Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022473.1 Corchorus olitorius cultivar O-4 contig22506, 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: 75177
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:10225 original size:14 final size:15
Alignment explanation
Indices: 10190--10228 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 15
10180 CGAACCCGAT
10190 TATGAAAATATACTA
1 TATGAAAATATACTA
10205 TAT---AATATA-TA
1 TATGAAAATATACTA
10216 TATGAAAATATAC
1 TATGAAAATATAC
10229 AGTAGTGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 8
0.71 0.00 0.29
Matches are distributed among these distances:
11 5 0.25
12 6 0.30
14 6 0.30
15 3 0.15
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (15 bp):
TATGAAAATATACTA
Found at i:11048 original size:20 final size:20
Alignment explanation
Indices: 10998--11038 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
10988 TAATTCATCC
*
10998 TATGTAATGTTTCTGAATAT
1 TATGTAATGTTTCTGAAAAT
11018 TATGTAATGTTTCTGAAAAT
1 TATGTAATGTTTCTGAAAAT
11038 T
1 T
11039 GTTTGATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.05, G:0.15, T:0.49
Consensus pattern (20 bp):
TATGTAATGTTTCTGAAAAT
Found at i:11677 original size:11 final size:11
Alignment explanation
Indices: 11663--11689 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
11653 TAACTATTAC
11663 TTAACCATAGA
1 TTAACCATAGA
11674 TTAACCATAGA
1 TTAACCATAGA
11685 TTAAC
1 TTAAC
11690 TATAACTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.07, T:0.30
Consensus pattern (11 bp):
TTAACCATAGA
Found at i:11690 original size:33 final size:33
Alignment explanation
Indices: 11640--11705 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
11630 TATATATACA
*
11640 ATTAACCTATAACTAACTATTACTTAACCATAG
1 ATTAACCTATAACTAACTATAACTTAACCATAG
* *
11673 ATTAACC-ATAGATTAACTATAACTTGACCATAG
1 ATTAACCTATA-ACTAACTATAACTTAACCATAG
11706 GTTAGTAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 3 0.10
33 26 0.90
ACGTcount: A:0.42, C:0.20, G:0.06, T:0.32
Consensus pattern (33 bp):
ATTAACCTATAACTAACTATAACTTAACCATAG
Found at i:13741 original size:6 final size:6
Alignment explanation
Indices: 13730--13757 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
13720 TAGACAATGG
13730 ATGGTC ATGGTC ATGGTC ATGGTC ATGG
1 ATGGTC ATGGTC ATGGTC ATGGTC ATGG
13758 ACCCCTAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.36, T:0.32
Consensus pattern (6 bp):
ATGGTC
Found at i:28755 original size:19 final size:19
Alignment explanation
Indices: 28731--28767 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
28721 ATACAGTACC
*
28731 TAATCTAATTTGTACAGTG
1 TAATCTAATCTGTACAGTG
*
28750 TAATCTCATCTGTACAGT
1 TAATCTAATCTGTACAGT
28768 TGCTAAACAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.41
Consensus pattern (19 bp):
TAATCTAATCTGTACAGTG
Found at i:39665 original size:22 final size:22
Alignment explanation
Indices: 39637--39684 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
39627 AAGAAATTTG
39637 CCTACATAGTTTGCTAATGTCC
1 CCTACATAGTTTGCTAATGTCC
39659 CCTACATAGTTTGCTAATGTCC
1 CCTACATAGTTTGCTAATGTCC
39681 CCTA
1 CCTA
39685 TCCTCTCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.23, C:0.29, G:0.12, T:0.35
Consensus pattern (22 bp):
CCTACATAGTTTGCTAATGTCC
Found at i:40438 original size:31 final size:32
Alignment explanation
Indices: 40379--40455 Score: 102
Period size: 31 Copynumber: 2.4 Consensus size: 32
40369 ATTACTAACG
40379 TGGCAATGCCACATCGGACCAAAAATGCCATA
1 TGGCAATGCCACATCGGACCAAAAATGCCATA
* * *
40411 TGGCAATGTCACATTGGACC-AAAATGCCATG
1 TGGCAATGCCACATCGGACCAAAAATGCCATA
* *
40442 TAGCAAGGCCACAT
1 TGGCAATGCCACAT
40456 AAGACCAAGG
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 21 0.54
32 18 0.46
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.18
Consensus pattern (32 bp):
TGGCAATGCCACATCGGACCAAAAATGCCATA
Found at i:42231 original size:124 final size:124
Alignment explanation
Indices: 42067--42316 Score: 482
Period size: 124 Copynumber: 2.0 Consensus size: 124
42057 TACTGGACTC
42067 TTAGTTCCAGCCTACCTAGACCAAGAGGTCTTAGGTTCAACTCTCACGGAATGTGAACTTGTTTG
1 TTAGTTCCAGCCTACCTAGACCAAGAGGTCTTAGGTTCAACTCTCACGGAATGTGAACTTGTTTG
42132 TAATTTGTTTGTTTATTTGGTAGGTATATATGTAGTTTATTTATGGTTTAGTTTCTAGT
66 TAATTTGTTTGTTTATTTGGTAGGTATATATGTAGTTTATTTATGGTTTAGTTTCTAGT
**
42191 TTAGTTCCAGCCTACCTAGACCAAGAGGTCTTAGGTTCAACTCTCACGGAATGTGAGTTTGTTTG
1 TTAGTTCCAGCCTACCTAGACCAAGAGGTCTTAGGTTCAACTCTCACGGAATGTGAACTTGTTTG
42256 TAATTTGTTTGTTTATTTGGTAGGTATATATGTAGTTTATTTATGGTTTAGTTTCTAGT
66 TAATTTGTTTGTTTATTTGGTAGGTATATATGTAGTTTATTTATGGTTTAGTTTCTAGT
42315 TT
1 TT
42317 GGGTTGAATT
Statistics
Matches: 124, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
124 124 1.00
ACGTcount: A:0.22, C:0.12, G:0.21, T:0.44
Consensus pattern (124 bp):
TTAGTTCCAGCCTACCTAGACCAAGAGGTCTTAGGTTCAACTCTCACGGAATGTGAACTTGTTTG
TAATTTGTTTGTTTATTTGGTAGGTATATATGTAGTTTATTTATGGTTTAGTTTCTAGT
Found at i:46343 original size:43 final size:44
Alignment explanation
Indices: 46295--46423 Score: 179
Period size: 48 Copynumber: 2.8 Consensus size: 44
46285 TCTGTTCCTT
*
46295 CCCCTGTTCTCTCTGTTTTTCTGTCATTGGCTTTGCCGCCCCAC
1 CCCCTGTTCTCTCTGTTTTTCTGTCATTTGCTTTGCCGCCCCAC
*
46339 CCCTGTTCTGTTCTCTCTGTTTTTCTGTCATTTGCTTTGCCTCCCCA-
1 CCC----CTGTTCTCTCTGTTTTTCTGTCATTTGCTTTGCCGCCCCAC
*
46386 CCCCTGTTCTCTCTGTTTTTTTGTTCATTTGCTTTGCC
1 CCCCTGTTCTCTCTGTTTTTCTG-TCATTTGCTTTGCC
46424 ACCCAAAAGA
Statistics
Matches: 77, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
43 19 0.25
44 17 0.22
47 3 0.04
48 38 0.49
ACGTcount: A:0.04, C:0.34, G:0.14, T:0.48
Consensus pattern (44 bp):
CCCCTGTTCTCTCTGTTTTTCTGTCATTTGCTTTGCCGCCCCAC
Found at i:46929 original size:25 final size:25
Alignment explanation
Indices: 46895--46946 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
46885 TTTCACATGA
46895 AGGTATTAAAGATTTGAACAAGTTG
1 AGGTATTAAAGATTTGAACAAGTTG
46920 AGGTATTAAAGATTTGAACAAGTTG
1 AGGTATTAAAGATTTGAACAAGTTG
46945 AG
1 AG
46947 TTGATTGCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.31
Consensus pattern (25 bp):
AGGTATTAAAGATTTGAACAAGTTG
Found at i:54189 original size:98 final size:98
Alignment explanation
Indices: 54015--54191 Score: 282
Period size: 98 Copynumber: 1.8 Consensus size: 98
54005 GATCTTTATG
* * * *
54015 AAAAGGTGCTATTGTTCTGTAAAATTTGATAAATAGGATTAGAATAATAGTTATAGTATTTCAGT
1 AAAAAGTGCTATTGTTCTGTAAAATTTGATAAATAGGATAAGAAAAATAGTTATAATATTTCAGT
54080 TTTGCAGTTTTGAATTAAATTCTAATTTTAATA
66 TTTGCAGTTTTGAATTAAATTCTAATTTTAATA
* * *
54113 AAAAAGTGCTATTGTTCTGTAAAATTTGATGAATAGGGTAAGAAAAATAGTTATAATATTTGAGT
1 AAAAAGTGCTATTGTTCTGTAAAATTTGATAAATAGGATAAGAAAAATAGTTATAATATTTCAGT
*
54178 TTTGTAGTTTTGAA
66 TTTGCAGTTTTGAA
54192 AATATTTTGG
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
98 71 1.00
ACGTcount: A:0.37, C:0.04, G:0.18, T:0.41
Consensus pattern (98 bp):
AAAAAGTGCTATTGTTCTGTAAAATTTGATAAATAGGATAAGAAAAATAGTTATAATATTTCAGT
TTTGCAGTTTTGAATTAAATTCTAATTTTAATA
Found at i:64671 original size:1 final size:1
Alignment explanation
Indices: 64665--64700 Score: 63
Period size: 1 Copynumber: 36.0 Consensus size: 1
64655 TCTAAACTGG
*
64665 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
64701 CACACACACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.97, C:0.03, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:72223 original size:13 final size:13
Alignment explanation
Indices: 72207--72232 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
72197 TTTGAAACAT
72207 GGTAAATAATAAG
1 GGTAAATAATAAG
72220 GGTAAATAATAAG
1 GGTAAATAATAAG
72233 ATAGACATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (13 bp):
GGTAAATAATAAG
Found at i:75144 original size:2 final size:2
Alignment explanation
Indices: 75137--75177 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
75127 GTGAATAATG
75137 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
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
Done.