Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021412.1 Corchorus olitorius cultivar O-4 contig21445, 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: 42302
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32
Found at i:6327 original size:29 final size:29
Alignment explanation
Indices: 6255--6330 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 29
6245 TTGTTTTAGA
* *
6255 AGGGGCAAAACATCCAAAATTGAGAGTTC
1 AGGGGCAAAACGTCCAAAATTGAGAATTC
* * *
6284 ATGGG-AGAAATGTCCAAAATTGA-AATTT
1 AGGGGCA-AAACGTCCAAAATTGAGAATTC
6312 AGGGGGCAAAACGTCCAAA
1 A-GGGGCAAAACGTCCAAA
6331 TGCTACAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
28 5 0.14
29 31 0.84
30 1 0.03
ACGTcount: A:0.42, C:0.14, G:0.25, T:0.18
Consensus pattern (29 bp):
AGGGGCAAAACGTCCAAAATTGAGAATTC
Found at i:9063 original size:32 final size:31
Alignment explanation
Indices: 8976--9063 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 31
8966 CATCAGCGTC
* * *
8976 TTGGTCTGACGTGGCCTTGCCACATGGCATT
1 TTGGTCCGACGTGGCATTGCCACGTGGCATT
* * *
9007 TTGGTCCAATGTGGCAATGCCACGTGGCATTT
1 TTGGTCCGACGTGGCATTGCCACGTGGCA-TT
* *
9039 TTGGTCCGACGTGGTATTGTCACGT
1 TTGGTCCGACGTGGCATTGCCACGT
9064 CAGTAATACC
Statistics
Matches: 45, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
31 23 0.51
32 22 0.49
ACGTcount: A:0.15, C:0.23, G:0.30, T:0.33
Consensus pattern (31 bp):
TTGGTCCGACGTGGCATTGCCACGTGGCATT
Found at i:11112 original size:439 final size:436
Alignment explanation
Indices: 10196--11277 Score: 1324
Period size: 439 Copynumber: 2.5 Consensus size: 436
10186 AATCTTTGTT
* * * ** * * *
10196 AATCGGACATCTGGATAAAAAATAATATGATATTAAATAGATTGTCAATCGAAATGAAAAAATTT
1 AATCGGACATGTGGACAAAAAATTATATGATATTAAATAGACCGACAATCGAAACGAACAAATTT
* * * ** * *
10261 CA-AAAGCATTTTTTAGAATTGAAATATAAAAATTAACTTTTGAGTCTTTCATGAAAGTTGTAGA
66 -AGGAAGCATTTTTTAGAATTAAAAAATAAAAATTTGCTTTTGAGTCCTTCATGAAAGATGTAGA
* * * * *
10325 ACATAAAATTACCTTTTAATAGACACATGAATTACTTTAATTGGACAAATAGAACAAAGAAAATT
130 TCATGAAATTACCTTTTAATAGACACATGAATCACATTAATCGGACAAATAGAACAAAG--AA--
*
10390 TAAAAAAAAATAAAGTGTTAAATCGAGTAAGATAGAATTTGGAAAGGACTAAGTAGCATAAAATA
191 T-AAAAAAAATAAAGTGTTAAATCGAGTAAGATAGAATTTAGAAAGGACTAAGTAGCATAAAATA
* * * *
10455 GAAAAGTATGAGGGTGATTTGATAACTAATTCAAATAAGAAAATATTTGTTAATGGAGATCCTGA
255 GAAAAGTATGAGAGTCATTTGATAAATAATCCAAATAAGAAAATATTTGTTAATGGAGATCCTGA
* * *
10520 AACATAAAAATTCCCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTAACTTTCAGGTTCTTC
320 AACATAAAAATTCCCTTTTAAACCCTTCACGAAACTCGTAGATCAAATTAACTTTCAGGTCCTTC
* * * * * *
10585 ATGAAAGTCTTAGATTATACAGTAACCTTTTAACCGACACTTGAATAACTTT
385 ATGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTCAATAACTTC
* * * *
10637 AATTGGACATGTGGATC-GAAAATTATATGGTATTAAATAGACCAACAATCGAAACGAACAAATT
1 AATCGGACATGTGGA-CAAAAAATTATATGATATTAAATAGACCGACAATCGAAACGAACAAATT
* *
10701 TAGGAAGCATTTTTTTTGAATTAAAACATAAAAATTTGCTTTTGAGTCCTTCATGAAAGATGTAG
65 TAGGAAGCA-TTTTTTAGAATTAAAAAATAAAAATTTGCTTTTGAGTCCTTCATGAAAGATGTAG
* *
10766 ATCAGGAAATTACCTTTTAATAGACACATAAATCA-ACTTAATCGGACAAATAGAACAAAGAATA
129 ATCATGAAATTACCTTTTAATAGACACATGAATCACA-TTAATCGGACAAATAGAACAAAGAATA
* * *
10830 AAAAAAATAAAG-GTTAAA-CGTTAGATTAAGATAGAATTTATAAAGGACTAAGTAGTATAAAGT
193 AAAAAAATAAAGTGTTAAATCG--AG--TAAGATAGAATTTAGAAAGGACTAAGTAGCATAAAAT
* *
10893 AGAAAAGTATGAGAGTCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTAATGGAGATCTTG
254 AGAAAAGTATGAGAGTCATTTGATAAATAATCCAAATAAGAAAATATTTGTTAATGGAGATCCTG
* *
10958 AAACATAAAAATTCCC-TTTAAACCCTTCACGAAACTCGTAGATCAAATTTAGCTTTCGGGTCCT
319 AAACATAAAAATTCCCTTTTAAACCCTTCACGAAACTCGTAGATCAAA-TTAACTTTCAGGTCCT
*
11022 TCATGAAAGTCGTAAATCATGCAATAACCTTTTAACCGACACTTCAATAACTTC
383 TCATGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTCAATAACTTC
* * * * *
11076 AATCGGACATGTGGACAAAAAATTATACGATATTAAATTAG-CCGGCTATCAAAAC-CACAAAAT
1 AATCGGACATGTGGACAAAAAATTATATGATATTAAA-TAGACCGACAATCGAAACGAAC-AAAT
* * * * *
11139 TTCGGAAGCATTTTTTAGAATCAAAAAAATTAAAA-TTGACTTTTGAGTTCTTAATGAAA-ATTG
64 TTAGGAAGCATTTTTTAGAAT-TAAAAAATAAAAATTTG-CTTTTGAGTCCTTCATGAAAGA-TG
* * * *
11202 TGGATCATGAAATTACCTTTTAATAGATACTTGAATCACATTAATCGGACAAATAGAA-AAAAAA
126 TAGATCATGAAATTACCTTTTAATAGACACATGAATCACATTAATCGGACAAATAGAACAAAGAA
*
11266 T-ACAAAAATAAA
191 TAAAAAAAATAAA
11278 AGGTAACGCG
Statistics
Matches: 553, Mismatches: 72, Indels: 36
0.84 0.11 0.05
Matches are distributed among these distances:
435 2 0.00
436 6 0.01
437 25 0.05
438 53 0.10
439 303 0.55
440 7 0.01
441 57 0.10
442 100 0.18
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (436 bp):
AATCGGACATGTGGACAAAAAATTATATGATATTAAATAGACCGACAATCGAAACGAACAAATTT
AGGAAGCATTTTTTAGAATTAAAAAATAAAAATTTGCTTTTGAGTCCTTCATGAAAGATGTAGAT
CATGAAATTACCTTTTAATAGACACATGAATCACATTAATCGGACAAATAGAACAAAGAATAAAA
AAAATAAAGTGTTAAATCGAGTAAGATAGAATTTAGAAAGGACTAAGTAGCATAAAATAGAAAAG
TATGAGAGTCATTTGATAAATAATCCAAATAAGAAAATATTTGTTAATGGAGATCCTGAAACATA
AAAATTCCCTTTTAAACCCTTCACGAAACTCGTAGATCAAATTAACTTTCAGGTCCTTCATGAAA
GTCGTAAATCATACAATAACCTTTTAACCGACACTTCAATAACTTC
Found at i:16207 original size:119 final size:119
Alignment explanation
Indices: 15982--16214 Score: 337
Period size: 119 Copynumber: 2.0 Consensus size: 119
15972 TATTTTCAAT
*
15982 TACTCACGTTTCCCAGTTCTCATAAAACTCAAATTCCCATTTCTGATTATAGCATTTGACATACA
1 TACTCACGTTTCCCACTTCTCATAAAACTCAAATTCCCATTTCTGATTATAGCATTTGACATACA
*
16047 AAAAACGGTTGCTTGCATAATTCCTAAAATTTAAGAAGAAAAAAAGTTTGTTGC
66 AAAAACGATTGCTTGCATAATTCCTAAAATTTAAGAAGAAAAAAAGTTTGTTGC
* * * ** *
16101 TACTCACG-TTCCCTACTTCTTATAAAACTCAATTTCCTATTTCTGATTATAGCATTTGATTTAT
1 TACTCACGTTTCCC-ACTTCTCATAAAACTCAAATTCCCATTTCTGATTATAGCATTTGACATAC
* *
16165 AAAAAA-GATTGGC-TGCATAATTCCTAAAATTTAAGAAGGAAAACAGTTTG
65 AAAAAACGATT-GCTTGCATAATTCCTAAAATTTAAGAAGAAAAAAAGTTTG
16215 CTAAAATAAG
Statistics
Matches: 102, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
118 43 0.42
119 59 0.58
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.35
Consensus pattern (119 bp):
TACTCACGTTTCCCACTTCTCATAAAACTCAAATTCCCATTTCTGATTATAGCATTTGACATACA
AAAAACGATTGCTTGCATAATTCCTAAAATTTAAGAAGAAAAAAAGTTTGTTGC
Found at i:31180 original size:53 final size:53
Alignment explanation
Indices: 31120--31225 Score: 160
Period size: 53 Copynumber: 2.0 Consensus size: 53
31110 AGCCTTCTTA
*
31120 GTGAATAAATAATACATGATTTTATGGTCAATAAATGCT-TTTACATTCAACTG
1 GTGAATAAATAATACATGATTTTATGGTCAATAAAT-ATGTTTACATTCAACTG
* * *
31173 GTGAATAAATATTACATGATTTTATGTTCAATAAATATGTTTACATTGAACTG
1 GTGAATAAATAATACATGATTTTATGGTCAATAAATATGTTTACATTCAACTG
31226 ATTAAAAACC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
52 1 0.02
53 47 0.98
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (53 bp):
GTGAATAAATAATACATGATTTTATGGTCAATAAATATGTTTACATTCAACTG
Found at i:31329 original size:180 final size:181
Alignment explanation
Indices: 30991--31354 Score: 631
Period size: 180 Copynumber: 2.0 Consensus size: 181
30981 GTTTGATGAA
*
30991 GTGAATAAATAATACATGATTTTATGTTCAATAAATATGTTTACATTGAACTGGTTAAAAACCCT
1 GTGAATAAATAATACATGATTTTATGTTCAATAAATATGTTTACATTGAACTGATTAAAAACCCT
*
31056 TGTAATTACAAAAAAAAGGCTGGAGGAAAAAGGAATGGTGAGAAACTAATTGAAAGCCTTCTTAG
66 TGTAATTAC-AAAAAAAGACTGGAGGAAAAAGGAATGGTGAGAAACTAATTGAAAGCCTTCTTAG
* *
31121 TGAATAAATAATACATGATTTTATGGTCAATAAATGCTTTTACATTCAACTG
130 TAAATAAATAATACATGATTTTATGGTCAATAAATGCTTTCACATTCAACTG
*
31173 GTGAATAAATATTACATGATTTTATGTTCAATAAATATGTTTACATTGAACTGATTAAAAACCCT
1 GTGAATAAATAATACATGATTTTATGTTCAATAAATATGTTTACATTGAACTGATTAAAAACCCT
**
31238 TGTAATTAC-AAAAAAGACTGGAGGAAAAAGGAATGGTGAGAAACTAATTGAGGGCCTTCTTAGT
66 TGTAATTACAAAAAAAGACTGGAGGAAAAAGGAATGGTGAGAAACTAATTGAAAGCCTTCTTAGT
* *
31302 AAATAAATAGTACATGATTTTATGGTCAATAAATGCTTTCACATTCAATTG
131 AAATAAATAATACATGATTTTATGGTCAATAAATGCTTTCACATTCAACTG
31353 GT
1 GT
31355 TAAAAAACCC
Statistics
Matches: 173, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
180 101 0.58
182 72 0.42
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.32
Consensus pattern (181 bp):
GTGAATAAATAATACATGATTTTATGTTCAATAAATATGTTTACATTGAACTGATTAAAAACCCT
TGTAATTACAAAAAAAGACTGGAGGAAAAAGGAATGGTGAGAAACTAATTGAAAGCCTTCTTAGT
AAATAAATAATACATGATTTTATGGTCAATAAATGCTTTCACATTCAACTG
Found at i:31379 original size:127 final size:128
Alignment explanation
Indices: 31176--31432 Score: 367
Period size: 129 Copynumber: 2.0 Consensus size: 128
31166 TCAACTGGTG
* * * *
31176 AATAAATATTACATGATTTTATGTTCAATAAATATGTTTACATTGAACTGATTAAAAACCCTTGT
1 AATAAATAGTACATGATTTTATGGTCAATAAATATGTTTACATTCAACTGATTAAAAACCCTTGC
*
31241 AATTACAAAAAA-GACTGGAGGAAAAAGGAATGGTGAGAAACTAATTGAGGGCCTTCTTAGTA
66 AATTACAAAAAAGGACTGGAGGAAAAAGGAATGATGAGAAACTAATTGAGGGCCTTCTTAGTA
* *
31303 AATAAATAGTACATGATTTTATGGTCAAT-AA-ATGCTTTCACATTCAATTGGTTAAAAAACCCT
1 AATAAATAGTACATGATTTTATGGTCAATAAATATG-TTT-ACATTCAACTGATT-AAAAACCCT
** * *
31366 TGCAATTACAAAAAAGGGTTGGAGGAAAAGGGAATGATGAGAAACTAATTGAGGGCCTTCTTGGT
63 TGCAATTACAAAAAAGGACTGGAGGAAAAAGGAATGATGAGAAACTAATTGAGGGCCTTCTTAGT
31431 A
128 A
31432 A
1 A
31433 TTAACCAAGT
Statistics
Matches: 115, Mismatches: 11, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
125 3 0.03
126 5 0.04
127 38 0.33
128 23 0.20
129 46 0.40
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (128 bp):
AATAAATAGTACATGATTTTATGGTCAATAAATATGTTTACATTCAACTGATTAAAAACCCTTGC
AATTACAAAAAAGGACTGGAGGAAAAAGGAATGATGAGAAACTAATTGAGGGCCTTCTTAGTA
Found at i:37316 original size:131 final size:130
Alignment explanation
Indices: 37108--37372 Score: 440
Period size: 131 Copynumber: 2.0 Consensus size: 130
37098 CATTGTTTAA
*
37108 ACTTTTATATTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAC
1 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAC
* * * *
37173 TATTTAATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTAAATAT
66 TATTTAAGTTTTACCATTTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAAAT
* *
37238 ACTTTTATAGTTTTAGTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCCTTATAC
1 ACTTTTATAGTTTTACTCAACTAAAAACTCTA-TTTTTATTTAATTAAATCTAATATCCTTATAA
* *
37303 CTATTTTAGTTTTACCATTTTACTAATTTAATTAAAAAACTTAGATATATTAGATTTTTTAAAAA
65 CTATTTAAGTTTTACCATTTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAAA
37368 T
130 T
37369 ACTT
1 ACTT
37373 CTTAAATGAA
Statistics
Matches: 125, Mismatches: 9, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
130 30 0.24
131 95 0.76
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (130 bp):
ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAC
TATTTAAGTTTTACCATTTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAAAT
Found at i:41200 original size:32 final size:31
Alignment explanation
Indices: 41159--41251 Score: 159
Period size: 32 Copynumber: 2.9 Consensus size: 31
41149 GCAGTTAACT
41159 TTGGAGTTGACGAAGCCGTTAGTCACGTGCCA
1 TTGGAGTTGACGAA-CCGTTAGTCACGTGCCA
41191 TTGGAGTTGACGGAACCGTTAGTCACGTGCCA
1 TTGGAGTTGAC-GAACCGTTAGTCACGTGCCA
41223 TTGGAGTTGACGAAACCGTTAGTCACGTG
1 TTGGAGTTGACG-AACCGTTAGTCACGTG
41252 ATGGCACGTG
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
31 1 0.02
32 55 0.93
33 3 0.05
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.26
Consensus pattern (31 bp):
TTGGAGTTGACGAACCGTTAGTCACGTGCCA
Done.