Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022580.1 Corchorus olitorius cultivar O-4 contig22613, 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: 12611
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Found at i:641 original size:30 final size:31
Alignment explanation
Indices: 600--668 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
590 GTGTAAATGG
*
600 GTCCCTGAAGTGAACTT-AGTGAGCAATTGA
1 GTCCCTAAAGTGAACTTGAGTGAGCAATTGA
* * * *
630 GTCCCTAAAGTGGAGTTGATTGAGCAATTGG
1 GTCCCTAAAGTGAACTTGAGTGAGCAATTGA
661 GTCCCTAA
1 GTCCCTAA
669 CTCATTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
30 14 0.42
31 19 0.58
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (31 bp):
GTCCCTAAAGTGAACTTGAGTGAGCAATTGA
Found at i:3529 original size:20 final size:20
Alignment explanation
Indices: 3504--3547 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
3494 TGACTTCAAT
3504 AAATAGATG-ATAAATAATA
1 AAATAGATGAATAAATAATA
*
3523 GAAATAGATGAATAGATAATA
1 -AAATAGATGAATAAATAATA
3544 AAAT
1 AAAT
3548 TAAGGGAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.61, C:0.00, G:0.14, T:0.25
Consensus pattern (20 bp):
AAATAGATGAATAAATAATA
Found at i:4097 original size:93 final size:93
Alignment explanation
Indices: 3938--4400 Score: 811
Period size: 93 Copynumber: 5.0 Consensus size: 93
3928 TCATATTAAT
* *
3938 AGTAAAGACAAGGTGAGAACCATAGGTTGTCCCAATGAAAGGCTATGGTGGTTTTCTCAATCACC
1 AGTAAAGACAAGGTGAGAGCCATAGGTTGTCCCAATGAAGGGCTATGGTGGTTTTCTCAATCACC
*
4003 AATGCCTTGCCACAAGGTGGACTTTGGA
66 AATGCCTTGCCACAAGGTGGACTTTGTA
* *
4031 AGTAAAGACAAGGTTAGAGCCATAGGTTGTCCCAGTGAAGGGCTATGGTGGTTTTCTCAATCACC
1 AGTAAAGACAAGGTGAGAGCCATAGGTTGTCCCAATGAAGGGCTATGGTGGTTTTCTCAATCACC
4096 AATGCCTTGCCACAAGGTGGACTTTGTA
66 AATGCCTTGCCACAAGGTGGACTTTGTA
4124 AGTAAAGACAAGGTGAGAGCCATAGGTTGTCCCAATGAAGGGCTATGGTGGTTTTCTCAATCACC
1 AGTAAAGACAAGGTGAGAGCCATAGGTTGTCCCAATGAAGGGCTATGGTGGTTTTCTCAATCACC
4189 AATGCCTTGCCACAAGGTGGACTTTGTA
66 AATGCCTTGCCACAAGGTGGACTTTGTA
* * *
4217 AATGAAGACAAGGTGAGAGCCATAGGTTGTCGCAATGAAGGGCTATGGTGGTTTTCTCAATCACC
1 AGTAAAGACAAGGTGAGAGCCATAGGTTGTCCCAATGAAGGGCTATGGTGGTTTTCTCAATCACC
4282 AATGCCTTGCCACAAGGTGGACTTTGTA
66 AATGCCTTGCCACAAGGTGGACTTTGTA
* * * *
4310 AATGAAGACAAGGTGAGAGCCATAGGTTGTCCCAATGATGGGCTATGGT-ATTTTCTCAATCACC
1 AGTAAAGACAAGGTGAGAGCCATAGGTTGTCCCAATGAAGGGCTATGGTGGTTTTCTCAATCACC
4374 AATGCCTTGCCACAAGGTGGACTTTGT
66 AATGCCTTGCCACAAGGTGGACTTTGT
4401 GATGAACCAT
Statistics
Matches: 357, Mismatches: 13, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
92 41 0.11
93 316 0.89
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (93 bp):
AGTAAAGACAAGGTGAGAGCCATAGGTTGTCCCAATGAAGGGCTATGGTGGTTTTCTCAATCACC
AATGCCTTGCCACAAGGTGGACTTTGTA
Found at i:8791 original size:164 final size:162
Alignment explanation
Indices: 8517--8903 Score: 584
Period size: 164 Copynumber: 2.4 Consensus size: 162
8507 ATAGAAAGAT
* *
8517 GCCGCCATATTAATATATGGAGGGAGAGA-TTTTTTTCTCTTTTTTTGGAGGGAAAAATTCCCT-
1 GCCGCCATTTTAATATATGGAGGGAGAGATTTTTTTTCTTTTTTTTTGGAGGGAAAAATTCCCTC
* * * *
8580 CCTCTAAAACAAAGAAAGTTTCCAACTCTACGCCTATAATATATAGCGGCGTTTTGACATTAGAC
66 CCCCTAAAACAAACAAAGTTTCCAACTCTACGCCTATAATATATAGCGGCGTTTTCACATCAGAC
* *
8645 GTCGCTAAGTAGTGGTGTCTAGAAAAGGAAAC
131 GCCGCTAAGTAGTGGCGTCTAGAAAAGGAAAC
8677 GCCGCCATTTTAATATATGGAGGGAGAGATTTTTTTTTCTTTTTTTTTGGAGGGAAAAATTCCCT
1 GCCGCCATTTTAATATATGGAGGGAGAGA-TTTTTTTTCTTTTTTTTTGGAGGGAAAAATTCCCT
*
8742 CCCCCCTAAAACAAACAAAGTTTCCAACTCTACGCCTATAATATATAGCGGCGTTTTCTCATCAG
65 -CCCCCTAAAACAAACAAAGTTTCCAACTCTACGCCTATAATATATAGCGGCGTTTTCACATCAG
* *
8807 ACGCCGCTAATTAGTGGCGTCTAGGAAAGGAAAC
129 ACGCCGCTAAGTAGTGGCGTCTAGAAAAGGAAAC
* * * * *
8841 GTCGCAATTGTAATATATGGAGTGAGA-ATTTTTTTTC-TTTGTTTTGGAGGGAAAAATTCCCTC
1 GCCGCCATTTTAATATATGGAGGGAGAGATTTTTTTTCTTTTTTTTTGGAGGGAAAAATTCCCTC
8904 GCCTATAATA
Statistics
Matches: 207, Mismatches: 16, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
160 29 0.14
161 24 0.12
162 42 0.20
163 1 0.00
164 111 0.54
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (162 bp):
GCCGCCATTTTAATATATGGAGGGAGAGATTTTTTTTCTTTTTTTTTGGAGGGAAAAATTCCCTC
CCCCTAAAACAAACAAAGTTTCCAACTCTACGCCTATAATATATAGCGGCGTTTTCACATCAGAC
GCCGCTAAGTAGTGGCGTCTAGAAAAGGAAAC
Found at i:12085 original size:15 final size:15
Alignment explanation
Indices: 12055--12096 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
12045 TTACTTTGCT
12055 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
12071 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
12086 TTGCTTTCTGT
1 TTGTTTTCTGT
12097 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Done.