Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024334.1 Corchorus olitorius cultivar O-4 contig24367, 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: 55851
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:27 original size:3 final size:3
Alignment explanation
Indices: 21--45 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
11 TTTTTTTTTT
21 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
46 AATAGATAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:1890 original size:32 final size:32
Alignment explanation
Indices: 1849--1909 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
1839 TGTAAAACTT
*
1849 TTGAATCGACTATTATACCCTTATTTTTCTAA
1 TTGAATCGACCATTATACCCTTATTTTTCTAA
1881 TTGAATCGACCATTATACCCTTATTTTTC
1 TTGAATCGACCATTATACCCTTATTTTTC
1910 AGACATATCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.46
Consensus pattern (32 bp):
TTGAATCGACCATTATACCCTTATTTTTCTAA
Found at i:3754 original size:32 final size:32
Alignment explanation
Indices: 3695--3828 Score: 189
Period size: 32 Copynumber: 4.2 Consensus size: 32
3685 TAAATCTAGG
* *
3695 CTCTGCCATGGCGGAGGCGCCCTCCGGGGGCAC
1 CTCTGCCATGGC-GTGGCGCCCTCCGGGGGCGC
* *
3728 CTCTGCCATGGTGTGGTGCCCTCCGGGGGCGC
1 CTCTGCCATGGCGTGGCGCCCTCCGGGGGCGC
* *
3760 CTCTGCCATGGCGTCGCGCCCTCTGGGGGCGC
1 CTCTGCCATGGCGTGGCGCCCTCCGGGGGCGC
3792 CTCTGCCATGGCGTGGCGCCCTCCGGGGTGC-C
1 CTCTGCCATGGCGTGGCGCCCTCCGGGG-GCGC
3824 CTCTG
1 CTCTG
3829 GGGGCGCTTA
Statistics
Matches: 90, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
32 77 0.86
33 13 0.14
ACGTcount: A:0.04, C:0.39, G:0.38, T:0.19
Consensus pattern (32 bp):
CTCTGCCATGGCGTGGCGCCCTCCGGGGGCGC
Found at i:3778 original size:19 final size:19
Alignment explanation
Indices: 3755--3811 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
3745 GCCCTCCGGG
3755 GGCGCCTCTGCCATGGCGT
1 GGCGCCTCTGCCATGGCGT
*
3774 CGCGCC-CT--C-TGG-G-
1 GGCGCCTCTGCCATGGCGT
3787 GGCGCCTCTGCCATGGCGT
1 GGCGCCTCTGCCATGGCGT
3806 GGCGCC
1 GGCGCC
3812 CTCCGGGGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
13 5 0.17
14 3 0.10
15 3 0.10
16 2 0.07
17 3 0.10
18 3 0.10
19 11 0.37
ACGTcount: A:0.04, C:0.40, G:0.39, T:0.18
Consensus pattern (19 bp):
GGCGCCTCTGCCATGGCGT
Found at i:3856 original size:45 final size:45
Alignment explanation
Indices: 3777--3863 Score: 131
Period size: 44 Copynumber: 1.9 Consensus size: 45
3767 ATGGCGTCGC
*
3777 GCCCTCTGGGGGCGCCTCTGCCATGGCGTGGCG-CCCTCCGGGGT
1 GCCCTCTGGGGGCGCCTCTGCCATAGCGTGGCGCCCCTCCGGGGT
* *
3821 GCCCTCTGGGGGCGCTTACTGCCATAGTGTGGCGCCCCTCCGG
1 GCCCTCTGGGGGCGCCT-CTGCCATAGCGTGGCGCCCCTCCGG
3864 ACACGCCCAC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 16 0.42
45 14 0.37
46 8 0.21
ACGTcount: A:0.05, C:0.38, G:0.38, T:0.20
Consensus pattern (45 bp):
GCCCTCTGGGGGCGCCTCTGCCATAGCGTGGCGCCCCTCCGGGGT
Found at i:3949 original size:3 final size:3
Alignment explanation
Indices: 3935--3965 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
3925 TGTTATTCAT
3935 TTA TTA TATA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA
3966 ATTTTACAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:4267 original size:3 final size:3
Alignment explanation
Indices: 4259--4291 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
4249 TTTAAATTAG
*
4259 TAA TAA TAA TAA TAA TAA AAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4292 ATAACAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:5094 original size:2 final size:2
Alignment explanation
Indices: 5087--5127 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5077 TCTTTCCCTC
5087 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5128 AAGATTGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7493 original size:33 final size:33
Alignment explanation
Indices: 7456--7521 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
7446 TTTGACTTCA
*
7456 ATTAATAG-TGTTCCCACCTTTTTAAAGTGCATG
1 ATTAAT-GTTGTTCCCACCTTTTCAAAGTGCATG
* * *
7489 ATTAATGTTTTTTCCACCTTTTCAAATTGCATG
1 ATTAATGTTGTTCCCACCTTTTCAAAGTGCATG
7522 CCCTTGGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 1 0.04
33 27 0.96
ACGTcount: A:0.26, C:0.18, G:0.12, T:0.44
Consensus pattern (33 bp):
ATTAATGTTGTTCCCACCTTTTCAAAGTGCATG
Found at i:24254 original size:1 final size:1
Alignment explanation
Indices: 24248--24283 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
24238 TATCTGGGAG
24248 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
24284 GTGAAAATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:25764 original size:22 final size:23
Alignment explanation
Indices: 25734--25778 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
25724 CCTATATATA
25734 TACACGTAC-ATTTGCTTTAATT
1 TACACGTACAATTTGCTTTAATT
*
25756 TACATGTACATATTTGCTTTAAT
1 TACACGTACA-ATTTGCTTTAAT
25779 GTGTATTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 8 0.40
24 12 0.60
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.47
Consensus pattern (23 bp):
TACACGTACAATTTGCTTTAATT
Found at i:26976 original size:6 final size:6
Alignment explanation
Indices: 26967--26992 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
26957 ACATGACCAC
26967 CATGAA CATGAA CATGAA CATGAA CA
1 CATGAA CATGAA CATGAA CATGAA CA
26993 GCAAAACCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.19, G:0.15, T:0.15
Consensus pattern (6 bp):
CATGAA
Found at i:28793 original size:3 final size:3
Alignment explanation
Indices: 28785--28812 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
28775 TTTGAGGAGC
28785 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
28813 GTTGCTGCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:33151 original size:2 final size:2
Alignment explanation
Indices: 33146--33175 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
33136 TGTGCAAGAT
33146 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
33176 ATGCAATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35141 original size:18 final size:19
Alignment explanation
Indices: 35102--35141 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
35092 GTGCTCCCGT
35102 TGTGATGCTCCCATTTTTCAA
1 TGTGATGCTCCCA--TTTCAA
35123 TGTGATGCTCCCA-TTCAA
1 TGTGATGCTCCCATTTCAA
35141 T
1 T
35142 TCTAACCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
21 13 0.68
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (19 bp):
TGTGATGCTCCCATTTCAA
Found at i:37326 original size:2 final size:2
Alignment explanation
Indices: 37319--37353 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
37309 TGAAATTTTC
37319 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
37354 GATAGAGGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39834 original size:27 final size:25
Alignment explanation
Indices: 39784--39835 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
39774 CTTAAAAAAT
* *
39784 GCATCCTATATATCTTTTGTGCAAA
1 GCATCCTATATATCTGTTGAGCAAA
39809 GCATCCTATATATCTGGTTGAAGCAAA
1 GCATCCTATATATCT-GTTG-AGCAAA
39836 TTAGTATGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 15 0.65
26 3 0.13
27 5 0.22
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (25 bp):
GCATCCTATATATCTGTTGAGCAAA
Found at i:40324 original size:18 final size:19
Alignment explanation
Indices: 40284--40324 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
40274 AAAATCTGTG
* *
40284 GTAAAAATGTTTTCAAGTA
1 GTAAAAATGATTGCAAGTA
40303 -TAAAAATGATTGCAAG-A
1 GTAAAAATGATTGCAAGTA
40320 GTAAA
1 GTAAA
40325 TTGCAAGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 1 0.05
18 18 0.95
ACGTcount: A:0.49, C:0.05, G:0.17, T:0.29
Consensus pattern (19 bp):
GTAAAAATGATTGCAAGTA
Found at i:41616 original size:42 final size:42
Alignment explanation
Indices: 41557--41639 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
41547 TGGCTAGATA
41557 TTTTTATTCATTAGACTTCGACTAATTCGGAGTTGAACCTGC
1 TTTTTATTCATTAGACTTCGACTAATTCGGAGTTGAACCTGC
* * *
41599 TTTTTTTTTATTAGACTTCGACTGATTCGGAGTTGAACCTG
1 TTTTTATTCATTAGACTTCGACTAATTCGGAGTTGAACCTG
41640 TTTCAATTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.22, C:0.17, G:0.18, T:0.43
Consensus pattern (42 bp):
TTTTTATTCATTAGACTTCGACTAATTCGGAGTTGAACCTGC
Done.