Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020410.1 Corchorus olitorius cultivar O-4 contig20443, 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: 51781
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Found at i:898 original size:24 final size:25
Alignment explanation
Indices: 855--927 Score: 69
Period size: 24 Copynumber: 3.0 Consensus size: 25
845 TTTGTACTTA
* *
855 AAATATATCAATTAT-ATATATTATT
1 AAATATAT-AAATATGATATATTAAT
* * * *
880 AATTATGTAAA-ATGTTATATAAAT
1 AAATATATAAATATGATATATTAAT
904 AAATATATAAATATGATATATTAA
1 AAATATATAAATATGATATATTAA
928 ATTTTTATTA
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
23 2 0.06
24 18 0.50
25 16 0.44
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.42
Consensus pattern (25 bp):
AAATATATAAATATGATATATTAAT
Found at i:6092 original size:16 final size:16
Alignment explanation
Indices: 6071--6104 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
6061 TACAGAAGTA
6071 ATTGGTATTTTATCTG
1 ATTGGTATTTTATCTG
6087 ATTGGTATTTTATCTG
1 ATTGGTATTTTATCTG
6103 AT
1 AT
6105 CGAATGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.21, C:0.06, G:0.18, T:0.56
Consensus pattern (16 bp):
ATTGGTATTTTATCTG
Found at i:11272 original size:19 final size:19
Alignment explanation
Indices: 11248--11294 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
11238 GTTTGATTTA
11248 TAATTAAATAAT-AATAAAT
1 TAATTAAA-AATAAATAAAT
*
11267 TAATTAAAATTAAATAAAT
1 TAATTAAAAATAAATAAAT
11286 TAATTAAAA
1 TAATTAAAA
11295 TTAACTTGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 2 0.08
19 24 0.92
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TAATTAAAAATAAATAAAT
Found at i:11276 original size:10 final size:10
Alignment explanation
Indices: 11263--11298 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
11253 AAATAATAAT
11263 AAATTAATTA
1 AAATTAATTA
*
11273 AAATTAAAT-
1 AAATTAATTA
11282 AAATTAATTA
1 AAATTAATTA
11292 AAATTAA
1 AAATTAA
11299 CTTGTATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AAATTAATTA
Found at i:11295 original size:19 final size:19
Alignment explanation
Indices: 11260--11298 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
11250 ATTAAATAAT
11260 AATAAATTAATTAAAATTA
1 AATAAATTAATTAAAATTA
11279 AATAAATTAATTAAAATTA
1 AATAAATTAATTAAAATTA
11298 A
1 A
11299 CTTGTATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AATAAATTAATTAAAATTA
Found at i:11424 original size:19 final size:19
Alignment explanation
Indices: 11384--11420 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
11374 AATTTTTAAG
11384 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
*
11403 TAAAAATTTAATAT-TAAA
1 TAAAAATATAATATATAAA
11421 ATAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:14066 original size:22 final size:22
Alignment explanation
Indices: 14038--14355 Score: 183
Period size: 22 Copynumber: 14.6 Consensus size: 22
14028 TAGGATTATC
*
14038 ATCAAAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGTGTGGTT
*
14060 ATCAAAATGTT-ATTAG-GATAG-T
1 ATCAAAAT-TTCA-TAGTG-TGGTT
* *
14082 A-CTATAATTTCATAGTATGGTT
1 ATC-AAAATTTCATAGTGTGGTT
* * * *
14104 AACAAAGTTTCATAGAGAGGTT
1 ATCAAAATTTCATAGTGTGGTT
** * *
14126 ATC-AAATAACATAGGGAGGTT
1 ATCAAAATTTCATAGTGTGGTT
*
14147 ATCGAAATTTCATAG-GTAGGTT
1 ATCAAAATTTCATAGTGT-GGTT
14169 ATCAAAATTTCCATAGTGTGGTT
1 ATCAAAATTT-CATAGTGTGGTT
*
14192 ATCAAAATTT--TAGTGTGTTT
1 ATCAAAATTTCATAGTGTGGTT
* **
14212 ATTAAAATTTCATAG-G-AATAT
1 ATCAAAATTTCATAGTGTGGT-T
* * * *
14233 ATTAAAATCTCATAGGGAGGTT
1 ATCAAAATTTCATAGTGTGGTT
14255 ATCAAAATTTCATAGTGTGGTT
1 ATCAAAATTTCATAGTGTGGTT
* *
14277 ATGAAATTTTCATA-TAG-GGATT
1 ATCAAAATTTCATAGT-GTGG-TT
* * *
14299 ATCGAAATTTTATGGTGTGGTT
1 ATCAAAATTTCATAGTGTGGTT
** * * * *
14321 ATTGAAATTTTATATTGAGGAT
1 ATCAAAATTTCATAGTGTGGTT
14343 ATCAAAATTTCAT
1 ATCAAAATTTCAT
14356 GGTCATATCA
Statistics
Matches: 230, Mismatches: 45, Indels: 42
0.73 0.14 0.13
Matches are distributed among these distances:
20 19 0.08
21 45 0.20
22 134 0.58
23 30 0.13
24 2 0.01
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.39
Consensus pattern (22 bp):
ATCAAAATTTCATAGTGTGGTT
Found at i:14220 original size:65 final size:64
Alignment explanation
Indices: 14038--14332 Score: 176
Period size: 65 Copynumber: 4.5 Consensus size: 64
14028 TAGGATTATC
* * *
14038 ATCAAAATTTCATAGTGTGATTATCAAAATGTTA-T-TAGGATAGTACT-ATAATTTCATA-GTA
1 ATCAAAATTTCATAGTGTGGTTATCAAAATTTTAGTGT-GG-T--TA-TGAAAATTTCATAGGTA
14099 TGGTT
61 -GGTT
* * * * *** * *
14104 AACAAAGTTTCATAGAGAGGTTATCAAATAACATAGGGAGGTTATCG-AAATTTCATAGGTAGGT
1 ATCAAAATTTCATAGTGTGGTTATCAAA-ATTTTAGTGTGGTTAT-GAAAATTTCATAGGTAGGT
14168 T
64 T
* * *
14169 ATCAAAATTTCCATAGTGTGGTTATCAAAATTTTAGTGTGTTTATTAAAATTTCATAGG-A-ATA
1 ATCAAAATTT-CATAGTGTGGTTATCAAAATTTTAGTGTGGTTATGAAAATTTCATAGGTAGGT-
14232 T
64 T
* * * * *
14233 ATTAAAATCTCATAGGGAGGTTATCAAAATTTCATAGTGTGGTTATGAAATTTTCATA--TAGGG
1 ATCAAAATTTCATAGTGTGGTTATCAAAATTT--TAGTGTGGTTATGAAAATTTCATAGGTA-GG
14296 ATT
63 -TT
* * * **
14299 ATCGAAATTTTATGGTGTGGTTATTGAAATTTTA
1 ATCAAAATTTCATAGTGTGGTTATCAAAATTTTA
14333 TATTGAGGAT
Statistics
Matches: 174, Mismatches: 40, Indels: 32
0.71 0.16 0.13
Matches are distributed among these distances:
63 21 0.12
64 14 0.08
65 66 0.38
66 66 0.38
67 5 0.03
68 2 0.01
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.39
Consensus pattern (64 bp):
ATCAAAATTTCATAGTGTGGTTATCAAAATTTTAGTGTGGTTATGAAAATTTCATAGGTAGGTT
Found at i:14255 original size:108 final size:108
Alignment explanation
Indices: 14135--14330 Score: 265
Period size: 108 Copynumber: 1.8 Consensus size: 108
14125 TATCAAATAA
*
14135 CATAGGGAGGTTATCGAAATTTCATAG-GTAGGTTATCAAAATTTCCATAGT-GTGG-TTATCAA
1 CATAGGGAGGTTATCAAAATTTCATAGTGT-GGTTAT-AAAATTTCCATA-TAG-GGATTATCAA
*
14197 AATTTTA-GTGTGTTTATTAAAATTTCATAGGAATATATTAAAATCT
62 AATTTTAGGTGTGGTTATTAAAATTTCATAGGAATATATTAAAATCT
* * *
14243 CATAGGGAGGTTATCAAAATTTCATAGTGTGGTTATGAAATTTTCATATAGGGATTATCGAAATT
1 CATAGGGAGGTTATCAAAATTTCATAGTGTGGTTATAAAATTTCCATATAGGGATTATCAAAATT
*
14308 TTATGGTGTGGTTATTGAAATTT
66 TTA-GGTGTGGTTATTAAAATTT
14331 TATATTGAGG
Statistics
Matches: 77, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
106 3 0.04
107 24 0.31
108 32 0.42
109 18 0.23
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (108 bp):
CATAGGGAGGTTATCAAAATTTCATAGTGTGGTTATAAAATTTCCATATAGGGATTATCAAAATT
TTAGGTGTGGTTATTAAAATTTCATAGGAATATATTAAAATCT
Found at i:14547 original size:2 final size:2
Alignment explanation
Indices: 14540--14571 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
14530 TAAAGCAGTG
14540 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14572 AGCATTTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31499 original size:22 final size:22
Alignment explanation
Indices: 31471--31512 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
31461 AAGAGAATCA
31471 TCACAACCATAAATACATTGGC
1 TCACAACCATAAATACATTGGC
31493 TCACAACCATAAATACATTG
1 TCACAACCATAAATACATTG
31513 TCAAGACAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.26, G:0.07, T:0.24
Consensus pattern (22 bp):
TCACAACCATAAATACATTGGC
Found at i:31918 original size:13 final size:13
Alignment explanation
Indices: 31900--31926 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31890 AATGCTTCTA
31900 AATAAAGTGTTCG
1 AATAAAGTGTTCG
31913 AATAAAGTGTTCG
1 AATAAAGTGTTCG
31926 A
1 A
31927 GTATAAGACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.30
Consensus pattern (13 bp):
AATAAAGTGTTCG
Found at i:32213 original size:22 final size:22
Alignment explanation
Indices: 32171--32222 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
32161 AACCACACTT
*
32171 TTCATAAT-TAAATAATAACTAA
1 TTCATCATCTAAATAATAACT-A
*
32193 TTCATCATCTAAA-AATTACTA
1 TTCATCATCTAAATAATAACTA
32214 TT-ATCATCT
1 TTCATCATCT
32223 TATTCCCACA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 7 0.26
21 3 0.11
22 13 0.48
23 4 0.15
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.40
Consensus pattern (22 bp):
TTCATCATCTAAATAATAACTA
Found at i:33842 original size:22 final size:22
Alignment explanation
Indices: 33798--33844 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
33788 TATTCTTATA
* *
33798 ACTATTTTACTTTTACCATTTT
1 ACTATTTTACTTTTACAAATTT
*
33820 ACTATTTTACTTTTATAAATTT
1 ACTATTTTACTTTTACAAATTT
33842 ACT
1 ACT
33845 CAACTAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.28, C:0.15, G:0.00, T:0.57
Consensus pattern (22 bp):
ACTATTTTACTTTTACAAATTT
Found at i:33869 original size:93 final size:94
Alignment explanation
Indices: 33734--33921 Score: 281
Period size: 93 Copynumber: 2.0 Consensus size: 94
33724 CATTGTTTAA
** *
33734 ACTTTTATAGTTTTAGCCAACTAAAAAACTCTATTTTTATTTAATTAAATCTAATATTCTTATAA
1 ACTTTTATAAATTTAGCCAACTAAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAA
* *
33799 CTATTTTACTTTTACCATTTTACTATTTT
66 CTATTTTACTTTTACCATATTACTAATTT
*
33828 ACTTTTATAAATTTA-CTCAACT-AAAAACTCTTTTTTTATTTAATTAAATCTAATATCCTTATA
1 ACTTTTATAAATTTAGC-CAACTAAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATA
* *
33891 CCTATTTTATTTTTACCATATTACTAATTT
65 ACTATTTTACTTTTACCATATTACTAATTT
33921 A
1 A
33922 ATTAAAAAGC
Statistics
Matches: 85, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
93 67 0.79
94 18 0.21
ACGTcount: A:0.34, C:0.14, G:0.01, T:0.51
Consensus pattern (94 bp):
ACTTTTATAAATTTAGCCAACTAAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAA
CTATTTTACTTTTACCATATTACTAATTT
Found at i:51500 original size:22 final size:22
Alignment explanation
Indices: 51472--51514 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
51462 TTTATTCTCA
51472 CCAAAATTAAATACTTAATTTT
1 CCAAAATTAAATACTTAATTTT
* *
51494 CCAAAATTAATTATTTAATTT
1 CCAAAATTAAATACTTAATTT
51515 CCTCTCATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (22 bp):
CCAAAATTAAATACTTAATTTT
Done.