Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014899.1 Corchorus capsularis cultivar CVL-1 contig14920, 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: 62839
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:2138 original size:25 final size:25
Alignment explanation
Indices: 2110--2168 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
2100 GGAATATATA
*
2110 AAATGAGA-TACTAAGAAGATAATCC
1 AAAT-AGACTACTAAAAAGATAATCC
2135 AAATAGACTACTAAAAAGATAATCC
1 AAATAGACTACTAAAAAGATAATCC
2160 AAATAGACT
1 AAATAGACT
2169 TCAATAAGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 3 0.09
25 29 0.91
ACGTcount: A:0.54, C:0.14, G:0.12, T:0.20
Consensus pattern (25 bp):
AAATAGACTACTAAAAAGATAATCC
Found at i:2822 original size:6 final size:6
Alignment explanation
Indices: 2811--2844 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
2801 CTTGGGGCTC
*
2811 TCTTTA TCTTTA TCTTTA TCTTTT TCTTTCA TCT
1 TCTTTA TCTTTA TCTTTA TCTTTA TCTTT-A TCT
2845 CCTCCTCAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 22 0.88
7 3 0.12
ACGTcount: A:0.12, C:0.21, G:0.00, T:0.68
Consensus pattern (6 bp):
TCTTTA
Found at i:3155 original size:19 final size:18
Alignment explanation
Indices: 3117--3155 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3107 TAAGAGTAAA
*
3117 AAATAAAACATAAAACAT
1 AAATAAAACAAAAAACAT
*
3135 AAATGAAACAAAAACACAT
1 AAATAAAACAAAAA-ACAT
3154 AA
1 AA
3156 TTAATCTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.72, C:0.13, G:0.03, T:0.13
Consensus pattern (18 bp):
AAATAAAACAAAAAACAT
Found at i:6084 original size:22 final size:22
Alignment explanation
Indices: 6041--6084 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
6031 CGACAAGCTT
* *
6041 TAGCTTATGATTGTGTCCTACA
1 TAGCTTATGATTGTATCATACA
6063 TAGCTTATGATTGTATCATACA
1 TAGCTTATGATTGTATCATACA
6085 ATTTACAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (22 bp):
TAGCTTATGATTGTATCATACA
Found at i:7668 original size:30 final size:31
Alignment explanation
Indices: 7634--7692 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
7624 GTTCCTAACG
* *
7634 TTGCAAAATTAGCTC-AATCGGTCCCTAATA
1 TTGCAAAATCAGCTCAAATCAGTCCCTAATA
*
7664 TTGCAAAATCAGTTCAAATCAGTCCCTAA
1 TTGCAAAATCAGCTCAAATCAGTCCCTAA
7693 CATTTTTGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 13 0.52
31 12 0.48
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.29
Consensus pattern (31 bp):
TTGCAAAATCAGCTCAAATCAGTCCCTAATA
Found at i:13774 original size:2 final size:2
Alignment explanation
Indices: 13767--13798 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
13757 TAGCCTTTAA
13767 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13799 GGACTTTGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23136 original size:2 final size:2
Alignment explanation
Indices: 23129--23164 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
23119 CTGACACAAA
23129 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23165 CATTCCATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46153 original size:33 final size:33
Alignment explanation
Indices: 46075--46157 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 33
46065 AGAAGTCCTC
* * *
46075 CGCCTCCATCGCCACCTCCACCAGTAGTATATT
1 CGCCACCACCGCCTCCTCCACCAGTAGTATATT
*** *
46108 ATTCACCGCCGCCTCCTCCACCAGT-GTATCATT
1 CGCCACCACCGCCTCCTCCACCAGTAGTAT-ATT
46141 CGCCACCACCGCCTCCT
1 CGCCACCACCGCCTCCT
46158 AAACGTTCAC
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
32 4 0.11
33 34 0.89
ACGTcount: A:0.18, C:0.47, G:0.12, T:0.23
Consensus pattern (33 bp):
CGCCACCACCGCCTCCTCCACCAGTAGTATATT
Found at i:46204 original size:30 final size:30
Alignment explanation
Indices: 46170--46270 Score: 166
Period size: 30 Copynumber: 3.4 Consensus size: 30
46160 ACGTTCACCA
46170 CCACCTCCACCAGTATATCACTCGCCGCCG
1 CCACCTCCACCAGTATATCACTCGCCGCCG
* *
46200 CCACCTCCACCAGTATATCACTCGCCACCA
1 CCACCTCCACCAGTATATCACTCGCCGCCG
* *
46230 CCTCCTCCACCAGTATATCATTCGCCGCCG
1 CCACCTCCACCAGTATATCACTCGCCGCCG
46260 CCACCTCCACC
1 CCACCTCCACC
46271 TCCTCAATAT
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.21, C:0.51, G:0.10, T:0.18
Consensus pattern (30 bp):
CCACCTCCACCAGTATATCACTCGCCGCCG
Found at i:46207 original size:81 final size:82
Alignment explanation
Indices: 46086--46237 Score: 216
Period size: 81 Copynumber: 1.8 Consensus size: 82
46076 GCCTCCATCG
* * * * *
46086 CCACCTCCACCAGTAGTATATTATTCACCGCCGCCTCCTCCACCAGTGTATCATTCGCCACCACC
1 CCACCTCCACCA--AGTATATCACTCACCGCCGCCACCTCCACCAGTATATCACTCGCCACCACC
46151 GCCTCCTAAACGTTCACCA
64 GCCTCCTAAACGTTCACCA
* *
46170 CCACCTCCACC-AGTATATCACTCGCCGCCGCCACCTCCACCAGTATATCACTCGCCACCACCTC
1 CCACCTCCACCAAGTATATCACTCACCGCCGCCACCTCCACCAGTATATCACTCGCCACCACCGC
46234 CTCC
66 CTCC
46238 ACCAGTATAT
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
81 50 0.82
84 11 0.18
ACGTcount: A:0.22, C:0.48, G:0.10, T:0.20
Consensus pattern (82 bp):
CCACCTCCACCAAGTATATCACTCACCGCCGCCACCTCCACCAGTATATCACTCGCCACCACCGC
CTCCTAAACGTTCACCA
Found at i:46367 original size:27 final size:27
Alignment explanation
Indices: 46337--46394 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
46327 TGCATGATTT
*
46337 GCCACATTTTCCACCAGGACAAGATAA
1 GCCACACTTTCCACCAGGACAAGATAA
*
46364 GCCACACTTTCCACCAGGGCAAGATAA
1 GCCACACTTTCCACCAGGACAAGATAA
46391 GCCA
1 GCCA
46395 AGACCAGGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.34, C:0.33, G:0.17, T:0.16
Consensus pattern (27 bp):
GCCACACTTTCCACCAGGACAAGATAA
Found at i:60487 original size:18 final size:18
Alignment explanation
Indices: 60464--60502 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
60454 TTGAGGGAAA
60464 AAAAAG-AAGAAGAAAAAG
1 AAAAAGAAAGAA-AAAAAG
*
60482 AAAAAGAAAGAAAGAAAG
1 AAAAAGAAAGAAAAAAAG
60500 AAA
1 AAA
60503 GAAAGGATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAGAAAAAAAG
Found at i:60491 original size:22 final size:21
Alignment explanation
Indices: 60460--60506 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
60450 AATTTTGAGG
60460 GAAAAAAAAG-AAGAAGAAAAA
1 GAAAAAAAAGAAAGAA-AAAAA
*
60481 GAAAAAGAAAGAAAGAAAGAAA
1 GAAAAA-AAAGAAAGAAAAAAA
60503 GAAA
1 GAAA
60507 GGATGAGCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 6 0.26
22 12 0.52
23 5 0.22
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (21 bp):
GAAAAAAAAGAAAGAAAAAAA
Found at i:60492 original size:16 final size:15
Alignment explanation
Indices: 60460--60507 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
60450 AATTTTGAGG
60460 GAAAAAAAAGAAG-AA
1 GAAAAAAAA-AAGAAA
60475 GAAAAAGAAAAAGAAA
1 GAAAAA-AAAAAGAAA
*
60491 GAAAGAAAGAAAGAAA
1 GAAA-AAAAAAAGAAA
60507 G
1 G
60508 GATGAGCATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
15 9 0.31
16 18 0.62
17 2 0.07
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
GAAAAAAAAAAGAAA
Found at i:62750 original size:29 final size:30
Alignment explanation
Indices: 62670--62777 Score: 94
Period size: 30 Copynumber: 3.6 Consensus size: 30
62660 ACTAATCTAC
* * * **
62670 CATTTTGCCCCCTGAACTTGTAGTGTTTAGA
1 CATTTTGCCCCCTGAACTT-CAATCTTGGGA
*
62701 CGTTTTGCCCCC-GAACTTCAATCTT-GGA
1 CATTTTGCCCCCTGAACTTCAATCTTGGGA
* *
62729 CATTTTGCCCCCTGAATTTCAATTTTGGGA
1 CATTTTGCCCCCTGAACTTCAATCTTGGGA
* * *
62759 CGTTTTGCTCCCTCAACTT
1 CATTTTGCCCCCTGAACTT
62778 AACGGTTCCG
Statistics
Matches: 63, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
28 13 0.21
29 15 0.24
30 24 0.38
31 11 0.17
ACGTcount: A:0.18, C:0.28, G:0.17, T:0.38
Consensus pattern (30 bp):
CATTTTGCCCCCTGAACTTCAATCTTGGGA
Done.