Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021587.1 Corchorus olitorius cultivar O-4 contig21620, 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: 52200
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:3156 original size:22 final size:22
Alignment explanation
Indices: 3131--3177 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
3121 GTTTTAGTTG
*
3131 AGTAAAACT-ATAAAAGTAAAAT
1 AGTAAAA-TGATAAAAATAAAAT
*
3153 AGTAAAATGGTAAAAATAAAAT
1 AGTAAAATGATAAAAATAAAAT
3175 AGT
1 AGT
3178 TATAAGGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.62, C:0.02, G:0.13, T:0.23
Consensus pattern (22 bp):
AGTAAAATGATAAAAATAAAAT
Found at i:3176 original size:92 final size:93
Alignment explanation
Indices: 3055--3238 Score: 298
Period size: 92 Copynumber: 2.0 Consensus size: 93
3045 TCTTTTTAAT
* *
3055 TAAATTAGTAATATCGTAAAAACAAAATAGGTATAAGGATATTAGATTTAATCAAATAAAAATAG
1 TAAAATAGTAAAATCGTAAAAACAAAATAGGTATAAGGATATTAGATTTAATCAAATAAAAATAG
*
3120 AG-TTTTAGTTGAGTAAAACTATAAAAG
66 AGTTTTTAGTTGACTAAAACTATAAAAG
* * * *
3147 TAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATCGTAAAAACAAAATAGGTATAAGGATATTAGATTTAATCAAATAAAAATAG
3212 AGTTTTTAGTTGACTAAAACTATAAAA
66 AGTTTTTAGTTGACTAAAACTATAAAA
3239 ATTTAAAGAA
Statistics
Matches: 84, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
92 61 0.73
93 23 0.27
ACGTcount: A:0.52, C:0.03, G:0.13, T:0.32
Consensus pattern (93 bp):
TAAAATAGTAAAATCGTAAAAACAAAATAGGTATAAGGATATTAGATTTAATCAAATAAAAATAG
AGTTTTTAGTTGACTAAAACTATAAAAG
Found at i:3310 original size:31 final size:31
Alignment explanation
Indices: 3275--3336 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
3265 TATTCGAAAA
*
3275 AATAAGGGTATGATAGGCGATTCAAAAGTTT
1 AATAAGGGTATAATAGGCGATTCAAAAGTTT
3306 AATAAGGGTATAATAGGCGATTCAAAAGTTT
1 AATAAGGGTATAATAGGCGATTCAAAAGTTT
3337 TACAAAACTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.40, C:0.06, G:0.24, T:0.29
Consensus pattern (31 bp):
AATAAGGGTATAATAGGCGATTCAAAAGTTT
Found at i:4356 original size:17 final size:17
Alignment explanation
Indices: 4334--4367 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
4324 CATAGAGCTG
4334 ACTATCTAGTGTAACAA
1 ACTATCTAGTGTAACAA
4351 ACTATCTAGTGTAACAA
1 ACTATCTAGTGTAACAA
4368 TTTTACGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (17 bp):
ACTATCTAGTGTAACAA
Found at i:7837 original size:14 final size:14
Alignment explanation
Indices: 7818--7849 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
7808 TGTTCTTCAT
*
7818 TCAGAAATAACATA
1 TCAGAAATAACAGA
7832 TCAGAAATAACAGA
1 TCAGAAATAACAGA
7846 TCAG
1 TCAG
7850 TTTGTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.16, G:0.12, T:0.19
Consensus pattern (14 bp):
TCAGAAATAACAGA
Found at i:8198 original size:5 final size:5
Alignment explanation
Indices: 8188--8222 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
8178 TAAGCATACA
8188 GGCCG GGCCG GGCTCG GGCCG GGCTCG GGCCG GGC
1 GGCCG GGCCG GGC-CG GGCCG GGC-CG GGCCG GGC
8223 TTTTATGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 18 0.64
6 10 0.36
ACGTcount: A:0.00, C:0.37, G:0.57, T:0.06
Consensus pattern (5 bp):
GGCCG
Found at i:8207 original size:11 final size:11
Alignment explanation
Indices: 8191--8223 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
8181 GCATACAGGC
8191 CGGGCCGGGCT
1 CGGGCCGGGCT
8202 CGGGCCGGGCT
1 CGGGCCGGGCT
8213 CGGGCCGGGCT
1 CGGGCCGGGCT
8224 TTTATGGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.55, T:0.09
Consensus pattern (11 bp):
CGGGCCGGGCT
Found at i:8209 original size:16 final size:16
Alignment explanation
Indices: 8188--8222 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
8178 TAAGCATACA
8188 GGCCGGGCCGGGCTCG
1 GGCCGGGCCGGGCTCG
8204 GGCCGGGCTCGGGC-CG
1 GGCCGGGC-CGGGCTCG
8220 GGC
1 GGC
8223 TTTTATGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.00, C:0.37, G:0.57, T:0.06
Consensus pattern (16 bp):
GGCCGGGCCGGGCTCG
Found at i:24928 original size:1 final size:1
Alignment explanation
Indices: 24922--24954 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
24912 TTAAGTATCG
24922 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
24955 CCTCAAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:29894 original size:16 final size:16
Alignment explanation
Indices: 29873--29904 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
29863 CGTTCGTTTC
29873 AAGATTATGATAAAAT
1 AAGATTATGATAAAAT
*
29889 AAGATTATTATAAAAT
1 AAGATTATGATAAAAT
29905 GTTGTCATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.34
Consensus pattern (16 bp):
AAGATTATGATAAAAT
Found at i:35132 original size:1 final size:1
Alignment explanation
Indices: 35126--35155 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
35116 AATTTACCAC
35126 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
35156 CTGTAGAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:42253 original size:21 final size:21
Alignment explanation
Indices: 42208--42266 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
42198 CTGTTTGGCA
* *
42208 ACTGTACAGATGAGATTA--C
1 ACTGTACAGATAAGATTATGT
* *
42227 ACTGTACATATTAGATTATGT
1 ACTGTACAGATAAGATTATGT
42248 ACTGTACAGATAAGATTAT
1 ACTGTACAGATAAGATTAT
42267 TAGAGCAACG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
19 16 0.48
21 17 0.52
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (21 bp):
ACTGTACAGATAAGATTATGT
Found at i:43268 original size:18 final size:18
Alignment explanation
Indices: 43245--43291 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
43235 AGAGGTTTTG
43245 GCAGAGGTAATTTTGATC
1 GCAGAGGTAATTTTGATC
* *
43263 GCAGAGGCAAATTTGATC
1 GCAGAGGTAATTTTGATC
* *
43281 GAAAAGGTAAT
1 GCAGAGGTAAT
43292 ACTGATCAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.36, C:0.11, G:0.28, T:0.26
Consensus pattern (18 bp):
GCAGAGGTAATTTTGATC
Found at i:49770 original size:21 final size:21
Alignment explanation
Indices: 49746--49828 Score: 81
Period size: 21 Copynumber: 4.3 Consensus size: 21
49736 TTTAACGTGA
* * *
49746 TTTGACTATTAAACTTTGGGG
1 TTTGACAATCAAAATTTGGGG
49767 TTTGACAATCAAAATTTGGGG
1 TTTGACAATCAAAATTTGGGG
*
49788 TTTGAC---CAAATTTTGGGG
1 TTTGACAATCAAAATTTGGGG
49806 TTTG--AA-CAAAATTT-GGG
1 TTTGACAATCAAAATTTGGGG
49823 TTTGAC
1 TTTGAC
49829 CATGCATATA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
17 7 0.13
18 22 0.42
21 24 0.45
ACGTcount: A:0.28, C:0.10, G:0.24, T:0.39
Consensus pattern (21 bp):
TTTGACAATCAAAATTTGGGG
Found at i:49802 original size:18 final size:18
Alignment explanation
Indices: 49760--49830 Score: 90
Period size: 18 Copynumber: 3.8 Consensus size: 18
49750 ACTATTAAAC
49760 TTTGGGGTTTGACAATCAAAA
1 TTTGGGGTTTGAC---CAAAA
*
49781 TTTGGGGTTTGACCAAAT
1 TTTGGGGTTTGACCAAAA
*
49799 TTTGGGGTTTGAACAAAA
1 TTTGGGGTTTGACCAAAA
49817 TTT-GGGTTTGACCA
1 TTTGGGGTTTGACCA
49831 TGCATATACA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
17 10 0.22
18 23 0.50
21 13 0.28
ACGTcount: A:0.27, C:0.10, G:0.27, T:0.37
Consensus pattern (18 bp):
TTTGGGGTTTGACCAAAA
Found at i:50862 original size:32 final size:32
Alignment explanation
Indices: 50821--50889 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
50811 AATTCAAGAT
50821 CAAA-CCTTTGACCAATTTCTCAATTAAGCGC
1 CAAACCCTTTGACCAATTTCTCAATTAAGCGC
50852 CAAACCCTTTGACCAATTTCTCAATTAAGCGC
1 CAAACCCTTTGACCAATTTCTCAATTAAGCGC
50884 CAAACC
1 CAAACC
50890 TTTATCTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 4 0.11
32 33 0.89
ACGTcount: A:0.33, C:0.32, G:0.09, T:0.26
Consensus pattern (32 bp):
CAAACCCTTTGACCAATTTCTCAATTAAGCGC
Done.