Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016205.1 Corchorus capsularis cultivar CVL-1 contig16226, 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: 39162
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2967 original size:18 final size:18
Alignment explanation
Indices: 2944--2982 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
2934 AAATTTAAGA
*
2944 AATATATTTAAAATTTTT
1 AATATATCTAAAATTTTT
2962 AATATATCTAAAATTTTT
1 AATATATCTAAAATTTTT
2980 AAT
1 AAT
2983 TAAAATAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
AATATATCTAAAATTTTT
Found at i:3321 original size:4 final size:4
Alignment explanation
Indices: 3312--3354 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
3302 TAGTATAGAT
* *
3312 ATAG ATAG ATAG ATAA ATAG AT-- ATAA ATAG ATAG ATAG ATAG A
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG A
3355 AAAAAAGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
2 2 0.06
4 32 0.94
ACGTcount: A:0.56, C:0.00, G:0.19, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:3331 original size:22 final size:22
Alignment explanation
Indices: 3306--3354 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
3296 TTAATATAGT
*
3306 ATAGATATAGATAGATAGATAA
1 ATAGATATAAATAGATAGATAA
*
3328 ATAGATATAAATAGATAGATAG
1 ATAGATATAAATAGATAGATAA
3350 ATAGA
1 ATAGA
3355 AAAAAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.55, C:0.00, G:0.18, T:0.27
Consensus pattern (22 bp):
ATAGATATAAATAGATAGATAA
Found at i:5231 original size:16 final size:15
Alignment explanation
Indices: 5210--5243 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
5200 ACCCCAATTT
5210 GAAAAGGAAAAGAAAA
1 GAAAAGGAAAA-AAAA
5226 GAAAAGGAAAAAAAA
1 GAAAAGGAAAAAAAA
5241 GAA
1 GAA
5244 GTAATAACAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
GAAAAGGAAAAAAAA
Found at i:6328 original size:13 final size:12
Alignment explanation
Indices: 6292--6334 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
6282 GTTTTATTAC
6292 TGTTTTG-TAATA
1 TGTTTTGATAA-A
6304 TGTTTT-ATAAA
1 TGTTTTGATAAA
6315 TGGTTTTGATAAA
1 T-GTTTTGATAAA
6328 TGTTTTG
1 TGTTTTG
6335 GGTGCATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 2 0.07
12 20 0.71
13 6 0.21
ACGTcount: A:0.26, C:0.00, G:0.19, T:0.56
Consensus pattern (12 bp):
TGTTTTGATAAA
Found at i:8330 original size:30 final size:29
Alignment explanation
Indices: 8263--8334 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
8253 ACACCGAACC
****
8263 GTCAAATAAGCCCCTGAACTATTATTTCA
1 GTCAAATAAGCCCCTGAACTATTAAAAAA
* *
8292 GCCAAATAAGCCCCTGAACTCTTAAAAAAA
1 GTCAAATAAGCCCCTGAACTATT-AAAAAA
8322 GTCAAATAAGCCC
1 GTCAAATAAGCCC
8335 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
29 21 0.60
30 14 0.40
ACGTcount: A:0.40, C:0.26, G:0.11, T:0.22
Consensus pattern (29 bp):
GTCAAATAAGCCCCTGAACTATTAAAAAA
Found at i:10790 original size:33 final size:33
Alignment explanation
Indices: 10712--10816 Score: 120
Period size: 33 Copynumber: 3.2 Consensus size: 33
10702 TTGCAAAGAG
* *
10712 TGTTTTAGATGTTGTTTGCAATGATACTAAACC
1 TGTTTTAGGTGTTGTTTGCAATGATACTAAATC
** *
10745 TAATTTAAGTGTTGTTTGCAATGATACTAAATC
1 TGTTTTAGGTGTTGTTTGCAATGATACTAAATC
* * ** *
10778 TGTTTTAGGTGTTATTGGTGATGACACTAAATC
1 TGTTTTAGGTGTTGTTTGCAATGATACTAAATC
10811 TGTTTT
1 TGTTTT
10817 GGATGCTAAT
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.45
Consensus pattern (33 bp):
TGTTTTAGGTGTTGTTTGCAATGATACTAAATC
Found at i:10832 original size:33 final size:33
Alignment explanation
Indices: 10765--10851 Score: 99
Period size: 33 Copynumber: 2.6 Consensus size: 33
10755 GTTGTTTGCA
* *
10765 ATGATACTAAATCTGTTTTAGGTGTTATTGGTG
1 ATGAAACTAAATCTGTTTTAGGTGTAATTGGTG
*
10798 ATGACACTAAATCTGTTTT-GGATGCTAATT-GTG
1 ATGAAACTAAATCTGTTTTAGG-TG-TAATTGGTG
10831 ATGAAAAC-AAATCTGTTTTAG
1 ATG-AAACTAAATCTGTTTTAG
10852 TTTATCATAG
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
32 2 0.04
33 37 0.79
34 8 0.17
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (33 bp):
ATGAAACTAAATCTGTTTTAGGTGTAATTGGTG
Found at i:10879 original size:33 final size:33
Alignment explanation
Indices: 10842--10915 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 33
10832 TGAAAACAAA
*
10842 TCTGTTTTAGTTTATCATAGCATTGCAAATAAT
1 TCTGTTTTAGTTGATCATAGCATTGCAAATAAT
10875 TCTGTTTTAGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTAGTTGATCATAGCATTGCAAATAAT
*
10908 TCTATTTT
1 TCTGTTTT
10916 GGGTGAAAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (33 bp):
TCTGTTTTAGTTGATCATAGCATTGCAAATAAT
Found at i:15651 original size:22 final size:22
Alignment explanation
Indices: 15553--15649 Score: 169
Period size: 22 Copynumber: 4.5 Consensus size: 22
15543 TTCTGAGGTT
15553 GCCCGCTCCCGGGCAAGGGGTC
1 GCCCGCTCCCGGGCAAGGGGTC
15575 GCCCGCTCCCGGGCAAGGGGTC
1 GCCCGCTCCCGGGCAAGGGGTC
15597 GCCCGCTCCCGGGCAAGGGGTC
1 GCCCGCTCCCGGGCAAGGGGTC
* *
15619 GCCCGCTCCTGGACAA-GGGTC
1 GCCCGCTCCCGGGCAAGGGGTC
15640 GCCCGCTCCC
1 GCCCGCTCCC
15650 TGATTTGCCT
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
21 14 0.19
22 58 0.81
ACGTcount: A:0.09, C:0.43, G:0.37, T:0.10
Consensus pattern (22 bp):
GCCCGCTCCCGGGCAAGGGGTC
Found at i:20195 original size:2 final size:2
Alignment explanation
Indices: 20161--20185 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20151 TGAGTAAATC
20161 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
20186 GCACATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21509 original size:13 final size:13
Alignment explanation
Indices: 21491--21515 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21481 ATCCCAAATT
21491 ATGAAATTCAAAG
1 ATGAAATTCAAAG
21504 ATGAAATTCAAA
1 ATGAAATTCAAA
21516 AACATCCAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.12, T:0.24
Consensus pattern (13 bp):
ATGAAATTCAAAG
Found at i:22973 original size:25 final size:25
Alignment explanation
Indices: 22945--22994 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
22935 ATATTAGAAC
**
22945 TTTTAAAATATATTCTTTTACAATTT
1 TTTTAAAA-ATAAACTTTTACAATTT
22971 TTTTAAAAATAAACTTTTACAATT
1 TTTTAAAAATAAACTTTTACAATT
22995 ATTCTACTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (25 bp):
TTTTAAAAATAAACTTTTACAATTT
Found at i:23017 original size:29 final size:29
Alignment explanation
Indices: 22984--23046 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
22974 TAAAAATAAA
22984 CTTTTACAATTATTCTACTAAAACTCTAT
1 CTTTTACAATTATTCTACTAAAACTCTAT
23013 CTTTTACAATTATTCTACTAAAACTCTAT
1 CTTTTACAATTATTCTACTAAAACTCTAT
23042 -TTTTA
1 CTTTTA
23047 TTCGATTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 5 0.15
29 29 0.85
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.48
Consensus pattern (29 bp):
CTTTTACAATTATTCTACTAAAACTCTAT
Found at i:24082 original size:1 final size:1
Alignment explanation
Indices: 24076--24116 Score: 82
Period size: 1 Copynumber: 41.0 Consensus size: 1
24066 AGCCCAAAAG
24076 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
24117 AAAGCATCAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:24278 original size:19 final size:19
Alignment explanation
Indices: 24254--24290 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
24244 AAAGTTAAAG
*
24254 AACCCATATGAGAAGGAAC
1 AACCCAGATGAGAAGGAAC
24273 AACCCAGATGAGAAGGAA
1 AACCCAGATGAGAAGGAA
24291 GAAGATGGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.19, G:0.24, T:0.08
Consensus pattern (19 bp):
AACCCAGATGAGAAGGAAC
Found at i:35954 original size:21 final size:22
Alignment explanation
Indices: 35930--35977 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
35920 AGGGTGGGCG
* *
35930 CCCAGGCGCTTTGCC-TGAGCA
1 CCCAGGCCCGTTGCCTTGAGCA
*
35951 CCCA-GCCCGTTGCCTTGGGCA
1 CCCAGGCCCGTTGCCTTGAGCA
35972 CCCAGG
1 CCCAGG
35978 TGCCGCGGGC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 8 0.36
21 13 0.59
22 1 0.05
ACGTcount: A:0.12, C:0.42, G:0.29, T:0.17
Consensus pattern (22 bp):
CCCAGGCCCGTTGCCTTGAGCA
Found at i:36852 original size:19 final size:19
Alignment explanation
Indices: 36828--36877 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
36818 TCAAAGGTAA
36828 CATTTGTATCTATCTTTTC
1 CATTTGTATCTATCTTTTC
36847 CATTTGTATCTATCTTTTC
1 CATTTGTATCTATCTTTTC
36866 CATTTGTATCTA
1 CATTTGTATCTA
36878 AGTACATTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.18, C:0.20, G:0.06, T:0.56
Consensus pattern (19 bp):
CATTTGTATCTATCTTTTC
Found at i:37616 original size:19 final size:18
Alignment explanation
Indices: 37592--37627 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
37582 TGAAGATTTC
37592 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
37611 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
37628 ATTATTTCAA
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:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Done.