Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007592.1 Hibiscus syriacus cultivar Beakdansim tig00021875_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: 81369
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:15501 original size:9 final size:9
Alignment explanation
Indices: 15489--15522 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
15479 TAATATTTTG
15489 TATTTAATT
1 TATTTAATT
15498 TATTTAA-T
1 TATTTAATT
15506 TATTTAATT
1 TATTTAATT
15515 TATTTAAT
1 TATTTAAT
15523 ATTTTACTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TATTTAATT
Found at i:15528 original size:17 final size:17
Alignment explanation
Indices: 15489--15526 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
15479 TAATATTTTG
15489 TATTTAATTTATTTAAT
1 TATTTAATTTATTTAAT
15506 TATTTAATTTATTTAA-
1 TATTTAATTTATTTAAT
15522 TATTT
1 TATTT
15527 TACTTAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTTAATTTATTTAAT
Found at i:15533 original size:21 final size:21
Alignment explanation
Indices: 15462--15540 Score: 64
Period size: 21 Copynumber: 4.0 Consensus size: 21
15452 TCTCTACGAT
15462 ATATTTTA-TT-ATATT-TTTA
1 ATATTTTATTTAAT-TTATTTA
15481 ATATTTTGTATTTAATTTATTT-
1 ATA-TTT-TATTTAATTTATTTA
15503 A-A--TTATTTAATTTATTTA
1 ATATTTTATTTAATTTATTTA
* *
15521 ATATTTTACTTAATTAATTT
1 ATATTTTATTTAATTTATTT
15541 TTTTACAGAT
Statistics
Matches: 49, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
17 14 0.29
18 2 0.04
19 4 0.08
20 3 0.06
21 16 0.33
22 5 0.10
23 5 0.10
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (21 bp):
ATATTTTATTTAATTTATTTA
Found at i:17769 original size:13 final size:13
Alignment explanation
Indices: 17728--17771 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
17718 TATTTAATAC
*
17728 TTTTTATTGTAGT
1 TTTTTATTGTAAT
* * *
17741 TGTTTATTGGACT
1 TTTTTATTGTAAT
17754 TTTTTATTGTAAT
1 TTTTTATTGTAAT
17767 TTTTT
1 TTTTT
17772 TATTATTTAT
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:27617 original size:15 final size:15
Alignment explanation
Indices: 27596--27647 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
27586 TGAGACATTA
*
27596 CCCGCCCCGCATCTG
1 CCCGCCCCGCATCCG
*
27611 TCCGCCCCGCATCCG
1 CCCGCCCCGCATCCG
*
27626 CCCGCCCCACATCCG
1 CCCGCCCCGCATCCG
27641 CCCGCCC
1 CCCGCCC
27648 AGCTAAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.08, C:0.65, G:0.17, T:0.10
Consensus pattern (15 bp):
CCCGCCCCGCATCCG
Found at i:31056 original size:30 final size:31
Alignment explanation
Indices: 31017--31146 Score: 86
Period size: 31 Copynumber: 4.2 Consensus size: 31
31007 GAAGGACCTA
* * * *
31017 TCCAGAGGTCATAAAGATCCTCGGT-AACTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
* *
31047 TCCATAGGTCCCGAAGAACCTAGGTAAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
* ** * *
31078 TCCATATGTTC-CTTAGAACATAGGTATACTG
1 TCCATA-GGTCACAAAGAACCTAGGTAAACTG
* * *
31109 TCCATATGTCTCGAAAG-ACATAGGTAAAACTG
1 TCCATAGGTCAC-AAAGAACCTAGGT-AAACTG
31141 TCCATA
1 TCCATA
31147 TGTTCCGTAG
Statistics
Matches: 79, Mismatches: 16, Indels: 8
0.77 0.16 0.08
Matches are distributed among these distances:
30 21 0.27
31 42 0.53
32 16 0.20
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.26
Consensus pattern (31 bp):
TCCATAGGTCACAAAGAACCTAGGTAAACTG
Found at i:31152 original size:63 final size:61
Alignment explanation
Indices: 31039--31167 Score: 188
Period size: 63 Copynumber: 2.1 Consensus size: 61
31029 AAAGATCCTC
* *
31039 GGTAACTGTCCATAGGTCCCGAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATA
* *
31100 GGTATACTGTCCATATGTCTCGAA-AGACATAGGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGTA-ACTGTCCATAGGTCCCGAAGA-ACATAGGT-AAACTGTCCATATGTTCCGTAGAACATA
31163 GGTAA
1 GGTAA
31168 ACCCTCGACT
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
61 5 0.08
62 25 0.41
63 31 0.51
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (61 bp):
GGTAACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATA
Found at i:31162 original size:32 final size:31
Alignment explanation
Indices: 31042--31169 Score: 152
Period size: 31 Copynumber: 4.1 Consensus size: 31
31032 GATCCTCGGT
* * * *
31042 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
*
31073 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
* *
31104 TACTGTCCATATG-TCTCG-AAAGACATAGGTAA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGT-A
31136 AACTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
31167 AAC
1 AAC
31170 CCTCGACTCT
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
30 4 0.05
31 51 0.62
32 23 0.28
33 4 0.05
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTA
Found at i:32082 original size:21 final size:21
Alignment explanation
Indices: 32056--32101 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
32046 ATTTTATTCG
*
32056 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTATCGATTCCC
*
32077 CTTGAATGGGTATCGATTCCC
1 CTTGAAGGGGTATCGATTCCC
32098 CTTG
1 CTTG
32102 CCCAGAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.15, C:0.24, G:0.28, T:0.33
Consensus pattern (21 bp):
CTTGAAGGGGTATCGATTCCC
Found at i:34863 original size:23 final size:23
Alignment explanation
Indices: 34828--34886 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 23
34818 TTGTGACATG
*
34828 TTCTCTG-TCTTTATGATAC-TTT
1 TTCTCTGCT-TTTATGACACGTTT
34850 TATCTCTGCTTTTATGACACGTTT
1 T-TCTCTGCTTTTATGACACGTTT
34874 TTCTCTGCATTTT
1 TTCTCTGC-TTTT
34887 GGTAGCTTAC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 1 0.03
23 22 0.69
24 9 0.28
ACGTcount: A:0.14, C:0.20, G:0.10, T:0.56
Consensus pattern (23 bp):
TTCTCTGCTTTTATGACACGTTT
Found at i:42956 original size:40 final size:40
Alignment explanation
Indices: 42909--42990 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
42899 TCATTCAATT
*
42909 TTCAATTTGATCAACTTGTTCACTGAACTTTACAATTGAA
1 TTCAATTTGATCAACTTGTTCACTAAACTTTACAATTGAA
42949 TTCAATTTGATCAACTTGTTCACTAAACTTTACAATTGAA
1 TTCAATTTGATCAACTTGTTCACTAAACTTTACAATTGAA
42989 TT
1 TT
42991 ATTTTGCTCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (40 bp):
TTCAATTTGATCAACTTGTTCACTAAACTTTACAATTGAA
Found at i:44389 original size:32 final size:32
Alignment explanation
Indices: 44282--44399 Score: 103
Period size: 32 Copynumber: 3.6 Consensus size: 32
44272 AACTTATATG
* * *
44282 ATATTAACTCGATCCGAAAATCAAATCGATCTG
1 ATATTAACCCGA-CCAAAAATCAAATCGATCTA
* * * * *
44315 ATATTGACCCGACCCAAAATCTAACCGATCGA
1 ATATTAACCCGACCAAAAATCAAATCGATCTA
44347 ATATTAACCCGACCTAAAAATC-AATCGATCTA
1 ATATTAACCCGACC-AAAAATCAAATCGATCTA
* * *
44379 ATAGTCACCCGAACCGAAAAT
1 ATATTAACCCG-ACCAAAAAT
44400 TGATCCGACC
Statistics
Matches: 69, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
32 50 0.72
33 19 0.28
ACGTcount: A:0.41, C:0.26, G:0.11, T:0.22
Consensus pattern (32 bp):
ATATTAACCCGACCAAAAATCAAATCGATCTA
Found at i:46593 original size:10 final size:10
Alignment explanation
Indices: 46578--46602 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
46568 TCAAATTTGT
46578 ATATTTTATA
1 ATATTTTATA
46588 ATATTTTATA
1 ATATTTTATA
46598 ATATT
1 ATATT
46603 ACGAAGTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
ATATTTTATA
Found at i:60500 original size:23 final size:23
Alignment explanation
Indices: 60463--60526 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
60453 CAGCTCATAT
*
60463 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* * *
60486 AGTTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
60509 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
60527 TATAATAATA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.25, C:0.27, G:0.28, T:0.20
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:60724 original size:103 final size:103
Alignment explanation
Indices: 60545--60759 Score: 385
Period size: 103 Copynumber: 2.1 Consensus size: 103
60535 TATCCATAAG
*
60545 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATAATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
60610 CTCACACATGTTCCAAAGAATACATATATGTCCCAAAA
66 CTCACACATGTTCCAAAGAATACATATATGTCCCAAAA
*
60648 GACCACATATAATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACTAGAC
1 GACCACATATAATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
* * *
60713 CTCACACATGTTCCAAAGAATATATATATGTCCCGAAG
66 CTCACACATGTTCCAAAGAATACATATATGTCCCAAAA
60751 GACCACATA
1 GACCACATA
60760 GACCCTCTAC
Statistics
Matches: 107, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.26
Consensus pattern (103 bp):
GACCACATATAATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
CTCACACATGTTCCAAAGAATACATATATGTCCCAAAA
Found at i:67429 original size:23 final size:22
Alignment explanation
Indices: 67403--67466 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 22
67393 TAGCTCATAT
67403 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
* *
67426 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACC-TAGTGCCACGTAG
67449 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
67467 TATAATAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:67648 original size:105 final size:103
Alignment explanation
Indices: 67482--67701 Score: 386
Period size: 105 Copynumber: 2.1 Consensus size: 103
67472 TAATATCCAT
* *
67482 AAGGACCACATATCATTCCTTAAGAATTATATACATATACCAAGGATCATGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
67547 GACCTCACACATGTTCCAAAGAATATATATATATGTCCCG
66 GACCTCACACATGTTCCAAAG-A-ATACATATATGTCCCG
67587 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
67652 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
*
67690 AATGACCACATA
1 AAGGACCACATA
67702 GACCCTCTAC
Statistics
Matches: 111, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
103 26 0.23
104 1 0.01
105 84 0.76
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:68269 original size:21 final size:21
Alignment explanation
Indices: 68245--68287 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
68235 TTCATATTCG
* *
68245 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
68266 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
68287 T
1 T
68288 AGCCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:70561 original size:21 final size:23
Alignment explanation
Indices: 70507--70556 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
70497 ATCGATACCC
*
70507 TTGAAGGGGAACCGATTCCCCCT
1 TTGAATGGGAACCGATTCCCCCT
* * *
70530 TTGAATAGGAACTGATTCCCTCT
1 TTGAATGGGAACCGATTCCCCCT
70553 TTGA
1 TTGA
70557 GGGAATCGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (23 bp):
TTGAATGGGAACCGATTCCCCCT
Found at i:71022 original size:14 final size:13
Alignment explanation
Indices: 70994--71032 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
70984 CTATGTGTAT
70994 TATTATTTTCAAA
1 TATTATTTTCAAA
71007 TATTATTTTCCAAA
1 TATTATTTT-CAAA
*
71021 TAGT-TTTTCAAA
1 TATTATTTTCAAA
71033 ACATTGCCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 4 0.17
13 13 0.54
14 7 0.29
ACGTcount: A:0.36, C:0.10, G:0.03, T:0.51
Consensus pattern (13 bp):
TATTATTTTCAAA
Found at i:72219 original size:227 final size:227
Alignment explanation
Indices: 71824--72281 Score: 907
Period size: 227 Copynumber: 2.0 Consensus size: 227
71814 CTTTAGTGAG
71824 TTTCCATAAACATTGTTCCCTCCAAGAATATAGAAACCTTGGTTTATGGTTGTCTCCTTAGTAAT
1 TTTCCATAAACATTGTTCCCTCCAAGAATATAGAAACCTTGGTTTATGGTTGTCTCCTTAGTAAT
71889 TTGTTTATCAAACTCGGTCTTAGGGTCAATGGATTTATCGTCCCGAACTCAGAACTTTTAATTGT
66 TTGTTTATCAAACTCGGTCTTAGGGTCAATGGATTTATCGTCCCGAACTCAGAACTTTTAATTGT
71954 GAAACATTTTGATGTTCATGAATTATTTTATTTTGGGTGTTTGAATTTGTTGAATAATTGGATAT
131 GAAACATTTTGATGTTCATGAATTATTTTATTTTGGGTGTTTGAATTTGTTGAATAATTGGATAT
72019 TTGAACTTACATGCTTATATATTTGGTTTGAT
196 TTGAACTTACATGCTTATATATTTGGTTTGAT
*
72051 TTTCCATAAACATTGTTCCTTCCAAGAATATAGAAACCTTGGTTTATGGTTGTCTCCTTAGTAAT
1 TTTCCATAAACATTGTTCCCTCCAAGAATATAGAAACCTTGGTTTATGGTTGTCTCCTTAGTAAT
72116 TTGTTTATCAAACTCGGTCTTAGGGTCAATGGATTTATCGTCCCGAACTCAGAACTTTTAATTGT
66 TTGTTTATCAAACTCGGTCTTAGGGTCAATGGATTTATCGTCCCGAACTCAGAACTTTTAATTGT
72181 GAAACATTTTGATGTTCATGAATTATTTTATTTTGGGTGTTTGAATTTGTTGAATAATTGGATAT
131 GAAACATTTTGATGTTCATGAATTATTTTATTTTGGGTGTTTGAATTTGTTGAATAATTGGATAT
72246 TTGAACTTACATGCTTATATATTTGGTTTGAT
196 TTGAACTTACATGCTTATATATTTGGTTTGAT
72278 TTTC
1 TTTC
72282 AGTTTCATTT
Statistics
Matches: 230, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
227 230 1.00
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.44
Consensus pattern (227 bp):
TTTCCATAAACATTGTTCCCTCCAAGAATATAGAAACCTTGGTTTATGGTTGTCTCCTTAGTAAT
TTGTTTATCAAACTCGGTCTTAGGGTCAATGGATTTATCGTCCCGAACTCAGAACTTTTAATTGT
GAAACATTTTGATGTTCATGAATTATTTTATTTTGGGTGTTTGAATTTGTTGAATAATTGGATAT
TTGAACTTACATGCTTATATATTTGGTTTGAT
Found at i:72907 original size:22 final size:21
Alignment explanation
Indices: 72882--72922 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
72872 CAGAATGTCC
72882 AGAGGGAACCGATTCTCCCCCA
1 AGAGGGAACCGATTC-CCCCCA
* *
72904 AGAGGGTATCGATTCCCCC
1 AGAGGGAACCGATTCCCCC
72923 TGAATGGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.24, C:0.34, G:0.24, T:0.17
Consensus pattern (21 bp):
AGAGGGAACCGATTCCCCCCA
Found at i:75685 original size:12 final size:12
Alignment explanation
Indices: 75668--75707 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
75658 GCTCGATTCA
75668 AGCTCGATTTTG
1 AGCTCGATTTTG
**
75680 AGCTCGA-TTCA
1 AGCTCGATTTTG
75691 AGCTCGATTTTG
1 AGCTCGATTTTG
75703 AGCTC
1 AGCTC
75708 AATTCAAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.35
Consensus pattern (12 bp):
AGCTCGATTTTG
Found at i:75686 original size:23 final size:23
Alignment explanation
Indices: 75632--75720 Score: 124
Period size: 23 Copynumber: 3.8 Consensus size: 23
75622 AAAAATTCAG
* ** *
75632 GAGCTCGATTGAAGCTCGAGACTC
1 GAGCTCGATTCAAGCTCGA-TTTT
75656 GAGCTCGATTCAAGCTCGATTTT
1 GAGCTCGATTCAAGCTCGATTTT
75679 GAGCTCGATTCAAGCTCGATTTT
1 GAGCTCGATTCAAGCTCGATTTT
*
75702 GAGCTCAATTCAAGCTCGA
1 GAGCTCGATTCAAGCTCGA
75721 ACTCGATTCA
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
23 42 0.70
24 18 0.30
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.28
Consensus pattern (23 bp):
GAGCTCGATTCAAGCTCGATTTT
Found at i:75731 original size:17 final size:17
Alignment explanation
Indices: 75709--75741 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
75699 TTTGAGCTCA
*
75709 ATTCAAGCTCGAACTCG
1 ATTCAAGATCGAACTCG
75726 ATTCAAGATCGAACTC
1 ATTCAAGATCGAACTC
75742 AAGCTCGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.24
Consensus pattern (17 bp):
ATTCAAGATCGAACTCG
Found at i:77971 original size:23 final size:23
Alignment explanation
Indices: 77940--78005 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
77930 CCTTATATGC
77940 CACTTCGGTGCATTTCTACGCAG
1 CACTTCGGTGCATTTCTACGCAG
* * ***
77963 CACTACGGTGCAATTCTACATGG
1 CACTTCGGTGCATTTCTACGCAG
*
77986 CACTTCGGTGCATTTATACG
1 CACTTCGGTGCATTTCTACG
78006 AGCTGTGGTG
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.30
Consensus pattern (23 bp):
CACTTCGGTGCATTTCTACGCAG
Done.