Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold17
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: 1562583
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.27
Warning! 255143 characters in sequence are not A, C, G, or T
File 8 of 9
Found at i:1305656 original size:22 final size:23
Alignment explanation
Indices: 1305631--1305675 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1305621 ATTCTTAGTA
*
1305631 ATTAAGCAAATATTG-ATGAATG
1 ATTAAGAAAATATTGAATGAATG
*
1305653 ATTATGAAAATATTGAATGAATG
1 ATTAAGAAAATATTGAATGAATG
1305676 CCATGAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.47, C:0.02, G:0.18, T:0.33
Consensus pattern (23 bp):
ATTAAGAAAATATTGAATGAATG
Found at i:1305681 original size:22 final size:22
Alignment explanation
Indices: 1305638--1305682 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1305628 GTAATTAAGC
**
1305638 AAATATTGATGAATGATTATGA
1 AAATATTGATGAATGACCATGA
1305660 AAATATTGAATGAATG-CCATGA
1 AAATATTG-ATGAATGACCATGA
1305682 A
1 A
1305683 TATGAATGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.47, C:0.04, G:0.18, T:0.31
Consensus pattern (22 bp):
AAATATTGATGAATGACCATGA
Found at i:1306889 original size:82 final size:82
Alignment explanation
Indices: 1306639--1306895 Score: 208
Period size: 82 Copynumber: 3.1 Consensus size: 82
1306629 ACAGTAAATG
* * * *
1306639 TATCGATACATAAGTGTTGTATCCATATAGTGTATCACTACAAAGCTACTGCCAAGGAAATGTAT
1 TATCGATAAATAAGTGTTGTATCGATACAGTGTATCGCTACAAAGCTACTGCCAAGGAAATGTAT
1306704 TGATACATTATTCAATT
66 TGATACATTATTCAATT
* * * * ** * *
1306721 TATCGATACAT-TGTATCGATACATCGAT-CTTTGTATCGATAC-AAGGT-C--CCAACGGTCAA
1 TATCGATAAATAAGTGTTG-T--ATCGATACAGTGTATCGCTACAAAGCTACTGCCAA-GG--AA
** * * *
1306780 AAATTTTGA-A-TTTCAAT-AATTT
60 ATGTATTGATACATT-ATTCAA-TT
1306802 GTATCGATAAATAAGTGTTGTATCGATACAGTGTATCGCTACAAAGCTACTGCCAAGGAAATGTA
1 -TATCGATAAATAAGTGTTGTATCGATACAGTGTATCGCTACAAAGCTACTGCCAAGGAAATGTA
*
1306867 TCGATACATTATTCAATT
65 TTGATACATTATTCAATT
1306885 TATCGATAAAT
1 TATCGATAAAT
1306896 TGTATCGATA
Statistics
Matches: 128, Mismatches: 29, Indels: 36
0.66 0.15 0.19
Matches are distributed among these distances:
79 4 0.03
80 12 0.09
81 21 0.16
82 57 0.45
83 19 0.15
84 11 0.09
85 4 0.03
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (82 bp):
TATCGATAAATAAGTGTTGTATCGATACAGTGTATCGCTACAAAGCTACTGCCAAGGAAATGTAT
TGATACATTATTCAATT
Found at i:1306972 original size:20 final size:19
Alignment explanation
Indices: 1306947--1307020 Score: 94
Period size: 20 Copynumber: 3.7 Consensus size: 19
1306937 TTTACCCAGA
1306947 TGTATCGATACATTTTGCAT
1 TGTATCGATACATTTT-CAT
*
1306967 TGTATCGATACATTGCTCAT
1 TGTATCGATACATT-TTCAT
* *
1306987 TGTATTGATACATTTTACAA
1 TGTATCGATACATTTT-CAT
1307007 TGTATCGATACATT
1 TGTATCGATACATT
1307021 CTAGTCCTCA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 1 0.02
20 45 0.96
21 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (19 bp):
TGTATCGATACATTTTCAT
Found at i:1307140 original size:55 final size:55
Alignment explanation
Indices: 1307056--1307333 Score: 272
Period size: 55 Copynumber: 4.8 Consensus size: 55
1307046 TTTTTTTTTA
* *
1307056 AAGCCCACACAAGTTGGTGGCATTGTCCAGTCCTTAAAGAGCAGGACGCCTCTTG
1 AAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTCTTG
* * *
1307111 AAGCCCACATAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCCT-TTCA
1 AAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTCTT-G
* * * *
1307166 AAGCCCACACAAGTTGGTGGCAATTTCTAGTCCTCCAAGAGCAGGATGCTTTCTCTTTG
1 AAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGC---CTC-TTG
** * *
1307225 CAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGTAGGACGCCTTTCCTTTTCA
1 --AAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCC--T-C--TT-G
* * *
1307288 AAGCCCACACGAGTTGGTGGCACTTTT-TAGTCTTCAAAGAGCAGGA
1 AAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGA
1307334 TGCACTTTAT
Statistics
Matches: 186, Mismatches: 23, Indels: 22
0.81 0.10 0.10
Matches are distributed among these distances:
54 2 0.01
55 92 0.49
58 3 0.02
60 3 0.02
61 81 0.44
62 5 0.03
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.25
Consensus pattern (55 bp):
AAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTCTTG
Found at i:1307347 original size:61 final size:60
Alignment explanation
Indices: 1307023--1307347 Score: 323
Period size: 61 Copynumber: 5.5 Consensus size: 60
1307013 GATACATTCT
* ** * *
1307023 AGTCCTCAAAGAGTAGGACACCTTTTTTTTTTAAAGCCCACACAAGTTGGTGGCA-TTGTCC
1 AGTCCTCAAAGAGCAGGATGCC-TTTCTTTTCAAAGCCCACACAAGTTGGTGGCACTT-TCC
* * * * *
1307084 AGTCCTTAAAGAGCAGGACGCC--TC--TT-GAAGCCCACATAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGATGCCTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTCC
* *
1307139 AGTCCTCAAAGAGCAGGATG-C---C-TTTCAAAGCCCACACAAGTTGGTGGCAATTTCT
1 AGTCCTCAAAGAGCAGGATGCCTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTCC
* *
1307194 AGTCCTCCAAGAGCAGGATG-CTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCC
1 AGTCCTCAAAGAGCAGGATGCCTTTCT-TTT-CAAAGCCCACACAAGTTGGTGGCACTTTCC
* * * **
1307255 AGTCCTCAAAGAGTAGGACGCCTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGATGCCTTT-CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTCC
* *
1307316 AGTCTTCAAAGAGCAGGATGCACTTTATTTTC
1 AGTCCTCAAAGAGCAGGATGC-CTTTCTTTTC
1307348 CTCTTTCTTT
Statistics
Matches: 225, Mismatches: 27, Indels: 24
0.82 0.10 0.09
Matches are distributed among these distances:
53 1 0.00
54 3 0.01
55 87 0.39
56 4 0.02
58 2 0.01
60 3 0.01
61 112 0.50
62 11 0.05
63 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (60 bp):
AGTCCTCAAAGAGCAGGATGCCTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTCC
Found at i:1308332 original size:116 final size:112
Alignment explanation
Indices: 1308117--1308396 Score: 352
Period size: 116 Copynumber: 2.4 Consensus size: 112
1308107 GACACCTTTT
* * *
1308117 CTTTTTAAAGCCCACATAAGTTGGTGGCATTTTCCAGTCCTC-AAGAGCATGACGCCTCTTAAAG
1 CTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAAGACGCCTCTTAAAG
** *
1308181 CCCACACAAGTTGGTGGCATTTTCCAGTCTTCAAAGAGCAGGACG-C
66 CCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGTC
**
1308227 C-TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAAGGTGCTTTCTCTTT
1 CTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAAGACGC---CTC-TT
1308291 GCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCTTTC
62 --AAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACG---TC
* *
1308347 CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-TAGTCCTTAAAGAGCA
1 CTTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCA
1308397 GGATGCACTT
Statistics
Matches: 147, Mismatches: 10, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
109 38 0.26
110 11 0.07
113 3 0.02
114 2 0.01
116 46 0.31
120 2 0.01
121 41 0.28
122 4 0.03
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.26
Consensus pattern (112 bp):
CTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAAGACGCCTCTTAAAG
CCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGTC
Found at i:1308376 original size:60 final size:60
Alignment explanation
Indices: 1308091--1308399 Score: 365
Period size: 55 Copynumber: 5.3 Consensus size: 60
1308081 GATACATTCT
* * * * *
1308091 AGTCCTCAAAGAGTAGGACACCTTTTCTTTTTAAAGCCCACATAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGAC-GCTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* *
1308152 AGTCCTC-AAGAGCATGACG----CCTCTT-AAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
*
1308206 AGTCTTCAAAGAGCAGGACG----CC-TTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* * **
1308261 AGTCCTCAAAGAGCAAGG-TGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCC
1 AGTCCTCAAAGAGC-AGGACGCTTTC-CTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
*
1308322 AGTCCTCAAAGAGCAGGACGCTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-T
1 AGTCCTCAAAGAGCAGGACGCTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
*
1308382 AGTCCTTAAAGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
1308400 TGCACTTTAT
Statistics
Matches: 217, Mismatches: 20, Indels: 23
0.83 0.08 0.09
Matches are distributed among these distances:
54 36 0.17
55 60 0.28
56 3 0.01
59 1 0.00
60 58 0.27
61 59 0.27
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.26
Consensus pattern (60 bp):
AGTCCTCAAAGAGCAGGACGCTTTCCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
Found at i:1309821 original size:51 final size:51
Alignment explanation
Indices: 1309756--1309975 Score: 214
Period size: 51 Copynumber: 4.3 Consensus size: 51
1309746 ATTTTTCATC
*
1309756 TCGGGGATACTCCAA-TCCCGGTTTCATTTCCAAAACATCAATTTTTCTTAA
1 TCGGGGATACTCCAACT-CCGATTTCATTTCCAAAACATCAATTTTTCTTAA
* * * * * * ** **
1309807 TCGGGAATACTCCAACTCCAATTTTATTTCTAAAGCATCGATTTACCGCAA
1 TCGGGGATACTCCAACTCCGATTTCATTTCCAAAACATCAATTTTTCTTAA
* * *
1309858 -CTGGGGATACTCCAA-TCCCGGTTTCATCTCGAAAACATCAATTTTTCTTAA
1 TC-GGGGATACTCCAACT-CCGATTTCATTTCCAAAACATCAATTTTTCTTAA
* * **
1309909 TCGGGGATACTCCAACTCCGATTTAATTTCCAAAACACCAATTTTTCACAA
1 TCGGGGATACTCCAACTCCGATTTCATTTCCAAAACATCAATTTTTCTTAA
1309960 -CTGGGGATACTCCAAC
1 TC-GGGGATACTCCAAC
1309976 CCCGTTATTT
Statistics
Matches: 133, Mismatches: 30, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
50 3 0.02
51 127 0.95
52 3 0.02
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (51 bp):
TCGGGGATACTCCAACTCCGATTTCATTTCCAAAACATCAATTTTTCTTAA
Found at i:1309938 original size:102 final size:102
Alignment explanation
Indices: 1309758--1309979 Score: 327
Period size: 102 Copynumber: 2.2 Consensus size: 102
1309748 TTTTCATCTC
*
1309758 GGGGATACTCCAATCCCGGTTTCATTTCCAAAACATCAATTTTTCTTAATCGGGAATACTCCAAC
1 GGGGATACTCCAATCCCGGTTTCATCTCCAAAACATCAATTTTTCTTAATCGGGAATACTCCAAC
* * * * * *
1309823 TCCAATTTTATTTCTAAAGCATCGATTTACCGCAACT
66 TCCAATTTAATTTCCAAAACACCAATTTACCACAACT
* *
1309860 GGGGATACTCCAATCCCGGTTTCATCTCGAAAACATCAATTTTTCTTAATCGGGGATACTCCAAC
1 GGGGATACTCCAATCCCGGTTTCATCTCCAAAACATCAATTTTTCTTAATCGGGAATACTCCAAC
* **
1309925 TCCGATTTAATTTCCAAAACACCAATTTTTCACAACT
66 TCCAATTTAATTTCCAAAACACCAATTTACCACAACT
*
1309962 GGGGATACTCCAACCCCG
1 GGGGATACTCCAATCCCG
1309980 TTATTTCCGA
Statistics
Matches: 107, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
102 107 1.00
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (102 bp):
GGGGATACTCCAATCCCGGTTTCATCTCCAAAACATCAATTTTTCTTAATCGGGAATACTCCAAC
TCCAATTTAATTTCCAAAACACCAATTTACCACAACT
Found at i:1310143 original size:28 final size:28
Alignment explanation
Indices: 1310050--1310145 Score: 97
Period size: 28 Copynumber: 3.4 Consensus size: 28
1310040 ATCGGGGGGC
* * *
1310050 ACTCTAACCCCGTTA-TGTCATCAGGGAT
1 ACTCCAACCCCGTTATTTTCAT-GGGGAT
* * *
1310078 ACTCCAATCACATTATTTTCGA-GGGGAT
1 ACTCCAACCCCGTTATTTTC-ATGGGGAT
1310106 ACTCCAACCCCGTTATTTTCATGGGGAT
1 ACTCCAACCCCGTTATTTTCATGGGGAT
*
1310134 GCTCCAACCCCG
1 ACTCCAACCCCG
1310146 GCCTTATTTC
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
27 1 0.02
28 50 0.91
29 3 0.05
30 1 0.02
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (28 bp):
ACTCCAACCCCGTTATTTTCATGGGGAT
Found at i:1315019 original size:16 final size:15
Alignment explanation
Indices: 1314993--1315023 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1314983 GATGAAAACA
1314993 ATTTTTTATTATTTT
1 ATTTTTTATTATTTT
1315008 ATTTTGTTATTATTTT
1 ATTTT-TTATTATTTT
1315024 TTTAATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (15 bp):
ATTTTTTATTATTTT
Found at i:1315045 original size:23 final size:26
Alignment explanation
Indices: 1314992--1315046 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
1314982 AGATGAAAAC
* *
1314992 AATTTTTTATTATTTTATTTTGTTAT
1 AATTTTTTATAATTATATTTTGTTAT
*
1315018 TATTTTTT-TAATTATATTTT-TTA-
1 AATTTTTTATAATTATATTTTGTTAT
1315041 AATTTT
1 AATTTT
1315047 ACTTTCGTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
23 5 0.20
24 3 0.12
25 10 0.40
26 7 0.28
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (26 bp):
AATTTTTTATAATTATATTTTGTTAT
Found at i:1315982 original size:21 final size:21
Alignment explanation
Indices: 1315925--1315989 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
1315915 AGAGGCTCGA
* * *
1315925 GCTGCTGTTGTGTTCTTGGAT
1 GCTGCTGCTATGTTCGTGGAT
*
1315946 GCTGCCGCTGCCATGTTCGTGGAT
1 GCT---GCTGCTATGTTCGTGGAT
1315970 GCTGCTGCTATGTTCGTGGA
1 GCTGCTGCTATGTTCGTGGA
1315990 AGTTGGAAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
21 19 0.53
24 17 0.47
ACGTcount: A:0.08, C:0.22, G:0.34, T:0.37
Consensus pattern (21 bp):
GCTGCTGCTATGTTCGTGGAT
Found at i:1317305 original size:16 final size:16
Alignment explanation
Indices: 1317284--1317314 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1317274 TTCTTTTCAA
*
1317284 AAAAAAGAAAAAAAAT
1 AAAAAACAAAAAAAAT
1317300 AAAAAACAAAAAAAA
1 AAAAAACAAAAAAAA
1317315 AACTATGGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.90, C:0.03, G:0.03, T:0.03
Consensus pattern (16 bp):
AAAAAACAAAAAAAAT
Found at i:1317305 original size:18 final size:18
Alignment explanation
Indices: 1317282--1317316 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1317272 TGTTCTTTTC
1317282 AAAAAA-AAGAAAAAAAAT
1 AAAAAACAA-AAAAAAAAT
1317300 AAAAAACAAAAAAAAAA
1 AAAAAACAAAAAAAAAA
1317317 CTATGGTGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.91, C:0.03, G:0.03, T:0.03
Consensus pattern (18 bp):
AAAAAACAAAAAAAAAAT
Found at i:1318500 original size:27 final size:27
Alignment explanation
Indices: 1318456--1318553 Score: 110
Period size: 27 Copynumber: 3.6 Consensus size: 27
1318446 TAATGATCTC
1318456 CCTTTTAAGTCTACAACTCCGTGGCAA
1 CCTTTTAAGTCTACAACTCCGTGGCAA
* *
1318483 CCTTTTAAGT-TCATAACTCCGTGG-TA
1 CCTTTTAAGTCT-ACAACTCCGTGGCAA
* *
1318509 CTCTTTTAAAGTCTACAACTCTGTGGCAC
1 C-CTTTT-AAGTCTACAACTCCGTGGCAA
*
1318538 CCTTTTAAGTCCACAA
1 CCTTTTAAGTCTACAA
1318554 TGTAGACACC
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
26 3 0.05
27 35 0.59
28 19 0.32
29 2 0.03
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.34
Consensus pattern (27 bp):
CCTTTTAAGTCTACAACTCCGTGGCAA
Found at i:1318865 original size:23 final size:23
Alignment explanation
Indices: 1318815--1318866 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
1318805 AAGTAGAAAT
* *
1318815 AAAAAATTAAAAATAAAAATTAA
1 AAAAAATCAAAAATAAAAATGAA
* * *
1318838 TAAAAATCAATAATAAGAATGAA
1 AAAAAATCAAAAATAAAAATGAA
1318861 AAAAAA
1 AAAAAA
1318867 AATCCTGAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (23 bp):
AAAAAATCAAAAATAAAAATGAA
Found at i:1318866 original size:24 final size:24
Alignment explanation
Indices: 1318799--1318867 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 24
1318789 TATAAAATAT
* *
1318799 AATAATAAGTA-GAAATAAAAAATT
1 AATAATAAGAATGAAA-AAAAAATC
* * * *
1318823 AAAAATAAAAAT-TAATAAAAATC
1 AATAATAAGAATGAAAAAAAAATC
1318846 AATAATAAGAATGAAAAAAAAA
1 AATAATAAGAATGAAAAAAAAA
1318868 ATCCTGAAAT
Statistics
Matches: 33, Mismatches: 10, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
23 16 0.48
24 17 0.52
ACGTcount: A:0.72, C:0.01, G:0.06, T:0.20
Consensus pattern (24 bp):
AATAATAAGAATGAAAAAAAAATC
Found at i:1319633 original size:61 final size:61
Alignment explanation
Indices: 1319535--1319724 Score: 231
Period size: 61 Copynumber: 3.1 Consensus size: 61
1319525 CAAAAACTCC
* * * *
1319535 AGCACGAACAGTAGCCAAACAACAGCACGAC-GACAACAATAACAGCTCCAACAAGAAGGCA
1 AGCATGAACAGCAGCCAAACAATAGCACGACAG-CAACAATAACAGCTCCAACAAGCAGGCA
* * *
1319596 AGCATGAATAGCAGCCAAACAATAGCATGACAGCAACAACAACAG-TCCAACAAGCAGGCA
1 AGCATGAACAGCAGCCAAACAATAGCACGACAGCAACAATAACAGCTCCAACAAGCAGGCA
* * * * * **
1319656 AGCATAAACAGCAACAAAACAATAGCACGGCAGCAGCAATAGTAGCTCCAACAAGCAGGCA
1 AGCATGAACAGCAGCCAAACAATAGCACGACAGCAACAATAACAGCTCCAACAAGCAGGCA
1319717 AGCATGAA
1 AGCATGAA
1319725 AAATGACCAA
Statistics
Matches: 109, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
60 49 0.45
61 59 0.54
62 1 0.01
ACGTcount: A:0.47, C:0.27, G:0.19, T:0.07
Consensus pattern (61 bp):
AGCATGAACAGCAGCCAAACAATAGCACGACAGCAACAATAACAGCTCCAACAAGCAGGCA
Found at i:1319676 original size:60 final size:61
Alignment explanation
Indices: 1319551--1319721 Score: 211
Period size: 60 Copynumber: 2.8 Consensus size: 61
1319541 AACAGTAGCC
* * * * * *
1319551 AAACAACAGCACGAC-GACAACAATAACAGCTCCAACAAGAAGGCAAGCATGAATAGCAGCC
1 AAACAATAGCACGACAG-CAACAATAACAGCTCCAACAAGCAGGCAAGCATAAACAGCAACA
* *
1319612 AAACAATAGCATGACAGCAACAACAACAG-TCCAACAAGCAGGCAAGCATAAACAGCAACA
1 AAACAATAGCACGACAGCAACAATAACAGCTCCAACAAGCAGGCAAGCATAAACAGCAACA
* * **
1319672 AAACAATAGCACGGCAGCAGCAATAGTAGCTCCAACAAGCAGGCAAGCAT
1 AAACAATAGCACGACAGCAACAATAACAGCTCCAACAAGCAGGCAAGCAT
1319722 GAAAAATGAC
Statistics
Matches: 94, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
60 49 0.52
61 44 0.47
62 1 0.01
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.08
Consensus pattern (61 bp):
AAACAATAGCACGACAGCAACAATAACAGCTCCAACAAGCAGGCAAGCATAAACAGCAACA
Found at i:1319741 original size:61 final size:61
Alignment explanation
Indices: 1319549--1319754 Score: 206
Period size: 61 Copynumber: 3.4 Consensus size: 61
1319539 CGAACAGTAG
* * * * *
1319549 CCAAACAACAGCACGAC-GACAACAATAACAGCTCCAACAAGAAGGCAAGCATG-AATAGCA
1 CCAAACAATAGCACGGCAG-CAACAACAACAGCTCCAACAAGCAGGCAAGCATGAAAAAGCA
* * *
1319609 GCCAAACAATAGCATGACAGCAACAACAACAG-TCCAACAAGCAGGCAAGCAT-AAACAGCAA
1 -CCAAACAATAGCACGGCAGCAACAACAACAGCTCCAACAAGCAGGCAAGCATGAAAAAGC-A
* * * **
1319670 CAAAACAATAGCACGGCAGCAGCAATAGTAGCTCCAACAAGCAGGCAAGCATGAAAAATG-A
1 CCAAACAATAGCACGGCAGCAACAACAACAGCTCCAACAAGCAGGCAAGCATGAAAAA-GCA
* *
1319731 CCAAAGAATAGCACGGTAGCAACA
1 CCAAACAATAGCACGGCAGCAACA
1319755 TTGAACAACT
Statistics
Matches: 122, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
60 48 0.39
61 68 0.56
62 5 0.04
63 1 0.01
ACGTcount: A:0.48, C:0.26, G:0.18, T:0.08
Consensus pattern (61 bp):
CCAAACAATAGCACGGCAGCAACAACAACAGCTCCAACAAGCAGGCAAGCATGAAAAAGCA
Found at i:1323587 original size:16 final size:16
Alignment explanation
Indices: 1323562--1323593 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1323552 GATGAAAAGA
*
1323562 ATTTTTTTATTATTTT
1 ATTTTGTTATTATTTT
1323578 ATTTTGTTATTATTTT
1 ATTTTGTTATTATTTT
1323594 TTAATTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (16 bp):
ATTTTGTTATTATTTT
Found at i:1324587 original size:31 final size:31
Alignment explanation
Indices: 1324552--1324621 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
1324542 CTGCTGTGTT
*
1324552 CGTGGAAGTTGGAAA-AGGCTCAAGCTGATGC
1 CGTGGAAGAT-GAAAGAGGCTCAAGCTGATGC
** * *
1324583 CGTGGAAGATGAAAGAGGCTTGAGCTGTTGG
1 CGTGGAAGATGAAAGAGGCTCAAGCTGATGC
1324614 CGTGGAAG
1 CGTGGAAG
1324622 CTAGAAGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.27, C:0.13, G:0.40, T:0.20
Consensus pattern (31 bp):
CGTGGAAGATGAAAGAGGCTCAAGCTGATGC
Found at i:1325348 original size:37 final size:36
Alignment explanation
Indices: 1325299--1325370 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 36
1325289 TTTCATGATT
* *
1325299 TTTTTTTATTTTTTATTTCTA-TTAATTATTATTATTA
1 TTTTTTAATTTTTGATTTCTACTT-ATTATT-TTATTA
1325336 TTTTTTAATTTTTGATTTCTACTTATTATTTTATT
1 TTTTTTAATTTTTGATTTCTACTTATTATTTTATT
1325371 TTATAGCGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 5 0.16
37 25 0.78
38 2 0.06
ACGTcount: A:0.22, C:0.04, G:0.01, T:0.72
Consensus pattern (36 bp):
TTTTTTAATTTTTGATTTCTACTTATTATTTTATTA
Found at i:1327092 original size:28 final size:27
Alignment explanation
Indices: 1327019--1327116 Score: 103
Period size: 27 Copynumber: 3.6 Consensus size: 27
1327009 TAATGATCTC
1327019 CCTTTTAAGTCTACAACTCCGTGGCAA
1 CCTTTTAAGTCTACAACTCCGTGGCAA
*
1327046 CCTTTTAAGT-TCACAACTCCAG-GG-TA
1 CCTTTTAAGTCT-ACAACTCC-GTGGCAA
* *
1327072 CTCTTTTAAAGTCTACAACTCTGTGGCAC
1 C-CTTTT-AAGTCTACAACTCCGTGGCAA
*
1327101 CCTTTTAAGTCCACAA
1 CCTTTTAAGTCTACAA
1327117 AGTAGACACC
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
26 3 0.05
27 35 0.59
28 19 0.32
29 2 0.03
ACGTcount: A:0.27, C:0.29, G:0.13, T:0.32
Consensus pattern (27 bp):
CCTTTTAAGTCTACAACTCCGTGGCAA
Found at i:1327409 original size:30 final size:32
Alignment explanation
Indices: 1327374--1327440 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
1327364 TAATAAGTAG
* * *
1327374 AAATCAAA-AATTAAA-AATAAAAATTAATAA
1 AAATCAAATAATAAAACAATAAAAATGAAAAA
*
1327404 AAATCAAATAATAAAACAATAACAATGAAAAA
1 AAATCAAATAATAAAACAATAAAAATGAAAAA
1327436 AAATC
1 AAATC
1327441 CTGAAATGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 8 0.26
31 6 0.19
32 17 0.55
ACGTcount: A:0.72, C:0.07, G:0.01, T:0.19
Consensus pattern (32 bp):
AAATCAAATAATAAAACAATAAAAATGAAAAA
Found at i:1327986 original size:41 final size:41
Alignment explanation
Indices: 1327922--1328003 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 41
1327912 AACTCTAGCG
* * * *
1327922 AGCAGCAGCTTCTAGTAGCAGGAGTA-TCTGCAACCAACACC
1 AGCAGCAGCTTCCAATAGCAGGAGCATTC-GAAACCAACACC
*
1327963 AGCAGCAGCTTCCAATAGTAGGAGCATTCGAAACCAACACC
1 AGCAGCAGCTTCCAATAGCAGGAGCATTCGAAACCAACACC
1328004 GGTAGTAGCT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 33 0.94
42 2 0.06
ACGTcount: A:0.34, C:0.29, G:0.21, T:0.16
Consensus pattern (41 bp):
AGCAGCAGCTTCCAATAGCAGGAGCATTCGAAACCAACACC
Found at i:1328179 original size:61 final size:61
Alignment explanation
Indices: 1328103--1328292 Score: 231
Period size: 61 Copynumber: 3.1 Consensus size: 61
1328093 CAAAAACGCT
* *
1328103 AGCACGAACACCAGCCAAACAACAGCACGACAGCAACAATAACAGCTCCAACAAGCAGGCA
1 AGCACGAATAGCAGCCAAACAACAGCACGACAGCAACAATAACAGCTCCAACAAGCAGGCA
* ** * * *
1328164 AGCACGAATAGCAGCCACACAATGGCATGATAGCAACAATAACAG-TCCAACGAGCAGGCA
1 AGCACGAATAGCAGCCAAACAACAGCACGACAGCAACAATAACAGCTCCAACAAGCAGGCA
* * * * * *
1328224 AGCATGAATAGCAACGAAACAACAGCACGGCAGCAGCAATAGCAGCTCCAACAAAG-AGGCA
1 AGCACGAATAGCAGCCAAACAACAGCACGACAGCAACAATAACAGCTCCAAC-AAGCAGGCA
1328285 AGCACGAA
1 AGCACGAA
1328293 AAATGACCAA
Statistics
Matches: 106, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
60 48 0.45
61 56 0.53
62 2 0.02
ACGTcount: A:0.44, C:0.29, G:0.21, T:0.06
Consensus pattern (61 bp):
AGCACGAATAGCAGCCAAACAACAGCACGACAGCAACAATAACAGCTCCAACAAGCAGGCA
Found at i:1333717 original size:21 final size:21
Alignment explanation
Indices: 1333692--1333754 Score: 81
Period size: 24 Copynumber: 2.9 Consensus size: 21
1333682 AGAGGCTCGA
* *
1333692 GCTGCTGTTGTGTTCTTGGAT
1 GCTGCTGCTGTGTTCGTGGAT
1333713 GCTGCTGCTGCCATGTTCGTGGAT
1 GCTGCTGCTG---TGTTCGTGGAT
1333737 GCTGCTGCTGTGTTCGTG
1 GCTGCTGCTGTGTTCGTG
1333755 AAAGTTGGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
21 17 0.46
24 20 0.54
ACGTcount: A:0.05, C:0.21, G:0.35, T:0.40
Consensus pattern (21 bp):
GCTGCTGCTGTGTTCGTGGAT
Found at i:1333801 original size:31 final size:32
Alignment explanation
Indices: 1333763--1333842 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 32
1333753 TGAAAGTTGG
1333763 AAGAGGCTCAAGCTACTGCCGTGGAAGCTA-A
1 AAGAGGCTCAAGCTACTGCCGTGGAAGCTAGA
* ** *
1333794 AAGAGGCTCGAGCTGTTGGCGTGGAAGCTAGA
1 AAGAGGCTCAAGCTACTGCCGTGGAAGCTAGA
**
1333826 AA-AATCTCAAGCTACTG
1 AAGAGGCTCAAGCTACTG
1333843 GTTTCGGGTG
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
31 36 0.92
32 3 0.08
ACGTcount: A:0.31, C:0.20, G:0.30, T:0.19
Consensus pattern (32 bp):
AAGAGGCTCAAGCTACTGCCGTGGAAGCTAGA
Found at i:1335165 original size:33 final size:32
Alignment explanation
Indices: 1335123--1335190 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
1335113 CGTTACAGGC
**
1335123 CAATGTATCGATACATTTTATGATGTATCGATA
1 CAATGTATCGATACATACTATG-TGTATCGATA
* *
1335156 CAATGTATCGATATATACTGTGTGTATCGATA
1 CAATGTATCGATACATACTATGTGTATCGATA
1335188 CAA
1 CAA
1335191 GTTTGGCTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 13 0.42
33 18 0.58
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
CAATGTATCGATACATACTATGTGTATCGATA
Found at i:1335269 original size:20 final size:21
Alignment explanation
Indices: 1335224--1335274 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
1335214 GAAAGACCTA
**
1335224 TATCGATACATCTTTTTCAAG
1 TATCGATACATCTTGGTCAAG
*
1335245 TATCGATACAT-TTGGTCATG
1 TATCGATACATCTTGGTCAAG
1335265 TATCGATACA
1 TATCGATACA
1335275 ATGTATCGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (21 bp):
TATCGATACATCTTGGTCAAG
Found at i:1335280 original size:13 final size:13
Alignment explanation
Indices: 1335262--1335290 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1335252 ACATTTGGTC
1335262 ATGTATCGATACA
1 ATGTATCGATACA
1335275 ATGTATCGATACA
1 ATGTATCGATACA
1335288 ATG
1 ATG
1335291 CAATCTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1335301 original size:20 final size:20
Alignment explanation
Indices: 1335276--1335326 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1335266 ATCGATACAA
*
1335276 TGTATCGATACAATGCAATC
1 TGTATCGATACAATGAAATC
* * *
1335296 TGTATCGATACATTTAAATG
1 TGTATCGATACAATGAAATC
1335316 TGTATCGATAC
1 TGTATCGATAC
1335327 TTTTCATGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (20 bp):
TGTATCGATACAATGAAATC
Found at i:1337783 original size:13 final size:13
Alignment explanation
Indices: 1337765--1337803 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1337755 ATAATCCCCT
1337765 TGTATCGATACAG
1 TGTATCGATACAG
*
1337778 TGTATCGATACAA
1 TGTATCGATACAG
1337791 TGTATCGATACAG
1 TGTATCGATACAG
1337804 AGAATGCTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1344005 original size:13 final size:13
Alignment explanation
Indices: 1343987--1344012 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1343977 ACATTTTATG
1343987 ATGTATCGATACA
1 ATGTATCGATACA
1344000 ATGTATCGATACA
1 ATGTATCGATACA
1344013 TACTGTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1344007 original size:33 final size:32
Alignment explanation
Indices: 1343965--1344032 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
1343955 CATTACAGGC
**
1343965 CAATGTATCGATACATTTTATGATGTATCGATA
1 CAATGTATCGATACATACTATG-TGTATCGATA
*
1343998 CAATGTATCGATACATACTGTGTGTATCGATA
1 CAATGTATCGATACATACTATGTGTATCGATA
1344030 CAA
1 CAA
1344033 GTTTGGCTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATACTATGTGTATCGATA
Found at i:1344118 original size:20 final size:20
Alignment explanation
Indices: 1344095--1344145 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1344085 CATTTGGTCA
*
1344095 TGTATCGATACAATGCAATC
1 TGTATCGATACAATGAAATC
* * *
1344115 TGTATCGATACATTTAAATG
1 TGTATCGATACAATGAAATC
1344135 TGTATCGATAC
1 TGTATCGATAC
1344146 TTTTCAGGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (20 bp):
TGTATCGATACAATGAAATC
Found at i:1344569 original size:18 final size:18
Alignment explanation
Indices: 1344546--1344597 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
1344536 GATTTTTTTT
1344546 ATTTTTTTATTTCTATTA
1 ATTTTTTTATTTCTATTA
* * *
1344564 ATTTTTATTGTTATATTTTA
1 ATTTTT-TTATT-TCTATTA
1344584 A-TTTTTTATTTCTA
1 ATTTTTTTATTTCTA
1344598 CTTATTATTA
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
17 2 0.08
18 10 0.38
19 8 0.31
20 6 0.23
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (18 bp):
ATTTTTTTATTTCTATTA
Found at i:1345113 original size:15 final size:14
Alignment explanation
Indices: 1345089--1345124 Score: 63
Period size: 15 Copynumber: 2.5 Consensus size: 14
1345079 TGTTCTTTTC
1345089 AAAAAAAAAAAACA
1 AAAAAAAAAAAACA
1345103 AAAAAATAAAAAACA
1 AAAAAA-AAAAAACA
1345118 AAAAAAA
1 AAAAAAA
1345125 CTATGGTGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.92, C:0.06, G:0.00, T:0.03
Consensus pattern (14 bp):
AAAAAAAAAAAACA
Found at i:1346322 original size:27 final size:27
Alignment explanation
Indices: 1346264--1346337 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 27
1346254 TAATGATCTC
1346264 CCTTTTAAGTCTACAACTCCGTGGCAA
1 CCTTTTAAGTCTACAACTCCGTGGCAA
* *
1346291 CCTTTTAAGT-TCACAACTCC-TTGCTA
1 CCTTTTAAGTCT-ACAACTCCGTGGCAA
*
1346317 CACTTTTAAAGTATACAACTC
1 C-CTTTT-AAGTCTACAACTC
1346338 TACGGTACCC
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
26 6 0.15
27 23 0.56
28 11 0.27
29 1 0.02
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.34
Consensus pattern (27 bp):
CCTTTTAAGTCTACAACTCCGTGGCAA
Found at i:1347212 original size:41 final size:41
Alignment explanation
Indices: 1347167--1347264 Score: 117
Period size: 41 Copynumber: 2.4 Consensus size: 41
1347157 AACTCTAGCA
* *
1347167 AGCAGTAGCTTCTAGCAGCAGGAGTA-TCTGAAACCAACACC
1 AGCAGTAGCTTCCAGCAGCAGGAGCATTC-GAAACCAACACC
* * *
1347208 AGCAGCAGCTTCCAGCAGTAGGAGCATTCGAAACCAATACC
1 AGCAGTAGCTTCCAGCAGCAGGAGCATTCGAAACCAACACC
* *
1347249 GGCAGTAGCTTTCAGC
1 AGCAGTAGCTTCCAGC
1347265 CCACGAGCAC
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 46 0.96
42 2 0.04
ACGTcount: A:0.32, C:0.28, G:0.23, T:0.17
Consensus pattern (41 bp):
AGCAGTAGCTTCCAGCAGCAGGAGCATTCGAAACCAACACC
Found at i:1347425 original size:61 final size:61
Alignment explanation
Indices: 1347354--1347533 Score: 193
Period size: 61 Copynumber: 3.0 Consensus size: 61
1347344 CTCCAGCAGA
*
1347354 AATAGCAGCCAAACAACAGCACGGTAGCAACAATAACAGCTCCAAGAAGCAGGCAAGCACG
1 AATAGCAGCCAAACAACAGCACGGTAGCAACAATAACAGCTCCAACAAGCAGGCAAGCACG
* *** * *
1347415 AATAGCAGCCAAACAATAGCGTAGTAGCAACAACAACAG-TCCAACAAGCAGGCAAGCATG
1 AATAGCAGCCAAACAACAGCACGGTAGCAACAATAACAGCTCCAACAAGCAGGCAAGCACG
*** ** * * * *
1347475 AACT-GCAATGAAACAACAGCACGACAGCAGCAATAGCAGCTCCAATAAGAAGGCAAGCA
1 AA-TAGCAGCCAAACAACAGCACGGTAGCAACAATAACAGCTCCAACAAGCAGGCAAGCA
1347534 TGAAAAATGA
Statistics
Matches: 96, Mismatches: 21, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
60 44 0.46
61 52 0.54
ACGTcount: A:0.45, C:0.26, G:0.21, T:0.08
Consensus pattern (61 bp):
AATAGCAGCCAAACAACAGCACGGTAGCAACAATAACAGCTCCAACAAGCAGGCAAGCACG
Found at i:1348449 original size:20 final size:23
Alignment explanation
Indices: 1348404--1348449 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1348394 GAATAAATTC
*
1348404 TTGATGTATTTTCACTTTTGATT
1 TTGATGTATTTACACTTTTGATT
1348427 TTGATGTA-TTACA-TTTT-ATT
1 TTGATGTATTTACACTTTTGATT
1348447 TTG
1 TTG
1348450 TAGATTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 6 0.27
21 4 0.18
22 4 0.18
23 8 0.36
ACGTcount: A:0.20, C:0.07, G:0.13, T:0.61
Consensus pattern (23 bp):
TTGATGTATTTACACTTTTGATT
Found at i:1351452 original size:13 final size:13
Alignment explanation
Indices: 1351434--1351459 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1351424 TACACCAAGT
1351434 ATGTATCGATACA
1 ATGTATCGATACA
1351447 ATGTATCGATACA
1 ATGTATCGATACA
1351460 CCAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1351478 original size:34 final size:32
Alignment explanation
Indices: 1351416--1351480 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
1351406 TAGCCAAACT
**
1351416 TGTATCGATACACCAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAATGTATCGATACAA
1351448 TGTATCGATACACCAAAAAATTGTATCGATACA
1 TGTATCGATACACC-AAAAA-TGTATCGATACA
1351481 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 14 0.48
33 3 0.10
34 12 0.41
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACCAAAAATGTATCGATACAA
Found at i:1353095 original size:12 final size:12
Alignment explanation
Indices: 1353063--1353096 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1353053 AACCATCAAG
*
1353063 GATGAAGAAGAT
1 GATGAAGATGAT
*
1353075 GATGAAGATGTT
1 GATGAAGATGAT
1353087 GATGAAGATG
1 GATGAAGATG
1353097 GTGACTCGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.35, T:0.24
Consensus pattern (12 bp):
GATGAAGATGAT
Found at i:1357823 original size:20 final size:20
Alignment explanation
Indices: 1357780--1357826 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
1357770 AAATCTTTTG
1357780 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1357801 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1357821 CAAAAT
1 CAAAAT
1357827 CAGCCTCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.32, C:0.19, G:0.04, T:0.45
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1360215 original size:21 final size:20
Alignment explanation
Indices: 1360169--1360221 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
1360159 GTAACCAAAC
**
1360169 TTGTATCGATACACCAAGTA
1 TTGTATCGATACACCAAAAA
1360189 -TGTATCGATACACCAAAAAA
1 TTGTATCGATACACC-AAAAA
1360209 TTGTATCGATACA
1 TTGTATCGATACA
1360222 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 14 0.48
20 3 0.10
21 12 0.41
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (20 bp):
TTGTATCGATACACCAAAAA
Found at i:1361515 original size:16 final size:16
Alignment explanation
Indices: 1361490--1361521 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1361480 GATGAAAAGA
*
1361490 ATTTTTTTATTATTTT
1 ATTTTGTTATTATTTT
1361506 ATTTTGTTATTATTTT
1 ATTTTGTTATTATTTT
1361522 TTTAATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (16 bp):
ATTTTGTTATTATTTT
Found at i:1362453 original size:24 final size:24
Alignment explanation
Indices: 1362421--1362478 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
1362411 AGAGGCTCGA
**
1362421 GCTGCTGCTGCCATGTTTGTGGAT
1 GCTGCTGCTGCCATGTTCATGGAT
1362445 GCTGCTGCTGCCATGTTCATGGAT
1 GCTGCTGCTGCCATGTTCATGGAT
1362469 GCTGCTGCTG
1 GCTGCTGCTG
1362479 TGTTCGTGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.09, C:0.24, G:0.33, T:0.34
Consensus pattern (24 bp):
GCTGCTGCTGCCATGTTCATGGAT
Found at i:1362482 original size:21 final size:22
Alignment explanation
Indices: 1362421--1362488 Score: 66
Period size: 24 Copynumber: 3.0 Consensus size: 22
1362411 AGAGGCTCGA
**
1362421 GCTGCTGCTGCCATGTTTGTGGAT
1 GCTGCTGCTG-C-TGTTCATGGAT
1362445 GCTGCTGCTGCCATGTTCATGGAT
1 GCTGCTGCTG-C-TGTTCATGGAT
*
1362469 GCTGCTGCTG-TGTTCGTGGA
1 GCTGCTGCTGCTGTTCATGGA
1362489 AGTTGGAAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
21 9 0.22
24 32 0.78
ACGTcount: A:0.09, C:0.22, G:0.34, T:0.35
Consensus pattern (22 bp):
GCTGCTGCTGCTGTTCATGGAT
Found at i:1365001 original size:28 final size:27
Alignment explanation
Indices: 1364914--1365012 Score: 112
Period size: 27 Copynumber: 3.6 Consensus size: 27
1364904 CTAATGATCT
1364914 CCCTTTTAAGTCTACAACTCCGTGGCA
1 CCCTTTTAAGTCTACAACTCCGTGGCA
*
1364941 ACCTTTTAAGT-TCACAACTCCGT-GCTA
1 CCCTTTTAAGTCT-ACAACTCCGTGGC-A
* **
1364968 CTCTTTTAAAGTCTACAACTTTGTGGCA
1 CCCTTTT-AAGTCTACAACTCCGTGGCA
*
1364996 CCCTTTTAAGTCCACAA
1 CCCTTTTAAGTCTACAA
1365013 TGTAGACACC
Statistics
Matches: 60, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
26 3 0.05
27 35 0.58
28 19 0.32
29 3 0.05
ACGTcount: A:0.25, C:0.29, G:0.12, T:0.33
Consensus pattern (27 bp):
CCCTTTTAAGTCTACAACTCCGTGGCA
Found at i:1365929 original size:41 final size:41
Alignment explanation
Indices: 1365823--1365944 Score: 165
Period size: 44 Copynumber: 2.9 Consensus size: 41
1365813 CTCTAGCAAG
1365823 CAGCAGCTTCTAGCAGCAGGAGTATCTGAAACCAACACCAC
1 CAGCAGCTTCTAGCAGCAGGAGTATCTGAAACCAACACCAC
*
1365864 CAGTAGCAGCTTCTAGCAACAGGAGTATCTGAAACCAACACCAC
1 C---AGCAGCTTCTAGCAGCAGGAGTATCTGAAACCAACACCAC
* * *
1365908 CAGCAGCTTCCAGCAGTAGGAGCAT-TCGAAACCAACA
1 CAGCAGCTTCTAGCAGCAGGAGTATCT-GAAACCAACA
1365945 ACGGCAGTAG
Statistics
Matches: 72, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
40 1 0.01
41 31 0.43
44 40 0.56
ACGTcount: A:0.35, C:0.30, G:0.20, T:0.15
Consensus pattern (41 bp):
CAGCAGCTTCTAGCAGCAGGAGTATCTGAAACCAACACCAC
Found at i:1366128 original size:61 final size:60
Alignment explanation
Indices: 1366052--1366254 Score: 212
Period size: 61 Copynumber: 3.3 Consensus size: 60
1366042 CTCCAACACG
* *
1366052 AACAGCAGCCAAACAACAGCATGGCAGCAACAATAATAGCTCCAACAAGCAGGCAAGCACA
1 AACAG-AGCCAAACAATAGCATGGCAGCAACAATAACAGCTCCAACAAGCAGGCAAGCACA
* ** * **
1366113 AATAGAAGCCAAACAATAGCATGATAGCAACAACAACAG-TCCAACAAGCAGGCAAGCATG
1 AACAG-AGCCAAACAATAGCATGGCAGCAACAATAACAGCTCCAACAAGCAGGCAAGCACA
* * * * *
1366173 AACAGCGACAAAACAATAGCACGGCAGCAGCAATAGCAGCTCCAACAAGCAGGCAAGCACGA
1 AACAGAG-CCAAACAATAGCATGGCAGCAACAATAACAGCTCCAACAAGCAGGCAAGCAC-A
* *
1366235 AAAATGA-CCAAAGAATAGCA
1 AACA-GAGCCAAACAATAGCA
1366255 CAGTAGCAAC
Statistics
Matches: 114, Mismatches: 24, Indels: 8
0.78 0.16 0.05
Matches are distributed among these distances:
59 1 0.01
60 47 0.41
61 62 0.54
62 3 0.03
63 1 0.01
ACGTcount: A:0.47, C:0.26, G:0.19, T:0.07
Consensus pattern (60 bp):
AACAGAGCCAAACAATAGCATGGCAGCAACAATAACAGCTCCAACAAGCAGGCAAGCACA
Found at i:1375687 original size:13 final size:13
Alignment explanation
Indices: 1375669--1375693 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1375659 TTCAACAATT
1375669 TGTATCGATACAA
1 TGTATCGATACAA
1375682 TGTATCGATACA
1 TGTATCGATACA
1375694 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1375765 original size:20 final size:20
Alignment explanation
Indices: 1375740--1375777 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1375730 TATTGCCAAG
1375740 GAAATGTATCAATACATTAC
1 GAAATGTATCAATACATTAC
*
1375760 GAAATGTATCGATACATT
1 GAAATGTATCAATACATT
1375778 GCATCGATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (20 bp):
GAAATGTATCAATACATTAC
Found at i:1378717 original size:20 final size:20
Alignment explanation
Indices: 1378692--1378729 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1378682 GTATCGATGC
1378692 AATGTATCGATACATTTCGT
1 AATGTATCGATACATTTCGT
1378712 AATGTATCGATACATTTC
1 AATGTATCGATACATTTC
1378730 CTTGGCAATA
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:0.16, G:0.13, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACATTTCGT
Found at i:1380074 original size:34 final size:35
Alignment explanation
Indices: 1380036--1380102 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1380026 CCTTACAACA
1380036 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
1380070 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
1380103 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:1380578 original size:13 final size:13
Alignment explanation
Indices: 1380560--1380585 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1380550 CAATTTTTTG
1380560 TGTATCGATACAT
1 TGTATCGATACAT
1380573 TGTATCGATACAT
1 TGTATCGATACAT
1380586 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1380600 original size:32 final size:33
Alignment explanation
Indices: 1380540--1380603 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1380530 TACAAGCCAA
** *
1380540 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
1380573 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
1380604 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:1381159 original size:47 final size:46
Alignment explanation
Indices: 1381096--1381269 Score: 219
Period size: 47 Copynumber: 3.7 Consensus size: 46
1381086 TAAAGACAAA
1381096 GTGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTCGTGAGAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCT-GTGAGAAG
*
1381143 GTGCCAATATGCTGATTCAAGGCCAGTGATATTAGGCT-T-A-AAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTGTGAGAAG
* * *
1381186 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTAGTCTTAAAGATGAGAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTAGGC-T---G-TGAG-AAG
*
1381238 GTGCCAATATGCTGATTCAAGGCCAGCAATAT
1 GTGCCAATATGCTGATTCAAGGCCAGCGATAT
1381270 AGGGCTTAGA
Statistics
Matches: 110, Mismatches: 8, Indels: 13
0.84 0.06 0.10
Matches are distributed among these distances:
43 36 0.33
44 2 0.02
45 1 0.01
47 37 0.34
49 1 0.01
50 1 0.01
52 32 0.29
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.25
Consensus pattern (46 bp):
GTGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTGTGAGAAG
Found at i:1381164 original size:95 final size:94
Alignment explanation
Indices: 1381049--1381263 Score: 276
Period size: 95 Copynumber: 2.3 Consensus size: 94
1381039 ATTGGGCTTA
* *
1381049 TGCCAATGTGCTGATTCAAGGCCAGTGACATTACTCTTAAAGACAAAGTGCCAATATGCTGATTC
1 TGCCAATATGCTGATTCAAGGCCAGTGACATTACGCTTAAAG-----GTGCCAATATGCTGATTC
* *
1381114 AAGGCCAGCGATATTAGGC-T-CG-TGAG-AAGG
61 AAGGCCAGCGACATTAGGCTTAAGATGAGAAAGG
* * *
1381144 TGCCAATATGCTGATTCAAGGCCAGTGATATTAGGCTTAAAGGTGCCAATGTGCTGATTCAAGGC
1 TGCCAATATGCTGATTCAAGGCCAGTGACATTACGCTTAAAGGTGCCAATATGCTGATTCAAGGC
*
1381209 CAGCGACATTAGTCTTAAAGATGAGAAAGG
66 CAGCGACATTAGGCTT-AAGATGAGAAAGG
1381239 TGCCAATATGCTGATTCAAGGCCAG
1 TGCCAATATGCTGATTCAAGGCCAG
1381264 CAATATAGGG
Statistics
Matches: 107, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
90 34 0.32
91 1 0.01
93 1 0.01
94 4 0.04
95 67 0.63
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.25
Consensus pattern (94 bp):
TGCCAATATGCTGATTCAAGGCCAGTGACATTACGCTTAAAGGTGCCAATATGCTGATTCAAGGC
CAGCGACATTAGGCTTAAGATGAGAAAGG
Found at i:1381276 original size:95 final size:91
Alignment explanation
Indices: 1381096--1381282 Score: 252
Period size: 95 Copynumber: 2.0 Consensus size: 91
1381086 TAAAGACAAA
* *
1381096 GTGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTCGTGAGAAGGTGCCAATATGCTGATTC
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTAGGCTAGTGAGAAGGTGCCAATATGCTGATTC
**
1381161 AAGGCCAGTGATATTAGGCTTA-AAG
66 AAGGCCAGCAATATTAGGCTTAGAAG
* *
1381186 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTAGTCTTAAAGATGAGAAAGGTGCCAATATGCT
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTAGGC-T--AG-TGAG-AAGGTGCCAATATGCT
1381251 GATTCAAGGCCAGCAATA-TAGGGCTTAGAAG
61 GATTCAAGGCCAGCAATATTA-GGCTTAGAAG
1381282 G
1 G
1381283 GTTGCCACCG
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
90 34 0.40
91 1 0.01
93 1 0.01
94 6 0.07
95 38 0.45
96 4 0.05
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (91 bp):
GTGCCAATATGCTGATTCAAGGCCAGCGACATTAGGCTAGTGAGAAGGTGCCAATATGCTGATTC
AAGGCCAGCAATATTAGGCTTAGAAG
Found at i:1381310 original size:31 final size:31
Alignment explanation
Indices: 1381271--1381347 Score: 111
Period size: 33 Copynumber: 2.5 Consensus size: 31
1381261 CAGCAATATA
1381271 GGGC-TTAGAAGGGTTGCCACCGACTTGTGT
1 GGGCTTTAGAAGGGTTGCCACCGACTTGTGT
* *
1381301 GGGTTTTAGAGAATGGTTGCCACCGACTTGTGT
1 GGGCTTT--AGAAGGGTTGCCACCGACTTGTGT
1381334 GGGCTTTAGAAGGG
1 GGGCTTTAGAAGGG
1381348 GGTGCCACGA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
30 3 0.08
31 8 0.20
33 29 0.73
ACGTcount: A:0.18, C:0.16, G:0.38, T:0.29
Consensus pattern (31 bp):
GGGCTTTAGAAGGGTTGCCACCGACTTGTGT
Found at i:1381319 original size:33 final size:33
Alignment explanation
Indices: 1381277--1381343 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
1381267 TATAGGGCTT
*
1381277 AGAAGGGTTGCCACCGACTTGTGTGGGTTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
1381310 AGAATGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1381343 A
1 A
1381344 AGGGGGTGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.19, C:0.16, G:0.34, T:0.30
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:1381413 original size:32 final size:33
Alignment explanation
Indices: 1381347--1381435 Score: 92
Period size: 32 Copynumber: 2.7 Consensus size: 33
1381337 CTTTAGAAGG
* * *
1381347 GGGTGCCACGAAGTTGTGGACTTAAAAGGAAAA
1 GGGTGCCACGGAGTTATGGGCTTAAAAGGAAAA
*
1381380 -GGTGCCACGGAGTTATGGGCTT-ACAGGAGAAA
1 GGGTGCCACGGAGTTATGGGCTTAAAAGGA-AAA
* *
1381412 GGGATGCCACAGAGGTATGGGCTT
1 GGG-TGCCACGGAGTTATGGGCTT
1381436 TTGGAAAAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
31 5 0.11
32 22 0.47
33 2 0.04
34 18 0.38
ACGTcount: A:0.29, C:0.15, G:0.37, T:0.19
Consensus pattern (33 bp):
GGGTGCCACGGAGTTATGGGCTTAAAAGGAAAA
Found at i:1381594 original size:109 final size:110
Alignment explanation
Indices: 1381349--1381657 Score: 410
Period size: 109 Copynumber: 2.8 Consensus size: 110
1381339 TTAGAAGGGG
* ** * *
1381349 GTGCCACGAAGTTGTGGACTTAAAAGG-AAAAGGTGCCACGGAGTTATGGGCTTACAGGAGAAAG
1 GTGCCACGGAGTTGTGGACTTAACTGGAAAAAAGTGCCACGGAGTTGTGGGCTTA-A--AG-AAG
** * * *
1381413 GGATGCCACAGAGGT-ATGGGCTTTT-GGAAAAAGATGCATAGGAAAAAAAA
62 AAATGCCACTGA-GTCAT-GGATTTTGGGAAAAAGATGCACAGG-AAAAAAA
*
1381463 GTGCCACAGAGTTGTGGACTTAACTGGAAAAAAGTGCCACGGAGTTGTGGGCTTAAAGAAGAAAT
1 GTGCCACGGAGTTGTGGACTTAACTGGAAAAAAGTGCCACGGAGTTGTGGGCTTAAAGAAGAAAT
*
1381528 GCCATTGAGTCATGGATTTTGGGAAAAAGATGCACAGG-AAAAAA
66 GCCACTGAGTCATGGATTTTGGGAAAAAGATGCACAGGAAAAAAA
1381572 GTGCCACGGAGTTGTGGACTTAACTGGAAAAAAGTGCCACGGAGTTGTGGGCTTAAAGAAGAAAT
1 GTGCCACGGAGTTGTGGACTTAACTGGAAAAAAGTGCCACGGAGTTGTGGGCTTAAAGAAGAAAT
*
1381637 GCCACTGAGTCATGGACTTTG
66 GCCACTGAGTCATGGATTTTG
1381658 AAGAAAAGAC
Statistics
Matches: 177, Mismatches: 15, Indels: 11
0.87 0.07 0.05
Matches are distributed among these distances:
109 89 0.50
110 8 0.05
111 29 0.16
112 2 0.01
114 24 0.14
115 25 0.14
ACGTcount: A:0.35, C:0.14, G:0.31, T:0.21
Consensus pattern (110 bp):
GTGCCACGGAGTTGTGGACTTAACTGGAAAAAAGTGCCACGGAGTTGTGGGCTTAAAGAAGAAAT
GCCACTGAGTCATGGATTTTGGGAAAAAGATGCACAGGAAAAAAA
Found at i:1381606 original size:33 final size:33
Alignment explanation
Indices: 1381564--1381627 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
1381554 AAGATGCACA
1381564 GGAAAAAAGTGCCACGGAGTTGTGGACTTAACT
1 GGAAAAAAGTGCCACGGAGTTGTGGACTTAACT
*
1381597 GGAAAAAAGTGCCACGGAGTTGTGGGCTTAA
1 GGAAAAAAGTGCCACGGAGTTGTGGACTTAA
1381628 AGAAGAAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.14, G:0.33, T:0.20
Consensus pattern (33 bp):
GGAAAAAAGTGCCACGGAGTTGTGGACTTAACT
Found at i:1381672 original size:31 final size:31
Alignment explanation
Indices: 1381627--1381781 Score: 188
Period size: 31 Copynumber: 4.9 Consensus size: 31
1381617 TGTGGGCTTA
1381627 AAGAAGAA-ATGCCACTGAGTCATGGACTTTG
1 AAGAA-AAGATGCCACTGAGTCATGGACTTTG
* *
1381658 AAGAAAAGACGCCACTGAGTCGTGGACTTTG
1 AAGAAAAGATGCCACTGAGTCATGGACTTTG
* * *
1381689 -GGAACAGATTGCCACTGAGTCATGGACTTTC
1 AAGAAAAGA-TGCCACTGAGTCATGGACTTTG
*
1381720 AAGAAAGAAGATGCCACTGAGTCATGGACTTGG
1 AAG-AA-AAGATGCCACTGAGTCATGGACTTTG
* *
1381753 AAGAAAAAATGCCACTGAGTCGTGGACTT
1 AAGAAAAGATGCCACTGAGTCATGGACTT
1381782 AAAAAAGAGA
Statistics
Matches: 106, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
30 8 0.08
31 67 0.63
32 3 0.03
33 25 0.24
34 3 0.03
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.21
Consensus pattern (31 bp):
AAGAAAAGATGCCACTGAGTCATGGACTTTG
Found at i:1381769 original size:64 final size:63
Alignment explanation
Indices: 1381627--1381781 Score: 199
Period size: 64 Copynumber: 2.5 Consensus size: 63
1381617 TGTGGGCTTA
* * *
1381627 AAGAAGAAATGCCACTGAGTCATGGACTTTGAAGAAAAGACGCCACTGAGTCGTGGACTTTGG
1 AAGAAAAAATGCCACTGAGTCATGGACTTTCAAGAAAAGACGCCACTGAGTCATGGACTTTGG
* * *
1381690 --GAACAGATTGCCACTGAGTCATGGACTTTCAAGAAAGAAGATGCCACTGAGTCATGGAC-TTG
1 AAGAA-AAAATGCCACTGAGTCATGGACTTTCAAG-AA-AAGACGCCACTGAGTCATGGACTTTG
1381752 G
63 G
*
1381753 AAGAAAAAATGCCACTGAGTCGTGGACTT
1 AAGAAAAAATGCCACTGAGTCATGGACTT
1381782 AAAAAAGAGA
Statistics
Matches: 78, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
61 3 0.04
62 25 0.32
63 6 0.08
64 41 0.53
65 3 0.04
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.21
Consensus pattern (63 bp):
AAGAAAAAATGCCACTGAGTCATGGACTTTCAAGAAAAGACGCCACTGAGTCATGGACTTTGG
Found at i:1383029 original size:6 final size:6
Alignment explanation
Indices: 1383020--1383061 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
1383010 TTTGCACTTT
1383020 TTTTTG TTTTTG TTTTTG TTGTTT- TTTTTG TGTTTT- TTTTTG
1 TTTTTG TTTTTG TTTTTG TT-TTTG TTTTTG T-TTTTG TTTTTG
1383062 GTGTTTGTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
5 7 0.22
6 18 0.56
7 7 0.22
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (6 bp):
TTTTTG
Found at i:1383035 original size:12 final size:11
Alignment explanation
Indices: 1383017--1383061 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 11
1383007 GCCTTTGCAC
1383017 TTTTTTTTGTT
1 TTTTTTTTGTT
1383028 TTTGTTTTTGTT
1 TTT-TTTTTGTT
1383040 GTTTTTTTTGTGT
1 -TTTTTTTTGT-T
1383053 TTTTTTTTG
1 TTTTTTTTG
1383062 GTGTTTGTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.10
12 24 0.77
13 4 0.13
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (11 bp):
TTTTTTTTGTT
Found at i:1383035 original size:15 final size:15
Alignment explanation
Indices: 1383017--1383058 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1383007 GCCTTTGCAC
*
1383017 TTTTTTTTGTTTTTG
1 TTTTTGTTGTTTTTG
1383032 TTTTTGTTGTTTTT-
1 TTTTTGTTGTTTTTG
*
1383046 TTTGTGTT-TTTTT
1 TTTTTGTTGTTTTT
1383059 TTGGTGTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 5 0.20
14 7 0.28
15 13 0.52
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (15 bp):
TTTTTGTTGTTTTTG
Found at i:1383037 original size:24 final size:24
Alignment explanation
Indices: 1383010--1383061 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1383000 TGATTTTGCC
1383010 TTTGCACTTTTTTTTGT-TTTTGTT
1 TTTGCACTTTTTTTTGTGTTTT-TT
***
1383034 TTTGTTGTTTTTTTTGTGTTTTTT
1 TTTGCACTTTTTTTTGTGTTTTTT
1383058 TTTG
1 TTTG
1383062 GTGTTTGTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.02, C:0.04, G:0.15, T:0.79
Consensus pattern (24 bp):
TTTGCACTTTTTTTTGTGTTTTTT
Found at i:1383066 original size:24 final size:24
Alignment explanation
Indices: 1383017--1383067 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
1383007 GCCTTTGCAC
*
1383017 TTTTTTTTGTTTTTGTTTTTGTTG
1 TTTTTTTTGTTTTTGTTTTTGGTG
1383041 TTTTTTTTGTGTTTT-TTTTTGGTG
1 TTTTTTTTGT-TTTTGTTTTTGGTG
1383065 TTT
1 TTT
1383068 GTACTTTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (24 bp):
TTTTTTTTGTTTTTGTTTTTGGTG
Found at i:1394101 original size:42 final size:42
Alignment explanation
Indices: 1394055--1395337 Score: 768
Period size: 42 Copynumber: 30.4 Consensus size: 42
1394045 ACCCTTAGTG
** *
1394055 TGCCTGTCGGCTTTGACTTTGGAGACTACCTCATCTTAAGTC
1 TGCCTGTCGGCTTTGACCCTGGAGACTTCCTCATCTTAAGTC
* * * *
1394097 TGCCTGTCGGCTTTGACCCTAGAGACTTTCCT-ACCCTCAGTC
1 TGCCTGTCGGCTTTGACCCTGGAGAC-TTCCTCATCTTAAGTC
* * * * * * *
1394139 TGTCTGTCGGCTTTGACCCTGAAGGCTACCTTATCTAAAGTT
1 TGCCTGTCGGCTTTGACCCTGGAGACTTCCTCATCTTAAGTC
* * *
1394181 TGCCTGTCGGCTTTGACCCTGGAGACTTTCCT-ACCCTCAA-TT
1 TGCCTGTCGGCTTTGACCCTGGAGAC-TTCCTCA-TCTTAAGTC
* * * *
1394223 TTCTTGTCGGCTTTGACCCTGGAGACTACCTCATCTAAAGTC
1 TGCCTGTCGGCTTTGACCCTGGAGACTTCCTCATCTTAAGTC
* * * * * * *
1394265 TGTCTGTCAGCATTGACCTTGGAGACTTTCCT-ACCCTCAGTC
1 TGCCTGTCGGCTTTGACCCTGGAGAC-TTCCTCATCTTAAGTC
* * * * *
1394307 TGCCTGTCGACTTTGACCCTAGAGACTGCCTTATCTAAAGTC
1 TGCCTGTCGGCTTTGACCCTGGAGACTTCCTCATCTTAAGTC
* * * * * *
1394349 TGCCTGTCGACTTTGACCTTGGAGACTT-TTCTACCCTCAGTC
1 TGCCTGTCGGCTTTGACCCTGGAGACTTCCTC-ATCTTAAGTC
** * * *
1394391 TGCCTGTCATCTTTGACCCTGGAGACTGCCTTATTCTT-TGTC
1 TGCCTGTCGGCTTTGACCCTGGAGACTTCCTCA-TCTTAAGTC
* * * * * * *
1394433 TAG-CTATTGACTTTGACCCTAGAGACTGCCTTAT-TCAAAGTC
1 T-GCCTGTCGGCTTTGACCCTGGAGACTTCCTCATCT-TAAGTC
* * * * *
1394475 TGCCTATCAGCTTTGACCTTGGAGACTGCCTCATCTAAAGTC
1 TGCCTGTCGGCTTTGACCCTGGAGACTTCCTCATCTTAAGTC
* * * * *
1394517 TGCTTGTTGGCTTTGACCTTGGAGACTTTTCTTC-CCTT-AGTC
1 TGCCTGTCGGCTTTGACCCTGGAGAC--TTCCTCATCTTAAGTC
* * * * *
1394559 TGCCTGTCAGCTCTGACCCTGAAGACTACCTTAT-TCTAAGTC
1 TGCCTGTCGGCTTTGACCCTGGAGACTTCCTCATCT-TAAGTC
* * * *** *
1394601 TGCTTGTCGGCTTTGACCTTGGAGACTTTCTTGCCTTCAA-TT
1 TGCCTGTCGGCTTTGACCCTGGAGACTTCCTCATCTT-AAGTC
* * * *
1394643 TACCTGTCGGCTTTGACCCTAGAGACTGCCTCAATC-TAAATC
1 TGCCTGTCGGCTTTGACCCTGGAGACTTCCTC-ATCTTAAGTC
* * * * * * *
1394685 TGCTTGTTGGCTTTGACCTTAGAGACTTTCCT-ACCCTCAGTC
1 TGCCTGTCGGCTTTGACCCTGGAGAC-TTCCTCATCTTAAGTC
* * * *
1394727 TGCCTATCGGCTTTGACCCTGGAGACTGCGTCATTTTAAGTC
1 TGCCTGTCGGCTTTGACCCTGGAGACTTCCTCATCTTAAGTC
* * *
1394769 TGCCTGTCGGCTTTGACCCTAGAGACTT-TTCTATCCCTCAA-TC
1 TGCCTGTCGGCTTTGACCCTGGAGACTTCCTC-AT--CTTAAGTC
* * * * * *
1394812 TGCCTGTCGGCTTTGACCTTAGAGACTT-TTCTACCCTCAGTC
1 TGCCTGTCGGCTTTGACCCTGGAGACTTCCTC-ATCTTAAGTC
* * * * *
1394854 TGCCTGTCGACTTTGACCTTAGAGACTACCTTAT-TCTAAGTC
1 TGCCTGTCGGCTTTGACCCTGGAGACTTCCTCATCT-TAAGTC
* * * * *
1394896 TGCCTATCGGCTTTGACCCTGGAGACTTTCCT-ACCCTCAGTT
1 TGCCTGTCGGCTTTGACCCTGGAGAC-TTCCTCATCTTAAGTC
** * * * *
1394938 TGCCTGTCCACTTTGACCTTGGAGACTGCCTCGTTTTAAGTC
1 TGCCTGTCGGCTTTGACCCTGGAGACTTCCTCATCTTAAGTC
* *
1394980 TGGCC-GTCGGCTTTGACCCTAGAGACTTTCCT-ACCCTT-AGTC
1 T-GCCTGTCGGCTTTGACCCTGGAGAC-TTCCTCA-TCTTAAGTC
* * * *
1395022 TGCCTGTCGACTTTGACCCTAGAGACCTTTCT-ACCCTT-AGTC
1 TGCCTGTCGGCTTTGACCCTGGAGA-CTTCCTCA-TCTTAAGTC
* * * * *
1395064 TGCCTGTCGACTTTGACCTTGGAGACTACCTCATTTTAAAGTT
1 TGCCTGTCGGCTTTGACCCTGGAGACTTCCTCATCTT-AAGTC
* * *
1395107 TGCCTGTCGGCTTTGACCTTGGAGACTACCTCATTTTAAAGTC
1 TGCCTGTCGGCTTTGACCCTGGAGACTTCCTCATCTT-AAGTC
* * *
1395150 TGTCTGTCAGCTTTGACCCTGGAGACTTTCCT-ATCCCTAAGTC
1 TGCCTGTCGGCTTTGACCCTGGAGAC-TTCCTCAT-CTTAAGTC
* * * *
1395193 TGCCTATCGGCTTTGACCCTGGAGACCTTTCT-ACCCTT-AGTT
1 TGCCTGTCGGCTTTGACCCTGGAGA-CTTCCTCA-TCTTAAGTC
* * ** *
1395235 TGCCTGTCAGCTTTGACCCTGGAGACCTTCCT-ATCCCTCGGTA
1 TGCCTGTCGGCTTTGACCCTGGAGA-CTTCCTCAT-CTTAAGTC
* * * * *
1395278 TACCTGTCGGCTTTGACCCTGGAGACTGCCTTATCTAAAGGC
1 TGCCTGTCGGCTTTGACCCTGGAGACTTCCTCATCTTAAGTC
*
1395320 TGCCTGTCTGCTTTGACC
1 TGCCTGTCGGCTTTGACC
1395338 TAGGAGAATC
Statistics
Matches: 962, Mismatches: 227, Indels: 104
0.74 0.18 0.08
Matches are distributed among these distances:
40 5 0.01
41 44 0.05
42 690 0.72
43 210 0.22
44 13 0.01
ACGTcount: A:0.17, C:0.29, G:0.19, T:0.35
Consensus pattern (42 bp):
TGCCTGTCGGCTTTGACCCTGGAGACTTCCTCATCTTAAGTC
Found at i:1394185 original size:84 final size:83
Alignment explanation
Indices: 1394032--1395304 Score: 963
Period size: 84 Copynumber: 15.1 Consensus size: 83
1394022 TTAAACTATC
* * ** *
1394032 TGGAGACTTTCCTACCCTTAGTGTGCCTGTCGGCTTTGACTTTGGAGACTACCTCATCTTAAGTC
1 TGGAGACTTTCCTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTACCTTATC-TAAGTC
*
1394097 TGCCTGTCGGCTTTGACCC
65 TGCCTGTCGGCTTTGACCT
* * * * *
1394116 TAGAGACTTTCCTACCCTCAGTCTGTCTGTCGGCTTTGACCCTGAAGGCTACCTTATCTAAAGTT
1 TGGAGACTTTCCTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTACCTTATCT-AAGTC
*
1394181 TGCCTGTCGGCTTTGACCC
65 TGCCTGTCGGCTTTGACCT
* * * * *
1394200 TGGAGACTTTCCTACCCTCAATTTTCTTGTCGGCTTTGACCCTGGAGACTACCTCATCTAAAGTC
1 TGGAGACTTTCCTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTACCTTATCT-AAGTC
* * *
1394265 TGTCTGTCAGCATTGACCT
65 TGCCTGTCGGCTTTGACCT
* * *
1394284 TGGAGACTTTCCTACCCTCAGTCTGCCTGTCGACTTTGACCCTAGAGACTGCCTTATCTAAAGTC
1 TGGAGACTTTCCTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTACCTTATCT-AAGTC
*
1394349 TGCCTGTCGACTTTGACCT
65 TGCCTGTCGGCTTTGACCT
* ** * **
1394368 TGGAGACTTTTCTACCCTCAGTCTGCCTGTCATCTTTGACCCTGGAGACTGCCTTATTCTTTGTC
1 TGGAGACTTTCCTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTACCTTA-TCTAAGTC
* * * *
1394433 TAG-CTATTGACTTTGACCC
65 T-GCCTGTCGGCTTTGACCT
* * ** ** * * * * *
1394452 TAGAGAC-TGCCTTATTCAAAGTCTGCCTATCAGCTTTGACCTTGGAGACTGCCTCATCTAAAGT
1 TGGAGACTTTCC-TACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTACCTTATCT-AAGT
* *
1394516 CTGCTTGTTGGCTTTGACCT
64 CTGCCTGTCGGCTTTGACCT
* * * * * *
1394536 TGGAGACTTTTCTTCCCTTAGTCTGCCTGTCAGCTCTGACCCTGAAGACTACCTTATTCTAAGTC
1 TGGAGACTTTCCTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTACCTTA-TCTAAGTC
*
1394601 TGCTTGTCGGCTTTGACCT
65 TGCCTGTCGGCTTTGACCT
* * * * * * * * * *
1394620 TGGAGACTTTCTTGCCTTCAATTTACCTGTCGGCTTTGACCCTAGAGACTGCCTCAATCTAAATC
1 TGGAGACTTTCCTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTACCT-TATCTAAGTC
* *
1394685 TGCTTGTTGGCTTTGACCT
65 TGCCTGTCGGCTTTGACCT
* * * * * *
1394704 TAGAGACTTTCCTACCCTCAGTCTGCCTATCGGCTTTGACCCTGGAGACTGCGTCATTTTAAGTC
1 TGGAGACTTTCCTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTACCTTA-TCTAAGTC
*
1394769 TGCCTGTCGGCTTTGACCC
65 TGCCTGTCGGCTTTGACCT
* * * * * ** * *
1394788 TAGAGACTTTTCTATCCCTCAATCTGCCTGTCGGCTTTGACCTTAGAGACT-TTTCTACCCTCAG
1 TGGAGACTTTCCTA-CCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTACCT-TA-TCTAAG
*
1394852 TCTGCCTGTCGACTTTGACCT
63 TCTGCCTGTCGGCTTTGACCT
* * ** * * * * *
1394873 TAGAGAC-TACCTTATTCTAAGTCTGCCTATCGGCTTTGACCCTGGAGACTTTCC-TACCCTCAG
1 TGGAGACTTTCC-TACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TACCTTA-TCTAAG
* **
1394936 TTTGCCTGTCCACTTTGACCT
63 TCTGCCTGTCGGCTTTGACCT
* ** * * * * *
1394957 TGGAGAC-TGCCT-CGTTTTAAGTCTGGCC-GTCGGCTTTGACCCTAGAGACTTTCC-TACCCTT
1 TGGAGACTTTCCTAC--CCTCAGTCT-GCCTGTCGGCTTTGACCCTGGAGAC-TACCTTA-TCTA
* *
1395018 AGTCTGCCTGTCGACTTTGACCC
61 AGTCTGCCTGTCGGCTTTGACCT
* * * * * *
1395041 TAGAGACCTTT-CTACCCTTAGTCTGCCTGTCGACTTTGACCTTGGAGACTACCTCATTTTAAAG
1 TGGAGA-CTTTCCTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTACCTTA-TCT-AAG
*
1395105 TTTGCCTGTCGGCTTTGACCT
63 TCTGCCTGTCGGCTTTGACCT
* *** * * * *
1395126 TGGAGAC-TACCTCATTTTAAAGTCTGTCTGTCAGCTTTGACCCTGGAGACTTTCC-TATCCCTA
1 TGGAGACTTTCCT-ACCCT-CAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TACCTTAT--CTA
* *
1395189 AGTCTGCCTATCGGCTTTGACCC
61 AGTCTGCCTGTCGGCTTTGACCT
* * * * **
1395212 TGGAGACCTTT-CTACCCTTAGTTTGCCTGTCAGCTTTGACCCTGGAGACCTTCC-TATCCCTCG
1 TGGAGA-CTTTCCTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGA-CTACCTTAT--CTAA
* * *
1395275 GTATACCTGTCGGCTTTGACCC
62 GTCTGCCTGTCGGCTTTGACCT
1395297 TGGAGACT
1 TGGAGACT
1395305 GCCTTATCTA
Statistics
Matches: 965, Mismatches: 191, Indels: 66
0.79 0.16 0.05
Matches are distributed among these distances:
83 16 0.02
84 710 0.74
85 172 0.18
86 59 0.06
87 7 0.01
88 1 0.00
ACGTcount: A:0.17, C:0.29, G:0.19, T:0.35
Consensus pattern (83 bp):
TGGAGACTTTCCTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTACCTTATCTAAGTCT
GCCTGTCGGCTTTGACCT
Found at i:1394311 original size:126 final size:126
Alignment explanation
Indices: 1394031--1395304 Score: 845
Period size: 126 Copynumber: 10.1 Consensus size: 126
1394021 GTTAAACTAT
* * ** * * *
1394031 CTGGAGACTTTCCTACCCTTAGTGTGCCTGTCGGCTTTGACTTTGGAGACTACCT-CATCTTAAG
1 CTGGAGACTTTCCTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTCCTAC-CCTCAAG
* * * * * *
1394095 TCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCT-ACCCTCAGTCTGTCTGTCGGCTTTGACC
65 TCTGCCTGTCGGCTTTGACCTTGGAGAC-TACCTCACTCTAAGTCTGCCTGTCGGCTTTGACC
* * * * * *
1394157 CTGAAGGC-TACCTTA-TCTAAAGTTTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTACCCTCA
1 CTGGAGACTTTCC-TACCCT-CAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTCCTACCCTCA
* * * * * * *
1394220 A-TTTTCTTGTCGGCTTTGACCCTGGAGACTACCTCA-TCTAAAGTCTGTCTGTCAGCATTGACC
63 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTACCTCACTCT-AAGTCTGCCTGTCGGCTTTGACC
* * * * * *
1394283 TTGGAGACTTTCCTACCCTCAGTCTGCCTGTCGACTTTGACCCTAGAGACTGCCTTA-TCTAAAG
1 CTGGAGACTTTCCTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTCC-TACCCTCAAG
* ** * * **
1394347 TCTGCCTGTCGACTTTGACCTTGGAGACT-TTTCTACCCTCAGTCTGCCTGTCATCTTTGACC
65 TCTGCCTGTCGGCTTTGACCTTGGAGACTACCTC-ACTCTAAGTCTGCCTGTCGGCTTTGACC
* ** ** * * * * * *
1394409 CTGGAGAC-TGCCTTATTCTTTGTCTAG-CTATTGACTTTGACCCTAGAGACTGCCTTA--TTCA
1 CTGGAGACTTTCC-TACCCTCAGTCT-GCCTGTCGGCTTTGACCCTGGAGACTTCC-TACCCTC-
* * * * *
1394470 AAGTCTGCCTATCAGCTTTGACCTTGGAGACTGCCTCA-TCTAAAGTCTGCTTGTTGGCTTTGAC
62 AAGTCTGCCTGTCGGCTTTGACCTTGGAGACTACCTCACTCT-AAGTCTGCCTGTCGGCTTTGAC
1394534 C
126 C
* * * * * * * * **
1394535 TTGGAGACTTTTCTTCCCTTAGTCTGCCTGTCAGCTCTGACCCTGAAGACTACCTTATTCT-AAG
1 CTGGAGACTTTCCTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTCC-TACCCTCAAG
* * * * *
1394599 TCTGCTTGTCGGCTTTGACCTTGGAGACTTTCTTGC-CT-TCAA-TTTACCTGTCGGCTTTGACC
65 TCTGCCTGTCGGCTTTGACCTTGGAGAC-TACCT-CACTCT-AAGTCTGCCTGTCGGCTTTGACC
* * ** * * * * * *
1394661 CTAGAGAC-TGCCTCAATCTAAATCTGCTTGTTGGCTTTGACCTTAGAGACTTTCCTACCCTC-A
1 CTGGAGACTTTCCT-ACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTCCTACCCTCAA
* * * * * *
1394724 GTCTGCCTATCGGCTTTGACCCTGGAGACTGCGTCATTTTAAGTCTGCCTGTCGGCTTTGACC
64 GTCTGCCTGTCGGCTTTGACCTTGGAGACTACCTCACTCTAAGTCTGCCTGTCGGCTTTGACC
* * * * * *
1394787 CTAGAGACTTTTCTATCCCTCAATCTGCCTGTCGGCTTTGACCTTAGAGACTTTTCTACCCTC-A
1 CTGGAGACTTTCCTA-CCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTCCTACCCTCAA
* * * * *
1394851 GTCTGCCTGTCGACTTTGACCTTAGAGACTACCTTATTCTAAGTCTGCCTATCGGCTTTGACC
64 GTCTGCCTGTCGGCTTTGACCTTGGAGACTACCTCACTCTAAGTCTGCCTGTCGGCTTTGACC
* ** * * ** *
1394914 CTGGAGACTTTCCTACCCTCAGTTTGCCTGTCCACTTTGACCTTGGAGACTGCCT-CGTTTTAAG
1 CTGGAGACTTTCCTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTCCTAC-CCTCAAG
* * * * * *
1394978 TCTGGCC-GTCGGCTTTGACCCTAGAGACTTTCCT-ACCCTTAGTCTGCCTGTCGACTTTGACC
65 TCT-GCCTGTCGGCTTTGACCTTGGAGAC-TACCTCACTCTAAGTCTGCCTGTCGGCTTTGACC
* * * * * *** *
1395040 CTAGAGACCTTT-CTACCCTTAGTCTGCCTGTCGACTTTGACCTTGGAGACTACCTCATTTTAAA
1 CTGGAGA-CTTTCCTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTCCT-ACCCTCAA
* * * * *
1395104 GTTTGCCTGTCGGCTTTGACCTTGGAGACTACCTCATTTTAAAGTCTGTCTGTCAGCTTTGACC
64 GTCTGCCTGTCGGCTTTGACCTTGGAGACTACCTCACTCT-AAGTCTGCCTGTCGGCTTTGACC
* * * *
1395168 CTGGAGACTTTCCTATCCCTAAGTCTGCCTATCGGCTTTGACCCTGGAGACCTTTCTACCCT-TA
1 CTGGAGACTTTCCTA-CCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGA-CTTCCTACCCTCAA
* * * * * ** * *
1395232 GTTTGCCTGTCAGCTTTGACCCTGGAGACCTTCCT-ATCCCTCGGTATACCTGTCGGCTTTGACC
64 GTCTGCCTGTCGGCTTTGACCTTGGAGA-CTACCTCA-CTCTAAGTCTGCCTGTCGGCTTTGACC
1395296 CTGGAGACT
1 CTGGAGACT
1395305 GCCTTATCTA
Statistics
Matches: 905, Mismatches: 196, Indels: 92
0.76 0.16 0.08
Matches are distributed among these distances:
124 2 0.00
125 40 0.04
126 550 0.61
127 185 0.20
128 86 0.10
129 38 0.04
130 4 0.00
ACGTcount: A:0.17, C:0.29, G:0.19, T:0.35
Consensus pattern (126 bp):
CTGGAGACTTTCCTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTCCTACCCTCAAGT
CTGCCTGTCGGCTTTGACCTTGGAGACTACCTCACTCTAAGTCTGCCTGTCGGCTTTGACC
Found at i:1396578 original size:30 final size:30
Alignment explanation
Indices: 1396544--1396639 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
1396534 TGACAGCAAC
1396544 AACAGTAGCTCCAACAAGTAGGCAAGCACG
1 AACAGTAGCTCCAACAAGTAGGCAAGCACG
* *
1396574 AACAGTAGC-CAAACAA-TA-GCACGACAGCAG
1 AACAGTAGCTCCAACAAGTAGGCAAG-CA-C-G
* * * *
1396604 CAACAGCAACTCCAACAAGCAGGCAAGCATG
1 -AACAGTAGCTCCAACAAGTAGGCAAGCACG
1396635 AACAG
1 AACAG
1396640 CAACGAAACA
Statistics
Matches: 51, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
27 4 0.08
28 4 0.08
29 7 0.14
30 15 0.29
31 8 0.16
32 6 0.12
33 3 0.06
34 4 0.08
ACGTcount: A:0.44, C:0.28, G:0.21, T:0.07
Consensus pattern (30 bp):
AACAGTAGCTCCAACAAGTAGGCAAGCACG
Found at i:1396694 original size:61 final size:61
Alignment explanation
Indices: 1396530--1396697 Score: 237
Period size: 61 Copynumber: 2.8 Consensus size: 61
1396520 ATAGCAGCTA
* * * * * *
1396530 AGCATGACAGCAACAACAGTAGCTCCAACAAGTAGGCAAGCACGAACAGTAGCCAAACAAT
1 AGCATGACAGCAGCAACAGCAGCTCCAACAAGTAGGCAAGCATGAACAGCAACCAAACAAC
* * * *
1396591 AGCACGACAGCAGCAACAGCAACTCCAACAAGCAGGCAAGCATGAACAGCAACGAAACAAC
1 AGCATGACAGCAGCAACAGCAGCTCCAACAAGTAGGCAAGCATGAACAGCAACCAAACAAC
*
1396652 AGCATGGCAGCAGCAACAGCAGCTCCAACAAGTAGGCAAGCATGAA
1 AGCATGACAGCAGCAACAGCAGCTCCAACAAGTAGGCAAGCATGAA
1396698 AAATGACCAA
Statistics
Matches: 93, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 93 1.00
ACGTcount: A:0.43, C:0.28, G:0.21, T:0.07
Consensus pattern (61 bp):
AGCATGACAGCAGCAACAGCAGCTCCAACAAGTAGGCAAGCATGAACAGCAACCAAACAAC
Found at i:1399196 original size:27 final size:27
Alignment explanation
Indices: 1399005--1399180 Score: 129
Period size: 27 Copynumber: 6.1 Consensus size: 27
1398995 TGCGACACAT
1399005 AACTCTGTGGCACCCTTTTAAAGTCCAC
1 AACTCTGTGGCACCCTTTT-AAGTCCAC
* * * * *
1399033 AACTCTATGGTATCCTTTAAAGTTCAC
1 AACTCTGTGGCACCCTTTTAAGTCCAC
* * *
1399060 AACTCCGTGGCACCCTTTCAAGTCCAT
1 AACTCTGTGGCACCCTTTTAAGTCCAC
*
1399087 AACT-TCGTGGCAACCTTTTCTGTTAAAGTCCAC
1 AACTCT-GTGGC-ACC----CT-TTTAAGTCCAC
*
1399120 AACTCCGTGGCACTTTCCTTTTTTAAGTCCAC
1 AACTCTGTGGCAC---CC--TTTTAAGTCCAC
*
1399152 AACTCTGTTGCACCCTTTTAAGTCCAC
1 AACTCTGTGGCACCCTTTTAAGTCCAC
1399179 AA
1 AA
1399181 GTTAGTGGCA
Statistics
Matches: 116, Mismatches: 19, Indels: 27
0.72 0.12 0.17
Matches are distributed among these distances:
27 50 0.43
28 18 0.16
29 2 0.02
31 1 0.01
32 25 0.22
33 19 0.16
35 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.13, T:0.32
Consensus pattern (27 bp):
AACTCTGTGGCACCCTTTTAAGTCCAC
Found at i:1399218 original size:28 final size:28
Alignment explanation
Indices: 1399184--1399737 Score: 527
Period size: 28 Copynumber: 19.8 Consensus size: 28
1399174 TCCACAAGTT
* ** *
1399184 AGTGGCACTCTTTCAAAGCTAATGAGAC
1 AGTGGCACCCTTTCAAAGCCCATGAGTC
*** **
1399212 AGTGGCATATTTTCAAAGCCCACAAGTC
1 AGTGGCACCCTTTCAAAGCCCATGAGTC
* *
1399240 AGTGGCACCCTTTAAAAGCCCATGAGTG
1 AGTGGCACCCTTTCAAAGCCCATGAGTC
* **
1399268 AGTGGCACCCTTT-TAAGCTGATGAGTC
1 AGTGGCACCCTTTCAAAGCCCATGAGTC
** **
1399295 AGTGGCACTATTTCAAAGCCCACAAGTC
1 AGTGGCACCCTTTCAAAGCCCATGAGTC
*
1399323 AGTGGCACCCTTTCAAAGCCCA-CAGTC
1 AGTGGCACCCTTTCAAAGCCCATGAGTC
* *
1399350 AGTGGCACCATTTCAAAGCCCATGAGTG
1 AGTGGCACCCTTTCAAAGCCCATGAGTC
* * *
1399378 AGTGGCATCTTTTCAAAGCCCATGAGTG
1 AGTGGCACCCTTTCAAAGCCCATGAGTC
** * * **
1399406 AGCAGCATCCTTTCAAAGCTCAAAAGTC
1 AGTGGCACCCTTTCAAAGCCCATGAGTC
* * *
1399434 TGTGGCATCCTTTCAAAGCCCACGAGTC
1 AGTGGCACCCTTTCAAAGCCCATGAGTC
*** * *
1399462 AGTGATGCCATTTCAAAAGCCCACGAGTC
1 AGTGGCACCCTTTC-AAAGCCCATGAGTC
*
1399491 AGTGGCACCCTTTCAAAGCCCATGAGTT
1 AGTGGCACCCTTTCAAAGCCCATGAGTC
*
1399519 AGTGGCATCCTTTCAAAGCCCATGAGTC
1 AGTGGCACCCTTTCAAAGCCCATGAGTC
* *
1399547 AGTGGCATCCTTTCAAAGCCCACGAGTC
1 AGTGGCACCCTTTCAAAGCCCATGAGTC
*** * *
1399575 AGTGATGCCATTTCAAAAGCCCACGAGTC
1 AGTGGCACCCTTTC-AAAGCCCATGAGTC
** *
1399604 AGTGGCACCCTTTCAAAGCCCACAAGCC
1 AGTGGCACCCTTTCAAAGCCCATGAGTC
*
1399632 AGTGGCACCATTTCAAAGCCCATGAGTC
1 AGTGGCACCCTTTCAAAGCCCATGAGTC
* * *
1399660 AGTGGCATCCTTTCAAAGCCAATGAGTT
1 AGTGGCACCCTTTCAAAGCCCATGAGTC
* * *
1399688 AGTGGCATCCTTTCAAAGCCCATAAGTT
1 AGTGGCACCCTTTCAAAGCCCATGAGTC
* ** *
1399716 ACTCACATCCTTTCAAAGCCCA
1 AGTGGCACCCTTTCAAAGCCCA
1399738 CAAGTTAGTC
Statistics
Matches: 436, Mismatches: 86, Indels: 8
0.82 0.16 0.02
Matches are distributed among these distances:
27 46 0.11
28 342 0.78
29 48 0.11
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.23
Consensus pattern (28 bp):
AGTGGCACCCTTTCAAAGCCCATGAGTC
Found at i:1399527 original size:113 final size:112
Alignment explanation
Indices: 1399184--1399709 Score: 573
Period size: 113 Copynumber: 4.7 Consensus size: 112
1399174 TCCACAAGTT
* * ** * *
1399184 AGTGGCACTCTTTCAAAG-CTAATGAGACAGTGGCATATTTTCAAAGCCCACAAGTCAGTGGCAC
1 AGTGGCAC-CTTTCAAAGCCCAA-GAGTCAGTGGCATCCTTTCAAAGCCCACGAGTCAGTGACAC
* * * * **
1399248 CCTTT-AAAAGCCCATGAGTGAGTGGCACCCTTT-TAAGCTGATGAGTC
64 CATTTCAAAAGCCCACGAGTCAGTGGCACCCTTTCAAAGCCCATGAGTC
* * *
1399295 AGTGGCACTATTTCAAAGCCCACA-AGTCAGTGGCACCCTTTCAAAGCCCAC-AGTCAGTGGCAC
1 AGTGGCAC-CTTTCAAAGCCCA-AGAGTCAGTGGCATCCTTTCAAAGCCCACGAGTCAGTGACAC
* * * * *
1399358 CATTTC-AAAGCCCATGAGTGAGTGGCATCTTTTCAAAGCCCATGAGTG
64 CATTTCAAAAGCCCACGAGTCAGTGGCACCCTTTCAAAGCCCATGAGTC
** * * * **
1399406 AGCAGCATCCTTTCAAAGCTCAAAAGTCTGTGGCATCCTTTCAAAGCCCACGAGTCAGTGATGCC
1 AGTGGCA-CCTTTCAAAGCCCAAGAGTCAGTGGCATCCTTTCAAAGCCCACGAGTCAGTGACACC
*
1399471 ATTTCAAAAGCCCACGAGTCAGTGGCACCCTTTCAAAGCCCATGAGTT
65 ATTTCAAAAGCCCACGAGTCAGTGGCACCCTTTCAAAGCCCATGAGTC
* **
1399519 AGTGGCATCCTTTCAAAGCCCATGAGTCAGTGGCATCCTTTCAAAGCCCACGAGTCAGTGATGCC
1 AGTGGCA-CCTTTCAAAGCCCAAGAGTCAGTGGCATCCTTTCAAAGCCCACGAGTCAGTGACACC
** *
1399584 ATTTCAAAAGCCCACGAGTCAGTGGCACCCTTTCAAAGCCCACAAGCC
65 ATTTCAAAAGCCCACGAGTCAGTGGCACCCTTTCAAAGCCCATGAGTC
* * * * *
1399632 AGTGGCACCATTTCAAAGCCCATGAGTCAGTGGCATCCTTTCAAAGCCAATGAGTTAGTGGCATC
1 AGTGGCACC-TTTCAAAGCCCAAGAGTCAGTGGCATCCTTTCAAAGCCCACGAGTCAGTGACA-C
1399697 C-TTTC-AAAGCCCA
64 CATTTCAAAAGCCCA
1399710 TAAGTTACTC
Statistics
Matches: 362, Mismatches: 43, Indels: 19
0.85 0.10 0.04
Matches are distributed among these distances:
110 42 0.12
111 91 0.25
112 28 0.08
113 199 0.55
114 2 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (112 bp):
AGTGGCACCTTTCAAAGCCCAAGAGTCAGTGGCATCCTTTCAAAGCCCACGAGTCAGTGACACCA
TTTCAAAAGCCCACGAGTCAGTGGCACCCTTTCAAAGCCCATGAGTC
Found at i:1399527 original size:141 final size:139
Alignment explanation
Indices: 1399222--1399738 Score: 637
Period size: 141 Copynumber: 3.7 Consensus size: 139
1399212 AGTGGCATAT
** * * * *
1399222 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTAAAAGCCCATGAGTGAGTGGCACCCTTT-TAAGC
1 TTTCAAAGCCCATGAGTCAGTGGCATCCTTTCAAAGCCCATGAGTGAGTGGCATCCTTTCAAAGC
** * * *
1399286 TGATGAGTCAGTGGCA-CTATTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAGTC
66 CCATAAGTCAGTGGCATC-CTTTCAAAGCCCACGAGTCAGTGGCACCCTTTCAAAGCCCACAGTC
1399350 AGTGGCACCA
130 AGTGGCACCA
* * **
1399360 TTTCAAAGCCCATGAGTGAGTGGCATCTTTTCAAAGCCCATGAGTGAGCAGCATCCTTTCAAAGC
1 TTTCAAAGCCCATGAGTCAGTGGCATCCTTTCAAAGCCCATGAGTGAGTGGCATCCTTTCAAAGC
* * * *** *
1399425 TCAAAAGTCTGTGGCATCCTTTCAAAGCCCACGAGTCAGTGATGCCATTTCAAAAGCCCACGAGT
66 CCATAAGTCAGTGGCATCCTTTCAAAGCCCACGAGTCAGTGGCACCCTTTC-AAAGCCCAC-AGT
*
1399490 CAGTGGCACCC
129 CAGTGGCACCA
* *
1399501 TTTCAAAGCCCATGAGTTAGTGGCATCCTTTCAAAGCCCATGAGTCAGTGGCATCCTTTCAAAGC
1 TTTCAAAGCCCATGAGTCAGTGGCATCCTTTCAAAGCCCATGAGTGAGTGGCATCCTTTCAAAGC
**
1399566 CCACGAGTCAGT-G-ATGCCATTTCAAAAGCCCACGAGTCAGTGGCACCCTTTCAAAGCCCACAA
66 CCATAAGTCAGTGGCAT-CC-TTTC-AAAGCCCACGAGTCAGTGGCACCCTTTCAAAGCCCAC-A
*
1399629 GCCAGTGGCACCA
127 GTCAGTGGCACCA
* *
1399642 TTTCAAAGCCCATGAGTCAGTGGCATCCTTTCAAAGCCAATGAGTTAGTGGCATCCTTTCAAAGC
1 TTTCAAAGCCCATGAGTCAGTGGCATCCTTTCAAAGCCCATGAGTGAGTGGCATCCTTTCAAAGC
* * **
1399707 CCATAAGTTACTCACATCCTTTCAAAGCCCAC
66 CCATAAGTCAGTGGCATCCTTTCAAAGCCCAC
1399739 AAGTTAGTCA
Statistics
Matches: 325, Mismatches: 45, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
138 50 0.15
139 45 0.14
140 22 0.07
141 180 0.55
142 26 0.08
143 2 0.01
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (139 bp):
TTTCAAAGCCCATGAGTCAGTGGCATCCTTTCAAAGCCCATGAGTGAGTGGCATCCTTTCAAAGC
CCATAAGTCAGTGGCATCCTTTCAAAGCCCACGAGTCAGTGGCACCCTTTCAAAGCCCACAGTCA
GTGGCACCA
Found at i:1399759 original size:113 final size:113
Alignment explanation
Indices: 1399161--1399771 Score: 503
Period size: 113 Copynumber: 5.5 Consensus size: 113
1399151 CAACTCTGTT
* * ** * * **
1399161 GCACCCTTT-TAAGTCCACAAGTTAGTGGCAC-T-CTTTCAAAGCTAATGAGACAGTGGCATATT
1 GCACCCTTTCAAAGCCCACAAGTTAGT--CACATCCTTTCAAAGCCCATAAGTCAGTGGCATCCT
* *** * * *
1399223 TTCAAAGCCCACAAGTCAGTGGCACCCTTT-AAAAGCCCATGAGTGAGTG
64 TTCAAAGCCCACGAGTCAGTGATGCCATTTCAAAAGCCCACGAGTCAGTG
* ** ** * * * *
1399272 GCACCCTTT-TAAGCTGATGAGTCAGTGGCAC-T-ATTTCAAAGCCCACAAGTCAGTGGCACCCT
1 GCACCCTTTCAAAGCCCACAAGTTAGT--CACATCCTTTCAAAGCCCATAAGTCAGTGGCATCCT
*** * *
1399334 TTCAAAGCCCAC-AGTCAGTGGCACCATTTC-AAAGCCCATGAGTGAGTG
64 TTCAAAGCCCACGAGTCAGTGATGCCATTTCAAAAGCCCACGAGTCAGTG
* * ** * * * *
1399382 GCATCTTTTCAAAGCCCATGAGTGAG-CAGCATCCTTTCAAAGCTCAAAAGTCTGTGGCATCCTT
1 GCACCCTTTCAAAGCCCACAAGTTAGTCA-CATCCTTTCAAAGCCCATAAGTCAGTGGCATCCTT
1399446 TCAAAGCCCACGAGTCAGTGATGCCATTTCAAAAGCCCACGAGTCAGTG
65 TCAAAGCCCACGAGTCAGTGATGCCATTTCAAAAGCCCACGAGTCAGTG
** ** *
1399495 GCACCCTTTCAAAGCCCATGAGTTAGTGGCATCCTTTCAAAGCCCATGAGTCAGTGGCATCCTTT
1 GCACCCTTTCAAAGCCCACAAGTTAGTCACATCCTTTCAAAGCCCATAAGTCAGTGGCATCCTTT
1399560 CAAAGCCCACGAGTCAGTGATGCCATTTCAAAAGCCCACGAGTCAGTG
66 CAAAGCCCACGAGTCAGTGATGCCATTTCAAAAGCCCACGAGTCAGTG
** ** *
1399608 GCACCCTTTCAAAGCCCACAAGCCAGTGGCA-CCATTTCAAAGCCCATGAGTCAGTGGCATCCTT
1 GCACCCTTTCAAAGCCCACAAGTTAGTCACATCC-TTTCAAAGCCCATAAGTCAGTGGCATCCTT
* * * ** * * *
1399672 TCAAAGCCAATGAGTTAGTGGCAT-CC-TTTC-AAAGCCCATAAGTTACTC
65 TCAAAGCCCACGAGTCAGT-G-ATGCCATTTCAAAAGCCCACGAGTCAGTG
* * * * *
1399720 ACATCCTTTCAAAGCCCACAAGTTAGTCATATCCGTTTCAAGGCCCACAAGT
1 GCACCCTTTCAAAGCCCACAAGTTAGTCACATCC-TTTCAAAGCCCATAAGT
1399772 TAGAGAGTCA
Statistics
Matches: 424, Mismatches: 64, Indels: 22
0.83 0.13 0.04
Matches are distributed among these distances:
108 2 0.00
109 1 0.00
110 42 0.10
111 108 0.25
112 54 0.13
113 212 0.50
114 3 0.01
115 2 0.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (113 bp):
GCACCCTTTCAAAGCCCACAAGTTAGTCACATCCTTTCAAAGCCCATAAGTCAGTGGCATCCTTT
CAAAGCCCACGAGTCAGTGATGCCATTTCAAAAGCCCACGAGTCAGTG
Found at i:1400824 original size:13 final size:13
Alignment explanation
Indices: 1400806--1400830 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1400796 CTGCCAGTTT
1400806 ATGTATCGATACA
1 ATGTATCGATACA
1400819 ATGTATCGATAC
1 ATGTATCGATAC
1400831 TAAGCAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1405878 original size:32 final size:36
Alignment explanation
Indices: 1405837--1405919 Score: 104
Period size: 36 Copynumber: 2.4 Consensus size: 36
1405827 ACTATCTTTC
1405837 AAGGCTAAGATAGAAACC-TC-C-CTATCTTTT-CA
1 AAGGCTAAGATAGAAACCTTCTCTCTATCTTTTACA
**
1405869 CGGGCTAAGATAG-AACCTTTCTCTCTATCTTTTACA
1 AAGGCTAAGATAGAAACC-TTCTCTCTATCTTTTACA
1405905 AAGGCTAAGATAGAA
1 AAGGCTAAGATAGAA
1405920 CTTCACAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
31 4 0.10
32 11 0.27
33 2 0.05
34 1 0.02
35 9 0.22
36 13 0.32
37 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.29
Consensus pattern (36 bp):
AAGGCTAAGATAGAAACCTTCTCTCTATCTTTTACA
Found at i:1405915 original size:36 final size:31
Alignment explanation
Indices: 1405828--1405920 Score: 100
Period size: 36 Copynumber: 2.9 Consensus size: 31
1405818 CCTTACAATA
1405828 CTATC-TTTC-AAGGCTAAGATAGAAACCTCC
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCC
**
1405858 CTATCTTTTCACGGGCTAAGATAGAACCTTTCTC
1 CTATCTTTTCAAAGGCTAAGATAGAACC--TC-C
1405892 TCTATCTTTTACAAAGGCTAAGATAGAAC
1 -CTATCTTTT-CAAAGGCTAAGATAGAAC
1405921 TTCACAATTA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
30 5 0.10
31 8 0.15
32 11 0.21
33 2 0.04
34 1 0.02
35 9 0.17
36 16 0.31
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (31 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCC
Found at i:1406485 original size:32 final size:32
Alignment explanation
Indices: 1406398--1406487 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
1406388 GTCGATACAC
*
1406398 TGTATCGATAAATGAACAGCGATGAACAGTGA
1 TGTATCGATAAATGAACAGTGATGAACAGTGA
*
1406430 TGTATCGATAAATGAATAGTGATGAACAGTGA
1 TGTATCGATAAATGAACAGTGATGAACAGTGA
* *
1406462 TGTATCGATACATGAACATTGATGAA
1 TGTATCGATAAATGAACAGTGATGAA
1406488 TAGGGATAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.27
Consensus pattern (32 bp):
TGTATCGATAAATGAACAGTGATGAACAGTGA
Found at i:1406549 original size:13 final size:13
Alignment explanation
Indices: 1406531--1406555 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1406521 TGTCAGTTTT
1406531 ATGTATCGATACA
1 ATGTATCGATACA
1406544 ATGTATCGATAC
1 ATGTATCGATAC
1406556 TAAGCAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1409041 original size:29 final size:28
Alignment explanation
Indices: 1409009--1409092 Score: 71
Period size: 29 Copynumber: 2.9 Consensus size: 28
1408999 AAAATATGGC
1409009 AAATTACTAAAATGACCCTAAAATG-CAT
1 AAATTAC-AAAATGACCCTAAAATGTCAT
* ** * *
1409037 GAAATTGCATAAATGGTCCAAAAATGTGAT
1 -AAATTACA-AAATGACCCTAAAATGTCAT
*
1409067 AAATTACAAAAATGACCATAAAATGT
1 AAATTAC-AAAATGACCCTAAAATGT
1409093 ATGGATGACA
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
28 1 0.02
29 38 0.90
30 3 0.07
ACGTcount: A:0.50, C:0.13, G:0.12, T:0.25
Consensus pattern (28 bp):
AAATTACAAAATGACCCTAAAATGTCAT
Found at i:1411687 original size:21 final size:20
Alignment explanation
Indices: 1411661--1411714 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
1411651 ATTGTGCTTA
1411661 AAAAGAAATAAGAAGAATTAG
1 AAAAGAAATAAG-AGAATTAG
* *
1411682 GAAAGAAAATAAGTGAATTAG
1 AAAAG-AAATAAGAGAATTAG
1411703 AAAAGAAGATAA
1 AAAAGAA-ATAA
1411715 TTAAATTCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 2 0.07
21 19 0.68
22 7 0.25
ACGTcount: A:0.65, C:0.00, G:0.20, T:0.15
Consensus pattern (20 bp):
AAAAGAAATAAGAGAATTAG
Found at i:1411721 original size:21 final size:21
Alignment explanation
Indices: 1411661--1411721 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
1411651 ATTGTGCTTA
*
1411661 AAAAG-AAATAAGAAGAATTAG
1 AAAAGAAAATAAGTA-AATTAG
* *
1411682 GAAAGAAAATAAGTGAATTAG
1 AAAAGAAAATAAGTAAATTAG
* *
1411703 AAAAGAAGATAATTAAATT
1 AAAAGAAAATAAGTAAATT
1411722 CCAAGTTGGT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
21 25 0.78
22 7 0.22
ACGTcount: A:0.62, C:0.00, G:0.18, T:0.20
Consensus pattern (21 bp):
AAAAGAAAATAAGTAAATTAG
Found at i:1412850 original size:13 final size:13
Alignment explanation
Indices: 1412832--1412862 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1412822 ACATTTCTTC
1412832 ATGTATCGATACA
1 ATGTATCGATACA
1412845 ATGTATCGATACA
1 ATGTATCGATACA
*
1412858 TTGTA
1 ATGTA
1412863 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1412854 original size:33 final size:33
Alignment explanation
Indices: 1412812--1412875 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 33
1412802 GTTACATGCT
1412812 ATGTATCGATACATT-T-CTTCATGTATCGATACA
1 ATGTATCGATACATTGTAC--CATGTATCGATACA
1412845 ATGTATCGATACATTGTACCATGTATCGATA
1 ATGTATCGATACATTGTACCATGTATCGATA
1412876 TAAATAGTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (33 bp):
ATGTATCGATACATTGTACCATGTATCGATACA
Found at i:1412933 original size:21 final size:20
Alignment explanation
Indices: 1412907--1412962 Score: 78
Period size: 19 Copynumber: 2.8 Consensus size: 20
1412897 CTGCCAGTTT
**
1412907 CATGTATCGATACAATTTGGC
1 CATGTATCGATACAA-TTGAA
1412928 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
1412947 CATGTATCGATACAAT
1 CATGTATCGATACAAT
1412963 CCATCGATAC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 17 0.53
21 15 0.47
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:1414835 original size:13 final size:13
Alignment explanation
Indices: 1414817--1414869 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
1414807 GATACATGGC
1414817 ACATTGTATCGAT
1 ACATTGTATCGAT
*
1414830 ACATTGTATTGAT
1 ACATTGTATCGAT
1414843 ACA-TG-A---AT
1 ACATTGTATCGAT
1414851 A-ATTGTATCGAT
1 ACATTGTATCGAT
1414863 ACATTGT
1 ACATTGT
1414870 CCCAAATGTC
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
7 1 0.03
8 5 0.15
9 1 0.03
11 1 0.03
12 5 0.15
13 20 0.61
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:1416076 original size:15 final size:15
Alignment explanation
Indices: 1416056--1416090 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
1416046 AACCATCAAA
1416056 GATGATGAA-GATAAT
1 GATGAT-AATGATAAT
1416071 GATGATAATGATAAT
1 GATGATAATGATAAT
1416086 GATGA
1 GATGA
1416091 AGTTGACTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 2 0.11
15 17 0.89
ACGTcount: A:0.46, C:0.00, G:0.26, T:0.29
Consensus pattern (15 bp):
GATGATAATGATAAT
Found at i:1420634 original size:13 final size:13
Alignment explanation
Indices: 1420618--1420650 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1420608 TCTTTGTGTT
1420618 GATACATTGTATC
1 GATACATTGTATC
*
1420631 GATACAATGTATC
1 GATACATTGTATC
1420644 GATACAT
1 GATACAT
1420651 GGGTTACTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
GATACATTGTATC
Found at i:1424615 original size:20 final size:21
Alignment explanation
Indices: 1424581--1424620 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1424571 AATTTTCTAG
1424581 AATGTATCGAAACAT-TGAAT
1 AATGTATCGAAACATCTGAAT
1424601 AATGTATC-AATACATCTGAA
1 AATGTATCGAA-ACATCTGAA
1424621 AAACCTAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 12 0.67
21 4 0.22
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (21 bp):
AATGTATCGAAACATCTGAAT
Found at i:1427164 original size:21 final size:21
Alignment explanation
Indices: 1427135--1427175 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
1427125 AAAGGTTAAA
1427135 ACCCTAGAAAGTATCGATACAG
1 ACCCTAG-AAGTATCGATACAG
1427157 ACCC-AGAAGTATCGATACA
1 ACCCTAGAAGTATCGATACA
1427176 TATTGCCTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.68
21 2 0.11
22 4 0.21
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.17
Consensus pattern (21 bp):
ACCCTAGAAGTATCGATACAG
Found at i:1427202 original size:13 final size:13
Alignment explanation
Indices: 1427184--1427208 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1427174 CATATTGCCT
1427184 TGTATCGATACAG
1 TGTATCGATACAG
1427197 TGTATCGATACA
1 TGTATCGATACA
1427209 TGATCTTGGT
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:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1431146 original size:33 final size:32
Alignment explanation
Indices: 1431088--1431151 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 32
1431078 GTTACAAGCT
*
1431088 ATGTATCGATACATTTCTTCTTGTATCGATATA
1 ATGTATCGATACATTTC-TCATGTATCGATATA
1431121 ATGTATCGATACATTGTAC-CATGTATCGATA
1 ATGTATCGATACATT-T-CTCATGTATCGATA
1431152 CAAAGAGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 26 0.93
34 1 0.04
35 1 0.04
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.41
Consensus pattern (32 bp):
ATGTATCGATACATTTCTCATGTATCGATATA
Found at i:1431228 original size:19 final size:19
Alignment explanation
Indices: 1431183--1431239 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
1431173 CTACCAGTTT
**
1431183 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAA--TGAA
1431204 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
1431223 CATGTATCGATATAATG
1 CATGTATCGATACAATG
1431240 TATCGATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 18 0.55
21 15 0.45
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1431246 original size:32 final size:33
Alignment explanation
Indices: 1431205--1431267 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
1431195 CAATTTGTCC
*
1431205 ATGTATCGATACAATG-AACATGTATCGATATA
1 ATGTATCGATACAAAGCAACATGTATCGATATA
*
1431237 ATGTATCGATACAAAGCAGCATGTATCGATA
1 ATGTATCGATACAAAGCAACATGTATCGATA
1431268 CATCTAGGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 15 0.54
33 13 0.46
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (33 bp):
ATGTATCGATACAAAGCAACATGTATCGATATA
Found at i:1431812 original size:16 final size:16
Alignment explanation
Indices: 1431787--1431835 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
1431777 GTTTTCGTTT
1431787 TTCT-CCCCTTAAAAA
1 TTCTCCCCCTTAAAAA
1431802 TTCTCCCCCTTAAACAA
1 TTCTCCCCCTTAAA-AA
* *
1431819 TTATCTCCTCTTAAAAA
1 TTCTC-CCCCTTAAAAA
1431836 AAATTCTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 4 0.14
16 9 0.31
17 8 0.28
18 8 0.28
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.35
Consensus pattern (16 bp):
TTCTCCCCCTTAAAAA
Found at i:1441307 original size:22 final size:20
Alignment explanation
Indices: 1441280--1441398 Score: 107
Period size: 22 Copynumber: 5.5 Consensus size: 20
1441270 TTTCATGATT
1441280 TTTTATTATTTTTATTTTTCA
1 TTTTATTATTTTTATTTTT-A
1441301 TTGTTATTA-TTTTATTATTTAA
1 TT-TTATTATTTTTATT-TTT-A
*
1441323 TTTTTATTAATTTTTATTATTA
1 -TTTTATT-ATTTTTATTTTTA
1441345 TTTTATTTATTTTTTATTTTTTA
1 TTTTA-TTA-TTTTTA-TTTTTA
* *
1441368 TTTT-TGATTTTTACTTATTA
1 TTTTATTATTTTTA-TTTTTA
1441388 TTTTATTATTT
1 TTTTATTATTT
1441399 GACTTTCTGA
Statistics
Matches: 82, Mismatches: 7, Indels: 18
0.77 0.07 0.17
Matches are distributed among these distances:
20 15 0.18
21 22 0.27
22 24 0.29
23 14 0.17
24 7 0.09
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.75
Consensus pattern (20 bp):
TTTTATTATTTTTATTTTTA
Found at i:1441326 original size:35 final size:35
Alignment explanation
Indices: 1441280--1441365 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 35
1441270 TTTCATGATT
*
1441280 TTTTA-TT-ATTTTTATTTTTCATTGTTATTATT-
1 TTTTATTTAATTTTTATTTTTAATTGTTATTATTA
*
1441312 TTATTATTTAATTTTTA---TTAATTTTTATTATTA
1 TT-TTATTTAATTTTTATTTTTAATTGTTATTATTA
*
1441345 TTTTATTTATTTTTTATTTTT
1 TTTTATTTAATTTTTATTTTT
1441366 TATTTTTGAT
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
32 28 0.64
33 5 0.11
34 2 0.05
35 9 0.20
ACGTcount: A:0.22, C:0.01, G:0.01, T:0.76
Consensus pattern (35 bp):
TTTTATTTAATTTTTATTTTTAATTGTTATTATTA
Found at i:1441329 original size:11 final size:11
Alignment explanation
Indices: 1441315--1441363 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
1441305 TATTATTTTA
1441315 TTATTTAATTT
1 TTATTTAATTT
1441326 TTA-TTAATTT
1 TTATTTAATTT
*
1441336 TTA-TTATTATT
1 TTATTTAAT-TT
*
1441347 TTATTTATTTT
1 TTATTTAATTT
1441358 TTATTT
1 TTATTT
1441364 TTTATTTTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
10 14 0.40
11 16 0.46
12 5 0.14
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTATTTAATTT
Found at i:1441359 original size:32 final size:31
Alignment explanation
Indices: 1441304--1441398 Score: 97
Period size: 32 Copynumber: 3.0 Consensus size: 31
1441294 TTTTTCATTG
*
1441304 TTATTATT-TTATTATTTAATTTTTATTAATTT
1 TTATTATTATT-TTATTTATTTTTTATT-ATTT
1441336 TTATTATTATTTTATTTATTTTTTA-T-TTT
1 TTATTATTATTTTATTTATTTTTTATTATTT
* *
1441365 TTATTTTTGATTTTTACTTATTATTTTATTATTT
1 TTATTATT-A-TTTTATTTATT-TTTTATTATTT
1441399 GACTTTCTGA
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
29 10 0.19
30 1 0.02
31 11 0.20
32 26 0.48
33 3 0.06
34 3 0.06
ACGTcount: A:0.23, C:0.01, G:0.01, T:0.75
Consensus pattern (31 bp):
TTATTATTATTTTATTTATTTTTTATTATTT
Found at i:1441362 original size:54 final size:56
Alignment explanation
Indices: 1441277--1441397 Score: 146
Period size: 54 Copynumber: 2.2 Consensus size: 56
1441267 GCATTTCATG
1441277 ATTTT-TTATTATTTTTATTTTTCATTGTTATTATTTTATTATTTAATTTTTA-TTAAT
1 ATTTTATTATTATTTTTATTTTT-ATTGTTATT-TTTTATT-TTTAATTTTTACTTAAT
* *
1441334 -TTTTATTATTA-TTTTATTTATT-TT-TTATTTTTTATTTTTGATTTTTACTTATT
1 ATTTTATTATTATTTTTATTT-TTATTGTTATTTTTTATTTTTAATTTTTACTTAAT
1441387 ATTTTATTATT
1 ATTTTATTATT
1441398 TGACTTTCTG
Statistics
Matches: 58, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
52 10 0.17
53 11 0.19
54 15 0.26
55 2 0.03
56 12 0.21
57 8 0.14
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (56 bp):
ATTTTATTATTATTTTTATTTTTATTGTTATTTTTTATTTTTAATTTTTACTTAAT
Found at i:1441371 original size:35 final size:34
Alignment explanation
Indices: 1441280--1441398 Score: 97
Period size: 35 Copynumber: 3.5 Consensus size: 34
1441270 TTTCATGATT
* *
1441280 TTTTATTA-TTTTTATTTTTCA---TTGTTATTA
1 TTTTATTATTTTTTATTTTTAATTTTTATTATTA
*
1441310 TTTTATTATTTAATTT-TTATTAATTTTTATTATTA
1 TTTTATTATTT--TTTATTTTTAATTTTTATTATTA
* *
1441345 TTTTATTTATTTTTTATTTTTTATTTTTGATTTTTA
1 TTTTA-TTATTTTTTATTTTTAATTTTT-ATTATTA
*
1441381 -CTTATTATTTTATTATTT
1 TTTTATTATTTT-TTATTT
1441399 GACTTTCTGA
Statistics
Matches: 72, Mismatches: 7, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
30 8 0.11
31 2 0.03
32 5 0.07
33 3 0.04
34 10 0.14
35 32 0.44
36 12 0.17
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.75
Consensus pattern (34 bp):
TTTTATTATTTTTTATTTTTAATTTTTATTATTA
Found at i:1447479 original size:44 final size:44
Alignment explanation
Indices: 1447412--1447991 Score: 341
Period size: 44 Copynumber: 13.3 Consensus size: 44
1447402 ATTGCGACAA
* * *
1447412 GTGGT-ACCATACATCAAATCAAAATGAAAAGAATCTGACCAGG
1 GTGGTAACCATACGTCAAATTAAAATGAAAAGAATTTGACCAGG
* * ** * * *
1447455 GTGGTAACCATACATCAGACCAAAAT-AAGAGGAGTTTGACTAGG
1 GTGGTAACCATACGTCAAATTAAAATGAA-AAGAATTTGACCAGG
** * * *
1447499 GTGGTAACTGTATGTCAAA-TAGGAAAT-AAGCAG-ATTTGACTAGG
1 GTGGTAACCATACGTCAAATTA--AAATGAA-AAGAATTTGACCAGG
* * * * * *
1447543 GTAGTAACCATATGTCAAATTAAAATAAAAAGAATCTAACTAGG
1 GTGGTAACCATACGTCAAATTAAAATGAAAAGAATTTGACCAGG
* * * *
1447587 GTGGTAACCATATGTCAAACT--GA-G-AAAG--TTTGACTAGG
1 GTGGTAACCATACGTCAAATTAAAATGAAAAGAATTTGACCAGG
* ** * * *** *
1447625 GTGATAATGATACATC-AATTAGAAAAGAGGTGAATTTGACGAGG
1 GTGGTAACCATACGTCAAATTA-AAATGAAAAGAATTTGACCAGG
* * ** *
1447669 GTGGTAACCATATGTCAAATTAGAATGAAACCAATCTGACCAGG
1 GTGGTAACCATACGTCAAATTAAAATGAAAAGAATTTGACCAGG
* ** * *
1447713 GTGGTAACCATACGTCACACCAAAATGAGAAGAGTTTGACCAGG
1 GTGGTAACCATACGTCAAATTAAAATGAAAAGAATTTGACCAGG
** ** *
1447757 GTGGTAACCATTTGTCAAA-TAGAAATGAGGTAG-ATTTGACGAGG
1 GTGGTAACCATACGTCAAATTA-AAATGA-AAAGAATTTGACCAGG
* *
1447801 GTGGTAACCATATGTCAAATAAAAATG--AAGTATATTTGACCAGG
1 GTGGTAACCATACGTCAAATTAAAATGAAAAG-A-ATTTGACCAGG
* * * * *
1447845 ATGATAACCATACATCAAA-TAATAATGAAAAGATTTTGACTAGG
1 GTGGTAACCATACGTCAAATTAA-AATGAAAAGAATTTGACCAGG
* ** * *
1447889 GTGGTAACCATACGTCATACCAAAAT-AAGAAGCATTTGACCAGA
1 GTGGTAACCATACGTCAAATTAAAATGAA-AAGAATTTGACCAGG
* *** *
1447933 GTGGTAATCATACGTCAAACGGAAATGAAAAGAGTTTGACCAGG
1 GTGGTAACCATACGTCAAATTAAAATGAAAAGAATTTGACCAGG
1447977 GTGGTAACCATACGT
1 GTGGTAACCATACGT
1447992 TAAGCAGGAA
Statistics
Matches: 414, Mismatches: 96, Indels: 53
0.74 0.17 0.09
Matches are distributed among these distances:
37 3 0.01
38 19 0.05
40 5 0.01
41 3 0.01
42 2 0.00
43 19 0.05
44 336 0.81
45 24 0.06
46 3 0.01
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.24
Consensus pattern (44 bp):
GTGGTAACCATACGTCAAATTAAAATGAAAAGAATTTGACCAGG
Found at i:1447763 original size:88 final size:86
Alignment explanation
Indices: 1447412--1447991 Score: 392
Period size: 88 Copynumber: 6.7 Consensus size: 86
1447402 ATTGCGACAA
** * * * *
1447412 GTGGT-ACCATACATCAAATCAAAATGAAAAGAATCTGACCAGGGTGGTAACCATACATCAGACC
1 GTGGTAACCATATGTCAAAT-AGAATGAAAAGAATTTGACCAGGGTGGTAACCATACGTCAAACC
* *
1447476 AAAATAAGAGGAGTTTGACTAGG
65 AAAATAAGAAGA-TTTGACCAGG
** * * * *
1447499 GTGGTAACTGTATGTCAAATAGGAA--ATAAGCAGATTTGACTAGGGTAGTAACCATATGTCAAA
1 GTGGTAACCATATGTCAAATA-GAATGAAAAG-A-ATTTGACCAGGGTGGTAACCATACGTCAAA
** * * * *
1447562 TTAAAATAAAAAGAATCTAACTAGG
63 CCAAAATAAGAAG-ATTTGACCAGG
* * ** *
1447587 GTGGTAACCATATGTCAAACT-G-A-G-AAAG--TTTGACTAGGGTGATAATGATACATCAATTA
1 GTGGTAACCATATGTCAAA-TAGAATGAAAAGAATTTGACCAGGGTGGTAACCATACGTCAA--A
* * ** *
1447646 -GAAAA-GAGGTGAATTTGACGAGG
63 CCAAAATAAGAAG-ATTTGACCAGG
** * *
1447669 GTGGTAACCATATGTCAAATTAGAATGAAACCAATCTGACCAGGGTGGTAACCATACGTCACACC
1 GTGGTAACCATATGTCAAA-TAGAATGAAAAGAATTTGACCAGGGTGGTAACCATACGTCAAACC
*
1447734 AAAATGAGAAGAGTTTGACCAGG
65 AAAATAAGAAGA-TTTGACCAGG
* ** * * *
1447757 GTGGTAACCATTTGTCAAATAGAAATGAGGTAG-ATTTGACGAGGGTGGTAACCATATGTCAAAT
1 GTGGTAACCATATGTCAAATAG-AATGA-AAAGAATTTGACCAGGGTGGTAACCATACGTCAAAC
* * *
1447821 AAAAATGAAGTATATTTGACCAGG
64 CAAAAT-AAGAAGATTTGACCAGG
* * ** * * * *
1447845 ATGATAACCATACATCAAATAATAATGAAAAGATTTTGACTAGGGTGGTAACCATACGTCATACC
1 GTGGTAACCATATGTCAAAT-AGAATGAAAAGAATTTGACCAGGGTGGTAACCATACGTCAAACC
*
1447910 AAAATAAGAAGCATTTGACCAGA
65 AAAATAAGAAG-ATTTGACCAGG
* * ** *
1447933 GTGGTAATCATACGTCAAACGGAAATGAAAAGAGTTTGACCAGGGTGGTAACCATACGT
1 GTGGTAACCATATGTCAAATAG-AATGAAAAGAATTTGACCAGGGTGGTAACCATACGT
1447992 TAAGCAGGAA
Statistics
Matches: 379, Mismatches: 89, Indels: 49
0.73 0.17 0.09
Matches are distributed among these distances:
82 53 0.14
83 5 0.01
84 2 0.01
85 1 0.00
86 11 0.03
87 22 0.06
88 278 0.73
89 7 0.02
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.24
Consensus pattern (86 bp):
GTGGTAACCATATGTCAAATAGAATGAAAAGAATTTGACCAGGGTGGTAACCATACGTCAAACCA
AAATAAGAAGATTTGACCAGG
Found at i:1447803 original size:132 final size:131
Alignment explanation
Indices: 1447412--1447989 Score: 523
Period size: 132 Copynumber: 4.4 Consensus size: 131
1447402 ATTGCGACAA
** *
1447412 GTGGT-ACCATACATCAAATCAAAATGAAAAGAATCTGACCAGGGTGGTAACCATACATCAGACC
1 GTGGTAACCATATGTCAAATTAAAATGAAAAGAATCTGACCAGGGTGGTAACCATACATCA-ACC
* * ** * * *
1447476 AAAATAAGAGGAGTTTGACTAGGGTGGTAACTGTATGTCAAATAGGAAAT-AAGCAGATTTGACT
65 AAAATGAGAAGAGTTTGACTAGGGTGGTAACCATATGTCAAATA-GAAATGAGGTAGATTTGACG
1447540 AGG
129 AGG
* * * * **
1447543 GTAGTAACCATATGTCAAATTAAAATAAAAAGAATCTAACTAGGGTGGTAACCAT--AT--GTCA
1 GTGGTAACCATATGTCAAATTAAAATGAAAAGAATCTGACCAGGGTGGTAACCATACATCAACCA
* * ** ** * *
1447604 AACTGAGAA-AGTTTGACTAGGGTGATAATGATACATCAATTAGAAAAGAGGT-GAATTTGACGA
66 AAATGAGAAGAGTTTGACTAGGGTGGTAACCATATGTCAAATAGAAATGAGGTAG-ATTTGACGA
1447667 GG
130 GG
* ** *
1447669 GTGGTAACCATATGTCAAATTAGAATGAAACCAATCTGACCAGGGTGGTAACCATACGTCACACC
1 GTGGTAACCATATGTCAAATTAAAATGAAAAGAATCTGACCAGGGTGGTAACCATACATCA-ACC
* *
1447734 AAAATGAGAAGAGTTTGACCAGGGTGGTAACCATTTGTCAAATAGAAATGAGGTAGATTTGACGA
65 AAAATGAGAAGAGTTTGACTAGGGTGGTAACCATATGTCAAATAGAAATGAGGTAGATTTGACGA
1447799 GG
130 GG
* * * * *
1447801 GTGGTAACCATATGTCAAATAAAAATG--AAGTATATTTGACCAGGATGATAACCATACATCAAA
1 GTGGTAACCATATGTCAAATTAAAATGAAAAG-A-ATCTGACCAGGGTGGTAACCATACATCAAC
* * * * ** * *
1447864 TAATAATGAAAAGATTTTGACTAGGGTGGTAACCATACGTCATACCA-AAAT-AAGAAGCATTTG
64 CAA-AATGAGAAGAGTTTGACTAGGGTGGTAACCATATGTCA-AATAGAAATGAGGTAG-ATTTG
* *
1447927 ACCAGA
126 ACGAGG
* * *** * *
1447933 GTGGTAATCATACGTCAAACGGAAATGAAAAGAGTTTGACCAGGGTGGTAACCATAC
1 GTGGTAACCATATGTCAAATTAAAATGAAAAGAATCTGACCAGGGTGGTAACCATAC
1447990 GTTAAGCAGG
Statistics
Matches: 358, Mismatches: 72, Indels: 33
0.77 0.16 0.07
Matches are distributed among these distances:
125 5 0.01
126 86 0.24
127 8 0.02
128 1 0.00
130 3 0.01
131 22 0.06
132 226 0.63
133 4 0.01
134 3 0.01
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.24
Consensus pattern (131 bp):
GTGGTAACCATATGTCAAATTAAAATGAAAAGAATCTGACCAGGGTGGTAACCATACATCAACCA
AAATGAGAAGAGTTTGACTAGGGTGGTAACCATATGTCAAATAGAAATGAGGTAGATTTGACGAG
G
Found at i:1449010 original size:16 final size:15
Alignment explanation
Indices: 1448989--1449018 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1448979 AGTGGCCTAA
1448989 CAAGATCAAGGTTCAT
1 CAAGATCAA-GTTCAT
1449005 CAAGATCAAGTTCA
1 CAAGATCAAGTTCA
1449019 AGATGTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (15 bp):
CAAGATCAAGTTCAT
Found at i:1452359 original size:20 final size:20
Alignment explanation
Indices: 1452336--1452391 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
1452326 TACATAAGAA
*
1452336 ATTGTATTGATACATTTCTC
1 ATTGTATCGATACATTTCTC
1452356 ATTGTATCGATACATTTCTC
1 ATTGTATCGATACATTTCTC
1452376 ATTGTATCGATACATT
1 ATTGTATCGATACATT
1452392 CTAGGTTTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.46
Consensus pattern (20 bp):
ATTGTATCGATACATTTCTC
Found at i:1456168 original size:13 final size:13
Alignment explanation
Indices: 1456150--1456175 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1456140 CAATTTTTTG
1456150 TGTATCGATACAT
1 TGTATCGATACAT
1456163 TGTATCGATACAT
1 TGTATCGATACAT
1456176 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Done.