Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008275.1 Corchorus capsularis cultivar CVL-1 contig08296, 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: 22291
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:1185 original size:9 final size:9
Alignment explanation
Indices: 1171--1202 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
1161 CAGACCAAGA
1171 AAATTAGTT
1 AAATTAGTT
1180 AAATTAGTT
1 AAATTAGTT
*
1189 AAAATAGTT
1 AAATTAGTT
1198 AAATT
1 AAATT
1203 GATAAGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (9 bp):
AAATTAGTT
Found at i:3868 original size:13 final size:12
Alignment explanation
Indices: 3843--3867 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3833 AAGGAAATAG
3843 TGGTAGTTTTTT
1 TGGTAGTTTTTT
3855 TGGTAGTTTTTT
1 TGGTAGTTTTTT
3867 T
1 T
3868 TTTGGCATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (12 bp):
TGGTAGTTTTTT
Found at i:3869 original size:15 final size:15
Alignment explanation
Indices: 3849--3895 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 15
3839 ATAGTGGTAG
3849 TTTTTTTGGTAGTTT
1 TTTTTTTGGTAGTTT
3864 TTTTTTTGGCATAAG-TT
1 TTTTTTTGG--T-AGTTT
3881 TTTTTTTGGTAGTTT
1 TTTTTTTGGTAGTTT
3896 AAAGAGTGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 2 0.07
15 12 0.43
17 12 0.43
18 2 0.07
ACGTcount: A:0.11, C:0.02, G:0.19, T:0.68
Consensus pattern (15 bp):
TTTTTTTGGTAGTTT
Found at i:5571 original size:12 final size:13
Alignment explanation
Indices: 5549--5577 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
5539 ACATGAATTT
5549 TTTTTTAAATAAA
1 TTTTTTAAATAAA
5562 TTTTTT-AATAAA
1 TTTTTTAAATAAA
5574 TTTT
1 TTTT
5578 ATTTTTCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTTTAAATAAA
Found at i:6718 original size:18 final size:18
Alignment explanation
Indices: 6695--6731 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
6685 ATTCAATTTT
6695 AAGGTTAAGATTTAGTTA
1 AAGGTTAAGATTTAGTTA
6713 AAGGTTAAGATTTAGTTA
1 AAGGTTAAGATTTAGTTA
6731 A
1 A
6732 GGTAATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (18 bp):
AAGGTTAAGATTTAGTTA
Found at i:13806 original size:31 final size:31
Alignment explanation
Indices: 13768--13903 Score: 127
Period size: 31 Copynumber: 4.5 Consensus size: 31
13758 ATTGGCTCAT
*
13768 TGCTCAAATAAGGGATTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGACTAACGTTTGCCAAAA
** ** **
13799 TGCTCAAATAA-GGA-TATGGTATT-TTAATT
1 TGCTCAAATAAGGGACTAACGT-TTGCCAAAA
*
13828 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGACTAACGTTTGCCAAAA
* * *
13859 TGCTTAAATAATGGCCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGACTAACGTTTGCCAAAA
13890 TGCTCAAATAAGGG
1 TGCTCAAATAAGGG
13904 TCCGTCTCAC
Statistics
Matches: 82, Mismatches: 17, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
29 14 0.17
30 13 0.16
31 55 0.67
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (31 bp):
TGCTCAAATAAGGGACTAACGTTTGCCAAAA
Found at i:14012 original size:60 final size:60
Alignment explanation
Indices: 13936--14098 Score: 256
Period size: 60 Copynumber: 2.7 Consensus size: 60
13926 CTGACACCAA
* **
13936 GCCCTTATTTGAGCATTTTCGATAACGTTAGGCCTTTATTTGGCCAAATTAAAAGATCGG
1 GCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGAACAAATTAAAAGATCGG
*
13996 GCCCTTATTTAAGCATTTTCGATAACGTTAGGCCCTTATTTGAACAAATTAAAAGATCGG
1 GCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGAACAAATTAAAAGATCGG
* *
14056 ACCCTTATTTGAGCATTTTGGCA-AACGTTAGGCCCTTATTTGA
1 GCCCTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTTGA
14099 GCATTTTGTT
Statistics
Matches: 95, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
60 94 0.99
61 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (60 bp):
GCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGAACAAATTAAAAGATCGG
Found at i:14031 original size:31 final size:29
Alignment explanation
Indices: 13995--14106 Score: 93
Period size: 31 Copynumber: 3.7 Consensus size: 29
13985 TAAAAGATCG
13995 GGCCCTTATTTAAGCATTTTCGATAACGTTA
1 GGCCCTTATTTAAGCATTTT-GA-AACGTTA
** * * *
14026 GGCCCTTATTTGAA-CAAATT-AAAAGATC
1 GGCCCTTATTT-AAGCATTTTGAAACGTTA
*
14054 GGACCCTTATTTGAGCATTTTGGCAAACGTTA
1 GG-CCCTTATTTAAGCATTTT-G-AAACGTTA
*
14086 GGCCCTTATTTGAGCATTTTG
1 GGCCCTTATTTAAGCATTTTG
14107 TTAACTGCTA
Statistics
Matches: 64, Mismatches: 11, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
28 7 0.11
29 14 0.22
30 1 0.02
31 33 0.52
32 9 0.14
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (29 bp):
GGCCCTTATTTAAGCATTTTGAAACGTTA
Found at i:17769 original size:12 final size:13
Alignment explanation
Indices: 17728--17772 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
17718 AATTATTGTT
17728 TGCTTTATTAATC
1 TGCTTTATTAATC
*
17741 TGCTTTATTAATT
1 TGCTTTATTAATC
17754 TGCTTTA-TAATC
1 TGCTTTATTAATC
17766 TGCTTTA
1 TGCTTTA
17773 GATTTAGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56
Consensus pattern (13 bp):
TGCTTTATTAATC
Found at i:17780 original size:6 final size:6
Alignment explanation
Indices: 17769--17795 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
17759 TATAATCTGC
17769 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
17796 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:17844 original size:14 final size:15
Alignment explanation
Indices: 17816--17848 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
17806 ATTTTTAGTT
*
17816 TAATTGTTTTCTTCA
1 TAATTGTTATCTTCA
17831 TAATTGTTAT-TTCA
1 TAATTGTTATCTTCA
17845 TAAT
1 TAAT
17849 CCCTGTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.27, C:0.09, G:0.06, T:0.58
Consensus pattern (15 bp):
TAATTGTTATCTTCA
Found at i:18245 original size:38 final size:35
Alignment explanation
Indices: 18172--18251 Score: 88
Period size: 36 Copynumber: 2.1 Consensus size: 35
18162 TAAAATTAGG
18172 GTTTCCGATTTTTCTTTAAAAAAAATTTAATTTTTCT
1 GTTTCCG--TTTTCTTTAAAAAAAATTTAATTTTTCT
* **
18209 TTTTCCGTTTTCTTTTAAAAAAAATATTTTTATTTTCT
1 GTTTCCGTTTTC-TTTAAAAAAAAT-TTAAT-TTTTCT
18247 GTTTC
1 GTTTC
18252 TGCTTTTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
35 5 0.14
36 12 0.33
37 9 0.25
38 10 0.28
ACGTcount: A:0.26, C:0.11, G:0.05, T:0.57
Consensus pattern (35 bp):
GTTTCCGTTTTCTTTAAAAAAAATTTAATTTTTCT
Done.