Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004341.1 Corchorus capsularis cultivar CVL-1 contig04349, 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, 637
Length: 1062
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.39
Found at i:460 original size:15 final size:15
Alignment explanation
Indices: 440--483 Score: 88
Period size: 15 Copynumber: 2.9 Consensus size: 15
430 TTAATTTCGA
440 TATAGTACTATATAG
1 TATAGTACTATATAG
455 TATAGTACTATATAG
1 TATAGTACTATATAG
470 TATAGTACTATATA
1 TATAGTACTATATA
484 ACTGCAAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (15 bp):
TATAGTACTATATAG
Found at i:644 original size:27 final size:30
Alignment explanation
Indices: 615--678 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 30
605 TTATTTTTAT
615 TCTATTTTCTATATTC-T-ATT-TATTTAT
1 TCTATTTTCTATATTCATAATTCTATTTAT
* *
642 TCTATATTCTTTATTCTATAATTCTATTTAT
1 TCTATTTTCTATATTC-ATAATTCTATTTAT
673 TCTATT
1 TCTATT
679 ATATATAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 14 0.47
29 1 0.03
30 3 0.10
31 12 0.40
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.64
Consensus pattern (30 bp):
TCTATTTTCTATATTCATAATTCTATTTAT
Found at i:649 original size:7 final size:7
Alignment explanation
Indices: 612--668 Score: 62
Period size: 7 Copynumber: 8.1 Consensus size: 7
602 AATTTATTTT
612 TATTCTA
1 TATTCTA
*
619 TTTTCTA
1 TATTCTA
626 TATTCTA
1 TATTCTA
* *
633 T-TTATT
1 TATTCTA
639 TATTCTA
1 TATTCTA
*
646 TATTCTT
1 TATTCTA
653 TATTCTA
1 TATTCTA
660 TAATTCTA
1 T-ATTCTA
668 T
1 T
669 TTATTCTATT
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
6 4 0.10
7 29 0.73
8 7 0.17
ACGTcount: A:0.25, C:0.12, G:0.00, T:0.63
Consensus pattern (7 bp):
TATTCTA
Found at i:661 original size:14 final size:14
Alignment explanation
Indices: 606--677 Score: 76
Period size: 14 Copynumber: 5.1 Consensus size: 14
596 ATTCGAAATT
606 TATT-TTTATTCTA
1 TATTCTTTATTCTA
* *
619 TTTTCTATATTCTA
1 TATTCTTTATTCTA
*
633 T-TTATTTATTCTA
1 TATTCTTTATTCTA
646 TATTCTTTATTCTA
1 TATTCTTTATTCTA
660 TAATTCTATTTATTCTA
1 T-ATTC--TTTATTCTA
677 T
1 T
678 TATATATAGT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
13 14 0.29
14 21 0.43
15 4 0.08
17 10 0.20
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.65
Consensus pattern (14 bp):
TATTCTTTATTCTA
Found at i:678 original size:22 final size:22
Alignment explanation
Indices: 626--683 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
616 CTATTTTCTA
*
626 TATTCTATTTATTTATTCTATAT
1 TATTCTATTTA-TAATTCTATAT
*
649 TCTT-TATTCTATAATTCTAT-T
1 TATTCTATT-TATAATTCTATAT
670 TATTCTATTATATA
1 TATTCTATT-TATA
684 TAGTTAGAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 4 0.14
22 20 0.69
23 5 0.17
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTCTATTTATAATTCTATAT
Found at i:705 original size:23 final size:23
Alignment explanation
Indices: 677--724 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
667 ATTTATTCTA
677 TTATATATAGTTAGAATATATTT
1 TTATATATAGTTAGAATATATTT
700 TTATATATAGTTAGAATATATTT
1 TTATATATAGTTAGAATATATTT
723 TT
1 TT
725 GAGAATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (23 bp):
TTATATATAGTTAGAATATATTT
Found at i:731 original size:14 final size:14
Alignment explanation
Indices: 712--740 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
702 ATATATAGTT
712 AGAATATATTTTTG
1 AGAATATATTTTTG
726 AGAATATATTTTTG
1 AGAATATATTTTTG
740 A
1 A
741 TTTTCTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (14 bp):
AGAATATATTTTTG
Found at i:732 original size:25 final size:23
Alignment explanation
Indices: 681--733 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 23
671 ATTCTATTAT
*
681 ATATAGTTAGAATATATTTTTAT
1 ATATAGTTAGAATATATTTTTAA
704 ATATAGTTAGAATATATTTTTGAGA
1 ATATAGTTAGAATATATTTTT-A-A
729 ATATA
1 ATATA
734 TTTTTGATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 21 0.78
24 1 0.04
25 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (23 bp):
ATATAGTTAGAATATATTTTTAA
Found at i:813 original size:12 final size:12
Alignment explanation
Indices: 796--832 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
786 AATAAAAATT
796 TATGAAATTATG
1 TATGAAATTATG
808 TATGAAATTATG
1 TATGAAATTATG
820 TATGAAATTATG
1 TATGAAATTATG
832 T
1 T
833 TTATGAATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.43
Consensus pattern (12 bp):
TATGAAATTATG
Found at i:846 original size:13 final size:13
Alignment explanation
Indices: 794--852 Score: 54
Period size: 12 Copynumber: 4.6 Consensus size: 13
784 AGAATAAAAA
794 TTTATGAAATTATG
1 TTTATG-AATTATG
808 --TATGAAATTATG
1 TTTATG-AATTATG
820 --TATGAAATTATG
1 TTTATG-AATTATG
*
832 TTTATGAATTCTG
1 TTTATGAATTATG
845 TTTATGAA
1 TTTATGAA
853 AAGATCTATC
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
12 24 0.57
13 14 0.33
14 4 0.10
ACGTcount: A:0.36, C:0.02, G:0.15, T:0.47
Consensus pattern (13 bp):
TTTATGAATTATG
Found at i:921 original size:38 final size:38
Alignment explanation
Indices: 870--946 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
860 ATCTTTGTTT
870 TTCAAAATCTAACGTGTCAACAAATACATACAATACAA
1 TTCAAAATCTAACGTGTCAACAAATACATACAATACAA
908 TTCAAAATCTAACGTGTCAACAAATACATACAATACAA
1 TTCAAAATCTAACGTGTCAACAAATACATACAATACAA
946 T
1 T
947 AAGGCGTTCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.49, C:0.21, G:0.05, T:0.25
Consensus pattern (38 bp):
TTCAAAATCTAACGTGTCAACAAATACATACAATACAA
Done.