Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017768.1 Corchorus olitorius cultivar O-4 contig17801, 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: 24121
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Found at i:5380 original size:24 final size:24
Alignment explanation
Indices: 5347--5392 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
5337 AAAGGTAAAG
5347 GGGTTCTTTTTTTTTTCTTTTTCT
1 GGGTTCTTTTTTTTTTCTTTTTCT
* *
5371 GGGTTGTTTTTTTTTTTTTTTT
1 GGGTTCTTTTTTTTTTCTTTTT
5393 TGAGAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.00, C:0.07, G:0.15, T:0.78
Consensus pattern (24 bp):
GGGTTCTTTTTTTTTTCTTTTTCT
Found at i:11851 original size:22 final size:21
Alignment explanation
Indices: 11803--11856 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
11793 GACAAATCGC
* *
11803 AAACCCTAATTTCAAACCTTT
1 AAACCCTAATTTCAAACCATG
*
11824 AGAACCCTAATTTGAAACCCATG
1 A-AACCCTAATTTCAAA-CCATG
11847 AAACCC-AATT
1 AAACCCTAATT
11857 GAATTTCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 5 0.18
22 19 0.68
23 4 0.14
ACGTcount: A:0.41, C:0.28, G:0.06, T:0.26
Consensus pattern (21 bp):
AAACCCTAATTTCAAACCATG
Found at i:17685 original size:33 final size:33
Alignment explanation
Indices: 17643--17708 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
17633 TATATAGTGG
17643 ATGGACTCGGCTCAAACAAGAGTAATTCTGTGT
1 ATGGACTCGGCTCAAACAAGAGTAATTCTGTGT
17676 ATGGACTCGGCTCAAACAAGAGTAATTCTGTGT
1 ATGGACTCGGCTCAAACAAGAGTAATTCTGTGT
17709 GTATATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.27
Consensus pattern (33 bp):
ATGGACTCGGCTCAAACAAGAGTAATTCTGTGT
Found at i:17861 original size:21 final size:21
Alignment explanation
Indices: 17837--17910 Score: 70
Period size: 21 Copynumber: 3.7 Consensus size: 21
17827 AAACACTAAT
17837 GAAAAAAAAGGGGATTACCGA
1 GAAAAAAAAGGGGATTACCGA
*
17858 GAAATAAAAA--CG-TTA---A
1 GAAA-AAAAAGGGGATTACCGA
17874 TGAAAAAAAAGGGGATTACCGA
1 -GAAAAAAAAGGGGATTACCGA
*
17896 GAAATAAAAGGGGAT
1 GAAAAAAAAGGGGAT
17911 ATTAGAAAGA
Statistics
Matches: 42, Mismatches: 3, Indels: 16
0.69 0.05 0.26
Matches are distributed among these distances:
16 6 0.14
17 4 0.10
18 1 0.02
19 6 0.14
20 1 0.02
21 18 0.43
22 6 0.14
ACGTcount: A:0.54, C:0.07, G:0.26, T:0.14
Consensus pattern (21 bp):
GAAAAAAAAGGGGATTACCGA
Found at i:17926 original size:12 final size:12
Alignment explanation
Indices: 17909--17942 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
17899 ATAAAAGGGG
17909 ATATTAGAAAGA
1 ATATTAGAAAGA
**
17921 ATATTAGATGGA
1 ATATTAGAAAGA
17933 ATATTAGAAA
1 ATATTAGAAA
17943 AGGGGATAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.18, T:0.29
Consensus pattern (12 bp):
ATATTAGAAAGA
Found at i:23126 original size:2 final size:2
Alignment explanation
Indices: 23119--23149 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
23109 AATTATATGA
*
23119 AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
23150 CTAGTTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:23725 original size:29 final size:29
Alignment explanation
Indices: 23693--23851 Score: 173
Period size: 29 Copynumber: 5.6 Consensus size: 29
23683 GGTCACTTAA
*
23693 GGGCATTTTGATCATTTCTGCACATTCAG
1 GGGCATTTTGGTCATTTCTGCACATTCAG
* **
23722 GGGCATTTTGGTCATTTCTACGTATTCAG
1 GGGCATTTTGGTCATTTCTGCACATTCAG
* * * *
23751 TGGTATTTTGGTCGTTTCTGCATGATTCAG
1 GGGCATTTTGGTCATTTCTGCA-CATTCAG
*
23781 GGGCATTTTGGTCA-TT-TGCACATTCAA
1 GGGCATTTTGGTCATTTCTGCACATTCAG
**
23808 GGGCATTTTGGTCA-TT-TGCATGTTCAG
1 GGGCATTTTGGTCATTTCTGCACATTCAG
*
23835 GGGCATTTTGATCATTT
1 GGGCATTTTGGTCATTT
23852 TAAGTTCACT
Statistics
Matches: 109, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
27 42 0.39
28 6 0.06
29 44 0.40
30 17 0.16
ACGTcount: A:0.18, C:0.16, G:0.25, T:0.42
Consensus pattern (29 bp):
GGGCATTTTGGTCATTTCTGCACATTCAG
Found at i:23811 original size:27 final size:27
Alignment explanation
Indices: 23691--23851 Score: 137
Period size: 27 Copynumber: 5.7 Consensus size: 27
23681 AGGGTCACTT
*
23691 AAGGGCATTTTGATCATTTCTGCACATTC
1 AAGGGCATTTTGGTCA-TT-TGCACATTC
*
23720 AGGGGCATTTTGGTCATTT-CTACGTATTC
1 AAGGGCATTTTGGTCATTTGC-AC--ATTC
* * *
23749 -AGTGGTATTTTGGTCGTTTCTGCATGATTC
1 AAG-GGCATTTTGGTC-ATT-TGCA-CATTC
*
23779 AGGGGCATTTTGGTCATTTGCACATTC
1 AAGGGCATTTTGGTCATTTGCACATTC
**
23806 AAGGGCATTTTGGTCATTTGCATGTTC
1 AAGGGCATTTTGGTCATTTGCACATTC
* *
23833 AGGGGCATTTTGATCATTT
1 AAGGGCATTTTGGTCATTT
23852 TAAGTTCACT
Statistics
Matches: 108, Mismatches: 15, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
26 1 0.01
27 48 0.44
28 7 0.06
29 31 0.29
30 17 0.16
31 3 0.03
32 1 0.01
ACGTcount: A:0.19, C:0.16, G:0.24, T:0.41
Consensus pattern (27 bp):
AAGGGCATTTTGGTCATTTGCACATTC
Done.