Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015151.1 Corchorus olitorius cultivar O-4 contig15184, 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: 18492
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:62 original size:12 final size:12
Alignment explanation
Indices: 45--69 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35 TTACAAAATC
45 CGACATGATTTT
1 CGACATGATTTT
57 CGACATGATTTT
1 CGACATGATTTT
69 C
1 C
70 TTCAAGATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (12 bp):
CGACATGATTTT
Found at i:191 original size:22 final size:20
Alignment explanation
Indices: 162--204 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
152 CAAAGGGCAA
*
162 AAGTGTAAAAATGGGGGCGGT
1 AAGTGT-AAAAGGGGGGCGGT
183 AAGTAGTAAAAGGGGGGCGGT
1 AAGT-GTAAAAGGGGGGCGGT
204 A
1 A
205 TTTAGCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.35, C:0.05, G:0.44, T:0.16
Consensus pattern (20 bp):
AAGTGTAAAAGGGGGGCGGT
Found at i:662 original size:53 final size:52
Alignment explanation
Indices: 552--689 Score: 233
Period size: 53 Copynumber: 2.6 Consensus size: 52
542 CATCGTTAGG
*
552 ATGTGCAAATACATCGGTTTTCCTATTTAC-AAACTCAATCTTTCGCTAGAGA
1 ATGTGCAAATACATTGG-TTTCCTATTTACAAAACTCAATCTTTCGCTAGAGA
604 ATGTGCAAATACATTGGTTTCCCTATTTACAAAACTCAATCTTTCGCTAGAGA
1 ATGTGCAAATACATTGGTTT-CCTATTTACAAAACTCAATCTTTCGCTAGAGA
657 ATGTGCAAATACATTGGATTTCCTATTTACAAA
1 ATGTGCAAATACATTGG-TTTCCTATTTACAAA
690 TTGAAATATA
Statistics
Matches: 82, Mismatches: 1, Indels: 5
0.93 0.01 0.06
Matches are distributed among these distances:
51 3 0.04
52 25 0.30
53 51 0.62
54 3 0.04
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.35
Consensus pattern (52 bp):
ATGTGCAAATACATTGGTTTCCTATTTACAAAACTCAATCTTTCGCTAGAGA
Found at i:805 original size:16 final size:16
Alignment explanation
Indices: 779--822 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
769 ACAAACCAAA
* *
779 TACACAAATAAATGAAT
1 TACA-AAATAAATAAAC
796 TACAAAATAAATAAAC
1 TACAAAATAAATAAAC
*
812 TACAAACTAAA
1 TACAAAATAAA
823 CTCACATTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 20 0.83
17 4 0.17
ACGTcount: A:0.64, C:0.14, G:0.02, T:0.20
Consensus pattern (16 bp):
TACAAAATAAATAAAC
Found at i:1285 original size:66 final size:64
Alignment explanation
Indices: 1181--1310 Score: 233
Period size: 66 Copynumber: 2.0 Consensus size: 64
1171 AATGAACAAA
1181 TATGGTAATATCAATATTTCTATCTAGGTATCAACTAATGATACAATAGATTAATCATTTTTGT
1 TATGGTAATATCAATATTTCTATCTAGGTATCAACTAATGATACAATAGATTAATCATTTTTGT
*
1245 TATGGTAATATATCAATATTTCTATCTAGGTTTCAACTAATGATACAATAGATTAATCATTTTTG
1 TATGGT-A-ATATCAATATTTCTATCTAGGTATCAACTAATGATACAATAGATTAATCATTTTTG
1310 T
64 T
1311 CAACTTTTAT
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
64 6 0.10
65 1 0.02
66 56 0.89
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (64 bp):
TATGGTAATATCAATATTTCTATCTAGGTATCAACTAATGATACAATAGATTAATCATTTTTGT
Found at i:3192 original size:19 final size:18
Alignment explanation
Indices: 3155--3194 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
3145 TGCTCTTGGG
*
3155 ATGGCGTCAAGTGTGATA
1 ATGGCGTCAAGTGTCATA
*
3173 ATGGCGTCAAAGTTTCATA
1 ATGGCGTC-AAGTGTCATA
3192 ATG
1 ATG
3195 ATTGTTACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.30
Consensus pattern (18 bp):
ATGGCGTCAAGTGTCATA
Found at i:3570 original size:30 final size:30
Alignment explanation
Indices: 3492--3784 Score: 372
Period size: 30 Copynumber: 9.6 Consensus size: 30
3482 GAAATTTATT
* * *
3492 ATGACAACTTCTGATGTTAATTGTAAGAAC
1 ATGACAACTTCTGGTGTCAATTGTAAGATC
*
3522 ATTGACAACTTCTGGTGTCAATTATAAGATC
1 A-TGACAACTTCTGGTGTCAATTGTAAGATC
* * *
3553 ATGACAATTTTTTGTGTCAATTGTAAGATC
1 ATGACAACTTCTGGTGTCAATTGTAAGATC
* *
3583 ATGACAACTTCTGGTGTCATTTGTAAAATC
1 ATGACAACTTCTGGTGTCAATTGTAAGATC
*
3613 ATGACAACTTCTGGTGTCAATTGTATGATC
1 ATGACAACTTCTGGTGTCAATTGTAAGATC
3643 ATGACAACTT-TCGGTGTCAATTGTAAGATC
1 ATGACAACTTCT-GGTGTCAATTGTAAGATC
* *
3673 ATTACAACTTCCGGTGTCAATTGTAAGATC
1 ATGACAACTTCTGGTGTCAATTGTAAGATC
*
3703 ATTACAACTTCTGGTGTCAATTGTAAGATC
1 ATGACAACTTCTGGTGTCAATTGTAAGATC
* * * *
3733 TTGACAACTTCCGGTGTCAATTGGAGATTTATC
1 ATGACAACTTCTGGTGTCAATTGTA-A--GATC
*
3766 ATGACAACTTTTGGTGTCA
1 ATGACAACTTCTGGTGTCA
3785 TTTGGAGAGT
Statistics
Matches: 229, Mismatches: 28, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
29 1 0.00
30 182 0.79
31 27 0.12
33 19 0.08
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (30 bp):
ATGACAACTTCTGGTGTCAATTGTAAGATC
Found at i:4312 original size:30 final size:30
Alignment explanation
Indices: 4234--4496 Score: 314
Period size: 30 Copynumber: 8.6 Consensus size: 30
4224 GAAATTTATT
* *
4234 ATGACAACTTCTGATGTTAATTGTAAGAAT-
1 ATGACAACTTCTGGTGTCAATTGTAAG-ATC
*
4264 ATTGACAACTTCTGGTGTCAATTATAAGATC
1 A-TGACAACTTCTGGTGTCAATTGTAAGATC
* * *
4295 ATGACAATTTTTTGTGTCAATTGTAAGATC
1 ATGACAACTTCTGGTGTCAATTGTAAGATC
* * *
4325 ATGATAATTTCTGGTGTCATTTGTAAGATC
1 ATGACAACTTCTGGTGTCAATTGTAAGATC
4355 ATGACAACTTCTGGTGTCAATTGTAAGATC
1 ATGACAACTTCTGGTGTCAATTGTAAGATC
4385 ATGACAACTT-TCGGTGTCAATTGTAAGATC
1 ATGACAACTTCT-GGTGTCAATTGTAAGATC
* *
4415 ATTACAACTTCCGGTGTCAATTGTAAGATC
1 ATGACAACTTCTGGTGTCAATTGTAAGATC
* * * *
4445 ATGACAATTTCCGGTGTCAATTGGAGATTTATC
1 ATGACAACTTCTGGTGTCAATTGTA-A--GATC
*
4478 ATGACAACTTTTGGTGTCA
1 ATGACAACTTCTGGTGTCA
4497 TTTGGAGAGT
Statistics
Matches: 203, Mismatches: 23, Indels: 11
0.86 0.10 0.05
Matches are distributed among these distances:
29 1 0.00
30 158 0.78
31 25 0.12
33 19 0.09
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (30 bp):
ATGACAACTTCTGGTGTCAATTGTAAGATC
Found at i:6937 original size:30 final size:30
Alignment explanation
Indices: 6859--7121 Score: 330
Period size: 30 Copynumber: 8.6 Consensus size: 30
6849 GAGATTTATT
* * *
6859 ATGACAACTTCTGATGTTAATTGTAAGAAC
1 ATGACAACTTCTGGTGTCAATTGTAAGATC
*
6889 ATTGACAACTTCTGGTGTCAATTATAAGATC
1 A-TGACAACTTCTGGTGTCAATTGTAAGATC
* * * * *
6920 ATGATAATTTTTTGTGTCAATTTTAAGATC
1 ATGACAACTTCTGGTGTCAATTGTAAGATC
*
6950 ATGACAACTTCTGGTGTCATTTGTAAGATC
1 ATGACAACTTCTGGTGTCAATTGTAAGATC
6980 ATGACAACTTCTGGTGTCAATTGTAAGATC
1 ATGACAACTTCTGGTGTCAATTGTAAGATC
7010 ATGACAACTT-TCGGTGTCAATTGTAAGATC
1 ATGACAACTTCT-GGTGTCAATTGTAAGATC
* *
7040 ATTACAACTTCCGGTGTCAATTGTAAGATC
1 ATGACAACTTCTGGTGTCAATTGTAAGATC
* * *
7070 ATGACAACTTCCGGTGTCAATTGGAGATTTATC
1 ATGACAACTTCTGGTGTCAATTGTA-A--GATC
*
7103 ATGACAACTTTTGGTGTCA
1 ATGACAACTTCTGGTGTCA
7122 TTTGGAGAGT
Statistics
Matches: 204, Mismatches: 23, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
29 1 0.00
30 156 0.76
31 27 0.13
33 20 0.10
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (30 bp):
ATGACAACTTCTGGTGTCAATTGTAAGATC
Found at i:16835 original size:6 final size:7
Alignment explanation
Indices: 16818--16849 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
16808 AAACATAGAT
16818 AAAAATC
1 AAAAATC
16825 AAAAATC
1 AAAAATC
16832 AAAAATC
1 AAAAATC
*
16839 AAAAACC
1 AAAAATC
16846 AAAA
1 AAAA
16850 TAGGAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.75, C:0.16, G:0.00, T:0.09
Consensus pattern (7 bp):
AAAAATC
Done.