Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011905.1 Corchorus olitorius cultivar O-4 contig11938, 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: 21245
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:2291 original size:14 final size:15
Alignment explanation
Indices: 2272--2305 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
2262 GCAGCTTCCT
2272 AAAAAAACTCAAAA-
1 AAAAAAACTCAAAAG
2286 AAAAAAACTCAAAAG
1 AAAAAAACTCAAAAG
2301 AAAAA
1 AAAAA
2306 TTGTTAGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.79, C:0.12, G:0.03, T:0.06
Consensus pattern (15 bp):
AAAAAAACTCAAAAG
Found at i:2884 original size:16 final size:16
Alignment explanation
Indices: 2848--2886 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
2838 GCAGAGATTG
2848 ACAG-AAAGCAATTAA
1 ACAGAAAAGCAATTAA
2863 ACAGAAAAG-AATTAA
1 ACAGAAAAGCAATTAA
2878 ACTAGAAAA
1 AC-AGAAAA
2887 CAAAGCAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.64, C:0.10, G:0.13, T:0.13
Consensus pattern (16 bp):
ACAGAAAAGCAATTAA
Found at i:3883 original size:12 final size:12
Alignment explanation
Indices: 3866--3892 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3856 AGGTCTAAGT
3866 CTTGGACTCCAA
1 CTTGGACTCCAA
3878 CTTGGACTCCAA
1 CTTGGACTCCAA
3890 CTT
1 CTT
3893 CAACAGCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.33, G:0.15, T:0.30
Consensus pattern (12 bp):
CTTGGACTCCAA
Found at i:10523 original size:39 final size:39
Alignment explanation
Indices: 10469--10543 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
10459 GGAATTCCGC
10469 CGGTGTTGCGCGTCGGGGATCGTCTGATGTTTTTTTCGT
1 CGGTGTTGCGCGTCGGGGATCGTCTGATGTTTTTTTCGT
* * *
10508 CGGTGTTGCGCGTCGGGGATTGTTTGGTGTTTTTTT
1 CGGTGTTGCGCGTCGGGGATCGTCTGATGTTTTTTT
10544 AAAATGCCAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.04, C:0.15, G:0.37, T:0.44
Consensus pattern (39 bp):
CGGTGTTGCGCGTCGGGGATCGTCTGATGTTTTTTTCGT
Found at i:10801 original size:118 final size:119
Alignment explanation
Indices: 10665--10894 Score: 311
Period size: 118 Copynumber: 1.9 Consensus size: 119
10655 TTGGTATATT
* * * * * *
10665 AATTAAGTGATGAAAATTTTAGTTAGTGACAATTTAAACGCCAGG-AAATCTCAAAAGATCTTTA
1 AATTAAGTGATGAAAATTTCAATCAGTGACAATCTAAACGCCAGGAAAAGCT-AAAAAATCTTTA
* * * *
10729 TTTGTGGCATTTTAAATGCCGGGAAACCTATTTTATAAATATTATATATAGTGAA
65 ATTATGGCATTTTAAATGCCGGGAAACCCATCTTATAAATATTATATATAGTGAA
* * *
10784 AATT-AGTGATGAAAATTTCAATCAGTGGCAATCTAAACGCCGGGAAAAGGTAAAAAATCTTTAA
1 AATTAAGTGATGAAAATTTCAATCAGTGACAATCTAAACGCCAGGAAAAGCTAAAAAATCTTTAA
*
10848 TTATGGCATTTTGAATGCCGGGAAACCCATCTTATAAATATTATATA
66 TTATGGCATTTTAAATGCCGGGAAACCCATCTTATAAATATTATATA
10895 GTAATTCTTA
Statistics
Matches: 96, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
118 88 0.92
119 8 0.08
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.33
Consensus pattern (119 bp):
AATTAAGTGATGAAAATTTCAATCAGTGACAATCTAAACGCCAGGAAAAGCTAAAAAATCTTTAA
TTATGGCATTTTAAATGCCGGGAAACCCATCTTATAAATATTATATATAGTGAA
Found at i:14658 original size:2 final size:2
Alignment explanation
Indices: 14651--14719 Score: 95
Period size: 2 Copynumber: 33.5 Consensus size: 2
14641 CATATAAATC
*
14651 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
14694 AT AT CAT AT AT CAT AT AT -T AT AT AT A
1 AT AT -AT AT AT -AT AT AT AT AT AT AT A
14720 ATGATAACAA
Statistics
Matches: 61, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
1 1 0.02
2 54 0.89
3 6 0.10
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:15862 original size:43 final size:43
Alignment explanation
Indices: 15814--15895 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
15804 CTCAATTTCC
* * *
15814 GTAA-TTAACTTTGATATCCTCAATTTTGGCAATTAGTATTGAT
1 GTAATTTAACTAT-ATATCCTCAAATTTGCCAATTAGTATTGAT
*
15857 GTAATTTCACTATATATCCTCAAATTTGCCAATTAGTAT
1 GTAATTTAACTATATATCCTCAAATTTGCCAATTAGTAT
15896 CATGTAACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 28 0.82
44 6 0.18
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.43
Consensus pattern (43 bp):
GTAATTTAACTATATATCCTCAAATTTGCCAATTAGTATTGAT
Found at i:16100 original size:35 final size:37
Alignment explanation
Indices: 16061--16135 Score: 93
Period size: 35 Copynumber: 2.1 Consensus size: 37
16051 TTCCATGATC
* *
16061 TTTATTCAATTTTTTGTCTCC-ATTATT-TT-ACAAAT
1 TTTATTCAAGTTTCT-TCTCCTATTATTCTTGACAAAT
*
16096 TTTATTCAAGTTTCTTCTCCTATTCTTCTTGACAAAT
1 TTTATTCAAGTTTCTTCTCCTATTATTCTTGACAAAT
16133 TTT
1 TTT
16136 GTTGGCCTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
34 5 0.15
35 18 0.53
36 2 0.06
37 9 0.26
ACGTcount: A:0.23, C:0.17, G:0.04, T:0.56
Consensus pattern (37 bp):
TTTATTCAAGTTTCTTCTCCTATTATTCTTGACAAAT
Found at i:17121 original size:106 final size:107
Alignment explanation
Indices: 16937--17182 Score: 404
Period size: 106 Copynumber: 2.3 Consensus size: 107
16927 AAATAAAGAT
* * *
16937 TTAGTTATATATTTTATTTATAAAACCCTATAACAATATATTATTAATTATGCAATTTACCCTTA
1 TTAGTTTTATATTTTATTTCTAAAACCCTATAACAATATATTATTAATTATGAAATTTACCCTTA
* *
17002 AAATAAAGATAAAATTTTAATTTGGGGCTAAACTTAGTGAAA
66 AAATAAAAATAAAATTTCAATTTGGGGCTAAACTTAGTGAAA
* * *
17044 TTAGTTTTGTATTTTATTTCTAAAACCCTATAACAATA-ATTATTAATTTTGAAATTTACCTTTA
1 TTAGTTTTATATTTTATTTCTAAAACCCTATAACAATATATTATTAATTATGAAATTTACCCTTA
17108 AAATAAAAATAAAATTTCAATTTGGGGCTAAACTTAGTGAAA
66 AAATAAAAATAAAATTTCAATTTGGGGCTAAACTTAGTGAAA
*
17150 TTAGTTTTATATTTTATTTCTAAAACTCTATAA
1 TTAGTTTTATATTTTATTTCTAAAACCCTATAA
17183 TAAAACCTTT
Statistics
Matches: 129, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
106 94 0.73
107 35 0.27
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (107 bp):
TTAGTTTTATATTTTATTTCTAAAACCCTATAACAATATATTATTAATTATGAAATTTACCCTTA
AAATAAAAATAAAATTTCAATTTGGGGCTAAACTTAGTGAAA
Found at i:17217 original size:106 final size:105
Alignment explanation
Indices: 16937--17215 Score: 368
Period size: 106 Copynumber: 2.6 Consensus size: 105
16927 AAATAAAGAT
* * * *
16937 TTAGTTATATATTTTATTTATAAAACCCTATAACAATATATTATTAATTATGC-AATTTACCCTT
1 TTAGTTTTATATTTTATTTCTAAAACCCTATAACAATA-ACTATTAATT-TTCAAATTTA-CCTT
* *
17001 AAAATAAAGATAAAATTTTAATTTGGGGCTAAACTTAGTGAAA
63 AAAATAAAAATAAAATTTCAATTTGGGGCTAAACTTAGTGAAA
* * *
17044 TTAGTTTTGTATTTTATTTCTAAAACCCTATAACAATAATTATTAATTTTGAAATTTACCTTTAA
1 TTAGTTTTATATTTTATTTCTAAAACCCTATAACAATAACTATTAATTTTCAAATTTACC-TTAA
17109 AATAAAAATAAAATTTCAATTTGGGGCTAAACTTAGTGAAA
65 AATAAAAATAAAATTTCAATTTGGGGCTAAACTTAGTGAAA
* *
17150 TTAGTTTTATATTTTATTTCTAAAACTCTATAATAA-AACCT-TTAA-TTTCATAATTTACTCTT
1 TTAGTTTTATATTTTATTTCTAAAACCCTATAACAATAA-CTATTAATTTTCA-AATTTAC-CTT
17212 AAAA
63 AAAA
17216 ATTAAATTTC
Statistics
Matches: 155, Mismatches: 12, Indels: 12
0.87 0.07 0.07
Matches are distributed among these distances:
104 4 0.03
105 22 0.14
106 94 0.61
107 35 0.23
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.43
Consensus pattern (105 bp):
TTAGTTTTATATTTTATTTCTAAAACCCTATAACAATAACTATTAATTTTCAAATTTACCTTAAA
ATAAAAATAAAATTTCAATTTGGGGCTAAACTTAGTGAAA
Found at i:17918 original size:25 final size:25
Alignment explanation
Indices: 17884--17933 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
17874 AATCAGAAAT
**
17884 AATCAATCAATAATTATTTACTTTC
1 AATCAATCAATAACAATTTACTTTC
17909 AATCAATCAATAACAATTTACTTTC
1 AATCAATCAATAACAATTTACTTTC
17934 CATAAACAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.40
Consensus pattern (25 bp):
AATCAATCAATAACAATTTACTTTC
Found at i:21130 original size:200 final size:199
Alignment explanation
Indices: 20787--21236 Score: 638
Period size: 200 Copynumber: 2.3 Consensus size: 199
20777 TATAAGTTTA
* ***
20787 TTATAAGAAAAATTATACAATACATCGTCAGTGGAGTTTAGCAGACTGCATGTTTGAGGTTTAAG
1 TTATAAGAAAAATTATACAATACATCGTCAGTGGAGTTTAGCAGACTGCACGCGCGAGGTTTAAG
*
20852 GGTTGACATGTGTCCCCTTGGGGAATATCTATTAATATTAAATATTTAATTAATTATAAAGTGAA
66 GGTTGACATGTGTCCCCTTAGGGAATATCTATTAATATTAAATATTTAATTAATTATAAAGTGAA
* *
20917 ATATGTGTCAACTTCTTAAC-CTGCTTAT-GAAGTCCAAAATTTACACTGACAGTGTATTGTATA
131 ATATGTGTCAACTTCTTAACTC-GCTTATAG-AGTCCAAAATTTACACTGACAATGTATTATATA
**
20980 ATTTTTC
194 A-TAATC
* * *
20987 TTATAAGAAAAATTATACAATACATTGTCTA-TGGAGTTTAGCAGACTGCACGCGCGGGGTTTGA
1 TTATAAGAAAAATTATACAATACATCGTC-AGTGGAGTTTAGCAGACTGCACGCGCGAGGTTTAA
** *
21051 GGGTTGACATGTGTCTGCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATTAAA-TG
65 GGGTTGACATGTGTCCCCTTAGGGAATATCTATTAATATTAAATATTTAATTAATTA-TAAAGTG
***
21115 GGGTATGTGTCAACTTCTTAACTCGCTTATAGAGTCCAAAATTTACACTGACAATGTATTATATA
129 AAATATGTGTCAACTTCTTAACTCGCTTATAGAGTCCAAAATTTACACTGACAATGTATTATATA
21180 ATAATC
194 ATAATC
** *
21186 CCATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCAC
1 TTATAAGAAAAATTATACAATACATCGTCAGTGGAGTTTAGCAGACTGCAC
21237 ATTCGGGGG
Statistics
Matches: 223, Mismatches: 22, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
198 1 0.00
199 48 0.22
200 167 0.75
201 7 0.03
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (199 bp):
TTATAAGAAAAATTATACAATACATCGTCAGTGGAGTTTAGCAGACTGCACGCGCGAGGTTTAAG
GGTTGACATGTGTCCCCTTAGGGAATATCTATTAATATTAAATATTTAATTAATTATAAAGTGAA
ATATGTGTCAACTTCTTAACTCGCTTATAGAGTCCAAAATTTACACTGACAATGTATTATATAAT
AATC
Done.