Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020787.1 Corchorus olitorius cultivar O-4 contig20820, 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: 46259
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:589 original size:325 final size:320
Alignment explanation
Indices: 1--861 Score: 1023
Period size: 325 Copynumber: 2.7 Consensus size: 320
* *
1 AATTAATTTCTAATTAAATC-ATAACAAGATTCAGATGCTCGTAAAAGCAAATTCTTATAT-TCA
1 AATTAATTTCTAATTAAATCGA-AACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCT-A
*
64 ATGTGGCTGA-TATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATG
64 ATGTGGCTGACTATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATG
* *
128 CAAAATTGAGTCGGGGCTCGAGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTT
129 CAAAATTGAGTCGGGCCCCGA-AACGCGTTTTTAGCCAAAAACTGTGATGG-TAGTACACGATTT
* * *
193 CGGCTAAAAACTGATCGGAAAAGGTTTTTTCTTAATTTTTTGCCACAATACTCAGAAAAATATAT
192 CGGCTAAAAACTGATCGGAAAAGGTTTTTTCTGAATCTATTGCCACAATACTCAGAAAAATATAT
* * * *
258 AATTCAACACCAAAAAGA-AT-AT-TTTTCTCGCTTCAAATATCATTTTTCTATTTTTTTTCCG
257 AATTCAAAACCAAAAAGATATGATCTTTTCACGCTTCAAATATCATTTTTCCAATTTTTTTCCG
* *
319 AATCT-ATTTCTAATTAAATCGAAACAATATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAA
1 AAT-TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCTAA
* *
383 TGTGGCTGAGAGCCTTAGATTGGTTAGATGAATATAGATATTTCAAGGAGTCGTT-CTGCCAAAA
65 TGTGGCT--GA--C-TA-TTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGC-GCCAAAA
* *
447 ATCATGCAAAACTGAGCCGGGACCCCCGAAACGCGTTTTTAGCCCAAAAA-T-T-AT-G-ACGTA
123 ATCATGCAAAATTGAGTCGGG--CCCCGAAACGCGTTTTTAG-CCAAAAACTGTGATGGTA-GTA
* * **** * *
507 CATGATTTTCGTCTAAAAACTGACTC-GAATTTTTTTTTTTCTGAATCTATTGCCACAATGCTCT
184 CACGA-TTTCGGCTAAAAACTGA-TCGGAA-AAGGTTTTTTCTGAATCTATTGCCACAATACTCA
* **
571 GAAAAAATATATAATTCAAAACCAAAAAGATTGATGGTCTTTTCACGCTTTTAATATCATTTTTC
246 G-AAAAATATATAATTCAAAACCAAAAAGA-T-ATGATCTTTTCACGCTTCAAATATCATTTTTC
636 CAATTTTTTTCCG
308 CAATTTTTTTCCG
* * *
649 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTATATCCATT
1 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCTAAT
* * * * *
714 GTGGTTGAC-ATTTGGTTCGTTGAATATAGATATTTCAAGGATTTTTTGCGCCAAAAATCATGCA
66 GTGGCTGACTATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCA
* * * **
778 AAATTGAGTCGGTGCTCGGAAACGCGTTTTTAGCCAAAAACCGTGATAATTAGTACACGATTTCG
131 AAATTGAGTCGG-GCCCCGAAACGCGTTTTTAGCCAAAAACTGTGAT-GGTAGTACACGATTTCG
843 GCTAAAAACTGATCGGAAA
194 GCTAAAAACTGATCGGAAA
862 TTTTTGAGTT
Statistics
Matches: 459, Mismatches: 50, Indels: 62
0.80 0.09 0.11
Matches are distributed among these distances:
318 61 0.13
319 3 0.01
320 2 0.00
321 8 0.02
322 24 0.05
323 77 0.17
324 40 0.09
325 107 0.23
326 22 0.05
327 12 0.03
328 4 0.01
329 2 0.00
330 97 0.21
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (320 bp):
AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCTAAT
GTGGCTGACTATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCA
AAATTGAGTCGGGCCCCGAAACGCGTTTTTAGCCAAAAACTGTGATGGTAGTACACGATTTCGGC
TAAAAACTGATCGGAAAAGGTTTTTTCTGAATCTATTGCCACAATACTCAGAAAAATATATAATT
CAAAACCAAAAAGATATGATCTTTTCACGCTTCAAATATCATTTTTCCAATTTTTTTCCG
Found at i:1564 original size:19 final size:19
Alignment explanation
Indices: 1540--1576 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1530 CTATTTAGTA
1540 ACTGTACAGATTAGATTAC
1 ACTGTACAGATTAGATTAC
1559 ACTGTACAGATTAGATTA
1 ACTGTACAGATTAGATTA
1577 GGTACTGTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (19 bp):
ACTGTACAGATTAGATTAC
Found at i:19658 original size:64 final size:64
Alignment explanation
Indices: 19548--19675 Score: 229
Period size: 64 Copynumber: 2.0 Consensus size: 64
19538 AAAAAGAGAA
* * *
19548 TTCTACAAATAATATAACACATAACCAGGTACCCGAGACGGGTCGAATCCGGATTAATCAGGGC
1 TTCTACAAATAATATAACACATAACCAGGTACCCAACACGGATCGAATCCGGATTAATCAGGGC
19612 TTCTACAAATAATATAACACATAACCAGGTACCCAACACGGATCGAATCCGGATTAATCAGGGC
1 TTCTACAAATAATATAACACATAACCAGGTACCCAACACGGATCGAATCCGGATTAATCAGGGC
19676 AAAGCCCTGG
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (64 bp):
TTCTACAAATAATATAACACATAACCAGGTACCCAACACGGATCGAATCCGGATTAATCAGGGC
Found at i:20271 original size:2 final size:2
Alignment explanation
Indices: 20264--20301 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
20254 CCCATAATCC
20264 AT AT AT 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 AT AT AT
20302 GCTAGTTAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25195 original size:24 final size:24
Alignment explanation
Indices: 25168--25219 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
25158 ACCATCTCCA
* *
25168 TAGAAACCGCGATCACCGATGCGG
1 TAGAAACAGCGACCACCGATGCGG
25192 TAGAAACAGCGACCACCGATGCGG
1 TAGAAACAGCGACCACCGATGCGG
25216 TAGA
1 TAGA
25220 TTCGAGAACC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.33, C:0.27, G:0.29, T:0.12
Consensus pattern (24 bp):
TAGAAACAGCGACCACCGATGCGG
Found at i:25489 original size:42 final size:42
Alignment explanation
Indices: 25438--25546 Score: 209
Period size: 42 Copynumber: 2.6 Consensus size: 42
25428 TATACGCTTC
25438 TCCGGTTCGGAAACCTTACGATCAGCCGTTGAAGGCTTCAAA
1 TCCGGTTCGGAAACCTTACGATCAGCCGTTGAAGGCTTCAAA
*
25480 TCCGGTTCGGAAACCTTACGACCAGCCGTTGAAGGCTTCAAA
1 TCCGGTTCGGAAACCTTACGATCAGCCGTTGAAGGCTTCAAA
25522 TCCGGTTCGGAAACCTTACGATCAG
1 TCCGGTTCGGAAACCTTACGATCAG
25547 GCGTCAACTT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.26, C:0.28, G:0.24, T:0.23
Consensus pattern (42 bp):
TCCGGTTCGGAAACCTTACGATCAGCCGTTGAAGGCTTCAAA
Found at i:25699 original size:2 final size:2
Alignment explanation
Indices: 25692--25722 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
25682 CTACTTTACA
25692 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
25723 AACCCGACCC
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
Found at i:28447 original size:1 final size:1
Alignment explanation
Indices: 28441--28466 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
28431 CTAAGTTGAT
28441 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
28467 GAAGAACACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:30458 original size:18 final size:18
Alignment explanation
Indices: 30405--30458 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
30395 CCTCCCCTTC
*
30405 GAGGACCACGTTCAGTAC
1 GAGGACCACGTTCAGTAT
30423 GAGGACCACGTTCAGTAT
1 GAGGACCACGTTCAGTAT
*
30441 GAGTACCACGTTCAGTAT
1 GAGGACCACGTTCAGTAT
30459 ATGTACGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.22
Consensus pattern (18 bp):
GAGGACCACGTTCAGTAT
Found at i:30464 original size:18 final size:17
Alignment explanation
Indices: 30409--30464 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 17
30399 CCCTTCGAGG
* *
30409 ACCACGTTCAGTACGAGG
1 ACCACGTTCAGTA-TAGT
30427 ACCACGTTCAGTATGAGT
1 ACCACGTTCAGTAT-AGT
30445 ACCACGTTCAGTATATGT
1 ACCACGTTCAGTATA-GT
30463 AC
1 AC
30465 GAAACTTCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 1 0.03
18 33 0.97
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (17 bp):
ACCACGTTCAGTATAGT
Found at i:34187 original size:8 final size:8
Alignment explanation
Indices: 34174--34198 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
34164 TATAGCACAA
34174 TGATTGAG
1 TGATTGAG
34182 TGATTGAG
1 TGATTGAG
34190 TGATTGAG
1 TGATTGAG
34198 T
1 T
34199 TACATATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.36, T:0.40
Consensus pattern (8 bp):
TGATTGAG
Found at i:39812 original size:13 final size:13
Alignment explanation
Indices: 39794--39818 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39784 ATAAGATCTC
39794 TCAATTTTTTTTT
1 TCAATTTTTTTTT
39807 TCAATTTTTTTT
1 TCAATTTTTTTT
39819 ATAAAATAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (13 bp):
TCAATTTTTTTTT
Found at i:40154 original size:28 final size:27
Alignment explanation
Indices: 40097--40149 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
40087 TTAGGGAAAA
**
40097 AACACTAGGATATTTTTTTTCTACATAT
1 AACACTAGGATA-TTTTGGTCTACATAT
40125 AACACTAGGATA-TTTGGTCTACATA
1 AACACTAGGATATTTTGGTCTACATA
40150 AATAAAGTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 11 0.48
28 12 0.52
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (27 bp):
AACACTAGGATATTTTGGTCTACATAT
Found at i:40357 original size:13 final size:13
Alignment explanation
Indices: 40339--40365 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40329 GGAAAATCCG
40339 GAAGTGTTTTTCA
1 GAAGTGTTTTTCA
40352 GAAGTGTTTTTCA
1 GAAGTGTTTTTCA
40365 G
1 G
40366 TTGTTTTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.26, T:0.44
Consensus pattern (13 bp):
GAAGTGTTTTTCA
Found at i:43819 original size:21 final size:21
Alignment explanation
Indices: 43793--43837 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
43783 TTAATTACCC
43793 ATTATA-TATGAAGAAAAAAAA
1 ATTATATTA-GAAGAAAAAAAA
*
43814 ATTATATTAGAAGTAAAAAAA
1 ATTATATTAGAAGAAAAAAAA
43835 ATT
1 ATT
43838 TCCTTTGCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.29
Consensus pattern (21 bp):
ATTATATTAGAAGAAAAAAAA
Found at i:45801 original size:13 final size:13
Alignment explanation
Indices: 45783--45808 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
45773 TGAAAATACA
45783 CCTATTTATAGCT
1 CCTATTTATAGCT
45796 CCTATTTATAGCT
1 CCTATTTATAGCT
45809 GCATATTTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (13 bp):
CCTATTTATAGCT
Done.