Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 127 of 163
Found at i:34959707 original size:33 final size:32
Alignment explanation
Indices: 34959653--34959714 Score: 79
Period size: 33 Copynumber: 1.9 Consensus size: 32
34959643 ACTAACCCAT
* *
34959653 TTTATTTACACCATCATCACAACAAGCACCAA
1 TTTATTTACACCAACACCACAACAAGCACCAA
* *
34959685 TTTATTTTACACCAAGACCACAACATGCAC
1 TTTA-TTTACACCAACACCACAACAAGCAC
34959715 ATTCATTCCC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 4 0.16
33 21 0.84
ACGTcount: A:0.39, C:0.31, G:0.05, T:0.26
Consensus pattern (32 bp):
TTTATTTACACCAACACCACAACAAGCACCAA
Found at i:34961555 original size:11 final size:12
Alignment explanation
Indices: 34961532--34961560 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
34961522 AAAGATCCAA
34961532 TCCTTTCCCCCT
1 TCCTTTCCCCCT
34961544 TCCTTT-CCCCT
1 TCCTTTCCCCCT
34961555 TCCTTT
1 TCCTTT
34961561 TCTTCCACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (12 bp):
TCCTTTCCCCCT
Found at i:34966879 original size:22 final size:22
Alignment explanation
Indices: 34966854--34966895 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
34966844 TTTATAATAA
34966854 ATAAATGTAAA-ATGAATAAATT
1 ATAAATG-AAATATGAATAAATT
*
34966876 ATAAATGAAATTTGAATAAA
1 ATAAATGAAATATGAATAAA
34966896 ATTAAAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.31
Consensus pattern (22 bp):
ATAAATGAAATATGAATAAATT
Found at i:34975459 original size:52 final size:53
Alignment explanation
Indices: 34975391--34975497 Score: 198
Period size: 52 Copynumber: 2.0 Consensus size: 53
34975381 TTGATCTAAC
34975391 TTCTTAGCCTTTATTGCCTCCCCAATTGCTCCC-TTTTTTCTCTAATTCTATT
1 TTCTTAGCCTTTATTGCCTCCCCAATTGCTCCCTTTTTTTCTCTAATTCTATT
*
34975443 TTCTTAGCCTTTATTGCCTCCCCAGTTGCTCCCTTTTTTTCTCTAATTCTATT
1 TTCTTAGCCTTTATTGCCTCCCCAATTGCTCCCTTTTTTTCTCTAATTCTATT
34975496 TT
1 TT
34975498 ACTTGTTATT
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 32 0.60
53 21 0.40
ACGTcount: A:0.12, C:0.30, G:0.07, T:0.51
Consensus pattern (53 bp):
TTCTTAGCCTTTATTGCCTCCCCAATTGCTCCCTTTTTTTCTCTAATTCTATT
Found at i:35000330 original size:22 final size:24
Alignment explanation
Indices: 35000305--35000352 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 24
35000295 TTATTTCTTT
*
35000305 AACTAAAATTAACATTT-G-AAAA
1 AACTAAAATTAAAATTTAGTAAAA
*
35000327 AACTAAATTTAAAATTTAGTAAAA
1 AACTAAAATTAAAATTTAGTAAAA
35000351 AA
1 AA
35000353 GGCAATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 15 0.68
23 1 0.05
24 6 0.27
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.29
Consensus pattern (24 bp):
AACTAAAATTAAAATTTAGTAAAA
Found at i:35000553 original size:21 final size:20
Alignment explanation
Indices: 35000529--35000593 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
35000519 TACATGCAAT
*
35000529 ATAATGAAAATGAAAAATAAA
1 ATAAAGAAAAT-AAAAATAAA
* *
35000550 ATAAAGTAAATAGAAATAAA
1 ATAAAGAAAATAAAAATAAA
*
35000570 AT-TA-AAAATAAAGAATAATA
1 ATAAAGAAAATAAA-AATAA-A
35000590 ATAA
1 ATAA
35000594 TATTAATTAC
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
18 6 0.18
19 6 0.18
20 13 0.38
21 9 0.26
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.22
Consensus pattern (20 bp):
ATAAAGAAAATAAAAATAAA
Found at i:35000586 original size:25 final size:26
Alignment explanation
Indices: 35000547--35000599 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 26
35000537 AATGAAAAAT
35000547 AAAATAAAGTAAATAGA-AATAAAATTA
1 AAAATAAAG-AAATA-ATAATAAAATTA
*
35000574 AAAATAAAG-AATAATAATAATATTA
1 AAAATAAAGAAATAATAATAAAATTA
35000599 A
1 A
35000600 TTACGGAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 1 0.04
25 14 0.58
27 9 0.38
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.25
Consensus pattern (26 bp):
AAAATAAAGAAATAATAATAAAATTA
Found at i:35002286 original size:17 final size:17
Alignment explanation
Indices: 35002264--35002300 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
35002254 GTTTTTTTTA
*
35002264 AAATTTAAACTTAATAT
1 AAATTTAAACTTAAAAT
*
35002281 AAATTTAAATTTAAAAT
1 AAATTTAAACTTAAAAT
35002298 AAA
1 AAA
35002301 AATTAAATGT
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:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATTTAAACTTAAAAT
Found at i:35002324 original size:20 final size:19
Alignment explanation
Indices: 35002294--35002339 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
35002284 TTTAAATTTA
35002294 AAATA-AAAATTAAATGTCC
1 AAATACAAAATTAAA-GTCC
35002313 AAATACAAAATTAAAGTCC
1 AAATACAAAATTAAAGTCC
*
35002332 AATTACAA
1 AAATACAA
35002340 GTCCAATGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.59, C:0.13, G:0.04, T:0.24
Consensus pattern (19 bp):
AAATACAAAATTAAAGTCC
Found at i:35003118 original size:19 final size:19
Alignment explanation
Indices: 35003094--35003130 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
35003084 TAATTAATAG
*
35003094 TAATAAGTATTATAATAAA
1 TAATAAATATTATAATAAA
*
35003113 TAATAAATGTTATAATAA
1 TAATAAATATTATAATAA
35003131 TATTTTTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
TAATAAATATTATAATAAA
Found at i:35004305 original size:29 final size:29
Alignment explanation
Indices: 35004268--35004443 Score: 125
Period size: 29 Copynumber: 6.1 Consensus size: 29
35004258 ACTTCTAAAT
35004268 ATTAC-ATTTTACCCTCAAACTTTCCAAA
1 ATTACAATTTTACCCTCAAACTTTCCAAA
*
35004296 ATTACAATTTTACCCT-GAACTTTCCAAA
1 ATTACAATTTTACCCTCAAACTTTCCAAA
* *
35004324 ATTTCATTTTTAACCC-C-AA-TTTCACCAAAA
1 ATTACAATTTT-ACCCTCAAACTTT--CC-AAA
* *
35004354 ATTACCATTTTACCCTCAAACTTTCCAGA
1 ATTACAATTTTACCCTCAAACTTTCCAAA
* * *
35004383 ATTCCATTTTTGACCC-C-GA-TTTCACCAAAA
1 ATTACAATTTT-ACCCTCAAACTTT--CC-AAA
* * *
35004413 ATTGCCATTTTACCCCCAAACTTTCCAAA
1 ATTACAATTTTACCCTCAAACTTTCCAAA
35004442 AT
1 AT
35004444 CTAATTTTTA
Statistics
Matches: 116, Mismatches: 16, Indels: 31
0.71 0.10 0.19
Matches are distributed among these distances:
27 6 0.05
28 28 0.24
29 42 0.36
30 31 0.27
31 3 0.03
32 6 0.05
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.35
Consensus pattern (29 bp):
ATTACAATTTTACCCTCAAACTTTCCAAA
Found at i:35004365 original size:30 final size:30
Alignment explanation
Indices: 35004331--35004487 Score: 102
Period size: 29 Copynumber: 5.3 Consensus size: 30
35004321 AAAATTTCAT
35004331 TTTTAACCCCAATTTCACCAAAAATTACCA
1 TTTTAACCCCAATTTCACCAAAAATTACCA
*
35004361 TTTT-ACCCTCAAACTTT--CC-AGAATT-CCA
1 TTTTAACCC-C-AA-TTTCACCAAAAATTACCA
* * *
35004389 TTTTTGACCCCGATTTCACCAAAAATTGCCA
1 -TTTTAACCCCAATTTCACCAAAAATTACCA
*
35004420 TTTTACCCCCAAACTTT--CC-AAAATCTA--A
1 TTTTAACCCC-AA-TTTCACCAAAAAT-TACCA
* *
35004448 TTTTTAACCCCGATTTCACTAAAAATTACCA
1 -TTTTAACCCCAATTTCACCAAAAATTACCA
35004479 TTTT-ACCCC
1 TTTTAACCCC
35004488 TGAACTTTTC
Statistics
Matches: 99, Mismatches: 10, Indels: 37
0.68 0.07 0.25
Matches are distributed among these distances:
27 6 0.06
28 6 0.06
29 38 0.38
30 36 0.36
31 7 0.07
32 6 0.06
ACGTcount: A:0.32, C:0.31, G:0.03, T:0.34
Consensus pattern (30 bp):
TTTTAACCCCAATTTCACCAAAAATTACCA
Found at i:35004487 original size:59 final size:58
Alignment explanation
Indices: 35004293--35004501 Score: 267
Period size: 59 Copynumber: 3.6 Consensus size: 58
35004283 CAAACTTTCC
* ** *
35004293 AAAATTACAATTTTA-CCCTGAACTTTCCAAAATTTCATTTTTAACCCCAATTTCACCA
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAA-TTCATTTTTAACCCCGATTTCACCA
* * *
35004351 AAAATTACCATTTTACCCTCAAACTTTCCAGAATTCCATTTTTGACCCCGATTTCACCA
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAATT-CATTTTTAACCCCGATTTCACCA
* * *
35004410 AAAATTGCCATTTTACCCCCAAACTTTCCAAAATCTAATTTTTAACCCCGATTTCACTA
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAAT-TCATTTTTAACCCCGATTTCACCA
** *
35004469 AAAATTACCATTTTACCCCTGAACTTTTCAAAA
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAA
35004502 ATTACCATTC
Statistics
Matches: 131, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
58 16 0.12
59 114 0.87
60 1 0.01
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.34
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCATTTTTAACCCCGATTTCACCA
Found at i:35004501 original size:89 final size:90
Alignment explanation
Indices: 35004408--35004577 Score: 218
Period size: 89 Copynumber: 1.9 Consensus size: 90
35004398 CCGATTTCAC
* * *
35004408 CAAAAATTGCCATTTTACCCCCAAACTTTCCAAAATCT-AATTTTTAACCCCGATTTCA-CTAAA
1 CAAAAATTACCATTCTA-CCCCAAACTTTCCAAAATCTCAATTTTTAACCCCGATTTCACCAAAA
*
35004471 AATTACCATTTTACCCCTGAACTTTT
65 AAATACCATTTTACCCCTGAACTTTT
*** * * *
35004497 CAAAAATTACCATTCTACCTTGAACTTTCCAAATTTTCATTTTTTAACCCCGATTTCACCAAAAA
1 CAAAAATTACCATTCTACCCCAAACTTTCCAAAATCTCAATTTTTAACCCCGATTTCACCAAAAA
*
35004562 AATACTATTTTACCCC
66 AATACCATTTTACCCC
35004578 CAAGAATCCA
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
88 15 0.22
89 34 0.50
90 19 0.28
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (90 bp):
CAAAAATTACCATTCTACCCCAAACTTTCCAAAATCTCAATTTTTAACCCCGATTTCACCAAAAA
AATACCATTTTACCCCTGAACTTTT
Found at i:35004502 original size:30 final size:29
Alignment explanation
Indices: 35004468--35004529 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 29
35004458 CGATTTCACT
* *
35004468 AAAAATTACCATTTTACCCCTGAACTTTTC
1 AAAAATTACCATTCTA-CCCTGAACTTTCC
*
35004498 AAAAATTACCATTCTACCTTGAACTTTCC
1 AAAAATTACCATTCTACCCTGAACTTTCC
35004527 AAA
1 AAA
35004530 TTTTCATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 14 0.48
30 15 0.52
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAAATTACCATTCTACCCTGAACTTTCC
Found at i:35004529 original size:118 final size:117
Alignment explanation
Indices: 35004285--35004529 Score: 268
Period size: 118 Copynumber: 2.1 Consensus size: 117
35004275 TTTACCCTCA
** * *
35004285 AACTTTCC-AAAATTACAATTTTACCCTGAACTTTCCAAAATTTCATTTTTAACCCCAATTTCAC
1 AACTTTCCAAAAATTACAATTTTACCCCAAACTTTCCAAAATCTAATTTTTAACCCCAATTTCAC
* * *
35004349 CAAAAATTACCATTTTACCCTCAAACTTTCCAGAATTCCATTTTTGACCCCG
66 CAAAAATTACCATTTTACCCTCAAACTTTCAAAAATTCCATTTCTGACCCCG
* * *
35004401 -A-TTTCACCAAAAATTGCCATTTTACCCCCAAACTTTCCAAAATCTAATTTTTAACCCCGATTT
1 AACTTT--CCAAAAATTACAATTTTA-CCCCAAACTTTCCAAAATCTAATTTTTAACCCCAATTT
* * **
35004464 CACTAAAAATTACCATTTTACCC-CTGAACTTTTCAAAAATTACCA-TTCT-ACCTTG
63 CACCAAAAATTACCATTTTACCCTC-AAAC-TTTCAAAAATT-CCATTTCTGACCCCG
35004519 AACTTTCCAAA
1 AACTTTCCAAA
35004530 TTTTCATTTT
Statistics
Matches: 106, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
114 3 0.03
115 1 0.01
116 2 0.02
117 14 0.13
118 67 0.63
119 13 0.12
120 6 0.06
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (117 bp):
AACTTTCCAAAAATTACAATTTTACCCCAAACTTTCCAAAATCTAATTTTTAACCCCAATTTCAC
CAAAAATTACCATTTTACCCTCAAACTTTCAAAAATTCCATTTCTGACCCCG
Found at i:35007544 original size:24 final size:26
Alignment explanation
Indices: 35007497--35007544 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
35007487 AAAAATTATA
*
35007497 ATATTTATAATAAATAATTGAAAAAT
1 ATATTTAGAATAAATAATTGAAAAAT
*
35007523 ATATTTAGAGTAAA-AATT-AAAA
1 ATATTTAGAATAAATAATTGAAAA
35007545 TAGAGAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 4 0.20
26 12 0.60
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (26 bp):
ATATTTAGAATAAATAATTGAAAAAT
Found at i:35007846 original size:14 final size:15
Alignment explanation
Indices: 35007813--35007852 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
35007803 TTTACATTTG
*
35007813 AATTATATTTTATTT
1 AATTATATTTTATAT
*
35007828 CATTAT-TTTTATAT
1 AATTATATTTTATAT
35007842 AATTATATTTT
1 AATTATATTTT
35007853 GAACTTAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (15 bp):
AATTATATTTTATAT
Found at i:35016100 original size:7 final size:7
Alignment explanation
Indices: 35016085--35016130 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
35016075 TAACATTATT
*
35016085 TAAACCC
1 TAAATCC
35016092 TAAATCC
1 TAAATCC
35016099 TAAATCC
1 TAAATCC
*
35016106 TAAATCA
1 TAAATCC
*
35016113 TAAACCC
1 TAAATCC
*
35016120 TAAATTC
1 TAAATCC
35016127 TAAA
1 TAAA
35016131 CTCTAAACTC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (7 bp):
TAAATCC
Found at i:35016107 original size:14 final size:14
Alignment explanation
Indices: 35016085--35016147 Score: 74
Period size: 14 Copynumber: 4.5 Consensus size: 14
35016075 TAACATTATT
35016085 TAAACCCTAAATCC
1 TAAACCCTAAATCC
* *
35016099 TAAATCCTAAATCA
1 TAAACCCTAAATCC
*
35016113 TAAACCCTAAATTC
1 TAAACCCTAAATCC
*
35016127 TAAACTCTAAA-CTC
1 TAAACCCTAAATC-C
35016141 TAAACCC
1 TAAACCC
35016148 GTCAAATTCA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
14 40 1.00
ACGTcount: A:0.44, C:0.30, G:0.00, T:0.25
Consensus pattern (14 bp):
TAAACCCTAAATCC
Found at i:35016118 original size:28 final size:28
Alignment explanation
Indices: 35016085--35016147 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 28
35016075 TAACATTATT
35016085 TAAACCCTAAATCCTAAA-TCCTAAA-TC
1 TAAACCCTAAATCCTAAACT-CTAAACTC
*
35016112 ATAAACCCTAAATTCTAAACTCTAAACTC
1 -TAAACCCTAAATCCTAAACTCTAAACTC
35016141 TAAACCC
1 TAAACCC
35016148 GTCAAATTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 29 0.91
29 3 0.09
ACGTcount: A:0.44, C:0.30, G:0.00, T:0.25
Consensus pattern (28 bp):
TAAACCCTAAATCCTAAACTCTAAACTC
Found at i:35016122 original size:58 final size:57
Alignment explanation
Indices: 35015997--35016123 Score: 134
Period size: 58 Copynumber: 2.2 Consensus size: 57
35015987 AACATTATTT
*
35015997 TAAACCCTAAACCCTATACCCAACATTATTTTAAAATATAAACCTAAACCATAAAAA
1 TAAACCCTAAACCCTATACCCAACATTATTTTAAAACATAAACCTAAACCATAAAAA
* * * * *
35016054 TATAATCCTAAA-CCTGATACCTAACATTA-TTTAAACCCTAAATCCTAAATCC-TAAATCA
1 TA-AACCCTAAACCCT-ATACCCAACATTATTTTAAAACATAAA-CCTAAA-CCATAAA-AA
35016113 TAAACCCTAAA
1 TAAACCCTAAA
35016124 TTCTAAACTC
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
57 15 0.26
58 38 0.66
59 5 0.09
ACGTcount: A:0.47, C:0.25, G:0.01, T:0.27
Consensus pattern (57 bp):
TAAACCCTAAACCCTATACCCAACATTATTTTAAAACATAAACCTAAACCATAAAAA
Found at i:35016137 original size:21 final size:21
Alignment explanation
Indices: 35016085--35016144 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
35016075 TAACATTATT
* *
35016085 TAAACCCTAAATCCTAAATCC
1 TAAACTCTAAACCCTAAATCC
*
35016106 TAAA-TCATAAACCCTAAATTC
1 TAAACTC-TAAACCCTAAATCC
*
35016127 TAAACTCTAAACTCTAAA
1 TAAACTCTAAACCCTAAA
35016145 CCCGTCAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.03
21 30 0.91
22 2 0.06
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.27
Consensus pattern (21 bp):
TAAACTCTAAACCCTAAATCC
Found at i:35017410 original size:146 final size:146
Alignment explanation
Indices: 35017157--35017420 Score: 393
Period size: 146 Copynumber: 1.8 Consensus size: 146
35017147 AAACAGGACC
* * *
35017157 TTTTGGATACCCGAGGGCAAAATAGTAATTTTAAACTGTCGAGGGTAAAATGGTAATTTTGAGAA
1 TTTTGGATACCCGAAGGCAAAATAGTAATTTTAAACTCTCGAGGGCAAAATGGTAATTTTGAGAA
***
35017222 AATTTAGGGTTAAAAATGACATTTTAGATGTTCGAGGGTAAAACGGTAATTTTCAAAAGAATCGG
66 AATTTAGGGTTAAAAATGACATTTTAGACAATCGAGGGTAAAACGGTAATTTTCAAAAGAATCGG
35017287 GATAAAAAACGAGACT
131 GATAAAAAACGAGACT
* * * * * *
35017303 TTTTGGATGCTCGAAGGCAAAATGGTAATTTTAGACTCTCGGGGGCAAAATGGTAATTTTGGGAA
1 TTTTGGATACCCGAAGGCAAAATAGTAATTTTAAACTCTCGAGGGCAAAATGGTAATTTTGAGAA
* * *
35017368 AATTTGGGGTTAAAAATGATATTTTAGACAATCGAGGGTAAAATGGTAATTTT
66 AATTTAGGGTTAAAAATGACATTTTAGACAATCGAGGGTAAAACGGTAATTTT
35017421 TATAAAAATT
Statistics
Matches: 103, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
146 103 1.00
ACGTcount: A:0.36, C:0.08, G:0.25, T:0.31
Consensus pattern (146 bp):
TTTTGGATACCCGAAGGCAAAATAGTAATTTTAAACTCTCGAGGGCAAAATGGTAATTTTGAGAA
AATTTAGGGTTAAAAATGACATTTTAGACAATCGAGGGTAAAACGGTAATTTTCAAAAGAATCGG
GATAAAAAACGAGACT
Found at i:35017419 original size:28 final size:27
Alignment explanation
Indices: 35017321--35017420 Score: 76
Period size: 28 Copynumber: 3.5 Consensus size: 27
35017311 GCTCGAAGGC
** *
35017321 AAAATGGTAATTTTAGACTCTCGGGGGC
1 AAAATGGTAATTTTAGACAATC-GGGGT
* * *
35017349 AAAATGGTAATTTTGGGAAAATTTGGGGTT
1 AAAATGGTAATTTT-AGACAA-TCGGGG-T
*
35017379 AAAAATGAT-ATTTTAGACAATCGAGGGT
1 -AAAATGGTAATTTTAGACAATCG-GGGT
35017407 AAAATGGTAATTTT
1 AAAATGGTAATTTT
35017421 TATAAAAATT
Statistics
Matches: 55, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
27 7 0.13
28 22 0.40
29 13 0.24
30 6 0.11
31 7 0.13
ACGTcount: A:0.36, C:0.06, G:0.25, T:0.33
Consensus pattern (27 bp):
AAAATGGTAATTTTAGACAATCGGGGT
Found at i:35017510 original size:30 final size:30
Alignment explanation
Indices: 35017466--35017610 Score: 142
Period size: 29 Copynumber: 4.9 Consensus size: 30
35017456 ATCCGAGGGT
* *
35017466 AAAATGGTAA-TTTT-GAGAGTTTTAGGGTTA
1 AAAATGG-AATTTTTGGA-AGTTTCAGGGTCA
35017496 AAAATGGAATTTTTGGAAG-TTC-GAGGTCA
1 AAAATGGAATTTTTGGAAGTTTCAG-GGTCA
35017525 AAAATGGAATTTTTGGAAG-TTCAGGGGT-A
1 AAAATGGAATTTTTGGAAGTTTCA-GGGTCA
** * *
35017554 AAAATATAATTTTGGGAAGTTTCGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTCAGGGTCA
35017584 AAAATGGAATTTTTGGACAGTTT-AGGG
1 AAAATGGAATTTTTGGA-AGTTTCAGGG
35017611 ACGTCCAGGG
Statistics
Matches: 97, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
28 1 0.01
29 51 0.53
30 37 0.38
31 8 0.08
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGTTTCAGGGTCA
Found at i:35017521 original size:58 final size:57
Alignment explanation
Indices: 35017438--35017610 Score: 149
Period size: 58 Copynumber: 2.9 Consensus size: 57
35017428 ATTGGTATCC
* * * *
35017438 AAAATGGGATTTTTGGACA-TCCGAGGGT-AAAATGGTAATTTT-GAGAGTTTTAGGGTTA
1 AAAATGGAATTTTTGGA-AGTTCGAGGGTAAAAATGG-AATTTTGGA-AG-TTCAGGGGTA
35017496 AAAATGGAATTTTTGGAAGTTCGA-GGTCAAAAATGGAATTTTTGGAAGTTCAGGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGT-AAAAATGGAA-TTTTGGAAGTTCAGGGGTA
** * *
35017554 AAAATATAATTTTGGGAAGTTTCG-GGGTCAAAAATGGAATTTTTGGACAGTTTAGGG
1 AAAATGGAATTTTTGGAAG-TTCGAGGGT-AAAAATGGAA-TTTTGGA-AGTTCAGGG
35017611 ACGTCCAGGG
Statistics
Matches: 99, Mismatches: 8, Indels: 14
0.82 0.07 0.12
Matches are distributed among these distances:
57 4 0.04
58 46 0.46
59 39 0.39
60 10 0.10
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (57 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTGGAAGTTCAGGGGTA
Found at i:35017527 original size:29 final size:29
Alignment explanation
Indices: 35017490--35017605 Score: 153
Period size: 29 Copynumber: 3.9 Consensus size: 29
35017480 GAGAGTTTTA
*
35017490 GGGTTAAAAATGGAATTTTTGGAAGTTCG
1 GGGTCAAAAATGGAATTTTTGGAAGTTCG
*
35017519 AGGTCAAAAATGGAATTTTTGGAAGTTCAG
1 GGGTCAAAAATGGAATTTTTGGAAGTTC-G
** *
35017549 GGGT-AAAAATATAATTTTGGGAAGTTTCG
1 GGGTCAAAAATGGAATTTTTGGAAG-TTCG
35017578 GGGTCAAAAATGGAATTTTTGGACAGTT
1 GGGTCAAAAATGGAATTTTTGGA-AGTT
35017606 TAGGGACGTC
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
29 48 0.65
30 24 0.32
31 2 0.03
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.33
Consensus pattern (29 bp):
GGGTCAAAAATGGAATTTTTGGAAGTTCG
Found at i:35017529 original size:59 final size:58
Alignment explanation
Indices: 35017466--35017610 Score: 159
Period size: 59 Copynumber: 2.4 Consensus size: 58
35017456 ATCCGAGGGT
* * * *
35017466 AAAATGGTAATTTT-GAGAGTTTTAGGGTTAAAAATGGAATTTTTGGAAG-TTCGAGGTCA
1 AAAATGG-AATTTTGGA-AG-TTCAGGGGTAAAAATAGAATTTTGGGAAGTTTCGAGGTCA
* *
35017525 AAAATGGAATTTTTGGAAGTTCAGGGGTAAAAATATAATTTTGGGAAGTTTCGGGGTCA
1 AAAATGGAA-TTTTGGAAGTTCAGGGGTAAAAATAGAATTTTGGGAAGTTTCGAGGTCA
*
35017584 AAAATGGAATTTTTGGACAGTTTAGGG
1 AAAATGGAA-TTTTGGA-AGTTCAGGG
35017611 ACGTCCAGGG
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
58 26 0.35
59 39 0.52
60 10 0.13
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (58 bp):
AAAATGGAATTTTGGAAGTTCAGGGGTAAAAATAGAATTTTGGGAAGTTTCGAGGTCA
Found at i:35018199 original size:92 final size:92
Alignment explanation
Indices: 35018042--35018763 Score: 1146
Period size: 92 Copynumber: 8.0 Consensus size: 92
35018032 TAGGAATTGA
* **
35018042 TATCCAACTTTACTACAACTTCAAGAGGATAAGAATTGATGTTTGAAACTTCATCTTGCTCTTAC
1 TATCCAACTTTACTACAACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTCTTAC
*
35018107 TACAACTTCAGAGAGATAAAGACTTGT
66 TACAACTTCAGAGAGATAAAGACTTGC
* *
35018134 TATCCAACTTTACTATAACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCACCTTGCTCTTAC
1 TATCCAACTTTACTACAACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTCTTAC
35018199 TACAACTTCAGAGAGATAAAGA--T--
66 TACAACTTCAGAGAGATAAAGACTTGC
**
35018222 T-T---AC--TAC-A-ACTT-CAAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTCTTAC
1 TATCCAACTTTACTACAACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTCTTAC
*
35018278 TACAACTTCAAAGAGATAAAGACTTGC
66 TACAACTTCAGAGAGATAAAGACTTGC
* * *
35018305 AATCCAACTTTACTACAACTTCAAGAGGATAGAAATTGATGTTTGATGCTTCACCTTGCTCTTAC
1 TATCCAACTTTACTACAACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTCTTAC
35018370 TACAACTTCAGAGAGATAAAGACTTGC
66 TACAACTTCAGAGAGATAAAGACTTGC
35018397 TATCCAACTTTACTACAACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTCTTAC
1 TATCCAACTTTACTACAACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTCTTAC
35018462 TACAACTTCAGAGAGATAAAGACTTGC
66 TACAACTTCAGAGAGATAAAGACTTGC
* * *
35018489 AATCCAACTTTACTACAACTTCAAGAGGATAGAAATTGATGTTTGATGCTTCACCTTGCTCTTAC
1 TATCCAACTTTACTACAACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTCTTAC
*
35018554 TACAACTTCAGAGAGATAAAAACTTGC
66 TACAACTTCAGAGAGATAAAGACTTGC
* ** *
35018581 TATCCAACTTTACTACAACTTCAAAAGGATAGGAATTGATGTTTGAAACTTCATATTGCTCTTAC
1 TATCCAACTTTACTACAACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTCTTAC
35018646 TACAACTTCAGAGAGATAAAGACTTGC
66 TACAACTTCAGAGAGATAAAGACTTGC
* **
35018673 TATCCAACTTTACTACAACTTCAAGAGGATAGGAATTGATGTTCGAAACTTCATCTTGCTCTTAC
1 TATCCAACTTTACTACAACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTCTTAC
35018738 TACAACTTCAGAGAGATAAAGACTTG
66 TACAACTTCAGAGAGATAAAGACTTG
35018764 GTATTTTGAT
Statistics
Matches: 584, Mismatches: 33, Indels: 26
0.91 0.05 0.04
Matches are distributed among these distances:
79 64 0.11
80 2 0.00
81 2 0.00
82 3 0.01
84 3 0.01
87 3 0.01
88 1 0.00
89 3 0.01
90 2 0.00
91 2 0.00
92 499 0.85
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (92 bp):
TATCCAACTTTACTACAACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTCTTAC
TACAACTTCAGAGAGATAAAGACTTGC
Found at i:35019009 original size:101 final size:100
Alignment explanation
Indices: 35018852--35019184 Score: 336
Period size: 100 Copynumber: 3.3 Consensus size: 100
35018842 CCGGGTTCGT
* * *
35018852 TGTTGCGACTTAAACCATTCCCTTTTATGTC--TTTGCGGAACTGGAT-TCGCCATTGCGGTCTT
1 TGTTGCGACTTAAACC-TTTCCTTTT-TGTCTTTTTGCGGTACTGGATCT-GCCGTTGCGGTCTT
*
35018914 AGATCTTTCCTGAT-GTATTTTCTGGGGTAC-ACGGTCCGC
63 AGATCTTTCCTG-TCGTATTTT-TGGGGTACTA-GATCCGC
* *
35018953 TGTTGCGACTTAAACCTTTCCTTTTTGTCTTTTTGCGGTACTAGATCTGCTGTTGCGGTCTTAGA
1 TGTTGCGACTTAAACCTTTCCTTTTTGTCTTTTTGCGGTACTGGATCTGCCGTTGCGGTCTTAGA
* *
35019018 TCTTTCCTGTCGTGTTTTTGTGGTACTAGATCCGC
66 TCTTTCCTGTCGTATTTTTGGGGTACTAGATCCGC
* * * ** * * * * * *
35019053 CGTCGCGGCTTTGATCTTTCATTTGTGTCTTTGTGTGGTACTGGATCCGCCGTTGCGGTCTTAGA
1 TGTTGCGACTTAAACCTTTCCTTTTTGTCTTTTTGCGGTACTGGATCTGCCGTTGCGGTCTTAGA
* *
35019118 TCTTTCCTGTCGTGTTTTTGTGGTACTAGATCCG-
66 TCTTTCCTGTCGTATTTTTGGGGTACTAGATCCGC
* * * *
35019152 TCGTTGCGGCTTAGATCTTTCCTTTGTGTCTTT
1 T-GTTGCGACTTAAACCTTTCCTTTTTGTCTTT
35019185 GCGTGGTATT
Statistics
Matches: 201, Mismatches: 25, Indels: 13
0.84 0.10 0.05
Matches are distributed among these distances:
99 4 0.02
100 136 0.68
101 60 0.30
102 1 0.00
ACGTcount: A:0.12, C:0.22, G:0.24, T:0.43
Consensus pattern (100 bp):
TGTTGCGACTTAAACCTTTCCTTTTTGTCTTTTTGCGGTACTGGATCTGCCGTTGCGGTCTTAGA
TCTTTCCTGTCGTATTTTTGGGGTACTAGATCCGC
Found at i:35019093 original size:100 final size:100
Alignment explanation
Indices: 35018899--35019192 Score: 376
Period size: 100 Copynumber: 2.9 Consensus size: 100
35018889 GAACTGGATT
* * * * * *
35018899 CGCCATTGCGGTCTTAGATCTTTCCTGAT-GTATTTTCTGGGGTAC-ACGGTCCGCTGTTGCGAC
1 CGCCGTTGCGGTCTTAGATCTTTCCTG-TCGTGTTTT-TGTGGTACTA-GATCCGCCGTTGCGGC
* * * * *
35018962 TTAAACCTTTCCTTTTTGTCTTTTTGCGGTACTAGATC
63 TTAGATCTTTCCTTTGTGTCTTTGTGTGGTACTAGATC
* * * *
35019000 TGCTGTTGCGGTCTTAGATCTTTCCTGTCGTGTTTTTGTGGTACTAGATCCGCCGTCGCGGCTTT
1 CGCCGTTGCGGTCTTAGATCTTTCCTGTCGTGTTTTTGTGGTACTAGATCCGCCGTTGCGGCTTA
* *
35019065 GATCTTTCATTTGTGTCTTTGTGTGGTACTGGATC
66 GATCTTTCCTTTGTGTCTTTGTGTGGTACTAGATC
*
35019100 CGCCGTTGCGGTCTTAGATCTTTCCTGTCGTGTTTTTGTGGTACTAGATCCGTCGTTGCGGCTTA
1 CGCCGTTGCGGTCTTAGATCTTTCCTGTCGTGTTTTTGTGGTACTAGATCCGCCGTTGCGGCTTA
*
35019165 GATCTTTCCTTTGTGTCTTTGCGTGGTA
66 GATCTTTCCTTTGTGTCTTTGTGTGGTA
35019193 TTGAGACCTG
Statistics
Matches: 167, Mismatches: 24, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
100 136 0.81
101 31 0.19
ACGTcount: A:0.11, C:0.22, G:0.25, T:0.43
Consensus pattern (100 bp):
CGCCGTTGCGGTCTTAGATCTTTCCTGTCGTGTTTTTGTGGTACTAGATCCGCCGTTGCGGCTTA
GATCTTTCCTTTGTGTCTTTGTGTGGTACTAGATC
Found at i:35019192 original size:50 final size:49
Alignment explanation
Indices: 35018899--35019184 Score: 274
Period size: 50 Copynumber: 5.7 Consensus size: 49
35018889 GAACTGGATT
* * * * *
35018899 CGCCATTGCGGTCTTAGATCTTTCCTGATGTAT-TTTCTGGGGTAC-ACGGTC
1 CGCCGTTGCGG-CTTAGATCTTTCCT-TTGTGTCTTT-TGTGGTACTA-GATC
* * * * * *
35018950 CGCTGTTGCGACTTAAACCTTTCCTTTTTGTCTTTTTGCGGTACTAGATC
1 CGCCGTTGCGGCTTAGATCTTTCCTTTGTGTC-TTTTGTGGTACTAGATC
* * *
35019000 TGCTGTTGCGGTCTTAGATCTTTCCTGTCGTGT-TTTTGTGGTACTAGATC
1 CGCCGTTGCGG-CTTAGATCTTTCCT-TTGTGTCTTTTGTGGTACTAGATC
* * * *
35019050 CGCCGTCGCGGCTTTGATCTTTCATTTGTGTCTTTGTGTGGTACTGGATC
1 CGCCGTTGCGGCTTAGATCTTTCCTTTGTGTCTTT-TGTGGTACTAGATC
*
35019100 CGCCGTTGCGGTCTTAGATCTTTCCTGTCGTGT-TTTTGTGGTACTAGATC
1 CGCCGTTGCGG-CTTAGATCTTTCCT-TTGTGTCTTTTGTGGTACTAGATC
*
35019150 CGTCGTTGCGGCTTAGATCTTTCCTTTGTGTCTTT
1 CGCCGTTGCGGCTTAGATCTTTCCTTTGTGTCTTT
35019185 GCGTGGTATT
Statistics
Matches: 194, Mismatches: 31, Indels: 22
0.79 0.13 0.09
Matches are distributed among these distances:
48 10 0.05
49 35 0.18
50 101 0.52
51 39 0.20
52 9 0.05
ACGTcount: A:0.10, C:0.22, G:0.24, T:0.43
Consensus pattern (49 bp):
CGCCGTTGCGGCTTAGATCTTTCCTTTGTGTCTTTTGTGGTACTAGATC
Found at i:35026138 original size:28 final size:28
Alignment explanation
Indices: 35026098--35026159 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
35026088 AAACGGGACT
*
35026098 TTTTGGATGCTCG-GTGGCAAAATGGTAA
1 TTTTAGATGCTCGAG-GGCAAAATGGTAA
*
35026126 TTTTAGATTCTCGAGGGCAAAATGGTAA
1 TTTTAGATGCTCGAGGGCAAAATGGTAA
35026154 TTTTAG
1 TTTTAG
35026160 GAAAATTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 30 0.97
29 1 0.03
ACGTcount: A:0.27, C:0.10, G:0.27, T:0.35
Consensus pattern (28 bp):
TTTTAGATGCTCGAGGGCAAAATGGTAA
Found at i:35026207 original size:58 final size:58
Alignment explanation
Indices: 35026136--35026304 Score: 164
Period size: 58 Copynumber: 2.9 Consensus size: 58
35026126 TTTTAGATTC
* *
35026136 TCGAGGGCAAAATGGTAATTTTAGGAAAATTTGGGGTTAAAAATGACA-TTTTAGACAA
1 TCGAGGGTAAAATGGTAATTTTAGGAAAATTTGGGGTCAAAAATGACATTTTTAGAC-A
* * ** ** ** *
35026194 TCGAGGGTAAAATGATAATTTTTGGAAAATCCGGTATCAAAAATGGGATTTTTGGACA
1 TCGAGGGTAAAATGGTAATTTTAGGAAAATTTGGGGTCAAAAATGACATTTTTAGACA
* **
35026252 TCCGAGGATAAAATGGTAATTTTAGG-AGTTTTGGGGTCAAAAATGGA-ATTTTT
1 T-CGAGGGTAAAATGGTAATTTTAGGAAAATTTGGGGTCAAAAAT-GACATTTTT
35026305 GGAAGTTTGG
Statistics
Matches: 87, Mismatches: 21, Indels: 6
0.76 0.18 0.05
Matches are distributed among these distances:
58 58 0.67
59 29 0.33
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.32
Consensus pattern (58 bp):
TCGAGGGTAAAATGGTAATTTTAGGAAAATTTGGGGTCAAAAATGACATTTTTAGACA
Found at i:35026214 original size:28 final size:28
Alignment explanation
Indices: 35026116--35026224 Score: 69
Period size: 29 Copynumber: 3.8 Consensus size: 28
35026106 GCTCGGTGGC
* *** *
35026116 AAAATGGTAATTTTAGATTCTCGAGGGC
1 AAAATGATAATTTTAGAAAATCGAGGGT
* *
35026144 AAAATGGTAATTTTAGGAAAATTTG-GGGTT
1 AAAATGATAATTTTA-GAAAA-TCGAGGG-T
* *
35026174 AAAAATGA-CATTTTAGACAATCGAGGGT
1 -AAAATGATAATTTTAGAAAATCGAGGGT
*
35026202 AAAATGATAATTTTTGGAAAATC
1 AAAATGATAA-TTTTAGAAAATC
35026225 CGGTATCAAA
Statistics
Matches: 62, Mismatches: 12, Indels: 13
0.71 0.14 0.15
Matches are distributed among these distances:
27 7 0.11
28 19 0.31
29 22 0.35
30 8 0.13
31 6 0.10
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.32
Consensus pattern (28 bp):
AAAATGATAATTTTAGAAAATCGAGGGT
Found at i:35026293 original size:29 final size:28
Alignment explanation
Indices: 35026261--35026476 Score: 123
Period size: 29 Copynumber: 7.5 Consensus size: 28
35026251 ATCCGAGGAT
35026261 AAAATGGTAATTTTAGGAGTTTTGGGGTCA
1 AAAAT-GTAATTTTAGGAGTTTTGGGGT-A
* *
35026291 AAAATGGAATTTTTGGAAG-TTTGGGGTGA
1 AAAATGTAATTTTAGG-AGTTTTGGGGT-A
* * ** * *
35026320 AAAATGAAATTTTTGGAAATTTAGGGTT
1 AAAATGTAATTTTAGGAGTTTTGGGGTA
* * ** *
35026348 AAAATGGAATTTTTGGAAGTTTAAGGGTG
1 AAAATGTAATTTTAGG-AGTTTTGGGGTA
** *
35026377 AAAATGTAATTTTCAAAAGTTTTAGGGTTA
1 AAAATGTAATTTT-AGGAGTTTT-GGGGTA
* *
35026407 AAAATGAAATTTCT-GGAAGTTTTGGGG-G
1 AAAATGTAATTT-TAGG-AGTTTTGGGGTA
* ** *
35026435 AAAATGTAATTTTAGTAAGTTTTAAGGTC
1 AAAATGTAATTTTAG-GAGTTTTGGGGTA
35026464 AAAATGTAATTTT
1 AAAATGTAATTTT
35026477 CGGACAGTTT
Statistics
Matches: 146, Mismatches: 30, Indels: 21
0.74 0.15 0.11
Matches are distributed among these distances:
27 1 0.01
28 36 0.25
29 81 0.55
30 27 0.18
31 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.38
Consensus pattern (28 bp):
AAAATGTAATTTTAGGAGTTTTGGGGTA
Found at i:35026331 original size:58 final size:57
Alignment explanation
Indices: 35026261--35026486 Score: 226
Period size: 57 Copynumber: 3.9 Consensus size: 57
35026251 ATCCGAGGAT
* *
35026261 AAAATGGTAATTTTAGGAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTGGGGTG
1 AAAAT-GTAATTTTAGAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAGTTTGGGGTG
* * * * *
35026319 AAAAATGAAATTTTTGGAA-ATTTAGGGT-TAAAATGGAATTTTTGGAAGTTTAAGGGTG
1 -AAAATGTAA-TTTTAGAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAGTTT-GGGGTG
* * * *
35026377 AAAATGTAATTTTCAAAAGTTTTAGGGTTAAAAATGAAATTTCTGGAAGTTTTGGGG-G
1 AAAATGTAATTTT-AGAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAG-TTTGGGGTG
* * *
35026435 AAAATGTAATTTTAGTAAGTTTTAAGGTC-AAAATGTAATTTTCGGACAGTTT
1 AAAATGTAATTTTAG-AAGTTTTAGGGTCAAAAATGGAATTTTTGGA-AGTTT
35026487 AGGGACTTTC
Statistics
Matches: 138, Mismatches: 21, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
56 4 0.03
57 50 0.36
58 50 0.36
59 31 0.22
60 3 0.02
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (57 bp):
AAAATGTAATTTTAGAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAGTTTGGGGTG
Found at i:35026351 original size:87 final size:86
Alignment explanation
Indices: 35026260--35026490 Score: 250
Period size: 87 Copynumber: 2.7 Consensus size: 86
35026250 CATCCGAGGA
* * * *
35026260 TAAAATGGTAATTTTAGGAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTGGGGTGAAAAAT
1 TAAAATGGTAATTTTAGGAGTTTTAGGGTC-AAAATGTAATTTTCGGAAGTTTAGGGTGAAAAAT
* *
35026325 GAAATTTTTGGAAATTTAGGGT
65 GAAATTTCTGGAAATTTAGGGG
* * * ** *
35026347 TAAAATGG-AATTTTTGGAAGTTTAAGGGTGAAAATGTAATTTTCAAAAGTTTTAGGGTTAAAAA
1 TAAAATGGTAATTTTAGG-AGTTTTAGGGTCAAAATGTAATTTTCGGAAG-TTTAGGGTGAAAAA
* *
35026411 TGAAATTTCTGGAAGTTTTGGGG
64 TGAAATTTCTGGAAATTTAGGGG
* * *
35026434 GAAAAT-GTAATTTTAGTAAGTTTTAAGGTCAAAATGTAATTTTCGGACAGTTTAGGG
1 TAAAATGGTAATTTTAG-GAGTTTTAGGGTCAAAATGTAATTTTCGGA-AGTTTAGGG
35026491 ACTTTCAAGG
Statistics
Matches: 117, Mismatches: 22, Indels: 10
0.79 0.15 0.07
Matches are distributed among these distances:
86 24 0.21
87 91 0.78
88 2 0.02
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.37
Consensus pattern (86 bp):
TAAAATGGTAATTTTAGGAGTTTTAGGGTCAAAATGTAATTTTCGGAAGTTTAGGGTGAAAAATG
AAATTTCTGGAAATTTAGGGG
Found at i:35026352 original size:28 final size:28
Alignment explanation
Indices: 35026291--35026490 Score: 166
Period size: 29 Copynumber: 6.9 Consensus size: 28
35026281 TTTGGGGTCA
* *
35026291 AAAATGGAATTTTTGGAAGTTTGGGGTG
1 AAAATGAAATTTTTGGAAGTTTAGGGTG
* *
35026319 AAAAATGAAATTTTTGGAAATTTAGGGTT
1 -AAAATGAAATTTTTGGAAGTTTAGGGTG
*
35026348 AAAATGGAATTTTTGGAAGTTTAAGGGTG
1 AAAATGAAATTTTTGGAAGTTT-AGGGTG
* *** *
35026377 AAAATGTAATTTTCAAAAGTTTTAGGGTTA
1 AAAATGAAATTTTTGGAAG-TTTAGGG-TG
* * *
35026407 AAAATGAAATTTCTGGAAGTTTTGGGGG
1 AAAATGAAATTTTTGGAAGTTTAGGGTG
* * * * *
35026435 AAAATGTAATTTTAGTAAGTTTTAAGGTC
1 AAAATGAAATTTTTGGAAG-TTTAGGGTG
* *
35026464 AAAATGTAATTTTCGGACAGTTTAGGG
1 AAAATGAAATTTTTGGA-AGTTTAGGG
35026491 ACTTTCAAGG
Statistics
Matches: 135, Mismatches: 31, Indels: 10
0.77 0.18 0.06
Matches are distributed among these distances:
28 35 0.26
29 80 0.59
30 20 0.15
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (28 bp):
AAAATGAAATTTTTGGAAGTTTAGGGTG
Found at i:35027628 original size:18 final size:18
Alignment explanation
Indices: 35027605--35027645 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
35027595 TTTATGCCAT
35027605 TTATTATTACTAAT-ATAA
1 TTATTATTACTAATGA-AA
*
35027623 TTATTATTATTAATGAAA
1 TTATTATTACTAATGAAA
35027641 TTATT
1 TTATT
35027646 TAATACTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (18 bp):
TTATTATTACTAATGAAA
Found at i:35028500 original size:17 final size:17
Alignment explanation
Indices: 35028478--35028541 Score: 78
Period size: 17 Copynumber: 3.8 Consensus size: 17
35028468 ATGGACATTT
35028478 TATTAAATTTATAA-TAA
1 TATTAAATTTA-AATTAA
35028495 TATTAAATTTAAATTAA
1 TATTAAATTTAAATTAA
35028512 -ATTCAAATTTAAATTAA
1 TATT-AAATTTAAATTAA
* *
35028529 AATTAAAATTAAA
1 TATTAAATTTAAA
35028542 ATAAATTTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
16 5 0.12
17 35 0.81
18 3 0.07
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
TATTAAATTTAAATTAA
Found at i:35028512 original size:11 final size:11
Alignment explanation
Indices: 35028496--35028571 Score: 71
Period size: 11 Copynumber: 6.8 Consensus size: 11
35028486 TTATAATAAT
35028496 ATTAAATTTAA
1 ATTAAATTTAA
*
35028507 ATTAAATTCAA
1 ATTAAATTTAA
*
35028518 ATTTAAATTAAA
1 A-TTAAATTTAA
*
35028530 ATTAAAATTAA
1 ATTAAATTTAA
*
35028541 AATAAATTTAA
1 ATTAAATTTAA
* **
35028552 AATAAAAATAA
1 ATTAAATTTAA
*
35028563 ATTTAATTT
1 ATTAAATTT
35028572 CAAAGTAAAA
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
11 42 0.81
12 10 0.19
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:35028534 original size:34 final size:34
Alignment explanation
Indices: 35028482--35028548 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
35028472 ACATTTTATT
* * *
35028482 AAATTTATAATAATATTAAATTTAAATTAAATTC
1 AAATTTATAATAAAATTAAAATTAAAATAAATTC
35028516 AAATTTA-AATTAAAATTAAAATTAAAATAAATT
1 AAATTTATAA-TAAAATTAAAATTAAAATAAATT
35028549 TAAAATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 2 0.07
34 27 0.93
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (34 bp):
AAATTTATAATAAAATTAAAATTAAAATAAATTC
Found at i:35028546 original size:17 final size:17
Alignment explanation
Indices: 35028479--35028568 Score: 74
Period size: 17 Copynumber: 5.3 Consensus size: 17
35028469 TGGACATTTT
* * *
35028479 ATTAAATTTATAATAAT
1 ATTAAAATTAAAATAAA
* *
35028496 ATT-AAATTTAAATTAA
1 ATTAAAATTAAAATAAA
* *
35028512 ATTCAAATTTAAATTAAA
1 ATT-AAAATTAAAATAAA
35028530 ATTAAAATTAAAATAAA
1 ATTAAAATTAAAATAAA
* *
35028547 TTTAAAATAAAAATAAA
1 ATTAAAATTAAAATAAA
*
35028564 TTTAA
1 ATTAA
35028569 TTTCAAAGTA
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
16 11 0.19
17 35 0.60
18 12 0.21
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (17 bp):
ATTAAAATTAAAATAAA
Found at i:35028559 original size:23 final size:23
Alignment explanation
Indices: 35028521--35028583 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
35028511 AATTCAAATT
*
35028521 TAAA-TTAAAATTAAAATTAAAA
1 TAAATTTAAAATAAAAATTAAAA
*
35028543 TAAATTTAAAATAAAAA-TAAAT
1 TAAATTTAAAATAAAAATTAAAA
* *
35028565 TTAATTTCAAAGTAAAAAT
1 TAAATTT-AAAATAAAAAT
35028584 GGTTTGGGCC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
22 14 0.41
23 20 0.59
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (23 bp):
TAAATTTAAAATAAAAATTAAAA
Found at i:35028563 original size:6 final size:6
Alignment explanation
Indices: 35028499--35028560 Score: 65
Period size: 6 Copynumber: 10.7 Consensus size: 6
35028489 TAATAATATT
* * *
35028499 AAATTT AAATT- AAATTC AAATTT AAATTA AAATTA AAATTA AAA-TA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
* *
35028545 AATTTA AAATAA AAAT
1 AAATTA AAATTA AAAT
35028561 AAATTTAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
5 9 0.18
6 40 0.82
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (6 bp):
AAATTA
Found at i:35029471 original size:14 final size:16
Alignment explanation
Indices: 35029433--35029473 Score: 50
Period size: 14 Copynumber: 2.6 Consensus size: 16
35029423 AAACTCAACC
35029433 TTTAAATATTTTCAATA
1 TTTAAA-ATTTTCAATA
35029450 TATTAAAATTTTC-AT-
1 T-TTAAAATTTTCAATA
35029465 TTTAAAATT
1 TTTAAAATT
35029474 AAAATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 8 0.35
15 1 0.04
16 2 0.09
17 7 0.30
18 5 0.22
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (16 bp):
TTTAAAATTTTCAATA
Found at i:35053862 original size:38 final size:38
Alignment explanation
Indices: 35053806--35053907 Score: 134
Period size: 38 Copynumber: 2.7 Consensus size: 38
35053796 AATGATCGTA
*
35053806 TGGTGTTTATTGGGCTTAGTGCCTA-AAAGGAGATGTGC
1 TGGTGTTTATCGGGCTTAGTGCCTAGAAA-GAGATGTGC
* * **
35053844 TGGTGTTTATCGGACTTAGTGCCTAGCAAGCTATGTGC
1 TGGTGTTTATCGGGCTTAGTGCCTAGAAAGAGATGTGC
*
35053882 TGGTGTTTATCGGGTTTAGTGCCTAG
1 TGGTGTTTATCGGGCTTAGTGCCTAG
35053908 TAAGTTTCGT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
38 54 0.96
39 2 0.04
ACGTcount: A:0.18, C:0.14, G:0.32, T:0.36
Consensus pattern (38 bp):
TGGTGTTTATCGGGCTTAGTGCCTAGAAAGAGATGTGC
Found at i:35055813 original size:2 final size:2
Alignment explanation
Indices: 35055806--35055830 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35055796 TTCCATTTTC
35055806 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
35055831 TAAACAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35056701 original size:6 final size:6
Alignment explanation
Indices: 35056692--35056748 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
35056682 CAAATTTAAC
* *
35056692 TAAATT TAAA-G TAAATT TAAATT TACAA-- TAAATT TAAATT TAAAGAT
1 TAAATT TAAATT TAAATT TAAATT TA-AATT TAAATT TAAATT TAAA-TT
35056739 T-AATT TAAAT
1 TAAATT TAAAT
35056749 CAATTTAAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
4 2 0.05
5 8 0.20
6 27 0.66
7 4 0.10
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (6 bp):
TAAATT
Found at i:35056708 original size:27 final size:27
Alignment explanation
Indices: 35056670--35056730 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
35056660 TATATTAAGT
*
35056670 TTTAAATAAATTCAAATTTA-ACTAAA
1 TTTAAATAAATTCAAATTTACAATAAA
*
35056696 TTTAAAGTAAATTTAAATTTACAATAAA
1 TTTAAA-TAAATTCAAATTTACAATAAA
35056724 TTTAAAT
1 TTTAAAT
35056731 TTAAAGATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
26 6 0.19
27 14 0.45
28 11 0.35
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (27 bp):
TTTAAATAAATTCAAATTTACAATAAA
Found at i:35056714 original size:17 final size:17
Alignment explanation
Indices: 35056692--35056748 Score: 80
Period size: 17 Copynumber: 3.3 Consensus size: 17
35056682 CAAATTTAAC
35056692 TAAATTTAAAGTAAATT
1 TAAATTTAAAGTAAATT
35056709 TAAATTTACAA-TAAATT
1 TAAATTTA-AAGTAAATT
*
35056726 TAAATTTAAAGATTAATT
1 TAAATTTAAAG-TAAATT
35056744 TAAAT
1 TAAAT
35056749 CAATTTAAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
16 2 0.06
17 22 0.61
18 12 0.33
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (17 bp):
TAAATTTAAAGTAAATT
Found at i:35065489 original size:114 final size:114
Alignment explanation
Indices: 35065286--35065518 Score: 346
Period size: 114 Copynumber: 2.0 Consensus size: 114
35065276 GATTAAGAGT
*
35065286 ACTCCTTGTTGAGACCCAAAAAGAACATTAGGTTCGCATTCTCGATTCTGCTTTGCTTTGCCACA
1 ACTCCTTGTTGAGACCCAAAAAGAACATCAGGTTCGCATTCTCGATTCTGCTTTGCTTTGCCACA
* * *
35065351 GCAACATCTCTTTGCCTCGATGGTTTTTGCTACAGCATTGTCGAGCTCC
66 GCAACATCACTTTGCCTAGATGGTTCTTGCTACAGCATTGTCGAGCTCC
*
35065400 ACTCCTTGTTGAGACCCAAAAAGAACATCAGGCTT-GCATTC-CTGATTCTTCTTTGCTTTGCCA
1 ACTCCTTGTTGAGACCCAAAAAGAACATCAGG-TTCGCATTCTC-GATTCTGCTTTGCTTTGCCA
* *
35065463 CAGCAACATCACTTTGCTTTAG-TGGTTCTTGCTACAGTATTGTCGAGCTCC
64 CAGCAACATCACTTTGC-CTAGATGGTTCTTGCTACAGCATTGTCGAGCTCC
*
35065514 GCTCC
1 ACTCC
35065519 CAGTGATGGC
Statistics
Matches: 108, Mismatches: 8, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
113 1 0.01
114 103 0.95
115 4 0.04
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.33
Consensus pattern (114 bp):
ACTCCTTGTTGAGACCCAAAAAGAACATCAGGTTCGCATTCTCGATTCTGCTTTGCTTTGCCACA
GCAACATCACTTTGCCTAGATGGTTCTTGCTACAGCATTGTCGAGCTCC
Found at i:35069252 original size:32 final size:32
Alignment explanation
Indices: 35069211--35069274 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
35069201 TGCTTGATTC
35069211 TATCAACATGTGGGGAAGATGTATATATGTTA
1 TATCAACATGTGGGGAAGATGTATATATGTTA
35069243 TATCAACATGTGGGGAAGATGTATATATGTTA
1 TATCAACATGTGGGGAAGATGTATATATGTTA
35069275 ATTTAAAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.34
Consensus pattern (32 bp):
TATCAACATGTGGGGAAGATGTATATATGTTA
Found at i:35072352 original size:37 final size:38
Alignment explanation
Indices: 35072302--35072375 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 38
35072292 GCATTGTTCC
*
35072302 TTGTCGCTGCATTGTTGCCAACATTCAACA-TCCTCCA
1 TTGTCGCTACATTGTTGCCAACATTCAACACTCCTCCA
*
35072339 TTGTCGCTACATTGTTGCCAACATTTAACACTCCTCC
1 TTGTCGCTACATTGTTGCCAACATTCAACACTCCTCC
35072376 TTGGCTACTA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 28 0.82
38 6 0.18
ACGTcount: A:0.22, C:0.32, G:0.12, T:0.34
Consensus pattern (38 bp):
TTGTCGCTACATTGTTGCCAACATTCAACACTCCTCCA
Found at i:35078604 original size:22 final size:22
Alignment explanation
Indices: 35078579--35078623 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
35078569 TATGAAAGAT
35078579 TTAACAATAAGCTCAAAGTGAC
1 TTAACAATAAGCTCAAAGTGAC
35078601 TTAACAATAAGCTCAAAGTGAC
1 TTAACAATAAGCTCAAAGTGAC
35078623 T
1 T
35078624 ATGTGCAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.24
Consensus pattern (22 bp):
TTAACAATAAGCTCAAAGTGAC
Found at i:35079342 original size:24 final size:24
Alignment explanation
Indices: 35079307--35079385 Score: 104
Period size: 24 Copynumber: 3.3 Consensus size: 24
35079297 CTTCCAAATA
*
35079307 AAACTCTGTTTATTTGTTTCAATT
1 AAACTCTATTTATTTGTTTCAATT
* *
35079331 AAATTTTATTTATTTGTTTCAATT
1 AAACTCTATTTATTTGTTTCAATT
* * *
35079355 AAACTCTGTTTATTTGTTTCAGTC
1 AAACTCTATTTATTTGTTTCAATT
35079379 AAACTCT
1 AAACTCT
35079386 TATTAGTCTA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.27, C:0.13, G:0.08, T:0.53
Consensus pattern (24 bp):
AAACTCTATTTATTTGTTTCAATT
Found at i:35080315 original size:23 final size:23
Alignment explanation
Indices: 35080285--35080332 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
35080275 TTATGGTAGA
35080285 GATAAACTCTCGTTCAAGGATGT
1 GATAAACTCTCGTTCAAGGATGT
35080308 GATAAACTCTCGTTCAAGGATGT
1 GATAAACTCTCGTTCAAGGATGT
35080331 GA
1 GA
35080333 AGGATCATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (23 bp):
GATAAACTCTCGTTCAAGGATGT
Found at i:35081162 original size:6 final size:6
Alignment explanation
Indices: 35081153--35081245 Score: 83
Period size: 6 Copynumber: 16.7 Consensus size: 6
35081143 TATTTTAAGA
* * * *
35081153 TTAATT TTAAAT TT-TAT TTAAAT TTAAAT TT-ATT TTAAGT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
35081199 TT--AT TTAAAT TT-ATT TTAAAT TTAAAT TT-AA- TTAAAT TTAAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
35081242 TTAA
1 TTAA
35081246 TCTTAAAATT
Statistics
Matches: 71, Mismatches: 9, Indels: 14
0.76 0.10 0.15
Matches are distributed among these distances:
4 6 0.08
5 16 0.23
6 49 0.69
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (6 bp):
TTAAAT
Found at i:35081204 original size:27 final size:27
Alignment explanation
Indices: 35081141--35081238 Score: 117
Period size: 27 Copynumber: 3.5 Consensus size: 27
35081131 TTGGATTTCG
* *
35081141 TTTATTTTAAGATTAATTTTAAATTT-TA
1 TTTA-TTTAA-ATTTATTTTAAATTTAAA
*
35081169 TTTAAATTTAAATTTATTTTAAGTTTAAA
1 TTT--ATTTAAATTTATTTTAAATTTAAA
35081198 TTTATTTAAATTTATTTTAAATTTAAA
1 TTTATTTAAATTTATTTTAAATTTAAA
*
35081225 TTTAATTAAATTTA
1 TTTATTTAAATTTA
35081239 AAATTAATCT
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
27 36 0.58
28 16 0.26
29 9 0.15
30 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (27 bp):
TTTATTTAAATTTATTTTAAATTTAAA
Found at i:35081222 original size:11 final size:11
Alignment explanation
Indices: 35081141--35081222 Score: 71
Period size: 11 Copynumber: 7.4 Consensus size: 11
35081131 TTGGATTTCG
35081141 TTTATTTTAAGA
1 TTTATTTTAA-A
*
35081153 TTAATTTTAAA
1 TTTATTTTAAA
35081164 TTT-TATTTAAA
1 TTTAT-TTTAAA
* *
35081175 TTTAAATTT-AT
1 TTT-ATTTTAAA
*
35081186 TTTAAGTTTAAA
1 TTT-ATTTTAAA
35081198 TTTA-TTTAAA
1 TTTATTTTAAA
35081208 TTTATTTTAAA
1 TTTATTTTAAA
35081219 TTTA
1 TTTA
35081223 AATTTAATTA
Statistics
Matches: 59, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
10 11 0.19
11 32 0.54
12 16 0.27
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (11 bp):
TTTATTTTAAA
Found at i:35081243 original size:12 final size:12
Alignment explanation
Indices: 35081213--35081257 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
35081203 TTAAATTTAT
*
35081213 TTTAAATTTAAA
1 TTTAAAATTAAA
35081225 TTT--AATTAAA
1 TTTAAAATTAAA
35081235 TTTAAAATT-AA
1 TTTAAAATTAAA
35081246 TCTTAAAATTAA
1 T-TTAAAATTAA
35081258 TGAATTAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
10 9 0.32
11 3 0.11
12 15 0.54
13 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (12 bp):
TTTAAAATTAAA
Found at i:35081243 original size:17 final size:16
Alignment explanation
Indices: 35081153--35081240 Score: 96
Period size: 17 Copynumber: 5.7 Consensus size: 16
35081143 TATTTTAAGA
*
35081153 TTAATTTTAAATTTTAT
1 TTAAATTTAAA-TTTAT
35081170 TTAAATTTAAATTTATT
1 TTAAATTTAAATTTA-T
*
35081187 TTAAGTTTAAATTTAT
1 TTAAATTTAAATTTAT
35081203 TTAAATTT--A--T-T
1 TTAAATTTAAATTTAT
*
35081214 TTAAATTTAAATTTAA
1 TTAAATTTAAATTTAT
35081230 TTAAATTTAAA
1 TTAAATTTAAA
35081241 ATTAATCTTA
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
11 9 0.15
12 1 0.02
13 1 0.02
14 1 0.02
15 1 0.02
16 23 0.38
17 25 0.41
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (16 bp):
TTAAATTTAAATTTAT
Found at i:35081245 original size:16 final size:16
Alignment explanation
Indices: 35081214--35081246 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
35081204 TAAATTTATT
*
35081214 TTAAATTTAAATTTAA
1 TTAAATTTAAAATTAA
35081230 TTAAATTTAAAATTAA
1 TTAAATTTAAAATTAA
35081246 T
1 T
35081247 CTTAAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTAAATTTAAAATTAA
Found at i:35082058 original size:10 final size:12
Alignment explanation
Indices: 35082027--35082062 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
35082017 GATGAAACAG
35082027 TGAATGATATTAA
1 TGAAT-ATATTAA
35082040 TGAATATATTAA
1 TGAATATATTAA
*
35082052 TAAATATATTA
1 TGAATATATTA
35082063 CAATAATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 17 0.77
13 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (12 bp):
TGAATATATTAA
Found at i:35082518 original size:33 final size:33
Alignment explanation
Indices: 35082476--35082549 Score: 148
Period size: 33 Copynumber: 2.2 Consensus size: 33
35082466 CCCTGATTGA
35082476 CGCGTGAACGACGGCCGGAAGGCCCAGGAACGG
1 CGCGTGAACGACGGCCGGAAGGCCCAGGAACGG
35082509 CGCGTGAACGACGGCCGGAAGGCCCAGGAACGG
1 CGCGTGAACGACGGCCGGAAGGCCCAGGAACGG
35082542 CGCGTGAA
1 CGCGTGAA
35082550 AGACTCTCGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.24, C:0.30, G:0.42, T:0.04
Consensus pattern (33 bp):
CGCGTGAACGACGGCCGGAAGGCCCAGGAACGG
Found at i:35083110 original size:162 final size:162
Alignment explanation
Indices: 35082932--35083254 Score: 461
Period size: 162 Copynumber: 2.0 Consensus size: 162
35082922 ATTAGCTTTC
* * *
35082932 AAATAAGTCCTTTGACTATTTGACTGTACCAGAGG-CTGCCACGTGTCACTTTTTGGCTTATTTA
1 AAATAAGTCCTTTGACTATGTGACTGCACCAG-GGACTGCCACGTGTCACTTTTTGACTTATTTA
* *** * *
35082996 TGCATTTAGTCCTCTTTTA-TTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTTATTTAAT
65 CGCATTTAGTCC-CTGACATTTTTAATTTATTTTAATTTAATCCCCAAATCAACTTTTACTTAAT
* *
35083060 TACGAAATTGGCCCAATAATTTTTCAAGATTTAT
129 TACAAAATTGGCCCAAGAATTTTTCAAGATTTAT
* * *
35083094 AAATTAGTCCTTTGACTGTGTGGCTGCACCAGGGACTGCCACGTGTCACTTTTTGACTTATTTAC
1 AAATAAGTCCTTTGACTATGTGACTGCACCAGGGACTGCCACGTGTCACTTTTTGACTTATTTAC
* *
35083159 GTATTTAGTCCCTGACATTTTTAATTTATTTTAATTTAATCCCTAAATCAACTTTTACTTAATTA
66 GCATTTAGTCCCTGACATTTTTAATTTATTTTAATTTAATCCCCAAATCAACTTTTACTTAATTA
*
35083224 CAAAATTGGCCCAAGAATTTTTTAAGATTTA
131 CAAAATTGGCCCAAGAATTTTTCAAGATTTA
35083255 CAATTTGGTC
Statistics
Matches: 142, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
161 5 0.04
162 137 0.96
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (162 bp):
AAATAAGTCCTTTGACTATGTGACTGCACCAGGGACTGCCACGTGTCACTTTTTGACTTATTTAC
GCATTTAGTCCCTGACATTTTTAATTTATTTTAATTTAATCCCCAAATCAACTTTTACTTAATTA
CAAAATTGGCCCAAGAATTTTTCAAGATTTAT
Found at i:35083468 original size:30 final size:30
Alignment explanation
Indices: 35083434--35083527 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
35083424 TAAATCTTTT
35083434 AAAATTCTATTTTTAACCCCAATTTCACCA
1 AAAATTCTATTTTTAACCCCAATTTCACCA
* *
35083464 AAAATTACCA-TTTT-ACCCCGAATCTT---CT
1 AAAATT-CTATTTTTAACCCC-AAT-TTCACCA
* *
35083492 AAAATTCTATTTTTAACCTCGATTTCACCA
1 AAAATTCTATTTTTAACCCCAATTTCACCA
35083522 AAAATT
1 AAAATT
35083528 ACCATTTTAC
Statistics
Matches: 50, Mismatches: 6, Indels: 16
0.69 0.08 0.22
Matches are distributed among these distances:
27 4 0.08
28 13 0.26
29 9 0.18
30 20 0.40
31 4 0.08
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.37
Consensus pattern (30 bp):
AAAATTCTATTTTTAACCCCAATTTCACCA
Found at i:35083505 original size:58 final size:58
Alignment explanation
Indices: 35083402--35083612 Score: 323
Period size: 59 Copynumber: 3.6 Consensus size: 58
35083392 CCCGAAACTT
* * * * *
35083402 CCAAAAATTATCATTTTACCCCTAAATCTTTTAAAATTCTATTTTTAACCCCAATTTCA
1 CCAAAAATTACCATTTTACCCC-GAATCTTCTAAAATTCTATTTTTAACCTCGATTTCA
35083461 CCAAAAATTACCATTTTACCCCGAATCTTCTAAAATTCTATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCGAATCTTCTAAAATTCTATTTTTAACCTCGATTTCA
* *
35083519 CCAAAAATTACCATTTTACCCTCGAATCTTTTAAAATTCCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCC-CGAATCTTCTAAAATTCTATTTTTAACCTCGATTTCA
* *
35083578 CCAAAAATTACCATTTTACCCCGAAACTTCCAAAA
1 CCAAAAATTACCATTTTACCCCGAATCTTCTAAAA
35083613 AATTACCATT
Statistics
Matches: 141, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
58 64 0.45
59 77 0.55
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.36
Consensus pattern (58 bp):
CCAAAAATTACCATTTTACCCCGAATCTTCTAAAATTCTATTTTTAACCTCGATTTCA
Found at i:35083536 original size:30 final size:30
Alignment explanation
Indices: 35083444--35083631 Score: 131
Period size: 30 Copynumber: 6.4 Consensus size: 30
35083434 AAAATTCTAT
*
35083444 TTTTAACCCCAATTTCACCAAAAATTACCA
1 TTTTAACCCCGATTTCACCAAAAATTACCA
* ** * *
35083474 TTTT-ACCCCGA-ATCTTCTAAAATT-CTA
1 TTTTAACCCCGATTTCACCAAAAATTACCA
*
35083501 TTTTTAACCTCGATTTCACCAAAAATTACCA
1 -TTTTAACCCCGATTTCACCAAAAATTACCA
* ****
35083532 TTTT-ACCCTCGA-ATCTTTTAAAATT-CCA
1 TTTTAACCC-CGATTTCACCAAAAATTACCA
*
35083560 TTTTTAACCTCGATTTCACCAAAAATTACCA
1 -TTTTAACCCCGATTTCACCAAAAATTACCA
* *
35083591 TTTT-ACCCCGAAACTTC-CAAAAAATTACCA
1 TTTTAACCCCG--ATTTCACCAAAAATTACCA
*
35083621 TTTTACCCCCG
1 TTTTAACCCCG
35083632 GGTATCCACA
Statistics
Matches: 118, Mismatches: 28, Indels: 23
0.70 0.17 0.14
Matches are distributed among these distances:
27 2 0.02
28 16 0.14
29 35 0.30
30 51 0.43
31 14 0.12
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (30 bp):
TTTTAACCCCGATTTCACCAAAAATTACCA
Found at i:35083539 original size:117 final size:117
Alignment explanation
Indices: 35083402--35083612 Score: 343
Period size: 117 Copynumber: 1.8 Consensus size: 117
35083392 CCCGAAACTT
* *
35083402 CCAAAAATTATCATTTTACCC-CTAAATCTTTTAAAATTCTATTTTTAACCCCAATTTCACCAAA
1 CCAAAAATTACCATTTTACCCTC-AAATCTTTTAAAATTCCATTTTTAACCCCAATTTCACCAAA
* *
35083466 AATTACCATTTTACCCCGAATCTTCTAAAATTCTATTTTTAACCTCGATTTCA
65 AATTACCATTTTACCCCGAAACTTCCAAAATTCTATTTTTAACCTCGATTTCA
* * *
35083519 CCAAAAATTACCATTTTACCCTCGAATCTTTTAAAATTCCATTTTTAACCTCGATTTCACCAAAA
1 CCAAAAATTACCATTTTACCCTCAAATCTTTTAAAATTCCATTTTTAACCCCAATTTCACCAAAA
35083584 ATTACCATTTTACCCCGAAACTTCCAAAA
66 ATTACCATTTTACCCCGAAACTTCCAAAA
35083613 AATTACCATT
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
117 85 0.99
118 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.36
Consensus pattern (117 bp):
CCAAAAATTACCATTTTACCCTCAAATCTTTTAAAATTCCATTTTTAACCCCAATTTCACCAAAA
ATTACCATTTTACCCCGAAACTTCCAAAATTCTATTTTTAACCTCGATTTCA
Found at i:35090212 original size:30 final size:30
Alignment explanation
Indices: 35090176--35090240 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
35090166 AAAACATGTA
* * *
35090176 GGGGTGTTCTAGAACCACTTGGAAATGTGG
1 GGGGTGTCCTAGAACCACTTGAAAATATGG
35090206 GGGGTGTCCTAGAACCACTTGAAAATATGG
1 GGGGTGTCCTAGAACCACTTGAAAATATGG
35090236 GGGGT
1 GGGGT
35090241 CTTGCTAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.25, C:0.14, G:0.37, T:0.25
Consensus pattern (30 bp):
GGGGTGTCCTAGAACCACTTGAAAATATGG
Found at i:35092544 original size:20 final size:21
Alignment explanation
Indices: 35092508--35092546 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
35092498 AAAAATATAT
35092508 AATTGTTAATTTAAATTTTCA
1 AATTGTTAATTTAAATTTTCA
35092529 AATT-TTAA-TTATAATTTT
1 AATTGTTAATTTA-AATTTT
35092547 AATATAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.18
20 10 0.59
21 4 0.24
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (21 bp):
AATTGTTAATTTAAATTTTCA
Found at i:35092719 original size:19 final size:19
Alignment explanation
Indices: 35092688--35092738 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
35092678 TTTTTATTTC
*
35092688 TATATTATA-TATAGTTTA
1 TATATTTTATTATAGTTTA
* *
35092706 T-TATTTTATGTATATTTTT
1 TATATTTTAT-TATAGTTTA
35092725 TATATTTTATTATA
1 TATATTTTATTATA
35092739 AATTATTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
17 6 0.22
18 1 0.04
19 12 0.44
20 8 0.30
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (19 bp):
TATATTTTATTATAGTTTA
Found at i:35092730 original size:9 final size:10
Alignment explanation
Indices: 35092707--35092766 Score: 52
Period size: 10 Copynumber: 5.8 Consensus size: 10
35092697 TATAGTTTAT
35092707 TATTTTATGTA
1 TATTTTAT-TA
35092718 TATTTT-TTA
1 TATTTTATTA
35092727 TATTTTATTA
1 TATTTTATTA
**
35092737 TAAATTATT-
1 TATTTTATTA
35092746 TATTTTTATTTA
1 TA-TTTTA-TTA
35092758 TATATTTAT
1 TAT-TTTAT
35092767 GTTATTAATG
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
9 10 0.25
10 14 0.35
11 10 0.25
12 6 0.15
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (10 bp):
TATTTTATTA
Found at i:35092747 original size:21 final size:19
Alignment explanation
Indices: 35092690--35092766 Score: 68
Period size: 20 Copynumber: 3.8 Consensus size: 19
35092680 TTTATTTCTA
35092690 TATTATATATAGTTTATTATTT
1 TATTATAT-TA-TTTA-TATTT
*
35092712 TATGTATATTTTTTATATTT
1 TAT-TATATTATTTATATTT
35092732 TATTATAAATTATTTAT-TTT
1 TATTAT--ATTATTTATATTT
35092752 TATT-TATATATTTAT
1 TATTATAT-TATTTAT
35092767 GTTATTAATG
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
17 2 0.04
18 7 0.14
19 4 0.08
20 15 0.31
21 12 0.24
22 4 0.08
23 5 0.10
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (19 bp):
TATTATATTATTTATATTT
Found at i:35095466 original size:30 final size:29
Alignment explanation
Indices: 35095432--35095555 Score: 135
Period size: 30 Copynumber: 4.1 Consensus size: 29
35095422 AAACGGAGTC
*
35095432 AAATTTTAATTTTT-GAAAACTTTAGGGGTT
1 AAATTTGAATTTTTGGAAAA-TTT-GGGGTT
*
35095462 AAATTTGAATTTTTGGAAAATTTGAGGGTG
1 AAATTTGAATTTTTGGAAAATTTG-GGGTT
*
35095492 AAATTTGAATTTTTTGGAAAATTTGGGGGT
1 AAATTTGAA-TTTTTGGAAAATTTGGGGTT
*
35095522 AAATTTTGAATTTTT-AAAAACTTTAGGGGTT
1 AAA-TTTGAATTTTTGGAAAA-TTT-GGGGTT
35095553 AAA
1 AAA
35095556 AATGGTTTTA
Statistics
Matches: 82, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
29 5 0.06
30 43 0.52
31 34 0.41
ACGTcount: A:0.35, C:0.02, G:0.21, T:0.43
Consensus pattern (29 bp):
AAATTTGAATTTTTGGAAAATTTGGGGTT
Found at i:35095720 original size:6 final size:6
Alignment explanation
Indices: 35095709--35095754 Score: 60
Period size: 6 Copynumber: 8.0 Consensus size: 6
35095699 ACCAAACCAT
**
35095709 TTTAAA TTTAAA TTT-AA TTTAAA TTTGGA TTT-AA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
35095755 ATTATTATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
5 9 0.26
6 26 0.74
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:35095729 original size:11 final size:11
Alignment explanation
Indices: 35095713--35095771 Score: 59
Period size: 11 Copynumber: 5.3 Consensus size: 11
35095703 AACCATTTTA
35095713 AATTTAAATTT
1 AATTTAAATTT
35095724 AATTTAAATTT
1 AATTTAAATTT
*
35095735 GGATTT-AATTT
1 -AATTTAAATTT
*
35095746 AAATTTAAAATT
1 -AATTTAAATTT
35095758 -ATTATAAATTT
1 AATT-TAAATTT
35095769 AAT
1 AAT
35095772 AAAATATAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
10 3 0.08
11 26 0.67
12 10 0.26
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:35095731 original size:17 final size:17
Alignment explanation
Indices: 35095709--35095770 Score: 81
Period size: 17 Copynumber: 3.6 Consensus size: 17
35095699 ACCAAACCAT
35095709 TTTAAATTTAAATTTAA
1 TTTAAATTTAAATTTAA
**
35095726 TTTAAATTTGGATTTAA
1 TTTAAATTTAAATTTAA
*
35095743 TTTAAATTTAAAATT-A
1 TTTAAATTTAAATTTAA
35095759 TTATAAATTTAA
1 TT-TAAATTTAA
35095771 TAAAATATAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
16 3 0.08
17 36 0.92
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
TTTAAATTTAAATTTAA
Found at i:35097786 original size:59 final size:60
Alignment explanation
Indices: 35097634--35097969 Score: 343
Period size: 59 Copynumber: 5.7 Consensus size: 60
35097624 AACTATTTAG
* *
35097634 AAATTATATTTTGACCCTAAAACTTTCTAAAAATTATATTTTGACCCCTAAACTTCTCTA
1 AAATTATATTTTAACCCTAAAACTTTCTAAAAATTACATTTTGACCCCTAAACTTCTCTA
* * * * *
35097694 AAATTATATTTTAATCGTAAAACTTTTTGAAAATTACATTTTGACCCCTAAACTT-ACTA
1 AAATTATATTTTAACCCTAAAACTTTCTAAAAATTACATTTTGACCCCTAAACTTCTCTA
*
35097753 AAATTATATTTTAACCCTAAAACTTTCTAAAAATTACATTTTAACCCC-AAACTTCTCTA
1 AAATTATATTTTAACCCTAAAACTTTCTAAAAATTACATTTTGACCCCTAAACTTCTCTA
* * * * * *
35097812 AAATTATATTTTAACCCTAAAACTTTTTAAAATTTATATTTT-AACCCTAAATTTTTCTAA
1 AAATTATATTTTAACCCTAAAACTTTCTAAAAATTACATTTTGACCCCTAAACTTCTCT-A
* * * * * *
35097872 AAATTACT-TTTT-ACCTCT-AAATTTTC-CAAAATTCCATTTTTACCCCT--GCTTTCCCTA
1 AAATTA-TATTTTAACC-CTAAAACTTTCTAAAAATTACATTTTGACCCCTAAAC-TTCTCTA
* * *
35097929 AAATTACCATTTTACCCCT-AAACTTTCT-AAAATTTCATTTT
1 AAATTA-TATTTTAACCCTAAAACTTTCTAAAAATTACATTTT
35097970 TAACCTCAAT
Statistics
Matches: 232, Mismatches: 34, Indels: 22
0.81 0.12 0.08
Matches are distributed among these distances:
57 8 0.03
58 49 0.21
59 112 0.48
60 62 0.27
61 1 0.00
ACGTcount: A:0.36, C:0.20, G:0.02, T:0.42
Consensus pattern (60 bp):
AAATTATATTTTAACCCTAAAACTTTCTAAAAATTACATTTTGACCCCTAAACTTCTCTA
Found at i:35097796 original size:89 final size:88
Alignment explanation
Indices: 35097634--35097884 Score: 294
Period size: 89 Copynumber: 2.8 Consensus size: 88
35097624 AACTATTTAG
*
35097634 AAATTATATTTTGACCCTAAAACTTTCTAAAAATTATATTTTGACCCCT-AAACTTCTCT-AAAA
1 AAATTATATTTTGACCCTAAAACTTTCT-AAAATTATATTTT-AACCCTAAAACTT-TCTAAAAA
* ** *
35097697 TTATATTTTAATCGTAAAACTT-TTTGA
63 TTACATTTTAA-CCCAAAACTTCTCT-A
* *
35097724 AAATTACATTTTGACCCCT-AAACTTACTAAAATTATATTTTAACCCTAAAACTTTCTAAAAATT
1 AAATTATATTTTGA-CCCTAAAACTTTCTAAAATTATATTTTAACCCTAAAACTTTCTAAAAATT
*
35097788 ACATTTTAACCCCAAACTTCTCTA
65 ACATTTTAACCCAAAACTTCTCTA
* * **
35097812 AAATTATATTTTAACCCTAAAACTTTTTAAAATTTATATTTTAACCCTAAATTTTTCTAAAAATT
1 AAATTATATTTTGACCCTAAAACTTTCTAAAA-TTATATTTTAACCCTAAAACTTTCTAAAAATT
*
35097877 ACTTTTTA
65 ACATTTTA
35097885 CCTCTAAATT
Statistics
Matches: 140, Mismatches: 15, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
87 4 0.03
88 39 0.28
89 72 0.51
90 21 0.15
91 4 0.03
ACGTcount: A:0.39, C:0.17, G:0.02, T:0.42
Consensus pattern (88 bp):
AAATTATATTTTGACCCTAAAACTTTCTAAAATTATATTTTAACCCTAAAACTTTCTAAAAATTA
CATTTTAACCCAAAACTTCTCTA
Found at i:35097952 original size:117 final size:118
Alignment explanation
Indices: 35097772--35098060 Score: 313
Period size: 117 Copynumber: 2.5 Consensus size: 118
35097762 TTTAACCCTA
* * * * *
35097772 AAACTTTCTAAAAATTACATTTTAACCCCAAAC-TT-CTCTAAAATTA-TATTTTAACCCTAAAA
1 AAACTTTC-CAAAATTCCATTTTAACCCC-GACTTTAC-CTAAAATTACCATTTTACCCCTAAAA
* * * * *
35097834 CTTTTTAAAATTT-ATATTTTAACCCTAAATTTTTCTAAAAATTA-CTTTTTACCTCT
63 CTTTCTAAAATTTCAT-TTTTAA-CCTAAATTTTTATAAAAATTACCATTTTACCCCC
* * *
35097890 AAATTTTCCAAAATTCCATTTTTACCCCTG-CTTTCCCTAAAATTACCATTTTACCCCT-AAACT
1 AAACTTTCCAAAATTCCATTTTAACCCC-GACTTTACCTAAAATTACCATTTTACCCCTAAAACT
* *
35097953 TTCTAAAATTTCATTTTTAACCTCAATTTTTATCAAAATTACCATTTTACCCCC
65 TTCTAAAATTTCATTTTTAACCTAAATTTTTATAAAAATTACCATTTTACCCCC
* * *
35098007 AAACTTTCCAAAATTCCATTTTAACCTCGATTTTACCAAAAATTACCATTTTAC
1 AAACTTTCCAAAATTCCATTTTAACCCCGACTTTACCTAAAATTACCATTTTAC
35098061 TCTCGAACTT
Statistics
Matches: 144, Mismatches: 21, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
116 20 0.14
117 104 0.72
118 20 0.14
ACGTcount: A:0.35, C:0.23, G:0.01, T:0.41
Consensus pattern (118 bp):
AAACTTTCCAAAATTCCATTTTAACCCCGACTTTACCTAAAATTACCATTTTACCCCTAAAACTT
TCTAAAATTTCATTTTTAACCTAAATTTTTATAAAAATTACCATTTTACCCCC
Found at i:35097958 original size:29 final size:28
Alignment explanation
Indices: 35097619--35098029 Score: 276
Period size: 30 Copynumber: 14.0 Consensus size: 28
35097609 CCCTAAAAGT
*
35097619 CCCTAAACTATT-TAGAAATTATATTTTGA-
1 CCCTAAACT-TTCTA-AAATTACATTTT-AC
*
35097648 CCCTAAAACTTTCTAAAAATTATATTTTGAC
1 CCCT-AAACTTTCT-AAAATTACATTTT-AC
* *
35097679 CCCTAAACTTCTCTAAAATTATATTTTAA
1 CCCTAAACTT-TCTAAAATTACATTTTAC
* * *
35097708 TCGTAAAACTTTTTGAAAATTACATTTTGAC
1 CCCT-AAACTTTCT-AAAATTACATTTT-AC
* * *
35097739 CCCTAAACTTACTAAAATTATATTTTAA
1 CCCTAAACTTTCTAAAATTACATTTTAC
35097767 CCCTAAAACTTTCTAAAAATTACATTTTAAC
1 CCCT-AAACTTTCT-AAAATTACATTTT-AC
* *
35097798 CCC-AAACTTCTCTAAAATTATATTTTAA
1 CCCTAAACTT-TCTAAAATTACATTTTAC
* * *
35097826 CCCTAAAACTTTTTAAAATTTATATTTTAA
1 CCCT-AAACTTTCTAAAA-TTACATTTTAC
* *
35097856 CCCTAAATTTTTCTAAAAATTACTTTTTAC
1 CCCTAAA-CTTTCT-AAAATTACATTTTAC
* * * *
35097886 CTCTAAATTTTCCAAAATTCCATTTTTAC
1 CCCTAAACTTTCTAAAATTACA-TTTTAC
*
35097915 CCCT--GCTTTCCCTAAAATTACCATTTTAC
1 CCCTAAACTTT--CTAAAATTA-CATTTTAC
*
35097944 CCCTAAACTTTCTAAAATTTCATTTTTA-
1 CCCTAAACTTTCTAAAATTACA-TTTTAC
* ** *
35097972 ACCTCAATTTTTATCAAAATTACCATTTTAC
1 CCCT-AAACTTTCT-AAAATTA-CATTTTAC
* * *
35098003 CCCCAAACTTTCCAAAATTCCATTTTA
1 CCCTAAACTTTCTAAAATTACATTTTA
35098030 ACCTCGATTT
Statistics
Matches: 308, Mismatches: 46, Indels: 57
0.75 0.11 0.14
Matches are distributed among these distances:
27 3 0.01
28 28 0.09
29 114 0.37
30 136 0.44
31 27 0.09
ACGTcount: A:0.36, C:0.21, G:0.02, T:0.41
Consensus pattern (28 bp):
CCCTAAACTTTCTAAAATTACATTTTAC
Found at i:35098005 original size:59 final size:60
Alignment explanation
Indices: 35097750--35098121 Score: 231
Period size: 59 Copynumber: 6.3 Consensus size: 60
35097740 CCTAAACTTA
* * * * * **
35097750 CTAAAATTATATTTTAACCCTAAAACTTTCTAAAAATTACA-TTTTAACCCCAA-ACTT-C
1 CTAAAATTACATTTTACCCCTAAAACTTTC-CAAAATTTCATTTTTAACCTCAATTTTTAC
* * ** *
35097808 TCTAAAATTATATTTTAACCCTAAAACTTTTTAAAATTT-ATATTTTAACCCTAAATTTTT--
1 -CTAAAATTACATTTTACCCCTAAAACTTTCCAAAATTTCAT-TTTTAA-CCTCAATTTTTAC
* * * * * * *
35097868 CTAAAAATTACTTTTTACCTCT-AAATTTTCCAAAATTCCATTTTT-ACC-C-CTGCTTTCC
1 CT-AAAATTACATTTTACCCCTAAAACTTTCCAAAATTTCATTTTTAACCTCAAT-TTTTAC
* *
35097926 CTAAAATTACCATTTTACCCCT-AAACTTTCTAAAATTTCATTTTTAACCTCAATTTTTAT
1 CTAAAATTA-CATTTTACCCCTAAAACTTTCCAAAATTTCATTTTTAACCTCAATTTTTAC
* * *
35097986 C-AAAATTACCATTTTACCCC-CAAACTTTCCAAAATTCCA-TTTTAACCTCGA-TTTTAC
1 CTAAAATTA-CATTTTACCCCTAAAACTTTCCAAAATTTCATTTTTAACCTCAATTTTTAC
* * ** * * * *
35098043 CAAAAATTACCATTTTA-CTCTCGAACTTTCCAAAATCTCGTTTTTGACC-CAATTTTGAC
1 CTAAAATTA-CATTTTACCCCTAAAACTTTCCAAAATTTCATTTTTAACCTCAATTTTTAC
*
35098102 C-AAAATTATCATTTTGCCCC
1 CTAAAATTA-CATTTTACCCC
35098122 CGAGTATCCA
Statistics
Matches: 252, Mismatches: 42, Indels: 38
0.76 0.13 0.11
Matches are distributed among these distances:
55 1 0.00
56 3 0.01
57 18 0.07
58 95 0.38
59 106 0.42
60 26 0.10
61 3 0.01
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.41
Consensus pattern (60 bp):
CTAAAATTACATTTTACCCCTAAAACTTTCCAAAATTTCATTTTTAACCTCAATTTTTAC
Found at i:35098070 original size:117 final size:116
Alignment explanation
Indices: 35097811--35098122 Score: 310
Period size: 117 Copynumber: 2.7 Consensus size: 116
35097801 AAACTTCTCT
* * * * * *
35097811 AAAATTA-TATTTTAACCCTAAAACTTTTTAAAATTT-ATATTTTAACCCTAAATTTTTCTAAAA
1 AAAATTACCATTTTACCCCT-AAACTTTCTAAAATTTCAT-TTTTAA-CCTCAATTTTTATCAAA
* * * * * * *
35097874 ATTACTTTTTACCTCTAAATTTTCCAAAATTCCATTTTTACCCCTGCTTTCCCT
63 ATTACATTTTACCCCCAAACTTTCCAAAATTCCATTTTAACCCCTGCTTTACCA
35097928 AAAATTACCATTTTACCCCTAAACTTTCTAAAATTTCATTTTTAACCTCAATTTTTATCAAAATT
1 AAAATTACCATTTTACCCCTAAACTTTCTAAAATTTCATTTTTAACCTCAATTTTTATCAAAATT
* *
35097993 ACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTAACCTC-GATTTTACCA
66 A-CATTTTACCCCCAAACTTTCCAAAATTCCATTTTAACCCCTG-CTTTACCA
* * * * * * * *
35098045 AAAATTACCATTTTA-CTCTCGAACTTTCCAAAATCTCGTTTTTGACC-CAATTTTGACCAAAAT
1 AAAATTACCATTTTACCCCT-AAACTTTCTAAAATTTCATTTTTAACCTCAATTTTTATCAAAAT
*
35098108 TATCATTTTGCCCCC
65 TA-CATTTTACCCCC
35098123 GAGTATCCAA
Statistics
Matches: 165, Mismatches: 25, Indels: 11
0.82 0.12 0.05
Matches are distributed among these distances:
116 49 0.30
117 104 0.63
118 12 0.07
ACGTcount: A:0.33, C:0.24, G:0.02, T:0.41
Consensus pattern (116 bp):
AAAATTACCATTTTACCCCTAAACTTTCTAAAATTTCATTTTTAACCTCAATTTTTATCAAAATT
ACATTTTACCCCCAAACTTTCCAAAATTCCATTTTAACCCCTGCTTTACCA
Found at i:35098076 original size:30 final size:29
Alignment explanation
Indices: 35097987--35098077 Score: 98
Period size: 30 Copynumber: 3.1 Consensus size: 29
35097977 AATTTTTATC
* *
35097987 AAAATTACCATTTTACCCCCAAACTTTCC-
1 AAAATTACCATTTTA-CCTCGAACTTTCCA
*
35098016 AAAATT-CCATTTTAACCTCG-ATTTTACCA
1 AAAATTACCATTTT-ACCTCGAACTTT-CCA
35098045 AAAATTACCATTTTACTCTCGAACTTTCCA
1 AAAATTACCATTTTAC-CTCGAACTTTCCA
35098075 AAA
1 AAA
35098078 TCTCGTTTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
27 4 0.08
28 12 0.23
29 15 0.29
30 17 0.33
31 4 0.08
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.34
Consensus pattern (29 bp):
AAAATTACCATTTTACCTCGAACTTTCCA
Found at i:35098077 original size:29 final size:28
Alignment explanation
Indices: 35097871--35098078 Score: 108
Period size: 29 Copynumber: 7.2 Consensus size: 28
35097861 AATTTTTCTA
* * *
35097871 AAAATTA-CTTTTTACCTCTAAATTTTCC
1 AAAATTACCATTTTACCTC-GAACTTTCC
*
35097899 AAAATT-CCATTTTTACCCCTG--CTTTCCC
1 AAAATTACCA-TTTTACCTC-GAACTTT-CC
* * *
35097927 TAAAATTACCATTTTACCCCTAAACTTTCT
1 -AAAATTACCATTTTACCTC-GAACTTTCC
* * *
35097957 AAAATT-TCATTTTTAACCTC-AATTTTTATC
1 AAAATTACCA-TTTT-ACCTCGAA-CTTT-CC
* *
35097987 AAAATTACCATTTTACCCCCAAACTTTCC
1 AAAATTACCATTTTA-CCTCGAACTTTCC
*
35098016 AAAATT-CCATTTTAACCTCG-ATTTTACC
1 AAAATTACCATTTT-ACCTCGAACTTT-CC
35098044 AAAAATTACCATTTTACTCTCGAACTTTCC
1 -AAAATTACCATTTTAC-CTCGAACTTTCC
35098074 AAAAT
1 AAAAT
35098079 CTCGTTTTTG
Statistics
Matches: 141, Mismatches: 19, Indels: 39
0.71 0.10 0.20
Matches are distributed among these distances:
27 7 0.05
28 25 0.18
29 60 0.43
30 37 0.26
31 12 0.09
ACGTcount: A:0.33, C:0.26, G:0.01, T:0.40
Consensus pattern (28 bp):
AAAATTACCATTTTACCTCGAACTTTCC
Found at i:35098098 original size:58 final size:56
Alignment explanation
Indices: 35097871--35098121 Score: 213
Period size: 58 Copynumber: 4.3 Consensus size: 56
35097861 AATTTTTCTA
* * * * *** *
35097871 AAAATTA-CTTTTTACCTCTAAATTTTCCAAAATTCCATTTTT-ACCCCTGCTTTCCC
1 AAAATTACCATTTTACC-CCAAACTTTCCAAAATT-CATTTTTAACCTCAATTTTACC
* *
35097927 TAAAATTACCATTTTACCCCTAAACTTTCTAAAATTTCATTTTTAACCTCAATTTTTATC
1 -AAAATTACCATTTTACCCC-AAACTTTCCAAAA-TTCATTTTTAACCTCAA-TTTTACC
*
35097987 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCA-TTTTAACCTCGATTTTACC
1 AAAATTACCATTTTA-CCCCAAACTTTCCAAAATT-CATTTTTAACCTCAATTTTACC
* * * *
35098044 AAAAATTACCATTTTACTCTCGAACTTTCCAAAATCTCGTTTTTGACC-CAATTTTGACC
1 -AAAATTACCATTTTAC-CCCAAACTTTCCAAAAT-TCATTTTTAACCTCAATTTT-ACC
* *
35098103 AAAATTATCATTTTGCCCC
1 AAAATTACCATTTTACCCC
35098122 CGAGTATCCA
Statistics
Matches: 161, Mismatches: 21, Indels: 24
0.78 0.10 0.12
Matches are distributed among these distances:
57 17 0.11
58 90 0.56
59 46 0.29
60 8 0.05
ACGTcount: A:0.31, C:0.26, G:0.03, T:0.40
Consensus pattern (56 bp):
AAAATTACCATTTTACCCCAAACTTTCCAAAATTCATTTTTAACCTCAATTTTACC
Found at i:35098615 original size:11 final size:11
Alignment explanation
Indices: 35098593--35098696 Score: 68
Period size: 11 Copynumber: 9.0 Consensus size: 11
35098583 GCTTGGGCTT
35098593 TTAAAGTTTAAA
1 TTAAA-TTTAAA
*
35098605 TTAATTTTAAA
1 TTAAATTTAAA
*
35098616 TTAATTTTAAA
1 TTAAATTTAAA
35098627 TTTAAATTTAAGA
1 -TTAAATTTAA-A
35098640 -TAAATTTAAA
1 TTAAATTTAAA
*
35098650 TTTACTTATTTAAA
1 -TTA--AATTTAAA
* * *
35098664 TTTATTTTAGAT
1 TTAAATTTA-AA
35098676 TTAAATTT-AA
1 TTAAATTTAAA
*
35098686 TCAAATTTAAA
1 TTAAATTTAAA
35098697 ATAATATTAA
Statistics
Matches: 73, Mismatches: 11, Indels: 17
0.72 0.11 0.17
Matches are distributed among these distances:
10 9 0.12
11 32 0.44
12 22 0.30
13 3 0.04
14 7 0.10
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:35098625 original size:6 final size:6
Alignment explanation
Indices: 35098592--35098685 Score: 72
Period size: 6 Copynumber: 15.8 Consensus size: 6
35098582 GGCTTGGGCT
* *
35098592 TTTAAA GTTTAAA -TTAAT TTTAAA -TTAAT TTTAAA TTTAAA TTTAAGA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A
* * *
35098640 --TAAA TTTAAA TTTACTTA TTTAAA TTT-AT TTTAGA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
35098686 TCAAATTTAA
Statistics
Matches: 69, Mismatches: 10, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
4 1 0.01
5 15 0.22
6 41 0.59
7 7 0.10
8 5 0.07
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:35098630 original size:17 final size:18
Alignment explanation
Indices: 35098592--35098653 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 18
35098582 GGCTTGGGCT
*
35098592 TTTAAAGTTTAA-ATTAAT
1 TTTAAA-TTTAAGATTAAA
**
35098610 TTTAAA-TTAATTTTAAA
1 TTTAAATTTAAGATTAAA
35098627 TTTAAATTTAAGA-TAAA
1 TTTAAATTTAAGATTAAA
35098644 TTTAAATTTA
1 TTTAAATTTA
35098654 CTTATTTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
16 4 0.11
17 24 0.63
18 10 0.26
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TTTAAATTTAAGATTAAA
Found at i:35098679 original size:17 final size:17
Alignment explanation
Indices: 35098605--35098684 Score: 76
Period size: 17 Copynumber: 4.9 Consensus size: 17
35098595 AAAGTTTAAA
* *
35098605 TTAATTTTAAATTAATT
1 TTAAATTTAAATTTATT
**
35098622 TTAAATTTAAATTTAAG
1 TTAAATTTAAATTTATT
* *
35098639 ATAAATTTAAATTTA-C
1 TTAAATTTAAATTTATT
35098655 TT--ATTTAAATTTATT
1 TTAAATTTAAATTTATT
*
35098670 TTAGATTTAAATTTA
1 TTAAATTTAAATTTA
35098685 ATCAAATTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 11 0.21
15 2 0.04
16 1 0.02
17 38 0.73
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (17 bp):
TTAAATTTAAATTTATT
Found at i:35100700 original size:30 final size:30
Alignment explanation
Indices: 35100666--35100884 Score: 111
Period size: 29 Copynumber: 7.4 Consensus size: 30
35100656 CAAACTTTCC
*
35100666 AAAATTCTATTTTTAACCTCGATTTCACCA
1 AAAATTCCATTTTTAACCTCGATTTCACCA
*
35100696 AAAATTACCA-TTTTACCCTCGAACTTT--CC-
1 AAAATT-CCATTTTTAACCTCG-A-TTTCACCA
*
35100725 AAAATTCCATTTTTAACCCCGATTTCACCA
1 AAAATTCCATTTTTAACCTCGATTTCACCA
* * * * ** *
35100755 AAAATTATCA-TCTTACCCCCGAACTCTCC-
1 AAAATT-CCATTTTTAACCTCGATTTCACCA
* * *
35100784 AAAATTCCATTTTTAATCGCGATTTCATC-
1 AAAATTCCATTTTTAACCTCGATTTCACCA
* * * * *
35100813 GAAATTACCA-TCTTACCCCCAAACTTT--CC-
1 AAAATT-CCATTTTTAACCTC-GA-TTTCACCA
*
35100842 AAAATTCCATTTTTAACCCCGATTTCACC-
1 AAAATTCCATTTTTAACCTCGATTTCACCA
35100871 AAAATTACCATTTT
1 AAAATT-CCATTTT
35100885 ACCCCTAAAT
Statistics
Matches: 143, Mismatches: 30, Indels: 32
0.70 0.15 0.16
Matches are distributed among these distances:
27 6 0.04
28 10 0.07
29 67 0.47
30 49 0.34
31 8 0.06
32 3 0.02
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.35
Consensus pattern (30 bp):
AAAATTCCATTTTTAACCTCGATTTCACCA
Found at i:35100707 original size:59 final size:58
Alignment explanation
Indices: 35100634--35100942 Score: 379
Period size: 59 Copynumber: 5.3 Consensus size: 58
35100624 CCAGAAACTT
* * *
35100634 CCAAAATTTACCATTTAACCCCCAAACTTTCCAAAATTCTATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTT-ACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* *
35100693 CCAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCA-TTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * * *
35100752 CCAAAAATTATCATCTTACCCCCGAACTCTCCAAAATTCCATTTTTAATCGCGATTTCA
1 CCAAAAATTACCAT-TTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* *
35100811 TC-GAAATTACCATCTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCAT-TTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * ** * ** *
35100869 CC-AAAATTACCATTTTACCCCTAAATTTTTTAAAATTCCATTTTTGACCCTAATTTTA
1 CCAAAAATTACCA-TTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
35100927 CCAAAAATTACCATTT
1 CCAAAAATTACCATTT
35100943 TGCCCCCGGG
Statistics
Matches: 219, Mismatches: 27, Indels: 9
0.86 0.11 0.04
Matches are distributed among these distances:
58 102 0.47
59 114 0.52
60 3 0.01
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (58 bp):
CCAAAAATTACCATTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:35100944 original size:30 final size:31
Alignment explanation
Indices: 35100814--35100949 Score: 94
Period size: 29 Copynumber: 4.6 Consensus size: 31
35100804 GATTTCATCG
* * *
35100814 AAATTACCATCTT-ACCCCCAAACTTT-CCA
1 AAATTACCATTTTGACCCCTAAATTTTACCA
* * *
35100843 AAATT-CCATTTTTAACCCC--GATTTCACCA
1 AAATTACCA-TTTTGACCCCTAAATTTTACCA
**
35100872 AAATTACCATTTT-ACCCCTAAATTTT-TTA
1 AAATTACCATTTTGACCCCTAAATTTTACCA
35100901 AAATT-CCATTTTTGA-CCCT-AATTTTACCAA
1 AAATTACCA-TTTTGACCCCTAAATTTTACC-A
*
35100931 AAATTACCATTTTGCCCCC
1 AAATTACCATTTTGACCCC
35100950 GGGTATCCAA
Statistics
Matches: 84, Mismatches: 11, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
28 20 0.24
29 34 0.40
30 24 0.29
31 6 0.07
ACGTcount: A:0.32, C:0.29, G:0.02, T:0.36
Consensus pattern (31 bp):
AAATTACCATTTTGACCCCTAAATTTTACCA
Found at i:35112755 original size:13 final size:13
Alignment explanation
Indices: 35112737--35112764 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
35112727 AGGCATCGAT
35112737 GAAGTAACTCCAA
1 GAAGTAACTCCAA
35112750 GAAGTAACTCCAA
1 GAAGTAACTCCAA
35112763 GA
1 GA
35112765 TCTCTAGAGA
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:0.46, C:0.21, G:0.18, T:0.14
Consensus pattern (13 bp):
GAAGTAACTCCAA
Found at i:35113692 original size:92 final size:92
Alignment explanation
Indices: 35113576--35114626 Score: 1861
Period size: 92 Copynumber: 11.4 Consensus size: 92
35113566 AATAGCAAGT
* *
35113576 CTTTATCTCTCTGAAGTTATAGTAAGAGTAAGATGAAGCTTCAAACGTCAATTCTTATCCTGTTG
1 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTG
35113641 AAGTTATAGTAAAGCTT-GATAACGAAC
66 AAGTTATAGTAAAG-TTGGATAACGAAC
35113668 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTG
1 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTG
35113733 AAGTTATAGTAAAGTTGGATAACGAAC
66 AAGTTATAGTAAAGTTGGATAACGAAC
35113760 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTG
1 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTG
35113825 AAGTTATAGTAAAGTTGGATAACGAAC
66 AAGTTATAGTAAAGTTGGATAACGAAC
* *
35113852 CTTTATCTCTCTAAAGTTATAGTAAGAGCAAGATGAAGCTTCAAATGTCAATTCTTATCCTCTTG
1 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTG
* *
35113917 AAGTTATAGTAAAGCTCGATAACGAAC
66 AAGTTATAGTAAAGTTGGATAACGAAC
35113944 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTG
1 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTG
*
35114009 AAGTTACAGTAAAGTTGGATAACGAAC
66 AAGTTATAGTAAAGTTGGATAACGAAC
*
35114036 CTTTATCTCTCTAAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTG
1 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTG
* *
35114101 AAGTTATAGTAAAGTTAGATAATGAAC
66 AAGTTATAGTAAAGTTGGATAACGAAC
35114128 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTG
1 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTG
35114193 AAGTTATAGTAAAGTTGGATAACGAAC
66 AAGTTATAGTAAAGTTGGATAACGAAC
* *
35114220 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAGTTCTTACCCTCTTG
1 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTG
35114285 AAGTTATAGTAAAGTTGGATAACGAAC
66 AAGTTATAGTAAAGTTGGATAACGAAC
* *
35114312 CTTTATCTCTCTGATGTTATAGTAAGAGCAAGATGAAGCTTCAAACCTCAATTCTTATCCTCTTG
1 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTG
*
35114377 AAGTTATAGTAAAGTTGGATAACAAAC
66 AAGTTATAGTAAAGTTGGATAACGAAC
* *
35114404 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATAAAGCTTTAAACGTCAATTCTTATCCTCTTG
1 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTG
35114469 AAGTTATAGTAAAGTTGGATAACGAAC
66 AAGTTATAGTAAAGTTGGATAACGAAC
* * *
35114496 CTTTATCTCTCTAAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTTAATTCTTATCCTCATG
1 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTG
*
35114561 AAGTTATAGTAAAGTTGGATAACAAAC
66 AAGTTATAGTAAAGTTGGATAACGAAC
* * * *
35114588 CTTTCTCTCTCTAAAGTTGTAGTAAGAGCAAGATAAAGC
1 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGC
35114627 CTCGACATCA
Statistics
Matches: 919, Mismatches: 39, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
91 2 0.00
92 917 1.00
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (92 bp):
CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTG
AAGTTATAGTAAAGTTGGATAACGAAC
Found at i:35114891 original size:6 final size:6
Alignment explanation
Indices: 35114880--35114942 Score: 62
Period size: 6 Copynumber: 11.0 Consensus size: 6
35114870 ACCAAACCAT
**
35114880 TTTAAA TTTAAA TTT-AA TTTAAA TTTGGA TTT-AA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
35114926 ATT--A TTATAAA TTTAAA
1 TTTAAA TT-TAAA TTTAAA
35114943 AAAATATAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
4 2 0.04
5 10 0.21
6 32 0.68
7 3 0.06
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:35114900 original size:11 final size:11
Alignment explanation
Indices: 35114884--35114941 Score: 57
Period size: 11 Copynumber: 5.2 Consensus size: 11
35114874 AACCATTTTA
35114884 AATTTAAATTT
1 AATTTAAATTT
35114895 AATTTAAATTT
1 AATTTAAATTT
*
35114906 GGATTT-AATTT
1 -AATTTAAATTT
*
35114917 AAATTTAAAATT
1 -AATTTAAATTT
35114929 -ATTATAAATTT
1 AATT-TAAATTT
35114940 AA
1 AA
35114942 AAAAATATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
10 3 0.08
11 26 0.68
12 9 0.24
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:35114902 original size:17 final size:17
Alignment explanation
Indices: 35114880--35114942 Score: 83
Period size: 17 Copynumber: 3.7 Consensus size: 17
35114870 ACCAAACCAT
35114880 TTTAAATTTAAATTTAA
1 TTTAAATTTAAATTTAA
**
35114897 TTTAAATTTGGATTTAA
1 TTTAAATTTAAATTTAA
*
35114914 TTTAAATTTAAAATT-A
1 TTTAAATTTAAATTTAA
35114930 TTATAAATTTAAA
1 TT-TAAATTTAAA
35114943 AAAATATAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
16 3 0.08
17 37 0.93
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (17 bp):
TTTAAATTTAAATTTAA
Found at i:35114952 original size:16 final size:17
Alignment explanation
Indices: 35114916--35114953 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
35114906 GGATTTAATT
* *
35114916 TAAATTTAAAATTATTA
1 TAAATTTAAAATAAATA
35114933 TAAATTTAAAA-AAATA
1 TAAATTTAAAATAAATA
35114949 TAAAT
1 TAAAT
35114954 GTCCAAATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAATTTAAAATAAATA
Found at i:35115702 original size:3 final size:3
Alignment explanation
Indices: 35115694--35115753 Score: 57
Period size: 3 Copynumber: 19.3 Consensus size: 3
35115684 ATAACAATTT
* * * * *
35115694 TAA TAA TAA TAT TAG TAG TAA TAAA TAT TAG TAA TAGA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TA-A TAA TAA TAA
35115741 TAA TAA TAA TAA T
1 TAA TAA TAA TAA T
35115754 GTTATTATTA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
3 43 0.88
4 6 0.12
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:35115722 original size:16 final size:15
Alignment explanation
Indices: 35115697--35115751 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
35115687 ACAATTTTAA
35115697 TAATAATATTAGTAG
1 TAATAATATTAGTAG
*
35115712 TAATAAATATTAGTAA
1 TAAT-AATATTAGTAG
* * *
35115728 TAGATAATAATAATAA
1 TA-ATAATATTAGTAG
35115744 TAATAATA
1 TAATAATA
35115752 ATGTTATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
15 10 0.29
16 23 0.66
17 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.36
Consensus pattern (15 bp):
TAATAATATTAGTAG
Found at i:35116860 original size:30 final size:30
Alignment explanation
Indices: 35116813--35117069 Score: 238
Period size: 30 Copynumber: 8.6 Consensus size: 30
35116803 TCTTGAAAGT
* *
35116813 CCCT-AAACTATCCAAAAATTATATTTTAA
1 CCCTAAAACTTTCTAAAAATTATATTTTAA
*
35116842 CCCTAAAACTTTCTAAAAATTATATTTTGAC
1 CCCTAAAACTTTCTAAAAATTATATTTT-AA
35116873 CCCT-AAACTTCTCT-AAAATTATATTTTAA
1 CCCTAAAACTT-TCTAAAAATTATATTTTAA
* * *
35116902 CCCCAAAACTTTTTAAAAATTACATTTTAA
1 CCCTAAAACTTTCTAAAAATTATATTTTAA
* * **
35116932 CCCTTAAAC-TTCTCCAAAATTATATTTTGT
1 CCCTAAAACTTTCT-AAAAATTATATTTTAA
* * **
35116962 CCCCAAAACATTCTAAAAATTGCATTTTAA
1 CCCTAAAACTTTCTAAAAATTATATTTTAA
*
35116992 CCCCT-AAACTTCTCT-AAAATTGTATTTTAA
1 -CCCTAAAACTT-TCTAAAAATTATATTTTAA
* * * *
35117022 CCTTAAAACTTTTTAAAATTTATATTTTGA
1 CCCTAAAACTTTCTAAAAATTATATTTTAA
* *
35117052 CCCCAAAATTTTCTAAAA
1 CCCTAAAACTTTCTAAAA
35117070 TTACTTTTTA
Statistics
Matches: 184, Mismatches: 33, Indels: 21
0.77 0.14 0.09
Matches are distributed among these distances:
29 18 0.10
30 148 0.80
31 18 0.10
ACGTcount: A:0.39, C:0.21, G:0.02, T:0.39
Consensus pattern (30 bp):
CCCTAAAACTTTCTAAAAATTATATTTTAA
Found at i:35116881 original size:60 final size:60
Alignment explanation
Indices: 35116813--35117072 Score: 317
Period size: 60 Copynumber: 4.3 Consensus size: 60
35116803 TCTTGAAAGT
* * * *
35116813 CCCTAAACTATC-CAAAAATTATATTTTAACCCTAAAACTTTCTAAAAATTATATTTTGAC
1 CCCTAAACT-TCTCTAAAATTATATTTTAACCCCAAAACTTTCTAAAAATTACATTTTAAC
*
35116873 CCCTAAACTTCTCTAAAATTATATTTTAACCCCAAAACTTTTTAAAAATTACATTTTAAC
1 CCCTAAACTTCTCTAAAATTATATTTTAACCCCAAAACTTTCTAAAAATTACATTTTAAC
* * ** * *
35116933 CCTTAAACTTCTCCAAAATTATATTTTGTCCCCAAAACATTCTAAAAATTGCATTTTAAC
1 CCCTAAACTTCTCTAAAATTATATTTTAACCCCAAAACTTTCTAAAAATTACATTTTAAC
* ** * * * *
35116993 CCCTAAACTTCTCTAAAATTGTATTTTAACCTTAAAACTTTTTAAAATTTATATTTTGAC
1 CCCTAAACTTCTCTAAAATTATATTTTAACCCCAAAACTTTCTAAAAATTACATTTTAAC
* *
35117053 CCC-AAAATTTTCTAAAATTA
1 CCCTAAACTTCTCTAAAATTA
35117073 CTTTTTACCC
Statistics
Matches: 171, Mismatches: 28, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
59 16 0.09
60 155 0.91
ACGTcount: A:0.39, C:0.20, G:0.02, T:0.39
Consensus pattern (60 bp):
CCCTAAACTTCTCTAAAATTATATTTTAACCCCAAAACTTTCTAAAAATTACATTTTAAC
Found at i:35116981 original size:90 final size:89
Alignment explanation
Indices: 35116826--35117079 Score: 282
Period size: 90 Copynumber: 2.8 Consensus size: 89
35116816 TAAACTATCC
* * *
35116826 AAAAATTATATTTTAACCCTAAAACTTTCTAAAAATTATATTTTGACCCCTAAACTTCTCTAAAA
1 AAAAATTATATTTTAACCCTTAAACTTTC-AAAAATTATATTTTGACCCCAAAACTTCT-AAAAA
* *
35116891 TTATATTTTAACCCCAAAACTT-TTT
64 TTACATTTTAACCCCAAAACTTCTCT
* * *
35116916 AAAAATTACATTTTAACCCTTAAACTTCTCCAAAATTATATTTTGTCCCCAAAACATTCTAAAAA
1 AAAAATTATATTTTAACCCTTAAACTT-TCAAAAATTATATTTTGACCCCAAAAC-TTCTAAAAA
* *
35116981 TTGCATTTTAACCCCTAAACTTCTCT
64 TTACATTTTAACCCCAAAACTTCTCT
* * * *
35117007 -AAAATTGTATTTTAA-CCTTAAAACTTTTTAAAATTTATATTTTGACCCCAAAATTTTCT-AAA
1 AAAAATTATATTTTAACCCTT-AAAC-TTTCAAAAATTATATTTTGACCCCAAAA-CTTCTAAAA
*
35117069 ATTACTTTTTA
63 ATTACATTTTA
35117080 CCCTTAAGTT
Statistics
Matches: 139, Mismatches: 19, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
89 16 0.12
90 113 0.81
91 10 0.07
ACGTcount: A:0.39, C:0.19, G:0.02, T:0.41
Consensus pattern (89 bp):
AAAAATTATATTTTAACCCTTAAACTTTCAAAAATTATATTTTGACCCCAAAACTTCTAAAAATT
ACATTTTAACCCCAAAACTTCTCT
Found at i:35118317 original size:25 final size:26
Alignment explanation
Indices: 35118289--35118342 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 26
35118279 TATTTGATTA
35118289 TTTCCATTAAAA-A-AATAACCCATTC
1 TTTCCATTAAAAGACAA-AACCCATTC
35118314 TTTCCATTAAAAGACAAAACCCATTC
1 TTTCCATTAAAAGACAAAACCCATTC
35118340 TTT
1 TTT
35118343 AATTTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 12 0.44
26 13 0.48
27 2 0.07
ACGTcount: A:0.41, C:0.24, G:0.02, T:0.33
Consensus pattern (26 bp):
TTTCCATTAAAAGACAAAACCCATTC
Found at i:35119290 original size:13 final size:13
Alignment explanation
Indices: 35119257--35119290 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
35119247 TTTATTTATT
*
35119257 TAATAAAAAAAAA
1 TAATAAAATAAAA
35119270 TAAT-AAATAAAA
1 TAATAAAATAAAA
35119282 TAATAAAAT
1 TAATAAAAT
35119291 TTGGATTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAATAAAATAAAA
Found at i:35119911 original size:39 final size:40
Alignment explanation
Indices: 35119809--35120061 Score: 246
Period size: 40 Copynumber: 6.4 Consensus size: 40
35119799 TATAACTTTA
* * * * *
35119809 AGGGTAAAAGATTGGGTTGT-TTTAATCCGTCC-TATGGTC
1 AGGGTAAAAGATTGGATTGTCTTCAATCTG-CCTTCTGGTT
* * * * * *
35119848 AAGGTAAGAGATCT-GATGGTCTTCAATCAGCCTTTTAGTT
1 AGGGTAAAAGAT-TGGATTGTCTTCAATCTGCCTTCTGGTT
* *
35119888 AGGGTAAAAGACTGGATTG-CTTCAATCTGCCCTCTGGTT
1 AGGGTAAAAGATTGGATTGTCTTCAATCTGCCTTCTGGTT
* * *
35119927 AGGGTAAAAGATTAGATTGT-TTCAATCTGCCCTATGGTT
1 AGGGTAAAAGATTGGATTGTCTTCAATCTGCCTTCTGGTT
* * * *
35119966 GGGGTAAGAGATTGGATTGTCTTCAATCTACCTTCTGATT
1 AGGGTAAAAGATTGGATTGTCTTCAATCTGCCTTCTGGTT
* *
35120006 AGGGCAAAAGATTGGATGGTCTTCAATCTGCCTTCTGGTT
1 AGGGTAAAAGATTGGATTGTCTTCAATCTGCCTTCTGGTT
*
35120046 AGGGTAAGAGATTGGA
1 AGGGTAAAAGATTGGA
35120062 GGTTGTAACT
Statistics
Matches: 173, Mismatches: 35, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
39 85 0.49
40 88 0.51
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (40 bp):
AGGGTAAAAGATTGGATTGTCTTCAATCTGCCTTCTGGTT
Found at i:35120022 original size:118 final size:119
Alignment explanation
Indices: 35119809--35120058 Score: 310
Period size: 118 Copynumber: 2.1 Consensus size: 119
35119799 TATAACTTTA
* * * *
35119809 AGGGTAAAAGATTGGGTTGTTTTAATCCGTCCTATGGTCAAGGTAAGAGATCTGATGGTCTTCAA
1 AGGGTAAAAGATTAGATTGTTTCAATCCGCCCTATGGTCAAGGTAAGAGATCTGATGGTCTTCAA
* * *
35119874 TCAGCCTTTTAGTTAGGGTAAAAGACTGGATTG-CTTCAATCTGCCCTCTGGTT
66 TCAGCCTTTGAGTTAGGGCAAAAGACTGGATGGTCTTCAATCTGCCCTCTGGTT
* *** *
35119927 AGGGTAAAAGATTAGATTGTTTCAATCTGCCCTATGGTTGGGGTAAGAGAT-TGGATTGTCTTCA
1 AGGGTAAAAGATTAGATTGTTTCAATCCGCCCTATGGTCAAGGTAAGAGATCT-GATGGTCTTCA
* *
35119991 ATCTA-CCTTCTGA-TTAGGGCAAAAGATTGGATGGTCTTCAATCTGCCTTCTGGTT
65 ATC-AGCCTT-TGAGTTAGGGCAAAAGACTGGATGGTCTTCAATCTGCCCTCTGGTT
*
35120046 AGGGTAAGAGATT
1 AGGGTAAAAGATT
35120059 GGAGGTTGTA
Statistics
Matches: 113, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
117 1 0.01
118 78 0.69
119 34 0.30
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (119 bp):
AGGGTAAAAGATTAGATTGTTTCAATCCGCCCTATGGTCAAGGTAAGAGATCTGATGGTCTTCAA
TCAGCCTTTGAGTTAGGGCAAAAGACTGGATGGTCTTCAATCTGCCCTCTGGTT
Found at i:35120202 original size:50 final size:50
Alignment explanation
Indices: 35120115--35120254 Score: 185
Period size: 50 Copynumber: 2.8 Consensus size: 50
35120105 ATCCTTGTGA
35120115 CTTCAATCTG-CCCTCTACAGCTTTAGGTGAATAAGATTTGCCATTGCGG
1 CTTCAATCTGCCCCTCTACAGCTTTAGGTGAATAAGATTTGCCATTGCGG
* * * *
35120164 CTTCATTCTGCCCCTCTACAACTTTAGGTGTATGAGATTTGCCATTGCGG
1 CTTCAATCTGCCCCTCTACAGCTTTAGGTGAATAAGATTTGCCATTGCGG
* * * *
35120214 TTTCAATCTGCACCTCCACAGCTTTAGGGGTAA-AAGATTTG
1 CTTCAATCTGCCCCTCTACAGCTTTAGGTG-AATAAGATTTG
35120255 TCGTTCTATT
Statistics
Matches: 77, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
49 9 0.12
50 67 0.87
51 1 0.01
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (50 bp):
CTTCAATCTGCCCCTCTACAGCTTTAGGTGAATAAGATTTGCCATTGCGG
Found at i:35122541 original size:263 final size:263
Alignment explanation
Indices: 35122074--35122601 Score: 1047
Period size: 263 Copynumber: 2.0 Consensus size: 263
35122064 GAAGTCATAA
35122074 CATGGAGAGGTGAAGGAAGTACATGAATTTTGTCTCCATAAATTTGACACTTGTGACATTTTTTA
1 CATGGAGAGGTGAAGGAAGTACATGAATTTTGTCTCCATAAATTTGACACTTGTGACATTTTTTA
35122139 GCATATTTAATGCAATCTCCTTTCATGGTTTACCAGTAATATACCCAAATCTCATAATCTATCTA
66 GCATATTTAATGCAATCTCCTTTCATGGTTTACCAGTAATATACCCAAATCTCATAATCTATCTA
35122204 GTCATCATGAAACCATTGGCATGTGTTCCACAAACTCCTTCATGAACTTCTTCTAAGATTTTCTT
131 GTCATCATGAAACCATTGGCATGTGTTCCACAAACTCCTTCATGAACTTCTTCTAAGATTTTCTT
35122269 GGCCTCAATAGAATCAACACACCTCAACAAGACTTGATCTTTTCTCTTTTTATACAATATATCCC
196 GGCCTCAATAGAATCAACACACCTCAACAAGACTTGATCTTTTCTCTTTTTATACAATATATCCC
35122334 CGT
261 CGT
*
35122337 CATGGAGAGGTGAAGGAAGTACATGAATTTTGTCTTCATAAATTTGACACTTGTGACATTTTTTA
1 CATGGAGAGGTGAAGGAAGTACATGAATTTTGTCTCCATAAATTTGACACTTGTGACATTTTTTA
35122402 GCATATTTAATGCAATCTCCTTTCATGGTTTACCAGTAATATACCCAAATCTCATAATCTATCTA
66 GCATATTTAATGCAATCTCCTTTCATGGTTTACCAGTAATATACCCAAATCTCATAATCTATCTA
35122467 GTCATCATGAAACCATTGGCATGTGTTCCACAAACTCCTTCATGAACTTCTTCTAAGATTTTCTT
131 GTCATCATGAAACCATTGGCATGTGTTCCACAAACTCCTTCATGAACTTCTTCTAAGATTTTCTT
35122532 GGCCTCAATAGAATCAACACACCTCAACAAGACTTGATCTTTTCTCTTTTTATACAATATATCCC
196 GGCCTCAATAGAATCAACACACCTCAACAAGACTTGATCTTTTCTCTTTTTATACAATATATCCC
35122597 CGT
261 CGT
35122600 CA
1 CA
35122602 AGGACATAGT
Statistics
Matches: 264, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
263 264 1.00
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.35
Consensus pattern (263 bp):
CATGGAGAGGTGAAGGAAGTACATGAATTTTGTCTCCATAAATTTGACACTTGTGACATTTTTTA
GCATATTTAATGCAATCTCCTTTCATGGTTTACCAGTAATATACCCAAATCTCATAATCTATCTA
GTCATCATGAAACCATTGGCATGTGTTCCACAAACTCCTTCATGAACTTCTTCTAAGATTTTCTT
GGCCTCAATAGAATCAACACACCTCAACAAGACTTGATCTTTTCTCTTTTTATACAATATATCCC
CGT
Found at i:35132880 original size:30 final size:29
Alignment explanation
Indices: 35132846--35132977 Score: 106
Period size: 31 Copynumber: 4.3 Consensus size: 29
35132836 AATATTAAAA
* *
35132846 AGGGGTCAAATTTTAATTTTTGAAAACTTT
1 AGGGGTAAAATTTGAATTTTTGAAAA-TTT
* *
35132876 AGGGGTTAAATTTGAATCTTTGGAAAATTT
1 AGGGGTAAAATTTGAAT-TTTTGAAAATTT
*
35132906 -GAGGGTGAAATTTGAATTTTTAGGAAAA-TT
1 AG-GGGTAAAATTTGAATTTTT--GAAAATTT
* *
35132936 CGAGGGTAAAATTTTAATTTTTGAAAACTTT
1 AG-GGGTAAAATTTGAATTTTTGAAAA-TTT
*
35132967 GGGGGTGAAAA
1 AGGGGT-AAAA
35132978 AATGATTTTA
Statistics
Matches: 86, Mismatches: 8, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
29 9 0.10
30 38 0.44
31 39 0.45
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.38
Consensus pattern (29 bp):
AGGGGTAAAATTTGAATTTTTGAAAATTT
Found at i:35132932 original size:31 final size:30
Alignment explanation
Indices: 35132848--35132976 Score: 129
Period size: 30 Copynumber: 4.3 Consensus size: 30
35132838 TATTAAAAAG
* *
35132848 GGGTCAAATTTTAATTTTTGAAAACTTT-A
1 GGGTGAAATTTGAATTTTTGAAAACTTTGA
* *
35132877 GGGGTTAAATTTGAATCTTTGGAAAA-TTTGA
1 -GGGTGAAATTTGAAT-TTTTGAAAACTTTGA
*
35132908 GGGTGAAATTTGAATTTTTAGGAAAA-TTCGA
1 GGGTGAAATTTGAATTTTT--GAAAACTTTGA
* * *
35132939 GGGTAAAATTTTAATTTTTGAAAACTTTGG
1 GGGTGAAATTTGAATTTTTGAAAACTTTGA
35132969 GGGTGAAA
1 GGGTGAAA
35132977 AAATGATTTT
Statistics
Matches: 83, Mismatches: 11, Indels: 10
0.80 0.11 0.10
Matches are distributed among these distances:
29 8 0.10
30 40 0.48
31 35 0.42
ACGTcount: A:0.34, C:0.04, G:0.23, T:0.39
Consensus pattern (30 bp):
GGGTGAAATTTGAATTTTTGAAAACTTTGA
Found at i:35143807 original size:17 final size:17
Alignment explanation
Indices: 35143748--35143807 Score: 86
Period size: 17 Copynumber: 3.5 Consensus size: 17
35143738 AAATCTTTAT
* *
35143748 TTTAAATTTATTCTAAG
1 TTTAAATTTATTTTAAA
35143765 TTTAGAA-TTATTTTAAA
1 TTTA-AATTTATTTTAAA
35143782 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
35143799 TTTAAATTT
1 TTTAAATTT
35143808 TGAAATATTG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
16 2 0.05
17 35 0.90
18 2 0.05
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:35145885 original size:29 final size:28
Alignment explanation
Indices: 35145740--35146180 Score: 168
Period size: 29 Copynumber: 15.1 Consensus size: 28
35145730 CTTAAAAGGT
* *
35145740 CCCTAAACTGTT-CAAAAATCATATTTTAA
1 CCCTAAACT-TTCCAAAAATTACATTTT-A
* *
35145769 CCCCCCAAAC-TTCCAAAAATTACATTTAAA
1 --CCCTAAACTTTCCAAAAATTACATTT-TA
* **
35145799 CCCCCAAACTTTTTAAAAATTACATTATTA
1 -CCCTAAACTTTCCAAAAATTACATT-TTA
* *
35145829 CCCCTAAATTTTCC-AAAATTCCAATTTTGA
1 -CCCTAAACTTTCCAAAAATTAC-ATTTT-A
35145859 CCCTAAACTTTCCAAAAATTACATTTTA
1 CCCTAAACTTTCCAAAAATTACATTTTA
* *
35145887 -CCTCAATA-TTTCCCAAAATTCCATTTTAA
1 CCCT-AA-ACTTTCCAAAAATTACATTTT-A
* * *
35145916 CCTTGAACCTTCCAAAAATTACCATTTTA
1 CCCTAAACTTTCCAAAAATTA-CATTTTA
* * * *
35145945 CCCCTGAA-TGTCTAAAAATTCCATTTTTGA
1 -CCCTAAACTTTCCAAAAATTACA-TTTT-A
*
35145975 CCTTAAACTTTCCAAAAATTACCATTTTA
1 CCCTAAACTTTCCAAAAATTA-CATTTTA
* * *
35146004 CCCTCGAA-TGTT--TAAAATTCCATCTTTGA
1 CCCT-AAACT-TTCCAAAAATTACAT-TTT-A
* * *
35146033 CCCTGAACCTTCCAAAAATTACCACTTTA
1 CCCTAAACTTTCCAAAAATTA-CATTTTA
* ** * *
35146062 CCCCTAAA-TATATAAAAACTCCATTTTTTA
1 -CCCTAAACTTTCCAAAAATTACA--TTTTA
* * * * *
35146092 CCCCAAAATTT-TAGAAATTACCCTTTTA
1 CCCTAAACTTTCCAAAAATTA-CATTTTA
* *
35146120 CCCCTAAA-TATCCAAAAATTCCATTTTTGA
1 -CCCTAAACTTTCCAAAAATTACA-TTTT-A
* *
35146150 CCCTAAAATTTCTAAAAATTACCATTTTA
1 CCCTAAACTTTCCAAAAATTA-CATTTTA
35146179 CC
1 CC
35146181 TCGAAGTGTT
Statistics
Matches: 311, Mismatches: 62, Indels: 76
0.69 0.14 0.17
Matches are distributed among these distances:
27 6 0.02
28 47 0.15
29 125 0.40
30 119 0.38
31 14 0.05
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.35
Consensus pattern (28 bp):
CCCTAAACTTTCCAAAAATTACATTTTA
Found at i:35145943 original size:30 final size:29
Alignment explanation
Indices: 35145839--35146061 Score: 118
Period size: 30 Copynumber: 7.7 Consensus size: 29
35145829 CCCCTAAATT
* * * *
35145839 TTCC-AAAATTCCAATTTTGACCCTAAACT
1 TTCCAAAAATTCC-ATTTTAACCTTGAACC
* * **
35145868 TTCCAAAAATTACATTTT-ACC-TCAATAT
1 TTCCAAAAATTCCATTTTAACCTTGAA-CC
*
35145896 TTCCCAAAATTCCATTTTAACCTTGAACC
1 TTCCAAAAATTCCATTTTAACCTTGAACC
* *
35145925 TTCCAAAAATTACCATTTTACCCCTGAA--
1 TTCCAAAAATT-CCATTTTAACCTTGAACC
* * * *
35145953 TGTCTAAAAATTCCATTTTTGACCTTAAACT
1 T-TCCAAAAATTCCA-TTTTAACCTTGAACC
* * **
35145984 TTCCAAAAATTACCATTTTACCCTCGAATG
1 TTCCAAAAATT-CCATTTTAACCTTGAACC
* * *
35146014 TT--TAAAATTCCATCTTTGACCCTGAACC
1 TTCCAAAAATTCCAT-TTTAACCTTGAACC
*
35146042 TTCCAAAAATTACCACTTTA
1 TTCCAAAAATT-CCATTTTA
35146062 CCCCTAAATA
Statistics
Matches: 147, Mismatches: 33, Indels: 27
0.71 0.16 0.13
Matches are distributed among these distances:
27 7 0.05
28 40 0.27
29 40 0.27
30 53 0.36
31 7 0.05
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (29 bp):
TTCCAAAAATTCCATTTTAACCTTGAACC
Found at i:35146138 original size:117 final size:116
Alignment explanation
Indices: 35145813--35146180 Score: 352
Period size: 117 Copynumber: 3.2 Consensus size: 116
35145803 CAAACTTTTT
* * * * * *
35145813 AAAAATTA-CATTATTACCCCTAAAT-TTTCCAAAATTCCAATTTTGACCCTAAACTTTCCAAAA
1 AAAAATTACCATT-TTACCCCTAAATATAT-AAAAACTCCATTTTTGACCCCAAAATTTCCAAAA
* * * *
35145876 ATTA-CATTTTA-CCTCAATATTTCCCAAAATTCCATTTTAACCTTGAACCTTCC
64 ATTACCATTTTACCCTCAA-ATAT-CAAAAATTCCATTTTGACCCTGAACCTTCC
* * * * ** *
35145929 AAAAATTACCATTTTACCCCTGAATGTCTAAAAATTCCATTTTTGACCTTAAACTTTCCAAAAAT
1 AAAAATTACCATTTTACCCCTAAATATATAAAAACTCCATTTTTGACCCCAAAATTTCCAAAAAT
* * **
35145994 TACCATTTTACCCTCGAATGTTTAAAATTCCATCTTTGACCCTGAACCTTCC
66 TACCATTTTACCCTCAAATATCAAAAATTCCAT-TTTGACCCTGAACCTTCC
* * * *
35146046 AAAAATTACCACTTTACCCCTAAATATATAAAAACTCCATTTTTTACCCCAAAATTT-TAGAAAT
1 AAAAATTACCATTTTACCCCTAAATATATAAAAACTCCATTTTTGACCCCAAAATTTCCAAAAAT
* * ** *
35146110 TACCCTTTTACCC-CTAAATATCCAAAAATTCCATTTTTGACCCTAAAATTTCT
66 TACCATTTTACCCTC-AAATAT-CAAAAATTCCA-TTTTGACCCTGAACCTTCC
35146163 AAAAATTACCATTTTACC
1 AAAAATTACCATTTTACC
35146181 TCGAAGTGTT
Statistics
Matches: 212, Mismatches: 32, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
115 1 0.00
116 85 0.40
117 120 0.57
118 6 0.03
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (116 bp):
AAAAATTACCATTTTACCCCTAAATATATAAAAACTCCATTTTTGACCCCAAAATTTCCAAAAAT
TACCATTTTACCCTCAAATATCAAAAATTCCATTTTGACCCTGAACCTTCC
Done.