Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006571.1 Corchorus capsularis cultivar CVL-1 contig06592, 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: 8564
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:831 original size:11 final size:11
Alignment explanation
Indices: 815--844 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
805 GAAGTTCGTG
*
815 TTTGAAGATTA
1 TTTGAAGATAA
826 TTTGAAGATAA
1 TTTGAAGATAA
837 TTTGAAGA
1 TTTGAAGA
845 ATTGGAGACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (11 bp):
TTTGAAGATAA
Found at i:2184 original size:6 final size:6
Alignment explanation
Indices: 2173--2209 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
2163 ATAATTTCTA
2173 TAGATT TAGATT TAGATT TAGATT TAGATT TA-ATT TA
1 TAGATT TAGATT TAGATT TAGATT TAGATT TAGATT TA
2210 CTTTGCTTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (6 bp):
TAGATT
Found at i:2792 original size:15 final size:15
Alignment explanation
Indices: 2774--2808 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2764 TAAGGTTCCA
2774 GATTTCTCAGTATTT
1 GATTTCTCAGTATTT
*
2789 GATTTCTCGGTATTT
1 GATTTCTCAGTATTT
*
2804 TATTT
1 GATTT
2809 TTTGTCAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.17, C:0.11, G:0.14, T:0.57
Consensus pattern (15 bp):
GATTTCTCAGTATTT
Found at i:5235 original size:4 final size:4
Alignment explanation
Indices: 5228--5272 Score: 65
Period size: 4 Copynumber: 11.2 Consensus size: 4
5218 ATAATAATAA
*
5228 TAAT TAAT ATTAT T-AT TAAT TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT -TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT T
5273 TAAAATTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
3 3 0.08
4 32 0.84
5 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (4 bp):
TAAT
Found at i:6844 original size:24 final size:24
Alignment explanation
Indices: 6812--6859 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
6802 TCTTATTAAT
*
6812 TTCAGTGGCATTCCCACTGCGGTG
1 TTCAGTGGCATTCCCACTACGGTG
6836 TTCAGTGGCATTCCCACTACGGTG
1 TTCAGTGGCATTCCCACTACGGTG
6860 AGAATCAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.15, C:0.29, G:0.27, T:0.29
Consensus pattern (24 bp):
TTCAGTGGCATTCCCACTACGGTG
Found at i:7286 original size:122 final size:126
Alignment explanation
Indices: 7136--7384 Score: 400
Period size: 122 Copynumber: 2.0 Consensus size: 126
7126 GTGGTAGACC
* *
7136 AAACCTATATATCTAATAATTCTCCGTTTTATGTTTGAAAAACATACAGTTAATTATTTTTT-AT
1 AAACCTATATATCGAATAATTCTCCGTTTTATATTTGAAAAACATACAGTTAATTATTTTTTAAT
7200 GAATATTTAAATAAACACTTTCACATGTA-TT-TTTTTAAAATTTAAATCTGTAGATAATAA
66 GAATATTTAAATAAACACTTTCACATGTATTTCTTTTTAAAA-TTAAATCTGTAGATAATAA
* * *
7260 AAACCTATAT-T-GAATAATTCTCCGTTTTATATTTGTAAAACATATAGTTATTTATTTTTTAAT
1 AAACCTATATATCGAATAATTCTCCGTTTTATATTTGAAAAACATACAGTTAATTATTTTTTAAT
*
7323 GAATTTTTAAATAAACACTTTCACATGTATTTCTTTTTAAAATTAAATCTGTAGATAATAA
66 GAATATTTAAATAAACACTTTCACATGTATTTCTTTTTAAAATTAAATCTGTAGATAATAA
7384 A
1 A
7385 TGGTTGGTAG
Statistics
Matches: 116, Mismatches: 6, Indels: 6
0.91 0.05 0.05
Matches are distributed among these distances:
122 44 0.38
123 31 0.27
124 32 0.28
125 9 0.08
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (126 bp):
AAACCTATATATCGAATAATTCTCCGTTTTATATTTGAAAAACATACAGTTAATTATTTTTTAAT
GAATATTTAAATAAACACTTTCACATGTATTTCTTTTTAAAATTAAATCTGTAGATAATAA
Found at i:8220 original size:107 final size:105
Alignment explanation
Indices: 8048--8309 Score: 420
Period size: 107 Copynumber: 2.5 Consensus size: 105
8038 AGTTTAGCCT
*
8048 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
8113 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
66 AATAA--TATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
*
8155 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
* * *
8220 AATAATATTGTTATAGGGTTTTAGAAATAAAATATATAAT
66 AATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
** *
8260 TAA-TTCACTAAGTTTAG-CCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
8310 TAGAAAAATA
Statistics
Matches: 147, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
103 30 0.20
104 14 0.10
105 35 0.24
107 68 0.46
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (105 bp):
TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
AATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
Done.