Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005345.1 Hibiscus syriacus cultivar Beakdansim tig00012107_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: 79369
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:546 original size:6 final size:7
Alignment explanation
Indices: 526--551 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
516 CTTTTTAATT
526 ATTAAAA
1 ATTAAAA
533 ATTAAAA
1 ATTAAAA
540 ATTAAAA
1 ATTAAAA
547 ATTAA
1 ATTAA
552 TCTCTTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
ATTAAAA
Found at i:4872 original size:39 final size:39
Alignment explanation
Indices: 4829--4903 Score: 150
Period size: 39 Copynumber: 1.9 Consensus size: 39
4819 CGACTACGAC
4829 CGGTAGATTCGACACCATTTTGATGCCATGAATGCTAGT
1 CGGTAGATTCGACACCATTTTGATGCCATGAATGCTAGT
4868 CGGTAGATTCGACACCATTTTGATGCCATGAATGCT
1 CGGTAGATTCGACACCATTTTGATGCCATGAATGCT
4904 CTTCTTAGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (39 bp):
CGGTAGATTCGACACCATTTTGATGCCATGAATGCTAGT
Found at i:5521 original size:30 final size:31
Alignment explanation
Indices: 5465--5522 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
5455 GGGGAGGAAA
* *
5465 AAATATAGAGAAAATGAGGGAAAAAAAACAC
1 AAATATAGAGAAAAAGAGGAAAAAAAAACAC
5496 AAATA-AGAGAAAAAGA-GAAACAAAAAA
1 AAATATAGAGAAAAAGAGGAAA-AAAAAA
5523 GAGGGAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 3 0.12
30 16 0.67
31 5 0.21
ACGTcount: A:0.71, C:0.05, G:0.17, T:0.07
Consensus pattern (31 bp):
AAATATAGAGAAAAAGAGGAAAAAAAAACAC
Found at i:6595 original size:30 final size:29
Alignment explanation
Indices: 6539--6652 Score: 102
Period size: 30 Copynumber: 3.9 Consensus size: 29
6529 TTATTTGTAA
* * * *
6539 TTACTGTTTAGCCCTTCAAATTTCTATTT
1 TTACTATTTAGTCCTTTAACTTTCTATTT
6568 TTACTATTTAAGTCCTTTAACTTTCTATTT
1 TTACTATTT-AGTCCTTTAACTTTCTATTT
** * * *
6598 TTGTTATTTTGGTCTTTTAACTTTTTATTT
1 TTACTA-TTTAGTCCTTTAACTTTCTATTT
* * *
6628 TTTCAATTTAGTCCTTTAAGTTTCT
1 TTACTATTTAGTCCTTTAACTTTCT
6653 GTTATTTTAT
Statistics
Matches: 67, Mismatches: 16, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
29 23 0.34
30 41 0.61
31 3 0.04
ACGTcount: A:0.19, C:0.15, G:0.07, T:0.59
Consensus pattern (29 bp):
TTACTATTTAGTCCTTTAACTTTCTATTT
Found at i:6646 original size:29 final size:29
Alignment explanation
Indices: 6545--6679 Score: 101
Period size: 30 Copynumber: 4.6 Consensus size: 29
6535 GTAATTACTG
* * * *
6545 TTTAGCCCTTCAAATTTCTATTTTTACTA
1 TTTAGTCCTTTAAATTTCTATTTTTTCAA
* * *
6574 TTTAAGTCCTTTAACTTTCTATTTTTGTTAT
1 TTT-AGTCCTTTAAATTTCTATTTTT-TCAA
* * * *
6605 TTTGGTCTTTTAACTTTTTATTTTTTCAA
1 TTTAGTCCTTTAAATTTCTATTTTTTCAA
* * *
6634 TTTAGTCCTTTAAGTTTCTGTTATTTT-AT
1 TTTAGTCCTTTAAATTTCTATT-TTTTCAA
*
6663 TTTGGTCCTTTAAATTT
1 TTTAGTCCTTTAAATTT
6680 TTGAATATGT
Statistics
Matches: 83, Mismatches: 20, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
29 38 0.46
30 42 0.51
31 3 0.04
ACGTcount: A:0.19, C:0.13, G:0.07, T:0.60
Consensus pattern (29 bp):
TTTAGTCCTTTAAATTTCTATTTTTTCAA
Found at i:6652 original size:59 final size:59
Alignment explanation
Indices: 6551--6681 Score: 165
Period size: 58 Copynumber: 2.2 Consensus size: 59
6541 ACTGTTTAGC
* * * *
6551 CCTTCAAATTTCTATTTTTACTATTTAAGTCCTTTAACTTTCTATTTTTGTTATTTTGGT
1 CCTTTAAATTTTTATTTTTACAATTTAAGTCCTTTAACTTTCTATTATT-TTATTTTGGT
* * * * *
6611 CTTTTAACTTTTTATTTTTTCAATTT-AGTCCTTTAAGTTTCTGTTATTTTATTTTGGT
1 CCTTTAAATTTTTATTTTTACAATTTAAGTCCTTTAACTTTCTATTATTTTATTTTGGT
6669 CCTTTAAATTTTT
1 CCTTTAAATTTTT
6682 GAATATGTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
58 21 0.35
59 19 0.32
60 20 0.33
ACGTcount: A:0.19, C:0.13, G:0.07, T:0.61
Consensus pattern (59 bp):
CCTTTAAATTTTTATTTTTACAATTTAAGTCCTTTAACTTTCTATTATTTTATTTTGGT
Found at i:11731 original size:19 final size:19
Alignment explanation
Indices: 11704--11741 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
11694 TTTTAACTGT
*
11704 AGCATAATTAAGTTTCCTA
1 AGCAGAATTAAGTTTCCTA
11723 AGCAGAATTAAGTTTCCTA
1 AGCAGAATTAAGTTTCCTA
11742 TAATCCACAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (19 bp):
AGCAGAATTAAGTTTCCTA
Found at i:19761 original size:32 final size:32
Alignment explanation
Indices: 19725--19788 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
19715 TCTTACATGT
* *
19725 ACTAACTAATTTCTTTTCTTTTGTTTGTGTAC
1 ACTAACTAAGTTATTTTCTTTTGTTTGTGTAC
*
19757 ACTAACTTAGTTATTTTCTTTTGTTTGTGTAC
1 ACTAACTAAGTTATTTTCTTTTGTTTGTGTAC
19789 TAACATAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.19, C:0.14, G:0.11, T:0.56
Consensus pattern (32 bp):
ACTAACTAAGTTATTTTCTTTTGTTTGTGTAC
Found at i:21630 original size:12 final size:12
Alignment explanation
Indices: 21613--21669 Score: 59
Period size: 12 Copynumber: 5.0 Consensus size: 12
21603 AAAAACAAAG
21613 AGCAAAGAAAAA
1 AGCAAAGAAAAA
21625 AGCAAAGAAAATA
1 AGCAAAGAAAA-A
* *
21638 AGGAAA-AAAAC
1 AGCAAAGAAAAA
21649 A--AAAGAAAAA
1 AGCAAAGAAAAA
21659 A-CAAAGAAAAA
1 AGCAAAGAAAAA
21670 GAAGACAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
9 3 0.08
10 5 0.13
11 10 0.26
12 15 0.38
13 6 0.15
ACGTcount: A:0.77, C:0.07, G:0.14, T:0.02
Consensus pattern (12 bp):
AGCAAAGAAAAA
Found at i:21635 original size:28 final size:28
Alignment explanation
Indices: 21576--21674 Score: 93
Period size: 28 Copynumber: 3.7 Consensus size: 28
21566 AGATCGAATC
* *
21576 AAAACAAAGAGAAAAGAAGTAAAGGAAA
1 AAAACAAAGAGAAAAGAAGAAAAGCAAA
*
21604 AAAACAAAGAGCAAAGAA-AAAAGCAAA
1 AAAACAAAGAGAAAAGAAGAAAAGCAAA
* * *
21631 GAAAA-TAAG-GAAAAAAACAAAAG--AA
1 -AAAACAAAGAGAAAAGAAGAAAAGCAAA
21656 AAAACAAAGA-AAAAGAAGA
1 AAAACAAAGAGAAAAGAAGA
21675 CAATAAGCAT
Statistics
Matches: 58, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
24 4 0.07
25 12 0.21
26 6 0.10
27 15 0.26
28 21 0.36
ACGTcount: A:0.75, C:0.06, G:0.17, T:0.02
Consensus pattern (28 bp):
AAAACAAAGAGAAAAGAAGAAAAGCAAA
Found at i:21669 original size:17 final size:17
Alignment explanation
Indices: 21602--21672 Score: 58
Period size: 19 Copynumber: 4.1 Consensus size: 17
21592 AAGTAAAGGA
*
21602 AAAAAACAAAGAGCAAAG
1 AAAAAACAAAGA-AAAAG
21620 AAAAAAGCAAAGAAAATA-
1 AAAAAA-CAAAGAAAA-AG
* *
21638 AGGAAAA-AAA-CAAAAG
1 A-AAAAACAAAGAAAAAG
21654 AAAAAACAAAGAAAAAG
1 AAAAAACAAAGAAAAAG
21671 AA
1 AA
21673 GACAATAAGC
Statistics
Matches: 42, Mismatches: 5, Indels: 13
0.70 0.08 0.22
Matches are distributed among these distances:
15 5 0.12
16 7 0.17
17 10 0.24
18 9 0.21
19 11 0.26
ACGTcount: A:0.77, C:0.07, G:0.14, T:0.01
Consensus pattern (17 bp):
AAAAAACAAAGAAAAAG
Found at i:22984 original size:68 final size:66
Alignment explanation
Indices: 22860--23027 Score: 218
Period size: 68 Copynumber: 2.6 Consensus size: 66
22850 AGTTTTCTTA
* *
22860 AAAACAAA-TTTTGTCTCTC--GAGATAGTGTCTTTT-GAAAAAAATCTTTGAGTATGTTTCTCT
1 AAAACAAAGTTTTGTCTCTCTTGAGATAATTTCTTTTGGAAAAAAATCTTTGAGTATGTTTCTCT
22921 G
66 G
* *
22922 AAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTTTTGGAAAAAAAATTCTTTGAGTCTGTTTCT
1 AAAACAAAGTTTTGTCTCTCTTGAGATAATTTCTTTTGG-AAAAAAA-TCTTTGAGTATGTTTCT
*
22987 GTG
64 CTG
* * *
22990 GAAATAAAGTTTTGTTTCTCTTGAGATAATTTCTTTTG
1 AAAACAAAGTTTTGTCTCTCTTGAGATAATTTCTTTTG
23028 AAACACCAAT
Statistics
Matches: 91, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
62 8 0.09
63 11 0.12
65 12 0.13
66 1 0.01
67 7 0.08
68 52 0.57
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (66 bp):
AAAACAAAGTTTTGTCTCTCTTGAGATAATTTCTTTTGGAAAAAAATCTTTGAGTATGTTTCTCT
G
Found at i:23081 original size:68 final size:69
Alignment explanation
Indices: 22888--23085 Score: 196
Period size: 68 Copynumber: 3.0 Consensus size: 69
22878 CGAGATAGTG
* * * *
22888 TCTTTT-G-AAAAAAA-TCTTTGAGTATGTTTCTCTGAAAACAAAGTTTTGTCTCT-CTTGAGAC
1 TCTTTTGGAAAAAAAATTATTTGAGTCTGTTTCTGTGGAAACAAAGTTTTGTCTCTCCTTGAGAC
22949 AATT
66 AATT
* * * *
22953 TCTTTTGGAAAAAAAATTCTTTGAGTCTGTTTCTGTGGAAATAAAGTTTTGTTTCT-CTTGAGAT
1 TCTTTTGGAAAAAAAATTATTTGAGTCTGTTTCTGTGGAAACAAAGTTTTGTCTCTCCTTGAGAC
23017 AATT
66 AATT
** * * * *
23021 TCTTTT-GAAACACCAA-TATTTGATTCTGTTTCTTTTGAACCAAA-TTTTGTCTCTCCCTTGAG
1 TCTTTTGGAAA-AAAAATTATTTGAGTCTGTTTCTGTGGAAACAAAGTTTTGTCTCT-CCTTGAG
23083 ACA
64 ACA
23086 GCTTATCTTG
Statistics
Matches: 111, Mismatches: 16, Indels: 9
0.82 0.12 0.07
Matches are distributed among these distances:
65 6 0.05
66 10 0.09
67 33 0.30
68 62 0.56
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (69 bp):
TCTTTTGGAAAAAAAATTATTTGAGTCTGTTTCTGTGGAAACAAAGTTTTGTCTCTCCTTGAGAC
AATT
Found at i:23445 original size:134 final size:135
Alignment explanation
Indices: 23134--23587 Score: 469
Period size: 134 Copynumber: 3.4 Consensus size: 135
23124 AAAACCAAAA
* * * * * * * * * *
23134 TCCCTAAAAATGGCC-TATCATCATCATCGCGTAGGAACCGTGTTATCCCCCGACTAGACCTTCT
1 TCCCTAAAGATGGCCATAAC-TCTTCATCACGTAAGAACCGTGTCATCCACCAACCAGACCTCCT
* * * * * *
23198 CGTCACGTAGAAGCCATGTCA-CCCTAGATAACTAGCTGTCCTTATCATGTAGGAACTGTGTTAT
65 CATCACGTAGGAGCCATGTCACCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACTGTGTTAT
23262 CA----
130 CACCCT
* * * *
23264 TCCCTAAAGATGG-CATATCGTCCTCATCACGTAGGAACCGTGTCATCCACCAACCAGGCCTCCT
1 TCCCTAAAGATGGCCATAAC-TCTTCATCACGTAAGAACCGTGTCATCCACCAACCAGACCTCCT
* * * *
23328 CATCACTTAGGAGCCATGTCACCCCT-GATAACCAGCCGTCGTCATCACGTAAGAACTGTTTTAT
65 CATCACGTAGGAGCCATGTCACCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACTGTGTTAT
23392 CACCCT
130 CACCCT
** * *
23398 TCCCTAAAGATGGCCATAACTCTTCATCACGTAAGAGTCGTGTCATCCACCGACCATACCTCCTC
1 TCCCTAAAGATGGCCATAACTCTTCATCACGTAAGAACCGTGTCATCCACCAACCAGACCTCCTC
* ** * * *
23463 ATCACGTAGGATCTGTGTCACCCCTAGATAACCAACCGTCCTCAT-AGCATAGGAATTGTGTTAT
66 ATCACGTAGGAGCCATGTCACCCCTAGATAACCAGCCGTCCTCATCA-CGTAGGAACTGTGTTAT
23527 CACCCT
130 CACCCT
* * * *
23533 T-CCTAAAGATGACCAGAACTCTTCATCACGTATGAACCGTGTAATCCACCAACCA
1 TCCCTAAAGATGGCCATAACTCTTCATCACGTAAGAACCGTGTCATCCACCAACCA
23588 TATCTCTTCA
Statistics
Matches: 270, Mismatches: 45, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
129 1 0.00
130 103 0.38
131 4 0.01
134 120 0.44
135 42 0.16
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.25
Consensus pattern (135 bp):
TCCCTAAAGATGGCCATAACTCTTCATCACGTAAGAACCGTGTCATCCACCAACCAGACCTCCTC
ATCACGTAGGAGCCATGTCACCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACTGTGTTATC
ACCCT
Found at i:23959 original size:91 final size:91
Alignment explanation
Indices: 23804--23976 Score: 292
Period size: 91 Copynumber: 1.9 Consensus size: 91
23794 TTTTACAACA
*** *
23804 CAGTTTTCAAATTTGCAACGCGATTCTCCAAAATCGCAACGCGAATTTCGTTTTCGCAATGCTAA
1 CAGTTTTCAAATTCAAAACGCGATTCTCCAAAATCGCAACGCGAATTTCATTTTCGCAATGCTAA
23869 TTACCGATATAGGTAAATATGAAACT
66 TTACCGATATAGGTAAATATGAAACT
* *
23895 CAGTTTTCAAATTCAAAACGCGATTCTCCAAAATCGTAACGCGTATTTCATTTTCGCAATGCTAA
1 CAGTTTTCAAATTCAAAACGCGATTCTCCAAAATCGCAACGCGAATTTCATTTTCGCAATGCTAA
23960 TTACCGATATAGGTAAA
66 TTACCGATATAGGTAAA
23977 CACAACTATT
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
91 76 1.00
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (91 bp):
CAGTTTTCAAATTCAAAACGCGATTCTCCAAAATCGCAACGCGAATTTCATTTTCGCAATGCTAA
TTACCGATATAGGTAAATATGAAACT
Found at i:24198 original size:20 final size:20
Alignment explanation
Indices: 24173--24210 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
24163 ATTAGCGTTG
24173 CGAAATTCGAGTTGCGAAAA
1 CGAAATTCGAGTTGCGAAAA
*
24193 CGAAATTCGCGTTGCGAA
1 CGAAATTCGAGTTGCGAA
24211 TTTGGAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.21
Consensus pattern (20 bp):
CGAAATTCGAGTTGCGAAAA
Found at i:24335 original size:21 final size:21
Alignment explanation
Indices: 24280--24327 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
24270 TCGGTAATTA
*
24280 GCGTTGTGATTTTGGAGAATC
1 GCGTTGCGATTTTGGAGAATC
*
24301 GCGTTGCGATTTTGGATAATC
1 GCGTTGCGATTTTGGAGAATC
24322 GCGTTG
1 GCGTTG
24328 GGAATTTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.17, C:0.12, G:0.33, T:0.38
Consensus pattern (21 bp):
GCGTTGCGATTTTGGAGAATC
Found at i:26287 original size:29 final size:29
Alignment explanation
Indices: 26194--26298 Score: 104
Period size: 30 Copynumber: 3.5 Consensus size: 29
26184 TTTTTTTTTC
26194 TATTTAAGTCCTTTAACTTTCTATTTTTGT
1 TATTT-AGTCCTTTAACTTTCTATTTTTGT
* * * *
26224 TATTTTGAACCTTTAACATTCTATTTTTGC
1 TATTTAG-TCCTTTAACTTTCTATTTTTGT
* *
26254 AATTTAGTCCTTTAAGTTTCTATTATTT-T
1 TATTTAGTCCTTTAACTTTCTATT-TTTGT
*
26283 TATTTTGGTCCTTTAA
1 TA-TTTAGTCCTTTAA
26299 ATTTTTGAAT
Statistics
Matches: 60, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
29 16 0.27
30 44 0.73
ACGTcount: A:0.22, C:0.13, G:0.08, T:0.57
Consensus pattern (29 bp):
TATTTAGTCCTTTAACTTTCTATTTTTGT
Found at i:35781 original size:3 final size:3
Alignment explanation
Indices: 35761--35822 Score: 76
Period size: 3 Copynumber: 21.3 Consensus size: 3
35751 GACTATAATG
* *
35761 TAT TA- TAT TAT TAA TAT TAT TAT TAT TAC TAT TAT TAT TAT TAAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
35806 T-T TAT T-T TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT T
35823 TTCATAGTAC
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
2 6 0.12
3 42 0.82
4 3 0.06
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:44572 original size:20 final size:21
Alignment explanation
Indices: 44549--44629 Score: 74
Period size: 21 Copynumber: 3.8 Consensus size: 21
44539 TTGGTACAGA
*
44549 GGGAATCGATCCCCCCTTGA-
1 GGGAACCGATCCCCCCTTGAG
*
44569 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGA-TCCCCCCTTG-AG
* **
44592 GGGAACCGATTCCCCCTACAG
1 GGGAACCGATCCCCCCTTGAG
*
44613 GGGAATCGATACCCCCC
1 GGGAACCGAT-CCCCCC
44630 CTGGGGTTCT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
20 8 0.16
21 20 0.41
22 12 0.24
23 9 0.18
ACGTcount: A:0.22, C:0.36, G:0.25, T:0.17
Consensus pattern (21 bp):
GGGAACCGATCCCCCCTTGAG
Found at i:44599 original size:23 final size:21
Alignment explanation
Indices: 44547--44608 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
44537 TTTTGGTACA
* *
44547 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCTTT
44567 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCTTT
44588 GAAGGGGAACCGATTCCCCCT
1 G-A-GGGAACCGATTCCCCCT
44609 ACAGGGGAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 10 0.27
21 9 0.24
22 1 0.03
23 17 0.46
ACGTcount: A:0.21, C:0.34, G:0.26, T:0.19
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCTTT
Found at i:45025 original size:26 final size:25
Alignment explanation
Indices: 44996--45047 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
44986 AGAATTTTCA
44996 AAAAAAAAAAATTAATTTTCGAAATT
1 AAAAAAAAAAATTAATTTTC-AAATT
**
45022 AAAAAAAAATGTTAATTTTCAAATT
1 AAAAAAAAAAATTAATTTTCAAATT
45047 A
1 A
45048 TTGTGTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.33
Consensus pattern (25 bp):
AAAAAAAAAAATTAATTTTCAAATT
Found at i:48713 original size:13 final size:13
Alignment explanation
Indices: 48695--48719 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48685 ACTGACATAA
48695 TTCTATTTTTTGT
1 TTCTATTTTTTGT
48708 TTCTATTTTTTG
1 TTCTATTTTTTG
48720 GTATTGTTGC
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:0.08, C:0.08, G:0.08, T:0.76
Consensus pattern (13 bp):
TTCTATTTTTTGT
Found at i:55996 original size:4 final size:4
Alignment explanation
Indices: 55987--57663 Score: 3183
Period size: 4 Copynumber: 423.0 Consensus size: 4
55977 CATGAAAGTT
55987 TGTA TGTA TGGTA TGTA TGTA TGGTA TGTA TGTA TGGTA TGTA TGTA TGTA
1 TGTA TGTA T-GTA TGTA TGTA T-GTA TGTA TGTA T-GTA TGTA TGTA TGTA
56038 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
56086 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
56134 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
56182 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
56230 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
56278 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
56326 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA --TA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
56372 TGT- TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
56419 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
56467 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
56515 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
56563 TGTA TGTA TGTA TGTA TG-- TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
56609 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
56657 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
56705 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
56753 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
56801 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
56849 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
56897 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
56945 TG-- TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
56991 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
57039 TATA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
57087 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA -GTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
57134 TGTA TGTA TGTA TGTA TG-- TGTA TGTA TGTA TGTA TGTA TG-- TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
57178 TGTA TG-- TGTA TGTA TGTA TGTA TGTA TGTA -GTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
57223 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
57271 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
57319 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
57367 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
57415 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
57463 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
57511 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
57559 TGTA TGTA TGTA TGTA --TA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
57605 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
57653 TGTA T-TA TGTA
1 TGTA TGTA TGTA
57664 ATGATATGCT
Statistics
Matches: 1648, Mismatches: 4, Indels: 42
0.97 0.00 0.02
Matches are distributed among these distances:
2 14 0.01
3 12 0.01
4 1610 0.98
5 12 0.01
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:57801 original size:26 final size:26
Alignment explanation
Indices: 57719--57801 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
57709 CAATAATCTA
*
57719 AAAGACTAAATAAATATTTAATAAAT
1 AAAGACTAAATAAATAATTAATAAAT
* *
57745 ACAGTAGCCTAAAT---TAATTAATATCAT
1 A-A--AGACTAAATAAATAATTAATA-AAT
*
57772 -AAGACTAAATAAATAGTTAATAAAT
1 AAAGACTAAATAAATAATTAATAAAT
57797 AAAGA
1 AAAGA
57802 GATGTGAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
23 8 0.19
25 3 0.07
26 21 0.49
27 3 0.07
29 8 0.19
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (26 bp):
AAAGACTAAATAAATAATTAATAAAT
Found at i:60224 original size:163 final size:168
Alignment explanation
Indices: 59952--60282 Score: 627
Period size: 163 Copynumber: 2.0 Consensus size: 168
59942 AAAAAAATAC
59952 ATGGAGGCTTCTTTGAAACTGGTCATCTTCTTCACTCTTTTGCTTTCATCTGGTAAGTTCTTTGT
1 ATGGAGGCTTCTTTGAAACTGGTCATCTTCTTCACTCTTTTGCTTTCATCTGGTAAGTTCTTTGT
60017 TGACAACCAATATATATATGGATATTTTTTATTATTCTTAATTGTTTTTATGTTTTTT-AA-ATA
66 TGACAACCAATATATATATGGATATTTTTTATTATTCTTAATTGTTTTTATGTTTTTTAAATATA
60080 TATAATTACATTC-TTAATAATTGTTTTGAAGAGTTGA
131 TATAATTACATTCTTTAATAATTGTTTTGAAGAGTTGA
60117 ATGGAGGCTTCTTTGAAACT-GTCATCTTCTTCACTC-TTTGCTTTCATCTGGTAAGTTCTTTGT
1 ATGGAGGCTTCTTTGAAACTGGTCATCTTCTTCACTCTTTTGCTTTCATCTGGTAAGTTCTTTGT
60180 TGACAACCAATATATATATGGATATTTTTTATTATTCTTAATTGTTTTTATGTTTTTTAAATATA
66 TGACAACCAATATATATATGGATATTTTTTATTATTCTTAATTGTTTTTATGTTTTTTAAATATA
60245 TATAATTACATTCTTTAATAATTGTTTTGAAGAGTTGA
131 TATAATTACATTCTTTAATAATTGTTTTGAAGAGTTGA
60283 GGGTTTGATT
Statistics
Matches: 163, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
163 85 0.52
164 18 0.11
165 36 0.22
166 24 0.15
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.49
Consensus pattern (168 bp):
ATGGAGGCTTCTTTGAAACTGGTCATCTTCTTCACTCTTTTGCTTTCATCTGGTAAGTTCTTTGT
TGACAACCAATATATATATGGATATTTTTTATTATTCTTAATTGTTTTTATGTTTTTTAAATATA
TATAATTACATTCTTTAATAATTGTTTTGAAGAGTTGA
Found at i:60563 original size:15 final size:15
Alignment explanation
Indices: 60517--60579 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
60507 TCAACCATAT
*
60517 TAATAATTACAATCAA
1 TAATAATTA-AATAAA
* *
60533 T-AT-ATAAAATATA
1 TAATAATTAAATAAA
60546 TAA-AATTAAATTAAA
1 TAATAATTAAA-TAAA
*
60561 TAATAATTCAATAAA
1 TAATAATTAAATAAA
60576 TAAT
1 TAAT
60580 TCATGTTAAC
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
13 5 0.14
14 9 0.24
15 16 0.43
16 7 0.19
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (15 bp):
TAATAATTAAATAAA
Found at i:64690 original size:128 final size:131
Alignment explanation
Indices: 64540--64819 Score: 395
Period size: 138 Copynumber: 2.1 Consensus size: 131
64530 TGTCTTTAAA
* * *
64540 CCTTTAATTTAGGAGAATTTTTTATTTGGTCCTCGCTTTTATGCTCGAGGTTCAATTTTGACTAT
1 CCTTT-ATTTAGGAGAATTTTTTATCTAGTCCTAGCTTTTATGCTCGAGGTTCAATTTTGACTAT
64605 TCAATTC-AA-T-AATTGGTTAAGTTAACAATTAGAGCATCCATTTTAGTTTTAATTTCACTTTA
65 TCAATTCAAATTAAATTGGTTAAGTTAACAATTAGAGCATCCATTTTAGTTTTAATTTCACTTTA
64667 GT
130 GT
* * *
64669 CCTTTATTTAGGAGATTTTTTTATCTAGTCCTAGCTTTTATGCTTGAGGTTCCATTTTGACTATT
1 CCTTTATTTAGGAGAATTTTTTATCTAGTCCTAGCTTTTATGCTCGAGGTTCAATTTTGACTATT
* *
64734 CGATTCAATAATTGGTTAAAATTGGTTAAGTTAATAATTAGAGCATCCATTTTAGTTTTAATTTC
66 CAATTC-A-AA----TT-AAATTGGTTAAGTTAACAATTAGAGCATCCATTTTAGTTTTAATTTC
64799 ACTTTAGT
124 ACTTTAGT
64807 CCTTTATTTAGGA
1 CCTTTATTTAGGA
64820 AAGTTAACCT
Statistics
Matches: 133, Mismatches: 8, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
128 59 0.44
129 5 0.04
131 2 0.02
136 1 0.01
138 66 0.50
ACGTcount: A:0.26, C:0.13, G:0.14, T:0.46
Consensus pattern (131 bp):
CCTTTATTTAGGAGAATTTTTTATCTAGTCCTAGCTTTTATGCTCGAGGTTCAATTTTGACTATT
CAATTCAAATTAAATTGGTTAAGTTAACAATTAGAGCATCCATTTTAGTTTTAATTTCACTTTAG
T
Found at i:67911 original size:23 final size:23
Alignment explanation
Indices: 67877--67985 Score: 80
Period size: 23 Copynumber: 4.8 Consensus size: 23
67867 ATAAATTGCA
67877 CCGAAGTG-CCACGTAGAAATGTC
1 CCGAAG-GACCACGTAGAAATGTC
* *
67900 CCGAAGGACCACATAG--ATTTCC
1 CCGAAGGACCACGTAGAAATGT-C
* **
67922 CCAAAGGACTGCGTAGAAATGTC
1 CCGAAGGACCACGTAGAAATGTC
* * * *
67945 CCTAATGACCACGTAGAATTATC
1 CCGAAGGACCACGTAGAAATGTC
* *
67968 CTGAAGGACCGCGTAGAA
1 CCGAAGGACCACGTAGAA
67986 CCCTCGACTC
Statistics
Matches: 65, Mismatches: 17, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
21 3 0.05
22 14 0.22
23 45 0.69
24 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.18
Consensus pattern (23 bp):
CCGAAGGACCACGTAGAAATGTC
Found at i:68110 original size:15 final size:15
Alignment explanation
Indices: 68061--68113 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
68051 TTATAATAAT
*
68061 TCACATAACTTA-TA
1 TCACATAGCTTATTA
*
68075 TCACATAAGCATT-TAA
1 TCACAT-AGC-TTATTA
68091 TCACATAGCTTATTA
1 TCACATAGCTTATTA
68106 TCACATAG
1 TCACATAG
68114 TTAATGTCAC
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 8 0.25
15 15 0.47
16 9 0.28
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.34
Consensus pattern (15 bp):
TCACATAGCTTATTA
Found at i:68125 original size:14 final size:15
Alignment explanation
Indices: 68057--68125 Score: 56
Period size: 14 Copynumber: 4.7 Consensus size: 15
68047 CCATTTATAA
*
68057 TAAT-TCACATAACT
1 TAATATCACATAGCT
68071 T-ATATCACATAAGCAT
1 TAATATCACAT-AGC-T
*
68087 TTA-ATCACATAGCT
1 TAATATCACATAGCT
*
68101 TATTATCACATAG-T
1 TAATATCACATAGCT
*
68115 TAATGTCACAT
1 TAATATCACAT
68126 TTGTAAAATC
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
13 2 0.04
14 19 0.42
15 14 0.31
16 9 0.20
17 1 0.02
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.36
Consensus pattern (15 bp):
TAATATCACATAGCT
Found at i:69677 original size:15 final size:15
Alignment explanation
Indices: 69657--69694 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
69647 AAATGATATA
*
69657 AGCTATGTGACTATG
1 AGCTATGTAACTATG
69672 AGCTATGTAACTATG
1 AGCTATGTAACTATG
69687 AGCTATGT
1 AGCTATGT
69695 TATAATCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (15 bp):
AGCTATGTAACTATG
Found at i:72267 original size:16 final size:16
Alignment explanation
Indices: 72233--72285 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
72223 ATATAAAATT
* *
72233 AAATAAAACAAAATGA
1 AAATAAAATAAAATAA
* **
72249 AAATGAAATATTATAA
1 AAATAAAATAAAATAA
72265 AAATAAAATAAAATAA
1 AAATAAAATAAAATAA
72281 AAATA
1 AAATA
72286 TTATTATAAT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.21
Consensus pattern (16 bp):
AAATAAAATAAAATAA
Found at i:72272 original size:5 final size:5
Alignment explanation
Indices: 72225--72282 Score: 53
Period size: 5 Copynumber: 11.2 Consensus size: 5
72215 ACATGTCAAT
* * * **
72225 ATAAA ATTAA ATAAA ACAAA ATGAAA ATGAA ATATT ATAAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA AT-AAA ATAAA ATAAA AT-AAA ATAAA ATAAA
72277 ATAAA A
1 ATAAA A
72283 ATATTATTAT
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
5 33 0.80
6 8 0.20
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.22
Consensus pattern (5 bp):
ATAAA
Found at i:72284 original size:27 final size:27
Alignment explanation
Indices: 72237--72289 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
72227 AAAATTAAAT
*
72237 AAAACAAAATGAAAATGAAATATTATA
1 AAAACAAAATGAAAATAAAATATTATA
*
72264 AAAATAAAAT-AAAATAAAAATATTAT
1 AAAACAAAATGAAAAT-AAAATATTAT
72290 TATAATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.25
Consensus pattern (27 bp):
AAAACAAAATGAAAATAAAATATTATA
Found at i:72499 original size:22 final size:22
Alignment explanation
Indices: 72474--72523 Score: 86
Period size: 20 Copynumber: 2.4 Consensus size: 22
72464 AAATACGAAT
72474 TGAAATATATAGATATAAAGAA
1 TGAAATATATAGATATAAAGAA
72496 TG-AA-ATATAGATATAAAGAA
1 TGAAATATATAGATATAAAGAA
72516 TGAAATAT
1 TGAAATAT
72524 CTATTGCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 18 0.69
21 4 0.15
22 4 0.15
ACGTcount: A:0.58, C:0.00, G:0.14, T:0.28
Consensus pattern (22 bp):
TGAAATATATAGATATAAAGAA
Found at i:72505 original size:20 final size:20
Alignment explanation
Indices: 72480--72523 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
72470 GAATTGAAAT
72480 ATATAGATATAAAGAATGAA
1 ATATAGATATAAAGAATGAA
72500 ATATAGATATAAAGAATGAA
1 ATATAGATATAAAGAATGAA
72520 ATAT
1 ATAT
72524 CTATTGCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.14, T:0.27
Consensus pattern (20 bp):
ATATAGATATAAAGAATGAA
Found at i:72615 original size:2 final size:2
Alignment explanation
Indices: 72608--72638 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
72598 GCATGTACAA
72608 AT AT AT 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 AT AT AT A
72639 CATAAAGGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:73506 original size:18 final size:18
Alignment explanation
Indices: 73475--73510 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
73465 GATTATTACT
*
73475 CTGATAAAGTAATGGTGG
1 CTGATAAAGCAATGGTGG
*
73493 CTGATGAAGCAATGGTGG
1 CTGATAAAGCAATGGTGG
73511 TCGAGTCTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.36, T:0.25
Consensus pattern (18 bp):
CTGATAAAGCAATGGTGG
Found at i:74247 original size:3 final size:3
Alignment explanation
Indices: 74239--74347 Score: 92
Period size: 3 Copynumber: 36.3 Consensus size: 3
74229 TGTAAATTAA
* * * * * * *
74239 AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT GAT GAT GAT GAT GAT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * *
74287 GAT GAT GAT GAT AAT AAT AAT AAT AAT AAC AAT AAT AAT ATT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
74335 AAT AAT ATT AAT A
1 AAT AAT AAT AAT A
74348 TGCAAAATTT
Statistics
Matches: 98, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 98 1.00
ACGTcount: A:0.55, C:0.01, G:0.10, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:74814 original size:24 final size:24
Alignment explanation
Indices: 74764--74815 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
74754 ATTGTTTTGA
*
74764 ATAAAATAATAATAATGATTTTTT
1 ATAAAATAATAATAATGATTTTAT
* *
74788 ATAAAAT-ATAATATTTATATTTAT
1 ATAAAATAATAATAATGAT-TTTAT
74812 ATAA
1 ATAA
74816 TTGTTTCAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (24 bp):
ATAAAATAATAATAATGATTTTAT
Found at i:74884 original size:13 final size:13
Alignment explanation
Indices: 74866--74892 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
74856 CTCACATTTA
74866 ATTTATAAAATAT
1 ATTTATAAAATAT
74879 ATTTATAAAATAT
1 ATTTATAAAATAT
74892 A
1 A
74893 ATATTTATAT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTTATAAAATAT
Found at i:74902 original size:22 final size:22
Alignment explanation
Indices: 74876--74918 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
74866 ATTTATAAAA
74876 TATATTTATAAAATATAATATT
1 TATATTTATAAAATATAATATT
*
74898 TATATTTATATAATATAATAT
1 TATATTTATAAAATATAATAT
74919 AATCACTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TATATTTATAAAATATAATATT
Found at i:75234 original size:16 final size:17
Alignment explanation
Indices: 75213--75246 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
75203 TTTTATTATT
*
75213 ATTTAATATA-AAAATA
1 ATTTAAAATATAAAATA
75229 ATTTAAAATATAAAATA
1 ATTTAAAATATAAAATA
75246 A
1 A
75247 AAATAGAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTTAAAATATAAAATA
Done.