Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021147.1 Corchorus olitorius cultivar O-4 contig21180, 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: 60734
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:512 original size:285 final size:285
Alignment explanation
Indices: 21--535 Score: 829
Period size: 285 Copynumber: 1.8 Consensus size: 285
11 CCCAATGCAG
* * *
21 TTTTGCATGATTTTTATAGTCAAGACTCCTTAAAATATCTATATTCATCTAATAAAAACTTAGTC
1 TTTTGCATGATTTTTAGAGTCAAGACTCCATAAAATATCTATATTCATCTAATAAAAACTTAGCC
*
86 ACGTTGCATTTAAGGATTTATTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAA
66 ACGTTGCATTTAAGGATTTATTTTTACGAGCATTTCAATCTTGTTTCGATTTAATTAGAAATTAA
* * *
151 TTCAGAAAAAATATGAACAACGATATTAAAAGCTTGAAAAGTCCTTCAATAATTTTGGCGTTAGA
131 TTCAGAAAAAATATGAAAAACGAGATTAAAAGCTTGAAAAGTCCTTCAATAATTTTGGCGTTAAA
* *
216 TTATGTATATTTTATGATTATTT-TATCCAAAAATTGAGTACTAACCATCACGGTTTTTGGCTAA
196 TTATATATATTTTATGAGTATTTGT-TCCAAAAATTGAGTACTAACCATCACGGTTTTTGGCTAA
280 AAACGCGTTTCGGGGTCCCGGCTCAA
260 AAACGCGTTTCGGGGTCCCGGCTCAA
* * * *
306 TTTTGTATGATTTTTGGCGTCAAGACTCCATGAAATATCTATATTCATCTAATAAAAACTTAGCC
1 TTTTGCATGATTTTTAGAGTCAAGACTCCATAAAATATCTATATTCATCTAATAAAAACTTAGCC
371 ACGTTGCATTTAAGGATTTATTTTTACGAGCATTTCAATCTTGTTTCGATTTAATTAGAAATTAA
66 ACGTTGCATTTAAGGATTTATTTTTACGAGCATTTCAATCTTGTTTCGATTTAATTAGAAATTAA
** *
436 TTCAGAAAAAATATGAAAAACGAGATTAAAAG-TATGAAAAGTCC-TCTAATGTTTTTGGGGTTA
131 TTCAGAAAAAATATGAAAAACGAGATTAAAAGCT-TGAAAAGTCCTTC-AATAATTTTGGCGTTA
*
499 AATTATATATATTTTTTGAGTATTTGTTCCAAAAATT
194 AATTATATATATTTTATGAGTATTTGTTCCAAAAATT
536 AAGGAAAAAA
Statistics
Matches: 210, Mismatches: 17, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
284 3 0.01
285 206 0.98
286 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (285 bp):
TTTTGCATGATTTTTAGAGTCAAGACTCCATAAAATATCTATATTCATCTAATAAAAACTTAGCC
ACGTTGCATTTAAGGATTTATTTTTACGAGCATTTCAATCTTGTTTCGATTTAATTAGAAATTAA
TTCAGAAAAAATATGAAAAACGAGATTAAAAGCTTGAAAAGTCCTTCAATAATTTTGGCGTTAAA
TTATATATATTTTATGAGTATTTGTTCCAAAAATTGAGTACTAACCATCACGGTTTTTGGCTAAA
AACGCGTTTCGGGGTCCCGGCTCAA
Found at i:981 original size:334 final size:333
Alignment explanation
Indices: 235--4590 Score: 6156
Period size: 333 Copynumber: 13.1 Consensus size: 333
225 TTTTATGATT
* * *
235 ATTTTATCCAAAAATTGAGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCG
1 ATTTTAGCC-AAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCG
* *
300 GCTCAATTTTGTATGATTTTTGGCGTCAAGACTCCATGAAATATCTATATTCATCTAATAAAAAC
65 GCTCAATTTTGCATGATTTTTGGCGTCAAGACTCCTTGAAATATCTATATTCATCTAATAAAAAC
* *
365 TTAGCCACGTTGCATTTAAGGATTTATTTTTACGAGCATTTCAATCTTGTTTCGATTTAATTAGA
130 TTAGCCACGTTGCATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGA
* * * *
430 AATTAATTCAGAAAAAATATGAAAAACGAGATTAAAAGTATGAAAAGTCCTCTAATGTTTTTGGG
195 AATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCCAATGTTTTTGGC
* * *
495 GTTAAATTATATATATTTTTTGAGTATTTGT-TCCAAAAATTAAGGAAAAAATTTTCGCTGTAAT
260 GTTAAATTATATATATTTTATGAGTATTT-TATCCAAAAATTAAGGAAAAATTTTTCGCGGTAA-
*
559 TTTTTTTGGAAA
323 -TTTTTTGCAAA
* * * * *
571 GTTTTAGACAAAATCGTGTACTAACTATCACGGTTTTTAGCTAAAAACGCGTTTCGGAGTCCCGG
1 ATTTTAGCCAAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGG
* * * *
636 CTCAATTTTGCATGATTTTTTGTGTCAAGACTCCTTCAAATATCTATATTCATCAAATAAAAACT
66 CTCAATTTTGCATGATTTTTGGCGTCAAGACTCCTTGAAATATCTATATTCATCTAATAAAAACT
* * *
701 TAGCCACGTTGCATTTAAGGATTTGTTTTTACGAGTATTTGAATCTTGTTTCAAGTTAATTAGAA
131 TAGCCACGTTGCATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAA
* * *
766 ATTAATTCTG-AAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATGTTTTTGGCA
196 ATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCCAATGTTTTTGGCG
* *
830 TTAAATTATATATATTTTATGAGTATTTTATCCAAAAATTAAGGAAAAAGTTTTCGCGGTCATTT
261 TTAAATTATATATATTTTATGAGTATTTTATCCAAAAATTAAGGAAAAATTTTTCGCGGTAATTT
895 TTTGCAAA
326 TTTGCAAA
* ** * * *
903 ATTTTAGCCATAATCGTAAACTAACAATCACAGTTTTTTTGGCTAAAAACGCGTTTCGAGGTCCC
1 ATTTTAGCCAAAATCGTGTACTAACCATCAC-G-GTTTTTGGCTAAAAACGCGTTTCGGGGTCCC
* * * ** *
968 AGCGCAGTTTTGCATGATTTTTATCGTCAAGACTCCTTGAAATATCTATAGTCATCTAATAAAAA
64 GGCTCAATTTTGCATGATTTTTGGCGTCAAGACTCCTTGAAATATCTATATTCATCTAATAAAAA
* * * *
1033 CTTAGTCACGTTGCATTTAAGAATTTGTTTTTACGAGCATTTGAATCTTGTTTCGAGTTAATTTG
129 CTTAGCCACGTTGCATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAG
* *
1098 AAATTAATTCAGAAAAAAATATGAAAAACGATAATT-AAAGCGTAAAAAGTCCTCCAATGTTTTT
194 AAATTAATTCAG-AAAAAATATGAAAAACGAT-ATTAAAAGCATGAAAAGTCCTCCAATGTTTTT
* * *
1162 GGCATTAAATTATATATATTTTATGAGTATTTTATCCAAATATTAAGGAAAAA-ATTTCGCGGTA
257 GGCGTTAAATTATATATATTTTATGAGTATTTTATCCAAAAATTAAGGAAAAATTTTTCGCGGTA
1226 ATTTTTTGCAAA
322 ATTTTTTGCAAA
** * **
1238 ATTTTAGCCAAAATCGTAAACTAATCATCACGGTTTTTTTTTTACTAAAAACGCGTTTCGGGGTC
1 ATTTTAGCCAAAATCGTGTACTAACCATCACGG----TTTTTGGCTAAAAACGCGTTTCGGGGTC
** * ***
1303 CC-AATGCAGTTTTGCATGATTTTTATAGTCAAGACTCCTTGAAATATCTATATTCATCTAATAA
62 CCGGCT-CAATTTTGCATGATTTTTGGCGTCAAGACTCCTTGAAATATCTATATTCATCTAATAA
* * *
1367 AAACTTAGTCACATTGCATTTAAGGATTTATTTTTACGAGCATTTGAATCTTGTTTCGATTTAAT
126 AAACTTAGCCACGTTGCATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAAT
** * **
1432 TAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGTTTG-AAAGTCCTTCAATAATTT
191 TAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCCAATGTTTT
* * * * * *
1496 TGGCGTTAGATTATGTATATTTTATGATTATTTTATCTAAAAATTGAGGAAAAATTTTTCGCGAT
256 TGGCGTTAAATTATATATATTTTATGAGTATTTTATCCAAAAATTAAGGAAAAATTTTTCGCGGT
1561 AATTTTTTGCAAA
321 AATTTTTTGCAAA
* *
1574 ATTTTAGCCAAAATCGTG---T-A-CATCACGGTTTTTGGTTAAAAACGCGTTTCGGGATCCCGG
1 ATTTTAGCCAAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGG
* * * *
1634 CTCAATTTTGTATGATTTTTGGCGTCAAGACTCCTTTAAATATTTATATTCATTTAATAAAAACT
66 CTCAATTTTGCATGATTTTTGGCGTCAAGACTCCTTGAAATATCTATATTCATCTAATAAAAACT
* *
1699 TAGCCACGTTGCATTTAAGGATTTGTTTTTACGAGAATTTGAATCTAGTTTCGATTTAATTAGAA
131 TAGCCACGTTGCATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAA
1764 ATTAATTTC-GAAAAAATATGAAAAACGATATTTAAAAGCATGAAAAAGTCCTCCAATGTTTTTG
196 ATTAA-TTCAGAAAAAATATGAAAAACGATA-TTAAAAGCATG-AAAAGTCCTCCAATGTTTTTG
* * *
1828 GTGTTAAATTATATATATTTTATGAGTAATGTTT-TCCACAAATTAAGGAAAAATTTTTCGCTGT
258 GCGTTAAATTATATATATTTTATGAGT-AT-TTTATCCAAAAATTAAGGAAAAATTTTTCGCGGT
1892 AATTTTTTTGCAAA
321 AA-TTTTTTGCAAA
* * ** * *
1906 GTTTTAGCCAAAATCGTGTACTAACTATCACGGTTTTTACCTAAAAACGCGTTTCGGAGTACCGG
1 ATTTTAGCCAAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGG
*
1971 CTCAATTTTGCATGTTTTTTGGCGTCAAGACTCCTTGAAATATCTATATTCATCTAATAAAAACT
66 CTCAATTTTGCATGATTTTTGGCGTCAAGACTCCTTGAAATATCTATATTCATCTAATAAAAACT
* *
2036 TAGCCACGTTGCATTTAAGGATTTATTTTTACGAGCATTTCAATCTTGTTTCGATTTAATTAGAA
131 TAGCCACGTTGCATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAA
*
2101 ATTAATTCCGAAAAAATATGAAAAACGATATTTAAAAGCATGAAAAAGTCCTCCAATGTTTTTGG
196 ATTAATTCAGAAAAAATATGAAAAACGATA-TTAAAAGCATG-AAAAGTCCTCCAATGTTTTTGG
* * ** *
2166 TGTTAAATTATGTATATTTTATGAGTAATGTTT-TCCAAAAATTAAGGAAAAAAATTTCGCTGTA
259 CGTTAAATTATATATATTTTATGAGT-AT-TTTATCCAAAAATTAAGGAAAAATTTTTCGCGGTA
2230 ATTTTTTTGCAAA
322 A-TTTTTTGCAAA
* * * * * * *
2243 GTTTTAGCCAAAATCGTGTGCTAACTATCACGGTTTTTAGATAAAAACGCGTTTCGGAGTACCGG
1 ATTTTAGCCAAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGG
* * *
2308 CTTAATTTTGCATGATTTTTGGCATCAAGACTCCTTGAAATATCTATATTTATCTAAT-AAAACT
66 CTCAATTTTGCATGATTTTTGGCGTCAAGACTCCTTGAAATATCTATATTCATCTAATAAAAACT
2372 TAGCCACGTTGCATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAA
131 TAGCCACGTTGCATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAA
* * *
2437 ATTATTTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATGTTTTTGGCA
196 ATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCCAATGTTTTTGGCG
* *
2502 TTAAATTATATATATTTTATGAGTATTTTATCCAAATATTAAGGAAAAAGTTTTCGCGGTAATTT
261 TTAAATTATATATATTTTATGAGTATTTTATCCAAAAATTAAGGAAAAATTTTTCGCGGTAATTT
2567 TTTGCAAA
326 TTTGCAAA
* * * *
2575 GTTTTAGCCAAAATCGTGTACTAACCATCACTGTTTTTAGCTAAAAACGCGTTTCGGAGTCCCGG
1 ATTTTAGCCAAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGG
* * *
2640 CTCAATTTTGCATAATTTTTGGCGTAAAGACTCCTTGAAATATCTATAGTCATCTAATAAAAACT
66 CTCAATTTTGCATGATTTTTGGCGTCAAGACTCCTTGAAATATCTATATTCATCTAATAAAAACT
* * * * *
2705 TAGTCACGTTGCATTTAAGAATTTGTTTTTACGAGCATTTAAATCTTGTTTTGAGTTAAATT-GA
131 TAGCCACGTTGCATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGA-TTTAATTAGA
*
2769 AATTAATTCAGGAAAAAATATGAAAAACGATAATT-AAAGCATAAAAAGTCCTCCAATGTTTTTG
195 AATTAATTCA-GAAAAAATATGAAAAACGAT-ATTAAAAGCATGAAAAGTCCTCCAATGTTTTTG
* *
2833 GCATTAAATTATATATATATTATGAGTATTTTATCCAAAAATTAAGGAAAAAATTTTT-GCGGTA
258 GCGTTAAATTATATATATTTTATGAGTATTTTATCCAAAAATTAAGG-AAAAATTTTTCGCGGTA
2897 ATTTTTTGCAAA
322 ATTTTTTGCAAA
* * *
2909 ATTTTAGCCAAAATCGTGAACTAATCATCACGGTTTTTTTCTTTTGACTAAAAACGCGTTTCGGG
1 ATTTTAGCCAAAATCGTGTACTAACCATCACGG------T-TTTTGGCTAAAAACGCGTTTCGGG
** * *** *
2974 GTCCC-AATGCAGTTTTGCATGATTTTTATAGTCAAGACT-CTTGGAAATATCTATATTCAACTA
59 GTCCCGGCT-CAATTTTGCATGATTTTTGGCGTCAAGACTCCTT-GAAATATCTATATTCATCTA
* *
3037 ATAAAAACTTAGTCACGTTGCATTTAAGGATTTATTTTTACGAGCATTTGAATCTTGTTTCGATT
122 ATAAAAACTTAGCCACGTTGCATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATT
* * * *
3102 TAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTTAAAGCTTGAAAAGTCCTTCAATA
187 TAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCCAATG
* * * * * *
3167 ATTTTGGCGTTAGATTATGTATATTTTATGATTATTTTATTCAAAAATTGAGGAAAAATTTTTCG
252 TTTTTGGCGTTAAATTATATATATTTTATGAGTATTTTATCCAAAAATTAAGGAAAAATTTTTCG
*
3232 CGTTAATTTTTTGCAAA
317 CGGTAATTTTTTGCAAA
* * *
3249 AGTTTAGCCAAAATCGTATACTAGCCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGG
1 ATTTTAGCCAAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGG
* *
3314 CTCAATTGTGTATGATTTTTGGCGTCAAGACTCCTTGAAATATCTATATTCATCTAATAAAAACT
66 CTCAATTTTGCATGATTTTTGGCGTCAAGACTCCTTGAAATATCTATATTCATCTAATAAAAACT
* *
3379 TAACCACGTTGCATTTATGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAA
131 TAGCCACGTTGCATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAA
* *
3444 ATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGTATGAAAAGTCCTCCAATGTTTTTGGGG
196 ATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCCAATGTTTTTGGCG
* * * **
3509 TTAAATTATATATATTTTTTGAGTATTTTTTCCAAAAATTAAGGAAAAAATTTTCGCTTTAATTT
261 TTAAATTATATATATTTTATGAGTATTTTATCCAAAAATTAAGGAAAAATTTTTCGCGGTAATTT
3574 TTTGCAAA
326 TTTGCAAA
* *
3582 GTTTTAGCCAAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGG
1 ATTTTAGCCAAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGG
*
3647 CTCAATTTTGTATGATTTTTGGCGTCAAGACTCCTTGAAATATCTATATTCATCTAATAAAAACT
66 CTCAATTTTGCATGATTTTTGGCGTCAAGACTCCTTGAAATATCTATATTCATCTAATAAAAACT
* * *
3712 TAGCCACATTGCATTTAAGGATTTGTTTTTACGAGAATTTGAATCTTGTTTCGATTTAATCAGAA
131 TAGCCACGTTGCATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAA
* * * **
3777 ATTAATTCAGAAAAAATATGTAAAACGATATTAAAAGCTTGAAAAGTCCTTCAATAATTTTGGCG
196 ATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCCAATGTTTTTGGCG
* * * * *
3842 TTAGATTATGTATATTTTATGATTATTTTATCCAAAAATTGAGGAAAAATTTTTCGCGTTAATTT
261 TTAAATTATATATATTTTATGAGTATTTTATCCAAAAATTAAGGAAAAATTTTTCGCGGTAATTT
3907 TTTGCAAA
326 TTTGCAAA
*
3915 AGTTTAGCCAAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGG
1 ATTTTAGCCAAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGG
* *
3980 CTCAATTGTGTATGATTTTTGGCGTCAAGACTCCTTGAAATATCTATATTCATCTAATAAAAACT
66 CTCAATTTTGCATGATTTTTGGCGTCAAGACTCCTTGAAATATCTATATTCATCTAATAAAAACT
* *
4045 TAACCACGTTGCATTTATGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAA
131 TAGCCACGTTGCATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAA
* * *
4110 ATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGTATGAAAAGTCCTCAAATGTTTTTGGCA
196 ATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCCAATGTTTTTGGCG
* * * *
4175 TTAAATTATGTATATTTTATGAGTATTTTATCCCAAAATTGAGGAAAAATTTTCCGCGGTAATTT
261 TTAAATTATATATATTTTATGAGTATTTTATCCAAAAATTAAGGAAAAATTTTTCGCGGTAATTT
4240 TTTGCAAA
326 TTTGCAAA
* *
4248 ATTTTAG------TC----A--AA--ATCACGGTTTTTGGCTAAAAAAGCGTTTCAGGGTCCCGG
1 ATTTTAGCCAAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGG
* * * *
4299 TTCAATTTTGCATG-TATTTTGGCGTTAAGACTCATTGAAATATTTATATTCATCTAATAAAAAC
66 CTCAATTTTGCATGAT-TTTTGGCGTCAAGACTCCTTGAAATATCTATATTCATCTAATAAAAAC
*
4363 TTAGCCACGTTGCATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTATTTAGA
130 TTAGCCACGTTGCATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGA
* * * * *
4428 AATTAATTCAG-AAAAATATGAAAAATGGTATTTAAAGCTTGAAAAGACCTCCAATGTTTTTGGC
195 AATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCCAATGTTTTTGGC
* * * * *
4492 GTTAAGTTATATATATTTTATGAGTATTTTTTCCAAAAATTGAGGAAAAATTTTTCACCGTAATT
260 GTTAAATTATATATATTTTATGAGTATTTTATCCAAAAATTAAGGAAAAATTTTTCGCGGTAATT
**
4557 TTTTGCCGA
325 TTTTGCAAA
4566 ATTTTAGCCAAAATCGTGTACTAAC
1 ATTTTAGCCAAAATCGTGTACTAAC
4591 TAATTAACTA
Statistics
Matches: 3624, Mismatches: 335, Indels: 127
0.89 0.08 0.03
Matches are distributed among these distances:
318 118 0.03
319 166 0.05
321 2 0.00
323 1 0.00
324 2 0.00
327 169 0.05
328 14 0.00
330 42 0.01
331 37 0.01
332 193 0.05
333 987 0.27
334 454 0.13
335 316 0.09
336 266 0.07
337 565 0.16
339 13 0.00
340 140 0.04
341 139 0.04
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (333 bp):
ATTTTAGCCAAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGTCCCGG
CTCAATTTTGCATGATTTTTGGCGTCAAGACTCCTTGAAATATCTATATTCATCTAATAAAAACT
TAGCCACGTTGCATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAA
ATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCCAATGTTTTTGGCG
TTAAATTATATATATTTTATGAGTATTTTATCCAAAAATTAAGGAAAAATTTTTCGCGGTAATTT
TTTGCAAA
Found at i:9871 original size:14 final size:14
Alignment explanation
Indices: 9852--9881 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
9842 TCATATCCTG
9852 GCCTTCAATGACAT
1 GCCTTCAATGACAT
9866 GCCTTCAATGACAT
1 GCCTTCAATGACAT
9880 GC
1 GC
9882 ACGTCAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.27
Consensus pattern (14 bp):
GCCTTCAATGACAT
Found at i:11646 original size:81 final size:79
Alignment explanation
Indices: 11557--11705 Score: 219
Period size: 81 Copynumber: 1.9 Consensus size: 79
11547 CTTAAAGATA
* *
11557 ATTCATGTAACAAGAGATCCTCTTTTGTGATTTTGAAC-AAGGAAAATATATGTTTGGCCCTACC
1 ATTCATGTAACAAGAGATCCTCTCTTGTGATTTT-AACAAAGGAAAATAT-T-TTTAGCCCTACC
11621 AAATTATGTATTAATTT
63 AAATTATGTATTAATTT
* * *
11638 ATTCATGTAATATGAGATCCTCTCTTGTGATTTTATCAAAGGAAAATATTTTTAGCCCTACCAAA
1 ATTCATGTAACAAGAGATCCTCTCTTGTGATTTTAACAAAGGAAAATATTTTTAGCCCTACCAAA
11703 TTA
66 TTA
11706 CATATAATCG
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
79 17 0.27
80 3 0.05
81 42 0.68
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (79 bp):
ATTCATGTAACAAGAGATCCTCTCTTGTGATTTTAACAAAGGAAAATATTTTTAGCCCTACCAAA
TTATGTATTAATTT
Found at i:15829 original size:12 final size:12
Alignment explanation
Indices: 15808--15843 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
15798 ATTTCTTTTA
*
15808 TATATATATATC
1 TATATCTATATC
15820 TATATCTATATC
1 TATATCTATATC
15832 TATATACTATAT
1 TATAT-CTATAT
15844 AAGTCTAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 16 0.73
13 6 0.27
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (12 bp):
TATATCTATATC
Found at i:17011 original size:36 final size:36
Alignment explanation
Indices: 16964--17033 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
16954 GAGATTTTGG
*
16964 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATTACAAAAAATGTAATA
*
17000 AGAAATATGATAACCAAAATTACAAAAAGTGTAA
1 AGAAATATGATAACCAAAATTACAAAAAATGTAA
17034 GGTTACTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.60, C:0.07, G:0.10, T:0.23
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATTACAAAAAATGTAATA
Found at i:23154 original size:13 final size:13
Alignment explanation
Indices: 23136--23177 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
23126 GATTTTTTAA
23136 AATTAAAATATTG
1 AATTAAAATATTG
23149 AATTAAAATATT-
1 AATTAAAATATTG
* *
23161 TATAAAAATATTG
1 AATTAAAATATTG
23174 AATT
1 AATT
23178 TAATTAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (13 bp):
AATTAAAATATTG
Found at i:24167 original size:19 final size:21
Alignment explanation
Indices: 24134--24174 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
24124 TTCTTAAAAG
*
24134 TAATGAGAAATAAAACCTTAT
1 TAATGAGAAATAAAAACTTAT
24155 TAATGA-AAA-AAAAACTTAT
1 TAATGAGAAATAAAAACTTAT
24174 T
1 T
24175 TTTTTAATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
20 3 0.16
21 6 0.32
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.29
Consensus pattern (21 bp):
TAATGAGAAATAAAAACTTAT
Found at i:24697 original size:12 final size:12
Alignment explanation
Indices: 24680--24718 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
24670 TGGGATTTTT
24680 ATAAATAATAAA
1 ATAAATAATAAA
*
24692 ATAAATAAGAAA
1 ATAAATAATAAA
*
24704 TAAAAATAATAAA
1 -ATAAATAATAAA
24717 AT
1 AT
24719 TAAAAAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (12 bp):
ATAAATAATAAA
Found at i:24941 original size:6 final size:7
Alignment explanation
Indices: 24922--24951 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
24912 CAATAAATTG
24922 AATTTTT
1 AATTTTT
24929 AATTTTT
1 AATTTTT
24936 AATTTTT
1 AATTTTT
24943 AATTTTT
1 AATTTTT
24950 AA
1 AA
24952 CCTGATTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (7 bp):
AATTTTT
Found at i:30739 original size:2 final size:2
Alignment explanation
Indices: 30732--30757 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30722 GGTTATATGA
30732 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
30758 TTTAAGAGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33892 original size:17 final size:17
Alignment explanation
Indices: 33870--33905 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
33860 ATAAAAAGAG
33870 CTATCTAGTATAACAAA
1 CTATCTAGTATAACAAA
* *
33887 CTATCTGGTGTAACAAA
1 CTATCTAGTATAACAAA
33904 CT
1 CT
33906 TTACAAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (17 bp):
CTATCTAGTATAACAAA
Found at i:36377 original size:18 final size:18
Alignment explanation
Indices: 36323--36382 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
36313 TTGCGGTAGC
*
36323 GGAACATCCTGCGGCAAT
1 GGAACATCCTGCGGCAGT
* * * *
36341 GCAACATTCTGCAGTAGT
1 GGAACATCCTGCGGCAGT
36359 GGAACATCCTGCGGCAGT
1 GGAACATCCTGCGGCAGT
*
36377 GTAACA
1 GGAACA
36383 ATATTTTGTA
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.28, C:0.25, G:0.27, T:0.20
Consensus pattern (18 bp):
GGAACATCCTGCGGCAGT
Found at i:42099 original size:114 final size:113
Alignment explanation
Indices: 41963--42184 Score: 401
Period size: 114 Copynumber: 2.0 Consensus size: 113
41953 AAGGTTGACA
41963 TATGTTATTTTAAGTAATAATTTTAAATAATAAATTAAG-AAATTAGTATACCTATAAAATATTA
1 TATGTTATTTTAAGTAATAATTTTAAATAATAAATTAAGAAAATTAGTATACCTATAAAATATTA
*
42027 AGAAATCAGTATGTATCCTATTTTCCCTCAAAAAAAAATAAAACACTTCT
66 AGAAATCAGTATGTATCCTA-TATCCCTC-AAAAAAAATAAAACACTTCT
42077 TATGTTATTTTAAGTAATAATTTTAAATAATAAATTAAGAAAATTAGTATACCTATAAAATATTA
1 TATGTTATTTTAAGTAATAATTTTAAATAATAAATTAAGAAAATTAGTATACCTATAAAATATTA
*
42142 AGAAATTAGTATGTATCCTATATCCCTCAAAAAAAATAAAACA
66 AGAAATCAGTATGTATCCTATATCCCTCAAAAAAAATAAAACA
42185 GTTGTTAACC
Statistics
Matches: 105, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
113 15 0.14
114 46 0.44
115 44 0.42
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.36
Consensus pattern (113 bp):
TATGTTATTTTAAGTAATAATTTTAAATAATAAATTAAGAAAATTAGTATACCTATAAAATATTA
AGAAATCAGTATGTATCCTATATCCCTCAAAAAAAATAAAACACTTCT
Found at i:49620 original size:22 final size:22
Alignment explanation
Indices: 49594--49868 Score: 265
Period size: 22 Copynumber: 12.7 Consensus size: 22
49584 AGAGAGGTAA
*
49594 TTACCACAATTTCATAGGGAGG
1 TTACCAAAATTTCATAGGGAGG
*
49616 TTACCAAAATTTTATAGGGTA-G
1 TTACCAAAATTTCATAGGG-AGG
* * * *
49638 TTACCCAAATTTTATAGTGTGG
1 TTACCAAAATTTCATAGGGAGG
* * * ** *
49660 TGATCAAAAGTTCATAGAAAAG
1 TTACCAAAATTTCATAGGGAGG
*
49682 TTACAAAAATTTCATA---AGG
1 TTACCAAAATTTCATAGGGAGG
*
49701 TTACAAAAATTTCATAGGGAGG
1 TTACCAAAATTTCATAGGGAGG
* *
49723 TTACCAAAATTACATA-GTAGG
1 TTACCAAAATTTCATAGGGAGG
* *
49744 TTACCAAAATTTTATAGGGAAG
1 TTACCAAAATTTCATAGGGAGG
* *
49766 TTACAAAAATTCCATAGGGAGG
1 TTACCAAAATTTCATAGGGAGG
* *
49788 TTACCGAAATTTCATA-GTATGG
1 TTACCAAAATTTCATAGGGA-GG
**
49810 TTACCAAAATTTCATAATGAGG
1 TTACCAAAATTTCATAGGGAGG
*
49832 TTACCAAAATGTCATAGGGAGG
1 TTACCAAAATTTCATAGGGAGG
49854 TTACCAAAATTTCAT
1 TTACCAAAATTTCAT
49869 CCTTATTCTA
Statistics
Matches: 204, Mismatches: 41, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
19 18 0.09
21 20 0.10
22 164 0.80
23 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.31
Consensus pattern (22 bp):
TTACCAAAATTTCATAGGGAGG
Found at i:55403 original size:41 final size:41
Alignment explanation
Indices: 55358--55442 Score: 134
Period size: 41 Copynumber: 2.1 Consensus size: 41
55348 TCCAATTTGC
* * *
55358 CCCTCCTAGTAATTAAGGTAATAAATTAATTCCAGTTTTAG
1 CCCTCCTAATAATTAAGGTAATAAATTAAATCCAGATTTAG
*
55399 CCCTCTTAATAATTAAGGTAATAAATTAAATCCAGATTTAG
1 CCCTCCTAATAATTAAGGTAATAAATTAAATCCAGATTTAG
55440 CCC
1 CCC
55443 CTAGTTATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (41 bp):
CCCTCCTAATAATTAAGGTAATAAATTAAATCCAGATTTAG
Found at i:58711 original size:21 final size:21
Alignment explanation
Indices: 58672--58713 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
58662 CATTATTTAA
58672 TATTTAAAATATATTTATTATT
1 TATTTAAAATATA-TTATTATT
58694 TATTTAATAATATA-TATTAT
1 TATTTAA-AATATATTATTAT
58714 ATCTAAGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 7 0.37
23 6 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTTAAAATATATTATTATT
Done.