Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011937.1 Corchorus capsularis cultivar CVL-1 contig11958, 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: 9975
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:212 original size:17 final size:17
Alignment explanation
Indices: 190--243 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
180 GTAAAAAGGG
190 CAATAAGTAATTAAGTT
1 CAATAAGTAATTAAGTT
*
207 CAATAAG-AA-AAAG-T
1 CAATAAGTAATTAAGTT
* *
221 -AATCAGTGATTAAGTT
1 CAATAAGTAATTAAGTT
237 CAATAAG
1 CAATAAG
244 AAAAAGCAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 8
0.68 0.12 0.20
Matches are distributed among these distances:
13 5 0.18
14 2 0.07
15 6 0.21
16 3 0.11
17 12 0.43
ACGTcount: A:0.50, C:0.07, G:0.15, T:0.28
Consensus pattern (17 bp):
CAATAAGTAATTAAGTT
Found at i:234 original size:30 final size:30
Alignment explanation
Indices: 161--257 Score: 122
Period size: 30 Copynumber: 3.1 Consensus size: 30
151 GGGTGATCAG
* *
161 AGTGATTAAGTTCGAAAAAGTAAAAAGGGCAATA
1 AGTGATTAAGTTC-AATAAG-AAAAA--GCAATC
* *
195 AGTAATTAAGTTCAATAAGAAAAAGTAATC
1 AGTGATTAAGTTCAATAAGAAAAAGCAATC
225 AGTGATTAAGTTCAATAAGAAAAAGCAATC
1 AGTGATTAAGTTCAATAAGAAAAAGCAATC
255 AGT
1 AGT
258 AAAGAGTAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
30 35 0.61
32 5 0.09
33 5 0.09
34 12 0.21
ACGTcount: A:0.51, C:0.07, G:0.19, T:0.24
Consensus pattern (30 bp):
AGTGATTAAGTTCAATAAGAAAAAGCAATC
Found at i:345 original size:22 final size:22
Alignment explanation
Indices: 292--480 Score: 76
Period size: 22 Copynumber: 8.8 Consensus size: 22
282 AATTAAATTC
* **
292 AAATAGTAATCAGTAAAA-AAA
1 AAATGGTAATCAGTAAAAGGTA
*
313 ATAATGATAATCAGTAAAAGGTA
1 A-AATGGTAATCAGTAAAAGGTA
* *
336 AAATGGTAATTAGT-AAAGAGCA
1 AAATGGTAATCAGTAAAAG-GTA
* *
358 ATATGGTAAGT-AGT-AGAGAGT-
1 AAATGGTAA-TCAGTAAAAG-GTA
*
379 -AATAGTAATCAGTAAGAA-GT-
1 AAATGGTAATCAGTAA-AAGGTA
*
399 -AACGGTAATCAGTAATAA-GTA
1 AAATGGTAATCAGTAA-AAGGTA
* * **
420 AAATGGTAGTTAGTAATGGGTA
1 AAATGGTAATCAGTAAAAGGTA
* *
442 CAATGGTAATTAGT-AAAGAGTA
1 AAATGGTAATCAGTAAAAG-GTA
* *
464 AAGTGATAATCAGTAAA
1 AAATGGTAATCAGTAAA
481 GAGTAATAGA
Statistics
Matches: 127, Mismatches: 29, Indels: 22
0.71 0.16 0.12
Matches are distributed among these distances:
19 1 0.01
20 28 0.22
21 8 0.06
22 85 0.67
23 5 0.04
ACGTcount: A:0.49, C:0.04, G:0.22, T:0.25
Consensus pattern (22 bp):
AAATGGTAATCAGTAAAAGGTA
Found at i:392 original size:20 final size:20
Alignment explanation
Indices: 376--420 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
366 AGTAGTAGAG
*
376 AGTAATAGTAATCAGTAAGA
1 AGTAACAGTAATCAGTAAGA
* *
396 AGTAACGGTAATCAGTAATA
1 AGTAACAGTAATCAGTAAGA
416 AGTAA
1 AGTAA
421 AATGGTAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.07, G:0.20, T:0.24
Consensus pattern (20 bp):
AGTAACAGTAATCAGTAAGA
Found at i:407 original size:106 final size:106
Alignment explanation
Indices: 297--499 Score: 250
Period size: 106 Copynumber: 1.9 Consensus size: 106
287 AATTCAAATA
297 GTAATCAGTAA-AAAAAATAATGATAATCAGTAAAAGGTAAAATGGTAATTAGTAAAGAGCAATA
1 GTAATCAGTAATAAAAAA-AATGATAATCAGTAAAAGGTAAAATGGTAATTAGTAAAGAGCAA-A
* * *
361 -TGGTAAGT-AGTAGAGAGTAATAGTAATCAGTAAGAAGTAACG
64 GTGATAA-TCAGTAAAGAGTAATAGAAATCAGTAAGAAGTAACG
** * * * ** * *
403 GTAATCAGTAATAAGTAAAATGGTAGTTAGTAATGGGTACAATGGTAATTAGTAAAGAGTAAAGT
1 GTAATCAGTAATAAAAAAAATGATAATCAGTAAAAGGTAAAATGGTAATTAGTAAAGAGCAAAGT
468 GATAATCAGTAAAGAGTAATAGAAATCAGTAA
66 GATAATCAGTAAAGAGTAATAGAAATCAGTAA
500 ATCAGTAATT
Statistics
Matches: 82, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
105 2 0.02
106 76 0.93
107 4 0.05
ACGTcount: A:0.48, C:0.04, G:0.22, T:0.25
Consensus pattern (106 bp):
GTAATCAGTAATAAAAAAAATGATAATCAGTAAAAGGTAAAATGGTAATTAGTAAAGAGCAAAGT
GATAATCAGTAAAGAGTAATAGAAATCAGTAAGAAGTAACG
Found at i:448 original size:84 final size:85
Alignment explanation
Indices: 293--464 Score: 206
Period size: 84 Copynumber: 2.0 Consensus size: 85
283 ATTAAATTCA
*
293 AATAGTAATCAGTAAAAAAAATAATGATAATCAGTAAAAGGTAAAATGGTAATTAGTAAAGAGCA
1 AATAGTAATCAGT-AAAAAAATAACGATAATCAGTAAAAGGTAAAATGGTAATTAGTAAAGAGCA
*
358 ATATGGTAAGTAGTAGAGAGT
65 ATATGGTAAGTAGTAAAGAGT
* * * * * * *
379 AATAGTAATCAGT-AAGAAGTAACGGTAATCAGTAATAA-GTAAAATGGTAGTTAGTAATGGGTA
1 AATAGTAATCAGTAAAAAAATAACGATAATCAGTAA-AAGGTAAAATGGTAATTAGTAAAGAGCA
*
442 CA-ATGGTAATTAGTAAAGAGT
65 -ATATGGTAAGTAGTAAAGAGT
463 AA
1 AA
465 AGTGATAATC
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
84 58 0.78
85 3 0.04
86 13 0.18
ACGTcount: A:0.48, C:0.04, G:0.22, T:0.26
Consensus pattern (85 bp):
AATAGTAATCAGTAAAAAAATAACGATAATCAGTAAAAGGTAAAATGGTAATTAGTAAAGAGCAA
TATGGTAAGTAGTAAAGAGT
Found at i:496 original size:20 final size:21
Alignment explanation
Indices: 448--500 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
438 GGTACAATGG
*
448 TAATTAGTAAAGAGTAAAGTGA
1 TAATCAGTAAAGAGTAAAG-GA
470 TAATCAGTAAAGAGTAATA-GA
1 TAATCAGTAAAGAGTAA-AGGA
491 -AATCAGTAAA
1 TAATCAGTAAA
501 TCAGTAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 10 0.34
21 2 0.07
22 16 0.55
23 1 0.03
ACGTcount: A:0.53, C:0.04, G:0.19, T:0.25
Consensus pattern (21 bp):
TAATCAGTAAAGAGTAAAGGA
Found at i:544 original size:55 final size:55
Alignment explanation
Indices: 482--843 Score: 600
Period size: 55 Copynumber: 6.6 Consensus size: 55
472 ATCAGTAAAG
* * *
482 AGTAATAGAAATCAGTAAATCAGTAATTAAGTGAAAAGAAATTAATCAGAGTCAA
1 AGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
* * * *
537 GGTAATAGAAATCAGTAAATCAATAATTAAGTGAAAAAGAAATTAATCAGAGTCAA
1 AGTAATAGTAATCAGTAAATCAGTAATTAAGT-AAAAAGAGATTAATCAGAGTCAA
*
593 GGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
1 AGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
*
648 AATAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
1 AGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
703 AGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
1 AGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
*
758 AGTAGTAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
1 AGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
*
813 GGTAATAGTAATCAGTAAATC-GATAATTAAG
1 AGTAATAGTAATCAGTAAATCAG-TAATTAAG
844 AGTTAAAATG
Statistics
Matches: 293, Mismatches: 12, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
54 1 0.00
55 240 0.82
56 52 0.18
ACGTcount: A:0.51, C:0.07, G:0.17, T:0.25
Consensus pattern (55 bp):
AGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAA
Found at i:1126 original size:43 final size:42
Alignment explanation
Indices: 1079--1418 Score: 233
Period size: 43 Copynumber: 7.7 Consensus size: 42
1069 TAAATTAGTA
1079 AAGAGTAAAATAGTAATCAGTAAAAAGTAAGAAGGTAATCAAC
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAA-AAGGTAATCAAC
* * **
1122 AAGAGTAAAATAGTAGTCAGTAAAATGTAAATA-GTAATCAGT
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAA-AGGTAATCAAC
* * **
1164 AAGAGTAAAA-AGGTAATAAGTAAGAAGTAAAAGG-AGATCAGT
1 AAGAGTAAAATA-GTAATCAGTAAAAAGTAAAAGGTA-ATCAAC
* * * *
1206 AAGAGTAAAA-AGGTGATCAGTAAAGAGTAAAAAGCTAATCAGC
1 AAGAGTAAAATA-GTAATCAGTAAAAAGT-AAAAGGTAATCAAC
* * *
1249 AAGAAGGAAAA-AGGTAATCAGTAAAAAGCAAAAGGCAATCAGTA-
1 AAG-AGTAAAATA-GTAATCAGTAAAAAGTAAAAGGTAATCA--AC
* * * * * *
1293 AAAAGTAAAAGAATAATCAGTAAAAAAGGAGAAGAAAATAGTAATCAGTAA
1 AAGAGTAAAATAGTAATCAGT--AAAA--AG--TAAAA-GGTAATCA--AC
* *
1344 AAGAGTAAAATTGTAATCAGTAAAAAGTAAGAAGGTAATTAAC
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAA-AAGGTAATCAAC
*
1387 AAGAGTAAAAATAGTAATCAGTACAAAGTAAA
1 AAGAGT-AAAATAGTAATCAGTAAAAAGTAAA
1419 GAATAATCAG
Statistics
Matches: 240, Mismatches: 37, Indels: 40
0.76 0.12 0.13
Matches are distributed among these distances:
41 3 0.01
42 64 0.27
43 74 0.31
44 47 0.20
45 12 0.05
46 2 0.01
47 4 0.02
49 8 0.03
50 9 0.04
51 17 0.07
ACGTcount: A:0.56, C:0.06, G:0.20, T:0.18
Consensus pattern (42 bp):
AAGAGTAAAATAGTAATCAGTAAAAAGTAAAAGGTAATCAAC
Found at i:1179 original size:21 final size:21
Alignment explanation
Indices: 1028--1431 Score: 189
Period size: 21 Copynumber: 18.4 Consensus size: 21
1018 AATAGCATGC
*
1028 AATCAGTAAAAAGTAAAAAGGT
1 AATCAGT-AAGAGTAAAAAGGT
* * * *
1050 -ATCTGAAAGGGTAAAATGGT
1 AATCAGTAAGAGTAAAAAGGT
*
1070 AAATTAGTAAAGAGTAAAATA-GT
1 -AATCAGT-AAGAGTAAAA-AGGT
* *
1093 AATCAGTAAAAAGTAAGAAGGT
1 AATCAGT-AAGAGTAAAAAGGT
**
1115 AATCAACAAGAGTAAAATA-GT
1 AATCAGTAAGAGTAAAA-AGGT
* * *
1136 AGTCAGTAAAATGTAAATA-GT
1 AATCAGTAAGA-GTAAAAAGGT
1157 AATCAGTAAGAGTAAAAAGGT
1 AATCAGTAAGAGTAAAAAGGT
*
1178 AATAAGTAAGAAGT-AAAAGG-
1 AATCAGTAAG-AGTAAAAAGGT
1198 AGATCAGTAAGAGTAAAAAGGT
1 A-ATCAGTAAGAGTAAAAAGGT
* *
1220 GATCAGTAAAGAGTAAAAAGCT
1 AATCAGT-AAGAGTAAAAAGGT
* *
1242 AATCAGCAAGAAGGAAAAAGGT
1 AATCAGTAAG-AGTAAAAAGGT
* * *
1264 AATCAGTAAAAAG-CAAAAGGC
1 AATCAGT-AAGAGTAAAAAGGT
* *
1285 AATCAGTAAAAAGT-AAAAGAAT
1 AATCAGT-AAGAGTAAAAAG-GT
* *
1307 AATCAGTAAAAAAGGAGAAGAAAATAGT
1 AATCAGT----AA-GAGTA-AAAA-GGT
**
1335 AATCAGTAAAAGAGTAAAATTGT
1 AATCAGT--AAGAGTAAAAAGGT
* *
1358 AATCAGTAAAAAGTAAGAAGGT
1 AATCAGT-AAGAGTAAAAAGGT
* ** *
1380 AATTAACAAGAGTAAAAATAGT
1 AATCAGTAAGAGTAAAAA-GGT
*
1402 AATCAGTACAAAGTAAAGAA--T
1 AATCAGTA-AGAGTAAA-AAGGT
1423 AATCAGTAA
1 AATCAGTAA
1432 AATAGTGATG
Statistics
Matches: 295, Mismatches: 60, Indels: 56
0.72 0.15 0.14
Matches are distributed among these distances:
20 22 0.07
21 116 0.39
22 98 0.33
23 29 0.10
24 5 0.02
25 7 0.02
26 6 0.02
28 12 0.04
ACGTcount: A:0.55, C:0.06, G:0.20, T:0.19
Consensus pattern (21 bp):
AATCAGTAAGAGTAAAAAGGT
Found at i:1362 original size:116 final size:115
Alignment explanation
Indices: 1221--1433 Score: 256
Period size: 116 Copynumber: 1.8 Consensus size: 115
1211 TAAAAAGGTG
* *
1221 ATCAGTAAAGAGTAAAAAGCTAATCAGCAAGAAGGAAAAAGGTAATCAGTAA-AA-AG-CAAAA-
1 ATCAGTAAAGAGTAAAAAGCTAATCAGCAAAAAGGAAAAAGGTAAT---TAACAAGAGTAAAAAT
*
1282 GGCAATCAGTAAAAAGTAAAAGAATAATCAGTAAAAAAGGAGAAGAAAATAGTA
63 AGCAATCAGTAAAAAGT-AAAGAATAATCAGTAAAAAAGGAGAAGAAAATAGTA
* * * *
1336 ATCAGTAAAAGAGTAAAATTG-TAATCAGTAAAAAGTAAGAAGGTAATTAACAAGAGTAAAAATA
1 ATCAGT-AAAGAGTAAAA-AGCTAATCAGCAAAAAGGAAAAAGGTAATTAACAAGAGTAAAAATA
* *
1400 GTAATCAGTACAAAGTAAAGAATAATCAGTAAAA
64 GCAATCAGTAAAAAGTAAAGAATAATCAGTAAAA
1434 TAGTGATGGT
Statistics
Matches: 83, Mismatches: 9, Indels: 11
0.81 0.09 0.11
Matches are distributed among these distances:
113 3 0.04
114 2 0.02
115 8 0.10
116 55 0.66
117 15 0.18
ACGTcount: A:0.57, C:0.07, G:0.18, T:0.17
Consensus pattern (115 bp):
ATCAGTAAAGAGTAAAAAGCTAATCAGCAAAAAGGAAAAAGGTAATTAACAAGAGTAAAAATAGC
AATCAGTAAAAAGTAAAGAATAATCAGTAAAAAAGGAGAAGAAAATAGTA
Found at i:4382 original size:21 final size:21
Alignment explanation
Indices: 4354--4396 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
4344 ACGAACCCTA
4354 AATTTTTTTTT-GAAAAACGC
1 AATTTTTTTTTAGAAAAACGC
*
4374 AATTTTTTTTTAGAAAAATGC
1 AATTTTTTTTTAGAAAAACGC
4395 AA
1 AA
4397 AAAAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (21 bp):
AATTTTTTTTTAGAAAAACGC
Found at i:4649 original size:20 final size:21
Alignment explanation
Indices: 4624--4671 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
4614 TAAAATTATC
* *
4624 AATTAAAAAGAAAGC-AATTA
1 AATTAAAAACAAAGCAAAGTA
4644 AATTAAAAACAAAGCAAAGTA
1 AATTAAAAACAAAGCAAAGTA
4665 AATTAAA
1 AATTAAA
4672 TCTAAATCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.67, C:0.06, G:0.08, T:0.19
Consensus pattern (21 bp):
AATTAAAAACAAAGCAAAGTA
Found at i:8870 original size:19 final size:18
Alignment explanation
Indices: 8846--8882 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
8836 TTGAAGATTT
8846 CTTGAAGATAATTTGAAGA
1 CTTGAAGATAA-TTGAAGA
*
8865 CTTGAAGATCATTGAAGA
1 CTTGAAGATAATTGAAGA
8883 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (18 bp):
CTTGAAGATAATTGAAGA
Done.