Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009921.1 Corchorus capsularis cultivar CVL-1 contig09942, 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: 17393
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.32
Found at i:665 original size:13 final size:14
Alignment explanation
Indices: 643--675 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
633 TATATTGCAA
*
643 ATTATAATATTTAT
1 ATTATTATATTTAT
657 -TTATTATATTTAT
1 ATTATTATATTTAT
670 ATTATT
1 ATTATT
676 TTAATAGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTATTATATTTAT
Found at i:714 original size:51 final size:51
Alignment explanation
Indices: 638--740 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
628 TTATATATAT
638 TGCAAATTATAATATTTATTTATTATATTTATATTATTTTAATAGTTCTTA
1 TGCAAATTATAATATTTATTTATTATATTTATATTATTTTAATAGTTCTTA
689 TGCAAATTATAATATTTATTTATTATATTTATATTATTTTAATAGTTCTTA
1 TGCAAATTATAATATTTATTTATTATATTTATATTATTTTAATAGTTCTTA
740 T
1 T
741 ATGTTTTATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (51 bp):
TGCAAATTATAATATTTATTTATTATATTTATATTATTTTAATAGTTCTTA
Found at i:716 original size:13 final size:14
Alignment explanation
Indices: 694--726 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
684 TCTTATGCAA
*
694 ATTATAATATTTAT
1 ATTATTATATTTAT
708 -TTATTATATTTAT
1 ATTATTATATTTAT
721 ATTATT
1 ATTATT
727 TTAATAGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTATTATATTTAT
Found at i:802 original size:4 final size:4
Alignment explanation
Indices: 793--818 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
783 TACTAGTTAC
793 TAAA TAAA TAAA TAAA TAAA TAAA TA
1 TAAA TAAA TAAA TAAA TAAA TAAA TA
819 GGGTACTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:6851 original size:94 final size:93
Alignment explanation
Indices: 6690--6868 Score: 245
Period size: 94 Copynumber: 1.9 Consensus size: 93
6680 TCAATCATTT
* * *
6690 TTCATAAATGAATAATGCATATTGGATCAATAAAAATCTTCTGTAAGCCATAAATTCTGATGAAA
1 TTCATAAATGAATAATACATATTGGACCAATAAAAATCTTCTGTAAGCCATAAATTCAGATGAAA
*
6755 TCC-TCTTTCAGAGTTTTCTAAAAGCAATG
66 TCCTTC-TT-AAAGTTTTCTAAAAGCAATG
* * **
6784 TTCATAAATGAATAATACATGTTGGACCAATAAAAATCTTTTGTAAGCTGTAAATTCCAG-TGAA
1 TTCATAAATGAATAATACATATTGGACCAATAAAAATCTTCTGTAAGCCATAAATT-CAGATGAA
6848 ATCCTTCTTAAAGTTTTCTAA
65 ATCCTTCTTAAAGTTTTCTAA
6869 GAGTAGTTAG
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
93 11 0.15
94 60 0.80
95 4 0.05
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (93 bp):
TTCATAAATGAATAATACATATTGGACCAATAAAAATCTTCTGTAAGCCATAAATTCAGATGAAA
TCCTTCTTAAAGTTTTCTAAAAGCAATG
Found at i:7057 original size:30 final size:31
Alignment explanation
Indices: 6998--7062 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
6988 AACTTTATGT
* * **
6998 TTTCCGATTGTACCTTTATTTTTAAAACATA
1 TTTCCAATTGTACCCTTATTTAAAAAACATA
7029 TTTCCAATTGTACCCTT-TTTAAAAAACATA
1 TTTCCAATTGTACCCTTATTTAAAAAACATA
7059 TTTC
1 TTTC
7063 TAAATTGTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 15 0.50
31 15 0.50
ACGTcount: A:0.31, C:0.18, G:0.05, T:0.46
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTATTTAAAAAACATA
Found at i:7533 original size:196 final size:198
Alignment explanation
Indices: 7199--7588 Score: 626
Period size: 196 Copynumber: 2.0 Consensus size: 198
7189 ATTATAAGAA
* *
7199 AGTCAATTTGACTTTTTGTTTCTAACGTCCTATTTAATTTTACATTTTGTCGTTATTTCCAATCA
1 AGTCAATTTGACTTTTTGTTTCCAACGTCCTATTTAATTTTACATTATGTCGTTATTTCCAATCA
* *
7264 TTGTATTTAATTTTGCTTTTTGTCTTTTTCTCCAACGTCGTATTTGGGCTTAGATAATCTGAAGC
66 TTGTATTTAATTTTCCTTTTTGTCTTTTTCTCCAACGTCCTATTTGGGCTTAGATAATCTGAAGC
* * * *
7329 AAGTGTGCATTGGGTCTTTGCTTT-AGATGGTCC-A-ATTTCTCATTCCTATAGGGCCTTTTTTT
131 AAGTGTGCAATGAGTCTTTGCTTTGA-ATGATCCAATATTTCTCAATCCTATAGGGCCTTTTTTT
7391 TATC
195 TATC
* * *
7395 AGTCAATTTGACTTTTTGTTTCCAACGTCCTATTTAATTTTGCCA-TATGTCTTTGTTTCCAATC
1 AGTCAATTTGACTTTTTGTTTCCAACGTCCTATTTAATTTT-ACATTATGTCGTTATTTCCAATC
7459 ATTGTATTTAATTTTCCTTTTTGTCTTTTTCTCCAACGTCCTATTTGGGCTTAGATAATCTGAAG
65 ATTGTATTTAATTTTCCTTTTTGTCTTTTTCTCCAACGTCCTATTTGGGCTTAGATAATCTGAAG
*
7524 CAAGTGTGCAATGAGTTTTTGCTTTGAATGATCCAATATTTCTCAATCCTATAGGGCCTTTTTTT
130 CAAGTGTGCAATGAGTCTTTGCTTTGAATGATCCAATATTTCTCAATCCTATAGGGCCTTTTTTT
7589 GATCCGTTTT
Statistics
Matches: 178, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
196 147 0.83
197 4 0.02
198 27 0.15
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.48
Consensus pattern (198 bp):
AGTCAATTTGACTTTTTGTTTCCAACGTCCTATTTAATTTTACATTATGTCGTTATTTCCAATCA
TTGTATTTAATTTTCCTTTTTGTCTTTTTCTCCAACGTCCTATTTGGGCTTAGATAATCTGAAGC
AAGTGTGCAATGAGTCTTTGCTTTGAATGATCCAATATTTCTCAATCCTATAGGGCCTTTTTTTT
ATC
Found at i:7667 original size:19 final size:20
Alignment explanation
Indices: 7640--7677 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
7630 TACTATTATT
7640 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
7660 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
7678 ACTGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:7668 original size:196 final size:193
Alignment explanation
Indices: 7258--7625 Score: 454
Period size: 196 Copynumber: 1.9 Consensus size: 193
7248 TCGTTATTTC
* *
7258 CAATCATTGTATTTAATTTTGCTTTTTGTCTTTTTCTCCAACGTCGTATTTGGGCTTAGATAATC
1 CAATCATTGTATTTAATTTTCCTTTTTGTCTTTTTCTCCAACGTCCTATTTGGGCTTAGATAATC
* * * *
7323 TGAAGCAAGTGTGCATTGGGTCTTTGCTTTAGATGGTCCAATTTCTCATTCCTATAGGGCCTTTT
66 TGAAGCAAGTGTGCAATGAGTCTTTGCTTTAGATGATCCAATTTCTCAATCCTATAGGGCCTTTT
* *** ** * ** * *
7388 TTTTATCAGTCAATTTGACTTTTTGTTTCCAACGTCCTATTTAATTTTGCCATATGTCTTTGTTT
131 TTTGATCAGT--ATTTGACTTTTTAAGTAAAACATCAAATTTAACTTTACCATATGTCTTTGTTT
7453 CCAATCATTGTATTTAATTTTCCTTTTTGTCTTTTTCTCCAACGTCCTATTTGGGCTTAGATAAT
1 -CAATCATTGTATTTAATTTTCCTTTTTGTCTTTTTCTCCAACGTCCTATTTGGGCTTAGATAAT
*
7518 CTGAAGCAAGTGTGCAATGAGTTTTTGCTTT-GAATGATCCAATATTTCTCAATCCTATAGGGCC
65 CTGAAGCAAGTGTGCAATGAGTCTTTGCTTTAG-ATGATCC-A-ATTTCTCAATCCTATAGGGCC
* * *
7582 TTTTTTTGATCCGT-TTT-ACTATTATTAAGTAAAATATTAAATTT
127 TTTTTTTGATCAGTATTTGACT-TT-TTAAGTAAAACATCAAATTT
7626 CCTTTACTAT
Statistics
Matches: 148, Mismatches: 19, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
194 3 0.02
195 6 0.04
196 106 0.72
197 1 0.01
198 32 0.22
ACGTcount: A:0.22, C:0.17, G:0.15, T:0.46
Consensus pattern (193 bp):
CAATCATTGTATTTAATTTTCCTTTTTGTCTTTTTCTCCAACGTCCTATTTGGGCTTAGATAATC
TGAAGCAAGTGTGCAATGAGTCTTTGCTTTAGATGATCCAATTTCTCAATCCTATAGGGCCTTTT
TTTGATCAGTATTTGACTTTTTAAGTAAAACATCAAATTTAACTTTACCATATGTCTTTGTTT
Found at i:7975 original size:22 final size:22
Alignment explanation
Indices: 7842--7982 Score: 86
Period size: 22 Copynumber: 6.3 Consensus size: 22
7832 TTGTCTCTAT
* * *
7842 GTGGTTATCAAAATTTTATAAG
1 GTGGTTATTAAAATTTCATAGG
* * *
7864 ATGGTTAGTATAATTTCAT-GAG
1 GTGGTTATTAAAATTTCATAG-G
* * * *
7886 GAGGTTATCAAAATTCCATAGT
1 GTGGTTATTAAAATTTCATAGG
**
7908 GTGGTTACCAAAATTTCATAGG
1 GTGGTTATTAAAATTTCATAGG
* * **
7930 ATCAAGTTATTAAAATTTTTTAGG
1 GT--GGTTATTAAAATTTCATAGG
* *
7954 TTGGTTATTGAAATTTCATAGG
1 GTGGTTATTAAAATTTCATAGG
7976 GTGGTTA
1 GTGGTTA
7983 ATTATCACAA
Statistics
Matches: 86, Mismatches: 29, Indels: 8
0.70 0.24 0.07
Matches are distributed among these distances:
22 69 0.80
23 1 0.01
24 16 0.19
ACGTcount: A:0.33, C:0.07, G:0.21, T:0.40
Consensus pattern (22 bp):
GTGGTTATTAAAATTTCATAGG
Found at i:8043 original size:22 final size:21
Alignment explanation
Indices: 8018--8409 Score: 136
Period size: 22 Copynumber: 17.7 Consensus size: 21
8008 ATCAAAGAGA
*
8018 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
*
8040 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAG-GAGG
*
8062 TTAACAAAATTTCATTAGGAGG
1 TTATCAAAATTTCA-TAGGAGG
* * *
8084 TTA-CTAATATTTCATGGGGAGA
1 TTATC-AAAATTTCAT-AGGAGG
* * *
8106 TTGTCAAAATTTTATAGCGTGG
1 TTATCAAAATTTCATAG-GAGG
* *
8128 TCATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATA-GGAGG
*
8150 TTATAAAAGTCTCAATTTCATA--AGG
1 TTAT-CAA-----AATTTCATAGGAGG
* * * *
8175 AGTACCAAAATTTGATAGAAGG
1 -TTATCAAAATTTCATAGGAGG
*
8197 TTATC-AAATCTCATA-GAGTG
1 TTATCAAAATTTCATAGGAG-G
* *
8217 ATTATCGAAATTTCATAGAGATCAGA
1 -TTATCAAAATTTCATAG-G---AGG
*
8243 TTATCAAAATTT-ATAGGAAGA
1 TTATCAAAATTTCATAGG-AGG
**
8264 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAG-GAGG
*
8286 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
* * * *
8308 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCAT-AGGAGG
* *
8330 TTATTAGAATTTCATA-GAGG
1 TTATCAAAATTTCATAGGAGG
* * * *
8350 -GATCAAAAAATTTTTATAAAGATG
1 TTATC--AAAA-TTTCAT-AGGAGG
*
8374 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
8396 TTATCAAATTTTCA
1 TTATCAAAATTTCA
8410 AAATGTGATT
Statistics
Matches: 276, Mismatches: 60, Indels: 68
0.68 0.15 0.17
Matches are distributed among these distances:
19 4 0.01
20 19 0.07
21 32 0.12
22 164 0.59
23 17 0.06
24 8 0.03
25 19 0.07
26 2 0.01
27 2 0.01
28 9 0.03
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:8540 original size:20 final size:20
Alignment explanation
Indices: 8515--8566 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
8505 TTATGGAGTA
*
8515 ATCAAAATTTCAATGAGGAT
1 ATCAAAATTTCAAGGAGGAT
*
8535 ATCAAAATTTCAGGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
*
8555 ATCACAATTTCA
1 ATCAAAATTTCA
8567 TAGTTTAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.29
Consensus pattern (20 bp):
ATCAAAATTTCAAGGAGGAT
Found at i:8603 original size:22 final size:22
Alignment explanation
Indices: 8578--8826 Score: 92
Period size: 22 Copynumber: 11.5 Consensus size: 22
8568 AGTTTAGTTT
8578 TCAAAATTTCATAAGAGGGTTA
1 TCAAAATTTCATAAGAGGGTTA
* *
8600 TCAAAATTTCAT-AGTA-TGTAGA
1 TCAAAATTTCATAAG-AGGGT-TA
*
8622 TCAAAATTTTAT-AG-GGAGATTA
1 TCAAAATTTCATAAGAGG-G-TTA
* * *
8644 ACAAAATTTCATAATAAGGTTA
1 TCAAAATTTCATAAGAGGGTTA
* ** *
8666 TTAAAAAATCAT-AGCGAGGTTA
1 TCAAAATTTCATAAGAG-GGTTA
*
8688 TCAAAATTT-GT---A--GTTA
1 TCAAAATTTCATAAGAGGGTTA
* **
8704 TCAAGATTTCATAAGAAAGTTA
1 TCAAAATTTCATAAGAGGGTTA
* * *
8726 TCAAAATTTTATAGGGAGGTTTA
1 TCAAAATTTCATA-AGAGGGTTA
* * **
8749 TCAAAATTTTATAGGAAGATTTA
1 TCAAAATTTCATAAG-AGGGTTA
** *
8772 TCAAAATTTCATATCAAGGTTA
1 TCAAAATTTCATAAGAGGGTTA
* *
8794 T-AACAATTTCAT-AGTGTGATTA
1 TCAA-AATTTCATAAGAG-GGTTA
8816 TCAAAATTTCA
1 TCAAAATTTCA
8827 GATTGTGATT
Statistics
Matches: 167, Mismatches: 41, Indels: 38
0.68 0.17 0.15
Matches are distributed among these distances:
16 12 0.07
17 1 0.01
20 1 0.01
21 8 0.05
22 103 0.62
23 41 0.25
24 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (22 bp):
TCAAAATTTCATAAGAGGGTTA
Found at i:8751 original size:23 final size:23
Alignment explanation
Indices: 8701--8780 Score: 99
Period size: 23 Copynumber: 3.5 Consensus size: 23
8691 AAATTTGTAG
* * * *
8701 TTATCAAGATTTCATAAGAA-AG
1 TTATCAAAATTTTATAGGAAGAT
* *
8723 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGAAGAT
8746 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGAAGAT
8769 TTATCAAAATTT
1 TTATCAAAATTT
8781 CATATCAAGG
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 16 0.33
23 33 0.67
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGAT
Found at i:8998 original size:22 final size:22
Alignment explanation
Indices: 8973--9072 Score: 76
Period size: 22 Copynumber: 4.6 Consensus size: 22
8963 TTGAGGTCTT
* * *
8973 CAAAATTCCTTAGGGAGGTTAA
1 CAAAATTCCATAAGAAGGTTAA
*
8995 CAAAATTTCATAAGAAGGTTAA
1 CAAAATTCCATAAGAAGGTTAA
* * **
9017 CAAAATT-TATAAAAAGGTTCT
1 CAAAATTCCATAAGAAGGTTAA
* * * *
9038 CGAAATTTCATAGGAAGGTTAT
1 CAAAATTCCATAAGAAGGTTAA
*
9060 CAAAATTTCATAA
1 CAAAATTCCATAA
9073 TGGGATCATA
Statistics
Matches: 62, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
21 16 0.26
22 46 0.74
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (22 bp):
CAAAATTCCATAAGAAGGTTAA
Found at i:9021 original size:44 final size:43
Alignment explanation
Indices: 8923--9023 Score: 116
Period size: 44 Copynumber: 2.3 Consensus size: 43
8913 TAATAGTGTT
*
8923 GGTTATCAAAATTTCATTGGGAAGTTAACAAAATTTCATATTGA
1 GGTTATCAAAA-TTCATTGGGAAGTTAACAAAATTTCATATAGA
* *
8967 GGTCT-TCAAAATTCCTTAGGGAGGTTAACAAAATTTCATA-AGAA
1 GGT-TATCAAAATTCATT-GGGAAGTTAACAAAATTTCATATAG-A
*
9011 GGTTAACAAAATT
1 GGTTATCAAAATT
9024 TATAAAAAGG
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
43 7 0.14
44 41 0.84
45 1 0.02
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.33
Consensus pattern (43 bp):
GGTTATCAAAATTCATTGGGAAGTTAACAAAATTTCATATAGA
Found at i:10031 original size:79 final size:78
Alignment explanation
Indices: 9918--10166 Score: 331
Period size: 79 Copynumber: 3.2 Consensus size: 78
9908 GTTTTTTAAT
*
9918 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGAATATTAGATTTAATTATATAAAAATGGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGAATATTAGATTTAATTATATAAAAATAGA
9983 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
** * *
9996 TAAAATAGTAAAATGGTTAAAATATTTTAGTTATAAGGATATTAGCTTTAATTATATAAAAATAG
1 TAAAATAGTAAAATGG-TAAAATATAATAGTTATAAGAATATTAGATTTAATTATATAAAAATAG
*
10061 AGTTTTTAGTTTAG
65 AGTTTTTAGTTGAG
* * * * * *
10075 TAAAATAGTAAAATAGTCAAATAAAAATAGTTATAA-AGATGTTATATTTAATTAAATAAAAATA
1 TAAAATAGTAAAATGGTAAAAT-ATAATAGTTATAAGA-ATATTAGATTTAATTATATAAAAATA
*
10139 GAGTTTTTAGTTGAC
64 GAGTTTTTAGTTGAG
10154 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
10167 ACCTAAACAA
Statistics
Matches: 149, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
78 21 0.14
79 126 0.85
80 2 0.01
ACGTcount: A:0.48, C:0.02, G:0.13, T:0.37
Consensus pattern (78 bp):
TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGAATATTAGATTTAATTATATAAAAATAGA
GTTTTTAGTTGAG
Found at i:10272 original size:6 final size:6
Alignment explanation
Indices: 10254--10290 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
10244 GTACTTTTTA
10254 ATATAG TATATAG ATATAG --ATAG ATATAG ATATAG AT
1 ATATAG -ATATAG ATATAG ATATAG ATATAG ATATAG AT
10291 TATTTAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
4 4 0.14
6 18 0.64
7 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.35
Consensus pattern (6 bp):
ATATAG
Found at i:10282 original size:16 final size:17
Alignment explanation
Indices: 10256--10290 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
10246 ACTTTTTAAT
10256 ATAGTATATAGATATAG
1 ATAGTATATAGATATAG
10273 ATAG-ATATAGATATAG
1 ATAGTATATAGATATAG
10289 AT
1 AT
10291 TATTTAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (17 bp):
ATAGTATATAGATATAG
Done.