Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011170.1 Corchorus capsularis cultivar CVL-1 contig11191, 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: 25136
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:42 original size:32 final size:32
Alignment explanation
Indices: 1--81 Score: 117
Period size: 32 Copynumber: 2.5 Consensus size: 32
* *
1 TCCCACCGGGGCGGCCTGCTGTGGCGAAGCCG
1 TCCCACCGGGGCGGCCTACCGTGGCGAAGCCG
*
33 TCCCACCGGGGCGGCCTACCGTGGTGAAGCCG
1 TCCCACCGGGGCGGCCTACCGTGGCGAAGCCG
* *
65 CCCCACTGGGGCGGCCT
1 TCCCACCGGGGCGGCCT
82 TTTCATGGTG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.10, C:0.40, G:0.38, T:0.12
Consensus pattern (32 bp):
TCCCACCGGGGCGGCCTACCGTGGCGAAGCCG
Found at i:96 original size:33 final size:32
Alignment explanation
Indices: 2--112 Score: 114
Period size: 32 Copynumber: 3.4 Consensus size: 32
1 T
* * ** * *
2 CCCACCGGGGCGGCCTGCTGTGGCGAAGCCGT
1 CCCACTGGGGCGGCCTACCATGGTGAAGCCGC
* *
34 CCCACCGGGGCGGCCTACCGTGGTGAAGCCGC
1 CCCACTGGGGCGGCCTACCATGGTGAAGCCGC
**
66 CCCACTGGGGCGGCCTTTTCATGGTGAAGCCGC
1 CCCACTGGGGCGGCC-TACCATGGTGAAGCCGC
*
99 CCCAGTGGGGCGGC
1 CCCACTGGGGCGGC
113 TTCGCCACGG
Statistics
Matches: 69, Mismatches: 9, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
32 42 0.61
33 27 0.39
ACGTcount: A:0.11, C:0.37, G:0.39, T:0.14
Consensus pattern (32 bp):
CCCACTGGGGCGGCCTACCATGGTGAAGCCGC
Found at i:225 original size:42 final size:42
Alignment explanation
Indices: 177--257 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
167 CGTCAAAAAT
**
177 TTCATTTTTCTGAAATCGTCATCAAAATACGGCACGTTATCG
1 TTCATTTTTCTGAAATCGTCATCAAAATACAACACGTTATCG
*
219 TTCATTTTTCTTAAATCGTCATCAAAATACAACACGTTA
1 TTCATTTTTCTGAAATCGTCATCAAAATACAACACGTTA
258 ACGCTATTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.37
Consensus pattern (42 bp):
TTCATTTTTCTGAAATCGTCATCAAAATACAACACGTTATCG
Found at i:17485 original size:44 final size:44
Alignment explanation
Indices: 17435--17519 Score: 161
Period size: 44 Copynumber: 1.9 Consensus size: 44
17425 AACTGGCGTT
*
17435 AACATGGACTAATAATAACCTTTTCTTGCTAAATGTTTCAAGTA
1 AACATGGACTAACAATAACCTTTTCTTGCTAAATGTTTCAAGTA
17479 AACATGGACTAACAATAACCTTTTCTTGCTAAATGTTTCAA
1 AACATGGACTAACAATAACCTTTTCTTGCTAAATGTTTCAA
17520 CCAAGATCAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (44 bp):
AACATGGACTAACAATAACCTTTTCTTGCTAAATGTTTCAAGTA
Found at i:20646 original size:49 final size:48
Alignment explanation
Indices: 20584--20744 Score: 120
Period size: 49 Copynumber: 3.4 Consensus size: 48
20574 GATTTCAGAT
*
20584 TAAATAAGATATAATGTGATTGTTCAATATTGGGAACTTGTATCATTA
1 TAAAGAAGATATAATGTGATTGTTCAATATTGGGAACTTGTATCATTA
* *** * * *
20632 TAAAGAAGATTATAATGTATTACTTGTTTTCTCTT-TG-A-TT-TCA-GATTA
1 TAAAGAAGA-TATAATG--TGA-TTGTTCAATATTGGGAACTTGT-ATCATTA
* *
20680 -AACG-AGATATAATGTGATTGTTCAGTATTGGGAACTTGTATCATTA
1 TAAAGAAGATATAATGTGATTGTTCAATATTGGGAACTTGTATCATTA
*
20726 TAAAGAAGATTATATTGTG
1 TAAAGAAGA-TATAATGTG
20745 TTACTTGTTT
Statistics
Matches: 82, Mismatches: 18, Indels: 25
0.66 0.14 0.20
Matches are distributed among these distances:
42 8 0.10
43 3 0.04
44 1 0.01
45 10 0.12
46 8 0.10
47 6 0.07
48 16 0.20
49 18 0.22
50 1 0.01
51 3 0.04
52 8 0.10
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.41
Consensus pattern (48 bp):
TAAAGAAGATATAATGTGATTGTTCAATATTGGGAACTTGTATCATTA
Found at i:20696 original size:94 final size:94
Alignment explanation
Indices: 20571--20755 Score: 325
Period size: 94 Copynumber: 2.0 Consensus size: 94
20561 ATATGACCTG
*
20571 TTTGATTTCAGATTAAATAAGATATAATGTGATTGTTCAATATTGGGAACTTGTATCATTATAAA
1 TTTGATTTCAGATTAAACAAGATATAATGTGATTGTTCAATATTGGGAACTTGTATCATTATAAA
20636 GAAGATTATAATGTATTACTTGTTTTCTC
66 GAAGATTATAATGTATTACTTGTTTTCTC
* *
20665 TTTGATTTCAGATTAAACGAGATATAATGTGATTGTTCAGTATTGGGAACTTGTATCATTATAAA
1 TTTGATTTCAGATTAAACAAGATATAATGTGATTGTTCAATATTGGGAACTTGTATCATTATAAA
* *
20730 GAAGATTATATTGTGTTACTTGTTTT
66 GAAGATTATAATGTATTACTTGTTTT
20756 AAAAAAAATT
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
94 86 1.00
ACGTcount: A:0.32, C:0.07, G:0.17, T:0.44
Consensus pattern (94 bp):
TTTGATTTCAGATTAAACAAGATATAATGTGATTGTTCAATATTGGGAACTTGTATCATTATAAA
GAAGATTATAATGTATTACTTGTTTTCTC
Found at i:21566 original size:1 final size:1
Alignment explanation
Indices: 21560--21593 Score: 59
Period size: 1 Copynumber: 34.0 Consensus size: 1
21550 ATGCTTTAGC
*
21560 TTTTTTTTTTTTTTTTTTTTTTTATTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
21594 GTTCTAATGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.03, C:0.00, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Done.