Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015337.1 Corchorus olitorius cultivar O-4 contig15370, 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: 48012
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1888 original size:8 final size:7
Alignment explanation
Indices: 1872--1906 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
1862 ATTCATTTTC
1872 TTTTCTT
1 TTTTCTT
*
1879 TTTCCTT
1 TTTTCTT
1886 TTTTCTT
1 TTTTCTT
1893 TTTTC-T
1 TTTTCTT
1899 TTTTCTT
1 TTTTCTT
1906 T
1 T
1907 ACCTTCTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTCTT
Found at i:8051 original size:7 final size:7
Alignment explanation
Indices: 8039--8067 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
8029 GTAGTATGAT
8039 GAAATTA
1 GAAATTA
8046 GAAATTA
1 GAAATTA
8053 GAAATTA
1 GAAATTA
8060 GAAATTA
1 GAAATTA
8067 G
1 G
8068 TGTAGCATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.17, T:0.28
Consensus pattern (7 bp):
GAAATTA
Found at i:16375 original size:14 final size:13
Alignment explanation
Indices: 16352--16383 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
16342 AATTTCAGAT
16352 GAAAAAAAAAAAA
1 GAAAAAAAAAAAA
16365 GAAAAAGAAAAAAA
1 GAAAAA-AAAAAAA
16379 GAAAA
1 GAAAA
16384 GGCAAGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
GAAAAAAAAAAAA
Found at i:21224 original size:42 final size:42
Alignment explanation
Indices: 21153--21349 Score: 247
Period size: 42 Copynumber: 4.7 Consensus size: 42
21143 CCTATTGCAG
*
21153 TTTCTTCTGGTTTCTCTTCAGCCAGTTTTTGTTCCTCTACAA
1 TTTCTTCTTGTTTCTCTTCAGCCAGTTTTTGTTCCTCTACAA
* * *
21195 TTGCTTCTTGTTTCTCTTC-GACCAATTTTTGTTCCTCCACAA
1 TTTCTTCTTGTTTCTCTTCAG-CCAGTTTTTGTTCCTCTACAA
*
21237 TTTCTTCCTT-TTTCTCTTCAGCCAGTTTTTGTTCCTTTACAA
1 TTTCTT-CTTGTTTCTCTTCAGCCAGTTTTTGTTCCTCTACAA
* * * * *
21279 ATTCTTCCTGCTTCTCTTCGGCCAGTTTTTGTTCCTCTATAA
1 TTTCTTCTTGTTTCTCTTCAGCCAGTTTTTGTTCCTCTACAA
*
21321 TTTCTTCCTT-TTTCTCTTCAGGCAGTTTT
1 TTTCTT-CTTGTTTCTCTTCAGCCAGTTTT
21350 GTTTCTTGCA
Statistics
Matches: 131, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
41 3 0.02
42 122 0.93
43 6 0.05
ACGTcount: A:0.12, C:0.27, G:0.10, T:0.51
Consensus pattern (42 bp):
TTTCTTCTTGTTTCTCTTCAGCCAGTTTTTGTTCCTCTACAA
Found at i:21294 original size:84 final size:84
Alignment explanation
Indices: 21163--21349 Score: 286
Period size: 84 Copynumber: 2.2 Consensus size: 84
21153 TTTCTTCTGG
* *
21163 TTTCTCTTCAGCCAGTTTTTGTTCCTCTACAATTGCTTCTTGTTTCTCTTCGACCAATTTTTGTT
1 TTTCTCTTCAGCCAGTTTTTGTTCCTCTACAATTGCTTCCTGCTTCTCTTCGACCAATTTTTGTT
21228 CCTCCACAATTTCTTCCTT
66 CCTCCACAATTTCTTCCTT
* * *
21247 TTTCTCTTCAGCCAGTTTTTGTTCCTTTACAAATT-CTTCCTGCTTCTCTTCGGCCAGTTTTTGT
1 TTTCTCTTCAGCCAGTTTTTGTTCCTCTAC-AATTGCTTCCTGCTTCTCTTCGACCAATTTTTGT
* *
21311 TCCTCTATAATTTCTTCCTT
65 TCCTCCACAATTTCTTCCTT
*
21331 TTTCTCTTCAGGCAGTTTT
1 TTTCTCTTCAGCCAGTTTT
21350 GTTTCTTGCA
Statistics
Matches: 94, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
84 90 0.96
85 4 0.04
ACGTcount: A:0.12, C:0.27, G:0.10, T:0.51
Consensus pattern (84 bp):
TTTCTCTTCAGCCAGTTTTTGTTCCTCTACAATTGCTTCCTGCTTCTCTTCGACCAATTTTTGTT
CCTCCACAATTTCTTCCTT
Found at i:21448 original size:57 final size:57
Alignment explanation
Indices: 21360--21549 Score: 253
Period size: 54 Copynumber: 3.3 Consensus size: 57
21350 GTTTCTTGCA
* *
21360 TGGTTTCTACTTTT-GTTTCCTCAGCCAATGGTTTAGTCTCCACAACATTTTCCCCTT
1 TGGTTTCTA-TTTTCGTCTCCTCAGCCAATGGTTTGGTCTCCACAACATTTTCCCCTT
* * * *
21417 TGGTTTCTATTTTTGTCTCCTCAACCAATGGTTTGGTCT-C-C-ATATTTTCCACTT
1 TGGTTTCTATTTTCGTCTCCTCAGCCAATGGTTTGGTCTCCACAACATTTTCCCCTT
*
21471 TTGTTTCTATTTTCGTCTCCTCAGCCAATGGTTTGGTCTCCACAGCCACATTTTCCCCTT
1 TGGTTTCTATTTTCGTCTCCTCAGCCAATGGTTTGGTCTCCACA---ACATTTTCCCCTT
21531 TGGTTTCTATTTTCGTCTC
1 TGGTTTCTATTTTCGTCTC
21550 TTGATTTTTT
Statistics
Matches: 115, Mismatches: 11, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
54 47 0.41
55 2 0.02
56 6 0.05
57 31 0.27
60 29 0.25
ACGTcount: A:0.14, C:0.27, G:0.13, T:0.46
Consensus pattern (57 bp):
TGGTTTCTATTTTCGTCTCCTCAGCCAATGGTTTGGTCTCCACAACATTTTCCCCTT
Found at i:21952 original size:18 final size:20
Alignment explanation
Indices: 21929--21966 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
21919 TTTTTTTTTT
21929 TTTTGGTTTC-GTT-TGTTG
1 TTTTGGTTTCTGTTCTGTTG
21947 TTTTGGTTTCTGTTCTGTTG
1 TTTTGGTTTCTGTTCTGTTG
21967 GATACATAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.56
19 3 0.17
20 5 0.28
ACGTcount: A:0.00, C:0.08, G:0.26, T:0.66
Consensus pattern (20 bp):
TTTTGGTTTCTGTTCTGTTG
Found at i:32287 original size:2 final size:2
Alignment explanation
Indices: 32280--32322 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
32270 ATAGATAGAT
32280 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
32322 A
1 A
32323 AGTTCACTCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:39159 original size:85 final size:85
Alignment explanation
Indices: 39016--39181 Score: 314
Period size: 85 Copynumber: 2.0 Consensus size: 85
39006 ATGAGCCAAC
*
39016 TAGAAACTATACCATAAATAAACTACCTACCTACCAAATAAACAAACAAATTACAAACAAATTCA
1 TAGAAACTATACCATAAATAAACTACCTACCTACCAAATAAACAAACAAATTACAAACAAACTCA
39081 CATTCCGTGAGAGTTGGGCA
66 CATTCCGTGAGAGTTGGGCA
*
39101 TAGAAACTATACCATAAATAAACTACTTACCTACCAAATAAACAAACAAATTACAAACAAACTCA
1 TAGAAACTATACCATAAATAAACTACCTACCTACCAAATAAACAAACAAATTACAAACAAACTCA
39166 CATTCCGTGAGAGTTG
66 CATTCCGTGAGAGTTG
39182 AACCCAAGAC
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 79 1.00
ACGTcount: A:0.48, C:0.22, G:0.08, T:0.22
Consensus pattern (85 bp):
TAGAAACTATACCATAAATAAACTACCTACCTACCAAATAAACAAACAAATTACAAACAAACTCA
CATTCCGTGAGAGTTGGGCA
Found at i:42720 original size:328 final size:327
Alignment explanation
Indices: 41470--43053 Score: 1229
Period size: 328 Copynumber: 4.8 Consensus size: 327
41460 GGATTCTTAA
* * * * * *
41470 CGCCAAAAATCATGCAAAACTGA-CCTGGGGTCCTGGAACGTGTTTTTAGCCAAAAACCGTGATG
1 CGCCAAAAATCATGCAAAACTGAGCC-GAGGCCCCGAAATGCGTTTTTAGCCAAAAA-CGTGATG
* * *
41534 ATTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCGAAA-ATAATCTTTCATCAATTTT
64 ATTATTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCGAAAGAT-A--TTTCCTCAATTTT
* * * * * * * * *
41598 TGGCTAAAATACTCATAAAAAATATATAATTCATCACCAAATATATTGAAGGGTTTTTTACG-TT
126 TGGATAAAATACTCAT-AAAATTATATAATTTAACGCCAAAAAGATTGAA-GGCTTTTCACGCTT
** * *
41662 TCTAAT-TTTTTTTTC-TACTTTTTTTCGAATTAATTTCTAATCAAATCGAAACAAGATAT-AGA
189 T-TAATATCGTTTTTCATA-TTTTTCTC-AATTAATTTCTAATTAAATCGAAACAAGAT-TCAGA
* * * * *
41724 TGCTCGTAAAAAAACAATCCTTAATTCCAATGTGGATGAGATTTGATTAGATGAATATAGATATT
250 TGCTCGTAAAAACA-AATCCTTAAATCCAATGTGGCTAACATTTGATTAGATGAATATAGATATT
* * * *
41789 T-ACATGATTTTTTG
314 TCA-AGGAGTCTCTG
* * * * * * * **** **
41803 CGCCAAAAATCATGCAAAACTGACCCG-GGCCACGGAACGCGGTTTTGGCTAAAAAAAAAAAAAA
1 CGCCAAAAATCATGCAAAACTGAGCCGAGGCCCCGAAATGCGTTTTTAGC-CAAAAACGTGATGA
* * * * * * *
41867 CTGTGATGTTACACGATTTCGACTAATATTTTGCAAAAATTGACCCAAA-ATATTTTTTCTCAAC
65 -T-T-A--TTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCGAAAGATA--TTTCCTCAAT
* ** * * * ** * * * *
41931 TTTTAGCCACAATAGTCATAAAAAAATATATAATTCGACGTCAAAAAGATTAAAGGGTTTTTCAT
123 TTTTGGATAAAATACTCAT--AAAATTATATAATTTAACGCCAAAAAGATTGAA-GGCTTTTCAC
* * * * * * *
41996 GCTTCTAATACCATTTTTCTTATTTATTTTCGAATTAATTTCTAATTAAAACGAAACATGATTCA
185 GCTTTTAATATCGTTTTTCATATTT-TTCTC-AATTAATTTCTAATTAAATCGAAACAAGATTCA
** ** * *
42061 GATGCTTTTAAAAAC-AA----T---GGC----TGG---A-ATTTGGTTATATGAATATAGATAT
248 GATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAACATTTGATTAGATGAATATAGATAT
* *
42110 TTCAAGGAGTTTCGG
313 TTCAAGGAGTCTCTG
* * *
42125 CGCCAAAAATCATTCAAAACTGAACCGA-GCCCCGGAATGCGTTTTTAGCCAAAAACCGTGATGA
1 CGCCAAAAATCATGCAAAACTGAGCCGAGGCCCCGAAATGCGTTTTTAGCCAAAAA-CGTGATGA
* * ** * *
42189 TTATTACATGATTTTGACTAAAATTTTGCAAAAGTTGACCTGAAAGATATTTCTTCAATTTTTAG
65 TTATTACACGATTTTGGCTAAAATTTTGCAAAAAATGACC-GAAAGATATTTCCTCAATTTTTGG
** * * ** *
42254 CCATAATACTCA-ACAAAATATATAATTCGACGCCAAAAAGATTGAAGGGCTTTTCGCGCTTTTA
129 ATAAAATACTCATA-AAATTATATAATTTAACGCCAAAAAGATTGAA-GGCTTTTCACGCTTTTA
* *
42318 ATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTGAATCGAAACAAGATTCAGATGCTCG
192 ATATCGTTTTTCATA-TTTTTCTCAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG
* * * * *
42383 T-ACAACAAATCCTTAAATGCAATGTTGCTAAGATTTTATTAGATGAATATAGATATTTCAAGGA
256 TAAAAACAAATCCTTAAATCCAATGTGGCTAACATTTGATTAGATGAATATAGATATTTCAAGGA
*
42447 GTGTCTG
321 GTCTCTG
* *
42454 CGCCAAAAATCATGCAAAACTGAGTCGAGGCCCCGAAATGCGTTTTTAGCCAAAAA-G-CATGAT
1 CGCCAAAAATCATGCAAAACTGAGCCGAGGCCCCGAAATGCGTTTTTAGCCAAAAACGTGATGAT
* * * * *
42517 AACGTACACGATTTTGGCTAAAATTCTGCAAAAAATGACTCGAAAAATTTTTCCTCAATTTTTGG
66 TA-TTACACGATTTTGGCTAAAATTTTGCAAAAAATGAC-CGAAAGATATTTCCTCAATTTTTGG
* ** *
42582 ATAAAATACTCATAAAATTTTATAATTTAACTTCAAAACA-ATTGGAGGACTTTTCACGCTTTTA
129 ATAAAATACTCATAAAATTATATAATTTAACGCCAAAA-AGATTGAAGG-CTTTTCACGCTTTTA
* * * *
42646 ATATCATTTTTCATATTTTTCTCAATTAATTTCTAATTAAATTGAAACAAAATTCAGATGCTTGT
192 ATATCGTTTTTCATATTTTTCTCAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
* * * * *
42711 AAAAACAAATTCTTAAATCCAATGTGGCTGACATTTGATTAGATGAATATGGATATCTAAAGGAG
257 AAAAACAAATCCTTAAATCCAATGTGGCTAACATTTGATTAGATGAATATAGATATTTCAAGGAG
42776 TCT-TGG
322 TCTCT-G
* * * * ** * * * *
42782 CGCCAAAAATCAGGCAAAACTGAGGCGGGGTCCTAAAACGCATTTTTAGCCAAAAATTGTGATGG
1 CGCCAAAAATCATGCAAAACTGAGCCGAGGCCCCGAAATGCGTTTTTAGCCAAAAA-CGTGATGA
* * * *
42847 TTATTACACGATTTCGGCTAAAATTTTGTAAAAAATTGACCCGAAAGGTATTTCCTAAATTTTTG
65 TTATTACACGATTTTGGCTAAAATTTTGCAAAAAA-TGA-CCGAAAGATATTTCCTCAATTTTTG
* * * * *
42912 GTTAAAATACTCATAAAAATCATATAATTTAACGCCAAAAAGATTGAATGGTTTTTGA-GGTTTC
128 GATAAAATACTCAT-AAAATTATATAATTTAACGCCAAAAAGATTGAA-GGCTTTTCACGCTTT-
* * *
42976 TAATATCGTTTTTCCTATTTTT-TCCAAATTAATTTCTAATTAAATCGAAACAAGATTTAAATGC
190 TAATATCGTTTTTCATATTTTTCT-C-AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGC
*
43040 TCATAAAAACAAAT
253 TCGTAAAAACAAAT
43054 TTATAAATCT
Statistics
Matches: 1018, Mismatches: 178, Indels: 110
0.78 0.14 0.08
Matches are distributed among these distances:
313 4 0.00
314 40 0.04
315 59 0.06
316 3 0.00
317 56 0.06
318 4 0.00
319 4 0.00
320 1 0.00
321 8 0.01
322 75 0.07
323 2 0.00
325 2 0.00
326 3 0.00
327 54 0.05
328 217 0.21
329 62 0.06
330 56 0.06
331 47 0.05
332 71 0.07
333 79 0.08
334 3 0.00
335 1 0.00
336 24 0.02
337 83 0.08
338 12 0.01
339 48 0.05
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (327 bp):
CGCCAAAAATCATGCAAAACTGAGCCGAGGCCCCGAAATGCGTTTTTAGCCAAAAACGTGATGAT
TATTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCGAAAGATATTTCCTCAATTTTTGGAT
AAAATACTCATAAAATTATATAATTTAACGCCAAAAAGATTGAAGGCTTTTCACGCTTTTAATAT
CGTTTTTCATATTTTTCTCAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
ACAAATCCTTAAATCCAATGTGGCTAACATTTGATTAGATGAATATAGATATTTCAAGGAGTCTC
TG
Found at i:43412 original size:15 final size:16
Alignment explanation
Indices: 43394--43423 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
43384 ATAAATAATA
43394 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
43409 ATATTATAATCTAAA
1 ATATTATAATCTAAA
43424 AATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:43730 original size:8 final size:8
Alignment explanation
Indices: 43717--43750 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
43707 TTTTATATAG
43717 TAGTAAGA
1 TAGTAAGA
43725 TAGTAAGA
1 TAGTAAGA
*
43733 TAGAAAGA
1 TAGTAAGA
43741 TAGTAAGA
1 TAGTAAGA
43749 TA
1 TA
43751 AAATAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.24, T:0.24
Consensus pattern (8 bp):
TAGTAAGA
Found at i:43758 original size:5 final size:5
Alignment explanation
Indices: 43720--43780 Score: 62
Period size: 5 Copynumber: 13.4 Consensus size: 5
43710 TATATAGTAG
* *
43720 TAAGA T-AG- TAAGA T-AGA -AAGA T-AG- TAAGA TAAAA TAAAA TAAGA
1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA
43764 TAAGA TAAGA TAAGA TA
1 TAAGA TAAGA TAAGA TA
43781 TATTCAATAT
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
3 2 0.04
4 14 0.29
5 32 0.67
ACGTcount: A:0.61, C:0.00, G:0.18, T:0.21
Consensus pattern (5 bp):
TAAGA
Done.