Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019190.1 Corchorus olitorius cultivar O-4 contig19223, 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: 59612
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:7551 original size:29 final size:34
Alignment explanation
Indices: 7483--7551 Score: 76
Period size: 34 Copynumber: 2.2 Consensus size: 34
7473 TATAATTTAT
*
7483 TTTTCTAAATATTTTATATAAATATTATATTTGA
1 TTTTCTAAATATTATATATAAATATTATATTTGA
**
7517 AATTCTAAATA-TATA-AT-AATA-TATATTTG-
1 TTTTCTAAATATTATATATAAATATTATATTTGA
7546 TTTTCT
1 TTTTCT
7552 CCCAACCAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
29 4 0.13
30 8 0.27
31 4 0.13
32 2 0.07
33 3 0.10
34 9 0.30
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.54
Consensus pattern (34 bp):
TTTTCTAAATATTATATATAAATATTATATTTGA
Found at i:8329 original size:16 final size:17
Alignment explanation
Indices: 8298--8332 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
8288 AAGAATTAAT
8298 ATTATATATATTAATTA
1 ATTATATATATTAATTA
*
8315 ATTAT-TATGTTAATTA
1 ATTATATATATTAATTA
8331 AT
1 AT
8333 CATTTCGGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
ATTATATATATTAATTA
Found at i:10427 original size:16 final size:16
Alignment explanation
Indices: 10406--10438 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
10396 AATTTTTACA
10406 AGTCTTTCCCATTGGT
1 AGTCTTTCCCATTGGT
10422 AGTCTTTCCCATTGGT
1 AGTCTTTCCCATTGGT
10438 A
1 A
10439 ATCAATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.42
Consensus pattern (16 bp):
AGTCTTTCCCATTGGT
Found at i:37641 original size:30 final size:30
Alignment explanation
Indices: 37607--37665 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
37597 TTTTTATCTT
*
37607 GACTTTTCTCTTATATCCTCAAATTTTAAA
1 GACTTTTCTCTTATACCCTCAAATTTTAAA
*
37637 GACTTTTTTCTTATACCCTCAAATTTTAA
1 GACTTTTCTCTTATACCCTCAAATTTTAA
37666 TGGTTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.29, C:0.20, G:0.03, T:0.47
Consensus pattern (30 bp):
GACTTTTCTCTTATACCCTCAAATTTTAAA
Found at i:44027 original size:65 final size:66
Alignment explanation
Indices: 43942--44069 Score: 231
Period size: 65 Copynumber: 2.0 Consensus size: 66
43932 ATAAAATAAA
*
43942 AAAAGTAAGGTGAGGAATTGCCTGGAAAATTATTTTGAGGACAATTTTAAAACAAATAGCTATCA
1 AAAAGTAAGGTGAGGAATTGCCTGGAAAATTATTTTGAGGACAATTTAAAAACAAATAGCTATCA
44007 T
66 T
*
44008 AAAA-TAAGGTGAGGAATTGCCTGGAAAATTATTTTGAGGATAATTTAAAAACAAATAGCTAT
1 AAAAGTAAGGTGAGGAATTGCCTGGAAAATTATTTTGAGGACAATTTAAAAACAAATAGCTAT
44070 ATATCATAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
65 56 0.93
66 4 0.07
ACGTcount: A:0.44, C:0.08, G:0.20, T:0.29
Consensus pattern (66 bp):
AAAAGTAAGGTGAGGAATTGCCTGGAAAATTATTTTGAGGACAATTTAAAAACAAATAGCTATCA
T
Found at i:55195 original size:41 final size:41
Alignment explanation
Indices: 55074--55199 Score: 103
Period size: 41 Copynumber: 3.0 Consensus size: 41
55064 AATTAGTTAT
* *
55074 AGAAATATATTATTTTGTTTCTTATATTGATCATGAAAAAA
1 AGAAATATATTAATTTGTTTCTTATTTTGATCATGAAAAAA
* ***** * *
55115 AGAAA-A-ACTTAATGTGAATAAAAAATTCTTGAACTTGAAAAAA
1 AGAAATATA-TTAATTTG--TTTCTTATT-TTGATCATGAAAAAA
*
55158 CGAAATATATTAATTTGTTTCTTATTTTGATCATGAAAAAA
1 AGAAATATATTAATTTGTTTCTTATTTTGATCATGAAAAAA
55199 A
1 A
55200 AAACCTTAAT
Statistics
Matches: 59, Mismatches: 20, Indels: 12
0.65 0.22 0.13
Matches are distributed among these distances:
39 1 0.02
40 7 0.12
41 18 0.31
42 7 0.12
43 17 0.29
44 8 0.14
45 1 0.02
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.37
Consensus pattern (41 bp):
AGAAATATATTAATTTGTTTCTTATTTTGATCATGAAAAAA
Found at i:55281 original size:143 final size:145
Alignment explanation
Indices: 55073--55367 Score: 447
Period size: 143 Copynumber: 2.0 Consensus size: 145
55063 TAATTAGTTA
*
55073 TAGAAATATATTATTTTGTTTCTTATATTGATCATGAAAAAAAGAAAAACTTAATGTGAATAAAA
1 TAGAAATATATTAATTTGTTTCTTATATTGATCATG--AAAAAGAAAAA--TAA--TGAATAAAA
*
55138 AATTCTTGAACTTGAAAAAACGAAATATATTAATTTGTTTCTTATTTTGATCATGAAAAAAAAAA
60 AATTCTTGAACTTGAAAAAACGAAATATATTAATTTGTTTCTTATTTTGATAATG---AAAAAAA
55203 CCTTAATGTGAAT-AAAAAATTCT
122 CCTTAATGTGAATAAAAAAATTCT
*
55226 TAGAAATATATTAATTTGTTTCTTATTTTGATCATG-AAAA-AAAAA-AA-GAATAAAAAATTCT
1 TAGAAATATATTAATTTGTTTCTTATATTGATCATGAAAAAGAAAAATAATGAATAAAAAATTCT
55287 TGAACTTGAAAAAACGAAATATATTAATTTGTTTCTTATTTTGATAATGAAAAAAACCTTAATGT
66 TGAACTTGAAAAAACGAAATATATTAATTTGTTTCTTATTTTGATAATGAAAAAAACCTTAATGT
55352 GAATAAAAAAATTCT
131 GAATAAAAAAATTCT
55367 T
1 T
55368 GAACTTGAAA
Statistics
Matches: 138, Mismatches: 3, Indels: 14
0.89 0.02 0.09
Matches are distributed among these distances:
140 20 0.14
141 11 0.08
143 62 0.45
146 2 0.01
149 5 0.04
150 4 0.03
153 34 0.25
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (145 bp):
TAGAAATATATTAATTTGTTTCTTATATTGATCATGAAAAAGAAAAATAATGAATAAAAAATTCT
TGAACTTGAAAAAACGAAATATATTAATTTGTTTCTTATTTTGATAATGAAAAAAACCTTAATGT
GAATAAAAAAATTCT
Found at i:55321 original size:74 final size:77
Alignment explanation
Indices: 55228--55381 Score: 233
Period size: 74 Copynumber: 2.0 Consensus size: 77
55218 AAAATTCTTA
*
55228 GAAATATATTAATTTGTTTCTTATTTTGATCATGAAAAAAA-AA-AAGAAT-AAAAAATTCTTGA
1 GAAATATATTAATTTGTTTCTTATTTTGATAATGAAAAAAACAATAAGAATAAAAAAATTCTTGA
55290 ACTTGAAAAAAC
66 ACTTGAAAAAAC
**
55302 GAAATATATTAATTTGTTTCTTATTTTGATAATGAAAAAAACCTTAATGTGAATAAAAAAATTCT
1 GAAATATATTAATTTGTTTCTTATTTTGATAATGAAAAAAA-C--AATAAGAATAAAAAAATTCT
55367 TGAACTTGAAAAAAC
63 TGAACTTGAAAAAAC
55382 TAGTGGTAGA
Statistics
Matches: 71, Mismatches: 3, Indels: 6
0.89 0.04 0.08
Matches are distributed among these distances:
74 40 0.56
78 2 0.03
79 4 0.06
80 25 0.35
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.35
Consensus pattern (77 bp):
GAAATATATTAATTTGTTTCTTATTTTGATAATGAAAAAAACAATAAGAATAAAAAAATTCTTGA
ACTTGAAAAAAC
Found at i:55501 original size:13 final size:13
Alignment explanation
Indices: 55483--55507 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55473 TGTAATGAGA
55483 TTTTTCACTTGTG
1 TTTTTCACTTGTG
55496 TTTTTCACTTGT
1 TTTTTCACTTGT
55508 ATTTGTTGCC
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:0.08, C:0.16, G:0.12, T:0.64
Consensus pattern (13 bp):
TTTTTCACTTGTG
Found at i:56346 original size:14 final size:14
Alignment explanation
Indices: 56327--56353 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
56317 ACATACGGAT
56327 ATATTAATTCAATC
1 ATATTAATTCAATC
56341 ATATTAATTCAAT
1 ATATTAATTCAAT
56354 GGTTTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (14 bp):
ATATTAATTCAATC
Found at i:56593 original size:32 final size:32
Alignment explanation
Indices: 56543--56614 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
56533 TTCAAAGAAC
* * *
56543 ATTTTGTCCTACTTTGTCAAAATTTGAGAGTT
1 ATTTTGTCCTACTATGTCAAAATTCGAGAGCT
* * *
56575 ATTTTGTTCTTCTATGTCAAAATTCGAGGGCT
1 ATTTTGTCCTACTATGTCAAAATTCGAGAGCT
56607 ATTTTGTC
1 ATTTTGTC
56615 TATCAATTTG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.47
Consensus pattern (32 bp):
ATTTTGTCCTACTATGTCAAAATTCGAGAGCT
Found at i:58981 original size:337 final size:331
Alignment explanation
Indices: 58025--59612 Score: 2017
Period size: 333 Copynumber: 4.7 Consensus size: 331
58015 TTTGTAACGT
* * * ** * * * *
58025 TAAAGATATTTCAAGGAGTCTTGGTACCAAAAATCAAGCAAAACTAAGCCAAGATCCAAGAACGC
1 TAAAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGAGCCGGGACCCCATAGCGC
* * * * ** ** *
58090 ATTTTTAGCCAAAAACCATTAAT-GTACAGGATTTCGGGCTTCGGCTAAAATTTTTGAAAAAACT
66 ATTTTTAGCCAAAAATCA-TGATGGT-TAGTA-CAC-GATTTCAGCTAAAATTTTTGAAAAAACT
* * * *
58154 GACCC-AAAAATTTTTCCTCCATTTTTTGCCACAATACTCA-CAAAAATATATGATTCAACGCCA
127 GACCCGAAAAATTTTTCCT-CAATTTTTGCCACAATACTCATAAAAAATATATAATTCAATGCCA
* * * *
58217 GAAAGATTGAAGGTTTTTTTCGCGCTTTTAATATCGTTTTTCAAAATTTTTTCCAAATTAATTTC
191 -AAAAATTGAAGG--GTTTTCACGCTTCTAATATCGTTTTTCAAAATTTTTTCCAAATTAATTTC
* * * *
58282 TAACTGAATCGAAACATGATTCAGACGTTCGCAAAAACAAATCCTTAAATCCATTGCGGCTGAA-
253 TAACTAAATCGAAACATGATTCAGATGCTCGCAAAAACAAATCCTTAAACCCATTGCGGCT-AAG
*
58346 ATTTGATTAGATGAA
317 ATTTGGTTAGATGAA
* * * * *
58361 TAAAGATATTTCAAGGAATCTTGGCACAAAAAAATCATGCAAAACTGAGGCGGG-CCCCAGAACG
1 TAAAGATATTTCAAGGAGTCTTGGCAC-CAAAAATCATGCAAAACTGAGCCGGGACCCCATAGCG
* * * * * *
58425 CATTTTTAGCC-AAAACCATGATGGTTA-CATATGATTTCGGCTAAAAATTTTTGAAAAAATTGA
65 CATTTTTAGCCAAAAATCATGATGGTTAGTACACGATTTCAGCT-AAAATTTTTGAAAAAACTGA
* * * * *
58488 CCCGAAAAATATTTCCTTAATTTTTGACCATAATATTCATAGAAAATATATAATTCAATGCCGAA
129 CCCGAAAAATTTTTCCTCAATTTTTG-CCACAATACTCATAAAAAATATATAATTCAATGCC-AA
* * * * *
58553 AAGATTGAAGGGCTATTCGCGCTTCTAATATTGTTTTTCAAAATTTTTTCCAAATTAATTTTTAA
192 AAAATTGAAGGG-TTTTCACGCTTCTAATATCGTTTTTCAAAATTTTTTCCAAATTAATTTCTAA
* * *
58618 CTAAATCGAAACATCATTCAGATGCTCGCAAAAACAAATCCTTAAACCCATTGCAGCTAAGAATT
256 CTAAATCGAAACATGATTCAGATGCTCGCAAAAACAAATCCTTAAACCCATTGCGGCTAAGATTT
*
58683 GGTTAGATAAA
321 GGTTAGATGAA
*
58694 TAAAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGAGCCGGGACCCCATAGTGC
1 TAAAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGAGCCGGGACCCCATAGCGC
*
58759 ATTTTTAGCCAAAAATCATATGATGGTTAGTACACGATTTTAGCTAAAATTTTTGAAAAAACTGA
66 ATTTTTAGCCAAAAATC--ATGATGGTTAGTACACGATTTCAGCTAAAATTTTTGAAAAAACTGA
** * *
58824 CCCGAAAGTTTTTTACTCAAGTTTTTTGCCACAATACTCATAAAAAATTATATAGTTCAATGCCA
129 CCCGAAAAATTTTTCCTCAA--TTTTTGCCACAATACTCATAAAAAA-TATATAATTCAATGCCA
* * *
58889 AAATAATTGAAGGGTTCTCACGCTTCTAATATCGTCTGTCAAAATTTTTTCCAAATTAATTTCTA
191 AAA-AATTGAAGGGTTTTCACGCTTCTAATATCGTTTTTCAAAATTTTTTCCAAATTAATTTCTA
* * *
58954 ACTAAATCGAAACATGATTCAGATGCTCGCAAAAACAATTCCTTAAATCCATTGCGGCTGAGATT
255 ACTAAATCGAAACATGATTCAGATGCTCGCAAAAACAAATCCTTAAACCCATTGCGGCTAAGATT
59019 TGGTTAGATGAA
320 TGGTTAGATGAA
* * * *
59031 CAAAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGAGCCGGGGCCCTATAGTGC
1 TAAAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGAGCCGGGACCCCATAGCGC
* * * * * * *
59096 ATTTTTAGGCAAAAATCATGATGGTTAGTAGAGGATTTCAACTAAGATTTTTGAAGAAACTAACC
66 ATTTTTAGCCAAAAATCATGATGGTTAGTACACGATTTCAGCTAAAATTTTTGAAAAAACTGACC
* * * *
59161 C-AAAACATTTTTCCTCAACTTTTGGCCACAATACTGA-CAAAAATATATAATTCAACGCCAAAA
131 CGAAAA-ATTTTTCCTCAA-TTTTTGCCACAATACTCATAAAAAATATATAATTCAATGCCAAAA
* * *
59224 ATATTGAAGGGTTTTTCACGTTTCTAATATCATTTCTCAAAATTTTTTCCAAATTAATTTCTAAC
194 A-ATTGAAGGG-TTTTCACGCTTCTAATATCGTTTTTCAAAATTTTTTCCAAATTAATTTCTAAC
59289 TAAATCGAAACATGATTCAGATGCTCGCAAAAACAAATCCTTAAACCCATTGCGGCTAAGATTTG
257 TAAATCGAAACATGATTCAGATGCTCGCAAAAACAAATCCTTAAACCCATTGCGGCTAAGATTTG
59354 GTTAGATGAA
322 GTTAGATGAA
* *
59364 TAAAGATATTTCAAGGAGTCTTGACACCAAAAATCATGCAAAACTGAGCC-GGAGTCCCATAGCG
1 TAAAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGAGCCGGGA-CCCCATAGCG
*
59428 CATTTTTAGCCAAAAATCATGATGGTTAGTACACGATTTCGGCTAAAATTTTTGAAAAAACTGAC
65 CATTTTTAGCCAAAAATCATGATGGTTAGTACACGATTTCAGCTAAAATTTTTGAAAAAACTGAC
** *
59493 CCGAAAGTTTTTTACTCAATTTTTGCCACAATACTCATAAAAAATTATATAATTCAATGCCAAAA
130 CCGAAAAATTTTTCCTCAATTTTTGCCACAATACTCATAAAAAA-TATATAATTCAATGCCAAAA
* *
59558 TAATTGAAGGGTTTTCACGCTTCTAATATCATCTTTCAAAATTTTTTCCAAATTA
194 -AATTGAAGGGTTTTCACGCTTCTAATATCGTTTTTCAAAATTTTTTCCAAATTA
Statistics
Matches: 1096, Mismatches: 130, Indels: 55
0.86 0.10 0.04
Matches are distributed among these distances:
331 9 0.01
332 101 0.09
333 474 0.43
334 89 0.08
335 63 0.06
336 88 0.08
337 242 0.22
338 30 0.03
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (331 bp):
TAAAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTGAGCCGGGACCCCATAGCGC
ATTTTTAGCCAAAAATCATGATGGTTAGTACACGATTTCAGCTAAAATTTTTGAAAAAACTGACC
CGAAAAATTTTTCCTCAATTTTTGCCACAATACTCATAAAAAATATATAATTCAATGCCAAAAAA
TTGAAGGGTTTTCACGCTTCTAATATCGTTTTTCAAAATTTTTTCCAAATTAATTTCTAACTAAA
TCGAAACATGATTCAGATGCTCGCAAAAACAAATCCTTAAACCCATTGCGGCTAAGATTTGGTTA
GATGAA
Done.