Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014564.1 Corchorus capsularis cultivar CVL-1 contig14585, 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: 77682
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1796 original size:324 final size:319
Alignment explanation
Indices: 236--2131 Score: 1911
Period size: 324 Copynumber: 5.8 Consensus size: 319
226 TTTCGGATAA
* ** *
236 AATTTT-GC-AAAAATTGACCCGAAAAA-TTTCCT-TCAA-TTTTTGCCACCATACTAAA-AAAA
1 AATTTTGGCTAAAAACTGACCC-AAAAATTTTTTTCTCAATTTTTTGCCACAATAC-AAAGAAAA
* * * * * * * ** * *
295 ATGTATATAACTCAATGCAAAAAATATTGAAAGGGCTTCTCACATTTCTAATATTGTTTTCCCNA
64 A-ATATATAATTCAATGCCAAAAATATTG-ACGGACTTTTTACGCTTCTAATATCGTTTTTCC-A
** * * *
360 -TTTTTTCATAATTAATTTCTAATGAAATCGAAAC-CGAATTGAGATGCTCAAAAAAAAATCAAA
126 TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAG-ATTGAGATGCTC---GAAAAA-CAAA
* * * ** *
423 TCCTTATATCCAGTATTGCTGATATTTGGTTCGATGAGTATAGGGATTTCAAGGAGTGTTTGTGC
186 TCCTTATATCCAATATTGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGT-TTT-TAC
* * * *
488 -CAAAAAATCATGCAAAATTAAGCCGGGGCTCCGGAACGCATTTTTAGCCAAAAACCGTGATGGT
249 ACCAAAAATCATGCAAAATTGAGCC-GGGCTCCAGAACG-ATTTTTAACCAAAAACCGTGATGGT
*
552 TAGAACAC
312 TAGTACAC
* * * ** **
560 AATTTCGGCTAAAAACTAACCCAAAAAATTTTTTCCTCAATTTTTTGCCACAATACGCAGAAACG
1 AATTTTGGCTAAAAACTGACCC-AAAAATTTTTTTCTCAATTTTTTGCCACAATACAAAGAAAAA
** * * * * *
625 GCATATAATTCACTGACAGATATATTGACGGACTTTTCACGCTTCTAATATCGTTTTTCCATTTT
65 ATATATAATTCAATGCCAAAAATATTGACGGACTTTTTACGCTTCTAATATCGTTTTTCCATTTT
* * * * *
690 TTTCCGAATTATTTTTTAATTAAATCGAAACAAAATTGAGATGATCGAAAAAACAAATCCTGATA
130 TTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCG-AAAAACAAATCCTTATA
* *
755 TCCAATATTGTTGAGATTTGGTTCAATGAATATAGATATTTCAAGGAGTTTTTACACCAAAAATC
194 TCCAATATTGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTTTTTACACCAAAAATC
* *** *
820 ATGTAAAATTGAGCCGGTGCTCC-GAAACGAATTTTTTTGTCAAAAATCGTGATGGTTAGTACAC
259 ATGCAAAATTGAGCCGG-GCTCCAG-AACG-A-TTTTTAACCAAAAACCGTGATGGTTAGTACAC
*** * *
884 AATTTTGGCTAAAAACTGACCCCTAAAAA--AAATTCTTAATTTTTTGCCAC-A-ACAAACAGAA
1 AATTTTGGCTAAAAACTGA-CCC-AAAAATTTTTTTCTCAATTTTTTGCCACAATACAAAGA-AA
* *
945 AAATATATAATTCAATGCCAAAAATATTGACGGAATTTTTAGGCTTCTAATATCGTTTTTCCATT
63 AAATATATAATTCAATGCCAAAAATATTGACGGACTTTTTACGCTTCTAATATCGTTTTTCCATT
* *
1010 TTTTTCCCGAATTAATTTCCAATTAAATCGAAACAAGATTTAGATGCTCGAAATAACAAATCCTT
128 TTTTT-CCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGAAA-AACAAATCCTT
* * * *
1075 ATATCCAATATTGCTAAGATTTGGTTCGATAAATATATATATATATATATATATTTCATGGAGTC
191 ATATCCAATATTGCTGAGATTTGGTTCG----------AT-GA-ATATAGATATTTCAAGGAGT-
* * ** *
1140 TTTT-CGCCAAAAATCATACAAAATTGAGCCGGGGCTCCAGAACGCGTTTTAAGCCAAAAACCAT
243 TTTTACACCAAAAATCATGCAAAATTGAGCC-GGGCTCCAGAACGATTTTTAA-CCAAAAACCGT
1204 GATGGTTAGTACAC
306 GATGGTTAGTACAC
* * * * * *
1218 AATTTTGGCGAAAAACTGA-CAAAAAATTTTTTTTCTTAATTTTTTGTCACAACAAAAAGAAAAA
1 AATTTTGGCTAAAAACTGACCCAAAAA-TTTTTTTCTCAATTTTTTGCCACAATACAAAGAAAAA
** * * * *
1282 ATATATAATTCAATGCCATGAATATTGACGGATTTTTTAGGCTTCTAATATCATTTTTACATTTT
65 ATATATAATTCAATGCCAAAAATATTGACGGACTTTTTACGCTTCTAATATCGTTTTTCCATTTT
* * *
1347 TTTCTGAATTAATTTCCAATTAAATCGAAACAAGATTTAGATGCTCGAAATAACAAATCCTTATA
130 TTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGAAA-AACAAATCCTTATA
* * * * * *
1412 TCCAATATTGCTAAGATTTGGTTCAAT-AA-ATATATATTTCATGGAGTCTTGT-CGCCAAAAAT
194 TCCAATATTGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGT-TTTTACACCAAAAAT
* *
1474 CATACAAAATTGAGTCGGGACTCCAGAACG-TGTTTTAACACAAAAACCGTGATGGTTAGTACAC
258 CATGCAAAATTGAGCCGGG-CTCCAGAACGAT-TTTTAAC-CAAAAACCGTGATGGTTAGTACAC
* * ** * *
1538 AATTTTTGACTAAAAACTTTACCCTAAATTTTTTTTTCTCAATTTTTTTTGTCACAATACAAATA
1 AA-TTTTGGCTAAAAAC-TGACCC-AAAAATTTTTTTCTCAA--TTTTTTGCCACAATACAAAGA
* *
1603 ATAAATATATAATTCAATGCCAAAAATATTGAC-GACTTTTTACGCTTCCAATATCGTTTTTCCA
61 AAAAATATATAATTCAATGCCAAAAATATTGACGGACTTTTTACGCTTCTAATATCGTTTTTCCA
* * *
1667 TTTTTTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTAAGATGCTCGAAAAA-AAATCCTA
126 TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAACAAATCCTT
*
1731 ATATCCAATATTGCTGAGATTTGGTTCGATGAATATATATATTTCAAGGA-TTTCTTACACCAAA
191 ATATCCAATATTGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTTT-TTACACCAAA
* * * * * * * *
1795 AATCTTGTAAAATTGAGTCAGGGCTCCGGAATGACTTTTTAGCCAAAAGCCGTGATGGTTAATAC
255 AATCATGCAAAATTGAG-CCGGGCTCCAGAACGA-TTTTTAACCAAAAACCGTGATGGTTAGTAC
1860 AC
318 AC
* * * *
1862 AATTTTGGCTAAAAATTGACCCGAAAATTTTTTTCTCAATTTTTTGCCACAAGA-AACATAAAAA
1 AATTTTGGCTAAAAACTGACCCAAAAATTTTTTTCTCAATTTTTTGCCACAATACAA-AGAAAAA
* * *
1926 ATATATAATTCAATGCCAAAAATATTGACGAACTTTTCACGTTTCTAATATCGTTTTTCCATTTT
65 ATATATAATTCAATGCCAAAAATATTGACGGACTTTTTACGCTTCTAATATCGTTTTTCCATTTT
*
1991 TTT-CGAATTAATTTGTAATTAAATCGTAAA-AAGATTGAGATGCAT-GAAAAAACAAATCCTTA
130 TTTCCGAATTAATTTCTAATTAAATCG-AAACAAGATTGAGATGC-TCG-AAAAACAAATCCTTA
* ***
2053 TATCCAATATTGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTTCCAAAAA
192 TATCCAATATTGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTTTTTACACCAAAAA
2118 TCATGCAAAATTGA
257 TCATGCAAAATTGA
2132 ATCGGGACTC
Statistics
Matches: 1334, Mismatches: 177, Indels: 125
0.82 0.11 0.08
Matches are distributed among these distances:
318 2 0.00
319 87 0.07
320 131 0.10
321 108 0.08
322 117 0.09
323 153 0.11
324 251 0.19
325 72 0.05
326 17 0.01
327 69 0.05
328 25 0.02
329 17 0.01
331 5 0.00
332 1 0.00
333 6 0.00
334 143 0.11
335 118 0.09
336 12 0.01
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (319 bp):
AATTTTGGCTAAAAACTGACCCAAAAATTTTTTTCTCAATTTTTTGCCACAATACAAAGAAAAAA
TATATAATTCAATGCCAAAAATATTGACGGACTTTTTACGCTTCTAATATCGTTTTTCCATTTTT
TTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATGCTCGAAAAACAAATCCTTATATC
CAATATTGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTTTTTACACCAAAAATCAT
GCAAAATTGAGCCGGGCTCCAGAACGATTTTTAACCAAAAACCGTGATGGTTAGTACAC
Found at i:2192 original size:15 final size:15
Alignment explanation
Indices: 2172--2223 Score: 68
Period size: 15 Copynumber: 3.3 Consensus size: 15
2162 AAAAATCATG
2172 AAATAAATATAATTA
1 AAATAAATATAATTA
2187 AAATAAATATAAGTTA
1 AAATAAATATAA-TTA
*
2203 TAAATAAATAGTATTTA
1 -AAATAAATA-TAATTA
2220 AAAT
1 AAAT
2224 GATTATGGGG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
15 12 0.36
16 7 0.21
17 12 0.36
18 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (15 bp):
AAATAAATATAATTA
Found at i:2511 original size:29 final size:29
Alignment explanation
Indices: 2452--2511 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
2442 TTTCCATAAT
* * *
2452 TAATAAAAAAGTTGAATCATCTCAAAAAA
1 TAATAAAAAAGTTAAATCAACTAAAAAAA
2481 TAATAAAAAAGTTAAAT-AACTAAAAAGAA
1 TAATAAAAAAGTTAAATCAACTAAAAA-AA
2510 TA
1 TA
2512 CTTATTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 7 0.26
29 20 0.74
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.23
Consensus pattern (29 bp):
TAATAAAAAAGTTAAATCAACTAAAAAAA
Found at i:37501 original size:55 final size:55
Alignment explanation
Indices: 37435--37545 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
37425 ACAAAGATTG
37435 AACCTCAAAAGAGTCCGACTCAATCTCTTAACTGGCGTTCTATTCTAGTTGTTCA
1 AACCTCAAAAGAGTCCGACTCAATCTCTTAACTGGCGTTCTATTCTAGTTGTTCA
37490 AACCTCAAAAGAGTCCGACTCAATCTCTTAACTGGCGTTCTATTCTAGTTGTTCA
1 AACCTCAAAAGAGTCCGACTCAATCTCTTAACTGGCGTTCTATTCTAGTTGTTCA
37545 A
1 A
37546 GGGGAACTCT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.32
Consensus pattern (55 bp):
AACCTCAAAAGAGTCCGACTCAATCTCTTAACTGGCGTTCTATTCTAGTTGTTCA
Found at i:39089 original size:16 final size:16
Alignment explanation
Indices: 39068--39120 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
39058 AGAAAGCCTA
39068 AGCAAATACAAGAAAC
1 AGCAAATACAAGAAAC
**
39084 AGCAAATACAAGTTTA-
1 AGCAAATACAAG-AAAC
*
39100 AGAAAATACAAGAAAC
1 AGCAAATACAAGAAAC
39116 AGCAA
1 AGCAA
39121 GTCTAACAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 1 0.03
16 27 0.93
17 1 0.03
ACGTcount: A:0.60, C:0.15, G:0.13, T:0.11
Consensus pattern (16 bp):
AGCAAATACAAGAAAC
Found at i:39397 original size:21 final size:21
Alignment explanation
Indices: 39359--39398 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
39349 AGCCAATTTA
*
39359 AAAAAAAAAAAGAAAGAAAAG
1 AAAAAAAAAAACAAAGAAAAG
* *
39380 AAAAGAAAAAACAGAGAAA
1 AAAAAAAAAAACAAAGAAA
39399 CTGGTGGAGT
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:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAAACAAAGAAAAG
Found at i:47435 original size:1 final size:1
Alignment explanation
Indices: 47429--47453 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
47419 TTTGTGCTTC
47429 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
47454 GTGATTGCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:56017 original size:6 final size:6
Alignment explanation
Indices: 56001--56036 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
55991 AGAAAGAAGA
*
56001 GCACAC ACACAC GCACAC GCACAC GCACAC GCACAC
1 GCACAC GCACAC GCACAC GCACAC GCACAC GCACAC
56037 ACTCTTGACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.36, C:0.50, G:0.14, T:0.00
Consensus pattern (6 bp):
GCACAC
Found at i:70963 original size:20 final size:20
Alignment explanation
Indices: 70938--70977 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
70928 GTCCCTCAAG
*
70938 TGGACCGAACATAGCAAATT
1 TGGACCGAACATAACAAATT
70958 TGGACCGAACATAACAAATT
1 TGGACCGAACATAACAAATT
70978 GGTCCTTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.20
Consensus pattern (20 bp):
TGGACCGAACATAACAAATT
Found at i:71524 original size:69 final size:69
Alignment explanation
Indices: 71410--71552 Score: 277
Period size: 69 Copynumber: 2.1 Consensus size: 69
71400 GAAGTTGCAA
71410 AGCAGTCGATTTTCCAAGCAATTGAGCTCGGTTATAGGCACTTTGATATAGGTTCAATGTATGGG
1 AGCAGTCGATTTTCCAAGCAATTGAGCTCGGTTATAGGCACTTTGATATAGGTTCAATGTATGGG
71475 TTAG
66 TTAG
*
71479 AGCAGTCGATTTTCCAAGCAATTGAGCTCGGTTATAGGCATTTTGATATAGGTTCAATGTATGGG
1 AGCAGTCGATTTTCCAAGCAATTGAGCTCGGTTATAGGCACTTTGATATAGGTTCAATGTATGGG
71544 TTAG
66 TTAG
71548 AGCAG
1 AGCAG
71553 CCGCCTGGTG
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 73 1.00
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.33
Consensus pattern (69 bp):
AGCAGTCGATTTTCCAAGCAATTGAGCTCGGTTATAGGCACTTTGATATAGGTTCAATGTATGGG
TTAG
Found at i:72319 original size:15 final size:15
Alignment explanation
Indices: 72299--72328 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
72289 CACAAAAGTG
72299 TTTTTTCGCCCCTTT
1 TTTTTTCGCCCCTTT
72314 TTTTTTCGCCCCTTT
1 TTTTTTCGCCCCTTT
72329 AAACCATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.33, G:0.07, T:0.60
Consensus pattern (15 bp):
TTTTTTCGCCCCTTT
Found at i:74324 original size:46 final size:47
Alignment explanation
Indices: 74252--74342 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 47
74242 GTTTTTGAAT
***
74252 ATTTATTTTCTTCTTTCTGGTGGCCCAAATGAACAAT-AGTAAAAGA
1 ATTTATTTTCTTCTTTCTGAAAGCCCAAATGAACAATGAGTAAAAGA
*
74298 ATTTATTTTCTTCTTTTTGAAAGCCCAAATGAACAATGAGTAAAA
1 ATTTATTTTCTTCTTTCTGAAAGCCCAAATGAACAATGAGTAAAA
74343 TAATACAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
46 33 0.82
47 7 0.17
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.37
Consensus pattern (47 bp):
ATTTATTTTCTTCTTTCTGAAAGCCCAAATGAACAATGAGTAAAAGA
Found at i:76094 original size:2 final size:2
Alignment explanation
Indices: 76087--76117 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
76077 ACAGGCATGA
76087 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
76118 GAAAATTAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.