Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021511.1 Corchorus olitorius cultivar O-4 contig21544, 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: 17579
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:4076 original size:29 final size:29
Alignment explanation
Indices: 3993--4219 Score: 257
Period size: 29 Copynumber: 7.8 Consensus size: 29
3983 CCTTTTGTGA
3993 ATCCAGGGGCATTTTGGTCATTTTTTGCAC
1 ATCCAGGGGCATTTTGGTCA-TTTTTGCAC
* * *
4023 ATCTAGGGGCGTTTTGGTCA-TTTTGTAC
1 ATCCAGGGGCATTTTGGTCATTTTTGCAC
*
4051 ATCCAAGGGCATTTTGGTCATTTTTGCAC
1 ATCCAGGGGCATTTTGGTCATTTTTGCAC
* * * * *
4080 ATTCAGGAGCATTTTAGTCATTTCTGCAA
1 ATCCAGGGGCATTTTGGTCATTTTTGCAC
4109 ATCC-GGGGCATTTTGGTCATTTTT-CACCC
1 ATCCAGGGGCATTTTGGTCATTTTTGCA--C
*
4138 ATCC-GTGGGCATTTTGGTCATTTTCGCAC
1 ATCCAG-GGGCATTTTGGTCATTTTTGCAC
* *
4167 ATCCAGGGGCATTTTAGTCATTTCTGCAC
1 ATCCAGGGGCATTTTGGTCATTTTTGCAC
*
4196 AATCC-GGGGCCTTTTGGTCATTTT
1 -ATCCAGGGGCATTTTGGTCATTTT
4220 AGTTTTATTT
Statistics
Matches: 165, Mismatches: 25, Indels: 15
0.80 0.12 0.07
Matches are distributed among these distances:
27 2 0.01
28 41 0.25
29 79 0.48
30 41 0.25
31 2 0.01
ACGTcount: A:0.18, C:0.21, G:0.22, T:0.39
Consensus pattern (29 bp):
ATCCAGGGGCATTTTGGTCATTTTTGCAC
Found at i:4141 original size:87 final size:85
Alignment explanation
Indices: 3993--4219 Score: 294
Period size: 87 Copynumber: 2.6 Consensus size: 85
3983 CCTTTTGTGA
* * * * *
3993 ATCCAGGGGCATTTTGGTCATTTTTTGCACATCTAGGGGCGTTTTGGTCATTTTGTACATCCAAG
1 ATCCAGGGGCATTTTAGTCA-TTTCTGCAAATC-CGGGGCATTTTGGTCATTTTGTACATCCAAG
*
4058 GGCATTTTGGTCATTTTTGCAC
64 GGCATTTTGGTCATTTTCGCAC
* * **
4080 ATTCAGGAGCATTTTAGTCATTTCTGCAAATCCGGGGCATTTTGGTCATTTT-TCACCCATCCGT
1 ATCCAGGGGCATTTTAGTCATTTCTGCAAATCCGGGGCATTTTGGTCATTTTGT-A--CATCCAA
4144 GGGCATTTTGGTCATTTTCGCAC
63 GGGCATTTTGGTCATTTTCGCAC
*
4167 ATCCAGGGGCATTTTAGTCATTTCTGCACAATCCGGGGCCTTTTGGTCATTTT
1 ATCCAGGGGCATTTTAGTCATTTCTGCA-AATCCGGGGCATTTTGGTCATTTT
4220 AGTTTTATTT
Statistics
Matches: 123, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
84 1 0.01
85 19 0.15
86 10 0.08
87 70 0.57
88 23 0.19
ACGTcount: A:0.18, C:0.21, G:0.22, T:0.39
Consensus pattern (85 bp):
ATCCAGGGGCATTTTAGTCATTTCTGCAAATCCGGGGCATTTTGGTCATTTTGTACATCCAAGGG
CATTTTGGTCATTTTCGCAC
Found at i:8907 original size:19 final size:18
Alignment explanation
Indices: 8883--8918 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
8873 TGAAGATTTA
8883 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
8902 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
8919 ATTATTTCCA
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:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:9548 original size:18 final size:19
Alignment explanation
Indices: 9520--9557 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
9510 CTCTTCTTCT
9520 TTTTCTCTTCTAGTTCTAG
1 TTTTCTCTTCTAGTTCTAG
*
9539 TTTT-TCTTCTAGTTTTAG
1 TTTTCTCTTCTAGTTCTAG
9557 T
1 T
9558 GCTAGGGTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.11, C:0.16, G:0.11, T:0.63
Consensus pattern (19 bp):
TTTTCTCTTCTAGTTCTAG
Found at i:13669 original size:17 final size:18
Alignment explanation
Indices: 13647--13688 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
13637 TTGACAACAT
13647 AACAAACAC-AAAAC-AAA
1 AACAAA-ACGAAAACAAAA
13664 AACAAAACGAAAACAAAA
1 AACAAAACGAAAACAAAA
13682 AACAAAA
1 AACAAAA
13689 AAACGGAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.09
17 11 0.48
18 10 0.43
ACGTcount: A:0.79, C:0.19, G:0.02, T:0.00
Consensus pattern (18 bp):
AACAAAACGAAAACAAAA
Found at i:15193 original size:18 final size:20
Alignment explanation
Indices: 15170--15206 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
15160 GCAATTAGGT
15170 TGTC-AATCCCT-CTAATTC
1 TGTCAAATCCCTACTAATTC
15188 TGTCAAATCCCTACTAATT
1 TGTCAAATCCCTACTAATT
15207 AGTCTGTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 7 0.41
20 6 0.35
ACGTcount: A:0.27, C:0.30, G:0.05, T:0.38
Consensus pattern (20 bp):
TGTCAAATCCCTACTAATTC
Done.