Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008295.1 Hibiscus syriacus cultivar Beakdansim tig00110962_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 741301
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:396347 original size:15 final size:15
Alignment explanation
Indices: 396329--396358 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
396319 AAAACCATGT
*
396329 TAGATAAAAATGTAA
1 TAGATAAAAAGGTAA
396344 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
396359 GAAATAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:396539 original size:32 final size:35
Alignment explanation
Indices: 396486--396591 Score: 105
Period size: 36 Copynumber: 3.1 Consensus size: 35
396476 GAAAAAGAAG
*
396486 AAATAAAAATATAGAAA-TAAAACAA-ATA-A-ATA
1 AAATAAAAATA-AAAAAGTAAAACAATATATATATA
* *
396518 AAATAATAATAAAAAAGTAAAAATAATATATATATA
1 AAATAAAAATAAAAAAGT-AAAACAATATATATATA
*
396554 AAATAAAAAATAAAAAAGTAAATA-TATATATATATA
1 AAAT-AAAAATAAAAAAGTAAA-ACAATATATATATA
396590 AA
1 AA
396592 TTAATAAAAC
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
31 4 0.06
32 11 0.18
33 6 0.10
34 3 0.05
35 1 0.02
36 23 0.37
37 14 0.23
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.25
Consensus pattern (35 bp):
AAATAAAAATAAAAAAGTAAAACAATATATATATA
Found at i:396542 original size:29 final size:29
Alignment explanation
Indices: 396509--396569 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
396499 GAAATAAAAC
396509 AAATAA-ATA-AAATAATAATAAAAAAGTAA
1 AAATAATATATAAATAA-AATAAAAAA-TAA
*
396538 AAATAATATATATATAAAATAAAAAATAA
1 AAATAATATATAAATAAAATAAAAAATAA
396567 AAA
1 AAA
396570 AGTAAATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 12 0.41
30 12 0.41
31 5 0.17
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (29 bp):
AAATAATATATAAATAAAATAAAAAATAA
Found at i:396561 original size:30 final size:33
Alignment explanation
Indices: 396500--396590 Score: 97
Period size: 30 Copynumber: 2.9 Consensus size: 33
396490 AAAAATATAG
*
396500 AAATAAAACAAATAAATA-A-A-ATAATAATAAA
1 AAATAAAA-AAGTAAATATATATATAATAATAAA
396531 AAAGT-AAAAA-T-AATATATATATAA-AATAAA
1 AAA-TAAAAAAGTAAATATATATATAATAATAAA
396561 AAATAAAAAAGTAAATATATATATATATAA
1 AAATAAAAAAGTAAATATATATATA-ATAA
396591 ATTAATAAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 15
0.77 0.00 0.23
Matches are distributed among these distances:
28 4 0.08
29 3 0.06
30 17 0.33
31 11 0.22
32 13 0.25
33 1 0.02
34 2 0.04
ACGTcount: A:0.71, C:0.01, G:0.02, T:0.25
Consensus pattern (33 bp):
AAATAAAAAAGTAAATATATATATAATAATAAA
Found at i:396617 original size:36 final size:36
Alignment explanation
Indices: 396515--396626 Score: 122
Period size: 36 Copynumber: 3.1 Consensus size: 36
396505 AAACAAATAA
*
396515 ATAAAAT-AATAATAAAAAAGTAAAAATAATATATAT
1 ATAAAATAAAAAATAAAAAAGTAAAAAT-ATATATAT
*
396551 ATAAAATAAAAAATAAAAAAGTAAATATATATATAT
1 ATAAAATAAAAAATAAAAAAGTAAAAATATATATAT
* * *
396587 ATAAATTAATAAAACT-GATAA-TAAAAATATATATTAT
1 ATAAAATAA-AAAA-TAAAAAAGTAAAAATATATA-TAT
396624 ATA
1 ATA
396627 TATAATCTAA
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
36 34 0.52
37 31 0.47
38 1 0.02
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (36 bp):
ATAAAATAAAAAATAAAAAAGTAAAAATATATATAT
Found at i:396699 original size:23 final size:22
Alignment explanation
Indices: 396644--396705 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
396634 TAAAAAAAAT
396644 AAAAATATATAC-T-AAAGTAAA
1 AAAAATAT-TACATAAAAGTAAA
*
396665 AAAGAA-AATACATAAAATGTAAA
1 AAA-AATATTACATAAAA-GTAAA
396688 AAAAATATTACATGAAAA
1 AAAAATATTACAT-AAAA
396706 AAAGAAAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
20 3 0.09
21 5 0.15
22 7 0.21
23 14 0.42
24 4 0.12
ACGTcount: A:0.68, C:0.05, G:0.06, T:0.21
Consensus pattern (22 bp):
AAAAATATTACATAAAAGTAAA
Found at i:397093 original size:33 final size:34
Alignment explanation
Indices: 397030--397097 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
397020 GAATCCTAGC
*
397030 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
1 AAAATTCTATCCTATCTTTAGGAGTTTGAATCCT
*
397064 AAAATTCTATCCTATTTTTA-GAGTTTGAATCCT
1 AAAATTCTATCCTATCTTTAGGAGTTTGAATCCT
397097 A
1 A
397098 GTAGGACGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 14 0.44
34 18 0.56
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (34 bp):
AAAATTCTATCCTATCTTTAGGAGTTTGAATCCT
Found at i:397946 original size:105 final size:104
Alignment explanation
Indices: 397651--398265 Score: 875
Period size: 105 Copynumber: 5.9 Consensus size: 104
397641 TTCCAAGTCT
* * ** * * *
397651 AATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTTTTTGTTGACAACCAGT
1 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGG-AAGTTGTTGTTGACAAGCAG-
* * * *
397715 C-GTCCCTTCGTTGTGAATTTGAACTTGTGTTGTCTCGAGTCC
63 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-GAATCC
** *
397757 AATATCCTTCGTTGTGAAGTTGAAATTGAATCTGA-A-T--GAAATT-TTGTTGACAAGCAGCGG
1 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGCAGCGG
397817 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAATCC
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-GAATCC
*
397857 AATATCCTTCGTTGTGAAATTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGCAGCGG
1 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGCAGCGG
* * *
397922 TCCCTTCGTCGTGAAGTTGAACTTGCATTGTATGGAGTCC
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-GAATCC
* *
397962 AATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGCGATTGGGAAGTTGTTGTTGACAAGCAGCGG
1 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGCAGCGG
*
398027 TCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGAAGTCC
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAA-TCC
* *
398067 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGG
1 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGCAGCGG
398132 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCC
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAA-TCC
* * *
398172 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCTG
1 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGCAGCGG
398237 TCCCTTCGTCGTGAAGTTGAACTTGCGTT
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTT
398266 TTCTCGAGTG
Statistics
Matches: 471, Mismatches: 30, Indels: 17
0.91 0.06 0.03
Matches are distributed among these distances:
99 1 0.00
100 81 0.17
101 5 0.01
102 2 0.00
104 7 0.01
105 345 0.73
106 30 0.06
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (104 bp):
AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGCAGCGG
TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAATCC
Found at i:399082 original size:65 final size:67
Alignment explanation
Indices: 398873--399092 Score: 196
Period size: 65 Copynumber: 3.3 Consensus size: 67
398863 AAAGAGATAG
* * * * * *
398873 AATTCGTTTCAAGGGAAAT-GATCTCAAAGATATATGTTGTTTCATGAGAAAC-GATCTCAAGGG
1 AATTTGTTTTAAGGGAAATAAAT-TCAAAGAT-TTTG-TGTTTCAAGAGAAACTG-TCTCAAGAG
*
398936 AAACAA
62 AGACAA
** * * * *
398942 AATTATGTTTTAAGGGAAATAAATTTGAAGATTTTGTGTTTCAAGAGTAATTGTCTTAAGGGAGA
1 AATT-TGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGA
399007 CAA
65 CAA
* * *
399010 AATTTGTTTTAGGGGAAATAAATTCAAAGA-TTT-TGTTTCAAGGGAAACTGTCTCAAGATAGAC
1 AATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGAC
*
399073 GA
66 AA
* *
399075 AATTTGTTTCAAGAGAAA
1 AATTTGTTTTAAGGGAAA
399093 CTGTCTCAAG
Statistics
Matches: 124, Mismatches: 24, Indels: 10
0.78 0.15 0.06
Matches are distributed among these distances:
65 40 0.32
66 3 0.02
67 23 0.19
68 29 0.23
69 8 0.06
70 19 0.15
71 2 0.02
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (67 bp):
AATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGAC
AA
Found at i:399138 original size:37 final size:36
Alignment explanation
Indices: 399053--399252 Score: 123
Period size: 36 Copynumber: 5.7 Consensus size: 36
399043 TGTTTCAAGG
* * * * *
399053 GAAACTGTCTCAAGATAGACGAAATTTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAA
399089 GAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAA
1 GAAACTGTCTCAAGAGAGACAAAA-TTAGTTCCAAAA
* ** * *
399126 GAAACTGTCTCAAGGGAGATGAAATTTGTTTC-AAA
1 GAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAA
* * * * * **
399161 GAAAACATAT-TC-----A-A-ATATTTTGTTTCAAGG
1 G-AAAC-TGTCTCAAGAGAGACAAAATTAGTTCCAAAA
* *
399191 GAAACTGTCTCAAGAGAGACAAAATTTA-TTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAA-TTAGTTCCAAAA
399227 GAAACTGTCTCAAGAGAGACAAAATT
1 GAAACTGTCTCAAGAGAGACAAAATT
399253 TTGTTTAAAG
Statistics
Matches: 130, Mismatches: 21, Indels: 27
0.73 0.12 0.15
Matches are distributed among these distances:
28 2 0.02
29 15 0.12
30 3 0.02
31 1 0.01
34 1 0.01
35 7 0.05
36 67 0.52
37 34 0.26
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (36 bp):
GAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAA
Found at i:399173 original size:138 final size:137
Alignment explanation
Indices: 399031--399390 Score: 447
Period size: 138 Copynumber: 2.6 Consensus size: 137
399021 GGGGAAATAA
*
399031 ATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTTCAAGAGAAACTG
1 ATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGAGAAACTG
* * * * *
399096 TCTCAAGAGAGACAAAACTTAGTTCCAAA-AGAAACTGTCTCAAGGGAGATGAAATTTGTTTCAA
66 TCTCAAGAGAGACAAAACTTAGTT-CAAAGAGAAACTATCCCAAGAGAGACGAAA-TTATTTCAA
399160 AGAAAACAT
129 AGAAAACAT
* * *
399169 ATTCAAATATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTG
1 ATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGAGAAACTG
* * * * *
399234 TCTCAAGAGAGACAAAATTTTGTTTAAAGGGAAACTATCCCAAGAGAGACGAAATTATTTCAAGG
66 TCTCAAGAGAGACAAAACTTAGTTCAAAGAGAAACTATCCCAAGAGAGACGAAATTATTTCAAAG
* **
399299 GAAATGT
131 AAAACAT
* * * * *
399306 TTTCAATG-TTTATGTTTCAAGAGAAACTGTCTCAATG-GAGACGGAATTTTGTTTCAAGGGAAA
1 ATTCAAAGATTT-TGTTTCAAGGGAAACTGTCTCAA-GAGAGAC-GAAATTTGTTTCAAGAGAAA
*
399369 CTATCTCAAGAGAGACAAAACT
63 CTGTCTCAAGAGAGACAAAACT
399391 CATTTCAAGG
Statistics
Matches: 191, Mismatches: 27, Indels: 8
0.85 0.12 0.04
Matches are distributed among these distances:
136 3 0.02
137 48 0.25
138 140 0.73
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.28
Consensus pattern (137 bp):
ATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGAGAAACTG
TCTCAAGAGAGACAAAACTTAGTTCAAAGAGAAACTATCCCAAGAGAGACGAAATTATTTCAAAG
AAAACAT
Found at i:399207 original size:102 final size:101
Alignment explanation
Indices: 399077--399262 Score: 284
Period size: 102 Copynumber: 1.8 Consensus size: 101
399067 ATAGACGAAA
*
399077 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGG
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA-TTCCAAAAGAAACTGTCTCAAGAG
**
399142 AGATGAAA-TTTGTTTCAAAGAAAACATATTCAAATAT
65 AGACAAAATTTTGTTT-AAAGAAAACATATTCAAATAT
* * * *
399179 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGA
399244 GACAAAATTTTGTTTAAAG
66 GACAAAATTTTGTTTAAAG
399263 GGAAACTATC
Statistics
Matches: 76, Mismatches: 7, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
101 31 0.41
102 45 0.59
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (101 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGA
GACAAAATTTTGTTTAAAGAAAACATATTCAAATAT
Found at i:399268 original size:37 final size:37
Alignment explanation
Indices: 399172--399523 Score: 245
Period size: 37 Copynumber: 10.1 Consensus size: 37
399162 AAAACATATT
399172 CAAATATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
1 CAAA-ATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
* *
399210 CAAAA-TTTATTTCAAGAGAAACTGTCTCAAGAGAGA
1 CAAAATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
* * *
399246 CAAAATTTTGTTTAAAGGGAAACTATCCCAAGAGAGA
1 CAAAATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
* * * *
399283 CGAAA--TTATTTCAAGGGAAA-TGTTTTC-A-A-TG-
1 CAAAATTTTGTTTCAAGGGAAACTG-TCTCAAGAGAGA
*
399314 -----TTTATGTTTCAAGAGAAACTGTCTCAATG-GAGA
1 CAAAATTT-TGTTTCAAGGGAAACTGTCTCAA-GAGAGA
** *
399347 CGGAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGA
1 CAAAATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
* ** * *
399384 CAAAA-CTCATTTCAAGGGAAA-TGTTTTC-A-A-TG-
1 CAAAATTTTGTTTCAAGGGAAACTG-TCTCAAGAGAGA
* *
399416 -----TTTATGTTTCAAGAGAAACTGTCTCAAGGGAGA
1 CAAAATTT-TGTTTCAAGGGAAACTGTCTCAAGAGAGA
*
399449 CAAAATTTTGTTTCAAGGGAAACTTTCTCAAGAGAGA
1 CAAAATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
* * *
399486 C-AAAGTTTGTTTCAAGGGAAACT-TTTCAAGAGAAA
1 CAAAATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
399521 CAA
1 CAA
399524 TAGTGAGCAC
Statistics
Matches: 242, Mismatches: 41, Indels: 64
0.70 0.12 0.18
Matches are distributed among these distances:
28 2 0.01
29 29 0.12
30 6 0.02
32 3 0.01
33 2 0.01
34 3 0.01
35 28 0.12
36 73 0.30
37 86 0.36
38 10 0.04
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (37 bp):
CAAAATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
Found at i:399499 original size:102 final size:100
Alignment explanation
Indices: 399219--399514 Score: 450
Period size: 102 Copynumber: 2.9 Consensus size: 100
399209 ACAAAATTTA
* * *
399219 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTAAAGGGAAACTATCCCAAGAGAGAC
1 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGAC
399284 GAAATTATTTCAAGGGAAATGTTTTCAATGTTTATG
66 -AAATTATTTCAAGGGAAATGTTTTCAATGTTTATG
* **
399320 TTTCAAGAGAAACTGTCTCAATGGAGACGGAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGAC
1 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGAC
*
399385 AAAACTCATTTCAAGGGAAATGTTTTCAATGTTTATG
66 -AAA-TTATTTCAAGGGAAATGTTTTCAATGTTTATG
*
399422 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTTTCTCAAGAGAGAC
1 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGAC
* *
399487 AAAGTTTGTTTCAAGGGAAA-CTTTTCAA
66 AAA--TTATTTCAAGGGAAATGTTTTCAA
399515 GAGAAACAAT
Statistics
Matches: 177, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
101 72 0.41
102 105 0.59
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (100 bp):
TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGAC
AAATTATTTCAAGGGAAATGTTTTCAATGTTTATG
Found at i:400332 original size:2 final size:2
Alignment explanation
Indices: 400321--400374 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
400311 AAGGAAAAAA
*
400321 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
400363 AT AT AT AT AT AT
1 AT AT AT AT AT AT
400375 CAAAGTATTA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:400857 original size:2 final size:2
Alignment explanation
Indices: 400850--400886 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
400840 AAATAATTTA
*
400850 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
400887 ATAATAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:400905 original size:18 final size:17
Alignment explanation
Indices: 400884--400926 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
400874 ATATATACAT
400884 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
* *
400902 ATAATAAAAATAAGTGA
1 ATAATAATAATAAATGA
400919 ATAA-AATA
1 ATAATAATA
400927 TCCATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:401350 original size:37 final size:37
Alignment explanation
Indices: 401263--401360 Score: 117
Period size: 37 Copynumber: 2.6 Consensus size: 37
401253 ATAATTTTAG
* * *
401263 GATTCAAACTCCTAAAAATAGGATAACATTTTGCTAG
1 GATTCAAACTCCTAAAAATAGGATAACATTCTACTAA
*
401300 GATTCAAACTCCTAAAAATAGGATAGA-GTTCTACTAA
1 GATTCAAACTCCTAAAAATAGGATA-ACATTCTACTAA
* * *
401337 GATTTAAATTCCTAAAGATAGGAT
1 GATTCAAACTCCTAAAAATAGGAT
401361 CCACAAGCAC
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
37 52 0.98
38 1 0.02
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
GATTCAAACTCCTAAAAATAGGATAACATTCTACTAA
Found at i:401659 original size:22 final size:21
Alignment explanation
Indices: 401629--401697 Score: 54
Period size: 23 Copynumber: 3.3 Consensus size: 21
401619 CTTTTCTTTT
401629 TTTTCATGTAATATTTTTTTAC
1 TTTT-ATGTAATATTTTTTTAC
* *
401651 ATTTTATGTATTTTCTTTTTTAC
1 -TTTTATGTAATAT-TTTTTTAC
* *
401674 -TTTA-GT-ATATATTTTTAT
1 TTTTATGTAATATTTTTTTAC
401692 TTTTAT
1 TTTTAT
401698 TTTTAGATTA
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
18 6 0.16
19 6 0.16
20 2 0.05
21 4 0.11
22 7 0.19
23 12 0.32
ACGTcount: A:0.22, C:0.06, G:0.04, T:0.68
Consensus pattern (21 bp):
TTTTATGTAATATTTTTTTAC
Found at i:401686 original size:24 final size:22
Alignment explanation
Indices: 401642--401696 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 22
401632 TCATGTAATA
*
401642 TTTTTTTACATTTTATGTATTT
1 TTTTTTTACATTTTATATATTT
401664 TCTTTTTTAC-TTTAGTATATATTT
1 T-TTTTTTACATTT--TATATATTT
401688 TTATTTTTA
1 TT-TTTTTA
401697 TTTTTAGATT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
22 4 0.14
23 9 0.32
24 15 0.54
ACGTcount: A:0.20, C:0.05, G:0.04, T:0.71
Consensus pattern (22 bp):
TTTTTTTACATTTTATATATTT
Found at i:401793 original size:30 final size:33
Alignment explanation
Indices: 401747--401824 Score: 106
Period size: 34 Copynumber: 2.3 Consensus size: 33
401737 GTTTTATTAA
401747 TTTA-TATATATATATATATATATATATATTACTTT
1 TTTATTAT-TATATATATATAT-TAT-TATTACTTT
*
401782 TTT-TTATTATATATATATATTATTTTTACTTT
1 TTTATTATTATATATATATATTATTATTACTTT
401814 TTTATTATTAT
1 TTTATTATTAT
401825 TTTATTTATT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
32 11 0.28
33 10 0.25
34 13 0.32
35 6 0.15
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (33 bp):
TTTATTATTATATATATATATTATTATTACTTT
Found at i:401795 original size:2 final size:2
Alignment explanation
Indices: 401749--401775 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
401739 TTTATTAATT
401749 TA 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 TA T
401776 TACTTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:401867 original size:9 final size:9
Alignment explanation
Indices: 401853--401878 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
401843 TTCTATATTT
401853 TTTTTCTTC
1 TTTTTCTTC
401862 TTTTTCTTC
1 TTTTTCTTC
401871 TTTTTCTT
1 TTTTTCTT
401879 TATTTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:402003 original size:15 final size:15
Alignment explanation
Indices: 401985--402014 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
401975 AATTTATTTC
401985 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
402000 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
402015 ACATGATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
TTACCTTTTTATCTA
Found at i:403964 original size:18 final size:18
Alignment explanation
Indices: 403941--403980 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
403931 TTCCTTCAAG
403941 TCTGGATTCACATCCACT
1 TCTGGATTCACATCCACT
403959 TCTGGATTCACATCCACT
1 TCTGGATTCACATCCACT
403977 TCTG
1 TCTG
403981 AAAGACTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.35
Consensus pattern (18 bp):
TCTGGATTCACATCCACT
Found at i:405690 original size:22 final size:22
Alignment explanation
Indices: 405667--405728 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
405657 CAAAAAGGGC
405667 AAAAAGAAAAAAGAAAAGAAGCA
1 AAAAAGAAAAAA-AAAAGAAGCA
* *
405690 AAAAAGGAAAAAACAAGAA-CA
1 AAAAAGAAAAAAAAAAGAAGCA
405711 AAAAAGAAAGAACAAAAA
1 AAAAAGAAA-AA-AAAAA
405729 TAAAAAAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.30
22 8 0.24
23 15 0.45
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAAAAAAAGAAGCA
Found at i:405719 original size:20 final size:20
Alignment explanation
Indices: 405667--405735 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 20
405657 CAAAAAGGGC
*
405667 AAAAAGAAAAAAGAAAAGAAGCA
1 AAAAAG-AAAAA-ACAAGAA-CA
405690 AAAAAGGAAAAAACAAGAACA
1 AAAAA-GAAAAAACAAGAACA
* * *
405711 AAAAAGAAAGAACAAAAATA
1 AAAAAGAAAAAACAAGAACA
405731 AAAAA
1 AAAAA
405736 AGGGACAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 17 0.41
21 7 0.17
22 6 0.15
23 10 0.24
24 1 0.02
ACGTcount: A:0.80, C:0.06, G:0.13, T:0.01
Consensus pattern (20 bp):
AAAAAGAAAAAACAAGAACA
Found at i:406389 original size:23 final size:22
Alignment explanation
Indices: 406347--406389 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
406337 CCATCAATCT
* *
406347 TTTGAGCATCCAATGTCAAACC
1 TTTGAGCATCAAATGACAAACC
406369 TTTGAGCATCAAATGAACAAA
1 TTTGAGCATCAAATG-ACAAA
406390 AATGCCAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.26
Consensus pattern (22 bp):
TTTGAGCATCAAATGACAAACC
Found at i:407370 original size:37 final size:36
Alignment explanation
Indices: 407283--407483 Score: 143
Period size: 37 Copynumber: 5.8 Consensus size: 36
407273 CACTATTGTT
* * *
407283 TCTCTTGA-AAAGTTTCCCTTGAAACAAACTTTGTC
1 TCTCTTGAGACAGTTTCCCTTGAAACAAAATTCGTC
*
407318 TCTCTTGAGATAGTTTCCCTTGAAACAAAATTCCGTC
1 TCTCTTGAGACAGTTTCCCTTGAAACAAAATT-CGTC
*
407355 TC-CATTGAGACAGTTTCTCTTGAAACATAAA-----C
1 TCTC-TTGAGACAGTTTCCCTTGAAACA-AAATTCGTC
* * * * ** * *
407387 -AT-TGGAAACA-TTTCCTTTGAAATGAATTTTGTC
1 TCTCTTGAGACAGTTTCCCTTGAAACAAAATTCGTC
* *
407420 TCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTC
1 TCTCTTGAGACAGTTTCCCTTGAAACAAAA-TTCGTC
* *
407457 TCCCTTGAGACAGTTTCTCTTGAAACA
1 TCTCTTGAGACAGTTTCCCTTGAAACA
407484 TAAACATTGA
Statistics
Matches: 128, Mismatches: 24, Indels: 26
0.72 0.13 0.15
Matches are distributed among these distances:
28 2 0.02
29 10 0.08
30 6 0.05
32 1 0.01
33 1 0.01
34 1 0.01
35 13 0.10
36 35 0.27
37 56 0.44
38 3 0.02
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (36 bp):
TCTCTTGAGACAGTTTCCCTTGAAACAAAATTCGTC
Found at i:407471 original size:102 final size:102
Alignment explanation
Indices: 407287--407685 Score: 656
Period size: 102 Copynumber: 3.9 Consensus size: 102
407277 ATTGTTTCTC
* ** * *
407287 TTGAAAA-GTTTCCCTTGAAACAAACTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTC
1 TTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTT
* *
407351 CGTCTCCATTGAGACAGTTTCTCTTGAAACATAAACA
66 TGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* *
407388 TTGGAAACATTTCCTTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTT
1 TTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTT
407453 TGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
66 TGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
*
407490 TTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTCGAAACAAAATTT
1 TTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTT
*
407555 TGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAATA
66 TGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* * *
407592 TTGAAAACATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATTT
1 TTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTT
407657 TGTCTCCCTTGAGACAGATTTCTCTTGAA
66 TGTCTCCCTTGAGACAG-TTTCTCTTGAA
407686 GCATCATCTT
Statistics
Matches: 279, Mismatches: 17, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
101 6 0.02
102 262 0.94
103 11 0.04
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (102 bp):
TTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTT
TGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
Found at i:407556 original size:37 final size:38
Alignment explanation
Indices: 407513--407590 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 38
407503 CCTTGAAATG
* *
407513 AATTTTGTCTCTCTTGAGATAGTTTCCCTCGAAACA-A
1 AATTTTGTCTCCCTTGAGACAGTTTCCCTCGAAACATA
* *
407550 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATA
1 AATTTTGTCTCCCTTGAGACAGTTTCCCTCGAAACATA
407588 AAT
1 AAT
407591 ATTGAAAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
37 32 0.89
38 4 0.11
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (38 bp):
AATTTTGTCTCCCTTGAGACAGTTTCCCTCGAAACATA
Found at i:407772 original size:104 final size:102
Alignment explanation
Indices: 407331--407795 Score: 495
Period size: 102 Copynumber: 4.5 Consensus size: 102
407321 CTTGAGATAG
* ** * * *
407331 TTTCCCTTGAAACAAAATTCCGTCTCCATTGAGACAGTTTCTCTTGAAACATAAACATTGGAAAC
1 TTTCTCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAATATTGAAAAC
* ** * * * *
407396 ATTTCCTTTGAAATGAATTTTGTCTCTCTTGAGATAG
66 ATTTCCCTTGAAATGAATTTCATCTCCCGTGAGACAA
* *
407433 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCTCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAATATTGAAAAC
** * * * *
407498 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
66 ATTTCCCTTGAAATGAATTTCATCTCCCGTGAGACAA
* *
407535 TTTCCCTCGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAATATTGAAAAC
1 TTTCTCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAATATTGAAAAC
* * * *
407600 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAG
66 ATTTCCCTTGAAATGAATTTCATCTCCCGTGAGACAA
* * * *
407637 TTTCTCTTGAAACAAAATTTTGTCTCCCTTGAGACAGATTTCTCTTGAAGCAT-CATCTTTGAAT
1 TTTCTCTTGAAACAAAATTTTGTCTCCCTTGAGACAG-TTTCTCTTGAAACATAAAT-ATTGAAA
** * *
407701 ATGTTTTCCTTGGAACT-AATTTCATCTCCCCGTGAGACAA
64 ACATTTCCCTT-GAAATGAATTTCATCT-CCCGTGAGACAA
* * * * * * *
407741 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTTTCTTAAAACA-AAAT
1 TTTCTCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAT
407796 TTTGTCTCCC
Statistics
Matches: 326, Mismatches: 32, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
102 232 0.71
103 49 0.15
104 45 0.14
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (102 bp):
TTTCTCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAATATTGAAAAC
ATTTCCCTTGAAATGAATTTCATCTCCCGTGAGACAA
Found at i:408689 original size:105 final size:105
Alignment explanation
Indices: 408183--409226 Score: 1133
Period size: 105 Copynumber: 9.9 Consensus size: 105
408173 TAGAGTCAAT
* * * * * * * *
408183 TTCAACTTCACAACGAAGGGACGGCTGGTTGCCAACAACAATTTCCCAATTTC-GAAACCGATTT
1 TTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAG-AGCCAATTT
* * * * *
408247 CAACTCCACGACGGAGGATATCGTG-CTACCCGAGACAACACAAG
65 CAACTTCACAACGAAGGATATTG-GACT--CC-AGACAACGCAAG
* * * * * * *
408291 TTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTCCCAATTCCAGAACCGATTT
1 TTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAGAGCCAATTT
* * * * * * *
408356 CAACTCCACGATGGAGGATATCGTG-CTACCCGAGAAAACACAAG
65 CAACTTCACAACGAAGGATATTG-GACT--CC-AGACAACGCAAG
* * * * * * ** *
408400 TCCAACTTCACAACGAATGGA-CGACTGGTTGTCAACGAACAACTTTTCAGTTTCATCTG-CGAT
1 TTCAACTTCACGACGAAGGGACCG-CTGCTTGTCAAC-AACAACTTCTCAATTTCA-GAGCCAAT
* * * * *
408463 TTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAG
63 TTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAG
* *
408509 TTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATT
1 TTCAACTTCACGACGAAGGGACCG-CTGCTTGTCAAC-AACAACTTCTCAATTTCAGAGCCAATT
*
408573 TCAACTTCACAACGAAGAATATTGGACTCCAGACAACGCAAG
64 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
** *
408615 TTCAACTTCACGGTGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTC
1 TTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTC
*
408680 AACTTCACAACGAAGGATATTGGACTCCAGATAACGCAAG
66 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
408720 TTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTTAATTTCAGAGCCAATTTC
1 TTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTC
* * *
408785 AACTTCACAACAAATGATATTGGACTTCAGACAACGCAAG
66 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *
408825 TTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTC
1 TTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTC
* * *
408890 AACTTCACAACAAAGGATATTGGACTCCATACAATGCAAG
66 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* * * *
408930 TTCAACTTCACGACGAAGGGACCGCTGCTTGTTAACAACAACTTCCCAATCTCAGAGCCAATTTT
1 TTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTC
* *
408995 AATTTCACAACGAAGGATATTGGATTCCAGACAACGCAAG
66 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
**
409035 TTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGATTCAATTTC
1 TTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTC
* *
409095 AACTTCACAACGAAGGATATTGGACTCGAGACAACACAAG
66 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* * * ** *
409135 TTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAA-TTTTCCGGTTCCAGAGCCAAT
1 TTCAACTTCACGACGAAGGGACCG-CTGCTTGTCAAC-AACAACTTCT-CAATTTCAGAGCCAAT
* *
409198 TTCAACTTCACGACGGAGGATATTGGACT
63 TTCAACTTCACAACGAAGGATATTGGACT
409227 TGGAACAATG
Statistics
Matches: 839, Mismatches: 80, Indels: 36
0.88 0.08 0.04
Matches are distributed among these distances:
99 2 0.00
100 78 0.09
101 3 0.00
102 5 0.01
103 3 0.00
104 3 0.00
105 397 0.47
106 79 0.09
107 5 0.01
108 37 0.04
109 221 0.26
110 3 0.00
111 1 0.00
112 2 0.00
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
TTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTC
AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:409818 original size:34 final size:34
Alignment explanation
Indices: 409775--409899 Score: 129
Period size: 34 Copynumber: 3.8 Consensus size: 34
409765 TTCGTCCTAC
409775 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
409809 TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
409844 GCTAGGATTC--A-----AAAAATAGGATAGAATTT
1 --TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * *
409873 TATGATTTAAACTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
409900 CCACAAGCAC
Statistics
Matches: 74, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
27 6 0.08
29 4 0.05
30 13 0.18
34 39 0.53
35 4 0.05
37 8 0.11
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.31
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:410195 original size:23 final size:22
Alignment explanation
Indices: 410164--410225 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
410154 TTTTTCTTTT
410164 TTTTCATGTAATATTTTTTTTAC
1 TTTT-ATGTAATATTTTTTTTAC
*
410187 ATTTTATGT-ATTTTCTTTTTTAC
1 -TTTTATGTAATATT-TTTTTTAC
410210 -TTTA-GTATATATTTTT
1 TTTTATGTA-ATATTTTT
410226 ATTTTTTTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
20 2 0.06
21 7 0.21
22 8 0.24
23 12 0.36
24 4 0.12
ACGTcount: A:0.21, C:0.06, G:0.05, T:0.68
Consensus pattern (22 bp):
TTTTATGTAATATTTTTTTTAC
Found at i:410222 original size:24 final size:23
Alignment explanation
Indices: 410179--410224 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
410169 ATGTAATATT
*
410179 TTTTTTACATTTTATGTATTTTC
1 TTTTTTACATTTTATATATTTTC
410202 TTTTTTAC-TTTAGTATATATTTT
1 TTTTTTACATTT--TATATATTTT
410225 TATTTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 8 0.40
24 9 0.45
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.70
Consensus pattern (23 bp):
TTTTTTACATTTTATATATTTTC
Found at i:410315 original size:8 final size:7
Alignment explanation
Indices: 410304--410397 Score: 57
Period size: 7 Copynumber: 12.4 Consensus size: 7
410294 TATATATATA
410304 TTTACTTT
1 TTTA-TTT
410312 TTTATTT
1 TTTATTT
410319 TTTATTT
1 TTTATTT
410326 TTTATTT
1 TTTATTT
*
410333 TATATATAT
1 T-T-TATTT
*
410342 ATTA-TT
1 TTTATTT
410348 TTTACTTT
1 TTTA-TTT
410356 TTTATTAT
1 TTTATT-T
*
410364 TATT-TTA
1 T-TTATTT
410371 TTTATTTGT
1 TTTA-TT-T
410380 TTTATTT
1 TTTATTT
*
410387 CTATATTT
1 -TTTATTT
410395 TTT
1 TTT
410398 TTCTTCTTTT
Statistics
Matches: 68, Mismatches: 8, Indels: 21
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.09
7 26 0.38
8 26 0.38
9 10 0.15
ACGTcount: A:0.20, C:0.03, G:0.01, T:0.76
Consensus pattern (7 bp):
TTTATTT
Found at i:410319 original size:6 final size:6
Alignment explanation
Indices: 410310--410439 Score: 52
Period size: 6 Copynumber: 19.7 Consensus size: 6
410300 TATATTTACT
410310 TTTTTA TTTTTTA TTTTTTA TTTTATA TATATATTA TTTTTA CTTTTTTA
1 TTTTTA -TTTTTA -TTTTTA TTTT-TA T-T-T-TTA TTTTTA --TTTTTA
* * *
410360 TTATTA -TTTTA TTTATT- TGTTTTA TTTCTATA TTTTT- TTTCTTC TTTTTC
1 TTTTTA TTTTTA TTT-TTA T-TTTTA TTT-T-TA TTTTTA TTT-TTA TTTTTA
*
410410 TTCTTT- TTCTTTA TTTTTTA TATTTA TTTT
1 TT-TTTA TT-TTTA -TTTTTA TTTTTA TTTT
410440 ACTTACTATT
Statistics
Matches: 102, Mismatches: 4, Indels: 35
0.72 0.03 0.25
Matches are distributed among these distances:
5 7 0.07
6 41 0.40
7 34 0.33
8 15 0.15
9 4 0.04
10 1 0.01
ACGTcount: A:0.17, C:0.05, G:0.01, T:0.77
Consensus pattern (6 bp):
TTTTTA
Found at i:410333 original size:13 final size:13
Alignment explanation
Indices: 410304--410439 Score: 71
Period size: 14 Copynumber: 9.6 Consensus size: 13
410294 TATATATATA
410304 TTTACTTTTTTATTT
1 TTTA-TTTTTTA-TT
410319 TTTATTTTTTATT
1 TTTATTTTTTATT
*
410332 TTATATATATATTATT
1 TT-TAT-T-TTTTATT
410348 TTTACTTTTTTATT
1 TTTA-TTTTTTATT
*
410362 ATTATTTTATTTATT
1 TTTA-TTT-TTTATT
410377 TGTT-TTATTTCTATAT
1 T-TTATT-TTT-TAT-T
*
410393 TTT-TTTTCTTCTT
1 TTTATTTT-TTATT
* *
410406 TTTCTTCTTTT-TC
1 TTTATT-TTTTATT
*
410419 TTTATTTTTTATA
1 TTTATTTTTTATT
410432 TTTATTTT
1 TTTATTTT
410440 ACTTACTATT
Statistics
Matches: 99, Mismatches: 9, Indels: 28
0.73 0.07 0.21
Matches are distributed among these distances:
12 4 0.04
13 23 0.23
14 34 0.34
15 25 0.25
16 13 0.13
ACGTcount: A:0.17, C:0.06, G:0.01, T:0.76
Consensus pattern (13 bp):
TTTATTTTTTATT
Found at i:410350 original size:37 final size:38
Alignment explanation
Indices: 410294--410371 Score: 108
Period size: 36 Copynumber: 2.1 Consensus size: 38
410284 TATATATATA
*
410294 TATATATATATTTACTTTTTTA-TTTTTTATTTTTTATTT
1 TATATATATATTTAC-TTTTTACTTTTTTA-TTATTATTT
410333 TATATATATA-TTA-TTTTTACTTTTTTATTATTATTT
1 TATATATATATTTACTTTTTACTTTTTTATTATTATTT
410369 TAT
1 TAT
410372 TTATTTGTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
36 17 0.46
37 7 0.19
38 3 0.08
39 10 0.27
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (38 bp):
TATATATATATTTACTTTTTACTTTTTTATTATTATTT
Found at i:410383 original size:49 final size:49
Alignment explanation
Indices: 410222--410407 Score: 154
Period size: 49 Copynumber: 3.9 Consensus size: 49
410212 TAGTATATAT
* ** * * *
410222 TTTTATTTTTTTAGATTATATATATA-AATATATTA-TTTTTTATTATCA
1 TTTTATTTATTTATTTTATATATATATTAT-TTTTACTTTTTTATTATTA
* * *
410270 GTTTTATTAATTTATATATATATATATATATATATTTAC--TTTT-TTATT-
1 -TTTTATTTATTTAT-TTTATATATATAT-TATTTTTACTTTTTTATTATTA
410318 TTTTATTT-TTTATTTTATATATATATTATTTTTACTTTTTTATTATTA
1 TTTTATTTATTTATTTTATATATATATTATTTTTACTTTTTTATTATTA
* * * *
410366 TTTTATTTATTTGTTTTATTTCTATATT-TTTTTTCTTCTTTT
1 TTTTATTTATTTATTTTATATATATATTATTTTTACTT-TTTT
410408 TCTTCTTTTT
Statistics
Matches: 111, Mismatches: 16, Indels: 20
0.76 0.11 0.14
Matches are distributed among these distances:
44 8 0.07
45 12 0.11
46 9 0.08
47 12 0.11
48 16 0.14
49 35 0.32
50 14 0.13
51 3 0.03
52 2 0.02
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (49 bp):
TTTTATTTATTTATTTTATATATATATTATTTTTACTTTTTTATTATTA
Found at i:410407 original size:8 final size:9
Alignment explanation
Indices: 410395--410420 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
410385 TTCTATATTT
410395 TTTTTCTTC
1 TTTTTCTTC
410404 TTTTTCTTC
1 TTTTTCTTC
410413 TTTTTCTT
1 TTTTTCTT
410421 TATTTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:410545 original size:15 final size:15
Alignment explanation
Indices: 410527--410556 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
410517 TATTTATTTC
410527 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
410542 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
410557 ACATGGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
TTACCTTTTTATCTA
Found at i:412553 original size:2 final size:2
Alignment explanation
Indices: 412542--412597 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
412532 AAGGAAAAAA
* *
412542 AT AT AA AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
412584 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
412598 CAAAGTATTA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:413129 original size:18 final size:17
Alignment explanation
Indices: 413106--413148 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
413096 ATATATACAT
413106 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
* *
413124 ATAATAAAAATAAGTGA
1 ATAATAATAATAAATGA
413141 ATAA-AATA
1 ATAATAATA
413149 TCCATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:413616 original size:34 final size:35
Alignment explanation
Indices: 413538--413640 Score: 147
Period size: 34 Copynumber: 2.9 Consensus size: 35
413528 TTAGTAGAAC
*
413538 TCTATCCTATTTTTTAGGAGTTTGAATACTAGCAAAATG
1 TCTATCCTA-TTTTTAGGAGTTTGAATCCT---AAAATG
413577 T-TATCCTATTTTTAGGAGTTTGAATCCTAAAAT-
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
413610 TCTATCCTATTTTTAGGAGTTTGAATCCTAA
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAA
413641 TAGGACGAAA
Statistics
Matches: 62, Mismatches: 1, Indels: 7
0.89 0.01 0.10
Matches are distributed among these distances:
33 1 0.02
34 34 0.55
37 19 0.31
38 7 0.11
39 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.44
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
Found at i:414485 original size:105 final size:105
Alignment explanation
Indices: 414186--414741 Score: 744
Period size: 105 Copynumber: 5.3 Consensus size: 105
414176 CATTGTTCCA
* * * * ** * * *
414186 AGTCCAATATCCTCCATCGTGAAGTTGAAATTGGCTCTGGAACCGAGAAATTGTTTGTTAACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * * * * *
414251 CAGCCGTCCCTTCATTGTGACGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
**
414292 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCT-AAA-TGA-AA-TT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
414352 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
414392 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
414457 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
414497 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* * *
414562 AGCGGTCCTTTCATCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
414602 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * * *
414667 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
414708 AGTGCCACGATATCCTCCGTTGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
414742 CGCGGATGGC
Statistics
Matches: 403, Mismatches: 38, Indels: 15
0.88 0.08 0.03
Matches are distributed among these distances:
100 80 0.20
101 2 0.00
102 4 0.01
103 4 0.01
104 4 0.01
105 204 0.51
106 79 0.20
107 3 0.01
109 23 0.06
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:415438 original size:31 final size:31
Alignment explanation
Indices: 415403--415530 Score: 82
Period size: 31 Copynumber: 3.9 Consensus size: 31
415393 AGGAAATAAA
415403 CTCAAAG-ATTTTGTGTTTCAAGAGAAACTGT
1 CTCAAAGAATTTTGTGTTTCAAGAGAAACT-T
** * *
415434 CTCAAGGGAGACAAAATT-TGTTTCAAGGGAAACAAT
1 CTCAA---AG--AATTTTGTGTTTCAAGAGAAAC-TT
*
415470 CTCAAAG-GTTTTGTGTTTCAAGAGAAACATT
1 CTCAAAGAATTTTGTGTTTCAAGAGAAAC-TT
* **
415501 TTCAAAGGTTTTTTGTGTTTCAAGAGAAAC
1 CTCAAA-GAATTTTGTGTTTCAAGAGAAAC
415531 AATTTCAAAG
Statistics
Matches: 76, Mismatches: 11, Indels: 18
0.72 0.10 0.17
Matches are distributed among these distances:
30 2 0.03
31 26 0.34
32 1 0.01
33 22 0.29
34 2 0.03
36 20 0.26
37 3 0.04
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.33
Consensus pattern (31 bp):
CTCAAAGAATTTTGTGTTTCAAGAGAAACTT
Found at i:415490 original size:67 final size:67
Alignment explanation
Indices: 415309--415497 Score: 243
Period size: 67 Copynumber: 2.8 Consensus size: 67
415299 TAAAAAAGAT
* * * * *
415309 AAAATTCGTTTCAAGGGAAACGATCTTAAAGATATATGTTGTTTCATGAGAAACGGCCTCAAGGG
1 AAAATTTGTTTCAAGGGAAACAATCTCAAAGAT-TTTG-TGTTTCAAGAGAAACGGCCTCAAGGG
415374 AGAC
64 AGAC
* * * * * *
415378 AAAATTTTGTTTTAAAGGAAATAAACTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGA
1 AAAA-TTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACGGCCTCAAGGGA
415443 GAC
65 GAC
*
415446 AAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTTTGTGTTTCAAGAGAAAC
1 AAAATTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAAC
415498 ATTTTCAAAG
Statistics
Matches: 103, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
67 43 0.42
68 31 0.30
69 7 0.07
70 22 0.21
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (67 bp):
AAAATTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACGGCCTCAAGGGAG
AC
Found at i:415557 original size:36 final size:33
Alignment explanation
Indices: 415452--415566 Score: 162
Period size: 33 Copynumber: 3.5 Consensus size: 33
415442 AGACAAAATT
* *
415452 TGTTTCAAGGGAAACAATCTCAAAGG--TTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTG
*
415483 TGTTTCAAGAGAAACATTTTCAAAGGTTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTG
415516 TGTTTCAAGAGAAACAATTTCAAAGGTTTCTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGG--T-TTTTTG
415552 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
415567 TGTATCAAGG
Statistics
Matches: 75, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
31 23 0.31
33 30 0.40
35 1 0.01
36 21 0.28
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.37
Consensus pattern (33 bp):
TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTG
Found at i:415649 original size:37 final size:36
Alignment explanation
Indices: 415608--415722 Score: 149
Period size: 37 Copynumber: 3.1 Consensus size: 36
415598 CAAGGATTGA
* *
415608 TGTTTCAAGATAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAA-TT
* * *
415645 TGTTTTAAGAAAAACATGTCTTAAGATAGACAAAATT
1 TGTTTCAAGAAAAAC-TGTCTCAAGAGAGACAAAATT
* *
415682 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATT
1 TGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAATT
415718 TGTTT
1 TGTTT
415723 AATGTAAAAC
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
36 23 0.34
37 28 0.42
38 16 0.24
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.31
Consensus pattern (36 bp):
TGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAATT
Found at i:415717 original size:36 final size:36
Alignment explanation
Indices: 415608--416082 Score: 227
Period size: 36 Copynumber: 13.9 Consensus size: 36
415598 CAAGGATTGA
* *
415608 TGTTTCAAGATAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * *
415645 TGTTTTAAGAAAAACATGTCTTAAGATAGACAAAATT
1 TGTTTCAAGAGAAAC-TGTCTCAAGAGAGACAAAATT
*
415682 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
415718 TGTTT-AATGTA-AAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAA-G-AGAAAC-TGTCTCAAGAGAGACAAAATT
* * *
415747 TGTTTCAAGGGAAACTGTTTTC-A-A-AG-----TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAATT
*
415776 ATGTTTCAATAGAAACTGTCTCAA-AGGAGACAAAATT
1 -TGTTTCAAGAGAAACTGTCTCAAGA-GAGACAAAATT
* *
415813 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
** * * * *
415849 CATTTCAAGGGAAA-TGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAATT
* *
415877 ATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * *
415915 TGATTCAAGGGAAACTATCTCAAGAGAGAC--AATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * * *
415949 TATTTCAAGGGAAA-TGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAATT
* *
415977 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* *
416015 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
416051 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
416083 TGGTGAGCAC
Statistics
Matches: 341, Mismatches: 55, Indels: 85
0.71 0.11 0.18
Matches are distributed among these distances:
28 5 0.01
29 49 0.14
30 31 0.09
31 1 0.00
32 5 0.01
33 5 0.01
34 19 0.06
35 7 0.02
36 110 0.32
37 89 0.26
38 20 0.06
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:415772 original size:30 final size:30
Alignment explanation
Indices: 415736--415794 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
415726 GTAAAACATA
*
415736 TTCAAAGATTT-TGTTTCAAGGGAAACTGTT
1 TTCAAAG-TTTATGTTTCAAGAGAAACTGTT
*
415766 TTCAAAGTTTATGTTTCAATAGAAACTGT
1 TTCAAAGTTTATGTTTCAAGAGAAACTGT
415795 CTCAAAGGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (30 bp):
TTCAAAGTTTATGTTTCAAGAGAAACTGTT
Found at i:415936 original size:37 final size:36
Alignment explanation
Indices: 415878--416082 Score: 189
Period size: 37 Copynumber: 5.9 Consensus size: 36
415868 TCAATGTTTA
* * *
415878 TGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAATTT
* *
415915 TGATTCAAGGGAAACTATCTCAAGAGAGAC-AA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAATTT
* * *
415949 TATTTCAAGGGAAA-TGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAATTT
* * *
415977 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAG-ACAAATTT
*
416015 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAATTT
416051 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
416083 TGGTGAGCAC
Statistics
Matches: 136, Mismatches: 19, Indels: 27
0.75 0.10 0.15
Matches are distributed among these distances:
28 2 0.01
29 15 0.11
30 3 0.02
31 1 0.01
32 2 0.01
33 2 0.01
34 17 0.12
35 2 0.01
36 38 0.28
37 51 0.38
38 3 0.02
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAATTT
Found at i:415945 original size:102 final size:102
Alignment explanation
Indices: 415749--416064 Score: 512
Period size: 100 Copynumber: 3.1 Consensus size: 102
415739 AAAGATTTTG
* * *
415749 TTTCAAGGGAAACTGTTTTCAAAGTTTATGTTTCAATAGAAACTGTCTCAAAGGAGACAAAA-TT
1 TTTCAAGGGAAA-TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
415813 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
65 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTA
*
415851 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
*
415916 GATTCAAGGGAAACTATCTCAAGAGAGAC--AATTTA
66 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTA
*
415951 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
* * *
416016 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTTTG
66 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTA
416053 TTTCAAGGGAAA
1 TTTCAAGGGAAA
416065 CTGTCTCAAG
Statistics
Matches: 199, Mismatches: 12, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
100 95 0.48
101 45 0.23
102 59 0.30
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (102 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTA
Found at i:416963 original size:19 final size:19
Alignment explanation
Indices: 416939--416985 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 19
416929 GGTCATTGTG
416939 TTTGATCAAAGGTTTGGCA
1 TTTGATCAAAGGTTTGGCA
*
416958 TTTGATGCTCAAAGGTTTGGTA
1 TTTGA---TCAAAGGTTTGGCA
416980 TTTGAT
1 TTTGAT
416986 GCTCAAAGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
19 6 0.25
22 18 0.75
ACGTcount: A:0.23, C:0.09, G:0.26, T:0.43
Consensus pattern (19 bp):
TTTGATCAAAGGTTTGGCA
Found at i:416971 original size:22 final size:22
Alignment explanation
Indices: 416944--416994 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
416934 TTGTGTTTGA
416944 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
416966 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
416988 TCAAAGG
1 TCAAAGG
416995 ATTGATGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:419325 original size:18 final size:18
Alignment explanation
Indices: 419302--419336 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
419292 TTAGTCTTTC
419302 AGAAGTGGATGTGAATCT
1 AGAAGTGGATGTGAATCT
419320 AGAAGTGGATGTGAATC
1 AGAAGTGGATGTGAATC
419337 CAGACTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.06, G:0.34, T:0.26
Consensus pattern (18 bp):
AGAAGTGGATGTGAATCT
Found at i:421387 original size:14 final size:14
Alignment explanation
Indices: 421368--421409 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
421358 AAAAAGGAAA
421368 AAATATAAATATAT
1 AAATATAAATATAT
421382 AAATATAAATATAT
1 AAATATAAATATAT
* *
421396 ATATATATATATAT
1 AAATATAAATATAT
421410 CAAAGTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AAATATAAATATAT
Found at i:421407 original size:6 final size:6
Alignment explanation
Indices: 421370--421409 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
421360 AAAGGAAAAA
* * *
421370 ATATAA ATATAT AAATAT AAATAT ATATAT ATATAT ATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATAT
421410 CAAAGTATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (6 bp):
ATATAT
Found at i:421407 original size:8 final size:8
Alignment explanation
Indices: 421370--421409 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
421360 AAAGGAAAAA
*
421370 ATATAAAT
1 ATATATAT
*
421378 ATATAAAT
1 ATATATAT
*
421386 ATAAATAT
1 ATATATAT
421394 ATATATAT
1 ATATATAT
421402 ATATATAT
1 ATATATAT
421410 CAAAGTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
ATATATAT
Found at i:421462 original size:36 final size:38
Alignment explanation
Indices: 421397--421472 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 38
421387 TAAATATATA
*
421397 TATATATATATATCAAAGTATTAATAAAATA-AATAAGC
1 TATATATATATACCAAAGTATTAATAAAATAGAA-AAGC
421435 TATATATATATACCAAA-TACTT-A-AAAATAGAAAAGC
1 TATATATATATACCAAAGTA-TTAATAAAATAGAAAAGC
421471 TA
1 TA
421473 CCCTCCCAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
36 12 0.34
37 5 0.14
38 18 0.51
ACGTcount: A:0.55, C:0.08, G:0.05, T:0.32
Consensus pattern (38 bp):
TATATATATATACCAAAGTATTAATAAAATAGAAAAGC
Found at i:421927 original size:18 final size:17
Alignment explanation
Indices: 421906--421948 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
421896 ATATATACAT
421906 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
* *
421924 ATAATAAAAATAAGTGA
1 ATAATAATAATAAATGA
421941 ATAA-AATA
1 ATAATAATA
421949 TCCATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:422354 original size:37 final size:35
Alignment explanation
Indices: 422304--422438 Score: 155
Period size: 37 Copynumber: 3.8 Consensus size: 35
422294 GTGCTTGTGG
* * * * *
422304 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAG-A-AAATCT
*
422341 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATGTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT-CT
*
422378 ATCCTATTTTTAGGAGTTTGAATCCTA-AAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGAAAATCT
*
422412 ATCCTATTTTTAAGAGTTTGAATCCTA
1 ATCCTATTTTTAGGAGTTTGAATCCTA
422439 ATAGGACGAA
Statistics
Matches: 87, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
34 27 0.31
35 4 0.05
36 3 0.03
37 53 0.61
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (35 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGAAAATCT
Found at i:422415 original size:34 final size:35
Alignment explanation
Indices: 422338--422439 Score: 154
Period size: 34 Copynumber: 2.9 Consensus size: 35
422328 TTAGTAGAAC
422338 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATG
1 TCTATCCTATTTTTAGGAGTTTGAATCCT---AAAATG
422376 T-TATCCTATTTTTAGGAGTTTGAATCCTAAAAT-
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
*
422409 TCTATCCTATTTTTAAGAGTTTGAATCCTAA
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAA
422440 TAGGACGAAA
Statistics
Matches: 62, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
33 1 0.02
34 33 0.53
37 27 0.44
38 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
Found at i:423670 original size:20 final size:22
Alignment explanation
Indices: 423624--423667 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
423614 AATATCCAAC
423624 AATAACAAAATCAATAGAAAAA
1 AATAACAAAATCAATAGAAAAA
*
423646 AATAACAAAATCGAT-GAAAAA
1 AATAACAAAATCAATAGAAAAA
423667 A
1 A
423668 TAATATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.70, C:0.09, G:0.07, T:0.14
Consensus pattern (22 bp):
AATAACAAAATCAATAGAAAAA
Found at i:429055 original size:9 final size:9
Alignment explanation
Indices: 429041--429074 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
429031 TAAGTAAAAT
429041 ATTAAATAA
1 ATTAAATAA
429050 ATTAAAT-A
1 ATTAAATAA
*
429058 CTTAAATAA
1 ATTAAATAA
429067 ATTAAATA
1 ATTAAATA
429075 CAAAATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (9 bp):
ATTAAATAA
Found at i:429073 original size:17 final size:17
Alignment explanation
Indices: 429037--429075 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
429027 TAATTAAGTA
429037 AAATA-TTAAATAAATT
1 AAATACTTAAATAAATT
429053 AAATACTTAAATAAATT
1 AAATACTTAAATAAATT
429070 AAATAC
1 AAATAC
429076 AAAATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATACTTAAATAAATT
Found at i:438934 original size:2 final size:2
Alignment explanation
Indices: 438927--438992 Score: 75
Period size: 2 Copynumber: 34.0 Consensus size: 2
438917 TAATTCAATA
* *
438927 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T CT AT CA- AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
*
438968 AT A- AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
438993 TGCAACGCCC
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
1 3 0.05
2 52 0.93
3 1 0.02
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:440457 original size:19 final size:20
Alignment explanation
Indices: 440418--440457 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
440408 TAAGTGTTAA
*
440418 TGAATTTTAAGATTTTATAT
1 TGAATTTTAAGATTATATAT
440438 TGAATTTTAA-ATTATATAT
1 TGAATTTTAAGATTATATAT
440457 T
1 T
440458 CGATTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (20 bp):
TGAATTTTAAGATTATATAT
Found at i:440701 original size:35 final size:36
Alignment explanation
Indices: 440650--440720 Score: 126
Period size: 35 Copynumber: 2.0 Consensus size: 36
440640 ATCACCCATA
440650 GGGAACAGATTCCCCCCCA-GGGGTACCGATTCCCC
1 GGGAACAGATTCCCCCCCAGGGGGTACCGATTCCCC
*
440685 GGGACCAGATTCCCCCCCAGGGGGTACCGATTCCCC
1 GGGAACAGATTCCCCCCCAGGGGGTACCGATTCCCC
440721 CTGCAGGTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 18 0.53
36 16 0.47
ACGTcount: A:0.18, C:0.41, G:0.27, T:0.14
Consensus pattern (36 bp):
GGGAACAGATTCCCCCCCAGGGGGTACCGATTCCCC
Found at i:443622 original size:27 final size:27
Alignment explanation
Indices: 443592--443646 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
443582 CAAAACACAA
443592 TAATTT-GAAAATTAACAATTTTTTTTT
1 TAATTTCGAAAATTAA-AATTTTTTTTT
*
443619 TAATTTCGAAAATTTAAATTTTTTTTT
1 TAATTTCGAAAATTAAAATTTTTTTTT
443646 T
1 T
443647 GGAAATTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 18 0.69
28 8 0.31
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (27 bp):
TAATTTCGAAAATTAAAATTTTTTTTT
Found at i:443854 original size:20 final size:20
Alignment explanation
Indices: 443817--443855 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
443807 AGATTGAGTG
* * *
443817 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
443837 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
443856 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:444074 original size:20 final size:21
Alignment explanation
Indices: 444028--444088 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
444018 TCCCCTGTGG
444028 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
444051 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
444071 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
444089 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:447792 original size:20 final size:20
Alignment explanation
Indices: 447767--447817 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
447757 GTTTGTTTTC
*
447767 AATTTTCA-ATTTTGAAACAT
1 AATTTTCATATTTT-AAAAAT
*
447787 AATTTTTATATTTTAAAAAT
1 AATTTTCATATTTTAAAAAT
447807 AATTTCTCATA
1 AATTT-TCATA
447818 ATCCGAAGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.49
Consensus pattern (20 bp):
AATTTTCATATTTTAAAAAT
Found at i:454255 original size:3 final size:3
Alignment explanation
Indices: 454247--454278 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
454237 TCTTGAATTC
454247 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
454279 CGATATGGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:456162 original size:26 final size:25
Alignment explanation
Indices: 456133--456181 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
456123 TAATAAAATT
456133 AAACAA-AGATAAATAAATAAAATAGA
1 AAACAACA-ATAAATAAA-AAAATAGA
*
456159 AAACAACAATGAATAAAAAAATA
1 AAACAACAATAAATAAAAAAATA
456182 CATGAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 6 0.29
26 14 0.67
27 1 0.05
ACGTcount: A:0.73, C:0.06, G:0.06, T:0.14
Consensus pattern (25 bp):
AAACAACAATAAATAAAAAAATAGA
Found at i:456235 original size:17 final size:15
Alignment explanation
Indices: 456206--456264 Score: 54
Period size: 15 Copynumber: 4.0 Consensus size: 15
456196 ATGAATATTC
456206 ATATTTATTA-AAATA
1 ATATTTATTATAAA-A
*
456221 AT-TTCATTATAAAA
1 ATATTTATTATAAAA
456235 ATTATTTA-TATAGAAA
1 A-TATTTATTATA-AAA
456251 ATATTTATT-TAAAA
1 ATATTTATTATAAAA
456265 TAAATATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
14 11 0.30
15 18 0.49
16 8 0.22
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (15 bp):
ATATTTATTATAAAA
Found at i:456496 original size:2 final size:2
Alignment explanation
Indices: 456485--456517 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
456475 ATAGCTTACT
456485 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
456518 AAATACCTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:460321 original size:25 final size:23
Alignment explanation
Indices: 460248--460330 Score: 62
Period size: 24 Copynumber: 3.5 Consensus size: 23
460238 AGCTCGTATA
* **
460248 AATTTGCACCAAAGTGCCACGTAG
1 AATTTGCACCGAA-TGCTGCGTAG
* *
460272 AATTTGTC-CCGAATGATCGCTTAG
1 AATTTG-CACCGAATGCT-GCGTAG
460296 AAATTTGCACCGAATTGCTGCGTAG
1 -AATTTGCACCGAA-TGCTGCGTAG
460321 AA-TTGCACCG
1 AATTTGCACCG
460331 TAGTGCCATA
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
23 10 0.21
24 17 0.36
25 17 0.36
26 3 0.06
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.27
Consensus pattern (23 bp):
AATTTGCACCGAATGCTGCGTAG
Found at i:460611 original size:30 final size:31
Alignment explanation
Indices: 460572--460642 Score: 117
Period size: 31 Copynumber: 2.3 Consensus size: 31
460562 TCACATAGTA
* *
460572 TATCTCATAGACATATTA-TTTCCATACCTT
1 TATCACATAGACATATCATTTTCCATACCTT
460602 TATCACATAGACATATCATTTTCCATACCTT
1 TATCACATAGACATATCATTTTCCATACCTT
460633 TATCACATAG
1 TATCACATAG
460643 CTCATATAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 16 0.42
31 22 0.58
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.39
Consensus pattern (31 bp):
TATCACATAGACATATCATTTTCCATACCTT
Found at i:462098 original size:36 final size:38
Alignment explanation
Indices: 462057--462128 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
462047 TATATATATG
*
462057 TTTTCATAACTATAT-TA-CATATGTTTTCAAAAATCA
1 TTTTCAAAACTATATATATCATATGTTTTCAAAAATCA
* *
462093 TTTTCAAAATTATATATATTATATGTTTTCAAAAAT
1 TTTTCAAAACTATATATATCATATGTTTTCAAAAAT
462129 GTGTTTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 13 0.42
37 2 0.06
38 16 0.52
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (38 bp):
TTTTCAAAACTATATATATCATATGTTTTCAAAAATCA
Found at i:462135 original size:14 final size:14
Alignment explanation
Indices: 462116--462154 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
462106 ATATATTATA
462116 TGTTTTCAAAAATG
1 TGTTTTCAAAAATG
*
462130 TGTTTTTAAAAATG
1 TGTTTTCAAAAATG
462144 TGTTTTCAAAA
1 TGTTTTCAAAA
462155 CTATATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.46
Consensus pattern (14 bp):
TGTTTTCAAAAATG
Found at i:462171 original size:37 final size:36
Alignment explanation
Indices: 462130--462289 Score: 135
Period size: 37 Copynumber: 4.3 Consensus size: 36
462120 TTCAAAAATG
*
462130 TGTTTTTAAAAATGTGTTTTCAAAACTATATAATATA
1 TGTTTTCAAAAATGTGTTTTCAAAACTATAT-ATATA
*
462167 TGTTTTCAAAAATGTGTTTTCAAAACCATAT-TATA
1 TGTTTTCAAAAATGTGTTTTCAAAACTATATATATA
* **** *
462202 TATTTTCAAAAACCAATTTTAAAAACTATATATTATA
1 TGTTTTCAAAAATGTGTTTTCAAAACTATATA-TATA
* * * *
462239 TGCTTTTAAAAAAAGT-TTTCTAAAAAGATATATATTATA
1 TG-TTTTCAAAAATGTGTTT-TCAAAA-CTATATA-TATA
*
462278 TATTTTCAAAAA
1 TGTTTTCAAAAA
462290 ATATTTTTAA
Statistics
Matches: 101, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
35 28 0.28
37 37 0.37
38 24 0.24
39 12 0.12
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (36 bp):
TGTTTTCAAAAATGTGTTTTCAAAACTATATATATA
Found at i:462171 original size:51 final size:53
Alignment explanation
Indices: 462078--462191 Score: 171
Period size: 51 Copynumber: 2.2 Consensus size: 53
462068 ATATTACATA
** *
462078 TGTTTTCAAAAAT-CATTTTCAAAATTATATATATTATATGTTTTCAAAAATG
1 TGTTTTCAAAAATGTGTTTTCAAAACTATATATATTATATGTTTTCAAAAATG
*
462130 TGTTTTTAAAAATGTGTTTTCAAAACTATATA-A-TATATGTTTTCAAAAATG
1 TGTTTTCAAAAATGTGTTTTCAAAACTATATATATTATATGTTTTCAAAAATG
462181 TGTTTTCAAAA
1 TGTTTTCAAAA
462192 CCATATTATA
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
51 28 0.50
52 13 0.23
53 15 0.27
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (53 bp):
TGTTTTCAAAAATGTGTTTTCAAAACTATATATATTATATGTTTTCAAAAATG
Found at i:462239 original size:35 final size:36
Alignment explanation
Indices: 462146--462289 Score: 107
Period size: 35 Copynumber: 3.9 Consensus size: 36
462136 TAAAAATGTG
* ****
462146 TTTTCAAAACTATATAATATATGTTTTCAAAAATGTG
1 TTTTCAAAACTATAT-ATATATATTTTCAAAAACCAA
*
462183 TTTTCAAAACCATAT-TATATATTTTCAAAAACCAA
1 TTTTCAAAACTATATATATATATTTTCAAAAACCAA
* *
462218 TTTTAAAAACTATATAT-TATATGCTTTTAAAAA--AA
1 TTTTCAAAACTATATATATATAT--TTTCAAAAACCAA
*
462253 GTTTTCTAAAAAGATATATATTATATATTTTCAAAAA
1 -TTTTC--AAAA-CTATATA-TATATATTTTCAAAAA
462290 ATATTTTTAA
Statistics
Matches: 86, Mismatches: 12, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
35 35 0.41
36 5 0.06
37 22 0.26
38 4 0.05
39 14 0.16
40 1 0.01
41 5 0.06
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (36 bp):
TTTTCAAAACTATATATATATATTTTCAAAAACCAA
Found at i:462271 original size:39 final size:37
Alignment explanation
Indices: 462194--462314 Score: 131
Period size: 39 Copynumber: 3.2 Consensus size: 37
462184 TTTCAAAACC
** * *
462194 ATATTATATATTTTCAAAAACCAATTTTAAAAACTAT
1 ATATTATATATTTTCAAAAAATATTTTTAAAAAATAT
*
462231 ATATTATATGCTTTT-AAAAAA-AGTTTTCTAAAAAGATAT
1 ATATTATAT-ATTTTCAAAAAATA-TTTT-TAAAAA-ATAT
462270 ATATTATATATTTTCAAAAAATATTTTTAAAAAAT-T
1 ATATTATATATTTTCAAAAAATATTTTTAAAAAATAT
*
462306 ACATTATAT
1 ATATTATAT
462315 TATTATATAT
Statistics
Matches: 72, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
36 10 0.14
37 19 0.26
38 20 0.28
39 22 0.31
40 1 0.01
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (37 bp):
ATATTATATATTTTCAAAAAATATTTTTAAAAAATAT
Found at i:463697 original size:31 final size:31
Alignment explanation
Indices: 463636--463699 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
463626 CCGAGACCCG
*
463636 ACCCAACCCAACCCGAATATATGAATTAAAA
1 ACCCAACCCAACCCGAATAAATGAATTAAAA
* *
463667 ACCCGACCCAACCCGACATGAAAT-AATAAAAA
1 ACCCAACCCAACCCGA-AT-AAATGAATTAAAA
463699 A
1 A
463700 ATATTTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 15 0.54
32 10 0.36
33 3 0.11
ACGTcount: A:0.50, C:0.30, G:0.08, T:0.12
Consensus pattern (31 bp):
ACCCAACCCAACCCGAATAAATGAATTAAAA
Found at i:464005 original size:28 final size:29
Alignment explanation
Indices: 463929--464009 Score: 92
Period size: 33 Copynumber: 2.7 Consensus size: 29
463919 CCCTAAAATT
* * *
463929 TTTAAAAAAACCCGACCTGAATATCACAC
1 TTTAAAAAAATCCGACCCGAATATCAAAC
463958 TTTAAAAAACATGACCCGACCCGAATATCAAAC
1 TTTAAAAAA-AT---CCGACCCGAATATCAAAC
463991 -TTAAAAAAATCCGACCCGA
1 TTTAAAAAAATCCGACCCGA
464010 TCTCGAATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
28 9 0.20
29 9 0.20
30 1 0.02
31 2 0.04
32 8 0.18
33 16 0.36
ACGTcount: A:0.46, C:0.27, G:0.09, T:0.19
Consensus pattern (29 bp):
TTTAAAAAAATCCGACCCGAATATCAAAC
Found at i:475375 original size:19 final size:19
Alignment explanation
Indices: 475351--475389 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
475341 TCGAATGCAT
475351 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
475370 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
475389 T
1 T
475390 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:475407 original size:65 final size:64
Alignment explanation
Indices: 475307--475497 Score: 217
Period size: 64 Copynumber: 3.0 Consensus size: 64
475297 ATACATCAGT
** * * * **
475307 CCATGCATCGATGCATCGATGAAT-TAATT-GAACATCGAATGCATTCCATGCACCGATGCACTC
1 CCATGCATCGATGCATC-A-GAATATTTTTCAAACATCGAATGCATTTCATGCATCGATGCACAA
*
475370 T
64 G
* *
475371 CCATGCATCGATGCACTCTGAATA-TTTTCAAAACATCGAATGCATTTGATGCATCGATGCACAA
1 CCATGCATCGATGCA-TCAGAATATTTTTC-AAACATCGAATGCATTTCATGCATCGATGCACAA
475435 G
64 G
**
475436 CCATGCATCGATGCATCAGGCTATTTTTCAAACATCGAATGCATTTCATGCATCGATGCACA
1 CCATGCATCGATGCATCAGAATATTTTTCAAACATCGAATGCATTTCATGCATCGATGCACA
475498 CTTGGTGCAC
Statistics
Matches: 108, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
63 6 0.06
64 52 0.48
65 50 0.46
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (64 bp):
CCATGCATCGATGCATCAGAATATTTTTCAAACATCGAATGCATTTCATGCATCGATGCACAAG
Found at i:475490 original size:64 final size:65
Alignment explanation
Indices: 475337--475497 Score: 218
Period size: 65 Copynumber: 2.5 Consensus size: 65
475327 GAATTAATTG
* * *** *
475337 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
* **
475402 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCA-TCAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATA-TTTTCA
475465 A
65 A
475466 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
475498 CTTGGTGCAC
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 37 0.44
65 48 0.56
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:475512 original size:64 final size:64
Alignment explanation
Indices: 475337--475517 Score: 220
Period size: 64 Copynumber: 2.8 Consensus size: 64
475327 GAATTAATTG
* * * *
475337 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAA
* ** **
475402 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTC-A
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAA
*** *
475466 AACATCGAATGCATTTCATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCA
475518 AGTGTTCCAA
Statistics
Matches: 99, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
64 51 0.52
65 48 0.48
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAA
Found at i:481303 original size:20 final size:21
Alignment explanation
Indices: 481274--481330 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
481264 TTTGCGCTTC
*
481274 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATATTGAA-A
*
481294 ATGCATCGATGCATCATTGAAT
1 ATGCATCGATGCAT-ATTGAAA
481316 ATGCATCGATGCATA
1 ATGCATCGATGCATA
481331 AGACCATGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 13 0.41
21 1 0.03
22 16 0.50
23 2 0.06
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (21 bp):
ATGCATCGATGCATATTGAAA
Found at i:482049 original size:21 final size:21
Alignment explanation
Indices: 482007--482050 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
481997 ACCCCGGGAG
*
482007 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
482028 CTAGTTCTTCTCGCGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
482049 CT
1 CT
482051 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.39, G:0.16, T:0.36
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:483114 original size:19 final size:19
Alignment explanation
Indices: 483090--483128 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
483080 TCGAATGCAT
483090 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
483109 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
483128 T
1 T
483129 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:483145 original size:65 final size:64
Alignment explanation
Indices: 483028--483236 Score: 219
Period size: 65 Copynumber: 3.2 Consensus size: 64
483018 ATTCAAAGGT
* ** *
483028 ATGCACCGATGCATC-AGTCCATGCATCGATGCATCGATGAAT-TAATT-GAACATCGAATGCAT
1 ATGCATCGATGCA-CAAG-CCATGCATCGATGCATC-A-GAATATTTTTCAAACATCGAATGCAT
*
483090 TCC
62 TTC
* *** *
483093 ATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATA-TTTTCAAAACATCGAATGCATTT
1 ATGCATCGATGCACAAGCCATGCATCGATGCA-TCAGAATATTTTTC-AAACATCGAATGCATTT
*
483157 G
64 C
**
483158 ATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTCAAACATCGAATGCATTTC
1 ATGCATCGATGCACAAGCCATGCATCGATGCATCAGAATATTTTTCAAACATCGAATGCATTTC
483222 ATGCATCGATGCACA
1 ATGCATCGATGCACA
483237 CTTGGTGCAC
Statistics
Matches: 122, Mismatches: 16, Indels: 13
0.81 0.11 0.09
Matches are distributed among these distances:
63 6 0.05
64 53 0.43
65 63 0.52
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.27
Consensus pattern (64 bp):
ATGCATCGATGCACAAGCCATGCATCGATGCATCAGAATATTTTTCAAACATCGAATGCATTTC
Found at i:483251 original size:64 final size:64
Alignment explanation
Indices: 483028--483256 Score: 223
Period size: 64 Copynumber: 3.5 Consensus size: 64
483018 ATTCAAAGGT
* * * *
483028 ATGCACCGATGCATCAGTCCATGCATCGATGCATCGATGAAT-TAATT--GAACATCGAATGCAT
1 ATGCATCGATGCA-CACTCCATGCATCGATGCATC-A-GAATAT-TTTCAAAACATCGAATGCAT
*
483090 TCC
62 TTC
* * * *
483093 ATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTTG
1 ATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAAAACATCGAATGCATTTC
** **
483158 ATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTC-AAACATCGAATGCATTTC
1 ATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAAAACATCGAATGCATTTC
*** *
483222 ATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 ATGCATCGATGCACACTCCATGCATCGATGCATCA
483257 AGTGTTCCAA
Statistics
Matches: 138, Mismatches: 21, Indels: 11
0.81 0.12 0.06
Matches are distributed among these distances:
63 6 0.04
64 69 0.50
65 63 0.46
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (64 bp):
ATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAAAACATCGAATGCATTTC
Found at i:484180 original size:41 final size:40
Alignment explanation
Indices: 484130--484305 Score: 124
Period size: 41 Copynumber: 4.2 Consensus size: 40
484120 TATATATATC
*
484130 GTGGCGTTTTTAGACAAACACCGCTAAAACCTAGTACTTTA
1 GTGGTGTTTTTA-ACAAACACCGCTAAAACCTAGTACTTTA
* * *
484171 GTGGTGTTTTTCAACAAACTCCGCTAAAACGTAATACTTTA
1 GTGGTGTTTTT-AACAAACACCGCTAAAACCTAGTACTTTA
* * ***
484212 ATGTTG-TTTTAAGCAAAAAACATTACTAAATA-CTCA-TACTTTA
1 GTGGTGTTTTTAA-C---AAACACCGCTAAA-ACCT-AGTACTTTA
* * * *
484255 ATGGTGTTTTCCAACAAATACCGCTAAAACGTAGTACTTTA
1 GTGGTGTTTT-TAACAAACACCGCTAAAACCTAGTACTTTA
*
484296 GTGGCGTTTT
1 GTGGTGTTTT
484306 AATTAAAAAA
Statistics
Matches: 104, Mismatches: 20, Indels: 22
0.71 0.14 0.15
Matches are distributed among these distances:
39 2 0.02
40 7 0.07
41 64 0.62
42 1 0.01
43 22 0.21
44 6 0.06
45 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (40 bp):
GTGGTGTTTTTAACAAACACCGCTAAAACCTAGTACTTTA
Found at i:484260 original size:84 final size:85
Alignment explanation
Indices: 484164--484350 Score: 227
Period size: 84 Copynumber: 2.2 Consensus size: 85
484154 TAAAACCTAG
* ** *
484164 TACTTTAGTGGTGTTTTTCAACAAACT-CCGCTAAAACGTAATACTTTAATGTTGTTTTAA-GCA
1 TACTTTAATGGTGTTTTTCAACAAA-TACCGCTAAAACGTAATACTTTAATGGCGTTTTAATGAA
* *
484227 AAAAAC-ATTACTAAATACTCA
65 AAAAACGACT-CTAAAGACTCA
* * * *
484248 TACTTTAATGGTGTTTTCCAACAAATACCGCTAAAACGTAGTACTTTAGTGGCGTTTTAATTAAA
1 TACTTTAATGGTGTTTTTCAACAAATACCGCTAAAACGTAATACTTTAATGGCGTTTTAATGAAA
*
484313 AAAACGCCTCTAAAGACTCA
66 AAAACGACTCTAAAGACTCA
*
484333 TACTTTATTGGTGTTTTT
1 TACTTTAATGGTGTTTTT
484351 TGAATAAACG
Statistics
Matches: 87, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
83 1 0.01
84 52 0.60
85 33 0.38
86 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.37
Consensus pattern (85 bp):
TACTTTAATGGTGTTTTTCAACAAATACCGCTAAAACGTAATACTTTAATGGCGTTTTAATGAAA
AAAACGACTCTAAAGACTCA
Found at i:489110 original size:20 final size:20
Alignment explanation
Indices: 489085--489123 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
489075 CACGCTGAAT
489085 GTTGAATGGAACCATTCAGC
1 GTTGAATGGAACCATTCAGC
**
489105 GTTGAATGGTTCCATTCAG
1 GTTGAATGGAACCATTCAG
489124 AGCCAAACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (20 bp):
GTTGAATGGAACCATTCAGC
Found at i:491148 original size:42 final size:41
Alignment explanation
Indices: 491083--491247 Score: 170
Period size: 43 Copynumber: 3.9 Consensus size: 41
491073 ATTAGCGGCA
* *
491083 TTTGTATCAAAAAACGCTACTATAGATCTGACCTTTTGCAGCA
1 TTTGT-TC-AAAAACGCCACTATAGATCTGACCTTTTGCAGCG
* * * *
491126 TTTCTTCTAAAAACGCCGCTATAGATCTTGATCTTTTGCGGCG
1 TTTGTTC-AAAAACGCCACTATAGATC-TGACCTTTTGCAGCG
* * *
491169 TTTGTTACAAAAATGCCTCTATAGATCTGACCTTTTG-TGACG
1 TTTGTT-CAAAAACGCCACTATAGATCTGACCTTTTGCAG-CG
* *
491211 TTTGTTAAAAAATGCCACTATAGATCTGACCTTTTGC
1 TTTGTTCAAAAACGCCACTATAGATCTGACCTTTTGC
491248 GGCGCTGGTA
Statistics
Matches: 104, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
41 29 0.28
42 36 0.35
43 38 0.37
44 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (41 bp):
TTTGTTCAAAAACGCCACTATAGATCTGACCTTTTGCAGCG
Found at i:491233 original size:41 final size:40
Alignment explanation
Indices: 491091--491246 Score: 159
Period size: 42 Copynumber: 3.8 Consensus size: 40
491081 CATTTGTATC
* * * *
491091 AAAAAACGCTACTATAGATCTGACCTTTTGCAGCATTTCTT
1 AAAAAACGCCACTATAGATCTGACCTTTTGGA-CGTTTGTT
* * * *
491132 CTAAAAACGCCGCTATAGATCTTGATCTTTTGCGGCGTTTGTT
1 -AAAAAACGCCACTATAGATC-TGACCTTTTG-GACGTTTGTT
* *
491175 ACAAAAATGCCTCTATAGATCTGACCTTTTGTGACGTTTGTT
1 A-AAAAACGCCACTATAGATCTGACCTTTTG-GACGTTTGTT
*
491217 AAAAAATGCCACTATAGATCTGACCTTTTG
1 AAAAAACGCCACTATAGATCTGACCTTTTG
491247 CGGCGCTGGT
Statistics
Matches: 96, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
41 28 0.29
42 36 0.38
43 32 0.33
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (40 bp):
AAAAAACGCCACTATAGATCTGACCTTTTGGACGTTTGTT
Found at i:494015 original size:28 final size:29
Alignment explanation
Indices: 493960--494021 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 29
493950 AGGTTAGCTC
493960 GATTAACAGTTAAATTTTTTTTAAACATT
1 GATTAACAGTTAAATTTTTTTTAAACATT
493989 GATTAACAGTTAAA-TTTTTTTAAACATT
1 GATTAACAGTTAAATTTTTTTTAAACATT
494017 GATTA
1 GATTA
494022 TCAGCTAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 19 0.58
29 14 0.42
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (29 bp):
GATTAACAGTTAAATTTTTTTTAAACATT
Found at i:494032 original size:27 final size:28
Alignment explanation
Indices: 493960--494029 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
493950 AGGTTAGCTC
*
493960 GATTAACAGTTAAATTTTTTTTAAACATT
1 GATTAACAGCTAAA-TTTTTTTAAACATT
*
493989 GATTAACAGTTAAATTTTTTTAAACATT
1 GATTAACAGCTAAATTTTTTTAAACATT
*
494017 GATTATCAGCTAA
1 GATTAACAGCTAA
494030 TTTGATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 25 0.64
29 14 0.36
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.44
Consensus pattern (28 bp):
GATTAACAGCTAAATTTTTTTAAACATT
Found at i:494039 original size:27 final size:28
Alignment explanation
Indices: 493960--494039 Score: 81
Period size: 28 Copynumber: 2.9 Consensus size: 28
493950 AGGTTAGCTC
* **
493960 GATTAACAGTTAAATTTTTTTTAAACATT
1 GATTAACAGCTAAA-TTTGATTAAACATT
* **
493989 GATTAACAGTTAAATTTTTTTAAACATT
1 GATTAACAGCTAAATTTGATTAAACATT
*
494017 GATTATCAGCT-AATTTGATTAAA
1 GATTAACAGCTAAATTTGATTAAA
494040 AATCAGTTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
27 10 0.21
28 23 0.49
29 14 0.30
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.45
Consensus pattern (28 bp):
GATTAACAGCTAAATTTGATTAAACATT
Found at i:520962 original size:64 final size:62
Alignment explanation
Indices: 520893--521071 Score: 191
Period size: 64 Copynumber: 2.8 Consensus size: 62
520883 TGGGACACTT
*
520893 AGTGCATCGGTGCACTAAGGATGCATCGATGCATAAAATGCATTCGATGTTTGAAAA-ATAGCCT
1 AGTGCATCGATGCA-T-AGGATGCATCGATGCATAAAATGCATTCGATGTTTGAAAATAT-GCC-
520957 G
62 G
* ** * *
520958 -GTGCATCGATGCATTGCTTGTACATCGATGCATCAAATGCATTCGATGTTTGAAAATATTCCG
1 AGTGCATCGATGCATAGGATG--CATCGATGCATAAAATGCATTCGATGTTTGAAAATATGCCG
* * *
521021 AGTGCATCGATGCATGGAGAGTGCATCGGTGCATGAAATGCATTCGATGTT
1 AGTGCATCGATGCATAG-GA-TGCATCGATGCATAAAATGCATTCGATGTT
521072 CAATTAAATC
Statistics
Matches: 97, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
62 3 0.03
63 2 0.02
64 88 0.91
65 2 0.02
66 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.29
Consensus pattern (62 bp):
AGTGCATCGATGCATAGGATGCATCGATGCATAAAATGCATTCGATGTTTGAAAATATGCCG
Found at i:526076 original size:22 final size:21
Alignment explanation
Indices: 526050--526096 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 21
526040 AAGGTCAAAA
*
526050 ATCAAATTGTTTGAAAATTG-AT
1 ATCAAATGGTTT-AAAA-TGAAT
526072 ATC-AATGGTTTAAAATGAAT
1 ATCAAATGGTTTAAAATGAAT
526092 ATCAA
1 ATCAA
526097 TTACGTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 2 0.09
20 9 0.41
21 8 0.36
22 3 0.14
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (21 bp):
ATCAAATGGTTTAAAATGAAT
Found at i:528215 original size:64 final size:64
Alignment explanation
Indices: 528147--528304 Score: 212
Period size: 64 Copynumber: 2.5 Consensus size: 64
528137 GCACTAAGGA
* ***
528147 TGCATCGATGCATAAAATGCATTCGATGTTTGAAAA-ATAGCCTG-GTGCATCGATGCATTGCTT
1 TGCATCGATGCATAAAATGCATTCGATGTTTGAAAATAT-GCC-GAGTGCATCGATGCATGGAGA
528210 G
64 G
* *
528211 TGCATCGATGCATCAAATGCATTCGATGTTTGAAAATATTCCGAGTGCATCGATGCATGGAGAG
1 TGCATCGATGCATAAAATGCATTCGATGTTTGAAAATATGCCGAGTGCATCGATGCATGGAGAG
* *
528275 TGCATCGGTGCATGAAATGCATTCGATGTT
1 TGCATCGATGCATAAAATGCATTCGATGTT
528305 CAATTAAATC
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
63 1 0.01
64 81 0.96
65 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (64 bp):
TGCATCGATGCATAAAATGCATTCGATGTTTGAAAATATGCCGAGTGCATCGATGCATGGAGAG
Found at i:528323 original size:64 final size:61
Alignment explanation
Indices: 528147--528334 Score: 180
Period size: 64 Copynumber: 2.9 Consensus size: 61
528137 GCACTAAGGA
* * * ***
528147 TGCATCGATGCATAAAATGCATTCGATGTTTGAAAAATAGCCTGGTGCATCGATGCATTGCTTG
1 TGCATCGATGCATAAAATGCATTCGATG-TTCAAAAAT--CATGGTGCATCGATGCATGGAGAG
* * *
528211 TGCATCGATGCATCAAATGCATTCGATGTTTGAAAATATTC-CGAGTGCATCGATGCATGGAGAG
1 TGCATCGATGCATAAAATGCATTCGATG-TTCAAAA-A-TCATG-GTGCATCGATGCATGGAGAG
* *
528275 TGCATCGGTGCATGAAATGCATTCGATGTTCAATTAAATCATAGGTGCATCGATGCATGG
1 TGCATCGATGCATAAAATGCATTCGATGTTCAA--AAATCAT-GGTGCATCGATGCATGG
528335 TTTGATGCAT
Statistics
Matches: 107, Mismatches: 10, Indels: 14
0.82 0.08 0.11
Matches are distributed among these distances:
63 7 0.07
64 95 0.89
65 4 0.04
66 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (61 bp):
TGCATCGATGCATAAAATGCATTCGATGTTCAAAAATCATGGTGCATCGATGCATGGAGAG
Found at i:529572 original size:27 final size:27
Alignment explanation
Indices: 529534--529618 Score: 143
Period size: 27 Copynumber: 3.1 Consensus size: 27
529524 ATAATAAAAT
* *
529534 AATATATCATCGATGAATTTTTATTTA
1 AATATATTATCGATGAATTTTTATATA
*
529561 AATATATTATCGATGAATTTTTATCTA
1 AATATATTATCGATGAATTTTTATATA
529588 AATATATTATCGATGAATTTTTATATA
1 AATATATTATCGATGAATTTTTATATA
529615 AATA
1 AATA
529619 ATTTTTATTT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.47
Consensus pattern (27 bp):
AATATATTATCGATGAATTTTTATATA
Found at i:529920 original size:2 final size:2
Alignment explanation
Indices: 529913--529941 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
529903 TTATAAAAAT
529913 TA TA 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 TA TA T
529942 GGAATTGGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:531137 original size:38 final size:36
Alignment explanation
Indices: 531061--531137 Score: 100
Period size: 37 Copynumber: 2.1 Consensus size: 36
531051 TTTTTATATT
* *
531061 TTTAATTTTATAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTATAAAAAAAATATATAAATATTATCAA
* *
531097 TTTAATTTTTTAAAGAAAAATATATAAATATTTTACAA
1 TTTAATTTTATAAA-AAAAATATATAAATATTAT-CAA
531135 TTT
1 TTT
531138 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 17 0.49
38 5 0.14
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (36 bp):
TTTAATTTTATAAAAAAAATATATAAATATTATCAA
Found at i:533974 original size:21 final size:22
Alignment explanation
Indices: 533950--533996 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
533940 AGTCGAGTTA
**
533950 TAAAATA-TAATTTTAATAACT
1 TAAAATAGTAATTCAAATAACT
533971 T-AAATAGTAATTCAAATAACT
1 TAAAATAGTAATTCAAATAACT
*
533992 CAAAA
1 TAAAA
533997 AAATTAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 5 0.24
21 13 0.62
22 3 0.14
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (22 bp):
TAAAATAGTAATTCAAATAACT
Found at i:535764 original size:40 final size:39
Alignment explanation
Indices: 535671--535769 Score: 110
Period size: 40 Copynumber: 2.5 Consensus size: 39
535661 TTCGTTCGAG
*
535671 GGAGATCTAGGCGTCTTCAATACAATTGCATGCAAAATC
1 GGAGATCTAGGCGTCTTCAACACAATTGCATGCAAAATC
* ** * *
535710 AGATCTCTAAGCGTCTTCAACACAATTTGCATTCAAACAT-
1 GGAGATCTAGGCGTCTTCAACACAA-TTGCATGCAAA-ATC
*
535750 GGAGGTCTAGGCGTCTTCAA
1 GGAGATCTAGGCGTCTTCAA
535770 ATTATTTTCC
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
39 20 0.42
40 26 0.54
41 2 0.04
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.27
Consensus pattern (39 bp):
GGAGATCTAGGCGTCTTCAACACAATTGCATGCAAAATC
Found at i:536183 original size:20 final size:20
Alignment explanation
Indices: 536158--536196 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
536148 TGCACGCAAA
*
536158 AGGGAATTCACGTGGTGAGC
1 AGGGAATTCACGGGGTGAGC
536178 AGGGAATTCACGGGGTGAG
1 AGGGAATTCACGGGGTGAG
536197 TTGATAATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.13, G:0.44, T:0.18
Consensus pattern (20 bp):
AGGGAATTCACGGGGTGAGC
Found at i:536303 original size:33 final size:33
Alignment explanation
Indices: 536251--536316 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
536241 CGTCTTCTTC
* * * *
536251 ATTTTGGGTGGATTACTCGGCGTTTTTTTCACA
1 ATTTGGGGTGGAATACTCGGCATTTTCTTCACA
*
536284 ATTTGGGGTGGAATGCTCGGCATTTTCTTCACA
1 ATTTGGGGTGGAATACTCGGCATTTTCTTCACA
536317 TGGGAGGGGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.41
Consensus pattern (33 bp):
ATTTGGGGTGGAATACTCGGCATTTTCTTCACA
Found at i:536570 original size:13 final size:13
Alignment explanation
Indices: 536552--536577 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
536542 TTAAGGTTTA
536552 GTGATTATATGTT
1 GTGATTATATGTT
536565 GTGATTATATGTT
1 GTGATTATATGTT
536578 ATTACATTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (13 bp):
GTGATTATATGTT
Found at i:538619 original size:42 final size:42
Alignment explanation
Indices: 538570--539190 Score: 234
Period size: 37 Copynumber: 14.8 Consensus size: 42
538560 ATATATTTAA
*
538570 TATTATTATATCATTAAA-TATAAATCATTAAAGTCAAGTAAT
1 TATTATTAAATCATTAAAGT-TAAATCATTAAAGTCAAGTAAT
*
538612 TATTATTAAATCATTAAAGTTAAATCATTAAAGTTAAGTAAT
1 TATTATTAAATCATTAAAGTTAAATCATTAAAGTCAAGTAAT
* * * * *
538654 TATTATTAAATCATTAAAGTTAAATAATTATTA-TTAAATCAT
1 TATTATTAAATCATTAAAGTTAAATCATTA-AAGTCAAGTAAT
* * *
538696 TA-AAGTTAAATCATTAAAG-TAATTATTATTAAA-TC-ATTAA-
1 TATTA-TTAAATCATTAAAGTTAA--ATCATTAAAGTCAAGTAAT
* * * * *
538736 -A--ATTAAATCATTAAAGTTAAATAATTATTA-TTAAATCAT
1 TATTATTAAATCATTAAAGTTAAATCATTA-AAGTCAAGTAAT
* * *
538775 TA-AAGTTAAATCATTAAAG-TAATTATTATTAAA-TC-ATTAA-
1 TATTA-TTAAATCATTAAAGTTAA--ATCATTAAAGTCAAGTAAT
* *
538815 -A--ATTAAATCATTAAAG-TAATTATTATTAAA-TC-ATTAAAGT
1 TATTATTAAATCATTAAAGTTAA--ATCATTAAAGTCAAGT-AA-T
* * * * *
538855 TAAATCATTAAAGTAATTATTA-TTAAATTATTAAAATTAAATCATTAAAGTAAT
1 T--ATTATTAAA-TCATTA-AAGTTAAATCATT---A--AAGTC----AAGTAAT
* *
538909 TATTATTAAATCATTAAAGTTAAGTAATTATTATTAAATCATTAAAGTAAT
1 TATTATTAAATCATTAAAGTT-A--AATCATTA--AAGTC----AAGTAAT
*
538960 TATTATTAAATCATTAAAATTAAATCATT--A---AAGTAAT
1 TATTATTAAATCATTAAAGTTAAATCATTAAAGTCAAGTAAT
538997 TATTATTAAATCATT-AAGTTAAATCATT--A---AAGTAAT
1 TATTATTAAATCATTAAAGTTAAATCATTAAAGTCAAGTAAT
* *
539033 TATTA-TAAATTATTAAAATTAAATCATT--A---AAGTAAT
1 TATTATTAAATCATTAAAGTTAAATCATTAAAGTCAAGTAAT
* *
539069 TATTATTAAATCATTAAAGTTAAGTAATTATTATTAAATCATTAAAGTAAT
1 TATTATTAAATCATTAAAGTT-A--AATCATTA--AAGTC----AAGTAAT
*
539120 TATTATTAAATCATTAAAATTAAATCATT--A---AAGTAAT
1 TATTATTAAATCATTAAAGTTAAATCATTAAAGTCAAGTAAT
539157 TATTATTAAATCATTAAAGTTAAATCATTAAAGT
1 TATTATTAAATCATTAAAGTTAAATCATTAAAGT
539191 AATTGAAATA
Statistics
Matches: 480, Mismatches: 39, Indels: 121
0.75 0.06 0.19
Matches are distributed among these distances:
35 8 0.02
36 56 0.12
37 119 0.25
38 11 0.02
39 3 0.01
40 7 0.01
41 14 0.03
42 108 0.22
43 15 0.03
44 3 0.01
45 12 0.03
46 5 0.01
47 4 0.01
48 13 0.03
50 5 0.01
51 75 0.16
52 9 0.02
54 9 0.02
55 2 0.00
56 2 0.00
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (42 bp):
TATTATTAAATCATTAAAGTTAAATCATTAAAGTCAAGTAAT
Found at i:538726 original size:37 final size:37
Alignment explanation
Indices: 538673--539194 Score: 557
Period size: 37 Copynumber: 14.3 Consensus size: 37
538663 ATCATTAAAG
538673 TTAAA-TAATTATTATTAAATCATTAAAGTTAAATCA
1 TTAAAGTAATTATTATTAAATCATTAAAGTTAAATCA
*
538709 TTAAAGTAATTATTATTAAATCATTAAAATTAAATCA
1 TTAAAGTAATTATTATTAAATCATTAAAGTTAAATCA
538746 TTAAAGTTAAATAATTATTATTAAATCATTAAAGTTAAATCA
1 TTAAAG-----TAATTATTATTAAATCATTAAAGTTAAATCA
*
538788 TTAAAGTAATTATTATTAAATCATTAAAATTAAATCA
1 TTAAAGTAATTATTATTAAATCATTAAAGTTAAATCA
538825 TTAAAGTAATTATTATTAAATCATTAAAGTTAAATCA
1 TTAAAGTAATTATTATTAAATCATTAAAGTTAAATCA
* *
538862 TTAAAGTAATTATTATTAAATTATTAAAATTAAATCA
1 TTAAAGTAATTATTATTAAATCATTAAAGTTAAATCA
538899 TTAAAGTAATTATTATTAAATCATTAAAG--------
1 TTAAAGTAATTATTATTAAATCATTAAAGTTAAATCA
*
538928 TT-AAGTAATTATTATTAAATCATTAAAG-TAATTATTA
1 TTAAAGTAATTATTATTAAATCATTAAAGTTAA--ATCA
* ** *
538965 TTAAA-TCATTAAAATTAAATCATTAAAG-TAATTATTA
1 TTAAAGTAATTATTATTAAATCATTAAAGTTAA--ATCA
* *
539002 TTAAA-TCATTA--AGTTAAATCATTAAAG-T-AATTA
1 TTAAAGTAATTATTA-TTAAATCATTAAAGTTAAATCA
* * ** *
539035 TTATAAATTATTAAAATTAAATCATTAAAG-TAATTATTA
1 TTA-AAGTAATTATTATTAAATCATTAAAGTTAA--ATCA
* * * * *
539074 TTAAA-TCATTA-AAGTTAAGTAATTATTA-TTAAATCA
1 TTAAAGTAATTATTA-TTAAATCATTA-AAGTTAAATCA
*
539110 TTAAAGTAATTATTATTAAATCATTAAAATTAAATCA
1 TTAAAGTAATTATTATTAAATCATTAAAGTTAAATCA
539147 TTAAAGTAATTATTATTAAATCATTAAAGTTAAATCA
1 TTAAAGTAATTATTATTAAATCATTAAAGTTAAATCA
539184 TTAAAGTAATT
1 TTAAAGTAATT
539195 GAAATATAAT
Statistics
Matches: 433, Mismatches: 23, Indels: 59
0.84 0.04 0.11
Matches are distributed among these distances:
28 26 0.06
29 2 0.00
33 7 0.02
34 2 0.00
35 7 0.02
36 46 0.11
37 291 0.67
38 9 0.02
39 7 0.02
42 36 0.08
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.42
Consensus pattern (37 bp):
TTAAAGTAATTATTATTAAATCATTAAAGTTAAATCA
Done.