Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008283.1 Hibiscus syriacus cultivar Beakdansim tig00110945_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: 2862730
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 14
Found at i:1491030 original size:19 final size:19
Alignment explanation
Indices: 1491006--1491042 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1490996 TTTTCACTTG
*
1491006 TTTTTTTATCTTTATTTTA
1 TTTTTTTATATTTATTTTA
1491025 TTTTTTTATATTTATTTT
1 TTTTTTTATATTTATTTT
1491043 GTTTCGGCCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTTTTATATTTATTTTA
Found at i:1491675 original size:18 final size:18
Alignment explanation
Indices: 1491652--1491686 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1491642 TTTTCATCAT
1491652 GATTTTGCTTT-ATTTTTG
1 GATTTTG-TTTCATTTTTG
1491670 GATTTTGTTTCATTTTT
1 GATTTTGTTTCATTTTT
1491687 TCCCTTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.11, C:0.06, G:0.14, T:0.69
Consensus pattern (18 bp):
GATTTTGTTTCATTTTTG
Found at i:1494733 original size:22 final size:20
Alignment explanation
Indices: 1494693--1494737 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1494683 TATCATCGTT
*
1494693 TTAATTTTATATTATAAATA
1 TTAAATTTATATTATAAATA
*
1494713 TTAAATTTATATCATATAA-A
1 TTAAATTTATATTATA-AATA
1494733 TTAAA
1 TTAAA
1494738 AATTATTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTAAATTTATATTATAAATA
Found at i:1496166 original size:31 final size:32
Alignment explanation
Indices: 1496082--1496170 Score: 117
Period size: 33 Copynumber: 2.8 Consensus size: 32
1496072 GAGCAACGAG
* * *
1496082 TTTAACGAGCAATGAGTCGAGCGACAAATTTT
1 TTTAACGAGCAATGAGTCGAGCAATAAAATTT
*
1496114 TCTTAACAAGCAATGAGTCGAGCAATAAAATTT
1 T-TTAACGAGCAATGAGTCGAGCAATAAAATTT
*
1496147 TTTAACGAGC-ACGAGTCGAGCAAT
1 TTTAACGAGCAATGAGTCGAGCAAT
1496171 GCCCTACTCG
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
31 13 0.26
32 9 0.18
33 28 0.56
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (32 bp):
TTTAACGAGCAATGAGTCGAGCAATAAAATTT
Found at i:1502756 original size:23 final size:23
Alignment explanation
Indices: 1502714--1502775 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
1502704 ATATGGCAGA
* *
1502714 GGGAATTGATACCCCC-TTGAA-
1 GGGAACTGATTCCCCCTTTGAAT
1502735 GGAGAACTGATTCCCCCTTTGAAT
1 GG-GAACTGATTCCCCCTTTGAAT
*
1502759 GGGAACTGATTTCCCCT
1 GGGAACTGATTCCCCCT
1502776 AGGGGAATCG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 2 0.06
22 12 0.34
23 19 0.54
24 2 0.06
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (23 bp):
GGGAACTGATTCCCCCTTTGAAT
Found at i:1505515 original size:21 final size:21
Alignment explanation
Indices: 1505491--1505540 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
1505481 TTAGGGAACT
1505491 GATTCCCCATGAGGGGGTACC
1 GATTCCCCATGAGGGGGTACC
1505512 GATTCCCCATGAGGGGGTACC
1 GATTCCCCATGAGGGGGTACC
1505533 GATTCCCC
1 GATTCCCC
1505541 CCACGCTCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.32, G:0.30, T:0.20
Consensus pattern (21 bp):
GATTCCCCATGAGGGGGTACC
Found at i:1506721 original size:24 final size:23
Alignment explanation
Indices: 1506680--1506725 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
1506670 CAAAATAATA
*
1506680 TATTTATTAAAAAAATATTATTTT
1 TATTTAATAAAAAAATA-TATTTT
* *
1506704 TATTTAATAACAATATATATTT
1 TATTTAATAAAAAAATATATTT
1506726 AATTAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TATTTAATAAAAAAATATATTTT
Found at i:1506726 original size:21 final size:19
Alignment explanation
Indices: 1506671--1506744 Score: 76
Period size: 21 Copynumber: 3.6 Consensus size: 19
1506661 CACCAAACCC
1506671 AAAATAATATATTTATTAAA
1 AAAAT-ATATATTTATTAAA
*
1506691 AAAATATTATTTTTATTTAATA
1 AAAATA-TATATTTA-TTAA-A
*
1506713 ACAATATATATTTAATTAAA
1 AAAATATATATTT-ATTAAA
1506733 AAAATAATATAT
1 AAAAT-ATATAT
1506745 GGATGTGTAC
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
19 1 0.02
20 17 0.38
21 20 0.44
22 7 0.16
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (19 bp):
AAAATATATATTTATTAAA
Found at i:1510760 original size:19 final size:19
Alignment explanation
Indices: 1510738--1510775 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1510728 CGGCGACAAA
1510738 GAGAAAGA-AGAGAGGTTTT
1 GAGAAAGAGAGAG-GGTTTT
*
1510757 GAGAGAGAGAGAGGGTTTT
1 GAGAAAGAGAGAGGGTTTT
1510776 TTGGCGTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.37, C:0.00, G:0.42, T:0.21
Consensus pattern (19 bp):
GAGAAAGAGAGAGGGTTTT
Found at i:1510883 original size:23 final size:22
Alignment explanation
Indices: 1510801--1510884 Score: 82
Period size: 23 Copynumber: 3.8 Consensus size: 22
1510791 CAGAACCCTC
* *
1510801 AGGGGGTATCGATTCCCCTAC-
1 AGGGGGAATCGATTCCCCTTCA
*
1510822 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGATTCCCCTTC-A
*
1510845 AGAGGGAATC-AGTTCCCCTTCA
1 AGGGGGAATCGA-TTCCCCTTCA
*
1510867 AGGGGGGTATCGATTCCC
1 A-GGGGGAATCGATTCCC
1510885 TCTGCACTAA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
21 18 0.35
22 2 0.04
23 30 0.59
24 1 0.02
ACGTcount: A:0.21, C:0.26, G:0.30, T:0.23
Consensus pattern (22 bp):
AGGGGGAATCGATTCCCCTTCA
Found at i:1524581 original size:17 final size:16
Alignment explanation
Indices: 1524550--1524588 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
1524540 GGGAGATCAT
1524550 TAAAAAAAAACCAAAA
1 TAAAAAAAAACCAAAA
1524566 -AAAAGAAAAACACAAAA
1 TAAAA-AAAAAC-CAAAA
1524583 TAAAAA
1 TAAAAA
1524589 CGAAAGAGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
15 4 0.20
16 6 0.30
17 6 0.30
18 4 0.20
ACGTcount: A:0.82, C:0.10, G:0.03, T:0.05
Consensus pattern (16 bp):
TAAAAAAAAACCAAAA
Found at i:1525169 original size:25 final size:25
Alignment explanation
Indices: 1525137--1525192 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
1525127 TAAGTGAAAT
1525137 TTTA-AATAAAGATGTATAAATGAA
1 TTTAGAATAAAGATGTATAAATGAA
1525161 TTTAGAATAAAGATGTATAAATGAA
1 TTTAGAATAAAGATGTATAAATGAA
1525186 TTTAGAA
1 TTTAGAA
1525193 GTTAAATTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 4 0.13
25 27 0.87
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (25 bp):
TTTAGAATAAAGATGTATAAATGAA
Found at i:1525818 original size:24 final size:24
Alignment explanation
Indices: 1525786--1525831 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1525776 ATAAGTCTAG
* *
1525786 ATTTAATATTTTGATATATGATTC
1 ATTTAATATTATGATACATGATTC
*
1525810 ATTTCATATTATGATACATGAT
1 ATTTAATATTATGATACATGAT
1525832 ATGAGTTCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.50
Consensus pattern (24 bp):
ATTTAATATTATGATACATGATTC
Found at i:1533090 original size:20 final size:20
Alignment explanation
Indices: 1533061--1533102 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1533051 ATTCCACAAC
*
1533061 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
1533081 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
1533101 AT
1 AT
1533103 AGGCTTTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:1538479 original size:20 final size:20
Alignment explanation
Indices: 1538450--1538492 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1538440 ATTCCACCAC
*
1538450 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
1538470 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
1538490 ATG
1 ATG
1538493 GGCTTTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:1540232 original size:23 final size:23
Alignment explanation
Indices: 1540195--1540238 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1540185 GAGTAGAGGG
1540195 TCTACGCGGTACTTCGGGACAAT
1 TCTACGCGGTACTTCGGGACAAT
* *
1540218 TCTACGTGGTCCTTCGGGACA
1 TCTACGCGGTACTTCGGGACA
1540239 TATATGTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
TCTACGCGGTACTTCGGGACAAT
Found at i:1540974 original size:21 final size:22
Alignment explanation
Indices: 1540939--1540981 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
1540929 ACCGAAATTT
1540939 ACTGTAGCAAGGGTATCAATAC
1 ACTGTAGCAAGGGTATCAATAC
1540961 ACTGTAGC-AGGGTATCAATAC
1 ACTGTAGCAAGGGTATCAATAC
1540982 CCCTTTTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (22 bp):
ACTGTAGCAAGGGTATCAATAC
Found at i:1541709 original size:14 final size:14
Alignment explanation
Indices: 1541690--1541731 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
1541680 TCTTTCGAGC
*
1541690 ACTTACATTTCAGT
1 ACTTACATTTAAGT
1541704 ACTTACATTTAAGT
1 ACTTACATTTAAGT
1541718 ACTTACATTTAAGT
1 ACTTACATTTAAGT
1541732 CACTAGTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (14 bp):
ACTTACATTTAAGT
Found at i:1549365 original size:107 final size:108
Alignment explanation
Indices: 1549232--1549485 Score: 323
Period size: 107 Copynumber: 2.4 Consensus size: 108
1549222 CTGATGAGAC
* *
1549232 CTTAGAAATCCGACTATAACAAAATATGTTAATTACTTAATTTGTTATCAATATTATCAACATAT
1 CTTAGAAATCTGACAATAACAAAATATGTTAATTACTTAATTTGTTATCAATATTATCAACATAT
* * * *
1549297 TAAGTAGCGCCTAAAATATTATCAAAGTTTAAGGTAATGGGCT
66 TAAGCAGCACCTAAAATATTACCAAAGTTTAAGCTAATGGGCT
* * * *
1549340 -TTAGAAATCTGACGATAACAAAATATGCTAATTACTTATTTTGTTATTAATATTATCAACATAT
1 CTTAGAAATCTGACAATAACAAAATATGTTAATTACTTAATTTGTTATCAATATTATCAACATAT
* * * *
1549404 TAGGCAGCACCTAAAATGTTACCAAAGTTTAAGCTGATGGGGT
66 TAAGCAGCACCTAAAATATTACCAAAGTTTAAGCTAATGGGCT
* * * *
1549447 CTTCGAAAT-TCCACAATAACAAAATAAGTTAATTTCTTA
1 CTTAGAAATCT-GACAATAACAAAATATGTTAATTACTTA
1549486 TTTTTTTTAT
Statistics
Matches: 125, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
107 95 0.76
108 30 0.24
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (108 bp):
CTTAGAAATCTGACAATAACAAAATATGTTAATTACTTAATTTGTTATCAATATTATCAACATAT
TAAGCAGCACCTAAAATATTACCAAAGTTTAAGCTAATGGGCT
Found at i:1550021 original size:23 final size:23
Alignment explanation
Indices: 1549994--1550065 Score: 101
Period size: 23 Copynumber: 3.1 Consensus size: 23
1549984 CGGTAGTTAG
* *
1549994 TTTAACGTAATAGGTAGCGCTTA
1 TTTAACGTAATAGGTAGCACCTA
1550017 TTTAACGTAATAGGTAGCACCTA
1 TTTAACGTAATAGGTAGCACCTA
*
1550040 TTTAACATAATAGGT-GACACCTA
1 TTTAACGTAATAGGTAG-CACCTA
1550063 TTT
1 TTT
1550066 TATTTTATCG
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
22 1 0.02
23 44 0.98
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (23 bp):
TTTAACGTAATAGGTAGCACCTA
Found at i:1550140 original size:75 final size:75
Alignment explanation
Indices: 1550040--1550300 Score: 362
Period size: 75 Copynumber: 3.5 Consensus size: 75
1550030 GTAGCACCTA
* *
1550040 TTTAACATAATAGGT-GACACCTATTTTATTTTATCGTTTACATTATTATTAACCTTTAAACAAA
1 TTTAACATAATAGGTAG-CACCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAA
* *
1550104 CCGGTAGCTAT
65 CCGGTAGGTAG
* * *
1550115 TTTAACGTAATAGGTAGTACCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAAT
1 TTTAACATAATAGGTAGCACCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAAC
1550180 CGGTAGGTAG
66 CGGTAGGTAG
** ** * * *
1550190 TTTAACGCAATAGGTAGTTCCTATTTTATTTCACCGTTTACATTATTAGTAACATTCAAACAAAC
1 TTTAACATAATAGGTAGCACCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAAC
1550255 CGGTAGGTAG
66 CGGTAGGTAG
* *
1550265 TTTAACATAATAGATAGCGCCTATTTTATTTTACCG
1 TTTAACATAATAGGTAGCACCTATTTTATTTTACCG
1550301 GTTAAGTTTT
Statistics
Matches: 166, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
75 165 0.99
76 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (75 bp):
TTTAACATAATAGGTAGCACCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAAC
CGGTAGGTAG
Found at i:1550992 original size:29 final size:29
Alignment explanation
Indices: 1550959--1551040 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 29
1550949 ATACTAGCGA
*
1550959 CTAAAATGAAATTTTTAAAAGTTTAGTGG-
1 CTAAAATGAAATTTTGAAAAGTTTAG-GGT
1550988 CTAAAGTAT-AAATTTTGAAAAGTTTAGGGT
1 CTAAA--ATGAAATTTTGAAAAGTTTAGGGT
* * *
1551018 CGAAAATGTAATTTTGATAAGTT
1 CTAAAATGAAATTTTGAAAAGTT
1551041 ATAGATTTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
28 2 0.04
29 20 0.44
30 21 0.47
31 2 0.04
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.38
Consensus pattern (29 bp):
CTAAAATGAAATTTTGAAAAGTTTAGGGT
Found at i:1552892 original size:3 final size:3
Alignment explanation
Indices: 1552884--1552927 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1552874 TTTGACTTAA
1552884 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1552928 AGCGTTAAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1553319 original size:41 final size:41
Alignment explanation
Indices: 1553274--1553354 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 41
1553264 AAGTGAGTTC
1553274 TTATCAGTTCAGCTTTGATACATTCATGTATCAATGTTCAG
1 TTATCAGTTCAGCTTTGATACATTCATGTATCAATGTTCAG
* *
1553315 TTATCAGTTCAGCTTTGGTACATTCGTGTATCAATGTTCA
1 TTATCAGTTCAGCTTTGATACATTCATGTATCAATGTTCA
1553355 ACACCGTTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.42
Consensus pattern (41 bp):
TTATCAGTTCAGCTTTGATACATTCATGTATCAATGTTCAG
Found at i:1554462 original size:19 final size:19
Alignment explanation
Indices: 1554396--1554463 Score: 50
Period size: 23 Copynumber: 3.4 Consensus size: 19
1554386 TTATGTAGCC
1554396 TAATAGTTTAAATAATTTTAAT
1 TAATAGTTTAAATAA-TTT--T
* * *
1554418 TTATAAATTTAATATTATTTT
1 TAAT-AGTTTAA-ATAATTTT
1554439 T--TAGTTTAAATAATTTT
1 TAATAGTTTAAATAATTTT
1554456 TAATAGTT
1 TAATAGTT
1554464 CATTGTTAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 11
0.70 0.09 0.21
Matches are distributed among these distances:
17 8 0.22
18 6 0.16
19 6 0.16
21 2 0.05
22 3 0.08
23 9 0.24
24 3 0.08
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (19 bp):
TAATAGTTTAAATAATTTT
Found at i:1555617 original size:23 final size:23
Alignment explanation
Indices: 1555583--1555641 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
1555573 CTGAACCAGT
* *
1555583 CCCGA-CCATTGACCTGATCTAA
1 CCCGACCCGTTGACCTGATCCAA
*
1555605 CCCGACCCGTTGACCTGATCCGA
1 CCCGACCCGTTGACCTGATCCAA
*
1555628 TCCGACCCGTTGAC
1 CCCGACCCGTTGAC
1555642 TATGACTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 5 0.16
23 27 0.84
ACGTcount: A:0.20, C:0.41, G:0.19, T:0.20
Consensus pattern (23 bp):
CCCGACCCGTTGACCTGATCCAA
Found at i:1557505 original size:11 final size:11
Alignment explanation
Indices: 1557459--1557521 Score: 58
Period size: 11 Copynumber: 5.7 Consensus size: 11
1557449 TTAAAATAAT
1557459 TAAAATAACAAA
1 TAAAATAA-AAA
*
1557471 TAATA-AAAAA
1 TAAAATAAAAA
* *
1557481 TAGTAA-AAACA
1 TA-AAATAAAAA
1557492 TAAAATAAAAA
1 TAAAATAAAAA
*
1557503 TAAAATAAACA
1 TAAAATAAAAA
1557514 TAAAATAA
1 TAAAATAA
1557522 GGACCTAATT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
10 7 0.17
11 31 0.74
12 4 0.10
ACGTcount: A:0.75, C:0.05, G:0.02, T:0.19
Consensus pattern (11 bp):
TAAAATAAAAA
Found at i:1583872 original size:22 final size:22
Alignment explanation
Indices: 1583847--1583893 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
1583837 TTTTTCTCTA
*
1583847 AATAGGTTTACGGATATTTTTT
1 AATAAGTTTACGGATATTTTTT
1583869 AATAAGTTTACGGATATTTTTT
1 AATAAGTTTACGGATATTTTTT
1583891 AAT
1 AAT
1583894 GAGATTTGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.32, C:0.04, G:0.15, T:0.49
Consensus pattern (22 bp):
AATAAGTTTACGGATATTTTTT
Found at i:1584541 original size:20 final size:20
Alignment explanation
Indices: 1584516--1584561 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1584506 TTAGAAGCTC
1584516 GATTGAAGCCTAAAATTCGA
1 GATTGAAGCCTAAAATTCGA
1584536 GATTGAAGCCTAAAATTCGA
1 GATTGAAGCCTAAAATTCGA
*
1584556 GCTTGA
1 GATTGA
1584562 TTGAAGTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (20 bp):
GATTGAAGCCTAAAATTCGA
Found at i:1585006 original size:23 final size:22
Alignment explanation
Indices: 1584980--1585022 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
1584970 TATAAAAAAT
1584980 TATTTTTTATTAAATATTTTTGG
1 TATTTTTTATTAAAT-TTTTTGG
*
1585003 TATTTTTTATTTAATTTTTT
1 TATTTTTTATTAAATTTTTT
1585023 AAATAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (22 bp):
TATTTTTTATTAAATTTTTTGG
Found at i:1593272 original size:13 final size:13
Alignment explanation
Indices: 1593231--1593274 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
1593221 TATTTAGTAC
*
1593231 TTTTTATTGTAGT
1 TTTTTATTGTAAT
* * *
1593244 TGTTTATTGGACT
1 TTTTTATTGTAAT
1593257 TTTTTATTGTAAT
1 TTTTTATTGTAAT
1593270 TTTTT
1 TTTTT
1593275 TATTTATCAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.16, C:0.02, G:0.14, T:0.68
Consensus pattern (13 bp):
TTTTTATTGTAAT
Found at i:1602353 original size:21 final size:21
Alignment explanation
Indices: 1602329--1602370 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1602319 GCGTAGAATT
1602329 TGTCCCGAAGGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
1602350 TGTCCCGAAGGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
1602371 CCCTCAACTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.29, G:0.24, T:0.14
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATAGA
Found at i:1603218 original size:24 final size:20
Alignment explanation
Indices: 1603165--1603222 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
1603155 TTCCCATTGA
*
1603165 AGTGCATCGGTGCATTCTTC
1 AGTGCATCGATGCATTCTTC
1603185 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TT--C
1603208 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1603223 CTACCATGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
21 2 0.06
23 2 0.06
24 13 0.39
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTTC
Found at i:1606017 original size:24 final size:24
Alignment explanation
Indices: 1605990--1606048 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
1605980 ATACATGACC
* *
1605990 TGGATTCTGTTCTAATTTCTTATA
1 TGGATTCTGTTCTAATATCTAATA
* * *
1606014 TGGATTATGCTCTGATATCTAATA
1 TGGATTCTGTTCTAATATCTAATA
*
1606038 TGAATTCTGTT
1 TGGATTCTGTT
1606049 TTGATTTATG
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.49
Consensus pattern (24 bp):
TGGATTCTGTTCTAATATCTAATA
Found at i:1606726 original size:18 final size:17
Alignment explanation
Indices: 1606703--1606745 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
1606693 TAAAGTTTAC
1606703 TTTTATATTTATAAATAA
1 TTTTATATTT-TAAATAA
* *
1606721 TTTTATGATTTTACATAT
1 TTTTAT-ATTTTAAATAA
1606739 TTTTATA
1 TTTTATA
1606746 AAAGTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 1 0.05
18 17 0.77
19 4 0.18
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (17 bp):
TTTTATATTTTAAATAA
Found at i:1610135 original size:24 final size:24
Alignment explanation
Indices: 1610108--1610174 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
1610098 ATTTGAATTT
*
1610108 TGTTCTGATACCT-TTCTTGGATTC
1 TGTTCTGATACCTGATC-TGGATTC
**
1610132 TGTTCTGATTTCTGATCTGGATTC
1 TGTTCTGATACCTGATCTGGATTC
*
1610156 TGTTCTGATATCTGATCTG
1 TGTTCTGATACCTGATCTG
1610175 AATACTATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
24 36 0.95
25 2 0.05
ACGTcount: A:0.13, C:0.18, G:0.19, T:0.49
Consensus pattern (24 bp):
TGTTCTGATACCTGATCTGGATTC
Found at i:1610150 original size:12 final size:12
Alignment explanation
Indices: 1610129--1610175 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
1610119 CTTTCTTGGA
*
1610129 TTCTGTTCTGAT
1 TTCTGATCTGAT
1610141 TTCTGATCTGGA-
1 TTCTGATCT-GAT
*
1610153 TTCTGTTCTGAT
1 TTCTGATCTGAT
*
1610165 ATCTGATCTGA
1 TTCTGATCTGA
1610176 ATACTATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 2 0.07
12 25 0.86
13 2 0.07
ACGTcount: A:0.15, C:0.17, G:0.19, T:0.49
Consensus pattern (12 bp):
TTCTGATCTGAT
Found at i:1610188 original size:24 final size:24
Alignment explanation
Indices: 1610134--1610188 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
1610124 TTGGATTCTG
* * * *
1610134 TTCTGATTTCTGATCTGGATTCTG
1 TTCTGATATCTGATCTGAATACTA
1610158 TTCTGATATCTGATCTGAATACTA
1 TTCTGATATCTGATCTGAATACTA
*
1610182 TTTTGAT
1 TTCTGAT
1610189 TTATGATATC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.20, C:0.15, G:0.16, T:0.49
Consensus pattern (24 bp):
TTCTGATATCTGATCTGAATACTA
Found at i:1614365 original size:24 final size:24
Alignment explanation
Indices: 1614295--1614353 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
1614285 ATTTTTTATT
* *
1614295 TGAATTCTGTTCTGATACTTAATC
1 TGAATTCTGTTCTGATATTTGATC
*
1614319 TGGATTCTGTTCTGATATTTGATC
1 TGAATTCTGTTCTGATATTTGATC
1614343 TGAATTCTGTT
1 TGAATTCTGTT
1614354 TTTATTTCTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.20, C:0.14, G:0.17, T:0.49
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATTTGATC
Found at i:1615144 original size:32 final size:32
Alignment explanation
Indices: 1615103--1615166 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
1615093 AGTGACCCTA
1615103 ATATAACACCCCAGATCGGATCGGATTACCTG
1 ATATAACACCCCAGATCGGATCGGATTACCTG
1615135 ATATAACACCCCAGATCGGATCGGATTACCTG
1 ATATAACACCCCAGATCGGATCGGATTACCTG
1615167 CATTGGTCTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (32 bp):
ATATAACACCCCAGATCGGATCGGATTACCTG
Found at i:1615555 original size:39 final size:39
Alignment explanation
Indices: 1615482--1615888 Score: 543
Period size: 39 Copynumber: 10.5 Consensus size: 39
1615472 GTTTTAAGAA
* *
1615482 AAACAATCTCAAGGGAGAT-AAATCTTCTGTTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* *
1615520 AAACTATCTCAAGCAAGATAAAATCTTTTGTTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* *
1615559 AAACTATTTCAAGCGAGATAAAATCTTCTGTTTCTAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* * * *
1615598 GAACTATCTCAAGCGAGATAAAATATTTTATTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* * *
1615637 CAATTATCTCAAGCAAGATAAAAATCTTCTGTTTCGAGTG
1 AAACTATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTG
*
1615677 AAACTATCTCAAGCGAGATAAAATCTTCTATTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
*
1615716 AAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
** *
1615755 AAACTATCTCAAGATAGAT-AAATCTTCTGTTTCAAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
* *
1615793 AAACTATCTCAAGCAAGATAAAATCTTAC-GTTTCAAGTG
1 AAACTATCTCAAGCGAGATAAAATCTT-CTGTTTCGAGTG
* * * *
1615832 AAACTATATTAAGCGAGAT-AAATCTTTTGTTTCAAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
*
1615870 AAACTATCTCAAGGGAGAT
1 AAACTATCTCAAGCGAGAT
1615889 GTTGATCCTT
Statistics
Matches: 325, Mismatches: 39, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
38 83 0.26
39 208 0.64
40 34 0.10
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.32
Consensus pattern (39 bp):
AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTG
Found at i:1615604 original size:78 final size:78
Alignment explanation
Indices: 1615482--1615888 Score: 552
Period size: 77 Copynumber: 5.2 Consensus size: 78
1615472 GTTTTAAGAA
* * *
1615482 AAACAATCTCAAGGGAGAT-AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCAAGATAAAATCT
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCT
1615546 TTTGTTTCGAGTG
66 TTTGTTTCGAGTG
* * * *
1615559 AAACTATTTCAAGCGAGATAAAATCTTCTGTTTCTAGTGGAACTATCTCAAGCGAGATAAAATAT
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCT
*
1615624 TTTATTTCGAGTG
66 TTTGTTTCGAGTG
* * *
1615637 CAATTATCTCAAGCAAGATAAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATC
1 AAACTATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATC
* *
1615702 TTCTATTTCGAGTG
65 TTTTGTTTCGAGTG
* **
1615716 AAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGTGAAACTATCTCAAGATAGAT-AAATCT
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCT
* *
1615780 TCTGTTTCAAGTG
66 TTTGTTTCGAGTG
* * * *
1615793 AAACTATCTCAAGCAAGATAAAATCTTAC-GTTTCAAGTGAAACTATATTAAGCGAGAT-AAATC
1 AAACTATCTCAAGCGAGATAAAATCTT-CTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATC
*
1615856 TTTTGTTTCAAGTG
65 TTTTGTTTCGAGTG
*
1615870 AAACTATCTCAAGGGAGAT
1 AAACTATCTCAAGCGAGAT
1615889 GTTGATCCTT
Statistics
Matches: 293, Mismatches: 34, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
77 118 0.40
78 104 0.35
79 71 0.24
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.32
Consensus pattern (78 bp):
AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCT
TTTGTTTCGAGTG
Found at i:1615698 original size:157 final size:155
Alignment explanation
Indices: 1615482--1615888 Score: 559
Period size: 157 Copynumber: 2.6 Consensus size: 155
1615472 GTTTTAAGAA
* ** *
1615482 AAACAATCTCAAGGGAGAT-AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCAAGATAAAATCT
1 AAACTATCTCAAGCAAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCT
* * * *
1615546 TTTGTTTCGAGTGAAACTATTTCAAGCGAGATAAAATCTTCTGTTTCTAGTGGAACTATCTCAAG
66 TTTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGTGAAACTATCTCAAG
* * *
1615611 CGAGATAAAATATTTTATTTCGAGTG
131 AGAGAT-AAATATTCTATTTCAAGTG
* *
1615637 CAATTATCTCAAGCAAGATAAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATC
1 AAACTATCTCAAGCAAGAT-AAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATC
* *
1615702 TTCTATTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGTGAAACTATCTCAA
65 TTTTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGTGAAACTATCTCAA
* * *
1615767 GATAGATAAATCTTCTGTTTCAAGTG
130 GAGAGATAAATATTCTATTTCAAGTG
* * *
1615793 AAACTATCTCAAGCAAGATAAAATCTTAC-GTTTCAAGTGAAACTATATTAAGCGAGAT-AAATC
1 AAACTATCTCAAGCAAGATAAAATCTT-CTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATC
* *
1615856 TTTTGTTTCAAGTGAAACTATCTCAAGGGAGAT
65 TTTTGTTTCGAGTGAAACTATCTCAAGCGAGAT
1615889 GTTGATCCTT
Statistics
Matches: 222, Mismatches: 27, Indels: 7
0.87 0.11 0.03
Matches are distributed among these distances:
154 34 0.15
155 48 0.22
156 33 0.15
157 107 0.48
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.32
Consensus pattern (155 bp):
AAACTATCTCAAGCAAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCT
TTTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGTGAAACTATCTCAAG
AGAGATAAATATTCTATTTCAAGTG
Found at i:1616532 original size:110 final size:109
Alignment explanation
Indices: 1616117--1616528 Score: 531
Period size: 110 Copynumber: 3.8 Consensus size: 109
1616107 TTTCAATTGT
* * * * * *
1616117 CATCAAGAAACCTCTAAAAATTAGGTTTAACTTC-TTTAAAAATTCTTTGGAAATAATCATCAAA
1 CATCAATAAACCCCTAAAAATTAGGCTTAGCTTCTTTTAAAAATTCATTGGAAATAATCATCAAG
* * * *
1616181 AAACCCCTAAAAATCAGACTTAGTATATAAAAGCACATTTAAAAA
66 AAACCCCTGAAAATCAGACTTAGTTTATAAAAACTCATTT-AAAA
* *
1616226 CAT-AATAAAACCCCCTAAAAATTAGGCTTAGCTTCTTTTAAAAAATCATTGGAAATAATCATCG
1 CATCAAT-AAA-CCCCTAAAAATTAGGCTTAGCTTCTTTTAAAAATTCATTGGAAATAATCATCA
* *
1616290 AGAAACCCCTGAAAATCAGACTTAGTTTTTAAAAACTTATTTAAAA
64 AGAAACCCCTGAAAATCAGACTTAGTTTATAAAAACTCATTTAAAA
* * ** * *
1616336 CATCAATAAACCACTAAAAATTAGGCTTAGCTTCTTTTAAAAAATTCACTATAACTCATCATCAA
1 CATCAATAAACCCCTAAAAATTAGGCTTAGCTTCTTTT-AAAAATTCATTGGAAATAATCATCAA
* * * *
1616401 GAAACCCATGAAAATCAGGCTTAGTTTCTAAAAACTCATTTGGAAA
65 GAAACCCCTGAAAATCAGACTTAGTTTATAAAAACTCATTT-AAAA
* *
1616447 CATCAATAAACCCCTACAAATTAGGCTTAGCTTCTTTTAAAAATTCGTTGGAAATAATCATCAAG
1 CATCAATAAACCCCTAAAAATTAGGCTTAGCTTCTTTTAAAAATTCATTGGAAATAATCATCAAG
1616512 AAACCCCTGAAAATCAG
66 AAACCCCTGAAAATCAG
1616529 GCTTTGCTTC
Statistics
Matches: 261, Mismatches: 36, Indels: 11
0.85 0.12 0.04
Matches are distributed among these distances:
108 2 0.01
109 33 0.13
110 124 0.48
111 102 0.39
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.29
Consensus pattern (109 bp):
CATCAATAAACCCCTAAAAATTAGGCTTAGCTTCTTTTAAAAATTCATTGGAAATAATCATCAAG
AAACCCCTGAAAATCAGACTTAGTTTATAAAAACTCATTTAAAA
Found at i:1616568 original size:58 final size:57
Alignment explanation
Indices: 1616118--1616608 Score: 248
Period size: 58 Copynumber: 8.8 Consensus size: 57
1616108 TTCAATTGTC
* * * * *
1616118 ATCAAGAAACCTCTAAAAATTAGGTTTAACTTCTTTAAAAATTC-TTTGGAAATA-ATC-
1 ATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTT-AAAATTCATTT-GAAA-ACATCA
* * * * * ** *
1616175 ATCAAAAAACCCCTAAAAATCAGACTTAG--TATATAAAAGCACATTTAAAAACAT-A
1 ATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTAAAA-TTCATTTGAAAACATCA
* * * * *
1616230 AT-AA-AACCCCCTAAAAATTAGGCTTAGCTTCTTTTAAAAAATCATTGGAAATA-ATC-
1 ATCAAGAAACCCCTGAAAATCAGGCTTAGCTTC-TTT-AAAATTCATTTGAAA-ACATCA
* *
1616286 ATCGAGAAACCCCTGAAAATCAGACTTAG-TT-TTTAAAAACTT-ATTT-AAAACATCA
1 ATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTT-AAAA-TTCATTTGAAAACATCA
* * * * **
1616341 AT----AAACCACTAAAAATTAGGCTTAGCTTCTTTTAAAAAATTCACTAT-AACTCATC-
1 ATCAAGAAACCCCTGAAAATCAGGCTTAGCTTC-TTT--AAAATTCA-TTTGAAAACATCA
* * * * *
1616396 ATCAAGAAACCCATGAAAATCAGGCTTAGTTTC-TAAAAACTCATTTGGAAACATCA
1 ATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTAAAATTCATTTGAAAACATCA
* * *
1616452 AT----AAACCCCT-ACAAATTAGGCTTAGCTTCTTTTAAAAATTCGTTGGAAATA-ATC-
1 ATCAAGAAACCCCTGA-AAATCAGGCTTAGCTTC-TTT-AAAATTCATTTGAAA-ACATCA
* *
1616506 ATCAAGAAACCCCTGAAAATCAGGCTTTGCTTCTTTCAAATTCATTTGAAAACATCA
1 ATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTAAAATTCATTTGAAAACATCA
* ** *
1616563 TATCAAGAAACCTCTGAAAATCAAAAC-TAGCTTATTTAAAATTCAT
1 -ATCAAGAAACCCCTGAAAATC-AGGCTTAGCTTCTTTAAAATTCAT
1616609 CGATTGGGTA
Statistics
Matches: 329, Mismatches: 64, Indels: 81
0.69 0.14 0.17
Matches are distributed among these distances:
51 20 0.06
52 24 0.07
53 21 0.06
54 23 0.07
55 60 0.18
56 43 0.13
57 35 0.11
58 78 0.24
59 25 0.08
ACGTcount: A:0.43, C:0.19, G:0.09, T:0.30
Consensus pattern (57 bp):
ATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTAAAATTCATTTGAAAACATCA
Found at i:1618488 original size:4 final size:4
Alignment explanation
Indices: 1618475--1618523 Score: 52
Period size: 4 Copynumber: 12.8 Consensus size: 4
1618465 TATGTTTACA
1618475 TTTC -TTC TTTC TTTC -TTC TATT- TTTC -TTC TTTC TCTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC T-TTC TTTC TTTC TTTC T-TTC TTTC TTTC
1618521 TTT
1 TTT
1618524 TTCTCTCTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
3 11 0.28
4 22 0.56
5 6 0.15
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTC
Found at i:1618514 original size:27 final size:26
Alignment explanation
Indices: 1618479--1618533 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
1618469 TTTACATTTC
1618479 TTCTTTCTTTCTTCTATTTTTCT-TCT
1 TTCTTTCTTTCTT-TATTTTTCTCTCT
*
1618505 TTCTCTTCTTTCTTTCTTTTTCTCTCT
1 TTCT-TTCTTTCTTTATTTTTCTCTCT
1618532 TT
1 TT
1618534 TTGTGTGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 12 0.46
27 14 0.54
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (26 bp):
TTCTTTCTTTCTTTATTTTTCTCTCT
Found at i:1618989 original size:34 final size:32
Alignment explanation
Indices: 1618935--1619004 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1618925 ACCTTACAAC
* *
1618935 TCCCTAGTTTTTCCGGGCTAAACTATAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
1618967 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
1619001 TCCC
1 TCCC
1619005 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.21, C:0.31, G:0.14, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:1619312 original size:21 final size:21
Alignment explanation
Indices: 1619286--1619327 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1619276 CCCAGAATGG
*
1619286 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1619307 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1619328 ATATTCAAAT
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:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:1619480 original size:30 final size:31
Alignment explanation
Indices: 1619429--1619519 Score: 159
Period size: 31 Copynumber: 3.0 Consensus size: 31
1619419 AAATTTTGAA
*
1619429 TAAATTCAATT-AAGTCTAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1619458 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1619489 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1619520 CCTTAAATTG
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
29 11 0.19
30 10 0.17
31 38 0.64
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:1620639 original size:18 final size:18
Alignment explanation
Indices: 1620586--1620639 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
1620576 TAATGCATGT
*
1620586 TGAGATGCAATGTATACA
1 TGAGATGCAATGTATACC
1620604 TGAGATGCAATGTATACC
1 TGAGATGCAATGTATACC
*
1620622 TGAGATGAAATGTATACC
1 TGAGATGCAATGTATACC
1620640 ATGTAATGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (18 bp):
TGAGATGCAATGTATACC
Found at i:1624614 original size:28 final size:28
Alignment explanation
Indices: 1624577--1624654 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
1624567 AGTCCCTAAT
*
1624577 CTATCTTGTATGGGATTTGTTCTCCGAA
1 CTATTTTGTATGGGATTTGTTCTCCGAA
* * *
1624605 C-AGTTTTGTATGGGATTTGTTATCTGAT
1 CTA-TTTTGTATGGGATTTGTTCTCCGAA
1624633 CTATTTTGTATGGGATTTGTTC
1 CTATTTTGTATGGGATTTGTTC
1624655 CTCGATATGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
27 1 0.02
28 41 0.95
29 1 0.02
ACGTcount: A:0.17, C:0.12, G:0.23, T:0.49
Consensus pattern (28 bp):
CTATTTTGTATGGGATTTGTTCTCCGAA
Found at i:1627815 original size:20 final size:20
Alignment explanation
Indices: 1627786--1627823 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1627776 CCATTGATCA
1627786 TTGACCGTTGAAAGTTGACT
1 TTGACCGTTGAAAGTTGACT
* *
1627806 TTGACTGTTGACAGTTGA
1 TTGACCGTTGAAAGTTGA
1627824 ATTTTTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.13, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGACCGTTGAAAGTTGACT
Found at i:1628503 original size:28 final size:29
Alignment explanation
Indices: 1628441--1628513 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 29
1628431 CGATTTGTCC
1628441 TGTATAAGATTTGTTCCCCTGATCTATATA
1 TGTATAAGATTTGTT-CCCTGATCTATATA
* *
1628471 T-TATATGATTTGTTCCCTGATCTGT-TA
1 TGTATAAGATTTGTTCCCTGATCTATATA
*
1628498 TGTATAGGATTTGTTC
1 TGTATAAGATTTGTTC
1628514 TCTAATTTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
27 3 0.08
28 23 0.59
29 12 0.31
30 1 0.03
ACGTcount: A:0.22, C:0.14, G:0.16, T:0.48
Consensus pattern (29 bp):
TGTATAAGATTTGTTCCCTGATCTATATA
Found at i:1628530 original size:28 final size:28
Alignment explanation
Indices: 1628472--1628592 Score: 84
Period size: 28 Copynumber: 4.3 Consensus size: 28
1628462 ATCTATATAT
* * *
1628472 TATATGATTTGTTCCCTGATCTGTT-ATG
1 TATAGGATTTGTTCCCTAATATGTTCA-G
* *
1628500 TATAGGATTTGTTCTCTAATTTGTTCAG
1 TATAGGATTTGTTCCCTAATATGTTCAG
* * *
1628528 TAT-GAGATTTTTTCCCCAATATGTTCTG
1 TATAG-GATTTGTTCCCTAATATGTTCAG
* * * * *
1628556 TATGGGATTTATTCCTTGATATGTTCTG
1 TATAGGATTTGTTCCCTAATATGTTCAG
*
1628584 TATGGGATT
1 TATAGGATT
1628593 ATATCCCCGT
Statistics
Matches: 77, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
27 1 0.01
28 74 0.96
29 2 0.03
ACGTcount: A:0.20, C:0.12, G:0.19, T:0.49
Consensus pattern (28 bp):
TATAGGATTTGTTCCCTAATATGTTCAG
Found at i:1628608 original size:28 final size:28
Alignment explanation
Indices: 1628521--1628620 Score: 94
Period size: 28 Copynumber: 3.5 Consensus size: 28
1628511 TTCTCTAATT
* * * *
1628521 TGTTCAGTATGAGATTTTTTCCCCAATA
1 TGTTCTGTATGGGATTTATTCCCCGATA
**
1628549 TGTTCTGTATGGGATTTATTCCTTGATA
1 TGTTCTGTATGGGATTTATTCCCCGATA
* *
1628577 TGTTCTGTATGGGA-TTATATCCCCGTTC
1 TGTTCTGTATGGGATTTAT-TCCCCGATA
*
1628605 TGTTTCTGTTTGGGAT
1 TG-TTCTGTATGGGAT
1628621 CCTCTATGGA
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
27 4 0.07
28 43 0.74
29 11 0.19
ACGTcount: A:0.17, C:0.15, G:0.21, T:0.47
Consensus pattern (28 bp):
TGTTCTGTATGGGATTTATTCCCCGATA
Found at i:1642094 original size:21 final size:21
Alignment explanation
Indices: 1642065--1642117 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
1642055 ATTCTGACTA
1642065 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
1642086 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
1642107 TCGCAATGCGA
1 TCGCATTGCGA
1642118 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:1642132 original size:20 final size:20
Alignment explanation
Indices: 1642107--1642200 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
1642097 TTTTCCTAAT
1642107 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
1642127 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
1642148 TCGTAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
1642168 TCGCAATGCGCATACGTAAA
1 TCGCAATGCGAATACGTAAA
1642188 TCGCAATGCGAAT
1 TCGCAATGCGAAT
1642201 CTGACTATCG
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 46 0.75
21 15 0.25
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1642210 original size:20 final size:20
Alignment explanation
Indices: 1642187--1642234 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1642177 GCATACGTAA
*
1642187 ATCGCAATGCGAATCTGACT
1 ATCGCAATGAGAATCTGACT
* *
1642207 ATCGCAACGAGATTCTGACT
1 ATCGCAATGAGAATCTGACT
1642227 ATCGCAAT
1 ATCGCAAT
1642235 ACAGAATTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAATGAGAATCTGACT
Found at i:1643102 original size:24 final size:24
Alignment explanation
Indices: 1643075--1643128 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
1643065 GTATTCGAAA
1643075 TTTGATCTTGGTCAATACTCGGAC
1 TTTGATCTTGGTCAATACTCGGAC
*
1643099 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACTCGGAC
1643123 TTTGAT
1 TTTGAT
1643129 GATTTTTCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACTCGGAC
Found at i:1645557 original size:20 final size:21
Alignment explanation
Indices: 1645532--1645643 Score: 171
Period size: 20 Copynumber: 5.6 Consensus size: 21
1645522 GACATTCATT
*
1645532 TGACTATCGCACCGC-GAATA
1 TGACTATCGCAACGCGGAATA
*
1645552 TGACTATCGCAACACGGAA-A
1 TGACTATCGCAACGCGGAATA
1645572 TGACTATCGCAACGCGGAAT-
1 TGACTATCGCAACGCGGAATA
1645592 TGACTATCGCAACGCGGAAT-
1 TGACTATCGCAACGCGGAATA
1645612 TGACTATCGCAACGCGGAA-A
1 TGACTATCGCAACGCGGAATA
1645632 TGACTATCGCAA
1 TGACTATCGCAA
1645644 TGAGAGAATC
Statistics
Matches: 86, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
20 83 0.97
21 3 0.03
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.19
Consensus pattern (21 bp):
TGACTATCGCAACGCGGAATA
Found at i:1645624 original size:60 final size:60
Alignment explanation
Indices: 1645531--1645643 Score: 192
Period size: 60 Copynumber: 1.9 Consensus size: 60
1645521 AGACATTCAT
*
1645531 TTGACTATCGCACCGCGAATATGACTATCGCAACACGGAAATGACTATCGCAACGCGGAA
1 TTGACTATCGCAACGCGAATATGACTATCGCAACACGGAAATGACTATCGCAACGCGGAA
*
1645591 TTGACTATCGCAACGCGGAAT-TGACTATCGCAACGCGGAAATGACTATCGCAA
1 TTGACTATCGCAACGC-GAATATGACTATCGCAACACGGAAATGACTATCGCAA
1645644 TGAGAGAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
60 46 0.92
61 4 0.08
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.19
Consensus pattern (60 bp):
TTGACTATCGCAACGCGAATATGACTATCGCAACACGGAAATGACTATCGCAACGCGGAA
Found at i:1645674 original size:33 final size:33
Alignment explanation
Indices: 1645617--1645745 Score: 177
Period size: 33 Copynumber: 3.8 Consensus size: 33
1645607 GGAATTGACT
* ** *
1645617 ATCGCAACGCGGAAATGACTATCGCAATGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
1645651 ATCGTAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1645684 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1645717 ATCACAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
1645746 CGAATTTAGT
Statistics
Matches: 86, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
33 61 0.71
34 25 0.29
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1645821 original size:33 final size:33
Alignment explanation
Indices: 1645760--1645855 Score: 120
Period size: 33 Copynumber: 2.8 Consensus size: 33
1645750 TTTAGTTTCG
*
1645760 CGTTGCGATTTTCATTTTTGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
*
1645794 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
* ** *
1645827 CATTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
1645856 AGTCTATTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 31 0.56
34 24 0.44
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:1645980 original size:14 final size:14
Alignment explanation
Indices: 1645961--1645997 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1645951 CATCAATTAA
1645961 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1645975 ACAAATCATCTTTT
1 ACAAATCAACATTT
1645989 ACAAATCAA
1 ACAAATCAA
1645998 TTAAATAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1647035 original size:55 final size:54
Alignment explanation
Indices: 1646975--1647082 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
1646965 AAAAAAAGAC
1646975 ATATATTAGTGAATTACATAAATTTTAAAAAAAAATTAATCAAACTGAAATATAT
1 ATATATTAGTGAATTACATAAATTTT-AAAAAAAATTAATCAAACTGAAATATAT
1647030 ATATATTAGTGAATTACATAAATTTTAAAAAAAATTAATCAAACTGAAATATA
1 ATATATTAGTGAATTACATAAATTTTAAAAAAAATTAATCAAACTGAAATATA
1647083 AGAAGAAATA
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 27 0.51
55 26 0.49
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.34
Consensus pattern (54 bp):
ATATATTAGTGAATTACATAAATTTTAAAAAAAATTAATCAAACTGAAATATAT
Found at i:1647523 original size:42 final size:42
Alignment explanation
Indices: 1647444--1647536 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
1647434 CCTCTTCAAC
* * *
1647444 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
1647486 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
1647528 GATGACAGG
1 GATGACAGG
1647537 TGAGTCAAGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:1649568 original size:20 final size:20
Alignment explanation
Indices: 1649545--1649599 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
1649535 CTGAAACTTT
*
1649545 AAATTGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
*
1649565 AAATCGCAATACGAAAATGA
1 AAATCGCAACACGAAAATGA
** *
1649585 CTATCGCAACGCGAA
1 AAATCGCAACACGAA
1649600 TTTGACTATC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.49, C:0.20, G:0.16, T:0.15
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:1649655 original size:33 final size:34
Alignment explanation
Indices: 1649587--1649659 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 34
1649577 GAAAATGACT
* **
1649587 ATCGCAACGCGAATTTGACTATCGCAACGCAAGA
1 ATCGCAACGCGAATATGAAAATCGCAACGCAAGA
1649621 ATCGCAACGCGAA-ATGAAAATCGCAACG-ACAGA
1 ATCGCAACGCGAATATGAAAATCGCAACGCA-AGA
1649654 ATCGCA
1 ATCGCA
1649660 TTGCGATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 1 0.03
33 21 0.60
34 13 0.37
ACGTcount: A:0.40, C:0.26, G:0.21, T:0.14
Consensus pattern (34 bp):
ATCGCAACGCGAATATGAAAATCGCAACGCAAGA
Found at i:1650046 original size:22 final size:22
Alignment explanation
Indices: 1649984--1650049 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
1649974 TGACCGTGAA
* *
1649984 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
*
1650006 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
1650028 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
1650050 GGATGTCGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.21, C:0.15, G:0.39, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:1650269 original size:20 final size:20
Alignment explanation
Indices: 1650246--1650399 Score: 236
Period size: 20 Copynumber: 7.7 Consensus size: 20
1650236 CGATAGTCAG
1650246 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1650266 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1650286 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
1650306 ATTTGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1650326 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * **
1650346 AATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
*
1650367 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
1650387 ATTCACATTGCGA
1 ATTCGCATTGCGA
1650400 ATTAGAAAAA
Statistics
Matches: 120, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
20 105 0.88
21 15 0.12
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1650321 original size:60 final size:61
Alignment explanation
Indices: 1650226--1650399 Score: 244
Period size: 60 Copynumber: 2.9 Consensus size: 61
1650216 GCGCTATGTA
** *
1650226 AATCGCATTGCGATAGT-CAGATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTTACAAATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
* ** *
1650286 ATTCGCATTGCGA-TTTACGTATTTGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTTACAAATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
* * *
1650346 AATCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACGTATTCACATTGCGA
1 AATCGCATTGCGATTTTACAAATTCGCATTGCGATTTACGTATTCGCATTGCGA
1650400 ATTAGAAAAA
Statistics
Matches: 99, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
59 1 0.01
60 64 0.65
61 34 0.34
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.37
Consensus pattern (61 bp):
AATCGCATTGCGATTTTACAAATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
Found at i:1650422 original size:21 final size:21
Alignment explanation
Indices: 1650396--1650441 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1650386 TATTCACATT
1650396 GCGAATTAGAAAAATCGCAAC
1 GCGAATTAGAAAAATCGCAAC
* * *
1650417 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGAAAAATCGCAAC
1650438 GCGA
1 GCGA
1650442 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.17
Consensus pattern (21 bp):
GCGAATTAGAAAAATCGCAAC
Found at i:1651062 original size:21 final size:21
Alignment explanation
Indices: 1651038--1651120 Score: 121
Period size: 21 Copynumber: 4.0 Consensus size: 21
1651028 CCAAATTCGT
* *
1651038 GTTGCGATAGCACTGTTTATC
1 GTTGCGATAGCACTGTTCACC
1651059 GTTGCGATAGCACTGTTCACC
1 GTTGCGATAGCACTGTTCACC
* *
1651080 GTTGCGATAGTATTGTTCACC
1 GTTGCGATAGCACTGTTCACC
*
1651101 GTTGCGATAACACTGTTCAC
1 GTTGCGATAGCACTGTTCAC
1651121 ATTGCGAATT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (21 bp):
GTTGCGATAGCACTGTTCACC
Found at i:1651304 original size:16 final size:17
Alignment explanation
Indices: 1651277--1651328 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
1651267 TTTATTTATG
1651277 ATAAACTATAAATTTTAA
1 ATAAA-TATAAATTTTAA
*
1651295 AT-AATATAAA-ATTAA
1 ATAAATATAAATTTTAA
*
1651310 ATAAATATAAATTCTAA
1 ATAAATATAAATTTTAA
1651327 AT
1 AT
1651329 TATTTATGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 6 0.21
16 14 0.48
17 7 0.24
18 2 0.07
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (17 bp):
ATAAATATAAATTTTAA
Found at i:1651723 original size:16 final size:15
Alignment explanation
Indices: 1651696--1651765 Score: 52
Period size: 15 Copynumber: 4.5 Consensus size: 15
1651686 ACTATTAATT
1651696 TTAAATAATATAAAA
1 TTAAATAATATAAAA
*
1651711 TTAAATAAATATAAAT
1 TTAAAT-AATATAAAA
* * **
1651727 TCTAAATTATTTATGA
1 T-TAAATAATATAAAA
*
1651743 -TAGAATAAAATAAAA
1 TTA-AATAATATAAAA
1651758 TTAAATAA
1 TTAAATAA
1651766 AATCCCAAGT
Statistics
Matches: 40, Mismatches: 11, Indels: 8
0.68 0.19 0.14
Matches are distributed among these distances:
14 2 0.05
15 18 0.45
16 15 0.38
17 5 0.12
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (15 bp):
TTAAATAATATAAAA
Found at i:1651855 original size:21 final size:21
Alignment explanation
Indices: 1651829--1651928 Score: 173
Period size: 21 Copynumber: 4.8 Consensus size: 21
1651819 ATTATAAAAT
1651829 GTGAACAGTGCTATCGCAACG
1 GTGAACAGTGCTATCGCAACG
* *
1651850 GTGAACAATACTATCGCAACG
1 GTGAACAGTGCTATCGCAACG
1651871 GTGAACAGTGCTATCGCAACG
1 GTGAACAGTGCTATCGCAACG
*
1651892 GTGAACAGTGTTATCGCAACG
1 GTGAACAGTGCTATCGCAACG
1651913 GTGAACAGTGCTATCG
1 GTGAACAGTGCTATCG
1651929 TAATGATTTT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 73 1.00
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (21 bp):
GTGAACAGTGCTATCGCAACG
Found at i:1651962 original size:21 final size:21
Alignment explanation
Indices: 1651936--1651976 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1651926 TCGTAATGAT
1651936 TTTGGACTATCGCAACGCGAA
1 TTTGGACTATCGCAACGCGAA
1651957 TTTGGACTATCGCAACGCGA
1 TTTGGACTATCGCAACGCGA
1651977 TAGTCAGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (21 bp):
TTTGGACTATCGCAACGCGAA
Found at i:1652067 original size:19 final size:19
Alignment explanation
Indices: 1652043--1652079 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1652033 TGCGATACTG
* *
1652043 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTACGATTTA
1652062 GAGATCGCATTACGATTT
1 GAGATCGCATTACGATTT
1652080 TGTTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTACGATTTA
Found at i:1653117 original size:37 final size:37
Alignment explanation
Indices: 1653060--1653132 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
1653050 TATGTTTCAG
*
1653060 AAAGAAAACTGGAACCAAGACAATATAGATGAATACC
1 AAAGAAAACTAGAACCAAGACAATATAGATGAATACC
* *
1653097 AAAGAAAACTAGTACTAAGACAATATAGATGAATAC
1 AAAGAAAACTAGAACCAAGACAATATAGATGAATAC
1653133 AAAACCTTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.55, C:0.14, G:0.15, T:0.16
Consensus pattern (37 bp):
AAAGAAAACTAGAACCAAGACAATATAGATGAATACC
Found at i:1653315 original size:22 final size:22
Alignment explanation
Indices: 1653290--1653357 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
1653280 CGATACTCAA
1653290 TACTTTGTTTAAGGGAGATAGT
1 TACTTTGTTTAAGGGAGATAGT
* * ***
1653312 TAC-TT-ATTAA-GCAGATTCA
1 TACTTTGTTTAAGGGAGATAGT
1653331 TACTTTGTTTAAGGGAGATAGT
1 TACTTTGTTTAAGGGAGATAGT
1653353 TACTT
1 TACTT
1653358 ATTAAGTAGA
Statistics
Matches: 33, Mismatches: 10, Indels: 6
0.67 0.20 0.12
Matches are distributed among these distances:
19 8 0.24
20 6 0.18
21 6 0.18
22 13 0.39
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (22 bp):
TACTTTGTTTAAGGGAGATAGT
Found at i:1653334 original size:41 final size:41
Alignment explanation
Indices: 1653289--1653371 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
1653279 TCGATACTCA
1653289 ATACTTTGTTTAAGGGAGATAGTTACTTATTAAGCAGATTC
1 ATACTTTGTTTAAGGGAGATAGTTACTTATTAAGCAGATTC
*
1653330 ATACTTTGTTTAAGGGAGATAGTTACTTATTAAGTAGATTC
1 ATACTTTGTTTAAGGGAGATAGTTACTTATTAAGCAGATTC
1653371 A
1 A
1653372 AACGACGATA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.40
Consensus pattern (41 bp):
ATACTTTGTTTAAGGGAGATAGTTACTTATTAAGCAGATTC
Found at i:1654176 original size:17 final size:17
Alignment explanation
Indices: 1654156--1654194 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1654146 TTTGGTAACG
*
1654156 GGTAAACTTTGGTTATC
1 GGTAAACTTTAGTTATC
*
1654173 GGTAAATTTTAGTTATC
1 GGTAAACTTTAGTTATC
1654190 GGTAA
1 GGTAA
1654195 GTATCGATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.28, C:0.08, G:0.23, T:0.41
Consensus pattern (17 bp):
GGTAAACTTTAGTTATC
Found at i:1654848 original size:111 final size:113
Alignment explanation
Indices: 1654550--1655034 Score: 705
Period size: 112 Copynumber: 4.3 Consensus size: 113
1654540 AACTTTCAAC
* ** * *
1654550 AAAGTATCGATACATGTACA-AAAAGTATCTATACTTTCAACATATCAGGTAG-TC-TTACCGGT
1 AAAGTATCGATACATTTTTATAAAAGTATCGATACTTTCAACATATCAGGTAGCTCTTTACCGAT
* * * *
1654612 TTTGTCATAATAAAACTAGTTTTGTCATATTTGTACCTGTTATATTAT
66 TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* * * * *
1654660 AAAATATCGATATATTTTTATAAAAAGGATCGATACTTTCAACATATCAAGTAGTTCTTTACCGA
1 AAAGTATCGATACATTTTTAT-AAAAGTATCGATACTTTCAACATATCAGGTAGCTCTTTACCGA
1654725 TTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
65 TTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
1654774 AAAGTA-CGATACATTTTTAT-AAAGTATCGATACTTTCAACATATCAGGTAGCTCTTTACCGAT
1 AAAGTATCGATACATTTTTATAAAAGTATCGATACTTTCAACATATCAGGTAGCTCTTTACCGAT
*
1654837 TTTGTCATAATGAAACTGGTTTTGTCATATTTTTATCTGTTATATTGT
66 TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* * *
1654885 AAAGTATCGATACATTTTTATAAAAG-ATCGATACTTTCAACATATCATGTAACTCTTTACCGGT
1 AAAGTATCGATACATTTTTATAAAAGTATCGATACTTTCAACATATCAGGTAGCTCTTTACCGAT
* * *
1654949 TTTGTCATAATGAAACTGATTTTGTCATATTTTTTACCTGTTAAATTGA
66 TTTGTCATAATGAAACTGGTTTTGTCATA-TTTTTACCTGTTATATTGT
*
1654998 AAAGTATCAATACATTTTTAT-AAAGTATCGATACTTT
1 AAAGTATCGATACATTTTTATAAAAGTATCGATACTTT
1655035 ATAGGCGCTA
Statistics
Matches: 340, Mismatches: 27, Indels: 13
0.89 0.07 0.03
Matches are distributed among these distances:
110 15 0.04
111 93 0.27
112 110 0.32
113 66 0.19
114 56 0.16
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (113 bp):
AAAGTATCGATACATTTTTATAAAAGTATCGATACTTTCAACATATCAGGTAGCTCTTTACCGAT
TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
Found at i:1654945 original size:223 final size:225
Alignment explanation
Indices: 1654571--1655034 Score: 729
Period size: 225 Copynumber: 2.1 Consensus size: 225
1654561 ACATGTACAA
* *
1654571 AAAGTATCTATACTTTCAACATATCAGGTAGTCTTACCGGTTTTGTCATAATAAAACTAGTTTTG
1 AAAGTATCGATACTTTCAACATATCAGGTAGTCTTACCGATTTTGTCATAATAAAACTAGTTTTG
*
1654636 TCATATTTGTACCTGTTATATTATAAAATATCGATATATTTTTATAAAAAGGATCGATACTTTCA
66 TCATATTTGTACCTGTTATATTATAAAATATCGATACATTTTTATAAAAAGGATCGATACTTTCA
** *
1654701 ACATATCAAGTAGTTCTTTACCGATTTTGTCATAATGAAACTGGTTTTGTCATA-TTTTTACCTG
131 ACATATCAAGTAACTCTTTACCGATTTTGTCATAATGAAACTGATTTTGTCATATTTTTTACCTG
* * *
1654765 TTATATTGTAAAGTA-CGATACATTTTTAT
196 TTAAATTGAAAAGTATCAATACATTTTTAT
* *
1654794 AAAGTATCGATACTTTCAACATATCAGGTAGCTCTTTACCGATTTTGTCATAATGAAACTGGTTT
1 AAAGTATCGATACTTTCAACATATCAGGTAG-TC-TTACCGATTTTGTCATAATAAAACTAGTTT
* * * *
1654859 TGTCATATTTTTATCTGTTATATTGTAAAGTATCGATACATTTTTAT-AAAA-GATCGATACTTT
64 TGTCATATTTGTACCTGTTATATTATAAAATATCGATACATTTTTATAAAAAGGATCGATACTTT
* *
1654922 CAACATATCATGTAACTCTTTACCGGTTTTGTCATAATGAAACTGATTTTGTCATATTTTTTACC
129 CAACATATCAAGTAACTCTTTACCGATTTTGTCATAATGAAACTGATTTTGTCATATTTTTTACC
1654987 TGTTAAATTGAAAAGTATCAATACATTTTTAT
194 TGTTAAATTGAAAAGTATCAATACATTTTTAT
1655019 AAAGTATCGATACTTT
1 AAAGTATCGATACTTT
1655035 ATAGGCGCTA
Statistics
Matches: 220, Mismatches: 17, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
223 93 0.42
224 29 0.13
225 98 0.45
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.42
Consensus pattern (225 bp):
AAAGTATCGATACTTTCAACATATCAGGTAGTCTTACCGATTTTGTCATAATAAAACTAGTTTTG
TCATATTTGTACCTGTTATATTATAAAATATCGATACATTTTTATAAAAAGGATCGATACTTTCA
ACATATCAAGTAACTCTTTACCGATTTTGTCATAATGAAACTGATTTTGTCATATTTTTTACCTG
TTAAATTGAAAAGTATCAATACATTTTTAT
Found at i:1655264 original size:73 final size:73
Alignment explanation
Indices: 1655119--1655357 Score: 354
Period size: 76 Copynumber: 3.2 Consensus size: 73
1655109 CATATCATGT
* * * * *
1655119 GGTAGTTTAATGTAATAGGTATCACCTATTTGTTTTACCTTTTACATTATTAGCAACCTT-AAAA
1 GGTATTTTAATGTAATAGGTAACA-CTATTTTTTTTACCGTTTACATTATTAACAACCTTAAAAA
*
1655183 AAATCGGTA
65 AAACCGGTA
1655192 GGTATTTTAATGTAATAGGTAACACTATTTTTTTTACCGTTTACATTATTAACAACCTTAAAAAA
1 GGTATTTTAATGTAATAGGTAACACTATTTTTTTTACCGTTTACATTATTAACAACCTTAAAAAA
1655257 AACCGGTA
66 AACCGGTA
** *
1655265 GGTATTTTAATGTAATAGGTAGTACTTATTTTTTTTTTACCGTTTACACTATTAACAACCTTAAA
1 GGTATTTTAATGTAATAGGTAACAC-TA--TTTTTTTTACCGTTTACATTATTAACAACCTTAAA
1655330 AAAAACCGGTA
63 AAAAACCGGTA
1655341 GGTATTTTAATGTAATA
1 GGTATTTTAATGTAATA
1655358 TATAATTTAA
Statistics
Matches: 153, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
72 32 0.21
73 57 0.37
74 2 0.01
76 62 0.41
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (73 bp):
GGTATTTTAATGTAATAGGTAACACTATTTTTTTTACCGTTTACATTATTAACAACCTTAAAAAA
AACCGGTA
Found at i:1655626 original size:23 final size:23
Alignment explanation
Indices: 1655578--1655627 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1655568 ACCTATTTTA
* *
1655578 TTATATAAGTGCTATCTATTACG
1 TTATATAAGCGCTATCTAATACG
*
1655601 TTATATAAGCGCTA-CATAATATG
1 TTATATAAGCGCTATC-TAATACG
1655624 TTAT
1 TTAT
1655628 TGTGCTTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (23 bp):
TTATATAAGCGCTATCTAATACG
Found at i:1655713 original size:158 final size:157
Alignment explanation
Indices: 1655433--1655944 Score: 760
Period size: 158 Copynumber: 3.2 Consensus size: 157
1655423 AGTAAGTAAT
** * * * * *
1655433 TACCTATTTTGTTATATAAACGCTACTTAGTATGTTATTATGTTTGATAATGTTTCCAG-AATTA
1 TACCTATTACGTTATATAAGCGCTACTTAATATGTTATTGTGCTTGATAATGTTTTCAGTAATTA
*
1655497 ACCGATTATGTTATCCTTGGTAACATTTTAAGCGTTTACCTAATATGTTGTAATAACAAATTAAG
66 ACCGATTATGTTAT-CTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAG
*
1655562 TAATTAACCTATTTTATTATATAAGTGC
130 TAATTAACCTATTTTATTATATAAGCGC
* *
1655590 TATCTATTACGTTATATAAGCGCTACATAATATGTTATTGTGCTTGATAATGTTTTCAGTAATTA
1 TACCTATTACGTTATATAAGCGCTACTTAATATGTTATTGTGCTTGATAATGTTTTCAGTAATTA
* * *
1655655 ACCGGTTATGTTATCATTGGTAACATTTTAGGCGTTTACCTTATATGTTGTAATAACAAATTAAA
66 ACCGATTATGTTATC-TTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAG
1655720 TAATTAACCTATTTTATTATATAAGCGC
130 TAATTAACCTATTTTATTATATAAGCGC
* * *
1655748 TACCTATTACGTTATATAAGCGCTATTTAATATGTTATTGTGCTTGATAATG-TTTCTAATAAAT
1 TACCTATTACGTTATATAAGCGCTACTTAATATGTTATTGTGCTTGATAATGTTTTC-AGTAATT
1655812 AACCGATTATGTTATCTCTGGTAACATTTTAAGG-GTTTACCTAATATGTTGTAATAACAAATTA
65 AACCGATTATGTTATCT-TGGTAACATTTT-AGGCGTTTACCTAATATGTTGTAATAACAAATTA
* *
1655876 AGTAATTAACATATTTTATTATATAAGCGT
128 AGTAATTAACCTATTTTATTATATAAGCGC
* * *
1655906 TACCTATTACATTATATAAGCGCTACCTAATATATTATT
1 TACCTATTACGTTATATAAGCGCTACTTAATATGTTATT
1655945 ATATTTAATA
Statistics
Matches: 322, Mismatches: 28, Indels: 9
0.90 0.08 0.03
Matches are distributed among these distances:
157 56 0.17
158 263 0.82
159 3 0.01
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (157 bp):
TACCTATTACGTTATATAAGCGCTACTTAATATGTTATTGTGCTTGATAATGTTTTCAGTAATTA
ACCGATTATGTTATCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGT
AATTAACCTATTTTATTATATAAGCGC
Found at i:1655945 original size:26 final size:25
Alignment explanation
Indices: 1655886--1655948 Score: 76
Period size: 23 Copynumber: 2.6 Consensus size: 25
1655876 AGTAATTAAC
* *
1655886 ATATTTTATTATATAAGCGTTACCT
1 ATATATTATTATATAAGCGCTACCT
*
1655911 AT-TA-CATTATATAAGCGCTACCT
1 ATATATTATTATATAAGCGCTACCT
1655934 AATATATTATTATAT
1 -ATATATTATTATAT
1655949 TTAATAATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
23 17 0.55
24 3 0.10
25 4 0.13
26 7 0.23
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.44
Consensus pattern (25 bp):
ATATATTATTATATAAGCGCTACCT
Found at i:1660692 original size:23 final size:23
Alignment explanation
Indices: 1660666--1660749 Score: 132
Period size: 23 Copynumber: 3.7 Consensus size: 23
1660656 CTCGTATAAA
*
1660666 TGCACCAAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
1660689 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1660712 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
1660735 TGTACCGTAGTGCCA
1 TGCACCGAAGTGCCA
1660750 TATAAGATGT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1661373 original size:20 final size:21
Alignment explanation
Indices: 1661348--1661403 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 21
1661338 AATAAAGGTA
1661348 TGTATCGATGCACT-CTACA-G
1 TGTATCGATGCACTCCTA-ATG
1661368 TGTATCGA-GCACTCCTAATG
1 TGTATCGATGCACTCCTAATG
1661388 TGTGCATCGATGCACT
1 TGT--ATCGATGCACT
1661404 ACCAGTGCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
19 6 0.19
20 15 0.48
22 5 0.16
23 5 0.16
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.30
Consensus pattern (21 bp):
TGTATCGATGCACTCCTAATG
Found at i:1664314 original size:183 final size:186
Alignment explanation
Indices: 1663988--1664357 Score: 701
Period size: 183 Copynumber: 2.0 Consensus size: 186
1663978 GTTCAAAACC
1663988 AAATTGTGGAAAATAAGAAAGAATGGGCAGAAAAAGGTTGTTCAATACTATCGGATGGATGGCGT
1 AAATTGTGGAAAATAAGAAAGAATGGGCAGAAAAAGGTTGTTCAATACTATCGGATGGATGGCGT
1664053 GATTCCGTTGTTCAAAAAGATATCATCAACTTCCTGGTAAACTCCCAAAAGGGTTCGGTCTTCGT
66 GATTCCGTTGTTCAAAAAGATATCA-CAACTTCCTGGTAAACTCCCAAAAGGGTTCGGTCTTCGT
1664118 GAAGTCACTTGATGTATCTGATGTTTCAAAGGATGCTGATTTGTTGGTTCATGTTCT
130 GAAGTCACTTGATGTATCTGATGTTTCAAAGGATGCTGATTTGTTGGTTCATGTTCT
1664175 AAATTGTGG-AAATAAGAAAGAATGGGCAGAAAAAGGTTGTTCAATACTATCGGATGGATGG-GT
1 AAATTGTGGAAAATAAGAAAGAATGGGCAGAAAAAGGTTGTTCAATACTATCGGATGGATGGCGT
1664238 GATTCCGTTGTTCAAAAAGATATCA-AACTTCCTGGTAAACTCCCAAAAGGGTTCGGTCTTCGTG
66 GATTCCGTTGTTCAAAAAGATATCACAACTTCCTGGTAAACTCCCAAAAGGGTTCGGTCTTCGTG
*
1664302 AAGTCACTTGATGTATCTGATGTTTCAAAGGATGCTGATTTGTTGTTTCATGTTCT
131 AAGTCACTTGATGTATCTGATGTTTCAAAGGATGCTGATTTGTTGGTTCATGTTCT
1664358 TGATAAAATG
Statistics
Matches: 182, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
183 94 0.52
185 27 0.15
186 52 0.29
187 9 0.05
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (186 bp):
AAATTGTGGAAAATAAGAAAGAATGGGCAGAAAAAGGTTGTTCAATACTATCGGATGGATGGCGT
GATTCCGTTGTTCAAAAAGATATCACAACTTCCTGGTAAACTCCCAAAAGGGTTCGGTCTTCGTG
AAGTCACTTGATGTATCTGATGTTTCAAAGGATGCTGATTTGTTGGTTCATGTTCT
Found at i:1672975 original size:3 final size:3
Alignment explanation
Indices: 1672967--1673039 Score: 101
Period size: 3 Copynumber: 24.3 Consensus size: 3
1672957 TAATATATTT
** * *
1672967 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGT TTA TAA CAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1673015 TAA TAA TTA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
1673040 TTTAAAATGG
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1674729 original size:54 final size:54
Alignment explanation
Indices: 1674647--1674806 Score: 266
Period size: 54 Copynumber: 3.0 Consensus size: 54
1674637 CTGGTTTATG
*
1674647 AAACATTTGACAATACATTCATCATTTCCTGTGGCTTCTGCACAGATGTTCGTA
1 AAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCACAGATGTTCGTA
* * * *
1674701 AAACATTTGACAACACATTCATCCTTTCCTATAGTTTCTGCACAGATGTTCGTA
1 AAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCACAGATGTTCGTA
*
1674755 AAACATTTGACAACACATTCATCATTTCTTGTGGCTTCTGCACAGATGTTCG
1 AAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCACAGATGTTCG
1674807 CCAGTGAAGC
Statistics
Matches: 96, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 96 1.00
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (54 bp):
AAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCACAGATGTTCGTA
Found at i:1679888 original size:42 final size:43
Alignment explanation
Indices: 1679842--1679926 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
1679832 CGGTACATCA
**
1679842 AACAAAACTTTACATATA-GGGATAGTTTTCACT-CATAACTTC
1 AACAAAACTTTACATATAGGGGATAACTTTCACTAC-TAACTTC
1679884 AACAAAACTTTACATATAGGGGATAACTTTCACTACTAACTTC
1 AACAAAACTTTACATATAGGGGATAACTTTCACTACTAACTTC
1679927 TCTAAAGCCA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
42 18 0.46
43 20 0.51
44 1 0.03
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (43 bp):
AACAAAACTTTACATATAGGGGATAACTTTCACTACTAACTTC
Found at i:1682068 original size:16 final size:17
Alignment explanation
Indices: 1682037--1682069 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1682027 CCATTTCTTC
1682037 AATATGAAAAATAAATA
1 AATATGAAAAATAAATA
*
1682054 AATATTAAAAA-AAATA
1 AATATGAAAAATAAATA
1682070 GATAATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (17 bp):
AATATGAAAAATAAATA
Found at i:1682122 original size:2 final size:2
Alignment explanation
Indices: 1682115--1682141 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1682105 TAAAGTAAAT
1682115 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1682142 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1683252 original size:21 final size:22
Alignment explanation
Indices: 1683219--1683261 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
1683209 TTGGGTGTTC
* *
1683219 TTGCTCTGTTTTTGT-TTGGTG
1 TTGCTCTGCTTTTCTCTTGGTG
*
1683240 TTGCTGTGCTTTTCTCTTGGTG
1 TTGCTCTGCTTTTCTCTTGGTG
1683262 GATGTTCGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.00, C:0.14, G:0.28, T:0.58
Consensus pattern (22 bp):
TTGCTCTGCTTTTCTCTTGGTG
Found at i:1683721 original size:3 final size:3
Alignment explanation
Indices: 1683713--1683785 Score: 74
Period size: 3 Copynumber: 24.3 Consensus size: 3
1683703 TAATATATTT
** * * *
1683713 TAA TAA TAA TAA TAA TAA TAA TAA TGT TTA TAA TAA TAA TAA TTA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
1683761 TTA TTA TAA TTA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
1683786 TTTAAAATGG
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (3 bp):
TAA
Found at i:1684948 original size:44 final size:43
Alignment explanation
Indices: 1684901--1685241 Score: 173
Period size: 43 Copynumber: 7.9 Consensus size: 43
1684891 GGCCCCCATT
* *
1684901 TTTTTCATCTTTATAATT-AGGTTCTTAATTTTTTTAAATTTTA
1 TTTTTCATCTTTATAATTGAGG-TCTTAATTTTTTTAAATCTAA
* * * * *
1684944 TTTTTCACCTTTATAATTGAGGTCCTAATATTATTCAATCTAA
1 TTTTTCATCTTTATAATTGAGGTCTTAATTTTTTTAAATCTAA
* * **
1684987 CTTTTT-ATCTTTATAATTGAAGTCTCTAATTTTTTTCAATC-CC
1 -TTTTTCATCTTTATAATTGAGGTCT-TAATTTTTTTAAATCTAA
* * * *
1685030 TTCTTT-ACCTTTATAATTGAGGCCTCTAA-TTTTGT-AATCTCA
1 TT-TTTCATCTTTATAATTGAGGTCT-TAATTTTTTTAAATCTAA
* * * * * * *
1685072 CTTTT-AACTTTATAATTGAAGCTTTTAAGTTTTTTCAATCTTA
1 TTTTTCATCTTTATAATTG-AGGTCTTAATTTTTTTAAATCTAA
* * * * *
1685115 -CTTTCTACCTTT-TCAATTGAGGCCTCTAAGTTTTTTCAATCTCAA
1 TTTTTC-ATCTTTAT-AATTGAGGTCT-TAATTTTTTTAAATCT-AA
* * * * *
1685160 TTTCT-ACCTTTATAATTGAGGCCCCTAATTTTTTT-AATCTCAC
1 TTTTTCATCTTTATAATTGAGG-TCTTAATTTTTTTAAATCT-AA
* *
1685203 TTTTTTAACTTTATAATTGAGGTCCTTAAGTTTTTTTAA
1 TTTTTCATCTTTATAATTGAGGT-CTTAA-TTTTTTTAA
1685242 TCTCACTTTC
Statistics
Matches: 237, Mismatches: 41, Indels: 37
0.75 0.13 0.12
Matches are distributed among these distances:
41 22 0.09
42 20 0.08
43 92 0.39
44 89 0.38
45 11 0.05
46 3 0.01
ACGTcount: A:0.25, C:0.16, G:0.07, T:0.51
Consensus pattern (43 bp):
TTTTTCATCTTTATAATTGAGGTCTTAATTTTTTTAAATCTAA
Found at i:1685221 original size:88 final size:88
Alignment explanation
Indices: 1684944--1685326 Score: 374
Period size: 88 Copynumber: 4.4 Consensus size: 88
1684934 TTAAATTTTA
* * * * *
1684944 TTTTTCACCTTTATAATTGAGGTC-CTAATATTATTCAATCT-AACTTTTTATCTTTATAATTGA
1 TTTTTTACCTTTATAATTGAGGCCTCTAAT-TTTTTCAATCTCAA-TTTCTAACTTTATAATTGA
* * *
1685007 AGTCTCTAATTTTTTTCAATC-C-C
64 GGCCCCTAATTTTTTTCAATCTCAC
* * * *
1685030 TTCTTTACCTTTATAATTGAGGCCTCTAATTTTGT-AATCTCACTTT-TAACTTTATAATTGAAG
1 TTTTTTACCTTTATAATTGAGGCCTCTAATTTTTTCAATCTCAATTTCTAACTTTATAATTGAGG
*** * *
1685093 CTTTTAAGTTTTTTCAATCTTAC
66 CCCCTAATTTTTTTCAATCTCAC
* *
1685116 -TTTCTACCTTT-TCAATTGAGGCCTCTAAGTTTTTTCAATCTCAATTTCTACCTTTATAATTGA
1 TTTTTTACCTTTAT-AATTGAGGCCTCTAA-TTTTTTCAATCTCAATTTCTAACTTTATAATTGA
1685179 GGCCCCTAATTTTTTT-AATCTCAC
64 GGCCCCTAATTTTTTTCAATCTCAC
* * * * *
1685203 TTTTTTAACTTTATAATTGAGGTCCT-TAAGTTTTTTTAATCTCACTTTCTAGCTTTCTAATTGA
1 TTTTTTACCTTTATAATTGAGG-CCTCTAA-TTTTTTCAATCTCAATTTCTAACTTTATAATTGA
*
1685267 GGCCCCTATTTTTTTTTCAATCTCA-
64 GGCCCCTA-ATTTTTTTCAATCTCAC
* * *
1685292 ATTTCTACCTTTATAATTAAGGCCTCTAATTTTTT
1 TTTTTTACCTTTATAATTGAGGCCTCTAATTTTTT
1685327 TTTTTTGCAA
Statistics
Matches: 249, Mismatches: 34, Indels: 26
0.81 0.11 0.08
Matches are distributed among these distances:
84 32 0.13
85 32 0.13
86 31 0.12
87 22 0.09
88 93 0.37
89 32 0.13
90 7 0.03
ACGTcount: A:0.24, C:0.19, G:0.08, T:0.50
Consensus pattern (88 bp):
TTTTTTACCTTTATAATTGAGGCCTCTAATTTTTTCAATCTCAATTTCTAACTTTATAATTGAGG
CCCCTAATTTTTTTCAATCTCAC
Found at i:1685340 original size:44 final size:43
Alignment explanation
Indices: 1684946--1685327 Score: 332
Period size: 44 Copynumber: 8.8 Consensus size: 43
1684936 AAATTTTATT
* * *
1684946 TTTC-ACCTTTATAATTGAGGTC-CTAATATTATTCAATCT-AA
1 TTTCTACCTTTATAATTGAGGCCTCTAAT-TTTTTTAATCTCAA
* * * * *
1684987 CTTTTTATCTTTATAATTGAAGTCTCTAATTTTTTTCAATC-C-C
1 -TTTCTACCTTTATAATTGAGGCCTCTAATTTTTTT-AATCTCAA
* * *
1685030 TTCTTTACCTTTATAATTGAGGCCTCTAA-TTTTGTAATCTCAC
1 TT-TCTACCTTTATAATTGAGGCCTCTAATTTTTTTAATCTCAA
* * * * * * *
1685073 TTT-TAACTTTATAATTGAAGCTTTTAAGTTTTTTCAATCTTAC
1 TTTCTACCTTTATAATTGAGGCCTCTAA-TTTTTTTAATCTCAA
*
1685116 TTTCTACCTTT-TCAATTGAGGCCTCTAAGTTTTTTCAATCTCAA
1 TTTCTACCTTTAT-AATTGAGGCCTCTAA-TTTTTTTAATCTCAA
* *
1685160 TTTCTACCTTTATAATTGAGGCCCCTAATTTTTTTAATCTCACT
1 TTTCTACCTTTATAATTGAGGCCTCTAATTTTTTTAATCTCA-A
* * *
1685204 TTTTTAACTTTATAATTGAGGTCCT-TAAGTTTTTTTAATCTCAC
1 TTTCTACCTTTATAATTGAGG-CCTCTAA-TTTTTTTAATCTCAA
* * * *
1685248 TTTCTAGCTTTCTAATTGAGGCCCCTATTTTTTTTTCAATCTCAA
1 TTTCTACCTTTATAATTGAGGCCTCTA-ATTTTTTT-AATCTCAA
*
1685293 TTTCTACCTTTATAATTAAGGCCTCTAATTTTTTT
1 TTTCTACCTTTATAATTGAGGCCTCTAATTTTTTT
1685328 TTTTTGCAAT
Statistics
Matches: 281, Mismatches: 41, Indels: 34
0.79 0.12 0.10
Matches are distributed among these distances:
41 24 0.09
42 12 0.04
43 76 0.27
44 122 0.43
45 47 0.17
ACGTcount: A:0.24, C:0.19, G:0.08, T:0.49
Consensus pattern (43 bp):
TTTCTACCTTTATAATTGAGGCCTCTAATTTTTTTAATCTCAA
Found at i:1685625 original size:23 final size:23
Alignment explanation
Indices: 1685582--1685625 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1685572 TAAGATGTTT
*
1685582 TATTAACAAAAAAATGAAATTAA
1 TATTAACAAAAAAATAAAATTAA
*
1685605 TATTAA-AAAAAATTAATAATT
1 TATTAACAAAAAAATAA-AATT
1685626 TTTCTACGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (23 bp):
TATTAACAAAAAAATAAAATTAA
Found at i:1688149 original size:19 final size:20
Alignment explanation
Indices: 1688125--1688165 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1688115 AATTAATAAT
1688125 TTTTA-TCTAATAA-AAAATA
1 TTTTATTCTAA-AATAAAATA
1688144 TTTTATTCTAAAATAAAATA
1 TTTTATTCTAAAATAAAATA
1688164 TT
1 TT
1688166 GAAAGTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTTATTCTAAAATAAAATA
Found at i:1688453 original size:41 final size:40
Alignment explanation
Indices: 1688408--1688499 Score: 123
Period size: 41 Copynumber: 2.2 Consensus size: 40
1688398 CTCAGTTTCC
** *
1688408 AAAATCGCAATGTGAATAGTAAAAATCGTAACGTGAA-TAG
1 AAAATCGCAACATGAATAGT-AAAATCGCAACGTGAATTAG
1688448 TAAAATCGCAACATGAATAGTAAAATCGCAACGTGAATTTAG
1 -AAAATCGCAACATGAATAGTAAAATCGCAACGTGAA-TTAG
1688490 AAAATCGCAA
1 AAAATCGCAA
1688500 AATCGTGTTG
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
40 15 0.33
41 28 0.61
42 3 0.07
ACGTcount: A:0.48, C:0.13, G:0.17, T:0.22
Consensus pattern (40 bp):
AAAATCGCAACATGAATAGTAAAATCGCAACGTGAATTAG
Found at i:1688454 original size:20 final size:20
Alignment explanation
Indices: 1688408--1688499 Score: 123
Period size: 20 Copynumber: 4.5 Consensus size: 20
1688398 CTCAGTTTCC
*
1688408 AAAATCGCAATGTGAATAGT
1 AAAATCGCAACGTGAATAGT
*
1688428 AAAAATCGTAACGTGAATAGT
1 -AAAATCGCAACGTGAATAGT
*
1688449 AAAATCGCAACATGAATAGT
1 AAAATCGCAACGTGAATAGT
1688469 AAAATCGCAACGTGAATTTAG-
1 AAAATCGCAACGTGAA--TAGT
1688490 AAAATCGCAA
1 AAAATCGCAA
1688500 AATCGTGTTG
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
20 33 0.52
21 28 0.44
22 3 0.05
ACGTcount: A:0.48, C:0.13, G:0.17, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGTGAATAGT
Found at i:1688883 original size:21 final size:21
Alignment explanation
Indices: 1688849--1688922 Score: 132
Period size: 21 Copynumber: 3.6 Consensus size: 21
1688839 CATATAGATT
*
1688849 CGTTGCGA-TTTTACTATTTA
1 CGTTGCGATTTTTACTATTCA
1688869 CGTTGCGATTTTTACTATTCA
1 CGTTGCGATTTTTACTATTCA
1688890 CGTTGCGATTTTTACTATTCA
1 CGTTGCGATTTTTACTATTCA
1688911 CGTTGCGATTTT
1 CGTTGCGATTTT
1688923 GGAAACTGAG
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
20 8 0.15
21 44 0.85
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.49
Consensus pattern (21 bp):
CGTTGCGATTTTTACTATTCA
Found at i:1688974 original size:19 final size:19
Alignment explanation
Indices: 1688930--1688977 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1688920 TTTGGAAACT
* *
1688930 GAGTTGCGAAATTGGAGTTC
1 GAGTTGCG-AATTCGAGATC
*
1688950 GCGTTGCGAATTCGAGATC
1 GAGTTGCGAATTCGAGATC
1688969 GAGTTGCGA
1 GAGTTGCGA
1688978 TTTTGTTAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.23, C:0.15, G:0.35, T:0.27
Consensus pattern (19 bp):
GAGTTGCGAATTCGAGATC
Found at i:1689177 original size:20 final size:20
Alignment explanation
Indices: 1689140--1689371 Score: 140
Period size: 20 Copynumber: 11.7 Consensus size: 20
1689130 AACTAAAACC
*
1689140 TGTTGCGAAATT-AAATTCG
1 TGTTGCGAATTTGAAATTCG
*
1689159 TGTTGTGAATTTGAAATTC-
1 TGTTGCGAATTTGAAATTCG
*
1689178 AGTTGCGAATTTGAAATTCCG
1 TGTTGCGAATTTGAAATT-CG
* ** *
1689199 CGTTGCGAATTTGACTTTTG
1 TGTTGCGAATTTGAAATTCG
*
1689219 TGTTGCGAATTTG-ACTTCTG
1 TGTTGCGAATTTGAAATTC-G
* *
1689239 TGTTGCG-ATTTACAAATCCG
1 TGTTGCGAATTT-GAAATTCG
* *
1689259 CGTTGCGAATTTG-ACTATCG
1 TGTTGCGAATTTGAAAT-TCG
*
1689279 TGTTGCGAATTTG-ACTTCTG
1 TGTTGCGAATTTGAAATTC-G
*
1689299 TGTTGCG-ATTTATAAATTCG
1 TGTTGCGAATTT-GAAATTCG
*
1689319 CGTTGCG-ATTT-ACATATTCG
1 TGTTGCGAATTTGA-A-ATTCG
* * * * *
1689339 CGTTGTGAAATTGGAGTTCG
1 TGTTGCGAATTTGAAATTCG
*
1689359 CGTTGCGAATTTG
1 TGTTGCGAATTTG
1689372 TTGGTTATTT
Statistics
Matches: 169, Mismatches: 29, Indels: 29
0.74 0.13 0.13
Matches are distributed among these distances:
18 1 0.01
19 41 0.24
20 97 0.57
21 30 0.18
ACGTcount: A:0.22, C:0.14, G:0.24, T:0.40
Consensus pattern (20 bp):
TGTTGCGAATTTGAAATTCG
Found at i:1689182 original size:19 final size:19
Alignment explanation
Indices: 1689141--1689212 Score: 74
Period size: 19 Copynumber: 3.7 Consensus size: 19
1689131 ACTAAAACCT
* *
1689141 GTTGCGAAATT-AAATTCGT
1 GTTGCGAATTTGAAATTC-A
*
1689160 GTTGTGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
*
1689179 GTTGCGAATTTGAAATTCCGC
1 GTTGCGAATTTGAAATT-C-A
1689200 GTTGCGAATTTGA
1 GTTGCGAATTTGA
1689213 CTTTTGTGTT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
19 25 0.56
20 7 0.16
21 13 0.29
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.38
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:1689229 original size:60 final size:60
Alignment explanation
Indices: 1689156--1689326 Score: 188
Period size: 60 Copynumber: 2.9 Consensus size: 60
1689146 GAAATTAAAT
* * *
1689156 TCGTGTTGTGAATTTGAAATTC-AGTTGCGAATTTGA-AATTCCGCGTTGCGAATTTGACTT
1 TCGTGTTGCGAATTTGAAATTCGAGTTGCG-ATTT-ACAAATCCGCGTTGCGAATTTGACTA
* * *
1689216 TTGTGTTGCGAATTTG-ACTTCTGTGTTGCGATTTACAAATCCGCGTTGCGAATTTGACTA
1 TCGTGTTGCGAATTTGAAATTC-GAGTTGCGATTTACAAATCCGCGTTGCGAATTTGACTA
* * * *
1689276 TCGTGTTGCGAATTTG-ACTTCTGTGTTGCGATTTATAAATTCGCGTTGCGA
1 TCGTGTTGCGAATTTGAAATTC-GAGTTGCGATTTACAAATCCGCGTTGCGA
1689327 TTTACATATT
Statistics
Matches: 99, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
59 5 0.05
60 88 0.89
61 6 0.06
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.40
Consensus pattern (60 bp):
TCGTGTTGCGAATTTGAAATTCGAGTTGCGATTTACAAATCCGCGTTGCGAATTTGACTA
Found at i:1689286 original size:80 final size:80
Alignment explanation
Indices: 1689179--1689371 Score: 219
Period size: 80 Copynumber: 2.4 Consensus size: 80
1689169 TTGAAATTCA
* * * * * * *
1689179 GTTGCGAATTTGAAATTCCGCGTTGCGAATTTGACTTTTGTGTTGCGAATT-TGACTTCTGTGTT
1 GTTGCGAAATTGGACTT-CGCGTTGCGAATTTGACTTCTGTGTTGCGAATTATAAATTC-GCGTT
1689243 GCGATTTACAAATCCGC
64 GCGATTTACAAATCCGC
* * *
1689260 GTTGCG-AATTTGACTATCGTGTTGCGAATTTGACTTCTGTGTTGCGATTTATAAATTCGCGTTG
1 GTTGCGAAATTGGACT-TCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTATAAATTCGCGTTG
* *
1689324 CGATTTACATATTCGC
65 CGATTTACAAATCCGC
* *
1689340 GTTGTGAAATTGGAGTTCGCGTTGCGAATTTG
1 GTTGCGAAATTGGACTTCGCGTTGCGAATTTG
1689372 TTGGTTATTT
Statistics
Matches: 93, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
80 74 0.80
81 19 0.20
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.40
Consensus pattern (80 bp):
GTTGCGAAATTGGACTTCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTATAAATTCGCGTTGC
GATTTACAAATCCGC
Found at i:1689364 original size:60 final size:60
Alignment explanation
Indices: 1689195--1689366 Score: 188
Period size: 60 Copynumber: 2.9 Consensus size: 60
1689185 AATTTGAAAT
* * * * *
1689195 TCCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTCTGTGTTGCGATTTACAAA
1 TCCGCGTTGCGAATTTGACTATCGCGTTGCGAATTGGACTTCTGCGTTGCGATTTACAAA
* * * *
1689255 TCCGCGTTGCGAATTTGACTATCGTGTTGCGAATTTGACTTCTGTGTTGCGATTTATAAA
1 TCCGCGTTGCGAATTTGACTATCGCGTTGCGAATTGGACTTCTGCGTTGCGATTTACAAA
* * *
1689315 TTCGCGTTGCG-ATTT-ACATATTCGCGTTGTGAAATTGGAGTTC-GCGTTGCGA
1 TCCGCGTTGCGAATTTGAC-TA-TCGCGTTGCG-AATTGGACTTCTGCGTTGCGA
1689367 ATTTGTTGGT
Statistics
Matches: 100, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
58 2 0.02
59 6 0.06
60 83 0.83
61 9 0.09
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.40
Consensus pattern (60 bp):
TCCGCGTTGCGAATTTGACTATCGCGTTGCGAATTGGACTTCTGCGTTGCGATTTACAAA
Found at i:1694325 original size:17 final size:18
Alignment explanation
Indices: 1694291--1694330 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
1694281 TTCTTATTAT
1694291 TTTTGTTTCTTATTTTTA
1 TTTTGTTTCTTATTTTTA
1694309 TTTT-TTTC-TATTGTTTA
1 TTTTGTTTCTTATT-TTTA
1694326 TTTTG
1 TTTTG
1694331 CTGATCTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 4 0.20
17 12 0.60
18 4 0.20
ACGTcount: A:0.10, C:0.05, G:0.07, T:0.78
Consensus pattern (18 bp):
TTTTGTTTCTTATTTTTA
Found at i:1695147 original size:15 final size:15
Alignment explanation
Indices: 1695119--1695158 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
1695109 TTTACGTAAG
*
1695119 GCGCGTTTCTAGGGAT
1 GCGC-TTTCCAGGGAT
1695135 GCGCTTTCCAGGGAT
1 GCGCTTTCCAGGGAT
*
1695150 GCACTTTCC
1 GCGCTTTCC
1695159 TGCCACGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.12, C:0.28, G:0.30, T:0.30
Consensus pattern (15 bp):
GCGCTTTCCAGGGAT
Found at i:1695822 original size:97 final size:98
Alignment explanation
Indices: 1695647--1695824 Score: 281
Period size: 97 Copynumber: 1.8 Consensus size: 98
1695637 ATTAATTATT
* *
1695647 AAAATATCATCTCTTTATTTAAAAATATTCCTTTTAATATTAATTTAAAAAAATATAAAATACAT
1 AAAATATCAACTCTTTATTTAAAAATATTCCTTTTAATATTAATTTAAAAAAATATAAAATAAAT
*
1695712 ATTAAATTATAATGAAATAGAATGTAAAGCTAA
66 ATTAAAATATAATGAAATAGAATGTAAAGCTAA
*
1695745 AAAATATCAACTCTTTATTT-AAAATATT-CTTTCTAATATTAATTTTAAAAAATATAAAATAAA
1 AAAATATCAACTCTTTATTTAAAAATATTCCTTT-TAATATTAATTTAAAAAAATATAAAATAAA
1695808 TATTAAAA-ATTAATGAA
65 TATTAAAATA-TAATGAA
1695825 TAATAATTCA
Statistics
Matches: 74, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
96 5 0.07
97 50 0.68
98 19 0.26
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.39
Consensus pattern (98 bp):
AAAATATCAACTCTTTATTTAAAAATATTCCTTTTAATATTAATTTAAAAAAATATAAAATAAAT
ATTAAAATATAATGAAATAGAATGTAAAGCTAA
Found at i:1704590 original size:31 final size:31
Alignment explanation
Indices: 1704548--1704626 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
1704538 ATAATAGTGG
*
1704548 AGTGACAATTTTGTTACAAATCAATAACGTT
1 AGTGACCATTTTGTTACAAATCAATAACGTT
*
1704579 AGTGACCATTTTGTTACAAATCAATAATGTT
1 AGTGACCATTTTGTTACAAATCAATAACGTT
* *
1704610 AGTGATCAATTTGTTAC
1 AGTGACCATTTTGTTAC
1704627 TTTTGAAACT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (31 bp):
AGTGACCATTTTGTTACAAATCAATAACGTT
Found at i:1704792 original size:15 final size:16
Alignment explanation
Indices: 1704767--1704796 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1704757 AATATTTAGA
1704767 AAAATATATATTTTAT
1 AAAATATATATTTTAT
1704783 AAAA-ATATATTTTA
1 AAAATATATATTTTA
1704797 AAACTATTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAAATATATATTTTAT
Found at i:1705284 original size:77 final size:77
Alignment explanation
Indices: 1705196--1705346 Score: 241
Period size: 77 Copynumber: 2.0 Consensus size: 77
1705186 TCAGGTGCGC
*
1705196 ATATTATTTTTTGTATGGATATTAGAAA-ATTTTGTCCAACTTTCATTCACATTTTACTTTACAT
1 ATATTATTTTTTGTATGGATATTAGAAACA-TTTGTCCAACTTTCATTCACATTTTACTTCACAT
1705260 ATATTCAGAGCAT
65 ATATTCAGAGCAT
* * * *
1705273 ATATTGTTTTTTGTATGGATATTTGAAACATTTGTCCAAGTTTCATTCGCATTTTACTTCACATA
1 ATATTATTTTTTGTATGGATATTAGAAACATTTGTCCAACTTTCATTCACATTTTACTTCACATA
1705338 TATTCAGAG
66 TATTCAGAG
1705347 ACGAGATGTT
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
77 67 0.99
78 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.46
Consensus pattern (77 bp):
ATATTATTTTTTGTATGGATATTAGAAACATTTGTCCAACTTTCATTCACATTTTACTTCACATA
TATTCAGAGCAT
Found at i:1706080 original size:21 final size:21
Alignment explanation
Indices: 1706050--1706108 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
1706040 TGATTTATTA
*
1706050 TTATGGATTTCAAGTTTCTTG
1 TTATGAATTTCAAGTTTCTTG
* *
1706071 TTATGTATTTCAAGTTTGTTG
1 TTATGAATTTCAAGTTTCTTG
* *
1706092 CTATGAATGTCAAGTTT
1 TTATGAATTTCAAGTTT
1706109 ATTGGATAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.22, C:0.08, G:0.19, T:0.51
Consensus pattern (21 bp):
TTATGAATTTCAAGTTTCTTG
Done.