Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022566.1 Corchorus olitorius cultivar O-4 contig22599, 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: 37653
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Found at i:3663 original size:28 final size:28
Alignment explanation
Indices: 3623--3728 Score: 140
Period size: 28 Copynumber: 3.8 Consensus size: 28
3613 AGTGTCCCTG
* * *
3623 AAATGATCAAAATACCCCTGGACGTGCA
1 AAATGACCAAAATGCCCCTGGACTTGCA
* *
3651 AAATGACCAAAATGCCCCTGGACTTACG
1 AAATGACCAAAATGCCCCTGGACTTGCA
*
3679 AAATGACCAAAATGCCCCTAGACTTGCA
1 AAATGACCAAAATGCCCCTGGACTTGCA
* *
3707 AAATGCCCAAAATGCCCTTGGA
1 AAATGACCAAAATGCCCCTGGA
3729 TCCGAAAAAT
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 67 1.00
ACGTcount: A:0.38, C:0.27, G:0.17, T:0.18
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTGGACTTGCA
Found at i:3708 original size:56 final size:56
Alignment explanation
Indices: 3622--3728 Score: 160
Period size: 56 Copynumber: 1.9 Consensus size: 56
3612 AAGTGTCCCT
* *
3622 GAAATGATCAAAATACCCCTGGACGTGCAAAATGACCAAAATGCCCCTGGACTTAC
1 GAAATGACCAAAATACCCCTAGACGTGCAAAATGACCAAAATGCCCCTGGACTTAC
* * * *
3678 GAAATGACCAAAATGCCCCTAGACTTGCAAAATGCCCAAAATGCCCTTGGA
1 GAAATGACCAAAATACCCCTAGACGTGCAAAATGACCAAAATGCCCCTGGA
3729 TCCGAAAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 45 1.00
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (56 bp):
GAAATGACCAAAATACCCCTAGACGTGCAAAATGACCAAAATGCCCCTGGACTTAC
Found at i:4006 original size:27 final size:25
Alignment explanation
Indices: 3945--4041 Score: 83
Period size: 26 Copynumber: 3.8 Consensus size: 25
3935 TTCTTTGAGA
*
3945 TGAATCGTCTCCCAA-TCAACTTCTT
1 TGAATCGTCTTCCAATTCAAC-TCTT
* *
3970 CGAATTGTCTTCCAATTCAA-TCTT
1 TGAATCGTCTTCCAATTCAACTCTT
*
3994 TGGGGAATCGTCTTCCGAA-CCAACTTCTT
1 T---GAATCGTCTTCC-AATTCAAC-TCTT
4023 TGAATCGTCTTCCAATTCA
1 TGAATCGTCTTCCAATTCA
4042 CATATAAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
24 4 0.07
25 14 0.25
26 18 0.32
27 14 0.25
28 2 0.04
29 5 0.09
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.36
Consensus pattern (25 bp):
TGAATCGTCTTCCAATTCAACTCTT
Found at i:4121 original size:50 final size:50
Alignment explanation
Indices: 4020--4190 Score: 227
Period size: 50 Copynumber: 3.4 Consensus size: 50
4010 GAACCAACTT
* * *
4020 CTTTGAA-TCGTCTTCCAATTCACATATAAAAAGGACCGTCTTCTGCTTATC
1 CTTTGAACT-GTCTTCCAATTTA-ATCTAAAAAGGACCGTCTTCCGCTTATC
*
4071 CTTTGAACTGTCTTCCAATTTAATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTTAATCTAAAAAGGACCGTCTTCCGCTTATC
* * * * * *
4121 CCTTAAACTGTTTTCCAATTTACTCTCAAAAGAACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTTAATCTAAAAAGGACCGTCTTCCGCTTATC
4171 CTTTGAACTGTCTTCCAATT
1 CTTTGAACTGTCTTCCAATT
4191 CGCTTTTCTG
Statistics
Matches: 106, Mismatches: 13, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
50 86 0.81
51 19 0.18
52 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.11, T:0.37
Consensus pattern (50 bp):
CTTTGAACTGTCTTCCAATTTAATCTAAAAAGGACCGTCTTCCGCTTATC
Found at i:8787 original size:2 final size:2
Alignment explanation
Indices: 8782--8818 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
8772 ACCAAAGAAA
* *
8782 AT AT AT AA AT AT AT AT AT AT AT AT AT CT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8819 GCTAGTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:12727 original size:16 final size:17
Alignment explanation
Indices: 12706--12746 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
12696 TTACTCTGCT
12706 TTGTTTTCTA-GTTTAA
1 TTGTTTTCTATGTTTAA
12722 TTGTTTT-TATGTTTAA
1 TTGTTTTCTATGTTTAA
12738 TTGTTTTCT
1 TTGTTTTCT
12747 GTCAACCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 2 0.09
16 20 0.87
17 1 0.04
ACGTcount: A:0.15, C:0.05, G:0.12, T:0.68
Consensus pattern (17 bp):
TTGTTTTCTATGTTTAA
Found at i:13170 original size:21 final size:22
Alignment explanation
Indices: 13144--13186 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
13134 TTGTTTTGTG
13144 TTTTGCGTC-GAAAAAAAAAAA
1 TTTTGCGTCAGAAAAAAAAAAA
*
13165 TTTTGCGTCATAAAAAAAAAAA
1 TTTTGCGTCAGAAAAAAAAAAA
13187 AATTTGTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.26
Consensus pattern (22 bp):
TTTTGCGTCAGAAAAAAAAAAA
Found at i:13184 original size:23 final size:24
Alignment explanation
Indices: 13154--13263 Score: 80
Period size: 24 Copynumber: 4.3 Consensus size: 24
13144 TTTTGCGTCG
13154 AAAAAAAAAAATTTTGCGTCATAA
1 AAAAAAAAAAATTTTGCGTCATAA
13178 AAAAAAAAAAATTTGTTTCTGCGTCAT-A
1 AAAAAAAAAAA----TTT-TGCGTCATAA
****
13206 AAAAAAAGGGTTTTTGCGTTTTTC-TAA
1 AAAAAAAAAAATTTTGCG----TCATAA
*
13233 AAAAAAAAAAAGTTTGCGTCATAA
1 AAAAAAAAAAATTTTGCGTCATAA
13257 AAAAAAA
1 AAAAAAA
13264 TTTCTTGTTT
Statistics
Matches: 66, Mismatches: 9, Indels: 22
0.68 0.09 0.23
Matches are distributed among these distances:
23 6 0.09
24 24 0.36
26 1 0.02
27 16 0.24
28 11 0.17
29 8 0.12
ACGTcount: A:0.52, C:0.08, G:0.12, T:0.28
Consensus pattern (24 bp):
AAAAAAAAAAATTTTGCGTCATAA
Found at i:16462 original size:11 final size:11
Alignment explanation
Indices: 16448--16484 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
16438 TACCGCCCAT
16448 TCACCGTGCCA
1 TCACCGTGCCA
16459 TCACCG-GCCA
1 TCACCGTGCCA
16469 TGC-CCGTGCCA
1 T-CACCGTGCCA
16480 TCACC
1 TCACC
16485 ATTCCAAGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.16, C:0.49, G:0.19, T:0.16
Consensus pattern (11 bp):
TCACCGTGCCA
Found at i:19765 original size:16 final size:15
Alignment explanation
Indices: 19744--19786 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 15
19734 TTACTCTGCT
19744 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
19760 TTGTTTTTCTGTTTAA
1 TTG-TTTTCTGTTTAA
19776 TTGTTTTCTGT
1 TTGTTTTCTGT
19787 CAACCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.31
16 12 0.46
17 6 0.23
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:22401 original size:19 final size:18
Alignment explanation
Indices: 22377--22412 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
22367 TGAAGACTTA
22377 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
22396 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
22413 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:22419 original size:30 final size:30
Alignment explanation
Indices: 22365--22424 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
22355 GAAGTTCGTG
* *
22365 TTTGAAGACTTATTGAAGACAATTTGAAGA
1 TTTGAAGACTCATTGAAGACAATTTCAAGA
*
22395 TTTGAAGAC-CATTGAAGAATAATTTCAAGA
1 TTTGAAGACTCATTGAAG-ACAATTTCAAGA
22425 GCAAGAATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (30 bp):
TTTGAAGACTCATTGAAGACAATTTCAAGA
Found at i:29033 original size:18 final size:18
Alignment explanation
Indices: 28993--29056 Score: 58
Period size: 18 Copynumber: 3.3 Consensus size: 18
28983 GAGGCAACCC
28993 AATTTTAATTTTTTGAGTAATT
1 AATTTTAATTTTTT---T-ATT
29015 AATTTTAATTTTTTTATT
1 AATTTTAATTTTTTTATT
* *
29033 -ATTCTTAATTTTTATACT
1 AATT-TTAATTTTTTTATT
29051 AATTTT
1 AATTTT
29057 TCTTTGAGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
17 3 0.08
18 17 0.45
19 4 0.11
22 14 0.37
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (18 bp):
AATTTTAATTTTTTTATT
Found at i:31658 original size:19 final size:18
Alignment explanation
Indices: 31636--31671 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
31626 AGGGTAATTA
*
31636 AAAAAAAATTGTTTTCAT
1 AAAAAAAAGTGTTTTCAT
*
31654 AAAAAGAAGTGTTTTCAT
1 AAAAAAAAGTGTTTTCAT
31672 GATAGAGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (18 bp):
AAAAAAAAGTGTTTTCAT
Found at i:32029 original size:13 final size:13
Alignment explanation
Indices: 32011--32035 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
32001 AAACATGAGC
32011 TTATAGAAAGTAG
1 TTATAGAAAGTAG
32024 TTATAGAAAGTA
1 TTATAGAAAGTA
32036 AAGAATGGTA
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:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (13 bp):
TTATAGAAAGTAG
Found at i:32535 original size:19 final size:18
Alignment explanation
Indices: 32511--32546 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
32501 TGAAGATTTA
32511 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
32530 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
32547 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:34789 original size:16 final size:16
Alignment explanation
Indices: 34768--34799 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
34758 AATGGCGACC
34768 TCTCTTCCTTTCAGCT
1 TCTCTTCCTTTCAGCT
34784 TCTCTTCCTTTCAGCT
1 TCTCTTCCTTTCAGCT
34800 CTATGGCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.38, G:0.06, T:0.50
Consensus pattern (16 bp):
TCTCTTCCTTTCAGCT
Done.