Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013952.1 Corchorus capsularis cultivar CVL-1 contig13973, 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: 22168
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:1140 original size:64 final size:64
Alignment explanation
Indices: 940--1219 Score: 314
Period size: 64 Copynumber: 4.3 Consensus size: 64
930 GACATGTCCA
* * * * *
940 AAAGGGCGTTTTGGGAAAACTAGAACCTCA-ATGCAAGAATGTGACAAAACCAACCCTTTGTCCG
1 AAAGGGCGTTTTGGGAAAACTAGAACCT-AGATGCAGGAATATGAAAAAACTAACCCTTTGTCTG
** * * * * **
1004 AAAGGGTATTTTGGGAATCGAA-AATGTTAAACTTAGATGCTA-GAATGTGACAAAACTGGCCCT
1 AAAGGGCGTTTTGGGAA---AACTA-G---AACCTAGATGC-AGGAATATGAAAAAACTAACCCT
1067 TTGTCTG
58 TTGTCTG
*
1074 AAAGGGCGTTTTGGGAAAACTAGAACCTAGATGCAGGAATATGAAAAAACTAACCCTTTGTTTG
1 AAAGGGCGTTTTGGGAAAACTAGAACCTAGATGCAGGAATATGAAAAAACTAACCCTTTGTCTG
*
1138 AAAGGGCGTTTTGGGAAAACTAGAACCTAAATGCAGGAATATGAAAAAACTAACCCTTTGTCTG
1 AAAGGGCGTTTTGGGAAAACTAGAACCTAGATGCAGGAATATGAAAAAACTAACCCTTTGTCTG
*
1202 AAAGAGCGTTTTGGGAAA
1 AAAGGGCGTTTTGGGAAA
1220 CTGAAAATGT
Statistics
Matches: 185, Mismatches: 20, Indels: 22
0.81 0.09 0.10
Matches are distributed among these distances:
63 1 0.01
64 127 0.69
66 1 0.01
67 6 0.03
68 1 0.01
69 1 0.01
70 47 0.25
71 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (64 bp):
AAAGGGCGTTTTGGGAAAACTAGAACCTAGATGCAGGAATATGAAAAAACTAACCCTTTGTCTG
Found at i:4927 original size:27 final size:27
Alignment explanation
Indices: 4889--4956 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
4879 ATCCTAGGGA
*
4889 ACTAACTTTGAATGGGGAACTGT-TTT
1 ACTAACTTTGAATGGAGAACTGTCTTT
* *
4915 GACTAGCTTTGAATGGAGATCTGTCTTT
1 -ACTAACTTTGAATGGAGAACTGTCTTT
*
4943 ACTAACTTGGAATG
1 ACTAACTTTGAATG
4957 AGAGTCTGTG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 32 0.91
28 3 0.09
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (27 bp):
ACTAACTTTGAATGGAGAACTGTCTTT
Found at i:4964 original size:27 final size:27
Alignment explanation
Indices: 4889--4965 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 27
4879 ATCCTAGGGA
* * *
4889 ACTAACTTTGAATGGGGAACTGTTTTG
1 ACTAACTTGGAATGGAGATCTGTTTTG
* *
4916 ACTAGCTTTGAATGGAGATCTGTCTTT-
1 ACTAACTTGGAATGGAGATCTGT-TTTG
4943 ACTAACTTGGAAT-GAGAGTCTGT
1 ACTAACTTGGAATGGAGA-TCTGT
4966 GTCTTTGAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
26 4 0.09
27 36 0.84
28 3 0.07
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.36
Consensus pattern (27 bp):
ACTAACTTGGAATGGAGATCTGTTTTG
Found at i:6788 original size:84 final size:84
Alignment explanation
Indices: 6633--6799 Score: 210
Period size: 84 Copynumber: 2.0 Consensus size: 84
6623 GTGCGACTAT
* * *
6633 TCTGTAGAGCTGGTGGCACTAAAGAACCATGAGTGGCTAGAGAATCAAAACAAATTTCTTGTGAA
1 TCTGTAGAGCTAGTGACACTAAAGAACCATGAGTGGCTAGAGAATCAAAACAAATTTCCTGTGAA
*
6698 ATTAGTGGCACTAAAGAGA
66 AGTAGTGGCACTAAAGAGA
* * * ** * *
6717 TCTGTGGAGCTAGTGACACTAAAGAACCATGAGTGGGC-AGGGAATCAGAATGATTTTCCTGTGG
1 TCTGTAGAGCTAGTGACACTAAAGAACCATGAGT-GGCTAGAGAATCAAAACAAATTTCCTGTGA
*
6781 AAGTAGTGGCACTGAAGAG
65 AAGTAGTGGCACTAAAGAG
6800 GAAGCATTAG
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
84 67 0.96
85 3 0.04
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.23
Consensus pattern (84 bp):
TCTGTAGAGCTAGTGACACTAAAGAACCATGAGTGGCTAGAGAATCAAAACAAATTTCCTGTGAA
AGTAGTGGCACTAAAGAGA
Found at i:9468 original size:27 final size:26
Alignment explanation
Indices: 9394--9469 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 26
9384 ATCCTAGGGA
* *
9394 ACTAACTTTGAATGGGAAACTGTTTTG
1 ACTAACTTTGAAT-GGAATCTGTCTTG
*
9421 ACTAGCTTTGAATGGAGATCTGTCTTG
1 ACTAACTTTGAATGGA-ATCTGTCTTG
*
9448 ACTAACTTGGAATGAGAATCTG
1 ACTAACTTTGAATG-GAATCTG
9470 ACTTTGAATG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 3 0.07
27 37 0.88
28 2 0.05
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (26 bp):
ACTAACTTTGAATGGAATCTGTCTTG
Found at i:12177 original size:11 final size:10
Alignment explanation
Indices: 12159--12192 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
12149 AATTGACTTC
12159 AAATCTTCAA
1 AAATCTTCAA
12169 AATATCTTCAA
1 AA-ATCTTCAA
12180 GAAATCTTCAA
1 -AAATCTTCAA
12191 AA
1 AA
12193 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:13312 original size:24 final size:24
Alignment explanation
Indices: 13283--13329 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
13273 AAACATTCTT
13283 AAAAATTCAAAGCAATC-ATCAATC
1 AAAAA-TCAAAGCAATCGATCAATC
*
13307 AAAAATCAAATCAATCGATCAAT
1 AAAAATCAAAGCAATCGATCAAT
13330 ACATTCATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.55, C:0.19, G:0.04, T:0.21
Consensus pattern (24 bp):
AAAAATCAAAGCAATCGATCAATC
Found at i:18661 original size:11 final size:10
Alignment explanation
Indices: 18643--18676 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
18633 AATTGACTTC
18643 AAATCTTCAA
1 AAATCTTCAA
18653 AATATCTTCAA
1 AA-ATCTTCAA
18664 GAAATCTTCAA
1 -AAATCTTCAA
18675 AA
1 AA
18677 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:19764 original size:16 final size:16
Alignment explanation
Indices: 19740--19770 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19730 TAGTATTGAA
*
19740 TTCGTGTATTTTCGGC
1 TTCGGGTATTTTCGGC
19756 TTCGGGTATTTTCGG
1 TTCGGGTATTTTCGG
19771 GATCAGATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.06, C:0.16, G:0.29, T:0.48
Consensus pattern (16 bp):
TTCGGGTATTTTCGGC
Done.