Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014922.1 Corchorus capsularis cultivar CVL-1 contig14943, 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: 10931
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Found at i:357 original size:25 final size:25
Alignment explanation
Indices: 323--372 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
313 CAAAAAATGA
*
323 CATGATATGAAA-CTCAAACCCTAAC
1 CATGACATGAAAGCT-AAACCCTAAC
*
348 CATGACATGAAAGCTAAACTCTAAC
1 CATGACATGAAAGCTAAACCCTAAC
373 ATGTCATCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.44, C:0.26, G:0.10, T:0.20
Consensus pattern (25 bp):
CATGACATGAAAGCTAAACCCTAAC
Found at i:2671 original size:1 final size:1
Alignment explanation
Indices: 2665--2694 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
2655 CCCAAGTATT
2665 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2695 TAAACTAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3777 original size:31 final size:31
Alignment explanation
Indices: 3742--3800 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
3732 AAAGTGGAGC
3742 TATATATATATATATAAACAATATGTTGATA
1 TATATATATATATATAAACAATATGTTGATA
3773 TATATATATATATATAAACAATATGTTG
1 TATATATATATATATAAACAATATGTTG
3801 CTCTCGTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (31 bp):
TATATATATATATATAAACAATATGTTGATA
Found at i:4265 original size:15 final size:16
Alignment explanation
Indices: 4231--4287 Score: 64
Period size: 15 Copynumber: 3.7 Consensus size: 16
4221 GGCAATTGGG
* **
4231 CGGGTTCGGGCAGGTT
1 CGGGTTCGGGTATTTT
*
4247 CGGGTTTGGGTA-TTT
1 CGGGTTCGGGTATTTT
4262 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
4278 CGGG-TCGGGT
1 CGGGTTCGGGT
4288 TTGGGTTCGG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
15 19 0.53
16 17 0.47
ACGTcount: A:0.05, C:0.14, G:0.46, T:0.35
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:4280 original size:16 final size:15
Alignment explanation
Indices: 4231--4298 Score: 63
Period size: 15 Copynumber: 4.7 Consensus size: 15
4221 GGCAATTGGG
* *
4231 CGGGTTCGGGCAGGTT
1 CGGGTTCGGGTA-TTT
*
4247 CGGGTTTGGGTATTT
1 CGGGTTCGGGTATTT
4262 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTA-TTT
4278 CGGG-TCGGG--TTT
1 CGGGTTCGGGTATTT
4290 -GGGTTCGGG
1 CGGGTTCGGG
4299 CCCGGGTCGG
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
11 3 0.07
12 8 0.17
15 18 0.39
16 17 0.37
ACGTcount: A:0.04, C:0.13, G:0.47, T:0.35
Consensus pattern (15 bp):
CGGGTTCGGGTATTT
Found at i:5102 original size:16 final size:17
Alignment explanation
Indices: 5075--5107 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
5065 TCAGGTCGAG
5075 TCGGGTCGGGTTCGGGT
1 TCGGGTCGGGTTCGGGT
5092 TCGGG-CGGGTTCGGGT
1 TCGGGTCGGGTTCGGGT
5108 ATTTTCGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.00, C:0.18, G:0.55, T:0.27
Consensus pattern (17 bp):
TCGGGTCGGGTTCGGGT
Found at i:5116 original size:16 final size:17
Alignment explanation
Indices: 5097--5135 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
5087 CGGGTTCGGG
5097 CGGGTTCGGGT-ATTTT
1 CGGGTTCGGGTAATTTT
5113 CGGGTTCGGGTAATTTT
1 CGGGTTCGGGTAATTTT
5130 -GGGTTC
1 CGGGTTC
5136 AGGTTCGGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.08, C:0.13, G:0.38, T:0.41
Consensus pattern (17 bp):
CGGGTTCGGGTAATTTT
Found at i:9787 original size:27 final size:26
Alignment explanation
Indices: 9757--9849 Score: 87
Period size: 26 Copynumber: 3.5 Consensus size: 26
9747 TTCCTCAATA
**
9757 AAAAGAATACATTTTTTTTTTAGAAAC
1 AAAAGAATA-ATTTTTTTTGAAGAAAC
*
9784 AAAAGAATAACTTTCTTTTTGAAGAAAG
1 AAAAGAATAA-TTT-TTTTTGAAGAAAC
* * *
9812 AAAAGAACAAATTTTTTTGAAGTAAC
1 AAAAGAATAATTTTTTTTGAAGAAAC
* *
9838 CAAAGAACAATT
1 AAAAGAATAATT
9850 ATTCTTCAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
26 22 0.40
27 14 0.25
28 19 0.35
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.32
Consensus pattern (26 bp):
AAAAGAATAATTTTTTTTGAAGAAAC
Found at i:9802 original size:28 final size:27
Alignment explanation
Indices: 9757--9844 Score: 81
Period size: 28 Copynumber: 3.3 Consensus size: 27
9747 TTCCTCAATA
**
9757 AAAAGAATACATTTTTTTTTTAGAAAC
1 AAAAGAATACATTTTTTTTGAAGAAAC
*
9784 AAAAGAATA-ACTTTCTTTTTGAAGAAAG
1 AAAAGAATACA-TTT-TTTTTGAAGAAAC
* * *
9812 AAAAGAACA-AATTTTTTTGAAGTAAC
1 AAAAGAATACATTTTTTTTGAAGAAAC
*
9838 CAAAGAA
1 AAAAGAA
9845 CAATTATTCT
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
26 18 0.35
27 14 0.27
28 19 0.37
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (27 bp):
AAAAGAATACATTTTTTTTGAAGAAAC
Done.