Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011831.1 Corchorus olitorius cultivar O-4 contig11864, 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: 26680
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Found at i:157 original size:18 final size:18
Alignment explanation
Indices: 134--175 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
124 AAGATTAAGG
*
134 TAATAATAATT-TTACTAC
1 TAATAATAATTATTA-TAA
152 TAATAATAATTATTATAA
1 TAATAATAATTATTATAA
170 TAATAA
1 TAATAA
176 GAAGTTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATAATAATTATTATAA
Found at i:190 original size:24 final size:24
Alignment explanation
Indices: 158--208 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
148 CTACTAATAA
*
158 TAATTATTATAATAATAAGAA-GTT
1 TAATAATTATAATAATAA-AATGTT
*
182 TAATAATTATAATGATAAAATGTT
1 TAATAATTATAATAATAAAATGTT
206 TAA
1 TAA
209 CGTAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (24 bp):
TAATAATTATAATAATAAAATGTT
Found at i:7294 original size:21 final size:21
Alignment explanation
Indices: 7268--7309 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
7258 AACAAAACCT
7268 AAAAAATAAGAGAA-AACACAA
1 AAAAAATAAGA-AAGAACACAA
*
7289 AAAAAATTAGAAAGAACACAA
1 AAAAAATAAGAAAGAACACAA
7310 GACGCGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.74, C:0.10, G:0.10, T:0.07
Consensus pattern (21 bp):
AAAAAATAAGAAAGAACACAA
Found at i:12439 original size:11 final size:12
Alignment explanation
Indices: 12423--12456 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
12413 TATTAAAGGA
12423 TAAAAGGAAAT-
1 TAAAAGGAAATC
*
12434 TAAAAGAAAATC
1 TAAAAGGAAATC
12446 TAAAAGGAAAT
1 TAAAAGGAAAT
12457 ATATATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.65, C:0.03, G:0.15, T:0.18
Consensus pattern (12 bp):
TAAAAGGAAATC
Found at i:12697 original size:32 final size:33
Alignment explanation
Indices: 12622--12698 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 33
12612 TCCTGTTTTT
* ** **
12622 TTTTAATCCTTATAGATTTTTTTTTTCTTTTTT
1 TTTTAATCCTTATAGATTTTTCTTTAATTTTCC
12655 TTTTAAATCCTTATAGATTTTTCTTTAATTTTCC
1 TTTT-AATCCTTATAGATTTTTCTTTAATTTTCC
12689 TTTT-ATCCTT
1 TTTTAATCCTT
12699 TAATAAGTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
32 6 0.16
33 4 0.11
34 28 0.74
ACGTcount: A:0.18, C:0.13, G:0.03, T:0.66
Consensus pattern (33 bp):
TTTTAATCCTTATAGATTTTTCTTTAATTTTCC
Found at i:14154 original size:15 final size:15
Alignment explanation
Indices: 14130--14160 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
14120 ATTCTTTTTT
*
14130 TTTATTTTATATGTA
1 TTTATATTATATGTA
14145 TTTATATTATATGTA
1 TTTATATTATATGTA
14160 T
1 T
14161 GGCTGGGTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (15 bp):
TTTATATTATATGTA
Found at i:16174 original size:6 final size:6
Alignment explanation
Indices: 16163--16197 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
16153 AAATAGCCTC
16163 TATATG TATATG TATATG TATATG TATATG TATAT
1 TATATG TATATG TATATG TATATG TATATG TATAT
16198 ATTCAAATCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:22579 original size:31 final size:31
Alignment explanation
Indices: 22421--22590 Score: 205
Period size: 31 Copynumber: 5.5 Consensus size: 31
22411 TCCTTTTGTG
* *
22421 CACGTGGCATGCCACGTGTCACTTTTTGGTA
1 CACGTGGCGTGCCACATGTCACTTTTTGGTA
** ** *
22452 CACACGGCGTGATACATGTCACTTTTTGATA
1 CACGTGGCGTGCCACATGTCACTTTTTGGTA
* *
22483 CACCTGGCGTGCCACATGTCGCTTTTTGGTA
1 CACGTGGCGTGCCACATGTCACTTTTTGGTA
* * *
22514 CAAGTGGTGAGCCACATGTCACTTTTTGGTA
1 CACGTGGCGTGCCACATGTCACTTTTTGGTA
**
22545 CACGTGGCGTGCCACATGTCGTTTTTTGGTA
1 CACGTGGCGTGCCACATGTCACTTTTTGGTA
*
22576 CACGTGGCATGCCAC
1 CACGTGGCGTGCCAC
22591 GTCGGACACC
Statistics
Matches: 115, Mismatches: 24, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 115 1.00
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.31
Consensus pattern (31 bp):
CACGTGGCGTGCCACATGTCACTTTTTGGTA
Found at i:24850 original size:22 final size:24
Alignment explanation
Indices: 24815--24873 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 24
24805 ATAAATGTTG
* *
24815 CTGATAA-TCTTCT-CTTTTATCT
1 CTGATAATTCTTCTCCATTTATCA
24837 CTGATAATTC-TCTCCATTTATCA
1 CTGATAATTCTTCTCCATTTATCA
24860 CTTGATAATATCTT
1 C-TGATAAT-TCTT
24874 GCCAGATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
22 10 0.33
23 10 0.33
24 7 0.23
25 2 0.07
26 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.05, T:0.49
Consensus pattern (24 bp):
CTGATAATTCTTCTCCATTTATCA
Done.