Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012370.1 Corchorus olitorius cultivar O-4 contig12403, 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: 55474
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:1464 original size:17 final size:17
Alignment explanation
Indices: 1444--1476 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1434 GAGTGTGGAT
*
1444 TGTGAGAGAGAGGGGAA
1 TGTGAGAGAAAGGGGAA
1461 TGTGAGAGAAAGGGGA
1 TGTGAGAGAAAGGGGA
1477 CAGGGCATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.52, T:0.12
Consensus pattern (17 bp):
TGTGAGAGAAAGGGGAA
Found at i:3227 original size:27 final size:28
Alignment explanation
Indices: 3161--3236 Score: 120
Period size: 27 Copynumber: 2.8 Consensus size: 28
3151 CAGTGAACTT
*
3161 AAAATGACCAAAATGCCCCTGAACATGC
1 AAAATGACCAAAATGCCCCTGAACATGA
3189 AAAATGACCAAAATGCCCCTG-A-ATGTA
1 AAAATGACCAAAATGCCCCTGAACATG-A
3216 AAAATGACCAAAATGCCCCTG
1 AAAATGACCAAAATGCCCCTG
3237 GATTTTGAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
26 3 0.07
27 22 0.48
28 21 0.46
ACGTcount: A:0.43, C:0.26, G:0.14, T:0.16
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTGAACATGA
Found at i:5312 original size:18 final size:18
Alignment explanation
Indices: 5286--5331 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
5276 TAATTGGTTT
*
5286 GCCATGTCATCCTCAATA
1 GCCACGTCATCCTCAATA
5304 GCCACGTCATCCTCAATA
1 GCCACGTCATCCTCAATA
5322 GCCACGTCAT
1 GCCACGTCAT
5332 TGCACTCCAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.26, C:0.37, G:0.13, T:0.24
Consensus pattern (18 bp):
GCCACGTCATCCTCAATA
Found at i:13080 original size:1 final size:1
Alignment explanation
Indices: 13074--13105 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
13064 ATATATATTT
13074 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
13106 CATGCAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:21766 original size:11 final size:11
Alignment explanation
Indices: 21742--21776 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
21732 TTGACAGCAC
21742 AACAAAAACAA
1 AACAAAAACAA
* *
21753 AACGAAAACGA
1 AACAAAAACAA
21764 AACAAAAACAA
1 AACAAAAACAA
21775 AA
1 AA
21777 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:24793 original size:60 final size:60
Alignment explanation
Indices: 24695--24856 Score: 209
Period size: 60 Copynumber: 2.7 Consensus size: 60
24685 GCTAATTGCT
* * * *
24695 CAAATAAGGGCCTAACATTTTTC-AACATGTTCAAATAAGGGCCCGATCTTTTAATTTGAC
1 CAAATAAAGGCCTAACA-TTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
* * * *
24755 CAAATAAAGGCCTAACATTATCGAAAATGCTCACATAAGGGCCCGGTTTTTTAATTTGGC
1 CAAATAAAGGCCTAACATTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
* **
24815 CAAATAAAGGTCTAATGTTATCGAAAATGCTCAAATAAGGGC
1 CAAATAAAGGCCTAACATTATCGAAAATGCTCAAATAAGGGC
24857 TTGGTGTCAG
Statistics
Matches: 89, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
59 4 0.04
60 85 0.96
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (60 bp):
CAAATAAAGGCCTAACATTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
Found at i:25863 original size:99 final size:99
Alignment explanation
Indices: 25692--25881 Score: 326
Period size: 99 Copynumber: 1.9 Consensus size: 99
25682 TTGACTTTTG
* * *
25692 AGGTGAAAATTAGCTTTTGACACAAACCATGACTTATTCGACATTGTGTTTAAGGTGAAAAGTAG
1 AGGTGAAAATTAGCTTTTGACACAAACCATGACTTATTCGACATTATATTTAAGGTGAAAAGTAA
25757 CTTTTTTATCTCCAAACTCAATCCCGAACCAAGT
66 CTTTTTTATCTCCAAACTCAATCCCGAACCAAGT
* * *
25791 AGGTGAAAATTAGCTTTTGGCACAAATCATGACTTATTTGACATTATATTTAAGGTGAAAAGTAA
1 AGGTGAAAATTAGCTTTTGACACAAACCATGACTTATTCGACATTATATTTAAGGTGAAAAGTAA
25856 CTTTTTTATCTCCAAACTCAATCCCG
66 CTTTTTTATCTCCAAACTCAATCCCG
25882 GACCCAGCAT
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
99 85 1.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (99 bp):
AGGTGAAAATTAGCTTTTGACACAAACCATGACTTATTCGACATTATATTTAAGGTGAAAAGTAA
CTTTTTTATCTCCAAACTCAATCCCGAACCAAGT
Found at i:28922 original size:180 final size:180
Alignment explanation
Indices: 28620--28978 Score: 646
Period size: 180 Copynumber: 2.0 Consensus size: 180
28610 TGAAAGATTT
* *
28620 AGGGAATTTACCAAAGACCCCTTTTGAGAATCGATGGGGAGGCTTCATTTGAGTTTTTTTTGTCC
1 AGGGAATTTACCAAAGACCCCTTTTGAGAATCGATGAGGAGGCTTCATTTGAATTTTTTTTGTCC
*
28685 TTTTCTGTCTTTTCTCACTTGCCAAATTACTTAAAAGACCCTAGGTTACTTTCTAGCCAGTTCTT
66 TTTTCTGTCTTTTCTCACTTGCCAAATTACTTAAAAGACCCTACGTTACTTTCTAGCCAGTTCTT
*
28750 GCCCTTAAGTCCTTTTTTGTAATTATCCTTTCCTTTCACATAAATGTTAC
131 GCCCTTAAGCCCTTTTTTGTAATTATCCTTTCCTTTCACATAAATGTTAC
* *
28800 AGGGAATTTACCAAAGGCCCCTTTTGAGGATCGATGAGGAGGCTTCATTTGAATTTTTTTTGTCC
1 AGGGAATTTACCAAAGACCCCTTTTGAGAATCGATGAGGAGGCTTCATTTGAATTTTTTTTGTCC
*
28865 TTTTCTGTCTTTTCTCACTTGCCAAATTACTTAGAAGACCCTACGTTACTTTCTAGCCAGTTCTT
66 TTTTCTGTCTTTTCTCACTTGCCAAATTACTTAAAAGACCCTACGTTACTTTCTAGCCAGTTCTT
*
28930 GCCCTTAAGCCCTTTTTTGTAATTATTCTTTCCTTTCACATAAATGTTA
131 GCCCTTAAGCCCTTTTTTGTAATTATCCTTTCCTTTCACATAAATGTTA
28979 TAATAAATCA
Statistics
Matches: 171, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
180 171 1.00
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (180 bp):
AGGGAATTTACCAAAGACCCCTTTTGAGAATCGATGAGGAGGCTTCATTTGAATTTTTTTTGTCC
TTTTCTGTCTTTTCTCACTTGCCAAATTACTTAAAAGACCCTACGTTACTTTCTAGCCAGTTCTT
GCCCTTAAGCCCTTTTTTGTAATTATCCTTTCCTTTCACATAAATGTTAC
Found at i:29853 original size:29 final size:29
Alignment explanation
Indices: 29788--29854 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
29778 TTTATTAGTG
*
29788 CCAAATTAATTTGATCAGTTTAGAATAAAT
1 CCAAATTAATTTGATCAG-TGAGAATAAAT
29818 CCAAATTAATTATGAGTCA-TGAGAA-AAAT
1 CCAAATTAATT-TGA-TCAGTGAGAATAAAT
29847 CCAAATTA
1 CCAAATTA
29855 TGGGTTAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
29 12 0.35
30 16 0.47
31 3 0.09
32 3 0.09
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.31
Consensus pattern (29 bp):
CCAAATTAATTTGATCAGTGAGAATAAAT
Found at i:30218 original size:1 final size:1
Alignment explanation
Indices: 30212--30239 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
30202 ATCTTGTTGC
30212 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
30240 CTCTTCCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:30700 original size:19 final size:20
Alignment explanation
Indices: 30676--30733 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 20
30666 CTGTTTAGGA
30676 ACTGTACAGATGAGATTA-C
1 ACTGTACAGATGAGATTAGC
* * *
30695 ACTGTACATATTAGATTAGGT
1 ACTGTACAGATGAGATTA-GC
30716 ACTGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
30734 TTAGAACAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (20 bp):
ACTGTACAGATGAGATTAGC
Found at i:30721 original size:21 final size:21
Alignment explanation
Indices: 30670--30733 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
30660 TTGACACTGT
30670 TTAGGAACTGTACAGATGAGA
1 TTAGGAACTGTACAGATGAGA
* * *
30691 TTA--CACTGTACATATTAGA
1 TTAGGAACTGTACAGATGAGA
*
30710 TTAGGTACTGTACAGATGAGA
1 TTAGGAACTGTACAGATGAGA
30731 TTA
1 TTA
30734 TTAGAACAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 16 0.46
21 19 0.54
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (21 bp):
TTAGGAACTGTACAGATGAGA
Done.