Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013306.1 Corchorus olitorius cultivar O-4 contig13339, 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: 26206
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:6618 original size:3 final size:3
Alignment explanation
Indices: 6610--6637 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
6600 AGCTTTAACC
6610 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
6638 AACCTGCTAG
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:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:9067 original size:18 final size:18
Alignment explanation
Indices: 9044--9079 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
9034 GACGGTATTT
9044 TGAATAACTTTCGGGTGA
1 TGAATAACTTTCGGGTGA
9062 TGAATAACTTTCGGGTGA
1 TGAATAACTTTCGGGTGA
9080 GGAGTTGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.11, G:0.28, T:0.33
Consensus pattern (18 bp):
TGAATAACTTTCGGGTGA
Found at i:13436 original size:40 final size:39
Alignment explanation
Indices: 13400--13688 Score: 350
Period size: 40 Copynumber: 7.3 Consensus size: 39
13390 ATCTTCCAAC
*** *
13400 TGGGAAGGGCAAATTGGGAATAAAAACAACACCTTCCGACG
1 TGGGAAGGGCAAAACAGGAATTAAAACAACACCTTCCG--G
* * *
13441 -GGGAAGGGCAAAAAAAGAATAAAAACAACACCTTCCGG
1 TGGGAAGGGCAAAACAGGAATTAAAACAACACCTTCCGG
*
13479 TGGGGAAGGGCGAAACAGGAATTAAAACAACACCTTCCGG
1 T-GGGAAGGGCAAAACAGGAATTAAAACAACACCTTCCGG
* **
13519 TGGGGAAGGGCAAAACATGTTTTAAAACAACACCTTCCGG
1 T-GGGAAGGGCAAAACAGGAATTAAAACAACACCTTCCGG
*
13559 TGGGAAGGGCAAAACAAGAA-TAAAACAACACCTTCCGG
1 TGGGAAGGGCAAAACAGGAATTAAAACAACACCTTCCGG
* *
13597 CAGGGAAGGGCAAAACAGGAATTAAAACAACACCTT-CGA
1 -TGGGAAGGGCAAAACAGGAATTAAAACAACACCTTCCGG
* *
13636 TGGGGAAGGGCAAACCAGGAATTAAAACAGCACCTTCCGG
1 T-GGGAAGGGCAAAACAGGAATTAAAACAACACCTTCCGG
13676 TGGGAAAGGGCAA
1 TGGG-AAGGGCAA
13689 TTTGGGAAAA
Statistics
Matches: 219, Mismatches: 22, Indels: 15
0.86 0.09 0.06
Matches are distributed among these distances:
38 19 0.09
39 71 0.32
40 129 0.59
ACGTcount: A:0.41, C:0.20, G:0.27, T:0.12
Consensus pattern (39 bp):
TGGGAAGGGCAAAACAGGAATTAAAACAACACCTTCCGG
Found at i:13733 original size:48 final size:48
Alignment explanation
Indices: 13657--13796 Score: 217
Period size: 48 Copynumber: 2.9 Consensus size: 48
13647 AAACCAGGAA
* * *
13657 TTAAAACAGCACCTTCCGGTGGGAAAGGGCAATTTGGGAAAAAGCAGAC
1 TTAAACCA-CACCTTCCGATGGGGAAGGGCAATTTGGGAAAAAGCAGAC
*
13706 TTAAACCACACCTTCCGATGGGGAAGGGCAATTTGGGAAAAAGCATAC
1 TTAAACCACACCTTCCGATGGGGAAGGGCAATTTGGGAAAAAGCAGAC
*
13754 TTAAACAACACCTTCCGATGGGGAAGGGCAATTTTGGGAAAAA
1 TTAAACCACACCTTCCGATGGGGAAGGGCAA-TTTGGGAAAAA
13797 ATGGAAATAG
Statistics
Matches: 85, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
48 67 0.79
49 18 0.21
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (48 bp):
TTAAACCACACCTTCCGATGGGGAAGGGCAATTTGGGAAAAAGCAGAC
Found at i:14250 original size:51 final size:50
Alignment explanation
Indices: 14169--14269 Score: 141
Period size: 51 Copynumber: 2.0 Consensus size: 50
14159 AATGAAAAGC
** * *
14169 TCAATCTTTTTCTTTAAAGGTTTCATCTTTATTACAATTTAATCAAAGAT
1 TCAATCTTTTTCTTTAAAGACTTCATCTTTATTACAAATTAACCAAAGAT
14219 TCAATCTTTTTAGC-TTAAAGACTTCATCTTTATTACAAATTAACCAAAGAT
1 TCAATCTTTTT--CTTTAAAGACTTCATCTTTATTACAAATTAACCAAAGAT
14270 CTCATTTTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
50 11 0.24
51 33 0.73
52 1 0.02
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.44
Consensus pattern (50 bp):
TCAATCTTTTTCTTTAAAGACTTCATCTTTATTACAAATTAACCAAAGAT
Found at i:14319 original size:51 final size:51
Alignment explanation
Indices: 14271--14432 Score: 236
Period size: 51 Copynumber: 3.2 Consensus size: 51
14261 ACCAAAGATC
* * * ** *
14271 TCATTTTTATTTACAAATTGATTAGAAGTCAAATCTTTTAGGCTAAAGACT
1 TCATTTTTACTTACAAATTGATCAAAAGTTTAATCTTTTAGCCTAAAGACT
*
14322 TCATTTTTACTTACAAATTGATCAAAAGTTTAATCTTTTAATCC-AAAGACT
1 TCATTTTTACTTACAAATTGATCAAAAGTTTAATCTTTT-AGCCTAAAGACT
14373 TCATTTTTACTTACAAATTGATCAAAAGTTTAATCTTTTAGCCTAAAGACT
1 TCATTTTTACTTACAAATTGATCAAAAGTTTAATCTTTTAGCCTAAAGACT
*
14424 TCATCTTTA
1 TCATTTTTA
14433 TTATTACTTT
Statistics
Matches: 100, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
50 3 0.03
51 95 0.95
52 2 0.02
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (51 bp):
TCATTTTTACTTACAAATTGATCAAAAGTTTAATCTTTTAGCCTAAAGACT
Found at i:14623 original size:51 final size:51
Alignment explanation
Indices: 14568--14672 Score: 158
Period size: 51 Copynumber: 2.1 Consensus size: 51
14558 TTTTTCGATC
* * * *
14568 AAAGATTATGTTTTTATTATGAATTCACCAAAGTTTAAAGCTCTTT-AAACT
1 AAAGATTATATTTTTATTATCAACTCACCAAAATTTAAAGCT-TTTAAAACT
14619 AAAGATTATATTTTTATTATCAACTCACCAAAATTTAAAGCTTTTAAAACT
1 AAAGATTATATTTTTATTATCAACTCACCAAAATTTAAAGCTTTTAAAACT
14670 AAA
1 AAA
14673 TCTACTCTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
50 3 0.06
51 46 0.94
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (51 bp):
AAAGATTATATTTTTATTATCAACTCACCAAAATTTAAAGCTTTTAAAACT
Found at i:14873 original size:20 final size:20
Alignment explanation
Indices: 14839--14879 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
14829 TCAAAGCAGC
** *
14839 CTCTTCTTCTTTTTCTTTTT
1 CTCTTCTTCCCTTTCCTTTT
14859 CTCTTCTTCCCTTTCCTTTT
1 CTCTTCTTCCCTTTCCTTTT
14879 C
1 C
14880 CGCCTTTATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (20 bp):
CTCTTCTTCCCTTTCCTTTT
Found at i:19268 original size:31 final size:31
Alignment explanation
Indices: 19230--19293 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
19220 CACTTAAGTA
*
19230 AAAGAAATGGACTTATCAAGCAACAGACACC
1 AAAGAAATGGACTAATCAAGCAACAGACACC
**
19261 AAAGAAATGGACTAATCAAGCAATGGACACC
1 AAAGAAATGGACTAATCAAGCAACAGACACC
19292 AA
1 AA
19294 TTGGATAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.50, C:0.20, G:0.17, T:0.12
Consensus pattern (31 bp):
AAAGAAATGGACTAATCAAGCAACAGACACC
Found at i:23938 original size:21 final size:21
Alignment explanation
Indices: 23912--23955 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
23902 GTGTAGACAT
23912 ATAAAATTTGACCAATCAACA
1 ATAAAATTTGACCAATCAACA
23933 ATAAAATTTGACCAATCAACA
1 ATAAAATTTGACCAATCAACA
23954 AT
1 AT
23956 GGTTTAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.52, C:0.18, G:0.05, T:0.25
Consensus pattern (21 bp):
ATAAAATTTGACCAATCAACA
Found at i:24194 original size:19 final size:19
Alignment explanation
Indices: 24172--24209 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
24162 CCCTAGTCTT
24172 TCCTAAAAAAAACCTAGCC
1 TCCTAAAAAAAACCTAGCC
* *
24191 TCCTCAAGAAAACCTAGCC
1 TCCTAAAAAAAACCTAGCC
24210 GCCTCAGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.34, G:0.08, T:0.16
Consensus pattern (19 bp):
TCCTAAAAAAAACCTAGCC
Found at i:24341 original size:31 final size:31
Alignment explanation
Indices: 24303--24368 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
24293 AACAACAAAC
24303 ACAGTTCGCAACAACAAAACCCATCCGATCT
1 ACAGTTCGCAACAACAAAACCCATCCGATCT
*
24334 ACAGTTCGCAACAACAAAGCCCATCCGATCT
1 ACAGTTCGCAACAACAAAACCCATCCGATCT
24365 ACAG
1 ACAG
24369 AAAACAACAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.38, C:0.35, G:0.12, T:0.15
Consensus pattern (31 bp):
ACAGTTCGCAACAACAAAACCCATCCGATCT
Found at i:24377 original size:31 final size:31
Alignment explanation
Indices: 24311--24378 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
24301 ACACAGTTCG
****
24311 CAACAACAAAACCCATCCGATCTACAGTTCG
1 CAACAACAAAACCCATCCGATCTACAGAAAA
*
24342 CAACAACAAAGCCCATCCGATCTACAGAAAA
1 CAACAACAAAACCCATCCGATCTACAGAAAA
24373 CAACAA
1 CAACAA
24379 GTTCGCAACA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.46, C:0.34, G:0.09, T:0.12
Consensus pattern (31 bp):
CAACAACAAAACCCATCCGATCTACAGAAAA
Found at i:24388 original size:73 final size:73
Alignment explanation
Indices: 24272--24410 Score: 210
Period size: 73 Copynumber: 1.9 Consensus size: 73
24262 GCAAATCAAG
* * *
24272 CAACAAAGCCCATCTGATCGCAACAACAAACACAGTTCGCAACAACAAAACCCATCCGATCTACA
1 CAACAAAGCCCATCCGATCACAAAAACAAACACAGTTCGCAACAACAAAACCCATCCGATCTACA
24337 GTTCGCAA
66 GTTCGCAA
*
24345 CAACAAAGCCCATCCGATCTACAGAAAAC-AACA-AGTTCGCAACAACAAAGCCCATCCGATCTA
1 CAACAAAGCCCATCCGATC-ACA-AAAACAAACACAGTTCGCAACAACAAAACCCATCCGATCTA
24408 CAG
64 CAG
24411 AAAACAACAA
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
73 50 0.83
74 6 0.10
75 4 0.07
ACGTcount: A:0.42, C:0.34, G:0.12, T:0.13
Consensus pattern (73 bp):
CAACAAAGCCCATCCGATCACAAAAACAAACACAGTTCGCAACAACAAAACCCATCCGATCTACA
GTTCGCAA
Found at i:24395 original size:42 final size:42
Alignment explanation
Indices: 24336--24452 Score: 234
Period size: 42 Copynumber: 2.8 Consensus size: 42
24326 TCCGATCTAC
24336 AGTTCGCAACAACAAAGCCCATCCGATCTACAGAAAACAACA
1 AGTTCGCAACAACAAAGCCCATCCGATCTACAGAAAACAACA
24378 AGTTCGCAACAACAAAGCCCATCCGATCTACAGAAAACAACA
1 AGTTCGCAACAACAAAGCCCATCCGATCTACAGAAAACAACA
24420 AGTTCGCAACAACAAAGCCCATCCGATCTACAG
1 AGTTCGCAACAACAAAGCCCATCCGATCTACAG
24453 CTCATCCGAT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.43, C:0.32, G:0.13, T:0.13
Consensus pattern (42 bp):
AGTTCGCAACAACAAAGCCCATCCGATCTACAGAAAACAACA
Found at i:25475 original size:22 final size:22
Alignment explanation
Indices: 25447--25491 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
25437 CCATCGTGAC
*
25447 TTCCCCTTTTTTACTTCCCATT
1 TTCCCCTTTTTTACTTCACATT
25469 TTCCCCTTTTTTACTTCACATT
1 TTCCCCTTTTTTACTTCACATT
25491 T
1 T
25492 CTTTCCACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.11, C:0.33, G:0.00, T:0.56
Consensus pattern (22 bp):
TTCCCCTTTTTTACTTCACATT
Done.