Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020863.1 Corchorus olitorius cultivar O-4 contig20896, 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: 167105
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:830 original size:32 final size:32
Alignment explanation
Indices: 789--849 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
779 AAATATGTTT
*
789 GAAAAATAAGGATATAATGGTCGATTCAATTA
1 GAAAAATAAGGATATAATAGTCGATTCAATTA
*
821 GAAAAATAAGGGTATAATAGTCGATTCAA
1 GAAAAATAAGGATATAATAGTCGATTCAA
850 AAGTTTTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.48, C:0.07, G:0.20, T:0.26
Consensus pattern (32 bp):
GAAAAATAAGGATATAATAGTCGATTCAATTA
Found at i:1855 original size:22 final size:22
Alignment explanation
Indices: 1801--1851 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
1791 TGAATCGCTC
1801 AAACCCAATTTTCGAAACCCCT
1 AAACCCAATTTTCGAAACCCCT
* *
1823 AAAGCCAATTTTTGAAA-CCCT
1 AAACCCAATTTTCGAAACCCCT
1844 AAACCCAA
1 AAACCCAA
1852 ATTTGGAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.41, C:0.31, G:0.06, T:0.22
Consensus pattern (22 bp):
AAACCCAATTTTCGAAACCCCT
Found at i:7412 original size:90 final size:90
Alignment explanation
Indices: 7240--7404 Score: 273
Period size: 88 Copynumber: 1.9 Consensus size: 90
7230 ATACCTGTTA
*
7240 ATACACATAAACAATAAATATTTATTAAACTTTTTATAAAAATTTTAAGATTTGAAATAATTTAC
1 ATACACATAAACAATAAATATTTATTAAACTTTTTATAAAAATTTTAAGATTTGAAATAACTTAC
7305 TTATATAATTAACAAAAACTTAATG
66 TTATATAATTAACAAAAACTTAATG
*
7330 ATACATATAAACAATAAATATTTATTAAAC-TTTT-TAAAAATTTTAAGATTTGAAATAACTTA-
1 ATACACATAAACAATAAATATTTATTAAACTTTTTATAAAAATTTTAAGATTTGAAATAACTTAC
*
7392 TTGTTATAATTAA
66 TT-ATATAATTAA
7405 ATCAAAAAAA
Statistics
Matches: 71, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
87 2 0.03
88 36 0.51
89 4 0.06
90 29 0.41
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.41
Consensus pattern (90 bp):
ATACACATAAACAATAAATATTTATTAAACTTTTTATAAAAATTTTAAGATTTGAAATAACTTAC
TTATATAATTAACAAAAACTTAATG
Found at i:14230 original size:128 final size:129
Alignment explanation
Indices: 14050--14304 Score: 460
Period size: 128 Copynumber: 2.0 Consensus size: 129
14040 GAGATTGACG
**
14050 GCCTTTTCACGCTTCTAATATAGTTTTTTCATTGTTTTTTCGAATTAATTTCTAATTAAATCGAA
1 GCCTTTTCACGCTTCTAATATAGTTTTCCCATTGTTTTTTCGAATTAATTTCTAATTAAATCGAA
14115 ACAACATTCAGATGCTCGTAAAAACAAATTTTTATATATAATATGGCTGAGATTTGGTTCGACA
66 ACAACATTCAGATGCTCGTAAAAACAAATTTTTATATATAATATGGCTGAGATTTGGTTCGACA
*
14179 GCCTTTTCACGCTTCTAATATCGTTTTCCCA-T-TTTTTTCGGAATTAATTTCTAATTAAATCGA
1 GCCTTTTCACGCTTCTAATATAGTTTTCCCATTGTTTTTTC-GAATTAATTTCTAATTAAATCGA
14242 AACAACATTCAGATGCTCGTAAAAACAAATTTTTATATATAATATGGCTGAGATTTGGTTCGA
65 AACAACATTCAGATGCTCGTAAAAACAAATTTTTATATATAATATGGCTGAGATTTGGTTCGA
14305 TTAATATAGA
Statistics
Matches: 122, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
127 7 0.06
128 87 0.71
129 28 0.23
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (129 bp):
GCCTTTTCACGCTTCTAATATAGTTTTCCCATTGTTTTTTCGAATTAATTTCTAATTAAATCGAA
ACAACATTCAGATGCTCGTAAAAACAAATTTTTATATATAATATGGCTGAGATTTGGTTCGACA
Found at i:15572 original size:18 final size:18
Alignment explanation
Indices: 15549--15584 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
15539 TTCTAATTTC
*
15549 TATGTGTATTAAATTACT
1 TATGTGTATTAAAGTACT
15567 TATGTGTATTAAAGTACT
1 TATGTGTATTAAAGTACT
15585 ATAGTATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.47
Consensus pattern (18 bp):
TATGTGTATTAAAGTACT
Found at i:15629 original size:44 final size:43
Alignment explanation
Indices: 15566--15654 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 43
15556 ATTAAATTAC
15566 TTATGTGTATTAAAGTACTATAGTATGATATATATATATATCTT
1 TTATGTGTATTAAAGTACTATAGTATGATATATATAT-TATCTT
* *
15610 TTATGTGTATTAAATTACTATAGTATGATATATATATTTTCTT
1 TTATGTGTATTAAAGTACTATAGTATGATATATATATTATCTT
15653 TT
1 TT
15655 TTTTTATTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
43 7 0.16
44 36 0.84
ACGTcount: A:0.34, C:0.04, G:0.10, T:0.52
Consensus pattern (43 bp):
TTATGTGTATTAAAGTACTATAGTATGATATATATATTATCTT
Found at i:17172 original size:323 final size:321
Alignment explanation
Indices: 16370--18459 Score: 1249
Period size: 323 Copynumber: 6.1 Consensus size: 321
16360 TGAGATTTAA
* * *
16370 TCAGATGCTCGTAAAAACAAATCGTTATATCCAATGTGGCTG-GATTTAGTTCGATGAATATAGA
1 TCAGATGCTCGTAAAAACAAATCCTAATATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGA
* ** * * * *
16434 TATTTCAAGGAGTCTTTACGCCAAATTTCATGTAAAATTGAG-CTGCGTCTCCGGT-ACGCATTT
66 TATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAATTGAGCCGGC-ACTCC-GTAACGC-GTT
**
16497 TTAGCCAAAAACCGTGAAAATTAGTACACGATTTCGGCTAAATTTTTGCAAAAAAACTGACCCGA
128 TTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGC-------TT---AAAAAACTGACCCGA
* * **
16562 AAATTTTTTTCCTCAATTTTTTGTCACAATACTCAGAAAAAATATATAATTCAACACCAAAAAAA
183 AAA-GTTTTT-CTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAAA
* * **
16627 TTGAAGGGTTTTTCACGCTTCTAATATCATTTTTCC-TTTTTTTCTGAATTTATTTCTAAGAAAA
246 TT-AAGGGTTTTTCACGCTTCTAATATCGTTTTTCCTTTTTTTTCCGAATTTATTTCTAATTAAA
16691 TCAAAACAAGAT
310 TCAAAACAAGAT
* * * * *
16703 TTAGATGCTCGTAAAAATAAATCCTTAA-ATCCTATGTGGCTTAGATTTGGTTAGATGAATATAG
1 TCAGATGCTCGTAAAAACAAATCC-TAATATCCAATGTGGCTGAGATTTGGTTCGATGAATATAG
* * * ** * *
16767 ATATTTCAAGGAGTCTTTCTGCAAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTT
65 ATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAATTGAGCCGGCACTCCGTAACGCGTTTT
* * *
16832 CAGCCGAAAACCGTGATGGTTAGTATACGATTTCGGC-T-AAAAACTGACCCGAAAAGATTTTTC
130 -AGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTTAAAAAACTGACCCGAAAAG-TTTTTC
** * * *
16895 TCAATTTCTTTG-CGGAATATTCAGAAAAAATATATAATTCAATGCCAAAAAGATTAACGGGCTT
193 TCAATTT-TTTGCCACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAAATTAA-GGGTTT
**
16959 TTCACGCTTCTAATATCGTTTTTCCATTTTTTTTCCGAATGAATTTCTAATTAAATCAAAACAAG
256 TTCACGCTTCTAATATCGTTTTTCC-TTTTTTTTCCGAATTTATTTCTAATTAAATCAAAACAAG
17024 AT
320 AT
* * *
17026 TGAGATGCTCGTAAAAACAAATCCTAATATCCAATGTAGCTGACATTTGGTTCGATGAATATAGA
1 TCAGATGCTCGTAAAAACAAATCCTAATATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGA
17091 TATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAATTGAGCCGGCACTCCGTAACGCGTATTT
66 TATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAATTGAGCCGGCACTCCGTAACGCGT-TTT
* ** * * * * *
17156 AGCCAAAAATCGTGATGCAAAAATTGACACGATTTCGGCTTTGCAAACATTGACCCGGAAAGTTT
130 AGCCAAAAACCGTGATG--ATTAGT-ACACGATTTCGGC-TT-AAAAAACTGACCCGAAAAGTTT
* * * * *
17221 TCCTCAATTTTTTGCCACAATACTCAGCAAAATTATATAATTCAATGCAAAAACAAATGGAAGGG
190 TTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAATGCCAAAA-AAAT-TAAGGG
17286 TTTTTCACGCTTCTAATATCGTTTTTTTCTTCTTCTTTTTTTCCGAATTTATTTCTAATTAAAT-
253 TTTTTCACGCTTCTAATATCG--TTTTTC--C-T-TTTTTTTCCGAATTTATTTCTAATTAAATC
17350 AGAAACAAGAT
312 A-AAACAAGAT
* * * ** ** * *
17361 TCAGATGCTCGTAAAAACATATTCTTAA-ATCCAAAGTGGCTGAGATTTAATGAGATTTAAT-CA
1 TCAGATGCTCGTAAAAACA-AATCCTAATATCCAATGTGGCTGAGATTTGGTTCGA-TGAATATA
* ** ** * ** * * * ***** *
17424 GATGCTCGTAAAAACAAATCGTTATAT-CC-AATGTGGC-TGGATTTAGTTCGATGAATATAGAT
64 GAT-AT--T-TCAAGGAGTC-TT-TATGCCAAAAAT--CATGCA--AAATT-GA-GCCGGCA-CT
*** * * ** * * * *
17486 ATTTCAAGGAGTCTTTACGCCAAATTTCATGTAAAATTGAGCTGT-GTCTCCGGTACGCATTTTT
116 CCGT-AACGCGT-TTTA-GCCAAA-AAC-CGT--GA-TGA--T-TAG--TAC---ACG-A-TTTC
* * * *** * * * * * * * * *
17550 AGC-CAAAAACCGTGAAAATTAGTACACG-ATTTCGGCTAAATTTTTGCAAAAAAACTGACCCGA
163 GGCTTAAAAAAC-TG---ACCCG-AAAAGTTTTTC-TC-AATTTTTTGCCACAATACT---CAGA
* * * *
17613 AATTTTTTTTCCTCAATTTGTTGTCACAATACTCAGAAAAAATATATAATTCAACACCAAAAAAC
218 AA------------AA----ATAT-ATAAT--TC------AAT-------GC--CA--AAAAAA-
* * **
17678 TTGAAGGGTTTTTCACGCTTCTAATATCATTTTTCC-TTTTTTTCTGAATTTATTTCTAAGAAAA
246 TT-AAGGGTTTTTCACGCTTCTAATATCGTTTTTCCTTTTTTTTCCGAATTTATTTCTAATTAAA
*
17742 TCAAAACAAGCT
310 TCAAAACAAGAT
* * * * * *
17754 TTAGATGCTCGTAAAAATAAATCATTAA-ATCCTATGTGGCTTAGATTTGGTTAGATGAATATAG
1 TCAGATGCTCGTAAAAACAAATC-CTAATATCCAATGTGGCTGAGATTTGGTTCGATGAATATAG
* * * * ** * *
17818 ATATTTCAAGGAGTCTTTCTGCAAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTT
65 ATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAATTGAGCCGGCACTCCGTAACGCGTTTT
* * * *
17883 CAGCCGAAAACCGTGATGGTTAGTATACGATTTCGGC-T-AAAAACTTACCCGAAAAGATTTTTC
130 -AGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTTAAAAAACTGACCCGAAAAG-TTTTTC
** * * * *
17946 TCAATTTCTTTG-CGGAATATTTAGAAAAAAATATATAATTCAATGCCAAAAAGATTAACGGGCT
193 TCAATTT-TTTGCCACAATACTCAG-AAAAAATATATAATTCAATGCCAAAAAAATTAA-GGGTT
* **
18010 TTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATGAATTTCTAATTAAATCAAAACAAG
255 TTTCACGCTTCTAATATCGTTTTTCCTTTTTTTTCCGAATTTATTTCTAATTAAATCAAAACAAG
18075 AT
320 AT
* * *
18077 TGAGATGCTCGTAAAAACAAATCCTAATATCCAATGTAGCTGACATTTGGTTCGATGAATATAGA
1 TCAGATGCTCGTAAAAACAAATCCTAATATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGA
*
18142 TATTTTAAGGAGTCTTTATGCCAAAAATCATGCAAAATTGAGCCGGCACTCCGTAACGCGTATTT
66 TATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAATTGAGCCGGCACTCCGTAACGCGT-TTT
* ** * * * *
18207 AGCCAAAAATCGTGATGCAAAAATTGACACGATTTCGGCTTTGCAAACATTGACCCGAAAAGTTT
130 AGCCAAAAACCGTGATG--ATTAGT-ACACGATTTCGGC-TT-AAAAAACTGACCCGAAAAGTTT
* * * * *
18272 TCCTCAATTTTTTGCCACAATACTCAGCAAAATTATATAATTCAATGCAAAAACAAATGGAAGGG
190 TTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAATGCCAAAA-AAAT-TAAGGG
*
18337 TTTTTCACGCTTCTAATATCGTTTTTTTCTTTTTCTTTTTTTCCGAATTTATTTCTAATTAAAT-
253 TTTTTCACGCTTCTAATATCG--TTTTTC---CT-TTTTTTTCCGAATTTATTTCTAATTAAATC
18401 AGAAACAAGAT
312 A-AAACAAGAT
* * * *
18412 TCAGATGCTCATAAAAACATATTCTTAA-ATCCAAAGTGGCTGAGATTT
1 TCAGATGCTCGTAAAAACA-AATCCTAATATCCAATGTGGCTGAGATTT
18460 AATGAGATTT
Statistics
Matches: 1333, Mismatches: 282, Indels: 282
0.70 0.15 0.15
Matches are distributed among these distances:
320 2 0.00
321 76 0.06
322 63 0.05
323 317 0.24
324 6 0.00
325 6 0.00
326 25 0.02
327 1 0.00
328 33 0.02
329 90 0.07
330 58 0.04
331 8 0.01
332 6 0.00
333 38 0.03
334 102 0.08
335 150 0.11
336 17 0.01
338 1 0.00
339 8 0.01
340 9 0.01
341 4 0.00
342 7 0.01
343 4 0.00
344 2 0.00
345 2 0.00
346 9 0.01
347 8 0.01
349 2 0.00
350 1 0.00
351 1 0.00
352 2 0.00
353 1 0.00
354 1 0.00
355 3 0.00
356 5 0.00
357 1 0.00
358 6 0.00
359 8 0.01
360 3 0.00
361 26 0.02
362 7 0.01
363 4 0.00
364 4 0.00
365 1 0.00
366 5 0.00
367 5 0.00
368 1 0.00
369 3 0.00
372 1 0.00
373 1 0.00
374 2 0.00
376 4 0.00
377 1 0.00
379 2 0.00
380 4 0.00
381 12 0.01
382 6 0.00
383 2 0.00
384 1 0.00
385 2 0.00
386 2 0.00
387 3 0.00
388 6 0.00
389 11 0.01
390 1 0.00
392 8 0.01
393 80 0.06
394 1 0.00
396 2 0.00
398 7 0.01
399 3 0.00
400 29 0.02
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Consensus pattern (321 bp):
TCAGATGCTCGTAAAAACAAATCCTAATATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGA
TATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAATTGAGCCGGCACTCCGTAACGCGTTTTA
GCCAAAAACCGTGATGATTAGTACACGATTTCGGCTTAAAAAACTGACCCGAAAAGTTTTTCTCA
ATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAAATTAAGGGTTTTTCAC
GCTTCTAATATCGTTTTTCCTTTTTTTTCCGAATTTATTTCTAATTAAATCAAAACAAGAT
Found at i:19081 original size:330 final size:329
Alignment explanation
Indices: 18472--19277 Score: 966
Period size: 330 Copynumber: 2.4 Consensus size: 329
18462 TGAGATTTAA
* *
18472 TCAGATGCTCGTAAAAACAAATCGTTATATCCAATGTGGCTG-GATTTAGTTCGATGAATATAGA
1 TCAGATGCTCGTAAAAACAAATCCTAATATCCAATGTGGCTGAGATTTAGTTCGATGAATATAGA
* ** * * * * *
18536 TATTTCAAGGAGTCTTTACGCCAAATTTCATGTAAAATTGAGCTGCGTCTCCGGTACGCATTTTT
66 TATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAATTGAGCGGC-ACTCCGGAACGCGTTTTT
**
18601 AGCCAAAAACCGTGAAAATTAGTACACGATTTCGGCTAAATTTTTGCAAAAAAACTGACCCGAAA
130 AGCCAAAAACCGTGAAAAAAAGTACACGATTTCGGC---A--TTTGC-AAAAAACTGACCCGAAA
* * *
18666 ATTTTTTTCCTCAATTTTTTGTCACAATACTCAGAAAAAATATATAATTCAACACCAAAAAAATT
189 A-TGTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAAAATG
*
18731 GAAGGGTTTTTCACGCTTCTAATATC-ATTTTTCCATT-TTTTTTCTGAATTTATTTCTAAGAAA
253 GAAGGGTTTTTCACGCTTCTAATATCGATTTTTCC-TTCTTTTTTCCGAATTTATTTCTAAGAAA
18794 ATCA-AAACAATGAT
317 AT-AGAAACAA-GAT
* * * * *
18808 TGAGATGCTCGTAAAAACAAATCCTAATATCCAATGTAGCTGACATTTGGTTCGACGAATATAGA
1 TCAGATGCTCGTAAAAACAAATCCTAATATCCAATGTGGCTGAGATTTAGTTCGATGAATATAGA
*
18873 TATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAATTGAGCCGGCACTCCGGAACGCGTATTT
66 TATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAATTGAG-CGGCACTCCGGAACGCGTTTTT
* * *
18938 AGCCAAAAATCGTGATGAAAAAATTGACACGATTTCGGC-TTTGC-AAAAATTGACCCCG-AAA-
130 AGCCAAAAACCGTGA--AAAAAAGT-ACACGATTTCGGCATTTGCAAAAAACTGA-CCCGAAAAT
* * *
18999 GTTTTCCTCAATTTTTTGCCACAATACTCAGCAAAATTATATAATTCAAC-GCAGAAAAAATGGA
191 GTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACCA-AAAAAATGGA
* * **
19063 AGGGTTTTTCACGCTTCTAATATCGTTTTTTTCTTCTTTTTTCCGAATTTATTTCTAATTAAATA
255 AGGGTTTTTCACGCTTCTAATATCGATTTTTCCTTCTTTTTTCCGAATTTATTTCTAAGAAAATA
19128 GAAACAAGAT
320 GAAACAAGAT
* * *
19138 TCAGATGCTCGTAAAAACAAATTCTTAA-ATCCAATGTGGCTGAGATTTAATTAGATGAATATAG
1 TCAGATGCTCGTAAAAACAAA-TCCTAATATCCAATGTGGCTGAGATTTAGTTCGATGAATATAG
* * * * * * ** * *
19202 ATGTTTCATGGAGACTTTCTGCCTAAAATCATGCAAAACTGAGGCGGGGCCCCGAAACGCGTTTT
65 ATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAATTGA-GCGGCACTCCGGAACGCGTTTT
19267 TAGCCAAAAAC
129 TAGCCAAAAAC
19278 AAAAACAAAA
Statistics
Matches: 406, Mismatches: 52, Indels: 30
0.83 0.11 0.06
Matches are distributed among these distances:
329 2 0.00
330 197 0.49
331 43 0.11
332 11 0.03
333 4 0.01
334 5 0.01
336 38 0.09
337 85 0.21
338 3 0.01
339 5 0.01
340 13 0.03
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (329 bp):
TCAGATGCTCGTAAAAACAAATCCTAATATCCAATGTGGCTGAGATTTAGTTCGATGAATATAGA
TATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAATTGAGCGGCACTCCGGAACGCGTTTTTA
GCCAAAAACCGTGAAAAAAAGTACACGATTTCGGCATTTGCAAAAAACTGACCCGAAAATGTTTT
CCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAAAATGGAAGGGTT
TTTCACGCTTCTAATATCGATTTTTCCTTCTTTTTTCCGAATTTATTTCTAAGAAAATAGAAACA
AGAT
Found at i:24144 original size:22 final size:22
Alignment explanation
Indices: 24119--24175 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
24109 AAAAGGCATG
*
24119 CATTTAAGATGGGCCAATCTCA
1 CATTTAAGATGGGCCAACCTCA
**
24141 CATTTAAGATGGGCCAACCTTG
1 CATTTAAGATGGGCCAACCTCA
24163 CATTTAAGATGGG
1 CATTTAAGATGGG
24176 ACATTCACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (22 bp):
CATTTAAGATGGGCCAACCTCA
Found at i:26295 original size:18 final size:19
Alignment explanation
Indices: 26252--26296 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
26242 TATTTTTTGT
26252 TGTTTTTGTTTTTTTTTAA
1 TGTTTTTGTTTTTTTTTAA
26271 TGTTTTTGTTTTTTTTTAA
1 TGTTTTTGTTTTTTTTTAA
26290 TGTTTTT
1 TGTTTTT
26297 ATTATTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.09, C:0.00, G:0.11, T:0.80
Consensus pattern (19 bp):
TGTTTTTGTTTTTTTTTAA
Found at i:26304 original size:19 final size:19
Alignment explanation
Indices: 26241--26305 Score: 85
Period size: 19 Copynumber: 3.4 Consensus size: 19
26231 AAAAATCTAT
**
26241 TTATTTTTTGTTGTTTTTG
1 TTATTTTTTAATGTTTTTG
*
26260 TTTTTTTTTAATGTTTTTG
1 TTATTTTTTAATGTTTTTG
* *
26279 TTTTTTTTTAATGTTTTTA
1 TTATTTTTTAATGTTTTTG
26298 TTATTTTT
1 TTATTTTT
26306 AAATTTTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.11, C:0.00, G:0.09, T:0.80
Consensus pattern (19 bp):
TTATTTTTTAATGTTTTTG
Found at i:26404 original size:13 final size:13
Alignment explanation
Indices: 26381--26412 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
26371 AAGTTACTCC
26381 ATTATTTAGTTTAT
1 ATTA-TTAGTTTAT
26395 ATTATTAGTTTAT
1 ATTATTAGTTTAT
26408 ATTAT
1 ATTAT
26413 ATATCAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62
Consensus pattern (13 bp):
ATTATTAGTTTAT
Found at i:36966 original size:42 final size:41
Alignment explanation
Indices: 36905--37160 Score: 314
Period size: 42 Copynumber: 6.1 Consensus size: 41
36895 TCGTAATGTG
* * *** * *
36905 ATGGAGGTGGATTCTGAGGCTAGTTGGAAAAGAAATGAAATT
1 ATGGAGGAGGCTTCTGAGGCTAAAGGGAAAA-AACTGAAAAT
* * *
36947 ATGGAGGAGGCTTCCGAGGCTAAACGGCAAAAAACCGAAAAT
1 ATGGAGGAGGCTTCTGAGGCTAAA-GGGAAAAAACTGAAAAT
*
36989 ATGGAGGAGGCTTCTGAGGCTAACCGGGAAAAAACTGAAAAT
1 ATGGAGGAGGCTTCTGAGGCTAA-AGGGAAAAAACTGAAAAT
* *
37031 ATAGAGGAGGCTTCTGAGGCTAAATGGCAAAAAACTGAAAAT
1 ATGGAGGAGGCTTCTGAGGCTAAA-GGGAAAAAACTGAAAAT
*
37073 ATGGAGGAGGCTTCTGAGGCTAACCGGGAAAAAACTGAAAAT
1 ATGGAGGAGGCTTCTGAGGCTAA-AGGGAAAAAACTGAAAAT
* *
37115 ATGGAGGAGGCTTCTGAGGCTAAATGGCAAAAATCTGAAAAT
1 ATGGAGGAGGCTTCTGAGGCTAAA-GGGAAAAAACTGAAAAT
37157 ATGG
1 ATGG
37161 GTTCCTTTCC
Statistics
Matches: 186, Mismatches: 23, Indels: 10
0.85 0.11 0.05
Matches are distributed among these distances:
42 181 0.97
43 5 0.03
ACGTcount: A:0.39, C:0.12, G:0.30, T:0.19
Consensus pattern (41 bp):
ATGGAGGAGGCTTCTGAGGCTAAAGGGAAAAAACTGAAAAT
Found at i:37050 original size:84 final size:84
Alignment explanation
Indices: 36930--37160 Score: 390
Period size: 84 Copynumber: 2.7 Consensus size: 84
36920 GAGGCTAGTT
* * * * *
36930 GGAAAAGAAATGAAATTATGGAGGAGGCTTCCGAGGCTAAACGGCAAAAAACCGAAAATATGGAG
1 GGAAAA-AACTGAAAATATGGAGGAGGCTTCTGAGGCTAAATGGCAAAAAACTGAAAATATGGAG
36995 GAGGCTTCTGAGGCTAACCG
65 GAGGCTTCTGAGGCTAACCG
*
37015 GGAAAAAACTGAAAATATAGAGGAGGCTTCTGAGGCTAAATGGCAAAAAACTGAAAATATGGAGG
1 GGAAAAAACTGAAAATATGGAGGAGGCTTCTGAGGCTAAATGGCAAAAAACTGAAAATATGGAGG
37080 AGGCTTCTGAGGCTAACCG
66 AGGCTTCTGAGGCTAACCG
*
37099 GGAAAAAACTGAAAATATGGAGGAGGCTTCTGAGGCTAAATGGCAAAAATCTGAAAATATGG
1 GGAAAAAACTGAAAATATGGAGGAGGCTTCTGAGGCTAAATGGCAAAAAACTGAAAATATGG
37161 GTTCCTTTCC
Statistics
Matches: 138, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
84 132 0.96
85 6 0.04
ACGTcount: A:0.41, C:0.13, G:0.29, T:0.17
Consensus pattern (84 bp):
GGAAAAAACTGAAAATATGGAGGAGGCTTCTGAGGCTAAATGGCAAAAAACTGAAAATATGGAGG
AGGCTTCTGAGGCTAACCG
Found at i:37147 original size:126 final size:126
Alignment explanation
Indices: 36916--37158 Score: 362
Period size: 126 Copynumber: 1.9 Consensus size: 126
36906 TGGAGGTGGA
** *
36916 TTCTGAGGCTAGTTGGAAAAGAAATGAAATTATGGAGGAGGCTTCCGAGGCTAAACGGCAAAAAA
1 TTCTGAGGCTAAATGGAAAAGAAATGAAAATATGGAGGAGGCTTCCGAGGCTAAACGGCAAAAAA
* *
36981 CCGAAAATATGGAGGAGGCTTCTGAGGCTAACCGGGAAAAAACTGAAAATATAGAGGAGGC
66 CCGAAAATATGGAGGAGGCTTCTGAGGCTAAACGGCAAAAAACTGAAAATATAGAGGAGGC
* * * *
37042 TTCTGAGGCTAAATGGCAAAA-AACTGAAAATATGGAGGAGGCTTCTGAGGCTAACCGGGAAAAA
1 TTCTGAGGCTAAATGG-AAAAGAAATGAAAATATGGAGGAGGCTTCCGAGGCTAAACGGCAAAAA
* * *
37106 ACTGAAAATATGGAGGAGGCTTCTGAGGCTAAATGGCAAAAATCTGAAAATAT
65 ACCGAAAATATGGAGGAGGCTTCTGAGGCTAAACGGCAAAAAACTGAAAATAT
37159 GGGTTCCTTT
Statistics
Matches: 104, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
126 100 0.96
127 4 0.04
ACGTcount: A:0.40, C:0.13, G:0.28, T:0.19
Consensus pattern (126 bp):
TTCTGAGGCTAAATGGAAAAGAAATGAAAATATGGAGGAGGCTTCCGAGGCTAAACGGCAAAAAA
CCGAAAATATGGAGGAGGCTTCTGAGGCTAAACGGCAAAAAACTGAAAATATAGAGGAGGC
Found at i:40068 original size:2 final size:2
Alignment explanation
Indices: 40061--40093 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
40051 TCTTTATCTT
40061 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40094 TTAGAACTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40911 original size:24 final size:24
Alignment explanation
Indices: 40879--40966 Score: 140
Period size: 24 Copynumber: 3.7 Consensus size: 24
40869 TTGGGGCTAA
*
40879 AGATGAAGATAAGAAAGGAGGAGG
1 AGATGAAGATAAGAAAGGAGCAGG
*
40903 AGATGAAGATAAGAAAGAAGCAGG
1 AGATGAAGATAAGAAAGGAGCAGG
*
40927 AGATGGAGATAAGAAAGGAGCAGG
1 AGATGAAGATAAGAAAGGAGCAGG
*
40951 AGATGAAGGTAAGAAA
1 AGATGAAGATAAGAAA
40967 AAAGCTAGGA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.51, C:0.02, G:0.38, T:0.09
Consensus pattern (24 bp):
AGATGAAGATAAGAAAGGAGCAGG
Found at i:40952 original size:48 final size:49
Alignment explanation
Indices: 40879--40976 Score: 153
Period size: 48 Copynumber: 2.0 Consensus size: 49
40869 TTGGGGCTAA
* *
40879 AGATGAAGATAAGAAAGGAGGAGGAGATGAAGATAAGAAAGAAGC-AGG
1 AGATGAAGATAAGAAAGGAGCAGGAGATGAAGATAAGAAAAAAGCTAGG
* *
40927 AGATGGAGATAAGAAAGGAGCAGGAGATGAAGGTAAGAAAAAAGCTAGG
1 AGATGAAGATAAGAAAGGAGCAGGAGATGAAGATAAGAAAAAAGCTAGG
40976 A
1 A
40977 CATCCAACCC
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
48 41 0.91
49 4 0.09
ACGTcount: A:0.51, C:0.03, G:0.37, T:0.09
Consensus pattern (49 bp):
AGATGAAGATAAGAAAGGAGCAGGAGATGAAGATAAGAAAAAAGCTAGG
Found at i:47347 original size:15 final size:15
Alignment explanation
Indices: 47327--47358 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
47317 GCAGAGAGTG
*
47327 CTCATCAGTTCCTTC
1 CTCATCAGTTACTTC
47342 CTCATCAGTTACTTC
1 CTCATCAGTTACTTC
47357 CT
1 CT
47359 TTGCCTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.38, G:0.06, T:0.41
Consensus pattern (15 bp):
CTCATCAGTTACTTC
Found at i:51870 original size:41 final size:41
Alignment explanation
Indices: 51813--51896 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
51803 TCTAGTTATC
51813 TTGATATAAATTATAGGCTTTGTAATTTGGGCTATTCTGGT
1 TTGATATAAATTATAGGCTTTGTAATTTGGGCTATTCTGGT
*
51854 TTGATATAAATTATAGGCTTTGTAATTTGGGTTATTCTGGT
1 TTGATATAAATTATAGGCTTTGTAATTTGGGCTATTCTGGT
51895 TT
1 TT
51897 AAATTTAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.24, C:0.06, G:0.21, T:0.49
Consensus pattern (41 bp):
TTGATATAAATTATAGGCTTTGTAATTTGGGCTATTCTGGT
Found at i:55473 original size:42 final size:42
Alignment explanation
Indices: 55391--55474 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
55381 GAGTTACCAG
**
55391 ATTTTCAAGTTTTTGCCGTTTAGCATCAGAAGCCTCCTCCAT
1 ATTTTCAAGTTTTTGCCGTTTAGCATCAGAAGCCGACTCCAT
*
55433 ATTTTC-AGTTTTTTGCCGTTTAGCCTCAGAAGCCGACTCCAT
1 ATTTTCAAG-TTTTTGCCGTTTAGCATCAGAAGCCGACTCCAT
55475 CACAACAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 2 0.05
42 36 0.95
ACGTcount: A:0.20, C:0.26, G:0.15, T:0.38
Consensus pattern (42 bp):
ATTTTCAAGTTTTTGCCGTTTAGCATCAGAAGCCGACTCCAT
Found at i:58703 original size:60 final size:60
Alignment explanation
Indices: 58627--58744 Score: 182
Period size: 60 Copynumber: 2.0 Consensus size: 60
58617 ATTTTCCTTG
*
58627 ATTTCAAATTTCCCTAAAATTTTCCTTTCCCTAGTATTTTTCTTACTTCCAAACTAAGCC
1 ATTTCAAATTTCCCTAAAATTTTCCTTTCCCTAGTATTTTTCCTACTTCCAAACTAAGCC
* * * * *
58687 ATTTCAATTTTTCCTAAAATTTTCCTTTTCTTAGTATTTTTCCTACTTCCAAAGTAAG
1 ATTTCAAATTTCCCTAAAATTTTCCTTTCCCTAGTATTTTTCCTACTTCCAAACTAAG
58745 ACATGAGGTG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.26, C:0.23, G:0.04, T:0.47
Consensus pattern (60 bp):
ATTTCAAATTTCCCTAAAATTTTCCTTTCCCTAGTATTTTTCCTACTTCCAAACTAAGCC
Found at i:59122 original size:14 final size:14
Alignment explanation
Indices: 59101--59151 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
59091 ATATTCCACT
*
59101 AGAAAAAAAAAAAA
1 AGAAAAAAAAAGAA
*
59115 AAAAAAAAAAAGAA
1 AGAAAAAAAAAGAA
*
59129 AGAAAGAAAAAGAA
1 AGAAAAAAAAAGAA
59143 AGAAAAAAA
1 AGAAAAAAA
59152 GCTTTCTCCC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (14 bp):
AGAAAAAAAAAGAA
Found at i:59169 original size:1 final size:1
Alignment explanation
Indices: 59103--59151 Score: 53
Period size: 1 Copynumber: 49.0 Consensus size: 1
59093 ATTCCACTAG
* * * * *
59103 AAAAAAAAAAAAAAAAAAAAAAAGAAAGAAAGAAAAAGAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
59152 GCTTTCTCCC
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (1 bp):
A
Found at i:75981 original size:23 final size:23
Alignment explanation
Indices: 75950--75995 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
75940 GACAGTGTCA
*
75950 AGTTTTGGTAGAATTAATGTTCC
1 AGTTCTGGTAGAATTAATGTTCC
*
75973 AGTTCTGGTATAATTAATGTTCC
1 AGTTCTGGTAGAATTAATGTTCC
75996 TTTGCAGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.43
Consensus pattern (23 bp):
AGTTCTGGTAGAATTAATGTTCC
Found at i:79885 original size:2 final size:2
Alignment explanation
Indices: 79880--79912 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
79870 CTAATCAAAC
*
79880 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
79913 GTGTGTGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:82772 original size:11 final size:11
Alignment explanation
Indices: 82756--82782 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
82746 AAGCATCACA
82756 GAATCAATACC
1 GAATCAATACC
82767 GAATCAATACC
1 GAATCAATACC
82778 GAATC
1 GAATC
82783 CTGGTCTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.44, C:0.26, G:0.11, T:0.19
Consensus pattern (11 bp):
GAATCAATACC
Found at i:83265 original size:13 final size:13
Alignment explanation
Indices: 83249--83273 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
83239 AAGAAAACCT
83249 AAAAATAGCTAAG
1 AAAAATAGCTAAG
83262 AAAAATAGCTAA
1 AAAAATAGCTAA
83274 ATATTAGTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.08, G:0.12, T:0.16
Consensus pattern (13 bp):
AAAAATAGCTAAG
Found at i:84371 original size:30 final size:30
Alignment explanation
Indices: 84335--84392 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
84325 AGAGGAGTTG
84335 ATTTTGAGAAATAAGATGGCTGTAAGCTGT
1 ATTTTGAGAAATAAGATGGCTGTAAGCTGT
*
84365 ATTTTGAGTAATAAGATGGCTGTAAGCT
1 ATTTTGAGAAATAAGATGGCTGTAAGCT
84393 TTTGTATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.33, C:0.07, G:0.26, T:0.34
Consensus pattern (30 bp):
ATTTTGAGAAATAAGATGGCTGTAAGCTGT
Found at i:102368 original size:18 final size:18
Alignment explanation
Indices: 102328--102368 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
102318 CATTAAAACA
*
102328 AGAACCCGAAACAGAGCC
1 AGAACCCGAAACAGAACC
* *
102346 GGAACCCGAACCAGAACC
1 AGAACCCGAAACAGAACC
102364 AGAAC
1 AGAAC
102369 AAGAAGCTGC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.44, C:0.34, G:0.22, T:0.00
Consensus pattern (18 bp):
AGAACCCGAAACAGAACC
Found at i:113575 original size:60 final size:59
Alignment explanation
Indices: 113511--113670 Score: 212
Period size: 60 Copynumber: 2.7 Consensus size: 59
113501 GCTAATTGCT
* *** *
113511 CAAATAAGGGCCTAACATTTAAAAAAATGCTCAAATAAGGATCTGATATTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGA-CCGATATTTTAATTTGGC
* ** * *
113571 CAAATAAGGGCCTGACGTTTGCCAAAATATTTAAATAACAGACCGATATTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAA-GGACCGATATTTTAATTTGGC
113631 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGG
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGG
113671 GTTTGACATT
Statistics
Matches: 84, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
59 1 0.01
60 81 0.96
61 2 0.02
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (59 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGACCGATATTTTAATTTGGC
Found at i:117994 original size:20 final size:19
Alignment explanation
Indices: 117941--117996 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
117931 TTTATCCTGT
117941 AATGAGTAGTTTTATTTAA
1 AATGAGTAGTTTTATTTAA
117960 AATGAGTAGTTTTATTTAA
1 AATGAGTAGTTTTATTTAA
117979 AATG-GATAGTTTTTATTT
1 AATGAG-TAG-TTTTATTT
117997 TGATTTGAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
18 1 0.03
19 26 0.74
20 8 0.23
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (19 bp):
AATGAGTAGTTTTATTTAA
Found at i:125302 original size:121 final size:121
Alignment explanation
Indices: 125157--125385 Score: 397
Period size: 121 Copynumber: 1.9 Consensus size: 121
125147 TTGCTTGCTG
125157 TGATGTTCCTTTTTCTGCTCTGATGGTTT-TTTGATAATGTTTGTTCTCTTCTGCAGTTATCTCC
1 TGATGTTCCTTTTTCTGCTCTGATGGTTTCTTT-ATAATGTTTGTTCTCTTCTGCAGTTATCTCC
*
125221 CCATTGGAGTTGAGCATATCCCTGTGGCAGCAAGGATTGCCTTCGGATTTGCTGGTA
65 CCATTGGAGCTGAGCATATCCCTGTGGCAGCAAGGATTGCCTTCGGATTTGCTGGTA
* * * *
125278 TGATTTTCCTTTTTCTGCTTTGATGGTTTCTTTATAATGTTTTTTCTCTTCTGCAGTTGTCTCCC
1 TGATGTTCCTTTTTCTGCTCTGATGGTTTCTTTATAATGTTTGTTCTCTTCTGCAGTTATCTCCC
125343 CATTGGAGCTGAGCATATCCCTGTGGCAGCAAGGATTGCCTTC
66 CATTGGAGCTGAGCATATCCCTGTGGCAGCAAGGATTGCCTTC
125386 CTGCTGTGGG
Statistics
Matches: 102, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
121 99 0.97
122 3 0.03
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.43
Consensus pattern (121 bp):
TGATGTTCCTTTTTCTGCTCTGATGGTTTCTTTATAATGTTTGTTCTCTTCTGCAGTTATCTCCC
CATTGGAGCTGAGCATATCCCTGTGGCAGCAAGGATTGCCTTCGGATTTGCTGGTA
Found at i:125487 original size:20 final size:20
Alignment explanation
Indices: 125460--125658 Score: 92
Period size: 20 Copynumber: 9.4 Consensus size: 20
125450 GGCAAGTTCA
125460 ATGTGAATTGGGAAAATTGG
1 ATGTGAATTGGGAAAATTGG
* ** * * **
125480 AGGTGAATCAAGGCAAGTTCA
1 ATGTGAAT-TGGGAAAATTGG
125501 ATGTGAATTGGGAAAATTGG
1 ATGTGAATTGGGAAAATTGG
** * * **
125521 ATGTGAATCAAGGCAAGTTCA
1 ATGTGAAT-TGGGAAAATTGG
*
125542 ATGTGAATTGGGAAATTTGG
1 ATGTGAATTGGGAAAATTGG
* * * **
125562 ATGTGAATTATCAAGGCAAGTTCA
1 ATGTGAA-T-T--GGGAAAATTGG
125586 ATGTGAATTGGGAAAATTGG
1 ATGTGAATTGGGAAAATTGG
* * * **
125606 ATGTGAATTATCAAGGCAAGTTCA
1 ATGTGAA-T-T--GGGAAAATTGG
125630 ATGTGAATTGGGAAAATTGG
1 ATGTGAATTGGGAAAATTGG
125650 ATGTGAATT
1 ATGTGAATT
125659 ATCAAGGCAA
Statistics
Matches: 123, Mismatches: 46, Indels: 20
0.65 0.24 0.11
Matches are distributed among these distances:
20 62 0.50
21 29 0.24
22 4 0.03
23 2 0.02
24 26 0.21
ACGTcount: A:0.36, C:0.06, G:0.29, T:0.29
Consensus pattern (20 bp):
ATGTGAATTGGGAAAATTGG
Found at i:125590 original size:44 final size:42
Alignment explanation
Indices: 125448--125826 Score: 523
Period size: 44 Copynumber: 8.9 Consensus size: 42
125438 CCAATGTGAG
*
125448 AAGGCAAGTTCAATGTGAATTGGGAAAATTGGAGGTG-AATC
1 AAGGCAAGTTCAATGTGAATTGGGAAAATTGGATGTGAAATC
125489 AAGGCAAGTTCAATGTGAATTGGGAAAATTGGATGTG-AATC
1 AAGGCAAGTTCAATGTGAATTGGGAAAATTGGATGTGAAATC
*
125530 AAGGCAAGTTCAATGTGAATTGGGAAATTTGGATGTGAATTATC
1 AAGGCAAGTTCAATGTGAATTGGGAAAATTGGATGTGAA--ATC
125574 AAGGCAAGTTCAATGTGAATTGGGAAAATTGGATGTGAATTATC
1 AAGGCAAGTTCAATGTGAATTGGGAAAATTGGATGTGAA--ATC
125618 AAGGCAAGTTCAATGTGAATTGGGAAAATTGGATGTGAATTATC
1 AAGGCAAGTTCAATGTGAATTGGGAAAATTGGATGTGAA--ATC
*
125662 AAGGCAAGTTCAATGTGAATTGGGAAAATTGGATTTG-AATC
1 AAGGCAAGTTCAATGTGAATTGGGAAAATTGGATGTGAAATC
* * *
125703 AAGGCAAGTTCAATGTTAATTGGGAAAGTTGAATGTGAGAAT-
1 AAGGCAAGTTCAATGTGAATTGGGAAAATTGGATGTGA-AATC
* ** * *
125745 AAGGCAAGTTCAATGTCAATTGGGAATGTTGAATGTGAGAATT
1 AAGGCAAGTTCAATGTGAATTGGGAAAATTGGATGTGA-AATC
* * **
125788 AAGGAAAGTTCAATGTCAATTGGGAAAATTCAATGTGAA
1 AAGGCAAGTTCAATGTGAATTGGGAAAATTGGATGTGAA
125827 TGCGCCGCGT
Statistics
Matches: 318, Mismatches: 14, Indels: 11
0.93 0.04 0.03
Matches are distributed among these distances:
41 112 0.35
42 42 0.13
43 38 0.12
44 126 0.40
ACGTcount: A:0.37, C:0.07, G:0.28, T:0.28
Consensus pattern (42 bp):
AAGGCAAGTTCAATGTGAATTGGGAAAATTGGATGTGAAATC
Found at i:125594 original size:24 final size:24
Alignment explanation
Indices: 125562--125682 Score: 96
Period size: 24 Copynumber: 5.4 Consensus size: 24
125552 GGAAATTTGG
125562 ATGTGAATTATCAAGGCAAGTTCA
1 ATGTGAATTATCAAGGCAAGTTCA
* * * **
125586 ATGTGAA-T-T--GGGAAAATTGG
1 ATGTGAATTATCAAGGCAAGTTCA
125606 ATGTGAATTATCAAGGCAAGTTCA
1 ATGTGAATTATCAAGGCAAGTTCA
* * * **
125630 ATGTGAA-T-T--GGGAAAATTGG
1 ATGTGAATTATCAAGGCAAGTTCA
125650 ATGTGAATTATCAAGGCAAGTTCA
1 ATGTGAATTATCAAGGCAAGTTCA
125674 ATGTGAATT
1 ATGTGAATT
125683 GGGAAAATTG
Statistics
Matches: 69, Mismatches: 20, Indels: 16
0.66 0.19 0.15
Matches are distributed among these distances:
20 26 0.38
21 2 0.03
22 4 0.06
23 2 0.03
24 35 0.51
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.31
Consensus pattern (24 bp):
ATGTGAATTATCAAGGCAAGTTCA
Found at i:125819 original size:20 final size:20
Alignment explanation
Indices: 125708--125823 Score: 88
Period size: 20 Copynumber: 5.5 Consensus size: 20
125698 GAATCAAGGC
*
125708 AAGTTCAATGTTAATTGGGA
1 AAGTTCAATGTCAATTGGGA
* * ** *
125728 AAGTTGAATGTGAGAATAAGGC
1 AAGTTCAATGT--CAATTGGGA
125750 AAGTTCAATGTCAATTGGGA
1 AAGTTCAATGTCAATTGGGA
* * * *
125770 ATGTTGAATGTGAGAATTAAGGA
1 AAGTTCAATGT--CAATT-GGGA
125793 AAGTTCAATGTCAATTGGGA
1 AAGTTCAATGTCAATTGGGA
*
125813 AAATTCAATGT
1 AAGTTCAATGT
125824 GAATGCGCCG
Statistics
Matches: 72, Mismatches: 19, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
20 37 0.51
21 4 0.06
22 19 0.26
23 12 0.17
ACGTcount: A:0.38, C:0.06, G:0.26, T:0.30
Consensus pattern (20 bp):
AAGTTCAATGTCAATTGGGA
Found at i:127215 original size:26 final size:26
Alignment explanation
Indices: 127168--127224 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
127158 TGGAAAATAT
* * * *
127168 TTAACGGTATTCCCGTAAAGAATAAC
1 TTAACCGTATTCCCGGAAAGAACAAA
* *
127194 TTAACCGTATTCCGGGATAGAACAAA
1 TTAACCGTATTCCCGGAAAGAACAAA
127220 TTAAC
1 TTAAC
127225 GGTACTCCTG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (26 bp):
TTAACCGTATTCCCGGAAAGAACAAA
Found at i:128032 original size:26 final size:25
Alignment explanation
Indices: 127998--128053 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 25
127988 CAGTTAACAC
127998 TAACGTAACAG-TATACGGCATATAAT
1 TAACGTAAC-GTTATACGGCA-ATAAT
*
128024 TAACTTAACGTTATACGGCAATAAT
1 TAACGTAACGTTATACGGCAATAAT
128049 TAACG
1 TAACG
128054 GAATATAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 10 0.37
26 17 0.63
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (25 bp):
TAACGTAACGTTATACGGCAATAAT
Found at i:129178 original size:56 final size:56
Alignment explanation
Indices: 129108--129219 Score: 152
Period size: 56 Copynumber: 2.0 Consensus size: 56
129098 CCAACTTCAT
*** *
129108 ATTCAGCTAGACAAATAGGATAGTCCTTGTGCACAAATGAACTCCATGGAGAAACC
1 ATTCAGCTAGACAAATAGGATAGTCCCCATGCACAAATGAACTACATGGAGAAACC
* * * *
129164 ATTCAGTTGGACAAATAGGATTGTCCCCATGCACAAATGAACTATATGGAGAAACC
1 ATTCAGCTAGACAAATAGGATAGTCCCCATGCACAAATGAACTACATGGAGAAACC
129220 TAAGAGTGAA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.22
Consensus pattern (56 bp):
ATTCAGCTAGACAAATAGGATAGTCCCCATGCACAAATGAACTACATGGAGAAACC
Found at i:129253 original size:32 final size:31
Alignment explanation
Indices: 129217--129438 Score: 199
Period size: 32 Copynumber: 7.3 Consensus size: 31
129207 ATATGGAGAA
* *
129217 ACCTAAGAGTGAACTATATGCTATAACAATAG
1 ACCTAA-AATGAACTATATGCTATAACGATAG
* * *
129249 ACCT---A-CAACCATATGCTAAAACGATAG
1 ACCTAAAATGAACTATATGCTATAACGATAG
* * *
129276 AGCT--AA--AACTATATGTTGTAACGATAG
1 ACCTAAAATGAACTATATGCTATAACGATAG
*
129303 ACCTAAAATGAACTATATGCTGTAACGATAG
1 ACCTAAAATGAACTATATGCTATAACGATAG
* * * *
129334 ACCTAAAAGGAACTATATGTTGTAACGATGG
1 ACCTAAAATGAACTATATGCTATAACGATAG
* *
129365 ACCTAAAAATGAATTATATGCTATAACGATGG
1 ACCT-AAAATGAACTATATGCTATAACGATAG
* *
129397 ACCTTAAAATGAATTATATGCTATAACGATAA
1 ACC-TAAAATGAACTATATGCTATAACGATAG
129429 ACCTGAAAAT
1 ACCT-AAAAT
129439 AAACGGCTTA
Statistics
Matches: 161, Mismatches: 21, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
27 41 0.25
28 1 0.01
29 2 0.01
31 53 0.33
32 63 0.39
33 1 0.01
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.26
Consensus pattern (31 bp):
ACCTAAAATGAACTATATGCTATAACGATAG
Found at i:129275 original size:27 final size:27
Alignment explanation
Indices: 129232--129341 Score: 103
Period size: 27 Copynumber: 3.9 Consensus size: 27
129222 AGAGTGAACT
* *
129232 ATATGCTATAACAATAGACCTACAACC
1 ATATGCTATAACGATAGACCTAAAACC
* * *
129259 ATATGCTAAAACGATAGAGCTAAAACT
1 ATATGCTATAACGATAGACCTAAAACC
* * *
129286 ATATGTTGTAACGATAGACCTAAAATGAACT
1 ATATGCTATAACGATAGACCT--AA--AACC
*
129317 ATATGCTGTAACGATAGACCTAAAA
1 ATATGCTATAACGATAGACCTAAAA
129342 GGAACTATAT
Statistics
Matches: 69, Mismatches: 10, Indels: 8
0.79 0.11 0.09
Matches are distributed among these distances:
27 41 0.59
29 4 0.06
31 24 0.35
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.25
Consensus pattern (27 bp):
ATATGCTATAACGATAGACCTAAAACC
Found at i:135727 original size:4 final size:4
Alignment explanation
Indices: 135718--135757 Score: 66
Period size: 4 Copynumber: 10.5 Consensus size: 4
135708 ATCCTGTTGA
135718 TTGT TTGT TTGT TTGT TTGT TTGT TTG- TT-T TTGT TTGT TT
1 TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT TT
135758 TTGTTTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 4 0.12
4 30 0.88
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.78
Consensus pattern (4 bp):
TTGT
Found at i:135752 original size:10 final size:10
Alignment explanation
Indices: 135725--135768 Score: 63
Period size: 10 Copynumber: 4.3 Consensus size: 10
135715 TGATTGTTTG
135725 TTTGTTTGTTT
1 TTTGTTTG-TT
135736 GTTTGTTTGTT
1 -TTTGTTTGTT
135747 TTTGTTTGTT
1 TTTGTTTGTT
135757 TTTGTTT-TT
1 TTTGTTTGTT
135766 TTT
1 TTT
135769 TTTTTTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
9 5 0.16
10 17 0.53
11 2 0.06
12 8 0.25
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (10 bp):
TTTGTTTGTT
Found at i:135766 original size:8 final size:8
Alignment explanation
Indices: 135718--135774 Score: 55
Period size: 8 Copynumber: 7.2 Consensus size: 8
135708 ATCCTGTTGA
*
135718 TTGTTTGT
1 TTGTTTTT
*
135726 TTGTTTGT
1 TTGTTTTT
*
135734 TTGTTTGT
1 TTGTTTTT
135742 TTGTTTTT
1 TTGTTTTT
*
135750 GTT-TGTTT
1 -TTGTTTTT
135758 TTGTTTTT
1 TTGTTTTT
135766 TT-TTTTT
1 TTGTTTTT
135773 TT
1 TT
135775 TAATGACATG
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
7 9 0.20
8 33 0.75
9 2 0.05
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (8 bp):
TTGTTTTT
Found at i:135769 original size:10 final size:10
Alignment explanation
Indices: 135725--135775 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
135715 TGATTGTTTG
135725 TTTGTTTGTTT
1 TTTGTTT-TTT
*
135736 GTTTGTTTGTT
1 -TTTGTTTTTT
*
135747 TTTGTTTGTT
1 TTTGTTTTTT
135757 TTTGTTTTTT
1 TTTGTTTTTT
135767 TTT-TTTTTT
1 TTTGTTTTTT
135776 AATGACATGG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
9 6 0.16
10 22 0.59
11 2 0.05
12 7 0.19
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (10 bp):
TTTGTTTTTT
Found at i:135908 original size:18 final size:18
Alignment explanation
Indices: 135885--135922 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
135875 TTGACCTTAA
135885 GTCTAACTTTGGCAATGT
1 GTCTAACTTTGGCAATGT
135903 GTCTAACTTTGGCAATGT
1 GTCTAACTTTGGCAATGT
135921 GT
1 GT
135923 AATGAAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.39
Consensus pattern (18 bp):
GTCTAACTTTGGCAATGT
Found at i:141235 original size:31 final size:31
Alignment explanation
Indices: 141197--141266 Score: 140
Period size: 31 Copynumber: 2.3 Consensus size: 31
141187 CAAAAAGGCC
141197 CCTGAACTTACACAAAACGACCAAATAAGCT
1 CCTGAACTTACACAAAACGACCAAATAAGCT
141228 CCTGAACTTACACAAAACGACCAAATAAGCT
1 CCTGAACTTACACAAAACGACCAAATAAGCT
141259 CCTGAACT
1 CCTGAACT
141267 CTAATTGCAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.43, C:0.30, G:0.10, T:0.17
Consensus pattern (31 bp):
CCTGAACTTACACAAAACGACCAAATAAGCT
Found at i:142049 original size:19 final size:19
Alignment explanation
Indices: 142013--142049 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
142003 TGTATTTGTA
*
142013 ACTGTTTCACTACCGTTTG
1 ACTGTTTCACCACCGTTTG
*
142032 ACTGTTTCACCACTGTTT
1 ACTGTTTCACCACCGTTT
142050 TGAACTCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.27, G:0.14, T:0.43
Consensus pattern (19 bp):
ACTGTTTCACCACCGTTTG
Done.