Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013721.1 Corchorus capsularis cultivar CVL-1 contig13742, 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: 28699
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:5203 original size:2 final size:2
Alignment explanation
Indices: 5196--5222 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5186 TTTAGAGCGT
5196 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5223 TATTCTTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5922 original size:109 final size:108
Alignment explanation
Indices: 5766--6135 Score: 576
Period size: 109 Copynumber: 3.5 Consensus size: 108
5756 AGTTTAGCCT
* *
5766 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTATATTTTTATTTTAAGGGTAAATTTCATAATT
5831 AATAATTTATTGTTATATGGTTTTAGAAATAAAATATATAAAAC
66 AATAATTTATTGTTATA-GGTTTTAGAAATAAAATATATAAAAC
* *
5875 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGATAAATTTCATAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTATATTTTTATTTTAAGGGTAAATTTCATAATT
*
5940 AATAATTTATTGTTATAGGGTTTTAGAAAT-AAA-ATACAAAAC
66 AATAATTTATTGTTATA-GGTTTTAGAAATAAAATATATAAAAC
5982 TAATTTCACTAAGTTTAGCCCCAAATT---ATTAT-TTTTTATTTTAAGGGTAAATTTCATAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTATATTTTTATTTTAAGGGTAAATTTCATAATT
* *
6043 AATAATTTATTGTTATAGGGTTTAGAAATAAAATATATATAAC
66 AATAATTTATTGTTATAGGTTTTAGAAATAAAATATATAAAAC
* * *
6086 TAA-TTCACTAAATTTAG-CCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTATATTTTTATTTTAAGGGT
6136 TAGAAAAATT
Statistics
Matches: 243, Mismatches: 12, Indels: 15
0.90 0.04 0.06
Matches are distributed among these distances:
102 19 0.08
103 61 0.25
104 14 0.06
105 4 0.02
106 15 0.06
107 35 0.14
108 3 0.01
109 92 0.38
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.43
Consensus pattern (108 bp):
TAATTTCACTAAGTTTAGCCCCAAATTAAAATTATATTTTTATTTTAAGGGTAAATTTCATAATT
AATAATTTATTGTTATAGGTTTTAGAAATAAAATATATAAAAC
Found at i:14820 original size:12 final size:12
Alignment explanation
Indices: 14803--14833 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
14793 TCTTCCCTTC
14803 AAACTAAACTTG
1 AAACTAAACTTG
14815 AAACTAAACTTG
1 AAACTAAACTTG
*
14827 AAGCTAA
1 AAACTAA
14834 TATGACTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.52, C:0.16, G:0.10, T:0.23
Consensus pattern (12 bp):
AAACTAAACTTG
Found at i:15162 original size:2 final size:2
Alignment explanation
Indices: 15155--15189 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
15145 TTCTCCAAAG
15155 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15190 TTATTTCTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17142 original size:20 final size:20
Alignment explanation
Indices: 17117--17156 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
17107 TTGGTCTTCA
17117 GACTT-GCAATACTTCAATTG
1 GACTTGGCAAT-CTTCAATTG
*
17137 GACTTGGCCATCTTCAATTG
1 GACTTGGCAATCTTCAATTG
17157 CTTCTCTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (20 bp):
GACTTGGCAATCTTCAATTG
Found at i:21090 original size:52 final size:52
Alignment explanation
Indices: 21025--21129 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
21015 TTTCCTTCCT
*
21025 AGTGGTTTTGTTTTGCCTAGTTTCTGAGAAAATTAAGATAAGAGTTCATAAG
1 AGTGGTTTCGTTTTGCCTAGTTTCTGAGAAAATTAAGATAAGAGTTCATAAG
*
21077 AGTGGTTTCGTTTTGCCTGGTTTCTGAGAAAATTAAGATAAGAGTTCATAAG
1 AGTGGTTTCGTTTTGCCTAGTTTCTGAGAAAATTAAGATAAGAGTTCATAAG
21129 A
1 A
21130 ATCAGTAATG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.30, C:0.09, G:0.24, T:0.37
Consensus pattern (52 bp):
AGTGGTTTCGTTTTGCCTAGTTTCTGAGAAAATTAAGATAAGAGTTCATAAG
Found at i:24968 original size:1 final size:1
Alignment explanation
Indices: 24962--24992 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
24952 CTAGCAATGC
24962 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
24993 CGCAGTATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:25288 original size:2 final size:2
Alignment explanation
Indices: 25281--25320 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
25271 ACGGACATAC
* *
25281 AT AT AT AT AT AT AT AT AT AT CT AT AT CT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25321 AGTCTAAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26440 original size:2 final size:2
Alignment explanation
Indices: 26433--26459 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
26423 TTCCTATGTA
26433 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 A
26460 ATAACTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28124 original size:183 final size:180
Alignment explanation
Indices: 27806--28145 Score: 511
Period size: 183 Copynumber: 1.9 Consensus size: 180
27796 GTTATTAAGC
* *
27806 ATGTAAGGATTGGTAAATACAATTTTAAAAACTTTTATAACTTTTTAGTAGATTACTCAAGTTAT
1 ATGTAAGGATTGGTAAATACAATTTTAAAAACTTTTATAACTATTTAGTAG--TACTCAAGTAAT
**
27871 TAAATTGGTAACTTTCATTATTGATCATAAAAAGTTACTAAAATCAATAAGGATGTAGGATTACT
64 TAAATTGGTAACTTTCATTATTGATCATAAAAAGTTACTAAAATCAATAAGGATGTAAAATTACT
27936 TGAATCTAGATAATAGTACTATAATGTTTTTCGGCAAAAAAAAATAAAAATAAAA
129 TGAATCTAG---ATAGTACTATAATGTTTTTCGGCAAAAAAAAATAAAAATAAAA
* * * * *
27991 ATGTGAGGATTGGTAAATACAATTTTAATAACTTTTTTAGCCTATTTAGTAG-ACTTAAGTAATT
1 ATGTAAGGATTGGTAAATACAATTTTAAAAACTTTTATA-ACTATTTAGTAGTACTCAAGTAATT
* * *
28055 AAATTGGTACCTTTCATTATTGATCATAAAAAGTTACTAAAATTAATAAGGATGTAAAATTATTT
65 AAATTGGTAACTTTCATTATTGATCATAAAAAGTTACTAAAATCAATAAGGATGTAAAATTACTT
28120 GAATCTAGATAGTACTATAATGTTTT
130 GAATCTAGATAGTACTATAATGTTTT
28146 CATAACTTTT
Statistics
Matches: 142, Mismatches: 12, Indels: 7
0.88 0.07 0.04
Matches are distributed among these distances:
180 18 0.13
183 78 0.55
185 36 0.25
186 10 0.07
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (180 bp):
ATGTAAGGATTGGTAAATACAATTTTAAAAACTTTTATAACTATTTAGTAGTACTCAAGTAATTA
AATTGGTAACTTTCATTATTGATCATAAAAAGTTACTAAAATCAATAAGGATGTAAAATTACTTG
AATCTAGATAGTACTATAATGTTTTTCGGCAAAAAAAAATAAAAATAAAA
Done.