Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012537.1 Corchorus capsularis cultivar CVL-1 contig12558, 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: 39247
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:9574 original size:2 final size:2
Alignment explanation
Indices: 9567--9601 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
9557 AATTATCTTT
9567 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9602 GATTTTTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11367 original size:6 final size:6
Alignment explanation
Indices: 11356--11423 Score: 100
Period size: 6 Copynumber: 11.3 Consensus size: 6
11346 ATCAAAAGAA
* * *
11356 TTTTCC TTTTCC TTTTCC TTCTCC TTTTCC TTTTCC TTCTCC TTCTCC
1 TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC
*
11404 TTTTCC TTTTCC TTCTCC TT
1 TTTTCC TTTTCC TTTTCC TT
11424 ATCTTGCTTC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 57 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (6 bp):
TTTTCC
Found at i:11388 original size:24 final size:24
Alignment explanation
Indices: 11356--11423 Score: 127
Period size: 24 Copynumber: 2.8 Consensus size: 24
11346 ATCAAAAGAA
*
11356 TTTTCCTTTTCCTTTTCCTTCTCC
1 TTTTCCTTTTCCTTCTCCTTCTCC
11380 TTTTCCTTTTCCTTCTCCTTCTCC
1 TTTTCCTTTTCCTTCTCCTTCTCC
11404 TTTTCCTTTTCCTTCTCCTT
1 TTTTCCTTTTCCTTCTCCTT
11424 ATCTTGCTTC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTTCCTTTTCCTTCTCCTTCTCC
Found at i:11774 original size:57 final size:57
Alignment explanation
Indices: 11668--11776 Score: 148
Period size: 57 Copynumber: 1.9 Consensus size: 57
11658 TTTTGGCAGT
* *
11668 TCCCTTGCTGCCTCTTCGCGACCAGGATCAGCTGCGGCTGGTTGTTGATGATGATCG
1 TCCCTTGCTGCCTCTTCGCGACCAGGATCAGCTGCAGCTGGTTGATGATGATGATCG
* ** *
11725 TCCCTTGCTGCCTCTTGGCGACCAGGATCATTTGCTAG-TTGTTGATGATGAT
1 TCCCTTGCTGCCTCTTCGCGACCAGGATCAGCTGC-AGCTGGTTGATGATGAT
11777 CCAAGTTATC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
57 44 0.98
58 1 0.02
ACGTcount: A:0.14, C:0.26, G:0.28, T:0.33
Consensus pattern (57 bp):
TCCCTTGCTGCCTCTTCGCGACCAGGATCAGCTGCAGCTGGTTGATGATGATGATCG
Found at i:15073 original size:2 final size:2
Alignment explanation
Indices: 15066--15097 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
15056 TCACCCATTA
15066 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15098 GATGATGATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28708 original size:25 final size:25
Alignment explanation
Indices: 28674--28723 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
28664 ATTCTATAAG
28674 TGGGTTGTGGAGTTGACACATGTTC
1 TGGGTTGTGGAGTTGACACATGTTC
28699 TGGGTTGTGGAGTTGACACATGTTC
1 TGGGTTGTGGAGTTGACACATGTTC
28724 ATTTTTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.16, C:0.12, G:0.36, T:0.36
Consensus pattern (25 bp):
TGGGTTGTGGAGTTGACACATGTTC
Found at i:28928 original size:18 final size:18
Alignment explanation
Indices: 28905--28940 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
28895 TATTTGATTT
28905 AATTTGGTAATGGAAACA
1 AATTTGGTAATGGAAACA
28923 AATTTGGTAATGGAAACA
1 AATTTGGTAATGGAAACA
28941 GTCTAATGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.22, T:0.28
Consensus pattern (18 bp):
AATTTGGTAATGGAAACA
Found at i:28982 original size:31 final size:31
Alignment explanation
Indices: 28947--29010 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
28937 AACAGTCTAA
28947 TGGGTCCAATTGGAAAGTTTAGGGTCTAGTC
1 TGGGTCCAATTGGAAAGTTTAGGGTCTAGTC
28978 TGGGTCCAATTGGAAAGTTTAGGGTCTAGTC
1 TGGGTCCAATTGGAAAGTTTAGGGTCTAGTC
29009 TG
1 TG
29011 TCGTGTTAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.22, C:0.12, G:0.33, T:0.33
Consensus pattern (31 bp):
TGGGTCCAATTGGAAAGTTTAGGGTCTAGTC
Found at i:29645 original size:14 final size:14
Alignment explanation
Indices: 29628--29662 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
29618 ACGAGAACTA
29628 GAGAGAGAGAAGGG
1 GAGAGAGAGAAGGG
*
29642 GAGAGGGAGAAGGG
1 GAGAGAGAGAAGGG
*
29656 AAGAGAG
1 GAGAGAG
29663 GAGCGGCTAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (14 bp):
GAGAGAGAGAAGGG
Found at i:31363 original size:17 final size:18
Alignment explanation
Indices: 31327--31363 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
31317 CCGACGTGGC
31327 ATGCCACGTGTACCCAAAA
1 ATGCCACGTGTA-CCAAAA
31346 ATGCCACGTGTA-CAAAA
1 ATGCCACGTGTACCAAAA
31363 A
1 A
31364 GGACACATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
19 12 0.67
ACGTcount: A:0.41, C:0.27, G:0.16, T:0.16
Consensus pattern (18 bp):
ATGCCACGTGTACCAAAA
Found at i:39158 original size:334 final size:332
Alignment explanation
Indices: 36285--39247 Score: 3407
Period size: 333 Copynumber: 8.9 Consensus size: 332
36275 CGGTTAAGGT
* * ** *
36285 AACAAATCCTTAAATCGAAT--ATGACTGAGATTTGCTTAGATTCA-TATAGATATTATCAAGCA
1 AACAAATCCTTAAATCCAATGCA-G-CTGAGATTTGGTTAGATAAATTA-AGATATT-TCAAGGA
* * * * * * * * *
36347 GTCTTGGTGCCAACAATCATTCAAAACTGAGCCG-GGTCCCAAAACGTATTTTTAGCAAAAAACC
62 GTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGAGGCCCCGAAGCGCATTTTTAGCCAAAATCC
* * * * * *
36411 GTAATGGTCAGTACACGATTTC-G------TCTTTG-AAAACTGACCCGAAAAATTTTTCTTCAA
127 GTGATGATTAGTACACGATTTCGGCTAAAATTTTTGAAAAACTGACCTGAAAAATTTTTCCTCAA
* * * * *
36468 TTTTTGGCCATAATAGTCATAAAAAATATATAATTCAACGCCAAAAAGATTAAAGGGCTTTACAT
192 TTTTTGGCCACAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCAC
* * * * * *
36533 ACTTCAAATATCGTTTTTCTAAACTTTTCCAAATAAATTTCTAATTATATCGAAACATGATTCAG
257 GCTTCTAATATCGTTTTTCTAAATTTTTTCAAATTAATTTCTAATTAAATCGAAACATGATTCAG
*
36598 ATGCCCGTAAA
322 ATGCTCGTAAA
* * *
36609 AACAAATCCTTAAATCCAATGCAGCTGAGATTTGGTTATATAAATTAAGATATTTAAAGGAGTAT
1 AACAAATCCTTAAATCCAATGCAGCTGAGATTTGGTTAGATAAATTAAGATATTTCAAGGAGTCT
* * *
36674 TGGCG-CAAAAATTCATGCAAAACTGAGAC-AGCGCCCCGAAGCGCATTTTTAGTCAAAACCCGT
66 TGGCGCCAAAAA-TCATGCAAAACTGAGCCGAG-GCCCCGAAGCGCATTTTTAGCCAAAATCCGT
*
36737 GATGATTAGTACACGATTTCGGCTAAAATTTTTGAAAAACTGACCTGAAAAAATTTTCCTCAATT
129 GATGATTAGTACACGATTTCGGCTAAAATTTTTGAAAAACTGACCTGAAAAATTTTTCCTCAATT
** ** **
36802 TTTGGCCACAATACTCATAAAAAATATATAATTCAGTGTAAAAAAGATTGAAGCACTTTTCACGC
194 TTTGGCCACAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGC
* *
36867 TTATAATATCGTTTTTCTAAATTTGTTTCAAATTAATTTCTAATTAAATTGAAACATGATTCAGA
259 TTCTAATATCGTTTTTCTAAATTT-TTTCAAATTAATTTCTAATTAAATCGAAACATGATTCAGA
36932 TGCTCGTAAA
323 TGCTCGTAAA
* *
36942 AACAAATCCTTAAAACCAATGCAGCTGACATTTGGTTAGATAAATTAAGATATTTCAAGGA-T-T
1 AACAAATCCTTAAATCCAATGCAGCTGAGATTTGGTTAGATAAATTAAGATATTTCAAGGAGTCT
* ** * * * * *
37005 TGACATCAAAAATCATGCAAAACTGGGCCGAGGCCTCGGAGTGCATTTTTAGCCAAAATCCATGA
66 TGGCGCCAAAAATCATGCAAAACTGAGCCGAGGCCCCGAAGCGCATTTTTAGCCAAAATCCGTGA
* * * * *
37070 TGATTAGTACACGATTTCGGCTAGAATTTTTGAAAAATTGACATGGAAAGTTTTTCCTCAATTTT
131 TGATTAGTACACGATTTCGGCTAAAATTTTTGAAAAACTGACCTGAAAAATTTTTCCTCAATTTT
* *
37135 TGGCCACAATACTCATAAAAAATATATAATTCAACGTCAAAAAGATTGAAGGGCTTTTCACACTT
196 TGGCCACAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTT
*
37200 -TCAATATCGTTTTTCTAAATTTGTTTCAAATTAATTTCTAATTAAATCGAAACATTATTCAGAT
261 CT-AATATCGTTTTTCTAAATTT-TTTCAAATTAATTTCTAATTAAATCGAAACATGATTCAGAT
37264 GCTCGTAAA
324 GCTCGTAAA
* * *
37273 AACAAATTCTTAAAACCAATGCAGTTGAGATTTGG-TAGATAAATTAAGATATTTCAAGGAGTCT
1 AACAAATCCTTAAATCCAATGCAGCTGAGATTTGGTTAGATAAATTAAGATATTTCAAGGAGTCT
* * **
37337 TGGCACAAAAAATCATGCAAAACTGAGCCG-GTGCCCCGAAGCATATTTTTAGCCAAAATCCGTG
66 TGGCGCCAAAAATCATGCAAAACTGAGCCGAG-GCCCCGAAGCGCATTTTTAGCCAAAATCCGTG
* ** * * * *
37401 ATGATTATTACACGATTTCAACTAAAATTTTTGAAAAACTGTCCTGAAAAAATTTTCCTTAATAT
130 ATGATTAGTACACGATTTCGGCTAAAATTTTTGAAAAACTGACCTGAAAAATTTTTCCTCAATTT
* * * * * * *
37466 TTGGCTACAATACTCATAGAAAATATATAATTCAATGGC--GAAGATTGGAGGGCTTTTCGCGCT
195 TTGGCCACAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCT
** * *
37529 TCTAATATTATTTTTC-AAATTGTTTTCAAATTAATTTCTAATTATATCGAAAAATGATTCAGAT
260 TCTAATATCGTTTTTCTAAATT-TTTTCAAATTAATTTCTAATTAAATCGAAACATGATTCAGAT
* *
37593 ACTCGTGAA
324 GCTCGTAAA
* * * * * *
37602 AACAAATCCTTAAACCCATTGCAGCTAAGATTTGGTTAGATAGATTAAGATATTTCAAGTAGTTT
1 AACAAATCCTTAAATCCAATGCAGCTGAGATTTGGTTAGATAAATTAAGATATTTCAAGGAGTCT
* ** * *
37667 TGGCG-CAACAAATCACGCAAAACTGAGCCGAGGCTTCGGAGCGCATTTTTAGCCAAAAT--TTG
66 TGGCGCCAA-AAATCATGCAAAACTGAGCCGAGGCCCCGAAGCGCATTTTTAGCCAAAATCCGTG
* * * * ** **
37729 -T-AAT-GTAAACGATATCGGCTAAAATTTTTGAAAAATTGACCTGAAATTTTTTTTTTGTCAA-
130 ATGATTAGTACACGATTTCGGCTAAAATTTTTGAAAAACTGACCTGAAA--AATTTTTCCTCAAT
* ** * * * *
37790 -ATTGGCCACAATGTTGATGATAAAATATATAATTCAACTCCAAAAAGATTGAAGGGTTTTTCAC
193 TTTTGGCCACAATACTCAT-AAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCAC
* * * * * **
37854 GTTTCTAATATCATTTTTTTAAA-CTTTTCAAATTAATTCCTAATTAGCTCGAAACATGATTCAG
257 GCTTCTAATATCGTTTTTCTAAATTTTTTCAAATTAATTTCTAATTAAATCGAAACATGATTCAG
37918 ATGCTCGTAAA
322 ATGCTCGTAAA
* ** *
37929 AACAAAT-TTATAAATCCAATGCAGCCT-AGATTTACTTAGATAAATCAAGATATTTTTCAAGGA
1 AACAAATCCT-TAAATCCAATGCAG-CTGAGATTTGGTTAGATAAATTAAGATA--TTTCAAGGA
* * * ** ** * * * * *
37992 GTGTAGGCACCAAAAAAAATGTGAAACTGAGCTG-GGGCCCAAGAGCACATTTTTAGTCAAAATC
62 GTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGAGGCCCCGA-AGCGCATTTTTAGCCAAAATC
* * * *
38056 CGTGATGATTTGTACACGTTTTCGGCTAAAGTTTTTGAAAAACT-ATCCTAAAAAATTTTTCCTC
126 CGTGATGATTAGTACACGATTTCGGCTAAAATTTTTGAAAAACTGA-CCTGAAAAATTTTTCCTC
* *
38120 AATTTTTGGCCACAATACTCATAAAAAATATATAATTCAACGGCAAAAAGATTGATGGGCTTTTC
190 AATTTTTGGCCACAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTC
*
38185 ACGCTTCTAATAAT-GTTTTTTTAAATTTTTTCCAAATTAATTTCTAATTAAATCGAAACATGAT
255 ACGCTTCTAAT-ATCGTTTTTCTAAATTTTTT-CAAATTAATTTCTAATTAAATCGAAACATGAT
* *
38249 TTAGATGCTTGTAAA
318 TCAGATGCTCGTAAA
* * *
38264 AACAAATCCTTAAATCTAATACGGCTGAGATTTGGTTAGATAAATTAAGATATTTCAAGGAGTCT
1 AACAAATCCTTAAATCCAATGCAGCTGAGATTTGGTTAGATAAATTAAGATATTTCAAGGAGTCT
* * * * * * *
38329 TGGCGCCAAAAATCATGCAAAACTGGGCCGGGGTCCCGGAGTGCTTTTTTAGTCAAAATCCGTGA
66 TGGCGCCAAAAATCATGCAAAACTGAGCCGAGGCCCCGAAGCGCATTTTTAGCCAAAATCCGTGA
* * * *
38394 TTATTAATACACGATTTCGGCTAAAATTTTTGAAAAAACGGACATGAAAAATTTTTCCTCAATTT
131 TGATTAGTACACGATTTCGGCTAAAATTTTTG-AAAAACTGACCTGAAAAATTTTTCCTCAATTT
** * * * *
38459 TTGGCCACAATACTCATAAAAAATATATAATTCAACG-CGGAAACATAGGAGGGCTTTTCACGTT
195 TTGGCCACAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCT
** * *
38523 TCTAATATTATTTTTC-AAATTTTCTTCCAAATTAATTTCTAATTATATCGAAACAAGATTCAGA
260 TCTAATATCGTTTTTCTAAATTTT-TT-CAAATTAATTTCTAATTAAATCGAAACATGATTCAGA
38587 TGCTCGTAAA
323 TGCTCGTAAA
* * * *
38597 AACAAATCCTTAAATCGATTGCAGCTAAGATTTGGTTAGATAAATTAAGATATTTCAAGGAGTTT
1 AACAAATCCTTAAATCCAATGCAGCTGAGATTTGGTTAGATAAATTAAGATATTTCAAGGAGTCT
* * * *
38662 TGGCGCAAAAAAT-ATGCAAAACTGAGCCGAGGCCCCGGAGCACATTTTTAGCCAAAATCAGTGA
66 TGGCGCCAAAAATCATGCAAAACTGAGCCGAGGCCCCGAAGCGCATTTTTAGCCAAAATCCGTGA
* * *
38726 TGATTAGTACACTATTTTTGGATAAAATTTTTGAAAAACTGACCTGAAAAATTTTTCCTCAATTT
131 TGATTAGTACACGA-TTTCGGCTAAAATTTTTGAAAAACTGACCTGAAAAATTTTTCCTCAATTT
* * *
38791 TTGGCCACAATACTCCA-AAAAAATAAAATAATTCTACGCCAAAAAGATTGAAGGGCTTCTCACG
195 TTGGCCACAATACT-CATAAAAAAT-ATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACG
* * * *
38855 CTTCTAATTTCATTTTTCTAAATTTTTTGAAAATTAATTTCTAATTAGATCGAAACATGATTCAG
258 CTTCTAATATCGTTTTTCTAAATTTTTT-CAAATTAATTTCTAATTAAATCGAAACATGATTCAG
*
38920 ATGCTCATAAA
322 ATGCTCGTAAA
** * * * * * *
38931 AGTAAATCCTTAAATCCAACGCGGCTGAGAGTTGTTTAAATAAATTAAGGTATTTCAAGGAGTCT
1 AACAAATCCTTAAATCCAATGCAGCTGAGATTTGGTTAGATAAATTAAGATATTTCAAGGAGTCT
* * * *
38996 TGGCGCCAAAAACCATGCAAAACTGAGCCGAGTCCCCGAAACGCATTTTTAGCCAAAATCTGTGA
66 TGGCGCCAAAAATCATGCAAAACTGAGCCGAGGCCCCGAAGCGCATTTTTAGCCAAAATCCGTGA
* * * ** *
39061 TG-TAATGTACACGATTTCGGCTAAATTTTTTTAAAAAACTGACCTGAAATTTTTTTTCTCAATT
131 TGATTA-GTACACGATTTCGGCTAAA-ATTTTTGAAAAACTGACCTGAAAAATTTTTCCTCAATT
* *
39125 TTTGGCCACAATACTCATAAAAAATATATAATTCAATGCCAAAAAAGATTGATGGGCTTTTCACG
194 TTTGGCCACAATACTCATAAAAAATATATAATTCAACGCC-AAAAAGATTGAAGGGCTTTTCACG
**
39190 CTTCTAATATCGTTTTTCTAAATTTTACCAAATTAATTTCTAATTAAATCGAAACATG
258 CTTCTAATATCGTTTTTCTAAATTTTTTCAAATTAATTTCTAATTAAATCGAAACATG
Statistics
Matches: 2232, Mismatches: 341, Indels: 122
0.83 0.13 0.05
Matches are distributed among these distances:
322 5 0.00
323 28 0.01
324 83 0.04
325 52 0.02
326 22 0.01
327 93 0.04
328 40 0.02
329 132 0.06
330 134 0.06
331 276 0.12
332 375 0.17
333 424 0.19
334 321 0.14
335 246 0.11
336 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (332 bp):
AACAAATCCTTAAATCCAATGCAGCTGAGATTTGGTTAGATAAATTAAGATATTTCAAGGAGTCT
TGGCGCCAAAAATCATGCAAAACTGAGCCGAGGCCCCGAAGCGCATTTTTAGCCAAAATCCGTGA
TGATTAGTACACGATTTCGGCTAAAATTTTTGAAAAACTGACCTGAAAAATTTTTCCTCAATTTT
TGGCCACAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTT
CTAATATCGTTTTTCTAAATTTTTTCAAATTAATTTCTAATTAAATCGAAACATGATTCAGATGC
TCGTAAA
Done.