Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024208.1 Corchorus olitorius cultivar O-4 contig24241, 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: 10287
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:2150 original size:22 final size:22
Alignment explanation
Indices: 2114--2155 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2104 TGGCACGGGC
**
2114 ATGGCCGGTGGTGGCATGGTGT
1 ATGGCCGGTAATGGCATGGTGT
*
2136 ATGGCCGGTAATGGCTTGGT
1 ATGGCCGGTAATGGCATGGT
2156 AGTGGCGCGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.12, C:0.14, G:0.45, T:0.29
Consensus pattern (22 bp):
ATGGCCGGTAATGGCATGGTGT
Found at i:5373 original size:30 final size:29
Alignment explanation
Indices: 5298--5373 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 29
5288 CAAGAAAGTT
*
5298 TTTTTTTTTTAG-AAAACGCAAAACAAAA
1 TTTTTTTTTTAGAAAAACACAAAACAAAA
* * *
5326 -ATTTTTATGACGCAAAAACACAAAACAAATA
1 TTTTTTTTTTA-G-AAAAACACAAAACAAA-A
5357 TTTTTTTTTTAGAAAAA
1 TTTTTTTTTTAGAAAAA
5374 AAAATGCAGA
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
27 7 0.19
28 1 0.03
30 19 0.53
31 2 0.06
32 7 0.19
ACGTcount: A:0.47, C:0.11, G:0.07, T:0.36
Consensus pattern (29 bp):
TTTTTTTTTTAGAAAAACACAAAACAAAA
Found at i:5727 original size:15 final size:16
Alignment explanation
Indices: 5703--5742 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
5693 AGAGGTTGAA
*
5703 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
5718 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
5734 AGAAAACAA
1 AGAAAACAA
5743 AGCAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:6558 original size:9 final size:10
Alignment explanation
Indices: 6527--6562 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
6517 TAAAGAGAAT
*
6527 TATGTGAAGA
1 TATGTGAAGG
6537 TATGTGAAGG
1 TATGTGAAGG
6547 TATGTG-AGG
1 TATGTGAAGG
6556 TATGTGA
1 TATGTGA
6563 TTTGTGTTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 9 0.38
10 15 0.62
ACGTcount: A:0.31, C:0.00, G:0.36, T:0.33
Consensus pattern (10 bp):
TATGTGAAGG
Found at i:7550 original size:11 final size:11
Alignment explanation
Indices: 7507--7555 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
7497 TTGAATAAAT
7507 TCTTC-AATAG
1 TCTTCAAATAG
7517 TCTTC--A-AG
1 TCTTCAAATAG
*
7525 TCTTCAACTTAG
1 TCTTCAA-ATAG
7537 TCTTCAAATAG
1 TCTTCAAATAG
7548 TCTTCAAA
1 TCTTCAAA
7556 CACGAACTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
8 7 0.21
9 1 0.03
10 5 0.15
11 11 0.33
12 9 0.27
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (11 bp):
TCTTCAAATAG
Found at i:9879 original size:21 final size:21
Alignment explanation
Indices: 9833--9905 Score: 103
Period size: 21 Copynumber: 3.4 Consensus size: 21
9823 TGCTAGGAGA
9833 TCATTGGAGCAA-GTTCCAAGAGC
1 TCATTGGAG-AAGGTTCC-A-AGC
9856 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
9877 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
9898 TCATTGGA
1 TCATTGGA
9906 ATTGCCTAAG
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
21 31 0.65
22 3 0.06
23 14 0.29
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:10041 original size:11 final size:11
Alignment explanation
Indices: 10022--10074 Score: 81
Period size: 11 Copynumber: 4.9 Consensus size: 11
10012 CTTGACGAGT
*
10022 TCATCTGAAGA
1 TCATTTGAAGA
10033 TCATTTGAAGA
1 TCATTTGAAGA
10044 TCATTTGAAGA
1 TCATTTGAAGA
*
10055 TCA-TTGGAGA
1 TCATTTGAAGA
10065 TCATTTGAAG
1 TCATTTGAAG
10075 CCCATTGGAG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
10 9 0.24
11 29 0.76
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (11 bp):
TCATTTGAAGA
Found at i:10067 original size:21 final size:21
Alignment explanation
Indices: 10022--10089 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
10012 CTTGACGAGT
* *
10022 TCATCTGAAGATCATTTGAAGA
1 TCATTTGAAGATCA-TTGGAGA
10044 TCATTTGAAGATCATTGGAGA
1 TCATTTGAAGATCATTGGAGA
**
10065 TCATTTGAAGCCCATTGGAGA
1 TCATTTGAAGATCATTGGAGA
10086 TCAT
1 TCAT
10090 CACCAAAGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
21 29 0.69
22 13 0.31
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (21 bp):
TCATTTGAAGATCATTGGAGA
Done.