Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01007880.1 Corchorus olitorius cultivar O-4 contig07907, 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, 676
Length: 1127
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.40
Found at i:301 original size:77 final size:77
Alignment explanation
Indices: 209--541 Score: 273
Period size: 77 Copynumber: 4.3 Consensus size: 77
199 AAAGTTGCCA
*
209 TTTAAGTAAACCTGCTTAGGTCCTCCTTTAGAATTTCCATTTTAGTAAACCTGCTTAGG-CCTCT
1 TTTAAGTAAACCTGCTTAGGTCCTCCTTTAGAATTT-CATTTAAGTAAACCTGCTTAGGACCTCT
*
273 GCTTAGAGCTTCG
65 GCTTAGAGTTTCG
** * * * *
286 TTTAAGTAAACCTGCTTAGGT-CTATGTTTAGAATTTCATCTAAGAAAACCTGCTTAGGTCC-CG
1 TTTAAGTAAACCTGCTTAGGTCCT-CCTTTAGAATTTCATTTAAGTAAACCTGCTTAGGACCTCT
* *
349 GCCTAGAATTTCTG
65 GCTTAGAGTTTC-G
* * * * * * *** *
363 CTTAAGAAAACCTGCTTAGGTCC-CCGCTAAGAATCTCGTTTGTTTAAACCTGCTTAGG-TCTCT
1 TTTAAGTAAACCTGCTTAGGTCCTCC-TTTAGAATTTCATTTAAGTAAACCTGCTTAGGACCTCT
* *
426 GTTTAGAATTTTCG
65 GCTTAG-AGTTTCG
* * * * *
440 TTTAAGTAAACCTGTTTAGGTCACT-ATTTAAAATTATCATTAAAGTAAACCTGCTTAGGATCTC
1 TTTAAGTAAACCTGCTTAGGTC-CTCCTTTAGAATT-TCATTTAAGTAAACCTGCTTAGGACCTC
* *
504 TGCTAATAGTTTCG
64 TGCTTAGAGTTTCG
* *
518 TTTAAAGTAAACCCGCTGAGGTCC
1 TTT-AAGTAAACCTGCTTAGGTCC
542 CTCTTTACAA
Statistics
Matches: 197, Mismatches: 47, Indels: 23
0.74 0.18 0.09
Matches are distributed among these distances:
76 32 0.16
77 106 0.54
78 35 0.18
79 24 0.12
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.36
Consensus pattern (77 bp):
TTTAAGTAAACCTGCTTAGGTCCTCCTTTAGAATTTCATTTAAGTAAACCTGCTTAGGACCTCTG
CTTAGAGTTTCG
Found at i:303 original size:38 final size:39
Alignment explanation
Indices: 129--541 Score: 278
Period size: 39 Copynumber: 10.6 Consensus size: 39
119 GTCTCTGTTC
* *
129 CGTTTAAGTAAACCTGTTTAGGAT-CTCTGCTTAGAGTTT
1 CGTTTAAGTAAACCTGCTTAGG-TCCTCTGCTTAGAATTT
* * * * *
168 TGGTCAAGTAAACCTGCTTAGGTCC-CT-ATATA-AAGTTGC
1 CGTTTAAGTAAACCTGCTTAGGTCCTCTGCT-TAGAA-TT-T
*
207 CATTTAAGTAAACCTGCTTAGGTCCTC--CTTTAGAATTT
1 CGTTTAAGTAAACCTGCTTAGGTCCTCTGC-TTAGAATTT
* * **
245 CCATTTTAGTAAACCTGCTTAGG-CCTCTGCTTAGAGCTT
1 -CGTTTAAGTAAACCTGCTTAGGTCCTCTGCTTAGAATTT
* *
284 CGTTTAAGTAAACCTGCTTAGGT-CTATGTTTAGAATTT
1 CGTTTAAGTAAACCTGCTTAGGTCCTCTGCTTAGAATTT
* * * * *
322 CATCTAAGAAAACCTGCTTAGGTCC-CGGCCTAGAATTT
1 CGTTTAAGTAAACCTGCTTAGGTCCTCTGCTTAGAATTT
* * * * *
360 CTGCTTAAGAAAACCTGCTTAGGTCC-CCGCTAAGAATCT
1 C-GTTTAAGTAAACCTGCTTAGGTCCTCTGCTTAGAATTT
*** *
399 CGTTTGTTTAAACCTGCTTAGGT-CTCTGTTTAGAATTTT
1 CGTTTAAGTAAACCTGCTTAGGTCCTCTGCTTAGAA-TTT
* * *
438 CGTTTAAGTAAACCTGTTTAGGTCACTAT--TTAAAATTAT
1 CGTTTAAGTAAACCTGCTTAGGTC-CTCTGCTTAGAATT-T
* * * * *
477 CATTAAAGTAAACCTGCTTAGGAT-CTCTGCTAATAGTTT
1 CGTTTAAGTAAACCTGCTTAGG-TCCTCTGCTTAGAATTT
* *
516 CGTTTAAAGTAAACCCGCTGAGGTCC
1 CGTTT-AAGTAAACCTGCTTAGGTCC
542 CTCTTTACAA
Statistics
Matches: 289, Mismatches: 62, Indels: 45
0.73 0.16 0.11
Matches are distributed among these distances:
37 3 0.01
38 101 0.35
39 155 0.54
40 27 0.09
41 3 0.01
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (39 bp):
CGTTTAAGTAAACCTGCTTAGGTCCTCTGCTTAGAATTT
Found at i:769 original size:4 final size:4
Alignment explanation
Indices: 762--801 Score: 53
Period size: 4 Copynumber: 9.5 Consensus size: 4
752 CATGATTTTT
*
762 TTTC TTTC TTTC TTTT TTTC TTTTC TTTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC -TTTC -TTTC TTTC TTTC TT
802 CTTCTTCTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
4 24 0.73
5 9 0.27
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (4 bp):
TTTC
Found at i:794 original size:26 final size:26
Alignment explanation
Indices: 757--810 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
747 ATTCTCATGA
*
757 TTTTTTTTCTTTCTTTCTT-TTTTTC
1 TTTTTTTTCTTTCTTTCTTCTTCTTC
782 TTTTCTTTTCTTTCTTTCTTCTTCTTC
1 TTTT-TTTTCTTTCTTTCTTCTTCTTC
809 TT
1 TT
811 CTTTCCTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 4 0.15
26 15 0.58
27 7 0.27
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (26 bp):
TTTTTTTTCTTTCTTTCTTCTTCTTC
Found at i:796 original size:30 final size:30
Alignment explanation
Indices: 757--814 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
747 ATTCTCATGA
* *
757 TTTTTTTTCTTTCTTTCTT-TTTTTCTTTTC
1 TTTTCTTTCTTTC-TTCTTCTTCTTCTTTTC
787 TTTTCTTTCTTTCTTCTTCTTCTTCTTT
1 TTTTCTTTCTTTCTTCTTCTTCTTCTTT
815 CCTCATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (30 bp):
TTTTCTTTCTTTCTTCTTCTTCTTCTTTTC
Found at i:799 original size:13 final size:13
Alignment explanation
Indices: 761--807 Score: 69
Period size: 13 Copynumber: 3.5 Consensus size: 13
751 TCATGATTTT
761 TTTTCTTTCTTTC
1 TTTTCTTTCTTTC
774 TTTT-TTTCTTTTC
1 TTTTCTTTC-TTTC
787 TTTTCTTTCTTTC
1 TTTTCTTTCTTTC
800 TTCTTCTT
1 TT-TTCTT
808 CTTCTTTCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.13
13 18 0.58
14 9 0.29
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTCTTTCTTTC
Found at i:809 original size:13 final size:12
Alignment explanation
Indices: 761--814 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 12
751 TCATGATTTT
761 TTTTCTTTCTTTC
1 TTTTC-TTCTTTC
*
774 TTTTTTTCTTTTC
1 TTTTCTTC-TTTC
787 TTTTCTTTCTTTC
1 TTTTC-TTCTTTC
800 TTCTTCTTC-TTC
1 TT-TTCTTCTTTC
812 TTT
1 TTT
815 CCTCATTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
11 1 0.03
12 8 0.22
13 21 0.58
14 6 0.17
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTCTTCTTTC
Done.