Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012964.1 Corchorus capsularis cultivar CVL-1 contig12985, 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: 15497
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Found at i:222 original size:20 final size:21
Alignment explanation
Indices: 197--238 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
187 AAACGGAAAA
*
197 AGAAAAAT-TAATTTTTTTTT
1 AGAAAAATCGAATTTTTTTTT
217 AGAAAAATCGGAATTTTTTTTT
1 AGAAAAATC-GAATTTTTTTTT
239 TTTTAGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
22 11 0.58
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.50
Consensus pattern (21 bp):
AGAAAAATCGAATTTTTTTTT
Found at i:231 original size:26 final size:26
Alignment explanation
Indices: 202--255 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
192 GAAAAAGAAA
*
202 AATTAATTTTTTTTTAGAAAAATCGG
1 AATTAATTTTTTTTTAGAAAAAACGG
**
228 AATTTTTTTTTTTTTAGAAAAAACGG
1 AATTAATTTTTTTTTAGAAAAAACGG
254 AA
1 AA
256 AATCAAAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.39, C:0.04, G:0.11, T:0.46
Consensus pattern (26 bp):
AATTAATTTTTTTTTAGAAAAAACGG
Found at i:554 original size:6 final size:6
Alignment explanation
Indices: 545--578 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
535 AAAGCAAAGC
545 AAATCT AAATCT AAATCTT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATC-T AAATCT AAATCT AAA
579 GCAGATTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATCT
Found at i:568 original size:13 final size:13
Alignment explanation
Indices: 545--575 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
535 AAAGCAAAGC
545 AAATC-TAAATCT
1 AAATCTTAAATCT
557 AAATCTTAAATCT
1 AAATCTTAAATCT
570 AAATCT
1 AAATCT
576 AAAGCAGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.35
Consensus pattern (13 bp):
AAATCTTAAATCT
Found at i:590 original size:12 final size:13
Alignment explanation
Indices: 575--619 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
565 AATCTAAATC
575 TAAAGCAGATT-A
1 TAAAGCAGATTAA
*
587 TAAAGCAAATTAA
1 TAAAGCAGATTAA
600 TAAAGCAGATTAA
1 TAAAGCAGATTAA
613 TAAAGCA
1 TAAAGCA
620 AACAATAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22
Consensus pattern (13 bp):
TAAAGCAGATTAA
Found at i:626 original size:25 final size:25
Alignment explanation
Indices: 575--627 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
565 AATCTAAATC
*
575 TAAAGCAGATTATAAAGCAAATTAA
1 TAAAGCAGATTATAAAGCAAATCAA
600 TAAAGCAGATTAATAAAGCAAA-CAA
1 TAAAGCAGATT-ATAAAGCAAATCAA
625 TAA
1 TAA
628 TTAAAAAGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.58, C:0.09, G:0.11, T:0.21
Consensus pattern (25 bp):
TAAAGCAGATTATAAAGCAAATCAA
Found at i:1950 original size:19 final size:18
Alignment explanation
Indices: 1926--1962 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1916 TTGAAGATTT
1926 CTTGAAGATAATTTGAAGA
1 CTTGAAGATAA-TTGAAGA
*
1945 CTTGAAGATCATTGAAGA
1 CTTGAAGATAATTGAAGA
1963 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (18 bp):
CTTGAAGATAATTGAAGA
Found at i:3293 original size:21 final size:21
Alignment explanation
Indices: 3267--3310 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
3257 AATTTTCTTG
3267 ATTGTTCTCTTAG-TTAATTTT
1 ATTGTT-TCTTAGATTAATTTT
*
3288 ATTGTTTGTTAGATTTAATTTT
1 ATTGTTTCTTAGA-TTAATTTT
3310 A
1 A
3311 AACTCTTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 6 0.30
22 9 0.45
ACGTcount: A:0.23, C:0.05, G:0.11, T:0.61
Consensus pattern (21 bp):
ATTGTTTCTTAGATTAATTTT
Found at i:4647 original size:18 final size:17
Alignment explanation
Indices: 4590--4654 Score: 55
Period size: 16 Copynumber: 3.9 Consensus size: 17
4580 CGACCGATTG
*
4590 AATTTATATA-ATTTAT
1 AATTTATATATATATAT
* *
4606 AATATAAATTATATATAT
1 AATTTATA-TATATATAT
4624 AA--TATATGATATATAT
1 AATTTATAT-ATATATAT
*
4640 AATTTATATTTATAT
1 AATTTATATATATAT
4655 TATTAATATT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
15 1 0.03
16 19 0.49
17 7 0.18
18 12 0.31
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
AATTTATATATATATAT
Found at i:5474 original size:41 final size:42
Alignment explanation
Indices: 5410--5493 Score: 127
Period size: 41 Copynumber: 2.0 Consensus size: 42
5400 ATGCATTTAC
5410 TGATACTTGAATACTTGAATACTTAAATTCTG-AATTTCTTTT
1 TGATACTTGAATACTTGAATACTTAAATTCTGAAATTT-TTTT
* *
5452 TGATACTTG-ATACTTGACTACTTGAATTCTGAAATTTTTTT
1 TGATACTTGAATACTTGAATACTTAAATTCTGAAATTTTTTT
5493 T
1 T
5494 ACTTGTTTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
41 25 0.64
42 14 0.36
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.49
Consensus pattern (42 bp):
TGATACTTGAATACTTGAATACTTAAATTCTGAAATTTTTTT
Found at i:6308 original size:18 final size:18
Alignment explanation
Indices: 6285--6319 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6275 ATTTGACTCT
*
6285 TAAAGTTTCTGCATCTAC
1 TAAAGTTACTGCATCTAC
*
6303 TAAAGTTACTTCATCTA
1 TAAAGTTACTGCATCTA
6320 ACTTGCTTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (18 bp):
TAAAGTTACTGCATCTAC
Found at i:8134 original size:20 final size:19
Alignment explanation
Indices: 8111--8152 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
8101 ATTAAATGAA
*
8111 TTAGGATTTAGGGTTAGGGT
1 TTAGGATTTAAGGTTA-GGT
*
8131 TTAGGGTTTAAGGTTAGGT
1 TTAGGATTTAAGGTTAGGT
8150 TTA
1 TTA
8153 ATAAAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.43
Consensus pattern (19 bp):
TTAGGATTTAAGGTTAGGT
Found at i:8376 original size:29 final size:29
Alignment explanation
Indices: 8343--8410 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
8333 CAAGTCTTCT
*
8343 AAGTTTT-AGATTTAGGGAAAGATCCCGTC
1 AAGTTTTCA-ATTTAGGGAAAGATCCCATC
*
8372 AAGTTTTCAATTTTGGGAAAGATCCCATC
1 AAGTTTTCAATTTAGGGAAAGATCCCATC
*
8401 CAGTTTTCAA
1 AAGTTTTCAA
8411 AATTTTTCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 34 0.97
30 1 0.03
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (29 bp):
AAGTTTTCAATTTAGGGAAAGATCCCATC
Found at i:11175 original size:14 final size:14
Alignment explanation
Indices: 11143--11188 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
11133 TTTAAAAATT
11143 GTTTTCAAGAAAAGA
1 GTTTTCAA-AAAAGA
*
11158 -TTTTCAAAAATGA
1 GTTTTCAAAAAAGA
*
11171 GTTTT-AAAAAAGG
1 GTTTTCAAAAAAGA
11184 GTTTT
1 GTTTT
11189 AGTTTTTAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 16 0.59
14 11 0.41
ACGTcount: A:0.41, C:0.04, G:0.17, T:0.37
Consensus pattern (14 bp):
GTTTTCAAAAAAGA
Found at i:11865 original size:15 final size:15
Alignment explanation
Indices: 11842--11871 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11832 ACTTAAATGG
11842 GAAAAAAAGAAAGAA
1 GAAAAAAAGAAAGAA
*
11857 GAAAGAAAGAAAGAA
1 GAAAAAAAGAAAGAA
11872 ACTGGGCCTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
GAAAAAAAGAAAGAA
Done.