Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 1 of 198
Found at i:16 original size:7 final size:7
Alignment explanation
Indices: 5--462 Score: 559
Period size: 7 Copynumber: 64.1 Consensus size: 7
1 ATTA
5 CTAAACC
1 CTAAACC
12 CTAAACC
1 CTAAACC
19 CTAAACC
1 CTAAACC
26 CTAAACC
1 CTAAACC
33 CTAAACC
1 CTAAACC
40 CTAAACC
1 CTAAACC
47 CTAAAACC
1 CT-AAACC
*
55 TTAAACC
1 CTAAACC
62 CTAAACC
1 CTAAACC
69 CTAAACC
1 CTAAACC
76 CTAAACC
1 CTAAACC
83 CTAAACC
1 CTAAACC
90 CTAAAAACC
1 CT--AAACC
99 CTAAACC
1 CTAAACC
106 CTAAACC
1 CTAAACC
113 CTAAACC
1 CTAAACC
120 CTAAACC
1 CTAAACC
127 CTAAACC
1 CTAAACC
134 CTAAAACC
1 CT-AAACC
142 CTAAAACC
1 CT-AAACC
150 CTAAACC
1 CTAAACC
157 CTAAACC
1 CTAAACC
164 CTAAACC
1 CTAAACC
171 CTAAACC
1 CTAAACC
*
178 CTAGACC
1 CTAAACC
185 CTAAACC
1 CTAAACC
192 CTAAACC
1 CTAAACC
199 CTAAACC
1 CTAAACC
206 CTAAACC
1 CTAAACC
213 CTAAACC
1 CTAAACC
220 CTAAACC
1 CTAAACC
227 CTAAACC
1 CTAAACC
234 CTAAACC
1 CTAAACC
241 CTAAA-C
1 CTAAACC
247 CTAAA-C
1 CTAAACC
253 CTAAA-C
1 CTAAACC
259 CTAAA-C
1 CTAAACC
265 CTAAACC
1 CTAAACC
272 CTAAACC
1 CTAAACC
279 C-AAACCCC
1 CTAAA--CC
*
287 CTAACCC
1 CTAAACC
*
294 TCTAACCC
1 -CTAAACC
302 CTTAAACC
1 C-TAAACC
310 CTTAAACC
1 C-TAAACC
*
318 CTAACCCC
1 CTAA-ACC
*
326 CTAACCC
1 CTAAACC
333 CTTAAACC
1 C-TAAACC
*
341 CTAAATC
1 CTAAACC
348 CTAAACC
1 CTAAACC
* *
355 CTTAACA
1 CTAAACC
362 CTAAACC
1 CTAAACC
369 CTAAACC
1 CTAAACC
*
376 CTACACC
1 CTAAACC
* *
383 CGACACC
1 CTAAACC
* *
390 CGACA-C
1 CTAAACC
*
396 CTGACACC
1 CT-AAACC
*
404 CCAAACC
1 CTAAACC
*
411 CCAAACC
1 CTAAACC
*
418 CCAAACC
1 CTAAACC
425 CTAAAACC
1 CT-AAACC
*
433 CCAAACC
1 CTAAACC
*
440 CCAAACC
1 CTAAACC
447 CTAAACC
1 CTAAACC
454 CTTAAACC
1 C-TAAACC
462 C
1 C
463 AAGCCGGGAT
Statistics
Matches: 413, Mismatches: 22, Indels: 31
0.89 0.05 0.07
Matches are distributed among these distances:
6 29 0.07
7 303 0.73
8 72 0.17
9 9 0.02
ACGTcount: A:0.41, C:0.44, G:0.01, T:0.14
Consensus pattern (7 bp):
CTAAACC
Found at i:302 original size:16 final size:16
Alignment explanation
Indices: 281--333 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
271 CCTAAACCCA
281 AACCCCCTAACCCTCT
1 AACCCCCTAACCCTCT
*
297 AACCCCTTAAACCCT-T
1 AACCCCCT-AACCCTCT
* *
313 AA-ACCCTAACCCCCT
1 AACCCCCTAACCCTCT
328 AACCCC
1 AACCCC
334 TTAAACCCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
14 5 0.17
15 6 0.21
16 12 0.41
17 6 0.21
ACGTcount: A:0.30, C:0.53, G:0.00, T:0.17
Consensus pattern (16 bp):
AACCCCCTAACCCTCT
Found at i:507 original size:32 final size:32
Alignment explanation
Indices: 456--579 Score: 144
Period size: 32 Copynumber: 3.9 Consensus size: 32
446 CCTAAACCCT
* * ** *
456 TAAACCCAAGCCGGGATATGCAAAGAATAGAA
1 TAAACCTAAACCGGGATATGCATGGAATGGAA
*
488 TAAATCC-AAACCGGGATATGCGTGGAATGGAA
1 TAAA-CCTAAACCGGGATATGCATGGAATGGAA
520 TAAACCTAAACCGGGATATG-AGTGGAATGGAA
1 TAAACCTAAACCGGGATATGCA-TGGAATGGAA
* *
552 TAAACCTAAACCGGGATATCCGTGGAAT
1 TAAACCTAAACCGGGATATGCATGGAAT
580 AGGATATCCC
Statistics
Matches: 80, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
31 2 0.03
32 76 0.95
33 2 0.03
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (32 bp):
TAAACCTAAACCGGGATATGCATGGAATGGAA
Found at i:537 original size:64 final size:64
Alignment explanation
Indices: 456--579 Score: 162
Period size: 64 Copynumber: 1.9 Consensus size: 64
446 CCTAAACCCT
* *
456 TAAACCCAAGCCGGGATATGCA-AAGAATAGAATAAATCC-AAACCGGGATATGCGTGGAATGGA
1 TAAACCCAAACCGGGATATG-AGAAGAATAGAATAAA-CCTAAACCGGGATATCCGTGGAATGGA
519 A
64 A
* ** *
520 TAAACCTAAACCGGGATATGAGTGGAATGGAATAAACCTAAACCGGGATATCCGTGGAAT
1 TAAACCCAAACCGGGATATGAGAAGAATAGAATAAACCTAAACCGGGATATCCGTGGAAT
580 AGGATATCCC
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
63 3 0.06
64 49 0.94
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (64 bp):
TAAACCCAAACCGGGATATGAGAAGAATAGAATAAACCTAAACCGGGATATCCGTGGAATGGAA
Found at i:782 original size:31 final size:31
Alignment explanation
Indices: 701--782 Score: 78
Period size: 31 Copynumber: 2.6 Consensus size: 31
691 GGGATTTGAA
*
701 TGGGATATCCCC-AGAATACCTTAAATCAAGT
1 TGGGATATCCCCGA-AATAGCTTAAATCAAGT
* * * * *
732 TGGTATTTCCGCGACATAGCTTAATTC-AGCT
1 TGGGATATCCCCGAAATAGCTTAAATCAAG-T
763 TGGGATATCCCCGAAATAGC
1 TGGGATATCCCCGAAATAGC
783 CCTCCAACAG
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
30 2 0.05
31 36 0.92
32 1 0.03
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (31 bp):
TGGGATATCCCCGAAATAGCTTAAATCAAGT
Found at i:5529 original size:46 final size:46
Alignment explanation
Indices: 5462--5554 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
5452 AAATAAATTT
5462 CCTTGTTTCTATGGTTTTCCTATTGGGTTGCTTTGCAGCTTCACCA
1 CCTTGTTTCTATGGTTTTCCTATTGGGTTGCTTTGCAGCTTCACCA
5508 CCTTGTTTCTATGGTTTTCCTATTGGGTTGCTTTGCAGCTTCACCA
1 CCTTGTTTCTATGGTTTTCCTATTGGGTTGCTTTGCAGCTTCACCA
5554 C
1 C
5555 GAGATCTCCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.45
Consensus pattern (46 bp):
CCTTGTTTCTATGGTTTTCCTATTGGGTTGCTTTGCAGCTTCACCA
Found at i:8002 original size:79 final size:80
Alignment explanation
Indices: 7870--8031 Score: 308
Period size: 79 Copynumber: 2.0 Consensus size: 80
7860 ACAAAATCAG
*
7870 CTTTATAATAAATAGGTAAACCCGAAACAATTGTTGGCTTTGTTTAAAGCCCTCCATTCATTAGT
1 CTTTATAACAAATAGGTAAACCCGAAACAATTGTTGGCTTTGTTTAAAGCCCTCCATTCATTAGT
7935 TTAACGGATTATTAA
66 TTAACGGATTATTAA
7950 CTTTATAACAAATAGGTAAACCCG-AACAATTGTTGGCTTTGTTTAAAGCCCTCCATTCATTAGT
1 CTTTATAACAAATAGGTAAACCCGAAACAATTGTTGGCTTTGTTTAAAGCCCTCCATTCATTAGT
8014 TTAACGGATTATTAA
66 TTAACGGATTATTAA
8029 CTT
1 CTT
8032 GAAAGCTTCA
Statistics
Matches: 81, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
79 58 0.72
80 23 0.28
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (80 bp):
CTTTATAACAAATAGGTAAACCCGAAACAATTGTTGGCTTTGTTTAAAGCCCTCCATTCATTAGT
TTAACGGATTATTAA
Found at i:10039 original size:26 final size:26
Alignment explanation
Indices: 10010--10061 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
10000 AATTATATAT
*
10010 ATTTCT-TTAACATTTTTGTTACTTAA
1 ATTTCTATTAACA-TTTTGGTACTTAA
* *
10036 ATTTTTATTCACATTTTGGTACTTAA
1 ATTTCTATTAACATTTTGGTACTTAA
10062 TTATCAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.27, C:0.12, G:0.06, T:0.56
Consensus pattern (26 bp):
ATTTCTATTAACATTTTGGTACTTAA
Found at i:10599 original size:25 final size:26
Alignment explanation
Indices: 10538--10600 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 26
10528 AGTTTAATGC
* *
10538 TTAAATCAAAGATAAAGAAACAAAAA
1 TTAAAGCAAAGAAAAAGAAACAAAAA
* *
10564 TTAAAGC-AAGAAAAATAAACAAAAT
1 TTAAAGCAAAGAAAAAGAAACAAAAA
10589 TTAAA-CAAAGAA
1 TTAAAGCAAAGAA
10601 GAAAAAGAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 1 0.03
25 25 0.78
26 6 0.19
ACGTcount: A:0.68, C:0.08, G:0.08, T:0.16
Consensus pattern (26 bp):
TTAAAGCAAAGAAAAAGAAACAAAAA
Found at i:10756 original size:7 final size:7
Alignment explanation
Indices: 10744--10819 Score: 71
Period size: 7 Copynumber: 10.3 Consensus size: 7
10734 AGTAAAAGAA
10744 CCAAGCC
1 CCAAGCC
10751 CCAAGCC
1 CCAAGCC
*
10758 CCTAAAACC
1 CC--AAGCC
10767 CCAAGCC
1 CCAAGCC
10774 CCAAGCC
1 CCAAGCC
10781 CCAAGCC
1 CCAAGCC
*
10788 CCTAAAACC
1 CC--AAGCC
*
10797 CCAACCC
1 CCAAGCC
*
10804 CCAACCC
1 CCAAGCC
*
10811 CCAAACC
1 CCAAGCC
10818 CC
1 CC
10820 CAATCCGGGA
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
7 48 0.80
9 12 0.20
ACGTcount: A:0.33, C:0.58, G:0.07, T:0.03
Consensus pattern (7 bp):
CCAAGCC
Found at i:10780 original size:30 final size:30
Alignment explanation
Indices: 10744--10819 Score: 125
Period size: 30 Copynumber: 2.5 Consensus size: 30
10734 AGTAAAAGAA
*
10744 CCAAGCCCCAAGCCCCTAAAACCCCAAGCC
1 CCAAGCCCCAAGCCCCTAAAACCCCAACCC
10774 CCAAGCCCCAAGCCCCTAAAACCCCAACCC
1 CCAAGCCCCAAGCCCCTAAAACCCCAACCC
* *
10804 CCAACCCCCAAACCCC
1 CCAAGCCCCAAGCCCC
10820 CAATCCGGGA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.33, C:0.58, G:0.07, T:0.03
Consensus pattern (30 bp):
CCAAGCCCCAAGCCCCTAAAACCCCAACCC
Found at i:10848 original size:21 final size:22
Alignment explanation
Indices: 10813--10860 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
10803 CCCAACCCCC
*
10813 AAACCCCCAATCCGGGAACCTA
1 AAACCCCCAATCCGGAAACCTA
*
10835 AAACCCCTAA-CCGGAAACCTA
1 AAACCCCCAATCCGGAAACCTA
10856 AAACC
1 AAACC
10861 TAAAGAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.42, C:0.40, G:0.10, T:0.08
Consensus pattern (22 bp):
AAACCCCCAATCCGGAAACCTA
Found at i:18032 original size:31 final size:31
Alignment explanation
Indices: 17997--18061 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
17987 ATATTTTGGT
17997 CCCTGAAATCACAATCTGATGTAGTCCAAAA
1 CCCTGAAATCACAATCTGATGTAGTCCAAAA
18028 CCCTGAAATCACAATCTGATGTAGTCCAAAA
1 CCCTGAAATCACAATCTGATGTAGTCCAAAA
18059 CCC
1 CCC
18062 AGTAATCCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.37, C:0.29, G:0.12, T:0.22
Consensus pattern (31 bp):
CCCTGAAATCACAATCTGATGTAGTCCAAAA
Found at i:18499 original size:31 final size:31
Alignment explanation
Indices: 18425--18505 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
18415 AAGAATGAAT
* * *
18425 TAAATTCAGTGCCTACTAAATCGTTGTAAAA
1 TAAATTCAGTGCTTATTAAAACGTTGTAAAA
*
18456 TAAATTTAGTGCTTATTAAAACGTTGTAAAA
1 TAAATTCAGTGCTTATTAAAACGTTGTAAAA
18487 TAAATTCAGTGCTTATTAA
1 TAAATTCAGTGCTTATTAA
18506 TACCCGGCTC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (31 bp):
TAAATTCAGTGCTTATTAAAACGTTGTAAAA
Found at i:28364 original size:15 final size:15
Alignment explanation
Indices: 28346--28397 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
28336 TAAATTTTTA
28346 TTTAATATACTTATT
1 TTTAATATACTTATT
* *
28361 TTTAATATTCTCATT
1 TTTAATATACTTATT
* *
28376 GTCTGAATATATTTATT
1 -T-TTAATATACTTATT
28393 TTTAA
1 TTTAA
28398 AATAATACTA
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
15 16 0.57
16 2 0.07
17 10 0.36
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.58
Consensus pattern (15 bp):
TTTAATATACTTATT
Found at i:28447 original size:20 final size:20
Alignment explanation
Indices: 28422--28461 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
28412 CTATATCAAA
28422 TATATAAAGAGTTAAAAAGT
1 TATATAAAGAGTTAAAAAGT
28442 TATATAAAGAGTTAAAAAGT
1 TATATAAAGAGTTAAAAAGT
28462 AAGTCAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.15, T:0.30
Consensus pattern (20 bp):
TATATAAAGAGTTAAAAAGT
Found at i:29790 original size:21 final size:21
Alignment explanation
Indices: 29758--29798 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
29748 TCCTGCAGCA
29758 TAAAAAATCTGAACCGGACAC
1 TAAAAAATCTGAACCGGACAC
29779 TAAAAGAA-CTGAACCGGACA
1 TAAAA-AATCTGAACCGGACA
29799 GGGGAAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (21 bp):
TAAAAAATCTGAACCGGACAC
Found at i:30739 original size:40 final size:40
Alignment explanation
Indices: 30684--30767 Score: 168
Period size: 40 Copynumber: 2.1 Consensus size: 40
30674 CTACGTGCGT
30684 CACAACTCCCACCGGGTTCCTAGAACCAAAATCAAGCCAA
1 CACAACTCCCACCGGGTTCCTAGAACCAAAATCAAGCCAA
30724 CACAACTCCCACCGGGTTCCTAGAACCAAAATCAAGCCAA
1 CACAACTCCCACCGGGTTCCTAGAACCAAAATCAAGCCAA
30764 CACA
1 CACA
30768 GATGCAGTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.38, C:0.38, G:0.12, T:0.12
Consensus pattern (40 bp):
CACAACTCCCACCGGGTTCCTAGAACCAAAATCAAGCCAA
Found at i:40273 original size:31 final size:30
Alignment explanation
Indices: 40227--40288 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 30
40217 GCAGATTATA
* *
40227 TTTTACCTAAGTCATTCGATTTTGAGGTATT
1 TTTTACCTAAATCATTCGATTTTAAGG-ATT
*
40258 TTTTATCTAAATCATTCGATTTTAAGGATT
1 TTTTACCTAAATCATTCGATTTTAAGGATT
40288 T
1 T
40289 AGCTTTTCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 4 0.14
31 24 0.86
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.50
Consensus pattern (30 bp):
TTTTACCTAAATCATTCGATTTTAAGGATT
Found at i:40898 original size:13 final size:13
Alignment explanation
Indices: 40880--40940 Score: 86
Period size: 13 Copynumber: 4.7 Consensus size: 13
40870 CTCAAATTTT
*
40880 TCAAAAGTACTTC
1 TCAAAAGCACTTC
*
40893 TCAAAAGCATTTC
1 TCAAAAGCACTTC
40906 TCAAAAGCACTTC
1 TCAAAAGCACTTC
* *
40919 TTAAAAGCATTTC
1 TCAAAAGCACTTC
40932 TCAAAAGCA
1 TCAAAAGCA
40941 ATGAAGAACT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 42 1.00
ACGTcount: A:0.41, C:0.23, G:0.08, T:0.28
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:40911 original size:26 final size:26
Alignment explanation
Indices: 40875--40940 Score: 105
Period size: 26 Copynumber: 2.5 Consensus size: 26
40865 AAACACTCAA
* *
40875 ATTTTTCAAAAGTACTTCTCAAAAGC
1 ATTTCTCAAAAGCACTTCTCAAAAGC
*
40901 ATTTCTCAAAAGCACTTCTTAAAAGC
1 ATTTCTCAAAAGCACTTCTCAAAAGC
40927 ATTTCTCAAAAGCA
1 ATTTCTCAAAAGCA
40941 ATGAAGAACT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.32
Consensus pattern (26 bp):
ATTTCTCAAAAGCACTTCTCAAAAGC
Found at i:44009 original size:16 final size:18
Alignment explanation
Indices: 43972--44009 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
43962 TTTCGGAATT
*
43972 TTCAAGATTTTTTTATAC
1 TTCAAGATTTTTTAATAC
43990 TTCAA-ATTTTTTAATA-
1 TTCAAGATTTTTTAATAC
44006 TTCA
1 TTCA
44010 TTTTAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 10 0.53
18 5 0.26
ACGTcount: A:0.32, C:0.11, G:0.03, T:0.55
Consensus pattern (18 bp):
TTCAAGATTTTTTAATAC
Found at i:51582 original size:6 final size:6
Alignment explanation
Indices: 51571--51600 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
51561 ATGAGATTGC
51571 CATAGT CATAGT CATAGT CATAGT CATAGT
1 CATAGT CATAGT CATAGT CATAGT CATAGT
51601 AATACTCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (6 bp):
CATAGT
Found at i:65303 original size:33 final size:34
Alignment explanation
Indices: 65228--65292 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 34
65218 TTGAGAAGTT
* **
65228 GAAGTATGCCTTGAAGGCTAAGTGTCTTGGAAGAC
1 GAAGCATGCCTTGAAGGCT-AGTGTCTAAGAAGAC
65263 GAAGCATGCCTTGAAGGCT-GTGTCTAAGAA
1 GAAGCATGCCTTGAAGGCTAGTGTCTAAGAA
65293 TAGCAAGCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 9 0.33
35 18 0.67
ACGTcount: A:0.29, C:0.15, G:0.31, T:0.25
Consensus pattern (34 bp):
GAAGCATGCCTTGAAGGCTAGTGTCTAAGAAGAC
Found at i:74521 original size:2 final size:2
Alignment explanation
Indices: 74516--74546 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
74506 AATAAAGTGC
74516 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
74547 AAAACTATTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:80311 original size:2 final size:2
Alignment explanation
Indices: 80306--80336 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
80296 AATAAAGTGC
80306 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
80337 AAAACTATTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:89146 original size:56 final size:56
Alignment explanation
Indices: 89060--89173 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
89050 CCAAGGTATA
89060 TCTTTATTTGATTGTTATTTTCTATTCGCAAGACTATTAATGTTTATTTTGCACCT
1 TCTTTATTTGATTGTTATTTTCTATTCGCAAGACTATTAATGTTTATTTTGCACCT
89116 TCTTTATTTGATTGTTATTTTCTATTCGCAAGACTATTAATGTTTATTTTGCACCT
1 TCTTTATTTGATTGTTATTTTCTATTCGCAAGACTATTAATGTTTATTTTGCACCT
89172 TC
1 TC
89174 CATATAAATT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.21, C:0.15, G:0.11, T:0.54
Consensus pattern (56 bp):
TCTTTATTTGATTGTTATTTTCTATTCGCAAGACTATTAATGTTTATTTTGCACCT
Found at i:89272 original size:2 final size:2
Alignment explanation
Indices: 89265--89290 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
89255 TGAAATTTGG
89265 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
89291 TCTTTCTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:99077 original size:18 final size:19
Alignment explanation
Indices: 99054--99089 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
99044 TATTTATTAT
99054 TCTC-TTTCCTTTCCCATC
1 TCTCTTTTCCTTTCCCATC
*
99072 TCTCTTTTTCTTTCCCAT
1 TCTCTTTTCCTTTCCCAT
99090 TCGAATTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.06, C:0.39, G:0.00, T:0.56
Consensus pattern (19 bp):
TCTCTTTTCCTTTCCCATC
Found at i:105197 original size:12 final size:12
Alignment explanation
Indices: 105180--105206 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
105170 TTTTTATTAT
105180 TAAAAATTTGTG
1 TAAAAATTTGTG
105192 TAAAAATTTGTG
1 TAAAAATTTGTG
105204 TAA
1 TAA
105207 TTGACTTGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (12 bp):
TAAAAATTTGTG
Found at i:105520 original size:17 final size:17
Alignment explanation
Indices: 105474--105521 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
105464 CTGCTTTTGG
* *
105474 CCAAAAATATATTGTCT
1 CCAAAAATATTTTTTCT
*
105491 -CAAAACATTTTTTTTCT
1 CCAAAA-ATATTTTTTCT
105508 CCAAAAATATTTTT
1 CCAAAAATATTTTT
105522 AAAAAATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 5 0.20
17 15 0.60
18 5 0.20
ACGTcount: A:0.38, C:0.17, G:0.02, T:0.44
Consensus pattern (17 bp):
CCAAAAATATTTTTTCT
Found at i:113152 original size:18 final size:18
Alignment explanation
Indices: 113129--113189 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
113119 AATTTTATCT
113129 ATTTATTTATAAAGACTA
1 ATTTATTTATAAAGACTA
*
113147 ATTTATTTATTTAA-AC--
1 ATTTATTTA-TAAAGACTA
113163 ATTT-TTTATAAAGACTA
1 ATTTATTTATAAAGACTA
113180 ATTTATTTAT
1 ATTTATTTAT
113190 TTTTTAAGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 3 0.08
15 6 0.17
16 4 0.11
17 4 0.11
18 16 0.44
19 3 0.08
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.52
Consensus pattern (18 bp):
ATTTATTTATAAAGACTA
Found at i:118710 original size:12 final size:13
Alignment explanation
Indices: 118686--118710 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
118676 TTTATTTATT
118686 TATTTAATAAAAA
1 TATTTAATAAAAA
118699 TATTTAATAAAA
1 TATTTAATAAAA
118711 CATTAATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TATTTAATAAAAA
Found at i:121368 original size:14 final size:14
Alignment explanation
Indices: 121349--121376 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
121339 ATATTAACAT
121349 GGGTCAAAACTGAA
1 GGGTCAAAACTGAA
121363 GGGTCAAAACTGAA
1 GGGTCAAAACTGAA
121377 AACTGTTCTT
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:0.43, C:0.14, G:0.29, T:0.14
Consensus pattern (14 bp):
GGGTCAAAACTGAA
Found at i:141500 original size:28 final size:28
Alignment explanation
Indices: 141459--141512 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
141449 GTAATTTTTT
141459 TTTAAAAAAATTGTGATAGGAACATTGG
1 TTTAAAAAAATTGTGATAGGAACATTGG
*
141487 TTTAAAAAATTTGTGATAGGAACATT
1 TTTAAAAAAATTGTGATAGGAACATT
141513 AAATTCAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.35
Consensus pattern (28 bp):
TTTAAAAAAATTGTGATAGGAACATTGG
Found at i:145431 original size:2 final size:2
Alignment explanation
Indices: 145424--145457 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
145414 GAACAAAGGG
145424 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
145458 CGGGCGTATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:149012 original size:15 final size:16
Alignment explanation
Indices: 148992--149024 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
148982 AAAAGAAAAA
*
148992 TTTTAATTAA-TTAAT
1 TTTTAAATAATTTAAT
149007 TTTTAAATAATTTAAT
1 TTTTAAATAATTTAAT
149023 TT
1 TT
149025 AAATTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTAAATAATTTAAT
Found at i:158526 original size:6 final size:6
Alignment explanation
Indices: 158518--158552 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
158508 AGACAAGCCG
* *
158518 GTTCCG GTTCCA GTTCCT GTTCCA GTTCCA GTTCC
1 GTTCCA GTTCCA GTTCCA GTTCCA GTTCCA GTTCC
158553 GGTACTGGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.09, C:0.34, G:0.20, T:0.37
Consensus pattern (6 bp):
GTTCCA
Found at i:158545 original size:18 final size:18
Alignment explanation
Indices: 158518--158552 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
158508 AGACAAGCCG
*
158518 GTTCCGGTTCCAGTTCCT
1 GTTCCAGTTCCAGTTCCT
158536 GTTCCAGTTCCAGTTCC
1 GTTCCAGTTCCAGTTCC
158553 GGTACTGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.09, C:0.34, G:0.20, T:0.37
Consensus pattern (18 bp):
GTTCCAGTTCCAGTTCCT
Found at i:163166 original size:18 final size:18
Alignment explanation
Indices: 163126--163174 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
163116 ATGGTGCTGG
163126 TGATGATGATGATGAAGA
1 TGATGATGATGATGAAGA
* **
163144 CGATGATGATGATGAATT
1 TGATGATGATGATGAAGA
*
163162 TGATGATGCTGAT
1 TGATGATGATGAT
163175 TCAGGAGCAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.04, G:0.31, T:0.33
Consensus pattern (18 bp):
TGATGATGATGATGAAGA
Found at i:178951 original size:15 final size:16
Alignment explanation
Indices: 178927--178961 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
178917 ACTTAATAAT
*
178927 TAAAATATTTAATTA-
1 TAAAAAATTTAATTAC
178942 TAAAAAATTTAATTAC
1 TAAAAAATTTAATTAC
178958 TAAA
1 TAAA
178962 TAAAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
TAAAAAATTTAATTAC
Found at i:183307 original size:27 final size:27
Alignment explanation
Indices: 183270--183324 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
183260 TTAACCACAT
183270 TTTTCTTCTGATTCACTCCACTGAAAA
1 TTTTCTTCTGATTCACTCCACTGAAAA
183297 TTTTCTTCTGATTCACTCCACTGAAAA
1 TTTTCTTCTGATTCACTCCACTGAAAA
183324 T
1 T
183325 CTCGGGTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.25, G:0.07, T:0.42
Consensus pattern (27 bp):
TTTTCTTCTGATTCACTCCACTGAAAA
Found at i:187879 original size:269 final size:269
Alignment explanation
Indices: 187354--187882 Score: 697
Period size: 269 Copynumber: 2.0 Consensus size: 269
187344 TCCATAATTA
* * *
187354 AATCTTGACAAGAAATAACGTTTTAATTTACTAATAACAATTAAAATTGAAAGTTTCCAAATCTT
1 AATCTTGACAAGAAATAAAGTTTTAATTTAATAATAACAATTAAAATTGAAAGTTTCCAAATCTG
* *
187419 GTGGCAATGTTTATTACTCTAAAGGAAAATTCTCCTTCTTGATCCTTAATTATATAAGCTTGGCA
66 GTGGCAATGCTTATTACTCTAAAGGAAAATTATCCTTCTTGATCCTTAATTATATAAGCTTGGCA
* * * *
187484 ATTAATTTTCAACTTGTTTAACAAGTAAAATCTCAGCTTGAATTGAATGTAGCAAGAAGGTAAAA
131 ATTAATTTTCAACTTATTTAACAAGTAAAATCTCAGCTTGAATTGAATATAACAAGAAGATAAAA
* * * * * *
187549 ATCGAGTTTGTTATATGATCTTGTGTTAGTAAATGTGGTGGGAAATAATATTAGATTGAAATGTA
196 ATCGAGTCTATTATATGATCTTATATTAGTAAATATGGTGAGAAATAATATTAGATTGAAATGTA
187614 TCATTATTG
261 TCATTATTG
** * *
187623 AATCTTGAGGAGAAATAAAGTTTTAATTTAATAATTACAATTAAAATTGAAAGTTTTCAAATCTG
1 AATCTTGACAAGAAATAAAGTTTTAATTTAATAATAACAATTAAAATTGAAAGTTTCCAAATCTG
* * *
187688 GTGGCAATGCTTATTA-TCCTAAAGGAAAATTATGCTTCTTTATCCTTAATTATATAAGTTTGGG
66 GTGGCAATGCTTATTACT-CTAAAGGAAAATTATCCTTCTTGATCCTTAATTATATAAGCTT-GG
* * * * * * * *
187752 GATTTAGTTTTCAACTTATTTAACAAGTAAAATCTTATCTTGATTTGGATATAATAAGGAA-ATA
129 CAATTAATTTTCAACTTATTTAACAAGTAAAATCTCAGCTTGAATTGAATATAACAA-GAAGATA
* * *
187816 AAAGTCGAGTCTATTGTATGTTCTTATATT-GATAAATATGGTGAGAAATAATATTAG-TTGAAA
193 AAAATCGAGTCTATTATATGATCTTATATTAG-TAAATATGGTGAGAAATAATATTAGATTGAAA
187879 TGTA
257 TGTA
187883 AATAAAGCTG
Statistics
Matches: 223, Mismatches: 33, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
268 1 0.00
269 123 0.55
270 96 0.43
271 3 0.01
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (269 bp):
AATCTTGACAAGAAATAAAGTTTTAATTTAATAATAACAATTAAAATTGAAAGTTTCCAAATCTG
GTGGCAATGCTTATTACTCTAAAGGAAAATTATCCTTCTTGATCCTTAATTATATAAGCTTGGCA
ATTAATTTTCAACTTATTTAACAAGTAAAATCTCAGCTTGAATTGAATATAACAAGAAGATAAAA
ATCGAGTCTATTATATGATCTTATATTAGTAAATATGGTGAGAAATAATATTAGATTGAAATGTA
TCATTATTG
Found at i:195942 original size:18 final size:18
Alignment explanation
Indices: 195919--195955 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
195909 TAACACTATA
* *
195919 ATATATTATGTTATTTAT
1 ATATATTATATAATTTAT
195937 ATATATTATATAATTTAT
1 ATATATTATATAATTTAT
195955 A
1 A
195956 ACACAAAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
ATATATTATATAATTTAT
Found at i:196388 original size:22 final size:22
Alignment explanation
Indices: 196360--196405 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
196350 CTTCCAACAC
*
196360 AAGTATGAAATGTTTATGAGCA
1 AAGTATGAAATATTTATGAGCA
196382 AAGTATGAAATATTTATGAGCA
1 AAGTATGAAATATTTATGAGCA
196404 AA
1 AA
196406 TTTCAAGAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.46, C:0.04, G:0.20, T:0.30
Consensus pattern (22 bp):
AAGTATGAAATATTTATGAGCA
Found at i:203510 original size:31 final size:30
Alignment explanation
Indices: 203466--203527 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
203456 TATATTTTTA
*
203466 AATAAATACAATTAAATCAAAATTAAAATTT
1 AATAAATACAATTAAA-CAAAACTAAAATTT
* * * *
203497 AATATATATAATTATACGAAACTAAAATTT
1 AATAAATACAATTAAACAAAACTAAAATTT
203527 A
1 A
203528 TGTCTCAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.34
Consensus pattern (30 bp):
AATAAATACAATTAAACAAAACTAAAATTT
Found at i:203595 original size:3 final size:3
Alignment explanation
Indices: 203587--203619 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
203577 TATATACTAT
203587 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
203620 GTGGTTAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:204222 original size:31 final size:31
Alignment explanation
Indices: 204168--204227 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
204158 CTTAAAAAAA
204168 GACTTAAATAAAATCTTTCGAATAGTTTATT
1 GACTTAAATAAAATCTTTCGAATAGTTTATT
* *
204199 GACTTGAATGAAAA-CTTTTGAATAGTTTA
1 GACTTAAAT-AAAATCTTTCGAATAGTTTA
204228 ATGATCATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.40
Consensus pattern (31 bp):
GACTTAAATAAAATCTTTCGAATAGTTTATT
Found at i:207175 original size:28 final size:27
Alignment explanation
Indices: 207131--207191 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
207121 TTTAGTGTAG
* * *
207131 AAAATATTAAATTAATT-TTATTTTATT
1 AAAAAATTAAATAAATTATT-TTTTATA
207158 AAAAAATTGAAATAAATTATTTTTTATA
1 AAAAAATT-AAATAAATTATTTTTTATA
207186 AAAAAA
1 AAAAAA
207192 ATTCAAAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 7 0.24
28 20 0.69
29 2 0.07
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (27 bp):
AAAAAATTAAATAAATTATTTTTTATA
Found at i:208632 original size:60 final size:59
Alignment explanation
Indices: 208554--208667 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 59
208544 AGTTGGTTGA
* * * * *
208554 TATTTTTTAACTTTTCATAATTGGGTGACCAAAAAAGAAATTTACTCATAGTTGAAAGAT
1 TATTTTATAACTTTTCATAATTGGATGACC-AAAAACAAATTCACTAATAGTTGAAAGAT
* * *
208614 TATTTTATAATTTTTCATAGTTGGATGACCTAAAACAAATTCACTAATAGTTGA
1 TATTTTATAACTTTTCATAATTGGATGACCAAAAACAAATTCACTAATAGTTGA
208668 GTGACTATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
59 20 0.43
60 26 0.57
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (59 bp):
TATTTTATAACTTTTCATAATTGGATGACCAAAAACAAATTCACTAATAGTTGAAAGAT
Found at i:214403 original size:23 final size:23
Alignment explanation
Indices: 214376--214430 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
214366 AAATAATATG
214376 AATTGAATTCATATTTAAGTAAT
1 AATTGAATTCATATTTAAGTAAT
214399 AATTGAATTCATATTTAAGTAAT
1 AATTGAATTCATATTTAAGTAAT
214422 AATTGAATT
1 AATTGAATT
214431 AAAAATAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.44
Consensus pattern (23 bp):
AATTGAATTCATATTTAAGTAAT
Found at i:221071 original size:21 final size:21
Alignment explanation
Indices: 221045--221086 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
221035 AGGTAGTTTC
221045 ATGGAATTTTCGGAGACAAGT
1 ATGGAATTTTCGGAGACAAGT
221066 ATGGAATTTTCGGAGACAAGT
1 ATGGAATTTTCGGAGACAAGT
221087 TCGGTTCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.29
Consensus pattern (21 bp):
ATGGAATTTTCGGAGACAAGT
Found at i:244134 original size:15 final size:15
Alignment explanation
Indices: 244114--244156 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
244104 TGGCACCAAA
244114 AGCTGAGAAGAAGCC
1 AGCTGAGAAGAAGCC
244129 AGCTGAGAAGAAGCC
1 AGCTGAGAAGAAGCC
* *
244144 AGCGGAGGAGAAG
1 AGCTGAGAAGAAG
244157 AAGACGGTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.40, C:0.16, G:0.40, T:0.05
Consensus pattern (15 bp):
AGCTGAGAAGAAGCC
Found at i:251273 original size:16 final size:17
Alignment explanation
Indices: 251252--251284 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
251242 ATGTCTAGGT
251252 AAATT-ATTAATTGAGA
1 AAATTAATTAATTGAGA
251268 AAATTAGATTAATTGAG
1 AAATTA-ATTAATTGAG
251285 GGGTTAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
18 10 0.67
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
AAATTAATTAATTGAGA
Found at i:252633 original size:46 final size:46
Alignment explanation
Indices: 252566--252728 Score: 258
Period size: 46 Copynumber: 3.6 Consensus size: 46
252556 TTTGAGTACT
* * *
252566 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
*
252612 TCTGATCAAGTGACAAAGTGATAAGTGCTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
252658 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
* *
252704 TCTGAT-TAGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
252729 ATCATACGTA
Statistics
Matches: 110, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
44 12 0.11
45 5 0.05
46 93 0.85
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
Found at i:257716 original size:26 final size:27
Alignment explanation
Indices: 257635--257719 Score: 82
Period size: 31 Copynumber: 3.0 Consensus size: 27
257625 TTTTCTTCAT
* * *
257635 ATTTTTTAATAATATAAACAACTATGA
1 ATTTTTGAATAACATAAAGAACTATGA
257662 ATTTTTGAATAACATAAAATGAAGGACTATG-
1 ATTTTTGAATAACAT-AAA-G-A--ACTATGA
*
257693 GTTTTTGAATAACATAAAGAACTATGA
1 ATTTTTGAATAACATAAAGAACTATGA
257720 GCTGTCATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
26 6 0.12
27 13 0.27
28 4 0.08
29 1 0.02
30 4 0.08
31 14 0.29
32 6 0.12
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.35
Consensus pattern (27 bp):
ATTTTTGAATAACATAAAGAACTATGA
Found at i:258087 original size:23 final size:22
Alignment explanation
Indices: 258045--258089 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
258035 AATAATATCA
*
258045 TATTAAAATTATTATTAAATAT
1 TATTAAAATTATTATAAAATAT
258067 TATTAACAATTATGT-TAAAATAT
1 TATTAA-AATTAT-TATAAAATAT
258090 GAATAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 6 0.30
23 13 0.65
24 1 0.05
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
TATTAAAATTATTATAAAATAT
Found at i:261711 original size:14 final size:14
Alignment explanation
Indices: 261692--261731 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
261682 TTGATTGACA
261692 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
261706 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
261720 GGAAAATGTTTT
1 GTAAAATGTTTT
261732 ACTTTTCTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:263649 original size:13 final size:13
Alignment explanation
Indices: 263631--263656 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
263621 CCAGAAACTG
263631 ATTTGCAGAAAAC
1 ATTTGCAGAAAAC
263644 ATTTGCAGAAAAC
1 ATTTGCAGAAAAC
263657 TACCCATTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (13 bp):
ATTTGCAGAAAAC
Found at i:278153 original size:35 final size:34
Alignment explanation
Indices: 278071--278153 Score: 82
Period size: 33 Copynumber: 2.4 Consensus size: 34
278061 ATTTTAGGTC
*
278071 TATTCATATTATATTTTAATTTTTTAAAAATATTTA
1 TATT-ATATT-TATTTTAATTATTTAAAAATATTTA
278107 TATTATA-TTATTTTAA-TATTTAATAAA-AGTTTA
1 TATTATATTTATTTTAATTATTTAA-AAATA-TTTA
*
278140 TATTTTTATTTATT
1 TA-TTATATTTATT
278154 GAAAATTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
32 7 0.17
33 17 0.41
34 5 0.12
35 8 0.20
36 4 0.10
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (34 bp):
TATTATATTTATTTTAATTATTTAAAAATATTTA
Found at i:283504 original size:18 final size:16
Alignment explanation
Indices: 283481--283516 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
283471 GTTTAAAATT
283481 TTTAATTAATTAAATTTA
1 TTTAATTAA--AAATTTA
283499 TTTAATTAAAAATTTA
1 TTTAATTAAAAATTTA
283515 TT
1 TT
283517 CTCATCCCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTAATTAAAAATTTA
Found at i:291595 original size:18 final size:18
Alignment explanation
Indices: 291569--291603 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
291559 TCATTTAAAG
* *
291569 ATTATAAAGATATAAATT
1 ATTAAAAAGATAAAAATT
291587 ATTAAAAAGATAAAAAT
1 ATTAAAAAGATAAAAAT
291604 ACACTTTTAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (18 bp):
ATTAAAAAGATAAAAATT
Found at i:301185 original size:39 final size:39
Alignment explanation
Indices: 301131--301210 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
301121 TTGTCAGAAT
*
301131 TTGGGTATTTATGTATGAGTTACGTGAAGAATAAGAAAA
1 TTGGGTATTTATGTATGAGTTACATGAAGAATAAGAAAA
*
301170 TTGGGTATTTATGTATGAGTTACATGAATAATAAGAAAA
1 TTGGGTATTTATGTATGAGTTACATGAAGAATAAGAAAA
301209 TT
1 TT
301211 ATTAACTCTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.36
Consensus pattern (39 bp):
TTGGGTATTTATGTATGAGTTACATGAAGAATAAGAAAA
Found at i:304797 original size:17 final size:17
Alignment explanation
Indices: 304775--304852 Score: 61
Period size: 17 Copynumber: 4.5 Consensus size: 17
304765 TTAAAAAACT
304775 TTAAAAAATTAAATATA
1 TTAAAAAATTAAATATA
304792 TTAAAAAATGTTAAATATA
1 TTAAAAAA--TTAAATATA
* ** *
304811 --ACCAATTTTAAAATATT
1 TTA-AAAAATT-AAATATA
*
304828 TTTAAAAATTAAATATA
1 TTAAAAAATTAAATATA
304845 TTAAAAAA
1 TTAAAAAA
304853 ATGTTAAGTA
Statistics
Matches: 45, Mismatches: 10, Indels: 12
0.67 0.15 0.18
Matches are distributed among these distances:
16 2 0.04
17 28 0.62
18 6 0.13
19 9 0.20
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (17 bp):
TTAAAAAATTAAATATA
Found at i:304835 original size:53 final size:54
Alignment explanation
Indices: 304761--304878 Score: 193
Period size: 53 Copynumber: 2.2 Consensus size: 54
304751 ATATATTTAA
*
304761 AATTTTAAAAAACTTTAAAAAATTAAATATATT-AAAAAATGTTAAATATAACC
1 AATTTTAAAATACTTTAAAAAATTAAATATATTAAAAAAATGTTAAATATAACC
* * *
304814 AATTTTAAAATATTTTTAAAAATTAAATATATTAAAAAAATGTTAAGTATAACC
1 AATTTTAAAATACTTTAAAAAATTAAATATATTAAAAAAATGTTAAATATAACC
304868 AATTTTAAAAT
1 AATTTTAAAAT
304879 TTTAATATTT
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
53 30 0.50
54 30 0.50
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (54 bp):
AATTTTAAAATACTTTAAAAAATTAAATATATTAAAAAAATGTTAAATATAACC
Found at i:304875 original size:27 final size:27
Alignment explanation
Indices: 304794--304877 Score: 82
Period size: 27 Copynumber: 3.1 Consensus size: 27
304784 TAAATATATT
304794 AAAAAATGTTAAATATAACCAATTTTA
1 AAAAAATGTTAAATATAACCAATTTTA
* * * * *
304821 AAATATTTTTAAAAATTAA--ATATATTA
1 AAAAAATGTTAAATA-TAACCA-ATTTTA
*
304848 AAAAAATGTTAAGTATAACCAATTTTA
1 AAAAAATGTTAAATATAACCAATTTTA
304875 AAA
1 AAA
304878 TTTTAATATT
Statistics
Matches: 42, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
26 4 0.10
27 34 0.81
28 4 0.10
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.36
Consensus pattern (27 bp):
AAAAAATGTTAAATATAACCAATTTTA
Found at i:305921 original size:16 final size:16
Alignment explanation
Indices: 305896--305930 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
305886 GAATACTTTT
*
305896 TAAAAGTATTTTTAAA
1 TAAAAATATTTTTAAA
305912 TAAAAATATTTTTAAA
1 TAAAAATATTTTTAAA
305928 TAA
1 TAA
305931 GCTGTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
TAAAAATATTTTTAAA
Found at i:307018 original size:5 final size:5
Alignment explanation
Indices: 307008--307033 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
306998 GTAGGCTAAA
307008 CGCAC CGCAC CGCAC CGCAC CGCAC C
1 CGCAC CGCAC CGCAC CGCAC CGCAC C
307034 CAATCGACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.62, G:0.19, T:0.00
Consensus pattern (5 bp):
CGCAC
Found at i:317597 original size:20 final size:20
Alignment explanation
Indices: 317574--317612 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
317564 ATTAAAAATT
317574 TTGAACTAAA-ATGGTCTTAA
1 TTGAA-TAAATATGGTCTTAA
*
317594 TTGAATAAATATTGTCTTA
1 TTGAATAAATATGGTCTTA
317613 TAGGGTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (20 bp):
TTGAATAAATATGGTCTTAA
Found at i:318526 original size:232 final size:231
Alignment explanation
Indices: 318091--318547 Score: 736
Period size: 231 Copynumber: 2.0 Consensus size: 231
318081 AATTCAGTTT
* *
318091 TTTTTTTTATGAAATAGCTTTGAAGTCATCAATCTGTGAATCAAAATCGAAATAACTTTCTTCTT
1 TTTTTTTTATGAAATAGCTTTGAAGTCACCAATCTGTGAATCAAAATCGAAACAACTTTCTTCTT
* * *
318156 CGATCTTCGACATTGACCATCAGATCGCTTGAAACCCACTAATCAATCTTCTTTTTTTGAAAAAA
66 CAATCTTCGACATTGACCATCAGATCGCCTGAAACCCACTAATCAATCTTCTTTTTTTAAAAAAA
* * *
318221 AAACTTAACAACCAAATGATTTAAATAAAAACGTTCTAATAGTTTATTGGCTAAAATGAAAATTT
131 AAACTTAACAACCAAATGATTTAAATAAAAACGTTCTAATAGTTTAGTGACTAAAATGAAAATTG
318286 TCAAATATTTCAGGTCTAAAATAATTTTTTTGAATC
196 TCAAATATTTCAGGTCTAAAATAATTTTTTTGAATC
**
318322 TTTTTTTTATGAAATAGCTTTGAAGTCACCAATCTGTGAATCAAAATCGAAACAGTTTTCTTCTT
1 TTTTTTTTATGAAATAGCTTTGAAGTCACCAATCTGTGAATCAAAATCGAAACAACTTTCTTCTT
* **
318387 CAATCTTCGACATTGACCATCAGATCGCCTGAAACTCACTAATCGGTCTTCTTTTTTTAAAAAAA
66 CAATCTTCGACATTGACCATCAGATCGCCTGAAACCCACTAATCAATCTTCTTTTTTT-AAAAAA
* * * *
318452 AAAACTTAGCAATCTAATTATTTAAATAAAAACGTT-TGAATAGTTTAGTGACTAAAATGAAAAT
130 AAAACTTAACAACCAAATGATTTAAATAAAAACGTTCT-AATAGTTTAGTGACTAAAATGAAAAT
318516 TGTCAAATATTTCAGGTCTAAAATAATTTTTT
194 TGTCAAATATTTCAGGTCTAAAATAATTTTTT
318548 AATAGCTTAG
Statistics
Matches: 207, Mismatches: 17, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
231 115 0.56
232 92 0.44
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (231 bp):
TTTTTTTTATGAAATAGCTTTGAAGTCACCAATCTGTGAATCAAAATCGAAACAACTTTCTTCTT
CAATCTTCGACATTGACCATCAGATCGCCTGAAACCCACTAATCAATCTTCTTTTTTTAAAAAAA
AAACTTAACAACCAAATGATTTAAATAAAAACGTTCTAATAGTTTAGTGACTAAAATGAAAATTG
TCAAATATTTCAGGTCTAAAATAATTTTTTTGAATC
Found at i:318762 original size:118 final size:117
Alignment explanation
Indices: 318490--318737 Score: 408
Period size: 118 Copynumber: 2.1 Consensus size: 117
318480 AAAACGTTTG
*
318490 AATAGTTTAGTGACTAAAATGAAAATTG-TCAAATATTTCAGGTCTAAAATAATTTTTTAATAGC
1 AATAGTTTAGTGACTAAAATGAAAA-CGATCAAATATTTCAGGTCTAAAATAATTTTTTAATAGC
* * *
318554 TTAGTGATCATTTTGTAACTTTTTGAAATTAATAACTAAAACGTAAGCTTATT
65 TTAGTGACCATTTTGCAACTTTTTGAAATTAATAACTAAAACATAAGCTTATT
*
318607 AATAGTTTAGTGACTAAAATGAAAACGATCAAATATTTCATGTCTAAAATAATTTTTTTAATAGC
1 AATAGTTTAGTGACTAAAATGAAAACGATCAAATATTTCAGGTCTAAAATAA-TTTTTTAATAGC
* *
318672 TTAGTGACCATTTTGCAATTTTTTGAAATTAATAACTGAAACATAAGCTTATT
65 TTAGTGACCATTTTGCAACTTTTTGAAATTAATAACTAAAACATAAGCTTATT
318725 AATAGTTTAGTGA
1 AATAGTTTAGTGA
318738 TACTGGGAGT
Statistics
Matches: 122, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
116 1 0.01
117 48 0.39
118 73 0.60
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.40
Consensus pattern (117 bp):
AATAGTTTAGTGACTAAAATGAAAACGATCAAATATTTCAGGTCTAAAATAATTTTTTAATAGCT
TAGTGACCATTTTGCAACTTTTTGAAATTAATAACTAAAACATAAGCTTATT
Found at i:322473 original size:26 final size:26
Alignment explanation
Indices: 322437--322486 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
322427 TCTATTTTTC
*
322437 AATAGTTTAATATCACATCAGTAAAA
1 AATAATTTAATATCACATCAGTAAAA
*
322463 AATAATTTAATATCATATCAGTAA
1 AATAATTTAATATCACATCAGTAA
322487 TTTCATCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.50, C:0.10, G:0.06, T:0.34
Consensus pattern (26 bp):
AATAATTTAATATCACATCAGTAAAA
Found at i:327045 original size:17 final size:17
Alignment explanation
Indices: 326992--327046 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
326982 TAATAATACC
*
326992 AAAAATATTTAAAATTA
1 AAAAATATTTTAAATTA
** *
327009 AAAAA-ATAAT-AATTT
1 AAAAATATTTTAAATTA
*
327024 TAAAATATTTTAAATTA
1 AAAAATATTTTAAATTA
327041 AAAAAT
1 AAAAAT
327047 TTACAAAGTA
Statistics
Matches: 27, Mismatches: 9, Indels: 4
0.68 0.22 0.10
Matches are distributed among these distances:
15 8 0.30
16 5 0.19
17 14 0.52
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAAATATTTTAAATTA
Found at i:327069 original size:11 final size:11
Alignment explanation
Indices: 327038--327113 Score: 53
Period size: 11 Copynumber: 7.5 Consensus size: 11
327028 ATATTTTAAA
327038 TTAAAAA-A-T
1 TTAAAAATATT
*
327047 TTACAAAGTATT
1 TTA-AAAATATT
327059 TTAAAAATATT
1 TTAAAAATATT
327070 TT--AAA-A--
1 TTAAAAATATT
327076 TTAAAAA-A-T
1 TTAAAAATATT
327085 TTAAAAAGTATT
1 TTAAAAA-TATT
*
327097 TTAAAAGTATT
1 TTAAAAATATT
327108 TTAAAA
1 TTAAAA
327114 TTAAAAATAA
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
6 2 0.04
8 5 0.09
9 13 0.24
10 3 0.05
11 21 0.38
12 11 0.20
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.39
Consensus pattern (11 bp):
TTAAAAATATT
Found at i:327077 original size:38 final size:37
Alignment explanation
Indices: 326992--327120 Score: 171
Period size: 38 Copynumber: 3.6 Consensus size: 37
326982 TAATAATACC
* *
326992 AAAAATA-TTTAAAATTAAAAAA-ATAATA--ATTTT
1 AAAAATATTTTAAAATTAAAAAATTTAAAAGTATTTT
327025 -AAAATATTTT-AAATTAAAAAATTTACAAAGTATTTT
1 AAAAATATTTTAAAATTAAAAAATTTA-AAAGTATTTT
327061 AAAAATATTTTAAAATTAAAAAATTTAAAAAGTATTTT
1 AAAAATATTTTAAAATTAAAAAATTT-AAAAGTATTTT
*
327099 AAAAGTATTTTAAAATTAAAAA
1 AAAAATATTTTAAAATTAAAAA
327121 TAAAAAATAA
Statistics
Matches: 85, Mismatches: 3, Indels: 11
0.86 0.03 0.11
Matches are distributed among these distances:
32 17 0.20
33 5 0.06
34 2 0.02
36 5 0.06
37 10 0.12
38 45 0.53
39 1 0.01
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (37 bp):
AAAAATATTTTAAAATTAAAAAATTTAAAAGTATTTT
Found at i:338381 original size:29 final size:29
Alignment explanation
Indices: 338348--338405 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
338338 TTGGTCTAAT
* *
338348 GTGCAATT-TGATATATGAACTTTGAATTG
1 GTGCAATTGT-ATACATGAAATTTGAATTG
338377 GTGCAATTGTATACATGAAATTTGAATTG
1 GTGCAATTGTATACATGAAATTTGAATTG
338406 TGGTTCACGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 25 0.96
30 1 0.04
ACGTcount: A:0.33, C:0.07, G:0.21, T:0.40
Consensus pattern (29 bp):
GTGCAATTGTATACATGAAATTTGAATTG
Found at i:338657 original size:2 final size:2
Alignment explanation
Indices: 338650--338694 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
338640 GAATCTAAGT
338650 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
338690 TA TA T
1 TA TA T
338695 GTCGATAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:341535 original size:20 final size:20
Alignment explanation
Indices: 341508--341567 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
341498 ATATTTATTG
341508 ATATTAAATATTTTATAAATA
1 ATATTAAATATTTT-TAAATA
*
341529 A-ATTAAAATAATTTTAAATA
1 ATATT-AAATATTTTTAAATA
*
341549 ATATTACAT-TTTTGTAAAT
1 ATATTAAATATTTT-TAAAT
341568 TTCTACTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 3 0.09
20 18 0.55
21 12 0.36
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (20 bp):
ATATTAAATATTTTTAAATA
Found at i:361082 original size:12 final size:13
Alignment explanation
Indices: 361060--361088 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
361050 TAGAAAATTA
361060 AAAAAAGTATTTT
1 AAAAAAGTATTTT
361073 AAAAAA-TATTTT
1 AAAAAAGTATTTT
361085 AAAA
1 AAAA
361089 TTAAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (13 bp):
AAAAAAGTATTTT
Found at i:366249 original size:2 final size:2
Alignment explanation
Indices: 366242--366269 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
366232 TTCAGCAAGA
366242 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
366270 CACAAAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:386541 original size:20 final size:20
Alignment explanation
Indices: 386518--386561 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
386508 TTTTTAAACC
386518 TTTTTAAT-AATTTTACAAA
1 TTTTTAATAAATTTTACAAA
386537 TTTTTAATAAATTTTACAAA
1 TTTTTAATAAATTTTACAAA
386557 TTTTT
1 TTTTT
386562 TTGTAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTTAATAAATTTTACAAA
Found at i:400414 original size:21 final size:21
Alignment explanation
Indices: 400375--400415 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
400365 AATAAAATCT
* *
400375 AATAACAGCATAAGCACACAC
1 AATAACAGCACAAGAACACAC
*
400396 AATAACAGGACAAGAACACA
1 AATAACAGCACAAGAACACA
400416 TCAAATAGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.24, G:0.12, T:0.07
Consensus pattern (21 bp):
AATAACAGCACAAGAACACAC
Found at i:404050 original size:10 final size:10
Alignment explanation
Indices: 404035--404059 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
404025 TTTTATTAAA
404035 ATTTTCATCC
1 ATTTTCATCC
404045 ATTTTCATCC
1 ATTTTCATCC
404055 ATTTT
1 ATTTT
404060 TACATGTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.24, G:0.00, T:0.56
Consensus pattern (10 bp):
ATTTTCATCC
Found at i:404751 original size:21 final size:21
Alignment explanation
Indices: 404728--404768 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
404718 CTCAGTTCAC
* *
404728 TTTCCTTCTTCTCTTCTTCCCT
1 TTTCC-TCTCCTCTCCTTCCCT
404750 TTTCCTCTCCTCTCCTTCC
1 TTTCCTCTCCTCTCCTTCC
404769 GCTAAACTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTCCTCTCCTCTCCTTCCCT
Found at i:407035 original size:7 final size:7
Alignment explanation
Indices: 407025--407050 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
407015 ACTAAGGACT
407025 AAATGCA
1 AAATGCA
407032 AAATGCA
1 AAATGCA
407039 AAATGCA
1 AAATGCA
407046 AAATG
1 AAATG
407051 GTGCACGACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.12, G:0.15, T:0.15
Consensus pattern (7 bp):
AAATGCA
Found at i:412154 original size:29 final size:27
Alignment explanation
Indices: 412055--412153 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 27
412045 AAAAATAAAA
*
412055 ATTTACCAAAATATTGCAACTTTTTTTT
1 ATTTACCAAAATATT-AAACTTTTTTTT
* *
412083 ATTTATCAAAATATTACAATTTTTTTTT
1 ATTTACCAAAATATTA-AACTTTTTTTT
412111 ATTTACCAAAATATATAAACTTTTTTATT
1 ATTTACCAAAATAT-TAAACTTTTTT-TT
412140 ATTTACCAAAATAT
1 ATTTACCAAAATAT
412154 AAAAAAAAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
28 45 0.71
29 18 0.29
ACGTcount: A:0.38, C:0.11, G:0.01, T:0.49
Consensus pattern (27 bp):
ATTTACCAAAATATTAAACTTTTTTTT
Found at i:412262 original size:27 final size:27
Alignment explanation
Indices: 412232--412325 Score: 152
Period size: 27 Copynumber: 3.5 Consensus size: 27
412222 CGCCAATGGT
* *
412232 ATTGGCGGCACCAAAGGTGCCAAAACC
1 ATTGGCGGCACCAATGGTGCCAATACC
412259 ATTGGCGGCACCAATGGTGCCAATACC
1 ATTGGCGGCACCAATGGTGCCAATACC
*
412286 ATTGGCGGCACCAATGGTGCCAATGCC
1 ATTGGCGGCACCAATGGTGCCAATACC
*
412313 ATTGGCAGCACCA
1 ATTGGCGGCACCA
412326 CTCGTATTAT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 63 1.00
ACGTcount: A:0.28, C:0.30, G:0.27, T:0.16
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAATACC
Found at i:412410 original size:27 final size:29
Alignment explanation
Indices: 412353--412409 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
412343 ACTTCTACCC
412353 AGCTGAAGAGAGAAAAATAATAAAAAAAA
1 AGCTGAAGAGAGAAAAATAATAAAAAAAA
*
412382 AGCTGAAGAGAGAAAATTAA-AAAAAAAA
1 AGCTGAAGAGAGAAAAATAATAAAAAAAA
412410 GAAGAGTTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 8 0.30
29 19 0.70
ACGTcount: A:0.68, C:0.04, G:0.18, T:0.11
Consensus pattern (29 bp):
AGCTGAAGAGAGAAAAATAATAAAAAAAA
Found at i:412505 original size:19 final size:21
Alignment explanation
Indices: 412467--412505 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
412457 AATAATTGAT
*
412467 TATATTATTGTTATTATTTTG
1 TATATTATTGTTAATATTTTG
412488 TATATT-TTG-TAATATTTT
1 TATATTATTGTTAATATTTT
412506 TTGTTGTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.67
Consensus pattern (21 bp):
TATATTATTGTTAATATTTTG
Found at i:412569 original size:3 final size:3
Alignment explanation
Indices: 412551--412585 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
412541 AAAATAAAAG
*
412551 TAT TAGT TAG TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT T
412586 GTTGTTGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:412590 original size:3 final size:3
Alignment explanation
Indices: 412584--412615 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
412574 ATTATTATTA
412584 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
412616 AGTTATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:412640 original size:19 final size:18
Alignment explanation
Indices: 412613--412648 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
412603 TGTTGTTGTT
*
412613 GTTAGTTATTATTATTATG
1 GTTACTTATTATT-TTATG
412632 GTTACTTATTATTTTAT
1 GTTACTTATTATTTTAT
412649 TTACGAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.25, C:0.03, G:0.11, T:0.61
Consensus pattern (18 bp):
GTTACTTATTATTTTATG
Found at i:412652 original size:16 final size:18
Alignment explanation
Indices: 412612--412652 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
412602 TTGTTGTTGT
*
412612 TGTTAGTTATTATTATTA
1 TGTTACTTATTATTATTA
412630 TGGTTACTTATTATT-TTA
1 T-GTTACTTATTATTATTA
412648 T-TTAC
1 TGTTAC
412653 GAAAATAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 4 0.19
18 5 0.24
19 12 0.57
ACGTcount: A:0.24, C:0.05, G:0.10, T:0.61
Consensus pattern (18 bp):
TGTTACTTATTATTATTA
Found at i:412748 original size:36 final size:36
Alignment explanation
Indices: 412708--412806 Score: 92
Period size: 26 Copynumber: 3.0 Consensus size: 36
412698 ATTTTTTTAG
412708 TAAAATTAATAATTTTAGTGTGTATTATTTTGAGTA
1 TAAAATTAATAATTTTAGTGTGTATTATTTTGAGTA
* **
412744 TAAAATTATTAA---TA---T-TA-T-TCGT-AGTA
1 TAAAATTAATAATTTTAGTGTGTATTATTTTGAGTA
*
412770 TAAAATTAATAATTTTAGTGTGTATTATTTTGTGTA
1 TAAAATTAATAATTTTAGTGTGTATTATTTTGAGTA
412806 T
1 T
412807 TATTGTGAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 20
0.63 0.10 0.27
Matches are distributed among these distances:
26 15 0.33
27 2 0.04
28 1 0.02
29 4 0.09
30 1 0.02
32 1 0.02
33 4 0.09
34 1 0.02
35 2 0.04
36 15 0.33
ACGTcount: A:0.36, C:0.01, G:0.12, T:0.51
Consensus pattern (36 bp):
TAAAATTAATAATTTTAGTGTGTATTATTTTGAGTA
Found at i:413415 original size:18 final size:18
Alignment explanation
Indices: 413372--413416 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
413362 TTGACATGGT
* *
413372 TGGTGGTGAAGAAGAATG
1 TGGTGGCGAAGAAGAAGG
**
413390 TGCCGGCGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
413408 TGGTGGCGA
1 TGGTGGCGA
413417 TCATTGGGAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.29, C:0.09, G:0.47, T:0.16
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:414984 original size:22 final size:22
Alignment explanation
Indices: 414922--414993 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
414912 CACGTTCAAA
* **
414922 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
414944 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
414966 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
414988 CATGAG
1 CATGAG
414994 GGTGACCAGA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:417430 original size:37 final size:38
Alignment explanation
Indices: 417389--417503 Score: 128
Period size: 39 Copynumber: 3.0 Consensus size: 38
417379 CTTCCCTCTT
417389 CTTCTTT-TTTTTTTCTCTTCTCCTTTCCCTTTCTTTC
1 CTTCTTTCTTTTTTTCTCTTCTCCTTTCCCTTTCTTTC
* *
417426 CTTCTTTCTTTCTTTTTTCTTCT-CTTCTCCTTTTCTTCTTC
1 CTTCTTTCTTT-TTTTCTCTTCTCCTT-TCCCTTTC-T-TTC
* * *
417467 TTTCTTTCCTTTTTTCTCTTCTCCTCT-CCTTTCTTTC
1 CTTCTTTCTTTTTTTCTCTTCTCCTTTCCCTTTCTTTC
417504 TTTCCTCTCC
Statistics
Matches: 65, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
37 10 0.15
38 7 0.11
39 22 0.34
40 12 0.18
41 14 0.22
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (38 bp):
CTTCTTTCTTTTTTTCTCTTCTCCTTTCCCTTTCTTTC
Found at i:417432 original size:8 final size:8
Alignment explanation
Indices: 417419--417539 Score: 52
Period size: 8 Copynumber: 14.5 Consensus size: 8
417409 TCCTTTCCCT
417419 TTCTTTCC
1 TTCTTTCC
*
417427 TTCTTTCT
1 TTCTTTCC
*
417435 TTCTTT-T
1 TTCTTTCC
417442 TTCTTCTCTTC
1 TTCTT-TC--C
* *
417453 TCCTTTTC
1 TTCTTTCC
*
417461 TTC-TTCT
1 TTCTTTCC
417468 TTCTTTCC
1 TTCTTTCC
*
417476 TT-TTTTC
1 TTCTTTCC
417483 -TCTTCTCC
1 TTCTT-TCC
*
417491 TCTCCTTTCT
1 T-T-CTTTCC
417501 TTCTTTCC
1 TTCTTTCC
*
417509 TCTCCTTTCT
1 T-T-CTTTCC
417519 TTCTTTCC
1 TTCTTTCC
*
417527 TTTTTTCTC
1 TTCTTTC-C
417536 TTCT
1 TTCT
417540 GCCCCCACCA
Statistics
Matches: 84, Mismatches: 16, Indels: 25
0.67 0.13 0.20
Matches are distributed among these distances:
6 1 0.01
7 17 0.20
8 41 0.49
9 7 0.08
10 11 0.13
11 7 0.08
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (8 bp):
TTCTTTCC
Found at i:417452 original size:23 final size:23
Alignment explanation
Indices: 417418--417534 Score: 72
Period size: 23 Copynumber: 5.2 Consensus size: 23
417408 CTCCTTTCCC
417418 TTTCTT-TCCTTCTTTCTTTCTTT
1 TTTCTTCT-CTTCTTTCTTTCTTT
417441 TTTCTTCTCTTC--TC---CTTT
1 TTTCTTCTCTTCTTTCTTTCTTT
*
417459 TCTTCTTCT-TTCTTTCCTT-TTT
1 T-TTCTTCTCTTCTTTCTTTCTTT
* * *
417481 TCTCTTCTCCTC-TCCTTTCTTT
1 TTTCTTCTCTTCTTTCTTTCTTT
*
417503 CTTTCCTCTCCTTTCTTTCTTTCCTTT
1 -TTTCTTCT-C-TTCTTTCTTT-CTTT
417530 TTTCT
1 TTTCT
417535 CTTCTGCCCC
Statistics
Matches: 71, Mismatches: 9, Indels: 25
0.68 0.09 0.24
Matches are distributed among these distances:
18 8 0.11
19 7 0.10
20 2 0.03
21 12 0.17
22 9 0.13
23 16 0.23
24 2 0.03
25 2 0.03
26 9 0.13
27 4 0.06
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (23 bp):
TTTCTTCTCTTCTTTCTTTCTTT
Found at i:417466 original size:58 final size:57
Alignment explanation
Indices: 417399--417539 Score: 131
Period size: 58 Copynumber: 2.6 Consensus size: 57
417389 CTTCTTTTTT
* * *
417399 TTTTC-TCTTCTCCTTTCCCTTTCTTTC-CTTCT-TTCTTTCTTT-TTTCTTCTCTTCTCC
1 TTTTCTTCTTCTCCTTT-CCTTT-TTTCTCTTCTCCTC-TCCTTTCTTTCTT-TCCTCTCC
*
417456 TTTTCTTCTTCTTTCTTTCCTTTTTTCTCTTCTCCTCTCCTTTCTTTCTTTCCTCTCC
1 TTTTCTTCTTC-TCCTTTCCTTTTTTCTCTTCTCCTCTCCTTTCTTTCTTTCCTCTCC
417514 ---T-TTCTT-T-CTTTCCTTTTTTCTCTTCT
1 TTTTCTTCTTCTCCTTTCCTTTTTTCTCTTCT
417540 GCCCCCACCA
Statistics
Matches: 75, Mismatches: 4, Indels: 16
0.79 0.04 0.17
Matches are distributed among these distances:
51 19 0.25
52 1 0.01
54 5 0.07
55 1 0.01
57 9 0.12
58 27 0.36
59 13 0.17
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (57 bp):
TTTTCTTCTTCTCCTTTCCTTTTTTCTCTTCTCCTCTCCTTTCTTTCTTTCCTCTCC
Found at i:417474 original size:49 final size:45
Alignment explanation
Indices: 417388--417539 Score: 142
Period size: 44 Copynumber: 3.5 Consensus size: 45
417378 TCTTCCCTCT
*
417388 TCTTCTTTTTTTTTTCTCTTCTCCTTTCCCTTTCTTTCCTTCTTTC
1 TCTTC-TTTTTTCTTCTCTTCTCCTTTCCCTTTCTTTCCTTCTTTC
* *
417434 T-TTCTTTTTTCTTCTCTTCTCCTTT-TC-TTC-TTCTTTCTTTC
1 TCTTCTTTTTTCTTCTCTTCTCCTTTCCCTTTCTTTCCTTCTTTC
* *
417475 -CTT-TTTTCTCTTCTCCTCTCCTTT--CTTTCTTTCCTCTCCTTTC
1 TCTTCTTTTTTCTTCTCTTCTCCTTTCCCTTTCTTTCCT-T-CTTTC
*
417518 T-TTCTTTCCTTTTTTCTCTTCT
1 TCTTCTTT--TTTCTTCTCTTCT
417540 GCCCCCACCA
Statistics
Matches: 88, Mismatches: 9, Indels: 18
0.77 0.08 0.16
Matches are distributed among these distances:
39 1 0.01
40 22 0.25
41 16 0.18
42 4 0.05
43 8 0.09
44 23 0.26
45 3 0.03
46 11 0.12
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (45 bp):
TCTTCTTTTTTCTTCTCTTCTCCTTTCCCTTTCTTTCCTTCTTTC
Found at i:417486 original size:18 final size:18
Alignment explanation
Indices: 417397--417537 Score: 89
Period size: 18 Copynumber: 7.6 Consensus size: 18
417387 TTCTTCTTTT
417397 TTTTTTCTCTTCTCCTTTCCC
1 TTTTTTCTCTT-T-CTTT-CC
417418 TTTCTTTCCTTCTTTCTTT-C
1 TTT-TTT-C-TCTTTCTTTCC
*
417438 TTTTTTCT-TCTCTTCTCC
1 TTTTTTCTCTTTCTT-TCC
417456 TTTTCTTCTTCTTTCTTTCC
1 TTTT-TTC-TCTTTCTTTCC
417476 TTTTTTCTC-TTC--TCC
1 TTTTTTCTCTTTCTTTCC
**
417491 TCTCCTT-TCTTTCTTTCC
1 T-TTTTTCTCTTTCTTTCC
**
417509 TCTCCTT-TCTTTCTTTCC
1 T-TTTTTCTCTTTCTTTCC
417527 TTTTTTCTCTT
1 TTTTTTCTCTT
417538 CTGCCCCCAC
Statistics
Matches: 101, Mismatches: 6, Indels: 29
0.74 0.04 0.21
Matches are distributed among these distances:
15 6 0.06
16 11 0.11
17 8 0.08
18 34 0.34
19 9 0.09
20 12 0.12
21 8 0.08
22 7 0.07
23 2 0.02
24 4 0.04
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTTTCTCTTTCTTTCC
Found at i:417501 original size:33 final size:34
Alignment explanation
Indices: 417429--417509 Score: 105
Period size: 33 Copynumber: 2.4 Consensus size: 34
417419 TTCTTTCCTT
*
417429 CTTTCTTTCTTT--TTTCTTCTCTTCTCCTTTTC
1 CTTTCTTTCTTTCCTTTCTTCTCTTCTCCTTCTC
* *
417461 TTCTTCTTTCTTTCCTTTTTTCTCTTCTCC-TCTC
1 CT-TTCTTTCTTTCCTTTCTTCTCTTCTCCTTCTC
417495 CTTTCTTTCTTTCCT
1 CTTTCTTTCTTTCCT
417510 CTCCTTTCTT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
32 1 0.02
33 23 0.55
34 4 0.10
35 14 0.33
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (34 bp):
CTTTCTTTCTTTCCTTTCTTCTCTTCTCCTTCTC
Found at i:417505 original size:37 final size:37
Alignment explanation
Indices: 417421--417522 Score: 111
Period size: 37 Copynumber: 2.7 Consensus size: 37
417411 CTTTCCCTTT
* *
417421 CTTTCCTTCTTTCTTT-C-TTTTT-TCTTCTCTTCTC
1 CTTTCTTTCTTTCTTTCCTTTTTTCTCTTCTCCTCTC
417455 CTTTTCTTCTTCTTTCTTTCCTTTTTTCTCTTCTCCTCTC
1 C-TTTC-T-TTCTTTCTTTCCTTTTTTCTCTTCTCCTCTC
*
417495 CTTTCTTTCTTTCCTCTCCTTTCTTTCT
1 CTTTCTTTCTTT-CTTTCCTTT-TTTCT
417523 TTCCTTTTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 11
0.80 0.04 0.15
Matches are distributed among these distances:
34 1 0.02
35 4 0.07
37 16 0.28
38 10 0.18
39 14 0.25
40 12 0.21
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (37 bp):
CTTTCTTTCTTTCTTTCCTTTTTTCTCTTCTCCTCTC
Found at i:417505 original size:40 final size:39
Alignment explanation
Indices: 417385--417505 Score: 151
Period size: 40 Copynumber: 3.1 Consensus size: 39
417375 CTTTCTTCCC
* *
417385 TCTTC-TTCTTTTTTTTTTCTCTTCTCCTTTCCCTTTCTT
1 TCTTCTTTCTTTCTTTTTTCTCTTCTCCTCT-CCTTTCTT
*
417424 TCCTTCTTTCTTTC-TTTTT-TCTTCTCTTCTCCTTT-TCT
1 T-CTTCTTTCTTTCTTTTTTCTCTTCTCCTCTCCTTTCT-T
417462 TCTTCTTTCTTTCCTTTTTTCTCTTCTCCTCTCCTTTCTT
1 TCTTCTTTCTTT-CTTTTTTCTCTTCTCCTCTCCTTTCTT
417502 TCTT
1 TCTT
417506 TCCTCTCCTT
Statistics
Matches: 71, Mismatches: 4, Indels: 13
0.81 0.05 0.15
Matches are distributed among these distances:
37 12 0.17
38 8 0.11
39 15 0.21
40 29 0.41
41 7 0.10
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (39 bp):
TCTTCTTTCTTTCTTTTTTCTCTTCTCCTCTCCTTTCTT
Found at i:417649 original size:27 final size:27
Alignment explanation
Indices: 417573--417639 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
417563 TAAAACCAAC
417573 TGGTGCCGCCAATGGTATTGGCACCAT
1 TGGTGCCGCCAATGGTATTGGCACCAT
* *
417600 TGGTGCCGCCAATGGTTTTGGCACCTT
1 TGGTGCCGCCAATGGTATTGGCACCAT
417627 TGGTGCCGCCAAT
1 TGGTGCCGCCAAT
417640 ACCATTGGCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.15, C:0.27, G:0.30, T:0.28
Consensus pattern (27 bp):
TGGTGCCGCCAATGGTATTGGCACCAT
Found at i:417762 original size:28 final size:29
Alignment explanation
Indices: 417707--417777 Score: 117
Period size: 28 Copynumber: 2.5 Consensus size: 29
417697 TTTTTTTGAT
417707 ATATTTTGGTAAATAAAAAAAAAATTGTA
1 ATATTTTGGTAAATAAAAAAAAAATTGTA
* *
417736 ATATTTTGGTAAAT-AAAAACAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAAAATTGTA
417764 ATATTTTGGTAAAT
1 ATATTTTGGTAAAT
417778 TTTTATTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 26 0.65
29 14 0.35
ACGTcount: A:0.48, C:0.01, G:0.13, T:0.38
Consensus pattern (29 bp):
ATATTTTGGTAAATAAAAAAAAAATTGTA
Found at i:437448 original size:21 final size:21
Alignment explanation
Indices: 437424--437463 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
437414 TAGTTGTGTT
437424 ATAACTACCTTACTAAAAAAA
1 ATAACTACCTTACTAAAAAAA
* *
437445 ATAATTACTTTACTAAAAA
1 ATAACTACCTTACTAAAAA
437464 TTATCATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (21 bp):
ATAACTACCTTACTAAAAAAA
Found at i:442036 original size:26 final size:28
Alignment explanation
Indices: 441980--442040 Score: 81
Period size: 26 Copynumber: 2.2 Consensus size: 28
441970 TGACTTAAAC
441980 CCAAAATGATACCAAAAAAAAAAAAAAAA
1 CCAAAATGATACC-AAAAAAAAAAAAAAA
* *
442009 CCAAAATGATA-C-AAACAAAAAAATAA
1 CCAAAATGATACCAAAAAAAAAAAAAAA
442035 CCAAAA
1 CCAAAA
442041 AATTTAGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 18 0.60
28 1 0.03
29 11 0.37
ACGTcount: A:0.72, C:0.16, G:0.03, T:0.08
Consensus pattern (28 bp):
CCAAAATGATACCAAAAAAAAAAAAAAA
Found at i:450500 original size:18 final size:18
Alignment explanation
Indices: 450473--450507 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
450463 TGTCACATTA
*
450473 ATAAATAATTAAAAAATC
1 ATAAAAAATTAAAAAATC
450491 ATAAAAAATTAAAAAAT
1 ATAAAAAATTAAAAAAT
450508 AACATAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
ATAAAAAATTAAAAAATC
Found at i:450516 original size:18 final size:18
Alignment explanation
Indices: 450479--450517 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
450469 ATTAATAAAT
* *
450479 AATTAAAAAATCATAAAA
1 AATTAAAAAATAACAAAA
*
450497 AATTAAAAAATAACATAA
1 AATTAAAAAATAACAAAA
450515 AAT
1 AAT
450518 ACTCTTTAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (18 bp):
AATTAAAAAATAACAAAA
Found at i:458253 original size:12 final size:12
Alignment explanation
Indices: 458233--458266 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
458223 GGCCACACGT
* *
458233 CCGTTTCCTTGC
1 CCGTGTCCTAGC
458245 CCGTGTCCTAGC
1 CCGTGTCCTAGC
458257 CCGTGTCCTA
1 CCGTGTCCTA
458267 ACTAGTGAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.06, C:0.41, G:0.21, T:0.32
Consensus pattern (12 bp):
CCGTGTCCTAGC
Found at i:463729 original size:2 final size:2
Alignment explanation
Indices: 463722--463749 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
463712 TATATGCATA
463722 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
463750 TCATCTGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:464758 original size:24 final size:25
Alignment explanation
Indices: 464731--464793 Score: 60
Period size: 25 Copynumber: 2.6 Consensus size: 25
464721 GTACATGTAT
464731 GCTCATACGAGC-G-ATAAACGGTAA
1 GCTCATACGAGCTGAAT-AACGGTAA
* * *
464755 GCTCTTCCGAGCTGAATAATGGTAA
1 GCTCATACGAGCTGAATAACGGTAA
464780 GCTCAT-CAGAGCTG
1 GCTCATAC-GAGCTG
464794 GAATCAGTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
24 11 0.34
25 19 0.59
26 2 0.06
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.22
Consensus pattern (25 bp):
GCTCATACGAGCTGAATAACGGTAA
Found at i:467135 original size:30 final size:30
Alignment explanation
Indices: 467099--467164 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
467089 GTCCGCATGG
* *
467099 CCGTGTGTCACACACGGTTGAGACACACGC
1 CCGTGTGCCACACACGATTGAGACACACGC
* *
467129 CCGTGTGCCACACACGATTGAGACATATGC
1 CCGTGTGCCACACACGATTGAGACACACGC
467159 CCGTGT
1 CCGTGT
467165 ATCTACCCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.23, C:0.32, G:0.26, T:0.20
Consensus pattern (30 bp):
CCGTGTGCCACACACGATTGAGACACACGC
Found at i:468726 original size:5 final size:5
Alignment explanation
Indices: 468697--468743 Score: 58
Period size: 5 Copynumber: 9.2 Consensus size: 5
468687 AAATTTAACA
* * *
468697 TCAAT TTAAT ACATT TCATAT TCAAT TCAAT TCAAT TCAAT TCAAT T
1 TCAAT TCAAT TCAAT TCA-AT TCAAT TCAAT TCAAT TCAAT TCAAT T
468744 TACATCTTAG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
5 31 0.89
6 4 0.11
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.45
Consensus pattern (5 bp):
TCAAT
Found at i:475472 original size:25 final size:25
Alignment explanation
Indices: 475371--475558 Score: 98
Period size: 25 Copynumber: 7.5 Consensus size: 25
475361 CTATAACTGT
* * * *
475371 AGCTCCTAAGAGCTATTAATCGGGG
1 AGCTCCAAAGAGCCATTAATCAGGA
* * *
475396 AGCTCCAGATAGCCATTTATC-GAGA
1 AGCTCCAAAGAGCCATTAATCAG-GA
* * *
475421 AG-TTCAAGCGAGCCA-T-ATCGGGA
1 AGCTCCAA-AGAGCCATTAATCAGGA
**
475444 AGCTCCGGAGAGCCATTAATCAGGA
1 AGCTCCAAAGAGCCATTAATCAGGA
* * * *
475469 AGCTTACAAATAGCCTTTAAT-TGGAA
1 AGC-TCCAAAGAGCCATTAATCAGG-A
* *
475495 AGCTCCAGAGAGCCATTTATCAGGA
1 AGCTCCAAAGAGCCATTAATCAGGA
* *
475520 AGCTCACAAAGAGCCTTTAATTAGGA
1 AGCTC-CAAAGAGCCATTAATCAGGA
**
475546 AGCTTAAAAGAGC
1 AGCTCCAAAGAGC
475559 TAAGGTGTGC
Statistics
Matches: 120, Mismatches: 33, Indels: 20
0.69 0.19 0.12
Matches are distributed among these distances:
23 13 0.11
24 9 0.08
25 60 0.50
26 38 0.32
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.22
Consensus pattern (25 bp):
AGCTCCAAAGAGCCATTAATCAGGA
Found at i:475488 original size:26 final size:26
Alignment explanation
Indices: 475452--475558 Score: 105
Period size: 26 Copynumber: 4.2 Consensus size: 26
475442 GAAGCTCCGG
*
475452 AGAGCCATTAATCAGGAAGCTTACAA
1 AGAGCCTTTAATCAGGAAGCTTACAA
* * * *
475478 ATAGCCTTTAAT-TGGAAAGC-TCCAG
1 AGAGCCTTTAATCAGG-AAGCTTACAA
*
475503 AGAGCCATTT-ATCAGGAAGCTCACAA
1 AGAGCC-TTTAATCAGGAAGCTTACAA
*
475529 AGAGCCTTTAATTAGGAAGCTTA-AA
1 AGAGCCTTTAATCAGGAAGCTTACAA
475554 AGAGC
1 AGAGC
475559 TAAGGTGTGC
Statistics
Matches: 64, Mismatches: 12, Indels: 11
0.74 0.14 0.13
Matches are distributed among these distances:
25 26 0.41
26 38 0.59
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (26 bp):
AGAGCCTTTAATCAGGAAGCTTACAA
Found at i:475506 original size:51 final size:52
Alignment explanation
Indices: 475443--475546 Score: 165
Period size: 51 Copynumber: 2.0 Consensus size: 52
475433 CCATATCGGG
* * *
475443 AAGCTCCGGAGAGCCATTAATCAGGAAGCTTACAAATAGCCTTTAATT-GGA
1 AAGCTCCAGAGAGCCATTAATCAGGAAGCTCACAAAGAGCCTTTAATTAGGA
*
475494 AAGCTCCAGAGAGCCATTTATCAGGAAGCTCACAAAGAGCCTTTAATTAGGA
1 AAGCTCCAGAGAGCCATTAATCAGGAAGCTCACAAAGAGCCTTTAATTAGGA
475546 A
1 A
475547 GCTTAAAAGA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
51 44 0.92
52 4 0.08
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (52 bp):
AAGCTCCAGAGAGCCATTAATCAGGAAGCTCACAAAGAGCCTTTAATTAGGA
Found at i:475558 original size:51 final size:51
Alignment explanation
Indices: 475452--475558 Score: 144
Period size: 51 Copynumber: 2.1 Consensus size: 51
475442 GAAGCTCCGG
* * * *
475452 AGAGCCATTAATCAGGAAGCTTACAAATAGCCTTTAATTGGAAAGCTCCAG
1 AGAGCCATTAATCAGGAAGCTCACAAAGAGCCTTTAATTGGAAAGCTCAAA
* *
475503 AGAGCCATTTATCAGGAAGCTCACAAAGAGCCTTTAATTAGG-AAGCTTAAA
1 AGAGCCATTAATCAGGAAGCTCACAAAGAGCCTTTAATT-GGAAAGCTCAAA
475554 AGAGC
1 AGAGC
475559 TAAGGTGTGC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
51 47 0.96
52 2 0.04
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (51 bp):
AGAGCCATTAATCAGGAAGCTCACAAAGAGCCTTTAATTGGAAAGCTCAAA
Done.