Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015203.1 Corchorus capsularis cultivar CVL-1 contig15224, 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: 20351
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5605 original size:16 final size:17
Alignment explanation
Indices: 5581--5614 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5571 CCACTTTCCC
*
5581 AAAACTTGAT-AATTTG
1 AAAAATTGATGAATTTG
5597 AAAAATTGATGAATTTG
1 AAAAATTGATGAATTTG
5614 A
1 A
5615 TGGAAAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.47, C:0.03, G:0.15, T:0.35
Consensus pattern (17 bp):
AAAAATTGATGAATTTG
Found at i:9476 original size:29 final size:30
Alignment explanation
Indices: 9401--9476 Score: 72
Period size: 29 Copynumber: 2.7 Consensus size: 30
9391 AAGTAATTTG
*
9401 GAAAAAT-AAAAAG-TAAGGAAAAATTAAC
1 GAAAAATAAAAAAGATAAAGAAAAATTAAC
* * *
9429 -TAAACTAAAAATTGA-AAAGAAAAA-TAAC
1 GAAAAATAAAAA-AGATAAAGAAAAATTAAC
9457 GAAAAATAAAAAAGATAAAG
1 GAAAAATAAAAAAGATAAAG
9477 GTAAGAAATT
Statistics
Matches: 36, Mismatches: 7, Indels: 9
0.69 0.13 0.17
Matches are distributed among these distances:
27 4 0.11
28 10 0.28
29 22 0.61
ACGTcount: A:0.70, C:0.04, G:0.12, T:0.14
Consensus pattern (30 bp):
GAAAAATAAAAAAGATAAAGAAAAATTAAC
Found at i:12460 original size:13 final size:13
Alignment explanation
Indices: 12442--12468 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12432 ATCTATGATC
12442 ATCTTATCTTACT
1 ATCTTATCTTACT
12455 ATCTTATCTTACT
1 ATCTTATCTTACT
12468 A
1 A
12469 GAGTACTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.22, G:0.00, T:0.52
Consensus pattern (13 bp):
ATCTTATCTTACT
Found at i:12684 original size:269 final size:269
Alignment explanation
Indices: 12203--12711 Score: 919
Period size: 269 Copynumber: 1.9 Consensus size: 269
12193 AATCTTATAC
*
12203 TACTATTTAAAATCACGAACTCAACAATTCTAATTGGAAAATTTCATAAATACACTTATTATTGT
1 TACTATTTAAAATCACGAACTCAACAATCCTAATTGGAAAATTTCATAAATACACTTATTATTGT
12268 AGTATAATATTTTTTTAATAAATATTCTTTTTGGTCATTGAAATTTTTTTATTAATTATGCAAAG
66 AGTATAATATTTTTTTAATAAATATTCTTTTTGGTCATTGAAATTTTTTTATTAATTATGCAAAG
12333 ATATTGTAAATATGCTATAATTATAATTAATAATTTATTTCTCATTGATATTGTTATTTATATAA
131 ATATTGTAAATATGCTATAATTATAATTAATAATTTATTTCTCATTGATATTGTTATTTATATAA
* * *
12398 TTTATGTTCATTAATTTAATTTACTCAATAATAGATCTATGATCATCTTATCTTACTATCTTATC
196 TTTATATTCACTAATTTAATTTAATCAATAATAGATCTATGATCATCTTATCTTACTATCTTATC
12463 TTACTAGAG
261 TTACTAGAG
* *
12472 TACTATTTAAAATCACGAACTCAACAATCCTAATTGGGAAATTTCATAAATACCCTTATTATTGT
1 TACTATTTAAAATCACGAACTCAACAATCCTAATTGGAAAATTTCATAAATACACTTATTATTGT
* * *
12537 AGTATAATATTTTTTTAATCAGTATTCTTTTTGGTCATTGAACTTTTTTTATTAATTATGCAAAG
66 AGTATAATATTTTTTTAATAAATATTCTTTTTGGTCATTGAAATTTTTTTATTAATTATGCAAAG
*
12602 ATATTGTAAATCTGCTATAATTATAATTAATAATTTATTTCTCATTGATATTGTTATTTATATAA
131 ATATTGTAAATATGCTATAATTATAATTAATAATTTATTTCTCATTGATATTGTTATTTATATAA
*
12667 TTTATATTTACTAATTTAATTTAATCAATAATAGATCTATGATCA
196 TTTATATTCACTAATTTAATTTAATCAATAATAGATCTATGATCA
12712 GGTTATATTT
Statistics
Matches: 229, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
269 229 1.00
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.47
Consensus pattern (269 bp):
TACTATTTAAAATCACGAACTCAACAATCCTAATTGGAAAATTTCATAAATACACTTATTATTGT
AGTATAATATTTTTTTAATAAATATTCTTTTTGGTCATTGAAATTTTTTTATTAATTATGCAAAG
ATATTGTAAATATGCTATAATTATAATTAATAATTTATTTCTCATTGATATTGTTATTTATATAA
TTTATATTCACTAATTTAATTTAATCAATAATAGATCTATGATCATCTTATCTTACTATCTTATC
TTACTAGAG
Found at i:16097 original size:14 final size:14
Alignment explanation
Indices: 16078--16111 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
16068 TTCATACGAA
16078 GGTTATTATAGCGT
1 GGTTATTATAGCGT
16092 GGTTATTATAGCGT
1 GGTTATTATAGCGT
16106 GGTTAT
1 GGTTAT
16112 CAAAATTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.21, C:0.06, G:0.29, T:0.44
Consensus pattern (14 bp):
GGTTATTATAGCGT
Found at i:16200 original size:119 final size:116
Alignment explanation
Indices: 15991--16202 Score: 295
Period size: 119 Copynumber: 1.8 Consensus size: 116
15981 TCATAGTGTA
* *
15991 GTTATCAAAATTTCATACAGATTGTACCAAAATTTCATTAAAAGGTTATCAAAATTTCTTAGGAA
1 GTTATCAAAATTTCATACAGAATGTAACAAAATTTCATTAAAAGGTTATCAAAATTTCTTAGGAA
16056 GGTTAACAAAATTTCATACGAAGGTTATTATAGCGTGGTTATTATAGCGTG
66 GGTTAACAAAATTTCATACGAAGGTTATTATAGCGTGGTTATTATAGCGTG
*
16107 GTTATCAAAATTTCATA-AGAATGTTAACAAAATTTCA-TAGGAGTAAGGTTATCAGAATTT-TC
1 GTTATCAAAATTTCATACAGAATG-TAACAAAATTTCATTA--A--AAGGTTATCAAAATTTCT-
* * *
16169 TAGGGAGGTTAACAAAATTTCATAGGGAGGTTAT
60 TAGGAAGGTTAACAAAATTTCATACGAAGGTTAT
16203 GAAAATTTTA
Statistics
Matches: 84, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
115 7 0.08
116 29 0.35
117 1 0.01
118 1 0.01
119 46 0.55
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (116 bp):
GTTATCAAAATTTCATACAGAATGTAACAAAATTTCATTAAAAGGTTATCAAAATTTCTTAGGAA
GGTTAACAAAATTTCATACGAAGGTTATTATAGCGTGGTTATTATAGCGTG
Found at i:16208 original size:69 final size:66
Alignment explanation
Indices: 16106--16231 Score: 153
Period size: 69 Copynumber: 1.9 Consensus size: 66
16096 ATTATAGCGT
* * *
16106 GGTTATCAAAATTTCATAAGAATGTTAACAAAATTTCATAGGAGTAAGGTTATCAGAATTTTCTA
1 GGTTAACAAAATTTCATAAGAAGGTTAACAAAATTTCAT-GGAG--AGGTTATCAAAATTTTCTA
16171 GGGA
63 GGGA
* * ** *
16175 GGTTAACAAAATTTCATAGGGAGGTTATGAAAATTTTATGGAGAGGTTATCAAAATT
1 GGTTAACAAAATTTCATAAGAAGGTTAACAAAATTTCATGGAGAGGTTATCAAAATT
16232 ACATAGAGAG
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
66 13 0.27
68 4 0.08
69 32 0.65
ACGTcount: A:0.39, C:0.07, G:0.21, T:0.33
Consensus pattern (66 bp):
GGTTAACAAAATTTCATAAGAAGGTTAACAAAATTTCATGGAGAGGTTATCAAAATTTTCTAGGG
A
Found at i:16240 original size:22 final size:22
Alignment explanation
Indices: 15925--16497 Score: 200
Period size: 22 Copynumber: 25.6 Consensus size: 22
15915 GAATTACATA
* * **
15925 GTTATCAAAGTTTCATAGTGTT
1 GTTATCAAAATTTCATAGAGAG
*
15947 GTTACCAAAATTTCATATG-GAG
1 GTTATCAAAATTTCATA-GAGAG
* *
15969 GTTATCAAAACTTCATAGTGTA-
1 GTTATCAAAATTTCATAGAG-AG
*
15991 GTTATCAAAATTTCATACAGA-
1 GTTATCAAAATTTCATAGAGAG
* * *
16012 TTGTACCAAAATTTCATTA-AAAG
1 GT-TATCAAAATTTCA-TAGAGAG
*
16035 GTTATCAAAATTTCTTAG-GAAG
1 GTTATCAAAATTTCATAGAG-AG
*
16057 GTTAACAAAATTTCATACGA-AG
1 GTTATCAAAATTTCATA-GAGAG
* ** * * *
16079 GTTATTATAGCGTGGTTATTATAGCGTG
1 GTTATCA-A----AATT-TCATAGAGAG
*
16107 GTTATCAAAATTTCATA-AGAAT
1 GTTATCAAAATTTCATAGAG-AG
*
16129 GTTAACAAAATTTCATAGGAGTAAG
1 GTTATCAAAATTTCATA-GAG--AG
* *
16154 GTTATCAGAATTTTC-TAGGGAG
1 GTTATCA-AAATTTCATAGAGAG
* *
16176 GTTAACAAAATTTCATAGGGAG
1 GTTATCAAAATTTCATAGAGAG
* * *
16198 GTTATGAAAATTTTATGGAGAG
1 GTTATCAAAATTTCATAGAGAG
*
16220 GTTATCAAAATTACATAGAGAG
1 GTTATCAAAATTTCATAGAGAG
* * *
16242 GATATCATAGTTTCATTCTCATAGGGAG
1 GTTATCA-A----AATT-TCATAGAGAG
* *
16270 GTTATCAAGATTTCGT-G-GTACG
1 GTTATCAAAATTTCATAGAG-A-G
*
16292 GTTATCAAAATTTTATA-AGGAG
1 GTTATCAAAATTTCATAGA-GAG
* *
16314 GTCATCAAAATTTTCAT---GCG
1 GTTATCAAAA-TTTCATAGAGAG
* * * *
16334 GTTA-C-CAATTTTATAGTGTG
1 GTTATCAAAATTTCATAGAGAG
* * * *
16354 ATTATCAGAATTTTATAGTGAG
1 GTTATCAAAATTTCATAGAGAG
* *
16376 ATTATCAAAATTTCATAGTGTA-
1 GTTATCAAAATTTCATAGAG-AG
*
16398 GTTATCAAAATTTCAGT-GTGA-
1 GTTATCAAAATTTCA-TAGAGAG
* *
16419 -TTATCAAATTTTCATAG-GAAA
1 GTTATCAAAATTTCATAGAG-AG
*
16440 GTTATCAAAATTTCGTA-ATGAG
1 GTTATCAAAATTTCATAGA-GAG
* * * * *
16462 ATTATCAAATTTTCACAGTGTG
1 GTTATCAAAATTTCATAGAGAG
*
16484 GTTATCAATATTTC
1 GTTATCAAAATTTC
16498 TACATTTGAG
Statistics
Matches: 418, Mismatches: 84, Indels: 98
0.70 0.14 0.16
Matches are distributed among these distances:
17 5 0.01
18 2 0.00
19 3 0.01
20 26 0.06
21 16 0.04
22 290 0.69
23 22 0.05
24 5 0.01
25 10 0.02
26 6 0.01
27 8 0.02
28 25 0.06
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGAGAG
Found at i:16445 original size:64 final size:64
Alignment explanation
Indices: 16343--16496 Score: 179
Period size: 64 Copynumber: 2.4 Consensus size: 64
16333 GGTTACCAAT
* * *
16343 TTTATAGTGTGATTATCAGAATTTTATAGTGAGATTATCAAAATTTCATAGTGTAG-TTATCAAA
1 TTTACAGTGTGATTATCA-AATTTTATAGTGAAATTATCAAAATTTCATAATG-AGATTATCAAA
16407 A
64 A
*
16408 TTT-CAGTGTGATTATCAAATTTTCATAG-GAAAGTTATCAAAATTTCGTAATGAGATTATCAAA
1 TTTACAGTGTGATTATCAAATTTT-ATAGTGAAA-TTATCAAAATTTCATAATGAGATTATCAAA
*
16471 T
64 A
*
16472 TTTCACAGTGTGGTTATCAATATTT
1 TTT-ACAGTGTGATTATCAA-ATTT
16497 CTACATTTGA
Statistics
Matches: 77, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
63 11 0.14
64 45 0.58
65 3 0.04
66 14 0.18
67 4 0.05
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (64 bp):
TTTACAGTGTGATTATCAAATTTTATAGTGAAATTATCAAAATTTCATAATGAGATTATCAAAA
Done.