Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016110.1 Corchorus capsularis cultivar CVL-1 contig16131, 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: 22386
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:3239 original size:40 final size:40
Alignment explanation
Indices: 3195--3275 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
3185 ATAACATAAC
*
3195 AATTCAAACCCAGAAATATAGTCATATTTCAATCCCAGAA
1 AATTCAAACCAAGAAATATAGTCATATTTCAATCCCAGAA
3235 AATTCAAACCAAGAAATATAGTCATATTTCAATCCCAGAA
1 AATTCAAACCAAGAAATATAGTCATATTTCAATCCCAGAA
3275 A
1 A
3276 TATATAACAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.47, C:0.21, G:0.07, T:0.25
Consensus pattern (40 bp):
AATTCAAACCAAGAAATATAGTCATATTTCAATCCCAGAA
Found at i:3332 original size:15 final size:15
Alignment explanation
Indices: 3312--3341 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3302 AAACAGAGCT
3312 TTTTAAACCCAGAAA
1 TTTTAAACCCAGAAA
3327 TTTTAAACCCAGAAA
1 TTTTAAACCCAGAAA
3342 ACCCAGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.27
Consensus pattern (15 bp):
TTTTAAACCCAGAAA
Found at i:3666 original size:11 final size:10
Alignment explanation
Indices: 3649--3685 Score: 51
Period size: 9 Copynumber: 3.8 Consensus size: 10
3639 ATCGAGTTCG
3649 AAGAGAGAGA
1 AAGAGAGAGA
3659 ACAGAGAGA-A
1 A-AGAGAGAGA
3669 AAGAGAGAGA
1 AAGAGAGAGA
3679 AA-AGAGA
1 AAGAGAGA
3686 AATTCTCGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 12 0.48
10 6 0.24
11 7 0.28
ACGTcount: A:0.62, C:0.03, G:0.35, T:0.00
Consensus pattern (10 bp):
AAGAGAGAGA
Found at i:3735 original size:23 final size:24
Alignment explanation
Indices: 3685--3737 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
3675 GAGAAAAGAG
* *
3685 AAATTCTCGGGTTGAAAGGGGTTT
1 AAATTTTCGGGCTGAAAGGGGTTT
3709 -AATTTTCGGGCTGAAA-GGGTTT
1 AAATTTTCGGGCTGAAAGGGGTTT
3731 AAATTTT
1 AAATTTT
3738 TTTAACCCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 6 0.23
23 20 0.77
ACGTcount: A:0.26, C:0.08, G:0.28, T:0.38
Consensus pattern (24 bp):
AAATTTTCGGGCTGAAAGGGGTTT
Found at i:6066 original size:14 final size:14
Alignment explanation
Indices: 6032--6070 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
6022 TTTTGTTTCC
**
6032 AAAAACAGAAAATT
1 AAAAACAGAAAACA
*
6046 AACAACAGAAAACA
1 AAAAACAGAAAACA
6060 AAAAACAGAAA
1 AAAAACAGAAA
6071 CAATACCAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.74, C:0.13, G:0.08, T:0.05
Consensus pattern (14 bp):
AAAAACAGAAAACA
Found at i:8794 original size:24 final size:23
Alignment explanation
Indices: 8752--8808 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
8742 GCGACCCGCA
**
8752 TATTATTTTTTAATTAATAATTATT
1 TATTA-TTTTTAAAAAATAATTA-T
*
8777 TATTATTTTTAAAAAATAGTTAT
1 TATTATTTTTAAAAAATAATTAT
8800 TATTATTTT
1 TATTATTTT
8809 ATATGATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 10 0.34
24 14 0.48
25 5 0.17
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (23 bp):
TATTATTTTTAAAAAATAATTAT
Found at i:10651 original size:2 final size:2
Alignment explanation
Indices: 10644--10678 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
10634 TGGGGACCAA
*
10644 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10679 GTAGAAAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:10958 original size:3 final size:3
Alignment explanation
Indices: 10939--10991 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
10929 TCCAACTCTC
* *
10939 ATT ATT -TT ATAT ATT ATT ATT ATT ATT ATT ATT TTT ATT GTT ATT
1 ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
10984 ATT ATT AT
1 ATT ATT AT
10992 ATAATATAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 39 0.89
4 3 0.07
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:11650 original size:23 final size:23
Alignment explanation
Indices: 11620--11665 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
11610 ACGCCTTTCT
11620 TATGTGATTTTGGAGAAAGTTCA
1 TATGTGATTTTGGAGAAAGTTCA
11643 TATGTGATTTTGGAGAAAGTTCA
1 TATGTGATTTTGGAGAAAGTTCA
11666 GCAGAAGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.04, G:0.26, T:0.39
Consensus pattern (23 bp):
TATGTGATTTTGGAGAAAGTTCA
Found at i:14003 original size:21 final size:21
Alignment explanation
Indices: 13977--14040 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
13967 CAGTTAGGGG
*
13977 TGTGCGATTTTAGAGCGTTTT
1 TGTGCGATTATAGAGCGTTTT
* **
13998 TGTGCGATTATATAG-G--GG
1 TGTGCGATTATAGAGCGTTTT
*
14016 TGTGCGATTGTAGAGCGTTTT
1 TGTGCGATTATAGAGCGTTTT
14037 TGTG
1 TGTG
14041 GACCACTCTC
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
18 13 0.41
19 1 0.03
20 1 0.03
21 17 0.53
ACGTcount: A:0.16, C:0.08, G:0.34, T:0.42
Consensus pattern (21 bp):
TGTGCGATTATAGAGCGTTTT
Found at i:17178 original size:6 final size:6
Alignment explanation
Indices: 17167--17216 Score: 54
Period size: 6 Copynumber: 9.0 Consensus size: 6
17157 GTTTGGCATC
* *
17167 GTTTTT GTTTTT -CTGTT -TTTTT GTTTTT G-TTTT GTTTTT G-TTTT
1 GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT
17211 GTTTTT
1 GTTTTT
17217 ATTGCGCTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
5 16 0.43
6 21 0.57
ACGTcount: A:0.00, C:0.02, G:0.16, T:0.82
Consensus pattern (6 bp):
GTTTTT
Found at i:17187 original size:16 final size:17
Alignment explanation
Indices: 17167--17210 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
17157 GTTTGGCATC
17167 GTTTTTGTTTTTCTGTT
1 GTTTTTGTTTTTCTGTT
* *
17184 -TTTTTGTTTTTGTTTT
1 GTTTTTGTTTTTCTGTT
17200 GTTTTTGTTTT
1 GTTTTTGTTTT
17211 GTTTTTATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.00, C:0.02, G:0.16, T:0.82
Consensus pattern (17 bp):
GTTTTTGTTTTTCTGTT
Found at i:17199 original size:11 final size:11
Alignment explanation
Indices: 17167--17216 Score: 68
Period size: 11 Copynumber: 4.5 Consensus size: 11
17157 GTTTGGCATC
17167 GTTTTTGTTTT
1 GTTTTTGTTTT
17178 -TCTGTTT-TTTT
1 GT-T-TTTGTTTT
17189 GTTTTTGTTTT
1 GTTTTTGTTTT
17200 GTTTTTGTTTT
1 GTTTTTGTTTT
17211 GTTTTT
1 GTTTTT
17217 ATTGCGCTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
10 4 0.11
11 27 0.77
12 4 0.11
ACGTcount: A:0.00, C:0.02, G:0.16, T:0.82
Consensus pattern (11 bp):
GTTTTTGTTTT
Found at i:17211 original size:16 final size:16
Alignment explanation
Indices: 17167--17215 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 16
17157 GTTTGGCATC
17167 GTTTTTGTTTT-TCTGTT
1 GTTTTTGTTTTGT-T-TT
17184 -TTTTTGTTTTTGTTTT
1 GTTTTTG-TTTTGTTTT
17200 GTTTTTGTTTTGTTTT
1 GTTTTTGTTTTGTTTT
17216 TATTGCGCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 17 0.59
17 11 0.38
18 1 0.03
ACGTcount: A:0.00, C:0.02, G:0.16, T:0.82
Consensus pattern (16 bp):
GTTTTTGTTTTGTTTT
Found at i:18438 original size:31 final size:31
Alignment explanation
Indices: 18367--18438 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
18357 GTCCATTAAC
*
18367 TTTTAATTTGTTTAATCTAAGACTTGCATTT
1 TTTTAATTTGTTTAATCTAAGACTTGAATTT
** * * *
18398 TGATCATTTGTTTAATTTAATACTT-AATTT
1 TTTTAATTTGTTTAATCTAAGACTTGAATTT
18428 GTTTTAATTTG
1 -TTTTAATTTG
18439 CTACAATTTA
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:0.26, C:0.07, G:0.10, T:0.57
Consensus pattern (31 bp):
TTTTAATTTGTTTAATCTAAGACTTGAATTT
Found at i:18984 original size:16 final size:16
Alignment explanation
Indices: 18965--19016 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
18955 CGAATCCGAT
*
18965 CCGAAAATACCCAAAT
1 CCGAAAATACCCAAAC
*
18981 CCGAAAATACCCGAAC
1 CCGAAAATACCCAAAC
*
18997 CCG-AAATATCCAAAC
1 CCGAAAATACCCAAAC
19012 CCGAA
1 CCGAA
19017 CCTGAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
15 13 0.42
16 18 0.58
ACGTcount: A:0.46, C:0.35, G:0.10, T:0.10
Consensus pattern (16 bp):
CCGAAAATACCCAAAC
Found at i:19012 original size:15 final size:15
Alignment explanation
Indices: 18969--19016 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
18959 TCCGATCCGA
*
18969 AAATACCCAAATCCG
1 AAATACCCAAACCCG
*
18984 AAAATACCCGAACCCG
1 -AAATACCCAAACCCG
*
19000 AAATATCCAAACCCG
1 AAATACCCAAACCCG
19015 AA
1 AA
19017 CCTGAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
15 15 0.54
16 13 0.46
ACGTcount: A:0.48, C:0.33, G:0.08, T:0.10
Consensus pattern (15 bp):
AAATACCCAAACCCG
Found at i:19013 original size:21 final size:22
Alignment explanation
Indices: 18989--19041 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
18979 ATCCGAAAAT
*
18989 ACCCGAACCCG-AAATATCCAA
1 ACCCGAACCCGAAAATACCCAA
*
19010 ACCCGAACCTGAAAATACCCAA
1 ACCCGAACCCGAAAATACCCAA
19032 ACCCGAACCC
1 ACCCGAACCC
19042 ATCCAATTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 10 0.36
22 18 0.64
ACGTcount: A:0.42, C:0.42, G:0.09, T:0.08
Consensus pattern (22 bp):
ACCCGAACCCGAAAATACCCAA
Found at i:21272 original size:25 final size:25
Alignment explanation
Indices: 21223--21269 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
21213 TAATGGACAC
*
21223 TTGAATCACCTTAATCATGAAAATA
1 TTGAATCACCTTAATCAGGAAAATA
21248 TTGAATCACCTTAATC-GGAAAA
1 TTGAATCACCTTAATCAGGAAAA
21270 ATAGAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.30
Consensus pattern (25 bp):
TTGAATCACCTTAATCAGGAAAATA
Found at i:22006 original size:22 final size:22
Alignment explanation
Indices: 21981--22028 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
21971 TTATTGCACC
*
21981 ATTACAAGGTGTTATAGAAAAG
1 ATTACAAGGTGTAATAGAAAAG
*
22003 ATTACAAGGTGTAATAGAAAGG
1 ATTACAAGGTGTAATAGAAAAG
22025 ATTA
1 ATTA
22029 TACATTCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.46, C:0.04, G:0.23, T:0.27
Consensus pattern (22 bp):
ATTACAAGGTGTAATAGAAAAG
Done.