Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021031.1 Corchorus olitorius cultivar O-4 contig21064, 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: 42830
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:3604 original size:99 final size:98
Alignment explanation
Indices: 3484--3679 Score: 374
Period size: 99 Copynumber: 2.0 Consensus size: 98
3474 AGAGGTTCAA
*
3484 GAGTCTGGTTTCTTTCTTTTGACTTGGCTCCCTTGATAACCCAATTAAACATGGCTTTTCTCTTG
1 GAGTCTGATTTCTTTCTTTTGACTTGGCTCCCTTGATAACCCAATTAAACATGGC-TTTCTCTTG
3549 CCTGCACCCAGTTACAGCTCCTGCCAAATCCCAC
65 CCTGCACCCAGTTACAGCTCCTGCCAAATCCCAC
3583 GAGTCTGATTTCTTTCTTTTGACTTGGCTCCCTTGATAACCCAATTAAACATGGCTTTCTCTTGC
1 GAGTCTGATTTCTTTCTTTTGACTTGGCTCCCTTGATAACCCAATTAAACATGGCTTTCTCTTGC
3648 CTGCACCCAGTTACAGCTCCTGCCAAATCCCA
66 CTGCACCCAGTTACAGCTCCTGCCAAATCCCA
3680 GCACATAGCA
Statistics
Matches: 96, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
98 42 0.44
99 54 0.56
ACGTcount: A:0.20, C:0.31, G:0.15, T:0.34
Consensus pattern (98 bp):
GAGTCTGATTTCTTTCTTTTGACTTGGCTCCCTTGATAACCCAATTAAACATGGCTTTCTCTTGC
CTGCACCCAGTTACAGCTCCTGCCAAATCCCAC
Found at i:4886 original size:22 final size:22
Alignment explanation
Indices: 4857--4909 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
4847 TATTCTTAGC
*
4857 AACCAAAAAA-GTACAGAAAAAA
1 AACCAAAAAATATACA-AAAAAA
*
4879 TACCAAAAAATATACAAAAAAA
1 AACCAAAAAATATACAAAAAAA
4901 AACCAAAAA
1 AACCAAAAA
4910 CAGAAAACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 23 0.85
23 4 0.15
ACGTcount: A:0.74, C:0.15, G:0.04, T:0.08
Consensus pattern (22 bp):
AACCAAAAAATATACAAAAAAA
Found at i:4887 original size:11 final size:11
Alignment explanation
Indices: 4858--4909 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
4848 ATTCTTAGCA
*
4858 ACCAAAAAAGT
1 ACCAAAAAAAT
4869 A-CAGAAAAAAT
1 ACCA-AAAAAAT
4880 ACCAAAAAATAT
1 ACCAAAAAA-AT
*
4892 A-CAAAAAAAA
1 ACCAAAAAAAT
4902 ACCAAAAA
1 ACCAAAAA
4910 CAGAAAACAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
10 4 0.11
11 26 0.74
12 5 0.14
ACGTcount: A:0.73, C:0.15, G:0.04, T:0.08
Consensus pattern (11 bp):
ACCAAAAAAAT
Found at i:13742 original size:15 final size:16
Alignment explanation
Indices: 13712--13750 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
13702 TTACTTTGCT
13712 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
13728 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTTTAA
13743 TTGCTTTT
1 TTG-TTTT
13751 TGTCAATCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.13, C:0.08, G:0.13, T:0.67
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:23984 original size:20 final size:20
Alignment explanation
Indices: 23938--23986 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
23928 GCTCATTCAA
*
23938 TCTTATCAAGGATTATTAAG
1 TCTTATGAAGGATTATTAAG
* *
23958 TCTTATGAAGGCTTATTTAG
1 TCTTATGAAGGATTATTAAG
23978 TCTTATGAA
1 TCTTATGAA
23987 TACCTCATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (20 bp):
TCTTATGAAGGATTATTAAG
Found at i:27566 original size:13 final size:13
Alignment explanation
Indices: 27548--27572 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27538 CATCTCTTTC
27548 TCTTTTTTTTTTT
1 TCTTTTTTTTTTT
27561 TCTTTTTTTTTT
1 TCTTTTTTTTTT
27573 CTTTTCTGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TCTTTTTTTTTTT
Found at i:27568 original size:11 final size:11
Alignment explanation
Indices: 27552--27577 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
27542 TCTTTCTCTT
27552 TTTTTTTTTTC
1 TTTTTTTTTTC
27563 TTTTTTTTTTC
1 TTTTTTTTTTC
27574 TTTT
1 TTTT
27578 CTGTTAATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:27568 original size:15 final size:16
Alignment explanation
Indices: 27544--27579 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
27534 TATTCATCTC
27544 TTTCTCTTTTTTTT-T
1 TTTCTCTTTTTTTTCT
*
27559 TTTCTTTTTTTTTTCT
1 TTTCTCTTTTTTTTCT
27575 TTTCT
1 TTTCT
27580 GTTAATGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (16 bp):
TTTCTCTTTTTTTTCT
Found at i:31854 original size:2 final size:2
Alignment explanation
Indices: 31847--31879 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
31837 TAATATTTAG
*
31847 TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31880 TCTTTAGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:38542 original size:19 final size:19
Alignment explanation
Indices: 38496--38561 Score: 57
Period size: 18 Copynumber: 3.6 Consensus size: 19
38486 TATTTTCTAT
* *
38496 AAAGCTCATTTCTTC-CTA
1 AAAGCCCATTACTTCACTA
**
38514 AAAGGGCATTACTTCACTA
1 AAAGCCCATTACTTCACTA
*
38533 AAAGCCCATTA-TTTA-TCA
1 AAAGCCCATTACTTCACT-A
38551 AAAGCCCATTA
1 AAAGCCCATTA
38562 TTTACAAATA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
17 1 0.03
18 27 0.68
19 12 0.30
ACGTcount: A:0.36, C:0.24, G:0.09, T:0.30
Consensus pattern (19 bp):
AAAGCCCATTACTTCACTA
Found at i:38555 original size:18 final size:17
Alignment explanation
Indices: 38532--38569 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
38522 TTACTTCACT
38532 AAAAGCCCATTATTTATC
1 AAAAGCCCATTATTTA-C
38550 AAAAGCCCATTATTTAC
1 AAAAGCCCATTATTTAC
38567 AAA
1 AAA
38570 TAATTAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (17 bp):
AAAAGCCCATTATTTAC
Found at i:39731 original size:26 final size:27
Alignment explanation
Indices: 39696--39766 Score: 90
Period size: 26 Copynumber: 2.7 Consensus size: 27
39686 GGTCATCTAG
*
39696 GGGCATTTTGGTCATTTTTACACT-AA
1 GGGCATTTTGGTCATTTTCACACTCAA
* * *
39722 GGGCATTTTGGTCATTTGCATATTCAA
1 GGGCATTTTGGTCATTTTCACACTCAA
*
39749 GGGCATGTTGGTCATTTT
1 GGGCATTTTGGTCATTTT
39767 GAGTCAACTT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
26 20 0.53
27 18 0.47
ACGTcount: A:0.20, C:0.14, G:0.24, T:0.42
Consensus pattern (27 bp):
GGGCATTTTGGTCATTTTCACACTCAA
Found at i:40207 original size:14 final size:14
Alignment explanation
Indices: 40190--40217 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40180 TCATGCATAT
40190 TACATCATTCTAAG
1 TACATCATTCTAAG
40204 TACATCATTCTAAG
1 TACATCATTCTAAG
40218 CTTAGACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (14 bp):
TACATCATTCTAAG
Found at i:42158 original size:13 final size:14
Alignment explanation
Indices: 42140--42168 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
42130 GAGTCTCGTC
42140 GAAGAAGAAGA-AA
1 GAAGAAGAAGATAA
42153 GAAGAAGAAGATAA
1 GAAGAAGAAGATAA
42167 GA
1 GA
42169 GGCTTAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.03
Consensus pattern (14 bp):
GAAGAAGAAGATAA
Found at i:42391 original size:72 final size:72
Alignment explanation
Indices: 42271--42415 Score: 263
Period size: 72 Copynumber: 2.0 Consensus size: 72
42261 TGGGTGCCTC
*
42271 TGTTTGTTATTTGAGTTAATTTAAAAGTTGATTTGGTGATTGAGGCATGTAAATGTTCTAAATTT
1 TGTTTGTTATTTGAGTTAAATTAAAAGTTGATTTGGTGATTGAGGCATGTAAATGTTCTAAATTT
42336 AGCTAAT
66 AGCTAAT
*
42343 TGTTTGTTATTTGAGTTAAATTAAAAGTTGATTTGGTGATTGATGCATGTAAATGTTCTAAATTT
1 TGTTTGTTATTTGAGTTAAATTAAAAGTTGATTTGGTGATTGAGGCATGTAAATGTTCTAAATTT
*
42408 ATCTAAT
66 AGCTAAT
42415 T
1 T
42416 TATGAATACA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.30, C:0.04, G:0.19, T:0.47
Consensus pattern (72 bp):
TGTTTGTTATTTGAGTTAAATTAAAAGTTGATTTGGTGATTGAGGCATGTAAATGTTCTAAATTT
AGCTAAT
Done.