Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007293.1 Corchorus capsularis cultivar CVL-1 contig07314, 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: 33006
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2163 original size:24 final size:22
Alignment explanation
Indices: 2101--2161 Score: 86
Period size: 24 Copynumber: 2.7 Consensus size: 22
2091 TAAACCCAAT
2101 TTTTTTTTTAAAAAAGAGCTAA
1 TTTTTTTTTAAAAAAGAGCTAA
* *
2123 TTATTATTTTTTAAAAATAGCTAA
1 TT-TT-TTTTTAAAAAAGAGCTAA
2147 TTTTTTTTTAAAAAA
1 TTTTTTTTTAAAAAA
2162 AAATATAGCC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 12 0.35
23 4 0.12
24 18 0.53
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (22 bp):
TTTTTTTTTAAAAAAGAGCTAA
Found at i:2939 original size:106 final size:106
Alignment explanation
Indices: 2670--3004 Score: 553
Period size: 106 Copynumber: 3.1 Consensus size: 106
2660 GAATTGATTA
* * * * **
2670 TATATTGTATTTCTAAAATCCTATAATAATAAGTCATTAATTTTGAAATTTACCCTCGACATAAA
1 TATATT-TATTTCTAAAACCCTATAATAATAAATTATTAATTTTGGAATTTACCCTTAACATAAA
* * * *
2735 ATTATAATTTTAATTTGGGGTTAAATTTAGTGAAATTAGTTT
65 ATTATAATTTTAATTTGGAGCTAAACTTAGTGAAACTAGTTT
2777 TATATTTTATTTCTAAAACCCTATAATAATAAATTATTAATTTTGGAATTTACCCTTAACATAAA
1 TATA-TTTATTTCTAAAACCCTATAATAATAAATTATTAATTTTGGAATTTACCCTTAACATAAA
2842 ATTATAATTTTAATTTGGAGCTAAACTTAGTGAAACTAGTTT
65 ATTATAATTTTAATTTGGAGCTAAACTTAGTGAAACTAGTTT
*
2884 TATATTTATTTCTAAAACCCTATAACAATAAATTATTAATTTTGGAATTTACCCTTAACATAAAA
1 TATATTTATTTCTAAAACCCTATAATAATAAATTATTAATTTTGGAATTTACCCTTAACATAAAA
2949 TTATAATTTTAATTTGGAGCTAAACTTAGTGAAACTAGTTT
66 TTATAATTTTAATTTGGAGCTAAACTTAGTGAAACTAGTTT
2990 TATATTTATTTCTAA
1 TATATTTATTTCTAA
3005 TTACTCTTAA
Statistics
Matches: 216, Mismatches: 11, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
106 116 0.54
107 98 0.45
108 2 0.01
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.44
Consensus pattern (106 bp):
TATATTTATTTCTAAAACCCTATAATAATAAATTATTAATTTTGGAATTTACCCTTAACATAAAA
TTATAATTTTAATTTGGAGCTAAACTTAGTGAAACTAGTTT
Found at i:7615 original size:20 final size:20
Alignment explanation
Indices: 7590--7627 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
7580 ATTATTGATG
*
7590 TGTTAAGTGGGTTTTTAATA
1 TGTTAAGTGGGTTCTTAATA
7610 TGTTAAGTGGGTTCTTAA
1 TGTTAAGTGGGTTCTTAA
7628 GACATCTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.03, G:0.26, T:0.47
Consensus pattern (20 bp):
TGTTAAGTGGGTTCTTAATA
Found at i:16012 original size:22 final size:22
Alignment explanation
Indices: 15984--16028 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
15974 AAAACCGAAT
15984 TGAAACCATCTAGTGGTTAAGG
1 TGAAACCATCTAGTGGTTAAGG
16006 TGAAACCATCTAGTGGTTAAGG
1 TGAAACCATCTAGTGGTTAAGG
16028 T
1 T
16029 TCCAGTTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (22 bp):
TGAAACCATCTAGTGGTTAAGG
Found at i:16522 original size:1 final size:1
Alignment explanation
Indices: 16516--16548 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
16506 TTCACACTTT
16516 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
16549 TCTTTTTGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:16783 original size:2 final size:2
Alignment explanation
Indices: 16778--16803 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16768 TTTTTTTACA
16778 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
16804 TCATAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23830 original size:104 final size:104
Alignment explanation
Indices: 23648--23857 Score: 366
Period size: 104 Copynumber: 2.0 Consensus size: 104
23638 CAGAATAAAA
*
23648 ATATTTATATTGAATTATTAAAGTAGATCAATATGTTTAGCTCTATTTACAGTATTCTGATTTCT
1 ATATTTATATTGAATTATTAAAGTAGATCAATATGTTTAGCTCTATTTACAGTATTCTAATTTCT
* *
23713 TCAATGCTTTTTTACACTGTCTTTCAACTTTCAAAATCT
66 TCAATGCTGTTTTACACTGTCTTTCAACTTTCAAAACCT
* *
23752 ATATTTATATTGAATTATTAATGTAGATCAATATGTTTAGCTTTATTTACAGTATTCTAATTTCT
1 ATATTTATATTGAATTATTAAAGTAGATCAATATGTTTAGCTCTATTTACAGTATTCTAATTTCT
*
23817 TCAATGCTGTTTTACGCTGTCTTTCAACTTTCAAAACCT
66 TCAATGCTGTTTTACACTGTCTTTCAACTTTCAAAACCT
23856 AT
1 AT
23858 CTGCAAAAGC
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
104 100 1.00
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.47
Consensus pattern (104 bp):
ATATTTATATTGAATTATTAAAGTAGATCAATATGTTTAGCTCTATTTACAGTATTCTAATTTCT
TCAATGCTGTTTTACACTGTCTTTCAACTTTCAAAACCT
Found at i:25665 original size:13 final size:13
Alignment explanation
Indices: 25647--25672 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25637 AGCAGAATGC
25647 TGGGGCCTGAGAG
1 TGGGGCCTGAGAG
25660 TGGGGCCTGAGAG
1 TGGGGCCTGAGAG
25673 ATGGTCTCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.54, T:0.15
Consensus pattern (13 bp):
TGGGGCCTGAGAG
Found at i:26664 original size:42 final size:42
Alignment explanation
Indices: 26617--26697 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
26607 AGTTTGTAAT
*
26617 TTGTTTATTTGTGTATTTGGTAGGTAGATGGTTTATTTATGG
1 TTGTTTATTTGTGTATTTGGTAGGTAGATGATTTATTTATGG
26659 TTGTTTATTTGTGTATTTGGTAGGTAGATGATTTATTTA
1 TTGTTTATTTGTGTATTTGGTAGGTAGATGATTTATTTA
26698 CAAACTAGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.56
Consensus pattern (42 bp):
TTGTTTATTTGTGTATTTGGTAGGTAGATGATTTATTTATGG
Done.