Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012820.1 Corchorus olitorius cultivar O-4 contig12853, 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: 4887
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Found at i:255 original size:4 final size:4
Alignment explanation
Indices: 240--268 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
230 TGCAATTAGA
240 AATT AA-T AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AATT AA
269 AAAAATACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (4 bp):
AATT
Found at i:2366 original size:2 final size:2
Alignment explanation
Indices: 2361--2399 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
2351 CATGTGTCCT
*
2361 TA TA TA TA TA TA TT TA TA TA TA TA TA TA TA CTA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
2400 AAAGTACGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3583 original size:22 final size:21
Alignment explanation
Indices: 3527--3740 Score: 124
Period size: 22 Copynumber: 9.7 Consensus size: 21
3517 GTCTCTGTGT
*
3527 GGTTATCAAAATTTCATAAGA
1 GGTTATCAAAATTTCATAGGA
* * *
3548 TGATTATTATAATTTCATGAGGA
1 -GGTTATCAAAATTTCAT-AGGA
* * *
3571 GGTTATGAAAATTCCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
* *
3593 GCTTACCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATA-GGA
* *
3615 AGTTATCAAAATTTCATGGGAA
1 GGTTATCAAAATTTCATAGG-A
3637 GGTTATCAAAATTTCATAGTGTA
1 GGTTATCAAAATTTCATAG-G-A
* *
3660 -GTTACCAAAATTTCATAGCATCA
1 GGTTATCAAAATTTCATAG---GA
* ** *
3683 GGTTATTAAAATTTTTTAGAAA
1 GGTTATCAAAATTTCATAG-GA
** *
3705 GGTTATTGAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
*
3727 GGTTATCACAATTT
1 GGTTATCAAAATTT
3741 TCTGGAAAGG
Statistics
Matches: 146, Mismatches: 38, Indels: 16
0.73 0.19 0.08
Matches are distributed among these distances:
21 4 0.03
22 120 0.82
23 7 0.05
24 15 0.10
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGGA
Found at i:3629 original size:66 final size:65
Alignment explanation
Indices: 3523--3676 Score: 186
Period size: 66 Copynumber: 2.3 Consensus size: 65
3513 TCTTGTCTCT
* * * * *
3523 GTGTGGTTATCAAAATTTCATAAGATGATTATTATAATTTCATGAGG-AGGTTATGAAAATTCCA
1 GTGT-GTTACCAAAATTTCATAAGAAGATTATCAAAATTTCATG-GGAAGGTTATCAAAATTCCA
3587 TA
64 TA
* *
3589 GTGTGCTTACCAAAATTTCATATGGAAG-TTATCAAAATTTCATGGGAAGGTTATCAAAATTTCA
1 GTGTG-TTACCAAAATTTCATA-AGAAGATTATCAAAATTTCATGGGAAGGTTATCAAAATTCCA
3653 TA
64 TA
3655 GTGTAGTTACCAAAATTTCATA
1 GTGT-GTTACCAAAATTTCATA
3677 GCATCAGGTT
Statistics
Matches: 77, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
65 3 0.04
66 70 0.91
67 4 0.05
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.36
Consensus pattern (65 bp):
GTGTGTTACCAAAATTTCATAAGAAGATTATCAAAATTTCATGGGAAGGTTATCAAAATTCCATA
Found at i:3717 original size:68 final size:65
Alignment explanation
Indices: 3570--3727 Score: 167
Period size: 68 Copynumber: 2.4 Consensus size: 65
3560 TTTCATGAGG
* * *
3570 AGGTTA-TGAAAATTCCATAGTGTGCTTACCAAAATTTCATATGGAAGTTATCAAAATTTCATGG
1 AGGTTATTG-AAATTTCATAGTGTG-TTACCAAAATTTCATATGCAAGTTATCAAAATTTCATAG
*
3634 GA
64 AA
** * **
3636 AGGTTATCAAAATTTCATAGTGTAGTTACCAAAATTTCATA-GCATCAGGTTATTAAAATTTTTT
1 AGGTTATTGAAATTTCATAGTGT-GTTACCAAAATTTCATATGCA--A-GTTATCAAAATTTCAT
3700 AGAA
62 AGAA
3704 AGGTTATTGAAATTTCATAGTGTG
1 AGGTTATTGAAATTTCATAGTGTG
3728 GTTATCACAA
Statistics
Matches: 76, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
65 2 0.03
66 35 0.46
67 3 0.04
68 36 0.47
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (65 bp):
AGGTTATTGAAATTTCATAGTGTGTTACCAAAATTTCATATGCAAGTTATCAAAATTTCATAGAA
Found at i:3935 original size:22 final size:21
Alignment explanation
Indices: 3907--4073 Score: 81
Period size: 22 Copynumber: 7.6 Consensus size: 21
3897 AGGAAGATTG
3907 TCAAAATTTCATAATGTTGTTA
1 TCAAAATTTCATAATG-TGTTA
* * *
3929 TCAAAATTTCA-AAGCGAGGCTA
1 TCAAAATTTCATAA-TG-TGTTA
*
3951 TCAAAATTACATAATGTGATTA
1 TCAAAATTTCATAATGTG-TTA
* * *
3973 TCAAAATTTCATAGAGGGGTCA
1 TCAAAATTTCATA-ATGTGTTA
* *
3995 ACGAAAGTTT-ATAGA-GATGTTA
1 TC-AAAATTTCATA-ATG-TGTTA
* *
4017 TCAAAATTTCATAAAGAGGTTA
1 TCAAAATTTCATAATG-TGTTA
* *
4039 TC-AAATTTGCAAAATGGGATTA
1 TCAAAATTT-CATAATGTG-TTA
*
4061 CCAAAATTTCATA
1 TCAAAATTTCATA
4074 GTGGTATTTT
Statistics
Matches: 111, Mismatches: 23, Indels: 22
0.71 0.15 0.14
Matches are distributed among these distances:
21 19 0.17
22 75 0.68
23 17 0.15
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.32
Consensus pattern (21 bp):
TCAAAATTTCATAATGTGTTA
Found at i:4361 original size:38 final size:38
Alignment explanation
Indices: 4306--4379 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
4296 TTCATAATGA
*
4306 AGTTATCAAAAAATCATAGGGAGGTTATCAAAATTTGT
1 AGTTATCAAAAAATCATAAGGAGGTTATCAAAATTTGT
* *
4344 AGTTATCAAGAATTCATAAGGAGGTTATCAAAATTT
1 AGTTATCAAAAAATCATAAGGAGGTTATCAAAATTT
4380 TATAGGTAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (38 bp):
AGTTATCAAAAAATCATAAGGAGGTTATCAAAATTTGT
Found at i:4398 original size:23 final size:21
Alignment explanation
Indices: 4155--4649 Score: 231
Period size: 22 Copynumber: 22.7 Consensus size: 21
4145 TTATGGAGTA
* *
4155 ATCAAAATTTCA-GGGAGGAT
1 ATCAAAATTTCATAGGAGGTT
*
4175 AGCAAAATTTCATATGATGAAGGTT
1 ATCAAAATTTCATA-G--G-AGGTT
*
4200 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG--GAGGTT
* *
4222 TTCAAAATTTCATAAGAGGATT
1 ATCAAAATTTCATAGGAGG-TT
* * * *
4244 ATTAAAATTTCATAGTATGTAG
1 ATCAAAATTTCATAGGAGGT-T
*
4266 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATA-GGAGGTT
* * *
4288 AACAAAATTTCATAATGAAGTT
1 ATCAAAATTTCAT-AGGAGGTT
**
4310 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATA-GGAGGTT
*
4332 ATCAAAA-TT--T-GTA-GTT
1 ATCAAAATTTCATAGGAGGTT
4348 ATCAAGAA-TTCATAAGGAGGTT
1 ATCAA-AATTTCAT-AGGAGGTT
*
4370 ATCAAAATTTTATAGGTAGGTT
1 ATCAAAATTTCATAGG-AGGTT
* *
4392 AATCAAAATTTTATTGGAAGGTTT
1 -ATCAAAATTTCATAGG-AGG-TT
4416 ATC-AAATTTCATAGCGAGGTT
1 ATCAAAATTTCATAG-GAGGTT
* ***
4437 ATCACAATTTCATAGTGTCATT
1 ATCAAAATTTCATAG-GAGGTT
* * *
4459 ATCAAAATTTCAGAGTGTGATT
1 ATCAAAATTTCATAG-GAGGTT
4481 A-CTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATA-GGAGGTT
* * * * *
4503 TTTAAATTTTCATAACGTGGTT
1 ATCAAAATTTCAT-AGGAGGTT
* *
4525 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATA-GGAGGTT
* * *
4547 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAG-G-AGGTT
* *
4570 ATCAAAATTTCATTGGGAAGTT
1 ATCAAAATTTCA-TAGGAGGTT
*
4592 ATCAAAATTTCATAGTGATGTCT
1 ATCAAAATTTCATAG-GAGGT-T
* * *
4615 -TCAAAATTCCTTAAAGAGGTT
1 ATCAAAATTTCAT-AGGAGGTT
*
4636 AACAAAATTTCATA
1 ATCAAAATTTCATA
4650 AGAAAGTTAA
Statistics
Matches: 361, Mismatches: 77, Indels: 73
0.71 0.15 0.14
Matches are distributed among these distances:
16 8 0.02
17 6 0.02
19 2 0.01
20 12 0.03
21 24 0.07
22 237 0.66
23 48 0.13
24 7 0.02
25 17 0.05
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (21 bp):
ATCAAAATTTCATAGGAGGTT
Found at i:4863 original size:2 final size:2
Alignment explanation
Indices: 4856--4887 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4846 CTAAAACTAG
4856 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.