Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019108.1 Corchorus olitorius cultivar O-4 contig19141, 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: 52513
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:864 original size:331 final size:328
Alignment explanation
Indices: 1--1253 Score: 1311
Period size: 331 Copynumber: 3.8 Consensus size: 328
* ** * *
1 GTTATTACACGATTTCGGCTAAAATTTTGCAAAAAATTGG-CCCCAAAGTTATTTCCACAATTTT
1 GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAA-TGGACCAAAAAATT-TTTCCTCAATTTT
* * * * * *
65 TAGCCACAATACTCATAAAAATTATATAATTCAATTCCAAAAAGATTGAAGGGCTTTTCAAGCTT
64 TGGCTAAAATACTCATAAAAA-TATATAATTCAACTCCAAAAAGATTGAAGGACTTTTCACGCTT
* * * *
130 CTAATATTATTTTTCCTATTATTTTCCGAATTAATTTCTAATTAAATCCAAACATGATTCAGATG
128 CTAATATCATTTTTCATATT-TTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATG
* *** * *
195 CTTGT-TTTACAAATCCTTAAATGCAATGTGGCTGAGATTTGGTTAGATGAATCTAGATATTTCA
192 CTCGTAAAAACAAATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCA
* * * * * * * *
259 AGGAGTCTCTACGCCAATAATCATGCAACACTGAACTAGGGCCTCGGAACGCGTTTTTAGCCAAA
257 AGGAGTCTCGATGCCAAAAATCATGCAAAACTG-ATTCGGGCCT-GAAACGCGTTTTTAGCAAAA
324 ACCGTGATTTCG
320 ACCGTGA--T-G
* * * * * *
336 ACTAACGTACACGATTTCGACTAATATTTTGAAAAAAAAAT-GACCAGAAATATTTTTCCTCAA-
1 -GTTA-GTACACGATTTCGGCTAAAATTTTG--CAAAAAATGGACCA-AAAAATTTTTCCTCAAT
* *
399 TTTTGTCTAAAATACTCATAAAATACAATATATAAAATTCAACTCCAAAAAGATTGGAGGACTTT
61 TTTTGGCTAAAATACTCAT--AA-A-AATATAT--AATTCAACTCCAAAAAGATTGAAGGACTTT
* * * * *
464 TCACGTTTTTCATATCATTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAATAAGAT
120 TCACGCTTCTAATATCATTTTTCATATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGAT
*
529 TCAGATGCTCGTAAAAACAAAACCTTAAATGCAATGTGGCTG-GATTTGATTAGATCG-ATATAG
185 TCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTGAGATTTGATTAGAT-GAATATAG
** * *
592 ATATTTCAAGGAGTCTCGATGGAAAAAATCATACAAAATTGATTCGGTGCCCTGAAACGCGTTTT
249 ATATTTCAAGGAGTCTCGATGCCAAAAATCATGCAAAACTGATTCGG-G-CCTGAAACGCGTTTT
657 TAGCAAAAACCGTGATG
312 TAGCAAAAACCGTGATG
* * * *
674 GTTAGTACACGATTCCTGCTAAAATTTTGCAAAAAATGGTCCAAAAAATTTTTCCTTAATTTTTG
1 GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGGACCAAAAAATTTTTCCTCAATTTTTG
* * * * * * *
739 GCTAAAATAGTCATGAAATATATATAATTTAA-TACAAAAAAATATTGGAGAACTTTTCACGCTT
66 GCTAAAATACTCAT-AAAAATATATAATTCAACT-C-CAAAAAGATTGAAGGACTTTTCACGCTT
* * * *
803 TTCATATCATTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAAATTCAGATGC
128 CTAATATCATTTTTCATATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGC
* * * * *
868 TCGTTAAAACAAATCCTTAAATGCATTGTGGCTGAGATTTGATTAGCTGAATATGGATATCTCAA
193 TCGTAAAAACAAATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAA
* * * *
933 GGAGTCTTGGTGTCAAAAATCATGCAAAACTGATCCGAGGTCCT-AGAACGCGTTTTTAGCCAAA
258 GGAGTCTCGATGCCAAAAATCATGCAAAACTGATTCG-GG-CCTGA-AACGCGTTTTTAG-CAAA
997 AACCGTGATG
319 AACCGTGATG
* * * * * *
1007 ATTATTACACGATTTCGGCTAAAATTTTGC-AAAAATTGACCTGAAAGATGTTTCCTCAATTTTT
1 GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGGACC-AAAAAATTTTTCCTCAATTTTT
* * * * **
1071 GGATAAAATACTCATAAAAAAATATAATTCAACTCCATAAATATTGAAGGGTTTTTCACGCTTCT
65 GGCTAAAATACTCATAAAAATATATAATTCAACTCCAAAAAGATTGAAGGACTTTTCACGCTTCT
* * * * * * *
1136 AATATCGTTCTTCCTA-GTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTTAAATGCTC
130 AATATCATTTTTCATATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTC
* * * *
1200 GTAAGAACAAATCCTTAAATCCGATGTGGTTGAGATTTGATTAGATGAATATAG
195 GTAAAAACAAATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATGAATATAG
1254 CGCCAAAAAT
Statistics
Matches: 769, Mismatches: 122, Indels: 58
0.81 0.13 0.06
Matches are distributed among these distances:
329 1 0.00
330 95 0.12
331 155 0.20
332 102 0.13
333 74 0.10
334 23 0.03
335 21 0.03
336 23 0.03
337 40 0.05
338 12 0.02
339 13 0.02
340 10 0.01
341 122 0.16
342 78 0.10
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (328 bp):
GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGGACCAAAAAATTTTTCCTCAATTTTTG
GCTAAAATACTCATAAAAATATATAATTCAACTCCAAAAAGATTGAAGGACTTTTCACGCTTCTA
ATATCATTTTTCATATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG
TAAAAACAAATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGA
GTCTCGATGCCAAAAATCATGCAAAACTGATTCGGGCCTGAAACGCGTTTTTAGCAAAAACCGTG
ATG
Found at i:2385 original size:21 final size:21
Alignment explanation
Indices: 2361--2412 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
2351 AATATCTTTA
2361 CATAATTAAAATAAAAAGT-TT
1 CATAATTAAAATAAAAA-TATT
* *
2382 CATAACTATAAATAATAATATT
1 CATAATTA-AAATAAAAATATT
2404 -ATAATTAAA
1 CATAATTAAA
2413 TATATTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 2 0.08
21 14 0.54
22 10 0.38
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.35
Consensus pattern (21 bp):
CATAATTAAAATAAAAATATT
Found at i:2423 original size:18 final size:18
Alignment explanation
Indices: 2390--2466 Score: 66
Period size: 18 Copynumber: 4.1 Consensus size: 18
2380 TTCATAACTA
*
2390 TAAATAATAATATTATAAT
1 TAAAT-ATATTATTATAAT
2409 TAAATATATTATTATAAT
1 TAAATATATTATTATAAT
* * *
2427 CTAAAAATAATTATTAGAAG
1 -TAAATAT-ATTATTATAAT
*
2447 TAAA-ATATTAATTACAAT
1 TAAATATATT-ATTATAAT
2465 TA
1 TA
2467 TAGTGGATTA
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
17 3 0.06
18 22 0.45
19 15 0.31
20 9 0.18
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (18 bp):
TAAATATATTATTATAAT
Found at i:2660 original size:5 final size:5
Alignment explanation
Indices: 2642--2733 Score: 149
Period size: 5 Copynumber: 19.4 Consensus size: 5
2632 TATATAGTAG
2642 TAAGA T-AG- TAAGA TAAGA TAAGA TAAGA T-AG- TAAGA TAAGA TAAGA
1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA
2688 T-AGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TA
1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TA
2734 TATCACCTTA
Statistics
Matches: 82, Mismatches: 0, Indels: 10
0.89 0.00 0.11
Matches are distributed among these distances:
3 2 0.02
4 12 0.15
5 68 0.83
ACGTcount: A:0.58, C:0.00, G:0.21, T:0.22
Consensus pattern (5 bp):
TAAGA
Found at i:4251 original size:29 final size:28
Alignment explanation
Indices: 4226--4294 Score: 111
Period size: 29 Copynumber: 2.4 Consensus size: 28
4216 AAATAAGCAA
4226 CTGAACTTTTATTTTGGCCAGATAAGCC
1 CTGAACTTTTATTTTGGCCAGATAAGCC
*
4254 CTTGAACTCTTATTTTGGCCAGATAAGCCC
1 C-TGAACTTTTATTTTGGCCAGATAAG-CC
4284 CTGAACTTTTA
1 CTGAACTTTTA
4295 AAAAAGTCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 1 0.03
29 33 0.89
30 3 0.08
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (28 bp):
CTGAACTTTTATTTTGGCCAGATAAGCC
Found at i:5661 original size:31 final size:32
Alignment explanation
Indices: 5620--5696 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
5610 TGGTCCAATA
* *
5620 TGGCAATGCCACATGGCA-TTTTAATCCGATG
1 TGGCATTGCCACATGGCATTTTTAATCCGACG
* ** *
5651 TGGCATTGCCACATGGTATTTTTGGTCCTACG
1 TGGCATTGCCACATGGCATTTTTAATCCGACG
5683 TGGCATTGCCACAT
1 TGGCATTGCCACAT
5697 CAGCAATACC
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 16 0.41
32 23 0.59
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.32
Consensus pattern (32 bp):
TGGCATTGCCACATGGCATTTTTAATCCGACG
Found at i:7464 original size:25 final size:25
Alignment explanation
Indices: 7436--7484 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
7426 TGTTAGTTTG
7436 TAGAGACCGAGCGAGAGTGCTCAAT
1 TAGAGACCGAGCGAGAGTGCTCAAT
7461 TAGAGACCGAGCGAGAGTGCTCAA
1 TAGAGACCGAGCGAGAGTGCTCAA
7485 GATTGTTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.20, G:0.33, T:0.14
Consensus pattern (25 bp):
TAGAGACCGAGCGAGAGTGCTCAAT
Found at i:12652 original size:16 final size:16
Alignment explanation
Indices: 12631--12662 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
12621 GAACTTGTAA
12631 GAAAGTGACAAATTAG
1 GAAAGTGACAAATTAG
12647 GAAAGTGACAAATTAG
1 GAAAGTGACAAATTAG
12663 CACTTGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.25, T:0.19
Consensus pattern (16 bp):
GAAAGTGACAAATTAG
Found at i:15941 original size:32 final size:32
Alignment explanation
Indices: 15882--15964 Score: 141
Period size: 32 Copynumber: 2.6 Consensus size: 32
15872 ATTTGATTTC
15882 GGATGAGTTAAAATGTAA-TTTTTTTTTTGAA
1 GGATGAGTTAAAATGTAACTTTTTTTTTTGAA
15913 GGATGAGTTAAAATGTAACTTTTTTTTTTGAA
1 GGATGAGTTAAAATGTAACTTTTTTTTTTGAA
* *
15945 GGAAGAGTTAAAACGTAACT
1 GGATGAGTTAAAATGTAACT
15965 GACTATGGAT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
31 18 0.37
32 31 0.63
ACGTcount: A:0.35, C:0.04, G:0.20, T:0.41
Consensus pattern (32 bp):
GGATGAGTTAAAATGTAACTTTTTTTTTTGAA
Found at i:26994 original size:1 final size:1
Alignment explanation
Indices: 26990--27017 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
26980 TATTTTTTGA
26990 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
27018 GTCTTGGAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:38953 original size:31 final size:31
Alignment explanation
Indices: 38918--38981 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
38908 ATCATCCACG
*
38918 TTTTATTTTATTTCATTTTTATTACAATAAA
1 TTTTATTTTATTTCATTTTCATTACAATAAA
38949 TTTTATTTTATTTCATTTTCATTACAATAAA
1 TTTTATTTTATTTCATTTTCATTACAATAAA
38980 TT
1 TT
38982 ATGGTTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.61
Consensus pattern (31 bp):
TTTTATTTTATTTCATTTTCATTACAATAAA
Found at i:39598 original size:20 final size:20
Alignment explanation
Indices: 39573--39611 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
39563 TGGGTAGAAA
39573 TGTATATAAGATGACAGATG
1 TGTATATAAGATGACAGATG
39593 TGTATATAAGATGACAGAT
1 TGTATATAAGATGACAGAT
39612 ATGAAACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.31
Consensus pattern (20 bp):
TGTATATAAGATGACAGATG
Found at i:40325 original size:90 final size:90
Alignment explanation
Indices: 40203--40379 Score: 295
Period size: 91 Copynumber: 2.0 Consensus size: 90
40193 ATACCTTTCT
*
40203 CTTTTACAATAATCTGCAGATTATAATGATCAAAGGG-TAAATCATTGAAA-CTTTTTGACACTT
1 CTTTTACAATAATCTGCAGATTATAATAATCAAAGGGTTAAATCATT-AAACCTTTTTGACACTT
40266 TTGACAGCAAAGTTAATAGGAAAAAG
65 TTGACAGCAAAGTTAATAGGAAAAAG
* *
40292 CTTTTAACAATAATCTGCAGATTATGATAATCAAAGGGTTAAATTATTAAACCTTTTTGACACTT
1 CTTTT-ACAATAATCTGCAGATTATAATAATCAAAGGGTTAAATCATTAAACCTTTTTGACACTT
40357 TTGACAGCAAAGTTAATAGGAAA
65 TTGACAGCAAAGTTAATAGGAAA
40380 TTAAGCCTAA
Statistics
Matches: 82, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
89 5 0.06
90 33 0.40
91 44 0.54
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (90 bp):
CTTTTACAATAATCTGCAGATTATAATAATCAAAGGGTTAAATCATTAAACCTTTTTGACACTTT
TGACAGCAAAGTTAATAGGAAAAAG
Found at i:43089 original size:2 final size:2
Alignment explanation
Indices: 43082--43118 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
43072 ATTAATTAAT
43082 TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43119 AATAGTATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:43089 original size:17 final size:18
Alignment explanation
Indices: 43080--43117 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 18
43070 ATATTAATTA
43080 ATTATATATA-TATATAT
1 ATTATATATATTATATAT
43097 ATTATATATATATATATAT
1 ATTATATATAT-TATATAT
43116 AT
1 AT
43118 AAATAGTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.53
19 9 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTATATATATTATATAT
Found at i:52333 original size:85 final size:87
Alignment explanation
Indices: 52238--52416 Score: 308
Period size: 88 Copynumber: 2.1 Consensus size: 87
52228 CTCATTACGA
52238 TATCTTTCTATATGCTCAACCAATCC-GAAAAATCATAAATATAATTAGGGTAAACTATAAATTT
1 TATCTTTCTATATGCTCAACCAATCCTGAAAAATCATAAATATAATTAGGGTAAACTATAAATTT
52302 AATCAC-TAAAATTTAGGTGAG
66 AATCACTTAAAATTTAGGTGAG
*
52323 TATCTTTCTATATGCTCAACCAATCCATTGAGAAATCATAAATATAATTAGGGTAAACTATAAAT
1 TATCTTTCTATATGCTCAACCAATCC--TGAAAAATCATAAATATAATTAGGGTAAACTATAAAT
*
52388 TTAATCACTTAAATTTTAGGTGAG
64 TTAATCACTTAAAATTTAGGTGAG
52412 TATCT
1 TATCT
52417 GTTTTGGGAG
Statistics
Matches: 88, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
85 26 0.30
88 43 0.49
89 19 0.22
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (87 bp):
TATCTTTCTATATGCTCAACCAATCCTGAAAAATCATAAATATAATTAGGGTAAACTATAAATTT
AATCACTTAAAATTTAGGTGAG
Done.