Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007371.1 Corchorus capsularis cultivar CVL-1 contig07392, 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: 15726
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.29
Found at i:893 original size:30 final size:30
Alignment explanation
Indices: 857--970 Score: 120
Period size: 33 Copynumber: 3.6 Consensus size: 30
847 CTCGTCACCT
*
857 AAAACAGATTTATTTTCAATGCTATCAACC
1 AAAACAGAATTATTTTCAATGCTATCAACC
* *
887 AAAACAGGATTATTTGCAATGCTATAATCAACC
1 AAAACAGAATTATTTTCAATGC--T-ATCAACC
* *
920 AAAACAGAATTGTTTTTAATGCTATGTTCAACC
1 AAAACAGAATTATTTTCAATGCTA---TCAACC
*
953 AAAACAGAATTGTTTTCA
1 AAAACAGAATTATTTTCA
971 TCACAATTAG
Statistics
Matches: 70, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
30 20 0.29
31 1 0.01
32 1 0.01
33 48 0.69
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (30 bp):
AAAACAGAATTATTTTCAATGCTATCAACC
Found at i:1043 original size:33 final size:33
Alignment explanation
Indices: 994--1092 Score: 137
Period size: 33 Copynumber: 3.0 Consensus size: 33
984 CCAAAACAGA
994 TTTAGTGTCATTGCAAACAACACTTAAATTAGG
1 TTTAGTGTCATTGCAAACAACACTTAAATTAGG
* * * *
1027 TTTAGTATCATCGCAAACAACA-TCTAAAATAGA
1 TTTAGTGTCATTGCAAACAACACT-TAAATTAGG
*
1060 TTTAGTGTCATTGCAAACAACACTCAAATTAGG
1 TTTAGTGTCATTGCAAACAACACTTAAATTAGG
1093 GGTTGTTTTA
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
32 1 0.02
33 53 0.96
34 1 0.02
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.30
Consensus pattern (33 bp):
TTTAGTGTCATTGCAAACAACACTTAAATTAGG
Found at i:2952 original size:12 final size:12
Alignment explanation
Indices: 2935--2966 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2925 GCCGCGCAAC
*
2935 ACCGGCCACATG
1 ACCGGCCACAGG
2947 ACCGGCCACAGG
1 ACCGGCCACAGG
2959 ACCGGCCA
1 ACCGGCCA
2967 TCGCATGCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.25, C:0.44, G:0.28, T:0.03
Consensus pattern (12 bp):
ACCGGCCACAGG
Found at i:4382 original size:49 final size:49
Alignment explanation
Indices: 4200--4958 Score: 867
Period size: 49 Copynumber: 15.6 Consensus size: 49
4190 CTCAAATGTA
* * * *
4200 AAGACAAATCTGGCACCTTCCGACCGGGAA-GGGCACTTTGGGAATAAATT
1 AAGA-AAA-CTGGGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAATG
* * * *
4250 AGGAAAAGTGGGACCTTCCGACCGGGAAGGGGTATTTTTGGAGTAAATG
1 AAGAAAACTGGGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAATG
* ** * * *
4299 ACG-AAA-T-GGACCTTCCGATTGGGAAAGGGCATTTTTAGAGTAAATG
1 AAGAAAACTGGGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAATG
* * * *
4345 AGGAAAACTGGGATCTTCCGACCGGGAAGGGGTATTTTTGGAATAAGTG
1 AAGAAAACTGGGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAATG
** *
4394 AAGAAAACTGGGATGTTCAGACCGGGAAGGGGCATTTTTGGAATAAAT-
1 AAGAAAACTGGGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAATG
* * *
4442 AAGGAAAACTGCGACCTTCCGACCGGGAAGGGGCATTTTTGGAGTACATG
1 AA-GAAAACTGGGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAATG
* * *
4492 ACGAAAACTGGGACCTTCCGACCGAGAAGGGGCATTTTTGGAATAATTG
1 AAGAAAACTGGGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAATG
* *
4541 AAGAAAACTGGGACCTTCCGACCAGGAAGGGGCATTTTTGGAATAAGTG
1 AAGAAAACTGGGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAATG
* * *
4590 AAGAAAACTGGAACCTTTCGACCGGGAAGGGGCATTTTTGGAATAAGTG
1 AAGAAAACTGGGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAATG
* * *
4639 AAGAAAA-TTGGACCTTCCGACCGGGAA-GGGTATTTTTGGAATAAGTG
1 AAGAAAACTGGGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAATG
* * *
4686 AAGAAATCT-GGACCTTCCGACCGGGAA-GGGTATTTTTGGAATAAGTG
1 AAGAAAACTGGGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAATG
* *
4733 AAGAAAACTGGGACCTTCCGACCGGGAAGGGGCATTTTTGGAGTAACTG
1 AAGAAAACTGGGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAATG
* * * * *
4782 AGGAAAATTAGGACCTTCCGATCGGGAAGGGGCATTTTTGGAGTAAATG
1 AAGAAAACTGGGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAATG
* * * ** * * *
4831 -AGAAAAACTAGGACCTTTCGACCGAGAATCGGTATTTTTCGAATAAA-C
1 AAG-AAAACTGGGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAATG
* **
4879 AAGGAAAACTGGGACCTTCCGACCGGGAA-GGGCATTTTTTGAATAAGGG
1 AA-GAAAACTGGGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAATG
* *
4928 AAGAAAACTCGGACTTTCCGACCGGGAAGGG
1 AAGAAAACTGGGACCTTCCGACCGGGAAGGG
4959 CAAAATAGGA
Statistics
Matches: 613, Mismatches: 82, Indels: 29
0.85 0.11 0.04
Matches are distributed among these distances:
46 36 0.06
47 75 0.12
48 100 0.16
49 397 0.65
50 5 0.01
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.22
Consensus pattern (49 bp):
AAGAAAACTGGGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAATG
Found at i:10332 original size:15 final size:15
Alignment explanation
Indices: 10312--10361 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
10302 CATTTTAGAT
10312 TAATTGCTTTCTTTA
1 TAATTGCTTTCTTTA
* *
10327 TAATTGGTAT-TTT-
1 TAATTGCTTTCTTTA
*
10340 TAATCTTCTTTCTTTA
1 TAAT-TGCTTTCTTTA
10356 TAATTG
1 TAATTG
10362 GTAGTTTAAG
Statistics
Matches: 26, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
13 4 0.15
14 6 0.23
15 12 0.46
16 4 0.15
ACGTcount: A:0.22, C:0.10, G:0.08, T:0.60
Consensus pattern (15 bp):
TAATTGCTTTCTTTA
Found at i:11640 original size:33 final size:33
Alignment explanation
Indices: 11597--11663 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
11587 GTTATGCGCG
*
11597 GATGGCCCATGCAATGCCCGGTTGTGGCCGGTT
1 GATGCCCCATGCAATGCCCGGTTGTGGCCGGTT
* * *
11630 GATGCCCCATGCGATGGCTGGTTGTGGCCGGTT
1 GATGCCCCATGCAATGCCCGGTTGTGGCCGGTT
11663 G
1 G
11664 CTCCATGCGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.10, C:0.25, G:0.39, T:0.25
Consensus pattern (33 bp):
GATGCCCCATGCAATGCCCGGTTGTGGCCGGTT
Found at i:11672 original size:30 final size:32
Alignment explanation
Indices: 11602--11677 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 32
11592 GCGCGGATGG
* * *
11602 CCCATGCAATGCCCGGTTGTGGCCGGTTGATGC
1 CCCATGCGATGGCTGGTTGTGGCCGGTT-ATGC
11635 CCCATGCGATGGCTGGTTGTGGCCGG-T-TGC
1 CCCATGCGATGGCTGGTTGTGGCCGGTTATGC
*
11665 TCCATGCGATGGC
1 CCCATGCGATGGC
11678 GAATGCGATG
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
30 15 0.38
32 1 0.03
33 23 0.59
ACGTcount: A:0.11, C:0.29, G:0.36, T:0.25
Consensus pattern (32 bp):
CCCATGCGATGGCTGGTTGTGGCCGGTTATGC
Done.