Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011886.1 Corchorus olitorius cultivar O-4 contig11919, 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: 8610
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Found at i:1047 original size:37 final size:37
Alignment explanation
Indices: 934--1047 Score: 122
Period size: 37 Copynumber: 3.1 Consensus size: 37
924 GTTTGACTAC
* ** *
934 GATAACTACGGAAAGATGACCCGTTTCAAGTCGACTTT
1 GATAACTACGGAAAGATGACCTGTTTCCCGTCAAC-TT
* * *
972 GATACCTACGGAAAGATGACAT-TTTCCCGTCGATCTT
1 GATAACTACGGAAAGATGACCTGTTTCCCGTC-AACTT
* *
1009 GATAACTGCTGAAAGATGACCTGTTTCCCGTCAACTT
1 GATAACTACGGAAAGATGACCTGTTTCCCGTCAACTT
1046 GA
1 GA
1048 AAGCTTGAGG
Statistics
Matches: 62, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
37 33 0.53
38 29 0.47
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (37 bp):
GATAACTACGGAAAGATGACCTGTTTCCCGTCAACTT
Found at i:3486 original size:213 final size:213
Alignment explanation
Indices: 3119--3528 Score: 786
Period size: 213 Copynumber: 1.9 Consensus size: 213
3109 AGTTTTTCTC
*
3119 TTTTTTGATGGGAATTTGATGATTGATGACTTTTGCCTCATTGACTTGTCTGACGTCCTTCGATG
1 TTTTTTGATGGGAATTTGATGATTAATGACTTTTGCCTCATTGACTTGTCTGACGTCCTTCGATG
3184 AAGGTGAGCGTATTATTCTTACATCGAATGTTGCCCCCTATTAATCACAAATGCGGTAATGGTGT
66 AAGGTGAGCGTATTATTCTTACATCGAATGTTGCCCCCTATTAATCACAAATGCGGTAATGGTGT
*
3249 TTTAACAACATAAATGGTTTGAAATGTGCCATTTTA-TTGGGCTTAATTGTTCTCCGAATCAATT
131 TTTAACAACATAAATGGTTTGAAATGTGCCA-TTTAGGTGGGCTTAATTGTTCTCCGAATCAATT
3313 TGTAGTTTTTCTCTTCTTT
195 TGTAGTTTTTCTCTTCTTT
3332 TTTTTTGATGGGAATTTGATGATTAATGACTTTTGCCTCATTGACTTGTCTGACGTCCTTCGATG
1 TTTTTTGATGGGAATTTGATGATTAATGACTTTTGCCTCATTGACTTGTCTGACGTCCTTCGATG
3397 AAGGTGAGCGTATTATTCTTACATCGAATGTTGCCCCCTATTAATCACAAATGCGGTAATGGTGT
66 AAGGTGAGCGTATTATTCTTACATCGAATGTTGCCCCCTATTAATCACAAATGCGGTAATGGTGT
3462 TTTAACAACATAAATGGTTTGAAATGTGCCATTTAGGTGGGCTTAATTGTTCTCCGAATCAATTT
131 TTTAACAACATAAATGGTTTGAAATGTGCCATTTAGGTGGGCTTAATTGTTCTCCGAATCAATTT
3527 GT
196 GT
3529 CTTCTCAAGG
Statistics
Matches: 194, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
212 4 0.02
213 190 0.98
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (213 bp):
TTTTTTGATGGGAATTTGATGATTAATGACTTTTGCCTCATTGACTTGTCTGACGTCCTTCGATG
AAGGTGAGCGTATTATTCTTACATCGAATGTTGCCCCCTATTAATCACAAATGCGGTAATGGTGT
TTTAACAACATAAATGGTTTGAAATGTGCCATTTAGGTGGGCTTAATTGTTCTCCGAATCAATTT
GTAGTTTTTCTCTTCTTT
Found at i:5946 original size:49 final size:49
Alignment explanation
Indices: 5888--6067 Score: 171
Period size: 49 Copynumber: 3.8 Consensus size: 49
5878 TGCTTACTCT
**
5888 TTCTTTTACTCTTTAACTTAATTACCCAAAATTAAACTTCTCTGTTTAC
1 TTCTTTTACTCTTTAGTTTAATTACCCAAAATTAAACTTCTCTGTTTAC
* *
5937 TTCTTTTACTTTTTAGTTTAATTAACCC--------A-GTCTCTGTTTACTTC
1 TTCTTTTACTCTTTAGTTTAATT-ACCCAAAATTAAACTTCTCTGTTTA---C
* *
5981 TTCTTTTCCTCTTTAGTTTAATTACCCGAAATTAAACTTCTCTGTTTAC
1 TTCTTTTACTCTTTAGTTTAATTACCCAAAATTAAACTTCTCTGTTTAC
* * * *
6030 TTCCTTTACTTTTTAGTTTGATTACCCAGAATTAAACT
1 TTCTTTTACTCTTTAGTTTAATTACCCAAAATTAAACT
6068 AATTACTGTT
Statistics
Matches: 105, Mismatches: 13, Indels: 26
0.73 0.09 0.18
Matches are distributed among these distances:
41 10 0.10
42 1 0.01
43 4 0.04
44 22 0.21
49 53 0.50
50 4 0.04
51 1 0.01
52 10 0.10
ACGTcount: A:0.24, C:0.21, G:0.06, T:0.49
Consensus pattern (49 bp):
TTCTTTTACTCTTTAGTTTAATTACCCAAAATTAAACTTCTCTGTTTAC
Found at i:6002 original size:93 final size:92
Alignment explanation
Indices: 5888--6058 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 92
5878 TGCTTACTCT
*
5888 TTCTTTTACTCTTTAACTTAATTACCCAAAATTAAACTTCTCTGTTTACTTCTTTTACTTTTTAG
1 TTCTTTTACTCTTTAACTTAATTACCCAAAATTAAACTTCTCTGTTTACTTCCTTTACTTTTTAG
5953 TTTAATTAACCCAGTCTCTGTTTACTTC
66 TTTAATT-ACCCAGTCTCTGTTTACTTC
* ** *
5981 TTCTTTTCCTCTTTAGTTTAATTACCCGAAATTAAACTTCTCTGTTTACTTCCTTTACTTTTTAG
1 TTCTTTTACTCTTTAACTTAATTACCCAAAATTAAACTTCTCTGTTTACTTCCTTTACTTTTTAG
*
6046 TTTGATTACCCAG
66 TTTAATTACCCAG
6059 AATTAAACTA
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
92 6 0.08
93 66 0.92
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (92 bp):
TTCTTTTACTCTTTAACTTAATTACCCAAAATTAAACTTCTCTGTTTACTTCCTTTACTTTTTAG
TTTAATTACCCAGTCTCTGTTTACTTC
Found at i:6151 original size:36 final size:36
Alignment explanation
Indices: 6091--6163 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
6081 CATTCGCTAC
* * *
6091 TTAGTTTAATTTCCTGGAACTAAACTAACCTCTTCT
1 TTAGTTCAATTACCTAGAACTAAACTAACCTCTTCT
* * *
6127 TTAGTTCAATTACCTAGAATTAAACTTATCTCTTCT
1 TTAGTTCAATTACCTAGAACTAAACTAACCTCTTCT
6163 T
1 T
6164 CTTTTATTAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.44
Consensus pattern (36 bp):
TTAGTTCAATTACCTAGAACTAAACTAACCTCTTCT
Found at i:6196 original size:47 final size:47
Alignment explanation
Indices: 6127--6626 Score: 598
Period size: 47 Copynumber: 10.6 Consensus size: 47
6117 AACCTCTTCT
* * *
6127 TTAGTTCAATTACCTAGAATTAAACTTATCTCTTCTTCTTTTATTAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
6174 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
*
6221 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTCTACTAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
6268 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
* *
6315 TTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTTTTTTACTAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
*
6362 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTATTTAGTTT
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTAC----TA---C
* * * *
6416 TTAGTTTAATTGCCCAGAATTTAACTAACCTCTTCTTC-TTT--T--
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
* * * * * * *
6458 TTAGTTTAATTGCCCAGAATTAAACAAACCTCTTCTTCTTTCATTAT
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
* * * * *
6505 TTAATTTAATTACCT-GAGATTAAACTAACCTTTTCTTCTTTCACTAT
1 TTAGTTTAATTACCTAGA-ATTAAACTAATCTCTTCTTCTTTTACTAC
* * * * * *
6552 TTAGTTTAATTACTTGGAATTAAAACTAACCTTTTCTTCTTTCACTAT
1 TTAGTTTAATTACCTAGAATT-AAACTAATCTCTTCTTCTTTTACTAC
* *
6600 TTAGTTTAATTACCTGGAATCAAACTA
1 TTAGTTTAATTACCTAGAATTAAACTA
6627 TCCTTTGTTT
Statistics
Matches: 411, Mismatches: 27, Indels: 30
0.88 0.06 0.06
Matches are distributed among these distances:
42 36 0.09
43 2 0.00
45 1 0.00
46 2 0.00
47 284 0.69
48 47 0.11
51 2 0.00
53 3 0.01
54 34 0.08
ACGTcount: A:0.29, C:0.18, G:0.05, T:0.47
Consensus pattern (47 bp):
TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
Found at i:6471 original size:42 final size:42
Alignment explanation
Indices: 6413--6498 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
6403 TACTATTTAG
* *
6413 TTTTTAGTTTAATTGCCCAGAATTTAACTAACCTCTTCTTCT
1 TTTTTAGTTTAATTGCCCAGAATTAAACAAACCTCTTCTTCT
6455 TTTTTAGTTTAATTGCCCAGAATTAAACAAACCTCTTCTTCT
1 TTTTTAGTTTAATTGCCCAGAATTAAACAAACCTCTTCTTCT
6497 TT
1 TT
6499 CATTATTTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.47
Consensus pattern (42 bp):
TTTTTAGTTTAATTGCCCAGAATTAAACAAACCTCTTCTTCT
Found at i:6508 original size:42 final size:42
Alignment explanation
Indices: 6416--6510 Score: 147
Period size: 42 Copynumber: 2.3 Consensus size: 42
6406 TATTTAGTTT
* * *
6416 TTAGTTTAATTGCCCAGAATTTAACTAACCTCTTCTTCTTTT
1 TTAGTTTAATTGCCCAGAATTAAACAAACCTCTTCTTCTTTA
6458 TTAGTTTAATTGCCCAGAATTAAACAAACCTCTTCTTCTTTCA
1 TTAGTTTAATTGCCCAGAATTAAACAAACCTCTTCTTCTTT-A
6501 TTA-TTTAATT
1 TTAGTTTAATT
6511 TAATTACCTG
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
42 46 0.94
43 3 0.06
ACGTcount: A:0.27, C:0.20, G:0.06, T:0.46
Consensus pattern (42 bp):
TTAGTTTAATTGCCCAGAATTAAACAAACCTCTTCTTCTTTA
Found at i:7108 original size:25 final size:25
Alignment explanation
Indices: 7057--7138 Score: 80
Period size: 25 Copynumber: 3.3 Consensus size: 25
7047 AAACTAAATT
*
7057 AAGCCCAAATGCAAGGGAAAGTTAA
1 AAGCCCAAATGCAAAGGAAAGTTAA
7082 AAGCCCAAATG-AAAGGAAA-TTAA
1 AAGCCCAAATGCAAAGGAAAGTTAA
** *
7105 AAAACCAAGTATGCAAATG-AAGTTAA
1 AAGCCCAA--ATGCAAAGGAAAGTTAA
*
7131 AAGTCCAA
1 AAGCCCAA
7139 GTGATACTAC
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
23 10 0.21
24 7 0.15
25 16 0.34
26 14 0.30
ACGTcount: A:0.52, C:0.15, G:0.18, T:0.15
Consensus pattern (25 bp):
AAGCCCAAATGCAAAGGAAAGTTAA
Found at i:7138 original size:26 final size:25
Alignment explanation
Indices: 7075--7140 Score: 64
Period size: 26 Copynumber: 2.7 Consensus size: 25
7065 ATGCAAGGGA
*
7075 AAGTTAAAAGCCCAA--ATGAAAGG
1 AAGTTAAAAGACCAAGTATGAAAGG
* * *
7098 AAATTAAAAAACCAAGTATGCAAATG
1 AAGTTAAAAGACCAAGTATG-AAAGG
*
7124 AAGTTAAAAGTCCAAGT
1 AAGTTAAAAGACCAAGT
7141 GATACTACCC
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
23 12 0.36
25 3 0.09
26 18 0.55
ACGTcount: A:0.53, C:0.12, G:0.17, T:0.18
Consensus pattern (25 bp):
AAGTTAAAAGACCAAGTATGAAAGG
Done.