Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011952.1 Corchorus capsularis cultivar CVL-1 contig11973, 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: 6718
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Found at i:1134 original size:188 final size:188
Alignment explanation
Indices: 817--1193 Score: 754
Period size: 188 Copynumber: 2.0 Consensus size: 188
807 CGAACGTTTC
817 GACAATCATCATCAATCCAAATGTTCAGATTCCTCCTCCACTCATCTTTCCCCTATCTTTAAAGC
1 GACAATCATCATCAATCCAAATGTTCAGATTCCTCCTCCACTCATCTTTCCCCTATCTTTAAAGC
882 CTTTGTTTGAGGAACTTTTTCTTCATCATCTAATCTGTTTTGTCGAGTTTATGCTCTTCTTCTTG
66 CTTTGTTTGAGGAACTTTTTCTTCATCATCTAATCTGTTTTGTCGAGTTTATGCTCTTCTTCTTG
947 TTGCTTCTTTGCTTTGTTAATCCTTGATTCTTGTTTAATTTTGGATTCCCGATTTCTT
131 TTGCTTCTTTGCTTTGTTAATCCTTGATTCTTGTTTAATTTTGGATTCCCGATTTCTT
1005 GACAATCATCATCAATCCAAATGTTCAGATTCCTCCTCCACTCATCTTTCCCCTATCTTTAAAGC
1 GACAATCATCATCAATCCAAATGTTCAGATTCCTCCTCCACTCATCTTTCCCCTATCTTTAAAGC
1070 CTTTGTTTGAGGAACTTTTTCTTCATCATCTAATCTGTTTTGTCGAGTTTATGCTCTTCTTCTTG
66 CTTTGTTTGAGGAACTTTTTCTTCATCATCTAATCTGTTTTGTCGAGTTTATGCTCTTCTTCTTG
1135 TTGCTTCTTTGCTTTGTTAATCCTTGATTCTTGTTTAATTTTGGATTCCCGATTTCTT
131 TTGCTTCTTTGCTTTGTTAATCCTTGATTCTTGTTTAATTTTGGATTCCCGATTTCTT
1193 G
1 G
1194 CTTTTGATTG
Statistics
Matches: 189, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
188 189 1.00
ACGTcount: A:0.18, C:0.23, G:0.12, T:0.47
Consensus pattern (188 bp):
GACAATCATCATCAATCCAAATGTTCAGATTCCTCCTCCACTCATCTTTCCCCTATCTTTAAAGC
CTTTGTTTGAGGAACTTTTTCTTCATCATCTAATCTGTTTTGTCGAGTTTATGCTCTTCTTCTTG
TTGCTTCTTTGCTTTGTTAATCCTTGATTCTTGTTTAATTTTGGATTCCCGATTTCTT
Found at i:1506 original size:27 final size:27
Alignment explanation
Indices: 1459--1539 Score: 108
Period size: 27 Copynumber: 3.0 Consensus size: 27
1449 GCATTAGGGT
*
1459 CACCCAAGGGCATTTTGGGTCATTTTTG
1 CACCCAGGGGCATTTT-GGTCATTTTTG
*
1487 TACCCAGGGGCATTTTGGTCATTTTTG
1 CACCCAGGGGCATTTTGGTCATTTTTG
* * *
1514 CACTCAGGGGTATTTTAGTCATTTTT
1 CACCCAGGGGCATTTTGGTCATTTTT
1540 AGGTTCACCT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 33 0.70
28 14 0.30
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.41
Consensus pattern (27 bp):
CACCCAGGGGCATTTTGGTCATTTTTG
Found at i:2228 original size:16 final size:16
Alignment explanation
Indices: 2207--2240 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2197 ATTTGGACCT
2207 TGCAAAGAAAAAGAAA
1 TGCAAAGAAAAAGAAA
* *
2223 TGCAAAGCACAAGAAA
1 TGCAAAGAAAAAGAAA
2239 TG
1 TG
2241 TTCCCCAAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.12, G:0.21, T:0.09
Consensus pattern (16 bp):
TGCAAAGAAAAAGAAA
Found at i:4384 original size:51 final size:50
Alignment explanation
Indices: 4273--4721 Score: 373
Period size: 51 Copynumber: 8.8 Consensus size: 50
4263 AAGTTTATCA
* * * * * *
4273 TTTGAATAAAAGATTGAATTTTTGAGTAATTGGAAAATAAAAATGTCATC
1 TTTGAATAAAAGATTGAATTTTTAAGTAATTAGTAAATAAAAATTTAAGC
** * * *
4323 TTTGGGTAAAAGATTGAATTTTTAAAGTGATTAGCAAATAAAGATTTAAGC
1 TTTGAATAAAAGATTGAATTTTT-AAGTAATTAGTAAATAAAAATTTAAGC
* * * *** **
4374 TTTGAATAAAAGATTGAATTTTTATGTAATTGGAAAATAAAAATGCCATA
1 TTTGAATAAAAGATTGAATTTTTAAGTAATTAGTAAATAAAAATTTAAGC
** * * *
4424 TTTGGGTAAAAGATTGAATTTTTAAAGTGATTAGCAAATAAAATTTTAAGC
1 TTTGAATAAAAGATTGAATTTTT-AAGTAATTAGTAAATAAAAATTTAAGC
* * ** * *
4475 TTTGAATAAAAGATTGAATTTTTATGTAATTGGTAAATAAAAAACGTCATC
1 TTTGAATAAAAGATTGAATTTTTAAGTAATTAGTAAAT-AAAAATTTAAGC
* * * *
4526 TTTGAGTTAAAAAGATTGAATCTTTAGAGTAATTAGTAAATTAAAGATTTAACC
1 TTTGA-AT-AAAAGATTGAATTTTTA-AGTAATTAGTAAA-TAAAAATTTAAGC
* * * *
4580 TTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAGT-AAAATGTCATG-
1 TTTGAATAAAAGATTGAATTTTTAAGTAATTAGTAAATAAAAAT-TTAAGC
** * * **
4629 TTTGGGTAAAAGATTGAATCTTTAGAGTGATTAGTAAATAAAGCTTTAA-C
1 TTTGAATAAAAGATTGAATTTTTA-AGTAATTAGTAAATAAAAATTTAAGC
* *
4679 ATTTGAATGAAAGATTGAACTTTTAAGTAATTAGTAAATAAAA
1 -TTTGAATAAAAGATTGAATTTTTAAGTAATTAGTAAATAAAA
4722 TGTTACCTTT
Statistics
Matches: 308, Mismatches: 79, Indels: 24
0.75 0.19 0.06
Matches are distributed among these distances:
49 25 0.08
50 102 0.33
51 123 0.40
52 17 0.06
53 17 0.06
54 23 0.07
55 1 0.00
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (50 bp):
TTTGAATAAAAGATTGAATTTTTAAGTAATTAGTAAATAAAAATTTAAGC
Found at i:4448 original size:101 final size:101
Alignment explanation
Indices: 4273--4721 Score: 616
Period size: 101 Copynumber: 4.4 Consensus size: 101
4263 AAGTTTATCA
* *
4273 TTTGAATAAAAGATTGAATTTTTGAGTAATTGGAAAATAAAAATGTCATCTTTGGGTAAAAGATT
1 TTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAAATGTCATCTTTGGGTAAAAGATT
*
4338 GAATTTTTAAAGTGATTAGCAAATAAAGATTTAAGC
66 GAATCTTTAAAGTGATTAGCAAATAAAGATTTAAGC
* * * *
4374 TTTGAATAAAAGATTGAATTTTTATGTAATTGGAAAATAAAAATGCCATATTTGGGTAAAAGATT
1 TTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAAATGTCATCTTTGGGTAAAAGATT
*
4439 GAATTTTTAAAGTGATTAGCAAATAAA-ATTTTAAGC
66 GAATCTTTAAAGTGATTAGCAAATAAAGA-TTTAAGC
* * *
4475 TTTGAATAAAAGATTGAATTTTTATGTAATTGGTAAATAAAAAACGTCATCTTTGAGTTAAAAAG
1 TTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAAT-AAAAATGTCATCTTTG-GGT-AAAAG
* * * *
4540 ATTGAATCTTTAGAGTAATTAGTAAATTAAAGATTTAACC
63 ATTGAATCTTTAAAGTGATTAGCAAA-TAAAGATTTAAGC
* *
4580 TTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAGT-AAAATGTCATGTTTGGGTAAAAGATT
1 TTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAAATGTCATCTTTGGGTAAAAGATT
* * *
4644 GAATCTTTAGAGTGATTAGTAAATAAAGCTTTAA-C
66 GAATCTTTAAAGTGATTAGCAAATAAAGATTTAAGC
* * *
4679 ATTTGAATGAAAGATTGAACTTTTAAGTAATTAGTAAATAAAA
1 -TTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAA
4722 TGTTACCTTT
Statistics
Matches: 315, Mismatches: 25, Indels: 16
0.88 0.07 0.04
Matches are distributed among these distances:
99 1 0.00
100 45 0.14
101 165 0.52
102 15 0.05
103 15 0.05
104 27 0.09
105 46 0.15
106 1 0.00
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (101 bp):
TTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAAATGTCATCTTTGGGTAAAAGATT
GAATCTTTAAAGTGATTAGCAAATAAAGATTTAAGC
Found at i:4670 original size:205 final size:202
Alignment explanation
Indices: 4266--4721 Score: 630
Period size: 205 Copynumber: 2.2 Consensus size: 202
4256 GGCTAAGAAG
* * *
4266 TTTATCATTTGAATAAAAGATTGAATTTTTGAGTAATTGGAAAAT-AAAAATGTCATCTTTGGGT
1 TTTAACATTTGAATAAAAGATTGAATTTTT-AGTAATTGGTAAATAAAAAACGTCATCTTTGGGT
* * *
4330 AAAAGATTGAATTTTTAAAGTGATTAGCAAATAAAGATTTAAGCTTTGAATAAAAGATTGAATTT
65 AAAAGATTGAATCTTTAAAGTAATTAGCAAATAAAGATTTAACCTTTGAATAAAAGATTGAATTT
* *
4395 TTATGTAATTGGAAAATAAAAATGCCATATTTGGGTAAAAGATTGAATTTTTAAAGTGATTAGCA
130 TTAAGTAATTGGAAAATAAAAATGCCATATTTGGGTAAAAGATTGAATCTTTAAAGTGATTAGCA
*
4460 AATAAAAT
195 AATAAAAC
4468 TTTAAGC-TTTGAATAAAAGATTGAATTTTTATGTAATTGGTAAATAAAAAACGTCATCTTTGAG
1 TTTAA-CATTTGAATAAAAGATTGAATTTTTA-GTAATTGGTAAATAAAAAACGTCATCTTTG-G
* * *
4532 TTAAAAAGATTGAATCTTTAGAGTAATTAGTAAATTAAAGATTTAACCTTTGAATAAAAGATTGA
63 GT-AAAAGATTGAATCTTTAAAGTAATTAGCAAA-TAAAGATTTAACCTTTGAATAAAAGATTGA
* * * * *
4597 ATTTTTAAGTAATTGGTAAGT-AAAATGTCATGTTTGGGTAAAAGATTGAATCTTTAGAGTGATT
126 ATTTTTAAGTAATTGGAAAATAAAAATGCCATATTTGGGTAAAAGATTGAATCTTTAAAGTGATT
* *
4661 AGTAAATAAAGC
191 AGCAAATAAAAC
* * *
4673 TTTAACATTTGAATGAAAGATTGAACTTTTAAGTAATTAGTAAATAAAA
1 TTTAACATTTGAATAAAAGATTGAA-TTTTTAGTAATTGGTAAATAAAA
4722 TGTTACCTTT
Statistics
Matches: 224, Mismatches: 22, Indels: 13
0.86 0.08 0.05
Matches are distributed among these distances:
201 1 0.00
202 39 0.17
203 16 0.07
204 3 0.01
205 113 0.50
206 52 0.23
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (202 bp):
TTTAACATTTGAATAAAAGATTGAATTTTTAGTAATTGGTAAATAAAAAACGTCATCTTTGGGTA
AAAGATTGAATCTTTAAAGTAATTAGCAAATAAAGATTTAACCTTTGAATAAAAGATTGAATTTT
TAAGTAATTGGAAAATAAAAATGCCATATTTGGGTAAAAGATTGAATCTTTAAAGTGATTAGCAA
ATAAAAC
Found at i:4750 original size:50 final size:51
Alignment explanation
Indices: 4273--4771 Score: 270
Period size: 51 Copynumber: 9.8 Consensus size: 51
4263 AAGTTTATCA
* * * * * * * *
4273 TTTGAA-TAAAAGATTGAATTTTTGAGTAATTGGAAAATAAAAATGTCATC
1 TTTGAATTAAAAGATTGAACTTTTAAGTAATTAGTAAATAAAGATTTAACC
** * * * *
4323 TTTG-GGTAAAAGATTGAATTTTTAAAGTGATTAGCAAATAAAGATTTAAGC
1 TTTGAATTAAAAGATTGAACTTTT-AAGTAATTAGTAAATAAAGATTTAACC
* * * * * *** **
4374 TTTGAA-TAAAAGATTGAATTTTTATGTAATTGGAAAATAAAAATGCCATA
1 TTTGAATTAAAAGATTGAACTTTTAAGTAATTAGTAAATAAAGATTTAACC
** * * * *
4424 TTTG-GGTAAAAGATTGAATTTTTAAAGTGATTAGCAAATAAA-ATTTTAAGC
1 TTTGAATTAAAAGATTGAACTTTT-AAGTAATTAGTAAATAAAGA-TTTAACC
* * * * ** * *
4475 TTTGAA-TAAAAGATTGAATTTTTATGTAATTGGTAAATAAAAAACGTCATC
1 TTTGAATTAAAAGATTGAACTTTTAAGTAATTAGTAAAT-AAAGATTTAACC
*
4526 TTTGAGTTAAAAAGATTGAA-TCTTTAGAGTAATTAGTAAATTAAAGATTTAACC
1 TTTGAATT-AAAAGATTGAACT-TTTA-AGTAATTAGTAAA-TAAAGATTTAACC
* * * * * **
4580 TTTGAA-TAAAAGATTGAATTTTTAAGTAATTGGTAAGTAAA-ATGTCATG
1 TTTGAATTAAAAGATTGAACTTTTAAGTAATTAGTAAATAAAGATTTAACC
** * * *
4629 TTTG-GGTAAAAGATTGAA-TCTTTAGAGTGATTAGTAAATAAAGCTTTAACA
1 TTTGAATTAAAAGATTGAACT-TTTA-AGTAATTAGTAAATAAAGATTTAACC
*
4680 TTTGAA-TGAAAGATTGAACTTTTAAGTAATTAGTAAATAAA-ATGTT-ACC
1 TTTGAATTAAAAGATTGAACTTTTAAGTAATTAGTAAATAAAGAT-TTAACC
* * * * **
4729 TTTGAATTAGAAGTTTAAACTTTTTAGGCCATTAGTAAATAAA
1 TTTGAATTAAAAGATTGAAC-TTTTAAGTAATTAGTAAATAAA
4772 TTGATTAGTT
Statistics
Matches: 350, Mismatches: 75, Indels: 47
0.74 0.16 0.10
Matches are distributed among these distances:
48 1 0.00
49 33 0.09
50 116 0.33
51 140 0.40
52 19 0.05
53 17 0.05
54 23 0.07
55 1 0.00
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.37
Consensus pattern (51 bp):
TTTGAATTAAAAGATTGAACTTTTAAGTAATTAGTAAATAAAGATTTAACC
Found at i:5594 original size:48 final size:47
Alignment explanation
Indices: 5441--5602 Score: 252
Period size: 47 Copynumber: 3.4 Consensus size: 47
5431 ATAGTAAAAA
5441 GGTAATCAGTAAATCAGTAAAAAGAGATTAATCGGAGTCAAAGTGAT
1 GGTAATCAGTAAATCAGTAAAAAGAGATTAATCGGAGTCAAAGTGAT
*
5488 GGTAATCAGTAAAACAGTAAAAAGAGATTAATCGGAGTCAAAGTGAT
1 GGTAATCAGTAAATCAGTAAAAAGAGATTAATCGGAGTCAAAGTGAT
* ** * *
5535 GGTAATCAGTAAATCAGTGAAAAGAGATTAATCAAAAGTCAAGGTAAT
1 GGTAATCAGTAAATCAGTAAAAAGAGATTAATC-GGAGTCAAAGTGAT
*
5583 AGTAATCAGTAAATCAGTAA
1 GGTAATCAGTAAATCAGTAA
5603 TCAAGTAAAA
Statistics
Matches: 105, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
47 77 0.73
48 28 0.27
ACGTcount: A:0.47, C:0.09, G:0.22, T:0.23
Consensus pattern (47 bp):
GGTAATCAGTAAATCAGTAAAAAGAGATTAATCGGAGTCAAAGTGAT
Found at i:5720 original size:74 final size:71
Alignment explanation
Indices: 5563--5721 Score: 169
Period size: 74 Copynumber: 2.2 Consensus size: 71
5553 GAAAAGAGAT
* * * *
5563 TAATCAAAAGTCAAGGTAATAGTAATCAGTAAATCAGTAATCAAGTAAAAACATAGTAATCAGTA
1 TAATTAAAAGTCAAGGTAAGAGTAATCAGTAAATAAGTAATCAAGTAAAAAAATAGTAATCAGTA
*
5628 AATTGA
66 AATAGA
** * *
5634 TAATTACGAGTCAAGGTAAGAGATTAATCAGTAATTAAG-AGTCAAGGTAAAAAAAATAGTAATC
1 TAATTAAAAGTCAAGGTAAGAG--TAATCAGTAAATAAGTAATCAA-GT-AAAAAAATAGTAATC
5698 AGTAAATCAG-
62 AGTAAAT-AGA
*
5708 TGATTAAAAGTCAA
1 TAATTAAAAGTCAA
5722 TAGATTGATC
Statistics
Matches: 71, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
71 18 0.25
72 5 0.07
73 15 0.21
74 32 0.45
75 1 0.01
ACGTcount: A:0.50, C:0.09, G:0.16, T:0.25
Consensus pattern (71 bp):
TAATTAAAAGTCAAGGTAAGAGTAATCAGTAAATAAGTAATCAAGTAAAAAAATAGTAATCAGTA
AATAGA
Found at i:5855 original size:35 final size:36
Alignment explanation
Indices: 5815--5964 Score: 112
Period size: 35 Copynumber: 4.2 Consensus size: 36
5805 TTCTAAAGAG
*
5815 TAATCAGTAAAGGAGA-AATGATAAAGAGTAAATAA
1 TAATCAGTAAAGGAGAGAATGATAAAGAGTAAAAAA
* * *
5850 TAATCACT-AAGGAG-TAATTAGTAAAGAGTAAAAAAA
1 TAATCAGTAAAGGAGAGAATGA-TAAAGAGT-AAAAAA
* * * * * *
5886 GTAATCAGCAAAAGA-AGAACGGTAAAAAGTAAAGAA
1 -TAATCAGTAAAGGAGAGAATGATAAAGAGTAAAAAA
* * *
5922 TAATCAGTAAA-GAAAGAATGGTAAAGAGTAAAAGGA
1 TAATCAGTAAAGGAGAGAATGATAAAGAGTAAAA-AA
5958 TAATCAG
1 TAATCAG
5965 CAAAAAGTAA
Statistics
Matches: 90, Mismatches: 17, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
34 12 0.13
35 41 0.46
36 18 0.20
37 13 0.14
38 6 0.07
ACGTcount: A:0.56, C:0.05, G:0.21, T:0.18
Consensus pattern (36 bp):
TAATCAGTAAAGGAGAGAATGATAAAGAGTAAAAAA
Found at i:5924 original size:72 final size:71
Alignment explanation
Indices: 5836--5969 Score: 164
Period size: 72 Copynumber: 1.9 Consensus size: 71
5826 GGAGAAATGA
* * *
5836 TAAAGAGTAAATAATAATCACT-AAG-GAGTAATTAGTAAAGAGTAAAAAAAGTAATCAGCAAAA
1 TAAAAAGTAAAGAATAATCACTAAAGAAAG-AA-TAGTAAAGAGTAAAAAAA-TAATCAGCAAAA
5899 GAAGAACGG
63 GAAGAACGG
* * **
5908 TAAAAAGTAAAGAATAATCAGTAAAGAAAGAATGGTAAAGAGTAAAAGGATAATCAGCAAAA
1 TAAAAAGTAAAGAATAATCACTAAAGAAAGAATAGTAAAGAGTAAAAAAATAATCAGCAAAA
5970 AGTAAAAAGA
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
71 12 0.23
72 34 0.64
73 5 0.09
74 2 0.04
ACGTcount: A:0.57, C:0.06, G:0.19, T:0.17
Consensus pattern (71 bp):
TAAAAAGTAAAGAATAATCACTAAAGAAAGAATAGTAAAGAGTAAAAAAATAATCAGCAAAAGAA
GAACGG
Found at i:6154 original size:22 final size:21
Alignment explanation
Indices: 6072--6159 Score: 79
Period size: 21 Copynumber: 4.1 Consensus size: 21
6062 AGGTAACCAT
* *
6072 TAAGAGTAAAACAGTAACCAG
1 TAAGAGTAAAAGAGTAATCAG
* * * *
6093 TGAGAG-CAAAGTGGTAATTAG
1 TAAGAGTAAAAG-AGTAATCAG
* *
6114 TAAGAGTCAAATAGTAATCAG
1 TAAGAGTAAAAGAGTAATCAG
6135 TAAGAAGTAAAAGAGTAATCAG
1 TAAG-AGTAAAAGAGTAATCAG
6157 TAA
1 TAA
6160 AAAAGGAGCA
Statistics
Matches: 52, Mismatches: 12, Indels: 5
0.75 0.17 0.07
Matches are distributed among these distances:
20 3 0.06
21 27 0.52
22 22 0.42
ACGTcount: A:0.49, C:0.08, G:0.23, T:0.20
Consensus pattern (21 bp):
TAAGAGTAAAAGAGTAATCAG
Found at i:6158 original size:15 final size:15
Alignment explanation
Indices: 6140--6195 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
6130 ATCAGTAAGA
6140 AGTAAAAGAGTAATC
1 AGTAAAAGAGTAATC
* * *
6155 AGTAAAAAAG-GAGC
1 AGTAAAAGAGTAATC
*
6169 AG-AAAATAGTAATC
1 AGTAAAAGAGTAATC
6183 AGTAAAAGAGTAA
1 AGTAAAAGAGTAA
6196 AATGGTAATC
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
13 6 0.19
14 8 0.25
15 18 0.56
ACGTcount: A:0.57, C:0.05, G:0.21, T:0.16
Consensus pattern (15 bp):
AGTAAAAGAGTAATC
Found at i:6240 original size:43 final size:41
Alignment explanation
Indices: 6191--6295 Score: 122
Period size: 43 Copynumber: 2.5 Consensus size: 41
6181 TCAGTAAAAG
6191 AGTAAAATGGTAATCAGTAAAAAGT-AAGAAGGTAATCAACAA
1 AGTAAAATGGTAATCAGTAAAAAGTAAAGAA--TAATCAACAA
* * **
6233 CAGTAAAATAGTAATCAGTACAAAGTAAAGAATAATCAGTAA
1 -AGTAAAATGGTAATCAGTAAAAAGTAAAGAATAATCAACAA
*
6275 AATAATAATGGTAATCAGTAA
1 AGTAA-AATGGTAATCAGTAA
6296 TTCAGTAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
41 4 0.08
42 21 0.40
43 23 0.43
44 5 0.09
ACGTcount: A:0.54, C:0.08, G:0.16, T:0.22
Consensus pattern (41 bp):
AGTAAAATGGTAATCAGTAAAAAGTAAAGAATAATCAACAA
Found at i:6268 original size:21 final size:22
Alignment explanation
Indices: 6176--6273 Score: 82
Period size: 21 Copynumber: 4.5 Consensus size: 22
6166 AGCAGAAAAT
*
6176 AGTAATCAGTAAAAGAGTAAA-A
1 AGTAATCAGTACAA-AGTAAAGA
* *
6198 TGGTAATCAGTAAAAAGT-AAGA
1 -AGTAATCAGTACAAAGTAAAGA
6220 AGGTAATCA--ACAACAGTAAA-A
1 A-GTAATCAGTACAA-AGTAAAGA
6241 TAGTAATCAGTACAAAGTAAAGA
1 -AGTAATCAGTACAAAGTAAAGA
6264 A-TAATCAGTA
1 AGTAATCAGTA
6274 AAATAATAAT
Statistics
Matches: 64, Mismatches: 3, Indels: 18
0.75 0.04 0.21
Matches are distributed among these distances:
20 3 0.05
21 22 0.34
22 21 0.33
23 18 0.28
ACGTcount: A:0.54, C:0.08, G:0.17, T:0.20
Consensus pattern (22 bp):
AGTAATCAGTACAAAGTAAAGA
Found at i:6289 original size:21 final size:20
Alignment explanation
Indices: 6171--6295 Score: 76
Period size: 21 Copynumber: 5.8 Consensus size: 20
6161 AAAGGAGCAG
*
6171 AAAATAGTAATCAGTAAAAGAGT
1 AAAATGGTAATCAGT-AAA-A-T
6194 AAAATGGTAATCAGTAAAAAGT
1 AAAATGGTAATCAGT-AAAA-T
** *
6216 AAGAA-GGTAATCAACAACAGT
1 AA-AATGGTAATCAGTAA-AAT
*
6237 AAAATAGTAATCAGTACAAAGT
1 AAAATGGTAATCAGTA-AAA-T
*
6259 -AAA-GAATAATCAGTAAAAT
1 AAAATG-GTAATCAGTAAAAT
6278 AATAATGGTAATCAGTAA
1 AA-AATGGTAATCAGTAA
6296 TTCAGTAAAA
Statistics
Matches: 82, Mismatches: 11, Indels: 20
0.73 0.10 0.18
Matches are distributed among these distances:
19 1 0.01
20 6 0.07
21 38 0.46
22 17 0.21
23 20 0.24
ACGTcount: A:0.55, C:0.07, G:0.16, T:0.22
Consensus pattern (20 bp):
AAAATGGTAATCAGTAAAAT
Done.