Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007980.1 Hibiscus syriacus cultivar Beakdansim tig00110419_pilon, whole genome shotgun sequence
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: 1499237
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 8
Found at i:1197590 original size:14 final size:12
Alignment explanation
Indices: 1197571--1197631 Score: 67
Period size: 11 Copynumber: 5.2 Consensus size: 12
1197561 ATTTGTTCTC
1197571 TTTCTTCTTTTCCT
1 TTTCTTCTTTT--T
1197585 TTTCTT-TTTTT
1 TTTCTTCTTTTT
1197596 TTTCTTC-TTTT
1 TTTCTTCTTTTT
*
1197607 TTTCTT-TTTCT
1 TTTCTTCTTTTT
1197618 TTTC-TCTTTTT
1 TTTCTTCTTTTT
1197629 TTT
1 TTT
1197632 GAATATGAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
10 1 0.02
11 31 0.74
13 4 0.10
14 6 0.14
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTCTTCTTTTT
Found at i:1197612 original size:33 final size:34
Alignment explanation
Indices: 1197566--1197631 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 34
1197556 ACTTGATTTG
*
1197566 TTCTCTTTCTTCTTTTCCTTTTCTTTTTTTTTTC
1 TTCTCTTTCTTCTTTTCCTTTTCTCTTTTTTTTC
* *
1197600 TTCT-TTTTTTCTTTTTCTTTTCTCTTTTTTTT
1 TTCTCTTTCTTCTTTTCCTTTTCTCTTTTTTTT
1197632 GAATATGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 25 0.86
34 4 0.14
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (34 bp):
TTCTCTTTCTTCTTTTCCTTTTCTCTTTTTTTTC
Found at i:1197614 original size:21 final size:22
Alignment explanation
Indices: 1197585--1197630 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 22
1197575 TTCTTTTCCT
1197585 TTTCTTTTTT-TTTTCTTCTTTT
1 TTTCTTTTTTCTTTTC-TCTTTT
1197607 TTTC-TTTTTCTTTTCTCTTTT
1 TTTCTTTTTTCTTTTCTCTTTT
1197628 TTT
1 TTT
1197631 TGAATATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (22 bp):
TTTCTTTTTTCTTTTCTCTTTT
Found at i:1200002 original size:32 final size:32
Alignment explanation
Indices: 1199966--1200036 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
1199956 GATTCGATAC
1199966 ATCTTGTAGAGAACTCAGTG-TTGATTCCTCAT
1 ATCTTGTAG-GAACTCAGTGATTGATTCCTCAT
* * *
1199998 ATCTTGTTGTAACTCGGTGATTGATTCCTCAT
1 ATCTTGTAGGAACTCAGTGATTGATTCCTCAT
1200030 ATCTTGT
1 ATCTTGT
1200037 TGTAACTCGG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
31 8 0.23
32 27 0.77
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.42
Consensus pattern (32 bp):
ATCTTGTAGGAACTCAGTGATTGATTCCTCAT
Found at i:1200037 original size:32 final size:31
Alignment explanation
Indices: 1199977--1200047 Score: 124
Period size: 32 Copynumber: 2.3 Consensus size: 31
1199967 TCTTGTAGAG
*
1199977 AACTCAGTGTTGATTCCTCATATCTTGTTGT
1 AACTCGGTGTTGATTCCTCATATCTTGTTGT
1200008 AACTCGGTGATTGATTCCTCATATCTTGTTGT
1 AACTCGGTG-TTGATTCCTCATATCTTGTTGT
1200040 AACTCGGT
1 AACTCGGT
1200048 CAACTGCTCT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 8 0.21
32 30 0.79
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (31 bp):
AACTCGGTGTTGATTCCTCATATCTTGTTGT
Found at i:1203235 original size:21 final size:21
Alignment explanation
Indices: 1203217--1203255 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1203207 ATGTTTAATG
1203217 AAAA-GATACCAATTGTTAAC
1 AAAATGATACCAATTGTTAAC
*
1203237 AAAATGATATCAATTGTTA
1 AAAATGATACCAATTGTTA
1203256 CCAATTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.31
Consensus pattern (21 bp):
AAAATGATACCAATTGTTAAC
Found at i:1205755 original size:21 final size:21
Alignment explanation
Indices: 1205687--1205807 Score: 131
Period size: 21 Copynumber: 5.8 Consensus size: 21
1205677 TTGCAGCCTT
*
1205687 GGTGCATGGATGCACAGTA-G
1 GGTGCATGGATGCACTGTAGG
*
1205707 GGTGCATCG-TGCACTAGT-GG
1 GGTGCATGGATGCACT-GTAGG
*
1205727 CAGGTGCATGGATGCACTGCAGG
1 --GGTGCATGGATGCACTGTAGG
*
1205750 GGTGCATGAATGCACTGTAGG
1 GGTGCATGGATGCACTGTAGG
* *
1205771 AGTGCATGGATACACTGTAGG
1 GGTGCATGGATGCACTGTAGG
*
1205792 AGTGCATGGATGCACT
1 GGTGCATGGATGCACT
1205808 TTGACACCTT
Statistics
Matches: 85, Mismatches: 10, Indels: 11
0.80 0.09 0.10
Matches are distributed among these distances:
19 5 0.06
20 11 0.13
21 52 0.61
22 9 0.11
23 8 0.09
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.22
Consensus pattern (21 bp):
GGTGCATGGATGCACTGTAGG
Found at i:1205797 original size:63 final size:63
Alignment explanation
Indices: 1205687--1205807 Score: 158
Period size: 63 Copynumber: 1.9 Consensus size: 63
1205677 TTGCAGCCTT
* *
1205687 GGTGCATGGATGCACAGTAGGGTGCATCGTGCACTAGTGGCAGGTGCATGGATGCACTGCAGG
1 GGTGCATGAATGCACAGTAGGGTGCATCGTACACTAGTGGCAGGTGCATGGATGCACTGCAGG
* *
1205750 GGTGCATGAATGCACTGTAGGAGTGCATGGATACACT-GTAGG-A-GTGCATGGATGCACT
1 GGTGCATGAATGCACAGTAGG-GTGCATCG-TACACTAGT-GGCAGGTGCATGGATGCACT
1205808 TTGACACCTT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
63 34 0.67
64 10 0.20
65 7 0.14
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.22
Consensus pattern (63 bp):
GGTGCATGAATGCACAGTAGGGTGCATCGTACACTAGTGGCAGGTGCATGGATGCACTGCAGG
Found at i:1207812 original size:46 final size:45
Alignment explanation
Indices: 1207760--1207866 Score: 144
Period size: 45 Copynumber: 2.4 Consensus size: 45
1207750 TGCACATACC
*
1207760 ATGCATCGATACACTCAGGGCT-TTATGAAAACATCGAATGCATTTG
1 ATGCATCGATGCACTCA-GGCTATTATG-AAACATCGAATGCATTTG
* * *
1207806 ATGCATCGACGCACTCAGGCTATTTTGAAACATCGAATGCATTTT
1 ATGCATCGATGCACTCAGGCTATTATGAAACATCGAATGCATTTG
*
1207851 ATACATCGATGCACTC
1 ATGCATCGATGCACTC
1207867 TTAGTGCACC
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
45 35 0.65
46 19 0.35
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (45 bp):
ATGCATCGATGCACTCAGGCTATTATGAAACATCGAATGCATTTG
Found at i:1213690 original size:23 final size:22
Alignment explanation
Indices: 1213660--1213740 Score: 83
Period size: 23 Copynumber: 3.6 Consensus size: 22
1213650 GCACTTAACA
*
1213660 GTGCATCGATGCATCCCTTGTAT
1 GTGCATCGATGCA-CCCTTGAAT
* * *
1213683 GTGCATCGATTCA-CCATGAAG
1 GTGCATCGATGCACCCTTGAAT
*
1213704 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCAC-CCTTGAAT
*
1213727 GAGCATCGATGCAC
1 GTGCATCGATGCAC
1213741 AAGGTCATGC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
21 16 0.35
23 30 0.65
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCACCCTTGAAT
Found at i:1216559 original size:64 final size:64
Alignment explanation
Indices: 1216402--1216562 Score: 236
Period size: 65 Copynumber: 2.5 Consensus size: 64
1216392 GAATAAATTG
* * *
1216402 AACATCGAATGCATTTTATGCATCGATGTACATACCATGCATCGATGCACTCAGGGCTTTATGAA
1 AACATCGAATGCATTTTATGCATCGATGCAC-TAACATGCATCAATGCACTCAGGGCTTTATGAA
* *
1216467 AACATCGAATGCATTTGATGCATCGATGCACTAGACATGCATCAATGCACTCA-GGCTATT-TGG
1 AACATCGAATGCATTTTATGCATCGATGCACTA-ACATGCATCAATGCACTCAGGGCT-TTATGA
1216530 A
64 A
1216531 AACATCGAATGCATTTTATGCATCGATGCACT
1 AACATCGAATGCATTTTATGCATCGATGCACT
1216563 CTTAGTGCAC
Statistics
Matches: 88, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
64 40 0.45
65 48 0.55
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCATTTTATGCATCGATGCACTAACATGCATCAATGCACTCAGGGCTTTATGAA
Found at i:1216579 original size:64 final size:63
Alignment explanation
Indices: 1216402--1216586 Score: 221
Period size: 64 Copynumber: 2.9 Consensus size: 63
1216392 GAATAAATTG
*
1216402 AACATCGAATGCATTTTATGCATCGATGTACATACCATGCATCGATGCACTCAGGGCTTTATGAA
1 AACATCGAATGCATTTTATGCATCGATGCAC-T-CCATGCATCGATGCACTCAGGGCTTTATGAA
* * * *
1216467 AACATCGAATGCATTTGATGCATCGATGCACTAGACATGCATCAATGCACTCA-GGCTATT-TGG
1 AACATCGAATGCATTTTATGCATCGATGCACT--CCATGCATCGATGCACTCAGGGCT-TTATGA
1216530 A
63 A
* * *
1216531 AACATCGAATGCATTTTATGCATCGATGCACTCTTAGTGCACCGATGCACTAAGGG
1 AACATCGAATGCATTTTATGCATCGATGCACTC-CA-TGCATCGATGCACTCAGGG
1216587 TCCAACGGTC
Statistics
Matches: 103, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
63 1 0.01
64 52 0.50
65 50 0.49
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTTTATGCATCGATGCACTCCATGCATCGATGCACTCAGGGCTTTATGAA
Found at i:1218148 original size:15 final size:14
Alignment explanation
Indices: 1218110--1218162 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
1218100 TTTAAAGGCT
1218110 GAAATTAGAATA-ACA
1 GAAATTA-AATAGA-A
*
1218125 GAAATTAAATGGAA
1 GAAATTAAATAGAA
*
1218139 GAAATATAAATAGTA
1 GAAAT-TAAATAGAA
1218154 GAAATTAAA
1 GAAATTAAA
1218163 GAGCAAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
14 13 0.39
15 20 0.61
ACGTcount: A:0.60, C:0.02, G:0.15, T:0.23
Consensus pattern (14 bp):
GAAATTAAATAGAA
Found at i:1221145 original size:20 final size:20
Alignment explanation
Indices: 1221122--1221160 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1221112 AGAATTGAAA
* *
1221122 GTTATAATATTGAATTTGAT
1 GTTAGAATATTAAATTTGAT
*
1221142 GTTAGAATGTTAAATTTGA
1 GTTAGAATATTAAATTTGA
1221161 CTATTTTAGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (20 bp):
GTTAGAATATTAAATTTGAT
Found at i:1222823 original size:19 final size:19
Alignment explanation
Indices: 1222799--1222893 Score: 75
Period size: 19 Copynumber: 5.0 Consensus size: 19
1222789 TATGCATTGG
1222799 GCTATGAATTTGAAAATAA
1 GCTATGAATTTGAAAATAA
* * *
1222818 GCTATGATTTTGACAGTAA
1 GCTATGAATTTGAAAATAA
* * *
1222837 GCTATGAGTCTGACAATAA
1 GCTATGAATTTGAAAATAA
* * *
1222856 GTTATGAATCTGTAAATAA
1 GCTATGAATTTGAAAATAA
* *
1222875 GTTATG-GTTTAGAAAATAA
1 GCTATGAATTT-GAAAATAA
1222894 ATTCTGAAAT
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
18 2 0.03
19 60 0.97
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.34
Consensus pattern (19 bp):
GCTATGAATTTGAAAATAA
Found at i:1222945 original size:12 final size:12
Alignment explanation
Indices: 1222918--1222961 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
1222908 AAGTATTTAT
*
1222918 TATGAACATGGAA
1 TATGAAAAT-GAA
1222931 TATGAAAATGAA
1 TATGAAAATGAA
**
1222943 TATGTGAATGAA
1 TATGAAAATGAA
1222955 TATGAAA
1 TATGAAA
1222962 GTGGAAAATG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 18 0.69
13 8 0.31
ACGTcount: A:0.50, C:0.02, G:0.20, T:0.27
Consensus pattern (12 bp):
TATGAAAATGAA
Found at i:1225883 original size:30 final size:31
Alignment explanation
Indices: 1225815--1225883 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 31
1225805 AAATTATACA
* *
1225815 TTTGGTAAAGTTTGGTGACCAAAGTATAAGC
1 TTTGGAAAAGTTTGGTGACCAAAATATAAGC
* *
1225846 TTT-GAAAAGTTTAGG-GACCAAAATGTAA-T
1 TTTGGAAAAGTTT-GGTGACCAAAATATAAGC
1225875 TTTGGAAAA
1 TTTGGAAAA
1225884 TTACAAATGG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
29 3 0.09
30 24 0.75
31 5 0.16
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.32
Consensus pattern (31 bp):
TTTGGAAAAGTTTGGTGACCAAAATATAAGC
Found at i:1232052 original size:91 final size:91
Alignment explanation
Indices: 1231930--1232111 Score: 346
Period size: 91 Copynumber: 2.0 Consensus size: 91
1231920 GCCCCACAGG
* *
1231930 AGCATTAGTCAACCCGAATAACATCGGGTACTCGATGTCCAAGTAAATTAACAAACCTTTATCTC
1 AGCATTAGTCAACCCGAACAAAATCGGGTACTCGATGTCCAAGTAAATTAACAAACCTTTATCTC
1231995 CTTTCTCTAGATGTGCCTGCAAAGAT
66 CTTTCTCTAGATGTGCCTGCAAAGAT
1232021 AGCATTAGTCAACCCGAACAAAATCGGGTACTCGATGTCCAAGTAAATTAACAAACCTTTATCTC
1 AGCATTAGTCAACCCGAACAAAATCGGGTACTCGATGTCCAAGTAAATTAACAAACCTTTATCTC
1232086 CTTTCTCTAGATGTGCCTGCAAAGAT
66 CTTTCTCTAGATGTGCCTGCAAAGAT
1232112 CTAAATGAAT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 89 1.00
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.28
Consensus pattern (91 bp):
AGCATTAGTCAACCCGAACAAAATCGGGTACTCGATGTCCAAGTAAATTAACAAACCTTTATCTC
CTTTCTCTAGATGTGCCTGCAAAGAT
Found at i:1238687 original size:24 final size:23
Alignment explanation
Indices: 1238622--1238687 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
1238612 TTCGCTAAAT
* *
1238622 GAATGCTAAAT-AATATGTTCAC
1 GAATACTAAATGAACATGTTCAC
* * *
1238644 GAATGCAAAACGAACATGTTCAC
1 GAATACTAAATGAACATGTTCAC
1238667 GAATACTTAAATGAACATGTT
1 GAATAC-TAAATGAACATGTT
1238688 TACAAACATT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
22 9 0.25
23 15 0.42
24 12 0.33
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (23 bp):
GAATACTAAATGAACATGTTCAC
Found at i:1238709 original size:23 final size:24
Alignment explanation
Indices: 1238636--1238711 Score: 77
Period size: 23 Copynumber: 3.2 Consensus size: 24
1238626 GCTAAATAAT
* *
1238636 ATGTTCACGAATGC-AAAACGAAC
1 ATGTTCACGAATACTTAAACGAAC
*
1238659 ATGTTCACGAATACTTAAATGAAC
1 ATGTTCACGAATACTTAAACGAAC
* *
1238683 ATGTTTAC-AA-ACATTAAACGAAT
1 ATGTTCACGAATAC-TTAAACGAAC
1238706 ATGTTC
1 ATGTTC
1238712 GTGAACGTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
22 2 0.05
23 28 0.64
24 14 0.32
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (24 bp):
ATGTTCACGAATACTTAAACGAAC
Found at i:1239473 original size:18 final size:18
Alignment explanation
Indices: 1239450--1239501 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
1239440 ATTAGTAAAT
* *
1239450 AAAGTTCAAAGAGAAAGC
1 AAAGTTCAATGAGAAAAC
*
1239468 AAAGTTGAATGAGAAAAC
1 AAAGTTCAATGAGAAAAC
1239486 AAAGTTCAATGAGAAA
1 AAAGTTCAATGAGAAA
1239502 TAATAAAGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.56, C:0.08, G:0.21, T:0.15
Consensus pattern (18 bp):
AAAGTTCAATGAGAAAAC
Found at i:1239591 original size:99 final size:99
Alignment explanation
Indices: 1239448--1239648 Score: 341
Period size: 99 Copynumber: 2.0 Consensus size: 99
1239438 ATATTAGTAA
* * *
1239448 ATAAAGTTCAAAGAGAAAGCAAAGTTGAATGAGAAAACAAAGTTCAATGAGAAATAATAAAGTTT
1 ATAAAATTCAAAGAGAAAGCAAAGTTCAAAGAGAAAACAAAGTTCAATGAGAAATAATAAAGTTT
**
1239513 ACCTTTAATGATTTAGAGAATGTAAGTATTAAACC
66 ACCTTTAATGA-TTAGAGAATGTAAACATTAAACC
1239548 ATAAAATTCAAAGAGAAA-CAAAGTTCAAAGAGAAAACAAAGTTCAATGAGAAATAATAAAGTTT
1 ATAAAATTCAAAGAGAAAGCAAAGTTCAAAGAGAAAACAAAGTTCAATGAGAAATAATAAAGTTT
1239612 ACCTTTAATGATTAGAGAATGTAAACATTAAACC
66 ACCTTTAATGATTAGAGAATGTAAACATTAAACC
1239646 ATA
1 ATA
1239649 GTTGTATTGC
Statistics
Matches: 96, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
98 24 0.25
99 55 0.57
100 17 0.18
ACGTcount: A:0.51, C:0.09, G:0.15, T:0.25
Consensus pattern (99 bp):
ATAAAATTCAAAGAGAAAGCAAAGTTCAAAGAGAAAACAAAGTTCAATGAGAAATAATAAAGTTT
ACCTTTAATGATTAGAGAATGTAAACATTAAACC
Found at i:1239610 original size:20 final size:18
Alignment explanation
Indices: 1239554--1239600 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
1239544 AACCATAAAA
1239554 TTCAAAGAG-AAACAAAG
1 TTCAAAGAGAAAACAAAG
1239571 TTCAAAGAGAAAACAAAG
1 TTCAAAGAGAAAACAAAG
*
1239589 TTCAATGAGAAA
1 TTCAAAGAGAAA
1239601 TAATAAAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 9 0.32
18 19 0.68
ACGTcount: A:0.57, C:0.11, G:0.17, T:0.15
Consensus pattern (18 bp):
TTCAAAGAGAAAACAAAG
Found at i:1240893 original size:13 final size:13
Alignment explanation
Indices: 1240875--1240901 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1240865 GTGAGTGGAG
1240875 GTTCCATTATATA
1 GTTCCATTATATA
1240888 GTTCCATTATATA
1 GTTCCATTATATA
1240901 G
1 G
1240902 GAAGAATTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (13 bp):
GTTCCATTATATA
Found at i:1244756 original size:2 final size:2
Alignment explanation
Indices: 1244749--1244818 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
1244739 TAAGTTCAGG
1244749 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1244791 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1244819 CAAGGTAATT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1251179 original size:89 final size:91
Alignment explanation
Indices: 1251051--1251230 Score: 337
Period size: 89 Copynumber: 2.0 Consensus size: 91
1251041 GCCCCACAGG
*
1251051 AGCATTAGTCAACCCGAATAACATCGGGTACTCGATGTCCAAGTAAATTAACAAACCTTTATCTC
1 AGCATTAGTCAACCCGAACAACATCGGGTACTCGATGTCCAAGTAAATTAACAAACCTTTATCTC
1251116 CTTTCTCTAGA-GTGCCTGCAAAGAT
66 CTTTCTCTAGATGTGCCTGCAAAGAT
1251141 AGCATTAGTCAACCCGAACAA-ATCGGGTACTCGATGTCCAAGTAAATTAACAAACCTTTATCTC
1 AGCATTAGTCAACCCGAACAACATCGGGTACTCGATGTCCAAGTAAATTAACAAACCTTTATCTC
1251205 CTTTCTCTAGATGTGCCTGCAAAGAT
66 CTTTCTCTAGATGTGCCTGCAAAGAT
1251231 CTAAATGAAT
Statistics
Matches: 88, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
89 54 0.61
90 34 0.39
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (91 bp):
AGCATTAGTCAACCCGAACAACATCGGGTACTCGATGTCCAAGTAAATTAACAAACCTTTATCTC
CTTTCTCTAGATGTGCCTGCAAAGAT
Found at i:1252319 original size:24 final size:23
Alignment explanation
Indices: 1252268--1252319 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
1252258 CTAAACAAGT
*
1252268 ATGTTCACGAATGCAAAACGAAC
1 ATGTTCACGAATACAAAACGAAC
* *
1252291 ATGTTCACGAATACTTAAATGAAC
1 ATGTTCACGAATAC-AAAACGAAC
1252315 ATGTT
1 ATGTT
1252320 TACAAACATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 13 0.52
24 12 0.48
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.27
Consensus pattern (23 bp):
ATGTTCACGAATACAAAACGAAC
Found at i:1252341 original size:23 final size:24
Alignment explanation
Indices: 1252283--1252343 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 24
1252273 CACGAATGCA
*
1252283 AAACGAACATGTTCACGAATACTT
1 AAACGAACATGTTTACGAATACTT
*
1252307 AAATGAACATGTTTAC-AA-ACATT
1 AAACGAACATGTTTACGAATAC-TT
*
1252330 AAACGAATATGTTT
1 AAACGAACATGTTT
1252344 GTGAACGTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 2 0.06
23 16 0.50
24 14 0.44
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (24 bp):
AAACGAACATGTTTACGAATACTT
Found at i:1253111 original size:75 final size:76
Alignment explanation
Indices: 1252952--1253128 Score: 266
Period size: 75 Copynumber: 2.3 Consensus size: 76
1252942 AATTATAGAT
* * **
1252952 TGCTCAGAGGGAACCGATTCCCCCCCATATGAGGAACCGATCCCCCCTAAATGGTTTTGGCCCCG
1 TGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATCCCCCCTAAACAGTTTTGGCCCCG
*
1253017 AGATTTCCAGAA
65 AGAATTCCAGAA
* *
1253029 TGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTTT-GCTCCGA
1 TGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATCCCCCCTAAACAGTTTTGGCCCCGA
*
1253093 GAATTCCAGTA
66 GAATTCCAGAA
1253104 TGCTCGGAGGGAACCGATTCCCCCC
1 TGCTCGGAGGGAACCGATTCCCCCC
1253129 TTGTACAACG
Statistics
Matches: 92, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
75 40 0.43
76 34 0.37
77 18 0.20
ACGTcount: A:0.24, C:0.33, G:0.23, T:0.20
Consensus pattern (76 bp):
TGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATCCCCCCTAAACAGTTTTGGCCCCGA
GAATTCCAGAA
Found at i:1258917 original size:19 final size:19
Alignment explanation
Indices: 1258893--1258953 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 19
1258883 TTTTGGTGCA
*
1258893 GAGGGAATCGATCCCCCCT
1 GAGGGAACCGATCCCCCCT
*
1258912 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGA-TCCCCC-CT
1258933 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGA-TCCCCCC
1258954 CACAGGGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 10 0.29
20 6 0.17
21 2 0.06
22 1 0.03
23 16 0.46
ACGTcount: A:0.21, C:0.36, G:0.26, T:0.16
Consensus pattern (19 bp):
GAGGGAACCGATCCCCCCT
Found at i:1260922 original size:17 final size:17
Alignment explanation
Indices: 1260900--1260947 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
1260890 TTTCAACATT
1260900 TTTGATATTTTGGATTG
1 TTTGATATTTTGGATTG
1260917 TTTGAT-TTTGTGGATTG
1 TTTGATATTT-TGGATTG
*
1260934 -TTG-GATTTTGGATT
1 TTTGATATTTTGGATT
1260948 TATGAATAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 6 0.21
16 9 0.32
17 13 0.46
ACGTcount: A:0.15, C:0.00, G:0.27, T:0.58
Consensus pattern (17 bp):
TTTGATATTTTGGATTG
Found at i:1261689 original size:76 final size:76
Alignment explanation
Indices: 1261567--1261724 Score: 228
Period size: 76 Copynumber: 2.1 Consensus size: 76
1261557 CGATTCCCCC
* * ** *
1261567 CCCCCCATATGAGGAATCGGTCCCCCCTAAATGGTTTTGGCCCCGAGATTTCCAGAATGCTCGGA
1 CCCCCCATAGGAGGAACCGGTCCCCCCTAAACAGTTTTGGCCCCGAGAATTCCAGAATGCTCGGA
1261632 GGGAACCGATT
66 GGGAACCGATT
* * *
1261643 CCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTT-GCTCCGAGAATTCCAGTATGCTCGG
1 CCCCCCATAGGAGGAACCG-GTCCCCCCTAAACAGTTTTGGCCCCGAGAATTCCAGAATGCTCGG
1261707 AGGGAACCGATT
65 AGGGAACCGATT
1261719 CCCCCC
1 CCCCCC
1261725 TTGTACAACG
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
76 57 0.78
77 16 0.22
ACGTcount: A:0.23, C:0.34, G:0.23, T:0.21
Consensus pattern (76 bp):
CCCCCCATAGGAGGAACCGGTCCCCCCTAAACAGTTTTGGCCCCGAGAATTCCAGAATGCTCGGA
GGGAACCGATT
Found at i:1261724 original size:77 final size:77
Alignment explanation
Indices: 1261543--1261724 Score: 224
Period size: 76 Copynumber: 2.3 Consensus size: 77
1261533 AATTATAGAT
* * * **
1261543 TGCTCAGAGGGAACCGATTCCCCCCCCCCCATATGAGGAATCGGTCCCCCCTAAATGGTTTTGGC
1 TGCTCGGAGGGAACCGATT----CCCCCCCATAGGAGGAACCGGTCCCCCCTAAACAGTTTTGGC
*
1261608 CCCGAGATTTCCAGAA
62 CCCGAGAATTCCAGAA
* *
1261624 TGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTT-GCTCC
1 TGCTCGGAGGGAACCGATTCCCCCCCATAGGAGGAACCG-GTCCCCCCTAAACAGTTTTGGCCCC
*
1261687 GAGAATTCCAGTA
65 GAGAATTCCAGAA
1261700 TGCTCGGAGGGAACCGATTCCCCCC
1 TGCTCGGAGGGAACCGATTCCCCCC
1261725 TTGTACAACG
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
76 51 0.57
77 21 0.23
81 18 0.20
ACGTcount: A:0.23, C:0.34, G:0.23, T:0.20
Consensus pattern (77 bp):
TGCTCGGAGGGAACCGATTCCCCCCCATAGGAGGAACCGGTCCCCCCTAAACAGTTTTGGCCCCG
AGAATTCCAGAA
Found at i:1262841 original size:18 final size:18
Alignment explanation
Indices: 1262818--1262869 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
1262808 ATTAGTAAAT
*
1262818 AAAGTTCAAAGAGAAAGA-
1 AAAGTTCAATGAGAAA-AC
*
1262836 AAAGTTGAATGAGAAAAC
1 AAAGTTCAATGAGAAAAC
1262854 AAAGTTCAATGAGAAA
1 AAAGTTCAATGAGAAA
1262870 TAATAAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
17 1 0.03
18 29 0.97
ACGTcount: A:0.58, C:0.06, G:0.21, T:0.15
Consensus pattern (18 bp):
AAAGTTCAATGAGAAAAC
Found at i:1262950 original size:100 final size:100
Alignment explanation
Indices: 1262816--1263014 Score: 337
Period size: 100 Copynumber: 2.0 Consensus size: 100
1262806 ATATTAGTAA
* * *
1262816 ATAAAGTTCAAAGAGAAAGAAAAGTTGAATGAGAAAACAAAGTTCAATGAGAAATAATAAAGTTT
1 ATAAAATTCAAAGAGAAAGAAAAGTTCAAAGAGAAAACAAAGTTCAATGAGAAATAATAAAGTTT
**
1262881 ACCTTTAATGATTTAGAGAATGTAAGTATTAAACC
66 ACCTTTAATGATTTAGAGAATGTAAACATTAAACC
1262916 ATAAAATTCAAAGAGAAA-ACAAAGTTCAAAGAGAAAACAAAGTTCAATGAGAAATAATAAAGTT
1 ATAAAATTCAAAGAGAAAGA-AAAGTTCAAAGAGAAAACAAAGTTCAATGAGAAATAATAAAGTT
1262980 TACCTTTAATGATTTAGAGAATGTAAACATTAAAC
65 TACCTTTAATGATTTAGAGAATGTAAACATTAAAC
1263015 TATAGTTGTA
Statistics
Matches: 93, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
99 1 0.01
100 92 0.99
ACGTcount: A:0.52, C:0.08, G:0.15, T:0.25
Consensus pattern (100 bp):
ATAAAATTCAAAGAGAAAGAAAAGTTCAAAGAGAAAACAAAGTTCAATGAGAAATAATAAAGTTT
ACCTTTAATGATTTAGAGAATGTAAACATTAAACC
Found at i:1262979 original size:20 final size:18
Alignment explanation
Indices: 1262922--1262969 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
1262912 AACCATAAAA
1262922 TTCAAAGAGAAAACAAAG
1 TTCAAAGAGAAAACAAAG
1262940 TTCAAAGAGAAAACAAAG
1 TTCAAAGAGAAAACAAAG
*
1262958 TTCAATGAGAAA
1 TTCAAAGAGAAA
1262970 TAATAAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.58, C:0.10, G:0.17, T:0.15
Consensus pattern (18 bp):
TTCAAAGAGAAAACAAAG
Found at i:1266115 original size:2 final size:2
Alignment explanation
Indices: 1266108--1266153 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1266098 TAAGTTCAGG
1266108 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1266150 AT AT
1 AT AT
1266154 CAAGGTAATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1269887 original size:3 final size:3
Alignment explanation
Indices: 1269868--1269932 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
1269858 TTGTAATATT
**
1269868 TAA TAAA TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA TTT TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
1269915 TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
1269933 ACTTAAATGA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
3 46 0.88
4 6 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:1270169 original size:46 final size:45
Alignment explanation
Indices: 1270058--1270206 Score: 262
Period size: 45 Copynumber: 3.3 Consensus size: 45
1270048 GATGGAAATG
*
1270058 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGT
1270103 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-T
* *
1270149 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGC
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGT
1270194 TTTGAAAACATCA
1 TTTGAAAACATCA
1270207 AAAAGCTCCC
Statistics
Matches: 100, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
45 56 0.56
46 44 0.44
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (45 bp):
TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGT
Found at i:1270237 original size:76 final size:76
Alignment explanation
Indices: 1270139--1270586 Score: 729
Period size: 76 Copynumber: 5.9 Consensus size: 76
1270129 TTACAGATGA
*
1270139 CCCGAAGG-TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
1270203 ATCAAAAAGCT
66 ATCAAAAAGCT
* * *
1270214 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
1270279 ATCAAAAAGCT
66 ATCAAAAAGCT
** * * * * *
1270290 CTTGAAGGCTTTTTGAAAACATCTTGCACTGCAGGGCTTACAGATGACCCGAAGGTTTTGAAAAT
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
1270355 ATCAAAAAGCT
66 ATCAAAAAGCT
*
1270366 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
1270431 ATCAAAAAGCT
66 ATCAAAAAGCT
* *
1270442 CCTGAAGGCTTTTTGAAAACATCATGCACTGAAGGGA-TCACAGATGACCCGAAGGCTTTGAAAA
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAA-GGACTTACAGATGACCCGAAGGCTTTGAAAA
*
1270506 CATCAAAAAGTT
65 CATCAAAAAGCT
*
1270518 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
1270583 ATCA
66 ATCA
1270587 TGCACTGAAG
Statistics
Matches: 346, Mismatches: 24, Indels: 5
0.92 0.06 0.01
Matches are distributed among these distances:
75 10 0.03
76 334 0.97
77 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (76 bp):
CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
ATCAAAAAGCT
Found at i:1270582 original size:121 final size:121
Alignment explanation
Indices: 1270453--1270684 Score: 419
Period size: 121 Copynumber: 1.9 Consensus size: 121
1270443 CTGAAGGCTT
* *
1270453 TTTGAAAACATCATGCACTGAAGGGATCACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGTT
1 TTTGAAAACATCATGCACTGAAGGGATCACAGATAACCCGAAGGCTTTGAAAACATCAAAAAGCT
1270518 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGC
66 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGC
* * *
1270574 TTTGAAAACATCATGCACTGAAGGGCTTACAGATAACCCGAAGGCTTTGAAAACGTCAAAAAGCT
1 TTTGAAAACATCATGCACTGAAGGGATCACAGATAACCCGAAGGCTTTGAAAACATCAAAAAGCT
1270639 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATG
66 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATG
1270685 TGAGAAATAG
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
121 106 1.00
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (121 bp):
TTTGAAAACATCATGCACTGAAGGGATCACAGATAACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGC
Found at i:1270585 original size:45 final size:45
Alignment explanation
Indices: 1270518--1270627 Score: 193
Period size: 45 Copynumber: 2.4 Consensus size: 45
1270508 TCAAAAAGTT
*
1270518 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGC--TTTGAAAACATCATGCACTGAAGGGCTTACAGATAA
1270565 CCCGAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATAA
1 CCCGAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATAA
1270610 CCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTGAAAAC
1270628 GTCAAAAAGC
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
45 53 0.85
47 9 0.15
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.21
Consensus pattern (45 bp):
CCCGAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATAA
Found at i:1270654 original size:152 final size:151
Alignment explanation
Indices: 1270183--1270662 Score: 483
Period size: 152 Copynumber: 3.2 Consensus size: 151
1270173 ACTTACAGAT
* * *
1270183 GACCCTAAGGC-TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTA
1 GACCCGAAGGCTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAA
* * ***
1270247 GGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT-CTTGAAGGCTTTTTGAAAACA
66 GGGCTTACAGATGACCCGAAGGCTTTGAAAACATC--AAAGCTAC-TGAAGGCTTACAGAAAACA
* ** * ** * * * *
1270311 TCTTGCACTGCAGGGCTTACAGAT
128 CCAGGCACTGAAACGATCACAAAA
*
1270335 GACCCGAAGG-TTTTGAAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAA
1 GACCCGAAGGCTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAA
* *** *
1270399 GGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCTGAAGGCTTTTTGAAAACAT
66 GGGCTTACAGATGACCCGAAGGCTTTGAAAACATC--AAAGCTACTGAAGGCTTACAGAAAACAC
* ** * *
1270464 CATGCACTGAAGGGATCACAGAT
129 CAGGCACTGAAACGATCACAAAA
*
1270487 GACCCGAAGGC-TTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGAAAACATCATGCACTGAA
1 GACCCGAAGGCTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAA
* *
1270551 GGGCTTACAGATGACCCGAAGGCTTTGAAAACATC-ATGC-ACTGAAGGGCTTACAGATAAC-CC
66 GGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAGCTACTGAA-GGCTTACAGAAAACACC
**
1270613 GAAGGCTTTGAAAACG-TCA-AAAA
130 --AGGCACTG-AAACGATCACAAAA
*
1270636 GCTCCCGAAGGCTTTTTGAAAACATCA
1 G-ACCCGAAGGC-TTTTGAAAACATCA
1270663 TGCACTGAAG
Statistics
Matches: 291, Mismatches: 27, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
148 6 0.02
149 16 0.05
150 17 0.06
151 3 0.01
152 248 0.85
153 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (151 bp):
GACCCGAAGGCTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAA
GGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAGCTACTGAAGGCTTACAGAAAACACCA
GGCACTGAAACGATCACAAAA
Found at i:1270656 original size:228 final size:226
Alignment explanation
Indices: 1270183--1270662 Score: 558
Period size: 228 Copynumber: 2.1 Consensus size: 226
1270173 ACTTACAGAT
* * *
1270183 GACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAG
1 GACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAG
* * **
1270248 GACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCTTGAAGGCTTTTTGAAAACATC
66 GACTCACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATC
* * * * * *
1270313 TTGCACTGCAGGGCTTACAGATGACCCGAAGGTTTTGAAAATATCAAAAAGCTCCCGAAGGCTTT
131 ATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATC--AAAGCTACCGAAGGCTTA
** * * ** * * *
1270378 TTGAAAACATCATGCACTGAAGGGCTTACAGAT
194 CAGAAAACACCAGGCACTGAAACGCTCACAAAA
*
1270411 GACCCGAAGGCTTTGAAAACATCAAAAAGCTCCTGAAGGCTTTTTGAAAACATCATGCACTGAAG
1 GACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAA-
*
1270476 GGA-TCACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGAAAACAT
65 GGACTCACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACAT
* *
1270540 CATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATC-ATGC-ACTGAAGGGCTTA
130 CATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAGCTACCGAA-GGCTTA
* **
1270603 CAGATAAC-CCGAAGGCTTTGAAAACG-TCA-AAAA
194 CAGAAAACACC--AGGCACTG-AAACGCTCACAAAA
*
1270636 GCTCCCGAAGGCTTTTTGAAAACATCA
1 G-ACCCGAAGGC--TTTGAAAACATCA
1270663 TGCACTGAAG
Statistics
Matches: 214, Mismatches: 30, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
224 5 0.02
225 16 0.07
226 16 0.07
227 3 0.01
228 171 0.80
229 3 0.01
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (226 bp):
GACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAG
GACTCACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATC
ATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAGCTACCGAAGGCTTACA
GAAAACACCAGGCACTGAAACGCTCACAAAA
Found at i:1274253 original size:114 final size:114
Alignment explanation
Indices: 1274053--1274269 Score: 362
Period size: 114 Copynumber: 1.9 Consensus size: 114
1274043 GATCATGCAG
* * * *
1274053 TTCATCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCATATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
1274118 ACACTTCCAGAAGATGCTATTGGATCTCCTTATTTTTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGAGCTCCTTATTTTTACTATGAGCAAA
* *
1274167 TTCATCTTTCAAATCTAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
1274232 ACACTTCCAGAAGATGCTATTGGGGCTCCTTATTTTTA
66 ACACTTCCAGAAGATGCTATTGGAGCTCCTTATTTTTA
1274270 ATACGAGAAC
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 95 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGAGCTCCTTATTTTTACTATGAGCAAA
Found at i:1278686 original size:7 final size:7
Alignment explanation
Indices: 1278676--1278713 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
1278666 TAAAAATGAA
1278676 AAAATGC
1 AAAATGC
1278683 AAAATGC
1 AAAATGC
1278690 AAAATGC
1 AAAATGC
1278697 AAAATGC
1 AAAATGC
1278704 AAAATGC
1 AAAATGC
1278711 AAA
1 AAA
1278714 TTTAAATATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.61, C:0.13, G:0.13, T:0.13
Consensus pattern (7 bp):
AAAATGC
Found at i:1282817 original size:3 final size:3
Alignment explanation
Indices: 1282784--1282827 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
1282774 TTGTAATATT
* *
1282784 TAA TAAA TAA TATA TAA TTA TAA TTA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1282828 ACTTAAATGA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
3 29 0.83
4 6 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:1283582 original size:21 final size:21
Alignment explanation
Indices: 1283516--1283583 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
1283506 TAGAATATAT
*
1283516 TATTTTGAAATTAAT-TTTAAA
1 TATTTT-AAATTATTATTTAAA
* * *
1283537 TCTTTAAAGATT-TTAATTAAA
1 TATTTTAA-ATTATTATTTAAA
1283558 -ATTTTAAATTATTATTTAAA
1 TATTTTAAATTATTATTTAAA
1283578 TATTTT
1 TATTTT
1283584 TATTAAGTTA
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
19 3 0.08
20 16 0.44
21 17 0.47
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (21 bp):
TATTTTAAATTATTATTTAAA
Found at i:1283976 original size:24 final size:24
Alignment explanation
Indices: 1283948--1283994 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1283938 TTTTTGCATA
*
1283948 TTTTTCTCTGCTTTTGTGGCACGC
1 TTTTTCTCTGCTCTTGTGGCACGC
1283972 TTTTTCTCTGCTCTTGTGGCACG
1 TTTTTCTCTGCTCTTGTGGCACG
1283995 TTTCTTATGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.04, C:0.26, G:0.21, T:0.49
Consensus pattern (24 bp):
TTTTTCTCTGCTCTTGTGGCACGC
Found at i:1284890 original size:18 final size:18
Alignment explanation
Indices: 1284867--1284905 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1284857 CCCTAAAAAA
1284867 TTTAAAATTATTATATAT
1 TTTAAAATTATTATATAT
* *
1284885 TTTAAATTTTTTATATAT
1 TTTAAAATTATTATATAT
1284903 TTT
1 TTT
1284906 TTATTAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTAAAATTATTATATAT
Found at i:1286094 original size:41 final size:41
Alignment explanation
Indices: 1285962--1286340 Score: 334
Period size: 41 Copynumber: 9.2 Consensus size: 41
1285952 TAACTTTTGC
* * * * * *
1285962 GGCGTTTTTCTTAAAAAGGCCGCTATAGAGTAGTACTTTAGC
1 GGCGTTTTT-ATACAAACGCCGCTATAGACTTGTACTTTAGT
* * * *
1286004 GGCGTTTGTATACAAACGCCG-TAATAG-GTT-CATTTATAGT
1 GGCGTTTTTATACAAACGCCGCT-ATAGACTTGTACTT-TAGT
* * * *
1286044 GGTGTTTTT-TCAACAAACGCCGCAATAGAGTAGTACTTTAGT
1 GGCGTTTTTAT--ACAAACGCCGCTATAGACTTGTACTTTAGT
* *
1286086 GGCGTTTTTGTACAAACGCCGCTATAGACTCGTACTTTAGT
1 GGCGTTTTTATACAAACGCCGCTATAGACTTGTACTTTAGT
** * *
1286127 GGCGTTTTTATACAAACGTTGCTATACAATTGTACTTTAGT
1 GGCGTTTTTATACAAACGCCGCTATAGACTTGTACTTTAGT
* * * * *
1286168 GGCATTTGTGTTTATAAACCCCGCTATACACTTGTACTTTAGT
1 GGCGTTT-T-TATACAAACGCCGCTATAGACTTGTACTTTAGT
* * * *
1286211 GGCGTTTATATACAAACGCCGCTATACACTGGTACTTTGGT
1 GGCGTTTTTATACAAACGCCGCTATAGACTTGTACTTTAGT
* * * *
1286252 GGCGTTTTTATATAAACACCGCTATATAATTGTACTTTAGT
1 GGCGTTTTTATACAAACGCCGCTATAGACTTGTACTTTAGT
* * * *
1286293 GGCGTTTATATACATACGCCACTATAGACTCGTACTTTAGT
1 GGCGTTTTTATACAAACGCCGCTATAGACTTGTACTTTAGT
1286334 GGCGTTT
1 GGCGTTT
1286341 GTATTTATAA
Statistics
Matches: 274, Mismatches: 53, Indels: 21
0.79 0.15 0.06
Matches are distributed among these distances:
39 4 0.01
40 13 0.05
41 197 0.72
42 23 0.08
43 37 0.14
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (41 bp):
GGCGTTTTTATACAAACGCCGCTATAGACTTGTACTTTAGT
Found at i:1286256 original size:166 final size:166
Alignment explanation
Indices: 1286056--1286357 Score: 406
Period size: 166 Copynumber: 1.8 Consensus size: 166
1286046 TGTTTTTTCA
* * * * *
1286056 ACAAACGCCGCAATAGAGTAGTACTTTAGTGGCGTTTTTGTACAAACGCCGCTATAGACTCGTAC
1 ACAAACGCCGCAATACACTAGTACTTTAGTGGCGTTTTTATACAAACACCGCTATAGAATCGTAC
* *** * *
1286121 TTTAGTGGCGTTTTTATACAAACGTTGCTATACAATTGTACTTTAGTGGCATTTGTGTTTATAAA
66 TTTAGTGGCGTTTATATACAAACGCCACTATACAATCGTACTTTAGTGGCATTTGTATTTATAAA
1286186 CCCCGCTATACACTTGTACTTTAGTGGCGTTTATAT
131 CCCCGCTATACACTTGTACTTTAGTGGCGTTTATAT
* * * * * *
1286222 ACAAACGCCGCTATACACTGGTACTTTGGTGGCGTTTTTATATAAACACCGCTATATAATTGTAC
1 ACAAACGCCGCAATACACTAGTACTTTAGTGGCGTTTTTATACAAACACCGCTATAGAATCGTAC
* * * *
1286287 TTTAGTGGCGTTTATATACATACGCCACTATAGACTCGTACTTTAGTGGCGTTTGTATTTATAAA
66 TTTAGTGGCGTTTATATACAAACGCCACTATACAATCGTACTTTAGTGGCATTTGTATTTATAAA
*
1286352 CGCCGC
131 CCCCGC
1286358 AAATTTATAA
Statistics
Matches: 114, Mismatches: 22, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
166 114 1.00
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (166 bp):
ACAAACGCCGCAATACACTAGTACTTTAGTGGCGTTTTTATACAAACACCGCTATAGAATCGTAC
TTTAGTGGCGTTTATATACAAACGCCACTATACAATCGTACTTTAGTGGCATTTGTATTTATAAA
CCCCGCTATACACTTGTACTTTAGTGGCGTTTATAT
Found at i:1286353 original size:125 final size:126
Alignment explanation
Indices: 1286076--1286357 Score: 347
Period size: 125 Copynumber: 2.3 Consensus size: 126
1286066 CAATAGAGTA
* *
1286076 GTACTTTAGTGGCGTTTT-TGTACAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAC
1 GTACTTTAGTGGCGTTTTATATACAAACGCCGCTATACACTCGTACTTTAGTGGCGTTTTTATAC
*** * * * * * *
1286140 AAACGTTGCTATACAATTGTACTTTAGTGGCATTTGTGTTTATAAACCCCGCTATACACTT
66 AAACACCGCTATACAATTGTACTTTAGTGGCAGTTGTATATACAAACCCCACTATACACTC
* * *
1286201 GTACTTTAGTGGCG-TTTATATACAAACGCCGCTATACACTGGTACTTTGGTGGCGTTTTTATAT
1 GTACTTTAGTGGCGTTTTATATACAAACGCCGCTATACACTCGTACTTTAGTGGCGTTTTTATAC
* * * *
1286265 AAACACCGCTATATAATTGTACTTTAGTGGC-GTT-TATATACATACGCCACTATAGACTC
66 AAACACCGCTATACAATTGTACTTTAGTGGCAGTTGTATATACAAACCCCACTATACACTC
* *
1286324 GTACTTTAGTGGCGTTTGTATTTATAAACGCCGC
1 GTACTTTAGTGGCGTTT-TATATACAAACGCCGC
1286358 AAATTTATAA
Statistics
Matches: 134, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
123 31 0.23
124 7 0.05
125 96 0.72
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (126 bp):
GTACTTTAGTGGCGTTTTATATACAAACGCCGCTATACACTCGTACTTTAGTGGCGTTTTTATAC
AAACACCGCTATACAATTGTACTTTAGTGGCAGTTGTATATACAAACCCCACTATACACTC
Found at i:1286464 original size:21 final size:21
Alignment explanation
Indices: 1286439--1286479 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1286429 CGCCTTTTAC
*
1286439 CCAAACCCATCTGCTTCACTA
1 CCAAACCCATCTGCGTCACTA
1286460 CCAAACCCATCTGCGTCACT
1 CCAAACCCATCTGCGTCACT
1286480 GCCATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.44, G:0.07, T:0.22
Consensus pattern (21 bp):
CCAAACCCATCTGCGTCACTA
Found at i:1290289 original size:43 final size:42
Alignment explanation
Indices: 1290221--1290659 Score: 309
Period size: 43 Copynumber: 10.5 Consensus size: 42
1290211 AACAGAGTGC
* * * *
1290221 TAGATCTGACCTTTTGCGACATTTGTATCTAAAAACACCGCCA
1 TAGATCTGACCTTTTGCG-CGTTTGTATCCAAAAACGCCGCTA
* * *
1290264 TAGATCTGACCTTTTACAGCGTTTGTA-CCAAAAATGCCACTA
1 TAGATCTGACCTTTTGC-GCGTTTGTATCCAAAAACGCCGCTA
* *
1290306 TAGATTTGATCTTTTGCGGCGTTTGTATCCAAAAACGCCGCTA
1 TAGATCTGACCTTTTGC-GCGTTTGTATCCAAAAACGCCGCTA
* * *
1290349 TAGAACTGACCTTTTGCGACGTTTGTATCAAAAAATGCCGCTA
1 TAGATCTGACCTTTTGCG-CGTTTGTATCCAAAAACGCCGCTA
* *
1290392 TAGATCTAACCTTTTGCGGCGTTTCTATCCAAAAACGCCGCTA
1 TAGATCTGACCTTTTGC-GCGTTTGTATCCAAAAACGCCGCTA
* *
1290435 TAGATATGACCTTTT--GC------A---AAAAA-GCCACTA
1 TAGATCTGACCTTTTGCGCGTTTGTATCCAAAAACGCCGCTA
* * * *
1290465 TAGATCTAACCTTTTGCGGTGTTTGT-TCTAAAAACGCTGCTA
1 TAGATCTGACCTTTTGC-GCGTTTGTATCCAAAAACGCCGCTA
* * * * * *
1290507 TAGATATGACATTTTACGGCGTTTGT-TCTAAAAACGTCGTTA
1 TAGATCTGACCTTTTGC-GCGTTTGTATCCAAAAACGCCGCTA
* * * *
1290549 TAGATCTCTAACTTTTGCGGCGTTTGT-TCCAAAAACGTCGTTA
1 TAGATCT-GACCTTTTGC-GCGTTTGTATCCAAAAACGCCGCTA
* * * * *
1290592 TAGATATCAACCTTTCGCGACGTTTGT-TCCGAAAACGCCGCGA
1 TAGATCT-GACCTTTTGCG-CGTTTGTATCCAAAAACGCCGCTA
* *
1290635 TAGATCTTTACCTATTGCGGCGTTT
1 TAGATC-TGACCTTTTGC-GCGTTT
1290660 TTTGTTCTCA
Statistics
Matches: 318, Mismatches: 57, Indels: 42
0.76 0.14 0.10
Matches are distributed among these distances:
30 19 0.06
31 5 0.02
33 1 0.00
34 1 0.00
40 2 0.01
41 5 0.02
42 80 0.25
43 201 0.63
44 4 0.01
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (42 bp):
TAGATCTGACCTTTTGCGCGTTTGTATCCAAAAACGCCGCTA
Found at i:1290421 original size:86 final size:85
Alignment explanation
Indices: 1290221--1290595 Score: 316
Period size: 85 Copynumber: 4.6 Consensus size: 85
1290211 AACAGAGTGC
* * * * * * *
1290221 TAGATCTGACCTTTTGCGACATTTGTATCTAAAAACACCGCCATAGATCTGACCTTTTACAGCGT
1 TAGATCTGACCTTTTGCGGCGTTTGTATCCAAAAACGCCGCTATAGAACTGACCTTTTGCAGCGT
*
1290286 TTGTACCAAAAATGCCACTA
66 TTGTACAAAAAATGCCACTA
* *
1290306 TAGATTTGATCTTTTGCGGCGTTTGTATCCAAAAACGCCGCTATAGAACTGACCTTTTGC-GACG
1 TAGATCTGACCTTTTGCGGCGTTTGTATCCAAAAACGCCGCTATAGAACTGACCTTTTGCAG-CG
*
1290370 TTTGTATCAAAAAATGCCGCTA
65 TTTGTA-CAAAAAATGCCACTA
* *
1290392 TAGATCTAACCTTTTGCGGCGTTTCTATCCAAAAACGCCGCTATAGATA-TGACC---T------
1 TAGATCTGACCTTTTGCGGCGTTTGTATCCAAAAACGCCGCTATAGA-ACTGACCTTTTGCAGCG
1290447 TTTG--CAAAAAA-GCCACTA
65 TTTGTACAAAAAATGCCACTA
* * * * * * *
1290465 TAGATCTAACCTTTTGCGGTGTTTGT-TCTAAAAACGCTGCTATAGATA-TGACATTTTACGGCG
1 TAGATCTGACCTTTTGCGGCGTTTGTATCCAAAAACGCCGCTATAGA-ACTGACCTTTTGCAGCG
* * * * **
1290528 TTTGTTCTAAAAACGTCGTTA
65 TTTGTACAAAAAATGCCACTA
* * * *
1290549 TAGATCTCTAACTTTTGCGGCGTTTGT-TCCAAAAACGTCGTTATAGA
1 TAGATCT-GACCTTTTGCGGCGTTTGTATCCAAAAACGCCGCTATAGA
1290596 TATCAACCTT
Statistics
Matches: 242, Mismatches: 32, Indels: 32
0.79 0.10 0.10
Matches are distributed among these distances:
72 24 0.10
73 30 0.12
74 7 0.03
75 1 0.00
77 4 0.02
81 4 0.02
83 7 0.03
84 12 0.05
85 91 0.38
86 61 0.25
87 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.33
Consensus pattern (85 bp):
TAGATCTGACCTTTTGCGGCGTTTGTATCCAAAAACGCCGCTATAGAACTGACCTTTTGCAGCGT
TTGTACAAAAAATGCCACTA
Found at i:1290466 original size:30 final size:30
Alignment explanation
Indices: 1290421--1290481 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
1290411 CGTTTCTATC
* * *
1290421 CAAAAACGCCGCTATAGATATGACCTTTTG
1 CAAAAAAGCCACTATAGATATAACCTTTTG
*
1290451 CAAAAAAGCCACTATAGATCTAACCTTTTG
1 CAAAAAAGCCACTATAGATATAACCTTTTG
1290481 C
1 C
1290482 GGTGTTTGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (30 bp):
CAAAAAAGCCACTATAGATATAACCTTTTG
Found at i:1294258 original size:2 final size:2
Alignment explanation
Indices: 1294251--1294275 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1294241 ATCATATAAT
1294251 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1294276 TTAATTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1299730 original size:18 final size:18
Alignment explanation
Indices: 1299709--1299751 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
1299699 TAAATCTAAA
1299709 AAATTCTACAAAATTCTT
1 AAATTCTACAAAATTCTT
* * * *
1299727 AAATTATTCAAACTTTTT
1 AAATTCTACAAAATTCTT
1299745 AAATTCT
1 AAATTCT
1299752 TTAAATCTCT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATTCTACAAAATTCTT
Found at i:1300096 original size:20 final size:20
Alignment explanation
Indices: 1300073--1300113 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1300063 GTACTTATAT
*
1300073 TATTCTTAAAGTACCGATAC
1 TATTCTTAAAATACCGATAC
*
1300093 TATTCTTAAAATATCGATAC
1 TATTCTTAAAATACCGATAC
1300113 T
1 T
1300114 CCATGAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (20 bp):
TATTCTTAAAATACCGATAC
Found at i:1305476 original size:20 final size:19
Alignment explanation
Indices: 1305453--1305497 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1305443 TATTTTTTAT
* *
1305453 TATTTATTTATTTTTAATAA
1 TATTTATATATATTTAAT-A
*
1305473 TATTTATATGTATTTAATA
1 TATTTATATATATTTAATA
1305492 TATTTA
1 TATTTA
1305498 ATAATAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TATTTATATATATTTAATA
Found at i:1305487 original size:26 final size:30
Alignment explanation
Indices: 1305448--1305503 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
1305438 AATTATATTT
*
1305448 TTTATTATTTATTT-AT-T-TTTAATAATA
1 TTTATTATGTATTTAATATATTTAATAATA
1305475 TTTA-TATGTATTTAATATATTTAATAATA
1 TTTATTATGTATTTAATATATTTAATAATA
1305504 ATAATAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 8 0.32
27 6 0.24
28 1 0.04
29 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (30 bp):
TTTATTATGTATTTAATATATTTAATAATA
Found at i:1305504 original size:3 final size:3
Alignment explanation
Indices: 1305496--1305562 Score: 107
Period size: 3 Copynumber: 22.3 Consensus size: 3
1305486 TTAATATATT
* *
1305496 TAA TAA TAA TAA TAA TAA TGA TGA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1305544 TAA TAA TAA TAA TGA TAA T
1 TAA TAA TAA TAA TAA TAA T
1305563 GATATGGGTA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1306025 original size:112 final size:113
Alignment explanation
Indices: 1305887--1306122 Score: 377
Period size: 112 Copynumber: 2.1 Consensus size: 113
1305877 GAATTATGCC
* * *
1305887 AAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
1305951 TATGAAC-TTCTCCGGAAAAGATAATCCATCAATTGATGGATTCAGGT
66 TATGAACTTTCTCCGGAAAAAATAATCCATCAAGTGATGAATTCAGGT
1305998 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
1306063 TATGAACTTTTTCTGGAAAAAATGATCCATCAAGTGATGAATTCAGGT
66 TATGAACTTTCTCCGGAAAAAATAATCCATCAAGTGATGAATTCAGGT
1306111 AAAAGGTTGAAC
1 AAAAGGTTGAAC
1306123 TCTACCTGGC
Statistics
Matches: 114, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
111 4 0.04
112 64 0.56
113 46 0.40
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCCGGAAAAAATAATCCATCAAGTGATGAATTCAGGT
Found at i:1306248 original size:166 final size:166
Alignment explanation
Indices: 1305974--1306288 Score: 612
Period size: 166 Copynumber: 1.9 Consensus size: 166
1305964 GGAAAAGATA
* *
1305974 ATCCATCAATTGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
1 ATCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
1306039 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAAATGATCCATCAAGTGATGAA
66 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAAATGATCCATCAAGTGATGAA
1306104 TTCAGGTAAAAGGTTGAACTCTACCTGGCAATGTTG
131 TTCAGGTAAAAGGTTGAACTCTACCTGGCAATGTTG
1306140 ATCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
1 ATCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
1306205 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAAATGATCCATCAAGTGATGAA
66 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAAATGATCCATCAAGTGATGAA
1306270 TTCAGGTAAAAGGTTGAAC
131 TTCAGGTAAAAGGTTGAAC
1306289 AAATTCTTCT
Statistics
Matches: 147, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
166 147 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35
Consensus pattern (166 bp):
ATCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAAATGATCCATCAAGTGATGAA
TTCAGGTAAAAGGTTGAACTCTACCTGGCAATGTTG
Found at i:1306316 original size:113 final size:113
Alignment explanation
Indices: 1306138--1306948 Score: 1543
Period size: 113 Copynumber: 7.2 Consensus size: 113
1306128 CTGGCAATGT
*
1306138 TGATCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCT
1 TGATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCT
*
1306203 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAAA
66 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAAA
1306251 TGATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCT
1 TGATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCT
1306316 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG-AAAAA
66 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAAA
1306363 TGATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCT
1 TGATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCT
*
1306428 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAAA
66 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAAA
1306476 TGATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCT
1 TGATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCT
1306541 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAAA
66 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAAA
1306589 TGATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCT
1 TGATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCT
*
1306654 TCCTTCTTTAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAAA
66 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAAA
1306702 TGATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCT
1 TGATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCT
*
1306767 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGA
66 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAAA
1306815 TGATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCT
1 TGATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCT
*
1306880 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGA
66 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAAA
* *
1306928 TGATCCATCAAATGATAAATT
1 TGATCCATCAAGTGATGAATT
1306949 TGAATCTTTG
Statistics
Matches: 688, Mismatches: 9, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
112 111 0.16
113 577 0.84
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.37
Consensus pattern (113 bp):
TGATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCT
TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAAA
Found at i:1307915 original size:136 final size:134
Alignment explanation
Indices: 1307667--1307921 Score: 429
Period size: 136 Copynumber: 1.9 Consensus size: 134
1307657 CTACTGAATC
**
1307667 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTTTAAACTCAAT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAACTCAAT
* *
1307732 GATTGTTTTGTCAAATCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTTGATTCTGTCC
66 GATTGATTTGTCAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTTGATTCTGTCC
1307797 AATT
131 AATT
* *
1307801 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGAGCACATTCATCTTCCAAATTCAA
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT-GAACACATTCATCTTCCAAACTCAA
*
1307866 TGATTGGATTTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
65 TGATT-GATTTGTCAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCT
1307922 ATTGGCACAT
Statistics
Matches: 112, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
134 39 0.35
135 26 0.23
136 47 0.42
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (134 bp):
AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAACTCAAT
GATTGATTTGTCAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTTGATTCTGTCC
AATT
Found at i:1307967 original size:83 final size:84
Alignment explanation
Indices: 1307801--1308004 Score: 376
Period size: 83 Copynumber: 2.4 Consensus size: 84
1307791 CTGTCCAATT
1307801 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGAGCACATTCATCTTCCAAATTCAA
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGAGCACATTCATCTTCCAAATTCAA
1307866 TGATTGGATTTGTCAAACC
66 TGATTGGATTTGTCAAACC
*
1307885 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCACATTCATCTTCCAAATTCAA
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGAGCACATTCATCTTCCAAATTCAA
1307949 TGATTGG-TTCTGTCAAACC
66 TGATTGGATT-TGTCAAACC
1307968 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1308005 TGATTCTGTC
Statistics
Matches: 118, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
82 2 0.02
83 76 0.64
84 40 0.34
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.25
Consensus pattern (84 bp):
AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGAGCACATTCATCTTCCAAATTCAA
TGATTGGATTTGTCAAACC
Found at i:1308044 original size:219 final size:218
Alignment explanation
Indices: 1307666--1308071 Score: 697
Period size: 219 Copynumber: 1.9 Consensus size: 218
1307656 CCTACTGAAT
**
1307666 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTTTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAACTCAA
* *
1307731 TGATTGTTTTGTCAAATCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTTGATTCTGTC
66 TGATTGTTCTGTCAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTTGATTCTGTC
*
1307796 CAATTAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGAGCACATTCATCTTCCAAA
131 CAATTAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGAGCAAATTCATCTTCCAAA
1307861 TTCAATGATTGGATTTGTCAAAC
196 TTCAATGATTGGATTTGTCAAAC
* *
1307884 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCACATTCATCTTCCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCCAAACTCA
*
1307948 ATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTTGATTCTG
65 ATGATT-GTTCTGTCAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTTGATTCTG
* *
1308013 TCCCATTAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCAT
129 TCCAATTAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGAGCAAATTCAT
1308072 TTGTTCTATT
Statistics
Matches: 176, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
218 63 0.36
219 113 0.64
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.27
Consensus pattern (218 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAACTCAA
TGATTGTTCTGTCAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTTGATTCTGTC
CAATTAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGAGCAAATTCATCTTCCAAA
TTCAATGATTGGATTTGTCAAAC
Found at i:1312976 original size:202 final size:200
Alignment explanation
Indices: 1312633--1313034 Score: 770
Period size: 202 Copynumber: 2.0 Consensus size: 200
1312623 ATAAATGTAA
1312633 AAATGTAAGAAAATGTAAAGAATCATTGCCATCTAAAATTTTAAAGAAATTTCTTATATTTACAT
1 AAATGTAAGAAAATGTAAAGAATCATTGCCATCTAAAATTTTAAAGAAATTTCTTATATTTACAT
1312698 AATTTCTTTTACAAGATAACAAAAAGTTTCATATTTTTGAGCTAAACATAAAGATTAGTTCTGAA
66 AATTTCTTTTACAAGATAACAAAAAGTTTCATATTTTTGAGCTAAACATAAAGATTAGTTCTGAA
1312763 TATTACTCTGCATTAATATTAAAAACTATAGGAAGATCTTCAGTGGTCCAATTGGTGAGGGTTT-
131 TATTACTCTGCATTAATATTAAAAACTATAGGAAGATCTTCAGTGGTCCAATTGGTGAGGGTTTC
1312827 TCCAG
196 TCCAG
1312832 AAATGTAAGAAAATGTAAAGAATCATTGCCATCTAAAATTTTAAAGAAAATTTCTTATATTTAAC
1 AAATGTAAGAAAATGTAAAGAATCATTGCCATCTAAAATTTTAAAG-AAATTTCTTATATTT-AC
1312897 ATAATTTCTTTTACAAGATAACAAAAAGTTTTCATATTTTTGAGCTAAACATAAAGATTAGTTCT
64 ATAATTTCTTTTACAAGATAACAAAAAG-TTTCATATTTTTGAGCTAAACATAAAGATTAGTTCT
1312962 GAATATTACTCTGCATTAATATTAAAAACTATAGGAAGATCTTCAGTGGTCCAATTGGTGAGGGT
128 GAATATTACTCTGCATTAATATTAAAAACTATAGGAAGATCTTCAGTGGTCCAATTGGTGAGGGT
1313027 TTCTCCAG
193 TTCTCCAG
1313035 GAAGACATGG
Statistics
Matches: 199, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
199 46 0.23
200 15 0.08
201 30 0.15
202 103 0.52
203 5 0.03
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (200 bp):
AAATGTAAGAAAATGTAAAGAATCATTGCCATCTAAAATTTTAAAGAAATTTCTTATATTTACAT
AATTTCTTTTACAAGATAACAAAAAGTTTCATATTTTTGAGCTAAACATAAAGATTAGTTCTGAA
TATTACTCTGCATTAATATTAAAAACTATAGGAAGATCTTCAGTGGTCCAATTGGTGAGGGTTTC
TCCAG
Found at i:1321959 original size:3 final size:3
Alignment explanation
Indices: 1321951--1322008 Score: 98
Period size: 3 Copynumber: 19.3 Consensus size: 3
1321941 TTAATATATT
*
1321951 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1321999 TAA TGA TAA T
1 TAA TAA TAA T
1322009 GATATGGGTA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1324233 original size:21 final size:21
Alignment explanation
Indices: 1324200--1324268 Score: 111
Period size: 21 Copynumber: 3.3 Consensus size: 21
1324190 TTTACACTCA
* * *
1324200 ATGCACCGATGCACAATCACC
1 ATGCATCGGTGCACCATCACC
1324221 ATGCATCGGTGCACCATCACC
1 ATGCATCGGTGCACCATCACC
1324242 ATGCATCGGTGCACCATCACC
1 ATGCATCGGTGCACCATCACC
1324263 ATGCAT
1 ATGCAT
1324269 TGATGCATAC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.28, C:0.36, G:0.17, T:0.19
Consensus pattern (21 bp):
ATGCATCGGTGCACCATCACC
Found at i:1330924 original size:10 final size:11
Alignment explanation
Indices: 1330890--1330924 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
1330880 TATTGAAAAG
*
1330890 AAATAATATTA
1 AAATAAGATTA
1330901 AAATAAGATTA
1 AAATAAGATTA
1330912 AAATAAG-TTA
1 AAATAAGATTA
1330922 AAA
1 AAA
1330925 ATAATTAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 6 0.26
11 17 0.74
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.29
Consensus pattern (11 bp):
AAATAAGATTA
Found at i:1331221 original size:15 final size:15
Alignment explanation
Indices: 1331201--1331229 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1331191 ATTATTAATA
1331201 AATTATTAAAATTAT
1 AATTATTAAAATTAT
1331216 AATTATTAAAATTA
1 AATTATTAAAATTA
1331230 AAGATTCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTATTAAAATTAT
Found at i:1332414 original size:13 final size:13
Alignment explanation
Indices: 1332398--1332422 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1332388 TTTTAATATA
1332398 ATATAATAATAAT
1 ATATAATAATAAT
1332411 ATATAATAATAA
1 ATATAATAATAA
1332423 ATAAATGGGT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATATAATAATAAT
Found at i:1332919 original size:112 final size:113
Alignment explanation
Indices: 1332759--1333311 Score: 759
Period size: 112 Copynumber: 4.9 Consensus size: 113
1332749 CTAGAGTCAT
* ** *
1332759 GCAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTTCTT-CTTCTTCAGATGAGTTCTTCT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTC-TTCTTCCTTCTTCAGATGAGTTCTTCT
* * * *
1332823 CATTATGAACTCTCTCTGGAAAAG-TGATCCATCGAGTGATGAATTCGA
65 CATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGAATTCGA
* * *
1332871 GCGAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCT
1 GC-AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * * * *
1332935 C---ATGAACTCTTTCACTGGGGATA-CTGGTCCATCAAATGATGAATTCAA
65 CATTATGAACT-TTT-TCT-GGAAAAGCTGATCCATCAAATGATGAATTCGA
* * *
1332983 ACAAAAGATTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTATTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
1333048 ATTATGAACTTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
66 ATTATGAAC-TTTTTCTGGAAAAGCTGATCCATCAAATGATGAATTCGA
1333097 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
1333162 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGAATTCGA
1333210 GCAAAAGGTTGAAC-AATTCTTCTCATTATGAATTTCTTCTT-C--CTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
1333271 ATTATGAACTTTTTCTGGAAAAGTTGATCCATCAAATGATG
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATG
1333312 GATTTGAATC
Statistics
Matches: 400, Mismatches: 29, Indels: 27
0.88 0.06 0.06
Matches are distributed among these distances:
109 66 0.17
110 1 0.00
111 12 0.03
112 156 0.39
113 61 0.15
114 94 0.23
115 9 0.02
116 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGAATTCGA
Found at i:1332925 original size:24 final size:23
Alignment explanation
Indices: 1332890--1332934 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
1332880 TGAACAAGTT
1332890 CTTCTCATTATGAACTTCTTCTTC
1 CTTCTCATTATG-ACTTCTTCTTC
*
1332914 CTTCTTCA-TATGAGTTCTTCT
1 CTTC-TCATTATGACTTCTTCT
1332935 CATGAACTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 8 0.42
25 3 0.16
ACGTcount: A:0.16, C:0.27, G:0.07, T:0.51
Consensus pattern (23 bp):
CTTCTCATTATGACTTCTTCTTC
Found at i:1333139 original size:226 final size:221
Alignment explanation
Indices: 1332777--1333318 Score: 754
Period size: 226 Copynumber: 2.4 Consensus size: 221
1332767 TCGAACAAGC
* * *
1332777 TCTTCTCATTATGAACTTCTTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTG
1 TCTTCTCATTATGAATTTC-TTCTTCCTT-TTCAGATGAGTTCTTCTCATTATGAACTTTTTCTG
* * * * *
1332841 GAAAAGTGATCCATCGAGTGATGAATTCGAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACT
64 GAAAAGTGATCCATCAAATGATGGATTTGAGCGAAAAGTTGAACAAATTCTTCTCATTATGAACT
* * * *
1332906 TCTTCTTCCTTCTTCATATGAGTTCTTCTC-ATGAACTCTTTCACTGGGGATA-CTGGTCCATCA
129 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCTATGAACT-TTT-ACT-GGAAAAGCTGATCCATCA
1332969 AATGATGAATTCAAACAAAAGATTGAACAAAT
191 AATGATGAATTCAAACAAAAGATTGAAC-AAT
1333001 TCTTCTCATTATGAATTTCTTCTTCCTTATTCAGATGAGTTCTTCTCATTATGAACTTTTTTCTG
1 TCTTCTCATTATGAATTTCTTCTTCCTT-TTCAGATGAGTTCTTCTCATTATGAAC-TTTTTCTG
1333066 GAAAAGCTGATCCATCAAATGATGGATTTGAGC-AAAAGGTTGAACAAATTCTTCTCATTATGAA
64 GAAAAG-TGATCCATCAAATGATGGATTTGAGCGAAAA-GTTGAACAAATTCTTCTCATTATGAA
* *
1333130 TTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATC
127 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC--TATGAACTTTTACTGGAAAAGCTGATCCATC
* ** * *
1333195 AAATGATGGATTTGAGCAAAAGGTTGAACAAT
190 AAATGATGAATTCAAACAAAAGATTGAACAAT
1333227 TCTTCTCATTATGAATTTCTTCTTCC--TTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGA
1 TCTTCTCATTATGAATTTCTTCTTCCTTTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGA
1333290 AAAGTTGATCCATCAAATGATGGATTTGA
66 AAAG-TGATCCATCAAATGATGGATTTGA
1333319 ATCTATGCTA
Statistics
Matches: 289, Mismatches: 21, Indels: 18
0.88 0.06 0.05
Matches are distributed among these distances:
222 38 0.13
223 32 0.11
224 48 0.17
225 16 0.06
226 110 0.38
227 35 0.12
228 3 0.01
229 7 0.02
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.39
Consensus pattern (221 bp):
TCTTCTCATTATGAATTTCTTCTTCCTTTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGA
AAAGTGATCCATCAAATGATGGATTTGAGCGAAAAGTTGAACAAATTCTTCTCATTATGAACTTC
TTCTTCCTTCTTCAGATGAGTTCTTCTCTATGAACTTTTACTGGAAAAGCTGATCCATCAAATGA
TGAATTCAAACAAAAGATTGAACAAT
Found at i:1333808 original size:115 final size:115
Alignment explanation
Indices: 1333606--1333838 Score: 403
Period size: 115 Copynumber: 2.0 Consensus size: 115
1333596 AGAAGAACTC
* * * * *
1333606 ATGAGCAAATTCATCTTTTAAATCTAATGATTGGTTTTTGGGGTTCATACCAAATCAGATCAGAT
1 ATGAGCAAATTCATATTTCAAATCCAATGATTGGTTTTTAGGGTTCATACCAAACCAGATCAGAT
1333671 AACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACT
66 AACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACT
* *
1333721 ATGAGCACATTCATATTTCAAATCCAATGATTGGTTTTTAGGGTTCATATCAAACCAGATCAGAT
1 ATGAGCAAATTCATATTTCAAATCCAATGATTGGTTTTTAGGGTTCATACCAAACCAGATCAGAT
1333786 AACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACT
66 AACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACT
1333836 ATG
1 ATG
1333839 CACATGGCAC
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
115 111 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (115 bp):
ATGAGCAAATTCATATTTCAAATCCAATGATTGGTTTTTAGGGTTCATACCAAACCAGATCAGAT
AACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACT
Found at i:1339486 original size:21 final size:22
Alignment explanation
Indices: 1339436--1339501 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 22
1339426 AACCTCTAAC
*
1339436 ATATAAATAAAATAATTAAT-AC
1 ATATAAA-AAAATAATTAATAAA
1339458 ATGA-AAAAAAAT-ATTAATAAA
1 AT-ATAAAAAAATAATTAATAAA
* *
1339479 ATATAAAATAATAAGTAATAAA
1 ATATAAAAAAATAATTAATAAA
1339501 A
1 A
1339502 AATTTGAAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
20 7 0.19
21 15 0.41
22 14 0.38
23 1 0.03
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (22 bp):
ATATAAAAAAATAATTAATAAA
Found at i:1341717 original size:3 final size:3
Alignment explanation
Indices: 1341705--1341751 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
1341695 AATTATTTTT
*
1341705 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1341752 AAAATGGGTA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1344655 original size:19 final size:22
Alignment explanation
Indices: 1344618--1344771 Score: 88
Period size: 21 Copynumber: 7.6 Consensus size: 22
1344608 AATAATTAAA
1344618 ATAATATATATTATATATATTT
1 ATAATATATATTATATATATTT
1344640 ATAAT-TAT-TTAT-TATATTT
1 ATAATATATATTATATATATTT
* *
1344659 A-AATCTTAAATTA-ATATATTT
1 ATAAT-ATATATTATATATATTT
1344680 -T-ATA-ATATT-T-TATATTT
1 ATAATATATATTATATATATTT
* *
1344697 TTAATAT-TAATA-ATATATTT
1 ATAATATATATTATATATATTT
** * *
1344717 -TAATAATATAAAATAAAAATTCT
1 ATAAT-ATATATTATATATATT-T
*
1344740 -TAATATATA-TATATATATAT
1 ATAATATATATTATATATATTT
1344760 AT-ATATATATTA
1 ATAATATATATTA
1344772 ACCGGATCGG
Statistics
Matches: 104, Mismatches: 11, Indels: 35
0.69 0.07 0.23
Matches are distributed among these distances:
17 7 0.07
18 8 0.08
19 18 0.17
20 25 0.24
21 26 0.25
22 15 0.14
23 5 0.05
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (22 bp):
ATAATATATATTATATATATTT
Found at i:1344749 original size:2 final size:2
Alignment explanation
Indices: 1344742--1344769 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1344732 AAAATTCTTA
1344742 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1344770 TAACCGGATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1350971 original size:2 final size:2
Alignment explanation
Indices: 1350964--1350993 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1350954 TATGTTTAAA
1350964 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1350994 GAAGTTGTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1351126 original size:17 final size:17
Alignment explanation
Indices: 1351104--1351136 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1351094 AGAAAAATGT
1351104 TAAAGATTTACTTTAAG
1 TAAAGATTTACTTTAAG
1351121 TAAAGATTTACTTTAA
1 TAAAGATTTACTTTAA
1351137 ATGCAAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.42
Consensus pattern (17 bp):
TAAAGATTTACTTTAAG
Found at i:1353016 original size:4 final size:4
Alignment explanation
Indices: 1353009--1353099 Score: 60
Period size: 4 Copynumber: 21.8 Consensus size: 4
1352999 ATTTTGTTTG
** * *
1353009 ATTT ATTT ATTT ATTT -TGA ATTT ATTT ATTT -TTGG ATTT ATTT AATTAA
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATT-T ATTT ATTT -ATT-T
* *
1353058 ATTC ATTT ATTT AATTT TTTT GAATTT ATTT ATTT ATTT ATT
1 ATTT ATTT ATTT -ATTT ATTT --ATTT ATTT ATTT ATTT ATT
1353100 GAAGGAATAT
Statistics
Matches: 68, Mismatches: 11, Indels: 16
0.72 0.12 0.17
Matches are distributed among these distances:
3 3 0.04
4 50 0.74
5 12 0.18
6 3 0.04
ACGTcount: A:0.27, C:0.01, G:0.04, T:0.67
Consensus pattern (4 bp):
ATTT
Found at i:1354769 original size:26 final size:27
Alignment explanation
Indices: 1354740--1354793 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
1354730 TTCACCCACT
1354740 CGACTCGGTCATCATTT-AGCATATGG
1 CGACTCGGTCATCATTTAAGCATATGG
**
1354766 CGACTTTGTCATCATTTAAGCATATGG
1 CGACTCGGTCATCATTTAAGCATATGG
1354793 C
1 C
1354794 ACCACCGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.33
Consensus pattern (27 bp):
CGACTCGGTCATCATTTAAGCATATGG
Found at i:1355052 original size:20 final size:20
Alignment explanation
Indices: 1355024--1355062 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1355014 TGTAGATGAG
*
1355024 GGTGATGATGGTGATGGTGT
1 GGTGATGATGATGATGGTGT
*
1355044 GGTGGTGATGATGATGGTG
1 GGTGATGATGATGATGGTG
1355063 ATGATCAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.00, G:0.51, T:0.33
Consensus pattern (20 bp):
GGTGATGATGATGATGGTGT
Found at i:1356632 original size:324 final size:324
Alignment explanation
Indices: 1356010--1356659 Score: 1202
Period size: 324 Copynumber: 2.0 Consensus size: 324
1356000 GCGAGATTAT
*
1356010 TGACTATAAATATCCTCCTTCTGCTGATATTGTAAATTTTAACACAGTATATACTTATAAGAGGC
1 TGACTATAAATATCCTCCCTCTGCTGATATTGTAAATTTTAACACAG-ATATACTTATAAGAGGC
1356075 TTTTCTTCTGGTGGCACAACTTGGCACTAAACTTATGTTAATATTAGTGCTATAAGTTATGCCAC
65 TTTTCTTCTGGTGGCACAACTTGGCACTAAACTTATGTTAATATTAGTGCTATAAGTTATGCCAC
1356140 GCGAAAAGAATGTTTTATTATTATAAAAGATATGACATTCTCGACAAAATTCTTGTCTCATAAAT
130 GCGAAAAGAATGTTTTATTATTATAAAAGATATGACATTCTCGACAAAATTCTTGTCTCATAAAT
1356205 TCCACCTTTTTGGTCAAACCACAGGTTTATAAAAGACATTCTCTTCGGTGGCTCCTCTGCAACTT
195 TCCACCTTTTTGGTCAAACCACAGGTTTATAAAAGACATTCTCTTCGGTGGCTCCTCTGCAACTT
1356270 GCCTTTTATATAATATATTTATAAAGTCTATTAAACATGAATACCCCGATCTTCTTGGGAAACTC
260 GCCTTTTATATAATATATTTATAAAGTCTATTAAACATGAATACCCCGATCTTCTTGGGAAACTC
1356335 TGACTATAAATATCCTCTCCTCTGCTGATATTGTAAATTTTAACACAG-TATACTTATAAGA-GC
1 TGACTATAAATATCCTC-CCTCTGCTGATATTGTAAATTTTAACACAGATATACTTATAAGAGGC
1356398 TTTTCTTCTGGTGGCACAACTTGGCACTAAACTTATGTTAATATTAGTGCTATAAGTTATGCCAC
65 TTTTCTTCTGGTGGCACAACTTGGCACTAAACTTATGTTAATATTAGTGCTATAAGTTATGCCAC
1356463 GCGAAAA-AATG-TTTATTATTAT-AAAGATATGACATTCTCGACAAAATTCTTGTCTCATAAAT
130 GCGAAAAGAATGTTTTATTATTATAAAAGATATGACATTCTCGACAAAATTCTTGTCTCATAAAT
1356525 TCCACCTTTTTGGTCAAACCAACAGTGTTTATAAAAGACATTCTCTTCGGGTGGCCTCCTCTGCA
195 TCCACCTTTTTGGTCAAACC-ACAG-GTTTATAAAAGACATTCTCTTC-GGTGG-CTCCTCTGCA
1356590 ACTTGCCTTTTATATAATATATTTATAAAGTCTATTAAACATGAATACCCCGATCTTCTTGGGAA
256 ACTTGCCTTTTATATAATATATTTATAAAGTCTATTAAACATGAATACCCCGATCTTCTTGGGAA
1356655 ACTC
321 ACTC
1356659 T
1 T
1356660 ACGAAGGCAT
Statistics
Matches: 319, Mismatches: 1, Indels: 11
0.96 0.00 0.03
Matches are distributed among these distances:
320 60 0.19
321 15 0.05
322 26 0.08
323 79 0.25
324 93 0.29
325 17 0.05
326 29 0.09
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.36
Consensus pattern (324 bp):
TGACTATAAATATCCTCCCTCTGCTGATATTGTAAATTTTAACACAGATATACTTATAAGAGGCT
TTTCTTCTGGTGGCACAACTTGGCACTAAACTTATGTTAATATTAGTGCTATAAGTTATGCCACG
CGAAAAGAATGTTTTATTATTATAAAAGATATGACATTCTCGACAAAATTCTTGTCTCATAAATT
CCACCTTTTTGGTCAAACCACAGGTTTATAAAAGACATTCTCTTCGGTGGCTCCTCTGCAACTTG
CCTTTTATATAATATATTTATAAAGTCTATTAAACATGAATACCCCGATCTTCTTGGGAAACTC
Found at i:1356924 original size:16 final size:16
Alignment explanation
Indices: 1356903--1356942 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
1356893 TCTCAAAAGA
*
1356903 CATCCTCTTCTGGTGG
1 CATCCTCTTCCGGTGG
1356919 CATCCTCTTCCGGTGG
1 CATCCTCTTCCGGTGG
1356935 CATCCTCT
1 CATCCTCT
1356943 ACTTAAGGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.07, C:0.38, G:0.20, T:0.35
Consensus pattern (16 bp):
CATCCTCTTCCGGTGG
Found at i:1358036 original size:2 final size:2
Alignment explanation
Indices: 1358029--1358054 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1358019 AAAGCTTTTA
1358029 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1358055 TGTAACAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1358755 original size:23 final size:23
Alignment explanation
Indices: 1358720--1358781 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
1358710 ACCACATAGA
* *
1358720 TTTGCATCGAAGTGCCAAAAAGG
1 TTTGCACCAAAGTGCCAAAAAGG
* *
1358743 TTTGCACCAAAGTG-CGAATAGG
1 TTTGCACCAAAGTGCCAAAAAGG
1358765 TTTGCACCGAAA-TGCCA
1 TTTGCACC-AAAGTGCCA
1358782 CATAATTGTC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
22 16 0.50
23 16 0.50
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (23 bp):
TTTGCACCAAAGTGCCAAAAAGG
Found at i:1359919 original size:113 final size:110
Alignment explanation
Indices: 1359754--1359976 Score: 419
Period size: 113 Copynumber: 2.0 Consensus size: 110
1359744 AGCTTAATTT
1359754 TGCTTAGTCTTGCTGTATTATCAAAGAAAAAAGTCTTGTGCTTATTCCAAACTTAGAAGATGTGT
1 TGCTTAGTCTTGCTGTATTATCAAAGAAAAAAGTCTTGTGCTTATTCCAAACTTAGAAGATGTG-
1359819 TTATGATTGAGTATATTTTGATCATTTAAGCTTTACAAAGTGACTAA
65 TTATGATTGAGTATA-TTTGATCATTTAAGCTTTACAAAGTGACTAA
1359866 TGCTTAGTCTTGCTGTATTATCAAAAGAAAAAAGTCTTGTGCTTATTCCAAACTTAGAAGATGTG
1 TGCTTAGTCTTGCTGTATTATC-AAAGAAAAAAGTCTTGTGCTTATTCCAAACTTAGAAGATGTG
1359931 TTATGATTGAGTATATTTGATCATTTAAGCTTTACAAAGTGACTAA
65 TTATGATTGAGTATATTTGATCATTTAAGCTTTACAAAGTGACTAA
1359977 ATATTAATCA
Statistics
Matches: 110, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
111 31 0.28
112 37 0.34
113 42 0.38
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.39
Consensus pattern (110 bp):
TGCTTAGTCTTGCTGTATTATCAAAGAAAAAAGTCTTGTGCTTATTCCAAACTTAGAAGATGTGT
TATGATTGAGTATATTTGATCATTTAAGCTTTACAAAGTGACTAA
Found at i:1360199 original size:48 final size:48
Alignment explanation
Indices: 1360114--1360209 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
1360104 TAAATTAAAG
1360114 CTTCTAATTTATGTACTATTTATGGTGAATTTGTTTAAGTAACTGTCC
1 CTTCTAATTTATGTACTATTTATGGTGAATTTGTTTAAGTAACTGTCC
1360162 CTTCTAATTTATTGTACTATTTATGGTGAATTT-TTTAAGTAACTGTCC
1 CTTCTAATTTA-TGTACTATTTATGGTGAATTTGTTTAAGTAACTGTCC
1360210 ATGTTGTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
48 26 0.55
49 21 0.45
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (48 bp):
CTTCTAATTTATGTACTATTTATGGTGAATTTGTTTAAGTAACTGTCC
Found at i:1364319 original size:29 final size:30
Alignment explanation
Indices: 1364271--1364331 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
1364261 AATTTGGGTC
1364271 CTAAACTTTTCAAAAATTACACTTTAGCCA
1 CTAAACTTTTCAAAAATTACACTTTAGCCA
* * *
1364301 CTAAAC-TTTCAAAACTTACATTTTAGTCA
1 CTAAACTTTTCAAAAATTACACTTTAGCCA
1364330 CT
1 CT
1364332 GGTCAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 22 0.79
30 6 0.21
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (30 bp):
CTAAACTTTTCAAAAATTACACTTTAGCCA
Found at i:1367648 original size:21 final size:21
Alignment explanation
Indices: 1367622--1367682 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
1367612 ACAGAACCTC
1367622 CAGGGGGTATCGATTCCCCTA
1 CAGGGGGTATCGATTCCCCTA
* * *
1367643 CAGGGGGAATCGGTTCCCCTT
1 CAGGGGGTATCGATTCCCCTA
*
1367664 CAAGGGGGTATTGATTCCC
1 C-AGGGGGTATCGATTCCC
1367683 TCTGCAGCAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 19 0.58
22 14 0.42
ACGTcount: A:0.18, C:0.26, G:0.31, T:0.25
Consensus pattern (21 bp):
CAGGGGGTATCGATTCCCCTA
Found at i:1371269 original size:18 final size:18
Alignment explanation
Indices: 1371230--1371269 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1371220 TTTTAAGATC
*
1371230 ATCAATTTTCTTTTAATT
1 ATCAATTTTCTTTTAATG
*
1371248 ATCAATTTTCTTTTGATG
1 ATCAATTTTCTTTTAATG
1371266 ATCA
1 ATCA
1371270 TCATTGACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.55
Consensus pattern (18 bp):
ATCAATTTTCTTTTAATG
Found at i:1378875 original size:36 final size:36
Alignment explanation
Indices: 1378835--1378937 Score: 197
Period size: 36 Copynumber: 2.9 Consensus size: 36
1378825 ACGGTGCTGG
*
1378835 ACATTGATACATGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1378871 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1378907 ACATTGATACACGAATGTACCAAAGCTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
1378938 ATACTCAACT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
36 66 1.00
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.25
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATATGATA
Found at i:1382778 original size:57 final size:57
Alignment explanation
Indices: 1382691--1382858 Score: 264
Period size: 57 Copynumber: 2.9 Consensus size: 57
1382681 AACCATACAA
* * *
1382691 CCCGTCACGAACAGAAAGGCCCTGAGCATAAAGCCGAGGAACCTGCAAGTATTCAAC
1 CCCGTCACGAACAGTAAGGCCCTCAACATAAAGCCGAGGAACCTGCAAGTATTCAAC
* *
1382748 CCCGTCACAAACAGTAAGGCCCTCAACATAAAGCCGAGGAACCTGTAAGTATTCAAC
1 CCCGTCACGAACAGTAAGGCCCTCAACATAAAGCCGAGGAACCTGCAAGTATTCAAC
* * *
1382805 CCCGTCACGAACAGTAAGGCCCTCAACACAAAGCCGATGAACCTACAAGTATTC
1 CCCGTCACGAACAGTAAGGCCCTCAACATAAAGCCGAGGAACCTGCAAGTATTC
1382859 TTCCTCCAAC
Statistics
Matches: 101, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 101 1.00
ACGTcount: A:0.36, C:0.31, G:0.19, T:0.14
Consensus pattern (57 bp):
CCCGTCACGAACAGTAAGGCCCTCAACATAAAGCCGAGGAACCTGCAAGTATTCAAC
Found at i:1382960 original size:24 final size:24
Alignment explanation
Indices: 1382933--1383023 Score: 96
Period size: 24 Copynumber: 3.8 Consensus size: 24
1382923 CATAATTCAG
*
1382933 GTCAAGTATCATATCAGAATCCAA
1 GTCATGTATCATATCAGAATCCAA
1382957 GTCATGTATCATATCAGAATCCATA
1 GTCATGTATCATATCAGAATCCA-A
* * * *
1382982 -TC-TGTATTAGATCATAATCCAG
1 GTCATGTATCATATCAGAATCCAA
* *
1383004 GTCAGGTATCATAACAGAAT
1 GTCATGTATCATATCAGAAT
1383024 TCAAATCGGA
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
23 18 0.33
24 35 0.65
25 1 0.02
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (24 bp):
GTCATGTATCATATCAGAATCCAA
Found at i:1387412 original size:57 final size:55
Alignment explanation
Indices: 1387337--1387504 Score: 192
Period size: 57 Copynumber: 3.0 Consensus size: 55
1387327 ACCATACAAC
* *
1387337 CCCGTCACGAACAGTAAGGCCATGAGCACAAAGACGAGGAACCTGCAAGTATTCAA
1 CCCGTCACGAACAGTAAGGCCCTCAGCACAAAG-CGAGGAACCTGCAAGTATTCAA
* * * * * *
1387393 CTCCGTCATGAATAGTAAGGCCCTCAGCACAAAGCCGACGTACGTGTAAGTATTCAA
1 C-CCGTCACGAACAGTAAGGCCCTCAGCACAAAG-CGAGGAACCTGCAAGTATTCAA
* * *
1387450 CCCTATCACAAACAGTAAGGCCCTCAGCACAAAGCTGAGGAACCTGGAAGTATTC
1 CCC-GTCACGAACAGTAAGGCCCTCAGCACAAAGC-GAGGAACCTGCAAGTATTC
1387505 TTCCTCCAAC
Statistics
Matches: 92, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
56 4 0.04
57 88 0.96
ACGTcount: A:0.35, C:0.27, G:0.21, T:0.17
Consensus pattern (55 bp):
CCCGTCACGAACAGTAAGGCCCTCAGCACAAAGCGAGGAACCTGCAAGTATTCAA
Found at i:1387639 original size:23 final size:24
Alignment explanation
Indices: 1387579--1387669 Score: 94
Period size: 24 Copynumber: 3.8 Consensus size: 24
1387569 CATAATTCAA
* *
1387579 GTCAAGTATCATATCAGAATCCAG
1 GTCATGTATCAGATCAGAATCCAG
*
1387603 GTCATGTATCAGATCAGAATCCAT
1 GTCATGTATCAGATCAGAATCCAG
* *
1387627 GTC-TGTATTAGATCATAATCCAG
1 GTCATGTATCAGATCAGAATCCAG
* * * *
1387650 GCCAGGTATCATAACAGAAT
1 GTCATGTATCAGATCAGAAT
1387670 TCAAATCGAA
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
23 19 0.35
24 35 0.65
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (24 bp):
GTCATGTATCAGATCAGAATCCAG
Found at i:1389141 original size:12 final size:12
Alignment explanation
Indices: 1389124--1389148 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1389114 TTGCTTTCCC
1389124 GAACATTCTCTG
1 GAACATTCTCTG
1389136 GAACATTCTCTG
1 GAACATTCTCTG
1389148 G
1 G
1389149 TCTTGAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (12 bp):
GAACATTCTCTG
Found at i:1393735 original size:21 final size:21
Alignment explanation
Indices: 1393709--1393756 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1393699 ATCCTTTGGA
1393709 TGTTCT-CTTCATACCGTTGAT
1 TGTTCTCCTT-ATACCGTTGAT
*
1393730 TGTTCTCCTTATACCTTTGAT
1 TGTTCTCCTTATACCGTTGAT
*
1393751 TCTTCT
1 TGTTCT
1393757 TCTTTCTCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.12, C:0.25, G:0.10, T:0.52
Consensus pattern (21 bp):
TGTTCTCCTTATACCGTTGAT
Found at i:1394748 original size:17 final size:17
Alignment explanation
Indices: 1394723--1394763 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1394713 CATTGAGAAT
*
1394723 TTTAAATTTTTATATAA
1 TTTATATTTTTATATAA
* *
1394740 TTTATATTTTTTTATAT
1 TTTATATTTTTATATAA
1394757 TTTATAT
1 TTTATAT
1394764 ATATAATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTATATTTTTATATAA
Found at i:1395094 original size:43 final size:43
Alignment explanation
Indices: 1395047--1395264 Score: 341
Period size: 43 Copynumber: 5.1 Consensus size: 43
1395037 TCAAGACATA
1395047 TAGCGGCGTTTGTCTTTGAAAACGCCGCTATTGACTGTGTATT
1 TAGCGGCGTTTGTCTTTGAAAACGCCGCTATTGACTGTGTATT
* *
1395090 TAGCGGCGTTTGACTTT-ATAAACGCCGTTATTGACTGTGTATT
1 TAGCGGCGTTTGTCTTTGA-AAACGCCGCTATTGACTGTGTATT
1395133 TAGCGGCGTTTGTCTTTGAAAACGCCGCTATTGACTGTGTATT
1 TAGCGGCGTTTGTCTTTGAAAACGCCGCTATTGACTGTGTATT
*
1395176 TAGCGGCGTTTGTCTTTGAAAACGCCGCTATTGACTGTGTATC
1 TAGCGGCGTTTGTCTTTGAAAACGCCGCTATTGACTGTGTATT
* * * *
1395219 TAACGGCGTTTATCTTT-ATAAACGCGGCTATTAACTGTGTATT
1 TAGCGGCGTTTGTCTTTGA-AAACGCCGCTATTGACTGTGTATT
1395262 TAG
1 TAG
1395265 TGCATTTGTA
Statistics
Matches: 161, Mismatches: 11, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
42 2 0.01
43 158 0.98
44 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.38
Consensus pattern (43 bp):
TAGCGGCGTTTGTCTTTGAAAACGCCGCTATTGACTGTGTATT
Found at i:1395324 original size:43 final size:43
Alignment explanation
Indices: 1395261--1395378 Score: 186
Period size: 43 Copynumber: 2.8 Consensus size: 43
1395251 AACTGTGTAT
* *
1395261 TTAGT-GCATTTGTAAT-TAAAAATGCCGCAAATAAGCCCAATA
1 TTAGTGGCATTT-TCATCTAAAAACGCCGCAAATAAGCCCAATA
*
1395303 TTAGTGGCATTTTCATCTAAAAACGCCGCAAATAAGCCCATTA
1 TTAGTGGCATTTTCATCTAAAAACGCCGCAAATAAGCCCAATA
1395346 TTAGTGGCATTTTCATCTAAAAACGCCGCAAAT
1 TTAGTGGCATTTTCATCTAAAAACGCCGCAAAT
1395379 GACGCTATTA
Statistics
Matches: 71, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
42 8 0.11
43 63 0.89
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.29
Consensus pattern (43 bp):
TTAGTGGCATTTTCATCTAAAAACGCCGCAAATAAGCCCAATA
Found at i:1398785 original size:125 final size:124
Alignment explanation
Indices: 1398540--1398795 Score: 359
Period size: 125 Copynumber: 2.1 Consensus size: 124
1398530 CCTGTTGCAA
* * * * *
1398540 CGTTTGTCTTTGAAAACGCTGCTAAACTATTACTCTGTTGCGGCGTTTATTAAAAACACCACTAA
1 CGTTTGTCTTTGAAAACGCCGCTAAACTACTACTCTATTACGACGTTTATTAAAAACACCACTAA
** * * *
1398605 AGATGGAATATATTACGGTGTTTTTATAAAAACGTCGCTAAAGTAAAACTTTGTTGCGG
66 AGATGGAATATATTACGGCATTTTTATAAAAACGCCACTAAAGTAAAACTGTGTTGCGG
* *
1398664 CGTTTGTCTTTGAAAACGCCGCTAAAGTACTACTCTATTACGACGTTTATTAAAAAACGCCACTA
1 CGTTTGTCTTTGAAAACGCCGCTAAACTACTACTCTATTACGACGTTTATT-AAAAACACCACTA
* * * *
1398729 AAGATGGAATCTATTGCGGCATTTTTATAAAAACGCCATTAAAGTAATACTGTGTTGCGG
65 AAGATGGAATATATTACGGCATTTTTATAAAAACGCCACTAAAGTAAAACTGTGTTGCGG
1398789 CGTTTGT
1 CGTTTGT
1398796 TGATAAAACG
Statistics
Matches: 115, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
124 45 0.39
125 70 0.61
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Consensus pattern (124 bp):
CGTTTGTCTTTGAAAACGCCGCTAAACTACTACTCTATTACGACGTTTATTAAAAACACCACTAA
AGATGGAATATATTACGGCATTTTTATAAAAACGCCACTAAAGTAAAACTGTGTTGCGG
Found at i:1398787 original size:41 final size:41
Alignment explanation
Indices: 1398625--1398894 Score: 149
Period size: 41 Copynumber: 6.5 Consensus size: 41
1398615 TATTACGGTG
* * * * *
1398625 TTTTTATAAAAACGTCGCTAAAGTAAAACTTTGTTGCGGCG
1 TTTTTATAAAAACGCCACTAAAGTAATACTATGTTGCGGCA
* * * * * * * * *
1398666 TTTGTCTTTGAAAACGCCGCTAAAGTACTACTCTATTACGACG
1 TTT-T-TATAAAAACGCCACTAAAGTAATACTATGTTGCGGCA
1398709 TTTATTA-AAAAACGCCACTAAAGATGGAAT-CTA--TTGCGGCA
1 TTT-TTATAAAAACGCCACTAAAG-T--AATACTATGTTGCGGCA
* * *
1398750 TTTTTATAAAAACGCCATTAAAGTAATACTGTGTTGCGGCG
1 TTTTTATAAAAACGCCACTAAAGTAATACTATGTTGCGGCA
* ** *
1398791 TTTGTTGAT-AAAACGCCACTATAGATGAACCCTA--TTACGGCA
1 TTT-TT-ATAAAAACGCCACTAAAG-T-AATACTATGTTGCGGCA
* * * *
1398833 TTTGTATAAAAACGCCACTAAAGTACTACTATGTTGCGACG
1 TTTTTATAAAAACGCCACTAAAGTAATACTATGTTGCGGCA
* *
1398874 TTTGTTAAAAAAATGCCACTA
1 TTT-TTATAAAAACGCCACTA
1398895 TAGATGAACC
Statistics
Matches: 173, Mismatches: 39, Indels: 33
0.71 0.16 0.13
Matches are distributed among these distances:
38 3 0.02
39 6 0.03
40 7 0.04
41 73 0.42
42 41 0.24
43 37 0.21
44 6 0.03
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (41 bp):
TTTTTATAAAAACGCCACTAAAGTAATACTATGTTGCGGCA
Found at i:1398826 original size:83 final size:83
Alignment explanation
Indices: 1398676--1398939 Score: 316
Period size: 83 Copynumber: 3.2 Consensus size: 83
1398666 TTTGTCTTTG
* * * * * * * *
1398676 AAAACGCCGCTAAAGTACTACTCTATTACGACGTTTATT-AAAAAACGCCACTAAAGATGGAA-T
1 AAAACGCCACTAAAGTAATACTATGTTGCGACGTTTGTTAAAAAAACGCCACTATAGAT-GAACC
* *
1398739 CTATTGCGGCATTTTTATA
65 CTATTACGGCATTTGTATA
* * * * *
1398758 AAAACGCCATTAAAGTAATACTGTGTTGCGGCGTTTGTTGATAAAACGCCACTATAGATGAACCC
1 AAAACGCCACTAAAGTAATACTATGTTGCGACGTTTGTTAAAAAAACGCCACTATAGATGAACCC
1398823 TATTACGGCATTTGTATA
66 TATTACGGCATTTGTATA
* *
1398841 AAAACGCCACTAAAGTACTACTATGTTGCGACGTTTGTTAAAAAAATGCCACTATAGATGAACCC
1 AAAACGCCACTAAAGTAATACTATGTTGCGACGTTTGTTAAAAAAACGCCACTATAGATGAACCC
* **
1398906 TACTACGATATTTGTATA
66 TATTACGGCATTTGTATA
*
1398924 AAAACGCCGCTAAAGT
1 AAAACGCCACTAAAGT
1398940 TACAATTTTG
Statistics
Matches: 156, Mismatches: 24, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
82 34 0.22
83 122 0.78
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.28
Consensus pattern (83 bp):
AAAACGCCACTAAAGTAATACTATGTTGCGACGTTTGTTAAAAAAACGCCACTATAGATGAACCC
TATTACGGCATTTGTATA
Found at i:1398843 original size:125 final size:123
Alignment explanation
Indices: 1398585--1398855 Score: 314
Period size: 125 Copynumber: 2.2 Consensus size: 123
1398575 TGTTGCGGCG
* ** * *
1398585 TTTATTAAAAACACCACTAAAGATGGAATATATTACGGTGTTTTTATAAAAACGTCGCTAAAGTA
1 TTTATTAAAAACGCCACTAAAGATGGAATATATTACGGCATTTTTATAAAAACGCCACTAAAGTA
* * * * *
1398650 AAACTTTGTTGCGGCGTTTGTCTTTGAAAACGCCGCTAAAGTACTACTCTATTACGACG
66 AAACTGTGTTGCGGCGTTTGTCTATGAAAACGCCACTAAAGTAC-ACCCTATTACGACA
* * *
1398709 TTTATTAAAAAACGCCACTAAAGATGGAATCTATTGCGGCATTTTTATAAAAACGCCATTAAAGT
1 TTTATT-AAAAACGCCACTAAAGATGGAATATATTACGGCATTTTTATAAAAACGCCACTAAAGT
* * *
1398774 AATACTGTGTTGCGGCGTTTGT-TGAT-AAAACGCCACTATAGATGA-ACCCTATTACGGCA
65 AAAACTGTGTTGCGGCGTTTGTCT-ATGAAAACGCCACTAAAG-T-ACACCCTATTACGACA
*
1398833 TTTGTATAAAAACGCCACTAAAG
1 TTTAT-TAAAAACGCCACTAAAG
1398856 TACTACTATG
Statistics
Matches: 125, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
124 51 0.41
125 73 0.58
126 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (123 bp):
TTTATTAAAAACGCCACTAAAGATGGAATATATTACGGCATTTTTATAAAAACGCCACTAAAGTA
AAACTGTGTTGCGGCGTTTGTCTATGAAAACGCCACTAAAGTACACCCTATTACGACA
Found at i:1399755 original size:51 final size:51
Alignment explanation
Indices: 1399687--1399801 Score: 176
Period size: 51 Copynumber: 2.3 Consensus size: 51
1399677 GTAATTATTG
* * * *
1399687 AATAAAATAATAATAAACTAAAAATAATGTTTTGATTTTATCCTAATTCCT
1 AATAAAATAATAATAAACTAAAAATAATATTTTAACTCTATCCTAATTCCT
* *
1399738 AATAAAATAATAATAAACTACAAATAATATTTTAACTCTATCTTAATTCCT
1 AATAAAATAATAATAAACTAAAAATAATATTTTAACTCTATCCTAATTCCT
1399789 AATAAAATAATAA
1 AATAAAATAATAA
1399802 ATCTAATCCT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (51 bp):
AATAAAATAATAATAAACTAAAAATAATATTTTAACTCTATCCTAATTCCT
Found at i:1400919 original size:23 final size:23
Alignment explanation
Indices: 1400861--1400919 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
1400851 CCAAAAAAAA
1400861 AAAATCTATTTTACTTCATCTTTT
1 AAAAT-TATTTTACTTCATCTTTT
* * *
1400885 ACAATTACTTTTA-TTGATGTTTT
1 AAAATTA-TTTTACTTCATCTTTT
1400908 CAAAATTATTTT
1 -AAAATTATTTT
1400920 TAGTAAAACA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
23 14 0.48
24 15 0.52
ACGTcount: A:0.31, C:0.12, G:0.03, T:0.54
Consensus pattern (23 bp):
AAAATTATTTTACTTCATCTTTT
Found at i:1403944 original size:2 final size:2
Alignment explanation
Indices: 1403937--1403971 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1403927 GTGAGGTATG
1403937 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1403972 GCATATCTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1406635 original size:33 final size:33
Alignment explanation
Indices: 1406588--1406686 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
1406578 AACTCAACAT
* * *
1406588 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
*
1406621 AATTCAAATACTTAAAAACTTCTAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1406654 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1406686 A
1 A
1406687 TTGAAACAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 11 0.18
33 50 0.82
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.33
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:1406705 original size:21 final size:21
Alignment explanation
Indices: 1406681--1406722 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1406671 ACTTCAAGTT
1406681 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
1406702 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
1406723 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:1409036 original size:12 final size:12
Alignment explanation
Indices: 1409019--1409058 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 12
1409009 TGTGGATAAA
1409019 AACCGGTTTTTT
1 AACCGGTTTTTT
1409031 AACCGGTTTTTTT
1 AACCGG-TTTTTT
1409044 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
1409058 A
1 A
1409059 TCAGGTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 7 0.28
13 6 0.24
14 6 0.24
15 6 0.24
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:1409049 original size:15 final size:14
Alignment explanation
Indices: 1409018--1409057 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
1409008 TTGTGGATAA
1409018 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
1409031 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
1409044 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
1409058 ATCAGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:1414480 original size:2 final size:2
Alignment explanation
Indices: 1414473--1414497 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1414463 TTCAAAAATA
1414473 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1414498 CAAATAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1414571 original size:15 final size:14
Alignment explanation
Indices: 1414553--1414601 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
1414543 TCTAAACTAT
1414553 AATAAAAATATAAAA
1 AATAAAAATA-AAAA
1414568 AATAAAAATAAAAA
1 AATAAAAATAAAAA
**
1414582 ATATAATTATAATAAA
1 A-ATAAAAATAA-AAA
1414598 AATA
1 AATA
1414602 TAATAACTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 5 0.17
15 21 0.70
16 4 0.13
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AATAAAAATAAAAA
Done.