Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004905.1 Hibiscus syriacus cultivar Beakdansim tig00011034_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: 84868
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:5446 original size:33 final size:34
Alignment explanation
Indices: 5406--5513 Score: 93
Period size: 33 Copynumber: 3.2 Consensus size: 34
5396 GTGGTAAGAA
* *
5406 ATTTATTTTATGTTAGTAT-TTT-T-TAAATAGTT
1 ATTTATTTTATATTAATATATTTATGTAAATA-TT
5438 ATTATATTTTATATTAATATATTTATGTAAATATT
1 ATT-TATTTTATATTAATATATTTATGTAAATATT
* * *
5473 A-TT-TTTT-TATTAAAATAATATTATATAATTATT
1 ATTTATTTTATATTAATAT-AT-TTATGTAAATATT
5506 ATTTATTT
1 ATTTATTT
5514 ATAATTATTA
Statistics
Matches: 63, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
31 8 0.13
32 9 0.14
33 27 0.43
34 6 0.10
35 7 0.11
36 6 0.10
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (34 bp):
ATTTATTTTATATTAATATATTTATGTAAATATT
Found at i:5515 original size:33 final size:30
Alignment explanation
Indices: 5427--5515 Score: 79
Period size: 32 Copynumber: 2.8 Consensus size: 30
5417 GTTAGTATTT
* * *
5427 TTTAAATAGTTATTATATTTTATATTAATATA
1 TTTATATAATTATTAT-TTTT-TATTAAAATA
* *
5459 TTTATGTAAATATTATTTTTTTATTAAAATAA
1 TTTATATAATTATTA-TTTTTTATTAAAAT-A
5491 TATTATATAATTATTATTTATTTAT
1 T-TTATATAATTATTATTT-TTTAT
5516 AATTATTAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
31 8 0.17
32 20 0.43
33 18 0.39
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.58
Consensus pattern (30 bp):
TTTATATAATTATTATTTTTTATTAAAATA
Found at i:7258 original size:21 final size:21
Alignment explanation
Indices: 7228--7275 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
7218 GCAGGGGTAC
* *
7228 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
7249 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
7270 ATGCCA
1 ATGCCA
7276 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:7305 original size:21 final size:21
Alignment explanation
Indices: 7279--7346 Score: 102
Period size: 21 Copynumber: 3.2 Consensus size: 21
7269 TATGCCATCT
*
7279 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCTAGC
7300 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
7321 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
7342 CCGCA
1 CCGCA
7347 CCATATGGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
20 2 0.05
21 40 0.91
22 2 0.05
ACGTcount: A:0.19, C:0.37, G:0.25, T:0.19
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:7966 original size:34 final size:34
Alignment explanation
Indices: 7861--7967 Score: 151
Period size: 34 Copynumber: 3.1 Consensus size: 34
7851 ATAAATGTTT
7861 TTAAAATATAAATTATATTATTCGAAATTTAAAA
1 TTAAAATATAAATTATATTATTCGAAATTTAAAA
* * *
7895 TAAAAATAAAAATAATATTATTCGAAATTTAAAA
1 TTAAAATATAAATTATATTATTCGAAATTTAAAA
** * *
7929 TTAAAATATAAATTATAGAATTCGAAAATTAACA
1 TTAAAATATAAATTATATTATTCGAAATTTAAAA
7963 TTAAA
1 TTAAA
7968 TTTCAACTTA
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 63 1.00
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.36
Consensus pattern (34 bp):
TTAAAATATAAATTATATTATTCGAAATTTAAAA
Found at i:14703 original size:29 final size:29
Alignment explanation
Indices: 14670--14738 Score: 120
Period size: 29 Copynumber: 2.4 Consensus size: 29
14660 GCATGCTTGA
*
14670 AGGTCGCCATGCACGCCCTGCTGAAATGG
1 AGGTCGCCATGCACGCCCTGCTGAAATAG
14699 AGGTCGCCATGCACGCCCTGCTGAAATAG
1 AGGTCGCCATGCACGCCCTGCTGAAATAG
*
14728 AGGTCTCCATG
1 AGGTCGCCATG
14739 TTTCAGATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.22, C:0.30, G:0.29, T:0.19
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCTGCTGAAATAG
Found at i:18841 original size:11 final size:11
Alignment explanation
Indices: 18825--18885 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
18815 ATGACATGAT
18825 ATATTTTATTA
1 ATATTTTATTA
18836 ATA-TTT-TT-
1 ATATTTTATTA
*
18844 A-A-TCTATTA
1 ATATTTTATTA
*
18853 ATGTTTTATTA
1 ATATTTTATTA
18864 ATATTTTATTA
1 ATATTTTATTA
*
18875 TTATTATTATT
1 ATATT-TTATT
18886 CACCTCATTC
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
7 3 0.08
8 3 0.08
9 3 0.08
10 3 0.08
11 23 0.57
12 5 0.12
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (11 bp):
ATATTTTATTA
Found at i:19282 original size:57 final size:57
Alignment explanation
Indices: 19207--19384 Score: 266
Period size: 57 Copynumber: 3.1 Consensus size: 57
19197 CCTTCACTGC
*
19207 ATAATCAGCAGTAAATCTCACAAATTTTGTCTCCACCTCCCACGCCTCTTACCCAACA
1 ATAA-CAGCAGTAAATCTCACAAATTTTGTCTTCACCTCCCACGCCTCTTACCCAACA
* * *
19265 ATAACAGTAGTAAATCTCACAAATTTTGCCTTCACCTCCCACGCCTCATACCCAACA
1 ATAACAGCAGTAAATCTCACAAATTTTGTCTTCACCTCCCACGCCTCTTACCCAACA
* ** * *
19322 ATAACAACAGTAAATCTCGTAAATTTTATCTTCACCTCCCACGCCTCTTACCTAACA
1 ATAACAGCAGTAAATCTCACAAATTTTGTCTTCACCTCCCACGCCTCTTACCCAACA
19379 ATAACA
1 ATAACA
19385 ACATCAACAA
Statistics
Matches: 108, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
57 104 0.96
58 4 0.04
ACGTcount: A:0.34, C:0.34, G:0.06, T:0.26
Consensus pattern (57 bp):
ATAACAGCAGTAAATCTCACAAATTTTGTCTTCACCTCCCACGCCTCTTACCCAACA
Found at i:19993 original size:16 final size:15
Alignment explanation
Indices: 19972--20014 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
19962 ATCAAATAAC
19972 TAAATTTAATAAAAT
1 TAAATTTAATAAAAT
*
19987 ATAAATTTAA-GAAAT
1 -TAAATTTAATAAAAT
20002 TAAATTATAATAA
1 TAAATT-TAATAA
20015 CTTATATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 6 0.26
15 7 0.30
16 10 0.43
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (15 bp):
TAAATTTAATAAAAT
Found at i:30352 original size:2 final size:2
Alignment explanation
Indices: 30347--30396 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
30337 TCACACACAC
* *
30347 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30389 AT AT AT AT
1 AT AT AT AT
30397 TGAATAATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:37322 original size:43 final size:43
Alignment explanation
Indices: 37256--37338 Score: 157
Period size: 43 Copynumber: 1.9 Consensus size: 43
37246 ACACCCTCCT
37256 TAATATTTCTGTCCTTATGGTAAATGTGAATTAGATTCATTTG
1 TAATATTTCTGTCCTTATGGTAAATGTGAATTAGATTCATTTG
*
37299 TAATATTTCTGTCCTTATTGTAAATGTGAATTAGATTCAT
1 TAATATTTCTGTCCTTATGGTAAATGTGAATTAGATTCAT
37339 CTGTTTATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (43 bp):
TAATATTTCTGTCCTTATGGTAAATGTGAATTAGATTCATTTG
Found at i:42510 original size:16 final size:16
Alignment explanation
Indices: 42481--42517 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
42471 CCTTTGTGCG
42481 CCCATCTCTTTGTTTC
1 CCCATCTCTTTGTTTC
42497 CCCATCTCTTTGTTTC
1 CCCATCTCTTTGTTTC
42513 CCCAT
1 CCCAT
42518 TTCCTTTGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.08, C:0.41, G:0.05, T:0.46
Consensus pattern (16 bp):
CCCATCTCTTTGTTTC
Found at i:53301 original size:24 final size:24
Alignment explanation
Indices: 53250--53301 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
53240 CAGCTCGTAT
*** *
53250 AAATTGCACCGAAGTGCCGTGTAG
1 AAATTGCACCGAAGTGCCACATAA
*
53274 AAATTGCTCCGAAGTGCCACATAA
1 AAATTGCACCGAAGTGCCACATAA
53298 AAAT
1 AAAT
53302 GTCCCGAAGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (24 bp):
AAATTGCACCGAAGTGCCACATAA
Found at i:56208 original size:14 final size:14
Alignment explanation
Indices: 56189--56216 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
56179 CAATGATCAT
56189 ACAAAGAACATGAA
1 ACAAAGAACATGAA
56203 ACAAAGAACATGAA
1 ACAAAGAACATGAA
56217 TAAGAAAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.14, G:0.14, T:0.07
Consensus pattern (14 bp):
ACAAAGAACATGAA
Found at i:63018 original size:20 final size:20
Alignment explanation
Indices: 62880--63029 Score: 89
Period size: 20 Copynumber: 7.6 Consensus size: 20
62870 AAATGACCAA
*
62880 CAAATTCGCAACGCGAATTC
1 CAAATTCGCAACGCGAATTT
* * *
62900 CAATTTCTCAAC-C-AGTTTT
1 CAAATTCGCAACGCGA-ATTT
* *
62919 CAATTTCGCAACGCAAATATGT
1 CAAATTCGCAACGCGAAT-T-T
** *
62941 -AAA-TCGCATTGCGATTTT
1 CAAATTCGCAACGCGAATTT
*
62959 CCAAATTCGCAACGCG-ATAGT
1 -CAAATTCGCAACGCGAAT-TT
*
62980 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAATTT
*
62999 CAAATTTGCAACGCGAATTT
1 CAAATTCGCAACGCGAATTT
*
63019 -AATTTCGCAAC
1 CAAATTCGCAAC
63030 AGGTTTTAGT
Statistics
Matches: 98, Mismatches: 21, Indels: 23
0.69 0.15 0.16
Matches are distributed among these distances:
18 2 0.02
19 37 0.38
20 45 0.46
21 13 0.13
22 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.29
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTT
Found at i:63948 original size:24 final size:24
Alignment explanation
Indices: 63921--63974 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
63911 GTATTCGAAA
63921 TTTGATCTTGGTCAATACTCGGAC
1 TTTGATCTTGGTCAATACTCGGAC
*
63945 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACTCGGAC
63969 TTTGAT
1 TTTGAT
63975 GATGTGATGG
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:66587 original size:20 final size:20
Alignment explanation
Indices: 66539--66588 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
66529 ATGTTGCGAT
66539 CAACGCGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
*
66559 CAACACGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
*
66579 CAATGCGAAA
1 CAACGCGAAA
66589 TAAGCGTTGC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.44, C:0.24, G:0.18, T:0.14
Consensus pattern (20 bp):
CAACGCGAAAGTCAAATTCG
Found at i:67134 original size:24 final size:24
Alignment explanation
Indices: 67107--67157 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
67097 TTTCATATGT
67107 AATTAGAGTTTGAATTTAAATTTC
1 AATTAGAGTTTGAATTTAAATTTC
* * *
67131 AATTTGAGTTTGAGTTTGAATTTC
1 AATTAGAGTTTGAATTTAAATTTC
67155 AAT
1 AAT
67158 ATAAATTTCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (24 bp):
AATTAGAGTTTGAATTTAAATTTC
Found at i:67511 original size:39 final size:39
Alignment explanation
Indices: 67468--67554 Score: 149
Period size: 39 Copynumber: 2.2 Consensus size: 39
67458 TCTGATGCTC
67468 ATCAAAATCCAAAGCTCATATGGTG-CAAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGTC-AAGCAAAAGGAA
*
67507 ATCAAAATCCAAATCTCATATGGTGTCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGTCAAGCAAAAGGAA
67546 ATCAAAATC
1 ATCAAAATC
67555 TACAACTTGA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
39 45 0.98
40 1 0.02
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGTCAAGCAAAAGGAA
Found at i:67753 original size:20 final size:20
Alignment explanation
Indices: 67728--67770 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
67718 ATGTTGCGAT
*
67728 CAACGCGAAAGTCAAATTCG
1 CAACGCAAAAGTCAAATTCG
67748 CAACGCAAAAGTCAAATTCG
1 CAACGCAAAAGTCAAATTCG
67768 CAA
1 CAA
67771 ACCGAAAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.44, C:0.26, G:0.16, T:0.14
Consensus pattern (20 bp):
CAACGCAAAAGTCAAATTCG
Found at i:69446 original size:21 final size:21
Alignment explanation
Indices: 69422--69517 Score: 97
Period size: 21 Copynumber: 4.6 Consensus size: 21
69412 GGCGAGACCA
*
69422 CTTGAACGATGACAGGGGCCT
1 CTTGAACGATGAGAGGGGCCT
* *
69443 CTTGAACGATGGGAGGGGCTT
1 CTTGAACGATGAGAGGGGCCT
*
69464 CTTCG-ATGATGAGAGGGGCCT
1 CTT-GAACGATGAGAGGGGCCT
* *
69485 ATTGAACGAT-AGGAGGCGCCT
1 CTTGAACGATGA-GAGGGGCCT
*
69506 CTTGAATGATGA
1 CTTGAACGATGA
69518 TAGGTGCATC
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
20 2 0.03
21 56 0.93
22 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.23
Consensus pattern (21 bp):
CTTGAACGATGAGAGGGGCCT
Found at i:69475 original size:42 final size:42
Alignment explanation
Indices: 69422--69517 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 42
69412 GGCGAGACCA
* * * * *
69422 CTTGAACGATGACAGGGGCCTCTTGAACGATGGGAGGGGCTT
1 CTTGAATGATGACAGGGGCCTATTGAACGATAGGAGGCGCCT
*
69464 CTTCG-ATGATGAGAGGGGCCTATTGAACGATAGGAGGCGCCT
1 CTT-GAATGATGACAGGGGCCTATTGAACGATAGGAGGCGCCT
69506 CTTGAATGATGA
1 CTTGAATGATGA
69518 TAGGTGCATC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
41 1 0.02
42 44 0.96
43 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.23
Consensus pattern (42 bp):
CTTGAATGATGACAGGGGCCTATTGAACGATAGGAGGCGCCT
Found at i:71695 original size:20 final size:20
Alignment explanation
Indices: 71672--71709 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
71662 AGAAGTTTCT
*
71672 GAAACTGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACGC
71692 GAAAATGAAAATCGCAAC
1 GAAAATGAAAATCGCAAC
71710 ACGATTTTAG
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:0.50, C:0.21, G:0.18, T:0.11
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACGC
Found at i:71935 original size:14 final size:14
Alignment explanation
Indices: 71918--71965 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
71908 AATTTCAAAA
71918 TAAAAATAAGAGAT
1 TAAAAATAAGAGAT
* * *
71932 TAAAAA-AACTATAA
1 TAAAAATAA-GAGAT
71946 TAAAAATAAGAGAT
1 TAAAAATAAGAGAT
71960 TAAAAA
1 TAAAAA
71966 AACTAACCAT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
13 2 0.08
14 22 0.85
15 2 0.08
ACGTcount: A:0.69, C:0.02, G:0.08, T:0.21
Consensus pattern (14 bp):
TAAAAATAAGAGAT
Found at i:71936 original size:28 final size:28
Alignment explanation
Indices: 71914--71971 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
71904 CAAAAATTTC
71914 AAAATAAAAATAAGAGATTAAAAAAACT
1 AAAATAAAAATAAGAGATTAAAAAAACT
*
71942 ATAATAAAAATAAGAGATTAAAAAAACT
1 AAAATAAAAATAAGAGATTAAAAAAACT
71970 AA
1 AA
71972 CCATCGGTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.71, C:0.03, G:0.07, T:0.19
Consensus pattern (28 bp):
AAAATAAAAATAAGAGATTAAAAAAACT
Found at i:72240 original size:20 final size:20
Alignment explanation
Indices: 72217--72260 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
72207 TGCGTAAAAT
* * *
72217 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTATCACGTTGCAA
72237 ATTTGACTATCACGTTGCAA
1 ATTTGACTATCACGTTGCAA
72257 ATTT
1 ATTT
72261 AGAAAATCGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTTGACTATCACGTTGCAA
Found at i:74120 original size:6 final size:6
Alignment explanation
Indices: 74098--74138 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
74088 GTATATCCAT
*
74098 CTCAT- CTCATG -TCATG CTCATG CTGATG CTCATG CTCATG C
1 CTCATG CTCATG CTCATG CTCATG CTCATG CTCATG CTCATG C
74139 ATGCCAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
5 10 0.31
6 22 0.69
ACGTcount: A:0.17, C:0.32, G:0.17, T:0.34
Consensus pattern (6 bp):
CTCATG
Found at i:75295 original size:21 final size:22
Alignment explanation
Indices: 75269--75314 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
75259 TCAAACAATC
*
75269 AAAATT-ACTAAAAACATAAAA
1 AAAATTAACCAAAAACATAAAA
* *
75290 AAAATTAACCATAAAGATAAAA
1 AAAATTAACCAAAAACATAAAA
75312 AAA
1 AAA
75315 TATACCAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.72, C:0.09, G:0.02, T:0.17
Consensus pattern (22 bp):
AAAATTAACCAAAAACATAAAA
Found at i:77399 original size:13 final size:13
Alignment explanation
Indices: 77383--77446 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 13
77373 TGTGTAAATA
77383 TATTAAATATTTT
1 TATTAAATATTTT
*
77396 TATTTAATATTTTT
1 TATTAAATA-TTTT
**
77410 TGAACAAATATTTT
1 T-ATTAAATATTTT
* *
77424 TATTTAATATTAT
1 TATTAAATATTTT
77437 T-TT-AATATTT
1 TATTAAATATTT
77447 AAACGGTGTT
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
11 6 0.15
12 2 0.05
13 17 0.43
14 10 0.25
15 5 0.12
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (13 bp):
TATTAAATATTTT
Found at i:77949 original size:24 final size:24
Alignment explanation
Indices: 77922--77983 Score: 61
Period size: 27 Copynumber: 2.4 Consensus size: 24
77912 GAAATTTATT
* *
77922 TTCGTCCTCTTAAAATTTTTTAAG
1 TTCGTCCTCTTAAAATTCTATAAG
*
77946 TTCGTCTCTCCTTTAAAGTTCTATAAG
1 TTCGTC-CT-C-TTAAAATTCTATAAG
77973 TTCGCTCCTCT
1 TTCG-TCCTCT
77984 AACATAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
24 6 0.19
25 3 0.10
26 2 0.06
27 18 0.58
28 2 0.06
ACGTcount: A:0.19, C:0.24, G:0.10, T:0.47
Consensus pattern (24 bp):
TTCGTCCTCTTAAAATTCTATAAG
Found at i:83507 original size:23 final size:23
Alignment explanation
Indices: 83481--83530 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
83471 ATATTAAACG
* *
83481 AATCCCAAGTAACATCCTACTCA
1 AATCACAAGGAACATCCTACTCA
* * *
83504 AATCACAGGGACCATTCTACTCA
1 AATCACAAGGAACATCCTACTCA
83527 AATC
1 AATC
83531 TTCAACTAGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.32, G:0.08, T:0.22
Consensus pattern (23 bp):
AATCACAAGGAACATCCTACTCA
Done.