Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015947.1 Corchorus capsularis cultivar CVL-1 contig15968, 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: 97543
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1519 original size:24 final size:25
Alignment explanation
Indices: 1483--1534 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
1473 CTACTACTAA
*
1483 TAATTATTATAATAA-TAAGAAGTT
1 TAATAATTATAATAATTAAGAAGTT
* *
1507 TAATAATTCTAATAATTAAGATGTT
1 TAATAATTATAATAATTAAGAAGTT
1532 TAA
1 TAA
1535 CGTGAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.42
Consensus pattern (25 bp):
TAATAATTATAATAATTAAGAAGTT
Found at i:2585 original size:63 final size:65
Alignment explanation
Indices: 2469--2600 Score: 241
Period size: 63 Copynumber: 2.0 Consensus size: 65
2459 TCAACCAACA
2469 TCAATTGGCAACAAAAATTTATATACTTTTATATATATATATATATAGTATCACTTATTTTATAT
1 TCAATTGGCAACAAAAATTTATATAC-TTTATATATATATATATATAGTATCACTTATTTTATAT
2534 T
65 T
2535 TCAATTGGCAACAAAAA-TTATATAC-TTATATATATATATATATAGTATCACTTATTTTATATT
1 TCAATTGGCAACAAAAATTTATATACTTTATATATATATATATATAGTATCACTTATTTTATATT
2598 TCA
1 TCA
2601 TTATTATAGT
Statistics
Matches: 66, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
63 41 0.62
65 8 0.12
66 17 0.26
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (65 bp):
TCAATTGGCAACAAAAATTTATATACTTTATATATATATATATATAGTATCACTTATTTTATATT
Found at i:6269 original size:20 final size:22
Alignment explanation
Indices: 6236--6281 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
6226 TCCATTATTT
*
6236 TTTTCTT-AATTTAATATTTAA
1 TTTTCTTAAATTAAATATTTAA
*
6257 TTTT-TTAAATTAAATATTTGA
1 TTTTCTTAAATTAAATATTTAA
6278 TTTT
1 TTTT
6282 AATTTAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (22 bp):
TTTTCTTAAATTAAATATTTAA
Found at i:10196 original size:18 final size:19
Alignment explanation
Indices: 10173--10223 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
10163 AATGTTGAAG
10173 TTATAATCTTA-AATTTTT
1 TTATAATCTTATAATTTTT
* *
10191 TTATAACCTCAATAATTTTT
1 TTATAATCT-TATAATTTTT
10211 TTAGTAATCTTAT
1 TTA-TAATCTTAT
10224 TAAATATGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 8 0.31
19 1 0.04
20 12 0.46
21 5 0.19
ACGTcount: A:0.33, C:0.10, G:0.02, T:0.55
Consensus pattern (19 bp):
TTATAATCTTATAATTTTT
Found at i:22021 original size:12 final size:12
Alignment explanation
Indices: 22002--22069 Score: 82
Period size: 12 Copynumber: 5.7 Consensus size: 12
21992 TTAAAAACAT
22002 GTTTTGTAATAA
1 GTTTTGTAATAA
* *
22014 GCTTTGTACTAA
1 GTTTTGTAATAA
22026 GTTTTGTAATAA
1 GTTTTGTAATAA
* *
22038 GTATTGTAACAA
1 GTTTTGTAATAA
* *
22050 ATTCTGTAATAA
1 GTTTTGTAATAA
22062 GTTTTGTA
1 GTTTTGTA
22070 CTTTCTCCAA
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 44 1.00
ACGTcount: A:0.32, C:0.06, G:0.16, T:0.46
Consensus pattern (12 bp):
GTTTTGTAATAA
Found at i:23665 original size:33 final size:33
Alignment explanation
Indices: 23605--23699 Score: 118
Period size: 33 Copynumber: 2.9 Consensus size: 33
23595 ATAAACTGCC
* * * *
23605 TCTTAACAACTTGCCTCCACATAATTCTACGCA
1 TCTTGACAAGTTGCCTCCAAATGATTCTACGCA
*
23638 TCTTGACAAGTTGCCTCCAAATGATTCTACGCC
1 TCTTGACAAGTTGCCTCCAAATGATTCTACGCA
* * *
23671 TCTTGACAAGTTCCCTCGAAACGATTCTA
1 TCTTGACAAGTTGCCTCCAAATGATTCTA
23700 AGATGCTTCA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.27, C:0.31, G:0.12, T:0.31
Consensus pattern (33 bp):
TCTTGACAAGTTGCCTCCAAATGATTCTACGCA
Found at i:25032 original size:33 final size:33
Alignment explanation
Indices: 24956--25037 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 33
24946 ACAAGCTGCT
*
24956 TCTTTACAAGTTG-CTCCAAATAATTTTAAGCA
1 TCTTTACAAGTTGCCTCCAAATAATTCTAAGCA
** * *
24988 TCTCGACAAGTTGCCTCCAAATAATTCTATGCC
1 TCTTTACAAGTTGCCTCCAAATAATTCTAAGCA
* *
25021 TCTTTAAAAGTTCCCTC
1 TCTTTACAAGTTGCCTC
25038 AAAACAAACT
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
32 11 0.28
33 29 0.73
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.35
Consensus pattern (33 bp):
TCTTTACAAGTTGCCTCCAAATAATTCTAAGCA
Found at i:27257 original size:16 final size:16
Alignment explanation
Indices: 27221--27259 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
27211 GAAAAGCAAT
27221 TAAACTAAAAATAAATC
1 TAAACT-AAAATAAATC
*
27238 -AAACTAAATTAAATC
1 TAAACTAAAATAAATC
27253 TAAACTA
1 TAAACTA
27260 TGACAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAACTAAAATAAATC
Found at i:33056 original size:18 final size:18
Alignment explanation
Indices: 33033--33067 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
33023 TGAAGATTTC
33033 TTGAAGA-TATTTGAAGAT
1 TTGAAGACTA-TTGAAGAT
33051 TTGAAGACTATTGAAGA
1 TTGAAGACTATTGAAGA
33068 ATTATTTCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (18 bp):
TTGAAGACTATTGAAGAT
Found at i:35174 original size:14 final size:13
Alignment explanation
Indices: 35150--35184 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
35140 AAGTTCTTAA
*
35150 AAAAATAAAAATT
1 AAAAATAAAAAAT
35163 AAAAATACAAAAAT
1 AAAAATA-AAAAAT
35177 AAAAATAA
1 AAAAATAA
35185 GAGAAAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:36230 original size:14 final size:15
Alignment explanation
Indices: 36198--36236 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
36188 GAAGAAAAAC
36198 TAGA-AAAATAGATG
1 TAGAGAAAATAGATG
*
36212 AAGAGAAAA-AGATG
1 TAGAGAAAATAGATG
36226 TAGAGAAAATA
1 TAGAGAAAATA
36237 TTGTGATTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (15 bp):
TAGAGAAAATAGATG
Found at i:44358 original size:50 final size:50
Alignment explanation
Indices: 44283--44377 Score: 163
Period size: 50 Copynumber: 1.9 Consensus size: 50
44273 TAAAATTTGG
* *
44283 TAAAAGGATATTTAGAGATATAGTGTAGAGCTGAACTTGCTGAACAAAGC
1 TAAAACGATATTTAGAGATATAGTGTAGAGATGAACTTGCTGAACAAAGC
*
44333 TAAAACGATATTTAGGGATATAGTGTAGAGATGAACTTGCTGAAC
1 TAAAACGATATTTAGAGATATAGTGTAGAGATGAACTTGCTGAAC
44378 CTTATTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.39, C:0.09, G:0.24, T:0.27
Consensus pattern (50 bp):
TAAAACGATATTTAGAGATATAGTGTAGAGATGAACTTGCTGAACAAAGC
Found at i:49294 original size:33 final size:33
Alignment explanation
Indices: 49252--49360 Score: 173
Period size: 33 Copynumber: 3.3 Consensus size: 33
49242 TTCTTTTCAC
* ** **
49252 CCAAAACAGAATTTTTTTTAATGCTACAATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
49285 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
49318 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
49351 CCAAAACAGA
1 CCAAAACAGA
49361 TTTGTTTTCA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 71 1.00
ACGTcount: A:0.44, C:0.19, G:0.10, T:0.27
Consensus pattern (33 bp):
CCAAAACAGAATTATTTGCAATGCTATGATCAA
Found at i:52838 original size:47 final size:47
Alignment explanation
Indices: 52766--52901 Score: 227
Period size: 47 Copynumber: 2.9 Consensus size: 47
52756 TCTAGTTAAT
* *
52766 TTTAATTGACACCAGAAGTTGTCAAATTAAAATTTTATTTTAGTAAA
1 TTTAATTGACACTAGAAGTTGTCAAATTAAAATTTTACTTTAGTAAA
* *
52813 TTTAATTGACACTAGAAGTTTTCAAATTAAAATTTTACTTAAGTAAA
1 TTTAATTGACACTAGAAGTTGTCAAATTAAAATTTTACTTTAGTAAA
*
52860 TTTAATTGACACTAGAAGTTGTCAAATTAAAATCTTACTTTA
1 TTTAATTGACACTAGAAGTTGTCAAATTAAAATTTTACTTTA
52902 CAAATAAAAA
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 82 1.00
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (47 bp):
TTTAATTGACACTAGAAGTTGTCAAATTAAAATTTTACTTTAGTAAA
Found at i:52925 original size:67 final size:67
Alignment explanation
Indices: 52835--52968 Score: 216
Period size: 67 Copynumber: 2.0 Consensus size: 67
52825 TAGAAGTTTT
* *
52835 CAAATTAAAATTTTACTTAAGTAAATTTAATTGACACTAGAAGTTGTCAAATTAAAATCTTACTT
1 CAAATAAAAATCTTACTTAAGTAAATTTAATTGACACTAGAAGTTGTCAAATTAAAATCTTACTT
52900 TA
66 TA
* *
52902 CAAATAAAAATCTTACATT-AGTAAATTTAATTGACACTAGAAGTTGTCAAATTAAATTTTTACT
1 CAAATAAAAATCTTAC-TTAAGTAAATTTAATTGACACTAGAAGTTGTCAAATTAAAATCTTACT
52966 TTA
65 TTA
52969 GTTGACACCG
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
67 60 0.97
68 2 0.03
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.39
Consensus pattern (67 bp):
CAAATAAAAATCTTACTTAAGTAAATTTAATTGACACTAGAAGTTGTCAAATTAAAATCTTACTT
TA
Found at i:52983 original size:38 final size:38
Alignment explanation
Indices: 52927--53004 Score: 111
Period size: 38 Copynumber: 2.1 Consensus size: 38
52917 CATTAGTAAA
* * *
52927 TTTAATTGACACTAGAAGTTGTCAAATTAAATTTTTAC
1 TTTAATTGACACCAGAAGTTGTCAAATTAAAATCTTAC
* *
52965 TTTAGTTGACACCGGAAGTTGTCAAATTAAAATCTTAC
1 TTTAATTGACACCAGAAGTTGTCAAATTAAAATCTTAC
53003 TT
1 TT
53005 GAGTAAACAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (38 bp):
TTTAATTGACACCAGAAGTTGTCAAATTAAAATCTTAC
Found at i:53039 original size:47 final size:47
Alignment explanation
Indices: 52970--53082 Score: 163
Period size: 47 Copynumber: 2.4 Consensus size: 47
52960 TTTACTTTAG
* *
52970 TTGACACCGGAAGTTGTCAAATTAAAATCTTACTTGAGTAAACATAA
1 TTGACACCAGAAGTTGTCAAATTAAAATCTTACTTAAGTAAACATAA
* * * **
53017 TTGACACAAGAAGTTGTCAAATTAAATTTTTACTTAAGTAAATTTAA
1 TTGACACCAGAAGTTGTCAAATTAAAATCTTACTTAAGTAAACATAA
53064 TTGACACCAGAAGTTGTCA
1 TTGACACCAGAAGTTGTCA
53083 CACAGATAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 58 1.00
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (47 bp):
TTGACACCAGAAGTTGTCAAATTAAAATCTTACTTAAGTAAACATAA
Found at i:53162 original size:43 final size:42
Alignment explanation
Indices: 53064--53251 Score: 163
Period size: 41 Copynumber: 4.5 Consensus size: 42
53054 GTAAATTTAA
* * **
53064 TTGACACCAGAAGTTGTCACAC-AGATAAAATTAAAATCTACGA
1 TTGACACCAGAAGTTGTCAC-CTTGGTAAAATTAAAAT-TACCT
* * **
53107 TTGACACAAGAAGCTGTCATTTTGGTAAAAATTAAAATTACCT
1 TTGACACCAGAAGTTGTCACCTTGGT-AAAATTAAAATTACCT
* *
53150 TTAACACCAGAAGTTGTTACCTTGGT-AAATTAAAATTACCT
1 TTGACACCAGAAGTTGTCACCTTGGTAAAATTAAAATTACCT
* *
53191 TTGACACCAGAAGTTGTC-GCTCCGGT-AAATTAAATTATTA--T
1 TTGACACCAGAAGTTGTCACCT-TGGTAAAATTAAA--ATTACCT
*
53232 TTGACACTAGAAGTTGTCAC
1 TTGACACCAGAAGTTGTCAC
53252 GTTGAAGTTT
Statistics
Matches: 119, Mismatches: 20, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
40 2 0.02
41 60 0.50
43 46 0.39
44 11 0.09
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (42 bp):
TTGACACCAGAAGTTGTCACCTTGGTAAAATTAAAATTACCT
Found at i:55127 original size:30 final size:30
Alignment explanation
Indices: 55091--55180 Score: 171
Period size: 30 Copynumber: 3.0 Consensus size: 30
55081 GGCATCTTAA
55091 TGGCATCTCCATGAGACTTTGCGATTCCAT
1 TGGCATCTCCATGAGACTTTGCGATTCCAT
55121 TGGCATCTCCATGAGACTTTGCGATTCCAT
1 TGGCATCTCCATGAGACTTTGCGATTCCAT
*
55151 TGGCATCTCCATGAGAATTTGCGATTCCAT
1 TGGCATCTCCATGAGACTTTGCGATTCCAT
55181 CCTCTCCTTT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.21, C:0.26, G:0.20, T:0.33
Consensus pattern (30 bp):
TGGCATCTCCATGAGACTTTGCGATTCCAT
Found at i:59879 original size:167 final size:165
Alignment explanation
Indices: 59524--59967 Score: 622
Period size: 167 Copynumber: 2.7 Consensus size: 165
59514 TGAGTCATTT
*
59524 GTCAATTGAGAAATGACCAAAAAGTTTAATTATTTAATCCCCTCAAGAATCAAAAGTTAAGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAATTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* * * * ** *
59589 TTAAGTAATCTGCCAAGTAGGTAAATACGAAAAAGATTAGTTCTCTAGCTCATCATCAATCCTTG
65 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACTCAAAATCAAGCCTTG
* * *
59654 ATGGGGATCTTTTATTAATTCCACTACTCTATTCAA
130 ATAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
* * *
59690 GTCCATTGAGAAATGACCAAAAAGATTACTTATTTAAT-CTCTCAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAATTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
*
59754 TTAAGTAATCTGCCAAGTAGGAAAAGACGGAAAAAAATAAGTTCTCTAACTCCAAAAGT-AAGCC
65 TTAAGTAATCTGCCAAGTAGGAAAAGAC-GAAAAAAATTAGTTCTCTAACT-CAAAA-TCAAGCC
* * *
59818 TTGGTATGGATCTTTTAGTAATTCCACTACTCTGTTAAA
127 TTGATAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
* *
59857 GTCAATTGAGAAATGACCAAAAAGTCTAGTTATTTAATCCCCTCAAGAATCAAAACTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAGT-TAATTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* *
59922 TTAAGTAATCTACCAAGTGGGAAAAGACGAAAAAAATTAGTTCTCT
65 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCT
59968 CGCTCCTCAT
Statistics
Matches: 247, Mismatches: 26, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
165 50 0.20
166 55 0.22
167 91 0.37
168 51 0.21
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (165 bp):
GTCAATTGAGAAATGACCAAAAAGTTAATTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATT
TAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACTCAAAATCAAGCCTTGA
TAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
Found at i:63412 original size:10 final size:10
Alignment explanation
Indices: 63397--63423 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
63387 TATTTAGGGT
63397 TCGGGTTCTA
1 TCGGGTTCTA
63407 TCGGGTTCTA
1 TCGGGTTCTA
63417 TCGGGTT
1 TCGGGTT
63424 TGGGTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.07, C:0.19, G:0.33, T:0.41
Consensus pattern (10 bp):
TCGGGTTCTA
Found at i:63414 original size:16 final size:15
Alignment explanation
Indices: 63345--63414 Score: 61
Period size: 16 Copynumber: 4.5 Consensus size: 15
63335 GGCAATTGGG
**
63345 CGGGTTCGGGTGGGTT
1 CGGGTTCGGGT-TCTT
63361 CGGGTTCGGGTTCTGT
1 CGGGTTCGGGTTCT-T
*
63377 CAGGTTCGGGTAT-TT
1 CGGGTTCGGGT-TCTT
*
63392 AGGGTTCGGGTTCTAT
1 CGGGTTCGGGTTCT-T
63408 CGGGTTC
1 CGGGTTC
63415 TATCGGGTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
14 1 0.02
15 12 0.27
16 30 0.68
17 1 0.02
ACGTcount: A:0.06, C:0.16, G:0.43, T:0.36
Consensus pattern (15 bp):
CGGGTTCGGGTTCTT
Found at i:63429 original size:41 final size:42
Alignment explanation
Indices: 63366--63446 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 42
63356 GGGTTCGGGT
* *
63366 TCGGGTTCTGTCAGGTTCGGGTA-TTTAGGGTTCGGGTTCTA
1 TCGGGTTCTATCAGGTTCGGGTATTTTAGGGTTCGAGTTCTA
* * *
63407 TCGGGTTCTATCGGGTTTGGGTATTTTCGGGTTCGAGTTC
1 TCGGGTTCTATCAGGTTCGGGTATTTTAGGGTTCGAGTTC
63447 GAGCCCAGGT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
41 20 0.59
42 14 0.41
ACGTcount: A:0.09, C:0.15, G:0.36, T:0.41
Consensus pattern (42 bp):
TCGGGTTCTATCAGGTTCGGGTATTTTAGGGTTCGAGTTCTA
Found at i:63997 original size:31 final size:31
Alignment explanation
Indices: 63962--64033 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
63952 TAAATTGTAG
* *
63962 CAAATTAAAACAAAT-TAAGTATTAAATTAAA
1 CAAATTAAAA-AAATGCAAGCATTAAATTAAA
* ** *
63993 CAAATCATCAAAATGCAAGCCTTAAATTAAA
1 CAAATTAAAAAAATGCAAGCATTAAATTAAA
64024 CAAATTAAAA
1 CAAATTAAAA
64034 GCTAATGAAC
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.58, C:0.12, G:0.04, T:0.25
Consensus pattern (31 bp):
CAAATTAAAAAAATGCAAGCATTAAATTAAA
Found at i:82166 original size:16 final size:16
Alignment explanation
Indices: 82142--82218 Score: 64
Period size: 16 Copynumber: 4.8 Consensus size: 16
82132 CATTTTCAGA
*
82142 TTCGTGTTCGGGTTTT
1 TTCGGGTTCGGGTTTT
* *
82158 TTCGGGTTCCGATTTT
1 TTCGGGTTCGGGTTTT
* * ***
82174 TTTGGGTTTGAACTTT
1 TTCGGGTTCGGGTTTT
* *
82190 TTCAGATTCGGGTTTT
1 TTCGGGTTCGGGTTTT
82206 TTCGGGTTCGGGT
1 TTCGGGTTCGGGT
82219 ATTTGACTTT
Statistics
Matches: 44, Mismatches: 17, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.06, C:0.13, G:0.30, T:0.51
Consensus pattern (16 bp):
TTCGGGTTCGGGTTTT
Found at i:96375 original size:12 final size:11
Alignment explanation
Indices: 96335--96385 Score: 52
Period size: 12 Copynumber: 4.5 Consensus size: 11
96325 CATCTTTTAA
96335 TTTTTTCA--T
1 TTTTTTCATTT
*
96344 TTTTTCCAATTT
1 TTTTTTC-ATTT
96356 TTTTTTCATTT
1 TTTTTTCATTT
96367 TTCTTTTCATCTT
1 TT-TTTTCAT-TT
96380 TTTTTT
1 TTTTTT
96386 TTCTTCAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
9 6 0.17
10 1 0.03
11 6 0.17
12 18 0.51
13 4 0.11
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTTTCATTT
Done.