Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 174 of 226
Found at i:53336897 original size:17 final size:17
Alignment explanation
Indices: 53336182--53338152 Score: 317
Period size: 17 Copynumber: 115.9 Consensus size: 17
53336172 TCCCCTCCCT
*
53336182 CTCCCTCC-CCTTCTCC
1 CTCCCTCCTCCTCCTCC
* *
53336198 TCTCCCTCTTCCTCCCCC
1 -CTCCCTCCTCCTCCTCC
*
53336216 CT-CC-CCTAACTTCCGTCC
1 CTCCCTCCT--CCTCC-TCC
53336234 CT-CCTCCTCC-CCTACC
1 CTCCCTCCTCCTCCT-CC
* *
53336250 CTCCCCCCT-CTCCTAC
1 CTCCCTCCTCCTCCTCC
*
53336266 TTCCCTCCT-C-CCTCC
1 CTCCCTCCTCCTCCTCC
*
53336281 CTTCCC-CCT-CTCCCCCC
1 C-TCCCTCCTCCT-CCTCC
*
53336298 CTTTCCCCTCC-CCCCCTCC
1 C--T-CCCTCCTCCTCCTCC
*
53336317 CTCCATCCT-CTCCT-C
1 CTCCCTCCTCCTCCTCC
*
53336332 CTCCC-CCCCTCTCCCTCC
1 CTCCCTCCTC-CT-CCTCC
*
53336350 CTCCCTTCTCTCCTCCCCC
1 CTCCC-TC-CTCCTCCTCC
*
53336369 CTCCCTCCCTCTCCCCTCC
1 CTCCCT-CCTC-CTCCTCC
*
53336388 CTCCCTTCCTACTCCTCC
1 CTCCC-TCCTCCTCCTCC
* * *
53336406 CTCTCCTCTTCTTCCCCC
1 CTC-CCTCCTCCTCCTCC
53336424 CTCCTCTCC-CTCTACCCTTCCC
1 CTCC-CTCCTC-CT--CC-T-CC
*
53336446 CTTCCCTCTCTCCCCCTCC
1 C-TCCCTC-CTCCTCCTCC
53336465 CTCCCGTCC-CTCTCC-CC
1 CTCCC-TCCTC-CTCCTCC
*
53336482 CTCCC-CC-CCACC-CC
1 CTCCCTCCTCCTCCTCC
53336496 C-CCCTCCTCC-CC-CC
1 CTCCCTCCTCCTCCTCC
* *
53336510 CTCCC-CCT-TTCCCCC
1 CTCCCTCCTCCTCCTCC
*
53336525 CT-CC-CCTCCCCCT-C
1 CTCCCTCCTCCTCCTCC
*
53336539 TTCCC-CC-CCT-CTCC
1 CTCCCTCCTCCTCCTCC
**
53336553 CTTTCTCCTCCTCCTCC
1 CTCCCTCCTCCTCCTCC
*
53336570 CTCCC-CCTCCCCCTCC
1 CTCCCTCCTCCTCCTCC
* *
53336586 C-CTCTTCC-CCCCCTCC
1 CTC-CCTCCTCCTCCTCC
*
53336602 CTACC-CCTCC-CCTCTC
1 CTCCCTCCTCCTCCTC-C
53336618 CTCCCT-CTCC-CCTCCC
1 CTCCCTCCTCCTCCT-CC
53336634 CTCCCCTCCTCTTCTCCTCC
1 CT-CCCTCCTC--CTCCTCC
*
53336654 TCTTCCCTCTTTCCCTCTTCTCCC
1 -C-TCCCTC-CT-CCTC--CT-CC
*
53336678 TCTCCCTCC-CCCCCTCC
1 -CTCCCTCCTCCTCCTCC
*
53336695 CTTCCTCTCCCCCTCCTCC
1 C-TCC-CTCCTCCTCCTCC
* * *
53336714 CCCCCCCCTTCTCC-CAC
1 CTCCCTCCTCCTCCTC-C
* *
53336731 CCCCCTCTTCCT-CTCC
1 CTCCCTCCTCCTCCTCC
53336747 TCTCCCGTCTCTCTCTCCTACTC
1 -CTCCC-TC-CTC-CTCCT-C-C
* *
53336770 CCCCCTCCTCC-CCTCTT
1 CTCCCTCCTCCTCCTC-C
* * *
53336787 CTCCCACCCCCTGTTCTCC
1 CTCCCTCCTCC--TCCTCC
*
53336806 CTCTC-CCTCTCTCCTCTC
1 CTCCCTCCTC-CTCCTC-C
* *
53336824 CT-CCTCTTCCTGCTTCC
1 CTCCCTCCTCCT-CCTCC
*
53336841 C-CCCTTCCTCTTCCCTCTC
1 CTCCC-TCCTCCT-CCTC-C
53336860 C-CCC-CCTCCTCCT-C
1 CTCCCTCCTCCTCCTCC
*
53336874 C-CCCTCCTCCTACTCC
1 CTCCCTCCTCCTCCTCC
53336890 CTCCCTCCTCC-CCTCC
1 CTCCCTCCTCCTCCTCC
* * *
53336906 CCCCCTCCCCCTCCTAC
1 CTCCCTCCTCCTCCTCC
*
53336923 CT-CC-CCGCCTCC-CC
1 CTCCCTCCTCCTCCTCC
*
53336937 C-CCCCCCTCCT--TCC
1 CTCCCTCCTCCTCCTCC
* **
53336951 CTCTCTTTTCTCTCCT-C
1 CTCCCTCCTC-CTCCTCC
*
53336968 TTCTCC-CCTCCT-CTCC
1 CTC-CCTCCTCCTCCTCC
*
53336984 CTCCC-CCTCC-CCCCC
1 CTCCCTCCTCCTCCTCC
53336999 CAT-CCTCC-CCTCCTCTC
1 C-TCCCTCCTCCTCCTC-C
*
53337016 TCTCCC-CTTACC-CCTCC
1 -CTCCCTCCT-CCTCCTCC
53337033 CTCCCTCCTCCT-CTCC
1 CTCCCTCCTCCTCCTCC
*
53337049 CTCTCCTCCCTCTTCC-CC
1 CTC-CCT-CCTCCTCCTCC
*
53337067 TCCCCCTCC-CCTCCTCC
1 -CTCCCTCCTCCTCCTCC
*
53337084 CTCCCCTCCCTCCTCCTCT
1 CT-CCCT-CCTCCTCCTCC
* *
53337103 TTCCCT--TCC-CCCCC
1 CTCCCTCCTCCTCCTCC
* *
53337117 CTCCCTTACTCCCCCTCC
1 CTCCC-TCCTCCTCCTCC
53337135 CTCCC-CCGTCC-CCT-C
1 CTCCCTCC-TCCTCCTCC
*
53337150 CTCCC-CCTTCCCCCTCC
1 CTCCCTCC-TCCTCCTCC
* *
53337167 CCCCCTCC-CCTTTCCTTC
1 CTCCCTCCTCC--TCCTCC
53337185 C-CCCT-CTCC-CC-CC
1 CTCCCTCCTCCTCCTCC
* *
53337198 CTCCC-CTTCCTCTCTTC
1 CTCCCTCCTCCTC-CTCC
* *
53337215 CTCCCCCCTCTTCC-CTC
1 CTCCCTCCTCCTCCTC-C
*
53337232 CTCCC-CTTCCTCTCTCC
1 CTCCCTCCTCCTC-CTCC
*
53337249 CTCCCTCCTCC-CCTCT
1 CTCCCTCCTCCTCCTCC
* **
53337265 CT-CCTCCCCCTTTTCC
1 CTCCCTCCTCCTCCTCC
*
53337281 CCCCTCTCCCTCCTTCC-CC
1 CTCC-CT-CCTCC-TCCTCC
*
53337300 CCCCCTCCT-CTCCTTCTTC
1 CTCCCTCCTCCTCC-TC--C
*
53337319 TCTCCCTCTTCC-CCTTCC
1 -CTCCCTCCTCCTCC-TCC
* *
53337337 CTCCTCTCTCTTTCTTCTCC
1 CTCC-CTC-C-TCCTCCTCC
53337357 CTCTACCTTTCCTTTCC-CTCTCC
1 CTC--CC--TCC--TCCTC-CTCC
*
53337380 CTTCCT-CTCC-CTCTCC
1 CTCCCTCCTCCTC-CTCC
*
53337396 CTCTCTCC-CCTCCTCC
1 CTCCCTCCTCCTCCTCC
* *
53337412 C-CCTTCTCTCCCCTCTCC
1 CTCCCTC-CTCCTC-CTCC
* *
53337430 CTTCCCCCCT-CTACCT-T
1 C-TCCCTCCTCCT-CCTCC
* *
53337447 CTTCCTCTTCCT-CTCC
1 CTCCCTCCTCCTCCTCC
*
53337463 TCTCCCTCC-CCTTCCTCT
1 -CTCCCTCCTCC-TCCTCC
53337481 CTCCCT-CT-C-CC-CC
1 CTCCCTCCTCCTCCTCC
53337494 CTACCC-CCTCCTCC-CC
1 CT-CCCTCCTCCTCCTCC
*
53337510 TTCCCTTCCTCCT-CTCC
1 CTCCC-TCCTCCTCCTCC
* * **
53337527 CCCCCTCCTCTTTTTTCC
1 CTCCCTCCTC-CTCCTCC
*
53337545 C-CTTCTCCCTCCTCCTCC
1 CTC-CCT-CCTCCTCCTCC
* *
53337563 CTTCTCTAC-CCT-CTCC
1 C-TCCCTCCTCCTCCTCC
53337579 CTCCTTCTCTTCTCCTCCTCC
1 CTCC--CTC--CTCCTCCTCC
53337600 CTCCC-CTCTCC-CCT-C
1 CTCCCTC-CTCCTCCTCC
53337615 CTCCC-CCTCC-CCT-C
1 CTCCCTCCTCCTCCTCC
*
53337629 CTCCC-CC-CCTCTTCC
1 CTCCCTCCTCCTCCTCC
53337644 C-CCCT-CTCGCTCCCTCTC
1 CTCCCTCCTC-CT-CCTC-C
53337662 CTCCCTCCTCC-CCTCC
1 CTCCCTCCTCCTCCTCC
53337678 C-CCCT--T-CTCC-CC
1 CTCCCTCCTCCTCCTCC
*
53337690 C-CCCTACTCC-CCTCC
1 CTCCCTCCTCCTCCTCC
* *
53337705 TCTCCCCCCCCCTCCT-C
1 -CTCCCTCCTCCTCCTCC
*
53337722 C-CCCTCC-CCTTCCCCC
1 CTCCCTCCTCC-TCCTCC
*
53337738 CTCTCTCTCTCTCTCC-CC
1 CTCCCTC-CTC-CTCCTCC
*
53337756 TTCTCCTCC-CC-CCTCCC
1 CTC-CCTCCTCCTCCT-CC
53337773 CTCCCTCCTCCTTCCTCC
1 CTCCCTCCTCC-TCCTCC
**
53337791 CTCTCCTCC-CCTTTTTCC
1 CTC-CCTCCTCC-TCCTCC
* * *
53337809 CCCCCCCCT-CTCCCCC
1 CTCCCTCCTCCTCCTCC
* *
53337825 CTTCCT-CTCCTCCACCC
1 CTCCCTCCTCCTCC-TCC
53337842 CTCCCT-CTCCTCCCTACC
1 CTCCCTCCTCCT-CCT-CC
*
53337860 CTCCCTCCTCCCCCT-C
1 CTCCCTCCTCCTCCTCC
*
53337876 CTACCC-CCCCCTACCTCCC
1 CT-CCCTCCTCCT-CCT-CC
*
53337895 CTCTCCTCTCTCCCCCTCTCC
1 CTC-CCTC-CT-CCTC-CTCC
* *
53337916 CTCCC-CCTTCTCCCCC
1 CTCCCTCCTCCTCCTCC
* *
53337932 CGTCCC-CC-CCCCCCCC
1 C-TCCCTCCTCCTCCTCC
53337948 CTCTCCTTCC-CCTCCTCC
1 CTC-CC-TCCTCCTCCTCC
53337966 GC-CCTCTCCTCCT-CTCTC
1 -CTCC-CTCCTCCTCCTC-C
53337984 CT-CCTCCTACC-CCTTCC
1 CTCCCTCCT-CCTCC-TCC
* *
53338001 CCCCCTCCTACTCCTCC
1 CTCCCTCCTCCTCCTCC
53338018 CTCACCCTCC-CCTCC-CC
1 CT--CCCTCCTCCTCCTCC
*
53338035 CCCCCTCCCTCCTCC-CC
1 CTCCCT-CCTCCTCCTCC
* *
53338052 TTCCC-CTCTCCTTCTCC
1 CTCCCTC-CTCCTCCTCC
53338069 C-CCCTCCT-CTCCCTCCC
1 CTCCCTCCTCCT-CCT-CC
53338086 CTCCCTCC-CTCTCC-CC
1 CTCCCTCCTC-CTCCTCC
* *
53338102 CCCCCTCCTCCCCCCTCC
1 CTCCCTCCT-CCTCCTCC
*
53338120 CTCCC-CTCTCCCCCTTCC
1 CTCCCTC-CTCCTCC-TCC
53338138 CTCCCTCCTCCTCCT
1 CTCCCTCCTCCTCCT
53338153 TCAACCTTGG
Statistics
Matches: 1456, Mismatches: 224, Indels: 548
0.65 0.10 0.25
Matches are distributed among these distances:
12 8 0.01
13 15 0.01
14 92 0.06
15 159 0.11
16 278 0.19
17 340 0.23
18 276 0.19
19 139 0.10
20 59 0.04
21 40 0.03
22 19 0.01
23 26 0.02
24 5 0.00
ACGTcount: A:0.01, C:0.68, G:0.01, T:0.30
Consensus pattern (17 bp):
CTCCCTCCTCCTCCTCC
Found at i:53336904 original size:37 final size:35
Alignment explanation
Indices: 53336158--53338152 Score: 342
Period size: 36 Copynumber: 57.4 Consensus size: 35
53336148 CACCCCCTTT
*
53336158 CTCCCCCT-TTCCTCTCCCCTCCCT-CT-CCCTCCC
1 CTCCCCCTCCTCCTCT-CCCTCCCTCCTCCCCTCCC
* * * * **
53336191 CTTCTCCT-CTCCCTCTTCCTCCCCCCTCCCCTAAC
1 CTCCCCCTCCT-CCTCTCCCTCCCTCCTCCCCTCCC
* *
53336226 TTCCGTCCCTCCTCCTC-CCCTACCCTCC-CCCCTCTC
1 CTCC--CCCTCCTCCTCTCCCT-CCCTCCTCCCCTCCC
*
53336262 CTACTTCCCTCCTCC-CTCCCTTCCC-CCTCTCCC-CCC
1 CT-C-CCCCTCCTCCTCTCCC-TCCCTCCTC-CCCTCCC
* * * * *
53336298 CTTTCCCCTCCCCCCCTCCCTCCATCCTCTCCTCCTC
1 C-TCCCCCTCCTCCTCTCCCTCCCTCCTCCCCTCC-C
* *
53336335 C-CCCCCT-CTCC-CTCCCTCCCTTCTCTCCTCCC
1 CTCCCCCTCCTCCTCTCCCTCCCTCCTCCCCTCCC
* *
53336367 C-CCTCCCT-C-CCTCTCCCCTCCCTCC-CTTCCTACTC
1 CTCC-CCCTCCTCCTCT-CCCTCCCTCCTC-CCCT-CCC
* *
53336402 CTCCCTCTCCTCTTCTTCCC-CCCTCCTCTCCCTCTACC
1 CTCCCCCTCCTCCTC-TCCCTCCCTCCTC-CCCTC--CC
* * *
53336440 CTTCCCCTTC-CCTCTCTCC-CCCTCCCTCCCGTCCC
1 CTCCCCCTCCTCCTCTC-CCTCCCT-CCTCCCCTCCC
* * * *
53336475 TCTCCCCCTCCCCCCCACCC-CCC-CCTCCTCCCCCC
1 -CTCCCCCTCCTCCTCTCCCTCCCTCCTCC-CCTCCC
* *
53336510 CTCCCCCT-TTCC-C-CCCT-CC-CCTCCCCCTCTTC
1 CTCCCCCTCCTCCTCTCCCTCCCTCCT-CCCCTC-CC
*
53336542 C-CCCCCT-CTCCCTTTCTCCT-CCTCCT-CCCTCCCC
1 CTCCCCCTCCT-CCTCTC-CCTCCCTCCTCCCCT-CCC
*
53336576 CTCCCCCTCC-CCTCTTCCCCCCCTCCCTACCCCTCCC
1 CTCCCCCTCCTCCTC-TCCCTCCCT-CCT-CCCCTCCC
*
53336613 CT-CTCCT-C-CCTCTCCC-CTCC-CCTCCCCTCCTC
1 CTCCCCCTCCTCCTCTCCCTC-CCTCCTCCCCTCC-C
* * ** *
53336645 TTCTCCTCCTCTTCC-CTCTTTCCCTCTTCTCCCTCTCC
1 --CTCCCCCTCCTCCTCTCCCTCCCTCCTC-CCCTC-CC
53336683 CTCCCCC-CCTCC-CTTCCTCTCCC-CCT--CCTCCC
1 CTCCCCCTCCTCCTC-TCC-CTCCCTCCTCCCCTCCC
* * * * * *
53336715 CCCCCCCTTCTCC-CACCC-CCCTCTTCCTCTCCT
1 CTCCCCCTCCTCCTCTCCCTCCCTCCTCCCCTCCC
**
53336748 CTCCCGTCTCTCTCTCCTACTCCC-CCCTCCTCCCCTCTT
1 CTCCC--C-CTC-CTCCT-CTCCCTCCCTCCTCCCCTCCC
* ** * * *
53336787 CTCCCACCCCCTGTTCTCCCTCTC-CCT-CTCTCCT
1 CTCCC-CCTCCTCCTCTCCCTCCCTCCTCCCCTCCC
* * *
53336821 CTCCTCCTCTTCCTGCTTCCC-CCCTTCCTCTTCCCTCTC
1 CTCCCCCTCCTCCT-C-TCCCTCCC-TCCTC--CCCTCCC
*
53336860 C-CCCCCTCCTCCTCCCCCT-CCTCCTACTCCCT-CC
1 CTCCCCCTCCTCCTCTCCCTCCCTCCT-C-CCCTCCC
* * * *
53336894 CTCCTCCCCTCCCCCCCTCCCCCTCCTACCTCCCCGCCTC
1 CT-C-CCCCTCCTCCTCTCCCTC-CCT-CCTCCCCTCC-C
* * * * * * *
53336934 CCCCCCCCCCTCCT-TCCCTCTCT-TTTCTCTCCT
1 CTCCCCCTCCTCCTCTCCCTCCCTCCTCCCCTCCC
* *
53336967 CTTCTCC-CCTCCTCTCCCTCCC-CCTCCCC-CCC
1 CTCCCCCTCCTCCTCTCCCTCCCTCCTCCCCTCCC
* * *
53336999 CATCCTCC-CCTCCTCTCTCTCCC-CTTACCCCT-CC
1 C-TCCCCCTCCTCCTCTCCCTCCCTCCT-CCCCTCCC
* *
53337033 CTCCCTCCTCCTCTCCCTCTCCTCCCTCTTCCCCTCCC
1 CTCCC-CCTCCTC-CTCTC-CCTCCCTCCTCCCCTCCC
*
53337071 C-CTCCCCTCCTCC-CTCCCCTCCCTCCTCCTCTTTCCC
1 CTC-CCCCTCCTCCTCT-CCCTCCCTCCTCC-C-CTCCC
* * **
53337108 TTCCCCCCCCTCC-CTTACTCCC-CCT-CCCTCCC
1 CTCCCCCTCCTCCTCTCCCTCCCTCCTCCCCTCCC
*
53337140 C-CGTCCCCTCCTCC-C-CCTTCCC-CCT-CCC-CCC
1 CTC--CCCCTCCTCCTCTCCCTCCCTCCTCCCCTCCC
* *
53337171 CT-CCCCT-TTCCT-TCCC-CCTCTCCCCCCCTCCC
1 CTCCCCCTCCTCCTCTCCCTCC-CTCCTCCCCTCCC
* * * *
53337203 CTTCCTCT-CTTC-CTCCC-CCCT-CTTCCCT--C
1 CTCCCCCTCCTCCTCTCCCTCCCTCCTCCCCTCCC
*
53337232 CTCCCCTTCCT-CTCTCCCTCCCTCCTCCCCTCTCTC
1 CTCCCCCTCCTCCTCTCCCTCCCTCCTCCCCTC-C-C
** * *
53337268 CTCCCCCTTTTCC-CCCCTCTCCCTCCTTCCCCCCCC
1 CTCCCCCTCCTCCTCTCC-CTCCCTCC-TCCCCTCCC
* * * * *
53337304 CT-CCTCTCCTTCT-TCTCTCCCTCTTCCCCTTCC
1 CTCCCCCTCCTCCTCTCCCTCCCTCCTCCCCTCCC
* * * * * *
53337337 CTCCTCTCTCTTTCTTCTCCCT--CTACCTTTCCTTTCC
1 CTCC-CCCTC-CTCCTCTCCCTCCCT-CC-TCCCCTCCC
*
53337374 CTCTCCCT--TCCTCTCCCTCTCCCTCTCTCCCCT--C
1 CTCCCCCTCCTCCTCT-CC-CTCCCTC-CTCCCCTCCC
* * *
53337408 CTCCCCCTTCT-CTC-CCCTCTC-CCT-TCC-CCC
1 CTCCCCCTCCTCCTCTCCCTCCCTCCTCCCCTCCC
* * * *
53337438 CTCTACCTTCTTCCTCTTCCT--CTCCTCTCCCTCCC
1 CTC-CCCCTCCTCCTCTCCCTCCCTCCTC-CCCTCCC
* * *
53337473 CTTCCTCT-CTCCCTCTCCC-CCCTACCCCCTCCTCCC
1 CTCCCCCTCCT-CCTCTCCCTCCCT-CCTCC-CCTCCC
* * * ***
53337509 CTTCCCTTCCTCCTCTCCCCCCCTCCTCTTTTTTCCC
1 CTCCCCCTCCTCCTCTCCCTCCCTCCTC--CCCTCCC
* * *
53337546 CTTCTCCCTCCT-C-CTCCCT-TCT-CTACCCTCTCC
1 C-TCCCCCTCCTCCTCTCCCTCCCTCCTCCCCTC-CC
* *
53337579 CTCCTTCTCTTCTCCTCCTCCCTCCC-CTCTCCCCT--C
1 CTCC--CCCTCCTCCT-CTCCCTCCCTC-CTCCCCTCCC
* * *
53337615 CTCCCCCTCC-CCTCCTCCCCCCCTCTTCCCC-CCT
1 CTCCCCCTCCTCCT-CTCCCTCCCTCCTCCCCTCCC
*
53337649 CTCGCTCCCT-CTCCTCCCTCCTCCCCTCC-CCCCTTCTCC
1 CTC-C-CCCTCCTCCTCTC-CCT-CCCTCCTCCCC-TC-CC
* *
53337688 C-CCCCCTACTCCCCTCCTCTCCC-CC-CCCCT--C
1 CTCCCCCTCCTCCTCTCC-CTCCCTCCTCCCCTCCC
53337719 CTCCCCCTCC-CCT-TCCC-CCCTCTCTCTCTCTCTCCC
1 CTCCCCCTCCTCCTCTCCCTCCCTC-CTC-C-C-CTCCC
* * *
53337755 CTTCTCCTCC-CCCCTCCCCTCCCTCCTCCTTCCTCCC
1 CTCCCCCTCCTCCTCT-CCCTCCCTCCTCC--CCTCCC
* * * * *
53337792 TCTCCTCC-CCT-TTTTCCCCCCCCCCTCTCCC-CCC
1 -CTCCCCCTCCTCCTCTCCCTCCCTCCTC-CCCTCCC
* * * *
53337826 TTCCTCTCCTCCACCCCTCCCTCTCCTCCCTACCCT-CC
1 CTCC-C-CCTCCTCCTCTCCCTC-CCT-CCTCCCCTCCC
* *
53337864 CTCCTCCC-CCTCCTAC-CCCCCCCTACCTCCCCTCTC
1 CTCC-CCCTCCTCCT-CTCCCTCCCT-CCTCCCCTCCC
* *
53337900 CT--CTCTCCCCCTCTCCCTCCC-CCTTCTCCC-CCC
1 CTCCCCCTCCTCCTCTCCCTCCCTCC-TC-CCCTCCC
* *
53337933 GTCCCCC-CC-CC-C-CCC-CTCTCCTTCCCCTCCTC
1 CTCCCCCTCCTCCTCTCCCTCCCTCC-TCCCCTCC-C
* * *
53337965 CGCCCTCTCCTCCTCTCTCCT-CCTCCTACCCCT-TC
1 CTCCCCCTCCTCCTCTC-CCTCCCTCCT-CCCCTCCC
* *
53338000 C-CCCCCTCCTACTCCTCCCTCAC-CCTCCCCTCCC
1 CTCCCCCTCCTCCT-CTCCCTCCCTCCTCCCCTCCC
* * *
53338034 C-CCCCCTCCCTCCTC-CCCTTCC-CCTCTCCT--T
1 CTCCCCCT-CCTCCTCTCCCTCCCTCCTCCCCTCCC
53338065 CT-CCCC-CCTCCTCTCCCTCCCCTCCCTCCCTCTCCC
1 CTCCCCCTCCTCCTCTCCCT-CCCT-CCTCCC-CTCCC
* *
53338101 C-CCCCCTCCTCCCCCCTCCCTCCC-CTCTCCCCCTTCC
1 CTCCCCCTCCT--CCTCTCCCTCCCTC-CT-CCCCTCCC
53338138 CTCCCTCCTCCTCCT
1 CTCCC-CCTCCTCCT
53338153 TCAACCTTGG
Statistics
Matches: 1441, Mismatches: 275, Indels: 488
0.65 0.12 0.22
Matches are distributed among these distances:
28 8 0.01
29 26 0.02
30 31 0.02
31 73 0.05
32 93 0.06
33 203 0.14
34 180 0.12
35 182 0.13
36 248 0.17
37 222 0.15
38 107 0.07
39 63 0.04
40 5 0.00
ACGTcount: A:0.01, C:0.68, G:0.01, T:0.30
Consensus pattern (35 bp):
CTCCCCCTCCTCCTCTCCCTCCCTCCTCCCCTCCC
Found at i:53336935 original size:45 final size:46
Alignment explanation
Indices: 53336842--53336935 Score: 111
Period size: 45 Copynumber: 2.1 Consensus size: 46
53336832 CCTGCTTCCC
* * * * *
53336842 CCCTTCCTCTTCCCTCTCCCCCCCTCCTCCTCCCCCTCCTCCTACT
1 CCCTCCCTCCTCCCTCTCCCCCCCTCCCCCTCCACCTCCTCCGACT
*
53336888 CCCTCCCTCCTCCC-CTCCCCCCCTCCCCCTCCTACCTCC-CCGCCT
1 CCCTCCCTCCTCCCTCTCCCCCCCTCCCCCTCC-ACCTCCTCCGACT
53336933 CCC
1 CCC
53336936 CCCCCCCCTC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
45 24 0.59
46 17 0.41
ACGTcount: A:0.02, C:0.72, G:0.01, T:0.24
Consensus pattern (46 bp):
CCCTCCCTCCTCCCTCTCCCCCCCTCCCCCTCCACCTCCTCCGACT
Found at i:53337049 original size:55 final size:55
Alignment explanation
Indices: 53336930--53337102 Score: 151
Period size: 55 Copynumber: 3.1 Consensus size: 55
53336920 TACCTCCCCG
* * * * *
53336930 CCTCCCCCCCCCCCTCCTTCCCTCTCTTTTCTCTCCTCTTCTCCCCTCCTCTCCCTCC-
1 CCTCTCCCCCCCCCTCC-TCCC-CTCCTCTCTCTCCCCTT-ACCCCTCC-CTCCCTCCT
*
53336988 CC-CTCCCCCCCCATCCTCCCCTCCTCTCTCTCCCCTTACCCCTCCCTCCCTCCT
1 CCTCTCCCCCCCCCTCCTCCCCTCCTCTCTCTCCCCTTACCCCTCCCTCCCTCCT
* *
53337042 CCTCTCCCTCTCCTCCCTCTTCCCCTCC-C-C-CTCCCC-TCCTCCCTCCCCTCCCTCCT
1 CCTCTCCC-C-CC-CCCTCCTCCCCTCCTCTCTCTCCCCTTAC-CCCT-CCCTCCCTCCT
53337098 CCTCT
1 CCTCT
53337103 TTCCCTTCCC
Statistics
Matches: 99, Mismatches: 9, Indels: 16
0.80 0.07 0.13
Matches are distributed among these distances:
53 8 0.08
54 11 0.11
55 29 0.29
56 22 0.22
57 15 0.15
58 14 0.14
ACGTcount: A:0.01, C:0.69, G:0.00, T:0.30
Consensus pattern (55 bp):
CCTCTCCCCCCCCCTCCTCCCCTCCTCTCTCTCCCCTTACCCCTCCCTCCCTCCT
Found at i:53337099 original size:106 final size:104
Alignment explanation
Indices: 53336970--53338151 Score: 333
Period size: 103 Copynumber: 11.3 Consensus size: 104
53336960 CTCTCCTCTT
53336970 CTCCCCTCCT--CT-CCCTCCC-CCTCCCCCCCCATCCTCCCCTCCTCTCTCTCCCCTTACCCCT
1 CTCCCCTCCTCCCTCCCCTCCCTCCTCCCCCCCC-TCCTCCCCTCCTCTCTCTCCCCTT-CCCCT
53337031 CCCTCCCTCCTCCTCTCCCTCTCCTCCCTCTTCCCCTCCCC
64 CCCTCCCTCCTCCTCTCCCTCTCCTCCCTCTTCCCCTCCCC
* *** * *
53337072 CTCCCCTCCTCCCTCCCCTCCCTCCTCCTCTTTC-CCTTCCC-CC-C-C-CT-CCCTTACTCC-C
1 CTCCCCTCCTCCCTCCCCTCCCTCCTCCCCCCCCTCCTCCCCTCCTCTCTCTCCCCTT-CCCCTC
* *
53337130 CCTCCCTCC-CC-CGTCCC-CTCCTCCCCCTTCCCC-CTCC
65 CCTCCCTCCTCCTC-TCCCTCTCCTCCCTCTTCCCCTCCCC
* * * *
53337167 C-CCCCTCC-CCTTTCCTTCCC-CCTCTCCCCCCCT-C-CCCTTCCTCTCT-TCCTCC--CCCCT
1 CTCCCCTCCTCCCTCCCCTCCCTCCTC-CCCCCCCTCCTCCCCTCCTCTCTCTCC-CCTTCCCCT
* * * *
53337224 -CTTCCCTCCTCCCCTTCCTCTCTCCCTCCCTCCTCCCCTCTCTC
64 CCCTCCCTCCTCCTC-TCC-CTCT-CCTCCCTCTTCCCCTC-CCC
** * *
53337268 CTCCCCCTTTTCCC-CCCTCTCCCTCCTTCCCCCCC-CCTCCTCTCCTTCTTCTCTCCCTCTTCC
1 CT-CCCCTCCTCCCTCCC-CTCCCTCCTCCCCCCCCTCCTCCCCTCC-TC-TCTCTCCC-CTTCC
* *
53337331 CCTTCCCTCCTCTCTCTTTCTTCTCCCTCTACCTTTCCT-TTCCCTCTCCCTTC
61 CC-TCCCTCC-CTC-C--TCCTCTCCCTCT-CC-TCCCTCTTCCC-CTCCC--C
* ** * *
53337384 CTCTCCCT-CTCCCT-CTCTCCCCTCCTCCCCCTTCT-CTCCCCT-CTCCCTTCCCCCCTCTACC
1 CTC-CCCTCCTCCCTCCCCT-CCCTCCTCCCCCCCCTCCTCCCCTCCTCTC-TCTCCCCT-T-CC
* * * *
53337445 TTCTTCCTCTTCCT-CTCCTCTCCCTCCCCTTCCTCTCTCCCTCTCCCCC
61 --CCTCC-CTCCCTCCTCCTCTCCCTCTCCTCCCTCT-TCCC-CT-CCCC
* * * * * *
53337494 CTACCC-CCT-CCTCCCCTTCCCT--T-CCTCCTCTCCCCCCCTCCTCTTTTTTCCCCTTCTCCC
1 CTCCCCTCCTCCCTCCCC-TCCCTCCTCCCCCCCCTCCTCCCCTCCTC-TCTCTCCCCTTC-CCC
* * ** *
53337554 T-CCT-CCTCCCTTCTCTACCCTCTCCCTCCTTC-TCTTCTCCTC
63 TCCCTCCCT-CCTCCTCT-CCCTCT-CCTCCCTCTTCCCCTCCCC
* * * *
53337596 CT-CCCTCC-CCTCTCCCCT-CCTCC-CCCTCCCCTCCTCCCCCCCTCT-TC-CCCCCTCTCGCT
1 CTCCCCTCCTCC-CTCCCCTCCCTCCTCCCCCCCCTCCTCCCCTCCTCTCTCTCCCCTTC-CCCT
53337655 CCCTCTCCTCCCTCCTC-CCCTC-CC-CCCT-TCTCCCC-CCCC
64 CCCTC-CCT-CCTCCTCTCCCTCTCCTCCCTCT-TCCCCTCCCC
*
53337694 TACTCCCCTCCTCTCC-CCCC-CCCTCCTCCCCCTCCCCTTCCCCCCTCTCTCTCTCTCTCCCCT
1 --CTCCCCTCCTC-CCTCCCCTCCCTCCT-CCCC-CCCC-TCCTCCC-CTC-CTCTCTCTCCCCT
* *
53337757 TCTCCTCCC-CCCTCC-CCTCCCTCCTCCTTCCTCCCTCTCCTCCCCTTTTTCCCC
58 TCCCCTCCCTCCCTCCTCCTCTC-CCT-C-TCCTCCCTCT--TCCCC----TCCCC
* * * * * *
53337811 CCCCCCT-CTCCC-CCCTTCCTCTCCT-CCACCCCTCCCTCTCCTCC-CTACCCTCCCTCCTCCC
1 CTCCCCTCCTCCCTCCCCTCC-CTCCTCCCCCCCCT-CCTCCCCTCCTCT-CTCT-CC-CCTTCC
* * * *
53337872 CCTCCTACCCCCCCCTACCTC-CCCTCTCCT--CTCTCCCCCTCTCC
61 CCTCC--CTCCCTCCT-CCTCTCCCTCTCCTCCCTCTTCCCCTCCCC
* * * * * * * *
53337916 CTCCCCCTTCTCCC-CCCGTCCCCCCCCCCCCCCTCTCCTTCCCCTCCTCCGCCCTCTCC-TCCT
1 CT-CCCCTCCTCCCTCCCCTCCCTCCTCCCCCCC-CTCC-TCCCCTCCT-CTCTCTCCCCTTCCC
* * * *
53337979 CTCTCCT-CCTCCTACCCCTTCCC-CCCCT-CCTACTCCTCCCTCACC
62 CTC-CCTCCCTCCT-CCTC-TCCCTCTCCTCCCT-CTTC-CCCTCCCC
*
53338024 CTCCCCTCC-CCC-CCCCTCCCTCCTCCCCTTCCCCTCTCCTTCTCCCCCCTC-CTCT-CCC-TC
1 CTCCCCTCCTCCCTCCCCTCCCTCCT-CCC--CCCC-CTCC-TC-CCCTCCTCTCTCTCCCCTTC
* * * *
53338084 CCCTCCCTCCCT-CTCC-CCCCCCCTCCTCCCCCCT-CCCTCCCC
60 CCCTCCCTCCCTCCTCCTCTCCCTCTCCTCCCTCTTCCCCTCCCC
*
53338126 TCTCCCC-CTTCCCT-CCCT-CCTCCTCC
1 -CTCCCCTCCTCCCTCCCCTCCCTCCTCC
53338152 TTCAACCTTG
Statistics
Matches: 814, Mismatches: 126, Indels: 281
0.67 0.10 0.23
Matches are distributed among these distances:
92 6 0.01
93 15 0.02
94 19 0.02
95 8 0.01
96 21 0.03
97 9 0.01
98 18 0.02
99 26 0.03
100 15 0.02
101 35 0.04
102 40 0.05
103 66 0.08
104 54 0.07
105 45 0.06
106 65 0.08
107 64 0.08
108 45 0.06
109 47 0.06
110 26 0.03
111 29 0.04
112 33 0.04
113 23 0.03
114 24 0.03
115 58 0.07
116 15 0.02
117 8 0.01
ACGTcount: A:0.01, C:0.69, G:0.00, T:0.30
Consensus pattern (104 bp):
CTCCCCTCCTCCCTCCCCTCCCTCCTCCCCCCCCTCCTCCCCTCCTCTCTCTCCCCTTCCCCTCC
CTCCCTCCTCCTCTCCCTCTCCTCCCTCTTCCCCTCCCC
Found at i:53337258 original size:41 final size:40
Alignment explanation
Indices: 53336167--53337791 Score: 96
Period size: 41 Copynumber: 40.6 Consensus size: 40
53336157 TCTCCCCCTT
* *
53336167 TCCTCTCCCCTC-CCTCTCCCTCCCCTT-CTCCTCTCCCT-CT
1 TCCTCCCCCCTCTCC-CT-CCTCCCCTTCCT-CTCTCCCTCCC
* * * *
53336207 TCCTCCCCCCTC-CCCTAACTTCCGTCCCTC-CT-CCTCCCC
1 TCCTCCCCCCTCTCCCT-CCTCCCCTTCCTCTCTCCCT-CCC
* * *
53336246 TACCCTCCCCCCTCT-CCTACTTCCC-TCCTCCCTCCCTTCCC
1 T--CCTCCCCCCTCTCCCTCCTCCCCTTCCTCTCTCCC-TCCC
* * * *
53336287 CCTCTCCCCCCCTTTCCCCTCCCCCCCTCCCTC-CAT-CCTCTCC
1 TC-CT-CCCCCCTCT-CCCTCCTCCCCTTCCTCTC-TCCCTC-CC
*
53336330 TCCTCCCCCCCTCTCCCTCC-CTCCCTTCTCTCCTCCCCCCTCCC
1 TCCT-CCCCCCTCTCCCTCCTC-CCCTTC-CT-CT-CTCCCTCCC
* * * *
53336374 TCCCTCTCCCCTCCCTCCCTTCCTACTCCTCCCTCTCCTCTTCTTCCC
1 T-CCTC-CCCC-CTCTCCC-TCCT-CCCCTTCCTCT-CTC--CCTCCC
*
53336422 CCCTCCTCTCCCTCTACCCT--TCCCCTTCC-CTCTCTCC-CCC
1 TCCTCC-C-CCCTCT-CCCTCCTCCCCTTCCTCTCTC-CCTCCC
* *
53336462 TCCCTCCCGTCCCTCTCCC-CCTCCCC--CC-CAC-CCCCCCC
1 T-CCTCCC--CCCTCTCCCTCCTCCCCTTCCTCTCTCCCTCCC
*
53336500 TCCTCCCCCC-CTCCC-CCTTTCCCC--CCTC-C-CCTCCCCC
1 TCCTCCCCCCTCTCCCTCC--TCCCCTTCCTCTCTCC-CTCCC
* * *
53336537 TCTTCCCCCCCTCTCCCT-TTCTCC-TCCTC-CTCCCTCCC
1 TCCT-CCCCCCTCTCCCTCCTCCCCTTCCTCTCTCCCTCCC
* *
53336575 -CCT-CCCCCTC-CCCT-CTTCCC--CC-C-CTCCCTACC
1 TCCTCCCCCCTCTCCCTCCTCCCCTTCCTCTCTCCCTCCC
* *
53336607 -CCTCCCCTCTCCTCCCT-CTCCCC-TCCCCTC-CCCT-CC
1 TCCTCCCCCCT-CTCCCTCCTCCCCTTCCTCTCTCCCTCCC
* * * * *
53336643 TCTTCTCCTCCTCTTCCCTCTTTCCC-T-CT-TCTCCCTCTC
1 TCCTC-CCCCCTC-TCCCTCCTCCCCTTCCTCTCTCCCTCCC
* * * *
53336682 -CCTCCCCCC-CTCCCTTCCTCTCCCCCTCCTCCCCCCCCCCTTC
1 TCCTCCCCCCTCTCCC-T-C-CTCCCCTTCCTCTCTCCCTCC--C
* *
53336725 TCCCACCCCCCTCTTCCTCTCCTCTCCCGTCTCTCTCTCCTACTCCC
1 T-CCTCCCCCCTC-TCC-CTCCTC-CCCTTC-CTCTCTCC--CTCCC
* * *
53336772 CCCTCCTCCCCTCTTCTCC-CAC-CCCCTGTTCTCCCTCTCCCTCTC
1 TCCTCC-CCCCTC-TC-CCTC-CTCCCC--TTC-CTCTCTCCCTCCC
* * * *
53336817 TCCTCTCCTCCTCTTCCTGCTTCCCC--CCT-TC-CTCTTCCC
1 TCCTC-CCCCCTCTCCCT-CCTCCCCTTCCTCTCTC-CCTCCC
*
53336856 T-CTCCCCCC-CT-CCTCCTCCCCCTCCTCCTACTCCCTCCC
1 TCCTCCCCCCTCTCCCTCCTCCCCTTCCT-CT-CTCCCTCCC
* *
53336895 TCCT--CCCCTC-CCCCCCTCCCCCTCCTAC-CTCCC-CGCC
1 TCCTCCCCCCTCTCCCTCCTCCCCTTCCT-CTCTCCCTC-CC
* * * * * * *
53336932 TCCCCCCCCCCCTCCTTCCCTCTCTTTTCTCTCCTCTTCTCCCC
1 TCCTCCCCCCTCTCCCT-CCTCCCCTTCCTCT-CTC-CCT-CCC
* *
53336976 TCCT-CTCCCTCCCCCTCC-CCCC--CCATC-CTCCC-CTCC
1 TCCTCCCCCCTCTCCCTCCTCCCCTTCC-TCTCTCCCTC-CC
* * *
53337012 TCTCTCTCCCCT-TACC-CCT-CCCTCCCTC-CTCCTCTCCC
1 TC-CTCCCCCCTCTCCCTCCTCCCCTTCCTCTCTCC-CTCCC
* * *
53337050 T-CTCCTCCCTCTTCC-CCTCCCCCTCC-C-CT-CCTCCC
1 TCCTCCCCCCTCTCCCTCCTCCCCTTCCTCTCTCCCTCCC
* * * *
53337085 TCC-CCTCCCTC-CTCCTCTTTCCCTTCC-C-CCCCCTCCC
1 TCCTCCCCCCTCTC-CCTCCTCCCCTTCCTCTCTCCCTCCC
* *
53337122 TTACTCCCCCTCCCTCCC-CCGTCCCC-TCCTC-C-CCCTTCCC
1 -TCCTCCCCC-CTCTCCCTCC-TCCCCTTCCTCTCTCCC-TCCC
*
53337162 -CCTCCCCCC-CTCCCCTTTCCTTCCC--CCTCTC-CCC-CCC
1 TCCTCCCCCCTCT-CCC--TCCTCCCCTTCCTCTCTCCCTCCC
** *
53337199 TCC-CCTTCCTCT-CTTCCTCCCC--CCTCT-TCCCT-CC
1 TCCTCCCCCCTCTCCCTCCTCCCCTTCCTCTCTCCCTCCC
* *
53337233 TCC-CCTTCCTCTCTCCCTCCCTCCTCC--CCTCTCTCCTCCCCC
1 TCCTCC--CCCCTCTCCCT-CCTCC-CCTTCCTCTCTCC-CTCCC
** ** *
53337275 TTTTCCCCCCTCTCCCTCCTTCCCCCCCCCTCCTCTCCTTCTTCTC
1 TCCTCCCCCCTCTCCCTCC-T-CCCCTTCCT-CTCTCC--C-TCCC
* * *
53337321 TCCCTCTTCCCCT-TCCCTCCTCTCTCTTTCT-TCTCCCTCTACC
1 T-CCTC-CCCCCTCTCCCTCCTC-CCCTTCCTCTCTCCCTC--CC
** *
53337364 TTTCCT-TTCCCTCTCCCTTCCTCTCCCTCTCC-CTCTCTC-CCC
1 --TCCTCCCCCCTCTCCC-TCCTC-CCCT-TCCTCTCTCCCTCCC
* * * * *
53337406 TCCTCCCCCTTCTCTCC-CCTCTCCCTTCCCCCCTCTACCTTCT
1 TCCTCCCCCCTCTC-CCTCCTC-CCCTT--CCTCTCTCCCTCCC
**
53337449 TCCT-CTTCCTCTCCTCTCCCTCCCCTTCCTCTCTCCCTCTCCC
1 TCCTCCCCCCTCTCC-CT-CCTCCCCTTCCTCTCT-CC-CTCCC
* * * *
53337492 CCCTACCCCCTC-CTCC-CCTTCCCTTCCTCCTCTCCCCCCC
1 TCCTCCCCCCTCTC-CCTCCTCCCCTTCCT-CTCTCCCTCCC
*
53337532 TCCTCTTTTTTCCCCTTCTCCCTCCTCCTCCCTT-CTCTAC-CCTCTCCC
1 TCCTC------CCCCCTCTCCCTCCT-C-CCCTTCCTCT-CTCC-CTCCC
* * * *
53337580 TCCT-TCTCTTCT-CCTCCT-CCC-TCC-C-CTCTC-CCC
1 TCCTCCCCCCTCTCCCTCCTCCCCTTCCTCTCTCCCTCCC
*
53337613 TCCT-CCCCCTC-CCCTCCTCCCC-CCCTCT-TCCC-CCC
1 TCCTCCCCCCTCTCCCTCCTCCCCTTCCTCTCTCCCTCCC
* * *
53337648 T-CTCGCTCCCTCTCCTCCCTCCTCCCCTCCCCCCTTCTCCCCCCCC
1 TCCTC-C-CCC-CT-CTCCCTCCTCCCCT-TCCTC-TCT-CCCTCCC
*
53337694 TACTCCCCTCCTCTCCC-CC-CCCC-TCCTC-C-CCCTCCC
1 TCCTCCCC-CCTCTCCCTCCTCCCCTTCCTCTCTCCCTCCC
*
53337730 -CTTCCCCCCTCTCTCTCTCTCTCCCCTT-CTC-CTCCC-CCC
1 TCCTCCCCCCTCTC-C-CTC-CTCCCCTTCCTCTCTCCCTCCC
* *
53337769 TCC-CCTCCCTCCTCCTTCCTCCC
1 TCCTCCCCCCT-CTCCCTCCTCCC
53337792 TCTCCTCCCC
Statistics
Matches: 1182, Mismatches: 185, Indels: 439
0.65 0.10 0.24
Matches are distributed among these distances:
32 12 0.01
33 24 0.02
34 58 0.05
35 58 0.05
36 67 0.06
37 108 0.09
38 99 0.08
39 116 0.10
40 113 0.10
41 124 0.10
42 64 0.05
43 59 0.05
44 61 0.05
45 64 0.05
46 48 0.04
47 66 0.06
48 32 0.03
49 9 0.01
ACGTcount: A:0.01, C:0.68, G:0.00, T:0.30
Consensus pattern (40 bp):
TCCTCCCCCCTCTCCCTCCTCCCCTTCCTCTCTCCCTCCC
Found at i:53337325 original size:20 final size:19
Alignment explanation
Indices: 53337029--53337326 Score: 72
Period size: 19 Copynumber: 16.4 Consensus size: 19
53337019 CCCCTTACCC
53337029 CTCCCTCCCTCC-TCCTCT
1 CTCCCTCCCTCCTTCCTCT
*
53337047 CCCTCTCCTCCCT-CTTCCCCT
1 --CTC-CCTCCCTCCTTCCTCT
*
53337068 CCCCCTCCCCTCC-TCC-CT
1 CTCCCT-CCCTCCTTCCTCT
53337086 C-CCCTCCCTCC-TCCTCT
1 CTCCCTCCCTCCTTCCTCT
* * *
53337103 TTCCCTTCCC-CC-CCCTCC
1 CTCCC-TCCCTCCTTCCTCT
**
53337121 CTTACTCCC-CC-TCC-CT
1 CTCCCTCCCTCCTTCCTCT
* * *
53337137 CCCCCGTCCCCTCCTCCCCCTT
1 CTCCC-T-CCCTCCTTCCTC-T
* * * *
53337159 CCCCCTCCCCCCCTCCCCT
1 CTCCCTCCCTCCTTCCTCT
* *
53337178 TTCCTTCCC-CCTCTCC-C-
1 CTCCCTCCCTCCT-TCCTCT
53337195 C-CCCT-CC-CCTTCCTCT
1 CTCCCTCCCTCCTTCCTCT
*
53337211 CTTCCT-CC-CC--CCTCT
1 CTCCCTCCCTCCTTCCTCT
*
53337226 -TCCCTCCTCCCCTTCCTCT
1 CTCCCTCC-CTCCTTCCTCT
*
53337245 CTCCCTCCCTCC-TCCCCT
1 CTCCCTCCCTCCTTCCTCT
* *
53337263 CTCTCCTCCC-CCTT-TTCC
1 CTC-CCTCCCTCCTTCCTCT
* *
53337281 CCCCTCTCCCTCCTTCC-CC
1 CTCC-CTCCCTCCTTCCTCT
* *
53337300 CCCCCTCCTCTCCTTCTTCT
1 CTCCCTCC-CTCCTTCCTCT
53337320 CTCCCTC
1 CTCCCTC
53337327 TTCCCCTTCC
Statistics
Matches: 213, Mismatches: 35, Indels: 60
0.69 0.11 0.19
Matches are distributed among these distances:
14 7 0.03
15 12 0.06
16 17 0.08
17 25 0.12
18 45 0.21
19 57 0.27
20 30 0.14
21 14 0.07
22 6 0.03
ACGTcount: A:0.00, C:0.69, G:0.00, T:0.30
Consensus pattern (19 bp):
CTCCCTCCCTCCTTCCTCT
Found at i:53337460 original size:61 final size:61
Alignment explanation
Indices: 53337389--53337802 Score: 151
Period size: 62 Copynumber: 6.7 Consensus size: 61
53337379 CCTTCCTCTC
* * * * *
53337389 CCTCTCCCTCTCTCCCCTCCTCC-CCCTTCTCTCCC-CTCTCCCTTCCCCCCT-CTACCTTCTT
1 CCTCTTCCTCTCTCCCCTCCTCCTCCC-TCTCTCCCTCTCCCCCCTACCCCCTCCT-CC-CCTT
*
53337450 CCTCTTCCTCTCCTCTCCCTCC-CCTTCCTCTCTCCCTCTCCCCCCTACCCCCTCCTCCCCTT
1 CCTCTTCCTCT-CTC-CCCTCCTCCTCCCTCTCTCCCTCTCCCCCCTACCCCCTCCTCCCCTT
* * * * * *
53337512 CC-CTTCCTCCTCTCCCCCCCTCCT-CTTTTTTCCCCTTCTCCCTCCT-CCTCCCTTCTCTACCC
1 CCTCTTCCT-CTCTCCCCTCCTCCTCCCTCTCT-CCC-TCTCCCCCCTACC-CCC-TC-CTCCCC
53337574 TCT
60 T-T
*
53337577 CC-C-TCCTTCTCTTCTCCTCCTCCCTCCC-CTCTCCC-CTCCTCCCC--CTCCCCTCCTCCCC-
1 CCTCTTCC-TCTC-TCCCCTCCT-CCTCCCTCTCTCCCTCTCC-CCCCTAC-CCCCTCCTCCCCT
*
53337635 C
61 T
* * *
53337636 CCTCTTCCCCCCTCTCGCTCC-CTCTCCTCCCTC-CTCCC-CTCCCCCCT-TCTCC-CC-CCCCT
1 CCTCTT--CCTCTCTC-C-CCTC-CTCCTCCCTCTCTCCCTCTCCCCCCTACCCCCTCCTCCCCT
53337695 ACT
61 --T
* * * * *
53337698 CC-CCTCCTCTCCCCCCCCCTCCTCCCCCTC-CCCT-TCCCCCCT-CTCTCTCTCTCTCCCCTT
1 CCTCTTCCTCTCTCCCCTCCTCCTCCCTCTCTCCCTCTCCCCCCTAC-C-CCCTC-CTCCCCTT
* * * *
53337758 -CTCCTCCCCCCTCCCCTCCCTCCTCCTTC-CTCCCTCTCCTCCCCT
1 CCTCTTCCTCTCTCCCCT-CCTCCTCCCTCTCTCCCTCTCC-CCCCT
53337803 TTTTCCCCCC
Statistics
Matches: 271, Mismatches: 38, Indels: 86
0.69 0.10 0.22
Matches are distributed among these distances:
57 22 0.08
58 4 0.01
59 14 0.05
60 26 0.10
61 58 0.21
62 63 0.23
63 45 0.17
64 18 0.07
65 15 0.06
66 5 0.02
67 1 0.00
ACGTcount: A:0.01, C:0.67, G:0.00, T:0.31
Consensus pattern (61 bp):
CCTCTTCCTCTCTCCCCTCCTCCTCCCTCTCTCCCTCTCCCCCCTACCCCCTCCTCCCCTT
Found at i:53337711 original size:99 final size:99
Alignment explanation
Indices: 53337596--53338141 Score: 260
Period size: 91 Copynumber: 5.3 Consensus size: 99
53337586 TCTTCTCCTC
* *
53337596 CTCCCTCCCCTCTCCCCTCCTCCCCCTCCCCTCCTCCCCCCCTCTTCCCCCCTCTCGCTCCCTCT
1 CTCCCTCTCCTCTCCCC-CCTCCCCCTCCCCTCCTCCCCCCCTCTTCCCCCCTCTCCCTCCCTCT
53337661 CCTCCCTCCTCCCCTCCCCCCTTCTCCCCCCCCTA
65 CCTCCCTCCTCCCCTCCCCCCTTCTCCCCCCCCTA
* * *
53337696 CTCCC-CTCCTCT--CCCC-CCCCCT--CCTCC-CCCTCCC-CTTCCCCCCTCTCTCTCTCTCTC
1 CTCCCTCTCCTCTCCCCCCTCCCCCTCCCCTCCTCCCCCCCTCTTCCCCCCTCTCCCTCCCTCTC
* * *
53337753 C-CCTTCTCCTCCCC-CCTCCCC-TC-CCTCCTCCTTC
66 CTCC--CTCCTCCCCTCC-CCCCTTCTCC-CCCCCCTA
*** * * *
53337787 CTCCCTCTCCTC-CCCTTTTTCCCCCCCCCCT-CTCCCCCCTTCCTCTCCTCCACCCCTCCCTCT
1 CTCCCTCTCCTCTCCC-CCCTCCCCCTCCCCTCCTCCCCCCCT-CT-TCC-CC-CCTCTCCCTC-
* *
53337850 CCTC-CCTACCCTCC-CTCCT-CCCCCTCCTACCCCCCCCTA
60 CCTCTCCT-CCCTCCTCCCCTCCCCCCTTCT-CCCCCCCCTA
* * *
53337889 CCTCCCCTCTCCTCTCTCCCCCTCTCCCTCCCCCTTCTCCCCCCGTC--CCCCCC-C-CCC-CCC
1 -CT-CCCTCTCCTCTC-CCCCCTCCCCCT-CCCCTCCTCCCCCCCTCTTCCCCCCTCTCCCTCCC
*
53337949 TCTCCTTCCCCTCCTCCGCCCTCTCCTCCTCTCTCCTCCTCCTACCCCTT
62 TCTCC-T-CCCTCCT-C-CCCTC-CC-CC-CT-T-CTCC-CC--CCCCTA
* * * * *
53337999 CCCCCCCTCCTACTCCTCCCTCACCCTCCCCTCC-CCCCCCCTCCCTCCTCCCCT-TCCCCTCTC
1 CTCCCTCTCCT-CTCCCCCCTCCCCCTCCCCTCCTCCCCCCCT-CTTCC-CCCCTCT-CCCTC-C
* *
53338062 CTTCTCCCCCCTCCTCTCCCTCCCCTCCCTCCCTCTCCCCCCCCCTC
61 C-TCTCCTCCCTCCTC-CCCT-CCC-CCCT---TCT-CCCCCCCCTA
* * *
53338109 CTCCCCCCTCC-CTCCCCTCTCCCCCTTCCCTCC
1 CT-CCCTCTCCTCTCCCCCCTCCCCCTCCCCTCC
53338142 CTCCTCCTCC
Statistics
Matches: 341, Mismatches: 45, Indels: 111
0.69 0.09 0.22
Matches are distributed among these distances:
90 4 0.01
91 36 0.11
92 25 0.07
93 6 0.02
95 11 0.03
96 3 0.01
97 14 0.04
98 3 0.01
99 18 0.05
100 13 0.04
101 10 0.03
102 24 0.07
103 9 0.03
104 14 0.04
105 8 0.02
106 17 0.05
107 18 0.05
108 22 0.06
109 24 0.07
110 15 0.04
111 10 0.03
112 17 0.05
113 13 0.04
114 2 0.01
115 5 0.01
ACGTcount: A:0.01, C:0.72, G:0.01, T:0.26
Consensus pattern (99 bp):
CTCCCTCTCCTCTCCCCCCTCCCCCTCCCCTCCTCCCCCCCTCTTCCCCCCTCTCCCTCCCTCTC
CTCCCTCCTCCCCTCCCCCCTTCTCCCCCCCCTA
Found at i:53337944 original size:23 final size:23
Alignment explanation
Indices: 53337901--53337945 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
53337891 TCCCCTCTCC
* *
53337901 TCTCTCCCCCTCTCCCTCCCCCT
1 TCTCTCCCCCTCCCCCCCCCCCT
53337924 TCTC-CCCCCGTCCCCCCCCCCC
1 TCTCTCCCCC-TCCCCCCCCCCC
53337946 CCCTCTCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.00, C:0.76, G:0.02, T:0.22
Consensus pattern (23 bp):
TCTCTCCCCCTCCCCCCCCCCCT
Found at i:53338017 original size:55 final size:56
Alignment explanation
Indices: 53337943--53338127 Score: 143
Period size: 55 Copynumber: 3.3 Consensus size: 56
53337933 GTCCCCCCCC
* * * * * *
53337943 CCCCCCTCTCCTTCCCCT-CCTCCGCCCTCTCCTCCTCTCTCCT-CCTCCTACCCCTT
1 CCCCCCTCTCCTACCCCTCCCT-CACCCTCCCCTCCCCCCCCCTCCCTCCT-CCCCTT
*
53337999 CCCCCC-CTCCTACTCCTCCCTCACCCTCCCCTCCCCCCCCCTCCCTCCTCCCCTT
1 CCCCCCTCTCCTACCCCTCCCTCACCCTCCCCTCCCCCCCCCTCCCTCCTCCCCTT
* * * * * *
53338054 CCCCTCTCCTTCT-CCCCCCTCCTCTCCCTCCCCTCCCTCCCTCTCCC-CC-CCCCTCCT
1 CCCCCCT-CTCCTACCCCTC-CCTCACCCTCCCCTCCCCCCCCCTCCCTCCTCCCCT--T
53338111 CCCCCCTC-CCT-CCCCTC
1 CCCCCCTCTCCTACCCCTC
53338128 TCCCCCTTCC
Statistics
Matches: 105, Mismatches: 17, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
55 48 0.46
56 22 0.21
57 35 0.33
ACGTcount: A:0.02, C:0.72, G:0.01, T:0.25
Consensus pattern (56 bp):
CCCCCCTCTCCTACCCCTCCCTCACCCTCCCCTCCCCCCCCCTCCCTCCTCCCCTT
Found at i:53338032 original size:67 final size:61
Alignment explanation
Indices: 53337593--53338133 Score: 186
Period size: 67 Copynumber: 8.9 Consensus size: 61
53337583 TTCTCTTCTC
* *
53337593 CTCCTCCCTCCCCTCTCCCCTCCTCCC-CCTCC-C-CTCCTCCCC-CCCTCTTCCCCCCTCTCGC
1 CTCCTCCC-CACC-CTCCCCTCCCCCCTCCTCCTCTCTCCTCCCCTCCC-CTTCCCCCC-CTC-C
53337654 T
61 T
* * * * * *
53337655 C-CCTCTCCTCCCTCCTCCCCTCCCCCCTTCTCCCCCCCCTACTCCCCTCCTC-T-CCCCCC-CC
1 CTCCTC-CC-CAC-CCTCCCCTCCCCCC-TC-CTCCTCTCTCCTCCCCTCCCCTTCCCCCCCTCC
53337716 -
61 T
* *
53337716 CTCCT--CC-CCCTCCCCTTCCCCCCT-CT-CTCTCTCTCTCCCCTTCTCC-T-CCCCCCTCCC
1 CTCCTCCCCACCCTCCCC-TCCCCCCTCCTCCTCTCTC-CTCCCC-TCCCCTTCCCCCCCTCCT
** *
53337773 CTCCCTCCTCCTTCCTCCCTCTCCTCCCCT--T--T-T-TCC-CCCC-CCCCTCTCCCCCCTTCC
1 CT-CCTCC-CCACCCTCCC-CTCC-CCCCTCCTCCTCTCTCCTCCCCTCCCCT-TCCCCCCCTCC
53337830 T
61 T
* * * * * *
53337831 CTCCTCCAC-CCCTCCCTCTCCTCCCTAC-CCTCCCTCCTCCCC-CTCCTACCCCCCCCTACCT
1 CTCCTCCCCACCCTCCC-CTCCCCCCTCCTCCTCTCTCCTCCCCTCCCCT-TCCCCCCCT-CCT
* * * * * * *
53337892 CCCCTCTCCTCTCTCCCC-CTCTCCCTCCCCCT-TCTCC-CCCCGTCCCC--CCCCCCCCCCT
1 CTCCTCCCCACCCTCCCCTC-CCCCCTCCTCCTCTCTCCTCCCC-TCCCCTTCCCCCCCTCCT
*
53337950 CTCCT--TC-CCCT--CCTCCGCCCTCTCCTCCTCTCTCCTCCTCCTACCCCTTCCCCCCCTCCT
1 CTCCTCCCCACCCTCCCCTCC-CCC-CTCCTCCTCTCTCCTCC-CCT-CCCCTTCCCCCCCTCCT
* * *
53338010 ACTCCTCCCTCACCCTCCCCTCCCCCCCCCTCCCTCCTCCCCTTCCCCTCTCCTTCTCCCCCCTC
1 -CTCCTCCC-CACCCTCCCCTCCCCCCTCCT-CCT-CTCTCC-TCCCCTCCCCTTC-CCCCCCTC
53338075 CT
60 CT
* * * *
53338077 CTCCCTCCCCTCCCTCCCTCTCCCCCCCCCTCCTCCCCCCT-CCCTCCCCTCTCCCCC
1 CT-CCTCCCCACCCTCCC-CTCCCCCCTCCTCCTCTCTCCTCCCCTCCCCT-TCCCCC
53338134 TTCCCTCCCT
Statistics
Matches: 376, Mismatches: 43, Indels: 119
0.70 0.08 0.22
Matches are distributed among these distances:
53 7 0.02
54 14 0.04
55 34 0.09
56 17 0.05
57 24 0.06
58 28 0.07
59 13 0.03
60 31 0.08
61 34 0.09
62 45 0.12
63 20 0.05
64 6 0.02
65 21 0.06
66 27 0.07
67 50 0.13
68 5 0.01
ACGTcount: A:0.01, C:0.72, G:0.01, T:0.26
Consensus pattern (61 bp):
CTCCTCCCCACCCTCCCCTCCCCCCTCCTCCTCTCTCCTCCCCTCCCCTTCCCCCCCTCCT
Found at i:53377875 original size:27 final size:27
Alignment explanation
Indices: 53377845--53377993 Score: 214
Period size: 27 Copynumber: 5.6 Consensus size: 27
53377835 TTATTAAGTC
* *
53377845 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
53377872 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCA-ACT
*
53377900 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
53377927 CGCACACTTAGTGCTACAT-ATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* *
53377954 CGCACACTTAGTGCTACAT--TTAATT
1 CGCACACTTAGTGCTACATAATCAACT
53377979 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
53377994 GCACAATTTA
Statistics
Matches: 114, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
25 18 0.16
26 3 0.03
27 67 0.59
28 26 0.23
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:53377929 original size:55 final size:53
Alignment explanation
Indices: 53377845--53377993 Score: 219
Period size: 55 Copynumber: 2.8 Consensus size: 53
53377835 TTATTAAGTC
* * *
53377845 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACAT-ATCAACTCGCACACTTAGTGCTACAT-ATCAAACT
53377900 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATATCAAACT
1 CGCACACTTAGTGCTACATA-TCAACTCGCACACTTAGTGCTACATATCAAACT
* *
53377954 CGCACACTTAGTGCTACAT-TTAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATATCAACTCGCACACTTAGTGCT
53377994 GCACAATTTA
Statistics
Matches: 88, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
52 19 0.22
54 27 0.31
55 42 0.48
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.28
Consensus pattern (53 bp):
CGCACACTTAGTGCTACATATCAACTCGCACACTTAGTGCTACATATCAAACT
Found at i:53387995 original size:50 final size:52
Alignment explanation
Indices: 53387866--53388107 Score: 198
Period size: 50 Copynumber: 4.7 Consensus size: 52
53387856 AGGGATGAAA
**
53387866 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTATTAAGGATATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAC---CGAGGATA-GAGAGG
*
53387922 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA-GATA-AGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGGATAGAGAGG
* * * * **
53387972 TCCC-TCGTAAGACCATGTGTGGGACATGGCATGGGCACCGA-TAT-GAAAAC
1 TCCCAT-GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGGATAGAGAGG
* * * * * * *
53388022 TCTCATGTAAGACCATATCTGGGATATGACATTTGCAGTAC-AGGA-A-ACA--
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA--CCGAGGATAGAGAGG
*
53388071 TCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
53388108 TGTTATTATC
Statistics
Matches: 153, Mismatches: 26, Indels: 21
0.76 0.13 0.10
Matches are distributed among these distances:
49 32 0.21
50 73 0.48
51 4 0.03
52 6 0.04
53 1 0.01
56 37 0.24
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (52 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGGATAGAGAGG
Found at i:53403243 original size:20 final size:20
Alignment explanation
Indices: 53403218--53403447 Score: 336
Period size: 20 Copynumber: 11.5 Consensus size: 20
53403208 AAGCTTATAC
*
53403218 TAAGTAAATGGAATGGAAAG
1 TAAGTAAATGAAATGGAAAG
53403238 TAAGTAAATGAAATGGAAAG
1 TAAGTAAATGAAATGGAAAG
53403258 TAAGTAAATGAAATGGAAAG
1 TAAGTAAATGAAATGGAAAG
* *
53403278 CAAGTAAAAGAAACT-GAAAG
1 TAAGTAAATGAAA-TGGAAAG
*
53403298 TAAGTAAATGAAATAGAAAG
1 TAAGTAAATGAAATGGAAAG
*
53403318 TAAGTAAAAGAAATGGAAAG
1 TAAGTAAATGAAATGGAAAG
53403338 TAAGTAAATGAAATGGAAAG
1 TAAGTAAATGAAATGGAAAG
** *
53403358 TAAACAAAAGAAATGGAAAG
1 TAAGTAAATGAAATGGAAAG
*
53403378 TAAGTAAATGTAATGGAAAG
1 TAAGTAAATGAAATGGAAAG
* *
53403398 TAAGTAAATGTAATGGGAAG
1 TAAGTAAATGAAATGGAAAG
*
53403418 TAAGTAAATGTAATGGAAAG
1 TAAGTAAATGAAATGGAAAG
53403438 TAAGTAAATG
1 TAAGTAAATG
53403448 GAGTGGTTCA
Statistics
Matches: 191, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
19 1 0.01
20 189 0.99
21 1 0.01
ACGTcount: A:0.55, C:0.01, G:0.24, T:0.20
Consensus pattern (20 bp):
TAAGTAAATGAAATGGAAAG
Found at i:53403390 original size:10 final size:10
Alignment explanation
Indices: 53403377--53403447 Score: 58
Period size: 10 Copynumber: 7.1 Consensus size: 10
53403367 GAAATGGAAA
53403377 GTAAGTAAAT
1 GTAAGTAAAT
*
53403387 GTAATGGAAA-
1 GTAA-GTAAAT
53403397 GTAAGTAAAT
1 GTAAGTAAAT
**
53403407 GTAATGGGAA-
1 GTAA-GTAAAT
53403417 GTAAGTAAAT
1 GTAAGTAAAT
*
53403427 GTAATGGAAA-
1 GTAA-GTAAAT
53403437 GTAAGTAAAT
1 GTAAGTAAAT
53403447 G
1 G
53403448 GAGTGGTTCA
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
9 11 0.23
10 25 0.53
11 11 0.23
ACGTcount: A:0.48, C:0.00, G:0.27, T:0.25
Consensus pattern (10 bp):
GTAAGTAAAT
Found at i:53408555 original size:48 final size:48
Alignment explanation
Indices: 53408484--53408576 Score: 159
Period size: 48 Copynumber: 1.9 Consensus size: 48
53408474 TTTCTTTACT
*
53408484 TAAAAACGCCTAAGTCAGCCTAACTCGCAATGATAAAGGATTCAATAG
1 TAAAAACGCCTAAGTCAGCCTAACTCGCAAAGATAAAGGATTCAATAG
* *
53408532 TAAAAACGCCTAAGTCCGCCTAACTTGCAAAGATAAAGGATTCAA
1 TAAAAACGCCTAAGTCAGCCTAACTCGCAAAGATAAAGGATTCAA
53408577 CTGAATTCCT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.20
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAACTCGCAAAGATAAAGGATTCAATAG
Found at i:53408842 original size:17 final size:17
Alignment explanation
Indices: 53408786--53408846 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
53408776 CAAAAGCTAA
*
53408786 AATTAAAAGCTGTATAC
1 AATTAGAAGCTGTATAC
* *
53408803 AATTAGAA-CTCTAAGACAC
1 AATTAGAAGCTGT---ATAC
53408822 AATTAGAAGCTGTATAC
1 AATTAGAAGCTGTATAC
53408839 AATTAGAA
1 AATTAGAA
53408847 CTCTAAGTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
16 3 0.09
17 18 0.51
19 11 0.31
20 3 0.09
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (17 bp):
AATTAGAAGCTGTATAC
Found at i:53412504 original size:40 final size:40
Alignment explanation
Indices: 53412413--53412582 Score: 207
Period size: 40 Copynumber: 4.3 Consensus size: 40
53412403 TCCTCGTTCA
* * * * *
53412413 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
53412452 CATGCCTTCGGGACGTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
53412492 AATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * *
53412532 AATGCCCTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
53412572 AAGGCCTTCGG
1 AATGCCTTCGG
53412583 ATCTTAGTCC
Statistics
Matches: 112, Mismatches: 18, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
39 32 0.29
40 80 0.71
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:53416747 original size:48 final size:48
Alignment explanation
Indices: 53416666--53416759 Score: 143
Period size: 48 Copynumber: 2.0 Consensus size: 48
53416656 TCTTTACTTA
* * *
53416666 AAAATGCCTAATTCAGCCTAACTCGCAATGATAAAGGATTCAACAGTG
1 AAAACGCCTAAGTCAGCCTAACTCGCAAAGATAAAGGATTCAACAGTG
* *
53416714 AAAACGCCTAAGTCGGCCTAACTTGCAAAGATAAAGGATTCAACAG
1 AAAACGCCTAAGTCAGCCTAACTCGCAAAGATAAAGGATTCAACAG
53416760 AATTCCCTCA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.20
Consensus pattern (48 bp):
AAAACGCCTAAGTCAGCCTAACTCGCAAAGATAAAGGATTCAACAGTG
Found at i:53417005 original size:19 final size:19
Alignment explanation
Indices: 53416981--53417034 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 19
53416971 AAAGCTGTAT
53416981 ACAATTAGAACTCTAAGAC
1 ACAATTAGAACTCTAAGAC
* *
53417000 ACAATTAGAA-GCT--GTAT
1 ACAATTAGAACTCTAAG-AC
53417017 ACAATTAGAACTCTAAGA
1 ACAATTAGAACTCTAAGA
53417035 TTACATAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
16 1 0.04
17 11 0.39
18 4 0.14
19 11 0.39
20 1 0.04
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.24
Consensus pattern (19 bp):
ACAATTAGAACTCTAAGAC
Found at i:53417013 original size:36 final size:36
Alignment explanation
Indices: 53416966--53417034 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
53416956 CAAAGGCTAA
53416966 AATTAAAAGCTGTATACAATTAGAACTCTAAGACAC
1 AATTAAAAGCTGTATACAATTAGAACTCTAAGACAC
*
53417002 AATTAGAAGCTGTATACAATTAGAACTCTAAGA
1 AATTAAAAGCTGTATACAATTAGAACTCTAAGA
53417035 TTACATAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.26
Consensus pattern (36 bp):
AATTAAAAGCTGTATACAATTAGAACTCTAAGACAC
Found at i:53417022 original size:17 final size:17
Alignment explanation
Indices: 53416966--53417026 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
53416956 CAAAGGCTAA
*
53416966 AATTAAAAGCTGTATAC
1 AATTAGAAGCTGTATAC
* *
53416983 AATTAGAA-CTCTAAGACAC
1 AATTAGAAGCTGT---ATAC
53417002 AATTAGAAGCTGTATAC
1 AATTAGAAGCTGTATAC
53417019 AATTAGAA
1 AATTAGAA
53417027 CTCTAAGATT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
16 3 0.09
17 18 0.51
19 11 0.31
20 3 0.09
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (17 bp):
AATTAGAAGCTGTATAC
Found at i:53421523 original size:5 final size:5
Alignment explanation
Indices: 53421513--53421546 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
53421503 TATTTGTTAT
53421513 CTATA CTATA CTATA CTATA CTATA CTATA CTAT
1 CTATA CTATA CTATA CTATA CTATA CTATA CTAT
53421547 TATATTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (5 bp):
CTATA
Found at i:53422925 original size:18 final size:18
Alignment explanation
Indices: 53422894--53422941 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
53422884 TGTCGTTCGT
**
53422894 TTTCAAAACATTATTC-A
1 TTTCAAAATGTTATTCAA
*
53422911 TTTACAAATTGTTATTCAA
1 TTT-CAAAATGTTATTCAA
53422930 TTTCAAAATGTT
1 TTTCAAAATGTT
53422942 TTTTTATTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 3 0.12
18 18 0.72
19 4 0.16
ACGTcount: A:0.38, C:0.12, G:0.04, T:0.46
Consensus pattern (18 bp):
TTTCAAAATGTTATTCAA
Found at i:53425164 original size:18 final size:18
Alignment explanation
Indices: 53425143--53425184 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
53425133 AATTCGTTTT
53425143 CAAAACATTATTC-ATTCA
1 CAAAACATTATTCAATT-A
* *
53425161 CAAATCGTTATTCAATTA
1 CAAAACATTATTCAATTA
53425179 CAAAAC
1 CAAAAC
53425185 GGTTTTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.45, C:0.21, G:0.02, T:0.31
Consensus pattern (18 bp):
CAAAACATTATTCAATTA
Found at i:53437672 original size:21 final size:21
Alignment explanation
Indices: 53437648--53437692 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
53437638 CTACTGGTAT
*
53437648 AACTGTGAGTTCTACCAAGAC
1 AACTCTGAGTTCTACCAAGAC
* *
53437669 AACTCTGGGTTCTACCAATAC
1 AACTCTGAGTTCTACCAAGAC
53437690 AAC
1 AAC
53437693 CCAAACTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (21 bp):
AACTCTGAGTTCTACCAAGAC
Found at i:53440826 original size:50 final size:50
Alignment explanation
Indices: 53440761--53440893 Score: 160
Period size: 50 Copynumber: 2.7 Consensus size: 50
53440751 TAATGACATA
* ** * * *
53440761 TCCCAGATATAGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATG
1 TCCCAGATATGGTCTTACATGGGACCTCTCATATCGGTGACAACGCCATG
* *
53440811 TCCCAGATATGGTCTTA-AGGGGGACCTCTCATCTCGGTGACAACGCCATG
1 TCCCAGATATGGTCTTACA-TGGGACCTCTCATATCGGTGACAACGCCATG
* *
53440861 TCCCAGACATGGTCTTACGTGGGACCTCTCATA
1 TCCCAGATATGGTCTTACATGGGACCTCTCATA
53440894 ACCTCAATAA
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
49 1 0.01
50 68 0.99
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.27
Consensus pattern (50 bp):
TCCCAGATATGGTCTTACATGGGACCTCTCATATCGGTGACAACGCCATG
Found at i:53442311 original size:21 final size:21
Alignment explanation
Indices: 53442285--53442324 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
53442275 TACTTTCACA
53442285 AGTGCAATACTTTTATTCCTT
1 AGTGCAATACTTTTATTCCTT
*
53442306 AGTGCAATACTTTTGTTCC
1 AGTGCAATACTTTTATTCC
53442325 ATAATACTCT
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:0.23, C:0.20, G:0.12, T:0.45
Consensus pattern (21 bp):
AGTGCAATACTTTTATTCCTT
Found at i:53447603 original size:13 final size:13
Alignment explanation
Indices: 53447581--53447619 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
53447571 AAGTTCTTAG
53447581 TTCTTTTTTTCTT
1 TTCTTTTTTTCTT
*
53447594 TTCTTCTTTTCTT
1 TTCTTTTTTTCTT
*
53447607 TTATTTTTTTCTT
1 TTCTTTTTTTCTT
53447620 ATTGTTGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (13 bp):
TTCTTTTTTTCTT
Found at i:53449816 original size:45 final size:45
Alignment explanation
Indices: 53449748--53450008 Score: 283
Period size: 45 Copynumber: 5.8 Consensus size: 45
53449738 TTGGTTTGAA
53449748 AAACGAATAAGACCATAAG-TGAAAGACACTATGGCACTATACCAG
1 AAACGAATAAGACCAT-AGTTGAAAGACACTATGGCACTATACCAG
*
53449793 AAACGAATAAGACCATAGTTGAAAGACACTATGGCACTATA-CTG
1 AAACGAATAAGACCATAGTTGAAAGACACTATGGCACTATACCAG
* * * ** *
53449837 AAAATGAATAAGACCATAATTGAAAGACACTATGTCACGCTACCAA
1 -AAACGAATAAGACCATAGTTGAAAGACACTATGGCACTATACCAG
* * *
53449883 AAATGAATAAGACCATAGTTGAAAGACACTACGGCACTGTACCAG
1 AAACGAATAAGACCATAGTTGAAAGACACTATGGCACTATACCAG
* * * * ***
53449928 AAACGAATAAGACCATACTTGAATGACACAATGGCATTATGTTAG
1 AAACGAATAAGACCATAGTTGAAAGACACTATGGCACTATACCAG
* ** * * *
53449973 AGATAAATAAGACTATGGCTGAAAGACACTATGGCA
1 AAACGAATAAGACCATAGTTGAAAGACACTATGGCA
53450009 TCTCTGAACA
Statistics
Matches: 180, Mismatches: 33, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
44 4 0.02
45 175 0.97
46 1 0.01
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.20
Consensus pattern (45 bp):
AAACGAATAAGACCATAGTTGAAAGACACTATGGCACTATACCAG
Found at i:53449996 original size:135 final size:135
Alignment explanation
Indices: 53449746--53450005 Score: 353
Period size: 135 Copynumber: 1.9 Consensus size: 135
53449736 TATTGGTTTG
* *
53449746 AAAAACGAATAAGACCATAAGTGAAAGACACTATGGCACTATACCAGAAACGAATAAGACCATAG
1 AAAAACGAATAAGACCATAAGTGAAAGACACTACGGCACTATACCAGAAACGAATAAGACCATAC
* * *
53449811 TTGAAAGACACTATGGCACTATACTGAAAATGAATAAGACCATAATTGAAAGACACTATGTCACG
66 TTGAAAGACACAATGGCACTATACTGAAAATAAATAAGACCATAACTGAAAGACACTATGTCACG
53449876 CTACC
131 CTACC
* *
53449881 AAAAATGAATAAGACCAT-AGTTGAAAGACACTACGGCACTGTACCAGAAACGAATAAGACCATA
1 AAAAACGAATAAGACCATAAG-TGAAAGACACTACGGCACTATACCAGAAACGAATAAGACCATA
* * * * * * **
53449945 CTTGAATGACACAATGGCATTAT-GTTAGAGATAAATAAGACTATGGCTGAAAGACACTATG
65 CTTGAAAGACACAATGGCACTATACTGA-AAATAAATAAGACCATAACTGAAAGACACTATG
53450006 GCATCTCTGA
Statistics
Matches: 108, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
134 4 0.04
135 104 0.96
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.20
Consensus pattern (135 bp):
AAAAACGAATAAGACCATAAGTGAAAGACACTACGGCACTATACCAGAAACGAATAAGACCATAC
TTGAAAGACACAATGGCACTATACTGAAAATAAATAAGACCATAACTGAAAGACACTATGTCACG
CTACC
Found at i:53450187 original size:40 final size:40
Alignment explanation
Indices: 53450109--53450200 Score: 98
Period size: 40 Copynumber: 2.3 Consensus size: 40
53450099 TGTAAAATGA
*** *
53450109 ATATATGAAATGATTTTATGAATTGGTTCTATGAAAATAG
1 ATATATGAAATGATTTTATGAATCAATTATATGAAAATAG
*
53450149 ATATATTG-AATGATTTTATGAATCAATTATATGTAAATA-
1 ATATA-TGAAATGATTTTATGAATCAATTATATGAAAATAG
*
53450188 ATAATATAAAATG
1 AT-ATATGAAATG
53450201 TTTATACGAA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
39 3 0.07
40 38 0.88
41 2 0.05
ACGTcount: A:0.45, C:0.02, G:0.13, T:0.40
Consensus pattern (40 bp):
ATATATGAAATGATTTTATGAATCAATTATATGAAAATAG
Found at i:53453317 original size:15 final size:15
Alignment explanation
Indices: 53453297--53453326 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
53453287 GCTAAGTGAT
53453297 AACATGGTGATTGAA
1 AACATGGTGATTGAA
53453312 AACATGGTGATTGAA
1 AACATGGTGATTGAA
53453327 GCATGAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.27, T:0.27
Consensus pattern (15 bp):
AACATGGTGATTGAA
Found at i:53455707 original size:5 final size:5
Alignment explanation
Indices: 53455697--53455730 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
53455687 TATTTGTTAT
53455697 CTATA CTATA CTATA CTATA CTATA CTATA CTAT
1 CTATA CTATA CTATA CTATA CTATA CTATA CTAT
53455731 TATATTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (5 bp):
CTATA
Found at i:53466451 original size:24 final size:24
Alignment explanation
Indices: 53466424--53466474 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 24
53466414 GTAGGAGGTT
53466424 AATTTCATCTAAAATC-GATTAAAC
1 AATTTCATCTAAAATCAG-TTAAAC
53466448 AATTTCATCTAAAATCAGTTAAAC
1 AATTTCATCTAAAATCAGTTAAAC
53466472 AAT
1 AAT
53466475 AACCCAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (24 bp):
AATTTCATCTAAAATCAGTTAAAC
Found at i:53472171 original size:19 final size:19
Alignment explanation
Indices: 53472143--53472184 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
53472133 TCATCAATTA
53472143 ATTTAATAAT-ATTACTATT
1 ATTTAATAATCA-TACTATT
* *
53472162 ATTTATTAATCATATTATT
1 ATTTAATAATCATACTATT
53472181 ATTT
1 ATTT
53472185 GTATTATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTAATAATCATACTATT
Found at i:53474715 original size:45 final size:45
Alignment explanation
Indices: 53474623--53474716 Score: 134
Period size: 45 Copynumber: 2.1 Consensus size: 45
53474613 AACCCCTGTT
* *
53474623 GTGCGAGCCCCTATCATGCGAACCCTAGTATAGGCCAGCCCTATC
1 GTGCGAGCCCCTATCATGCAAACCCTAGTATAAGCCAGCCCTATC
* * * *
53474668 GTGCGAGCCCCTATCTTGCAAACCCTAGTATAAGCGAGCCTTGTC
1 GTGCGAGCCCCTATCATGCAAACCCTAGTATAAGCCAGCCCTATC
53474713 GTGC
1 GTGC
53474717 AAACCCTAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.21, C:0.33, G:0.23, T:0.22
Consensus pattern (45 bp):
GTGCGAGCCCCTATCATGCAAACCCTAGTATAAGCCAGCCCTATC
Found at i:53475511 original size:43 final size:43
Alignment explanation
Indices: 53475454--53475683 Score: 298
Period size: 43 Copynumber: 5.3 Consensus size: 43
53475444 ATTTTTAGAA
* **
53475454 ACAAACGCCACTAAAGACCGCGACCTTTAGCGGCGCTTTTCCC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCC
* * **
53475497 ACAAACGCCGCTAAAGACCAAGACCTTTAGCCGTGCTTTTATC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCC
*
53475540 ACAAAGGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCC
* * * *
53475583 ACAAACGCTGCTAAAGCCCATGACCTTTAGCAGCGCTTTTCCC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCC
* * * * *
53475626 ACAAACACCGCTAAAGAACATGACCTTTAGCGGCGCTTCTCGC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCC
*
53475669 AAAAACGCCGCTAAA
1 ACAAACGCCGCTAAA
53475684 AACATAGCCT
Statistics
Matches: 161, Mismatches: 26, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 161 1.00
ACGTcount: A:0.30, C:0.33, G:0.18, T:0.20
Consensus pattern (43 bp):
ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCC
Found at i:53480405 original size:7 final size:7
Alignment explanation
Indices: 53480395--53480453 Score: 82
Period size: 7 Copynumber: 8.4 Consensus size: 7
53480385 CACTAACTCT
*
53480395 TAACCTC
1 TAACCCC
53480402 TAACCCC
1 TAACCCC
*
53480409 TAACCCT
1 TAACCCC
53480416 TAACCCC
1 TAACCCC
53480423 TAACCCC
1 TAACCCC
53480430 TAACCCC
1 TAACCCC
**
53480437 TAACTAC
1 TAACCCC
53480444 TAACCCC
1 TAACCCC
53480451 TAA
1 TAA
53480454 ACCTTATTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 45 1.00
ACGTcount: A:0.32, C:0.47, G:0.00, T:0.20
Consensus pattern (7 bp):
TAACCCC
Found at i:53480411 original size:21 final size:21
Alignment explanation
Indices: 53480387--53480459 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
53480377 CCATGAATCA
*
53480387 CTAACTCTTAACCTCTAACCC
1 CTAACCCTTAACCTCTAACCC
*
53480408 CTAACCCTTAACCCCTAACCC
1 CTAACCCTTAACCTCTAACCC
*
53480429 CTAACCCCTAA-CTACTAACCC
1 CTAACCCTTAACCT-CTAACCC
*
53480450 CTAAACCTTA
1 CTAACCCTTA
53480460 TTTAATATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 1 0.02
21 44 0.98
ACGTcount: A:0.32, C:0.45, G:0.00, T:0.23
Consensus pattern (21 bp):
CTAACCCTTAACCTCTAACCC
Found at i:53480566 original size:68 final size:70
Alignment explanation
Indices: 53480443--53480577 Score: 247
Period size: 68 Copynumber: 2.0 Consensus size: 70
53480433 CCCCTAACTA
53480443 CTAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCTTAAACCCT
1 CTAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCTTAAACCCT
53480508 AATCC
66 AATCC
*
53480513 CTAACCCCTAAACCTTATTT-A-ATATAAATTAAAATACACTAATTAATCTAAACCTTAAACCCT
1 CTAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCTTAAACCCT
53480576 AA
66 AA
53480578 CCTAACATCG
Statistics
Matches: 64, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
68 43 0.67
69 1 0.02
70 20 0.31
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (70 bp):
CTAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCTTAAACCCT
AATCC
Found at i:53480634 original size:7 final size:7
Alignment explanation
Indices: 53480622--53480653 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
53480612 CTCTTAATCT
53480622 CTAACCC
1 CTAACCC
*
53480629 CTAACCA
1 CTAACCC
53480636 CTAACCC
1 CTAACCC
53480643 CTAACCC
1 CTAACCC
53480650 CTAA
1 CTAA
53480654 ATCACAACCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.34, C:0.50, G:0.00, T:0.16
Consensus pattern (7 bp):
CTAACCC
Found at i:53480692 original size:14 final size:15
Alignment explanation
Indices: 53480673--53480705 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
53480663 CTTAAACCAG
53480673 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
53480687 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
53480702 AATC
1 AATC
53480706 TATAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:53481092 original size:41 final size:41
Alignment explanation
Indices: 53481035--53481192 Score: 219
Period size: 41 Copynumber: 3.9 Consensus size: 41
53481025 AAATATTTTT
*
53481035 GCGGCGCTTTTTCAAAAACGCCGCTAAA-AGCCCGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGA-CCCGAGCATCA
* * *
53481076 GCGGCGCTTTTTCAAAAACGCCGTTAAAGATCTGAGCATCA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGACCCGAGCATCA
* * *
53481117 GCGGTGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATCA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGACCCGAGCATCA
* *
53481158 GCGGCGCTTTTTCAAAAACGTCGCTAAAGCCCCGA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGACCCGA
53481193 AAGGTCAAAA
Statistics
Matches: 105, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
41 104 0.99
42 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.22
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAGACCCGAGCATCA
Found at i:53485630 original size:3 final size:3
Alignment explanation
Indices: 53485622--53485646 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
53485612 ATTTGCATCC
53485622 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
53485647 AAACGGGCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:53486574 original size:3 final size:3
Alignment explanation
Indices: 53486566--53486601 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
53486556 AAAGCACTTA
53486566 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
53486602 GGGCATGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:53486693 original size:8 final size:8
Alignment explanation
Indices: 53486682--53486755 Score: 50
Period size: 8 Copynumber: 9.6 Consensus size: 8
53486672 TATAAAAATA
53486682 TATATATG
1 TATATATG
53486690 TATATATG
1 TATATATG
53486698 TACGTATAT-
1 TA--TATATG
*
53486707 TA-AAAT-
1 TATATATG
*
53486713 TATA-AAG
1 TATATATG
*
53486720 TATA-ATA
1 TATATATG
53486727 TATATATG
1 TATATATG
* *
53486735 TAGATATA
1 TATATATG
53486743 TATATATG
1 TATATATG
53486751 TATAT
1 TATAT
53486756 GTAAGTTGTA
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
6 6 0.12
7 10 0.19
8 29 0.56
9 2 0.04
10 5 0.10
ACGTcount: A:0.45, C:0.01, G:0.09, T:0.45
Consensus pattern (8 bp):
TATATATG
Found at i:53487046 original size:23 final size:23
Alignment explanation
Indices: 53487001--53487052 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
53486991 CGTACATGTA
53487001 TATATGTATATATATTATAAAAG
1 TATATGTATATATATTATAAAAG
*
53487024 TGTATGTATATATAATTAT-AAAG
1 TATATGTATATAT-ATTATAAAAG
53487047 TATATG
1 TATATG
53487053 AAGTATGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (23 bp):
TATATGTATATATATTATAAAAG
Found at i:53487676 original size:40 final size:40
Alignment explanation
Indices: 53487621--53487702 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
53487611 ATTAAAGATT
*
53487621 GACCAACCAAGAAGCAACAAGTTATACATGAACAATCAAC
1 GACCAACCAAGAAGCAACAAGTTATACATGAACAACCAAC
*
53487661 GACCAATCAAGAAGCAACAAGTTATACATGAACAACCAAC
1 GACCAACCAAGAAGCAACAAGTTATACATGAACAACCAAC
53487701 GA
1 GA
53487703 GCATGTGTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.50, C:0.24, G:0.13, T:0.12
Consensus pattern (40 bp):
GACCAACCAAGAAGCAACAAGTTATACATGAACAACCAAC
Found at i:53490491 original size:40 final size:40
Alignment explanation
Indices: 53490380--53490533 Score: 132
Period size: 40 Copynumber: 3.9 Consensus size: 40
53490370 AGCAGCACTT
** * *
53490380 TTAGCGGCGTTTGGACAAAAAACGCCGGTAAAAATCAAGCA
1 TTAGCGGCGTTTTTAAAAAAAACGCCGCTAAAAAT-AAGCA
** *** * * * *
53490421 TTAGCGGC-ACTTTATGGAAATCGCCACTAAAGATTGAGCA
1 TTAGCGGCGTTTTTAAAAAAAACGCCGCTAAA-AATAAGCA
* *
53490461 TTAGTGGCGTTTTT-CAAAAAACGCCGCTAAAAATAAGCA
1 TTAGCGGCGTTTTTAAAAAAAACGCCGCTAAAAATAAGCA
*
53490500 TTAGCGGCGTTTTTAAAAAAAACGCCGCAAAAAA
1 TTAGCGGCGTTTTTAAAAAAAACGCCGCTAAAAA
53490534 CATAAGCCCA
Statistics
Matches: 85, Mismatches: 25, Indels: 7
0.73 0.21 0.06
Matches are distributed among these distances:
39 19 0.22
40 53 0.62
41 13 0.15
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (40 bp):
TTAGCGGCGTTTTTAAAAAAAACGCCGCTAAAAATAAGCA
Found at i:53490633 original size:41 final size:42
Alignment explanation
Indices: 53490569--53490887 Score: 354
Period size: 41 Copynumber: 7.8 Consensus size: 42
53490559 GACCTTTCGT
* * *
53490569 GGCTTTAACGGCGTTTTTAGAAAAGCGCTGCTAATGCCT-GG
1 GGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCCTAGG
*
53490610 GTCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCCT--G
1 GGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCCTAGG
** * *
53490650 GTTTTTAGCGGCGTTTTTGGAAAAAGTGCCG-TAATG-GTAGG
1 GGCTTTAGCGGCGTTTTTGG-AAAAGCGCCGCTAATGCCTAGG
* **
53490691 GGCTTTAGTGGC-TTTTTGGAAAAGCGCCGCTAAT-TATAGG
1 GGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCCTAGG
53490731 GGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCCTA--
1 GGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCCTAGG
** * * *
53490771 GATTTTAGCGGCGTTTTTGGAAAAAGTGTCGCTAATG-GTAGG
1 GGCTTTAGCGGCGTTTTTGG-AAAAGCGCCGCTAATGCCTAGG
* ** *
53490813 GGCTTTAGTGGCGTTTTTGGAAAAGCGCCGCTAAT-TATAAG
1 GGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCCTAGG
*
53490854 GGCTTTAGCGCCGTTTTTGGAAAAGCGCCGCTAA
1 GGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAA
53490888 AAATATTTTA
Statistics
Matches: 238, Mismatches: 29, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
39 10 0.04
40 71 0.30
41 138 0.58
42 19 0.08
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.31
Consensus pattern (42 bp):
GGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCCTAGG
Found at i:53491302 original size:21 final size:20
Alignment explanation
Indices: 53491268--53491308 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
53491258 TTATGTATCA
*
53491268 GGGATTATGGTTTAAGGGTT
1 GGGATTAAGGTTTAAGGGTT
*
53491288 GGGATTTAAGGTTTAGGGGTT
1 GGGA-TTAAGGTTTAAGGGTT
53491309 AGGGGTTAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.20, C:0.00, G:0.41, T:0.39
Consensus pattern (20 bp):
GGGATTAAGGTTTAAGGGTT
Found at i:53491310 original size:7 final size:7
Alignment explanation
Indices: 53491300--53491332 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
53491290 GATTTAAGGT
53491300 TTAGGGG
1 TTAGGGG
53491307 TTAGGGG
1 TTAGGGG
53491314 TTAGGGG
1 TTAGGGG
53491321 CTTAGGGG
1 -TTAGGGG
53491329 TTAG
1 TTAG
53491333 ACATTATGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.15, C:0.03, G:0.52, T:0.30
Consensus pattern (7 bp):
TTAGGGG
Found at i:53491325 original size:15 final size:14
Alignment explanation
Indices: 53491300--53491332 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
53491290 GATTTAAGGT
53491300 TTAGGGGTTAGGGG
1 TTAGGGGTTAGGGG
53491314 TTAGGGGCTTAGGGG
1 TTAGGGG-TTAGGGG
53491329 TTAG
1 TTAG
53491333 ACATTATGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.15, C:0.03, G:0.52, T:0.30
Consensus pattern (14 bp):
TTAGGGGTTAGGGG
Found at i:53492541 original size:22 final size:22
Alignment explanation
Indices: 53492510--53492555 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
53492500 TATGTCCCAC
*
53492510 GCGCTGTTCTCATGGATCTGGA
1 GCGCTATTCTCATGGATCTGGA
53492532 GCGCTATTCTCATGGATCTGGA
1 GCGCTATTCTCATGGATCTGGA
53492554 GC
1 GC
53492556 CGGGCACTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.15, C:0.24, G:0.30, T:0.30
Consensus pattern (22 bp):
GCGCTATTCTCATGGATCTGGA
Found at i:53495192 original size:42 final size:42
Alignment explanation
Indices: 53495146--53495317 Score: 186
Period size: 43 Copynumber: 4.0 Consensus size: 42
53495136 TTTAATAAAA
* *
53495146 ATGCT-TTTAGTGGCGTTTTCTATAAAAGCGTCGCTAAAGGTC
1 ATGCTCTTTAGCGGCGTTTT-TATAAAAGCGCCGCTAAAGGTC
* * *
53495188 ATGCTTTTTAGCTGCGTTTGTGATAAAAGCGCCGCTAAAGGTC
1 ATGCTCTTTAGCGGCGTTT-TTATAAAAGCGCCGCTAAAGGTC
* * *
53495231 CTGTTCTTTAGCGGCGTTTTTGGGT-AAAGCGCCGCTAAAGGTC
1 ATGCTCTTTAGCGGCGTTTTT--ATAAAAGCGCCGCTAAAGGTC
* * * *
53495274 CTGTTCTTTAGCGGCGTTTTTTTCAAAGCGCCGCTAAAGGTC
1 ATGCTCTTTAGCGGCGTTTTTATAAAAGCGCCGCTAAAGGTC
53495316 AT
1 AT
53495318 AAAAACGCCG
Statistics
Matches: 113, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
41 1 0.01
42 25 0.22
43 85 0.75
44 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (42 bp):
ATGCTCTTTAGCGGCGTTTTTATAAAAGCGCCGCTAAAGGTC
Found at i:53498393 original size:3 final size:3
Alignment explanation
Indices: 53498387--53498413 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
53498377 TTTTTTTAAT
53498387 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
53498414 GCGTAAGTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:53498524 original size:23 final size:21
Alignment explanation
Indices: 53498498--53498541 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
53498488 TATCCTAGTT
53498498 TTTTATCAA-GTATTATTATTTAA
1 TTTTAT-AATGTATT-TT-TTTAA
53498521 TTTTATAATGTATTTTTTTAA
1 TTTTATAATGTATTTTTTTAA
53498542 AAAAATCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 5 0.25
22 4 0.20
23 11 0.55
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (21 bp):
TTTTATAATGTATTTTTTTAA
Found at i:53503666 original size:118 final size:118
Alignment explanation
Indices: 53503458--53503690 Score: 322
Period size: 118 Copynumber: 2.0 Consensus size: 118
53503448 CACCCACTAA
* * * *
53503458 AAAGAATACAGAGATAATAATAAGGCATATAAAATTTCAAAACCAAACAAAAGTCATGACTAGAT
1 AAAGAACACAGAGATAATAATAAGGCATATAAAAATTCAAAACCAAACAAAAGACAGGACTAGAT
* *
53503523 TTAAATCTAGAAATTTCTTTTTACAGCCTATCTAGCCCAAGAATTACTAGTAG
66 TTAAACCTAGAAATTTCTTTTTACAGCCTATCTAGCCCAAGAATAACTAGTAG
* * * * *
53503576 AAAGAACACGGAGATAATAATGAGGCATATAAAAATTCAATACCATACACAAGACAGGACTAGAT
1 AAAGAACACAGAGATAATAATAAGGCATATAAAAATTCAAAACCAAACAAAAGACAGGACTAGAT
* * * * *
53503641 TTGAACCTTGGAATTTCTTTTTACAGTCTATCTAGTCCAAGAATAACTAG
66 TTAAACCTAGAAATTTCTTTTTACAGCCTATCTAGCCCAAGAATAACTAG
53503691 CAGTGCACAG
Statistics
Matches: 99, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
118 99 1.00
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.27
Consensus pattern (118 bp):
AAAGAACACAGAGATAATAATAAGGCATATAAAAATTCAAAACCAAACAAAAGACAGGACTAGAT
TTAAACCTAGAAATTTCTTTTTACAGCCTATCTAGCCCAAGAATAACTAGTAG
Found at i:53505069 original size:18 final size:18
Alignment explanation
Indices: 53505046--53505082 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
53505036 GCAGAGTTTC
53505046 TCCTCCTGTCCCTTGACT
1 TCCTCCTGTCCCTTGACT
53505064 TCCTCCTGTCCCTTGACT
1 TCCTCCTGTCCCTTGACT
53505082 T
1 T
53505083 GGAATGCCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.43, G:0.11, T:0.41
Consensus pattern (18 bp):
TCCTCCTGTCCCTTGACT
Found at i:53506089 original size:5 final size:5
Alignment explanation
Indices: 53506079--53506150 Score: 64
Period size: 5 Copynumber: 14.8 Consensus size: 5
53506069 TGTTAAAAAA
* *
53506079 ATATT ATATT ATAGTA ATGATT ATGTT -T-TT ATATT ATATT ATTATT
1 ATATT ATATT ATA-TT AT-ATT ATATT ATATT ATATT ATATT A-TATT
53506125 A-A-T ATATT ATATT ATATT ATA-T ATAT
1 ATATT ATATT ATATT ATATT ATATT ATAT
53506151 ACATAAAACA
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
3 4 0.07
4 8 0.14
5 32 0.57
6 11 0.20
7 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (5 bp):
ATATT
Found at i:53506132 original size:19 final size:19
Alignment explanation
Indices: 53506108--53506150 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
53506098 ATTATGTTTT
53506108 TATATTATATTATTATTA-A
1 TATATTATATTA-TATTATA
53506127 TATATTATATTATATTATA
1 TATATTATATTATATTATA
53506146 TATAT
1 TATAT
53506151 ACATAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:53506183 original size:18 final size:19
Alignment explanation
Indices: 53506155--53506194 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
53506145 ATATATACAT
*
53506155 AAAACAAAAGAAAGAATAG
1 AAAACAAAAGAAAGAAAAG
53506174 AAAA-AAAAGAAAGAAAAG
1 AAAACAAAAGAAAGAAAAG
53506192 AAA
1 AAA
53506195 GAGAATAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.03
Consensus pattern (19 bp):
AAAACAAAAGAAAGAAAAG
Found at i:53506195 original size:9 final size:9
Alignment explanation
Indices: 53506160--53506196 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
53506150 TACATAAAAC
53506160 AAAAGAAAG
1 AAAAGAAAG
* *
53506169 AATAGAAAA
1 AAAAGAAAG
53506178 AAAAGAAAG
1 AAAAGAAAG
53506187 AAAAGAAAG
1 AAAAGAAAG
53506196 A
1 A
53506197 GAATAGAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:53507159 original size:44 final size:45
Alignment explanation
Indices: 53507064--53507197 Score: 162
Period size: 44 Copynumber: 3.0 Consensus size: 45
53507054 ACAGGACAGA
* *
53507064 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
53507110 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * *
53507154 ACAGGAATAATTCATGTAAGTCCATGTTAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
53507198 CAGGATATTG
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
44 37 0.49
45 1 0.01
46 37 0.49
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:53512237 original size:5 final size:5
Alignment explanation
Indices: 53512227--53512298 Score: 64
Period size: 5 Copynumber: 14.8 Consensus size: 5
53512217 TGTTAAAAAA
* *
53512227 ATATT ATATT ATAGTA ATGATT ATGTT -T-TT ATATT ATATT ATTATT
1 ATATT ATATT ATA-TT AT-ATT ATATT ATATT ATATT ATATT A-TATT
53512273 A-A-T ATATT ATATT ATATT ATA-T ATAT
1 ATATT ATATT ATATT ATATT ATATT ATAT
53512299 ACATAAAACA
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
3 4 0.07
4 8 0.14
5 32 0.57
6 11 0.20
7 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (5 bp):
ATATT
Found at i:53512280 original size:19 final size:19
Alignment explanation
Indices: 53512256--53512298 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
53512246 ATTATGTTTT
53512256 TATATTATATTATTATTA-A
1 TATATTATATTA-TATTATA
53512275 TATATTATATTATATTATA
1 TATATTATATTATATTATA
53512294 TATAT
1 TATAT
53512299 ACATAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:53512331 original size:18 final size:19
Alignment explanation
Indices: 53512303--53512342 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
53512293 ATATATACAT
*
53512303 AAAACAAAAGAAAGAATAG
1 AAAACAAAAGAAAGAAAAG
53512322 AAAA-AAAAGAAAGAAAAG
1 AAAACAAAAGAAAGAAAAG
53512340 AAA
1 AAA
53512343 GAATAGAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.03
Consensus pattern (19 bp):
AAAACAAAAGAAAGAAAAG
Found at i:53512343 original size:9 final size:9
Alignment explanation
Indices: 53512308--53512350 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
53512298 TACATAAAAC
53512308 AAAAGAAAG
1 AAAAGAAAG
* *
53512317 AATAGAAAA
1 AAAAGAAAG
53512326 AAAAGAAAG
1 AAAAGAAAG
53512335 AAAAGAAAG
1 AAAAGAAAG
*
53512344 AATAGAA
1 AAAAGAA
53512351 GAGACGAAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.05
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:53513305 original size:44 final size:45
Alignment explanation
Indices: 53513210--53513343 Score: 162
Period size: 44 Copynumber: 3.0 Consensus size: 45
53513200 ACAGGACAGA
* *
53513210 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
53513256 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * *
53513300 ACAGGAATAATTCATGTAAGTCCATGTTAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
53513344 CAGGATATTG
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
44 37 0.49
45 1 0.01
46 37 0.49
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:53515532 original size:24 final size:25
Alignment explanation
Indices: 53515488--53515535 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
53515478 TAATAGCCAA
*
53515488 ATTAATAATAAAAAAAGTATATTTG
1 ATTAAAAATAAAAAAAGTATATTTG
*
53515513 ATTAAAAATAAAAATA-TATATTT
1 ATTAAAAATAAAAAAAGTATATTT
53515536 AATATATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (25 bp):
ATTAAAAATAAAAAAAGTATATTTG
Found at i:53518266 original size:42 final size:41
Alignment explanation
Indices: 53518100--53518277 Score: 157
Period size: 41 Copynumber: 4.3 Consensus size: 41
53518090 TTTAGAGGGC
* * *
53518100 TTTAGTGGCG-TTTTTAAACAAACGCCGCTAATGTTATGGTT
1 TTTAGTGGCGTTTTTTATA-AAGCGCCGCTAATGTTAGGGTT
* * *
53518141 TTTAGTGGCGTTTTTT-TCTAAGCGCCGCTAATTTTAGGGCT
1 TTTAGTGGCGTTTTTTAT-AAAGCGCCGCTAATGTTAGGGTT
* * * * * *
53518182 TTTAGCGGCATTTTTAATAATGCGCCGCTAAAGTTAAGGTT
1 TTTAGTGGCGTTTTTTATAAAGCGCCGCTAATGTTAGGGTT
* *
53518223 TTTAGTTGCGTTTGTTTGTAAAGCGCCGCTAATGTT-GGAG-T
1 TTTAGTGGCGTTT-TTTATAAAGCGCCGCTAATGTTAGG-GTT
*
53518264 TTTAGCGGCGTTTT
1 TTTAGTGGCGTTTT
53518278 GATGGAAACA
Statistics
Matches: 107, Mismatches: 25, Indels: 11
0.75 0.17 0.08
Matches are distributed among these distances:
40 1 0.01
41 81 0.76
42 25 0.23
ACGTcount: A:0.20, C:0.15, G:0.25, T:0.41
Consensus pattern (41 bp):
TTTAGTGGCGTTTTTTATAAAGCGCCGCTAATGTTAGGGTT
Found at i:53518267 original size:82 final size:82
Alignment explanation
Indices: 53518122--53518277 Score: 217
Period size: 82 Copynumber: 1.9 Consensus size: 82
53518112 TTTAAACAAA
* * * *
53518122 CGCCGCTAATGTTATGGTTTTTAGTGGCGTTTTTTTCTAAGCGCCGCTAATTTTAGGGCTTTTAG
1 CGCCGCTAAAGTTAAGGTTTTTAGTGGCGTTTGTTTCTAAGCGCCGCTAATGTTAGGGCTTTTAG
53518187 CGGCATTTTTAATAATG
66 CGGCATTTTTAATAATG
* *
53518204 CGCCGCTAAAGTTAAGGTTTTTAGTTGCGTTTGTTTGTAAAGCGCCGCTAATGTT-GGAG-TTTT
1 CGCCGCTAAAGTTAAGGTTTTTAGTGGCGTTTGTTTCT-AAGCGCCGCTAATGTTAGG-GCTTTT
*
53518267 AGCGGCGTTTT
64 AGCGGCATTTT
53518278 GATGGAAACA
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
82 49 0.75
83 16 0.25
ACGTcount: A:0.18, C:0.15, G:0.26, T:0.41
Consensus pattern (82 bp):
CGCCGCTAAAGTTAAGGTTTTTAGTGGCGTTTGTTTCTAAGCGCCGCTAATGTTAGGGCTTTTAG
CGGCATTTTTAATAATG
Found at i:53518894 original size:7 final size:7
Alignment explanation
Indices: 53518884--53518990 Score: 88
Period size: 7 Copynumber: 14.3 Consensus size: 7
53518874 TAAGGTTTAA
53518884 GGGTTAG
1 GGGTTAG
53518891 GGGTTAG
1 GGGTTAG
**
53518898 GAATTTAG
1 G-GGTTAG
53518906 GGGTTAG
1 GGGTTAG
53518913 GGGTTAG
1 GGGTTAG
**
53518920 TGATTTAAG
1 -GGGTT-AG
53518929 GGGTTAG
1 GGGTTAG
*
53518936 GGTTTAGG
1 GGGTTA-G
53518944 GGGATTTAG
1 GGG--TTAG
53518953 GGGTTAG
1 GGGTTAG
53518960 GGGTTAG
1 GGGTTAG
53518967 GGGTTAG
1 GGGTTAG
**
53518974 AGATTTAG
1 -GGGTTAG
53518982 GGGTTAG
1 GGGTTAG
53518989 GG
1 GG
53518991 TGTCAAGGGT
Statistics
Matches: 79, Mismatches: 14, Indels: 14
0.74 0.13 0.13
Matches are distributed among these distances:
7 51 0.65
8 19 0.24
9 6 0.08
10 3 0.04
ACGTcount: A:0.20, C:0.00, G:0.49, T:0.32
Consensus pattern (7 bp):
GGGTTAG
Found at i:53518959 original size:24 final size:25
Alignment explanation
Indices: 53518879--53518969 Score: 106
Period size: 22 Copynumber: 3.9 Consensus size: 25
53518869 GGGATTAAGG
*
53518879 TTTAA-GGGTTAGGGGTTA--GGAA
1 TTTAAGGGGTTAGGGGTTAGGGGGA
*
53518901 TTT-AGGGGTTAGGGGTTA--GTGA
1 TTTAAGGGGTTAGGGGTTAGGGGGA
*
53518923 TTTAAGGGGTTAGGGTTTAGGGGGA
1 TTTAAGGGGTTAGGGGTTAGGGGGA
53518948 TTT-AGGGGTTAGGGGTTAGGGG
1 TTTAAGGGGTTAGGGGTTAGGGG
53518970 TTAGAGATTT
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
21 1 0.02
22 21 0.35
23 14 0.23
24 18 0.30
25 6 0.10
ACGTcount: A:0.20, C:0.00, G:0.47, T:0.33
Consensus pattern (25 bp):
TTTAAGGGGTTAGGGGTTAGGGGGA
Found at i:53518983 original size:15 final size:14
Alignment explanation
Indices: 53518909--53518989 Score: 80
Period size: 15 Copynumber: 5.9 Consensus size: 14
53518899 AATTTAGGGG
53518909 TTAGGGGTTAGTGAT
1 TTAGGGGTTAG-GAT
*
53518924 TTAAGGGGTTAGGGT
1 TT-AGGGGTTAGGAT
53518939 TTA-GGG---GGAT
1 TTAGGGGTTAGGAT
**
53518949 TTAGGGGTTAGGGG
1 TTAGGGGTTAGGAT
53518963 TTAGGGGTTAGAGAT
1 TTAGGGGTTAG-GAT
53518978 TTAGGGGTTAGG
1 TTAGGGGTTAGG
53518990 GTGTCAAGGG
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
10 6 0.11
11 3 0.06
13 3 0.06
14 15 0.28
15 18 0.33
16 9 0.17
ACGTcount: A:0.20, C:0.00, G:0.47, T:0.33
Consensus pattern (14 bp):
TTAGGGGTTAGGAT
Found at i:53518986 original size:47 final size:46
Alignment explanation
Indices: 53518880--53518966 Score: 108
Period size: 47 Copynumber: 1.9 Consensus size: 46
53518870 GGATTAAGGT
* *
53518880 TTAAGG-GTTAGGGGTTA--GGAATTTAGGGGTTAGGGGTTAGTGAT
1 TTAAGGAGTTA-GGGTTAGGGGGATTTAGGGGTTAGGGGTTAGTGAG
*
53518924 TTAAGGGGTTAGGGTTTAGGGGGATTTAGGGGTTAGGGGTTAG
1 TTAAGGAGTTAGGG-TTAGGGGGATTTAGGGGTTAGGGGTTAG
53518967 GGGTTAGAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
44 9 0.24
45 7 0.18
47 22 0.58
ACGTcount: A:0.21, C:0.00, G:0.46, T:0.33
Consensus pattern (46 bp):
TTAAGGAGTTAGGGTTAGGGGGATTTAGGGGTTAGGGGTTAGTGAG
Found at i:53520505 original size:24 final size:22
Alignment explanation
Indices: 53520476--53520519 Score: 70
Period size: 24 Copynumber: 1.9 Consensus size: 22
53520466 ATCACTTTTC
53520476 TCCCCAAAAATTCCCCCTAAATTT
1 TCCCCAAAAA-TCCCCC-AAATTT
53520500 TCCCCAAAAATCCCCCAAAT
1 TCCCCAAAAATCCCCCAAAT
53520520 CTAGAACCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 4 0.20
23 6 0.30
24 10 0.50
ACGTcount: A:0.36, C:0.41, G:0.00, T:0.23
Consensus pattern (22 bp):
TCCCCAAAAATCCCCCAAATTT
Found at i:53521631 original size:26 final size:26
Alignment explanation
Indices: 53521602--53521659 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
53521592 CTCGTTGCAT
*
53521602 AATAATTCTCACTCTATAGCTTATCA
1 AATAATTCTCACTCTATAGCTTATAA
*
53521628 AATAATTCTTACTCTATAGCTTATAA
1 AATAATTCTCACTCTATAGCTTATAA
53521654 AATAAT
1 AATAAT
53521660 ATAAATCTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.40, C:0.17, G:0.03, T:0.40
Consensus pattern (26 bp):
AATAATTCTCACTCTATAGCTTATAA
Found at i:53522146 original size:16 final size:16
Alignment explanation
Indices: 53522125--53522155 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
53522115 CCAATTCAAA
53522125 TAGTATTATTTAATAC
1 TAGTATTATTTAATAC
53522141 TAGTATTATTTAATA
1 TAGTATTATTTAATA
53522156 TGGTTCCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (16 bp):
TAGTATTATTTAATAC
Found at i:53522950 original size:9 final size:9
Alignment explanation
Indices: 53522936--53523019 Score: 85
Period size: 9 Copynumber: 10.0 Consensus size: 9
53522926 TTAGAAATAA
53522936 TACATAACT
1 TACATAACT
53522945 TACATAA--
1 TACATAACT
53522952 TATC-TAACT
1 TA-CATAACT
53522961 TACATAACT
1 TACATAACT
53522970 TACATAACT
1 TACATAACT
53522979 TACATAA--
1 TACATAACT
*
53522986 TACACAACT
1 TACATAACT
53522995 TACATAA--
1 TACATAACT
53523002 TACATAACCT
1 TACATAA-CT
53523012 T-CATAACT
1 TACATAACT
53523020 CATAGATACT
Statistics
Matches: 64, Mismatches: 2, Indels: 19
0.75 0.02 0.22
Matches are distributed among these distances:
7 18 0.28
8 4 0.06
9 41 0.64
10 1 0.02
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.32
Consensus pattern (9 bp):
TACATAACT
Found at i:53523017 original size:16 final size:16
Alignment explanation
Indices: 53522932--53523009 Score: 113
Period size: 16 Copynumber: 4.8 Consensus size: 16
53522922 AATTTTAGAA
53522932 ATAATACATAACTTAC
1 ATAATACATAACTTAC
53522948 ATAATATC-TAACTTAC
1 ATAATA-CATAACTTAC
53522964 ATAACTTACATAACTTAC
1 ATAA--TACATAACTTAC
*
53522982 ATAATACACAACTTAC
1 ATAATACATAACTTAC
53522998 ATAATACATAAC
1 ATAATACATAAC
53523010 CTTCATAACT
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
16 40 0.71
17 2 0.04
18 14 0.25
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAATACATAACTTAC
Found at i:53523019 original size:25 final size:24
Alignment explanation
Indices: 53522938--53523019 Score: 87
Period size: 25 Copynumber: 3.3 Consensus size: 24
53522928 AGAAATAATA
53522938 CATAACTTACATAATATC-TAACTT
1 CATAACTTACATAATA-CATAACTT
*
53522962 ACATAACTTACATAACTTACATAA-TA
1 -CATAACTTACATAA--TACATAACTT
*
53522988 CACAACTTACATAATACATAACCTT
1 CATAACTTACATAATACATAA-CTT
53523013 CATAACT
1 CATAACT
53523020 CATAGATACT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
23 7 0.15
25 34 0.71
26 2 0.04
27 5 0.10
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.32
Consensus pattern (24 bp):
CATAACTTACATAATACATAACTT
Found at i:53528977 original size:43 final size:43
Alignment explanation
Indices: 53528883--53529241 Score: 447
Period size: 43 Copynumber: 8.3 Consensus size: 43
53528873 TCTGCCAAAA
** * *
53528883 TTAGCGGCGTTTGTG-GAAAAAGCGTCGCTAAAAGGTCTTAGTCT
1 TTAGCGGCGTTTGTGTG-GGAAGCGCCGCT-AAAGGTCTTGGTCT
* * ** * *
53528927 TTTGCGGCGTTTGTGAGAAAAGCGCCACTAAAGGTCTTGATCT
1 TTAGCGGCGTTTGTGTGGGAAGCGCCGCTAAAGGTCTTGGTCT
* *
53528970 TTAGCGGCGTTTGTCGT-GTAAGCGCCGCTAAAAAGGTCATT-GTTT
1 TTAGCGGCGTTTGT-GTGGGAAGCGCCGCT--AAAGGTC-TTGGTCT
* * *
53529015 TTAGCGACGTTTGTGTGGGAAGCGCTGCTAAAGGTCTTAGTCT
1 TTAGCGGCGTTTGTGTGGGAAGCGCCGCTAAAGGTCTTGGTCT
*
53529058 TTAGCGGCGTTTGTGTGGGAAGC-CTCGCTAAAAGTCTTGGTCT
1 TTAGCGGCGTTTGTGTGGGAAGCGC-CGCTAAAGGTCTTGGTCT
53529101 TTAGCGGCGTTTGTGTGGGAAGCGCCGCTAAAGGTCTTGGTCT
1 TTAGCGGCGTTTGTGTGGGAAGCGCCGCTAAAGGTCTTGGTCT
* *
53529144 TTAGCGGCGTTTGTGTGGAAAGCGCCACTAAAGGTCTTGGTCT
1 TTAGCGGCGTTTGTGTGGGAAGCGCCGCTAAAGGTCTTGGTCT
* *
53529187 TTAGCGGCGTTTGTGTTGGAAGCGCCGCTAAAGGTCTTGGCCT
1 TTAGCGGCGTTTGTGTGGGAAGCGCCGCTAAAGGTCTTGGTCT
53529230 TTAGCGGCGTTT
1 TTAGCGGCGTTT
53529242 TTTCCTAGAA
Statistics
Matches: 279, Mismatches: 27, Indels: 19
0.86 0.08 0.06
Matches are distributed among these distances:
42 3 0.01
43 213 0.76
44 28 0.10
45 33 0.12
46 2 0.01
ACGTcount: A:0.18, C:0.18, G:0.32, T:0.31
Consensus pattern (43 bp):
TTAGCGGCGTTTGTGTGGGAAGCGCCGCTAAAGGTCTTGGTCT
Found at i:53531330 original size:125 final size:124
Alignment explanation
Indices: 53530873--53531328 Score: 624
Period size: 125 Copynumber: 3.7 Consensus size: 124
53530863 GCAAAAAGCG
* * * *
53530873 CCGCAAACAATTAAGTAGAACGCCTTCGTTTAACTTTGACCTGTAGTGGCACTAGCGGCATTTAT
1 CCGCAAATAATTAAGCAGAACGCCGTCGTTTAACTTTGACCTGTAGTGGCACTAGCGGCGTTTAT
** *
53530938 CTGGAAACGCCGGTAAAGATCTAGCATTTGCGGCACTTATCAAAAAACGCCACTAATGCT
66 CTGGAAACGCCACTAAAGATCTAGCATTTGCGGC-CATATCAAAAAACGCCACTAATGCT
* *
53530998 CCTCAAATAATTAAGCAGAACGCCGTCGTTTAACTTTGACCTGTAGTGACACTAGCGGCGTTTAT
1 CCGCAAATAATTAAGCAGAACGCCGTCGTTTAACTTTGACCTGTAGTGGCACTAGCGGCGTTTAT
* * * * * * *
53531063 CAGGAAATGCCGCCAAAGATCAAGCATTTGTGGCAATTATCAAAAAACGCCACTAATGCT
66 CTGGAAACGCCACTAAAGATCTAGCATTTGCGGCCA-TATCAAAAAACGCCACTAATGCT
** * **
53531123 CAACAAAAAATTAAGCAGAACGCCGTCGTTTAACTTTGACCTGTAGTGGCACTAGTAGCGTTTAT
1 CCGCAAATAATTAAGCAGAACGCCGTCGTTTAACTTTGACCTGTAGTGGCACTAGCGGCGTTTAT
** * * *
53531188 CTAAAAACGCCAGTAATGATCTAGCATTTGCGGCGCATACCAAAAAACGCCACTAATGCT
66 CTGGAAACGCCACTAAAGATCTAGCATTTGCGGC-CATATCAAAAAACGCCACTAATGCT
* *
53531248 CCGCAAATAATTAAGCAGAACGCTGTCGTTTAACTTTGACCTGTAGTGGCACTAGCGGTGTTTAT
1 CCGCAAATAATTAAGCAGAACGCCGTCGTTTAACTTTGACCTGTAGTGGCACTAGCGGCGTTTAT
*
53531313 CTGGAAATGCCACTAA
66 CTGGAAACGCCACTAA
53531329 TGCTCTGCAA
Statistics
Matches: 286, Mismatches: 43, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
125 285 1.00
126 1 0.00
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (124 bp):
CCGCAAATAATTAAGCAGAACGCCGTCGTTTAACTTTGACCTGTAGTGGCACTAGCGGCGTTTAT
CTGGAAACGCCACTAAAGATCTAGCATTTGCGGCCATATCAAAAAACGCCACTAATGCT
Found at i:53531614 original size:166 final size:168
Alignment explanation
Indices: 53531321--53531621 Score: 430
Period size: 166 Copynumber: 1.8 Consensus size: 168
53531311 ATCTGGAAAT
**
53531321 GCCACTAATGCTCTGCAAATAATTAAGCAGAATGATATCATTTAACTTTGATAATATTAGCGGCA
1 GCCACTAATGCTCCACAAATAATTAAGCAGAATGATATCATTTAACTTTGATAATATTAGCGGCA
* *
53531386 CTAGCGGCGTTTATATGAAAACGCCGGTAAAGATCTAGCATTTGTGACGCTTATAGAAAAACGCC
66 CTAGCGGCGTTTATATGAAAACGCCGGTAAAAATCTAGCATTTGAGACGCTTATAGAAAAACGCC
*
53531451 GCTAAAGCTCGGTACATTAGCGACGCTACCATAAAAAC
131 ACTAAAGCTCGGTACATTAGCGACGCTACCATAAAAAC
* * * * ** *
53531489 GCCACTAATGCTCCACAAATAATTAAGCAGAATGCTGTCGTTTAGCTTTGA-CCT-TTAGTGGCA
1 GCCACTAATGCTCCACAAATAATTAAGCAGAATGATATCATTTAACTTTGATAATATTAGCGGCA
* *
53531552 CTAGCGGCGTTTATATGGAAACGCCGGTAAAAATCTAGCATTTGCAG-CGTTTATCA-AAAAACG
66 CTAGCGGCGTTTATATGAAAACGCCGGTAAAAATCTAGCATTTG-AGACGCTTAT-AGAAAAACG
53531615 CCACTAA
129 CCACTAA
53531622 TGATCGATCT
Statistics
Matches: 117, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
166 69 0.59
167 3 0.03
168 45 0.38
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (168 bp):
GCCACTAATGCTCCACAAATAATTAAGCAGAATGATATCATTTAACTTTGATAATATTAGCGGCA
CTAGCGGCGTTTATATGAAAACGCCGGTAAAAATCTAGCATTTGAGACGCTTATAGAAAAACGCC
ACTAAAGCTCGGTACATTAGCGACGCTACCATAAAAAC
Found at i:53532056 original size:22 final size:24
Alignment explanation
Indices: 53532015--53532059 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
53532005 TCTTAGTTAT
53532015 TATTCATGGTTTAACAGGTTAGGC
1 TATTCATGGTTTAACAGGTTAGGC
*
53532039 TATT-ATGGTTTAA-GGGTTAGG
1 TATTCATGGTTTAACAGGTTAGG
53532060 GTTATTGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 9 0.45
24 4 0.20
ACGTcount: A:0.24, C:0.07, G:0.29, T:0.40
Consensus pattern (24 bp):
TATTCATGGTTTAACAGGTTAGGC
Found at i:53532065 original size:23 final size:24
Alignment explanation
Indices: 53532014--53532065 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
53532004 GTCTTAGTTA
53532014 TTATTCATGGTTTAACAGGTTAGG
1 TTATTCATGGTTTAACAGGTTAGG
* *
53532038 CTATT-ATGGTTTAA-GGGTTAGGG
1 TTATTCATGGTTTAACAGGTTA-GG
53532061 TTATT
1 TTATT
53532066 GATAAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 5 0.21
23 15 0.62
24 4 0.17
ACGTcount: A:0.23, C:0.06, G:0.27, T:0.44
Consensus pattern (24 bp):
TTATTCATGGTTTAACAGGTTAGG
Found at i:53532163 original size:13 final size:13
Alignment explanation
Indices: 53532145--53532189 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
53532135 TAGTGTTTAC
53532145 GGTTTATGGTGTA
1 GGTTTATGGTGTA
*
53532158 GGTTTATGGTTTA
1 GGTTTATGGTGTA
53532171 GTGTTTATGGTGTA
1 G-GTTTATGGTGTA
*
53532185 CGTTT
1 GGTTT
53532190 TCAATTTACA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 17 0.61
14 11 0.39
ACGTcount: A:0.13, C:0.02, G:0.33, T:0.51
Consensus pattern (13 bp):
GGTTTATGGTGTA
Found at i:53532232 original size:21 final size:21
Alignment explanation
Indices: 53532208--53532301 Score: 75
Period size: 21 Copynumber: 4.4 Consensus size: 21
53532198 CATGTTGAGT
*
53532208 GTTTAGGGGTGAGGGCTTAAG
1 GTTTAGGGGTTAGGGCTTAAG
*
53532229 GTTTAGGGGTTATAGGCTT-AG
1 GTTTAGGGGTTA-GGGCTTAAG
* *
53532250 GGTCAGGGGTTAGTGGCTTAAG
1 GTTTAGGGGTTAG-GGCTTAAG
* * *
53532272 G-TTACGGGTTTAAGGGTTTAGG
1 GTTTA-GGGGTT-AGGGCTTAAG
53532294 GTTTAGGG
1 GTTTAGGG
53532302 TATAGGGTAT
Statistics
Matches: 58, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
21 30 0.52
22 23 0.40
23 5 0.09
ACGTcount: A:0.18, C:0.05, G:0.44, T:0.33
Consensus pattern (21 bp):
GTTTAGGGGTTAGGGCTTAAG
Found at i:53532309 original size:14 final size:15
Alignment explanation
Indices: 53532277--53532309 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
53532267 TTAAGGTTAC
*
53532277 GGGTTTAAGGGTTTA
1 GGGTTTAAGGGTATA
53532292 GGGTTT-AGGGTATA
1 GGGTTTAAGGGTATA
53532306 GGGT
1 GGGT
53532310 ATAAAAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.18, C:0.00, G:0.45, T:0.36
Consensus pattern (15 bp):
GGGTTTAAGGGTATA
Found at i:53532450 original size:14 final size:14
Alignment explanation
Indices: 53532368--53532451 Score: 57
Period size: 14 Copynumber: 6.1 Consensus size: 14
53532358 CTTATATAGT
53532368 GTTTACGATTTAGG
1 GTTTACGATTTAGG
* *
53532382 GTGTAC-ATTTACG
1 GTTTACGATTTAGG
* *
53532395 GTTTAAAGA-TTAAG
1 GTTT-ACGATTTAGG
* *
53532409 GTTTAGGATATA-G
1 GTTTACGATTTAGG
* *
53532422 TTTTAAGAGTTTAGG
1 GTTTACGA-TTTAGG
53532437 GTTTACGATTTAGG
1 GTTTACGATTTAGG
53532451 G
1 G
53532452 GTTAATGGTT
Statistics
Matches: 53, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
13 19 0.36
14 26 0.49
15 8 0.15
ACGTcount: A:0.27, C:0.05, G:0.27, T:0.40
Consensus pattern (14 bp):
GTTTACGATTTAGG
Found at i:53532514 original size:21 final size:21
Alignment explanation
Indices: 53532490--53532542 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
53532480 GGTTAGGGGC
53532490 TTATGGTTTAGGGTTTAA-ATT
1 TTATGGTTTAGGGTTTAATA-T
*
53532511 TTAT-ATTTGAGGGTTTAATAT
1 TTATGGTTT-AGGGTTTAATAT
*
53532532 TTAGGGTTTAG
1 TTATGGTTTAG
53532543 CTAAAAACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
20 3 0.12
21 19 0.73
22 4 0.15
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (21 bp):
TTATGGTTTAGGGTTTAATAT
Found at i:53533017 original size:23 final size:23
Alignment explanation
Indices: 53532926--53533025 Score: 87
Period size: 23 Copynumber: 4.3 Consensus size: 23
53532916 TCCCCCAACT
* * *
53532926 CAATTTCCCCAAATTGATTTCCC
1 CAATTTCCCCGATTTCATTTCCC
*
53532949 TAATTT-CCC-ATTTCATATTCTCC
1 CAATTTCCCCGATTTCAT-TTC-CC
* **
53532972 CAATTTCCCTGATTTCAAATCCC
1 CAATTTCCCCGATTTCATTTCCC
*
53532995 CAATTTCCCCGATATCATTTCCC
1 CAATTTCCCCGATTTCATTTCCC
53533018 CAAATTTC
1 C-AATTTC
53533026 GAACTGAGGT
Statistics
Matches: 61, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
21 5 0.08
22 6 0.10
23 34 0.56
24 10 0.16
25 6 0.10
ACGTcount: A:0.25, C:0.34, G:0.03, T:0.38
Consensus pattern (23 bp):
CAATTTCCCCGATTTCATTTCCC
Found at i:53534741 original size:30 final size:31
Alignment explanation
Indices: 53534691--53534748 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
53534681 TATTTTAAAG
*
53534691 TTCAAATTTACATAACTTACATAATTTACGA
1 TTCAAATTTACATAAATTACATAATTTACGA
53534722 TTCAAATTT-CATAAATTACATAATTTA
1 TTCAAATTTACATAAATTACATAATTTA
53534749 AATATAATAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 17 0.65
31 9 0.35
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.41
Consensus pattern (31 bp):
TTCAAATTTACATAAATTACATAATTTACGA
Found at i:53534864 original size:12 final size:12
Alignment explanation
Indices: 53534847--53534958 Score: 52
Period size: 12 Copynumber: 10.1 Consensus size: 12
53534837 TACATAATGC
53534847 ATAACTTACATA
1 ATAACTTACATA
53534859 ATAACTTAC---
1 ATAACTTACATA
*
53534868 ATAACTTATAT-
1 ATAACTTACATA
*
53534879 ATAAACTTATAT-
1 AT-AACTTACATA
*
53534891 ATAAACTTGC---
1 AT-AACTTACATA
53534901 ATAACTTACATA
1 ATAACTTACATA
53534913 AT-A---ACATA
1 ATAACTTACATA
53534921 ATAACTTACATA
1 ATAACTTACATA
* *
53534933 AT-ACATAGCCTA
1 ATAACTTA-CATA
53534945 CATAACTTACATA
1 -ATAACTTACATA
53534958 A
1 A
53534959 CTTACATGAT
Statistics
Matches: 79, Mismatches: 8, Indels: 26
0.70 0.07 0.23
Matches are distributed among these distances:
8 7 0.09
9 15 0.19
10 2 0.03
11 7 0.09
12 39 0.49
13 5 0.06
14 4 0.05
ACGTcount: A:0.48, C:0.17, G:0.02, T:0.33
Consensus pattern (12 bp):
ATAACTTACATA
Found at i:53534871 original size:9 final size:9
Alignment explanation
Indices: 53534859--53535344 Score: 276
Period size: 9 Copynumber: 54.9 Consensus size: 9
53534849 AACTTACATA
53534859 ATAACTTAC
1 ATAACTTAC
*
53534868 ATAACTTATAT
1 ATAAC-T-TAC
*
53534879 ATAAACTTATAT
1 AT-AAC-T-TAC
*
53534891 ATAAACTTGC
1 ATAA-CTTAC
53534901 ATAACTTAC
1 ATAACTTAC
*
53534910 ATAA-TAAC
1 ATAACTTAC
53534918 ATAATAACTTAC
1 --A-TAACTTAC
53534930 ATAA--TAC
1 ATAACTTAC
* *
53534937 ATAGCCTAC
1 ATAACTTAC
53534946 ATAACTTAC
1 ATAACTTAC
53534955 ATAACTTAC
1 ATAACTTAC
*
53534964 ATGA--TAC
1 ATAACTTAC
*
53534971 ACAACTTATTAC
1 ATAAC---TTAC
*
53534983 ATAACTTAA
1 ATAACTTAC
53534992 ATAACTTA-
1 ATAACTTAC
53535000 ATAA--TAC
1 ATAACTTAC
*
53535007 ATAACTTTC
1 ATAACTTAC
53535016 ATAACTTAC
1 ATAACTTAC
*
53535025 ATTA--TAC
1 ATAACTTAC
*
53535032 ACAACTTAC
1 ATAACTTAC
53535041 ATAACTTA-
1 ATAACTTAC
* *
53535049 ATTAATATTAT
1 A-TAA-CTTAC
53535060 ATAGAACTTAC
1 AT--AACTTAC
53535071 ATAA--TAC
1 ATAACTTAC
* *
53535078 ATTACGTAC
1 ATAACTTAC
53535087 ATAACTTAC
1 ATAACTTAC
*
53535096 ATTA--TAC
1 ATAACTTAC
*
53535103 ACAACTTAC
1 ATAACTTAC
*
53535112 ATAACTTAT
1 ATAACTTAC
* *
53535121 TTAATATTATAC
1 AT-A-ACT-TAC
53535133 ATAACTTAC
1 ATAACTTAC
53535142 ATAA--TAC
1 ATAACTTAC
*
53535149 ATAACTTAT
1 ATAACTTAC
53535158 ATAACTTAC
1 ATAACTTAC
53535167 ATAACTTAC
1 ATAACTTAC
53535176 ATAACTTAC
1 ATAACTTAC
53535185 --AACTTAC
1 ATAACTTAC
*
53535192 ATAACTTAG
1 ATAACTTAC
*
53535201 ATACATTATAC
1 ATA-ACT-TAC
*
53535212 AGAACTTAC
1 ATAACTTAC
53535221 ATAACTTAC
1 ATAACTTAC
*
53535230 ATAGCTTAC
1 ATAACTTAC
*
53535239 AT-TC-TAC
1 ATAACTTAC
*
53535246 ATAACATAC
1 ATAACTTAC
*
53535255 ATAACATAC
1 ATAACTTAC
53535264 ATAA--TAC
1 ATAACTTAC
53535271 ATAACTTAC
1 ATAACTTAC
53535280 ATAA--TAC
1 ATAACTTAC
53535287 ATAGA-TTAC
1 ATA-ACTTAC
53535296 ATAA--TAC
1 ATAACTTAC
*
53535303 ACAACTTAC
1 ATAACTTAC
*
53535312 ATAGCTTAC
1 ATAACTTAC
53535321 ATAA--TAC
1 ATAACTTAC
53535328 ATAACTTAC
1 ATAACTTAC
*
53535337 ATAGCTTA
1 ATAACTTA
53535345 ATTATACTTA
Statistics
Matches: 377, Mismatches: 52, Indels: 96
0.72 0.10 0.18
Matches are distributed among these distances:
6 2 0.01
7 76 0.20
8 12 0.03
9 218 0.58
10 19 0.05
11 23 0.06
12 27 0.07
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.34
Consensus pattern (9 bp):
ATAACTTAC
Found at i:53534926 original size:20 final size:19
Alignment explanation
Indices: 53534901--53534939 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
53534891 ATAAACTTGC
53534901 ATAACTTACATAATAACATA
1 ATAACTTACATAAT-ACATA
53534921 ATAACTTACATAATACATA
1 ATAACTTACATAATACATA
53534940 GCCTACATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (19 bp):
ATAACTTACATAATACATA
Found at i:53534952 original size:54 final size:53
Alignment explanation
Indices: 53534837--53534965 Score: 140
Period size: 54 Copynumber: 2.4 Consensus size: 53
53534827 ATAAACTAAT
* * *
53534837 TACATAA--TGCATAACTTACATAATAACTTACATAACTTATATATAAACTTA
1 TACATAACTTGCATAACTTACATAATAACATACATAACTTACATATAAACATA
* *
53534888 TATATAAACTTGCATAACTTACATAATAACATA-ATAACTTACATA-ATACATA
1 TACAT-AACTTGCATAACTTACATAATAACATACATAACTTACATATAAACATA
*
53534940 GCCTACATAACTTACATAACTTACAT
1 ---TACATAACTTGCATAACTTACAT
53534966 GATACACAAC
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
51 4 0.06
52 7 0.11
53 11 0.17
54 39 0.60
55 4 0.06
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.33
Consensus pattern (53 bp):
TACATAACTTGCATAACTTACATAATAACATACATAACTTACATATAAACATA
Found at i:53534984 original size:37 final size:34
Alignment explanation
Indices: 53534913--53535324 Score: 111
Period size: 34 Copynumber: 12.4 Consensus size: 34
53534903 AACTTACATA
* * * *
53534913 ATAACATA-ATAACTTACATAATACATAGC-CTAC
1 ATAACTTACATAACTTA-ATAATACACAACTTTAC
*
53534946 ATAACTTACATAACTTACATGATACACAACTTATTAC
1 ATAACTTACATAACTTA-ATAATACACAAC-T-TTAC
* *
53534983 ATAACTTAAATAACTTAATAATACATAACTTT-C
1 ATAACTTACATAACTTAATAATACACAACTTTAC
53535016 ATAACTTAC---A--T--T-ATACACAAC-TTAC
1 ATAACTTACATAACTTAATAATACACAACTTTAC
* *
53535041 ATAACTTA-ATTAATATTATATAGA-ACTTAC-A-TAATAC
1 ATAACTTACA-TAA-CTTA-ATA-ATAC--ACAACT-TTAC
* * *
53535078 ATTACGTACATAACTTACATTATACACAAC-TTAC
1 ATAACTTACATAACTTA-ATAATACACAACTTTAC
** * *
53535112 ATAACTTATTTAA--T-ATTATACATAAC-TTAC
1 ATAACTTACATAACTTAATAATACACAACTTTAC
*
53535142 ATAA--TACATAACTTATATAACTTACATAAC-TTAC
1 ATAACTTACATAACTTA-ATAA--TACACAACTTTAC
* *
53535176 ATAACTTAC--AACTTACATAACTTAGA-TACATTATAC
1 ATAACTTACATAACTTA-ATAA--TACACAAC-TT-TAC
* * *
53535212 AGAACTTACATAACTTACATAGCT-TAC-A-TTCTAC
1 ATAACTTACATAACTTA-ATA-ATACACAACTT-TAC
* * *
53535246 ATAACATACATAACATACATAATACATAAC-TTAC
1 ATAACTTACATAACTTA-ATAATACACAACTTTAC
53535280 ATAA--TACATAGA-TTACATAATACACAAC-TTAC
1 ATAACTTACATA-ACTTA-ATAATACACAACTTTAC
*
53535312 ATAGCTTACATAA
1 ATAACTTACATAA
53535325 TACATAACTT
Statistics
Matches: 292, Mismatches: 41, Indels: 92
0.69 0.10 0.22
Matches are distributed among these distances:
24 2 0.01
25 17 0.06
26 1 0.00
28 7 0.02
30 21 0.07
31 1 0.00
32 31 0.11
33 21 0.07
34 103 0.35
35 8 0.03
36 35 0.12
37 34 0.12
38 11 0.04
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.33
Consensus pattern (34 bp):
ATAACTTACATAACTTAATAATACACAACTTTAC
Found at i:53535096 original size:71 final size:71
Alignment explanation
Indices: 53534994--53535348 Score: 308
Period size: 71 Copynumber: 4.8 Consensus size: 71
53534984 TAACTTAAAT
*
53534994 AACTTA-ATAATACATAACTTTCATAACTTACATTATACACAACTTACATAACTTAATTAATATT
1 AACTTACATAATACATAACTTACATAACTTACATTATACACAACTTACATAACTTAATTAATATT
*
53535058 ATATAG
66 ATACAG
* * *
53535064 AACTTACATAATACATTACGTACATAACTTACATTATACACAACTTACATAACTTATTTAATATT
1 AACTTACATAATACATAACTTACATAACTTACATTATACACAACTTACATAACTTAATTAATATT
*
53535129 ATACAT
66 ATACAG
* * * * *
53535135 AACTTACATAATACATAACTTATATAACTTACATAACTTACATAACTTACAACTTACATAACTTA
1 AACTTACATAATACATAACTTACATAACTTACATTA--TACACAACTTAC-A-TAACTTAA-TTA
53535200 GATACATTATACAG
61 -AT--ATTATACAG
* * * * * *
53535214 AACTTACATAACTTACATAGCTTACAT-TC-TACATAACATACATAACATACATAATACATAACT
1 AACTTACATAA--TACATAACTTACATAACTTACAT--TATACACAACTTACAT-A-ACTTAA-T
*
53535277 TACATA--ATACAT
59 TA-ATATTATACAG
* * * * *
53535289 AGA-TTACATAATACACAACTTACATAGCTTACATAATACATAACTTACATAGCTTAATTA
1 A-ACTTACATAATACATAACTTACATAACTTACATTATACACAACTTACATAACTTAATTA
53535349 TACTTATTCA
Statistics
Matches: 237, Mismatches: 30, Indels: 36
0.78 0.10 0.12
Matches are distributed among these distances:
70 9 0.04
71 94 0.40
72 1 0.00
73 37 0.16
74 2 0.01
75 24 0.10
76 4 0.02
77 4 0.02
78 1 0.00
79 47 0.20
80 1 0.00
81 13 0.05
ACGTcount: A:0.45, C:0.19, G:0.02, T:0.34
Consensus pattern (71 bp):
AACTTACATAATACATAACTTACATAACTTACATTATACACAACTTACATAACTTAATTAATATT
ATACAG
Found at i:53535329 original size:32 final size:31
Alignment explanation
Indices: 53535251--53535331 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 31
53535241 TCTACATAAC
* *
53535251 ATACATAACATACATAATACATAACTTACATA
1 ATACAT-AGATACATAATACACAACTTACATA
53535283 ATACATAGATTACATAATACACAACTTACATA
1 ATACATAGA-TACATAATACACAACTTACATA
*
53535315 GCTTACATA-ATACATAA
1 --ATACATAGATACATAA
53535332 CTTACATAGC
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
31 2 0.05
32 34 0.79
33 1 0.02
34 6 0.14
ACGTcount: A:0.51, C:0.19, G:0.02, T:0.28
Consensus pattern (31 bp):
ATACATAGATACATAATACACAACTTACATA
Found at i:53535339 original size:16 final size:16
Alignment explanation
Indices: 53534900--53535314 Score: 164
Period size: 16 Copynumber: 24.8 Consensus size: 16
53534890 TATAAACTTG
53534900 CATAACTTACATAATAA
1 CATAACTTACATAAT-A
53534917 CATAATAACTTACATAATA
1 C---ATAACTTACATAATA
* *
53534936 CATAGCCTACATAACTTA
1 CATAACTTACATAA--TA
*
53534954 CATAACTTACATGATA
1 CATAACTTACATAATA
*
53534970 CACAACTT--AT--TA
1 CATAACTTACATAATA
*
53534982 CATAACTTAAATAACTTA
1 CATAACTTACATAA--TA
*
53535000 -ATAA--TACATAACTTT
1 CATAACTTACATAA--TA
*
53535015 CATAACTTACATTATA
1 CATAACTTACATAATA
*
53535031 CACAACTTACAT-A-A
1 CATAACTTACATAATA
*
53535045 CTTAA-TTA-ATATTATA
1 CATAACTTACATA--ATA
* *
53535061 TAGAACTTACATAATA
1 CATAACTTACATAATA
* *
53535077 CATTACGTACATAACTTA
1 CATAACTTACATAA--TA
* *
53535095 CATTA--TACACAACTTA
1 CATAACTTACATAA--TA
*
53535111 CATAACTTATTTAATATTATA
1 CATAACTTA---CATA--ATA
53535132 CATAACTTACATAATA
1 CATAACTTACATAATA
*
53535148 CATAACTTATATAACTTA
1 CATAACTTACATAA--TA
53535166 CATAACTTACATAACTTA
1 CATAACTTACATAA--TA
53535184 C--AACTTACATAACTTA
1 CATAACTTACATAA--TA
* * *
53535200 GATACATTATACAGAACTTA
1 CATA-ACT-TACATAA--TA
*
53535220 CATAACTTACATAGCTTA
1 CATAACTTACATA--ATA
*
53535238 CAT-TC-TACATAACATA
1 CATAACTTACAT-A-ATA
*
53535254 CATAACATACATAATA
1 CATAACTTACATAATA
53535270 CATAACTTACATAATA
1 CATAACTTACATAATA
53535286 CATAGA-TTACATAATA
1 CATA-ACTTACATAATA
*
53535302 CACAACTTACATA
1 CATAACTTACATA
53535315 GCTTACATAA
Statistics
Matches: 316, Mismatches: 40, Indels: 85
0.72 0.09 0.19
Matches are distributed among these distances:
12 11 0.03
13 3 0.01
14 8 0.03
15 12 0.04
16 150 0.47
17 13 0.04
18 72 0.23
19 6 0.02
20 27 0.09
21 13 0.04
23 1 0.00
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.33
Consensus pattern (16 bp):
CATAACTTACATAATA
Found at i:53535344 original size:25 final size:25
Alignment explanation
Indices: 53534894--53535331 Score: 171
Period size: 25 Copynumber: 16.8 Consensus size: 25
53534884 CTTATATATA
*
53534894 AACTTGCATAACTTACATAATAACATAAT
1 AACTTACATAACTTACATAAT-AC---AT
*
53534923 AACTTACATAA--TACATAGCCTACAT
1 AACTTACATAACTTACATA--ATACAT
* *
53534948 AACTTACATAACTTACATGATACAC
1 AACTTACATAACTTACATAATACAT
*
53534973 AACTTATTACATAACTTAAATAACTTA-AT
1 AAC---TTACATAACTTACATAA--TACAT
*
53535002 AA--TACATAACTTTCATAACTTACAT
1 AACTTACATAACTTACATAA--TACAT
* *
53535027 TA--TACACAACTTACATAACTTA-ATT
1 AACTTACATAACTTACATAA--TACA-T
* *
53535052 AATATTATATAGAACTTACATAATACAT
1 AA-CTTACAT--AACTTACATAATACAT
* * * *
53535080 TACGTACATAACTTACATTATACAC
1 AACTTACATAACTTACATAATACAT
*
53535105 AACTTACATAACTTATTTAATATTATACAT
1 AACTTACATAACTTA---CATA--ATACAT
*
53535135 AACTTACATAA--TACATAACTTATAT
1 AACTTACATAACTTACATAA--TACAT
53535160 AACTTACATAACTTACATAACTTAC--
1 AACTTACATAACTTACATAA--TACAT
* *
53535185 AACTTACATAACTTAGATACATTATACAG
1 AACTTACATAAC-T---TACATAATACAT
*
53535214 AACTTACATAACTTACATAGCTTACAT
1 AACTTACATAACTTACATA--ATACAT
* *
53535241 -TC-TACATAACATACATAACATACAT
1 AACTTACATAACTTACAT-A-ATACAT
53535266 AA--TACATAACTTACATAATACAT
1 AACTTACATAACTTACATAATACAT
*
53535289 AGA-TTACATAA--TACACAACTTACAT
1 A-ACTTACATAACTTACATAA--TACAT
*
53535314 AGCTTACATAA--TACATAA
1 AACTTACATAACTTACATAA
53535332 CTTACATAGC
Statistics
Matches: 326, Mismatches: 42, Indels: 86
0.72 0.09 0.19
Matches are distributed among these distances:
23 14 0.04
24 21 0.06
25 164 0.50
26 3 0.01
27 33 0.10
28 29 0.09
29 33 0.10
30 29 0.09
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.33
Consensus pattern (25 bp):
AACTTACATAACTTACATAATACAT
Found at i:53540944 original size:21 final size:21
Alignment explanation
Indices: 53540920--53540970 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
53540910 GGCAACGAGG
53540920 GAAGCAGAGGC-AGCAGTGAGA
1 GAAGCAGAGGCTA-CAGTGAGA
*
53540941 GAAGCAGAGGCTACAGTGAGG
1 GAAGCAGAGGCTACAGTGAGA
53540962 GAAGCAGAG
1 GAAGCAGAG
53540971 TAGAGCAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.37, C:0.14, G:0.43, T:0.06
Consensus pattern (21 bp):
GAAGCAGAGGCTACAGTGAGA
Found at i:53541369 original size:43 final size:42
Alignment explanation
Indices: 53541321--53541673 Score: 319
Period size: 43 Copynumber: 8.2 Consensus size: 42
53541311 ATAGTCTTTC
* **
53541321 GCGGCGTTTGTGTGAAAAGCACCGCCAAAGGTCTTGGCCTATA
1 GCGGCGTTTGTG-GAAAAGCACCGCTAAAGGTCTTGATCTATA
* *** *
53541364 GCGGCGTTTTTGGAAAAAGTGTCGCTAAAGGTCATGATCTATA
1 GCGGCGTTTGTGG-AAAAGCACCGCTAAAGGTCTTGATCTATA
* ** ** ** *
53541407 GCAGCGTTTGTAAACAAAGCGTCAATAAAGGTCTTGAGCTATA
1 GCGGCGTTTGTGGA-AAAGCACCGCTAAAGGTCTTGATCTATA
*
53541450 GCGGCGTTTGTGGAAAAAGCACAGCTAAAGGTCTTGATCTATA
1 GCGGCGTTTGTGG-AAAAGCACCGCTAAAGGTCTTGATCTATA
*
53541493 GCGGCGTTTGTGGGAAAGGCACCGCTAAAGGTCTTGATCTATA
1 GCGGCGTTTGT-GGAAAAGCACCGCTAAAGGTCTTGATCTATA
* * ** * * * *
53541536 GCGGCATTTTTGGAAAAAAGTGCCGTTACAGATCTTGAGCTATA
1 GCGGCGTTTGTGG--AAAAGCACCGCTAAAGGTCTTGATCTATA
** * * * *
53541580 ATGGCGTTTGTGTAAAAGCGCCCCTAAAGGTCCTGATCTATA
1 GCGGCGTTTGTGGAAAAGCACCGCTAAAGGTCTTGATCTATA
* *
53541622 GCGGCGTTTCTGGAAGAAGCACCGCTAAAGGTCATGATCTATA
1 GCGGCGTTTGTGGAA-AAGCACCGCTAAAGGTCTTGATCTATA
*
53541665 GTGGCGTTT
1 GCGGCGTTT
53541674 ATTTCTAAAA
Statistics
Matches: 246, Mismatches: 57, Indels: 14
0.78 0.18 0.04
Matches are distributed among these distances:
42 37 0.15
43 176 0.72
44 33 0.13
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (42 bp):
GCGGCGTTTGTGGAAAAGCACCGCTAAAGGTCTTGATCTATA
Found at i:53541597 original size:129 final size:128
Alignment explanation
Indices: 53541322--53541665 Score: 386
Period size: 129 Copynumber: 2.7 Consensus size: 128
53541312 TAGTCTTTCG
* ** * * ***
53541322 CGGCGTTTGTGTGAAAAGCACCGCCAAAGGTCTTGGCCTATAGCGGCGTTTTTGGAAAAAGTGTC
1 CGGCGTTTGTGT-AAAAGCACCGCTAAAGGTCTTGATCTATAGCGGCGTTTCTGGGAAAAGCACC
* * * *
53541387 GCTAAAGGTCATGATCTATAGCAGCGTTTGTAAACAAAGCGTCAATAAAGGTCTTGAGCTATAG
65 GCTAAAGGTCATGATCTATAGCAGCGTTTGGAAACAAAGCGCCAATAAAGATCTTGAGCTATAA
* * * *
53541451 CGGCGTTTGTGGAAAAAGCACAGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGGAAAGGCACC
1 CGGCGTTTGT-GTAAAAGCACCGCTAAAGGTCTTGATCTATAGCGGCGTTTCTGGGAAAAGCACC
* * * * ** *
53541516 GCTAAAGGTCTTGATCTATAGCGGCATTTTTGGAAA-AAAGTGCCGTTACAGATCTTGAGCTATA
65 GCTAAAGGTCATGATCTATAGCAGC--GTTTGGAAACAAAGCGCCAATAAAGATCTTGAGCTATA
53541580 A
128 A
* * * *
53541581 TGGCGTTTGTGTAAAAGCGCCCCTAAAGGTCCTGATCTATAGCGGCGTTTCT-GGAAGAAGCACC
1 CGGCGTTTGTGTAAAAGCACCGCTAAAGGTCTTGATCTATAGCGGCGTTTCTGGGAA-AAGCACC
53541645 GCTAAAGGTCATGATCTATAG
65 GCTAAAGGTCATGATCTATAG
53541666 TGGCGTTTAT
Statistics
Matches: 180, Mismatches: 31, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
128 4 0.02
129 137 0.76
130 32 0.18
131 7 0.04
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.26
Consensus pattern (128 bp):
CGGCGTTTGTGTAAAAGCACCGCTAAAGGTCTTGATCTATAGCGGCGTTTCTGGGAAAAGCACCG
CTAAAGGTCATGATCTATAGCAGCGTTTGGAAACAAAGCGCCAATAAAGATCTTGAGCTATAA
Found at i:53542309 original size:16 final size:16
Alignment explanation
Indices: 53542288--53542343 Score: 85
Period size: 16 Copynumber: 3.5 Consensus size: 16
53542278 CGTTTGGTTC
53542288 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
* *
53542304 GCTGTAATTGAAGAGA
1 GCTGTAATGGAATAGA
53542320 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
53542336 GTTGTAAT
1 GCTGTAAT
53542344 AAGTAATTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.36, C:0.05, G:0.30, T:0.29
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:53542418 original size:44 final size:46
Alignment explanation
Indices: 53542325--53542418 Score: 122
Period size: 44 Copynumber: 2.1 Consensus size: 46
53542315 AGAGAGCTGT
** *
53542325 AATGGAATAGAGTTGTAATAAGTAATTCAATTGTTTGGTTGAATTG
1 AATGGAATAGAACTGTAATAAGTAATTCAATTGTTTGGTTGAATGG
*
53542371 AATGGAATAGAACTGTAAT-AGT-ATTC-TTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAAGTAATTCAAT-TGTTTGGTTGAATGG
53542415 AATG
1 AATG
53542419 ATGTTGTACT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
43 1 0.02
44 22 0.51
45 3 0.07
46 17 0.40
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.38
Consensus pattern (46 bp):
AATGGAATAGAACTGTAATAAGTAATTCAATTGTTTGGTTGAATGG
Found at i:53542616 original size:37 final size:37
Alignment explanation
Indices: 53542536--53542633 Score: 103
Period size: 37 Copynumber: 2.7 Consensus size: 37
53542526 AAAATAATAA
* * *
53542536 ATAATTTAATCATATT-TTAACATAATTATTATTAAAT
1 ATAATTTAATAAAATTCTTAATATAATTATTATT-AAT
*
53542573 ATAATTTAATAAAATTCTTAATATAATTATTCTT-AT
1 ATAATTTAATAAAATTCTTAATATAATTATTATTAAT
* *
53542609 ATGAATTTACTAAAA-TCATAATATA
1 AT-AATTTAATAAAATTCTTAATATA
53542634 TAATACTATA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
36 13 0.25
37 25 0.47
38 15 0.28
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.46
Consensus pattern (37 bp):
ATAATTTAATAAAATTCTTAATATAATTATTATTAAT
Found at i:53542641 original size:21 final size:21
Alignment explanation
Indices: 53542616--53542658 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
53542606 TATATGAATT
53542616 TACTA-AAATCATAATATATAA
1 TACTATAAA-CATAATATATAA
*
53542637 TACTATAAAGATAATATATAA
1 TACTATAAACATAATATATAA
53542658 T
1 T
53542659 CTACTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (21 bp):
TACTATAAACATAATATATAA
Found at i:53543326 original size:24 final size:24
Alignment explanation
Indices: 53543293--53543343 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
53543283 AATACAAGCA
53543293 TCAAGACAATAGTTTAATACATCC
1 TCAAGACAATAGTTTAATACATCC
*
53543317 TCAAGGCAATAGTTTAATACATCC
1 TCAAGACAATAGTTTAATACATCC
53543341 TCA
1 TCA
53543344 TGATACTCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (24 bp):
TCAAGACAATAGTTTAATACATCC
Found at i:53547464 original size:24 final size:24
Alignment explanation
Indices: 53547437--53547499 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
53547427 ATAATTTAGC
*
53547437 CATTTTTATTTTTATTATAATTTT
1 CATTTTTATTTTAATTATAATTTT
* * *
53547461 CATTTTTAGTTTAATTTTTATTTT
1 CATTTTTATTTTAATTATAATTTT
53547485 CTAATTTTTATTTTA
1 C--ATTTTTATTTTA
53547500 TTTGCTTCTG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 21 0.66
26 11 0.34
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.70
Consensus pattern (24 bp):
CATTTTTATTTTAATTATAATTTT
Found at i:53547465 original size:18 final size:18
Alignment explanation
Indices: 53547438--53547484 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
53547428 TAATTTAGCC
53547438 ATTTTTATTTTTA-TTATA
1 ATTTTTATTTTTAGTT-TA
*
53547456 ATTTTCATTTTTAGTTTA
1 ATTTTTATTTTTAGTTTA
53547474 ATTTTTATTTT
1 ATTTTTATTTT
53547485 CTAATTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 24 0.92
19 2 0.08
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (18 bp):
ATTTTTATTTTTAGTTTA
Found at i:53547480 original size:7 final size:6
Alignment explanation
Indices: 53547438--53547502 Score: 60
Period size: 6 Copynumber: 10.7 Consensus size: 6
53547428 TAATTTAGCC
* * * * *
53547438 ATTTTT ATTTTT ATTATA ATTTTC ATTTTT AGTTTA ATTTTT ATTTTCT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTT-T
53547487 AATTTTT A-TTTT ATTT
1 -ATTTTT ATTTTT ATTT
53547503 GCTTCTGGCA
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
5 5 0.11
6 35 0.74
7 2 0.04
8 5 0.11
ACGTcount: A:0.23, C:0.03, G:0.02, T:0.72
Consensus pattern (6 bp):
ATTTTT
Found at i:53547491 original size:14 final size:14
Alignment explanation
Indices: 53547472--53547498 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53547462 ATTTTTAGTT
53547472 TAATTTTTATTTTC
1 TAATTTTTATTTTC
53547486 TAATTTTTATTTT
1 TAATTTTTATTTT
53547499 ATTTGCTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (14 bp):
TAATTTTTATTTTC
Found at i:53549950 original size:22 final size:22
Alignment explanation
Indices: 53549925--53549981 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
53549915 TACCCTTTTC
* *
53549925 TTTATTTTATTTTCTTTTATTT
1 TTTATTTTATTTTCTTATATTA
*
53549947 TTTATTATT-TTTTGTTATATTA
1 TTTATT-TTATTTTCTTATATTA
53549969 TTTATTTTTATTT
1 TTTA-TTTTATTT
53549982 GAATAATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 22 0.76
23 7 0.24
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.79
Consensus pattern (22 bp):
TTTATTTTATTTTCTTATATTA
Found at i:53549979 original size:15 final size:15
Alignment explanation
Indices: 53549940--53549979 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
53549930 TTTATTTTCT
53549940 TTTATTTTT-TATTA
1 TTTATTTTTATATTA
53549954 TTT-TTTGTTATATTA
1 TTTATTT-TTATATTA
53549969 TTTATTTTTAT
1 TTTATTTTTAT
53549980 TTGAATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 3 0.13
14 5 0.22
15 12 0.52
16 3 0.13
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.78
Consensus pattern (15 bp):
TTTATTTTTATATTA
Done.