Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007665.1 Corchorus capsularis cultivar CVL-1 contig07686, 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: 9743
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Found at i:229 original size:41 final size:41
Alignment explanation
Indices: 164--248 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 41
154 GTTCATGTTT
* * *
164 TTTCTTTTTATCTCACTTATGGTTTA-ATATGTTTTTTGAGGG
1 TTTCTTTTTATCTCACCTAGGGTTTATAT-TGTTTGTT-AGGG
206 TTTC-TTTTATCTCACCTAGGGTTTATATTGTTTGTTAGGG
1 TTTCTTTTTATCTCACCTAGGGTTTATATTGTTTGTTAGGG
246 TTT
1 TTT
249 GGGTTTCATA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
40 7 0.18
41 26 0.67
42 6 0.15
ACGTcount: A:0.15, C:0.11, G:0.18, T:0.56
Consensus pattern (41 bp):
TTTCTTTTTATCTCACCTAGGGTTTATATTGTTTGTTAGGG
Found at i:4936 original size:50 final size:50
Alignment explanation
Indices: 4859--4961 Score: 181
Period size: 50 Copynumber: 2.1 Consensus size: 50
4849 GTTTCAATTT
4859 CAATGTACTTTGCAGATAGTTTCATTCACTTTCTATGGCCTTTAAGATGG
1 CAATGTACTTTGCAGATAGTTTCATTCACTTTCTATGGCCTTTAAGATGG
*
4909 CAATGTACTTTGCAGAT-GTTTTTATTCACTTTCTATGGCCTTTAAGATGG
1 CAATGTACTTTGCAGATAG-TTTCATTCACTTTCTATGGCCTTTAAGATGG
4959 CAA
1 CAA
4962 GATATATATA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
49 1 0.02
50 50 0.98
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.41
Consensus pattern (50 bp):
CAATGTACTTTGCAGATAGTTTCATTCACTTTCTATGGCCTTTAAGATGG
Found at i:4970 original size:2 final size:2
Alignment explanation
Indices: 4963--4994 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4953 AGATGGCAAG
4963 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4995 TACACCTGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5988 original size:447 final size:447
Alignment explanation
Indices: 5154--6052 Score: 1771
Period size: 447 Copynumber: 2.0 Consensus size: 447
5144 TTGATTTTGG
*
5154 ACATATTGAAGCCGAGAGAGAATGAAGCTAATACAAAAAATGCGTTTTCACTTTGCTACAGAACC
1 ACATATTGAAGCCGAGAGAGAATGAAGCTAATACAAAAAATGCGTTTTCACTTTACTACAGAACC
5219 AAGTCTATGAAGGTAGGAGGCAACTTATTTCCTTGGCACACTCTATTTGCAGGTTTTCTTTTGTC
66 AAGTCTATGAAGGTAGGAGGCAACTTATTTCCTTGGCACACTCTATTTGCAGGTTTTCTTTTGTC
5284 TCCAATGCTTGATTTTGGGGGACATGATTATACATCTCAGTATTATACCTGCTTTGTATCGAGAA
131 TCCAATGCTTGATTTTGGGGGACATGATTATACATCTCAGTATTATACCTGCTTTGTATCGAGAA
5349 CACACATTCAGTTTATCTCAACTTTACCAAAATGCAGTCCTTCTCAATTGTTCTGTACAAAATAT
196 CACACATTCAGTTTATCTCAACTTTACCAAAATGCAGTCCTTCTCAATTGTTCTGTACAAAATAT
5414 TCCCCATTTCTTTCATGTATATTTTGCAGCGACTTTAATTTTTCCAAGAAAATGGACCAACTAAA
261 TCCCCATTTCTTTCATGTATATTTTGCAGCGACTTTAATTTTTCCAAGAAAATGGACCAACTAAA
5479 TGTAGAACACCAACTCAATTACAATGGGAGAGAATCAATTGGTCCATTTATATAGAAATTTCAAC
326 TGTAGAACACCAACTCAATTACAATGGGAGAGAATCAATTGGTCCATTTATATAGAAATTTCAAC
5544 TCCTCATTACATTTTATCATTCCTAACTAATAGAGATATACAACAATCAAAATGACC
391 TCCTCATTACATTTTATCATTCCTAACTAATAGAGATATACAACAATCAAAATGACC
5601 ACATATTGAAGCCGAGAGAGAATGAAGCTAATACAAAAAATGCGTTTTCACTTTACTACAGAACC
1 ACATATTGAAGCCGAGAGAGAATGAAGCTAATACAAAAAATGCGTTTTCACTTTACTACAGAACC
*
5666 AAGTCTATGAAGGTATGAGGCAACTTATTTCCTTGGCACACTCTATTTGCAGGTTTTCTTTTGTC
66 AAGTCTATGAAGGTAGGAGGCAACTTATTTCCTTGGCACACTCTATTTGCAGGTTTTCTTTTGTC
5731 TCCAATGCTTGATTTTGGGGGACATGATTATACATCTCAGTATTATACCTGCTTTGTATCGAGAA
131 TCCAATGCTTGATTTTGGGGGACATGATTATACATCTCAGTATTATACCTGCTTTGTATCGAGAA
5796 CACACATTCAGTTTATCTCAACTTTACCAAAATGCAGTCCTTCTCAATTGTTCTGTACAAAATAT
196 CACACATTCAGTTTATCTCAACTTTACCAAAATGCAGTCCTTCTCAATTGTTCTGTACAAAATAT
5861 TCCCCATTTCTTTCATGTATATTTTGCAGCGACTTTAATTTTTCCAAGAAAATGGACCAACTAAA
261 TCCCCATTTCTTTCATGTATATTTTGCAGCGACTTTAATTTTTCCAAGAAAATGGACCAACTAAA
5926 TGTAGAACACCAACTCAATTACAATGGGAGAGAATCAATTGGTCCATTTATATAGAAATTTCAAC
326 TGTAGAACACCAACTCAATTACAATGGGAGAGAATCAATTGGTCCATTTATATAGAAATTTCAAC
*
5991 TCCTCGTTACATTTTATCATTCCTAACTAATAGAGATATACAACAATCAAAATGACC
391 TCCTCATTACATTTTATCATTCCTAACTAATAGAGATATACAACAATCAAAATGACC
6048 ACATA
1 ACATA
6053 CACTTCATCA
Statistics
Matches: 449, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
447 449 1.00
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (447 bp):
ACATATTGAAGCCGAGAGAGAATGAAGCTAATACAAAAAATGCGTTTTCACTTTACTACAGAACC
AAGTCTATGAAGGTAGGAGGCAACTTATTTCCTTGGCACACTCTATTTGCAGGTTTTCTTTTGTC
TCCAATGCTTGATTTTGGGGGACATGATTATACATCTCAGTATTATACCTGCTTTGTATCGAGAA
CACACATTCAGTTTATCTCAACTTTACCAAAATGCAGTCCTTCTCAATTGTTCTGTACAAAATAT
TCCCCATTTCTTTCATGTATATTTTGCAGCGACTTTAATTTTTCCAAGAAAATGGACCAACTAAA
TGTAGAACACCAACTCAATTACAATGGGAGAGAATCAATTGGTCCATTTATATAGAAATTTCAAC
TCCTCATTACATTTTATCATTCCTAACTAATAGAGATATACAACAATCAAAATGACC
Found at i:6171 original size:53 final size:53
Alignment explanation
Indices: 6091--6197 Score: 196
Period size: 53 Copynumber: 2.0 Consensus size: 53
6081 CGAAGCGCGG
*
6091 GCAAGAAATCTAGTTATGTAGAAAAGTATTATGAGAGATTCACTAGGGTTCTA
1 GCAAGAAACCTAGTTATGTAGAAAAGTATTATGAGAGATTCACTAGGGTTCTA
*
6144 GCAAGAAACCTAGTTATGTAGAAAAGTATTATGAGAGGTTCACTAGGGTTCTA
1 GCAAGAAACCTAGTTATGTAGAAAAGTATTATGAGAGATTCACTAGGGTTCTA
6197 G
1 G
6198 ACTTAAGAGG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.29
Consensus pattern (53 bp):
GCAAGAAACCTAGTTATGTAGAAAAGTATTATGAGAGATTCACTAGGGTTCTA
Found at i:6755 original size:21 final size:21
Alignment explanation
Indices: 6711--6758 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
6701 CGTTGGGCGT
* * * *
6711 CCATGTGGTTTGCTTGGTGCC
1 CCATGTGGTTTGCCTCGCGAC
6732 CCATGTGGTTTGCCTCGCGAC
1 CCATGTGGTTTGCCTCGCGAC
6753 CCATGT
1 CCATGT
6759 ACTCCAGTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.08, C:0.29, G:0.29, T:0.33
Consensus pattern (21 bp):
CCATGTGGTTTGCCTCGCGAC
Found at i:7838 original size:142 final size:142
Alignment explanation
Indices: 7582--7868 Score: 574
Period size: 142 Copynumber: 2.0 Consensus size: 142
7572 ATTTCCAAGA
7582 TTTGGGGCTCAATTGATTAAAAGAAGAGTTTTTAGATCTGATTGAAAAGTGGAATAAAGCCAATA
1 TTTGGGGCTCAATTGATTAAAAGAAGAGTTTTTAGATCTGATTGAAAAGTGGAATAAAGCCAATA
7647 GACCATTTGGAAATTTTTCCAAATTGGAAAATATTTGAACAACTTCTCCTTCCCTCACCGTCACT
66 GACCATTTGGAAATTTTTCCAAATTGGAAAATATTTGAACAACTTCTCCTTCCCTCACCGTCACT
7712 TCCTTTCTTCAT
131 TCCTTTCTTCAT
7724 TTTGGGGCTCAATTGATTAAAAGAAGAGTTTTTAGATCTGATTGAAAAGTGGAATAAAGCCAATA
1 TTTGGGGCTCAATTGATTAAAAGAAGAGTTTTTAGATCTGATTGAAAAGTGGAATAAAGCCAATA
7789 GACCATTTGGAAATTTTTCCAAATTGGAAAATATTTGAACAACTTCTCCTTCCCTCACCGTCACT
66 GACCATTTGGAAATTTTTCCAAATTGGAAAATATTTGAACAACTTCTCCTTCCCTCACCGTCACT
7854 TCCTTTCTTCAT
131 TCCTTTCTTCAT
7866 TTT
1 TTT
7869 CCCTCATAGC
Statistics
Matches: 145, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
142 145 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.35
Consensus pattern (142 bp):
TTTGGGGCTCAATTGATTAAAAGAAGAGTTTTTAGATCTGATTGAAAAGTGGAATAAAGCCAATA
GACCATTTGGAAATTTTTCCAAATTGGAAAATATTTGAACAACTTCTCCTTCCCTCACCGTCACT
TCCTTTCTTCAT
Done.