Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold187
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: 870467
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 27366 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:1306 original size:26 final size:26
Alignment explanation
Indices: 1277--1327 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
1267 AATTAATGCA
*
1277 AATTAAACTGAAACATTGAATGTTTT
1 AATTAAACTAAAACATTGAATGTTTT
*
1303 AATTAAACTAAAATATTGAATGTTT
1 AATTAAACTAAAACATTGAATGTTT
1328 GCTTTTATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (26 bp):
AATTAAACTAAAACATTGAATGTTTT
Found at i:3343 original size:26 final size:26
Alignment explanation
Indices: 3304--3353 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
3294 AATTAATACA
*
3304 AATTAAACTTAAATATTGAATGTTCT
1 AATTAAACTGAAATATTGAATGTTCT
3330 AATTAAACTGAAATATTGAATGTT
1 AATTAAACTGAAATATTGAATGTT
3354 TTCATTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (26 bp):
AATTAAACTGAAATATTGAATGTTCT
Found at i:7326 original size:26 final size:26
Alignment explanation
Indices: 7297--7346 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
7287 AATTAATACA
7297 AATTAAACTGAAATATTGAATGTTCT
1 AATTAAACTGAAATATTGAATGTTCT
7323 AATTAAACTGAAATATTGAATGTT
1 AATTAAACTGAAATATTGAATGTT
7347 TTCTATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (26 bp):
AATTAAACTGAAATATTGAATGTTCT
Found at i:9149 original size:26 final size:26
Alignment explanation
Indices: 9120--9169 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
9110 AATTAATACA
9120 AATTAAACTGAAATATTGAATGTTCT
1 AATTAAACTGAAATATTGAATGTTCT
9146 AATTAAACTGAAATATTGAATGTT
1 AATTAAACTGAAATATTGAATGTT
9170 TTCTATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (26 bp):
AATTAAACTGAAATATTGAATGTTCT
Found at i:11763 original size:26 final size:26
Alignment explanation
Indices: 11734--11783 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
11724 AATTAATACA
* *
11734 AATTAAATTGTAATATTGAATGTTCT
1 AATTAAACTGAAATATTGAATGTTCT
11760 AATTAAACTGAAATATTGAATGTT
1 AATTAAACTGAAATATTGAATGTT
11784 TTCTATTATT
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:0.42, C:0.04, G:0.12, T:0.42
Consensus pattern (26 bp):
AATTAAACTGAAATATTGAATGTTCT
Found at i:14369 original size:26 final size:26
Alignment explanation
Indices: 14338--14387 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
14328 AATTAATGCA
14338 AATTAAACTGAAACATTAAATGTTCT
1 AATTAAACTGAAACATTAAATGTTCT
* *
14364 AATTAAACTGAAATATTGAATGTT
1 AATTAAACTGAAACATTAAATGTT
14388 TTCTTTTATT
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:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (26 bp):
AATTAAACTGAAACATTAAATGTTCT
Found at i:16419 original size:26 final size:26
Alignment explanation
Indices: 16390--16439 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
16380 AATTAATGCA
16390 AATTAAACTGAAATATTGAATGTTCT
1 AATTAAACTGAAATATTGAATGTTCT
16416 AATTAAACTGAAATATTGAATGTT
1 AATTAAACTGAAATATTGAATGTT
16440 TTCTTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (26 bp):
AATTAAACTGAAATATTGAATGTTCT
Found at i:18496 original size:26 final size:26
Alignment explanation
Indices: 18439--18488 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
18429 AATTAATGCA
*
18439 AATTAAACTGAAACATTAAATGTTCT
1 AATTTAACTGAAACATTAAATGTTCT
* *
18465 AATTTAACTGAAATATTGAATGTT
1 AATTTAACTGAAACATTAAATGTT
18489 TTCTTTTAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (26 bp):
AATTTAACTGAAACATTAAATGTTCT
Found at i:20521 original size:26 final size:26
Alignment explanation
Indices: 20492--20541 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
20482 AATTAATGCA
* *
20492 AATTAAACTGAACTATTGAATGTTCT
1 AATTAAACTGAAATATAGAATGTTCT
20518 AATTAAACTGAAATATAGAATGTT
1 AATTAAACTGAAATATAGAATGTT
20542 TTCTTTTATT
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:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (26 bp):
AATTAAACTGAAATATAGAATGTTCT
Found at i:22300 original size:35 final size:35
Alignment explanation
Indices: 22261--22328 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
22251 ACGACACACG
22261 TAACGAATATGTGTGCCTGTAATGCAAGTGTACCA
1 TAACGAATATGTGTGCCTGTAATGCAAGTGTACCA
* *
22296 TAACGAATATGTTTGCTTGTAATGCAAGTGTAC
1 TAACGAATATGTGTGCCTGTAATGCAAGTGTAC
22329 TATATCCCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (35 bp):
TAACGAATATGTGTGCCTGTAATGCAAGTGTACCA
Found at i:22598 original size:26 final size:26
Alignment explanation
Indices: 22567--22617 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
22557 AAATTAATGT
* *
22567 TAATTAAGCTTAAATATTGAATGTTC
1 TAATTAAACTAAAATATTGAATGTTC
22593 TAATTAAACTAAAATATTGAATGTT
1 TAATTAAACTAAAATATTGAATGTT
22618 TTCTTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.41
Consensus pattern (26 bp):
TAATTAAACTAAAATATTGAATGTTC
Found at i:24360 original size:26 final size:26
Alignment explanation
Indices: 24331--24380 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
24321 AATTAATGCA
*
24331 AATTAAACTGAAATATTGAATGTTCT
1 AATTAAACTAAAATATTGAATGTTCT
24357 AATTAAACTAAAATATTGAATGTT
1 AATTAAACTAAAATATTGAATGTT
24381 TTCTTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (26 bp):
AATTAAACTAAAATATTGAATGTTCT
Found at i:28058 original size:26 final size:26
Alignment explanation
Indices: 28021--28070 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
28011 AATTAATACA
28021 AATTAAAATGAAATATTGAATGTTCT
1 AATTAAAATGAAATATTGAATGTTCT
*
28047 AATTAAACTGAAATATTGAATGTT
1 AATTAAAATGAAATATTGAATGTT
28071 TTCTTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.46, C:0.04, G:0.12, T:0.38
Consensus pattern (26 bp):
AATTAAAATGAAATATTGAATGTTCT
Found at i:32061 original size:16 final size:16
Alignment explanation
Indices: 32040--32074 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
32030 AATTAGTAAT
*
32040 TTTTTTATATTTCTTA
1 TTTTTTATATTTCATA
*
32056 TTTTTTATTTTTCATA
1 TTTTTTATATTTCATA
32072 TTT
1 TTT
32075 AATTATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTTATATTTCATA
Found at i:32072 original size:23 final size:24
Alignment explanation
Indices: 32040--32085 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
32030 AATTAGTAAT
* *
32040 TTTTTTATATTT-CTTATTTTTTA
1 TTTTTCATATTTAATTATTTTTTA
32063 TTTTTCATATTTAATTATTTTTT
1 TTTTTCATATTTAATTATTTTTT
32086 GAAATCTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (24 bp):
TTTTTCATATTTAATTATTTTTTA
Found at i:32191 original size:30 final size:28
Alignment explanation
Indices: 32140--32200 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 28
32130 CATACGCATA
32140 TTTATTTTTTTAATATAATGTAATTATT
1 TTTATTTTTTTAATATAATGTAATTATT
* * *
32168 TTTATTTTATTTTATTTATATGTATTTATT
1 TTTATTTT-TTTAATATA-ATGTAATTATT
32198 TTT
1 TTT
32201 TCTAANNNNN
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 8 0.29
29 7 0.25
30 13 0.46
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.70
Consensus pattern (28 bp):
TTTATTTTTTTAATATAATGTAATTATT
Found at i:33898 original size:24 final size:25
Alignment explanation
Indices: 33854--33900 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
33844 TTTTCTAAGG
33854 TCCATTGCATATCCCACTAAAAGCT
1 TCCATTGCATATCCCACTAAAAGCT
* *
33879 TCCATT-CATATTCCAGTAAAAG
1 TCCATTGCATATCCCACTAAAAG
33901 TGGGTCGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.34, C:0.28, G:0.09, T:0.30
Consensus pattern (25 bp):
TCCATTGCATATCCCACTAAAAGCT
Found at i:36674 original size:26 final size:26
Alignment explanation
Indices: 36645--36699 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
36635 ATTAATGCAA
36645 ATTAAACTGAAATATTGAATGTTCTC
1 ATTAAACTGAAATATTGAATGTTCTC
*
36671 ATTAAACTGAAATATTGAATGTTTTC
1 ATTAAACTGAAATATTGAATGTTCTC
36697 ATT
1 ATT
36700 TATTGTAACG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (26 bp):
ATTAAACTGAAATATTGAATGTTCTC
Found at i:38706 original size:26 final size:26
Alignment explanation
Indices: 38677--38731 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
38667 ATTAATGCAA
38677 ATTAAACTGAAATACTGAATGTTCTC
1 ATTAAACTGAAATACTGAATGTTCTC
* *
38703 ATTAAACTGAAATATTGAATGTTTTC
1 ATTAAACTGAAATACTGAATGTTCTC
38729 ATT
1 ATT
38732 TATTGTAACG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (26 bp):
ATTAAACTGAAATACTGAATGTTCTC
Found at i:46315 original size:26 final size:26
Alignment explanation
Indices: 46286--46340 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
46276 ATTAATGCAA
46286 ATTAAACTGAAATATTGAATGTTCTC
1 ATTAAACTGAAATATTGAATGTTCTC
*
46312 ATTAAACTGAAATATTGAATGTTTTC
1 ATTAAACTGAAATATTGAATGTTCTC
46338 ATT
1 ATT
46341 TATTGTAACG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (26 bp):
ATTAAACTGAAATATTGAATGTTCTC
Found at i:59020 original size:26 final size:26
Alignment explanation
Indices: 58991--59040 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
58981 AATTAATGCA
58991 AATTAAACTGAAATATTGAATGTTCT
1 AATTAAACTGAAATATTGAATGTTCT
59017 AATTAAACTGAAATATTGAATGTT
1 AATTAAACTGAAATATTGAATGTT
59041 TTCTTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (26 bp):
AATTAAACTGAAATATTGAATGTTCT
Found at i:62925 original size:26 final size:26
Alignment explanation
Indices: 62887--62938 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
62877 ATTAAAATTA
*
62887 ATTCTAATTAAACTAAAATATTGAAT
1 ATTCTAATCAAACTAAAATATTGAAT
*
62913 ATTCTAATCAAACTGAAATATTGAAT
1 ATTCTAATCAAACTAAAATATTGAAT
62939 GTTTTCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.37
Consensus pattern (26 bp):
ATTCTAATCAAACTAAAATATTGAAT
Found at i:64702 original size:15 final size:15
Alignment explanation
Indices: 64682--64757 Score: 57
Period size: 15 Copynumber: 5.1 Consensus size: 15
64672 TTTATGGAAA
64682 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
64697 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
64711 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
64727 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
64741 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
64757 A
1 A
64758 CCGAGATATT
Statistics
Matches: 43, Mismatches: 14, Indels: 7
0.67 0.22 0.11
Matches are distributed among these distances:
14 8 0.19
15 27 0.63
16 8 0.19
ACGTcount: A:0.46, C:0.07, G:0.22, T:0.25
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:64719 original size:30 final size:30
Alignment explanation
Indices: 64678--64757 Score: 133
Period size: 30 Copynumber: 2.7 Consensus size: 30
64668 CATATTTATG
*
64678 GAAAATCAAAGATATGGGTATCAAATAATA
1 GAAAGTCAAAGATATGGGTATCAAATAATA
* *
64708 GAAAGTCAAAGATATGGGTATCAAATATTG
1 GAAAGTCAAAGATATGGGTATCAAATAATA
64738 GAAAGTCAAAGATATGGGTA
1 GAAAGTCAAAGATATGGGTA
64758 CCGAGATATT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.47, C:0.06, G:0.23, T:0.24
Consensus pattern (30 bp):
GAAAGTCAAAGATATGGGTATCAAATAATA
Found at i:69216 original size:30 final size:30
Alignment explanation
Indices: 69172--69251 Score: 124
Period size: 30 Copynumber: 2.7 Consensus size: 30
69162 CATATTTATG
*
69172 GAAAATCAAAGATATGGGTATCAAATAATA
1 GAAAGTCAAAGATATGGGTATCAAATAATA
* * *
69202 GAAAGTCGAAGATATGGGTATCAAATATTG
1 GAAAGTCAAAGATATGGGTATCAAATAATA
69232 GAAAGTCAAAGATATGGGTA
1 GAAAGTCAAAGATATGGGTA
69252 CCGAGATATT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.46, C:0.06, G:0.24, T:0.24
Consensus pattern (30 bp):
GAAAGTCAAAGATATGGGTATCAAATAATA
Found at i:69859 original size:12 final size:12
Alignment explanation
Indices: 69836--69866 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
69826 CTTATTGCTT
69836 TTTCCATATGTTG
1 TTTCC-TATGTTG
69849 TTTCCTATGTTG
1 TTTCCTATGTTG
69861 TTTCCT
1 TTTCCT
69867 CCATATTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.72
13 5 0.28
ACGTcount: A:0.10, C:0.19, G:0.13, T:0.58
Consensus pattern (12 bp):
TTTCCTATGTTG
Found at i:70085 original size:26 final size:26
Alignment explanation
Indices: 70056--70105 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
70046 AACTAATGCA
*
70056 AATTAAACGGAAACATTGAATGTTCT
1 AATTAAACGAAAACATTGAATGTTCT
* *
70082 AATTAAACTAAAATATTGAATGTT
1 AATTAAACGAAAACATTGAATGTT
70106 TTTTTTTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.34
Consensus pattern (26 bp):
AATTAAACGAAAACATTGAATGTTCT
Found at i:78591 original size:432 final size:432
Alignment explanation
Indices: 77776--78621 Score: 1620
Period size: 432 Copynumber: 2.0 Consensus size: 432
77766 AGTGTTGCGG
77776 TGAACTTGTTATGTTGGGAAAAGTTTGCCACTCAGAATTAGTAAAGAGGACTCTTGAAAATCCTC
1 TGAACTTGTTATGTTGGGAAAAGTTTGCCACTCAGAATTAGTAAAGAGGACTCTTGAAAATCCTC
77841 TATTCAAAGACCTAAGCCAAGGACAATTATAGCGAAGAGCATTCAAACATGGAATAATTGCCTTA
66 TATTCAAAGACCTAAGCCAAGGACAATTATAGCGAAGAGCATTCAAACATGGAATAATTGCCTTA
77906 CATTGATCGATTCACCATCTGCGTCTGCTTAAGGATATATGATTGCTTAAGCTAACAAACGGTTA
131 CATTGATCGATTCACCATCTGCGTCTGCTTAAGGATATATGATTGCTTAAGCTAACAAACGGTTA
77971 CAAGAAGTAACAGGCCCAAAATTGTTCTTTTGTATTTATTTTTGATATTGTTCCGAAAGCTTCAT
196 CAAGAAGTAACAGGCCCAAAATTGTTCTTTTGTATTTATTTTTGATATTGTTCCGAAAGCTTCAT
78036 TAAAATGTGTCATTAAATTTAAGCCCAGTTAAATTATATTTAGTTTAAAGAAAATTAAATGGTTC
261 TAAAATGTGTCATTAAATTTAAGCCCAGTTAAATTATATTTAGTTTAAAGAAAATTAAATGGTTC
* * *
78101 TAAAGAAGCCATTACTTAATACACTATGATTTTATGCATGCCATTATTTTTTACTTTATAGCATT
326 TAAAGAAGCCATTACTTAATACACTATGATTTTATACATGCCATTAGTTTTAACTTTATAGCATT
78166 GGAACTCGGTAACCATCTAAAATCGAGAACTAGATTTTGTTT
391 GGAACTCGGTAACCATCTAAAATCGAGAACTAGATTTTGTTT
78208 TGAACTTGTTATGTTGGGAAAAGTTTGCCACTCAGAATTAGTAAAGAGGACTCTTGAAAATCCTC
1 TGAACTTGTTATGTTGGGAAAAGTTTGCCACTCAGAATTAGTAAAGAGGACTCTTGAAAATCCTC
78273 TATTCAAAGACCTAAGCCAAGGACAATTATAGCGAAGAGCATTCAAACATGGAATAATTGCCTTA
66 TATTCAAAGACCTAAGCCAAGGACAATTATAGCGAAGAGCATTCAAACATGGAATAATTGCCTTA
78338 CATTGATCGATTCACCATCTGCGTCTGCTTAAGGATATATGATTGCTTAAGCTAACAAACGGTTA
131 CATTGATCGATTCACCATCTGCGTCTGCTTAAGGATATATGATTGCTTAAGCTAACAAACGGTTA
78403 CAAGAAGTAACAGGCCCAAAATTGTTCTTTTGTATTTATTTTTGATATTGTTCCGAAAGCTTCAT
196 CAAGAAGTAACAGGCCCAAAATTGTTCTTTTGTATTTATTTTTGATATTGTTCCGAAAGCTTCAT
*
78468 TAAAATGTGTCATTAAATTTAAGCCCAGTTAAATTATATTTAGTTTTAAGAAAATTAAATGGTTC
261 TAAAATGTGTCATTAAATTTAAGCCCAGTTAAATTATATTTAGTTTAAAGAAAATTAAATGGTTC
* *
78533 TAGAGAAGCCATTACTTAATACACTATGATTTTATACATGCCATTAGTTTTAACTTTATATCATT
326 TAAAGAAGCCATTACTTAATACACTATGATTTTATACATGCCATTAGTTTTAACTTTATAGCATT
* *
78598 GGAACTTGGTAACCATCTTAAATC
391 GGAACTCGGTAACCATCTAAAATC
78622 AAGCACTACA
Statistics
Matches: 406, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
432 406 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (432 bp):
TGAACTTGTTATGTTGGGAAAAGTTTGCCACTCAGAATTAGTAAAGAGGACTCTTGAAAATCCTC
TATTCAAAGACCTAAGCCAAGGACAATTATAGCGAAGAGCATTCAAACATGGAATAATTGCCTTA
CATTGATCGATTCACCATCTGCGTCTGCTTAAGGATATATGATTGCTTAAGCTAACAAACGGTTA
CAAGAAGTAACAGGCCCAAAATTGTTCTTTTGTATTTATTTTTGATATTGTTCCGAAAGCTTCAT
TAAAATGTGTCATTAAATTTAAGCCCAGTTAAATTATATTTAGTTTAAAGAAAATTAAATGGTTC
TAAAGAAGCCATTACTTAATACACTATGATTTTATACATGCCATTAGTTTTAACTTTATAGCATT
GGAACTCGGTAACCATCTAAAATCGAGAACTAGATTTTGTTT
Found at i:80322 original size:23 final size:23
Alignment explanation
Indices: 80279--80324 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
80269 ATAAATATAT
*
80279 AAATATACATATTTTAATATGTA
1 AAATATACATATTATAATATGTA
*
80302 AAATATATATA-TATAAGTATGTA
1 AAATATACATATTATAA-TATGTA
80325 TATAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (23 bp):
AAATATACATATTATAATATGTA
Found at i:80866 original size:16 final size:16
Alignment explanation
Indices: 80845--80909 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
80835 TTGATTTGCT
80845 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
80861 ATTACGTCTCTATTCC
1 ATTACGCCTCTATTCC
80877 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
80893 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
80909 A
1 A
80910 ATACAGCGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.20, C:0.35, G:0.06, T:0.38
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:80979 original size:21 final size:21
Alignment explanation
Indices: 80953--81007 Score: 96
Period size: 19 Copynumber: 2.7 Consensus size: 21
80943 AATCATATCT
80953 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
80974 TCTAAGATTGC--ATATCATA
1 TCTAAGATTGCATATATCATA
80993 TCTAAGATTGCATAT
1 TCTAAGATTGCATAT
81008 CCTTGAAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 19 0.59
21 13 0.41
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:82562 original size:3 final size:3
Alignment explanation
Indices: 82554--82593 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
82544 ATAAAGAAGG
82554 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
82594 GGATTAAAAA
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:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:82638 original size:5 final size:6
Alignment explanation
Indices: 82619--82676 Score: 53
Period size: 6 Copynumber: 9.2 Consensus size: 6
82609 TTTGGAATTC
* * *
82619 AAATAA AAATAA AAATAA AACATTAC AAATAG AAATAA AAAGGAA AAATAA
1 AAATAA AAATAA AAATAA AA-A-TAA AAATAA AAATAA AAA-TAA AAATAA
*
82670 AGATAA A
1 AAATAA A
82677 CTAAATTGGT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
6 32 0.74
7 7 0.16
8 4 0.09
ACGTcount: A:0.74, C:0.03, G:0.07, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:88960 original size:33 final size:33
Alignment explanation
Indices: 88923--89000 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 33
88913 TAGTTTGTTG
88923 GGACAATAAACACAAAACAAAGATAGTCCT-CCA
1 GGACAATAAACACAAAACAAAGATAGT-CTGCCA
* * * *
88956 GGACAGTAAACACGAAACAGAGATAGTCTGTCA
1 GGACAATAAACACAAAACAAAGATAGTCTGCCA
88989 GGACAATAAACA
1 GGACAATAAACA
89001 TGAGGTAAGT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 2 0.05
33 37 0.95
ACGTcount: A:0.49, C:0.21, G:0.18, T:0.13
Consensus pattern (33 bp):
GGACAATAAACACAAAACAAAGATAGTCTGCCA
Found at i:98433 original size:27 final size:27
Alignment explanation
Indices: 98401--98456 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
98391 AAAGGTTGTT
*
98401 AAATGATCGTAATACCCCTATAAGGTA
1 AAATGATCGTAATACCCCTAGAAGGTA
* *
98428 AAATGATCGTAATGCCCCTAGAGGGTA
1 AAATGATCGTAATACCCCTAGAAGGTA
98455 AA
1 AA
98457 TGACTATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (27 bp):
AAATGATCGTAATACCCCTAGAAGGTA
Found at i:98469 original size:26 final size:27
Alignment explanation
Indices: 98440--98492 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 27
98430 ATGATCGTAA
98440 TGCCCCTAGAGGGTAAATGACT-ATTT
1 TGCCCCTAGAGGGTAAATGACTGATTT
*
98466 TGCCCCTCGAGGGTAAATGACTGATTT
1 TGCCCCTAGAGGGTAAATGACTGATTT
98493 GTGCTATGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (27 bp):
TGCCCCTAGAGGGTAAATGACTGATTT
Found at i:103051 original size:26 final size:28
Alignment explanation
Indices: 102997--103057 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
102987 TATTATCAAG
* *
102997 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
103025 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
103051 AATTATA
1 AATTATA
103058 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:103713 original size:45 final size:44
Alignment explanation
Indices: 103633--103723 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 44
103623 ACCTCTATTC
103633 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
* *
103677 CATTCAACCAAACA-ATTGATTTGCTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACA-AGA-TTACTATTACGCCTCTATTCCATTA
103722 CA
1 CA
103724 CCTCTATTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 16 0.37
45 26 0.60
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
Found at i:103727 original size:16 final size:16
Alignment explanation
Indices: 103702--103766 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
103692 TTGATTTGCT
103702 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
* *
103718 ATTACACCTCTATTTC
1 ATTACGCCTCTATTCC
*
103734 ATTACGCCTCTATTTC
1 ATTACGCCTCTATTCC
103750 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
103766 A
1 A
103767 ATACAGCGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.22, C:0.34, G:0.05, T:0.40
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:107961 original size:21 final size:22
Alignment explanation
Indices: 107937--107979 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
107927 TAAATTTGTA
*
107937 AAAACTCATTATA-AAATAATT
1 AAAACTCAATATATAAATAATT
* *
107958 AAAATTCAATATATTAATAATT
1 AAAACTCAATATATAAATAATT
107980 TAAGTGAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAACTCAATATATAAATAATT
Found at i:110801 original size:13 final size:13
Alignment explanation
Indices: 110785--110860 Score: 84
Period size: 13 Copynumber: 5.8 Consensus size: 13
110775 ATTCATTTAA
*
110785 CATTTCATATGTC
1 CATTTCATATATC
*
110798 CATTTCA-AGTAAC
1 CATTTCATA-TATC
110811 CATTTCATATATC
1 CATTTCATATATC
*
110824 TATTTCGATATAAT-
1 CATTTC-ATAT-ATC
110838 CATTTCATATATC
1 CATTTCATATATC
110851 CATTTCATAT
1 CATTTCATAT
110861 CACCATTTTC
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
12 3 0.06
13 38 0.72
14 10 0.19
15 2 0.04
ACGTcount: A:0.32, C:0.20, G:0.04, T:0.45
Consensus pattern (13 bp):
CATTTCATATATC
Found at i:115993 original size:33 final size:33
Alignment explanation
Indices: 115956--116020 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
115946 AAGTTTAAGT
*
115956 GGTGAGTCAAGTCACTAATAAGAAATGATATTG
1 GGTGAGTCAAGTCACTAATAAGAAAGGATATTG
115989 GGTGAGTCAAGTCACTAATAAGAAAGGATATT
1 GGTGAGTCAAGTCACTAATAAGAAAGGATATT
116021 AGGTTTTGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.40, C:0.09, G:0.25, T:0.26
Consensus pattern (33 bp):
GGTGAGTCAAGTCACTAATAAGAAAGGATATTG
Found at i:118571 original size:20 final size:18
Alignment explanation
Indices: 118534--118573 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
118524 CAAACAAACA
*
118534 TATTTTTTTTTGTGTACT
1 TATTTTTTTTTGTATACT
118552 TATTTTTTCTTTGGTATACT
1 TATTTTTT-TTT-GTATACT
118572 TA
1 TA
118574 ACACACTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 3 0.16
20 8 0.42
ACGTcount: A:0.15, C:0.07, G:0.10, T:0.68
Consensus pattern (18 bp):
TATTTTTTTTTGTATACT
Found at i:127417 original size:81 final size:81
Alignment explanation
Indices: 127282--127444 Score: 281
Period size: 81 Copynumber: 2.0 Consensus size: 81
127272 TTTCTTAAAC
* * *
127282 TCTTTTCTTTTATTATATGTCTACCATGTGTTTAATAAAATGTTTGATTGAAATTAAAGTTTGAT
1 TCTTTACTTTTATTATATGCCTACCATGTGTTTAATAAAATGCTTGATTGAAATTAAAGTTTGAT
*
127347 TATGTGCTAAATTGGT
66 TATGTGCTAAAGTGGT
*
127363 TCTTTACTTTTATTATATGCCTACCATGTGTTTAATAAAATGCTTGTTTGAAATTAAAGTTTGAT
1 TCTTTACTTTTATTATATGCCTACCATGTGTTTAATAAAATGCTTGATTGAAATTAAAGTTTGAT
127428 TATGTGCTAAAGTGGT
66 TATGTGCTAAAGTGGT
127444 T
1 T
127445 GTTGGTTGAT
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 77 1.00
ACGTcount: A:0.28, C:0.09, G:0.15, T:0.48
Consensus pattern (81 bp):
TCTTTACTTTTATTATATGCCTACCATGTGTTTAATAAAATGCTTGATTGAAATTAAAGTTTGAT
TATGTGCTAAAGTGGT
Found at i:128219 original size:370 final size:370
Alignment explanation
Indices: 127519--128253 Score: 1177
Period size: 370 Copynumber: 2.0 Consensus size: 370
127509 TTATTATATT
* * * *
127519 GAATTGCTTAATAGCTAGAATTGATGCCTCTAGTAGACAATCTAGATTAACAAGACAGAGAGGAG
1 GAATTGCTTAATAGCTAGAATTGATGCCTCTAGTAGAAAATCTAGATAAAAAAGACAAAGAGGAG
* *
127584 AGTTTATCCTTAATAGTTCGATATAATTGTACCAAGTAGTGAGATTGAGAGAAGAACTACTTGTC
66 AGTTTATCCTTAATAGTTAGACATAATTGTACCAAGTAGTGAGATTGAGAGAAGAACTACTTGTC
* * * * * *
127649 AAAGTGAGATTGAGAGAATAACTTAGGCTGTAATTTCAAATTAGGATGAGACTGAGAGGAGATTC
131 AAAGTGAGACTGAGAGAAAAACTTAGGCTGCAATTCCAAATTAGGATGAGACTAAGACGAGATTC
* * *
127714 TAGTGAGGAGTGACAAGTGATCTAATCGGTATAGGTTATTGGCTTAGTTAGTAATCGACTAATCA
196 TAGTGAGGAGTGACAAGCGATCTAATCGGGATAGGTTATTGGCTTAATTAGTAATCGACTAATCA
* * * *
127779 ATCAACCATCATTTTTATCATTTTCATAGTCGAATGCAATAGGAAGAAATCTTAGTTTAGGTAGT
261 ATCAACCATCATTTTTATCATTTGCATAGTCGAATACAACAGGAAGAAATCTTAATTTAGGTAGT
127844 TTAATTGATAATTTAGAATTAGTCTCATT-TATTTTCATACGCTA
326 TTAATTGATAATTTAGAATTAGTCTCATTATATTTTCATACGCTA
*
127888 GAATTGCTTAATACGCTAGAATTGATGCCTCTAGTGGAAAATCTAGATAAAAAAGACAAAGAGGA
1 GAATTGCTTAATA-GCTAGAATTGATGCCTCTAGTAGAAAATCTAGATAAAAAAGACAAAGAGGA
***
127953 GAGTTTATCCTTAATAGTTAGACATAATTGTATTGAGTAGTGAGATTGAGAGAAGAACTACTTGT
65 GAGTTTATCCTTAATAGTTAGACATAATTGTACCAAGTAGTGAGATTGAGAGAAGAACTACTTGT
* * *
128018 CTAAGTGAGACTGAGAGAAAAACTTA-GTTGGCAATTCCGAATTAGGATGAGACTAAGACGAGAT
130 CAAAGTGAGACTGAGAGAAAAACTTAGGCT-GCAATTCCAAATTAGGATGAGACTAAGACGAGAT
* *
128082 TCTAGTGAGGAGTGGCAAGCGATCTAATCGGGATAGGTTATTGGCTTAATTAGTAATTGACTAAT
194 TCTAGTGAGGAGTGACAAGCGATCTAATCGGGATAGGTTATTGGCTTAATTAGTAATCGACTAAT
128147 CAATCAACCATCATTTTTATCATTTGCATAGTCGAATACAACAGGAAGAAATCTTAATTTAGGTA
259 CAATCAACCATCATTTTTATCATTTGCATAGTCGAATACAACAGGAAGAAATCTTAATTTAGGTA
*
128212 TTTTAATTGATAATTTAGAATTAGTCTCATTATATTTTCATA
324 GTTTAATTGATAATTTAGAATTAGTCTCATTATATTTTCATA
128254 TCTAGTTTGC
Statistics
Matches: 334, Mismatches: 29, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
369 15 0.04
370 309 0.93
371 10 0.03
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.32
Consensus pattern (370 bp):
GAATTGCTTAATAGCTAGAATTGATGCCTCTAGTAGAAAATCTAGATAAAAAAGACAAAGAGGAG
AGTTTATCCTTAATAGTTAGACATAATTGTACCAAGTAGTGAGATTGAGAGAAGAACTACTTGTC
AAAGTGAGACTGAGAGAAAAACTTAGGCTGCAATTCCAAATTAGGATGAGACTAAGACGAGATTC
TAGTGAGGAGTGACAAGCGATCTAATCGGGATAGGTTATTGGCTTAATTAGTAATCGACTAATCA
ATCAACCATCATTTTTATCATTTGCATAGTCGAATACAACAGGAAGAAATCTTAATTTAGGTAGT
TTAATTGATAATTTAGAATTAGTCTCATTATATTTTCATACGCTA
Found at i:130208 original size:12 final size:12
Alignment explanation
Indices: 130191--130218 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
130181 ACCTGTAATC
130191 AAAATTAATCCA
1 AAAATTAATCCA
130203 AAAATTAATCCA
1 AAAATTAATCCA
130215 AAAA
1 AAAA
130219 CCAAAAGCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.64, C:0.14, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAATTAATCCA
Found at i:131105 original size:14 final size:13
Alignment explanation
Indices: 131086--131129 Score: 61
Period size: 14 Copynumber: 3.2 Consensus size: 13
131076 AGGATTAATA
131086 TATTATAACATTGT
1 TATTATAACA-TGT
131100 TATTATAACACTGT
1 TATTATAACA-TGT
*
131114 TATTATAGCATGT
1 TATTATAACATGT
131127 TAT
1 TAT
131130 GAAACAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
13 6 0.21
14 22 0.79
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.48
Consensus pattern (13 bp):
TATTATAACATGT
Found at i:133970 original size:35 final size:35
Alignment explanation
Indices: 133931--134025 Score: 109
Period size: 35 Copynumber: 2.7 Consensus size: 35
133921 GTTTTCACGG
133931 TGTCACCCCGAAGGACCTATATACCATTTATACGA
1 TGTCACCCCGAAGGACCTATATACCATTTATACGA
* * * * *
133966 TGTCACCCTGAATGACCTATATATCATTTATATGG
1 TGTCACCCCGAAGGACCTATATACCATTTATACGA
** * *
134001 TGTTGCCCCAAAGGACCAATATACC
1 TGTCACCCCGAAGGACCTATATACC
134026 GTTGTCATAG
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
35 48 1.00
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (35 bp):
TGTCACCCCGAAGGACCTATATACCATTTATACGA
Found at i:138130 original size:18 final size:18
Alignment explanation
Indices: 138090--138145 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
138080 TTTCGCGATA
*
138090 AATAACGTTTTGAAAATT
1 AATAACGTTTTGAAAATG
*
138108 TATAACGTTTTG-AAATAG
1 AATAACGTTTTGAAAAT-G
* *
138126 AATAAC-TTATGAATATG
1 AATAACGTTTTGAAAATG
138143 AAT
1 AAT
138146 CAAATTTGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
17 12 0.39
18 19 0.61
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (18 bp):
AATAACGTTTTGAAAATG
Found at i:138159 original size:16 final size:16
Alignment explanation
Indices: 138116--138162 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
138106 TTTATAACGT
*
138116 TTTGAAATAGAAT-AAC
1 TTTGAAAT-GAATCAAA
138132 TTATGAATATGAATCAAA
1 TT-TGAA-ATGAATCAAA
138150 TTTGAAATGAATC
1 TTTGAAATGAATC
138163 GGCACGTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 9 0.33
17 12 0.44
18 6 0.22
ACGTcount: A:0.47, C:0.06, G:0.13, T:0.34
Consensus pattern (16 bp):
TTTGAAATGAATCAAA
Found at i:144936 original size:18 final size:18
Alignment explanation
Indices: 144896--144951 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
144886 TTTCGCGATA
*
144896 AATAACGTTTTGAAAATT
1 AATAACGTTTTGAAAATG
*
144914 TATAACGTTTTGAAAGA-G
1 AATAACGTTTTGAAA-ATG
* *
144932 AATAAC-TTATGAATATG
1 AATAACGTTTTGAAAATG
144949 AAT
1 AAT
144952 CACATTTGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
16 1 0.03
17 10 0.32
18 19 0.61
19 1 0.03
ACGTcount: A:0.45, C:0.05, G:0.14, T:0.36
Consensus pattern (18 bp):
AATAACGTTTTGAAAATG
Found at i:145464 original size:14 final size:13
Alignment explanation
Indices: 145445--145483 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
145435 TTGATTGCCA
145445 GTAAAATGTCTTCT
1 GTAAAATGT-TTCT
145459 GTAAAATGATTTCT
1 GTAAAATG-TTTCT
*
145473 GGAAAATGTTT
1 GTAAAATGTTT
145484 TACTTTTCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 3 0.13
14 19 0.83
15 1 0.04
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (13 bp):
GTAAAATGTTTCT
Found at i:145493 original size:20 final size:20
Alignment explanation
Indices: 145468--145507 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
145458 TGTAAAATGA
*
145468 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
145488 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
145508 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:145523 original size:14 final size:15
Alignment explanation
Indices: 145455--145523 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 15
145445 GTAAAATGTC
*
145455 TTCTGTAAAATGA-T
1 TTCTGGAAAATGATT
145469 TTCTGGAAAATGTTTTACTT
1 TTCTGGAAAATG----A-TT
*
145489 TTCTGTAAAATGATT
1 TTCTGGAAAATGATT
*
145504 TACTGGAAAAT-ATT
1 TTCTGGAAAATGATT
145518 TTCTGG
1 TTCTGG
145524 TGTTTGATTG
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
14 19 0.43
15 11 0.25
16 1 0.02
18 1 0.02
20 12 0.27
ACGTcount: A:0.30, C:0.09, G:0.16, T:0.45
Consensus pattern (15 bp):
TTCTGGAAAATGATT
Found at i:145702 original size:22 final size:24
Alignment explanation
Indices: 145677--145727 Score: 56
Period size: 26 Copynumber: 2.2 Consensus size: 24
145667 TTATTTATAA
145677 ATAAATAA-A-TCAA-ATT-AAAT
1 ATAAATAATACTCAATATTAAAAT
145697 ATATAATAATACTCAATTATTAAAAT
1 ATA-AATAATACTCAA-TATTAAAAT
145723 ATAAA
1 ATAAA
145728 AGCATTGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
20 3 0.12
21 5 0.20
22 1 0.04
23 4 0.16
25 5 0.20
26 7 0.28
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (24 bp):
ATAAATAATACTCAATATTAAAAT
Found at i:164952 original size:32 final size:32
Alignment explanation
Indices: 164913--164973 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
164903 TTTCTGGTTG
* *
164913 TGTGGGATGGATGAATTTATGTGCAATTTGGT
1 TGTGGGATAGATGAACTTATGTGCAATTTGGT
* *
164945 TGTGGGATAGATGCACTTGTGTGCAATTT
1 TGTGGGATAGATGAACTTATGTGCAATTT
164974 TCTTGTATTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.21, C:0.07, G:0.33, T:0.39
Consensus pattern (32 bp):
TGTGGGATAGATGAACTTATGTGCAATTTGGT
Found at i:165183 original size:20 final size:21
Alignment explanation
Indices: 165151--165190 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
165141 ATTAAGATTC
165151 AACTATAAACCATACAATTTT
1 AACTATAAACCATACAATTTT
*
165172 AACTAT-AACCATACGATTT
1 AACTATAAACCATACAATTT
165191 AATTGGAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.33
Consensus pattern (21 bp):
AACTATAAACCATACAATTTT
Found at i:168812 original size:6 final size:6
Alignment explanation
Indices: 168803--168844 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
168793 GGTTATCTCC
*
168803 AAAATG AAAATG AAAATG AAAATG AAAATG GAAATG AAAATG
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG
168845 GAGAAATGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.64, C:0.00, G:0.19, T:0.17
Consensus pattern (6 bp):
AAAATG
Found at i:172574 original size:43 final size:43
Alignment explanation
Indices: 172520--172646 Score: 154
Period size: 43 Copynumber: 3.0 Consensus size: 43
172510 CATAGGATTT
172520 TCGATATGTGTTATCGTGTAAGACCACGTCTGGGACATTGGCA
1 TCGATATGTGTTATCGTGTAAGACCACGTCTGGGACATTGGCA
*
172563 TCGACT-TGTGTT-TACGTGTAAGACC-CTGTCTGGGACAGTGGCA
1 TCGA-TATGTGTTAT-CGTGTAAGACCAC-GTCTGGGACATTGGCA
* * *
172606 TCGATATGTGATTA-CATGTAAGACCACGTCTAGGACGTTGG
1 TCGATATGTG-TTATCGTGTAAGACCACGTCTGGGACATTGG
172647 TATTGTACGA
Statistics
Matches: 72, Mismatches: 5, Indels: 14
0.79 0.05 0.15
Matches are distributed among these distances:
42 3 0.04
43 65 0.90
44 4 0.06
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (43 bp):
TCGATATGTGTTATCGTGTAAGACCACGTCTGGGACATTGGCA
Found at i:173513 original size:23 final size:23
Alignment explanation
Indices: 173486--173603 Score: 128
Period size: 23 Copynumber: 5.0 Consensus size: 23
173476 ATGAGTTGAA
*
173486 CCAATTTGTTACATATATGCTGT
1 CCAATTTGTTGCATATATGCTGT
* * * *
173509 CCAATTTTGATGCTTAAATGCTGC
1 CCAA-TTTGTTGCATATATGCTGT
*
173533 CCAATTTGTTACATATATGCTGT
1 CCAATTTGTTGCATATATGCTGT
* * * *
173556 CCAATTTTGATGCTTAAATGCTGC
1 CCAA-TTTGTTGCATATATGCTGT
173580 CCAATTTGTTGCATATATGCTGT
1 CCAATTTGTTGCATATATGCTGT
173603 C
1 C
173604 TAGTTTTGGT
Statistics
Matches: 74, Mismatches: 19, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
23 38 0.51
24 36 0.49
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.41
Consensus pattern (23 bp):
CCAATTTGTTGCATATATGCTGT
Found at i:173529 original size:24 final size:23
Alignment explanation
Indices: 173486--174064 Score: 159
Period size: 24 Copynumber: 24.3 Consensus size: 23
173476 ATGAGTTGAA
* * *
173486 CCAATTTGTTACATATATGCTGT
1 CCAATTTGATGCATAAATGCTGT
* *
173509 CCAATTTTGATGCTTAAATGCTGC
1 CCAA-TTTGATGCATAAATGCTGT
* * *
173533 CCAATTTGTTACATATATGCTGT
1 CCAATTTGATGCATAAATGCTGT
* *
173556 CCAATTTTGATGCTTAAATGCTGC
1 CCAA-TTTGATGCATAAATGCTGT
* *
173580 CCAATTTGTTGCATATATGCTGT
1 CCAATTTGATGCATAAATGCTGT
* * * * * *
173603 CTAGTTTTGGTGTAAAAATGTTGCT
1 CCA-ATTTGATGCATAAATGCTG-T
* * *
173628 CAAACTATTGTAT--ATATATGCTGC
1 CCAA-T-TTG-ATGCATAAATGCTGT
* * * *
173652 CCAAATTGATGTATAAAAGTTGT
1 CCAATTTGATGCATAAATGCTGT
** * * *
173675 CCAAATAGGGTAG-ATTACTGCTGT
1 CC-AATTTGAT-GCATAAATGCTGT
* *
173699 CCAATTTTGATGTATAAATGCT-A
1 CCAA-TTTGATGCATAAATGCTGT
* * *
173722 CCTAATTTGGTGTC-TATATGCAGT
1 CC-AATTTGATG-CATAAATGCTGT
* * * *
173746 CCAATTTTGGTGTAAAAATGTTGT
1 CCAA-TTTGATGCATAAATGCTGT
** * *
173770 CCAATTTGATATATATATGCTGC
1 CCAATTTGATGCATAAATGCTGT
* *
173793 CCAAATTGATGTATAAATGCTGT
1 CCAATTTGATGCATAAATGCTGT
* * **
173816 CCAATTTTAGTGTATAAATGGGGT
1 CCAATTTGA-TGCATAAATGCTGT
* *
173840 TCAATTTTGATGTATAAATGCT-T
1 CCAA-TTTGATGCATAAATGCTGT
* * *
173863 CCTAATTTGGTGTC-TATATGCAGT
1 CC-AATTTGATG-CATAAATGCTGT
* * *
173887 CCAATTTTGGTGTAAAAATGCTGT
1 CCAA-TTTGATGCATAAATGCTGT
* ** *
173911 CCAATTTAATATATATATATATATGCTGC
1 CCAA-TT--T-GATGCATA-A-ATGCTGT
* *
173940 CCAAATTGATGTATAAATGCTGT
1 CCAATTTGATGCATAAATGCTGT
* * **
173963 CCAATTTTAGTGTATAAATGGGGT
1 CCAATTTGA-TGCATAAATGCTGT
* *
173987 TCAATTTTGATGTATAAATGCT-T
1 CCAA-TTTGATGCATAAATGCTGT
* * *
174010 CCTAATTTGGTGTC-TATATGCAGT
1 CC-AATTTGATG-CATAAATGCTGT
* * *
174034 CCAATTTTGGTGTAAAAATGCTGT
1 CCAA-TTTGATGCATAAATGCTGT
174058 CCAATTT
1 CCAATTT
174065 AATATATATA
Statistics
Matches: 403, Mismatches: 116, Indels: 74
0.68 0.20 0.12
Matches are distributed among these distances:
21 2 0.00
22 3 0.01
23 154 0.38
24 196 0.49
25 26 0.06
26 5 0.01
27 5 0.01
28 2 0.00
29 10 0.02
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (23 bp):
CCAATTTGATGCATAAATGCTGT
Found at i:174002 original size:147 final size:144
Alignment explanation
Indices: 173557--174139 Score: 815
Period size: 147 Copynumber: 4.0 Consensus size: 144
173547 ATATGCTGTC
* * * * * *
173557 CAATTTTGATGCT-TAAATGCTGCCCAATTTGTTG-CATATATGCTGTCTAGTTTTGGTGTAAAA
1 CAATTTTGATG-TATAAATGCTTCCTAATTTGGTGTC-TATATGCAGTCCAATTTTGGTGTAAAA
* * * * * *
173620 ATGTTG-CTCAA-ACTATTGTATATATATGCTGCCCAAATTGATGTATAAAAGTTGTCCAA--AT
64 ATGCTGTC-CAATAATATTATATATATATGCTGCCCAAATTGATGTATAAATGCTGTCCAATTTT
* * * ** *
173681 AGGGTAGATTACTGCTGTC
128 AGTGT--ATAAATGGGGTT
*
173700 CAATTTTGATGTATAAATGCTACCTAATTTGGTGTCTATATGCAGTCCAATTTTGGTGTAAAAAT
1 CAATTTTGATGTATAAATGCTTCCTAATTTGGTGTCTATATGCAGTCCAATTTTGGTGTAAAAAT
* *
173765 GTTGTCCAAT--T-TGATATATATATGCTGCCCAAATTGATGTATAAATGCTGTCCAATTTTAGT
66 GCTGTCCAATAATATTATATATATATGCTGCCCAAATTGATGTATAAATGCTGTCCAATTTTAGT
173827 GTATAAATGGGGTT
131 GTATAAATGGGGTT
173841 CAATTTTGATGTATAAATGCTTCCTAATTTGGTGTCTATATGCAGTCCAATTTTGGTGTAAAAAT
1 CAATTTTGATGTATAAATGCTTCCTAATTTGGTGTCTATATGCAGTCCAATTTTGGTGTAAAAAT
173906 GCTGTCCAATTTAATATATATATATATATGCTGCCCAAATTGATGTATAAATGCTGTCCAATTTT
66 GCTGTCCAA--TAATAT-TATATATATATGCTGCCCAAATTGATGTATAAATGCTGTCCAATTTT
173971 AGTGTATAAATGGGGTT
128 AGTGTATAAATGGGGTT
173988 CAATTTTGATGTATAAATGCTTCCTAATTTGGTGTCTATATGCAGTCCAATTTTGGTGTAAAAAT
1 CAATTTTGATGTATAAATGCTTCCTAATTTGGTGTCTATATGCAGTCCAATTTTGGTGTAAAAAT
174053 GCTGTCCAATTTAATATATATATATATATGCTGCCCAAATTGATGTATAAATGCTGTCCAATTTT
66 GCTGTCCAA--TAATAT-TATATATATATGCTGCCCAAATTGATGTATAAATGCTGTCCAATTTT
174118 AGTGTATAAATGGGGTT
128 AGTGTATAAATGGGGTT
174135 CAATT
1 CAATT
174140 GTGGTGCCTT
Statistics
Matches: 408, Mismatches: 20, Indels: 20
0.91 0.04 0.04
Matches are distributed among these distances:
141 119 0.29
142 2 0.00
143 68 0.17
144 2 0.00
145 1 0.00
146 1 0.00
147 215 0.53
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.39
Consensus pattern (144 bp):
CAATTTTGATGTATAAATGCTTCCTAATTTGGTGTCTATATGCAGTCCAATTTTGGTGTAAAAAT
GCTGTCCAATAATATTATATATATATGCTGCCCAAATTGATGTATAAATGCTGTCCAATTTTAGT
GTATAAATGGGGTT
Found at i:174075 original size:47 final size:47
Alignment explanation
Indices: 173498--174125 Score: 368
Period size: 47 Copynumber: 13.1 Consensus size: 47
173488 AATTTGTTAC
* *
173498 ATATATGCTGTCCAATTTTGATGCT-TAAATGCTGCCCAATTT-GT-T
1 ATATATGCAGTCCAATTTTGATG-TATAAATGCTGTCCAATTTAGTGT
* * *
173543 ACATATATGCTGTCCAATTTTGATGCT-TAAATGCTGCCCAATTT-GTTGC
1 --ATATATGCAGTCCAATTTTGATG-TATAAATGCTGTCCAATTTAG-TGT
* * * * * * * *
173592 ATATATGCTGTCTAGTTTTGGTGTAAAAATGTTGCTCAAACTATT-GTAT
1 ATATATGCAGTCCAATTTTGATGTATAAATGCTG-TCCAA-T-TTAGTGT
* * * * * * *
173641 ATATATGCTGCCCAA-ATTGATGTATAAAAGTTGTCCAA-ATAGGGT
1 ATATATGCAGTCCAATTTTGATGTATAAATGCTGTCCAATTTAGTGT
* * * *
173686 AGATTACTGCTGTCCAATTTTGATGTATAAATGCT-ACCTAATTTGGTGT
1 ATA-TA-TGCAGTCCAATTTTGATGTATAAATGCTGTCC-AATTTAGTGT
* * * * *
173735 CTATATGCAGTCCAATTTTGGTGTAAAAATGTTGTCCAATTT-GATAT
1 ATATATGCAGTCCAATTTTGATGTATAAATGCTGTCCAATTTAG-TGT
* * *
173782 ATATATGCTGCCCAA-ATTGATGTATAAATGCTGTCCAATTTTAGTGT
1 ATATATGCAGTCCAATTTTGATGTATAAATGCTGTCCAA-TTTAGTGT
* ** * *
173829 ATAAATGGGGTTCAATTTTGATGTATAAATGCT-TCCTAATTTGGTGT
1 ATATATGCAGTCCAATTTTGATGTATAAATGCTGTCC-AATTTAGTGT
* * * * *
173876 CTATATGCAGTCCAATTTTGGTGTAAAAATGCTGTCCAATTTAATATATATAT
1 ATATATGCAGTCCAATTTTGATGTATAAATGCTGTCCAA--T--T-TA-GTGT
* * *
173929 ATATATGCTGCCCAA-ATTGATGTATAAATGCTGTCCAATTTTAGTGT
1 ATATATGCAGTCCAATTTTGATGTATAAATGCTGTCCAA-TTTAGTGT
* ** * *
173976 ATAAATGGGGTTCAATTTTGATGTATAAATGCT-TCCTAATTTGGTGT
1 ATATATGCAGTCCAATTTTGATGTATAAATGCTGTCC-AATTTAGTGT
* * * * *
174023 CTATATGCAGTCCAATTTTGGTGTAAAAATGCTGTCCAATTTAATATATATAT
1 ATATATGCAGTCCAATTTTGATGTATAAATGCTGTCCAA--T--T-TA-GTGT
* * *
174076 ATATATGCTGCCCAA-ATTGATGTATAAATGCTGTCCAATTTTAGTGT
1 ATATATGCAGTCCAATTTTGATGTATAAATGCTGTCCAA-TTTAGTGT
174123 ATA
1 ATA
174126 AATGGGGTTC
Statistics
Matches: 451, Mismatches: 96, Indels: 68
0.73 0.16 0.11
Matches are distributed among these distances:
44 1 0.00
45 4 0.01
46 23 0.05
47 236 0.52
48 85 0.19
49 23 0.05
50 3 0.01
51 6 0.01
52 42 0.09
53 28 0.06
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.40
Consensus pattern (47 bp):
ATATATGCAGTCCAATTTTGATGTATAAATGCTGTCCAATTTAGTGT
Found at i:174123 original size:24 final size:24
Alignment explanation
Indices: 173693--174129 Score: 261
Period size: 24 Copynumber: 18.1 Consensus size: 24
173683 GGTAGATTAC
173693 TGCTGTCCAATTTT-GATGTATAAA
1 TGCTGTCCAATTTTAG-TGTATAAA
* * * *
173717 TGCT-ACCTAA-TTTGGTGTCTATA
1 TGCTGTCC-AATTTTAGTGTATAAA
* * *
173740 TGCAGTCCAATTTTGGTGTAAAAA
1 TGCTGTCCAATTTTAGTGTATAAA
* * * *
173764 TGTTGTCCAATTTGA-TATATATA
1 TGCTGTCCAATTTTAGTGTATAAA
* * *
173787 TGCTGCCCAAATTGA-TGTATAAA
1 TGCTGTCCAATTTTAGTGTATAAA
173810 TGCTGTCCAATTTTAGTGTATAAA
1 TGCTGTCCAATTTTAGTGTATAAA
** *
173834 TGGGGTTCAATTTT-GATGTATAAA
1 TGCTGTCCAATTTTAG-TGTATAAA
* * *
173858 TGCT-TCCTAA-TTTGGTGTCTATA
1 TGCTGTCC-AATTTTAGTGTATAAA
* * *
173881 TGCAGTCCAATTTTGGTGTAAAAA
1 TGCTGTCCAATTTTAGTGTATAAA
* *
173905 TGCTGTCCAATTTAATATATATATATATA
1 TGCTGTCCAATTT--TA-GTGTATA-A-A
* * *
173934 TGCTGCCCAAATTGA-TGTATAAA
1 TGCTGTCCAATTTTAGTGTATAAA
173957 TGCTGTCCAATTTTAGTGTATAAA
1 TGCTGTCCAATTTTAGTGTATAAA
** *
173981 TGGGGTTCAATTTT-GATGTATAAA
1 TGCTGTCCAATTTTAG-TGTATAAA
* * *
174005 TGCT-TCCTAA-TTTGGTGTCTATA
1 TGCTGTCC-AATTTTAGTGTATAAA
* * *
174028 TGCAGTCCAATTTTGGTGTAAAAA
1 TGCTGTCCAATTTTAGTGTATAAA
* *
174052 TGCTGTCCAATTTAATATATATATATATA
1 TGCTGTCCAATTT--TA-GTGTATA-A-A
* * *
174081 TGCTGCCCAAATTGA-TGTATAAA
1 TGCTGTCCAATTTTAGTGTATAAA
174104 TGCTGTCCAATTTTAGTGTATAAA
1 TGCTGTCCAATTTTAGTGTATAAA
174128 TG
1 TG
174130 GGGTTCAATT
Statistics
Matches: 315, Mismatches: 71, Indels: 54
0.72 0.16 0.12
Matches are distributed among these distances:
23 111 0.35
24 156 0.50
25 10 0.03
26 2 0.01
27 10 0.03
28 2 0.01
29 24 0.08
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (24 bp):
TGCTGTCCAATTTTAGTGTATAAA
Found at i:176218 original size:16 final size:16
Alignment explanation
Indices: 176199--176230 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
176189 CCAATTACAA
176199 CCAAAACTAAACTAAG
1 CCAAAACTAAACTAAG
176215 CCAAAACTAAACTAAG
1 CCAAAACTAAACTAAG
176231 TCCCGGAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.25, G:0.06, T:0.12
Consensus pattern (16 bp):
CCAAAACTAAACTAAG
Found at i:176681 original size:11 final size:11
Alignment explanation
Indices: 176663--176694 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
176653 ATATTTTGAA
176663 GCTGTTGATTT
1 GCTGTTGATTT
*
176674 GTTGTTGATTT
1 GCTGTTGATTT
176685 GCTGTTGATT
1 GCTGTTGATT
176695 AAGAGTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.09, C:0.06, G:0.28, T:0.56
Consensus pattern (11 bp):
GCTGTTGATTT
Found at i:177481 original size:79 final size:80
Alignment explanation
Indices: 177350--177511 Score: 308
Period size: 79 Copynumber: 2.0 Consensus size: 80
177340 CACTGAGGGG
177350 AAATGTGTTCCCATTGAGCTTGGGAATGCATTCAAAACTAATGCTCAAAACAACCAAAACTGCCT
1 AAATGTGTTCCCATTGAGCTTGGGAATGCATTCAAAACTAATGCTCAAAACAACCAAAACTGCCT
177415 TAAGTAATGCATT-A
66 TAAGTAATGCATTCA
*
177429 AAATGTGTTCCCATTGAGCTTGGGAATGCATTCAAAACTAATGCTCAAAACAACTAAAACTGCCT
1 AAATGTGTTCCCATTGAGCTTGGGAATGCATTCAAAACTAATGCTCAAAACAACCAAAACTGCCT
177494 TAAGTAATGCATTCA
66 TAAGTAATGCATTCA
177509 AAA
1 AAA
177512 CTACTAACTT
Statistics
Matches: 81, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
79 77 0.95
80 4 0.05
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.27
Consensus pattern (80 bp):
AAATGTGTTCCCATTGAGCTTGGGAATGCATTCAAAACTAATGCTCAAAACAACCAAAACTGCCT
TAAGTAATGCATTCA
Found at i:179228 original size:13 final size:13
Alignment explanation
Indices: 179210--179245 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
179200 ACTCAAATTT
179210 CTCAAAAGCACTA
1 CTCAAAAGCACTA
*
179223 CTCAAAAGCACTT
1 CTCAAAAGCACTA
179236 CTCAAAAGCA
1 CTCAAAAGCA
179246 ATAAAGAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.44, C:0.31, G:0.08, T:0.17
Consensus pattern (13 bp):
CTCAAAAGCACTA
Found at i:185271 original size:8 final size:8
Alignment explanation
Indices: 185258--185287 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
185248 CTTTGGGGTG
185258 AATTTTGT
1 AATTTTGT
185266 AATTTTGT
1 AATTTTGT
185274 AATTTTGT
1 AATTTTGT
185282 AATTTT
1 AATTTT
185288 TTTTATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (8 bp):
AATTTTGT
Found at i:194923 original size:2 final size:2
Alignment explanation
Indices: 194916--194944 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
194906 AACAACCATA
194916 AG AG 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 AG AG A
194945 TTAGACTCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:202623 original size:49 final size:50
Alignment explanation
Indices: 202517--202657 Score: 164
Period size: 49 Copynumber: 2.9 Consensus size: 50
202507 ATATCTGAAT
* ** *
202517 ATGATGGGCCACTGGTAGGACATGTTAGTTGCTAACTAGATTGGTGTATG
1 ATGATGGGCCACTGGTAGGACATGTTAGTTGCTAACAAGATTGGTCAAAG
* * * *
202567 -TGTTGGGCCACTAGTAGGGCATGCTAGTTGCTAACCAAG-TTGG-CAAAG
1 ATGATGGGCCACTGGTAGGACATGTTAGTTGCTAA-CAAGATTGGTCAAAG
202615 ATGATGGGCCACTGGTAGGACATGTTAGTTGCTAATCAA-ATTG
1 ATGATGGGCCACTGGTAGGACATGTTAGTTGCTAA-CAAGATTG
202658 ACGTATGTGC
Statistics
Matches: 75, Mismatches: 13, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
48 2 0.03
49 70 0.93
50 3 0.04
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.29
Consensus pattern (50 bp):
ATGATGGGCCACTGGTAGGACATGTTAGTTGCTAACAAGATTGGTCAAAG
Found at i:202686 original size:98 final size:98
Alignment explanation
Indices: 202517--202701 Score: 246
Period size: 98 Copynumber: 1.9 Consensus size: 98
202507 ATATCTGAAT
* ** * *
202517 ATGATGGGCCACTGGTAGGACATGTTAGTTGCTAACTAGATTGGTGTATGTGTTGGGCCACTAGT
1 ATGATGGGCCACTGGTAGGACATGTTAGTTGCTAACTAAATTGACGTATGTGCTGAGCCACTAGT
*
202582 AGGGCATGCTAGTTGCTAACCAAGTTGGCAAAG
66 AAGGCATGCTAGTTGCTAACCAAGTTGGCAAAG
**** *
202615 ATGATGGGCCACTGGTAGGACATGTTAGTTGCTAA-TCAAATTGACGTATGTGCTGAGTTTTTGG
1 ATGATGGGCCACTGGTAGGACATGTTAGTTGCTAACT-AAATTGACGTATGTGCTGAGCCACTAG
*
202679 TAAGGCATGTTAGTTGCTAACCA
65 TAAGGCATGCTAGTTGCTAACCA
202702 GCCTGACGTT
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
97 1 0.01
98 73 0.99
ACGTcount: A:0.25, C:0.15, G:0.30, T:0.31
Consensus pattern (98 bp):
ATGATGGGCCACTGGTAGGACATGTTAGTTGCTAACTAAATTGACGTATGTGCTGAGCCACTAGT
AAGGCATGCTAGTTGCTAACCAAGTTGGCAAAG
Found at i:204360 original size:50 final size:50
Alignment explanation
Indices: 204304--204493 Score: 227
Period size: 50 Copynumber: 3.7 Consensus size: 50
204294 GGTTCCCATG
* **
204304 CCATGTCCCAGACATAGTCTTACGGGGGACCTCTCATCTCGGTGCCAACA
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACA
* *
204354 CCATGTCCCAGACATGGTCTTACATAGGACCTCTCATCTCGGTGCCAACG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACA
** * **
204404 CCATGTCTGAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAATG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC---GGTGCCAACA
*
204460 CCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCT
204494 TTACCCAAAT
Statistics
Matches: 121, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
50 77 0.64
53 5 0.04
56 39 0.32
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.26
Consensus pattern (50 bp):
CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACA
Found at i:208225 original size:30 final size:31
Alignment explanation
Indices: 208186--208243 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
208176 TTTTTATTTT
208186 TCCCTCAAAACTTTTACTCCTTCCCACTTTC
1 TCCCTCAAAACTTTTACTCCTTCCCACTTTC
*
208217 TCCC-CAAAATTTTTACTCCTTCCCACT
1 TCCCTCAAAACTTTTACTCCTTCCCACT
208244 CCCTCCCCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.21, C:0.41, G:0.00, T:0.38
Consensus pattern (31 bp):
TCCCTCAAAACTTTTACTCCTTCCCACTTTC
Found at i:208250 original size:30 final size:30
Alignment explanation
Indices: 208186--208256 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
208176 TTTTTATTTT
**
208186 TCCCTCAAAACTTTTACTCCTTCCCACTTTC
1 TCCC-CAAAACTTTTACTCCTTCCCACTCCC
*
208217 TCCCCAAAATTTTTACTCCTTCCCACTCCC
1 TCCCCAAAACTTTTACTCCTTCCCACTCCC
*
208247 TCCCCTAAAC
1 TCCCCAAAAC
208257 AAAATTTTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
30 31 0.89
31 4 0.11
ACGTcount: A:0.21, C:0.45, G:0.00, T:0.34
Consensus pattern (30 bp):
TCCCCAAAACTTTTACTCCTTCCCACTCCC
Found at i:208483 original size:21 final size:21
Alignment explanation
Indices: 208454--208493 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
208444 TCCTTCAAAC
208454 TTTTACTCCCCAAAACTTTTTA
1 TTTTACT-CCCAAAACTTTTTA
*
208476 TTTT-CTCCCTAAACTTTT
1 TTTTACTCCCAAAACTTTT
208494 ACTTCTCGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.23, C:0.28, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTTACTCCCAAAACTTTTTA
Found at i:212036 original size:7 final size:7
Alignment explanation
Indices: 212024--212076 Score: 106
Period size: 7 Copynumber: 7.6 Consensus size: 7
212014 TTTCCAGGTC
212024 TTTTTCA
1 TTTTTCA
212031 TTTTTCA
1 TTTTTCA
212038 TTTTTCA
1 TTTTTCA
212045 TTTTTCA
1 TTTTTCA
212052 TTTTTCA
1 TTTTTCA
212059 TTTTTCA
1 TTTTTCA
212066 TTTTTCA
1 TTTTTCA
212073 TTTT
1 TTTT
212077 GAAGAAAAAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTTCA
Found at i:212169 original size:58 final size:58
Alignment explanation
Indices: 212047--212181 Score: 166
Period size: 58 Copynumber: 2.3 Consensus size: 58
212037 ATTTTTCATT
* * * *
212047 TTTCATTT-TTCATTTTTCATTTTTCATTTTGAAGAAAAACACATTCATTTCCAAATGA
1 TTTCATTTCTCCA-TTTTCATTTTTCATTTTGAAGAAAAACACAGTAATTTCCAAACGA
* * * *
212105 TTTCATTTCTCCATTTTCATTTTT-ATTTTGCAGAAAACCATAGTAATTTCCAAACGT
1 TTTCATTTCTCCATTTTCATTTTTCATTTTGAAGAAAAACACAGTAATTTCCAAACGA
212162 TTCTCATTTCTCCATTTTCA
1 TT-TCATTTCTCCATTTTCA
212182 CTATTTCTAT
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
57 28 0.42
58 36 0.54
59 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.05, T:0.48
Consensus pattern (58 bp):
TTTCATTTCTCCATTTTCATTTTTCATTTTGAAGAAAAACACAGTAATTTCCAAACGA
Found at i:214106 original size:70 final size:70
Alignment explanation
Indices: 214018--214154 Score: 265
Period size: 70 Copynumber: 2.0 Consensus size: 70
214008 TATTTCAAGT
214018 TTTTTTTATATACCTTATTTATTTTAAATATATATATACATTATCTACTTTAGTTCATTGTTTTG
1 TTTTTTTATATACCTTATTTATTTTAAATATATATATACATTATCTACTTTAGTTCATTGTTTTG
214083 TTAGG
66 TTAGG
*
214088 TTTTTTTATATACGTTATTTATTTTAAATATATATATACATTATCTACTTTAGTTCATTGTTTTG
1 TTTTTTTATATACCTTATTTATTTTAAATATATATATACATTATCTACTTTAGTTCATTGTTTTG
214153 TT
66 TT
214155 TAAAAAAATT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 66 1.00
ACGTcount: A:0.27, C:0.08, G:0.07, T:0.58
Consensus pattern (70 bp):
TTTTTTTATATACCTTATTTATTTTAAATATATATATACATTATCTACTTTAGTTCATTGTTTTG
TTAGG
Found at i:219086 original size:7 final size:7
Alignment explanation
Indices: 219076--219101 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
219066 GTAGTTGTTG
219076 ATTTTAA
1 ATTTTAA
219083 ATTTTAA
1 ATTTTAA
219090 ATTTTAA
1 ATTTTAA
219097 ATTTT
1 ATTTT
219102 TCGAACCAAA
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
ATTTTAA
Found at i:224219 original size:22 final size:21
Alignment explanation
Indices: 224194--224235 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
224184 CCAGCTAGAC
224194 TTTGACGAATTTAATAAAAAAA
1 TTTGAC-AATTTAATAAAAAAA
* *
224216 TTTGTCTATTTAATAAAAAA
1 TTTGACAATTTAATAAAAAA
224236 CCTGCTCAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (21 bp):
TTTGACAATTTAATAAAAAAA
Found at i:224300 original size:3 final size:3
Alignment explanation
Indices: 224292--224339 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
224282 TTCAACTTGT
224292 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
224340 ATAAGATAGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:228746 original size:54 final size:55
Alignment explanation
Indices: 228619--228748 Score: 158
Period size: 54 Copynumber: 2.4 Consensus size: 55
228609 CATCTCATAG
*
228619 ACTGTGTAACTCACTGACTTGACTCACACAACCGTGTCGCAGGCTGTGTGCTAGT
1 ACTGTGTAACTCACTGACTTGACTCACACAACCATGTCGCAGGCTGTGTGCTAGT
* ** * * *
228674 AC-GTGTAACCCACTGACTTGGTTCACACAGCCATGTCGTAGGTTGTGTGCTAG-
1 ACTGTGTAACTCACTGACTTGACTCACACAACCATGTCGCAGGCTGTGTGCTAGT
*
228727 CCTGTGTAACTCA-TGGACTTGA
1 ACTGTGTAACTCACT-GACTTGA
228749 GACACACGAT
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
53 2 0.03
54 59 0.94
55 2 0.03
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.28
Consensus pattern (55 bp):
ACTGTGTAACTCACTGACTTGACTCACACAACCATGTCGCAGGCTGTGTGCTAGT
Found at i:230612 original size:42 final size:40
Alignment explanation
Indices: 230502--230618 Score: 126
Period size: 42 Copynumber: 2.8 Consensus size: 40
230492 ATTTATATGC
230502 CATACGGCTTGGACACTAGCCCATGTCCTTGCCCGTATAGCT
1 CATACGGC-TGGACAC-AGCCCATGTCCTTGCCCGTATAGCT
* * ** *
230544 CACATGGCCTGGACACATGTACATGTCCTTGCCCGTGTAGCT
1 CATACGG-CTGGACACA-GCCCATGTCCTTGCCCGTATAGCT
*
230586 CATACGGTCTGGACACACCCCTATGTCCTTGCC
1 CATACGG-CTGGACACAGCCC-ATGTCCTTGCC
230619 TTTGTGACTT
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
41 2 0.03
42 58 0.95
43 1 0.02
ACGTcount: A:0.19, C:0.34, G:0.21, T:0.26
Consensus pattern (40 bp):
CATACGGCTGGACACAGCCCATGTCCTTGCCCGTATAGCT
Found at i:230828 original size:105 final size:105
Alignment explanation
Indices: 230634--230831 Score: 256
Period size: 104 Copynumber: 1.9 Consensus size: 105
230624 GACTTACACG
* * * *
230634 GCCTGGGCACACGCCCATGTCCTCTGTGCGTGTGGTTCTAAAACATAAGTAGTGAGTTACACGGT
1 GCCTGGGCACACGCCCATGTCCTCTGTGCGTGTGGTACTAAAACACAAATAGTGAGTTACACGGC
* * * *
230699 CTGGACACACGCCCGTGTCCTTGCCCGTATACCTCACATA
66 CTAGACAAACGCCCATCTCCTTGCCCGTATACCTCACATA
** *
230739 GCCTGGGCACACGCCCATGTCC-CTG-GCCGTGTGGTACTAAGTCACAAATAGTGAGTTACATGG
1 GCCTGGGCACACGCCCATGTCCTCTGTG-CGTGTGGTACTAAAACACAAATAGTGAGTTACACGG
*
230802 CCTAGACAAACGCTCATCTCCTTTGCCCGT
65 CCTAGACAAACGCCCATCTCC-TTGCCCGT
230832 GTGAACCCTA
Statistics
Matches: 79, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
103 1 0.01
104 48 0.61
105 30 0.38
ACGTcount: A:0.21, C:0.31, G:0.24, T:0.24
Consensus pattern (105 bp):
GCCTGGGCACACGCCCATGTCCTCTGTGCGTGTGGTACTAAAACACAAATAGTGAGTTACACGGC
CTAGACAAACGCCCATCTCCTTGCCCGTATACCTCACATA
Found at i:234302 original size:20 final size:20
Alignment explanation
Indices: 234277--234324 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
234267 AAATGATATT
234277 GATACTTTGTGAAAG-GTATC
1 GATACTTTGT-AAAGAGTATC
*
234297 GATACTTTGTTAAGAGTATC
1 GATACTTTGTAAAGAGTATC
*
234317 AATACTTT
1 GATACTTT
234325 TGATTTTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (20 bp):
GATACTTTGTAAAGAGTATC
Found at i:243037 original size:40 final size:41
Alignment explanation
Indices: 242975--243051 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 41
242965 AGGTTAAAAT
*
242975 ATGTGTAAGTTTATTATATATATTATAAT-ATAAAATCTTA
1 ATGTGTAAGTATATTATATATATTATAATAATAAAATCTTA
* *
243015 ATGTTTAAGTATA-TATATTATATTATAGTAATAAAAT
1 ATGTGTAAGTATATTATA-TATATTATAATAATAAAAT
243052 AAGTAATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
39 4 0.12
40 21 0.66
41 7 0.22
ACGTcount: A:0.44, C:0.01, G:0.08, T:0.47
Consensus pattern (41 bp):
ATGTGTAAGTATATTATATATATTATAATAATAAAATCTTA
Found at i:243147 original size:87 final size:83
Alignment explanation
Indices: 243044--243201 Score: 221
Period size: 87 Copynumber: 1.9 Consensus size: 83
243034 ATATTATAGT
*
243044 AATAAAATAAGTAATAAAAAGAAATAGAA-AAAGGAAACAAAATA-AAATGAAACAGAAAATAAA
1 AATAAAATAAGTAATAAAAAGAAATA-AAGAAA-G-AA-AAAATAGAAACGAAACAG-AAA-AAA
243107 GAAAGAAAGAAAAAAGACAGGGAA
60 GAAAGAAAGAAAAAAGACAGGGAA
* *
243131 AATAAAATAAGTAATAAAAAGAAATAAAGAAAGAAAGAATAGAAACGAAACAGAAAGAAGAAAGA
1 AATAAAATAAGTAATAAAAAGAAATAAAGAAAGAAAAAATAGAAACGAAACAGAAAAAAGAAAGA
243196 AAGAAA
66 AAGAAA
243202 TGAGAATGAC
Statistics
Matches: 66, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
83 14 0.21
84 8 0.12
85 12 0.18
86 3 0.05
87 29 0.44
ACGTcount: A:0.72, C:0.03, G:0.16, T:0.09
Consensus pattern (83 bp):
AATAAAATAAGTAATAAAAAGAAATAAAGAAAGAAAAAATAGAAACGAAACAGAAAAAAGAAAGA
AAGAAAAAAGACAGGGAA
Found at i:243165 original size:4 final size:4
Alignment explanation
Indices: 243148--243201 Score: 56
Period size: 4 Copynumber: 12.8 Consensus size: 4
243138 TAAGTAATAA
*
243148 AAAG AAAT AAAG AAAG AAAG AATAG AAACG AAACAG AAAG -AAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AA-AG AAA-G -AA-AG AAAG AAAG AAAG
243195 AAAG AAA
1 AAAG AAA
243202 TGAGAATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
3 3 0.07
4 29 0.67
5 7 0.16
6 3 0.07
7 1 0.02
ACGTcount: A:0.72, C:0.04, G:0.20, T:0.04
Consensus pattern (4 bp):
AAAG
Found at i:244176 original size:40 final size:39
Alignment explanation
Indices: 244055--244189 Score: 121
Period size: 40 Copynumber: 3.4 Consensus size: 39
244045 GACTTCGAGT
* *
244055 CGATGAGACACTGGGTGTCAATTTATTATTTCAGATTTATT
1 CGATGAGACACTGGGTGTCAATTTA-TACTTCA-ATTTATC
* * * * ** *
244096 TGATGAGGCATTGGGTGCCAA-TT-TACTTCGGTTTAAC
1 CGATGAGACACTGGGTGTCAATTTATACTTCAATTTATC
*
244133 CGATGAGACACTGGGTGTCAATTTACTACTTCAAATTATC
1 CGATGAGACACTGGGTGTCAATTTA-TACTTCAATTTATC
* *
244173 CGATGAGGCACTAGGTG
1 CGATGAGACACTGGGTG
244190 CCAGGCTGGT
Statistics
Matches: 72, Mismatches: 19, Indels: 7
0.73 0.19 0.07
Matches are distributed among these distances:
37 21 0.29
38 7 0.10
40 27 0.38
41 17 0.24
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAATTTATACTTCAATTTATC
Found at i:244380 original size:16 final size:16
Alignment explanation
Indices: 244344--244398 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 16
244334 ATTGAGACAC
244344 ATGAATTG-TGTAT-T
1 ATGAATTGATGTATGT
244358 CATGAATTGA-GTATGGT
1 -ATGAATTGATGTAT-GT
*
244375 ATGAA-TGATGTATTT
1 ATGAATTGATGTATGT
244390 ATGAATTGA
1 ATGAATTGA
244399 ATAATTGAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
15 21 0.62
16 12 0.35
17 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.24, T:0.42
Consensus pattern (16 bp):
ATGAATTGATGTATGT
Found at i:247738 original size:9 final size:9
Alignment explanation
Indices: 247707--247764 Score: 55
Period size: 9 Copynumber: 6.3 Consensus size: 9
247697 TTAAAACAAT
247707 AAAGTAAATA
1 AAAG-AAATA
*
247717 AAATAAA-A
1 AAAGAAATA
247725 TAAAGAAATA
1 -AAAGAAATA
*
247735 AAAGAAACA
1 AAAGAAATA
*
247744 AAAGAAGTA
1 AAAGAAATA
*
247753 AAAGAAACA
1 AAAGAAATA
247762 AAA
1 AAA
247765 AGAACAGGAG
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
8 1 0.03
9 34 0.87
10 4 0.10
ACGTcount: A:0.76, C:0.03, G:0.10, T:0.10
Consensus pattern (9 bp):
AAAGAAATA
Found at i:247760 original size:18 final size:18
Alignment explanation
Indices: 247707--247764 Score: 73
Period size: 18 Copynumber: 3.2 Consensus size: 18
247697 TTAAAACAAT
*
247707 AAAGTAAATAAAATAAA-A
1 AAAG-AAATAAAAGAAACA
247725 TAAAGAAATAAAAGAAACA
1 -AAAGAAATAAAAGAAACA
*
247744 AAAGAAGTAAAAGAAACA
1 AAAGAAATAAAAGAAACA
247762 AAA
1 AAA
247765 AGAACAGGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
18 31 0.86
19 5 0.14
ACGTcount: A:0.76, C:0.03, G:0.10, T:0.10
Consensus pattern (18 bp):
AAAGAAATAAAAGAAACA
Found at i:248490 original size:23 final size:23
Alignment explanation
Indices: 248463--248596 Score: 143
Period size: 23 Copynumber: 6.0 Consensus size: 23
248453 GGCTTTGCCG
*
248463 ATCAGACACTTTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTAT
248486 ATCAGGCACTTTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTAT
248509 ATCAGGCACTTTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTAT
* * **
248532 TTCAGGCACCTCGTGTGTCG--T
1 ATCAGGCACTTTATGTGTCGTAT
* ** *
248553 ATCAGGCACCTCGTGTGTTGT-T
1 ATCAGGCACTTTATGTGTCGTAT
*
248575 -TCAGGCA-TCTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTAT
248596 A
1 A
248597 CTAATTAGGT
Statistics
Matches: 96, Mismatches: 12, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
20 7 0.07
21 27 0.28
22 1 0.01
23 61 0.64
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.37
Consensus pattern (23 bp):
ATCAGGCACTTTATGTGTCGTAT
Found at i:260197 original size:31 final size:31
Alignment explanation
Indices: 260156--260527 Score: 219
Period size: 31 Copynumber: 12.2 Consensus size: 31
260146 CAACAATATA
* *
260156 TATATTCATATACGAATCAAATTCGGCAATG
1 TATAATCATATACAAATCAAATTCGGCAATG
*
260187 TATAATCATATACAAATC-AATTTGGCAATG
1 TATAATCATATACAAATCAAATTCGGCAATG
* ** **
260217 TATAACCATATATGAATCATGTTCGGCAATG
1 TATAATCATATACAAATCAAATTCGGCAATG
* *
260248 TATAATCATATACAAAT-TAATTCGGTAACT-
1 TATAATCATATACAAATCAAATTCGGCAA-TG
* * ** *
260278 TAT-ATCCATATACAAATTAATTTTAGCAAAG
1 TATAAT-CATATACAAATCAAATTCGGCAATG
* *
260309 TATAATCATATACGAATC-AATTCTGCAACT-
1 TATAATCATATACAAATCAAATTCGGCAA-TG
** * **
260339 TATCTTCATATACAAATCAATTTCGATAATG
1 TATAATCATATACAAATCAAATTCGGCAATG
* ** *
260370 TATAACCATATACAAAT-AAATTTCAACAATT
1 TATAATCATATACAAATCAAA-TTCGGCAATG
* * * *
260401 TACAACCATATACAAAT-TAATTCAGCAACT-
1 TATAATCATATACAAATCAAATTCGGCAA-TG
* * **
260431 TAT-ATCCATATACAATTCAATTTCAACAATG
1 TATAAT-CATATACAAATCAAATTCGGCAATG
* * * *
260462 TATAA-CTATATACAAATTAATTTCAGCAATT
1 TATAATC-ATATACAAATCAAATTCGGCAATG
* * * *
260493 TATAATTATATACGAAT-TAATTCGGCAATA
1 TATAATCATATACAAATCAAATTCGGCAATG
260523 TATAA
1 TATAA
260528 AACAATCAAA
Statistics
Matches: 263, Mismatches: 61, Indels: 35
0.73 0.17 0.10
Matches are distributed among these distances:
29 3 0.01
30 107 0.41
31 150 0.57
32 3 0.01
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (31 bp):
TATAATCATATACAAATCAAATTCGGCAATG
Found at i:260234 original size:61 final size:60
Alignment explanation
Indices: 260162--260527 Score: 267
Period size: 61 Copynumber: 6.0 Consensus size: 60
260152 TATATATATT
* * *
260162 CATATACGAATCAAATTCGGCAATGTATAATCATATACAAATCAATTTGGCAATGTATAAC
1 CATATACAAATCAATTTCAGCAATGTATAATCATATACAAATCAATTTGGCAAT-TATAAC
** * * * * *
260223 CATATATGAATC-ATGTTCGGCAATGTATAATCATATACAAATTAATTCGGTAACTTATATC
1 CATATACAAATCAAT-TTCAGCAATGTATAATCATATACAAATCAATTTGGCAA-TTATAAC
* * * * ***
260284 CATATACAAATTAATTTTAGCAAAGTATAATCATATACGAATCAATTCT-GCAACTTATCTT
1 CATATACAAATCAATTTCAGCAATGTATAATCATATACAAATCAATT-TGGCAA-TTATAAC
* * * ** *
260345 CATATACAAATCAATTTC-GATAATGTATAACCATATACAAATAAATTTCAACAATTTACAAC
1 CATATACAAATCAATTTCAG-CAATGTATAATCATATACAAATCAATTT-GGCAA-TTATAAC
* * **
260407 CATATACAAATTAA-TTCAGCAACT-TAT-ATCCATATACAATTCAATTTCAACAATGTATAAC
1 CATATACAAATCAATTTCAGCAA-TGTATAAT-CATATACAAATCAATTT-GGCAAT-TATAAC
* * * * * * *
260468 TATATACAAATTAATTTCAGCAATTTATAATTATATACGAATTAATTCGGCAATATATAA
1 CATATACAAATCAATTTCAGCAATGTATAATCATATACAAATCAATTTGGCAAT-TATAA
260528 AACAATCAAA
Statistics
Matches: 245, Mismatches: 46, Indels: 28
0.77 0.14 0.09
Matches are distributed among these distances:
60 5 0.02
61 191 0.78
62 47 0.19
63 2 0.01
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (60 bp):
CATATACAAATCAATTTCAGCAATGTATAATCATATACAAATCAATTTGGCAATTATAAC
Found at i:260411 original size:92 final size:92
Alignment explanation
Indices: 260156--260520 Score: 369
Period size: 92 Copynumber: 4.0 Consensus size: 92
260146 CAACAATATA
* * * * * *
260156 TATATTCATATACGAATCAAATTCGGCAATGTATAATCATATACAAATCAATTT-GGCAATGTAT
1 TATATTCATATACAAATCAATTTCGACAATGTATAACCATATACAAATTAATTTCAGCAATGTAT
* *
260220 AACCATATATGAATCATGTTCGGCAA-T
66 AACCATATACGAATCA-ATTCGGCAACT
* * ** * * *
260247 GTATAATCATATACAAATTAA-TTCGGTAACT-TATATCCATATACAAATTAATTTTAGCAAAGT
1 -TATATTCATATACAAATCAATTTCGACAA-TGTATAACCATATACAAATTAATTTCAGCAATGT
* *
260310 ATAATCATATACGAATCAATTCTGCAACT
64 ATAACCATATACGAATCAATTCGGCAACT
* * * * * *
260339 TATCTTCATATACAAATCAATTTCGATAATGTATAACCATATACAAATAAATTTCAACAATTTAC
1 TATATTCATATACAAATCAATTTCGACAATGTATAACCATATACAAATTAATTTCAGCAATGTAT
* * *
260404 AACCATATACAAATTAATTCAGCAACT
66 AACCATATACGAATCAATTCGGCAACT
* * * * *
260431 TATATCCATATACAATTCAATTTCAACAATGTATAACTATATACAAATTAATTTCAGCAATTTAT
1 TATATTCATATACAAATCAATTTCGACAATGTATAACCATATACAAATTAATTTCAGCAATGTAT
** *
260496 AATTATATACGAATTAATTCGGCAA
66 AACCATATACGAATCAATTCGGCAA
260521 TATATAAAAC
Statistics
Matches: 227, Mismatches: 41, Indels: 10
0.82 0.15 0.04
Matches are distributed among these distances:
91 52 0.23
92 175 0.77
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (92 bp):
TATATTCATATACAAATCAATTTCGACAATGTATAACCATATACAAATTAATTTCAGCAATGTAT
AACCATATACGAATCAATTCGGCAACT
Found at i:260465 original size:153 final size:153
Alignment explanation
Indices: 260136--260514 Score: 403
Period size: 153 Copynumber: 2.5 Consensus size: 153
260126 ATCCAATGCT
*
260136 CAAA-TCAA-TTCAACAATATATATATTCATATACGAATCAAATTCGGCAATGTATAATCATATA
1 CAAATTCAATTTCAACAATGTATA-A-TCATATACGAATC-AATTCGGCAATGTATAATCATATA
* ** * ** * *
260199 CAAATCAATTTGGCAATGTATAACCATATATGAATCATGTTCGGCAATGTATAATCATATACAAA
63 CAAATCAATTTGACAATGTATAACCATATACAAATAATGTTCAACAATGTACAACCATATACAAA
* *
260264 TTAATTCGGTAACTTATATCCATATA
128 TTAATTCAGCAACTTATATCCATATA
* * * * **
260290 CAAATT-AATTTTAGCAAAGTATAATCATATACGAATCAATTCTGCAACT-TATCTTCATATACA
1 CAAATTCAATTTCAACAATGTATAATCATATACGAATCAATTCGGCAA-TGTATAATCATATACA
* *
260353 AATCAATTTCGATAATGTATAACCATATACAAATAAAT-TTCAACAATTTACAACCATATACAAA
65 AATCAATTT-GACAATGTATAACCATATACAAAT-AATGTTCAACAATGTACAACCATATACAAA
260417 TTAATTCAGCAACTTATATCCATATA
128 TTAATTCAGCAACTTATATCCATATA
* * * * *
260443 C-AATTCAATTTCAACAATGTATAA-CTATATACAAATTAATTTCAGCAATTTATAATTATATAC
1 CAAATTCAATTTCAACAATGTATAATC-ATATACGAATCAA-TTCGGCAATGTATAATCATATAC
* *
260506 GAATTAATT
64 AAATCAATT
260515 CGGCAATATA
Statistics
Matches: 186, Mismatches: 30, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
152 35 0.19
153 107 0.58
154 33 0.18
155 11 0.06
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34
Consensus pattern (153 bp):
CAAATTCAATTTCAACAATGTATAATCATATACGAATCAATTCGGCAATGTATAATCATATACAA
ATCAATTTGACAATGTATAACCATATACAAATAATGTTCAACAATGTACAACCATATACAAATTA
ATTCAGCAACTTATATCCATATA
Found at i:267930 original size:20 final size:20
Alignment explanation
Indices: 267877--267922 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
267867 CAGTGGTTTT
267877 CACACGGGCGTGTGCCTATC
1 CACACGGGCGTGTGCCTATC
* *
267897 CGCACGGGCGTGTGCCTGTC
1 CACACGGGCGTGTGCCTATC
267917 CACACG
1 CACACG
267923 AGCATGTGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.13, C:0.37, G:0.33, T:0.17
Consensus pattern (20 bp):
CACACGGGCGTGTGCCTATC
Found at i:271126 original size:29 final size:31
Alignment explanation
Indices: 271075--271132 Score: 93
Period size: 29 Copynumber: 1.9 Consensus size: 31
271065 TGAAAATATT
*
271075 AAAATTATTAAAATTATTTTTAAAAAAATAA
1 AAAATTATTAAAATTATTCTTAAAAAAATAA
271106 AAAATT-TTAAAATT-TTCTTAAAAAAAT
1 AAAATTATTAAAATTATTCTTAAAAAAAT
271133 GAAATTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 12 0.46
30 8 0.31
31 6 0.23
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (31 bp):
AAAATTATTAAAATTATTCTTAAAAAAATAA
Found at i:271204 original size:22 final size:22
Alignment explanation
Indices: 271174--271215 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
271164 ATTTGGAGAT
*
271174 TTTTTGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
271196 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
271216 TTTGAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:271236 original size:52 final size:51
Alignment explanation
Indices: 271165--271267 Score: 129
Period size: 52 Copynumber: 2.0 Consensus size: 51
271155 TTAATATGGA
* * *
271165 TTTGGAGATTTTTTGAAGGAAATTGAGAG-GATTTTGGAA-GGAATTTGAGAG
1 TTTGGAGAATTTTGGAAGGAAATTGAGAGAAATTTT-GAAGGGAA-TTGAGAG
*
271216 TTTGAGAGAATTTTGGAAGGAAATTGATAGAAATTTTGAAGGGAATTGAGAG
1 TTTG-GAGAATTTTGGAAGGAAATTGAGAGAAATTTTGAAGGGAATTGAGAG
271268 AAATTTTGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
51 4 0.09
52 32 0.71
53 9 0.20
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.33
Consensus pattern (51 bp):
TTTGGAGAATTTTGGAAGGAAATTGAGAGAAATTTTGAAGGGAATTGAGAG
Found at i:271242 original size:22 final size:23
Alignment explanation
Indices: 271217--271308 Score: 111
Period size: 22 Copynumber: 4.2 Consensus size: 23
271207 ATTTGAGAGT
271217 TTGAGAG-AATTTTGGAAGGAAA
1 TTGAGAGAAATTTTGGAAGGAAA
* *
271239 TTGATAGAAATTTT-GAAGGGAA
1 TTGAGAGAAATTTTGGAAGGAAA
*
271261 TTGAGAGAAATTTTGAAAGG-AA
1 TTGAGAGAAATTTTGGAAGGAAA
* *
271283 TTGAGAG-AATTTTTGAAAGAAA
1 TTGAGAGAAATTTTGGAAGGAAA
271305 TTGA
1 TTGA
271309 TATTGAATTT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
21 9 0.15
22 41 0.68
23 10 0.17
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.30
Consensus pattern (23 bp):
TTGAGAGAAATTTTGGAAGGAAA
Found at i:271266 original size:44 final size:44
Alignment explanation
Indices: 271217--271308 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
271207 ATTTGAGAGT
* * * *
271217 TTGAGAG-AATTTTGGAAGGAAATTGATAGAAATTTTGAAGGGAA
1 TTGAGAGAAATTTTGAAAGG-AATTGAGAGAAATTTTGAAAGAAA
*
271261 TTGAGAGAAATTTTGAAAGGAATTGAGAGAATTTTTGAAAGAAA
1 TTGAGAGAAATTTTGAAAGGAATTGAGAGAAATTTTGAAAGAAA
271305 TTGA
1 TTGA
271309 TATTGAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 31 0.74
45 11 0.26
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.30
Consensus pattern (44 bp):
TTGAGAGAAATTTTGAAAGGAATTGAGAGAAATTTTGAAAGAAA
Found at i:272009 original size:19 final size:18
Alignment explanation
Indices: 271968--272027 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 18
271958 ATGAATTTAA
**
271968 AAAAAATAAAAAATTAGGA
1 AAAAAATAAAAAATT-TTA
*
271987 AAAAGAATAAAAATCTTTTA
1 AAAA-AATAAAAA-ATTTTA
272007 AAAAAATAAAAAATTTTA
1 AAAAAATAAAAAATTTTA
272025 AAA
1 AAA
272028 TTATAATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 8 0.23
19 12 0.34
20 13 0.37
21 2 0.06
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (18 bp):
AAAAAATAAAAAATTTTA
Found at i:272513 original size:12 final size:12
Alignment explanation
Indices: 272496--272535 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
272486 ATTTTTATAT
272496 TTTAAATTTTTA
1 TTTAAATTTTTA
272508 TTTAAA--TTTA
1 TTTAAATTTTTA
272518 TTTAATATTTTT-
1 TTTAA-ATTTTTA
272530 TTTAAA
1 TTTAAA
272536 GGCAAACTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
10 9 0.36
11 2 0.08
12 11 0.44
13 3 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTAAATTTTTA
Found at i:282340 original size:61 final size:62
Alignment explanation
Indices: 282271--282391 Score: 181
Period size: 61 Copynumber: 2.0 Consensus size: 62
282261 TAGTTCACTC
* *
282271 ATTATCTTCGTATCACTAATACATAGTATAATCTTGTTTTATT-TGACTCCAGAACCTATTT
1 ATTATCTTCGTATCACTAATACATACTATAATCTTATTTTATTGTGACTCCAGAACCTATTT
* ** *
282332 ATTATCTTCTTATCACTGGTACATACTATAATCTTATTTTATTGTGACTCCATAACCTAT
1 ATTATCTTCGTATCACTAATACATACTATAATCTTATTTTATTGTGACTCCAGAACCTAT
282392 GTCTATATCC
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
61 38 0.72
62 15 0.28
ACGTcount: A:0.29, C:0.19, G:0.07, T:0.45
Consensus pattern (62 bp):
ATTATCTTCGTATCACTAATACATACTATAATCTTATTTTATTGTGACTCCAGAACCTATTT
Found at i:283431 original size:12 final size:13
Alignment explanation
Indices: 283402--283439 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
283392 GATGTATTTA
283402 TCTTCTTTCTTTCTT
1 TCTTC-TTCTTTC-T
283417 TCTTCTTC-TTCT
1 TCTTCTTCTTTCT
283429 TCTTCTTCTTT
1 TCTTCTTCTTT
283440 TTTTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 9 0.41
13 5 0.23
14 3 0.14
15 5 0.23
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (13 bp):
TCTTCTTCTTTCT
Found at i:283443 original size:1 final size:1
Alignment explanation
Indices: 283437--283491 Score: 101
Period size: 1 Copynumber: 55.0 Consensus size: 1
283427 CTTCTTCTTC
*
283437 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
283492 GCGTTTATTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.02, C:0.00, G:0.00, T:0.98
Consensus pattern (1 bp):
T
Found at i:287729 original size:255 final size:254
Alignment explanation
Indices: 287237--287750 Score: 942
Period size: 255 Copynumber: 2.0 Consensus size: 254
287227 AAAATATTTA
*
287237 AATGATAATAAAAATTACTTTTATTTAAATGTGAAATAATATATTTAAAATGATTAACTTGGTCT
1 AATGATAATAAAAATTACTTTTATTTAAATGTGAAATAATATATTTAAAACGATTAACTTGGTCT
287302 TTGAACTTCTTTATCTCCATTAGCCTTAGTTTTTTTTTTCTATTTTGATACTTGAATTTAGATTC
66 TTGAACTTCTTTATCTCCATTAGCCTTAGTTTTTTTTTTCTATTTTGATACTTGAATTTAGATTC
*
287367 CATTTAAATTGTCACATCTCATTTAATTGTTTTAATTTATATGTTTTTAATAATTTATGTATATA
131 CATTTAAATTGTCACATCTCATTTAATTGTTTTAATTTATATATTTTTAATAATTTATG-ATATA
287432 TATATATATATTATTTTTTCAGGTATTAACACAGTAAAAAAAAAGTCAAATTTTGAGGCT
195 TATATATATATTATTTTTTCAGGTATTAACACAGTAAAAAAAAAGTCAAATTTTGAGGCT
287492 AATGATAATAAAAATTACTTTTATTTAAATGTGAAATAATATATTTAAAACGATTAACTTGGTCT
1 AATGATAATAAAAATTACTTTTATTTAAATGTGAAATAATATATTTAAAACGATTAACTTGGTCT
*
287557 TTGAACTTCTTTATCTCCATTAGCCTTAGTTTTTTTTTTTTTCTATTTTGATCCTTGAATTTAGA
66 TTGAACTTCTTTATCTCCATTAGCCTTAG---TTTTTTTTTTCTATTTTGATACTTGAATTTAGA
287622 TTCCATTTAAATTGTCACATCTCATTTAATTGTTTTAATTTATATATTTTTAATAATTTATG-TA
128 TTCCATTTAAATTGTCACATCTCATTTAATTGTTTTAATTTATATATTTTTAATAATTTATGATA
*
287686 TATATATATATATTATTTTTTCAGGTATTAACACAGT-AAAAAAATGTCAAATTTTGAGGCT
193 TATATATATATATTATTTTTTCAGGTATTAACACAGTAAAAAAAAAGTCAAATTTTGAGGCT
287747 AATG
1 AATG
287751 TTAACCAAAA
Statistics
Matches: 252, Mismatches: 4, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
255 120 0.48
256 39 0.15
258 93 0.37
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.48
Consensus pattern (254 bp):
AATGATAATAAAAATTACTTTTATTTAAATGTGAAATAATATATTTAAAACGATTAACTTGGTCT
TTGAACTTCTTTATCTCCATTAGCCTTAGTTTTTTTTTTCTATTTTGATACTTGAATTTAGATTC
CATTTAAATTGTCACATCTCATTTAATTGTTTTAATTTATATATTTTTAATAATTTATGATATAT
ATATATATATTATTTTTTCAGGTATTAACACAGTAAAAAAAAAGTCAAATTTTGAGGCT
Found at i:293592 original size:43 final size:43
Alignment explanation
Indices: 293530--293754 Score: 153
Period size: 43 Copynumber: 5.2 Consensus size: 43
293520 TTTGAAAAAG
*
293530 CGCCGCTAAAGACCATGACCTATAGCGGCGCTTCTCTAACAAA
1 CGCCGCTAAAGACCATGACCTATAGCGGCGCTTCTCCAACAAA
* * *
293573 CGCCGCTAAAGA-CATTGACCTTTAGCGGCGCTTTTCCCACAAA
1 CGCCGCTAAAGACCA-TGACCTATAGCGGCGCTTCTCCAACAAA
* * * * *
293616 TGCCGCTATAG-CTCATGAGCTTTAGCGGCGCTTTTTCC-ACAAA
1 CGCCGCTAAAGAC-CATGACCTATAGCGGCGC-TTCTCCAACAAA
* * * * *
293659 CGTCGCTATAG-CTCTAT-ACCTTTAGCGGTGCATT-TCCCACAAA
1 CGCCGCTAAAGAC-C-ATGACCTATAGCGGCGC-TTCTCCAACAAA
* *
293702 CGCCGCTATAG-CTCGAT-ACCTTTAGCGGCGCTTCTCACAA-AAA
1 CGCCGCTAAAGAC-C-ATGACCTATAGCGGCGCTTCTC-CAACAAA
*
293745 CGCCACTAAA
1 CGCCGCTAAA
293755 AATATAACAT
Statistics
Matches: 156, Mismatches: 18, Indels: 16
0.82 0.09 0.08
Matches are distributed among these distances:
42 7 0.04
43 137 0.88
44 12 0.08
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (43 bp):
CGCCGCTAAAGACCATGACCTATAGCGGCGCTTCTCCAACAAA
Found at i:293642 original size:86 final size:86
Alignment explanation
Indices: 293530--293754 Score: 237
Period size: 86 Copynumber: 2.6 Consensus size: 86
293520 TTTGAAAAAG
* *
293530 CGCCGCTAAAGAC-CATGACCTATAGCGGCGCTTCTCTAACAAACGCCGCTAAAGACAT-T-GAC
1 CGCCGCTATAG-CTCATGACCTTTAGCGGCGCTTCTCTAACAAACGCCGCTAAAG-C-TCTAGAC
*
293592 CTTTAGCGGCGCTTTTCCCACAAA
63 CTTTAGCGGCGCATTTCCCACAAA
* * * * * * *
293616 TGCCGCTATAGCTCATGAGCTTTAGCGGCGCTT-TTTCCACAAACGTCGCTATAGCTCTATACCT
1 CGCCGCTATAGCTCATGACCTTTAGCGGCGCTTCTCT-AACAAACGCCGCTAAAGCTCTAGACCT
*
293680 TTAGCGGTGCATTTCCCACAAA
65 TTAGCGGCGCATTTCCCACAAA
* *
293702 CGCCGCTATAGCTCGAT-ACCTTTAGCGGCGCTTCTC-ACAAAAACGCCACTAAA
1 CGCCGCTATAGCTC-ATGACCTTTAGCGGCGCTTCTCTA-ACAAACGCCGCTAAA
293755 AATATAACAT
Statistics
Matches: 113, Mismatches: 19, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
84 1 0.01
85 5 0.04
86 104 0.92
87 3 0.03
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (86 bp):
CGCCGCTATAGCTCATGACCTTTAGCGGCGCTTCTCTAACAAACGCCGCTAAAGCTCTAGACCTT
TAGCGGCGCATTTCCCACAAA
Found at i:295451 original size:19 final size:20
Alignment explanation
Indices: 295423--295465 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
295413 AAATTATAAA
*
295423 TTTTAGTTTTTTTATTTCAT
1 TTTTAGTTTTTGTATTTCAT
*
295443 TTTTA-TTTTTGTATTTTAT
1 TTTTAGTTTTTGTATTTCAT
295462 TTTT
1 TTTT
295466 TCTTATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.79
Consensus pattern (20 bp):
TTTTAGTTTTTGTATTTCAT
Found at i:295780 original size:21 final size:20
Alignment explanation
Indices: 295756--295796 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
295746 TCTAACCCCT
*
295756 AACCCCTAAACCTTAAATCCC
1 AACCCCTAAACCAT-AATCCC
*
295777 AACCCTTAAACCATAATCCC
1 AACCCCTAAACCATAATCCC
295797 TAGTCCTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.39, C:0.41, G:0.00, T:0.20
Consensus pattern (20 bp):
AACCCCTAAACCATAATCCC
Found at i:297001 original size:41 final size:41
Alignment explanation
Indices: 296944--297159 Score: 324
Period size: 41 Copynumber: 5.3 Consensus size: 41
296934 AAATGTTTTT
*
296944 GCGGCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGTATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGCATTA
* * *
296985 GCGGCGCTATTACAAAAACGCCGCTAAAGAACTGAACATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGCATTA
* *
297026 GCGGCGCTTTTCCAAAAATGCCGGTAAAGAACTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGCATTA
* *
297067 GCGGCGCTTTTACAAAAACGCCGCTAAAGAACTAAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGCATTA
* * *
297108 GCGACGCTTCTCCAAAAACGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGCATTA
*
297149 GCGGTGCTTTT
1 GCGGCGCTTTT
297160 TTTTAAAAAG
Statistics
Matches: 154, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 154 1.00
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (41 bp):
GCGGCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGCATTA
Found at i:297261 original size:40 final size:39
Alignment explanation
Indices: 297217--297353 Score: 139
Period size: 40 Copynumber: 3.4 Consensus size: 39
297207 GGGCTTAGGG
* **
297217 TTTTTTGCGGCGTTTTTCCAAAAATTGCCGCTAATGCTCA
1 TTTTTAGCGGCGTTTTT-CAAAAAGCGCCGCTAATGCTCA
* * *
297257 TTTTTAGCAGCGTTTTTGAAAAAGCGTCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTC-A
* * * ** *
297297 TCTCTAGCGGCGTTTTACGTAAAGCGCCGCTAATGCTTGA
1 TTTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGC-TCA
297337 TTTTTAGCGGCGTTTTT
1 TTTTTAGCGGCGTTTTT
297354 TTGTCTAAAC
Statistics
Matches: 77, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
39 17 0.22
40 59 0.77
41 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (39 bp):
TTTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCA
Found at i:298003 original size:41 final size:41
Alignment explanation
Indices: 297946--298161 Score: 324
Period size: 41 Copynumber: 5.3 Consensus size: 41
297936 AAATGTTTTT
*
297946 GCGGCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGTATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGCATTA
* * *
297987 GCGGCGCTATTACAAAAACGCCGCTAAAGAACTGAACATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGCATTA
* *
298028 GCGGCGCTTTTCCAAAAATGCCGGTAAAGAACTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGCATTA
* *
298069 GCGGCGCTTTTACAAAAACGCCGCTAAAGAACTAAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGCATTA
* * *
298110 GCGACGCTTCTCCAAAAACGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGCATTA
*
298151 GCGGTGCTTTT
1 GCGGCGCTTTT
298162 TTTTAAAAAG
Statistics
Matches: 154, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 154 1.00
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (41 bp):
GCGGCGCTTTTCCAAAAACGCCGCTAAAGAACTGAGCATTA
Found at i:298263 original size:40 final size:39
Alignment explanation
Indices: 298219--298355 Score: 139
Period size: 40 Copynumber: 3.4 Consensus size: 39
298209 GGGCTTAGGG
* **
298219 TTTTTTGCGGCGTTTTTCCAAAAATTGCCGCTAATGCTCA
1 TTTTTAGCGGCGTTTTT-CAAAAAGCGCCGCTAATGCTCA
* * *
298259 TTTTTAGCAGCGTTTTTGAAAAAGCGTCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTC-A
* * * ** *
298299 TCTCTAGCGGCGTTTTACGTAAAGCGCCGCTAATGCTTGA
1 TTTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGC-TCA
298339 TTTTTAGCGGCGTTTTT
1 TTTTTAGCGGCGTTTTT
298356 TTGTCTAAAC
Statistics
Matches: 77, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
39 17 0.22
40 59 0.77
41 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (39 bp):
TTTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCA
Found at i:301109 original size:13 final size:13
Alignment explanation
Indices: 301091--301141 Score: 75
Period size: 13 Copynumber: 3.9 Consensus size: 13
301081 AGTTCTTCAT
301091 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
301104 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
* *
301117 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
301130 TGCTTTTGAAAA
1 TGCTTTTGAAAA
301142 ATTTGAGTGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.29, C:0.08, G:0.27, T:0.35
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:313211 original size:18 final size:18
Alignment explanation
Indices: 313173--313212 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
313163 GACTCGGAAA
* *
313173 AGGATACATATAAGGGTT
1 AGGATACATATAAGAGCT
313191 AGGATACATATAAGAGCT
1 AGGATACATATAAGAGCT
313209 AGGA
1 AGGA
313213 AACGCACCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.07, G:0.28, T:0.23
Consensus pattern (18 bp):
AGGATACATATAAGAGCT
Done.