Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012588.1 Corchorus capsularis cultivar CVL-1 contig12609, 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: 26034
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:161 original size:2 final size:2
Alignment explanation
Indices: 156--210 Score: 60
Period size: 2 Copynumber: 28.0 Consensus size: 2
146 TATACATAAA
* * *
156 AT AT AT AT ACT AT GT GT AT AT AT AT AT AT AT AT AT AT AT AT TT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
199 AT -T A- AT AT AT AT
1 AT AT AT AT AT AT AT
211 GTTTTTTATA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
1 2 0.04
2 42 0.91
3 2 0.04
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.51
Consensus pattern (2 bp):
AT
Found at i:306 original size:20 final size:18
Alignment explanation
Indices: 281--325 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
271 ACATATGTTT
281 TACTAATAAATAATAATATA
1 TACTAATAAAT-A-AATATA
* *
301 TACTAACAAATAAATATT
1 TACTAATAAATAAATATA
319 TACTAAT
1 TACTAAT
326 TTTTGCTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 11 0.50
19 1 0.05
20 10 0.45
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.36
Consensus pattern (18 bp):
TACTAATAAATAAATATA
Found at i:819 original size:13 final size:14
Alignment explanation
Indices: 788--821 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
778 ACTATAAAAG
*
788 TTTAAACAATATCA
1 TTTAAAAAATATCA
802 TTTAAAAAATAT-A
1 TTTAAAAAATATCA
815 TTTAAAA
1 TTTAAAA
822 TGTTCCAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (14 bp):
TTTAAAAAATATCA
Found at i:1049 original size:3 final size:3
Alignment explanation
Indices: 1041--1111 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
1031 TGAAATTAGG
1041 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1089 ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT AT
1112 GGGTTGCTTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1241 original size:31 final size:31
Alignment explanation
Indices: 1172--1281 Score: 125
Period size: 31 Copynumber: 3.6 Consensus size: 31
1162 TTTGCTGCCG
* ***
1172 CAAGCAATTAAGGATATAACG-TTAC-AAAA
1 CAAGCAATTAAGGATATAACGTTTTCGATTT
* **
1201 CAAGCAATTAAGAATATAACGTTTTTTATTT
1 CAAGCAATTAAGGATATAACGTTTTCGATTT
**
1232 TGAGCAATTAAGGATATAACGTTTTCGATTT
1 CAAGCAATTAAGGATATAACGTTTTCGATTT
1263 CAAGCAATTAAGGATATAA
1 CAAGCAATTAAGGATATAA
1282 TCAGTTAGGG
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
29 20 0.30
30 2 0.03
31 44 0.67
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.32
Consensus pattern (31 bp):
CAAGCAATTAAGGATATAACGTTTTCGATTT
Found at i:1485 original size:29 final size:31
Alignment explanation
Indices: 1411--1477 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
1401 TCTAACGGGC
1411 TATATCCTTAATTGCTCGTTTTTCGTAACGT
1 TATATCCTTAATTGCTCGTTTTTCGTAACGT
*
1442 TATATCCTTAATTGCTTG-TTTT-GTAACGT
1 TATATCCTTAATTGCTCGTTTTTCGTAACGT
1471 TATATCC
1 TATATCC
1478 CAAATTGCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 14 0.40
30 4 0.11
31 17 0.49
ACGTcount: A:0.21, C:0.18, G:0.12, T:0.49
Consensus pattern (31 bp):
TATATCCTTAATTGCTCGTTTTTCGTAACGT
Found at i:4596 original size:20 final size:19
Alignment explanation
Indices: 4557--4596 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
4547 ATTATAGATT
*
4557 TTGAAAAAAAAAATTCTAA
1 TTGAAAAAAAAAATTATAA
*
4576 TTGAAATAAAAAATTTATAA
1 TTGAAA-AAAAAAATTATAA
4596 T
1 T
4597 AATTGAACAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.33
Consensus pattern (19 bp):
TTGAAAAAAAAAATTATAA
Found at i:5130 original size:12 final size:12
Alignment explanation
Indices: 5110--5172 Score: 51
Period size: 12 Copynumber: 5.2 Consensus size: 12
5100 AAACCGACCG
5110 AATTATATATAT
1 AATTATATATAT
*
5122 AATTTTATATAT
1 AATTATATATAT
* *
5134 TATTATAGATA-
1 AATTATATATAT
5145 ATATTA-ATATAT
1 A-ATTATATATAT
5157 -ATATATATATGAT
1 AAT-TATATAT-AT
5170 AAT
1 AAT
5173 CTGAAATATA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
10 2 0.05
11 6 0.15
12 27 0.69
13 2 0.05
14 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (12 bp):
AATTATATATAT
Found at i:8704 original size:18 final size:19
Alignment explanation
Indices: 8677--8721 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
8667 CCTTTCAAGA
*
8677 TTTTGGGTTTAG-ACAGTT
1 TTTTGAGTTTAGTACAGTT
*
8695 TTTTGAGTTTAGTTCAGTT
1 TTTTGAGTTTAGTACAGTT
8714 TTTTGAGT
1 TTTTGAGT
8722 CAGTTAGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.16, C:0.04, G:0.24, T:0.56
Consensus pattern (19 bp):
TTTTGAGTTTAGTACAGTT
Found at i:8726 original size:18 final size:19
Alignment explanation
Indices: 8690--8731 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
8680 TGGGTTTAGA
*
8690 CAGTTTTTTGAGTTTAGTT
1 CAGTTTTTTGAGTTCAGTT
8709 CAGTTTTTTGAG-TCAGTT
1 CAGTTTTTTGAGTTCAGTT
8727 -AGTTT
1 CAGTTT
8732 GAGTTTGAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.23
18 5 0.23
19 12 0.55
ACGTcount: A:0.17, C:0.07, G:0.21, T:0.55
Consensus pattern (19 bp):
CAGTTTTTTGAGTTCAGTT
Found at i:9634 original size:16 final size:16
Alignment explanation
Indices: 9588--9636 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
9578 TCGGGTCATA
9588 CATTCGGGTCTCGGGT
1 CATTCGGGTCTCGGGT
*
9604 CA-TCTGGAT-TACGGGT
1 CATTC-GGGTCT-CGGGT
9620 CATTCGGGTCTCGGGT
1 CATTCGGGTCTCGGGT
9636 C
1 C
9637 GGACGGGTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
15 3 0.11
16 21 0.78
17 3 0.11
ACGTcount: A:0.10, C:0.24, G:0.35, T:0.31
Consensus pattern (16 bp):
CATTCGGGTCTCGGGT
Found at i:9694 original size:15 final size:15
Alignment explanation
Indices: 9674--9705 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
9664 TGATCAAATT
*
9674 GGGTTGGGCAGGTTG
1 GGGTTGGGCAGATTG
9689 GGGTTGGGCAGATTG
1 GGGTTGGGCAGATTG
9704 GG
1 GG
9706 CGGGTTCTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.09, C:0.06, G:0.59, T:0.25
Consensus pattern (15 bp):
GGGTTGGGCAGATTG
Found at i:11428 original size:22 final size:22
Alignment explanation
Indices: 11403--11451 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
11393 TCATAAAGAA
* *
11403 GTTATCAAAATTTTATAGGGAT
1 GTTATCAAAATTTGATAGGGAG
**
11425 GTTATTGAAATTTGATAGGGAG
1 GTTATCAAAATTTGATAGGGAG
11447 GTTAT
1 GTTAT
11452 TTCATAGTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.02, G:0.24, T:0.41
Consensus pattern (22 bp):
GTTATCAAAATTTGATAGGGAG
Found at i:11452 original size:22 final size:22
Alignment explanation
Indices: 11410--11452 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
11400 GAAGTTATCA
* *
11410 AAATTTTATAGGGATGTTATTG
1 AAATTTGATAGGGAGGTTATTG
11432 AAATTTGATAGGGAGGTTATT
1 AAATTTGATAGGGAGGTTATT
11453 TCATAGTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.42
Consensus pattern (22 bp):
AAATTTGATAGGGAGGTTATTG
Found at i:12143 original size:66 final size:66
Alignment explanation
Indices: 12066--12190 Score: 250
Period size: 66 Copynumber: 1.9 Consensus size: 66
12056 ACACGACAAA
12066 AAAACCCGGATGATCCGCAACCCGATTGACCAGAGGTCAAAACTCGAATCCGCCTAACCAAAATC
1 AAAACCCGGATGATCCGCAACCCGATTGACCAGAGGTCAAAACTCGAATCCGCCTAACCAAAATC
12131 C
66 C
12132 AAAACCCGGATGATCCGCAACCCGATTGACCAGAGGTCAAAACTCGAATCCGCCTAACC
1 AAAACCCGGATGATCCGCAACCCGATTGACCAGAGGTCAAAACTCGAATCCGCCTAACC
12191 CAATTAGACC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.35, C:0.34, G:0.18, T:0.14
Consensus pattern (66 bp):
AAAACCCGGATGATCCGCAACCCGATTGACCAGAGGTCAAAACTCGAATCCGCCTAACCAAAATC
C
Found at i:13418 original size:32 final size:34
Alignment explanation
Indices: 13379--13459 Score: 103
Period size: 34 Copynumber: 2.4 Consensus size: 34
13369 TGCTTGTTCC
13379 AGCCTTCTAAGTAG-CTTTTTCCTTTCGGCC-CA
1 AGCCTTCTAAGTAGTCTTTTTCCTTTCGGCCACA
* ** * *
13411 AGCCTTCTAAGTAGTTTTTTTTTTTTTGGCCAGA
1 AGCCTTCTAAGTAGTCTTTTTCCTTTCGGCCACA
13445 AGCCTTCTAAGTAGT
1 AGCCTTCTAAGTAGT
13460 TGACTATAGG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
32 14 0.33
33 12 0.29
34 16 0.38
ACGTcount: A:0.19, C:0.22, G:0.17, T:0.42
Consensus pattern (34 bp):
AGCCTTCTAAGTAGTCTTTTTCCTTTCGGCCACA
Found at i:25831 original size:32 final size:33
Alignment explanation
Indices: 25790--25872 Score: 100
Period size: 33 Copynumber: 2.5 Consensus size: 33
25780 AGAGTATAGT
*
25790 AAAGTGATTTTTTCTTTTCTC-CTG-GCAAAAAA
1 AAAGTGATTTTTTCTTTTCTCTC-GAACAAAAAA
* *
25822 AAAGTGATTTTTT-TTAATCTTTCGAACAAAAAA
1 AAAGTGATTTTTTCTT-TTCTCTCGAACAAAAAA
25855 AAAGTGATTTTTTCTTTT
1 AAAGTGATTTTTTCTTTT
25873 TTTTTTAAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
31 2 0.05
32 17 0.40
33 22 0.51
34 2 0.05
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.45
Consensus pattern (33 bp):
AAAGTGATTTTTTCTTTTCTCTCGAACAAAAAA
Done.