Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014376.1 Corchorus olitorius cultivar O-4 contig14409, 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: 60190
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:7377 original size:5 final size:5
Alignment explanation
Indices: 7367--7400 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
7357 GTCTTTCTTT
7367 TTTTC TTTTC TTTTC TTTT- TTTTC TTTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC TTTT
7401 TGAGTTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 18 0.67
6 5 0.19
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (5 bp):
TTTTC
Found at i:7388 original size:19 final size:19
Alignment explanation
Indices: 7360--7400 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
7350 TATCATTGTC
7360 TTTCTTTTTTTC-TTTTCT
1 TTTCTTTTTTTCTTTTTCT
7378 TTTCTTTTTTTTCTTTTTCT
1 TTTC-TTTTTTTCTTTTTCT
7398 TTT
1 TTT
7401 TGAGTTGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 4 0.19
19 8 0.38
20 9 0.43
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (19 bp):
TTTCTTTTTTTCTTTTTCT
Found at i:14486 original size:3 final size:3
Alignment explanation
Indices: 14473--14523 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
14463 GCTTTTGTTT
* * *
14473 TAC TCC TAC TAC TAC TAC TAT TAC TAC TAC GT-C TAC AGAC TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC -TAC TAC -TAC TAC TAC
14519 TAC TA
1 TAC TA
14524 TGCTTATTGC
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
2 1 0.03
3 35 0.90
4 3 0.08
ACGTcount: A:0.31, C:0.31, G:0.04, T:0.33
Consensus pattern (3 bp):
TAC
Found at i:18637 original size:109 final size:109
Alignment explanation
Indices: 18496--18713 Score: 357
Period size: 109 Copynumber: 2.0 Consensus size: 109
18486 TAAAAAAGAG
*
18496 GATTTATTACACTTATCGGTTGAGCTCAAGTTATGAAATATGCAATCACAAGCAAACCCCAAATG
1 GATTTATTACACTTATCGGTTGAGCTCAAGTTATGAAATATGCAATCACAAGCAAACCCCAAATC
18561 GATAGAATCCATACATGCAAAAAGTATGCATGG-TGTTCTATTCA
66 GATAGAATCCATACATGCAAAAAGTATGCA-GGATGTTCTATTCA
* ** *
18605 GATTTATTACACTTCTCGGTTGAGCTCAAGTTATGTTATATGCAATCACAAGCAAATCCCAAATC
1 GATTTATTACACTTATCGGTTGAGCTCAAGTTATGAAATATGCAATCACAAGCAAACCCCAAATC
**
18670 GATAGAATCCATACATGCAAATGGTATGCAGGATGTTCTATTCA
66 GATAGAATCCATACATGCAAAAAGTATGCAGGATGTTCTATTCA
18714 CTGCTCACAA
Statistics
Matches: 101, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
108 2 0.02
109 99 0.98
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.30
Consensus pattern (109 bp):
GATTTATTACACTTATCGGTTGAGCTCAAGTTATGAAATATGCAATCACAAGCAAACCCCAAATC
GATAGAATCCATACATGCAAAAAGTATGCAGGATGTTCTATTCA
Found at i:24757 original size:25 final size:25
Alignment explanation
Indices: 24728--24806 Score: 78
Period size: 25 Copynumber: 3.2 Consensus size: 25
24718 ATCTCTATGT
*
24728 CCAAACATCTAAATGAGAGTTCAAC
1 CCAAACATCTAAATGAGAATTCAAC
*
24753 CC-AA-A-CTAAAT-A-AATCTCTATGC
1 CCAAACATCTAAATGAGAAT-TC-A-AC
24776 CCAAACATCTAAATGAGAATTCAAC
1 CCAAACATCTAAATGAGAATTCAAC
24801 CCAAAC
1 CCAAAC
24807 TAAAAACTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 16
0.69 0.05 0.26
Matches are distributed among these distances:
20 2 0.05
21 3 0.07
22 7 0.16
23 4 0.09
24 4 0.09
25 10 0.23
26 7 0.16
27 3 0.07
28 3 0.07
ACGTcount: A:0.46, C:0.27, G:0.08, T:0.20
Consensus pattern (25 bp):
CCAAACATCTAAATGAGAATTCAAC
Found at i:24764 original size:48 final size:48
Alignment explanation
Indices: 24712--24810 Score: 180
Period size: 48 Copynumber: 2.1 Consensus size: 48
24702 ATTACAATTC
* *
24712 AAATAAATCTCTATGTCCAAACATCTAAATGAGAGTTCAACCCAAACT
1 AAATAAATCTCTATGCCCAAACATCTAAATGAGAATTCAACCCAAACT
24760 AAATAAATCTCTATGCCCAAACATCTAAATGAGAATTCAACCCAAACT
1 AAATAAATCTCTATGCCCAAACATCTAAATGAGAATTCAACCCAAACT
24808 AAA
1 AAA
24811 AACTATACCA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.46, C:0.23, G:0.07, T:0.23
Consensus pattern (48 bp):
AAATAAATCTCTATGCCCAAACATCTAAATGAGAATTCAACCCAAACT
Found at i:24787 original size:26 final size:26
Alignment explanation
Indices: 24712--24789 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 26
24702 ATTACAATTC
*
24712 AAATAAATCTCTATGTCCAAACATCT
1 AAATAAATCTCTATGCCCAAACATCT
* *
24738 AAATGAGAGT-TC-A-ACCC-AA-A-CT
1 AAAT-A-AATCTCTATGCCCAAACATCT
24760 AAATAAATCTCTATGCCCAAACATCT
1 AAATAAATCTCTATGCCCAAACATCT
24786 AAAT
1 AAAT
24790 GAGAATTCAA
Statistics
Matches: 39, Mismatches: 5, Indels: 16
0.65 0.08 0.27
Matches are distributed among these distances:
20 2 0.05
21 3 0.08
22 7 0.18
23 4 0.10
24 4 0.10
25 3 0.08
26 11 0.28
27 3 0.08
28 2 0.05
ACGTcount: A:0.45, C:0.23, G:0.06, T:0.26
Consensus pattern (26 bp):
AAATAAATCTCTATGCCCAAACATCT
Found at i:24809 original size:22 final size:22
Alignment explanation
Indices: 24736--24810 Score: 64
Period size: 22 Copynumber: 3.2 Consensus size: 22
24726 GTCCAAACAT
*
24736 CTAAATGAGAGTTCAACCCAAA
1 CTAAATGAGAATTCAACCCAAA
*
24758 CTAAAT-A-AATCTCTATGCCCAAACA
1 CTAAATGAGAAT-TC-A-ACCC-AA-A
24783 TCTAAATGAGAATTCAACCCAAA
1 -CTAAATGAGAATTCAACCCAAA
24806 CTAAA
1 CTAAA
24811 AACTATACCA
Statistics
Matches: 42, Mismatches: 3, Indels: 16
0.69 0.05 0.26
Matches are distributed among these distances:
20 2 0.05
21 3 0.07
22 12 0.29
23 4 0.10
24 4 0.10
25 4 0.10
26 7 0.17
27 3 0.07
28 3 0.07
ACGTcount: A:0.47, C:0.24, G:0.08, T:0.21
Consensus pattern (22 bp):
CTAAATGAGAATTCAACCCAAA
Found at i:25929 original size:20 final size:21
Alignment explanation
Indices: 25898--25941 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
25888 CCTGCGGCGG
*
25898 TTTCCTTTTTTATTTTTTTCT
1 TTTCCTTTTTTATTTTTTCCT
25919 TTTCC-TTTTTATTTTTTCCT
1 TTTCCTTTTTTATTTTTTCCT
25939 TTT
1 TTT
25942 AGGTTTAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTCCTTTTTTATTTTTTCCT
Found at i:36186 original size:27 final size:27
Alignment explanation
Indices: 36135--36196 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
36125 TGGGTATGTT
* * * *
36135 GGAGGATAACCTGCAGGAGGGGCCTGC
1 GGAGGGTAACCTACAGCAGGCGCCTGC
* *
36162 GGTGGGTAACCTACAGCAGGCGCCTGT
1 GGAGGGTAACCTACAGCAGGCGCCTGC
36189 GGAGGGTA
1 GGAGGGTA
36197 GCCGGTATAT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.21, C:0.21, G:0.44, T:0.15
Consensus pattern (27 bp):
GGAGGGTAACCTACAGCAGGCGCCTGC
Found at i:58392 original size:20 final size:20
Alignment explanation
Indices: 58369--58406 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
58359 AAAAACAAAA
58369 TAAAATAAAACTACCCATCT
1 TAAAATAAAACTACCCATCT
*
58389 TAAATTAAAACTACCCAT
1 TAAAATAAAACTACCCAT
58407 TATAGATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (20 bp):
TAAAATAAAACTACCCATCT
Done.