Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold126
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: 2080828
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 191490 characters in sequence are not A, C, G, or T
File 9 of 13
Found at i:1430858 original size:28 final size:28
Alignment explanation
Indices: 1430825--1430907 Score: 80
Period size: 28 Copynumber: 2.9 Consensus size: 28
1430815 TTAAAATGGC
*
1430825 CCTAAAATGCATGAAATTACATAAAATA
1 CCTAAAATGCATGAAATTACATAAAAAA
*
1430853 CCT-AAAT-CATGAAAAATTACCTAAAAAA
1 CCTAAAATGCATG--AAATTACATAAAAAA
* * *
1430881 CCATAAAATGAATAAAATTACACAAAA
1 CC-TAAAATGCATGAAATTACATAAAA
1430908 GTCCTTAAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
26 4 0.09
27 4 0.09
28 18 0.41
29 12 0.27
30 4 0.09
31 2 0.05
ACGTcount: A:0.58, C:0.16, G:0.05, T:0.22
Consensus pattern (28 bp):
CCTAAAATGCATGAAATTACATAAAAAA
Found at i:1445598 original size:52 final size:51
Alignment explanation
Indices: 1445482--1445828 Score: 418
Period size: 52 Copynumber: 6.8 Consensus size: 51
1445472 TTACGGATGC
* * *
1445482 CAATATGCTGATTCAAGGCCAGTGATATTGGACTT-AA-A-GACGAAGGTG
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGGCG
* * * *
1445530 CTAATGTGCTGATTCAAGGTCAGCGAAATTTGACTTAAAGATGACAAAGGCG
1 C-AATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGGCG
* *
1445582 TCAATATGCTGCTTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGACG
1 -CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGGCG
* * * * *
1445634 CCGATATGTTGATTCAAGGCTAGCGATATTGGACTTAAAGATGA-AGATGC-
1 -CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGGCG
* * * * * *
1445684 CAATGTGCTGATTCAAGGCGAACAACATTGGACTTAAAGACGACAAAGGCG
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGGCG
**
1445735 TCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGATG
1 -CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGGCG
1445787 C-ATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGA
1445829 AGGTGCCACC
Statistics
Matches: 252, Mismatches: 39, Indels: 14
0.83 0.13 0.05
Matches are distributed among these distances:
48 1 0.00
49 64 0.25
50 47 0.19
51 5 0.02
52 134 0.53
53 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (51 bp):
CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGGCG
Found at i:1445599 original size:101 final size:99
Alignment explanation
Indices: 1445482--1445834 Score: 381
Period size: 101 Copynumber: 3.5 Consensus size: 99
1445472 TTACGGATGC
* *
1445482 CAATATGCTGATTCAAGGCCAGTGATATTGGACTTAAAGACGAAGGTGCTAATGTGCTGATTCAA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACGAAGGTGCTAATATGCTGATTCAA
* *
1445547 GGTCAGCGAAATTTGACTTAAAGATGACAAAGGCG
66 GG-CAGCGATATTGGACTTAAAGATGACAAAGGCG
* * ** ** *
1445582 TCAATATGCTGCTTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGACGCCGATATGTTGAT
1 -CAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-GACGAAGGTGCTAATATGCTGAT
* *
1445647 TCAAGGCTAGCGATATTGGACTTAAAGATGA-AGATGC-
62 TCAAGGC-AGCGATATTGGACTTAAAGATGACAAAGGCG
* * * * * *
1445684 CAATGTGCTGATTCAAGGCGAACAACATTGGACTTAAAGACGACAAAG-GCGTCAATATGCTGAT
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACG--AAGGTGC-T-AATATGCTGAT
**
1445748 TCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGATG
62 TCAAGG-CAGCGATATTGGACTTAAAGATGACAAAGGCG
*
1445787 C-ATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACGAAGGTGC
1445835 CACCAACTTG
Statistics
Matches: 204, Mismatches: 36, Indels: 24
0.77 0.14 0.09
Matches are distributed among these distances:
98 3 0.01
99 3 0.01
100 7 0.03
101 102 0.50
102 39 0.19
103 7 0.03
104 43 0.21
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.24
Consensus pattern (99 bp):
CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACGAAGGTGCTAATATGCTGATTCAA
GGCAGCGATATTGGACTTAAAGATGACAAAGGCG
Found at i:1445697 original size:153 final size:151
Alignment explanation
Indices: 1445484--1445836 Score: 557
Period size: 153 Copynumber: 2.3 Consensus size: 151
1445474 ACGGATGCCA
* * *
1445484 ATATGCTGATTCAAGGCCAGTGATATTGGACTTAAAGACGAAGGTGCTAATGTGCTGATTCAAGG
1 ATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGG
* * * *
1445549 TC-AGCGAA-ATTTGACTTAAAGATGACAAAGGCGTCAATATGCTGCTTCAAGGCCAGCGATATT
66 -CGAAC-AACATTGGACTTAAAGACGACAAAGGCGTCAATATGCTGATTCAAGGCCAGCGATATT
1445612 GGACTTAAAGATGACAAAGACGCC
129 GGACTTAAAGATGACAAAGACG-C
* * *
1445636 GATATGTTGATTCAAGGCTAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAG
1 -ATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAG
1445701 GCGAACAACATTGGACTTAAAGACGACAAAGGCGTCAATATGCTGATTCAAGGCCAGCGATATTG
65 GCGAACAACATTGGACTTAAAGACGACAAAGGCGTCAATATGCTGATTCAAGGCCAGCGATATTG
*
1445766 GACTTAAAGATGACAAAGATGC
130 GACTTAAAGATGACAAAGACGC
1445788 ATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCA
1 ATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCA
1445837 CCAACTTGTG
Statistics
Matches: 184, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
151 46 0.25
152 4 0.02
153 134 0.73
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.24
Consensus pattern (151 bp):
ATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGG
CGAACAACATTGGACTTAAAGACGACAAAGGCGTCAATATGCTGATTCAAGGCCAGCGATATTGG
ACTTAAAGATGACAAAGACGC
Found at i:1445910 original size:28 final size:28
Alignment explanation
Indices: 1445845--1446246 Score: 465
Period size: 28 Copynumber: 14.4 Consensus size: 28
1445835 CACCAACTTG
**
1445845 TGTGGGCTTTTGAAAAGGTTG-CACCAACT
1 TGTGGGCTTTT--AAAGGTTGCCACTGACT
* *
1445874 TGTGTGCTTTTAAAGGTTGCCACTGCCT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
*
1445902 TGTGGGCTTTGAAAAGG-TGCCACTGACT
1 TGTGGGCTTT-TAAAGGTTGCCACTGACT
*
1445930 TGTGGGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
*
1445958 TGTGGGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
* *
1445986 TGTGAGC-TTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
* * *
1446013 TATGGGCTTTGAAAAGTTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
* *
1446041 TGTGGGCTTCTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
*
1446069 TGTGGGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
*
1446097 TGTGGGC-TTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
*** *
1446124 TGTGGGCTTTTGAAAAAATGCCACTCACT
1 TGTGGGCTTTT-AAAGGTTGCCACTGACT
*
1446153 TGTGGGCTTTGAAAAGG-TGCCACTGACT
1 TGTGGGCTTT-TAAAGGTTGCCACTGACT
***
1446181 TGTGGGC-TTCGGAGGTTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
* * *
1446208 TGTGGGCTTTTGAAAAGATGCCACCGACT
1 TGTGGGCTTTT-AAAGGTTGCCACTGACT
1446237 TGTGGGCTTT
1 TGTGGGCTTT
1446247 GAAAAGGTGA
Statistics
Matches: 324, Mismatches: 39, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
26 3 0.01
27 84 0.26
28 175 0.54
29 62 0.19
ACGTcount: A:0.18, C:0.19, G:0.30, T:0.33
Consensus pattern (28 bp):
TGTGGGCTTTTAAAGGTTGCCACTGACT
Found at i:1445974 original size:84 final size:83
Alignment explanation
Indices: 1445845--1446255 Score: 535
Period size: 84 Copynumber: 4.9 Consensus size: 83
1445835 CACCAACTTG
** * * *
1445845 TGTGGGCTTTTGAAAAGGTTG-CACCAACTTGTGTGCTTTTAAAGGTTGCCACTGCCTTGTGGGC
1 TGTGGGC-TTTG--AAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGC
1445909 TTTGAAAAGGTGCCACTGACT
63 TTTGAAAAGGTGCCACTGACT
*
1445930 TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGAGCTT
1 TGTGGGC-TTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTT
1445995 TG--AAGGTTGCCACTGACT
65 TGAAAAGG-TGCCACTGACT
* * *
1446013 TATGGGCTTTGAAAAGTTGCCACTGACTTGTGGGCTTCTGAAGGTTGCCACTGACTTGTGGGCTT
1 TGTGGGCTTTG-AAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGC-T
1446078 TTG--AAGGTTGCCACTGACT
64 TTGAAAAGG-TGCCACTGACT
*** *
1446097 TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAAATGCCACTCACTTGTGGGCTT
1 TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTG-AAGGTTGCCACTGACTTGTGGGCTT
1446162 TGAAAAGGTGCCACTGACT
65 TGAAAAGGTGCCACTGACT
* * * * *
1446181 TGTGGGCTTCGGAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACCGACTTGTGGGCTT
1 TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTG-AAGGTTGCCACTGACTTGTGGGCTT
1446246 TGAAAAGGTG
65 TGAAAAGGTG
1446256 AGGAATGTCT
Statistics
Matches: 297, Mismatches: 22, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
82 8 0.03
83 102 0.34
84 171 0.58
85 16 0.05
ACGTcount: A:0.19, C:0.18, G:0.30, T:0.32
Consensus pattern (83 bp):
TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTT
GAAAAGGTGCCACTGACT
Found at i:1446055 original size:111 final size:111
Alignment explanation
Indices: 1445845--1446252 Score: 565
Period size: 111 Copynumber: 3.6 Consensus size: 111
1445835 CACCAACTTG
** * * *
1445845 TGTGGGCTTTTGAAAAGGTTG-CACCAACTTGTGTGCTTTTAAAGGTTGCCACTGCCTTGTGGGC
1 TGTGGGCTTTTG--AAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGC
*
1445909 TTTGAAAAGGTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACT
64 TTTGAAAAGATGCCACTGACTTGTGGGC-TTTGAAGGTTGCCACTGACT
* *
1445958 TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGAGC-TTTGAAGGTTGCCACTGACTTATGGGCTT
1 TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTT
*
1446022 TGAAAAGTTGCCACTGACTTGTGGGCTTCTGAAGGTTGCCACTGACT
66 TGAAAAGATGCCACTGACTTGTGGGCTT-TGAAGGTTGCCACTGACT
1446069 TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGC-TTTGAAGGTTGCCACTGACTTGTGGGCTT
1 TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGC-T
* *
1446133 TTGAAAAAATGCCACTCACTTGTGGGCTTTGAAAAGG-TGCCACTGACT
65 TTGAAAAGATGCCACTGACTTGTGGGCTTTG--AAGGTTGCCACTGACT
* * * * *
1446181 TGTGGGC-TTCGGAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACCGACTTGTGGGCT
1 TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTG-AAGGTTGCCACTGACTTGTGGGCT
1446245 TTGAAAAG
65 TTGAAAAG
1446253 GTGAGGAATG
Statistics
Matches: 270, Mismatches: 18, Indels: 15
0.89 0.06 0.05
Matches are distributed among these distances:
110 2 0.01
111 163 0.60
112 69 0.26
113 36 0.13
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.32
Consensus pattern (111 bp):
TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTT
TGAAAAGATGCCACTGACTTGTGGGCTTTGAAGGTTGCCACTGACT
Found at i:1447640 original size:4 final size:4
Alignment explanation
Indices: 1447627--1447696 Score: 55
Period size: 4 Copynumber: 18.8 Consensus size: 4
1447617 CCGGACCCTT
* *
1447627 TTTG -TTG TTTG TTTG TTT- TTTT TGTTG TTT- TTT- TTGTT TTTG TTT-
1 TTTG TTTG TTTG TTTG TTTG TTTG T-TTG TTTG TTTG TT-TG TTTG TTTG
1447672 TTT- TTTG TTTG TTTG TTT- TTTG TTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTT
1447697 TTTTTCTCTT
Statistics
Matches: 57, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
3 20 0.35
4 32 0.56
5 5 0.09
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (4 bp):
TTTG
Found at i:1447646 original size:1 final size:1
Alignment explanation
Indices: 1447642--1447730 Score: 61
Period size: 1 Copynumber: 89.0 Consensus size: 1
1447632 TGTTTGTTTG
* * * * * * * * * *
1447642 TTTTTTTTGTTGTTTTTTTTGTTTTTGTTTTTTTTTGTTTGTTTGTTTTTTGTTTTTTTTCTCTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
1447707 TTTTTTTGTTTTGTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTT
1447731 ACGGAAGACG
Statistics
Matches: 62, Mismatches: 26, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 62 1.00
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.85
Consensus pattern (1 bp):
T
Found at i:1447650 original size:20 final size:19
Alignment explanation
Indices: 1447625--1447730 Score: 97
Period size: 20 Copynumber: 5.3 Consensus size: 19
1447615 ATCCGGACCC
1447625 TTTTTGTTGTTTGTTTGTTT
1 TTTTTGTTGTTT-TTTGTTT
*
1447645 TTTTTGTTGTTTTTT-TTG
1 TTTTTGTTGTTTTTTGTTT
*
1447663 TTTTTGTTTTTTTTTGTTTGT
1 TTTTTGTTGTTTTTTG-TT-T
* *
1447684 TTGTTTTTTGTTTTTTTTCTCT
1 TT-TTTGTTGTTTTTTGT-T-T
*
1447706 TTTTTTTTGTTTTGTTGTTT
1 TTTTTGTTGTTTT-TTGTTT
1447726 TTTTT
1 TTTTT
1447731 ACGGAAGACG
Statistics
Matches: 72, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
18 16 0.22
19 3 0.04
20 20 0.28
21 15 0.21
22 18 0.25
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.84
Consensus pattern (19 bp):
TTTTTGTTGTTTTTTGTTT
Found at i:1447672 original size:25 final size:27
Alignment explanation
Indices: 1447634--1447730 Score: 107
Period size: 25 Copynumber: 3.7 Consensus size: 27
1447624 CTTTTTGTTG
*
1447634 TTTG-TTTGTT-TTTTTTGTTGTTTTT
1 TTTGTTTTGTTGTTTTTTTTTGTTTTT
*
1447659 TTTG-TTT-TTGTTTTTTTTTG-TTTG
1 TTTGTTTTGTTGTTTTTTTTTGTTTTT
*
1447683 TTTGTTTT-TTGTTTTTTTTCTCTTTTTT
1 TTTGTTTTGTTGTTTTTTTT-T-GTTTTT
1447711 TTTGTTTTGTTGTTTTTTTT
1 TTTGTTTTGTTGTTTTTTTT
1447731 ACGGAAGACG
Statistics
Matches: 62, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
24 9 0.15
25 30 0.48
26 1 0.02
28 11 0.18
29 11 0.18
ACGTcount: A:0.00, C:0.02, G:0.13, T:0.85
Consensus pattern (27 bp):
TTTGTTTTGTTGTTTTTTTTTGTTTTT
Found at i:1447694 original size:52 final size:54
Alignment explanation
Indices: 1447627--1447730 Score: 153
Period size: 52 Copynumber: 2.0 Consensus size: 54
1447617 CCGGACCCTT
*
1447627 TTTGTTGTTTGTTTGTTTTTTTTGT-TGTTTTTTTTG-TTT-TTGTTTTTTTTTG
1 TTTGTTGTTTGTTTGTTTTTTTTCTCT-TTTTTTTTGTTTTGTTGTTTTTTTTTG
1447679 TTTGTTTGTTT-TTTGTTTTTTTTCTCTTTTTTTTTGTTTTGTTGTTTTTTTT
1 TTTG-TTGTTTGTTTGTTTTTTTTCTCTTTTTTTTTGTTTTGTTGTTTTTTTT
1447731 ACGGAAGACG
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
52 26 0.55
53 10 0.21
54 11 0.23
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.84
Consensus pattern (54 bp):
TTTGTTGTTTGTTTGTTTTTTTTCTCTTTTTTTTTGTTTTGTTGTTTTTTTTTG
Found at i:1447699 original size:41 final size:39
Alignment explanation
Indices: 1447625--1447730 Score: 119
Period size: 41 Copynumber: 2.7 Consensus size: 39
1447615 ATCCGGACCC
* *
1447625 TTTTTGTTG-TTTGTTTGTTTTTTTTGTTGTTTTTTT-TGT
1 TTTTTTTTGTTTTGTTTG-TTTTTTT-TTGTTTTTTTCTCT
*
1447664 TTTTGTTTTTTTTTGTTTGTTTGTTTTTTGTTTTTTTTCTCT
1 TTTT-TTTTGTTTTGTTTGTTT-TTTTTTG-TTTTTTTCTCT
1447706 TTTTTTTTGTTTTG-TTGTTTTTTTT
1 TTTTTTTTGTTTTGTTTGTTTTTTTT
1447731 ACGGAAGACG
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
39 9 0.16
40 15 0.26
41 28 0.48
42 6 0.10
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.84
Consensus pattern (39 bp):
TTTTTTTTGTTTTGTTTGTTTTTTTTTGTTTTTTTCTCT
Found at i:1447709 original size:36 final size:34
Alignment explanation
Indices: 1447644--1447730 Score: 113
Period size: 36 Copynumber: 2.4 Consensus size: 34
1447634 TTTGTTTGTT
*
1447644 TTTTTTGTTGTTTTTTTTGTTTTTGTTTTTTTTTG
1 TTTTTTGTT-TTTTTTTTGTTTTTCTTTTTTTTTG
1447679 TTTGTTTGTTTTTTGTTTT-TTTTCTCTTTTTTTTTG
1 TTT-TTTGTTTTTT-TTTTGTTTT-TCTTTTTTTTTG
1447715 TTTTGTTGTTTTTTTT
1 TTTT-TTGTTTTTTTT
1447731 ACGGAAGACG
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
35 14 0.30
36 33 0.70
ACGTcount: A:0.00, C:0.02, G:0.13, T:0.85
Consensus pattern (34 bp):
TTTTTTGTTTTTTTTTTGTTTTTCTTTTTTTTTG
Found at i:1457669 original size:52 final size:51
Alignment explanation
Indices: 1457603--1457739 Score: 202
Period size: 52 Copynumber: 2.6 Consensus size: 51
1457593 ATTTGCTTGT
1457603 ATGTATCGATACATTGAATAGTGTATCGATACATCTGGGCAAATTTGCCTAC
1 ATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGCAAATTTGCCTAC
* * *
1457655 ATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCCTGC
1 ATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGCAAATTTGCCTAC
**
1457707 ATGTATCGATACAAAGATCAGTGTATCGATACA
1 ATGTATCGATACATTGAT-AGTGTATCGATACA
1457740 ATGTATCGAT
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
51 2 0.03
52 72 0.95
53 2 0.03
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (51 bp):
ATGTATCGATACATTGATAGTGTATCGATACATCTGGGCAAATTTGCCTAC
Found at i:1457746 original size:13 final size:13
Alignment explanation
Indices: 1457728--1457752 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1457718 CAAAGATCAG
1457728 TGTATCGATACAA
1 TGTATCGATACAA
1457741 TGTATCGATACA
1 TGTATCGATACA
1457753 TTTAAGTGAT
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:1457830 original size:33 final size:33
Alignment explanation
Indices: 1457793--1457859 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1457783 AGTAGCTTAA
*
1457793 ATTGTATCGATACAATAAAATATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
***
1457826 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
1457859 A
1 A
1457860 AATCGTTGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAACAAAATATGTATCGATAC
Found at i:1457833 original size:13 final size:13
Alignment explanation
Indices: 1457815--1457839 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1457805 CAATAAAATA
1457815 TGTATCGATACAT
1 TGTATCGATACAT
1457828 TGTATCGATACA
1 TGTATCGATACA
1457840 ACACTTTATG
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:1465820 original size:15 final size:15
Alignment explanation
Indices: 1465800--1465829 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1465790 GAGTAACTTT
1465800 ATCATTATCATCATC
1 ATCATTATCATCATC
1465815 ATCATTATCATCATC
1 ATCATTATCATCATC
1465830 TTTAATGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.40
Consensus pattern (15 bp):
ATCATTATCATCATC
Found at i:1468338 original size:25 final size:25
Alignment explanation
Indices: 1468278--1468336 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
1468268 AGAGATTCAT
* *
1468278 ATATTTATTCATATATTTGAATATG
1 ATATATATTTATATATTTGAATATG
*
1468303 ATATGTATTTATATATTT-AATTAT-
1 ATATATATTTATATATTTGAA-TATG
1468327 ATATATATTT
1 ATATATATTT
1468337 TAAAAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 11 0.37
25 19 0.63
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (25 bp):
ATATATATTTATATATTTGAATATG
Found at i:1473699 original size:13 final size:12
Alignment explanation
Indices: 1473677--1473837 Score: 50
Period size: 12 Copynumber: 13.2 Consensus size: 12
1473667 TATTGTATTC
1473677 ATATTATATTTAT
1 ATATTATA-TTAT
*
1473690 ATATTTTATTAT
1 ATATTATATTAT
* *
1473702 ATTATAAATATTTT
1 A-TAT-TATATTAT
** *
1473716 A-AAAATATTTT
1 ATATTATATTAT
*
1473727 AAATT-TATATAT
1 ATATTATAT-TAT
1473739 AATATTATATTCAT
1 -ATATTATATT-AT
1473753 AT-TTA-A-TAT
1 ATATTATATTAT
* *
1473762 ATTTTAAATT-T
1 ATATTATATTAT
*
1473773 ATATTAATTTTAAT
1 ATATT-ATATT-AT
1473787 ATATTAATAATT-T
1 ATATT-AT-ATTAT
* *
1473800 ATATTATATAAA
1 ATATTATATTAT
*
1473812 ATTTTATA-TAT
1 ATATTATATTAT
1473823 ATATTTATATTAT
1 ATA-TTATATTAT
1473836 AT
1 AT
1473838 CATATTTTAA
Statistics
Matches: 112, Mismatches: 19, Indels: 34
0.68 0.12 0.21
Matches are distributed among these distances:
9 4 0.04
10 4 0.04
11 24 0.21
12 30 0.27
13 28 0.25
14 20 0.18
15 2 0.02
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (12 bp):
ATATTATATTAT
Found at i:1473707 original size:709 final size:694
Alignment explanation
Indices: 1472313--1473707 Score: 2266
Period size: 709 Copynumber: 2.0 Consensus size: 694
1472303 AAGTTGTATC
*
1472313 TTGCAACACTAAGTTACCTGAATCCAGTAGCTTGGCAAATGTTTTGCTGTCGTTGCTAGCTATAC
1 TTGCAACACTAAGTTACCTGAATCCAGTAGCATGGCAAATGTTTTGCTGTCGTTGCTAGCTATAC
1472378 TGCGTGTTACCTGGTACGACATTGGGCCATCTGATATCACGAGCTTTCCCTCAGAGTTGATGGTG
66 TGCGTGTTACCTGGTACGACATTGGGCCATCTGATATCACGAGCTTTCCCTCAGAGTTGATGGTG
* *
1472443 AGATTAGAAGAGTCACTCAGGCAAGGGTATTCTCTATTTGCCACCCAAACTATTGGTTGCTTAGA
131 AGATTAGAAGAGTCACTCAGGCAAGGGTATGCTCTATTTGCCACCCAAACTATTGCTTGCTTAGA
*
1472508 CACTTTATGCCATATTCCAAGGTAGTACTTGGAGGTATTTACTGGCGAAAAAAACCCAAGTTCGA
196 CACTTTATGCCATATTCCAAGGTAGTACTTGGAGGTACTTACTGGCGAAAAAAACCCAAGTTCGA
*
1472573 ATTTCCCACCAGATGATATAAGGGTATTTGGATAGGTGATTGTTTGGCCTTGATGAATTGTATCA
261 ATTTCCCACCAGATGATATAAGGGTATTTGGATAGGTGATTGTTTGGCCTCGATGAATTGTATCA
* * * *
1472638 CTGCCATTTGTAAACCGTAAGGCAAGGCATAAGAAAGCCAGCAAACTAACAAGAAGAGAAAACCA
326 CTGCCATTCGTAAACCGGAAGGCAAGGCATAAGAAAACCAGCAAACTAACAAAAAGAGAAAACCA
1472703 ATCTCCCATCATTTACAGATGTTTAATGCTGATCAGAGTGAGAATCATATAGATGAAATTCGGGG
391 ATCTCCCATCATTTACAGATGTTTAATGCTGATCAGAGTGAGAATCATATAGATGAAATTCGGGG
1472768 ATTAAAGAAACGATTCAAGTCAACTCTCTCTGCAAATCTTCGCTTGCTTTGGGCTAACTAAAAAA
456 ATTAAAGAAACGATTCAAGTCAACTCTCTCTGCAAATCTTCGCTTGCTTTGGGCTAACTAAAAAA
*
1472833 AATCTTGTTCTTTAGCCTTGGATCAAGTCATCGTCTGCCCCACGTTCGAGAAGAGAGATACAAAT
521 AATCTTGTTCTTCAGCCTT-G-TCAAGTCATCGTCTGCCCCA---TC--------AGAT--AAAT
* * *
1472898 CAAGCATTTTTTATGGTCATGTTGTATAATCAAATGAAAACAATTACATTTAGTCACTATCAATA
571 CAAGCATTTTTTATGGTCACGTTGAATAATCAAATGAAAACAATTACATTTAGTCACCATCAATA
* *
1472963 AAAGTATTTATATATGGCTATTATATTCGTATTATATTTATATATTTTATCATATTATA
636 AAAATATTTATATATGGCTATTATATTCATATTATATTTATATATTTTATCATATTATA
* *
1473022 TTGCAATACTAAGTTACCTGAATCCAGTAGCATGGCAAATGTTTTGCTGTTGTTGCTAGCTATAC
1 TTGCAACACTAAGTTACCTGAATCCAGTAGCATGGCAAATGTTTTGCTGTCGTTGCTAGCTATAC
*
1473087 TGCGTGTTACCTGGTACGACATTGGGCCATCTGGTATCACGAGCTTTCCCTCAGAGTTGATGGTG
66 TGCGTGTTACCTGGTACGACATTGGGCCATCTGATATCACGAGCTTTCCCTCAGAGTTGATGGTG
* *
1473152 AGATTAGAAGAGTCACTCAGGGAAGGGTATGCTCTATTTGCCATCCAAACTATTGCTTGCTTAGA
131 AGATTAGAAGAGTCACTCAGGCAAGGGTATGCTCTATTTGCCACCCAAACTATTGCTTGCTTAGA
*
1473217 CACTTTATGCCATATTCCAAGGTAGTACTTGGAGGTACTTCCTGGCGAAAAAAACCCAAGTTCGA
196 CACTTTATGCCATATTCCAAGGTAGTACTTGGAGGTACTTACTGGCGAAAAAAACCCAAGTTCGA
* *
1473282 ATTTCCCACCAGATGATATAATGGTATTTGGATAGGTGATTGTTTGGCCTCGATGAATTGTGTCA
261 ATTTCCCACCAGATGATATAAGGGTATTTGGATAGGTGATTGTTTGGCCTCGATGAATTGTATCA
* * *
1473347 CTGCCATTCGTAAATCGGAAGGCGAGGCATAAGAAAACCAGCAAGCTAACAAAAAGAGAAAACCA
326 CTGCCATTCGTAAACCGGAAGGCAAGGCATAAGAAAACCAGCAAACTAACAAAAAGAGAAAACCA
1473412 ATCTCCCATCATTTACAGATGTTTAATGCTGATCAGAGTGAGAATCATATAGATGAAATTCGGGG
391 ATCTCCCATCATTTACAGATGTTTAATGCTGATCAGAGTGAGAATCATATAGATGAAATTCGGGG
*
1473477 ATTAAAGAAACGATTCAAGTCAACTCTCTCTGCAAGTCTTCGCTTGCTTTGGGCTAACT-AAAAA
456 ATTAAAGAAACGATTCAAGTCAACTCTCTCTGCAAATCTTCGCTTGCTTTGGGCTAACTAAAAAA
* * *
1473541 TATGTTGTTCTTCAGCC-T-T-AGGTCATCGTCTGCCCCA-C-G-T-AATCAAGCATTTTTTATG
521 AATCTTGTTCTTCAGCCTTGTCAAGTCATCGTCTGCCCCATCAGATAAATCAAGCATTTTTTATG
* *
1473599 GTCACGTTGAATTATCAAATGAAAACAATTACATTTAGTCACCATCAATAAAAATAATTATATAT
586 GTCACGTTGAATAATCAAATGAAAACAATTACATTTAGTCACCATCAATAAAAATATTTATATAT
*** * *
1473664 AATTATTGTATTCATATTATATTTATATATTTTATTATATTATA
651 GGCTATTATATTCATATTATATTTATATATTTTATCATATTATA
1473708 AATATTTTAA
Statistics
Matches: 649, Mismatches: 37, Indels: 23
0.92 0.05 0.03
Matches are distributed among these distances:
686 115 0.18
689 1 0.00
690 1 0.00
699 1 0.00
703 17 0.03
704 1 0.00
707 1 0.00
708 19 0.03
709 493 0.76
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (694 bp):
TTGCAACACTAAGTTACCTGAATCCAGTAGCATGGCAAATGTTTTGCTGTCGTTGCTAGCTATAC
TGCGTGTTACCTGGTACGACATTGGGCCATCTGATATCACGAGCTTTCCCTCAGAGTTGATGGTG
AGATTAGAAGAGTCACTCAGGCAAGGGTATGCTCTATTTGCCACCCAAACTATTGCTTGCTTAGA
CACTTTATGCCATATTCCAAGGTAGTACTTGGAGGTACTTACTGGCGAAAAAAACCCAAGTTCGA
ATTTCCCACCAGATGATATAAGGGTATTTGGATAGGTGATTGTTTGGCCTCGATGAATTGTATCA
CTGCCATTCGTAAACCGGAAGGCAAGGCATAAGAAAACCAGCAAACTAACAAAAAGAGAAAACCA
ATCTCCCATCATTTACAGATGTTTAATGCTGATCAGAGTGAGAATCATATAGATGAAATTCGGGG
ATTAAAGAAACGATTCAAGTCAACTCTCTCTGCAAATCTTCGCTTGCTTTGGGCTAACTAAAAAA
AATCTTGTTCTTCAGCCTTGTCAAGTCATCGTCTGCCCCATCAGATAAATCAAGCATTTTTTATG
GTCACGTTGAATAATCAAATGAAAACAATTACATTTAGTCACCATCAATAAAAATATTTATATAT
GGCTATTATATTCATATTATATTTATATATTTTATCATATTATA
Found at i:1473742 original size:20 final size:19
Alignment explanation
Indices: 1473719--1473833 Score: 59
Period size: 18 Copynumber: 6.3 Consensus size: 19
1473709 ATATTTTAAA
1473719 AATATTTTAAATTTATATAT
1 AATATTTTAAATTTATAT-T
* *
1473739 AATA--TTATATTCATATTT
1 AATATTTTAAATTTATA-TT
1473757 AATATATTTTAAATTTATATT
1 -A-ATATTTTAAATTTATATT
1473778 -A-ATTTT-AA--TATATT
1 AATATTTTAAATTTATATT
* *
1473792 AATAATTTATA-TTATA-T
1 AATATTTTAAATTTATATT
* * *
1473809 AAAATTTTATATATATATT
1 AATATTTTAAATTTATATT
*
1473828 TATATT
1 AATATT
1473834 ATATCATATT
Statistics
Matches: 73, Mismatches: 11, Indels: 23
0.68 0.10 0.21
Matches are distributed among these distances:
14 6 0.08
15 1 0.01
16 6 0.08
17 16 0.22
18 19 0.26
19 7 0.10
20 7 0.10
21 2 0.03
22 9 0.12
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (19 bp):
AATATTTTAAATTTATATT
Found at i:1473745 original size:45 final size:44
Alignment explanation
Indices: 1473684--1473847 Score: 126
Period size: 45 Copynumber: 3.8 Consensus size: 44
1473674 TTCATATTAT
**
1473684 ATTTATATATTTTATTATATTATAAATATTTTAAAAATATTTTAA
1 ATTTATATATAATATTATATTATAAATATTTT-AAAATATTTTAA
* *
1473729 ATTTATATATAATATTATA-T-T-CATA-TTTAATATATTTTAA
1 ATTTATATATAATATTATATTATAAATATTTTAAAATATTTTAA
* * * * * * *
1473769 ATTTATAT-TAATTTTA-ATATATTAATAATTTATATTATATAAA
1 ATTTATATATAATATTATAT-TATAAATATTTTAAAATATTTTAA
*
1473812 ATTT-TATATATATATTTATATTATATCATATTTTAA
1 ATTTATATATA-ATA-TTATATTATA-AATATTTTAA
1473848 TTACTTTATA
Statistics
Matches: 93, Mismatches: 16, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
38 1 0.01
39 7 0.08
40 20 0.22
41 4 0.04
42 9 0.10
43 17 0.18
44 3 0.03
45 23 0.25
46 9 0.10
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (44 bp):
ATTTATATATAATATTATATTATAAATATTTTAAAATATTTTAA
Found at i:1473784 original size:27 final size:28
Alignment explanation
Indices: 1473737--1473805 Score: 88
Period size: 27 Copynumber: 2.5 Consensus size: 28
1473727 AAATTTATAT
*
1473737 ATAATATTATATTCATATTTAATATATT-
1 ATAAT-TTATATTAATATTTAATATATTA
*
1473765 TTAAATTTATATTAAT-TTTAATATATTA
1 AT-AATTTATATTAATATTTAATATATTA
1473793 ATAATTTATATTA
1 ATAATTTATATTA
1473806 TATAAAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 22 0.61
28 11 0.31
29 3 0.08
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (28 bp):
ATAATTTATATTAATATTTAATATATTA
Found at i:1473797 original size:17 final size:17
Alignment explanation
Indices: 1473751--1473824 Score: 59
Period size: 17 Copynumber: 4.4 Consensus size: 17
1473741 TATTATATTC
1473751 ATAT-TTAATATATTTTA
1 ATATATTAATA-ATTTTA
1473768 A-AT-TTATATTAATTTTA
1 ATATATTA-A-TAATTTTA
1473785 ATATATTAATAATTTATA
1 ATATATTAATAATTT-TA
*
1473803 TTATA-TAA-AATTTTA
1 ATATATTAATAATTTTA
1473818 TATATAT
1 -ATATAT
1473825 ATTTATATTA
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
15 2 0.04
16 14 0.29
17 18 0.38
18 11 0.23
19 3 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATATATTAATAATTTTA
Found at i:1473850 original size:16 final size:16
Alignment explanation
Indices: 1473760--1473850 Score: 59
Period size: 17 Copynumber: 5.8 Consensus size: 16
1473750 CATATTTAAT
1473760 ATATTTTAAATT-TATA
1 ATATTTT-AATTATATA
*
1473776 TTAATTTTAA-TATATTA
1 AT-ATTTTAATTATA-TA
*
1473793 ATAATTTATATTATATA
1 ATATTTTA-ATTATATA
*
1473810 AAATTTT-A-TATAT-
1 ATATTTTAATTATATA
*
1473823 ATA-TTTATATTATATC
1 ATATTTTA-ATTATATA
1473839 ATATTTTAATTA
1 ATATTTTAATTA
1473851 CTTTATATAC
Statistics
Matches: 59, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
12 3 0.05
13 2 0.03
14 6 0.10
15 7 0.12
16 17 0.29
17 20 0.34
18 4 0.07
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (16 bp):
ATATTTTAATTATATA
Found at i:1474284 original size:32 final size:31
Alignment explanation
Indices: 1474248--1474307 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
1474238 TATTTAGATC
1474248 TTATTTATTATCTAGTTTAT-TTTAAATTAGTT
1 TTATTTATT-TCTA-TTTATATTTAAATTAGTT
*
1474280 TTATTTATTTTTATTTATATTTAAATTA
1 TTATTTATTTCTATTTATATTTAAATTA
1474308 TATAGTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 5 0.19
31 12 0.46
32 9 0.35
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (31 bp):
TTATTTATTTCTATTTATATTTAAATTAGTT
Found at i:1476226 original size:12 final size:12
Alignment explanation
Indices: 1476209--1476250 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1476199 TGGTTATTTT
*
1476209 ATTTTTTTTAAA
1 ATTTTTTATAAA
*
1476221 ATTTTTTATAAC
1 ATTTTTTATAAA
*
1476233 A-TTTTTAAAAA
1 ATTTTTTATAAA
1476244 ATTTTTT
1 ATTTTTT
1476251 GTTTGGTAGC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (12 bp):
ATTTTTTATAAA
Found at i:1476416 original size:16 final size:17
Alignment explanation
Indices: 1476395--1476428 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1476385 GCTCTATAAA
*
1476395 TAGAGCTTGAAAC-CTT
1 TAGAGCTCGAAACTCTT
1476411 TAGAGCTCGAAACTCTT
1 TAGAGCTCGAAACTCTT
1476428 T
1 T
1476429 CATTCATACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (17 bp):
TAGAGCTCGAAACTCTT
Found at i:1476781 original size:17 final size:16
Alignment explanation
Indices: 1476759--1476795 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
1476749 AAAAGTGTAC
*
1476759 TTTTTTGTTAGTGTTAT
1 TTTTTTGATAG-GTTAT
1476776 TTTTTTGATAGGTTAT
1 TTTTTTGATAGGTTAT
1476792 TTTT
1 TTTT
1476796 GTTTTTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.14, C:0.00, G:0.16, T:0.70
Consensus pattern (16 bp):
TTTTTTGATAGGTTAT
Found at i:1476807 original size:6 final size:7
Alignment explanation
Indices: 1476791--1476816 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1476781 TGATAGGTTA
1476791 TTTTTGT
1 TTTTTGT
1476798 TTTTTGT
1 TTTTTGT
1476805 TTTTTGT
1 TTTTTGT
1476812 TTTTT
1 TTTTT
1476817 TATTCTAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (7 bp):
TTTTTGT
Found at i:1476869 original size:38 final size:37
Alignment explanation
Indices: 1476827--1476900 Score: 103
Period size: 38 Copynumber: 2.0 Consensus size: 37
1476817 TATTCTAATG
*
1476827 ATTAGCTTTGTAATTTATTATTATGATTAAATATAAAA
1 ATTAGCTTTATAATTTATTATTATGATTAAAT-TAAAA
* * *
1476865 ATTAGTTTTATAATTTGTTCTTATGATTAAATTAAA
1 ATTAGCTTTATAATTTATTATTATGATTAAATTAAA
1476901 TTTTATTGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 4 0.12
38 28 0.88
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (37 bp):
ATTAGCTTTATAATTTATTATTATGATTAAATTAAAA
Found at i:1480215 original size:15 final size:15
Alignment explanation
Indices: 1480195--1480234 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
1480185 TTTATTTATT
1480195 ATTTCATTTTTCAAA
1 ATTTCATTTTTCAAA
*
1480210 ATTTCATTTTTGAAA
1 ATTTCATTTTTCAAA
*
1480225 ATTGCATTTT
1 ATTTCATTTT
1480235 GTACCTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.30, C:0.10, G:0.05, T:0.55
Consensus pattern (15 bp):
ATTTCATTTTTCAAA
Found at i:1482245 original size:20 final size:20
Alignment explanation
Indices: 1482220--1482276 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
1482210 TTTTACCTAG
*
1482220 ATGTATCAATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
1482240 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
1482260 ATGTATCGATACATTTT
1 ATGTATCGATACATTTT
1482277 GTCTTTTTAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1482280 original size:70 final size:71
Alignment explanation
Indices: 1482170--1482324 Score: 249
Period size: 71 Copynumber: 2.2 Consensus size: 71
1482160 TTTTACCTAG
* * *
1482170 ATGCATCGATACATTTTTCAATGTATCGATTCATTCTGTC-TTTTACCTAGATGTATCAATACAT
1 ATGCATCGATACATGTATCAATGTATCGATACATTCTGTCTTTTTACCTAGATGTATCAATACAT
1482234 TTTTCA
66 TTTTCA
* * *
1482240 ATGTATCGATACATGTATGAATGTATCGATACATTTTGTCTTTTTACCTAGATGTATCAATACAT
1 ATGCATCGATACATGTATCAATGTATCGATACATTCTGTCTTTTTACCTAGATGTATCAATACAT
1482305 TTTTCA
66 TTTTCA
1482311 ATGCATCGATACAT
1 ATGCATCGATACAT
1482325 CTAGTTAAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
70 34 0.44
71 43 0.56
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.43
Consensus pattern (71 bp):
ATGCATCGATACATGTATCAATGTATCGATACATTCTGTCTTTTTACCTAGATGTATCAATACAT
TTTTCA
Found at i:1483220 original size:20 final size:22
Alignment explanation
Indices: 1483181--1483220 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1483171 AGCCTTTGAC
*
1483181 CATGCATTTTTTTACTATGTTT
1 CATGCATTTTTTAACTATGTTT
1483203 CATGCA-TTTTTAAC-ATGT
1 CATGCATTTTTTAACTATGT
1483221 CTAGCATCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 7 0.41
22 6 0.35
ACGTcount: A:0.23, C:0.15, G:0.10, T:0.53
Consensus pattern (22 bp):
CATGCATTTTTTAACTATGTTT
Found at i:1486083 original size:10 final size:10
Alignment explanation
Indices: 1486068--1486092 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1486058 GAAAAAAATA
1486068 AAAATGAATG
1 AAAATGAATG
1486078 AAAATGAATG
1 AAAATGAATG
1486088 AAAAT
1 AAAAT
1486093 TTGAAACCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.16, T:0.20
Consensus pattern (10 bp):
AAAATGAATG
Found at i:1486208 original size:154 final size:153
Alignment explanation
Indices: 1485953--1486239 Score: 375
Period size: 154 Copynumber: 1.9 Consensus size: 153
1485943 AATATAAATC
* * *
1485953 AAATAATGATGTTTAATGAATTTTAAAATTAAAAACCGAGAAAAATCCTCTCGAAAAATATTATG
1 AAATAATGATGTTTAATGAATTTTAAAATTAAAAACCAAGAAAAATCCCCTCGAAAAATATTATA
* *
1486018 GAGTAGAAAATACTGTATTTCGAAAAAATAAAAGTTTCAAGAAAAAAATAAAAAT-GAATGAAAA
66 GAGTAGAAAACACTATATTTCGAAAAAATAAAAGTTTCAAG-AAAAAATAAAAATCGAATGAAAA
1486082 TGAATGAAAATTTGAAACCGAGAT
130 TGAATGAAAATTTGAAACCGAGAT
* *
1486106 AAATAATGATGTTTGATGAATTTTAAAAATTAAAAATCAAGAAAAATCCCCTCGAAAAA-ATTTA
1 AAATAATGATGTTTAATGAATTTT-AAAATTAAAAACCAAGAAAAATCCCCTCGAAAAATA-TTA
* ** * * **
1486170 TAGAGTAGAAAACA-TCATATTTTGAAAAAA-AGGGAGTTTCGAGGAAAAATAAAAATCTCATGA
64 TAGAGTAGAAAACACT-ATATTTCGAAAAAATA-AAAGTTTCAAGAAAAAATAAAAATCGAATGA
1486233 AAATGAA
127 AAATGAA
1486240 ATAAATTTTT
Statistics
Matches: 115, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
153 38 0.33
154 77 0.67
ACGTcount: A:0.52, C:0.08, G:0.14, T:0.26
Consensus pattern (153 bp):
AAATAATGATGTTTAATGAATTTTAAAATTAAAAACCAAGAAAAATCCCCTCGAAAAATATTATA
GAGTAGAAAACACTATATTTCGAAAAAATAAAAGTTTCAAGAAAAAATAAAAATCGAATGAAAAT
GAATGAAAATTTGAAACCGAGAT
Found at i:1488338 original size:20 final size:20
Alignment explanation
Indices: 1488313--1488350 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1488303 ATCATGTATG
1488313 AATGTATCGATACATTCTTC
1 AATGTATCGATACATTCTTC
1488333 AATGTATCGATACATTCT
1 AATGTATCGATACATTCT
1488351 ATTTTTTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACATTCTTC
Found at i:1491917 original size:89 final size:89
Alignment explanation
Indices: 1491795--1492057 Score: 332
Period size: 89 Copynumber: 3.0 Consensus size: 89
1491785 GTTCTAATAA
* * * * * * *
1491795 AATAAATTTCTTAGAACCCGAAAGATGTAACAGATACATGTGGGTATCGGATTTCTTATAACATG
1 AATAAATTTCTTAGAACACGAAAGATGTGACAGATGCATGTGGGTATCAGATTCCTTCTAACAAG
*
1491860 ATAGAAAATATTTGACTAATGCTT
66 ATAGAAAATATTTGACTAATGCCT
** *
1491884 AATAAATTTCTTAGAACTTGAAAGATGTGACAGATGCATGTGGGTATCAAATTCCTTCTAACAAG
1 AATAAATTTCTTAGAACACGAAAGATGTGACAGATGCATGTGGGTATCAGATTCCTTCTAACAAG
1491949 AT-GAAAAATATTTGACTAATGCCT
66 ATAG-AAAATATTTGACTAATGCCT
* * * * * * *
1491973 AATAAATTTGTTGGAACACGAAAGATGTGATAGATGCATGTAGGTATCAGACTCCTTCTGACACG
1 AATAAATTTCTTAGAACACGAAAGATGTGACAGATGCATGTGGGTATCAGATTCCTTCTAACAAG
*
1492038 ACA-AAAATATTTGACTAATG
66 ATAGAAAATATTTGACTAATG
1492058 ATATGACAAA
Statistics
Matches: 151, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
88 18 0.12
89 133 0.88
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (89 bp):
AATAAATTTCTTAGAACACGAAAGATGTGACAGATGCATGTGGGTATCAGATTCCTTCTAACAAG
ATAGAAAATATTTGACTAATGCCT
Found at i:1493306 original size:28 final size:28
Alignment explanation
Indices: 1493275--1493339 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
1493265 ACGGTGTTAC
** *
1493275 AGTATCCCCTTGAAAATGATAGGTTTGG
1 AGTATCCCCTCAAAAATGATAGGGTTGG
1493303 AGTATCCCCTCAAAAATGATAGGGTTGG
1 AGTATCCCCTCAAAAATGATAGGGTTGG
1493331 AGTATCCCC
1 AGTATCCCC
1493340 GATGGTGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (28 bp):
AGTATCCCCTCAAAAATGATAGGGTTGG
Found at i:1493430 original size:79 final size:79
Alignment explanation
Indices: 1493299--1493850 Score: 534
Period size: 79 Copynumber: 6.8 Consensus size: 79
1493289 AATGATAGGT
* * * **
1493299 TTGGAGTATCCCCTCAAAAATGATAGGGTTGGAGTATCCCCGATGGTGAAAAATCAATA-TTTGG
1 TTGGAGTATCCCTTCAGAAATGATGGGGTTGGAGTATCCCTAATGGTGAAAAATCAATATTTTGG
* *
1493363 TAAATACAAATGGGG
66 -AAATAAAAACGGGG
1493378 TTGGAGTATCCCTTCAGAAATGATGGGGTTGGAGTATCCCTAATGGTGAAAAATCAATATTTTGG
1 TTGGAGTATCCCTTCAGAAATGATGGGGTTGGAGTATCCCTAATGGTGAAAAATCAATATTTTGG
1493443 AAATAAAAACGGGG
66 AAATAAAAACGGGG
* * * ** ** ** *
1493457 TTGAAGTATCCCCTCAGAAATGATAGGGTTAAAGTATCCCCGATGGTGAAAAATTGATATTTTGA
1 TTGGAGTATCCCTTCAGAAATGATGGGGTTGGAGTATCCCTAATGGTGAAAAATCAATATTTTGG
*
1493522 AAATAAAAATGGGG
66 AAATAAAAACGGGG
* * * * * *
1493536 TTGGAGTATCCTCTGACCTCTTCGGATATGATGGGGTTGGAGTACCCCTAATGATGGAAAATTTT
1 TTGGAGTA-----T--CC-CTTCAGAAATGATGGGGTTGGAGTATCCCTAATGGT-GAAAA-ATC
* * *
1493601 GATATTTTGGAATTAAAAACGAGG
56 AATATTTTGGAAATAAAAACGGGG
* * * * * *
1493625 TTAGAGTATCCCCTCAGATATGATGGGGTTGAAGTAT-CCTCAATAGTAAAAAATCAATATTTTG
1 TTGGAGTATCCCTTCAGAAATGATGGGGTTGGAGTATCCCT-AATGGTGAAAAATCAATATTTTG
* **
1493689 GAAATAAAAATGGCA
65 GAAATAAAAACGGGG
* ** * * *
1493704 TCGGAGTATCCCTTTGGAAATGATAGGGTTGGAGTATCCCCAATGGTGAAAAATCGATATTTTGG
1 TTGGAGTATCCCTTCAGAAATGATGGGGTTGGAGTATCCCTAATGGTGAAAAATCAATATTTTGG
1493769 AAATAAAAACGGGG
66 AAATAAAAACGGGG
* ** * *
1493783 TTGGAGTATCCCTTCAGAAATAATGAAGTTGGAGTAT-CCTCGATGGTGAAAAATCGATACTTTT
1 TTGGAGTATCCCTTCAGAAATGATGGGGTTGGAGTATCCCT-AATGGTGAAAAATCAATA-TTTT
1493847 GGAA
64 GGAA
1493851 GGAGAAATTT
Statistics
Matches: 384, Mismatches: 74, Indels: 29
0.79 0.15 0.06
Matches are distributed among these distances:
78 2 0.01
79 268 0.70
80 22 0.06
81 26 0.07
82 2 0.01
84 2 0.01
86 2 0.01
87 26 0.07
88 5 0.01
89 29 0.08
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (79 bp):
TTGGAGTATCCCTTCAGAAATGATGGGGTTGGAGTATCCCTAATGGTGAAAAATCAATATTTTGG
AAATAAAAACGGGG
Found at i:1494390 original size:51 final size:53
Alignment explanation
Indices: 1494256--1494410 Score: 219
Period size: 51 Copynumber: 3.0 Consensus size: 53
1494246 GGTTCGAAAT
* * *
1494256 GGTCAAAATAGCCTGAATGTATCGATACAATGAAGAATGTATC-AGTACA-TTGA
1 GGTCAAAA-ACCCAGAATGTATCGATACAATGAAAAATGTATCGA-TACATTTGA
*
1494309 GGTCAAAAACCCAGAATGTATCGATACAATGAATAATGTATCGATACATTTG-
1 GGTCAAAAACCCAGAATGTATCGATACAATGAAAAATGTATCGATACATTTGA
*
1494361 GGTC-AAAACCTAGAATGTATCGATACAATGAAAAATGTATCGATACATTT
1 GGTCAAAAACCCAGAATGTATCGATACAATGAAAAATGTATCGATACATTT
1494411 TCTTTCTAGA
Statistics
Matches: 95, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
51 44 0.46
52 39 0.41
53 12 0.13
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (53 bp):
GGTCAAAAACCCAGAATGTATCGATACAATGAAAAATGTATCGATACATTTGA
Found at i:1495446 original size:66 final size:65
Alignment explanation
Indices: 1494994--1495678 Score: 506
Period size: 66 Copynumber: 10.6 Consensus size: 65
1494984 GGAAGTAGAT
* * **
1494994 AGGTGCCACCAACTTATGTGGGTTTTGAGAAAGAAAAAG--A-G--TCCCACTCTTTGAGGACTA
1 AGGTGCCACCAACTTGTGTGGGCTTT-A-AAAGAAAAAGAAAGGCATCCTGCTCTTTGAGGACT-
1495054 AAA
63 AAA
* * *
1495057 AGGAGTGCCACCAACTTGTGTGGGCTTTTAAAAAGAAAAAAAAGAGGCGTCCTGCTTTTTGAGGA
1 A-G-GTGCCACCAACTTGTGTGGGC-TTT-AAAAGAAAAAGAA-AGGCATCCTGCTCTTTGAGGA
1495122 CTAAA
61 CTAAA
** * *
1495127 AAATGCCACCAACTTGTGTGGGTTTTAAAAGAAAAAGAAAAGCATCCTG--C--T-----CT--A
1 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGAAAGGCATCCTGCTCTTTGAGGACTAAA
* * * ** * * ** *
1495181 AGGTGTCACTAATTTATGTG-GGCTTTAAAAGA-AAAAAA--A-GCATTTTGCACTTTGAGGACT
1 AGGTGCCACCAA-CT-TGTGTGGGCTTTAAA-AGAAAAAGAAAGGCATCCTGCTCTTTGAGGACT
1495241 AAA
63 AAA
**** * * *
1495244 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGAAAAATGTCTTACTCTATGAGGACTAAA
1 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGAAAGGCATCCTGCTCTTTGAGGACTAAA
** ** * * *
1495309 AGGTTTCACCAACTTGTGTAAGCTTTTTAAAG---GA-AAAGGCATCCTACTCTTTGAGGACTAA
1 AGGTGCCACCAACTTGTGTGGGC-TTTAAAAGAAAAAGAAAGGCATCCTGCTCTTTGAGGACTAA
1495370 A
65 A
* * ** ** *
1495371 AGGTGCCACCAACTTATGTGAGCTTTAAAAGGAAAAAGTTAGGTGTCCTGCTCTTTAAGGACTAA
1 AGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAAGAAAGGCATCCTGCTCTTTGAGGACTAA
1495436 A
65 A
* * *
1495437 AGGTACCACCAATTTGTGTGGGCTTTAAAAAGAAAAGGAGAA-GCATCCTGCTCTTTGAGGACTA
1 AGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAAGA-AAGGCATCCTGCTCTTTGAGGACTA
1495501 AA
64 AA
* *
1495503 AGGTGCCACCAACTTGTGTGAGCTTTAAAAGAAAAAGGAAAGGCATCTTGCTCTTTGAGGACTAT
1 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAA-GAAAGGCATCCTGCTCTTTGAGGACTA-
1495568 AA
64 AA
* * * * *
1495570 A-GTGCCACCACCTTGTGTGGGTTTTAAGAAAAAAAAGAAGAAGCGTCCTGCTCTTTGAGGACTA
1 AGGTGCCACCAACTTGTGTGGGCTTTAA-AAGAAAAAGAA-AGGCATCCTGCTCTTTGAGGACTA
1495634 AA
64 AA
* * *
1495636 AGGTGCCACTAACTTGTATGGGCTTTAAAAGGAAAAGGAAAGG
1 AGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAAGAAAGG
1495679 TGTTTTACTT
Statistics
Matches: 488, Mismatches: 91, Indels: 83
0.74 0.14 0.13
Matches are distributed among these distances:
52 6 0.01
53 1 0.00
54 10 0.02
55 14 0.03
56 8 0.02
61 14 0.03
62 55 0.11
63 13 0.03
64 2 0.00
65 84 0.17
66 173 0.35
67 68 0.14
68 20 0.04
69 1 0.00
70 4 0.01
71 15 0.03
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (65 bp):
AGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGAAAGGCATCCTGCTCTTTGAGGACTAAA
Found at i:1499397 original size:25 final size:24
Alignment explanation
Indices: 1499369--1499436 Score: 93
Period size: 23 Copynumber: 2.8 Consensus size: 24
1499359 TGAAAATCCA
1499369 TTTAATATTGACTAAACTTTCCTAT
1 TTTAATATTGACTAAA-TTTCCTAT
* *
1499394 TTTAATATTAAC-AATTTTCCTAT
1 TTTAATATTGACTAAATTTCCTAT
*
1499417 TTTAATATTGAGTAAATTTC
1 TTTAATATTGACTAAATTTC
1499437 AACCGTTGCT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
23 18 0.49
24 8 0.22
25 11 0.30
ACGTcount: A:0.34, C:0.12, G:0.04, T:0.50
Consensus pattern (24 bp):
TTTAATATTGACTAAATTTCCTAT
Found at i:1499579 original size:12 final size:10
Alignment explanation
Indices: 1499556--1499584 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1499546 CTTGCTTCGA
1499556 TTCTTCTCTT
1 TTCTTCTCTT
1499566 TTCTTCTCTT
1 TTCTTCTCTT
1499576 TT-TTCTCTT
1 TTCTTCTCTT
1499585 GTTGTTTCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 7 0.37
10 12 0.63
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (10 bp):
TTCTTCTCTT
Found at i:1499968 original size:23 final size:24
Alignment explanation
Indices: 1499938--1499991 Score: 83
Period size: 23 Copynumber: 2.2 Consensus size: 24
1499928 CGTTTCTGAG
1499938 TTCAGCAGCTTAATTG-TAGCTGT
1 TTCAGCAGCTTAATTGATAGCTGT
1499961 TTCAGCAGCTTAATTGCAATAGCTGT
1 TTCAGCAGCTTAATTG--ATAGCTGT
1499987 TTCAG
1 TTCAG
1499992 TTTTTATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 16 0.57
26 12 0.43
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (24 bp):
TTCAGCAGCTTAATTGATAGCTGT
Found at i:1500072 original size:30 final size:30
Alignment explanation
Indices: 1500037--1500103 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
1500027 TTCTTTGCTG
**
1500037 CTTGATTCATTTTTGTCTTCATTGTAGCAT
1 CTTGATTCATTTTTGTCTTCATTACAGCAT
*
1500067 CTTGATTCGTTTTTGTCTTCATTACAGCAT
1 CTTGATTCATTTTTGTCTTCATTACAGCAT
1500097 CTTGATT
1 CTTGATT
1500104 GCTTTAATTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.16, C:0.18, G:0.13, T:0.52
Consensus pattern (30 bp):
CTTGATTCATTTTTGTCTTCATTACAGCAT
Found at i:1500190 original size:12 final size:12
Alignment explanation
Indices: 1500175--1500216 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
1500165 ACTTTATCGT
1500175 TTGCTTTCTTCA
1 TTGCTTTCTTCA
1500187 TTGCATTTGCTTCA
1 TTGC-TTT-CTTCA
*
1500201 TTGGTTTCTTCA
1 TTGCTTTCTTCA
1500213 TTGC
1 TTGC
1500217 ACCTTGATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 12 0.46
13 6 0.23
14 8 0.31
ACGTcount: A:0.10, C:0.21, G:0.14, T:0.55
Consensus pattern (12 bp):
TTGCTTTCTTCA
Found at i:1500929 original size:42 final size:42
Alignment explanation
Indices: 1500870--1501043 Score: 165
Period size: 42 Copynumber: 4.2 Consensus size: 42
1500860 AAATGACCCA
** * **
1500870 GACAGGCAGACTAAGGGTTAGAAAGTCTCCAAAGTCAAAGCC
1 GACAGGCAGACCGAGGGTAAGAAAGTCTCCAGGGTCAAAGCC
* *
1500912 GACAGGCAGACCGAGGGTAAGAAAGTCTCTAGGGTCAAAGCT
1 GACAGGCAGACCGAGGGTAAGAAAGTCTCCAGGGTCAAAGCC
* * * ** * **
1500954 GACAGGTAGACTTGA-GGTGAGGCAGTCTCTAGGGTCAAAGGT
1 GACAGGCAGAC-CGAGGGTAAGAAAGTCTCCAGGGTCAAAGCC
* *
1500996 GATAGGCAGA-CTAGGGTAAGAAAGTCTCCAGGGTCAAAG-C
1 GACAGGCAGACCGAGGGTAAGAAAGTCTCCAGGGTCAAAGCC
1501036 GACAGGCA
1 GACAGGCA
1501044 CACTTGAGAA
Statistics
Matches: 107, Mismatches: 23, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
40 8 0.07
41 21 0.20
42 76 0.71
43 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.33, T:0.16
Consensus pattern (42 bp):
GACAGGCAGACCGAGGGTAAGAAAGTCTCCAGGGTCAAAGCC
Found at i:1501460 original size:134 final size:131
Alignment explanation
Indices: 1501295--1501535 Score: 313
Period size: 134 Copynumber: 1.8 Consensus size: 131
1501285 AAAAAAGGTG
* * *
1501295 GATTTAACTAGGATGGTAACCATACGTCAAATCAGAAT-GAAATGAATCTGACTAGAGTGGTAAC
1 GATTTAACTAGGATGGTAACCATACATCAAATCAAAATAGAAA-AAAT-TGACTAGAGTGGTAAC
* * *
1501359 CATACATCAGACCGAAATGAGAAAAGTTTGACTAGGGTGGTAACTAATACAATTAAATAAAACAG
64 CATACAT--GACCAAAATGAGAAAAATTTGACCAGGGTGGTAACTAATACAATTAAATAAAACAG
1501424 AGGCA
127 AGGCA
* * * *
1501429 GATTTGACTAGGGTGGTAACCATACATCAAATCAAAATAAGAAAAAATTGATTAGGGTGGTAACC
1 GATTTAACTAGGATGGTAACCATACATCAAATCAAAAT-AGAAAAAATTGACTAGAGTGGTAACC
* * *
1501494 ATACGTTATCAAAATGAGAAAAATTTGACCAGGGTGGTAACT
65 ATACATGACCAAAATGAGAAAAATTTGACCAGGGTGGTAACT
1501536 GTATGTCAAA
Statistics
Matches: 92, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
132 31 0.34
134 54 0.59
135 3 0.03
136 4 0.04
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (131 bp):
GATTTAACTAGGATGGTAACCATACATCAAATCAAAATAGAAAAAATTGACTAGAGTGGTAACCA
TACATGACCAAAATGAGAAAAATTTGACCAGGGTGGTAACTAATACAATTAAATAAAACAGAGGC
A
Found at i:1501494 original size:44 final size:44
Alignment explanation
Indices: 1501296--1501534 Score: 191
Period size: 44 Copynumber: 5.4 Consensus size: 44
1501286 AAAAAGGTGG
* * * *
1501296 ATTTAACTAGGATGGTAACCATACGTCAAATCAGAAT--GAAATGA
1 ATTTGACTAGGGTGGTAACCATACATCAAATCAAAATAAGAAA--A
* * * * * *
1501340 ATCTGACTAGAGTGGTAACCATACATCAGACCGAAATGAGAAAA
1 ATTTGACTAGGGTGGTAACCATACATCAAATCAAAATAAGAAAA
* * * * ** *
1501384 GTTTGACTAGGGTGGTAACTAATACAATTAAAT-AAAACAGAGGCAG
1 ATTTGACTAGGGTGGTAAC-CATAC-ATCAAATCAAAATA-AGAAAA
1501430 ATTTGACTAGGGTGGTAACCATACATCAAATCAAAATAAGAAAA
1 ATTTGACTAGGGTGGTAACCATACATCAAATCAAAATAAGAAAA
* * * * *
1501474 AATTGATTAGGGTGGTAACCATACGT--TATCAAAATGAGAAAA
1 ATTTGACTAGGGTGGTAACCATACATCAAATCAAAATAAGAAAA
*
1501516 ATTTGACCAGGGTGGTAAC
1 ATTTGACTAGGGTGGTAAC
1501535 TGTATGTCAA
Statistics
Matches: 152, Mismatches: 37, Indels: 14
0.75 0.18 0.07
Matches are distributed among these distances:
42 30 0.20
44 77 0.51
45 16 0.11
46 29 0.19
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.23
Consensus pattern (44 bp):
ATTTGACTAGGGTGGTAACCATACATCAAATCAAAATAAGAAAA
Found at i:1502529 original size:88 final size:88
Alignment explanation
Indices: 1502311--1502543 Score: 238
Period size: 88 Copynumber: 2.7 Consensus size: 88
1502301 AACATGCATG
* * ** *
1502311 AAACAATGCAAATACAAGCATCAGTAAAGTGGCAAATGCATATGAAAATGATGCAAATGTCAATG
1 AAACAATGCAAATGCAAGCATCAATAAAGTGGCAAATGCATATGAAAATGATGCAAATACCAATA
* *
1502376 TTATTTGAATGCAAATGCATGTA
66 TTATTTAAATGCAAATGCAGGTA
** * * * ** * *
1502399 AAATGATACAAATGCAAGCATCAACAAAGGGGCAAACACATATG-TAATGATGCAAATACCACTA
1 AAACAATGCAAATGCAAGCATCAATAAAGTGGCAAATGCATATGAAAATGATGCAAATACCAATA
* * *
1502463 TTATTTAAAATGTAAATGTAGGTG
66 TTATTT-AAATGCAAATGCAGGTA
* *
1502487 AGACAATGCAAATGCAATCATCAATAGAA-TGGCAAATGCATATGAAAAT-ATGCAAAT
1 AAACAATGCAAATGCAAGCATCAATA-AAGTGGCAAATGCATATGAAAATGATGCAAAT
1502544 GCTAATGCAG
Statistics
Matches: 113, Mismatches: 29, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
87 21 0.19
88 87 0.77
89 5 0.04
ACGTcount: A:0.46, C:0.13, G:0.17, T:0.24
Consensus pattern (88 bp):
AAACAATGCAAATGCAAGCATCAATAAAGTGGCAAATGCATATGAAAATGATGCAAATACCAATA
TTATTTAAATGCAAATGCAGGTA
Found at i:1508502 original size:23 final size:23
Alignment explanation
Indices: 1508476--1508560 Score: 134
Period size: 23 Copynumber: 3.7 Consensus size: 23
1508466 TTTGCTAATG
*
1508476 TTTGCTTGATGTTTTTGTTGGTA
1 TTTGCTTGATATTTTTGTTGGTA
*
1508499 TTTGCTTGTTATTTTTGTTGGTA
1 TTTGCTTGATATTTTTGTTGGTA
*
1508522 TTTGCTTGCTATTTTTGTTGGTA
1 TTTGCTTGATATTTTTGTTGGTA
*
1508545 TTTGCTTGCTATTTTT
1 TTTGCTTGATATTTTT
1508561 ACTGCCATTG
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.08, C:0.07, G:0.21, T:0.64
Consensus pattern (23 bp):
TTTGCTTGATATTTTTGTTGGTA
Found at i:1508571 original size:22 final size:23
Alignment explanation
Indices: 1508498--1508574 Score: 66
Period size: 23 Copynumber: 3.4 Consensus size: 23
1508488 TTTTGTTGGT
* ** **
1508498 ATTTGCTTGTTATTTTTGTTGGT
1 ATTTGCTTGCTATTTTTACTGCC
** **
1508521 ATTTGCTTGCTATTTTTGTTGGT
1 ATTTGCTTGCTATTTTTACTGCC
1508544 ATTTGCTTGCTATTTTTACTGCC
1 ATTTGCTTGCTATTTTTACTGCC
1508567 A-TTGCTTG
1 ATTTGCTTG
1508575 TTGCTTGTTG
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
22 7 0.14
23 42 0.86
ACGTcount: A:0.10, C:0.12, G:0.19, T:0.58
Consensus pattern (23 bp):
ATTTGCTTGCTATTTTTACTGCC
Found at i:1508580 original size:7 final size:7
Alignment explanation
Indices: 1508568--1508618 Score: 56
Period size: 7 Copynumber: 7.7 Consensus size: 7
1508558 TTTACTGCCA
1508568 TTGCTTG
1 TTGCTTG
1508575 TTGCTTG
1 TTGCTTG
1508582 TTGCTTG
1 TTGCTTG
1508589 TTCGCTTG
1 TT-GCTTG
1508597 -TG-TTG
1 TTGCTTG
1508602 TTGC-TG
1 TTGCTTG
*
1508608 TTAC-TG
1 TTGCTTG
1508614 TTGCT
1 TTGCT
1508619 GCTACTATTG
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
5 3 0.08
6 13 0.34
7 17 0.45
8 5 0.13
ACGTcount: A:0.02, C:0.16, G:0.27, T:0.55
Consensus pattern (7 bp):
TTGCTTG
Found at i:1509282 original size:23 final size:23
Alignment explanation
Indices: 1509250--1509301 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
1509240 CGTTTCTGAG
*
1509250 TTCAGTAGCTTAATTACAGCTAT
1 TTCAGCAGCTTAATTACAGCTAT
* *
1509273 TTCAGCAGCTTAATTGCAGCTGT
1 TTCAGCAGCTTAATTACAGCTAT
1509296 TTCAGC
1 TTCAGC
1509302 TTTTTTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (23 bp):
TTCAGCAGCTTAATTACAGCTAT
Found at i:1509693 original size:14 final size:14
Alignment explanation
Indices: 1509674--1509700 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1509664 TGAAAGAAAG
1509674 AATGCATGAAATGT
1 AATGCATGAAATGT
1509688 AATGCATGAAATG
1 AATGCATGAAATG
1509701 AACATATGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.26
Consensus pattern (14 bp):
AATGCATGAAATGT
Found at i:1509899 original size:20 final size:20
Alignment explanation
Indices: 1509874--1509911 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1509864 TTTATGTACA
1509874 TATTTTCTATTTAATTATTT
1 TATTTTCTATTTAATTATTT
* *
1509894 TATTTTTTATTTTATTAT
1 TATTTTCTATTTAATTAT
1509912 ATTTTTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (20 bp):
TATTTTCTATTTAATTATTT
Found at i:1509914 original size:17 final size:16
Alignment explanation
Indices: 1509893--1509922 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1509883 TTTAATTATT
1509893 TTAT-TTTTTATTTTA
1 TTATATTTTTATTTTA
1509908 TTATATTTTTATTTT
1 TTATATTTTTATTTT
1509923 TTAATGCCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (16 bp):
TTATATTTTTATTTTA
Found at i:1511499 original size:20 final size:20
Alignment explanation
Indices: 1511474--1511525 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1511464 CATTTACGGC
*
1511474 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTCACTA
* *
1511494 ATGTATTGACACATTCACTA
1 ATGTATCGATACATTCACTA
1511514 ATTGTATCGATA
1 A-TGTATCGATA
1511526 TAAATTGTAG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTCACTA
Found at i:1512304 original size:31 final size:31
Alignment explanation
Indices: 1512223--1512325 Score: 100
Period size: 31 Copynumber: 3.3 Consensus size: 31
1512213 CACTAGCTTA
* * *
1512223 TGTGGGCTTTAACTCA-AGTGCCGCCAACTCG
1 TGTGGGCTTTGACT-AGGGTGCCACCAACTCG
* ** * * * *
1512254 TGCGACCTTAGACTCGGGTGCCACCAGCTTG
1 TGTGGGCTTTGACTAGGGTGCCACCAACTCG
1512285 TGTGGGCTTTGACTAGGGTGCCACCAACTCG
1 TGTGGGCTTTGACTAGGGTGCCACCAACTCG
1512316 TGTGGGCTTT
1 TGTGGGCTTT
1512326 AACATTCTAA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
31 54 1.00
ACGTcount: A:0.16, C:0.27, G:0.30, T:0.27
Consensus pattern (31 bp):
TGTGGGCTTTGACTAGGGTGCCACCAACTCG
Found at i:1512316 original size:180 final size:180
Alignment explanation
Indices: 1512014--1512411 Score: 526
Period size: 180 Copynumber: 2.2 Consensus size: 180
1512004 TGTGCAGGCT
* * * * * ** * *
1512014 TTGACTCAGACTTTGGTGCCACCAGTTTGTGTGGGCTTTGACTCAAGTGTTGCCAATTCATGCGG
1 TTGACTCAAACTTAGGTGCCACTAGCTTGTGTGGGCTTTAACTCAAGTGCCGCCAACTCATGCGA
* * *** *
1512079 GCTTAGACTTGAGTGTTGCCAGCTTGTGCAGGCTTTAACTAGGGTGCCACTAACTCGTATAGGCT
66 CCTTAGACTCGAGTGCCACCAGCTTGTGCAGGCTTTAACTAGGGTGCCACCAACTCGTATAGGCT
* * *
1512144 TTGATATTCTAAGGCTTGACCTCCTCAAACAGGTGCTAACTAATTTGGAC
131 TTAACATTCTAAGGCTTGACCTCCTCAAACAGGTGCCAACTAATTTGGAC
* *
1512194 TTGACTCAAACTTAGGTGCCACTAGCTTATGTGGGCTTTAACTCAAGTGCCGCCAACTCGTGCGA
1 TTGACTCAAACTTAGGTGCCACTAGCTTGTGTGGGCTTTAACTCAAGTGCCGCCAACTCATGCGA
* ** * * *
1512259 CCTTAGACTCGGGTGCCACCAGCTTGTGTGGGCTTTGACTAGGGTGCCACCAACTCGTGTGGGCT
66 CCTTAGACTCGAGTGCCACCAGCTTGTGCAGGCTTTAACTAGGGTGCCACCAACTCGTATAGGCT
* *
1512324 TTAACATTCTAAGGCTTGACCTCCTTAGACAGGTGCCAACTAATTTGGAC
131 TTAACATTCTAAGGCTTGACCTCCTCAAACAGGTGCCAACTAATTTGGAC
* *
1512374 TTGACTTAAACTTAGATGCCACTAGCTTGTGTGGGCTT
1 TTGACTCAAACTTAGGTGCCACTAGCTTGTGTGGGCTT
1512412 ATAAAAGTGG
Statistics
Matches: 187, Mismatches: 31, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
180 187 1.00
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (180 bp):
TTGACTCAAACTTAGGTGCCACTAGCTTGTGTGGGCTTTAACTCAAGTGCCGCCAACTCATGCGA
CCTTAGACTCGAGTGCCACCAGCTTGTGCAGGCTTTAACTAGGGTGCCACCAACTCGTATAGGCT
TTAACATTCTAAGGCTTGACCTCCTCAAACAGGTGCCAACTAATTTGGAC
Found at i:1512739 original size:36 final size:36
Alignment explanation
Indices: 1512633--1512884 Score: 136
Period size: 37 Copynumber: 6.8 Consensus size: 36
1512623 AATAAAATGG
* *
1512633 GTCCTACT-TCTTGAAAACAAAGGAAAAAAGAGTAGGC
1 GTCCTACTCT-TTGAAGACAAAGG-AAAATGAGTAGGC
*
1512670 GTCCTACTCTTT-AAGGACAAAGGGAAAATGAGTAGGT
1 GTCCTACTCTTTGAA-GACAAA-GGAAAATGAGTAGGC
* * *
1512707 GTCTTTCTCTTTGAAGACAAAGGAAAATGAGTA--T
1 GTCCTACTCTTTGAAGACAAAGGAAAATGAGTAGGC
* * * * * *
1512741 GTCCTACTCTTTTAGGAAAAAGGAAAAAGAATAATGAAATGG
1 GTCCTACTCTTTGAAGACAAAGGAAAATGAGT-A-G----GC
* * * * * *
1512783 GTCTTGCTCTTTGAGGATATAGGAAAAAGGAGTAGGC
1 GTCCTACTCTTTGAAGACAAAGG-AAAATGAGTAGGC
* * *
1512820 ATCCTGCTCTTTGAGGACAAAGAGAAAATGAGTAGGC
1 GTCCTACTCTTTGAAGACAAAG-GAAAATGAGTAGGC
* *
1512857 ATCCTACTC-TTCAAGGACAAAGGGAAAA
1 GTCCTACTCTTTGAA-GACAAA-GGAAAA
1512885 AAGGAATAAA
Statistics
Matches: 170, Mismatches: 29, Indels: 32
0.74 0.13 0.14
Matches are distributed among these distances:
34 26 0.15
35 1 0.01
36 17 0.10
37 92 0.54
38 7 0.04
41 1 0.01
42 19 0.11
43 7 0.04
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.24
Consensus pattern (36 bp):
GTCCTACTCTTTGAAGACAAAGGAAAATGAGTAGGC
Found at i:1512907 original size:116 final size:113
Alignment explanation
Indices: 1512683--1512927 Score: 285
Period size: 116 Copynumber: 2.1 Consensus size: 113
1512673 CTACTCTTTA
* * ** * * *
1512683 AGGACAAAGGGAAAATGAGTAGGTGTCTTTCTCTTTGAAGACAAAGGAAAATGAGTATGTCCTAC
1 AGGACAAAGGAAAAAGGAGTAGGCATCCTGCTCTTTGAAGACAAAGGAAAATGAGTAGGTCCTAC
** * * * *
1512748 TCTTTTAGGAAAAAGGAAAAAGAATAATGAAATGGGTCTTGCTCTTTG
66 TCTTCAAGGAAAAAGGAAAAAGAAGAATAAAATGGGTCCTGCTCCTTG
* * *
1512796 AGGATATAGGAAAAAGGAGTAGGCATCCTGCTCTTTGAGGACAAAGAGAAAATGAGTAGGCATCC
1 AGGACAAAGGAAAAAGGAGTAGGCATCCTGCTCTTTGAAGACAAAG-GAAAATGAGTAGG--TCC
* *
1512861 TACTCTTCAAGGACAAAGGGAAAAA-AGGAATAAAATGGGTCCTGCTCCTTG
63 TACTCTTCAAGGA-AAAAGGAAAAAGAAGAATAAAATGGGTCCTGCTCCTTG
1512912 AGGACAAAGGAAAAAG
1 AGGACAAAGGAAAAAG
1512928 AAGAAAAGGA
Statistics
Matches: 108, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
113 37 0.34
114 12 0.11
116 49 0.45
117 10 0.09
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.22
Consensus pattern (113 bp):
AGGACAAAGGAAAAAGGAGTAGGCATCCTGCTCTTTGAAGACAAAGGAAAATGAGTAGGTCCTAC
TCTTCAAGGAAAAAGGAAAAAGAAGAATAAAATGGGTCCTGCTCCTTG
Found at i:1515501 original size:122 final size:121
Alignment explanation
Indices: 1515274--1515518 Score: 445
Period size: 122 Copynumber: 2.0 Consensus size: 121
1515264 CTGTGCAGCA
*
1515274 CCTGATCCCTACTCTTCTTGTATAGGATCATGCCATCTAAGAAGAATCCCATGCCAGTCTTCTGA
1 CCTGATCCCTACTCTTCTTGTATAGGATCATGCCATCTAAGAAGAATCCCATGCCAGTCTCCTGA
* *
1515339 TGGTCCTTTTGTTGTTTTCAGTCCTGTTCTTGGGGTATTATTGATCCTTGATGTAG
66 TGGTCCTTTTATTGTTTTCAGTCCTGTTCTTGGGGTATTATTGATCCCTGATGTAG
1515395 CCTGATCCCTACTCTTCTTGTATAGGATCATGCCATCTAAGAAGAATCCCATTGCCAGTCTCCTG
1 CCTGATCCCTACTCTTCTTGTATAGGATCATGCCATCTAAGAAGAATCCCA-TGCCAGTCTCCTG
*
1515460 ATGGTCCTTTTATTGTTTTTAGTCCTGTTCTTGGGGTATTATTGATCCCTGATGTAG
65 ATGGTCCTTTTATTGTTTTCAGTCCTGTTCTTGGGGTATTATTGATCCCTGATGTAG
1515517 CC
1 CC
1515519 AAGGATGTCA
Statistics
Matches: 119, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
121 51 0.43
122 68 0.57
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.39
Consensus pattern (121 bp):
CCTGATCCCTACTCTTCTTGTATAGGATCATGCCATCTAAGAAGAATCCCATGCCAGTCTCCTGA
TGGTCCTTTTATTGTTTTCAGTCCTGTTCTTGGGGTATTATTGATCCCTGATGTAG
Found at i:1518548 original size:19 final size:18
Alignment explanation
Indices: 1518523--1518586 Score: 75
Period size: 19 Copynumber: 3.7 Consensus size: 18
1518513 AATTCAACGA
1518523 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1518541 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1518557 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1518573 TTTTGTATCGATAC
1 -TTTGTATCGATAC
1518587 TAATGAAGCT
Statistics
Matches: 39, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
17 2 0.05
18 1 0.03
19 23 0.59
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.39
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:1518561 original size:32 final size:33
Alignment explanation
Indices: 1518525--1518591 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 33
1518515 TTCAACGATT
1518525 TGTATCGATACATAAGTGTTGTATCGATAC-AA
1 TGTATCGATACATAAGTGTTGTATCGATACTAA
*
1518557 TGTATCGATACATAAGTTTTGTATCGATACTAA
1 TGTATCGATACATAAGTGTTGTATCGATACTAA
1518590 TG
1 TG
1518592 AAGCTACTAC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 29 0.88
33 4 0.12
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (33 bp):
TGTATCGATACATAAGTGTTGTATCGATACTAA
Found at i:1518562 original size:13 final size:13
Alignment explanation
Indices: 1518544--1518568 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1518534 ACATAAGTGT
1518544 TGTATCGATACAA
1 TGTATCGATACAA
1518557 TGTATCGATACA
1 TGTATCGATACA
1518569 TAAGTTTTGT
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:1518652 original size:13 final size:13
Alignment explanation
Indices: 1518634--1518658 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1518624 ACTCAAATGA
1518634 ATCGATACATTGT
1 ATCGATACATTGT
1518647 ATCGATACATTG
1 ATCGATACATTG
1518659 ATCTTTGTAT
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):
ATCGATACATTGT
Found at i:1532402 original size:21 final size:21
Alignment explanation
Indices: 1532355--1532408 Score: 92
Period size: 20 Copynumber: 2.6 Consensus size: 21
1532345 CATTTAAGAC
*
1532355 TTGTATCGATACATTCACTTA
1 TTGTATCGATACATTCACTAA
1532376 -TGTATCGATACATTCACTAA
1 TTGTATCGATACATTCACTAA
1532396 TTGTATCGATACA
1 TTGTATCGATACA
1532409 AATTGTAGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 19 0.61
21 12 0.39
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (21 bp):
TTGTATCGATACATTCACTAA
Found at i:1532869 original size:63 final size:60
Alignment explanation
Indices: 1532718--1532953 Score: 242
Period size: 61 Copynumber: 3.9 Consensus size: 60
1532708 TGTCTACACC
* * *
1532718 ACTCTTTAAAGACTAAAAGGTGCCACCAACTTATGTGGGCTTTAAAAGAAAAAGGCATTCT
1 ACTCTTTGAAGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-AAAAAGGCATCCT
* * * ** * ***
1532779 GCTCTTTGAGGACTAAAAAGTATCACCAACTTGTGTGAGCTTTAAAAACAGGCGCAGCATCCT
1 ACTCTTTGAAGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAA-AAAAG--GCATCCT
* *
1532842 ACTCTTTGAAGACTAAAAGGTGCCACCAACTTGTATGGGCTTTAAAAAGAAAAAGGCATCTT
1 ACTCTTTGAAGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAA-AAAAAGGCATCCT
* * *
1532904 GCTCTTT-AAGGACT-AAAGTTGCCACCAACTTGTGTAGGCTTTAAAAAAAA
1 ACTCTTTGAA-GACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAAA
1532954 GGAAAAAGTT
Statistics
Matches: 142, Mismatches: 27, Indels: 14
0.78 0.15 0.08
Matches are distributed among these distances:
59 4 0.03
60 5 0.04
61 68 0.48
62 16 0.11
63 42 0.30
64 6 0.04
65 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (60 bp):
ACTCTTTGAAGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAAAAGGCATCCT
Found at i:1532938 original size:124 final size:123
Alignment explanation
Indices: 1532718--1532950 Score: 348
Period size: 124 Copynumber: 1.9 Consensus size: 123
1532708 TGTCTACACC
*
1532718 ACTCTTTAAAGACTAAAAGGTGCCACCAACTTATGTGGGCTTTAAAAGAAAAAGGCATTCTGCTC
1 ACTCTTTAAAGACTAAAAGGTGCCACCAACTTATATGGGCTTTAAAAGAAAAAGGCATTCTGCTC
*
1532783 TTTGAGGACTAAAAAGTATCACCAACTTGTGT-GAGCTTTAAAAACAGGCGCAGCATCCT
66 TTTAAGGACT-AAAAGTATCACCAACTTGTGTAG-GCTTTAAAAACAGGCGCAGCATCCT
* *
1532842 ACTCTTTGAAGACTAAAAGGTGCCACCAACTTGTATGGGCTTTAAAAAGAAAAAGGCA-TCTTGC
1 ACTCTTTAAAGACTAAAAGGTGCCACCAACTTATATGGGCTTT-AAAAGAAAAAGGCATTC-TGC
1532906 TCTTTAAGGACT-AAAGT-TGCCACCAACTTGTGTAGGCTTTAAAAA
64 TCTTTAAGGACTAAAAGTAT--CACCAACTTGTGTAGGCTTTAAAAA
1532951 AAAGGAAAAA
Statistics
Matches: 100, Mismatches: 4, Indels: 10
0.88 0.04 0.09
Matches are distributed among these distances:
122 1 0.01
123 5 0.05
124 65 0.65
125 29 0.29
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (123 bp):
ACTCTTTAAAGACTAAAAGGTGCCACCAACTTATATGGGCTTTAAAAGAAAAAGGCATTCTGCTC
TTTAAGGACTAAAAGTATCACCAACTTGTGTAGGCTTTAAAAACAGGCGCAGCATCCT
Found at i:1532992 original size:31 final size:31
Alignment explanation
Indices: 1532956--1533024 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
1532946 AAAAAAAAGG
* * *
1532956 AAAAAGTTTCCACAGAGTCGTGGACTTTAGA
1 AAAAAGGTGCCACAAAGTCGTGGACTTTAGA
* * *
1532987 AAAAAGGTGCCACAAAGTTGTGGACTTTTGG
1 AAAAAGGTGCCACAAAGTCGTGGACTTTAGA
1533018 AAAAAGG
1 AAAAAGG
1533025 CTTGGAGGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.23
Consensus pattern (31 bp):
AAAAAGGTGCCACAAAGTCGTGGACTTTAGA
Found at i:1535312 original size:23 final size:23
Alignment explanation
Indices: 1535286--1535370 Score: 134
Period size: 23 Copynumber: 3.7 Consensus size: 23
1535276 TTTGCTAATG
*
1535286 TTTGCTTGATGTTTTTGTTGGTA
1 TTTGCTTGATATTTTTGTTGGTA
*
1535309 TTTGCTTGTTATTTTTGTTGGTA
1 TTTGCTTGATATTTTTGTTGGTA
*
1535332 TTTGCTTGCTATTTTTGTTGGTA
1 TTTGCTTGATATTTTTGTTGGTA
*
1535355 TTTGCTTGCTATTTTT
1 TTTGCTTGATATTTTT
1535371 ACTGCCATTG
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.08, C:0.07, G:0.21, T:0.64
Consensus pattern (23 bp):
TTTGCTTGATATTTTTGTTGGTA
Found at i:1535381 original size:22 final size:23
Alignment explanation
Indices: 1535308--1535384 Score: 66
Period size: 23 Copynumber: 3.4 Consensus size: 23
1535298 TTTTGTTGGT
* ** **
1535308 ATTTGCTTGTTATTTTTGTTGGT
1 ATTTGCTTGCTATTTTTACTGCC
** **
1535331 ATTTGCTTGCTATTTTTGTTGGT
1 ATTTGCTTGCTATTTTTACTGCC
1535354 ATTTGCTTGCTATTTTTACTGCC
1 ATTTGCTTGCTATTTTTACTGCC
1535377 A-TTGCTTG
1 ATTTGCTTG
1535385 TTGCTTGTTG
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
22 7 0.14
23 42 0.86
ACGTcount: A:0.10, C:0.12, G:0.19, T:0.58
Consensus pattern (23 bp):
ATTTGCTTGCTATTTTTACTGCC
Found at i:1535390 original size:7 final size:7
Alignment explanation
Indices: 1535378--1535428 Score: 56
Period size: 7 Copynumber: 7.7 Consensus size: 7
1535368 TTTACTGCCA
1535378 TTGCTTG
1 TTGCTTG
1535385 TTGCTTG
1 TTGCTTG
1535392 TTGCTTG
1 TTGCTTG
1535399 TTCGCTTG
1 TT-GCTTG
1535407 -TG-TTG
1 TTGCTTG
1535412 TTGC-TG
1 TTGCTTG
*
1535418 TTAC-TG
1 TTGCTTG
1535424 TTGCT
1 TTGCT
1535429 GCTACTATTG
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
5 3 0.08
6 13 0.34
7 17 0.45
8 5 0.13
ACGTcount: A:0.02, C:0.16, G:0.27, T:0.55
Consensus pattern (7 bp):
TTGCTTG
Found at i:1536083 original size:23 final size:23
Alignment explanation
Indices: 1536051--1536102 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
1536041 CGTTTCTGAG
*
1536051 TTCAGTAGCTTAATTACAGCTAT
1 TTCAGCAGCTTAATTACAGCTAT
* *
1536074 TTCAGCAGCTTAATTGCAGCTGT
1 TTCAGCAGCTTAATTACAGCTAT
1536097 TTCAGC
1 TTCAGC
1536103 TTTTTTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (23 bp):
TTCAGCAGCTTAATTACAGCTAT
Found at i:1536494 original size:14 final size:14
Alignment explanation
Indices: 1536475--1536501 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1536465 TGAAAGAAAG
1536475 AATGCATGAAATGT
1 AATGCATGAAATGT
1536489 AATGCATGAAATG
1 AATGCATGAAATG
1536502 AACATATGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.26
Consensus pattern (14 bp):
AATGCATGAAATGT
Found at i:1536700 original size:20 final size:20
Alignment explanation
Indices: 1536675--1536712 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1536665 TTTATGTACA
1536675 TATTTTCTATTTAATTATTT
1 TATTTTCTATTTAATTATTT
* *
1536695 TATTTTTTATTTTATTAT
1 TATTTTCTATTTAATTAT
1536713 ATTTTTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (20 bp):
TATTTTCTATTTAATTATTT
Found at i:1536715 original size:17 final size:16
Alignment explanation
Indices: 1536694--1536723 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1536684 TTTAATTATT
1536694 TTAT-TTTTTATTTTA
1 TTATATTTTTATTTTA
1536709 TTATATTTTTATTTT
1 TTATATTTTTATTTT
1536724 TTAATGCCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (16 bp):
TTATATTTTTATTTTA
Found at i:1538297 original size:21 final size:21
Alignment explanation
Indices: 1538273--1538324 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
1538263 ATTTACGGCA
*
1538273 TGTATCGATACATTCACTTAT
1 TGTATCGATACATTCACTAAT
* *
1538294 TGTATTGACACATTCACTAAT
1 TGTATCGATACATTCACTAAT
1538315 TGTATCGATA
1 TGTATCGATA
1538325 TAAATTGTAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCACTAAT
Found at i:1539120 original size:31 final size:31
Alignment explanation
Indices: 1539022--1539123 Score: 91
Period size: 31 Copynumber: 3.3 Consensus size: 31
1539012 CACTAGCTTA
* * *
1539022 TGTGGGCTTTAACTCA-AGTGCCGCCAACTCG
1 TGTGGGCTTTGACT-AGGGTGCCACCAACTCG
* ** * * * *
1539053 TGCGACCTTAGACTCGGGTGCCA-CAGCTTG
1 TGTGGGCTTTGACTAGGGTGCCACCAACTCG
1539083 TGTGGGCTTTGACTAGGGTGCCACCAACTCG
1 TGTGGGCTTTGACTAGGGTGCCACCAACTCG
1539114 TGTGGGCTTT
1 TGTGGGCTTT
1539124 AAACATTCTA
Statistics
Matches: 52, Mismatches: 17, Indels: 4
0.71 0.23 0.05
Matches are distributed among these distances:
30 23 0.44
31 29 0.56
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.27
Consensus pattern (31 bp):
TGTGGGCTTTGACTAGGGTGCCACCAACTCG
Found at i:1539134 original size:180 final size:180
Alignment explanation
Indices: 1538814--1539210 Score: 505
Period size: 180 Copynumber: 2.2 Consensus size: 180
1538804 TGTGCAGGCT
* * * * * ** * *
1538814 TTGACTCAGACTT-TGTGCCACCAGTTTGTGTGGGCTTTGACTCAAGTGTTGCCAATTCATGCGG
1 TTGACTCAAACTTAGGTGCCACTAGCTTGTGTGGGCTTTAACTCAAGTGCCGCCAACTCATGCGA
* * *
1538878 GCTTAGACTTGAGTGTTGCCAGCTTGTGCAGGCTTTAACTAGGGTGCCACTAACTCGTATAGGCT
66 CCTTAGACTCGAGTGTTGCCAGCTTGTGCAGGCTTTAACTAGGGTGCCACCAACTCGTATAGGCT
* * *
1538943 TTGATATTCTAAGGCTTGACCTCCTCAAACAGGTGCTAACTAATTTGGAC
131 TTAACATTCTAAGGCTTGACCTCCTCAAACAGGTGCCAACTAATTTGGAC
* *
1538993 TTGACTCAAACTTAGGTGCCACTAGCTTATGTGGGCTTTAACTCAAGTGCCGCCAACTCGTGCGA
1 TTGACTCAAACTTAGGTGCCACTAGCTTGTGTGGGCTTTAACTCAAGTGCCGCCAACTCATGCGA
** * * *
1539058 CCTTAGACTCG-G-G-TGCCACAGCTTGTGTGGGCTTTGACTAGGGTGCCACCAACTCGTGTGGG
66 CCTTAGACTCGAGTGTTG-C-CAGCTTGTGCAGGCTTTAACTAGGGTGCCACCAACTCGTATAGG
* *
1539120 CTTTAAACATTCTAAGGCTTGACCTCCTTAGACAGGTGCCAACTAATTTGGAC
129 CTTT-AACATTCTAAGGCTTGACCTCCTCAAACAGGTGCCAACTAATTTGGAC
* *
1539173 TTGACTTAAACTTAGATGCCACTAGCTTGTGTGGGCTT
1 TTGACTCAAACTTAGGTGCCACTAGCTTGTGTGGGCTT
1539211 ATAAAAGTGG
Statistics
Matches: 187, Mismatches: 27, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
177 2 0.01
178 2 0.01
179 55 0.29
180 128 0.68
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (180 bp):
TTGACTCAAACTTAGGTGCCACTAGCTTGTGTGGGCTTTAACTCAAGTGCCGCCAACTCATGCGA
CCTTAGACTCGAGTGTTGCCAGCTTGTGCAGGCTTTAACTAGGGTGCCACCAACTCGTATAGGCT
TTAACATTCTAAGGCTTGACCTCCTCAAACAGGTGCCAACTAATTTGGAC
Found at i:1539488 original size:37 final size:37
Alignment explanation
Indices: 1539447--1539684 Score: 139
Period size: 37 Copynumber: 6.4 Consensus size: 37
1539437 CTTCTTGAAA
1539447 ACAAAGGAAAAAAGAGTAGGCGTCCTACTCTTTAAGG
1 ACAAAGGAAAAAAGAGTAGGCGTCCTACTCTTTAAGG
* * * * *
1539484 ACAAAGGGAAAATGAGTAGGTGTCTTTCTCTTTGAA-G
1 ACAAAGGAAAAAAGAGTAGGCGTCCTACTCTTT-AAGG
* * *
1539521 ACAAAGG--AAATGAGTA--TGTCCTACTCTTTTAGG
1 ACAAAGGAAAAAAGAGTAGGCGTCCTACTCTTTAAGG
* * * * * *
1539554 AAAAAGG-AAAAAGAATAATGAAATGGGTCTTGCTCTTTGAGG
1 ACAAAGGAAAAAAGAGT-A-G----GCGTCCTACTCTTTAAGG
* * * * * *
1539596 ATATAGGAAAAAGGAGTAGGCATCCTGCTCTTTGAGG
1 ACAAAGGAAAAAAGAGTAGGCGTCCTACTCTTTAAGG
* * *
1539633 ACAAA-GAGAAAATGAGTAGGCATCCTACTCTTCAAGG
1 ACAAAGGA-AAAAAGAGTAGGCGTCCTACTCTTTAAGG
1539670 ACAAAGGGAAAAAAG
1 ACAAA-GGAAAAAAG
1539685 GAATAAAATG
Statistics
Matches: 157, Mismatches: 29, Indels: 29
0.73 0.13 0.13
Matches are distributed among these distances:
32 1 0.01
33 18 0.11
34 6 0.04
35 10 0.06
36 2 0.01
37 84 0.54
38 7 0.04
39 2 0.01
41 1 0.01
42 19 0.12
43 7 0.04
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.23
Consensus pattern (37 bp):
ACAAAGGAAAAAAGAGTAGGCGTCCTACTCTTTAAGG
Found at i:1539560 original size:33 final size:34
Alignment explanation
Indices: 1539468--1539563 Score: 97
Period size: 33 Copynumber: 2.8 Consensus size: 34
1539458 AAGAGTAGGC
*
1539468 GTCCTACTCTTTAAGGACAAAGGGAAAATGAGTAGGT
1 GTCCTACTCTTTAAGGA-AAAAGG-AAATGAGTA-GT
* * *
1539505 GTCTTTCTCTTTGAA-GACAAAGGAAATGAGTA-T
1 GTCCTACTCTTT-AAGGAAAAAGGAAATGAGTAGT
*
1539538 GTCCTACTCTTTTAGGAAAAAGGAAA
1 GTCCTACTCTTTAAGGAAAAAGGAAA
1539564 AAGAATAATG
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
32 1 0.02
33 21 0.43
35 9 0.18
36 4 0.08
37 12 0.24
38 2 0.04
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (34 bp):
GTCCTACTCTTTAAGGAAAAAGGAAATGAGTAGT
Found at i:1539704 original size:116 final size:112
Alignment explanation
Indices: 1539481--1539727 Score: 280
Period size: 116 Copynumber: 2.2 Consensus size: 112
1539471 CTACTCTTTA
* * ** * * *
1539481 AGGACAAAGGGAAAATGAGTAGGTGTCTTTCTCTTTGAAGACAAAGGAAATGAGTATGTCCTACT
1 AGGACAAAGGAAAAAGGAGTAGGCATCCTGCTCTTTGAAGACAAAGGAAATGAGTAGGTCCTACT
** * * * *
1539546 CTTTTAGGAAAAAGGAAAAAGAATAATGAAATGGGTCTTGCTCTTTG
66 CTTCAAGGAAAAAGGAAAAAGAAGAATAAAATGGGTCCTGCTCCTTG
* * *
1539593 AGGATATAGGAAAAAGGAGTAGGCATCCTGCTCTTTGAGGACAAAGAGAAAATGAGTAGGCATCC
1 AGGACAAAGGAAAAAGGAGTAGGCATCCTGCTCTTTGAAGACAAAG-G-AAATGAGTAGG--TCC
* *
1539658 TACTCTTCAAGGACAAAGGGAAAAA-AGGAATAAAATGGGTCCTGCTCCTTG
62 TACTCTTCAAGGA-AAAAGGAAAAAGAAGAATAAAATGGGTCCTGCTCCTTG
1539709 AGGACAAAGGAAAAAGGAG
1 AGGACAAAGGAAAAAGGAG
1539728 AAAAGGAATG
Statistics
Matches: 110, Mismatches: 20, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
112 37 0.34
113 1 0.01
114 10 0.09
116 52 0.47
117 10 0.09
ACGTcount: A:0.39, C:0.13, G:0.27, T:0.22
Consensus pattern (112 bp):
AGGACAAAGGAAAAAGGAGTAGGCATCCTGCTCTTTGAAGACAAAGGAAATGAGTAGGTCCTACT
CTTCAAGGAAAAAGGAAAAAGAAGAATAAAATGGGTCCTGCTCCTTG
Found at i:1540510 original size:17 final size:17
Alignment explanation
Indices: 1540479--1540512 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1540469 TAAAAATCCC
**
1540479 TTTATCAATTTTTATCA
1 TTTATCAATCATTATCA
1540496 TTTATCAATCATTATCA
1 TTTATCAATCATTATCA
1540513 ACTAAATGCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.15, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTATCAATCATTATCA
Found at i:1545343 original size:19 final size:18
Alignment explanation
Indices: 1545318--1545381 Score: 75
Period size: 19 Copynumber: 3.7 Consensus size: 18
1545308 AATTCAACGA
1545318 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1545336 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1545352 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1545368 TTTTGTATCGATAC
1 -TTTGTATCGATAC
1545382 TAATGAAGCT
Statistics
Matches: 39, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
17 2 0.05
18 1 0.03
19 23 0.59
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.39
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:1545356 original size:32 final size:33
Alignment explanation
Indices: 1545320--1545386 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 33
1545310 TTCAACGATT
1545320 TGTATCGATACATAAGTGTTGTATCGATAC-AA
1 TGTATCGATACATAAGTGTTGTATCGATACTAA
*
1545352 TGTATCGATACATAAGTTTTGTATCGATACTAA
1 TGTATCGATACATAAGTGTTGTATCGATACTAA
1545385 TG
1 TG
1545387 AAGCTACTAC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 29 0.88
33 4 0.12
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (33 bp):
TGTATCGATACATAAGTGTTGTATCGATACTAA
Found at i:1545357 original size:13 final size:13
Alignment explanation
Indices: 1545339--1545363 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1545329 ACATAAGTGT
1545339 TGTATCGATACAA
1 TGTATCGATACAA
1545352 TGTATCGATACA
1 TGTATCGATACA
1545364 TAAGTTTTGT
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:1545447 original size:13 final size:13
Alignment explanation
Indices: 1545429--1545453 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1545419 ACTCAAATGA
1545429 ATCGATACATTGT
1 ATCGATACATTGT
1545442 ATCGATACATTG
1 ATCGATACATTG
1545454 ATCTTTGTAT
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):
ATCGATACATTGT
Found at i:1559196 original size:21 final size:21
Alignment explanation
Indices: 1559149--1559202 Score: 92
Period size: 20 Copynumber: 2.6 Consensus size: 21
1559139 CATTTAAGAC
*
1559149 TTGTATCGATACATTCACTTA
1 TTGTATCGATACATTCACTAA
1559170 -TGTATCGATACATTCACTAA
1 TTGTATCGATACATTCACTAA
1559190 TTGTATCGATACA
1 TTGTATCGATACA
1559203 AATTGTAGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 19 0.61
21 12 0.39
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (21 bp):
TTGTATCGATACATTCACTAA
Found at i:1559746 original size:127 final size:126
Alignment explanation
Indices: 1559515--1559756 Score: 366
Period size: 127 Copynumber: 1.9 Consensus size: 126
1559505 TGTCTACACC
*
1559515 ACTCTTTAAAGACTAAAAGGTGCCACCAACTTATGTGGGCTTTAAAAAGAAAAAGGCATTCTGCT
1 ACTCTTTAAAGACTAAAAGGTGCCACCAACTTATATGGGCTTTAAAAAGAAAAAGGCATTCTGCT
* *
1559580 CTTTGAGGACTAAAAAGTATCACCAACTTGTGTGAGCTTTAAAAACAAGGCGCAGCATCCT
66 CTTTAAGGACTAAAAAGTATCACCAACTTGTGTGAGCTTTAAAAAAAAGGCGCAGCATCCT
* *
1559641 ACTCTTTGAAGACTAAAAGGTGCCACCAACTTGTATGGGCTTTAAAAAAGAAAAAGGCA-TCTTG
1 ACTCTTTAAAGACTAAAAGGTGCCACCAACTTATATGGGCTTT-AAAAAGAAAAAGGCATTC-TG
1559705 CTCTTTAAGGACT-AAAAGT-TGCCACCAACTTGTGT-AGGCTTTAAAAAAAAGG
64 CTCTTTAAGGACTAAAAAGTAT--CACCAACTTGTGTGA-GCTTTAAAAAAAAGG
1559757 AAAAAGTTGC
Statistics
Matches: 106, Mismatches: 5, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
125 1 0.01
126 49 0.46
127 56 0.53
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (126 bp):
ACTCTTTAAAGACTAAAAGGTGCCACCAACTTATATGGGCTTTAAAAAGAAAAAGGCATTCTGCT
CTTTAAGGACTAAAAAGTATCACCAACTTGTGTGAGCTTTAAAAAAAAGGCGCAGCATCCT
Found at i:1559752 original size:63 final size:62
Alignment explanation
Indices: 1559516--1559751 Score: 269
Period size: 62 Copynumber: 3.8 Consensus size: 62
1559506 GTCTACACCA
* *
1559516 CTCTTTAAAGACTAAAAGGTGCCACCAACTTATGTGGGCTTTAAAAAGAAAAAGGCAT-TCTG
1 CTCTTTAAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGGCATCT-TG
* * ** * * *** * *
1559578 CTCTTTGAGGACTAAAAAGTATCACCAACTTGTGTGAGCTTTAAAAACAAGGCGCAGCATCCTA
1 CTCTTTAAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAG--GCATCTTG
*
1559642 CTCTTTGAA-GACTAAAAGGTGCCACCAACTTGTATGGGCTTTAAAAAAGAAAAAGGCATCTTG
1 CTCTTT-AAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAAGAAAAAGGCATCTTG
* *
1559705 CTCTTTAAGGACTAAAAGTTGCCACCAACTTGTGTAGGCTTTAAAAA
1 CTCTTTAAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAA
1559752 AAAGGAAAAA
Statistics
Matches: 140, Mismatches: 28, Indels: 12
0.78 0.16 0.07
Matches are distributed among these distances:
62 50 0.36
63 42 0.30
64 39 0.28
65 9 0.06
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (62 bp):
CTCTTTAAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGGCATCTTG
Found at i:1559793 original size:31 final size:31
Alignment explanation
Indices: 1559757--1559825 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
1559747 AAAAAAAAGG
* *
1559757 AAAAAGTTGCCACAGAGTCGTGGACTTTAGA
1 AAAAAGGTGCCACAAAGTCGTGGACTTTAGA
* * *
1559788 AAAAAGGTGCCACAAAGTTGTGGACTTTTGG
1 AAAAAGGTGCCACAAAGTCGTGGACTTTAGA
1559819 AAAAAGG
1 AAAAAGG
1559826 CTTGGAGGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.38, C:0.13, G:0.28, T:0.22
Consensus pattern (31 bp):
AAAAAGGTGCCACAAAGTCGTGGACTTTAGA
Found at i:1565741 original size:23 final size:22
Alignment explanation
Indices: 1565698--1565746 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
1565688 AACGAAAAAG
**
1565698 AAAATAACGAACAAATTTACAC
1 AAAATAACGAACAAAAATACAC
* *
1565720 AAAATAAACGCACAAAAATACAT
1 AAAAT-AACGAACAAAAATACAC
1565743 AAAA
1 AAAA
1565747 AGGAGGGAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.65, C:0.16, G:0.04, T:0.14
Consensus pattern (22 bp):
AAAATAACGAACAAAAATACAC
Found at i:1566173 original size:80 final size:80
Alignment explanation
Indices: 1566052--1566344 Score: 317
Period size: 79 Copynumber: 3.7 Consensus size: 80
1566042 GAAAAAATGG
* * * *
1566052 GGTTGGAGTAT-CCTTTCGAAAATTATGGGGTTAGAGTATCCTCGATGGTAAAAAAATCAATATT
1 GGTTGGAGTATCCCTTT-GGAAATGATGGGGTTGGAGTATCCTCGATGGTAAAAAAATTAATATT
* *
1566116 TTAGAAGTAAAAACGA
65 TTGGAAATAAAAACGA
* * * *** *
1566132 GGTTGGAGTATCCCTTTGGATATGATGGAGTTGGAGCATCCTCGACAAT-GAAAAATTAATATTT
1 GGTTGGAGTATCCCTTTGGAAATGATGGGGTTGGAGTATCCTCGATGGTAAAAAAATTAATATTT
1566196 TGGAAATAAAAACGA
66 TGGAAATAAAAACGA
1566211 GGTTGGAGTATTCCC-TTGGAAATGATGGGGTTGGAGTATCC-CGATGGTAAAAAAATTAATATT
1 GGTTGGAGTA-TCCCTTTGGAAATGATGGGGTTGGAGTATCCTCGATGGTAAAAAAATTAATATT
* *
1566274 TTGGAAATAAAAGCGG
65 TTGGAAATAAAAACGA
** * * * * * *
1566290 GGTTATAATATCTCC-TCGGAGATAATGGGGTTGGAGTATCCCCGATGGTGAAAAA
1 GGTTGGAGTATC-CCTTTGGAAATGATGGGGTTGGAGTATCCTCGATGGTAAAAAA
1566345 TCGATACTTT
Statistics
Matches: 179, Mismatches: 29, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
78 6 0.03
79 118 0.66
80 50 0.28
81 5 0.03
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (80 bp):
GGTTGGAGTATCCCTTTGGAAATGATGGGGTTGGAGTATCCTCGATGGTAAAAAAATTAATATTT
TGGAAATAAAAACGA
Found at i:1566342 original size:158 final size:160
Alignment explanation
Indices: 1566052--1566359 Score: 363
Period size: 158 Copynumber: 1.9 Consensus size: 160
1566042 GAAAAAATGG
* *
1566052 GGTTGGAGTATCCTTTCGAAAATTATGGGGTTAGAGTATCCTCGATGGTAAAAAAATCAATATTT
1 GGTTGGAGTATCCCTTCGAAAATGATGGGGTTAGAGTATCCTCGATGGTAAAAAAATCAATATTT
* * * * * * *
1566117 TAGAAGTAAAAACGAGGTTGGAGTATCCCTTTGGATATGATGGAGTTGGAGCATCCTCGACAATG
66 TAGAAATAAAAACGAGGTTAGAATATCCCTTCGGAGATAATGGAGTTGGAGCATCCCCGACAATG
*
1566182 AAAAATTAATA-TTTTGGAAATAAAAACGA
131 AAAAATCAATACTTTTGGAAATAAAAACGA
* * *
1566211 GGTTGGAGTATTCCCTT-GGAAATGATGGGGTTGGAGTATCC-CGATGGTAAAAAAATTAATATT
1 GGTTGGAGTA-TCCCTTCGAAAATGATGGGGTTAGAGTATCCTCGATGGTAAAAAAATCAATATT
* * * * * * ***
1566274 TTGGAAATAAAAGCGGGGTTATAATATCTCC-TCGGAGATAATGGGGTTGGAGTATCCCCGATGG
65 TTAGAAATAAAAACGAGGTTAGAATATC-CCTTCGGAGATAATGGAGTTGGAGCATCCCCGACAA
*
1566338 TGAAAAATCGATACTTTTGGAA
129 TGAAAAATCAATACTTTTGGAA
1566360 GGAGAAATTT
Statistics
Matches: 123, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
158 77 0.63
159 41 0.33
160 5 0.04
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.30
Consensus pattern (160 bp):
GGTTGGAGTATCCCTTCGAAAATGATGGGGTTAGAGTATCCTCGATGGTAAAAAAATCAATATTT
TAGAAATAAAAACGAGGTTAGAATATCCCTTCGGAGATAATGGAGTTGGAGCATCCCCGACAATG
AAAAATCAATACTTTTGGAAATAAAAACGA
Found at i:1568068 original size:51 final size:51
Alignment explanation
Indices: 1567960--1568125 Score: 151
Period size: 51 Copynumber: 3.3 Consensus size: 51
1567950 AAAAATAATG
* * * * *** *
1567960 GGGTTGGAGCATCCCCGATTGTGGAAAATCG--ATCTTTAGAAATAACGCCG
1 GGGTTGGAGTATCCCCGATTGTGAAAAATTGTAAT-TTTAAAAATAAAATCA
* * **
1568010 GGGTTGGAGTATCCCCGATTGTGAGAAATTGGT-GTTTTGGAAATAAAATC-
1 GGGTTGGAGTATCCCCGATTGTGAAAAATT-GTAATTTTAAAAATAAAATCA
* *
1568060 GGAGTTGGAGTATCCTCGATTGTGAAAAATTTTAATTTTAAAAATAAAATCA
1 GG-GTTGGAGTATCCCCGATTGTGAAAAATTGTAATTTTAAAAATAAAATCA
1568112 GGGTTGGAGTATCC
1 GGGTTGGAGTATCC
1568126 TCTCGGAAAT
Statistics
Matches: 96, Mismatches: 15, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
50 29 0.30
51 64 0.67
52 3 0.03
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.30
Consensus pattern (51 bp):
GGGTTGGAGTATCCCCGATTGTGAAAAATTGTAATTTTAAAAATAAAATCA
Found at i:1568162 original size:28 final size:28
Alignment explanation
Indices: 1568110--1568186 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 28
1568100 AAAATAAAAT
*
1568110 CAGGGTTGGAGTATCCTCTCG--GAAATAA
1 CAGGATTGGAGTATCC-C-CGATGAAATAA
1568138 CAGGATTGGAGTATCCCCGATGAAATAA
1 CAGGATTGGAGTATCCCCGATGAAATAA
* *
1568166 CGGGGA-TGGAGTACCCCCGAT
1 C-AGGATTGGAGTATCCCCGAT
1568187 TATGAAAACA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
26 2 0.05
27 1 0.02
28 37 0.86
29 3 0.07
ACGTcount: A:0.29, C:0.21, G:0.30, T:0.21
Consensus pattern (28 bp):
CAGGATTGGAGTATCCCCGATGAAATAA
Found at i:1568346 original size:51 final size:51
Alignment explanation
Indices: 1568252--1568367 Score: 130
Period size: 51 Copynumber: 2.3 Consensus size: 51
1568242 GAAATAACGG
* *
1568252 GGTTATAGTATCCCCGATGGTGGAAAATCGATGTTTTGAAAATAAAACCAG-
1 GGTTAGAGTATCCCCGATGGTGGAAAATCGATGTTTAGAAAATAAAA-CAGA
* * * *
1568303 GGTTGGAGTATCCCCGATTGT-GAGAAATTGATGTTTCAG-AAATAAAACTGA
1 GGTTAGAGTATCCCCGATGGTGGA-AAATCGATGTTT-AGAAAATAAAACAGA
1568354 GGTTAGAGTATCCC
1 GGTTAGAGTATCCC
1568368 TCAGAAATAA
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
50 4 0.07
51 50 0.91
52 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (51 bp):
GGTTAGAGTATCCCCGATGGTGGAAAATCGATGTTTAGAAAATAAAACAGA
Found at i:1570779 original size:20 final size:20
Alignment explanation
Indices: 1570754--1570823 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
1570744 TGCCTGAATA
* *
1570754 TATCGATATATTGTAAAATG
1 TATCGATACAATGTAAAATG
*
1570774 TATCGATACAATG-AGCAATG
1 TATCGATACAATGTA-AAATG
1570794 TATCGATACAATGTAAAATG
1 TATCGATACAATGTAAAATG
1570814 TATCGATACA
1 TATCGATACA
1570824 TCTGGGTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
19 1 0.02
20 42 0.95
21 1 0.02
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.31
Consensus pattern (20 bp):
TATCGATACAATGTAAAATG
Found at i:1570857 original size:13 final size:13
Alignment explanation
Indices: 1570839--1570868 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1570829 GTAAACCCAG
1570839 AATGTATCGATAC
1 AATGTATCGATAC
*
1570852 AATGTATCGATAT
1 AATGTATCGATAC
1570865 AATG
1 AATG
1570869 AGTAATATAT
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):
AATGTATCGATAC
Found at i:1570902 original size:20 final size:20
Alignment explanation
Indices: 1570850--1570906 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
1570840 ATGTATCGAT
*
1570850 ACAATGTATCGATATAATGA
1 ACAATGTATCGATACAATGA
** *
1570870 GTAATATATCGATACAATGA
1 ACAATGTATCGATACAATGA
*
1570890 ACAATGTACCGATACAA
1 ACAATGTATCGATACAA
1570907 ATTGTGAAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.26
Consensus pattern (20 bp):
ACAATGTATCGATACAATGA
Found at i:1572863 original size:51 final size:51
Alignment explanation
Indices: 1572797--1572926 Score: 170
Period size: 51 Copynumber: 2.5 Consensus size: 51
1572787 GCATGTACTA
* *
1572797 ATACATTGAAGAATGTATCGATACATTTGGGTCAAAAACCAGAATGTATCG
1 ATACAATGAAAAATGTATCGATACATTTGGGTCAAAAACCAGAATGTATCG
* * * * *
1572848 ATACAATGAATAATGTGTCAATACATTTGGGTCAAAACCCATAATGTATCG
1 ATACAATGAAAAATGTATCGATACATTTGGGTCAAAAACCAGAATGTATCG
* * *
1572899 ATATAATGAAAAATGTATTGATAGATTT
1 ATACAATGAAAAATGTATCGATACATTT
1572927 TCTTTCTAGA
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 67 1.00
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.31
Consensus pattern (51 bp):
ATACAATGAAAAATGTATCGATACATTTGGGTCAAAAACCAGAATGTATCG
Found at i:1573009 original size:20 final size:21
Alignment explanation
Indices: 1572965--1573017 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
1572955 CATGGTCCTT
* *
1572965 TATCGATACATTTTAGACATG
1 TATCGATACATTTTACACATC
*
1572986 TATCGATAC-TTTTACTCATC
1 TATCGATACATTTTACACATC
*
1573006 TATCAATACATT
1 TATCGATACATT
1573018 CACTATTTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.42
Consensus pattern (21 bp):
TATCGATACATTTTACACATC
Found at i:1576620 original size:19 final size:19
Alignment explanation
Indices: 1576596--1576639 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1576586 AGATTTAAGG
* *
1576596 AAAAAATAATGCAAAACTA
1 AAAAAATAAAGCAAAACCA
*
1576615 AAAAAATAAAGTAAAACCA
1 AAAAAATAAAGCAAAACCA
1576634 AAAAAA
1 AAAAAA
1576640 ATATTACAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.75, C:0.09, G:0.05, T:0.11
Consensus pattern (19 bp):
AAAAAATAAAGCAAAACCA
Found at i:1576702 original size:23 final size:24
Alignment explanation
Indices: 1576676--1576720 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1576666 ATTTTATATA
1576676 AATAA-TATTAAAAAAAATAAAAT
1 AATAACTATTAAAAAAAATAAAAT
* *
1576699 AATAACTTTTCAAAAAAATAAA
1 AATAACTATTAAAAAAAATAAA
1576721 GTCCAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (24 bp):
AATAACTATTAAAAAAAATAAAAT
Found at i:1576789 original size:18 final size:17
Alignment explanation
Indices: 1576748--1576850 Score: 50
Period size: 18 Copynumber: 5.6 Consensus size: 17
1576738 ATATAACTTA
1576748 AAAAACATATAAAAAATACTT
1 AAAAA-ATA-AAAAAATA--T
*
1576769 AAAAAATAGAAAAACTAT
1 AAAAAATA-AAAAAATAT
* *
1576787 AAACTAAA-AAATAATTAT
1 AAA--AAATAAAAAAATAT
*
1576805 AAAAAAATAAAAAAATTT
1 -AAAAAATAAAAAAATAT
*
1576823 AAAAAATTGAAAAAAT-T
1 AAAAAA-TAAAAAAATAT
1576840 GAAAAAA-AAAA
1 -AAAAAATAAAA
1576851 CATTAGGAAC
Statistics
Matches: 67, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
16 3 0.04
17 10 0.15
18 32 0.48
19 4 0.06
20 13 0.19
21 5 0.07
ACGTcount: A:0.73, C:0.04, G:0.03, T:0.20
Consensus pattern (17 bp):
AAAAAATAAAAAAATAT
Found at i:1576835 original size:8 final size:9
Alignment explanation
Indices: 1576814--1576846 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
1576804 TAAAAAAATA
*
1576814 AAAAAATTT
1 AAAAAATTG
1576823 AAAAAATTG
1 AAAAAATTG
1576832 AAAAAATTG
1 AAAAAATTG
1576841 AAAAAA
1 AAAAAA
1576847 AAAACATTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (9 bp):
AAAAAATTG
Found at i:1577843 original size:41 final size:40
Alignment explanation
Indices: 1577789--1577991 Score: 169
Period size: 41 Copynumber: 4.9 Consensus size: 40
1577779 CCAATCAAAT
* *
1577789 TTTATCTCCAATTAAATTAATTAAGAGATAAATAAAAGAG
1 TTTATCTCTAATTAAATTAATTAAGAGATAAATAAAAGAA
*
1577829 TTATATCTCTAATTAAACTAATTAAGAGATAAATAAAA-AA
1 TT-TATCTCTAATTAAATTAATTAAGAGATAAATAAAAGAA
* * *
1577869 TTTATCTTCGATTAAATTAAATTACTTATAG-GAAAAATAAAAAAA
1 TTTATC-TC---T-AATTAAATTAATTA-AGAGATAAATAAAAGAA
* *
1577914 TTT-TCTAATTAAATTAAATTAATTAAGAGATAAATAAAAGAGT
1 TTTATCT--CT-AATTAAATTAATTAAGAGATAAATAAAAGA-A
* * * * *
1577957 TTTATTTCTACTTAAATTAAATAAAAAATAAATAA
1 TTTATCTCTAATTAAATTAATTAAGAGATAAATAA
1577992 TAAAAAACTT
Statistics
Matches: 133, Mismatches: 17, Indels: 25
0.76 0.10 0.14
Matches are distributed among these distances:
39 4 0.03
40 7 0.05
41 57 0.43
42 27 0.20
43 5 0.04
44 26 0.20
45 7 0.05
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.35
Consensus pattern (40 bp):
TTTATCTCTAATTAAATTAATTAAGAGATAAATAAAAGAA
Found at i:1577994 original size:86 final size:85
Alignment explanation
Indices: 1577839--1577998 Score: 198
Period size: 86 Copynumber: 1.9 Consensus size: 85
1577829 TTATATCTCT
* ***
1577839 AATTAAACTAATTAAGAGATAAATAAAAAATTTATCTTCGATTAAATTAAATTACTTATAGGAAA
1 AATTAAACTAATTAAGAGATAAATAAAAAATTTATCTTCGATTAAATTAAATAAAAAATA-GAAA
1577904 AATAAAAAAATTTTCTAATTA
65 AATAAAAAAATTTTCTAATTA
* * *
1577925 AATTAAATTAATTAAGAGATAAATAAAAGAGTTTTAT-TTCTACTTAAATTAAATAAAAAATA-A
1 AATTAAACTAATTAAGAGATAAATAAAA-A-ATTTATCTTCGA-TTAAATTAAATAAAAAATAGA
*
1577988 ATAATAAAAAA
63 AAAATAAAAAA
1577999 CTTAATAATA
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
86 38 0.60
87 5 0.08
88 20 0.32
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (85 bp):
AATTAAACTAATTAAGAGATAAATAAAAAATTTATCTTCGATTAAATTAAATAAAAAATAGAAAA
ATAAAAAAATTTTCTAATTA
Found at i:1577995 original size:14 final size:15
Alignment explanation
Indices: 1577976--1578012 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1577966 ACTTAAATTA
1577976 AATAAAAAA-TAAAT
1 AATAAAAAACTAAAT
*
1577990 AATAAAAAACTTAAT
1 AATAAAAAACTAAAT
1578005 AATAAAAA
1 AATAAAAA
1578013 TAAGTTCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.22
Consensus pattern (15 bp):
AATAAAAAACTAAAT
Found at i:1578974 original size:32 final size:33
Alignment explanation
Indices: 1578933--1578998 Score: 125
Period size: 32 Copynumber: 2.0 Consensus size: 33
1578923 ATTTCATTTC
1578933 CTTTTCATTACTTAACC-AATGAAGGTTGTAAT
1 CTTTTCATTACTTAACCAAATGAAGGTTGTAAT
1578965 CTTTTCATTACTTAACCAAATGAAGGTTGTAAT
1 CTTTTCATTACTTAACCAAATGAAGGTTGTAAT
1578998 C
1 C
1578999 AATCCTTTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 17 0.52
33 16 0.48
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (33 bp):
CTTTTCATTACTTAACCAAATGAAGGTTGTAAT
Found at i:1580398 original size:38 final size:38
Alignment explanation
Indices: 1580356--1580438 Score: 89
Period size: 38 Copynumber: 2.2 Consensus size: 38
1580346 ACAACTAACT
*
1580356 CTAAAGACTT-AATTTTGCTTTAAAAAGTA-AAAATGATC
1 CTAAA-ACTTCAATTTTGATTTAAAAA-TATAAAATGATC
* *
1580394 CTAAAAGTTCAGTTTTGATTTAAAAATATTAAAATGATC
1 CTAAAACTTCAATTTTGATTTAAAAATA-TAAAATGATC
*
1580433 TTAAAA
1 CTAAAA
1580439 TTTTCAGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
37 5 0.13
38 19 0.50
39 14 0.37
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (38 bp):
CTAAAACTTCAATTTTGATTTAAAAATATAAAATGATC
Found at i:1580438 original size:39 final size:39
Alignment explanation
Indices: 1580368--1580448 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 39
1580358 AAAGACTTAA
*
1580368 TTTTGCTTTAAAAAGTAAAAATGATCCTAAAA-GTTCAG
1 TTTTGATTTAAAAAGTAAAAATGATCCTAAAATGTTCAG
* *
1580406 TTTTGATTTAAAAA-TATTAAAATGATCTTAAAATTTTCAG
1 TTTTGATTTAAAAAGTA--AAAATGATCCTAAAATGTTCAG
1580446 TTT
1 TTT
1580449 GAACATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 2 0.05
38 13 0.35
39 14 0.38
40 8 0.22
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (39 bp):
TTTTGATTTAAAAAGTAAAAATGATCCTAAAATGTTCAG
Found at i:1581259 original size:26 final size:24
Alignment explanation
Indices: 1581222--1581308 Score: 85
Period size: 22 Copynumber: 3.7 Consensus size: 24
1581212 TTTCAACAAT
1581222 TTATTGATAAAATAAAGT-TATAACTA
1 TTATT-ATAAAA-AAA-TATATAACTA
*
1581248 TTATTATAAAAAAATATATAATTA
1 TTATTATAAAAAAATATATAACTA
1581272 -TATTAT-AAAAAATAT-TAACT-
1 TTATTATAAAAAAATATATAACTA
* *
1581292 TTATAATAGAAAAATAT
1 TTATTATAAAAAAATAT
1581309 TATTCAGGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
21 9 0.17
22 17 0.31
23 7 0.13
24 10 0.19
25 6 0.11
26 5 0.09
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.39
Consensus pattern (24 bp):
TTATTATAAAAAAATATATAACTA
Found at i:1581282 original size:24 final size:23
Alignment explanation
Indices: 1581219--1581288 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 23
1581209 GTTTTTCAAC
*
1581219 AATT-TATTGATAAAATAAAGTTAT
1 AATTATATT-ATAAAA-AAAATTAT
*
1581243 AACTATTATTAT-AAAAAAATATAT
1 AATTA-TATTATAAAAAAAAT-TAT
*
1581267 AATTATATTATAAAAAATATTA
1 AATTATATTATAAAAAAAATTA
1581289 ACTTTATAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
23 12 0.32
24 20 0.53
25 2 0.05
26 4 0.11
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (23 bp):
AATTATATTATAAAAAAAATTAT
Done.