Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000648.1 Corchorus capsularis cultivar CVL-1 contig00648, 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: 4081
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Found at i:855 original size:59 final size:58
Alignment explanation
Indices: 788--951 Score: 213
Period size: 59 Copynumber: 2.8 Consensus size: 58
778 TTTTTTTTCA
* * * *
788 AAATTAAATATAGTGGCGTCTAGACACCGCTATATTAAAGTGTTTTAAAAAAAAAACTC
1 AAATTAAATATAGCGGCGTCTAGACGCCGCTATATTTAAGGGTTTT-AAAAAAAAACTC
* * * *
847 AAATTAAATATAGCGACGTTTAAACGCCGCTATATTTAAGGGATTTTAAAAAAAATCTC
1 AAATTAAATATAGCGGCGTCTAGACGCCGCTATATTTAAGGG-TTTTAAAAAAAAACTC
*
906 AAACTAAATATAGCGGCG-CTTAGACGCCGCTATATTTAAGGGTTTT
1 AAATTAAATATAGCGGCGTC-TAGACGCCGCTATATTTAAGGGTTTT
952 TTAAATATAG
Statistics
Matches: 91, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
58 4 0.04
59 83 0.91
60 4 0.04
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.30
Consensus pattern (58 bp):
AAATTAAATATAGCGGCGTCTAGACGCCGCTATATTTAAGGGTTTTAAAAAAAAACTC
Found at i:3646 original size:14 final size:14
Alignment explanation
Indices: 3621--3989 Score: 116
Period size: 14 Copynumber: 25.4 Consensus size: 14
3611 TTATGTAATG
*
3621 AAATATTATTTAGA
1 AAATAATATTTAGA
*
3635 AAACAATATTTAGA
1 AAATAATATTTAGA
*
3649 AATATATATGTTTAG-
1 AA-ATA-ATATTTAGA
*
3664 AAATTATATTTAGA
1 AAATAATATTTAGA
*
3678 AAATAATATTCAGA
1 AAATAATATTTAGA
3692 AATTATAA-ATTTA-A
1 AA--ATAATATTTAGA
* *
3706 TGAAATTATATTAAGA
1 --AAATAATATTTAGA
3722 AAATAATATTTAGA
1 AAATAATATTTAGA
* * *
3736 AATTGTATATGTAATGA
1 AAAT-AATAT-TTA-GA
* *
3753 AATTATATTTTCTA-A
1 AAATA-ATATT-TAGA
*
3768 AAAT--TATATA-A
1 AAATAATATTTAGA
* *
3779 AAATTGTATATGTA-A
1 AAA-T-AATATTTAGA
* *
3794 TGAAATTATAATTAGA
1 --AAATAATATTTAGA
3810 AAATAATATTTAGA
1 AAATAATATTTAGA
* *
3824 AATTATATATGTA-A
1 AAATA-ATATTTAGA
* * *
3838 TGAAATTATAATGAGA
1 --AAATAATATTTAGA
*
3854 AAATAATATTTGGA
1 AAATAATATTTAGA
*
3868 AATTATAAATTTTTAG-
1 AA--AT-AATATTTAGA
*
3884 AAATTATATTTAGA
1 AAATAATATTTAGA
*
3898 AAATAATAATTAGA
1 AAATAATATTTAGA
* *
3912 AATTATATATGTA-A
1 AAATA-ATATTTAGA
* *
3926 TGAAATTATAATTA-A
1 --AAATAATATTTAGA
3941 AAATAATATTTAGA
1 AAATAATATTTAGA
*
3955 AATTATAAATGTTTA-A
1 AA--AT-AATATTTAGA
*
3971 AAATTATATTTAGA
1 AAATAATATTTAGA
3985 AAATA
1 AAATA
3990 CAATTGGAAA
Statistics
Matches: 261, Mismatches: 57, Indels: 74
0.67 0.15 0.19
Matches are distributed among these distances:
11 6 0.02
12 3 0.01
13 30 0.11
14 107 0.41
15 53 0.20
16 35 0.13
17 27 0.10
ACGTcount: A:0.51, C:0.01, G:0.08, T:0.39
Consensus pattern (14 bp):
AAATAATATTTAGA
Found at i:3664 original size:16 final size:15
Alignment explanation
Indices: 3643--3776 Score: 57
Period size: 16 Copynumber: 8.9 Consensus size: 15
3633 GAAAACAATA
3643 TTTAGAAATATATATG
1 TTTAGAAAT-TATATG
3659 TTTAGAAATTATA--
1 TTTAGAAATTATATG
* *
3672 TTTAGAAAATA-ATA
1 TTTAGAAATTATATG
* **
3686 TTCAGAAATTATAAA
1 TTTAGAAATTATATG
3701 TTTAATGAAATTATA--
1 TTT-A-GAAATTATATG
* * *
3716 TTAAGAAAATA-ATA
1 TTTAGAAATTATATG
3730 TTTAGAAATTGTATATG
1 TTTAGAAA-T-TATATG
* *
3747 -TAATGAAATTATATT
1 TTTA-GAAATTATATG
*
3762 TTCTAAAAATTATAT
1 TT-TAGAAATTATAT
3777 AAAAATTGTA
Statistics
Matches: 91, Mismatches: 14, Indels: 26
0.69 0.11 0.20
Matches are distributed among these distances:
12 2 0.02
13 16 0.18
14 17 0.19
15 15 0.16
16 25 0.27
17 16 0.18
ACGTcount: A:0.49, C:0.01, G:0.08, T:0.42
Consensus pattern (15 bp):
TTTAGAAATTATATG
Found at i:3672 original size:29 final size:29
Alignment explanation
Indices: 3640--3961 Score: 105
Period size: 29 Copynumber: 11.1 Consensus size: 29
3630 TTAGAAAACA
*
3640 ATATTTAGAAATATATATGTTTAGAAATT
1 ATATTTAGAAATATATATGTTAAGAAATT
* *
3669 ATATTTAGAAA-ATA-ATATTCAGAAATT
1 ATATTTAGAAATATATATGTTAAGAAATT
*
3696 ATAAATTTAATGAAAT-TATA--TTAAGAAAATA
1 AT--ATTT-A-GAAATATATATGTTAAG-AAATT
*
3727 ATATTTAGAAATTGTATATG-TAATGAAATT
1 ATATTTAGAAA-TATATATGTTAA-GAAATT
** * *
3757 ATATTTTCTAAAAAT-TAT-ATAA-AAATTGT
1 ATA-TTTAGAAATATATATGTTAAGAAA-T-T
* * *
3786 ATATGTAATGAAAT-TATA-ATT-AGAAAATA
1 ATAT-TTA-GAAATATATATGTTAAG-AAATT
3815 ATATTTAGAAATTATATATG-TAATGAAATT
1 ATATTTAGAAA-TATATATGTTAA-GAAATT
* * *
3845 ATAATGAGAAA-ATAATAT-TT-GGAAATT
1 ATATTTAGAAATAT-ATATGTTAAGAAATT
*
3872 ATAAATTTTTAGAAAT-TATAT-TT-AGAAAATA
1 AT--A--TTTAGAAATATATATGTTAAG-AAATT
*
3903 ATAATTAGAAATTATATATG-TAATGAAATT
1 ATATTTAGAAA-TATATATGTTAA-GAAATT
* *
3933 ATAATTAAAAATA-ATAT-TT-AGAAATT
1 ATATTTAGAAATATATATGTTAAGAAATT
3959 ATA
1 ATA
3962 AATGTTTAAA
Statistics
Matches: 224, Mismatches: 28, Indels: 85
0.66 0.08 0.25
Matches are distributed among these distances:
26 9 0.04
27 40 0.18
28 18 0.08
29 60 0.27
30 59 0.26
31 37 0.17
32 1 0.00
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.40
Consensus pattern (29 bp):
ATATTTAGAAATATATATGTTAAGAAATT
Found at i:3723 original size:44 final size:44
Alignment explanation
Indices: 3612--3989 Score: 439
Period size: 44 Copynumber: 8.6 Consensus size: 44
3602 AAATCACTTT
*
3612 TATGTAATGAAA-TATTATTTAGAAAACAATATTTAGAAA-TATA
1 TATGTAATGAAATTA-TATTTAGAAAATAATATTTAGAAATTATA
* *
3655 TATGT-TTAGAAATTATATTTAGAAAATAATATTCAGAAATTATA
1 TATGTAAT-GAAATTATATTTAGAAAATAATATTTAGAAATTATA
* * * *
3699 AATTTAATGAAATTATATTAAGAAAATAATATTTAGAAATTGTA
1 TATGTAATGAAATTATATTTAGAAAATAATATTTAGAAATTATA
** * * * *
3743 TATGTAATGAAATTATATTTTCTAAAA-ATTATATAAAAATTGTA
1 TATGTAATGAAATTATA-TTTAGAAAATAATATTTAGAAATTATA
*
3787 TATGTAATGAAATTATAATTAGAAAATAATATTTAGAAATTATA
1 TATGTAATGAAATTATATTTAGAAAATAATATTTAGAAATTATA
* * *
3831 TATGTAATGAAATTATAATGAGAAAATAATATTTGGAAATTATA
1 TATGTAATGAAATTATATTTAGAAAATAATATTTAGAAATTATA
* ** *
3875 AAT-TTTTAGAAATTATATTTAGAAAATAATAATTAGAAATTATA
1 TATGTAAT-GAAATTATATTTAGAAAATAATATTTAGAAATTATA
*
3919 TATGTAATGAAATTATAATTA-AAAATAATATTTAGAAATTATA
1 TATGTAATGAAATTATATTTAGAAAATAATATTTAGAAATTATA
*
3962 AATGTTTAA--AAATTATATTTAGAAAATA
1 TATG--TAATGAAATTATATTTAGAAAATA
3990 CAATTGGAAA
Statistics
Matches: 284, Mismatches: 40, Indels: 21
0.82 0.12 0.06
Matches are distributed among these distances:
42 1 0.00
43 74 0.26
44 197 0.69
45 12 0.04
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.39
Consensus pattern (44 bp):
TATGTAATGAAATTATATTTAGAAAATAATATTTAGAAATTATA
Found at i:3971 original size:30 final size:28
Alignment explanation
Indices: 3853--3986 Score: 96
Period size: 30 Copynumber: 4.6 Consensus size: 28
3843 TTATAATGAG
*
3853 AAAATAATATTTGGAAATTATAAATTTTTA
1 AAAATAATATTTAGAAATTAT-AA-TTTTA
* * *
3883 GAAATTATATTTAGAAA--ATAATAATTA
1 AAAATAATATTTAGAAATTATAAT-TTTA
* *
3910 GAAATTATATATGTAATGAAATTATAA--TTA
1 -AAAATA-ATAT-TTA-GAAATTATAATTTTA
3940 AAAATAATATTTAGAAATTATAAATGTTTA
1 AAAATAATATTTAGAAATTAT-AAT-TTTA
*
3970 AAAATTATATTTAGAAA
1 AAAATAATATTTAGAAA
3987 ATACAATTGG
Statistics
Matches: 82, Mismatches: 11, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
26 9 0.11
27 9 0.11
28 9 0.11
29 9 0.11
30 38 0.46
31 4 0.05
33 4 0.05
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (28 bp):
AAAATAATATTTAGAAATTATAATTTTA
Found at i:4038 original size:33 final size:32
Alignment explanation
Indices: 4001--4075 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
3991 AATTGGAAAA
*
4001 TAGCGGCGTTTTAGCCAAAT-AAACGCCACCATT
1 TAGCGGCGTTTGAGCC--ATCAAACGCCACCATT
* *
4034 TAGCGGCGTTTGGGCCCTCAAACGCCACCATT
1 TAGCGGCGTTTGAGCCATCAAACGCCACCATT
*
4066 TAACGGCGTT
1 TAGCGGCGTT
4076 CAGGAC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 1 0.03
32 22 0.59
33 14 0.38
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.24
Consensus pattern (32 bp):
TAGCGGCGTTTGAGCCATCAAACGCCACCATT
Done.