Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016134.1 Corchorus olitorius cultivar O-4 contig16167, 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: 34379
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:3024 original size:33 final size:33
Alignment explanation
Indices: 2982--3052 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
2972 TCCGCGCCAT
*
2982 CCGAGCCTCATGCCCGGCTAGGACCGGCCACAG
1 CCGAGCCTCATGCCCAGCTAGGACCGGCCACAG
3015 CCGAGCCTCATGCCCAGCTAGGACCGGCCACAG
1 CCGAGCCTCATGCCCAGCTAGGACCGGCCACAG
3048 CCGAG
1 CCGAG
3053 TCAAGTGTCC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.20, C:0.42, G:0.30, T:0.08
Consensus pattern (33 bp):
CCGAGCCTCATGCCCAGCTAGGACCGGCCACAG
Found at i:3235 original size:21 final size:21
Alignment explanation
Indices: 3188--3237 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
3178 CGCCCATTCA
**
3188 CCGTGCCACCACCGGTTAAGC
1 CCGTGCCACCACCGGCCAAGC
*
3209 CCGTGCCACCACCGGCCATGC
1 CCGTGCCACCACCGGCCAAGC
*
3230 CTGTGCCA
1 CCGTGCCA
3238 TCGCCATTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.16, C:0.46, G:0.24, T:0.14
Consensus pattern (21 bp):
CCGTGCCACCACCGGCCAAGC
Found at i:8500 original size:17 final size:17
Alignment explanation
Indices: 8478--8514 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
8468 CCCTTGAGTG
*
8478 TGCAAAAATGACCAATA
1 TGCAAAAATGACCAAAA
8495 TGCAAAAATGACCAAAA
1 TGCAAAAATGACCAAAA
8512 TGC
1 TGC
8515 CCCTGGATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.51, C:0.19, G:0.14, T:0.16
Consensus pattern (17 bp):
TGCAAAAATGACCAAAA
Found at i:16441 original size:30 final size:30
Alignment explanation
Indices: 16385--16442 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
16375 AATTCTTGCT
**
16385 TCTTGAAATAATTCTTCAATGGTCTTCATA
1 TCTTGAAATAATTCTTCAATAATCTTCATA
*
16415 TCTTGAAATTA-TCTTCAATTAATCTTCA
1 TCTTGAAATAATTCTTCAA-TAATCTTCA
16443 ACCACGAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 7 0.29
30 17 0.71
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.45
Consensus pattern (30 bp):
TCTTGAAATAATTCTTCAATAATCTTCATA
Found at i:17569 original size:17 final size:17
Alignment explanation
Indices: 17547--17583 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
17537 TTCTTTGTCA
17547 AAGTAATAGGACACATC
1 AAGTAATAGGACACATC
17564 AAGTAATAGGACACATC
1 AAGTAATAGGACACATC
17581 AAG
1 AAG
17584 GAAGATGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.49, C:0.16, G:0.19, T:0.16
Consensus pattern (17 bp):
AAGTAATAGGACACATC
Found at i:18402 original size:17 final size:17
Alignment explanation
Indices: 18380--18416 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
18370 TTCTTTGTCA
*
18380 AAGTAATATGACACATC
1 AAGTAATAGGACACATC
18397 AAGTAATAGGACACATC
1 AAGTAATAGGACACATC
18414 AAG
1 AAG
18417 GAAGATGAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.19
Consensus pattern (17 bp):
AAGTAATAGGACACATC
Found at i:18661 original size:833 final size:833
Alignment explanation
Indices: 17056--18719 Score: 3150
Period size: 833 Copynumber: 2.0 Consensus size: 833
17046 GTCTCCTCCA
* *
17056 AGTCATCCTATTTCTTTATTTAGGTTGAGCAGGATGTTTGGGATGCTGCACATTCTGCCACACAC
1 AGTCATCCTATTTCTTTATATAGGTTGAGCAGGATGCTTGGGATGCTGCACATTCTGCCACACAC
*
17121 CATTCAGAGCATTTGATGGTGGCTTGACCATTCTAGGTCGTGCATGTTCTTTTCGCAGCTTCATC
66 CATTCAGAGCATTTGATGGTGGCTTGACCATTCTAGGTCGTGCATGTTCTTTTCGCAACTTCATC
17186 TCCCTTTCCACAGCTACATGGCGATATCCATCTTTCCTATGATCCAACCGAGGTCTGATTTCATG
131 TCCCTTTCCACAGCTACATGGCGATATCCATCTTTCCTATGATCCAACCGAGGTCTGATTTCATG
*
17251 CCTAGCCCTCTTTGAATGAGGCTTTGAACAAAATTCATCCTGTGGTTGCTGCTCATATCCCCTCT
196 CCTAGCCCTCTTTGAATGAGGCTTTGAACAAAATTCATCCTGTGGCTGCTGCTCATATCCCCTCT
*
17316 TGGAATGCTTCTGCGCTTTATGGGAAAGAGATGACGTCAAGCAAAAGGTATGAGGCGCCACCTTA
261 TGGAATGCTTCTACGCTTTATGGGAAAGAGATGACGTCAAGCAAAAGGTATGAGGCGCCACCTTA
17381 AAAGATGACTCTCCATGTTCTCTTTTGCTCGACTTGCGATATGGAAGATAGGCTTCTTTCTTATT
326 AAAGATGACTCTCCATGTTCTCTTTTGCTCGACTTGCGATATGGAAGATAGGCTTCTTTCTTATT
17446 CCTTGGATCATAAACGAGTTTTGTTTTTACTTTTTCTTCCTTTTGAAATGGAGTCTTTGAGGAAA
391 CCTTGGATCATAAACGAGTTTTGTTTTTACTTTTTCTTCCTTTTGAAATGGAGTCTTTGAGGAAA
17511 AGTCCAACCTCCTTTGAACTTCTTTTTTCTTTGTCAAAGTAATAGGACACATCAAGTAATAGGAC
456 AGTCCAACCTCCTTTGAACTTCTTTTTTCTTTGTCAAAGTAATAGGACACATCAAGTAATAGGAC
17576 ACATCAAGGAAGATGAAGAAAACTCCAACTTACTTCTTGGTGCTGTAAGCCTCATTGCGGCCGAT
521 ACATCAAGGAAGATGAAGAAAACTCCAACTTACTTCTTGGTGCTGTAAGCCTCATTGCGGCCGAT
*
17641 TTTGGGGACAAAGGTCGGTCTAAAATAAGGCCTAAAGGCTTGGGCTCAGTTCCATCACCATGCCT
586 TTTGGGGACAAAGGTCGGTCTAAAATAAGGCCTAAAGGCTTGGGCTCAATTCCATCACCATGCCT
17706 CTTGATTCTTGTAGAACGATGATGAGTCTTGTCCTTGTGTTGAGGGTCGACTGACAAGGGATACC
651 CTTGATTCTTGTAGAACGATGATGAGTCTTGTCCTTGTGTTGAGGGTCGACTGACAAGGGATACC
*
17771 TTGTAGCCGGACTTGTCCCTTTTGGTGTTACCTCTTCTTCCCTTGCATCCTTAATGGTCAACTAC
716 TTGTAGCCGGACTTGTCCCTTTTGGTGTTACCTCTTCTTCCCCTGCATCCTTAATGGTCAACTAC
17836 CCATCTTTTTGAAGATTAAGCGCAACCATATGAACTGGTGTTGGGAAAAAAAT
781 CCATCTTTTTGAAGATTAAGCGCAACCATATGAACTGGTGTTGGGAAAAAAAT
*
17889 AGTCATCCTATTTCTTTGTATAGGTTGAGCAGGATGCTTGGGATGCTGCACATTCTGCCACACAC
1 AGTCATCCTATTTCTTTATATAGGTTGAGCAGGATGCTTGGGATGCTGCACATTCTGCCACACAC
17954 CATTCAGAGCATTTGATGGTGGCTTGACCATTCTAGGTCGTGCATGTTCTTTTCGCAACTTCATC
66 CATTCAGAGCATTTGATGGTGGCTTGACCATTCTAGGTCGTGCATGTTCTTTTCGCAACTTCATC
* *
18019 TCCCTTTCCACAGCTACATGGCGATATTCATCTTTCCTATGATCCAACCGAGGTTTGATTTCATG
131 TCCCTTTCCACAGCTACATGGCGATATCCATCTTTCCTATGATCCAACCGAGGTCTGATTTCATG
*
18084 CCTAGCCCTCTTTGAATGAGGCTTTGAACAAAATTCATCTTGTGGCTGCTGCTCATATCCCCTCT
196 CCTAGCCCTCTTTGAATGAGGCTTTGAACAAAATTCATCCTGTGGCTGCTGCTCATATCCCCTCT
* * *
18149 TGGAATGCTTCTACGCTTTATGGGAAAGAGATGACGTCAAGCGAAAGGTATTAGGTGCCACCTTA
261 TGGAATGCTTCTACGCTTTATGGGAAAGAGATGACGTCAAGCAAAAGGTATGAGGCGCCACCTTA
18214 AAAGATGACTCTCCATGTTCTCTTTTGCTCGACTTGCGATATGGAAGATAGGCTTCTTTCTTATT
326 AAAGATGACTCTCCATGTTCTCTTTTGCTCGACTTGCGATATGGAAGATAGGCTTCTTTCTTATT
* *
18279 CCTTGGATCATAAACGAGTTTTGTTTTTACTTTTTCTTCCTTTTGAAGTGGAGTTTTTGAGGAAA
391 CCTTGGATCATAAACGAGTTTTGTTTTTACTTTTTCTTCCTTTTGAAATGGAGTCTTTGAGGAAA
*
18344 AGTCCAACCTCCTTTGAACTTCTTTTTTCTTTGTCAAAGTAATATGACACATCAAGTAATAGGAC
456 AGTCCAACCTCCTTTGAACTTCTTTTTTCTTTGTCAAAGTAATAGGACACATCAAGTAATAGGAC
*
18409 ACATCAAGGAAGATGAAGAAAACTCCAACTT-CTTTCTTGGTGTTGTAAGCCTCATTGCGGCCGA
521 ACATCAAGGAAGATGAAGAAAACTCCAACTTAC-TTCTTGGTGCTGTAAGCCTCATTGCGGCCGA
18473 TTTTGGGGACAAAGGTCGGTCTAAAATAAGGCCTAAAGGCTTGGGCTCAATTCCATCACCATGCC
585 TTTTGGGGACAAAGGTCGGTCTAAAATAAGGCCTAAAGGCTTGGGCTCAATTCCATCACCATGCC
18538 TCTTGATTCTTGTAGAACGATGATGAGTCTTGTCCTTGTGTTGAGGGTCGACTGACAAGGGATAC
650 TCTTGATTCTTGTAGAACGATGATGAGTCTTGTCCTTGTGTTGAGGGTCGACTGACAAGGGATAC
18603 CTTGTAGCCGGACTTGTCCCTTTTGGTGTTACCTCTTCTTCCCCTGCATCCTTAATGGTCAACTA
715 CTTGTAGCCGGACTTGTCCCTTTTGGTGTTACCTCTTCTTCCCCTGCATCCTTAATGGTCAACTA
18668 CCCATCTTTTTGAAGATTAAGCGCAACCATATGAACTGGTGTTGGGAAAAAA
780 CCCATCTTTTTGAAGATTAAGCGCAACCATATGAACTGGTGTTGGGAAAAAA
18720 TTCTTGTTAA
Statistics
Matches: 812, Mismatches: 18, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
832 1 0.00
833 811 1.00
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (833 bp):
AGTCATCCTATTTCTTTATATAGGTTGAGCAGGATGCTTGGGATGCTGCACATTCTGCCACACAC
CATTCAGAGCATTTGATGGTGGCTTGACCATTCTAGGTCGTGCATGTTCTTTTCGCAACTTCATC
TCCCTTTCCACAGCTACATGGCGATATCCATCTTTCCTATGATCCAACCGAGGTCTGATTTCATG
CCTAGCCCTCTTTGAATGAGGCTTTGAACAAAATTCATCCTGTGGCTGCTGCTCATATCCCCTCT
TGGAATGCTTCTACGCTTTATGGGAAAGAGATGACGTCAAGCAAAAGGTATGAGGCGCCACCTTA
AAAGATGACTCTCCATGTTCTCTTTTGCTCGACTTGCGATATGGAAGATAGGCTTCTTTCTTATT
CCTTGGATCATAAACGAGTTTTGTTTTTACTTTTTCTTCCTTTTGAAATGGAGTCTTTGAGGAAA
AGTCCAACCTCCTTTGAACTTCTTTTTTCTTTGTCAAAGTAATAGGACACATCAAGTAATAGGAC
ACATCAAGGAAGATGAAGAAAACTCCAACTTACTTCTTGGTGCTGTAAGCCTCATTGCGGCCGAT
TTTGGGGACAAAGGTCGGTCTAAAATAAGGCCTAAAGGCTTGGGCTCAATTCCATCACCATGCCT
CTTGATTCTTGTAGAACGATGATGAGTCTTGTCCTTGTGTTGAGGGTCGACTGACAAGGGATACC
TTGTAGCCGGACTTGTCCCTTTTGGTGTTACCTCTTCTTCCCCTGCATCCTTAATGGTCAACTAC
CCATCTTTTTGAAGATTAAGCGCAACCATATGAACTGGTGTTGGGAAAAAAAT
Found at i:25885 original size:21 final size:21
Alignment explanation
Indices: 25861--25923 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
25851 CTTAAAATTA
25861 AAATTTTTTGTGCGACTATTG
1 AAATTTTTTGTGCGACTATTG
* * * *
25882 AAATCTTCT-T-AGA--ATTA
1 AAATTTTTTGTGCGACTATTG
25899 AAATTTTTTGTGCGACTATTG
1 AAATTTTTTGTGCGACTATTG
25920 AAAT
1 AAAT
25924 AAAATTAAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 8
0.65 0.17 0.17
Matches are distributed among these distances:
17 10 0.33
18 1 0.03
19 4 0.13
20 1 0.03
21 14 0.47
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.44
Consensus pattern (21 bp):
AAATTTTTTGTGCGACTATTG
Found at i:25889 original size:38 final size:38
Alignment explanation
Indices: 25847--25923 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
25837 GTCACATTTT
25847 TCTTCTTAAAATTAAAATTTTTTGTGCGACTATTGAAA
1 TCTTCTTAAAATTAAAATTTTTTGTGCGACTATTGAAA
*
25885 TCTTCTTAGAATTAAAATTTTTTGTGCGACTATTGAAA
1 TCTTCTTAAAATTAAAATTTTTTGTGCGACTATTGAAA
25923 T
1 T
25924 AAAATTAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.45
Consensus pattern (38 bp):
TCTTCTTAAAATTAAAATTTTTTGTGCGACTATTGAAA
Found at i:27263 original size:360 final size:356
Alignment explanation
Indices: 26604--27288 Score: 1048
Period size: 360 Copynumber: 1.9 Consensus size: 356
26594 AGTCAAATGA
* * * * * * * * *
26604 AGATTTTGATGAGTCTAATTTCAGCTAATAATATTATAAAAGGGTTTATAGTGTGGATATTCAAA
1 AGATTTTAATGAGTCCAATTCCAACTAATAATATTACAAAAGAGTCTACAGTGTGGACATTCAAA
*
26669 GAAAATATAGTAATAAGATTCAATTACATCAGTGCACAGGTAGTAAGGATTAGGAATGGAGTTCC
66 GAAAATATAGTAATAAGATTCAATTACATCAGTGCACAGGTAGTAAGAATTAGGAATGGAGTTCC
* ** *
26734 TACATATGATAAAGCATTTCTGCGTAGCTAATTTATGATGTGCACACAGCCACATGAAAATCTTG
131 TACATATGATAAAGCATTTCTGCGTAGCTAATTTATGATGTGCACACAACCACACAAAAAACTTG
* *
26799 ACTCTAGTGATAGTTTTCACTTTCCATAAATAGTGCCAAGGTAAATTAGAGCCTAAAGAGGGTGA
196 ACCCTAGGGATAGTTTTCACTTTCCATAAATAGTGCCAAGGTAAATTAGAGCCTAAAGAGGGTGA
*
26864 TTTTCTCTAAATAAGAATTTGATATAATGAAACAGTAGTAAAATCACCATTATTTGTATAAGGGG
261 TTTTCTCCAAATAAGAATTTGATATAATGAAACAGTAGTAAAATCACCATTATTTGTATAAGGGG
26929 ATATGACAGCATCTTCAGATTCAGGGGCCAT
326 ATATGACAGCATCTTCAGATTCAGGGGCCAT
*
26960 AGATTTTAATGAGTCCAATTCCAACTAATAATATTACAAAAGAGTCTACATTGTGGACATTCAAA
1 AGATTTTAATGAGTCCAATTCCAACTAATAATATTACAAAAGAGTCTACAGTGTGGACATTCAAA
* * * *
27025 GAAAATATGGTAATCAGATTCAATTGCATCAGTGCACAGATGGTGGTAAGAATTAGGAATGGAGT
66 GAAAATATAGTAATAAGATTCAATTACATCAGTGCAC--A-GGTAGTAAGAATTAGGAATGGAGT
*
27090 TCCTATATATGATAAAGCATTTCTGCAGTAGCTAATTTATGATGTGCACACAACCACACAAAAAA
128 TCCTACATATGATAAAGCATTTCTGC-GTAGCTAATTTATGATGTGCACACAACCACACAAAAAA
* *
27155 CTTGACCCTAGGGATGGTTTTCACTTTCCATAAATAGTGCCAAGGTAAATTAG-GCCCTAAAGTG
192 CTTGACCCTAGGGATAGTTTTCACTTTCCATAAATAGTGCCAAGGTAAATTAGAG-CCTAAAGAG
* * ** *
27219 GGTGTTTTTCTCCGAATAAGAATTTGATATAATGAAGTAGTAGTAAAGTCACCATTATTTGTATA
256 GGTGATTTTCTCCAAATAAGAATTTGATATAATGAAACAGTAGTAAAATCACCATTATTTGTATA
27284 AGGGG
321 AGGGG
27289 CCATATTTCC
Statistics
Matches: 294, Mismatches: 30, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
356 89 0.30
358 1 0.00
359 48 0.16
360 156 0.53
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (356 bp):
AGATTTTAATGAGTCCAATTCCAACTAATAATATTACAAAAGAGTCTACAGTGTGGACATTCAAA
GAAAATATAGTAATAAGATTCAATTACATCAGTGCACAGGTAGTAAGAATTAGGAATGGAGTTCC
TACATATGATAAAGCATTTCTGCGTAGCTAATTTATGATGTGCACACAACCACACAAAAAACTTG
ACCCTAGGGATAGTTTTCACTTTCCATAAATAGTGCCAAGGTAAATTAGAGCCTAAAGAGGGTGA
TTTTCTCCAAATAAGAATTTGATATAATGAAACAGTAGTAAAATCACCATTATTTGTATAAGGGG
ATATGACAGCATCTTCAGATTCAGGGGCCAT
Found at i:27332 original size:113 final size:114
Alignment explanation
Indices: 27179--27645 Score: 544
Period size: 113 Copynumber: 4.0 Consensus size: 114
27169 TGGTTTTCAC
* *
27179 TTTCCATAAATAGTGCCAAGGTAAATTAGGCCCTAAAGTGGGTGTTTTTCTCCGAATAAGAATTT
1 TTTCCATAAACAG-GCCAAGGTAAATTAGGCCCTAAAGTGGGTGATTTTCTCCGAATAAGAATTT
** *
27244 GATATAATGAAGTAGTAGTAAAGTCACCATTATTTGTATAAGGGGCCATA
65 GATATAATGAAACAGTAGTAAAATCACCATTATTTGTATAAGGGGCCATA
* * *
27294 TTTCCATAAACA-GCCAAGGTAGATTAGGGCCTAAAGTGGGTGATTTTCTCTGAATAAGAATTTG
1 TTTCCATAAACAGGCCAAGGTAAATTAGGCCCTAAAGTGGGTGATTTTCTCCGAATAAGAATTTG
* *
27358 ATATAATGAAACAGTAGTAAAGTGACCATTATTTGTATAAGGGGCCATA
66 ATATAATGAAACAGTAGTAAAATCACCATTATTTGTATAAGGGGCCATA
* * ** * *
27407 TTTCCATAAACAGTGCCAAGGTAGATTAAGCCCTAAACCGAGTGATTTTCT-CGAATAAAAATTT
1 TTTCCATAAACAG-GCCAAGGTAAATTAGGCCCTAAAGTGGGTGATTTTCTCCGAATAAGAATTT
* * * * * *
27471 GATAGAATCAAAGTAGTAGTAAAATCATCATTATTTGTATAAAGGGCCACA
65 GATATAATGAAA-CAGTAGTAAAATCACCATTATTTGTATAAGGGGCCATA
* * * *
27522 TTTCCATAAATAGTGTCAAGGTAAATTAGGCCCTAATTCCTAAAATGGGTTATTTTCTCCGAATA
1 TTTCCATAAACAG-GCCAAGGTAAATTAGG--C-----CCTAAAGTGGGTGATTTTCTCCGAATA
* *
27587 AGATTTTTGATATAATGAAACAATAGTAAAATCACCA-TAGTTTGTATAAGGGGCCATA
58 AGA-ATTTGATATAATGAAACAGTAGTAAAATCACCATTA-TTTGTATAAGGGGCCATA
27645 T
1 T
27646 GACAGCATCT
Statistics
Matches: 299, Mismatches: 40, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
113 106 0.35
114 21 0.07
115 101 0.34
117 1 0.00
122 18 0.06
123 39 0.13
124 13 0.04
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (114 bp):
TTTCCATAAACAGGCCAAGGTAAATTAGGCCCTAAAGTGGGTGATTTTCTCCGAATAAGAATTTG
ATATAATGAAACAGTAGTAAAATCACCATTATTTGTATAAGGGGCCATA
Found at i:31685 original size:2 final size:2
Alignment explanation
Indices: 31678--31704 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31668 GTAGTACTGG
31678 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 T
31705 TTGTTCTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33302 original size:26 final size:24
Alignment explanation
Indices: 33261--33317 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 24
33251 AGGATTGTTA
33261 GAAAAAAAAAAAAAGAAAGAAAAGT
1 GAAAAAAAAAAAAAG-AAGAAAAGT
*
33286 GAAAAGAAAAAAAAAGAAGAAAAAAT
1 GAAAA-AAAAAAAAAGAAG-AAAAGT
33312 GAAAAA
1 GAAAAA
33318 TACTAGGTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 9 0.31
26 20 0.69
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.04
Consensus pattern (24 bp):
GAAAAAAAAAAAAAGAAGAAAAGT
Done.