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 410 of 438
Found at i:127444375 original size:12 final size:12
Alignment explanation
Indices: 127444358--127444388 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
127444348 GTAAATTTTT
127444358 TTTTTTTGTATA
1 TTTTTTTGTATA
127444370 TTTTTTTGTATA
1 TTTTTTTGTATA
127444382 TTTTTTT
1 TTTTTTT
127444389 ATGTTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.13, C:0.00, G:0.06, T:0.81
Consensus pattern (12 bp):
TTTTTTTGTATA
Found at i:127444799 original size:35 final size:34
Alignment explanation
Indices: 127444746--127444824 Score: 131
Period size: 35 Copynumber: 2.3 Consensus size: 34
127444736 GCAGGTGCGG
* *
127444746 TGGGAGTGTGTGATGGTGCTGGTGGCAGACAGCA
1 TGGGAGAGTGAGATGGTGCTGGTGGCAGACAGCA
127444780 TGGGAGAGTGAGAGTGGTGCTGGTGGCAGACAGCA
1 TGGGAGAGTGAGA-TGGTGCTGGTGGCAGACAGCA
127444815 TGGGAGAGTG
1 TGGGAGAGTG
127444825 GGAAGAGGCA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
34 11 0.26
35 31 0.74
ACGTcount: A:0.20, C:0.10, G:0.49, T:0.20
Consensus pattern (34 bp):
TGGGAGAGTGAGATGGTGCTGGTGGCAGACAGCA
Found at i:127445843 original size:142 final size:137
Alignment explanation
Indices: 127445478--127445990 Score: 362
Period size: 151 Copynumber: 3.6 Consensus size: 137
127445468 AAAACAAAAA
* ** *
127445478 TTGAAAATACCTCAGCAGGTGAACT-GAGGCTCAACTCATTTCTCGCAATATGGGTTGATTTTTG
1 TTGAAAATACCT-AGC--GTG-ACTAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
* * * *
127445542 AAACATAGAAATT-AAAAGCAGAAATTAAAAAGCTCAACTCACCTCTCGCAACATGAGTT-AATA
62 AAA-ACAGAAATTGAAAA-TAGAAATTAAAAAGCTCAACTCACCTCTCGCAATATGAATTGAAT-
127445605 ATTTGAAAAGTAG-AT
124 -TTTGAAAA-TAGAAT
** *
127445620 TTCGAAAA-A-C--G-GAAATTAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATCTTTGAAA
1 TT-GAAAATACCTAGCGTGACTAAAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTT----
* *
127445680 AATTAAAAACAGAACTTGAAAATAGAAATTAAAAAGACTCAACTCACCTCTCGCAATATGAATTG
59 --TTGAAAACAGAAATTGAAAATAGAAATTAAAAAG-CTCAACTCACCTCTCGCAATATGAATTG
*
127445745 ACTTTTGAAAATAGAAT
121 AATTTTGAAAATAGAAT
* **
127445762 TTGAAAATACCTTAGCGTGCCGCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGA
1 TTGAAAATACC-TAGCGTGACTAAAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGA
* * * *
127445827 AAGACAGAAATTGAAAATACCTCAGCATGTGAACCGAGGCTCAACTCACCTCTCGCAATAT-AAG
63 AA-ACAGAAATTGAAAATA---GA-AAT-T-AA--AAAGCTCAACTCACCTCTCGCAATATGAA-
* * *
127445891 TTGATTTTTTTGAAAACAGAAA
118 TTGA--ATTTTGAAAATAGAAT
* * ** ** *
127445913 TTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAA
1 TTGAAAATACCT-AGCGTGACTAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA
127445978 ACAGAAATTGAAA
65 ACAGAAATTGAAA
127445991 TTACCTCAAC
Statistics
Matches: 300, Mismatches: 38, Indels: 60
0.75 0.10 0.15
Matches are distributed among these distances:
134 2 0.01
135 30 0.10
137 3 0.01
138 1 0.00
141 14 0.05
142 51 0.17
143 40 0.13
144 2 0.01
145 1 0.00
146 3 0.01
147 39 0.13
148 17 0.06
149 34 0.11
150 3 0.01
151 60 0.20
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (137 bp):
TTGAAAATACCTAGCGTGACTAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
CAGAAATTGAAAATAGAAATTAAAAAGCTCAACTCACCTCTCGCAATATGAATTGAATTTTGAAA
ATAGAAT
Found at i:127445976 original size:223 final size:225
Alignment explanation
Indices: 127445717--127446226 Score: 641
Period size: 223 Copynumber: 2.2 Consensus size: 225
127445707 ATTAAAAAGA
* * * * * *
127445717 CTCAACTCACCTCTCGCAATATGAATTGACTTTTGAAAATAGAATTTGAAAATACCTTAGCGTGC
1 CTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAACGTGC
* *
127445782 CGCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT-TTTGAAAGACAGAAATTGAAAATA
66 CGCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAATTGAAAAACAGAAATTGAAAATA
* *
127445846 CCTCAGCATGTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTGA-AAACAG
131 CCTCAGCACGTGAACCGAGACTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTGATAAACAG
*
127445910 AAATTGAAAA-TACCTCAACGTGTCTTGAGG
196 AAATT-AAAATTACCTCAACGTGTCCTGAGG
** * *
127445940 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGT
1 CTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAACGTGC
*** * *
127446005 CTTGAGGTTCAATTCACCTCTCGCAATATGAGTTGATTTTGACGAACAGAAATTGAAAAACAGAA
66 CGCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT----------AATTGAAAAACAGAA
* * * *
127446070 ATTGAAAATACCTCAGCGCGTGAGCTGAGACTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
121 ATTGAAAATACCTCAGCACGTGAACCGAGACTCAACTCACCTCTCGCAATATAAGTTGATTTTTT
* *
127446135 TGATGAACAGAAATTAAAATTACCTCAACGTGTCCTGATG
186 TGATAAACAGAAATTAAAATTACCTCAACGTGTCCTGAGG
*
127446175 CTCAACTCACCTCTCGCAATATGAGTTG-ATTTTGACGAACAGAAATTGAAAA
1 CTCAACTCACCTCTCGCAATATGAGTTGAATTTTGA-AAACAGAAATTGAAAA
127446227 ACAGAAATTG
Statistics
Matches: 243, Mismatches: 30, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
223 90 0.37
234 85 0.35
235 68 0.28
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (225 bp):
CTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAACGTGC
CGCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAATTGAAAAACAGAAATTGAAAATA
CCTCAGCACGTGAACCGAGACTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTGATAAACAG
AAATTAAAATTACCTCAACGTGTCCTGAGG
Found at i:127446000 original size:72 final size:72
Alignment explanation
Indices: 127445717--127446063 Score: 401
Period size: 72 Copynumber: 4.7 Consensus size: 72
127445707 ATTAAAAAGA
* * * * * * *
127445717 CTCAACTCACCTCTCGCAATATGAATTGACTTTTGAAAATAGAATTTGAAAATACCTTAGCGTGC
1 CTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAACGTGT
* *
127445782 CGCAAGG
66 CTCGAGG
*
127445789 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCAGCA
1 CTCAACTCACCTCTCGCAATATGAGTTGA--ATTTTGAAA-ACAGAAATTGAAAATACCTCA--A
* *
127445854 TGTGAAC-CGAGG
61 CGTG-TCTCGAGG
* *
127445866 CTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTGAAAACAGAAATTGAAAATACCTCAACGT
1 CTCAACTCACCTCTCGCAATATGAGTTGA--ATTTTGAAAACAGAAATTGAAAATACCTCAACGT
*
127445931 GTCTTGAGG
64 GTCTCGAGG
** *
127445940 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGT
1 CTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAACGTGT
*
127446005 CTTGAGG
66 CTCGAGG
* * *
127446012 TTCAATTCACCTCTCGCAATATGAGTTG-ATTTTGACGAACAGAAATTGAAAA
1 CTCAACTCACCTCTCGCAATATGAGTTGAATTTTGA-AAACAGAAATTGAAAA
127446064 ACAGAAATTG
Statistics
Matches: 243, Mismatches: 24, Indels: 16
0.86 0.08 0.06
Matches are distributed among these distances:
71 7 0.03
72 107 0.44
73 1 0.00
74 42 0.17
75 18 0.07
76 21 0.09
77 46 0.19
78 1 0.00
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (72 bp):
CTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAACGTGT
CTCGAGG
Found at i:127446066 original size:14 final size:14
Alignment explanation
Indices: 127446049--127446077 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
127446039 GATTTTGACG
127446049 AACAGAAATTGAAA
1 AACAGAAATTGAAA
127446063 AACAGAAATTGAAA
1 AACAGAAATTGAAA
127446077 A
1 A
127446078 TACCTCAGCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.07, G:0.14, T:0.14
Consensus pattern (14 bp):
AACAGAAATTGAAA
Found at i:127446167 original size:163 final size:162
Alignment explanation
Indices: 127445903--127446297 Score: 629
Period size: 163 Copynumber: 2.5 Consensus size: 162
127445893 GATTTTTTTG
* * **
127445903 AAAACAGAAATTGAAAATACCTCA--ACGTG-TCTTGAGGCTCAACTCATTTCTCGCAATATGAG
1 AAAACAGAAATTGAAAATACCTCAGCGCGTGAGC-TGAGGCTCAACTCACCTCTCGCAATATGAG
* * * * *
127445965 TTGA--ATTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCTTGAGGTTCAATTCACCTCTCG
65 TTGATTTTTTTGAAAACAGAAATTAAAATTACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCG
127446028 CAATATGAGTTGATTTTGACGAACAGAAATTGA
130 CAATATGAGTTGATTTTGACGAACAGAAATTGA
*
127446061 AAAACAGAAATTGAAAATACCTCAGCGCGTGAGCTGAGACTCAACTCACCTCTCGCAATATGAGT
1 AAAACAGAAATTGAAAATACCTCAGCGCGTGAGCTGAGGCTCAACTCACCTCTCGCAATATGAGT
* *
127446126 TGATTTTTTTGATGAACAGAAATTAAAATTACCTCAACGTGTCCTGATGCTCAACTCACCTCTCG
66 TGATTTTTTTGA-AAACAGAAATTAAAATTACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCG
127446191 CAATATGAGTTGATTTTGACGAACAGAAATTGA
130 CAATATGAGTTGATTTTGACGAACAGAAATTGA
127446224 AAAACAGAAATTGAAAATACCTCAGCGCGTGAGCTGAGGCTCAACTCACCTCTCGCAATATGAGT
1 AAAACAGAAATTGAAAATACCTCAGCGCGTGAGCTGAGGCTCAACTCACCTCTCGCAATATGAGT
127446289 TGATTTTTT
66 TGATTTTTT
127446298 GGTAGAATTT
Statistics
Matches: 218, Mismatches: 13, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
158 24 0.11
160 35 0.16
161 1 0.00
162 6 0.03
163 152 0.70
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.28
Consensus pattern (162 bp):
AAAACAGAAATTGAAAATACCTCAGCGCGTGAGCTGAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTTTTTTGAAAACAGAAATTAAAATTACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGC
AATATGAGTTGATTTTGACGAACAGAAATTGA
Found at i:127446229 original size:14 final size:14
Alignment explanation
Indices: 127446212--127446240 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
127446202 GATTTTGACG
127446212 AACAGAAATTGAAA
1 AACAGAAATTGAAA
127446226 AACAGAAATTGAAA
1 AACAGAAATTGAAA
127446240 A
1 A
127446241 TACCTCAGCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.07, G:0.14, T:0.14
Consensus pattern (14 bp):
AACAGAAATTGAAA
Found at i:127458595 original size:2 final size:2
Alignment explanation
Indices: 127458588--127458612 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
127458578 GGTACTAAGA
127458588 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 A
127458613 AATAATAGTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:127458645 original size:33 final size:30
Alignment explanation
Indices: 127458598--127458667 Score: 86
Period size: 33 Copynumber: 2.2 Consensus size: 30
127458588 ATATATATAT
*
127458598 ATATATATATATATAAATAATAGTATTAGAA
1 ATATATATATATATAAATAATAATATTA-AA
* *
127458629 ATCATATAGTATATATAACTGATAATATTAAA
1 AT-ATATA-TATATATAAATAATAATATTAAA
127458661 ATATATA
1 ATATATA
127458668 CATAATATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 7 0.21
32 9 0.26
33 18 0.53
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.39
Consensus pattern (30 bp):
ATATATATATATATAAATAATAATATTAAA
Found at i:127458892 original size:3 final size:3
Alignment explanation
Indices: 127458884--127458940 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
127458874 ACAAGGATAT
127458884 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
127458932 ATA ATA ATA
1 ATA ATA ATA
127458941 TTGAAACACA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:127459060 original size:3 final size:3
Alignment explanation
Indices: 127459046--127459094 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
127459036 AATGTATTTC
*
127459046 AAT AAC 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
127459094 A
1 A
127459095 TTGAAATGCA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:127459589 original size:13 final size:12
Alignment explanation
Indices: 127459571--127459608 Score: 62
Period size: 11 Copynumber: 3.3 Consensus size: 12
127459561 GAAAAAAAAA
127459571 GAAGAGAG-AGG
1 GAAGAGAGAAGG
127459582 GAAGAGAGAAGG
1 GAAGAGAGAAGG
127459594 GAA-AGAGAAGG
1 GAAGAGAGAAGG
127459605 GAAG
1 GAAG
127459609 GGAATCCGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 19 0.76
12 6 0.24
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (12 bp):
GAAGAGAGAAGG
Found at i:127466033 original size:22 final size:23
Alignment explanation
Indices: 127465986--127466034 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
127465976 TTATAAAACC
*
127465986 TAAAGATGAAATAAAAATAGTAT
1 TAAAGATGAAATAAAAATAATAT
127466009 TAAAGA-GAAATAAAAAGTAAT-T
1 TAAAGATGAAATAAAAA-TAATAT
127466031 TAAA
1 TAAA
127466035 AACATAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.63, C:0.00, G:0.12, T:0.24
Consensus pattern (23 bp):
TAAAGATGAAATAAAAATAATAT
Found at i:127471059 original size:26 final size:26
Alignment explanation
Indices: 127471023--127471106 Score: 141
Period size: 26 Copynumber: 3.2 Consensus size: 26
127471013 TGATACAAAT
*
127471023 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
127471049 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
127471075 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
127471101 TCATAA
1 TGATAA
127471107 GAATTTCATG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:127472589 original size:28 final size:26
Alignment explanation
Indices: 127472547--127472621 Score: 89
Period size: 26 Copynumber: 2.8 Consensus size: 26
127472537 AAAAGTAGCT
*
127472547 AAATTACTATAATACCCCTATGTATAG-A
1 AAATTACTATTATACCCCTA-G-AT-GCA
*
127472575 AAATTACTATTATACCCCTAGGTGCA
1 AAATTACTATTATACCCCTAGATGCA
*
127472601 AAATTACTGTTATACCCCTAG
1 AAATTACTATTATACCCCTAG
127472622 GGTTAATTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
25 1 0.02
26 22 0.51
27 1 0.02
28 19 0.44
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.32
Consensus pattern (26 bp):
AAATTACTATTATACCCCTAGATGCA
Found at i:127472766 original size:27 final size:27
Alignment explanation
Indices: 127472725--127472851 Score: 173
Period size: 27 Copynumber: 4.7 Consensus size: 27
127472715 GAGGAAGCAT
*
127472725 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
127472752 TCTGGTGGCTCTGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * *
127472779 TCTGGTGGCTCTACCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
127472806 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* *
127472834 TCTGGTGACTCTGTCACA
1 TCTGGTGGCTCTGCCACA
127472852 TTATCTGTTT
Statistics
Matches: 87, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
27 72 0.83
28 15 0.17
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.33
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:127488584 original size:6 final size:6
Alignment explanation
Indices: 127488573--127488606 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
127488563 TATTTCTCTC
*
127488573 TTTTTA TTTTTA TTTTTA TTTTT- CTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
127488607 TCATTTTCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:127490002 original size:49 final size:49
Alignment explanation
Indices: 127489933--127490166 Score: 279
Period size: 49 Copynumber: 4.7 Consensus size: 49
127489923 ATTTGATACG
* * *
127489933 CATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTATA
1 CATAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCTGGTACA
* * ** *
127489982 CGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACA
1 CATAGTAGCCTGCACTTAGTACTACACACGCGACC-AATTATCTGGTACA
* * * ** * *
127490032 CGTAGTAGTCTGCACTTAGTACTACACACGTGATTGAAGTTATCGGGTACG
1 CATAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-TTATCTGGTACA
* *
127490083 CATAGTAGCCTGCACTTAGTACTACACATGCGACTAATTATCTGGTACA
1 CATAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCTGGTACA
*
127490132 CATAGTAGCCTGCACTTAGTACTACACACGTGACC
1 CATAGTAGCCTGCACTTAGTACTACACACGCGACC
127490167 TCACAATATA
Statistics
Matches: 155, Mismatches: 27, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
49 74 0.48
50 45 0.29
51 36 0.23
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.26
Consensus pattern (49 bp):
CATAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCTGGTACA
Found at i:127490155 original size:100 final size:99
Alignment explanation
Indices: 127489926--127490166 Score: 313
Period size: 100 Copynumber: 2.4 Consensus size: 99
127489916 CAAAGCTATT
* * * * *
127489926 TGATACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTATACGTAGTAGC
1 TGATACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACATAGTAGC
*
127489991 CTGCACTTAGTACTACACACGTGACCTAACCATC
66 CTGCACTTAGTACTACACACGCGACCTAACCATC
* * ** * *
127490025 TGATACACGTAGTAGTCTGCACTTAGTACTACACACGTGATTGAAGTTATCGGGTACGCATAGTA
1 TGATACACATAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-TTATCCGGTACACATAGTA
* **
127490090 GCCTGCACTTAGTACTACACATGCGA-CTAATTATC
64 GCCTGCACTTAGTACTACACACGCGACCTAACCATC
*
127490125 TGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACC
1 TGATACACATAGTAGCCTGCACTTAGTACTACACACGTGACC
127490167 TCACAATATA
Statistics
Matches: 120, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
99 35 0.29
100 46 0.38
101 39 0.32
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.27
Consensus pattern (99 bp):
TGATACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACATAGTAGC
CTGCACTTAGTACTACACACGCGACCTAACCATC
Found at i:127492737 original size:46 final size:46
Alignment explanation
Indices: 127492684--127493003 Score: 444
Period size: 46 Copynumber: 7.0 Consensus size: 46
127492674 AGTGTGCTCT
* *
127492684 CTGATATGAAATGTGTAAAACCGTGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
*
127492730 CTGATATGAAATGTGTAAGACCGTGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
127492776 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
* *
127492822 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGTAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
* *
127492868 CTAATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
* *** * *
127492914 GTGATATGAAATGAACAAGACCATGGTTGAAAGATATCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
* * * * * * *
127492960 ATGACA-GAAAATGAGTAAGCCCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
127493004 TCATGTCAAA
Statistics
Matches: 252, Mismatches: 21, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
45 1 0.00
46 251 1.00
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.23
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
Found at i:127496035 original size:15 final size:15
Alignment explanation
Indices: 127496012--127496051 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
127496002 CAAGCCCAGA
127496012 ATAAGGAAATCCAAG
1 ATAAGGAAATCCAAG
* *
127496027 ATAAAGAAATCCATG
1 ATAAGGAAATCCAAG
127496042 ATAAGGAAAT
1 ATAAGGAAAT
127496052 ACCATTTACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.55, C:0.10, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAGGAAATCCAAG
Found at i:127500291 original size:22 final size:22
Alignment explanation
Indices: 127500266--127500307 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
127500256 ATATTTTCAG
127500266 AATTT-TAATATTATTTTATATT
1 AATTTATAAT-TTATTTTATATT
*
127500288 AATTTATGATTTATTTTATA
1 AATTTATAATTTATTTTATA
127500308 CACAAACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
AATTTATAATTTATTTTATATT
Found at i:127510797 original size:28 final size:28
Alignment explanation
Indices: 127510755--127510815 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
127510745 CTGGTTTAGC
* *
127510755 TAGGGTTTTAGTTTCTGAAACCAAAGTT
1 TAGGGTTTCAATTTCTGAAACCAAAGTT
127510783 TAGGGTTTCAATTTCTGAAACCAAAGTT
1 TAGGGTTTCAATTTCTGAAACCAAAGTT
127510811 T-GGGT
1 TAGGGT
127510816 CATTTAAGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 4 0.13
28 27 0.87
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.38
Consensus pattern (28 bp):
TAGGGTTTCAATTTCTGAAACCAAAGTT
Found at i:127519827 original size:7 final size:7
Alignment explanation
Indices: 127519807--127519934 Score: 53
Period size: 7 Copynumber: 18.0 Consensus size: 7
127519797 ACCCCTATCC
127519807 CCATAAA
1 CCATAAA
127519814 -CACTAAA
1 CCA-TAAA
127519821 CCATAAA
1 CCATAAA
*
127519828 ACATAAA
1 CCATAAA
*
127519835 CCATAAT
1 CCATAAA
* *
127519842 CCCTAATC
1 CCATAA-A
* *
127519850 CCCTAAC
1 CCATAAA
*
127519857 CCTTAATA
1 CCATAA-A
* *
127519865 GC-TAAC
1 CCATAAA
*
127519871 CCCTAAA
1 CCATAAA
*
127519878 CCTTAAA
1 CCATAAA
127519885 CCATAAA
1 CCATAAA
127519892 CCATAAA
1 CCATAAA
* *
127519899 TCATAAT
1 CCATAAA
*
127519906 CCCTAAA
1 CCATAAA
*
127519913 CCCATAAT
1 -CCATAAA
*
127519921 TCATAAA
1 CCATAAA
*
127519928 CCTTAAA
1 CCATAAA
127519935 ATAGTAACTC
Statistics
Matches: 91, Mismatches: 24, Indels: 12
0.72 0.19 0.09
Matches are distributed among these distances:
6 3 0.03
7 74 0.81
8 14 0.15
ACGTcount: A:0.46, C:0.31, G:0.01, T:0.22
Consensus pattern (7 bp):
CCATAAA
Found at i:127519863 original size:22 final size:21
Alignment explanation
Indices: 127519831--127519883 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
127519821 CCATAAAACA
* *
127519831 TAAACCATAATCCCTAATCCCC
1 TAAACCTTAATACCTAA-CCCC
* *
127519853 TAACCCTTAATAGCTAACCCC
1 TAAACCTTAATACCTAACCCC
127519874 TAAACCTTAA
1 TAAACCTTAA
127519884 ACCATAAACC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 13 0.50
22 13 0.50
ACGTcount: A:0.38, C:0.36, G:0.02, T:0.25
Consensus pattern (21 bp):
TAAACCTTAATACCTAACCCC
Found at i:127519934 original size:22 final size:21
Alignment explanation
Indices: 127519881--127519934 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
127519871 CCCTAAACCT
127519881 TAAACCATAAACCATAAATCA
1 TAAACCATAAACCATAAATCA
* * *
127519902 TAATCCCTAAACCCATAATTCA
1 TAAACCATAAA-CCATAAATCA
*
127519924 TAAACCTTAAA
1 TAAACCATAAA
127519935 ATAGTAACTC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 9 0.33
22 18 0.67
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (21 bp):
TAAACCATAAACCATAAATCA
Found at i:127519963 original size:7 final size:7
Alignment explanation
Indices: 127519953--127519978 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
127519943 TCCTAAAACT
127519953 TAAACCC
1 TAAACCC
127519960 TAAACCC
1 TAAACCC
127519967 TAAACCC
1 TAAACCC
127519974 TAAAC
1 TAAAC
127519979 TATAATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.38, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAACCC
Found at i:127519963 original size:14 final size:14
Alignment explanation
Indices: 127519944--127519977 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
127519934 AATAGTAACT
*
127519944 CCTAAAACTTAAAC
1 CCTAAAACCTAAAC
*
127519958 CCTAAACCCTAAAC
1 CCTAAAACCTAAAC
127519972 CCTAAA
1 CCTAAA
127519978 CTATAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.35, G:0.00, T:0.18
Consensus pattern (14 bp):
CCTAAAACCTAAAC
Found at i:127520585 original size:40 final size:40
Alignment explanation
Indices: 127520509--127520603 Score: 100
Period size: 40 Copynumber: 2.4 Consensus size: 40
127520499 TATTTTTGCA
* * *
127520509 GCGTTTTTCAAAAAGCGCTGCTAATGGTCGACCTATAGCG
1 GCGTTTTTCAAAAAGCGCCGCTAATGCTCAACCTATAGCG
* ** * *
127520549 GCGTTTTTTAAAAAGTTCCGCTAATGCTCAATCTATAGTG
1 GCGTTTTTCAAAAAGCGCCGCTAATGCTCAACCTATAGCG
**
127520589 GTATTTTTCAAAAAG
1 GCGTTTTTCAAAAAG
127520604 AGTTAACATA
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (40 bp):
GCGTTTTTCAAAAAGCGCCGCTAATGCTCAACCTATAGCG
Found at i:127520722 original size:40 final size:40
Alignment explanation
Indices: 127520678--127520761 Score: 114
Period size: 40 Copynumber: 2.1 Consensus size: 40
127520668 ATGGTCGACT
* * *
127520678 TATAGCGTCGTTTTTCAAAAAGCACTTCCAATGCTCAATC
1 TATAGCGGCATTTTTCAAAAAGCACTGCCAATGCTCAATC
* * *
127520718 TATAGCGGCATTTTTCAAAAAGCGCTGCTAATGCTCGATC
1 TATAGCGGCATTTTTCAAAAAGCACTGCCAATGCTCAATC
127520758 TATA
1 TATA
127520762 ATGGCGTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (40 bp):
TATAGCGGCATTTTTCAAAAAGCACTGCCAATGCTCAATC
Found at i:127520731 original size:136 final size:136
Alignment explanation
Indices: 127520485--127520739 Score: 384
Period size: 136 Copynumber: 1.9 Consensus size: 136
127520475 GCTCATCGAT
127520485 GGCGTTGTGCTTAATATTTTTGCAGCGTTTTTCAAAAAGCGCTGCTAATGGTCGACCTATAGCGG
1 GGCGTTGTGCTTAATATTTTTGCAGCGTTTTTCAAAAAGCGCTGCTAATGGTCGACCTATAGCGG
* ** * * *
127520550 CGTTTTTTAAAAAGTTCCGCTAATGCTCAATCTATAGTGGTATTTTTCAAAAAGAGTTAACATAA
66 CGTTTTTCAAAAAGCACCGCCAATGCTCAATCTATAGCGGCATTTTTCAAAAAGAGTTAACATAA
127520615 AACGAC
131 AACGAC
* ** * * *
127520621 GGCGTTGTGCTTAATTTTTTTGTGGCGTTTTTCAAAAAGCGCTGGTAATGGTCGACTTATAGCGT
1 GGCGTTGTGCTTAATATTTTTGCAGCGTTTTTCAAAAAGCGCTGCTAATGGTCGACCTATAGCGG
**
127520686 CGTTTTTCAAAAAGCACTTCCAATGCTCAATCTATAGCGGCATTTTTCAAAAAG
66 CGTTTTTCAAAAAGCACCGCCAATGCTCAATCTATAGCGGCATTTTTCAAAAAG
127520740 CGCTGCTAAT
Statistics
Matches: 105, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
136 105 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.35
Consensus pattern (136 bp):
GGCGTTGTGCTTAATATTTTTGCAGCGTTTTTCAAAAAGCGCTGCTAATGGTCGACCTATAGCGG
CGTTTTTCAAAAAGCACCGCCAATGCTCAATCTATAGCGGCATTTTTCAAAAAGAGTTAACATAA
AACGAC
Found at i:127522617 original size:2 final size:2
Alignment explanation
Indices: 127522610--127522655 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
127522600 ATCATTTGAC
127522610 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
127522652 AT AT
1 AT AT
127522656 TTTATTTATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:127523469 original size:20 final size:21
Alignment explanation
Indices: 127523444--127523484 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
127523434 CTTTATAATT
127523444 TATTAT-TTTTTCAA-AATATA
1 TATTATATTTTT-AATAATATA
127523464 TATTATATTTTTAATAATATA
1 TATTATATTTTTAATAATATA
127523485 ATAAGTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTATATTTTTAATAATATA
Found at i:127528661 original size:6 final size:6
Alignment explanation
Indices: 127528650--127528686 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
127528640 CTGTTGATGC
127528650 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA A
127528687 CTTTATCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:127530045 original size:3 final size:3
Alignment explanation
Indices: 127530032--127530201 Score: 140
Period size: 3 Copynumber: 58.0 Consensus size: 3
127530022 TATTTTTAAA
*
127530032 TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
127530079 TAT TA- TATT TAT T-T TAT TAC TGT TAC TAT TAT T-T TAT ATATT TAT
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TA-T TAT
* * * * * *
127530124 TAC CAT TAT T-T GT-T TAT TAT TAT TAT TAA TAA CA- TAT TGT TAT
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
127530167 TTT TAT TAT T-T TAT TAT TAT TAT TGT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
127530202 CATGGTACTA
Statistics
Matches: 135, Mismatches: 21, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
2 13 0.10
3 115 0.85
4 6 0.04
5 1 0.01
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:127530354 original size:3 final size:3
Alignment explanation
Indices: 127530346--127530432 Score: 115
Period size: 3 Copynumber: 29.3 Consensus size: 3
127530336 TTTTTCCCTA
* * * *
127530346 TAT TAT TAT TAT TTT TAT AAT T-T TCAT TTT TAT TAA TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT
127530390 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
127530433 GTCTTCTATT
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
2 4 0.05
3 68 0.92
4 2 0.03
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:127531353 original size:125 final size:125
Alignment explanation
Indices: 127531129--127531358 Score: 300
Period size: 125 Copynumber: 1.8 Consensus size: 125
127531119 GGATTTCTAA
* *
127531129 AAAATAAGAAAATATTTCGTGTTTAGAAATTCGAGAAATCATGCCCAATCGTGCTGGGTTTCGAT
1 AAAATAAGAAAATATTTCGTGTTTAGAAATTCGAGAAATCATGCCCAATCGTGCTGAGTTTCGAC
** * ** *
127531194 TTTTCGTTCAACCGAATAACTGAATATCCTTTTGAAATTTTGTCCATGTTTTCTTAAATT
66 TTACCATTCAACCGAATAACCAAATATCCCTTTGAAATTTTGTCCATGTTTTCTTAAATT
* * * **
127531254 AAAATGAGACAATATTTTGTGTTTAGAAATTCGAGAAATTGTGCCCAATCGTGCTGAGTTTCGAC
1 AAAATAAGAAAATATTTCGTGTTTAGAAATTCGAGAAATCATGCCCAATCGTGCTGAGTTTCGAC
** *
127531319 TTACCATTTGACC-AGATAGCCAAATATCCCTTTGAAATTT
66 TTACCATTCAACCGA-ATAACCAAATATCCCTTTGAAATTT
127531359 CAAATGCATG
Statistics
Matches: 88, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
124 1 0.01
125 87 0.99
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (125 bp):
AAAATAAGAAAATATTTCGTGTTTAGAAATTCGAGAAATCATGCCCAATCGTGCTGAGTTTCGAC
TTACCATTCAACCGAATAACCAAATATCCCTTTGAAATTTTGTCCATGTTTTCTTAAATT
Found at i:127531696 original size:14 final size:14
Alignment explanation
Indices: 127531677--127531703 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
127531667 ACCGAAATGC
127531677 TTTATTAAAATGAG
1 TTTATTAAAATGAG
127531691 TTTATTAAAATGA
1 TTTATTAAAATGA
127531704 TCGATCACAA
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:0.00, G:0.11, T:0.44
Consensus pattern (14 bp):
TTTATTAAAATGAG
Found at i:127538014 original size:9 final size:9
Alignment explanation
Indices: 127537978--127538007 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
127537968 ATTCGAAAAA
127537978 AATTCGAGTT
1 AATTCGA-TT
127537988 AATTCGATT
1 AATTCGATT
127537997 AATTCGATT
1 AATTCGATT
127538006 AA
1 AA
127538008 CTTGATTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 13 0.65
10 7 0.35
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (9 bp):
AATTCGATT
Found at i:127541620 original size:21 final size:21
Alignment explanation
Indices: 127541596--127541635 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
127541586 CCAGAAGAAA
127541596 CTACATAGGAGCCAAAAGAGG
1 CTACATAGGAGCCAAAAGAGG
*
127541617 CTACATAGGAGCCAGAAGA
1 CTACATAGGAGCCAAAAGA
127541636 AACCATGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.20, G:0.28, T:0.10
Consensus pattern (21 bp):
CTACATAGGAGCCAAAAGAGG
Found at i:127541651 original size:20 final size:20
Alignment explanation
Indices: 127541626--127541670 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
127541616 GCTACATAGG
127541626 AGCCAGAAGAAACCATGAGA
1 AGCCAGAAGAAACCATGAGA
127541646 AGCCAGAAGAAACCATGAGA
1 AGCCAGAAGAAACCATGAGA
127541666 AGCCA
1 AGCCA
127541671 ATATCCGAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.49, C:0.22, G:0.24, T:0.04
Consensus pattern (20 bp):
AGCCAGAAGAAACCATGAGA
Found at i:127554109 original size:6 final size:6
Alignment explanation
Indices: 127554087--127554200 Score: 176
Period size: 6 Copynumber: 19.0 Consensus size: 6
127554077 AGGTAAAATT
*
127554087 AATAAA AACATAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
1 AATAAA AATA-AA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
*
127554136 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA GATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
* *
127554184 GAT-AA AATAAA ATTAAA
1 AATAAA AATAAA AATAAA
127554201 CATCATTATC
Statistics
Matches: 101, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
5 4 0.04
6 92 0.91
7 5 0.05
ACGTcount: A:0.80, C:0.01, G:0.02, T:0.18
Consensus pattern (6 bp):
AATAAA
Found at i:127582957 original size:2 final size:2
Alignment explanation
Indices: 127582950--127582991 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
127582940 ACAAACTAAT
127582950 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
127582992 CTCCTTCCCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:127584091 original size:16 final size:17
Alignment explanation
Indices: 127584070--127584107 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
127584060 TGTATTTATG
*
127584070 TATTTA-AATTTTATTT
1 TATTTATAATTTAATTT
127584086 TATTTATAATTTAATTT
1 TATTTATAATTTAATTT
*
127584103 AATTT
1 TATTT
127584108 TTTAATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTTATAATTTAATTT
Found at i:127592967 original size:2 final size:2
Alignment explanation
Indices: 127592960--127592991 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
127592950 AACTATGTAA
127592960 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
127592992 TTTTATATTT
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:127594818 original size:17 final size:17
Alignment explanation
Indices: 127594793--127594828 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
127594783 TGTGTTCAAA
127594793 TTATATTGTATTTAAAT
1 TTATATTGTATTTAAAT
* *
127594810 TTATTTTGTATTTATAT
1 TTATATTGTATTTAAAT
127594827 TT
1 TT
127594829 TTCTAATAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTATATTGTATTTAAAT
Found at i:127597563 original size:28 final size:27
Alignment explanation
Indices: 127597513--127597568 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
127597503 CTTTTATTAA
*
127597513 TTTAATTTTAAATAAAATTAAAATCATG
1 TTTAATTTTAAATAAAATGAAAA-CATG
*
127597541 TTTAATATTTAATTAAAA-GAAAACATG
1 TTTAAT-TTTAAATAAAATGAAAACATG
127597568 T
1 T
127597569 CTACCCCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.20
28 10 0.40
29 10 0.40
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.41
Consensus pattern (27 bp):
TTTAATTTTAAATAAAATGAAAACATG
Found at i:127599207 original size:2 final size:2
Alignment explanation
Indices: 127599200--127599228 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
127599190 TTCGTCATTA
127599200 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
127599229 GTGTGTGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:127599829 original size:18 final size:18
Alignment explanation
Indices: 127599798--127599838 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
127599788 AAAATAATAA
* *
127599798 TTATATTTAATTATTTTT
1 TTATAGTTAATTATTCTT
*
127599816 TTATAGTTAGTTATTCTT
1 TTATAGTTAATTATTCTT
127599834 TTATA
1 TTATA
127599839 ATAATAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (18 bp):
TTATAGTTAATTATTCTT
Found at i:127600291 original size:16 final size:15
Alignment explanation
Indices: 127600265--127600303 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
127600255 TAATGAAAAT
127600265 TAATTTT-TTTGAAA
1 TAATTTTATTTGAAA
127600279 CTAATTTTATTTGAAA
1 -TAATTTTATTTGAAA
*
127600295 TAATATTAT
1 TAATTTTAT
127600304 GTATATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (15 bp):
TAATTTTATTTGAAA
Found at i:127600385 original size:20 final size:20
Alignment explanation
Indices: 127600362--127600400 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
127600352 TAATTATAAA
*
127600362 ATTTATTTATTACATTAATT
1 ATTTATTTATTACAATAATT
127600382 ATTTATTTATTACAATAAT
1 ATTTATTTATTACAATAAT
127600401 AAAACATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTATTTATTACAATAATT
Found at i:127603957 original size:18 final size:19
Alignment explanation
Indices: 127603934--127603971 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
127603924 GGGCAAAATG
127603934 TAATAGAC-AAAATTAATA
1 TAATAGACTAAAATTAATA
*
127603952 TAATAGACTAATATTAATA
1 TAATAGACTAAAATTAATA
127603971 T
1 T
127603972 TTCCTAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (19 bp):
TAATAGACTAAAATTAATA
Found at i:127607544 original size:38 final size:38
Alignment explanation
Indices: 127607482--127607555 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 38
127607472 TTTCTGATGT
127607482 AGAATATTTTTCGGTTAAGAAAAATCCTCTAGCTATTGC
1 AGAATATTTTTCGGTTAAGAAAAATCCTCTA-CTATTGC
* * *
127607521 AGAATA-TTTTCTGTTGAGGAAAATCCTCTACTATT
1 AGAATATTTTTCGGTTAAGAAAAATCCTCTACTATT
127607556 TATGGAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
37 5 0.16
38 21 0.66
39 6 0.19
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (38 bp):
AGAATATTTTTCGGTTAAGAAAAATCCTCTACTATTGC
Found at i:127614005 original size:20 final size:20
Alignment explanation
Indices: 127613966--127614005 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
127613956 TAAGGTGGCC
*
127613966 CGTTAACTAGACACGTTGGA
1 CGTTAACTAGACACGGTGGA
127613986 CGTTAACTAG-CTACGGTGGA
1 CGTTAACTAGAC-ACGGTGGA
127614006 AACTCAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25
Consensus pattern (20 bp):
CGTTAACTAGACACGGTGGA
Found at i:127614054 original size:11 final size:12
Alignment explanation
Indices: 127614032--127614064 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
127614022 CCTAGCTGCT
127614032 AGAAGAAGAAGC
1 AGAAGAAGAAGC
127614044 AGAAG-AGAAGC
1 AGAAGAAGAAGC
*
127614055 AGAAAAAGAA
1 AGAAGAAGAA
127614065 TAATAAGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.64, C:0.06, G:0.30, T:0.00
Consensus pattern (12 bp):
AGAAGAAGAAGC
Found at i:127614784 original size:29 final size:29
Alignment explanation
Indices: 127614744--127614801 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
127614734 AACAACAAAG
127614744 TATTAGACATAGCAATTTAACCATGACAT
1 TATTAGACATAGCAATTTAACCATGACAT
127614773 TATTAGACATAGCAATTTAACCATGACAT
1 TATTAGACATAGCAATTTAACCATGACAT
127614802 AAGAATCGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.31
Consensus pattern (29 bp):
TATTAGACATAGCAATTTAACCATGACAT
Found at i:127616479 original size:46 final size:46
Alignment explanation
Indices: 127616412--127616586 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
127616402 TGTAACCCGC
127616412 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACAT
127616458 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCACAT
* * * * *
127616508 CTC-T---CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACAT
*
127616551 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
127616587 ATGCTCAACC
Statistics
Matches: 112, Mismatches: 6, Indels: 22
0.80 0.04 0.16
Matches are distributed among these distances:
42 3 0.03
43 5 0.04
44 1 0.01
46 64 0.57
47 27 0.24
48 1 0.01
49 1 0.01
50 6 0.05
51 4 0.04
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACAT
Found at i:127616532 original size:93 final size:93
Alignment explanation
Indices: 127616420--127616590 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
127616410 GCCCATAAGT
* *
127616420 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
127616485 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* *
127616513 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
*
127616578 CGAGTTCGGATGC
66 CGAGCTCGGATGC
127616591 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:127616606 original size:46 final size:45
Alignment explanation
Indices: 127616417--127616606 Score: 165
Period size: 46 Copynumber: 4.1 Consensus size: 45
127616407 CCCGCCCATA
** *
127616417 AGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTC-ACATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCTCAACATCC-T
127616462 AAGTGAACTCGGACTCAACTCAACGAGCTCGGATGC-CTAGTTACATCTCT
1 -AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCTC-A---ACATC-CT
* * *** *
127616512 --CGAACTCGGACTCAACTCAACGAGTTCGGACATTC-GCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCTCAACATCC-T
*
127616555 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCTCAA-CATCCT
127616602 AGTGA
1 AGTGA
127616607 CATGTCACTT
Statistics
Matches: 117, Mismatches: 14, Indels: 26
0.75 0.09 0.17
Matches are distributed among these distances:
42 1 0.01
43 5 0.04
45 1 0.01
46 68 0.58
47 29 0.25
48 6 0.05
50 6 0.05
51 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCTCAACATCCT
Found at i:127618388 original size:23 final size:24
Alignment explanation
Indices: 127618360--127618419 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 24
127618350 GTTCGCATGT
* *
127618360 ACACATATATAGGATTTGCGTA-AT
1 ACACATATATAGG-TTTGCATATAC
*
127618384 A-ACATGTATAAGGTTTGCATATAC
1 ACACATATAT-AGGTTTGCATATAC
127618408 ACACATATATAG
1 ACACATATATAG
127618420 AGAGAGTTCG
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
23 14 0.48
24 8 0.28
25 7 0.24
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (24 bp):
ACACATATATAGGTTTGCATATAC
Found at i:127621538 original size:2 final size:2
Alignment explanation
Indices: 127621531--127621565 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
127621521 ATGATTTGTG
127621531 AT 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 AT A
127621566 GTTAAAATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:127628575 original size:2 final size:2
Alignment explanation
Indices: 127628568--127628600 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
127628558 ATGATTTGTG
127628568 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
127628601 GTTAAAATGA
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:127629960 original size:15 final size:14
Alignment explanation
Indices: 127629942--127629973 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
127629932 TTTAAAATTG
127629942 TTTCTTTTTTTTCTT
1 TTTCTTTTTTTT-TT
127629957 TTTCTTTTTTTTTT
1 TTTCTTTTTTTTTT
127629971 TTT
1 TTT
127629974 GCAAATTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (14 bp):
TTTCTTTTTTTTTT
Found at i:127632461 original size:29 final size:29
Alignment explanation
Indices: 127632398--127632467 Score: 88
Period size: 28 Copynumber: 2.4 Consensus size: 29
127632388 CACAACCATG
* * *
127632398 TGTCCCTTTTTTTTTAGATTTTATAGTTT
1 TGTCCCCTATTTTTTAGATTTTACAGTTT
*
127632427 TG-CCCCTATTTTTTGGATTTTACAGTTT
1 TGTCCCCTATTTTTTAGATTTTACAGTTT
*
127632455 TGTCCCCTGTTTT
1 TGTCCCCTATTTT
127632468 ACAAATTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 24 0.69
29 11 0.31
ACGTcount: A:0.11, C:0.17, G:0.13, T:0.59
Consensus pattern (29 bp):
TGTCCCCTATTTTTTAGATTTTACAGTTT
Found at i:127632788 original size:34 final size:34
Alignment explanation
Indices: 127632740--127632842 Score: 107
Period size: 34 Copynumber: 3.0 Consensus size: 34
127632730 AGCATGACTT
* * **
127632740 TTGCCACTAAATTGAACAGTTATAAGCATATTAA
1 TTGCTACTATATTGAACTATTATAAGCATATTAA
**
127632774 TTGCTACTATATTGAACTATTATAAGCATATTGG
1 TTGCTACTATATTGAACTATTATAAGCATATTAA
* ** *
127632808 TTGCTACTGTATTGTTCTATTAAAAGCATAATTAA
1 TTGCTACTATATTGAACTATTATAAGCAT-ATTAA
127632843 ATACTATCAT
Statistics
Matches: 56, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
34 53 0.95
35 3 0.05
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.39
Consensus pattern (34 bp):
TTGCTACTATATTGAACTATTATAAGCATATTAA
Found at i:127633571 original size:25 final size:25
Alignment explanation
Indices: 127633543--127633611 Score: 75
Period size: 27 Copynumber: 2.7 Consensus size: 25
127633533 TATATTGTTT
*
127633543 TATTTATTTTGTGGCATGAAACTCA
1 TATTTATTTTGTGGCATAAAACTCA
* * * *
127633568 TATTTAAGGTTTATAGCTTAAAACTCA
1 TATTT-A-TTTTGTGGCATAAAACTCA
127633595 TATTTATTTTGTGGCAT
1 TATTTATTTTGTGGCAT
127633612 TAGTTTTCTT
Statistics
Matches: 33, Mismatches: 9, Indels: 4
0.72 0.20 0.09
Matches are distributed among these distances:
25 12 0.36
26 2 0.06
27 19 0.58
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.46
Consensus pattern (25 bp):
TATTTATTTTGTGGCATAAAACTCA
Found at i:127634542 original size:35 final size:33
Alignment explanation
Indices: 127634473--127634551 Score: 88
Period size: 35 Copynumber: 2.3 Consensus size: 33
127634463 AAAAATATTA
* *
127634473 TTTATTATATTATTAATTTGACATTTGAATAAT
1 TTTATTATATTATTAATTTGACATTTAAAAAAT
*
127634506 TTTATTTTATTATTAAATTTTGA-ATATTAAAAAAT
1 TTTATTATATTATT-AA-TTTGACAT-TTAAAAAAT
*
127634541 TTCATTATATT
1 TTTATTATATT
127634552 TAAGCTTAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
33 13 0.34
34 4 0.11
35 21 0.55
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.56
Consensus pattern (33 bp):
TTTATTATATTATTAATTTGACATTTAAAAAAT
Found at i:127635988 original size:2 final size:2
Alignment explanation
Indices: 127635983--127636009 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
127635973 GTTTATATGC
127635983 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 A
127636010 ACCATAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:127638962 original size:17 final size:17
Alignment explanation
Indices: 127638940--127638978 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
127638930 AAGACTATTT
127638940 AACATTAATAAATTACA
1 AACATTAATAAATTACA
127638957 AACATTAATAAATTACA
1 AACATTAATAAATTACA
127638974 AACAT
1 AACAT
127638979 CAACCATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.59, C:0.13, G:0.00, T:0.28
Consensus pattern (17 bp):
AACATTAATAAATTACA
Found at i:127640645 original size:21 final size:20
Alignment explanation
Indices: 127640621--127640689 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
127640611 AATACTAATA
127640621 ATAATAATCTAATATAAAACC
1 ATAATAAT-TAATATAAAACC
* **
127640642 ATAAT-GTTAAT-TAATAATT
1 ATAATAATTAATATAA-AACC
127640661 ATAATAATTTAATATAAAACC
1 ATAATAA-TTAATATAAAACC
127640682 ATAATAAT
1 ATAATAAT
127640690 AATCATTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
18 3 0.08
19 11 0.29
20 2 0.05
21 19 0.50
22 3 0.08
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.36
Consensus pattern (20 bp):
ATAATAATTAATATAAAACC
Found at i:127644636 original size:39 final size:39
Alignment explanation
Indices: 127644593--127644671 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
127644583 TCTTAATGAA
127644593 AAAAAAACGTACTAACTTAACTTACAAGCTTGTATTTAT
1 AAAAAAACGTACTAACTTAACTTACAAGCTTGTATTTAT
127644632 AAAAAAACGTACTAACTTAACTTACAAGCTTGTATTTAT
1 AAAAAAACGTACTAACTTAACTTACAAGCTTGTATTTAT
127644671 A
1 A
127644672 TCTTACTGCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (39 bp):
AAAAAAACGTACTAACTTAACTTACAAGCTTGTATTTAT
Found at i:127646356 original size:25 final size:25
Alignment explanation
Indices: 127646328--127646456 Score: 208
Period size: 25 Copynumber: 5.2 Consensus size: 25
127646318 CGAAATGACT
127646328 TGGCACTAAGTGTGCGGAAATTATA
1 TGGCACTAAGTGTGCGGAAATTATA
127646353 TGGCACTAAGTGTGCGGAAATTATA
1 TGGCACTAAGTGTGCGGAAATTATA
*
127646378 TGGCACTAAGTGTGCGGAAATTGTA
1 TGGCACTAAGTGTGCGGAAATTATA
*
127646403 TGGCACTAAGTGTGCGGAAATTTTA
1 TGGCACTAAGTGTGCGGAAATTATA
*
127646428 TGGCACTATGTGTGC-G-AATATATA
1 TGGCACTAAGTGTGCGGAAAT-TATA
127646452 TGGCA
1 TGGCA
127646457 TTGGTGTGTA
Statistics
Matches: 99, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
23 3 0.03
24 9 0.09
25 87 0.88
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (25 bp):
TGGCACTAAGTGTGCGGAAATTATA
Found at i:127651209 original size:12 final size:12
Alignment explanation
Indices: 127651192--127651216 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
127651182 CGGATTTCTC
127651192 GCTCGATAAATT
1 GCTCGATAAATT
127651204 GCTCGATAAATT
1 GCTCGATAAATT
127651216 G
1 G
127651217 GCAGAATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (12 bp):
GCTCGATAAATT
Found at i:127653790 original size:25 final size:25
Alignment explanation
Indices: 127653762--127653840 Score: 117
Period size: 25 Copynumber: 3.2 Consensus size: 25
127653752 CGAAATGACT
127653762 TGGCACTAAGTGTGCGGAAATTATA
1 TGGCACTAAGTGTGCGGAAATTATA
*
127653787 TGGCACTAAGTGTGCGGAAATTTTA
1 TGGCACTAAGTGTGCGGAAATTATA
*
127653812 TGGCACTATGTGTGC-G-AATATATA
1 TGGCACTAAGTGTGCGGAAAT-TATA
127653836 TGGCA
1 TGGCA
127653841 TTGGTGTGTA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
23 3 0.06
24 9 0.18
25 38 0.76
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.30
Consensus pattern (25 bp):
TGGCACTAAGTGTGCGGAAATTATA
Found at i:127669315 original size:16 final size:16
Alignment explanation
Indices: 127669294--127669364 Score: 106
Period size: 16 Copynumber: 4.4 Consensus size: 16
127669284 GTTTGGTTCA
*
127669294 CTGTAATGGAATAGGG
1 CTGTAATGGAATAGAG
*
127669310 CTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
*
127669326 CTGTAATGGAATAGAA
1 CTGTAATGGAATAGAG
*
127669342 CTGTAATGGAATAGAA
1 CTGTAATGGAATAGAG
127669358 CTGTAAT
1 CTGTAAT
127669365 AAGTAATTCA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.38, C:0.07, G:0.27, T:0.28
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:127669625 original size:17 final size:17
Alignment explanation
Indices: 127669603--127669635 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
127669593 AACTATTATT
127669603 AAATATAATTTAATAAA
1 AAATATAATTTAATAAA
127669620 AAATATAATTTAATAA
1 AAATATAATTTAATAA
127669636 CATTCATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATATAATTTAATAAA
Found at i:127670162 original size:18 final size:18
Alignment explanation
Indices: 127670139--127670173 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
127670129 ACGTGGTAGT
*
127670139 CCAACTAGATTTTAAGTG
1 CCAACTAGATCTTAAGTG
127670157 CCAACTAGATCTTAAGT
1 CCAACTAGATCTTAAGT
127670174 ATATCTGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (18 bp):
CCAACTAGATCTTAAGTG
Found at i:127670232 original size:40 final size:40
Alignment explanation
Indices: 127670181--127670425 Score: 382
Period size: 40 Copynumber: 6.1 Consensus size: 40
127670171 AGTATATCTG
* * *
127670181 TTAATACATACTTCATCCGGGTAAATTATACAATTTTCTG
1 TTAATACATACTTCACCCGGGTAAATTATACAGTTTTCTA
*
127670221 TTAATACATACTTTACCCGGGTAAATTATACAGTTTTCTA
1 TTAATACATACTTCACCCGGGTAAATTATACAGTTTTCTA
* * *
127670261 TTAATACATACTTCATCCGGATAAATTATACAGTTTTCTG
1 TTAATACATACTTCACCCGGGTAAATTATACAGTTTTCTA
*
127670301 TTAATACATACTTTACCCGGGTAAATTATACAGTTTTCTA
1 TTAATACATACTTCACCCGGGTAAATTATACAGTTTTCTA
*
127670341 TTAATACATACTTTACCCGGGTAAATTATACAGTTTTCTA
1 TTAATACATACTTCACCCGGGTAAATTATACAGTTTTCTA
* * *
127670381 TTAATATATACTTCATCCGGATAAATTATACAGTTTTCTA
1 TTAATACATACTTCACCCGGGTAAATTATACAGTTTTCTA
127670421 TTAAT
1 TTAAT
127670426 GTGCTTGTGA
Statistics
Matches: 189, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 189 1.00
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (40 bp):
TTAATACATACTTCACCCGGGTAAATTATACAGTTTTCTA
Found at i:127670392 original size:120 final size:120
Alignment explanation
Indices: 127670177--127670425 Score: 444
Period size: 120 Copynumber: 2.1 Consensus size: 120
127670167 CTTAAGTATA
* *
127670177 TCTGTTAATACATACTTCATCCGGGTAAATTATACAATTTTCTGTTAATACATACTTTACCCGGG
1 TCTGTTAATACATACTTCACCCGGGTAAATTATACAATTTTCTATTAATACATACTTTACCCGGG
127670242 TAAATTATACAGTTTTCTATTAATACATACTTCATCCGGATAAATTATACAGTTT
66 TAAATTATACAGTTTTCTATTAATACATACTTCATCCGGATAAATTATACAGTTT
* *
127670297 TCTGTTAATACATACTTTACCCGGGTAAATTATACAGTTTTCTATTAATACATACTTTACCCGGG
1 TCTGTTAATACATACTTCACCCGGGTAAATTATACAATTTTCTATTAATACATACTTTACCCGGG
*
127670362 TAAATTATACAGTTTTCTATTAATATATACTTCATCCGGATAAATTATACAGTTT
66 TAAATTATACAGTTTTCTATTAATACATACTTCATCCGGATAAATTATACAGTTT
*
127670417 TCTATTAAT
1 TCTGTTAAT
127670426 GTGCTTGTGA
Statistics
Matches: 123, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 123 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.41
Consensus pattern (120 bp):
TCTGTTAATACATACTTCACCCGGGTAAATTATACAATTTTCTATTAATACATACTTTACCCGGG
TAAATTATACAGTTTTCTATTAATACATACTTCATCCGGATAAATTATACAGTTT
Found at i:127671805 original size:15 final size:14
Alignment explanation
Indices: 127671769--127671803 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
127671759 ATAAAAAATC
*
127671769 TTTTTTTGAATTTT
1 TTTTTTTAAATTTT
127671783 TTTTTTTAAATTTT
1 TTTTTTTAAATTTT
127671797 TTTTTTT
1 TTTTTTT
127671804 TACTGAAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (14 bp):
TTTTTTTAAATTTT
Found at i:127674591 original size:21 final size:21
Alignment explanation
Indices: 127674545--127674592 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
127674535 TATATCTAAA
*
127674545 AATTGTTATCATAATGTTTTT
1 AATTATTATCATAATGTTTTT
*
127674566 -CTTATTATCAATAAT-TTTTT
1 AATTATTATC-ATAATGTTTTT
127674586 AATTATT
1 AATTATT
127674593 TATTTGATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.58
Consensus pattern (21 bp):
AATTATTATCATAATGTTTTT
Found at i:127681915 original size:43 final size:43
Alignment explanation
Indices: 127681849--127681933 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 43
127681839 TCACTGCCAA
*
127681849 AAGCCAAACATTATTACATTATTATTACTAACTCAATGTAGGG
1 AAGCCAAACATTATTACATTATTATTACTAACTCAACGTAGGG
* *
127681892 AAGCTAAACATTATTACATTATTATTACTAACTGAACGTAGG
1 AAGCCAAACATTATTACATTATTATTACTAACTCAACGTAGG
127681934 AAAACAAGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (43 bp):
AAGCCAAACATTATTACATTATTATTACTAACTCAACGTAGGG
Found at i:127683144 original size:27 final size:26
Alignment explanation
Indices: 127683107--127683158 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
127683097 CTTAAGACAA
** *
127683107 AAAAATTAAATTGATTTTATTTTATT
1 AAAAATTAAATAAATTATATTTTATT
127683133 AAAAATTAAAATAAATTATATTTTAT
1 AAAAATT-AAATAAATTATATTTTAT
127683159 CCAAAAGTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (26 bp):
AAAAATTAAATAAATTATATTTTATT
Found at i:127684622 original size:13 final size:13
Alignment explanation
Indices: 127684604--127684646 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
127684594 ATATATGAAG
127684604 ATTATTATTTAAA
1 ATTATTATTTAAA
127684617 ATTATTATTTTTAAA
1 ATTATTA--TTTAAA
127684632 ATTTATTA-TTAAA
1 A-TTATTATTTAAA
127684645 AT
1 AT
127684647 AAAATTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
12 1 0.04
13 13 0.48
15 7 0.26
16 6 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTATTATTTAAA
Found at i:127684625 original size:16 final size:17
Alignment explanation
Indices: 127684604--127684642 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
127684594 ATATATGAAG
127684604 ATTATTATTTAAAA-TT
1 ATTATTATTTAAAATTT
127684620 ATTATT-TTTAAAATTT
1 ATTATTATTTAAAATTT
127684636 ATTATTA
1 ATTATTA
127684643 AAATAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTATTATTTAAAATTT
Found at i:127684677 original size:13 final size:13
Alignment explanation
Indices: 127684657--127684686 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
127684647 AAAATTAAAA
127684657 TATT-AAATAATT
1 TATTAAAATAATT
127684669 TATTAAAATAATT
1 TATTAAAATAATT
127684682 TATTA
1 TATTA
127684687 TATGATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TATTAAAATAATT
Found at i:127684721 original size:22 final size:23
Alignment explanation
Indices: 127684696--127684741 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
127684686 ATATGATTAA
127684696 ATATTTAAAATTAT-AATATTTT
1 ATATTTAAAATTATAAATATTTT
* *
127684718 ATATTTATAATTTTAAATATTTT
1 ATATTTAAAATTATAAATATTTT
127684741 A
1 A
127684742 AAAATAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
ATATTTAAAATTATAAATATTTT
Found at i:127686595 original size:2 final size:2
Alignment explanation
Indices: 127686558--127686583 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
127686548 TTTTAATACC
127686558 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
127686584 TCTTTTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:127686832 original size:3 final size:3
Alignment explanation
Indices: 127686824--127686854 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
127686814 ATCTATATAG
127686824 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
127686855 CCTAATATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:127687190 original size:22 final size:20
Alignment explanation
Indices: 127687130--127687199 Score: 54
Period size: 22 Copynumber: 3.5 Consensus size: 20
127687120 TTGCTTTCAT
*
127687130 CATTATTATTAT-TACTA-A
1 CATTTTTATTATATACTATA
* *
127687148 CATGTATATATATATACTATA
1 CATTTTTAT-TATATACTATA
*
127687169 TATTTTTATTATATCACGTATA
1 CATTTTTATTATAT-AC-TATA
*
127687191 CGTTTTTAT
1 CATTTTTAT
127687200 ATGTACGCTA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
18 6 0.15
19 3 0.08
20 10 0.26
21 9 0.23
22 11 0.28
ACGTcount: A:0.34, C:0.10, G:0.04, T:0.51
Consensus pattern (20 bp):
CATTTTTATTATATACTATA
Found at i:127690448 original size:44 final size:45
Alignment explanation
Indices: 127690358--127690486 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
127690348 GACAGAACGA
*
127690358 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
127690404 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
127690448 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
127690487 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:127706996 original size:88 final size:87
Alignment explanation
Indices: 127706816--127706998 Score: 208
Period size: 88 Copynumber: 2.1 Consensus size: 87
127706806 TTGAAGATTT
* * * *
127706816 ACAGATCTTACCCCCTAAGCAGTAGGGAAACAGATCGAAGGTAACGAGCTTTAACCCTCCTAAGC
1 ACAGATCTTACACCCTAAGCAGTAGGGAAACAGATCGAAAGAAACGAGCCTTAACCCTCCTAAGC
* *
127706881 AGTAAGGTAACAAGCCGAATTT
66 AGTAAGGTAACAAGCCGAAATC
* * *
127706903 GCAGATCTTATCACCCTAAGCAGTAGGGAAACAGATC-AAAGAAGATGGGCCTTAA-CCTCCTAA
1 ACAGATCTTA-CACCCTAAGCAGTAGGGAAACAGATCGAAAGAA-ACGAGCCTTAACCCTCCTAA
* * * *
127706966 GCAGTAGGGTAATAGGCTGAAAATC
64 GCAGTAAGGTAACAAGCCG-AAATC
127706991 ACAGATCT
1 ACAGATCT
127706999 CACCTCCCTG
Statistics
Matches: 79, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
87 36 0.46
88 43 0.54
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (87 bp):
ACAGATCTTACACCCTAAGCAGTAGGGAAACAGATCGAAAGAAACGAGCCTTAACCCTCCTAAGC
AGTAAGGTAACAAGCCGAAATC
Found at i:127708018 original size:22 final size:21
Alignment explanation
Indices: 127707987--127708029 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
127707977 ATTTATACAT
*
127707987 ATAAATAAAAAAACATAAAAAA
1 ATAAAGAAAAAAACA-AAAAAA
*
127708009 ATAAAGAAAAAAAGAAAAAAA
1 ATAAAGAAAAAAACAAAAAAA
127708030 TTACCCCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.84, C:0.02, G:0.05, T:0.09
Consensus pattern (21 bp):
ATAAAGAAAAAAACAAAAAAA
Found at i:127708943 original size:2 final size:2
Alignment explanation
Indices: 127708901--127708932 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
127708891 TTTTAATACC
127708901 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
127708933 CTTTTATATA
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:127709180 original size:3 final size:3
Alignment explanation
Indices: 127709172--127709205 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
127709162 ATCTATATAG
127709172 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
127709206 CCTAATATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:127709541 original size:22 final size:20
Alignment explanation
Indices: 127709481--127709550 Score: 54
Period size: 22 Copynumber: 3.5 Consensus size: 20
127709471 TTGCTTTCAT
*
127709481 CATTATTATTAT-TACTA-A
1 CATTTTTATTATATACTATA
* *
127709499 CATGTATATATATATACTATA
1 CATTTTTAT-TATATACTATA
*
127709520 TATTTTTATTATATCACGTATA
1 CATTTTTATTATAT-AC-TATA
*
127709542 CGTTTTTAT
1 CATTTTTAT
127709551 ATGTACGCTA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
18 6 0.15
19 3 0.08
20 10 0.26
21 9 0.23
22 11 0.28
ACGTcount: A:0.34, C:0.10, G:0.04, T:0.51
Consensus pattern (20 bp):
CATTTTTATTATATACTATA
Found at i:127711056 original size:14 final size:14
Alignment explanation
Indices: 127711045--127711079 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 14
127711035 TTTAAAATTA
127711045 ATAAATATAAATAT
1 ATAAATATAAATAT
127711059 ATAAATATATAAATAT
1 AT-AA-ATATAAATAT
127711075 ATAAA
1 ATAAA
127711080 ACCCAACAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 3 0.16
15 4 0.21
16 12 0.63
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAAATATAAATAT
Found at i:127711060 original size:8 final size:8
Alignment explanation
Indices: 127711049--127711079 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
127711039 AAATTAATAA
127711049 ATATAAAT
1 ATATAAAT
127711057 ATATAAAT
1 ATATAAAT
127711065 ATATAAAT
1 ATATAAAT
127711073 ATATAAA
1 ATATAAA
127711080 ACCCAACAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
ATATAAAT
Found at i:127715663 original size:3 final size:3
Alignment explanation
Indices: 127715655--127715689 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
127715645 TTTTAAGCAC
127715655 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
127715690 TTCGACCCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:127720844 original size:15 final size:14
Alignment explanation
Indices: 127720817--127720847 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
127720807 TTTGATCAAG
127720817 TAAAATTAAATTAA
1 TAAAATTAAATTAA
127720831 TAAAATTAAAATTAA
1 TAAAATT-AAATTAA
127720846 TA
1 TA
127720848 TGATATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TAAAATTAAATTAA
Found at i:127721298 original size:37 final size:36
Alignment explanation
Indices: 127721235--127721341 Score: 94
Period size: 37 Copynumber: 2.9 Consensus size: 36
127721225 ATTCTAAAAA
*
127721235 TAATATTATTTTAATAGTTTAATATTAAATTAAATT
1 TAATATTATCTTAATAGTTTAATATTAAATTAAATT
* *
127721271 TAATACTTATCTTAATAGTATT-TTATTAATTTAATATT
1 TAATA-TTATCTTAATAGT-TTAATATTAAATTAA-ATT
* * *
127721309 AAATTGATTATCTTAAT-GTTAAAT-TTAATTTAA
1 TAA-T-ATTATCTTAATAGTTTAATATTAAATTAA
127721342 TGTTACATTC
Statistics
Matches: 59, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
36 5 0.08
37 32 0.54
38 10 0.17
39 11 0.19
40 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (36 bp):
TAATATTATCTTAATAGTTTAATATTAAATTAAATT
Found at i:127721310 original size:11 final size:11
Alignment explanation
Indices: 127721235--127721423 Score: 58
Period size: 11 Copynumber: 16.8 Consensus size: 11
127721225 ATTCTAAAAA
*
127721235 TAATATTATTT
1 TAATATTAATT
127721246 TAATAGTTTAATAT
1 TAATA--TTAAT-T
127721260 TAA-ATTAAATT
1 TAATATT-AATT
127721271 TAATACTT-ATCT
1 TAATA-TTAAT-T
*
127721283 TAATAGT-ATT
1 TAATATTAATT
127721293 T--TATTAATT
1 TAATATTAATT
127721302 TAATATTAAATT
1 TAATATT-AATT
* *
127721314 GATTATCTTAATGT
1 --TAATATTAAT-T
127721328 TAA-ATTTAATT
1 TAATA-TTAATT
*
127721339 TAATGTTACA-T
1 TAATATTA-ATT
* *
127721350 T-CTATTATTT
1 TAATATTAATT
*
127721360 TAATA-AAATT
1 TAATATTAATT
127721370 TAATATTAAATT
1 TAATATT-AATT
*
127721382 TAAT-CTAATAT
1 TAATATTAAT-T
* * *
127721393 CAAGATAAATAT
1 TAATATTAAT-T
127721405 T-ATATTAATT
1 TAATATTAATT
127721415 TAATATTAA
1 TAATATTAA
127721424 AGTAATTAAG
Statistics
Matches: 131, Mismatches: 23, Indels: 48
0.65 0.11 0.24
Matches are distributed among these distances:
8 3 0.02
9 4 0.03
10 21 0.16
11 48 0.37
12 35 0.27
13 10 0.08
14 10 0.08
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.50
Consensus pattern (11 bp):
TAATATTAATT
Found at i:127723830 original size:53 final size:53
Alignment explanation
Indices: 127723750--127723883 Score: 198
Period size: 53 Copynumber: 2.5 Consensus size: 53
127723740 TCATACTGAA
* * *
127723750 GCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTATCCCATTATACCGAT
1 GCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTATCACATTACACCGAT
* *
127723803 GCCATAGCCCAGCTATGGTCTTATACGGAATCACCTTATCACATTGCACCGAT
1 GCCATAGCCCAGCTATGGTCTTATACGGAATCACATTATCACATTACACCGAT
*
127723856 GCCATAGCCCAGCTATGGTCTTAAACGG
1 GCCATAGCCCAGCTATGGTCTTATACGG
127723884 GCGCACTTAT
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
52 1 0.01
53 73 0.99
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (53 bp):
GCCATAGCCCAGCTATGGTCTTATACGGAATCACATTATCACATTACACCGAT
Found at i:127726622 original size:39 final size:39
Alignment explanation
Indices: 127726564--127726685 Score: 165
Period size: 39 Copynumber: 3.1 Consensus size: 39
127726554 TTTTGAGTAT
* * * *
127726564 TGTGATATAT-TCTTGAATGTTATGTGATTAAATATGTAT
1 TGTGATATATGT-TTAAATGTTATGTGATTATATGTGTAC
*
127726603 TGTGATATATGTTTAAATGTTATGTGATTGTATGTGTAC
1 TGTGATATATGTTTAAATGTTATGTGATTATATGTGTAC
* *
127726642 TGTGATATATGCTTAAATGTTACGTGATTATATGTGTAC
1 TGTGATATATGTTTAAATGTTATGTGATTATATGTGTAC
127726681 TGTGA
1 TGTGA
127726686 CAGCCCTAAT
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
39 73 0.99
40 1 0.01
ACGTcount: A:0.28, C:0.04, G:0.21, T:0.47
Consensus pattern (39 bp):
TGTGATATATGTTTAAATGTTATGTGATTATATGTGTAC
Found at i:127729529 original size:43 final size:43
Alignment explanation
Indices: 127729296--127729516 Score: 388
Period size: 43 Copynumber: 5.1 Consensus size: 43
127729286 GTTAAATCCC
* *
127729296 GCAGGCTTCGTGTCGGTGATGTATATTCGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
127729339 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
** *
127729382 GCAGGCTTCGTGTTGGTGATGTATATTCGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
*
127729425 GCAGGCTTCGTGCCAGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
127729468 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
127729511 GCAGGC
1 GCAGGC
127729517 GTAATGCCGG
Statistics
Matches: 168, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 168 1.00
ACGTcount: A:0.11, C:0.24, G:0.34, T:0.31
Consensus pattern (43 bp):
GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
Found at i:127733482 original size:28 final size:27
Alignment explanation
Indices: 127733418--127733482 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
127733408 ACACAAATTG
* * *
127733418 AAAATATAATAAAAAGTGATTATATTA
1 AAAATAAAATAAAAAGTAAATATATTA
* *
127733445 AAATTGAAAATAAAATGTAAATATGATTA
1 AAAAT-AAAATAAAAAGTAAATAT-ATTA
127733474 AAAATAAAA
1 AAAATAAAA
127733483 ATATATATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
27 4 0.13
28 18 0.60
29 8 0.27
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (27 bp):
AAAATAAAATAAAAAGTAAATATATTA
Found at i:127735064 original size:3 final size:3
Alignment explanation
Indices: 127735058--127735319 Score: 182
Period size: 3 Copynumber: 87.3 Consensus size: 3
127735048 AAAATACAAC
* * *
127735058 AAT AAT AAT AGT AA- AAG ATAT AAT AACCT AAT AAT -AT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AA--T AAT AAT AAT AAT AAT AAT
* * * * * * *
127735104 AGT AAC AAT -AT GAC GAT AAT AGT AA- AAT AAT -AT ATT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
*
127735147 AGT 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
* *
127735195 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -CT ATT AAGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T
* * * * * *
127735240 TAT AAT GAA- AAT AAT GAT AAT GAT GAT -AT ATT AGAT AAT AAT AGT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT
* * *
127735285 AA- AAT AAT AAGT AAC AAT GAT AAAT TAT AAT AAT A
1 AAT AAT AAT AA-T AAT AAT AAT -AAT AAT AAT AAT A
127735320 GTGATGAGAA
Statistics
Matches: 205, Mismatches: 36, Indels: 36
0.74 0.13 0.13
Matches are distributed among these distances:
2 17 0.08
3 170 0.83
4 15 0.07
5 3 0.01
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:127735064 original size:22 final size:22
Alignment explanation
Indices: 127735013--127735073 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
127735003 ATAAGTAAAT
* *
127735013 ACAAAAATAA-AGGAAAATATA
1 ACAAAAATAATAGAAAAATACA
* *
127735034 ATAACAATAATAGAAAAATACA
1 ACAAAAATAATAGAAAAATACA
* *
127735056 ACAATAATAATAGTAAAA
1 ACAAAAATAATAGAAAAA
127735074 GATATAATAA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 8 0.25
22 24 0.75
ACGTcount: A:0.69, C:0.07, G:0.07, T:0.18
Consensus pattern (22 bp):
ACAAAAATAATAGAAAAATACA
Found at i:127735340 original size:16 final size:16
Alignment explanation
Indices: 127735319--127735350 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
127735309 TTATAATAAT
127735319 AGTGATGAGAATAACA
1 AGTGATGAGAATAACA
*
127735335 AGTGATGATAATAACA
1 AGTGATGAGAATAACA
127735351 GTAACAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.22
Consensus pattern (16 bp):
AGTGATGAGAATAACA
Found at i:127735483 original size:16 final size:15
Alignment explanation
Indices: 127735454--127735496 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
127735444 TATACGTATG
*
127735454 AAAAATAATGATAGT
1 AAAAATAATAATAGT
127735469 AAAATATAATAATAGT
1 AAAA-ATAATAATAGT
*
127735485 AATAATAATAAT
1 AAAAATAATAAT
127735497 GGAATGAAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (15 bp):
AAAAATAATAATAGT
Found at i:127735605 original size:3 final size:3
Alignment explanation
Indices: 127735599--127735631 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
127735589 CCATATTATT
127735599 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
127735632 TAGAAATACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:127735741 original size:3 final size:3
Alignment explanation
Indices: 127735727--127735762 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
127735717 AAATATACAC
127735727 TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
127735763 TTAAAATGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:127736256 original size:31 final size:30
Alignment explanation
Indices: 127736218--127736296 Score: 117
Period size: 28 Copynumber: 2.7 Consensus size: 30
127736208 GATTTTTTGT
127736218 TCTTGAATCTCAAAAAAAAAGAAAAATCCCC
1 TCTTGAATCTCAAAAAAAAA-AAAAATCCCC
* *
127736249 TCTTGAATCTC--AAAAAAAAAAAATCTCT
1 TCTTGAATCTCAAAAAAAAAAAAAATCCCC
127736277 TCTTGAATCTCAAAAAAAAA
1 TCTTGAATCTCAAAAAAAAA
127736297 TCTCTTCTCT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
28 19 0.43
29 7 0.16
30 7 0.16
31 11 0.25
ACGTcount: A:0.52, C:0.19, G:0.05, T:0.24
Consensus pattern (30 bp):
TCTTGAATCTCAAAAAAAAAAAAAATCCCC
Found at i:127736297 original size:25 final size:26
Alignment explanation
Indices: 127736233--127736304 Score: 92
Period size: 28 Copynumber: 2.7 Consensus size: 26
127736223 AATCTCAAAA
* *
127736233 AAAAAGAAAAATCCCCTCTTGAATCTC
1 AAAAA-AAAAATCTCTTCTTGAATCTC
127736260 AAAAAAAAAAAATCTCTTCTTGAATCTC
1 --AAAAAAAAAATCTCTTCTTGAATCTC
127736288 -AAAAAAAAATCTCTTCT
1 AAAAAAAAAATCTCTTCT
127736305 CTCCAAAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
25 17 0.41
28 19 0.46
29 5 0.12
ACGTcount: A:0.49, C:0.21, G:0.04, T:0.26
Consensus pattern (26 bp):
AAAAAAAAAATCTCTTCTTGAATCTC
Found at i:127736974 original size:44 final size:43
Alignment explanation
Indices: 127736769--127737012 Score: 181
Period size: 44 Copynumber: 5.6 Consensus size: 43
127736759 TGAGTTCTTG
* * *
127736769 ATCTGCT-TCTTCGATCTGCTCCCCATAAACACAGGGATGCCAA
1 ATCTGCTATCTTC-ATCTGTTCCCTATAAGCACAGGGATGCCAA
* * * * *
127736812 ATCCGCTGTCTTCAACTTGTTCCTTATAAACACAGGGATGCCAA
1 ATCTGCTATCTTCATC-TGTTCCCTATAAGCACAGGGATGCCAA
* * *
127736856 ATCTGCTATATTCAACTTGTTCCCTATAAGCACAGGGATTCC--
1 ATCTGCTATCTTCATC-TGTTCCCTATAAGCACAGGGATGCCAA
*** * * * *
127736898 ATGCTAAAATCTTCTATCTGCTTCACC-GTAAGCACAGGAATGTCAG
1 AT-CTGCTATCTTC-ATCTG-TTC-CCTATAAGCACAGGGATGCCAA
*
127736944 TTCTGCTATCTTCGATCTGTTCCCTATAAGCACAGGGATGCCAA
1 ATCTGCTATCTTC-ATCTGTTCCCTATAAGCACAGGGATGCCAA
* * *
127736988 ATCTGCTGTTTTCAACTTGTTCCCT
1 ATCTGCTATCTTCATC-TGTTCCCT
127737013 GACAATACGG
Statistics
Matches: 158, Mismatches: 33, Indels: 19
0.75 0.16 0.09
Matches are distributed among these distances:
42 2 0.01
43 21 0.13
44 119 0.75
45 15 0.09
46 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.32
Consensus pattern (43 bp):
ATCTGCTATCTTCATCTGTTCCCTATAAGCACAGGGATGCCAA
Found at i:127737521 original size:206 final size:204
Alignment explanation
Indices: 127737152--127737865 Score: 1045
Period size: 206 Copynumber: 3.5 Consensus size: 204
127737142 GGGAACATCC
* * * *
127737152 GAAAGTCAAATCTGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGG
1 GAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTTGG
*
127737217 ATCTTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCATTGAAGTGGA
66 ATC-TGCTTCAGTATAAACATCTGAAGGTCAGATCTGCTATGTATCTGCTCTCCATTGAAGTGGA
* *
127737282 GATGCCAGACTTCGATTTGCTCTCTGACAATACAGAGACCACAAATCATCTTAGATTTGCTTCAT
130 GATGCCAGACTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCAT
127737347 CATAATCACGT
195 C-TAATCACGT
* * * * *
127737358 GAAAGCCAAATCAGTTATGTCTTTGATTTGTTCCTTATAAGCACAAGGATGCCAAATCATCTTGG
1 GAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTTGG
127737423 ATCTTGCTTCAGTATAAACATCTGAAGGTCAGATCTGCTATGTATCTGCTCTCCATTGAAGTGGA
66 ATC-TGCTTCAGTATAAACATCTGAAGGTCAGATCTGCTATGTATCTGCTCTCCATTGAAGTGGA
*
127737488 GATG-CAGGACTTTGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTG---C-
130 GATGCCA-GACTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCA
127737548 T-T--TCACGT
194 TCTAATCACGT
127737556 GAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTTGG
1 GAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTTGG
* * * ** *
127737621 ATCTGCTTCAGTGA-AATCATCTGAAGG-CGAGATCTGCTATGTGTCTGCTCTCTATCAAAGTGA
66 ATCTGCTTCAGT-ATAAACATCTGAAGGTC-AGATCTGCTATGTATCTGCTCTCCATTGAAGTGG
* *
127737684 AGATGCCAAACTTCGATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCA
129 AGATGCCAGACTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCA
127737749 TCGTAATCACGT
194 TC-TAATCACGT
* * *
127737761 GAAAGCCAAATCAGCTATATCTTTGATTTGCTCCTTGTAAACACAAGGATGCCAAACCATCTTGG
1 GAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTTGG
* * *
127737826 ATCTGCTTCAGTAT-AACATCTGTAGGCCAGATCTGTTATG
66 ATCTGCTTCAGTATAAACATCTGAAGGTCAGATCTGCTATG
127737866 CTGCGGCCTA
Statistics
Matches: 465, Mismatches: 29, Indels: 30
0.89 0.06 0.06
Matches are distributed among these distances:
196 1 0.00
197 104 0.22
198 72 0.15
200 2 0.00
201 1 0.00
202 1 0.00
203 2 0.00
204 22 0.05
205 83 0.18
206 177 0.38
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (204 bp):
GAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAACCATCTTGG
ATCTGCTTCAGTATAAACATCTGAAGGTCAGATCTGCTATGTATCTGCTCTCCATTGAAGTGGAG
ATGCCAGACTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATC
TAATCACGT
Found at i:127745683 original size:13 final size:15
Alignment explanation
Indices: 127745653--127745683 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
127745643 TTCCAGATTT
127745653 TCTTTTCTACCTCTC
1 TCTTTTCTACCTCTC
127745668 TCTTTTCTACCTCTC
1 TCTTTTCTACCTCTC
127745683 T
1 T
127745684 GGAAAGTAAA
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:0.06, C:0.39, G:0.00, T:0.55
Consensus pattern (15 bp):
TCTTTTCTACCTCTC
Found at i:127745769 original size:15 final size:14
Alignment explanation
Indices: 127745727--127745776 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
127745717 ATAATTTTGA
*
127745727 ATGCAAATGATGTG
1 ATGCAAATGATGAG
127745741 ATG-AAATGTTATGAG
1 ATGCAAATG--ATGAG
127745756 ATGCAAATGCATGA-
1 ATGCAAATG-ATGAG
127745770 ATGCAAA
1 ATGCAAA
127745777 AAGAATATCG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 5 0.16
14 10 0.32
15 11 0.35
16 5 0.16
ACGTcount: A:0.42, C:0.08, G:0.24, T:0.26
Consensus pattern (14 bp):
ATGCAAATGATGAG
Found at i:127749545 original size:17 final size:17
Alignment explanation
Indices: 127749515--127749547 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
127749505 AAAAGTAATG
127749515 ATATGTAAATAAAATAA
1 ATATGTAAATAAAATAA
127749532 ATATGCTAAA-AAAATA
1 ATATG-TAAATAAAATA
127749548 TACAGTTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.27
Consensus pattern (17 bp):
ATATGTAAATAAAATAA
Done.