Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011179.1 Corchorus olitorius cultivar O-4 contig11212, 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: 4788
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Found at i:998 original size:154 final size:154
Alignment explanation
Indices: 659--1367 Score: 1122
Period size: 154 Copynumber: 4.6 Consensus size: 154
649 CTGCTAAAGC
* *
659 TGTTCCAGATGAGCCAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
1 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
* * *
724 AAACAATGGAAACAAAGGCATTGAGGGTTG-CAAATCGAAGACAATTCAAAACGTCACTAATGGG
66 AAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGG
* **
788 CCCCGATAGGCTCAACCTAACAAG
131 CCCCGATAGGCCCAAAATAACAAG
* *
812 TGTTCCAAAAT-AGCTAAAAATTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCTA
1 TGTTCC-AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
876 TAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGG
65 TAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGG
* *
941 GCCCTGATGGGCCCAAAATAACAAG
130 GCCCCGATAGGCCCAAAATAACAAG
* * *
966 TGTTCCAAATTAGCTAAAAACTTCACATTGGACTAATCTCACCAAAATGATTATAGTTAAGCCAT
1 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
* * *
1031 AGACAATGGAAATAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACAG-AACTAATGG
66 AAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAAC-GTCACTAATGG
1095 GCCCCGATAGGCCCAAAATAACAAG
130 GCCCCGATAGGCCCAAAATAACAAG
* *
1120 TGTTCGAAATGAGCTAAAAACTTTACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
1 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
*
1185 AAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGATGATTCAAAACGTCACTAATGGG
66 AAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGG
* *
1250 CCCCGATAGG--CTAAATAAAAAG
131 CCCCGATAGGCCCAAAATAACAAG
* *
1272 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGCTGGGCCAT
1 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
* *
1337 AAACAATGGAAAGAAAGGCATTGAGGATTGC
66 AAACAATGGAAAGAAAAGCATTGAGGGTTGC
1368 TAAAAATAAC
Statistics
Matches: 513, Mismatches: 38, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
152 100 0.19
153 90 0.18
154 322 0.63
155 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (154 bp):
TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
AAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGG
CCCCGATAGGCCCAAAATAACAAG
Found at i:1471 original size:109 final size:109
Alignment explanation
Indices: 1262--1461 Score: 355
Period size: 109 Copynumber: 1.8 Consensus size: 109
1252 CCGATAGGCT
*
1262 AAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
1 AAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAATAATCTCACCAAAATGATTATA
*
1327 GCTGGGCCATAAACAATGGAAAGAAAGGCATTGAGGATTGCTAA
66 GCTAGGCCATAAACAATGGAAAGAAAGGCATTGAGGATTGCTAA
* *
1371 AAATAACAAGTGTTCCAAATGAGCTAAAAATTTCACAGTGGAATAATCTCACCAAAATGATTATA
1 AAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAATAATCTCACCAAAATGATTATA
*
1436 GTTAGGCCATAAACAATGGAAAGAAA
66 GCTAGGCCATAAACAATGGAAAGAAA
1462 AGTCTTGAGG
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
109 86 1.00
ACGTcount: A:0.45, C:0.15, G:0.17, T:0.23
Consensus pattern (109 bp):
AAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAATAATCTCACCAAAATGATTATA
GCTAGGCCATAAACAATGGAAAGAAAGGCATTGAGGATTGCTAA
Found at i:2601 original size:25 final size:24
Alignment explanation
Indices: 2565--2611 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
2555 TCCTTCTATT
2565 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
2588 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
2612 AATTTTCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (24 bp):
CATCTATCATCAAAGTTTTTCATC
Found at i:3528 original size:15 final size:15
Alignment explanation
Indices: 3508--3539 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3498 CCTTGGGGGT
3508 TCAAAATCAACAAGC
1 TCAAAATCAACAAGC
*
3523 TCAAAATCGACAAGC
1 TCAAAATCAACAAGC
3538 TC
1 TC
3540 CACTTAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.28, G:0.09, T:0.16
Consensus pattern (15 bp):
TCAAAATCAACAAGC
Found at i:4231 original size:66 final size:66
Alignment explanation
Indices: 4124--4250 Score: 175
Period size: 66 Copynumber: 1.9 Consensus size: 66
4114 AGTAATTCTG
* *
4124 AACCTGATTTGAGTGTTGTTTGCAATGACATGAAATCTGTTTTAGATGTTGTTAGTGATGATACT
1 AACCTAATTTAAGTGTTGTTTGCAATGACATGAAATCTGTTTTAGATGTTGTTAGTGATGATACT
4189 A
66 A
** * * *
4190 AACCTAATTTAAGTGTTGTTTGTGATGACACT-AAATTTGTTTTAGGTGTTGTTTGTGATGA
1 AACCTAATTTAAGTGTTGTTTGCAATGACA-TGAAATCTGTTTTAGATGTTGTTAGTGATGA
4251 AACAAATTCT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
66 52 0.98
67 1 0.02
ACGTcount: A:0.26, C:0.08, G:0.23, T:0.43
Consensus pattern (66 bp):
AACCTAATTTAAGTGTTGTTTGCAATGACATGAAATCTGTTTTAGATGTTGTTAGTGATGATACT
A
Found at i:4239 original size:33 final size:33
Alignment explanation
Indices: 4136--4265 Score: 129
Period size: 33 Copynumber: 3.9 Consensus size: 33
4126 CCTGATTTGA
**
4136 GTGTTGTTTGCAATGACA-TGAAATCTGTTTTAG
1 GTGTTGTTTGTGATGACACT-AAATCTGTTTTAG
* * * * ** *
4169 ATGTTGTTAGTGATGATACTAAACCTAATTTAA
1 GTGTTGTTTGTGATGACACTAAATCTGTTTTAG
*
4202 GTGTTGTTTGTGATGACACTAAATTTGTTTTAG
1 GTGTTGTTTGTGATGACACTAAATCTGTTTTAG
*
4235 GTGTTGTTTGTGATGAAAC-AAATTCTGTTTT
1 GTGTTGTTTGTGATGACACTAAA-TCTGTTTT
4266 GGATGCTAAT
Statistics
Matches: 76, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
32 3 0.04
33 72 0.95
34 1 0.01
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.45
Consensus pattern (33 bp):
GTGTTGTTTGTGATGACACTAAATCTGTTTTAG
Done.