Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 19 of 438
Found at i:5205478 original size:12 final size:13
Alignment explanation
Indices: 5205464--5205528 Score: 53
Period size: 12 Copynumber: 5.0 Consensus size: 13
5205454 GATAATTTTT
5205464 TTATTATTATAT-
1 TTATTATTATATA
* *
5205476 TTACTATTATTTA
1 TTATTATTATATA
* *
5205489 TTGTTATTGGTATTA
1 TTATTATT-ATA-TA
*
5205504 TTATTATTATATG
1 TTATTATTATATA
5205517 TT-TTATTATATA
1 TTATTATTATATA
5205529 CGTATGAATA
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
12 19 0.47
13 9 0.22
14 3 0.08
15 9 0.22
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.63
Consensus pattern (13 bp):
TTATTATTATATA
Found at i:5205630 original size:27 final size:26
Alignment explanation
Indices: 5205561--5205626 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 26
5205551 CATTTTACAT
*
5205561 TATTATATTTATTATTTATTTCTAACA
1 TATTATATTTATT-TTTATTTATAACA
*
5205588 TATTATTATTTTATTTTT-TTTATATCA
1 TATTA-TA-TTTATTTTTATTTATAACA
5205615 TCATTATATTTA
1 T-ATTATATTTA
5205627 ATTTGTGCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
26 4 0.12
27 15 0.44
28 9 0.26
29 6 0.18
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (26 bp):
TATTATATTTATTTTTATTTATAACA
Found at i:5206027 original size:21 final size:22
Alignment explanation
Indices: 5205991--5206031 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
5205981 ATATATTTTC
5205991 TTTTATATATTATGTATATGCA
1 TTTTATATATTATGTATATGCA
*
5206013 TTTTTTATA-TATGTATATG
1 TTTTATATATTATGTATATG
5206032 TTTATACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.59
Consensus pattern (22 bp):
TTTTATATATTATGTATATGCA
Found at i:5206251 original size:15 final size:17
Alignment explanation
Indices: 5206231--5206263 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5206221 CCGTCACCTT
5206231 ACATAT-TAT-TATATA
1 ACATATGTATATATATA
5206246 ACATATGTATATATATA
1 ACATATGTATATATATA
5206263 A
1 A
5206264 TCCATTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 3 0.19
17 7 0.44
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (17 bp):
ACATATGTATATATATA
Found at i:5211530 original size:13 final size:14
Alignment explanation
Indices: 5211514--5211549 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
5211504 CAATCTCATA
5211514 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
5211527 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
5211540 TCTC-ATTTCA
1 TCTCAATTTCA
5211550 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:5211539 original size:18 final size:19
Alignment explanation
Indices: 5211501--5211541 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
5211491 TGGTTCATGT
5211501 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
5211520 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
5211538 TTTC
1 TTTC
5211542 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:5211731 original size:39 final size:38
Alignment explanation
Indices: 5211664--5211798 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
5211654 ACCAATATGG
* * *
5211664 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
5211703 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
5211741 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
5211782 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
5211799 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:5212064 original size:18 final size:19
Alignment explanation
Indices: 5212038--5212076 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
5212028 TTTCAATTCA
5212038 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
5212057 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
5212075 AT
1 AT
5212077 CTATATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:5212074 original size:2 final size:2
Alignment explanation
Indices: 5212069--5212099 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5212059 TCAATATTCA
*
5212069 AT AT AT AT CT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5212100 CGCCAATTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5213364 original size:5 final size:5
Alignment explanation
Indices: 5213354--5213406 Score: 61
Period size: 5 Copynumber: 10.0 Consensus size: 5
5213344 TTACTTATTT
* *
5213354 ATATA ATATAA TATATA ATATA ATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
5213402 ATATA
1 ATATA
5213407 TATTTTAACA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 30 0.73
6 7 0.17
7 4 0.10
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:5213370 original size:12 final size:12
Alignment explanation
Indices: 5213353--5213408 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
5213343 TTTACTTATT
5213353 TATATAATATAA
1 TATATAATATAA
5213365 TATATAATATAATA
1 TATATAATAT-A-A
5213379 TACTATAATATAA
1 TA-TATAATATAA
*
5213392 TA-ATAATTTAA
1 TATATAATATAA
5213403 TATATA
1 TATATA
5213409 TTTTAACACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 13 0.33
13 4 0.10
14 4 0.10
15 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Found at i:5221258 original size:73 final size:73
Alignment explanation
Indices: 5221178--5221326 Score: 217
Period size: 73 Copynumber: 2.0 Consensus size: 73
5221168 TTTATTTCTG
* * *
5221178 TTTCAAAAATCAACTCGTATGGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGCATTTTCAA
1 TTTCAAAAATCAACTCATATGGCGAGAGGTAAGTTGAGCCTCAGGACACGCTGAGGCATGTTCAA
5221243 TTTTTGTT
66 TTTTTGTT
* * * * * *
5221251 TTTCAAAAATCGACTCATATTGTGAGAGGTAAGTTGAGCCTCAGGGCACGCTGAGGTATGTTCAG
1 TTTCAAAAATCAACTCATATGGCGAGAGGTAAGTTGAGCCTCAGGACACGCTGAGGCATGTTCAA
5221316 TTTTTGTT
66 TTTTTGTT
5221324 TTT
1 TTT
5221327 TAATTTATGT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
73 67 1.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (73 bp):
TTTCAAAAATCAACTCATATGGCGAGAGGTAAGTTGAGCCTCAGGACACGCTGAGGCATGTTCAA
TTTTTGTT
Found at i:5221449 original size:74 final size:74
Alignment explanation
Indices: 5221342--5221723 Score: 471
Period size: 73 Copynumber: 5.0 Consensus size: 74
5221332 TATGTTTCAA
*
5221342 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
5221407 TTGTTTTTC
66 TTGTTTTTC
* * **
5221416 AAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATGTTCTGTTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
5221481 TTGTTTTTTAATTTATGTTTC
66 TTG----------T-T-TTTC
* *
5221502 AAAAAATCAACTCATATCGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
5221567 TTGTTTTTC
66 TTGTTTTTC
* * * *
5221576 -AAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAAATT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
* * *
5221640 CTATTTGTC
66 TTGTTTTTC
* * * *
5221649 -AAAAATCAACTCATATTGCGAGAAGTGAGTTGTGCCTCAGGGCACGCTGAGGAATTTTCAATTC
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
*
5221713 TTGCTTTTC
66 TTGTTTTTC
5221722 AA
1 AA
5221724 TTTCTGCTTT
Statistics
Matches: 263, Mismatches: 32, Indels: 26
0.82 0.10 0.08
Matches are distributed among these distances:
73 125 0.48
74 68 0.26
75 1 0.00
76 1 0.00
84 1 0.00
85 1 0.00
86 66 0.25
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.33
Consensus pattern (74 bp):
AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
TTGTTTTTC
Found at i:5221491 original size:162 final size:159
Alignment explanation
Indices: 5221166--5221866 Score: 790
Period size: 162 Copynumber: 4.4 Consensus size: 159
5221156 TATTCTGATA
* * *
5221166 TTTTT-ATTTCTGTTTC-AAAAATCAACTCGTATGGCGAGAGGTGAGTTGAGCCTCAGGACACGC
1 TTTTTAATTTATGTTTCAAAAAATCAACTCATATCGCGAGAGGTGAGTTGAGCCTCAGGACACGC
* * *
5221229 TGAGGCATTTTCAATTTTTGTTTTTCAAAAATCGACTCATATTGTGAGAGGTAAGTTGAGCCTCA
66 TGAGGTATTTTCAATTTTTGTTTTTCAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCA
5221294 GGGCACGCTGAGGTATGTTCAGTTTTTGT
131 GGGCACGCTGAGGTATGTTCAGTTTTTGT
*
5221323 TTTTTAATTTATGTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
1 TTTTTAATTTATGTTTC--AAAAAATCAACTCATATCGCGAGAGGTGAGTTGAGCCTCAGGACAC
5221388 GCTGAGGTATTTTCAATTTTTGTTTTTCAAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCC
64 GCTGAGGTATTTTCAATTTTTGTTTTTC-AAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCC
*
5221453 TCAGGGCACGCTGAGGTATGTTCTGTTTTTGT
128 TCAGGGCACGCTGAGGTATGTTCAGTTTTTGT
* *
5221485 TTTTTAATTTATGTTTCAAAAAATCAACTCATATCGCGAGAAGTGAGTTGAGCCTCAGGGCACGC
1 TTTTTAATTTATGTTTCAAAAAATCAACTCATATCGCGAGAGGTGAGTTGAGCCTCAGGACACGC
5221550 TGAGGTATTTTCAATTTTTGTTTTTCAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCA
66 TGAGGTATTTTCAATTTTTGTTTTTCAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCA
* *
5221615 GGACACGCTGAGGTAAT-TTCA-------A
131 GGGCACGCTGAGGT-ATGTTCAGTTTTTGT
* * * * * *
5221637 ATTCT-A-TT-TG--TC-AAAAATCAACTCATATTGCGAGAAGTGAGTTGTGCCTCAGGGCACGC
1 TTTTTAATTTATGTTTCAAAAAATCAACTCATATCGCGAGAGGTGAGTTGAGCCTCAGGACACGC
* * *
5221696 TGAGGAATTTTCAATTCTTGCTTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGA
66 TGAGG-----T--A-------TTTTCAATTTTTGTTTTTC--AAAAATCGACTCATATTGCGAGA
* * * *
5221761 GGTGAGTTGAGCCTC-GGCTCATATGCTGAGGTATTTTCAGTTTCTGTT
115 GGTGAGTTGAGCCTCAGG-GC--ACGCTGAGGTATGTTCAGTTTTTG-T
* *
5221809 TTTTTCAATTTATATTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
1 TTTTT-AA-TT-TATGTTTCAAAAAATCAACTCATATCGCGAGAGGTGAGTTGAGCCTC
5221867 GGGTCACATG
Statistics
Matches: 474, Mismatches: 28, Indels: 61
0.84 0.05 0.11
Matches are distributed among these distances:
146 50 0.11
147 2 0.00
149 2 0.00
150 2 0.00
151 2 0.00
152 3 0.01
153 1 0.00
157 5 0.01
158 10 0.02
159 55 0.12
160 90 0.19
161 72 0.15
162 120 0.25
163 2 0.00
164 13 0.03
172 3 0.01
174 1 0.00
176 1 0.00
177 1 0.00
178 1 0.00
180 38 0.08
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.36
Consensus pattern (159 bp):
TTTTTAATTTATGTTTCAAAAAATCAACTCATATCGCGAGAGGTGAGTTGAGCCTCAGGACACGC
TGAGGTATTTTCAATTTTTGTTTTTCAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCA
GGGCACGCTGAGGTATGTTCAGTTTTTGT
Found at i:5221557 original size:86 final size:86
Alignment explanation
Indices: 5221412--5221574 Score: 272
Period size: 86 Copynumber: 1.9 Consensus size: 86
5221402 AATTTTTGTT
* * * *
5221412 TTTCAAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATGTTCT
1 TTTCAAAAAATCAACTCATATCGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATGTTCA
*
5221477 GTTTTTGTTTTTTAATTTATG
66 ATTTTTGTTTTTTAATTTATG
*
5221498 TTTCAAAAAATCAACTCATATCGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCA
1 TTTCAAAAAATCAACTCATATCGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATGTTCA
5221563 ATTTTTGTTTTT
66 ATTTTTGTTTTT
5221575 CAAAAATCGA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
86 71 1.00
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (86 bp):
TTTCAAAAAATCAACTCATATCGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATGTTCA
ATTTTTGTTTTTTAATTTATG
Found at i:5221722 original size:14 final size:14
Alignment explanation
Indices: 5221703--5221737 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
5221693 CGCTGAGGAA
5221703 TTTTCAA-TTCTTGC
1 TTTTCAATTTC-TGC
5221717 TTTTCAATTTCTGC
1 TTTTCAATTTCTGC
5221731 TTTTCAA
1 TTTTCAA
5221738 AAAAATCAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 17 0.85
15 3 0.15
ACGTcount: A:0.17, C:0.20, G:0.06, T:0.57
Consensus pattern (14 bp):
TTTTCAATTTCTGC
Found at i:5221849 original size:91 final size:87
Alignment explanation
Indices: 5221631--5221888 Score: 295
Period size: 91 Copynumber: 2.9 Consensus size: 87
5221621 GCTGAGGTAA
* * * * * *
5221631 TTTCAAATTCTATTTGTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGTGCCTCAGGGC-ACG
1 TTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGTCAATG
*
5221695 CTGAGGAATTTTCAATTCTTGCT
65 CTGAGGTATTTTCAATTCTTGCT
**
5221718 TTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCAT
1 TTTCAATTTCTATTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG-TCA-
* **
5221783 ATGCTGAGGTATTTTCAGTTTCTGTTTT
62 ATGCTGAGGTATTTTCA-ATTCT-TGCT
*
5221811 TTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACAT
1 TTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGTCA-AT
5221876 G-TCGAGGTATTTT
64 GCT-GAGGTATTTT
5221889 TAAAATCTGC
Statistics
Matches: 146, Mismatches: 16, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
87 14 0.10
88 2 0.01
89 37 0.25
90 1 0.01
91 69 0.47
92 6 0.04
93 17 0.12
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (87 bp):
TTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTCAATGC
TGAGGTATTTTCAATTCTTGCT
Found at i:5223777 original size:3 final size:3
Alignment explanation
Indices: 5223741--5223765 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5223731 ATTTTGATAT
5223741 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
5223766 ATGTTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5223884 original size:27 final size:26
Alignment explanation
Indices: 5223815--5223880 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 26
5223805 TATTTTACAT
*
5223815 TATTATATTTATTATTTATTTCTAACA
1 TATTATATTTATT-TTTATTTATAACA
*
5223842 TATTATTATTTTATTTTT-TTTATATCA
1 TATTA-TA-TTTATTTTTATTTATAACA
5223869 TCATTATATTTA
1 T-ATTATATTTA
5223881 ATTTGTGCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
26 4 0.12
27 15 0.44
28 9 0.26
29 6 0.18
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (26 bp):
TATTATATTTATTTTTATTTATAACA
Found at i:5224505 original size:15 final size:17
Alignment explanation
Indices: 5224485--5224516 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
5224475 CCGTCTCCTT
5224485 ACATAT-TAT-TATATA
1 ACATATGTATATATATA
5224500 ACATATGTATATATATA
1 ACATATGTATATATATA
5224517 TAATCCATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 3 0.20
17 6 0.40
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (17 bp):
ACATATGTATATATATA
Found at i:5225984 original size:19 final size:20
Alignment explanation
Indices: 5225944--5225992 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
5225934 ATAATTAATT
* *
5225944 AATTAATTAAAATTTTATAA
1 AATTAATAAAAATATTATAA
5225964 AATTAATAAAAATATTA-AA
1 AATTAATAAAAATATTATAA
5225983 AATTAATAAA
1 AATTAATAAA
5225993 TAGATTCAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AATTAATAAAAATATTATAA
Found at i:5227578 original size:45 final size:45
Alignment explanation
Indices: 5227523--5228008 Score: 476
Period size: 45 Copynumber: 10.8 Consensus size: 45
5227513 AACTGGTGGC
* * * * * * *
5227523 TTCTTCGGAGGCTGATAAACTGGTGGTTTGGGTTCTGGTTTTTCT
1 TTCTTTGGAGGTTCATAAACTGGTGGCTTAGGTTCAGGCTTTTCT
* * * * * *
5227568 TTCTTTGGAGGTGCATAAACTGGTGACTTTGGCTCGGGCTTTTCC
1 TTCTTTGGAGGTTCATAAACTGGTGGCTTAGGTTCAGGCTTTTCT
* * * *
5227613 TTCTTTGGCGGTTCATACACTGGTGGCTTAGGTTCAAGCTTCTCT
1 TTCTTTGGAGGTTCATAAACTGGTGGCTTAGGTTCAGGCTTTTCT
* * *
5227658 TTCTTTGGTGGTGT-ATAAACTGGTGGCTTAGGCTCAGGCTTTTCC
1 TTCTTTGGAGGT-TCATAAACTGGTGGCTTAGGTTCAGGCTTTTCT
* * * *
5227703 TTCTTTGGTGGTTCATACACTGGTGGCTTGGGTTCAGGCTTCTCT
1 TTCTTTGGAGGTTCATAAACTGGTGGCTTAGGTTCAGGCTTTTCT
* * *
5227748 TTCTTTGGTGGTGT-ATAAACTGGTGGCTTAGGCTCAGGCTTTTCC
1 TTCTTTGGAGGT-TCATAAACTGGTGGCTTAGGTTCAGGCTTTTCT
* * * * *
5227793 TTCTTTGGTGGTTCATATACTGGTGGTTTGGGTTCAGGCTTCTCT
1 TTCTTTGGAGGTTCATAAACTGGTGGCTTAGGTTCAGGCTTTTCT
* * *
5227838 TTCTTTGGAGGTGT-ATAAACTGGTGGCTTTGGTTCGGGCTTTTCC
1 TTCTTTGGAGGT-TCATAAACTGGTGGCTTAGGTTCAGGCTTTTCT
* * * *
5227883 TTCTTTGGTGGTTCATACA-TCGGTGGCTTGGGTTCAGGTTTTTCT
1 TTCTTTGGAGGTTCATAAACT-GGTGGCTTAGGTTCAGGCTTTTCT
* * * * *
5227928 TTCTTTGGAGGTTCATAGACAGGTGGCTTATGCTCAGGTTTTTCT
1 TTCTTTGGAGGTTCATAAACTGGTGGCTTAGGTTCAGGCTTTTCT
* * * *
5227973 TTCTTTAGAGGTTCATAGACAGGTGGCTTATGTTCA
1 TTCTTTGGAGGTTCATAAACTGGTGGCTTAGGTTCA
5228009 TAAGGTGGGG
Statistics
Matches: 369, Mismatches: 64, Indels: 16
0.82 0.14 0.04
Matches are distributed among these distances:
44 4 0.01
45 362 0.98
46 3 0.01
ACGTcount: A:0.13, C:0.17, G:0.28, T:0.42
Consensus pattern (45 bp):
TTCTTTGGAGGTTCATAAACTGGTGGCTTAGGTTCAGGCTTTTCT
Found at i:5227659 original size:90 final size:90
Alignment explanation
Indices: 5227541--5228001 Score: 622
Period size: 90 Copynumber: 5.1 Consensus size: 90
5227531 AGGCTGATAA
* * * * * * *
5227541 ACTGGTGGTTTGGGTTCTGGTTTTTCTTTCTTTGGAGGTGCATAAACTGGTGACTTTGGCTCGGG
1 ACTGGTGGCTTGGGTTCAGGCTTCTCTTTCTTTGGAGGTGTATAAACTGGTGGCTTTGGCTCAGG
*
5227606 CTTTTCCTTCTTTGGCGGTTCATAC
66 CTTTTCCTTCTTTGGTGGTTCATAC
* * * *
5227631 ACTGGTGGCTTAGGTTCAAGCTTCTCTTTCTTTGGTGGTGTATAAACTGGTGGCTTAGGCTCAGG
1 ACTGGTGGCTTGGGTTCAGGCTTCTCTTTCTTTGGAGGTGTATAAACTGGTGGCTTTGGCTCAGG
5227696 CTTTTCCTTCTTTGGTGGTTCATAC
66 CTTTTCCTTCTTTGGTGGTTCATAC
* *
5227721 ACTGGTGGCTTGGGTTCAGGCTTCTCTTTCTTTGGTGGTGTATAAACTGGTGGCTTAGGCTCAGG
1 ACTGGTGGCTTGGGTTCAGGCTTCTCTTTCTTTGGAGGTGTATAAACTGGTGGCTTTGGCTCAGG
*
5227786 CTTTTCCTTCTTTGGTGGTTCATAT
66 CTTTTCCTTCTTTGGTGGTTCATAC
* * *
5227811 ACTGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTGGAGGTGTATAAACTGGTGGCTTTGGTTCGGG
1 ACTGGTGGCTTGGGTTCAGGCTTCTCTTTCTTTGGAGGTGTATAAACTGGTGGCTTTGGCTCAGG
5227876 CTTTTCCTTCTTTGGTGGTTCATAC
66 CTTTTCCTTCTTTGGTGGTTCATAC
* * * *
5227901 A-TCGGTGGCTTGGGTTCAGGTTTTTCTTTCTTTGGAGGT-TCATAGACAGGTGGCTTAT-GCTC
1 ACT-GGTGGCTTGGGTTCAGGCTTCTCTTTCTTTGGAGGTGT-ATAAACTGGTGGCTT-TGGCTC
* * * * *
5227963 AGGTTTTTCTTTCTTTAGAGGTTCATAG
63 AGGCTTTTCCTTCTTTGGTGGTTCATAC
*
5227991 ACAGGTGGCTT
1 ACTGGTGGCTT
5228002 ATGTTCATAA
Statistics
Matches: 333, Mismatches: 34, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
89 2 0.01
90 330 0.99
91 1 0.00
ACGTcount: A:0.12, C:0.17, G:0.29, T:0.42
Consensus pattern (90 bp):
ACTGGTGGCTTGGGTTCAGGCTTCTCTTTCTTTGGAGGTGTATAAACTGGTGGCTTTGGCTCAGG
CTTTTCCTTCTTTGGTGGTTCATAC
Found at i:5237790 original size:64 final size:64
Alignment explanation
Indices: 5237713--5237832 Score: 204
Period size: 64 Copynumber: 1.9 Consensus size: 64
5237703 AACACATCTA
* *
5237713 GTTAGAAGCATTTGATTTATTTCGATCATAGCATCCTAATTATTTGACATAAGCATCACATATG
1 GTTAGAAGAATTTGATTTATTTCAATCATAGCATCCTAATTATTTGACATAAGCATCACATATG
* *
5237777 GTTAGGAGAATTTGATTTATTTCAATCATAGCATCCTAATTATTTGGCATAAGCAT
1 GTTAGAAGAATTTGATTTATTTCAATCATAGCATCCTAATTATTTGACATAAGCAT
5237833 AGATACATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 52 1.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (64 bp):
GTTAGAAGAATTTGATTTATTTCAATCATAGCATCCTAATTATTTGACATAAGCATCACATATG
Found at i:5238132 original size:131 final size:129
Alignment explanation
Indices: 5237896--5238284 Score: 476
Period size: 130 Copynumber: 3.0 Consensus size: 129
5237886 ATCGGTGAAT
* * *
5237896 TTACAGATCTTGTCTCCTTGAAGTCAGTGGAACAGATCGAAAATGGTGAATCTTGTCTCTCTGAA
1 TTACAGATCTTGTCTCCCTGAAGTCAGTGGAACAGATCGAAGACGGTGAATCTTGTCTCTCT-AA
** * * * *
5237961 GTTGCAGTGGAGTAGATTTAAGCCACTATCCTATCTCCCTAAGTAATAGTGGAGTAGGCTGAAGA
65 GCAGTAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGTAGTAGTGGAGTAGGCTGAAGA
*
5238026 TTACAGATCTTGTCTCCCTGAAGTTGCAGTGGAACAGATCGAAGACGGTGAATCTTATCTCTCTA
1 TTACAGATCTTGTCTCCCTGAAG-T-CAGTGGAACAGATCGAAGACGGTGAATCTTGTCTCTCTA
* * * *
5238091 AACAGTAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAGGTAGTAGTAGAGTGGGCTGAAG
64 AGCAGTAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGTAGTAGTGGAGTAGGCTGAAG
5238156 A
129 A
* * * ** * *
5238157 TTAGAGATCTTATCTCCC-CAAG-CAATAGTGGAGTAGATCGAAGACGGCGAATCTTGTCTCCCT
1 TTACAGATCTTGTCTCCCTGAAGTC---AGTGGAACAGATCGAAGACGGTGAATCTTGTCTCTCT
* * * * *
5238220 AAGCAGTAGTGAAGCAGATTTAAGCCACCATCCTATCTTCCTAAGCAGTAGTGGAGCAGGTTGAA
63 AAGCAGTAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGTAGTAGTGGAGTAGGCTGAA
5238285 ATCAACAATT
Statistics
Matches: 223, Mismatches: 31, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
127 1 0.00
130 113 0.51
131 74 0.33
132 35 0.16
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (129 bp):
TTACAGATCTTGTCTCCCTGAAGTCAGTGGAACAGATCGAAGACGGTGAATCTTGTCTCTCTAAG
CAGTAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGTAGTAGTGGAGTAGGCTGAAGA
Found at i:5238395 original size:88 final size:88
Alignment explanation
Indices: 5238289--5238794 Score: 755
Period size: 88 Copynumber: 5.8 Consensus size: 88
5238279 GTTGAAATCA
* *
5238289 ACAATTCGTATCTCCTTGAAGTTTCAGCAGAGTAGATTGAAGCTACAAATCTCTTCTCCCTGAAA
1 ACAATTCGTATCTCCTTGAAGTTTCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAA
*
5238354 TGGCACTGGAGCGGCTCGAAGCC
66 TGGCACTAGAGCGGCTCGAAGCC
* * *
5238377 ACAATTCATATCTACTTGAAGTTTCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTGCCTGAAA
1 ACAATTCGTATCTCCTTGAAGTTTCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAA
*
5238442 TGGCACTAGAGCAGCTCGAAGCC
66 TGGCACTAGAGCGGCTCGAAGCC
* * * *
5238465 ACAATTCGTATCTCCTTAAAATTTCAGCGGAGTAAATCGAAGCTACAAATCTCTTCT-CTTGAAA
1 ACAATTCGTATCTCCTTGAAGTTTCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAA
*
5238529 TGTCACTAGAGCGGCTCGAAGCC
66 TGGCACTAGAGCGGCTCGAAGCC
* * * *
5238552 ACAATTCGTATCTCCTTGAAGTTCCAGCAGAGTAGATCGAAGCCACAAATCTCTTCTCCCTAAAA
1 ACAATTCGTATCTCCTTGAAGTTTCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAA
* * *
5238617 TGGCACTGGAGCGACTTGAAGCC
66 TGGCACTAGAGCGGCTCGAAGCC
* *
5238640 ACAATTCGTATCTCCTTGAAGTTCCAGCGAAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAA
1 ACAATTCGTATCTCCTTGAAGTTTCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAA
* *
5238705 TGGCACTAGAGTGGCTCAAAGCC
66 TGGCACTAGAGCGGCTCGAAGCC
* * *
5238728 ACAATTCGTATCTCCTTAAAG-TTCTAGTGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTAAA
1 ACAATTCGTATCTCCTTGAAGTTTC-AGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAA
5238792 ATG
65 ATG
5238795 ATTGTGGAAC
Statistics
Matches: 375, Mismatches: 41, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
87 80 0.21
88 295 0.79
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (88 bp):
ACAATTCGTATCTCCTTGAAGTTTCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAA
TGGCACTAGAGCGGCTCGAAGCC
Found at i:5238461 original size:44 final size:43
Alignment explanation
Indices: 5238317--5238715 Score: 176
Period size: 44 Copynumber: 9.1 Consensus size: 43
5238307 AAGTTTCAGC
* * *
5238317 AGAGTAGATTGAAGCTACAAATCTCTTCTCCCTGAAATGGCACT
1 AGAGCAGATCGAAGCCACAAATCTCTTCT-CCTGAAATGGCACT
* * * * * **
5238361 GGAGCGGCTCGAAGCCAC-AAT-TCATATCTACTTGAAGTTTCAGC-
1 AGAGCAGATCGAAGCCACAAATCTC-T-TCT-CCTGAAATGGCA-CT
* * *
5238405 GGAGTAGATCGAAGCTACAAATCTCTTCTGCCTGAAATGGCACT
1 AGAGCAGATCGAAGCCACAAATCTCTTCT-CCTGAAATGGCACT
* * **
5238449 AGAGCAGCTCGAAGCCAC-AAT-TCGTATCTCCTTAAAATTTCAGC-
1 AGAGCAGATCGAAGCCACAAATCTC-T-TCTCC-TGAAATGGCA-CT
* * * * * *
5238493 GGAGTAAATCGAAGCTACAAATCTCTTCTCTTGAAATGTCACT
1 AGAGCAGATCGAAGCCACAAATCTCTTCTCCTGAAATGGCACT
* * * **
5238536 AGAGCGGCTCGAAGCCAC-AAT-TCGTATCTCCTTGAAGTTCCAGC-
1 AGAGCAGATCGAAGCCACAAATCTC-T-TCTCC-TGAAATGGCA-CT
* *
5238580 AGAGTAGATCGAAGCCACAAATCTCTTCTCCCTAAAATGGCACT
1 AGAGCAGATCGAAGCCACAAATCTCTTCT-CCTGAAATGGCACT
* * * ** *
5238624 GGAGC-GACTTGAAGCCAC-AAT-TCGTATCTCCTTGAAGTTCCAGCG
1 AGAGCAGA-TCGAAGCCACAAATCTC-T-TCTCC-TGAAATGGCA-CT
* *
5238669 A-AGTAGATCGAAGCTACAAATCTCTTCTCCCTGAAATGGCACT
1 AGAGCAGATCGAAGCCACAAATCTCTTCT-CCTGAAATGGCACT
5238712 AGAG
1 AGAG
5238716 TGGCTCAAAG
Statistics
Matches: 256, Mismatches: 68, Indels: 62
0.66 0.18 0.16
Matches are distributed among these distances:
41 2 0.01
42 11 0.04
43 46 0.18
44 163 0.64
45 26 0.10
46 8 0.03
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (43 bp):
AGAGCAGATCGAAGCCACAAATCTCTTCTCCTGAAATGGCACT
Found at i:5238769 original size:263 final size:263
Alignment explanation
Indices: 5238289--5238785 Score: 825
Period size: 263 Copynumber: 1.9 Consensus size: 263
5238279 GTTGAAATCA
* * * *
5238289 ACAATTCGTATCTCCTTGAAGTTTCAGCAGAGTAGATTGAAGCTACAAATCTCTTCTCCCTGAAA
1 ACAATTCGTATCTCCTTGAAGTTCCAGCAGAGTAGATCGAAGCCACAAATCTCTTCTCCCTAAAA
* * *
5238354 TGGCACTGGAGCGGCTCGAAGCCACAATTCATATCTACTTGAAGTTTCAGCGGAGTAGATCGAAG
66 TGGCACTGGAGCGACTCGAAGCCACAATTCATATCTACTTGAAGTTCCAGCGAAGTAGATCGAAG
* *
5238419 CTACAAATCTCTTCTGCCTGAAATGGCACTAGAGCAGCTCGAAGCCACAATTCGTATCTCCTTAA
131 CTACAAATCTCTTCTCCCTGAAATGGCACTAGAGCAGCTCAAAGCCACAATTCGTATCTCCTTAA
5238484 AATTTCAGCGGAGTAAATCGAAGCTACAAATCTCTTCTCTTGAAATGTCACTAGAGCGGCTCGAA
196 AATTTCAGCGGAGTAAATCGAAGCTACAAATCTCTTCTCTTGAAATGTCACTAGAGCGGCTCGAA
5238549 GCC
261 GCC
5238552 ACAATTCGTATCTCCTTGAAGTTCCAGCAGAGTAGATCGAAGCCACAAATCTCTTCTCCCTAAAA
1 ACAATTCGTATCTCCTTGAAGTTCCAGCAGAGTAGATCGAAGCCACAAATCTCTTCTCCCTAAAA
* * *
5238617 TGGCACTGGAGCGACTTGAAGCCACAATTCGTATCTCCTTGAAGTTCCAGCGAAGTAGATCGAAG
66 TGGCACTGGAGCGACTCGAAGCCACAATTCATATCTACTTGAAGTTCCAGCGAAGTAGATCGAAG
**
5238682 CTACAAATCTCTTCTCCCTGAAATGGCACTAGAGTGGCTCAAAGCCACAATTCGTATCTCCTT-A
131 CTACAAATCTCTTCTCCCTGAAATGGCACTAGAGCAGCTCAAAGCCACAATTCGTATCTCCTTAA
* * *
5238746 AAGTTCTAGTGGAGTAGATCGAAGCTACAAATCTCTTCTC
196 AATTTC-AGCGGAGTAAATCGAAGCTACAAATCTCTTCTC
5238786 CCTAAAATGA
Statistics
Matches: 216, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
262 6 0.03
263 210 0.97
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (263 bp):
ACAATTCGTATCTCCTTGAAGTTCCAGCAGAGTAGATCGAAGCCACAAATCTCTTCTCCCTAAAA
TGGCACTGGAGCGACTCGAAGCCACAATTCATATCTACTTGAAGTTCCAGCGAAGTAGATCGAAG
CTACAAATCTCTTCTCCCTGAAATGGCACTAGAGCAGCTCAAAGCCACAATTCGTATCTCCTTAA
AATTTCAGCGGAGTAAATCGAAGCTACAAATCTCTTCTCTTGAAATGTCACTAGAGCGGCTCGAA
GCC
Found at i:5238870 original size:44 final size:44
Alignment explanation
Indices: 5238821--5239074 Score: 202
Period size: 45 Copynumber: 5.7 Consensus size: 44
5238811 AGCCACAAAC
* *
5238821 CTTATCTCCCTGAAGTTGTAGTGGAGCAGGTTGAAGTTACAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACAAGT
* *
5238865 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATA-CAAGT
* * ** * * * * **
5238910 CTTATCTCTCTGAAATCACAGTAGAGCAGAGTTAAAGCTATAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAG-GTTGAAGATACAAGT
* * * ** * *
5238955 CTTATCCCCCTGAAGTTGCAGTGGGGCAAGTCAAAGTTGCAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACAAGT
** * * ** *
5238999 CTTATCTCCCTGAAGCCGTAGTGGAACAGACTGAAGATAGCAGGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATA-CAAGT
* * *
5239044 CTTATCTCCTTGAAGTTGCAATAGAGCAGGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGT
5239075 CAAGCTACGA
Statistics
Matches: 156, Mismatches: 51, Indels: 5
0.74 0.24 0.02
Matches are distributed among these distances:
44 71 0.46
45 78 0.50
46 7 0.04
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACAAGT
Found at i:5238937 original size:45 final size:44
Alignment explanation
Indices: 5238805--5238968 Score: 121
Period size: 44 Copynumber: 3.7 Consensus size: 44
5238795 ATTGTGGAAC
** * * *** *
5238805 GATTGAAGCCACAAACCTTATCTCCCTGAAGTTGTAGTGGAGCA
1 GATTGAAGATACAAATCTTATCTCCCTGAAATCACAGTAGAGCA
* * * * ** *
5238849 GGTTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCA
1 GATTGAAGATACAAATCTTATCTCCCTGAAATCACAGTAGAGCA
*
5238893 GATTGAAGATAGCAAATCTTATCTCTCTGAAATCACAGTAGAGCA
1 GATTGAAGATA-CAAATCTTATCTCCCTGAAATCACAGTAGAGCA
* * * * *
5238938 GAGTTAAAGCTATAAACCTTATCCCCCTGAA
1 GA-TTGAAGATACAAATCTTATCTCCCTGAA
5238969 GTTGCAGTGG
Statistics
Matches: 98, Mismatches: 20, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
44 47 0.48
45 44 0.45
46 7 0.07
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (44 bp):
GATTGAAGATACAAATCTTATCTCCCTGAAATCACAGTAGAGCA
Found at i:5240180 original size:14 final size:14
Alignment explanation
Indices: 5240161--5240187 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5240151 CAGTCAGACA
5240161 TAGATACAGATATT
1 TAGATACAGATATT
5240175 TAGATACAGATAT
1 TAGATACAGATAT
5240188 AACAAATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.33
Consensus pattern (14 bp):
TAGATACAGATATT
Found at i:5241932 original size:19 final size:18
Alignment explanation
Indices: 5241904--5241942 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
5241894 TTAGCAAGTC
*
5241904 TTGAAAACTTCTATATAT
1 TTGAAAACTTCTATAAAT
*
5241922 TTGAGAAACTTGTATAAAT
1 TTGA-AAACTTCTATAAAT
5241941 TT
1 TT
5241943 ATTTACTAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (18 bp):
TTGAAAACTTCTATAAAT
Found at i:5243229 original size:1 final size:1
Alignment explanation
Indices: 5243223--5243252 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
5243213 AAAAGTAAGC
5243223 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5243253 GGAGAAGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:5245007 original size:10 final size:10
Alignment explanation
Indices: 5244992--5245017 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
5244982 ATTCCTACAT
5244992 AACATACAAG
1 AACATACAAG
5245002 AACATACAAG
1 AACATACAAG
5245012 AACATA
1 AACATA
5245018 GAACATGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.62, C:0.19, G:0.08, T:0.12
Consensus pattern (10 bp):
AACATACAAG
Found at i:5245323 original size:45 final size:44
Alignment explanation
Indices: 5245269--5245648 Score: 366
Period size: 45 Copynumber: 8.4 Consensus size: 44
5245259 CACTGGTGGC
* * * *
5245269 TTCTTTGGAGGCTTATAAACTGGTGGTTTGGGTTCTGGTTTTTCT
1 TTCTTTGGAGG-TTATAAACTGGTGGTTTAGGTTCAGGCTTCTCT
* * * *
5245314 TTCTTTGGAGGTGCATAAACTGGTGGCTTAGGTTCAGGTTTCTCC
1 TTCTTTGGAGGT-TATAAACTGGTGGTTTAGGTTCAGGCTTCTCT
* * *
5245359 TTCTTTGGTGGTTCATACACTGGTGGTTTAAGCTT-AGGCTTCTCT
1 TTCTTTGGAGGTT-ATAAACTGGTGGTTT-AGGTTCAGGCTTCTCT
* * * * * * *
5245404 TTCTTTGGTGGCATATAAATTGGTGGCTTAGGCTCAGGCTTTTCC
1 TTCTTTGGAGG-TTATAAACTGGTGGTTTAGGTTCAGGCTTCTCT
* * *
5245449 TTCTTTGGAGGTTCATATACTGGTGGTTTGGGCTCAGGCTTCTCT
1 TTCTTTGGAGGTT-ATAAACTGGTGGTTTAGGTTCAGGCTTCTCT
* * * * * *
5245494 TTCTTTGGTGGCGTATAAACTGGTGGCTTAGGCTCAGGCTTTTCC
1 TTCTTTGGAGG-TTATAAACTGGTGGTTTAGGTTCAGGCTTCTCT
* *
5245539 TTCTTTGGAGGTTCATATACTGGTGGTTTGGGTTCAGGCTTCTCT
1 TTCTTTGGAGGTT-ATAAACTGGTGGTTTAGGTTCAGGCTTCTCT
* * *
5245584 TTCTTTGGAGGCGTATAAACTGGTGGTTTAGGCTCAGGCTTCTCC
1 TTCTTTGGAGG-TTATAAACTGGTGGTTTAGGTTCAGGCTTCTCT
*
5245629 TTCTTTGGTGGTTCATAAAC
1 TTCTTTGGAGGTT-ATAAAC
5245649 AGGGGGCTTA
Statistics
Matches: 274, Mismatches: 51, Indels: 20
0.79 0.15 0.06
Matches are distributed among these distances:
44 7 0.03
45 260 0.95
46 7 0.03
ACGTcount: A:0.14, C:0.17, G:0.28, T:0.42
Consensus pattern (44 bp):
TTCTTTGGAGGTTATAAACTGGTGGTTTAGGTTCAGGCTTCTCT
Found at i:5245454 original size:135 final size:135
Alignment explanation
Indices: 5245268--5245658 Score: 482
Period size: 135 Copynumber: 2.9 Consensus size: 135
5245258 ACACTGGTGG
* * *
5245268 CTTCTTTGGAGGCTTATAAACTGGTGGTTTGGGTTCTGGTTTTTCTTTCTTTGGAGGTGCATAAA
1 CTTCTTTGGAGGCATATAAACTGGTGGTTTGGGTTCAGGCTTTTCTTTCTTTGGAGGTGCATAAA
* * * * * *
5245333 CTGGTGGCTTAGGTTCAGGTTTCTCCTTCTTTGGTGGTTCATACACTGGTGGTTTAAGCTTAGGC
66 CTGGTGGTTTAGGCTCAGGCTTCTCCTTCTTTGGTGGTTCATAAACTGGTGGCTTAAGCTCAGGC
5245398 TTCTC
131 TTCTC
* * * * * * * * *
5245403 TTTCTTTGGTGGCATATAAATTGGTGGCTTAGGCTCAGGCTTTTCCTTCTTTGGAGGTTCATATA
1 CTTCTTTGGAGGCATATAAACTGGTGGTTTGGGTTCAGGCTTTTCTTTCTTTGGAGGTGCATAAA
* * * *
5245468 CTGGTGGTTTGGGCTCAGGCTTCTCTTTCTTTGGTGGCGT-ATAAACTGGTGGCTTAGGCTCAGG
66 CTGGTGGTTTAGGCTCAGGCTTCTCCTTCTTTGGTGG-TTCATAAACTGGTGGCTTAAGCTCAGG
*
5245532 CTTTTC
130 CTTCTC
* * *
5245538 CTTCTTTGGAGGTTCATAT--ACTGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTGGAGGCGTATA
1 CTTCTTTGGAGG--CATATAAACTGGTGGTTTGGGTTCAGGCTTTTCTTTCTTTGGAGGTGCATA
* *
5245601 AACTGGTGGTTTAGGCTCAGGCTTCTCCTTCTTTGGTGGTTCATAAACAGGGGGCTTA
64 AACTGGTGGTTTAGGCTCAGGCTTCTCCTTCTTTGGTGGTTCATAAACTGGTGGCTTA
5245659 TGTTCATAAG
Statistics
Matches: 212, Mismatches: 40, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
134 1 0.00
135 205 0.97
136 1 0.00
137 5 0.02
ACGTcount: A:0.14, C:0.17, G:0.28, T:0.41
Consensus pattern (135 bp):
CTTCTTTGGAGGCATATAAACTGGTGGTTTGGGTTCAGGCTTTTCTTTCTTTGGAGGTGCATAAA
CTGGTGGTTTAGGCTCAGGCTTCTCCTTCTTTGGTGGTTCATAAACTGGTGGCTTAAGCTCAGGC
TTCTC
Found at i:5245664 original size:90 final size:90
Alignment explanation
Indices: 5245268--5245645 Score: 517
Period size: 90 Copynumber: 4.2 Consensus size: 90
5245258 ACACTGGTGG
* * * * * * *
5245268 CTTCTTTGGAGGCTT-ATAAACTGGTGGTTTGGGTTCTGGTTTTTCTTTCTTTGGAGGTGCATAA
1 CTTCTTTGGAGG-TTCATATACTGGTGGTTTAGGTTCAGGCTTCTCTTTCTTTGGAGGCGTATAA
* *
5245332 ACTGGTGGCTTAGGTTCAGGTTTCTC
65 ACTGGTGGCTTAGGCTCAGGCTTCTC
* * * * *
5245358 CTTCTTTGGTGGTTCATACACTGGTGGTTTAAGCTT-AGGCTTCTCTTTCTTTGGTGGCATATAA
1 CTTCTTTGGAGGTTCATATACTGGTGGTTT-AGGTTCAGGCTTCTCTTTCTTTGGAGGCGTATAA
* *
5245422 ATTGGTGGCTTAGGCTCAGGCTTTTC
65 ACTGGTGGCTTAGGCTCAGGCTTCTC
* * *
5245448 CTTCTTTGGAGGTTCATATACTGGTGGTTTGGGCTCAGGCTTCTCTTTCTTTGGTGGCGTATAAA
1 CTTCTTTGGAGGTTCATATACTGGTGGTTTAGGTTCAGGCTTCTCTTTCTTTGGAGGCGTATAAA
*
5245513 CTGGTGGCTTAGGCTCAGGCTTTTC
66 CTGGTGGCTTAGGCTCAGGCTTCTC
*
5245538 CTTCTTTGGAGGTTCATATACTGGTGGTTTGGGTTCAGGCTTCTCTTTCTTTGGAGGCGTATAAA
1 CTTCTTTGGAGGTTCATATACTGGTGGTTTAGGTTCAGGCTTCTCTTTCTTTGGAGGCGTATAAA
*
5245603 CTGGTGGTTTAGGCTCAGGCTTCTC
66 CTGGTGGCTTAGGCTCAGGCTTCTC
*
5245628 CTTCTTTGGTGGTTCATA
1 CTTCTTTGGAGGTTCATA
5245646 AACAGGGGGC
Statistics
Matches: 258, Mismatches: 27, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
89 4 0.02
90 251 0.97
91 3 0.01
ACGTcount: A:0.13, C:0.17, G:0.28, T:0.42
Consensus pattern (90 bp):
CTTCTTTGGAGGTTCATATACTGGTGGTTTAGGTTCAGGCTTCTCTTTCTTTGGAGGCGTATAAA
CTGGTGGCTTAGGCTCAGGCTTCTC
Found at i:5255778 original size:33 final size:33
Alignment explanation
Indices: 5255735--5255811 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 33
5255725 GCTAATGTGC
*
5255735 TTGATTTCCAACAGCAGATACAATGGCAAACTA
1 TTGATTTCCAACAGCAAATACAATGGCAAACTA
* * * *
5255768 TTGCTTTCCAACAGCAAATTCTATGGCAAACTC
1 TTGATTTCCAACAGCAAATACAATGGCAAACTA
5255801 TTGATTTCCAA
1 TTGATTTCCAA
5255812 AAGGAAACAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.30
Consensus pattern (33 bp):
TTGATTTCCAACAGCAAATACAATGGCAAACTA
Found at i:5257206 original size:13 final size:13
Alignment explanation
Indices: 5257174--5257233 Score: 77
Period size: 13 Copynumber: 4.6 Consensus size: 13
5257164 GGCAACCCAA
*
5257174 TTTTATTTATTTT
1 TTTTATTTATATT
5257187 ATTTTATTTATATT
1 -TTTTATTTATATT
5257201 TTTTATTTATA-T
1 TTTTATTTATATT
*
5257213 TTATATTTATATT
1 TTTTATTTATATT
*
5257226 TTATATTT
1 TTTTATTT
5257234 TCTTTATTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
12 11 0.26
13 20 0.47
14 12 0.28
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTTATTTATATT
Found at i:5257213 original size:6 final size:6
Alignment explanation
Indices: 5257181--5257233 Score: 65
Period size: 6 Copynumber: 8.8 Consensus size: 6
5257171 CAATTTTATT
*
5257181 TATTT- TATTT- TATTTA TATTTTT TATTTA TATTTA TATTTA TATTTTA
1 TATTTA TATTTA TATTTA TA-TTTA TATTTA TATTTA TATTTA TA-TTTA
5257229 TATTT
1 TATTT
5257234 TCTTTATTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
5 10 0.23
6 22 0.51
7 11 0.26
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (6 bp):
TATTTA
Found at i:5257213 original size:19 final size:18
Alignment explanation
Indices: 5257183--5257233 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
5257173 ATTTTATTTA
5257183 TTTTATTT-TATTTATATT
1 TTTTATTTATATTTATA-T
5257201 TTTTATTTATATTTATAT
1 TTTTATTTATATTTATAT
*
5257219 TTATATTTTATATTT
1 TTTTA-TTTATATTT
5257234 TCTTTATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 13 0.43
19 17 0.57
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTATTTATATTTATAT
Found at i:5258868 original size:44 final size:44
Alignment explanation
Indices: 5258805--5258892 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
5258795 AAAGTGCAAA
5258805 TGAAGGCCTAAAGGCACACTTTCAATGCGGCGCCGTTCCAAGGG
1 TGAAGGCCTAAAGGCACACTTTCAATGCGGCGCCGTTCCAAGGG
5258849 TGAAGGCCTAAAGGCACACTTTCAATGCGGCGCCGTTCCAAGGG
1 TGAAGGCCTAAAGGCACACTTTCAATGCGGCGCCGTTCCAAGGG
5258893 AATTAAGACC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.25, C:0.27, G:0.30, T:0.18
Consensus pattern (44 bp):
TGAAGGCCTAAAGGCACACTTTCAATGCGGCGCCGTTCCAAGGG
Found at i:5259771 original size:31 final size:32
Alignment explanation
Indices: 5259712--5259772 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
5259702 ATAACTTATG
*
5259712 TAAATATTTTTTATGTATATATCCTTTTTTTT
1 TAAATATTTTTTATGTATATATCATTTTTTTT
*
5259744 TAAA-ATTTTTTATGTGTATAAT-ATTTTTT
1 TAAATATTTTTTATGTATAT-ATCATTTTTT
5259773 AAGAACCCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 20 0.77
32 6 0.23
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (32 bp):
TAAATATTTTTTATGTATATATCATTTTTTTT
Found at i:5261418 original size:37 final size:38
Alignment explanation
Indices: 5261346--5261418 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
5261336 TTTTTTATTA
5261346 TTGGGTCTCAAAGCGCCCTTTACGGGTATTCACTTTAT
1 TTGGGTCTCAAAGCGCCCTTTACGGGTATTCACTTTAT
* * *
5261384 TTGGGTCTCAAAGTGCCCTTTGCGGGT-TTTACTTT
1 TTGGGTCTCAAAGCGCCCTTTACGGGTATTCACTTT
5261419 GGCCCCTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 7 0.22
38 25 0.78
ACGTcount: A:0.15, C:0.22, G:0.23, T:0.40
Consensus pattern (38 bp):
TTGGGTCTCAAAGCGCCCTTTACGGGTATTCACTTTAT
Found at i:5272345 original size:21 final size:20
Alignment explanation
Indices: 5272303--5272370 Score: 77
Period size: 21 Copynumber: 3.4 Consensus size: 20
5272293 AATAATAATA
*
5272303 ATAATAATAATAATA-ATA-
1 ATAATAATAATAATATACAC
5272321 ATAATAATAATAATATACAC
1 ATAATAATAATAATATACAC
* *
5272341 GATAATAAAAATATTATACAC
1 -ATAATAATAATAATATACAC
5272362 ATAAATAAT
1 AT-AATAAT
5272371 TTTAGAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
18 15 0.36
19 2 0.05
20 2 0.05
21 23 0.55
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.31
Consensus pattern (20 bp):
ATAATAATAATAATATACAC
Found at i:5272348 original size:3 final size:3
Alignment explanation
Indices: 5272293--5272335 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
5272283 TTATTACAAA
5272293 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5272336 TACACGATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5274679 original size:101 final size:101
Alignment explanation
Indices: 5274500--5274684 Score: 289
Period size: 101 Copynumber: 1.8 Consensus size: 101
5274490 ATTCAGCATT
* * *
5274500 TGCGAAGATCTGCTCCGCTGCAATCTCAAAGAGATAAGATCTTTAATTCTCAGTCTACTTCCTTA
1 TGCGAAGATCTGCTCCGCTACAAACTCAAAGAGATAAAATCTTTAATTCTCAGTCTACTTCCTTA
*
5274565 CTACCTCAGGAAGATAAGATACATTCTTCAACCATC
66 CTACCTCAAGAAGATAAGATACATTCTTCAACCATC
** * *
5274601 TGCGAAGATCTGCTCCGCTACAAACTCAGGGAGATAAAATCTTTAATTCTCAGTCTGCTTCCTTG
1 TGCGAAGATCTGCTCCGCTACAAACTCAAAGAGATAAAATCTTTAATTCTCAGTCTACTTCCTTA
*
5274666 TTACCTCAAGAAGATAAGA
66 CTACCTCAAGAAGATAAGA
5274685 CCTGCTCGCC
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
101 75 1.00
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (101 bp):
TGCGAAGATCTGCTCCGCTACAAACTCAAAGAGATAAAATCTTTAATTCTCAGTCTACTTCCTTA
CTACCTCAAGAAGATAAGATACATTCTTCAACCATC
Found at i:5274985 original size:180 final size:179
Alignment explanation
Indices: 5274697--5275324 Score: 785
Period size: 180 Copynumber: 3.5 Consensus size: 179
5274687 TGCTCGCCCA
* * * * * *
5274697 CTACCTCAGAGAGATGAGG-TTGGTGGTAAAATCTACTCCATTGCCAATACATGGAAATAAGATT
1 CTACCTTAGAGAGATAAGGCTTGGAGGTAAAATCTGCTCCATTGCCGATACATGGAGATAAGATT
* * * * * *
5274761 TACCATCTGTGAAAATCTGCTCTG-TGACGACTTTA-GAGAGATAAAATTTTCAATTCTCAGTCT
66 CACCATCTGCGAAGATCTGCTCCGCTG-CAACTTCAGGA-AGATAAAATTTTCAATTCTCAGTCT
* * *
5274824 ACTTCTTTGCTACCTCAGGAAGATAGGACTCATTCTTTAACCTGCTCTCTTA
129 ACTTCCTTGCTACCTCAGGAAGATA-GACTCATTCTTCAACCTGCTCTCTTG
** * *
5274876 CTACCTTAGAGAGATAAGGCTTAAAAGTAAAATCTGTTCCATTGCCGATACATGGAGATAAGATT
1 CTACCTTAGAGAGATAAGGCTTGGAGGTAAAATCTGCTCCATTGCCGATACATGGAGATAAGATT
* * * *
5274941 CACCATCTACGAAGATATGCTCCGCTGCAACTTCAGGAAGATAAAATCTTCAATTCTTAGTCTAC
66 CACCATCTGCGAAGATCTGCTCCGCTGCAACTTCAGGAAGATAAAATTTTCAATTCTCAGTCTAC
5275006 TTCCTTGCTACCTCAGGAAGATAAGACTCATTCTTCAACCTGCTCTCTTG
131 TTCCTTGCTACCTCAGGAAGAT-AGACTCATTCTTCAACCTGCTCTCTTG
* * * * *
5275056 CTACCTCAGAGAGATAAGGCTTGGTGGTAAAATCTGCTCCATTGTCGATATATGAAGATAAGATT
1 CTACCTTAGAGAGATAAGGCTTGGAGGTAAAATCTGCTCCATTGCCGATACATGGAGATAAGATT
* * * *
5275121 CACCATCTGCGAAGATCTACTCCGCTGTAACTTCAGCG-AGATAAAATTTTCAATTCTCAGCCTG
66 CACCATCTGCGAAGATCTGCTCCGCTGCAACTTCAG-GAAGATAAAATTTTCAATTCTCAGTCTA
*
5275185 CTTCCTTGCTACCTCA-G--GA-AGACTCATTCTTCAACCTGCTCCCTTG
130 CTTCCTTGCTACCTCAGGAAGATAGACTCATTCTTCAACCTGCTCTCTTG
** *
5275231 CTACCTTAGAGAGACGAGGC-TGGAGGTAAAATCTGCTCCATTGCTGATACATGGAGATAAGATT
1 CTACCTTAGAGAGATAAGGCTTGGAGGTAAAATCTGCTCCATTGCCGATACATGGAGATAAGATT
* *
5275295 CACCATCTTC---GATCTGCTCCGCTACAACTT
66 CACCATCTGCGAAGATCTGCTCCGCTGCAACTT
5275325 ACTTCAACTT
Statistics
Matches: 391, Mismatches: 53, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
171 17 0.04
174 48 0.12
175 43 0.11
177 2 0.01
179 18 0.05
180 257 0.66
181 6 0.02
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (179 bp):
CTACCTTAGAGAGATAAGGCTTGGAGGTAAAATCTGCTCCATTGCCGATACATGGAGATAAGATT
CACCATCTGCGAAGATCTGCTCCGCTGCAACTTCAGGAAGATAAAATTTTCAATTCTCAGTCTAC
TTCCTTGCTACCTCAGGAAGATAGACTCATTCTTCAACCTGCTCTCTTG
Found at i:5278420 original size:10 final size:10
Alignment explanation
Indices: 5278405--5278454 Score: 75
Period size: 10 Copynumber: 5.0 Consensus size: 10
5278395 TAATTTTAGC
5278405 ATTTATCTTT
1 ATTTATCTTT
5278415 ATTTATCTTT
1 ATTTATCTTT
*
5278425 AATTATCTTT
1 ATTTATCTTT
5278435 ATTTAT-TTT
1 ATTTATCTTT
5278444 CATTTATCTTT
1 -ATTTATCTTT
5278455 TAGAATTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
9 3 0.08
10 30 0.83
11 3 0.08
ACGTcount: A:0.22, C:0.10, G:0.00, T:0.68
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:5282643 original size:47 final size:45
Alignment explanation
Indices: 5282573--5282747 Score: 169
Period size: 46 Copynumber: 3.8 Consensus size: 45
5282563 GAGTTATTGT
*
5282573 GAGCAAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCC-CATTATGA
* *
5282619 GAGCCAGTGTAAGACCATGTCTGGGACACGGCATCGG--CATTGAGATGA
1 GAGCTAGTGTAAGA-CATGTCTGGGACA-TGCATCGGCCCATT---ATGA
* * *
5282667 GAGCTAGTGTAAGACATGTTTGGGACATGCATCGACCTCGA-GATGTA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCC-C-ATTATG-A
*
5282714 -AACTAGTGTAAGACATGTCTGGGACATGGCATCG
1 GAGCTAGTGTAAGACATGTCTGGGACAT-GCATCG
5282748 ACATCTTACC
Statistics
Matches: 109, Mismatches: 9, Indels: 21
0.78 0.06 0.15
Matches are distributed among these distances:
45 4 0.04
46 47 0.43
47 32 0.29
48 24 0.22
49 1 0.01
50 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.22
Consensus pattern (45 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCCATTATGA
Found at i:5285010 original size:12 final size:12
Alignment explanation
Indices: 5284995--5285028 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
5284985 AAATCGATCC
5284995 ATAAATATTTTT
1 ATAAATATTTTT
5285007 ATAAATATTTTT
1 ATAAATATTTTT
5285019 ATAAATATTT
1 ATAAATATTT
5285029 ATGGAGTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATAAATATTTTT
Found at i:5286871 original size:50 final size:49
Alignment explanation
Indices: 5286796--5286972 Score: 273
Period size: 50 Copynumber: 3.5 Consensus size: 49
5286786 CCATGGCAAC
*
5286796 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATTAAGGACTAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGAC-AATGA
*
5286846 AAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAA-TGA
5286896 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGAC-AATGA
* * *
5286946 CAAGTGAAAAGTGGTAGCTTCGACTAC
1 -AAGTGATAAGTGATAGCTTCGGCTAC
5286973 CTGACCAGTG
Statistics
Matches: 118, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
49 2 0.02
50 91 0.77
51 25 0.21
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.27
Consensus pattern (49 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAATGA
Found at i:5286986 original size:31 final size:31
Alignment explanation
Indices: 5286943--5287065 Score: 158
Period size: 31 Copynumber: 4.0 Consensus size: 31
5286933 CAAGGACAAA
*
5286943 TGACAAGTGAAAAGTGGTAGCTTCGACTACC
1 TGACCAGTGAAAAGTGGTAGCTTCGACTACC
*
5286974 TGACCAGTGAAAAGTGGTAGCTTCTG-CTATC
1 TGACCAGTGAAAAGTGGTAGCTTC-GACTACC
* * *
5287005 TGATCAGTGAAAAATGGTAGCTCCGACTACC
1 TGACCAGTGAAAAGTGGTAGCTTCGACTACC
* * *
5287036 TGATCAGTGAATAGTGGTAGCTTCGGCTAC
1 TGACCAGTGAAAAGTGGTAGCTTCGACTAC
5287066 AAGTGACAAG
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
30 1 0.01
31 78 0.98
32 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (31 bp):
TGACCAGTGAAAAGTGGTAGCTTCGACTACC
Found at i:5287045 original size:62 final size:62
Alignment explanation
Indices: 5286948--5287064 Score: 189
Period size: 62 Copynumber: 1.9 Consensus size: 62
5286938 ACAAATGACA
* * *
5286948 AGTGAAAAGTGGTAGCTTCGACTACCTGACCAGTGAAAAGTGGTAGCTTCTGCTATCTGATC
1 AGTGAAAAATGGTAGCTCCGACTACCTGACCAGTGAAAAGTGGTAGCTTCGGCTATCTGATC
* *
5287010 AGTGAAAAATGGTAGCTCCGACTACCTGATCAGTGAATAGTGGTAGCTTCGGCTA
1 AGTGAAAAATGGTAGCTCCGACTACCTGACCAGTGAAAAGTGGTAGCTTCGGCTA
5287065 CAAGTGACAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 50 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.26
Consensus pattern (62 bp):
AGTGAAAAATGGTAGCTCCGACTACCTGACCAGTGAAAAGTGGTAGCTTCGGCTATCTGATC
Found at i:5287236 original size:49 final size:46
Alignment explanation
Indices: 5287134--5287270 Score: 150
Period size: 49 Copynumber: 2.8 Consensus size: 46
5287124 TGCTACTGTA
* * * *
5287134 TAAGACCATATCTGGGATATGGCATCA-GTGAGATATGTGATTTGTG
1 TAAGACCATAT-TGGGCTATGGCATCATATGTGATATGTGATTCGTG
5287180 TAAGACCATAGTTGGGCTATGGCATCAATATGTGATATGTGATTACGTG
1 TAAGACCATA-TTGGGCTATGGCATC-ATATGTGATATGTGATT-CGTG
* *
5287229 TAAGACCATAACTGGGCTATGGCATCGATATATGAATATGTG
1 TAAGACCAT-ATTGGGCTATGGCATC-ATATGTG-ATATGTG
5287271 TAAGACCATA
Statistics
Matches: 78, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
46 23 0.29
47 2 0.03
48 13 0.17
49 32 0.41
50 8 0.10
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.31
Consensus pattern (46 bp):
TAAGACCATATTGGGCTATGGCATCATATGTGATATGTGATTCGTG
Found at i:5288527 original size:21 final size:18
Alignment explanation
Indices: 5288494--5288540 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 18
5288484 TGCATAAAAT
*
5288494 TTAATT-TGAATTTAAGATA
1 TTAATTATGGATTT-AGA-A
5288513 TTGAATTATGGATTTAGAA
1 TT-AATTATGGATTTAGAA
5288532 TTAATTATG
1 TTAATTATG
5288541 TATAAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 7 0.28
19 5 0.20
20 7 0.28
21 6 0.24
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (18 bp):
TTAATTATGGATTTAGAA
Found at i:5289988 original size:16 final size:16
Alignment explanation
Indices: 5289969--5289999 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5289959 CTTCTTCACT
5289969 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
5289985 TACTTACTTACTTAA
1 TACTCACTTACTTAA
5290000 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:5290005 original size:20 final size:20
Alignment explanation
Indices: 5289966--5290005 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5289956 AAACTTCTTC
* *
5289966 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
5289986 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
5290006 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:5290377 original size:55 final size:53
Alignment explanation
Indices: 5290251--5290446 Score: 164
Period size: 55 Copynumber: 3.6 Consensus size: 53
5290241 TTACCATTGT
* *
5290251 CATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATGC
1 CATGTCTTAACATGGTCTTACATGGGATCCTTGCCTTATGAACTCACCAATGC
* * * * * *
5290304 TATG-CCTAGGCATGGTCTTACTTGGGA-CCTTTGCCTTATAGTAACTTATCAATGC
1 CATGTCTTA-ACATGGTCTTACATGGGATCC-TTGCCTTAT-G-AACTCACCAATGC
*** *
5290359 CATGTCTTAACATGGTCTTACATGATTTCCTTGCCTTA-GAGACCTTACCAAATGC
1 CATGTCTTAACATGGTCTTACATGGGATCCTTGCCTTATGA-A-CTCACC-AATGC
* ** *
5290414 CATGCCTTGGCATGGTCTTACATGGTATCCTTG
1 CATGTCTTAACATGGTCTTACATGGGATCCTTG
5290447 AACCCTAATG
Statistics
Matches: 113, Mismatches: 21, Indels: 16
0.75 0.14 0.11
Matches are distributed among these distances:
52 5 0.04
53 29 0.26
54 6 0.05
55 68 0.60
56 5 0.04
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.35
Consensus pattern (53 bp):
CATGTCTTAACATGGTCTTACATGGGATCCTTGCCTTATGAACTCACCAATGC
Found at i:5291946 original size:30 final size:30
Alignment explanation
Indices: 5291913--5291984 Score: 103
Period size: 29 Copynumber: 2.4 Consensus size: 30
5291903 TTTAAAAATA
5291913 AAAAATTTAAATTTTTATA-TTTT-ATTTT
1 AAAAATTTAAATTTTTATATTTTTAATTTT
* *
5291941 CAAAAATTTTATTTTTTATATTTTTAATTTT
1 -AAAAATTTAAATTTTTATATTTTTAATTTT
5291972 AAAAATTTAAATT
1 AAAAATTTAAATT
5291985 CAATTATTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 17 0.46
30 15 0.41
31 5 0.14
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (30 bp):
AAAAATTTAAATTTTTATATTTTTAATTTT
Found at i:5292977 original size:2 final size:2
Alignment explanation
Indices: 5292970--5293003 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5292960 GCATTATGGC
5292970 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
5293004 TCTAAAAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5293997 original size:102 final size:102
Alignment explanation
Indices: 5293863--5294137 Score: 354
Period size: 102 Copynumber: 2.7 Consensus size: 102
5293853 CTTATGTACA
* * * * *
5293863 GGAGGTTTCTTTGGAGGTTCGTACATTGGTGGTTTTGGTTCTGGCTTCTCTTTCTTTGGTGGTGC
1 GGAGGCTTCTTTGGAGGTTCATACATTGGTGGTTTGGGTTCTGGCTTTTCTTTCTTTGGAGGTGC
* * * *
5293928 ATAAACCGGTGACTTTTGTGGCTTGGGCTCATACATT
66 ATAAACCGGTGACTTTGGTGGCTTAGGCTCATAAACT
* * * *
5293965 GGAGGCTTAC-TTGGTGGTTCATACATTGGTGGTTTGGGTTCAGGCTTTTCCTTCTTTGGAGATG
1 GGAGGCTT-CTTTGGAGGTTCATACATTGGTGGTTTGGGTTCTGGCTTTTCTTTCTTTGGAGGTG
*
5294029 CATAAACCGGTGGCTTTGGTGGCTTAGGCTCATAAACT
65 CATAAACCGGTGACTTTGGTGGCTTAGGCTCATAAACT
* * * * * *
5294067 GGTGGCTTCTTTGGAGGCTCATAAACTGGAGGTTTGGGTTCTGGTTTTTCTTTCTTTGGAGGTGC
1 GGAGGCTTCTTTGGAGGTTCATACATTGGTGGTTTGGGTTCTGGCTTTTCTTTCTTTGGAGGTGC
5294132 ATAAAC
66 ATAAAC
5294138 TAGCGGTTTA
Statistics
Matches: 147, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
101 1 0.01
102 145 0.99
103 1 0.01
ACGTcount: A:0.15, C:0.16, G:0.31, T:0.39
Consensus pattern (102 bp):
GGAGGCTTCTTTGGAGGTTCATACATTGGTGGTTTGGGTTCTGGCTTTTCTTTCTTTGGAGGTGC
ATAAACCGGTGACTTTGGTGGCTTAGGCTCATAAACT
Found at i:5294167 original size:45 final size:45
Alignment explanation
Indices: 5294115--5294552 Score: 354
Period size: 45 Copynumber: 9.7 Consensus size: 45
5294105 TTCTGGTTTT
* * *
5294115 TCTTTCTTTGGAGGTGCATAAACTAGCGGTTTAGGCTTAGGCTTC
1 TCTTTCTTTGGTGGTGCATAAACTAGTGGCTTAGGCTTAGGCTTC
* * * *
5294160 TCCTTCTTTGGTGGTTCATACA-TAGGTGGCTT-GGGTTCAGGCTTC
1 TCTTTCTTTGGTGGTGCATAAACTA-GTGGCTTAGGCTT-AGGCTTC
* * *
5294205 TCTTTCTTTGGTGGTGTATAAACTGGTGGCTTAGGCTCAGGCTTC
1 TCTTTCTTTGGTGGTGCATAAACTAGTGGCTTAGGCTTAGGCTTC
* * * * *
5294250 TCCTTCTTTGGTGGTTCATACACAAGTGGCTT-GGGTTCAGGCTTC
1 TCTTTCTTTGGTGGTGCATAAACTAGTGGCTTAGGCTT-AGGCTTC
*
5294295 TCTTTCTTTGGTGGTGTATAAACT-GATGGCTTAGGCTTAGGCTTC
1 TCTTTCTTTGGTGGTGCATAAACTAG-TGGCTTAGGCTTAGGCTTC
* * * * *
5294340 TCCTTCTTTGGTGGTTCATACACTGGTGGCTT-GGGTTCAGGCCTT-
1 TCTTTCTTTGGTGGTGCATAAACTAGTGGCTTAGGCTT-AGG-CTTC
* * * * * *
5294385 TCTTTCTTTGGAGGTGTATAAACTGGTGACTTAGGCTCAGGCTTT
1 TCTTTCTTTGGTGGTGCATAAACTAGTGGCTTAGGCTTAGGCTTC
* * * ** * * * *
5294430 TCTTTCTTTGGAGGTTCATATACCGGTGG-TTTGGGTTCATGCTTA
1 TCTTTCTTTGGTGGTGCATAAACTAGTGGCTTAGGCTT-AGGCTTC
* * * *
5294475 TCTTTCTTTGGTGATGTATAAAC-AGGTGGTTTAGGCTCAGGCTTC
1 TCTTTCTTTGGTGGTGCATAAACTA-GTGGCTTAGGCTTAGGCTTC
* *
5294520 TCCTTCTTTGGTGGTTCATAAAC-AGGTGGCTTA
1 TCTTTCTTTGGTGGTGCATAAACTA-GTGGCTTA
5294553 TGTTCATATG
Statistics
Matches: 311, Mismatches: 67, Indels: 30
0.76 0.16 0.07
Matches are distributed among these distances:
44 22 0.07
45 269 0.86
46 20 0.06
ACGTcount: A:0.15, C:0.18, G:0.27, T:0.40
Consensus pattern (45 bp):
TCTTTCTTTGGTGGTGCATAAACTAGTGGCTTAGGCTTAGGCTTC
Found at i:5294559 original size:90 final size:90
Alignment explanation
Indices: 5294072--5294551 Score: 638
Period size: 90 Copynumber: 5.3 Consensus size: 90
5294062 AAACTGGTGG
* * * * * * * * * * *
5294072 CTTCTTTGGAGGCTCATAAACTGGAGGTTTGGGTTCTGGTTTTTCTTTCTTTGGAGGTGCATAAA
1 CTTCTTTGGTGGTTCATACACAGGTGGCTTGGGTTCAGGCTTCTCTTTCTTTGGTGGTGTATAAA
* * * *
5294137 CTAGCGGTTTAGGCTTAGGCTTCTC
66 CTGGTGGCTTAGGCTCAGGCTTCTC
*
5294162 CTTCTTTGGTGGTTCATACATAGGTGGCTTGGGTTCAGGCTTCTCTTTCTTTGGTGGTGTATAAA
1 CTTCTTTGGTGGTTCATACACAGGTGGCTTGGGTTCAGGCTTCTCTTTCTTTGGTGGTGTATAAA
5294227 CTGGTGGCTTAGGCTCAGGCTTCTC
66 CTGGTGGCTTAGGCTCAGGCTTCTC
*
5294252 CTTCTTTGGTGGTTCATACACAAGTGGCTTGGGTTCAGGCTTCTCTTTCTTTGGTGGTGTATAAA
1 CTTCTTTGGTGGTTCATACACAGGTGGCTTGGGTTCAGGCTTCTCTTTCTTTGGTGGTGTATAAA
* *
5294317 CTGATGGCTTAGGCTTAGGCTTCTC
66 CTGGTGGCTTAGGCTCAGGCTTCTC
* *
5294342 CTTCTTTGGTGGTTCATACACTGGTGGCTTGGGTTCAGGCCTT-TCTTTCTTTGGAGGTGTATAA
1 CTTCTTTGGTGGTTCATACACAGGTGGCTTGGGTTCAGG-CTTCTCTTTCTTTGGTGGTGTATAA
* *
5294406 ACTGGTGACTTAGGCTCAGGCTTTTC
65 ACTGGTGGCTTAGGCTCAGGCTTCTC
* * * * * * * *
5294432 TTTCTTTGGAGGTTCATATACCGGTGGTTTGGGTTCATGCTTATCTTTCTTTGGTGATGTATAAA
1 CTTCTTTGGTGGTTCATACACAGGTGGCTTGGGTTCAGGCTTCTCTTTCTTTGGTGGTGTATAAA
* *
5294497 CAGGTGGTTTAGGCTCAGGCTTCTC
66 CTGGTGGCTTAGGCTCAGGCTTCTC
*
5294522 CTTCTTTGGTGGTTCATAAACAGGTGGCTT
1 CTTCTTTGGTGGTTCATACACAGGTGGCTT
5294552 ATGTTCATAT
Statistics
Matches: 344, Mismatches: 44, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
89 3 0.01
90 338 0.98
91 3 0.01
ACGTcount: A:0.14, C:0.18, G:0.28, T:0.40
Consensus pattern (90 bp):
CTTCTTTGGTGGTTCATACACAGGTGGCTTGGGTTCAGGCTTCTCTTTCTTTGGTGGTGTATAAA
CTGGTGGCTTAGGCTCAGGCTTCTC
Found at i:5295690 original size:15 final size:15
Alignment explanation
Indices: 5295672--5295726 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
5295662 CATCAAATTA
5295672 ACAAAAAAAAACTAG
1 ACAAAAAAAAACTAG
** *
5295687 ACAAAAATGAAATTTAAA
1 ACAAAAA--AAAACT-AG
5295705 ACAAAAAAAAACTAG
1 ACAAAAAAAAACTAG
5295720 ACAAAAA
1 ACAAAAA
5295727 TGAAATTTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
15 15 0.48
16 4 0.13
17 4 0.13
18 8 0.26
ACGTcount: A:0.73, C:0.11, G:0.05, T:0.11
Consensus pattern (15 bp):
ACAAAAAAAAACTAG
Found at i:5295713 original size:33 final size:33
Alignment explanation
Indices: 5295671--5295739 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
5295661 ACATCAAATT
5295671 AACAAAAAAAAACTAGACAAAAATGAAATTTAA
1 AACAAAAAAAAACTAGACAAAAATGAAATTTAA
*
5295704 AACAAAAAAAAACTAGACAAAAATGAAATTTGA
1 AACAAAAAAAAACTAGACAAAAATGAAATTTAA
5295737 AAC
1 AAC
5295740 TACCTGTTCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.68, C:0.10, G:0.07, T:0.14
Consensus pattern (33 bp):
AACAAAAAAAAACTAGACAAAAATGAAATTTAA
Found at i:5297461 original size:106 final size:106
Alignment explanation
Indices: 5297276--5297488 Score: 268
Period size: 106 Copynumber: 2.0 Consensus size: 106
5297266 AAATATCGCT
* **
5297276 AATTAAATCCAATTTTATAAAAAATGCCCTTGTATTTCAAGTTAATCGGGAAGAAAATCATGTGT
1 AATTAAATCAAATTTTATAAAAAATGCCCTTGTATTTCAAGTTAATCGGGAAGAAAATCATGCCT
* * *
5297341 CGTAAGTTAGGGCACGATGTCTCGAATTCCCAAAAATAAGA
66 CATAAATTAGGGCACGATGTCTCAAATTCCCAAAAATAAGA
* * * ** *
5297382 AATTAAATCAAATTTTATGAAGAATG-TCTTCGTATTTTGAGTTAATCTGGAAGAAAATCATGCC
1 AATTAAATCAAATTTTATAAAAAATGCCCTT-GTATTTCAAGTTAATCGGGAAGAAAATCATGCC
* *
5297446 -CTATAAATTAGGGCACGATGTCTCAAATTCCCGAATATAAGA
65 TC-ATAAATTAGGGCACGATGTCTCAAATTCCCAAAAATAAGA
5297488 A
1 A
5297489 TACTCATTTT
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
105 4 0.04
106 87 0.96
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (106 bp):
AATTAAATCAAATTTTATAAAAAATGCCCTTGTATTTCAAGTTAATCGGGAAGAAAATCATGCCT
CATAAATTAGGGCACGATGTCTCAAATTCCCAAAAATAAGA
Found at i:5301128 original size:3 final size:3
Alignment explanation
Indices: 5301120--5301187 Score: 127
Period size: 3 Copynumber: 22.7 Consensus size: 3
5301110 GAAAAATCAA
*
5301120 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5301168 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
5301188 ACAGTAAAAT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5301936 original size:31 final size:32
Alignment explanation
Indices: 5301889--5301948 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 32
5301879 TTAAATCTAG
5301889 CCCTAACCTTTTTAAAAAAAGTCAAATTTGAC
1 CCCTAACCTTTTTAAAAAAAGTCAAATTTGAC
*
5301921 CCCTAACC-TTTTAAAAAGAGTCAAATTT
1 CCCTAACCTTTTTAAAAAAAGTCAAATTT
5301949 CTATTTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 19 0.70
32 8 0.30
ACGTcount: A:0.40, C:0.22, G:0.07, T:0.32
Consensus pattern (32 bp):
CCCTAACCTTTTTAAAAAAAGTCAAATTTGAC
Found at i:5302782 original size:31 final size:31
Alignment explanation
Indices: 5302744--5302806 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
5302734 TGATTAAGGT
5302744 GCTTCTACTTAGTACGGTATTTTCTCTGTAA
1 GCTTCTACTTAGTACGGTATTTTCTCTGTAA
5302775 GCTTCTACTTAGTACGGTATTTTCTCTGTAA
1 GCTTCTACTTAGTACGGTATTTTCTCTGTAA
5302806 G
1 G
5302807 TAGATTTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.44
Consensus pattern (31 bp):
GCTTCTACTTAGTACGGTATTTTCTCTGTAA
Found at i:5302874 original size:2 final size:2
Alignment explanation
Indices: 5302867--5302972 Score: 194
Period size: 2 Copynumber: 53.0 Consensus size: 2
5302857 GGTATGGAAC
5302867 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
5302909 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* *
5302951 TG TG TG TG TG TT TG TG TT TG TG
1 TG TG TG TG TG TG TG TG TG TG TG
5302973 AGTTTCAATC
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 100 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:5306265 original size:24 final size:24
Alignment explanation
Indices: 5306235--5306394 Score: 71
Period size: 24 Copynumber: 6.7 Consensus size: 24
5306225 CTATATAACA
5306235 GGAAGCTCATAAGAGCCATAATTG
1 GGAAGCTCATAAGAGCCATAATTG
** *
5306259 GGAAGCTCATGTGAGCCTATAA-CG
1 GGAAGCTCATAAGAGCC-ATAATTG
* * *
5306283 GGTAGCTTC-GAAGAGCCATTAA-TA
1 GGAAGC-TCATAAGAGCCA-TAATTG
* * * *
5306307 GAAAGCTC-TGATAGCTATATATTG
1 GGAAGCTCATAAGAGCCATA-ATTG
* * *
5306331 GGAAGTTCA-AGCGAGCCAT-ATTA
1 GGAAGCTCATA-AGAGCCATAATTG
* * *
5306354 GGAAGCTCATTAAGAACCATTATCG
1 GGAAGCTCA-TAAGAGCCATAATTG
*
5306379 GGAAACTCATAAGAGC
1 GGAAGCTCATAAGAGC
5306395 TAAGGTGTGT
Statistics
Matches: 96, Mismatches: 30, Indels: 20
0.66 0.21 0.14
Matches are distributed among these distances:
22 2 0.02
23 20 0.21
24 52 0.54
25 22 0.23
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.23
Consensus pattern (24 bp):
GGAAGCTCATAAGAGCCATAATTG
Found at i:5308931 original size:23 final size:23
Alignment explanation
Indices: 5308882--5308953 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 23
5308872 AAGAAAAACC
* * *
5308882 GAAAGAAGAAGAAGAAAGAGAAA
1 GAAAGAAGAAAAAAAAACAGAAA
* *
5308905 GAAAGAAGAAAAAAAAACATAAG
1 GAAAGAAGAAAAAAAAACAGAAA
* *
5308928 GAAAGAAGGAAAACAATACA-AAA
1 GAAAGAA-GAAAAAAAAACAGAAA
5308951 GAA
1 GAA
5308954 GAACTAACAT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
23 30 0.75
24 10 0.25
ACGTcount: A:0.71, C:0.04, G:0.22, T:0.03
Consensus pattern (23 bp):
GAAAGAAGAAAAAAAAACAGAAA
Found at i:5315548 original size:135 final size:134
Alignment explanation
Indices: 5315295--5315578 Score: 338
Period size: 135 Copynumber: 2.1 Consensus size: 134
5315285 ACACTGGTGG
* * * * * *
5315295 CTTCTTTGGAGGCTTATAAACTGGTGGTTTGGGTTCTGGTTTTTCTTTCTTTGGAGGTGCATAAA
1 CTTCTTTGGTGG-TTATAAACTGGTGGTTTAGGCTCAGGCTTTTCCTTCTTTGGAGGTGCATAAA
* * * * * *
5315360 CTGGTGGTTTAGACTCAGGCTTTTCCTTCTTTGGTGGTTCATACATCGTTGGCTTGGGTTCATGC
65 CTGGTGGTTTAGACTCAGGCTTCTCCTTCTTTGGAGGTTCATAAATCGGTGGCTTAGGTTCAGGC
*
5315425 TTTTC
130 TTCTC
* * *
5315430 TTTCTTTGGTGGTGTATAAACTGGTGGTTTAGGCTCAGGCTTTTCCTTCTTTGGAGGTTCATATA
1 CTTCTTTGGTGGT-TATAAACTGGTGGTTTAGGCTCAGGCTTTTCCTTCTTTGGAGGTGCATAAA
* ** *
5315495 CTGGTGGTTTCGGTTCAGGCTTCTCTTTCTTTGGAGGTAT-ATAAA-CTGGTGGCTTAGGTTCAG
65 CTGGTGGTTTAGACTCAGGCTTCTCCTTCTTTGGAGGT-TCATAAATC-GGTGGCTTAGGTTCAG
5315558 GCTTCTC
128 GCTTCTC
5315565 CTTCTTTGGTGGTT
1 CTTCTTTGGTGGTT
5315579 CATAGACCGG
Statistics
Matches: 125, Mismatches: 21, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
134 3 0.02
135 121 0.97
136 1 0.01
ACGTcount: A:0.13, C:0.16, G:0.27, T:0.44
Consensus pattern (134 bp):
CTTCTTTGGTGGTTATAAACTGGTGGTTTAGGCTCAGGCTTTTCCTTCTTTGGAGGTGCATAAAC
TGGTGGTTTAGACTCAGGCTTCTCCTTCTTTGGAGGTTCATAAATCGGTGGCTTAGGTTCAGGCT
TCTC
Found at i:5315594 original size:90 final size:90
Alignment explanation
Indices: 5315295--5315594 Score: 377
Period size: 90 Copynumber: 3.3 Consensus size: 90
5315285 ACACTGGTGG
* * * * * *
5315295 CTTCTTTGGAGGCTT-ATAAACTGGTGGTTTGGGTTCTGGTTTTTCTTTCTTTGGAGGTGCATAA
1 CTTCTTTGGTGG-TTCATACACCGGTGGTTTGGGTTCAGGCTTTTCTTTCTTTGGAGGTGTATAA
*
5315359 ACTGGTGGTTTAGACTCAGGCTTTTC
65 ACTGGTGGTTTAGGCTCAGGCTTTTC
* * * * *
5315385 CTTCTTTGGTGGTTCATACATCGTTGGCTTGGGTTCATGCTTTTCTTTCTTTGGTGGTGTATAAA
1 CTTCTTTGGTGGTTCATACACCGGTGGTTTGGGTTCAGGCTTTTCTTTCTTTGGAGGTGTATAAA
5315450 CTGGTGGTTTAGGCTCAGGCTTTTC
66 CTGGTGGTTTAGGCTCAGGCTTTTC
* * * * * *
5315475 CTTCTTTGGAGGTTCATATACTGGTGGTTTCGGTTCAGGCTTCTCTTTCTTTGGAGGTATATAAA
1 CTTCTTTGGTGGTTCATACACCGGTGGTTTGGGTTCAGGCTTTTCTTTCTTTGGAGGTGTATAAA
* * *
5315540 CTGGTGGCTTAGGTTCAGGCTTCTC
66 CTGGTGGTTTAGGCTCAGGCTTTTC
* *
5315565 CTTCTTTGGTGGTTCATAGACCGGAGGTTT
1 CTTCTTTGGTGGTTCATACACCGGTGGTTT
5315595 ATGTTCATAT
Statistics
Matches: 179, Mismatches: 30, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
89 2 0.01
90 177 0.99
ACGTcount: A:0.13, C:0.16, G:0.27, T:0.43
Consensus pattern (90 bp):
CTTCTTTGGTGGTTCATACACCGGTGGTTTGGGTTCAGGCTTTTCTTTCTTTGGAGGTGTATAAA
CTGGTGGTTTAGGCTCAGGCTTTTC
Found at i:5315601 original size:45 final size:45
Alignment explanation
Indices: 5315295--5315601 Score: 298
Period size: 45 Copynumber: 6.8 Consensus size: 45
5315285 ACACTGGTGG
* * * *
5315295 CTTCTTTGGAGGCTT-ATAAACTGGTGGTTTGGGTTCTGGTTTTTC
1 CTTCTTTGGTGG-TTCATAAACTGGTGGTTTAGGTTCAGGCTTTTC
* * * **
5315340 TTTCTTTGGAGGTGCATAAACTGGTGGTTTAGACTCAGGCTTTTC
1 CTTCTTTGGTGGTTCATAAACTGGTGGTTTAGGTTCAGGCTTTTC
* * * * *
5315385 CTTCTTTGGTGGTTCATACA-TCGTTGGCTTGGGTTCATGCTTTTC
1 CTTCTTTGGTGGTTCATAAACT-GGTGGTTTAGGTTCAGGCTTTTC
* *
5315430 TTTCTTTGGTGGTGT-ATAAACTGGTGGTTTAGGCTCAGGCTTTTC
1 CTTCTTTGGTGGT-TCATAAACTGGTGGTTTAGGTTCAGGCTTTTC
* * * *
5315475 CTTCTTTGGAGGTTCATATACTGGTGGTTTCGGTTCAGGCTTCTC
1 CTTCTTTGGTGGTTCATAAACTGGTGGTTTAGGTTCAGGCTTTTC
* * * *
5315520 TTTCTTTGGAGGTAT-ATAAACTGGTGGCTTAGGTTCAGGCTTCTC
1 CTTCTTTGGTGGT-TCATAAACTGGTGGTTTAGGTTCAGGCTTTTC
* * * *
5315565 CTTCTTTGGTGGTTCATAGACCGGAGGTTTATGTTCA
1 CTTCTTTGGTGGTTCATAAACTGGTGGTTTAGGTTCA
5315602 TATGGTGGCG
Statistics
Matches: 214, Mismatches: 41, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
44 4 0.02
45 207 0.97
46 3 0.01
ACGTcount: A:0.14, C:0.16, G:0.27, T:0.43
Consensus pattern (45 bp):
CTTCTTTGGTGGTTCATAAACTGGTGGTTTAGGTTCAGGCTTTTC
Found at i:5319380 original size:2 final size:2
Alignment explanation
Indices: 5319373--5319402 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5319363 CTAGTGTATG
*
5319373 TA TA TA TA TA TG 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
5319403 ATAATCTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5319386 original size:12 final size:12
Alignment explanation
Indices: 5319369--5319402 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
5319359 TAATCTAGTG
5319369 TATGTATATATA
1 TATGTATATATA
5319381 TATGTATATATA
1 TATGTATATATA
*
5319393 TATATATATA
1 TATGTATATA
5319403 ATAATCTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (12 bp):
TATGTATATATA
Found at i:5321869 original size:24 final size:22
Alignment explanation
Indices: 5321830--5321875 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
5321820 GAACTTACTT
5321830 TTTTTAATATTTTTTTAATAAA
1 TTTTTAATATTTTTTTAATAAA
* *
5321852 TTTTTAGTGATTTATTTTACTAAA
1 TTTTTAAT-ATTT-TTTTAATAAA
5321876 CCCTAAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 7 0.35
23 4 0.20
24 9 0.45
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (22 bp):
TTTTTAATATTTTTTTAATAAA
Found at i:5322047 original size:14 final size:14
Alignment explanation
Indices: 5322028--5322054 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5322018 ATACTCTTTA
5322028 TAATATTTTTAATT
1 TAATATTTTTAATT
5322042 TAATATTTTTAAT
1 TAATATTTTTAAT
5322055 CGATTTCTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TAATATTTTTAATT
Found at i:5327188 original size:3 final size:3
Alignment explanation
Indices: 5327180--5327237 Score: 89
Period size: 3 Copynumber: 19.3 Consensus size: 3
5327170 ATTTGAATGC
* * *
5327180 TAA TAA TAA TAA CAA CAA CAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5327228 TAA TAA TAA T
1 TAA TAA TAA T
5327238 TTATTTGAAC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:5335757 original size:11 final size:11
Alignment explanation
Indices: 5335741--5335779 Score: 60
Period size: 11 Copynumber: 3.4 Consensus size: 11
5335731 TGGAGAAAAT
5335741 TTTTATATTAA
1 TTTTATATTAA
5335752 TTTTATATTAA
1 TTTTATATTAA
5335763 TATTTATATATAA
1 T-TTTATAT-TAA
5335776 TTTT
1 TTTT
5335780 TAAATTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 12 0.46
12 10 0.38
13 4 0.15
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TTTTATATTAA
Found at i:5335780 original size:25 final size:24
Alignment explanation
Indices: 5335737--5335792 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
5335727 AAAATGGAGA
* *
5335737 AAATTTTTATATTAATTTTATATT
1 AAATATTTATATTAATTTTAAATT
5335761 -AATATTTATATATAATTTTTAAATT
1 AAATATTTATAT-TAA-TTTTAAATT
5335786 AAATATT
1 AAATATT
5335793 GATTCAGATC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 10 0.37
24 3 0.11
25 8 0.30
26 6 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
AAATATTTATATTAATTTTAAATT
Found at i:5339738 original size:12 final size:12
Alignment explanation
Indices: 5339721--5339761 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
5339711 GCTATTTTTT
5339721 TTGTTTGTATTA
1 TTGTTTGTATTA
*
5339733 TTGTTTATATTA
1 TTGTTTGTATTA
* *
5339745 TTGTTAGTATCA
1 TTGTTTGTATTA
5339757 TTGTT
1 TTGTT
5339762 ATTCCTTAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.20, C:0.02, G:0.15, T:0.63
Consensus pattern (12 bp):
TTGTTTGTATTA
Found at i:5352479 original size:88 final size:88
Alignment explanation
Indices: 5352350--5352555 Score: 331
Period size: 88 Copynumber: 2.3 Consensus size: 88
5352340 TTTTGGCAAA
* * * *
5352350 TCTTATCTTCCTAAAGTTGCAGTGAAGCTGATTGAAACCACTAACTTTATCTCCCTGAAGATACG
1 TCTTATCTTCCTGAAGTTGCAGTGAAGCAGATCGAAACCACTAACCTTATCTCCCTGAAGATACG
*
5352415 GTGGAGTAGACTGAAGTTACAAG
66 GTGGAGTAGACTAAAGTTACAAG
*
5352438 TCTTATCTTCCTGAAGTTGCAGTGAAGCAGATCGAAGCCACTAACCTTATCTCCCTGAAGATACG
1 TCTTATCTTCCTGAAGTTGCAGTGAAGCAGATCGAAACCACTAACCTTATCTCCCTGAAGATACG
**
5352503 GTGGAGTAGGTTAAAGTTACAAG
66 GTGGAGTAGACTAAAGTTACAAG
*
5352526 TCTTATCTTCCTGAAGTTGCAGTGGAGCAG
1 TCTTATCTTCCTGAAGTTGCAGTGAAGCAG
5352556 GCTGAAGGTA
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 109 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (88 bp):
TCTTATCTTCCTGAAGTTGCAGTGAAGCAGATCGAAACCACTAACCTTATCTCCCTGAAGATACG
GTGGAGTAGACTAAAGTTACAAG
Found at i:5352551 original size:44 final size:44
Alignment explanation
Indices: 5352348--5352607 Score: 159
Period size: 44 Copynumber: 5.9 Consensus size: 44
5352338 AATTTTGGCA
* * * * *** *
5352348 AATCTTATCTTCCTAAAGTTGCAGTGAAGCTGATTGAAACCACT
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGACTGAAGTTACG
* * * * *
5352392 AA-CTTTATCTCCCTGAAGATACGGTGGAGTAGACTGAAGTTAC-
1 AATC-TTATCTTCCTGAAGTTGCAGTGGAGCAGACTGAAGTTACG
* ** *
5352435 AAGTCTTATCTTCCTGAAGTTGCAGTGAAGCAGA-TCGAAGCCACT
1 AA-TCTTATCTTCCTGAAGTTGCAGTGGAGCAGACT-GAAGTTACG
* * * * * * ** *
5352480 AACCTTATCTCCCTGAAGATACGGTGGAGTAGGTTAAAGTTAC-
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGACTGAAGTTACG
* *
5352523 AAGTCTTATCTTCCTGAAGTTGCAGTGGAGCAGGCTGAAGGTAGCG
1 AA-TCTTATCTTCCTGAAGTTGCAGTGGAGCAGACTGAAGTTA-CG
* * * *
5352569 AATCTTGTTTTCCTGAAGTTGCAGTGGAACAGATTGAAG
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGACTGAAG
5352608 CTATAAATTG
Statistics
Matches: 162, Mismatches: 45, Indels: 17
0.72 0.20 0.08
Matches are distributed among these distances:
43 6 0.04
44 117 0.72
45 37 0.23
46 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (44 bp):
AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGACTGAAGTTACG
Found at i:5352785 original size:137 final size:137
Alignment explanation
Indices: 5352521--5352785 Score: 368
Period size: 137 Copynumber: 1.9 Consensus size: 137
5352511 GGTTAAAGTT
* * * * *
5352521 ACAAGTCTTATCTTCCTGAAGTTGCAGTGGAGCAGGCTGAAGGTAGCGAATCTTGTTTTCCTGAA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGAAGCAGGCTGAAGATAGCAAATCTTGTTTCCCTGAA
*** * * ** * * *
5352586 GTTGCAGTGGAACAGATTGAAGCTATAAATTGTAGATCTTATCTCTCTGAAGTTACAGTAGAGTA
66 GTTGCAGTGGAACAGATTGAAGCTATAAATCACAGATCTTATCCCCCCAAAATGACAATAGAGTA
5352651 GATCAAA
131 GATCAAA
*
5352658 ACAAGTCTTATCTCCCTGAAGTTGCAGTGAAGCAGGCTGAAGATAGCAAATTTTGTTTCCCTGAA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGAAGCAGGCTGAAGATAGCAAATCTTGTTTCCCTGAA
* *
5352723 GTTGCAGTGGAATAGATTGAAGCTATAAATCACAGATCTTATCCCCCCAAAATGGCAATAGAG
66 GTTGCAGTGGAACAGATTGAAGCTATAAATCACAGATCTTATCCCCCCAAAATGACAATAGAG
5352786 CAGGTCGAAA
Statistics
Matches: 110, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
137 110 1.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (137 bp):
ACAAGTCTTATCTCCCTGAAGTTGCAGTGAAGCAGGCTGAAGATAGCAAATCTTGTTTCCCTGAA
GTTGCAGTGGAACAGATTGAAGCTATAAATCACAGATCTTATCCCCCCAAAATGACAATAGAGTA
GATCAAA
Found at i:5360669 original size:22 final size:20
Alignment explanation
Indices: 5360642--5360683 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
5360632 CCTATATTAA
*
5360642 TATTATAAATTTTTATATTTTT
1 TATTAT-AATTTAT-TATTTTT
5360664 TATTATAATTTATTATTTTT
1 TATTATAATTTATTATTTTT
5360684 ATACTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 6 0.32
22 6 0.32
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TATTATAATTTATTATTTTT
Found at i:5366771 original size:11 final size:11
Alignment explanation
Indices: 5366755--5366788 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
5366745 CAGGGCCACA
5366755 TTTTTTTATTT
1 TTTTTTTATTT
*
5366766 TTTTTTTGTTT
1 TTTTTTTATTT
*
5366777 TTTATTTATTT
1 TTTTTTTATTT
5366788 T
1 T
5366789 CCTTTTATTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.09, C:0.00, G:0.03, T:0.88
Consensus pattern (11 bp):
TTTTTTTATTT
Found at i:5371047 original size:27 final size:27
Alignment explanation
Indices: 5371017--5371073 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
5371007 ATTTAATTAC
* *
5371017 TTAAATTTATTATA-AATACATATTAAT
1 TTAAAATT-TTATACAATACACATTAAT
*
5371044 TTAAAATTTTATACAATACACATTATT
1 TTAAAATTTTATACAATACACATTAAT
5371071 TTA
1 TTA
5371074 CCACACAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.47
Consensus pattern (27 bp):
TTAAAATTTTATACAATACACATTAAT
Found at i:5374544 original size:2 final size:2
Alignment explanation
Indices: 5374537--5374573 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5374527 TTTCCATTGT
5374537 TA TA TA TA 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 TA TA TA TA T
5374574 GAATATGAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5379363 original size:2 final size:2
Alignment explanation
Indices: 5379356--5379403 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
5379346 TTATATTTTC
5379356 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5379398 AT -T AT A
1 AT AT AT A
5379404 AATAGAGGTG
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5379697 original size:30 final size:30
Alignment explanation
Indices: 5379663--5379723 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
5379653 CAACTTAACA
5379663 AGCAAATGCCTCTAAAATAATAACAAAATT
1 AGCAAATGCCTCTAAAATAATAACAAAATT
* * *
5379693 AGCAAATGCGTTTAAAATAATAACAGAATT
1 AGCAAATGCCTCTAAAATAATAACAAAATT
5379723 A
1 A
5379724 ACAATAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.52, C:0.13, G:0.10, T:0.25
Consensus pattern (30 bp):
AGCAAATGCCTCTAAAATAATAACAAAATT
Found at i:5381194 original size:17 final size:18
Alignment explanation
Indices: 5381172--5381208 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
5381162 AGGTATAAAG
*
5381172 AAAATAAAA-AAATATAA
1 AAAATAAAATAAAAATAA
5381189 AAAATAAAATAAAAATAA
1 AAAATAAAATAAAAATAA
5381207 AA
1 AA
5381209 TTATGATTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (18 bp):
AAAATAAAATAAAAATAA
Found at i:5393855 original size:40 final size:40
Alignment explanation
Indices: 5393810--5393888 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
5393800 TTTCATAAAT
5393810 TTTATATAGTTAAGCATTTGTTAAAGAGTTTCAAAAAAAA
1 TTTATATAGTTAAGCATTTGTTAAAGAGTTTCAAAAAAAA
*
5393850 TTTATATAGTTAAGCATTTGTTAAAGAGTTTCAGAAAAA
1 TTTATATAGTTAAGCATTTGTTAAAGAGTTTCAAAAAAA
5393889 TGAATGTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (40 bp):
TTTATATAGTTAAGCATTTGTTAAAGAGTTTCAAAAAAAA
Found at i:5396163 original size:3 final size:3
Alignment explanation
Indices: 5396155--5396203 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
5396145 GACGTATATG
5396155 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5396203 A
1 A
5396204 TATAGATATG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5396441 original size:2 final size:2
Alignment explanation
Indices: 5396436--5396467 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5396426 ATATAAAAGA
5396436 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
5396468 GGTATTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5396718 original size:17 final size:17
Alignment explanation
Indices: 5396692--5396726 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5396682 GATAATAGTG
5396692 AGCCATTAATAAAGATAC
1 AGCCATTAATAAA-ATAC
5396710 AGCCA-TAATAAAATAC
1 AGCCATTAATAAAATAC
5396726 A
1 A
5396727 ATAAATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 7 0.41
18 5 0.29
ACGTcount: A:0.54, C:0.17, G:0.09, T:0.20
Consensus pattern (17 bp):
AGCCATTAATAAAATAC
Found at i:5398421 original size:23 final size:22
Alignment explanation
Indices: 5398375--5398421 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
5398365 AGTAACAGAA
* *
5398375 GGGTAAAATAGTAAATATGCAG
1 GGGTAAAAGAGTAAATACGCAG
*
5398397 GGGTAAAAGAGTAAAATACGTAG
1 GGGTAAAAGAGT-AAATACGCAG
5398420 GG
1 GG
5398422 TTAGTCACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.45, C:0.04, G:0.32, T:0.19
Consensus pattern (22 bp):
GGGTAAAAGAGTAAATACGCAG
Found at i:5398802 original size:238 final size:235
Alignment explanation
Indices: 5398379--5398810 Score: 632
Period size: 237 Copynumber: 1.8 Consensus size: 235
5398369 ACAGAAGGGT
* * * * * *** *
5398379 AAAATAGTAAATATGCAGGGGTAAAAGAGTAAAATACGTAGGGTTAGTCACAACAGTGATCCACC
1 AAAATAATAAATATGCAGGGGTAAAAGAGTAAAAAACGCAGGGTCAGTCACAAAACCAACCCACC
* * *
5398444 ATTTCTACGCAACAGTAAAAAAATATATACTGTTCAGATTTTCGTAACAGTCAAAATCGAAAAAA
66 ATTTCCACGCAACAGTAAAAAAATATATACTGTTCAGATTTTCGTAACAGTCAAAAACCAAAAAA
5398509 GTCAAATTATTTTAAAGAAATTATTTTCTGAAAAATAATATAAGAATTTTATCCAAAAAGAAATA
131 GTCAAATTATTTTAAAGAAATTATTTTCTGAAAAATAATATAAGAATTTTATCCAAAAA-AAATA
5398574 TACGCGGTACATTTCAAAGACACGTGTTAACACAGTCATGA
195 TACGCGGTACATTTCAAAGACACGTGTTAACACAGTCATGA
* *
5398615 AAAATAATAAATATGTAGGGGTAAAAGAGTAAAAAACTGCAGGGTCAGTTACAAAACCAACCCAC
1 AAAATAATAAATATGCAGGGGTAAAAGAGTAAAAAAC-GCAGGGTCAGTCACAAAACCAACCCAC
* * * * * *
5398680 TATTTCCATGCAACAGTCAAAAAATATATAGTGTTTAGATTTTTGTAACAGTCAAAAACCAGAAA
65 CATTTCCACGCAACAGTAAAAAAATATATACTGTTCAGATTTTCGTAACAGTCAAAAACCA-AAA
*
5398745 AAGTCAAATTGTTTTAAAGAAATTATTTTCT-AGAAAATAATATAAGAATTTTATCCAAAAAAAA
129 AAGTCAAATTATTTTAAAGAAATTATTTTCTGA-AAAATAATATAAGAATTTTATCCAAAAAAAA
5398809 TA
193 TA
5398811 CAAATAGTAT
Statistics
Matches: 172, Mismatches: 21, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
236 34 0.20
237 77 0.45
238 61 0.35
ACGTcount: A:0.46, C:0.13, G:0.14, T:0.27
Consensus pattern (235 bp):
AAAATAATAAATATGCAGGGGTAAAAGAGTAAAAAACGCAGGGTCAGTCACAAAACCAACCCACC
ATTTCCACGCAACAGTAAAAAAATATATACTGTTCAGATTTTCGTAACAGTCAAAAACCAAAAAA
GTCAAATTATTTTAAAGAAATTATTTTCTGAAAAATAATATAAGAATTTTATCCAAAAAAAATAT
ACGCGGTACATTTCAAAGACACGTGTTAACACAGTCATGA
Found at i:5399914 original size:3 final size:3
Alignment explanation
Indices: 5399906--5399934 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5399896 ATTAAAGAAG
5399906 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5399935 TGTCCAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5407300 original size:3 final size:3
Alignment explanation
Indices: 5407292--5407330 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
5407282 GTAGACAAAG
5407292 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5407331 AAGGAAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5414905 original size:21 final size:20
Alignment explanation
Indices: 5414872--5414913 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
5414862 AAAAAACAAT
*
5414872 TTAATTACTTTAAGTAGGAAA
1 TTAATTACTTTAAATA-GAAA
5414893 TTAATT-CTCTTAAATAGAAA
1 TTAATTACT-TTAAATAGAAA
5414913 T
1 T
5414914 CAGTAGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (20 bp):
TTAATTACTTTAAATAGAAA
Found at i:5421030 original size:14 final size:14
Alignment explanation
Indices: 5421011--5421040 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5421001 TATCTTATAA
5421011 ATATGCGTGAATCT
1 ATATGCGTGAATCT
*
5421025 ATATGCGTTAATCT
1 ATATGCGTGAATCT
5421039 AT
1 AT
5421041 CTTGAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (14 bp):
ATATGCGTGAATCT
Found at i:5423454 original size:18 final size:19
Alignment explanation
Indices: 5423417--5423457 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
5423407 ATTTAGAATC
5423417 AAAACTAAAATAAATAATA
1 AAAACTAAAATAAATAATA
* *
5423436 AAAACTAGATTAAAT-ATA
1 AAAACTAAAATAAATAATA
5423454 AAAA
1 AAAA
5423458 TATCAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22
Consensus pattern (19 bp):
AAAACTAAAATAAATAATA
Found at i:5423459 original size:31 final size:31
Alignment explanation
Indices: 5423383--5423456 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 31
5423373 TCAAGTTATC
*
5423383 TTAAATATTAAAATAAAAATAAAAATTTAGAA
1 TTAAATA-TAAAATAAAAATAAAAATCTAGAA
*
5423415 TCAAA-ACTAAAATAAATAATAAAAA-CTAG-A
1 TTAAATA-TAAAATAAA-AATAAAAATCTAGAA
5423445 TTAAATATAAAA
1 TTAAATATAAAA
5423457 ATATCAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
30 10 0.28
31 14 0.39
32 12 0.33
ACGTcount: A:0.66, C:0.04, G:0.03, T:0.27
Consensus pattern (31 bp):
TTAAATATAAAATAAAAATAAAAATCTAGAA
Found at i:5423831 original size:78 final size:79
Alignment explanation
Indices: 5423701--5423857 Score: 307
Period size: 78 Copynumber: 2.0 Consensus size: 79
5423691 CCTCGAGTAA
5423701 AAAAAAATTATGTAAAAAATTATAACAATTAAGCATTAGTGACATACAATTAACGATTAAAATAA
1 AAAAAAATTATGTAAAAAATTATAACAATTAAGCATTAGTGACATACAATTAACGATTAAAATAA
5423766 AATAAAACATATAT
66 AATAAAACATATAT
5423780 AAAAAAATTATGT-AAAAATTATAACAATTAAGCATTAGTGACATACAATTAACGATTAAAATAA
1 AAAAAAATTATGTAAAAAATTATAACAATTAAGCATTAGTGACATACAATTAACGATTAAAATAA
5423844 AATAAAACATATAT
66 AATAAAACATATAT
5423858 GTAACAAATA
Statistics
Matches: 78, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
78 65 0.83
79 13 0.17
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.28
Consensus pattern (79 bp):
AAAAAAATTATGTAAAAAATTATAACAATTAAGCATTAGTGACATACAATTAACGATTAAAATAA
AATAAAACATATAT
Found at i:5427670 original size:16 final size:16
Alignment explanation
Indices: 5427649--5427684 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
5427639 TTATGCAACT
5427649 TTAATTAATCCCATCG
1 TTAATTAATCCCATCG
5427665 TTAATTAATCCCATCG
1 TTAATTAATCCCATCG
5427681 TTAA
1 TTAA
5427685 CTGGAGCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (16 bp):
TTAATTAATCCCATCG
Found at i:5428785 original size:14 final size:14
Alignment explanation
Indices: 5428746--5428810 Score: 58
Period size: 14 Copynumber: 4.6 Consensus size: 14
5428736 CTAATTAATT
* *
5428746 TAAACCCTAAATTCC
1 TAAACCCTAAA-ACA
* *
5428761 TAATCCCTAAACCA
1 TAAACCCTAAAACA
*
5428775 TAAATCCTAAAACA
1 TAAACCCTAAAACA
*
5428789 TAAACCCTAAATCA
1 TAAACCCTAAAACA
*
5428803 TGAACCCT
1 TAAACCCT
5428811 TAACCCTTAA
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
14 31 0.76
15 10 0.24
ACGTcount: A:0.45, C:0.31, G:0.02, T:0.23
Consensus pattern (14 bp):
TAAACCCTAAAACA
Found at i:5428829 original size:21 final size:20
Alignment explanation
Indices: 5428805--5428876 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 20
5428795 CTAAATCATG
5428805 AACCCTTAACCCTTAACCTCT
1 AACCCTTAACCCTTAACC-CT
*
5428826 AA-CCTCTAACCCCTAACACCT
1 AACCCT-TAACCCTTAAC-CCT
* *
5428847 AACACC-TAAACCTTAAACCCC
1 AAC-CCTTAACCCTT-AACCCT
5428868 AACCCTTAA
1 AACCCTTAA
5428877 ACCACACTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
20 5 0.12
21 30 0.73
22 4 0.10
23 2 0.05
ACGTcount: A:0.36, C:0.43, G:0.00, T:0.21
Consensus pattern (20 bp):
AACCCTTAACCCTTAACCCT
Found at i:5428890 original size:32 final size:32
Alignment explanation
Indices: 5428848--5428909 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
5428838 CTAACACCTA
* *
5428848 ACACCTAAACCTTAAACCCCAACCCTTAAACC
1 ACACCTAAACCATAAACCCCAAACCTTAAACC
* * *
5428880 ACACTTAAACCATAATCCCTAAACCTTAAA
1 ACACCTAAACCATAAACCCCAAACCTTAAA
5428910 ATAGTAACTC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.44, C:0.37, G:0.00, T:0.19
Consensus pattern (32 bp):
ACACCTAAACCATAAACCCCAAACCTTAAACC
Found at i:5429490 original size:41 final size:41
Alignment explanation
Indices: 5429427--5429686 Score: 337
Period size: 41 Copynumber: 6.4 Consensus size: 41
5429417 GTTATATGAC
* *
5429427 TTTTAGCGGCGTATTACAAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
*
5429468 TTATAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
*
5429509 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATTCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
* * *
5429550 TTTTAACGGCGTTTTACCAAAAGCACCGCAAATGCTCTGG-
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
* *
5429590 TTTTAGCGGCGTTTTACCAAAAGCGCCCGCTATTTCTCT-GT
1 TTTTAGCGGCGTTTTACCAAAAGCG-CCGCTAATGCTCTGGT
* * * * * *
5429631 TTTTAGCGGCATTTTAACAAAAAACGCCGGTATTGCTC-CGT
1 TTTTAGCGGCGTTTT-ACCAAAAGCGCCGCTAATGCTCTGGT
*
5429672 TTTTAGCGACGTTTT
1 TTTTAGCGGCGTTTT
5429687 TGGTAAAACG
Statistics
Matches: 194, Mismatches: 21, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
40 24 0.12
41 162 0.84
42 8 0.04
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.33
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
Found at i:5429709 original size:122 final size:123
Alignment explanation
Indices: 5429440--5429686 Score: 331
Period size: 122 Copynumber: 2.0 Consensus size: 123
5429430 TAGCGGCGTA
*
5429440 TTACAAAAAGCGCCGCTAATGCTCTGGTTTATAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTC
1 TTACCAAAAGCGCCGCTAATGCTCTGGTTTATAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTC
* * * * *
5429505 TGGTTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATTCTCTGGTTTTTAACGGCGTT
66 TGGTTTTTAGCGGCATTTTACAAAAAACGCCGCTAATTCTCTCGTTTTTAACGACGTT
* * * *
5429563 TTACCAAAAGCACCGCAAATGCTCTGGTTT-TAGCGGCGTTTTACCAAAAGCGCCCGCTATTTCT
1 TTACCAAAAGCGCCGCTAATGCTCTGGTTTATAGCGGCGTTTTACCAAAAGCG-CCGCTAATGCT
* *
5429627 CT-GTTTTTAGCGGCATTTTAACAAAAAACGCCGGT-ATTGCTC-CGTTTTTAGCGACGTT
65 CTGGTTTTTAGCGGCATTTT-ACAAAAAACGCCGCTAATT-CTCTCGTTTTTAACGACGTT
5429685 TT
1 TT
5429687 TGGTAAAACG
Statistics
Matches: 109, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
122 56 0.51
123 53 0.49
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.32
Consensus pattern (123 bp):
TTACCAAAAGCGCCGCTAATGCTCTGGTTTATAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTC
TGGTTTTTAGCGGCATTTTACAAAAAACGCCGCTAATTCTCTCGTTTTTAACGACGTT
Found at i:5431315 original size:3 final size:3
Alignment explanation
Indices: 5431307--5431375 Score: 129
Period size: 3 Copynumber: 23.0 Consensus size: 3
5431297 AAGTAGTCAG
5431307 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
5431355 ATT ATT ATT ATT ATT TTT ATT
1 ATT ATT ATT ATT ATT ATT ATT
5431376 TTGTTAGTAG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:5435698 original size:16 final size:16
Alignment explanation
Indices: 5435674--5435704 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5435664 AATAGTAAAC
*
5435674 ATAATATTAATATTAA
1 ATAAAATTAATATTAA
5435690 ATAAAATTAATATTA
1 ATAAAATTAATATTA
5435705 CAAATTTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAAATTAATATTAA
Found at i:5436823 original size:18 final size:18
Alignment explanation
Indices: 5436775--5436826 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
5436765 AAGGGTTGGT
*
5436775 TTAAGTGGGTTTGGGTAG
1 TTAAATGGGTTTGGGTAG
**
5436793 TTAGTTGGGTTTGGGTAG
1 TTAAATGGGTTTGGGTAG
5436811 -TAAATGGGTTTTGGGT
1 TTAAATGGG-TTTGGGT
5436827 TATAATGTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 6 0.21
18 23 0.79
ACGTcount: A:0.15, C:0.00, G:0.42, T:0.42
Consensus pattern (18 bp):
TTAAATGGGTTTGGGTAG
Found at i:5437854 original size:87 final size:86
Alignment explanation
Indices: 5437749--5437979 Score: 333
Period size: 85 Copynumber: 2.7 Consensus size: 86
5437739 CATGTGTGCC
5437749 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATGTAAATTGAAAAACAGAAAT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAT-TAAATTGAAAAACAGAAAT
* * *
5437814 TGAAAATACCTCAGCGTGTCTT
65 TGAAAATACCTCAACGTGCCCT
* *
5437836 GAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTTTG-AAAA--ACATTGAAAATAACAGAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATTAAATTG-AAA-AACAGAAA
*
5437898 TTGAAATTACCTCAACGTGCCCT
64 TTGAAAATACCTCAACGTGCCCT
5437921 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATATAAATTGAAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAAT-TAAATTGAAAA
5437980 TACCCAACAT
Statistics
Matches: 128, Mismatches: 8, Indels: 14
0.85 0.05 0.09
Matches are distributed among these distances:
83 5 0.04
84 3 0.02
85 59 0.46
86 4 0.03
87 44 0.34
88 4 0.03
89 1 0.01
90 3 0.02
91 5 0.04
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (86 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATTAAATTGAAAAACAGAAATT
GAAAATACCTCAACGTGCCCT
Found at i:5437944 original size:172 final size:167
Alignment explanation
Indices: 5437749--5438292 Score: 634
Period size: 172 Copynumber: 3.3 Consensus size: 167
5437739 CATGTGTGCC
*
5437749 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATGTAAATTGAAAAACAGAAAT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG--AAATGT-AATTGAAAAACAAAAAT
*
5437814 TGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTTTGAAAA
63 TGAAAATACCTCAGCGTGTCATGAGGCTCAACTCA-CTCTCGCAATATGAGTTGATTTTTGAAAA
*
5437879 ACATTGAAAATAACAGAAATTGAAATTACCTCAACGTGCCCT
127 ACATTGAAAATAACAGAAATTGAAA-TACCTCAGCGTGCCCT
* *
5437921 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTT----T-T--TTGAAAAATATAAATTGA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAATGTAATTGAAAAACAAAAATTGA
* * * *
5437977 AAATACC-CAACATGTCATGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTCTG-AAAACA
66 AAATACCTCAGCGTGTCATGAGGCTCAACTCA-CTCTCGCAATATGAGTTGATTTTTGAAAAACA
* * *
5438040 --GATTAATCAACAGAATTTGAGAATACCTCAGCGTGTCCT
130 TTGA-AAAT-AACAGAAATTGA-AATACCTCAGCGTGCCCT
* *
5438079 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTCTTTGAAACGTAACTT-AAAGAACAAAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TT-TTTGAAATGTAA-TTGAAA-AACAAAAA
* **
5438143 TTGAACATACCTCAGCGTGTCCCGAGGCTCAACTCACTCTCGCAATATGAGTTGATTTTTGAAAA
62 TTGAAAATACCTCAGCGTGTCATGAGGCTCAACTCACTCTCGCAATATGAGTTGATTTTTGAAAA
* * * *
5438208 CTAAATT-AAAACAACA-AGAATTGAAAATACCTTAGCATGCCCT
127 --ACATTGAAAATAACAGA-AATTG-AAATACCTCAGCGTGCCCT
5438251 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA
5438293 AACATAAATT
Statistics
Matches: 317, Mismatches: 31, Indels: 50
0.80 0.08 0.13
Matches are distributed among these distances:
156 2 0.01
157 3 0.01
158 63 0.20
159 46 0.15
160 23 0.07
162 3 0.01
163 1 0.00
164 1 0.00
167 1 0.00
169 3 0.01
170 51 0.16
171 26 0.08
172 88 0.28
173 5 0.02
174 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (167 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAATGTAATTGAAAAACAAAAATTGA
AAATACCTCAGCGTGTCATGAGGCTCAACTCACTCTCGCAATATGAGTTGATTTTTGAAAAACAT
TGAAAATAACAGAAATTGAAATACCTCAGCGTGCCCT
Found at i:5438100 original size:158 final size:156
Alignment explanation
Indices: 5437799--5438306 Score: 569
Period size: 158 Copynumber: 3.1 Consensus size: 156
5437789 AAAATGTAAA
* *
5437799 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGA
1 TTGAAAAACATAAATTGAAAATACCTCAGCGTGTCATGAGGCTCAACTCA-CTCTCGCAATATGA
* *
5437864 GTTGATTTTTGAAAAACATTGA-AAAT-AACAGAAATTGAAATTACCTCAACGTGCCCTGAGGCT
65 GTTGATTTTTG-AAAACA--GATTAATCAACAG-AATTGAAA-TACCTCAGCGTGCCCTGAGGCT
5437927 CAACTCACCTCTCGCAATATGAGTTGATTTTT
125 CAACTCACCTCTCGCAATATGAGTTGATTTTT
* * * *
5437959 TTGAAAAATATAAATTGAAAATACC-CAACATGTCATGAGGCTCAACTCACCTCTCACAATATGA
1 TTGAAAAACATAAATTGAAAATACCTCAGCGTGTCATGAGGCTCAACTCA-CTCTCGCAATATGA
* * *
5438023 GTTGATTTCTGAAAACAGATTAATCAACAGAATTTGAGAATACCTCAGCGTGTCCTAAGGCTCAA
65 GTTGATTTTTGAAAACAGATTAATCAACAGAA-TTGA-AATACCTCAGCGTGCCCTGAGGCTCAA
5438088 CTCACCTCTCGCAATATGAGTTGATTTCTTT
128 CTCACCTCTCGCAATATGAGTTGA-TT-TTT
* * * **
5438119 GAAACGTAACTTAAAGAACAAAAATTGAACATACCTCAGCGTGTCCCGAGGCTCAACTCACTCTC
1 ------T---TGAAA-AACATAAATTGAAAATACCTCAGCGTGTCATGAGGCTCAACTCACTCTC
* * * *
5438184 GCAATATGAGTTGATTTTTGAAAACTAAATTAAAACAACAAGAATTGAAAATACCTTAGCATGCC
56 GCAATATGAGTTGATTTTTGAAAAC-AGATT-AATCAAC-AGAATTG-AAATACCTCAGCGTGCC
5438249 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTT
117 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
5438287 TTGAAAAACATAAATT-AAAA
1 TTGAAAAACATAAATTGAAAA
5438307 GGCTCAACTC
Statistics
Matches: 296, Mismatches: 31, Indels: 45
0.80 0.08 0.12
Matches are distributed among these distances:
156 2 0.01
157 8 0.03
158 70 0.24
159 52 0.18
160 26 0.09
162 1 0.00
166 1 0.00
168 3 0.01
169 4 0.01
170 44 0.15
171 24 0.08
172 56 0.19
173 5 0.02
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (156 bp):
TTGAAAAACATAAATTGAAAATACCTCAGCGTGTCATGAGGCTCAACTCACTCTCGCAATATGAG
TTGATTTTTGAAAACAGATTAATCAACAGAATTGAAATACCTCAGCGTGCCCTGAGGCTCAACTC
ACCTCTCGCAATATGAGTTGATTTTT
Found at i:5438274 original size:86 final size:86
Alignment explanation
Indices: 5437971--5438305 Score: 398
Period size: 84 Copynumber: 3.9 Consensus size: 86
5437961 GAAAAATATA
* * * * *
5437971 AATTGAAAATACC-CAACATGTCATGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTCTGA
1 AATTGAAAATACCTCAGCATGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
* *
5438035 AAAC--AGATTAATCAAC-AG
66 AAACATAAATTAAACAACAAG
* * * *
5438053 AATTTGAGAATACCTCAGCGTGTCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTCTT
1 AA-TTGAAAATACCTCAGCATGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TT-TT
* * * *
5438118 TG-AAACGTAACTTAAAGAACAAA
63 TGAAAACATAAATTAAACAACAAG
* *
5438141 AATTGAACATACCTCAGCGTGTCCC-GAGGCTCAACTCA-CTCTCGCAATATGAGTTGATTTTTG
1 AATTGAAAATACCTCAGCATG-CCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
5438204 AAAAC-TAAATTAAAACAACAAG
65 AAAACATAAATT-AAACAACAAG
*
5438226 AATTGAAAATACCTTAGCATGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
1 AATTGAAAATACCTCAGCATGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-
5438291 AAAACATAAATTAAA
65 AAAACATAAATTAAA
5438306 AGGCTCAACT
Statistics
Matches: 217, Mismatches: 22, Indels: 23
0.83 0.08 0.09
Matches are distributed among these distances:
82 2 0.01
83 10 0.05
84 51 0.24
85 51 0.24
86 47 0.22
87 45 0.21
88 11 0.05
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (86 bp):
AATTGAAAATACCTCAGCATGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
AAACATAAATTAAACAACAAG
Done.