Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01008694.1 Corchorus olitorius cultivar O-4 contig08721, 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, 832
Length: 1387
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Found at i:146 original size:22 final size:22
Alignment explanation
Indices: 121--608 Score: 125
Period size: 22 Copynumber: 22.1 Consensus size: 22
111 ACCAAAGTTA
121 CATAGGAAGGTTATCAAAATTT
1 CATAGGAAGGTTATCAAAATTT
* * *
143 CATAATG-TGGTTACCAAAATTT
1 CAT-AGGAAGGTTATCAAAATTT
* *
165 CATATGG-TGGTTATCAAAACTT
1 CATA-GGAAGGTTATCAAAATTT
* *
187 CATA-CAGAGG-TACCAAAATTT
1 CATAGGA-AGGTTATCAAAATTT
** *
208 CATAAAAAGGTTATCGAAATTT
1 CATAGGAAGGTTATCAAAATTT
* * * *
230 CTTAGGGAGGTTAACCAAATTT
1 CATAGGAAGGTTATCAAAATTT
* *
252 CATATGAAGGTTATCAGAATTT
1 CATAGGAAGGTTATCAAAATTT
* * * *
274 TATAGTG-TGGGTATTAAAATTT
1 CATAG-GAAGGTTATCAAAATTT
* ** *
296 AATAAAAAGGTTAAC-AAATTT
1 CATAGGAAGGTTATCAAAATTT
*
317 CATAGGGAGGGAGGTTACCAAAA-TT
1 CATA-GGA---AGGTTATCAAAATTT
* * *
342 --T--G-TGCTTATCAAAATCT
1 CATAGGAAGGTTATCAAAATTT
* * * *
359 CCTAGGGAGGTTAACAAAATTA
1 CATAGGAAGGTTATCAAAATTT
* *
381 CATA-GAGAGGATATTACAGATTCATTCT
1 CATAGGA-AGGTTA-T-CA-A--AATT-T
* * *
409 CACATGG-AGGTTGTCGAAATTT
1 CATA-GGAAGGTTATCAAAATTT
**
431 CAT-GGTGCGGTTATCAAAATTTT
1 CATAGG-AAGGTTATCAAAA-TTT
* *
454 CATAGTG-CGGTTA-C-CAATTT
1 CATAG-GAAGGTTATCAAAATTT
* * *
474 TATAGTG-TGATTATCAAAATTT
1 CATAG-GAAGGTTATCAAAATTT
* * *
496 CATAGGGAGATTATCAAATTTT
1 CATAGGAAGGTTATCAAAATTT
* *
518 CATTGTGTA-GTTATCAAAATTTT
1 CATAG-GAAGGTTATCAAAA-TTT
* * * *
541 CACAGTACGGTTATCAAATTTT
1 CATAGGAAGGTTATCAAAATTT
*
563 CATAGGGAGGTTATCAAAATTT
1 CATAGGAAGGTTATCAAAATTT
** *
585 CATAATAAGGTTATCAAATTTT
1 CATAGGAAGGTTATCAAAATTT
607 CA
1 CA
609 CAACGTGGTT
Statistics
Matches: 334, Mismatches: 93, Indels: 78
0.66 0.18 0.15
Matches are distributed among these distances:
16 9 0.03
17 1 0.00
19 1 0.00
20 16 0.05
21 32 0.10
22 208 0.62
23 36 0.11
24 3 0.01
25 12 0.04
26 4 0.01
27 4 0.01
28 7 0.02
30 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (22 bp):
CATAGGAAGGTTATCAAAATTT
Found at i:160 original size:44 final size:44
Alignment explanation
Indices: 111--273 Score: 154
Period size: 44 Copynumber: 3.7 Consensus size: 44
101 TGACAATCAA
* * *
111 ACCAAAGTTACATAGGAAGGTTATCAAAATTTCATAATGTGGTT
1 ACCAAAATTTCATAGGAAGGTTATCAAAATTTCATAATGAGGTT
* *
155 ACCAAAATTTCATATGG-TGGTTATCAAAACTTCATACA-GAGG-T
1 ACCAAAATTTCATA-GGAAGGTTATCAAAATTTCATA-ATGAGGTT
** * * **
198 ACCAAAATTTCATAAAAAGGTTATCGAAATTTCTTAGGGAGGTT
1 ACCAAAATTTCATAGGAAGGTTATCAAAATTTCATAATGAGGTT
* *
242 AACC-AAATTTCATATGAAGGTTATCAGAATTT
1 -ACCAAAATTTCATAGGAAGGTTATCAAAATTT
274 TATAGTGTGG
Statistics
Matches: 97, Mismatches: 16, Indels: 12
0.78 0.13 0.10
Matches are distributed among these distances:
43 34 0.35
44 57 0.59
45 6 0.06
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.32
Consensus pattern (44 bp):
ACCAAAATTTCATAGGAAGGTTATCAAAATTTCATAATGAGGTT
Found at i:218 original size:21 final size:21
Alignment explanation
Indices: 179--218 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
169 TGGTGGTTAT
* *
179 CAAAACTTCATACAGAGGTAC
1 CAAAACTTCATAAAAAGGTAC
*
200 CAAAATTTCATAAAAAGGT
1 CAAAACTTCATAAAAAGGT
219 TATCGAAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.17, G:0.12, T:0.23
Consensus pattern (21 bp):
CAAAACTTCATAAAAAGGTAC
Found at i:257 original size:87 final size:87
Alignment explanation
Indices: 127--326 Score: 215
Period size: 87 Copynumber: 2.3 Consensus size: 87
117 GTTACATAGG
** * **
127 AAGGTTATCAAAATTTCATAATGTGGTTACCAAAATTTCATATGGTGGTTATCAAAACTTCATAC
1 AAGGTTATC-AAATTTCATAGGGAGGTTACCAAAATTTCATATGAAGGTTATCAAAACTTCATAC
*
192 AG-AGGTACCAAAATTTCATAAA
65 AGTAGGTACCAAAATTTAATAAA
* * * *
214 AAGGTTATCGAAATTTCTTAGGGAGGTTAACC-AAATTTCATATGAAGGTTATCAGAATTTTATA
1 AAGGTTATC-AAATTTCATAGGGAGGTT-ACCAAAATTTCATATGAAGGTTATCAAAACTTCATA
** * **
278 GTGTGGGTATTAAAATTTAATAAA
64 CAGTAGGTACCAAAATTTAATAAA
*
302 AAGGTTAACAAATTTCATAGGGAGG
1 AAGGTTATCAAATTTCATAGGGAGG
327 GAGGTTACCA
Statistics
Matches: 93, Mismatches: 18, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
87 66 0.71
88 27 0.29
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (87 bp):
AAGGTTATCAAATTTCATAGGGAGGTTACCAAAATTTCATATGAAGGTTATCAAAACTTCATACA
GTAGGTACCAAAATTTAATAAA
Found at i:538 original size:44 final size:45
Alignment explanation
Indices: 414--608 Score: 163
Period size: 44 Copynumber: 4.4 Consensus size: 45
404 ATTCTCACAT
* * **
414 GGAGGTTGTCGAAA-TTTCATGGTGCGGTTATCAAAATTTTCATAG
1 GGAGGTTATC-AAATTTTCATAGTGTAGTTATCAAAATTTTCATAG
* * *
459 TGCGGTTA-CCAATTTT-ATAGTGT-GATTATCAAAA-TTTCATAG
1 GGAGGTTATCAAATTTTCATAGTGTAG-TTATCAAAATTTTCATAG
* * *
501 GGAGATTATCAAATTTTCATTGTGTAGTTATCAAAATTTTCACA-
1 GGAGGTTATCAAATTTTCATAGTGTAGTTATCAAAATTTTCATAG
* * *
545 GTACGGTTATCAAATTTTCATAG-GGAGGTTATCAAAA-TTTCATAA
1 GGA-GGTTATCAAATTTTCATAGTGTA-GTTATCAAAATTTTCATAG
**
590 TAAGGTTATCAAATTTTCA
1 GGAGGTTATCAAATTTTCA
609 CAACGTGGTT
Statistics
Matches: 122, Mismatches: 19, Indels: 19
0.76 0.12 0.12
Matches are distributed among these distances:
42 14 0.11
43 23 0.19
44 45 0.37
45 40 0.33
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.38
Consensus pattern (45 bp):
GGAGGTTATCAAATTTTCATAGTGTAGTTATCAAAATTTTCATAG
Found at i:598 original size:67 final size:66
Alignment explanation
Indices: 484--610 Score: 175
Period size: 67 Copynumber: 1.9 Consensus size: 66
474 TATAGTGTGA
* ** *
484 TTATCAAAATTTCATAGGGAGATTATCAAATTTTCATTGTGTAGTTATCAAAATTTTCACAGTAC
1 TTATCAAAATTTCATAGGGAGATTATCAAAATTTCATAATGAAGTTATC-AAATTTTCACAGTAC
549 GG
65 GG
* *
551 TTATCAAATTTTCATAGGGAGGTTATCAAAATTTCATAAT-AAGGTTATCAAATTTTCACA
1 TTATCAAAATTTCATAGGGAGATTATCAAAATTTCATAATGAA-GTTATCAAATTTTCACA
611 ACGTGGTTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
66 12 0.23
67 41 0.77
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (66 bp):
TTATCAAAATTTCATAGGGAGATTATCAAAATTTCATAATGAAGTTATCAAATTTTCACAGTACG
G
Found at i:618 original size:22 final size:21
Alignment explanation
Indices: 527--628 Score: 80
Period size: 22 Copynumber: 4.6 Consensus size: 21
517 TCATTGTGTA
527 GTTATCAAAATTTTCAC-AGTACG
1 GTTATC-AAATTTTCACAAG-A-G
* *
550 GTTATCAAATTTTCATAGGGAG
1 GTTATCAAATTTTCACA-AGAG
* * *
572 GTTATCAAAATTTCATAATAAG
1 GTTATCAAATTTTCACAA-GAG
*
594 GTTATCAAATTTTCACAACGTG
1 GTTATCAAATTTTCACAA-GAG
616 GTTATCAATATTT
1 GTTATCAA-ATTT
629 CTATGTTGGA
Statistics
Matches: 65, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
22 53 0.82
23 11 0.17
24 1 0.02
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (21 bp):
GTTATCAAATTTTCACAAGAG
Found at i:619 original size:44 final size:44
Alignment explanation
Indices: 439--629 Score: 179
Period size: 44 Copynumber: 4.3 Consensus size: 44
429 TTCATGGTGC
** * *
439 GGTTATCAAAATTTTCATAGTGCGGTTA-CCAATTTT-ATAGTGT
1 GGTTATCAAAA-TTTCATAGTAAGGTTATCAAATTTTCATAGCGT
* ** * * *
482 GATTATCAAAATTTCATAGGGAGATTATCAAATTTTCATTGTGT
1 GGTTATCAAAATTTCATAGTAAGGTTATCAAATTTTCATAGCGT
* * * * *
526 AGTTATCAAAATTTTCACAGTACGGTTATCAAATTTTCATAGGGA
1 GGTTATCAAAA-TTTCATAGTAAGGTTATCAAATTTTCATAGCGT
* * *
571 GGTTATCAAAATTTCATAATAAGGTTATCAAATTTTCACAACGT
1 GGTTATCAAAATTTCATAGTAAGGTTATCAAATTTTCATAGCGT
*
615 GGTTATCAATATTTC
1 GGTTATCAAAATTTC
630 TATGTTGGAG
Statistics
Matches: 120, Mismatches: 25, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
42 13 0.11
43 17 0.14
44 55 0.46
45 35 0.29
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAGTAAGGTTATCAAATTTTCATAGCGT
Found at i:620 original size:89 final size:87
Alignment explanation
Indices: 439--628 Score: 218
Period size: 89 Copynumber: 2.2 Consensus size: 87
429 TTCATGGTGC
* * * * * * *
439 GGTTATCAAAATTTTCATAGTGCGGTTACCAATTTTATAGTGTGATTATCAAAATTTCATAGGGA
1 GGTTATCAAAATTTTCACAGTACGGTTACAAATTTTATAGGGAGATTATCAAAATTTCATAAGAA
****
504 GATTATCAAATTTTCATTGTGT
66 GATTATCAAATTTTCACAACGT
* * *
526 AGTTATCAAAATTTTCACAGTACGGTTATCAAATTTTCATAGGGAGGTTATCAAAATTTCATAAT
1 GGTTATCAAAATTTTCACAGTACGGTTA-CAAATTTT-ATAGGGAGATTATCAAAATTTCATAAG
*
591 AAGGTTATCAAATTTTCACAACGT
64 AAGATTATCAAATTTTCACAACGT
*
615 GGTTATCAATATTT
1 GGTTATCAAAATTT
629 CTATGTTGGA
Statistics
Matches: 84, Mismatches: 17, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
87 25 0.30
88 7 0.08
89 52 0.62
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (87 bp):
GGTTATCAAAATTTTCACAGTACGGTTACAAATTTTATAGGGAGATTATCAAAATTTCATAAGAA
GATTATCAAATTTTCACAACGT
Done.