Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015460.1 Corchorus capsularis cultivar CVL-1 contig15481, 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: 25518
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Found at i:2420 original size:55 final size:55
Alignment explanation
Indices: 2352--2604 Score: 279
Period size: 47 Copynumber: 4.9 Consensus size: 55
2342 GTCCGAACAA
* * *
2352 TAATCAGTCAATCAGTAATTAATTAAAAAGGGATTAATCAGAGTCAAGGTAATAG
1 TAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAG
2407 TAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAG
1 TAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAG
* *
2462 --A--AG----TCAGTAAATAAGTAAAAAGAGATTAATCAGTGTCAAGGTAATAG
1 TAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAG
*
2509 -AAGTCAGTAAATCAGTAA--AAG------GAGATTAATCAGAGACAAGGTAATAG
1 TAA-TCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAG
* * * *
2556 TAATCAGTAAATCAGTAAATAAGCAAAAAGATAGTAATCAGAGATCAAG
1 TAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAG-TCAAG
2605 AGTCAAAGTT
Statistics
Matches: 170, Mismatches: 10, Indels: 35
0.79 0.05 0.16
Matches are distributed among these distances:
47 81 0.48
48 3 0.02
49 3 0.02
51 4 0.02
53 4 0.02
55 71 0.42
56 4 0.02
ACGTcount: A:0.49, C:0.08, G:0.19, T:0.23
Consensus pattern (55 bp):
TAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAG
Found at i:2458 original size:26 final size:26
Alignment explanation
Indices: 2375--2458 Score: 64
Period size: 26 Copynumber: 3.1 Consensus size: 26
2365 AGTAATTAAT
*
2375 TAAAAAGGGATTAATCAGAGTCAAGG
1 TAAAAAGAGATTAATCAGAGTCAAGG
* * * *
2401 TAATAGTAATCAG-TAAATCAGTAATTAA-G
1 TAA-A--AA-GAGATTAATCAG-AGTCAAGG
2430 TAAAAAGAGATTAATCAGAGTCAAGG
1 TAAAAAGAGATTAATCAGAGTCAAGG
2456 TAA
1 TAA
2459 TAGAAGTCAG
Statistics
Matches: 42, Mismatches: 9, Indels: 14
0.65 0.14 0.22
Matches are distributed among these distances:
25 6 0.14
26 16 0.38
27 1 0.02
28 1 0.02
29 13 0.31
30 5 0.12
ACGTcount: A:0.49, C:0.07, G:0.20, T:0.24
Consensus pattern (26 bp):
TAAAAAGAGATTAATCAGAGTCAAGG
Found at i:2823 original size:24 final size:24
Alignment explanation
Indices: 2795--2841 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
2785 GAGATTGAAA
2795 ATTAAAGTAGTAATTAAGATTCAT
1 ATTAAAGTAGTAATTAAGATTCAT
* *
2819 ATTAAAGTGGTAATTGAGATTCA
1 ATTAAAGTAGTAATTAAGATTCA
2842 AGGTAAGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.04, G:0.17, T:0.36
Consensus pattern (24 bp):
ATTAAAGTAGTAATTAAGATTCAT
Found at i:3064 original size:26 final size:28
Alignment explanation
Indices: 3029--3111 Score: 98
Period size: 26 Copynumber: 2.9 Consensus size: 28
3019 TTAGAAGTAA
*
3029 AGAGTAAAAAGTGGTATTTAGTAAAAAGG
1 AGAGTAAAAA-TGGTATTGAGTAAAAAGG
3058 -G-GTAAAAATGGTATTGAGTAAAAAGG
1 AGAGTAAAAATGGTATTGAGTAAAAAGG
*
3084 AGAGTAAAAAAATGGTAATTAAGTAAAA
1 AGAGT--AAAAATGGT-ATTGAGTAAAA
3112 GGACTAAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
26 17 0.36
27 8 0.17
28 3 0.06
30 9 0.19
31 10 0.21
ACGTcount: A:0.52, C:0.00, G:0.25, T:0.23
Consensus pattern (28 bp):
AGAGTAAAAATGGTATTGAGTAAAAAGG
Found at i:3112 original size:30 final size:28
Alignment explanation
Indices: 3029--3186 Score: 105
Period size: 27 Copynumber: 5.6 Consensus size: 28
3019 TTAGAAGTAA
* *
3029 AGAGTAAAAAGTGGT-ATTTAGTAAAA-
1 AGAGTAAAAAATGGTAATTAAGTAAAAG
* *
3055 AGGGGT-AAAAATGGT-ATTGAGTAAAAAGG
1 A-GAGTAAAAAATGGTAATTAAGT-AAAA-G
3084 AGAGTAAAAAAATGGTAATTAAGTAAAAG
1 AGAGT-AAAAAATGGTAATTAAGTAAAAG
* * * *
3113 -GACTAAAAAGTGGTAATTCAAGCAAAAA
1 AGAGTAAAAAATGGTAATT-AAGTAAAAG
* *
3141 ACAGAAAGAAAATGGGTAATT-AGTAAAA-
1 AGAGTAA-AAAAT-GGTAATTAAGTAAAAG
*
3169 AGAGTAAAATATGGTAAT
1 AGAGTAAAAAATGGTAAT
3187 ACAGTAATTC
Statistics
Matches: 104, Mismatches: 17, Indels: 22
0.73 0.12 0.15
Matches are distributed among these distances:
26 21 0.20
27 24 0.23
28 18 0.17
29 11 0.11
30 17 0.16
31 13 0.12
ACGTcount: A:0.53, C:0.03, G:0.23, T:0.22
Consensus pattern (28 bp):
AGAGTAAAAAATGGTAATTAAGTAAAAG
Found at i:3313 original size:30 final size:29
Alignment explanation
Indices: 3249--3315 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
3239 AAGTGGTAAT
**
3249 AATAAAAGAGAGTAAGAAAAGAGTAAATT
1 AATAAAAGAGAGTAAGAAAAGAGTAAAAA
*
3278 GATAAAA-AGAGTAAGAAAAGAGTCAAAAAA
1 AATAAAAGAGAGTAAGAAAAGAGT--AAAAA
3308 AATAAAAG
1 AATAAAAG
3316 CAGCAAAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
28 16 0.52
29 6 0.19
30 9 0.29
ACGTcount: A:0.66, C:0.01, G:0.19, T:0.13
Consensus pattern (29 bp):
AATAAAAGAGAGTAAGAAAAGAGTAAAAA
Found at i:5283 original size:8 final size:8
Alignment explanation
Indices: 5270--5303 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
5260 CACCTTCTTG
5270 AAAAATTC
1 AAAAATTC
5278 AAAAATTC
1 AAAAATTC
*
5286 AGAAACTTC
1 A-AAAATTC
5295 AAAAATTC
1 AAAAATTC
5303 A
1 A
5304 TAGCCGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Found at i:5391 original size:10 final size:9
Alignment explanation
Indices: 5376--5409 Score: 50
Period size: 10 Copynumber: 3.6 Consensus size: 9
5366 AGTTATATCG
5376 AAAAAATATA
1 AAAAAATA-A
5386 AAAAAATAA
1 AAAAAATAA
5395 AACAAAATAA
1 AA-AAAATAA
5405 AAAAA
1 AAAAA
5410 GTTTTCGACC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 6 0.26
10 17 0.74
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAAATAA
Found at i:16135 original size:46 final size:46
Alignment explanation
Indices: 16085--16260 Score: 160
Period size: 46 Copynumber: 3.7 Consensus size: 46
16075 CTCAATTTTG
*
16085 TTTTTTACTTGCTTTTTCCCAAAATACCCTTCCTGGACGGAAGGCA
1 TTTTTTACTTGCTTTTTCCCAAAACACCCTTCCTGGACGGAAGGCA
* *
16131 TTTTTTACTTGCTTTTTCTCAAAGCACCCTTACC-GGACGGAAGGCA
1 TTTTTTACTTGCTTTTTCCCAAAACACCCTT-CCTGGACGGAAGGCA
* * *
16177 CTTCTTTTTACTTG-TTCTTT-CTAAAACGCCCTTCCTGGACGGAGGGCGTTA
1 --T-TTTTTACTTGCTT-TTTCCCAAAACACCCTTCCTGGACGGAAGGC---A
* * * **
16228 ATTTTTACTCGCTTTTTCTCAAAATGCCCTTCC
1 TTTTTTACTTGCTTTTTCCCAAAACACCCTTCC
16261 AAGCAAATGG
Statistics
Matches: 106, Mismatches: 13, Indels: 19
0.77 0.09 0.14
Matches are distributed among these distances:
46 40 0.38
47 4 0.04
48 34 0.32
49 27 0.25
51 1 0.01
ACGTcount: A:0.19, C:0.27, G:0.15, T:0.39
Consensus pattern (46 bp):
TTTTTTACTTGCTTTTTCCCAAAACACCCTTCCTGGACGGAAGGCA
Found at i:16452 original size:62 final size:62
Alignment explanation
Indices: 16367--16540 Score: 198
Period size: 62 Copynumber: 2.8 Consensus size: 62
16357 TCTTGCATTT
*
16367 TAGTTT-AGTATTCCCAAAATACCCTTTCAGATAAAGGGTCAGTT-TCTTCACATT-CCTGCACT
1 TAGTTTCAGT-TTCCCAAAATACCCTTTCAGATAAAGGGTCAGTTGT-GTCACATTGCCT-CA-T
16429 -
62 A
* *
16429 TAGATTAT-AG-TTCCCAAAATACCCTTTCAGACAAAGGGTCAGTTGTGTCACATTGTCTCATA
1 TAG-TT-TCAGTTTCCCAAAATACCCTTTCAGATAAAGGGTCAGTTGTGTCACATTGCCTCATA
* * *
16491 TAGTTTCAGTTTCCCAAAATACCCTTTCGGATAAAGGGTCAATTTTGTCA
1 TAGTTTCAGTTTCCCAAAATACCCTTTCAGATAAAGGGTCAGTTGTGTCA
16541 TGTTCTTGCA
Statistics
Matches: 98, Mismatches: 7, Indels: 14
0.82 0.06 0.12
Matches are distributed among these distances:
60 1 0.01
61 5 0.05
62 84 0.86
63 5 0.05
64 3 0.03
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (62 bp):
TAGTTTCAGTTTCCCAAAATACCCTTTCAGATAAAGGGTCAGTTGTGTCACATTGCCTCATA
Found at i:20400 original size:14 final size:14
Alignment explanation
Indices: 20381--20418 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
20371 ATGAGATATT
20381 TTTTCAAAAAAATG
1 TTTTCAAAAAAATG
*
20395 TTTTCAAGAAAATG
1 TTTTCAAAAAAATG
20409 TTTTCAAAAA
1 TTTTCAAAAA
20419 TGAGTTTTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (14 bp):
TTTTCAAAAAAATG
Found at i:20814 original size:19 final size:18
Alignment explanation
Indices: 20790--20825 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
20780 TGAAGATTTC
20790 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
20809 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
20826 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:23175 original size:23 final size:21
Alignment explanation
Indices: 23132--23175 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
23122 AAGATTAAGT
*
23132 ATGGTGAAAAATATGACCTGC
1 ATGGTGAAAAATATCACCTGC
*
23153 ATGGATGAAAATATATCAGCTGC
1 ATGG-TGAAAA-ATATCACCTGC
23176 TTATCAAAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 6 0.32
23 9 0.47
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.25
Consensus pattern (21 bp):
ATGGTGAAAAATATCACCTGC
Done.