Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019867.1 Corchorus olitorius cultivar O-4 contig19900, 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: 17894
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:8328 original size:53 final size:53
Alignment explanation
Indices: 8157--8471 Score: 454
Period size: 53 Copynumber: 5.9 Consensus size: 53
8147 AGGGTAACTA
*
8157 AGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAAAGTAATCAGTAG-T
1 AGTTTAATTCAGAGTAATTAAGCTAAAAAGT-AAAGAAAGAGTAATCAGTAGAT
8210 CAGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAGAT
1 -AGTTTAATTCAGAGTAATTAAGCTAAAAAGT-AAAGAAAGAGTAATCAGTAGAT
* * *
8265 ATTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAGGAAGAGTAATCATTAGAT
1 AGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAGAAAGAGTAATCAGTAGAT
* * *
8318 AGTTTAATTCAGAATAATTAAGCCAAAAAGTAATGGAAA-AGTAATCAGTAGAT
1 AGTTTAATTCAGAGTAATTAAGCTAAAAAGTAA-AGAAAGAGTAATCAGTAGAT
* * *
8371 AGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAGGAAGAGTAATCGGTGGAT
1 AGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAGAAAGAGTAATCAGTAGAT
* *
8424 AGTTTAATTCTGAGTAATTAAGCTAAAAAAGTAGAGAAAAGAGTAATC
1 AGTTTAATTCAGAGTAATTAAGCT-AAAAAGTAAAG-AAAGAGTAATC
8472 TGTAATTAAA
Statistics
Matches: 237, Mismatches: 19, Indels: 9
0.89 0.07 0.03
Matches are distributed among these distances:
52 3 0.01
53 129 0.54
54 94 0.40
55 11 0.05
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.27
Consensus pattern (53 bp):
AGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAGAAAGAGTAATCAGTAGAT
Found at i:9718 original size:42 final size:42
Alignment explanation
Indices: 9658--9740 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
9648 GTAAAAGAAA
9658 GAGTAATCAGTAGATAGTTTAATTC-AGAGTAATTAAGCTAAT
1 GAGTAATCAGTAGATAGTTTAATTCTA-AGTAATTAAGCTAAT
*
9700 GAGTAATTAGTA-ATTAGTTTAATTCTAAGTAATTAAGCTAA
1 GAGTAATCAGTAGA-TAGTTTAATTCTAAGTAATTAAGCTAA
9741 AAAAGTAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
41 1 0.03
42 36 0.95
43 1 0.03
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.36
Consensus pattern (42 bp):
GAGTAATCAGTAGATAGTTTAATTCTAAGTAATTAAGCTAAT
Found at i:9776 original size:97 final size:101
Alignment explanation
Indices: 9647--10009 Score: 377
Period size: 107 Copynumber: 3.5 Consensus size: 101
9637 ATCAATAATT
*
9647 AGTAAAAGAAAGAGTAATCAGTAGATAGTTTAATTCAGAGTAATTAAGCTAA-T-G-A-GTAATT
1 AGTAAAAGAAAGAGTAATCAGTAGATAGTTTAATTCAGAGTAATTAAGCTAAGTAGAAGGTAATC
*
9708 AGTA-ATTAGTTTAATTCTAAGTAATTAAGCTAAAAA
66 AGTAGA-TAGTTTAATTCAAAGTAATTAAGCTAAAAA
*
9744 AGTAAAAGAAAGAGTAATCAGTA-ATAAATTTAATTCAGAGTAATTAAGCTAAAAAGTAAAGAAA
1 AGTAAAAGAAAGAGTAATCAGTAGAT-AGTTTAATTCAGAGTAATTAAGCT---AAGT--AG-AA
9808 TGGTAATCAGTAGATAGTTTAATTCAAAGTAATTAAGCTAAAAA
59 -GGTAATCAGTAGATAGTTTAATTCAAAGTAATTAAGCTAAAAA
9852 AGT-AAAGAAATG-GTAATCAGTAGATAGTTTAATTCAGAGTAATTAAGCTAAAAAAGTAAAGAA
1 AGTAAAAGAAA-GAGTAATCAGTAGATAGTTTAATTCAGAGTAATTAAGCT----AAGT--AG-A
* * *
9915 ATGGT-TTCAGTAGATAGTTTAATTCAGAGTAATTAAGCAAAAAA
58 A-GGTAATCAGTAGATAGTTTAATTCAAAGTAATTAAGCTAAAAA
* * * * * * *
9959 AGT-AAAGAAATATTAATCAATAAATGGTTTAATTCTGAGTAATTAAACTAA
1 AGTAAAAGAAAGAGTAATCAGTAGATAGTTTAATTCAGAGTAATTAAGCTAA
10010 AAAAAAGTAA
Statistics
Matches: 235, Mismatches: 14, Indels: 28
0.85 0.05 0.10
Matches are distributed among these distances:
96 2 0.01
97 46 0.20
100 2 0.01
101 1 0.00
103 2 0.01
104 1 0.00
106 1 0.00
107 117 0.50
108 62 0.26
109 1 0.00
ACGTcount: A:0.49, C:0.06, G:0.16, T:0.29
Consensus pattern (101 bp):
AGTAAAAGAAAGAGTAATCAGTAGATAGTTTAATTCAGAGTAATTAAGCTAAGTAGAAGGTAATC
AGTAGATAGTTTAATTCAAAGTAATTAAGCTAAAAA
Found at i:9853 original size:54 final size:54
Alignment explanation
Indices: 9697--10030 Score: 432
Period size: 54 Copynumber: 6.2 Consensus size: 54
9687 TAATTAAGCT
*
9697 AATGAGTAATTAGTA-ATTAGTTTAATTCTA-AGTAATTAAGCTAAAAAAGTAAAAGA
1 AATG-GTAATCAGTAGA-TAGTTTAATTC-AGAGTAATTAAGCTAAAAAAGT-AAAGA
*
9753 AA-GAGTAATCAGTA-ATAAATTTAATTCAGAGTAATTAAGCT-AAAAAGTAAAGA
1 AATG-GTAATCAGTAGAT-AGTTTAATTCAGAGTAATTAAGCTAAAAAAGTAAAGA
*
9806 AATGGTAATCAGTAGATAGTTTAATTCAAAGTAATTAAGCTAAAAAAGTAAAGA
1 AATGGTAATCAGTAGATAGTTTAATTCAGAGTAATTAAGCTAAAAAAGTAAAGA
9860 AATGGTAATCAGTAGATAGTTTAATTCAGAGTAATTAAGCTAAAAAAGTAAAGA
1 AATGGTAATCAGTAGATAGTTTAATTCAGAGTAATTAAGCTAAAAAAGTAAAGA
* *
9914 AATGGT-TTCAGTAGATAGTTTAATTCAGAGTAATTAAGCAAAAAAAGTAAAGA
1 AATGGTAATCAGTAGATAGTTTAATTCAGAGTAATTAAGCTAAAAAAGTAAAGA
** * * * * *
9967 AATATTAATCAATAAATGGTTTAATTCTGAGTAATTAAACTAAAAAAAAGT-AA-A
1 AATGGTAATCAGTAGATAGTTTAATTCAGAGTAATTAAGCT--AAAAAAGTAAAGA
10021 AATGGTAATC
1 AATGGTAATC
10031 CGTGATTGAC
Statistics
Matches: 252, Mismatches: 18, Indels: 18
0.88 0.06 0.06
Matches are distributed among these distances:
53 88 0.35
54 119 0.47
55 35 0.14
56 10 0.04
ACGTcount: A:0.50, C:0.05, G:0.16, T:0.29
Consensus pattern (54 bp):
AATGGTAATCAGTAGATAGTTTAATTCAGAGTAATTAAGCTAAAAAAGTAAAGA
Found at i:10013 original size:107 final size:107
Alignment explanation
Indices: 9697--10030 Score: 437
Period size: 107 Copynumber: 3.1 Consensus size: 107
9687 TAATTAAGCT
* *
9697 AATGAGTAATTAGTA-ATTAGTTTAATTCTAAGTAATTAAGCTAAAAAAGTAAAAGAAAGAGTAA
1 AATG-GTAATCAGTAGA-TAGTTTAATTC-AAGTAATTAAGCTAAAAAAGT-AAAGAAATAGTAA
*
9761 TCAGT-AATAAATTTAATTCAGAGTAATTAAGCT-AAAAAGTAAAGA
62 TCAGTAAAT-AGTTTAATTCAGAGTAATTAAGCTAAAAAAGTAAAGA
*
9806 AATGGTAATCAGTAGATAGTTTAATTCAAAGTAATTAAGCTAAAAAAGTAAAGAAATGGTAATCA
1 AATGGTAATCAGTAGATAGTTTAATTC-AAGTAATTAAGCTAAAAAAGTAAAGAAATAGTAATCA
*
9871 GTAGATAGTTTAATTCAGAGTAATTAAGCTAAAAAAGTAAAGA
65 GTAAATAGTTTAATTCAGAGTAATTAAGCTAAAAAAGTAAAGA
* * *
9914 AATGGT-TTCAGTAGATAGTTTAATTCAGAGTAATTAAGCAAAAAAAGTAAAGAAATATTAATCA
1 AATGGTAATCAGTAGATAGTTTAATTCA-AGTAATTAAGCTAAAAAAGTAAAGAAATAGTAATCA
* * * *
9978 ATAAATGGTTTAATTCTGAGTAATTAAACTAAAAAAAAGT-AA-A
65 GTAAATAGTTTAATTCAGAGTAATTAAGCT--AAAAAAGTAAAGA
10021 AATGGTAATC
1 AATGGTAATC
10031 CGTGATTGAC
Statistics
Matches: 202, Mismatches: 16, Indels: 15
0.87 0.07 0.06
Matches are distributed among these distances:
106 1 0.00
107 123 0.61
108 65 0.32
109 13 0.06
ACGTcount: A:0.50, C:0.05, G:0.16, T:0.29
Consensus pattern (107 bp):
AATGGTAATCAGTAGATAGTTTAATTCAAGTAATTAAGCTAAAAAAGTAAAGAAATAGTAATCAG
TAAATAGTTTAATTCAGAGTAATTAAGCTAAAAAAGTAAAGA
Found at i:12672 original size:31 final size:29
Alignment explanation
Indices: 12620--12704 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 29
12610 ATAATGGCTG
**
12620 AATCTCAAATAAGTCCCCGAACTTT-GCCATA
1 AATCTCAAATAAGGGCCCGAACTTTAG--A-A
*
12651 AATCTCAAATAAGGGCTCGAACTTTAGAA
1 AATCTCAAATAAGGGCCCGAACTTTAGAA
**
12680 AAGATCAAATAAGGGCCCGAACTTT
1 AATCTCAAATAAGGGCCCGAACTTT
12705 TTTGGAAAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
29 23 0.49
30 1 0.02
31 22 0.47
32 1 0.02
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.24
Consensus pattern (29 bp):
AATCTCAAATAAGGGCCCGAACTTTAGAA
Found at i:12720 original size:32 final size:29
Alignment explanation
Indices: 12623--12722 Score: 85
Period size: 29 Copynumber: 3.3 Consensus size: 29
12613 ATGGCTGAAT
** *
12623 CTCAAATAAGTCCCCGAACTTT-GCCATAAAT
1 CTCAAATAAGGGCCCGAACTTTAG--A-AAAG
*
12654 CTCAAATAAGGGCTCGAACTTTAGAAAAG
1 CTCAAATAAGGGCCCGAACTTTAGAAAAG
* *
12683 ATCAAATAAGGGCCCGAACTTTTTTGGAAAAG
1 CTCAAATAAGGGCCCGAAC---TTTAGAAAAG
12715 CTCAAATA
1 CTCAAATA
12723 GGTCCATTCC
Statistics
Matches: 57, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
29 20 0.35
30 1 0.02
31 19 0.33
32 17 0.30
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (29 bp):
CTCAAATAAGGGCCCGAACTTTAGAAAAG
Found at i:14447 original size:31 final size:30
Alignment explanation
Indices: 14412--14479 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
14402 AGATTGGACC
* **
14412 TATTTGAGCTTTTTCGAAAAGTTGGGGCCCT
1 TATTTGAGCCTTTTC-AAAAGTTCAGGCCCT
*
14443 TATTTGA-CCTTTTCTAAAGTTCAGGCCCT
1 TATTTGAGCCTTTTCAAAAGTTCAGGCCCT
14472 TATTTGAG
1 TATTTGAG
14480 ATTTATGGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 19 0.59
30 6 0.19
31 7 0.22
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.41
Consensus pattern (30 bp):
TATTTGAGCCTTTTCAAAAGTTCAGGCCCT
Done.