Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014545.1 Corchorus capsularis cultivar CVL-1 contig14566, 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: 27943
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:662 original size:7 final size:7
Alignment explanation
Indices: 650--682 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
640 GTTTTTGGCC
650 TTTTCTT
1 TTTTCTT
657 TTTTCTT
1 TTTTCTT
664 TTTTCTT
1 TTTTCTT
671 TTTTCTT
1 TTTTCTT
678 TTTTC
1 TTTTC
683 CATTTCTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTCTT
Found at i:731 original size:3 final size:3
Alignment explanation
Indices: 723--761 Score: 60
Period size: 3 Copynumber: 12.3 Consensus size: 3
713 TATTTTATAG
723 TAA TAA TAA TAA TAA TAA TTAA TTAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA -TAA -TAA TAA TAA TAA TAA T
762 CCAATATCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 28 0.80
4 7 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:767 original size:17 final size:17
Alignment explanation
Indices: 726--767 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
716 TTTATAGTAA
726 TAAT-AATAATAATAAT
1 TAATCAATAATAATAAT
*
742 TAATTAATAATAATAA-
1 TAATCAATAATAATAAT
758 TAATCCAATA
1 TAAT-CAATA
768 TCAGCCATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (17 bp):
TAATCAATAATAATAAT
Found at i:4250 original size:142 final size:144
Alignment explanation
Indices: 4002--4273 Score: 476
Period size: 142 Copynumber: 1.9 Consensus size: 144
3992 ATGAGTAACG
* * *
4002 AAAAAATATCGGACCAAGAGACAGAGGGAAGGTTGGGATTGAATTCGACTAATTTTTATAGTTTC
1 AAAAAAAATCGGACCAAGAGACAGAGGGAAGGTTGGGATCGAATTCGACTAATTTTTATAATTTC
*
4067 GGTATCCAGTGATCACATTAAAGCTTTGATTAAATCATGAAACCCTATCAGATTTCAAA-TAAAA
66 GGTATCCAGTGATCACATTAAAGCTCTGATTAAATCATGAAACCCTATCAGATTTCAAATTAAAA
4131 CATGAGTAACCAAA
131 CATGAGTAACCAAA
4145 AAAAAAAATCGGACCAAGAGACAGAGGGAAGGTTGGGATCGAATTCGACT-ATTTTTATAATTTC
1 AAAAAAAATCGGACCAAGAGACAGAGGGAAGGTTGGGATCGAATTCGACTAATTTTTATAATTTC
* *
4209 GGTATCCAGTGATCACATTAAATCTCTGATTAAATCGTGAAACCCTATCAGATTTCAAATTAAAA
66 GGTATCCAGTGATCACATTAAAGCTCTGATTAAATCATGAAACCCTATCAGATTTCAAATTAAAA
4274 AAAAAACCTT
Statistics
Matches: 122, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
142 69 0.57
143 53 0.43
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (144 bp):
AAAAAAAATCGGACCAAGAGACAGAGGGAAGGTTGGGATCGAATTCGACTAATTTTTATAATTTC
GGTATCCAGTGATCACATTAAAGCTCTGATTAAATCATGAAACCCTATCAGATTTCAAATTAAAA
CATGAGTAACCAAA
Found at i:21708 original size:12 final size:12
Alignment explanation
Indices: 21693--21733 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
21683 ACCATCCTCG
*
21693 TCCTCATCTTCA
1 TCCTCATCATCA
21705 TCCTCATCATCA
1 TCCTCATCATCA
* *
21717 TCGTCGTCATCA
1 TCCTCATCATCA
21729 TCCTC
1 TCCTC
21734 TTCCTCCGGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.17, C:0.41, G:0.05, T:0.37
Consensus pattern (12 bp):
TCCTCATCATCA
Found at i:21771 original size:24 final size:24
Alignment explanation
Indices: 21703--21772 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
21693 TCCTCATCTT
* * *
21703 CATCCTCATCATCATCGTCGTCAT
1 CATCCTCTTCATCATCGTCTTCAC
* ***
21727 CATCCTCTTCCTCCGGGTCTTCAC
1 CATCCTCTTCATCATCGTCTTCAC
*
21751 CATCCTCTTCATCATCTTCTTC
1 CATCCTCTTCATCATCGTCTTC
21773 TTCCCCATTC
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.14, C:0.41, G:0.07, T:0.37
Consensus pattern (24 bp):
CATCCTCTTCATCATCGTCTTCAC
Found at i:25544 original size:34 final size:36
Alignment explanation
Indices: 25499--25566 Score: 95
Period size: 34 Copynumber: 1.9 Consensus size: 36
25489 CAAATGGGGT
* *
25499 AAAAATCAAACTTACA-TTCTAAA-AAATAAAAATA
1 AAAAATCAAACTTACACGTCAAAACAAATAAAAATA
*
25533 AAAAATGAAACTTACACGTCAAAACAAATAAAAA
1 AAAAATCAAACTTACACGTCAAAACAAATAAAAA
25567 GTAAGAAGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 15 0.52
35 5 0.17
36 9 0.31
ACGTcount: A:0.65, C:0.13, G:0.03, T:0.19
Consensus pattern (36 bp):
AAAAATCAAACTTACACGTCAAAACAAATAAAAATA
Found at i:26415 original size:3 final size:3
Alignment explanation
Indices: 26407--26461 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
26397 TATTATATAT
26407 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
26455 ATA ATA A
1 ATA ATA A
26462 GCTTTTTCAG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Done.