Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 99 of 196
Found at i:29402917 original size:14 final size:14
Alignment explanation
Indices: 29402898--29402930 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
29402888 AGTTAACTAA
29402898 CACACCAGTAATGG
1 CACACCAGTAATGG
29402912 CACACCAGTAATGG
1 CACACCAGTAATGG
29402926 CACAC
1 CACAC
29402931 AAGTGTCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.36, C:0.33, G:0.18, T:0.12
Consensus pattern (14 bp):
CACACCAGTAATGG
Found at i:29413161 original size:19 final size:18
Alignment explanation
Indices: 29413139--29413216 Score: 84
Period size: 20 Copynumber: 4.1 Consensus size: 18
29413129 AGTTATTAAG
29413139 AATTAGTAAAAATTATAAA
1 AATT-GTAAAAATTATAAA
29413158 AATTGTAAAAAAATTATAAA
1 AATTGT--AAAAATTATAAA
* **
29413178 AAATGTAACATTTTATAAAA
1 AATTGTAA-AAATTAT-AAA
29413198 AATTGTAAAAATTATAAA
1 AATTGTAAAAATTATAAA
29413216 A
1 A
29413217 TATATAGAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
18 8 0.16
19 14 0.29
20 27 0.55
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (18 bp):
AATTGTAAAAATTATAAA
Found at i:29413166 original size:9 final size:9
Alignment explanation
Indices: 29413139--29413327 Score: 71
Period size: 9 Copynumber: 19.7 Consensus size: 9
29413129 AGTTATTAAG
29413139 AATTAGTAAA
1 AATTA-TAAA
29413149 AATTATAAA
1 AATTATAAA
*
29413158 AATTGTAAAAA
1 AA-T-TATAAA
29413169 AATTATAAA
1 AATTATAAA
* *
29413178 AAATGTAACA
1 AATTATAA-A
**
29413188 TTTTATAAAA
1 AATTAT-AAA
*
29413198 AATTGTAAA
1 AATTATAAA
29413207 AATTAT-AA
1 AATTATAAA
*
29413215 AATATATAGA
1 AAT-TATAAA
*
29413225 AATATAGAAAA
1 AAT-TA-TAAA
29413236 AATTAT-AA
1 AATTATAAA
* *
29413244 ATTTTTATAA
1 AATTATA-AA
*
29413254 AGTTATAAGAA
1 AATTAT-A-AA
29413265 AATTGCA-AGAA
1 AATT--ATA-AA
*
29413276 AATTGTAAA
1 AATTATAAA
*
29413285 AATTTTAAA
1 AATTATAAA
29413294 AA-TATAAA
1 AATTATAAA
* *
29413302 ATTTGTAAAAA
1 A-AT-TATAAA
29413313 AATTATAAA
1 AATTATAAA
29413322 AATTAT
1 AATTAT
29413328 CATGTCTCTC
Statistics
Matches: 134, Mismatches: 29, Indels: 33
0.68 0.15 0.17
Matches are distributed among these distances:
8 17 0.13
9 51 0.38
10 31 0.23
11 34 0.25
13 1 0.01
ACGTcount: A:0.59, C:0.01, G:0.06, T:0.33
Consensus pattern (9 bp):
AATTATAAA
Found at i:29413169 original size:20 final size:20
Alignment explanation
Indices: 29413146--29413325 Score: 79
Period size: 20 Copynumber: 8.8 Consensus size: 20
29413136 AAGAATTAGT
29413146 AAAAATTATAAAAATTGTAA
1 AAAAATTATAAAAATTGTAA
*
29413166 AAAAATTATAAAAAATGT-A
1 AAAAATTATAAAAATTGTAA
* **
29413185 ACATTTTATAAAAAATTGT--
1 AAAAATTAT-AAAAATTGTAA
29413204 AAAAATTATAAAATATATAGAAATATAGA
1 AAAAATTATAAAA-AT-T-G-----TA-A
* *
29413233 AAAAATTAT--AAATTTTTA
1 AAAAATTATAAAAATTGTAA
* * *
29413251 TAAAGTTATAAGAAAATTGCAA
1 AAAAATTAT-A-AAAATTGTAA
* * *
29413273 GAAAATTGTAAAAATT-T-T
1 AAAAATTATAAAAATTGTAA
*
29413291 AAAAA-TATAAAATTTGTAA
1 AAAAATTATAAAAATTGTAA
29413310 AAAAATTATAAAAATT
1 AAAAATTATAAAAATT
29413326 ATCATGTCTC
Statistics
Matches: 116, Mismatches: 25, Indels: 38
0.65 0.14 0.21
Matches are distributed among these distances:
17 8 0.07
18 17 0.15
19 21 0.18
20 41 0.35
21 2 0.02
22 12 0.10
25 1 0.01
26 3 0.03
27 2 0.02
29 9 0.08
ACGTcount: A:0.60, C:0.01, G:0.06, T:0.33
Consensus pattern (20 bp):
AAAAATTATAAAAATTGTAA
Found at i:29414911 original size:19 final size:16
Alignment explanation
Indices: 29414886--29414928 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 16
29414876 TAACATATAA
29414886 AATTTATAATTATTTTAT
1 AATTTATAA-T-TTTTAT
29414904 ATATTTATAATTTTTAT
1 A-ATTTATAATTTTTAT
29414921 AATTTATA
1 AATTTATA
29414929 TTTCATAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.29
17 7 0.29
18 2 0.08
19 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
AATTTATAATTTTTAT
Found at i:29415609 original size:19 final size:20
Alignment explanation
Indices: 29415571--29415611 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
29415561 TAGAAAAATC
29415571 TTATTATGTATAAATTATAA
1 TTATTATGTATAAATTATAA
29415591 TTATTA-GT-TAAATTTATAA
1 TTATTATGTATAAA-TTATAA
29415610 TT
1 TT
29415612 TCCAGATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 10 0.50
20 6 0.30
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (20 bp):
TTATTATGTATAAATTATAA
Found at i:29415701 original size:22 final size:23
Alignment explanation
Indices: 29415676--29415720 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
29415666 TCAAGTGTAA
29415676 TTTGAACAA-AAA-AAAATTATTT
1 TTTGAA-AATAAATAAAATTATTT
*
29415698 TTTGAAAATAAATAAATTTATTT
1 TTTGAAAATAAATAAAATTATTT
29415721 CCAGTTAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 2 0.10
22 9 0.45
23 9 0.45
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.42
Consensus pattern (23 bp):
TTTGAAAATAAATAAAATTATTT
Found at i:29416057 original size:17 final size:17
Alignment explanation
Indices: 29416035--29416068 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
29416025 ACAAATATCT
29416035 ATTTTTGTA-ATTAATTA
1 ATTTTT-TATATTAATTA
29416052 ATTTTTTATATTAATTA
1 ATTTTTTATATTAATTA
29416069 TGTAAAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 14 0.88
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
ATTTTTTATATTAATTA
Found at i:29418193 original size:26 final size:26
Alignment explanation
Indices: 29418164--29418215 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
29418154 GCTTCAAGAT
*
29418164 CCAAAATGTATAACTTGTGTCAAATA
1 CCAAAATGCATAACTTGTGTCAAATA
*
29418190 CCAAAATGCATAACTTTTGTCAAATA
1 CCAAAATGCATAACTTGTGTCAAATA
29418216 TAGGTACCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.31
Consensus pattern (26 bp):
CCAAAATGCATAACTTGTGTCAAATA
Found at i:29421388 original size:17 final size:17
Alignment explanation
Indices: 29421368--29421402 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
29421358 ATTAGTTTTA
29421368 AAAAAATAAATATACAT
1 AAAAAATAAATATACAT
29421385 AAAAAATAAATATACAT
1 AAAAAATAAATATACAT
29421402 A
1 A
29421403 TATATTACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAAAATAAATATACAT
Found at i:29421446 original size:3 final size:3
Alignment explanation
Indices: 29421438--29421485 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
29421428 GCATATGAAT
* *
29421438 ATA ATA ATA ATA GTA ATA ATA ATA ATA ATAA ATA ATA ATG ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA
29421484 AT
1 AT
29421486 TTATTTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:29422847 original size:39 final size:39
Alignment explanation
Indices: 29422793--29422871 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
29422783 GCCAGGGAGA
29422793 TAGGATTTGTATGTTGTAGTTTCTTAAGAGAACAAAATT
1 TAGGATTTGTATGTTGTAGTTTCTTAAGAGAACAAAATT
29422832 TAGGATTTGTATGTTGTAGTTTCTTAAGAGAACAAAATT
1 TAGGATTTGTATGTTGTAGTTTCTTAAGAGAACAAAATT
29422871 T
1 T
29422872 TCTATTTGCT
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:0.33, C:0.05, G:0.20, T:0.42
Consensus pattern (39 bp):
TAGGATTTGTATGTTGTAGTTTCTTAAGAGAACAAAATT
Found at i:29423145 original size:44 final size:44
Alignment explanation
Indices: 29423094--29423205 Score: 136
Period size: 44 Copynumber: 2.5 Consensus size: 44
29423084 GTTCTGCTCT
* * *
29423094 CTGCAACTTCAGAGAGATAAGATTCA-AGGTTTTAATCCACTTCA
1 CTGCAACTTCAGGGAGATAAGATT-ATAGGCTTTAATCCACTCCA
* * **
29423138 CTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCA
1 CTGCAACTTCAGGGAGATAAGATTATAGGCTTTAATCCACTCCA
*
29423182 TTGCAACTTCAGGGAGATAAGATT
1 CTGCAACTTCAGGGAGATAAGATT
29423206 TTCCATATTC
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
43 1 0.02
44 57 0.98
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (44 bp):
CTGCAACTTCAGGGAGATAAGATTATAGGCTTTAATCCACTCCA
Found at i:29423589 original size:44 final size:43
Alignment explanation
Indices: 29423508--29424095 Score: 510
Period size: 44 Copynumber: 13.7 Consensus size: 43
29423498 ACTATTTTCC
* * * *
29423508 ACCTACTCCATTGCT-ACTCAGGG-GATAGGGTTCACAATCTTCA
1 ACCTATTCCACTGCTGAC-CAGGGAGATA-GGATCTCAATCTTCA
*
29423551 ACCTATTCCACTGCTGACCAGGGAGATAGGACCTACAATCTTCA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATCT-CAATCTTCA
* *
29423595 ATCTATTCCACTGCT-ACCCAGGGAGATAGAATTCTCAATCTTCA
1 ACCTATTCCACTGCTGA-CCAGGGAGATAGGA-TCTCAATCTTCA
* * *
29423639 ACCTATTCCACTGCTGACTAGGGAGATAGGATTCACAATCTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGA-TCTCAATCTTCA
* * *
29423683 ACCTATTCTACTACTGTCCAGGGAGATAGGAT-TC--T-TT-A
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATCTCAATCTTCA
* * *
29423721 ATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTTCA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGA-TCTCAATCTTCA
* * * *
29423765 GCCTATTCCACTGCTGACTAGGGAGATAGGATTCACAATCTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGA-TCTCAATCTTCA
* * *
29423809 ACCTATTCCACTACT-ATTCAGGGAGATA-GAGCTC--T-TT-A
1 ACCTATTCCACTGCTGA-CCAGGGAGATAGGATCTCAATCTTCA
* * *
29423847 ATCTATTCCACTGCTG-CCTAGGGAGATAGAATTCTCAATCTTTA
1 ACCTATTCCACTGCTGACC-AGGGAGATAGGA-TCTCAATCTTCA
* * *
29423891 ATCTATTCCACTGCTGATCAGGGAGATAGGACCTACAATCTTCA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATCT-CAATCTTCA
* * *
29423935 ATCTATTCCACTGCTGCCCAGGGAG--AGAATTCTCAATCTTCA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGA-TCTCAATCTTCA
*
29423977 ACCTATTCCACTGCTGACCAGGGAGATAGGAT-TCAGAATCTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATCTC--AATCTTCA
* ** * * * *
29424021 ACTTATTCCACTATTGTCCAGGGAGATAGGATTCTTTAATATTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGA-TC-TCAATCTTCA
* * *
29424066 GCCTATTCCACTACTGACCAGGAAGATAGG
1 ACCTATTCCACTGCTGACCAGGGAGATAGG
29424096 GCTGGGGTCA
Statistics
Matches: 450, Mismatches: 64, Indels: 60
0.78 0.11 0.10
Matches are distributed among these distances:
37 1 0.00
38 50 0.11
39 6 0.01
40 7 0.02
42 42 0.09
43 35 0.08
44 271 0.60
45 37 0.08
47 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (43 bp):
ACCTATTCCACTGCTGACCAGGGAGATAGGATCTCAATCTTCA
Found at i:29423728 original size:38 final size:38
Alignment explanation
Indices: 29423677--29423881 Score: 140
Period size: 38 Copynumber: 5.1 Consensus size: 38
29423667 GGATTCACAA
* * *
29423677 TCTTTAACCTATTCTACTACTGTCCAGGGAGATAGGAT
1 TCTTTAACCTATTCCACTACTGCCCAGGGAGATAGAAT
* *
29423715 TCTTTAATCTATTCCACTGCTGCCCAGGGAGATAGAATT
1 TCTTTAACCTATTCCACTACTGCCCAGGGAGATAGAA-T
* * * * *
29423754 CTCAATCTTCAGCCTATTCCACTGCTGACTAGGGAGATAGGATTCACAA
1 -TC--T-TT-AACCTATTCCACTACTGCCCAGGGAGATA-G----A-AT
*** **
29423803 TCTTTAACCTATTCCACTACTATTCAGGGAGATAGAGC
1 TCTTTAACCTATTCCACTACTGCCCAGGGAGATAGAAT
* * *
29423841 TCTTTAATCTATTCCACTGCTGCCTAGGGAGATAGAAT
1 TCTTTAACCTATTCCACTACTGCCCAGGGAGATAGAAT
29423879 TCT
1 TCT
29423882 CAATCTTTAA
Statistics
Matches: 129, Mismatches: 26, Indels: 24
0.72 0.15 0.13
Matches are distributed among these distances:
38 65 0.50
39 2 0.02
40 2 0.02
42 1 0.01
43 3 0.02
44 48 0.37
45 3 0.02
46 1 0.01
48 2 0.02
49 1 0.01
50 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (38 bp):
TCTTTAACCTATTCCACTACTGCCCAGGGAGATAGAAT
Found at i:29423762 original size:126 final size:128
Alignment explanation
Indices: 29423508--29424095 Score: 638
Period size: 126 Copynumber: 4.6 Consensus size: 128
29423498 ACTATTTTCC
* * * * *
29423508 ACCTACTCCATTGCT-ACTCAGGG-GATAGGGTTCACAATCTTCAACCTATTCCACTGCTGACCA
1 ACCTATTCCACTGCTGACT-AGGGAGATAGGATTCACAATCTTTAACCTATTCCACTACTGACCA
* *
29423571 GGGAGATAGGACCTACAATCTTCAATCTATTCCACTGCTACCCAGGGAGATAGAATTCTCAATCT
65 GGGAGATAGGA-CT---ATCTTTAATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATCT
29423636 TCA
126 TCA
* *
29423639 ACCTATTCCACTGCTGACTAGGGAGATAGGATTCACAATCTTTAACCTATTCTACTACTGTCCAG
1 ACCTATTCCACTGCTGACTAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTACTGACCAG
29423704 GGAGATAGGA-T-TCTTTAATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTTCA
66 GGAGATAGGACTATCTTTAATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTTCA
* *
29423765 GCCTATTCCACTGCTGACTAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTACT-ATTCA
1 ACCTATTCCACTGCTGACTAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTACTGA-CCA
* *
29423829 GGGAGATA-GAGC--TCTTTAATCTATTCCACTGCTGCCTAGGGAGATAGAATTCTCAATCTTTA
65 GGGAGATAGGA-CTATCTTTAATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTTCA
* * * * * *
29423891 ATCTATTCCACTGCTGA-TCAGGGAGATAGGA-CCTACAATCTTCAATCTATTCCACTGCTGCCC
1 ACCTATTCCACTGCTGACT-AGGGAGATAGGATTC-ACAATCTTTAACCTATTCCACTACTGACC
* *** * * * * **
29423954 AGGGAGAGAATTCTCAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCAGAATCTT
64 AGGGAGATAGGACT--ATCTTTAATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTT
*
29424019 TA
127 CA
* ** * * ** * *
29424021 ACTTATTCCACTATTGTCCAGGGAGATAGGATTCTTTAATATTTAGCCTATTCCACTACTGACCA
1 ACCTATTCCACTGCTGACTAGGGAGATAGGATTC-ACAATCTTTAACCTATTCCACTACTGACCA
*
29424086 GGAAGATAGG
65 GGGAGATAGG
29424096 GCTGGGGTCA
Statistics
Matches: 390, Mismatches: 52, Indels: 30
0.83 0.11 0.06
Matches are distributed among these distances:
125 4 0.01
126 222 0.57
130 68 0.17
131 47 0.12
132 49 0.13
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (128 bp):
ACCTATTCCACTGCTGACTAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTACTGACCAG
GGAGATAGGACTATCTTTAATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTTCA
Found at i:29423835 original size:170 final size:170
Alignment explanation
Indices: 29423553--29424060 Score: 637
Period size: 170 Copynumber: 3.0 Consensus size: 170
29423543 AATCTTCAAC
29423553 CTATTCCACTGCTGACCAGGGAGATAGGACCTACAATCTTCAATCTATTCCACTGCT-ACCCAGG
1 CTATTCCACTGCTGACCAGGGAGATAGGACCTACAATCTTCAATCTATTCCACTGCTGA-CCAGG
29423617 GAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTGA-CTAGGGAGATAGGATTCACAATCTT
65 GAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTGATC-AGGGAGATAGGATTCACAATCTT
*
29423681 TAACCTATTCTACTACTGTCCAGGGAGATAGGATTCTTTAAT
129 TAACCTATTCCACTACTGTCCAGGGAGATAGGATTCTTTAAT
* * * ** *
29423723 CTATTCCACTGCTGCCCAGGGAGATAGAATTCT-CAATCTTCAGCCTATTCCACTGCTGACTAGG
1 CTATTCCACTGCTGACCAGGGAGATAGGA-CCTACAATCTTCAATCTATTCCACTGCTGACCAGG
* * * * *
29423787 GAGATAGGATTCACAATCTTTAACCTATTCCACTACT-ATTCAGGGAGATA-GA---GC--TCTT
65 GAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTGA-TCAGGGAGATAGGATTCACAATCTT
* * *
29423845 TAATCTATTCCACTGCTG-CCTAGGGAGATAGAATTCTCAATCTTTAAT
129 TAACCTATTCCACTACTGTCC-AGGGAGATAGGA---T---TCTTTAAT
* *
29423893 CTATTCCACTGCTGATCAGGGAGATAGGACCTACAATCTTCAATCTATTCCACTGCTGCCCAGGG
1 CTATTCCACTGCTGACCAGGGAGATAGGACCTACAATCTTCAATCTATTCCACTGCTGACCAGGG
* *
29423958 AG--AGAATTCTCAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCAGAATCTTTA
66 AGATAGAATTCTCAATCTTCAACCTATTCCACTGCTGATCAGGGAGATAGGATTCACAATCTTTA
* *
29424021 ACTTATTCCACTATTGTCCAGGGAGATAGGATTCTTTAAT
131 ACCTATTCCACTACTGTCCAGGGAGATAGGATTCTTTAAT
29424061 ATTTAGCCTA
Statistics
Matches: 283, Mismatches: 35, Indels: 42
0.79 0.10 0.12
Matches are distributed among these distances:
163 2 0.01
164 30 0.11
166 1 0.00
167 1 0.00
168 46 0.16
169 8 0.03
170 159 0.56
171 5 0.02
174 29 0.10
175 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (170 bp):
CTATTCCACTGCTGACCAGGGAGATAGGACCTACAATCTTCAATCTATTCCACTGCTGACCAGGG
AGATAGAATTCTCAATCTTCAACCTATTCCACTGCTGATCAGGGAGATAGGATTCACAATCTTTA
ACCTATTCCACTACTGTCCAGGGAGATAGGATTCTTTAAT
Found at i:29424251 original size:88 final size:88
Alignment explanation
Indices: 29424095--29424505 Score: 599
Period size: 88 Copynumber: 4.7 Consensus size: 88
29424085 AGGAAGATAG
* * * * * *
29424095 GGCTGGGGTCATCAATCTGCTTCGCTATCGGTGTAGGAAGGCAAGATCTGCTATTTTTAACCTAC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
*
29424160 TCCGCTGCAACCTAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* * *
29424183 GGCTGGTGTCTTTGATCTGCTTCGCTGTCGGTGCA-GAAGGGTAAGATCTGCTATTTTTAGCCTG
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAA-GGCAAGATCTGCTATTTTTAACCTG
* *
29424247 CTCCGCTGCAACCTAGGAAGGCAA
65 CTCCGCTGCAACCCAGGGAGGCAA
* * *
29424271 GGCTGGCGTCTTCGATCTGCTTCGCTGTCCGTGCAGGAAGGCAAGATTTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
*
29424336 TCTGCTGCAACCCAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* *
29424359 GGCTGGTATCTTCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
* *
29424424 TCCGCTACAACCCAGGGAGACAA
66 TCCGCTGCAACCCAGGGAGGCAA
* * *
29424447 GGCTAGTGTCTTTGATCTGCCTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTA
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTA
29424506 CTGATCTGCT
Statistics
Matches: 289, Mismatches: 32, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
87 3 0.01
88 283 0.98
89 3 0.01
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.28
Consensus pattern (88 bp):
GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
TCCGCTGCAACCCAGGGAGGCAA
Found at i:29425881 original size:14 final size:15
Alignment explanation
Indices: 29425858--29425890 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
29425848 ATTGACACTT
*
29425858 TTCTAGATAAGG-CC
1 TTCTACATAAGGTCC
29425872 TTCTACATAAGGTCC
1 TTCTACATAAGGTCC
29425887 TTCT
1 TTCT
29425891 CAGCTTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.36
Consensus pattern (15 bp):
TTCTACATAAGGTCC
Found at i:29430254 original size:17 final size:17
Alignment explanation
Indices: 29430232--29430268 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 17
29430222 ATATTAGTTT
29430232 TAAAAATATAAATATACA
1 TAAAAA-ATAAATATACA
29430250 TAAAAAATAAATATACA
1 TAAAAAATAAATATACA
29430267 TA
1 TA
29430269 TATATATTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAAAAATAAATATACA
Found at i:29436000 original size:54 final size:54
Alignment explanation
Indices: 29435874--29436067 Score: 201
Period size: 54 Copynumber: 3.6 Consensus size: 54
29435864 ATGATCGAAT
* * * * * * * *
29435874 TACCCCCGAAAGGTAAAACTACCGAAACACCCTCGAAAGGTAAAATTATCGAAA
1 TACCCTCGAAGGGTAAAATTACTGAAATACCCTTGAAAGGTAAAATTACCAAAA
* * * * *
29435928 TACCTTTGAAGGGTAAAATTACTAAAATACCCTTGAAAGGTAATATTGCCAAAA
1 TACCCTCGAAGGGTAAAATTACTGAAATACCCTTGAAAGGTAAAATTACCAAAA
** * * *
29435982 TACCCTCGAAGGGTAAAATTTTTGAAATA-CATCTGAAAGATAAAATTACTAAAA
1 TACCCTCGAAGGGTAAAATTACTGAAATACCCT-TGAAAGGTAAAATTACCAAAA
*
29436036 TACCCTCGAAGGGTAAAATTACTGAGATACCC
1 TACCCTCGAAGGGTAAAATTACTGAAATACCC
29436068 CATAAGGGTA
Statistics
Matches: 111, Mismatches: 27, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
53 2 0.02
54 108 0.97
55 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.23
Consensus pattern (54 bp):
TACCCTCGAAGGGTAAAATTACTGAAATACCCTTGAAAGGTAAAATTACCAAAA
Found at i:29436057 original size:27 final size:27
Alignment explanation
Indices: 29435874--29436067 Score: 167
Period size: 27 Copynumber: 7.2 Consensus size: 27
29435864 ATGATCGAAT
* * *
29435874 TACCCCCGAAAGGTAAAACTACCGAAA
1 TACCCTCGAAAGGTAAAATTACTGAAA
*
29435901 CACCCTCGAAAGGTAAAATTA-TCGAAA
1 TACCCTCGAAAGGTAAAATTACT-GAAA
* * * *
29435928 TACCTTTGAAGGGTAAAATTACTAAAA
1 TACCCTCGAAAGGTAAAATTACTGAAA
* * * **
29435955 TACCCTTGAAAGGTAATATTGCCAAAA
1 TACCCTCGAAAGGTAAAATTACTGAAA
* **
29435982 TACCCTCGAAGGGTAAAATTTTTGAAA
1 TACCCTCGAAAGGTAAAATTACTGAAA
* * *
29436009 TA-CATCTGAAAGATAAAATTACTAAAA
1 TACCCTC-GAAAGGTAAAATTACTGAAA
* *
29436036 TACCCTCGAAGGGTAAAATTACTGAGA
1 TACCCTCGAAAGGTAAAATTACTGAAA
29436063 TACCC
1 TACCC
29436068 CATAAGGGTA
Statistics
Matches: 131, Mismatches: 32, Indels: 8
0.77 0.19 0.05
Matches are distributed among these distances:
26 3 0.02
27 124 0.95
28 4 0.03
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.23
Consensus pattern (27 bp):
TACCCTCGAAAGGTAAAATTACTGAAA
Found at i:29436066 original size:81 final size:81
Alignment explanation
Indices: 29435874--29436081 Score: 238
Period size: 81 Copynumber: 2.6 Consensus size: 81
29435864 ATGATCGAAT
* * * * * * *
29435874 TACCCCCGAAAGGTAAAACTACCGAAACACCCTCGAAAGGTAAAATTATCGAAATACCTTTGAAG
1 TACCCTCGAAAGGTAAAATTACCGAAATACCCTCGAAGGGTAAAATTATCGAAATACATCTGAAA
*
29435939 GGTAAAATTACTAAAA
66 GATAAAATTACTAAAA
* * * * * *
29435955 TACCCTTGAAAGGTAATATTGCCAAAATACCCTCGAAGGGTAAAATTTTTGAAATACATCTGAAA
1 TACCCTCGAAAGGTAAAATTACCGAAATACCCTCGAAGGGTAAAATTATCGAAATACATCTGAAA
29436020 GATAAAATTACTAAAA
66 GATAAAATTACTAAAA
* * * *
29436036 TACCCTCGAAGGGTAAAATTACTGAGATACCC-CATAAGGGTAAAAT
1 TACCCTCGAAAGGTAAAATTACCGAAATACCCTC-GAAGGGTAAAAT
29436082 GACTGTTATA
Statistics
Matches: 104, Mismatches: 22, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
80 1 0.01
81 103 0.99
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.23
Consensus pattern (81 bp):
TACCCTCGAAAGGTAAAATTACCGAAATACCCTCGAAGGGTAAAATTATCGAAATACATCTGAAA
GATAAAATTACTAAAA
Found at i:29436074 original size:27 final size:27
Alignment explanation
Indices: 29435857--29436095 Score: 162
Period size: 27 Copynumber: 8.9 Consensus size: 27
29435847 TGGGAATTAT
* * *
29435857 GGGTAAAATGA-TCGAATTACCCCCGAA
1 GGGTAAAATTACT-GAAATACCCTCGAA
* * * *
29435884 AGGTAAAACTACCGAAACACCCTCGAA
1 GGGTAAAATTACTGAAATACCCTCGAA
* * *
29435911 AGGTAAAATTA-TCGAAATACCTTTGAA
1 GGGTAAAATTACT-GAAATACCCTCGAA
* *
29435938 GGGTAAAATTACTAAAATACCCTTGAA
1 GGGTAAAATTACTGAAATACCCTCGAA
* * * **
29435965 AGGTAATATTGCCAAAATACCCTCGAA
1 GGGTAAAATTACTGAAATACCCTCGAA
** *
29435992 GGGTAAAATTTTTGAAATA-CATCTGAA
1 GGGTAAAATTACTGAAATACCCTC-GAA
* * *
29436019 AGATAAAATTACTAAAATACCCTCGAA
1 GGGTAAAATTACTGAAATACCCTCGAA
* *
29436046 GGGTAAAATTACTGAGATACCC-CATAA
1 GGGTAAAATTACTGAAATACCCTC-GAA
* **
29436073 GGGTAAAATGACTGTTATACCCT
1 GGGTAAAATTACTGAAATACCCT
29436096 TAAGAGTGGA
Statistics
Matches: 164, Mismatches: 41, Indels: 13
0.75 0.19 0.06
Matches are distributed among these distances:
26 4 0.02
27 156 0.95
28 4 0.02
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (27 bp):
GGGTAAAATTACTGAAATACCCTCGAA
Found at i:29436317 original size:26 final size:26
Alignment explanation
Indices: 29436264--29436332 Score: 84
Period size: 26 Copynumber: 2.7 Consensus size: 26
29436254 ACATATACTG
* * *
29436264 TTACTGGCAGCCTTGCTGCGTTACTA
1 TTACTGGCAGCTTTGCTGCATCACTA
* *
29436290 TTACTGGCAGCTTTGTTGCATCATTA
1 TTACTGGCAGCTTTGCTGCATCACTA
*
29436316 TTACTGGCAGCTCTGCT
1 TTACTGGCAGCTTTGCT
29436333 ACGATATTGG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.16, C:0.25, G:0.22, T:0.38
Consensus pattern (26 bp):
TTACTGGCAGCTTTGCTGCATCACTA
Found at i:29437008 original size:20 final size:20
Alignment explanation
Indices: 29436983--29437023 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
29436973 CCAAAATTAG
*
29436983 GAAACGAGTTTTATCAGCAA
1 GAAACGAGTTTTATCAACAA
29437003 GAAACGAGTTTTATCAACAA
1 GAAACGAGTTTTATCAACAA
29437023 G
1 G
29437024 TCTAAGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (20 bp):
GAAACGAGTTTTATCAACAA
Found at i:29442706 original size:17 final size:19
Alignment explanation
Indices: 29442674--29442723 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
29442664 GAACACACTC
*
29442674 TCTTCCTTCATCTTTT-ATTT
1 TCTT-CTTC-TCTTTTCAGTT
29442694 TCTTCTT-TCTTTTCAGTT
1 TCTTCTTCTCTTTTCAGTT
29442712 TCTTCTTCTCTT
1 TCTTCTTCTCTT
29442724 GTTGCCAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 6 0.22
18 10 0.37
19 7 0.26
20 4 0.15
ACGTcount: A:0.06, C:0.26, G:0.02, T:0.66
Consensus pattern (19 bp):
TCTTCTTCTCTTTTCAGTT
Found at i:29443666 original size:27 final size:27
Alignment explanation
Indices: 29443597--29443796 Score: 242
Period size: 27 Copynumber: 7.4 Consensus size: 27
29443587 TACGAATCGT
*
29443597 GGGTAAAATGACTGAAATACCCTC-AA
1 GGGTAAAATTACTGAAATACCCTCGAA
* *
29443623 AGGTAAAATTACTGAAATGCCCTCGAA
1 GGGTAAAATTACTGAAATACCCTCGAA
* *
29443650 GGGTAAAATTACCGAAATACCTTCGAA
1 GGGTAAAATTACTGAAATACCCTCGAA
** **
29443677 GGGTAAAATTTTTGAAATACCCTTAAA
1 GGGTAAAATTACTGAAATACCCTCGAA
* *
29443704 AGGTAAAATTACTGAAATACCCTCAAA
1 GGGTAAAATTACTGAAATACCCTCGAA
**
29443731 GAATAAAATTA-TCGAAATACCCTCGAA
1 GGGTAAAATTACT-GAAATACCCTCGAA
* *
29443758 GGGTAAAATTACTAAAATACCCTTGAA
1 GGGTAAAATTACTGAAATACCCTCGAA
29443785 GGGTAAAATTAC
1 GGGTAAAATTAC
29443797 CAAGATCCCT
Statistics
Matches: 146, Mismatches: 25, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
26 22 0.15
27 123 0.84
28 1 0.01
ACGTcount: A:0.43, C:0.17, G:0.16, T:0.24
Consensus pattern (27 bp):
GGGTAAAATTACTGAAATACCCTCGAA
Found at i:29443721 original size:81 final size:81
Alignment explanation
Indices: 29443597--29443796 Score: 276
Period size: 81 Copynumber: 2.5 Consensus size: 81
29443587 TACGAATCGT
* * * * **
29443597 GGGTAAAATGACTGAAATACCC-TCAAAGGTAAAATTACTGAAATGCCCTCGAAGGGTAAAATTA
1 GGGTAAAATTACTGAAATACCCTTAAAAGGTAAAATTACTGAAATACCCTCAAAGAATAAAATTA
*
29443661 CCGAAATACCTTCGAA
66 CCGAAATACCCTCGAA
**
29443677 GGGTAAAATTTTTGAAATACCCTTAAAAGGTAAAATTACTGAAATACCCTCAAAGAATAAAATTA
1 GGGTAAAATTACTGAAATACCCTTAAAAGGTAAAATTACTGAAATACCCTCAAAGAATAAAATTA
*
29443742 TCGAAATACCCTCGAA
66 CCGAAATACCCTCGAA
* * *
29443758 GGGTAAAATTACTAAAATACCCTTGAAGGGTAAAATTAC
1 GGGTAAAATTACTGAAATACCCTTAAAAGGTAAAATTAC
29443797 CAAGATCCCT
Statistics
Matches: 104, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
80 19 0.18
81 85 0.82
ACGTcount: A:0.43, C:0.17, G:0.16, T:0.24
Consensus pattern (81 bp):
GGGTAAAATTACTGAAATACCCTTAAAAGGTAAAATTACTGAAATACCCTCAAAGAATAAAATTA
CCGAAATACCCTCGAA
Found at i:29443813 original size:26 final size:27
Alignment explanation
Indices: 29443597--29443819 Score: 164
Period size: 27 Copynumber: 8.3 Consensus size: 27
29443587 TACGAATCGT
* ** *
29443597 GGGTAAAATGACTGAAATACCCTCAAA
1 GGGTAAAATTACCAAAATACCCTTAAA
** * **
29443624 -GGTAAAATTACTGAAATGCCCTCGAA
1 GGGTAAAATTACCAAAATACCCTTAAA
* *
29443650 GGGTAAAATTACCGAAATA-CCTTCGAA
1 GGGTAAAATTACCAAAATACCCTT-AAA
****
29443677 GGGTAAAATTTTTGAAATACCCTTAAA
1 GGGTAAAATTACCAAAATACCCTTAAA
* ** *
29443704 AGGTAAAATTACTGAAATACCCTCAAA
1 GGGTAAAATTACCAAAATACCCTTAAA
** * * **
29443731 GAATAAAATTATCGAAATACCCTCGAA
1 GGGTAAAATTACCAAAATACCCTTAAA
* *
29443758 GGGTAAAATTACTAAAATACCCTTGAA
1 GGGTAAAATTACCAAAATACCCTTAAA
*
29443785 GGGTAAAATTACCAAGAT-CCCTTAAA
1 GGGTAAAATTACCAAAATACCCTTAAA
29443811 GGGTAAAAT
1 GGGTAAAAT
29443820 GACTGTTATA
Statistics
Matches: 164, Mismatches: 29, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
26 42 0.26
27 118 0.72
28 4 0.02
ACGTcount: A:0.43, C:0.17, G:0.16, T:0.24
Consensus pattern (27 bp):
GGGTAAAATTACCAAAATACCCTTAAA
Found at i:29448700 original size:13 final size:13
Alignment explanation
Indices: 29448684--29448716 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
29448674 TTTAAACAAA
*
29448684 ACTTTTCAAAAGT
1 ACTTTTCAAAAGC
29448697 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
29448710 ACTTTTC
1 ACTTTTC
29448717 CGTAACACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.39
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:29449023 original size:7 final size:7
Alignment explanation
Indices: 29449013--29449048 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
29449003 ATAATTTTCA
*
29449013 AAAACTT
1 AAAATTT
29449020 AAAATTT
1 AAAATTT
29449027 AAAATTT
1 AAAATTT
29449034 AAAATTT
1 AAAATTT
29449041 AAAATTT
1 AAAATTT
29449048 A
1 A
29449049 GTATTTGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (7 bp):
AAAATTT
Found at i:29453368 original size:51 final size:50
Alignment explanation
Indices: 29453182--29453373 Score: 206
Period size: 51 Copynumber: 3.8 Consensus size: 50
29453172 TTATTATCAT
** * * *
29453182 TCGATACACGTAGTAGCCTTTACATAGTACTACACACGTGATCAAATTTT
1 TCGATACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAATCTA
* * *
29453232 TCGGTTCACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAAGCCT-
1 TCGATACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAA-TCTA
* * * * * * *
29453282 TCCGGTACACATAGTAGCGTGCACATGGTATTACACATGTGACCATTATCTA
1 T-CGATACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA-AATCTA
*
29453334 TCGATACACGTAGTAGCCTGCACTTAGTACTACACACGTG
1 TCGATACACGTAGTAGCCTGCACATAGTACTACACACGTG
29453374 TTTATAGGCA
Statistics
Matches: 116, Mismatches: 22, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
50 42 0.36
51 72 0.62
52 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (50 bp):
TCGATACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAATCTA
Found at i:29455905 original size:22 final size:20
Alignment explanation
Indices: 29455862--29455900 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
29455852 AAAATAAAAA
*
29455862 TATAAAAATTTATTAATATG
1 TATATAAATTTATTAATATG
29455882 TATATAAATTTATTAATAT
1 TATATAAATTTATTAATAT
29455901 ATGTAATAAC
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:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATATAAATTTATTAATATG
Found at i:29455962 original size:32 final size:33
Alignment explanation
Indices: 29455921--29455996 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 33
29455911 AACTTTTCCG
29455921 GAAAATATTTT-CA-AGAAATC-TGCCAAACAACA
1 GAAAATATTTTACACAG-AATCAT-CCAAACAACA
* *
29455953 GAAAATATTTTACACAGATTCATCCAAACACCA
1 GAAAATATTTTACACAGAATCATCCAAACAACA
29455986 GAAAATATTTT
1 GAAAATATTTT
29455997 TAGTAAATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
32 11 0.28
33 25 0.64
34 3 0.08
ACGTcount: A:0.47, C:0.18, G:0.08, T:0.26
Consensus pattern (33 bp):
GAAAATATTTTACACAGAATCATCCAAACAACA
Found at i:29456022 original size:19 final size:19
Alignment explanation
Indices: 29455998--29456036 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
29455988 AAATATTTTT
*
29455998 AGTAAATTATTTTCCAGAA
1 AGTAAATCATTTTCCAGAA
29456017 AGTAAATCATTTTCCAGAA
1 AGTAAATCATTTTCCAGAA
29456036 A
1 A
29456037 TCATTTTCCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (19 bp):
AGTAAATCATTTTCCAGAA
Found at i:29456039 original size:14 final size:14
Alignment explanation
Indices: 29456020--29456057 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
29456010 TCCAGAAAGT
29456020 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
29456034 AAATCATTTTCCGG
1 AAATCATTTTCCAG
*
29456048 AAAACATTTT
1 AAATCATTTT
29456058 ACTGGCAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:29460108 original size:6 final size:6
Alignment explanation
Indices: 29460097--29460184 Score: 142
Period size: 6 Copynumber: 14.3 Consensus size: 6
29460087 GAAGTTTAAG
29460097 AAATAA AAATAAA AAATAAA AAATAA AAATAA AAGA-AA AAATAA AAATAA
1 AAATAA AAAT-AA AAAT-AA AAATAA AAATAA AA-ATAA AAATAA AAATAA
29460147 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AA
29460185 GAAATAAAAT
Statistics
Matches: 79, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
5 1 0.01
6 64 0.81
7 14 0.18
ACGTcount: A:0.84, C:0.00, G:0.01, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:29460111 original size:1 final size:1
Alignment explanation
Indices: 29460101--29460184 Score: 51
Period size: 1 Copynumber: 84.0 Consensus size: 1
29460091 TTTAAGAAAT
* * * * * * * * * *
29460101 AAAAATAAAAAATAAAAAATAAAAATAAAAGAAAAAATAAAAATAAAAATAAAAATAAAAATAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
29460166 AATAAAAATAAAAATAAAA
1 AAAAAAAAAAAAAAAAAAA
29460185 GAAATAAAAT
Statistics
Matches: 57, Mismatches: 26, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 57 1.00
ACGTcount: A:0.85, C:0.00, G:0.01, T:0.14
Consensus pattern (1 bp):
A
Found at i:29468981 original size:29 final size:29
Alignment explanation
Indices: 29468929--29468997 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
29468919 GCCACAAAGC
*
29468929 CTCACATATATCAAATTTCTCCACTAGAG
1 CTCACATATAACAAATTTCTCCACTAGAG
* *
29468958 CTCACATATAACAAA-TTCTGCCACTGGGG
1 CTCACATATAACAAATTTCT-CCACTAGAG
29468987 CTCACATATAA
1 CTCACATATAA
29468998 TAGAAAAGAG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 4 0.11
29 32 0.89
ACGTcount: A:0.35, C:0.28, G:0.10, T:0.28
Consensus pattern (29 bp):
CTCACATATAACAAATTTCTCCACTAGAG
Found at i:29479937 original size:27 final size:26
Alignment explanation
Indices: 29479881--29479950 Score: 88
Period size: 27 Copynumber: 2.7 Consensus size: 26
29479871 CTGTACATGT
*
29479881 ATGCTCACACGAGCTGT-AAATCAGA
1 ATGCTCACACGAGCTGTGAAATAAGA
* *
29479906 ATGCTCACACGAACTGTGAAAATAAGC
1 ATGCTCACACGAGCTGTG-AAATAAGA
*
29479933 CTGCTCACACGAGCTGTG
1 ATGCTCACACGAGCTGTG
29479951 GTTCGGAACG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
25 16 0.42
27 22 0.58
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.20
Consensus pattern (26 bp):
ATGCTCACACGAGCTGTGAAATAAGA
Found at i:29489237 original size:50 final size:50
Alignment explanation
Indices: 29489183--29489278 Score: 129
Period size: 50 Copynumber: 1.9 Consensus size: 50
29489173 ATTAATCAAG
* *
29489183 ATGCAAACTAAATAAACAAATGAATTACGTAATGCATAACATAATTTAAT
1 ATGCAAACTAAATAAACAAAGGAATTACATAATGCATAACATAATTTAAT
* * * * *
29489233 ATGCAAACTTAATTAACATAGGAGTTACATAATGCATGACATAATT
1 ATGCAAACTAAATAAACAAAGGAATTACATAATGCATAACATAATT
29489279 AAAACACAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 39 1.00
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.29
Consensus pattern (50 bp):
ATGCAAACTAAATAAACAAAGGAATTACATAATGCATAACATAATTTAAT
Found at i:29492548 original size:26 final size:26
Alignment explanation
Indices: 29492493--29492550 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
29492483 TATAACATTT
* * *
29492493 CTCACACGAGCTGTGAAATGAGTCTG
1 CTCACACGAGCAGTGAAATGAGCCTA
*
29492519 CTCACACGAGCAGTGAAATGGGCCTA
1 CTCACACGAGCAGTGAAATGAGCCTA
29492545 CTCACA
1 CTCACA
29492551 TGAGTTGTGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.29, C:0.28, G:0.24, T:0.19
Consensus pattern (26 bp):
CTCACACGAGCAGTGAAATGAGCCTA
Found at i:29505527 original size:51 final size:50
Alignment explanation
Indices: 29505412--29505591 Score: 227
Period size: 51 Copynumber: 3.6 Consensus size: 50
29505402 GATACACGTT
* * *
29505412 GTAGCCTTCACATAGTACTACACACGTGATC-AAACTTTCCGGTTCACATA
1 GTAGCCTGCACATAGTACTACACACGTGACCAAAACTTT-CGGTACACATA
29505462 GTAGCCTGCACATAGTACTACACACGTGACCAAAACCTTTCGGTACACATA
1 GTAGCCTGCACATAGTACTACACACGTGACCAAAA-CTTTCGGTACACATA
* * * * * *
29505513 GTAGCCTGCACATAGTACTACACATGTGACCATTATCTATCGATACACGTA
1 GTAGCCTGCACATAGTACTACACACGTGACCA-AAACTTTCGGTACACATA
* *
29505564 GTAGCCTGCACTTAATACTACACACGTG
1 GTAGCCTGCACATAGTACTACACACGTG
29505592 TTTATAGGCA
Statistics
Matches: 115, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
50 29 0.25
51 81 0.70
52 5 0.04
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.26
Consensus pattern (50 bp):
GTAGCCTGCACATAGTACTACACACGTGACCAAAACTTTCGGTACACATA
Found at i:29512779 original size:25 final size:25
Alignment explanation
Indices: 29512738--29512795 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
29512728 TCCTGTACAT
* * *
29512738 GTATGCTCATACGAGCTGTGAATCG
1 GTATGCTCATACAAGCTGTAAATCA
29512763 GTATGCTCACT-CAAGCTGTAAATCA
1 GTATGCTCA-TACAAGCTGTAAATCA
*
29512788 GTGTGCTC
1 GTATGCTC
29512796 TCATAAGCTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 27 0.96
26 1 0.04
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (25 bp):
GTATGCTCATACAAGCTGTAAATCA
Found at i:29517570 original size:29 final size:29
Alignment explanation
Indices: 29517533--29517591 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
29517523 TCCTTTCTCC
* *
29517533 TCCTCCTTGCTATTCTGTCTCTCTATTTT
1 TCCTACTTGCTATTCTGTCTATCTATTTT
29517562 TCCTACTTGCTATTCTGTCTATCTATTTT
1 TCCTACTTGCTATTCTGTCTATCTATTTT
29517591 T
1 T
29517592 TCTATTTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.10, C:0.27, G:0.07, T:0.56
Consensus pattern (29 bp):
TCCTACTTGCTATTCTGTCTATCTATTTT
Found at i:29536633 original size:39 final size:39
Alignment explanation
Indices: 29536579--29536748 Score: 232
Period size: 39 Copynumber: 4.4 Consensus size: 39
29536569 GACGGCAAAA
29536579 AAGTGCGATCAGGGGTACCGAAGTACAACAGGGGCACGT
1 AAGTGCGATCAGGGGTACCGAAGTACAACAGGGGCACGT
* * * * * *
29536618 AAGTGTGATTAGGGGTACCGAAGTACAATAAGGACACAT
1 AAGTGCGATCAGGGGTACCGAAGTACAACAGGGGCACGT
* * * *
29536657 AGGTGCGATCAGGGGTATCGAAGTATAATAGGGGCACGT
1 AAGTGCGATCAGGGGTACCGAAGTACAACAGGGGCACGT
*
29536696 AAGTGCGATCAGGGGTACCGAAGTACAACAGGGGCATGT
1 AAGTGCGATCAGGGGTACCGAAGTACAACAGGGGCACGT
*
29536735 AACTGCGATCAGGG
1 AAGTGCGATCAGGG
29536749 TATAATTATA
Statistics
Matches: 111, Mismatches: 20, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 111 1.00
ACGTcount: A:0.32, C:0.16, G:0.35, T:0.17
Consensus pattern (39 bp):
AAGTGCGATCAGGGGTACCGAAGTACAACAGGGGCACGT
Found at i:29543667 original size:20 final size:20
Alignment explanation
Indices: 29543653--29543693 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
29543643 GCGAAGTGTG
29543653 AACAAGGGCACCGAAGTGCA
1 AACAAGGGCACCGAAGTGCA
**
29543673 AACTGGGGCACCGAAGTGCA
1 AACAAGGGCACCGAAGTGCA
29543693 A
1 A
29543694 TGTATAAGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.24, G:0.32, T:0.07
Consensus pattern (20 bp):
AACAAGGGCACCGAAGTGCA
Found at i:29548899 original size:251 final size:250
Alignment explanation
Indices: 29547997--29548999 Score: 1427
Period size: 250 Copynumber: 4.0 Consensus size: 250
29547987 TATTCGTTTG
* *
29547997 TAAACTTGTAATTTTTTTTGAAAAGATTGAAGAATAAAACAAATTCATGGATTACATTAATATAC
1 TAAACTTGTAA-TTTTTTCGAAAAGATTGAATAATAAAACAAATTCATGGATTACATTAATATAC
* * **
29548062 -TTTGTATGATTGTCCTCGTACGGTTTTTGCACGCAAAGAAAAATGGAAGCAAATGTTGGTCATT
65 ATTT-TATGATTTTCCTCGTACGGTTTTTGCACGCAAAGAAAAATGGAAGAAAATGTTACTCATT
** * *
29548126 GGTTGTCTAAAATTTAAACTAATACTAAGCAGTATTACATGGCTGGATCGTAATACAGAAATACA
129 GGTTGTCTAACGTTTAAACTAATACTAAGCAGTATTACATGGCCGGATCGTAATACAGAAAGACA
* * * * *
29548191 ACTTACATTACTCGATGAAACTTAACATGTCCTTAGTCTAATCGGAAATGAGCAAAC
194 ACTTATATTAGTAGACGAAACTTAACATGTCCTTAATCTAATCGGAAATGAGCAAAC
*
29548248 TAAACTTGTAATTTTTTCGAAAAGATTGAATAATAAAACAAATTCATGGATTACATTAATATATA
1 TAAACTTGTAATTTTTTCGAAAAGATTGAATAATAAAACAAATTCATGGATTACATTAATATACA
* * * * * *
29548313 TTGTATGACTTTCCTTGTACGGTTTTTGCAGGAAAAGAAAAATGGAAGAAAATGTTGCTCATTGG
66 TTTTATGATTTTCCTCGTACGGTTTTTGCACGCAAAGAAAAATGGAAGAAAATGTTACTCATTGG
* * *
29548378 TTGTCTAACGTTTAAACTAATACTAATC-GATATTACATGGCCAGATCGTAATACAGAAAAACAA
131 TTGTCTAACGTTTAAACTAATACTAAGCAG-TATTACATGGCCGGATCGTAATACAGAAAGACAA
* * *
29548442 CTTATATTAGTAGATGAAACTTAACATGTCCTTAATCTAATCAGAAATGAGCAAAA
195 CTTATATTAGTAGACGAAACTTAACATGTCCTTAATCTAATCGGAAATGAGCAAAC
* *
29548498 TAAACTTGTAATTTTTTCAAAAAGATTGAATAATAAAACAAATTCATGGATTACATTAATATACT
1 TAAACTTGTAATTTTTTCGAAAAGATTGAATAATAAAACAAATTCATGGATTACATTAATATACA
* * * * * * *
29548563 TTTTACGATTTTCCTCATACGGTTTTTGCACACAAAGGAAAATGGAAGCAAATGCTACTTATTGG
66 TTTTATGATTTTCCTCGTACGGTTTTTGCACGCAAAGAAAAATGGAAGAAAATGTTACTCATTGG
** * *
29548628 TTGTCTAACGTTTAAACTAATACTAAGTGGTATTACATGGCCGGATTGTAATATAGAAAGACAAC
131 TTGTCTAACGTTTAAACTAATACTAAGCAGTATTACATGGCCGGATCGTAATACAGAAAGACAAC
* * *
29548693 TTATATTAGTAGACGAAACTTATCATGTCCTTAACCTAATTGGAAATGAGCAAAC
196 TTATATTAGTAGACGAAACTTAACATGTCCTTAATCTAATCGGAAATGAGCAAAC
* *
29548748 TAAACTTGTAGTTTTTTTTGAAAAGATTGAATAATAAAGA-AAATTCATGGATTACATTAATATA
1 TAAACTTGTA-ATTTTTTCGAAAAGATTGAATAATAAA-ACAAATTCATGGATTACATTAATATA
*
29548812 CATTTTATGATTTTCCTTGTACGGTTTTTGCACGCAAAGAAAAATGGAAGAAAATGTTACTCATT
64 CATTTTATGATTTTCCTCGTACGGTTTTTGCACGCAAAGAAAAATGGAAGAAAATGTTACTCATT
* * * *
29548877 GGTTGTCTAACGTTTAAACTAATACTAAACAGTATTAAATGGCTGGATCGTAATACAAAAAGACA
129 GGTTGTCTAACGTTTAAACTAATACTAAGCAGTATTACATGGCCGGATCGTAATACAGAAAGACA
* * * * * *
29548942 ACTAATATTAGTAGTCGAAACTAAACATGACTTTAGTCTAATCGGAAATGAGCAAAC
194 ACTTATATTAGTAGACGAAACTTAACATGTCCTTAATCTAATCGGAAATGAGCAAAC
29548999 T
1 T
29549000 GATTGAAAGA
Statistics
Matches: 667, Mismatches: 80, Indels: 10
0.88 0.11 0.01
Matches are distributed among these distances:
249 1 0.00
250 441 0.66
251 224 0.34
252 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (250 bp):
TAAACTTGTAATTTTTTCGAAAAGATTGAATAATAAAACAAATTCATGGATTACATTAATATACA
TTTTATGATTTTCCTCGTACGGTTTTTGCACGCAAAGAAAAATGGAAGAAAATGTTACTCATTGG
TTGTCTAACGTTTAAACTAATACTAAGCAGTATTACATGGCCGGATCGTAATACAGAAAGACAAC
TTATATTAGTAGACGAAACTTAACATGTCCTTAATCTAATCGGAAATGAGCAAAC
Found at i:29568240 original size:20 final size:22
Alignment explanation
Indices: 29568191--29568251 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 22
29568181 TTCCATGTGG
29568191 TATCGATACCACTTAAAAAAAA
1 TATCGATACCACTTAAAAAAAA
* * *
29568213 TATTGATACC-CTT-AAGACAA
1 TATCGATACCACTTAAAAAAAA
*
29568233 TATCGATACCTACATAAAA
1 TATCGATACC-ACTTAAAA
29568252 GTTTTGGAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
20 14 0.47
21 3 0.10
22 11 0.37
23 2 0.07
ACGTcount: A:0.48, C:0.20, G:0.07, T:0.26
Consensus pattern (22 bp):
TATCGATACCACTTAAAAAAAA
Found at i:29569206 original size:132 final size:132
Alignment explanation
Indices: 29569033--29569293 Score: 375
Period size: 132 Copynumber: 2.0 Consensus size: 132
29569023 AAAATAGAGA
* *
29569033 GACTTTTATTCTCTAAAAATTAAATATATTTTCCGGAATAACGATTCTATC-GAT-TTCTATTTG
1 GACTATTATTCTCTAAAAATTAAATATATTTTCCGGAATAACGATTCTATCTG-TCTT-TATTTA
* *
29569096 AGAAAAGAATTTT-TGTTTTCACTTCAAAGGAAAAGAAAACTATTTCTAGTTTCTGTGTTTAATT
64 AGAAAAGAATTTTAT-TTTTCACCTCAAAAGAAAAGAAAACTATTTCTAGTTTCTGTGTTTAATT
29569160 CAAAT
128 CAAAT
* *
29569165 GACTATTATTCTCTAAGAATTAAATATATTTTTCGGAATAACGATTCTATCTGTCTTTATTTAAG
1 GACTATTATTCTCTAAAAATTAAATATATTTTCCGGAATAACGATTCTATCTGTCTTTATTTAAG
* * * *
29569230 AAGAGAATTTTCATTTTTCACCTCAAAAGAAAAGAAAGCTATTTCTAGTTTTTGTGTTTGATTC
66 AAAAGAATTTT-ATTTTTCACCTCAAAAGAAAAGAAAACTATTTCTAGTTTCTGTGTTTAATTC
29569294 GATTTGATTG
Statistics
Matches: 115, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
132 66 0.57
133 48 0.42
134 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (132 bp):
GACTATTATTCTCTAAAAATTAAATATATTTTCCGGAATAACGATTCTATCTGTCTTTATTTAAG
AAAAGAATTTTATTTTTCACCTCAAAAGAAAAGAAAACTATTTCTAGTTTCTGTGTTTAATTCAA
AT
Found at i:29574067 original size:18 final size:18
Alignment explanation
Indices: 29574046--29574128 Score: 85
Period size: 18 Copynumber: 4.6 Consensus size: 18
29574036 ACCCATATTG
*
29574046 TTATGCGAACCTTTGTTA
1 TTATGCGAACCTATGTTA
* * * *
29574064 TTATGCAAACTTTTGTTG
1 TTATGCGAACCTATGTTA
29574082 TTATGCGAACCTATGTTA
1 TTATGCGAACCTATGTTA
* * *
29574100 TTTTTCGAACCCATGTTA
1 TTATGCGAACCTATGTTA
*
29574118 TTGTGCGAACC
1 TTATGCGAACC
29574129 CTAACATTAA
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 53 1.00
ACGTcount: A:0.23, C:0.18, G:0.17, T:0.42
Consensus pattern (18 bp):
TTATGCGAACCTATGTTA
Found at i:29576648 original size:44 final size:42
Alignment explanation
Indices: 29576598--29576710 Score: 118
Period size: 44 Copynumber: 2.6 Consensus size: 42
29576588 GGTGCTTCGG
* *** *
29576598 TGGCATTCTATTAACCTTTATGGTGTATTTTGATTTGGCCTTTA
1 TGGCATTCTATTAGCCTTTATGGCACATTTTG--TTAGCCTTTA
*
29576642 TGGCATTCTAATCTAGCCTTTGTGGCACATTTTGTTAGCCTTTA
1 TGGCATTCT-AT-TAGCCTTTATGGCACATTTTGTTAGCCTTTA
* *
29576686 TGGCATTCTACTAGCCTTTGTGGCA
1 TGGCATTCTATTAGCCTTTATGGCA
29576711 TGTTCTATAT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
42 14 0.23
43 1 0.02
44 27 0.45
45 2 0.03
46 16 0.27
ACGTcount: A:0.18, C:0.19, G:0.19, T:0.44
Consensus pattern (42 bp):
TGGCATTCTATTAGCCTTTATGGCACATTTTGTTAGCCTTTA
Found at i:29576667 original size:22 final size:21
Alignment explanation
Indices: 29576635--29576711 Score: 77
Period size: 22 Copynumber: 3.6 Consensus size: 21
29576625 TTTTGATTTG
29576635 GCCTTTATGGCATTCTAATCTA
1 GCCTTTATGGCATTCT-ATCTA
* * *
29576657 GCCTTTGTGGCACATTTTGT-TA
1 GCCTTTATGG--CATTCTATCTA
29576679 GCCTTTATGGCATTCTA-CTA
1 GCCTTTATGGCATTCTATCTA
*
29576699 GCCTTTGTGGCAT
1 GCCTTTATGGCAT
29576712 GTTCTATATG
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
20 19 0.42
22 20 0.44
23 1 0.02
24 5 0.11
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (21 bp):
GCCTTTATGGCATTCTATCTA
Found at i:29578751 original size:19 final size:19
Alignment explanation
Indices: 29578727--29578766 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
29578717 ACATAAAATA
*
29578727 AACTAAGTAAAAACTTAAG
1 AACTAAATAAAAACTTAAG
29578746 AACTAAATAAAAACTTAAG
1 AACTAAATAAAAACTTAAG
29578765 AA
1 AA
29578767 TCAATCCCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.62, C:0.10, G:0.07, T:0.20
Consensus pattern (19 bp):
AACTAAATAAAAACTTAAG
Found at i:29582630 original size:30 final size:30
Alignment explanation
Indices: 29582587--29582649 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
29582577 CTTAACAAGA
*
29582587 AAATGCCTCTAAAATAATAACAAAATTAAC
1 AAATGCCTCTAAAATAAGAACAAAATTAAC
* *
29582617 AAATGTCTTTAAAATAAGAACAAAATTAAC
1 AAATGCCTCTAAAATAAGAACAAAATTAAC
29582647 AAA
1 AAA
29582650 AAAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.59, C:0.13, G:0.05, T:0.24
Consensus pattern (30 bp):
AAATGCCTCTAAAATAAGAACAAAATTAAC
Found at i:29584620 original size:69 final size:69
Alignment explanation
Indices: 29584484--29584636 Score: 166
Period size: 69 Copynumber: 2.2 Consensus size: 69
29584474 GACTGCCTTT
* **** *
29584484 GGTTTCCTCCTTTTGTCTCTACTCAGCTGCTACACTCTATTGTTGCCTTTGGATCTCTACACTCT
1 GGTTTCCTCCTTTTGTCCCTACTCAGCTGCTACACTCTATTGTTGCCTCCAAATCTCTACACCCT
29584549 TTAG
66 TTAG
* * * *
29584553 GGTTTCCT-CTTTTCGTCCCTACTTAGTTGCTACCCTTTATTGTTGCCTCCAAATCT-TCACACC
1 GGTTTCCTCCTTTT-GTCCCTACTCAGCTGCTACACTCTATTGTTGCCTCCAAATCTCT-ACACC
29584616 CTTTAG
64 CTTTAG
29584622 GGTTTTTCCTCCTTT
1 GG--TTTCCTCCTTT
29584637 GGCTTTTTAT
Statistics
Matches: 69, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
68 6 0.09
69 53 0.77
71 6 0.09
72 4 0.06
ACGTcount: A:0.12, C:0.30, G:0.13, T:0.44
Consensus pattern (69 bp):
GGTTTCCTCCTTTTGTCCCTACTCAGCTGCTACACTCTATTGTTGCCTCCAAATCTCTACACCCT
TTAG
Found at i:29591822 original size:7 final size:7
Alignment explanation
Indices: 29591810--29591856 Score: 85
Period size: 7 Copynumber: 6.7 Consensus size: 7
29591800 TCACGCCCTC
29591810 TAGGGTT
1 TAGGGTT
29591817 TAGGGTT
1 TAGGGTT
29591824 TAGGGTT
1 TAGGGTT
*
29591831 TAAGGTT
1 TAGGGTT
29591838 TAGGGTT
1 TAGGGTT
29591845 TAGGGTT
1 TAGGGTT
29591852 TAGGG
1 TAGGG
29591857 CGTGATTTGC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (7 bp):
TAGGGTT
Found at i:29592249 original size:23 final size:22
Alignment explanation
Indices: 29592205--29592671 Score: 507
Period size: 23 Copynumber: 21.0 Consensus size: 22
29592195 AGGATGCTAG
29592205 TTAAGGGTTTAGGG-TTTTAAT
1 TTAAGGGTTTAGGGTTTTTAAT
*
29592226 TATAAGGGTTTAAGGTTTTTAAT
1 T-TAAGGGTTTAGGGTTTTTAAT
* ** * *
29592249 TAAATTAGTTTAAGGTTTTTAAG
1 TTAA-GGGTTTAGGGTTTTTAAT
*
29592272 TTAAGGGCTTAGGGTTTTTAATT
1 TTAAGGGTTTAGGGTTTTTAA-T
29592295 TTAAGGGTTTA-GGTTTTATAAT
1 TTAAGGGTTTAGGGTTTT-TAAT
* *
29592317 TTAAGGG-TTAGGGTTTATAAG
1 TTAAGGGTTTAGGGTTTTTAAT
*
29592338 TTAATGGTTTAGGGTTTTTAATT
1 TTAAGGGTTTAGGGTTTTTAA-T
*
29592361 TTAAGGGTTTATGGTTTTTAAT
1 TTAAGGGTTTAGGGTTTTTAAT
* **
29592383 TAAATTAGTTTAGGGTTTTTAAGT
1 TTAA-GGGTTTAGGGTTTTTAA-T
*
29592407 TAAAGGG-TTAGGGTTTTTTAAT
1 TTAAGGGTTTAGGG-TTTTTAAT
* ** *
29592429 TAAATTAGTTTAGGGTTTTTAAG
1 TTAA-GGGTTTAGGGTTTTTAAT
* *
29592452 TTAAGGGCTTAGGGTTTTTATT
1 TTAAGGGTTTAGGGTTTTTAAT
*
29592474 TTAAGGGTTTAGGGTTCTTAAT
1 TTAAGGGTTTAGGGTTTTTAAT
* *
29592496 TTAAGGG-TTAGAGTTTTTAAG
1 TTAAGGGTTTAGGGTTTTTAAT
29592517 TTAAGGGTTTAGGGTTTTTAATT
1 TTAAGGGTTTAGGGTTTTTAA-T
*
29592540 TTAAGAGTTTAGGGTTTTTAACT
1 TTAAGGGTTTAGGGTTTTTAA-T
*
29592563 TTAAGGG-TTAGGGTTTTTAAA
1 TTAAGGGTTTAGGGTTTTTAAT
*
29592584 TTAAGGGTTTAGGG-TTTTAAG
1 TTAAGGGTTTAGGGTTTTTAAT
*
29592605 TCAAGGGTTTAGGGTTTTTAATT
1 TTAAGGGTTTAGGGTTTTTAA-T
*
29592628 TTAAAGGTTTAGGGTTTTTAATT
1 TTAAGGGTTTAGGGTTTTTAA-T
29592651 TTAAGGGTTTAGGGTTTTTAA
1 TTAAGGGTTTAGGGTTTTTAA
29592672 GTAATAACTC
Statistics
Matches: 376, Mismatches: 52, Indels: 34
0.81 0.11 0.07
Matches are distributed among these distances:
21 57 0.15
22 149 0.40
23 159 0.42
24 11 0.03
ACGTcount: A:0.26, C:0.01, G:0.25, T:0.48
Consensus pattern (22 bp):
TTAAGGGTTTAGGGTTTTTAAT
Found at i:29594039 original size:20 final size:20
Alignment explanation
Indices: 29594002--29594039 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
29593992 TTTATTTTTA
*
29594002 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
29594022 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
29594040 TTCCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:29596539 original size:11 final size:12
Alignment explanation
Indices: 29596525--29596591 Score: 81
Period size: 11 Copynumber: 5.9 Consensus size: 12
29596515 TTAAATATGG
29596525 ATTTGAGA-GAA
1 ATTTGAGAGGAA
29596536 ATTTG-GAAGG-A
1 ATTTGAG-AGGAA
29596547 ATTTGAGAGGAA
1 ATTTGAGAGGAA
29596559 ATTT-AGAGGAA
1 ATTTGAGAGGAA
29596570 A-TTGAGAGGAA
1 ATTTGAGAGGAA
*
29596581 ATTTGACAGGA
1 ATTTGAGAGGA
29596592 TTAGTTTGTG
Statistics
Matches: 49, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
10 3 0.06
11 31 0.63
12 15 0.31
ACGTcount: A:0.42, C:0.01, G:0.31, T:0.25
Consensus pattern (12 bp):
ATTTGAGAGGAA
Found at i:29596767 original size:26 final size:26
Alignment explanation
Indices: 29596710--29596767 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
29596700 CGACCATGTC
* *
29596710 AGCGCGCTTTGTTGACGTGGCAGAAA
1 AGCGCGATTTGTTGACATGGCAGAAA
* * * *
29596736 ATCGCGATTTGTTGCCATGTCAGCAA
1 AGCGCGATTTGTTGACATGGCAGAAA
29596762 AGCGCG
1 AGCGCG
29596768 CTGATGTTGC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.22, C:0.22, G:0.31, T:0.24
Consensus pattern (26 bp):
AGCGCGATTTGTTGACATGGCAGAAA
Found at i:29604560 original size:80 final size:80
Alignment explanation
Indices: 29604427--29604757 Score: 592
Period size: 80 Copynumber: 4.2 Consensus size: 80
29604417 ATTTGAATGA
29604427 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAA
29604492 TTGTGCTAGTGATTT
66 TTGTGCTAGTGATTT
29604507 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAA
29604572 TTGTGCTAGTGATTT
66 TTGTGCTAGTGATTT
29604587 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAA
29604652 TTGTGCTAGTGATTT
66 TTGTGCTAGTGATTT
* * * *
29604667 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATATATCCGGGCTAAGACCCGAAGGCAT
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAA
* * *
29604732 TTGTGCTTGTGGTTA
66 TTGTGCTAGTGATTT
29604747 TATCC-GGCTAA
1 TATCCGGGCTAA
29604758 ATTCCGAAGA
Statistics
Matches: 244, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
79 6 0.02
80 238 0.98
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.27
Consensus pattern (80 bp):
TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAA
TTGTGCTAGTGATTT
Found at i:29604749 original size:40 final size:40
Alignment explanation
Indices: 29604426--29604757 Score: 405
Period size: 40 Copynumber: 8.3 Consensus size: 40
29604416 CATTTGAATG
* *
29604426 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGGTT
* * * * *
29604466 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGGTT
* * *
29604506 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGGTT
* * * * *
29604546 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGGTT
* * *
29604586 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGGTT
* * * * *
29604626 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGGTT
* * *
29604666 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGGTT
**
29604706 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGGTT
29604746 ATATCC-GGCTAA
1 ATATCCGGGCTAA
29604758 ATTCCGAAGA
Statistics
Matches: 240, Mismatches: 52, Indels: 1
0.82 0.18 0.00
Matches are distributed among these distances:
39 6 0.03
40 234 0.98
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGGTT
Found at i:29607792 original size:23 final size:23
Alignment explanation
Indices: 29607766--29607989 Score: 142
Period size: 23 Copynumber: 9.7 Consensus size: 23
29607756 GAAAAATATT
* *
29607766 GAATATGCTACATAGGCATTACA
1 GAATATGCCACAAAGGCATTACA
** * * **
29607789 GAATACACCATAAAAGCATTGTA
1 GAATATGCCACAAAGGCATTACA
* * *
29607812 GAATAAGCCACATAGGCATTGCA
1 GAATATGCCACAAAGGCATTACA
* ** ** *
29607835 AAATACACCACAAAGAAAATACA
1 GAATATGCCACAAAGGCATTACA
* * *
29607858 TAATAAGCCACATAGGCATTACA
1 GAATATGCCACAAAGGCATTACA
* *
29607881 TAATATGCCACAAATGCATTACA
1 GAATATGCCACAAAGGCATTACA
* * **
29607904 AAATATGCCACATAGGCATTGTA
1 GAATATGCCACAAAGGCATTACA
** * *
29607927 GAATACACCATAAAGACATTACA
1 GAATATGCCACAAAGGCATTACA
* * *
29607950 AAATATGCTACAAAGGCATTATA
1 GAATATGCCACAAAGGCATTACA
*
29607973 GAATACGCCACAAAGGC
1 GAATATGCCACAAAGGC
29607990 TTCAAAAGTA
Statistics
Matches: 146, Mismatches: 55, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
23 146 1.00
ACGTcount: A:0.46, C:0.20, G:0.14, T:0.20
Consensus pattern (23 bp):
GAATATGCCACAAAGGCATTACA
Found at i:29607840 original size:46 final size:46
Alignment explanation
Indices: 29607766--29607978 Score: 178
Period size: 46 Copynumber: 4.6 Consensus size: 46
29607756 GAAAAATATT
* * **
29607766 GAATATGCTACATAGGCATTACAGAATACACCATAAAAGCATTGTA
1 GAATAAGCCACATAGGCATTACAGAATACACCATAAAAGCATTACA
* * * * *
29607812 GAATAAGCCACATAGGCATTGCAAAATACACCA-CAAAGAAAATACA
1 GAATAAGCCACATAGGCATTACAGAATACACCATAAAAG-CATTACA
* * ** * *
29607858 TAATAAGCCACATAGGCATTACATAATATGCCACAAATGCATTACA
1 GAATAAGCCACATAGGCATTACAGAATACACCATAAAAGCATTACA
* * **
29607904 AAATATGCCACATAGGCATTGTAGAATACACCAT-AAAGACATTACA
1 GAATAAGCCACATAGGCATTACAGAATACACCATAAAAG-CATTACA
* * * * *
29607950 AAATATGCTACAAAGGCATTATAGAATAC
1 GAATAAGCCACATAGGCATTACAGAATAC
29607979 GCCACAAAGG
Statistics
Matches: 134, Mismatches: 30, Indels: 6
0.79 0.18 0.04
Matches are distributed among these distances:
45 7 0.05
46 124 0.93
47 3 0.02
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.21
Consensus pattern (46 bp):
GAATAAGCCACATAGGCATTACAGAATACACCATAAAAGCATTACA
Found at i:29607915 original size:92 final size:92
Alignment explanation
Indices: 29607775--29607986 Score: 253
Period size: 92 Copynumber: 2.3 Consensus size: 92
29607765 TGAATATGCT
* * ** *
29607775 ACATAGGCATTACAGAATACACCATAAAAGCATTGTAGAATAAGCCACATAGGCATTGCAAAATA
1 ACATAGGCATTACAGAATACGCCACAAAAGCATTACAAAATAAGCCACATAGGCATTGCAAAATA
*
29607840 CACCACAAAGAAAATACATAATAAGCC
66 CACCACAAAGAAAATACAAAATAAGCC
* * * * * *
29607867 ACATAGGCATTACATAATATGCCACAAATGCATTACAAAATATGCCACATAGGCATTGTAGAATA
1 ACATAGGCATTACAGAATACGCCACAAAAGCATTACAAAATAAGCCACATAGGCATTGCAAAATA
* * * * *
29607932 CACCATAAAGACATTACAAAATATGCT
66 CACCACAAAGAAAATACAAAATAAGCC
* *
29607959 ACAAAGGCATTATAGAATACGCCACAAA
1 ACATAGGCATTACAGAATACGCCACAAA
29607987 GGCTTCAAAA
Statistics
Matches: 99, Mismatches: 21, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
92 99 1.00
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.20
Consensus pattern (92 bp):
ACATAGGCATTACAGAATACGCCACAAAAGCATTACAAAATAAGCCACATAGGCATTGCAAAATA
CACCACAAAGAAAATACAAAATAAGCC
Found at i:29610700 original size:15 final size:15
Alignment explanation
Indices: 29610679--29610713 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
29610669 ACTTTTTAAG
29610679 CTTTAGTTTAATGCA
1 CTTTAGTTTAATGCA
* *
29610694 TTTTAGTTTATTGCA
1 CTTTAGTTTAATGCA
29610709 CTTTA
1 CTTTA
29610714 AATCTATTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.23, C:0.11, G:0.11, T:0.54
Consensus pattern (15 bp):
CTTTAGTTTAATGCA
Found at i:29613553 original size:25 final size:25
Alignment explanation
Indices: 29613524--29613593 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
29613514 CGTTCTGACC
*
29613524 CACAGCTTGTGTAAGCATACCGATT
1 CACAGCTTGTGTAAGCATACCAATT
*
29613549 CACAGCTTGTGTGAGCATACCAATT
1 CACAGCTTGTGTAAGCATACCAATT
* *
29613574 CACAGATCGTGTAAGCATAC
1 CACAGCTTGTGTAAGCATAC
29613594 ATGTACAGGA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (25 bp):
CACAGCTTGTGTAAGCATACCAATT
Found at i:29623479 original size:12 final size:12
Alignment explanation
Indices: 29623462--29623503 Score: 84
Period size: 12 Copynumber: 3.5 Consensus size: 12
29623452 GTAGCAGTTT
29623462 TATAACTAAGCC
1 TATAACTAAGCC
29623474 TATAACTAAGCC
1 TATAACTAAGCC
29623486 TATAACTAAGCC
1 TATAACTAAGCC
29623498 TATAAC
1 TATAAC
29623504 ACCATTATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.43, C:0.24, G:0.07, T:0.26
Consensus pattern (12 bp):
TATAACTAAGCC
Found at i:29624453 original size:23 final size:23
Alignment explanation
Indices: 29624406--29624540 Score: 128
Period size: 23 Copynumber: 5.9 Consensus size: 23
29624396 CTACATAGGT
* * *
29624406 ATTGCAGAATTCACCACAAATGC
1 ATTGCAGAATACGCCACAAAGGC
* * *
29624429 ATTACAAAATACGCTACAAAGGC
1 ATTGCAGAATACGCCACAAAGGC
* *
29624452 ATTGCAGAATACGCCACATAGGT
1 ATTGCAGAATACGCCACAAAGGC
* * * *
29624475 ATTGTAGAATATGTCACTAAGGC
1 ATTGCAGAATACGCCACAAAGGC
* * *
29624498 ATTACATAATACGCCACATAGGC
1 ATTGCAGAATACGCCACAAAGGC
29624521 ATTGCAGAATACGCCA-AAAG
1 ATTGCAGAATACGCCACAAAG
29624541 TGTAACACCC
Statistics
Matches: 85, Mismatches: 27, Indels: 1
0.75 0.24 0.01
Matches are distributed among these distances:
22 3 0.04
23 82 0.96
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.21
Consensus pattern (23 bp):
ATTGCAGAATACGCCACAAAGGC
Found at i:29629651 original size:23 final size:22
Alignment explanation
Indices: 29629588--29629653 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 22
29629578 CAAAATGTGT
*
29629588 CACAAAGACTATATAAAATGCGC
1 CACAAAGAC-ATATAGAATGCGC
* *
29629611 CAAAAATGTCATATAGAATGCGC
1 CACAAA-GACATATAGAATGCGC
*
29629634 CACAAAGACAATACAGAATG
1 CACAAAGAC-ATATAGAATG
29629654 ACACAAAGTC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
22 2 0.06
23 31 0.89
24 2 0.06
ACGTcount: A:0.48, C:0.20, G:0.15, T:0.17
Consensus pattern (22 bp):
CACAAAGACATATAGAATGCGC
Found at i:29631972 original size:28 final size:28
Alignment explanation
Indices: 29631900--29632025 Score: 173
Period size: 28 Copynumber: 4.4 Consensus size: 28
29631890 ATTCAATGAT
29631900 AGTAA-AGTGTGGGCCTTAGCCCAATAC
1 AGTAACAGTGTGGGCCTTAGCCCAATAC
*
29631927 AGTAACAGTACAGTGTGGGCCTTAGCCCAATAT
1 AGT---A--ACAGTGTGGGCCTTAGCCCAATAC
*
29631960 AGTAATAGTGTGGGCCTTAGCCCAATAC
1 AGTAACAGTGTGGGCCTTAGCCCAATAC
*
29631988 AGTAACAATGTGGGCCTTAGCCCAATAC
1 AGTAACAGTGTGGGCCTTAGCCCAATAC
29632016 AGTAACAGTG
1 AGTAACAGTG
29632026 CAGTGCAATA
Statistics
Matches: 87, Mismatches: 6, Indels: 11
0.84 0.06 0.11
Matches are distributed among these distances:
27 3 0.03
28 57 0.66
30 2 0.02
32 1 0.01
33 24 0.28
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (28 bp):
AGTAACAGTGTGGGCCTTAGCCCAATAC
Found at i:29631973 original size:61 final size:55
Alignment explanation
Indices: 29631893--29632025 Score: 185
Period size: 61 Copynumber: 2.3 Consensus size: 55
29631883 CAGCCTTATT
29631893 CAATGATAGTAAAGTGTGGGCCTTAGCCCAATACAGTAACAGTACAGTGTGGGCCTTAGCC
1 CAAT-ATAGTAAAGTGTGGGCCTTAGCCCAATACAGTAAC---A-A-TGTGGGCCTTAGCC
29631954 CAATATAGTAATAGTGTGGGCCTTAGCCCAATACAGTAACAATGTGGGCCTTAGCC
1 CAATATAGTAA-AGTGTGGGCCTTAGCCCAATACAGTAACAATGTGGGCCTTAGCC
*
29632010 CAATACAGTAACAGTG
1 CAATATAGTAA-AGTG
29632026 CAGTGCAATA
Statistics
Matches: 69, Mismatches: 2, Indels: 7
0.88 0.03 0.09
Matches are distributed among these distances:
56 28 0.41
57 1 0.01
58 1 0.01
60 7 0.10
61 32 0.46
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (55 bp):
CAATATAGTAAAGTGTGGGCCTTAGCCCAATACAGTAACAATGTGGGCCTTAGCC
Found at i:29632448 original size:27 final size:26
Alignment explanation
Indices: 29632418--29632666 Score: 286
Period size: 27 Copynumber: 9.2 Consensus size: 26
29632408 TATAACAGTT
*
29632418 ATTTTACCTTATGGGGATATTTCGATC
1 ATTTTACCCTATGGGG-TATTTCGATC
29632445 ATTTTACCCTATAGGGGTATTTCGATC
1 ATTTTACCCTAT-GGGGTATTTCGATC
* *
29632472 ATTTTTCCCTATGGCGGTATTTTGATC
1 ATTTTACCCTATGG-GGTATTTCGATC
* * *
29632499 ATTTTAGCCTATGAGGGTATTTTGGTC
1 ATTTTACCCTATG-GGGTATTTCGATC
29632526 ATTTTACCCTATGGGGGTATTTC-AGTC
1 ATTTTACCCTAT-GGGGTATTTCGA-TC
29632553 ATTTTACCCTATAGGGGTATTTCGATC
1 ATTTTACCCTAT-GGGGTATTTCGATC
* *
29632580 ATTTTAACCTATGGGGGTATTTC-AGTT
1 ATTTTACCCTAT-GGGGTATTTCGA-TC
*
29632607 ATTTTACCCTATTGGGGTATTTTGATC
1 ATTTTACCCTA-TGGGGTATTTCGATC
*
29632634 ATTTTACACTATGGGGGGTATTTCGATC
1 ATTTTACCCTAT--GGGGTATTTCGATC
29632662 ATTTT
1 ATTTT
29632667 CATCTATTAG
Statistics
Matches: 193, Mismatches: 18, Indels: 21
0.83 0.08 0.09
Matches are distributed among these distances:
26 4 0.02
27 162 0.84
28 27 0.14
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.44
Consensus pattern (26 bp):
ATTTTACCCTATGGGGTATTTCGATC
Found at i:29635363 original size:28 final size:28
Alignment explanation
Indices: 29635322--29635528 Score: 251
Period size: 28 Copynumber: 7.4 Consensus size: 28
29635312 CTATTCAGTG
29635322 ACAGT-ACAGTGTGGGCCTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
*
29635349 ATAGTAACAGTGTGGGCCTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
* * *
29635377 ACAGTAACAATGTGGGCCTTAGTCTAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
* *
29635405 ATAG-AATCAGTGTGGGCCTTAGCCTAAT
1 ACAGTAA-CAGTGTGGGCCTTAGCCCAAT
* *
29635433 ACAG-AATCAGTGGGGGCCTTAGCTCAAT
1 ACAGTAA-CAGTGTGGGCCTTAGCCCAAT
* * *
29635461 ATAGTAACAGTGTGAGCCTTAGCCAAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
29635489 ACAG-AATCAGTGTGGGCCTTAGCCCAAT
1 ACAGTAA-CAGTGTGGGCCTTAGCCCAAT
*
29635517 ACAGTAATAGTG
1 ACAGTAACAGTG
29635529 CAGTGCAGTA
Statistics
Matches: 154, Mismatches: 21, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
27 8 0.05
28 142 0.92
29 4 0.03
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (28 bp):
ACAGTAACAGTGTGGGCCTTAGCCCAAT
Found at i:29635407 original size:56 final size:56
Alignment explanation
Indices: 29635328--29635528 Score: 280
Period size: 56 Copynumber: 3.6 Consensus size: 56
29635318 AGTGACAGTA
*
29635328 CAGTGTGGGCCTTAGCCCAATATAGTAACAGTGTGGGCCTTAGCCCAATACAGTAA-
1 CAGTGTGGGCCTTAGCCCAATATAGTAACAGTGTGGGCCTTAGCCAAATACAG-AAT
* * * *
29635384 CAATGTGGGCCTTAGTCTAATATAG-AATCAGTGTGGGCCTTAGCCTAATACAGAAT
1 CAGTGTGGGCCTTAGCCCAATATAGTAA-CAGTGTGGGCCTTAGCCAAATACAGAAT
* * *
29635440 CAGTGGGGGCCTTAGCTCAATATAGTAACAGTGTGAGCCTTAGCCAAATACAGAAT
1 CAGTGTGGGCCTTAGCCCAATATAGTAACAGTGTGGGCCTTAGCCAAATACAGAAT
* *
29635496 CAGTGTGGGCCTTAGCCCAATACAGTAATAGTG
1 CAGTGTGGGCCTTAGCCCAATATAGTAACAGTG
29635529 CAGTGCAGTA
Statistics
Matches: 127, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
55 4 0.03
56 121 0.95
57 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (56 bp):
CAGTGTGGGCCTTAGCCCAATATAGTAACAGTGTGGGCCTTAGCCAAATACAGAAT
Found at i:29635444 original size:84 final size:85
Alignment explanation
Indices: 29635328--29635528 Score: 291
Period size: 84 Copynumber: 2.4 Consensus size: 85
29635318 AGTGACAGTA
* * *
29635328 CAGTGTGGGCCTTAGCCCAATATAGTAA-CAGTGTGGGCCTTAGCCCAATACAGTAACAATGTGG
1 CAGTGTGGGCCTTAGCCCAATACAGTAATCAGTGGGGGCCTTAGCCCAATACAGTAACAATGTGA
* * *
29635392 GCCTTAGTCTAATATAGAAT
66 GCCTTAGCCAAATACAGAAT
* * * *
29635412 CAGTGTGGGCCTTAGCCTAATACAG-AATCAGTGGGGGCCTTAGCTCAATATAGTAACAGTGTGA
1 CAGTGTGGGCCTTAGCCCAATACAGTAATCAGTGGGGGCCTTAGCCCAATACAGTAACAATGTGA
29635476 GCCTTAGCCAAATACAGAAT
66 GCCTTAGCCAAATACAGAAT
29635496 CAGTGTGGGCCTTAGCCCAATACAGTAAT-AGTG
1 CAGTGTGGGCCTTAGCCCAATACAGTAATCAGTG
29635529 CAGTGCAGTA
Statistics
Matches: 104, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
83 2 0.02
84 99 0.95
85 3 0.03
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (85 bp):
CAGTGTGGGCCTTAGCCCAATACAGTAATCAGTGGGGGCCTTAGCCCAATACAGTAACAATGTGA
GCCTTAGCCAAATACAGAAT
Found at i:29635689 original size:26 final size:26
Alignment explanation
Indices: 29635635--29635710 Score: 71
Period size: 26 Copynumber: 2.9 Consensus size: 26
29635625 ACCAATATCA
* * * **
29635635 CAGCAAAGCTGCTAGTAATAGCACCG
1 CAGCAAAGCTGCCAGTAACAGTATTG
* * *
29635661 CAGTAGAGCTGCCAGTATCAGTATTG
1 CAGCAAAGCTGCCAGTAACAGTATTG
*
29635687 CAGCAAAGTTGCCAGTAACAGTAT
1 CAGCAAAGCTGCCAGTAACAGTAT
29635711 ATGTGCCAAA
Statistics
Matches: 38, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (26 bp):
CAGCAAAGCTGCCAGTAACAGTATTG
Found at i:29636326 original size:55 final size:54
Alignment explanation
Indices: 29636238--29636341 Score: 127
Period size: 55 Copynumber: 1.9 Consensus size: 54
29636228 GGGGTATTTC
*
29636238 AGTCACTTTACCCTATAGGGGTATGTCAATCATTTTCATCTATTAGGGGTAAAAT
1 AGTCACTTTACCCTATAGGGGTATGTCAATCATTTT-ACCTATTAGGGGTAAAAT
* * * *** *
29636293 AGTCATTTTACCCTTTAGGGGTATTTTGGTCATTTTACCTATTTGGGGT
1 AGTCACTTTACCCTATAGGGGTATGTCAATCATTTTACCTATTAGGGGT
29636342 CTCGGTGTAG
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
54 11 0.27
55 30 0.73
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.41
Consensus pattern (54 bp):
AGTCACTTTACCCTATAGGGGTATGTCAATCATTTTACCTATTAGGGGTAAAAT
Found at i:29636341 original size:27 final size:27
Alignment explanation
Indices: 29635932--29636331 Score: 340
Period size: 27 Copynumber: 14.8 Consensus size: 27
29635922 TTATCTCCTA
** *
29635932 GGGGTATAATAGTCATTTTACCCTCTG
1 GGGGTATTTTAGTCATTTTACCCTATG
** ** * * *
29635959 AAGGTATTTCGGTTATTTTACCGTATA
1 GGGGTATTTTAGTCATTTTACCCTATG
29635986 GGGGTATTTTAGTCATTTTACCCTATG
1 GGGGTATTTTAGTCATTTTACCCTATG
* * *
29636013 GGGGTATTTCAGTCATTTTACCTTGTG
1 GGGGTATTTTAGTCATTTTACCCTATG
* * *
29636040 GAGGTATTTTTGTCATTTTACCTTATG
1 GGGGTATTTTAGTCATTTTACCCTATG
* *
29636067 GTGGTATTTT-TTCATTTTACCCTATG
1 GGGGTATTTTAGTCATTTTACCCTATG
* ** *
29636093 GGGGAATTTCGGTCATTTTATCCTATG
1 GGGGTATTTTAGTCATTTTACCCTATG
29636120 GGGGTATTTT-GCTCATTTTACCCTATG
1 GGGGTATTTTAG-TCATTTTACCCTATG
*
29636147 GGGGTATTTTAGTCATTTTACCCAATG
1 GGGGTATTTTAGTCATTTTACCCTATG
* *
29636174 GAGCTATTTT-GCTCATTTTACCCTATG
1 GGGGTATTTTAG-TCATTTTACCCTATG
* ** * *
29636201 GGAGTATTTCGGTCATGTTACCTTATG
1 GGGGTATTTTAGTCATTTTACCCTATG
* * *
29636228 GGGGTATTTCAGTCACTTTACCCTATA
1 GGGGTATTTTAGTCATTTTACCCTATG
* * * * *
29636255 GGGGTATGTCAATCATTTT-CATCTATTA
1 GGGGTATTTTAGTCATTTTAC-CCTA-TG
*** * *
29636283 GGGGTAAAATAGTCATTTTACCCTTTA
1 GGGGTATTTTAGTCATTTTACCCTATG
*
29636310 GGGGTATTTTGGTCATTTTACC
1 GGGGTATTTTAGTCATTTTACC
29636332 TATTTGGGGT
Statistics
Matches: 299, Mismatches: 66, Indels: 16
0.78 0.17 0.04
Matches are distributed among these distances:
26 24 0.08
27 254 0.85
28 20 0.07
29 1 0.00
ACGTcount: A:0.20, C:0.16, G:0.21, T:0.43
Consensus pattern (27 bp):
GGGGTATTTTAGTCATTTTACCCTATG
Found at i:29656172 original size:21 final size:21
Alignment explanation
Indices: 29656148--29656194 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
29656138 AGGTTAACAG
*
29656148 AATGCCATAAAAGCCATACAA
1 AATGCCACAAAAGCCATACAA
* *
29656169 AATGCCACAAAGGCCATACAG
1 AATGCCACAAAAGCCATACAA
29656190 AATGC
1 AATGC
29656195 ATTATAAAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.47, C:0.26, G:0.15, T:0.13
Consensus pattern (21 bp):
AATGCCACAAAAGCCATACAA
Found at i:29661607 original size:21 final size:21
Alignment explanation
Indices: 29661583--29661636 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
29661573 TGAATTTTTA
**
29661583 AATTAGATTTTATTAAATTAT
1 AATTAGATTTTAAAAAATTAT
* *
29661604 AATTAAATTTAAAAAAATTAT
1 AATTAGATTTTAAAAAATTAT
*
29661625 AATATAGTTTTT
1 AAT-TAGATTTT
29661637 GTTTCTATTT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (21 bp):
AATTAGATTTTAAAAAATTAT
Found at i:29664584 original size:27 final size:27
Alignment explanation
Indices: 29664554--29664640 Score: 129
Period size: 27 Copynumber: 3.2 Consensus size: 27
29664544 TAAACACGTT
*
29664554 ATGAAAGAAATGTCTTTGTGGTGAATC
1 ATGAAAGAAATGCCTTTGTGGTGAATC
*
29664581 ATGAAAGAAATGCCTTTGTGGCGAATC
1 ATGAAAGAAATGCCTTTGTGGTGAATC
* * *
29664608 ATGAAAGAAAAGCCTTGGTGGTGAATT
1 ATGAAAGAAATGCCTTTGTGGTGAATC
29664635 ATGAAA
1 ATGAAA
29664641 AGAATTCTGT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.37, C:0.09, G:0.26, T:0.28
Consensus pattern (27 bp):
ATGAAAGAAATGCCTTTGTGGTGAATC
Found at i:29683414 original size:47 final size:46
Alignment explanation
Indices: 29683080--29683509 Score: 389
Period size: 45 Copynumber: 9.4 Consensus size: 46
29683070 AGACCACAAC
** *
29683080 TGAAAGAGTCTATGGCATCATTATTC--AAA-TGAGTAAGACCATAGT
1 TGAAAGACACTATGGCATCA-TA-TCAGAAAGTGAATAAGACCATAGT
** * *
29683125 TGAAAGAGGCTATGGCATCATGATTCAG--A-TGAGTAAGACCGTAGT
1 TGAAAGACACTATGGCATCAT-A-TCAGAAAGTGAATAAGACCATAGT
* *
29683170 TGAAAGACAGTATGTCATCATATCAGAAAGTGAATAAGACCATAGT
1 TGAAAGACACTATGGCATCATATCAGAAAGTGAATAAGACCATAGT
* * * * *
29683216 T-AAAGACATTATGGAATCCTATCA-AAAATGGATAAGACCATAGT
1 TGAAAGACACTATGGCATCATATCAGAAAGTGAATAAGACCATAGT
* * * *
29683260 TGAAAGACACTGTGGCATTATATCAAAAAGTGAATAAGACCATAAT
1 TGAAAGACACTATGGCATCATATCAGAAAGTGAATAAGACCATAGT
* * * *
29683306 TGAAAGACACTATGGCAACCTATC-GAAAATGGATAAGACCATAGT
1 TGAAAGACACTATGGCATCATATCAGAAAGTGAATAAGACCATAGT
* *
29683351 TGAAAGACACACTATGGCATCATATCAGAAACTGAATAAGACCATGGT
1 TGAAAG--ACACTATGGCATCATATCAGAAAGTGAATAAGACCATAGT
* * * *
29683399 TAAAAGAAACTTATGGCATCATATCGGAAAGTGAATAAGACCATGGT
1 TGAAAGACAC-TATGGCATCATATCAGAAAGTGAATAAGACCATAGT
** * * * *
29683446 TGAAATTCATTATGGCATCA-AGTC-GAGAA-TAAATAAGATCATGGT
1 TGAAAGACACTATGGCATCATA-TCAGA-AAGTGAATAAGACCATAGT
29683491 TGAAAGACACTATGGCATC
1 TGAAAGACACTATGGCATC
29683510 CTTCAATCAT
Statistics
Matches: 322, Mismatches: 49, Indels: 28
0.81 0.12 0.07
Matches are distributed among these distances:
43 4 0.01
44 21 0.07
45 150 0.47
46 69 0.21
47 55 0.17
48 23 0.07
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.24
Consensus pattern (46 bp):
TGAAAGACACTATGGCATCATATCAGAAAGTGAATAAGACCATAGT
Found at i:29689814 original size:38 final size:39
Alignment explanation
Indices: 29689676--29689854 Score: 186
Period size: 40 Copynumber: 4.5 Consensus size: 39
29689666 CTCATTCAAT
* *
29689676 GCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACGAAT
1 GCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCAC-AAA
* *
29689716 GCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAA
1 GCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAA
29689755 GGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAA
1 -GCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAA
** * * *
29689795 -CCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACAAA
1 GCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACAAA
*
29689834 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
29689855 CAGCATTCAA
Statistics
Matches: 119, Mismatches: 12, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
37 5 0.04
38 18 0.15
39 13 0.11
40 80 0.67
41 3 0.03
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.23
Consensus pattern (39 bp):
GCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAA
Found at i:29689853 original size:78 final size:80
Alignment explanation
Indices: 29689676--29689854 Score: 210
Period size: 78 Copynumber: 2.3 Consensus size: 80
29689666 CTCATTCAAT
* *
29689676 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGACTTAACCCGGAATTA
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACGAATACCTTCGGGACTTAACCCGGAATTA
*
29689741 GTATCTCGCACAAAG
66 GTATCTAGCACAAAG
**
29689756 GCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCAC-AA-ACCTTC-GGATCTTAGTCCGG-AT
1 GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACGAATACCTTCGGGA-CTTAACCCGGAAT
29689816 ATAGTCA-CTTAGCACAAA-
64 -TAGT-ATC-TAGCACAAAG
*
29689834 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
29689855 CAGCATTCAA
Statistics
Matches: 88, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
77 5 0.06
78 38 0.43
79 15 0.17
80 30 0.34
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.23
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACGAATACCTTCGGGACTTAACCCGGAATTA
GTATCTAGCACAAAG
Found at i:29697542 original size:39 final size:40
Alignment explanation
Indices: 29697465--29697571 Score: 119
Period size: 40 Copynumber: 2.7 Consensus size: 40
29697455 TAGCTCCTCG
* * *
29697465 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATATTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATATAAACTCA
* *
29697505 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATATAAACTCA
**
29697544 CACGAATGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
29697572 ATTAGTATCT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
39 25 0.43
40 33 0.57
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATATAAACTCA
Found at i:29697635 original size:41 final size:41
Alignment explanation
Indices: 29697511--29697692 Score: 198
Period size: 40 Copynumber: 4.5 Consensus size: 41
29697501 CTCATTCAAT
* * * *
29697511 GCCTTCGGGACTTAACCCGG-ATT-TTAAAACTCGCACGAAT
1 GCCTTCGGGACTTAACCCGGAATTAGT-AATCTCGCACAAAG
29697551 GCCTTCGGGACTTAACCCGGAATTAGT-ATCTCGCACAAAG
1 GCCTTCGGGACTTAACCCGGAATTAGTAATCTCGCACAAAG
29697591 GCCTTCGGGACTTAACCCGGAATTAGTAATCTCGCACAAAG
1 GCCTTCGGGACTTAACCCGGAATTAGTAATCTCGCACAAAG
** * *
29697632 GCCTTC-GGATCTTAGTCCGG-ATATAGTCA-CTTAGCACAAA-
1 GCCTTCGGGA-CTTAACCCGGAAT-TAGTAATC-TCGCACAAAG
*
29697672 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
29697693 CAGCATTCAA
Statistics
Matches: 125, Mismatches: 9, Indels: 15
0.84 0.06 0.10
Matches are distributed among these distances:
40 78 0.62
41 46 0.37
42 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (41 bp):
GCCTTCGGGACTTAACCCGGAATTAGTAATCTCGCACAAAG
Found at i:29697676 original size:81 final size:81
Alignment explanation
Indices: 29697511--29697692 Score: 205
Period size: 81 Copynumber: 2.3 Consensus size: 81
29697501 CTCATTCAAT
* * *
29697511 GCCTTCGGGACTTAACCCGG-ATTTTAAAACTCGCACGAATGCCTTCGGGACTTAACCCGGAATT
1 GCCTTCGGGACTTAACCCGGAATTGTAAAACTCGCACAAAGGCCTTCGGGACTTAACCCGGAATT
*
29697575 AGTATCTCGCACAAAG
66 AGTATCTAGCACAAAG
* **
29697591 GCCTTCGGGACTTAACCCGGAATTAGT-AATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGG-A
1 GCCTTCGGGACTTAACCCGGAATT-GTAAAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGAA
29697653 TATAGTCA-CTTAGCACAAA-
64 T-TAGT-ATC-TAGCACAAAG
*
29697672 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
29697693 CAGCATTCAA
Statistics
Matches: 88, Mismatches: 8, Indels: 11
0.82 0.07 0.10
Matches are distributed among these distances:
80 25 0.28
81 53 0.60
82 10 0.11
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (81 bp):
GCCTTCGGGACTTAACCCGGAATTGTAAAACTCGCACAAAGGCCTTCGGGACTTAACCCGGAATT
AGTATCTAGCACAAAG
Found at i:29702422 original size:25 final size:25
Alignment explanation
Indices: 29702391--29702483 Score: 114
Period size: 25 Copynumber: 3.7 Consensus size: 25
29702381 AGCTGTAAAT
29702391 GGTAAGCTCCTCCGAGCTGAATAAC
1 GGTAAGCTCCTCCGAGCTGAATAAC
* * *
29702416 GGTAAGCTCTTCTGAGCTAAATAAC
1 GGTAAGCTCCTCCGAGCTGAATAAC
* * *
29702441 GGTAAACTCCTCCAAGCTGAATAAT
1 GGTAAGCTCCTCCGAGCTGAATAAC
* *
29702466 GGTAAGCTCATACGAGCT
1 GGTAAGCTCCTCCGAGCT
29702484 AAGCATCGGT
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 55 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.24
Consensus pattern (25 bp):
GGTAAGCTCCTCCGAGCTGAATAAC
Found at i:29702483 original size:50 final size:49
Alignment explanation
Indices: 29702374--29702544 Score: 137
Period size: 50 Copynumber: 3.4 Consensus size: 49
29702364 ACATGTATGT
** * * *
29702374 TCATACGAGCTGTAAATGGTAAGCTCCTCCGAGCTGAATAACGGTAAGC
1 TCATACGAGCTAAAAACGGTAAACTCCTCCAAGCTGAATAACGGTAAGC
* *
29702423 TC-TTCTGAGCTAAATAACGGTAAACTCCTCCAAGCTGAATAATGGTAAGC
1 TCATAC-GAGCTAAA-AACGGTAAACTCCTCCAAGCTGAATAACGGTAAGC
* * * * * * * ** *
29702473 TCATACGAGCTAAGCATCGGTAAGCTCATACGAGTTGAGCATCGGTAAGC
1 TCATACGAGCTAA-AAACGGTAAACTCCTCCAAGCTGAATAACGGTAAGC
* *
29702523 TCATAAGAGCTAAAATCGGTAA
1 TCATACGAGCTAAAAACGGTAA
29702545 CCCTAATGAC
Statistics
Matches: 97, Mismatches: 21, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
48 2 0.02
49 16 0.16
50 77 0.79
51 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.23
Consensus pattern (49 bp):
TCATACGAGCTAAAAACGGTAAACTCCTCCAAGCTGAATAACGGTAAGC
Found at i:29702494 original size:25 final size:25
Alignment explanation
Indices: 29702466--29702544 Score: 115
Period size: 25 Copynumber: 3.2 Consensus size: 25
29702456 GCTGAATAAT
29702466 GGTAAGCTCATACGAGCTAAGCATC
1 GGTAAGCTCATACGAGCTAAGCATC
* *
29702491 GGTAAGCTCATACGAGTTGAGCATC
1 GGTAAGCTCATACGAGCTAAGCATC
* *
29702516 GGTAAGCTCATAAGAGCTAA-AATC
1 GGTAAGCTCATACGAGCTAAGCATC
29702540 GGTAA
1 GGTAA
29702545 CCCTAATGAC
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
24 8 0.17
25 40 0.83
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (25 bp):
GGTAAGCTCATACGAGCTAAGCATC
Found at i:29710232 original size:25 final size:25
Alignment explanation
Indices: 29710195--29710279 Score: 98
Period size: 25 Copynumber: 3.4 Consensus size: 25
29710185 ATACGAGCTG
29710195 TAAACGGTAAGCTCCTCTAAGCTAAA
1 TAAA-GGTAAGCTCCTCTAAGCTAAA
** *
29710221 TAAAGGTAAGCTCCTCCGAGCTAGA
1 TAAAGGTAAGCTCCTCTAAGCTAAA
* * *
29710246 TAATGGTAAGCTCGTCTAAGCTGAA
1 TAAAGGTAAGCTCCTCTAAGCTAAA
*
29710271 TAACGGTAA
1 TAAAGGTAA
29710280 CCTCATACGA
Statistics
Matches: 49, Mismatches: 10, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
25 45 0.92
26 4 0.08
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (25 bp):
TAAAGGTAAGCTCCTCTAAGCTAAA
Found at i:29710291 original size:50 final size:49
Alignment explanation
Indices: 29710182--29710293 Score: 136
Period size: 50 Copynumber: 2.3 Consensus size: 49
29710172 TACATGTATG
*
29710182 CTCATACGAGCTGTAAACGGTAAGCTCCTCTAAGCTAAATAAAGGTAAG
1 CTCATACGAGCTGTAAACGGTAAGCTCCTCTAAGCTAAATAAAGGTAAC
* * * * * *
29710231 CTCCTCCGAGCTAG-ATAATGGTAAGCTCGTCTAAGCTGAATAACGGTAAC
1 CTCATACGAGCT-GTA-AACGGTAAGCTCCTCTAAGCTAAATAAAGGTAAC
29710281 CTCATACGAGCTG
1 CTCATACGAGCTG
29710294 AGCATCGATA
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
49 12 0.23
50 40 0.77
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.23
Consensus pattern (49 bp):
CTCATACGAGCTGTAAACGGTAAGCTCCTCTAAGCTAAATAAAGGTAAC
Found at i:29710306 original size:50 final size:50
Alignment explanation
Indices: 29710202--29710308 Score: 117
Period size: 50 Copynumber: 2.1 Consensus size: 50
29710192 CTGTAAACGG
* * * * *
29710202 TAAGCTCCTCTAAGCTAAATAAAGGTAAGCTCCTCCGAGCTAGATAATGG
1 TAAGCTCCTCTAAGCTAAATAAAGGTAACCTCATACGAGCTAGAGAATGA
* * * *
29710252 TAAGCTCGTCTAAGCTGAATAACGGTAACCTCATACGAGCT-GAGCATCGA
1 TAAGCTCCTCTAAGCTAAATAAAGGTAACCTCATACGAGCTAGAGAAT-GA
29710302 TAAGCTC
1 TAAGCTC
29710309 ATAAGAGCTG
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
49 4 0.09
50 43 0.91
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (50 bp):
TAAGCTCCTCTAAGCTAAATAAAGGTAACCTCATACGAGCTAGAGAATGA
Found at i:29710309 original size:25 final size:24
Alignment explanation
Indices: 29710281--29710328 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
29710271 TAACGGTAAC
* *
29710281 CTCATACGAGCTGAGCATCGATAAG
1 CTCATAAGAGCTGA-AATCGATAAG
29710306 CTCATAAGAGCTGAAATCGATAA
1 CTCATAAGAGCTGAAATCGATAA
29710329 CCATAATGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (24 bp):
CTCATAAGAGCTGAAATCGATAAG
Found at i:29715198 original size:20 final size:20
Alignment explanation
Indices: 29715173--29715215 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
29715163 TCTTTAATTT
*
29715173 CTTCTTTATTTACTCTCTTA
1 CTTCTTTACTTACTCTCTTA
*
29715193 CTTCTTTACTTACTTTCTTA
1 CTTCTTTACTTACTCTCTTA
29715213 CTT
1 CTT
29715216 AAATAACTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.26, G:0.00, T:0.60
Consensus pattern (20 bp):
CTTCTTTACTTACTCTCTTA
Found at i:29715590 original size:50 final size:52
Alignment explanation
Indices: 29715530--29715653 Score: 153
Period size: 56 Copynumber: 2.3 Consensus size: 52
29715520 CCATGTCATA
* *
29715530 TCCCACACATGGTCTTACGGGGGACCTCTCAT-CTC-GATGCCAATGCCATG
1 TCCCAAACATGGTCTTACGGGGGACCTCTCATACTCAAATGCCAATGCCATG
* * *
29715580 TCCTAGACATGGTCTTACGTGGGACCTCTCATAACCTCAATAATGCCAATGCCATG
1 TCCCAAACATGGTCTTACGGGGGACCTCTCAT-A-CTC-A-AATGCCAATGCCATG
29715636 TCCCAAACATGGTCTTAC
1 TCCCAAACATGGTCTTAC
29715654 ATGGGATCTC
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
50 29 0.47
53 3 0.05
56 30 0.48
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (52 bp):
TCCCAAACATGGTCTTACGGGGGACCTCTCATACTCAAATGCCAATGCCATG
Found at i:29715628 original size:56 final size:50
Alignment explanation
Indices: 29715427--29715659 Score: 153
Period size: 50 Copynumber: 4.6 Consensus size: 50
29715417 ATACCAAAGT
* ** * * * * *
29715427 CATGTCCCAAACATGGTCTTACATGGGATGTTTCTTGT-ACTACCAATGC
1 CATGTCCCAAACATGGTCTTACGTGGGACCTCTCATCTCAATGCCAATGC
* * * * * ** * * ** * *
29715476 CATATCTCAGATATGGTCTTACATGGGAGTTATCATATCGGTGCCCATGT
1 CATGTCCCAAACATGGTCTTACGTGGGACCTCTCATCTCAATGCCAATGC
* * * *
29715526 CATATCCCACACATGGTCTTACGGGGGACCTCTCATCTCGATGCCAATGC
1 CATGTCCCAAACATGGTCTTACGTGGGACCTCTCATCTCAATGCCAATGC
* *
29715576 CATGTCCTAGACATGGTCTTACGTGGGACCTCTCATAACCTCAATAATGCCAATGC
1 CATGTCCCAAACATGGTCTTACGTGGGACCTCTCAT---CTC---AATGCCAATGC
*
29715632 CATGTCCCAAACATGGTCTTACATGGGA
1 CATGTCCCAAACATGGTCTTACGTGGGA
29715660 TCTCATTCCT
Statistics
Matches: 143, Mismatches: 34, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
49 29 0.20
50 76 0.53
53 3 0.02
56 35 0.24
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.29
Consensus pattern (50 bp):
CATGTCCCAAACATGGTCTTACGTGGGACCTCTCATCTCAATGCCAATGC
Found at i:29719273 original size:39 final size:39
Alignment explanation
Indices: 29719214--29719300 Score: 165
Period size: 39 Copynumber: 2.2 Consensus size: 39
29719204 TAGTTTATTT
*
29719214 TAAGCTTTAGTTGTAGTATCCATGCATTACATGTAGCTG
1 TAAGTTTTAGTTGTAGTATCCATGCATTACATGTAGCTG
29719253 TAAGTTTTAGTTGTAGTATCCATGCATTACATGTAGCTG
1 TAAGTTTTAGTTGTAGTATCCATGCATTACATGTAGCTG
29719292 TAAGTTTTA
1 TAAGTTTTA
29719301 TTTGGATAAG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.41
Consensus pattern (39 bp):
TAAGTTTTAGTTGTAGTATCCATGCATTACATGTAGCTG
Found at i:29725072 original size:45 final size:45
Alignment explanation
Indices: 29725016--29725139 Score: 140
Period size: 45 Copynumber: 2.8 Consensus size: 45
29725006 TTATTCAGAT
* * * *
29725016 GAGTAAGACCATAGCTGAAAGACGTTATGGCCTCATTAATCAAAC
1 GAGTAAAACCATAGCTGAAAGACGCTATGGCATCATGAATCAAAC
* * * * * *
29725061 GAGTAATACCATAGCTGAAAGATGCTATGGTATCATGACTCAGAT
1 GAGTAAAACCATAGCTGAAAGACGCTATGGCATCATGAATCAAAC
* *
29725106 GAGTAAAACCATAGTTGAAAGACACTATGGCATC
1 GAGTAAAACCATAGCTGAAAGACGCTATGGCATC
29725140 CTATCGAAAA
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 65 1.00
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (45 bp):
GAGTAAAACCATAGCTGAAAGACGCTATGGCATCATGAATCAAAC
Found at i:29725170 original size:90 final size:88
Alignment explanation
Indices: 29725001--29725503 Score: 431
Period size: 91 Copynumber: 5.6 Consensus size: 88
29724991 AGAGCAGGTT
* ** * * * *
29725001 CATCATTATTCAGATGAGTAAGACCATAGCTGAAAGACGTTATGGCCTCATTAATC--AAACGAG
1 CATCA-TA-TCAGATGAGTAAGACCATAGTTGAAAGACACTATGGCATC-CT-ATCGAAAATGAA
* * **
29725064 TAATACCATAGCTGAAAGATGCTATGG
62 TAAGACCATAGTTGAAAGACACTATGG
* *
29725091 TATCATGACTCAGATGAGTAAAACCATAGTTGAAAGACACTATGGCATCCTATCGAAAATGAATA
1 CATCAT-A-TCAGATGAGTAAGACCATAGTTGAAAGACACTATGGCATCCTATCGAAAATGAATA
* *
29725156 AGACCAGAGTTGAAA-ACATTATGG
64 AGACCATAGTTGAAAGACACTATGG
* * * * *
29725180 CATCATATCAGAAAGTGAATAAGGCCATAGTT-AAAGACACTATGGCATCCTATCGAAGACGGAT
1 CATCATATCAG--A-TGAGTAAGACCATAGTTGAAAGACACTATGGCATCCTATCGAAAATGAAT
* *
29725244 AAAACCATAGTTGAAAGACACAATGG
63 AAGACCATAGTTGAAAGACACTATGG
* ** *
29725270 CATCATATCAGAAAGTGAATAAGACCATAGTTGAAAGACACTATACCATTCTATCGAAAATGAAT
1 CATCATATCAG--A-TGAGTAAGACCATAGTTGAAAGACACTATGGCATCCTATCGAAAATGAAT
29725335 AAGACCATAGTTGAAAGACACTATGG
63 AAGACCATAGTTGAAAGACACTATGG
* * * * * * *
29725361 CATCATATTGGAAAATGAATAAGACCATGGTTGAAAGACACTATGGCATCATGTCGGAAAGTGAA
1 CATCATA-T--CAGATGAGTAAGACCATAGTTGAAAGACACTATGGCATCCTATC-GAAAATGAA
* * *
29725426 TAAGACCATGGTTGAAAAACATTATGG
62 TAAGACCATAGTTGAAAGACACTATGG
* * * * *
29725453 CTTCA-AGTCGAGAATAAATAAGACCATGGTTGAAAGACATTATGGCATCCT
1 CATCATA-TC-AG-ATGAGTAAGACCATAGTTGAAAGACACTATGGCATCCT
29725504 TTAATCATTA
Statistics
Matches: 344, Mismatches: 55, Indels: 27
0.81 0.13 0.06
Matches are distributed among these distances:
87 4 0.01
88 4 0.01
89 57 0.17
90 112 0.33
91 128 0.37
92 38 0.11
94 1 0.00
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (88 bp):
CATCATATCAGATGAGTAAGACCATAGTTGAAAGACACTATGGCATCCTATCGAAAATGAATAAG
ACCATAGTTGAAAGACACTATGG
Found at i:29725308 original size:46 final size:45
Alignment explanation
Indices: 29725113--29725501 Score: 450
Period size: 45 Copynumber: 8.6 Consensus size: 45
29725103 GATGAGTAAA
* *
29725113 ACCATAGTTGAAAGACACTATGGCATCCTATCGAAAATGAATAAG
1 ACCATAGTTGAAAGACACTATGGCATCATATCGAAAGTGAATAAG
* *
29725158 ACCAGAGTTGAAA-ACATTATGGCATCATATCAGAAAGTGAATAAG
1 ACCATAGTTGAAAGACACTATGGCATCATATC-GAAAGTGAATAAG
* * *
29725203 GCCATAGTT-AAAGACACTATGGCATCCTATCGAAGACG-G-ATAAA
1 ACCATAGTTGAAAGACACTATGGCATCATATCGAA-A-GTGAATAAG
*
29725247 ACCATAGTTGAAAGACACAATGGCATCATATCAGAAAGTGAATAAG
1 ACCATAGTTGAAAGACACTATGGCATCATATC-GAAAGTGAATAAG
** *
29725293 ACCATAGTTGAAAGACACTATACCATTC-TATCGAAAATGAATAAG
1 ACCATAGTTGAAAGACACTATGGCA-TCATATCGAAAGTGAATAAG
* *
29725338 ACCATAGTTGAAAGACACTATGGCATCATATTGGAAAATGAATAAG
1 ACCATAGTTGAAAGACACTATGGCATCATA-TCGAAAGTGAATAAG
* *
29725384 ACCATGGTTGAAAGACACTATGGCATCATGTCGGAAAGTGAATAAG
1 ACCATAGTTGAAAGACACTATGGCATCATATC-GAAAGTGAATAAG
* * * * *
29725430 ACCATGGTTGAAAAACATTATGGCTTCA-AGTCGAGAA-TAAATAAG
1 ACCATAGTTGAAAGACACTATGGCATCATA-TCGA-AAGTGAATAAG
* *
29725475 ACCATGGTTGAAAGACATTATGGCATC
1 ACCATAGTTGAAAGACACTATGGCATC
29725502 CTTTAATCAT
Statistics
Matches: 299, Mismatches: 31, Indels: 28
0.84 0.09 0.08
Matches are distributed among these distances:
44 37 0.12
45 143 0.48
46 117 0.39
47 2 0.01
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.23
Consensus pattern (45 bp):
ACCATAGTTGAAAGACACTATGGCATCATATCGAAAGTGAATAAG
Found at i:29725353 original size:91 final size:91
Alignment explanation
Indices: 29725113--29725503 Score: 495
Period size: 91 Copynumber: 4.3 Consensus size: 91
29725103 GATGAGTAAA
* *
29725113 ACCATAGTTGAAAGACACTATGGCATCCTATCGAAAATGAATAAGACCAGAGTTGAAA-ACATTA
1 ACCATAGTTGAAAGACACTATGGCATCCTATCGAAAATGAATAAGACCATAGTTGAAAGACACTA
29725177 TGGCATCATATCAGAAAGTGAATAAG
66 TGGCATCATATCAGAAAGTGAATAAG
* * * * * *
29725203 GCCATAGTT-AAAGACACTATGGCATCCTATCGAAGACGGATAAAACCATAGTTGAAAGACACAA
1 ACCATAGTTGAAAGACACTATGGCATCCTATCGAAAATGAATAAGACCATAGTTGAAAGACACTA
29725267 TGGCATCATATCAGAAAGTGAATAAG
66 TGGCATCATATCAGAAAGTGAATAAG
** *
29725293 ACCATAGTTGAAAGACACTATACCATTCTATCGAAAATGAATAAGACCATAGTTGAAAGACACTA
1 ACCATAGTTGAAAGACACTATGGCATCCTATCGAAAATGAATAAGACCATAGTTGAAAGACACTA
** *
29725358 TGGCATCATATTGGAAAATGAATAAG
66 TGGCATCATATCAGAAAGTGAATAAG
* * * * * * *
29725384 ACCATGGTTGAAAGACACTATGGCATCATGTCGGAAAGTGAATAAGACCATGGTTGAAAAACATT
1 ACCATAGTTGAAAGACACTATGGCATCCTATC-GAAAATGAATAAGACCATAGTTGAAAGACACT
* *
29725449 ATGGCTTCA-AGTC-GAGAA-TAAATAAG
65 ATGGCATCATA-TCAGA-AAGTGAATAAG
* *
29725475 ACCATGGTTGAAAGACATTATGGCATCCT
1 ACCATAGTTGAAAGACACTATGGCATCCT
29725504 TTAATCATTA
Statistics
Matches: 261, Mismatches: 35, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
89 43 0.16
90 46 0.18
91 133 0.51
92 39 0.15
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (91 bp):
ACCATAGTTGAAAGACACTATGGCATCCTATCGAAAATGAATAAGACCATAGTTGAAAGACACTA
TGGCATCATATCAGAAAGTGAATAAG
Found at i:29729162 original size:30 final size:31
Alignment explanation
Indices: 29729103--29729162 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
29729093 CAGTTTCTAA
* *
29729103 GTGTGAACAAAAGGAAATGAGCAGGCCTTGT
1 GTGTGAACAAAAGAAAATGAACAGGCCTTGT
29729134 GTGTGAACACAAA-AAAATGAAC-GGCCTTG
1 GTGTGAACA-AAAGAAAATGAACAGGCCTTG
29729163 GTGAGGGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 7 0.27
31 16 0.62
32 3 0.12
ACGTcount: A:0.38, C:0.15, G:0.28, T:0.18
Consensus pattern (31 bp):
GTGTGAACAAAAGAAAATGAACAGGCCTTGT
Found at i:29731613 original size:15 final size:14
Alignment explanation
Indices: 29731578--29731623 Score: 60
Period size: 12 Copynumber: 3.4 Consensus size: 14
29731568 TTTTCAAACT
29731578 CTCTTTCTTTTT--
1 CTCTTTCTTTTTCA
*
29731590 CTTTTTCTTTTTCCA
1 CTCTTTCTTTTT-CA
29731605 CTCTTTCTTTTTCA
1 CTCTTTCTTTTTCA
29731619 CTCTT
1 CTCTT
29731624 AATTTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 11 0.38
14 7 0.24
15 11 0.38
ACGTcount: A:0.04, C:0.28, G:0.00, T:0.67
Consensus pattern (14 bp):
CTCTTTCTTTTTCA
Found at i:29731715 original size:11 final size:12
Alignment explanation
Indices: 29731699--29731731 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
29731689 TTTGTTGTTC
29731699 TTTTTCTTTC-A
1 TTTTTCTTTCGA
29731710 TTTTTCTTCTCGA
1 TTTTTCTT-TCGA
29731723 TTTTTCTTT
1 TTTTTCTTT
29731732 ACAAGATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 8 0.40
12 3 0.15
13 9 0.45
ACGTcount: A:0.06, C:0.18, G:0.03, T:0.73
Consensus pattern (12 bp):
TTTTTCTTTCGA
Found at i:29732621 original size:12 final size:13
Alignment explanation
Indices: 29732604--29732637 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
29732594 AATCACGTAC
29732604 AAATTTTTTTT-G
1 AAATTTTTTTTCG
29732616 AAATTTTTTTTCG
1 AAATTTTTTTTCG
29732629 -AATTTTTTT
1 AAATTTTTTT
29732638 AAATCACATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 20 0.95
13 1 0.05
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.68
Consensus pattern (13 bp):
AAATTTTTTTTCG
Found at i:29735064 original size:27 final size:27
Alignment explanation
Indices: 29734993--29735051 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
29734983 GAATAGGAGG
** * *
29734993 ATTAACACCCTGAACATTTGGATTATC
1 ATTAACACCAGGACCATTTAGATTATC
29735020 ATTAACACCAGGACCATTTAGATTATC
1 ATTAACACCAGGACCATTTAGATTATC
29735047 ATTAA
1 ATTAA
29735052 GACTGGGATC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.32
Consensus pattern (27 bp):
ATTAACACCAGGACCATTTAGATTATC
Found at i:29745798 original size:35 final size:35
Alignment explanation
Indices: 29745683--29745955 Score: 298
Period size: 35 Copynumber: 8.1 Consensus size: 35
29745673 TTCACTTGCC
* * *
29745683 TTTTCTTGCAGGGAATATTTCCTGTTCACGCATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
* * * * *
29745718 TTCTG-T--AGGGAATATTTCCTGTTCA--CTTGTC
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCAT-TA
*
29745749 TTTTTTTGCAGGGAATCTCTCCTGTTCACGCATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
* *
29745784 TTTTGTTGCAGGGAATCTCTCCTGTTTACACATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
* *
29745819 TTTTGTTGCAGGGAATCTTTCCTGTTCA--CATCA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
*
29745852 TTTT-TTGCAGGGAATCTCTCCTGTTCACGGATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
*
29745886 TTTTGTTGCAGGGAATCTCTCCTGTTCA--CATCA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
* * *
29745919 -TTTCTTGCAGGGAATCTCTCCTGTTCATGTATTA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
29745953 TTT
1 TTT
29745956 CTTTTTGGAC
Statistics
Matches: 202, Mismatches: 24, Indels: 24
0.81 0.10 0.10
Matches are distributed among these distances:
30 2 0.01
31 4 0.02
32 68 0.34
33 11 0.05
34 28 0.14
35 87 0.43
36 2 0.01
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.43
Consensus pattern (35 bp):
TTTTGTTGCAGGGAATCTCTCCTGTTCACGCATTA
Found at i:29745873 original size:67 final size:67
Alignment explanation
Indices: 29745683--29745943 Score: 303
Period size: 67 Copynumber: 3.9 Consensus size: 67
29745673 TTCACTTGCC
* * * * * * * * *
29745683 TTTTCTTGCAGGGAATATTTCCTGTTCAC-GCATTATTCTGTAGGGAATATTTCCTG-TT-CACT
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACATCATT-TTTTGCAGGGAATCTCTCCTGTTTACACA
*
29745745 TGTC
65 T-TA
* *
29745749 TTTTTTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTCTCCTGTTTACA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCA--CATCATTTT-TTGCAGGGAATCTCTCCTGTTTACA
29745814 CATTA
63 CATTA
* * **
29745819 TTTTGTTGCAGGGAATCTTTCCTGTTCACATCATTTTTTGCAGGGAATCTCTCCTGTTCACGGAT
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACATCATTTTTTGCAGGGAATCTCTCCTGTTTACACAT
29745884 TA
66 TA
*
29745886 TTTTGTTGCAGGGAATCTCTCCTGTTCACATCATTTCTTGCAGGGAATCTCTCCTGTT
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACATCATTTTTTGCAGGGAATCTCTCCTGTT
29745944 CATGTATTAT
Statistics
Matches: 170, Mismatches: 19, Indels: 11
0.85 0.09 0.05
Matches are distributed among these distances:
66 25 0.15
67 83 0.49
68 11 0.06
69 18 0.11
70 29 0.17
71 4 0.02
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.43
Consensus pattern (67 bp):
TTTTGTTGCAGGGAATCTCTCCTGTTCACATCATTTTTTGCAGGGAATCTCTCCTGTTTACACAT
TA
Found at i:29749946 original size:22 final size:23
Alignment explanation
Indices: 29749921--29749980 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
29749911 TGGACTGAAT
29749921 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
29749943 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
29749965 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
29749981 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:29749948 original size:4 final size:4
Alignment explanation
Indices: 29749930--29749963 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
29749920 TATAAAAATT
29749930 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
29749964 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:29753946 original size:22 final size:23
Alignment explanation
Indices: 29753921--29753980 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
29753911 TGGACTGAAT
29753921 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
29753943 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
29753965 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
29753981 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:29753948 original size:4 final size:4
Alignment explanation
Indices: 29753930--29753963 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
29753920 TATAAAAATT
29753930 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
29753964 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:29757968 original size:17 final size:17
Alignment explanation
Indices: 29757937--29757969 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
29757927 TAACGCAAGG
29757937 GACCTTTTCATGATCCC
1 GACCTTTTCATGATCCC
29757954 GACCTGTTTCA-GATCC
1 GACCT-TTTCATGATCC
29757970 GTCACTGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.18, C:0.33, G:0.15, T:0.33
Consensus pattern (17 bp):
GACCTTTTCATGATCCC
Found at i:29768616 original size:25 final size:24
Alignment explanation
Indices: 29768588--29768639 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
29768578 CTGAATAATA
* *
29768588 GTAAGCTCATATGAGCTGAGCATCG
1 GTAAGCTCATAAGAGCT-AACATCG
29768613 GTAAGCTCATAAGAGCTAACATCG
1 GTAAGCTCATAAGAGCTAACATCG
29768637 GTA
1 GTA
29768640 GCCCTAATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 9 0.36
25 16 0.64
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (24 bp):
GTAAGCTCATAAGAGCTAACATCG
Found at i:29770078 original size:69 final size:68
Alignment explanation
Indices: 29769955--29770082 Score: 193
Period size: 69 Copynumber: 1.9 Consensus size: 68
29769945 AGTTTAATAG
* * *
29769955 TAAATTTAATTTAATACTTATCTTAATAGTATTTTATTAATTTAATATTAAAGTGATTATCTTAA
1 TAAATTAAATTTAATACTTATCTTAATAATATTATATTAATTTAATATTAAAGTGATTATCTTAA
29770020 AAT
66 AAT
** *
29770023 TAAATTAAATTTAATGTTTATCTTGATAAATATTATATTAATTTAATATTAAAGTGATTA
1 TAAATTAAATTTAATACTTATCTTAAT-AATATTATATTAATTTAATATTAAAGTGATTA
29770083 AGTTTATCAT
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
68 23 0.43
69 30 0.57
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.49
Consensus pattern (68 bp):
TAAATTAAATTTAATACTTATCTTAATAATATTATATTAATTTAATATTAAAGTGATTATCTTAA
AAT
Found at i:29791353 original size:533 final size:537
Alignment explanation
Indices: 29790339--29791412 Score: 1575
Period size: 533 Copynumber: 2.0 Consensus size: 537
29790329 TGTGACGTAT
* * * *
29790339 AGATATTCTGGTGTTGCTTTGGAACTCACTAAGTTTTATAAACTTACTTCGTTTATCTTCCCTTC
1 AGATATTCTGATGTTGCTTTGGAACTCACTAAGTTCTATAAACTTACTCCGTTGATCTTCCCTTC
* * *
29790404 TCAAGACCATTAAAGAAATAAATGAACCTTCAAGGAATACGCCAGAGGATATATTGTGTGTGAGG
66 TCAAGACCATTAAAGAAATAAAGGAACCTTCAAGGAATACGCCAGAGGATATATTATGTGTAAGG
*
29790469 CTTATAGTGATTTTGTATTATGCATGACAAATGAGAGTAGCATCAAGGCTTGAAATATGATAAAC
131 CTTATAGTGATTTTGTATTATGCATG---AA-GAGAGTAGCATCAAGGCTTGAAATATGAGAAAC
* * *
29790534 AATATTTTGTAACTAAAATTGTATCCACCAAATGGCGTCCTTTCCTTAGATCTTCATAATGAACA
192 AATATTTTGTAACTAAAATTGTATCCACCAAATGGCGTCCTCTCCTTAAATCTTCACAATGAACA
* * *
29790599 TTTGTGTTTTAAAGGTGTTTAGGCCCTAAAGTTTAAAAGTTTTATTTATTACTACTATAGCAAAT
257 TTTGTGTTTTAAAGGTGTTTAGGCCCTAAAGTCTAAAAGTTTTATTTACTACTACTATAGCAAAC
* ** *
29790664 ACCTTTTGTTCTTTTGTAAACTTGAGATTTTGCCAATTTCGTTACAGTAAGGAAAGGCTTCAAAG
322 ACCTTTTGCTCTTTTGTAAACTTGAGATTCCGCCAATTTCGTAACAGTAAGGAAAGGCTTCAAAG
* * ** * *
29790729 TTGTAACACACCACTCCTGGATCCTCCTTAAGGGTCGGGGATGGGGCGCTACAACTGAAAACTTG
387 TTGTAACACACCACTCCTGGATCCTCCTTAAAGGTCAGGGATCAGGCACTACAACCGAAAACTTG
29790794 TAACCTTGCACTTTTTGGATTAGTCACTA-ACACATGATAGATGAAAAACATGGCCCTCTTGTGT
452 TAACCTTGCACTTTTTGGATTAGTCACTAGA-ACATGATAGATGAAAAACATGGCCCTCTTGTGT
29790858 AATCGAAAAGTAATGTGGTCAC
516 AATCGAAAAGTAATGTGGTCAC
*
29790880 AGATATTCTGATGTTGCTTTGGAACTCACTAAGTTCTATGAACTTACTCCGTTGATCTTCCCTTC
1 AGATATTCTGATGTTGCTTTGGAACTCACTAAGTTCTATAAACTTACTCCGTTGATCTTCCCTTC
* * * * * * *
29790945 TCAGGACCCTTGAAGAAATAAAGGAACCTTTACA-GACTACTCTAGAGGATATATTATGTGTAAG
66 TCAAGACCATTAAAGAAATAAAGGAACCTTCA-AGGAATACGCCAGAGGATATATTATGTGTAAG
* *
29791009 GCTTATAGTGATTTTGTATTATGCATG-A-A-AGTGGCATCAAGGCTTGAAATCTGAGAAACAAT
130 GCTTATAGTGATTTTGTATTATGCATGAAGAGAGTAGCATCAAGGCTTGAAATATGAGAAACAAT
* * * * *
29791071 ATTTTGTAACTAAAATTGTATCCGCTAAAT-TCGTCCTCTCCTTAAATCTTTACAATGAACTTTT
195 ATTTTGTAACTAAAATTGTATCCACCAAATGGCGTCCTCTCCTTAAATCTTCACAATGAACATTT
* * * *
29791135 GTGTTTTAAAGGTGTTTGGGCCCTTAAGTCTAAAAGTTTTATTTACTACTGCTATAGCAAACGCC
260 GTGTTTTAAAGGTGTTTAGGCCCTAAAGTCTAAAAGTTTTATTTACTACTACTATAGCAAACACC
**
29791200 TTTTGCTCTTTTGTAAACTTGAGATTCCGCCAATTTCGTAATTGTAAGGAAAGGCTTCAAAGTTG
325 TTTTGCTCTTTTGTAAACTTGAGATTCCGCCAATTTCGTAACAGTAAGGAAAGGCTTCAAAGTTG
** * * * **
29791265 TAATGCACCATTCTTGGATCCTCCTTAAAGGTCAGGGATCAGGCACTACAGCCGGGAACTTGTAA
390 TAACACACCACTCCTGGATCCTCCTTAAAGGTCAGGGATCAGGCACTACAACCGAAAACTTGTAA
*
29791330 CCTTGCACTTTTTGGATTAGTCACTAGAACATGATAGATGGAAAACATGGCCCTCTTGTGTAATC
455 CCTTGCACTTTTTGGATTAGTCACTAGAACATGATAGATGAAAAACATGGCCCTCTTGTGTAATC
29791395 GAAAAGTAATGTGGTCAC
520 GAAAAGTAATGTGGTCAC
29791413 GGTTATTTGT
Statistics
Matches: 478, Mismatches: 53, Indels: 12
0.88 0.10 0.02
Matches are distributed among these distances:
533 277 0.58
534 59 0.12
535 1 0.00
537 1 0.00
541 139 0.29
542 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (537 bp):
AGATATTCTGATGTTGCTTTGGAACTCACTAAGTTCTATAAACTTACTCCGTTGATCTTCCCTTC
TCAAGACCATTAAAGAAATAAAGGAACCTTCAAGGAATACGCCAGAGGATATATTATGTGTAAGG
CTTATAGTGATTTTGTATTATGCATGAAGAGAGTAGCATCAAGGCTTGAAATATGAGAAACAATA
TTTTGTAACTAAAATTGTATCCACCAAATGGCGTCCTCTCCTTAAATCTTCACAATGAACATTTG
TGTTTTAAAGGTGTTTAGGCCCTAAAGTCTAAAAGTTTTATTTACTACTACTATAGCAAACACCT
TTTGCTCTTTTGTAAACTTGAGATTCCGCCAATTTCGTAACAGTAAGGAAAGGCTTCAAAGTTGT
AACACACCACTCCTGGATCCTCCTTAAAGGTCAGGGATCAGGCACTACAACCGAAAACTTGTAAC
CTTGCACTTTTTGGATTAGTCACTAGAACATGATAGATGAAAAACATGGCCCTCTTGTGTAATCG
AAAAGTAATGTGGTCAC
Done.