Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021818.1 Corchorus olitorius cultivar O-4 contig21851, 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: 10046
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Found at i:3336 original size:22 final size:22
Alignment explanation
Indices: 3287--3416 Score: 111
Period size: 22 Copynumber: 5.9 Consensus size: 22
3277 TGACAATCAA
* ** *
3287 ACCAAAATTACATAGAAAGATT
1 ACCAAAATTTCATAGTGAGGTT
* * *
3309 ATCAAAATTTCGTAGTGTGGTT
1 ACCAAAATTTCATAGTGAGGTT
3331 ACCAAAATTTCATA-TAGAGGTT
1 ACCAAAATTTCATAGT-GAGGTT
* *
3353 ATCAAAACTTCATAGTGTA-GTT
1 ACCAAAATTTCATAGTG-AGGTT
* **
3375 ATCAAAATTTCATACAGAGGTT
1 ACCAAAATTTCATAGTGAGGTT
*
3397 ACCAAAATTTCATAGGGAGG
1 ACCAAAATTTCATAGTGAGG
3417 GAGGTTACCA
Statistics
Matches: 86, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
21 2 0.02
22 82 0.95
23 2 0.02
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (22 bp):
ACCAAAATTTCATAGTGAGGTT
Found at i:3355 original size:44 final size:44
Alignment explanation
Indices: 3287--3411 Score: 160
Period size: 44 Copynumber: 2.8 Consensus size: 44
3277 TGACAATCAA
* * * * * *
3287 ACCAAAATTACATAGAAAGATTATCAAAATTTCGTAGTGTGGTT
1 ACCAAAATTTCATACAGAGGTTATCAAAATTTCATAGTGTAGTT
* *
3331 ACCAAAATTTCATATAGAGGTTATCAAAACTTCATAGTGTAGTT
1 ACCAAAATTTCATACAGAGGTTATCAAAATTTCATAGTGTAGTT
* *
3375 ATCAAAATTTCATACAGAGGTTACCAAAATTTCATAG
1 ACCAAAATTTCATACAGAGGTTATCAAAATTTCATAG
3412 GGAGGGAGGT
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 70 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32
Consensus pattern (44 bp):
ACCAAAATTTCATACAGAGGTTATCAAAATTTCATAGTGTAGTT
Found at i:3489 original size:22 final size:23
Alignment explanation
Indices: 3464--3513 Score: 77
Period size: 22 Copynumber: 2.2 Consensus size: 23
3454 AGAGATTAAC
3464 AAAATTTTATAGG-GAGGTTAT-G
1 AAAATTTTAT-GGAGAGGTTATCG
3486 AAAATTTTATGGAGAGGTTATCG
1 AAAATTTTATGGAGAGGTTATCG
3509 AAAAT
1 AAAAT
3514 ACATAGAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 2 0.08
22 18 0.69
23 6 0.23
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.34
Consensus pattern (23 bp):
AAAATTTTATGGAGAGGTTATCG
Found at i:3695 original size:22 final size:21
Alignment explanation
Indices: 3670--3745 Score: 71
Period size: 22 Copynumber: 3.5 Consensus size: 21
3660 GAGATTATCG
3670 AAATTTCATAGTGTGGTTACCC
1 AAATTTCATAGTGTGGTTA-CC
* **
3692 AAATTTCACAGTGTGGTTATT
1 AAATTTCATAGTGTGGTTACC
* * *
3713 AAATTTTCATAGGGAGGTTATCG
1 AAA-TTTCATAGTGTGGTTA-CC
3736 AAATTTCATA
1 AAATTTCATA
3746 TTAGGTTTAA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
21 3 0.07
22 38 0.86
23 3 0.07
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (21 bp):
AAATTTCATAGTGTGGTTACC
Found at i:4057 original size:49 final size:51
Alignment explanation
Indices: 3985--4088 Score: 169
Period size: 49 Copynumber: 2.1 Consensus size: 51
3975 GAGTGAGTAA
* *
3985 GCTAATTGGAAAGTGGGTTTGCC-AAAAAAAAAAAAA-CTTTCTTCAAAGC
1 GCTAAGTGGAAACTGGGTTTGCCAAAAAAAAAAAAAATCTTTCTTCAAAGC
4034 GCTAAGTGGAAACTGGGTTTGCCAAAAAAAAAAAAAATCTTTCTTCAAAGC
1 GCTAAGTGGAAACTGGGTTTGCCAAAAAAAAAAAAAATCTTTCTTCAAAGC
4085 -CTAA
1 GCTAA
4089 AACTTAAACT
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
49 21 0.41
50 17 0.33
51 13 0.25
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.24
Consensus pattern (51 bp):
GCTAAGTGGAAACTGGGTTTGCCAAAAAAAAAAAAAATCTTTCTTCAAAGC
Found at i:5542 original size:22 final size:22
Alignment explanation
Indices: 5501--6061 Score: 179
Period size: 22 Copynumber: 25.4 Consensus size: 22
5491 ACAATCAAAC
* *
5501 CAAAATTACATAGTAAGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* * *
5523 TAAAATTTCATAGTGTGGTTAC
1 CAAAATTTCATAGTGAGGTTAT
5545 CAAAATTTCATA-TGGAGGTTAT
1 CAAAATTTCATAGT-GAGGTTAT
* * *
5567 CAAAACTTCGTAGTGTA-ATTAT
1 CAAAATTTCATAGTG-AGGTTAT
** * *
5589 CAAAATTTCATACAGAGGTCAC
1 CAAAATTTCATAGTGAGGTTAT
***
5611 CAAAATTTCATAAAAAAAGGTTAT
1 CAAAATTTCAT--AGTGAGGTTAT
* * *
5635 CAAAATCTCTTA-TGGAGATTAT
1 CAAAATTTCATAGT-GAGGTTAT
***
5657 C-AAATTTCATACAAAGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
** * *
5678 TGAAATTTTATAGTGTA-ATTAT
1 CAAAATTTCATAGTG-AGGTTAT
* * *
5700 CAAAA-TTAATTAG-AAAGTTAT
1 CAAAATTTCA-TAGTGAGGTTAT
**
5721 CAAAA-TT--T-GT--TCTTAT
1 CAAAATTTCATAGTGAGGTTAT
* *
5737 CAAAATTTCCTAG-GATGGTTAA
1 CAAAATTTCATAGTGA-GGTTAT
* * *
5759 CAAAATTCCATAGGGAGCTTAT
1 CAAAATTTCATAGTGAGGTTAT
* * *
5781 AAAAATATT-ATGGAGAGGTTAT
1 CAAAAT-TTCATAGTGAGGTTAT
* **
5803 CAAAATTACATA-TAGAGAATAT
1 CAAAATTTCATAGT-GAGGTTAT
* * *
5825 CACAATTTCATTATTATAGGGAAGTTAT
1 CA-AA----ATT-TCATAGTGAGGTTAT
* * *
5853 CGAAATTTCATGGTGTGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* *
5875 CAAAATTTTCATAGTGCGATTA-
1 CAAAA-TTTCATAGTGAGGTTAT
* * * * *
5897 C-CAATTTTATAATGTGATTAT
1 CAAAATTTCATAGTGAGGTTAT
5918 CAAAATTTCATAGACAATGAGGTTAT
1 CAAAATTTCATAG----TGAGGTTAT
* * *
5944 CAAAACTTCATTGTGTGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* * * *
5966 CAGAATTCCACAGTGTGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* * *
5988 CAAAATTTCACATTGTGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* *
6010 CAAATTTTCATAGAGAGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* * *
6032 CGAAATTTCACAATGAGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
6054 C-AAATTTC
1 CAAAATTTC
6062 CGCAGTATGG
Statistics
Matches: 392, Mismatches: 109, Indels: 77
0.68 0.19 0.13
Matches are distributed among these distances:
16 9 0.02
17 3 0.01
18 1 0.00
19 1 0.00
20 15 0.04
21 41 0.10
22 250 0.64
23 24 0.06
24 16 0.04
26 18 0.05
27 5 0.01
28 9 0.02
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (22 bp):
CAAAATTTCATAGTGAGGTTAT
Found at i:6074 original size:44 final size:43
Alignment explanation
Indices: 5960--6084 Score: 128
Period size: 44 Copynumber: 2.8 Consensus size: 43
5950 TTCATTGTGT
* * *
5960 GGTTATCAGAA-TTCCACAGTGTGGTTATCAAAATTTCACATTGT
1 GGTTATCA-AATTTCCACAGTATGGTTATC-AAATTTCACAATGA
* * *
6004 GGTTATCAAATTTTCATAG-AGAGGTTATCGAAATTTCACAATGA
1 GGTTATCAAATTTCCACAGTA-TGGTTATC-AAATTTCACAATGA
*
6048 GGTTATCAAATTTCCGCAGTATGGTTATCAATATTTC
1 GGTTATCAAATTTCCACAGTATGGTTATCAA-ATTTC
6085 TACGTTGGAG
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
43 4 0.06
44 61 0.92
45 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (43 bp):
GGTTATCAAATTTCCACAGTATGGTTATCAAATTTCACAATGA
Found at i:7511 original size:19 final size:19
Alignment explanation
Indices: 7487--7523 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
7477 TCTAATGTCT
7487 ATTCAAATAATTATCTACA
1 ATTCAAATAATTATCTACA
7506 ATTCAAATAATTATCTAC
1 ATTCAAATAATTATCTAC
7524 TGGATCCCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.46, C:0.16, G:0.00, T:0.38
Consensus pattern (19 bp):
ATTCAAATAATTATCTACA
Found at i:8696 original size:118 final size:118
Alignment explanation
Indices: 8488--8720 Score: 421
Period size: 118 Copynumber: 2.0 Consensus size: 118
8478 TGGAAGAACA
*
8488 TCCACCACAACCATGAATATTGTTTTGAGGAATTTCAAGTCCTTAAATTTTCCACTTCAAACCAA
1 TCCACCACAACCATGAATATTGTTTTGAGGAATTCCAAGTCCTTAAATTTTCCACTTCAAACCAA
8553 CTCTTCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGATCCCAAATGC
66 CTCTTCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGATCCCAAATGC
* * *
8606 TCCACCATAACCATGAATATTGTTTTGAGGAATTCCAAGTCCTTGAATTTTCCACTTGAAACCAA
1 TCCACCACAACCATGAATATTGTTTTGAGGAATTCCAAGTCCTTAAATTTTCCACTTCAAACCAA
*
8671 CTTTTCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGATCCCAAA
66 CTCTTCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGATCCCAAA
8721 CGCGTTAACA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
118 110 1.00
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (118 bp):
TCCACCACAACCATGAATATTGTTTTGAGGAATTCCAAGTCCTTAAATTTTCCACTTCAAACCAA
CTCTTCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGATCCCAAATGC
Found at i:9997 original size:22 final size:21
Alignment explanation
Indices: 9964--10034 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 21
9954 TCAATCAAAC
*
9964 CAAAATTACATAGGAAGGTTAT
1 CAAAATTTCATAGG-AGGTTAT
* *
9986 CAAATTTTCATAGTGTGGTTA-
1 CAAAATTTCATAG-GAGGTTAT
10007 CTAAAATTTCATATGGAGGTTAT
1 C-AAAATTTCATA-GGAGGTTAT
10030 CAAAA
1 CAAAA
10035 CGTCATAGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
21 1 0.03
22 36 0.90
23 3 0.08
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (21 bp):
CAAAATTTCATAGGAGGTTAT
Done.