Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012565.1 Corchorus capsularis cultivar CVL-1 contig12586, 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: 17794
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:5793 original size:12 final size:13
Alignment explanation
Indices: 5757--5796 Score: 55
Period size: 15 Copynumber: 3.0 Consensus size: 13
5747 CTAAATTAAC
5757 ATTATTAAAATTT
1 ATTATTAAAATTT
5770 ATTATTTAAAAATTT
1 ATTA-TT-AAAATTT
5785 ATTA-TAAAATTT
1 ATTATTAAAATTT
5797 CAATTTAGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 7 0.28
13 5 0.20
14 2 0.08
15 11 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
ATTATTAAAATTT
Found at i:6015 original size:165 final size:164
Alignment explanation
Indices: 5704--6021 Score: 489
Period size: 165 Copynumber: 1.9 Consensus size: 164
5694 GAATAATTGA
*
5704 AAACCTTATGTTTTCCGATTGTACCCTTTTTTCAAATATATTTCTAAATTAACATTATTAAAATT
1 AAACCTTATGTTTTCCGATTGCACCCTTTTTTCAAATATATTTCTAAATTAACATTATTAAAATT
*
5769 TATTATTTAAAAATTTATTATAAAATTTCAATTTAGACCGAATTATAAGTTTGTAAAATTGATTT
66 TAGTA-TT-AAAATTTATTATAAAATTTCAATTTAGACCGAATTATAAGTTTGTAAAATTGATTT
5834 TCACTGATGAACATGCAAATTTCTACAAATGATGGG
129 TCACTGATGAACATGCAAATTTCTACAAATGATGGG
* *
5870 AAACTTTATGTTTTCCGATTGCACCCTTTTTTCAAATATATTTCTAAATT-GCTATTATTAAAAT
1 AAACCTTATGTTTTCCGATTGCACCCTTTTTTCAAATATATTTCTAAATTAAC-ATTATTAAAAT
* *
5934 TTAGTA-T-AATTTTATTATTTAAAAATTTCAATTTAGACCGAATTATAAGTTTGTCAAATTGAT
65 TTAGTATTAAAATTTATTA--T-AAAATTTCAATTTAGACCGAATTATAAGTTTGTAAAATTGAT
**
5997 TTTCGTTGATGAACATGCAAATTTC
127 TTTCACTGATGAACATGCAAATTTC
6022 CTTTACTATA
Statistics
Matches: 140, Mismatches: 8, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
162 9 0.06
164 2 0.01
165 65 0.46
166 64 0.46
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.44
Consensus pattern (164 bp):
AAACCTTATGTTTTCCGATTGCACCCTTTTTTCAAATATATTTCTAAATTAACATTATTAAAATT
TAGTATTAAAATTTATTATAAAATTTCAATTTAGACCGAATTATAAGTTTGTAAAATTGATTTTC
ACTGATGAACATGCAAATTTCTACAAATGATGGG
Found at i:6266 original size:22 final size:21
Alignment explanation
Indices: 6238--7252 Score: 150
Period size: 22 Copynumber: 47.8 Consensus size: 21
6228 TGTCTCTGTG
6238 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCAT-AGA
* *
6260 TGGTTATTATAATTTCAT-GA
1 TGGTTATCAAAATTTCATAGA
*
6280 -GGTTATCAAAATTTCATAGTG
1 TGGTTATCAAAATTTCATAG-A
*
6301 TGGTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA--GA
*
6324 -AGTTATCAAAATTTCATAG-
1 TGGTTATCAAAATTTCATAGA
*
6343 TGTAGTTACCAAAATTTCATAGGA
1 TG--GTTATCAAAATTTCATA-GA
* *
6367 TCAGGTTATTAAAATTTCTTAGGA
1 T--GGTTATCAAAATTTCATA-GA
* ** *
6391 AGGTTATTGAAATTTCATAGTG
1 TGGTTATCAAAATTTCATAG-A
* *
6413 TGGTTATCACAATTTTATAGAA
1 TGGTTATCAAAATTTCATAG-A
* *
6435 AGGTTATCAAAGAGATTATCA-AAA
1 TGGTTATC-AA-A-ATT-TCATAGA
* * *
6459 T-GTCATAGCGAGA-TT-ATA-A
1 TGGT--TATCAAAATTTCATAGA
*
6478 -GAATT-TC---A--T-AGT-G-
1 TG-GTTATCAAAATTTCA-TAGA
*
6491 TGGTTAACAAAATTTCAT-GA
1 TGGTTATCAAAATTTCATAGA
* * *
6511 -GGTTA-CTAATATTTAATGGGA
1 TGGTTATC-AAAATTTCAT-AGA
* *
6532 AGGTTATCAAAATTTCATAGTG
1 TGGTTATCAAAATTTCATAG-A
* ** *
6554 TGGTTATCAAATTTTTTTAGCG
1 TGGTTATCAAAATTTCATAG-A
*
6576 TGGTTATCAAAATTTCATATAA
1 TGGTTATCAAAATTTCATA-GA
* * * *
6598 AGGTTATAAAAATCTCAATTTCATA
1 TGGTTATCAAAATTTC-A--T-AGA
* * * *
6623 AGGAGTACCAAAATTTGATAGA
1 TGG-TTATCAAAATTTCATAGA
*
6645 AGGTTATC-AAATCTT-ATAGA
1 TGGTTATCAAAAT-TTCATAGA
* *
6665 GTGATTATCGAAATTTCATAGAGA
1 -TGGTTATCAAAATTTCAT--AGA
*
6689 TCAGATTATCAAAATTT-ATAGGA
1 T--GGTTATCAAAATTTCATA-GA
* * *
6712 AGATTATTAAAATTTCATAG-
1 TGGTTATCAAAATTTCATAGA
*
6732 TGTTGTTATCAAAAATTTCAAAGCGA
1 TG--GTTATC-AAAATTTCATA--GA
* * *
6758 -GATTATCAAAGTTACATA-A
1 TGGTTATCAAAATTTCATAGA
6777 TGTGATTATCAAAATTTCATAGA
1 TG-G-TTATCAAAATTTCATAGA
* * * *
6800 GGGGTCAACAAAATTTTATAGA
1 -TGGTTATCAAAATTTCATAGA
*
6822 GAGGTTATCAAAATTTCATA-A
1 -TGGTTATCAAAATTTCATAGA
* *
6843 AGAGTTATCAAATTTTCA-A-A
1 TG-GTTATCAAAATTTCATAGA
*
6863 TTGTGATTACCAAAATTTCATAG-
1 -TG-G-TTATCAAAATTTCATAGA
***
6886 TGG---T---A-TTTCTGGGGA
1 TGGTTATCAAAATTTC-ATAGA
6901 -GGTTATCAAAATTTCATAGTA
1 TGGTTATCAAAATTTCATAG-A
* *
6922 TGGTTA-CCAAA-TT-A-GGA
1 TGGTTATCAAAATTTCATAGA
* * * * *
6939 AGGTTATTAAACTTTTAT-TA
1 TGGTTATCAAAATTTCATAGA
* **
6959 TGGAGTAATCAAAATTTCAGGGA
1 T-G-GTTATCAAAATTTCATAGA
* *
6982 -GGATATCAAAATTTGATATGAA
1 TGGTTATCAAAATTTCATA-G-A
*
7004 T-GTTATCAAAATTTCATAGTT
1 TGGTTATCAAAATTTCATAG-A
* * *
7025 TAGTTTTCAAATTTTCATAAGA
1 TGGTTATCAAAATTTCAT-AGA
* *
7047 GGGTCATCAAAATTTCATAGGGA
1 TGGTTATCAAAATTTCATA--GA
* *
7070 -GATTAACAAAATTTCATA-A
1 TGGTTATCAAAATTTCATAGA
*
7089 TGAGGTTATCAAAA-ATCATAGAA
1 T--GGTTATCAAAATTTCATAG-A
* *
7112 AGGTTATCAAAATTT-GTAG-
1 TGGTTATCAAAATTTCATAGA
*
7131 T--TATATCAAGATTTCATAAGGA
1 TGGT-TATCAAAATTTCAT-A-GA
*
7153 -GGTTATCAAAATTT--TATA
1 TGGTTATCAAAATTTCATAGA
*
7171 -GG-TATCAAAATTTTATAGGA
1 TGGTTATCAAAATTTCATA-GA
* * *
7191 AGATTTATCAAAATTTCATAGCG
1 TG-GTTATCAAAATTTCATAG-A
* * *
7214 GGGTTATCACAATTTCATAGTG
1 TGGTTATCAAAATTTCATAG-A
7236 TGGTTATCAAAATTTCA
1 TGGTTATCAAAATTTCA
7253 GAGTGTGATT
Statistics
Matches: 721, Mismatches: 156, Indels: 232
0.65 0.14 0.21
Matches are distributed among these distances:
13 8 0.01
14 8 0.01
17 21 0.03
18 18 0.02
19 42 0.06
20 44 0.06
21 86 0.12
22 376 0.52
23 50 0.07
24 28 0.04
25 28 0.04
26 12 0.02
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.36
Consensus pattern (21 bp):
TGGTTATCAAAATTTCATAGA
Found at i:6337 original size:63 final size:65
Alignment explanation
Indices: 6235--6364 Score: 158
Period size: 63 Copynumber: 2.0 Consensus size: 65
6225 TCTTGTCTCT
* * * * *
6235 GTGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCAT-GAG-GTTATCAAAATTTCATA
1 GTGTGGTTACCAAAATTTCATAAGATAGTTATCAAAATTTCATAGAGAGTTACCAAAATTTCATA
* *
6298 GTGTGGTTACCAAAATTTCATATGGA-AGTTATCAAAATTTCATAGTGTAGTTACCAAAATTTCA
1 GTGTGGTTACCAAAATTTCATA-AGATAGTTATCAAAATTTCATAGAG-AGTTACCAAAATTTCA
6362 TA
64 TA
6364 G
1 G
6365 GATCAGGTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
63 35 0.62
64 4 0.07
66 17 0.30
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.38
Consensus pattern (65 bp):
GTGTGGTTACCAAAATTTCATAAGATAGTTATCAAAATTTCATAGAGAGTTACCAAAATTTCATA
Found at i:6656 original size:20 final size:22
Alignment explanation
Indices: 6633--6709 Score: 56
Period size: 25 Copynumber: 3.5 Consensus size: 22
6623 AGGAGTACCA
6633 AAATTTGATAGAAG-G-TTATC-
1 AAATTT-ATAGAAGTGATTATCG
6653 AAATCTTATAG-AGTGATTATCG
1 AAAT-TTATAGAAGTGATTATCG
*
6675 AAATTTCATAG-AGATCAGATTATCA
1 AAATTT-ATAGAAG-T--GATTATCG
6700 AAATTTATAG
1 AAATTTATAG
6710 GAAGATTATT
Statistics
Matches: 48, Mismatches: 1, Indels: 12
0.79 0.02 0.20
Matches are distributed among these distances:
19 2 0.04
20 9 0.19
21 9 0.19
22 10 0.21
23 1 0.02
24 4 0.08
25 13 0.27
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.35
Consensus pattern (22 bp):
AAATTTATAGAAGTGATTATCG
Found at i:6715 original size:21 final size:23
Alignment explanation
Indices: 6667--6731 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 23
6657 CTTATAGAGT
*
6667 GATTATCGAAATTTCATAGAGATCA
1 GATTATCAAAATTTCATAG-GA-CA
6692 GATTATCAAAATTT-ATAGGA-A
1 GATTATCAAAATTTCATAGGACA
*
6713 GATTATTAAAATTTCATAG
1 GATTATCAAAATTTCATAG
6732 TGTTGTTATC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
21 14 0.38
22 4 0.11
23 2 0.05
24 4 0.11
25 13 0.35
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (23 bp):
GATTATCAAAATTTCATAGGACA
Found at i:7177 original size:39 final size:38
Alignment explanation
Indices: 7052--7211 Score: 110
Period size: 40 Copynumber: 4.0 Consensus size: 38
7042 TAAGAGGGTC
* * *
7052 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGAAGGTTATCAAAATTT--T-AT-A-G-T
* *
7096 ATCAAAA-ATCATAGAAAGGTTATCAAAATTTGTAGTTA-T
1 ATCAAAATTTCATAGGAAGGTTATCAAAATTT-TA--TAGT
*
7135 ATCAAGATTTCATAAGG-AGGTTATCAAAATTTTATAGGT
1 ATCAAAATTTCAT-AGGAAGGTTATCAAAATTTTATA-GT
* * *
7174 ATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAG
1 ATCAAAATTTCATAGGAAG-GTTATCAAAATTTTATAG
7212 CGGGGTTATC
Statistics
Matches: 95, Mismatches: 13, Indels: 21
0.74 0.10 0.16
Matches are distributed among these distances:
37 2 0.02
38 3 0.03
39 24 0.25
40 34 0.36
41 3 0.03
42 2 0.02
43 20 0.21
44 7 0.07
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.34
Consensus pattern (38 bp):
ATCAAAATTTCATAGGAAGGTTATCAAAATTTTATAGT
Found at i:7178 original size:17 final size:17
Alignment explanation
Indices: 7156--7189 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
7146 ATAAGGAGGT
7156 TATCAAAATTTTATAGG
1 TATCAAAATTTTATAGG
7173 TATCAAAATTTTATAGG
1 TATCAAAATTTTATAGG
7190 AAGATTTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (17 bp):
TATCAAAATTTTATAGG
Found at i:7257 original size:22 final size:22
Alignment explanation
Indices: 7005--7389 Score: 133
Period size: 22 Copynumber: 17.9 Consensus size: 22
6995 TGATATGAAT
* *
7005 GTTATCAAAATTTCATAGTTTA
1 GTTATCAAAATTTCATAGTGTG
* * *
7027 GTTTTCAAATTTTCATAAGAG-G
1 GTTATCAAAATTTCAT-AGTGTG
* * *
7049 GTCATCAAAATTTCATAGGGAG
1 GTTATCAAAATTTCATAGTGTG
* * * *
7071 ATTAACAAAATTTCATAATGAG
1 GTTATCAAAATTTCATAGTGTG
* ***
7093 GTTATCAAAA-ATCATAGAAAG
1 GTTATCAAAATTTCATAGTGTG
*
7114 GTTATCAAAATTT-GTAGT-T-
1 GTTATCAAAATTTCATAGTGTG
* * *
7133 -ATATCAAGATTTCATAAG-GAG
1 GTTATCAAAATTTCAT-AGTGTG
*
7154 GTTATCAAAATTT--TA-T-AG
1 GTTATCAAAATTTCATAGTGTG
* *
7172 G-TATCAAAATTTTATAG-GAAG
1 GTTATCAAAATTTCATAGTG-TG
* * *
7193 ATTTATCAAAATTTCATAGCGGG
1 -GTTATCAAAATTTCATAGTGTG
*
7216 GTTATCACAATTTCATAGTGTG
1 GTTATCAAAATTTCATAGTGTG
*
7238 GTTATCAAAATTTCAGAGTGTG
1 GTTATCAAAATTTCATAGTGTG
* *
7260 ATTA-CTAACAA-TTCATA-TGGAG
1 GTTATC-AA-AATTTCATAGT-GTG
* * * ***
7282 GTTTTTAAATTTTCATAACATG
1 GTTATCAAAATTTCATAGTGTG
* *
7304 GTTATCAATATATCATA-TG-G
1 GTTATCAAAATTTCATAGTGTG
* *
7324 AGATTATCAACATCTCATAGTGTTG
1 -G-TTATCAAAATTTCATAGTG-TG
* * * **
7349 GTTATCAAATTTTTATTG-GAAA
1 GTTATCAAAATTTCATAGTG-TG
7371 GTTATCAAAATTTCATAGT
1 GTTATCAAAATTTCATAGT
7390 TATCAACATC
Statistics
Matches: 265, Mismatches: 69, Indels: 57
0.68 0.18 0.15
Matches are distributed among these distances:
17 11 0.04
18 13 0.05
19 4 0.02
20 4 0.02
21 29 0.11
22 167 0.63
23 34 0.13
24 2 0.01
25 1 0.00
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGTGTG
Found at i:7448 original size:22 final size:22
Alignment explanation
Indices: 7423--7471 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
7413 TTCCTTAGGG
*
7423 AGGTTAACAAAAT-TTCATAAGA
1 AGGTTAA-AAAATATTCATAAAA
*
7445 AGGTTAAAAAATATTTATAAAA
1 AGGTTAAAAAATATTCATAAAA
7467 AGGTT
1 AGGTT
7472 CTCGAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.51, C:0.04, G:0.14, T:0.31
Consensus pattern (22 bp):
AGGTTAAAAAATATTCATAAAA
Found at i:11477 original size:19 final size:20
Alignment explanation
Indices: 11453--11494 Score: 77
Period size: 19 Copynumber: 2.1 Consensus size: 20
11443 GCTTGTTTAA
11453 TCAACCTTGTC-TTTACTTT
1 TCAACCTTGTCTTTTACTTT
11472 TCAACCTTGTCTTTTACTTT
1 TCAACCTTGTCTTTTACTTT
11492 TCA
1 TCA
11495 TCACCCTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.17, C:0.26, G:0.05, T:0.52
Consensus pattern (20 bp):
TCAACCTTGTCTTTTACTTT
Found at i:14133 original size:17 final size:18
Alignment explanation
Indices: 14111--14151 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
14101 AATAAGATCC
14111 AATAAAACAAAAAAAC-A
1 AATAAAACAAAAAAACAA
* *
14128 AATAAAACATAAAAGCAA
1 AATAAAACAAAAAAACAA
14146 AATAAA
1 AATAAA
14152 GAAAATAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.78, C:0.10, G:0.02, T:0.10
Consensus pattern (18 bp):
AATAAAACAAAAAAACAA
Done.