Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016178.1 Corchorus capsularis cultivar CVL-1 contig16199, 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: 24300
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:2620 original size:55 final size:49
Alignment explanation
Indices: 2523--2620 Score: 178
Period size: 49 Copynumber: 2.0 Consensus size: 49
2513 ATGTACCTAC
*
2523 AATCAAGGAATTGGTAAGCTATTTGAAATAGTTAGTGTTAGTATTAGTA
1 AATCAAGCAATTGGTAAGCTATTTGAAATAGTTAGTGTTAGTATTAGTA
*
2572 AATCAAGCAATTTGTAAGCTATTTGAAATAGTTAGTGTTAGTATTAGTA
1 AATCAAGCAATTGGTAAGCTATTTGAAATAGTTAGTGTTAGTATTAGTA
2621 TTAGAAGTCT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.38
Consensus pattern (49 bp):
AATCAAGCAATTGGTAAGCTATTTGAAATAGTTAGTGTTAGTATTAGTA
Found at i:3211 original size:31 final size:31
Alignment explanation
Indices: 3173--3232 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
3163 TATATTAGAA
* *
3173 AAATAAGGATATAATAGGCGTTTCAAAAGTT
1 AAATAAGGATACAATAGACGTTTCAAAAGTT
3204 AAATAAGGATACAATAGACGTTTCAAAAG
1 AAATAAGGATACAATAGACGTTTCAAAAG
3233 CTTTACAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.48, C:0.08, G:0.18, T:0.25
Consensus pattern (31 bp):
AAATAAGGATACAATAGACGTTTCAAAAGTT
Found at i:3564 original size:31 final size:31
Alignment explanation
Indices: 3526--3584 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
3516 TATGTTAGAA
* *
3526 AAATAAGGATATAATAGGCGTTTCAAAAGTT
1 AAATAAGGATACAATAAGCGTTTCAAAAGTT
*
3557 AAATAAGGGTACAATAAGCGTTTCAAAA
1 AAATAAGGATACAATAAGCGTTTCAAAA
3585 ATTTTATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.47, C:0.08, G:0.19, T:0.25
Consensus pattern (31 bp):
AAATAAGGATACAATAAGCGTTTCAAAAGTT
Found at i:3617 original size:353 final size:354
Alignment explanation
Indices: 2908--3618 Score: 1183
Period size: 353 Copynumber: 2.0 Consensus size: 354
2898 ATTTATTAGT
* * *
2908 ATTAGTCTATTGGAAACGTTTGGTTCAAGAAGTTGAAATCTTTAAAAACTTCTGCTCTAACTTGG
1 ATTAATCTATTAGAAACGTTTGGTTCAAAAAGTTGAAATCTTTAAAAACTTCTGCTCTAACTTGG
2973 ATTGAAGTAAATTTTAGATATATATTTCGTAGATTTAATTAAATGCTATTAGTCTATTAGAAACA
66 ATTGAAGTAAATTTTAGATATATATTTCGTAGATTTAATTAAATGCTATTAGTCTATTAGAAACA
3038 TTTGGTTCAAGAAGTTGAAATCTATAAAAACTAAATTTGAGATATATATATATATATATTTGGTA
131 TTTGGTTCAAGAAGTTGAAATCTATAAAAACTAAATTTGAG--------A-ATATATATTTGGTA
*
3103 GATTTAATTAAATGCAAATTAACAAAAATAAAAAATAATTATATAATGGTAGTTTAGAAATATAT
187 GATTTAATTAAATGCAAATTAACAAAAATAAAAAATAATTATATAATGGTAATTTAGAAATATAT
*
3168 TAGAAAAATAAGGATATAATAGGCGTTTCAAAAGTTAAATAAGGATACAATAGACGTTTCAAAAG
252 TAGAAAAATAAGGATATAATAGGCGTTTCAAAAGTTAAATAAGGATACAATAGACGTTTCAAAAA
*
3233 CTTTACAAAACTCGTACTTTTATATATAGTATAGATAG
317 CTTTACAAAACTCGTACCTTTATATATAGTATAGATAG
**
3271 ATTAATCTATTAGAAACGTTTGGTTCAAAAAGTTGAAATCTTTAAAAACTTCTGCTCTAGTTTGG
1 ATTAATCTATTAGAAACGTTTGGTTCAAAAAGTTGAAATCTTTAAAAACTTCTGCTCTAACTTGG
* *
3336 ATTGAAGTAAGTTTTAGATATATATTTCGTAGATTTAATTAAATGCTATTAGTCTATTAGAAACG
66 ATTGAAGTAAATTTTAGATATATATTTCGTAGATTTAATTAAATGCTATTAGTCTATTAGAAACA
3401 TTTGGTTCAAGAAGTTGAAATCTATAAAAACTAAATTTGAG-ATATATATTTGGTAGATTTAATT
131 TTTGGTTCAAGAAGTTGAAATCTATAAAAACTAAATTTGAGAATATATATTTGGTAGATTTAATT
* *
3465 AAATGCAAATTAACAAAATTAAAAAATAATTATATAATGGTAATTTAGAAATATGTTAGAAAAAT
196 AAATGCAAATTAACAAAAATAAAAAATAATTATATAATGGTAATTTAGAAATATATTAGAAAAAT
* * *
3530 AAGGATATAATAGGCGTTTCAAAAGTTAAATAAGGGTACAATA-AGCGTTTCAAAAATTTTATAA
261 AAGGATATAATAGGCGTTTCAAAAGTTAAATAAGGATACAATAGA-CGTTTCAAAAACTTTACAA
3594 AACTCGTACCTTTATATATAGTATA
325 AACTCGTACCTTTATATATAGTATA
3619 TTATAAGAAA
Statistics
Matches: 332, Mismatches: 15, Indels: 12
0.92 0.04 0.03
Matches are distributed among these distances:
352 1 0.00
353 167 0.50
363 164 0.49
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (354 bp):
ATTAATCTATTAGAAACGTTTGGTTCAAAAAGTTGAAATCTTTAAAAACTTCTGCTCTAACTTGG
ATTGAAGTAAATTTTAGATATATATTTCGTAGATTTAATTAAATGCTATTAGTCTATTAGAAACA
TTTGGTTCAAGAAGTTGAAATCTATAAAAACTAAATTTGAGAATATATATTTGGTAGATTTAATT
AAATGCAAATTAACAAAAATAAAAAATAATTATATAATGGTAATTTAGAAATATATTAGAAAAAT
AAGGATATAATAGGCGTTTCAAAAGTTAAATAAGGATACAATAGACGTTTCAAAAACTTTACAAA
ACTCGTACCTTTATATATAGTATAGATAG
Found at i:5366 original size:1 final size:1
Alignment explanation
Indices: 5360--5395 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
5350 ATAGCTATTT
5360 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5396 CCTTGCCGCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:5462 original size:33 final size:33
Alignment explanation
Indices: 5400--5519 Score: 152
Period size: 33 Copynumber: 3.7 Consensus size: 33
5390 AAAAAACCTT
* * *
5400 GCCGCCCTAGTGGGGCGGCT-AGCCGTGGCAGA
1 GCCGTCCTAGTGGGGAGGCTCCGCCGTGGCAGA
* * *
5432 GCCGTCCTAGTGAGGTGGCTCCGTCGTGGCAGA
1 GCCGTCCTAGTGGGGAGGCTCCGCCGTGGCAGA
* *
5465 GTCGCCCTAGTGGGGAGGCTCCGCCGTGGCAGA
1 GCCGTCCTAGTGGGGAGGCTCCGCCGTGGCAGA
*
5498 GCCGTCTTAGTGGGGAGGCTCC
1 GCCGTCCTAGTGGGGAGGCTCC
5520 ACGTGGCTAA
Statistics
Matches: 74, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
32 17 0.23
33 57 0.77
ACGTcount: A:0.12, C:0.29, G:0.42, T:0.17
Consensus pattern (33 bp):
GCCGTCCTAGTGGGGAGGCTCCGCCGTGGCAGA
Found at i:6243 original size:2 final size:2
Alignment explanation
Indices: 6236--6266 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6226 TATGTATGTA
6236 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
6267 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:18133 original size:56 final size:56
Alignment explanation
Indices: 18042--18158 Score: 198
Period size: 56 Copynumber: 2.1 Consensus size: 56
18032 CTGAGGTATT
* *
18042 TGATCAATATGGCTCCATAGGCTTCAAATCTGTCTCCCAAAATAGTTGAAGATAAA
1 TGATAAATATGGCTCCACAGGCTTCAAATCTGTCTCCCAAAATAGTTGAAGATAAA
* *
18098 TGATAAATATGGCTCCACAGGCTTCAATTTTGTCTCCCAAAATAGTTGAAGATAAA
1 TGATAAATATGGCTCCACAGGCTTCAAATCTGTCTCCCAAAATAGTTGAAGATAAA
18154 TGATA
1 TGATA
18159 CTGCTTTATA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (56 bp):
TGATAAATATGGCTCCACAGGCTTCAAATCTGTCTCCCAAAATAGTTGAAGATAAA
Found at i:18462 original size:48 final size:45
Alignment explanation
Indices: 18372--18459 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 45
18362 GGTTTAGGAA
18372 AAAAAAAAAGAGAGAGAGAAGATAATTACGCTAAAGAGTAGTGTT
1 AAAAAAAAAGAGAGAGAGAAGATAATTACGCTAAAGAGTAGTGTT
*
18417 AAAAAAAAA-AGAGA-A-AAGATAATTACGCTTAAGAGTAGTGTT
1 AAAAAAAAAGAGAGAGAGAAGATAATTACGCTAAAGAGTAGTGTT
18459 A
1 A
18460 GTGAATAATA
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
42 27 0.64
43 1 0.02
44 5 0.12
45 9 0.21
ACGTcount: A:0.55, C:0.05, G:0.22, T:0.19
Consensus pattern (45 bp):
AAAAAAAAAGAGAGAGAGAAGATAATTACGCTAAAGAGTAGTGTT
Found at i:20063 original size:102 final size:101
Alignment explanation
Indices: 19857--20051 Score: 245
Period size: 102 Copynumber: 1.9 Consensus size: 101
19847 AACACCGTTC
* *
19857 AAAGGCTCCGAGCTTTAATTAATCATAAATCAAACAAAAATAGCCAACAAAAGACGTCAAACTTG
1 AAAGGCTACAAGCTTTAATTAATCATAAATCAAACAAAAATAGCCAAC-AAAGACGTCAAACTTG
* ** *
19922 TGAATTCAATATTGAAATTAGTATAGATTAATTACAA
65 TGAAATCAATATTGAAATTAGTATAGATTAAAGAAAA
* * *
19959 AAAGGCTACAAGCTTTAGTTAATGATAAATCAAA-AAAGAATAGCCAAC-AA-ACGTCAAAGTTG
1 AAAGGCTACAAGCTTTAATTAATCATAAATCAAACAAA-AATAGCCAACAAAGACGTCAAACTTG
*
20021 TGAAATCAAT-TATGAGATTAGTATAGATTAA
65 TGAAATCAATAT-TGAAATTAGTATAGATTAA
20052 CAAAGAAAAA
Statistics
Matches: 84, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
98 1 0.01
99 38 0.45
100 2 0.02
101 3 0.04
102 40 0.48
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.26
Consensus pattern (101 bp):
AAAGGCTACAAGCTTTAATTAATCATAAATCAAACAAAAATAGCCAACAAAGACGTCAAACTTGT
GAAATCAATATTGAAATTAGTATAGATTAAAGAAAA
Found at i:20736 original size:30 final size:29
Alignment explanation
Indices: 20671--20742 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
20661 ACACCGAACC
****
20671 GTCAAATAAGCCCCTGAACTATTATTTCA
1 GTCAAATAAGCCCCTGAACTATTAAAAAA
*
20700 GTCAAATAAGCCCCTGAACTCTTAAAAAA
1 GTCAAATAAGCCCCTGAACTATTAAAAAA
20729 TGTCAAATAAGCCC
1 -GTCAAATAAGCCC
20743 TGTTGCCAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 24 0.65
30 13 0.35
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.25
Consensus pattern (29 bp):
GTCAAATAAGCCCCTGAACTATTAAAAAA
Found at i:21428 original size:2 final size:2
Alignment explanation
Indices: 21421--21450 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
21411 TTATAGAAAG
*
21421 TA TA TA TA TA TA TA TT TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21451 AAAATTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:22966 original size:25 final size:25
Alignment explanation
Indices: 22936--23004 Score: 120
Period size: 25 Copynumber: 2.8 Consensus size: 25
22926 TGGATGACAT
22936 GTTAGGGTTTGGTTTTCATGTCATG
1 GTTAGGGTTTGGTTTTCATGTCATG
22961 GTTAGGGTTTGGTTTTCATGTCATG
1 GTTAGGGTTTGGTTTTCATGTCATG
* *
22986 GTTAGGGTTTAGTCTTCAT
1 GTTAGGGTTTGGTTTTCAT
23005 CTCACCAAGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.13, C:0.09, G:0.30, T:0.48
Consensus pattern (25 bp):
GTTAGGGTTTGGTTTTCATGTCATG
Done.