Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 1 of 120
Found at i:513 original size:7 final size:7
Alignment explanation
Indices: 1--497 Score: 527
Period size: 7 Copynumber: 71.3 Consensus size: 7
1 CCCGAAC
1 CCCGAAC
8 CCCGAAC
1 CCCGAAC
15 CCCGAAC
1 CCCGAAC
22 CCCGAAC
1 CCCGAAC
29 CCCGAAC
1 CCCGAAC
36 CCCGAAC
1 CCCGAAC
43 CCC-AAC
1 CCCGAAC
49 CCCGAAC
1 CCCGAAC
56 CCCGAAC
1 CCCGAAC
63 CCCGAAC
1 CCCGAAC
70 CCCGAAC
1 CCCGAAC
77 CCCGAAC
1 CCCGAAC
84 CCCGAAC
1 CCCGAAC
91 CCCGAAC
1 CCCGAAC
98 CCCGAAC
1 CCCGAAC
105 CCCGAAC
1 CCCGAAC
112 CCCGAAC
1 CCCGAAC
119 CCCGAAC
1 CCCGAAC
126 CCCGAAC
1 CCCGAAC
133 CCCGAAC
1 CCCGAAC
140 CCCGAAC
1 CCCGAAC
147 CCCGAAC
1 CCCGAAC
154 CCCGAAC
1 CCCGAAC
161 CCCGAAC
1 CCCGAAC
168 CCCGAAC
1 CCCGAAC
175 CCCGAAC
1 CCCGAAC
182 CCCGAAC
1 CCCGAAC
189 CCCGAAC
1 CCCGAAC
196 CCCGAAC
1 CCCGAAC
203 CCCGAAC
1 CCCGAAC
210 CCCGAAC
1 CCCGAAC
217 CCCGAAC
1 CCCGAAC
224 CCCGAAC
1 CCCGAAC
*
231 CCTG-AC
1 CCCGAAC
237 CCC-AGAC
1 CCCGA-AC
244 CCC-AGAC
1 CCCGA-AC
251 CCC-AGAC
1 CCCGA-AC
258 CCC-AGAC
1 CCCGA-AC
265 CCC-AGAC
1 CCCGA-AC
272 CCC-AGAC
1 CCCGA-AC
279 CCC-AGAC
1 CCCGA-AC
286 CCC-AGAC
1 CCCGA-AC
293 CCC-AGA-
1 CCCGA-AC
299 CCCGAGA-
1 CCCGA-AC
306 CCCGAGA-
1 CCCGA-AC
313 CCCGAGA-
1 CCCGA-AC
320 CCCGAGA-
1 CCCGA-AC
327 CCCGAGA-
1 CCCGA-AC
334 CCCGAGA-
1 CCCGA-AC
341 CCCGAGA-
1 CCCGA-AC
348 CCCGAGA-
1 CCCGA-AC
355 CCCGAGA-
1 CCCGA-AC
362 CCCGAGA-
1 CCCGA-AC
369 CCCGAGA-
1 CCCGA-AC
376 CCCGAGAC
1 CCCGA-AC
**
384 CCTAAAC
1 CCCGAAC
**
391 CCTAAAC
1 CCCGAAC
**
398 CCTAAAC
1 CCCGAAC
**
405 CCTAAAC
1 CCCGAAC
**
412 CCTAAAC
1 CCCGAAC
**
419 CCTAAAC
1 CCCGAAC
426 CCCGAAC
1 CCCGAAC
433 CCCGAAC
1 CCCGAAC
440 CCCGAAC
1 CCCGAAC
447 CCCGAAC
1 CCCGAAC
454 CCCGAAC
1 CCCGAAC
461 CCCGAAC
1 CCCGAAC
468 CCCGAAC
1 CCCGAAC
475 CCCGAAC
1 CCCGAAC
482 CCCGAAC
1 CCCGAAC
489 CCCGAAC
1 CCCGAAC
496 CC
1 CC
498 AAACCCTAAC
Statistics
Matches: 479, Mismatches: 6, Indels: 10
0.97 0.01 0.02
Matches are distributed among these distances:
6 13 0.03
7 463 0.97
8 3 0.01
ACGTcount: A:0.30, C:0.54, G:0.15, T:0.01
Consensus pattern (7 bp):
CCCGAAC
Found at i:713 original size:21 final size:22
Alignment explanation
Indices: 689--746 Score: 93
Period size: 21 Copynumber: 2.7 Consensus size: 22
679 GCCCTAATCC
*
689 TTAAACCCCAAACCT-GACACT
1 TTAAACCCTAAACCTCGACACT
710 TTAAACCCTAAA-CTCGACACT
1 TTAAACCCTAAACCTCGACACT
731 TTAAACCCTAAACCTC
1 TTAAACCCTAAACCTC
747 ATAATCTATA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 2 0.06
21 29 0.85
22 3 0.09
ACGTcount: A:0.38, C:0.36, G:0.03, T:0.22
Consensus pattern (22 bp):
TTAAACCCTAAACCTCGACACT
Found at i:779 original size:21 final size:23
Alignment explanation
Indices: 734--785 Score: 74
Period size: 21 Copynumber: 2.4 Consensus size: 23
724 CGACACTTTA
734 AACCC-TAAACCTCATAATCTAT
1 AACCCTTAAACCTCATAATCTAT
*
756 AACCTTTAAACCTCA-AAT-TAT
1 AACCCTTAAACCTCATAATCTAT
777 AACCCTTAA
1 AACCCTTAA
786 CTCTAACCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 11 0.41
22 7 0.26
23 9 0.33
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (23 bp):
AACCCTTAAACCTCATAATCTAT
Found at i:1798 original size:2 final size:2
Alignment explanation
Indices: 1791--1815 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1781 AAAGGGAACA
1791 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1816 AATGGGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2415 original size:3 final size:3
Alignment explanation
Indices: 2407--2446 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2397 ACCATATTTG
2407 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
2447 AAGCCACTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:7712 original size:362 final size:362
Alignment explanation
Indices: 6810--8265 Score: 2302
Period size: 362 Copynumber: 4.0 Consensus size: 362
6800 GCTTATCTCA
* * * *
6810 AACATTCTAAAATCCATTTTCTCCATAGCCTTAAGTTCATGAAAAATTATTAGAACTTGAATTAA
1 AACATTCTAAAATCCATTTTCTCCATAACCTTAAGTTCATGGAAAATTATTAGAACTCGGATTAA
* * *
6875 GAGGTTGTCAATTGTCGACTTCCTTAAACCCTATAATTTGTTTAAGAAACACTAATTTATGGTTT
66 GAGGTTGCCAATTGTCGACTTCCTTAAACCCTAGAATTTGTTTAAGAAACACTAATTTAT-GATT
* * * *
6940 TTGAAAAAAAAGTGTGATTCTAGAGTTTGATTACAAAATTGAACCATTATTTAATGAAATTGGCG
130 TTGAAAAAAAAGTATGGTTCTAGAGTTTGATTACAAAATTGAACCATTATTTAATGAAATAGGCA
* * * *
7005 AGAATAACACACTAAATTCACATACCAAAAAAATAAATTTAATATCAA-TTTTCCACCAATAGTT
195 AGAACAACATACTAAATTCACATACCAAAAAAATAAATTTAATATCAATTTTTCCACAAATAATT
*
7069 GCAAACAAAAAATAAATAAATTCAACATTGATACAAAAAATTAAATTTAATATTTTATCTATTAT
260 GCAAACAAAAAATAAATAAATTCAACATTGATAAAAAAAATTAAATTTAATATTTTATCTATTAT
7134 AAAAATTCAATACTTAAATTTTTTATTTTTTC-AAAAC
325 AAAAATTCAATACTTAAATTTTTTATTTTTTCAAAAAC
* * *
7171 AACATTCTAATATCCATTTTCTTCATAACCTTAAGTTCAAGGAAAATTATTAGAACTCGGATTAA
1 AACATTCTAAAATCCATTTTCTCCATAACCTTAAGTTCATGGAAAATTATTAGAACTCGGATTAA
* * *
7236 GAGGTTGTCAATTGTCGACTTCCTTACACCCTAGAATTTGTTTAAGAAACAGTAATTTATGATTT
66 GAGGTTGCCAATTGTCGACTTCCTTAAACCCTAGAATTTGTTTAAGAAACACTAATTTATGATTT
7301 TGAAAAAAAAAAGTATGGTTCTAGAGTTTGATTACAAAATTGAACCATTATTTAATGAAATAGGC
131 TG--AAAAAAAAGTATGGTTCTAGAGTTTGATTACAAAATTGAACCATTATTTAATGAAATAGGC
*
7366 AAGAACAACATACTAAATTCACATACCAAAAAATTAAATTTAATATCAATTTTTCCACAAATAAT
194 AAGAACAACATACTAAATTCACATACCAAAAAAATAAATTTAATATCAATTTTTCCACAAATAAT
*
7431 TGCAAACAAAAAATAAATAAATTCAACTTTGATAAAAAAAATTAAATTTAATATTTTATCTATTA
259 TGCAAACAAAAAATAAATAAATTCAACATTGATAAAAAAAATTAAATTTAATATTTTATCTATTA
*
7496 TAAAAATTCAATACTTAAATTTTTTATTTTTTCCAAAAAT
324 TAAAAATTCAATACTTAAATTTTTTATTTTTT-CAAAAAC
*
7536 AACATTCTAAAATCCATTTTCTCCATAACCTTAAGTTCATGGAAAATTATTAGAACTCAGATTAA
1 AACATTCTAAAATCCATTTTCTCCATAACCTTAAGTTCATGGAAAATTATTAGAACTCGGATTAA
* * *
7601 GAGGGTACCAATTGTCGACTTCCTTAAACCCTAGAATTTGTTTAAGAAACACTAATTTATGGTTT
66 GAGGTTGCCAATTGTCGACTTCCTTAAACCCTAGAATTTGTTTAAGAAACACTAATTTATGATTT
* * *
7666 TG-AAAAAAGGTATGGTTCTAGAGTTTGATTCCAAAATTGAACCATTATTTAATGAAATAGACAA
131 TGAAAAAAAAGTATGGTTCTAGAGTTTGATTACAAAATTGAACCATTATTTAATGAAATAGGCAA
* *
7730 GAACAACTTACTAAATTCACATACCAAAAAAATAAATTTAATATCAATTTTTTCACAAATAATTG
196 GAACAACATACTAAATTCACATACCAAAAAAATAAATTTAATATCAATTTTTCCACAAATAATTG
*
7795 CAAAC-AAAAATAAATAAATTCAACATTGATACAAAAAATTAAATTTAATATTTTATCTATTATA
261 CAAACAAAAAATAAATAAATTCAACATTGATAAAAAAAATTAAATTTAATATTTTATCTATTATA
*
7859 AAAATTCAATACTTAAATTTTTTATTTTTCCAAAAAC
326 AAAATTCAATACTTAAATTTTTTATTTTTTCAAAAAC
* * *
7896 AACATTCTAAAATCCATTTTATCCATAACCCTAAGTTCATGGAAAATTATTA-AGCCTCGGATTA
1 AACATTCTAAAATCCATTTTCTCCATAACCTTAAGTTCATGGAAAATTATTAGA-ACTCGGATTA
* * * *
7960 AGAGGTTGCCAATTTTCGACTTCTTTAAACTCTAGAATTTGTTTAAGAAACACTAATTTATAATT
65 AGAGGTTGCCAATTGTCGACTTCCTTAAACCCTAGAATTTGTTTAAGAAACACTAATTTATGATT
* *
8025 TTG-AAAAAAAGCATGGTTCTAGAGTTTGATTACAAAATTGAACCCTTATTTAATGAAATAGGCA
130 TTGAAAAAAAAGTATGGTTCTAGAGTTTGATTACAAAATTGAACCATTATTTAATGAAATAGGCA
* * *
8089 AGAACAACATACTAAATT-AGCATA-C-AAAAAGTAAATTTAAAATCAATTTTTCCACAAATAGT
195 AGAACAACATACTAAATTCA-CATACCAAAAAAATAAATTTAATATCAATTTTTCCACAAATAAT
* *
8151 TACAAATAAAAAATTAAATAAATTCAACATTGAT-AAAAAAATTAAATTTAATATTTTATCTATT
259 TGCAAACAAAAAA-TAAATAAATTCAACATTGATAAAAAAAATTAAATTTAATATTTTATCTATT
* *
8215 ATAAAAACTCAATACTTAAATTTTTTATATTTTCAAAAAC
323 ATAAAAATTCAATACTTAAATTTTTTATTTTTTCAAAAAC
*
8255 AACATACTAAA
1 AACATTCTAAA
8266 CTTGGATATT
Statistics
Matches: 1015, Mismatches: 71, Indels: 20
0.92 0.06 0.02
Matches are distributed among these distances:
358 38 0.04
359 84 0.08
360 228 0.22
361 201 0.20
362 229 0.23
363 108 0.11
364 1 0.00
365 126 0.12
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.35
Consensus pattern (362 bp):
AACATTCTAAAATCCATTTTCTCCATAACCTTAAGTTCATGGAAAATTATTAGAACTCGGATTAA
GAGGTTGCCAATTGTCGACTTCCTTAAACCCTAGAATTTGTTTAAGAAACACTAATTTATGATTT
TGAAAAAAAAGTATGGTTCTAGAGTTTGATTACAAAATTGAACCATTATTTAATGAAATAGGCAA
GAACAACATACTAAATTCACATACCAAAAAAATAAATTTAATATCAATTTTTCCACAAATAATTG
CAAACAAAAAATAAATAAATTCAACATTGATAAAAAAAATTAAATTTAATATTTTATCTATTATA
AAAATTCAATACTTAAATTTTTTATTTTTTCAAAAAC
Found at i:8043 original size:360 final size:362
Alignment explanation
Indices: 6810--8265 Score: 2304
Period size: 360 Copynumber: 4.0 Consensus size: 362
6800 GCTTATCTCA
* * * *
6810 AACATTCTAAAATCCATTTTCTCCATAGCCTTAAGTTCATGAAAAATTATTAGAACTTGAATTAA
1 AACATTCTAAAATCCATTTTCTCCATAACCTTAAGTTCATGGAAAATTATTAGAACTCGGATTAA
* * *
6875 GAGGTTGTCAATTGTCGACTTCCTTAAACCCTATAATTTGTTTAAGAAACACTAATTTATGGTTT
66 GAGGTTGCCAATTGTCGACTTCCTTAAACCCTAGAATTTGTTTAAGAAACACTAATTTAT-GATT
* * * *
6940 TTGAAAAAAAAGTGTGATTCTAGAGTTTGATTACAAAATTGAACCATTATTTAATGAAATTGGCG
130 TTGAAAAAAAAGTATGGTTCTAGAGTTTGATTACAAAATTGAACCATTATTTAATGAAATAGGCA
* * * *
7005 AGAATAACACACTAAATTCACATACCAAAAAAATAAATTTAATATCAA-TTTTCCACCAATAGTT
195 AGAACAACATACTAAATTCACATACCAAAAAAATAAATTTAATATCAATTTTTCCACAAATAATT
7069 GCAAACAAAAAATAAATAAATTCAACATTGATACAAAAAATTAAATTTAATATTTTATCTATTAT
260 GCAAACAAAAAATAAATAAATTCAACATTGATACAAAAAATTAAATTTAATATTTTATCTATTAT
*
7134 AAAAATTCAATACTTAAATTTTTTATTTTTTC-AAAAC
325 AAAAATTCAATACTTAAATTTTTTATTTTTCCAAAAAC
* * *
7171 AACATTCTAATATCCATTTTCTTCATAACCTTAAGTTCAAGGAAAATTATTAGAACTCGGATTAA
1 AACATTCTAAAATCCATTTTCTCCATAACCTTAAGTTCATGGAAAATTATTAGAACTCGGATTAA
* * *
7236 GAGGTTGTCAATTGTCGACTTCCTTACACCCTAGAATTTGTTTAAGAAACAGTAATTTATGATTT
66 GAGGTTGCCAATTGTCGACTTCCTTAAACCCTAGAATTTGTTTAAGAAACACTAATTTATGATTT
7301 TGAAAAAAAAAAGTATGGTTCTAGAGTTTGATTACAAAATTGAACCATTATTTAATGAAATAGGC
131 TG--AAAAAAAAGTATGGTTCTAGAGTTTGATTACAAAATTGAACCATTATTTAATGAAATAGGC
*
7366 AAGAACAACATACTAAATTCACATACCAAAAAATTAAATTTAATATCAATTTTTCCACAAATAAT
194 AAGAACAACATACTAAATTCACATACCAAAAAAATAAATTTAATATCAATTTTTCCACAAATAAT
* *
7431 TGCAAACAAAAAATAAATAAATTCAACTTTGATAAAAAAAATTAAATTTAATATTTTATCTATTA
259 TGCAAACAAAAAATAAATAAATTCAACATTGATACAAAAAATTAAATTTAATATTTTATCTATTA
*
7496 TAAAAATTCAATACTTAAATTTTTTATTTTTTCCAAAAAT
324 TAAAAATTCAATACTTAAATTTTTTA-TTTTTCCAAAAAC
*
7536 AACATTCTAAAATCCATTTTCTCCATAACCTTAAGTTCATGGAAAATTATTAGAACTCAGATTAA
1 AACATTCTAAAATCCATTTTCTCCATAACCTTAAGTTCATGGAAAATTATTAGAACTCGGATTAA
* * *
7601 GAGGGTACCAATTGTCGACTTCCTTAAACCCTAGAATTTGTTTAAGAAACACTAATTTATGGTTT
66 GAGGTTGCCAATTGTCGACTTCCTTAAACCCTAGAATTTGTTTAAGAAACACTAATTTATGATTT
* * *
7666 TG-AAAAAAGGTATGGTTCTAGAGTTTGATTCCAAAATTGAACCATTATTTAATGAAATAGACAA
131 TGAAAAAAAAGTATGGTTCTAGAGTTTGATTACAAAATTGAACCATTATTTAATGAAATAGGCAA
* *
7730 GAACAACTTACTAAATTCACATACCAAAAAAATAAATTTAATATCAATTTTTTCACAAATAATTG
196 GAACAACATACTAAATTCACATACCAAAAAAATAAATTTAATATCAATTTTTCCACAAATAATTG
7795 CAAAC-AAAAATAAATAAATTCAACATTGATACAAAAAATTAAATTTAATATTTTATCTATTATA
261 CAAACAAAAAATAAATAAATTCAACATTGATACAAAAAATTAAATTTAATATTTTATCTATTATA
7859 AAAATTCAATACTTAAATTTTTTATTTTTCCAAAAAC
326 AAAATTCAATACTTAAATTTTTTATTTTTCCAAAAAC
* * *
7896 AACATTCTAAAATCCATTTTATCCATAACCCTAAGTTCATGGAAAATTATTA-AGCCTCGGATTA
1 AACATTCTAAAATCCATTTTCTCCATAACCTTAAGTTCATGGAAAATTATTAGA-ACTCGGATTA
* * * *
7960 AGAGGTTGCCAATTTTCGACTTCTTTAAACTCTAGAATTTGTTTAAGAAACACTAATTTATAATT
65 AGAGGTTGCCAATTGTCGACTTCCTTAAACCCTAGAATTTGTTTAAGAAACACTAATTTATGATT
* *
8025 TTG-AAAAAAAGCATGGTTCTAGAGTTTGATTACAAAATTGAACCCTTATTTAATGAAATAGGCA
130 TTGAAAAAAAAGTATGGTTCTAGAGTTTGATTACAAAATTGAACCATTATTTAATGAAATAGGCA
* * *
8089 AGAACAACATACTAAATT-AGCATA-C-AAAAAGTAAATTTAAAATCAATTTTTCCACAAATAGT
195 AGAACAACATACTAAATTCA-CATACCAAAAAAATAAATTTAATATCAATTTTTCCACAAATAAT
* *
8151 TACAAATAAAAAATTAAATAAATTCAACATTGATA-AAAAAATTAAATTTAATATTTTATCTATT
259 TGCAAACAAAAAA-TAAATAAATTCAACATTGATACAAAAAATTAAATTTAATATTTTATCTATT
*
8215 ATAAAAACTCAATACTTAAATTTTTTATATTTT-CAAAAAC
323 ATAAAAATTCAATACTTAAATTTTTTAT-TTTTCCAAAAAC
*
8255 AACATACTAAA
1 AACATTCTAAA
8266 CTTGGATATT
Statistics
Matches: 1017, Mismatches: 68, Indels: 22
0.92 0.06 0.02
Matches are distributed among these distances:
358 38 0.04
359 81 0.08
360 239 0.24
361 196 0.19
362 229 0.23
363 102 0.10
364 6 0.01
365 126 0.12
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.35
Consensus pattern (362 bp):
AACATTCTAAAATCCATTTTCTCCATAACCTTAAGTTCATGGAAAATTATTAGAACTCGGATTAA
GAGGTTGCCAATTGTCGACTTCCTTAAACCCTAGAATTTGTTTAAGAAACACTAATTTATGATTT
TGAAAAAAAAGTATGGTTCTAGAGTTTGATTACAAAATTGAACCATTATTTAATGAAATAGGCAA
GAACAACATACTAAATTCACATACCAAAAAAATAAATTTAATATCAATTTTTCCACAAATAATTG
CAAACAAAAAATAAATAAATTCAACATTGATACAAAAAATTAAATTTAATATTTTATCTATTATA
AAAATTCAATACTTAAATTTTTTATTTTTCCAAAAAC
Found at i:11007 original size:29 final size:31
Alignment explanation
Indices: 10972--11030 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
10962 TTAAAGACAA
10972 ATCAAAC-TTTTC-AAAATGATCAAATAAGG
1 ATCAAACATTTTCGAAAATGATCAAATAAGG
* *
11001 ATCAAACATTTTCGAAAGTGCTCAAATAAG
1 ATCAAACATTTTCGAAAATGATCAAATAAG
11031 AACTTTTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 7 0.27
30 5 0.19
31 14 0.54
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (31 bp):
ATCAAACATTTTCGAAAATGATCAAATAAGG
Found at i:12051 original size:12 final size:12
Alignment explanation
Indices: 12034--12064 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
12024 TGGATGTAGA
12034 CTACGATAGTGC
1 CTACGATAGTGC
12046 CTACGATAGTGC
1 CTACGATAGTGC
*
12058 CAACGAT
1 CTACGAT
12065 CGAGGAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.23
Consensus pattern (12 bp):
CTACGATAGTGC
Found at i:22683 original size:25 final size:24
Alignment explanation
Indices: 22626--22684 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
22616 AAAAATAGAT
* *
22626 TATA-TATTATTTTTCTAATATTA
1 TATATTATAATTTTTCTAATATCA
22649 TATATTATAATTTTTACTAAT-TCA
1 TATATTATAATTTTT-CTAATATCA
*
22673 TATTTTAATAAT
1 TATATT-ATAAT
22685 AATTATATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 4 0.13
24 16 0.53
25 10 0.33
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (24 bp):
TATATTATAATTTTTCTAATATCA
Found at i:22753 original size:57 final size:58
Alignment explanation
Indices: 22658--22802 Score: 181
Period size: 58 Copynumber: 2.5 Consensus size: 58
22648 ATATATTATA
* *
22658 ATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAAATATTATTAAATT-A-T-AT
1 ATTTTTATTAAATT-ATA-TTTAATAATAATTATATT-AAAATATAATTAAATTAATTAAT
* * *
22715 ATTATTTTTTAAATTGTATTTAATAATAATTATGTTAAAATATAATTAAATTAATTAAT
1 ATT-TTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAATTAAT
22774 ATTTTTATTAAATTATATTTAATAATAAT
1 ATTTTTATTAAATTATATTTAATAATAAT
22803 CATTAAAATT
Statistics
Matches: 76, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
56 15 0.20
57 21 0.28
58 31 0.41
59 9 0.12
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (58 bp):
ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAATTAAT
Found at i:22809 original size:56 final size:53
Alignment explanation
Indices: 22652--22816 Score: 163
Period size: 56 Copynumber: 2.9 Consensus size: 53
22642 AATATTATAT
* *
22652 ATTATA-ATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAAATATTATTAA
1 ATTATATATTTTTATTAAATT-ATA-TTTAATAATAA-T-TATT-AAAATATAATTAA
* *
22708 ATTATATATTATTTTTTAAATTGTATTTAATAATAATTATGTTAAAATATAATTAA
1 ATTATATATT-TTTATTAAATTATATTTAATAATAATTA--TTAAAATATAATTAA
* *
22764 ATTAATTAATATTTTTATTAAATTATATTTAATAATAATCATTAAAATTTAAT
1 ATT-A-T-ATATTTTTATTAAATTATATTTAATAATAATTATTAAAATATAAT
22817 AACAATAATC
Statistics
Matches: 93, Mismatches: 8, Indels: 16
0.79 0.07 0.14
Matches are distributed among these distances:
55 2 0.02
56 33 0.35
57 17 0.18
58 32 0.34
59 9 0.10
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (53 bp):
ATTATATATTTTTATTAAATTATATTTAATAATAATTATTAAAATATAATTAA
Found at i:22993 original size:16 final size:16
Alignment explanation
Indices: 22972--23025 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
22962 TGAATTACTG
22972 ATTACAGTTCTATTCC
1 ATTACAGTTCTATTCC
22988 ATTACAGCTT-TATTCC
1 ATTACAG-TTCTATTCC
*
23004 ATTACACTTCTATTCC
1 ATTACAGTTCTATTCC
23020 ATTACA
1 ATTACA
23026 ACGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
15 2 0.06
16 31 0.89
17 2 0.06
ACGTcount: A:0.28, C:0.26, G:0.04, T:0.43
Consensus pattern (16 bp):
ATTACAGTTCTATTCC
Found at i:23410 original size:4 final size:4
Alignment explanation
Indices: 23401--23431 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
23391 TTTAAATTCA
23401 AATT AATT AATT AATT AATT AATT AAATT AA
1 AATT AATT AATT AATT AATT AATT -AATT AA
23432 AACTGTAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (4 bp):
AATT
Found at i:23418 original size:12 final size:13
Alignment explanation
Indices: 23395--23431 Score: 58
Period size: 12 Copynumber: 2.8 Consensus size: 13
23385 GATACTTTTA
23395 AATTCAAATTAATT
1 AATT-AAATTAATT
23409 AATT-AATTAATT
1 AATTAAATTAATT
23421 AATTAAATTAA
1 AATTAAATTAA
23432 AACTGTAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.55
13 6 0.27
14 4 0.18
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (13 bp):
AATTAAATTAATT
Found at i:26805 original size:12 final size:12
Alignment explanation
Indices: 26788--26812 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
26778 AGGATTAACT
26788 AAATCTTCTCCC
1 AAATCTTCTCCC
26800 AAATCTTCTCCC
1 AAATCTTCTCCC
26812 A
1 A
26813 GTTGACCTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.40, G:0.00, T:0.32
Consensus pattern (12 bp):
AAATCTTCTCCC
Found at i:36614 original size:14 final size:14
Alignment explanation
Indices: 36597--36624 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
36587 TAAGTAATTG
36597 TGTATAAAATTATA
1 TGTATAAAATTATA
36611 TGTATAAAATTATA
1 TGTATAAAATTATA
36625 CAAAATCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (14 bp):
TGTATAAAATTATA
Found at i:36906 original size:39 final size:40
Alignment explanation
Indices: 36852--36927 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 40
36842 CTAAGACGAA
*
36852 AAAATCACGAAAATAACTTTACACATTTTAAATAATTGAG
1 AAAATCACGAAAATAACCTTACACATTTTAAATAATTGAG
* **
36892 AAAATTAC-AAAATAACCTTACATGTTTTAAATAATT
1 AAAATCACGAAAATAACCTTACACATTTTAAATAATT
36928 TATATTATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
39 25 0.78
40 7 0.22
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.33
Consensus pattern (40 bp):
AAAATCACGAAAATAACCTTACACATTTTAAATAATTGAG
Found at i:36938 original size:39 final size:40
Alignment explanation
Indices: 36852--36945 Score: 100
Period size: 39 Copynumber: 2.4 Consensus size: 40
36842 CTAAGACGAA
* * *
36852 AAAATCACGAAAATAACTTTACACATTTTAAATAATTGAG
1 AAAATTACTAAAATAACCTTACACATTTTAAATAATTGAG
** * *
36892 AAAATTAC-AAAATAACCTTACATGTTTTAAATAATTTAT
1 AAAATTACTAAAATAACCTTACACATTTTAAATAATTGAG
**
36931 ATTATTACTAAAATA
1 AAAATTACTAAAATA
36946 TTATTATTAA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
39 32 0.71
40 13 0.29
ACGTcount: A:0.50, C:0.11, G:0.04, T:0.35
Consensus pattern (40 bp):
AAAATTACTAAAATAACCTTACACATTTTAAATAATTGAG
Found at i:37711 original size:22 final size:22
Alignment explanation
Indices: 37669--37709 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
37659 TTATATATAA
37669 ATTATAAAATTCATAAAAAATT
1 ATTATAAAATTCATAAAAAATT
*
37691 ATTAT-AAATTTATAAAAAA
1 ATTATAAAATTCATAAAAAA
37710 ATAAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
ATTATAAAATTCATAAAAAATT
Found at i:37713 original size:29 final size:29
Alignment explanation
Indices: 37659--37738 Score: 78
Period size: 27 Copynumber: 2.8 Consensus size: 29
37649 AACCATATTT
**
37659 TTATATATAAA-TTATAAAATTCATAAAAAA
1 TTAT-TATAAATTTATAAAA-AAATAAAAAA
37689 TTATTATAAATTTATAAAAAAATAAAAAA
1 TTATTATAAATTTATAAAAAAATAAAAAA
*
37718 --ATT-TAGATGTTATAAAAAAAT
1 TTATTATAAAT-TTATAAAAAAAT
37739 TTAGAAGAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
26 4 0.09
27 15 0.33
29 14 0.31
30 12 0.27
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (29 bp):
TTATTATAAATTTATAAAAAAATAAAAAA
Found at i:37880 original size:25 final size:25
Alignment explanation
Indices: 37849--37899 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
37839 ATAAAATTAT
37849 TAAAAATTAAT-AAAAGTTTATAAAA
1 TAAAAATTAATGAAAAG-TTATAAAA
*
37874 TAAAAATTATTGAAAAGTTATAAAA
1 TAAAAATTAATGAAAAGTTATAAAA
37899 T
1 T
37900 TTATAGGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (25 bp):
TAAAAATTAATGAAAAGTTATAAAA
Found at i:38451 original size:10 final size:10
Alignment explanation
Indices: 38436--38494 Score: 54
Period size: 10 Copynumber: 5.9 Consensus size: 10
38426 TAATTTCTAT
38436 ATTTTTAATA
1 ATTTTTAATA
38446 ATTTTTAA-A
1 ATTTTTAATA
38455 ATTATTT-ATAA
1 ATT-TTTAAT-A
38466 ATTTTTAAT-
1 ATTTTTAATA
38475 ATTTTT-ATGA
1 ATTTTTAAT-A
38485 ATTTTATAAT
1 ATTTT-TAAT
38495 TTATATTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
8 2 0.05
9 11 0.27
10 19 0.46
11 7 0.17
12 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:38468 original size:20 final size:19
Alignment explanation
Indices: 38436--38489 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
38426 TAATTTCTAT
38436 ATTTTTA-ATAATTTTTAAA
1 ATTTTTATA-AATTTTTAAA
*
38455 ATTATTTATAAATTTTTAAT
1 ATT-TTTATAAATTTTTAAA
*
38475 ATTTTTATGAATTTT
1 ATTTTTATAAATTTT
38490 ATAATTTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 14 0.45
20 16 0.52
21 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
ATTTTTATAAATTTTTAAA
Found at i:38470 original size:19 final size:18
Alignment explanation
Indices: 38436--38496 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
38426 TAATTTCTAT
*
38436 ATTTTTAATAATTTTTAAA
1 ATTTTT-ATAAATTTTAAA
*
38455 ATTATTTATAAATTTTTAAT
1 ATT-TTTATAAA-TTTTAAA
* *
38475 ATTTTTATGAATTTTATA
1 ATTTTTATAAATTTTAAA
38493 ATTT
1 ATTT
38497 ATATTTTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 9 0.26
19 14 0.40
20 12 0.34
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
ATTTTTATAAATTTTAAA
Found at i:39252 original size:127 final size:127
Alignment explanation
Indices: 39027--39280 Score: 438
Period size: 127 Copynumber: 2.0 Consensus size: 127
39017 GAGCAATCCT
39027 TTTGTAACAGAATTTTGGGGCATTTTTTATGGAATCATGCTTTTGCTTGAACAAGGATTCAAAAA
1 TTTGTAACAGAATTTTGGGGCATTTTTTATGGAATCATGCTTTTGCTTGAACAAGGATTCAAAAA
* *
39092 AGACATAATTAATACTGGCAATTTAAAGGTTGTAAAGGCACTAAATGATTCCAATAT-AAAA
66 AGACATAATTAATACTGACAATTTAAAGGTTGTAAAGGCACTAAATAATTCCAATATGAAAA
* *
39153 TTTGTAGCAGAATTTTGGGGCATTTTTTTATGGAATCATGCTTTTGCTTGAACGAGGATTCAAAA
1 TTTGTAACAGAATTTTGGGGCA-TTTTTTATGGAATCATGCTTTTGCTTGAACAAGGATTCAAAA
* *
39218 AGGACATAATTAATACTGACAATTTAGAGGTTGTAAAGGCACTAAATAATTCCAATATGAAAA
65 AAGACATAATTAATACTGACAATTTAAAGGTTGTAAAGGCACTAAATAATTCCAATATGAAAA
39281 ACTTGAGAAT
Statistics
Matches: 120, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
126 21 0.17
127 95 0.79
128 4 0.03
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (127 bp):
TTTGTAACAGAATTTTGGGGCATTTTTTATGGAATCATGCTTTTGCTTGAACAAGGATTCAAAAA
AGACATAATTAATACTGACAATTTAAAGGTTGTAAAGGCACTAAATAATTCCAATATGAAAA
Found at i:47020 original size:22 final size:21
Alignment explanation
Indices: 46995--47052 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 21
46985 TTTTAATGAT
46995 AATAATATATTAAATA-AAATAA
1 AATAATAT-TTAAA-AGAAATAA
*
47017 AATAATTTTTTAAAAGTAAATAA
1 AATAA-TATTTAAAAG-AAATAA
*
47040 AATAAAATTTAAA
1 AATAATATTTAAA
47053 CTATTTATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 1 0.03
22 16 0.53
23 13 0.43
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
AATAATATTTAAAAGAAATAA
Found at i:47791 original size:23 final size:23
Alignment explanation
Indices: 47765--47810 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
47755 TTAGTTATCA
*
47765 GTTATCAGCAGTTACTGTTAGTT
1 GTTATCAACAGTTACTGTTAGTT
* * *
47788 GTTATTAACTGTTATTGTTAGTT
1 GTTATCAACAGTTACTGTTAGTT
47811 AACAGCAGTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.09, G:0.20, T:0.50
Consensus pattern (23 bp):
GTTATCAACAGTTACTGTTAGTT
Found at i:47800 original size:17 final size:17
Alignment explanation
Indices: 47774--47813 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
47764 AGTTATCAGC
47774 AGTT-ACTGTTAGTTGTT
1 AGTTAACTGTTA-TTGTT
47791 A-TTAACTGTTATTGTT
1 AGTTAACTGTTATTGTT
47807 AGTTAAC
1 AGTTAAC
47814 AGCAGTTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.25, C:0.07, G:0.17, T:0.50
Consensus pattern (17 bp):
AGTTAACTGTTATTGTT
Found at i:55918 original size:29 final size:30
Alignment explanation
Indices: 55885--55951 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
55875 AAAAACAAAG
* *
55885 TAAAAGGGTTTAAA-AAATTTAATGAAA-AA
1 TAAAAGGGTTTAAATAAA-TAAATAAAAGAA
*
55914 TAAAAGGATTTAAATAAATAAATAAAAGAA
1 TAAAAGGGTTTAAATAAATAAATAAAAGAA
55944 TAAAAGGG
1 TAAAAGGG
55952 CCAAATTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 20 0.62
30 12 0.38
ACGTcount: A:0.61, C:0.00, G:0.15, T:0.24
Consensus pattern (30 bp):
TAAAAGGGTTTAAATAAATAAATAAAAGAA
Found at i:59228 original size:27 final size:27
Alignment explanation
Indices: 59190--59289 Score: 128
Period size: 27 Copynumber: 3.7 Consensus size: 27
59180 GAGTAATCTG
*
59190 ATTCTGGCTCGAAAAAGCGTTATTCTA
1 ATTCTGGCTCGAAAGAGCGTTATTCTA
* *
59217 ATTCTGGCTCGAAAGAGGGTTATTCTG
1 ATTCTGGCTCGAAAGAGCGTTATTCTA
* *
59244 ATTCTGGCTTGAAAGAGCATTATTCTA
1 ATTCTGGCTCGAAAGAGCGTTATTCTA
* *
59271 ATTTTGGGCTCGTAAGAGC
1 ATTCT-GGCTCGAAAGAGC
59290 AACCATTCTA
Statistics
Matches: 62, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
27 51 0.82
28 11 0.18
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (27 bp):
ATTCTGGCTCGAAAGAGCGTTATTCTA
Found at i:59350 original size:24 final size:24
Alignment explanation
Indices: 59277--59409 Score: 175
Period size: 23 Copynumber: 5.7 Consensus size: 24
59267 TCTAATTTTG
59277 GGCTCGTAAGAGC-AACCATTCTA
1 GGCTCGTAAGAGCTAACCATTCTA
* *
59300 GGCTCGTAAGAGCTAA-CATTTTG
1 GGCTCGTAAGAGCTAACCATTCTA
59323 GGCTCGTAAGAGCTAACCATTCTA
1 GGCTCGTAAGAGCTAACCATTCTA
*
59347 GGCTCGTAAGAGCTAA-CATTCTG
1 GGCTCGTAAGAGCTAACCATTCTA
*
59370 GGCTCATAAGAGCTAACC-TATCTA
1 GGCTCGTAAGAGCTAACCAT-TCTA
* *
59394 GGCTTGTATGAGCTAA
1 GGCTCGTAAGAGCTAA
59410 TTTTGTTTAG
Statistics
Matches: 96, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
23 56 0.58
24 40 0.42
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (24 bp):
GGCTCGTAAGAGCTAACCATTCTA
Found at i:59355 original size:47 final size:47
Alignment explanation
Indices: 59271--59409 Score: 219
Period size: 47 Copynumber: 3.0 Consensus size: 47
59261 CATTATTCTA
59271 ATTTTGGGCTCGTAAGAGC-AACCATTCTAGGCTCGTAAGAGCTAAC
1 ATTTTGGGCTCGTAAGAGCTAACCATTCTAGGCTCGTAAGAGCTAAC
59317 ATTTTGGGCTCGTAAGAGCTAACCATTCTAGGCTCGTAAGAGCTAAC
1 ATTTTGGGCTCGTAAGAGCTAACCATTCTAGGCTCGTAAGAGCTAAC
* * * *
59364 ATTCTGGGCTCATAAGAGCTAACC-TATCTAGGCTTGTATGAGCTAA
1 ATTTTGGGCTCGTAAGAGCTAACCAT-TCTAGGCTCGTAAGAGCTAA
59410 TTTTGTTTAG
Statistics
Matches: 87, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
46 20 0.23
47 67 0.77
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (47 bp):
ATTTTGGGCTCGTAAGAGCTAACCATTCTAGGCTCGTAAGAGCTAAC
Found at i:60885 original size:84 final size:84
Alignment explanation
Indices: 60744--60929 Score: 220
Period size: 84 Copynumber: 2.2 Consensus size: 84
60734 TCTTGGTTTA
60744 GGGGTAAAAGATTGGAT-AGTGGCTTCAATCTACCTCATGATCGGGGTAAGAGATTGGACGGAA-
1 GGGGT-AAAGATTGGATGAGTGGCTTCAATCTACCTCATGATCGGGGTAAGAGATTGGA--GAAT
60807 G-CTTCAATATGCCCTATGAAC
63 GTCTTCAATATGCCCTATGAAC
* * * *
60828 GGGGTAAGAGATTGGATGA-TGTCTTCAATCTGCC-CGATGATCGGGGTAAGAGGTTGGATAATG
1 GGGGTAA-AGATTGGATGAGTGGCTTCAATCTACCTC-ATGATCGGGGTAAGAGATTGGAGAATG
* **
60891 TCTTCAATCTGCCCTATGATT
64 TCTTCAATATGCCCTATGAAC
60912 GGGGTTAAAGATTGGATG
1 GGGG-TAAAGATTGGATG
60930 GCTTCAGTCT
Statistics
Matches: 89, Mismatches: 7, Indels: 12
0.82 0.06 0.11
Matches are distributed among these distances:
82 2 0.02
83 4 0.04
84 79 0.89
85 4 0.04
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.28
Consensus pattern (84 bp):
GGGGTAAAGATTGGATGAGTGGCTTCAATCTACCTCATGATCGGGGTAAGAGATTGGAGAATGTC
TTCAATATGCCCTATGAAC
Found at i:61097 original size:38 final size:37
Alignment explanation
Indices: 61049--61328 Score: 134
Period size: 38 Copynumber: 7.2 Consensus size: 37
61039 ATTGGTGTCT
61049 CTTCAATCTACCATCTGATTAGGGTAAAAGATTAAATG
1 CTTCAATCTACC-TCTGATTAGGGTAAAAGATTAAATG
* * **
61087 CTTCAATCTACCCCATGATCAGGGTAAAAGATTGATGTG
1 CTTCAATCTACCTC-TGATTAGGGTAAAAGATT-AAATG
* * * *
61126 TCTTCAATCTGCCCTCTGTTTAGGGTAAATGATTAGATG
1 -CTTCAATCT-ACCTCTGATTAGGGTAAAAGATTAAATG
* * ** ** ***
61165 CTTCAATCT-GCTCCATAATCGGGGTATGAGATTGGTGTG
1 CTTCAATCTACCT-C-TGATTAGGGTAAAAGATT-AAATG
* * ** *
61204 TCTTCAATCGACCTTCTGATTAAGGTAAAAGATTGGATT
1 -CTTCAATCTACC-TCTGATTAGGGTAAAAGATTAAATG
* * ***
61243 TTTCAATCTACC-CATGATT-GAGGTAAGAGATTGGTGTG
1 CTTCAATCTACCTC-TGATTAG-GGTAAAAGATT-AAATG
* * *
61281 TCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGAATA
1 -CTTCAATCT-ACCTCTGATTAGGGTAAAAGATTAAATG
61320 CTTCAATCT
1 CTTCAATCT
61329 TCCCTATGAT
Statistics
Matches: 179, Mismatches: 46, Indels: 34
0.69 0.18 0.13
Matches are distributed among these distances:
36 3 0.02
37 17 0.09
38 70 0.39
39 20 0.11
40 61 0.34
41 7 0.04
42 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.34
Consensus pattern (37 bp):
CTTCAATCTACCTCTGATTAGGGTAAAAGATTAAATG
Found at i:61120 original size:78 final size:78
Alignment explanation
Indices: 60745--61432 Score: 535
Period size: 78 Copynumber: 8.7 Consensus size: 78
60735 CTTGGTTTAG
* * *
60745 GGGTAAAAGATTGGATAGTGGCTTCAATCTACCTCATGATCGGGGTAAGAGATTGGACG-GAAGC
1 GGGTAAAAGATTGG--A-T-GCTTCAATCTACCCCATGATCGGGGTAAGAGATTGG-TGTG--TC
* * * ***
60809 TTCAATATGCCCTATGAACG
59 TTCAATCTACCCTCTGATTA
* * * * *
60829 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCGATGATCGGGGTAAGAGGTTGGATAATGTCT
1 GGGTAAAAGATT-G--GATG-CTTCAATCTACCCCATGATCGGGGTAAGAGATTGG-T-GTGTCT
* * *
60894 TCAATCTGCCCTATGATTG
60 TCAATCTACCCTCTGATTA
* * * * * * * * *
60913 GGGTTAAAGATTGGATGGCTTCAGTCTGCTCCATTA-CTGGCTAAAAGATTAGAT-TGAT-TTCA
1 GGGTAAAAGATTGGAT-GCTTCAATCTACCCCATGATCGGGGTAAGAGATT-GGTGTG-TCTTCA
* * **
60975 ATTTTCCC-CATGATCG
63 ATCTACCCTC-TGATTA
* * * * ** * *
60991 GGGTAAGAGATTGGACGACTGCAATTTGGCCCATGATCTGGGTAAGAGATTGGTGTCTCTTCAAT
1 GGGTAAAAGATTGGATG-CTTCAATCTACCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAAT
*
61056 CTACCATCTGATTA
65 CTACCCTCTGATTA
** * * *
61070 GGGTAAAAGATTAAATGCTTCAATCTACCCCATGATCAGGGTAAAAGATTGATGTGTCTTCAATC
1 GGGTAAAAGATTGGATGCTTCAATCTACCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATC
* *
61135 TGCCCTCTGTTTA
66 TACCCTCTGATTA
* * * * * *
61148 GGGTAAATGATTAGATGCTTCAATCTGCTCCATAATCGGGGTATGAGATTGGTGTGTCTTCAATC
1 GGGTAAAAGATTGGATGCTTCAATCTACCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATC
* *
61213 GACCTTCTGATTA
66 TACCCTCTGATTA
* ** * *
61226 AGGTAAAAGATTGGATTTTTCAATCTA-CCCATGATTGAGGTAAGAGATTGGTGTGTCTTCAATC
1 GGGTAAAAGATTGGATGCTTCAATCTACCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATC
*
61290 TGCCCTCTGATTA
66 TACCCTCTGATTA
* * * *
61303 GGGTAAAAGATTGAATACTTCAATCTTCCCTATGATCGGGGTAAGAGATTGGTGTGTCTTCAATC
1 GGGTAAAAGATTGGATGCTTCAATCTACCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATC
* *
61368 -AGCCTTCTAATTA
66 TA-CCCTCTGATTA
* * *
61381 GTGTAAAAGATTGGATGCTTTAATCTGCCCCATGATCGGGGTAAGAGATTGG
1 GGGTAAAAGATTGGATGCTTCAATCTACCCCATGATCGGGGTAAGAGATTGG
61433 ATGGTAGCTT
Statistics
Matches: 484, Mismatches: 103, Indels: 40
0.77 0.16 0.06
Matches are distributed among these distances:
77 65 0.13
78 270 0.56
79 40 0.08
80 12 0.02
81 18 0.04
82 1 0.00
83 2 0.00
84 72 0.15
85 2 0.00
86 1 0.00
87 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.32
Consensus pattern (78 bp):
GGGTAAAAGATTGGATGCTTCAATCTACCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATC
TACCCTCTGATTA
Found at i:61324 original size:155 final size:153
Alignment explanation
Indices: 61019--61432 Score: 505
Period size: 155 Copynumber: 2.7 Consensus size: 153
61009 CTGCAATTTG
* * * * **
61019 GCCCATGATCTGGGTAAGAGATTGGTGTCTCTTCAATCTACCATCTGATTAGGGTAAAAGATTAA
1 GCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATC-ACCTTCTGATTAAGGTAAAAGATTGG
* * * *
61084 ATGC-TTCAATCTACCCCATGA-TCAGGGTAAAAGATTGATGTGTCTTCAATCTGCCCTCTGTTT
65 AT-CTTTCAATCTA-CCCATGATTGA-GGTAAGAGATTGGTGTGTCTTCAATCTGCCCTCTGATT
* *
61147 AGGGTAAATGATTAGATGCTTCAATCT
127 AGGGTAAAAGATTAGATACTTCAATCT
* *
61174 GCTCCATAATCGGGGTATGAGATTGGTGTGTCTTCAATCGACCTTCTGATTAAGGTAAAAGATTG
1 GC-CCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATC-ACCTTCTGATTAAGGTAAAAGATTG
*
61239 GATTTTTCAATCTACCCATGATTGAGGTAAGAGATTGGTGTGTCTTCAATCTGCCCTCTGATTAG
64 GATCTTTCAATCTACCCATGATTGAGGTAAGAGATTGGTGTGTCTTCAATCTGCCCTCTGATTAG
61304 GGTAAAAGATT-GAATACTTCAATCT
129 GGTAAAAGATTAG-ATACTTCAATCT
* *
61329 TCCCTATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCAGCCTTCTAATT-AGTGTAAAAGATT
1 GCCC-ATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCA-CCTTCTGATTAAG-GTAAAAGATT
* * *
61393 GGATGCTTT-AATCTGCCCCATGATCGGGGTAAGAGATTGG
63 GGAT-CTTTCAATCT-ACCCATGATTGAGGTAAGAGATTGG
61433 ATGGTAGCTT
Statistics
Matches: 226, Mismatches: 24, Indels: 17
0.85 0.09 0.06
Matches are distributed among these distances:
154 6 0.03
155 128 0.57
156 92 0.41
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (153 bp):
GCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCACCTTCTGATTAAGGTAAAAGATTGGA
TCTTTCAATCTACCCATGATTGAGGTAAGAGATTGGTGTGTCTTCAATCTGCCCTCTGATTAGGG
TAAAAGATTAGATACTTCAATCT
Found at i:61756 original size:49 final size:49
Alignment explanation
Indices: 61703--62134 Score: 305
Period size: 49 Copynumber: 8.8 Consensus size: 49
61693 TCATCCTTAG
* *
61703 GGTATAAGATTCGCCGTTGTGGCCTCAATCTTTCCCTTCACATCTCTAA
1 GGTATAAGATTCGTCGTTGTGGCTTCAATCTTTCCCTTCACATCTCTAA
* * * *
61752 GGTATAAGGTTCGTCGTTGTGGCTTCAA-CTTTTCCCTCCACATCTTTAG
1 GGTATAAGATTCGTCGTTGTGGCTTCAATC-TTTCCCTTCACATCTCTAA
** * * * * * *
61801 GGTATAAGATTTATCATTGTTGTTTCAATCTTTCCCATCGCATCTCCAA
1 GGTATAAGATTCGTCGTTGTGGCTTCAATCTTTCCCTTCACATCTCTAA
** * *** ** * * *
61850 GGTACGAGGTTTACCGTTGCAGCTTCAACCTTTCCC-TCAACATCTCCAT
1 GGTATAAGATTCGTCGTTGTGGCTTCAATCTTTCCCTTC-ACATCTCTAA
* * * * * *
61899 GGTACAAGATTCGTTGTTGTGGCTTCAATCTTTGCCATCACATGTATAA
1 GGTATAAGATTCGTCGTTGTGGCTTCAATCTTTCCCTTCACATCTCTAA
* * * * * * *
61948 GGTACAAGGTTCTTTGTTGCT-GCTTCAACCTTTCCCTCCACATCTCTAT
1 GGTATAAGATTCGTCGTTG-TGGCTTCAATCTTTCCCTTCACATCTCTAA
* * * **
61997 GGTACAAGATTCGTCGTTGCGGCTTCAATCTTTCCCATCATGTCTCTAA
1 GGTATAAGATTCGTCGTTGTGGCTTCAATCTTTCCCTTCACATCTCTAA
* * * * * * *
62046 GGT-TCAAGGTTTGTCGTTGCGGCTTCAACCTTTCCCTCCATATCTCTAG
1 GGTAT-AAGATTCGTCGTTGTGGCTTCAATCTTTCCCTTCACATCTCTAA
* * * * *
62095 GGTATTAGATTTGCCATTGTGGCTTCAATATTTCCCTTCA
1 GGTATAAGATTCGTCGTTGTGGCTTCAATCTTTCCCTTCA
62135 AACCTAGAAC
Statistics
Matches: 297, Mismatches: 78, Indels: 16
0.76 0.20 0.04
Matches are distributed among these distances:
48 3 0.01
49 289 0.97
50 5 0.02
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (49 bp):
GGTATAAGATTCGTCGTTGTGGCTTCAATCTTTCCCTTCACATCTCTAA
Found at i:61805 original size:98 final size:98
Alignment explanation
Indices: 61700--62130 Score: 475
Period size: 98 Copynumber: 4.4 Consensus size: 98
61690 TTCTCATCCT
* * * *
61700 TAGGGTATAAGATTCGCCGTTGTGGCCTCAATCTTTCCCTTCACATCTCTAAGGTATAAGGTTCG
1 TAGGGTATAAGATTCGTCGTTGTGGCTTCAATCTTTCCCATCACATCTCTAAGGTACAAGGTTCG
* * *
61765 TCGTTGTGGCTTCAACTTTTCCCTCCACATCTT
66 TCGTTGCGGCTTCAACCTTTCCCTCCACATCTC
** * * * * * * **
61798 TAGGGTATAAGATTTATCATTGTTGTTTCAATCTTTCCCATCGCATCTCCAAGGTACGAGGTTTA
1 TAGGGTATAAGATTCGTCGTTGTGGCTTCAATCTTTCCCATCACATCTCTAAGGTACAAGGTTCG
* * *
61863 CCGTTGCAGCTTCAACCTTTCCCTCAACATCTC
66 TCGTTGCGGCTTCAACCTTTCCCTCCACATCTC
* * * * * * * *
61896 CATGGTACAAGATTCGTTGTTGTGGCTTCAATCTTTGCCATCACATGTATAAGGTACAAGGTTCT
1 TAGGGTATAAGATTCGTCGTTGTGGCTTCAATCTTTCCCATCACATCTCTAAGGTACAAGGTTCG
* *
61961 TTGTTGCTGCTTCAACCTTTCCCTCCACATCTC
66 TCGTTGCGGCTTCAACCTTTCCCTCCACATCTC
* * * ** * *
61994 TATGGTACAAGATTCGTCGTTGCGGCTTCAATCTTTCCCATCATGTCTCTAAGGTTCAAGGTTTG
1 TAGGGTATAAGATTCGTCGTTGTGGCTTCAATCTTTCCCATCACATCTCTAAGGTACAAGGTTCG
*
62059 TCGTTGCGGCTTCAACCTTTCCCTCCATATCTC
66 TCGTTGCGGCTTCAACCTTTCCCTCCACATCTC
* * * * *
62092 TAGGGTATTAGATTTGCCATTGTGGCTTCAATATTTCCC
1 TAGGGTATAAGATTCGTCGTTGTGGCTTCAATCTTTCCC
62131 TTCAAACCTA
Statistics
Matches: 270, Mismatches: 63, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
98 270 1.00
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.37
Consensus pattern (98 bp):
TAGGGTATAAGATTCGTCGTTGTGGCTTCAATCTTTCCCATCACATCTCTAAGGTACAAGGTTCG
TCGTTGCGGCTTCAACCTTTCCCTCCACATCTC
Found at i:62676 original size:109 final size:110
Alignment explanation
Indices: 62513--62713 Score: 287
Period size: 109 Copynumber: 1.8 Consensus size: 110
62503 TGTTAGACCA
* * *
62513 CTAACCGTCATTTCAATGCAAAAATGCTTGAACAGGGTTATAAGGTGGATAAAATTGAATTTTAT
1 CTAACCGTCATTTCAATGCAAAAATGCTTGAACAGAGTCATAAGGCGGATAAAATTGAATTTTAT
62578 TAGAGAAAAAACTCGCATGAA-AAAAATTAAAAATCAGCGGTCCG
66 TAGAGAAAAAACTCGCATGAATAAAAATTAAAAATCAGCGGTCCG
* ** * * *
62622 CTAACCGTTATTTTGATGCAAAAATTCTTGAATAGAGTCGTAAGGCGGATAAAATTGAATTTTAT
1 CTAACCGTCATTTCAATGCAAAAATGCTTGAACAGAGTCATAAGGCGGATAAAATTGAATTTTAT
* **
62687 TATAGGCAAAACTCGCATGAATAAAAA
66 TAGAGAAAAAACTCGCATGAATAAAAA
62714 GAGTAAAAAT
Statistics
Matches: 79, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
109 74 0.94
110 5 0.06
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (110 bp):
CTAACCGTCATTTCAATGCAAAAATGCTTGAACAGAGTCATAAGGCGGATAAAATTGAATTTTAT
TAGAGAAAAAACTCGCATGAATAAAAATTAAAAATCAGCGGTCCG
Found at i:63042 original size:7 final size:7
Alignment explanation
Indices: 63030--63071 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
63020 CACCTCGAGC
63030 TCTTTTT
1 TCTTTTT
63037 TCTTTTCT
1 TCTTTT-T
63045 TC-TTTT
1 TCTTTTT
*
63051 T-TATTT
1 TCTTTTT
63057 TCTTTTT
1 TCTTTTT
63064 TCTTTTT
1 TCTTTTT
63071 T
1 T
63072 TGGGTGAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
6 6 0.20
7 21 0.70
8 3 0.10
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.83
Consensus pattern (7 bp):
TCTTTTT
Found at i:63050 original size:15 final size:15
Alignment explanation
Indices: 63030--63064 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
63020 CACCTCGAGC
*
63030 TCTTTTTTCTTTTCT
1 TCTTTTTTATTTTCT
63045 TCTTTTTTATTTTCT
1 TCTTTTTTATTTTCT
63060 T-TTTT
1 TCTTTT
63065 CTTTTTTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (15 bp):
TCTTTTTTATTTTCT
Found at i:63072 original size:20 final size:20
Alignment explanation
Indices: 63034--63071 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
63024 TCGAGCTCTT
63034 TTTTCTTTTCTTCTTTTTTA
1 TTTTCTTTTCTTCTTTTTTA
63054 TTTTCTTTT-TTCTTTTTT
1 TTTTCTTTTCTTCTTTTTT
63072 TGGGTGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (20 bp):
TTTTCTTTTCTTCTTTTTTA
Found at i:67668 original size:28 final size:29
Alignment explanation
Indices: 67624--67690 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 29
67614 TAATGAAAAC
* *
67624 AATAAACAAATATATACAAAT-AACA-TAA
1 AATAAATAAATAAATACAAATCAA-AGTAA
*
67652 AATGAATAAATAAATACAAATCAAAGTAA
1 AATAAATAAATAAATACAAATCAAAGTAA
67681 AATAAATAAA
1 AATAAATAAA
67691 GTGGTAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 19 0.58
29 14 0.42
ACGTcount: A:0.69, C:0.07, G:0.03, T:0.21
Consensus pattern (29 bp):
AATAAATAAATAAATACAAATCAAAGTAA
Found at i:67722 original size:18 final size:19
Alignment explanation
Indices: 67696--67732 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
67686 ATAAAGTGGT
*
67696 AAAATGATTAAA-TTAAAA
1 AAAAAGATTAAATTTAAAA
67714 AAAAAGATTAAATTTAAAA
1 AAAAAGATTAAATTTAAAA
67733 GGATAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (19 bp):
AAAAAGATTAAATTTAAAA
Found at i:67753 original size:34 final size:35
Alignment explanation
Indices: 67710--67776 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
67700 TGATTAAATT
* *
67710 AAAAAAAAAGATTAAATTTAAAAG-GATAAAAAAC
1 AAAAAAAAAGAGTAAATTTAAAAGAGACAAAAAAC
* *
67744 AAAATAAAAGAGTAATTTTAAAAGAGACAAAAA
1 AAAAAAAAAGAGTAAATTTAAAAGAGACAAAAA
67777 TAAAAGGAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 21 0.75
35 7 0.25
ACGTcount: A:0.69, C:0.03, G:0.10, T:0.18
Consensus pattern (35 bp):
AAAAAAAAAGAGTAAATTTAAAAGAGACAAAAAAC
Found at i:67766 original size:25 final size:26
Alignment explanation
Indices: 67736--67798 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 26
67726 TTTAAAAGGA
67736 TAAAAAACAAAATAAAAGAGTAATTT
1 TAAAAAACAAAATAAAAGAGTAATTT
67762 TAAAAGAGACAAAAATAAAAGGAGTAATTT
1 TAAAA-A-AC-AAAATAAAA-GAGTAATTT
*
67792 TAGAAAA
1 TAAAAAA
67799 GAATAAAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 5 0.16
27 1 0.03
28 3 0.09
29 10 0.31
30 13 0.41
ACGTcount: A:0.63, C:0.03, G:0.13, T:0.21
Consensus pattern (26 bp):
TAAAAAACAAAATAAAAGAGTAATTT
Found at i:67890 original size:21 final size:21
Alignment explanation
Indices: 67851--67891 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
67841 GGTTTAAAAA
*
67851 ATTTAAATGAAAAATAAAAGG
1 ATTTAAATGAAAAAAAAAAGG
67872 ATTTAAAT-AAATAAAAAAAG
1 ATTTAAATGAAA-AAAAAAAG
67892 AATAAAAGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (21 bp):
ATTTAAATGAAAAAAAAAAGG
Found at i:67896 original size:29 final size:29
Alignment explanation
Indices: 67795--67900 Score: 76
Period size: 30 Copynumber: 3.5 Consensus size: 29
67785 GTAATTTTAG
*
67795 AAAAGAATAAAA-GATTTAATTACACA-ATAA
1 AAAAGAATAAAAGGATTTAAATA-A-ATA-AA
*
67825 AAAAGCAAAGTAAAAGGGTTTAAA-AAATTTAAA
1 AAAAG--AA-TAAAAGGATTTAAATAAA--TAAA
*
67858 TGAAA-AATAAAAGGATTTAAATAAATAAA
1 -AAAAGAATAAAAGGATTTAAATAAATAAA
67887 AAAAGAATAAAAGG
1 AAAAGAATAAAAGG
67901 GCCAAGTTTA
Statistics
Matches: 61, Mismatches: 5, Indels: 21
0.70 0.06 0.24
Matches are distributed among these distances:
28 3 0.05
29 13 0.21
30 18 0.30
31 6 0.10
32 3 0.05
33 8 0.13
34 10 0.16
ACGTcount: A:0.64, C:0.03, G:0.12, T:0.21
Consensus pattern (29 bp):
AAAAGAATAAAAGGATTTAAATAAATAAA
Found at i:69857 original size:108 final size:109
Alignment explanation
Indices: 69676--69887 Score: 268
Period size: 108 Copynumber: 1.9 Consensus size: 109
69666 TAAAGAACAC
* * ** * *
69676 TTATCGATTTTAAAGTTGGATGTTCAATTACTTAGGTTCCATGAAAAACCATACTCAATACGTTA
1 TTATCGATTTTAAAGTAGGATGCTCAATTACTTAGGTT-CAAAAAAAACCATACCCAACACGTTA
*
69741 GGGCACAATTT-TTCGAGCTCCCTAAAATAAAAGAACATTAAGCGT
65 GGGCACAATTTCTT-GAACTCCCTAAAATAAAAGAACATTAAGCGT
* * *
69786 TTATCGATTTTAAA-TAGGATGCTCTATTATTTAGGTT-AAAAAAAACCCGTACCCAACACGTTA
1 TTATCGATTTTAAAGTAGGATGCTCAATTACTTAGGTTCAAAAAAAA-CCATACCCAACACGTTA
* *
69849 GGGTACAATTTCTTGAATTCCCTAAAATAAAAGAACATT
65 GGGCACAATTTCTTGAACTCCCTAAAATAAAAGAACATT
69888 GCCTTGATAT
Statistics
Matches: 88, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
107 6 0.07
108 47 0.53
109 21 0.24
110 14 0.16
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (109 bp):
TTATCGATTTTAAAGTAGGATGCTCAATTACTTAGGTTCAAAAAAAACCATACCCAACACGTTAG
GGCACAATTTCTTGAACTCCCTAAAATAAAAGAACATTAAGCGT
Found at i:70115 original size:19 final size:20
Alignment explanation
Indices: 70083--70121 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
70073 ATAAAGTGAT
*
70083 AAAATGATTAAAATTTAAAA
1 AAAAGGATTAAAATTTAAAA
70103 AAAAGGATT-AAATTTAAAA
1 AAAAGGATTAAAATTTAAAA
70122 GGATAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (20 bp):
AAAAGGATTAAAATTTAAAA
Found at i:71821 original size:25 final size:25
Alignment explanation
Indices: 71761--71821 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 25
71751 ATTTTTAATC
71761 ATTTA-TATT-TAATAATATAATAA
1 ATTTATTATTGTAATAATATAATAA
71784 A-TTATTA--GT-ATAAT-TAATAGA
1 ATTTATTATTGTAATAATATAATA-A
71805 ATTTATTATTGTAATAA
1 ATTTATTATTGTAATAA
71822 ATTATTTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
20 5 0.16
21 7 0.23
22 10 0.32
23 3 0.10
24 2 0.06
25 4 0.13
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (25 bp):
ATTTATTATTGTAATAATATAATAA
Found at i:71850 original size:19 final size:18
Alignment explanation
Indices: 71826--71861 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
71816 TAATAAATTA
*
71826 TTTAATATTACAATTTTAT
1 TTTAATAATAC-ATTTTAT
71845 TTTAATAATACATTTTA
1 TTTAATAATACATTTTA
71862 AATAATATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTAATAATACATTTTAT
Found at i:71955 original size:23 final size:26
Alignment explanation
Indices: 71897--71958 Score: 85
Period size: 23 Copynumber: 2.5 Consensus size: 26
71887 TATTTAAACT
71897 TATGACATATTTTAATATAGTATAGAA
1 TATGA-ATATTTTAATATAGTATAGAA
*
71924 TATGGATATTTTAAT-TA-TATA-AA
1 TATGAATATTTTAATATAGTATAGAA
71947 TATGAATATTTT
1 TATGAATATTTT
71959 TAAAAATCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 13 0.39
24 4 0.12
25 2 0.06
26 10 0.30
27 4 0.12
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.47
Consensus pattern (26 bp):
TATGAATATTTTAATATAGTATAGAA
Found at i:73101 original size:39 final size:39
Alignment explanation
Indices: 73038--73149 Score: 116
Period size: 39 Copynumber: 2.9 Consensus size: 39
73028 GTTATCAATT
* * * * *
73038 TACTAAACTGACAGTGATACTGTAAACACTGCAATAAGC
1 TACTGAACTGGCAGTAACACTGTAAACACTGCAACAAGC
* * * *
73077 TATTGAACTGGCAGTAACATTGTAAACACTGTAACACGC
1 TACTGAACTGGCAGTAACACTGTAAACACTGCAACAAGC
* * *
73116 TACTGAACTGGCAGTGATACTGAAAACACTGCAA
1 TACTGAACTGGCAGTAACACTGTAAACACTGCAA
73150 AGAAATACTG
Statistics
Matches: 58, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
39 58 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (39 bp):
TACTGAACTGGCAGTAACACTGTAAACACTGCAACAAGC
Found at i:73175 original size:78 final size:78
Alignment explanation
Indices: 73038--73183 Score: 186
Period size: 78 Copynumber: 1.9 Consensus size: 78
73028 GTTATCAATT
* ** * *
73038 TACTAAACTGACAGTGATACTGTAAACACTGCAATAAGCTATTGAACTGGCAGTAACATTGTAAA
1 TACTAAACTGACAGTGATACTGAAAACACTGCAATAAAATACTGAACTGACAGTAACATTGTAAA
73103 CACTGTAACACGC
66 CACTGTAACACGC
* * * * *
73116 TACTGAACTGGCAGTGATACTGAAAACACTGCAA-AGAAATACTGAGCTGACGGTGACATTGTAA
1 TACTAAACTGACAGTGATACTGAAAACACTGCAATA-AAATACTGAACTGACAGTAACATTGTAA
73180 ACAC
65 ACAC
73184 CGAGTACTGT
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
77 1 0.02
78 56 0.98
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (78 bp):
TACTAAACTGACAGTGATACTGAAAACACTGCAATAAAATACTGAACTGACAGTAACATTGTAAA
CACTGTAACACGC
Found at i:80813 original size:17 final size:17
Alignment explanation
Indices: 80791--80831 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
80781 TGCATAGAGT
80791 TGAGTTCTCACTCTTAA
1 TGAGTTCTCACTCTTAA
80808 TGAGTTCTCACTCTTAA
1 TGAGTTCTCACTCTTAA
80825 TGAGTTC
1 TGAGTTC
80832 ATATTCCAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (17 bp):
TGAGTTCTCACTCTTAA
Found at i:82022 original size:19 final size:19
Alignment explanation
Indices: 81994--82054 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
81984 TGTCACATCA
*
81994 ATAAATAATTTAAAAAATT
1 ATAAAAAATTTAAAAAATT
*
82013 ATAAAAAATTTAAAAGA-T
1 ATAAAAAATTTAAAAAATT
* *
82031 -TCAAAACTTT-AAAAATT
1 ATAAAAAATTTAAAAAATT
82048 ATAAAAA
1 ATAAAAA
82055 TTTCAATTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
16 4 0.12
17 9 0.26
18 6 0.18
19 15 0.44
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (19 bp):
ATAAAAAATTTAAAAAATT
Found at i:82036 original size:17 final size:17
Alignment explanation
Indices: 82000--82057 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
81990 ATCAATAAAT
*
82000 AATTTAAAAAATTATAAAA
1 AATTT-AAAAATTA-CAAA
82019 AATTTAAAAGATT-CAAA
1 AATTTAAAA-ATTACAAA
* *
82036 ACTTTAAAAATTATAAA
1 AATTTAAAAATTACAAA
82053 AATTT
1 AATTT
82058 CAATTTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 3 0.09
17 18 0.55
18 4 0.12
19 8 0.24
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.34
Consensus pattern (17 bp):
AATTTAAAAATTACAAA
Found at i:82055 original size:9 final size:8
Alignment explanation
Indices: 81995--82057 Score: 54
Period size: 9 Copynumber: 7.1 Consensus size: 8
81985 GTCACATCAA
81995 TAAATAATT
1 TAAA-AATT
82004 TAAAAAATT
1 T-AAAAATT
82013 ATAAAAAATT
1 -T-AAAAATT
82023 TAAAAGATT
1 TAAAA-ATT
* *
82032 CAAAACTT
1 TAAAAATT
82040 TAAAAATT
1 TAAAAATT
82048 ATAAAAATT
1 -TAAAAATT
82057 T
1 T
82058 CAATTTTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
8 13 0.28
9 21 0.46
10 12 0.26
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (8 bp):
TAAAAATT
Found at i:85299 original size:16 final size:15
Alignment explanation
Indices: 85246--85301 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 15
85236 CGTTTGGTTC
85246 GCTGTAATGGAATAGG
1 GCTGTAATGGAATA-G
*
85262 GATGTAATGGAATAG
1 GCTGTAATGGAATAG
*
85277 AGCTGTAATAGAATAG
1 -GCTGTAATGGAATAG
85293 GCTTGTAAT
1 GC-TGTAAT
85302 CAATAATTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
15 3 0.09
16 32 0.91
ACGTcount: A:0.36, C:0.05, G:0.30, T:0.29
Consensus pattern (15 bp):
GCTGTAATGGAATAG
Found at i:94033 original size:15 final size:15
Alignment explanation
Indices: 94013--94042 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
94003 CGACTTAAAC
94013 CCATATTAAATGAGT
1 CCATATTAAATGAGT
94028 CCATATTAAATGAGT
1 CCATATTAAATGAGT
94043 GTTTAACAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (15 bp):
CCATATTAAATGAGT
Found at i:94846 original size:2 final size:2
Alignment explanation
Indices: 94839--94869 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
94829 TATTTCCATT
94839 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
94870 TTTTTGCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:115350 original size:11 final size:11
Alignment explanation
Indices: 115334--115363 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
115324 CGAAAGAGGG
115334 GATGAGACCGA
1 GATGAGACCGA
115345 GATGAGACCGA
1 GATGAGACCGA
*
115356 GGTGAGAC
1 GATGAGAC
115364 TAATCGGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.40, T:0.10
Consensus pattern (11 bp):
GATGAGACCGA
Found at i:117790 original size:6 final size:6
Alignment explanation
Indices: 117765--117803 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
117755 ACAATTCATA
* * *
117765 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
117804 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:126891 original size:19 final size:19
Alignment explanation
Indices: 126852--126890 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
126842 GCTACAAAAT
*
126852 AATTCAAAATAATTTCTAA
1 AATTCAAAATAATTTATAA
126871 AATTCAAAAT-ATTTATAA
1 AATTCAAAATAATTTATAA
126889 AA
1 AA
126891 AAATCCAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (19 bp):
AATTCAAAATAATTTATAA
Found at i:139333 original size:44 final size:44
Alignment explanation
Indices: 139244--139331 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 44
139234 TAGTGTCGAG
* * *
139244 TTAAGAGTTAGAATATGTGGTTAAAATAAGAAGATTAGGAAAAA
1 TTAAGAATTAGAATATGTAGTTAAAATAAGAAGATTAAGAAAAA
* *
139288 TTAAGAATTAGAATGTGTAGTCT-AAATAAGAAAGGTTAAGAAAA
1 TTAAGAATTAGAATATGTAGT-TAAAATAAG-AAGATTAAGAAAA
139332 TTCAAGGATT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
44 25 0.68
45 12 0.32
ACGTcount: A:0.50, C:0.01, G:0.22, T:0.27
Consensus pattern (44 bp):
TTAAGAATTAGAATATGTAGTTAAAATAAGAAGATTAAGAAAAA
Found at i:140911 original size:12 final size:12
Alignment explanation
Indices: 140894--140928 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
140884 TTTGTGATCA
140894 AAATTGAAAGTG
1 AAATTGAAAGTG
140906 AAATTGAAAGTG
1 AAATTGAAAGTG
140918 AAATTGAAAGT
1 AAATTGAAAGT
140929 TATATGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (12 bp):
AAATTGAAAGTG
Found at i:142535 original size:18 final size:17
Alignment explanation
Indices: 142514--142552 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
142504 ATTTTTTGTC
*
142514 AATTTAACTTTTTAGTTA
1 AATTTAAC-TTTTAGTCA
*
142532 AATTTGACTTTTAGTCA
1 AATTTAACTTTTAGTCA
142549 AATT
1 AATT
142553 GTTTTTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.51
Consensus pattern (17 bp):
AATTTAACTTTTAGTCA
Found at i:142677 original size:19 final size:20
Alignment explanation
Indices: 142633--142681 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
142623 TTACTTTTTG
* *
142633 TTTTTTTATGAATTTTTATA
1 TTTTTTTATGAAATTTTAAA
*
142653 TATTTTT-TGAAATTTTAAA
1 TTTTTTTATGAAATTTTAAA
142672 TTTTTTTATG
1 TTTTTTTATG
142682 TGTCATGTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (20 bp):
TTTTTTTATGAAATTTTAAA
Found at i:145385 original size:18 final size:19
Alignment explanation
Indices: 145348--145386 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
145338 ATTACAAAAT
*
145348 AATTCAAAATAATTTTTAA
1 AATTCAAAATAATTTATAA
145367 AATTCAAAAT-ATTTATAA
1 AATTCAAAATAATTTATAA
145385 AA
1 AA
145387 AATCCAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTCAAAATAATTTATAA
Found at i:145387 original size:19 final size:19
Alignment explanation
Indices: 145348--145401 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
145338 ATTACAAAAT
*
145348 AATTCAAAATAATTT-TTAA
1 AATTCAAAAT-ATTTATAAA
145367 AATTCAAAATATTTATAAA
1 AATTCAAAATATTTATAAA
* *
145386 AAATCCAAA-ATTTATA
1 AATTCAAAATATTTATA
145402 TTTTTAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 11 0.35
19 20 0.65
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (19 bp):
AATTCAAAATATTTATAAA
Found at i:153791 original size:17 final size:17
Alignment explanation
Indices: 153771--153829 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
153761 AGAAAATAGA
153771 AGGTTAAAAGTCAAGGG
1 AGGTTAAAAGTCAAGGG
* *
153788 AGGTT-AAGGT-AGATGGA
1 AGGTTAAAAGTCA-A-GGG
153805 AGGTTAAAAGTCAAGGG
1 AGGTTAAAAGTCAAGGG
153822 AGGTTAAA
1 AGGTTAAA
153830 GGTTAAACAT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 1 0.03
16 5 0.15
17 22 0.65
18 5 0.15
19 1 0.03
ACGTcount: A:0.41, C:0.03, G:0.36, T:0.20
Consensus pattern (17 bp):
AGGTTAAAAGTCAAGGG
Found at i:153794 original size:34 final size:34
Alignment explanation
Indices: 153754--153830 Score: 118
Period size: 34 Copynumber: 2.3 Consensus size: 34
153744 AGAATATGAA
153754 AGGTTAAAGAAAATAGAAGGTTAAAAGTCAAGGG
1 AGGTTAAAGAAAATAGAAGGTTAAAAGTCAAGGG
* * * *
153788 AGGTTAAGGTAGATGGAAGGTTAAAAGTCAAGGG
1 AGGTTAAAGAAAATAGAAGGTTAAAAGTCAAGGG
153822 AGGTTAAAG
1 AGGTTAAAG
153831 GTTAAACATC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.44, C:0.03, G:0.34, T:0.19
Consensus pattern (34 bp):
AGGTTAAAGAAAATAGAAGGTTAAAAGTCAAGGG
Found at i:155509 original size:23 final size:24
Alignment explanation
Indices: 155477--155522 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
155467 GTTATATTCT
155477 TTTTCTTAATTTCATACTTAAACA
1 TTTTCTTAATTTCATACTTAAACA
*
155501 TTTT-TTAATTTGATACTTAAAC
1 TTTTCTTAATTTCATACTTAAAC
155523 TTCGCGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.33, C:0.13, G:0.02, T:0.52
Consensus pattern (24 bp):
TTTTCTTAATTTCATACTTAAACA
Found at i:159298 original size:24 final size:24
Alignment explanation
Indices: 159269--159344 Score: 88
Period size: 24 Copynumber: 3.3 Consensus size: 24
159259 ATATCACATT
*
159269 AAAATTAATTAATTTTTAATTTAA
1 AAAATTAACTAATTTTTAATTTAA
** *
159293 AAAATTAAGAAATTATT-A-TT--
1 AAAATTAACTAATTTTTAATTTAA
159313 AAAATTAACTAATTTTTAATTTAA
1 AAAATTAACTAATTTTTAATTTAA
159337 AAAATTAA
1 AAAATTAA
159345 ACAATTGTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
20 14 0.33
21 1 0.02
22 4 0.10
23 1 0.02
24 22 0.52
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (24 bp):
AAAATTAACTAATTTTTAATTTAA
Found at i:159300 original size:20 final size:20
Alignment explanation
Indices: 159275--159344 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 20
159265 CATTAAAATT
159275 AATTAATTTTTAATTTAAAA
1 AATTAATTTTTAATTTAAAA
*** *
159295 AATTAAGAAATTATTATTAAAA
1 AATTAA-TTTTTAAT-TTAAAA
*
159317 TTAACTAATTTTTAATTTAAAA
1 --AATTAATTTTTAATTTAAAA
159339 AATTAA
1 AATTAA
159345 ACAATTGTTA
Statistics
Matches: 36, Mismatches: 10, Indels: 8
0.67 0.19 0.15
Matches are distributed among these distances:
20 11 0.31
21 4 0.11
22 12 0.33
23 4 0.11
24 5 0.14
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (20 bp):
AATTAATTTTTAATTTAAAA
Found at i:159350 original size:24 final size:24
Alignment explanation
Indices: 159269--159356 Score: 80
Period size: 24 Copynumber: 3.8 Consensus size: 24
159259 ATATCACATT
**
159269 AAAATTAATTAATTTTTAATTTAA
1 AAAATTAAACAATTTTTAATTTAA
*
159293 AAAATTAAGA-AATTATT-A-TT--
1 AAAATTAA-ACAATTTTTAATTTAA
159313 AAAATT-AACTAATTTTTAATTTAA
1 AAAATTAAAC-AATTTTTAATTTAA
*
159337 AAAATTAAACAATTGTTAAT
1 AAAATTAAACAATTTTTAAT
159357 ATGATATGCA
Statistics
Matches: 52, Mismatches: 4, Indels: 16
0.72 0.06 0.22
Matches are distributed among these distances:
18 1 0.02
19 1 0.02
20 12 0.23
21 1 0.02
22 4 0.08
23 1 0.02
24 29 0.56
25 3 0.06
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (24 bp):
AAAATTAAACAATTTTTAATTTAA
Found at i:166133 original size:150 final size:150
Alignment explanation
Indices: 165824--166130 Score: 575
Period size: 149 Copynumber: 2.1 Consensus size: 150
165814 CATTCCCATA
165824 TTTTTTTTAATTTTAATTAGTAAGGATGTTATTTTCAAGTTTTTAATTAACAAATATTTCTTTAT
1 TTTTTTTTAATTTTAATTAGTAAGGATGTTATTTTCAAGTTTTTAATTAACAAATATTTCTTTAT
165889 TTATATAGACAGATTAATAAATATGTAATTATCATTTTCAAAAAATAAATAAATATGTAATTATA
66 TTATATAGACAGATTAATAAATATGTAATTATCATTTTCAAAAAATAAATAAATATGTAATTATA
165954 TATATATCATGTTAAATATT
131 TATATATCATGTTAAATATT
165974 TTTTTTTTAATTTTAATTAGTAAGGATGTTATTTTCAAGTTTTTAATTAAC-AATATTTCTTTAT
1 TTTTTTTTAATTTTAATTAGTAAGGATGTTATTTTCAAGTTTTTAATTAACAAATATTTCTTTAT
166038 TTATATAGACAGATTAATAAATATGTAATTATCATTTTCAAAAAATAAATAAATATGTAA-T-TA
66 TTATATAGACAGATTAATAAATATGTAATTATCATTTTCAAAAAATAAATAAATATGTAATTATA
166101 TATATATCATGTTAAATATAT
131 TATATATCATGTTAAATAT-T
166122 TTTATTTTT
1 TTT-TTTTT
166131 TAAAAATAAC
Statistics
Matches: 155, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
147 21 0.14
148 5 0.03
149 78 0.50
150 51 0.33
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.49
Consensus pattern (150 bp):
TTTTTTTTAATTTTAATTAGTAAGGATGTTATTTTCAAGTTTTTAATTAACAAATATTTCTTTAT
TTATATAGACAGATTAATAAATATGTAATTATCATTTTCAAAAAATAAATAAATATGTAATTATA
TATATATCATGTTAAATATT
Found at i:167955 original size:21 final size:21
Alignment explanation
Indices: 167902--167957 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 21
167892 AGACTTAGTC
*
167902 AATTTGTTATTTTCTTTTTAT
1 AATTTGTTATTTTATTTTTAT
*
167923 --TTT-TT-GTTTATTTTTAT
1 AATTTGTTATTTTATTTTTAT
167940 AATTTGTTATTTTATTTT
1 AATTTGTTATTTTATTTT
167958 GACTAAACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
17 10 0.36
18 2 0.07
19 6 0.21
20 2 0.07
21 8 0.29
ACGTcount: A:0.18, C:0.02, G:0.05, T:0.75
Consensus pattern (21 bp):
AATTTGTTATTTTATTTTTAT
Found at i:173688 original size:17 final size:18
Alignment explanation
Indices: 173660--173694 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
173650 TTCCTAAGTC
173660 AACCCAATAACCATTAAA
1 AACCCAATAACCATTAAA
*
173678 AACCC-ATAACCTTTAAA
1 AACCCAATAACCATTAAA
173695 TTCACCATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.20
Consensus pattern (18 bp):
AACCCAATAACCATTAAA
Found at i:177412 original size:21 final size:21
Alignment explanation
Indices: 177359--177414 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 21
177349 AGACTTAGTC
*
177359 AATTTGTTATTTTCTTTTTAT
1 AATTTGTTATTTTATTTTTAT
*
177380 --TTT-TT-GTTTATTTTTAT
1 AATTTGTTATTTTATTTTTAT
177397 AATTTGTTATTTTATTTT
1 AATTTGTTATTTTATTTT
177415 GACTAAACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
17 10 0.36
18 2 0.07
19 6 0.21
20 2 0.07
21 8 0.29
ACGTcount: A:0.18, C:0.02, G:0.05, T:0.75
Consensus pattern (21 bp):
AATTTGTTATTTTATTTTTAT
Found at i:179512 original size:29 final size:29
Alignment explanation
Indices: 179453--179511 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
179443 TACGGTTTAA
179453 TGTACAATTGTATACAAAAACTTTGATTT
1 TGTACAATTGTATACAAAAACTTTGATTT
* *
179482 TGTACATTTTTATACATGAAAA-TTTGATTT
1 TGTACAATTGTATACA--AAAACTTTGATTT
179512 GATTTGATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 14 0.54
30 8 0.31
31 4 0.15
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (29 bp):
TGTACAATTGTATACAAAAACTTTGATTT
Found at i:180136 original size:144 final size:143
Alignment explanation
Indices: 179891--180153 Score: 345
Period size: 144 Copynumber: 1.8 Consensus size: 143
179881 AATGTTTTAC
* *
179891 TAATATAATATAATTATTTTGGGTATGGAAAGAAATAAAGAATTCGGTAAAAAATCATCTTCAGT
1 TAATATAATATAATTATTTTGAGTATGGAAAGAAATAAAGAATTCGGTAAAAAATCATATTCAGT
* * * * ** *
179956 CGACATTTTACAATTTGTAGTAAATTTTGATTTTTTTTAATTGTAAATTAACAAAATGGCAAATT
66 CGACATTTTACAATTTGTAGTAAA-TCTCAATATTTTTAATAATAAAATAACAAAATGGCAAATT
180021 ATAGAAAGTGTTAT
130 ATAGAAAGTGTTAT
*
180035 TAATATAATATAATTATTTTGAGTATGGAAAGAAATAAAGAATT-GTGT-AAAAATCAATATTTA
1 TAATATAATATAATTATTTTGAGTATGGAAAGAAATAAAGAATTCG-GTAAAAAATC-ATATTCA
* *
180098 TTTC-A-ATTTTAATAATTTGTAGTAAATCTCAATATTTTTAATAATAAAATAACAAA
64 -GTCGACATTTT-ACAATTTGTAGTAAATCTCAATATTTTTAATAATAAAATAACAAA
180154 TAATGCTTAC
Statistics
Matches: 103, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
143 36 0.35
144 65 0.63
145 2 0.02
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.39
Consensus pattern (143 bp):
TAATATAATATAATTATTTTGAGTATGGAAAGAAATAAAGAATTCGGTAAAAAATCATATTCAGT
CGACATTTTACAATTTGTAGTAAATCTCAATATTTTTAATAATAAAATAACAAAATGGCAAATTA
TAGAAAGTGTTAT
Found at i:185689 original size:23 final size:23
Alignment explanation
Indices: 185658--185708 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
185648 TTTTTATTGA
185658 AATT-TAT-TTTAAATATATAA-
1 AATTATATATTTAAATATATAAT
*
185678 AATTATATATTTAAATTTATAAT
1 AATTATATATTTAAATATATAAT
*
185701 CATTATAT
1 AATTATAT
185709 TTGAATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 4 0.15
21 3 0.12
22 12 0.46
23 7 0.27
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
AATTATATATTTAAATATATAAT
Found at i:187844 original size:16 final size:17
Alignment explanation
Indices: 187820--187860 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
187810 TTTGTTTAAG
*
187820 AATGCTTTTAT-CCAAA
1 AATGATTTTATCCCAAA
*
187836 AATGATTTTGTCCCAAA
1 AATGATTTTATCCCAAA
187853 AAT-ATTTT
1 AATGATTTT
187861 TTAAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (17 bp):
AATGATTTTATCCCAAA
Found at i:198386 original size:6 final size:6
Alignment explanation
Indices: 198375--198406 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
198365 AATTTTTAGA
198375 TTTTTC TTTTTC TTTTTC TTTTT- TTTTT- TTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTT
198407 GAAAAATTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 9 0.35
6 17 0.65
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (6 bp):
TTTTTC
Found at i:204559 original size:11 final size:11
Alignment explanation
Indices: 204539--204567 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
204529 ATTTCACTCA
204539 TTTA-TTTTAT
1 TTTAGTTTTAT
204549 TTTAGTTTTAT
1 TTTAGTTTTAT
204560 TTTAGTTT
1 TTTAGTTT
204568 GCGTTTCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (11 bp):
TTTAGTTTTAT
Found at i:209698 original size:11 final size:11
Alignment explanation
Indices: 209678--209706 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
209668 ATTTCACTTA
209678 TTTA-TTTTAT
1 TTTAGTTTTAT
209688 TTTAGTTTTAT
1 TTTAGTTTTAT
209699 TTTAGTTT
1 TTTAGTTT
209707 GACGTCTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (11 bp):
TTTAGTTTTAT
Found at i:211098 original size:25 final size:26
Alignment explanation
Indices: 211049--211100 Score: 81
Period size: 25 Copynumber: 2.0 Consensus size: 26
211039 AAATATGGTA
211049 ATCGAAAAGCACAATACGTGCTAAAT
1 ATCGAAAAGCACAATACGTGCTAAAT
211075 ATCGAATAA-CACAA-ACGTGCTAAAT
1 ATCGAA-AAGCACAATACGTGCTAAAT
211100 A
1 A
211101 ACGGAAAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 12 0.48
26 11 0.44
27 2 0.08
ACGTcount: A:0.48, C:0.19, G:0.13, T:0.19
Consensus pattern (26 bp):
ATCGAAAAGCACAATACGTGCTAAAT
Found at i:212576 original size:31 final size:31
Alignment explanation
Indices: 212541--212696 Score: 107
Period size: 31 Copynumber: 5.2 Consensus size: 31
212531 GAAAAGATAT
212541 CAAATTAGGAAAAAAAGTCAAGTTTAAGTAC
1 CAAATTAGGAAAAAAAGTCAAGTTTAAGTAC
***
212572 CAAATT-GGACCCCAAA---AAGTTTAAGTAC
1 CAAATTAGGA-AAAAAAGTCAAGTTTAAGTAC
* *
212600 CAACTTA--AAAAAAAGTGTCAAGTTTAGGTAC
1 CAAATTAGGAAAAAAA--GTCAAGTTTAAGTAC
* ** * *
212631 TAAATTAGGAAAAAGTGTCAAGTTTGAGTGC
1 CAAATTAGGAAAAAAAGTCAAGTTTAAGTAC
*
212662 CAAATT-GGACCAAAAA---AAGTTTAAGTAC
1 CAAATTAGGA-AAAAAAGTCAAGTTTAAGTAC
212690 CAAATTA
1 CAAATTA
212697 CAAAAAGTGA
Statistics
Matches: 93, Mismatches: 21, Indels: 24
0.67 0.15 0.17
Matches are distributed among these distances:
26 3 0.03
27 1 0.01
28 33 0.35
30 6 0.06
31 45 0.48
33 5 0.05
ACGTcount: A:0.46, C:0.13, G:0.17, T:0.24
Consensus pattern (31 bp):
CAAATTAGGAAAAAAAGTCAAGTTTAAGTAC
Found at i:212702 original size:90 final size:89
Alignment explanation
Indices: 212542--212712 Score: 252
Period size: 90 Copynumber: 1.9 Consensus size: 89
212532 AAAAGATATC
** *
212542 AAATTAGGAAAAAAAGTCAAGTTTAAGTACCAAATTGGACCCCAAAAAGTTTAAGTACCAACTTA
1 AAATTAGGAAAAAAAGTCAAGTTTAAGTACCAAATTGGACCAAAAAAAGTTTAAGTACCAAATT-
*
212607 AAAAAAAGTGTCAAGTTTAGGTACT
65 AAAAAAAGTGACAAGTTTAGGTACT
** * *
212632 AAATTAGGAAAAAGTGTCAAGTTTGAGTGCCAAATTGGACCAAAAAAAGTTTAAGTACCAAATTA
1 AAATTAGGAAAAAAAGTCAAGTTTAAGTACCAAATTGGACCAAAAAAAGTTTAAGTACCAAATTA
*
212697 CAAAAAGTGACAAGTT
66 AAAAAAGTGACAAGTT
212713 CAGATATCAA
Statistics
Matches: 72, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
89 15 0.21
90 57 0.79
ACGTcount: A:0.47, C:0.12, G:0.17, T:0.24
Consensus pattern (89 bp):
AAATTAGGAAAAAAAGTCAAGTTTAAGTACCAAATTGGACCAAAAAAAGTTTAAGTACCAAATTA
AAAAAAGTGACAAGTTTAGGTACT
Found at i:213301 original size:41 final size:41
Alignment explanation
Indices: 213146--213671 Score: 383
Period size: 42 Copynumber: 12.8 Consensus size: 41
213136 AAAGATAAAA
** * ***
213146 CATTAGCGGCGCTTT-TCTTAATGCGCCGCAAAAGGTAAAG-
1 CATTAGCGGCGCTTTATCACAA-GCGCCGCTAAAGGTCGGGT
* * *
213186 CATTAGCGGCGC-TTAACAAAAGCGGCGCTAAAGGT-GGTGT
1 CATTAGCGGCGCTTTATCACAAGCGCCGCTAAAGGTCGG-GT
* *
213226 CATTAGCGGCGCTTTACCCACAAGCGCCGCTAAAGGTGGGGT
1 CATTAGCGGCGCTTTA-TCACAAGCGCCGCTAAAGGTCGGGT
* **
213268 CATTAGCGGCGCTTTATCACAAGCGCCGCTAAAGTTCAAGT
1 CATTAGCGGCGCTTTATCACAAGCGCCGCTAAAGGTCGGGT
* * *
213309 CATTAGCGGCGCTTTCTCTA-ATA-CGCCGCTAAAGGCCAGGT
1 CATTAGCGGCGCTTTATC-ACA-AGCGCCGCTAAAGGTCGGGT
* * * ** *
213350 AATTAGCGGCGCTTTAACTCAAGCGCCGCTAAAGGTATGAT
1 CATTAGCGGCGCTTTATCACAAGCGCCGCTAAAGGTCGGGT
** * * * *
213391 CATTAGCGGCGCTTTCCCTCAAGCGCCACAAAAAGTTCGGGT
1 CATTAGCGGCGCTTTATCACAAGCGCCGC-TAAAGGTCGGGT
** * * *
213433 CATTAGCGGCGCTTTCCCTCAAGCGCCGCTAAAGGTAGGAT
1 CATTAGCGGCGCTTTATCACAAGCGCCGCTAAAGGTCGGGT
* *
213474 CATTTAGCGACGCTTTCAT-TCAAGCGCCGCTAAAAGGTCGGGT
1 CA-TTAGCGGCGCTTT-ATCACAAGCGCCGCT-AAAGGTCGGGT
* * * *
213517 CATTAGCGGCACTTT-TCCTCAAGTGCCGCTAAAGTTCGGGT
1 CATTAGCGGCGCTTTAT-CACAAGCGCCGCTAAAGGTCGGGT
* *
213558 CATTAGCGGCGCTTATAT-ATAAAGCGCCGCTAAAGGTCAGGT
1 CATTAGCGGCGCTT-TATCA-CAAGCGCCGCTAAAGGTCGGGT
* * * *
213600 CATTAGCGGCACTTT-TCTAATAAGCGTCGCTAAAGGT-GTG-
1 CATTAGCGGCGCTTTATC--ACAAGCGCCGCTAAAGGTCGGGT
* * ** *
213640 AATTAGCGGCACTTTCCCATAAGCGCCGCTAA
1 CATTAGCGGCGCTTTATCACAAGCGCCGCTAA
213672 TTTATTTAAA
Statistics
Matches: 399, Mismatches: 64, Indels: 47
0.78 0.13 0.09
Matches are distributed among these distances:
39 28 0.07
40 44 0.11
41 147 0.37
42 165 0.41
43 15 0.04
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.24
Consensus pattern (41 bp):
CATTAGCGGCGCTTTATCACAAGCGCCGCTAAAGGTCGGGT
Found at i:213311 original size:83 final size:81
Alignment explanation
Indices: 213146--213671 Score: 417
Period size: 83 Copynumber: 6.4 Consensus size: 81
213136 AAAGATAAAA
* * * *** **
213146 CATTAGCGGCGCTTTTCTTA-ATGCGCCGCAAAAGGTAAAG-CATTAGCGGCGC-TTAACAAAAG
1 CATTAGCGGCGC-TTTCCTACAAGCGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTTAACTCAAG
* *
213208 CGGCGCTAAAGGTGGTGT
65 CGCCGCTAAAGGTAG-GT
* * * *
213226 CATTAGCGGCGCTTTACCCACAAGCGCCGCTAAAGGTGGGGTCATTAGCGGCGCTTTATCACAAG
1 CATTAGCGGCGCTTT-CCTACAAGCGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTTAACTCAAG
* *
213291 CGCCGCTAAAGTTCAAGT
65 CGCCGCTAAAGGT-AGGT
* * *
213309 CATTAGCGGCGCTTTCTCTA-ATA-CGCCGCTAAAGGCCAGGTAATTAGCGGCGCTTTAACTCAA
1 CATTAGCGGCGCTTTC-CTACA-AGCGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTTAACTCAA
*
213372 GCGCCGCTAAAGGTATGAT
64 GCGCCGCTAAAGGTA-GGT
* * * **
213391 CATTAGCGGCGCTTTCCCT-CAAGCGCCACAAAAAGTTCGGGTCATTAGCGGCGCTTTCCCTCAA
1 CATTAGCGGCGCTTT-CCTACAAGCGCCGC-TAAAGGTCGGGTCATTAGCGGCGCTTTAACTCAA
213455 GCGCCGCTAAAGGTAGGAT
64 GCGCCGCTAAAGGTAGG-T
* * * * **
213474 CATTTAGCGACGCTTTCATTCAAGCGCCGCTAAAAGGTCGGGTCATTAGCGGCACTTTTCCTCAA
1 CA-TTAGCGGCGCTTTCCTACAAGCGCCGCT-AAAGGTCGGGTCATTAGCGGCGCTTTAACTCAA
* * *
213539 GTGCCGCTAAAGTTCGGGT
64 GCGCCGCTAAAGGT-AGGT
* * * *
213558 CATTAGCGGCGCTTAT-ATATAAAGCGCCGCTAAAGGTCAGGTCATTAGCGGCACTTTTCTAA-T
1 CATTAGCGGCGCTT-TCCTA-CAAGCGCCGCTAAAGGTCGGGTCATTAGCGGCGC--TT-TAACT
*
213621 -AAGCGTCGCTAAAGGT--GT
61 CAAGCGCCGCTAAAGGTAGGT
* * * *
213639 GAATTAGCGGCACTTTCCCATAAGCGCCGCTAA
1 -CATTAGCGGCGCTTTCCTACAAGCGCCGCTAA
213672 TTTATTTAAA
Statistics
Matches: 366, Mismatches: 56, Indels: 47
0.78 0.12 0.10
Matches are distributed among these distances:
79 3 0.01
80 14 0.04
81 32 0.09
82 99 0.27
83 122 0.33
84 90 0.25
85 5 0.01
86 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.24
Consensus pattern (81 bp):
CATTAGCGGCGCTTTCCTACAAGCGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTTAACTCAAGC
GCCGCTAAAGGTAGGT
Found at i:218181 original size:18 final size:18
Alignment explanation
Indices: 218130--219074 Score: 149
Period size: 18 Copynumber: 54.3 Consensus size: 18
218120 TATCAGCTTG
218130 ATTATAATTATTTAATTAT
1 ATTA-AATTATTTAATTAT
* **
218149 ATTAAACTAAATAATTAT
1 ATTAAATTATTTAATTAT
*
218167 ATTAAATTATTTAATCAT
1 ATTAAATTATTTAATTAT
*
218185 GTTTAATTATGTATTTAATTAT
1 -ATTAA--AT-TATTTAATTAT
* **
218207 A--AACACTA-TCGATTA-
1 ATTAA-ATTATTTAATTAT
*
218222 ATTAAA-TATTTAAGTTAAAAG
1 ATTAAATTATTTAA-TT---AT
* *
218243 ATTTAATT-TTTAATGAT
1 ATTAAATTATTTAATTAT
*
218260 ATTAAATT-TTATGATTAT
1 ATTAAATTATT-TAATTAT
218278 ATTAAATTA---AA-TAT
1 ATTAAATTATTTAATTAT
218292 -TT-AATTATTTAATTAT
1 ATTAAATTATTTAATTAT
* **
218308 ATTAAACTAAATAATTAT
1 ATTAAATTATTTAATTAT
*
218326 ATTAAATTATTTAATCAT
1 ATTAAATTATTTAATTAT
*
218344 GTTTAATTATGTATTTAATTAT
1 -ATTAA--AT-TATTTAATTAT
* *
218366 A--AACACTA-TTGATTA-
1 ATTAA-ATTATTTAATTAT
* *
218381 ATTAAA-TATTTAAGGTAAAAG
1 ATTAAATTATTTAA--T--TAT
*
218402 ATTTAATTATTTAATTAT
1 ATTAAATTATTTAATTAT
* ** *
218420 ATTAAAGTAAATGATTAT
1 ATTAAATTATTTAATTAT
* *
218438 ATTAAGTTA---AA--AG
1 ATTAAATTATTTAATTAT
*
218451 ATTTAATTATTTAATTAT
1 ATTAAATTATTTAATTAT
* ** *
218469 ATTAAAGTAAATGATTAT
1 ATTAAATTATTTAATTAT
* *
218487 ATTAAGTTA---AA--AG
1 ATTAAATTATTTAATTAT
*
218500 ATTTAATTATTTAATTAT
1 ATTAAATTATTTAATTAT
* ** *
218518 ATTAAAGTAAATGATTAT
1 ATTAAATTATTTAATTAT
* *
218536 ATTAAGTTA---AA--AG
1 ATTAAATTATTTAATTAT
*
218549 ATTTAATTATTTAATTAT
1 ATTAAATTATTTAATTAT
* **
218567 ATTAAAGTAAATAATTAT
1 ATTAAATTATTTAATTAT
**
218585 ATTAAATTAAATAATTAT
1 ATTAAATTATTTAATTAT
* **
218603 ATT-AA-T-TTAAAAGAT
1 ATTAAATTATTTAATTAT
218618 A-T-AATTATTTAATTAT
1 ATTAAATTATTTAATTAT
* **
218634 ATTAAACTAAATAATTAT
1 ATTAAATTATTTAATTAT
* *
218652 ATTAAGTTATTTAATCAT
1 ATTAAATTATTTAATTAT
*
218670 GTTTAATTATGTATTTAATTAT
1 -ATTAA--AT-TATTTAATTAT
* **
218692 A--AACACTA-TCGATTA-
1 ATTAA-ATTATTTAATTAT
*
218707 ATTAAA-TATTTAAGTTAAAAG
1 ATTAAATTATTTAA-TT---AT
* * *
218728 ATTTAATCATTTTATTAT
1 ATTAAATTATTTAATTAT
* * **
218746 ACTAAAGTAAATAATTAT
1 ATTAAATTATTTAATTAT
218764 ATTAAATTA---AA-TAT
1 ATTAAATTATTTAATTAT
218778 -TT-AATTATTTAATTAT
1 ATTAAATTATTTAATTAT
* ** **
218794 ATTAAAGTAAATAGGTAT
1 ATTAAATTATTTAATTAT
* **
218812 ATT-AA-T-TTAAAAGAT
1 ATTAAATTATTTAATTAT
218827 A-T-AATTATTTAATTAT
1 ATTAAATTATTTAATTAT
** *
218843 ATTAAATTAAATGATTAT
1 ATTAAATTATTTAATTAT
*
218861 ATTAAATTATTTAATCAT
1 ATTAAATTATTTAATTAT
*
218879 GTTTAATTATGTATTTAATTAT
1 -ATTAA--AT-TATTTAATTAT
* **
218901 A--AACACTA-TGGATTA-
1 ATTAA-ATTATTTAATTAT
*
218916 ATTAAA-TATTTAAGTTAAAAG
1 ATTAAATTATTTAA-TT---AT
*
218937 ATTTAATTATTTAATTAT
1 ATTAAATTATTTAATTAT
* ** *
218955 ATTAAAGTAAATGATTAT
1 ATTAAATTATTTAATTAT
* *
218973 ATTAAGTTA---AA--AG
1 ATTAAATTATTTAATTAT
* *
218986 ATTTAATCATTTAATTAT
1 ATTAAATTATTTAATTAT
* * **
219004 ACTAAAGTAAATAATTAT
1 ATTAAATTATTTAATTAT
219022 ATTAAATTA---AA-TAT
1 ATTAAATTATTTAATTAT
219036 -TT-AATTATTTAATTAT
1 ATTAAATTATTTAATTAT
* **
219052 ATTAAAGTAAATAATTAT
1 ATTAAATTATTTAATTAT
219070 ATTAA
1 ATTAA
219075 GTTAAAAGAT
Statistics
Matches: 649, Mismatches: 177, Indels: 201
0.63 0.17 0.20
Matches are distributed among these distances:
12 15 0.02
13 37 0.06
14 15 0.02
15 38 0.06
16 67 0.10
17 44 0.07
18 303 0.47
19 28 0.04
20 6 0.01
21 36 0.06
22 60 0.09
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (18 bp):
ATTAAATTATTTAATTAT
Found at i:218292 original size:30 final size:30
Alignment explanation
Indices: 218258--218329 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
218248 ATTTTTAATG
* *
218258 ATATTAAATT-TTATGATTATATTAAATTAA
1 ATATTAAATTATT-TAATTATATTAAACTAA
*
218288 ATATTTAATTATTTAATTATATTAAACTAA
1 ATATTAAATTATTTAATTATATTAAACTAA
*
218318 ATAATTATATTA
1 AT-ATTAAATTA
218330 AATTATTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 26 0.74
31 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (30 bp):
ATATTAAATTATTTAATTATATTAAACTAA
Found at i:218303 original size:48 final size:47
Alignment explanation
Indices: 218243--218334 Score: 130
Period size: 48 Copynumber: 1.9 Consensus size: 47
218233 AAGTTAAAAG
* ** *
218243 ATTTAATTTTTAATGATATTAAATTTTATGATTATATTAAATTAAAT
1 ATTTAATTTTTAATGATATTAAACTAAATAATTATATTAAATTAAAT
*
218290 ATTTAATTATTTAATTATATTAAACTAAATAATTATATTAAATTA
1 ATTTAATT-TTTAATGATATTAAACTAAATAATTATATTAAATTA
218335 TTTAATCATG
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
47 8 0.21
48 31 0.79
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (47 bp):
ATTTAATTTTTAATGATATTAAACTAAATAATTATATTAAATTAAAT
Found at i:218451 original size:49 final size:49
Alignment explanation
Indices: 218390--219110 Score: 406
Period size: 49 Copynumber: 14.8 Consensus size: 49
218380 AATTAAATAT
*
218390 TTAAGGTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATA
218439 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATA
218488 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATA
*
218537 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATA
* *
218586 TTAAATT--AA-A--TAATTATATTAATT-TA--AAAGATATAATTATT-TAA
1 TTAAGTTAAAAGATTTAATTAT-TTAATTATATTAAAG-TA-AATGATTAT-A
** ** * *
218630 TTATA-TTAAACTAAATAATTATATTAAGTTAT-TTAATCATGTTTAATTATGTAT-
1 TTA-AGTTAAAAGATTTAATTAT-TTAA-TTATATTAA--A-G-TAAATGAT-TATA
* ** * * *
218684 TTAA-TTATAAACACTATCGATTAATTAA--ATATTTAAGTTAAAAGATT-TAA
1 TTAAGTTA-AAAGA-T-TTAATTATTTAATTATATTAAAG-TAAATGATTAT-A
* ** ** * * * * ** *
218734 TCATTTTATTATACTAAAGTAAATAATTATATTAAATTAAAT-ATT-TAA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTAT-A
* * * * * ** ** ** *
218782 TT-ATTTAATTATATTAAAGTAAATAGGTATATTAATTTAAAAGA-TATAA
1 TTAAGTTAA-AAGATTTAATTATTTAATTATATTAAAGTAAATGATTAT-A
* * * * ** * * ** * * *
218831 TT-ATTTAATTATATTAAATTAAATGATTATATTAAATTATTTAATCATGT
1 TTAAGTTAA-AAGATTTAATTATTTAATTATATTAAAGTAAATGATTAT-A
* ** * *
218881 TTAA-TT--ATGTATTTAATTATAAACACTATGGATT-AA-TTAA--A-TAT-
1 TTAAGTTAAAAG-ATTTAATTATTTA-ATTAT--ATTAAAGTAAATGATTATA
218925 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATA
* * *
218974 TTAAGTTAAAAGATTTAATCATTTAATTATACTAAAGTAAATAATTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATA
* * *
219023 TTAAATT-AAATATTTAATTATTTAATTATATTAAAGTAAATAATTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATA
*
219071 TTAAGTTAAAAGATTTAATTATTTAATGATATTAAAGTAA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAA
219111 CTAATTATTT
Statistics
Matches: 547, Mismatches: 78, Indels: 94
0.76 0.11 0.13
Matches are distributed among these distances:
42 4 0.01
43 6 0.01
44 27 0.05
45 16 0.03
46 15 0.03
47 11 0.02
48 101 0.18
49 294 0.54
50 28 0.05
51 9 0.02
52 4 0.01
53 7 0.01
54 13 0.02
55 7 0.01
56 5 0.01
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (49 bp):
TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATA
Found at i:218582 original size:67 final size:67
Alignment explanation
Indices: 218511--218656 Score: 247
Period size: 67 Copynumber: 2.2 Consensus size: 67
218501 TTTAATTATT
* * *
218511 TAATTATATTAAAGTAAATGATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTA
1 TAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATATAATTATTTAATTATATTAAACTA
218576 AA
66 AA
* *
218578 TAATTATATTAAATTAAATAATTATATTAATTTAAAAGATATAATTATTTAATTATATTAAACTA
1 TAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATATAATTATTTAATTATATTAAACTA
218643 AA
66 AA
218645 TAATTATATTAA
1 TAATTATATTAA
218657 GTTATTTAAT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 74 1.00
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.45
Consensus pattern (67 bp):
TAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATATAATTATTTAATTATATTAAACTA
AA
Found at i:218831 original size:209 final size:210
Alignment explanation
Indices: 218578--219078 Score: 817
Period size: 209 Copynumber: 2.4 Consensus size: 210
218568 TTAAAGTAAA
*
218578 TAATTATATTAAATTAAATAATTATATTAATTTAAAAGATATAATTATTTAATTATATTAAACTA
1 TAATTATATTAAAGTAAATAATTATATTAATTTAAAAGATATAATTATTTAATTATATTAAACTA
218643 AATAATTATATTAAGTTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAA
66 AATAATTATATTAAGTTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAA
*
218708 TTAAATATTTAAGTTAAAAGATTTAATCATTTTATTATACTAAAGTAAATAATTATATTAAATT-
131 TTAAATATTTAAGTTAAAAGATTTAATCATTTAATTATACTAAAGTAAATAATTATATTAAATTA
* *
218772 AAATATTTAATTATT
196 AAAGATTTAATCATT
** *
218787 TAATTATATTAAAGTAAATAGGTATATTAATTTAAAAGATATAATTATTTAATTATATTAAATTA
1 TAATTATATTAAAGTAAATAATTATATTAATTTAAAAGATATAATTATTTAATTATATTAAACTA
* * *
218852 AATGATTATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATGGATTAA
66 AATAATTATATTAAGTTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAA
* * * *
218917 TTAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTA
131 TTAAATATTTAAGTTAAAAGATTTAATCATTTAATTATACTAAAGTAAATAATTATATTAAATTA
218982 AAAGATTTAATCATT
196 AAAGATTTAATCATT
* * * * *
218997 TAATTATACTAAAGTAAATAATTATATTAAATT-AAATATTTAATTATTTAATTATATTAAAGTA
1 TAATTATATTAAAGTAAATAATTATATTAATTTAAAAGATATAATTATTTAATTATATTAAACTA
219061 AATAATTATATTAAGTTA
66 AATAATTATATTAAGTTA
219079 AAAGATTTAA
Statistics
Matches: 268, Mismatches: 23, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
209 226 0.84
210 42 0.16
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (210 bp):
TAATTATATTAAAGTAAATAATTATATTAATTTAAAAGATATAATTATTTAATTATATTAAACTA
AATAATTATATTAAGTTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAA
TTAAATATTTAAGTTAAAAGATTTAATCATTTAATTATACTAAAGTAAATAATTATATTAAATTA
AAAGATTTAATCATT
Found at i:218860 original size:97 final size:98
Alignment explanation
Indices: 218716--219122 Score: 435
Period size: 97 Copynumber: 4.0 Consensus size: 98
218706 AATTAAATAT
* * * *
218716 TTAAGTTAAAAGATTTAATCATTTTATTATACTAAAGTAAATAATTATATTAAATT-AAATATTT
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTAAAAGATTT
**
218780 AATTATTTAATTATATTAAAGTAAATAGGTATA
66 AATTATTTAATTATATTAAAGTAAATAATTATA
* * * *
218813 TTAATTTAAAAGATATAATTATTTAATTATATTAAATTAAATGATTATATTAAATTATTTAATCA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTA---AA--A
* * * * *
218878 TG-TTTAATTATGTATTTAATTATAAACACTATGGATTAATTAAATA
61 -GATTTAATTATTTAATT-A-TATTAA-AGTA---AATAATT--ATA
* *
218924 TTTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTAAAAGATT
1 -TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTAAAAGATT
* *
218989 TAATCATTTAATTATACTAAAGTAAATAATTATA
65 TAATTATTTAATTATATTAAAGTAAATAATTATA
* * *
219023 TTAAATT-AAATATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATTT
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTAAAAGATTT
* *
219087 AATTATTTAATGATATTAAAGTAACTAATTAT-
66 AATTATTTAATTATATTAAAGTAAATAATTATA
219119 TTAA
1 TTAA
219123 TTATATTAAA
Statistics
Matches: 260, Mismatches: 33, Indels: 35
0.79 0.10 0.11
Matches are distributed among these distances:
96 4 0.02
97 132 0.51
98 6 0.02
99 3 0.01
101 8 0.03
103 14 0.05
104 4 0.02
105 9 0.03
106 5 0.02
107 13 0.05
109 6 0.02
111 3 0.01
112 53 0.20
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (98 bp):
TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTAAAAGATTT
AATTATTTAATTATATTAAAGTAAATAATTATA
Found at i:219049 original size:30 final size:31
Alignment explanation
Indices: 219015--219073 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
219005 CTAAAGTAAA
* *
219015 TAATTATATTAAATTAAATATTTA-ATTATT
1 TAATTATATTAAAGTAAATAATTATATTATT
219045 TAATTATATTAAAGTAAATAATTATATTA
1 TAATTATATTAAAGTAAATAATTATATTA
219074 AGTTAAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (31 bp):
TAATTATATTAAAGTAAATAATTATATTATT
Found at i:224654 original size:66 final size:66
Alignment explanation
Indices: 224548--224704 Score: 217
Period size: 66 Copynumber: 2.4 Consensus size: 66
224538 CAAATTGCTC
*
224548 AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGATGAACTCCATC-T
1 AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCA-CAT
224612 AA
65 AA
* ** *
224614 AACTTAAAGAGGAGGTTGCAGTGAGAGAAGCAGAGTCTCAAAAAAAATATGAAGAACTCCACATA
1 AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCACATA
*
224679 C
66 A
* * *
224680 AACTTAAAGCGGAGGCAGCAGCGAG
1 AACTTAAAGAGGAGGCTGCAACGAG
224705 GCAAGCGAAG
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
65 1 0.01
66 79 0.99
ACGTcount: A:0.44, C:0.17, G:0.25, T:0.15
Consensus pattern (66 bp):
AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCACATA
A
Found at i:225077 original size:43 final size:43
Alignment explanation
Indices: 225024--225149 Score: 207
Period size: 43 Copynumber: 2.9 Consensus size: 43
225014 GTTATATTAG
225024 CGGCGCTTGTGGAAAAAGCGCCGCTAAAGAACATGGCCTTCAA
1 CGGCGCTTGTGGAAAAAGCGCCGCTAAAGAACATGGCCTTCAA
* *
225067 CGGCACTTGTGGAAAAAGCGCCGCTAAAGAACATGGCCTTCAG
1 CGGCGCTTGTGGAAAAAGCGCCGCTAAAGAACATGGCCTTCAA
* * *
225110 CGGCGCTTCTGGAGAAAGCGCCGCTAAAGAACATAGCCTT
1 CGGCGCTTGTGGAAAAAGCGCCGCTAAAGAACATGGCCTT
225150 AGCGGTGCTT
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 77 1.00
ACGTcount: A:0.29, C:0.26, G:0.28, T:0.17
Consensus pattern (43 bp):
CGGCGCTTGTGGAAAAAGCGCCGCTAAAGAACATGGCCTTCAA
Found at i:232096 original size:15 final size:15
Alignment explanation
Indices: 232055--232097 Score: 56
Period size: 13 Copynumber: 3.0 Consensus size: 15
232045 ACAAATAACA
232055 ACAATTCTTATATTG
1 ACAATTCTTATATTG
232070 -CATATT-TT-TATTG
1 ACA-ATTCTTATATTG
232083 ACAATTCTTATATTG
1 ACAATTCTTATATTG
232098 TTCATCGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
13 8 0.33
14 8 0.33
15 8 0.33
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.51
Consensus pattern (15 bp):
ACAATTCTTATATTG
Found at i:237356 original size:25 final size:23
Alignment explanation
Indices: 237324--237369 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
237314 GTTAGATCCA
237324 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
237349 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
237370 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:238070 original size:9 final size:9
Alignment explanation
Indices: 238056--238082 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
238046 ACTAAAGATT
238056 CACTCAAAG
1 CACTCAAAG
238065 CACTCAAAG
1 CACTCAAAG
238074 CACTCAAAG
1 CACTCAAAG
238083 TGTTCAAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.33, G:0.11, T:0.11
Consensus pattern (9 bp):
CACTCAAAG
Found at i:238447 original size:19 final size:16
Alignment explanation
Indices: 238409--238476 Score: 57
Period size: 16 Copynumber: 3.9 Consensus size: 16
238399 TTAAACACAC
*
238409 TTTTGTTTTTTTTTT-C
1 TTTT-TTTTTTTTTTAA
238425 TTTTTCTTTTTTTTTCAAA
1 TTTTT-TTTTTTTTT--AA
238444 TTTTTTAATTTTTTTTAA
1 TTTTTT--TTTTTTTTAA
238462 TTTTTTTGTTTTTTT
1 TTTTTTT-TTTTTTT
238477 TAATAATAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
15 1 0.02
16 14 0.32
17 7 0.16
18 9 0.20
19 5 0.11
20 8 0.18
ACGTcount: A:0.10, C:0.04, G:0.03, T:0.82
Consensus pattern (16 bp):
TTTTTTTTTTTTTTAA
Found at i:238468 original size:10 final size:10
Alignment explanation
Indices: 238444--238480 Score: 51
Period size: 9 Copynumber: 3.9 Consensus size: 10
238434 TTTTTTCAAA
238444 TTTTTTAATT
1 TTTTTTAATT
238454 TTTTTTAA-T
1 TTTTTTAATT
*
238463 TTTTTT-GTT
1 TTTTTTAATT
238472 TTTTTTAAT
1 TTTTTTAAT
238481 AATAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (10 bp):
TTTTTTAATT
Found at i:238473 original size:18 final size:18
Alignment explanation
Indices: 238409--238480 Score: 67
Period size: 18 Copynumber: 3.9 Consensus size: 18
238399 TTAAACACAC
238409 TTTTGTTTTTTTT--TTCT
1 TTTTGTTTTTTTTAATT-T
*
238426 TTTTCTTTTTTTTTCAAATTT
1 TTTT-GTTTTTTTT--AATTT
**
238447 TTTAATTTTTTTTAATTT
1 TTTTGTTTTTTTTAATTT
238465 TTTTGTTTTTTTTAAT
1 TTTTGTTTTTTTTAAT
238481 AATAAAATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
17 4 0.09
18 27 0.60
20 8 0.18
21 4 0.09
22 2 0.04
ACGTcount: A:0.12, C:0.04, G:0.03, T:0.81
Consensus pattern (18 bp):
TTTTGTTTTTTTTAATTT
Found at i:239430 original size:6 final size:5
Alignment explanation
Indices: 239379--239426 Score: 60
Period size: 5 Copynumber: 8.8 Consensus size: 5
239369 ATTGCATAAT
239379 TAAAA TAAAA TAAAA TAAAA TAAAA CTAAAAA TGAAAA TAAATA TAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA -T-AAAA T-AAAA TAAA-A TAAA
239427 TATACTAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
5 23 0.59
6 12 0.31
7 4 0.10
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:243019 original size:15 final size:15
Alignment explanation
Indices: 242999--243037 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
242989 GCACATCAAA
*
242999 CAAGAATTAATATAT
1 CAAGAATTAATAAAT
*
243014 CAAGAA-TACTAAAT
1 CAAGAATTAATAAAT
243028 CAAGAATTAA
1 CAAGAATTAA
243038 GAACACATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.26
Consensus pattern (15 bp):
CAAGAATTAATAAAT
Found at i:243443 original size:25 final size:23
Alignment explanation
Indices: 243415--243460 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
243405 GTTGGATTCA
243415 AATTAAATTCTACAAAAATAATTAG
1 AATTAAA-TCTA-AAAAATAATTAG
*
243440 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
243461 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 4 0.20
25 7 0.35
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:245328 original size:23 final size:23
Alignment explanation
Indices: 245280--245330 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
245270 AAAAGCTATC
245280 TACAAAATCAAATCTCTAAGATT
1 TACAAAATCAAATCTCTAAGATT
* * *
245303 TACAGAATCATATCTTCTAATA-T
1 TACAAAATCAAATC-TCTAAGATT
245326 TACAA
1 TACAA
245331 GTCATCCAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.45, C:0.18, G:0.04, T:0.33
Consensus pattern (23 bp):
TACAAAATCAAATCTCTAAGATT
Found at i:248187 original size:13 final size:14
Alignment explanation
Indices: 248156--248188 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
248146 TTTGTTTGAT
248156 TGAAAATAATTTTC
1 TGAAAATAATTTTC
*
248170 GGAAAATAA-TTTC
1 TGAAAATAATTTTC
248183 TGAAAA
1 TGAAAA
248189 ATAAAATACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.33
Consensus pattern (14 bp):
TGAAAATAATTTTC
Found at i:248348 original size:22 final size:22
Alignment explanation
Indices: 248323--248390 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
248313 TACATTTGAA
*
248323 AATTTATTATTTTTTATTATTT
1 AATTTATTATTTTATATTATTT
* *
248345 AATTGATTTTATTTTATATCTATTA
1 AATT--TATTATTTTATAT-TATTT
248370 AATTTA-TATTTTATATTATTT
1 AATTTATTATTTTATATTATTT
248391 TTACATATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
21 4 0.11
22 14 0.37
23 1 0.03
24 11 0.29
25 8 0.21
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (22 bp):
AATTTATTATTTTATATTATTT
Found at i:248548 original size:46 final size:46
Alignment explanation
Indices: 248480--248567 Score: 113
Period size: 46 Copynumber: 1.9 Consensus size: 46
248470 AAGCGAATTG
* ** *** *
248480 ATGATAACTACAATATTTTCCAAGTGTATAACTAGTATTACACCAC
1 ATGATAACTACAACATCGTCCAAGCACATAACTAATATTACACCAC
248526 ATGATAACTACAACATCGTCCAAGCACATAACTAATATTACA
1 ATGATAACTACAACATCGTCCAAGCACATAACTAATATTACA
248568 AATTAGTAGT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
46 35 1.00
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.28
Consensus pattern (46 bp):
ATGATAACTACAACATCGTCCAAGCACATAACTAATATTACACCAC
Found at i:249851 original size:14 final size:14
Alignment explanation
Indices: 249832--249859 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
249822 AAATTGAAGC
249832 CACAACTTCAACAA
1 CACAACTTCAACAA
249846 CACAACTTCAACAA
1 CACAACTTCAACAA
249860 TTGCATTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.36, G:0.00, T:0.14
Consensus pattern (14 bp):
CACAACTTCAACAA
Found at i:250316 original size:17 final size:17
Alignment explanation
Indices: 250294--250327 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
250284 CCATATTTAG
250294 GATAAACTTCAAATTAA
1 GATAAACTTCAAATTAA
* *
250311 GATAAATTTCTAATTAA
1 GATAAACTTCAAATTAA
250328 ATTAGCCAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.35
Consensus pattern (17 bp):
GATAAACTTCAAATTAA
Found at i:250517 original size:17 final size:19
Alignment explanation
Indices: 250497--250539 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
250487 AAAAGAATCT
*
250497 AAACAAAACCA-GACAT-C
1 AAACAAAACCACCACATCC
*
250514 AAACCAAACCACCACATCC
1 AAACAAAACCACCACATCC
250533 AAACAAA
1 AAACAAA
250540 CTTGCCAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 10 0.48
18 4 0.19
19 7 0.33
ACGTcount: A:0.58, C:0.35, G:0.02, T:0.05
Consensus pattern (19 bp):
AAACAAAACCACCACATCC
Done.