Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007141.1 Corchorus capsularis cultivar CVL-1 contig07162, 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: 24297
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:4243 original size:20 final size:21
Alignment explanation
Indices: 4199--4247 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 21
4189 GAGAATTTTC
4199 AAAAAAA-AATCAAAATCAAT
1 AAAAAAATAATCAAAATCAAT
*
4219 -TAAAAATAAT-AAAATCAAT
1 AAAAAAATAATCAAAATCAAT
4238 AAAAAAATAA
1 AAAAAAATAA
4248 GAAATGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (21 bp):
AAAAAAATAATCAAAATCAAT
Found at i:4259 original size:14 final size:15
Alignment explanation
Indices: 4240--4277 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
4230 AAATCAATAA
4240 AAAAAT-AAGAAATG
1 AAAAATGAAGAAATG
*
4254 AAAAATGATGAAATG
1 AAAAATGAAGAAATG
*
4269 AAAATTGAA
1 AAAAATGAA
4278 AATTTAAGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (15 bp):
AAAAATGAAGAAATG
Found at i:4510 original size:13 final size:13
Alignment explanation
Indices: 4492--4520 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
4482 AAGTAGTCCG
4492 TTTTGAAAAGAGT
1 TTTTGAAAAGAGT
4505 TTTTGAAAAGAGT
1 TTTTGAAAAGAGT
4518 TTT
1 TTT
4521 CGAGTTAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (13 bp):
TTTTGAAAAGAGT
Found at i:4564 original size:10 final size:10
Alignment explanation
Indices: 4549--4584 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
4539 CCAAGTGCGG
4549 TGAAAAAAAA
1 TGAAAAAAAA
4559 TG--AAAAAA
1 TGAAAAAAAA
4567 TGAAAAAAAA
1 TGAAAAAAAA
4577 TGAAAAAA
1 TGAAAAAA
4585 GAGAAGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 8 0.33
10 16 0.67
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (10 bp):
TGAAAAAAAA
Found at i:4594 original size:18 final size:18
Alignment explanation
Indices: 4549--4584 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
4539 CCAAGTGCGG
4549 TGAAAAAAAATGAAAAAA
1 TGAAAAAAAATGAAAAAA
4567 TGAAAAAAAATGAAAAAA
1 TGAAAAAAAATGAAAAAA
4585 GAGAAGAAAA
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:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (18 bp):
TGAAAAAAAATGAAAAAA
Found at i:5844 original size:22 final size:22
Alignment explanation
Indices: 5819--5938 Score: 96
Period size: 22 Copynumber: 5.2 Consensus size: 22
5809 TCCAGGCACA
*
5819 AATTCAGAAACCTCCGGGTGTT
1 AATTCAGAAACCTCCGGGTATT
* * *
5841 AATTCTGATAAGTCCTCCGGGCACT
1 AATTCAGA-AA--CCTCCGGGTATT
*
5866 AATTCAGAAACCTCCGGGTGTT
1 AATTCAGAAACCTCCGGGTATT
* * **
5888 AATTCTGATAAGTCCTCCGGGCACA
1 AATTCAGA-AA--CCTCCGGGTATT
*
5913 AATTCAGAAACCTCCGAGTATT
1 AATTCAGAAACCTCCGGGTATT
5935 AATT
1 AATT
5939 TTGATAAGTC
Statistics
Matches: 74, Mismatches: 18, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
22 35 0.47
23 4 0.05
24 4 0.05
25 31 0.42
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (22 bp):
AATTCAGAAACCTCCGGGTATT
Found at i:5858 original size:25 final size:25
Alignment explanation
Indices: 5829--5955 Score: 113
Period size: 25 Copynumber: 5.3 Consensus size: 25
5819 AATTCAGAAA
*
5829 CCTCCGGGTGTTAATTCTGATAAGT
1 CCTCCGGGTATTAATTCTGATAAGT
* * *
5854 CCTCCGGGCACTAATTCAGA-AA--
1 CCTCCGGGTATTAATTCTGATAAGT
*
5876 CCTCCGGGTGTTAATTCTGATAAGT
1 CCTCCGGGTATTAATTCTGATAAGT
* ** *
5901 CCTCCGGGCACAAATTCAGA-AA--
1 CCTCCGGGTATTAATTCTGATAAGT
* *
5923 CCTCCGAGTATTAATTTTGATAAGT
1 CCTCCGGGTATTAATTCTGATAAGT
5948 CCTCCGGG
1 CCTCCGGG
5956 CAATTGGTAA
Statistics
Matches: 76, Mismatches: 20, Indels: 12
0.70 0.19 0.11
Matches are distributed among these distances:
22 30 0.39
23 4 0.05
24 4 0.05
25 38 0.50
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.28
Consensus pattern (25 bp):
CCTCCGGGTATTAATTCTGATAAGT
Found at i:5871 original size:47 final size:47
Alignment explanation
Indices: 5802--5957 Score: 267
Period size: 47 Copynumber: 3.3 Consensus size: 47
5792 TATGTATTGG
*
5802 TAAGTCCTCCAGGCACAAATTCAGAAACCTCCGGGTGTTAATTCTGA
1 TAAGTCCTCCGGGCACAAATTCAGAAACCTCCGGGTGTTAATTCTGA
*
5849 TAAGTCCTCCGGGCACTAATTCAGAAACCTCCGGGTGTTAATTCTGA
1 TAAGTCCTCCGGGCACAAATTCAGAAACCTCCGGGTGTTAATTCTGA
* * *
5896 TAAGTCCTCCGGGCACAAATTCAGAAACCTCCGAGTATTAATTTTGA
1 TAAGTCCTCCGGGCACAAATTCAGAAACCTCCGGGTGTTAATTCTGA
5943 TAAGTCCTCCGGGCA
1 TAAGTCCTCCGGGCA
5958 ATTGGTAAAA
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 103 1.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (47 bp):
TAAGTCCTCCGGGCACAAATTCAGAAACCTCCGGGTGTTAATTCTGA
Found at i:6668 original size:27 final size:28
Alignment explanation
Indices: 6638--6712 Score: 116
Period size: 27 Copynumber: 2.7 Consensus size: 28
6628 AGGGTCATAT
6638 AGGGGCATTTTGGTCATTTTTACATTC-
1 AGGGGCATTTTGGTCATTTTTACATTCA
* * *
6665 AGGGGTATTTAGGTCATTTTTGCATTCA
1 AGGGGCATTTTGGTCATTTTTACATTCA
6693 AGGGGCATTTTGGTCATTTT
1 AGGGGCATTTTGGTCATTTT
6713 GAGTCCATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 24 0.57
28 18 0.43
ACGTcount: A:0.19, C:0.12, G:0.25, T:0.44
Consensus pattern (28 bp):
AGGGGCATTTTGGTCATTTTTACATTCA
Found at i:8001 original size:23 final size:23
Alignment explanation
Indices: 7971--8016 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
7961 CAAACAATCT
7971 TGAGCACTCTCGCTCGGTCTCTA
1 TGAGCACTCTCGCTCGGTCTCTA
*
7994 TGAGCACTCTCGCTTGGTCTCTA
1 TGAGCACTCTCGCTCGGTCTCTA
8017 CAAACCAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.13, C:0.33, G:0.22, T:0.33
Consensus pattern (23 bp):
TGAGCACTCTCGCTCGGTCTCTA
Found at i:11088 original size:21 final size:20
Alignment explanation
Indices: 11047--11103 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 20
11037 ATTATGAGCT
* **
11047 AATTTTAATTTAAAGGTTAA
1 AATTTTAATTAAAAGACTAA
11067 AATTTTGAATTAAAAGACTAA
1 AATTTT-AATTAAAAGACTAA
*
11088 ATTATTTATATTAAAA
1 AAT-TTTA-ATTAAAA
11104 ATCAACTCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 6 0.20
21 14 0.47
22 10 0.33
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (20 bp):
AATTTTAATTAAAAGACTAA
Found at i:13068 original size:27 final size:27
Alignment explanation
Indices: 13030--13317 Score: 335
Period size: 27 Copynumber: 10.7 Consensus size: 27
13020 GGTCTCATCA
* *
13030 AGATGTCACTGAAACGAATCAACCCTG
1 AGATGTCACTGAAGCGAATCTACCCTG
* * * *
13057 AGATGTCTCTGAAGAGAATTTCCCCTG
1 AGATGTCACTGAAGCGAATCTACCCTG
* *
13084 AGATGTCACTGAAGCGAATCTGCCCTA
1 AGATGTCACTGAAGCGAATCTACCCTG
*
13111 AGATGTCACTGAAGGGAATCTACCCTG
1 AGATGTCACTGAAGCGAATCTACCCTG
* *
13138 CGATGTCACTGAAGCGAATCTACCCTA
1 AGATGTCACTGAAGCGAATCTACCCTG
*
13165 AGATGCCACTGAAGCGAATCTACCCTG
1 AGATGTCACTGAAGCGAATCTACCCTG
* * *
13192 CGATGCCACTGAAGCAAATCTACCCTG
1 AGATGTCACTGAAGCGAATCTACCCTG
* **
13219 AGATGCCACTGAAGATAATCTACCCTG
1 AGATGTCACTGAAGCGAATCTACCCTG
* * *
13246 AGATGTCAGTAAAGAGAATCTACCCT-
1 AGATGTCACTGAAGCGAATCTACCCTG
* * * * *
13272 AGATGTTATTAAAGAGAATCTACCATG
1 AGATGTCACTGAAGCGAATCTACCCTG
13299 AGATGTCACTGAAGCGAAT
1 AGATGTCACTGAAGCGAAT
13318 TTGCCCTTAG
Statistics
Matches: 224, Mismatches: 36, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
26 23 0.10
27 201 0.90
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.23
Consensus pattern (27 bp):
AGATGTCACTGAAGCGAATCTACCCTG
Found at i:17697 original size:21 final size:22
Alignment explanation
Indices: 17673--17713 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
17663 TTGATTTATG
*
17673 AATTTA-AATTGTTTTTCTTTC
1 AATTTAGAATTATTTTTCTTTC
*
17694 AATTTAGATTTATTTTTCTT
1 AATTTAGAATTATTTTTCTT
17714 GTTCTTCATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.24, C:0.07, G:0.05, T:0.63
Consensus pattern (22 bp):
AATTTAGAATTATTTTTCTTTC
Found at i:22587 original size:19 final size:18
Alignment explanation
Indices: 22563--22598 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
22553 TGAAGATTTC
22563 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
22582 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
22599 ATTATTTCAA
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:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Done.