Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005463.1 Corchorus capsularis cultivar CVL-1 contig05481, 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: 18656
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Found at i:62 original size:18 final size:19
Alignment explanation
Indices: 30--65 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
20 AACTACTAAA
*
30 TAATAAATAATACTAATAT
1 TAATAAATAACACTAATAT
49 TAAT-AATAACACTAATA
1 TAATAAATAACACTAATA
66 ATTATTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (19 bp):
TAATAAATAACACTAATAT
Found at i:314 original size:24 final size:24
Alignment explanation
Indices: 284--330 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
274 AGTTAAAAAT
*
284 TTAGAAAGTTATG-AATGATTTGAA
1 TTAGAAAATTA-GAAATGATTTGAA
308 TTAGAAAATTAGAAATGATTTGA
1 TTAGAAAATTAGAAATGATTTGA
331 GAGAATTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.45, C:0.00, G:0.19, T:0.36
Consensus pattern (24 bp):
TTAGAAAATTAGAAATGATTTGAA
Found at i:2503 original size:22 final size:23
Alignment explanation
Indices: 2468--2514 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
2458 GTATTTAATC
*
2468 ATAAATTAACTAATTAAA-ACTA
1 ATAAACTAACTAATTAAATACTA
*
2490 ATAAACTAAGTAATTAAATACTA
1 ATAAACTAACTAATTAAATACTA
2513 AT
1 AT
2515 TAATTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (23 bp):
ATAAACTAACTAATTAAATACTA
Found at i:2526 original size:22 final size:22
Alignment explanation
Indices: 2479--2527 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
2469 TAAATTAACT
*
2479 AATTAAAACTAATAAACTAAGT
1 AATTAAAACTAATAAACTAAGA
* *
2501 AATTAAATACTAATTAATTAA-A
1 AATTAAA-ACTAATAAACTAAGA
2523 AATTA
1 AATTA
2528 TTTTTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (22 bp):
AATTAAAACTAATAAACTAAGA
Found at i:2589 original size:32 final size:32
Alignment explanation
Indices: 2553--2677 Score: 146
Period size: 32 Copynumber: 3.9 Consensus size: 32
2543 AATTGGCTTT
* * *
2553 GCCGCCCATTTTGGGAGGCATGCCATGGGCAA
1 GCCGCCCAATTTGGGAGGCCTGCCATGTGCAA
* *
2585 GCCGCCCAATTTGGGCGGCCTACCATGTGCAA
1 GCCGCCCAATTTGGGAGGCCTGCCATGTGCAA
2617 GCCGCCCAATTTGGGCA-GCCT-CCAATGTGCAA
1 GCCGCCCAATTTGGG-AGGCCTGCC-ATGTGCAA
* *
2649 GCCGCCCAATTTGGGCGGCTTGCCCATGT
1 GCCGCCCAATTTGGGAGGCCTG-CCATGT
2678 ACAGTCCTAA
Statistics
Matches: 80, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
31 2 0.03
32 72 0.90
33 4 0.05
34 2 0.03
ACGTcount: A:0.18, C:0.33, G:0.30, T:0.20
Consensus pattern (32 bp):
GCCGCCCAATTTGGGAGGCCTGCCATGTGCAA
Found at i:2657 original size:16 final size:16
Alignment explanation
Indices: 2609--2658 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
2599 GCGGCCTACC
2609 ATGTGCAAGCCGCCCA
1 ATGTGCAAGCCGCCCA
* *
2625 ATTTGGGC-AGCC-TCCA
1 A--TGTGCAAGCCGCCCA
2641 ATGTGCAAGCCGCCCA
1 ATGTGCAAGCCGCCCA
2657 AT
1 AT
2659 TTGGGCGGCT
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
14 4 0.15
15 4 0.15
16 10 0.38
17 4 0.15
18 4 0.15
ACGTcount: A:0.24, C:0.34, G:0.24, T:0.18
Consensus pattern (16 bp):
ATGTGCAAGCCGCCCA
Found at i:2865 original size:21 final size:21
Alignment explanation
Indices: 2841--2884 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2831 CAAAAATGTA
*
2841 AAAAGGGGGGCGGTATTTTGC
1 AAAAGGGGGGCGGTATTTAGC
*
2862 AAAAGGGGGGCGGTGTTTAGC
1 AAAAGGGGGGCGGTATTTAGC
2883 AA
1 AA
2885 TCCAGTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.09, G:0.43, T:0.20
Consensus pattern (21 bp):
AAAAGGGGGGCGGTATTTAGC
Found at i:3135 original size:23 final size:21
Alignment explanation
Indices: 3109--3152 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
3099 AAAAAATATT
*
3109 TTTTGAAAAATTTAAGTTTTAAA
1 TTTTCAAAAATTT-A-TTTTAAA
*
3132 TTTTCCAAAATTTATTTTAAA
1 TTTTCAAAAATTTATTTTAAA
3153 AAATTATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
22 1 0.05
23 11 0.58
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (21 bp):
TTTTCAAAAATTTATTTTAAA
Found at i:4866 original size:4 final size:5
Alignment explanation
Indices: 4841--4872 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
4831 GTAGTGAGTG
4841 TTAAA TTAAA TTAAA TTAAA -TAAA -TAAA TTAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAA
4873 TGAGTATGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 8 0.31
5 18 0.69
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
TTAAA
Found at i:18305 original size:131 final size:131
Alignment explanation
Indices: 18071--18323 Score: 506
Period size: 131 Copynumber: 1.9 Consensus size: 131
18061 TGAGCTATAG
18071 TAGCGTGCTAAATATAGCGTCGTACTGTAGCAACGTAATTTTTATGTTTTTGGGGGGAACCATAG
1 TAGCGTGCTAAATATAGCGTCGTACTGTAGCAACGTAATTTTTATGTTTTTGGGGGGAACCATAG
18136 TTTGCCGTGTTCATTGGATTGGAAATTTGTGGATTTTTGCACCATTTTGGTGTTTTGCGGTGTTC
66 TTTGCCGTGTTCATTGGATTGGAAATTTGTGGATTTTTGCACCATTTTGGTGTTTTGCGGTGTTC
18201 A
131 A
18202 TAGCGTGCTAAATATAGCGTCGTACTGTAGCAACGTAATTTTTATGTTTTTGGGGGGAACCATAG
1 TAGCGTGCTAAATATAGCGTCGTACTGTAGCAACGTAATTTTTATGTTTTTGGGGGGAACCATAG
18267 TTTGCCGTGTTCATTGGATTGGAAATTTGTGGATTTTTGCACCATTTTGGTGTTTTG
66 TTTGCCGTGTTCATTGGATTGGAAATTTGTGGATTTTTGCACCATTTTGGTGTTTTG
18324 AGGTACTGTA
Statistics
Matches: 122, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
131 122 1.00
ACGTcount: A:0.20, C:0.13, G:0.26, T:0.41
Consensus pattern (131 bp):
TAGCGTGCTAAATATAGCGTCGTACTGTAGCAACGTAATTTTTATGTTTTTGGGGGGAACCATAG
TTTGCCGTGTTCATTGGATTGGAAATTTGTGGATTTTTGCACCATTTTGGTGTTTTGCGGTGTTC
A
Done.