Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006487.1 Corchorus capsularis cultivar CVL-1 contig06508, 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: 6190
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Found at i:2833 original size:19 final size:18
Alignment explanation
Indices: 2811--2849 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2801 GTTGAAGTCA
2811 AGTTAATCAATAAAAGTTG
1 AGTTAATCAAT-AAAGTTG
* *
2830 AGTTGATTAATAAAGTTG
1 AGTTAATCAATAAAGTTG
2848 AG
1 AG
2850 GATTATTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.44, C:0.03, G:0.21, T:0.33
Consensus pattern (18 bp):
AGTTAATCAATAAAGTTG
Found at i:3390 original size:5 final size:5
Alignment explanation
Indices: 3374--3403 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
3364 ATCGAAAAAC
3374 ATAAA A-AAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
3404 ATTCGACTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
ATAAA
Found at i:3861 original size:204 final size:204
Alignment explanation
Indices: 3511--3919 Score: 818
Period size: 204 Copynumber: 2.0 Consensus size: 204
3501 GGAAAATATT
3511 TAAAAAAATCAAAAAAATATGTGCTGTTATCGATTTTTTCCAGAAACTAGGGTTCTTAGTTTTGG
1 TAAAAAAATCAAAAAAATATGTGCTGTTATCGATTTTTTCCAGAAACTAGGGTTCTTAGTTTTGG
3576 AAATTTGGGGATTAGGGTTTTCTTGTGCAATTGATCTATTTAGTTGCAACTAATCCTAGTTGTTT
66 AAATTTGGGGATTAGGGTTTTCTTGTGCAATTGATCTATTTAGTTGCAACTAATCCTAGTTGTTT
3641 GTGTAATTGGATCCTTGGATTGCTTTTGCTGTTAATTGTGATTTGATTTGAAGAATTTCAGGTTA
131 GTGTAATTGGATCCTTGGATTGCTTTTGCTGTTAATTGTGATTTGATTTGAAGAATTTCAGGTTA
3706 CAAGCCCTA
196 CAAGCCCTA
3715 TAAAAAAATCAAAAAAATATGTGCTGTTATCGATTTTTTCCAGAAACTAGGGTTCTTAGTTTTGG
1 TAAAAAAATCAAAAAAATATGTGCTGTTATCGATTTTTTCCAGAAACTAGGGTTCTTAGTTTTGG
3780 AAATTTGGGGATTAGGGTTTTCTTGTGCAATTGATCTATTTAGTTGCAACTAATCCTAGTTGTTT
66 AAATTTGGGGATTAGGGTTTTCTTGTGCAATTGATCTATTTAGTTGCAACTAATCCTAGTTGTTT
3845 GTGTAATTGGATCCTTGGATTGCTTTTGCTGTTAATTGTGATTTGATTTGAAGAATTTCAGGTTA
131 GTGTAATTGGATCCTTGGATTGCTTTTGCTGTTAATTGTGATTTGATTTGAAGAATTTCAGGTTA
3910 CAAGCCCTA
196 CAAGCCCTA
3919 T
1 T
3920 TGTATTCAAA
Statistics
Matches: 205, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
204 205 1.00
ACGTcount: A:0.27, C:0.11, G:0.21, T:0.41
Consensus pattern (204 bp):
TAAAAAAATCAAAAAAATATGTGCTGTTATCGATTTTTTCCAGAAACTAGGGTTCTTAGTTTTGG
AAATTTGGGGATTAGGGTTTTCTTGTGCAATTGATCTATTTAGTTGCAACTAATCCTAGTTGTTT
GTGTAATTGGATCCTTGGATTGCTTTTGCTGTTAATTGTGATTTGATTTGAAGAATTTCAGGTTA
CAAGCCCTA
Found at i:5155 original size:33 final size:33
Alignment explanation
Indices: 5113--5221 Score: 157
Period size: 33 Copynumber: 3.3 Consensus size: 33
5103 GTCTTTTAGA
5113 TGTTGTTTGCGATGATACTAAACCTAATTTGAG
1 TGTTGTTTGCGATGATACTAAACCTAATTTGAG
* * * * *
5146 TGTTGTTTGCAATGACACTAAATCT-GTTTTAG
1 TGTTGTTTGCGATGATACTAAACCTAATTTGAG
5178 ATGTTGTTTGCGATGATACTAAACCTAATTTGAG
1 -TGTTGTTTGCGATGATACTAAACCTAATTTGAG
5212 TGTTGTTTGC
1 TGTTGTTTGC
5222 AATAAAACTA
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
32 5 0.08
33 54 0.84
34 5 0.08
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.42
Consensus pattern (33 bp):
TGTTGTTTGCGATGATACTAAACCTAATTTGAG
Found at i:5188 original size:66 final size:66
Alignment explanation
Indices: 5106--5246 Score: 255
Period size: 66 Copynumber: 2.1 Consensus size: 66
5096 GAAAAGAGTC
* *
5106 TTTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGTTGTTTGCAATGACACTAAATCT
1 TTTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGTTGTTTGCAATAAAACTAAATCT
5171 G
66 G
5172 TTTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGTTGTTTGCAATAAAACTAAATCT
1 TTTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGTTGTTTGCAATAAAACTAAATCT
5237 G
66 G
*
5238 TTTTGGATG
1 TTTTAGATG
5247 CTAATTGTGA
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 72 1.00
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.42
Consensus pattern (66 bp):
TTTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGTTGTTTGCAATAAAACTAAATCT
G
Found at i:5296 original size:33 final size:33
Alignment explanation
Indices: 5259--5346 Score: 122
Period size: 33 Copynumber: 2.7 Consensus size: 33
5249 AATTGTGATG
5259 AAAACAATTCTGTTTTGGTTGAACATAGCATTA
1 AAAACAATTCTGTTTTGGTTGAACATAGCATTA
** *
5292 AAAACAATTCTGTTTTGGTTGATTATAGCATTG
1 AAAACAATTCTGTTTTGGTTGAACATAGCATTA
* * *
5325 CAAATAATCCTGTTTTGGTTGA
1 AAAACAATTCTGTTTTGGTTGA
5347 TAGCATTGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (33 bp):
AAAACAATTCTGTTTTGGTTGAACATAGCATTA
Found at i:5352 original size:30 final size:31
Alignment explanation
Indices: 5257--5361 Score: 113
Period size: 33 Copynumber: 3.3 Consensus size: 31
5247 CTAATTGTGA
* *
5257 TGAAAACAATTCTGTTTTGGTTGAACATAGCAT
1 TGAAAATAATCCTGTTTTGGTTG-A-ATAGCAT
* * *
5290 TAAAAACAATTCTGTTTTGGTTGATTATAGCAT
1 TGAAAATAATCCTGTTTTGGTTGA--ATAGCAT
*
5323 TGCAAATAATCCTGTTTTGGTTG-ATAGCAT
1 TGAAAATAATCCTGTTTTGGTTGAATAGCAT
5353 TGAAAATAA
1 TGAAAATAA
5362 ATCTATTTTG
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
30 15 0.23
32 1 0.02
33 48 0.75
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.38
Consensus pattern (31 bp):
TGAAAATAATCCTGTTTTGGTTGAATAGCAT
Found at i:5783 original size:30 final size:30
Alignment explanation
Indices: 5747--5803 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
5737 TCTTCAAGGG
5747 GGAGGGAATGATGCGCCCAAGG-CTTATCAT
1 GGAGGGAATGATGCG-CCAAGGACTTATCAT
5777 GGAGGGAATGATGCGCCAAGGACTTAT
1 GGAGGGAATGATGCGCCAAGGACTTAT
5804 TATGCCTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.28, C:0.18, G:0.35, T:0.19
Consensus pattern (30 bp):
GGAGGGAATGATGCGCCAAGGACTTATCAT
Done.