Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024174.1 Corchorus olitorius cultivar O-4 contig24207, 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: 37381
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:5770 original size:49 final size:47
Alignment explanation
Indices: 5694--5822 Score: 159
Period size: 49 Copynumber: 2.7 Consensus size: 47
5684 CCAAGCAATA
**
5694 TTTTACTTTTACTGCACTTTTTCTCAATTTTTACTACAAAATTGAAC
1 TTTTACTTTTACTGCACTTTTTCTCAATTTTTAAGACAAAATTGAAC
* *
5741 TTTTATTTTTACTCGCACCTTTTTCTCAATTTTTAAGACAAAATTGATC
1 TTTTACTTTTACT-GCA-CTTTTTCTCAATTTTTAAGACAAAATTGAAC
* * * *
5790 TTTTAATATTCATTGCACTTTTTATCAATTTTT
1 TTTTACT-TTTACTGCACTTTTTCTCAATTTTT
5823 GGATAAAATT
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
47 12 0.17
48 18 0.25
49 37 0.52
50 4 0.06
ACGTcount: A:0.26, C:0.17, G:0.05, T:0.52
Consensus pattern (47 bp):
TTTTACTTTTACTGCACTTTTTCTCAATTTTTAAGACAAAATTGAAC
Found at i:6642 original size:15 final size:15
Alignment explanation
Indices: 6622--6658 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
6612 TGCTAGGGTG
6622 AATGGTGCAAACAAC
1 AATGGTGCAAACAAC
* *
6637 AATGGTGCGAATAAC
1 AATGGTGCAAACAAC
6652 AATGGTG
1 AATGGTG
6659 TGAACAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.41, C:0.14, G:0.27, T:0.19
Consensus pattern (15 bp):
AATGGTGCAAACAAC
Found at i:12713 original size:17 final size:18
Alignment explanation
Indices: 12678--12715 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
12668 CCCAAATTAC
*
12678 TTATGGAAATTAGGGAAA
1 TTATGGAAACTAGGGAAA
12696 TTATGGAAACTA-GGAAA
1 TTATGGAAACTAGGGAAA
12713 TTA
1 TTA
12716 AATGAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.45, C:0.03, G:0.24, T:0.29
Consensus pattern (18 bp):
TTATGGAAACTAGGGAAA
Found at i:14070 original size:49 final size:48
Alignment explanation
Indices: 13990--14120 Score: 165
Period size: 49 Copynumber: 2.7 Consensus size: 48
13980 TCCAAGCAAT
* * **
13990 CTTTTACTTTTACTGCACTTTTTTCTCAATTTTTACTACAAAATTGAA
1 CTTTTAATTTTACTGCACCTTTTTCTCAATTTTTAAGACAAAATTGAA
* *
14038 CTTTTATTTTTACTCGCACCTTTTTCTCAATTTTTAAGACAAAATTGAT
1 CTTTTAATTTTACT-GCACCTTTTTCTCAATTTTTAAGACAAAATTGAA
* *
14087 CTTTTAATTTTCATTGCA-CTTTTTATCAATTTTT
1 CTTTTAATTTT-ACTGCACCTTTTTCTCAATTTTT
14121 GGATAAAATT
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
48 28 0.38
49 43 0.59
50 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.05, T:0.53
Consensus pattern (48 bp):
CTTTTAATTTTACTGCACCTTTTTCTCAATTTTTAAGACAAAATTGAA
Found at i:15222 original size:2 final size:2
Alignment explanation
Indices: 15147--15211 Score: 62
Period size: 2 Copynumber: 33.0 Consensus size: 2
15137 GTGCCTTGGC
* ** *
15147 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AC AT AT AT GC AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
15188 AT AT AT TT AT AT CAT -T AT AT AT AT
1 AT AT AT AT AT AT -AT AT AT AT AT AT
15212 TTTTTATATA
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
1 2 0.04
2 48 0.92
3 2 0.04
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:19373 original size:11 final size:10
Alignment explanation
Indices: 19357--19409 Score: 56
Period size: 11 Copynumber: 5.2 Consensus size: 10
19347 GCTTCTTGGA
19357 AATAATTCTTC
1 AATAA-TCTTC
19368 AATAATCTTC
1 AATAATCTTC
19378 -A-AATCTTC
1 AATAATCTTC
*
19386 AAATTATCTTC
1 -AATAATCTTC
19397 AATAAGTCTTC
1 AATAA-TCTTC
19408 AA
1 AA
19410 ACACAAACCC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
8 7 0.19
9 1 0.03
10 10 0.28
11 18 0.50
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.40
Consensus pattern (10 bp):
AATAATCTTC
Found at i:19409 original size:22 final size:21
Alignment explanation
Indices: 19357--19410 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
19347 GCTTCTTGGA
19357 AATAATTCTTC-AATAATCTTC
1 AATAA-TCTTCAAATAATCTTC
*
19378 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATAATCTTC
19397 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
19411 CACAAACCCC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.41, C:0.19, G:0.02, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATAATCTTC
Found at i:30944 original size:22 final size:21
Alignment explanation
Indices: 30892--30945 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
30882 GCTTCTTGGA
30892 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
30913 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
30932 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
30946 CACGAACCTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Done.