Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005606.1 Corchorus capsularis cultivar CVL-1 contig05624, 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: 2606
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Found at i:222 original size:38 final size:38
Alignment explanation
Indices: 180--594 Score: 619
Period size: 38 Copynumber: 11.1 Consensus size: 38
170 ACCCCAATAA
180 AATTAAG-GACAAAAGTAATAGTAATCAGTAAAATTGAT
1 AATTAAGAGAC-AAAGTAATAGTAATCAGTAAAATTGAT
*
218 AATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTGAT
1 AATTAAGAGACAAAGTAATAGTAATCAGTAAAATTGAT
* **
256 AATTAAGAGTC-AAGGGAT--TAATCAGTAAAATTGAT
1 AATTAAGAGACAAAGTAATAGTAATCAGTAAAATTGAT
* *
291 AATTAAGAGGCAAAGTAATAGTAATCAGTAAGATTGAT
1 AATTAAGAGACAAAGTAATAGTAATCAGTAAAATTGAT
*
329 AATTAAGAGCCAAAGTAATAGTAATCAGTAAAATTGAT
1 AATTAAGAGACAAAGTAATAGTAATCAGTAAAATTGAT
*
367 AATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTGAT
1 AATTAAGAGACAAAGTAATAGTAATCAGTAAAATTGAT
* **
405 AATTAAGAGTC-AAGGGAT--TAATCAGTAAAATTGAT
1 AATTAAGAGACAAAGTAATAGTAATCAGTAAAATTGAT
* *
440 AATTAAGAGGCAAAGTAATAGTAATCAGTAAGATTGAT
1 AATTAAGAGACAAAGTAATAGTAATCAGTAAAATTGAT
*
478 AATTAAGAGGCAAAGTAATAGTAATCAGTAAAATTGAT
1 AATTAAGAGACAAAGTAATAGTAATCAGTAAAATTGAT
*
516 AATTAAGAGCCAAAGTAATAGTAATCAGTAAAATTGAT
1 AATTAAGAGACAAAGTAATAGTAATCAGTAAAATTGAT
* *
554 AATTAAGAGCCAAAGTAATAGCAATCAGTAAAATTGAT
1 AATTAAGAGACAAAGTAATAGTAATCAGTAAAATTGAT
592 AAT
1 AAT
595 CAAGGGTCAA
Statistics
Matches: 351, Mismatches: 19, Indels: 14
0.91 0.05 0.04
Matches are distributed among these distances:
35 54 0.15
36 10 0.03
37 10 0.03
38 275 0.78
39 2 0.01
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.27
Consensus pattern (38 bp):
AATTAAGAGACAAAGTAATAGTAATCAGTAAAATTGAT
Found at i:450 original size:149 final size:149
Alignment explanation
Indices: 191--594 Score: 727
Period size: 149 Copynumber: 2.7 Consensus size: 149
181 ATTAAGGACA
191 AAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTGAT
1 AAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTGAT
256 AATTAAGAGTCAAGGGATTAATCAGTAAAATTGATAATTAAGAGGCAAAGTAATAGTAATCAGTA
66 AATTAAGAGTCAAGGGATTAATCAGTAAAATTGATAATTAAGAGGCAAAGTAATAGTAATCAGTA
321 AGATTGATAATTAAGAGCC
131 AGATTGATAATTAAGAGCC
340 AAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTGAT
1 AAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTGAT
405 AATTAAGAGTCAAGGGATTAATCAGTAAAATTGATAATTAAGAGGCAAAGTAATAGTAATCAGTA
66 AATTAAGAGTCAAGGGATTAATCAGTAAAATTGATAATTAAGAGGCAAAGTAATAGTAATCAGTA
*
470 AGATTGATAATTAAGAGGC
131 AGATTGATAATTAAGAGCC
*
489 AAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGCCAAAGTAATAGTAATCAGTAAAATTGAT
1 AAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTGAT
* ** *
554 AATTAAGAGCCAAAGTAATAGCAATCAGTAAAATTGATAAT
66 AATTAAGAGTC-AAGGGAT--TAATCAGTAAAATTGATAAT
595 CAAGGGTCAA
Statistics
Matches: 246, Mismatches: 6, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
149 222 0.90
150 5 0.02
152 19 0.08
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.27
Consensus pattern (149 bp):
AAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTGAT
AATTAAGAGTCAAGGGATTAATCAGTAAAATTGATAATTAAGAGGCAAAGTAATAGTAATCAGTA
AGATTGATAATTAAGAGCC
Found at i:495 original size:187 final size:185
Alignment explanation
Indices: 191--672 Score: 684
Period size: 187 Copynumber: 2.6 Consensus size: 185
181 ATTAAGGACA
*
191 AAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTGAT
1 AAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGTC-AAGGAATA-TAATCAGTAAAATTGAT
* *
256 AATTAAGAGTCAAGGGATTAATCAGTAAAATTGATAATTAAGAGGCAAAGTAATAGTAATCAGTA
64 AATTAAGAGGCAAGGAATTAATCAGTAAAATTGATAATTAAGAGGCAAAGTAATAGTAATCAGTA
* *
321 AGATTGATAATTAAGAGCCAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGTC
129 AAATTGATAATTAAGAGCCAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGCC
*
378 AAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGTCAAGGGAT-TAATCAGTAAAATTGATAA
1 AAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGTCAAGGAATATAATCAGTAAAATTGATAA
* *
442 TTAAGAGGCAAAGTAATAGTAATCAGTAAGATTGATAATTAAGAGGCAAAGTAATAGTAATCAGT
66 TTAAGAGGC-AAGGAAT--TAATCAGTAAAATTGATAATTAAGAGGCAAAGTAATAGTAATCAGT
507 AAAATTGATAATTAAGAGCCAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGCC
128 AAAATTGATAATTAAGAGCCAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGCC
* * * *
565 AAAGTAATAGCAATCAGTAAAATTGATAATCAAGGGTCAAGGTAAAAATAGTAATCAG-CAAA-T
1 AAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGTCAAGG----AATA-TAATCAGTAAAATT
* * ** *
628 CAGTAATTAAGAGTCAAGGGTTTAATCAGT-AAATTGATACTTAAG
61 GA-TAATTAAGAGGCAAGGAATTAATCAGTAAAATTGATAATTAAG
673 GGAGAGAGTA
Statistics
Matches: 265, Mismatches: 20, Indels: 19
0.87 0.07 0.06
Matches are distributed among these distances:
184 27 0.10
185 5 0.02
186 5 0.02
187 178 0.67
188 13 0.05
189 8 0.03
191 8 0.03
192 14 0.05
193 7 0.03
ACGTcount: A:0.48, C:0.07, G:0.18, T:0.27
Consensus pattern (185 bp):
AAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGTCAAGGAATATAATCAGTAAAATTGATAA
TTAAGAGGCAAGGAATTAATCAGTAAAATTGATAATTAAGAGGCAAAGTAATAGTAATCAGTAAA
ATTGATAATTAAGAGCCAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGCC
Found at i:730 original size:32 final size:33
Alignment explanation
Indices: 689--763 Score: 125
Period size: 32 Copynumber: 2.3 Consensus size: 33
679 AGTAAAAGAG
689 TAATCAGTAATTAAGAAAGGAAATAAAAA-AAT
1 TAATCAGTAATTAAGAAAGGAAATAAAAAGAAT
* *
721 TAATCAGTAATTAAGAAAGGAAGTAAAAAGGAT
1 TAATCAGTAATTAAGAAAGGAAATAAAAAGAAT
754 TAATCAGTAA
1 TAATCAGTAA
764 ATTAGTAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 28 0.70
33 12 0.30
ACGTcount: A:0.57, C:0.04, G:0.16, T:0.23
Consensus pattern (33 bp):
TAATCAGTAATTAAGAAAGGAAATAAAAAGAAT
Found at i:1037 original size:14 final size:13
Alignment explanation
Indices: 1015--1114 Score: 69
Period size: 14 Copynumber: 7.3 Consensus size: 13
1005 CAGTAAAAAG
1015 GTAAAAGTAATCA
1 GTAAAAGTAATCA
1028 GTAAAGAGTAATCA
1 GTAAA-AGTAATCA
**
1042 GTAAAAAGTAAAAA
1 GT-AAAAGTAATCA
* *
1056 TGGCAAAGAGTAGT-A
1 --GTAAA-AGTAATCA
*
1071 -AAAAAGTAATCA
1 GTAAAAGTAATCA
*
1083 TGTAAAAGCAATCA
1 -GTAAAAGTAATCA
1097 GTAAGAAGTAATCA
1 GTAA-AAGTAATCA
1111 GTAA
1 GTAA
1115 GAAGGTCAAA
Statistics
Matches: 68, Mismatches: 10, Indels: 17
0.72 0.11 0.18
Matches are distributed among these distances:
11 5 0.07
12 4 0.06
13 9 0.13
14 38 0.56
15 7 0.10
16 5 0.07
ACGTcount: A:0.54, C:0.07, G:0.19, T:0.20
Consensus pattern (13 bp):
GTAAAAGTAATCA
Found at i:1205 original size:26 final size:25
Alignment explanation
Indices: 1176--1227 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
1166 AAAATGGTGT
*
1176 AGAGTAAAAAAATGGTATTAAGTAAA
1 AGAGT-AAAAAACGGTATTAAGTAAA
* *
1202 AGAGTAAAGAACGGTATTAATTAAA
1 AGAGTAAAAAACGGTATTAAGTAAA
1227 A
1 A
1228 AATGGTGTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.56, C:0.02, G:0.19, T:0.23
Consensus pattern (25 bp):
AGAGTAAAAAACGGTATTAAGTAAA
Found at i:1275 original size:42 final size:43
Alignment explanation
Indices: 1110--1280 Score: 158
Period size: 42 Copynumber: 4.0 Consensus size: 43
1100 AGAAGTAATC
* *
1110 AGTAAGAAGGTCAAAAATGGTATCAAGT-GAAATATGGTATTA
1 AGTAAGAAGGTCAAAAATGGTATCAAGTAAAAAAATGGTATTA
*
1152 AGTAAGAAGGTCAAAAAATGGTGT-AGAGTAAAAAAATGGTATTA
1 AGTAAGAAGGTC-AAAAATGGTATCA-AGTAAAAAAATGGTATTA
* * * *
1196 AGTAA-AAGAGT-AAAGAACGGTATTAA-TTAAAAAATGGTGTTA
1 AGTAAGAAG-GTCAAA-AATGGTATCAAGTAAAAAAATGGTATTA
* * *
1238 AGTAA-AATGGTCAAAAATGGTATCCAGT-AAGAGATGGTATTA
1 AGTAAGAA-GGTCAAAAATGGTATCAAGTAAAAAAATGGTATTA
1280 A
1 A
1281 ACAAAAATGG
Statistics
Matches: 107, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 59 0.55
43 28 0.26
44 20 0.19
ACGTcount: A:0.47, C:0.04, G:0.23, T:0.25
Consensus pattern (43 bp):
AGTAAGAAGGTCAAAAATGGTATCAAGTAAAAAAATGGTATTA
Found at i:1302 original size:16 final size:16
Alignment explanation
Indices: 1250--1302 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
1240 TAAAATGGTC
**
1250 AAAAATGGTATCCAGT
1 AAAAATGGTATTAAGT
* **
1266 AAGAGATGGTATTAAAC
1 AA-AAATGGTATTAAGT
1283 AAAAATGGTATTAAGT
1 AAAAATGGTATTAAGT
1299 AAAA
1 AAAA
1303 GAGTAAGAAA
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
16 17 0.61
17 11 0.39
ACGTcount: A:0.51, C:0.06, G:0.19, T:0.25
Consensus pattern (16 bp):
AAAAATGGTATTAAGT
Found at i:1330 original size:15 final size:15
Alignment explanation
Indices: 1310--1340 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1300 AAAGAGTAAG
*
1310 AAAAATGGTAAAAGT
1 AAAAATGATAAAAGT
1325 AAAAATGATAAAAGT
1 AAAAATGATAAAAGT
1340 A
1 A
1341 GCAAAAGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.16, T:0.19
Consensus pattern (15 bp):
AAAAATGATAAAAGT
Done.