Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015427.1 Corchorus capsularis cultivar CVL-1 contig15448, 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: 17182
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Found at i:2775 original size:36 final size:37
Alignment explanation
Indices: 2730--2804 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 37
2720 GCAGAAACAG
* *
2730 AAAATAAAAA-TATATTTTTTTTAAAAGGAAAA-CGGA
1 AAAAGAAAAATTA-ATTTTTTTTAAAAGAAAAATCGGA
*
2766 AAAAGAAAAATTAATTTTTTTTTAAAGAAAAATCGGA
1 AAAAGAAAAATTAATTTTTTTTAAAAGAAAAATCGGA
2803 AA
1 AA
2805 CCCTAATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 26 0.76
37 8 0.24
ACGTcount: A:0.56, C:0.03, G:0.11, T:0.31
Consensus pattern (37 bp):
AAAAGAAAAATTAATTTTTTTTAAAAGAAAAATCGGA
Found at i:2867 original size:42 final size:41
Alignment explanation
Indices: 2816--2901 Score: 122
Period size: 43 Copynumber: 2.1 Consensus size: 41
2806 CCTAATTTTG
*
2816 AAAACGGAAAAA-TA-TTTTTATTTTTTTTTAGAAAAATCGGA
1 AAAACGGAAAAAGAACTTTTT-TTTTTTTTTAGAAAAA-CGGA
2857 AAAATCGGAAAAAGAACTTTTTTTTTTTTTTAGAAAAACGGA
1 AAAA-CGGAAAAAGAACTTTTTTTTTTTTTTAGAAAAACGGA
2899 AAA
1 AAA
2902 TCAAAAACTA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
41 4 0.10
42 15 0.37
43 17 0.41
44 5 0.12
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (41 bp):
AAAACGGAAAAAGAACTTTTTTTTTTTTTTAGAAAAACGGA
Found at i:3205 original size:6 final size:6
Alignment explanation
Indices: 3189--3226 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
3179 AAAGCAAAGC
3189 AAATC- AAATCT AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAA
3227 GCAAAATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (6 bp):
AAATCT
Found at i:3217 original size:18 final size:17
Alignment explanation
Indices: 3189--3231 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 17
3179 AAAGCAAAGC
3189 AAATCAAATCTAAATCT
1 AAATCAAATCTAAATCT
3206 AAATCTAAATCTAAATCT
1 AAATC-AAATCTAAATCT
*
3224 AAAGCAAA
1 AAATCAAA
3232 ATTAATAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.56, C:0.16, G:0.02, T:0.26
Consensus pattern (17 bp):
AAATCAAATCTAAATCT
Found at i:3242 original size:14 final size:14
Alignment explanation
Indices: 3223--3258 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
3213 AATCTAAATC
3223 TAAAGCAAAATTAA
1 TAAAGCAAAATTAA
*
3237 TAAAGC-AGATTAA
1 TAAAGCAAAATTAA
3250 TAAAGCAAA
1 TAAAGCAAA
3259 CAATAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.61, C:0.08, G:0.11, T:0.19
Consensus pattern (14 bp):
TAAAGCAAAATTAA
Found at i:7388 original size:33 final size:33
Alignment explanation
Indices: 7314--7389 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 33
7304 TTCTTTTCAC
*
7314 CCAAAACAAAATTATTTCTAATGCTATAATCAA
1 CCAAAACAGAATTATTTCTAATGCTATAATCAA
*
7347 CCAAAACAGAATTATTTGC-AATGCTATGATCAA
1 CCAAAACAGAATTATTT-CTAATGCTATAATCAA
7380 CCAAAACAGA
1 CCAAAACAGA
7390 CTTGTTTTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
33 39 0.98
34 1 0.03
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.25
Consensus pattern (33 bp):
CCAAAACAGAATTATTTCTAATGCTATAATCAA
Found at i:7452 original size:33 final size:32
Alignment explanation
Indices: 7415--7519 Score: 111
Period size: 33 Copynumber: 3.2 Consensus size: 32
7405 ATTAGCATCC
* * *
7415 AAAACAGATTTAATTTCATCACAAACAACACCT
1 AAAACAGATTTAGTATCATCGCAAACAACA-CT
* *
7448 AAAACAGATTTAGTGTCATTGCAAACAACACT
1 AAAACAGATTTAGTATCATCGCAAACAACACT
** *
7480 GAAATTAGGTTTAGTATCATCGCAAACAACATCT
1 -AAAACAGATTTAGTATCATCGCAAACAACA-CT
7514 AAAACA
1 AAAACA
7520 CTCTTTGCAA
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
32 2 0.03
33 55 0.93
34 2 0.03
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.25
Consensus pattern (32 bp):
AAAACAGATTTAGTATCATCGCAAACAACACT
Found at i:12345 original size:16 final size:17
Alignment explanation
Indices: 12326--12360 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12316 TTCACTAGAG
12326 AAGC-AAAAGTTTTGAA
1 AAGCAAAAAGTTTTGAA
*
12342 AAGCAAAAATTTTTGAA
1 AAGCAAAAAGTTTTGAA
12359 AA
1 AA
12361 ATTTTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.54, C:0.06, G:0.14, T:0.26
Consensus pattern (17 bp):
AAGCAAAAAGTTTTGAA
Found at i:15662 original size:30 final size:30
Alignment explanation
Indices: 15622--15684 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
15612 TCTTCAAGGG
15622 GGAGGAAATGATGCGCCCAAGG-CTTATCAT
1 GGAGGAAATGATGCG-CCAAGGACTTATCAT
* **
15652 GGAGGGAATGATGCGTGAAGGACTTATCAT
1 GGAGGAAATGATGCGCCAAGGACTTATCAT
15682 GGA
1 GGA
15685 CTTGAAGACA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 4 0.14
30 25 0.86
ACGTcount: A:0.30, C:0.14, G:0.35, T:0.21
Consensus pattern (30 bp):
GGAGGAAATGATGCGCCAAGGACTTATCAT
Found at i:16526 original size:21 final size:21
Alignment explanation
Indices: 16500--16540 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
16490 TCTTGAAGGC
*
16500 TTGAAGTCCATTGAAGATCAA
1 TTGAAGACCATTGAAGATCAA
**
16521 TTGAAGAGTATTGAAGATCA
1 TTGAAGACCATTGAAGATCA
16541 TAAGCCAAGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (21 bp):
TTGAAGACCATTGAAGATCAA
Found at i:16800 original size:28 final size:28
Alignment explanation
Indices: 16768--16840 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
16758 GGGTCATCCA
16768 GGGGCATTTTGGTCATTTTCACATCTAG
1 GGGGCATTTTGGTCATTTTCACATCTAG
** *
16796 GGGGCATTTTGGTCATTTTTGCATTTAG
1 GGGGCATTTTGGTCATTTTCACATCTAG
*
16824 GGGGTATTTTGGTCATT
1 GGGGCATTTTGGTCATT
16841 CTTAGTCTAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.15, C:0.12, G:0.29, T:0.44
Consensus pattern (28 bp):
GGGGCATTTTGGTCATTTTCACATCTAG
Done.