Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015427.1 Corchorus olitorius cultivar O-4 contig15460, 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: 97686
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:4552 original size:18 final size:18
Alignment explanation
Indices: 4529--4566 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
4519 AATCCGTAAG
4529 AAGCAATCAAAAAAGAAA
1 AAGCAATCAAAAAAGAAA
*
4547 AAGCAATCAAACAAGAAA
1 AAGCAATCAAAAAAGAAA
4565 AA
1 AA
4567 AAGATGCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.71, C:0.13, G:0.11, T:0.05
Consensus pattern (18 bp):
AAGCAATCAAAAAAGAAA
Found at i:17009 original size:4 final size:4
Alignment explanation
Indices: 17000--17040 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
16990 CCTATCAAAT
* *
17000 GAAA GAAA GAAA GAAA GAAA GAAA GAAA -AAA AAAA AAAA GA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GA
17041 TTATGGAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
3 3 0.09
4 32 0.91
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:42808 original size:19 final size:21
Alignment explanation
Indices: 42769--42809 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
42759 CATGGTTCTG
42769 AATTTCTAAAATCATTTCAATT
1 AATTTCTAAAATCA-TTCAATT
42791 AATTTC-AAAATC-TTCAATT
1 AATTTCTAAAATCATTCAATT
42810 CTGAAGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
21 6 0.32
22 6 0.32
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (21 bp):
AATTTCTAAAATCATTCAATT
Found at i:63478 original size:32 final size:32
Alignment explanation
Indices: 63442--63505 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
63432 TTGTAGGAGA
63442 AAAAAACTATTTCA-A-TTTTTTTAAAGAAAAAT
1 AAAAAA-TATTTCATATTTTTTTTAAA-AAAAAT
* *
63474 AAAAAATTTTTTATATTTTTTTTAAAAAAAAT
1 AAAAAATATTTCATATTTTTTTTAAAAAAAAT
63506 TTCTGATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 5 0.18
32 13 0.46
33 10 0.36
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (32 bp):
AAAAAATATTTCATATTTTTTTTAAAAAAAAT
Found at i:68103 original size:13 final size:13
Alignment explanation
Indices: 68085--68111 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
68075 AAACAACTAA
68085 AAAGCACTTCTGG
1 AAAGCACTTCTGG
68098 AAAGCACTTCTGG
1 AAAGCACTTCTGG
68111 A
1 A
68112 TTTTCCGTTT
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:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (13 bp):
AAAGCACTTCTGG
Found at i:68241 original size:29 final size:29
Alignment explanation
Indices: 68209--68300 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 29
68199 AAACACATAA
68209 AGTTCAGGGTGAAATTACTAAACACCCTT
1 AGTTCAGGGTGAAATTACTAAACACCCTT
** * * * * *
68238 AGTTC--TCTCAAATTAATAAAAACACATAA
1 AGTTCAGGGTGAAATTACTAAACAC-CCT-T
68267 AGTTCAGGGTGAAATTACTAAACACCCTT
1 AGTTCAGGGTGAAATTACTAAACACCCTT
68296 AGTTC
1 AGTTC
68301 TCTCAAATTA
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
27 13 0.29
28 2 0.04
29 15 0.33
30 2 0.04
31 13 0.29
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (29 bp):
AGTTCAGGGTGAAATTACTAAACACCCTT
Found at i:68264 original size:58 final size:58
Alignment explanation
Indices: 68191--68340 Score: 300
Period size: 58 Copynumber: 2.6 Consensus size: 58
68181 CTAAATCTCC
68191 ATTAATAAAAACACATAAAGTTCAGGGTGAAATTACTAAACACCCTTAGTTCTCTCAA
1 ATTAATAAAAACACATAAAGTTCAGGGTGAAATTACTAAACACCCTTAGTTCTCTCAA
68249 ATTAATAAAAACACATAAAGTTCAGGGTGAAATTACTAAACACCCTTAGTTCTCTCAA
1 ATTAATAAAAACACATAAAGTTCAGGGTGAAATTACTAAACACCCTTAGTTCTCTCAA
68307 ATTAATAAAAACACATAAAGTTCAGGGTGAAATT
1 ATTAATAAAAACACATAAAGTTCAGGGTGAAATT
68341 CTCTCAAATC
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 92 1.00
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.27
Consensus pattern (58 bp):
ATTAATAAAAACACATAAAGTTCAGGGTGAAATTACTAAACACCCTTAGTTCTCTCAA
Found at i:68318 original size:29 final size:29
Alignment explanation
Indices: 68228--68320 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 29
68218 TGAAATTACT
68228 AAACACCCTTAGTTCTCTCAAATTAATAA
1 AAACACCCTTAGTTCTCTCAAATTAATAA
* * ** * *
68257 AAACA-CATAAAGTTCAGGGTGAAATTACT--
1 AAACACCCT-TAGTTC--TCTCAAATTAATAA
68286 AAACACCCTTAGTTCTCTCAAATTAATAA
1 AAACACCCTTAGTTCTCTCAAATTAATAA
68315 AAACAC
1 AAACAC
68321 ATAAAGTTCA
Statistics
Matches: 46, Mismatches: 12, Indels: 12
0.66 0.17 0.17
Matches are distributed among these distances:
27 8 0.17
28 2 0.04
29 26 0.57
30 2 0.04
31 8 0.17
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.27
Consensus pattern (29 bp):
AAACACCCTTAGTTCTCTCAAATTAATAA
Found at i:68328 original size:29 final size:29
Alignment explanation
Indices: 68238--68329 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 29
68228 AAACACCCTT
68238 AGTTCTCTCAAATTAATAAAAACACATAA
1 AGTTCTCTCAAATTAATAAAAACACATAA
** * * * * *
68267 AGTTCAGGGTGAAATTACTAAACAC-CCT-T
1 AGTTC--TCTCAAATTAATAAAAACACATAA
68296 AGTTCTCTCAAATTAATAAAAACACATAA
1 AGTTCTCTCAAATTAATAAAAACACATAA
68325 AGTTC
1 AGTTC
68330 AGGGTGAAAT
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
27 13 0.29
28 2 0.04
29 15 0.33
30 2 0.04
31 13 0.29
ACGTcount: A:0.45, C:0.18, G:0.09, T:0.28
Consensus pattern (29 bp):
AGTTCTCTCAAATTAATAAAAACACATAA
Found at i:75170 original size:178 final size:174
Alignment explanation
Indices: 74874--75207 Score: 544
Period size: 178 Copynumber: 1.9 Consensus size: 174
74864 TTTTTTTTTT
* *
74874 ATTTCTAAGGCTCGAATTCGAGATTTTATGTTGCATCAAGCTCCTCTCCACTTAACCTAACAGAT
1 ATTTCTAAGACTCGAATTCGAGACTTTATGTTGCATCAAGCTCCTCTCCACTTAACCTAACAGA-
74939 GTTGATTTACTGGTTGTTATTATTAAACATAACAACAAGGAATTACAAAGTTGGTAAGGGTTGGA
65 GTTGATTTACTGGTTGTTATTATTAAACATAACAACAAGGAATTACAAAGTTGGTAAGGGTTGGA
75004 TTGAAAAACTATATCCAAAACTGAAACTCTCAACACCTGTTTTCC
130 TTGAAAAACTATATCCAAAACTGAAACTCTCAACACCTGTTTTCC
* *
75049 ATTTCTAAGACTCGAATTCGTGACTTTATGTTGCATCAAGCTCCTCTCCTCTCTACTTAATCTAA
1 ATTTCTAAGACTCGAATTCGAGACTTTATGTTGCATCAAGCT-C-CT-CTC-C-ACTTAACCTAA
* * *
75114 CAGA-TTGGTTTACTGGTTGTTATTATTAAACATAACTACAGGGAATTACAAAGTTGGTAAGGGT
61 CAGAGTTGATTTACTGGTTGTTATTATTAAACATAACAACAAGGAATTACAAAGTTGGTAAGGGT
75178 TGGATTGAAAAACTATATCCAAAACTGAAA
126 TGGATTGAAAAACTATATCCAAAACTGAAA
75208 GGAGTTATTC
Statistics
Matches: 147, Mismatches: 7, Indels: 7
0.91 0.04 0.04
Matches are distributed among these distances:
175 39 0.27
176 1 0.01
177 2 0.01
178 90 0.61
179 1 0.01
180 14 0.10
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (174 bp):
ATTTCTAAGACTCGAATTCGAGACTTTATGTTGCATCAAGCTCCTCTCCACTTAACCTAACAGAG
TTGATTTACTGGTTGTTATTATTAAACATAACAACAAGGAATTACAAAGTTGGTAAGGGTTGGAT
TGAAAAACTATATCCAAAACTGAAACTCTCAACACCTGTTTTCC
Found at i:83239 original size:48 final size:46
Alignment explanation
Indices: 83152--83243 Score: 123
Period size: 48 Copynumber: 2.0 Consensus size: 46
83142 GAGGACCTCC
* *
83152 TCCAAGTCCAAAACCAAGCCCAAGAACTGATTGTTGTAAGCCAGAA
1 TCCAAGTCCAAAACCAAGCCCAAGAACAGATTGTCGTAAGCCAGAA
*
83198 TCCACAGTACCAAAAGCAAGCCCAAGAACCAGATT-TCGTAAGCCAG
1 TCCA-AGT-CCAAAACCAAGCCCAAGAA-CAGATTGTCGTAAGCCAG
83244 CAGGAATAGC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
46 4 0.10
47 3 0.08
48 28 0.70
49 5 0.12
ACGTcount: A:0.39, C:0.28, G:0.17, T:0.15
Consensus pattern (46 bp):
TCCAAGTCCAAAACCAAGCCCAAGAACAGATTGTCGTAAGCCAGAA
Found at i:96701 original size:333 final size:332
Alignment explanation
Indices: 95272--97313 Score: 2971
Period size: 333 Copynumber: 6.2 Consensus size: 332
95262 ATTATTATTA
* * *
95272 CCTTGAAATATCTATATTAATCTGACCAAAT-TCCAACCACAATGGACTTGGGGATTTGGTTTTA
1 CCTTGAAATATCTATATTAATCTAACCAAATCT-CAACCACAATGGACTTGAGGATTTGTTTTTA
* *
95336 CGAGCATTTACATTTTCTTTCGATATAATTAGAAATTAATTCAGAAAATATAGGAAAAACGATAT
65 CGAGCATTTAAATTTTCTTTCGATATAATTAAAAATTAATTCAGAAAATATAGGAAAAACGATAT
* * *** * *
95401 TAGAAGCGTGAAACGATCTTCAATCTTTTTGGTGTTGAATTATATATTATTTAAGAGTATTGTGG
130 TAGAAGCGTGAAACGCTCTTCAATCTTTTTGGCGTTGAATTATATATTCCATATGACTATTGTGG
* * * * * *
95466 CT-AAAAATTATGCAAAAATCTGACGGGTCACA-TTTTGCAAAATTTTA-TCCGAAATTGTGGCT
195 TTAAAAAATGA-GGAAAAACCTTACGGGTCA-ATTTTTGCAAAATTTTAGT-CGAAATCGT-G-T
** ** * *
95528 AAAAATTATCACAGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTCTGTTTTGCATG-TTTT
255 ACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTT
95592 TTGCGCCAATAAT
320 TTGCGCCAATAAT
* *
95605 CCTTTAAATATCTATATTAATCTAACCATATCTCAACCACAATGGACTTGAGGATTTGTTTTTAC
1 CCTTGAAATATCTATATTAATCTAACCAAATCTCAACCACAATGGACTTGAGGATTTGTTTTTAC
*
95670 GAGCATTCAAATTTTCTTTCGATATAATTAAAAATTAATTCAGAAAATATAGGAAAAACGATATT
66 GAGCATTTAAATTTTCTTTCGATATAATTAAAAATTAATTCAGAAAATATAGGAAAAACGATATT
* * * *
95735 AGAAGCGTGAAACGCTCATCAATATTTTTGGCATTGAATTATATATTCCATGTGACTATTGTGGT
131 AGAAGCGTGAAACGCTCTTCAATCTTTTTGGCGTTGAATTATATATTCCATATGACTATTGTGGT
* * ** *
95800 TAAAAAATGAGGAAAAAACTTACGGGTCAATTTTTGCAAAACTTTAGTCGAAATTATGTACTACC
196 TAAAAAATGAGGAAAAACCTTACGGGTCAATTTTTGCAAAATTTTAGTCGAAATCGTGTACTAAC
* *
95865 CATCACAGTTTTTGGCTAAAAACGCATTCCGGGGCCTCGGCTCAGTTTTGCATGATTTTTTGCGC
261 CATCACAGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTTGCGC
95930 CAATAAT
326 CAATAAT
* * **
95937 TCTTAAAATATCTATATTAATCTAACCAAATCTCAACCACAATAAACTTGAGGATTTGTTTTTAC
1 CCTTGAAATATCTATATTAATCTAACCAAATCTCAACCACAATGGACTTGAGGATTTGTTTTTAC
* *
96002 GAGCATTTAAATTTTCTTTCGTTATAATTAAAAATTAATTCAGAAAATATAGGAAAAATGATATT
66 GAGCATTTAAATTTTCTTTCGATATAATTAAAAATTAATTCAGAAAATATAGGAAAAACGATATT
* * * * * * *
96067 GGAAGCGTGAAAAGCCCTTAAATCTTTTTGGCGTTGAGTTATATATTCCTTATGGA-TATTATGG
131 AGAAGCGTGAAACGCTCTTCAATCTTTTTGGCGTTGAATTATATATTCCATAT-GACTATTGTGG
* * *
96131 CTAAAAAATGAGGAAAAATCTTACAGGTCAATTTTTGCAAAATTTTAG-CTGAAATC--G---T-
195 TTAAAAAATGAGGAAAAACCTTACGGGTCAATTTTTGCAAAATTTTAGTC-GAAATCGTGTACTA
* * *
96189 ---AT-ACAGTTTTTGGCTAAAAACGCGTTCCGAGACCCTGGCTCAGTTTTGCATGATTTTTTGC
259 ACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTTGC
*
96250 GCCAAGAAT
324 GCCAATAAT
*
96259 CCTTGAAATATCTATATTAATCAAACCAAATCTCAACCACAATGGACTTGAGGATTTGTTTTTAC
1 CCTTGAAATATCTATATTAATCTAACCAAATCTCAACCACAATGGACTTGAGGATTTGTTTTTAC
* * *
96324 GAGCAATTAAATTTTATTTGGATATAATTAAAAATTAATTCAGAAAATATAGGAAAAACGATATT
66 GAGCATTTAAATTTTCTTTCGATATAATTAAAAATTAATTCAGAAAATATAGGAAAAACGATATT
* *
96389 AGAAGCGTGAAACGCTCATCAATCTTTTTGGTGTTGAATTATATATTCCATATGACTATTGTGGT
131 AGAAGCGTGAAACGCTCTTCAATCTTTTTGGCGTTGAATTATATATTCCATATGACTATTGTGGT
*
96454 TAAAAAATGAGGAAAAACCTTATGGGTCAATTTTTGCAAAATTTTAGTCGAAATCGTGTACTAAC
196 TAAAAAATGAGGAAAAACCTTACGGGTCAATTTTTGCAAAATTTTAGTCGAAATCGTGTACTAAC
*
96519 CATCACAGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTTTGCG
261 CATCACAGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGA-TTTTTTGCG
96584 CCAATAAT
325 CCAATAAT
* *
96592 CCTTGAAATATCTATATTAATCTAACCAAATTTCAACCACATTGGACTTGAGGATTTGTTTTTAC
1 CCTTGAAATATCTATATTAATCTAACCAAATCTCAACCACAATGGACTTGAGGATTTGTTTTTAC
* * *
96657 GAGCATTTAAATTTTCATTCGATATAATTAAAAATTAATTCAGAAAATATACGAAAAATGATATT
66 GAGCATTTAAATTTTCTTTCGATATAATTAAAAATTAATTCAGAAAATATAGGAAAAACGATATT
* *
96722 AGAAGTGTGAAACGCTCTTCAATCTTTTTGGCGTTGAATTATATATTCCATATGACTAATGTGGT
131 AGAAGCGTGAAACGCTCTTCAATCTTTTTGGCGTTGAATTATATATTCCATATGACTATTGTGGT
* * *
96787 TAAAAAATGAGGAAAAACCTTACGTGTCAATTTTTGCAAAATGTTAGCCGAAATCGTG---T-A-
196 TAAAAAATGAGGAAAAACCTTACGGGTCAATTTTTGCAAAATTTTAGTCGAAATCGTGTACTAAC
* * *
96847 CATCACAGTTTTTGGTTAAAATCGCGTTCCGGGG-CCCGGCTCAGTTTTGCATGATTTTTTGCAC
261 CATCACAGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTTGCGC
96911 CAATAAT
326 CAATAAT
*
96918 CCTTGAAATATCTATATTAATCTAACCAAATCTCAACCACAATGGACTTGAGGATTTGTTTTTGC
1 CCTTGAAATATCTATATTAATCTAACCAAATCTCAACCACAATGGACTTGAGGATTTGTTTTTAC
* * *
96983 GAGCATTTAAATTTTCTTTCGATATAATTTAAAATTAATTCTGAAAATATACGAAAAACGATATT
66 GAGCATTTAAATTTTCTTTCGATATAATTAAAAATTAATTCAGAAAATATAGGAAAAACGATATT
* * *
97048 AGAAGTGTGAAACGCTCTTCAATCTTTTTGGCGTTGAATTATATATTCTATATGGCTATTGTGGT
131 AGAAGCGTGAAACGCTCTTCAATCTTTTTGGCGTTGAATTATATATTCCATATGACTATTGTGGT
* * * *
97113 TAAAAAATGAGGAAAAACCTTATGTGTAAATTTTTGCAAAATTTTAG-CTGAAATTGTGTACTAA
196 TAAAAAATGAGGAAAAACCTTACGGGTCAATTTTTGCAAAATTTTAGTC-GAAATCGTGTACTAA
* * *
97177 CCATCACAGTTTTTGGCTAAAAACGCGTTCCGGGGCCACGGCTCAGTTTTCCATGATTTTTAGCG
260 CCATCACAGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTTGCG
97242 CCAATAAT
325 CCAATAAT
* *
97250 CCTTGAAATATCTATATTAATCTAACCAAATCTCAACCACAATGGACTTAAGGATTTATTTTTA
1 CCTTGAAATATCTATATTAATCTAACCAAATCTCAACCACAATGGACTTGAGGATTTGTTTTTA
97314 GCGCCAACAA
Statistics
Matches: 1545, Mismatches: 137, Indels: 55
0.89 0.08 0.03
Matches are distributed among these distances:
321 2 0.00
322 284 0.18
323 3 0.00
324 1 0.00
325 1 0.00
326 253 0.16
327 22 0.01
328 31 0.02
329 2 0.00
330 3 0.00
331 87 0.06
332 381 0.25
333 466 0.30
334 9 0.01
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (332 bp):
CCTTGAAATATCTATATTAATCTAACCAAATCTCAACCACAATGGACTTGAGGATTTGTTTTTAC
GAGCATTTAAATTTTCTTTCGATATAATTAAAAATTAATTCAGAAAATATAGGAAAAACGATATT
AGAAGCGTGAAACGCTCTTCAATCTTTTTGGCGTTGAATTATATATTCCATATGACTATTGTGGT
TAAAAAATGAGGAAAAACCTTACGGGTCAATTTTTGCAAAATTTTAGTCGAAATCGTGTACTAAC
CATCACAGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTTGCGC
CAATAAT
Done.