Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008439.1 Hibiscus syriacus cultivar Beakdansim tig00111238_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2703160
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 9
Found at i:1788367 original size:37 final size:36
Alignment explanation
Indices: 1788290--1788426 Score: 129
Period size: 37 Copynumber: 3.8 Consensus size: 36
1788280 GTGCTTGTGG
* * * * *
1788290 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTAT
1 ATCCTATTTTTAGGAGTTTAAATCTTAGCA-AAATTT
*
1788327 ATCCTATTTTTAGGAGTTTGAATCTTAGCAAAATGTT
1 ATCCTATTTTTAGGAGTTTAAATCTTAGCAAAAT-TT
* *
1788364 ATCCTA-TTTTAGGAGTTTGAAT-TCTA--AAATTTT
1 ATCCTATTTTTAGGAGTTTAAATCT-TAGCAAAATTT
* *
1788397 ATCTTATTTTTAAGAGTTTAAATCTTAGCA
1 ATCCTATTTTTAGGAGTTTAAATCTTAGCA
1788427 GGACGAAAAA
Statistics
Matches: 84, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
33 7 0.08
34 20 0.24
35 2 0.02
36 22 0.26
37 33 0.39
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (36 bp):
ATCCTATTTTTAGGAGTTTAAATCTTAGCAAAATTT
Found at i:1788399 original size:33 final size:35
Alignment explanation
Indices: 1788326--1788423 Score: 112
Period size: 36 Copynumber: 2.8 Consensus size: 35
1788316 AGTAGAACTA
1788326 TATCCTATTTTTAGGAGTTTGAATCTTAGCAAAATGT
1 TATCCTATTTTTAGGAGTTTGAATCTTA--AAAATGT
*
1788363 TATCCTA-TTTTAGGAGTTTGAAT-TCT-AAAATTT
1 TATCCTATTTTTAGGAGTTTGAATCT-TAAAAATGT
* * *
1788396 TATCTTATTTTTAAGAGTTTAAATCTTA
1 TATCCTATTTTTAGGAGTTTGAATCTTA
1788424 GCAGGACGAA
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
33 12 0.23
34 15 0.28
35 2 0.04
36 17 0.32
37 7 0.13
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (35 bp):
TATCCTATTTTTAGGAGTTTGAATCTTAAAAATGT
Found at i:1789911 original size:21 final size:21
Alignment explanation
Indices: 1789851--1789922 Score: 108
Period size: 21 Copynumber: 3.4 Consensus size: 21
1789841 AGAAGACAGA
* *
1789851 AGCTCTTTTAATGTCTGCACG
1 AGCTCTTCTAATGTCTGCGCG
*
1789872 AACTCTTCTAATGTCTGCGCG
1 AGCTCTTCTAATGTCTGCGCG
*
1789893 AGCTCTTCTAATGTCTGCGCA
1 AGCTCTTCTAATGTCTGCGCG
1789914 AGCTCTTCT
1 AGCTCTTCT
1789923 TGGTACAAAC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.18, C:0.28, G:0.18, T:0.36
Consensus pattern (21 bp):
AGCTCTTCTAATGTCTGCGCG
Found at i:1790062 original size:15 final size:15
Alignment explanation
Indices: 1790028--1790088 Score: 77
Period size: 15 Copynumber: 4.0 Consensus size: 15
1790018 TAATAAGGTT
*
1790028 ATTTATTTTAAAATTA
1 ATTTATTATAAAA-TA
*
1790044 ATTTATTATAACATA
1 ATTTATTATAAAATA
*
1790059 ATTTATTTTAAAATA
1 ATTTATTATAAAATA
*
1790074 AATTATTATAAAATA
1 ATTTATTATAAAATA
1790089 TGGATTGATT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
15 28 0.72
16 11 0.28
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTTATTATAAAATA
Found at i:1790180 original size:32 final size:32
Alignment explanation
Indices: 1790142--1790354 Score: 137
Period size: 32 Copynumber: 6.7 Consensus size: 32
1790132 TATTTTAAAA
1790142 TATGAATTGATTTATTTTAAATAATTTATTAG
1 TATGAATTGATTTATTTTAAATAATTTATTAG
1790174 TATGAATTGATTTA-TTT---TAA---A--A-
1 TATGAATTGATTTATTTTAAATAATTTATTAG
1790196 TATGAATTGATTTATTTTAAATAATTTATTAG
1 TATGAATTGATTTATTTTAAATAATTTATTAG
* *
1790228 TAT-AGATTGATTTATTTTAAAATATAGATTGATTTAT
1 TATGA-ATTGATTTATTTT--AA-ATA-ATTTA-TTAG
* ** * *
1790265 TATTGTAGTTGTATAGATTGATT-TATTATTATAGTT-G
1 TA-TG-AATTG-ATTTATT--TTAAATAATT-TA-TTAG
* *
1790302 TATGGATTGATTTATTTTAAATAATTTATTAC
1 TATGAATTGATTTATTTTAAATAATTTATTAG
1790334 TATGAATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
1790355 ATATAGATTA
Statistics
Matches: 138, Mismatches: 18, Indels: 50
0.67 0.09 0.24
Matches are distributed among these distances:
22 14 0.10
23 4 0.03
25 1 0.01
26 3 0.02
28 3 0.02
29 1 0.01
31 7 0.05
32 54 0.39
33 5 0.04
34 7 0.05
35 6 0.04
36 6 0.04
37 10 0.07
38 6 0.04
39 3 0.02
40 6 0.04
42 2 0.01
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (32 bp):
TATGAATTGATTTATTTTAAATAATTTATTAG
Found at i:1790188 original size:54 final size:54
Alignment explanation
Indices: 1790076--1790371 Score: 344
Period size: 54 Copynumber: 5.5 Consensus size: 54
1790066 TTAAAATAAA
* * *
1790076 TTATTATAAAATATGGATTGATTTATTTTAAAATAATTTATTAGTTTGAATTGAT
1 TTATTTTAAAATATGAATTGATTTATTTT-AAATAATTTATTAGTATGAATTGAT
1790131 TTATTTTAAAATATGAATTGATTTATTTTAAATAATTTATTAGTATGAATTGAT
1 TTATTTTAAAATATGAATTGATTTATTTTAAATAATTTATTAGTATGAATTGAT
1790185 TTATTTTAAAATATGAATTGATTTATTTTAAATAATTTATTAGTAT-AGATTGAT
1 TTATTTTAAAATATGAATTGATTTATTTTAAATAATTTATTAGTATGA-ATTGAT
*
1790239 TTATTTTAAAATAT-AGATTGATTTA--TT--AT--TGTAGTT-GTAT-AGATTGAT
1 TTATTTTAAAATATGA-ATTGATTTATTTTAAATAATTTA-TTAGTATGA-ATTGAT
** * *
1790287 TTATTATTATAGTTGTATGGATTGATTTATTTTAAATAATTTATTACTATGAATTGAT
1 TTATT-TTA-A--AATATGAATTGATTTATTTTAAATAATTTATTAGTATGAATTGAT
*
1790345 TTATTTTAAAATAT-AGATTAATTTATT
1 TTATTTTAAAATATGA-ATTGATTTATT
1790372 ATTATAGTTG
Statistics
Matches: 211, Mismatches: 13, Indels: 35
0.81 0.05 0.14
Matches are distributed among these distances:
48 20 0.09
49 5 0.02
50 3 0.01
52 14 0.07
53 2 0.01
54 114 0.54
55 27 0.13
56 3 0.01
57 5 0.02
58 17 0.08
59 1 0.00
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.52
Consensus pattern (54 bp):
TTATTTTAAAATATGAATTGATTTATTTTAAATAATTTATTAGTATGAATTGAT
Found at i:1790199 original size:22 final size:22
Alignment explanation
Indices: 1790174--1790216 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1790164 AATTTATTAG
1790174 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
1790196 TATGAATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
1790217 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:1790240 original size:18 final size:18
Alignment explanation
Indices: 1790219--1790266 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
1790209 ATTTTAAATA
*
1790219 ATTTATTAGTATAGATTG
1 ATTTATTAATATAGATTG
1790237 ATTTATTTTAAAATATAGATTG
1 ATTTA--TT--AATATAGATTG
1790259 ATTTATTA
1 ATTTATTA
1790267 TTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATAGATTG
Found at i:1790279 original size:26 final size:26
Alignment explanation
Indices: 1790227--1790397 Score: 119
Period size: 26 Copynumber: 6.7 Consensus size: 26
1790217 TAATTTATTA
*
1790227 GTATAGATTGATTTATT-TTA-A--A
1 GTATAGATTGATTTATTATTATAGTT
* *
1790249 ATATAGATTGATTTATTATTGTAGTT
1 GTATAGATTGATTTATTATTATAGTT
1790275 GTATAGATTGATTTATTATTATAGTT
1 GTATAGATTGATTTATTATTATAGTT
* *
1790301 GTATGGATTGATTTATT-TTAAATAATTT
1 GTATAGATTGATTTATTATT--AT-AGTT
* *
1790329 ATTACTATGAATTGATTTATT-TTA-A--A
1 -GTA-TA-G-ATTGATTTATTATTATAGTT
* *
1790355 ATATAGATTAATTTATTATTATAGTT
1 GTATAGATTGATTTATTATTATAGTT
1790381 GTAT-GAATTGATTTATT
1 GTATAG-ATTGATTTATT
1790398 TTAATAATTT
Statistics
Matches: 118, Mismatches: 15, Indels: 28
0.73 0.09 0.17
Matches are distributed among these distances:
22 26 0.22
23 6 0.05
24 4 0.03
25 5 0.04
26 53 0.45
27 2 0.02
28 4 0.03
29 2 0.02
30 2 0.02
31 1 0.01
32 13 0.11
ACGTcount: A:0.34, C:0.01, G:0.13, T:0.53
Consensus pattern (26 bp):
GTATAGATTGATTTATTATTATAGTT
Found at i:1790343 original size:106 final size:102
Alignment explanation
Indices: 1790076--1790401 Score: 408
Period size: 106 Copynumber: 3.1 Consensus size: 102
1790066 TTAAAATAAA
* *
1790076 TTATTATAAAATATGGATTGATTTATTTTAAAATAATTTATTAGTTTGAATTGATTTATTTTAAA
1 TTATTTTAAAATATGGATTGATTTATTTT-AAATAATTTATTAGTATGAATTGATTTATTTTAAA
*
1790141 ATAT-GAATTGATTTATT-TTAAATAATTTATTAGTATGAATTGAT
65 ATATAG-ATTGATTTATTATT--AT-A---GTT-GTATGAATTGAT
*
1790185 TTATTTTAAAATATGAATTGATTTATTTTAAATAATTTATTAGTAT-AGATTGATTTATTTTAAA
1 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGA-ATTGATTTATTTTAAA
*
1790249 ATATAGATTGATTTATTATTGTAGTTGTAT-AGATTGAT
65 ATATAGATTGATTTATTATTATAGTTGTATGA-ATTGAT
** *
1790287 TTATTATTATAGTTGTATGGATTGATTTATTTTAAATAATTTATTACTATGAATTGATTTATTTT
1 TTATT-TTA-A--AATATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
*
1790352 AAAATATAGATTAATTTATTATTATAGTTGTATGAATTGAT
62 AAAATATAGATTGATTTATTATTATAGTTGTATGAATTGAT
1790393 TTATTTTAA
1 TTATTTTAA
1790402 TAATTTATTA
Statistics
Matches: 196, Mismatches: 11, Indels: 25
0.84 0.05 0.11
Matches are distributed among these distances:
101 1 0.01
102 15 0.08
103 5 0.03
104 2 0.01
105 3 0.02
106 89 0.45
107 4 0.02
108 47 0.24
109 30 0.15
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (102 bp):
TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAA
TATAGATTGATTTATTATTATAGTTGTATGAATTGAT
Found at i:1790465 original size:22 final size:22
Alignment explanation
Indices: 1790417--1790465 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1790407 TATTACTATG
* *
1790417 TATTGATTTATTTTAAATTATA
1 TATTAATTTATTTTAAATAATA
* *
1790439 AATTAATTTATTTTAAATAATT
1 TATTAATTTATTTTAAATAATA
1790461 TATTA
1 TATTA
1790466 TTGTAGTTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
TATTAATTTATTTTAAATAATA
Found at i:1790487 original size:79 final size:79
Alignment explanation
Indices: 1790276--1790450 Score: 215
Period size: 79 Copynumber: 2.2 Consensus size: 79
1790266 ATTGTAGTTG
* * * * * * *
1790276 TATAGATTGATTTATTATTATAGTTGTATGGATTGATTTATTTTAAATAATTTATTACTATGAAT
1 TATAAATTAATTTATTATTATAATTGTATGAATTGAGTTA-TATGAATAATTTATTACTATGAAT
1790341 TGATTTATTTTAAAA
65 TGATTTATTTTAAAA
* * * * * *
1790356 TATAGATTAATTTATTATTATAGTTGTATGAATTGATTTATTTTAATAATTTATTACTATGTATT
1 TATAAATTAATTTATTATTATAATTGTATGAATTGAGTTATATGAATAATTTATTACTATGAATT
*
1790421 GATTTATTTTAAAT
66 GATTTATTTTAAAA
1790435 TATAAATTAATTTATT
1 TATAAATTAATTTATT
1790451 TTAAATAATT
Statistics
Matches: 89, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
79 51 0.57
80 38 0.43
ACGTcount: A:0.35, C:0.01, G:0.09, T:0.54
Consensus pattern (79 bp):
TATAAATTAATTTATTATTATAATTGTATGAATTGAGTTATATGAATAATTTATTACTATGAATT
GATTTATTTTAAAA
Found at i:1794736 original size:73 final size:73
Alignment explanation
Indices: 1794617--1794780 Score: 213
Period size: 73 Copynumber: 2.2 Consensus size: 73
1794607 TCAAAAATAT
* * * * *
1794617 AAAATAGAGGTTACCTACTACATTAAAATATCTATCGGTTTTTTTAAGGTTACTAACAATGTAAA
1 AAAATAGACGCTACCTACTACATTAAAATACCTATCGATTTTTTTAAGATTACTAACAATGTAAA
1794682 CGGTAAAA
66 CGGTAAAA
* * *
1794690 AAAATAGACGCTACCTATTACATTAAACA-ACCTATCGATTTTTTTAAGATTGCTAATAATGTAA
1 AAAATAGACGCTACCTACTACATTAAA-ATACCTATCGATTTTTTTAAGATTACTAACAATGTAA
1794754 ACGGTAAAA
65 ACGGTAAAA
* * *
1794763 AAAACAGGCGTTACCTAC
1 AAAATAGACGCTACCTAC
1794781 CAGTTTTTTT
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
73 77 0.99
74 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.30
Consensus pattern (73 bp):
AAAATAGACGCTACCTACTACATTAAAATACCTATCGATTTTTTTAAGATTACTAACAATGTAAA
CGGTAAAA
Found at i:1794836 original size:58 final size:57
Alignment explanation
Indices: 1794728--1794837 Score: 157
Period size: 57 Copynumber: 1.9 Consensus size: 57
1794718 AACCTATCGA
* *
1794728 TTTTTTTAAGATTGCTAATAATGTAAACGGTAAAAAAAACAGGCGTTACCTACCAGT
1 TTTTTTTAAGATTACTAATAATGTAAACGGTAAAAAAAACAGGCGCTACCTACCAGT
* * * *
1794785 TTTTTTTAAGGTTACTAATAATGTAAATGGTAAAAAAAAATAGGTGCTACCTA
1 TTTTTTTAAGATTACTAATAATGTAAACGGT-AAAAAAAACAGGCGCTACCTA
1794838 TTACATTAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
57 28 0.61
58 18 0.39
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (57 bp):
TTTTTTTAAGATTACTAATAATGTAAACGGTAAAAAAAACAGGCGCTACCTACCAGT
Found at i:1795148 original size:112 final size:111
Alignment explanation
Indices: 1794938--1795280 Score: 499
Period size: 112 Copynumber: 3.1 Consensus size: 111
1794928 TAGCACCTAT
* * * *
1794938 AAAGTATTAATAATTTATAAAAATGTATCGATACGTAACAATATAACAGGTAAAAAATGATAAAA
1 AAAGTATCAATAATTTATAAAAATGTATCGATACATAACAATATAACATGTAAAAAATGACAAAA
* * *
1795003 TCAATTTTATTATGACAAAATCGGTAAAGAGCTATCGGATATGTTA
66 CCAATTTTATTATAACAAAACCGGTAAAGAGCTATCGGATATGTTA
* *
1795049 AAAGTATCAATATTTTTATAAAAATGTATCTATACATAACAATATAACATGTAAAAAATGACAAA
1 AAAGTATCAATA-ATTTATAAAAATGTATCGATACATAACAATATAACATGTAAAAAATGACAAA
* *
1795114 ACCTATTTCATTATAACAAAACCGGTAAAGAGCTATCGGATATGTTA
65 ACCAATTTTATTATAACAAAACCGGTAAAGAGCTATCGGATATGTTA
* * * * *
1795161 CAAGTATCGATACTTTATAAAAAAAGTATCGATAGATAACAATATAACATGTAAAAAATGACAAA
1 AAAGTATCAATAATTTAT-AAAAATGTATCGATACATAACAATATAACATGTAAAAAATGACAAA
*
1795226 ACCAATTTTATTATGAA-AAAACCGGTAAAGAGCTATCGTATATGTTA
65 ACCAATTTTATTAT-AACAAAACCGGTAAAGAGCTATCGGATATGTTA
1795273 AAAGTATC
1 AAAGTATC
1795281 GATAGATAAC
Statistics
Matches: 208, Mismatches: 21, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
111 16 0.08
112 190 0.91
113 2 0.01
ACGTcount: A:0.48, C:0.11, G:0.12, T:0.29
Consensus pattern (111 bp):
AAAGTATCAATAATTTATAAAAATGTATCGATACATAACAATATAACATGTAAAAAATGACAAAA
CCAATTTTATTATAACAAAACCGGTAAAGAGCTATCGGATATGTTA
Found at i:1795287 original size:90 final size:90
Alignment explanation
Indices: 1795182--1795374 Score: 325
Period size: 90 Copynumber: 2.1 Consensus size: 90
1795172 ACTTTATAAA
* *
1795182 AAAAGTATCGATAGATAACAATATAACATGTAAAAAATGACAAAACCAATTTTATTATGAAAAAA
1 AAAAGTATCGATAGATAACAATATAACAGGTAAAAAATGACAAAACCAATTTCATTATGAAAAAA
*
1795247 CCGGTAAAGAGCTATC-GTATATGTT
66 CCGGTAAAGAGCTACCAG-ATATGTT
* *
1795272 AAAAGTATCGATAGATAACAATATAACAGGTAAAAAATGACAAAACCAGTTTCATTATGATAAAA
1 AAAAGTATCGATAGATAACAATATAACAGGTAAAAAATGACAAAACCAATTTCATTATGAAAAAA
1795337 CCGGTAAAGAGCTACCAGATATGTT
66 CCGGTAAAGAGCTACCAGATATGTT
1795362 AAAAGTATCGATA
1 AAAAGTATCGATA
1795375 CTTTATAAAA
Statistics
Matches: 97, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
90 96 0.99
91 1 0.01
ACGTcount: A:0.49, C:0.12, G:0.15, T:0.25
Consensus pattern (90 bp):
AAAAGTATCGATAGATAACAATATAACAGGTAAAAAATGACAAAACCAATTTCATTATGAAAAAA
CCGGTAAAGAGCTACCAGATATGTT
Found at i:1795403 original size:21 final size:20
Alignment explanation
Indices: 1795362--1795403 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1795352 CAGATATGTT
* *
1795362 AAAAGTATCGATACTTTATA
1 AAAAGTATCGATACATAATA
1795382 AAAATGTATCGATACATAATA
1 AAAA-GTATCGATACATAATA
1795403 A
1 A
1795404 TATAATAGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.31
Consensus pattern (20 bp):
AAAAGTATCGATACATAATA
Found at i:1795580 original size:110 final size:109
Alignment explanation
Indices: 1795272--1795719 Score: 604
Period size: 110 Copynumber: 4.1 Consensus size: 109
1795262 CGTATATGTT
* * *
1795272 AAAA-GTATCGATAGATAACAATATAACAGGTAAAAAATGACAAAACCAGTTTCATTATGATAAA
1 AAAATGTATCGATACATAACAATATAACAGGT-AAAAAT-ATAAAACCAGTTTCATTATGACAAA
*
1795336 ACCGGTAAAGAGCTACCAGATATGTTAAAAGTATCGATACTTTATA
64 ACCGGTAAAGAGCTACCGGATATGTTAAAAGTATCGATACTTTATA
* * * *
1795382 AAAATGTATCGATACATAATAATATAATAGGT----A-A-AAAACCAGTTTCATTATGAAAAAAA
1 AAAATGTATCGATACATAACAATATAACAGGTAAAAATATAAAACCAGTTTCATTATGACAAAAC
** * **
1795441 TAGTAAAGAGCTACCGAATATGTTAAAAGTATTAATACTTTATA
66 CGGTAAAGAGCTACCGGATATGTTAAAAGTATCGATACTTTATA
1795485 AAAATGTATCGATACATAACAATATAACAGGTAAAAATTATAAAACCAGTTTCATTATGACAAAA
1 AAAATGTATCGATACATAACAATATAACAGGTAAAAA-TATAAAACCAGTTTCATTATGACAAAA
*
1795550 CCGGTAAATAGCTACCGGATATGTTAAAAGTATCGATACTTTATA
65 CCGGTAAAGAGCTACCGGATATGTTAAAAGTATCGATACTTTATA
* *
1795595 AAAATGTTTCGATACATAATAATATAACAGGTAAAAATATAAAAACCAGTTTCATTATGACAAAA
1 AAAATGTATCGATACATAACAATATAACAGGTAAAAATAT-AAAACCAGTTTCATTATGACAAAA
** * * *
1795660 CCGGTAAAGAATTACTGGATATGTTAAAAGTATCGATACTTTTTG
65 CCGGTAAAGAGCTACCGGATATGTTAAAAGTATCGATACTTTATA
* *
1795705 TACATGTATCGATAC
1 AAAATGTATCGATAC
1795720 TTTATTGAAA
Statistics
Matches: 297, Mismatches: 32, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
103 91 0.31
104 1 0.00
106 1 0.00
107 1 0.00
109 4 0.01
110 175 0.59
111 24 0.08
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.29
Consensus pattern (109 bp):
AAAATGTATCGATACATAACAATATAACAGGTAAAAATATAAAACCAGTTTCATTATGACAAAAC
CGGTAAAGAGCTACCGGATATGTTAAAAGTATCGATACTTTATA
Found at i:1795734 original size:21 final size:21
Alignment explanation
Indices: 1795684--1795734 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1795674 CTGGATATGT
*
1795684 TAAAAGTATCGATACTTTTTG
1 TAAAGGTATCGATACTTTTTG
* *
1795705 TACATGTATCGATACTTTATTG
1 TAAAGGTATCGATACTTT-TTG
1795727 -AAAGGTAT
1 TAAAGGTAT
1795735 GTAATTTATG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (21 bp):
TAAAGGTATCGATACTTTTTG
Found at i:1797454 original size:10 final size:10
Alignment explanation
Indices: 1797441--1797485 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
1797431 CTTTTTTTAA
1797441 ATTAAAATAT
1 ATTAAAATAT
1797451 ATT-AAAT-T
1 ATTAAAATAT
*
1797459 A-TAAAATAG
1 ATTAAAATAT
*
1797468 ATAAAAATAT
1 ATTAAAATAT
1797478 ATTAAAAT
1 ATTAAAAT
1797486 TAGATAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
7 1 0.04
8 6 0.21
9 5 0.18
10 16 0.57
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:1797521 original size:21 final size:21
Alignment explanation
Indices: 1797504--1797543 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1797494 TAATTTTACT
1797504 AATTTTTTTGTA-ATTTTTCGG
1 AATTTTTTT-TATATTTTTCGG
1797525 AATTTTTTTTATATTTTTC
1 AATTTTTTTTATATTTTTC
1797544 TGCTTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.20, C:0.05, G:0.07, T:0.68
Consensus pattern (21 bp):
AATTTTTTTTATATTTTTCGG
Found at i:1798979 original size:98 final size:98
Alignment explanation
Indices: 1798810--1798989 Score: 315
Period size: 98 Copynumber: 1.8 Consensus size: 98
1798800 GGTCGTGGTT
* *
1798810 TTGGGCGTTGACGCCAACATTTCAGGTTCATCTTTAGAAAATCAAAAAGGAATGAGCCAGCTTCA
1 TTGGGCCTTGACGCCAACATTTCAGGTTCATCTTTAGAAAACCAAAAAGGAATGAGCCAGCTTCA
1798875 GCATGTATACGATGCTTGAACCTTCGGCCGATA
66 GCATGTATACGATGCTTGAACCTTCGGCCGATA
* * *
1798908 TTGGGCCTTGATGCCAACATTTCAGGTTCATCTTTATAAAACCAAAATGGAATGAGCCAGCTTCA
1 TTGGGCCTTGACGCCAACATTTCAGGTTCATCTTTAGAAAACCAAAAAGGAATGAGCCAGCTTCA
1798973 GCATGTATACGATGCTT
66 GCATGTATACGATGCTT
1798990 TCACCAAGTT
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 77 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.28
Consensus pattern (98 bp):
TTGGGCCTTGACGCCAACATTTCAGGTTCATCTTTAGAAAACCAAAAAGGAATGAGCCAGCTTCA
GCATGTATACGATGCTTGAACCTTCGGCCGATA
Found at i:1809540 original size:17 final size:17
Alignment explanation
Indices: 1809520--1809556 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1809510 TAAAACAAAG
*
1809520 AAATTAATAATAATAAT
1 AAATAAATAATAATAAT
*
1809537 AAATAAATTATAATAAT
1 AAATAAATAATAATAAT
1809554 AAA
1 AAA
1809557 AATATAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAATAAATAATAATAAT
Found at i:1809568 original size:20 final size:20
Alignment explanation
Indices: 1809526--1809569 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1809516 AAAGAAATTA
*
1809526 ATAATAATAATAAATAAATT
1 ATAATAATAATAAATAAAAT
1809546 ATAATAATAA-AAATATAAAT
1 ATAATAATAATAAATA-AAAT
1809566 ATAA
1 ATAA
1809570 AACCCGGTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
ATAATAATAATAAATAAAAT
Found at i:1815552 original size:4 final size:4
Alignment explanation
Indices: 1815526--1815600 Score: 62
Period size: 4 Copynumber: 17.8 Consensus size: 4
1815516 AAGCTAATAC
** *
1815526 ATGT ATGT AACT ATAT ATG- ATGT ATGT ATGT ATGT ATGT ATGT ATTGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A-TGT
*
1815574 ATAAGCT GATAT ATGT ATGT ATGT ATG
1 AT--G-T -ATGT ATGT ATGT ATGT ATG
1815601 CACCACATTT
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
3 3 0.05
4 46 0.79
5 5 0.09
6 1 0.02
7 1 0.02
8 2 0.03
ACGTcount: A:0.31, C:0.03, G:0.21, T:0.45
Consensus pattern (4 bp):
ATGT
Found at i:1817777 original size:29 final size:28
Alignment explanation
Indices: 1817731--1817854 Score: 106
Period size: 29 Copynumber: 4.2 Consensus size: 28
1817721 CAGTTATTTT
1817731 AATATATTTTTAAAATTTAAGATAATAATAA
1 AATATATTTTT--AATTTAA-ATAATAATAA
* *
1817762 AATATATTTTTAATTTGAAATAAGAATGA
1 AATATATTTTTAATTT-AAATAATAATAA
* *
1817791 AATATATTTTTAAGTGAAGATAATAAT-A
1 AATATATTTTTAATTTAA-ATAATAATAA
* * *
1817819 TATATATATATATATATTAAATCAATAATAA
1 AATATATTTTTA-AT-TTAAAT-AATAATAA
1817850 AATAT
1 AATAT
1817855 TTAAATATAT
Statistics
Matches: 76, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
28 12 0.16
29 37 0.49
30 11 0.14
31 16 0.21
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.41
Consensus pattern (28 bp):
AATATATTTTTAATTTAAATAATAATAA
Found at i:1819206 original size:17 final size:17
Alignment explanation
Indices: 1819184--1819217 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1819174 TCAACCGTTG
1819184 TGCTTAGAATTTATCGT
1 TGCTTAGAATTTATCGT
1819201 TGCTTAGAATTTATCGT
1 TGCTTAGAATTTATCGT
1819218 CGTTTTATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.47
Consensus pattern (17 bp):
TGCTTAGAATTTATCGT
Found at i:1837858 original size:31 final size:31
Alignment explanation
Indices: 1837820--1837938 Score: 98
Period size: 31 Copynumber: 3.6 Consensus size: 31
1837810 AAACTACCTA
1837820 TTTGGTCACTTATATATTATCTAATTTATGT
1 TTTGGTCACTTATATATTATCTAATTTATGT
* * * **
1837851 TTTGGTCACTCGAT-TATTATTTAGGATAAACTACCT
1 TTTGGTCACT-TATATATTATCTA--AT---TTATGT
1837887 ATTTGGTCACTTATATATTATCTAATTTATGT
1 -TTTGGTCACTTATATATTATCTAATTTATGT
*
1837919 TTTGCTCAC-TATATTATTAT
1 TTTGGTCACTTATA-TATTAT
1837939 TTAGGGTAAA
Statistics
Matches: 68, Mismatches: 11, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
30 4 0.06
31 32 0.47
32 5 0.07
33 2 0.03
35 2 0.03
36 5 0.07
37 18 0.26
ACGTcount: A:0.27, C:0.13, G:0.10, T:0.50
Consensus pattern (31 bp):
TTTGGTCACTTATATATTATCTAATTTATGT
Found at i:1837883 original size:68 final size:68
Alignment explanation
Indices: 1837802--1838075 Score: 451
Period size: 68 Copynumber: 4.0 Consensus size: 68
1837792 TAGGGATTTT
1837802 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
1837867 TTA
66 TTA
* * **
1837870 TTTAGGATAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGCTCACTATATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
1837935 TTA
66 TTA
* * *
1837938 TTTAGGGTAAACTACCCATTTAGTCACTTATATATTATCTAATTTATATTTTGGTCACTCGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
1838003 TTA
66 TTA
* * *
1838006 TTTAGGGTAAACTACCTATTTGGTCACTTGTATATTATCTAATTTATG-TTTGGTCTCTTGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
1838070 TTA
66 TTA
1838073 TTT
1 TTT
1838076 TTTTCAAAAT
Statistics
Matches: 189, Mismatches: 17, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
67 20 0.11
68 169 0.89
ACGTcount: A:0.27, C:0.13, G:0.12, T:0.48
Consensus pattern (68 bp):
TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
TTA
Found at i:1839676 original size:43 final size:43
Alignment explanation
Indices: 1839628--1839749 Score: 217
Period size: 43 Copynumber: 2.8 Consensus size: 43
1839618 ATGCTCAAAG
1839628 ATCTGAATATATAAATTATATTTTAAAAGTTAAAATAAGATTA
1 ATCTGAATATATAAATTATATTTTAAAAGTTAAAATAAGATTA
*
1839671 ATCTGAATACATAAATTATATTTTAAAAGTTAAAATAAGATTA
1 ATCTGAATATATAAATTATATTTTAAAAGTTAAAATAAGATTA
**
1839714 ATCTCTATATATAAATTATATTTTAAAAGTTAAAAT
1 ATCTGAATATATAAATTATATTTTAAAAGTTAAAAT
1839750 TACACAAAAA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 75 1.00
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.40
Consensus pattern (43 bp):
ATCTGAATATATAAATTATATTTTAAAAGTTAAAATAAGATTA
Found at i:1848140 original size:20 final size:21
Alignment explanation
Indices: 1848076--1848141 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 21
1848066 GTACATTTTT
* *
1848076 TTTAATTTTAGATTCTCATATAA
1 TTTAATTTT-TATTCTC-TAAAA
*
1848099 TTTAATTTTT-TTAT-TAATAA
1 TTTAATTTTTATTCTCTAA-AA
1848119 TTT-ATTTTTATTCTCTAAAA
1 TTTAATTTTTATTCTCTAAAA
1848139 TTT
1 TTT
1848142 TATAAATTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
19 8 0.22
20 13 0.36
21 6 0.17
23 9 0.25
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.61
Consensus pattern (21 bp):
TTTAATTTTTATTCTCTAAAA
Found at i:1851225 original size:16 final size:17
Alignment explanation
Indices: 1851197--1851228 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1851187 GAATTTATAA
1851197 TTAAATAAAATAAATAT
1 TTAAATAAAATAAATAT
1851214 TTAAAT-AAATAAATA
1 TTAAATAAAATAAATA
1851229 AAAGAACTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TTAAATAAAATAAATAT
Found at i:1861108 original size:185 final size:184
Alignment explanation
Indices: 1860868--1861255 Score: 620
Period size: 185 Copynumber: 2.1 Consensus size: 184
1860858 ATTTCTAATT
* * * *
1860868 TATATAA-AAATTAAATA-TTTTTAATTCAAAAAAAGTGTATAATTAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTTAATTAAAAAAAAGTGTACAATTAATTTAAATAATATATAAT
1860931 TATAAAAT-AAAAATTCCAGATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTAT
66 TATAAAATAAAAAATT-CAGATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTAT
* *
1860995 TGGATCTTAAATTATTAATTGAGTTTTAAATTGTTTGGGCTTAGCCCAAATGTTA
130 TGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCAAATGTTA
*
1861050 TATATAATATATTTAATATTTTTTAATTAAAAAAACAGTTTACAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTAAAAAAA-AGTGTACAATTAATTTAAATAATATATAA
* * * *
1861115 TTATAAAATAAAAAATTTATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
65 TTATAAAATAAAAAATTCAGATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTAT
* *
1861180 TGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
130 TGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCAAATGTTA
1861235 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
1861256 AAAATTTAAT
Statistics
Matches: 189, Mismatches: 13, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
182 7 0.04
183 8 0.04
184 15 0.08
185 152 0.80
186 7 0.04
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.45
Consensus pattern (184 bp):
TATATAATATATTTAATATTTTTTAATTAAAAAAAAGTGTACAATTAATTTAAATAATATATAAT
TATAAAATAAAAAATTCAGATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATT
GGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCAAATGTTA
Found at i:1871454 original size:3 final size:3
Alignment explanation
Indices: 1871446--1871472 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1871436 CTCCATTAAT
1871446 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1871473 AGCACCGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:1875394 original size:30 final size:30
Alignment explanation
Indices: 1875358--1875417 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
1875348 CTTGAAGCAT
1875358 TGGTGCTTGAATAATTTGTTTCGATATTTC
1 TGGTGCTTGAATAATTTGTTTCGATATTTC
1875388 TGGTGCTTGAATAATTTGTTTCGATATTTC
1 TGGTGCTTGAATAATTTGTTTCGATATTTC
1875418 CAGCAGAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.20, C:0.10, G:0.20, T:0.50
Consensus pattern (30 bp):
TGGTGCTTGAATAATTTGTTTCGATATTTC
Found at i:1876110 original size:24 final size:23
Alignment explanation
Indices: 1876081--1876136 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 23
1876071 AGGATCAAAT
1876081 TTATAAAATTTTAAAAGAATAAAA
1 TTATAAAATTTTAAAAGAA-AAAA
*
1876105 TTATAAAATTTTAAGAGAAAAAA
1 TTATAAAATTTTAAAAGAAAAAA
1876128 TTAGTAAAA
1 TTA-TAAAA
1876137 GATATAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 7 0.23
24 23 0.77
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (23 bp):
TTATAAAATTTTAAAAGAAAAAA
Found at i:1882132 original size:111 final size:111
Alignment explanation
Indices: 1881566--1882121 Score: 686
Period size: 114 Copynumber: 5.0 Consensus size: 111
1881556 AGAGGGGCTT
* *
1881566 CTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGAGTTGTGCCTTGAGCATAGGACTGCTCATATC
1 CTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACTTGTGCCTTGAGCATATGACTGCTCATATC
* * *
1881631 GAGGTGATCCTATGTTTGATACAGTTCCATTTGCATGAAAATTATGCGG
66 GAGGTGATCCCATGTTTGATACAGTTCCATTCGCATGAAAA-T-T-CTG
* * * * * *
1881680 CTGCTGCTGAACCAGCTGGCCACTCCAGGCAGGACTTGTGCCTTGATCACATGTCTGCCCATAGC
1 CTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACTTGTGCCTTGAGCATATGACTGCTCATATC
*
1881745 GAGGTGATCCCATGTTTGATACAGTTCCATT-GACATGAATATTCTG
66 GAGGTGATCCCATGTTTGATACAGTTCCATTCG-CATGAAAATTCTG
* * * *
1881791 CGGGTGCTGCTGAACCAGCTGGCCACTCCAGGCAGGACTTGTGCCTTGAGAACATGTCTGCTCAT
1 C---TGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACTTGTGCCTTGAGCATATGACTGCTCAT
* * * *
1881856 AGCGAGGCGATCCCATGTTTAATACAGTTCCATTTGCATGAAAATTCTG
63 ATCGAGGTGATCCCATGTTTGATACAGTTCCATTCGCATGAAAATTCTG
* * * *
1881905 CTGCTGCTGAACCATCTGTCCATTCCAGGAAGGACCTGTGCCTTGAGCATATGACTGCTCATATC
1 CTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACTTGTGCCTTGAGCATATGACTGCTCATATC
* * *
1881970 CAGGTGATCCCATGTTTGGTACGGTTCCATTCGCA-GAAAAATTCTG
66 GAGGTGATCCCATGTTTGATACAGTTCCATTCGCATG-AAAATTCTG
* * * * *
1882016 CTGTTGCTGAACC-GTCTGTCCATTCCAGGCAGGACCTGTACCTTGAGCATATGACTGCTCAAAT
1 CTGCTGCTGAACCAG-CTGGCCATTCCAGGCAGGACTTGTGCCTTGAGCATATGACTGCTCATAT
** * *
1882080 CGAGGCAATCCCGTGTTTGGTACAGTTCCATTCGCATGAAAA
65 CGAGGTGATCCCATGTTTGATACAGTTCCATTCGCATGAAAA
1882122 CTTTGTTGTT
Statistics
Matches: 392, Mismatches: 42, Indels: 19
0.87 0.09 0.04
Matches are distributed among these distances:
110 1 0.00
111 189 0.48
112 2 0.01
113 2 0.01
114 197 0.50
115 1 0.00
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.28
Consensus pattern (111 bp):
CTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACTTGTGCCTTGAGCATATGACTGCTCATATC
GAGGTGATCCCATGTTTGATACAGTTCCATTCGCATGAAAATTCTG
Found at i:1883527 original size:123 final size:123
Alignment explanation
Indices: 1883308--1883529 Score: 302
Period size: 123 Copynumber: 1.8 Consensus size: 123
1883298 GTAAGAGCTA
* * **
1883308 GAAAAACATGAAGTTTAAATTCAAAAACTAGCTCACATACTGATGGATTCGAGAATTTACAACCA
1 GAAAAACATGAAGCTTAAACTCAAAAACTAGCTCACATACTGACAGATTCGAGAATTTACAACCA
* *
1883373 AATCATTACAAAAATGTCAGCTATATCAAGACTTGAGTAGCCACTTTAAATAGAGATG
66 AATCATGACAAAAATGCCAGCTATATCAAGACTTGAGTAGCCACTTTAAATAGAGATG
* * * * * *
1883431 GAAAAACATGAAGCTTACACTGAAAAATTGGCTCACATACTGACAGATTTGAGCATTTACAACCA
1 GAAAAACATGAAGCTTAAACTCAAAAACTAGCTCACATACTGACAGATTCGAGAATTTACAACCA
* *
1883496 AATTC-TGACACAAATGCCAGTTATATCAAGACTT
66 AA-TCATGACAAAAATGCCAGCTATATCAAGACTT
1883530 CAGTGGTCAC
Statistics
Matches: 84, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
123 82 0.98
124 2 0.02
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (123 bp):
GAAAAACATGAAGCTTAAACTCAAAAACTAGCTCACATACTGACAGATTCGAGAATTTACAACCA
AATCATGACAAAAATGCCAGCTATATCAAGACTTGAGTAGCCACTTTAAATAGAGATG
Found at i:1887309 original size:117 final size:119
Alignment explanation
Indices: 1887099--1887333 Score: 411
Period size: 117 Copynumber: 2.0 Consensus size: 119
1887089 ATTTACGAAA
* *
1887099 ATAATATTTATTTTTATAATTAAAATAAAAATATATTTCGTCAATAGCTAACAGATACTTTTAAT
1 ATAATATTTATTTTTATAATTAAAATAAAAATATATTTCGTCAACAGCTAACAGATACATTTAAT
1887164 ATAATATACTTTTATTTTATGTAATATTTTAATATATATATA-A-ATTATTAGC
66 ATAATATACTTTTATTTTATGTAATATTTTAATATATATATATATATTATTAGC
* *
1887216 ATAATATTTATTTTTATAATTAAAATAAATATATATTTCGTCAACAGTTAACAGATACATTTAAT
1 ATAATATTTATTTTTATAATTAAAATAAAAATATATTTCGTCAACAGCTAACAGATACATTTAAT
*
1887281 ATAATATACTTTTATTTTATGTATTATTTTAATATATATATATATATTATTAG
66 ATAATATACTTTTATTTTATGTAATATTTTAATATATATATATATATTATTAG
1887334 TTGAAATGAA
Statistics
Matches: 111, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
117 102 0.92
118 1 0.01
119 8 0.07
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (119 bp):
ATAATATTTATTTTTATAATTAAAATAAAAATATATTTCGTCAACAGCTAACAGATACATTTAAT
ATAATATACTTTTATTTTATGTAATATTTTAATATATATATATATATTATTAGC
Found at i:1887684 original size:25 final size:25
Alignment explanation
Indices: 1887650--1887697 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
1887640 AAATATTATA
1887650 ATTTAGAAAAATAATAGATAATATT
1 ATTTAGAAAAATAATAGATAATATT
* *
1887675 ATTTTGAAAAATAATATATAATA
1 ATTTAGAAAAATAATAGATAATA
1887698 ATCTTTAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (25 bp):
ATTTAGAAAAATAATAGATAATATT
Found at i:1891830 original size:13 final size:13
Alignment explanation
Indices: 1891812--1891836 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1891802 GACAATGAAA
1891812 TATTACATGAAGT
1 TATTACATGAAGT
1891825 TATTACATGAAG
1 TATTACATGAAG
1891837 CAGAAAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (13 bp):
TATTACATGAAGT
Found at i:1893164 original size:14 final size:14
Alignment explanation
Indices: 1893142--1893198 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 14
1893132 CGTTCATGAA
*
1893142 CGTTCGGTTATGTT
1 CGTTTGGTTATGTT
1893156 CGTTTGGTTATGTT
1 CGTTTGGTTATGTT
1893170 CG--T--TTATGTT
1 CGTTTGGTTATGTT
* *
1893180 CGTTCGATTATGTT
1 CGTTTGGTTATGTT
1893194 CGTTT
1 CGTTT
1893199 ATATTCATTC
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 9 0.25
12 1 0.03
14 26 0.72
ACGTcount: A:0.09, C:0.12, G:0.25, T:0.54
Consensus pattern (14 bp):
CGTTTGGTTATGTT
Found at i:1893170 original size:24 final size:24
Alignment explanation
Indices: 1893143--1893217 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
1893133 GTTCATGAAC
* * *
1893143 GTTCGGTTATGTTCGTTTGGTTAT
1 GTTCGTTTATGTTCGTTCGATTAT
1893167 GTTCGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTCGATTAT
* *
1893191 GTTCGTTTATATTCATTC-ATTTAT
1 GTTCGTTTATGTTCGTTCGA-TTAT
1893215 GTT
1 GTT
1893218 TAACCCAATC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
23 1 0.02
24 44 0.98
ACGTcount: A:0.13, C:0.11, G:0.20, T:0.56
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGATTAT
Found at i:1893301 original size:14 final size:14
Alignment explanation
Indices: 1893262--1893307 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
1893252 ATTTATAAGT
*
1893262 ATCTTCTTAAACCA
1 ATCTTCTTAAATCA
1893276 ATCTTCTTAAATCA
1 ATCTTCTTAAATCA
*
1893290 ATCTTCTTAAATTA
1 ATCTTCTTAAATCA
1893304 ATCT
1 ATCT
1893308 GATATTCTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.35, C:0.22, G:0.00, T:0.43
Consensus pattern (14 bp):
ATCTTCTTAAATCA
Found at i:1893993 original size:16 final size:16
Alignment explanation
Indices: 1893972--1894038 Score: 93
Period size: 16 Copynumber: 4.3 Consensus size: 16
1893962 GTCTCCAACG
*
1893972 TTTATGTTCGTATTCA
1 TTTATGTTCGTGTTCA
*
1893988 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
*
1894004 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
1894020 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
1894034 TTTAT
1 TTTAT
1894039 TAAATGAACG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
14 5 0.10
15 2 0.04
16 41 0.85
ACGTcount: A:0.12, C:0.10, G:0.18, T:0.60
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:1894011 original size:32 final size:32
Alignment explanation
Indices: 1893970--1894030 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
1893960 GGGTCTCCAA
1893970 CGTTTATGTTCGTATTCATTTATGTTCGTGTT
1 CGTTTATGTTCGTATTCATTTATGTTCGTGTT
* *
1894002 CGTTTATGTTCGTGTTCGTTTATGTTCGT
1 CGTTTATGTTCGTATTCATTTATGTTCGT
1894031 TTATTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.10, C:0.13, G:0.21, T:0.56
Consensus pattern (32 bp):
CGTTTATGTTCGTATTCATTTATGTTCGTGTT
Found at i:1894121 original size:16 final size:16
Alignment explanation
Indices: 1894100--1894132 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1894090 AAAAAAATTT
1894100 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1894116 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1894132 T
1 T
1894133 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1905650 original size:13 final size:13
Alignment explanation
Indices: 1905632--1905663 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
1905622 CAATTCCTTA
1905632 TTTTTATCTCATT
1 TTTTTATCTCATT
1905645 TTTTTATCTCATT
1 TTTTTATCTCATT
1905658 TCTTTT
1 T-TTTT
1905664 TTTTAGCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTATCTCATT
Found at i:1910100 original size:7 final size:7
Alignment explanation
Indices: 1910088--1910119 Score: 50
Period size: 6 Copynumber: 4.9 Consensus size: 7
1910078 TTCACTTAAT
1910088 TTATTTA
1 TTATTTA
1910095 TTATTTA
1 TTATTTA
1910102 TTA-TTA
1 TTATTTA
1910108 TTA-TTA
1 TTATTTA
1910114 TTATTT
1 TTATTT
1910120 TTTCATCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 12 0.50
7 12 0.50
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTATTTA
Found at i:1911002 original size:31 final size:28
Alignment explanation
Indices: 1910956--1911015 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 28
1910946 GCAAACTATA
1910956 CGTTTAGTACCTAAATTATCAGTTTTATTT
1 CGTTTAGTACCTAAATTATCA--TTTATTT
* *
1910986 CGTTTAAGTACTTAAATTTTCATTTATTT
1 CGTTT-AGTACCTAAATTATCATTTATTT
1911015 C
1 C
1911016 AAAATCATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 8 0.30
30 5 0.19
31 14 0.52
ACGTcount: A:0.27, C:0.13, G:0.08, T:0.52
Consensus pattern (28 bp):
CGTTTAGTACCTAAATTATCATTTATTT
Found at i:1911356 original size:32 final size:33
Alignment explanation
Indices: 1911272--1911359 Score: 92
Period size: 32 Copynumber: 2.7 Consensus size: 33
1911262 TATTAGTATA
1911272 TAATTACAATAAAAAATTAAATTTGAAAGTTAGAG
1 TAATTA-AATAAAAAATT-AATTTGAAAGTTAGAG
** *
1911307 TAATTAAACT--AGGATTAATTTGAATGTTA-AG
1 TAATTAAA-TAAAAAATTAATTTGAAAGTTAGAG
*
1911338 TGATTAAATAAAAAATTAATTT
1 TAATTAAATAAAAAATTAATTT
1911360 TTAGCGAACA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
30 1 0.02
31 9 0.20
32 21 0.48
33 4 0.09
34 2 0.05
35 7 0.16
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.36
Consensus pattern (33 bp):
TAATTAAATAAAAAATTAATTTGAAAGTTAGAG
Found at i:1916773 original size:59 final size:58
Alignment explanation
Indices: 1916617--1916778 Score: 155
Period size: 59 Copynumber: 2.7 Consensus size: 58
1916607 ATCATAATCT
* * *
1916617 TCAAATTATGACTCTCATTTTAAATTAGTACTTAAATTTTTTAAATATTTCAATTTCATCC
1 TCAAATTATGAC-CTCATTCTAAATTAGT-CTTAAA-CTTTTAAATATTTCAATTTCATCA
* * * * * * * *
1916678 CCAAACTACGACTTTCATTCTAATTTAGTTATTAAACTTTTGAATATTTCAATTTTAT-A
1 TCAAATTATGAC-CTCATTCTAAATTAG-TCTTAAACTTTTAAATATTTCAATTTCATCA
1916737 TCAAATTATGACCGTCATTCTAAATTAGTCTCTAAACTTTTA
1 TCAAATTATGACC-TCATTCTAAATTAGTCT-TAAACTTTTA
1916779 CACATTCTAA
Statistics
Matches: 80, Mismatches: 18, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
58 2 0.03
59 31 0.39
60 19 0.24
61 27 0.34
62 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.05, T:0.45
Consensus pattern (58 bp):
TCAAATTATGACCTCATTCTAAATTAGTCTTAAACTTTTAAATATTTCAATTTCATCA
Found at i:1917190 original size:18 final size:18
Alignment explanation
Indices: 1917167--1917204 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1917157 GGGTATAGAG
*
1917167 TATATGAGTTATTCAAAT
1 TATATGAATTATTCAAAT
*
1917185 TATATGAATTATTCTAAT
1 TATATGAATTATTCAAAT
1917203 TA
1 TA
1917205 AATTTAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.47
Consensus pattern (18 bp):
TATATGAATTATTCAAAT
Found at i:1923193 original size:18 final size:19
Alignment explanation
Indices: 1923155--1923196 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
1923145 GATCCGCCAC
*
1923155 TAAATAATATTTTAAAATT
1 TAAATAATATTCTAAAATT
*
1923174 TAAATAATA-TCTATAATT
1 TAAATAATATTCTAAAATT
1923192 TAAAT
1 TAAAT
1923197 CTTGATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
TAAATAATATTCTAAAATT
Found at i:1927125 original size:21 final size:21
Alignment explanation
Indices: 1927095--1927141 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
1927085 TGATTTATTA
* *
1927095 TTATGGATTTTAAGTTTGTTG
1 TTATGAATTTCAAGTTTGTTG
1927116 TTATGAATTTCAAGTTTGTTG
1 TTATGAATTTCAAGTTTGTTG
1927137 TTATG
1 TTATG
1927142 GAAGTCAAGT
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:0.21, C:0.02, G:0.21, T:0.55
Consensus pattern (21 bp):
TTATGAATTTCAAGTTTGTTG
Found at i:1927149 original size:21 final size:21
Alignment explanation
Indices: 1927106--1927153 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1927096 TATGGATTTT
*
1927106 AAGTTTGTTGTTATGAATTTC
1 AAGTTTGTTGTTATGAATGTC
1927127 AAGTTTGTTGTTATGGAA-GTC
1 AAGTTTGTTGTTAT-GAATGTC
1927148 AAGTTT
1 AAGTTT
1927154 ATTGGATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.25, C:0.04, G:0.23, T:0.48
Consensus pattern (21 bp):
AAGTTTGTTGTTATGAATGTC
Found at i:1927681 original size:18 final size:17
Alignment explanation
Indices: 1927647--1927679 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1927637 ATCTAACTAA
*
1927647 AGCTAAAATTGAATTTT
1 AGCTAAAAATGAATTTT
1927664 AGCTAAAAATG-ATTTT
1 AGCTAAAAATGAATTTT
1927680 TTTTATATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.39
Consensus pattern (17 bp):
AGCTAAAAATGAATTTT
Found at i:1930778 original size:23 final size:24
Alignment explanation
Indices: 1930742--1930795 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
1930732 GTTATTTGTT
* * *
1930742 AACATATCCTTTTA-ATGTTCATG
1 AACATGTCCATTTATATGTTCACG
1930765 AACATGTCCATTTATATGTTCACG
1 AACATGTCCATTTATATGTTCACG
1930789 AACATGT
1 AACATGT
1930796 TCGTTTAACG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 12 0.44
24 15 0.56
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (24 bp):
AACATGTCCATTTATATGTTCACG
Found at i:1934588 original size:66 final size:66
Alignment explanation
Indices: 1934507--1934711 Score: 347
Period size: 66 Copynumber: 3.1 Consensus size: 66
1934497 ACTTCCGTGG
*
1934507 ACGTCGGAAAGGGCGGAGTTGGAGTGAACACCGGGAAAGGAAAGCCAGGGGGTGGCACCCATGTA
1 ACGTCGGAAAGGGCGGAGTTGGAGTGAACACCGGGAAAGGAAAGCCAGGGGGTGGCACCCATGTG
1934572 A
66 A
1934573 ACGTCGGAAAGGGCGGAGTTGGAGTGAACACCGGGAAAGGAAAGCCAGGGGGTGGCACCCATGTG
1 ACGTCGGAAAGGGCGGAGTTGGAGTGAACACCGGGAAAGGAAAGCCAGGGGGTGGCACCCATGTG
1934638 A
66 A
* * * * *
1934639 ACGTTGGAAAGGGCGGAATTGGAGTGAACACCGGGAAAGGAAAGCGAGGAGGTGGCACTCATGTG
1 ACGTCGGAAAGGGCGGAGTTGGAGTGAACACCGGGAAAGGAAAGCCAGGGGGTGGCACCCATGTG
1934704 A
66 A
*
1934705 GCGTCGG
1 ACGTCGG
1934712 CGGCAAAGGT
Statistics
Matches: 131, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 131 1.00
ACGTcount: A:0.29, C:0.17, G:0.42, T:0.12
Consensus pattern (66 bp):
ACGTCGGAAAGGGCGGAGTTGGAGTGAACACCGGGAAAGGAAAGCCAGGGGGTGGCACCCATGTG
A
Found at i:1936099 original size:18 final size:19
Alignment explanation
Indices: 1936076--1936118 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
1936066 CAGTAATCAT
*
1936076 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGATAATCTTAC
*
1936094 ATTCCCACTGATAATCTTAT
1 ATT-CCACTGATAATCTTAC
1936114 ATTCC
1 ATTCC
1936119 GTGAACCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 3 0.14
19 4 0.19
20 14 0.67
ACGTcount: A:0.26, C:0.28, G:0.07, T:0.40
Consensus pattern (19 bp):
ATTCCACTGATAATCTTAC
Found at i:1947938 original size:69 final size:68
Alignment explanation
Indices: 1947805--1947943 Score: 269
Period size: 69 Copynumber: 2.0 Consensus size: 68
1947795 ATATGAAAAT
1947805 ATGAGAAAGAAGGATGAGAGTTTATGCTTTATTTGTATTTGGTATCTGTCTTTATAAGCTTATCC
1 ATGAGAAAGAAGGATGAGAGTTTATGCTTTATTTGTATTTGGTATCTGTCTTTATAAGCTTATCC
1947870 CAA
66 CAA
1947873 ATGAGAAAGAAGGATGAGAGTTTATGCTTTATTTTGTATTTGGTATCTGTCTTTATAAGCTTATC
1 ATGAGAAAGAAGGATGAGAGTTTATGCTTTA-TTTGTATTTGGTATCTGTCTTTATAAGCTTATC
1947938 CCAA
65 CCAA
1947942 AT
1 AT
1947944 TGCTTGTGTT
Statistics
Matches: 70, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
68 31 0.44
69 39 0.56
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.40
Consensus pattern (68 bp):
ATGAGAAAGAAGGATGAGAGTTTATGCTTTATTTGTATTTGGTATCTGTCTTTATAAGCTTATCC
CAA
Found at i:1950026 original size:2 final size:2
Alignment explanation
Indices: 1950021--1950074 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
1950011 TTCATGTGTG
1950021 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1950063 TA TA TA AA TA TA
1 TA TA TA TA TA TA
1950075 AAACGGGTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1950164 original size:31 final size:33
Alignment explanation
Indices: 1950129--1950201 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 33
1950119 TAAAACGATT
*
1950129 ATTAAATTTAT-CGAG-CTGATATAAAATGGT-G
1 ATTAAATTTATACCAGACTGATATAAAA-GGTCG
*
1950160 ATTAAATTT-TACCAGACTGTTATAAAAGGTCG
1 ATTAAATTTATACCAGACTGATATAAAAGGTCG
1950192 -TTAAATTTAT
1 ATTAAATTTAT
1950202 TAATATTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
30 1 0.03
31 23 0.64
32 12 0.33
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (33 bp):
ATTAAATTTATACCAGACTGATATAAAAGGTCG
Found at i:1955744 original size:41 final size:40
Alignment explanation
Indices: 1955699--1955802 Score: 117
Period size: 41 Copynumber: 2.6 Consensus size: 40
1955689 TACTTTGCGA
1955699 CGTTTCTACGAAAACGCCACTAAAGTACG-AGTCTATAGCGG
1 CGTTTCTACG-AAACGCCACTAAAGTA-GAAGTCTATAGCGG
* *
1955740 CGTTTTTATACG-AACGCAACTAAAGTAGAAGTCTATAGCGG
1 CG--TTTCTACGAAACGCCACTAAAGTAGAAGTCTATAGCGG
1955781 CG-TTCATAC-AAACGCCACTAAA
1 CGTTTC-TACGAAACGCCACTAAA
1955803 ATACAAATAT
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
38 2 0.04
39 14 0.26
40 1 0.02
41 30 0.56
43 7 0.13
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (40 bp):
CGTTTCTACGAAACGCCACTAAAGTAGAAGTCTATAGCGG
Found at i:1956223 original size:55 final size:57
Alignment explanation
Indices: 1956054--1956235 Score: 311
Period size: 55 Copynumber: 3.3 Consensus size: 57
1956044 ATTAAAACAG
1956054 AAGTACTTATGCATAAAACTACTTAACAACAAAATACA-T-T-ATTTAGAAACATTA
1 AAGTACTTATGCATAAAACTACTTAACAACAAAATACATTATAATTTAGAAACATTA
**
1956108 AAGTAGATATGCATAAAACTACTTAACAACAAAATACATTATAATTTAGAAACATTA
1 AAGTACTTATGCATAAAACTACTTAACAACAAAATACATTATAATTTAGAAACATTA
1956165 AAGTACTTATGCATAAAACTACTTAA-AAC-AAATACATTATAATTTAGAAACATTA
1 AAGTACTTATGCATAAAACTACTTAACAACAAAATACATTATAATTTAGAAACATTA
1956220 AAGTACTTATGCATAA
1 AAGTACTTATGCATAA
1956236 CAGTCTTCAC
Statistics
Matches: 121, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
54 36 0.30
55 43 0.36
56 4 0.03
57 38 0.31
ACGTcount: A:0.51, C:0.13, G:0.07, T:0.30
Consensus pattern (57 bp):
AAGTACTTATGCATAAAACTACTTAACAACAAAATACATTATAATTTAGAAACATTA
Found at i:1965398 original size:30 final size:29
Alignment explanation
Indices: 1965364--1965420 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
1965354 AATTTGATCA
*
1965364 TAATT-TTAATAAATTATAATATATTTATTT
1 TAATTCTT-ATAAATAAT-ATATATTTATTT
1965394 TAATTCTTATAAATAATATATATTTAT
1 TAATTCTTATAAATAATATATATTTAT
1965421 AGTTTACCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 10 0.40
30 13 0.52
31 2 0.08
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (29 bp):
TAATTCTTATAAATAATATATATTTATTT
Found at i:1976519 original size:12 final size:12
Alignment explanation
Indices: 1976502--1976533 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
1976492 ATTATTACAA
1976502 AATTATTATTAT
1 AATTATTATTAT
1976514 AATTATTATTAT
1 AATTATTATTAT
1976526 AATTATTA
1 AATTATTA
1976534 ACATAAGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AATTATTATTAT
Found at i:1982034 original size:21 final size:21
Alignment explanation
Indices: 1982010--1982062 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
1982000 ACCAACAAAA
1982010 TCGCAATGCGATTTT-CCAATT
1 TCGCAATGCGATTTTCCCAA-T
**
1982031 TCGCGTTGCGATTTTCCCAAT
1 TCGCAATGCGATTTTCCCAAT
1982052 TCGCAATGCGA
1 TCGCAATGCGA
1982063 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCCAAT
Found at i:1982077 original size:20 final size:21
Alignment explanation
Indices: 1982052--1982103 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1982042 TTTTCCCAAT
*
1982052 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGGAAA
**
1982072 TCGCAATGCGAATTTGGGAAA
1 TCGCAATGCGAATTAAGGAAA
1982093 TCGCAATGCGA
1 TCGCAATGCGA
1982104 TACTAACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGGAAA
Found at i:1982147 original size:21 final size:21
Alignment explanation
Indices: 1982123--1982185 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 21
1982113 TCGTAATGCA
*
1982123 ATTTTCCTAATTCGCATTGCG
1 ATTTTCATAATTCGCATTGCG
* * *
1982144 ATTTACGT-ATTCGCGTTGCG
1 ATTTTCATAATTCGCATTGCG
*
1982164 ATTTTCATAATTCGCAATGCG
1 ATTTTCATAATTCGCATTGCG
1982185 A
1 A
1982186 ATTAGGAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 17 0.50
21 17 0.50
ACGTcount: A:0.22, C:0.21, G:0.17, T:0.40
Consensus pattern (21 bp):
ATTTTCATAATTCGCATTGCG
Found at i:1982199 original size:21 final size:20
Alignment explanation
Indices: 1982175--1982228 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
1982165 TTTTCATAAT
*
1982175 TCGCAATGCGAATTAGGAAAA
1 TCGCAATG-GAATTACGAAAA
*
1982196 TCGCAATTGGAA-TACGTAAA
1 TCGCAA-TGGAATTACGAAAA
1982216 TCGCAATGTGAAT
1 TCGCAATG-GAAT
1982229 CTTACTATCG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 2 0.07
20 15 0.54
21 9 0.32
22 2 0.07
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (20 bp):
TCGCAATGGAATTACGAAAA
Found at i:1982808 original size:19 final size:19
Alignment explanation
Indices: 1982759--1982829 Score: 90
Period size: 19 Copynumber: 3.7 Consensus size: 19
1982749 TAGTTTCGAG
1982759 AATGAAAATCGCAACGCGGA
1 AATGAAAATCGCAACGC-GA
*
1982779 AAT-AACTATCGCAACGCGA
1 AATGAA-AATCGCAACGCGA
1982798 AATGAAAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
**
1982817 AACCAAAATCGCA
1 AATGAAAATCGCA
1982830 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
19 30 0.67
20 15 0.33
ACGTcount: A:0.46, C:0.24, G:0.18, T:0.11
Consensus pattern (19 bp):
AATGAAAATCGCAACGCGA
Found at i:1982847 original size:19 final size:19
Alignment explanation
Indices: 1982825--1982951 Score: 94
Period size: 20 Copynumber: 7.1 Consensus size: 19
1982815 GAAACCAAAA
*
1982825 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1982844 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1982858 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1982877 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1982891 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1982910 TCCGCGTGGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
* *
1982930 ATCTCGTTGCGATTTTCGTT
1 -TCGCGTTGCGATTTTCATT
1982950 TC
1 TC
1982952 AACCAAAAGA
Statistics
Matches: 84, Mismatches: 12, Indels: 24
0.70 0.10 0.20
Matches are distributed among these distances:
14 20 0.24
16 5 0.06
17 6 0.07
19 23 0.27
20 29 0.35
21 1 0.01
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1982866 original size:14 final size:14
Alignment explanation
Indices: 1982847--1982902 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
1982837 TTTCATTTCG
1982847 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1982861 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1982880 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1982894 CGTTGCGAT
1 CGTTGCGAT
1982903 AGTCATTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1982872 original size:33 final size:33
Alignment explanation
Indices: 1982830--1982923 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
1982820 CAAAATCGCA
1982830 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1982863 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
** *
1982896 TTGCGATAGTCATTTCCGCGTGGCGATT
1 TTGCGATTTTCATTT-CGCGTTGCGATT
1982924 TTCATTATCT
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 46 0.81
34 11 0.19
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.43
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1985106 original size:42 final size:42
Alignment explanation
Indices: 1985046--1985168 Score: 104
Period size: 42 Copynumber: 2.9 Consensus size: 42
1985036 GCCCGACTCG
* * * *
1985046 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCATCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * * *
1985088 CCTATCATTCATCGAGAGTCCCCTCCCACCGTTCAAGAGGTC
1 CCTATCATCCATCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
1985130 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCATCAAGA-GTCCACTCCCACCGTTCAAGAG
1985169 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 16, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
42 60 0.94
43 4 0.06
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.24
Consensus pattern (42 bp):
CCTATCATCCATCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:1985167 original size:21 final size:21
Alignment explanation
Indices: 1985108--1985168 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
1985098 ATCGAGAGTC
1985108 CCCTCCCACCGTTCAAGAGGT
1 CCCTCCCACCGTTCAAGAGGT
* ** * *
1985129 CACTGTCATCGTTGAAGAGGT
1 CCCTCCCACCGTTCAAGAGGT
*
1985150 CCCTCCCACCATTCAAGAG
1 CCCTCCCACCGTTCAAGAG
1985169 CCCGATTCAC
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.36, G:0.20, T:0.21
Consensus pattern (21 bp):
CCCTCCCACCGTTCAAGAGGT
Found at i:1986546 original size:14 final size:14
Alignment explanation
Indices: 1986527--1986562 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1986517 ATTGTTTAAT
1986527 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1986541 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1986555 TGATTTGT
1 TGATTTGT
1986563 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1986691 original size:19 final size:19
Alignment explanation
Indices: 1986669--1986730 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
1986659 AAAAATTACT
*
1986669 ATCGCAATACGAAA-TGAAA
1 ATCGCAACACGAAACT-AAA
*
1986688 ATCGCAACGCGAAACTAAA
1 ATCGCAACACGAAACTAAA
1986707 ATCGCAACACGAAACTAAA
1 ATCGCAACACGAAACTAAA
*
1986726 TTCGC
1 ATCGC
1986731 GTTGCGATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 37 0.97
20 1 0.03
ACGTcount: A:0.47, C:0.24, G:0.15, T:0.15
Consensus pattern (19 bp):
ATCGCAACACGAAACTAAA
Found at i:1986748 original size:19 final size:19
Alignment explanation
Indices: 1986726--1986876 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
1986716 CGAAACTAAA
1986726 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1986745 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1986760 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1986778 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1986793 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
** *
1986811 TTCGCACTACGA--TT-A-
1 TTCGCGTTGCGATTTTCAT
*
1986826 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
1986844 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
1986863 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1986877 AGACATTAAG
Statistics
Matches: 93, Mismatches: 23, Indels: 31
0.63 0.16 0.21
Matches are distributed among these distances:
14 24 0.26
16 9 0.10
17 9 0.10
19 41 0.44
20 10 0.11
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1986772 original size:33 final size:33
Alignment explanation
Indices: 1986730--1986856 Score: 209
Period size: 33 Copynumber: 3.8 Consensus size: 33
1986720 ACTAAATTCG
* *
1986730 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1986763 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* * *
1986796 CGTTGCGATTTTCATTTCGCACTACGATTATCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1986829 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1986857 AGTAATTTCC
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 87 1.00
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:1989434 original size:24 final size:24
Alignment explanation
Indices: 1989407--1989453 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1989397 CAAAATCCGA
*
1989407 GTATTGACCAATATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
1989431 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
1989454 AATACTGACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:1989462 original size:24 final size:24
Alignment explanation
Indices: 1989411--1989462 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1989401 ATCCGAGTAT
* ** *
1989411 TGACCAATATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
1989435 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
1989459 TGAC
1 TGAC
1989463 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:1990276 original size:21 final size:20
Alignment explanation
Indices: 1990230--1990281 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
1990220 TTTTCCTAAT
*
1990230 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* **
1990250 TAGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
1990271 TCGCAATGCGA
1 TCGCAATGCGA
1990282 TATTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:1990633 original size:20 final size:20
Alignment explanation
Indices: 1990571--1990637 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1990561 CAACGGGGAA
1990571 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
* * ***
1990591 ATCTCAATGCG-AAATGAAA
1 ATCGCAACGCGAAAATGGCT
*
1990610 ATCGCAACGTGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
1990630 ATCGCAAC
1 ATCGCAAC
1990638 TAGAAAATCG
Statistics
Matches: 35, Mismatches: 11, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
19 13 0.37
20 22 0.63
ACGTcount: A:0.39, C:0.22, G:0.21, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:1990688 original size:33 final size:33
Alignment explanation
Indices: 1990651--1990721 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
1990641 AAAATCGCAA
*
1990651 TGCGAAATGAAAATCGCATTGTGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
1990684 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1990717 TGCGA
1 TGCGA
1990722 TAGTCAGTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.41
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:1990692 original size:14 final size:14
Alignment explanation
Indices: 1990673--1990722 Score: 55
Period size: 14 Copynumber: 3.2 Consensus size: 14
1990663 ATCGCATTGT
1990673 GATTTTCTCGTTGC
1 GATTTTCTCGTTGC
1990687 GATTTTCATTTCGCATTGC
1 GATTTTC---TCG--TTGC
1990706 GATTTTCTCGTTGC
1 GATTTTCTCGTTGC
1990720 GAT
1 GAT
1990723 AGTCAGTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
14 14 0.45
16 3 0.10
17 3 0.10
19 11 0.35
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
GATTTTCTCGTTGC
Found at i:1992341 original size:42 final size:42
Alignment explanation
Indices: 1992295--1992383 Score: 128
Period size: 42 Copynumber: 2.1 Consensus size: 42
1992285 CCTCTTCAAC
*
1992295 GATGATAGTGGCCTCTTGAACG-GTGG-GGGGACTCTCTTGAGG
1 GATGATAGGGGCCTCTTGAACGAGTGGAGGGGA--CTCTTGAGG
*
1992337 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGATAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
1992379 GATGA
1 GATGA
1992384 CAGGTGAGTC
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
42 35 0.81
43 3 0.07
44 5 0.12
ACGTcount: A:0.20, C:0.15, G:0.40, T:0.25
Consensus pattern (42 bp):
GATGATAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:1992352 original size:21 final size:21
Alignment explanation
Indices: 1992328--1992383 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
1992318 TGGGGGGACT
* *
1992328 CTCTTGAGGGATGATAGGGGC
1 CTCTTGAGGGATGAGAGGGGA
**
1992349 CTCTTGAACGATTG-GAGGGGA
1 CTCTTGAGGGA-TGAGAGGGGA
1992370 CTCTTGAGGGATGA
1 CTCTTGAGGGATGA
1992384 CAGGTGAGTC
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
20 2 0.07
21 23 0.85
22 2 0.07
ACGTcount: A:0.21, C:0.14, G:0.39, T:0.25
Consensus pattern (21 bp):
CTCTTGAGGGATGAGAGGGGA
Found at i:1992750 original size:20 final size:20
Alignment explanation
Indices: 1992725--1992777 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1992715 GAAGAATAGT
*
1992725 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAA
*
1992745 TTACTTTCGCAACGCGAAAA
1 TTACTTTCGCAACACGAAAA
* *
1992765 TGACTATCGCAAC
1 TTACTTTCGCAAC
1992778 GCGGAAATGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.25
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAA
Found at i:1992778 original size:20 final size:20
Alignment explanation
Indices: 1992731--1992817 Score: 86
Period size: 20 Copynumber: 4.4 Consensus size: 20
1992721 TAGTTTACTT
* * * *
1992731 TCGCAACACGAAACTTACTT
1 TCGCAACGCGAAAATGACTA
1992751 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
* *
1992771 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGAAAATGACTA
* **
1992791 TCGCAATGCG-AAATGAAAA
1 TCGCAACGCGAAAATGACTA
1992810 TCGCAACG
1 TCGCAACG
1992818 ACAAAATCGC
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
19 13 0.23
20 43 0.77
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.17
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:1992872 original size:19 final size:19
Alignment explanation
Indices: 1992790--1992872 Score: 79
Period size: 19 Copynumber: 4.6 Consensus size: 19
1992780 GGAAATGGCT
*
1992790 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATCAAA
1992809 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATCAAA
*
1992823 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATCAAA
*
1992842 ATCGCAACGCGAAA-CACAA
1 ATCGCAATGCGAAATCA-AA
*
1992861 ATCGCATTGCGA
1 ATCGCAATGCGA
1992873 TTTTCATTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 2 0.04
19 35 0.67
ACGTcount: A:0.45, C:0.23, G:0.19, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATCAAA
Found at i:1992884 original size:19 final size:18
Alignment explanation
Indices: 1992862--1992958 Score: 75
Period size: 19 Copynumber: 5.7 Consensus size: 18
1992852 GAAACACAAA
1992862 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTT-ATT
* * *
1992881 TCGCGTTGTGA-TTT-TG
1 TCGCATTGCGATTTTATT
1992897 T--CATTGCGATTTTCATT
1 TCGCATTGCGATTTT-ATT
*
1992914 TCGCATTGCGA-TTT-TG
1 TCGCATTGCGATTTTATT
1992930 TCG--TTGCGATTTTTATT
1 TCGCATTGCGA-TTTTATT
1992947 TCGCATTGCGAT
1 TCGCATTGCGAT
1992959 AGCCATTTCC
Statistics
Matches: 60, Mismatches: 8, Indels: 21
0.67 0.09 0.24
Matches are distributed among these distances:
14 12 0.20
15 3 0.05
16 9 0.15
17 6 0.10
18 7 0.12
19 23 0.38
ACGTcount: A:0.13, C:0.18, G:0.21, T:0.48
Consensus pattern (18 bp):
TCGCATTGCGATTTTATT
Found at i:1992907 original size:33 final size:33
Alignment explanation
Indices: 1992865--1992958 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
1992855 ACACAAATCG
* *
1992865 CATTGCGATTTTCATTTCGCGTTGTGATTTTGT
1 CATTGCGATTTTCATTTCGCATTGCGATTTTGT
1992898 CATTGCGATTTTCATTTCGCATTGCGATTTTGT
1 CATTGCGATTTTCATTTCGCATTGCGATTTTGT
* *
1992931 CGTTGCGATTTTTATTTCGCATTGCGAT
1 CATTGCGATTTTCATTTCGCATTGCGAT
1992959 AGCCATTTCC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.14, C:0.17, G:0.20, T:0.49
Consensus pattern (33 bp):
CATTGCGATTTTCATTTCGCATTGCGATTTTGT
Found at i:1992966 original size:19 final size:20
Alignment explanation
Indices: 1992944--1992986 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1992934 TGCGATTTTT
1992944 ATTT-CGCATTGCGATAGCC
1 ATTTCCGCATTGCGATAGCC
* *
1992963 ATTTCCGCGTTGCGATAGTC
1 ATTTCCGCATTGCGATAGCC
1992983 ATTT
1 ATTT
1992987 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (20 bp):
ATTTCCGCATTGCGATAGCC
Found at i:1992977 original size:20 final size:20
Alignment explanation
Indices: 1992952--1992997 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1992942 TTATTTCGCA
1992952 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
1992972 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
1992992 TTGCGA
1 TTGCGA
1992998 AAGTAAACTA
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:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:1993537 original size:18 final size:18
Alignment explanation
Indices: 1993514--1993561 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
1993504 CGGGTCGATC
1993514 AGGTGATGGCTCTAGGTG
1 AGGTGATGGCTCTAGGTG
* *
1993532 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTAGGTG
1993550 AGGTGATGGCTC
1 AGGTGATGGCTC
1993562 CCGAAGTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.17, C:0.12, G:0.44, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTAGGTG
Found at i:1994913 original size:20 final size:20
Alignment explanation
Indices: 1994890--1994934 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1994880 AATAAAAATT
1994890 GCAACACGAAAATGACAATC
1 GCAACACGAAAATGACAATC
* ** *
1994910 GCAACGCGAATTTGACTATC
1 GCAACACGAAAATGACAATC
1994930 GCAAC
1 GCAAC
1994935 GAGAGAATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.27, G:0.18, T:0.16
Consensus pattern (20 bp):
GCAACACGAAAATGACAATC
Found at i:1995214 original size:22 final size:22
Alignment explanation
Indices: 1995184--1995227 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1995174 GATGGAGATA
1995184 GACGGATTTCGCCAGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
* * *
1995206 GACGTATTTCGTCGGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
1995228 TGAGAGAGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.20, C:0.16, G:0.41, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGCCAGAGATGGG
Found at i:1995465 original size:40 final size:41
Alignment explanation
Indices: 1995414--1995527 Score: 142
Period size: 40 Copynumber: 2.8 Consensus size: 41
1995404 GATTATGTAT
* * *
1995414 TATCTCGTTGCGAAAGTCAGTATTGAGTTGCGAAATTA-AG
1 TATCACGTTGCGAAAGTCAGTATCGCGTTGCGAAATTATAG
** *
1995454 TATCGA-GTTGCGAAAGTCAGTATCGCGTTGCGATTTTATAT
1 TATC-ACGTTGCGAAAGTCAGTATCGCGTTGCGAAATTATAG
*
1995495 TATCACGTTGCGATAGTCAGTATCGCGTTGCGA
1 TATCACGTTGCGAAAGTCAGTATCGCGTTGCGA
1995528 TTTTCCAAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
40 33 0.52
41 31 0.48
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.33
Consensus pattern (41 bp):
TATCACGTTGCGAAAGTCAGTATCGCGTTGCGAAATTATAG
Found at i:1995516 original size:41 final size:41
Alignment explanation
Indices: 1995394--1995531 Score: 163
Period size: 41 Copynumber: 3.4 Consensus size: 41
1995384 CGCTTTGAAA
* * * *
1995394 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTATATTATCACGTTGCGAAAGTCAGT
* * ** *
1995435 ATTGAGTTGCGAAATTA-AGTATCGA-GTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTATATTATC-ACGTTGCGAAAGTCAGT
*
1995475 ATCGCGTTGCGATTTTATATTATCACGTTGCGATAGTCAGT
1 ATCGCGTTGCGATTTTATATTATCACGTTGCGAAAGTCAGT
1995516 ATCGCGTTGCGATTTT
1 ATCGCGTTGCGATTTT
1995532 CCAAATTCAC
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
40 34 0.43
41 45 0.57
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTATATTATCACGTTGCGAAAGTCAGT
Found at i:1995528 original size:20 final size:20
Alignment explanation
Indices: 1995414--1995527 Score: 102
Period size: 20 Copynumber: 5.7 Consensus size: 20
1995404 GATTATGTAT
*
1995414 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * * *
1995434 TATTGAGTTGCGAAATTAAG
1 TATCGCGTTGCGAAAGTCAG
*
1995454 TATCGAGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*** * *
1995474 TATCGCGTTGCGATTTTATAT
1 TATCGCGTTGCGAAAGT-CAG
* *
1995495 TATCACGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
1995515 TATCGCGTTGCGA
1 TATCGCGTTGCGA
1995528 TTTTCCAAAT
Statistics
Matches: 73, Mismatches: 20, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
20 58 0.79
21 15 0.21
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.33
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1995547 original size:41 final size:41
Alignment explanation
Indices: 1995461--1995549 Score: 119
Period size: 41 Copynumber: 2.2 Consensus size: 41
1995451 AAGTATCGAG
* * *
1995461 TTGCGAAAGTCAGTATCGCGTTGCGATTTTATATTATCACG
1 TTGCGATAGTCAGTATCGCGTTGCGATTTTATAATATCACA
1995502 TTGCGATAGTCAGTATCGCGTTGCGATTTTCCA-AAT-TCACA
1 TTGCGATAGTCAGTATCGCGTTGCGATTTT--ATAATATCACA
1995543 TTGCGAT
1 TTGCGAT
1995550 TTACTTATTC
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
41 40 0.93
42 2 0.05
43 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (41 bp):
TTGCGATAGTCAGTATCGCGTTGCGATTTTATAATATCACA
Found at i:1995610 original size:21 final size:22
Alignment explanation
Indices: 1995558--1995610 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
1995548 ATTTACTTAT
1995558 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
1995579 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
1995600 TCGCATTGCGA
1 TCGCATTGCGA
1995611 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:1996185 original size:21 final size:19
Alignment explanation
Indices: 1996143--1996185 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
1996133 ATTATTATAT
*
1996143 TAATATTTTATAACATACA
1 TAATATTTTATAACATAAA
*
1996162 TAATATATTTATAAATATAAA
1 TAATAT-TTTAT-AACATAAA
1996183 TAA
1 TAA
1996186 ATAATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 6 0.30
20 5 0.25
21 9 0.45
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (19 bp):
TAATATTTTATAACATAAA
Found at i:1996429 original size:17 final size:17
Alignment explanation
Indices: 1996409--1996447 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1996399 AACTTATTAA
* * *
1996409 TAATATTATAATAATAT
1 TAATATCATAAAAATAC
1996426 TAATATCATAAAAATAC
1 TAATATCATAAAAATAC
1996443 TAATA
1 TAATA
1996448 ATATTAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATATCATAAAAATAC
Found at i:1996451 original size:26 final size:25
Alignment explanation
Indices: 1996415--1996472 Score: 98
Period size: 26 Copynumber: 2.3 Consensus size: 25
1996405 TTAATAATAT
1996415 TATAATAATATTAATATCATAAAAA
1 TATAATAATATTAATATCATAAAAA
*
1996440 TACTAATAATATTAATTTCATAAAAA
1 TA-TAATAATATTAATATCATAAAAA
1996466 TATAATA
1 TATAATA
1996473 TTTTTATGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 7 0.23
26 24 0.77
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (25 bp):
TATAATAATATTAATATCATAAAAA
Found at i:1996555 original size:31 final size:31
Alignment explanation
Indices: 1996489--1996555 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
1996479 TGGATGTAAT
** *
1996489 ATATATCGTGTCATCATTTTGGATACATAAT
1 ATATATCAAGTCATCATTTTGGATACATAAC
*
1996520 ATATATCAAGTCATCAATTTT-GATACATAGC
1 ATATATCAAGTCATC-ATTTTGGATACATAAC
1996551 ATATA
1 ATATA
1996556 CTACAACATC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 26 0.84
32 5 0.16
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.39
Consensus pattern (31 bp):
ATATATCAAGTCATCATTTTGGATACATAAC
Found at i:1996555 original size:33 final size:31
Alignment explanation
Indices: 1996485--1996548 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
1996475 TTTATGGATG
**
1996485 TAATATATATCGTGTCATCATTTTGGATACA
1 TAATATATATCAAGTCATCATTTTGGATACA
1996516 TAATATATATCAAGTCATCAATTTT-GATACA
1 TAATATATATCAAGTCATC-ATTTTGGATACA
1996547 TA
1 TA
1996549 GCATATACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 25 0.83
32 5 0.17
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (31 bp):
TAATATATATCAAGTCATCATTTTGGATACA
Found at i:2009900 original size:2 final size:2
Alignment explanation
Indices: 2009893--2009944 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
2009883 TTGAACTCGA
2009893 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
2009935 AT AT AT AT AT
1 AT AT AT AT AT
2009945 GTATGTATGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2015112 original size:2 final size:2
Alignment explanation
Indices: 2015100--2015137 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2015090 TCATTTATCC
*
2015100 AT AT AT GT 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
2015138 CATTTGTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2016221 original size:23 final size:23
Alignment explanation
Indices: 2016154--2016221 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 23
2016144 AAGGGGCAAT
2016154 ATTTTCAAAACTTTTGATTAA-AC
1 ATTTTCAAAACTTTTGA-TAATAC
* *
2016177 ATTTTTCAAAACTCTT-CTAATAC
1 A-TTTTCAAAACTTTTGATAATAC
*
2016200 ATTTTCAAAACTTTTGAAAATA
1 ATTTTCAAAACTTTTGATAATA
2016222 AAAGAAGAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
22 16 0.43
23 8 0.22
24 13 0.35
ACGTcount: A:0.40, C:0.15, G:0.03, T:0.43
Consensus pattern (23 bp):
ATTTTCAAAACTTTTGATAATAC
Found at i:2016421 original size:32 final size:32
Alignment explanation
Indices: 2016362--2016436 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
2016352 GCATCTTTAA
* * *
2016362 AGATTCAACAGTAAATGTTGGGGCATATTTGG
1 AGATTCAACATTAAATATTGGGCCATATTTGG
* *
2016394 AGATTCAACATTGAATATTGTGCCATATTTGG
1 AGATTCAACATTAAATATTGGGCCATATTTGG
*
2016426 GGATTCAACAT
1 AGATTCAACAT
2016437 CCTGATGCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (32 bp):
AGATTCAACATTAAATATTGGGCCATATTTGG
Found at i:2017049 original size:43 final size:43
Alignment explanation
Indices: 2016996--2017133 Score: 204
Period size: 43 Copynumber: 3.2 Consensus size: 43
2016986 GTCATCCGCA
2016996 ATTTCAACTCCACGACGGAGGATATCGTACCCACACATCCACG
1 ATTTCAACTCCACGACGGAGGATATCGTACCCACACATCCACG
* * *
2017039 ATTTTAACTCCACGACGGAGGATATCGTACCAACAGATCCACG
1 ATTTCAACTCCACGACGGAGGATATCGTACCCACACATCCACG
* * * *
2017082 ATTTCAACTCCACAACGGAGGATATCGTGCCCATACATTCACG
1 ATTTCAACTCCACGACGGAGGATATCGTACCCACACATCCACG
*
2017125 GTTTCAACT
1 ATTTCAACT
2017134 TCACAACGAA
Statistics
Matches: 84, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 84 1.00
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.22
Consensus pattern (43 bp):
ATTTCAACTCCACGACGGAGGATATCGTACCCACACATCCACG
Found at i:2017152 original size:86 final size:86
Alignment explanation
Indices: 2016996--2017153 Score: 219
Period size: 86 Copynumber: 1.8 Consensus size: 86
2016986 GTCATCCGCA
* * * *
2016996 ATTTCAACTCCACGACGGAGGATATCGTACCCACACATCCACGATTTTAACTCCACGACGGAGGA
1 ATTTCAACTCCACAACGGAGGATATCGTACCCACACATCCACGATTTCAACTCCACAACGAAGGA
2017061 TATCGTACCAACAGATCCACG
66 TATCGTACCAACAGATCCACG
* * * * *
2017082 ATTTCAACTCCACAACGGAGGATATCGTGCCCATACATTCACGGTTTCAACTTCACAACGAAGGG
1 ATTTCAACTCCACAACGGAGGATATCGTACCCACACATCCACGATTTCAACTCCACAACGAA-GG
2017147 A-ATCGTA
65 ATATCGTA
2017154 TACACGAGTA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
86 59 0.95
87 3 0.05
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.22
Consensus pattern (86 bp):
ATTTCAACTCCACAACGGAGGATATCGTACCCACACATCCACGATTTCAACTCCACAACGAAGGA
TATCGTACCAACAGATCCACG
Found at i:2017425 original size:43 final size:43
Alignment explanation
Indices: 2017363--2017465 Score: 136
Period size: 43 Copynumber: 2.4 Consensus size: 43
2017353 ACGAATGAGC
* * *
2017363 CATCCACAATTTCAACTCCACGATGGAGGATATCGTACCCACGA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCATACCCAC-A
* *
2017407 -ATCCATGATTTCAACTCCACGACGGAGGATATCATGCCCACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCATACCCACA
*
2017449 CATCCACGGTTTCAACT
1 CATCCACGATTTCAACT
2017466 TCATGACGAA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
42 1 0.02
43 50 0.98
ACGTcount: A:0.30, C:0.32, G:0.16, T:0.22
Consensus pattern (43 bp):
CATCCACGATTTCAACTCCACGACGGAGGATATCATACCCACA
Found at i:2017426 original size:332 final size:335
Alignment explanation
Indices: 2017031--2017734 Score: 951
Period size: 332 Copynumber: 2.1 Consensus size: 335
2017021 CGTACCCACA
* *
2017031 CATCCACGATTTTAACTCCACGACGGAGGATATCGTACCAACAGATCCACGATTTCAACTCCACA
1 CATCCACAATTTCAACTCCACGACGGAGGATATCGTACCAACAGATCCACGATTTCAACTCCACA
* * * * *
2017096 ACGGAGGATATCGTGCCCATACATTCACGGTTTCAACTTCACAACGAAGGGAATCGTATACACGA
66 ACGGAGGATATCATGCCCACACATCCACGGTTTCAACTTCACAACGAAGGGAATCGTACACACAA
* * *
2017161 GTATCATCCATCTCTTGATTGGATTTCAACTTCACGACGAATGATATCCAACTCAAAGAATGAGT
131 GCATCATCCATCTCTAGATTGGATTTCAACTTCACGACGAATGATATCCAACTCAAAGAAGGAGT
* * *
2017226 GTATGTCAATAAACTTTCCAGTTTCAGAGCCAATTTCAACTTCACGGCGAAGGATATTGGACTCG
196 GTATGTCAATAAACTTTCCAGTTTCAGAGCCAACTTCAACTTCACGACGAAAGATATTGGACTCG
*
2017291 AAAC-A-A-CAC-AAGCTTGGATTTCAACTTCACGATGAAGGATATTCAAGTTGCTCAACTTCAC
261 AAACAATATAACTAA-CTTGGATTTCAACTTCACGATGAAGGATATTCAAGTTGCTCAACTTCAC
2017352 GACGAATGAGC
325 GACGAATGAGC
* * *
2017363 CATCCACAATTTCAACTCCACGATGGAGGATATCGTACCCAC-GAATCCATGATTTCAACTCCAC
1 CATCCACAATTTCAACTCCACGACGGAGGATATCGTACCAACAG-ATCCACGATTTCAACTCCAC
* **
2017427 GACGGAGGATATCATGCCCACACATCCACGGTTTCAACTTCATGACGAAGGGAATCGTACACACA
65 AACGGAGGATATCATGCCCACACATCCACGGTTTCAACTTCACAACGAAGGGAATCGTACACACA
* * * * *
2017492 AGCATCATCTATCTCTAGGTTGGATTTCAACTTCAGGACGAATGATATCCAACTCAGAGAGGGAG
130 AGCATCATCCATCTCTAGATTGGATTTCAACTTCACGACGAATGATATCCAACTCAAAGAAGGAG
* * * *
2017557 TGTTTGTCAATAAACTTTCCAGTTTCATAGTCAACTTCAACTTCACGACGAAAGATATTGGCCTC
195 TGTATGTCAATAAACTTTCCAGTTTCAGAGCCAACTTCAACTTCACGACGAAAGATATTGGACTC
*
2017622 GAAACAATATAACTTAACTTGGATTTCAACTTCTCGATGAAGGATATCCAATTCAAGTT--TCAA
260 GAAACAATATAAC-TAACTTGGATTTCAACTTCACGATGAAGG--AT---ATTCAAGTTGCTCAA
2017685 CTTCACGACGAA-G-G-
319 CTTCACGACGAATGAGC
** * * *
2017699 GGTCCACGATTTCAACTTCACGACGAAGGATATCGT
1 CATCCACAATTTCAACTCCACGACGGAGGATATCGT
2017735 GTCCACCAGC
Statistics
Matches: 325, Mismatches: 36, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
331 1 0.00
332 234 0.72
333 1 0.00
334 1 0.00
335 2 0.01
336 55 0.17
337 3 0.01
338 3 0.01
339 16 0.05
341 9 0.03
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (335 bp):
CATCCACAATTTCAACTCCACGACGGAGGATATCGTACCAACAGATCCACGATTTCAACTCCACA
ACGGAGGATATCATGCCCACACATCCACGGTTTCAACTTCACAACGAAGGGAATCGTACACACAA
GCATCATCCATCTCTAGATTGGATTTCAACTTCACGACGAATGATATCCAACTCAAAGAAGGAGT
GTATGTCAATAAACTTTCCAGTTTCAGAGCCAACTTCAACTTCACGACGAAAGATATTGGACTCG
AAACAATATAACTAACTTGGATTTCAACTTCACGATGAAGGATATTCAAGTTGCTCAACTTCACG
ACGAATGAGC
Found at i:2017803 original size:118 final size:119
Alignment explanation
Indices: 2017639--2017856 Score: 321
Period size: 118 Copynumber: 1.8 Consensus size: 119
2017629 TATAACTTAA
* * ** * *
2017639 CTTGGATTTCAACTTCTCGATGAAGGATATCCAATTCAAGTTTCAACTTCACGACGAAGGGGTC-
1 CTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGAGTCT
2017703 CACGATTTCAACTTCACGACGAAGGATATCGTGTCCACCAGCATCAATGCAACT
66 CACGATTTCAACTTCACGACGAAGGATATCGTGTCCACCAGCATCAATGCAACT
* * *
2017757 CTTGGATTTCAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTTCACAATGAATGAGTCA
1 CTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGAGTC-
*
2017822 TTCACGATTTCAACTTCACGATGAAGGATATCGTG
65 -TCACGATTTCAACTTCACGACGAAGGATATCGTG
2017857 CTCATTTGCA
Statistics
Matches: 87, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
118 55 0.63
121 32 0.37
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (119 bp):
CTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGAGTCT
CACGATTTCAACTTCACGACGAAGGATATCGTGTCCACCAGCATCAATGCAACT
Found at i:2017999 original size:84 final size:84
Alignment explanation
Indices: 2017858--2018301 Score: 412
Period size: 84 Copynumber: 5.3 Consensus size: 84
2017848 GATATCGTGC
* * * *
2017858 TCATTTGCAGCTTAGCTCAAGGCAAGAAGGGTTATCTG-CTAACAAAAGACCTTCGAGTTCGATT
1 TCATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTC-AACTAAAGACCTTCGAGTTCGATT
2017922 ATACTCAGCTCAAAGGCACA
65 ATACTCAGCTCAAAGGCACA
* * * * * * * * *
2017942 TCATTTGTAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAACTAAAGACCTTCGAGTTTGACTA
1 TCATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACTAAAGACCTTCGAGTTCGATTA
** * *
2018007 CGCTCAGCTCCAAGGCACG
66 TACTCAGCTCAAAGGCACA
* *
2018026 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAA-TAAAAGACCTTCGAGTTCAATT
1 TCATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACT-AAAGACCTTCGAGTTCGATT
* * * *
2018090 ATATTCATCTCAAAGGAATA
65 ATACTCAGCTCAAAGGCACA
* * * ** * * * * *
2018110 TCATTTGCAGTATAGCTTAAGTTGAGAAGAGCTATCTGTCATC-AAATACCTTCAAGATTCGATT
1 TCATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACTAAAGACCTTCGAG-TTCGATT
* * * *
2018174 -TCATTCAGTTCCAAGGCACG
65 AT-ACTCAGCTCAAAGGCACA
* *
2018194 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAA-TAAAAGACCTTTTGAGTTCGAT
1 TCATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACT-AAAGACC-TTCGAGTTCGAT
* * *
2018258 TACACTCAGCTTAAAGACACA
64 TATACTCAGCTCAAAGGCACA
*
2018279 TCTTTTGCAGCATAACTCAAGGC
1 TCATTTGCAGCATAACTCAAGGC
2018302 TATAAGGATT
Statistics
Matches: 280, Mismatches: 71, Indels: 17
0.76 0.19 0.05
Matches are distributed among these distances:
83 13 0.05
84 215 0.77
85 48 0.17
86 4 0.01
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (84 bp):
TCATTTGCAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACTAAAGACCTTCGAGTTCGATTA
TACTCAGCTCAAAGGCACA
Found at i:2018146 original size:168 final size:168
Alignment explanation
Indices: 2017858--2018288 Score: 562
Period size: 168 Copynumber: 2.6 Consensus size: 168
2017848 GATATCGTGC
* * * * *
2017858 TCATTTGCAGCTTAGCTCAAGGCAAGAAGGGTTATCTG-CTAACAAAAGACCTTCGAGTTCGATT
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTC-AATAAAAGACCTTCGAGTTCAATT
* * *
2017922 ATACTCAGCTCAAAGGCACATCATTTGTAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAACTA
65 ATACTCAGCTCAAAGGAACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAAC-A
* * *
2017987 AAGACCTTCGAG-TTTGACTACGCTCAGCTCCAAGGCACG
129 AAGACCTTCAAGATTCGACTACACTCAGCTCCAAGGCACG
2018026 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAATAAAAGACCTTCGAGTTCAATTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAATAAAAGACCTTCGAGTTCAATTA
* * * * * *
2018091 TATTCATCTCAAAGGAATATCATTTGCAGTATAGCTTAAGTTGAGAAGAGCTATCTGTCATCAAA
66 TACTCAGCTCAAAGGAACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAACAAA
* * * * *
2018156 TACCTTCAAGATTCGATTTCATTCAGTTCCAAGGCACG
131 GACCTTCAAGATTCGACTACACTCAGCTCCAAGGCACG
* *
2018194 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAATAAAAGACCTTTTGAGTTCGATT
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAATAAAAGACC-TTCGAGTTCAATT
* * *
2018259 ACACTCAGCTTAAA-GACACATCTTTTGCAG
65 ATACTCAGCTCAAAGGA-ACATCATTTGCAG
2018289 CATAACTCAA
Statistics
Matches: 229, Mismatches: 30, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
167 11 0.05
168 185 0.81
169 33 0.14
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (168 bp):
TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAATAAAAGACCTTCGAGTTCAATTA
TACTCAGCTCAAAGGAACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAACAAA
GACCTTCAAGATTCGACTACACTCAGCTCCAAGGCACG
Done.