Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013204.1 Corchorus olitorius cultivar O-4 contig13237, 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: 42552
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Found at i:1298 original size:21 final size:21
Alignment explanation
Indices: 1255--1309 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1245 CCGCCCATTA
***
1255 CCGTGCCACCACCGGTTAAGC
1 CCGTGCCACCACCGACCAAGC
*
1276 CCGTGCCACCACCGACCATGC
1 CCGTGCCACCACCGACCAAGC
*
1297 CCGTGCCATCACC
1 CCGTGCCACCACC
1310 ATTCCAAGCC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.49, G:0.20, T:0.13
Consensus pattern (21 bp):
CCGTGCCACCACCGACCAAGC
Found at i:1682 original size:15 final size:14
Alignment explanation
Indices: 1662--1691 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1652 ATCTCTTTAA
1662 TTTTCCTTGCATTAT
1 TTTTCCTTG-ATTAT
1677 TTTTCCTTGATTAT
1 TTTTCCTTGATTAT
1691 T
1 T
1692 GCTTTAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTTCCTTGATTAT
Found at i:3138 original size:11 final size:11
Alignment explanation
Indices: 3122--3169 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
3112 GAAGTTCGTG
3122 TTTGAAGACCA
1 TTTGAAGACCA
**
3133 TTTGAAGATAA
1 TTTGAAGACCA
3144 TTTGAAGA-C-
1 TTTGAAGACCA
3153 -TTGAAGACCA
1 TTTGAAGACCA
3163 -TTGAAGA
1 TTTGAAGA
3170 TTTTGATGCC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
8 7 0.22
9 1 0.03
10 7 0.22
11 17 0.53
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (11 bp):
TTTGAAGACCA
Found at i:3491 original size:13 final size:13
Alignment explanation
Indices: 3473--3501 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3463 CGTTGGAAAG
3473 CTAACTCCGAGAT
1 CTAACTCCGAGAT
3486 CTAACTCCGAGAT
1 CTAACTCCGAGAT
3499 CTA
1 CTA
3502 CAACTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.31, G:0.14, T:0.24
Consensus pattern (13 bp):
CTAACTCCGAGAT
Found at i:4571 original size:15 final size:15
Alignment explanation
Indices: 4541--4582 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
4531 TTACTTTGTT
4541 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
4557 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
4572 TTGTTTTCTGT
1 TTGTTTTCTGT
4583 CAACCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:20966 original size:15 final size:15
Alignment explanation
Indices: 20935--20976 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
20925 TTACTTTGCT
*
20935 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-TTTTAA
20951 TTGTTTTCTTTTTAA
1 TTGTTTTCTTTTTAA
20966 TTGTTCTTCTT
1 TTGTT-TTCTT
20977 AACCCTCTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.12, C:0.10, G:0.10, T:0.69
Consensus pattern (15 bp):
TTGTTTTCTTTTTAA
Found at i:26539 original size:19 final size:19
Alignment explanation
Indices: 26512--26556 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
26502 TTGTTTTGCT
*
26512 TTGAATGATTAATGCTTGA
1 TTGAATGATTAATCCTTGA
* *
26531 TTGATTGATTATTCCTTGA
1 TTGAATGATTAATCCTTGA
26550 TTTGAAT
1 -TTGAAT
26557 TAGTTTTTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.27, C:0.07, G:0.18, T:0.49
Consensus pattern (19 bp):
TTGAATGATTAATCCTTGA
Found at i:26866 original size:47 final size:47
Alignment explanation
Indices: 26797--26893 Score: 194
Period size: 47 Copynumber: 2.1 Consensus size: 47
26787 GGGTGAATAC
26797 TTGATAGGGTTATTACTTGAATAATTGAGTCATATGATAATCCTTGT
1 TTGATAGGGTTATTACTTGAATAATTGAGTCATATGATAATCCTTGT
26844 TTGATAGGGTTATTACTTGAATAATTGAGTCATATGATAATCCTTGT
1 TTGATAGGGTTATTACTTGAATAATTGAGTCATATGATAATCCTTGT
26891 TTG
1 TTG
26894 CATGAGAAAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.43
Consensus pattern (47 bp):
TTGATAGGGTTATTACTTGAATAATTGAGTCATATGATAATCCTTGT
Found at i:26944 original size:22 final size:22
Alignment explanation
Indices: 26919--26964 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
26909 TAGAATTTGA
26919 TTGTTTTTGGATTAATCTTATT
1 TTGTTTTTGGATTAATCTTATT
26941 TTGTTTTTGGATTAATCTTATT
1 TTGTTTTTGGATTAATCTTATT
26963 TT
1 TT
26965 CCCCAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.04, G:0.13, T:0.65
Consensus pattern (22 bp):
TTGTTTTTGGATTAATCTTATT
Found at i:34908 original size:44 final size:42
Alignment explanation
Indices: 34840--34973 Score: 134
Period size: 41 Copynumber: 3.2 Consensus size: 42
34830 GATTGAAAAA
34840 TTGAAAACTACTAGATGGGATCTTTCCCTAAATT-AAAATTT
1 TTGAAAACTACTAGATGGGATCTTTCCCTAAATTGAAAATTT
*
34881 TTGAAAACTACTGGATGATGGGATCTTTCCCTAAATTGAAAAAACTT
1 TTGAAAACTACT--A-GATGGGATCTTTCCCTAAATTG--AAAATTT
* * * *
34928 TTGAAGA-T--TGGATGGGATCTTTCCCTAATTTTG-AAATCT
1 TTGAAAACTACTAGATGGGATCTTTCCCTAA-ATTGAAAATTT
34967 TTGAAAA
1 TTGAAAA
34974 AAAATACTTT
Statistics
Matches: 79, Mismatches: 7, Indels: 16
0.77 0.07 0.16
Matches are distributed among these distances:
39 10 0.13
41 30 0.38
42 3 0.04
43 1 0.01
44 22 0.28
46 1 0.01
47 12 0.15
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.36
Consensus pattern (42 bp):
TTGAAAACTACTAGATGGGATCTTTCCCTAAATTGAAAATTT
Found at i:35504 original size:2 final size:2
Alignment explanation
Indices: 35497--35524 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35487 ATAGTCAATA
35497 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35525 GATGCATATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36277 original size:11 final size:11
Alignment explanation
Indices: 36261--36295 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
36251 TTTTTCTGTT
36261 TTTTGTTTTTG
1 TTTTGTTTTTG
*
36272 TTTTGTTTTCG
1 TTTTGTTTTTG
36283 TTTTGTTTTTG
1 TTTTGTTTTTG
36294 TT
1 TT
36296 GCGCTGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.80
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:37096 original size:10 final size:10
Alignment explanation
Indices: 37081--37109 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
37071 TCTCAAACGT
37081 TGCCTCGAAG
1 TGCCTCGAAG
37091 TGCCTCGAAG
1 TGCCTCGAAG
37101 TGCCTCGAA
1 TGCCTCGAA
37110 TAAGCCCCGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.31, G:0.28, T:0.21
Consensus pattern (10 bp):
TGCCTCGAAG
Found at i:40355 original size:17 final size:17
Alignment explanation
Indices: 40330--40365 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
40320 TTTTAATCGA
*
40330 TTTCTTCTTCTTCTTCC
1 TTTCCTCTTCTTCTTCC
40347 TTTCCTCTTCTTCTTCC
1 TTTCCTCTTCTTCTTCC
40364 TT
1 TT
40366 GCAATTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTCCTCTTCTTCTTCC
Done.