Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013059.1 Corchorus capsularis cultivar CVL-1 contig13080, 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: 23851
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:171 original size:14 final size:13
Alignment explanation
Indices: 148--189 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
138 TCAAGATTTG
148 AAGAAAAAAGCAAA
1 AAGAAAAAAG-AAA
*
162 AAGAAGAAAG-AA
1 AAGAAAAAAGAAA
174 AAGAAAAAATGAAA
1 AAGAAAAAA-GAAA
188 AA
1 AA
190 ATGAAAATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 10 0.42
13 1 0.04
14 13 0.54
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (13 bp):
AAGAAAAAAGAAA
Found at i:339 original size:21 final size:22
Alignment explanation
Indices: 294--342 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
284 TAAAATTGGT
*
294 AATCA-AGAGTTTTCAAGATTT
1 AATCAGAGAGTTTTCAAGATTA
315 AATCAGAG-GTTTTCAA-ATTCA
1 AATCAGAGAGTTTTCAAGATT-A
336 AATCAGA
1 AATCAGA
343 CTTAGTTAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 3 0.12
21 20 0.80
22 2 0.08
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (22 bp):
AATCAGAGAGTTTTCAAGATTA
Found at i:5334 original size:75 final size:75
Alignment explanation
Indices: 5229--5377 Score: 172
Period size: 75 Copynumber: 2.0 Consensus size: 75
5219 ATCTAGACTA
* * ** * * * *
5229 TGAGCAAATGAATGATGGGTTTTAATCAAAACAGGTTTCATATTCAGTTTCAATCAAAGCAATGG
1 TGAGAAAAAGAATGATGAATTTTAAACAAAACAGGTTTCAAAATCAGTTTCAATCAAAGCAATGA
*
5294 TTTTAAGGTG
66 TTTCAAGGTG
* * * * *
5304 TGAGAAAAAGAATGATGAATTTTAAACAAAAGATGTTTCAAAATCAGTTTTAGTCAAAGGAATGA
1 TGAGAAAAAGAATGATGAATTTTAAACAAAACAGGTTTCAAAATCAGTTTCAATCAAAGCAATGA
5369 TTTCAAGGT
66 TTTCAAGGT
5378 AATAGAATCC
Statistics
Matches: 60, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
75 60 1.00
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.32
Consensus pattern (75 bp):
TGAGAAAAAGAATGATGAATTTTAAACAAAACAGGTTTCAAAATCAGTTTCAATCAAAGCAATGA
TTTCAAGGTG
Found at i:5915 original size:45 final size:44
Alignment explanation
Indices: 5803--5929 Score: 200
Period size: 44 Copynumber: 2.9 Consensus size: 44
5793 AAAAGCAACG
*
5803 ATGGTTTTCAAAAAGAGTCGTGGTTTTCAAAAGGTTTTGATAAA
1 ATGGTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAA
* *
5847 ATGGTTTTCAAAAAGAGTCATGGTTTTTAAAAGATTTTGATAAA
1 ATGGTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAA
* *
5891 ATGCTTTTTCAAAAGGAGTCATGGTTTTCAAAAGGTTTT
1 ATG-GTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTT
5930 CCAAAGTTAT
Statistics
Matches: 75, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
44 44 0.59
45 31 0.41
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (44 bp):
ATGGTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAA
Found at i:5945 original size:45 final size:43
Alignment explanation
Indices: 5806--5948 Score: 146
Period size: 45 Copynumber: 3.2 Consensus size: 43
5796 AGCAACGATG
* *
5806 GTTTTCAAAAAGAGTCGTGGTTTTCAAAAGGTTTTGATAA-AAT
1 GTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTCA-AATAAT
* * *
5849 GGTTTTCAAAAAGAGTCATGGTTTTTAAAAGATTTTGATAA-AAT
1 -GTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTCA-AATAAT
* *
5893 GCTTTTTCAAAAGGAGTCATGGTTTTCAAAAGGTTTTCCAAAGTTAT
1 G--TTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTT-CAAA-TAAT
5940 GTTTTCAAA
1 GTTTTCAAA
5949 CTCGTTTTTC
Statistics
Matches: 86, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
43 1 0.01
44 40 0.47
45 41 0.48
46 1 0.01
47 3 0.03
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.38
Consensus pattern (43 bp):
GTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTCAAATAAT
Found at i:7147 original size:15 final size:16
Alignment explanation
Indices: 7129--7181 Score: 60
Period size: 15 Copynumber: 3.6 Consensus size: 16
7119 GAAAAATGAT
7129 GAAAGAAAAAG-GAAA
1 GAAAGAAAAAGAGAAA
7144 GAAA-AAAAAGAGAAA
1 GAAAGAAAAAGAGAAA
* *
7159 -AAGGAAAAAGAGAAT
1 GAAAGAAAAAGAGAAA
7174 G-AAGAAAA
1 GAAAGAAAA
7182 GAGGCTCTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
14 8 0.25
15 24 0.75
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.02
Consensus pattern (16 bp):
GAAAGAAAAAGAGAAA
Found at i:7517 original size:50 final size:50
Alignment explanation
Indices: 7448--7554 Score: 153
Period size: 50 Copynumber: 2.1 Consensus size: 50
7438 AAACAAGAAG
* * * *
7448 TTTCAAAATGAGATGGCATTCCATTTGTGAGTCCAATATCAAGATTCGA-T
1 TTTCAAAATAAGATGGCATTCCACTTGTGAGTCCAAGATCAAAATTC-ACT
*
7498 TTTCAAAATAAGATTGCATTCCACTTGTGAGTCCAAGATCAAAATTCACT
1 TTTCAAAATAAGATGGCATTCCACTTGTGAGTCCAAGATCAAAATTCACT
7548 TTTCAAA
1 TTTCAAA
7555 GGGCATTTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
49 1 0.02
50 50 0.98
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.34
Consensus pattern (50 bp):
TTTCAAAATAAGATGGCATTCCACTTGTGAGTCCAAGATCAAAATTCACT
Found at i:8300 original size:139 final size:139
Alignment explanation
Indices: 8076--8438 Score: 566
Period size: 139 Copynumber: 2.6 Consensus size: 139
8066 CGAATGCTCC
* * * * **
8076 GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTTAGTTTAGCCTTGGTTCCATCCAAGCATT
1 GGCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGATAGTTTAGATTTGGTTCCATCCAAGCATT
* *
8141 CAGGGGCTTTTCCACAAGCCAAACTCGTTTCCACACGGGTCAGATCCAGCTTCGGTTCCATCCAG
66 CAGGGGCTTTTCCATAAGCCAAACTCGTTTCCACACGAGTCAGATCCAGCTTCGGTTCCATCCAG
* *
8206 GCAAGTGA-
131 ACAAGAGAG
*
8214 GGCTTTTCCATAAGCCGAACTCGCTTCCACGCGAGATAGTTTAAGATTTGGTTCCATCCAAGCAT
1 GGCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGATAGTTT-AGATTTGGTTCCATCCAAGCAT
* *
8279 TCAAGGGCTTTTCCATAAGCCAAACTCGTTTCCACACGAGTCAGATCCAGCTTTGGTTCCATCCA
65 TCAGGGGCTTTTCCATAAGCCAAACTCGTTTCCACACGAGTCAGATCCAGCTTCGGTTCCATCCA
8344 GACAAGAGAG
130 GACAAGAGAG
* *
8354 GGCTTTTCCATAAGCCAAACCCGCTTCCACGCGAGATAGTTTCAGATTTGGTTCTATCCAAGCAT
1 GGCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGATAGTTT-AGATTTGGTTCCATCCAAGCAT
8419 TCAGGGGCTTTTCCATAAGC
65 TCAGGGGCTTTTCCATAAGC
8439 TAAGTTCAGT
Statistics
Matches: 205, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
138 37 0.18
139 88 0.43
140 80 0.39
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (139 bp):
GGCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGATAGTTTAGATTTGGTTCCATCCAAGCATT
CAGGGGCTTTTCCATAAGCCAAACTCGTTTCCACACGAGTCAGATCCAGCTTCGGTTCCATCCAG
ACAAGAGAG
Found at i:8305 original size:70 final size:70
Alignment explanation
Indices: 8076--8438 Score: 389
Period size: 70 Copynumber: 5.2 Consensus size: 70
8066 CGAATGCTCC
* * *
8076 GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTTAGTTT-AGCCTTGGTTCCATCCAAGCAT
1 GGCTTTTCCATAAGCCAAACTCGTTTCCACACGAGATAGTTTCAGCTTTGGTTCCATCCAAGCAT
*
8140 TCAGG
66 TCAAG
* * * * * *
8145 GGCTTTTCCACAAGCCAAACTCGTTTCCACACG-GGTCAGATCCAGCTTCGGTTCCATCCAGGCA
1 GGCTTTTCCATAAGCCAAACTCGTTTCCACACGAGAT-AGTTTCAGCTTTGGTTCCATCCAAGC-
* *
8209 AGT-GA-
64 ATTCAAG
* * * * *
8214 GGCTTTTCCATAAGCCGAACTCGCTTCCACGCGAGATAGTTTAAGATTTGGTTCCATCCAAGCAT
1 GGCTTTTCCATAAGCCAAACTCGTTTCCACACGAGATAGTTTCAGCTTTGGTTCCATCCAAGCAT
8279 TCAAG
66 TCAAG
* *
8284 GGCTTTTCCATAAGCCAAACTCGTTTCCACACGAG-TCAGATCCAGCTTTGGTTCCATCC-AGAC
1 GGCTTTTCCATAAGCCAAACTCGTTTCCACACGAGAT-AGTTTCAGCTTTGGTTCCATCCAAG-C
**
8347 A-AGAGAG
64 ATTCA-AG
* * * * *
8354 GGCTTTTCCATAAGCCAAACCCGCTTCCACGCGAGATAGTTTCAGATTTGGTTCTATCCAAGCAT
1 GGCTTTTCCATAAGCCAAACTCGTTTCCACACGAGATAGTTTCAGCTTTGGTTCCATCCAAGCAT
*
8419 TCAGG
66 TCAAG
8424 GGCTTTTCCATAAGC
1 GGCTTTTCCATAAGC
8439 TAAGTTCAGT
Statistics
Matches: 241, Mismatches: 41, Indels: 23
0.79 0.13 0.08
Matches are distributed among these distances:
68 4 0.02
69 90 0.37
70 141 0.59
71 6 0.02
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (70 bp):
GGCTTTTCCATAAGCCAAACTCGTTTCCACACGAGATAGTTTCAGCTTTGGTTCCATCCAAGCAT
TCAAG
Found at i:8626 original size:47 final size:47
Alignment explanation
Indices: 8552--8876 Score: 551
Period size: 47 Copynumber: 6.9 Consensus size: 47
8542 ATCCAGGCAA
*
8552 TCTTGTCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAGATGG
1 TCTTTTCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAGATGG
*
8599 TCTTTTCTCGCTTCCACGCGAGTTTTCAATCTAGTGACCAAAGATGG
1 TCTTTTCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAGATGG
* *
8646 TCTTTTCTCGCTTCCATGCGAGTTTTCAATCTAGTGACCAAAGATGG
1 TCTTTTCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAGATGG
8693 TCTTTTCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAGATGG
1 TCTTTTCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAGATGG
* * *
8740 TCTTTTCTCGCTTCCATGCGAGTTTTCCATCTAGTGACCAAAGATGG
1 TCTTTTCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAGATGG
* *
8787 TCATTTCTCGCTTCCACGCGGGTTTTCAATTTAGTGACCAAAGATGG
1 TCTTTTCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAGATGG
* *
8834 TCTTCTCTCGCTTCCACGCGAGTTTTCAATTTAGTGGCCAAAG
1 TCTTTTCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAG
8877 TTGTTCAACG
Statistics
Matches: 261, Mismatches: 17, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 261 1.00
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.35
Consensus pattern (47 bp):
TCTTTTCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAGATGG
Found at i:9245 original size:27 final size:27
Alignment explanation
Indices: 9182--9251 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 27
9172 AGGGTCTTCT
* * *
9182 AGGGGCATTTGGGTCATCTTTACATTC
1 AGGGGCATTTAGGTCATCTTCACACTC
*
9209 AGGGGTATTTAGGTCAT-TTGCACACTC
1 AGGGGCATTTAGGTCATCTT-CACACTC
* *
9236 ATGGGCATTTTGGTCA
1 AGGGGCATTTAGGTCA
9252 CATTATTCCA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
26 2 0.06
27 33 0.94
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.36
Consensus pattern (27 bp):
AGGGGCATTTAGGTCATCTTCACACTC
Found at i:12194 original size:29 final size:29
Alignment explanation
Indices: 12152--12210 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
12142 CATGCATATA
12152 TCATGTGATGTTACTTGGTAAATTGGATT
1 TCATGTGATGTTACTTGGTAAATTGGATT
12181 TCATGTGATGTTACTTGGTAAATTGGATT
1 TCATGTGATGTTACTTGGTAAATTGGATT
12210 T
1 T
12211 AAAAGATGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.07, G:0.24, T:0.46
Consensus pattern (29 bp):
TCATGTGATGTTACTTGGTAAATTGGATT
Found at i:12273 original size:20 final size:20
Alignment explanation
Indices: 12248--12286 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12238 GATAAATTTG
12248 TTTAAAGATTAGATTTTTAA
1 TTTAAAGATTAGATTTTTAA
* *
12268 TTTAAAGCTTTGATTTTTA
1 TTTAAAGATTAGATTTTTA
12287 CTAATAAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.54
Consensus pattern (20 bp):
TTTAAAGATTAGATTTTTAA
Found at i:13511 original size:21 final size:22
Alignment explanation
Indices: 13466--13514 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
13456 TAAAATTGGT
*
13466 AATCA-AGAGTTTTCAAGATTT
1 AATCAGAGAGTTTTCAAGATTA
13487 AATCAGAG-GTTTTCAA-ATTCA
1 AATCAGAGAGTTTTCAAGATT-A
13508 AATCAGA
1 AATCAGA
13515 CTTAGTTAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 3 0.12
21 20 0.80
22 2 0.08
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (22 bp):
AATCAGAGAGTTTTCAAGATTA
Found at i:23821 original size:37 final size:39
Alignment explanation
Indices: 23768--23840 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 39
23758 AAATATAATT
23768 TTAAATTTTTTTAAAACA-AACTTTGAAAATTTTAAAGC
1 TTAAATTTTTTTAAAACATAACTTTGAAAATTTTAAAGC
** *
23806 TTAAA-TTTTTTAAAACATATTTTTTAAAATTTTAA
1 TTAAATTTTTTTAAAACATAACTTTGAAAATTTTAA
23841 TTGCATATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 12 0.39
38 19 0.61
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (39 bp):
TTAAATTTTTTTAAAACATAACTTTGAAAATTTTAAAGC
Done.