Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005626.1 Hibiscus syriacus cultivar Beakdansim tig00013101_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: 71111
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:1649 original size:21 final size:21
Alignment explanation
Indices: 1623--1673 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
1613 CTTGAAACTT
*
1623 TTTCGAGTTGAGTCAAAAATA
1 TTTCGAGTTGAGTCAAAAAAA
1644 TTTCGAGTTGAGTCAAAAAAA
1 TTTCGAGTTGAGTCAAAAAAA
*
1665 ATTCGAGTT
1 TTTCGAGTT
1674 ATTTATGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (21 bp):
TTTCGAGTTGAGTCAAAAAAA
Found at i:2384 original size:161 final size:156
Alignment explanation
Indices: 2132--2431 Score: 458
Period size: 161 Copynumber: 1.9 Consensus size: 156
2122 GGTATATGAG
* * *
2132 CATGTGGTTCAAATTTGGTAAAAGCGGACTTAAAATAAAGGTGAATTCAAGAAATAAGAAAATTA
1 CATGTGGATCAAATTTGGTAAAAGCGAACTTAAAATAAAGATGAATTCAAGAAATAAGAAAATTA
* *
2197 AAAAAAATTGAGGGACTAAATTGAAAAAT-AAAAGTTTATTATCAAAAAGAGGAATTGAAAGTAC
66 AAAAAAATTGAGGGACTAAATTGAAAAATAAAAAATTTATTATCAAAAAGAGAAATTGAAAGTAC
2261 ATATGTATTCTACGATGGTTTAGGAA
131 ATATGTATTCTACGATGGTTTAGGAA
*
2287 CATGTGGATCAAATTTGGTAAAAAAAAGACGAACTTAAAATAAATGATGAATTGAAGAAATAAGA
1 CATGTGGATCAAATTTGGT----AAAAG-CGAACTTAAAATAAA-GATGAATTCAAGAAATAAGA
* * *
2352 AAATTATAAAAAATTGAGGGACTAAATTGAAAAATAAAAAATTTGTTATCAAAAAGATAAATTGA
60 AAATTAAAAAAAATTGAGGGACTAAATTGAAAAATAAAAAATTTATTATCAAAAAGAGAAATTGA
2417 AAGTACATATGTATT
125 AAGTACATATGTATT
2432 TTATGATGAT
Statistics
Matches: 129, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
155 18 0.14
159 5 0.04
160 14 0.11
161 52 0.40
162 40 0.31
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.27
Consensus pattern (156 bp):
CATGTGGATCAAATTTGGTAAAAGCGAACTTAAAATAAAGATGAATTCAAGAAATAAGAAAATTA
AAAAAAATTGAGGGACTAAATTGAAAAATAAAAAATTTATTATCAAAAAGAGAAATTGAAAGTAC
ATATGTATTCTACGATGGTTTAGGAA
Found at i:5651 original size:31 final size:28
Alignment explanation
Indices: 5613--5679 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
5603 CTTTTAAAAC
5613 TTGCAATACAGTCCCCTAACATTTAGTCTAT
1 TTGCAATACAGTCCCC---CATTTAGTCTAT
** *
5644 TTGCAATATGGTCCCCCATTTAGTCTGT
1 TTGCAATACAGTCCCCCATTTAGTCTAT
5672 TTGCAATA
1 TTGCAATA
5680 TGGTCCCCGA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 19 0.58
31 14 0.42
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.37
Consensus pattern (28 bp):
TTGCAATACAGTCCCCCATTTAGTCTAT
Found at i:5674 original size:28 final size:28
Alignment explanation
Indices: 5632--5687 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
5622 AGTCCCCTAA
5632 CATTTAGTCTATTTGCAATATGGTCCCC
1 CATTTAGTCTATTTGCAATATGGTCCCC
*
5660 CATTTAGTCTGTTTGCAATATGGTCCCC
1 CATTTAGTCTATTTGCAATATGGTCCCC
5688 GACGTAACTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.20, C:0.25, G:0.16, T:0.39
Consensus pattern (28 bp):
CATTTAGTCTATTTGCAATATGGTCCCC
Found at i:5698 original size:27 final size:28
Alignment explanation
Indices: 5643--5699 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
5633 ATTTAGTCTA
** *
5643 TTTGCAATATGGTCCCCCATTTAGTCTG
1 TTTGCAATATGGTCCCCCACGTAGACTG
*
5671 TTTGCAATATGGTCCCCGACGTA-ACTG
1 TTTGCAATATGGTCCCCCACGTAGACTG
5698 TT
1 TT
5700 GGGGGACCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.37
Consensus pattern (28 bp):
TTTGCAATATGGTCCCCCACGTAGACTG
Found at i:6650 original size:2 final size:2
Alignment explanation
Indices: 6645--6673 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6635 TGCAAGCTTT
6645 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6674 TTGTTTTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9063 original size:138 final size:137
Alignment explanation
Indices: 8834--9081 Score: 356
Period size: 138 Copynumber: 1.8 Consensus size: 137
8824 TTATGAATTT
* *
8834 CATGGATGCACACATAGTGCCGAGAGTACATATAGTACTGATACGAAAAATGCAACATATGCATT
1 CATGGATGCACACATAGTGCCGAAAGTACACATAGTACTGATACGAAAAATGCAACATATGCATT
** *
8899 AAACAAAATCGATCGATAACTTTTATACATAATTGTATGTCGAAATAGTAATTCAAGAACTCATT
66 AAACAAAATCGATCGATAACCATTATACACAATT-TATGTCGAAATAGTAATTCAAGAACTCATT
8964 ATAAATAC
130 ATAAATAC
* * *
8972 CATGGTTGCACATC-TAGTGCCGAAAGTACACATAGTGCTGATACG-AAAATGCACCATTATGCA
1 CATGGATGCACA-CATAGTGCCGAAAGTACACATAGTACTGATACGAAAAATGCAACA-TATGCA
* * *
9035 TTACACAAAATCGATCGATAACCATTATATACAATTTATGTTGAAAT
64 TTAAACAAAATCGATCGATAACCATTATACACAATTTATGTCGAAAT
9082 GCACCTATGA
Statistics
Matches: 97, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
137 20 0.21
138 76 0.78
139 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (137 bp):
CATGGATGCACACATAGTGCCGAAAGTACACATAGTACTGATACGAAAAATGCAACATATGCATT
AAACAAAATCGATCGATAACCATTATACACAATTTATGTCGAAATAGTAATTCAAGAACTCATTA
TAAATAC
Found at i:10932 original size:74 final size:74
Alignment explanation
Indices: 10853--11011 Score: 230
Period size: 74 Copynumber: 2.1 Consensus size: 74
10843 AAATGACTAG
* * ** *
10853 GGGTATCGGTACCTCTAAG-GGGGTATCGGTACCCATTGGGCATTCTGTTTTTTTCGGAGCCAAA
1 GGGTATCGGTACC-CTAAGAAGGGTATCGATACCCATTGGGCATTCTGTTTTCCTCAGAGCCAAA
10917 ATTGGCATAC
65 ATTGGCATAC
* *
10927 GGGTATCGGTACCCTATGAAGGGTATCGATACCCATTTGGCATTCTGTTTTCCTCAGAGCCAAAA
1 GGGTATCGGTACCCTAAGAAGGGTATCGATACCCATTGGGCATTCTGTTTTCCTCAGAGCCAAAA
*
10992 TTGGCATAG
66 TTGGCATAC
11001 GGGTATCGGTA
1 GGGTATCGGTA
11012 TACCTTATGA
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
73 4 0.05
74 72 0.95
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (74 bp):
GGGTATCGGTACCCTAAGAAGGGTATCGATACCCATTGGGCATTCTGTTTTCCTCAGAGCCAAAA
TTGGCATAC
Found at i:12604 original size:12 final size:12
Alignment explanation
Indices: 12589--12616 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
12579 ATGAGGTGGA
12589 TTTGGAGGTCGG
1 TTTGGAGGTCGG
12601 TTTGGAGGTCGG
1 TTTGGAGGTCGG
12613 TTTG
1 TTTG
12617 AACGACTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.46, T:0.39
Consensus pattern (12 bp):
TTTGGAGGTCGG
Found at i:13330 original size:21 final size:20
Alignment explanation
Indices: 13259--13356 Score: 74
Period size: 21 Copynumber: 4.7 Consensus size: 20
13249 AACCCGACAG
* *
13259 GGGGTATCGGTACCCTT-ATA
1 GGGGTATCGATACACTTGA-A
*
13279 GGGGTATCGATACACATTAAAA
1 GGGGTATCGATACAC-TT-GAA
*
13301 GATGGTATCGATACACGTTGAA
1 G-GGGTATCGATACAC-TTGAA
*
13323 GGGGTATCGATAC-CTAGCAA
1 GGGGTATCGATACACTTG-AA
13343 GGGGGTATCGATAC
1 -GGGGTATCGATAC
13357 CTGGTACACA
Statistics
Matches: 65, Mismatches: 7, Indels: 11
0.78 0.08 0.13
Matches are distributed among these distances:
19 2 0.03
20 16 0.25
21 26 0.40
22 5 0.08
23 16 0.25
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.24
Consensus pattern (20 bp):
GGGGTATCGATACACTTGAA
Found at i:19198 original size:74 final size:74
Alignment explanation
Indices: 19115--19304 Score: 267
Period size: 74 Copynumber: 2.6 Consensus size: 74
19105 GACCGTTAAA
* * *
19115 TGAC-TAGGGGTATCGGTACCTCTAAG-GGGGTATCGGTACCCATTGGGTATTCTGTTTTTCTCG
1 TGACATAGGGGTATCGGTACC-CTATGAGGGGTATCGGTACCCATTGGGCATTCTGTTTTCCTCG
19178 GAGCCAAAAT
65 GAGCCAAAAT
* * *
19188 TGACATAGGGGTATCGGTACCCTATGAGGGGTATCGGTAACCATTTGGCATTTTGTTTTCCTCGG
1 TGACATAGGGGTATCGGTACCCTATGAGGGGTATCGGTACCCATTGGGCATTCTGTTTTCCTCGG
19253 AGCCAAAAT
66 AGCCAAAAT
* *
19262 TGGCATAGGGGTATCGGTACACCCTATGAGGGGTATCGATACC
1 TGACATAGGGGTATCGGT--ACCCTATGAGGGGTATCGGTACC
19305 TCCCTATTTA
Statistics
Matches: 104, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
73 8 0.08
74 75 0.72
76 21 0.20
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.29
Consensus pattern (74 bp):
TGACATAGGGGTATCGGTACCCTATGAGGGGTATCGGTACCCATTGGGCATTCTGTTTTCCTCGG
AGCCAAAAT
Found at i:19478 original size:17 final size:17
Alignment explanation
Indices: 19458--19500 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
19448 TGATATTCGA
19458 ATAATTTAATCGAATAT
1 ATAATTTAATCGAATAT
19475 ATAATTTAATCGAATAT
1 ATAATTTAATCGAATAT
19492 ATAATTTAA
1 ATAATTTAA
19501 GATATAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.42
Consensus pattern (17 bp):
ATAATTTAATCGAATAT
Found at i:19619 original size:8 final size:8
Alignment explanation
Indices: 19606--19642 Score: 74
Period size: 8 Copynumber: 4.6 Consensus size: 8
19596 AGTTTAAGCT
19606 TTTTCCCA
1 TTTTCCCA
19614 TTTTCCCA
1 TTTTCCCA
19622 TTTTCCCA
1 TTTTCCCA
19630 TTTTCCCA
1 TTTTCCCA
19638 TTTTC
1 TTTTC
19643 AACCTTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.11, C:0.35, G:0.00, T:0.54
Consensus pattern (8 bp):
TTTTCCCA
Found at i:21966 original size:16 final size:17
Alignment explanation
Indices: 21929--21965 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
21919 TTATTTAAGC
*
21929 ATTTTACTTAATTTAAT
1 ATTTTACTTAATATAAT
21946 ATTTTAC-TAATATAAT
1 ATTTTACTTAATATAAT
21962 -TTTT
1 ATTTT
21966 TTGCAGATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 4 0.21
16 8 0.42
17 7 0.37
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTACTTAATATAAT
Found at i:30517 original size:35 final size:33
Alignment explanation
Indices: 30454--30659 Score: 98
Period size: 35 Copynumber: 5.8 Consensus size: 33
30444 CAAAATAGAA
30454 ATATTTTAATATTTAAAT-TTAAATAGATAATAAAT
1 ATATTTT-A-ATTTAAATATTAAA-AGATAATAAAT
*
30489 ATATTTTAATTTAGAATATTCAAAAGATATATATAT
1 ATATTTTAATTTA-AATATT-AAAAGATA-ATAAAT
* * * *
30525 ACCTTTTTTATATTCAGA-ATT-AAAGATATATTATAT
1 A--TATTTTA-ATTTAAATATTAAAAGATA-A-TAAAT
* *
30561 ATCTTTTAATTTAAATTATTCAAAAGGAT-ATAATT
1 ATATTTTAATTTAAA-TATT-AAAA-GATAATAAAT
* *
30596 ATATTTTTATATTAAA-AGTTAATTAGATAATAAAT
1 ATATTTTAAT-TTAAATA-TTAA-AAGATAATAAAT
*
30631 ATCTTTTTAAATTTAAAGTATTCAAAAGA
1 AT-ATTTT-AATTTAAA-TATT-AAAAGA
30660 ATATAATTAT
Statistics
Matches: 133, Mismatches: 16, Indels: 42
0.70 0.08 0.22
Matches are distributed among these distances:
33 10 0.08
34 16 0.12
35 47 0.35
36 30 0.23
37 13 0.10
38 13 0.10
39 4 0.03
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (33 bp):
ATATTTTAATTTAAATATTAAAAGATAATAAAT
Found at i:30581 original size:72 final size:68
Alignment explanation
Indices: 30454--30669 Score: 208
Period size: 72 Copynumber: 3.0 Consensus size: 68
30444 CAAAATAGAA
* * * *
30454 ATATTTTAATATTTAAATTTAAATAGATAATAAATATATTTTAATTTAGAATATTCAAAAGATAT
1 ATATTTTTATATTAAAAGTT-AATAGATAATAAATATCTTTTAATTTA-AATATTCAAAAGATAT
30519 ATA-T
64 ATATT
* *
30523 ATACCTTTTTTATATTCAGAA-TTAA-AGATATATTATATATCTTTTAATTTAAATTATTCAAAA
1 ATA---TTTTTATATT-AAAAGTTAATAGATA-A-TAAATATCTTTTAATTTAAA-TATTCAAAA
30586 GGATATA-ATT
59 -GATATATATT
30596 ATATTTTTATATTAAAAGTTAATTAGATAATAAATATCTTTTTAAATTTAAAGTATTCAAAAGA-
1 ATATTTTTATATTAAAAGTTAA-TAGATAATAAATATC-TTTT-AATTTAAA-TATTCAAAAGAT
30660 ATATAATT
62 ATAT-ATT
30668 AT
1 AT
30670 TCTACAAATA
Statistics
Matches: 123, Mismatches: 8, Indels: 29
0.77 0.05 0.18
Matches are distributed among these distances:
69 6 0.05
70 29 0.24
71 12 0.10
72 64 0.52
73 12 0.10
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (68 bp):
ATATTTTTATATTAAAAGTTAATAGATAATAAATATCTTTTAATTTAAATATTCAAAAGATATAT
ATT
Found at i:35430 original size:15 final size:17
Alignment explanation
Indices: 35410--35442 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
35400 ATTCGATGAT
35410 CAAAAT-AAA-TTGAGG
1 CAAAATGAAACTTGAGG
35425 CAAAATGAAACTTGAGG
1 CAAAATGAAACTTGAGG
35442 C
1 C
35443 TATTTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 3 0.19
17 7 0.44
ACGTcount: A:0.48, C:0.12, G:0.21, T:0.18
Consensus pattern (17 bp):
CAAAATGAAACTTGAGG
Found at i:42375 original size:5 final size:5
Alignment explanation
Indices: 42362--42422 Score: 52
Period size: 5 Copynumber: 12.0 Consensus size: 5
42352 TTTATTTTTC
* * * *
42362 AATTT -ATTT AATTT TATTT ATTTTT AATTT AATTT TATTT ATTTTT AATTT
1 AATTT AATTT AATTT AATTT A-ATTT AATTT AATTT AATTT A-ATTT AATTT
*
42413 AATTT TATTT
1 AATTT AATTT
42423 TATTACATAT
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
4 4 0.09
5 32 0.73
6 8 0.18
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (5 bp):
AATTT
Found at i:42396 original size:26 final size:26
Alignment explanation
Indices: 42352--42426 Score: 90
Period size: 26 Copynumber: 3.1 Consensus size: 26
42342 GACAACCCAT
42352 TTTATTTTTCAATTT-ATTTAATTTTA
1 TTTATTTTT-AATTTAATTTAATTTTA
42378 TTTA---TT--TTTAATTTAATTTTA
1 TTTATTTTTAATTTAATTTAATTTTA
*
42399 TTTATTTTTAATTTAATTTTATTTTA
1 TTTATTTTTAATTTAATTTAATTTTA
42425 TT
1 TT
42427 ACATATTAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
20 3 0.07
21 15 0.36
23 2 0.05
24 2 0.05
26 20 0.48
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.72
Consensus pattern (26 bp):
TTTATTTTTAATTTAATTTAATTTTA
Found at i:42444 original size:5 final size:5
Alignment explanation
Indices: 42350--42426 Score: 50
Period size: 5 Copynumber: 14.6 Consensus size: 5
42340 AAGACAACCC
* * *
42350 ATTTT ATTTTT CAATTT ATTTA ATTTT A-TTT ATTTTT AATTTA ATTTT
1 ATTTT A-TTTT -ATTTT ATTTT ATTTT ATTTT A-TTTT -ATTTT ATTTT
*
42398 A-TTT ATTTTT AATTTA ATTTT ATTTT ATT
1 ATTTT A-TTTT -ATTTT ATTTT ATTTT ATT
42427 ACATATTAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
4 8 0.14
5 26 0.46
6 19 0.34
7 3 0.05
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.71
Consensus pattern (5 bp):
ATTTT
Found at i:42444 original size:21 final size:21
Alignment explanation
Indices: 42367--42443 Score: 113
Period size: 21 Copynumber: 3.7 Consensus size: 21
42357 TTTTCAATTT
42367 ATTTAATTTTATTTATTTTTA
1 ATTTAATTTTATTTATTTTTA
42388 ATTTAATTTTATTTATTTTTA
1 ATTTAATTTTATTTATTTTTA
*
42409 ATTTAATTTTA-TT-TTATTA
1 ATTTAATTTTATTTATTTTTA
42428 CATATTAATTTTATTT
1 -AT-TTAATTTTATTT
42444 TTCTTTGAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 5
0.90 0.02 0.09
Matches are distributed among these distances:
19 5 0.10
20 4 0.08
21 41 0.79
22 2 0.04
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (21 bp):
ATTTAATTTTATTTATTTTTA
Found at i:42614 original size:6 final size:6
Alignment explanation
Indices: 42603--42633 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
42593 TACCGAAACT
42603 CCCACC CCCACC CCCACC CCCACC CCCACC C
1 CCCACC CCCACC CCCACC CCCACC CCCACC C
42634 GACTCCATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.84, G:0.00, T:0.00
Consensus pattern (6 bp):
CCCACC
Found at i:47107 original size:23 final size:22
Alignment explanation
Indices: 47081--47130 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
47071 TAGCTCGTAG
47081 AAATGCACCGAAGTGTCGCATA-A
1 AAATGCACCGAAGTG-C-CATATA
*
47104 AAATGCACCGAGGTGCCATATA
1 AAATGCACCGAAGTGCCATATA
47126 AAATG
1 AAATG
47131 TCCATAAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 4 0.16
22 7 0.28
23 14 0.56
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (22 bp):
AAATGCACCGAAGTGCCATATA
Found at i:47213 original size:21 final size:21
Alignment explanation
Indices: 47175--47250 Score: 55
Period size: 21 Copynumber: 3.6 Consensus size: 21
47165 TATATACATA
* *
47175 TTCCCAAGGACCAAATATGTG
1 TTCCAAAGGACCAAATATATG
**
47196 -TCTCAAAGGACCGTATATATG
1 TTC-CAAAGGACCAAATATATG
** *
47217 TTCCAAAGGATTACATATATG
1 TTCCAAAGGACCAAATATATG
* *
47238 TCCCGAAGGACCA
1 TTCCAAAGGACCA
47251 CGTAGAACCC
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
20 2 0.05
21 37 0.90
22 2 0.05
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.25
Consensus pattern (21 bp):
TTCCAAAGGACCAAATATATG
Found at i:50681 original size:55 final size:54
Alignment explanation
Indices: 50544--50813 Score: 364
Period size: 55 Copynumber: 4.9 Consensus size: 54
50534 TTTATTAAGA
* * *
50544 TGCACACGTAGTGTCTATACGG-TAGTTCATCAACTCATGATGAATTTCGTGGA-T
1 TGCACACATAGTG-CTGTACGGTTA-TTCATCAACTCATGATGAATTCCGTGGATT
* * *
50598 TGCACACATTGTACATGTATGGTTATTCATCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGC-TGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
*
50653 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTTCGTGGATT
1 TGCACACATAGTGC-TGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * * * *
50708 TGTATACATAGTGGCTGTACGATTATTCATCAACTCATGATAAATTCTGTGGATT
1 TGCACACATAGT-GCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
50763 TGCACACATAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCCGTG
1 TGCACACATAGTGC-TGTACGGTTATTCATCAACTCATGATGAATTCCGTG
50814 AAATGCACAC
Statistics
Matches: 190, Mismatches: 21, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
53 1 0.01
54 44 0.23
55 143 0.75
56 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (54 bp):
TGCACACATAGTGCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
Found at i:50845 original size:54 final size:55
Alignment explanation
Indices: 50544--50883 Score: 299
Period size: 55 Copynumber: 6.2 Consensus size: 55
50534 TTTATTAAGA
* * *
50544 TGCACACGTAGTGTCTATACGG-TAGTTCATCAACTCATGATGAATTTCGTGG-AT
1 TGCACACATAGTGTCGATACGGTTA-TTCATCAACTCATGATGAATTCCGTGGAAT
* *
50598 TGCACACAT--TGTAC-ATGTATGGTTATTCATCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGT-CGA--TACGGTTATTCATCAACTCATGATGAATTCCGTGGAAT
* *
50653 TGCACACATAGTG-C-ATGTACGGTTATTCATCAACTCATGATGAATTTCGTGGATT
1 TGCACACATAGTGTCGA--TACGGTTATTCATCAACTCATGATGAATTCCGTGGAAT
* * * * * * *
50708 TGTATACATAGTGGCTG-TACGATTATTCATCAACTCATGATAAATTCTGTGGATT
1 TGCACACATAGTGTC-GATACGGTTATTCATCAACTCATGATGAATTCCGTGGAAT
* *
50763 TGCACACATAGTGCTTG-TACGGTTATTCATCAACTCATGATGAATTCCGT-GAAA
1 TGCACACATAGTG-TCGATACGGTTATTCATCAACTCATGATGAATTCCGTGGAAT
* * * * * * *
50817 TGCACACTTAGTGTCGAAATGATTATTCATCCACAT-AGGATGAATTCCGTAGAA-
1 TGCACACATAGTGTCGATACGGTTATTCATCAAC-TCATGATGAATTCCGTGGAAT
*
50871 TGCACACTTAGTG
1 TGCACACATAGTG
50884 CCTATTTGGT
Statistics
Matches: 244, Mismatches: 28, Indels: 28
0.81 0.09 0.09
Matches are distributed among these distances:
52 4 0.02
53 3 0.01
54 91 0.37
55 143 0.59
56 1 0.00
57 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (55 bp):
TGCACACATAGTGTCGATACGGTTATTCATCAACTCATGATGAATTCCGTGGAAT
Found at i:55004 original size:13 final size:13
Alignment explanation
Indices: 54986--55010 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54976 TGGAAAGATC
54986 ATTTTTATAATAA
1 ATTTTTATAATAA
54999 ATTTTTATAATA
1 ATTTTTATAATA
55011 TTCGATTTAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTTTTATAATAA
Found at i:55874 original size:4 final size:4
Alignment explanation
Indices: 55865--55935 Score: 142
Period size: 4 Copynumber: 17.8 Consensus size: 4
55855 AAGATAAAGT
55865 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
55913 TGTA TGTA TGTA TGTA TGTA TGT
1 TGTA TGTA TGTA TGTA TGTA TGT
55936 GTCTGAAATT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 67 1.00
ACGTcount: A:0.24, C:0.00, G:0.25, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:59426 original size:30 final size:30
Alignment explanation
Indices: 59390--59486 Score: 126
Period size: 30 Copynumber: 3.2 Consensus size: 30
59380 TATTAGATAA
59390 AAATGAATGATACATGCTATGAAATGAATT
1 AAATGAATGATACATGCTATGAAATGAATT
* *
59420 AAATGAATGATACATGCTATGAAATAAATG
1 AAATGAATGATACATGCTATGAAATGAATT
* *
59450 AAGTGAAT-AAAGCATGCTATGAAATGAA-T
1 AAATGAATGATA-CATGCTATGAAATGAATT
59479 AAAGTGAA
1 AAA-TGAA
59487 AGGTAAAGGT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
29 4 0.07
30 54 0.93
ACGTcount: A:0.49, C:0.06, G:0.19, T:0.26
Consensus pattern (30 bp):
AAATGAATGATACATGCTATGAAATGAATT
Found at i:61429 original size:7 final size:7
Alignment explanation
Indices: 61410--61455 Score: 83
Period size: 7 Copynumber: 6.4 Consensus size: 7
61400 CTCATCTATT
61410 AGAAAAA
1 AGAAAAA
61417 AGGAAAAA
1 A-GAAAAA
61425 AGAAAAA
1 AGAAAAA
61432 AGAAAAA
1 AGAAAAA
61439 AGAAAAA
1 AGAAAAA
61446 AGAAAAA
1 AGAAAAA
61453 AGA
1 AGA
61456 TGAAAAAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
7 31 0.82
8 7 0.18
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (7 bp):
AGAAAAA
Found at i:61643 original size:19 final size:18
Alignment explanation
Indices: 61598--61639 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
61588 CAAGAAGCGC
61598 AAGAAATGATGGAGATAT
1 AAGAAATGATGGAGATAT
61616 AAGAAATGATGGAGATAT
1 AAGAAATGATGGAGATAT
61634 AAGAAA
1 AAGAAA
61640 ATGAAAATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.26, T:0.19
Consensus pattern (18 bp):
AAGAAATGATGGAGATAT
Found at i:64194 original size:73 final size:73
Alignment explanation
Indices: 64074--64737 Score: 1010
Period size: 73 Copynumber: 9.1 Consensus size: 73
64064 CAACATTTTC
*
64074 AAAACAAAGATTTATCTCGCTT-AGACAGTTTCACTCGAAACAGAAATTTATCTCACTCGAGATA
1 AAAAC-AAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAAATTTATCTCACTCGAGATA
*
64138 ATTTTTCTT
65 GTTTTTCTT
* * * *
64147 AAAACATGATTTGTCTTGCTTGAGACAGTTTCACTCGAAACATAAATTTATATCACTCGAGATAG
1 AAAACAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAAATTTATCTCACTCGAGATAG
64212 TTTTTCTT
66 TTTTTCTT
* * *
64220 AAAACAAGATTTGTGTCGCTTGAGACAGTTTCACTCGAAATAGAAATTTATCTCACTTGAGATAG
1 AAAACAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAAATTTATCTCACTCGAGATAG
64285 TTTTTCTT
66 TTTTTCTT
64293 AAAACAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAAATTTATCTCACTCGAGATAG
1 AAAACAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAAATTTATCTCACTCGAGATAG
64358 TTTTTCTT
66 TTTTTCTT
* * *
64366 AAAA-AAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAAAAAAAATTTATCTCACTGGAGATAG
1 AAAACAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAAATTTATCTCACTCGAGATAG
64430 TTTTTCTT
66 TTTTTCTT
* ** *
64438 ATAACAAGATTTGTCTTACTTTAGACAGTTTCACTCGAAACAGAAATTTATCTCACTCGAGATAG
1 AAAACAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAAATTTATCTCACTCGAGATAG
64503 TTTTTCTT
66 TTTTTCTT
* * * * *
64511 AAAACAATATTTGTATCGCTTGAGACAGTTTCACTCGAAACAGAATTTTATCTCACTTGAGATTG
1 AAAACAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAAATTTATCTCACTCGAGATAG
64576 TTTTTCTT
66 TTTTTCTT
* * * * *
64584 AAAACAAGATTTTTCTCGCTTGAGATAGTTTCACTCGAAACAGAAATTTATCTCACTTGATATTG
1 AAAACAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAAATTTATCTCACTCGAGATAG
64649 TTTTTCTT
66 TTTTTCTT
** * * * *
64657 AAAACAAGAGATGTCTCGCTTGAGACAGTTTCACTCGAAACAAAAAATTATCTCACTTGAGATTG
1 AAAACAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAAATTTATCTCACTCGAGATAG
64722 TTTTTCTT
66 TTTTTCTT
64730 -AAACAAGA
1 AAAACAAGA
64738 GATTGTTTTT
Statistics
Matches: 541, Mismatches: 48, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
72 89 0.16
73 452 0.84
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (73 bp):
AAAACAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAAATTTATCTCACTCGAGATAG
TTTTTCTT
Found at i:64620 original size:291 final size:290
Alignment explanation
Indices: 64079--64737 Score: 1052
Period size: 291 Copynumber: 2.3 Consensus size: 290
64069 TTTTCAAAAC
* * * *
64079 AAAGATTTATCTCGCTT-AGACAGTTTCACTCGAAACAGAAATTTATCTCACTCGAGATAATTTT
1 AAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAAAAAAAATTTATCTCACTCGAGATAGTTTT
* * *
64143 TCTTAAAACATGATTTGTCTTGCTTGAGACAGTTTCACTCGAAACATAAATTTATATCACTCGAG
66 TCTT-AAACAAGATTTGTCTTACTTGAGACAGTTTCACTCGAAACAGAAATTTATATCACTCGAG
* *
64208 ATAGTTTTTCTTAAAACAAGATTTGTGTCGCTTGAGACAGTTTCACTCGAAATAGAAATTTATCT
130 ATAGTTTTTCTTAAAACAAGATTTGTATCGCTTGAGACAGTTTCACTCGAAACAGAAATTTATCT
64273 CACTTGAGATAGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAA
195 CACTTGAGATAGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAA
64338 ATTTATCTCACTCGAGATAGTTTTTCTTAAA
260 ATTTATCTCACTCGAGATAGTTTTTCTTAAA
*
64369 AAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAAAAAAAATTTATCTCACTGGAGATAGTTTT
1 AAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAAAAAAAATTTATCTCACTCGAGATAGTTTT
* *
64434 TCTTATAACAAGATTTGTCTTACTTTAGACAGTTTCACTCGAAACAGAAATTTATCTCACTCGAG
66 TCTTA-AACAAGATTTGTCTTACTTGAGACAGTTTCACTCGAAACAGAAATTTATATCACTCGAG
* *
64499 ATAGTTTTTCTTAAAACAATATTTGTATCGCTTGAGACAGTTTCACTCGAAACAGAATTTTATCT
130 ATAGTTTTTCTTAAAACAAGATTTGTATCGCTTGAGACAGTTTCACTCGAAACAGAAATTTATCT
* * *
64564 CACTTGAGATTGTTTTTCTTAAAACAAGATTTTTCTCGCTTGAGATAGTTTCACTCGAAACAGAA
195 CACTTGAGATAGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAA
* * *
64629 ATTTATCTCACTTGATATTGTTTTTCTTAAA
260 ATTTATCTCACTCGAGATAGTTTTTCTTAAA
** * *
64660 ACAAGAGATGTCTCGCTTGAGACAGTTTCACTCGAAACAAAAAA-TTATCTCACTTGAGATTGTT
1 A-AAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAA-AAAAAATTTATCTCACTCGAGATAGTT
64724 TTTCTTAAACAAGA
64 TTTCTTAAACAAGA
64738 GATTGTTTTT
Statistics
Matches: 341, Mismatches: 24, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
290 17 0.05
291 260 0.76
292 58 0.17
293 6 0.02
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (290 bp):
AAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAAAAAAAATTTATCTCACTCGAGATAGTTTT
TCTTAAACAAGATTTGTCTTACTTGAGACAGTTTCACTCGAAACAGAAATTTATATCACTCGAGA
TAGTTTTTCTTAAAACAAGATTTGTATCGCTTGAGACAGTTTCACTCGAAACAGAAATTTATCTC
ACTTGAGATAGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAAA
TTTATCTCACTCGAGATAGTTTTTCTTAAA
Found at i:64763 original size:20 final size:21
Alignment explanation
Indices: 64715--64758 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
64705 TATCTCACTT
64715 GAGATTGTTTTTCTTAAACAA
1 GAGATTGTTTTTCTTAAACAA
64736 GAGATTGTTTTTCTTAAACAA
1 GAGATTGTTTTTCTTAAACAA
64757 GA
1 GA
64759 TTTGTCTCGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (21 bp):
GAGATTGTTTTTCTTAAACAA
Found at i:64835 original size:94 final size:94
Alignment explanation
Indices: 64645--64835 Score: 233
Period size: 94 Copynumber: 2.0 Consensus size: 94
64635 CTCACTTGAT
*
64645 ATTGTTTTTCTTAAAACAAGAGATGTCTCGCTTGAGACAGTTTCACTCGAAACAAAAAATTATCT
1 ATTGTTTTTCTTAAAACAAGAGATGTCTCGCTTGAGACAATTTCACTCGAAACAAAAAATTATCT
* * *
64710 CACTTGAGATTGTTTTTCTTAAACAAGAG
66 CACTCGAGATAGTTTTTCTCAAACAAGAG
** * * * ** *
64739 ATTGTTTTTCTT-AAACAAGATTTGTCTCGCTTGAGATAATTTCACTCGCAGCAGAAATTTTATT
1 ATTGTTTTTCTTAAAACAAGAGATGTCTCGCTTGAGACAATTTCACTCGAAACA-AAAAATTATC
*
64803 TCGCTCGAGATAGTTTTTCTCAAAGCAA-AG
65 TCACTCGAGATAGTTTTTCTCAAA-CAAGAG
64833 ATT
1 ATT
64836 TGTCTCGCTT
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
93 35 0.43
94 44 0.54
95 3 0.04
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.37
Consensus pattern (94 bp):
ATTGTTTTTCTTAAAACAAGAGATGTCTCGCTTGAGACAATTTCACTCGAAACAAAAAATTATCT
CACTCGAGATAGTTTTTCTCAAACAAGAG
Found at i:65504 original size:139 final size:137
Alignment explanation
Indices: 65251--65564 Score: 409
Period size: 139 Copynumber: 2.3 Consensus size: 137
65241 AGATCAGTAG
* * * * *
65251 CAACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGGATAAGAAGTTCATAG
1 CAACATTTCCAATGGAGAATTCATAATGAGAAGAACTCATCCAATGAGGGAAAAGAAGTTCATAA
* * *
65316 TGAAAAGAACTTGTTCAACCTTAGTTCGATTCATCGCATATGGAGTTGAATCAACGACACCTAAC
66 TGAAAAGAACTTGTTAAACCTTAGTTCGATTCATCACATATGGAGTTGAATC-A-GAAACCTAAC
*
65381 TCGAGGGAT
129 TCGAGGCAT
* * * *
65390 CACCATTTCCATTGGAGAATTCATAATGAGAAGAACTCATCCGATGGGGGAAAAGAAGTTCATAA
1 CAACATTTCCAATGGAGAATTCATAATGAGAAGAACTCATCCAATGAGGGAAAAGAAGTTCATAA
* *
65455 TGAGAAGAACTTGTTAAACCTTA-TCTCGATTCATCACATATGGAGTTGAATCAGAAACCTCACT
66 TGAAAAGAACTTGTTAAACCTTAGT-TCGATTCATCACATATGGAGTTGAATCAGAAACCTAACT
65519 CGAGGCAT
130 CGAGGCAT
*
65527 CAACA-TTCTCAAAGGA-ATAGTTCATAATGAGAAGAACT
1 CAACATTTC-CAATGGAGA-A-TTCATAATGAGAAGAACT
65565 TGTTCAACCT
Statistics
Matches: 154, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
136 4 0.03
137 26 0.17
138 20 0.13
139 104 0.68
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (137 bp):
CAACATTTCCAATGGAGAATTCATAATGAGAAGAACTCATCCAATGAGGGAAAAGAAGTTCATAA
TGAAAAGAACTTGTTAAACCTTAGTTCGATTCATCACATATGGAGTTGAATCAGAAACCTAACTC
GAGGCAT
Found at i:66998 original size:33 final size:33
Alignment explanation
Indices: 66940--67019 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
66930 ATTTTGGGCA
*
66940 TTATATTTTGATATCTATTATTTTAGTTCTTTACT
1 TTATATTTT-A-ATCTATTATTTTAGTCCTTTACT
*
66975 TTATATTTTAATCTTTTATTTTAGTCCTTTACT
1 TTATATTTTAATCTATTATTTTAGTCCTTTACT
67008 TTATATTTTAAT
1 TTATATTTTAAT
67020 TTATGTCATT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
33 33 0.77
34 1 0.02
35 9 0.21
ACGTcount: A:0.24, C:0.09, G:0.04, T:0.64
Consensus pattern (33 bp):
TTATATTTTAATCTATTATTTTAGTCCTTTACT
Found at i:67021 original size:26 final size:25
Alignment explanation
Indices: 66988--67066 Score: 74
Period size: 26 Copynumber: 3.2 Consensus size: 25
66978 TATTTTAATC
*
66988 TTTTATTT-TAGTCCTTTACTTTATA
1 TTTTATTTAT-GTCATTTACTTTATA
*
67013 TTTTAATTTATGTCATTTACTTTTTA
1 TTTT-ATTTATGTCATTTACTTTATA
* *
67039 -TTTATTTAATTTCA-TTACTTTAAA
1 TTTTATTT-ATGTCATTTACTTTATA
67063 TTTT
1 TTTT
67067 TAATTTTTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
24 12 0.27
25 15 0.33
26 17 0.38
27 1 0.02
ACGTcount: A:0.24, C:0.09, G:0.03, T:0.65
Consensus pattern (25 bp):
TTTTATTTATGTCATTTACTTTATA
Found at i:67053 original size:25 final size:26
Alignment explanation
Indices: 66988--67072 Score: 79
Period size: 25 Copynumber: 3.3 Consensus size: 26
66978 TATTTTAATC
* *
66988 TTTTATTTTA-GTCCTTTACTTTATA
1 TTTTAATTTATGTCATTTACTTTATA
*
67013 TTTTAATTTATGTCATTTACTTTTTA
1 TTTTAATTTATGTCATTTACTTTATA
* *
67039 -TTT-ATTTAATTTCA-TTACTTTAAA
1 TTTTAATTT-ATGTCATTTACTTTATA
67063 TTTTTAATTT
1 -TTTTAATTT
67073 TTATTTATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
24 12 0.24
25 17 0.35
26 16 0.33
27 4 0.08
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.65
Consensus pattern (26 bp):
TTTTAATTTATGTCATTTACTTTATA
Found at i:68818 original size:11 final size:11
Alignment explanation
Indices: 68774--68831 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
68764 ACCAAAAGTT
68774 TAATATATACA
1 TAATATATACA
* * *
68785 AAATAAATTAAA
1 TAATATA-TACA
* *
68797 TGAACATATACT
1 T-AATATATACA
68809 TAATATATACA
1 TAATATATACA
68820 TAATATATACA
1 TAATATATACA
68831 T
1 T
68832 GCTTACGAAA
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
11 25 0.71
12 6 0.17
13 4 0.11
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (11 bp):
TAATATATACA
Done.