Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
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: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 37 of 153
Found at i:12576620 original size:13 final size:14
Alignment explanation
Indices: 12576590--12576630 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
12576580 TTCGCCATTA
12576590 TTTTC-TTTTGTCT
1 TTTTCTTTTTGTCT
*
12576603 GTTTCTTTTTGT-T
1 TTTTCTTTTTGTCT
12576616 TTTTCTTCTTTGTCT
1 TTTTCTT-TTTGTCT
12576631 ACTGCTATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 11 0.48
14 11 0.48
15 1 0.04
ACGTcount: A:0.00, C:0.15, G:0.10, T:0.76
Consensus pattern (14 bp):
TTTTCTTTTTGTCT
Found at i:12577158 original size:44 final size:44
Alignment explanation
Indices: 12577103--12577404 Score: 211
Period size: 44 Copynumber: 6.8 Consensus size: 44
12577093 TCATCGTTTT
* *
12577103 AATCTACTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTC
* * * * *
12577147 AACCTGTTCCACTACAACTTCAGGGAGATAAGGTT--T-GATAT-
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCT-TC
* * * * * * *
12577188 GATGC-GTTCTACTACAACTCCAGAGAGATAAGATCTGTTATTTAGCTTC
1 AAT-CTGCTCCACTGCAACTTCAGGGAGATAAGA----TTA-GTAGCTTC
* * * * *
12577237 AATCTGTTCCACTGCAACTTCAAGGAAATAAGATTTGCTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAG-TAGCTTC
* * * *
12577282 AGTTTGCTCCACTGCAACTTTAGGGAGATAAGACTT-GTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTAGTAGCTTC
* * * *
12577326 AATCTGCCCCACTGCAACTTTAGGGGGATAAGATTAGTGGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTC
* * *
12577370 ATTCTGCTCCACTGCAATTTTAGGGAGATAAGATT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
12577405 CGCCATTGTA
Statistics
Matches: 203, Mismatches: 40, Indels: 30
0.74 0.15 0.11
Matches are distributed among these distances:
41 27 0.13
42 3 0.01
43 2 0.01
44 102 0.50
45 38 0.19
46 2 0.01
48 3 0.01
49 26 0.13
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTC
Found at i:12577466 original size:50 final size:50
Alignment explanation
Indices: 12577377--12578380 Score: 530
Period size: 50 Copynumber: 20.1 Consensus size: 50
12577367 TTCATTCTGC
* * * * * *
12577377 TCCACTGCAATTTTAGGGAGATAAGATTCGCCATTGTAGCTTCAATCTAT
1 TCCACTGCAATGTCAGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTAT
** * * * **
12577427 TTAACTGTAATGTCGGGGAAACAAGATTCGTCGTCGTAGCTTCAATCTGC
1 TCCACTGCAATGTCAGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTAT
* * * * * * * *
12577477 TCCACTGCAATTTCAGGGAGATAAGATTCGTCATTGTAGTTTCAATTTAT
1 TCCACTGCAATGTCAGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTAT
** * * * * * *
12577527 TTAACTACAATTTCGGGGAAACAAGATTCACCGTCGTAGCATCAATCTGT
1 TCCACTGCAATGTCAGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTAT
* ** * ** * ** *
12577577 TCCACTACACCG-CTAGGTAAGTAAGATTTGCCGTTATAGCTTCAATAT-T
1 TCCACTGCAATGTC-AGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTAT
** * * *
12577626 TTAACTGCAATGTC-GGGAAAACAAGATTCACTGTCGTAGCTTCAATCTGT
1 TCCACTGCAATGTCAGGG-AAACAAGATTCGCCGTCGTAGCTTCAATCTAT
* * ** * * ** ** *
12577676 TCCATTACACCGCCAGGTAAGTAAGATTCGCCGTTATAGCTTCAATATAT
1 TCCACTGCAATGTCAGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTAT
** *
12577726 TTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTAT
1 TCCACTGCAATGTCAGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTAT
* **** * * *
12577776 TCCACTACACCACCAGGGAAACAAGATTCACCGTCGTAGCTTCAGTCTGT
1 TCCACTGCAATGTCAGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTAT
* * *** * *
12577826 TCCACTAC-ATCGCCAGGGAGGTAAGATTTGCCGTC-TAGCTTCAATATAT
1 TCCACTGCAAT-GTCAGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTAT
** ** * * *
12577875 TTAACTGCAATGTTGGGGAAACAAGATTCGCCGTTGTAGCTTCAATATGT
1 TCCACTGCAATGTCAGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTAT
* ** * * *** *
12577925 TCCACTACACCGCCAGGGAAGCAAGATTCATTGTCGTAGCTTCAATCTGT
1 TCCACTGCAATGTCAGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTAT
**** * ** *
12577975 TCCAC-GACACCACCAGAGAAGTAAGATTCGCCGTTGTAGCTTCAATCTAT
1 TCCACTG-CAATGTCAGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTAT
** * * *
12578025 TTAACTGCAATGTCATGGAAACAAGATTCGTCGTCGTAGCTTCAATCTGT
1 TCCACTGCAATGTCAGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTAT
* **** *** * * * *
12578075 TCCACTACACCACCAGGGAGGTAAGGTTTGCCATTGTAGCTTCAATCTAT
1 TCCACTGCAATGTCAGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTAT
** * * * * *
12578125 TTAACTACAATGTCGGGGAAACAAGATTCGCCATCGTAGCTTCAATTTGT
1 TCCACTGCAATGTCAGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTAT
* ** * *** * *
12578175 TCCACTACACCGCCAGGGAGGTAAGACTCGCCGTTGTAGCTTCAATCTAT
1 TCCACTGCAATGTCAGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTAT
** * * * *
12578225 TTAACTGCAATATC-GGGAAAACAAGATTCGCCATCATAGCTTCAATCTGT
1 TCCACTGCAATGTCAGGG-AAACAAGATTCGCCGTCGTAGCTTCAATCTAT
* ** * *** * * *
12578275 TCCACTACACCGCCAGGGAGGTAAGATTTGCCGTTGTAACTTCAATCTAT
1 TCCACTGCAATGTCAGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTAT
* * * ** *
12578325 T-TACCTGTAATGTCGGGGAAACAAGATTCAACGTCGTAGCTTCAATCTGT
1 TCCA-CTGCAATGTCAGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTAT
12578375 TCCACT
1 TCCACT
12578381 ACACTGCTAG
Statistics
Matches: 677, Mismatches: 263, Indels: 28
0.70 0.27 0.03
Matches are distributed among these distances:
48 2 0.00
49 67 0.10
50 601 0.89
51 7 0.01
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (50 bp):
TCCACTGCAATGTCAGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTAT
Found at i:12577827 original size:249 final size:250
Alignment explanation
Indices: 12577542--12578293 Score: 952
Period size: 249 Copynumber: 3.0 Consensus size: 250
12577532 TACAATTTCG
* * * *
12577542 GGGAAACAAGATTCACCGTCGTAGCATCAATCTGTTCCACTACACCGCTAGGTAAGTAAGATTTG
1 GGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAGGTAAGATTTG
* * *
12577607 CCGTTATAGCTTCAATAT-TTTAACTGCAATGTCGGGAAAACAAGATTCACTGTCGTAGCTTCAA
66 CCGTTATAGCTTCAATATATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAA
* * * * *
12577671 TCTGTTCCATTACACCGCCAGGTAAGTAAGATTCGCCGTTATAGCTTCAATATATTTAACTGCAA
131 TATGTTCCACTACACCGCCAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTATTTAACTGCAA
* *
12577736 TGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTATTCCACTACACCACCA
196 TATCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTATTCCACTACACCGCCA
* *
12577791 GGGAAACAAGATTCACCGTCGTAGCTTCAGTCTGTTCCACTACATCGCCAGGGAGGTAAGATTTG
1 GGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAGGTAAGATTTG
* * *
12577856 CCG-TCTAGCTTCAATATATTTAACTGCAATGTTGGGGAAACAAGATTCGCCGTTGTAGCTTCAA
66 CCGTTATAGCTTCAATATATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAA
* *** * * **
12577920 TATGTTCCACTACACCGCCAGGGAAGCAAGATTCATTGTCGTAGCTTCAATCTGTTCCAC-GACA
131 TATGTTCCACTACACCGCCAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTATTTAACTG-CA
** * * * ** * ** * ** *
12577984 CCACCAGAGAAGTAAGATTCGCCGTTGTAGCTTCAATCTATTTAACTGCAATGTCA
195 ATATCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTATTCCACTACACCGCCA
* ** * *
12578040 TGGAAACAAGATTCGTCGTCGTAGCTTCAATCTGTTCCACTACACCACCAGGGAGGTAAGGTTTG
1 GGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAGGTAAGATTTG
* * * * *
12578105 CCATTGTAGCTTCAATCTATTTAACTACAATGTCGGGGAAACAAGATTCGCCATCGTAGCTTCAA
66 CCGTTATAGCTTCAATATATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAA
* * *
12578170 TTTGTTCCACTACACCGCCAGGGAGGTAAGACTCGCCGTTGTAGCTTCAATCTATTTAACTGCAA
131 TATGTTCCACTACACCGCCAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTATTTAACTGCAA
* * * *
12578235 TATCGGGAAAACAAGATTCGCCATCATAGCTTCAATCTGTTCCACTACACCGCCA
196 TATCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTATTCCACTACACCGCCA
12578290 GGGA
1 GGGA
12578294 GGTAAGATTT
Statistics
Matches: 414, Mismatches: 85, Indels: 7
0.82 0.17 0.01
Matches are distributed among these distances:
248 14 0.03
249 252 0.61
250 147 0.36
251 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (250 bp):
GGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAGGTAAGATTTG
CCGTTATAGCTTCAATATATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAA
TATGTTCCACTACACCGCCAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTATTTAACTGCAA
TATCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTATTCCACTACACCGCCA
Found at i:12577828 original size:150 final size:150
Alignment explanation
Indices: 12577644--12578384 Score: 784
Period size: 150 Copynumber: 4.9 Consensus size: 150
12577634 AATGTCGGGA
* * *
12577644 AAACAAGATTCACTGTCGTAGCTTCAATCTGTTCCATTACACCGCCAGGTAAGTAAGATTCGCCG
1 AAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATTCGCCG
*
12577709 TTATAGCTTCAATATATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCT
66 TTGTAGCTTCAATATATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCT
*
12577774 ATTCCACTACACCACCAGGG
131 GTTCCACTACACCACCAGGG
* * * *
12577794 AAACAAGATTCACCGTCGTAGCTTCAGTCTGTTCCACTACATCGCCAGGGAGGTAAGATTTGCCG
1 AAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATTCGCCG
* * * *
12577859 -TCTAGCTTCAATATATTTAACTGCAATGTTGGGGAAACAAGATTCGCCGTTGTAGCTTCAATAT
66 TTGTAGCTTCAATATATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCT
*
12577923 GTTCCACTACACCGCCAGGG
131 GTTCCACTACACCACCAGGG
* ** * * *
12577943 AAGCAAGATTCATTGTCGTAGCTTCAATCTGTTCCACGACACCACCAGAGAAGTAAGATTCGCCG
1 AAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATTCGCCG
* ** *
12578008 TTGTAGCTTCAATCTATTTAACTGCAATGTCATGGAAACAAGATTCGTCGTCGTAGCTTCAATCT
66 TTGTAGCTTCAATATATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCT
12578073 GTTCCACTACACCACCAGGG
131 GTTCCACTACACCACCAGGG
*** * ** * * * ** ** * * ** *
12578093 AGGTAAGGTTTGCCATTGTAGCTTCAATCTATTTAACTACAATGTCGGGGAAACAAGATTCGCCA
1 AAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATTCGCCG
* * * ** * ** * * *** * *
12578158 TCGTAGCTTCAATTTGTTCCACTACACCGCCAGGGAGGTAAGACTCGCCGTTGTAGCTTCAATCT
66 TTGTAGCTTCAATATATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCT
* ** * ** *
12578223 ATTTAACTGCAATATC-GGG
131 GTTCCACTACACCACCAGGG
* * * * *
12578242 AAAACAAGATTCGCCATCATAGCTTCAATCTGTTCCACTACACCGCCAGGGAGGTAAGATTTGCC
1 -AAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATTCGCC
* * * * **
12578307 GTTGTAACTTCAATCTATTTACCTGTAATGTCGGGGAAACAAGATTCAACGTCGTAGCTTCAATC
65 GTTGTAGCTTCAATATATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATC
12578372 TGTTCCACTACAC
130 TGTTCCACTACAC
12578385 TGCTAGGGAG
Statistics
Matches: 468, Mismatches: 121, Indels: 4
0.79 0.20 0.01
Matches are distributed among these distances:
149 136 0.29
150 332 0.71
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (150 bp):
AAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATTCGCCG
TTGTAGCTTCAATATATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCT
GTTCCACTACACCACCAGGG
Found at i:12578436 original size:100 final size:100
Alignment explanation
Indices: 12577391--12578425 Score: 1068
Period size: 100 Copynumber: 10.4 Consensus size: 100
12577381 CTGCAATTTT
* * *
12577391 AGGGAGATAAGATTCGCCATTGTAGCTTCAATCTATTTAACTGTAATGTCGGGGAAACAAGATTC
1 AGGGAGGTAAGATTCGCCGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTC
* * * ****
12577456 GTCGTCGTAGCTTCAATCTGCTCCACTGCAATTTC
66 GCCGTCGTAGCTTCAATCTGTTCCACTACACCGCC
* * * * * * *
12577491 AGGGAGATAAGATTCGTCATTGTAGTTTCAATTTATTTAACTACAATTTCGGGGAAACAAGATTC
1 AGGGAGGTAAGATTCGCCGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTC
* * *
12577556 ACCGTCGTAGCATCAATCTGTTCCACTACACCGCT
66 GCCGTCGTAGCTTCAATCTGTTCCACTACACCGCC
* * * * * *
12577591 AGGTAAGTAAGATTTGCCGTTATAGCTTCAATAT-TTTAACTGCAATGTCGGGAAAACAAGATTC
1 AGGGAGGTAAGATTCGCCGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTC
* * *
12577655 ACTGTCGTAGCTTCAATCTGTTCCATTACACCGCC
66 GCCGTCGTAGCTTCAATCTGTTCCACTACACCGCC
* * * *
12577690 AGGTAAGTAAGATTCGCCGTTATAGCTTCAATATATTTAACTGCAATGTCGGGGAAACAAGATTC
1 AGGGAGGTAAGATTCGCCGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTC
* *
12577755 GCCGTCGTAGCTTCAATCTATTCCACTACACCACC
66 GCCGTCGTAGCTTCAATCTGTTCCACTACACCGCC
*** * * * * ** * * * ***
12577790 AGGGAAACAAGATTCACCGTCGTAGCTTCAGTCTGTTCCACTAC-ATCGCCAGGGAGGTAAGATT
1 AGGGAGGTAAGATTCGCCGTTGTAGCTTCAATCTATTTAACTGCAAT-GTCGGGGAAACAAGATT
* * * ** * ** **
12577854 TGCCGTC-TAGCTTCAATATATTTAACTGCAATGTT
65 CGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCC
* *** * * ** * ** * * *
12577889 GGGGAAACAAGATTCGCCGTTGTAGCTTCAATATGTTCCACTACACCGCCAGGGAAGCAAGATTC
1 AGGGAGGTAAGATTCGCCGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTC
*** * *
12577954 ATTGTCGTAGCTTCAATCTGTTCCACGACACCACC
66 GCCGTCGTAGCTTCAATCTGTTCCACTACACCGCC
* * **
12577989 AGAGAAGTAAGATTCGCCGTTGTAGCTTCAATCTATTTAACTGCAATGTCATGGAAACAAGATTC
1 AGGGAGGTAAGATTCGCCGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTC
* *
12578054 GTCGTCGTAGCTTCAATCTGTTCCACTACACCACC
66 GCCGTCGTAGCTTCAATCTGTTCCACTACACCGCC
* * * *
12578089 AGGGAGGTAAGGTTTGCCATTGTAGCTTCAATCTATTTAACTACAATGTCGGGGAAACAAGATTC
1 AGGGAGGTAAGATTCGCCGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTC
* *
12578154 GCCATCGTAGCTTCAATTTGTTCCACTACACCGCC
66 GCCGTCGTAGCTTCAATCTGTTCCACTACACCGCC
* * *
12578189 AGGGAGGTAAGACTCGCCGTTGTAGCTTCAATCTATTTAACTGCAATATCGGGAAAACAAGATTC
1 AGGGAGGTAAGATTCGCCGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTC
* *
12578254 GCCATCATAGCTTCAATCTGTTCCACTACACCGCC
66 GCCGTCGTAGCTTCAATCTGTTCCACTACACCGCC
* * * *
12578289 AGGGAGGTAAGATTTGCCGTTGTAACTTCAATCTATTTACCTGTAATGTCGGGGAAACAAGATTC
1 AGGGAGGTAAGATTCGCCGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTC
** * *
12578354 AACGTCGTAGCTTCAATCTGTTCCACTACACTGCT
66 GCCGTCGTAGCTTCAATCTGTTCCACTACACCGCC
* * * *
12578389 AGGGAGGTAAGATTCGTCGTTATAACTTCAATTTATT
1 AGGGAGGTAAGATTCGCCGTTGTAGCTTCAATCTATT
12578426 CCACTGTAAT
Statistics
Matches: 786, Mismatches: 145, Indels: 8
0.84 0.15 0.01
Matches are distributed among these distances:
99 169 0.22
100 617 0.78
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (100 bp):
AGGGAGGTAAGATTCGCCGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTC
GCCGTCGTAGCTTCAATCTGTTCCACTACACCGCC
Found at i:12579374 original size:45 final size:45
Alignment explanation
Indices: 12579302--12579388 Score: 102
Period size: 45 Copynumber: 1.9 Consensus size: 45
12579292 AGCTCGGAAT
* * * *
12579302 GAATGAATTAATCAAGATAGCAAATTTTGCTAGAATACAAAATGA
1 GAATAAATTAATCAAGATAGCAAATTTTACCAAAATACAAAATGA
* ***
12579347 GAATAAATTAATCAAGATGGTGTATTTTACCAAAATACAAAA
1 GAATAAATTAATCAAGATAGCAAATTTTACCAAAATACAAAA
12579389 ATGAATAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 34 1.00
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.28
Consensus pattern (45 bp):
GAATAAATTAATCAAGATAGCAAATTTTACCAAAATACAAAATGA
Found at i:12587777 original size:40 final size:40
Alignment explanation
Indices: 12587732--12587901 Score: 288
Period size: 40 Copynumber: 4.2 Consensus size: 40
12587722 GTTTGAATAA
* *
12587732 AAAACGCCGCTAAAAATTGAGCATTAGCGGCGCTTTATAT
1 AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTATAT
*
12587772 AAAACGCAGCTAAAGATCGAGCATTAGCGGCGCTTTATAT
1 AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTATAT
12587812 AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTATAT
1 AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTATAT
*
12587852 AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTA-AGG
1 AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTATA-T
12587892 AAAACGCCGC
1 AAAACGCCGC
12587902 AAAAAACCTA
Statistics
Matches: 124, Mismatches: 5, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
39 1 0.01
40 123 0.99
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.21
Consensus pattern (40 bp):
AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTATAT
Found at i:12587992 original size:41 final size:41
Alignment explanation
Indices: 12587935--12588169 Score: 321
Period size: 42 Copynumber: 5.7 Consensus size: 41
12587925 CCTTTCAGGC
*
12587935 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTAAGGG
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTAAGGG
* *
12587976 CTTTAGTC-GCGTTTTTGGAGAAGCGCCGCTAATGCTCAGGGG
1 CTTTAG-CGGCGTTTTTGGAAAAGCGCCGCTAATGCT-AAGGG
* * * *
12588018 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGATCAGCG
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTAAGGG
* *
12588059 CTTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGCTCAGGGG
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCT-AAGGG
* *
12588101 ATTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCA-GG
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTAAGGG
*
12588141 CTTTAGCGGCGTTTTTGTAAAAGCGCCGC
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGC
12588170 AAAAACATTT
Statistics
Matches: 173, Mismatches: 17, Indels: 9
0.87 0.09 0.05
Matches are distributed among these distances:
40 29 0.17
41 70 0.40
42 74 0.43
ACGTcount: A:0.20, C:0.21, G:0.31, T:0.28
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTAAGGG
Found at i:12588032 original size:42 final size:41
Alignment explanation
Indices: 12587929--12588169 Score: 351
Period size: 41 Copynumber: 5.9 Consensus size: 41
12587919 TTTTGACCTT
* *
12587929 TCAGGCCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGC
1 TCAGGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGC
* *
12587970 TAAGGGCTTTAGTC-GCGTTTTTGGAGAAGCGCCGCTAATGC
1 TCAGGGCTTTAG-CGGCGTTTTTGGAAAAGCGCCGCTAATGC
* *
12588011 TCAGGGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGA
1 TCA-GGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGC
* *
12588053 TCAGCGCTTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGC
1 TCAGGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGC
*
12588094 TCAGGGGATTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGC
1 TCA-GGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGC
*
12588136 TCA-GGCTTTAGCGGCGTTTTTGTAAAAGCGCCGC
1 TCAGGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGC
12588170 AAAAACATTT
Statistics
Matches: 183, Mismatches: 13, Indels: 9
0.89 0.06 0.04
Matches are distributed among these distances:
40 29 0.16
41 77 0.42
42 77 0.42
ACGTcount: A:0.20, C:0.22, G:0.32, T:0.27
Consensus pattern (41 bp):
TCAGGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGC
Found at i:12588037 original size:83 final size:83
Alignment explanation
Indices: 12587935--12588169 Score: 375
Period size: 83 Copynumber: 2.8 Consensus size: 83
12587925 CCTTTCAGGC
* *
12587935 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTAAGGGCTTTAGTC-GCGTTTTTGGAGAAG
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCAGGGCTTTAG-CGGCGTTTTTGGAAAAG
12587999 CGCCGCTAATGCTCAGGGG
65 CGCCGCTAATGCTCAGGGG
* * *
12588018 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGATCAGCGCTTTAGCGGCGTTTTTAGAAAAGC
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGAAAAGC
12588083 GCCGCTAATGCTCAGGGG
66 GCCGCTAATGCTCAGGGG
* * *
12588101 ATTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCA-GGCTTTAGCGGCGTTTTTGTAAAAGC
1 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGAAAAGC
12588165 GCCGC
66 GCCGC
12588170 AAAAACATTT
Statistics
Matches: 140, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
82 29 0.21
83 111 0.79
ACGTcount: A:0.20, C:0.21, G:0.31, T:0.28
Consensus pattern (83 bp):
CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGAAAAGC
GCCGCTAATGCTCAGGGG
Found at i:12588434 original size:14 final size:14
Alignment explanation
Indices: 12588405--12588529 Score: 99
Period size: 14 Copynumber: 8.9 Consensus size: 14
12588395 TATCTCTATA
* *
12588405 GTTTAAGGTTTTTG
1 GTTTAGGGTTTATG
*
12588419 GTTTAGGGTATATG
1 GTTTAGGGTTTATG
* * *
12588433 GTATAGAGTTTAAG
1 GTTTAGGGTTTATG
* *
12588447 GTTTATGGATTATGG
1 GTTTAGGGTTTAT-G
*
12588462 GTTTAGGGGTTATG
1 GTTTAGGGTTTATG
**
12588476 GTTTACCGTTTATG
1 GTTTAGGGTTTATG
*
12588490 GTTTAAGGTTTA-G
1 GTTTAGGGTTTATG
*
12588503 GATTTAGGGGTTATG
1 G-TTTAGGGTTTATG
*
12588518 GTTTATGGTTTA
1 GTTTAGGGTTTA
12588530 AGATTATAGA
Statistics
Matches: 85, Mismatches: 23, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
13 2 0.02
14 69 0.81
15 14 0.16
ACGTcount: A:0.20, C:0.02, G:0.32, T:0.46
Consensus pattern (14 bp):
GTTTAGGGTTTATG
Found at i:12588529 original size:21 final size:21
Alignment explanation
Indices: 12588411--12588529 Score: 91
Period size: 21 Copynumber: 5.6 Consensus size: 21
12588401 TATAGTTTAA
*
12588411 GGTTTTTGGTTTA-GGGTATAT
1 GGTTTATGGTTTAGGGGT-TAT
* * *
12588432 GGTATA-GAGTTTAAGGTTTAT
1 GGTTTATG-GTTTAGGGGTTAT
*
12588453 GGATTATGGGTTTAGGGGTTAT
1 GGTTTAT-GGTTTAGGGGTTAT
** * * *
12588475 GGTTTACCGTTTATGGTTTAA
1 GGTTTATGGTTTAGGGGTTAT
12588496 GGTTTA-GGATTTAGGGGTTAT
1 GGTTTATGG-TTTAGGGGTTAT
12588517 GGTTTATGGTTTA
1 GGTTTATGGTTTA
12588530 AGATTATAGA
Statistics
Matches: 75, Mismatches: 17, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
20 2 0.03
21 51 0.68
22 21 0.28
23 1 0.01
ACGTcount: A:0.19, C:0.02, G:0.33, T:0.46
Consensus pattern (21 bp):
GGTTTATGGTTTAGGGGTTAT
Found at i:12588589 original size:7 final size:7
Alignment explanation
Indices: 12588540--12588604 Score: 51
Period size: 7 Copynumber: 9.3 Consensus size: 7
12588530 AGATTATAGA
12588540 TTAAGGG
1 TTAAGGG
* *
12588547 TTGAGGT
1 TTAAGGG
*
12588554 TTAAGGT
1 TTAAGGG
*
12588561 TTAGGGG
1 TTAAGGG
12588568 TT-AGGG
1 TTAAGGG
*
12588574 GTAAGGGG
1 TTAA-GGG
*
12588582 TTGAGGG
1 TTAAGGG
*
12588589 TTAAGAG
1 TTAAGGG
12588596 TTAAGGG
1 TTAAGGG
12588603 TT
1 TT
12588605 TAGGATTTAG
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
6 4 0.09
7 35 0.80
8 5 0.11
ACGTcount: A:0.23, C:0.00, G:0.45, T:0.32
Consensus pattern (7 bp):
TTAAGGG
Found at i:12588740 original size:16 final size:17
Alignment explanation
Indices: 12588721--12588762 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
12588711 AAATTATTTA
12588721 TAAATAATTT-ATATAT
1 TAAATAATTTAATATAT
12588737 TAAATAATTTAATATAT
1 TAAATAATTTAATATAT
12588754 TAAAATAAT
1 T-AAATAAT
12588763 GATTATAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 10 0.42
17 7 0.29
18 7 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAATAATTTAATATAT
Found at i:12592617 original size:13 final size:13
Alignment explanation
Indices: 12592599--12592631 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
12592589 TACAAGTACC
12592599 TTTTTTTTTATT-
1 TTTTTTTTTATTA
12592611 TTTTTTTATTATTA
1 TTTTTTT-TTATTA
12592625 TTTTTTT
1 TTTTTTT
12592632 CTAAAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 5 0.26
14 7 0.37
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTATTA
Found at i:12593792 original size:5 final size:5
Alignment explanation
Indices: 12593782--12593807 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
12593772 TCAAATTTAA
12593782 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
12593808 TTTATCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:12593996 original size:43 final size:43
Alignment explanation
Indices: 12593904--12594111 Score: 222
Period size: 43 Copynumber: 4.8 Consensus size: 43
12593894 AAAGGTTTAT
** * * *
12593904 TCTTTAGCGGCG-TTGTGCTAAAAGCGTCGCTAAAGGTAATGCT
1 TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATG-G
* * *
12593947 TTTTTAGCGGCGTTTGTGGGAAAAGTGCCGCTATAGGTCATGG
1 TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGG
* *
12593990 TCTTTAGCGGCATTTGT-GGAAAATGCGCCGCTAAAGGTCGTGG
1 TCTTTAGCGGCGTTTGTGGGAAAA-GCGCCGCTAAAGGTCATGG
* * *
12594033 CCTTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCTTGG
1 TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGG
* * * * *
12594076 TCTTTAGCGACGCTTGTTGTAAAAGCGCCGTTAAAG
1 TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAG
12594112 TTAGCGACGC
Statistics
Matches: 141, Mismatches: 21, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
42 6 0.04
43 106 0.75
44 29 0.21
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.30
Consensus pattern (43 bp):
TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGG
Found at i:12596930 original size:20 final size:20
Alignment explanation
Indices: 12596896--12596935 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
12596886 GGGGTAAATT
12596896 GAAATCAAAACAAAATTAAAA
1 GAAATCAAAACAAAA-TAAAA
*
12596917 GAAAT-AAAATAAAATAAAA
1 GAAATCAAAACAAAATAAAA
12596936 TAGAATAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 8 0.44
21 5 0.28
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.15
Consensus pattern (20 bp):
GAAATCAAAACAAAATAAAA
Found at i:12597938 original size:17 final size:19
Alignment explanation
Indices: 12597916--12597953 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
12597906 GCCTATTTCT
*
12597916 TTGTAATTGGA-TTT-TTA
1 TTGTAAATGGACTTTGTTA
12597933 TTGTAAATGGACTTTGTTA
1 TTGTAAATGGACTTTGTTA
12597952 TT
1 TT
12597954 TTTGGAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 10 0.56
18 3 0.17
19 5 0.28
ACGTcount: A:0.24, C:0.03, G:0.18, T:0.55
Consensus pattern (19 bp):
TTGTAAATGGACTTTGTTA
Found at i:12601148 original size:20 final size:20
Alignment explanation
Indices: 12601125--12601163 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12601115 GTGACTAAAA
*
12601125 ATAAACTTACTAATAATTTC
1 ATAAACTTAATAATAATTTC
* *
12601145 ATAATCTTAATTATAATTT
1 ATAAACTTAATAATAATTT
12601164 ACCCTGATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (20 bp):
ATAAACTTAATAATAATTTC
Found at i:12604218 original size:27 final size:26
Alignment explanation
Indices: 12604188--12604241 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
12604178 TCACGCAAGA
* *
12604188 AGAAAATGAAAGAATAATAACAAAATC
1 AGAAAAAGAAAGAA-AATAAAAAAATC
*
12604215 AGAAAAAGAAAGAAACTAAAAAAATC
1 AGAAAAAGAAAGAAAATAAAAAAATC
12604241 A
1 A
12604242 CCTTTAACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 11 0.46
27 13 0.54
ACGTcount: A:0.70, C:0.07, G:0.11, T:0.11
Consensus pattern (26 bp):
AGAAAAAGAAAGAAAATAAAAAAATC
Found at i:12605049 original size:13 final size:12
Alignment explanation
Indices: 12605012--12605136 Score: 74
Period size: 12 Copynumber: 9.8 Consensus size: 12
12605002 AAAAACATAA
*
12605012 TGATTAAAAACT
1 TGATGAAAAACT
*
12605024 TGATGGAAAACT
1 TGATGAAAAACT
*
12605036 TTATGAAAAGACT
1 TGATGAAAA-ACT
12605049 TGATGAAAAACT
1 TGATGAAAAACT
*
12605061 T-A-AAAAGAACT
1 TGATGAAA-AACT
*
12605072 TGATGCAAAACT
1 TGATGAAAAACT
* *
12605084 TAATAAAAAAAAACT
1 TGAT---GAAAAACT
*
12605099 TGGTAATTAAAAACT
1 T-G--ATGAAAAACT
*
12605114 TGATAAAAGAACT
1 TGATGAAA-AACT
12605127 TGATGAAAAA
1 TGATGAAAAA
12605137 TACTTGAAGA
Statistics
Matches: 87, Mismatches: 15, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
10 3 0.03
11 6 0.07
12 36 0.41
13 24 0.28
14 1 0.01
15 15 0.17
18 2 0.02
ACGTcount: A:0.53, C:0.08, G:0.14, T:0.26
Consensus pattern (12 bp):
TGATGAAAAACT
Found at i:12605058 original size:25 final size:23
Alignment explanation
Indices: 12605017--12605084 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 23
12605007 CATAATGATT
*
12605017 AAAA-ACTTGATGGAAAACTTTA
1 AAAAGACTTGATGAAAAACTTTA
12605039 TGAAAAGACTTGATGAAAAAC-TTA
1 --AAAAGACTTGATGAAAAACTTTA
*
12605063 AAAAGAACTTGATGCAAAACTT
1 AAAAG-ACTTGATGAAAAACTT
12605085 AATAAAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.13
23 13 0.33
24 8 0.21
25 13 0.33
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (23 bp):
AAAAGACTTGATGAAAAACTTTA
Found at i:12605091 original size:25 final size:25
Alignment explanation
Indices: 12605020--12605136 Score: 98
Period size: 25 Copynumber: 4.6 Consensus size: 25
12605010 AATGATTAAA
* *
12605020 AACTTGATGGAAAACTTTATGAAAAG
1 AACTTGATGAAAAAC-TTATAAAAAG
12605046 -ACTTGATGAAAAAC-T-TAAAAAG
1 AACTTGATGAAAAACTTATAAAAAG
* *
12605068 AACTTGATGCAAAACTTAATAAAAAAA
1 AACTTGATGAAAAACTT-AT-AAAAAG
*
12605095 AACTTGGTAATTAAAAACTTGAT-AAAAG
1 AACTT-G--ATGAAAAACTT-ATAAAAAG
12605123 AACTTGATGAAAAA
1 AACTTGATGAAAAA
12605137 TACTTGAAGA
Statistics
Matches: 74, Mismatches: 9, Indels: 17
0.74 0.09 0.17
Matches are distributed among these distances:
22 6 0.08
23 14 0.19
24 1 0.01
25 20 0.27
26 1 0.01
27 11 0.15
28 10 0.14
30 11 0.15
ACGTcount: A:0.53, C:0.09, G:0.14, T:0.25
Consensus pattern (25 bp):
AACTTGATGAAAAACTTATAAAAAG
Found at i:12609329 original size:52 final size:52
Alignment explanation
Indices: 12609258--12609513 Score: 485
Period size: 52 Copynumber: 4.9 Consensus size: 52
12609248 ATCAAGTGAC
12609258 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
12609310 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
12609362 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
*
12609414 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
* *
12609466 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGACAA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
12609514 AGTGATAAGT
Statistics
Matches: 201, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 201 1.00
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (52 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
Found at i:12609534 original size:37 final size:37
Alignment explanation
Indices: 12609487--12609596 Score: 170
Period size: 37 Copynumber: 3.0 Consensus size: 37
12609477 TGATAGCTTC
*
12609487 GGCTATACTTATCTGATCAAGAGACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
* *
12609524 GGCTACACTTATCTGATCAAGAAACAAAGTGATAGGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
*
12609561 GGCTACACTTATCTGATC-AGGGAC-AAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
12609596 G
1 G
12609597 ATCATACGTA
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
35 11 0.16
36 4 0.06
37 52 0.78
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.25
Consensus pattern (37 bp):
GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
Found at i:12611147 original size:12 final size:12
Alignment explanation
Indices: 12611130--12611159 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
12611120 CCCCACATGT
12611130 CTGTGTGCCAAG
1 CTGTGTGCCAAG
*
12611142 CTGTGTGCCAGG
1 CTGTGTGCCAAG
12611154 CTGTGT
1 CTGTGT
12611160 AACTCACTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.10, C:0.23, G:0.37, T:0.30
Consensus pattern (12 bp):
CTGTGTGCCAAG
Found at i:12612088 original size:36 final size:36
Alignment explanation
Indices: 12612048--12612140 Score: 100
Period size: 36 Copynumber: 2.6 Consensus size: 36
12612038 GTACATCGAA
**
12612048 AATCCAACCAAAACACACCAGAT-G-TTTATAAGAGCT
1 AATCCAACCAAAACACACCA-ATGGCTCCA-AAGAGCT
** *
12612084 AATCCTTCCAAAACACATCAATGGCTCCAAAGAGCT
1 AATCCAACCAAAACACACCAATGGCTCCAAAGAGCT
*
12612120 AGTCCAACCAAAACACACCAA
1 AATCCAACCAAAACACACCAA
12612141 AACAGAGAGT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
35 2 0.04
36 42 0.91
37 2 0.04
ACGTcount: A:0.44, C:0.30, G:0.10, T:0.16
Consensus pattern (36 bp):
AATCCAACCAAAACACACCAATGGCTCCAAAGAGCT
Found at i:12614531 original size:4 final size:4
Alignment explanation
Indices: 12614524--12614782 Score: 131
Period size: 4 Copynumber: 66.8 Consensus size: 4
12614514 ATTCGCTGCT
* * * *
12614524 TCTC TCTC TCTC TCTC TCTC TCTC TCT- TC-C TCCC TCTC CCTC CCCC
1 TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC
* * * * * *
12614570 T-TC -CTC TCTC CCCC TCTC TCTC GCTC TCCC TCCC TCTC TCTC CCTC
1 TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC
* * * * * *
12614616 CCTC TCTC -CT- TCTC TCTC CCTC TCTC TCTC CCTC CCGC T-TGC TGTC
1 TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCT-C TCTC
* * * * * * * *
12614662 CCTC CCTC TCCC TCTC CCTC TCTC TCTC CCTC TCTC GCTT TCCC TCTC
1 TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC
* * * * * * * * * *
12614710 TCCC TCCC TGTC CCTC CCGC TC-C T-TG TCCC TCCC TCTC TCCC TCTC
1 TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC
*
12614756 TCCC TCTC TCTC TCTC TCTC TCTC TCT
1 TCTC TCTC TCTC TCTC TCTC TCTC TCT
12614783 TCTTGCAGAG
Statistics
Matches: 194, Mismatches: 51, Indels: 20
0.73 0.19 0.08
Matches are distributed among these distances:
3 14 0.07
4 179 0.92
5 1 0.01
ACGTcount: A:0.00, C:0.58, G:0.03, T:0.39
Consensus pattern (4 bp):
TCTC
Found at i:12614539 original size:10 final size:10
Alignment explanation
Indices: 12614524--12614782 Score: 131
Period size: 10 Copynumber: 26.7 Consensus size: 10
12614514 ATTCGCTGCT
12614524 TCTCTCTCTC
1 TCTCTCTCTC
12614534 TCTCTCTCTC
1 TCTCTCTCTC
12614544 TCTCTCT-TC
1 TCTCTCTCTC
*
12614553 -CTCCCTCTC
1 TCTCTCTCTC
* * *
12614562 CCTCCCCCT-
1 TCTCTCTCTC
12614571 TC-CTCTCTC
1 TCTCTCTCTC
* *
12614580 CCCCTCTCTC
1 TCTCTCTCTC
* *
12614590 TCGCTCTCCC
1 TCTCTCTCTC
*
12614600 TCCCTCTCTC
1 TCTCTCTCTC
* *
12614610 TCCCTCCCTC
1 TCTCTCTCTC
12614620 TCTC-CT-TC
1 TCTCTCTCTC
*
12614628 TCTCTCCCTC
1 TCTCTCTCTC
*
12614638 TCTCTCTCCC
1 TCTCTCTCTC
* *
12614648 TCCCGCT-TGC
1 TCTCTCTCT-C
* * *
12614658 TGTCCCTCCC
1 TCTCTCTCTC
*
12614668 TCTCCCTCTC
1 TCTCTCTCTC
*
12614678 CCTCTCTCTC
1 TCTCTCTCTC
*
12614688 TCCCTCTCTC
1 TCTCTCTCTC
* * *
12614698 GCTTTCCCTC
1 TCTCTCTCTC
* *
12614708 TCTCCCTCCC
1 TCTCTCTCTC
* * *
12614718 TGTCCCTCCC
1 TCTCTCTCTC
* *
12614728 GCTC-CT-TG
1 TCTCTCTCTC
* *
12614736 TCCCTCCCTC
1 TCTCTCTCTC
*
12614746 TCTCCCTCTC
1 TCTCTCTCTC
*
12614756 TCCCTCTCTC
1 TCTCTCTCTC
12614766 TCTCTCTCTC
1 TCTCTCTCTC
12614776 TCTCTCT
1 TCTCTCT
12614783 TCTTGCAGAG
Statistics
Matches: 185, Mismatches: 54, Indels: 20
0.71 0.21 0.08
Matches are distributed among these distances:
8 17 0.09
9 11 0.06
10 157 0.85
ACGTcount: A:0.00, C:0.58, G:0.03, T:0.39
Consensus pattern (10 bp):
TCTCTCTCTC
Found at i:12627376 original size:87 final size:87
Alignment explanation
Indices: 12627230--12627506 Score: 518
Period size: 87 Copynumber: 3.2 Consensus size: 87
12627220 CCGTTGGAGT
12627230 TGGAGGCCGAGGAGGTTGACATGAGGGAGGAAATGTACGAGGCGGTGGATATGAAGGAGTACGTC
1 TGGAGGCCGAGGAGGTTGACATGAGGGAGGAAATGTACGAGGCGGTGGATATGAAGGAGTACGTC
12627295 TAATAGGTGGACGACTTTGTGG
66 TAATAGGTGGACGACTTTGTGG
* *
12627317 TGGAGGCCGAGGAGGTTGACTTGAGGGAGGAAATGTACGAGGCGGTGGATATGAAGGAGTATGTC
1 TGGAGGCCGAGGAGGTTGACATGAGGGAGGAAATGTACGAGGCGGTGGATATGAAGGAGTACGTC
12627382 TAATAGGTGGACGACTTTGTGG
66 TAATAGGTGGACGACTTTGTGG
12627404 TGGAGGCCGAGGAGGTTGACATGAGGGAGGAAATGTACGAGGCGGTGGATATGAAGGAGTACGTC
1 TGGAGGCCGAGGAGGTTGACATGAGGGAGGAAATGTACGAGGCGGTGGATATGAAGGAGTACGTC
12627469 TAATAGGTGGACGACTTTGTGG
66 TAATAGGTGGACGACTTTGTGG
* *
12627491 TGGAGACCGAGAAGGT
1 TGGAGGCCGAGGAGGT
12627507 GATCGAGTAT
Statistics
Matches: 184, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 184 1.00
ACGTcount: A:0.26, C:0.10, G:0.43, T:0.21
Consensus pattern (87 bp):
TGGAGGCCGAGGAGGTTGACATGAGGGAGGAAATGTACGAGGCGGTGGATATGAAGGAGTACGTC
TAATAGGTGGACGACTTTGTGG
Found at i:12636226 original size:48 final size:48
Alignment explanation
Indices: 12636150--12636318 Score: 221
Period size: 48 Copynumber: 3.5 Consensus size: 48
12636140 GGTCGCATAT
* *
12636150 GTGGCACGGACTGTATGCAGGTCACCAATATTCTGTTAAGATACAAGG
1 GTGGCACGGACTGTGTGCAGGCCACCAATATTCTGTTAAGATACAAGG
*
12636198 GTGGTACGGACTGTGTGCAGGCCACCAATATTCTGTTAAGATACAAGG
1 GTGGCACGGACTGTGTGCAGGCCACCAATATTCTGTTAAGATACAAGG
* * * * ** * *
12636246 GTGGCACGGACTGTGTGCAGGCCACCGAGAGTCTATTATTACACAAAG
1 GTGGCACGGACTGTGTGCAGGCCACCAATATTCTGTTAAGATACAAGG
* *
12636294 GTGGTACGGACTGTGTGTAGGCCAC
1 GTGGCACGGACTGTGTGCAGGCCAC
12636319 TGAGAAAACT
Statistics
Matches: 107, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 107 1.00
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (48 bp):
GTGGCACGGACTGTGTGCAGGCCACCAATATTCTGTTAAGATACAAGG
Found at i:12638838 original size:20 final size:21
Alignment explanation
Indices: 12638813--12638852 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
12638803 TTTTCAATGA
12638813 ATTTTTATTTATA-AAATTAG
1 ATTTTTATTTATATAAATTAG
*
12638833 ATTTTTATTTTTATAAATTA
1 ATTTTTATTTATATAAATTA
12638853 AATAAAACAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (21 bp):
ATTTTTATTTATATAAATTAG
Found at i:12640351 original size:135 final size:135
Alignment explanation
Indices: 12640104--12640376 Score: 528
Period size: 135 Copynumber: 2.0 Consensus size: 135
12640094 AGTCAAACCA
12640104 GGTTTTGCATGTGAAGGCGTCGCAGAACCAGAAGGGTTTAGTTCCAGTGCCACTGATGATTCAGC
1 GGTTTTGCATGTGAAGGCGTCGCAGAACCAGAAGGGTTTAGTTCCAGTGCCACTGATGATTCAGC
*
12640169 CATCCCTTGAGATTGTGATATACATGTTAAGAAAGGTCGTGCTGCTAAAGCTGGACTTGGCTGCC
66 CATCCCTTGAGATTGTGATATACATGTTAAGAAAGGTCGTGCCGCTAAAGCTGGACTTGGCTGCC
12640234 TTAGC
131 TTAGC
12640239 GGTTTTGCATGTGAAGGCGTCGCAGAACCAGAAGGGTTTAGTTCCAGTGCCACTGATGATTCAGC
1 GGTTTTGCATGTGAAGGCGTCGCAGAACCAGAAGGGTTTAGTTCCAGTGCCACTGATGATTCAGC
*
12640304 CATCCCTTGAGATTGTGATGTACATGTTAAGAAAGGTCGTGCCGCTAAAGCTGGACTTGGCTGCC
66 CATCCCTTGAGATTGTGATATACATGTTAAGAAAGGTCGTGCCGCTAAAGCTGGACTTGGCTGCC
12640369 TTAGC
131 TTAGC
12640374 GGT
1 GGT
12640377 CTTGGACGTG
Statistics
Matches: 136, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
135 136 1.00
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (135 bp):
GGTTTTGCATGTGAAGGCGTCGCAGAACCAGAAGGGTTTAGTTCCAGTGCCACTGATGATTCAGC
CATCCCTTGAGATTGTGATATACATGTTAAGAAAGGTCGTGCCGCTAAAGCTGGACTTGGCTGCC
TTAGC
Found at i:12640676 original size:15 final size:16
Alignment explanation
Indices: 12640656--12640714 Score: 66
Period size: 18 Copynumber: 3.5 Consensus size: 16
12640646 GCGTCTAACA
12640656 GGTGGAGGC-GAAGGT
1 GGTGGAGGCAGAAGGT
*
12640671 GGTGGATGCCAAGAAGGT
1 GGTGGA-GGC-AGAAGGT
12640689 GGTGGAGGCCAAGAAGGT
1 GGTGGAGG-C-AGAAGGT
12640707 GGTGGAGG
1 GGTGGAGG
12640715 TGGACTATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
15 6 0.16
16 2 0.05
17 1 0.03
18 29 0.76
ACGTcount: A:0.24, C:0.08, G:0.54, T:0.14
Consensus pattern (16 bp):
GGTGGAGGCAGAAGGT
Found at i:12640710 original size:21 final size:18
Alignment explanation
Indices: 12640665--12640714 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
12640655 AGGTGGAGGC
*
12640665 GAAGGTGGTGGATGCCAA
1 GAAGGTGGTGGAGGCCAA
12640683 GAAGGTGGTGGAGGCCAA
1 GAAGGTGGTGGAGGCCAA
12640701 GAAGGTGGTGGAGG
1 GAAGGTGGTGGAGG
12640715 TGGACTATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.26, C:0.08, G:0.52, T:0.14
Consensus pattern (18 bp):
GAAGGTGGTGGAGGCCAA
Found at i:12643440 original size:6 final size:7
Alignment explanation
Indices: 12643423--12643451 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
12643413 TCATGCTTCT
12643423 TTTTTTA
1 TTTTTTA
12643430 TTTTTTA
1 TTTTTTA
12643437 TTTTTTA
1 TTTTTTA
12643444 TTTTTTA
1 TTTTTTA
12643451 T
1 T
12643452 CTTGAGTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTTA
Found at i:12672692 original size:42 final size:42
Alignment explanation
Indices: 12672642--12672731 Score: 155
Period size: 42 Copynumber: 2.2 Consensus size: 42
12672632 TTTTTAGTGA
*
12672642 AAAGAAAGAGATTGTCATCTCTTTCAATCAATTTTAGGAAAG
1 AAAGAAAGAGATTGTCATCTCCTTCAATCAATTTTAGGAAAG
*
12672684 AAAGAAAGAGATTGTCATCTCCTTCAATCAATTTTAGGCAAG
1 AAAGAAAGAGATTGTCATCTCCTTCAATCAATTTTAGGAAAG
12672726 -AAGAAA
1 AAAGAAA
12672732 ACACTTGATG
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 6 0.13
42 40 0.87
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (42 bp):
AAAGAAAGAGATTGTCATCTCCTTCAATCAATTTTAGGAAAG
Found at i:12672727 original size:38 final size:40
Alignment explanation
Indices: 12672633--12672721 Score: 135
Period size: 42 Copynumber: 2.2 Consensus size: 40
12672623 ATAAGCTAAT
*
12672633 TTTTAGTGA-AAAGAAAGAGATTGTCATCTCTTTCAATCAA
1 TTTTAG-GAGAAAGAAAGAGATTGTCATCTCCTTCAATCAA
12672673 TTTTAGGAAAGAAAGAAAGAGATTGTCATCTCCTTCAATCAA
1 TTTTAGG--AGAAAGAAAGAGATTGTCATCTCCTTCAATCAA
12672715 TTTTAGG
1 TTTTAGG
12672722 CAAGAAGAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
39 1 0.02
40 6 0.13
41 1 0.02
42 37 0.82
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (40 bp):
TTTTAGGAGAAAGAAAGAGATTGTCATCTCCTTCAATCAA
Found at i:12676782 original size:3 final size:3
Alignment explanation
Indices: 12676774--12676805 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
12676764 TATTCCTAGT
12676774 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
12676806 TATTTTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:12676954 original size:14 final size:14
Alignment explanation
Indices: 12676935--12676980 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
12676925 TATTTAAAAT
12676935 ATAATAATAATTTA
1 ATAATAATAATTTA
*
12676949 ATAATACTAATTTA
1 ATAATAATAATTTA
12676963 ATAATAATAATTTA
1 ATAATAATAATTTA
12676977 ATAA
1 ATAA
12676981 CATTTTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAATAATAATTTA
Found at i:12678592 original size:26 final size:25
Alignment explanation
Indices: 12678563--12678635 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 25
12678553 TCATCCCAAG
12678563 TTTACCCCAGTAAATTTTTTGACAAT
1 TTTACCCCAGTAAA-TTTTTGACAAT
** *
12678589 TTTA-CCTTGATAAAATTTTGACAAT
1 TTTACCCCAG-TAAATTTTTGACAAT
*
12678614 TTTACCCCTAGTAAAATTTTGA
1 TTTACCCC-AGTAAATTTTTGA
12678636 GAAAATTCGT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
25 17 0.44
26 21 0.54
27 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.42
Consensus pattern (25 bp):
TTTACCCCAGTAAATTTTTGACAAT
Found at i:12703311 original size:9 final size:9
Alignment explanation
Indices: 12703299--12703544 Score: 67
Period size: 10 Copynumber: 25.7 Consensus size: 9
12703289 AAAATCAAAA
12703299 AAAAATTAT
1 AAAAATTAT
12703308 AAAAATCATTAT
1 -AAAA--ATTAT
12703320 AAAAATT-T
1 AAAAATTAT
12703328 AAAATATT-T
1 AAAA-ATTAT
*
12703337 AAAAAATAAT
1 -AAAAATTAT
*
12703347 TAAAATTGAT
1 AAAAATT-AT
* *
12703357 ATAAACTTGT
1 A-AAAATTAT
12703367 AAAAATTAT
1 AAAAATTAT
12703376 AAAAAAATTTAAT
1 --AAAAA-TT-AT
12703389 AAAAACTTAT
1 AAAAA-TTAT
*
12703399 AAATATTATT
1 AAAAATTA-T
12703409 AAAAATCTA-
1 AAAAAT-TAT
* *
12703418 ACAAATTTT
1 AAAAATTAT
12703427 AATAAATTAT
1 AA-AAATTAT
*
12703437 -GAAATTAAT
1 AAAAATT-AT
12703446 AAAACA-TATT
1 AAAA-ATTA-T
*
12703456 TAAAA-TA-
1 AAAAATTAT
* *
12703463 AAAAAGTAA
1 AAAAATTAT
*
12703472 AAAAATTCTT
1 AAAAATT-AT
* *
12703482 AACAACTAT
1 AAAAATTAT
*
12703491 AAAAAATCAT
1 -AAAAATTAT
12703501 AAAAA-TAT
1 AAAAATTAT
*
12703509 TAAAATTGAT
1 AAAAATT-AT
*
12703519 ATAAAGTTAT
1 A-AAAATTAT
*
12703529 AATAATTATT
1 AAAAATTA-T
12703539 AAAAAT
1 AAAAAT
12703545 ATCATGAAAA
Statistics
Matches: 174, Mismatches: 35, Indels: 54
0.66 0.13 0.21
Matches are distributed among these distances:
7 4 0.02
8 19 0.11
9 53 0.30
10 60 0.34
11 29 0.17
12 7 0.04
13 2 0.01
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:12703311 original size:10 final size:10
Alignment explanation
Indices: 12703298--12703436 Score: 58
Period size: 9 Copynumber: 14.0 Consensus size: 10
12703288 AAAAATCAAA
12703298 AAAAAATTAT
1 AAAAAATTAT
12703308 AAAAATCATTAT
1 AAAAA--ATTAT
12703320 -AAAAATT-T
1 AAAAAATTAT
*
12703328 AAAATATT-T
1 AAAAAATTAT
*
12703337 AAAAAATAAT
1 AAAAAATTAT
*
12703347 -TAAAATTGAT
1 AAAAAATT-AT
* * *
12703357 ATAAACTTGT
1 AAAAAATTAT
12703367 -AAAAATTAT
1 AAAAAATTAT
12703376 AAAAAAATTTAAT
1 -AAAAAA-TT-AT
*
12703389 AAAAACTTAT
1 AAAAAATTAT
*
12703399 -AAATATTAT
1 AAAAAATTAT
* *
12703408 TAAAAA-TCT
1 AAAAAATTAT
* *
12703417 AACAAATTTT
1 AAAAAATTAT
*
12703427 AATAAATTAT
1 AAAAAATTAT
12703437 GAAATTAATA
Statistics
Matches: 97, Mismatches: 20, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
8 1 0.01
9 40 0.41
10 25 0.26
11 17 0.18
12 12 0.12
13 2 0.02
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.35
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:12704077 original size:10 final size:10
Alignment explanation
Indices: 12704062--12704167 Score: 62
Period size: 10 Copynumber: 10.9 Consensus size: 10
12704052 GGTCCAATTC
12704062 AAATTTTTAT
1 AAATTTTTAT
12704072 AAATTTTT-T
1 AAATTTTTAT
* *
12704081 AAGTTTATAT
1 AAATTTTTAT
*
12704091 CAA--TTTA-
1 AAATTTTTAT
*
12704098 ATATTTTTA-
1 AAATTTTTAT
12704107 ATAATTTTTAT
1 A-AATTTTTAT
* *
12704118 GATTTTTTAT
1 AAATTTTTAT
12704128 AAATTTTT-T
1 AAATTTTTAT
12704137 AAGAATTTTTAT
1 -A-AATTTTTAT
**
12704149 ACGTTTTTAT
1 AAATTTTTAT
*
12704159 AAAATTTTA
1 AAATTTTTA
12704168 AATATTTATT
Statistics
Matches: 71, Mismatches: 17, Indels: 16
0.68 0.16 0.15
Matches are distributed among these distances:
7 1 0.01
8 3 0.04
9 13 0.18
10 45 0.63
11 8 0.11
12 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (10 bp):
AAATTTTTAT
Found at i:12704144 original size:31 final size:31
Alignment explanation
Indices: 12704100--12704166 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
12704090 TCAATTTAAT
* *
12704100 ATTTTTAATAATTTTTATGA-TTTTTTATAAA
1 ATTTTTAAGAATTTTTAT-ACGTTTTTATAAA
*
12704131 TTTTTTAAGAATTTTTATACGTTTTTATAAA
1 ATTTTTAAGAATTTTTATACGTTTTTATAAA
12704162 ATTTT
1 ATTTT
12704167 AAATATTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 1 0.03
31 30 0.97
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.61
Consensus pattern (31 bp):
ATTTTTAAGAATTTTTATACGTTTTTATAAA
Found at i:12704261 original size:9 final size:9
Alignment explanation
Indices: 12704063--12704292 Score: 60
Period size: 10 Copynumber: 23.8 Consensus size: 9
12704053 GTCCAATTCA
12704063 AATTTTTAT
1 AATTTTTAT
12704072 AAATTTTT-T
1 -AATTTTTAT
*
12704081 AAGTTTATAT
1 AA-TTTTTAT
*
12704091 CAA-TTTAAT
1 -AATTTTTAT
12704100 -ATTTTTAAT
1 AATTTTT-AT
12704109 AATTTTTAT
1 AATTTTTAT
*
12704118 GATTTTTTAT
1 -AATTTTTAT
*
12704128 AAATTTTTTAAG
1 -AA-TTTTT-AT
12704140 AATTTTTAT
1 AATTTTTAT
*
12704149 ACGTTTTTAT
1 A-ATTTTTAT
* *
12704159 AAAATTTTAA
1 -AATTTTTAT
*
12704169 ATATTTATTGTT
1 A-ATTT-TT-AT
12704181 AA-TTTTAT
1 AATTTTTAT
*
12704189 AATTTATTAA
1 AATTT-TTAT
12704199 AATTTATTA-
1 AATTT-TTAT
*
12704208 GATTTATTA-
1 AATTT-TTAT
*
12704217 GATTTTTGAT
1 AATTTTT-AT
*
12704227 AATATTTA-
1 AATTTTTAT
12704235 AAGTTTTTAGT
1 AA-TTTTTA-T
*
12704246 ACTTTTTTAT
1 A-ATTTTTAT
*
12704256 AATTTTCAT
1 AATTTTTAT
* *
12704265 AAACCTTTTAG
1 -AA-TTTTTAT
12704276 ATATTTTTAT
1 A-ATTTTTAT
12704286 AATTTTT
1 AATTTTT
12704293 TCTGATTTTT
Statistics
Matches: 165, Mismatches: 30, Indels: 51
0.67 0.12 0.21
Matches are distributed among these distances:
7 1 0.01
8 12 0.07
9 52 0.32
10 73 0.44
11 25 0.15
12 2 0.01
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (9 bp):
AATTTTTAT
Found at i:12710545 original size:29 final size:29
Alignment explanation
Indices: 12710474--12710573 Score: 82
Period size: 30 Copynumber: 3.4 Consensus size: 29
12710464 AAAAATAAAT
*
12710474 AAAATTTATAAAAT-TATTAAATTTTAATA
1 AAAATTTATAAAATAT-TTAAAATTTAATA
*
12710503 AAAATATATTAAAATATTTAAAATTTAGA-A
1 AAAATTTA-TAAAATATTTAAAATTTA-ATA
* *
12710533 TAAATTTATAAAA-ATTGTAAAAAATT-ATA
1 AAAATTTATAAAATATT-T-AAAATTTAATA
*
12710562 AATATTTATAAA
1 AAAATTTATAAA
12710574 GTTATAAGAA
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
28 4 0.07
29 24 0.41
30 28 0.48
31 2 0.03
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (29 bp):
AAAATTTATAAAATATTTAAAATTTAATA
Found at i:12710573 original size:20 final size:19
Alignment explanation
Indices: 12710512--12710573 Score: 54
Period size: 20 Copynumber: 3.2 Consensus size: 19
12710502 AAAAATATAT
*
12710512 TAAAATATT-TAAAATTTA
1 TAAAAAATTATAAAATTTA
* * * *
12710530 GAATAAATTTATAAAAATTG
1 TAA-AAAATTATAAAATTTA
12710550 TAAAAAATTATAAATATTTA
1 TAAAAAATTATAAA-ATTTA
12710570 TAAA
1 TAAA
12710574 GTTATAAGAA
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
18 2 0.06
19 14 0.44
20 16 0.50
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (19 bp):
TAAAAAATTATAAAATTTA
Found at i:12710585 original size:29 final size:29
Alignment explanation
Indices: 12710536--12710592 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
12710526 TTTAGAATAA
* *
12710536 ATTTATAAAAATTGTAAAAAATTATAAAT
1 ATTTATAAAAATTATAAAAAAATATAAAT
*
12710565 ATTTAT-AAAGTTATAAGAAAAATATAAA
1 ATTTATAAAAATTATAA-AAAAATATAAA
12710593 AATGTAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (29 bp):
ATTTATAAAAATTATAAAAAAATATAAAT
Found at i:12710623 original size:18 final size:17
Alignment explanation
Indices: 12710582--12710631 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
12710572 AAGTTATAAG
* *
12710582 AAAAATATAAAAATGTA
1 AAAAATATAAAATTCTA
12710599 AATAAATATAAAATTCCTA
1 AA-AAATATAAAATT-CTA
*
12710618 AAAAATGTAAAATT
1 AAAAATATAAAATT
12710632 TTATATTACA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 2 0.07
18 22 0.79
19 4 0.14
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (17 bp):
AAAAATATAAAATTCTA
Found at i:12710798 original size:28 final size:28
Alignment explanation
Indices: 12710758--12710815 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
12710748 TTTTTAATAA
*
12710758 TTTATATA-TTTTATTAAAATTTTATGTTT
1 TTTATATACTTTAATT-AAATTTTAT-TTT
*
12710787 TTTATA-ACTTTAATTAATTTTTATTTT
1 TTTATATACTTTAATTAAATTTTATTTT
12710814 TT
1 TT
12710816 CATCATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 5 0.19
28 9 0.35
29 12 0.46
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (28 bp):
TTTATATACTTTAATTAAATTTTATTTT
Found at i:12712560 original size:23 final size:22
Alignment explanation
Indices: 12712534--12712583 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
12712524 TATAAAGTTT
*
12712534 AAATTAAAAATTAAAAACATATA
1 AAATTAAAAATTAAAAA-ACATA
*
12712557 AAATT-TAAATTAAAAAACATA
1 AAATTAAAAATTAAAAAACATA
12712578 AAATTA
1 AAATTA
12712584 GTAAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 9 0.38
22 10 0.42
23 5 0.21
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (22 bp):
AAATTAAAAATTAAAAAACATA
Found at i:12712588 original size:23 final size:22
Alignment explanation
Indices: 12712541--12712582 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
12712531 TTTAAATTAA
*
12712541 AAATTAAAAACATATAAAATTT
1 AAATTAAAAACACATAAAATTT
12712563 AAATTAAAAA-ACATAAAATT
1 AAATTAAAAACACATAAAATT
12712583 AGTAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (22 bp):
AAATTAAAAACACATAAAATTT
Found at i:12715341 original size:16 final size:16
Alignment explanation
Indices: 12715317--12715360 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
12715307 AAAAATATAT
*
12715317 ATTTATAATTTTAATG
1 ATTTTTAATTTTAATG
* *
12715333 ATTTTTAATTTAAATT
1 ATTTTTAATTTTAATG
*
12715349 TTTTTTAATTTT
1 ATTTTTAATTTT
12715361 TTATTTTTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (16 bp):
ATTTTTAATTTTAATG
Found at i:12722307 original size:36 final size:36
Alignment explanation
Indices: 12722260--12722452 Score: 215
Period size: 36 Copynumber: 5.0 Consensus size: 36
12722250 GCTAAGCTAC
*
12722260 CACTTATCACTTTGTCACTTGATCTGATAAGTATAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
*
12722296 CACTTATCACTTTTTTTCACTTGATCAGATAAGTATAG
1 CACTTATCAC--TTTGTCACTTGATCAGATAAGTATAG
*
12722334 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAG
1 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--T--AG
* * *
12722376 CTACCACTTATCACTTTGTCTCTTGATCAGATAAATGTAG
1 ----CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
*
12722416 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
12722452 C
1 C
12722453 TAAAGCTACC
Statistics
Matches: 137, Mismatches: 8, Indels: 24
0.81 0.05 0.14
Matches are distributed among these distances:
36 65 0.47
38 37 0.27
40 3 0.02
42 3 0.02
44 1 0.01
46 28 0.20
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.38
Consensus pattern (36 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
Found at i:12722384 original size:46 final size:46
Alignment explanation
Indices: 12722334--12722488 Score: 195
Period size: 46 Copynumber: 3.6 Consensus size: 46
12722324 ATAAGTATAG
*
12722334 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
12722380 CACTTATCACTTTGTCTCTTGATCAGATAA----A--T---G-TAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
12722416 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
12722462 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
12722489 AGTACTCAAA
Statistics
Matches: 92, Mismatches: 7, Indels: 20
0.77 0.06 0.17
Matches are distributed among these distances:
36 31 0.34
37 1 0.01
40 2 0.02
42 2 0.02
45 1 0.01
46 55 0.60
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:12722389 original size:120 final size:114
Alignment explanation
Indices: 12722218--12722452 Score: 344
Period size: 120 Copynumber: 2.0 Consensus size: 114
12722208 TACGTATGGT
12722218 CACTTATCATTTGTCCCTGATAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCACTTGAT
1 CACTTATCATTTGTCCCTGATAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCACTTGAT
* * *
12722283 CTGATAAGTATAGCACTTATCACTTTTTTTCACTTGATCAGATAAGTATAG
66 CAGATAAATATAGCACTTATCAC--TTTGTCACTTGATCAGATAAGTATAG
* * *
12722334 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCA-TTTGTC-CCTGAT-AGATAAGTGTAGCT-AAGCTACCACTTATCACTTTGTCACT
* *
12722399 TGATCAGATAAATGTAGCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
62 TGATCAGATAAATATAGCACTTATCACTTTGTCACTTGATCAGATAAGTATAG
12722452 C
1 C
12722453 TAAAGCTACC
Statistics
Matches: 107, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
116 9 0.08
117 5 0.05
118 30 0.28
119 14 0.13
120 49 0.46
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (114 bp):
CACTTATCATTTGTCCCTGATAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCACTTGAT
CAGATAAATATAGCACTTATCACTTTGTCACTTGATCAGATAAGTATAG
Found at i:12722403 original size:82 final size:82
Alignment explanation
Indices: 12722296--12722488 Score: 314
Period size: 82 Copynumber: 2.3 Consensus size: 82
12722286 ATAAGTATAG
* * * *
12722296 CACTTATCACTTTTTTTCACTTGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGA
1 CACTTATCAC--TTTATCTCTTGATCAGATAAATATAGCACTTATCACTTTGTCACTTGATCAGA
12722361 TAAGTGTAGCTAAAGCTAC
64 TAAGTGTAGCTAAAGCTAC
* *
12722380 CACTTATCACTTTGTCTCTTGATCAGATAAATGTAGCACTTATCACTTTGTCACTTGATCAGATA
1 CACTTATCACTTTATCTCTTGATCAGATAAATATAGCACTTATCACTTTGTCACTTGATCAGATA
12722445 AGTGTAGCTAAAGCTAC
66 AGTGTAGCTAAAGCTAC
12722462 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTATCTCTTGATCAGA
12722489 AGTACTCAAA
Statistics
Matches: 103, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
82 93 0.90
84 10 0.10
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.37
Consensus pattern (82 bp):
CACTTATCACTTTATCTCTTGATCAGATAAATATAGCACTTATCACTTTGTCACTTGATCAGATA
AGTGTAGCTAAAGCTAC
Found at i:12722815 original size:20 final size:20
Alignment explanation
Indices: 12722790--12722830 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
12722780 ACAATTTATG
12722790 CCCTTAAATTTTCGAAATTA
1 CCCTTAAATTTTCGAAATTA
*
12722810 CCCTTAAATTTTTGAAATTA
1 CCCTTAAATTTTCGAAATTA
12722830 C
1 C
12722831 ACTTTTACCC
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:0.34, C:0.20, G:0.05, T:0.41
Consensus pattern (20 bp):
CCCTTAAATTTTCGAAATTA
Found at i:12722929 original size:52 final size:52
Alignment explanation
Indices: 12722867--12722966 Score: 182
Period size: 52 Copynumber: 1.9 Consensus size: 52
12722857 TACAATTTGA
*
12722867 TCCCTACTCAATTAACCCCTCAATTGATCTAATTTTTCTTAATCAACAACGG
1 TCCCTACTCAATTAACCCCTCAATTGATCTAATTTTTCTCAATCAACAACGG
*
12722919 TCCCTACTCAATTAACCCCTCAATTGATCTAATTTTTCTCAATTAACA
1 TCCCTACTCAATTAACCCCTCAATTGATCTAATTTTTCTCAATCAACA
12722967 CCTTTTCCAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.36
Consensus pattern (52 bp):
TCCCTACTCAATTAACCCCTCAATTGATCTAATTTTTCTCAATCAACAACGG
Found at i:12732200 original size:4 final size:4
Alignment explanation
Indices: 12732191--12732215 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
12732181 TCCGAGATTT
12732191 GGTG GGTG GGTG GGTG GGTG GGTG G
1 GGTG GGTG GGTG GGTG GGTG GGTG G
12732216 CAAAACACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.76, T:0.24
Consensus pattern (4 bp):
GGTG
Found at i:12735028 original size:16 final size:16
Alignment explanation
Indices: 12735007--12735038 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12734997 TTTAGGAAGT
12735007 TTATTTTGCTAATTTA
1 TTATTTTGCTAATTTA
*
12735023 TTATTTTGTTAATTTA
1 TTATTTTGCTAATTTA
12735039 GATCTGGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.03, G:0.06, T:0.66
Consensus pattern (16 bp):
TTATTTTGCTAATTTA
Found at i:12738767 original size:18 final size:18
Alignment explanation
Indices: 12738740--12738832 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
12738730 TACGACCGTT
12738740 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
12738758 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
12738776 TACGGTACTATTTACGTA
1 TACGGTACTATTCACGTA
*
12738794 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
12738812 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
12738830 TAC
1 TAC
12738833 AGTAGTTGGG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:12738787 original size:36 final size:36
Alignment explanation
Indices: 12738740--12738832 Score: 168
Period size: 36 Copynumber: 2.6 Consensus size: 36
12738730 TACGACCGTT
12738740 TACGGTACTATTCACGTATACGGCACTATTCACGTA
1 TACGGTACTATTCACGTATACGGCACTATTCACGTA
*
12738776 TACGGTACTATTTACGTATACGGCACTATTCACGTA
1 TACGGTACTATTCACGTATACGGCACTATTCACGTA
*
12738812 TACGGTACTGTTCACGTATAC
1 TACGGTACTATTCACGTATAC
12738833 AGTAGTTGGG
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (36 bp):
TACGGTACTATTCACGTATACGGCACTATTCACGTA
Found at i:12744602 original size:25 final size:25
Alignment explanation
Indices: 12744543--12744696 Score: 168
Period size: 25 Copynumber: 6.2 Consensus size: 25
12744533 ACACACCACC
* * **
12744543 GCTCTCATGAGCTTCCCTGATATTTA
1 GCTCGCATGAGCTTCCC-GTTATACA
12744569 GCTCGCATGAGCTTCCCGTTATACA
1 GCTCGCATGAGCTTCCCGTTATACA
* * *
12744594 GCTCGCATGAGATTTCCATTATACA
1 GCTCGCATGAGCTTCCCGTTATACA
*
12744619 GCTCGCATGAGCTTCCCGTTATTCA
1 GCTCGCATGAGCTTCCCGTTATACA
* *
12744644 GCTCGCATGAACTTCCCGTTATTCA
1 GCTCGCATGAGCTTCCCGTTATACA
* *
12744669 GCTCAG-AGGAGCTTCTCGTT-TACA
1 GCTC-GCATGAGCTTCCCGTTATACA
12744693 GCTC
1 GCTC
12744697 ATATGAGCAT
Statistics
Matches: 111, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
24 7 0.06
25 87 0.78
26 17 0.15
ACGTcount: A:0.20, C:0.29, G:0.19, T:0.32
Consensus pattern (25 bp):
GCTCGCATGAGCTTCCCGTTATACA
Found at i:12745201 original size:25 final size:25
Alignment explanation
Indices: 12745173--12745284 Score: 134
Period size: 25 Copynumber: 4.5 Consensus size: 25
12745163 CCACCATTCT
*
12745173 CATGAGCTTCCCGATATTTAGCTTG
1 CATGAGCTTCCCGATATTTAGCTCG
* * *
12745198 CATGAGCTTCACAATATTTAGCTCT
1 CATGAGCTTCCCGATATTTAGCTCG
* *
12745223 CATGAACTTCCGGATATTTAGCTCG
1 CATGAGCTTCCCGATATTTAGCTCG
* * *
12745248 CATGAGCTTCCCGTTATATAGCTCA
1 CATGAGCTTCCCGATATTTAGCTCG
*
12745273 CATAAGCTTCCC
1 CATGAGCTTCCC
12745285 ATTATTCTGC
Statistics
Matches: 72, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 72 1.00
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (25 bp):
CATGAGCTTCCCGATATTTAGCTCG
Found at i:12745289 original size:25 final size:25
Alignment explanation
Indices: 12745241--12745289 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
12745231 TCCGGATATT
* * *
12745241 TAGCTCGCATGAGCTTCCCGTTATA
1 TAGCTCACATAAGCTTCCCATTATA
12745266 TAGCTCACATAAGCTTCCCATTAT
1 TAGCTCACATAAGCTTCCCATTAT
12745290 TCTGCTCAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (25 bp):
TAGCTCACATAAGCTTCCCATTATA
Found at i:12746858 original size:25 final size:25
Alignment explanation
Indices: 12746805--12746851 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
12746795 TTGAATTCAA
*
12746805 TAACCAACTCGATCATTTTTCCACT
1 TAACCAACTCGATCATTCTTCCACT
*
12746830 TAACCAACTC-ATTATTCTTCCA
1 TAACCAACTCGATCATTCTTCCA
12746852 TTCTAACTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.30, C:0.32, G:0.02, T:0.36
Consensus pattern (25 bp):
TAACCAACTCGATCATTCTTCCACT
Found at i:12746951 original size:29 final size:29
Alignment explanation
Indices: 12746893--12746951 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
12746883 ATTTGGTGTA
* * *
12746893 ATATATACATTAAATTTGAATTGTGCTTC
1 ATATATAAATGAAATTTGAATTGTGATTC
*
12746922 ATATATAAATGAAATTTTG-ATTTTGATTC
1 ATATATAAATGAAA-TTTGAATTGTGATTC
12746951 A
1 A
12746952 ACTGTACACA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.46
Consensus pattern (29 bp):
ATATATAAATGAAATTTGAATTGTGATTC
Found at i:12766503 original size:10 final size:9
Alignment explanation
Indices: 12766472--12766646 Score: 58
Period size: 9 Copynumber: 19.0 Consensus size: 9
12766462 AAATTTTAAG
*
12766472 TTATATAAAC
1 TTATA-AAAA
12766482 TTATAAAAA
1 TTATAAAAA
*
12766491 -TA-AAAAC
1 TTATAAAAA
*
12766498 TTATAAATA
1 TTATAAAAA
12766507 TTAT-AAAA
1 TTATAAAAA
*
12766515 -TATTAAAA
1 TTATAAAAA
12766523 TT-TAAAAA
1 TTATAAAAA
* *
12766531 TTCTAATCAA
1 TTATAA-AAA
12766541 TTATAAAAA
1 TTATAAAAA
*
12766550 ATAT-AAAA
1 TTATAAAAA
*
12766558 TTAACAAAACA
1 TT-ATAAAA-A
* **
12766569 TATTTAAATTT
1 T-TATAAA-AA
12766580 TTAATAAAAA
1 TT-ATAAAAA
12766590 -TATAAAAA
1 TTATAAAAA
**
12766598 CCATAAAATA
1 TTATAAAA-A
12766608 TTATAAAAA
1 TTATAAAAA
* *
12766617 TGTGTTAAAA
1 T-TATAAAAA
*
12766627 TTAACATAAAA
1 TT-ATA-AAAA
12766638 TTATAAAAA
1 TTATAAAAA
12766647 AGACTATAAA
Statistics
Matches: 120, Mismatches: 28, Indels: 35
0.66 0.15 0.19
Matches are distributed among these distances:
7 7 0.06
8 30 0.25
9 34 0.28
10 32 0.27
11 16 0.13
12 1 0.01
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.34
Consensus pattern (9 bp):
TTATAAAAA
Found at i:12766523 original size:32 final size:31
Alignment explanation
Indices: 12766430--12766558 Score: 84
Period size: 32 Copynumber: 4.0 Consensus size: 31
12766420 AACAAAATTA
* * *
12766430 AAAAATTATTAATATT-TAAAATATTTAAAG
1 AAAAATTATAAATATTATAAAATATTAAAAT
* * * *
12766460 AAAAATTTTAAGT-TATATAAACTTATAAAAAT
1 AAAAATTATAAATAT-TATAAA-ATATTAAAAT
12766492 AAAAACTTATAAATATTATAAAATATTAAAATTT
1 AAAAA-TTATAAATATTATAAAATATTAAAA--T
* *
12766526 AAAAATTCT-AATCAATTATAAAAAATATAAAAT
1 AAAAATTATAAAT--ATTATAAAATAT-TAAAAT
12766559 TAACAAAACA
Statistics
Matches: 76, Mismatches: 13, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
29 1 0.01
30 11 0.14
31 4 0.05
32 21 0.28
33 16 0.21
34 18 0.24
35 5 0.07
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (31 bp):
AAAAATTATAAATATTATAAAATATTAAAAT
Found at i:12776935 original size:3 final size:3
Alignment explanation
Indices: 12776927--12776959 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
12776917 AGCAGAAAAG
12776927 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
12776960 TCTCAATGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:12779858 original size:14 final size:14
Alignment explanation
Indices: 12779839--12779916 Score: 50
Period size: 14 Copynumber: 5.1 Consensus size: 14
12779829 TCGATTGCCA
12779839 GTAAAATATTTTCT
1 GTAAAATATTTTCT
12779853 GTAAAATGA-TTTCT
1 GTAAAAT-ATTTTCT
*
12779867 GGAAAATGTTTTACTTTTCT
1 GTAAAA-----TA-TTTTCT
*
12779887 GTAAAATGATTTACT
1 GTAAAAT-ATTTTCT
*
12779902 GGAAAATATTTTCT
1 GTAAAATATTTTCT
12779916 G
1 G
12779917 GTGTTTGATT
Statistics
Matches: 50, Mismatches: 5, Indels: 18
0.68 0.07 0.25
Matches are distributed among these distances:
14 24 0.48
15 13 0.26
16 1 0.02
18 1 0.02
19 1 0.02
20 10 0.20
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (14 bp):
GTAAAATATTTTCT
Found at i:12779887 original size:20 final size:20
Alignment explanation
Indices: 12779862--12779901 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
12779852 TGTAAAATGA
*
12779862 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
12779882 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
12779902 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:12779890 original size:34 final size:35
Alignment explanation
Indices: 12779847--12779913 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
12779837 CAGTAAAATA
*
12779847 TTTTCTGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCTGTAAAATGATTTACTGGAAAATATTTTAC
12779881 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
12779914 CTGGTGTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 18 0.58
35 13 0.42
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.48
Consensus pattern (35 bp):
TTTTCTGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:12794944 original size:259 final size:260
Alignment explanation
Indices: 12794484--12794982 Score: 750
Period size: 259 Copynumber: 1.9 Consensus size: 260
12794474 TCACCACTGC
* * * *
12794484 TCAAACTTGTCATTAAGTCATACACTTGCCACATTTGATCATTAAGTTTATAACATGCAATCTAG
1 TCAAACTTGTCATTAAGTCACACACTTGCCACATTTGATCATTAAGTTCATAACATGCAATATAA
** * * ** * * *
12794549 TTTCCACGCTTTACACCTTGTAAGATATTCGATGAAGCATCGTAAAAGAACTCGAATACACTAGT
66 TTTCCAAACTTCACACATTGTAAGATACCCGATGAAACATCATAAAAGAACTCAAATACACTAGT
* * * *
12794614 ACTAATCACATATGATGTTCGTCAGAGCTAATCACATCCATTTGTGTGAGGTTACCCGTCCGGGA
131 ACTAATCACATACGATGCTCGTCAGAGCTAATCACATCCATTTGTGTCAGGTTACCCATCCGGGA
12794679 TAAACCTTTT-AATGACACGTCAAATAACTTGGCTAAAGCTGTAAAATACAGATCAAGTTACCCG
196 TAAACCTTTTAAATGACACGTCAAATAACTTGGCTAAAGCTGTAAAATACAGATCAAGTTACCCG
12794743 TCAAACTTGTCATTAAGTCACACACTTGCCACATTTGATCATTAAGTTCATAACATGCAATATAA
1 TCAAACTTGTCATTAAGTCACACACTTGCCACATTTGATCATTAAGTTCATAACATGCAATATAA
* * *
12794808 TTTCCAAACTTCACATATTGTAAGTTACCCGATGAAACATCATAAAGGAACTCAAATACACTAGT
66 TTTCCAAACTTCACACATTGTAAGATACCCGATGAAACATCATAAAAGAACTCAAATACACTAGT
* ** *
12794873 ACTAATCACATCCGATGCTCGTTTGAGCTAATCATATCCATTTGTGTCAGGTTACCCATCC-GGA
131 ACTAATCACATACGATGCTCGTCAGAGCTAATCACATCCATTTGTGTCAGGTTACCCATCCGGGA
*
12794937 CTAAACCTTTTAAATGACACGTCAAATAACTTGGCTAAAGTTGTAA
196 -TAAACCTTTTAAATGACACGTCAAATAACTTGGCTAAAGCTGTAA
12794983 TCATATCCAT
Statistics
Matches: 213, Mismatches: 25, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
258 3 0.01
259 177 0.83
260 33 0.15
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (260 bp):
TCAAACTTGTCATTAAGTCACACACTTGCCACATTTGATCATTAAGTTCATAACATGCAATATAA
TTTCCAAACTTCACACATTGTAAGATACCCGATGAAACATCATAAAAGAACTCAAATACACTAGT
ACTAATCACATACGATGCTCGTCAGAGCTAATCACATCCATTTGTGTCAGGTTACCCATCCGGGA
TAAACCTTTTAAATGACACGTCAAATAACTTGGCTAAAGCTGTAAAATACAGATCAAGTTACCCG
Found at i:12801439 original size:22 final size:22
Alignment explanation
Indices: 12801408--12801451 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
12801398 GGCCCTTTAA
*
12801408 GGTTGGCTTATACATTGAAAAC
1 GGTTGACTTATACATTGAAAAC
12801430 GGTTGACTTATACATTGAAAAC
1 GGTTGACTTATACATTGAAAAC
12801452 CTGAAATCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (22 bp):
GGTTGACTTATACATTGAAAAC
Found at i:12803101 original size:32 final size:32
Alignment explanation
Indices: 12803060--12803122 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
12803050 CCTTTAAATT
*
12803060 AATACATACTGTTCCAGTCTTATATCAGTACA
1 AATACATACTGTTCCAGTCTTAAATCAGTACA
*
12803092 AATACATACTGTTCCAGTCTTAAATCGGTAC
1 AATACATACTGTTCCAGTCTTAAATCAGTAC
12803123 TAAAATTGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.33
Consensus pattern (32 bp):
AATACATACTGTTCCAGTCTTAAATCAGTACA
Found at i:12805956 original size:17 final size:19
Alignment explanation
Indices: 12805918--12805956 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
12805908 ATCAAACTTG
*
12805918 TTTGTGTTTGTAATGAATA
1 TTTGTGTTTATAATGAATA
12805937 TTTG-GTTTATAATG-ATA
1 TTTGTGTTTATAATGAATA
12805954 TTT
1 TTT
12805957 AAGCCCTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 9 0.47
19 4 0.21
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.56
Consensus pattern (19 bp):
TTTGTGTTTATAATGAATA
Found at i:12808231 original size:3 final size:3
Alignment explanation
Indices: 12808223--12808254 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
12808213 TTAACGAAGT
12808223 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
12808255 GCAAATCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:12813384 original size:18 final size:18
Alignment explanation
Indices: 12813357--12813449 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
12813347 TACGACCGTT
12813357 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
12813375 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
12813393 TACAGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
12813411 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
12813429 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
12813447 TAC
1 TAC
12813450 AGTAGTTGGG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:12820581 original size:17 final size:17
Alignment explanation
Indices: 12820559--12820592 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
12820549 ATCAACTCCC
12820559 AATAAAAGAATATATGT
1 AATAAAAGAATATATGT
12820576 AATAAAAGAATATATGT
1 AATAAAAGAATATATGT
12820593 TTTTATGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (17 bp):
AATAAAAGAATATATGT
Found at i:12824238 original size:3 final size:3
Alignment explanation
Indices: 12824230--12824264 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
12824220 TGAAGCAGTG
*
12824230 AGA AGA AGA AGA AGA AGA AGA AGA ACA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
12824265 GAAAACCCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.03, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:12831136 original size:82 final size:82
Alignment explanation
Indices: 12830999--12831162 Score: 319
Period size: 82 Copynumber: 2.0 Consensus size: 82
12830989 GTCCAAGTCC
*
12830999 AAACTGTCTGTCCATATTCCATAATTGGGTTTTTAATAGATTATCATATTTATTTTTGGATGTAA
1 AAACTGTCTGTCCATATTCCATAAGTGGGTTTTTAATAGATTATCATATTTATTTTTGGATGTAA
12831064 TTCAGATGATTGTTTTA
66 TTCAGATGATTGTTTTA
12831081 AAACTGTCTGTCCATATTCCATAAGTGGGTTTTTAATAGATTATCATATTTATTTTTGGATGTAA
1 AAACTGTCTGTCCATATTCCATAAGTGGGTTTTTAATAGATTATCATATTTATTTTTGGATGTAA
12831146 TTCAGATGATTGTTTTA
66 TTCAGATGATTGTTTTA
12831163 GAGTTTATCC
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.47
Consensus pattern (82 bp):
AAACTGTCTGTCCATATTCCATAAGTGGGTTTTTAATAGATTATCATATTTATTTTTGGATGTAA
TTCAGATGATTGTTTTA
Found at i:12842323 original size:4 final size:4
Alignment explanation
Indices: 12842314--12842343 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
12842304 CTTGGACTAA
12842314 GGAG GGAG GGAG GGAG GGAG GGAG GGAG GG
1 GGAG GGAG GGAG GGAG GGAG GGAG GGAG GG
12842344 GTACCTATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.77, T:0.00
Consensus pattern (4 bp):
GGAG
Found at i:12847795 original size:272 final size:272
Alignment explanation
Indices: 12847309--12847852 Score: 1079
Period size: 272 Copynumber: 2.0 Consensus size: 272
12847299 TTTAGGGGTC
12847309 TAATTTGGTATCTAATCTTTTTTTGTTCGAATTTGGTACTTGTCAAGCATTTTAAAAATTACTCT
1 TAATTTGGTATCTAATCTTTTTTTGTTCGAATTTGGTACTTGTCAAGCATTTTAAAAATTACTCT
12847374 AATATACTAACAATGCTATTTTTTTGAGGTAGCAAAAATAATCAATGTATGATCGACATGTGATA
66 AATATACTAACAATGCTATTTTTTTGAGGTAGCAAAAATAATCAATGTATGATCGACATGTGATA
12847439 GATTATATGATATTTTTTGTATTTTATATGTTCAATTATTTTTAGTTTTATTTAATTATTTATTT
131 GATTATATGATATTTTTTGTATTTTATATGTTCAATTATTTTTAGTTTTATTTAATTATTTATTT
12847504 TATTAATTGAAAATAATAAATTTCTTTTTAATTTGAAATTTAAAAAACATTTTTTTCTTATTAAT
196 TATTAATTGAAAATAATAAATTTCTTTTTAATTTGAAATTTAAAAAACATTTTTTTCTTATTAAT
12847569 TATTAATTCGTT
261 TATTAATTCGTT
12847581 TAATTTGGTATCTAATCTTTTTTTGTTCGAATTTGGTACTTGTCAAGCATTTTAAAAATTACTCT
1 TAATTTGGTATCTAATCTTTTTTTGTTCGAATTTGGTACTTGTCAAGCATTTTAAAAATTACTCT
12847646 AATATACTAACAATGCTATTTTTTTGAGGTAGCAAAAATAATCAATGTATGATCGACATGTGATA
66 AATATACTAACAATGCTATTTTTTTGAGGTAGCAAAAATAATCAATGTATGATCGACATGTGATA
12847711 GATTATATGATATTTTTTGTATTTTATATGTTCAATTATTTTTAGTTTTATTTAATTATTTATTT
131 GATTATATGATATTTTTTGTATTTTATATGTTCAATTATTTTTAGTTTTATTTAATTATTTATTT
*
12847776 TATTAATTGAAAATAATAAATTTCTTTTTAATTTGAAATTTAAAAAACATTTTTTTCTTATTTAT
196 TATTAATTGAAAATAATAAATTTCTTTTTAATTTGAAATTTAAAAAACATTTTTTTCTTATTAAT
12847841 TATTAATTCGTT
261 TATTAATTCGTT
12847853 AAGCATAGCT
Statistics
Matches: 271, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
272 271 1.00
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (272 bp):
TAATTTGGTATCTAATCTTTTTTTGTTCGAATTTGGTACTTGTCAAGCATTTTAAAAATTACTCT
AATATACTAACAATGCTATTTTTTTGAGGTAGCAAAAATAATCAATGTATGATCGACATGTGATA
GATTATATGATATTTTTTGTATTTTATATGTTCAATTATTTTTAGTTTTATTTAATTATTTATTT
TATTAATTGAAAATAATAAATTTCTTTTTAATTTGAAATTTAAAAAACATTTTTTTCTTATTAAT
TATTAATTCGTT
Found at i:12848099 original size:7 final size:7
Alignment explanation
Indices: 12848087--12848114 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
12848077 TAAAAAAAAT
12848087 ATATCAA
1 ATATCAA
12848094 ATATCAA
1 ATATCAA
12848101 ATATCAA
1 ATATCAA
12848108 ATATCAA
1 ATATCAA
12848115 GCATATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (7 bp):
ATATCAA
Found at i:12852476 original size:180 final size:181
Alignment explanation
Indices: 12852174--12852534 Score: 616
Period size: 180 Copynumber: 2.0 Consensus size: 181
12852164 TGGAACTACA
* * *
12852174 TTTATTTTATTTTAGAATAAGATTTTTTAAACTTTATTAAACTCCATCTATTTGATATTGATTAG
1 TTTATTTTATTTTAAAATAAGATTTTTAAAACCTTATTAAACTCCATCTATTTGATATTGATTAG
12852239 AATAAGGTGTTTCAATCTTACTACACTCCTATTAGAATATGGTTTTACAAGCCTATAAATAGACA
66 AATAAGGTGTTTCAATCTTACTACACTCCTATTAGAATATGGTTTTACAAGCCTATAAATAGACA
* * *
12852304 TAACCTACTCCTTTTGTAATTATTCGAATTCAACATGGTGAATTTT-TTCT
131 TAACCTACTCCTCTTGTAATTATTCGAATTCAACATAGTAAATTTTCTTCT
* *
12852354 TTTATTTTATTTTAAAATAAGGTTTTTAAAACCTTATTAAACTCTATCTATTTGATATTGATTAG
1 TTTATTTTATTTTAAAATAAGATTTTTAAAACCTTATTAAACTCCATCTATTTGATATTGATTAG
*
12852419 AATAAGGTGTTTCAATCTTACTACATTCCTATTAGAATATGGTTTTACAAGCCTATAAATAGACA
66 AATAAGGTGTTTCAATCTTACTACACTCCTATTAGAATATGGTTTTACAAGCCTATAAATAGACA
* *
12852484 TAATCTACTCCTCTTGTAATTATTCGAATTCGACATAGTAAATTTTCTTCT
131 TAACCTACTCCTCTTGTAATTATTCGAATTCAACATAGTAAATTTTCTTCT
12852535 CATTTGCCCG
Statistics
Matches: 169, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
180 165 0.98
181 4 0.02
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.44
Consensus pattern (181 bp):
TTTATTTTATTTTAAAATAAGATTTTTAAAACCTTATTAAACTCCATCTATTTGATATTGATTAG
AATAAGGTGTTTCAATCTTACTACACTCCTATTAGAATATGGTTTTACAAGCCTATAAATAGACA
TAACCTACTCCTCTTGTAATTATTCGAATTCAACATAGTAAATTTTCTTCT
Found at i:12855750 original size:22 final size:22
Alignment explanation
Indices: 12855722--12855765 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
12855712 TATATACATA
*
12855722 TATAAAA-AAAAACTTTAAGTAT
1 TATAAAATAAAAA-TGTAAGTAT
12855744 TATAAAATAAAAATGTAAGTAT
1 TATAAAATAAAAATGTAAGTAT
12855766 GTGCATATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (22 bp):
TATAAAATAAAAATGTAAGTAT
Found at i:12857883 original size:44 final size:44
Alignment explanation
Indices: 12857816--12858457 Score: 492
Period size: 44 Copynumber: 14.6 Consensus size: 44
12857806 TCCACCTCCT
* * * *
12857816 ACCAATATAGGAAGGCAGGATCTGCTATCGTCGATCTATTTCAC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * * * *
12857860 GCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-AC
* * *
12857905 ACCAATATGGGAAGACAAGATCTG-TAGCTTCGATCCACTTC-C
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
** * * * *
12857947 TACCAATATAGGAAGACCGGACCTGTTATTTTTGATCTACTTCAC
1 -ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * * *
12857992 GCCAATATATGAAGACAAAATCTGCTTTCTTTGATCTACTTC-C
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
*
12858035 TACCAATATAGGAAGACAAGATCTG-TAGCTTCGATCTACTTCAC
1 -ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * * * * * *
12858079 GCCAACACATGATGATAAGATCTGCTTTCTTCGATCTACTTCGCC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-AC
* * * * *
12858124 ACCAGTATGGGAAGACAAGATCTACTATCTTTGATCTACTTCAT
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * * * * *
12858168 GCCAATACATGAAGACAAGATCTGCTTTCTGCGATTTACTTCGCC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-AC
* * * *
12858213 ACCAATATGGGAAGATAAGATCTGC-ATCGTCGATCCACTTC-C
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * *
12858255 TACCAATATAGGAAGA-TAGAACCTACTATCTTTGATCTACTTCAC
1 -ACCAATATAGGAAGACAAG-ATCTGCTATCTTCGATCTACTTCAC
* * * * * * *
12858300 GCCAATACATGAAGATAAGATCTGCTTTCTGCGATCTACTTCGCC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-AC
* * *
12858345 ACCAATATGGGAAGACAAGATCTGC-ATCGTCGATCCACTTC-C
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * *
12858387 TACCAATATAGGAACACAAGACCTACTATCTTTGATCTACTTCAC
1 -ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * * *
12858432 GCCAATACATGAAGATAGGATCTGCT
1 ACCAATATAGGAAGACAAGATCTGCT
12858458 TTAATGACTT
Statistics
Matches: 454, Mismatches: 126, Indels: 36
0.74 0.20 0.06
Matches are distributed among these distances:
42 5 0.01
43 92 0.20
44 258 0.57
45 99 0.22
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.28
Consensus pattern (44 bp):
ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
Found at i:12858189 original size:132 final size:131
Alignment explanation
Indices: 12857993--12858459 Score: 566
Period size: 132 Copynumber: 3.5 Consensus size: 131
12857983 CTACTTCACG
* * * * * * * *
12857993 CCAATATATGAAGACAAAATCTGCTTTCTTTGATCTACTTC-CTACCAATATAGGAAGACAAGAT
1 CCAATATAGGAAGACAAGACCTACTATCTTTGATCTACTTCAC-GCCAATACATGAAGACAAGAT
** * * * * * * *
12858057 CTG-TAGCTTCGATCTACTTCACGCCAAC-ACAT-GATGATAAGATCTGCTTTCTTCGATCTACT
65 CTGCTTTCTGCGATCTACTT--CGCCACCAATATGGAAGATAAGATCTGC-ATCGTCGATCCACT
*
12858119 TCGCCA
127 TC-CTA
* * * *
12858125 CCAGTATGGGAAGACAAGATCTACTATCTTTGATCTACTTCATGCCAATACATGAAGACAAGATC
1 CCAATATAGGAAGACAAGACCTACTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATC
*
12858190 TGCTTTCTGCGATTTACTTCGCCACCAATATGGGAAGATAAGATCTGCATCGTCGATCCACTTCC
66 TGCTTTCTGCGATCTACTTCGCCACCAATAT-GGAAGATAAGATCTGCATCGTCGATCCACTTCC
12858255 TA
130 TA
* *
12858257 CCAATATAGGAAGA-TAGAACCTACTATCTTTGATCTACTTCACGCCAATACATGAAGATAAGAT
1 CCAATATAGGAAGACAAG-ACCTACTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGAT
*
12858321 CTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCGTCGATCCACTTC
65 CTGCTTTCTGCGATCTACTTCGCCACCAATAT-GGAAGATAAGATCTGCATCGTCGATCCACTTC
12858386 CTA
129 CTA
* * *
12858389 CCAATATAGGAACACAAGACCTACTATCTTTGATCTACTTCACGCCAATACATGAAGATAGGATC
1 CCAATATAGGAAGACAAGACCTACTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATC
12858454 TGCTTT
66 TGCTTT
12858460 AATGACTTCA
Statistics
Matches: 296, Mismatches: 32, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
131 8 0.03
132 247 0.83
133 27 0.09
134 14 0.05
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (131 bp):
CCAATATAGGAAGACAAGACCTACTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATC
TGCTTTCTGCGATCTACTTCGCCACCAATATGGAAGATAAGATCTGCATCGTCGATCCACTTCCT
A
Found at i:12879718 original size:23 final size:22
Alignment explanation
Indices: 12879692--12879736 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
12879682 ATATATATAT
*
12879692 TAAAAGATGTAATATTTTTAATA
1 TAAAA-ATGCAATATTTTTAATA
* *
12879715 TAAAAATGCATTGTTTTTAATA
1 TAAAAATGCAATATTTTTAATA
12879737 AGTGAAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.44
Consensus pattern (22 bp):
TAAAAATGCAATATTTTTAATA
Found at i:12905373 original size:34 final size:35
Alignment explanation
Indices: 12905316--12905382 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
12905306 CAAACACCAG
* *
12905316 AAAATATTTTCCAGTAAGTCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
12905351 AAAACATTTTCTAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
12905383 CATTTTACAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:12912472 original size:5 final size:5
Alignment explanation
Indices: 12912462--12912510 Score: 73
Period size: 5 Copynumber: 9.6 Consensus size: 5
12912452 CATAATTCAT
12912462 AATTC AATTC AATTC AATTC AATTC AATT- ACATTC AATTC AATATC AAT
1 AATTC AATTC AATTC AATTC AATTC AATTC A-ATTC AATTC AAT-TC AAT
12912511 ACTCACCTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
4 1 0.02
5 34 0.83
6 6 0.15
ACGTcount: A:0.43, C:0.18, G:0.00, T:0.39
Consensus pattern (5 bp):
AATTC
Found at i:12914222 original size:23 final size:23
Alignment explanation
Indices: 12914196--12914247 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
12914186 AGGGCTGGCT
12914196 TTGGATGCTATTCTTTATAGCTG
1 TTGGATGCTATTCTTTATAGCTG
12914219 TTGGATGCTATTCTTTATAGCTG
1 TTGGATGCTATTCTTTATAGCTG
12914242 TTGGAT
1 TTGGAT
12914248 TCAAAATGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.17, C:0.12, G:0.23, T:0.48
Consensus pattern (23 bp):
TTGGATGCTATTCTTTATAGCTG
Found at i:12927737 original size:69 final size:69
Alignment explanation
Indices: 12927617--12927790 Score: 201
Period size: 69 Copynumber: 2.5 Consensus size: 69
12927607 CTTTCCAAGG
* **
12927617 AAAATCAACTCATATTGCGAG-AGATGAATTGAGCCTCAAGACACGTTGAGGTATTTTTAATTT-
1 AAAATCAACTCATATTGCGAGAAG-TGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTA
12927680 T-TTAAA
65 TGTT--A
* * *
12927686 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCCGAGGTATTTTTAGTTTAT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTAT
*
12927751 GTTT
66 GTTA
* ** *
12927755 TAAATTGACTCATATTGCGAGAAGTGAGTTAAGCCT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
12927791 TTTAATTTTT
Statistics
Matches: 91, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
69 86 0.95
70 3 0.03
71 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.32
Consensus pattern (69 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTAT
GTTA
Found at i:12927930 original size:74 final size:75
Alignment explanation
Indices: 12927808--12928010 Score: 336
Period size: 74 Copynumber: 2.7 Consensus size: 75
12927798 TTTGTTTTTC
* * *
12927808 AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
12927873 GTTGTC-AAA
66 GTTGTCAAAA
*
12927882 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
12927947 GTTGTCAAAAA
66 GTTGTC-AAAA
* *
12927958 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCCGAGGTA
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTA
12928011 TTTTTAGTTT
Statistics
Matches: 120, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
74 67 0.56
76 53 0.44
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.27
Consensus pattern (75 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
GTTGTCAAAA
Found at i:12928206 original size:76 final size:76
Alignment explanation
Indices: 12928080--12928284 Score: 356
Period size: 76 Copynumber: 2.7 Consensus size: 76
12928070 TTTGTTTTTC
* * *
12928080 AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
12928145 GTTGTCAAAAA
66 GTTGTCAAAAA
*
12928156 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
12928221 GTTGTCAAAAA
66 GTTGTCAAAAA
* *
12928232 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCCGAGGTA
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTA
12928285 TTTTTAGTTT
Statistics
Matches: 122, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 122 1.00
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (76 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
GTTGTCAAAAA
Found at i:12928362 original size:274 final size:270
Alignment explanation
Indices: 12927617--12928559 Score: 1617
Period size: 274 Copynumber: 3.5 Consensus size: 270
12927607 CTTTCCAAGG
* * * * *
12927617 AAAATCAACTCATATTGCGAGAGATGAATTGAGCCTCAAGACACGTTGAGGTATTTTTAA-TT-T
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCT
12927680 -TT-T-AAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCCGAGGTATTT
66 GTTGTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCCGAGGTATTT
12927742 TTAGTTTATGTTTTAAATTGACTCATATTGCGAGAAGTGAGTTAAGCCTTTTAATTTTTGTTTTT
131 TTAGTTTATGTTTTAAATTGACTCATATTGCGAGAAGTGAGTTAAGCCTTTTAATTTTTGTTTTT
12927807 CAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCAATTTC
196 CAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCAATTTC
12927872 TGTTGTCAAA
261 TGTTGTCAAA
*
12927882 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCT
12927947 GTTGTCAAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCCGAGGTAT
66 GTTGTC--AAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCCGAGGTAT
12928012 TTTTAGTTTATGTTTTAAATTGACTCATATTGCGAGAAGTGAGTTAAGCCTTTTAATTTTTGTTT
129 TTTTAGTTTATGTTTTAAATTGACTCATATTGCGAGAAGTGAGTTAAGCCTTTTAATTTTTGTTT
12928077 TTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCAATT
194 TTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCAATT
12928142 TCTGTTGTCAAAAA
259 TCTGTTGTC--AAA
*
12928156 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCT
12928221 GTTGTCAAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCCGAGGTAT
66 GTTGTC--AAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCCGAGGTAT
12928286 TTTTAGTTTATGTTTTAAATTGACTCATATTGCGAGAAGTGAGTTAAGCCTTTTAATTTTTGTTT
129 TTTTAGTTTATGTTTTAAATTGACTCATATTGCGAGAAGTGAGTTAAGCCTTTTAATTTTTGTTT
12928351 TTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCAATT
194 TTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCAATT
12928416 TCTGTTGTCAAA
259 TCTGTTGTCAAA
** ** *
12928428 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACATTGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCT
* * * * * **
12928493 GCTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATT
66 G-TTGTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCCGAGGTATT
12928558 TT
130 TT
12928560 CAATTTCTGC
Statistics
Matches: 649, Mismatches: 19, Indels: 14
0.95 0.03 0.02
Matches are distributed among these distances:
265 54 0.08
266 2 0.00
267 1 0.00
268 2 0.00
269 1 0.00
271 54 0.08
272 259 0.40
273 4 0.01
274 272 0.42
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (270 bp):
AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCT
GTTGTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCCGAGGTATTT
TTAGTTTATGTTTTAAATTGACTCATATTGCGAGAAGTGAGTTAAGCCTTTTAATTTTTGTTTTT
CAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCAATTTC
TGTTGTCAAA
Found at i:12928539 original size:75 final size:75
Alignment explanation
Indices: 12928354--12928935 Score: 778
Period size: 75 Copynumber: 7.5 Consensus size: 75
12928344 TTTGTTTTTC
* * * * *
12928354 AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCT
* *
12928419 G-TTGTCAAA
66 GCTTTTCAAG
*
12928428 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACATTGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCT
12928493 GCTTTTCAAG
66 GCTTTTCAAG
12928503 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCT
12928568 GCTTTTCAAG
66 GCTTTTCAAG
12928578 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTCCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAA----T
*
12928643 GTTCAATTTATGTTTTTC-A-
62 -TTC------TGCTTTTCAAG
12928662 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTCCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAA----T
*
12928727 GTTCAATTTATGTTTTTC-A-
62 -TTC------TGCTTTTCAAG
*
12928746 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACATTGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCT
*
12928811 GATTTTCAAG
66 GCTTTTCAAG
*
12928821 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAAGTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCT
*
12928886 GCTTTTCAAAAAA
66 GCTTTTC---AAG
12928899 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
12928936 GGCTCTCACG
Statistics
Matches: 475, Mismatches: 16, Indels: 30
0.91 0.03 0.06
Matches are distributed among these distances:
73 7 0.01
74 61 0.13
75 209 0.44
78 39 0.08
79 4 0.01
80 4 0.01
84 143 0.30
85 1 0.00
86 7 0.01
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (75 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCT
GCTTTTCAAG
Found at i:12928701 original size:84 final size:86
Alignment explanation
Indices: 12928558--12928807 Score: 445
Period size: 84 Copynumber: 3.0 Consensus size: 86
12928548 TTGAGGTATT
* *
12928558 TTCAATTTCTGCTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACG
1 TTCAATTTATGTTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACG
12928623 TTGAGGTATTTTCAATTCCTG
66 TTGAGGTATTTTCAATTCCTG
12928644 TTCAATTTATGTTTTTC-A-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACG
1 TTCAATTTATGTTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACG
12928707 TTGAGGTATTTTCAATTCCTG
66 TTGAGGTATTTTCAATTCCTG
*
12928728 TTCAATTTATGTTTTTC-A-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACA
1 TTCAATTTATGTTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACG
12928791 TTGAGGTATTTTCAATT
66 TTGAGGTATTTTCAATT
12928808 TCTGATTTTC
Statistics
Matches: 161, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
84 145 0.90
85 1 0.01
86 15 0.09
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (86 bp):
TTCAATTTATGTTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACG
TTGAGGTATTTTCAATTCCTG
Found at i:12928722 original size:159 final size:156
Alignment explanation
Indices: 12928335--12929531 Score: 953
Period size: 159 Copynumber: 7.5 Consensus size: 156
12928325 TGAGTTAAGC
* * * * *
12928335 CTTTTAATTTTTGTTTTTC-AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACATG
1 CTTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACG
* *
12928399 CTGAGGTAATTTCAATTTCTG-TTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
66 CTGAGGTATTTTCAATTTCTGCTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
* **
12928463 TCAAGACACATTGAGGTATTTTCAA--
130 TCAGGACACGCTGAGGTATTTTCAATT
*
12928488 -TTTC------TGCTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
1 CTTTCAATTTATGTTTTTC-A-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
*
12928546 CGTTGAGGTATTTTCAATTTCTGCTTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
64 CGCTGAGGTATTTTCAATTTCTGCTTTTCAA-AAAATCAACTCATATTGCGAGAGGTGAGTTGAG
* *
12928611 CCTCAAGACACGTTGAGGTATTTTCAATT
128 CCTCAGGACACGCTGAGGTATTTTCAATT
12928640 CCTGTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
1 -CT-TTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
* *
12928705 CGTTGAGGTATTTTCAATTCCTGTTCAATTTATGTTTTTC-AAAAATCAACTCATATTGCGAGAG
64 CGCTGAGGTATTTTCAA----T-TTC------TGCTTTTCAAAAAATCAACTCATATTGCGAGAG
* **
12928769 GTGAGTTGAGCCTCAAGACACATTGAGGTATTTTCAA--
118 GTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
*
12928806 -TTTC------TGATTTTCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
1 CTTTCAATTTATGTTTTTC-A-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
* *
12928864 CGTTGAGGTATTTTCAAGTTCTGCTTTTCAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTT
64 CGCTGAGGTATTTTCAATTTCTGCTTTTC----AAAAAATCAACTCATATTGCGAGAGGTGAGTT
*
12928929 GAGCCTC-GGCTCTCACGCTGAGGTATTTTCAATTTTT
125 GAGCCTCAGG---ACACGCTGAGGTATTTTCAA---TT
* *
12928966 CGTTTTTTCAATTTATGCTTTTCAAATTCTACTTTTCCAAAATCAGCTCATATTGCAAGAGGTGA
1 C----TTTCAATTTATG--TTT----TTC-A-------AAAATCAACTCATATTGCGAGAGGTGA
** * * ** * *
12929031 GTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTACTG-TTTGGAAAAAACCAACTCATACTGC
48 GTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGCTTTTCAAAAAATCAACTCATATTGC
*
12929095 GAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAA--
113 GAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
* ** *
12929137 -TTTC----TGT-TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACG
1 CTTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACG
* * * *
12929196 CCGAGGTATTTTCAAATTCTAC-TTTCAAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCC
66 CTGAGGTATTTTCAATTTCTGCTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
* * * *
12929260 T-TGGCTCACG-TGTTGAGTCACTTTCAATTT
130 TCAGG-ACACGCTG-AG-GT-ATTTTCAA-TT
* * ** *
12929290 CTGTT---TTTATGTCTGTTTTC-TAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGG
1 CT-TTCAATTTATG--T-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGA
* ** * *
12929351 CACGCTGAGGTATTTTCAATTACTG-TTTGGAAAAAACCAACTCATACTGCGAGAGGTGAGTTGA
62 CACGCTGAGGTATTTTCAATTTCTGCTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
* *
12929415 GCCTCAGGACATGCTGAGGTATTTTCCGATT
127 GCCTCAGGACACGCTGAGGTATTTT-CAATT
* * * * *
12929446 CTATTTTTCAATTTATG-TTTTCAAAAATCAATTCATATTGCTAGAGGTGAATGGAGCCTCAGGT
1 C----TTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG-
* *
12929510 CATACGCCGAGGTATTTTCAAT
61 -ACACGCTGAGGTATTTTCAAT
12929532 AGATGTTTTT
Statistics
Matches: 868, Mismatches: 79, Indels: 186
0.77 0.07 0.16
Matches are distributed among these distances:
146 7 0.01
147 66 0.08
148 47 0.05
149 65 0.07
150 70 0.08
152 4 0.00
153 38 0.04
154 6 0.01
155 25 0.03
156 9 0.01
157 11 0.01
158 45 0.05
159 226 0.26
160 7 0.01
161 25 0.03
162 8 0.01
163 4 0.00
164 4 0.00
165 4 0.00
166 4 0.00
168 59 0.07
169 1 0.00
170 7 0.01
171 2 0.00
173 2 0.00
176 18 0.02
177 4 0.00
178 37 0.04
179 2 0.00
182 3 0.00
183 58 0.07
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.34
Consensus pattern (156 bp):
CTTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACG
CTGAGGTATTTTCAATTTCTGCTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
CAGGACACGCTGAGGTATTTTCAATT
Found at i:12929103 original size:73 final size:73
Alignment explanation
Indices: 12929004--12929440 Score: 437
Period size: 73 Copynumber: 5.8 Consensus size: 73
12928994 CTACTTTTCC
* *
12929004 AAAATCAGCTCATATTGCAAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTACT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTACT
12929069 GTTTGGAA
66 GTTTGGAA
* * * * * *
12929077 AAAACCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTACT
***
12929142 GTTTTTTCA
66 G-TTTGGAA
*
12929151 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTCAAATT-C
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTC-AATTAC
* **
12929215 TACTTTCAAA
65 T-GTTTGGAA
* * ** * *
12929225 AAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTTGGCTCACG-TGTTGAGTCACTTTCAATT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTG-AG-GT-ATTTTCAATT
* **
12929289 TCTGTTTTTATGTCTGTTTTC
63 ACTG---TT-TG---G---AA
* *
12929310 TAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTACT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTACT
12929375 GTTTGGAA
66 GTTTGGAA
* * * * *
12929383 AAAACCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTATTTTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTC
12929441 CGATTCTATT
Statistics
Matches: 295, Mismatches: 51, Indels: 36
0.77 0.13 0.09
Matches are distributed among these distances:
73 110 0.37
74 104 0.35
75 10 0.03
76 8 0.03
78 2 0.01
79 3 0.01
80 2 0.01
83 12 0.04
84 2 0.01
85 40 0.14
86 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (73 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTACT
GTTTGGAA
Found at i:12934834 original size:45 final size:45
Alignment explanation
Indices: 12934767--12934946 Score: 213
Period size: 45 Copynumber: 4.0 Consensus size: 45
12934757 ATAGATACAT
* * * **
12934767 GTGG-ATCAGCACACAAC-ACCACCCTTATAGTAAATGATACTAG
1 GTGGAATCAGCACACAGCAACCACCCTTATAATCAATGATACCCG
* * * *
12934810 GTGGAATTAGCACATAGCAACCA-CCTCCATAATCAATGGTACCCG
1 GTGGAATCAGCACACAGCAACCACCCT-TATAATCAATGATACCCG
* *
12934855 GTGAAATCAGCACACAGCAACCACCTTTATAATCAATGATACCCG
1 GTGGAATCAGCACACAGCAACCACCCTTATAATCAATGATACCCG
* *
12934900 GTGGAATCAGCACACAACAACCACCTTTATAATCAATGATACCCG
1 GTGGAATCAGCACACAGCAACCACCCTTATAATCAATGATACCCG
12934945 GT
1 GT
12934947 ACATGTAGTA
Statistics
Matches: 116, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
43 4 0.03
44 13 0.11
45 97 0.84
46 2 0.02
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.21
Consensus pattern (45 bp):
GTGGAATCAGCACACAGCAACCACCCTTATAATCAATGATACCCG
Found at i:12934923 original size:90 final size:89
Alignment explanation
Indices: 12934771--12934946 Score: 235
Period size: 90 Copynumber: 2.0 Consensus size: 89
12934761 ATACATGTGG
* * * * *
12934771 ATCAGCACACAACACCACCCTTATAGTAAATGATACTAGGTGGAATTAGCACATAGCAACCACCT
1 ATCAGCACACAACACCACCCTTATAATAAATGATACCAGGTGGAATCAGCACACAACAACCACCT
*
12934836 CCATAATCAATGGTACCCGGTGAA
66 CCATAATCAATGATACCCGGTGAA
* * * *
12934860 ATCAGCACACAGCAACCACCTTTATAATCAATGATACCCGGTGGAATCAGCACACAACAACCACC
1 ATCAGCACACAAC-ACCACCCTTATAATAAATGATACCAGGTGGAATCAGCACACAACAACCACC
**
12934925 TTTATAATCAATGATACCCGGT
65 TCCATAATCAATGATACCCGGT
12934947 ACATGTAGTA
Statistics
Matches: 74, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
89 12 0.16
90 62 0.84
ACGTcount: A:0.37, C:0.28, G:0.14, T:0.20
Consensus pattern (89 bp):
ATCAGCACACAACACCACCCTTATAATAAATGATACCAGGTGGAATCAGCACACAACAACCACCT
CCATAATCAATGATACCCGGTGAA
Found at i:12937419 original size:41 final size:39
Alignment explanation
Indices: 12937288--12937421 Score: 130
Period size: 40 Copynumber: 3.4 Consensus size: 39
12937278 CCAGTTTGGT
** * *
12937288 ACCCAGTACCTCATC-AGATAATTCGAAGTAATAAGTTGAT
1 ACCCAGTGTCTCATCGA-ATAATCCGAAGTAATAA-TTGAC
* * *
12937328 ACCCAGTGTCTTATCGAATAAACCGAAGT-A-AATTGGC
1 ACCCAGTGTCTCATCGAATAATCCGAAGTAATAATTGAC
*
12937365 ACCCAGTGCCTCATCGAATTAATCCGAAGTAATAGATTGAC
1 ACCCAGTGTCTCATCGAA-TAATCCGAAGTAATA-ATTGAC
*
12937406 ACTCAGTGTCTCATCG
1 ACCCAGTGTCTCATCG
12937422 GCTAAAAGTC
Statistics
Matches: 76, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
37 19 0.25
38 12 0.16
39 2 0.03
40 23 0.30
41 20 0.26
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (39 bp):
ACCCAGTGTCTCATCGAATAATCCGAAGTAATAATTGAC
Found at i:12937706 original size:40 final size:40
Alignment explanation
Indices: 12937662--12937798 Score: 163
Period size: 40 Copynumber: 3.5 Consensus size: 40
12937652 GGCGTTTGGA
12937662 TAAAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTT
1 TAAAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTT
* * * * * *
12937702 TAAAAAATGCCACTAAAGATCAAGTATTACCGGTGCTTTT
1 TAAAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTT
*
12937742 T-AAAAACGCCGCTAAAAAT-GAGCATTAGCGGCG-TTTT
1 TAAAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTT
* *
12937779 CTAAAAAGCGCCGCAAAAAA
1 -TAAAAAACGCCGCTAAAAA
12937799 CCTAAGTCCA
Statistics
Matches: 80, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
37 4 0.05
38 11 0.14
39 30 0.38
40 35 0.44
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (40 bp):
TAAAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTT
Found at i:12941385 original size:12 final size:12
Alignment explanation
Indices: 12941368--12941415 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
12941358 ATAAATACCA
12941368 AAAAATTATTTT
1 AAAAATTATTTT
*
12941380 AAAAATTA---A
1 AAAAATTATTTT
*
12941389 AAAAAGTATTTT
1 AAAAATTATTTT
12941401 AAAAA-TATTTT
1 AAAAATTATTTT
12941412 AAAA
1 AAAA
12941416 TTAAAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
9 7 0.23
11 10 0.33
12 13 0.43
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (12 bp):
AAAAATTATTTT
Found at i:12941393 original size:21 final size:21
Alignment explanation
Indices: 12941367--12941406 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
12941357 AATAAATACC
*
12941367 AAAAAATTATTTTAAAAATTA
1 AAAAAAGTATTTTAAAAATTA
12941388 AAAAAAGTATTTTAAAAAT
1 AAAAAAGTATTTTAAAAAT
12941407 ATTTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (21 bp):
AAAAAAGTATTTTAAAAATTA
Found at i:12941409 original size:11 final size:11
Alignment explanation
Indices: 12941368--12941455 Score: 55
Period size: 11 Copynumber: 8.4 Consensus size: 11
12941358 ATAAATACCA
12941368 AAAAATTATTTT
1 AAAAA-TATTTT
**
12941380 -AAAA-ATTAA
1 AAAAATATTTT
12941389 AAAAAGTATTTT
1 AAAAA-TATTTT
12941401 AAAAATATTTT
1 AAAAATATTTT
*
12941412 --AAA-A-TTA
1 AAAAATATTTT
* *
12941419 AAAAATA-ATA
1 AAAAATATTTT
12941429 AAAAAGTATTTT
1 AAAAA-TATTTT
12941441 AAAAATATTTT
1 AAAAATATTTT
12941452 AAAA
1 AAAA
12941456 TTAAAAATAT
Statistics
Matches: 60, Mismatches: 8, Indels: 17
0.71 0.09 0.20
Matches are distributed among these distances:
7 2 0.03
8 1 0.02
9 9 0.15
10 12 0.20
11 22 0.37
12 14 0.23
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:12941421 original size:17 final size:17
Alignment explanation
Indices: 12941399--12941485 Score: 66
Period size: 17 Copynumber: 4.8 Consensus size: 17
12941389 AAAAAGTATT
*
12941399 TTAAAAATATTTTAAAA
1 TTAAAAATATTTAAAAA
**
12941416 TTAAAAAATAATAAAAAAGTA
1 TT-AAAAAT-ATTTAAAA--A
*
12941437 TTTTAAAAATATTTTAAAA
1 -T-TAAAAATATTTAAAAA
12941456 TTAAAAATATTTAAAAA
1 TTAAAAATATTTAAAAA
* *
12941473 ATAAATATATTTA
1 TTAAAAATATTTA
12941486 TTATATCGGG
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
17 28 0.51
18 7 0.13
19 6 0.11
21 6 0.11
22 7 0.13
23 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (17 bp):
TTAAAAATATTTAAAAA
Found at i:12941471 original size:40 final size:39
Alignment explanation
Indices: 12941380--12941473 Score: 152
Period size: 40 Copynumber: 2.4 Consensus size: 39
12941370 AAATTATTTT
*
12941380 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTA
1 AAAAATTTAAAAAAGTATTTTAAAAATATTTTAAAATTA
*
12941419 AAAAATAATAAAAAAGTATTTTAAAAATATTTTAAAATTA
1 AAAAAT-TTAAAAAAGTATTTTAAAAATATTTTAAAATTA
12941459 AAAATATTTAAAAAA
1 AAAA-ATTTAAAAAA
12941474 TAAATATATT
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
39 6 0.12
40 42 0.84
41 2 0.04
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (39 bp):
AAAAATTTAAAAAAGTATTTTAAAAATATTTTAAAATTA
Found at i:12942169 original size:9 final size:9
Alignment explanation
Indices: 12942145--12942182 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
12942135 TACAAGTACC
12942145 TTTTATTA-
1 TTTTATTAT
12942153 TTTT-TTAT
1 TTTTATTAT
12942161 TTTTATTAT
1 TTTTATTAT
*
12942170 TATTATTAT
1 TTTTATTAT
12942179 TTTT
1 TTTT
12942183 TTCTAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
7 3 0.12
8 8 0.31
9 15 0.58
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTATTAT
Found at i:12944694 original size:43 final size:43
Alignment explanation
Indices: 12944568--12944893 Score: 288
Period size: 43 Copynumber: 7.6 Consensus size: 43
12944558 TATATTTTTT
* * * * * *
12944568 TAAAGGTTAT-GTTTTTAGCGGCGTTTTTGCGAGAAGCGCCGG
1 TAAAGGTTATGGTCTTTAGCAGCGTTTGTGGGAAAAGCGCCGC
* ** ** *
12944610 TAAAAGTTTAT--TCTTTAGTGGCGTTTGTGATAAAAACGCCGC
1 T-AAAGGTTATGGTCTTTAGCAGCGTTTGTGGGAAAAGCGCCGC
* * * *
12944652 TAAATGTTATGTTTTTTAGCAGC-TCTTGTGGGAAAAGTGCCGC
1 TAAAGGTTATGGTCTTTAGCAGCGT-TTGTGGGAAAAGCGCCGC
* * *
12944695 TAAAGGTCATGGTCTTTAGC-GACGTCTGTGGGAGAAGCGCCGC
1 TAAAGGTTATGGTCTTTAGCAG-CGTTTGTGGGAAAAGCGCCGC
* * *
12944738 TAAAGGTTATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGTCGC
1 TAAAGGTTATGGTCTTTAGCAGCGTTTGTGGGAAAAGCGCCGC
* * *
12944781 TAAAGGTCATGGTCTTTAGCAGCGTTTGTGGGAGAAGTGCCGC
1 TAAAGGTTATGGTCTTTAGCAGCGTTTGTGGGAAAAGCGCCGC
* * *
12944824 TAAATGTCT-TAGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
1 TAAAGGT-TATGGTCTTTAGCAGCGTTTGTGGGAAAAGCGCCGC
* *
12944867 TAAAGGTCT-TGTTCTTTAGCGGCGTTT
1 TAAAGGT-TATGGTCTTTAGCAGCGTTT
12944894 ATTTCTAAAA
Statistics
Matches: 231, Mismatches: 45, Indels: 15
0.79 0.15 0.05
Matches are distributed among these distances:
41 7 0.03
42 27 0.12
43 195 0.84
44 2 0.01
ACGTcount: A:0.21, C:0.16, G:0.30, T:0.33
Consensus pattern (43 bp):
TAAAGGTTATGGTCTTTAGCAGCGTTTGTGGGAAAAGCGCCGC
Found at i:12944767 original size:129 final size:128
Alignment explanation
Indices: 12944598--12944893 Score: 387
Period size: 129 Copynumber: 2.3 Consensus size: 128
12944588 GCGTTTTTGC
* * * * * * *
12944598 GAGAAGCGCCGGTAAAAGTTTATTCTTTAGTGGCGTTTGTGATAAAAACGCCGCTAAATGTTATG
1 GAGAAGCGCCGCTAAAGGTTTGTTCTTTAGCGGCGTTTGTGAGAAAAACGCCGCTAAAGGTCATG
* * *
12944663 TTTTTTAGCAGC-TCTTGTGGGAAAAGTGCCGCTAAAGGTCATGGTCTTTAGCGACGTCTGTGG
66 GTCTTTAGCAGCGT-TTGTGGGAAAAGTGCCGCTAAAGGTCATAGTCTTTAGCGACGTCTGTGG
* * *
12944726 GAGAAGCGCCGCTAAAGGTTATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCAT
1 GAGAAGCGCCGCTAAAGGTT-TGTTCTTTAGCGGCGTTTGTGAGAAAAACGCCGCTAAAGGTCAT
* * * * *
12944791 GGTCTTTAGCAGCGTTTGTGGGAGAAGTGCCGCTAAATGTCTTAGTCTTTAGCGGCGTTTGTGG
65 GGTCTTTAGCAGCGTTTGTGGGAAAAGTGCCGCTAAAGGTCATAGTCTTTAGCGACGTCTGTGG
*
12944855 GAAAAGCGCCGCTAAAGGTCTTGTTCTTTAGCGGCGTTT
1 GAGAAGCGCCGCTAAAGGT-TTGTTCTTTAGCGGCGTTT
12944894 ATTTCTAAAA
Statistics
Matches: 146, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
128 18 0.12
129 126 0.86
130 2 0.01
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (128 bp):
GAGAAGCGCCGCTAAAGGTTTGTTCTTTAGCGGCGTTTGTGAGAAAAACGCCGCTAAAGGTCATG
GTCTTTAGCAGCGTTTGTGGGAAAAGTGCCGCTAAAGGTCATAGTCTTTAGCGACGTCTGTGG
Found at i:12944892 original size:86 final size:86
Alignment explanation
Indices: 12944568--12944893 Score: 367
Period size: 86 Copynumber: 3.8 Consensus size: 86
12944558 TATATTTTTT
* * * * * * * *
12944568 TAAAGGTTATGTT-TTTAGCGGCGTTTTTGCGAGAAGCGCCGGTAAAAGTTTAT--TCTTTAGTG
1 TAAATGTTATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCT-AAAGGTCATGGTCTTTAGCG
** * *
12944630 GCGTTTGTGATAAAAACGCCGC
65 GCGTTTGTGGGAGAAGCGCCGC
* * *
12944652 TAAATGTTATGTTTTTTAGCAGC-TCTTGTGGGAAAAGTGCCGCTAAAGGTCATGGTCTTTAGCG
1 TAAATGTTATGTTCTTTAGCGGCGT-TTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCG
* *
12944716 ACGTCTGTGGGAGAAGCGCCGC
65 GCGTTTGTGGGAGAAGCGCCGC
* * *
12944738 TAAAGGTTATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCATGGTCTTTAGCAG
1 TAAATGTTATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGG
*
12944803 CGTTTGTGGGAGAAGTGCCGC
66 CGTTTGTGGGAGAAGCGCCGC
* *
12944824 TAAATGTCT-TAG-TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGTTCTTTAGC
1 TAAATGT-TAT-GTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGC
12944887 GGCGTTT
64 GGCGTTT
12944894 ATTTCTAAAA
Statistics
Matches: 205, Mismatches: 30, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
84 20 0.10
85 22 0.11
86 160 0.78
87 3 0.01
ACGTcount: A:0.21, C:0.16, G:0.30, T:0.33
Consensus pattern (86 bp):
TAAATGTTATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGG
CGTTTGTGGGAGAAGCGCCGC
Found at i:12945695 original size:7 final size:7
Alignment explanation
Indices: 12945679--12945746 Score: 54
Period size: 7 Copynumber: 9.9 Consensus size: 7
12945669 GTTTTATTAT
12945679 TATATAA
1 TATATAA
12945686 TATA-ATA
1 TATATA-A
12945693 TATATAA
1 TATATAA
*
12945700 TATATAC
1 TATATAA
12945707 T-TA-AA
1 TATATAA
*
12945712 CAT-TAA
1 TATATAA
*
12945718 GATATAA
1 TATATAA
12945725 TATTATAA
1 TA-TATAA
12945733 TATTATAA
1 TA-TATAA
12945741 TATATA
1 TATATA
12945747 TTTTAACTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
5 1 0.02
6 8 0.16
7 25 0.50
8 16 0.32
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (7 bp):
TATATAA
Found at i:12966565 original size:19 final size:19
Alignment explanation
Indices: 12966541--12966579 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
12966531 ATTCTTCACA
*
12966541 TCATTTGATGCTTGGATGT
1 TCATTTCATGCTTGGATGT
* *
12966560 TCATTTCTTGTTTGGATGT
1 TCATTTCATGCTTGGATGT
12966579 T
1 T
12966580 GATCTCATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.13, C:0.10, G:0.23, T:0.54
Consensus pattern (19 bp):
TCATTTCATGCTTGGATGT
Done.