Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012847.1 Corchorus olitorius cultivar O-4 contig12880, 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: 23981
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:671 original size:321 final size:319
Alignment explanation
Indices: 1--905 Score: 1089
Period size: 319 Copynumber: 2.8 Consensus size: 319
* *
1 TTCGGGTCAATATTTCACCGAAATCGTGTACTAATCATCACGGTTTTTGGCTAAAAACGCGTTTC
1 TTCGGGTCAATATTT-AGCGAAATCGTGTA-TAACCATCACGGTTTTTGGCTAAAAACGCGTTTC
* * * * **
66 GGGTTCCCGGCTCAGTTTTGCATGATTTTTGG-AGAAAAGACTCCTTAAAATATTTATATTTGTA
64 GGG-GCCCAGCTCAGTTTTGCATGATTTTTGGCAG-AAAGACTCCTTGAAATATCTATATTCATA
* * *
130 TAACCAAATCTCAACCAATTTGGATTTAAGGATTTCTTTTTACGAGCATCTGAATCTTGTTTCGA
127 TAACCAAATCTCAGCCAATTTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTTGA
* *
195 TTTAATTAGAAATAAATTC-GAAAAAAATTGGAAAAACGATATT-GTAAGCGTGGAAAA-CCCTT
192 TTTAATTAGAAATAAATTCGGAAAAAAAATGGAAAAACGATATTAG-AAGCGT-GAAAATCCC-G
* * ** * * * **
257 CAAATTTTTTTGGCATTCAATTATGTATATTCCAGAGTAGTGTGGCAAAAAATTAAGAATAAAGT
254 CCAATCTTTTACGCATTCAATTATATATATTCCAGAGTAGTGTGACAAAAAATTAAGAAAAAAAA
322 T
319 T
* *
323 TTCGGGTCAATTTTTAGCTGAAAATCGTGTAATAACCATCACGGTTTTTGGCTAAAAACGTGTTT
1 TTCGGGTCAATATTTAGC-G-AAATCGTGT-ATAACCATCACGGTTTTTGGCTAAAAACGCGTTT
*
388 CGGGGCTCAGCTCAGTTTTGCAT-ATTTTTGGCAGAAAGACT-CTGTGAAATATCTATATTCATA
63 CGGGGCCCAGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCT-TGAAATATCTATATTCATA
* * * *
451 TAACCAGATCTCGGCCAATTTGGA-TTAAGAATTTGTTTTTACGAGCATCTAAATCTTGTTTTGA
127 TAACCAAATCTCAGCCAATTTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTTGA
* *
515 TTTAATTA-AAATAAATTCGGAAAAAAAAATCGAAAAATGATATTAGAAGCGTGAAAATCCCGCC
192 TTTAATTAGAAATAAATTCGG-AAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAATCCCGCC
** * * * ** * * *
579 AATCTTTTACGTGTTTAACTATATATTTTTTTTAGAGTATTGTGACAATAAATTGAGAAAAAAAA
256 AATCTTTTACGCATTCAA-T-TATATATATTCCAGAGTAGTGTGACAAAAAATTAAGAAAAAAAA
644 T
319 T
*
645 TTCGGGTCAATATTTAGTCGAAATCGTG--T-ACCATCACGGTTTTTGGCTAAAAACGCGTTTTG
1 TTCGGGTCAATATTTAG-CGAAATCGTGTATAACCATCACGGTTTTTGGCTAAAAACGCGTTTCG
* *
707 GGGCCCCGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAGTATCTATATTCATATA
65 GGGCCCAG-CTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATA
* *
772 ACCAAATCTCAGCCAATTTGGATTTAAGGATTTGTTTTTACAAGCATCTGAAGCTTGTTTCTG-T
129 ACCAAATCTCAGCCAATTTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTT-TGAT
* * * * * * *
836 TTAACTAGAAATTAATTCGG-AAAAAGATGGGAAAACGATATTAGAAGCATGAAAATTCAGCCAA
193 TTAATTAGAAATAAATTCGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAATCCCGCCAA
900 TCTTTT
258 TCTTTT
906 GCCATCGGAC
Statistics
Matches: 503, Mismatches: 62, Indels: 39
0.83 0.10 0.06
Matches are distributed among these distances:
317 37 0.07
318 14 0.03
319 111 0.22
320 107 0.21
321 104 0.21
322 84 0.17
323 45 0.09
324 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Consensus pattern (319 bp):
TTCGGGTCAATATTTAGCGAAATCGTGTATAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGG
GGCCCAGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATAAC
CAAATCTCAGCCAATTTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTTGATTTA
ATTAGAAATAAATTCGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAATCCCGCCAATCT
TTTACGCATTCAATTATATATATTCCAGAGTAGTGTGACAAAAAATTAAGAAAAAAAAT
Found at i:6750 original size:16 final size:16
Alignment explanation
Indices: 6729--6759 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6719 AATAAAACCT
*
6729 TAAAAAAACAAATAAA
1 TAAAAAAAAAAATAAA
6745 TAAAAAAAAAAATAA
1 TAAAAAAAAAAATAA
6760 CCAAAATTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.13
Consensus pattern (16 bp):
TAAAAAAAAAAATAAA
Found at i:17250 original size:107 final size:105
Alignment explanation
Indices: 17022--17283 Score: 420
Period size: 107 Copynumber: 2.5 Consensus size: 105
17012 AATTTTTTTA
* **
17022 ACCCTTAAAATAAAATTTTAATTTTAATTT-GGGCTAAACTTAGTG-AATTAGTTATATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
17085 TTTCTAAAACCCTATAACAATATTATTAATTATGAAATTT
66 TTTCTAAAACCCTATAACAATATTATTAATTATGAAATTT
* * *
17125 ATCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
* *
17190 TTTCTAAAACTCTATAACAATAAATTATTAATTTTGAAATTT
66 TTTCTAAAACCCTATAACAAT--ATTATTAATTATGAAATTT
17232 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
17284 AGGCTAAACT
Statistics
Matches: 146, Mismatches: 9, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
103 26 0.18
104 15 0.10
105 36 0.25
107 69 0.47
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (105 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
TTTCTAAAACCCTATAACAATATTATTAATTATGAAATTT
Found at i:17535 original size:29 final size:29
Alignment explanation
Indices: 17493--17551 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
17483 TGCCATGATT
17493 GACTAAGTTGTATTTACACCCCTAATTTA
1 GACTAAGTTGTATTTACACCCCTAATTTA
17522 GACTAAGTTGTATTTACACCCCTAATTTA
1 GACTAAGTTGTATTTACACCCCTAATTTA
17551 G
1 G
17552 TAAATCCAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (29 bp):
GACTAAGTTGTATTTACACCCCTAATTTA
Found at i:18939 original size:3 final size:3
Alignment explanation
Indices: 18931--19070 Score: 264
Period size: 3 Copynumber: 47.0 Consensus size: 3
18921 AAGAGGAAAA
18931 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
18979 TAT TAT TGT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
19026 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
19071 ATGTGTTTAA
Statistics
Matches: 134, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
2 2 0.01
3 132 0.99
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:20167 original size:88 final size:88
Alignment explanation
Indices: 19999--20170 Score: 222
Period size: 88 Copynumber: 2.0 Consensus size: 88
19989 TCTCTGACTC
* * ** *
19999 TCAAAGACACTTGAGGATTAACTTATAAGGTTTTAGCCTTGTGAAAATGAGAATTATAAGGTTTT
1 TCAAAGACAATTGAGGATTAACTTATAAGGTATTAGCCTTGTGAAAATGAGAATTATAACCTTGT
20064 AGACTAAACCCTAATTAGTCTTG
66 AGACTAAACCCTAATTAGTCTTG
* * **
20087 TCAAAGACAATTGATGATTAACTTATAAGGTATTAGTCTTGTGAAAATGAGAA-TATTTCCTTGT
1 TCAAAGACAATTGAGGATTAACTTATAAGGTATTAGCCTTGTGAAAATGAGAATTATAACCTTGT
*
20151 AGA-TTAACCCGTTAATTAGT
66 AGACTAAACCC--TAATTAGT
20171 GTCTTAATGT
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
86 6 0.08
87 9 0.12
88 57 0.79
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (88 bp):
TCAAAGACAATTGAGGATTAACTTATAAGGTATTAGCCTTGTGAAAATGAGAATTATAACCTTGT
AGACTAAACCCTAATTAGTCTTG
Done.