Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 55 of 202
Found at i:16306154 original size:24 final size:23
Alignment explanation
Indices: 16306127--16306175 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
16306117 CACTATAATC
* * *
16306127 AACTTTTCACCTTTCATATTCCTT
1 AACTCTTCACATTTCAT-CTCCTT
16306151 AACTCTTCACATTTCATCTCCTT
1 AACTCTTCACATTTCATCTCCTT
16306174 AA
1 AA
16306176 AACCCATTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.24, C:0.31, G:0.00, T:0.45
Consensus pattern (23 bp):
AACTCTTCACATTTCATCTCCTT
Found at i:16318840 original size:18 final size:18
Alignment explanation
Indices: 16318817--16318853 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
16318807 TAAAGTCAGC
16318817 TCCATCAAAACGAAGGCA
1 TCCATCAAAACGAAGGCA
16318835 TCCATCAAAACGAAGGCA
1 TCCATCAAAACGAAGGCA
16318853 T
1 T
16318854 TCTAACCTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.27, G:0.16, T:0.14
Consensus pattern (18 bp):
TCCATCAAAACGAAGGCA
Found at i:16319693 original size:69 final size:71
Alignment explanation
Indices: 16319554--16319695 Score: 173
Period size: 76 Copynumber: 2.0 Consensus size: 71
16319544 AAATAATAAT
*
16319554 AATTTTCTATATTATTAGTTGATAGAAATTAACAATATGTGCAAATTAAAAATTATTTCTTTAAT
1 AATTTTCTATATTATTAGTTGATAGAAATTAACAATATGTGC-----AAAAATTATTGCTTTAAT
16319619 ATATTTTTCAA
61 ATATTTTTCAA
* * *
16319630 AATTTTCTATATTATTAGTTGATGGAAATTAAC-ATATGTGC-AAAA-TGTTGCTTTTATAATAT
1 AATTTTCTATATTATTAGTTGATAGAAATTAACAATATGTGCAAAAATTATTGCTTTAAT-ATAT
16319692 TTTT
65 TTTT
16319696 ATCATTTGTT
Statistics
Matches: 61, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
68 9 0.15
69 12 0.20
75 8 0.13
76 32 0.52
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.47
Consensus pattern (71 bp):
AATTTTCTATATTATTAGTTGATAGAAATTAACAATATGTGCAAAAATTATTGCTTTAATATATT
TTTCAA
Found at i:16320011 original size:35 final size:34
Alignment explanation
Indices: 16319962--16320029 Score: 91
Period size: 35 Copynumber: 2.0 Consensus size: 34
16319952 TTCAATTTTG
16319962 GAAAGTAATAATTATAATTCAATAAATACATTTA
1 GAAAGTAATAATTATAATTCAATAAATACATTTA
* * **
16319996 GAAAGTGATAAATTATCATTCAATGGATACATTT
1 GAAAGTAAT-AATTATAATTCAATAAATACATTT
16320030 TCATGGGACA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 8 0.28
35 21 0.72
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.35
Consensus pattern (34 bp):
GAAAGTAATAATTATAATTCAATAAATACATTTA
Found at i:16320332 original size:17 final size:17
Alignment explanation
Indices: 16320312--16320344 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
16320302 ATTTAATATA
16320312 TATATTTGATTAAAAAG
1 TATATTTGATTAAAAAG
16320329 TATATTTGATTAAAAA
1 TATATTTGATTAAAAA
16320345 TAAAAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (17 bp):
TATATTTGATTAAAAAG
Found at i:16326875 original size:26 final size:25
Alignment explanation
Indices: 16326846--16326900 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 25
16326836 TCCTTATATT
16326846 TTAATATAATATAACTT-TATCATTAA
1 TTAATATAA-ATAA-TTATATCATTAA
*
16326872 TTAATTTAAATAATTAATATCATTAA
1 TTAATATAAATAATT-ATATCATTAA
16326898 TTA
1 TTA
16326901 TTTTAGTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 2 0.08
25 4 0.15
26 20 0.77
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (25 bp):
TTAATATAAATAATTATATCATTAA
Found at i:16330109 original size:2 final size:2
Alignment explanation
Indices: 16330102--16330128 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16330092 AGAGAAAAGA
16330102 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 A
16330129 AAAGAAGGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16331536 original size:19 final size:19
Alignment explanation
Indices: 16331514--16331595 Score: 53
Period size: 19 Copynumber: 4.3 Consensus size: 19
16331504 TTATATATTT
*
16331514 TTTTATGATTTTTATAAAA
1 TTTTATAATTTTTATAAAA
* **
16331533 TTTTA-CATTTTTAATAATT
1 TTTTATAATTTTT-ATAAAA
*
16331552 TTTTACAATTTTTAT-AAA
1 TTTTATAATTTTTATAAAA
* *
16331570 TTTAATAAAATTTTA-ATAAA
1 TTTTAT-AATTTTTATA-AAA
16331590 TTTTAT
1 TTTTAT
16331596 TGATTTTTAC
Statistics
Matches: 48, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
18 11 0.23
19 23 0.48
20 14 0.29
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.57
Consensus pattern (19 bp):
TTTTATAATTTTTATAAAA
Found at i:16331571 original size:20 final size:20
Alignment explanation
Indices: 16331521--16331593 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
16331511 TTTTTTTATG
*
16331521 ATTTTTATAAA-ATTTTAC-
1 ATTTTTATAAATTTTTTACA
16331539 ATTTTTA-ATAATTTTTTACA
1 ATTTTTATA-AATTTTTTACA
** *
16331559 ATTTTTATAAATTTAATAAA
1 ATTTTTATAAATTTTTTACA
*
16331579 ATTTTAATAAATTTT
1 ATTTTTATAAATTTT
16331594 ATTGATTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
17 1 0.02
18 9 0.20
19 6 0.13
20 28 0.62
21 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTTTATAAATTTTTTACA
Found at i:16331594 original size:10 final size:10
Alignment explanation
Indices: 16331541--16331594 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
16331531 AATTTTACAT
16331541 TTTTAAT-AA
1 TTTTAATAAA
*
16331550 TTTT-TTACAA
1 TTTTAATA-AA
*
16331560 TTTTTATAAA
1 TTTTAATAAA
16331570 -TTTAATAAAA
1 TTTTAAT-AAA
16331580 TTTTAATAAA
1 TTTTAATAAA
16331590 TTTTA
1 TTTTA
16331595 TTGATTTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
8 1 0.03
9 9 0.24
10 19 0.51
11 8 0.22
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (10 bp):
TTTTAATAAA
Found at i:16331603 original size:20 final size:20
Alignment explanation
Indices: 16331539--16331604 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
16331529 AAAATTTTAC
16331539 ATTTTTAAT-AATTTT-TTACA
1 ATTTTTAATAAATTTTATT--A
* *
16331559 ATTTTT-ATAAATTTAATAA
1 ATTTTTAATAAATTTTATTA
* *
16331578 AATTTTAATAAATTTTATTG
1 ATTTTTAATAAATTTTATTA
16331598 ATTTTTA
1 ATTTTTA
16331605 CTTTTTGTCA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
19 8 0.22
20 27 0.75
21 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (20 bp):
ATTTTTAATAAATTTTATTA
Found at i:16334839 original size:3 final size:3
Alignment explanation
Indices: 16334831--16334896 Score: 132
Period size: 3 Copynumber: 22.0 Consensus size: 3
16334821 ATATGTCCAT
16334831 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
16334879 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
16334897 AAGAGATAAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:16344184 original size:58 final size:60
Alignment explanation
Indices: 16344122--16344235 Score: 144
Period size: 61 Copynumber: 1.9 Consensus size: 60
16344112 ACTTTAATAC
* *
16344122 TAAATTAATATAATACTTAT-T-AAGATAAATAATT-GATTAAATTTAATATTAAATCTGT
1 TAAATTAATAGAATACTTATCTAAAGATAAAT-ATTAAATTAAATTTAATATTAAATCTGT
* **
16344180 TAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTATTTTTAATATTAAA
1 TAAATTAATAGAATACTTATCTA-AAGATAAATATTAAATTAAATTTAATATTAAA
16344236 ATAATCATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
58 18 0.38
59 1 0.02
60 3 0.06
61 25 0.53
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (60 bp):
TAAATTAATAGAATACTTATCTAAAGATAAATATTAAATTAAATTTAATATTAAATCTGT
Found at i:16344232 original size:17 final size:18
Alignment explanation
Indices: 16344210--16344258 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 18
16344200 CTACAAGATA
16344210 AATATTAAATTAT-TTTT
1 AATATTAAATTATATTTT
*
16344227 AATATTAAAATAATCATTTT
1 AATATT-AAATTAT-ATTTT
16344247 AATATTAAATTA
1 AATATTAAATTA
16344259 ATAAAATACT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 6 0.22
18 6 0.22
19 5 0.19
20 10 0.37
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
AATATTAAATTATATTTT
Found at i:16344248 original size:20 final size:20
Alignment explanation
Indices: 16344223--16344260 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
16344213 ATTAAATTAT
16344223 TTTTAATATTAAAATAATCA
1 TTTTAATATTAAAATAATCA
*
16344243 TTTTAATATTAAATTAAT
1 TTTTAATATTAAAATAAT
16344261 AAAATACTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTTAATATTAAAATAATCA
Found at i:16344286 original size:68 final size:72
Alignment explanation
Indices: 16344179--16344321 Score: 170
Period size: 68 Copynumber: 2.0 Consensus size: 72
16344169 ATTAAATCTG
* * **
16344179 TTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTATTTTTAATATTAAAA-TAATCA
1 TTAAATTAATAAAATATCTATCTACAAGATAAATATTAAATTAAATTTAATATTAAAACT-ATCA
* *
16344243 TTTTAATA
65 ATATAATA
* *
16344251 TTAAATTAATAAAATA-CTATC-A-AA-ATAATTATTAAATTAAATTTAGTATTAAAACTATCAA
1 TTAAATTAATAAAATATCTATCTACAAGATAAATATTAAATTAAATTTAATATTAAAACTATCAA
16344312 TATAATA
66 TATAATA
16344319 TTA
1 TTA
16344322 TTTTTGAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
68 39 0.63
69 3 0.05
70 1 0.02
71 4 0.06
72 15 0.24
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (72 bp):
TTAAATTAATAAAATATCTATCTACAAGATAAATATTAAATTAAATTTAATATTAAAACTATCAA
TATAATA
Found at i:16351096 original size:32 final size:32
Alignment explanation
Indices: 16351055--16351124 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
16351045 TTTCGAGAAA
16351055 ATATGTTTAATATTTCACAACTCAACATGTTC
1 ATATGTTTAATATTTCACAACTCAACATGTTC
16351087 ATATGTTTAATATTTCACAACTCAACATGTTC
1 ATATGTTTAATATTTCACAACTCAACATGTTC
16351119 ACTATG
1 A-TATG
16351125 ACATGATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 33 0.89
33 4 0.11
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.40
Consensus pattern (32 bp):
ATATGTTTAATATTTCACAACTCAACATGTTC
Found at i:16356020 original size:52 final size:53
Alignment explanation
Indices: 16355933--16356076 Score: 141
Period size: 52 Copynumber: 2.7 Consensus size: 53
16355923 ATGTTGTGCG
* * * * * * **
16355933 ACATGTTATTTGGCTTTGTAAAGGTTGGGATGGATTGTTTGGAG-AATGCATAT
1 ACATGATATTTGGTTTTGTAGAGGATCGGTTGGATTGTAAGGAGAAAT-CATAT
*
16355986 ACATGATATTTGG-TTTGTAGAGGATCAGG-TGGATTGTAAGGAGAAATTATAT
1 ACATGATATTTGGTTTTGTAGAGGATC-GGTTGGATTGTAAGGAGAAATCATAT
* * *
16356038 GCATGATATTTGGTTTTGTGGAGGTTCGGTTGGATTGTA
1 ACATGATATTTGGTTTTGTAGAGGATCGGTTGGATTGTA
16356077 CAGAGACATA
Statistics
Matches: 77, Mismatches: 10, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
52 40 0.52
53 37 0.48
ACGTcount: A:0.25, C:0.05, G:0.31, T:0.39
Consensus pattern (53 bp):
ACATGATATTTGGTTTTGTAGAGGATCGGTTGGATTGTAAGGAGAAATCATAT
Found at i:16359664 original size:27 final size:27
Alignment explanation
Indices: 16359626--16359680 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
16359616 ATTTTGGATG
16359626 ATCCGAATCCAATGATAGTTAGACCAT
1 ATCCGAATCCAATGATAGTTAGACCAT
16359653 ATCCGAATCCAATGATAGTTAGACCAT
1 ATCCGAATCCAATGATAGTTAGACCAT
16359680 A
1 A
16359681 CATTTAAGCT
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:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (27 bp):
ATCCGAATCCAATGATAGTTAGACCAT
Found at i:16360577 original size:3 final size:3
Alignment explanation
Indices: 16360569--16360625 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
16360559 TTCCTTCGTT
16360569 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
16360617 ATC ATC ATC
1 ATC ATC ATC
16360626 TATTAAAGCT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:16374926 original size:16 final size:16
Alignment explanation
Indices: 16374907--16374938 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
16374897 TAGTTTTTTG
*
16374907 TTTTCTTTCTTTTTCT
1 TTTTCTTTCTATTTCT
16374923 TTTTCTTTCTATTTCT
1 TTTTCTTTCTATTTCT
16374939 ATTGTTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTCTTTCTATTTCT
Found at i:16374963 original size:15 final size:16
Alignment explanation
Indices: 16374934--16374963 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16374924 TTTCTTTCTA
16374934 TTTCTATTGTTATTTG
1 TTTCTATTGTTATTTG
16374950 TTTCTATT-TTATTT
1 TTTCTATTGTTATTT
16374964 TCTAGATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.13, C:0.07, G:0.07, T:0.73
Consensus pattern (16 bp):
TTTCTATTGTTATTTG
Found at i:16376341 original size:16 final size:16
Alignment explanation
Indices: 16376321--16376389 Score: 93
Period size: 16 Copynumber: 4.3 Consensus size: 16
16376311 TTGGTTCGCT
*
16376321 GTAATGGAATAGAAGT
1 GTAATGGAATAGAAGC
*
16376337 GTAATGGAATAGAGGC
1 GTAATGGAATAGAAGC
*
16376353 GTAATGGAATAGATGC
1 GTAATGGAATAGAAGC
* *
16376369 GTATTGGAATAGAGGC
1 GTAATGGAATAGAAGC
16376385 GTAAT
1 GTAAT
16376390 AGGTAATTCT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.38, C:0.04, G:0.33, T:0.25
Consensus pattern (16 bp):
GTAATGGAATAGAAGC
Found at i:16376362 original size:32 final size:32
Alignment explanation
Indices: 16376321--16376389 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
16376311 TTGGTTCGCT
*
16376321 GTAATGGAATAGAAGTGTAATGGAATAGAGGC
1 GTAATGGAATAGAAGCGTAATGGAATAGAGGC
* *
16376353 GTAATGGAATAGATGCGTATTGGAATAGAGGC
1 GTAATGGAATAGAAGCGTAATGGAATAGAGGC
16376385 GTAAT
1 GTAAT
16376390 AGGTAATTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.38, C:0.04, G:0.33, T:0.25
Consensus pattern (32 bp):
GTAATGGAATAGAAGCGTAATGGAATAGAGGC
Found at i:16376453 original size:44 final size:46
Alignment explanation
Indices: 16376373--16376463 Score: 141
Period size: 44 Copynumber: 2.0 Consensus size: 46
16376363 AGATGCGTAT
*
16376373 TGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATAGAA
1 TGGAATAGAGGCGTAATAGATAATTCTTTTGTTTGGTTGAATAGAA
* *
16376419 TGGAATAGAGGCGTAGT-GAT-ATTCTTTTGTTTGGTTGAATGGAA
1 TGGAATAGAGGCGTAATAGATAATTCTTTTGTTTGGTTGAATAGAA
16376463 T
1 T
16376464 AGAGGTGTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
44 24 0.57
45 2 0.05
46 16 0.38
ACGTcount: A:0.27, C:0.04, G:0.30, T:0.38
Consensus pattern (46 bp):
TGGAATAGAGGCGTAATAGATAATTCTTTTGTTTGGTTGAATAGAA
Found at i:16376459 original size:39 final size:44
Alignment explanation
Indices: 16376373--16376481 Score: 129
Period size: 39 Copynumber: 2.5 Consensus size: 44
16376363 AGATGCGTAT
*
16376373 TGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATAGAA
1 TGGAATAGAGGCGTAATAGATAATTCTTTTGTTTGGTT--ATAGAA
*
16376419 TGGAATAGAGGCGTAGT-GAT-ATTCTTTTGTTTGG-T-T-GAA
1 TGGAATAGAGGCGTAATAGATAATTCTTTTGTTTGGTTATAGAA
*
16376458 TGGAATAGAGGTGTAATAGCATAA
1 TGGAATAGAGGCGTAATAG-ATAA
16376482 GGAAAAAAAC
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
39 18 0.32
40 2 0.04
41 2 0.04
42 1 0.02
43 1 0.02
44 14 0.25
45 2 0.04
46 16 0.29
ACGTcount: A:0.30, C:0.05, G:0.29, T:0.36
Consensus pattern (44 bp):
TGGAATAGAGGCGTAATAGATAATTCTTTTGTTTGGTTATAGAA
Found at i:16376632 original size:26 final size:26
Alignment explanation
Indices: 16376603--16376742 Score: 96
Period size: 26 Copynumber: 5.5 Consensus size: 26
16376593 TTAATCATAT
*
16376603 TTTAACATAAATATTATTAAATATAA
1 TTTAATATAAATATTATTAAATATAA
* *
16376629 TTTAATAAAAATATATAATTTAATA-AA
1 TTTAATATAAATAT-T-ATTAAATATAA
* * * *
16376656 -AT-ATATGAAT-TTACTAAA-ATCA
1 TTTAATATAAATATTATTAAATATAA
* *
16376678 --TAATATATAATACTATAAAATATAA
1 TTTAATATA-AATATTATTAAATATAA
* *
16376703 TTTAAAATAATTATTATTAAATATAA
1 TTTAATATAAATATTATTAAATATAA
*
16376729 TTTAATAAAAATAT
1 TTTAATATAAATAT
16376743 ATAATTTGAT
Statistics
Matches: 84, Mismatches: 21, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
21 2 0.02
22 9 0.11
23 4 0.05
24 6 0.07
25 9 0.11
26 38 0.45
27 9 0.11
28 7 0.08
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.41
Consensus pattern (26 bp):
TTTAATATAAATATTATTAAATATAA
Found at i:16376646 original size:18 final size:18
Alignment explanation
Indices: 16376623--16376756 Score: 81
Period size: 18 Copynumber: 7.9 Consensus size: 18
16376613 ATATTATTAA
16376623 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
16376641 ATATAATTTAAT-AAAAT
1 ATATAATTTAATAAAAAT
*
16376658 ATATGAATTTACT-AAAAT
1 ATAT-AATTTAATAAAAAT
* * * *
16376676 -CATAATAT-ATAATACT
1 ATATAATTTAATAAAAAT
* * *
16376692 ATAAAATATAATTTAAAAT
1 ATATAATTTAA-TAAAAAT
* *
16376711 A-ATTA-TT-AT--TAA-
1 ATATAATTTAATAAAAAT
16376723 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
*
16376741 ATATAATTTGATAAAA
1 ATATAATTTAATAAAA
16376757 TTCTTTAGTA
Statistics
Matches: 87, Mismatches: 18, Indels: 22
0.69 0.14 0.17
Matches are distributed among these distances:
12 1 0.01
13 5 0.06
14 2 0.02
15 4 0.05
16 8 0.09
17 20 0.23
18 42 0.48
19 5 0.06
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:16394984 original size:22 final size:22
Alignment explanation
Indices: 16394930--16394975 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
16394920 ATACAACATA
16394930 CCATAACATCCATTCATGTTTT
1 CCATAACATCCATTCATGTTTT
16394952 CCATAACATCCATTCATGTTTT
1 CCATAACATCCATTCATGTTTT
16394974 CC
1 CC
16394976 TCAAGATCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.30, G:0.04, T:0.39
Consensus pattern (22 bp):
CCATAACATCCATTCATGTTTT
Found at i:16398288 original size:9 final size:9
Alignment explanation
Indices: 16398274--16398359 Score: 129
Period size: 9 Copynumber: 9.4 Consensus size: 9
16398264 TTTGGTTAAA
16398274 AATTACCCG
1 AATTACCCG
16398283 AATTACCCG
1 AATTACCCG
16398292 AATTACCCG
1 AATTACCCG
16398301 AATTACCCG
1 AATTACCCG
*
16398310 AATTAACCG
1 AATTACCCG
16398319 AATTACCCG
1 AATTACCCG
16398328 AATTA-CCG
1 AATTACCCG
*
16398336 AAAAATACCCG
1 --AATTACCCG
16398347 AATTACCCG
1 AATTACCCG
16398356 AATT
1 AATT
16398360 TTTTTATTTT
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
8 3 0.04
9 60 0.86
10 4 0.06
11 3 0.04
ACGTcount: A:0.38, C:0.29, G:0.10, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:16400647 original size:20 final size:20
Alignment explanation
Indices: 16400624--16400662 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16400614 AATGAAATGC
*
16400624 AATGTAATGAAATGGTTTAA
1 AATGCAATGAAATGGTTTAA
*
16400644 AATGCAATGGAATGGTTTA
1 AATGCAATGAAATGGTTTA
16400663 GCAGCAATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.23, T:0.33
Consensus pattern (20 bp):
AATGCAATGAAATGGTTTAA
Found at i:16409165 original size:16 final size:17
Alignment explanation
Indices: 16409144--16409175 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
16409134 AAATATGCAA
16409144 TCACATAA-TTCATATT
1 TCACATAACTTCATATT
16409160 TCACATAACTTCATAT
1 TCACATAACTTCATAT
16409176 CATCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCACATAACTTCATATT
Found at i:16409402 original size:43 final size:43
Alignment explanation
Indices: 16409336--16409504 Score: 179
Period size: 43 Copynumber: 4.0 Consensus size: 43
16409326 GACTCGTACA
* * *
16409336 ATGCCAACGTCCCAGAC-GTGGTCTTACATGTAATCACATATCG
1 ATGCCAATGTCCCAGACAG-GGTCTTACACGAAATCACATATCG
* *
16409379 ATGCCATTGTCCCAGACAGGGTCTTACAC-AAATCAAATA-CG
1 ATGCCAATGTCCCAGACAGGGTCTTACACGAAATCACATATCG
*
16409420 ATGCCAATGTCCCAGACATGGTCTTACAC-ATAA--ACATAAGTCG
1 ATGCCAATGTCCCAGACAGGGTCTTACACGA-AATCACAT-A-TCG
* * *
16409463 ATGCCAACGTCCCAGACATGGTCTTACACGAAAACACATATC
1 ATGCCAATGTCCCAGACAGGGTCTTACACGAAATCACATATC
16409505 AAAATCCTAT
Statistics
Matches: 109, Mismatches: 9, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
40 3 0.03
41 31 0.28
42 10 0.09
43 58 0.53
44 3 0.03
45 4 0.04
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACAGGGTCTTACACGAAATCACATATCG
Found at i:16409477 original size:84 final size:83
Alignment explanation
Indices: 16409336--16409491 Score: 215
Period size: 84 Copynumber: 1.9 Consensus size: 83
16409326 GACTCGTACA
* ** **
16409336 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCGATGCCATTGTCCCAGACAGGGT
1 ATGCCAACGTCCCAGACATGGTCTTACACATAA-CACATATCGATGCCAACGTCCCAGACAGGGT
16409401 CTTACACAAATCAAATACG
65 CTTACACAAATCAAATACG
* *
16409420 ATGCCAATGTCCCAGACATGGTCTTACACATAA-ACATAAGTCGATGCCAACGTCCCAGACATGG
1 ATGCCAACGTCCCAGACATGGTCTTACACATAACACAT-A-TCGATGCCAACGTCCCAGACAGGG
16409484 TCTTACAC
64 TCTTACAC
16409492 GAAAACACAT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
82 4 0.06
83 1 0.02
84 58 0.92
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.23
Consensus pattern (83 bp):
ATGCCAACGTCCCAGACATGGTCTTACACATAACACATATCGATGCCAACGTCCCAGACAGGGTC
TTACACAAATCAAATACG
Found at i:16417268 original size:21 final size:20
Alignment explanation
Indices: 16417230--16417273 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
16417220 TACAACAACC
* *
16417230 TTAACTACCACTGTTAACTG
1 TTAACTACAACTGCTAACTG
16417250 TTAACTACTAACTGCTAACTG
1 TTAACTAC-AACTGCTAACTG
16417271 TTA
1 TTA
16417274 TAACAGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (20 bp):
TTAACTACAACTGCTAACTG
Found at i:16418027 original size:3 final size:3
Alignment explanation
Indices: 16418019--16418049 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
16418009 AGAGTGTTTT
16418019 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
16418050 GAGAAAAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:16418997 original size:12 final size:12
Alignment explanation
Indices: 16418974--16419008 Score: 54
Period size: 11 Copynumber: 2.9 Consensus size: 12
16418964 TTTGTGTGTA
16418974 AAATAATTTTTTT
1 AAAT-ATTTTTTT
16418987 AAA-ATTTTTTT
1 AAATATTTTTTT
16418998 AAATATTTTTT
1 AAATATTTTTT
16419009 CTTTTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.52
12 7 0.33
13 3 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
AAATATTTTTTT
Found at i:16419970 original size:4 final size:4
Alignment explanation
Indices: 16419961--16419987 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
16419951 AAACAACACC
16419961 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
16419988 CCTTCGAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:16420662 original size:16 final size:16
Alignment explanation
Indices: 16420643--16420687 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
16420633 AATAGGGCTA
16420643 TAATGGAATAAAACTG
1 TAATGGAATAAAACTG
* ***
16420659 TAATTGAATAGGGCTG
1 TAATGGAATAAAACTG
16420675 TAATGGAATAAAA
1 TAATGGAATAAAA
16420688 TGACCATAGT
Statistics
Matches: 21, Mismatches: 8, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.47, C:0.04, G:0.22, T:0.27
Consensus pattern (16 bp):
TAATGGAATAAAACTG
Found at i:16420664 original size:32 final size:32
Alignment explanation
Indices: 16420622--16420687 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
16420612 TTTGGTTATT
16420622 AACTGGAATTGAATAGGGCTATAATGGAATAA
1 AACTGGAATTGAATAGGGCTATAATGGAATAA
* *
16420654 AACTGTAATTGAATAGGGCTGTAATGGAATAA
1 AACTGGAATTGAATAGGGCTATAATGGAATAA
16420686 AA
1 AA
16420688 TGACCATAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.44, C:0.06, G:0.24, T:0.26
Consensus pattern (32 bp):
AACTGGAATTGAATAGGGCTATAATGGAATAA
Found at i:16423179 original size:30 final size:29
Alignment explanation
Indices: 16423123--16423179 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
16423113 ATTTTTAAAA
**
16423123 TTTAGAATTTAGTTATTGTACTTTTTATT
1 TTTAGAATTTAGTTATTGTAAATTTTATT
*
16423152 TTTATGAATTTAGTTCTTGTAAATTTTA
1 TTTA-GAATTTAGTTATTGTAAATTTTA
16423180 GATTTCAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.26, C:0.04, G:0.11, T:0.60
Consensus pattern (29 bp):
TTTAGAATTTAGTTATTGTAAATTTTATT
Found at i:16423516 original size:2 final size:2
Alignment explanation
Indices: 16423509--16423568 Score: 102
Period size: 2 Copynumber: 30.0 Consensus size: 2
16423499 CTAAGAAAAG
* *
16423509 AT AT AT AT AT AT AC AT AT AT AT TT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16423551 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
16423569 TAGAGTTGTG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16423677 original size:24 final size:24
Alignment explanation
Indices: 16423643--16423694 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
16423633 TTTCTAGAAG
* **
16423643 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAACATAATAT
*
16423667 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATGAACATAATAT
16423691 ATTT
1 ATTT
16423695 GACTTTGATC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAACATAATAT
Found at i:16428092 original size:24 final size:24
Alignment explanation
Indices: 16428058--16428109 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
16428048 TTTCTAGAAG
* **
16428058 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAACATAATAT
*
16428082 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATGAACATAATAT
16428106 ATTT
1 ATTT
16428110 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAACATAATAT
Found at i:16434943 original size:21 final size:21
Alignment explanation
Indices: 16434919--16434971 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
16434909 CCTTGTATAA
16434919 AATTTAATTTGAGCATTT-A-AT
1 AATTTAATTTGA--ATTTCACAT
* *
16434940 AATTTTATTTTAATTTCACAT
1 AATTTAATTTGAATTTCACAT
16434961 AATTTAATTTG
1 AATTTAATTTG
16434972 TTTCTACAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 4 0.15
20 1 0.04
21 21 0.81
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.53
Consensus pattern (21 bp):
AATTTAATTTGAATTTCACAT
Found at i:16436746 original size:14 final size:14
Alignment explanation
Indices: 16436727--16436756 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
16436717 TTACCAATTC
*
16436727 AACATAAACTTCCA
1 AACATAAACATCCA
16436741 AACATAAACATCCA
1 AACATAAACATCCA
16436755 AA
1 AA
16436757 TCACTATTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.27, G:0.00, T:0.17
Consensus pattern (14 bp):
AACATAAACATCCA
Found at i:16437091 original size:40 final size:40
Alignment explanation
Indices: 16437037--16437174 Score: 195
Period size: 40 Copynumber: 3.5 Consensus size: 40
16437027 TACAAGTAGA
** * * *
16437037 GGCACGTAACTGCATTTAGGGGTACTAAAGTACAAATAGG
1 GGCACGTATGTGCATTCAGGGGTACCAAAGTACAAACAGG
*
16437077 GGCACGTATGTGCATTCAGGGGTACCGAAGTACAAACAGG
1 GGCACGTATGTGCATTCAGGGGTACCAAAGTACAAACAGG
* * *
16437117 GACATGTATGTGCATTCAAGGGTACCAAAGTACAAACAGG
1 GGCACGTATGTGCATTCAGGGGTACCAAAGTACAAACAGG
16437157 GGCACGTATGTGCATTCA
1 GGCACGTATGTGCATTCA
16437175 TTCAATAGTT
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 86 1.00
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (40 bp):
GGCACGTATGTGCATTCAGGGGTACCAAAGTACAAACAGG
Found at i:16437097 original size:20 final size:20
Alignment explanation
Indices: 16437074--16437174 Score: 51
Period size: 20 Copynumber: 5.0 Consensus size: 20
16437064 AAGTACAAAT
16437074 AGGGGCACGTATGTGCATTC
1 AGGGGCACGTATGTGCATTC
* * * **
16437094 AGGGGTACCG-AAGTACAAAC
1 AGGGGCA-CGTATGTGCATTC
* *
16437114 AGGGACATGTATGTGCATTC
1 AGGGGCACGTATGTGCATTC
* * ** * * **
16437134 AAGGGTACCAAAGTACAAAC
1 AGGGGCACGTATGTGCATTC
16437154 AGGGGCACGTATGTGCATTC
1 AGGGGCACGTATGTGCATTC
16437174 A
1 A
16437175 TTCAATAGTT
Statistics
Matches: 49, Mismatches: 30, Indels: 4
0.59 0.36 0.05
Matches are distributed among these distances:
19 1 0.02
20 46 0.94
21 2 0.04
ACGTcount: A:0.32, C:0.19, G:0.30, T:0.20
Consensus pattern (20 bp):
AGGGGCACGTATGTGCATTC
Found at i:16441461 original size:61 final size:58
Alignment explanation
Indices: 16441388--16441521 Score: 196
Period size: 61 Copynumber: 2.3 Consensus size: 58
16441378 TCAAAAAATA
* *
16441388 ATATTATTTTAATATATTTAATATTAAATTTAATTTAATATTTATCTTGTAGATAAATATT
1 ATATTAATTTAATATATTTAATATTAAATTTAATCTAATATTTATC-T-TA-ATAAATATT
* * *
16441449 CTATTAATTTAATAGATTTAATATTAAATTTAATCTAATATTTATCTTAATAAGTATT
1 ATATTAATTTAATATATTTAATATTAAATTTAATCTAATATTTATCTTAATAAATATT
16441507 ATATTAATTTAATAT
1 ATATTAATTTAATAT
16441522 TAAGGTGATC
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
58 21 0.32
59 2 0.03
60 1 0.02
61 42 0.64
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (58 bp):
ATATTAATTTAATATATTTAATATTAAATTTAATCTAATATTTATCTTAATAAATATT
Found at i:16445634 original size:45 final size:45
Alignment explanation
Indices: 16445559--16445651 Score: 109
Period size: 45 Copynumber: 2.1 Consensus size: 45
16445549 CTTGTCAAAG
* * * *
16445559 GATGTCATAGCGTCTTTCAGCCATGATCTTAGTCCTATT-TATCAT
1 GATGTCATAACGTATTTCAGCCATGATCTTACTCAT-TTATATCAT
*
16445604 GATGTCATAATGTATTTCAGCCATTG-TCTTACTCATTTATATCAT
1 GATGTCATAACGTATTTCAGCCA-TGATCTTACTCATTTATATCAT
16445649 GAT
1 GAT
16445652 ACCATATCAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
44 2 0.05
45 37 0.90
46 2 0.05
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (45 bp):
GATGTCATAACGTATTTCAGCCATGATCTTACTCATTTATATCAT
Found at i:16457709 original size:20 final size:20
Alignment explanation
Indices: 16457684--16457722 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
16457674 TGAGTTATTT
16457684 AAGCAAGCA-AGTAAGTAAAC
1 AAGCAAG-AGAGTAAGTAAAC
16457704 AAGCAAGAGAGTAAGTAAA
1 AAGCAAGAGAGTAAGTAAA
16457723 GAAGAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.10, G:0.23, T:0.10
Consensus pattern (20 bp):
AAGCAAGAGAGTAAGTAAAC
Found at i:16464680 original size:15 final size:16
Alignment explanation
Indices: 16464660--16464696 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
16464650 TCACTATCAA
16464660 TAATAAAATGA-GACT
1 TAATAAAATGACGACT
*
16464675 TAAT-AATTGACGACT
1 TAATAAAATGACGACT
16464690 TAATAAA
1 TAATAAA
16464697 TGTATATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 5 0.26
15 12 0.63
16 2 0.11
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (16 bp):
TAATAAAATGACGACT
Found at i:16473701 original size:321 final size:324
Alignment explanation
Indices: 16472962--16473766 Score: 997
Period size: 331 Copynumber: 2.5 Consensus size: 324
16472952 ATGACTTTTT
* * *
16472962 TTTTTAGCCATTATAAGATAATAATAAAATGGTAGTTTTGATCTTTCTATTATGCTTACATTTGA
1 TTTTTAGTCATTATAAGATAATGATAAAATGGTAGTTTTGATCTTTCTATTATGCTCACATTTGA
* *
16473027 GATTTAGTC-TT-TATTTTAATTTGACATAATTTAATTTTCTATTTTTACAATGACATTAGGTAG
66 GATTTAGTCTTTATATTTTAATTTGACATAATTTAATTTTCTACTTTTACTATGACATTAGGTAG
* * * *
16473090 TCCAAGTAATTAACATATTTAACTGTTCTGATTAAAATTTTTAGTCATTTAAAAAAAAGAAGCTA
131 TCCAAATAATTAACATCTTTAGCTATTCTGATTAAAATTTTTAGTCATTTAAAAAAAAGAAGCTA
** ** *
16473155 TTATATCAAAAAAATTATATTGGCATTATGATTTACTAAGCATGGTTAAAAAAATTCACATCATT
196 TTATATCAAAAAAATTATATTCACACAATGATTTACTAAGCATGGTTAAAAAAATTCACATCATC
* *
16473220 TACTAAAAATATTAAGGGTGCTAATTATTTAGATCAATAATGACATTACTTCTTTTTTTTCTTCT
261 TACTAAAAATATTAAGGGTGCTAATTATTTAGACCAATAATGACATGA-------TTTTTCTTCT
*
16473285 TCTATT
319 TCTATC
*
16473291 TTTTTAGTCATTATAAGATAATGATAAAATGGTAATTTTGATCTTTCTATTATGCTCACATTTGA
1 TTTTTAGTCATTATAAGATAATGATAAAATGGTAGTTTTGATCTTTCTATTATGCTCACATTTGA
* * *
16473356 TATTTAATCTTTATATTTTAATTTGACATAATTTGATTTTCTACTTTTACTATGACATTAGGTAG
66 GATTTAGTCTTTATATTTTAATTTGACATAATTTAATTTTCTACTTTTACTATGACATTAGGTAG
* * * * *
16473421 TCCAAATAATTAACAGCTTTAGCTATTTTGATTAAAATTTTTATTCTATTT-TAAAAAA-ATGCT
131 TCCAAATAATTAACATCTTTAGCTATTCTGATTAAAATTTTTAGTC-ATTTAAAAAAAAGAAGCT
* * *
16473484 ATTATAT-AAAGAAAATTATATTCACACAATGATTTGGCATAAGTATTGTTAAAAAAAATTCACA
195 ATTATATCAAA-AAAATTATATTCACACAATGATTT-AC-TAAGCATGGTT-AAAAAAATTCACA
* * *
16473548 TCATCTACT-AAAATATTAAGGGTGTTAATTATTTAGACCAATACTGGCATGA-TTTT-TT-TTC
256 TCATCTACTAAAAATATTAAGGGTGCTAATTATTTAGACCAATAATGACATGATTTTTCTTCTTC
16473609 TA-C
321 TATC
** * *
16473612 TTTTTAGTTTTTATAAGATAATGGTAAAATGATAGTTTTGATCCTTT-TATTATGCTCACATTTG
1 TTTTTAGTCATTATAAGATAATGATAAAATGGTAGTTTTGAT-CTTTCTATTATGCTCACATTTG
* ** * * * *
16473676 AGATTTAGTCTTTATATTTTAATTTGAAATAATTTAATCCTCTACGTTATAATA-G-TATTAGTT
65 AGATTTAGTCTTTATATTTTAATTTGACATAATTTAATTTTCTAC-TTTTACTATGACATTAGGT
*
16473739 AGCCCAAATAATTAACATCTTTAGCTAT
129 AGTCCAAATAATTAACATCTTTAGCTAT
16473767 ATCGGTTAAA
Statistics
Matches: 418, Mismatches: 49, Indels: 27
0.85 0.10 0.05
Matches are distributed among these distances:
320 32 0.08
321 94 0.22
322 15 0.04
323 2 0.00
324 4 0.01
329 71 0.17
330 33 0.08
331 95 0.23
332 51 0.12
333 21 0.05
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.44
Consensus pattern (324 bp):
TTTTTAGTCATTATAAGATAATGATAAAATGGTAGTTTTGATCTTTCTATTATGCTCACATTTGA
GATTTAGTCTTTATATTTTAATTTGACATAATTTAATTTTCTACTTTTACTATGACATTAGGTAG
TCCAAATAATTAACATCTTTAGCTATTCTGATTAAAATTTTTAGTCATTTAAAAAAAAGAAGCTA
TTATATCAAAAAAATTATATTCACACAATGATTTACTAAGCATGGTTAAAAAAATTCACATCATC
TACTAAAAATATTAAGGGTGCTAATTATTTAGACCAATAATGACATGATTTTTCTTCTTCTATC
Found at i:16477875 original size:14 final size:14
Alignment explanation
Indices: 16477856--16477886 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
16477846 GCACCAATAA
16477856 TATTTCCTCGGGTT
1 TATTTCCTCGGGTT
16477870 TATTTCCTCGGGTT
1 TATTTCCTCGGGTT
16477884 TAT
1 TAT
16477887 CAAAGTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.10, C:0.19, G:0.19, T:0.52
Consensus pattern (14 bp):
TATTTCCTCGGGTT
Found at i:16483219 original size:197 final size:200
Alignment explanation
Indices: 16482861--16483262 Score: 695
Period size: 197 Copynumber: 2.0 Consensus size: 200
16482851 ACTTTGAGTT
16482861 TTATTGAATCAACTAGTCATTAACCTAGTAGGGCCTCTCGACCTTCCACTAACCTAATGAGTTGA
1 TTATTGAATCAACTAGTCATTAACCTAGTAGGGCCTCTCGACCTTCCACTAACCTAATGAGTTGA
*
16482926 CAAGAACTAGTTATCTCTTAATGTCATAGTTTAGATCGGATTGGGGTAAGGTTTTCACGGATAGA
66 CAAGAAC---TTATCTC-TAATGTCATAGTTTAGACCGGATTGGGGTAAGGTTTTCACGGATAGA
*
16482991 AAATACCAATTTTGAGTTCATTCCCACCTATATGACTTCCTAGGGTCATCAAGTCTAGGGTTTTA
127 AAATACCAATTTTGAGTTCAATCCCACCTATATGACTTCCTAGGGTCATCAAGTCTAGGGTTTTA
16483056 AGTTCTTCC
192 AGTTCTTCC
*
16483065 TTATTGAATCAACTAGTCATTAACCTAGTAGGGCCTCTCGGCCTTCCACTAACCTAATGAGTTGA
1 TTATTGAATCAACTAGTCATTAACCTAGTAGGGCCTCTCGACCTTCCACTAACCTAATGAGTTGA
*
16483130 CAAGAAC-TA-C-C-CATCGTCATAGTTTAGACCGGATTGGGGTAAGGTTTTCACGGATAGAAAA
66 CAAGAACTTATCTCTAAT-GTCATAGTTTAGACCGGATTGGGGTAAGGTTTTCACGGATAGAAAA
16483191 TACCAATTTTGAGTTCAATCCCACCTATATGACTTCCTAGGGTCATCAAGTCTAGGGTTTTAAGT
130 TACCAATTTTGAGTTCAATCCCACCTATATGACTTCCTAGGGTCATCAAGTCTAGGGTTTTAAGT
16483256 TCTTCC
195 TCTTCC
16483262 T
1 T
16483263 ATCCCAACCA
Statistics
Matches: 193, Mismatches: 4, Indels: 9
0.94 0.02 0.04
Matches are distributed among these distances:
196 2 0.01
197 116 0.60
198 1 0.01
199 1 0.01
200 2 0.01
204 71 0.37
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (200 bp):
TTATTGAATCAACTAGTCATTAACCTAGTAGGGCCTCTCGACCTTCCACTAACCTAATGAGTTGA
CAAGAACTTATCTCTAATGTCATAGTTTAGACCGGATTGGGGTAAGGTTTTCACGGATAGAAAAT
ACCAATTTTGAGTTCAATCCCACCTATATGACTTCCTAGGGTCATCAAGTCTAGGGTTTTAAGTT
CTTCC
Found at i:16493610 original size:21 final size:22
Alignment explanation
Indices: 16493580--16493621 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
16493570 TTTAAGTAAA
16493580 GTTTGTAATTTTACATAATTTG
1 GTTTGTAATTTTACATAATTTG
*
16493602 GTTT-TAATTTTACGTAATTT
1 GTTTGTAATTTTACATAATTT
16493622 CATTGAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.26, C:0.05, G:0.12, T:0.57
Consensus pattern (22 bp):
GTTTGTAATTTTACATAATTTG
Found at i:16499991 original size:11 final size:11
Alignment explanation
Indices: 16499971--16500000 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
16499961 ATGCTATTGA
*
16499971 AATGGGAATGT
1 AATGGAAATGT
16499982 AATGGAAATGT
1 AATGGAAATGT
16499993 AATGGAAA
1 AATGGAAA
16500001 CATGATTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.30, T:0.23
Consensus pattern (11 bp):
AATGGAAATGT
Found at i:16500360 original size:8 final size:8
Alignment explanation
Indices: 16500347--16500371 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
16500337 TAAACTATAT
16500347 TTTAAATA
1 TTTAAATA
16500355 TTTAAATA
1 TTTAAATA
16500363 TTTAAATA
1 TTTAAATA
16500371 T
1 T
16500372 AACCATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTTAAATA
Found at i:16511314 original size:101 final size:102
Alignment explanation
Indices: 16511194--16511378 Score: 284
Period size: 101 Copynumber: 1.8 Consensus size: 102
16511184 AAAGTGATGG
* *
16511194 TCACGTGTGTAGTACTATGTGCAAGCTACTACATGTACCGG--AATGATAGGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAAGCTACTACATGTACCGGATAATAAT-GGTCACATGTGTAGT
*
16511257 ACTATTTACAGGCTACTATGCATACCAGATAGTTTCGA
65 ACTATGTACAGGCTACTATGCATACCAGATAGTTTCGA
* * *
16511295 TCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTATCGGATAATAATTGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAAGCTACTACATGTACCGGATAATAATGGTCACATGTGTAGTA
*
16511360 CTATGTATAGGCTACTATG
66 CTATGTACAGGCTACTATG
16511379 TGAATCGAAC
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
101 39 0.52
102 31 0.41
103 5 0.07
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAAGCTACTACATGTACCGGATAATAATGGTCACATGTGTAGTA
CTATGTACAGGCTACTATGCATACCAGATAGTTTCGA
Found at i:16511323 original size:51 final size:49
Alignment explanation
Indices: 16511194--16511326 Score: 126
Period size: 50 Copynumber: 2.7 Consensus size: 49
16511184 AAAGTGATGG
* *
16511194 TCACGTGTGTAGTACTATGTGCAAGCTACTACATGTACCGGAATGATAGG
1 TCACGTGTGTAGTACTATGTGCAAGCTACTACA-GTACCAGAATGATAGA
* * * * * * *
16511244 TCGCATGTGTAGTACTATTTACAGGCTACTATGCA-TACCAG-ATAGTTTCGA
1 TCACGTGTGTAGTACTATGTGCAAGCTACTA--CAGTACCAGAAT-G-ATAGA
16511295 TCACGTGTGTAGTACTATGTGCAAGCTACTAC
1 TCACGTGTGTAGTACTATGTGCAAGCTACTAC
16511327 GTGTATCGGA
Statistics
Matches: 65, Mismatches: 14, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
49 3 0.05
50 32 0.49
51 28 0.43
52 2 0.03
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.31
Consensus pattern (49 bp):
TCACGTGTGTAGTACTATGTGCAAGCTACTACAGTACCAGAATGATAGA
Found at i:16511355 original size:51 final size:50
Alignment explanation
Indices: 16511193--16511365 Score: 161
Period size: 51 Copynumber: 3.4 Consensus size: 50
16511183 GAAAGTGATG
* * * *
16511193 GTCACGTGTGTAGTACTATGTGCAAGCTACTACATGTACCGGAATGATA-G
1 GTCACATGTGTAGTACTATGTGCAAGCTACTACGTGTACCGG-ATAATATT
* * * * * ** * *
16511243 GTCGCATGTGTAGTACTATTTACAGGCTACTATGCATACCAGATAGT-TT
1 GTCACATGTGTAGTACTATGTGCAAGCTACTACGTGTACCGGATAATATT
* *
16511292 CGATCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTATCGGATAATAATT
1 -G-TCACATGTGTAGTACTATGTGCAAGCTACTACGTGTACCGGATAAT-ATT
16511345 GTCACATGTGTAGTACTATGT
1 GTCACATGTGTAGTACTATGT
16511366 ATAGGCTACT
Statistics
Matches: 93, Mismatches: 25, Indels: 9
0.73 0.20 0.07
Matches are distributed among these distances:
49 3 0.03
50 33 0.35
51 54 0.58
52 1 0.01
53 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (50 bp):
GTCACATGTGTAGTACTATGTGCAAGCTACTACGTGTACCGGATAATATT
Found at i:16520441 original size:22 final size:22
Alignment explanation
Indices: 16520415--16520500 Score: 100
Period size: 22 Copynumber: 3.9 Consensus size: 22
16520405 ATTTAGGGAC
*
16520415 TACGTGAAACATGAGAGCTTAG
1 TACGTTAAACATGAGAGCTTAG
**
16520437 TACGTTAGCCATGAGAGCTTAG
1 TACGTTAAACATGAGAGCTTAG
** * *
16520459 TACGTTAGCCATGAGGGTTTAG
1 TACGTTAAACATGAGAGCTTAG
*
16520481 TTCGTTAAACATGAGAGCTT
1 TACGTTAAACATGAGAGCTT
16520501 CTTGGAATAA
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (22 bp):
TACGTTAAACATGAGAGCTTAG
Found at i:16520993 original size:25 final size:25
Alignment explanation
Indices: 16520956--16521003 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
16520946 GACACACCAC
*
16520956 AGCTCCTAAGAGCATCCCGTTATCT
1 AGCTCCTAAGAGCATCACGTTATCT
* *
16520981 AGCTCTTATGAGCATCACGTTAT
1 AGCTCCTAAGAGCATCACGTTAT
16521004 ATGGCTCTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (25 bp):
AGCTCCTAAGAGCATCACGTTATCT
Found at i:16521018 original size:25 final size:25
Alignment explanation
Indices: 16520965--16521038 Score: 67
Period size: 25 Copynumber: 3.0 Consensus size: 25
16520955 CAGCTCCTAA
* * * * *
16520965 GAGCATCCCGTTATCTAGCTCTTAT
1 GAGCATCACGTTATATGGCTCTCAC
16520990 GAGCATCACGTTATATGGCTCTCAC
1 GAGCATCACGTTATATGGCTCTCAC
* * * *
16521015 GAGCTTCTCGATATTTGGCTCTCA
1 GAGCATCACGTTATATGGCTCTCA
16521039 TGAGATTCCT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.20, C:0.27, G:0.19, T:0.34
Consensus pattern (25 bp):
GAGCATCACGTTATATGGCTCTCAC
Found at i:16521159 original size:25 final size:25
Alignment explanation
Indices: 16521104--16521159 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
16521094 TCCTGATAAT
*
16521104 TGGCTCACAAGAGCTTCCCATTATA
1 TGGCTCACAAGAGCTTCCCATTACA
** *
16521129 CAGCTCACATGAGCTTCCCATTACA
1 TGGCTCACAAGAGCTTCCCATTACA
16521154 TGGCTC
1 TGGCTC
16521160 GATAGAACAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.27
Consensus pattern (25 bp):
TGGCTCACAAGAGCTTCCCATTACA
Found at i:16540587 original size:12 final size:12
Alignment explanation
Indices: 16540570--16540602 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
16540560 AATTGAATAA
16540570 AATGTAAAATTG
1 AATGTAAAATTG
*
16540582 AATGTAGAATTG
1 AATGTAAAATTG
16540594 AATGTAAAA
1 AATGTAAAA
16540603 ATAGGAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.18, T:0.30
Consensus pattern (12 bp):
AATGTAAAATTG
Found at i:16542369 original size:42 final size:42
Alignment explanation
Indices: 16542310--16542389 Score: 151
Period size: 42 Copynumber: 1.9 Consensus size: 42
16542300 AAAAGAATGC
*
16542310 TTGAAATAGAAGCTTTGGGTCGAGGTAAATGTGGGTCTATGA
1 TTGAAATAGAAGCTTTGGGCCGAGGTAAATGTGGGTCTATGA
16542352 TTGAAATAGAAGCTTTGGGCCGAGGTAAATGTGGGTCT
1 TTGAAATAGAAGCTTTGGGCCGAGGTAAATGTGGGTCT
16542390 TTGGTGAGTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.28, C:0.09, G:0.34, T:0.30
Consensus pattern (42 bp):
TTGAAATAGAAGCTTTGGGCCGAGGTAAATGTGGGTCTATGA
Found at i:16554505 original size:6 final size:6
Alignment explanation
Indices: 16554494--16554535 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
16554484 TTGCATGGGT
16554494 AACCAA AACCAA AACCAA AACCAA AACCAA AACCAA AACCAA
1 AACCAA AACCAA AACCAA AACCAA AACCAA AACCAA AACCAA
16554536 GGGAGGCAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (6 bp):
AACCAA
Found at i:16562854 original size:19 final size:18
Alignment explanation
Indices: 16562808--16562855 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
16562798 GATAGAATTT
*
16562808 TTGTCATAAAATAATCAAT
1 TTGT-ATAAAATAATCAAA
* *
16562827 TTTTATAAAATAATTAAA
1 TTGTATAAAATAATCAAA
16562845 TTGTATTAAAA
1 TTGTA-TAAAA
16562856 ATTTGAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (18 bp):
TTGTATAAAATAATCAAA
Found at i:16567560 original size:30 final size:30
Alignment explanation
Indices: 16567503--16567561 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
16567493 GCCTTTTGAA
* *
16567503 AATATTTACAAAAAGAGACATCTAATTTTT
1 AATATTTACAAAAAGAGACACCAAATTTTT
16567533 AATATTTACAAAAAGAG-CAACCAAATTTT
1 AATATTTACAAAAAGAGAC-ACCAAATTTT
16567562 GAAAATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (30 bp):
AATATTTACAAAAAGAGACACCAAATTTTT
Found at i:16577218 original size:50 final size:50
Alignment explanation
Indices: 16577091--16577434 Score: 467
Period size: 50 Copynumber: 6.9 Consensus size: 50
16577081 GATAATAACA
* ** * * *
16577091 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCTTGTAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* * ** *
16577140 TGCCAATGCCATGTCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
16577190 TGCCCATGCCATGTCCCAGACATTGTCTTACAAGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
16577240 TGCCAACGCCATGTCCCAAAGATGGTCTTACATGGGACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
16577290 TGCCAACGCCATGTCCTAGACATGGTCTTACATCGGACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
16577340 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
16577390 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT
16577435 AATTTCAATA
Statistics
Matches: 263, Mismatches: 30, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
48 1 0.00
49 40 0.15
50 222 0.84
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:16577361 original size:150 final size:151
Alignment explanation
Indices: 16577091--16577523 Score: 502
Period size: 150 Copynumber: 2.9 Consensus size: 151
16577081 GATAATAACA
* * * *
16577091 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA--TGT-TTCTTGTACTGCCAATGCCATG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTG-ACTGCCAACGCCATG
* * ** * *
16577153 TCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCCAGACATTGTCT
65 TCCCAGACATGGTCTTACATCGGACCTCTCATATCGGTGCCAATGCCATGTCCCAGACATGGTCT
16577218 TACAAGGGACCTCTCATCTCGG
130 TACAAGGGACCTCTCATCTCGG
* * *
16577240 TGCCAACGCCATGTCCCAAAGATGGTCTTACATGGGACCTCTCATCTTG-GTGCCAACGCCATGT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGACTGCCAACGCCATGT
* * *
16577304 CCTAGACATGGTCTTACATCGGACCTCTCATCTTGGTGCCAATGCCATGTCCCAGACATGGTCTT
66 CCCAGACATGGTCTTACATCGGACCTCTCATATCGGTGCCAATGCCATGTCCCAGACATGGTCTT
*
16577369 ACATGGGACCTCTCATCTCGG
131 ACAAGGGACCTCTCATCTCGG
* * * * *
16577390 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATTTCAATAATGTCAATGC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT--CTT---GACTGCCAACGC
* * * * * *
16577455 CATGTCCTAGACATGGTCTTACA-CTGG--CTCACACATCGATGTCGATGCCATGTCCCAGACAT
61 CATGTCCCAGACATGGTCTTACATC-GGACCTCTCATATCGGTGCCAATGCCATGTCCCAGACAT
16577517 GGTCTTA
125 GGTCTTA
16577524 TACGAGATCG
Statistics
Matches: 243, Mismatches: 31, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
149 34 0.14
150 132 0.54
151 2 0.01
152 7 0.03
154 35 0.14
155 1 0.00
156 32 0.13
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (151 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGACTGCCAACGCCATGT
CCCAGACATGGTCTTACATCGGACCTCTCATATCGGTGCCAATGCCATGTCCCAGACATGGTCTT
ACAAGGGACCTCTCATCTCGG
Found at i:16577561 original size:42 final size:41
Alignment explanation
Indices: 16577489--16577568 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 41
16577479 TGGCTCACAC
* * *
16577489 ATCGATGTCGATGCCATGTCCCAGACATGGTCTTATACGAG
1 ATCGATGCCGATGCCATATCCCAAACATGGTCTTATACGAG
*
16577530 ATCGCATGCCGATGCCATATCCCAAATATGGTCTTATAC
1 ATCG-ATGCCGATGCCATATCCCAAACATGGTCTTATAC
16577569 AGAAATCACA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
41 4 0.12
42 30 0.88
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (41 bp):
ATCGATGCCGATGCCATATCCCAAACATGGTCTTATACGAG
Found at i:16582899 original size:22 final size:22
Alignment explanation
Indices: 16582871--16582915 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
16582861 ATTCAATCAT
16582871 AAGATTAGTAGATTTCTGTAAC
1 AAGATTAGTAGATTTCTGTAAC
*
16582893 AAGATTAGTATATTTCTGTAAC
1 AAGATTAGTAGATTTCTGTAAC
16582915 A
1 A
16582916 CCCCTAACCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (22 bp):
AAGATTAGTAGATTTCTGTAAC
Found at i:16594708 original size:59 final size:58
Alignment explanation
Indices: 16594596--16594708 Score: 145
Period size: 58 Copynumber: 1.9 Consensus size: 58
16594586 TGTTGGGGCT
* * * *
16594596 TGAACTTGGCAATTGTTCTCATATTAGGCCTGAACTTTTTTTTATCCAAGTTAGGACC
1 TGAACTTGGCAATTGCTCCCACATTAGGCCTGAACTTATTTTTATCCAAGTTAGGACC
* * * *
16594654 TGAACTTGGCAATTGCTCCCACATTGGGGCTTAAGCTTATTTTTGTCCAAGTTAG
1 TGAACTTGGCAATTGCTCCCACATTAGGCCTGAA-CTTATTTTTATCCAAGTTAG
16594709 TCTTTGAAGA
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
58 28 0.61
59 18 0.39
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (58 bp):
TGAACTTGGCAATTGCTCCCACATTAGGCCTGAACTTATTTTTATCCAAGTTAGGACC
Found at i:16595196 original size:18 final size:18
Alignment explanation
Indices: 16595173--16595208 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
16595163 TTAGCATACT
*
16595173 TTAGATTTATTGAAACCC
1 TTAGATTTATCGAAACCC
16595191 TTAGATTTATCGAAACCC
1 TTAGATTTATCGAAACCC
16595209 AACCCAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.36
Consensus pattern (18 bp):
TTAGATTTATCGAAACCC
Found at i:16595334 original size:22 final size:23
Alignment explanation
Indices: 16595308--16595351 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
16595298 AAATATTTTT
16595308 TTTAAAATATATT-ATTTATTAA
1 TTTAAAATATATTAATTTATTAA
* *
16595330 TTTAATATATTTTAATTTATTA
1 TTTAAAATATATTAATTTATTA
16595352 CTTTTTGGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TTTAAAATATATTAATTTATTAA
Found at i:16595616 original size:30 final size:30
Alignment explanation
Indices: 16595577--16595643 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 30
16595567 ACTAATAAAA
*
16595577 GCCGTTTTTTTTCAAAATTTACCGAAATGG
1 GCCGATTTTTTTCAAAATTTACCGAAATGG
* ** *
16595607 GCCGA-TTTTTTGATTATTTACCGGAATGG
1 GCCGATTTTTTTCAAAATTTACCGAAATGG
16595636 GCC-ATTTT
1 GCCGATTTT
16595644 CCGCGAAATC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 1 0.03
29 26 0.84
30 4 0.13
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.42
Consensus pattern (30 bp):
GCCGATTTTTTTCAAAATTTACCGAAATGG
Found at i:16598947 original size:49 final size:50
Alignment explanation
Indices: 16598883--16599002 Score: 129
Period size: 49 Copynumber: 2.4 Consensus size: 50
16598873 CGTATTTTCC
* * * * *
16598883 TCAATCTTTACAATCCCATTTCCTCAAAATCTCGT-CTTTTTCTCC-TTGTT
1 TCAATCTTTAAAATCCCATTTCATCAAAATCCCATAC--TTTCCCCTTTGTT
* **
16598933 T-AATCTGTAAAATCCCGGTTCATCAAAATCCCATACTTTCCCCTTTGTT
1 TCAATCTTTAAAATCCCATTTCATCAAAATCCCATACTTTCCCCTTTGTT
16598982 TCAATCTTTAAAATCCCATTT
1 TCAATCTTTAAAATCCCATTT
16599003 GTTCAAAAAC
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
48 6 0.11
49 32 0.57
50 18 0.32
ACGTcount: A:0.25, C:0.28, G:0.05, T:0.42
Consensus pattern (50 bp):
TCAATCTTTAAAATCCCATTTCATCAAAATCCCATACTTTCCCCTTTGTT
Found at i:16599990 original size:2 final size:2
Alignment explanation
Indices: 16599983--16600028 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
16599973 TCTCACGTTC
16599983 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
16600025 AT AT
1 AT AT
16600029 GGATTTGCAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16602691 original size:18 final size:22
Alignment explanation
Indices: 16602649--16602693 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 22
16602639 ATTAAAATCG
16602649 ATTATTATAAGTACTAAATTTA
1 ATTATTATAAGTACTAAATTTA
16602671 ATTATT-TAAGT-CT-AA-TTA
1 ATTATTATAAGTACTAAATTTA
16602689 ATTAT
1 ATTAT
16602694 CTCACTCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 8 0.35
19 2 0.09
20 2 0.09
21 5 0.22
22 6 0.26
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.49
Consensus pattern (22 bp):
ATTATTATAAGTACTAAATTTA
Found at i:16618411 original size:39 final size:40
Alignment explanation
Indices: 16618283--16618418 Score: 161
Period size: 40 Copynumber: 3.4 Consensus size: 40
16618273 CGTTTGGATA
*
16618283 AAAAACGCCACTAAAAATCAAGCATTAGCGGTGCTTTTCT
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGTGCTTTTCT
* * ** *
16618323 AAAAACGCCGCCAAAGATGGAGCATTAGCGGCGCTTTT-T
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGTGCTTTTCT
*
16618362 GGAAAACGCCGCTAAAAAT-AAGCATTAGCGGTG-TTTTCT
1 -AAAAACGCCGCTAAAAATCAAGCATTAGCGGTGCTTTTCT
*
16618401 AAAAAGCGCCGCAAAAAA
1 AAAAA-CGCCGCTAAAAA
16618419 CCTAAGACCG
Statistics
Matches: 80, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
38 8 0.10
39 25 0.31
40 47 0.59
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATCAAGCATTAGCGGTGCTTTTCT
Found at i:16618523 original size:41 final size:41
Alignment explanation
Indices: 16618463--16618650 Score: 132
Period size: 41 Copynumber: 4.6 Consensus size: 41
16618453 CATTTAGCGG
16618463 CGTTTTTGAAGAACCGCCGCTAATGATCGGGCCTTTAACGA
1 CGTTTTTGAAGAACCGCCGCTAATGATCGGGCCTTTAACGA
** * *
16618504 CGTTTTTGAAGAATTGCCGCTAATGCTCGGGCCTTTAGC-A
1 CGTTTTTGAAGAACCGCCGCTAATGATCGGGCCTTTAACGA
* * * * * ** * *
16618544 GCATTTTTGAA-AATGCGCCTCTAATGCTTGTTCCTTTAGCGG
1 -CGTTTTTGAAGAA-CCGCCGCTAATGATCGGGCCTTTAACGA
* * * * * *
16618586 CGCTTTTTCAA-AAACGCCGCTAATGCTCGGGCCCTTAGCGG
1 CG-TTTTTGAAGAACCGCCGCTAATGATCGGGCCTTTAACGA
*
16618627 CGTTTTTG-AGAAAGCGCCGCTAAT
1 CGTTTTTGAAG-AACCGCCGCTAAT
16618651 AATAAAAAAA
Statistics
Matches: 119, Mismatches: 22, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
39 1 0.01
40 8 0.07
41 101 0.85
42 9 0.08
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.30
Consensus pattern (41 bp):
CGTTTTTGAAGAACCGCCGCTAATGATCGGGCCTTTAACGA
Found at i:16620780 original size:18 final size:17
Alignment explanation
Indices: 16620730--16620781 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
16620720 GTATAGGACC
*
16620730 AAAATATAAGAAA-AAAT
1 AAAATA-AAAAAATAAAT
*
16620747 AAAATAAAAATATAAAT
1 AAAATAAAAAAATAAAT
*
16620764 GAAATAAAAAAACTAAAT
1 AAAATAAAAAAA-TAAAT
16620782 TTATAAATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 4 0.14
17 20 0.69
18 5 0.17
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (17 bp):
AAAATAAAAAAATAAAT
Found at i:16621870 original size:25 final size:27
Alignment explanation
Indices: 16621842--16621894 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
16621832 GTCTTCCAAT
16621842 TTGTC-ATT-CTGCTATAATTCATGCC
1 TTGTCTATTACTGCTATAATTCATGCC
* *
16621867 TTGTCTTTTAATTGCTATAATTCATGCC
1 TTGTCTATT-ACTGCTATAATTCATGCC
16621895 ATGTTTGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 5 0.22
26 2 0.09
28 16 0.70
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.47
Consensus pattern (27 bp):
TTGTCTATTACTGCTATAATTCATGCC
Found at i:16622689 original size:8 final size:8
Alignment explanation
Indices: 16622676--16622714 Score: 60
Period size: 8 Copynumber: 4.9 Consensus size: 8
16622666 CCTCATGAAG
16622676 GCCTTGTT
1 GCCTTGTT
16622684 GCCTTGTT
1 GCCTTGTT
*
16622692 GCCTAGTT
1 GCCTTGTT
16622700 GCCTTGTT
1 GCCTTGTT
*
16622708 GCATTGT
1 GCCTTGT
16622715 AGGCTCGAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.05, C:0.23, G:0.26, T:0.46
Consensus pattern (8 bp):
GCCTTGTT
Found at i:16623102 original size:21 final size:21
Alignment explanation
Indices: 16623076--16623122 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
16623066 TTAATTAAAT
*
16623076 CAGAGGCGGTAGCGAGGGAAG
1 CAGAGGCGGCAGCGAGGGAAG
*
16623097 CAGAGGCTGCAGCGAGGGAAG
1 CAGAGGCGGCAGCGAGGGAAG
16623118 CAGAG
1 CAGAG
16623123 CAGAGCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.30, C:0.17, G:0.49, T:0.04
Consensus pattern (21 bp):
CAGAGGCGGCAGCGAGGGAAG
Found at i:16623285 original size:19 final size:19
Alignment explanation
Indices: 16623263--16623314 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
16623253 AAAAATAATA
16623263 TGATTTATATTTGA-TTTAT
1 TGATTTA-ATTTGATTTTAT
16623282 TGATATTAATATT-ATTTTAT
1 TGAT-TTAAT-TTGATTTTAT
*
16623302 TCATTTAATTTGA
1 TGATTTAATTTGA
16623315 AATAATTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
18 2 0.07
19 13 0.46
20 13 0.46
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.60
Consensus pattern (19 bp):
TGATTTAATTTGATTTTAT
Found at i:16623468 original size:43 final size:41
Alignment explanation
Indices: 16623420--16623538 Score: 114
Period size: 44 Copynumber: 2.7 Consensus size: 41
16623410 TATAAAAATC
* *
16623420 CCAAAATTAGTGGCGTTTTTAGAAAAAGCGCTGCAAAAGGTCA
1 CCAAAAATAG-GGCGTTTTTGGAAAAAGCGC-GCAAAAGGTCA
* *
16623463 CCAAAAAATAGCGGCGTTTGTGGGAAAAATGC-CGCTAAAGGTCA
1 CC-AAAAATAG-GGCGTTT-TTGGAAAAA-GCGCGCAAAAGGTCA
*
16623507 CCAAACAATAGGGACGTTTGTGGAAAAAGCGC
1 CCAAA-AATAGGG-CGTTTTTGGAAAAAGCGC
16623539 CGCTAAAGAA
Statistics
Matches: 63, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
42 2 0.03
43 15 0.24
44 36 0.57
45 8 0.13
46 2 0.03
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.19
Consensus pattern (41 bp):
CCAAAAATAGGGCGTTTTTGGAAAAAGCGCGCAAAAGGTCA
Found at i:16623503 original size:44 final size:44
Alignment explanation
Indices: 16623441--16623546 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
16623431 GGCGTTTTTA
* *
16623441 GAAAAAGCGCTGCAAAAGGTCACCAAAAAATAGCGG-CGTTTGTGG
1 GAAAAAGCGCCGCTAAAGGTCACCAAAAAATAG-GGACGTTTGT-G
* *
16623486 GAAAAA-TGCCGCTAAAGGTCACCAAACAATAGGGACGTTTGTG
1 GAAAAAGCGCCGCTAAAGGTCACCAAAAAATAGGGACGTTTGTG
16623529 GAAAAAGCGCCGCTAAAG
1 GAAAAAGCGCCGCTAAAG
16623547 AACATGACCT
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
43 9 0.17
44 39 0.72
45 6 0.11
ACGTcount: A:0.39, C:0.19, G:0.27, T:0.15
Consensus pattern (44 bp):
GAAAAAGCGCCGCTAAAGGTCACCAAAAAATAGGGACGTTTGTG
Found at i:16623567 original size:87 final size:86
Alignment explanation
Indices: 16623471--16623678 Score: 249
Period size: 86 Copynumber: 2.4 Consensus size: 86
16623461 CACCAAAAAA
* ** * *
16623471 TAGCGGCGTTTGTGGGAAAAATGCCGCTAAAGGTCACCAAACAATAG-GGACGTTTGTGGAAAAA
1 TAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGAACA-CAAACAATAGCAG-CATTTGTGGAAAAA
16623535 GCGCCGCTAAAGAACATGACCTT
64 GCGCCGCTAAAGAACATGACCTT
* ** * ** *
16623558 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATGACCTTTAGCAGCATTTGTGGGAAAAGC
1 TAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGAACACAAACAATAGCAGCATTTGTGGAAAAAGC
*
16623623 GCTGCTAAAGAACATGACCTT
66 GCCGCTAAAGAACATGACCTT
* *
16623644 TAGCGGCGTTTTTGTG-AAAGTGCCGCTAAAGAACA
1 TAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGAACA
16623679 TGACCTTTAG
Statistics
Matches: 104, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
85 18 0.17
86 53 0.51
87 33 0.32
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (86 bp):
TAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGAACACAAACAATAGCAGCATTTGTGGAAAAAGC
GCCGCTAAAGAACATGACCTT
Found at i:16623685 original size:42 final size:43
Alignment explanation
Indices: 16623521--16623689 Score: 268
Period size: 43 Copynumber: 4.0 Consensus size: 43
16623511 ACAATAGGGA
*
16623521 CGTTTGTGGAAAAAGCGCCGCTAAAGAACATGACCTTTAGCGG
1 CGTTTGTGGGAAAAGCGCCGCTAAAGAACATGACCTTTAGCGG
*
16623564 CGTTTGTGGGAAAAGCGCCGCTAAAGAACATGACCTTTAGCAG
1 CGTTTGTGGGAAAAGCGCCGCTAAAGAACATGACCTTTAGCGG
* *
16623607 CATTTGTGGGAAAAGCGCTGCTAAAGAACATGACCTTTAGCGG
1 CGTTTGTGGGAAAAGCGCCGCTAAAGAACATGACCTTTAGCGG
* * *
16623650 CGTTTTTGTG-AAAGTGCCGCTAAAGAACATGACCTTTAGC
1 CGTTTGTGGGAAAAGCGCCGCTAAAGAACATGACCTTTAGC
16623690 AGTGTTTATA
Statistics
Matches: 116, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
42 28 0.24
43 88 0.76
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.24
Consensus pattern (43 bp):
CGTTTGTGGGAAAAGCGCCGCTAAAGAACATGACCTTTAGCGG
Found at i:16625162 original size:38 final size:38
Alignment explanation
Indices: 16625114--16625208 Score: 140
Period size: 38 Copynumber: 2.5 Consensus size: 38
16625104 TGAGATTTGG
16625114 TTGCATGTTAAAACATGCCCTATATGAAATTATCCGAT
1 TTGCATGTTAAAACATGCCCTATATGAAATTATCCGAT
* * *
16625152 TTGCATGTTAAAACATGCCTTATATGATATTATTCGAT
1 TTGCATGTTAAAACATGCCCTATATGAAATTATCCGAT
16625190 TTGCATGATT--AACATGCCC
1 TTGCATG-TTAAAACATGCCC
16625209 AATGTGACAA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
37 8 0.15
38 42 0.81
39 2 0.04
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (38 bp):
TTGCATGTTAAAACATGCCCTATATGAAATTATCCGAT
Found at i:16625565 original size:191 final size:191
Alignment explanation
Indices: 16625241--16625632 Score: 705
Period size: 191 Copynumber: 2.1 Consensus size: 191
16625231 GATGAGTAAA
*
16625241 ATGTTTATATATGTTCATTATGGTCATATCACATGCATAGGGTGGGATATTATAAGGACGAGGAA
1 ATGTTTATATATGTTCATTATGATCATATCACATGCATAGGGTGGGATATTATAAGGACGAGGAA
* *
16625306 TTGGTGGCTTCGTCCACAACCTACATGGTAGCTTGTTTGCAAATATTGGTGGCTTCGTCCACATT
66 TTGGTGGCTTCGTCCACAACCTACATGGTAGCTTGTCTGCAAATATTGGTGGCTTCATCCACATT
* *
16625371 GGAGTGTTTGGATGGATGAGTTCTGGGGAACTCTTTTTGGAGTGTAGCGATGATGGGTAGG
131 GGAGTGTTTGGATGGATGAGTTCTGGGGAAATCTTTTTGAAGTGTAGCGATGATGGGTAGG
* *
16625432 ATGTTTATATATGTTCATTATGATCATATCACATGCATGGGGTGGGATATTATAAGGAGGAGGAA
1 ATGTTTATATATGTTCATTATGATCATATCACATGCATAGGGTGGGATATTATAAGGACGAGGAA
16625497 TTGGTGGCTTCGTCCACAACCTACATGGTAGCTTGTCTGCAAATATTGGTGGCTTCATCCACATT
66 TTGGTGGCTTCGTCCACAACCTACATGGTAGCTTGTCTGCAAATATTGGTGGCTTCATCCACATT
*
16625562 GGAGTGTTTGGATGGATGAGTTCTGGGGAAATCTTTTTGAAGTGTAGCGGTGATGGGTAGG
131 GGAGTGTTTGGATGGATGAGTTCTGGGGAAATCTTTTTGAAGTGTAGCGATGATGGGTAGG
16625623 ATGTTT-TATA
1 ATGTTTATATA
16625633 AAAACTTGCA
Statistics
Matches: 193, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
190 4 0.02
191 189 0.98
ACGTcount: A:0.24, C:0.12, G:0.29, T:0.34
Consensus pattern (191 bp):
ATGTTTATATATGTTCATTATGATCATATCACATGCATAGGGTGGGATATTATAAGGACGAGGAA
TTGGTGGCTTCGTCCACAACCTACATGGTAGCTTGTCTGCAAATATTGGTGGCTTCATCCACATT
GGAGTGTTTGGATGGATGAGTTCTGGGGAAATCTTTTTGAAGTGTAGCGATGATGGGTAGG
Found at i:16628187 original size:25 final size:27
Alignment explanation
Indices: 16628132--16628188 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 27
16628122 AATTCTTGCA
16628132 CTTATTTTATTATAATTTAATCCCAAAC
1 CTTATTTTATTAT-ATTTAATCCCAAAC
*
16628160 CTTATTTT-TTAT-TTTCAAT-CCAATC
1 CTTATTTTATTATATTT-AATCCCAAAC
16628185 CTTA
1 CTTA
16628189 GTCTATGTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 12 0.44
26 3 0.11
27 4 0.15
28 8 0.30
ACGTcount: A:0.30, C:0.19, G:0.00, T:0.51
Consensus pattern (27 bp):
CTTATTTTATTATATTTAATCCCAAAC
Found at i:16641094 original size:140 final size:140
Alignment explanation
Indices: 16640645--16641097 Score: 563
Period size: 140 Copynumber: 3.2 Consensus size: 140
16640635 AGTTACGAGT
* * * * * *
16640645 CTTATCTCCCTAAAGTTGTAGCGAAGCAAACTA-AAGACAGCGAATCTTATTTCCATAGCATTGC
1 CTTATCTCCCTGAAGTTGCAGCGGAGTAGAC-AGAAGACAGCGAATCTTATTTCCATGGCATTGC
* * * * *
16640709 AATGGAACAGATTAAAGCTACAAGTTACGGCAAATCTTATCT-TTCTGAAGTTGCAG-TGAAGTA
65 AGTAGAACAGATTAAAGCTAC-AG--ACAGCAAATCTTATCTCCT-TGAAGTTGCAGATG-AGCA
*
16640772 AATTAAAGCCACTAGC
125 AATTAAAGCCACCAGC
* * * *
16640788 CTTATCTCCCTGAAGTTGCAGCGGAGCAGACAGAAGACAGTGAATCTTATTTCCCTGGCATTGTA
1 CTTATCTCCCTGAAGTTGCAGCGGAGTAGACAGAAGACAGCGAATCTTATTTCCATGGCATTGCA
* * * * *
16640853 GCAGAACAGATTAAAGCTATAG-CTAGCAAATCTTATCTCCTTAAAGTTGCAGAGGAACAAATTA
66 GTAGAACAGATTAAAGCTACAGAC-AGCAAATCTTATCTCCTTGAAGTTGCAGATGAGCAAATTA
16640917 AAGCCACCAGC
130 AAGCCACCAGC
* *
16640928 CTTATCTCCCTGAAGTTGCAGCGGAGTAGACTGAAGACAGCGAATCTTATTTCCTTGGCATTGCA
1 CTTATCTCCCTGAAGTTGCAGCGGAGTAGACAGAAGACAGCGAATCTTATTTCCATGGCATTGCA
* *
16640993 GTAGAACAGATTAAAGCTACAGACAACAAATCTTATCTCCTTGAAGTTGCAGATGAGCAGATTAA
66 GTAGAACAGATTAAAGCTACAGACAGCAAATCTTATCTCCTTGAAGTTGCAGATGAGCAAATTAA
16641058 AGCCACCAGC
131 AGCCACCAGC
* * *
16641068 CTTATCTACTTGAAGTTGCAGTGGAGTAGA
1 CTTATCTCCCTGAAGTTGCAGCGGAGTAGA
16641098 TCGAAGCTAC
Statistics
Matches: 271, Mismatches: 34, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
139 1 0.00
140 193 0.71
141 3 0.01
142 3 0.01
143 71 0.26
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (140 bp):
CTTATCTCCCTGAAGTTGCAGCGGAGTAGACAGAAGACAGCGAATCTTATTTCCATGGCATTGCA
GTAGAACAGATTAAAGCTACAGACAGCAAATCTTATCTCCTTGAAGTTGCAGATGAGCAAATTAA
AGCCACCAGC
Found at i:16642854 original size:21 final size:21
Alignment explanation
Indices: 16642830--16642906 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 21
16642820 TTACCATTAT
*
16642830 TGTTA-TAGTTGTTATTATTCG
1 TGTTATTAGTTATT-TTATTCG
*
16642851 TGTTATTAGTTATTTTATTTG
1 TGTTATTAGTTATTTTATTCG
* *
16642872 -GTTGTTAGTTATTTTATTTG
1 TGTTATTAGTTATTTTATTCG
*
16642892 T-TTACTTATTTATTT
1 TGTTA-TTAGTTATTT
16642907 ATTTTTGATT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
20 21 0.44
21 20 0.42
22 7 0.15
ACGTcount: A:0.18, C:0.03, G:0.14, T:0.65
Consensus pattern (21 bp):
TGTTATTAGTTATTTTATTCG
Found at i:16643395 original size:18 final size:17
Alignment explanation
Indices: 16643368--16643401 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
16643358 AAGGGATCGT
16643368 ATTTTAAATTCTTTTCAA
1 ATTTTAAATT-TTTTCAA
*
16643386 ATTTTCAATTTTTTCA
1 ATTTTAAATTTTTTCA
16643402 CATTAAGACG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTAAATTTTTTCAA
Found at i:16645444 original size:27 final size:27
Alignment explanation
Indices: 16645332--16645545 Score: 118
Period size: 27 Copynumber: 8.0 Consensus size: 27
16645322 CCTCTACCAA
* *
16645332 AAGATAGTCCTGATAGACCTT-CCAAAT
1 AAGATAGTCCTGA-AGAACTTCCCACAT
* * * *
16645359 AAAATAGTCATGACAG-ACTTTCCACAA
1 AAGATAGTCCTGA-AGAACTTCCCACAT
* * *
16645386 AAGATAGTCCTGACGAACTTTCTACCA-
1 AAGATAGTCCTGAAGAACTTCCCA-CAT
16645413 AAGATAGTCCTGAAGAACTTCCCACAT
1 AAGATAGTCCTGAAGAACTTCCCACAT
* * * *
16645440 TAGATAGTCCTTG-TGGACTTCCCGCAT
1 AAGATAGTCC-TGAAGAACTTCCCACAT
* * *
16645467 AAGATAGT-CTTATGGACTTCCCACAT
1 AAGATAGTCCTGAAGAACTTCCCACAT
* * * * *
16645493 TAGATAGTCATTACGGACTT-CCAGCAT
1 AAGATAGTCCTGAAGAACTTCCCA-CAT
* * *
16645520 AAGATAATCCT-ACGAACTTCCTACAT
1 AAGATAGTCCTGAAGAACTTCCCACAT
16645546 TTACGGTAAT
Statistics
Matches: 150, Mismatches: 28, Indels: 19
0.76 0.14 0.10
Matches are distributed among these distances:
25 1 0.01
26 40 0.27
27 105 0.70
28 4 0.03
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (27 bp):
AAGATAGTCCTGAAGAACTTCCCACAT
Found at i:16645539 original size:53 final size:53
Alignment explanation
Indices: 16645413--16645546 Score: 169
Period size: 53 Copynumber: 2.5 Consensus size: 53
16645403 CTTTCTACCA
* ** *
16645413 AAGATAGTCCTGAAGAACTTCCCACATTAGATAGTCCTTGTGGACTTCCCGCAT
1 AAGATAGTCCT-AAGAACTTCCCACATTAGATAGTCATTACGGACTTCCAGCAT
* * *
16645467 AAGATAGTCTTATGGACTTCCCACATTAGATAGTCATTACGGACTTCCAGCAT
1 AAGATAGTCCTAAGAACTTCCCACATTAGATAGTCATTACGGACTTCCAGCAT
* * *
16645520 AAGATAATCCTACGAACTTCCTACATT
1 AAGATAGTCCTAAGAACTTCCCACATT
16645547 TACGGTAATG
Statistics
Matches: 68, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
53 58 0.85
54 10 0.15
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.29
Consensus pattern (53 bp):
AAGATAGTCCTAAGAACTTCCCACATTAGATAGTCATTACGGACTTCCAGCAT
Found at i:16647392 original size:60 final size:60
Alignment explanation
Indices: 16647319--16647449 Score: 163
Period size: 60 Copynumber: 2.2 Consensus size: 60
16647309 TCCCTTTTGA
* * * * *
16647319 AATTTTCAAAATTTGAACTAAATTGAGAAATTTTGTAAATCCTGAGAGCTAAATTTATTG
1 AATTTTTAGAATTTGAACTAAAATGACAAATTTTGTAAATACTGAGAGCTAAATTTATTG
* * * * *
16647379 AATTTTTAGAATTTGGACTAAAATGACAAATTTTGTAAATATTGAGGGTTAAATTTGTTG
1 AATTTTTAGAATTTGAACTAAAATGACAAATTTTGTAAATACTGAGAGCTAAATTTATTG
16647439 AACTTTTTAGA
1 AA-TTTTTAGA
16647450 TTTAGCGTCA
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
60 52 0.87
61 8 0.13
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.40
Consensus pattern (60 bp):
AATTTTTAGAATTTGAACTAAAATGACAAATTTTGTAAATACTGAGAGCTAAATTTATTG
Found at i:16647536 original size:20 final size:19
Alignment explanation
Indices: 16647512--16647549 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
16647502 TAGACCAATA
*
16647512 AAAAAAGACCCACGTCAGC
1 AAAAAAGACCCACATCAGC
16647531 AAAAAAGACCCACATCAGC
1 AAAAAAGACCCACATCAGC
16647550 TTTCTATCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.32, G:0.13, T:0.05
Consensus pattern (19 bp):
AAAAAAGACCCACATCAGC
Found at i:16647969 original size:2 final size:2
Alignment explanation
Indices: 16647956--16648007 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
16647946 ATGTTTCATA
* * *
16647956 AT AT AG AT AT AT AT AT AT AT AT TT AT AT CT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16647998 AT AT AT AT AT
1 AT AT AT AT AT
16648008 TTAGGATTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16650792 original size:12 final size:12
Alignment explanation
Indices: 16650775--16650812 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
16650765 TTGTTTAAAA
16650775 ATTTATTATTTT
1 ATTTATTATTTT
16650787 ATTTATTATTTT
1 ATTTATTATTTT
16650799 ATTTTATT-TTTT
1 A-TTTATTATTTT
16650811 AT
1 AT
16650813 AAATATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 1 0.04
12 18 0.72
13 6 0.24
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
ATTTATTATTTT
Found at i:16650802 original size:17 final size:17
Alignment explanation
Indices: 16650780--16650812 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
16650770 TAAAAATTTA
16650780 TTATTTTATTTATTATT
1 TTATTTTATTTATTATT
*
16650797 TTATTTTATTTTTTAT
1 TTATTTTATTTATTAT
16650813 AAATATTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (17 bp):
TTATTTTATTTATTATT
Found at i:16651688 original size:22 final size:22
Alignment explanation
Indices: 16651652--16651693 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
16651642 AAAATTGTTT
16651652 TAATGTTGCACGT-AATTTTCA
1 TAATGTTGCACGTAAATTTTCA
*
16651673 TAATAGTTGCATGTAAATTTT
1 TAAT-GTTGCACGTAAATTTT
16651694 TATTTAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 8 0.44
23 6 0.33
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45
Consensus pattern (22 bp):
TAATGTTGCACGTAAATTTTCA
Found at i:16652487 original size:26 final size:26
Alignment explanation
Indices: 16652458--16652513 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
16652448 ATTTTTATTG
16652458 TAAAAATTCTCATTATAGTTACTAAA
1 TAAAAATTCTCATTATAGTTACTAAA
16652484 TAAAAATTCTCATTATAGTTACTAAA
1 TAAAAATTCTCATTATAGTTACTAAA
16652510 TAAA
1 TAAA
16652514 TATAAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.48, C:0.11, G:0.04, T:0.38
Consensus pattern (26 bp):
TAAAAATTCTCATTATAGTTACTAAA
Found at i:16655901 original size:25 final size:25
Alignment explanation
Indices: 16655822--16655961 Score: 104
Period size: 25 Copynumber: 5.6 Consensus size: 25
16655812 CAACTCGCAA
* * *
16655822 GAGCATCCCGTTATTTAGATCTTAT
1 GAGCTTCCCGATATTTAGCTCTTAT
* * * * * *
16655847 GAGCATCCCGTTATATGGCTCTCAC
1 GAGCTTCCCGATATTTAGCTCTTAT
16655872 GAGCTTCCCGATATTTAGCTCTTAT
1 GAGCTTCCCGATATTTAGCTCTTAT
* * *
16655897 GAGCTTTCCGAT-TAATGGCTCTCT-T
1 GAGCTTCCCGATAT-TTAGCTCT-TAT
* * *
16655922 GAGTTTCCCGATAATTAGCTCTCAT
1 GAGCTTCCCGATATTTAGCTCTTAT
*
16655947 GAGCTTCCTGATATT
1 GAGCTTCCCGATATT
16655962 GGCGCGCATG
Statistics
Matches: 88, Mismatches: 23, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
24 1 0.01
25 86 0.98
26 1 0.01
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.37
Consensus pattern (25 bp):
GAGCTTCCCGATATTTAGCTCTTAT
Found at i:16655915 original size:50 final size:49
Alignment explanation
Indices: 16655815--16656077 Score: 199
Period size: 50 Copynumber: 5.3 Consensus size: 49
16655805 CACACCACAA
* * * * *
16655815 CTCGCAAGAGCATCCCGTTATTTAGATCTTATGAGCATCCCGTTATATGG
1 CTCGCATGAGCTTCCCGATATTTAGCTCTTATGAGCTTCCCGTTA-ATGG
* * *
16655865 CTCTCACGAGCTTCCCGATATTTAGCTCTTATGAGCTTTCCGATTAATGG
1 CTCGCATGAGCTTCCCGATATTTAGCTCTTATGAGCTTCCCG-TTAATGG
* * * * * * * *
16655915 CTCTCTTGAGTTTCCCGATAATTAGCTCTCATGAGCTTCCTGATATTGG
1 CTCGCATGAGCTTCCCGATATTTAGCTCTTATGAGCTTCCCGTTAATGG
* * * * *
16655964 CGCGCATGAGCTTCCC-AAATTTGGCTCCCT-TGAGCTTCCCGTTTATGG
1 CTCGCATGAGCTTCCCGATATTTAGCT-CTTATGAGCTTCCCGTTAATGG
* * ** * ** *
16656012 CTCGCATAAGCTTCCCGATA-TTGGCTCGCAGGAGCTTCTTGTTATATGA
1 CTCGCATGAGCTTCCCGATATTTAGCTCTTATGAGCTTCCCGTTA-ATGG
*
16656061 CTCACATGAGCTTCCCG
1 CTCGCATGAGCTTCCCG
16656078 TTACATGGCT
Statistics
Matches: 167, Mismatches: 41, Indels: 11
0.76 0.19 0.05
Matches are distributed among these distances:
47 1 0.01
48 51 0.31
49 38 0.23
50 74 0.44
51 3 0.02
ACGTcount: A:0.19, C:0.27, G:0.20, T:0.33
Consensus pattern (49 bp):
CTCGCATGAGCTTCCCGATATTTAGCTCTTATGAGCTTCCCGTTAATGG
Found at i:16655975 original size:24 final size:24
Alignment explanation
Indices: 16655845--16656077 Score: 146
Period size: 25 Copynumber: 9.5 Consensus size: 24
16655835 TTTAGATCTT
* * *
16655845 ATGAGCATCCCGTTATATGGCTCTC
1 ATGAGCTTCCCGATAT-TGGCTCGC
* * **
16655870 ACGAGCTTCCCGATATTTAGCTCTT
1 ATGAGCTTCCCGATA-TTGGCTCGC
* * *
16655895 ATGAGCTTTCCGATTAATGGCTCTC
1 ATGAGCTTCCCGA-TATTGGCTCGC
* * * *
16655920 TTGAGTTTCCCGATAATTAGCTCTC
1 ATGAGCTTCCCGAT-ATTGGCTCGC
* *
16655945 ATGAGCTTCCTGATATTGGCGCGC
1 ATGAGCTTCCCGATATTGGCTCGC
* *
16655969 ATGAGCTTCCC-AAATTTGGCTCCC
1 ATGAGCTTCCCGATA-TTGGCTCGC
* *
16655993 TTGAGCTTCCCG-TTTATGGCTCGC
1 ATGAGCTTCCCGATAT-TGGCTCGC
*
16656017 ATAAGCTTCCCGATATTGGCTCGC
1 ATGAGCTTCCCGATATTGGCTCGC
* ** * * *
16656041 AGGAGCTTCTTGTTATATGACTCAC
1 ATGAGCTTCCCGATAT-TGGCTCGC
16656066 ATGAGCTTCCCG
1 ATGAGCTTCCCG
16656078 TTACATGGCT
Statistics
Matches: 158, Mismatches: 42, Indels: 16
0.73 0.19 0.07
Matches are distributed among these distances:
23 3 0.02
24 71 0.45
25 81 0.51
26 3 0.02
ACGTcount: A:0.19, C:0.27, G:0.21, T:0.33
Consensus pattern (24 bp):
ATGAGCTTCCCGATATTGGCTCGC
Found at i:16656018 original size:48 final size:49
Alignment explanation
Indices: 16655845--16656077 Score: 159
Period size: 48 Copynumber: 4.7 Consensus size: 49
16655835 TTTAGATCTT
* * * * **
16655845 ATGAGCATCCCGTTATATGGCTCTCACGAGCTTCCCGATATTTAGCTCTT
1 ATGAGCTTCCCGTT-TATGGCTCGCATGAGCTTCCCGAAATTTAGCTCCC
* * * * * *
16655895 ATGAGCTTTCCGATTAATGGCTCTCTTGAGTTTCCCGATAA-TTAGCTCTC
1 ATGAGCTTCCCG-TTTATGGCTCGCATGAGCTTCCCGA-AATTTAGCTCCC
* * * *
16655945 ATGAGCTTCCTG-ATATTGGCGCGCATGAGCTTCCC-AAATTTGGCTCCC
1 ATGAGCTTCCCGTTTA-TGGCTCGCATGAGCTTCCCGAAATTTAGCTCCC
* * * * *
16655993 TTGAGCTTCCCGTTTATGGCTCGCATAAGCTTCCCGATA-TTGGCTCGC
1 ATGAGCTTCCCGTTTATGGCTCGCATGAGCTTCCCGAAATTTAGCTCCC
* ** * *
16656041 AGGAGCTTCTTGTTATATGACTCACATGAGCTTCCCG
1 ATGAGCTTCCCGTT-TATGGCTCGCATGAGCTTCCCG
16656078 TTACATGGCT
Statistics
Matches: 144, Mismatches: 32, Indels: 15
0.75 0.17 0.08
Matches are distributed among these distances:
47 2 0.01
48 54 0.38
49 38 0.26
50 47 0.33
51 3 0.02
ACGTcount: A:0.19, C:0.27, G:0.21, T:0.33
Consensus pattern (49 bp):
ATGAGCTTCCCGTTTATGGCTCGCATGAGCTTCCCGAAATTTAGCTCCC
Found at i:16656047 original size:72 final size:73
Alignment explanation
Indices: 16655912--16656049 Score: 179
Period size: 72 Copynumber: 1.9 Consensus size: 73
16655902 TTCCGATTAA
* * * * * *
16655912 TGGCTCTCTTGAGTTTCCCGATAATTAGCTCTCATGAGCTTCCTGATATTGGCGCGCATGAGCTT
1 TGGCTCCCTTGAGCTTCCCGATAATTAGCTCGCATAAGCTTCCCGATATTGGCGCGCAGGAGCTT
16655977 CCCAAATT
66 CCCAAATT
* * * *
16655985 TGGCTCCCTTGAGCTTCCCGTTTA-TGGCTCGCATAAGCTTCCCGATATTGGCTCGCAGGAGCTT
1 TGGCTCCCTTGAGCTTCCCGATAATTAGCTCGCATAAGCTTCCCGATATTGGCGCGCAGGAGCTT
16656049 C
66 C
16656050 TTGTTATATG
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
72 35 0.64
73 20 0.36
ACGTcount: A:0.17, C:0.28, G:0.22, T:0.33
Consensus pattern (73 bp):
TGGCTCCCTTGAGCTTCCCGATAATTAGCTCGCATAAGCTTCCCGATATTGGCGCGCAGGAGCTT
CCCAAATT
Found at i:16663712 original size:24 final size:24
Alignment explanation
Indices: 16663668--16663847 Score: 177
Period size: 24 Copynumber: 7.4 Consensus size: 24
16663658 GGCTCCCTCA
16663668 AGCTTCCCGATAATTGGCTCGCATG
1 AGCTTCCCGAT-ATTGGCTCGCATG
16663693 AGCTTCCCGATATTGGCTCGCATG
1 AGCTTCCCGATATTGGCTCGCATG
16663717 AGCTTCCCGATATTGGCTCG-AGTG
1 AGCTTCCCGATATTGGCTCGCA-TG
* *** *
16663741 AGCTTCTCGA-ATTTGGCTCTTTTA
1 AGCTTCCCGATA-TTGGCTCGCATG
* * *
16663765 AGCTTCTCG-TTTATGGCTCGCATA
1 AGCTTCCCGATAT-TGGCTCGCATG
*
16663789 AGCTTCCCGATATTGGCTCGCAAG
1 AGCTTCCCGATATTGGCTCGCATG
* * * *
16663813 AGCTTCCCGTTACATGGCTCGTAAG
1 AGCTTCCCGATA-TTGGCTCGCATG
16663838 AGCTTCCCGA
1 AGCTTCCCGA
16663848 CTACATGCTC
Statistics
Matches: 132, Mismatches: 16, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
23 3 0.02
24 97 0.73
25 32 0.24
ACGTcount: A:0.18, C:0.27, G:0.23, T:0.31
Consensus pattern (24 bp):
AGCTTCCCGATATTGGCTCGCATG
Found at i:16663769 original size:48 final size:49
Alignment explanation
Indices: 16663640--16663847 Score: 178
Period size: 48 Copynumber: 4.3 Consensus size: 49
16663630 TTTAGCTCTT
* * *
16663640 ATGAGCATCCCGTTATATGGCTC-CCTCAAGCTTCCCGATAATTGGCTCGC
1 ATGAGCTTCCCGATAT-TGGCTCGCAT-AAGCTTCCCGATAATTGGCTCGC
*
16663690 ATGAGCTTCCCGATATTGGCTCGCATGAGCTTCCCGAT-ATTGGCTCG-
1 ATGAGCTTCCCGATATTGGCTCGCATAAGCTTCCCGATAATTGGCTCGC
* *** * * *
16663737 AGTGAGCTTCTCGA-ATTTGGCTCTTTTAAGCTTCTCGTTTA-TGGCTCGC
1 A-TGAGCTTCCCGATA-TTGGCTCGCATAAGCTTCCCGATAATTGGCTCGC
* * *
16663786 ATAAGCTTCCCGATATTGGCTCGCA-AGAGCTTCCCGTTACA-TGGCTCGT
1 ATGAGCTTCCCGATATTGGCTCGCATA-AGCTTCCCGATA-ATTGGCTCGC
*
16663835 AAGAGCTTCCCGA
1 ATGAGCTTCCCGA
16663848 CTACATGCTC
Statistics
Matches: 129, Mismatches: 21, Indels: 17
0.77 0.13 0.10
Matches are distributed among these distances:
47 3 0.02
48 71 0.55
49 39 0.30
50 16 0.12
ACGTcount: A:0.19, C:0.28, G:0.23, T:0.31
Consensus pattern (49 bp):
ATGAGCTTCCCGATATTGGCTCGCATAAGCTTCCCGATAATTGGCTCGC
Found at i:16663857 original size:25 final size:25
Alignment explanation
Indices: 16663777--16663858 Score: 89
Period size: 25 Copynumber: 3.3 Consensus size: 25
16663767 CTTCTCGTTT
*
16663777 ATGGCTCGCATA-AGCTTCCCGATA-
1 ATGGCTCGCA-AGAGCTTCCCGCTAC
* *
16663801 TTGGCTCGCAAGAGCTTCCCGTTAC
1 ATGGCTCGCAAGAGCTTCCCGCTAC
*
16663826 ATGGCTCGTAAGAGCTTCCCGACTAC
1 ATGGCTCGCAAGAGCTTCCCG-CTAC
16663852 AT-GCTCG
1 ATGGCTCG
16663859 ATGAGCATAC
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.02
24 20 0.40
25 24 0.48
26 5 0.10
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (25 bp):
ATGGCTCGCAAGAGCTTCCCGCTAC
Found at i:16667943 original size:13 final size:13
Alignment explanation
Indices: 16667925--16667954 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
16667915 AGCCCAAACT
16667925 CAATTACCCAACC
1 CAATTACCCAACC
16667938 CAATTACCCAACC
1 CAATTACCCAACC
16667951 CAAT
1 CAAT
16667955 AAAACTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (13 bp):
CAATTACCCAACC
Found at i:16668111 original size:9 final size:9
Alignment explanation
Indices: 16668099--16668203 Score: 97
Period size: 9 Copynumber: 11.4 Consensus size: 9
16668089 AAATAAAAAA
*
16668099 AATTCAGGT
1 AATTCGGGT
16668108 AATTCGGGT
1 AATTCGGGT
*
16668117 ATTTTTC-GGT
1 A--ATTCGGGT
* *
16668127 AATTTGGTT
1 AATTCGGGT
16668136 AATTCGGGT
1 AATTCGGGT
16668145 AATTCGGGT
1 AATTCGGGT
*
16668154 ATTTTTC-GGT
1 A--ATTCGGGT
*
16668164 AATTCGGTT
1 AATTCGGGT
*
16668173 AATTTGGGT
1 AATTCGGGT
16668182 AATTCGGGT
1 AATTCGGGT
16668191 AATTCGGGT
1 AATTCGGGT
16668200 AATT
1 AATT
16668204 TTTAACCAAA
Statistics
Matches: 77, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
8 5 0.06
9 58 0.75
10 8 0.10
11 6 0.08
ACGTcount: A:0.22, C:0.09, G:0.27, T:0.43
Consensus pattern (9 bp):
AATTCGGGT
Found at i:16668149 original size:37 final size:37
Alignment explanation
Indices: 16668099--16668191 Score: 159
Period size: 37 Copynumber: 2.5 Consensus size: 37
16668089 AAATAAAAAA
* *
16668099 AATTCAGGTAATTCGGGTATTTTTCGGTAATTTGGTT
1 AATTCGGGTAATTCGGGTATTTTTCGGTAATTCGGTT
16668136 AATTCGGGTAATTCGGGTATTTTTCGGTAATTCGGTT
1 AATTCGGGTAATTCGGGTATTTTTCGGTAATTCGGTT
*
16668173 AATTTGGGTAATTCGGGTA
1 AATTCGGGTAATTCGGGTA
16668192 ATTCGGGTAA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.22, C:0.09, G:0.27, T:0.43
Consensus pattern (37 bp):
AATTCGGGTAATTCGGGTATTTTTCGGTAATTCGGTT
Found at i:16668917 original size:19 final size:19
Alignment explanation
Indices: 16668871--16668917 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
16668861 CAATTCACAT
16668871 ATTTTAATAATTTTAAAAA
1 ATTTTAATAATTTTAAAAA
* **
16668890 AGTAAAATAA-TTTAAAAA
1 ATTTTAATAATTTTAAAAA
16668908 ACTTTTAATA
1 A-TTTTAATA
16668918 TATATCAATT
Statistics
Matches: 21, Mismatches: 6, Indels: 2
0.72 0.21 0.07
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
ATTTTAATAATTTTAAAAA
Found at i:16669041 original size:21 final size:21
Alignment explanation
Indices: 16669017--16669069 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
16669007 CATTGTTTCT
*
16669017 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
16669038 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
16669059 AATCTCACCGC
1 AATCTCACCGC
16669070 CACCGCTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.38, G:0.09, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Done.