Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014010.1 Corchorus olitorius cultivar O-4 contig14043, 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: 37581
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:4679 original size:30 final size:30
Alignment explanation
Indices: 4643--4726 Score: 107
Period size: 31 Copynumber: 2.8 Consensus size: 30
4633 ATTTTATTAA
* *
4643 TTTCCAAAATTTTCTTTTGGGTT-TCTTTAT
1 TTTCCAAAATCTTCTTTTGGATTATC-TTAT
* *
4673 TTTCCAAAATCTTCTTGTAGAATTATCTTAT
1 TTTCCAAAATCTTCTT-TTGGATTATCTTAT
4704 TTTCCAAAATCTTCTTTTGGATT
1 TTTCCAAAATCTTCTTTTGGATT
4727 TGCTTAAGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
30 20 0.43
31 24 0.52
32 2 0.04
ACGTcount: A:0.23, C:0.15, G:0.08, T:0.54
Consensus pattern (30 bp):
TTTCCAAAATCTTCTTTTGGATTATCTTAT
Found at i:7144 original size:2 final size:2
Alignment explanation
Indices: 7134--7165 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
7124 GTTTTTTCGA
*
7134 GT GT AT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
7166 TTTTTTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.03, C:0.00, G:0.47, T:0.50
Consensus pattern (2 bp):
GT
Found at i:9178 original size:27 final size:27
Alignment explanation
Indices: 9148--9214 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
9138 AGTGCACTTG
* *
9148 AAATGACCAAAATGCCCCTGGACGTGC
1 AAATGACCAAAATGCCCCTGAACATGC
9175 AAATGACCAAAATGCCCCTGAACATGC
1 AAATGACCAAAATGCCCCTGAACATGC
*
9202 CAATGACCAAAAT
1 AAATGACCAAAAT
9215 AAGAAGTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.40, C:0.28, G:0.16, T:0.15
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGAACATGC
Found at i:9566 original size:50 final size:50
Alignment explanation
Indices: 9512--9710 Score: 328
Period size: 50 Copynumber: 4.0 Consensus size: 50
9502 TCCAATATAC
* *
9512 AAAGGACCGTCTTCCGCTTATCCTCTGAACCGTCTTCCAATTCAATCTTA
1 AAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTA
9562 AAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTA
1 AAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTA
*
9612 AAAGGACCGTC-TCCTGCTAATCCTTTGAACTGTCTTCCAATTCAATCTTA
1 AAAGGACCGTCTTCC-GCTTATCCTTTGAACTGTCTTCCAATTCAATCTTA
* * *
9662 AAAGGATCGTCTCCCGCTTATCCTTTGAACTGTCTTCCAATTCACTCTT
1 AAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTT
9711 CTGGATATCT
Statistics
Matches: 140, Mismatches: 7, Indels: 4
0.93 0.05 0.03
Matches are distributed among these distances:
49 3 0.02
50 135 0.96
51 2 0.01
ACGTcount: A:0.24, C:0.30, G:0.12, T:0.35
Consensus pattern (50 bp):
AAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTA
Found at i:10400 original size:2 final size:2
Alignment explanation
Indices: 10393--10426 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
10383 GGAATTTAAC
10393 AT AT AT 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 AT AT AT
10427 GTACCAACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16784 original size:11 final size:11
Alignment explanation
Indices: 16768--16793 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
16758 GTGCGTGAGC
16768 ATGCATGATGA
1 ATGCATGATGA
16779 ATGCATGATGA
1 ATGCATGATGA
16790 ATGC
1 ATGC
16794 CATGTAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.12, G:0.27, T:0.27
Consensus pattern (11 bp):
ATGCATGATGA
Found at i:20797 original size:14 final size:14
Alignment explanation
Indices: 20780--20810 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
20770 TTTTTTGAAA
*
20780 TTCTCCTTTTTCTT
1 TTCTCCTTTTCCTT
20794 TTCTCCTTTTCCTT
1 TTCTCCTTTTCCTT
20808 TTC
1 TTC
20811 CTTCGTCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (14 bp):
TTCTCCTTTTCCTT
Found at i:20827 original size:3 final size:3
Alignment explanation
Indices: 20819--20845 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
20809 TCCTTCGTCT
20819 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
20846 ACTAGCCTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:34934 original size:22 final size:21
Alignment explanation
Indices: 34864--34939 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 21
34854 CCCGGTTGTG
*
34864 GCCTGGTCGTGCTCGGGCTGCT
1 GCCTGGTCATGC-CGGGCTGCT
* *
34886 GTCTGGTCATG--GTGCGTGCGT
1 GCCTGGTCATGCCGGGC-TGC-T
34907 GCCTGGTCATGACCGGGCTGCT
1 GCCTGGTCATG-CCGGGCTGCT
34929 GCCTGGTCATG
1 GCCTGGTCATG
34940 GTGCGGAGCA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
19 3 0.07
20 3 0.07
21 11 0.25
22 21 0.48
23 3 0.07
24 3 0.07
ACGTcount: A:0.05, C:0.28, G:0.39, T:0.28
Consensus pattern (21 bp):
GCCTGGTCATGCCGGGCTGCT
Found at i:34954 original size:43 final size:43
Alignment explanation
Indices: 34864--34955 Score: 116
Period size: 43 Copynumber: 2.1 Consensus size: 43
34854 CCCGGTTGTG
* * * *
34864 GCCTGGTCGTGCTCGGGCTGCTGTCTGGTCATGGTGCGTGCGT
1 GCCTGGTCATGCTCGGGCTGCTGCCTGGTCATGGTGCGAGCGA
34907 GCCTGGTCATGAC-CGGGCTGCTGCCTGGTCATGGTGCGGAGC-A
1 GCCTGGTCATG-CTCGGGCTGCTGCCTGGTCATGGTGC-GAGCGA
34950 GCCTGG
1 GCCTGG
34956 CAGTGGCGCG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
43 39 0.91
44 4 0.09
ACGTcount: A:0.07, C:0.27, G:0.41, T:0.25
Consensus pattern (43 bp):
GCCTGGTCATGCTCGGGCTGCTGCCTGGTCATGGTGCGAGCGA
Found at i:35182 original size:16 final size:15
Alignment explanation
Indices: 35155--35185 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
35145 AAGTTAGAAA
35155 TTAAAAATAAAAAAT
1 TTAAAAATAAAAAAT
35170 TTAAAAGATAAAAAAT
1 TTAAAA-ATAAAAAAT
35186 AAAAATTGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (15 bp):
TTAAAAATAAAAAAT
Found at i:36003 original size:40 final size:40
Alignment explanation
Indices: 35959--37581 Score: 1997
Period size: 40 Copynumber: 40.6 Consensus size: 40
35949 AAGGAATAGG
* * * ** *
35959 AACAACACCTCCCGATGAGGAAGGGCAAACTAAGAACTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
* * ****
35999 AACAACACTTTCCGGTGGGGAAAGGCAAACTGTTTTTTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
* * * *
36039 AAAAACACCTTCCAGTGGGGAAGAGCAAATTGGGAATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
36079 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
*
36119 AACAACACCTTCCGGTGGGGAAGGGCAAATTGGGAATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
* *
36159 GACAACACCTTTCGGTGGGGAAGGGCAAACTGGGAATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
* *
36199 GACAACACCTTCCGATGGGGAAGGGCAAACTGGGAATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
* *
36239 GAC-ACACCTTCCGGTGGGGAAGGGCAAACTGGTTAATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGG-GAATTTA
* * * *
36279 AACAACACCTTCCGATGGGGAAGGGCAAAATGCGTATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
*
36319 CACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
* * *
36359 GACAACACCTTCCGATGGGGTAGGGCAAACTGGGAA-TTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
**
36398 AGACAACACCTTCCGGTGGAAAAGGGCAAACTGGGAATTTA
1 A-ACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
* * * * **
36439 GACAACACCTTCCGCTGGGGATGGGTAAACACGGAATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
* * * *
36479 GACAACACCTTCCGATGGGGAAGGGTAAACTGAGAATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
* * ** *
36519 GACAACACCTTCCGATGGGG-AGGATAAATTGGGAATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
* *
36558 GAC-ACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
* *
36597 GACAACACATTCCGGTGGGGAAGGGGCAAACTGGG--TTTA
1 AACAACACCTTCCGGTGGGGAA-GGGCAAACTGGGAATTTA
* * *
36636 AACAACACCTTCCGGTGGGGAAGGGCACATTGGGTATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
* * *
36676 AACAACACCTTCCGGTGGGGAAGAGCAGACTGGGTATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
* * * * *
36716 AACAACACCTTCCGGTGAGTAAGGGTACACTGGGTATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
* *
36756 AACAACACCTTCCGGTGGGGAAGGGCAGACTGGGTATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
* * * *
36796 AACAACACCTTCCGCTGGGGAAGGACAGACTGGGTATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
* *
36836 AACAACACCTTCCGGTGGGGAAGGGCAAACTGTGTATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
* * *
36876 AACAACACCTTCCGCTGGGGAAGGAC-AACTGGGTATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
* * * * *
36915 AACCACACCTTCCGCTGGAGAAGGGCAGACTGGGTATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
* * *
36955 AACAACACCTTCCGGTGTGGAACGGCACACTGGGTAATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGG-AATTTA
* * *
36996 AACAACACCTTCCGGTGGGGAATGGCAAAATGGGTATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
* * ***
37036 AATAACACCTTCCGTTGGGGAATACCAAACTGGGAATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
*
37076 GACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
* **
37116 GACAACACCTTCCAATGGGGAAGGGCAAACTGGGAATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
* *
37156 GACAACACCTTCCGATGGGGAAGGGCAAACTGGGAA-TTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
* *
37195 AGATAACACCTTTCGGT-GGGAAGGGCAAACTGGGAATTTA
1 A-ACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
* * *
37235 GACAACACCTTCCGATGGGGAAGGGCGAACTGGGAATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
* * *
37275 GACAACACCTTCCGATGGGGAAGGGCAAACTGGGTATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
* * * *
37315 GATAACACCTTACGATGGGGAAGGGCAAACTGGGAATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
* * * * * *
37355 GATAACACATTCCGGTGGGGAAAGGAAAACTGGGTATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
* * *
37395 AACAACTACCTTCCGGTGGGGAAGGGCACATTGGGTATTTA
1 AACAAC-ACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
* *
37436 AACAACACCTTCCGGAGGGGAAGGCCAAACTGGGAATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
*
37476 AGACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA
1 A-ACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
* * *
37517 GACAACACCTTCCGGT-GGGAAGGGCAGACTGGGTATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
*
37556 AACAACACCTTCCGATGGGGAAGGGC
1 AACAACACCTTCCGGTGGGGAAGGGC
Statistics
Matches: 1397, Mismatches: 169, Indels: 34
0.87 0.11 0.02
Matches are distributed among these distances:
38 25 0.02
39 197 0.14
40 1028 0.74
41 147 0.11
ACGTcount: A:0.31, C:0.20, G:0.29, T:0.20
Consensus pattern (40 bp):
AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTA
Done.