Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007716.1 Hibiscus syriacus cultivar Beakdansim tig00109945_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4364108
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 17
Found at i:3478219 original size:21 final size:21
Alignment explanation
Indices: 3478193--3478236 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
3478183 AATTAAGTAA
3478193 TTGGGTGGCGTCTAATCTTTC
1 TTGGGTGGCGTCTAATCTTTC
3478214 TTGGGTGGCGTCTAATCTTTC
1 TTGGGTGGCGTCTAATCTTTC
3478235 TT
1 TT
3478237 TGGTTGCGCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.45
Consensus pattern (21 bp):
TTGGGTGGCGTCTAATCTTTC
Found at i:3483569 original size:36 final size:38
Alignment explanation
Indices: 3483497--3483573 Score: 122
Period size: 38 Copynumber: 2.1 Consensus size: 38
3483487 TACATGGGAA
3483497 GAAACGACTTAAAGCAAGAAAGAGTGTGATATGTGGCG
1 GAAACGACTTAAAGCAAGAAAGAGTGTGATATGTGGCG
* *
3483535 GAAAGGACTTAAAGCAAGAAAG-G-GTGATGTGTGGCG
1 GAAACGACTTAAAGCAAGAAAGAGTGTGATATGTGGCG
3483571 GAA
1 GAA
3483574 GTGTATTCAG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 15 0.41
37 1 0.03
38 21 0.57
ACGTcount: A:0.39, C:0.09, G:0.35, T:0.17
Consensus pattern (38 bp):
GAAACGACTTAAAGCAAGAAAGAGTGTGATATGTGGCG
Found at i:3484971 original size:29 final size:29
Alignment explanation
Indices: 3484922--3484978 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
3484912 CCTAAGAGTT
*
3484922 CCAAGGCCGATAACCTTTATCTCATTTTTA
1 CCAAGGCCGACAACCTTTATCT-ATTTTTA
*
3484952 CCAAGGCTGACAA-CTTTATCTATTTTT
1 CCAAGGCCGACAACCTTTATCTATTTTT
3484979 CCTTGATTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 6 0.24
29 8 0.32
30 11 0.44
ACGTcount: A:0.26, C:0.25, G:0.11, T:0.39
Consensus pattern (29 bp):
CCAAGGCCGACAACCTTTATCTATTTTTA
Found at i:3496275 original size:31 final size:31
Alignment explanation
Indices: 3496239--3496342 Score: 129
Period size: 31 Copynumber: 3.4 Consensus size: 31
3496229 GGCCTATGGT
* *
3496239 CTACCCAAGAAAGTTCTCAGGGCCACAGGGC
1 CTACCCAAGAAAGATCTCAGGGCCGCAGGGC
* *
3496270 CTACCCAAGAAAGATCTCAAGGCCGTAGGGC
1 CTACCCAAGAAAGATCTCAGGGCCGCAGGGC
* **
3496301 CTACCCAAGAATA-ATCTCGGGGCCGCATAGC
1 CTACCCAAGAA-AGATCTCAGGGCCGCAGGGC
3496332 CTACCCAAGAA
1 CTACCCAAGAA
3496343 TCACATTAGG
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
31 62 0.98
32 1 0.02
ACGTcount: A:0.32, C:0.32, G:0.23, T:0.13
Consensus pattern (31 bp):
CTACCCAAGAAAGATCTCAGGGCCGCAGGGC
Found at i:3502151 original size:19 final size:19
Alignment explanation
Indices: 3502101--3502154 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
3502091 GAATGCAATT
*
3502101 AGTGTACCGATACACCCCA
1 AGTGTACCGATATACCCCA
3502120 AGTGTACCGATATACCCCA
1 AGTGTACCGATATACCCCA
3502139 AGTGTACCGATATACC
1 AGTGTACCGATATACC
3502155 AGGTCAACCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.20
Consensus pattern (19 bp):
AGTGTACCGATATACCCCA
Found at i:3502937 original size:2 final size:2
Alignment explanation
Indices: 3502930--3502962 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3502920 GGACGTTGTG
3502930 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3502963 ACGTATGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3508303 original size:45 final size:45
Alignment explanation
Indices: 3508252--3508341 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
3508242 GTCAAATGAT
3508252 ATAGCTTTGAGATTTTGAATGCCGCTTTTCTTAACTTATTTCATC
1 ATAGCTTTGAGATTTTGAATGCCGCTTTTCTTAACTTATTTCATC
3508297 ATAGCTTTGAGATTTTGAATGCCGCTTTTCTTAACTTATTTCATC
1 ATAGCTTTGAGATTTTGAATGCCGCTTTTCTTAACTTATTTCATC
3508342 CCACCAATTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.22, C:0.18, G:0.13, T:0.47
Consensus pattern (45 bp):
ATAGCTTTGAGATTTTGAATGCCGCTTTTCTTAACTTATTTCATC
Found at i:3508849 original size:85 final size:85
Alignment explanation
Indices: 3508706--3508875 Score: 331
Period size: 85 Copynumber: 2.0 Consensus size: 85
3508696 GAAGAGAAGG
*
3508706 TATGCCCACAGGAAGCAAGGAAGAATGCAAAACAAGGGCATACAGTACCATGACATGATATATAA
1 TATGCCCACAGGAAGCAAGGAAGAATGCAAAACAAGGGCATACAGTACCATGACATGATATAAAA
3508771 AGAACAAGGTATACTTCAAA
66 AGAACAAGGTATACTTCAAA
3508791 TATGCCCACAGGAAGCAAGGAAGAATGCAAAACAAGGGCATACAGTACCATGACATGATATAAAA
1 TATGCCCACAGGAAGCAAGGAAGAATGCAAAACAAGGGCATACAGTACCATGACATGATATAAAA
3508856 AGAACAAGGTATACTTCAAA
66 AGAACAAGGTATACTTCAAA
3508876 GGAGGTATGA
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 84 1.00
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.16
Consensus pattern (85 bp):
TATGCCCACAGGAAGCAAGGAAGAATGCAAAACAAGGGCATACAGTACCATGACATGATATAAAA
AGAACAAGGTATACTTCAAA
Found at i:3510837 original size:38 final size:38
Alignment explanation
Indices: 3510795--3510879 Score: 170
Period size: 38 Copynumber: 2.2 Consensus size: 38
3510785 TTTAATGAAA
3510795 GAATTCAACTATATAAATATAAATACCTGGATTCATGG
1 GAATTCAACTATATAAATATAAATACCTGGATTCATGG
3510833 GAATTCAACTATATAAATATAAATACCTGGATTCATGG
1 GAATTCAACTATATAAATATAAATACCTGGATTCATGG
3510871 GAATTCAAC
1 GAATTCAAC
3510880 AATGAATTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.31
Consensus pattern (38 bp):
GAATTCAACTATATAAATATAAATACCTGGATTCATGG
Found at i:3518807 original size:17 final size:17
Alignment explanation
Indices: 3518770--3518821 Score: 77
Period size: 17 Copynumber: 3.0 Consensus size: 17
3518760 TTTATTTAAT
* *
3518770 TTTAAAATATAAAAAATA
1 TTTAAAA-ATTAAATATA
3518788 TTTAAAAATTAAATATA
1 TTTAAAAATTAAATATA
3518805 TTTAAAAATTAAATATA
1 TTTAAAAATTAAATATA
3518822 AAAATACTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 25 0.78
18 7 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTTAAAAATTAAATATA
Found at i:3526098 original size:24 final size:26
Alignment explanation
Indices: 3526048--3526098 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
3526038 ATAAAATTTG
3526048 TGCATAAAATCTTTGATCTATTCTCA
1 TGCATAAAATCTTTGATCTATTCTCA
3526074 TGCATAAAATC-TTGAT-TATTCTCA
1 TGCATAAAATCTTTGATCTATTCTCA
3526098 T
1 T
3526099 TTCACACCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 9 0.36
25 5 0.20
26 11 0.44
ACGTcount: A:0.31, C:0.18, G:0.08, T:0.43
Consensus pattern (26 bp):
TGCATAAAATCTTTGATCTATTCTCA
Found at i:3528015 original size:19 final size:21
Alignment explanation
Indices: 3527969--3528008 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3527959 TAGCCTTTTA
3527969 AATTATTACAGTTTATATTTC
1 AATTATTACAGTTTATATTTC
3527990 AATTATTACA-TTTA-ATTTC
1 AATTATTACAGTTTATATTTC
3528009 CAATATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.26
20 4 0.21
21 10 0.53
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
AATTATTACAGTTTATATTTC
Found at i:3531315 original size:78 final size:77
Alignment explanation
Indices: 3531169--3531352 Score: 235
Period size: 78 Copynumber: 2.4 Consensus size: 77
3531159 GGCTGGGGTT
* * * * *
3531169 GCTGACCCCCTTATGTGGAAGGGAATGTTGTTGCATGTGTTTTTGGTTTGGTTGATCTTGGACAT
1 GCTGACCCCCTTGTGTGGAAGGGGATGTTGTTACATGTGCTTTTGGTTTGATTGATCTTGGACAT
3531234 GCTCTTGGAGTG
66 GCTCTTGGAGTG
* * *
3531246 GCTGGCCTCCTTTGTGTGGAAGGGGATGTTGTTACTTGTGCTTTTGGTTTGATTGATCTTGTG-C
1 GCTGACC-CCCTTGTGTGGAAGGGGATGTTGTTACATGTGCTTTTGGTTTGATTGATCTTG-GAC
* *
3531310 CTGCTCTTGGAGTT
64 ATGCTCTTGGAGTG
* *
3531324 GTTGACCCCCTTGTGTGGAGGGGGATGTT
1 GCTGACCCCCTTGTGTGGAAGGGGATGTT
3531353 ACCGCTCAGG
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
77 26 0.29
78 64 0.70
79 1 0.01
ACGTcount: A:0.11, C:0.15, G:0.34, T:0.40
Consensus pattern (77 bp):
GCTGACCCCCTTGTGTGGAAGGGGATGTTGTTACATGTGCTTTTGGTTTGATTGATCTTGGACAT
GCTCTTGGAGTG
Found at i:3535221 original size:17 final size:18
Alignment explanation
Indices: 3535189--3535222 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3535179 AAAATAGTTA
3535189 AAATAATAAATAAAAGAT
1 AAATAATAAATAAAAGAT
*
3535207 AAATAA-AATTAAAAGA
1 AAATAATAAATAAAAGA
3535223 AGATAATCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (18 bp):
AAATAATAAATAAAAGAT
Found at i:3535345 original size:63 final size:64
Alignment explanation
Indices: 3535267--3535396 Score: 244
Period size: 63 Copynumber: 2.0 Consensus size: 64
3535257 GAATGGTAGG
3535267 GATTGATCTAAGAATGCTAAACTTATCTCTCAGGCAG-ATAAGCTATCTGGTCTTTACTTACTC
1 GATTGATCTAAGAATGCTAAACTTATCTCTCAGGCAGAATAAGCTATCTGGTCTTTACTTACTC
3535330 GATTGATCTAAGAATGCTAAACTTATCTCTCAGGCAGATATAAGCTATCTGGTCTTTACTTACTC
1 GATTGATCTAAGAATGCTAAACTTATCTCTCAGGCAGA-ATAAGCTATCTGGTCTTTACTTACTC
3535395 GA
1 GA
3535397 CAGGGCTTTC
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
63 37 0.57
65 28 0.43
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (64 bp):
GATTGATCTAAGAATGCTAAACTTATCTCTCAGGCAGAATAAGCTATCTGGTCTTTACTTACTC
Found at i:3535797 original size:24 final size:24
Alignment explanation
Indices: 3535769--3535815 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3535759 GAGAACCAAG
*
3535769 ATAAA-CTTAAATATACCATTAAAA
1 ATAAAGCTTAAACAT-CCATTAAAA
*
3535793 ATAAAGTTTAAACATCCATTAAA
1 ATAAAGCTTAAACATCCATTAAA
3535816 CCAACCACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.55, C:0.13, G:0.02, T:0.30
Consensus pattern (24 bp):
ATAAAGCTTAAACATCCATTAAAA
Found at i:3537180 original size:13 final size:13
Alignment explanation
Indices: 3537163--3537198 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
3537153 AACTAATATT
3537163 AAAAATAAAGAAA
1 AAAAATAAAGAAA
*
3537176 TAAAATAAAGAAA
1 AAAAATAAAGAAA
3537189 AACAAATAAA
1 AA-AAATAAA
3537199 CAAACACTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.81, C:0.03, G:0.06, T:0.11
Consensus pattern (13 bp):
AAAAATAAAGAAA
Found at i:3542494 original size:29 final size:28
Alignment explanation
Indices: 3542444--3542498 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
3542434 TAAGCTCATT
3542444 AAAATTGTGATTGACTCATGCTCGTTAA
1 AAAATTGTGATTGACTCATGCTCGTTAA
* *
3542472 AAAATTGTTGCTTGACTCGTGCTCGTT
1 AAAATTG-TGATTGACTCATGCTCGTT
3542499 GCTCGTTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.38
Consensus pattern (28 bp):
AAAATTGTGATTGACTCATGCTCGTTAA
Found at i:3542750 original size:24 final size:24
Alignment explanation
Indices: 3542651--3542751 Score: 70
Period size: 24 Copynumber: 4.4 Consensus size: 24
3542641 GTCTGAATTA
* *
3542651 CAAACTAATAATCCACAAATACAC
1 CAAACTAACAATCCACAAATACAT
**
3542675 CAAACTAAC-AT--ATTAA-A-AT
1 CAAACTAACAATCCACAAATACAT
* * * *
3542694 CAAAGTAACAATCTAGAAATTCA-
1 CAAACTAACAATCCACAAATACAT
*
3542717 CTAAAGTAACAATCCACAAATACAT
1 C-AAACTAACAATCCACAAATACAT
3542742 CAAACTAACA
1 CAAACTAACA
3542752 TATTAAAAAC
Statistics
Matches: 58, Mismatches: 12, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
19 9 0.16
20 3 0.05
21 3 0.05
22 3 0.05
23 3 0.05
24 36 0.62
25 1 0.02
ACGTcount: A:0.54, C:0.23, G:0.03, T:0.20
Consensus pattern (24 bp):
CAAACTAACAATCCACAAATACAT
Found at i:3543391 original size:15 final size:15
Alignment explanation
Indices: 3543371--3543401 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3543361 TCAAATAAAA
3543371 CAGGAGTGTTATTTT
1 CAGGAGTGTTATTTT
3543386 CAGGAGTGTTATTTT
1 CAGGAGTGTTATTTT
3543401 C
1 C
3543402 CTCTACTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.10, G:0.26, T:0.45
Consensus pattern (15 bp):
CAGGAGTGTTATTTT
Found at i:3546830 original size:168 final size:171
Alignment explanation
Indices: 3546547--3546888 Score: 638
Period size: 168 Copynumber: 2.0 Consensus size: 171
3546537 TGATTTTTGC
3546547 TTTCAAAAACACTCATTGTGCTCAATTGTATCATTCTTGAGTGTTCTTTGTTTGTTATAGAATTG
1 TTTCAAAAACACTCATTGTGCTCAATTGTATCATTCTTGAGTGTTCTTTGTTTGTTATAGAATTG
3546612 TACAAACATCTTTCCTTATGAGGATTTTCTTGTAAGTTTGCGAAATTTGTATTGTTTCTCTTTGG
66 TACAAACATCTTTCCTTATGAGGATTTTCTTGTAAGTTTGCGAAATTTGTATTG-TTCTCTTTGG
3546677 GAGAG-G-GTTCTCAAGAA-TTGGAGTATAATTCTTGAGGGT
130 GAGAGAGTGTTCTCAAGAATTTGGAGTATAATTCTTGAGGGT
*
3546716 TTTC-AAAACACTTATTGTGCTCAATTGTATCATTCTTGAGTGTTCTTTGTTTGTTATAGAATTG
1 TTTCAAAAACACTCATTGTGCTCAATTGTATCATTCTTGAGTGTTCTTTGTTTGTTATAGAATTG
3546780 TACAAACATCTTTCCTTATGAGGATTTTCTTGTAAGTTTGCGAAATTTGTATTGTTCTCTTTGGG
66 TACAAACATCTTTCCTTATGAGGATTTTCTTGTAAGTTTGCGAAATTTGTATTGTTCTCTTTGGG
3546845 AGAGAGTGTTCTCAAGAATTTGGAGTATAATTCTTGAGGGT
131 AGAGAGTGTTCTCAAGAATTTGGAGTATAATTCTTGAGGGT
3546886 TTT
1 TTT
3546889 GTAAGGTTAC
Statistics
Matches: 169, Mismatches: 1, Indels: 5
0.97 0.01 0.03
Matches are distributed among these distances:
167 15 0.09
168 114 0.67
169 15 0.09
170 25 0.15
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.44
Consensus pattern (171 bp):
TTTCAAAAACACTCATTGTGCTCAATTGTATCATTCTTGAGTGTTCTTTGTTTGTTATAGAATTG
TACAAACATCTTTCCTTATGAGGATTTTCTTGTAAGTTTGCGAAATTTGTATTGTTCTCTTTGGG
AGAGAGTGTTCTCAAGAATTTGGAGTATAATTCTTGAGGGT
Found at i:3548294 original size:21 final size:22
Alignment explanation
Indices: 3548257--3548297 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3548247 AAGACTTTAT
3548257 TTTCAAAATACAAAAAATGATG
1 TTTCAAAATACAAAAAATGATG
*
3548279 TTTCAAAAT-TAAAAAATGA
1 TTTCAAAATACAAAAAATGA
3548298 AAATAGTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.29
Consensus pattern (22 bp):
TTTCAAAATACAAAAAATGATG
Found at i:3549307 original size:333 final size:333
Alignment explanation
Indices: 3548701--3549367 Score: 1253
Period size: 333 Copynumber: 2.0 Consensus size: 333
3548691 AGAATTTGGG
* *
3548701 TACCAAAAATCAAAAATCAATCTATGTTTGTAGGGAAAGGAGCATTGCTACAAGGCACGAGGAAC
1 TACCAAAAATCAAAAATCAATCTATGTTTGTAGGGAAAGGAGCATTACTACAAGGCACGAGAAAC
3548766 AAATTCAAACTCATGGTAGCTTGATAGTGGATGCTCAAGACACATGACCAGAGACAAGAGCCGGT
66 AAATTCAAACTCATGGTAGCTTGATAGTGGATGCTCAAGACACATGACCAGAGACAAGAGCCGGT
*
3548831 TCATAGAGCTTAACGCTAAAAATGGAGGAGAGGTGACTTCTGGAGATAAGTCAAAAGGTCACATT
131 TCATAGAGCTTAACGCTAAAAATAGAGGAGAGGTGACTTCTGGAGATAAGTCAAAAGGTCACATT
3548896 GAAGGTATAGGTACTATAGGTAATACATCTTCCATACAAATTAAAAATGTTTTATATGTGAATGG
196 GAAGGTATAGGTACTATAGGTAATACATCTTCCATACAAATTAAAAATGTTTTATATGTGAATGG
3548961 ATTAAATCATAATCTATTTAGTATTAGTCAATTATGCGATAAGAGATTCAATGTCATGTTTGAAA
261 ATTAAATCATAATCTATTTAGTATTAGTCAATTATGCGATAAGAGATTCAATGTCATGTTTGAAA
3549026 CTAATGGT
326 CTAATGGT
*
3549034 TACCAAAAATCAAAAATCAATCTATGTTTGTAGGGAAGGGAGCATTACTACAAGGCACGAGAAAC
1 TACCAAAAATCAAAAATCAATCTATGTTTGTAGGGAAAGGAGCATTACTACAAGGCACGAGAAAC
*
3549099 AAATTCAAACTCATGGTAGCTTGATAGTGGATGCTCAAGACACATGACCGGAGACAAGAGCCGGT
66 AAATTCAAACTCATGGTAGCTTGATAGTGGATGCTCAAGACACATGACCAGAGACAAGAGCCGGT
* *
3549164 TCATAGAGCTTAACGCTAAAAATAGAGGAGAGGTGACTTTTGGAGATAATTCAAAAGGTCACATT
131 TCATAGAGCTTAACGCTAAAAATAGAGGAGAGGTGACTTCTGGAGATAAGTCAAAAGGTCACATT
*
3549229 GAAGGTATAGGTACTATAGGTAATACATCTTCCATACAAATTAAAAATGTTTTATATGTGAATTG
196 GAAGGTATAGGTACTATAGGTAATACATCTTCCATACAAATTAAAAATGTTTTATATGTGAATGG
*
3549294 ATTAAATCATAATCTATTTAGTATTAGTCAATTATGCGATAAGGGATTCAATGTCATGTTTGAAA
261 ATTAAATCATAATCTATTTAGTATTAGTCAATTATGCGATAAGAGATTCAATGTCATGTTTGAAA
3549359 CTAATGGT
326 CTAATGGT
3549367 T
1 T
3549368 GTGTTGAAAA
Statistics
Matches: 325, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
333 325 1.00
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.28
Consensus pattern (333 bp):
TACCAAAAATCAAAAATCAATCTATGTTTGTAGGGAAAGGAGCATTACTACAAGGCACGAGAAAC
AAATTCAAACTCATGGTAGCTTGATAGTGGATGCTCAAGACACATGACCAGAGACAAGAGCCGGT
TCATAGAGCTTAACGCTAAAAATAGAGGAGAGGTGACTTCTGGAGATAAGTCAAAAGGTCACATT
GAAGGTATAGGTACTATAGGTAATACATCTTCCATACAAATTAAAAATGTTTTATATGTGAATGG
ATTAAATCATAATCTATTTAGTATTAGTCAATTATGCGATAAGAGATTCAATGTCATGTTTGAAA
CTAATGGT
Found at i:3549768 original size:64 final size:66
Alignment explanation
Indices: 3549611--3549770 Score: 220
Period size: 65 Copynumber: 2.5 Consensus size: 66
3549601 AATTAAATTG
* * *
3549611 AACATCGAATGCATTTCATGCATCGATGCA-CATACCATGCATCGATGCACTGAGGATTTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACCATACCATGAATCGATGCACTCAGGATTTTATGA
3549675 A
66 A
* * *
3549676 AACATCGAATGCATTTGATGCATCGATGCACCA-GCCATGAATCGATGCACTCTGGCTATTT-T-
1 AACATCGAATGCATTTGATGCATCGATGCACCATACCATGAATCGATGCACTCAGGAT-TTTATG
3549738 AA
65 AA
*
3549740 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
3549771 GCTTAGTGCA
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
64 32 0.37
65 49 0.57
66 5 0.06
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (66 bp):
AACATCGAATGCATTTGATGCATCGATGCACCATACCATGAATCGATGCACTCAGGATTTTATGA
A
Found at i:3555058 original size:42 final size:44
Alignment explanation
Indices: 3555011--3555105 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 44
3555001 TTGTGCTTCA
* *
3555011 TGCATCGATACACC-T-AACAGTGCATCGATGCA-TCCTTGAATG
1 TGCATCGATACACCATGAA-AGTGCACCGATGCACGCCTTGAATG
* *
3555053 TGCATCAATACACCATGAAGGTGCACCGATGCACGCCTTGAATG
1 TGCATCGATACACCATGAAAGTGCACCGATGCACGCCTTGAATG
3555097 TGCATCGAT
1 TGCATCGAT
3555106 GCACAAGGCC
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
42 13 0.29
43 13 0.29
44 19 0.42
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.24
Consensus pattern (44 bp):
TGCATCGATACACCATGAAAGTGCACCGATGCACGCCTTGAATG
Found at i:3555099 original size:23 final size:23
Alignment explanation
Indices: 3555030--3555110 Score: 87
Period size: 23 Copynumber: 3.7 Consensus size: 23
3555020 ACACCTAACA
*
3555030 GTGCATCGATGCA-TCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
* * *
3555052 GTGCATCAAT--ACACCATGAAG
1 GTGCATCGATGCACACCTTGAAT
* *
3555073 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
3555096 GTGCATCGATGCACA
1 GTGCATCGATGCACA
3555111 AGGCCATGCA
Statistics
Matches: 45, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
20 1 0.02
21 14 0.31
22 9 0.20
23 21 0.47
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.23
Consensus pattern (23 bp):
GTGCATCGATGCACACCTTGAAT
Found at i:3555126 original size:43 final size:42
Alignment explanation
Indices: 3555029--3555128 Score: 103
Period size: 43 Copynumber: 2.3 Consensus size: 42
3555019 TACACCTAAC
* * *
3555029 AGTGCATCGATGCATCCTTGAATGTGCATCAATACACCATGA
1 AGTGCATCGATGCAGCCTTGAATGTGCATCAATACACAAGGA
* * * *
3555071 AGGTGCACCGATGCACGCCTTGAATGTGCATCGATGCACAAGGCC
1 A-GTGCATCGATGCA-GCCTTGAATGTGCATCAATACACAAGG-A
3555116 A-TGCATCGATGCA
1 AGTGCATCGATGCA
3555129 TCCATCGGGT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
42 1 0.02
43 23 0.49
44 22 0.47
45 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (42 bp):
AGTGCATCGATGCAGCCTTGAATGTGCATCAATACACAAGGA
Found at i:3557423 original size:65 final size:63
Alignment explanation
Indices: 3557304--3557513 Score: 221
Period size: 65 Copynumber: 3.3 Consensus size: 63
3557294 TTTATCAAAG
* *
3557304 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATGC
1 TGATGCATCGATGCA-CAA-CCATGCATCGATGCACTCAGGATATT---TTGAAACATCGAATGC
3557366 ATT
61 ATT
* * *
3557369 TCATGCATCGATGCACATACCATGCATCGATGCACTGAGGAT-TTTATGAAAACATCGAATTCAT
1 TGATGCATCGATGCACA-ACCATGCATCGATGCACTCAGGATATTT-TG-AAACATCGAATGCAT
3557433 T
63 T
* * * * *
3557434 TGATGCATCGATGCACCAGCCATGTATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCA-CAACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
3557498 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
3557514 TCTTAGTGCA
Statistics
Matches: 124, Mismatches: 13, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
62 1 0.01
63 3 0.02
64 47 0.38
65 68 0.55
66 5 0.04
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (63 bp):
TGATGCATCGATGCACAACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:3557513 original size:17 final size:19
Alignment explanation
Indices: 3557485--3557533 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
3557475 TATTTTGAAA
3557485 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
3557503 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
3557522 CACCGATGCACT
1 CATCGATGCACT
3557534 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:3560213 original size:17 final size:18
Alignment explanation
Indices: 3560188--3560222 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3560178 GGTTATTAAA
*
3560188 TGCCCAAAA-CCTCTTTT
1 TGCCAAAAACCCTCTTTT
3560205 TGCCAAAAACCCTCTTTT
1 TGCCAAAAACCCTCTTTT
3560223 CTTCTTCTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.26, C:0.34, G:0.06, T:0.34
Consensus pattern (18 bp):
TGCCAAAAACCCTCTTTT
Found at i:3562043 original size:29 final size:28
Alignment explanation
Indices: 3562006--3562072 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 28
3561996 CTTGTTAAAC
*
3562006 ATTTTAATGTTTTTGGATTAAATGTTTGA
1 ATTTGAATGTTTTTGGATTAAATGTTT-A
* *
3562035 ATTTGAATGTTTTTGGTTTGAATGTTTA
1 ATTTGAATGTTTTTGGATTAAATGTTTA
3562063 ACTTTGAATG
1 A-TTTGAATG
3562073 CTTATATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 2 0.06
29 32 0.94
ACGTcount: A:0.25, C:0.01, G:0.19, T:0.54
Consensus pattern (28 bp):
ATTTGAATGTTTTTGGATTAAATGTTTA
Found at i:3562672 original size:19 final size:20
Alignment explanation
Indices: 3562631--3562671 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3562621 ACCATATTGT
3562631 CCAGAGGGTACCGATACCCC
1 CCAGAGGGTACCGATACCCC
3562651 CCAGAGGGTACCGATACCCC
1 CCAGAGGGTACCGATACCCC
3562671 C
1 C
3562672 ATGTAAGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.41, G:0.24, T:0.10
Consensus pattern (20 bp):
CCAGAGGGTACCGATACCCC
Found at i:3564171 original size:20 final size:21
Alignment explanation
Indices: 3564141--3564180 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
3564131 AGCCATTGGG
3564141 GCCTGATGGTATCGAAACTAT
1 GCCTGATGGTATCGAAACTAT
*
3564162 GCCT-ATGGTATCGATACTA
1 GCCTGATGGTATCGAAACTA
3564181 CTATGTATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.30
Consensus pattern (21 bp):
GCCTGATGGTATCGAAACTAT
Found at i:3565729 original size:17 final size:18
Alignment explanation
Indices: 3565707--3565753 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
3565697 TATGGAATTG
*
3565707 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
3565724 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
3565742 GATTCCAATTCC
1 GATTCCAATTCC
3565754 CTCAGAAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 12 0.43
18 16 0.57
ACGTcount: A:0.28, C:0.32, G:0.09, T:0.32
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:3570477 original size:21 final size:22
Alignment explanation
Indices: 3570437--3570484 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
3570427 AATATATTTT
* * *
3570437 TAAAATTTTTATTTAAAAAAAG
1 TAAAATTATTATTAAAAAAAAA
3570459 TAAAATTATT-TTAAAAAAAAA
1 TAAAATTATTATTAAAAAAAAA
3570480 TAAAA
1 TAAAA
3570485 GTCCCAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
TAAAATTATTATTAAAAAAAAA
Found at i:3572962 original size:49 final size:49
Alignment explanation
Indices: 3572905--3573005 Score: 184
Period size: 49 Copynumber: 2.1 Consensus size: 49
3572895 GAGACTTTGA
*
3572905 GTTGTGAAGGAAGCACCAGGGGAGTTGAAGAATGAAATTGAAAATTAGG
1 GTTGTGAAGGAAGCACCAGGGGAGTTAAAGAATGAAATTGAAAATTAGG
*
3572954 GTTGTGAAGGAGGCACCAGGGGAGTTAAAGAATGAAATTGAAAATTAGG
1 GTTGTGAAGGAAGCACCAGGGGAGTTAAAGAATGAAATTGAAAATTAGG
3573003 GTT
1 GTT
3573006 TCCTTTATTG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.38, C:0.06, G:0.35, T:0.22
Consensus pattern (49 bp):
GTTGTGAAGGAAGCACCAGGGGAGTTAAAGAATGAAATTGAAAATTAGG
Found at i:3573460 original size:29 final size:29
Alignment explanation
Indices: 3573418--3573476 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
3573408 CAAGTACTTG
3573418 AAATGGGACTCCTTTGCCGTCCCCGTGCT
1 AAATGGGACTCCTTTGCCGTCCCCGTGCT
*
3573447 AAATGGGACTCCTTTGCCGTCCCTGTGCT
1 AAATGGGACTCCTTTGCCGTCCCCGTGCT
3573476 A
1 A
3573477 CATAGCCATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.15, C:0.32, G:0.24, T:0.29
Consensus pattern (29 bp):
AAATGGGACTCCTTTGCCGTCCCCGTGCT
Found at i:3576971 original size:17 final size:17
Alignment explanation
Indices: 3576946--3576980 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3576936 GAAAATTCTC
3576946 ATATATCCTAATCATCT
1 ATATATCCTAATCATCT
* *
3576963 ATATGTCCTCATCATCT
1 ATATATCCTAATCATCT
3576980 A
1 A
3576981 AAAAGAGATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.31, C:0.26, G:0.03, T:0.40
Consensus pattern (17 bp):
ATATATCCTAATCATCT
Found at i:3580173 original size:16 final size:16
Alignment explanation
Indices: 3580149--3580185 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
3580139 TAAACCCATT
* *
3580149 AATATTTTTAAATTCA
1 AATAATTTTAAACTCA
3580165 AATAATTTTAAACTCA
1 AATAATTTTAAACTCA
3580181 AATAA
1 AATAA
3580186 AAAAAAACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (16 bp):
AATAATTTTAAACTCA
Found at i:3580311 original size:34 final size:34
Alignment explanation
Indices: 3580272--3580338 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
3580262 CCCAAATAAT
3580272 TTTATGTTCGTTCGTTTATATTCATTTACGTTTA
1 TTTATGTTCGTTCGTTTATATTCATTTACGTTTA
* * *
3580306 TTTATGTTCGTTTGTTTGTATTCGTTTACGTTT
1 TTTATGTTCGTTCGTTTATATTCATTTACGTTT
3580339 GCTCATTTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.13, C:0.10, G:0.15, T:0.61
Consensus pattern (34 bp):
TTTATGTTCGTTCGTTTATATTCATTTACGTTTA
Found at i:3583535 original size:20 final size:20
Alignment explanation
Indices: 3583510--3583556 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
3583500 TGACGGTGAG
3583510 GATGGATTTGTGGAAAAATA
1 GATGGATTTGTGGAAAAATA
3583530 GATGGATTTGTGGAAAAATA
1 GATGGATTTGTGGAAAAATA
3583550 GATGGAT
1 GATGGAT
3583557 AAGTGTCCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.30
Consensus pattern (20 bp):
GATGGATTTGTGGAAAAATA
Found at i:3592614 original size:59 final size:59
Alignment explanation
Indices: 3592526--3592695 Score: 171
Period size: 63 Copynumber: 2.8 Consensus size: 59
3592516 CAAGCTAACT
* * * * *
3592526 TTATTAACAAATTTCAAGTTATAGACTAAACTGA-TTTAATTAAGAAATTTAAGTTAAAC
1 TTATCAACTAATTTTAAATTATGGACTAAAC-GACTTTAATTAAGAAATTTAAGTTAAAC
* * *
3592585 TTATCAACTAATTTTAAATTATGGACTAAACGACTTTAGTTAAGAAATAAGACTAAATTAAAC
1 TTATCAACTAATTTTAAATTATGGACTAAACGACTTTAATTAAGAAAT----TTAAGTTAAAC
* * * * *
3592648 TTATCAAATAATTTTAAATTACGGACCAAACGACTTCAGTTAAGAAAT
1 TTATCAACTAATTTTAAATTATGGACTAAACGACTTTAATTAAGAAAT
3592696 AAGACTAAAC
Statistics
Matches: 94, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
58 2 0.02
59 39 0.41
63 53 0.56
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.34
Consensus pattern (59 bp):
TTATCAACTAATTTTAAATTATGGACTAAACGACTTTAATTAAGAAATTTAAGTTAAAC
Found at i:3592660 original size:63 final size:63
Alignment explanation
Indices: 3592579--3592704 Score: 216
Period size: 63 Copynumber: 2.0 Consensus size: 63
3592569 GAAATTTAAG
* * * *
3592579 TTAAACTTATCAACTAATTTTAAATTATGGACTAAACGACTTTAGTTAAGAAATAAGACTAAA
1 TTAAACTTATCAAATAATTTTAAATTACGGACCAAACGACTTCAGTTAAGAAATAAGACTAAA
3592642 TTAAACTTATCAAATAATTTTAAATTACGGACCAAACGACTTCAGTTAAGAAATAAGACTAAA
1 TTAAACTTATCAAATAATTTTAAATTACGGACCAAACGACTTCAGTTAAGAAATAAGACTAAA
3592705 CTGAGCAAGA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.31
Consensus pattern (63 bp):
TTAAACTTATCAAATAATTTTAAATTACGGACCAAACGACTTCAGTTAAGAAATAAGACTAAA
Found at i:3600836 original size:20 final size:20
Alignment explanation
Indices: 3600790--3600836 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
3600780 TACTACTGTT
3600790 AACTATGGGAAAATTTAGAG
1 AACTATGGGAAAATTTAGAG
*
3600810 AATTATGGGAAAATTTAGAG
1 AACTATGGGAAAATTTAGAG
*
3600830 TACTATG
1 AACTATG
3600837 CACATGATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.23, T:0.30
Consensus pattern (20 bp):
AACTATGGGAAAATTTAGAG
Found at i:3602045 original size:85 final size:85
Alignment explanation
Indices: 3601882--3602045 Score: 188
Period size: 85 Copynumber: 1.9 Consensus size: 85
3601872 AAATACAATC
* *
3601882 ATGACACACGAATATGTGCCATCTTCATTTATAACTGGGGCTTCAATGACACGCAATGTAAGTCA
1 ATGACACACAAATATGTGCCATCTTCATTTATAACTGGGGCTTCAATGACACGCAATGTAAGACA
* * *
3601947 TACATGCGTGTCATTAATTT
66 TAAATGAGCGTCATTAATTT
* * * * * * *
3601967 ATGACACACAAATGTGTGTCATCTTTATTTATGA-TGGGGGCTTTAATGACGCTCAATG-AACGA
1 ATGACACACAAATATGTGCCATCTTCATTTATAACT-GGGGCTTCAATGACACGCAATGTAA-GA
3602030 CATAAATGAGCGTCAT
64 CATAAATGAGCGTCAT
3602046 AAATGTGTGT
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
84 3 0.05
85 62 0.95
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (85 bp):
ATGACACACAAATATGTGCCATCTTCATTTATAACTGGGGCTTCAATGACACGCAATGTAAGACA
TAAATGAGCGTCATTAATTT
Found at i:3602046 original size:13 final size:13
Alignment explanation
Indices: 3602030--3602072 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
3602020 CAATGAACGA
3602030 CATAAATGAGCGT
1 CATAAATGAGCGT
* *
3602043 CATAAATGTGTGT
1 CATAAATGAGCGT
* *
3602056 TATAAATGCGCGT
1 CATAAATGAGCGT
3602069 CATA
1 CATA
3602073 GATTTATGAC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (13 bp):
CATAAATGAGCGT
Found at i:3613283 original size:22 final size:21
Alignment explanation
Indices: 3613253--3613296 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
3613243 TCAATACTGA
*
3613253 ATAGAGTATCGGTACCATAGT
1 ATAGAGTATCGATACCATAGT
3613274 ATAGAAGTATCGATACCATAGT
1 ATAG-AGTATCGATACCATAGT
3613296 A
1 A
3613297 GGGGTACCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (21 bp):
ATAGAGTATCGATACCATAGT
Found at i:3614122 original size:54 final size:55
Alignment explanation
Indices: 3614017--3614122 Score: 142
Period size: 54 Copynumber: 1.9 Consensus size: 55
3614007 CATAACTGTG
* **
3614017 CATTTTCGGCACTAAATGTGCAACCCATGGTATTCATAATGTGTTTATGAATAAC
1 CATTTTCGGCACTAAATGTGCAACCCATGGAATTCATAATAAGTTTATGAATAAC
** * *
3614072 CATTTT-GGCACTATGTGTGCAATCCATGGAATTCATAATAAGTTTGTGAAT
1 CATTTTCGGCACTAAATGTGCAACCCATGGAATTCATAATAAGTTTATGAAT
3614123 TTCTATTTCG
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
54 38 0.86
55 6 0.14
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (55 bp):
CATTTTCGGCACTAAATGTGCAACCCATGGAATTCATAATAAGTTTATGAATAAC
Found at i:3614136 original size:54 final size:54
Alignment explanation
Indices: 3614020--3614137 Score: 137
Period size: 54 Copynumber: 2.2 Consensus size: 54
3614010 AACTGTGCAT
* **
3614020 TTTCGGCACTAAATGTGCAACCCATGGTATTCATAATGTGTTTATGAATAACCA
1 TTTCGGCACTAAATGTGCAACCCATGGAATTCATAATAAGTTTATGAATAACCA
* ** * * ** *
3614074 TTTTGGCACTATGTGTGCAATCCATGGAATTCATAATAAGTTTGTGAATTTCTA
1 TTTCGGCACTAAATGTGCAACCCATGGAATTCATAATAAGTTTATGAATAACCA
3614128 TTTCGGCACT
1 TTTCGGCACT
3614138 TTGATGCAAT
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (54 bp):
TTTCGGCACTAAATGTGCAACCCATGGAATTCATAATAAGTTTATGAATAACCA
Found at i:3627597 original size:97 final size:97
Alignment explanation
Indices: 3627431--3627624 Score: 388
Period size: 97 Copynumber: 2.0 Consensus size: 97
3627421 GTGCGTTTTA
3627431 ATCAAATTTGGCCCATCCGAAATAGAGGTCTTCAAGTACTCCACTGTAAGTTTCATGGTCCACTT
1 ATCAAATTTGGCCCATCCGAAATAGAGGTCTTCAAGTACTCCACTGTAAGTTTCATGGTCCACTT
3627496 CAGCCATAAACTTCTTGTGTTGATCCTCCACT
66 CAGCCATAAACTTCTTGTGTTGATCCTCCACT
3627528 ATCAAATTTGGCCCATCCGAAATAGAGGTCTTCAAGTACTCCACTGTAAGTTTCATGGTCCACTT
1 ATCAAATTTGGCCCATCCGAAATAGAGGTCTTCAAGTACTCCACTGTAAGTTTCATGGTCCACTT
3627593 CAGCCATAAACTTCTTGTGTTGATCCTCCACT
66 CAGCCATAAACTTCTTGTGTTGATCCTCCACT
3627625 TTTCCAACAT
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 97 1.00
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.32
Consensus pattern (97 bp):
ATCAAATTTGGCCCATCCGAAATAGAGGTCTTCAAGTACTCCACTGTAAGTTTCATGGTCCACTT
CAGCCATAAACTTCTTGTGTTGATCCTCCACT
Found at i:3636259 original size:3 final size:3
Alignment explanation
Indices: 3636251--3636277 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3636241 TGCTTTTCCT
3636251 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
3636278 ACGTGGAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:3637954 original size:32 final size:32
Alignment explanation
Indices: 3637913--3638013 Score: 93
Period size: 31 Copynumber: 3.2 Consensus size: 32
3637903 AGTCGAGGGT
*
3637913 TTACCTATGTTCTACGGAACATATGGACA-TAA
1 TTACCTATGTTCTAAGGAACATATGGACAGT-A
** *
3637945 TTACCTATG-TCTTTTGGGACATATGGACAGTA
1 TTACCTATGTTC-TAAGGAACATATGGACAGTA
* * *
3637977 -TACCTATTTTCTAATGAACATATGGATAGT-
1 TTACCTATGTTCTAAGGAACATATGGACAGTA
3638007 TTACCTA
1 TTACCTA
3638014 GGTTATTCAG
Statistics
Matches: 56, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
31 29 0.52
32 26 0.46
33 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.37
Consensus pattern (32 bp):
TTACCTATGTTCTAAGGAACATATGGACAGTA
Found at i:3639686 original size:26 final size:26
Alignment explanation
Indices: 3639643--3639692 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
3639633 AAAGGATTAG
*
3639643 ATATGATAAAGGTTATATGGAAGTGT
1 ATATGATAAAGGTTATATAGAAGTGT
*
3639669 ATATGAT-AAGTTTGATATAGAAGT
1 ATATGATAAAGGTT-ATATAGAAGT
3639693 AAGAGAAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.40, C:0.00, G:0.24, T:0.36
Consensus pattern (26 bp):
ATATGATAAAGGTTATATAGAAGTGT
Found at i:3640802 original size:64 final size:64
Alignment explanation
Indices: 3640665--3640822 Score: 167
Period size: 64 Copynumber: 2.5 Consensus size: 64
3640655 AATTGTTCAG
* * * *
3640665 TGTGTATCGATGCACAGGAAGTGCATCGATGCACCCCTTAAAAATGGAAACATCGAATGCAATT
1 TGTGTATCGATGCATAGGAAGTGCATCGATACACCCCTTAAAAATGAAAACATCGAAGGCAATT
* * * * ***
3640729 AGTGCATCGATGCATAAGG-AGTGCATCGATACACCCCCTT-AAGATTAAAACATCGAAGGTGTT
1 TGTGTATCGATGCAT-AGGAAGTGCATCGATACA-CCCCTTAAAAATGAAAACATCGAAGGCAAT
3640792 T
64 T
* *
3640793 TGTGTATCGATGCATGGGTAGTGCATCGAT
1 TGTGTATCGATGCATAGGAAGTGCATCGAT
3640823 GCATATGTTA
Statistics
Matches: 77, Mismatches: 14, Indels: 6
0.79 0.14 0.06
Matches are distributed among these distances:
63 2 0.03
64 66 0.86
65 9 0.12
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (64 bp):
TGTGTATCGATGCATAGGAAGTGCATCGATACACCCCTTAAAAATGAAAACATCGAAGGCAATT
Found at i:3641881 original size:31 final size:31
Alignment explanation
Indices: 3641780--3641882 Score: 100
Period size: 31 Copynumber: 3.3 Consensus size: 31
3641770 AGAGTCGAGG
* * *
3641780 GTTTACCTATGTTCTACGAAACATATTGACA
1 GTTTACCTATGTTCTAAGGAACATATGGACA
* * *
3641811 GAATTACCTATGTCTTTTAGG-ACATATGGACA
1 G-TTTACCTATGT-TCTAAGGAACATATGGACA
* * *
3641843 ATATACCTATGTTCTAAGGAACATATGGATA
1 GTTTACCTATGTTCTAAGGAACATATGGACA
3641874 GTTTACCTA
1 GTTTACCTA
3641883 GGTTTTTCGG
Statistics
Matches: 55, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
30 5 0.09
31 27 0.49
32 20 0.36
33 3 0.05
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35
Consensus pattern (31 bp):
GTTTACCTATGTTCTAAGGAACATATGGACA
Found at i:3644360 original size:15 final size:15
Alignment explanation
Indices: 3644342--3644370 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3644332 CGCTTCTTCC
3644342 CCCTTTTTCTCTTTT
1 CCCTTTTTCTCTTTT
3644357 CCCTTTTTCTCTTT
1 CCCTTTTTCTCTTT
3644371 GCAGTAGTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (15 bp):
CCCTTTTTCTCTTTT
Found at i:3646381 original size:27 final size:27
Alignment explanation
Indices: 3646350--3646402 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
3646340 TCCTATAATC
*
3646350 GAATTAACTGGTTAATCCATCTAAACT
1 GAATTAACTGGTTAAGCCATCTAAACT
*
3646377 GAATTAACTGGTTAAGCCATGTAAAC
1 GAATTAACTGGTTAAGCCATCTAAAC
3646403 CGAGTATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (27 bp):
GAATTAACTGGTTAAGCCATCTAAACT
Found at i:3648074 original size:11 final size:11
Alignment explanation
Indices: 3648058--3648091 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
3648048 GATTGCTTAT
3648058 ATATAATATAA
1 ATATAATATAA
*
3648069 ATATAATATAT
1 ATATAATATAA
3648080 ATATATATATAA
1 ATATA-ATATAA
3648092 TTTACGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
ATATAATATAA
Found at i:3648258 original size:85 final size:85
Alignment explanation
Indices: 3648108--3648275 Score: 207
Period size: 85 Copynumber: 2.0 Consensus size: 85
3648098 AAATACAATC
* * * *
3648108 ATGACACAAGAATGTGTGTCATCTTTTTTAATGATGTGTGCTTCAATGACACACAATGTAAGTCA
1 ATGACACAAGAATGTGTGTCATCTTATTTAATGAAGAGGGCTTCAATGACACACAATGTAAGTCA
* *
3648173 TACATGCGTGTCAGAAATTT
66 TAAATACGTGTCAGAAATTT
* *
3648193 ATGACACACA-AATGTGTGTCATCTTCATTT-ATGAAGAGGGCTTCAATGACGCACAATG-AGCG
1 ATGACACA-AGAATGTGTGTCATCTT-ATTTAATGAAGAGGGCTTCAATGACACACAATGTA-AG
*
3648255 TCATAAATACGTGTCATAAAT
63 TCATAAATACGTGTCAGAAAT
3648276 GCTCGTCATA
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
84 1 0.01
85 66 0.93
86 4 0.06
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (85 bp):
ATGACACAAGAATGTGTGTCATCTTATTTAATGAAGAGGGCTTCAATGACACACAATGTAAGTCA
TAAATACGTGTCAGAAATTT
Found at i:3657117 original size:14 final size:14
Alignment explanation
Indices: 3657100--3657127 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3657090 ATCATAACAA
3657100 AATTATATAACTAT
1 AATTATATAACTAT
3657114 AATTATATAACTAT
1 AATTATATAACTAT
3657128 TCTTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:3658108 original size:27 final size:27
Alignment explanation
Indices: 3658077--3658132 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
3658067 ACAGGCCCAT
3658077 TACACGCAAACAAGAACAGCCCAAGGC
1 TACACGCAAACAAGAACAGCCCAAGGC
3658104 TACACGCAAACAAGAACAGCCCAAGGC
1 TACACGCAAACAAGAACAGCCCAAGGC
3658131 TA
1 TA
3658133 GTGACCCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.45, C:0.32, G:0.18, T:0.05
Consensus pattern (27 bp):
TACACGCAAACAAGAACAGCCCAAGGC
Found at i:3659612 original size:18 final size:19
Alignment explanation
Indices: 3659579--3659618 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
3659569 TCTTTTTCGG
3659579 TTTCTTATAATTTATTTAT
1 TTTCTTATAATTTATTTAT
*
3659598 TTTCTTAT-TTTTATTTAT
1 TTTCTTATAATTTATTTAT
3659616 TTT
1 TTT
3659619 GTTTGCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTCTTATAATTTATTTAT
Found at i:3659628 original size:18 final size:18
Alignment explanation
Indices: 3659579--3659631 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
3659569 TCTTTTTCGG
*
3659579 TTTCTTATAATTTATTTAT
1 TTTCTTAT-CTTTATTTAT
*
3659598 TTTCTTATTTTTATTTAT
1 TTTCTTATCTTTATTTAT
*
3659616 TTTGTT-TGCTTTATTT
1 TTTCTTAT-CTTTATTT
3659632 TCATTTTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
17 1 0.03
18 21 0.70
19 8 0.27
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.74
Consensus pattern (18 bp):
TTTCTTATCTTTATTTAT
Found at i:3663564 original size:95 final size:97
Alignment explanation
Indices: 3663395--3663631 Score: 284
Period size: 95 Copynumber: 2.5 Consensus size: 97
3663385 ATAATATATA
* * * * * *
3663395 TATACAATAAAGCTTGAGCTGCCCCTATAAAGCAATTAGTTAAACACCCCGACTTTATGAATAAG
1 TATACAATAAATCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACACCCCGACTTTATGAATAAG
**
3663460 ATTTTGCTAGCCTGATAAAGGT-AGTTAT-AA-
66 ATTCAGCTAGCCTGATAAAGGTGA-TTATAAAC
* * * * *
3663490 TGTACAATAAATCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGTATAAT
1 TATACAATAAATCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACACCCCGACTTTATGAATAAG
3663555 ATTCAGCTAGCCTGATAAAGGTGATTATAAAATC
66 ATTCAGCTAGCCTGATAAAGGTGATTAT-AAA-C
* *
3663589 TATACAAT-AATATTGAGTTGTCCCTCTAGAGGAATTGGTTAAA
1 TATACAATAAATCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAA
3663632 ATACCCCGGT
Statistics
Matches: 121, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
95 78 0.64
96 1 0.01
97 2 0.02
98 33 0.27
99 7 0.06
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (97 bp):
TATACAATAAATCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACACCCCGACTTTATGAATAAG
ATTCAGCTAGCCTGATAAAGGTGATTATAAAC
Found at i:3665065 original size:65 final size:65
Alignment explanation
Indices: 3664955--3665124 Score: 225
Period size: 65 Copynumber: 2.6 Consensus size: 65
3664945 TTAAGACTAA
*
3664955 TTCCCTTGAAACAAAATTTTGTCTCACTTGAGACAGTTTCTCTTGAAACATAAA-CATTGAAAAC
1 TTCCCTTGAAAC-AAATTTTGTCTCACTTGAGACAGTTTCCCTTGAAACA-AAATCATTGAAAAC
3665019 AT
64 AT
* * * * **
3665021 TTCCCTTGAAACAAATTTTGTTTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGT
1 TTCCCTTGAAACAAATTTTGTCTCACTTGAGACAGTTTCCCTTGAAACAAAATCATTGAAAACAT
* * *
3665086 TTACCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTC
1 TTCCCTTGAAACAAATTTTGTCTCACTTGAGACAGTTTC
3665125 TTTTGGAACT
Statistics
Matches: 92, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 3 0.03
65 77 0.84
66 12 0.13
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (65 bp):
TTCCCTTGAAACAAATTTTGTCTCACTTGAGACAGTTTCCCTTGAAACAAAATCATTGAAAACAT
Found at i:3665219 original size:102 final size:102
Alignment explanation
Indices: 3665020--3665281 Score: 267
Period size: 102 Copynumber: 2.6 Consensus size: 102
3665010 ATTGAAAACA
* * * * *
3665020 TTTCCCTTGAAAC-AAATTTTGTTTCTCTTGAGACAGTTTCCCTTGAAACA-AAATCTTTGAATA
1 TTTCCCTTGAAACAAAATTTTCTCTCTCTTGAGACAGTTTCTCTTGAAACATAAA-CATTGAAAA
** *
3665083 TGTTTACCTTGAAACAAATTTCGTCTCCCTTGAGACAG
65 CATTTACCTTGAAACAAATTTCATCTCCCTTGAGACAG
** * * * *
3665121 TTTCTTTTGGAACTAAGTTTTCTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAACAAAATTTTCTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
* * ** * * *
3665186 ATTTCCCTTTAAATGAATTTTATCTCTCTTGAGATAG
66 ATTTACCTTGAAACAAATTTCATCTCCCTTGAGACAG
* * * * *
3665223 TTTCCCTTGAAACAAAATTTTGTCTCCCTCGAGACAGGTTCTCTTAAAACATAAACATT
1 TTTCCCTTGAAACAAAATTTTCTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATT
3665282 TCCTTTGAAA
Statistics
Matches: 128, Mismatches: 31, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
101 10 0.08
102 115 0.90
103 3 0.02
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (102 bp):
TTTCCCTTGAAACAAAATTTTCTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
ATTTACCTTGAAACAAATTTCATCTCCCTTGAGACAG
Found at i:3665319 original size:36 final size:36
Alignment explanation
Indices: 3665279--3665365 Score: 102
Period size: 36 Copynumber: 2.4 Consensus size: 36
3665269 AAACATAAAC
* ** * *
3665279 ATTTCCTTTGAAATGAATTTTGTCTCTCTTGAGATA
1 ATTTCCCTTGAAACAAAATTTGTCTCCCTTGAGATA
*
3665315 ATTTCCCTTGAAACAAAATTTGTCTCCCTTGAGACA
1 ATTTCCCTTGAAACAAAATTTGTCTCCCTTGAGATA
* *
3665351 GTTTCTCTTGAAACA
1 ATTTCCCTTGAAACA
3665366 TAAACATTGA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.40
Consensus pattern (36 bp):
ATTTCCCTTGAAACAAAATTTGTCTCCCTTGAGATA
Found at i:3665367 original size:194 final size:195
Alignment explanation
Indices: 3665138--3665676 Score: 832
Period size: 194 Copynumber: 2.7 Consensus size: 195
3665128 TGGAACTAAG
* * *
3665138 TTTTCTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTTAAATGAA
1 TTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAA
* *
3665203 TTTTATCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTCGAGACAGGTTCTCTT
66 TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGGTTCTCTT
*
3665268 AAAACATAAACATTTCCTTTGAAATGAATTTTGTCTCTCTTGAGATAATTTCCCTTGAAACAAAA
131 AAAACATAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAATTTCCCTTGAAACAAAA
*
3665333 -TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAA
1 TTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAA
*
3665397 TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTT
66 TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGGTTCTCTT
*
3665462 GAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTT
131 -----A-AAACA-T--AAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAATTTCCCTT
3665527 GAAACAAAA
187 GAAACAAAA
* *
3665536 TTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACACAAACAATGAAAACATTTCCCTTGAAATGAA
1 TTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAA
* *
3665601 TTTTGTCTCTCTTGAGATAGTTTCCCCATGAAAC-TAATTTTGTCTCCCTTGAGACA-GTTCCTC
66 TTTTGTCTCTCTTGAGATAGTTT-CCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGGTT-CTC
*
3665664 TTGAAACATAAAC
129 TTAAAACATAAAC
3665677 TTTGAAAACG
Statistics
Matches: 316, Mismatches: 16, Indels: 24
0.89 0.04 0.07
Matches are distributed among these distances:
194 122 0.39
195 4 0.01
197 1 0.00
198 5 0.02
199 1 0.00
200 5 0.02
201 1 0.00
203 58 0.18
204 110 0.35
205 9 0.03
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.37
Consensus pattern (195 bp):
TTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAA
TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGGTTCTCTT
AAAACATAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAATTTCCCTTGAAACAAAA
Found at i:3665448 original size:37 final size:37
Alignment explanation
Indices: 3665381--3665467 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 37
3665371 ATTGAAAACA
** * *
3665381 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
3665417 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
3665454 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
3665468 TAAACATTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 12 0.27
37 33 0.73
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:3665486 original size:102 final size:102
Alignment explanation
Indices: 3665275--3665698 Score: 726
Period size: 102 Copynumber: 4.2 Consensus size: 102
3665265 CTTAAAACAT
* *
3665275 AAACATTTCCTTTGAAATGAATTTTGTCTCTCTTGAGATAATTTCCCTTGAAACAAAA-TTTGTC
1 AAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTC
3665339 TCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGA
66 TCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGA
3665376 AAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTC
1 AAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTC
3665441 TCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGA
66 TCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGA
3665478 AAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTC
1 AAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTC
* * *
3665543 TCCCTTGAGATAGTTTCTCTTGAAACACAAACAATGA
66 TCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGA
* *
3665580 AAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCCATGAAAC-TAATTTTGT
1 AAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTT-CCCTTGAAACAAAATTTTGT
* *
3665644 CTCCCTTGAGACAGTTCCTCTTGAAACATAAACTTTGA
65 CTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGA
* *
3665682 AAACGTTTCCCTAGAAA
1 AAACATTTCCCTTGAAA
3665699 CACAAAATAT
Statistics
Matches: 307, Mismatches: 14, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
101 56 0.18
102 242 0.79
103 9 0.03
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (102 bp):
AAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTC
TCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGA
Found at i:3665550 original size:37 final size:37
Alignment explanation
Indices: 3665483--3665569 Score: 131
Period size: 37 Copynumber: 2.4 Consensus size: 37
3665473 ATTGAAAACA
** *
3665483 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
3665519 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
*
3665556 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
3665570 CAAACAATGA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
36 12 0.26
37 34 0.74
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
Found at i:3665563 original size:296 final size:300
Alignment explanation
Indices: 3665019--3665700 Score: 969
Period size: 296 Copynumber: 2.3 Consensus size: 300
3665009 CATTGAAAAC
* * * *
3665019 ATTTCCCTTGAAACAAATTTTGTTTCTCTTGAGACAGTTTCCCTTGAAACA-AAATCTTTGAATA
1 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA-CTTTGAAAA
* * ** * * * *
3665083 TGTTTACCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTCTCTCT
65 CGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATTTTCTCTCC
* *
3665148 CTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTTAAATGAATTTTATCTCT
130 CTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTATCTCT
3665213 CTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTCGAGACAGGTTCTCTT-A-AAAC-AT
195 CTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTCGAGACAGGTTCTCTTAACAAACAAT
*
3665275 -AAACATTTCCTTTGAAATGAATTTTGTCTCTCTTGAGATA
260 AAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATA
* *
3665315 ATTTCCCTTGAAACAAAATTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
1 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAAC
* ** * * * *
3665380 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCC
66 GTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATTTTCTCTCCC
*
3665445 TTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTC
131 TTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTATCTCTC
* * *
3665510 TTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACACAAAC
196 TTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTCGAGACAGGTTCTCTT---A-ACAAAC
3665575 AATGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATA
257 AAT-AAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATA
* * * *
3665620 GTTTCCCCATGAAACTAATTTTGTCTCCCTTGAGACAGTTCCTCTTGAAACATAAACTTTGAAAA
1 ATTT-CCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAA
*
3665685 CGTTTCCCTAGAAACA
65 CGTTTCCCTTGAAACA
3665701 CAAAATATTT
Statistics
Matches: 337, Mismatches: 38, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
296 218 0.65
297 3 0.01
301 1 0.00
302 4 0.01
303 2 0.01
305 42 0.12
306 67 0.20
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.37
Consensus pattern (300 bp):
ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAAC
GTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATTTTCTCTCCC
TTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTATCTCTC
TTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTCGAGACAGGTTCTCTTAACAAACAATA
AAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATA
Found at i:3665730 original size:31 final size:30
Alignment explanation
Indices: 3665657--3665730 Score: 71
Period size: 30 Copynumber: 2.5 Consensus size: 30
3665647 CCTTGAGACA
* *
3665657 GTTCCTCTTGAAACATAAACTTTGAAAACG
1 GTTCCTCTTGAAACAAAAAATTTGAAAACG
* * *
3665687 TTTCC-CTAGAAACACAAAATATTTG-AATCG
1 GTTCCTCTTGAAACA-AAAA-ATTTGAAAACG
3665717 GTTCCTCTTGAAAC
1 GTTCCTCTTGAAAC
3665731 GAGTTTTGTG
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
29 8 0.24
30 15 0.44
31 11 0.32
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (30 bp):
GTTCCTCTTGAAACAAAAAATTTGAAAACG
Found at i:3667329 original size:15 final size:15
Alignment explanation
Indices: 3667303--3667350 Score: 51
Period size: 17 Copynumber: 3.0 Consensus size: 15
3667293 TTCAAACATA
*
3667303 CAAACAAATCCAAAGT
1 CAAAC-AATCCAAAAT
*
3667319 CTAACAATCCACAAAAT
1 CAAACAAT-C-CAAAAT
3667336 CAAACAATCCAAAAT
1 CAAACAATCCAAAAT
3667351 ATTCAAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 9 0.33
16 6 0.22
17 12 0.44
ACGTcount: A:0.56, C:0.27, G:0.02, T:0.15
Consensus pattern (15 bp):
CAAACAATCCAAAAT
Found at i:3669358 original size:23 final size:20
Alignment explanation
Indices: 3669325--3669383 Score: 57
Period size: 23 Copynumber: 2.8 Consensus size: 20
3669315 CCAGAACCCC
3669325 AGGGGGTATCGATTCCCCTTCAA
1 AGGGGG-ATCGATTCCCC-TC-A
*
3669348 AGGGGGAATCGGTT-CCCTCA
1 AGGGGG-ATCGATTCCCCTCA
*
3669368 TGGGGGATCGATTCCC
1 AGGGGGATCGATTCCC
3669384 TCTGCACCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
19 6 0.19
20 8 0.26
21 2 0.06
22 3 0.10
23 12 0.39
ACGTcount: A:0.19, C:0.25, G:0.32, T:0.24
Consensus pattern (20 bp):
AGGGGGATCGATTCCCCTCA
Found at i:3669374 original size:20 final size:19
Alignment explanation
Indices: 3669326--3669385 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 19
3669316 CAGAACCCCA
*
3669326 GGGGGTATCGATTCCCCTTCAAA
1 GGGGG-ATCGATT-CCC-TC-AT
*
3669349 GGGGGAATCGGTTCCCTCAT
1 GGGGG-ATCGATTCCCTCAT
3669369 GGGGGATCGATTCCCTC
1 GGGGGATCGATTCCCTC
3669386 TGCACCAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 11 0.33
20 6 0.18
21 2 0.06
22 3 0.09
23 11 0.33
ACGTcount: A:0.17, C:0.27, G:0.32, T:0.25
Consensus pattern (19 bp):
GGGGGATCGATTCCCTCAT
Found at i:3673228 original size:22 final size:21
Alignment explanation
Indices: 3673186--3673225 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3673176 GAGTTTATTT
*
3673186 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
3673207 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
3673226 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:3676885 original size:2 final size:2
Alignment explanation
Indices: 3676878--3676910 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3676868 CCGTCACTAT
3676878 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 T
3676911 TTGCTCATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3680022 original size:28 final size:30
Alignment explanation
Indices: 3679982--3680039 Score: 102
Period size: 28 Copynumber: 2.0 Consensus size: 30
3679972 ATGTCTCAAC
3679982 GTGGAGGTTTCATTCTCAT-A-ATTTTCTT
1 GTGGAGGTTTCATTCTCATAACATTTTCTT
3680010 GTGGAGGTTTCATTCTCATAACATTTTCTT
1 GTGGAGGTTTCATTCTCATAACATTTTCTT
3680040 AATGTTCTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 19 0.68
29 1 0.04
30 8 0.29
ACGTcount: A:0.19, C:0.16, G:0.17, T:0.48
Consensus pattern (30 bp):
GTGGAGGTTTCATTCTCATAACATTTTCTT
Found at i:3682106 original size:14 final size:14
Alignment explanation
Indices: 3682087--3682113 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3682077 TTTCGAATAG
3682087 AGTCGAGTTATTCA
1 AGTCGAGTTATTCA
3682101 AGTCGAGTTATTC
1 AGTCGAGTTATTC
3682114 GAGTTTCTAT
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:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (14 bp):
AGTCGAGTTATTCA
Found at i:3682885 original size:18 final size:19
Alignment explanation
Indices: 3682862--3682907 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
3682852 ATTATATATA
3682862 TATATATATATAATATT-T
1 TATATATATATAATATTAT
*
3682880 TATATAT-T-TTATATTAAT
1 TATATATATATAATATT-AT
3682898 TATATATATA
1 TATATATATA
3682908 ACATTTCATA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
16 6 0.26
17 1 0.04
18 15 0.65
19 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATATATATATAATATTAT
Found at i:3682903 original size:34 final size:34
Alignment explanation
Indices: 3682864--3682948 Score: 143
Period size: 34 Copynumber: 2.5 Consensus size: 34
3682854 TATATATATA
3682864 TATATATATAATATTTTATATATTTTATATTAAT
1 TATATATATAATATTTTATATATTTTATATTAAT
* * *
3682898 TATATATATAACATTTCATATTTTTTATATTAAT
1 TATATATATAATATTTTATATATTTTATATTAAT
3682932 TATATATATAATATTTT
1 TATATATATAATATTTT
3682949 CGGGTTCGGG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (34 bp):
TATATATATAATATTTTATATATTTTATATTAAT
Found at i:3691664 original size:59 final size:59
Alignment explanation
Indices: 3691601--3691726 Score: 162
Period size: 59 Copynumber: 2.1 Consensus size: 59
3691591 ATAGTTAAGT
* * * * * *
3691601 GATCATTTTGTAACTTTTAATAGTCGGTGGACTCAATAAAAAAACCTCATATAGTCGGG
1 GATCATTTTATAACTTTCAATAATCGATGGACTCAATAAAAAAACATCATATAATCGGG
* * *
3691660 GATCATTTTATAACTTTCAATAATCGATGGACTTAATAAAGAAACATCTTATAATCGGG
1 GATCATTTTATAACTTTCAATAATCGATGGACTCAATAAAAAAACATCATATAATCGGG
*
3691719 GACCATTT
1 GATCATTT
3691727 GGGTACTTTT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (59 bp):
GATCATTTTATAACTTTCAATAATCGATGGACTCAATAAAAAAACATCATATAATCGGG
Found at i:3694660 original size:15 final size:15
Alignment explanation
Indices: 3694640--3694676 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
3694630 GGTATTTAGT
* *
3694640 GGGCGGGCGGATGTG
1 GGGCGGGCAGATGCG
3694655 GGGCGGGCAGATGCG
1 GGGCGGGCAGATGCG
3694670 GGGCGGG
1 GGGCGGG
3694677 TAAGGTCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.08, C:0.16, G:0.68, T:0.08
Consensus pattern (15 bp):
GGGCGGGCAGATGCG
Found at i:3699787 original size:3 final size:3
Alignment explanation
Indices: 3699779--3699829 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
3699769 AATGCACCAT
*
3699779 TTA TTA TTA TTA TTA TTA TTA TTC TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3699827 TTA
1 TTA
3699830 ATAAATTACT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3707390 original size:17 final size:17
Alignment explanation
Indices: 3707368--3707405 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3707358 TTTTTGAATA
3707368 TTTAATATTTAATAATT
1 TTTAATATTTAATAATT
* *
3707385 TTTAATTTTTAATATTT
1 TTTAATATTTAATAATT
3707402 TTTA
1 TTTA
3707406 TGAAATTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTAATATTTAATAATT
Found at i:3707539 original size:62 final size:62
Alignment explanation
Indices: 3707459--3707581 Score: 210
Period size: 62 Copynumber: 2.0 Consensus size: 62
3707449 TCGACACGTC
* *
3707459 ATTAATTATTGTTGATTGTCACATCATCACTGTAGATCTCCGTGTCAATATCACGAACTGTA
1 ATTAATTATTGTTAATTGTCACATCATCACCGTAGATCTCCGTGTCAATATCACGAACTGTA
* *
3707521 ATTAATTATTGTTAATTGTCACATCATCACCGTGGATCTCCGTGTTAATATCACGAACTGT
1 ATTAATTATTGTTAATTGTCACATCATCACCGTAGATCTCCGTGTCAATATCACGAACTGT
3707582 TATGTTAATA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (62 bp):
ATTAATTATTGTTAATTGTCACATCATCACCGTAGATCTCCGTGTCAATATCACGAACTGTA
Found at i:3708567 original size:2 final size:2
Alignment explanation
Indices: 3708560--3708593 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3708550 GATCGATGTA
3708560 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
3708594 TGTTTTCTTT
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:3710083 original size:2 final size:2
Alignment explanation
Indices: 3710076--3710104 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3710066 AGCAAAATTA
3710076 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3710105 TTTAACCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3713242 original size:129 final size:132
Alignment explanation
Indices: 3712911--3713246 Score: 326
Period size: 134 Copynumber: 2.5 Consensus size: 132
3712901 GTTCTGGTCG
* * * * * *
3712911 TCTAAGGGTGACACGACTTCTATGTGATGAGGAGATTTGGTCGGTGGATGACATGGTTCCTACGC
1 TCTAAGGGTGACACGACCT-TACGTGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCCTACGT
* * *
3712976 GATGAGGACGGCTAGCCATATTTAGGGATGATGATAACATGATTCCTACGTGATAAGGACATTTG
65 GATGAGGACGGCAAGACATATTTAGGGATGATGATAACA-GATTCCTACGTGATAAGGACAGTTG
3713041 GTTA
129 GTTA
* * * * ** **
3713045 TCTAAGGTTGACACGGCTCCT-CTGTGATAAGGAGGTCTGGTCGGTGGATGACACAATTTTTACG
1 TCTAAGGGTGACACGAC-CTTAC-GTGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCCTACG
* * * * *
3713109 TGATGATGATGG-AAGGACATATTTAGGGATGAT-A-ACACA-ATT-CTATGTGATGAGGACGGT
64 TGATGAGGACGGCAA-GACATATTTAGGGATGATGATA-ACAGATTCCTACGTGATAAGGACAGT
3713169 TGGTTA
127 TGGTTA
** * *
3713175 TCT-AGGGTGACACGACACTTACGTGATGAGGAGGTCTGGTCGAAGGATGACAGGGTTCCTACAT
1 TCTAAGGGTGACACGAC-CTTACGTGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCCTACGT
3713239 GATGAGGA
65 GATGAGGA
3713247 TAATTAACCA
Statistics
Matches: 161, Mismatches: 36, Indels: 15
0.76 0.17 0.07
Matches are distributed among these distances:
129 53 0.33
130 24 0.15
131 3 0.02
132 1 0.01
133 5 0.03
134 75 0.47
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (132 bp):
TCTAAGGGTGACACGACCTTACGTGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCCTACGTG
ATGAGGACGGCAAGACATATTTAGGGATGATGATAACAGATTCCTACGTGATAAGGACAGTTGGT
TA
Found at i:3713379 original size:21 final size:20
Alignment explanation
Indices: 3713346--3713385 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3713336 GTTTCAAGAG
3713346 AAATTGTCTCAAGAGAAATA
1 AAATTGTCTCAAGAGAAATA
* *
3713366 AAATTCGTTTCAAGGGAAAT
1 AAATT-GTCTCAAGAGAAAT
3713386 GACTCAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.28
Consensus pattern (20 bp):
AAATTGTCTCAAGAGAAATA
Found at i:3713385 original size:36 final size:33
Alignment explanation
Indices: 3713335--3713441 Score: 96
Period size: 36 Copynumber: 3.2 Consensus size: 33
3713325 TCAAAGATAA
3713335 TGTTTCAAGAGAAATTGTCTCAAGAGAAATAAAAT
1 TGTTTCAAGAGAAA-TGTCTCAAGAG-AATAAAAT
* * *
3713370 TCGTTTCAAGGGAAATGACTCAA-AG-AT--GAT
1 T-GTTTCAAGAGAAATGTCTCAAGAGAATAAAAT
*
3713400 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAA-TGTCTCAAGAGA-ATAAAA-T
3713436 TGTTTC
1 TGTTTC
3713442 GAGGGAAACA
Statistics
Matches: 57, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
29 12 0.21
30 10 0.18
31 2 0.04
32 2 0.04
33 1 0.02
34 2 0.04
35 9 0.16
36 19 0.33
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (33 bp):
TGTTTCAAGAGAAATGTCTCAAGAGAATAAAAT
Found at i:3713434 original size:65 final size:64
Alignment explanation
Indices: 3713265--3713450 Score: 246
Period size: 64 Copynumber: 2.9 Consensus size: 64
3713255 CATCTTTAGG
** * * *
3713265 GATAATAGTTTCAAGAGAAACCATCTTAAGAGAGACAAAATTCGTTTAAATGGAAACGACTCAAA
1 GATAAT-GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGACTCAAA
* * * *
3713330 GATAATGTTTCAAGAGAAATTGTCTCAAGAGAAATAAAATTCGTTTCAAGGGAAATGACTCAAA
1 GATAATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGACTCAAA
* * *
3713394 GATGATTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCGAGGGAAAC
1 GAT-AATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAAC
3713451 AATCTTAAAA
Statistics
Matches: 104, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
64 52 0.50
65 52 0.50
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.25
Consensus pattern (64 bp):
GATAATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGACTCAAA
Found at i:3715075 original size:2 final size:2
Alignment explanation
Indices: 3715068--3715092 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3715058 AACTTTATTG
3715068 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3715093 CTGGATATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3721933 original size:20 final size:21
Alignment explanation
Indices: 3721908--3721967 Score: 77
Period size: 23 Copynumber: 2.8 Consensus size: 21
3721898 TTTTGGTGCA
3721908 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAATCGATTCCCCCCTT
* *
3721928 GAGGGAACCGATTCCCCCTTT
1 GAGGGAATCGATTCCCCCCTT
3721949 GAAGGGGAATCGATTCCCC
1 G-A-GGGAATCGATTCCCC
3721968 TAAGGGGAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.29
21 9 0.26
22 1 0.03
23 14 0.41
ACGTcount: A:0.22, C:0.32, G:0.27, T:0.20
Consensus pattern (21 bp):
GAGGGAATCGATTCCCCCCTT
Found at i:3721974 original size:19 final size:19
Alignment explanation
Indices: 3721930--3721986 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 19
3721920 CCCCCCTTGA
3721930 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATT-CCCC--T-AAG
*
3721953 GGGAATCGATTCCCCTAAG
1 GGGAACCGATTCCCCTAAG
3721972 GGGAACCGATTCCCC
1 GGGAACCGATTCCCC
3721987 CCCACAGGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 17 0.53
20 1 0.03
22 4 0.12
23 10 0.31
ACGTcount: A:0.23, C:0.32, G:0.26, T:0.19
Consensus pattern (19 bp):
GGGAACCGATTCCCCTAAG
Found at i:3721989 original size:22 final size:22
Alignment explanation
Indices: 3721930--3722009 Score: 69
Period size: 22 Copynumber: 3.7 Consensus size: 22
3721920 CCCCCCTTGA
**
3721930 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCCCT-AAG
*
3721953 GGGAATCGATT---CCCCTAAG
1 GGGAACCGATTCCCCCCCTAAG
3721972 GGGAACCGATTCCCCCCC-ACAG
1 GGGAACCGATTCCCCCCCTA-AG
* *
3721994 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
3722010 TGGGATTCTG
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
19 13 0.28
20 3 0.06
21 1 0.02
22 20 0.43
23 10 0.21
ACGTcount: A:0.24, C:0.35, G:0.25, T:0.16
Consensus pattern (22 bp):
GGGAACCGATTCCCCCCCTAAG
Found at i:3722010 original size:42 final size:41
Alignment explanation
Indices: 3721910--3722010 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 41
3721900 TTGGTGCAGA
* **
3721910 GGGAATCGATCCCCCCTTGAGGGAACCGATTCCCCCTTTGAAG
1 GGGAATCGAT-CCCCCTAGAGGGAACCGATTCCCCC-TCCAAG
*
3721953 GGGAATCGATTCCCCTA-AGGGGAACCGATTCCCCC-CCACAG
1 GGGAATCGATCCCCCTAGA-GGGAACCGATTCCCCCTCCA-AG
3721994 GGGAATCGATACCCCCT
1 GGGAATCGAT-CCCCCT
3722011 GGGATTCTGG
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
40 1 0.02
41 13 0.26
42 26 0.52
43 10 0.20
ACGTcount: A:0.23, C:0.35, G:0.25, T:0.18
Consensus pattern (41 bp):
GGGAATCGATCCCCCTAGAGGGAACCGATTCCCCCTCCAAG
Found at i:3724692 original size:33 final size:33
Alignment explanation
Indices: 3724639--3724720 Score: 128
Period size: 33 Copynumber: 2.4 Consensus size: 33
3724629 TGTCCAGGGG
3724639 GAACAGATTCCCCCCCAGGGGTATCGATTCCCCGA
1 GAACAGATT--CCCCCAGGGGTATCGATTCCCCGA
*
3724674 GAACAGATTCCCCCAGGGGTATCGATTCCCCGG
1 GAACAGATTCCCCCAGGGGTATCGATTCCCCGA
*
3724707 GTACAGATTCCCCC
1 GAACAGATTCCCCC
3724721 TGCATGGTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
33 36 0.80
35 9 0.20
ACGTcount: A:0.22, C:0.37, G:0.23, T:0.18
Consensus pattern (33 bp):
GAACAGATTCCCCCAGGGGTATCGATTCCCCGA
Found at i:3724702 original size:18 final size:18
Alignment explanation
Indices: 3724650--3724704 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
3724640 AACAGATTCC
3724650 CCCCCAGGGGTATCGATT
1 CCCCCAGGGGTATCGATT
* *
3724668 -CCCC--GAG-AACAGATT
1 CCCCCAGGGGTATC-GATT
3724683 CCCCCAGGGGTATCGATT
1 CCCCCAGGGGTATCGATT
3724701 CCCC
1 CCCC
3724705 GGGTACAGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 10
0.67 0.10 0.24
Matches are distributed among these distances:
14 2 0.07
15 6 0.21
16 4 0.14
17 4 0.14
18 10 0.36
19 2 0.07
ACGTcount: A:0.20, C:0.38, G:0.24, T:0.18
Consensus pattern (18 bp):
CCCCCAGGGGTATCGATT
Found at i:3724715 original size:15 final size:15
Alignment explanation
Indices: 3724664--3724719 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
3724654 CAGGGGTATC
* *
3724664 GATTCCCCGAGAACA
1 GATTCCCCGGGTACA
3724679 GATTCCCCCAGGGGTATC-
1 GATT-CCCC--GGGTA-CA
3724697 GATTCCCCGGGTACA
1 GATTCCCCGGGTACA
3724712 GATTCCCC
1 GATTCCCC
3724720 CTGCATGGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 1 0.03
15 17 0.50
16 4 0.12
17 4 0.12
18 7 0.21
19 1 0.03
ACGTcount: A:0.21, C:0.36, G:0.23, T:0.20
Consensus pattern (15 bp):
GATTCCCCGGGTACA
Found at i:3724857 original size:21 final size:21
Alignment explanation
Indices: 3724833--3724874 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3724823 ATTTGAATAT
*
3724833 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
3724854 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
3724875 CCCATTATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:3724936 original size:21 final size:21
Alignment explanation
Indices: 3724903--3724942 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
3724893 TTTTTGTAGA
*
3724903 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
3724925 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
3724943 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:3726551 original size:13 final size:14
Alignment explanation
Indices: 3726533--3726561 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3726523 TTAATGGAAT
3726533 AAGAAATG-AATGA
1 AAGAAATGAAATGA
3726546 AAGAAATGAAATGA
1 AAGAAATGAAATGA
3726560 AA
1 AA
3726562 ATGAATTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.66, C:0.00, G:0.21, T:0.14
Consensus pattern (14 bp):
AAGAAATGAAATGA
Found at i:3731988 original size:16 final size:16
Alignment explanation
Indices: 3731967--3731999 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3731957 GTAGGAGTTC
3731967 TTTTCTT-TTCTCTTTT
1 TTTTCTTCTT-TCTTTT
3731983 TTTTCTTCTTTCTTTT
1 TTTTCTTCTTTCTTTT
3731999 T
1 T
3732000 GTTTTGTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTCTTCTTTCTTTT
Found at i:3732208 original size:13 final size:14
Alignment explanation
Indices: 3732190--3732218 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3732180 TTAATGGAAT
3732190 AAGAAATG-AATGA
1 AAGAAATGAAATGA
3732203 AAGAAATGAAATGA
1 AAGAAATGAAATGA
3732217 AA
1 AA
3732219 ATAAAATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.66, C:0.00, G:0.21, T:0.14
Consensus pattern (14 bp):
AAGAAATGAAATGA
Found at i:3735842 original size:17 final size:17
Alignment explanation
Indices: 3735820--3735856 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
3735810 GGTTAGGTAG
3735820 GTCGAATACCTAAAAAC
1 GTCGAATACCTAAAAAC
3735837 GTCGAATACCTAAAAAC
1 GTCGAATACCTAAAAAC
3735854 GTC
1 GTC
3735857 TTATAAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.43, C:0.24, G:0.14, T:0.19
Consensus pattern (17 bp):
GTCGAATACCTAAAAAC
Found at i:3738241 original size:3 final size:3
Alignment explanation
Indices: 3738233--3738262 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
3738223 AATTAATATA
3738233 AAT AAT AAT AAT AAT AAT AAT AATT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AA
3738263 AAAAGACCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3748094 original size:20 final size:20
Alignment explanation
Indices: 3748066--3748103 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3748056 TAAAAAATTG
*
3748066 AATTCAATTCCACTGATCCA
1 AATTAAATTCCACTGATCCA
*
3748086 AATTAAATTTCACTGATC
1 AATTAAATTCCACTGATC
3748104 TAAAATATGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (20 bp):
AATTAAATTCCACTGATCCA
Found at i:3752497 original size:23 final size:23
Alignment explanation
Indices: 3752429--3752489 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
3752419 CAATCTTATA
*
3752429 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
3752452 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
3752475 TTGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
3752490 TTTATACGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:3758172 original size:64 final size:63
Alignment explanation
Indices: 3758086--3758205 Score: 150
Period size: 64 Copynumber: 1.9 Consensus size: 63
3758076 ATTATTCAAG
* * * * **
3758086 GTGTATCGATGCACATGAAGTGCATTGATGCACTCTTTTAAAATAAAAACATCGAATGCCATCA
1 GTGTATCGATGAACAAGAAGTGCATCGATGCACCCCCTT-AAATAAAAACATCGAATGCCATCA
* * *
3758150 GTGTATCGATGAATAAGTAGTGCATCGATGCACCCCCTTAAATACAAACATCGAAT
1 GTGTATCGATGAACAAGAAGTGCATCGATGCACCCCCTTAAATAAAAACATCGAAT
3758206 AGGATTTATG
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
63 16 0.34
64 31 0.66
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (63 bp):
GTGTATCGATGAACAAGAAGTGCATCGATGCACCCCCTTAAATAAAAACATCGAATGCCATCA
Found at i:3758954 original size:23 final size:23
Alignment explanation
Indices: 3758886--3758946 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
3758876 CAATCTTATA
* *
3758886 TGGCACTACAGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
3758909 CGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
3758932 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
3758947 TTTATACGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.28, G:0.26, T:0.26
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:3776868 original size:222 final size:225
Alignment explanation
Indices: 3776481--3776928 Score: 859
Period size: 222 Copynumber: 2.0 Consensus size: 225
3776471 CTAAATGAAG
3776481 GAAAGTCAGTATAGATAAGTAAATAAGAGTTTAATAGTAATGTTGGGGGTAAACACAAGGAAATT
1 GAAAGTCAGTATAGATAAGTAAATAAGAGTTTAATAGTAATGTTGGGGGTAAACACAAGGAAATT
3776546 TGACCCAATTTGGGTAATAATCGAGTTGAAAACTGAAAATTTGGGTACAGGTACCGATACTGATA
66 TGACCCAATTTGGGTAATAATCGAGTTGAAAACTGAAAATTTGGGTACAGGTACCGATACTGATA
3776611 GAAGAGTACCGATACTATAGGATTAAAAGGGGAAGAACAAC-GAGTAGTATCGATATTGATGCAA
131 GAAGAGTACCGATACTATAGGATTAAAAGGGGAAGAACAACTGAGTAGTATCGATATTGATGCAA
3776675 GCAGTATCGATACCGAGA-GGGTATCGATA
196 GCAGTATCGATACCGAGAGGGGTATCGATA
3776704 GAAAGTCAGTATAGATAAGTAAATAAGAGTTTAATAGTAATGTTGGGGGGT-AA-ACAAGGAAAT
1 GAAAGTCAGTATAGATAAGTAAATAAGAGTTTAATAGTAATGTT-GGGGGTAAACACAAGGAAAT
3776767 TTGACCCAATTTGGGTAATAATCGAGTTGAAAACTGAAAATTTGGGTACAGGTACCGATACTGAT
65 TTGACCCAATTTGGGTAATAATCGAGTTGAAAACTGAAAATTTGGGTACAGGTACCGATACTGAT
3776832 AGAAGAGTACCGATACTATAGGATTAAAAGGGGAAGAACAACTGAGTAGTATCGATATTGATGCA
130 AGAAGAGTACCGATACTATAGGATTAAAAGGGGAAGAACAACTGAGTAGTATCGATATTGATGCA
3776897 AGCAGTATCGATACCGAGAGGGGTATCGATA
195 AGCAGTATCGATACCGAGAGGGGTATCGATA
3776928 G
1 G
3776929 TGTGAGGAAG
Statistics
Matches: 222, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
222 117 0.53
223 87 0.39
224 18 0.08
ACGTcount: A:0.39, C:0.10, G:0.26, T:0.24
Consensus pattern (225 bp):
GAAAGTCAGTATAGATAAGTAAATAAGAGTTTAATAGTAATGTTGGGGGTAAACACAAGGAAATT
TGACCCAATTTGGGTAATAATCGAGTTGAAAACTGAAAATTTGGGTACAGGTACCGATACTGATA
GAAGAGTACCGATACTATAGGATTAAAAGGGGAAGAACAACTGAGTAGTATCGATATTGATGCAA
GCAGTATCGATACCGAGAGGGGTATCGATA
Found at i:3777330 original size:16 final size:16
Alignment explanation
Indices: 3777311--3777343 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3777301 TACATTAAGA
*
3777311 GTTATAAATATATGTT
1 GTTAAAAATATATGTT
3777327 GTTAAAAATATATGTT
1 GTTAAAAATATATGTT
3777343 G
1 G
3777344 CAATGGTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.45
Consensus pattern (16 bp):
GTTAAAAATATATGTT
Found at i:3777465 original size:55 final size:55
Alignment explanation
Indices: 3777381--3777663 Score: 390
Period size: 55 Copynumber: 5.2 Consensus size: 55
3777371 ACAGGCATTT
* *
3777381 TGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATCACCTTACATGCACTA
1 TGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATCACCGTACATGCACTA
*
3777436 TGTGTGCAAATCCACAGAATTCATCATGAGTTTATGAATCACCGTACATGCACTA
1 TGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATCACCGTACATGCACTA
* * * * *
3777491 TGCGTGCAAATCCATAGAATTCATCATGATTTGATTAATAACCGTACATGCACTA
1 TGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATCACCGTACATGCACTA
* * **
3777546 TGTGTACAAATCCACAGAATTCATCATGAGTTGATGAATAACCGTACAAACACTA
1 TGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATCACCGTACATGCACTA
* * * *
3777601 TGTTTGC-AACCCACAGAATTCATCATGAGTTGATGAA-CTACCGTATAGGCACTA
1 TGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATC-ACCGTACATGCACTA
*
3777655 CGTGTGCAA
1 TGTGTGCAA
3777664 CTTAATAAAT
Statistics
Matches: 201, Mismatches: 25, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
54 46 0.23
55 155 0.77
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (55 bp):
TGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATCACCGTACATGCACTA
Found at i:3783766 original size:19 final size:20
Alignment explanation
Indices: 3783742--3783789 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
3783732 ATGCAAGCAT
*
3783742 TATCGATACTGAGAGG-GGG
1 TATCGATACTGAGAGGAAGG
*
3783761 TATCGATACTGTGAGGAAGG
1 TATCGATACTGAGAGGAAGG
3783781 TATCGATAC
1 TATCGATAC
3783790 CATTGGTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.29, C:0.12, G:0.33, T:0.25
Consensus pattern (20 bp):
TATCGATACTGAGAGGAAGG
Found at i:3784319 original size:55 final size:55
Alignment explanation
Indices: 3784222--3784472 Score: 276
Period size: 55 Copynumber: 4.6 Consensus size: 55
3784212 GCAGGCACTT
* * * *
3784222 TGTGTGCAAATCCAC-GAAATACATCATGAGTTGATGAGTCACCGTACATGCAATA
1 TGTGTGCAAATCCACAG-AATTCATCATGAGTTGATGAATAACCATACATGCAATA
* * * * * * *
3784277 TGTGTGTAAATCCACGGAATTCATAATGGGTTTATGAATCACCATACAAG-AACTA
1 TGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCATACATGCAA-TA
* * *
3784332 TGAGTGCAAATCCACATAATTCATCATGAGTTGATGAATAACCATACATGCACTA
1 TGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCATACATGCAATA
* * *
3784387 TGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTA
1 TGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCATACATGCAATA
* *
3784442 TGTGTGC-AACCCAC-GAAATCCATCATGAGTT
1 TGTGTGCAAATCCACAG-AATTCATCATGAGTT
3784473 AGTTAACTAC
Statistics
Matches: 168, Mismatches: 24, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
53 1 0.01
54 22 0.13
55 143 0.85
56 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (55 bp):
TGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCATACATGCAATA
Found at i:3784368 original size:110 final size:110
Alignment explanation
Indices: 3784225--3784472 Score: 320
Period size: 110 Copynumber: 2.3 Consensus size: 110
3784215 GGCACTTTGT
* * * *
3784225 GTGCAAATCCACGAAATACATCATGAGTTGATGAGTCACCGTACATGCAATATGTGTGTAAATCC
1 GTGCAAATCCACGAAATACATCATGAGTTGATGAATAACCATACATGCAATATGTGTGCAAATCC
* * * *
3784290 ACGGAATTCATAATGGGTTTATGAATCACCATACAAGAACTATGA
66 ACAGAATTCATAATGAGTTGATGAATAACCATACAAGAACTATGA
* *
3784335 GTGCAAATCCAC-ATAATTCATCATGAGTTGATGAATAACCATACATGCACTATGTGTGCAAATC
1 GTGCAAATCCACGA-AATACATCATGAGTTGATGAATAACCATACATGCAATATGTGTGCAAATC
* * * * *
3784399 CACAGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGT
65 CACAGAATTCATAATGAGTTGATGAATAACCATACAAGAACTATGA
* *
3784445 GTGC-AACCCACGAAATCCATCATGAGTT
1 GTGCAAATCCACGAAATACATCATGAGTT
3784473 AGTTAACTAC
Statistics
Matches: 119, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
109 21 0.18
110 98 0.82
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.26
Consensus pattern (110 bp):
GTGCAAATCCACGAAATACATCATGAGTTGATGAATAACCATACATGCAATATGTGTGCAAATCC
ACAGAATTCATAATGAGTTGATGAATAACCATACAAGAACTATGA
Found at i:3784485 original size:54 final size:54
Alignment explanation
Indices: 3784213--3784505 Score: 225
Period size: 55 Copynumber: 5.4 Consensus size: 54
3784203 ATGTGTACTG
* * * * *
3784213 CAGGCACTTTGTGTGCAAATCCAC-GAAATACATCATGAGTTGATGAGTCACCGTA
1 CAGGCACTATGTGTGC-AACCCACAG-AATCCATCATGAGTTGATGAATAACCGTA
* * * * * * * * * * *
3784268 CATGCAATATGTGTGTAAATCCACGGAATTCATAATGGGTTTATGAATCACCATA
1 CAGGCACTATGTGTG-CAACCCACAGAATCCATCATGAGTTGATGAATAACCGTA
* * * * * * *
3784323 CAAGAACTATGAGTGCAAATCCACATAATTCATCATGAGTTGATGAATAACCATA
1 CAGGCACTATGTGTGC-AACCCACAGAATCCATCATGAGTTGATGAATAACCGTA
* * *
3784378 CATGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCGTA
1 CAGGCACTATGTGTGC-AACCCACAGAATCCATCATGAGTTGATGAATAACCGTA
*
3784433 CAGGCACTATGTGTGCAACCCAC-GAAATCCATCATGAGTT-AGTTAACT-ACCGTA
1 CAGGCACTATGTGTGCAACCCACAG-AATCCATCATGAGTTGA-TGAA-TAACCGTA
* *
3784487 TAGGCACTACGTGTGCAAC
1 CAGGCACTATGTGTGCAAC
3784506 TTAATAAATA
Statistics
Matches: 200, Mismatches: 32, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
53 2 0.01
54 46 0.23
55 151 0.75
56 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (54 bp):
CAGGCACTATGTGTGCAACCCACAGAATCCATCATGAGTTGATGAATAACCGTA
Found at i:3787964 original size:33 final size:32
Alignment explanation
Indices: 3787927--3788025 Score: 101
Period size: 33 Copynumber: 2.9 Consensus size: 32
3787917 TTAGTTTGTG
3787927 CAATAAAATAAAATGTTAGTAAGTTAGTAAGAA
1 CAATAAAATAAAA-GTTAGTAAGTTAGTAAGAA
* * *
3787960 CAATAAAAGTAAAAAAGTCAGTATGTTAGTATGAA
1 CAATAAAA-T--AAAAGTTAGTAAGTTAGTAAGAA
*
3787995 CAAACAAAATAAAAGTTAG-AATGTTAGTAAG
1 C-AATAAAATAAAAGTTAGTAA-GTTAGTAAG
3788026 TTAGAAAAGT
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
32 1 0.02
33 24 0.44
34 1 0.02
35 18 0.33
36 10 0.19
ACGTcount: A:0.54, C:0.05, G:0.16, T:0.25
Consensus pattern (32 bp):
CAATAAAATAAAAGTTAGTAAGTTAGTAAGAA
Done.