Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold42
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3911082
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Warning! 18191 characters in sequence are not A, C, G, or T
File 22 of 24
Found at i:3342731 original size:32 final size:32
Alignment explanation
Indices: 3342687--3342757 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
3342677 AGCTTCGTAG
*
3342687 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACAATGTATCGATACAACACTTATGTAT
*
3342719 CGATACAATGTATCGATACATCACTTATGTAT
1 CGATACAATGTATCGATACAACACTTATGTAT
3342751 CGATACA
1 CGATACA
3342758 GTTACTGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (32 bp):
CGATACAATGTATCGATACAACACTTATGTAT
Found at i:3342773 original size:21 final size:19
Alignment explanation
Indices: 3342695--3342757 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
3342685 AGCGATACAT
*
3342695 TGTATCGATACAACACTTA
1 TGTATCGATACATCACTTA
3342714 TGTATCGAT--A-CA---A
1 TGTATCGATACATCACTTA
3342727 TGTATCGATACATCACTTA
1 TGTATCGATACATCACTTA
3342746 TGTATCGATACA
1 TGTATCGATACA
3342758 GTTACTGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 10 0.26
15 1 0.03
16 4 0.11
17 1 0.03
19 22 0.58
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (19 bp):
TGTATCGATACATCACTTA
Found at i:3343658 original size:49 final size:49
Alignment explanation
Indices: 3343509--3343873 Score: 249
Period size: 42 Copynumber: 7.9 Consensus size: 49
3343499 AATGACAATG
* ** * * * *
3343509 TGATTCATGGCCAGTGACATTGGACTTGAAGAAG-A-ATGCCAATGTGC
1 TGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGATGCCAATATGC
** * * *
3343556 TGAGACAAGGCCAGCGACATTGGGCTTAGAA-ATGTTAAAGATGCCAATATGC
1 TGATTCAAGGCCAACGATATTGGACTTA-AAGATG---AAGATGCCAATATGC
* * *
3343608 TGATTCAAGGCCAACGATATCGGACTTAAAGATGAAGATACCAATGTGC
1 TGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGATGCCAATATGC
* *
3343657 TGATTCAAGGCCGACGACATTGGACTT-AA-A-G--G-TGCCAATATGC
1 TGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGATGCCAATATGC
* * *
3343700 TGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGT
1 TGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGATGCCAATATGC
** * * * *
3343749 TGATTCAAGGTTAGCGACATTGG--TTTAA-A-G--G-TGCCAATATGT
1 TGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGATGCCAATATGC
* *
3343791 TGATTCAAGGCCAACGATATTGG--TTTAA-A-G--G-TGCCAATATGT
1 TGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGATGCCAATATGC
* *
3343833 TGATTCAAGGCCAGCGATATTGGACTT--AGAAGAAGATGCCA
1 TGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGATGCCA
3343874 CCAACTTGTG
Statistics
Matches: 262, Mismatches: 36, Indels: 40
0.78 0.11 0.12
Matches are distributed among these distances:
42 71 0.27
43 35 0.13
44 6 0.02
45 2 0.01
46 4 0.02
47 34 0.13
48 5 0.02
49 66 0.25
51 3 0.01
52 36 0.14
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.25
Consensus pattern (49 bp):
TGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGATGCCAATATGC
Found at i:3343747 original size:92 final size:91
Alignment explanation
Indices: 3343590--3343813 Score: 342
Period size: 92 Copynumber: 2.5 Consensus size: 91
3343580 CTTAGAAATG
* *
3343590 TTAAAGATGCCAATATGCTGATTCAAGGCCAACGATATCGGACTTAAAGATGAAGATACCAATGT
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGATACCAATGT
3343655 GCTGATTCAAGGCCGA-CGACATTGGAC
66 GCTGATTCAAGG-CGAGCGACATTGG-C
* *
3343682 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGT
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGATACCAATGT
* ** *
3343747 GTTGATTCAAGGTTAGCGACATTGGT
66 GCTGATTCAAGGCGAGCGACATTGGC
*
3343773 TTAAAGGTGCCAATATGTTGATTCAAGGCCAACGATATTGG
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGG
3343814 TTTAAAGGTG
Statistics
Matches: 121, Mismatches: 10, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
91 40 0.33
92 81 0.67
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.26
Consensus pattern (91 bp):
TTAAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGATACCAATGT
GCTGATTCAAGGCGAGCGACATTGGC
Found at i:3343800 original size:21 final size:21
Alignment explanation
Indices: 3343776--3343842 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
3343766 CATTGGTTTA
3343776 AAGGTGCCAATATGTTGATTC
1 AAGGTGCCAATATGTTGATTC
* * * *
3343797 AA-G-GCCAACGATATTGGTTTA
1 AAGGTGCCAA-TATGTT-GATTC
3343818 AAGGTGCCAATATGTTGATTC
1 AAGGTGCCAATATGTTGATTC
3343839 AAGG
1 AAGG
3343843 CCAGCGATAT
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
19 5 0.15
20 5 0.15
21 14 0.41
22 5 0.15
23 5 0.15
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.30
Consensus pattern (21 bp):
AAGGTGCCAATATGTTGATTC
Found at i:3343852 original size:22 final size:21
Alignment explanation
Indices: 3343785--3343852 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
3343775 AAAGGTGCCA
3343785 ATATGTTGATTCAAGGCCAACG
1 ATATGTTGATTCAAGGCC-ACG
* * *
3343807 ATAT-TGGTTTAAAGGTGCCA--
1 ATATGTTGATTCAA-G-GCCACG
3343827 ATATGTTGATTCAAGGCCAGCG
1 ATATGTTGATTCAAGGCCA-CG
3343849 ATAT
1 ATAT
3343853 TGGACTTAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
19 4 0.12
20 5 0.15
21 12 0.35
22 10 0.29
23 3 0.09
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.31
Consensus pattern (21 bp):
ATATGTTGATTCAAGGCCACG
Found at i:3343947 original size:28 final size:28
Alignment explanation
Indices: 3343882--3344349 Score: 544
Period size: 28 Copynumber: 16.4 Consensus size: 28
3343872 CACCAACTTG
**
3343882 TGTGGGCTTTTGATAGGGTTG-CACCAACT
1 TGTGGGCTTTTGA-A-GGTTGCCACTGACT
*
3343911 TGTGTGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* *
3343939 TATGGGCTTTTGAAGGTTGCCACTAACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
3343967 TGTGGGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* * * *
3343995 TGTGGGCTTTGGAAAAGATGCCACGGACT
1 TGTGGGCTTTTG-AAGGTTGCCACTGACT
* *
3344024 CGTGGGCTTTTGAAAAGGGTGCCACTGACT
1 TGTGGGCTTTTG--AAGGTTGCCACTGACT
*
3344054 TGTGGGCTTTTAAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* * * *
3344082 TGCGGGCTTTGGAAAAGATGCCAC-GAACT
1 TGTGGGCTTTTG-AAGGTTGCCACTG-ACT
3344111 TGTGGGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
3344139 TGTGGGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* * *
3344167 TGTGGGCTTTGGAAAAGATGCCACTGACT
1 TGTGGGCTTTTG-AAGGTTGCCACTGACT
* * *
3344196 TGTGGGATTTGGAAAAGGGTGCCACTGACT
1 TGTGGGCTTTTG--AAGGTTGCCACTGACT
*
3344226 TGTGGGCTTTTGAAAGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* * * *
3344254 TGTGGGCTTTGGAAAAGATGCCACGGACT
1 TGTGGGCTTTTG-AAGGTTGCCACTGACT
3344283 TGTGGGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* * *
3344311 TGTGGGCTTTGGAAACGATGCCACTGACT
1 TGTGGGCTTTTG-AAGGTTGCCACTGACT
3344340 TGTGGGCTTT
1 TGTGGGCTTT
3344350 GAACAAGGTG
Statistics
Matches: 380, Mismatches: 49, Indels: 20
0.85 0.11 0.04
Matches are distributed among these distances:
27 5 0.01
28 194 0.51
29 132 0.35
30 49 0.13
ACGTcount: A:0.19, C:0.18, G:0.32, T:0.32
Consensus pattern (28 bp):
TGTGGGCTTTTGAAGGTTGCCACTGACT
Found at i:3343951 original size:57 final size:57
Alignment explanation
Indices: 3343882--3344349 Score: 568
Period size: 57 Copynumber: 8.2 Consensus size: 57
3343872 CACCAACTTG
** * * *
3343882 TGTGGGCTTTTGATAGGGTTG-CACCAACTTGTGTGCTTTTG-AAGGTTGCCACTGACT
1 TGTGGGCTTTTGA-A-GGTTGCCACTGACTTGTGGGCTTTGGAAAGGATGCCACTGACT
* * * *
3343939 TATGGGCTTTTGAAGGTTGCCACTAACTTGTGGGCTTTTG-AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAGGATGCCACTGACT
* * * * * * *
3343995 TGTGGGCTTTGGAAAAGATGCCACGGACTCGTGGGCTTTTGAAAAGGGTGCCACTGACT
1 TGTGGGCTTTTG-AAGGTTGCCACTGACTTGTGGGC-TTTGGAAAGGATGCCACTGACT
* * *
3344054 TGTGGGCTTTTAAAGGTTGCCACTGACTTGCGGGCTTTGGAAAAGATGCCAC-GAACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAGGATGCCACTG-ACT
* *
3344111 TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTG-AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAGGATGCCACTGACT
* * * * *
3344167 TGTGGGCTTTGGAAAAGATGCCACTGACTTGTGGGATTTGGAAAAGGGTGCCACTGACT
1 TGTGGGCTTTTG-AAGGTTGCCACTGACTTGTGGGCTTTGG-AAAGGATGCCACTGACT
* * *
3344226 TGTGGGCTTTTGAAAGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACGGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAGGATGCCACTGACT
*
3344283 TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAACGATGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAGGATGCCACTGACT
3344340 TGTGGGCTTT
1 TGTGGGCTTT
3344350 GAACAAGGTG
Statistics
Matches: 359, Mismatches: 43, Indels: 18
0.85 0.10 0.04
Matches are distributed among these distances:
55 5 0.01
56 69 0.19
57 187 0.52
58 47 0.13
59 51 0.14
ACGTcount: A:0.19, C:0.18, G:0.32, T:0.32
Consensus pattern (57 bp):
TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAGGATGCCACTGACT
Found at i:3344168 original size:172 final size:171
Alignment explanation
Indices: 3343928--3344350 Score: 704
Period size: 172 Copynumber: 2.5 Consensus size: 171
3343918 TTTTGAAGGT
* *
3343928 TGCCACTGACTTATGGGCTTTTGAAGGTTGCCACTAACTTGTGGGCTTTTGAAGGTTGCCACTGA
1 TGCCAC-GACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGA
* *
3343993 CTTGTGGGCTTTGGAAAAGATGCCACGGACTCGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTG
65 CTTGTGGGCTTTGGAAAAGATGCCACGGACTCGTGGGATTTGGAAAAGGGTGCCACTGACTTGTG
3344058 GGCTTTT-AAAGGTTGCCACTGACTTGCGGGCTTTGGAAAAGA
130 GGCTTTTGAAA-GTTGCCACTGACTTGCGGGCTTTGGAAAAGA
3344100 TGCCACGAACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGA
1 TGCCACG-ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGA
* *
3344165 CTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTGGGATTTGGAAAAGGGTGCCACTGACTTGTG
65 CTTGTGGGCTTTGGAAAAGATGCCACGGACTCGTGGGATTTGGAAAAGGGTGCCACTGACTTGTG
*
3344230 GGCTTTTGAAAGTTGCCACTGACTTGTGGGCTTTGGAAAAGA
130 GGCTTTTGAAAGTTGCCACTGACTTGCGGGCTTTGGAAAAGA
* * *
3344272 TGCCACGGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAACGATGCCACTG
1 TGCCAC-GACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTG-AAGGTTGCCACTG
3344337 ACTTGTGGGCTTTG
64 ACTTGTGGGCTTTG
3344351 AACAAGGTGA
Statistics
Matches: 237, Mismatches: 10, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
171 1 0.00
172 207 0.87
173 29 0.12
ACGTcount: A:0.19, C:0.18, G:0.32, T:0.31
Consensus pattern (171 bp):
TGCCACGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGAC
TTGTGGGCTTTGGAAAAGATGCCACGGACTCGTGGGATTTGGAAAAGGGTGCCACTGACTTGTGG
GCTTTTGAAAGTTGCCACTGACTTGCGGGCTTTGGAAAAGA
Found at i:3345806 original size:17 final size:17
Alignment explanation
Indices: 3345786--3345821 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
3345776 CTTTTTGTTG
3345786 TTGTTGTTGT-TTTTTTT
1 TTGTT-TTGTGTTTTTTT
3345803 TTGTTTTGTGTTTTTTT
1 TTGTTTTGTGTTTTTTT
3345820 TT
1 TT
3345822 TTGGGGAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (17 bp):
TTGTTTTGTGTTTTTTT
Found at i:3345816 original size:16 final size:17
Alignment explanation
Indices: 3345786--3345820 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
3345776 CTTTTTGTTG
*
3345786 TTGTTGTTGTTTTTTTT
1 TTGTTGTTGTGTTTTTT
3345803 TTGTT-TTGTGTTTTTT
1 TTGTTGTTGTGTTTTTT
3345819 TT
1 TT
3345821 TTTGGGGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (17 bp):
TTGTTGTTGTGTTTTTT
Found at i:3345824 original size:19 final size:20
Alignment explanation
Indices: 3345777--3345822 Score: 69
Period size: 18 Copynumber: 2.4 Consensus size: 20
3345767 ATCCGGACCC
*
3345777 TTTTTGTTGTTGTTGTTGTT
1 TTTTTTTTGTTGTTGTTGTT
3345797 TTTTTTTTGTT-TTG-TGTT
1 TTTTTTTTGTTGTTGTTGTT
3345815 TTTTTTTT
1 TTTTTTTT
3345823 TGGGGAGGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 12 0.48
19 3 0.12
20 10 0.40
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (20 bp):
TTTTTTTTGTTGTTGTTGTT
Found at i:3361136 original size:61 final size:60
Alignment explanation
Indices: 3361035--3361159 Score: 162
Period size: 61 Copynumber: 2.1 Consensus size: 60
3361025 CCTTTTTCTT
* * * * * *
3361035 TCTTAAGCCTAATATTGCTGGCCCTAGATCAGCATGTTGGCATCTTTTTCATTCTTCTCA
1 TCTTAAGCCTAATATCGCTGGCACTAGATCAGCATATTGGCACCTTTATCATTCTTCGCA
*
3361095 TCTTCAAGCCTAATATCGCTGGCAGT-GAATCAGCATATTGGCACCTTTATCATTCTTCGCA
1 TCTT-AAGCCTAATATCGCTGGCACTAG-ATCAGCATATTGGCACCTTTATCATTCTTCGCA
3361156 TCTT
1 TCTT
3361160 TAAGTCCAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
60 5 0.09
61 51 0.91
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.38
Consensus pattern (60 bp):
TCTTAAGCCTAATATCGCTGGCACTAGATCAGCATATTGGCACCTTTATCATTCTTCGCA
Found at i:3361185 original size:61 final size:61
Alignment explanation
Indices: 3361062--3361211 Score: 160
Period size: 61 Copynumber: 2.5 Consensus size: 61
3361052 CTGGCCCTAG
* * * * *
3361062 ATCAGCATGTTGGCATCTTTTTCATTCTTCTCATCTTCAAGCCTAATATCGCTGGCAGTGA
1 ATCAGCATATTGGCACCTTTATCATTCTTCGCATCTTCAAGCCTAATATCGCTGACAGTGA
* * * **
3361123 ATCAGCATATTGGCACCTTTATCATTCTTCGCATCTTTAAGTCC-AATGTTGCTGACTTTGA
1 ATCAGCATATTGGCACCTTTATCATTCTTCGCATCTTCAAG-CCTAATATCGCTGACAGTGA
* * *
3361184 ATCAGCACATTGACACTTTTATC-TTCTT
1 ATCAGCATATTGGCACCTTTATCATTCTT
3361212 ATCTTTAAGT
Statistics
Matches: 75, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
60 5 0.07
61 68 0.91
62 2 0.03
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.39
Consensus pattern (61 bp):
ATCAGCATATTGGCACCTTTATCATTCTTCGCATCTTCAAGCCTAATATCGCTGACAGTGA
Found at i:3371042 original size:51 final size:51
Alignment explanation
Indices: 3370985--3371096 Score: 136
Period size: 51 Copynumber: 2.2 Consensus size: 51
3370975 GACAGGGTTG
* * *
3370985 GAGTATCCTCGATTGTGGAAAATCAGTGTTTT-GAAAATAAAATCGAAGTTA
1 GAGTATCCCCGATTATGAAAAATCAGTGTTTTAG-AAATAAAATCGAAGTTA
** ** *
3371036 GAGTATCCCCGATTATGAAAAATGGGTGTTTTAGAAATAAAATCGGGGTTG
1 GAGTATCCCCGATTATGAAAAATCAGTGTTTTAGAAATAAAATCGAAGTTA
3371087 GAGTATCCCC
1 GAGTATCCCC
3371097 TTGGAAATAA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
51 51 0.98
52 1 0.02
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.29
Consensus pattern (51 bp):
GAGTATCCCCGATTATGAAAAATCAGTGTTTTAGAAATAAAATCGAAGTTA
Found at i:3371119 original size:79 final size:79
Alignment explanation
Indices: 3371036--3371254 Score: 312
Period size: 79 Copynumber: 2.8 Consensus size: 79
3371026 ATCGAAGTTA
* * * *
3371036 GAGTATCCCCGATTATGAAAAATGGGTGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTTGG
1 GAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGG
3371101 AAATAACGGGGTTG
66 AAATAACGGGGTTG
* * * * * *
3371115 GAGTATCCCTGATTGTGAGAAATTAATATTTTAGAAATAAAGCCGGGGTTGGAGTATCCCCTCGG
1 GAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGG
3371180 AAATAACGGGGTTG
66 AAATAACGGGGTTG
* * * *
3371194 GAGCATCCCCGATTATGAAAAATTGATGTTTTGGATATAAAACCGAGGTTGGAGTATCCCC
1 GAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCC
3371255 GAGATGAAAA
Statistics
Matches: 120, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
79 120 1.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.28
Consensus pattern (79 bp):
GAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGG
AAATAACGGGGTTG
Found at i:3371170 original size:130 final size:130
Alignment explanation
Indices: 3370932--3371175 Score: 316
Period size: 130 Copynumber: 1.9 Consensus size: 130
3370922 AGGAAATCGA
*
3370932 TGTTTTGAGAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATGACAGGGTTGGAGTATCCTCGA
1 TGTTTTGAGAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCTCGA
* * *
3370997 TTGTGGAAAATCAGTGTTTTGAAAATAAAATCGAAGTTAGAGTATCCCCGATTATGAAAAATGGG
66 TTGTGGAAAATCAATATTTTGAAAATAAAACCGAAGTTAGAGTATCCCCGATTATGAAAAATGGG
* * *
3371062 TGTTTT-AGAAATAAAATCGGGGTTGGAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCC-CT
1 TGTTTTGAG-AATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCTC-
* * ** *
3371125 GATTGT-GAGAAATTAATATTTT-AGAAATAAAGCCGGGGTTGGAGTATCCCC
64 GATTGTGGA-AAATCAATATTTTGA-AAATAAAACCGAAGTTAGAGTATCCCC
3371176 TCGGAAATAA
Statistics
Matches: 98, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
129 6 0.06
130 92 0.94
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.29
Consensus pattern (130 bp):
TGTTTTGAGAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCTCGA
TTGTGGAAAATCAATATTTTGAAAATAAAACCGAAGTTAGAGTATCCCCGATTATGAAAAATGGG
Found at i:3371951 original size:119 final size:119
Alignment explanation
Indices: 3371739--3371979 Score: 428
Period size: 119 Copynumber: 2.0 Consensus size: 119
3371729 GGTAGGCCTG
* * *
3371739 AATGGCCCAAATAGAATGCATTTTACTGACTCTAGCGTTTTTGAACAGCTTAGACTCAAAAAATC
1 AATGGCCCAAACAGAATGCATTTTACTAACTCAAGCGTTTTTGAACAGCTTAGACTCAAAAAATC
3371804 ATAACTCTCTAGTTTGGACTAATCTGGGGGCAAACAAGACATCGTTGAAAAGAT
66 ATAACTCTCTAGTTTGGACTAATCTGGGGGCAAACAAGACATCGTTGAAAAGAT
* *
3371858 AATGGCCCAAACAGAATGCATTTTACTAACTCAAGGGTTTTTGAACAGCTTCGACTCAAAAAATC
1 AATGGCCCAAACAGAATGCATTTTACTAACTCAAGCGTTTTTGAACAGCTTAGACTCAAAAAATC
*
3371923 ATAACTCTCTAGTTTGGACTAATTTGGGGGCAAACAAGACATCGTTGAAAAGAT
66 ATAACTCTCTAGTTTGGACTAATCTGGGGGCAAACAAGACATCGTTGAAAAGAT
3371977 AAT
1 AAT
3371980 TCAAAGCTCT
Statistics
Matches: 116, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
119 116 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (119 bp):
AATGGCCCAAACAGAATGCATTTTACTAACTCAAGCGTTTTTGAACAGCTTAGACTCAAAAAATC
ATAACTCTCTAGTTTGGACTAATCTGGGGGCAAACAAGACATCGTTGAAAAGAT
Found at i:3373751 original size:13 final size:13
Alignment explanation
Indices: 3373733--3373762 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3373723 GTAAACCCAG
*
3373733 AATGTATTGATAC
1 AATGTATTGACAC
3373746 AATGTATTGACAC
1 AATGTATTGACAC
3373759 AATG
1 AATG
3373763 AACAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (13 bp):
AATGTATTGACAC
Found at i:3374544 original size:42 final size:43
Alignment explanation
Indices: 3374497--3374633 Score: 156
Period size: 42 Copynumber: 3.2 Consensus size: 43
3374487 AAAGGAAAAA
3374497 AGGAAAATGAAATGCGTCCTGCTCTTTGAGGAC-AAGAGAAAG
1 AGGAAAATGAAATGCGTCCTGCTCTTTGAGGACAAAGAGAAAG
3374539 AGGAAAAT-AAAGTGCGTCCTGCTCTTTGAGGACAAAAGAGAAAAG
1 AGGAAAATGAAA-TGCGTCCTGCTCTTTGAGGAC-AAAGAG-AAAG
* * * * *
3374584 AAGG-GAATGAAGTGTGTCCTACTTTTTGAGGACAAAGGAGAAA-
1 -AGGAAAATGAAATGCGTCCTGCTCTTTGAGGACAAA-GAGAAAG
3374627 AGGAAAA
1 AGGAAAA
3374634 GGAGTCCTGC
Statistics
Matches: 81, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
41 3 0.04
42 32 0.40
43 2 0.02
44 11 0.14
45 28 0.35
46 5 0.06
ACGTcount: A:0.41, C:0.12, G:0.28, T:0.19
Consensus pattern (43 bp):
AGGAAAATGAAATGCGTCCTGCTCTTTGAGGACAAAGAGAAAG
Found at i:3374603 original size:45 final size:45
Alignment explanation
Indices: 3374487--3374628 Score: 168
Period size: 45 Copynumber: 3.2 Consensus size: 45
3374477 TTTCGAGGAT
* *
3374487 AAAG-GAAAAAAGGAAAATGAAATGCGTCCTGCTCTTTGAGGAC-
1 AAAGAGAAAAGAGGAAAATGAAGTGCGTCCTGCTCTTTGAGGACA
*
3374530 -AAGAG-AAAGAGGAAAATAAAGTGCGTCCTGCTCTTTGAGGACA
1 AAAGAGAAAAGAGGAAAATGAAGTGCGTCCTGCTCTTTGAGGACA
* * * *
3374573 AAAGAGAAAAGAAGG-GAATGAAGTGTGTCCTACTTTTTGAGGACA
1 AAAGAGAAAAG-AGGAAAATGAAGTGCGTCCTGCTCTTTGAGGACA
*
3374618 AAGGAGAAAAG
1 AAAGAGAAAAG
3374629 GAAAAGGAGT
Statistics
Matches: 85, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
42 37 0.44
43 1 0.01
44 5 0.06
45 39 0.46
46 3 0.04
ACGTcount: A:0.42, C:0.11, G:0.28, T:0.18
Consensus pattern (45 bp):
AAAGAGAAAAGAGGAAAATGAAGTGCGTCCTGCTCTTTGAGGACA
Found at i:3374703 original size:61 final size:62
Alignment explanation
Indices: 3374624--3375460 Score: 571
Period size: 61 Copynumber: 13.5 Consensus size: 62
3374614 GACAAAGGAG
* ** *
3374624 AAAAGGAAAAGG-AGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTAAGTTTTA
1 AAAAGAAAAAGGCA-TCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTA
* * ** * * *
3374686 AAAAG-AAAAGGCATCCTGCTTTTTGAGGATTGGAAGGTGCCACCAACTTGTGTGGGCTTTG
1 AAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTA
** * * * *
3374747 AAAAGAAAAAGGTGTACTGCTCTTTGAAGACT-AAAAGTGTCACCAACTCGTGTGGGCTTTG
1 AAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTA
* ** * * * *
3374808 AAAAGGAAAAGGTGTCCTGCTCCTTGAGGACT-AAAGGTGTCACCAACTCGTGTGGGCTTTG
1 AAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTA
* * ** *
3374869 AAAAGAAAAAGGCATCCTGTTTTTTGAGGACTAAAGCGTGCCACCAACTCGTGTGGGC-TTG
1 AAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTA
* * ** ** * *
3374930 AAAAGAAAAAGGCGTCCTGCACTTTGAGGACTAAAGCAAAAAAAAG-GAAATGAAGTGCGTCCTG
1 AAAAGAAAAAGGCATCCTGCTCTTTGAGGACT--------AAAAAGTGCCACCAACT-CGT-GTG
**
3374994 CTCTTT-
56 GGCTTTA
* * *** *** * * * * ** * **
3375000 -GAGGACAAAAGG-A----GAAATGAAAGGAATGAAACGTG--TCCTGCTC-TTTGAGGACAAAG
1 AAAAGA-AAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTG-GG-C--TT
*
3375056 AA
61 TA
* * *
3375058 GAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTG
1 -AAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTA
* ** * *
3375121 AAAAGAAAAAAGTGTCCTGCTCTTTGAAGACT-AAAAGTGCCACCAACTCGTGTGGGCTTTG
1 AAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTA
** * * *
3375182 AAAAGAAAAAGGTGTCCTGCTCTTTGAGGACTAAAAGGTGTCACCAACTTGTGTGGGCTTTA
1 AAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTA
* ** * * *
3375244 AAAAGGAAAAGGTGTCCTGCTCATTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTG
1 AAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTA
* ** * * *
3375305 AAAAGAAAAATGTGTCCTGCTCGTTGAGGA-TTAAAAGATGCCACCAACTTGTGTGGGCTTTA
1 AAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAAG-TGCCACCAACTCGTGTGGGCTTTA
* * * * *
3375367 AAAAGGAAAAGGCGTCCTCCTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTG
1 AAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTA
* *
3375428 AAAAGAAAAAGGCGTCCTACTCTTTGAGGACTA
1 AAAAGAAAAAGGCATCCTGCTCTTTGAGGACTA
3375461 GAAGGGCTAA
Statistics
Matches: 616, Mismatches: 123, Indels: 72
0.76 0.15 0.09
Matches are distributed among these distances:
53 2 0.00
54 1 0.00
55 2 0.00
56 1 0.00
57 4 0.01
58 1 0.00
59 6 0.01
60 3 0.00
61 355 0.58
62 182 0.30
63 1 0.00
64 13 0.02
65 9 0.01
66 7 0.01
67 3 0.00
68 5 0.01
69 10 0.02
70 9 0.01
71 2 0.00
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (62 bp):
AAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTA
Found at i:3374837 original size:184 final size:182
Alignment explanation
Indices: 3374623--3375465 Score: 781
Period size: 184 Copynumber: 4.5 Consensus size: 182
3374613 GGACAAAGGA
* ** *
3374623 GAAAAGGAAAAGGAGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTAAGTTTTAAA
1 GAAAAGGAAAAGGAGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTAAA
* * * * *
3374688 AAGAAAAGGCATCCTGCTTTTTGAGGATTGGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGA
65 AAGAAAAGGCGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGA
* *
3374753 AAAAGGTGTACTGCTCTTTGAAGACTAAAAGTGTCACCAACTCGTGTGGGCTTT
129 AAAAGGTGTCCTGCTCTTTGAAGACTAAAAGTGCCACCAACTCGTGTGGGCTTT
* * * *
3374807 GAAAAGGAAAAGGTGTCCTGCTCCTTGAGGACTAAAGGTGTCACCAACTCGTGTGGGCTTTGAAA
1 GAAAAGGAAAAGGAGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTAAAA
* * *
3374872 AGAAAAAGGCATCCTGTTTTTTGAGGACTAAAGCGTGCCACCAACTCGTGTGGGC-TTGAAAAGA
66 AG-AAAAGGCGTCCTGCTCTTTGAGGACTAAAG-GTGCCACCAACTCGTGTGGGCTTTGAAAAGA
* * * ** ** * * **
3374936 AAAAGGCGTCCTGCACTTTGAGGACTAAAGCAAAAAAAAG-GAAATGAAGTGCGTCCTGCTCTTT
129 AAAAGGTGTCCTGCTCTTTGAAGACT---------AAAAGTGCCACCAACT-CGT-GTGGGCTTT
** * *** ** * * * ** * **
3375000 GAGGA-CAAAAGGAGAAATG-----AAAGGAATGAAACGTG--TCCTGCTC-TTTGAGGACAAAG
1 GAAAAGGAAAAGGAGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTG-GG-C--TT
* *
3375056 AAGAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTG
61 TA-AAAA-GAAAAGGCGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTG
*
3375121 AAAAGAAAAAAGTGTCCTGCTCTTTGAAGACTAAAAGTGCCACCAACTCGTGTGGGCTTT
123 AAAAGAAAAAGGTGTCCTGCTCTTTGAAGACTAAAAGTGCCACCAACTCGTGTGGGCTTT
* * * *
3375181 GAAAAGAAAAAGGTGTCCTGCTCTTTGAGGACTAAAAGGTGTCACCAACTTGTGTGGGCTTTAAA
1 GAAAAGGAAAAGGAGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTAAA
* *
3375246 AAGGAAAAGGTGTCCTGCTCATTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGA
65 AA-GAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGA
* * * * *
3375311 AAAATGTGTCCTGCTCGTTGAGGATTAAAAGATGCCACCAACTTGTGTGGGCTTT
129 AAAAGGTGTCCTGCTCTTTGAAGACTAAAAG-TGCCACCAACTCGTGTGGGCTTT
* * * *
3375366 AAAAAGGAAAAGGCGTCCTCCTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAA
1 GAAAAGGAAAAGGAGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTAAAA
*
3375431 AGAAAAAGGCGTCCTACTCTTTGAGGACTAGAAGG
66 AG-AAAAGGCGTCCTGCTCTTTGAGGACTA-AAGG
3375466 GCTAAAAGAA
Statistics
Matches: 527, Mismatches: 97, Indels: 69
0.76 0.14 0.10
Matches are distributed among these distances:
181 9 0.02
182 17 0.03
183 68 0.13
184 190 0.36
185 88 0.17
186 8 0.02
187 17 0.03
188 7 0.01
189 6 0.01
190 51 0.10
191 40 0.08
192 17 0.03
193 9 0.02
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (182 bp):
GAAAAGGAAAAGGAGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTAAAA
AGAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAA
AAGGTGTCCTGCTCTTTGAAGACTAAAAGTGCCACCAACTCGTGTGGGCTTT
Found at i:3374992 original size:45 final size:42
Alignment explanation
Indices: 3374938--3375093 Score: 167
Period size: 46 Copynumber: 3.6 Consensus size: 42
3374928 TGAAAAGAAA
*
3374938 AAGGCGTCCTGCACTTTGAGGACTAAAGCAAAAAAAAGGAAATG
1 AAGGCGTCCTGCTCTTTGAGGACTAAAG-AAAAAAAAGG-AATG
* *
3374982 AAGTGCGTCCTGCTCTTTGAGGACAAAAGGAGAAATGAAAGGAATG
1 AAG-GCGTCCTGCTCTTTGAGGACTAAA-GA-AAA-AAAAGGAATG
* * *
3375028 AAACGTGTCCTGCTCTTTGAGGAC-AAAG-AAGAAAAGGAA--
1 -AAGGCGTCCTGCTCTTTGAGGACTAAAGAAAAAAAAGGAATG
3375067 AAGGCGTCCTGCTCTTTGAGGACTAAA
1 AAGGCGTCCTGCTCTTTGAGGACTAAA
3375094 AAGTGCCACC
Statistics
Matches: 97, Mismatches: 9, Indels: 17
0.79 0.07 0.14
Matches are distributed among these distances:
38 21 0.22
39 3 0.03
41 7 0.07
42 2 0.02
44 4 0.04
45 26 0.27
46 27 0.28
47 7 0.07
ACGTcount: A:0.38, C:0.16, G:0.27, T:0.19
Consensus pattern (42 bp):
AAGGCGTCCTGCTCTTTGAGGACTAAAGAAAAAAAAGGAATG
Found at i:3375078 original size:38 final size:40
Alignment explanation
Indices: 3374930--3375094 Score: 156
Period size: 45 Copynumber: 3.9 Consensus size: 40
3374920 TGTGGGCTTG
* *
3374930 AAAA-GAAAAAGGCGTCCTGCACTTTGAGGACTAAAGCAAAA
1 AAAAGGAAAAAGGCGTCCTGCTCTTTGAGGACAAAAG--AAA
3374971 AAAAGGAAATGAAGTGCGTCCTGCTCTTTGAGGACAAAAGGAGAA
1 AAAAGGAAA--AAG-GCGTCCTGCTCTTTGAGGACAAAA-GA-AA
* * *
3375016 ATGAAAGGAATGAAACGTGTCCTGCTCTTTGAGGAC-AAAGAAG
1 A--AAAGGAA--AAAGGCGTCCTGCTCTTTGAGGACAAAAGAAA
3375059 AAAAGG-AAAAGGCGTCCTGCTCTTTGAGGACTAAAA
1 AAAAGGAAAAAGGCGTCCTGCTCTTTGAGGAC-AAAA
3375095 AGTGCCACCA
Statistics
Matches: 105, Mismatches: 7, Indels: 25
0.77 0.05 0.18
Matches are distributed among these distances:
38 22 0.21
40 4 0.04
41 9 0.09
42 4 0.04
43 2 0.02
44 6 0.06
45 28 0.27
46 20 0.19
47 9 0.09
49 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.26, T:0.18
Consensus pattern (40 bp):
AAAAGGAAAAAGGCGTCCTGCTCTTTGAGGACAAAAGAAA
Found at i:3375207 original size:123 final size:123
Alignment explanation
Indices: 3374623--3375460 Score: 734
Period size: 123 Copynumber: 6.8 Consensus size: 123
3374613 GGACAAAGGA
* * ** * *
3374623 GAAAAGGAAAAGGAGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTAAGTTTTAAA
1 GAAAAGAAAAAGGTGTCCTGCTCTTTGAGGACT-AAAAGTGCCACCAACTCGTGTGGGCTTTGAA
* * * ** * *
3374688 AAG-AAAAGGCATCCTGCTTTTTGAGGATTGGAAGGTGCCACCAACTTGTGTGGGCTTT
65 AAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT
* * *
3374746 GAAAAGAAAAAGGTGTACTGCTCTTTGAAGACTAAAAGTGTCACCAACTCGTGTGGGCTTTGAAA
1 GAAAAGAAAAAGGTGTCCTGCTCTTTGAGGACTAAAAGTGCCACCAACTCGTGTGGGCTTTGAAA
* * * * *
3374811 AGGAAAAGGTGTCCTGCTCCTTGAGGACT-AAAGGTGTCACCAACTCGTGTGGGCTTT
66 AGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT
** * * *
3374868 GAAAAGAAAAAGGCATCCTGTTTTTTGAGGACTAAAGCGTGCCACCAACTCGTGTGGGC-TTGAA
1 GAAAAGAAAAAGGTGTCCTGCTCTTTGAGGACTAAA-AGTGCCACCAACTCGTGTGGGCTTTGAA
* ** ** * * **
3374932 AAGAAAAAGGCGTCCTGCACTTTGAGGACTAAAGCAAAAAAAAG-GAAATGAAGTGCGTCCTGCT
65 AAGAAAAAGGCGTCCTGCTCTTTGAGGACT--------AAAAAGTGCCACCAACT-CGT-GTGGG
3374996 CTTT
120 CTTT
* * *** ** * * * ** *
3375000 G--AGGACAAAAGGAGAAATG-----AAAGGAATGAAACGTG--TCCTGCTC-TTTGAGGACAAA
1 GAAAAGA-AAAAGGTGTCCTGCTCTTTGAGGACT-AAAAGTGCCACCAACTCGTGTG-GG-C---
*** *
3375055 GAAGAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT
59 TTTGAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT
* *
3375120 GAAAAGAAAAAAGTGTCCTGCTCTTTGAAGACTAAAAGTGCCACCAACTCGTGTGGGCTTTGAAA
1 GAAAAGAAAAAGGTGTCCTGCTCTTTGAGGACTAAAAGTGCCACCAACTCGTGTGGGCTTTGAAA
* * * *
3375185 AGAAAAAGGTGTCCTGCTCTTTGAGGACTAAAAGGTGTCACCAACTTGTGTGGGCTTT
66 AGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT
* * * *
3375243 AAAAAGGAAAAGGTGTCCTGCTCATTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAA
1 GAAAAGAAAAAGGTGTCCTGCTCTTTGAGGACTAAAAGTGCCACCAACTCGTGTGGGCTTTGAAA
* * * * *
3375308 AGAAAAATGTGTCCTGCTCGTTGAGGA-TTAAAAGATGCCACCAACTTGTGTGGGCTTT
66 AGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAG-TGCCACCAACTCGTGTGGGCTTT
* * * * *
3375366 AAAAAGGAAAAGGCGTCCTCCTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAA
1 GAAAAGAAAAAGGTGTCCTGCTCTTTGAGGACTAAAAGTGCCACCAACTCGTGTGGGCTTTGAAA
*
3375431 AGAAAAAGGCGTCCTACTCTTTGAGGACTA
66 AGAAAAAGGCGTCCTGCTCTTTGAGGACTA
3375461 GAAGGGCTAA
Statistics
Matches: 576, Mismatches: 105, Indels: 67
0.77 0.14 0.09
Matches are distributed among these distances:
120 7 0.01
121 17 0.03
122 128 0.22
123 321 0.56
124 8 0.01
125 7 0.01
126 14 0.02
127 10 0.02
128 3 0.01
129 31 0.05
130 8 0.01
131 15 0.03
132 7 0.01
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (123 bp):
GAAAAGAAAAAGGTGTCCTGCTCTTTGAGGACTAAAAGTGCCACCAACTCGTGTGGGCTTTGAAA
AGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT
Found at i:3380284 original size:79 final size:78
Alignment explanation
Indices: 3380120--3380285 Score: 219
Period size: 79 Copynumber: 2.1 Consensus size: 78
3380110 TCGGGGTTCC
* *
3380120 AGAAATAAAATCAGGGTTGGAGTATCTCCTCGAAAATAACAGGGTTGGAGTATCCTTGATTATAT
1 AGAAATAAAATCAGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCTCGATTATAT
*
3380185 AAAATCGGTATTT
66 AAAATCGATATTT
* * *
3380198 TGAAAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAAC-GAGGTTGGAGTATCCTCGATTGT
1 AG-AAATAAAATCAGGGTTGGAGTATCCCCTCGAAAATAACAG-GGTTGGAGTATCCTCGATTAT
*
3380262 GA-AAAATTGATGATTT
64 -ATAAAATCGAT-ATTT
3380278 AGAAATAA
1 AGAAATAA
3380286 GGTCGGGATT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
78 2 0.03
79 68 0.89
80 6 0.08
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (78 bp):
AGAAATAAAATCAGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCTCGATTATAT
AAAATCGATATTT
Found at i:3380303 original size:79 final size:79
Alignment explanation
Indices: 3380122--3380306 Score: 209
Period size: 79 Copynumber: 2.3 Consensus size: 79
3380112 GGGGTTCCAG
* *
3380122 AAATAAAATCAGGG-TTGGAGTATCTCCTCGAAAATAACAGGGTTGGAGTATCCTTGATTATATA
1 AAATAAAATC-GGGATTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCTCGATTATATA
* *
3380186 AAATCGGTATTTTGA
65 AAATCGATATTTAGA
* *
3380201 AAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAAC-GAGGTTGGAGTATCCTCGATTGTGA-
1 AAATAAAATCGGGATTGGAGTATCCCCTCGAAAATAACAG-GGTTGGAGTATCCTCGATTAT-AT
*
3380264 AAAATTGATGATTTAG-
64 AAAATCGAT-ATTTAGA
**
3380280 AAATAAGGTCGGGATT-GATGTATCCCC
1 AAATAAAATCGGGATTGGA-GTATCCCC
3380307 GATTATGAGA
Statistics
Matches: 92, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
78 6 0.07
79 80 0.87
80 6 0.07
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (79 bp):
AAATAAAATCGGGATTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCTCGATTATATAA
AATCGATATTTAGA
Found at i:3380310 original size:51 final size:51
Alignment explanation
Indices: 3380243--3380525 Score: 227
Period size: 51 Copynumber: 5.5 Consensus size: 51
3380233 AATAACGAGG
* * **
3380243 TTGGAGTATCCTCGATTGTGAAAAATTGATGA-TTTAGAAATAAGGTCGGGA
1 TTGGAGTATCCCCGATTGTGAAAAATCGAT-ATTTTAGAAATAAAATCGGGA
* * * * *
3380294 TT-GATGTATCCCCGATTATGAGAAATCAATATTTTGAAAAATAAAATC-AGA
1 TTGGA-GTATCCCCGATTGTGAAAAATCGATATTTT-AGAAATAAAATCGGGA
* *
3380345 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTAGAAATAAAATCGAGG-
1 -TTGGAGTATCCCCGATTGTGAAAAATCGATATTTTAGAAATAAAATCG-GGA
* * ** **
3380397 TTGGAGTATCCCCCGATTGCGATAAATCGATGCTTTAGAAATAAAATC-ATA
1 TTGGAGTAT-CCCCGATTGTGAAAAATCGATATTTTAGAAATAAAATCGGGA
** * * * * **
3380448 CTTGGAGTATCCCCGATTAAGAAAAATTGATGTCTTGGAAATGGAATCGGGA
1 -TTGGAGTATCCCCGATTGTGAAAAATCGATATTTTAGAAATAAAATCGGGA
*
3380500 TTGGAGTATCCCCGAGT-TGAAAAATC
1 TTGGAGTATCCCCGATTGTGAAAAATC
3380526 TAGAAATTTA
Statistics
Matches: 183, Mismatches: 38, Indels: 23
0.75 0.16 0.09
Matches are distributed among these distances:
50 10 0.05
51 92 0.50
52 78 0.43
53 3 0.02
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (51 bp):
TTGGAGTATCCCCGATTGTGAAAAATCGATATTTTAGAAATAAAATCGGGA
Found at i:3380356 original size:103 final size:104
Alignment explanation
Indices: 3380242--3380512 Score: 286
Period size: 103 Copynumber: 2.6 Consensus size: 104
3380232 AAATAACGAG
* **
3380242 GTTGGAGTATCCTCGATTGTGAAAAATTGATGA-TTTAGAAATAAGGTCG-GGATT-GATGTAT-
1 GTTGGAGTATCCCCGATTGTGAAAAATTGATGATTTTAGAAATAAAATCGAGG-TTGGA-GTATC
* *
3380303 CCCCGATTATGAGAAATCAATATTTTGAAAAATAAAATCAGA
64 CCCCGATTACGAGAAATCAATACTTT-AAAAATAAAATCAGA
*
3380345 GTTGGAGTATCCCCGATTGTGAAAAATTGGT-ATTTTAGAAATAAAATCGAGGTTGGAGTATCCC
1 GTTGGAGTATCCCCGATTGTGAAAAATTGATGATTTTAGAAATAAAATCGAGGTTGGAGTATCCC
* * * * * *
3380409 CCGATTGCGATAAATCGATGCTTTAGAAATAAAATCATA
66 CCGATTACGAGAAATCAATACTTTAAAAATAAAATCAGA
* ** * * **
3380448 CTTGGAGTATCCCCGATTAAGAAAAATTGATG-TCTTGGAAATGGAATCG-GGATTGGAGTATCC
1 GTTGGAGTATCCCCGATTGTGAAAAATTGATGATTTTAGAAATAAAATCGAGG-TTGGAGTATCC
3380511 CC
65 CC
3380513 GAGTTGAAAA
Statistics
Matches: 142, Mismatches: 20, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
102 3 0.02
103 115 0.81
104 24 0.17
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.30
Consensus pattern (104 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGATGATTTTAGAAATAAAATCGAGGTTGGAGTATCCC
CCGATTACGAGAAATCAATACTTTAAAAATAAAATCAGA
Found at i:3382839 original size:20 final size:20
Alignment explanation
Indices: 3382814--3382929 Score: 101
Period size: 20 Copynumber: 5.8 Consensus size: 20
3382804 AAAAATGCCT
*
3382814 GAATGTATTGATACATTGTA
1 GAATGTATCGATACATTGTA
*
3382834 GAATGTATTGATACATTGTA
1 GAATGTATCGATACATTGTA
* * *
3382854 AAATATATCGATACAATG-A
1 GAATGTATCGATACATTGTA
* *
3382873 GCAATGTATCGATACAAT-AA
1 G-AATGTATCGATACATTGTA
* * *
3382893 GCAATGTATCAATACAATGCA
1 G-AATGTATCGATACATTGTA
*
3382914 AAATGTATCGATACAT
1 GAATGTATCGATACAT
3382930 CTGGGTAAAC
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 1 0.01
20 80 0.98
21 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (20 bp):
GAATGTATCGATACATTGTA
Found at i:3383731 original size:134 final size:129
Alignment explanation
Indices: 3383428--3384219 Score: 683
Period size: 134 Copynumber: 6.0 Consensus size: 129
3383418 TCCTACTTTT
* ** * * * * * *
3383428 AAAGGAAAAAAGGAAAACGAAATGCGTCATGCTCTTTGAAGATAAAA-GAAAAAGGAAAATAAAG
1 AAAGGAGAAAAGGAAAATAAAATGCGTCCTACTCTTTGAGGACAAAAGGGAAAAGGAAAATGAAG
* * * *
3383492 TGCGTCTTGCTCTTTGAGGACAAAAGGGAAAAGAAGGGAATGAAGTGTTTCTGCTCTTTGAGGAC
66 TGCGTCCTACTCTTTGAGGACAAAAGGGAAAAGAAGGAAATGAAGTG-TCCTGCTCTTTGAGGAC
* * * * *
3383557 AAATGA-AGAAA-GAAAATGAAGTGCGTCCTACTCTTTGAGGACGAAAGGGAAAAGAAGGAAATG
1 AAAGGAGA-AAAGGAAAATAAAATGCGTCCTACTCTTTGAGGACAAAAGGGAAAAG--GAAAATG
* * * *
3383620 AAGTGTGTCCAACTCTTTGAGGACAAAAGGAGAAAAAAAAGAAATGGAACGTGTCCTGCTCTTTG
63 AAGTGCGTCCTACTCTTTGAGGACAAAAGG-GAAAAGAAGGAAAT-GAA-GTGTCCTGCTCTTTG
3383685 AGGAC
125 AGGAC
* * *
3383690 AGAGGAGAAAAGGAAAATAAAATGTGTCCTACTCTTTGAGGACAAAAGGGAAAA-GATTGGAATG
1 AAAGGAGAAAAGGAAAATAAAATGCGTCCTACTCTTTGAGGACAAAAGGGAAAAGGA---AAATG
* * *
3383754 AAGTGTGTCCTGCTCTTTGAGGACAAAAGGAGAAAAGAAGGGAATGGAACGTGTCCTGCTCTTTG
63 AAGTGCGTCCTACTCTTTGAGGACAAAAGG-GAAAAGAAGGAAAT-GAA-GTGTCCTGCTCTTTG
3383819 AGGAC
125 AGGAC
* * * *
3383824 AAAGGAGAAAAGGAAAATAAAGTGCGTCATGCTCTTTGAGGACAAAAGAGAAAAGGAAAAT-AAT
1 AAAGGAGAAAAGGAAAATAAAATGCGTCCTACTCTTTGAGGACAAAAGGGAAAAGGAAAATGAA-
* * *
3383888 GTGCGTCCTGCTCTTTAAAGACAAAAGGGAAAAGAAGGAAATGAAGTGCGTCCTGCTCTTTGAGG
65 GTGCGTCCTACTCTTTGAGGACAAAAGGGAAAAGAAGGAAATGAAGT--GTCCTGCTCTTTGAGG
3383953 ACC
128 A-C
* ** * * * *
3383956 AAAGGAGAAAAAAAGG-GAATGGAACGTGTCCTGCTCTTTGAGGAC-CAAGGAGAAAAGGAAAAT
1 AAAGGAG---AAAAGGAAAATAAAATGCGTCCTACTCTTTGAGGACAAAAGG-GAAAAGGAAAAT
* * *
3384019 AAAGTGCATTCTACTCTTTGAGGACAAAAGGGGAAAA-AAGGAAATGAAGTGTGTCCTGCTCTTT
62 GAAGTGCGTCCTACTCTTTGAGGACAAAA-GGGAAAAGAAGGAAATGAA--GTGTCCTGCTCTTT
3384083 GAGGAC
124 GAGGAC
** * * ** * * * *
3384089 AAAAGGAGAAAA-GAAGGGAATGGAACGTGTTTTGCCCTTTAAGGA-TAAAGGAGAAAAGGAAAA
1 -AAAGGAGAAAAGGAA---AATAAAATGCGTCCTACTCTTTGAGGACAAAAGG-GAAAAGGAAAA
* * *
3384152 T-ACAGTGCGTCCTACTCTTTGAGGACAAAAGAGAAGAGAA--AAATAAAGTACGTCCTGCTCTT
61 TGA-AGTGCGTCCTACTCTTTGAGGACAAAAGGGAAAAGAAGGAAATGAAGT--GTCCTGCTCTT
3384214 TGAGGA
123 TGAGGA
3384220 TAAGGAGGTG
Statistics
Matches: 560, Mismatches: 68, Indels: 67
0.81 0.10 0.10
Matches are distributed among these distances:
128 29 0.05
129 16 0.03
130 6 0.01
131 68 0.12
132 70 0.12
133 36 0.06
134 316 0.56
135 17 0.03
136 2 0.00
ACGTcount: A:0.40, C:0.12, G:0.28, T:0.20
Consensus pattern (129 bp):
AAAGGAGAAAAGGAAAATAAAATGCGTCCTACTCTTTGAGGACAAAAGGGAAAAGGAAAATGAAG
TGCGTCCTACTCTTTGAGGACAAAAGGGAAAAGAAGGAAATGAAGTGTCCTGCTCTTTGAGGAC
Found at i:3383913 original size:177 final size:175
Alignment explanation
Indices: 3383457--3384219 Score: 743
Period size: 177 Copynumber: 4.3 Consensus size: 175
3383447 AAATGCGTCA
* * * * *
3383457 TGCTCTTTGAAGATAAAAGA-AAAAGGAAAATAAAGTGCGTCTTGCTCTTTGAGGACAAAAGGGA
1 TGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAGAGA
* * * *
3383521 AAA-GAAGGGAATGAAGTGT-TTCTGCTCTTTGAGGAC-AAATGAAGAAAGA-AAATGAAGTGCG
66 AAAGGAA---AATGAAGTGTGTCCTGCTCTTTGAGGACAAAAGGGA-AAAGAGGAATGAAGTGCG
* * * *
3383582 TCCTACTCTTTGAGGACGAAAGG-GAAAAGAAGGAAAT-GAAGTGTGTCC
127 TCCTGCTCTTTGAGGACAAAAGGAGAAAAGAAGGGAATGGAA-CGTGTCC
** * *
3383630 AACTCTTTGAGGACAAAAGGAGAAAA--AAAAGAAA-TGGAACGTGTCCTGCTCTTTGAGGACAG
1 TGCTCTTTGAGGAC-AAAGGAGAAAAGGAAAATAAAGT-G--C--GTCCTGCTCTTTGAGGACAA
* * * *
3383692 AGGAGAAAAGGAAAATAAAATGTGTCCTACTCTTTGAGGACAAAAGGGAAAAGATTGGAATGAAG
60 AAGAGAAAAGGAAAATGAAGTGTGTCCTGCTCTTTGAGGACAAAAGGGAAAAGA--GGAATGAAG
*
3383757 TGTGTCCTGCTCTTTGAGGACAAAAGGAGAAAAGAAGGGAATGGAACGTGTCC
123 TGCGTCCTGCTCTTTGAGGACAAAAGGAGAAAAGAAGGGAATGGAACGTGTCC
*
3383810 TGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAAAGTGCGTCATGCTCTTTGAGGACAAAAGAGA
1 TGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAGAGA
* * *
3383875 AAAGGAAAAT-AATGTGCGTCCTGCTCTTTAAAGACAAAAGGGAAAAGAAGGAAATGAAGTGCGT
66 AAAGGAAAATGAA-GTGTGTCCTGCTCTTTGAGGACAAAAGGGAAAAG-AGG-AATGAAGTGCGT
* *
3383939 CCTGCTCTTTGAGGACCAAAGGAGAAAAAAAGGGAATGGAACGTGTCC
128 CCTGCTCTTTGAGGACAAAAGGAGAAAAGAAGGGAATGGAACGTGTCC
* * * *
3383987 TGCTCTTTGAGGACCAAGGAGAAAAGGAAAATAAAGTGCATTCTACTCTTTGAGGACAAAAGGGG
1 TGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAA---G
*
3384052 AAAAAAGG-AAATGAAGTGTGTCCTGCTCTTTGAGGACAAAAGGAGAAAAGAAGGGAATGGAACG
63 AGAAAAGGAAAATGAAGTGTGTCCTGCTCTTTGAGGACAAAAGG-GAAAAG-A-GGAAT-GAA-G
** * * * ** ** *
3384116 T--GTTTTGCCCTTTAAGGA-TAAAGGAGAAAAGGAA---AATACAGTGCGTCC
123 TGCGTCCTGCTCTTTGAGGACAAAAGGAGAAAA-GAAGGGAATGGAACGTGTCC
* * * * *
3384164 TACTCTTTGAGGACAAAAGAGAAGAGAAAAATAAAGTACGTCCTGCTCTTTGAGGA
1 TGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAAAGTGCGTCCTGCTCTTTGAGGA
3384220 TAAGGAGGTG
Statistics
Matches: 495, Mismatches: 65, Indels: 56
0.80 0.11 0.09
Matches are distributed among these distances:
172 1 0.00
173 18 0.04
174 5 0.01
175 13 0.03
176 24 0.05
177 261 0.53
178 4 0.01
179 83 0.17
180 67 0.14
181 16 0.03
182 3 0.01
ACGTcount: A:0.40, C:0.12, G:0.28, T:0.20
Consensus pattern (175 bp):
TGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAGAGA
AAAGGAAAATGAAGTGTGTCCTGCTCTTTGAGGACAAAAGGGAAAAGAGGAATGAAGTGCGTCCT
GCTCTTTGAGGACAAAAGGAGAAAAGAAGGGAATGGAACGTGTCC
Found at i:3384067 original size:311 final size:309
Alignment explanation
Indices: 3383499--3384214 Score: 1005
Period size: 311 Copynumber: 2.3 Consensus size: 309
3383489 AAGTGCGTCT
* ** *
3383499 TGCTCTTTGAGGACAAAAGG-GAAAA-GAAGGGAATGAAGTGTTTCTGCTCTTTGAGGACAAATG
1 TGCTCTTTGAGGAC-AAAGGAGAAAAGGAA---AATAAAGTGCGTCTGCTCTTTGAGGACAAAAG
* * * *
3383562 A-AGAAA-GAAAATGAAGTGCGTCCTACTCTTTGAGGACGAAAGGGAAAAGAAGGAAATGAAGTG
62 AGA-AAAGGAAAAT-AAGTGCGTCCTGCTCTTTAAAGACAAAAGGGAAAAGAAGGAAATGAAGTG
*
3383625 TGTCCAACTCTTTGAGGACAAAAGGAGAAAAAAAAGAAATGGAACGTGTCCTGCTCTTTGAGGAC
125 CGTCCAACTCTTTGAGGACAAAAGGAGAAAAAAAAGAAATGGAACGTGTCCTGCTCTTTGAGGAC
** *
3383690 AGAGGAGAAAAGGAAAATAAAATGTGTCCTACTCTTTGAGGACAAAAGGGAAAAGATTGGAATGA
190 AGAGGAGAAAAGGAAAATAAAATGCATCCTACTCTTTGAGGACAAAAGGGAAAAGATAGGAATGA
3383755 AGTGTGTCCTGCTCTTTGAGGACAAAAGGAGAAAAGAAGGGAATGGAACGTGTCC
255 AGTGTGTCCTGCTCTTTGAGGACAAAAGGAGAAAAGAAGGGAATGGAACGTGTCC
3383810 TGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAAAGTGCGTCATGCTCTTTGAGGACAAAAGAGA
1 TGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAAAGTGCGTC-TGCTCTTTGAGGACAAAAGAGA
3383875 AAAGGAAAATAATGTGCGTCCTGCTCTTTAAAGACAAAAGGGAAAAGAAGGAAATGAAGTGCGTC
65 AAAGGAAAATAA-GTGCGTCCTGCTCTTTAAAGACAAAAGGGAAAAGAAGGAAATGAAGTGCGTC
** * * *
3383940 CTGCTCTTTGAGGACCAAAGGAGAAAAAAAGGGAATGGAACGTGTCCTGCTCTTTGAGGACCA-A
129 CAACTCTTTGAGGACAAAAGGAGAAAAAAAAGAAATGGAACGTGTCCTGCTCTTTGAGGA-CAGA
* *
3384004 GGAGAAAAGGAAAATAAAGTGCATTCTACTCTTTGAGGACAAAAGGGGAAAA-A-AGGAAATGAA
193 GGAGAAAAGGAAAATAAAATGCATCCTACTCTTTGAGGACAAAA-GGGAAAAGATAGG-AATGAA
**
3384067 GTGTGTCCTGCTCTTTGAGGACAAAAGGAGAAAAGAAGGGAATGGAACGTGTTT
256 GTGTGTCCTGCTCTTTGAGGACAAAAGGAGAAAAGAAGGGAATGGAACGTGTCC
* * * * *
3384121 TGCCCTTTAAGGATAAAGGAGAAAAGGAAAATACAGTGCGTCCTACTCTTTGAGGACAAAAGAGA
1 TGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAAAGTGCGT-CTGCTCTTTGAGGACAAAAGAGA
* * *
3384186 AGAGAAAAATAAAGTACGTCCTGCTCTTT
65 AAAGGAAAAT-AAGTGCGTCCTGCTCTTT
3384215 GAGGATAAGG
Statistics
Matches: 365, Mismatches: 29, Indels: 22
0.88 0.07 0.05
Matches are distributed among these distances:
309 10 0.03
310 31 0.08
311 309 0.85
312 15 0.04
ACGTcount: A:0.39, C:0.13, G:0.28, T:0.20
Consensus pattern (309 bp):
TGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAAAGTGCGTCTGCTCTTTGAGGACAAAAGAGAA
AAGGAAAATAAGTGCGTCCTGCTCTTTAAAGACAAAAGGGAAAAGAAGGAAATGAAGTGCGTCCA
ACTCTTTGAGGACAAAAGGAGAAAAAAAAGAAATGGAACGTGTCCTGCTCTTTGAGGACAGAGGA
GAAAAGGAAAATAAAATGCATCCTACTCTTTGAGGACAAAAGGGAAAAGATAGGAATGAAGTGTG
TCCTGCTCTTTGAGGACAAAAGGAGAAAAGAAGGGAATGGAACGTGTCC
Found at i:3384291 original size:60 final size:61
Alignment explanation
Indices: 3384204--3384889 Score: 779
Period size: 61 Copynumber: 11.4 Consensus size: 61
3384194 ATAAAGTACG
*
3384204 TCCTGCTCTTTGAGGA-TAAGG-AGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCA
1 TCCTGCTCTTTGAGGACT--GGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
* * ** *
3384265 TCCT-TTCTTTGAGGACTGGAATGTGCCACCAACTTAAGTGGTCTTTAAAAGGAGAAA-GCA
1 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAAGGCA
** * *
3384325 TCCTGCTCTTTGAGGACTGGAAAATGCCCCCAACTTGTGTGGGCTCT-----G-AAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
* * **
3384380 TCCTGTTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
* * * * *
3384441 TCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTCTAAAAAGAAAAATGCA
1 TCCTGCTCTTTGAGGACT-GGAAGGTGCCACCAACTTGTGTGGGCT-TTAAAAGGAAAAGGCA
* * * *
3384504 TCCTGCTCTTTGAGGACTGGAAGGTGCCACTAACTTGAGTGGTCTTTAAAAGGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
* * *
3384565 TCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACG
1 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
* * * *
3384625 TCATGCTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGGCA
* * * * *
3384686 TCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAATGCG
1 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGGCA
* * * ** * * * * *
3384747 TCCTGCTCTTTAAAGACTGGAGGGTGCCACCAACTCATGTAGACTTT-GAAGGAGAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
** *
3384807 TCCTGCTCTTTGAGGACTAAAAGGTGCTACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
3384868 TCCTGCTCTTTGAGGACTGGAA
1 TCCTGCTCTTTGAGGACTGGAA
3384890 AGGCTAAAAG
Statistics
Matches: 536, Mismatches: 73, Indels: 32
0.84 0.11 0.05
Matches are distributed among these distances:
54 3 0.01
55 46 0.09
56 1 0.00
59 2 0.00
60 173 0.32
61 211 0.39
62 69 0.13
63 31 0.06
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.25
Consensus pattern (61 bp):
TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
Found at i:3384690 original size:121 final size:122
Alignment explanation
Indices: 3384204--3384889 Score: 808
Period size: 121 Copynumber: 5.7 Consensus size: 122
3384194 ATAAAGTACG
*
3384204 TCCTGCTCTTTGAGGA-T-AAGGAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCATC
1 TCCTGCTCTTTGAGGACTGAA--AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATC
* * ** *
3384267 CT-TTCTTTGAGGACTGGAATGTGCCACCAACTTAAGTGGTCTTTAAAAGGAGAAA-GCA
64 CTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAAGGCA
* * *
3384325 TCCTGCTCTTTGAGGACTGGAAA-ATGCCCCCAACTTGTGTGGGCTCT-----G-AAAGGCATCC
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCC
* * **
3384383 TGTTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
65 TGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
* * * *
3384441 TCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTCTAAAAAGAAAAATGCATC
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCT-TTAAAAGGAAAAGGCATC
* * * *
3384506 CTGCTCTTTGAGGACTGGAAGGTGCCACTAACTTGAGTGGTCTTTAAAAGGAAAAGGCG
64 CTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
* * *
3384565 TCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACGTCAT
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCT
* * *
3384629 GCTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCA
66 GCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGGCA
* * * *
3384686 TCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAATGCGTCC
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGGCATCC
* * * ** * * * * *
3384750 TGCTCTTTAAAGACTGGAGGGTGCCACCAACTCATGTAGACTTT-GAAGGAGAAGGCG
65 TGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
* *
3384807 TCCTGCTCTTTGAGGACTAAAAGGTGCTACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCT
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCT
3384872 GCTCTTTGAGGACTGGAA
66 GCTCTTTGAGGACTGGAA
3384890 AGGCTAAAAG
Statistics
Matches: 486, Mismatches: 62, Indels: 34
0.84 0.11 0.06
Matches are distributed among these distances:
115 14 0.03
116 69 0.14
117 20 0.04
120 23 0.05
121 179 0.37
122 79 0.16
123 23 0.05
124 79 0.16
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.25
Consensus pattern (122 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCT
GCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
Found at i:3388955 original size:52 final size:52
Alignment explanation
Indices: 3388877--3389005 Score: 204
Period size: 52 Copynumber: 2.5 Consensus size: 52
3388867 CGAAATATGA
* * **
3388877 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTACGC
*
3388929 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTACGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTACGC
*
3388981 AAATTTGCCTGCATGTACCGATACA
1 AAATTTGCCTGCATGTATCGATACA
3389006 AAGATCAGTG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTACGC
Found at i:3389018 original size:52 final size:51
Alignment explanation
Indices: 3388877--3389025 Score: 192
Period size: 52 Copynumber: 2.9 Consensus size: 51
3388867 CGAAATATGA
* **
3388877 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTACGC
* *
3388929 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTACGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTACGC
* *
3388981 AAATTTGCCTGCATGTACCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
3389026 ATGTATCGAT
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.98
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTACGC
Found at i:3389032 original size:13 final size:13
Alignment explanation
Indices: 3389014--3389038 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3389004 CAAAGATCAG
3389014 TGTATCGATACAA
1 TGTATCGATACAA
3389027 TGTATCGATACA
1 TGTATCGATACA
3389039 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3389119 original size:13 final size:13
Alignment explanation
Indices: 3389101--3389125 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3389091 CAAAAAAATA
3389101 TGTATCGATACAT
1 TGTATCGATACAT
3389114 TGTATCGATACA
1 TGTATCGATACA
3389126 ATACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3389485 original size:13 final size:13
Alignment explanation
Indices: 3389444--3389525 Score: 60
Period size: 13 Copynumber: 7.2 Consensus size: 13
3389434 CCGTTACAAG
3389444 CAATGTATCGATA
1 CAATGTATCGATA
3389457 CAAT-T-TC-AT-
1 CAATGTATCGATA
*
3389466 C-ATGTATTGATA
1 CAATGTATCGATA
3389478 CAATGTATCGATA
1 CAATGTATCGATA
*
3389491 C-A--T-T-G-TC
1 CAATGTATCGATA
*
3389498 CTATGTATCGATA
1 CAATGTATCGATA
3389511 CAATGTATCGATA
1 CAATGTATCGATA
3389524 CA
1 CA
3389526 TTGTCCCATG
Statistics
Matches: 53, Mismatches: 5, Indels: 22
0.66 0.06 0.28
Matches are distributed among these distances:
7 2 0.04
8 4 0.08
9 3 0.06
10 5 0.09
11 5 0.09
12 4 0.08
13 30 0.57
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.35
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:3389505 original size:20 final size:19
Alignment explanation
Indices: 3389480--3389545 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 19
3389470 TATTGATACA
3389480 ATGTATCGATACATTGTCC
1 ATGTATCGATACATTGTCC
3389499 TATGTATCGATACA------
1 -ATGTATCGATACATTGTCC
3389513 ATGTATCGATACATTGTCCC
1 ATGTATCGATACATTGT-CC
3389533 ATGTATCGATACA
1 ATGTATCGATACA
3389546 ATTAGTGGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 13 0.33
20 26 0.67
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (19 bp):
ATGTATCGATACATTGTCC
Found at i:3389511 original size:33 final size:33
Alignment explanation
Indices: 3389444--3389547 Score: 156
Period size: 33 Copynumber: 3.1 Consensus size: 33
3389434 CCGTTACAAG
* *
3389444 CAATGTATCGATACAATT-TCATCATGTATTGATA
1 CAATGTATCGATAC-ATTGTCCT-ATGTATCGATA
3389478 CAATGTATCGATACATTGTCCTATGTATCGATA
1 CAATGTATCGATACATTGTCCTATGTATCGATA
*
3389511 CAATGTATCGATACATTGTCCCATGTATCGATA
1 CAATGTATCGATACATTGTCCTATGTATCGATA
3389544 CAAT
1 CAAT
3389548 TAGTGGTAGG
Statistics
Matches: 66, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
33 49 0.74
34 17 0.26
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (33 bp):
CAATGTATCGATACATTGTCCTATGTATCGATA
Found at i:3389601 original size:20 final size:18
Alignment explanation
Indices: 3389576--3389667 Score: 78
Period size: 20 Copynumber: 4.7 Consensus size: 18
3389566 TGCCAGTTTC
3389576 ATGTATCGATACAACTGTCT
1 ATGTATCGATACAA-TG-CT
3389596 ATGTATCGATACAATGAGC-
1 ATGTATCGATACAAT--GCT
*
3389615 ATGTATCGATACAAAGCAGT
1 ATGTATCGATACAATGC--T
* *
3389635 ATGTATCGATACATCTGGT
1 ATGTATCGATACA-ATGCT
3389654 AGTGTATCGATACA
1 A-TGTATCGATACA
3389668 TTCAAGGGTT
Statistics
Matches: 61, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
17 2 0.03
19 17 0.28
20 40 0.66
21 2 0.03
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (18 bp):
ATGTATCGATACAATGCT
Found at i:3390258 original size:16 final size:17
Alignment explanation
Indices: 3390219--3390260 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
3390209 AATTTATATC
*
3390219 TTCTCCCCCTTAAAGAAT
1 TTCT-CCCCTTAAAGAAA
3390237 TTCTCCCCTTAAA-AAA
1 TTCTCCCCTTAAAGAAA
3390253 TTCTCCCC
1 TTCTCCCC
3390261 CTTTGTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.43
17 9 0.39
18 4 0.17
ACGTcount: A:0.26, C:0.38, G:0.02, T:0.33
Consensus pattern (17 bp):
TTCTCCCCTTAAAGAAA
Found at i:3390261 original size:17 final size:17
Alignment explanation
Indices: 3390219--3390263 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
3390209 AATTTATATC
*
3390219 TTCTCCCCCTTAAAGAA
1 TTCTCCCCCTTAAAAAA
3390236 TT-TCTCCCCTTAAAAAA
1 TTCTC-CCCCTTAAAAAA
3390253 TTCTCCCCCTT
1 TTCTCCCCCTT
3390264 TGTCAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 2 0.08
17 21 0.84
18 2 0.08
ACGTcount: A:0.24, C:0.38, G:0.02, T:0.36
Consensus pattern (17 bp):
TTCTCCCCCTTAAAAAA
Found at i:3390983 original size:13 final size:13
Alignment explanation
Indices: 3390965--3390989 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3390955 AGTAGCCAGG
3390965 GTATCGATACAAT
1 GTATCGATACAAT
3390978 GTATCGATACAA
1 GTATCGATACAA
3390990 GGAATGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (13 bp):
GTATCGATACAAT
Found at i:3397126 original size:21 final size:21
Alignment explanation
Indices: 3397100--3397155 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
3397090 ATTACAAGCA
3397100 ATGTATCGATACGATT-TCAT
1 ATGTATCGATACGATTGTCAT
*
3397120 CATGTATCGATAC-ATTGTCCT
1 -ATGTATCGATACGATTGTCAT
*
3397141 ATGTATTGATACGAT
1 ATGTATCGATACGAT
3397156 GTATCGATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (21 bp):
ATGTATCGATACGATTGTCAT
Found at i:3397146 original size:20 final size:20
Alignment explanation
Indices: 3397100--3397186 Score: 73
Period size: 20 Copynumber: 4.7 Consensus size: 20
3397090 ATTACAAGCA
*
3397100 ATGTATCGATACGATT-TCAT
1 ATGTATCGATAC-ATTGTCCT
3397120 CATGTATCGATACATTGTCCT
1 -ATGTATCGATACATTGTCCT
*
3397141 ATGTATTGATAC---G----
1 ATGTATCGATACATTGTCCT
*
3397154 ATGTATCGATACATTGTCCC
1 ATGTATCGATACATTGTCCT
3397174 ATGTATCGATACA
1 ATGTATCGATACA
3397187 AATAGTGGTA
Statistics
Matches: 55, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
13 11 0.20
16 1 0.02
17 1 0.02
20 27 0.49
21 15 0.27
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGTCCT
Found at i:3397163 original size:33 final size:33
Alignment explanation
Indices: 3397121--3397185 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
3397111 CGATTTCATC
* *
3397121 ATGTATCGATACATTGTCCTATGTATTGATACG
1 ATGTATCGATACATTGTCCCATGTATCGATACG
3397154 ATGTATCGATACATTGTCCCATGTATCGATAC
1 ATGTATCGATACATTGTCCCATGTATCGATAC
3397186 AAATAGTGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (33 bp):
ATGTATCGATACATTGTCCCATGTATCGATACG
Found at i:3397274 original size:13 final size:13
Alignment explanation
Indices: 3397256--3397282 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3397246 TAGAATGAGC
3397256 ATGTATCGATACA
1 ATGTATCGATACA
3397269 ATGTATCGATACA
1 ATGTATCGATACA
3397282 A
1 A
3397283 AGCAGTATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3397298 original size:33 final size:32
Alignment explanation
Indices: 3397237--3397301 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
3397227 TCAACTATCT
* *
3397237 ATGTATCGATAGAATGAGCATGTATCGATACA
1 ATGTATCGATACAAAGAGCATGTATCGATACA
*
3397269 ATGTATCGATACAAAGCAGTATGTATCGATACA
1 ATGTATCGATACAAAG-AGCATGTATCGATACA
3397302 TCTGGTAGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (32 bp):
ATGTATCGATACAAAGAGCATGTATCGATACA
Found at i:3403223 original size:16 final size:17
Alignment explanation
Indices: 3403198--3403235 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
3403188 TTGTGCTGTA
* *
3403198 ATCATGACATC-ATGAC
1 ATCATAACATCAATAAC
3403214 ATCATAACATCAATAAC
1 ATCATAACATCAATAAC
3403231 ATCAT
1 ATCAT
3403236 TATTTGCATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.45, C:0.24, G:0.05, T:0.26
Consensus pattern (17 bp):
ATCATAACATCAATAAC
Found at i:3403390 original size:31 final size:31
Alignment explanation
Indices: 3403334--3403565 Score: 148
Period size: 31 Copynumber: 7.2 Consensus size: 31
3403324 CTTCAAATAC
* * * *
3403334 CTTCTTAAAGTCCACGACTCAGTGGCAATCT
1 CTTCTCAAAGCCCACAACTCCGTGGCAATCT
* * *
3403365 CTTCTCAAAGCCCATAACTCCGTGGCACTTTTTT
1 CTTCTCAAAGCCCACAACTCCGTGGCA---ATCT
* * * *
3403399 CTTTTTAAAGCCCACAACTCCGTGGCACTTTTT
1 CTTCTCAAAGCCCACAACTCCGTGGCA--ATCT
* * *
3403432 CCTTTTTAAAGCCCACAACTCCGTGGC-ACCTT
1 -CTTCTCAAAGCCCACAACTCCGTGGCAATC-T
* *
3403464 CTTTTCAAAGCCCACAACTCCGTGGCACTCTT
1 CTTCTCAAAGCCCACAACTCCGTGGCAATC-T
* * *
3403496 TTTCCCTTTTAAAGCCCACAACTCCGTGGC-ACCTT
1 CTT--C--TCAAAGCCCACAACTCCGTGGCAATC-T
3403531 CTTCTCAAAGCCCACAACTCCGTGGC-ATCT
1 CTTCTCAAAGCCCACAACTCCGTGGCAATCT
3403561 -TTCTC
1 CTTCTC
3403566 CTTCCCAAAG
Statistics
Matches: 166, Mismatches: 25, Indels: 22
0.78 0.12 0.10
Matches are distributed among these distances:
29 5 0.03
30 1 0.01
31 70 0.42
32 6 0.04
33 6 0.04
34 52 0.31
35 5 0.03
36 21 0.13
ACGTcount: A:0.22, C:0.35, G:0.12, T:0.31
Consensus pattern (31 bp):
CTTCTCAAAGCCCACAACTCCGTGGCAATCT
Found at i:3403410 original size:34 final size:34
Alignment explanation
Indices: 3403371--3403562 Score: 243
Period size: 34 Copynumber: 5.7 Consensus size: 34
3403361 ATCTCTTCTC
*
3403371 AAAGCCCATAACTCCGTGGCACTTTTTTCTTTTT
1 AAAGCCCACAACTCCGTGGCACTTTTTTCTTTTT
*
3403405 AAAGCCCACAACTCCGTGGCACTTTTTCCTTTTT
1 AAAGCCCACAACTCCGTGGCACTTTTTTCTTTTT
* *
3403439 AAAGCCCACAACTCCGTGGCAC---CTTCTTTTC
1 AAAGCCCACAACTCCGTGGCACTTTTTTCTTTTT
*
3403470 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCACT-TTTTT-CTTTTT
* * *
3403506 AAAGCCCACAACTCCGTGGCAC---CTTCTTCTC
1 AAAGCCCACAACTCCGTGGCACTTTTTTCTTTTT
3403537 AAAGCCCACAACTCCGTGGCATCTTT
1 AAAGCCCACAACTCCGTGGCA-CTTT
3403563 CTCCTTCCCA
Statistics
Matches: 137, Mismatches: 12, Indels: 17
0.83 0.07 0.10
Matches are distributed among these distances:
31 52 0.38
32 3 0.02
34 54 0.39
35 2 0.01
36 26 0.19
ACGTcount: A:0.22, C:0.35, G:0.12, T:0.31
Consensus pattern (34 bp):
AAAGCCCACAACTCCGTGGCACTTTTTTCTTTTT
Found at i:3403523 original size:67 final size:66
Alignment explanation
Indices: 3403371--3403562 Score: 296
Period size: 67 Copynumber: 2.9 Consensus size: 66
3403361 ATCTCTTCTC
* * * *
3403371 AAAGCCCATAACTCCGTGGCACTTTTTTCTTTTTAAAGCCCACAACTCCGTGGCA-CTTTTTCCT
1 AAAGCCCACAACTCCGTGGCAC---CTTCTTTTCAAAGCCCACAACTCCGTGGCATCTTTTTCCC
3403435 TTTT
63 TTTT
3403439 AAAGCCCACAACTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTT
1 AAAGCCCACAACTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCA-TCTTTTTCCCTT
3403504 TT
65 TT
*
3403506 AAAGCCCACAACTCCGTGGCACCTTCTTCTCAAAGCCCACAACTCCGTGGCATCTTT
1 AAAGCCCACAACTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCATCTTT
3403563 CTCCTTCCCA
Statistics
Matches: 117, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
65 28 0.24
66 5 0.04
67 63 0.54
68 21 0.18
ACGTcount: A:0.22, C:0.35, G:0.12, T:0.31
Consensus pattern (66 bp):
AAAGCCCACAACTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCATCTTTTTCCCTTT
T
Found at i:3403773 original size:33 final size:33
Alignment explanation
Indices: 3403572--3403960 Score: 567
Period size: 33 Copynumber: 11.9 Consensus size: 33
3403562 TCTCCTTCCC
*
3403572 AAAGCCCACACAAGTCGGTGGCAACC-CTCTCT
1 AAAGCCCACACAAGTCGGTGGCAACCTTTCTCT
* *
3403604 AAAGCCCACACAAGTTGGTGGCAACCCTTCT-T
1 AAAGCCCACACAAGTCGGTGGCAACCTTTCTCT
*
3403636 AAAGCCCACACAAGTTGGTGGCAACCTTTCTC-
1 AAAGCCCACACAAGTCGGTGGCAACCTTTCTCT
* *
3403668 AAAGCCCACATAAGTCGGTGGCAACC-CTCTCT
1 AAAGCCCACACAAGTCGGTGGCAACCTTTCTCT
* *
3403700 AAAGCCCACACAAGTCGGTGGTAACCTTT-TTT
1 AAAGCCCACACAAGTCGGTGGCAACCTTTCTCT
* *
3403732 AAAGCCCACACAAGTCGGTGGAAACCTTTTTCT
1 AAAGCCCACACAAGTCGGTGGCAACCTTTCTCT
3403765 AAAGCCCACACAAGTCGGTGGCAAACC-TTCTCT
1 AAAGCCCACACAAGTCGGTGGC-AACCTTTCTCT
*
3403798 AAAGCCCACACAAGTCGGTGGCAACCTTTTTCT
1 AAAGCCCACACAAGTCGGTGGCAACCTTTCTCT
3403831 AAAGCCCACACAAGTCGGTGGCAAACC-TTCTCT
1 AAAGCCCACACAAGTCGGTGGC-AACCTTTCTCT
*
3403864 AAAGCCCACACAAGTCGGTGGCAACCTTTTTCT
1 AAAGCCCACACAAGTCGGTGGCAACCTTTCTCT
* *
3403897 AAAGCCCACACAAGTTGGTGGCAACCATTCTCT
1 AAAGCCCACACAAGTCGGTGGCAACCTTTCTCT
* *
3403930 AAAGCCCACACAAGTTGGTGGCAACCCTTCT
1 AAAGCCCACACAAGTCGGTGGCAACCTTTCT
3403961 AAGCCCAATA
Statistics
Matches: 327, Mismatches: 21, Indels: 17
0.90 0.06 0.05
Matches are distributed among these distances:
31 4 0.01
32 142 0.43
33 173 0.53
34 8 0.02
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (33 bp):
AAAGCCCACACAAGTCGGTGGCAACCTTTCTCT
Found at i:3404028 original size:49 final size:49
Alignment explanation
Indices: 3403960--3404489 Score: 655
Period size: 49 Copynumber: 11.1 Consensus size: 49
3403950 GCAACCCTTC
* * *
3403960 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * *
3404009 TAAGTCTAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
3404052 TAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCACCTTCTTCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * *
3404101 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
3404144 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
*
3404193 TAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * *
3404242 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TC--C--
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
3404286 -AAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCGCCTTTGTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCATCTT
* *
3404337 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * *
3404386 CAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGTCTTTGTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC-AC-CT-TCATCTT
* *
3404438 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
3404487 TAA
1 TAA
3404490 CATTCCTAAG
Statistics
Matches: 417, Mismatches: 40, Indels: 48
0.83 0.08 0.10
Matches are distributed among these distances:
43 111 0.27
45 2 0.00
46 1 0.00
47 4 0.01
48 2 0.00
49 214 0.51
50 3 0.01
51 2 0.00
52 78 0.19
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (49 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
Found at i:3404122 original size:92 final size:92
Alignment explanation
Indices: 3403955--3404489 Score: 587
Period size: 92 Copynumber: 5.6 Consensus size: 92
3403945 TGGTGGCAAC
* * * * * *
3403955 CCTTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCTAATG
1 CCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATA
* *
3404020 TAGCTGGCCTTGAATCAGCACATTGGCA
65 TCGCTGGCCTTGAATCAGCATATTGGCA
* * * *
3404048 CCTTTAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCACCTTCTTCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATAT
* *
3404113 AGCTGGCCTTGAATCAGCACATTGGCA
66 CGCTGGCCTTGAATCAGCATATTGGCA
*
3404140 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATAT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATAT
*
3404205 CGCTAGCCTTGAATCAGCATATTGGCA
66 CGCTGGCCTTGAATCAGCATATTGGCA
* *
3404232 CCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TC--C---AAGTC
1 ----C--CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTC
*
3404291 CAATATCGCTGGCCTTGAATCAACATATTGGCGCCTTTGTCA
60 CAATATCGCTGGCCTTGAATCAGCATATT---G-----G-CA
* * *
3404333 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTCAAGTCCAATAT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATAT
3404398 CGCTGGCCTTGAATCAGCATATTGGCGTCTTTGTCA
66 CGCTGGCCTTGAATCAGCATATT---G-----G-CA
* *
3404434 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAA
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAA
3404490 CATTCCTAAG
Statistics
Matches: 399, Mismatches: 22, Indels: 34
0.88 0.05 0.07
Matches are distributed among these distances:
92 200 0.50
93 4 0.01
95 45 0.11
96 3 0.01
97 2 0.01
98 42 0.11
100 1 0.00
101 102 0.26
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (92 bp):
CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATAT
CGCTGGCCTTGAATCAGCATATTGGCA
Found at i:3404224 original size:141 final size:141
Alignment explanation
Indices: 3403960--3404489 Score: 649
Period size: 141 Copynumber: 3.7 Consensus size: 141
3403950 GCAACCCTTC
* * * * *
3403960 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCTAATGTAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATCGCT
*
3404025 GGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATCGCTGGCCTTGAATTAGCAT
60 GGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCAT
*
3404084 ATTGGCACCTTCTTCTT
125 ATTGGCACCTTCATCTT
*
3404101 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTT
* *
3404166 GAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGC
66 GAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC
3404231 ACCTTCATCTT
131 ACCTTCATCTT
* **
3404242 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCCAAGTCCAATATCGCTGGCCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTT
* * * * *
3404307 GAATCAACATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATT
66 GAATCAGCACATTGGCACC--T-TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATT
3404372 GGCACCTTCATCTT
128 GGCACCTTCATCTT
* * * * *
3404386 CAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGTCTTTGTCATCTTTAAGTCCAATGTC
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATT---G-----G-CACCTTTAAGTCCAATATC
3404451 GCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAA
57 GCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAA
3404490 CATTCCTAAG
Statistics
Matches: 343, Mismatches: 28, Indels: 27
0.86 0.07 0.07
Matches are distributed among these distances:
135 38 0.11
137 1 0.00
139 1 0.00
141 165 0.48
143 1 0.00
144 84 0.24
147 1 0.00
150 10 0.03
151 1 0.00
152 1 0.00
153 40 0.12
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (141 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTT
GAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC
ACCTTCATCTT
Found at i:3404364 original size:52 final size:52
Alignment explanation
Indices: 3404286--3404480 Score: 288
Period size: 52 Copynumber: 3.8 Consensus size: 52
3404276 TGGCACCTCC
* * *
3404286 AAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCGCCTTTGTCATCTTT
1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTCATCTTT
* *
3404338 AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCATCTTC
1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTCATCTTT
* **
3404387 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGTCTTTGTCATCTTT
1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTCATCTTT
*
3404439 AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT
1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT
3404481 CATCTTTAAC
Statistics
Matches: 126, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
49 43 0.34
50 1 0.01
51 1 0.01
52 81 0.64
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.32
Consensus pattern (52 bp):
AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTCATCTTT
Found at i:3404435 original size:101 final size:101
Alignment explanation
Indices: 3404141--3404486 Score: 548
Period size: 101 Copynumber: 3.5 Consensus size: 101
3404131 ACATTGGCAC
* * *
3404141 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATC
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTCAAGTCCAATATC
* *
3404206 GCTAGCCTTGAATCAGCATATTGGC-AC-CT-TCAT
66 GCTGGCCTTGAATCAGCATATTGGCGACTTTGTCAT
*
3404239 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C--C-TC--CAAGTCCAATATC
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTCAAGTCCAATATC
* *
3404298 GCTGGCCTTGAATCAACATATTGGCGCCTTTGTCAT
66 GCTGGCCTTGAATCAGCATATTGGCGACTTTGTCAT
3404334 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTCAAGTCCAATATC
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTCAAGTCCAATATC
*
3404399 GCTGGCCTTGAATCAGCATATTGGCGTCTTTGTCAT
66 GCTGGCCTTGAATCAGCATATTGGCGACTTTGTCAT
3404435 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
3404487 TAACATTCCT
Statistics
Matches: 228, Mismatches: 11, Indels: 15
0.90 0.04 0.06
Matches are distributed among these distances:
92 35 0.15
93 1 0.00
94 3 0.01
95 46 0.20
96 1 0.00
97 1 0.00
98 40 0.18
99 2 0.01
101 99 0.43
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (101 bp):
CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTCAAGTCCAATATC
GCTGGCCTTGAATCAGCATATTGGCGACTTTGTCAT
Found at i:3405314 original size:13 final size:13
Alignment explanation
Indices: 3405296--3405320 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3405286 CATAAAGTGT
3405296 TGTATCGATACAA
1 TGTATCGATACAA
3405309 TGTATCGATACA
1 TGTATCGATACA
3405321 TATTTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3405336 original size:32 final size:33
Alignment explanation
Indices: 3405276--3405341 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
3405266 TTCAATGATT
3405276 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
** *
3405309 TGTATCGATACAT-ATTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
3405341 T
1 T
3405342 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:3405400 original size:13 final size:13
Alignment explanation
Indices: 3405382--3405409 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3405372 ATTACTCAAA
3405382 TGTATCGATACAT
1 TGTATCGATACAT
3405395 TGTATCGATACAT
1 TGTATCGATACAT
3405408 TG
1 TG
3405410 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3405459 original size:52 final size:50
Alignment explanation
Indices: 3405395--3405539 Score: 209
Period size: 52 Copynumber: 2.8 Consensus size: 50
3405385 ATCGATACAT
*
3405395 TGTATCGATACATTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACATT-AT-TATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
3405447 TGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACATTAT--TATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
3405499 TGTATCGATACACTATTAAATGTATCGATACATGCAGGCAA
1 TGTATCGATACATTATT--ATGTATCGATACATGCAGGCAA
3405540 CTTTTCATAT
Statistics
Matches: 85, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
51 2 0.02
52 83 0.98
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (50 bp):
TGTATCGATACATTATTATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:3408642 original size:79 final size:78
Alignment explanation
Indices: 3408548--3408766 Score: 262
Period size: 79 Copynumber: 2.8 Consensus size: 78
3408538 CAACGGGCTA
* **
3408548 GAGTATCCCCGATTATGGAAAATCGGTGTTCTAGAAATAAAATCGGGGTTGGAGTATCCCCTCGA
1 GAGTATCCCTGATTATGGAAAATCAATGTT-TAGAAATAAAATCGGGGTTGGAGTATCCCCTCGA
3408613 AAATAAC-AGGGTTG
65 AAATAACGA-GGTTG
* * *
3408627 GAGTATCCCTGATTATAGAAAATCAATATTTTGAAAATAAAATCGGGGTTGGAGTATCCCCTCGA
1 GAGTATCCCTGATTATGGAAAATCAATGTTTAG-AAATAAAATCGGGGTTGGAGTATCCCCTCGA
3408692 AAATAACGAGGTTG
65 AAATAACGAGGTTG
* * * ** * *
3408706 GAGAAT-CTTCGATTATGAAAAATCAATGATTTAGAAATAAGGTTGGGGTTGAAGTATCCCC
1 GAGTATCCCT-GATTATGGAAAATCAATG-TTTAGAAATAAAATCGGGGTTGGAGTATCCCC
3408767 GATTATGAGA
Statistics
Matches: 120, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
78 4 0.03
79 111 0.93
80 5 0.04
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (78 bp):
GAGTATCCCTGATTATGGAAAATCAATGTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCGAA
AATAACGAGGTTG
Found at i:3408770 original size:51 final size:51
Alignment explanation
Indices: 3408715--3408924 Score: 178
Period size: 51 Copynumber: 4.1 Consensus size: 51
3408705 GGAGAATCTT
** *
3408715 CGATTATGAAAAATCAATGA-TTTAGAAATAAGGTTGGGGTTGAAGTATCCC
1 CGATTATGAAAAATCAAT-ATTTTAGAAATAAAATTGGAGTTGAAGTATCCC
* * * *
3408766 CGATTATGAGAAATCAATATTTTGGAAATAAAATTGGAGTTGGAGTATGCC
1 CGATTATGAAAAATCAATATTTTAGAAATAAAATTGGAGTTGAAGTATCCC
* *** *
3408817 CGATTATGGAAAATTGGTATTTTAGAAATAAAATCAGG-GTT-AGAGTATCCC
1 CGATTATGAAAAATCAATATTTTAGAAATAAAAT-TGGAGTTGA-AGTATCCC
* * * ** *
3408868 CGATTA-CAGTAAATCGATGCTTTAGAAATAAAATCGGAGTTTG-AGTATCCC
1 CGATTATGA-AAAATCAATATTTTAGAAATAAAATTGGAG-TTGAAGTATCCC
3408919 CGATTA
1 CGATTA
3408925 AGAGAAATTG
Statistics
Matches: 128, Mismatches: 24, Indels: 14
0.77 0.14 0.08
Matches are distributed among these distances:
50 3 0.02
51 121 0.95
52 4 0.03
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (51 bp):
CGATTATGAAAAATCAATATTTTAGAAATAAAATTGGAGTTGAAGTATCCC
Found at i:3408821 original size:102 final size:102
Alignment explanation
Indices: 3408715--3408924 Score: 228
Period size: 102 Copynumber: 2.1 Consensus size: 102
3408705 GGAGAATCTT
** ** *
3408715 CGATTATGAAAAATCAATGA-TTTAGAAATAAGGTTGGGGTT-GAAGTATCCCCGATTATGAG-A
1 CGATTATGAAAAATCAAT-ATTTTAGAAATAAAATCAGGGTTAG-AGTATCCCCGATTA-CAGTA
* * * *
3408777 AATCAATATTTTGGAAATAAAATTGGAGTTGGAGTATGCC
63 AATCAATACTTTAGAAATAAAATCGGAGTTGGAGTATCCC
* ***
3408817 CGATTATGGAAAATTGGTATTTTAGAAATAAAATCAGGGTTAGAGTATCCCCGATTACAGTAAAT
1 CGATTATGAAAAATCAATATTTTAGAAATAAAATCAGGGTTAGAGTATCCCCGATTACAGTAAAT
* * *
3408882 CGATGCTTTAGAAATAAAATCGGAGTTTGAGTATCCC
66 CAATACTTTAGAAATAAAATCGGAGTTGGAGTATCCC
3408919 CGATTA
1 CGATTA
3408925 AGAGAAATTG
Statistics
Matches: 89, Mismatches: 16, Indels: 6
0.80 0.14 0.05
Matches are distributed among these distances:
101 3 0.03
102 85 0.96
103 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (102 bp):
CGATTATGAAAAATCAATATTTTAGAAATAAAATCAGGGTTAGAGTATCCCCGATTACAGTAAAT
CAATACTTTAGAAATAAAATCGGAGTTGGAGTATCCC
Found at i:3408947 original size:51 final size:50
Alignment explanation
Indices: 3408758--3408947 Score: 159
Period size: 51 Copynumber: 3.7 Consensus size: 50
3408748 TTGGGGTTGA
* * * * * *
3408758 AGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAATTGGAGTTGG
1 AGTATCCCCGATTAAG-GAAATCGATATCTTAGAAATAAAATCGGAGTTAG
* * * * *
3408809 AGTATGCCCGATTATGGAAAATTGGTATTTTAGAAATAAAATCAGG-GTTAG
1 AGTATCCCCGATTAAGG-AAATCGATATCTTAGAAATAAAATC-GGAGTTAG
* * *
3408860 AGTATCCCCGATTACAGTAAATCGAT-GCTTTAGAAATAAAATCGGAGTTTG
1 AGTATCCCCGATTA-AGGAAATCGATATC-TTAGAAATAAAATCGGAGTTAG
* * *
3408911 AGTATCCCCGATTAAGAGAAATTGATGTCTTGGAAAT
1 AGTATCCCCGATTAAG-GAAATCGATATCTTAGAAAT
3408948 GGAACCGAGA
Statistics
Matches: 113, Mismatches: 19, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
50 5 0.04
51 104 0.92
52 4 0.04
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.31
Consensus pattern (50 bp):
AGTATCCCCGATTAAGGAAATCGATATCTTAGAAATAAAATCGGAGTTAG
Found at i:3408947 original size:102 final size:102
Alignment explanation
Indices: 3408758--3408947 Score: 231
Period size: 102 Copynumber: 1.9 Consensus size: 102
3408748 TTGGGGTTGA
* * * * *
3408758 AGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAATTGGAGTTGGAGTATGCCCGATTA
1 AGTATCCCCGATTATCAGAAATCAATACTTTAGAAATAAAATCGGAGTTGGAGTATCCCCGATTA
* * *
3408823 TGGAAAATTGGTATTTTAGAAATAAAATCAGGGTTAG
66 AGGAAAATTGATATCTTAGAAATAAAATCAGGGTTAG
* * *
3408860 AGTATCCCCGATTA-CAGTAAATCGATGCTTTAGAAATAAAATCGGAGTTTGAGTATCCCCGATT
1 AGTATCCCCGATTATCAG-AAATCAATACTTTAGAAATAAAATCGGAGTTGGAGTATCCCCGATT
* *
3408924 AA-GAGAAATTGATGTCTTGGAAAT
65 AAGGA-AAATTGATATCTTAGAAAT
3408948 GGAACCGAGA
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
101 4 0.05
102 69 0.95
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.31
Consensus pattern (102 bp):
AGTATCCCCGATTATCAGAAATCAATACTTTAGAAATAAAATCGGAGTTGGAGTATCCCCGATTA
AGGAAAATTGATATCTTAGAAATAAAATCAGGGTTAG
Found at i:3411295 original size:20 final size:19
Alignment explanation
Indices: 3411265--3411338 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
3411255 AAAATGCCTG
* *
3411265 AATGCATCGATACATTGTAA
1 AATGTATCGATACAATG-AA
* *
3411285 AATATATCGATACAATGAGC
1 AATGTATCGATACAATGA-A
*
3411305 AGTGTATCGATACAATGCAA
1 AATGTATCGATACAATG-AA
3411325 AATGTATCGATACA
1 AATGTATCGATACA
3411339 TCTGGGTAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 1 0.02
20 42 0.95
21 1 0.02
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (19 bp):
AATGTATCGATACAATGAA
Found at i:3413874 original size:78 final size:78
Alignment explanation
Indices: 3413783--3414003 Score: 302
Period size: 78 Copynumber: 2.8 Consensus size: 78
3413773 TAAAATCAAA
* * *
3413783 GTTGGAGTATCCCCGATTATGGAAATGGGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCT
1 GTTGGAGTATCCCCGATTATGGAAATTGATGTTTTAGAAATAAAGCCGGGGTTGGAGTATCCCCT
*
3413848 CGA-AAATAATGGG
66 C-ATAAATAACGGG
* * * *
3413861 GTTGGAGTATCCCCGATTGT-GAGAATTAATATTATAGAAATAAAGCCGGGGTTGGAGTATCCCC
1 GTTGGAGTATCCCCGATTATGGA-AATTGATGTTTTAGAAATAAAGCCGGGGTTGGAGTATCCCC
3413925 TCATAAATAACGGG
65 TCATAAATAACGGG
* * *
3413939 GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTGGAAATAAAGCTGGGGTTGGAGTATCCCC
1 GTTGGAGTATCCCCGATTATG-GAAATTGATGTTTTAGAAATAAAGCCGGGGTTGGAGTATCCCC
3414004 GAGATGAAAA
Statistics
Matches: 124, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
77 3 0.02
78 84 0.68
79 36 0.29
80 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (78 bp):
GTTGGAGTATCCCCGATTATGGAAATTGATGTTTTAGAAATAAAGCCGGGGTTGGAGTATCCCCT
CATAAATAACGGG
Found at i:3416184 original size:20 final size:20
Alignment explanation
Indices: 3416159--3416209 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
3416149 AAAATGCCTG
*
3416159 AATGTATCGATACAATG-AGC
1 AATGTATCGATACAATGCA-A
3416179 AATGTATCGATACAATGCAA
1 AATGTATCGATACAATGCAA
3416199 AATGTATCGAT
1 AATGTATCGAT
3416210 TCATCTGGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (20 bp):
AATGTATCGATACAATGCAA
Found at i:3418024 original size:65 final size:64
Alignment explanation
Indices: 3417941--3418070 Score: 152
Period size: 65 Copynumber: 2.0 Consensus size: 64
3417931 GTGGCACCCA
* * * * * *
3417941 TCTCAAAGTCCACAACTTAATGGCATCTTTTTTTAAAGTCCACGACTCCGTGGCACCCTTTTTTC
1 TCTCAAAATCCACAACTTAATGGCATATCTTCTAAAAATCCACGACTCCGTGGCA-CCTTTTTTC
** * * *
3418006 TCTCAAAATCCATGACTTAGTGGCATATCTTCTAAAAATCCATGACTCTGTGGCACCTTTTTTC
1 TCTCAAAATCCACAACTTAATGGCATATCTTCTAAAAATCCACGACTCCGTGGCACCTTTTTTC
3418070 T
1 T
3418071 TTTTAAGTCC
Statistics
Matches: 54, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
64 10 0.19
65 44 0.81
ACGTcount: A:0.25, C:0.27, G:0.12, T:0.36
Consensus pattern (64 bp):
TCTCAAAATCCACAACTTAATGGCATATCTTCTAAAAATCCACGACTCCGTGGCACCTTTTTTC
Found at i:3418112 original size:33 final size:32
Alignment explanation
Indices: 3418056--3418463 Score: 256
Period size: 33 Copynumber: 12.9 Consensus size: 32
3418046 CATGACTCTG
3418056 TGGCACCTTTTTTCTTTTTAAGTCCACAACTCCA
1 TGGCACC-TTTTT-TTTTTAAGTCCACAACTCCA
* *
3418090 TGGCACCCTTTTTTTTTTAAGTCCATAACTCCG
1 TGGCA-CCTTTTTTTTTTAAGTCCACAACTCCA
** * * *
3418123 TGGCACAGTTTTCTTCTAAGTCCACAACTTCA
1 TGGCACCTTTTTTTTTTAAGTCCACAACTCCA
3418155 TGGCA-CTTTTTTCTTTCTAAGTCCACAACTCCA
1 TGGCACCTTTTTT-TTT-TAAGTCCACAACTCCA
* * *
3418188 TGGCACCTTTTTCCTTTTAAATCCACAACTCTA
1 TGGCACCTTTTT-TTTTTAAGTCCACAACTCCA
* * * *
3418221 TGACACC-----CTTTTAGGTCCACAACTCCG
1 TGGCACCTTTTTTTTTTAAGTCCACAACTCCA
* ** * * * *
3418248 TGGCACCTTTTTCTTCAAAGTCTAGAACTTCT
1 TGGCACCTTTTTTTTTTAAGTCCACAACTCCA
* *
3418280 TGGCACCTTTTTCTTTTTAAGTCCATAAATCCA
1 TGGCACCTTTTT-TTTTTAAGTCCACAACTCCA
* * * * *
3418313 TAGTACC-----CTTTTAAGTCCCCAACTCCG
1 TGGCACCTTTTTTTTTTAAGTCCACAACTCCA
* * *
3418340 TGGCACCTTTTTCCTTTTAAGTTCATAACTCCA
1 TGGCACCTTTTT-TTTTTAAGTCCACAACTCCA
* * * * *
3418373 TAGAACCTTTTTCCTTTTAAGACCACAACTCTA
1 TGGCACCTTTTT-TTTTTAAGTCCACAACTCCA
*
3418406 TGGCACC-----TTTTTAAGTCCACAACTCCG
1 TGGCACCTTTTTTTTTTAAGTCCACAACTCCA
*
3418433 TGGCA-CTTTTTTCCTTTTAAGTTCACAACTC
1 TGGCACCTTTTTT--TTTTAAGTCCACAACTC
3418464 TATGAAACAT
Statistics
Matches: 286, Mismatches: 64, Indels: 49
0.72 0.16 0.12
Matches are distributed among these distances:
26 1 0.00
27 63 0.22
31 5 0.02
32 52 0.18
33 144 0.50
34 19 0.07
35 2 0.01
ACGTcount: A:0.23, C:0.29, G:0.10, T:0.38
Consensus pattern (32 bp):
TGGCACCTTTTTTTTTTAAGTCCACAACTCCA
Found at i:3418150 original size:65 final size:64
Alignment explanation
Indices: 3418050--3418504 Score: 285
Period size: 60 Copynumber: 7.2 Consensus size: 64
3418040 AAAATCCATG
* *
3418050 ACTCTGTGGCACCTTTTTTCTTTTTAAGTCCACAACTCCATGGCACCCTTTTTTTTTTAAGTCCA
1 ACTCCGTGGCACC-TTTTTC-TTCTAAGTCCACAACTCCATGGCA-CCTTTTTTTTTTAAGTCCA
*
3418115 TA
63 CA
** *
3418117 ACTCCGTGGCACAGTTTTCTTCTAAGTCCACAACTTCATGGCA-CTTTTTTCTTTCTAAGTCCAC
1 ACTCCGTGGCACCTTTTTCTTCTAAGTCCACAACTCCATGGCACCTTTTTT-TTT-TAAGTCCAC
3418181 A
64 A
* * * * * * *
3418182 ACTCCATGGCACCTTTTTCCTTTTAAATCCACAACTCTATGACACC-----CTTTTAGGTCCACA
1 ACTCCGTGGCACCTTTTT-CTTCTAAGTCCACAACTCCATGGCACCTTTTTTTTTTAAGTCCACA
* * * * * *
3418242 ACTCCGTGGCACCTTTTTCTTCAAAGTCTAGAACTTCTTGGCACCTTTTTCTTTTTAAGTCCATA
1 ACTCCGTGGCACCTTTTTCTTCTAAGTCCACAACTCCATGGCACCTTTTT-TTTTTAAGTCCACA
* * * * * * * * * *
3418307 AATCCATAGTACC-----CTTTTAAGTCCCCAACTCCGTGGCACCTTTTTCCTTTTAAGTTCATA
1 ACTCCGTGGCACCTTTTTCTTCTAAGTCCACAACTCCATGGCACCTTTTT-TTTTTAAGTCCACA
* * * * * *
3418367 ACTCCATAGAACCTTTTTCCTTTTAAGACCACAACTCTATGGCACC-----TTTTTAAGTCCACA
1 ACTCCGTGGCACCTTTTT-CTTCTAAGTCCACAACTCCATGGCACCTTTTTTTTTTAAGTCCACA
* * * * ** * * ** *
3418427 ACTCCGTGGCACTTTTTTCCTTTTAAGTTCACAACTCTATGAAACATTTTTCTTCAAAGTCTACA
1 ACTCCGTGGCACCTTTTT-CTTCTAAGTCCACAACTCCATGGCACCTTTTTTTTTTAAGTCCACA
*
3418492 ACTCTGTGGCACC
1 ACTCCGTGGCACC
3418505 CTTCTTTAAA
Statistics
Matches: 301, Mismatches: 66, Indels: 44
0.73 0.16 0.11
Matches are distributed among these distances:
59 18 0.06
60 123 0.41
61 3 0.01
63 7 0.02
64 3 0.01
65 87 0.29
66 48 0.16
67 12 0.04
ACGTcount: A:0.23, C:0.29, G:0.11, T:0.38
Consensus pattern (64 bp):
ACTCCGTGGCACCTTTTTCTTCTAAGTCCACAACTCCATGGCACCTTTTTTTTTTAAGTCCACA
Found at i:3418356 original size:125 final size:127
Alignment explanation
Indices: 3418071--3418417 Score: 318
Period size: 125 Copynumber: 2.8 Consensus size: 127
3418061 CCTTTTTTCT
* **
3418071 TTTTAAGTCCACAACTCCATGGCACCCTTTTT-TTTTTAAGTCCATAACTCCGTGGCACAGTTTT
1 TTTTAAGTCCACAACTCCATGGCA-CCTTTTTCCTTTTAAGTCCATAACTCCGTGGCACCTTTTT
* * * *
3418135 CTTCTAAGTCCACAACTTCATGGCACTTTTTTCTTTCTAAGTCCACAACTCCATGGCACCTTTTT
65 CTTCAAAGTCCACAACTTCATGGCACCTTTTTCTTTCTAAGTCCACAAATCCATAGCACC----T
3418200 CC
126 CC
* * * * *
3418202 TTTTAAATCCACAACTCTATGACA-C-----CCTTTTAGGTCCACAACTCCGTGGCACCTTTTTC
1 TTTTAAGTCCACAACTCCATGGCACCTTTTTCCTTTTAAGTCCATAACTCCGTGGCACCTTTTTC
* * * * * *
3418261 TTCAAAGTCTAGAACTTCTTGGCACCTTTTTCTTTTTAAGTCCATAAATCCATAGTA-C-CC
66 TTCAAAGTCCACAACTTCATGGCACCTTTTTCTTTCTAAGTCCACAAATCCATAGCACCTCC
* * * * * *
3418321 TTTTAAGTCCCCAACTCCGTGGCACCTTTTTCCTTTTAAGTTCATAACTCCATAGAACCTTTTTC
1 TTTTAAGTCCACAACTCCATGGCACCTTTTTCCTTTTAAGTCCATAACTCCGTGGCACCTTTTT-
** *
3418386 CTTTTAAGACCACAAC-TCTATGGCACCTTTTT
65 CTTCAAAGTCCACAACTTC-ATGGCACCTTTTT
3418418 AAGTCCACAA
Statistics
Matches: 172, Mismatches: 35, Indels: 23
0.75 0.15 0.10
Matches are distributed among these distances:
119 21 0.12
120 1 0.01
124 1 0.01
125 104 0.60
126 23 0.13
129 1 0.01
131 21 0.12
ACGTcount: A:0.23, C:0.29, G:0.10, T:0.38
Consensus pattern (127 bp):
TTTTAAGTCCACAACTCCATGGCACCTTTTTCCTTTTAAGTCCATAACTCCGTGGCACCTTTTTC
TTCAAAGTCCACAACTTCATGGCACCTTTTTCTTTCTAAGTCCACAAATCCATAGCACCTCC
Found at i:3418429 original size:93 final size:93
Alignment explanation
Indices: 3418050--3418478 Score: 382
Period size: 93 Copynumber: 4.6 Consensus size: 93
3418040 AAAATCCATG
* * * * * *
3418050 ACTCTGTGGCACCTTTTTTCTTTTTAAGTCCACAACTCCATGGCACCCTTTTT-TTTTTAAGTCC
1 ACTCCGTGGCACC-TTTTTCCTTTTAAGTTCACAACTCCATGG-AACCTTTTTCCTTTTAAGACC
* * * *
3418114 ATAACTCCGTGGCACAGTTTTCTTCTAAGTCCACA
64 ACAACTCCATGGCAC-----CCTTTTAAGTCCACA
* * * * *
3418149 ACTTCATGGCA-CTTTTTTCTTTCTAAGTCCACAACTCCATGGCACCTTTTTCCTTTTAA-ATCC
1 ACTCCGTGGCACCTTTTTCCTTT-TAAGTTCACAACTCCATGGAACCTTTTTCCTTTTAAGA-CC
* * *
3418212 ACAACTCTATGACACCCTTTTAGGTCCACA
64 ACAACTCCATGGCACCCTTTTAAGTCCACA
** * * * * * *
3418242 ACTCCGTGGCACCTTTTT-CTTCAAAG-TCTAGAACTTCTTGGCACCTTTTTCTTTTTAAGTCCA
1 ACTCCGTGGCACCTTTTTCCTTTTAAGTTC-ACAACTCCATGGAACCTTTTTCCTTTTAAGACCA
* * * * *
3418305 TAAATCCATAGTACCCTTTTAAGTCCCCA
65 CAACTCCATGGCACCCTTTTAAGTCCACA
* *
3418334 ACTCCGTGGCACCTTTTTCCTTTTAAGTTCATAACTCCATAGAACCTTTTTCCTTTTAAGACCAC
1 ACTCCGTGGCACCTTTTTCCTTTTAAGTTCACAACTCCATGGAACCTTTTTCCTTTTAAGACCAC
* *
3418399 AACTCTATGGCACCTTTTTAAGTCCACA
66 AACTCCATGGCACCCTTTTAAGTCCACA
* * * *
3418427 ACTCCGTGGCACTTTTTTCCTTTTAAGTTCACAACTCTATGAAACATTTTTC
1 ACTCCGTGGCACCTTTTTCCTTTTAAGTTCACAACTCCATGGAACCTTTTTC
3418479 TTCAAAGTCT
Statistics
Matches: 266, Mismatches: 56, Indels: 22
0.77 0.16 0.06
Matches are distributed among these distances:
91 1 0.00
92 70 0.26
93 125 0.47
94 8 0.03
97 15 0.06
98 39 0.15
99 8 0.03
ACGTcount: A:0.23, C:0.29, G:0.10, T:0.38
Consensus pattern (93 bp):
ACTCCGTGGCACCTTTTTCCTTTTAAGTTCACAACTCCATGGAACCTTTTTCCTTTTAAGACCAC
AACTCCATGGCACCCTTTTAAGTCCACA
Found at i:3418441 original size:26 final size:27
Alignment explanation
Indices: 3418387--3418444 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
3418377 ACCTTTTTCC
*
3418387 TTTTAAGACCACAACTCTATGGCACCT
1 TTTTAAGACCACAACTCCATGGCACCT
* * *
3418414 TTTTAAGTCCACAACTCCGTGGCACTT
1 TTTTAAGACCACAACTCCATGGCACCT
3418441 TTTT
1 TTTT
3418445 CCTTTTAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.36
Consensus pattern (27 bp):
TTTTAAGACCACAACTCCATGGCACCT
Found at i:3418477 original size:33 final size:33
Alignment explanation
Indices: 3418319--3418495 Score: 93
Period size: 33 Copynumber: 5.6 Consensus size: 33
3418309 TCCATAGTAC
* * ** *
3418319 CCTTTTAAGTCCCCAACTCCGTGGCACCTTTTT
1 CCTTTTAAGTCCACAACTCCATGAAACATTTTT
* * *
3418352 CCTTTTAAGTTCATAACTCCAT-AGAACCTTTTT
1 CCTTTTAAGTCCACAACTCCATGA-AACATTTTT
* * *
3418385 CCTTTTAAGACCACAACTCTATG--GCA-----
1 CCTTTTAAGTCCACAACTCCATGAAACATTTTT
* ** *
3418411 CCTTTTTAAGTCCACAACTCCGTGGCACTTTTTT
1 CC-TTTTAAGTCCACAACTCCATGAAACATTTTT
* *
3418445 CCTTTTAAGTTCACAACTCTATGAAACATTTTT
1 CCTTTTAAGTCCACAACTCCATGAAACATTTTT
** *
3418478 -CTTCAAAGTCTACAACTC
1 CCTTTTAAGTCCACAACTC
3418496 TGTGGCACCC
Statistics
Matches: 107, Mismatches: 27, Indels: 21
0.69 0.17 0.14
Matches are distributed among these distances:
26 2 0.02
27 18 0.17
29 1 0.01
31 1 0.01
32 14 0.13
33 69 0.64
34 2 0.02
ACGTcount: A:0.25, C:0.29, G:0.09, T:0.37
Consensus pattern (33 bp):
CCTTTTAAGTCCACAACTCCATGAAACATTTTT
Found at i:3418533 original size:32 final size:32
Alignment explanation
Indices: 3418497--3418900 Score: 229
Period size: 32 Copynumber: 12.4 Consensus size: 32
3418487 CTACAACTCT
*
3418497 GTGGCACCCTTCTTTAAAGCCCACACAAGTTG
1 GTGGCACCCTTCTTTAAAGCCCACACAAGTCG
* * *
3418529 GTGGCA-ACTTCTTTTAAAGCCCACACAAATTG
1 GTGGCACCCTTC-TTTAAAGCCCACACAAGTCG
* **
3418561 GTGGTAACCCTT-TCAAAAGCCCACACAAGTCG
1 GTGG-CACCCTTCTTTAAAGCCCACACAAGTCG
* * *
3418593 GTGGAAACC-TCTTTCAAAAG-CC-CACAAGTTG
1 GTGGCACCCTTCTTT--AAAGCCCACACAAGTCG
* *
3418624 GTGGCAACCC-TCTCTAAAGCCCACACAAGTCA
1 GTGGC-ACCCTTCTTTAAAGCCCACACAAGTCG
** *
3418656 GTGGCAACCCTTCTCAAAAGCCCACACAAGTCA
1 GTGGC-ACCCTTCTTTAAAGCCCACACAAGTCG
* * *
3418689 GAGGCA-ACATCTTTCAAAAGCCCACACAAGTCG
1 GTGGCACCCTTCTTT--AAAGCCCACACAAGTCG
* *
3418722 GTGGCAACC-TCTTTCAAAAGCCCACATAAGTCG
1 GTGGCACCCTTCTTT--AAAGCCCACACAAGTCG
* * *
3418755 GTGGTAACCTT-TTTCAAAGCCCACACAAGTTG
1 GTGGCACCCTTCTTT-AAAGCCCACACAAGTCG
* * * *
3418787 GTGGTA-ACTTCTTTTCTAAAGCCCACAAAAGTCA
1 GTGGCACCCTTC--TT-TAAAGCCCACACAAGTCG
* * * *
3418821 GTGGCAACCC-CCTTCAAAAGCCCACATAAGTTG
1 GTGGC-ACCCTTCTT-TAAAGCCCACACAAGTCG
* ** * *
3418854 GTGGTAACCC-TCTCAAAAGCCCACATATGTCG
1 GTGG-CACCCTTCTTTAAAGCCCACACAAGTCG
3418886 GTGGCATCTCCTTCT
1 GTGGCA-C-CCTTCT
3418901 AAGCCCAATG
Statistics
Matches: 300, Mismatches: 48, Indels: 46
0.76 0.12 0.12
Matches are distributed among these distances:
30 5 0.02
31 31 0.10
32 118 0.39
33 114 0.38
34 28 0.09
35 3 0.01
36 1 0.00
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.22
Consensus pattern (32 bp):
GTGGCACCCTTCTTTAAAGCCCACACAAGTCG
Found at i:3418612 original size:33 final size:33
Alignment explanation
Indices: 3418512--3418891 Score: 407
Period size: 33 Copynumber: 11.7 Consensus size: 33
3418502 ACCCTTCTTT
* * *
3418512 AAAGCCCACACAAGTTGGTGGCAACTTCTTT-T
1 AAAGCCCACACAAGTCGGTGGCAACCTCTTTCA
* * *
3418544 AAAGCCCACACAAATTGGTGGTAACC-CTTTCA
1 AAAGCCCACACAAGTCGGTGGCAACCTCTTTCA
*
3418576 AAAGCCCACACAAGTCGGTGGAAACCTCTTTCA
1 AAAGCCCACACAAGTCGGTGGCAACCTCTTTCA
* * *
3418609 AAAG-CC-CACAAGTTGGTGGCAACC-CTCTCT
1 AAAGCCCACACAAGTCGGTGGCAACCTCTTTCA
*
3418639 AAAGCCCACACAAGTCAGTGGCAACC-CTTCTCA
1 AAAGCCCACACAAGTCGGTGGCAACCTCTT-TCA
* * *
3418672 AAAGCCCACACAAGTCAGAGGCAACATCTTTCA
1 AAAGCCCACACAAGTCGGTGGCAACCTCTTTCA
3418705 AAAGCCCACACAAGTCGGTGGCAACCTCTTTCA
1 AAAGCCCACACAAGTCGGTGGCAACCTCTTTCA
* * *
3418738 AAAGCCCACATAAGTCGGTGGTAACCTTTTTC-
1 AAAGCCCACACAAGTCGGTGGCAACCTCTTTCA
* * * *
3418770 AAAGCCCACACAAGTTGGTGGTAACTTCTTTTCT
1 AAAGCCCACACAAGTCGGTGGCAACCTC-TTTCA
* * * *
3418804 AAAGCCCACAAAAGTCAGTGGCAACCCCCTTCA
1 AAAGCCCACACAAGTCGGTGGCAACCTCTTTCA
* * * *
3418837 AAAGCCCACATAAGTTGGTGGTAACC-CTCTCA
1 AAAGCCCACACAAGTCGGTGGCAACCTCTTTCA
* *
3418869 AAAGCCCACATATGTCGGTGGCA
1 AAAGCCCACACAAGTCGGTGGCA
3418892 TCTCCTTCTA
Statistics
Matches: 296, Mismatches: 44, Indels: 16
0.83 0.12 0.04
Matches are distributed among these distances:
30 8 0.03
31 22 0.07
32 114 0.39
33 127 0.43
34 25 0.08
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.21
Consensus pattern (33 bp):
AAAGCCCACACAAGTCGGTGGCAACCTCTTTCA
Found at i:3419047 original size:52 final size:52
Alignment explanation
Indices: 3418975--3419270 Score: 234
Period size: 52 Copynumber: 5.5 Consensus size: 52
3418965 CAACGTCATC
* * * * ** *
3418975 GGCCTTGAATCAACACATTGGCACCTTTTTTTTTCTT-AAGTCTAATATCGTT
1 GGCCTTAAATCAGCATATTGGCACC-TTTGTCATCTTCAAGTCTAATATCGCT
* ** * *
3419027 GGCCTTAAATTAGCATATTGGTGCCTTTGTCATCTTTAAGTCTAATATTGCT
1 GGCCTTAAATCAGCATATTGGCACCTTTGTCATCTTCAAGTCTAATATCGCT
* * * * *
3419079 GGCCTTAAATCAGCATATCGACATCTTATCATTCTTCTCATCTTCAAGTCTAATGTCACT
1 GGCCTTAAATCAGCATATTGGCA-C----C--T-TTGTCATCTTCAAGTCTAATATCGCT
* * * * *
3419139 GGCCTTGAATCAGCATATTAGCACCTTTGTCATCTTGAAGCCCAATATCGCT
1 GGCCTTAAATCAGCATATTGGCACCTTTGTCATCTTCAAGTCTAATATCGCT
* ** * *
3419191 GGCCTTGAATCAGCATATTGGCACCTTCATCATCTTCAAGCCTGATATCGCT
1 GGCCTTAAATCAGCATATTGGCACCTTTGTCATCTTCAAGTCTAATATCGCT
* * *
3419243 GGCCGTAAATTAGAATATTGGCACCTTT
1 GGCCTTAAATCAGCATATTGGCACCTTT
3419271 AAGTCCAATG
Statistics
Matches: 193, Mismatches: 42, Indels: 18
0.76 0.17 0.07
Matches are distributed among these distances:
51 8 0.04
52 139 0.72
53 2 0.01
55 1 0.01
57 1 0.01
59 2 0.01
60 40 0.21
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.36
Consensus pattern (52 bp):
GGCCTTAAATCAGCATATTGGCACCTTTGTCATCTTCAAGTCTAATATCGCT
Found at i:3419142 original size:112 final size:111
Alignment explanation
Indices: 3419008--3419208 Score: 276
Period size: 112 Copynumber: 1.8 Consensus size: 111
3418998 CCTTTTTTTT
** * * ** * * *
3419008 TCTTAAGTCTAATATCGTTGGCCTTAAATTAGCATATTGGTGCCTTTGTCATCTTTAAGTCTAAT
1 TCTTAAGTCTAATATCACTGGCCTTAAATCAGCATATTAGCACCTTTGTCATCTTGAAGCCCAAT
*
3419073 ATTGCTGGCCTTAAATCAGCATATCGACATCTTATCATTCTTCTCA
66 ATCGCTGGCCTTAAATCAGCATATCGACATCTTATCATTCTTCTCA
* *
3419119 TCTTCAAGTCTAATGTCACTGGCCTTGAATCAGCATATTAGCACCTTTGTCATCTTGAAGCCCAA
1 TCTT-AAGTCTAATATCACTGGCCTTAAATCAGCATATTAGCACCTTTGTCATCTTGAAGCCCAA
*
3419184 TATCGCTGGCCTTGAATCAGCATAT
65 TATCGCTGGCCTTAAATCAGCATAT
3419209 TGGCACCTTC
Statistics
Matches: 76, Mismatches: 13, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
111 4 0.05
112 72 0.95
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (111 bp):
TCTTAAGTCTAATATCACTGGCCTTAAATCAGCATATTAGCACCTTTGTCATCTTGAAGCCCAAT
ATCGCTGGCCTTAAATCAGCATATCGACATCTTATCATTCTTCTCA
Found at i:3420012 original size:20 final size:21
Alignment explanation
Indices: 3419964--3420017 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
3419954 TTCTATAATT
* *
3419964 TGTATCAATACAAATAGTAAA
1 TGTATCGATACATATAGTAAA
* *
3419985 TTTATCGATACATA-AGTGAA
1 TGTATCGATACATATAGTAAA
3420005 TGTATCGATACAT
1 TGTATCGATACAT
3420018 GCTCGAAATG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (21 bp):
TGTATCGATACATATAGTAAA
Found at i:3421540 original size:19 final size:20
Alignment explanation
Indices: 3421498--3421549 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
3421488 AAGCTCAAAA
* *
3421498 GTATCGATACATATTGCTTT
1 GTATCGATACATGTTGCATT
3421518 GTATCGATACATGTT-CATT
1 GTATCGATACATGTTGCATT
3421537 GTATCGATACATG
1 GTATCGATACATG
3421550 AAATTGGTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.40
Consensus pattern (20 bp):
GTATCGATACATGTTGCATT
Found at i:3424581 original size:166 final size:166
Alignment explanation
Indices: 3424398--3424968 Score: 611
Period size: 166 Copynumber: 3.4 Consensus size: 166
3424388 CTTATTTTTA
* * *
3424398 AAATACGTGTTTTTTCTTCTCTGTAAATTTTTTCGAGAGAAGTTTTCTTAATTTTTAATTTTTAA
1 AAATACG-GTATTTTCTTCTTTGTAAATTTTTTCGAGAGAATTTTTCTTAATTTTTAATTTTTAA
* ** **
3424463 AATTCGTCAAATGTTTTTATTTATTTTATATTAATTCAGTTTTCAAAAATTCATTCATTTTCATT
65 AATTCATCAAACATCATTATTTATTTTATATTAATTCAGTTTTCAAAAATTCATTCATTTTCATT
3424528 AGTTTTTGAATTTTTTCTTGAAATTTTCCTTTTTTCG
130 AGTTTTTGAATTTTTTCTTGAAATTTTCCTTTTTTCG
* * * *
3424565 AAATACGGTGTTTTCTTCTTTGTAAATTTTTTTGAGTAG-ATTTTTCTTAGTTTTTAACTTTTAA
1 AAATACGGTATTTTCTTCTTTGTAAATTTTTTCGAG-AGAATTTTTCTTAATTTTTAATTTTTAA
* *
3424629 AATTCATCAAACATCATTATTTATTTTGTATTAATTCTGTTTTCAAAAATTCATTCATTTTCATT
65 AATTCATCAAACATCATTATTTATTTTATATTAATTCAGTTTTCAAAAATTCATTCATTTTCATT
*
3424694 CA-TTTTT-AATTTTTTCCTTGAAATTTTTCTTTTTTCG
130 -AGTTTTTGAATTTTTT-CTTGAAATTTTCCTTTTTTCG
* ** * * * * *
3424731 AAATACGGTATTTTCTACTTCATAAA--TTTTCAAGGGGATTTTTCTCAGTTTTTAATTTTTAAA
1 AAATACGGTATTTTCTTCTTTGTAAATTTTTTCGAGAGAATTTTTCTTAATTTTTAATTTTTAAA
* * * *
3424794 ATTCATCAAACATCATTATTTGA-TTCATAGTT-ATTCATTTTTCAAAAAATTAATTCTTTTTCA
66 ATTCATCAAACATCATTATTT-ATTTTATA-TTAATTCAGTTTTC-AAAAATTCATTCATTTTCA
* * * * *
3424857 TGAG-TTTTGAATTTTTTTTGTTGAAATTCTCCTTTTTCCC
128 TTAGTTTTTGAA--TTTTTTCTTGAAATTTTCCTTTTTTCG
* * * * * * ** *
3424897 AAGAAACCGAAATTTCTTCTTTGTAAATTTTTTCGGGAGAA-TTTTCTTGATTTAGAATTTTGAA
1 AA-ATACGGTATTTTCTTCTTTGTAAATTTTTTCGAGAGAATTTTTCTTAATTTTTAATTTTTAA
*
3424961 AACTCATC
65 AATTCATC
3424969 TTGTAAGCTC
Statistics
Matches: 337, Mismatches: 53, Indels: 27
0.81 0.13 0.06
Matches are distributed among these distances:
163 1 0.00
164 69 0.20
165 31 0.09
166 171 0.51
167 33 0.10
168 24 0.07
169 8 0.02
ACGTcount: A:0.27, C:0.12, G:0.09, T:0.52
Consensus pattern (166 bp):
AAATACGGTATTTTCTTCTTTGTAAATTTTTTCGAGAGAATTTTTCTTAATTTTTAATTTTTAAA
ATTCATCAAACATCATTATTTATTTTATATTAATTCAGTTTTCAAAAATTCATTCATTTTCATTA
GTTTTTGAATTTTTTCTTGAAATTTTCCTTTTTTCG
Found at i:3425742 original size:20 final size:18
Alignment explanation
Indices: 3425717--3425769 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 18
3425707 GCTGGGTTTA
3425717 ATGTATCGATACAATGCAC
1 ATGTATCGATACAATG-AC
* *
3425736 TATGTATTGATACAAT-TC
1 -ATGTATCGATACAATGAC
3425754 ATGTATCGATACAATG
1 ATGTATCGATACAATG
3425770 TATCGATACT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 14 0.48
18 1 0.03
20 14 0.48
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (18 bp):
ATGTATCGATACAATGAC
Found at i:3425772 original size:13 final size:13
Alignment explanation
Indices: 3425754--3425778 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3425744 GATACAATTC
3425754 ATGTATCGATACA
1 ATGTATCGATACA
3425767 ATGTATCGATAC
1 ATGTATCGATAC
3425779 TAAGTGAGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3428982 original size:154 final size:155
Alignment explanation
Indices: 3428698--3429374 Score: 539
Period size: 154 Copynumber: 4.4 Consensus size: 155
3428688 GGTAGAATCA
* * * * * *
3428698 TCATTATTTATCCTTTTAAGTCCTTTAAGGGTA-TCAGGTATTTTTACATTGAAGGTATCCGCCA
1 TCATTATTTATCCTTTTAAGTCCTTTAGGGGTATTGA-GTACTTTTACGTCGAAGGTATCC-CCT
* * * * * *
3428762 AGGA-CATTTTCATAAATTTTCAGAACTGAGTCCTTA-GTTGTCATCGA-ATCTGCTTTTATGCT
64 AGGAGCATTTTCATAATTTTTCAAAACTAAGTCC-TAGGTTGTCATCGAGGTCCGCTTTTATGCC
* *
3428824 GAAGGTAGATATTTAGGATAGGTTCATT
128 GAAGGTAGGTATTTAGGATAGGTTCATC
* *
3428852 TCATTATTTATCCTTTTAAGTCCTTTAGGGGTATTGAATACTTTTATGTCGAAGGTATCCCCTAG
1 TCATTATTTATCCTTTTAAGTCCTTTAGGGGTATTGAGTACTTTTACGTCGAAGGTATCCCCTAG
**
3428917 GAGCATTTT-AGTAATTTTTCAAAA-TCAAGTCCTAGGTTGTCATCGA-GTTTG-TTTTCATGCC
66 GAGCATTTTCA-TAATTTTTCAAAACT-AAGTCCTAGGTTGTCATCGAGGTCCGCTTTT-ATGCC
* * *
3428978 GAAGGTGGGTATTTAGGATACGTTCACC
128 GAAGGTAGGTATTTAGGATAGGTTCATC
* * * * * *
3429006 CCATCTA--TATCCTTTTTAAGTCCTTTAGGGGTATCGGGTACTTTTACGTCAAAGTTATCTCCT
1 TCAT-TATTTATCC-TTTTAAGTCCTTTAGGGGTATTGAGTACTTTTACGTCGAAGGTATCCCCT
* *
3429069 AGG-GCCATTTTCATAA-TTTTCTAAAACTAAGT-CTTGAGTTGCCATC-AGGTCCGCTTTTATG
64 AGGAG-CATTTTCATAATTTTTC-AAAACTAAGTCCTAG-GTTGTCATCGAGGTCCGCTTTTATG
* * * * * *
3429130 CCAAAAGTGGGCATTTAGGATAGATTCATT
126 CCGAAGGTAGGTATTTAGGATAGGTTCATC
* * * * ** * *
3429160 TCATCAATAATCTTTTTAAGTCCTTTAGGGGTATTGAACACTTCTACGTCGAAGATATCCCCT-G
1 TCATTATTTATCCTTTTAAGTCCTTTAGGGGTATTGAGTACTTTTACGTCGAAGGTATCCCCTAG
* * * * * ** * * * *
3429224 CAGGCATTTTGATAATTTTTTAGAA-TCGAGTTTTAGGTTATCA-CCAGGTTCGCTTTTATGCTG
66 GA-GCATTTTCATAATTTTTCAAAACT-AAGTCCTAGGTTGTCATCGAGGTCCGCTTTTATGCCG
3429287 AAGGTAGGTATTTAGGATAGGTTCATC
129 AAGGTAGGTATTTAGGATAGGTTCATC
* * * *
3429314 TCATT-TATAATCTTTTTTAAGTCCTTTAGGGGTA--GCAGGTACTTTTATGTCAAAGGTATCC
1 TCATTAT-TTATC-CTTTTAAGTCCTTTAGGGGTATTG-A-GTACTTTTACGTCGAAGGTATCC
3429375 TTTAGAGGTA
Statistics
Matches: 421, Mismatches: 75, Indels: 53
0.77 0.14 0.10
Matches are distributed among these distances:
153 34 0.08
154 329 0.78
155 58 0.14
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (155 bp):
TCATTATTTATCCTTTTAAGTCCTTTAGGGGTATTGAGTACTTTTACGTCGAAGGTATCCCCTAG
GAGCATTTTCATAATTTTTCAAAACTAAGTCCTAGGTTGTCATCGAGGTCCGCTTTTATGCCGAA
GGTAGGTATTTAGGATAGGTTCATC
Found at i:3432103 original size:13 final size:13
Alignment explanation
Indices: 3432085--3432109 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3432075 CATAAAGTGT
3432085 TGTATCGATACAA
1 TGTATCGATACAA
3432098 TGTATCGATACA
1 TGTATCGATACA
3432110 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3432120 original size:32 final size:33
Alignment explanation
Indices: 3432065--3432128 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 33
3432055 TTCAACGATT
3432065 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
3432098 TGTATCGATACAT-AAGTGTTGTATCGATACA
1 TGTATCGATACATAAAGTGTTGTATCGATACA
3432129 TAAGTTTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 18 0.58
33 13 0.42
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:3432122 original size:19 final size:19
Alignment explanation
Indices: 3432064--3432147 Score: 108
Period size: 19 Copynumber: 4.7 Consensus size: 19
3432054 TTTCAACGAT
3432064 TTGTATCGATACATAAAGTG
1 TTGTATCGATACAT-AAGTG
3432084 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
3432098 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
*
3432116 TTGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
3432135 TTGTATCGATACA
1 TTGTATCGATACA
3432148 ATGTAAGCTA
Statistics
Matches: 57, Mismatches: 1, Indels: 13
0.80 0.01 0.18
Matches are distributed among these distances:
13 11 0.19
15 2 0.04
17 2 0.04
19 30 0.53
20 12 0.21
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:3432208 original size:13 final size:13
Alignment explanation
Indices: 3432190--3432214 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3432180 ATTACTCAAA
3432190 TGTATCGATACAT
1 TGTATCGATACAT
3432203 TGTATCGATACA
1 TGTATCGATACA
3432215 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3432264 original size:52 final size:52
Alignment explanation
Indices: 3432223--3432351 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
3432213 CACTGATCTT
* *
3432223 TGTATCGATATATGCAGGCAAATTTGCCTAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
3432275 TGTATCGATACATGAAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
3432327 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
3432352 TCATATTTCG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:3438715 original size:14 final size:15
Alignment explanation
Indices: 3438708--3438746 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
3438698 AAAAGTCAAA
3438708 AAAAAAAAGAAGAGT
1 AAAAAAAAGAAGAGT
3438723 AAAAAAAA-AAGAGT
1 AAAAAAAAGAAGAGT
3438737 CAAAAAAAAG
1 -AAAAAAAAG
3438747 TGTAAAGGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.77, C:0.03, G:0.15, T:0.05
Consensus pattern (15 bp):
AAAAAAAAGAAGAGT
Found at i:3438726 original size:13 final size:13
Alignment explanation
Indices: 3438709--3438752 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
3438699 AAAGTCAAAA
3438709 AAAAAAAGAAGAGT
1 AAAAAAA-AAGAGT
3438723 AAAAAAAAAAGAGT
1 -AAAAAAAAAGAGT
* *
3438737 CAAAAAAAAGTGT
1 AAAAAAAAAGAGT
3438750 AAA
1 AAA
3438753 GGCAAAATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 13 0.50
14 6 0.23
15 7 0.27
ACGTcount: A:0.73, C:0.02, G:0.16, T:0.09
Consensus pattern (13 bp):
AAAAAAAAAGAGT
Found at i:3438743 original size:17 final size:18
Alignment explanation
Indices: 3438701--3438745 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 18
3438691 CACAAACAAA
3438701 AGTCAAAAAAAAAAAGAAG
1 AGTC-AAAAAAAAAAGAAG
3438720 AGT---AAAAAAAA-AAG
1 AGTCAAAAAAAAAAGAAG
3438734 AGTCAAAAAAAA
1 AGTCAAAAAAAA
3438746 GTGTAAAGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
14 6 0.26
15 8 0.35
17 6 0.26
19 3 0.13
ACGTcount: A:0.76, C:0.04, G:0.13, T:0.07
Consensus pattern (18 bp):
AGTCAAAAAAAAAAGAAG
Found at i:3440095 original size:30 final size:30
Alignment explanation
Indices: 3440027--3440432 Score: 331
Period size: 31 Copynumber: 13.1 Consensus size: 30
3440017 TTCAAATACC
* * *
3440027 TTCTTAAAGTCCATGACTCAGTGGCAATCTC
1 TTCTCAAAGTCCACGACTCAGTGGC-ATCTT
* *
3440058 TTCTCAAAGCCCACAACTCAGTGGCAT-TT
1 TTCTCAAAGTCCACGACTCAGTGGCATCTT
* *
3440087 TGTCTCAAAGTCCACGATTCTGTGGCATCCTT
1 T-TCTCAAAGTCCACGACTCAGTGGCAT-CTT
3440119 TTCTTCAAAGTCCACGACTCAGTGGCAT-TT
1 TTC-TCAAAGTCCACGACTCAGTGGCATCTT
*
3440149 TATCTCAAAGTCCATGACTCAGTGGCATCCGTT
1 T-TCTCAAAGTCCACGACTCAGTGGCAT-C-TT
3440182 TT-TCAAAGTCCACGACTCAGTGGCAT-TT
1 TTCTCAAAGTCCACGACTCAGTGGCATCTT
* *
3440210 TGTCTCAAAGTCCACGGCTTAGTGGCATCCTT
1 T-TCTCAAAGTCCACGACTCAGTGGCAT-CTT
*
3440242 TTCTTCAAAGTCCACGACTCAGTGGCGT-TT
1 TTC-TCAAAGTCCACGACTCAGTGGCATCTT
*
3440272 TGTCTCAAAGTCCACGACTTAGTGGCATCCTT
1 T-TCTCAAAGTCCACGACTCAGTGGCAT-CTT
* * *
3440304 TTCTTCAAAGTCCACAACTTC-GTGGTACCTT
1 TTC-TCAAAGTCCACGAC-TCAGTGGCATCTT
** * *
3440335 GTTCTTTGTAAGTCCACGACTCCGTGGCACCTT
1 -TTC--TCAAAGTCCACGACTCAGTGGCATCTT
* * * *
3440368 CCTT-TCAAAGTCAAAGACTCCGTGGCACCTTT
1 --TTCTCAAAGTCCACGACTCAGTGGCATC-TT
* * * *
3440400 TTTTCAAAGCCCACAACTCCGTGGCACTCTT
1 TTCTCAAAGTCCACGACTCAGTGGCA-TCTT
3440431 TT
1 TT
3440433 TCCCTTTTAA
Statistics
Matches: 312, Mismatches: 38, Indels: 50
0.78 0.09 0.12
Matches are distributed among these distances:
28 3 0.01
29 3 0.01
30 99 0.32
31 101 0.32
32 79 0.25
33 25 0.08
34 2 0.01
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.32
Consensus pattern (30 bp):
TTCTCAAAGTCCACGACTCAGTGGCATCTT
Found at i:3440251 original size:123 final size:122
Alignment explanation
Indices: 3440032--3440322 Score: 433
Period size: 123 Copynumber: 2.4 Consensus size: 122
3440022 ATACCTTCTT
* *
3440032 AAAGTCCATGACTCAGTGGCAAT-CTCTTCTCAAAGCCCACAACTCAGTGGCATTTTGTCTCAAA
1 AAAGTCCATGACTCAGTGGC-ATCCT-TTTTCAAAGTCCACAACTCAGTGGCATTTTGTCTCAAA
*
3440096 GTCCACGATTCTGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGCATTTTATCTC
64 GTCCACGATTCAGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGCATTTTATCTC
*
3440155 AAAGTCCATGACTCAGTGGCATCCGTTTTTCAAAGTCCACGACTCAGTGGCATTTTGTCTCAAAG
1 AAAGTCCATGACTCAGTGGCATCC-TTTTTCAAAGTCCACAACTCAGTGGCATTTTGTCTCAAAG
* * *
3440220 TCCACGGCTT-AGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGCGTTTTGTCTC
65 TCCAC-GATTCAGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGCATTTTATCTC
* *
3440278 AAAGTCCACGACTTAGTGGCATCCTTTTCTTCAAAGTCCACAACT
1 AAAGTCCATGACTCAGTGGCATCC-TTT-TTCAAAGTCCACAACT
3440323 TCGTGGTACC
Statistics
Matches: 153, Mismatches: 11, Indels: 7
0.89 0.06 0.04
Matches are distributed among these distances:
122 2 0.01
123 132 0.86
124 19 0.12
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.31
Consensus pattern (122 bp):
AAAGTCCATGACTCAGTGGCATCCTTTTTCAAAGTCCACAACTCAGTGGCATTTTGTCTCAAAGT
CCACGATTCAGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGCATTTTATCTC
Found at i:3440387 original size:31 final size:30
Alignment explanation
Indices: 3440307--3440657 Score: 211
Period size: 31 Copynumber: 10.8 Consensus size: 30
3440297 CATCCTTTTC
* * *
3440307 TTCAAAGTCCACAACTTCGTGGTACCTTGTTCT
1 TTCAAAGT-CACAACTCCGTGGCACC-T-TCCT
** *
3440340 TTGTAAGTCCACGACTCCGTGGCACCTTCCT
1 TTCAAAGT-CACAACTCCGTGGCACCTTCCT
* **
3440371 TTCAAAGTCAAAGACTCCGTGGCACCTTTTT
1 TTCAAAGTCACA-ACTCCGTGGCACCTTCCT
*
3440402 TTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCT
1 TTCAAAG-TCACAACTCCGTGGCAC-C---TT-CCT
* *
3440438 TTTAAAGTCCACAACTTCGTGGCACCTTGTTCCT
1 TTCAAAGT-CACAACTCCGTGGCACC---TTCCT
* *
3440472 TT-TAAGTCCACAACTCCGTGGCACCTTCTT
1 TTCAAAGT-CACAACTCCGTGGCACCTTCCT
*
3440502 TTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCT
1 TTCAAAG-TCACAACTCCGTGGCAC-C---TT-CCT
* *
3440538 TTTAAAGTCCACAACCCCGTGGCACCTTGTTCCT
1 TTCAAAGT-CACAACTCCGTGGCACC---TTCCT
* *
3440572 TT-TAAGTCCACAACTCCGTGGCACCTTTCT
1 TTCAAAGT-CACAACTCCGTGGCACCTTCCT
* * **
3440602 TTCAAAGTCCGCGACTCCGTGGCACCTTATT
1 TTCAAAGT-CACAACTCCGTGGCACCTTCCT
*
3440633 TTCAAAGCCCACAACTCCGTGGCAC
1 TTCAAAG-TCACAACTCCGTGGCAC
3440658 TCTTTTTCCC
Statistics
Matches: 259, Mismatches: 41, Indels: 38
0.77 0.12 0.11
Matches are distributed among these distances:
30 14 0.05
31 107 0.41
32 6 0.02
33 63 0.24
34 10 0.04
35 14 0.05
36 45 0.17
ACGTcount: A:0.21, C:0.34, G:0.15, T:0.31
Consensus pattern (30 bp):
TTCAAAGTCACAACTCCGTGGCACCTTCCT
Found at i:3440504 original size:100 final size:99
Alignment explanation
Indices: 3440279--3440750 Score: 461
Period size: 100 Copynumber: 4.8 Consensus size: 99
3440269 TTTTGTCTCA
* ** * * *
3440279 AAGTCCACGACTTAGTGGCATCCTTTTCTTCAAAGTCCACAACTTCGTGGTAC-CTTGTT--CTT
1 AAGTCCACAACTCCGTGGCA-CCTTTT-TTCAAAGTCCACAACTCCGTGGCACTCTTTTTCCCTT
* *
3440341 TGT-AAGTCCACGACTCCGTGGCACC---TTCCTTTCA
64 T-TAAAGTCCACAACTCCGTGGCACCTTGTTCCTTT-T
* *
3440375 AAGT-CAAAGACTCCGTGGCACCTTTTTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTT
1 AAGTCCACA-ACTCCGTGGCACC-TTTTTTCAAAGTCCACAACTCCGTGGCACTCTTTTTCCCTT
*
3440439 TTAAAGTCCACAACTTCGTGGCACCTTGTTCCTTTT
64 TTAAAGTCCACAACTCCGTGGCACCTTGTTCCTTTT
*
3440475 AAGTCCACAACTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT
1 AAGTCCACAACTCCGTGGCACCTT-TTTTCAAAGTCCACAACTCCGTGGCACTCTTTTTCCCTTT
*
3440540 TAAAGTCCACAACCCCGTGGCACCTTGTTCCTTTT
65 TAAAGTCCACAACTCCGTGGCACCTTGTTCCTTTT
* * *
3440575 AAGTCCACAACTCCGTGGCACCTTTCTTTCAAAGTCCGCGACTCCGTGGCAC-C-TTAT---TTT
1 AAGTCCACAACTCCGTGGCACCTTT-TTTCAAAGTCCACAACTCCGTGGCACTCTTTTTCCCTTT
* * *
3440635 CAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
65 TAAAGTCCACAACTCCGTGGCAC-CTTGTT-CCTTTT
* ** * **
3440672 AAAG-CCTATAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTTCGTGGCA-TCTTTCACC
1 -AAGTCC-ACAACTCCGTGGCACCTT-TT--TTCAAAGTCCACAACTCCGTGGCACTCTTTTTCC
*
3440735 CTTTTTAAAGCCCACA
61 C-TTTTAAAGTCCACA
3440751 CAAGTCGATG
Statistics
Matches: 320, Mismatches: 31, Indels: 41
0.82 0.08 0.10
Matches are distributed among these distances:
95 49 0.15
96 27 0.08
97 9 0.03
98 48 0.15
99 5 0.02
100 157 0.49
101 12 0.04
105 13 0.04
ACGTcount: A:0.21, C:0.33, G:0.14, T:0.32
Consensus pattern (99 bp):
AAGTCCACAACTCCGTGGCACCTTTTTTCAAAGTCCACAACTCCGTGGCACTCTTTTTCCCTTTT
AAAGTCCACAACTCCGTGGCACCTTGTTCCTTTT
Found at i:3440640 original size:231 final size:231
Alignment explanation
Indices: 3440310--3440725 Score: 692
Period size: 231 Copynumber: 1.8 Consensus size: 231
3440300 CCTTTTCTTC
** * *
3440310 AAAGTCCACAACTTCGTGGTACCTTGTTCTTTGTAAGTCCACGACTCCGTGGCACCTTCCTTTCA
1 AAAGTCCACAACCCCGTGGCACCTTGTTCTTTGTAAGTCCACAACTCCGTGGCACCTTCCTTTCA
*
3440375 AAGTCAAAGACTCCGTGGCACCTTTTTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT
66 AAGTCAAAGACTCCGTGGCACCTTATTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT
*
3440440 TAAAGTCC-ACAACTTCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCTTCTTTT
131 TAAAG-CCTACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCTTCTTTT
3440504 CAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
195 CAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
*
3440541 AAAGTCCACAACCCCGTGGCACCTTGTTCCTTT-TAAGTCCACAACTCCGTGGCACCTTTCTTTC
1 AAAGTCCACAACCCCGTGGCACCTTGTT-CTTTGTAAGTCCACAACTCCGTGGCACCTTCCTTTC
***
3440605 AAAGTCCGCGACTCCGTGGCACCTTATTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTT
65 AAAGTCAAAGACTCCGTGGCACCTTATTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTT
* *
3440670 TTAAAGCCTATAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTTCGTGGCA
130 TTAAAGCCTACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCA
3440726 TCTTTCACCC
Statistics
Matches: 171, Mismatches: 12, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
230 2 0.01
231 165 0.96
232 4 0.02
ACGTcount: A:0.21, C:0.33, G:0.15, T:0.32
Consensus pattern (231 bp):
AAAGTCCACAACCCCGTGGCACCTTGTTCTTTGTAAGTCCACAACTCCGTGGCACCTTCCTTTCA
AAGTCAAAGACTCCGTGGCACCTTATTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT
TAAAGCCTACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCTTCTTTTC
AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
Found at i:3440655 original size:62 final size:61
Alignment explanation
Indices: 3440032--3440662 Score: 419
Period size: 62 Copynumber: 9.9 Consensus size: 61
3440022 ATACCTTCTT
* * * * * * * * * *
3440032 AAAGTCCATGACTCAGTGGCAATCTCTTCTCAAAGCCCACAACTCAGTGGCA-TTTTGTCTC
1 AAAGTCCACGACTCCGTGGC-ACCTTTTTTCAAAGTCCACAACTCCGTGGCACCTTTCTTTC
* * * * * * *
3440093 AAAGTCCACGATTCTGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGCA-TTTTATCTC
1 AAAGTCCACGACTCCGTGGCA-CCTTTT-TTCAAAGTCCACAACTCCGTGGCACCTTTCTTTC
* * * * * * * *
3440155 AAAGTCCATGACTCAGTGGCATCCGTTTTTCAAAGTCCACGACTCAGTGGCA-TTTTGTCTC
1 AAAGTCCACGACTCCGTGGCA-CCTTTTTTCAAAGTCCACAACTCCGTGGCACCTTTCTTTC
* ** * * ** * *
3440216 AAAGTCCACGGCTTAGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGC-GTTTTGTCTC
1 AAAGTCCACGACTCCGTGGCA-CCTTTT-TTCAAAGTCCACAACTCCGTGGCACCTTTCTTTC
** * * *
3440278 AAAGTCCACGACTTAGTGGCATCCTTTTCTTCAAAGTCCACAACTTCGTGGTACCTTGTTCTTTG
1 AAAGTCCACGACTCCGTGGCA-CCTTTT-TTCAAAGTCCACAACTCCGTGGCACC-T-TTCTTTC
* * * *
3440343 TAAGTCCACGACTCCGTGGCACCTTCCTTTCAAAGT-CAAAGACTCCGTGGCACCTTTTTTTC
1 AAAGTCCACGACTCCGTGGCACCTT-TTTTCAAAGTCCACA-ACTCCGTGGCACCTTTCTTTC
* * * *
3440405 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAAGTCCACAACTTCGTGGCACCTTGTTC
1 AAAGTCCACGACTCCGTGGCAC-C--TTT---TTTCAAAGTCCACAACTCCGTGGCACC-T-TT-
3440470 CTTT-
57 CTTTC
* * *
3440474 TAAGTCCACAACTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTT
1 AAAGTCCACGACTCCGTGGCACCTT-TTTTCAAAGTCCACAACTCCGTGGCAC-C--TTT--CTT
*
3440539 TT
60 TC
* * **
3440541 AAAGTCCACAACCCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCTTTCTTTC
1 AAAGTCCACGACTCCGTGGCACCTT-TT--TTCAAAGTCCACAACTCCGTGGCACCTTTCTTTC
* *
3440605 AAAGTCCGCGACTCCGTGGCACCTTATTTTCAAAGCCCACAACTCCGTGGCACTCTTT
1 AAAGTCCACGACTCCGTGGCACCTT-TTTTCAAAGTCCACAACTCCGTGGCAC-CTTT
3440663 TTCCCTTTTA
Statistics
Matches: 479, Mismatches: 64, Indels: 52
0.81 0.11 0.09
Matches are distributed among these distances:
60 1 0.00
61 77 0.16
62 178 0.37
63 9 0.02
64 75 0.16
65 28 0.06
66 12 0.03
67 46 0.10
68 6 0.01
69 44 0.09
70 3 0.01
ACGTcount: A:0.22, C:0.31, G:0.16, T:0.31
Consensus pattern (61 bp):
AAAGTCCACGACTCCGTGGCACCTTTTTTCAAAGTCCACAACTCCGTGGCACCTTTCTTTC
Found at i:3440731 original size:131 final size:131
Alignment explanation
Indices: 3440311--3440725 Score: 567
Period size: 131 Copynumber: 3.2 Consensus size: 131
3440301 CTTTTCTTCA
* *
3440311 AAGTCCACAACTTCGTGGTACCTTGTTCTTTGTAAGTCCACGACTCCGTGGCACCTTCCTTTCAA
1 AAGTCCACAACTTCGTGGCACCTTGTTCTTT-TAAGTCCACGACTCCGTGGCACCTTCTTTTCAA
* * * *
3440376 AG-TCAAAGACTCCGTGGCAC-C-TTTT---TTTCAAAGCCCACAACTCCGTGGCACTCTTTTTC
65 AGCCCACA-ACTCCGTGGCACTCTTTTTCCCTTTTAAAG-CCACAACTCCGTGGCAC-CTTGTT-
3440435 CCTTTT
126 CCTTTT
*
3440441 AAAGTCCACAACTTCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCTTCTTTTCA
1 -AAGTCCACAACTTCGTGGCACCTTGTT-CTTTTAAGTCCACGACTCCGTGGCACCTTCTTTTCA
*
3440506 AAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAAGTCCACAACCCCGTGGCACCTTGTTCC
64 AAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAAG-CCACAACTCCGTGGCACCTTGTTCC
3440571 TTTT
128 TTTT
* * * *
3440575 AAGTCCACAACTCCGTGGCACC-T-TTCTTTCAAAGTCCGCGACTCCGTGGCACCTTATTTTCAA
1 AAGTCCACAACTTCGTGGCACCTTGTTCTTT-TAAGTCCACGACTCCGTGGCACCTTCTTTTCAA
*
3440638 AGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAAGCCTATAACTCCGTGGCACCTTGTTCCT
65 AGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAAGCC-ACAACTCCGTGGCACCTTGTTCCT
3440703 TTT
129 TTT
3440706 AAGTCCACAACTTCGTGGCA
1 AAGTCCACAACTTCGTGGCA
3440726 TCTTTCACCC
Statistics
Matches: 258, Mismatches: 17, Indels: 18
0.88 0.06 0.06
Matches are distributed among these distances:
130 6 0.02
131 184 0.71
132 9 0.03
133 25 0.10
134 6 0.02
135 5 0.02
136 23 0.09
ACGTcount: A:0.20, C:0.33, G:0.15, T:0.32
Consensus pattern (131 bp):
AAGTCCACAACTTCGTGGCACCTTGTTCTTTTAAGTCCACGACTCCGTGGCACCTTCTTTTCAAA
GCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAAGCCACAACTCCGTGGCACCTTGTTCCTTT
T
Found at i:3440769 original size:32 final size:32
Alignment explanation
Indices: 3440740--3440875 Score: 179
Period size: 32 Copynumber: 4.3 Consensus size: 32
3440730 TCACCCTTTT
3440740 TAAAGCCCACACAAGTCGATGGCAACCCTTCC
1 TAAAGCCCACACAAGTCGATGGCAACCCTTCC
*
3440772 CAAAGCCCACACAAGTC-AGTGGCAACCCTTCC
1 TAAAGCCCACACAAGTCGA-TGGCAACCCTTCC
* * * *
3440804 TAAAGCCCACACAAGTTGGTGACAACCATTCTC
1 TAAAGCCCACACAAGTCGATGGCAACCCTTC-C
*
3440837 TAAAGCCCACACAAGTCGGTGGCAACCCTT-C
1 TAAAGCCCACACAAGTCGATGGCAACCCTTCC
3440868 T-AAGCCCA
1 TAAAGCCCA
3440876 ATATCGCTGG
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
30 7 0.08
31 3 0.03
32 54 0.59
33 28 0.30
ACGTcount: A:0.32, C:0.36, G:0.16, T:0.16
Consensus pattern (32 bp):
TAAAGCCCACACAAGTCGATGGCAACCCTTCC
Found at i:3441030 original size:92 final size:92
Alignment explanation
Indices: 3440868--3441185 Score: 351
Period size: 92 Copynumber: 3.5 Consensus size: 92
3440858 GCAACCCTTC
*
3440868 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAATCCAATGTAGCT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAATCCAATGTAGCT
* *
3440933 GGCCTTGAATCAGTACATTGGCACCTG
66 AGCCTTGAATCAGCACATTGGCACCTG
* * * *
3440960 TAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGTCCACTGTAGCT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAATCCAATGTAGCT
*
3441025 AGCCTTGAATCAGCACATTGGCACCTT
66 AGCCTTGAATCAGCACATTGGCACCTG
** * * * * *
3441052 TAAGTCCAACGTAGCTGGCCTTGAATCAGCACATTGGCA-C-----CTTTAAGTCCAATATCGCT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAATCCAATGTAGCT
* *
3441111 GGCCTTGAATCAGCATATTGGCACCTTTG
66 AGCCTTGAATCAGCACATTGGCACC--TG
* * * *
3441140 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGAACATTGGCACCT
1 ----TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCT
3441186 CCAAGTCTAA
Statistics
Matches: 197, Mismatches: 21, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
86 39 0.20
88 1 0.01
91 1 0.01
92 155 0.79
93 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.30
Consensus pattern (92 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAATCCAATGTAGCT
AGCCTTGAATCAGCACATTGGCACCTG
Found at i:3441192 original size:92 final size:92
Alignment explanation
Indices: 3441049--3441736 Score: 1112
Period size: 92 Copynumber: 7.4 Consensus size: 92
3441039 ACATTGGCAC
*
3441049 CTTTAAGTCCAACGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGC
*
3441114 CTTGAATCAGCATATTGGCACCTTTGT
66 CTTGAATCAGCATATTGGCACCTTTAT
* ** *
3441141 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGAACATTGGCACCTCCAAGTCTAATATCGCTGGC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGC
*
3441206 CTTGAATCAGCATATTGGCACTTTTAT
66 CTTGAATCAGCATATTGGCACCTTTAT
* * *
3441233 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAACACATCGGCACCTTTAAGTCCAATATCGTTGGC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGC
*
3441298 CTTGAATCAGCATATTGGCACCTTTGT
66 CTTGAATCAGCATATTGGCACCTTTAT
**
3441325 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCCAAGTCCAATATCGCTGGC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGC
3441390 CTTGAATCAGCATATTGGCACCTTTAT
66 CTTGAATCAGCATATTGGCACCTTTAT
*
3441417 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAACACATTGGCACCTTTAAGTCCAATATCGCTGGC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGC
3441482 CTTGAATCAGCATATTGGCACCTTTAT
66 CTTGAATCAGCATATTGGCACCTTTAT
3441509 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGC
*
3441574 CTTGAATCAGCATATTGGCACC-TCAT
66 CTTGAATCAGCATATTGGCACCTTTAT
3441600 CTTTTAAG-CCTAATGTCA-CTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCT
1 C-TTTAAGTCC-AATGT-AGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCT
* *
3441663 GGCCTTGAATTAGCATATTGGCGCCTCTGTCAT
63 GGCCTTGAATCAGCATATTGGCACCT-T-T-AT
* * * *
3441696 CTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGC
3441737 GTCTTTGTCA
Statistics
Matches: 553, Mismatches: 34, Indels: 15
0.92 0.06 0.02
Matches are distributed among these distances:
91 6 0.01
92 508 0.92
93 1 0.00
94 1 0.00
95 32 0.06
96 5 0.01
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (92 bp):
CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGC
CTTGAATCAGCATATTGGCACCTTTAT
Found at i:3441788 original size:52 final size:52
Alignment explanation
Indices: 3441644--3441778 Score: 225
Period size: 52 Copynumber: 2.6 Consensus size: 52
3441634 ACATTGGCAC
*
3441644 CTTTAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCGCCTCTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTCTGTCAT
* * *
3441696 CTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCGTCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTCTGTCAT
*
3441748 CTTTAAGTCCAATGTCGCTGGCCTTGAATCA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCA
3441779 ATACATTGGC
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 77 1.00
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (52 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTCTGTCAT
Found at i:3447148 original size:15 final size:16
Alignment explanation
Indices: 3447124--3447157 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
3447114 AACTATTTAT
*
3447124 TTTCAGAATATTAATA
1 TTTCAGAATAGTAATA
3447140 TTTCA-AATAGTAATA
1 TTTCAGAATAGTAATA
3447155 TTT
1 TTT
3447158 TAATCATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (16 bp):
TTTCAGAATAGTAATA
Found at i:3447276 original size:12 final size:11
Alignment explanation
Indices: 3447242--3447313 Score: 64
Period size: 10 Copynumber: 6.9 Consensus size: 11
3447232 TTAATTATAT
3447242 AAATATT-TTA
1 AAATATTATTA
3447252 AAATATTA-TA
1 AAATATTATTA
*
3447262 ATA-ATTATTA
1 AAATATTATTA
3447272 AAATATTATT-
1 AAATATTATTA
* *
3447282 -TATATTAATA
1 AAATATTATTA
*
3447292 TAATTATTATTA
1 -AAATATTATTA
3447304 AAATATTATT
1 AAATATTATT
3447314 TTACAATTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
9 11 0.23
10 15 0.31
11 15 0.31
12 7 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AAATATTATTA
Found at i:3447291 original size:15 final size:17
Alignment explanation
Indices: 3447265--3447314 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 17
3447255 TATTATAATA
3447265 ATTATTAAAATATTATTT
1 ATTATT-AAATATTATTT
*
3447283 A-TATT-AATA-TAATT
1 ATTATTAAATATTATTT
3447297 ATTATTAAAATATTATTT
1 ATTATT-AAATATTATTT
3447315 TACAATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
14 5 0.19
15 8 0.31
17 8 0.31
18 5 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTATTAAATATTATTT
Found at i:3447356 original size:8 final size:8
Alignment explanation
Indices: 3447343--3447376 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
3447333 ATATTAACAT
3447343 AAATATTA
1 AAATATTA
3447351 AAATATT-
1 AAATATTA
*
3447358 AATTATTA
1 AAATATTA
3447366 AAATATTA
1 AAATATTA
3447374 AAA
1 AAA
3447377 ACTATTTATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
AAATATTA
Found at i:3447366 original size:15 final size:15
Alignment explanation
Indices: 3447346--3447374 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3447336 TTAACATAAA
3447346 TATTAAAATATTAAT
1 TATTAAAATATTAAT
3447361 TATTAAAATATTAA
1 TATTAAAATATTAA
3447375 AAACTATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTAAAATATTAAT
Found at i:3447838 original size:22 final size:21
Alignment explanation
Indices: 3447787--3447839 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
3447777 AATAATAGAT
* *
3447787 TATAAATACTCTATTATTAAA
1 TATAAATATTATATTATTAAA
* *
3447808 AAAATAATATTATATTATTGAAA
1 TATA-AATATTATATTATT-AAA
3447831 TATAAATAT
1 TATAAATAT
3447840 GCATGTTTAA
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
21 2 0.08
22 17 0.71
23 5 0.21
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (21 bp):
TATAAATATTATATTATTAAA
Found at i:3448785 original size:20 final size:19
Alignment explanation
Indices: 3448759--3448831 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
3448749 CTGCTAGTTT
*
3448759 CATGTATCGATACAATTGAG
1 CATGTATCGATACAA-TGAA
* *
3448779 TATGTATCGATGCAATGAA
1 CATGTATCGATACAATGAA
*
3448798 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAATG-A-A
3448819 -ATGTATCGATACA
1 CATGTATCGATACA
3448832 TCTGGATGTG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 17 0.38
20 27 0.60
21 1 0.02
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:3448804 original size:19 final size:20
Alignment explanation
Indices: 3448759--3448812 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
3448749 CTGCTAGTTT
*
3448759 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATTGAA
* *
3448779 TATGTATCGATGCAA-TGAA
1 CATGTATCGATACAATTGAA
3448798 CATGTATCGATACAA
1 CATGTATCGATACAA
3448813 AGCATAATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:3452389 original size:52 final size:52
Alignment explanation
Indices: 3452244--3452368 Score: 241
Period size: 52 Copynumber: 2.4 Consensus size: 52
3452234 ATATGAAAAT
3452244 TTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAAC
1 TTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAAC
*
3452296 TTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGCAAAC
1 TTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAAC
3452348 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
3452369 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAAC
Found at i:3452455 original size:19 final size:19
Alignment explanation
Indices: 3452431--3452512 Score: 104
Period size: 19 Copynumber: 4.6 Consensus size: 19
3452421 TAGCTCACAT
* *
3452431 TGTATCAATACAAAACTTA
1 TGTATCGATACAACACTTA
3452450 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
3452463 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
3452482 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
3452501 TGTATCGATACA
1 TGTATCGATACA
3452513 TTATATCGAT
Statistics
Matches: 55, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
13 9 0.16
14 1 0.02
16 5 0.09
18 1 0.02
19 39 0.71
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Done.