Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023202.1 Corchorus olitorius cultivar O-4 contig23235, 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: 39217
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Found at i:5557 original size:2 final size:2
Alignment explanation
Indices: 5507--5537 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5497 CAACAAAATA
5507 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5538 CCAAAGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17978 original size:28 final size:27
Alignment explanation
Indices: 17893--17990 Score: 90
Period size: 28 Copynumber: 3.5 Consensus size: 27
17883 GGTGTCCCTG
*
17893 AAATGACCAAAATGCCCCTAGCCTAGCA
1 AAATGACCAAAATGCCCCTGGCC-AGCA
* * **
17921 AAATGTCCAAAATGCCACTGGATTTA-CA
1 AAATGACCAAAATGCCCCTGG--CCAGCA
*
17949 AAATGACCAAAATGCCCCCGGCCACGCAA
1 AAATGACCAAAATGCCCCTGGCCA-GC-A
17978 AAATGACCAAAAT
1 AAATGACCAAAAT
17991 AAAAGTAAAT
Statistics
Matches: 55, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
26 1 0.02
28 39 0.71
29 15 0.27
ACGTcount: A:0.42, C:0.29, G:0.14, T:0.15
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGGCCAGCA
Found at i:22064 original size:157 final size:159
Alignment explanation
Indices: 21781--22193 Score: 641
Period size: 157 Copynumber: 2.6 Consensus size: 159
21771 TTTTTTCATC
*
21781 TTTTACCACTTGACAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAG
1 TTTTCCCACTTGACAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAG
* * *
21846 ACGTTTTGGTCATTTCTCAATTGACTTTAATAGAGTACTGGAATTACTAAAAGATCCCTACCCCG
66 ACATTTTGGTCATTTCTCAATTGACTTTAATAGAGTACTAGAATTACTAAAAGATCCCTACCCCA
21911 GATTAATGATGAGTTGGAGAACTAATC-T
131 GATTAATGATGAGTTGGAGAACTAATCTT
*
21939 TTTTCCCACTTGACAGATTACTTAAATGTCCTAACTTTTGATTCTTGA-GGGATTAAATGACTAG
1 TTTTCCCACTTGACAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAG
* *
22003 ACATTTTGGTCATTTCTCAATTGACTTTAATAGAGTAGTAGAATTACTAAAAGATCCCTACCGCA
66 ACATTTTGGTCATTTCTCAATTGACTTTAATAGAGTACTAGAATTACTAAAAGATCCCTACCCCA
22068 GATTAATGATGAGTTGGAGAACTAATCTT
131 GATTAATGATGAGTTGGAGAACTAATCTT
* * *
22097 TTTCGTCTTTACCTACTTGGCAGATTACTTAAATGCCCTAACTTTTTATTCTTGAGGGGATTAAA
1 TTT--TC----CC-ACTTGACAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAA
* *
22162 TAACTAAACTTTTTGGTCATTTCTCAATTGAC
59 TAACTAGACATTTTGGTCATTTCTCAATTGAC
22194 CAATGACTCA
Statistics
Matches: 233, Mismatches: 13, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
157 102 0.44
158 51 0.22
160 2 0.01
164 2 0.01
165 38 0.16
166 38 0.16
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (159 bp):
TTTTCCCACTTGACAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAG
ACATTTTGGTCATTTCTCAATTGACTTTAATAGAGTACTAGAATTACTAAAAGATCCCTACCCCA
GATTAATGATGAGTTGGAGAACTAATCTT
Found at i:24327 original size:20 final size:21
Alignment explanation
Indices: 24283--24330 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
24273 TAGAATTAGA
* *
24283 TTTAATTTACTTTGCTTTGTT
1 TTTAATTTACATTGCTTTCTT
*
24304 TTTAATTTA-ATTGTTTTCTT
1 TTTAATTTACATTGCTTTCTT
24324 TTTAATT
1 TTTAATT
24331 AATCTTTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (21 bp):
TTTAATTTACATTGCTTTCTT
Found at i:24594 original size:35 final size:35
Alignment explanation
Indices: 24555--24654 Score: 96
Period size: 39 Copynumber: 2.8 Consensus size: 35
24545 AATATTTTTC
24555 TTGTTTCTGCGTTTTTGTAAAAAAAAAAAAAGATT
1 TTGTTTCTGCGTTTTTGTAAAAAAAAAAAAAGATT
* * * * *
24590 TTGTTTCTACGTTTTTTTTTAAATTTAAAAGAAAATATT
1 TTGTTTCTGCG--TTTTTGTAAA--AAAAAAAAAAGATT
*
24629 TTGTTTTTGCG-TTTTG-AAAAAAAAAA
1 TTGTTTCTGCGTTTTTGTAAAAAAAAAA
24655 GATTTTCTTA
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
33 5 0.10
35 13 0.25
36 4 0.08
37 9 0.18
39 20 0.39
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.46
Consensus pattern (35 bp):
TTGTTTCTGCGTTTTTGTAAAAAAAAAAAAAGATT
Found at i:27782 original size:21 final size:21
Alignment explanation
Indices: 27752--27793 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
27742 TGCAAGCCAT
27752 GCCATCACCGAGCCACCACCA
1 GCCATCACCGAGCCACCACCA
* * *
27773 GCCATGACCGTGCCATCACCA
1 GCCATCACCGAGCCACCACCA
27794 TTGCAAGCCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.48, G:0.17, T:0.10
Consensus pattern (21 bp):
GCCATCACCGAGCCACCACCA
Found at i:28709 original size:18 final size:16
Alignment explanation
Indices: 28678--28712 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
28668 AAAGGGTAGT
28678 TAAAAAAAATTTTTCA
1 TAAAAAAAATTTTTCA
28694 TAAAAAAAAGTGTTTTCA
1 TAAAAAAAA-T-TTTTCA
28712 T
1 T
28713 GCAAGAGGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 1 0.06
18 7 0.41
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (16 bp):
TAAAAAAAATTTTTCA
Found at i:34843 original size:11 final size:11
Alignment explanation
Indices: 34827--34854 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
34817 ATGTCTCTTG
34827 GTCTTGACTTT
1 GTCTTGACTTT
34838 GTCTTGACTTT
1 GTCTTGACTTT
34849 GTCTTG
1 GTCTTG
34855 TGAGGATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.18, G:0.21, T:0.54
Consensus pattern (11 bp):
GTCTTGACTTT
Found at i:37617 original size:19 final size:18
Alignment explanation
Indices: 37593--37628 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
37583 TGAAGACTTA
37593 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
37612 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
37629 ATTATTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:38939 original size:22 final size:22
Alignment explanation
Indices: 38897--38939 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
38887 TTTCTAATTA
**
38897 ATTGTTTTCTTTAATTTTCTTG
1 ATTGTTTTCTTTAATAGTCTTG
38919 ATTGTTTTC-TTAGATAGTCTT
1 ATTGTTTTCTTTA-ATAGTCTT
38940 AATTACTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.16, C:0.09, G:0.12, T:0.63
Consensus pattern (22 bp):
ATTGTTTTCTTTAATAGTCTTG
Done.