Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167938.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_20, 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: 19866354
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 74000 characters in sequence are not A, C, G, or T
File 90 of 100
Found at i:17987282 original size:23 final size:22
Alignment explanation
Indices: 17987223--17987303 Score: 92
Period size: 23 Copynumber: 3.6 Consensus size: 22
17987213 ATGCCTAGAA
*
17987223 GTCTT-AGAAATCATGCTCGAAG
1 GTCTTAAG-AATCATGCTCGGAG
* * *
17987245 ATCTTAAGATTCATGTTCGGAG
1 GTCTTAAGAATCATGCTCGGAG
17987267 GTCTTATAGAATCATGCTCGGAG
1 GTCTTA-AGAATCATGCTCGGAG
17987290 GTCTTACAGAATCA
1 GTCTTA-AGAATCA
17987304 ACTAGATAAC
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
22 20 0.41
23 29 0.59
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (22 bp):
GTCTTAAGAATCATGCTCGGAG
Found at i:17987452 original size:87 final size:86
Alignment explanation
Indices: 17987285--17987468 Score: 217
Period size: 87 Copynumber: 2.1 Consensus size: 86
17987275 GAATCATGCT
* * * *
17987285 CGGAGGTCTTACAGAATCAACTAGATAACATCACAGTCGAAAGATAAGGAATCGATCGGGATAAC
1 CGGAGGTCTTACAGAATCAACTAGATAACATCAAAGTCGAAAAATAAAGAATCGATCGAGATAAC
* * * *
17987350 ATCACGAATTAAAATTATGCC
66 ACCACAAATCAAAATTATACC
* **
17987371 TGGAGGTCTTACAGAATTGACTAGGATAACATCATAAGTC-AAAAATAAAGAATCGATCGAGATA
1 CGGAGGTCTTACAGAATCAACTA-GATAACATCA-AAGTCGAAAAATAAAGAATCGATCGAGATA
* *
17987435 ACACCGCAAATCGAAATTATACC
64 ACACCACAAATCAAAATTATACC
*
17987458 CGAAGGTCTTA
1 CGGAGGTCTTA
17987469 GAAATCATGC
Statistics
Matches: 81, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
86 20 0.25
87 57 0.70
88 4 0.05
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22
Consensus pattern (86 bp):
CGGAGGTCTTACAGAATCAACTAGATAACATCAAAGTCGAAAAATAAAGAATCGATCGAGATAAC
ACCACAAATCAAAATTATACC
Found at i:17987481 original size:22 final size:22
Alignment explanation
Indices: 17987447--17987490 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
17987437 ACCGCAAATC
*
17987447 GAAATTATACCCGAAGGTCTTA
1 GAAATCATACCCGAAGGTCTTA
* *
17987469 GAAATCATGCCCGGAGGTCTTA
1 GAAATCATACCCGAAGGTCTTA
17987491 CAGAATTGAA
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:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (22 bp):
GAAATCATACCCGAAGGTCTTA
Found at i:17987530 original size:109 final size:109
Alignment explanation
Indices: 17987361--17987607 Score: 334
Period size: 109 Copynumber: 2.3 Consensus size: 109
17987351 TCACGAATTA
* * * * *
17987361 AAATTATGCCTGGAGGTCTTACAGAATTGACTAGGATAACATCATAAGTCAAAAATAAAGAATCG
1 AAATCATGCCCGGAGGTCTTACAGAATTGAATAGGATAACACCATAAGTCAAAAACAAAGAATCG
*
17987426 ATCGAGATAACACCGCAAATCGAAATTATACCCGAAGGTCTTAG
66 ATCGAGATAACACCGCAAATCAAAATTATACCCGAAGGTCTTAG
* *
17987470 AAATCATGCCCGGAGGTCTTACAGAATTGAAT-GAGATAACACCATAAGTTAGAAACAAAGAATC
1 AAATCATGCCCGGAGGTCTTACAGAATTGAATAG-GATAACACCATAAGTCAAAAACAAAGAATC
* * *** *
17987534 GATCGGGATAACACCGCGAATCAAAATTATGTTCGGAGGTCTTAG
65 GATCGAGATAACACCGCAAATCAAAATTATACCCGAAGGTCTTAG
* *
17987579 AAATCATGCCCGGAGCTCTTACAAAATTG
1 AAATCATGCCCGGAGGTCTTACAGAATTG
17987608 CCTGAAGGTC
Statistics
Matches: 121, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
108 1 0.01
109 120 0.99
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (109 bp):
AAATCATGCCCGGAGGTCTTACAGAATTGAATAGGATAACACCATAAGTCAAAAACAAAGAATCG
ATCGAGATAACACCGCAAATCAAAATTATACCCGAAGGTCTTAG
Found at i:17987592 original size:22 final size:22
Alignment explanation
Indices: 17987567--17987642 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
17987557 AAATTATGTT
*
17987567 CGGAGGTCTTAGAAATCATGCC
1 CGGAGGTCTTAAAAATCATGCC
*
17987589 CGGAGCTCTTACAAAAT--TGCC
1 CGGAGGTCTTA-AAAATCATGCC
* *
17987610 TGAAGGTCTTAAAAATCATGCC
1 CGGAGGTCTTAAAAATCATGCC
* *
17987632 TGGAAGTCTTA
1 CGGAGGTCTTA
17987643 CAGAATTGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
20 5 0.11
21 12 0.27
22 23 0.52
23 4 0.09
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
CGGAGGTCTTAAAAATCATGCC
Found at i:17987619 original size:21 final size:21
Alignment explanation
Indices: 17987595--17987650 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
17987585 TGCCCGGAGC
17987595 TCTTACAAAATTGCCT-GAAGG
1 TCTTACAAAATTGCCTGGAA-G
17987616 TCTTA-AAAATCATGCCTGGAAG
1 TCTTACAAAAT--TGCCTGGAAG
*
17987638 TCTTACAGAATTG
1 TCTTACAAAATTG
17987651 AATAGGATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
20 5 0.17
21 7 0.23
22 11 0.37
23 7 0.23
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (21 bp):
TCTTACAAAATTGCCTGGAAG
Found at i:17987660 original size:152 final size:152
Alignment explanation
Indices: 17987459--17987735 Score: 450
Period size: 152 Copynumber: 1.8 Consensus size: 152
17987449 AATTATACCC
* * *
17987459 GAAGGTCTTAGAAATCATGCCCGGAGGTCTTACAGAATTGAATGAGATAACACCATAAGTTAGAA
1 GAAGGTCTTAAAAATCATGCCCGGAAGTCTTACAGAATTGAATGAGATAACACCACAAGTTAGAA
*
17987524 ACAAAGAATCGATCGGGATAACACCGCGAATCAAAATTATG-TTCGGAGGTCTTAGAAATCATGC
66 ACAAAAAATCGATCGGGATAACACCGCGAATCAAAATTATGCTT-GGAGGTCTTAGAAATCATGC
17987588 CCGGAGCTCTTACAAAATTGCCT
130 CCGGAGCTCTTACAAAATTGCCT
* *
17987611 GAAGGTCTTAAAAATCATGCCTGGAAGTCTTACAGAATTGAAT-AGGATAACACCACGAGTTAGA
1 GAAGGTCTTAAAAATCATGCCCGGAAGTCTTACAGAATTGAATGA-GATAACACCACAAGTTAGA
* *
17987675 AACAAAAAATTGATCGGGATAACACCGCGAATCGAAATTATGCTTGGAGGTCTTAGAAATC
65 AACAAAAAATCGATCGGGATAACACCGCGAATCAAAATTATGCTTGGAGGTCTTAGAAATC
17987736 TCAAAATCTT
Statistics
Matches: 115, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
151 1 0.01
152 112 0.97
153 2 0.02
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.23
Consensus pattern (152 bp):
GAAGGTCTTAAAAATCATGCCCGGAAGTCTTACAGAATTGAATGAGATAACACCACAAGTTAGAA
ACAAAAAATCGATCGGGATAACACCGCGAATCAAAATTATGCTTGGAGGTCTTAGAAATCATGCC
CGGAGCTCTTACAAAATTGCCT
Found at i:17988011 original size:23 final size:23
Alignment explanation
Indices: 17987946--17988027 Score: 98
Period size: 23 Copynumber: 3.7 Consensus size: 23
17987936 AATCAAATTT
* *
17987946 ATGCCTGGAGGTCTT-AGAAATC
1 ATGCCCGGAGGTCTTAAAAAATC
* *
17987968 ATGCCCAGAGGTCTTATAAAATC
1 ATGCCCGGAGGTCTTAAAAAATC
17987991 ATGCCCGGAGGTCTTAAAAAAT-
1 ATGCCCGGAGGTCTTAAAAAATC
*
17988013 -TACCCGGAGGTCTTA
1 ATGCCCGGAGGTCTTA
17988028 CAGAATCGAC
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
21 14 0.27
22 13 0.25
23 25 0.48
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (23 bp):
ATGCCCGGAGGTCTTAAAAAATC
Found at i:17988262 original size:103 final size:104
Alignment explanation
Indices: 17988141--17988344 Score: 383
Period size: 104 Copynumber: 2.0 Consensus size: 104
17988131 GGTCTTACAC
* *
17988141 ATCTCAAAATCTTTGAATGCTCCTCATAATCAGAGGCAATGAAA-TTTTAAAATTTGAAAATCTT
1 ATCTCAAAATCTTTGAATGCTCCTCATAATCAGAGGCAATGAAACTTTAAAAATTTAAAAATCTT
17988205 TTAATCTTGAAAGTCATGCACAGAGGCTTTTAGAAACAA
66 TTAATCTTGAAAGTCATGCACAGAGGCTTTTAGAAACAA
17988244 ATCTCAAAATCTTTGAATGCTCCTCATAATCAGAGGCAATGAAACTTTAAAAATTTAAAAATCTT
1 ATCTCAAAATCTTTGAATGCTCCTCATAATCAGAGGCAATGAAACTTTAAAAATTTAAAAATCTT
17988309 TTAATCTTGAAAGTCATGCACAGAGGCTTTTAGAAA
66 TTAATCTTGAAAGTCATGCACAGAGGCTTTTAGAAA
17988345 TTATGCCCGG
Statistics
Matches: 98, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
103 44 0.45
104 54 0.55
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (104 bp):
ATCTCAAAATCTTTGAATGCTCCTCATAATCAGAGGCAATGAAACTTTAAAAATTTAAAAATCTT
TTAATCTTGAAAGTCATGCACAGAGGCTTTTAGAAACAA
Found at i:17988305 original size:52 final size:52
Alignment explanation
Indices: 17988146--17988309 Score: 128
Period size: 52 Copynumber: 3.2 Consensus size: 52
17988136 TACACATCTC
* *
17988146 AAAATCTTTGAATGCTCCTCATAATCAGAGGCAATGAAA-TTTTAAAATTTG
1 AAAATCTTTGAATGCTCCTCATAATCAGAGGCAATGAAACTTTAAAAATTTA
* * * ** * *
17988197 AAAATCTTTTAAT-CT--TGA-AAGTC--ATGCACA-GAGGCTTTTAGAAACAAATCTC
1 AAAATCTTTGAATGCTCCTCATAA-TCAGAGGCA-ATGAAAC-TTT---AA-AAATTTA
17988249 AAAATCTTTGAATGCTCCTCATAATCAGAGGCAATGAAACTTTAAAAATTTA
1 AAAATCTTTGAATGCTCCTCATAATCAGAGGCAATGAAACTTTAAAAATTTA
17988301 AAAATCTTT
1 AAAATCTTT
17988310 TAATCTTGAA
Statistics
Matches: 83, Mismatches: 15, Indels: 29
0.65 0.12 0.23
Matches are distributed among these distances:
46 6 0.07
47 3 0.04
48 7 0.08
50 2 0.02
51 13 0.16
52 31 0.37
53 4 0.05
55 4 0.05
56 6 0.07
57 7 0.08
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.32
Consensus pattern (52 bp):
AAAATCTTTGAATGCTCCTCATAATCAGAGGCAATGAAACTTTAAAAATTTA
Found at i:17988476 original size:121 final size:121
Alignment explanation
Indices: 17988240--17988551 Score: 500
Period size: 121 Copynumber: 2.6 Consensus size: 121
17988230 GCTTTTAGAA
17988240 ACAAATCTCAAAATCTTTGAATGCTCCTCATAATCAGAGGCAATGAAACTTTAAAAATTTAAAAA
1 ACAAATCTCAAAATCTTTGAATGCTCCTCATAATCAGAGGCAATGAAACTTT-AAAATTTAAAAA
*
17988305 TCTTTTAATCTTGAAAGTCATGCACAGAGGCTTTTAGAAATTATGCCCGGAGGTCTT
65 TCTTTTAATCTTGAAAGTCACGCACAGAGGCTTTTAGAAATTATGCCCGGAGGTCTT
* *
17988362 ACAAATCTCAAAATCTTTGAATGCTCCTCACAATCAGAGGCAATGAAACTTTAAAATTTGAAAAT
1 ACAAATCTCAAAATCTTTGAATGCTCCTCATAATCAGAGGCAATGAAACTTTAAAATTTAAAAAT
** * *
17988427 CTTTTAATCTTGAAAGTCACGCGTAGAGGCTTTTAGAGATTATGTCCGGAGGTCTT
66 CTTTTAATCTTGAAAGTCACGCACAGAGGCTTTTAGAAATTATGCCCGGAGGTCTT
* * * *
17988483 ACAAATCTCAAAATCTTTAAATGCTCCTTATAATCAGAGGCGATGAAAGTTTAAAA-TTAAAAAT
1 ACAAATCTCAAAATCTTTGAATGCTCCTCATAATCAGAGGCAATGAAACTTTAAAATTTAAAAAT
*
17988547 TTTTT
66 CTTTT
17988552 TTTTGAAAAT
Statistics
Matches: 176, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
120 11 0.06
121 114 0.65
122 51 0.29
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (121 bp):
ACAAATCTCAAAATCTTTGAATGCTCCTCATAATCAGAGGCAATGAAACTTTAAAATTTAAAAAT
CTTTTAATCTTGAAAGTCACGCACAGAGGCTTTTAGAAATTATGCCCGGAGGTCTT
Found at i:17988566 original size:16 final size:15
Alignment explanation
Indices: 17988542--17988571 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
17988532 TTTAAAATTA
17988542 AAAATTTTTTTTTTG
1 AAAATTTTTTTTTTG
17988557 AAAATGTTTTTTTTT
1 AAAAT-TTTTTTTTT
17988572 TCAATAAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (15 bp):
AAAATTTTTTTTTTG
Found at i:17989180 original size:65 final size:65
Alignment explanation
Indices: 17989072--17989413 Score: 354
Period size: 65 Copynumber: 5.2 Consensus size: 65
17989062 TTGGGACTAA
* * * * * * *
17989072 ATAAACTTGGCTT-AAATTTTATCGAAGGCCAGCTAAACTGGGCTTAAATTTTATTGATGGCCAG
1 ATAAACTGGGCTTAAAACTTCATTGATGGCCAGATAAACTGGGCTTAAATTTCATTGATGGCCAG
* * *
17989136 ATAAACTGGGCTTAAAACCTCATTGATGGCCAGATGAACTGGGCTTAAAGCTTT-ATTAATGGCC
1 ATAAACTGGGCTTAAAACTTCATTGATGGCCAGATAAACTGGGCTTAAA--TTTCATTGATGGCC
17989200 AG
64 AG
* * * *
17989202 ATAAACTCGGCTT-AAA-TGTCATTGTTGGCTAGATAAACTGAGCTTAAAGTTTCATTGA-GAGC
1 ATAAACTGGGCTTAAAACT-TCATTGATGGCCAGATAAACTGGGCTTAAA-TTTCATTGATG-GC
17989264 CAG
63 CAG
* * * * * *
17989267 ATAAACTGGGCTTAAAGCTTCATTAATGACTAAATAAACTGGGCTTAAATATCATTGATGGCCAG
1 ATAAACTGGGCTTAAAACTTCATTGATGGCCAGATAAACTGGGCTTAAATTTCATTGATGGCCAG
* * * *
17989332 ATAAACTGAGCTTAAAACTTCATTGATGGCCAAATAAACTAGGCTTAAATCTTCATTTGA-GGCT
1 ATAAACTGGGCTTAAAACTTCATTGATGGCCAGATAAACTGGGCTTAAAT-TTCA-TTGATGGCC
17989396 AG
64 AG
*
17989398 ATAAATTGGGCTTAAA
1 ATAAACTGGGCTTAAA
17989414 TATTATTTTA
Statistics
Matches: 232, Mismatches: 35, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
64 16 0.07
65 135 0.58
66 73 0.31
67 8 0.03
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (65 bp):
ATAAACTGGGCTTAAAACTTCATTGATGGCCAGATAAACTGGGCTTAAATTTCATTGATGGCCAG
Found at i:17989207 original size:98 final size:98
Alignment explanation
Indices: 17989098--17989416 Score: 408
Period size: 98 Copynumber: 3.3 Consensus size: 98
17989088 TTTTATCGAA
* * * * *
17989098 GGCCAGCTAAACTGGGCTTAAATTTTATTGATGGCCAGATAAACTGGGCTTAAAACCTCATTGAT
1 GGCCAGATAAACTGGGCTTAAATATCATTGATGGCCAGATAAACTGAGCTTAAAACTTCATTGAT
* *
17989163 GGCCAGATGAACTGGGCTTAAAGCTTTATTAAT
66 GGCCAGATAAACTGGGCTTAAAGCTTCATTAAT
* * * * **
17989196 GGCCAGATAAACTCGGCTTAAATGTCATTGTTGGCTAGATAAACTGAGCTTAAAGTTTCATTGA-
1 GGCCAGATAAACTGGGCTTAAATATCATTGATGGCCAGATAAACTGAGCTTAAAACTTCATTGAT
17989260 GAGCCAGATAAACTGGGCTTAAAGCTTCATTAAT
66 G-GCCAGATAAACTGGGCTTAAAGCTTCATTAAT
* * *
17989294 GACTAAATAAACTGGGCTTAAATATCATTGATGGCCAGATAAACTGAGCTTAAAACTTCATTGAT
1 GGCCAGATAAACTGGGCTTAAATATCATTGATGGCCAGATAAACTGAGCTTAAAACTTCATTGAT
* * * *
17989359 GGCCAAATAAACTAGGCTTAAATCTTCATTTGA-
66 GGCCAGATAAACTGGGCTTAAAGCTTCA-TTAAT
* *
17989392 GGCTAGATAAATTGGGCTTAAATAT
1 GGCCAGATAAACTGGGCTTAAATAT
17989417 TATTTTATTT
Statistics
Matches: 190, Mismatches: 28, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
97 1 0.01
98 185 0.97
99 4 0.02
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (98 bp):
GGCCAGATAAACTGGGCTTAAATATCATTGATGGCCAGATAAACTGAGCTTAAAACTTCATTGAT
GGCCAGATAAACTGGGCTTAAAGCTTCATTAAT
Found at i:17989414 original size:33 final size:33
Alignment explanation
Indices: 17989072--17989414 Score: 349
Period size: 33 Copynumber: 10.5 Consensus size: 33
17989062 TTGGGACTAA
* * * *
17989072 ATAAACTTGGCTTAAAT-TTTATCGAAGGCCAG
1 ATAAACTGGGCTTAAATCTTCATTGATGGCCAG
* *
17989104 CTAAACTGGGCTTAAAT-TTTATTGATGGCCAG
1 ATAAACTGGGCTTAAATCTTCATTGATGGCCAG
* *
17989136 ATAAACTGGGCTTAAAACCTCATTGATGGCCAG
1 ATAAACTGGGCTTAAATCTTCATTGATGGCCAG
* * * *
17989169 ATGAACTGGGCTTAAAGCTTTATTAATGGCCAG
1 ATAAACTGGGCTTAAATCTTCATTGATGGCCAG
* * * *
17989202 ATAAACTCGGCTTAAAT-GTCATTGTTGGCTAG
1 ATAAACTGGGCTTAAATCTTCATTGATGGCCAG
*
17989234 ATAAACTGAGCTTAAAGT-TTCATTGA-GAGCCAG
1 ATAAACTGGGCTTAAA-TCTTCATTGATG-GCCAG
* * * * *
17989267 ATAAACTGGGCTTAAAGCTTCATTAATGACTAA
1 ATAAACTGGGCTTAAATCTTCATTGATGGCCAG
*
17989300 ATAAACTGGGCTTAAAT-ATCATTGATGGCCAG
1 ATAAACTGGGCTTAAATCTTCATTGATGGCCAG
* * *
17989332 ATAAACTGAGCTTAAAACTTCATTGATGGCCAA
1 ATAAACTGGGCTTAAATCTTCATTGATGGCCAG
* *
17989365 ATAAACTAGGCTTAAATCTTCATTTGA-GGCTAG
1 ATAAACTGGGCTTAAATCTTCA-TTGATGGCCAG
*
17989398 ATAAATTGGGCTTAAAT
1 ATAAACTGGGCTTAAAT
17989415 ATTATTTTAT
Statistics
Matches: 255, Mismatches: 49, Indels: 13
0.80 0.15 0.04
Matches are distributed among these distances:
32 93 0.36
33 157 0.62
34 5 0.02
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (33 bp):
ATAAACTGGGCTTAAATCTTCATTGATGGCCAG
Found at i:17997257 original size:17 final size:17
Alignment explanation
Indices: 17997235--17997274 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
17997225 CATTTTAAGA
17997235 GGTTTT-GAATTTTAGG
1 GGTTTTGGAATTTTAGG
*
17997251 GGATTTTGGATTTTTAGG
1 GG-TTTTGGAATTTTAGG
17997269 GGTTTT
1 GGTTTT
17997275 AAAAACTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 2 0.10
17 8 0.38
18 11 0.52
ACGTcount: A:0.15, C:0.00, G:0.33, T:0.53
Consensus pattern (17 bp):
GGTTTTGGAATTTTAGG
Found at i:17998665 original size:13 final size:12
Alignment explanation
Indices: 17998647--17998685 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
17998637 GTTTTTCTGC
17998647 TTTTTTTGTATT
1 TTTTTTTGTATT
*
17998659 ATTTTTTGGTATT
1 -TTTTTTTGTATT
17998672 TATTTTTTGTATT
1 T-TTTTTTGTATT
17998685 T
1 T
17998686 CGTATAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 1 0.04
13 22 0.96
ACGTcount: A:0.13, C:0.00, G:0.10, T:0.77
Consensus pattern (12 bp):
TTTTTTTGTATT
Found at i:18000474 original size:23 final size:25
Alignment explanation
Indices: 18000431--18000476 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
18000421 GGAAATTTTC
*
18000431 TTACTTAGGGATTTTTCAAGAATCA
1 TTACTTAGGGATTTTTAAAGAATCA
18000456 TTACTT-GGG-TTTTTAAAGAAT
1 TTACTTAGGGATTTTTAAAGAAT
18000477 TTTATCATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 11 0.55
24 3 0.15
25 6 0.30
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.43
Consensus pattern (25 bp):
TTACTTAGGGATTTTTAAAGAATCA
Found at i:18001736 original size:16 final size:16
Alignment explanation
Indices: 18001714--18001747 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18001704 TTTCCCTCCT
*
18001714 TTTTTTTTATTTTTTGA
1 TTTTTTTT-TTTGTTGA
18001731 TTTTTTTTTTTGTTGA
1 TTTTTTTTTTTGTTGA
18001747 T
1 T
18001748 GTTTCAGCGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.09, C:0.00, G:0.09, T:0.82
Consensus pattern (16 bp):
TTTTTTTTTTTGTTGA
Found at i:18001864 original size:21 final size:21
Alignment explanation
Indices: 18001822--18001866 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
18001812 TTTTTTTCAA
* *
18001822 TTTTTTGGTTTGGAATGATTT
1 TTTTTTAGTTTGCAATGATTT
* *
18001843 TTTTTTAGTTTGCAGTGCTTT
1 TTTTTTAGTTTGCAATGATTT
18001864 TTT
1 TTT
18001867 ATGGTTTTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.11, C:0.04, G:0.20, T:0.64
Consensus pattern (21 bp):
TTTTTTAGTTTGCAATGATTT
Found at i:18003477 original size:37 final size:37
Alignment explanation
Indices: 18003377--18003495 Score: 152
Period size: 37 Copynumber: 3.2 Consensus size: 37
18003367 TTAATTAATC
* * * *
18003377 ATAAAATTAATCATATAAAAATTAACTGTATGATTGG
1 ATAAAATTAATCATTTAGAAATTAATTGTATGATTAG
*
18003414 ATAAAATTAATCATTTAGAAACTAATTGTATGATTAG
1 ATAAAATTAATCATTTAGAAATTAATTGTATGATTAG
*
18003451 ATAAAATTATTCATTTAGAAATTAATT-T-TGGATTAG
1 ATAAAATTAATCATTTAGAAATTAATTGTAT-GATTAG
*
18003487 ATAATATTA
1 ATAAAATTA
18003496 TTTGTTTCAC
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
35 1 0.01
36 15 0.21
37 57 0.78
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.39
Consensus pattern (37 bp):
ATAAAATTAATCATTTAGAAATTAATTGTATGATTAG
Found at i:18010166 original size:3 final size:3
Alignment explanation
Indices: 18010160--18010197 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
18010150 GCAAGTTCAA
18010160 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
18010198 CACAAATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:18014453 original size:3 final size:3
Alignment explanation
Indices: 18014447--18014494 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
18014437 CATTTTAACT
18014447 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
18014495 GAATAAGTGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:18016135 original size:32 final size:32
Alignment explanation
Indices: 18016099--18016161 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
18016089 CAAAAATAAA
* *
18016099 TATAATATAAAAATTTACACATTGAGAATGCG
1 TATAATATAAAAATCTACAAATTGAGAATGCG
18016131 TATAATATAAAAATCTACAAATTGAGAATGC
1 TATAATATAAAAATCTACAAATTGAGAATGC
18016162 TCAATTTGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.49, C:0.10, G:0.11, T:0.30
Consensus pattern (32 bp):
TATAATATAAAAATCTACAAATTGAGAATGCG
Found at i:18019474 original size:16 final size:16
Alignment explanation
Indices: 18019453--18019487 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
18019443 AAGCTTGATG
18019453 ATTGGTATGCAAACAA
1 ATTGGTATGCAAACAA
18019469 ATTGGTATGCAAACAA
1 ATTGGTATGCAAACAA
18019485 ATT
1 ATT
18019488 CCAAGTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.29
Consensus pattern (16 bp):
ATTGGTATGCAAACAA
Found at i:18020371 original size:3 final size:3
Alignment explanation
Indices: 18020329--18020424 Score: 81
Period size: 3 Copynumber: 32.0 Consensus size: 3
18020319 ATGTTCAATG
* ** * *
18020329 TTA TTA TTT TTA GGA TTA TTT TTA TT- TTA TTA TATG TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
* *
18020373 GTA -TA TTA TATA TTA TTG TTA TATA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA
18020419 TTA TTA
1 TTA TTA
18020425 GTTAAAAAAA
Statistics
Matches: 75, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
2 6 0.08
3 61 0.81
4 8 0.11
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:18020397 original size:25 final size:25
Alignment explanation
Indices: 18020350--18020419 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
18020340 AGGATTATTT
18020350 TTATT-TTATTATATGTTATTATAGTA
1 TTATTATTATTAT-TGTTA-TATAGTA
*
18020376 -TATTATATATTATTGTTATATATTA
1 TTATTAT-TATTATTGTTATATAGTA
*
18020401 TTATTATTATTATTATTAT
1 TTATTATTATTATTGTTAT
18020420 TATTAGTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
25 21 0.54
26 12 0.31
27 6 0.15
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (25 bp):
TTATTATTATTATTGTTATATAGTA
Found at i:18020510 original size:37 final size:37
Alignment explanation
Indices: 18020460--18020554 Score: 147
Period size: 37 Copynumber: 2.6 Consensus size: 37
18020450 AAGAAGGAAA
18020460 TTGGTGATTCAATCTCGGATTCGTTGGAGCATGATTC
1 TTGGTGATTCAATCTCGGATTCGTTGGAGCATGATTC
* *
18020497 TTGGTGATTCAATCAT-GGATCCGTTGGAGCGTGATTC
1 TTGGTGATTCAATC-TCGGATTCGTTGGAGCATGATTC
*
18020534 TTGGTGATTCAATCTCAGATT
1 TTGGTGATTCAATCTCGGATT
18020555 TGGTGGGCAT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
36 1 0.02
37 50 0.96
38 1 0.02
ACGTcount: A:0.20, C:0.16, G:0.26, T:0.38
Consensus pattern (37 bp):
TTGGTGATTCAATCTCGGATTCGTTGGAGCATGATTC
Found at i:18026472 original size:32 final size:32
Alignment explanation
Indices: 18026436--18026500 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
18026426 AATTTTAATG
* * *
18026436 ACAGATAATTTCTTTTTACTTATGGGTAATTT
1 ACAGATAATTTCTCTTTACTTATAGGCAATTT
18026468 ACAGATAATTTCTCTTTACTTATAGGCAATTT
1 ACAGATAATTTCTCTTTACTTATAGGCAATTT
18026500 A
1 A
18026501 AGTATTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.46
Consensus pattern (32 bp):
ACAGATAATTTCTCTTTACTTATAGGCAATTT
Found at i:18032220 original size:19 final size:18
Alignment explanation
Indices: 18032188--18032223 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
18032178 AAATTGAGTA
*
18032188 TAAAAATATTAATATAAT
1 TAAAAATATGAATATAAT
18032206 TAAAAATAATGAATATAA
1 TAAAAAT-ATGAATATAA
18032224 CATAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (18 bp):
TAAAAATATGAATATAAT
Found at i:18032966 original size:15 final size:16
Alignment explanation
Indices: 18032921--18032969 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
18032911 TGGATTGATC
*
18032921 AACTCAAAATAATTCA
1 AACTCAAAATAATTTA
*
18032937 AACTCAAAATGATTTA
1 AACTCAAAATAATTTA
18032953 AACTC-AAATAATTTA
1 AACTCAAAATAATTTA
18032968 AA
1 AA
18032970 TTTGAATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 11 0.37
16 19 0.63
ACGTcount: A:0.55, C:0.14, G:0.02, T:0.29
Consensus pattern (16 bp):
AACTCAAAATAATTTA
Found at i:18033025 original size:16 final size:16
Alignment explanation
Indices: 18033002--18033050 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
18032992 ACCTAAATTG
*
18033002 ATAC-AACTCAAAATA
1 ATACAAACTTAAAATA
*
18033017 ATATAAACTTAAAATA
1 ATACAAACTTAAAATA
*
18033033 ATCCAAACTTAAAATA
1 ATACAAACTTAAAATA
18033049 AT
1 AT
18033051 TCCACTTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
15 3 0.10
16 26 0.90
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.27
Consensus pattern (16 bp):
ATACAAACTTAAAATA
Found at i:18033727 original size:2 final size:2
Alignment explanation
Indices: 18033720--18033748 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18033710 CTCAAAAGAC
18033720 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18033749 GAGAGAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18033753 original size:2 final size:2
Alignment explanation
Indices: 18033748--18033780 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
18033738 ATATATATAT
18033748 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
18033781 AAACTAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:18035828 original size:11 final size:11
Alignment explanation
Indices: 18035812--18035836 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
18035802 AAAAAAAAGC
18035812 AAAATGAAATA
1 AAAATGAAATA
18035823 AAAATGAAATA
1 AAAATGAAATA
18035834 AAA
1 AAA
18035837 GAACTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (11 bp):
AAAATGAAATA
Found at i:18035866 original size:13 final size:14
Alignment explanation
Indices: 18035843--18035885 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
18035833 AAAAGAACTT
18035843 AAAATAAAAAATAAA
1 AAAAT-AAAAATAAA
* *
18035858 AAAAT-AAAATTAG
1 AAAATAAAAATAAA
18035871 AAAATAAAAATAAA
1 AAAATAAAAATAAA
18035885 A
1 A
18035886 TGAAAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 11 0.48
14 7 0.30
15 5 0.22
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.16
Consensus pattern (14 bp):
AAAATAAAAATAAA
Found at i:18035876 original size:21 final size:20
Alignment explanation
Indices: 18035842--18035897 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
18035832 TAAAAGAACT
18035842 TAAAATAAAAAATAAAAAAA
1 TAAAATAAAAAATAAAAAAA
*
18035862 TAAAATTAGAAAAT--AAAAA
1 TAAAA-TAAAAAATAAAAAAA
18035881 TAAAATGAAAAAA-AAAA
1 TAAAAT-AAAAAATAAAA
18035898 CCTGCAATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
18 1 0.03
19 15 0.50
20 7 0.23
21 7 0.23
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (20 bp):
TAAAATAAAAAATAAAAAAA
Found at i:18035892 original size:26 final size:25
Alignment explanation
Indices: 18035818--18035893 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 25
18035808 AAGCAAAATG
*
18035818 AAATAAAAATGAAATAAAAGAACTTA
1 AAATAAAAATAAAATAAAA-AACTTA
*
18035844 AAATAAAAAATAAAA-AAATAAAATTAGA
1 AAAT-AAAAATAAAATAAA-AAACTT--A
18035872 AAATAAAAATAAAATGAAAAAA
1 AAATAAAAATAAAAT-AAAAAA
18035894 AAAACCTGCA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
26 11 0.26
27 20 0.48
28 8 0.19
29 3 0.07
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.17
Consensus pattern (25 bp):
AAATAAAAATAAAATAAAAAACTTA
Found at i:18036693 original size:22 final size:22
Alignment explanation
Indices: 18036665--18036710 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
18036655 CACAAATTGA
18036665 AAAAAAAAAGAAAAATAATAAT
1 AAAAAAAAAGAAAAATAATAAT
* * *
18036687 AAAAAAATATAATAATAATAAT
1 AAAAAAAAAGAAAAATAATAAT
18036709 AA
1 AA
18036711 TACATAATAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (22 bp):
AAAAAAAAAGAAAAATAATAAT
Found at i:18036698 original size:13 final size:14
Alignment explanation
Indices: 18036675--18036717 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
18036665 AAAAAAAAAG
18036675 AAAAATAATAATAA
1 AAAAATAATAATAA
18036689 AAAAAT-ATAATAA
1 AAAAATAATAATAA
*
18036702 TAATAATAATACATAA
1 -AAAAATAATA-ATAA
18036718 TACAATGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 7 0.28
14 11 0.44
15 3 0.12
16 4 0.16
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAAATAATAATAA
Found at i:18036700 original size:16 final size:15
Alignment explanation
Indices: 18036675--18036719 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
18036665 AAAAAAAAAG
18036675 AAAAATAATAATAAA
1 AAAAATAATAATAAA
*
18036690 AAAATATAATAATAAT
1 AAAA-ATAATAATAAA
*
18036706 AATAATACATAATA
1 AAAAATA-ATAATA
18036720 CAATGTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 7 0.27
16 19 0.73
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAAATAATAATAAA
Found at i:18036701 original size:3 final size:3
Alignment explanation
Indices: 18036678--18036799 Score: 116
Period size: 3 Copynumber: 42.3 Consensus size: 3
18036668 AAAAAAGAAA
* *
18036678 AAT AAT AAT AA- AAA AAT -AT AAT AAT AAT AAT AAT ACAT AAT -AC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
* *
18036721 AAT -GT AAT AAT AAT -AT AAT AGT AAT -AT AAT -AT ACCAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A--AT AAT AAT
*
18036763 AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
18036800 TCACCATATA
Statistics
Matches: 99, Mismatches: 9, Indels: 22
0.76 0.07 0.17
Matches are distributed among these distances:
2 14 0.14
3 80 0.81
4 3 0.03
5 2 0.02
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:18036769 original size:18 final size:17
Alignment explanation
Indices: 18036704--18036819 Score: 84
Period size: 15 Copynumber: 6.8 Consensus size: 17
18036694 TATAATAATA
18036704 ATAATAATACATAATACAAT
1 ATAATAATA-AT-ATAC-AT
*
18036724 GTAATAATAATATA-AT
1 ATAATAATAATATACAT
18036740 AGTAAT-ATAATATACCAT
1 A-TAATAATAATATA-CAT
*
18036758 ATAATAATAATA-ATA-
1 ATAATAATAATATACAT
* *
18036773 ATAATAATAGTA-ATA-
1 ATAATAATAATATACAT
18036788 ATAATAATAATATCACCAT
1 ATAATAATAATAT-A-CAT
18036807 ATAAT-ATAATATA
1 ATAATAATAATATA
18036820 ATACACTATA
Statistics
Matches: 82, Mismatches: 6, Indels: 19
0.77 0.06 0.18
Matches are distributed among these distances:
15 25 0.30
16 11 0.13
17 11 0.13
18 20 0.24
19 7 0.09
20 8 0.10
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.34
Consensus pattern (17 bp):
ATAATAATAATATACAT
Found at i:18036812 original size:66 final size:63
Alignment explanation
Indices: 18036693--18036819 Score: 177
Period size: 63 Copynumber: 2.0 Consensus size: 63
18036683 TAATAAAAAA
*
18036693 ATATAATAATAATAATAATACATAATACAATGTAATAATAATATAATAGTAATATAATATACC
1 ATATAATAATAATAATAATACATAATACAATATAATAATAATATAATAGTAATATAATATACC
*
18036756 ATATAATAATAATAATAATA-ATAATAGTAATAATAATAATAATATCACCATA-TAATATAATAT
1 ATATAATAATAATAATAATACATAATA-CAAT-ATAATAATAATAT-A--ATAGTAATATAATAT
18036819 A
61 A
18036820 ATACACTATA
Statistics
Matches: 57, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
62 6 0.11
63 23 0.40
64 12 0.21
65 1 0.02
66 12 0.21
67 3 0.05
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.34
Consensus pattern (63 bp):
ATATAATAATAATAATAATACATAATACAATATAATAATAATATAATAGTAATATAATATACC
Found at i:18036849 original size:71 final size:72
Alignment explanation
Indices: 18036733--18036866 Score: 180
Period size: 71 Copynumber: 1.9 Consensus size: 72
18036723 TGTAATAATA
* * * * *
18036733 ATATAATAGTAATATAATATACCATATAATAATAATAATAATAATAATAGTAATAATAATAATAA
1 ATATAATAGTAATATAATACACCATATAATAATAACAAAAATAATAACAGTAAGAATAATAATAA
18036798 TATCACC
66 TATCACC
* * * *
18036805 ATATAATA-TAATATAATACACTATATTATGATAACAAAAATAATAACAGTAAGAGTAATAAT
1 ATATAATAGTAATATAATACACCATATAATAATAACAAAAATAATAACAGTAAGAATAATAAT
18036867 TGACCCGATT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
71 45 0.85
72 8 0.15
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.32
Consensus pattern (72 bp):
ATATAATAGTAATATAATACACCATATAATAATAACAAAAATAATAACAGTAAGAATAATAATAA
TATCACC
Found at i:18037127 original size:55 final size:55
Alignment explanation
Indices: 18037067--18037198 Score: 140
Period size: 56 Copynumber: 2.4 Consensus size: 55
18037057 GATTGAATTG
* ** * *
18037067 CAAGTCTGAAAAATGATCTGGCCTAAGTTGAGATCGAATGACCAAGATTGAACCA
1 CAAGTCTGAAAAATGATCTGGACTAAGCCGAGATCAAATGACCAAGATTAAACCA
* * * * * *
18037122 TAAGTCTAGAAAACTAACCTGGACTAAGCCGAGGTCAAATGACCAGGATTAAACCA
1 CAAGTCT-GAAAAATGATCTGGACTAAGCCGAGATCAAATGACCAAGATTAAACCA
18037178 CAAGTCT-AGAAAATGATCTGG
1 CAAGTCTGA-AAAATGATCTGG
18037199 GCTTAGTCAA
Statistics
Matches: 60, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
54 1 0.02
55 15 0.25
56 44 0.73
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.20
Consensus pattern (55 bp):
CAAGTCTGAAAAATGATCTGGACTAAGCCGAGATCAAATGACCAAGATTAAACCA
Found at i:18037416 original size:110 final size:110
Alignment explanation
Indices: 18037109--18037419 Score: 293
Period size: 110 Copynumber: 2.8 Consensus size: 110
18037099 ATCGAATGAC
* * ** * * * *
18037109 CAAGATTGAACCATAAGTCTAGAAAACTAACCTGGACTAAGCCGAGGTCAAATGACCAGGATTAA
1 CAAGATTGAACCATAAGTCTAGAAAA-TAATCTGGACTGAGCTAAGATCGAGTGACCAAGATTAA
* * * * * *
18037174 ACCACAAGTCTAGAAAATGATCTGGGCTTAGTCAAGATCAAGCGAT
65 ACCACAAGTCTAGAAAATGATTTGGACTAAGCCAAGATCAAACAAT
*** * * * * * * *
18037220 TGGGATTGAACCATAA-ACCAGAAAGATGATTTGGACTGAGCTAAGATCGAGCGATCGAGATTAA
1 CAAGATTGAACCATAAGTCTAGAAA-ATAATCTGGACTGAGCTAAGATCGAGTGACCAAGATTAA
* * * *
18037284 ACTACAAGTTTGGAAAACGATTTGGACTAAGCCAAGATCAAACAAT
65 ACCACAAGTCTAGAAAATGATTTGGACTAAGCCAAGATCAAACAAT
* *
18037330 CAAGATTGAACCATAAGTCTA-AAATATAATCTGGATTGAGCTAAGATCGAGTGACCAAGAATAA
1 CAAGATTGAACCATAAGTCTAGAAA-ATAATCTGGACTGAGCTAAGATCGAGTGACCAAGATTAA
* *
18037394 ACCACAAGTCAAGAAGATGATTTGGA
65 ACCACAAGTCTAGAAAATGATTTGGA
18037420 TTTAGTCGAG
Statistics
Matches: 151, Mismatches: 47, Indels: 5
0.74 0.23 0.02
Matches are distributed among these distances:
110 135 0.89
111 16 0.11
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.21
Consensus pattern (110 bp):
CAAGATTGAACCATAAGTCTAGAAAATAATCTGGACTGAGCTAAGATCGAGTGACCAAGATTAAA
CCACAAGTCTAGAAAATGATTTGGACTAAGCCAAGATCAAACAAT
Found at i:18043044 original size:12 final size:12
Alignment explanation
Indices: 18043022--18043051 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
18043012 AAAAGAACTT
18043022 AAAATATAAAATC
1 AAAA-ATAAAATC
18043035 AAAAATAAAATC
1 AAAAATAAAATC
18043047 AAAAA
1 AAAAA
18043052 ATTAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.17
Consensus pattern (12 bp):
AAAAATAAAATC
Found at i:18043853 original size:3 final size:3
Alignment explanation
Indices: 18043847--18044043 Score: 118
Period size: 3 Copynumber: 69.0 Consensus size: 3
18043837 AAATAAGGAA
*
18043847 AAT AAT AA- AAA AAT AA- AA- AAT AAT ATAT AAT AAT AAT AAT ACAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT A-AT
* * * *
18043891 AAT -AC AAT -GT AAT AAT AAT -AT AAT -AT AAT -CT AAT -AT AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
18043933 AAT -CT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * *
18043978 CAC CAT -AT AAT -AT AAT -AT AAT ACACT ATAT TAT GAT AAT AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-A-T A-AT AAT AAT AAT AAT AAT
* *
18044023 AAT AAC AAT AAT AGT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT
18044044 TGACCCGATT
Statistics
Matches: 153, Mismatches: 23, Indels: 36
0.72 0.11 0.17
Matches are distributed among these distances:
2 26 0.17
3 116 0.76
4 8 0.05
5 3 0.02
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:18043866 original size:18 final size:19
Alignment explanation
Indices: 18043833--18043871 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
18043823 TCACAGATTG
18043833 AAAAAAATAAGGAAAATAAT
1 AAAAAAATAA-GAAAATAAT
18043853 AAAAAAATAA-AAAATAAT
1 AAAAAAATAAGAAAATAAT
18043871 A
1 A
18043872 TATAATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
20 10 0.53
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.15
Consensus pattern (19 bp):
AAAAAAATAAGAAAATAAT
Found at i:18043887 original size:26 final size:26
Alignment explanation
Indices: 18043848--18044043 Score: 124
Period size: 26 Copynumber: 7.5 Consensus size: 26
18043838 AATAAGGAAA
* *
18043848 ATAATAA-AAAAATAAAAAATAATAT
1 ATAATAATAATAATAAATAATAATAT
*
18043873 ATAATAATAATAATACATAATACA-AT
1 ATAATAATAATAATAAATAATA-ATAT
*
18043899 GTAATAATAAT-ATAATATAATCTAATAT
1 ATAATAATAATAATAA-ATAA--TAATAT
* *
18043927 AATAGTAAT-CTAATATAATAATAATA-
1 -ATAATAATAATAATA-AATAATAATAT
18043953 ATAATAATAATAAT-AATAATAATAT
1 ATAATAATAATAATAAATAATAATAT
**
18043978 CACCAT-ATAAT-ATAATATAATACACTAT
1 -ATAATAATAATAATAA-ATAATA-A-TAT
* * *
18044006 ATTATGATAATAA-AAATAATAACA-
1 ATAATAATAATAATAAATAATAATAT
*
18044030 ATAATAGTAATAAT
1 ATAATAATAATAAT
18044044 TGACCCGATT
Statistics
Matches: 134, Mismatches: 18, Indels: 38
0.71 0.09 0.20
Matches are distributed among these distances:
24 22 0.16
25 24 0.18
26 41 0.31
27 17 0.13
28 15 0.11
29 14 0.10
30 1 0.01
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (26 bp):
ATAATAATAATAATAAATAATAATAT
Found at i:18043926 original size:15 final size:15
Alignment explanation
Indices: 18043866--18043999 Score: 99
Period size: 16 Copynumber: 8.1 Consensus size: 15
18043856 AAAATAAAAA
18043866 ATAATAT-ATAATAAT
1 ATAATATAAT-ATAAT
*
18043881 AATAATACATAATACAAT
1 -ATAAT--ATAATATAAT
*
18043899 GTAATAATAATATAAT
1 ATAAT-ATAATATAAT
*
18043915 ATAATCTAATATAAT
1 ATAATATAATATAAT
*
18043930 AGTAATCTAATATAAT
1 A-TAATATAATATAAT
18043946 AATAATAATAATAATAAT
1 -ATAAT-ATAAT-ATAAT
18043964 AATAATAATAATATCACCAT
1 -ATAAT-ATAATAT-A--AT
18043984 ATAATATAATATAAT
1 ATAATATAATATAAT
18043999 A
1 A
18044000 CACTATATTA
Statistics
Matches: 101, Mismatches: 7, Indels: 21
0.78 0.05 0.16
Matches are distributed among these distances:
15 13 0.13
16 36 0.36
17 12 0.12
18 31 0.31
19 7 0.07
20 2 0.02
ACGTcount: A:0.58, C:0.05, G:0.01, T:0.35
Consensus pattern (15 bp):
ATAATATAATATAAT
Found at i:18043940 original size:11 final size:10
Alignment explanation
Indices: 18043866--18043999 Score: 99
Period size: 10 Copynumber: 12.1 Consensus size: 10
18043856 AAAATAAAAA
18043866 ATAATAT-AT
1 ATAATATAAT
18043875 AATAATAATAAT
1 -ATAAT-ATAAT
*
18043887 ACATAATACAAT
1 --ATAATATAAT
*
18043899 GTAATAATAAT
1 ATAAT-ATAAT
18043910 ATAATATAAT
1 ATAATATAAT
*
18043920 CTAATATAAT
1 ATAATATAAT
*
18043930 AGTAATCTAAT
1 A-TAATATAAT
18043941 ATAATAATAAT
1 ATAAT-ATAAT
18043952 AATAATAATAAT
1 -ATAAT-ATAAT
18043964 AATAATAATAAT
1 -ATAAT-ATAAT
18043976 ATCACCATATAAT
1 AT-A--ATATAAT
18043989 ATAATATAAT
1 ATAATATAAT
18043999 A
1 A
18044000 CACTATATTA
Statistics
Matches: 105, Mismatches: 9, Indels: 20
0.78 0.07 0.15
Matches are distributed among these distances:
10 35 0.33
11 25 0.24
12 31 0.30
13 12 0.11
14 2 0.02
ACGTcount: A:0.58, C:0.05, G:0.01, T:0.35
Consensus pattern (10 bp):
ATAATATAAT
Found at i:18043987 original size:74 final size:69
Alignment explanation
Indices: 18043867--18044043 Score: 175
Period size: 71 Copynumber: 2.5 Consensus size: 69
18043857 AAATAAAAAA
* * * *
18043867 TAATAT-ATAATAATAATAATACATAAT-ACAAT-GTAATAATAATATAATATAATCTAATATAA
1 TAATATAATAATAATAATAATA-ATAATAATAATAATAATAATAATATAATATAATATAATACAA
18043929 TAGTAAT
65 TA-T-AT
18043936 CTAATATAATAATAATAATAATAATAATAATAATAATAAT-ATCACCATATAATATAATATAATA
1 -TAATATAATAATAATAATAATAATAATAATAATAATAATAAT-A--ATATAATATAATATAATA
*
18044000 CACTATAT
62 CAATATAT
* * *
18044008 T-ATGATAATAAAAATAATAACAATAATAGTAATAAT
1 TAAT-ATAATAATAATAATAATAATAATAATAATAAT
18044044 TGACCCGATT
Statistics
Matches: 92, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
70 13 0.14
71 51 0.55
72 7 0.08
73 1 0.01
74 20 0.22
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.34
Consensus pattern (69 bp):
TAATATAATAATAATAATAATAATAATAATAATAATAATAATAATATAATATAATATAATACAAT
ATAT
Found at i:18045449 original size:30 final size:31
Alignment explanation
Indices: 18045400--18045457 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
18045390 GCTTAATGTC
*
18045400 TTGGTTTTTAAGATATAGTTGGTAGTAGACG
1 TTGGATTTTAAGATATAGTTGGTAGTAGACG
*
18045431 TTGGATTTTAGGAT-TAGTTGGTAGTAG
1 TTGGATTTTAAGATATAGTTGGTAGTAG
18045458 TTGTTAAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 13 0.52
31 12 0.48
ACGTcount: A:0.24, C:0.02, G:0.31, T:0.43
Consensus pattern (31 bp):
TTGGATTTTAAGATATAGTTGGTAGTAGACG
Found at i:18051550 original size:36 final size:36
Alignment explanation
Indices: 18051503--18051571 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
18051493 CCCTTTTTAG
18051503 TAAAAAATGTCTTAAATAATACCCTTCAATTTTGAA
1 TAAAAAATGTCTTAAATAATACCCTTCAATTTTGAA
18051539 TAAAAAATGTCTTAAATAATACCCTTCAATTTT
1 TAAAAAATGTCTTAAATAATACCCTTCAATTTT
18051572 AAAGGGTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.43, C:0.14, G:0.04, T:0.38
Consensus pattern (36 bp):
TAAAAAATGTCTTAAATAATACCCTTCAATTTTGAA
Found at i:18052311 original size:32 final size:31
Alignment explanation
Indices: 18052246--18052312 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 31
18052236 TCTTTTTTAA
* *
18052246 TTTTATTTTTGTATTTTTATTTTATTTACAT
1 TTTTATTATTGTATTTTTATTTTATATACAT
*
18052277 TTTTATTATTGTTATTGTTT-TTTTATATATAT
1 TTTTATTATTG-TATT-TTTATTTTATATACAT
18052309 TTTT
1 TTTT
18052313 CTTTTATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 10 0.32
32 18 0.58
33 3 0.10
ACGTcount: A:0.19, C:0.01, G:0.04, T:0.75
Consensus pattern (31 bp):
TTTTATTATTGTATTTTTATTTTATATACAT
Found at i:18052339 original size:19 final size:19
Alignment explanation
Indices: 18052315--18052359 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
18052305 ATATTTTTCT
18052315 TTTATT-TTTATCTTATGTA
1 TTTATTATTTAT-TTATGTA
*
18052334 TTTATTATTTATTTATTTA
1 TTTATTATTTATTTATGTA
18052353 TTTATTA
1 TTTATTA
18052360 CTACTATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTATTATTTATTTATGTA
Found at i:18052345 original size:4 final size:4
Alignment explanation
Indices: 18052321--18052541 Score: 52
Period size: 4 Copynumber: 53.5 Consensus size: 4
18052311 TTCTTTTATT
* *
18052321 TTTA TCTTA TGTA TTTA -TTA TTTA TTTA TTTA TTTA -TTA CTACTA TTTA
1 TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -T-TTA TTTA
* *
18052370 -TTA GTATA TATA TCCTTA -TTA -TTA TTT- TTT- TTCTA TTAATA TTTA
1 TTTA -TTTA TTTA T--TTA TTTA TTTA TTTA TTTA TT-TA TT--TA TTTA
* * * *
18052415 TATATA TTTA TCTGA TTATA TGTTA -TAA TTTA TCTA -TTA TTTA ATT-
1 T-T-TA TTTA T-TTA TT-TA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * * *
18052461 TTAA TTTA TCTG TTAA TTT- TTTA TTTA TTTGA TTTA TTTTCA TTAA TATT-
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT-A TTTA -TTT-A TTTA T-TTA
* *
18052511 TTTA TTTGA TTTT TTTA TTTT TTTA TTTA TT
1 TTTA TTT-A TTTA TTTA TTTA TTTA TTTA TT
18052542 CGGCTGAAAA
Statistics
Matches: 160, Mismatches: 29, Indels: 56
0.65 0.12 0.23
Matches are distributed among these distances:
3 30 0.19
4 85 0.53
5 32 0.20
6 13 0.08
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.66
Consensus pattern (4 bp):
TTTA
Found at i:18052345 original size:15 final size:16
Alignment explanation
Indices: 18052317--18052354 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
18052307 ATTTTTCTTT
18052317 TATTT-TTATCTTATG
1 TATTTATTATCTTATG
*
18052332 TATTTATTAT-TTATT
1 TATTTATTATCTTATG
18052347 TATTTATT
1 TATTTATT
18052355 TATTACTACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (16 bp):
TATTTATTATCTTATG
Found at i:18052355 original size:12 final size:12
Alignment explanation
Indices: 18052321--18052541 Score: 52
Period size: 11 Copynumber: 17.8 Consensus size: 12
18052311 TTCTTTTATT
*
18052321 TTTATCTTATGTA
1 TTTAT-TTATTTA
18052334 TTTA-TTATTTA
1 TTTATTTATTTA
18052345 TTTATTTATTTA
1 TTTATTTATTTA
*
18052357 -TTACTACTATTTA
1 TTTA-T-TTATTTA
* *
18052370 -TTAGTATATATA
1 TTTA-TTTATTTA
18052382 TCCTTA-TTA-TTA
1 T--TTATTTATTTA
18052394 TTT-TTT-TTCTA
1 TTTATTTATT-TA
18052405 TTAATATTTATATATA
1 TT--TATTTAT-T-TA
*
18052421 TTTATCTGATTATA
1 TTTAT-TTATT-TA
*
18052435 TGTTA-TAATTTA
1 T-TTATTTATTTA
*
18052447 TCTA-TTATTTA
1 TTTATTTATTTA
* *
18052458 ATT-TTAATTTA
1 TTTATTTATTTA
* * *
18052469 TCTGTTAATTT-
1 TTTATTTATTTA
18052480 TTTATTTATTTGA
1 TTTATTTATTT-A
*
18052493 TTTATTTTCATTAA
1 TTTA-TTT-ATTTA
18052507 TATT-TTTATTTGA
1 T-TTATTTATTT-A
* *
18052520 TTTTTTTATTTT
1 TTTATTTATTTA
18052532 TTTATTTATT
1 TTTATTTATT
18052542 CGGCTGAAAA
Statistics
Matches: 159, Mismatches: 24, Indels: 51
0.68 0.10 0.22
Matches are distributed among these distances:
10 5 0.03
11 41 0.26
12 40 0.25
13 37 0.23
14 16 0.10
15 15 0.09
16 5 0.03
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.66
Consensus pattern (12 bp):
TTTATTTATTTA
Found at i:18052448 original size:22 final size:23
Alignment explanation
Indices: 18052415--18052472 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
18052405 TTAATATTTA
*
18052415 TATATATTTATCTGATTATAT-GT
1 TATA-ATTTATCTGATTATATAAT
*
18052438 TATAATTTATCT-ATTATTTAAT
1 TATAATTTATCTGATTATATAAT
*
18052460 TTTAATTTATCTG
1 TATAATTTATCTG
18052473 TTAATTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 6 0.20
22 20 0.67
23 4 0.13
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (23 bp):
TATAATTTATCTGATTATATAAT
Found at i:18052516 original size:31 final size:30
Alignment explanation
Indices: 18052473--18052531 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 30
18052463 AATTTATCTG
18052473 TTAATTTTTTATTT-ATTTGATTTATTTTCA
1 TTAATTTTTTATTTGATTT-ATTTATTTTCA
*
18052503 TTAATATTTTTATTTGATTTTTTTATTTT
1 TTAAT-TTTTTATTTGATTTATTTATTTT
18052532 TTTATTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 5 0.19
31 17 0.65
32 4 0.15
ACGTcount: A:0.22, C:0.02, G:0.03, T:0.73
Consensus pattern (30 bp):
TTAATTTTTTATTTGATTTATTTATTTTCA
Found at i:18053370 original size:9 final size:9
Alignment explanation
Indices: 18053356--18053413 Score: 71
Period size: 9 Copynumber: 6.3 Consensus size: 9
18053346 GCTCCAGGTT
18053356 TTTTTTTTA
1 TTTTTTTTA
18053365 TTTTTTTTA
1 TTTTTTTTA
*
18053374 TTATTTTTA
1 TTTTTTTTA
* *
18053383 TTATTTTTG
1 TTTTTTTTA
18053392 TTTTATTTTA
1 TTTT-TTTTA
*
18053402 TTTTATTTA
1 TTTTTTTTA
18053411 TTT
1 TTT
18053414 ATTATTATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
9 35 0.81
10 8 0.19
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.83
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:18053396 original size:32 final size:35
Alignment explanation
Indices: 18053354--18053422 Score: 108
Period size: 32 Copynumber: 2.1 Consensus size: 35
18053344 CCGCTCCAGG
*
18053354 TTTTTTTTTTATTTT-TTTTA-TTATTT-TTATTA
1 TTTTTGTTTTATTTTATTTTATTTATTTATTATTA
18053386 TTTTTGTTTTATTTTATTTTATTTATTTATTATTA
1 TTTTTGTTTTATTTTATTTTATTTATTTATTATTA
18053421 TT
1 TT
18053423 ATATTAGGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 14 0.42
33 5 0.15
34 6 0.18
35 8 0.24
ACGTcount: A:0.17, C:0.00, G:0.01, T:0.81
Consensus pattern (35 bp):
TTTTTGTTTTATTTTATTTTATTTATTTATTATTA
Found at i:18053400 original size:28 final size:27
Alignment explanation
Indices: 18053360--18053512 Score: 57
Period size: 28 Copynumber: 5.5 Consensus size: 27
18053350 CAGGTTTTTT
* *
18053360 TTTTATTTTTTTTATTATTTTTATTAT
1 TTTTATTTTATTTATTATTTTTATTTT
*
18053387 TTTTGTTTTATTTTATT-TTATTTATTTAT
1 TTTTATTTTA-TTTATTATT-TTTATTT-T
* * * *
18053416 TATTATTATA-TTAGGGTTGTTTAATATTTT
1 TTTTATTTTATTTA---TTATTT-TTATTTT
* *
18053446 TTTTCTTCTT-TCTA-T-TTTTTATTTAT
1 TTTTATT-TTATTTATTATTTTTATTT-T
*
18053472 TTTCATTTTATTTACTT-TTATTTATTTT
1 TTTTATTTTATTTA-TTATT-TTTATTTT
* *
18053500 ATTTATTTCATTT
1 TTTTATTTTATTT
18053513 TCTTTAAATA
Statistics
Matches: 93, Mismatches: 18, Indels: 29
0.66 0.13 0.21
Matches are distributed among these distances:
25 7 0.08
26 12 0.13
27 14 0.15
28 26 0.28
29 15 0.16
30 9 0.10
31 10 0.11
ACGTcount: A:0.19, C:0.04, G:0.03, T:0.74
Consensus pattern (27 bp):
TTTTATTTTATTTATTATTTTTATTTT
Found at i:18053427 original size:19 final size:18
Alignment explanation
Indices: 18053360--18053427 Score: 57
Period size: 19 Copynumber: 3.7 Consensus size: 18
18053350 CAGGTTTTTT
* *
18053360 TTTTATTTTTTTTA-TTA
1 TTTTATTATATTTATTTA
* *
18053377 TTTTTATTATTTTTGTTTTA
1 -TTTTATTATATTT-ATTTA
*
18053397 TTTTATTTTATTTATTTA
1 TTTTATTATATTTATTTA
18053415 TTATTATTATATT
1 TT-TTATTATATT
18053428 AGGGTTGTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
18 18 0.44
19 20 0.49
20 3 0.07
ACGTcount: A:0.21, C:0.00, G:0.01, T:0.78
Consensus pattern (18 bp):
TTTTATTATATTTATTTA
Found at i:18053501 original size:9 final size:9
Alignment explanation
Indices: 18053463--18053512 Score: 57
Period size: 9 Copynumber: 5.3 Consensus size: 9
18053453 CTTTCTATTT
18053463 TTTA-TTTA
1 TTTATTTTA
18053471 TTTTCATTTTA
1 -TTT-ATTTTA
18053482 TTTACTTTTA
1 TTTA-TTTTA
18053492 TTTATTTTA
1 TTTATTTTA
*
18053501 TTTATTTCA
1 TTTATTTTA
18053510 TTT
1 TTT
18053513 TCTTTAAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
9 20 0.54
10 13 0.35
11 4 0.11
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTATTTTA
Found at i:18053699 original size:130 final size:119
Alignment explanation
Indices: 18053542--18053951 Score: 449
Period size: 117 Copynumber: 3.4 Consensus size: 119
18053532 AAAAAAAACA
* * * *
18053542 AAAAAAAATGT-TTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAGAATAAATATTCAAAAA
1 AAAAAAAATATATTTTG-GAAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTTCAAAAA
*
18053606 GGTTTTTTTTTTTTTAAGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAGAATTC
65 GG---TTTTTTTTTTAGGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAGAATTC
18053664 AAAATATATATATCTATATATTTAGGAAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTT
1 AAAA-A-A-A-A--TATAT-TTT-GGAAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTT
* * **
18053729 TCAAGAAAGG-TTTTTTTTTAGGAAAAATTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTTC
58 TCAA-AAAGGTTTTTTTTTTAGGAAAAGTTGAAAGTATCAATTTTTCTCGAAATT-AAGAATTC
* * * *
18053792 --AAAAAATAT-TTTTGGGAAAAGTTGAAACTATCAATTTTCCTTAAAAATAAATTTTTAAAAA-
1 AAAAAAAATATATTTTGGAAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTTCAAAAAG
*** * *
18053853 -TGAGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAA-AATTT
66 GTTTTTTTTTTAGGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAGAATTC
*
18053905 AAAAAAAATATATTTTGGAGAAATGTTGAAAGTATCAATTTTTCCTT
1 AAAAAAAATATATTTTGGA-AAAAGTTGAAAGTATCAA-TTTTCCTT
18053952 GTACAAAAGC
Statistics
Matches: 246, Mismatches: 25, Indels: 38
0.80 0.08 0.12
Matches are distributed among these distances:
113 2 0.01
114 2 0.01
115 47 0.19
116 9 0.04
117 57 0.23
118 11 0.04
119 1 0.00
120 3 0.01
122 5 0.02
123 2 0.01
124 2 0.01
125 2 0.01
126 3 0.01
127 41 0.17
128 8 0.03
129 1 0.00
130 44 0.18
131 6 0.02
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39
Consensus pattern (119 bp):
AAAAAAAATATATTTTGGAAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTTCAAAAAG
GTTTTTTTTTTAGGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAGAATTC
Found at i:18053910 original size:58 final size:56
Alignment explanation
Indices: 18053691--18053946 Score: 246
Period size: 57 Copynumber: 4.4 Consensus size: 56
18053681 ATATTTAGGA
* * ** * *
18053691 AAAAGTTGAAAGTATCAATTTTCCT-TAAGAATAAATTTTCAAGAAAGGTTTTTTTTTAGG
1 AAAAGTTGAAAGTATCAATTTTCCTCGAA-ATTAAATTTT-AA-AAA--AATATTTTTGGG
* *
18053751 AAAAATTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTTCAAAAAATATTTTTGGG
1 AAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAA-TTTTAAAAAAATATTTTTGGG
* ** * *
18053808 AAAAGTTGAAACTATCAATTTTCCTTAAAAATAAATTTT-TAAAAATGAGTTTTTGAGG
1 AAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAATTTTAAAAAAAT-A-TTTTTG-GG
* *
18053866 AAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAATTTAAAAAAAATATATTTTGGAG
1 AAAAGTTGAAAGTATCAATTTTCCTCGAAATT-AAATTTTAAAAAAATAT-TTTTGG-G
*
18053925 AAATGTTGAAAGTATCAATTTT
1 AAAAGTTGAAAGTATCAATTTT
18053947 TCCTTGTACA
Statistics
Matches: 165, Mismatches: 22, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
55 6 0.04
56 5 0.03
57 44 0.27
58 31 0.19
59 37 0.22
60 36 0.22
61 6 0.04
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.38
Consensus pattern (56 bp):
AAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAATTTTAAAAAAATATTTTTGGG
Found at i:18057080 original size:28 final size:28
Alignment explanation
Indices: 18057048--18057104 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
18057038 TTTTTTGGAA
18057048 TAAATGAAATCTTCTAGTTGAATACCGT
1 TAAATGAAATCTTCTAGTTGAATACCGT
18057076 TAAATGAAATCTTCTAGTTGAATACCGT
1 TAAATGAAATCTTCTAGTTGAATACCGT
18057104 T
1 T
18057105 TTTGAGGCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (28 bp):
TAAATGAAATCTTCTAGTTGAATACCGT
Found at i:18064364 original size:8 final size:8
Alignment explanation
Indices: 18064351--18064419 Score: 68
Period size: 8 Copynumber: 8.6 Consensus size: 8
18064341 ATGCTTAAAG
18064351 AAAAATAA
1 AAAAATAA
*
18064359 AAAAATGA
1 AAAAATAA
*
18064367 AAAAAT-G
1 AAAAATAA
*
18064374 AAAAATGA
1 AAAAATAA
* *
18064382 AAGAATGA
1 AAAAATAA
18064390 AAAAATAA
1 AAAAATAA
18064398 AAAAATGAA
1 AAAAAT-AA
*
18064407 AAAAAGAA
1 AAAAATAA
18064415 AAAAA
1 AAAAA
18064420 AAGTGAATGA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
7 6 0.12
8 39 0.75
9 7 0.13
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (8 bp):
AAAAATAA
Found at i:18064370 original size:15 final size:15
Alignment explanation
Indices: 18064359--18064409 Score: 75
Period size: 15 Copynumber: 3.3 Consensus size: 15
18064349 AGAAAAATAA
18064359 AAAAATGAAAAAATG
1 AAAAATGAAAAAATG
*
18064374 AAAAATGAAAGAATG
1 AAAAATGAAAAAATG
*
18064389 AAAAAATAAAAAAATG
1 -AAAAATGAAAAAATG
18064405 AAAAA
1 AAAAA
18064410 AAGAAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
15 19 0.59
16 13 0.41
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (15 bp):
AAAAATGAAAAAATG
Found at i:18064395 original size:39 final size:39
Alignment explanation
Indices: 18064351--18064434 Score: 125
Period size: 39 Copynumber: 2.1 Consensus size: 39
18064341 ATGCTTAAAG
* *
18064351 AAAAATAAAAAAATGAAAAAATGAAAAATGAAA-GAATGA
1 AAAAATAAAAAAATGAAAAAAAGAAAAA-AAAAGGAATGA
18064390 AAAAATAAAAAAATGAAAAAAAGAAAAAAAAAGTGAATGA
1 AAAAATAAAAAAATGAAAAAAAGAAAAAAAAAG-GAATGA
18064430 AAAAA
1 AAAAA
18064435 GAGGACTTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
38 3 0.07
39 27 0.66
40 11 0.27
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.11
Consensus pattern (39 bp):
AAAAATAAAAAAATGAAAAAAAGAAAAAAAAAGGAATGA
Found at i:18065479 original size:13 final size:13
Alignment explanation
Indices: 18065461--18065490 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
18065451 GGTGCCTCTG
18065461 TTTAGAGGAGCAA
1 TTTAGAGGAGCAA
18065474 TTTAGAGGAGCAA
1 TTTAGAGGAGCAA
18065487 TTTA
1 TTTA
18065491 CTTTTCAAAG
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:0.37, C:0.07, G:0.27, T:0.30
Consensus pattern (13 bp):
TTTAGAGGAGCAA
Found at i:18065488 original size:54 final size:54
Alignment explanation
Indices: 18065425--18065531 Score: 214
Period size: 54 Copynumber: 2.0 Consensus size: 54
18065415 ATGATTGTCA
18065425 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTAG
18065479 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTA
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTA
18065532 TTTTTCAAAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (54 bp):
AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTAG
Found at i:18065531 original size:41 final size:41
Alignment explanation
Indices: 18065475--18065653 Score: 214
Period size: 41 Copynumber: 4.2 Consensus size: 41
18065465 GAGGAGCAAT
* * * *
18065475 TTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGT
1 TTAGAGGAGCAATTTATTTTTCAAAGTCGTTGAGCCTCTGA
*
18065516 TTAGAGGAGCAATTTATTTTTCAAAGTGGTTGAGCCTCTGA
1 TTAGAGGAGCAATTTATTTTTCAAAGTCGTTGAGCCTCTGA
* *
18065557 TTAGAAGAGCCATTTATTTTTCTAAAAGTCGTTGAGCCTCTGA
1 TTAGAGGAGCAATTTATTTTTC--AAAGTCGTTGAGCCTCTGA
* * * *
18065600 TTAGAATGAGCTATTTATGTTTCTCAAAGTCATTGAGCCTCTGC
1 TTAG-AGGAGCAATTTAT-TTT-TCAAAGTCGTTGAGCCTCTGA
18065644 TTAGAGGAGC
1 TTAGAGGAGC
18065654 TTTGATCAAA
Statistics
Matches: 120, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
41 56 0.47
43 27 0.22
44 32 0.27
45 3 0.03
46 2 0.02
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (41 bp):
TTAGAGGAGCAATTTATTTTTCAAAGTCGTTGAGCCTCTGA
Found at i:18065648 original size:87 final size:82
Alignment explanation
Indices: 18065475--18065653 Score: 214
Period size: 87 Copynumber: 2.1 Consensus size: 82
18065465 GAGGAGCAAT
* *
18065475 TTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAA
1 TTAGAGGAGCAATTTACTTTTCAAAGTCGTGGAGCCTCTGATTAGAGGAGCAATTTATTTTTCAA
**
18065540 AGTGGTTGAGCCTCTGA
66 AGTCATTGAGCCTCTGA
* * * * * *
18065557 TTAGAAGAGCCATTTATTTTTCTAAAAGTCGTTGAGCCTCTGATTAGAATGAGCTATTTATGTTT
1 TTAGAGGAGCAATTTACTTTTC--AAAGTCGTGGAGCCTCTGATTAG-AGGAGCAATTTAT-TTT
*
18065622 CTCAAAGTCATTGAGCCTCTGC
62 -TCAAAGTCATTGAGCCTCTGA
18065644 TTAGAGGAGC
1 TTAGAGGAGC
18065654 TTTGATCAAA
Statistics
Matches: 80, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
82 19 0.24
84 20 0.25
85 11 0.14
86 3 0.04
87 27 0.34
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (82 bp):
TTAGAGGAGCAATTTACTTTTCAAAGTCGTGGAGCCTCTGATTAGAGGAGCAATTTATTTTTCAA
AGTCATTGAGCCTCTGA
Found at i:18065767 original size:43 final size:44
Alignment explanation
Indices: 18065706--18065815 Score: 141
Period size: 45 Copynumber: 2.5 Consensus size: 44
18065696 TAAAAAAATT
* * *
18065706 GCCTCTGTTTAGAGGAGCTTTGTTTA-TTTTTCAAAGTCGTTGA
1 GCCTCTGATTAGAGGAGCTTTGTTTAGTTTTTCAAAGTAGTTAA
*
18065749 GCCTCTGATTAGAGGAGCTTTGTTTATGTTTTTCGAAGTAGTTAA
1 GCCTCTGATTAGAGGAGCTTTGTTTA-GTTTTTCAAAGTAGTTAA
* * *
18065794 GCTTCTGCTTAGAGGAGTTTTG
1 GCCTCTGATTAGAGGAGCTTTG
18065816 ATCAAATCTT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
43 25 0.43
45 33 0.57
ACGTcount: A:0.19, C:0.13, G:0.25, T:0.43
Consensus pattern (44 bp):
GCCTCTGATTAGAGGAGCTTTGTTTAGTTTTTCAAAGTAGTTAA
Found at i:18066024 original size:31 final size:33
Alignment explanation
Indices: 18065988--18066060 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 33
18065978 TATTTTTTTA
*
18065988 TTTTATTTTTG-TATT-TTTATTTTATTTACAT
1 TTTTATTTTTGTTATTGTTTATTTTATATACAT
* * *
18066019 TTTTATTATTGTTATTGTTTTTTTTATATATAT
1 TTTTATTTTTGTTATTGTTTATTTTATATACAT
*
18066052 TTTTCTTTT
1 TTTTATTTT
18066061 ATTTTTAGCT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
31 10 0.29
32 4 0.12
33 20 0.59
ACGTcount: A:0.18, C:0.03, G:0.04, T:0.75
Consensus pattern (33 bp):
TTTTATTTTTGTTATTGTTTATTTTATATACAT
Found at i:18066188 original size:22 final size:23
Alignment explanation
Indices: 18066160--18066212 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
18066150 ATTTATATTT
*
18066160 ATTTATCTGATTATAT-GTTATA
1 ATTTATCTGATTATATAATTATA
* *
18066182 ATTTATCT-ATTATTTAATTTTA
1 ATTTATCTGATTATATAATTATA
18066204 ATTTATCTG
1 ATTTATCTG
18066213 TTAATTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58
Consensus pattern (23 bp):
ATTTATCTGATTATATAATTATA
Found at i:18067190 original size:4 final size:4
Alignment explanation
Indices: 18067177--18067234 Score: 50
Period size: 4 Copynumber: 14.0 Consensus size: 4
18067167 CTTCTTTTTA
18067177 ATTT -TTT ATTT ATTTT CATTTT ATTT ATTT A-TT -TTT ATTT ATTTT
1 ATTT ATTT ATTT A-TTT -A-TTT ATTT ATTT ATTT ATTT ATTT A-TTT
18067222 ATTT ATTT CATTT
1 ATTT ATTT -ATTT
18067235 TCTTTAAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
3 7 0.15
4 23 0.49
5 12 0.26
6 5 0.11
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (4 bp):
ATTT
Found at i:18067197 original size:6 final size:5
Alignment explanation
Indices: 18067180--18067235 Score: 50
Period size: 5 Copynumber: 11.8 Consensus size: 5
18067170 CTTTTTAATT
18067180 TTTTA -TTTA TTTTCA TTTTA -TTTA -TTTA TTTT- TATTTA TTTTA -TTTA
1 TTTTA TTTTA TTTT-A TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA TTTTA
*
18067227 TTTCA TTTT
1 TTTTA TTTT
18067236 CTTTAAATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
4 17 0.40
5 20 0.47
6 6 0.14
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:18067205 original size:19 final size:19
Alignment explanation
Indices: 18067181--18067240 Score: 79
Period size: 19 Copynumber: 3.2 Consensus size: 19
18067171 TTTTTAATTT
18067181 TTTATTTATTTTCATTTTA
1 TTTATTTATTTTCATTTTA
*
18067200 TTTATTTATTTTTA-TTTA
1 TTTATTTATTTTCATTTTA
*
18067218 TTTTATTTA-TTTCATTTTC
1 -TTTATTTATTTTCATTTTA
18067237 TTTA
1 TTTA
18067241 AATAAAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
18 12 0.33
19 24 0.67
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTATTTATTTTCATTTTA
Found at i:18067240 original size:23 final size:23
Alignment explanation
Indices: 18067106--18067235 Score: 85
Period size: 23 Copynumber: 5.5 Consensus size: 23
18067096 TTCATTTCTT
*
18067106 TTTA-TTATTTTT-TTTGTTTTA
1 TTTATTTATTTTTATTTATTTTA
*
18067127 TTTATTTATTTATTA-TTATATTA
1 TTTATTTATTT-TTATTTATTTTA
*
18067150 GGGTTTAATATT-TTTTTCTTCT-TTTTAA
1 ---TTT-AT-TTATTTTTATT-TATTTT-A
*
18067178 TTT-TTTATTTATT-TTCATTTTA
1 TTTATTTATTT-TTATTTATTTTA
18067200 TTTATTTATTTTTATTTATTTTA
1 TTTATTTATTTTTATTTATTTTA
18067223 TTTATTTCATTTT
1 TTTATTT-ATTTT
18067236 CTTTAAATAA
Statistics
Matches: 86, Mismatches: 6, Indels: 31
0.70 0.05 0.25
Matches are distributed among these distances:
21 4 0.05
22 14 0.16
23 40 0.47
24 7 0.08
25 3 0.03
26 5 0.06
27 9 0.10
28 4 0.05
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (23 bp):
TTTATTTATTTTTATTTATTTTA
Found at i:18067334 original size:59 final size:57
Alignment explanation
Indices: 18067262--18067608 Score: 270
Period size: 58 Copynumber: 5.8 Consensus size: 57
18067252 AAAAAAAACA
* * *
18067262 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCGATTTTTCTTAAGAATAAATTTTC
1 AAAAAAATTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAA-ATTAAATTTTC
* * * *
18067320 AAAAAAGGTTTTTTTTTAGGAAAAATTGAAAGTATCAA-TTTTCTTCGAAATTAAGA-ATTC
1 AAAAAA--ATTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTT--AAATTAA-ATTTTC
* * *
18067380 AAAATATATATATATATTTTTTAGGGAAAAGTTGAAAGTATCAATTTTACTCGAAATTAAAGTTT
1 -AAA-A-A-A-AT-T-TTTTTGA-GGAAAAGTTGAAAGTATCAATTTTTCT-TAAATTAAA-TTT
18067445 TC
56 TC
* * * *
18067447 -AAAAAATATTTTTG-GAAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
1 AAAAAAATTTTTTTGAG-GAAAAGTTGAAAGTATCAATTTTTCTT-AAATTAAATTTTC
**** * * *
18067504 AAAAATGGGTTTTTGAGGAAAAATTGAAAGTATCAATTTTTCTCGAAATTAAAATTTC
1 AAAAAAATTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCT-TAAATTAAATTTTC
* *
18067562 AAAAAAATATATTTTGGGGAAAAGTTGAAAGTATCAATTTTTTCTTA
1 AAAAAAAT-TTTTTTGAGGAAAAGTTGAAAGTATCAA-TTTTTCTTA
18067609 TACAAAAGCA
Statistics
Matches: 229, Mismatches: 37, Indels: 45
0.74 0.12 0.14
Matches are distributed among these distances:
57 6 0.03
58 86 0.38
59 38 0.17
60 39 0.17
61 8 0.03
62 2 0.01
63 3 0.01
64 3 0.01
65 10 0.04
66 26 0.11
67 8 0.03
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.38
Consensus pattern (57 bp):
AAAAAAATTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAATTAAATTTTC
Found at i:18070623 original size:27 final size:27
Alignment explanation
Indices: 18070547--18070623 Score: 70
Period size: 29 Copynumber: 2.8 Consensus size: 27
18070537 TTAAATTCAA
*
18070547 AAAAATTAACAAAAACTTTAAAAATTTTG
1 AAAAATTACCAAAAA--TTAAAAATTTTG
*
18070576 AAAAATTACCAAAAACT-AAAATTCTCTG
1 AAAAATTACCAAAAATTAAAAATT-T-TG
*
18070604 AAAAA-TA-TAAAAATTAAAAA
1 AAAAATTACCAAAAATTAAAAA
18070624 AAATAAAACT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
26 12 0.29
27 8 0.20
28 7 0.17
29 14 0.34
ACGTcount: A:0.62, C:0.09, G:0.03, T:0.26
Consensus pattern (27 bp):
AAAAATTACCAAAAATTAAAAATTTTG
Found at i:18070661 original size:9 final size:9
Alignment explanation
Indices: 18070637--18070670 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
18070627 TAAAACTTAT
18070637 GAAAATTTCA
1 GAAAA-TTCA
*
18070647 GAAAATTCT
1 GAAAATTCA
18070656 GAAAATTCA
1 GAAAATTCA
18070665 GAAAAT
1 GAAAAT
18070671 ATGTTAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 17 0.77
10 5 0.23
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.26
Consensus pattern (9 bp):
GAAAATTCA
Found at i:18070798 original size:19 final size:20
Alignment explanation
Indices: 18070774--18070813 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
18070764 TTAAAAAGTC
*
18070774 AAAAAATAAAACTT-AAAAA
1 AAAAAACAAAACTTCAAAAA
18070793 AAAAAACAAAACTTCAAAAA
1 AAAAAACAAAACTTCAAAAA
18070813 A
1 A
18070814 GCTGATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.78, C:0.10, G:0.00, T:0.12
Consensus pattern (20 bp):
AAAAAACAAAACTTCAAAAA
Found at i:18070861 original size:19 final size:19
Alignment explanation
Indices: 18070837--18070877 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
18070827 TTTAAATCTG
18070837 AAAAATAAAAAAAATC-TAA
1 AAAAAT-AAAAAAATCGTAA
18070856 AAAAATAAAAAAATCGTAA
1 AAAAATAAAAAAATCGTAA
18070875 AAA
1 AAA
18070878 TCCTTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.78, C:0.05, G:0.02, T:0.15
Consensus pattern (19 bp):
AAAAATAAAAAAATCGTAA
Found at i:18071273 original size:29 final size:29
Alignment explanation
Indices: 18071241--18071296 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
18071231 TATATAGATT
*
18071241 ATTT-TATTTTTTTAATTTTATTTTTTAGA
1 ATTTCTATTTTTTT-ATTTTAATTTTTAGA
* *
18071270 ATTTCTCTTTTTTTTTTTTAATTTTTA
1 ATTTCTATTTTTTTATTTTAATTTTTA
18071297 AAACATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 15 0.65
30 8 0.35
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.75
Consensus pattern (29 bp):
ATTTCTATTTTTTTATTTTAATTTTTAGA
Found at i:18071916 original size:20 final size:21
Alignment explanation
Indices: 18071879--18071917 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
18071869 AATTTTTGGA
*
18071879 ATTTTTAAAACAATATTTTAG
1 ATTTTTAAAACAAAATTTTAG
18071900 ATTTTTAAAA-AAAATTTT
1 ATTTTTAAAACAAAATTTT
18071918 GGGAATGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (21 bp):
ATTTTTAAAACAAAATTTTAG
Found at i:18071980 original size:27 final size:26
Alignment explanation
Indices: 18071955--18072078 Score: 112
Period size: 26 Copynumber: 4.7 Consensus size: 26
18071945 GCAAAATTTA
18071955 TGATTTTTTTAAATTTTCATATATTTT
1 TGATTTTTTTAAATTTTCATAT-TTTT
18071982 TGGA--TTTTTAAATTTCTCATATTTTT
1 T-GATTTTTTTAAATTT-TCATATTTTT
* *
18072008 TGAATTTTTTAAAATTTTTA-ATTTTT
1 TG-ATTTTTTTAAATTTTCATATTTTT
* *
18072034 TAGATTTTTTTGAAAATTTTAATGTTTTT
1 T-GATTTTTTT--AAATTTTCATATTTTT
*
18072063 AGA-TTTTTTAAATTTT
1 TGATTTTTTTAAATTTT
18072079 TTAAGTTTTT
Statistics
Matches: 82, Mismatches: 6, Indels: 20
0.76 0.06 0.19
Matches are distributed among these distances:
25 8 0.10
26 31 0.38
27 16 0.20
28 22 0.27
29 5 0.06
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.64
Consensus pattern (26 bp):
TGATTTTTTTAAATTTTCATATTTTT
Found at i:18072014 original size:9 final size:8
Alignment explanation
Indices: 18072002--18072090 Score: 70
Period size: 9 Copynumber: 10.1 Consensus size: 8
18071992 AATTTCTCAT
18072002 ATTTTTTGA
1 ATTTTTT-A
18072011 ATTTTTTAA
1 ATTTTTT-A
*
18072020 AATTTTTA
1 ATTTTTTA
18072028 ATTTTTTA
1 ATTTTTTA
18072036 GATTTTTTTGA
1 -A-TTTTTT-A
**
18072047 AAATTTTA
1 ATTTTTTA
18072055 ATGTTTTTA
1 AT-TTTTTA
18072064 GATTTTTTAA
1 -ATTTTTT-A
18072074 ATTTTTTA
1 ATTTTTTA
*
18072082 AGTTTTTA
1 ATTTTTTA
18072090 A
1 A
18072091 GATTCTTAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
8 19 0.29
9 36 0.55
10 10 0.15
11 1 0.02
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (8 bp):
ATTTTTTA
Found at i:18072043 original size:26 final size:26
Alignment explanation
Indices: 18071951--18072106 Score: 122
Period size: 27 Copynumber: 5.8 Consensus size: 26
18071941 TTTTGCAAAA
* *
18071951 TTTATGATTTTTTTAAATTTTCATATATT
1 TTTA-GATTTTTTAAAATTTTTA-AT-TT
* *
18071980 TTTGGA-TTTTT-AAATTTCTCATATTT
1 TTTAGATTTTTTAAAATTT-TTA-ATTT
18072006 TTT-GAATTTTTTAAAATTTTTAATTT
1 TTTAG-ATTTTTTAAAATTTTTAATTT
18072032 TTTAGATTTTTTTGAAAA-TTTTAATGTT
1 TTTAGA-TTTTTT-AAAATTTTTAAT-TT
*
18072060 TTTAGATTTTTTAAATTTTTTAAGTTT
1 TTTAGATTTTTTAAAATTTTTAA-TTT
* * *
18072087 TTAAGATTCTTAAAAATTTT
1 TTTAGATTTTTTAAAATTTT
18072107 AGGATTTCTT
Statistics
Matches: 110, Mismatches: 7, Indels: 22
0.79 0.05 0.16
Matches are distributed among these distances:
25 1 0.01
26 23 0.21
27 62 0.56
28 21 0.19
29 3 0.03
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.62
Consensus pattern (26 bp):
TTTAGATTTTTTAAAATTTTTAATTT
Found at i:18074929 original size:19 final size:18
Alignment explanation
Indices: 18074905--18074945 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
18074895 TAGGTTTCGA
*
18074905 GTTTCACCTAAATTTTAGG
1 GTTTCACCTAAA-ATTAGG
*
18074924 GTTTCACTTAAAATTAGG
1 GTTTCACCTAAAATTAGG
18074942 GTTT
1 GTTT
18074946 TACTTAAGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (18 bp):
GTTTCACCTAAAATTAGG
Found at i:18074942 original size:18 final size:19
Alignment explanation
Indices: 18074905--18074952 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
18074895 TAGGTTTCGA
* *
18074905 GTTTCACCTAAATTTTAGG
1 GTTTCACTTAAATATTAGG
18074924 GTTTCACTTAAA-ATTAGG
1 GTTTCACTTAAATATTAGG
*
18074942 GTTTTACTTAA
1 GTTTCACTTAA
18074953 GGTTTCGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 15 0.58
19 11 0.42
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (19 bp):
GTTTCACTTAAATATTAGG
Found at i:18075150 original size:26 final size:27
Alignment explanation
Indices: 18075109--18075166 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 27
18075099 TTTTATTAAA
18075109 ATTTTATTCTTCTTATTAGTATTCAAT
1 ATTTTATTCTTCTTATTAGTATTCAAT
* * * *
18075136 CTTTTATT-TTTTTATTATTATTTAAT
1 ATTTTATTCTTCTTATTAGTATTCAAT
18075162 ATTTT
1 ATTTT
18075167 CTCAATATCT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 19 0.73
27 7 0.27
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (27 bp):
ATTTTATTCTTCTTATTAGTATTCAAT
Found at i:18075567 original size:17 final size:15
Alignment explanation
Indices: 18075487--18075568 Score: 71
Period size: 14 Copynumber: 5.3 Consensus size: 15
18075477 AATAATATGT
*
18075487 AAAT-TAAAAATTAA
1 AAATATAAAAAATAA
*
18075501 AATTA-AAAAAATAA
1 AAATATAAAAAATAA
18075515 AAATA-AAAACGACATAA
1 AAATATAAAA--A-ATAA
*
18075532 AAATATAAAAATTAA
1 AAATATAAAAAATAA
18075547 AAATATAATAAAATAA
1 AAATATAA-AAAATAA
18075563 TAAATA
1 -AAATA
18075569 ATGTGTAATA
Statistics
Matches: 56, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
14 19 0.34
15 11 0.20
16 8 0.14
17 14 0.25
18 4 0.07
ACGTcount: A:0.73, C:0.02, G:0.01, T:0.23
Consensus pattern (15 bp):
AAATATAAAAAATAA
Found at i:18076145 original size:17 final size:17
Alignment explanation
Indices: 18076105--18076146 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
18076095 GCAGCAGCTC
18076105 AAAACAAAAGGCAGAAA
1 AAAACAAAAGGCAGAAA
*
18076122 AGGAACAAAA-GCAGTAAA
1 A-AAACAAAAGGCAG-AAA
18076140 AAAACAA
1 AAAACAA
18076147 GGGAGGCAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.69, C:0.12, G:0.17, T:0.02
Consensus pattern (17 bp):
AAAACAAAAGGCAGAAA
Found at i:18077105 original size:3 final size:3
Alignment explanation
Indices: 18077097--18077126 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
18077087 ATAACTTTTA
*
18077097 CAT CAT CAT CAT CAT CAT CAC CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
18077127 TATTATTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (3 bp):
CAT
Found at i:18086449 original size:161 final size:160
Alignment explanation
Indices: 18086150--18087574 Score: 1114
Period size: 161 Copynumber: 8.8 Consensus size: 160
18086140 AAACACATAT
* * * ** * * * * *
18086150 TATTGAAGCTATCCAAACTATTAAAACCGAATAATAACAATAAATTTGTATTTGTGCCTTTTAAC
1 TATTTAAGCTATCGAAACTGTTAAAATAGAACAATAACAACAAATTTGCATTTTTGCCTTTTAAT
* * * * * * * *
18086215 GACACAAAAAGTCCTAAATAGATCCTAAACAATAATTTTTTCACACATATCAACT-GTGAAAACC
66 GGCATAAAAAG-CCTAAACA-AACGTAAACGATAACTTTTTCACACATATCAA-TAGTGAAAATC
* ** * * *
18086279 AAATTCAATCATTCTGATAAGTTTAGTATGATG
128 AAGTTCAATCATTCAAACAAGTTTAATATCATG
* * * * * * *
18086312 TATTTAAGCTATCGAAACTATTAAAATAGAACAATAATAGCAATTTTGTATTTTTACCTCTTAAT
1 TATTTAAGCTATCGAAACTGTTAAAATAGAACAATAACAACAAATTTGCATTTTTGCCTTTTAAT
* * * *
18086377 GGCATAAAAAGCCTTAAACAGATGTAAATGGTAACTTTTTCACACATATCAATAGTGAAAATCAA
66 GGCATAAAAAGCC-TAAACAAACGTAAACGATAACTTTTTCACACATATCAATAGTGAAAATCAA
** **
18086442 GTTCAATCATTCGGACAAGTTTTGTATCATG
130 GTTCAATCATTCAAACAAGTTTAATATCATG
* * * * ** *
18086473 AATTTAAGCTATTGAAACTATTAAAATAGAACAATAACAGCATTTTTGCTTTTTTG-CTTTTCAA
1 TATTTAAGCTATCGAAACTGTTAAAATAGAACAATAACAACAAATTTGCATTTTTGCCTTTT-AA
* * * * * * *
18086537 TGGCATAAAAAGCCCTAAACAGACGTAAATGACAACTTTTTCATACATATGAACCA-TGGAAA-C
65 TGGCATAAAAAG-CCTAAACAAACGTAAACGATAACTTTTTCACACATATCAA-TAGTGAAAATC
* * ** ** *
18086600 TAAATTCAATTATTTGAACCTGTTTAGTATCATG
128 -AAGTTCAATCATTCAAACAAGTTTAATATCATG
* * * * ** *
18086634 CATTTAAGCTATCAAAACTGTTAAAATAGAACAATAATAACAAATTTACATTTTTAACTTTTAAC
1 TATTTAAGCTATCGAAACTGTTAAAATAGAACAATAACAACAAATTTGCATTTTTGCCTTTTAAT
* * * * *
18086699 GACATAAAAAGTCCTAAACAAACCCTAAACGATAACATTTTCACACATATCAGTTGTGGAAAA-C
66 GGCATAAAAAG-CCTAAACAAA-CGTAAACGATAACTTTTTCACACATATCAATAGT-GAAAATC
*
18086763 AAGTTAAATCATTCAAACAAGTTTAATATCATG
128 AAGTTCAATCATTCAAACAAGTTTAATATCATG
* * *
18086796 TA-TTAAACTATTGAAACTGTTAAAATAGAACAATAACAACAAATTTGCATTTGTGCCTTTTAAT
1 TATTTAAGCTATCGAAACTGTTAAAATAGAACAATAACAACAAATTTGCATTTTTGCCTTTTAAT
* * * *
18086860 GGCATAAAAAGTCCTAAACAAACATAAACGGTAACGTTTTCACACATATCAATCA-TGAAAACCA
66 GGCATAAAAAG-CCTAAACAAACGTAAACGATAACTTTTTCACACATATCAAT-AGTGAAAATCA
* * * * *
18086924 AGTTTAATCATTCAATCAAATTTTAGTATTATG
129 AGTTCAATCATTCAAAC-AAGTTTAATATCATG
** * * * * *
18086957 TATTTAAGCTA-CCCAA-TGGTTAAAATAGAAAAATAACAATAAATTTGTATTTTTACCTCTTAA
1 TATTTAAGCTATCGAAACT-GTTAAAATAGAACAATAACAACAAATTTGCATTTTTGCCTTTTAA
* ** * * *
18087020 CGGCATAAAAAGTTTTAAACAAACCTTAAACGATAATTTTTTCACATATATCAACT-GTGAAAAT
65 TGGCATAAAAAG-CCTAAACAAA-CGTAAACGATAACTTTTTCACACATATCAA-TAGTGAAAAT
* * * *
18087084 CAAATTCAATCATTCGAACAAGTTTAATATGATA
127 CAAGTTCAATCATTCAAACAAGTTTAATATCATG
* * *
18087118 TATTTAAACTATCGAAACTGTTAAAATAGAACAATAACAACAATTTTCCATTTTTGCCTTTTAAT
1 TATTTAAGCTATCGAAACTGTTAAAATAGAACAATAACAACAAATTTGCATTTTTGCCTTTTAAT
* * *** * ** *
18087183 GGCACAAAAAGCCTTAAATAGTTGTAAATGGCAACTTTTTCACACATATTAATAGT-AGAAATCA
66 GGCATAAAAAGCC-TAAACAAACGTAAACGATAACTTTTTCACACATATCAATAGTGA-AAATCA
18087247 AGTTCAATCATTCAAACAAGTTTAATATCATG
129 AGTTCAATCATTCAAACAAGTTTAATATCATG
* * * * * ** * *
18087279 TATTTAAGCTACCCAAA-TGTTTAAAATAAAAGAATAATAGGAAATTTGTATTTTTGCCGTTTAA
1 TATTTAAGCTATCGAAACTG-TTAAAATAGAACAATAACAACAAATTTGCATTTTTGCCTTTTAA
** * * * * *
18087343 TTACACAAAAAGCCTAAACAAACATAAACAATAAATTTTTCACAGATATCAACT-GT-AGAAATC
65 TGGCATAAAAAGCCTAAACAAACGTAAACGATAACTTTTTCACACATATCAA-TAGTGA-AAATC
* * *
18087406 AAGTTCAATTATTCAAAAAAGTTTAATATCATA
128 AAGTTCAATCATTCAAACAAGTTTAATATCATG
* ** * * * * * ** * *
18087439 TATTGAAATTACCCAAATTGTTAAAATAGAACAATAATAGCCTATTTGCATTTTGGCCTTTTAAC
1 TATTTAAGCTATCGAAACTGTTAAAATAGAACAATAACAACAAATTTGCATTTTTGCCTTTTAAT
** * * * * * * * * * * *
18087504 ACCACAAAAAGTCATAAAAAAATGTTAATGGTAACTTTTTCATACATATCAATTGTGAAACTTAA
66 GGCATAAAAAG-CCTAAACAAACGTAAACGATAACTTTTTCACACATATCAATAGTGAAAATCAA
18087569 GTTCAA
130 GTTCAA
18087575 ATATTTGGAT
Statistics
Matches: 1016, Mismatches: 218, Indels: 59
0.79 0.17 0.05
Matches are distributed among these distances:
159 5 0.00
160 181 0.18
161 589 0.58
162 234 0.23
163 7 0.01
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (160 bp):
TATTTAAGCTATCGAAACTGTTAAAATAGAACAATAACAACAAATTTGCATTTTTGCCTTTTAAT
GGCATAAAAAGCCTAAACAAACGTAAACGATAACTTTTTCACACATATCAATAGTGAAAATCAAG
TTCAATCATTCAAACAAGTTTAATATCATG
Found at i:18091667 original size:21 final size:19
Alignment explanation
Indices: 18091633--18091671 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
18091623 AGCATAACAT
*
18091633 TTTGAAGATTAGAAACAAAG
1 TTTGAAAATTAG-AACAAAG
18091653 TTTGAAAACTTAGAACAAA
1 TTTGAAAA-TTAGAACAAA
18091672 ATGATTTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.51, C:0.08, G:0.15, T:0.26
Consensus pattern (19 bp):
TTTGAAAATTAGAACAAAG
Found at i:18100246 original size:37 final size:39
Alignment explanation
Indices: 18100147--18100250 Score: 131
Period size: 40 Copynumber: 2.7 Consensus size: 39
18100137 TGGGTGTTTA
** * **
18100147 TTTATTTTTAAAGTTGTGTATCTCTATTAAGATGAGCCT
1 TTTATTTTTAAAGTTGTGTGCCTCTATTAAAATGAGAAT
18100186 TTTATTTTTAAAAGTTGTGTGCCTCTATTAAAAT-A-AAT
1 TTTATTTTT-AAAGTTGTGTGCCTCTATTAAAATGAGAAT
*
18100224 TTTATTTTTAAAGTTATGTGCCTCTAT
1 TTTATTTTTAAAGTTGTGTGCCTCTAT
18100251 CATAAGGAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
37 17 0.29
38 10 0.17
39 10 0.17
40 21 0.36
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (39 bp):
TTTATTTTTAAAGTTGTGTGCCTCTATTAAAATGAGAAT
Found at i:18100267 original size:38 final size:37
Alignment explanation
Indices: 18100187--18100280 Score: 107
Period size: 38 Copynumber: 2.5 Consensus size: 37
18100177 GATGAGCCTT
* * * *
18100187 TTATTTTTAAAAGTTGTGTGCCTCTATTAAAATAAATT
1 TTATTTTT-AAAGTTATGTGCCTCTATCAAAAGAAATC
* *
18100225 TTATTTTTAAAGTTATGTGCCTCTATCATAAGGAATCC
1 TTATTTTTAAAGTTATGTGCCTCTATCAAAAGAAAT-C
*
18100263 TTATTTTGAAAGTTATGT
1 TTATTTTTAAAGTTATGT
18100281 ACCTTTGTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
37 23 0.48
38 25 0.52
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.47
Consensus pattern (37 bp):
TTATTTTTAAAGTTATGTGCCTCTATCAAAAGAAATC
Found at i:18100385 original size:116 final size:116
Alignment explanation
Indices: 18100225--18100492 Score: 290
Period size: 116 Copynumber: 2.3 Consensus size: 116
18100215 AAAATAAATT
* * ** * * * *
18100225 TTATTTTTAAAGTTATGTGCCTCTATCATA-AGGAATCCTTATTTTGAAAGTTATGTACCTTTGT
1 TTATTTTTAAAGTTGTGTGCCTCTATTA-AGAGGAGCCCTCATTTTGAAAGTTATGCACCTCTAT
* *
18100289 TATGGAGAAGCTCTTATTTTTAAAAGTTGCATGTCTCTGTTAT-GAAAAGCTC
65 TATGGAGAAGCTCTTATTTTT-AAAGTCGCATATCTCTGTTATGGAAAAGCTC
* * *
18100341 TTATTTTCAAAGTTGTGTGCCTCTATTAAGAGGAGCCCTCATTTTTAAAGTTGTGCACCTCTATT
1 TTATTTTTAAAGTTGTGTGCCTCTATTAAGAGGAGCCCTCATTTTGAAAGTTATGCACCTCTATT
* * * ** * *
18100406 TTGGATAAGTTCTTATTTTTAAAGTCGTGTATCTCTGTTATGGAAGAGCTT
66 ATGGAGAAGCTCTTATTTTTAAAGTCGCATATCTCTGTTATGGAAAAGCTC
* **
18100457 TTATTTTTAAAGTTGTATGTTTCTATTAAGA-GAGCC
1 TTATTTTTAAAGTTGTGTGCCTCTATTAAGAGGAGCC
18100493 TTTATTTTTT
Statistics
Matches: 126, Mismatches: 24, Indels: 5
0.81 0.15 0.03
Matches are distributed among these distances:
115 23 0.18
116 103 0.82
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.44
Consensus pattern (116 bp):
TTATTTTTAAAGTTGTGTGCCTCTATTAAGAGGAGCCCTCATTTTGAAAGTTATGCACCTCTATT
ATGGAGAAGCTCTTATTTTTAAAGTCGCATATCTCTGTTATGGAAAAGCTC
Found at i:18101323 original size:13 final size:13
Alignment explanation
Indices: 18101305--18101332 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
18101295 TTCTTCTTTA
18101305 TTTAAAATAAATT
1 TTTAAAATAAATT
18101318 TTTAAAATAAATT
1 TTTAAAATAAATT
18101331 TT
1 TT
18101333 CAATCCTACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTAAAATAAATT
Found at i:18102723 original size:33 final size:32
Alignment explanation
Indices: 18102678--18102750 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
18102668 TATCTTATTG
*
18102678 TAAATAATAAAGCAAATAGACCTTAT-CCATTA
1 TAAAAAATAAAGC-AATAGACCTTATCCCATTA
* *
18102710 TAAAAAATAAAAGCAATGGGCCTTATCCCATTA
1 TAAAAAAT-AAAGCAATAGACCTTATCCCATTA
18102743 TAATAAAA
1 TAA-AAAA
18102751 AGGCTAACTG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 17 0.49
33 14 0.40
34 4 0.11
ACGTcount: A:0.51, C:0.15, G:0.08, T:0.26
Consensus pattern (32 bp):
TAAAAAATAAAGCAATAGACCTTATCCCATTA
Found at i:18102734 original size:32 final size:32
Alignment explanation
Indices: 18102658--18102750 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 32
18102648 TATAAAAATG
* * * *
18102658 AAATTGGCCTTATCTTATTGTAAATAATAAAGC
1 AAATAGGCCTTATC-CATTATAAAAAATAAAGC
*
18102691 AAATAGACCTTATCCATTATAAAAAATAAAAGC
1 AAATAGGCCTTATCCATTATAAAAAAT-AAAGC
*
18102724 -AATGGGCCTTATCCCATTATAATAAAA
1 AAATAGGCCTTAT-CCATTATAA-AAAA
18102751 AGGCTAACTG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
32 20 0.40
33 26 0.52
34 4 0.08
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.30
Consensus pattern (32 bp):
AAATAGGCCTTATCCATTATAAAAAATAAAGC
Found at i:18103598 original size:76 final size:74
Alignment explanation
Indices: 18103452--18103599 Score: 181
Period size: 75 Copynumber: 2.0 Consensus size: 74
18103442 TACATTATCT
* * *
18103452 AGTAAATTTACTAGTATTTTTTGGTGTTTTTGTTGGTATTTATTTCCTAATTTTTTTTAGTGTGA
1 AGTAAATTTACTAGTATTTTTTGGTGTTTTTGTTAGAATTTATTTCCTAATTTTCTTTAGTGTGA
18103517 ATGTAGGCC
66 ATGTAGGCC
* * ** *
18103526 AGTAAATTTATTGGTATTTCTTTGGTGTTTTT-TCTAGAATTTATTTTTTGATATTTCTTTAGTG
1 AGTAAATTTACTAGTATTT-TTTGGTGTTTTTGT-TAGAATTTATTTCCTAAT-TTTCTTTAGTG
*
18103590 TGATTGTAGG
63 TGAATGTAGG
18103600 GCATTGTTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
74 18 0.29
75 25 0.40
76 19 0.31
ACGTcount: A:0.20, C:0.05, G:0.19, T:0.55
Consensus pattern (74 bp):
AGTAAATTTACTAGTATTTTTTGGTGTTTTTGTTAGAATTTATTTCCTAATTTTCTTTAGTGTGA
ATGTAGGCC
Found at i:18104961 original size:36 final size:36
Alignment explanation
Indices: 18104872--18104992 Score: 100
Period size: 36 Copynumber: 3.3 Consensus size: 36
18104862 AATAGCATTG
*** * *
18104872 ACTGGATTTGAAACTTTTGTTGAAACTGGAATGGAA
1 ACTGGATTTGAAACTGGAGTTGAAACTAGAATTGAA
* *
18104908 AGTGGATCT-AAAGCTGGAGTTGAAACTAGAATTGAA
1 ACTGGATTTGAAA-CTGGAGTTGAAACTAGAATTGAA
* *
18104944 ACTGAATTTGAAACTGGATTTGTTGAAACTAGATTTGAA
1 ACTGGATTTGAAACTGGA---GTTGAAACTAGAATTGAA
* *
18104983 GCTAGATTTG
1 ACTGGATTTG
18104993 GGGTTTGTGC
Statistics
Matches: 66, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
35 3 0.05
36 36 0.55
37 3 0.05
39 24 0.36
ACGTcount: A:0.35, C:0.08, G:0.25, T:0.32
Consensus pattern (36 bp):
ACTGGATTTGAAACTGGAGTTGAAACTAGAATTGAA
Found at i:18104964 original size:12 final size:12
Alignment explanation
Indices: 18104872--18104965 Score: 66
Period size: 12 Copynumber: 7.8 Consensus size: 12
18104862 AATAGCATTG
18104872 ACTGGATTTGAA
1 ACTGGATTTGAA
**
18104884 ACT-TTTGTTGAA
1 ACTGGAT-TTGAA
* *
18104896 ACTGGAATGGAA
1 ACTGGATTTGAA
* *
18104908 AGTGGATCT-AA
1 ACTGGATTTGAA
*
18104919 AGCTGGAGTTGAA
1 A-CTGGATTTGAA
* *
18104932 ACTAGAATTGAA
1 ACTGGATTTGAA
*
18104944 ACTGAATTTGAA
1 ACTGGATTTGAA
18104956 ACTGGATTTG
1 ACTGGATTTG
18104966 TTGAAACTAG
Statistics
Matches: 59, Mismatches: 19, Indels: 8
0.69 0.22 0.09
Matches are distributed among these distances:
11 4 0.07
12 52 0.88
13 3 0.05
ACGTcount: A:0.35, C:0.09, G:0.26, T:0.31
Consensus pattern (12 bp):
ACTGGATTTGAA
Found at i:18104971 original size:15 final size:15
Alignment explanation
Indices: 18104951--18104980 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18104941 GAAACTGAAT
*
18104951 TTGAAACTGGATTTG
1 TTGAAACTAGATTTG
18104966 TTGAAACTAGATTTG
1 TTGAAACTAGATTTG
18104981 AAGCTAGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.40
Consensus pattern (15 bp):
TTGAAACTAGATTTG
Found at i:18104973 original size:27 final size:27
Alignment explanation
Indices: 18104939--18104992 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
18104929 GAAACTAGAA
*
18104939 TTGAAACT-GAATTTGAAACTGGATTTG
1 TTGAAACTAG-ATTTGAAACTAGATTTG
*
18104966 TTGAAACTAGATTTGAAGCTAGATTTG
1 TTGAAACTAGATTTGAAACTAGATTTG
18104993 GGGTTTGTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.33, C:0.07, G:0.22, T:0.37
Consensus pattern (27 bp):
TTGAAACTAGATTTGAAACTAGATTTG
Found at i:18104981 original size:12 final size:12
Alignment explanation
Indices: 18104927--18104992 Score: 62
Period size: 12 Copynumber: 5.2 Consensus size: 12
18104917 AAAGCTGGAG
*
18104927 TTGAAACTAGAA
1 TTGAAACTAGAT
18104939 TTGAAACT-GAAT
1 TTGAAACTAG-AT
*
18104951 TTGAAACTGGATTT
1 TTGAAACTAGA--T
18104965 GTTGAAACTAGAT
1 -TTGAAACTAGAT
*
18104978 TTGAAGCTAGAT
1 TTGAAACTAGAT
18104990 TTG
1 TTG
18104993 GGGTTTGTGC
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
11 1 0.02
12 32 0.70
13 2 0.04
14 1 0.02
15 10 0.22
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.35
Consensus pattern (12 bp):
TTGAAACTAGAT
Found at i:18108254 original size:32 final size:31
Alignment explanation
Indices: 18108204--18108280 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
18108194 TACATGTCCC
* **
18108204 TTACATTGTTATCTAATTTCTATTATAA-TCTT
1 TTACTTTGTTATAAAATTT-TATTATAAGT-TT
*
18108236 TTACTTTGTTATAAAATTTTGTTATAAGTTT
1 TTACTTTGTTATAAAATTTTATTATAAGTTT
*
18108267 GTACTTTGTTATAA
1 TTACTTTGTTATAA
18108281 CCAAGAATCT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
31 22 0.56
32 17 0.44
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.56
Consensus pattern (31 bp):
TTACTTTGTTATAAAATTTTATTATAAGTTT
Found at i:18108857 original size:42 final size:42
Alignment explanation
Indices: 18108795--18109009 Score: 159
Period size: 42 Copynumber: 5.1 Consensus size: 42
18108785 TTAAACACAG
* * * * * *
18108795 AAACCCTAATTGTAAATTCGAGTAATTAAGAACAATAATATA
1 AAACCCTAACTATAATTTCGAGCAATTAAGAACAACAATAAA
*
18108837 AAGCCCTAACTATAATTTCGAGCAATTAAGAACAACAATAAA
1 AAACCCTAACTATAATTTCGAGCAATTAAGAACAACAATAAA
* * * * * *
18108879 AAATCCTAACTATTATTTCAACCAATTAAGAATAACAAT-AG
1 AAACCCTAACTATAATTTCGAGCAATTAAGAACAACAATAAA
** * ** * * *
18108920 AAAGTCTCAAATATATATTT-GAAAAATTAAAAACAACAGTAGA
1 AAACCCT-AACTATA-ATTTCGAGCAATTAAGAACAACAATAAA
**
18108963 AAACGTTAACTATAAAGTTT--AGCAATTAAGAACAACAATAAA
1 AAACCCTAACTAT-AA-TTTCGAGCAATTAAGAACAACAATAAA
18109005 AAACC
1 AAACC
18109010 ATAAATCAGA
Statistics
Matches: 132, Mismatches: 36, Indels: 10
0.74 0.20 0.06
Matches are distributed among these distances:
41 6 0.05
42 114 0.86
43 12 0.09
ACGTcount: A:0.52, C:0.14, G:0.08, T:0.25
Consensus pattern (42 bp):
AAACCCTAACTATAATTTCGAGCAATTAAGAACAACAATAAA
Found at i:18109164 original size:12 final size:12
Alignment explanation
Indices: 18109147--18109171 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18109137 AATATACATA
18109147 CATATTATTCAC
1 CATATTATTCAC
18109159 CATATTATTCAC
1 CATATTATTCAC
18109171 C
1 C
18109172 TTACACAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.28, G:0.00, T:0.40
Consensus pattern (12 bp):
CATATTATTCAC
Found at i:18110536 original size:11 final size:11
Alignment explanation
Indices: 18110520--18110544 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
18110510 TTAAAAAACA
18110520 TTTTTAGAAAT
1 TTTTTAGAAAT
18110531 TTTTTAGAAAT
1 TTTTTAGAAAT
18110542 TTT
1 TTT
18110545 CATATTTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (11 bp):
TTTTTAGAAAT
Found at i:18111737 original size:49 final size:48
Alignment explanation
Indices: 18111630--18111737 Score: 146
Period size: 48 Copynumber: 2.3 Consensus size: 48
18111620 TTTCTTTCCA
* * * *
18111630 AAAAATT-AAAAAAAAATTTCTAAATTGACCCAAATGTTGAAAATTTT
1 AAAAATTAAAAAAAAAAATTCTAAATAGACCCAAATGATGAAAAATTT
* *
18111677 AAAAATAAAAAAAAAAAATTCTAAATAGGCCCAAATGATGAAAAATTT
1 AAAAATTAAAAAAAAAAATTCTAAATAGACCCAAATGATGAAAAATTT
*
18111725 AAAAATTCAAAAA
1 AAAAATTAAAAAA
18111738 GAGAAAATAT
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
47 6 0.12
48 46 0.88
ACGTcount: A:0.60, C:0.08, G:0.06, T:0.25
Consensus pattern (48 bp):
AAAAATTAAAAAAAAAAATTCTAAATAGACCCAAATGATGAAAAATTT
Done.