Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 20 of 120
Found at i:6133673 original size:29 final size:29
Alignment explanation
Indices: 6133641--6133769 Score: 83
Period size: 29 Copynumber: 4.6 Consensus size: 29
6133631 CCCTAAACAC
6133641 TAAATCTAAAACCATAAAACCTAAAACCA
1 TAAATCTAAAACCATAAAACCTAAAACCA
* * * * * *
6133670 TAAACCCAAAATCATAAATCAT-AAACCC
1 TAAATCTAAAACCATAAAACCTAAAACCA
* *
6133698 TAAATAT-AAACCATAAATCCTAAAA-CA
1 TAAATCTAAAACCATAAAACCTAAAACCA
* * * *
6133725 CTAAAT-AATAAACCTTAAAATCTAAAACCC
1 -TAAATCTA-AAACCATAAAACCTAAAACCA
6133755 TAAA-C--AAACCATAAA
1 TAAATCTAAAACCATAAA
6133770 CATAAACACT
Statistics
Matches: 76, Mismatches: 18, Indels: 15
0.70 0.17 0.14
Matches are distributed among these distances:
26 9 0.12
27 13 0.17
28 17 0.22
29 36 0.47
30 1 0.01
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.19
Consensus pattern (29 bp):
TAAATCTAAAACCATAAAACCTAAAACCA
Found at i:6133713 original size:7 final size:7
Alignment explanation
Indices: 6133585--6133714 Score: 58
Period size: 7 Copynumber: 18.7 Consensus size: 7
6133575 AACATCAAAT
6133585 ATAAACC
1 ATAAACC
*
6133592 ATAAATC
1 ATAAACC
*
6133599 -TAGAATC
1 ATA-AACC
6133606 ATAAACC
1 ATAAACC
* *
6133613 CTAAAGC
1 ATAAACC
*
6133620 TTAAA-C
1 ATAAACC
6133626 ATAAACC
1 ATAAACC
*
6133633 CTAAA-C
1 ATAAACC
*
6133639 ACTAAATC
1 A-TAAACC
6133647 -TAAAACC
1 AT-AAACC
6133654 ATAAAACC
1 AT-AAACC
6133662 -TAAAACC
1 AT-AAACC
6133669 ATAAACCC
1 ATAAA-CC
*
6133677 A-AAATC
1 ATAAACC
*
6133683 ATAAATC
1 ATAAACC
6133690 ATAAACC
1 ATAAACC
* *
6133697 CTAAA-T
1 ATAAACC
6133703 ATAAACC
1 ATAAACC
6133710 ATAAA
1 ATAAA
6133715 TCCTAAAACA
Statistics
Matches: 97, Mismatches: 15, Indels: 22
0.72 0.11 0.16
Matches are distributed among these distances:
6 15 0.15
7 68 0.70
8 14 0.14
ACGTcount: A:0.55, C:0.24, G:0.02, T:0.19
Consensus pattern (7 bp):
ATAAACC
Found at i:6133743 original size:14 final size:13
Alignment explanation
Indices: 6133547--6133739 Score: 54
Period size: 14 Copynumber: 13.9 Consensus size: 13
6133537 AGCAAATCTT
6133547 AATCACTAAACCTTA
1 AATCA-TAAACC-TA
*
6133562 AA-CATCTAACCTA
1 AATCAT-AAACCTA
**
6133575 AA-CATCAAATATA
1 AATCAT-AAACCTA
* *
6133588 AACCATAAATCTA
1 AATCATAAACCTA
6133601 GAATCATAAACCCTA
1 -AATCATAAA-CCTA
* * *
6133616 AAGCTTAAACATA
1 AATCATAAACCTA
* *
6133629 AACCCTAAACACTA
1 AATCATAAAC-CTA
6133643 AATC-TAAAACCATA
1 AATCAT-AAACC-TA
* *
6133657 AAACCTAAAACCATA
1 AATCAT-AAACC-TA
* *
6133672 AACCCA-AAATCATA
1 AA-TCATAAA-CCTA
6133686 AATCATAAACCCTA
1 AATCATAAA-CCTA
6133700 AAT-ATAAACCATA
1 AATCATAAACC-TA
*
6133713 AATCCTAAAACACTA
1 AATCAT-AAAC-CTA
*
6133728 AATAATAAACCT
1 AATCATAAACCT
6133740 TAAAATCTAA
Statistics
Matches: 139, Mismatches: 24, Indels: 32
0.71 0.12 0.16
Matches are distributed among these distances:
12 2 0.01
13 48 0.35
14 59 0.42
15 28 0.20
16 2 0.01
ACGTcount: A:0.54, C:0.24, G:0.01, T:0.21
Consensus pattern (13 bp):
AATCATAAACCTA
Found at i:6133810 original size:40 final size:40
Alignment explanation
Indices: 6133607--6133896 Score: 162
Period size: 41 Copynumber: 6.9 Consensus size: 40
6133597 TCTAGAATCA
*
6133607 TAAACCCTAAAGCT-TAAA-CATAAACCCTAAACACTAAA-TC
1 TAAACCCTAAA--TATAAACCATAAACCCTAAACA-TAAACAC
* *
6133647 TAAAACCATAAA-ACCTAAAACCATAAACCCAAAATCATAAATCA-
1 T-AAACCCTAAATA--T-AAACCATAAACCCTAAA-CATAAA-CAC
* * *
6133691 TAAACCCTAAATATAAACCATAAATCCTAAAACACTAAATAA
1 TAAACCCTAAATATAAACCATAAACCCT-AAACA-TAAACAC
* * *
6133733 TAAACCTTAAAATCTAAAACCCTAAACAAACCATAAACATAAACAC
1 TAAACCCT-AAATAT-AAACCATAAAC---CC-TAAACATAAACAC
** * * * * *
6133779 TAAACCCTTTATAT-AACTTATAAACCCTAAACTTTACCCC
1 TAAACCCTAAATATAAAC-CATAAACCCTAAACATAAACAC
*
6133819 TAAACCCTAAATATAAACCATAAACCCTAAATCATAAATAC
1 TAAACCCTAAATATAAACCATAAACCCTAAA-CATAAACAC
* * * *
6133860 TAAACACTAAACACTAAACCCTAAACAC-AAACATAAA
1 TAAACCCTAAATA-TAAACCATAAACCCTAAACATAAA
6133897 ACCCTAAAAC
Statistics
Matches: 192, Mismatches: 35, Indels: 46
0.70 0.13 0.17
Matches are distributed among these distances:
40 40 0.21
41 48 0.25
42 30 0.16
43 33 0.17
44 18 0.09
45 3 0.02
46 12 0.06
47 7 0.04
48 1 0.01
ACGTcount: A:0.53, C:0.26, G:0.00, T:0.20
Consensus pattern (40 bp):
TAAACCCTAAATATAAACCATAAACCCTAAACATAAACAC
Found at i:6133826 original size:7 final size:7
Alignment explanation
Indices: 6133816--6133885 Score: 52
Period size: 7 Copynumber: 10.1 Consensus size: 7
6133806 TAAACTTTAC
6133816 CCCTAAA
1 CCCTAAA
6133823 CCCTAAA
1 CCCTAAA
**
6133830 -TATAAA
1 CCCTAAA
*
6133836 CCATAAA
1 CCCTAAA
6133843 CCCTAAA
1 CCCTAAA
* *
6133850 TCATAAA
1 CCCTAAA
**
6133857 TACTAAA
1 CCCTAAA
*
6133864 CACTAAA
1 CCCTAAA
*
6133871 CACTAAA
1 CCCTAAA
6133878 CCCTAAA
1 CCCTAAA
6133885 C
1 C
6133886 ACAAACATAA
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
6 4 0.08
7 48 0.92
ACGTcount: A:0.51, C:0.30, G:0.00, T:0.19
Consensus pattern (7 bp):
CCCTAAA
Found at i:6133854 original size:14 final size:13
Alignment explanation
Indices: 6133832--6133896 Score: 60
Period size: 14 Copynumber: 4.8 Consensus size: 13
6133822 ACCCTAAATA
*
6133832 TAAACCATAAACCC
1 TAAA-CATAAACAC
*
6133846 TAAATCATAAATAC
1 TAAA-CATAAACAC
6133860 TAAACACTAAACAC
1 TAAACA-TAAACAC
*
6133874 TAAACCCTAAACAC
1 TAAA-CATAAACAC
6133888 -AAACATAAA
1 TAAACATAAA
6133897 ACCCTAAAAC
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
12 5 0.12
13 5 0.12
14 32 0.74
15 1 0.02
ACGTcount: A:0.57, C:0.26, G:0.00, T:0.17
Consensus pattern (13 bp):
TAAACATAAACAC
Found at i:6133877 original size:21 final size:20
Alignment explanation
Indices: 6133818--6133896 Score: 72
Period size: 21 Copynumber: 3.9 Consensus size: 20
6133808 AACTTTACCC
* *
6133818 CTAAACCCTAAATATAAAC-
1 CTAAACACTAAACATAAACA
* *
6133837 CATAAACCCTAAATCATAAATA
1 C-TAAACACTAAA-CATAAACA
*
6133859 CTAAACACTAAACACTAAACC
1 CTAAACACTAAACA-TAAACA
6133880 CTAAACAC-AAACATAAA
1 CTAAACACTAAACATAAA
6133897 ACCCTAAAAC
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
19 5 0.10
20 18 0.35
21 27 0.53
22 1 0.02
ACGTcount: A:0.56, C:0.27, G:0.00, T:0.18
Consensus pattern (20 bp):
CTAAACACTAAACATAAACA
Found at i:6133948 original size:6 final size:7
Alignment explanation
Indices: 6133936--6134145 Score: 55
Period size: 7 Copynumber: 31.7 Consensus size: 7
6133926 CCCTAAATCT
6133936 TAAACTA
1 TAAACTA
6133943 -AAACTA
1 TAAACTA
*
6133949 TAAACTT
1 TAAACTA
* **
6133956 TATACCC
1 TAAACTA
6133963 TAAAC-A
1 TAAACTA
*
6133969 TAAACAA
1 TAAACTA
6133976 TAAA-TA
1 TAAACTA
6133982 TAAAACCTA
1 T-AAA-CTA
*
6133991 -AACCT-
1 TAAACTA
6133996 TAAAC-A
1 TAAACTA
6134002 TAAACCT-
1 TAAA-CTA
6134009 TAAACCT-
1 TAAA-CTA
6134016 TAAA-TA
1 TAAACTA
*
6134022 TAAACCA
1 TAAACTA
6134029 TAAACCT-
1 TAAA-CTA
6134036 TAAAC-A
1 TAAACTA
6134042 TAAACCT-
1 TAAA-CTA
6134049 TAAAC-A
1 TAAACTA
**
6134055 TAAACCC
1 TAAACTA
*
6134062 TAAACTC
1 TAAACTA
6134069 TAAAC-A
1 TAAACTA
**
6134075 TAAACCC
1 TAAACTA
*
6134082 TAAACCA
1 TAAACTA
6134089 TACAA-T-
1 TA-AACTA
6134095 TAAATCT-
1 TAAA-CTA
6134102 TAAACT-
1 TAAACTA
6134108 TAAACT-
1 TAAACTA
**
6134114 TAAACCC
1 TAAACTA
*
6134121 TAAACTT
1 TAAACTA
6134128 TAAA-TA
1 TAAACTA
*
6134134 TAAAATA
1 TAAACTA
6134141 TAAAC
1 TAAAC
6134146 CCTAAACCCT
Statistics
Matches: 158, Mismatches: 22, Indels: 46
0.70 0.10 0.20
Matches are distributed among these distances:
5 3 0.02
6 62 0.39
7 88 0.56
8 3 0.02
9 2 0.01
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.25
Consensus pattern (7 bp):
TAAACTA
Found at i:6134000 original size:13 final size:13
Alignment explanation
Indices: 6133984--6134131 Score: 108
Period size: 13 Copynumber: 11.2 Consensus size: 13
6133974 AATAAATATA
6133984 AAACCTAAACCTT
1 AAACCTAAACCTT
*
6133997 AAACATAAACCTT
1 AAACCTAAACCTT
6134010 AAACCTTAAA--TAT
1 AAACC-TAAACCT-T
6134023 AAACCATAAACCTT
1 AAACC-TAAACCTT
*
6134037 AAACATAAACCTT
1 AAACCTAAACCTT
* *
6134050 AAACATAAACCCT
1 AAACCTAAACCTT
*
6134063 AAACTCTAAA-CAT
1 AAAC-CTAAACCTT
*
6134076 AAACCCTAAACCAT
1 AAA-CCTAAACCTT
* *
6134090 ACAA-TTAAATCTT
1 A-AACCTAAACCTT
*
6134103 AAACTTAAA-CTT
1 AAACCTAAACCTT
*
6134115 AAACCCTAAACTTT
1 AAA-CCTAAACCTT
6134129 AAA
1 AAA
6134132 TATAAAATAT
Statistics
Matches: 112, Mismatches: 12, Indels: 21
0.77 0.08 0.14
Matches are distributed among these distances:
12 9 0.08
13 77 0.69
14 23 0.21
15 3 0.03
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (13 bp):
AAACCTAAACCTT
Found at i:6134080 original size:33 final size:32
Alignment explanation
Indices: 6133922--6134086 Score: 125
Period size: 33 Copynumber: 5.0 Consensus size: 32
6133912 TTACAAATCC
* * *
6133922 TAAACCCTAAATCTTAAAC-TAAAACTATAAACTT
1 TAAACCCTAAA-CCTAAACATAAACCT-TAAAC-A
* * ** * *
6133956 TATACCCTAAACATAAACAATAAATATAAAACC
1 TAAACCCTAAACCTAAAC-ATAAACCTTAAACA
* * * *
6133989 TAAACCTTAAACATAAACCTTAAACCTTAAATA
1 TAAACCCTAAACCTAAA-CATAAACCTTAAACA
*
6134022 TAAACCATAAACCTTAAACATAAACCTTAAACA
1 TAAACCCTAAACC-TAAACATAAACCTTAAACA
*
6134055 TAAACCCTAAACTCTAAACATAAACCCTAAAC
1 TAAACCCTAAAC-CTAAACATAAACCTTAAAC
6134087 CATACAATTA
Statistics
Matches: 106, Mismatches: 20, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
33 81 0.76
34 20 0.19
35 5 0.05
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.24
Consensus pattern (32 bp):
TAAACCCTAAACCTAAACATAAACCTTAAACA
Found at i:6134165 original size:20 final size:20
Alignment explanation
Indices: 6133581--6134151 Score: 124
Period size: 20 Copynumber: 28.1 Consensus size: 20
6133571 CCTAAACATC
* *
6133581 AAATATAAACCATAAA-TCT
1 AAATATAAACCCTAAACCCT
* *
6133600 AGAATCATAAACCCTAAAGCTT
1 A-AAT-ATAAACCCTAAACCCT
* *
6133622 AAACATAAACCCTAAACACT
1 AAATATAAACCCTAAACCCT
* * *
6133642 AAATCTAAAACCATAAAACC-
1 AAATAT-AAACCCTAAACCCT
* *
6133662 ---TA-AAACCATAAACCCA
1 AAATATAAACCCTAAACCCT
* *
6133678 AAATCATAAATCATAAACCCT
1 AAAT-ATAAACCCTAAACCCT
* *
6133699 AAATATAAACCATAAATCCT
1 AAATATAAACCCTAAACCCT
* *** *
6133719 AAAACACTAAATAATAAACCTT
1 -AAATA-TAAACCCTAAACCCT
*
6133741 AAAATCTAAAACCCTAAACAAACCAT
1 -AAATAT-AAACCCTAAAC---CC-T
* *
6133767 AAACATAAACACTAAACCCT
1 AAATATAAACCCTAAACCCT
** **
6133787 TTATAT-AACTTATAAACCCT
1 AAATATAAAC-CCTAAACCCT
* *
6133807 AAACT-TTACCCCTAAACCCT
1 AAA-TATAAACCCTAAACCCT
*
6133827 AAATATAAACCATAAACCCT
1 AAATATAAACCCTAAACCCT
** *
6133847 AAATCATAAATACTAAACACT
1 AAAT-ATAAACCCTAAACCCT
* *
6133868 AAACACTAAACCCTAAACAC-
1 AAATA-TAAACCCTAAACCCT
* *
6133888 AAACATAAAACCCTAAA-ACT
1 AAATAT-AAACCCTAAACCCT
* * *
6133908 AGTATTACAAATCCTAAACCCT
1 A--AATATAAACCCTAAACCCT
* **
6133930 AAATCTTAAA--CTAAAACTAT
1 AAAT-ATAAACCCT-AAACCCT
* * *
6133950 AAACTTTATACCCTAAACATAAACAAT
1 AAA-TATAAACCCTAAAC-----C-CT
* *
6133977 AAATATAAAACCTAAACCTT
1 AAATATAAACCCTAAACCCT
* * *
6133997 AAACATAAACCTTAAACCTT
1 AAATATAAACCCTAAACCCT
*
6134017 AAATATAAACCATAAA-CC-
1 AAATATAAACCCTAAACCCT
* *
6134035 ---T-TAAA-CATAAACCTT
1 AAATATAAACCCTAAACCCT
* *
6134050 AAACATAAACCCTAAACTCT
1 AAATATAAACCCTAAACCCT
* *
6134070 AAACATAAACCCTAAACCAT
1 AAATATAAACCCTAAACCCT
* * *
6134090 ACAAT-TAAATCTTAAA-CTT
1 A-AATATAAACCCTAAACCCT
**
6134109 AAACT-TAAACCCTAAACTTT
1 AAA-TATAAACCCTAAACCCT
***
6134129 AAATATAAAATATAAACCCT
1 AAATATAAACCCTAAACCCT
6134149 AAA
1 AAA
6134152 CCCTAAATAT
Statistics
Matches: 409, Mismatches: 93, Indels: 99
0.68 0.15 0.16
Matches are distributed among these distances:
13 6 0.01
14 5 0.01
15 13 0.03
17 1 0.00
18 2 0.00
19 30 0.07
20 192 0.47
21 96 0.23
22 32 0.08
24 10 0.02
25 5 0.01
26 12 0.03
27 5 0.01
ACGTcount: A:0.53, C:0.24, G:0.01, T:0.23
Consensus pattern (20 bp):
AAATATAAACCCTAAACCCT
Found at i:6134360 original size:21 final size:21
Alignment explanation
Indices: 6134334--6134375 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6134324 AAACCCTAAA
*
6134334 TATAAATAATAAATCTAGAAT
1 TATAAACAATAAATCTAGAAT
**
6134355 TATAAACCCTAAATCTAGAAT
1 TATAAACAATAAATCTAGAAT
6134376 CACAAAACTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.31
Consensus pattern (21 bp):
TATAAACAATAAATCTAGAAT
Found at i:6134546 original size:20 final size:20
Alignment explanation
Indices: 6134523--6134589 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
6134513 AAAAACTAAG
* * *
6134523 CCCTATACTTAAACTATAAA
1 CCCTAAACTCAAACCATAAA
*
6134543 CCCTAAACTCAAACCATCAA
1 CCCTAAACTCAAACCATAAA
*
6134563 CCCTAAA-TATAAACCATAAA
1 CCCTAAACT-CAAACCATAAA
*
6134583 TCCTAAA
1 CCCTAAA
6134590 TTATAAATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 1 0.03
20 38 0.97
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (20 bp):
CCCTAAACTCAAACCATAAA
Found at i:6134547 original size:122 final size:121
Alignment explanation
Indices: 6134357--6134610 Score: 323
Period size: 122 Copynumber: 2.1 Consensus size: 121
6134347 TCTAGAATTA
* * * * * *
6134357 TAAACCCTAAATCTAGAATCACAAAACTAAACCTAAACATTAAACCCTATATTTAAATCATAAAC
1 TAAACCCTAAAACCAAAATCACAAAACTAAACCTAAAAACTAAACCCTATACTTAAATCATAAAC
** *
6134422 CCTAAACTCTAATTC-TAAACCCAAAATATAAACCATAAATCCTAAATCCTAAACAT
66 CCTAAACTC-AAACCATAAACCCAAAATATAAACCATAAATCCTAAATCATAAACAT
* *
6134478 TAAACCCTAAAACCAAAATCACAAACCGTAAACCTAAAAACTAAGCCCTATACTTAAA-CTATAA
1 TAAACCCTAAAACCAAAATCACAAAAC-TAAACCTAAAAACTAAACCCTATACTTAAATC-ATAA
* * * *
6134542 ACCCTAAACTCAAACCATCAACCCTAAATATAAACCATAAATCCTAAATTATAAATAT
64 ACCCTAAACTCAAACCATAAACCCAAAATATAAACCATAAATCCTAAATCATAAACAT
*
6134600 TAAACCTTAAA
1 TAAACCCTAAA
6134611 CCCTAAAACT
Statistics
Matches: 114, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
121 27 0.24
122 87 0.76
ACGTcount: A:0.50, C:0.25, G:0.01, T:0.23
Consensus pattern (121 bp):
TAAACCCTAAAACCAAAATCACAAAACTAAACCTAAAAACTAAACCCTATACTTAAATCATAAAC
CCTAAACTCAAACCATAAACCCAAAATATAAACCATAAATCCTAAATCATAAACAT
Found at i:6134625 original size:28 final size:27
Alignment explanation
Indices: 6134566--6134673 Score: 69
Period size: 28 Copynumber: 3.9 Consensus size: 27
6134556 CCATCAACCC
* *
6134566 TAAATATAAACCATAAATCCTAAATTA
1 TAAATATAAACCATAAACCCTAAACTA
*
6134593 TAAATATTAAACCTTAAACCCTAAAACTA
1 TAAATA-TAAACCATAAACCCT-AAACTA
* * * *
6134622 -AAATCACAAACAAAAAACCTTACAA-T-
1 TAAAT-ATAAACCATAAACCCTA-AACTA
* *
6134648 TAAACTCTAAACCCTAAACCCTAAAC
1 TAAA-TATAAACCATAAACCCTAAAC
6134674 CTTAAACTAA
Statistics
Matches: 60, Mismatches: 14, Indels: 14
0.68 0.16 0.16
Matches are distributed among these distances:
26 2 0.03
27 22 0.37
28 30 0.50
29 6 0.10
ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (27 bp):
TAAATATAAACCATAAACCCTAAACTA
Found at i:6134746 original size:7 final size:7
Alignment explanation
Indices: 6134736--6134760 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6134726 CTTTAAACCC
6134736 TAAATTA
1 TAAATTA
6134743 TAAATTA
1 TAAATTA
6134750 TAAATTA
1 TAAATTA
6134757 TAAA
1 TAAA
6134761 CCTTAAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
TAAATTA
Found at i:6134782 original size:14 final size:15
Alignment explanation
Indices: 6134722--6134782 Score: 60
Period size: 14 Copynumber: 4.3 Consensus size: 15
6134712 ACACTAACTC
*
6134722 TAAACTT-TAAACCC
1 TAAACTTATAAACCT
6134736 TAAA-TTATAAA--T
1 TAAACTTATAAACCT
*
6134748 TATAAATTATAAACCT
1 TA-AACTTATAAACCT
6134764 TAAACTT-TAAACCT
1 TAAACTTATAAACCT
6134778 TAAAC
1 TAAAC
6134783 CCTAAACATA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
12 2 0.05
13 4 0.10
14 27 0.68
15 4 0.10
16 3 0.08
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.34
Consensus pattern (15 bp):
TAAACTTATAAACCT
Found at i:6134942 original size:7 final size:7
Alignment explanation
Indices: 6134905--6134976 Score: 58
Period size: 7 Copynumber: 10.0 Consensus size: 7
6134895 ATTACCAAAT
6134905 CTTAAAC
1 CTTAAAC
6134912 CTTTAAAC
1 C-TTAAAC
6134920 CTTAAAAC
1 CTT-AAAC
*
6134928 CATAAAAC
1 C-TTAAAC
6134936 CTTAAAC
1 CTTAAAC
6134943 AC-TAAA-
1 -CTTAAAC
*
6134949 ATTAAAC
1 CTTAAAC
*
6134956 TTTAAAC
1 CTTAAAC
*
6134963 CATAAAC
1 CTTAAAC
6134970 CTTAAAC
1 CTTAAAC
6134977 TCAAACACTA
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
6 4 0.08
7 29 0.56
8 18 0.35
9 1 0.02
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (7 bp):
CTTAAAC
Found at i:6134960 original size:20 final size:19
Alignment explanation
Indices: 6134936--6134989 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
6134926 ACCATAAAAC
6134936 CTTAAACACTAAAATTAAA
1 CTTAAACACTAAAATTAAA
*
6134955 CTTTAAAC-CATAAACCTTAAA
1 C-TTAAACAC-TAAA-ATTAAA
*
6134976 CTCAAACACTAAAA
1 CTTAAACACTAAAA
6134990 AATATACCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
19 2 0.07
20 19 0.68
21 7 0.25
ACGTcount: A:0.54, C:0.22, G:0.00, T:0.24
Consensus pattern (19 bp):
CTTAAACACTAAAATTAAA
Found at i:6134974 original size:14 final size:14
Alignment explanation
Indices: 6134905--6135085 Score: 52
Period size: 14 Copynumber: 12.5 Consensus size: 14
6134895 ATTACCAAAT
*
6134905 CTTAAACCTTTAAAC
1 CTTAAACC-ATAAAC
6134920 CTTAAAACCATAAAAC
1 CTT-AAACCAT-AAAC
6134936 CTTAAACACTAAAATTAAAC
1 CTTAAAC-C----A-TAAAC
*
6134956 TTTAAACCATAAAC
1 CTTAAACCATAAAC
6134970 CTTAAA-C-TCAAAC
1 CTTAAACCAT-AAAC
** *
6134983 AC-TAAAAAATATAC
1 -CTTAAACCATAAAC
* *
6134997 CCTAAACGATAAA-
1 CTTAAACCATAAAC
*
6135010 CTATAAACCCTAAA-
1 CT-TAAACCATAAAC
*
6135024 CTTAAACAATAAAC
1 CTTAAACCATAAAC
* *
6135038 CCTAAA-TATAAAC
1 CTTAAACCATAAAC
* * * *
6135051 CATAAATCTTAAAT
1 CTTAAACCATAAAC
*
6135065 CTTAAA-AACTAAAC
1 CTTAAACCA-TAAAC
6135079 CTTAAAC
1 CTTAAAC
6135086 ACTAAACCCT
Statistics
Matches: 125, Mismatches: 23, Indels: 36
0.68 0.12 0.20
Matches are distributed among these distances:
12 1 0.01
13 31 0.25
14 57 0.46
15 10 0.08
16 13 0.10
19 1 0.01
20 11 0.09
21 1 0.01
ACGTcount: A:0.52, C:0.23, G:0.01, T:0.24
Consensus pattern (14 bp):
CTTAAACCATAAAC
Found at i:6135003 original size:21 final size:20
Alignment explanation
Indices: 6134979--6135092 Score: 86
Period size: 21 Copynumber: 5.5 Consensus size: 20
6134969 CCTTAAACTC
* *
6134979 AAACACTAAAAAATATACCCT
1 AAACA-TAAACAATAAACCCT
*
6135000 AAACGATAAACTATAAACCCT
1 AAAC-ATAAACAATAAACCCT
*
6135021 AAACTTAAACAATAAACCCT
1 AAACATAAACAATAAACCCT
* * * *
6135041 AAATATAAACCATAAATCTT
1 AAACATAAACAATAAACCCT
* *
6135061 AAATCTTAAA-AACTAAACCTT
1 AAA-CATAAACAA-TAAACCCT
6135082 AAACACTAAAC
1 AAACA-TAAAC
6135093 CCTAATCACA
Statistics
Matches: 73, Mismatches: 15, Indels: 9
0.75 0.15 0.09
Matches are distributed among these distances:
20 34 0.47
21 38 0.52
22 1 0.01
ACGTcount: A:0.55, C:0.22, G:0.01, T:0.22
Consensus pattern (20 bp):
AAACATAAACAATAAACCCT
Found at i:6135017 original size:41 final size:41
Alignment explanation
Indices: 6134932--6135085 Score: 100
Period size: 41 Copynumber: 3.8 Consensus size: 41
6134922 TAAAACCATA
* * **
6134932 AAACCTTAAACACT-AAAATTAAACTTTAAACCATAAACCT-T
1 AAACCCTAAAC-CTAAAAAATAAACCCTAAACCATAAA-CTAT
* * *
6134973 AAACTC-AAACACTAAAAAATATACCCTAAACGATAAACTAT
1 AAACCCTAAAC-CTAAAAAATAAACCCTAAACCATAAACTAT
* * * *
6135014 AAACCCTAAACTTAAACAATAAACCCTAAA-TATAAACCAT
1 AAACCCTAAACCTAAAAAATAAACCCTAAACCATAAACTAT
* * * * *
6135054 AAATCTTAAATCTTAAAAACTAAACCTTAAAC
1 AAACCCTAAA-CCTAAAAAATAAACCCTAAAC
6135086 ACTAAACCCT
Statistics
Matches: 90, Mismatches: 18, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
40 25 0.28
41 61 0.68
42 4 0.04
ACGTcount: A:0.54, C:0.22, G:0.01, T:0.23
Consensus pattern (41 bp):
AAACCCTAAACCTAAAAAATAAACCCTAAACCATAAACTAT
Found at i:6135035 original size:20 final size:20
Alignment explanation
Indices: 6134985--6135085 Score: 80
Period size: 20 Copynumber: 5.0 Consensus size: 20
6134975 ACTCAAACAC
* * *
6134985 TAAAAAATATACCCTAAACGA
1 TAAACAATAAACCCTAAAC-T
*
6135006 TAAACTATAAACCCTAAACT
1 TAAACAATAAACCCTAAACT
6135026 TAAACAATAAACCCTAAA-T
1 TAAACAATAAACCCTAAACT
* * *
6135045 ATAAACCATAAATCTTAAATCT
1 -TAAACAATAAACCCTAAA-CT
*
6135067 TAAA-AACTAAACCTTAAAC
1 TAAACAA-TAAACCCTAAAC
6135086 ACTAAACCCT
Statistics
Matches: 66, Mismatches: 10, Indels: 9
0.78 0.12 0.11
Matches are distributed among these distances:
19 1 0.02
20 34 0.52
21 30 0.45
22 1 0.02
ACGTcount: A:0.54, C:0.21, G:0.01, T:0.24
Consensus pattern (20 bp):
TAAACAATAAACCCTAAACT
Found at i:6135089 original size:14 final size:14
Alignment explanation
Indices: 6135013--6135093 Score: 60
Period size: 14 Copynumber: 5.9 Consensus size: 14
6135003 CGATAAACTA
*
6135013 TAAACCCTAAA-CT
1 TAAACACTAAACCT
* *
6135026 TAAACAATAAACCC
1 TAAACACTAAACCT
* *
6135040 TAAATA-TAAACCA
1 TAAACACTAAACCT
* *
6135053 TAAATC-TTAAATCT
1 TAAA-CACTAAACCT
*
6135067 TAAAAACTAAACCT
1 TAAACACTAAACCT
6135081 TAAACACTAAACC
1 TAAACACTAAACC
6135094 CTAATCACAA
Statistics
Matches: 52, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
13 19 0.37
14 33 0.63
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAACACTAAACCT
Found at i:6135133 original size:21 final size:20
Alignment explanation
Indices: 6135109--6135169 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
6135099 CACAAATAAT
6135109 AAACTATACACATAAACCCTA
1 AAACTATA-ACATAAACCCTA
** *
6135130 AAACTAATATTAAAAACCCTA
1 AAACT-ATAACATAAACCCTA
6135151 AAACCTA-AACATAAACCCT
1 AAA-CTATAACATAAACCCT
6135170 CATTATATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
20 9 0.28
21 18 0.56
22 5 0.16
ACGTcount: A:0.54, C:0.26, G:0.00, T:0.20
Consensus pattern (20 bp):
AAACTATAACATAAACCCTA
Found at i:6135226 original size:13 final size:13
Alignment explanation
Indices: 6135208--6135237 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
6135198 ACAAAATCTT
6135208 AAACCCTAAAATA
1 AAACCCTAAAATA
*
6135221 AAACCCTAAGATA
1 AAACCCTAAAATA
6135234 AAAC
1 AAAC
6135238 TAAAAACCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.60, C:0.23, G:0.03, T:0.13
Consensus pattern (13 bp):
AAACCCTAAAATA
Found at i:6135345 original size:80 final size:80
Alignment explanation
Indices: 6135261--6135481 Score: 193
Period size: 80 Copynumber: 2.8 Consensus size: 80
6135251 ACCTATATAT
* * * *
6135261 AAACCATAAACCTAAA-CTCGAACACTACACACTAAACCTTAAA-TATAAATTATAAACCCTAAA
1 AAACCATAAACATAAACCTCAAACACTACA-ACTAAACCATAAACCATAAA-TATAAACCCTAAA
6135324 CACTATAATTATATCAC
64 CACTATAATTATATCAC
* * * * * * * *
6135341 AAACCTTAAATATAAACCTTAAACACTATAATTATATCATAAACCATAAATATAAACCTTAAACA
1 AAACCATAAACATAAACCTCAAACACTACAACTAAACCATAAACCATAAATATAAACCCTAAACA
*
6135406 CTATAATTATATCAT
66 CTATAATTATATCAC
* * * ** *
6135421 AAACCCTAAATATAAACC-CTAAACCCT--AA-TAAAAAACTAAACCATAAACATAAACCCTAAA
1 AAACCATAAACATAAACCTC-AAACACTACAACTAAACCA-TAAACCATAAATATAAACCCTAAA
6135482 ACATAAGCAT
Statistics
Matches: 116, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
77 4 0.03
78 24 0.21
80 73 0.63
81 15 0.13
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.24
Consensus pattern (80 bp):
AAACCATAAACATAAACCTCAAACACTACAACTAAACCATAAACCATAAATATAAACCCTAAACA
CTATAATTATATCAC
Found at i:6135355 original size:40 final size:40
Alignment explanation
Indices: 6135305--6135481 Score: 234
Period size: 40 Copynumber: 4.5 Consensus size: 40
6135295 AACCTTAAAT
*
6135305 ATAAATTATAAACCCTAAACACTATAATTATATCACAAACC
1 ATAAA-TATAAACCCTAAACACTATAATTATATCATAAACC
* *
6135346 TTAAATATAAACCTTAAACACTATAATTATATCATAAACC
1 ATAAATATAAACCCTAAACACTATAATTATATCATAAACC
*
6135386 ATAAATATAAACCTTAAACACTATAATTATATCATAAACC
1 ATAAATATAAACCCTAAACACTATAATTATATCATAAACC
* * * *
6135426 CTAAATATAAACCCTAAACCCTAATAA--AAAAC-TAAACC
1 ATAAATATAAACCCTAAACACT-ATAATTATATCATAAACC
*
6135464 ATAAACATAAACCCTAAA
1 ATAAATATAAACCCTAAA
6135482 ACATAAGCAT
Statistics
Matches: 124, Mismatches: 11, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
38 22 0.18
39 3 0.02
40 91 0.73
41 8 0.06
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (40 bp):
ATAAATATAAACCCTAAACACTATAATTATATCATAAACC
Found at i:6135359 original size:13 final size:13
Alignment explanation
Indices: 6135341--6135443 Score: 61
Period size: 13 Copynumber: 7.8 Consensus size: 13
6135331 ATTATATCAC
6135341 AAACCTTAAATAT
1 AAACCTTAAATAT
*
6135354 AAACCTTAAACACT
1 AAACCTTAAATA-T
*
6135368 ATAA--TTATATCAT
1 A-AACCTTAAAT-AT
*
6135381 AAACCATAAATAT
1 AAACCTTAAATAT
*
6135394 AAACCTTAAACACT
1 AAACCTTAAATA-T
*
6135408 ATAA--TTATATCAT
1 A-AACCTTAAAT-AT
*
6135421 AAACCCTAAATAT
1 AAACCTTAAATAT
*
6135434 AAACCCTAAA
1 AAACCTTAAA
6135444 CCCTAATAAA
Statistics
Matches: 69, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
12 4 0.06
13 47 0.68
14 14 0.20
15 4 0.06
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.28
Consensus pattern (13 bp):
AAACCTTAAATAT
Found at i:6135443 original size:20 final size:20
Alignment explanation
Indices: 6135306--6135500 Score: 96
Period size: 20 Copynumber: 9.8 Consensus size: 20
6135296 ACCTTAAATA
*
6135306 TAAATTATAAACCCTAAACAC
1 TAAA-TATAAACCCTAAACCC
* * *
6135327 TATAAT-TATATCAC-AAACCT
1 TA-AATATA-AACCCTAAACCC
* *
6135347 TAAATATAAACCTTAAACAC
1 TAAATATAAACCCTAAACCC
* * * *
6135367 TATAAT-TATATCATAAACCA
1 TA-AATATAAACCCTAAACCC
* *
6135387 TAAATATAAACCTTAAACAC
1 TAAATATAAACCCTAAACCC
* * *
6135407 TATAAT-TATATCATAAACCC
1 TA-AATATAAACCCTAAACCC
6135427 TAAATATAAACCCTAAACCC
1 TAAATATAAACCCTAAACCC
** *
6135447 T-AATA-AAAAACTAAACCA
1 TAAATATAAACCCTAAACCC
* * *
6135465 TAAACATAAACCCTAAAACA
1 TAAATATAAACCCTAAACCC
**
6135485 TAAGCATAAACCCTAA
1 TAAATATAAACCCTAA
6135501 CTATATCCTA
Statistics
Matches: 130, Mismatches: 34, Indels: 21
0.70 0.18 0.11
Matches are distributed among these distances:
18 11 0.08
19 18 0.14
20 87 0.67
21 12 0.09
22 2 0.02
ACGTcount: A:0.53, C:0.22, G:0.01, T:0.25
Consensus pattern (20 bp):
TAAATATAAACCCTAAACCC
Found at i:6135690 original size:21 final size:21
Alignment explanation
Indices: 6135664--6135705 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6135654 AAACCCTAAA
6135664 TATAAACAATAAATCTAGAAT
1 TATAAACAATAAATCTAGAAT
** *
6135685 TATAAACCCTAAATTTAGAAT
1 TATAAACAATAAATCTAGAAT
6135706 CACAAAAACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.31
Consensus pattern (21 bp):
TATAAACAATAAATCTAGAAT
Found at i:6135751 original size:7 final size:7
Alignment explanation
Indices: 6135741--6135772 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
6135731 ACCCTATATT
6135741 TAAATCA
1 TAAATCA
6135748 TAAATCA
1 TAAATCA
6135755 TAAATCA
1 TAAATCA
*
6135762 TAAATGA
1 TAAATCA
6135769 TAAA
1 TAAA
6135773 CCCTAAACTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.28
Consensus pattern (7 bp):
TAAATCA
Found at i:6135779 original size:21 final size:20
Alignment explanation
Indices: 6135686--6135840 Score: 91
Period size: 21 Copynumber: 7.6 Consensus size: 20
6135676 ATCTAGAATT
*
6135686 ATAAACCCTAAATTTAGAATC
1 ATAAACCCTAAATATA-AATC
* ** **
6135707 ACAAAAACTAAACCTAAA-C
1 ATAAACCCTAAATATAAATC
* *
6135726 ATTAAACCCTATATTTAAATC
1 A-TAAACCCTAAATATAAATC
* * *
6135747 ATAAATCATAAATCATAAATG
1 ATAAACCCTAAAT-ATAAATC
* *
6135768 ATAAACCCTAAACTCTAATTC
1 ATAAACCCTAAA-TATAAATC
* *
6135789 -TAAACCCAAAATATAAACC
1 ATAAACCCTAAATATAAATC
*
6135808 ATAAATCCTAAATACTAAA-C
1 ATAAACCCTAAATA-TAAATC
6135828 ATTAAACCCTAAA
1 A-TAAACCCTAAA
6135841 ACCAAAATCA
Statistics
Matches: 99, Mismatches: 28, Indels: 14
0.70 0.20 0.10
Matches are distributed among these distances:
19 7 0.07
20 45 0.45
21 46 0.46
22 1 0.01
ACGTcount: A:0.52, C:0.21, G:0.01, T:0.25
Consensus pattern (20 bp):
ATAAACCCTAAATATAAATC
Found at i:6135866 original size:48 final size:48
Alignment explanation
Indices: 6135788--6135879 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
6135778 AACTCTAATT
* * *
6135788 CTAAACCCAAAATATAAACCATAAATCCTAAATACTAAACATTAAACC
1 CTAAAACCAAAATACAAACCATAAATCCTAAAAACTAAACATTAAACC
6135836 CTAAAACCAAAATCACAAACCATAAA-CCTAAAAACTAAACATTA
1 CTAAAACCAAAAT-ACAAACCATAAATCCTAAAAACTAAACATTA
6135880 TACTTAAACT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
48 29 0.73
49 11 0.28
ACGTcount: A:0.57, C:0.25, G:0.00, T:0.18
Consensus pattern (48 bp):
CTAAAACCAAAATACAAACCATAAATCCTAAAAACTAAACATTAAACC
Found at i:6135962 original size:14 final size:14
Alignment explanation
Indices: 6135913--6135962 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
6135903 TCCAACCATC
*
6135913 AACCCTAAATA-TA
1 AACCTTAAATACTA
*
6135926 AACCATAAATACTA
1 AACCTTAAATACTA
*
6135940 AA-TTATAAATACTA
1 AACCT-TAAATACTA
6135954 AACCTTAAA
1 AACCTTAAA
6135963 CCCTAAAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
13 10 0.33
14 19 0.63
15 1 0.03
ACGTcount: A:0.56, C:0.18, G:0.00, T:0.26
Consensus pattern (14 bp):
AACCTTAAATACTA
Found at i:6136064 original size:20 final size:19
Alignment explanation
Indices: 6136013--6136064 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
6136003 TTCTAAACCC
* *
6136013 TAAATCCTAAACCTTAAAC
1 TAAAACCTAAACCTTAAAA
6136032 TAAAA-CTACAAACCTTAAAAA
1 TAAAACCT--AAACCTT-AAAA
6136053 TAAAACCTAAAC
1 TAAAACCTAAAC
6136065 ACTAAATCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
18 2 0.07
19 4 0.15
20 11 0.41
21 8 0.30
22 2 0.07
ACGTcount: A:0.56, C:0.23, G:0.00, T:0.21
Consensus pattern (19 bp):
TAAAACCTAAACCTTAAAA
Found at i:6136070 original size:14 final size:14
Alignment explanation
Indices: 6136005--6136070 Score: 50
Period size: 14 Copynumber: 4.9 Consensus size: 14
6135995 CAATTAAATT
* *
6136005 CTAAACCCTAAATC
1 CTAAACACTAAAAC
*
6136019 CTAAAC-CTTAAA-
1 CTAAACACTAAAAC
6136031 CTAAA-ACTACAAAC
1 CTAAACACTA-AAAC
*
6136045 CTTAAA-AATAAAAC
1 C-TAAACACTAAAAC
6136059 CTAAACACTAAA
1 CTAAACACTAAA
6136071 TCTAAACTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
12 7 0.17
13 11 0.26
14 17 0.40
15 7 0.17
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.20
Consensus pattern (14 bp):
CTAAACACTAAAAC
Found at i:6136276 original size:15 final size:15
Alignment explanation
Indices: 6136209--6136277 Score: 56
Period size: 15 Copynumber: 4.7 Consensus size: 15
6136199 ATTATATAAT
6136209 AAACCCTAAATCTTA
1 AAACCCTAAATCTTA
*
6136224 AAACCCTAAAAC-T-
1 AAACCCTAAATCTTA
6136237 AAACTACC-AAATCTT-
1 AAAC--CCTAAATCTTA
*
6136252 AAACCTTTAAATCTTA
1 AAACC-CTAAATCTTA
*
6136268 AAACCTTAAA
1 AAACCCTAAA
6136278 CCCTAAAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
13 5 0.11
14 5 0.11
15 30 0.67
16 5 0.11
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (15 bp):
AAACCCTAAATCTTA
Found at i:6136371 original size:20 final size:20
Alignment explanation
Indices: 6136342--6136421 Score: 74
Period size: 20 Copynumber: 4.0 Consensus size: 20
6136332 CCCTAAATAA
*
6136342 TAAACTATAAACCCTAAACT
1 TAAACAATAAACCCTAAACT
6136362 TAAACAATAAACCCTAAA-T
1 TAAACAATAAACCCTAAACT
* * *
6136381 ATAAACCATAAATCCTAAATCC
1 -TAAACAATAAACCCTAAA-CT
*
6136403 TAAA-AACTAAACCTTAAAC
1 TAAACAA-TAAACCCTAAAC
6136422 ACTAAACCCT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
19 1 0.02
20 35 0.71
21 13 0.27
ACGTcount: A:0.54, C:0.24, G:0.00, T:0.23
Consensus pattern (20 bp):
TAAACAATAAACCCTAAACT
Found at i:6136379 original size:14 final size:14
Alignment explanation
Indices: 6136331--6136433 Score: 52
Period size: 14 Copynumber: 7.5 Consensus size: 14
6136321 CAAAAACTAG
*
6136331 ACCCTAAATAATAA
1 ACCCTAAACAATAA
** **
6136345 ACTATAAACCCTAA
1 ACCCTAAACAATAA
*
6136359 A-CTTAAACAATAA
1 ACCCTAAACAATAA
*
6136372 ACCCTAAA-TATAA
1 ACCCTAAACAATAA
* *
6136385 ACCATAAATC-CTAA
1 ACCCTAAA-CAATAA
*
6136399 ATCCTAAA-AACTAA
1 ACCCTAAACAA-TAA
* *
6136413 ACCTTAAACACTAA
1 ACCCTAAACAATAA
6136427 ACCCTAA
1 ACCCTAA
6136434 TCACAAATAA
Statistics
Matches: 63, Mismatches: 20, Indels: 12
0.66 0.21 0.13
Matches are distributed among these distances:
13 20 0.32
14 42 0.67
15 1 0.02
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.21
Consensus pattern (14 bp):
ACCCTAAACAATAA
Found at i:6136420 original size:28 final size:27
Alignment explanation
Indices: 6136362--6136433 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
6136352 ACCCTAAACT
* *
6136362 TAAACAATAAACCCTAAATATAAACCA
1 TAAACACTAAACCCTAAAAATAAACCA
* *
6136389 TAAATC-CTAAATCCTAAAAACTAAACCT
1 TAAA-CACTAAACCCTAAAAA-TAAACCA
6136417 TAAACACTAAACCCTAA
1 TAAACACTAAACCCTAA
6136434 TCACAAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
27 16 0.43
28 21 0.57
ACGTcount: A:0.54, C:0.25, G:0.00, T:0.21
Consensus pattern (27 bp):
TAAACACTAAACCCTAAAAATAAACCA
Found at i:6136607 original size:27 final size:27
Alignment explanation
Indices: 6136577--6136693 Score: 71
Period size: 27 Copynumber: 4.4 Consensus size: 27
6136567 ATAAAACTAG
*
6136577 AAACCCTAAAACCTATATATAAACCAT
1 AAACCCTAAAACCTATACATAAACCAT
* *
6136604 AAA--CTTAAACGCGA-ACACTAAA-CACT
1 AAACCCTAAAAC-CTATACA-TAAACCA-T
* * * *
6136630 AAACCCTAAACCCTAAACACAAACCCT
1 AAACCCTAAAACCTATACATAAACCAT
* ** * *
6136657 AAACCCTAAACCCTATATTTATATCAT
1 AAACCCTAAAACCTATACATAAACCAT
6136684 AAACCCTAAA
1 AAACCCTAAA
6136694 TATAAACCTT
Statistics
Matches: 68, Mismatches: 15, Indels: 14
0.70 0.15 0.14
Matches are distributed among these distances:
25 10 0.15
26 10 0.15
27 39 0.57
28 9 0.13
ACGTcount: A:0.49, C:0.30, G:0.02, T:0.20
Consensus pattern (27 bp):
AAACCCTAAAACCTATACATAAACCAT
Found at i:6136629 original size:7 final size:7
Alignment explanation
Indices: 6136621--6136671 Score: 77
Period size: 7 Copynumber: 7.4 Consensus size: 7
6136611 AACGCGAACA
*
6136621 CTAAACA
1 CTAAACC
6136628 CTAAACC
1 CTAAACC
6136635 CTAAACC
1 CTAAACC
*
6136642 CTAAACA
1 CTAAACC
6136649 C-AAACC
1 CTAAACC
6136655 CTAAACC
1 CTAAACC
6136662 CTAAACC
1 CTAAACC
6136669 CTA
1 CTA
6136672 TATTTATATC
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
6 5 0.12
7 35 0.88
ACGTcount: A:0.47, C:0.39, G:0.00, T:0.14
Consensus pattern (7 bp):
CTAAACC
Found at i:6136655 original size:20 final size:21
Alignment explanation
Indices: 6136621--6136667 Score: 87
Period size: 20 Copynumber: 2.3 Consensus size: 21
6136611 AACGCGAACA
6136621 CTAAACACTAAACCCTAAACC
1 CTAAACACTAAACCCTAAACC
6136642 CTAAACAC-AAACCCTAAACC
1 CTAAACACTAAACCCTAAACC
6136662 CTAAAC
1 CTAAAC
6136668 CCTATATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.49, C:0.38, G:0.00, T:0.13
Consensus pattern (21 bp):
CTAAACACTAAACCCTAAACC
Found at i:6136700 original size:40 final size:40
Alignment explanation
Indices: 6136656--6136783 Score: 145
Period size: 40 Copynumber: 3.3 Consensus size: 40
6136646 ACACAAACCC
* * *
6136656 TAAACCCTAAACCCTATATTTATATCATAAACCCTAAATA
1 TAAACCCTAAACCCTATAATCATATCATAAACCATAAATA
* * *
6136696 TAAACCTTAAACACTATAATCATATCATAAACCATAAATC
1 TAAACCCTAAACCCTATAATCATATCATAAACCATAAATA
* * * *
6136736 TAAACCCTAAACCC--TAATGAAAAC-TAAACCATAAAGA
1 TAAACCCTAAACCCTATAATCATATCATAAACCATAAATA
6136773 TAAACCCTAAA
1 TAAACCCTAAA
6136784 ACATAAACAT
Statistics
Matches: 75, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
37 22 0.29
38 7 0.09
40 46 0.61
ACGTcount: A:0.50, C:0.24, G:0.02, T:0.24
Consensus pattern (40 bp):
TAAACCCTAAACCCTATAATCATATCATAAACCATAAATA
Found at i:6136746 original size:20 final size:20
Alignment explanation
Indices: 6136635--6136802 Score: 71
Period size: 20 Copynumber: 8.6 Consensus size: 20
6136625 ACACTAAACC
**
6136635 CTAAACCCTAAACACA-AACC
1 CTAAACCCTAAAC-CATAAAT
* *
6136655 CTAAACCCTAAACCCTATAT
1 CTAAACCCTAAACCATAAAT
* * * * *
6136675 TTATATCATAAACCCTAAAT
1 CTAAACCCTAAACCATAAAT
* *
6136695 ATAAACCTTAAA-CACTATAAT
1 CTAAACCCTAAACCA-TA-AAT
* * *
6136716 C-ATATCATAAACCATAAAT
1 CTAAACCCTAAACCATAAAT
*
6136735 CTAAACCCTAAACCCT-AAT
1 CTAAACCCTAAACCATAAAT
* * *
6136754 -GAAA-ACTAAACCATAAAG
1 CTAAACCCTAAACCATAAAT
* *
6136772 ATAAACCCTAAAACATAAA-
1 CTAAACCCTAAACCATAAAT
6136791 CATAAACCCTAA
1 C-TAAACCCTAA
6136803 TTATATCCTA
Statistics
Matches: 109, Mismatches: 30, Indels: 18
0.69 0.19 0.11
Matches are distributed among these distances:
17 8 0.07
18 5 0.05
19 12 0.11
20 79 0.72
21 5 0.05
ACGTcount: A:0.51, C:0.27, G:0.01, T:0.21
Consensus pattern (20 bp):
CTAAACCCTAAACCATAAAT
Found at i:6136889 original size:28 final size:28
Alignment explanation
Indices: 6136825--6136892 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
6136815 CCATAACCTC
* * **
6136825 AAACACTAAACACTAAACCTTAAATTAT
1 AAACAATAAACCCTAAACCTTAAACCAT
*
6136853 AAACCATAAACCCTAAACCTTAAAACCAT
1 AAACAATAAACCCTAAACCTT-AAACCAT
6136882 AAA-AATAAACC
1 AAACAATAAACC
6136893 TTCAACCCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 25 0.76
29 8 0.24
ACGTcount: A:0.56, C:0.25, G:0.00, T:0.19
Consensus pattern (28 bp):
AAACAATAAACCCTAAACCTTAAACCAT
Found at i:6136991 original size:21 final size:21
Alignment explanation
Indices: 6136940--6136999 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
6136930 TTCTAAACCC
6136940 TAAACCCTAAATCTTA-AA-TA
1 TAAACCCTAAATC-TAGAATTA
***
6136960 TAAATAATAAATCTAGAATTA
1 TAAACCCTAAATCTAGAATTA
*
6136981 TAAACCCTAAATATAGAAT
1 TAAACCCTAAATCTAGAAT
6137000 CACAAAAACT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
19 2 0.06
20 12 0.39
21 17 0.55
ACGTcount: A:0.53, C:0.13, G:0.03, T:0.30
Consensus pattern (21 bp):
TAAACCCTAAATCTAGAATTA
Found at i:6137270 original size:14 final size:14
Alignment explanation
Indices: 6137251--6137327 Score: 61
Period size: 14 Copynumber: 5.6 Consensus size: 14
6137241 TAAACCTTAC
*
6137251 AACCCTAAACTCTA
1 AACCCTAAAATCTA
6137265 AACCCTAAAAT-TA
1 AACCCTAAAATCTA
* * *
6137278 AA-CTTTAAACCATA
1 AACCCTAAAATC-TA
*
6137292 AACCTTAAAATC-A
1 AACCCTAAAATCTA
* *
6137305 AACACTAAAAACTA
1 AACCCTAAAATCTA
6137319 AACCCTAAA
1 AACCCTAAA
6137328 TGATAAGCTA
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
12 5 0.10
13 14 0.29
14 23 0.47
15 7 0.14
ACGTcount: A:0.53, C:0.26, G:0.00, T:0.21
Consensus pattern (14 bp):
AACCCTAAAATCTA
Found at i:6137274 original size:989 final size:984
Alignment explanation
Indices: 6136210--6138205 Score: 2948
Period size: 989 Copynumber: 2.0 Consensus size: 984
6136200 TTATATAATA
* * * *
6136210 AACCCTAAATCTTAAAACCCTAAAACTAAACTACCAAATCTTAAACCTTTAAATCTTAAAACCTT
1 AACCCTAAATCTCAAAACCCTAAAACTAAACTACCAAATCTAAAACCTTTAAACCTTAAAAACTT
* *
6136275 AAACCCTAAAAATAAACTTTAAACCACAAACCTTAAACTCAAACACCAAAAACTAGACCCTAAAT
66 AAACCCTAAAAATAAACTTTAAACCACAAACCTTAAAATCAAACACCAAAAACTAAACCCTAAAT
*
6136340 AATAAACTATAAACCCTAAACTTAAACAATAAACCCTAAATATAAACCATAAATCCTAAATCCTA
131 AATAAACTATAAACCCTAAACTTAAACAATAAACCCAAAATATAAACCATAAATCCTAAATCCTA
* * *
6136405 AAAACTAAACCTTAAACACTAAACCCTAATCACAAATAATAAACTATACACATAAACCCTAAAAC
196 AAAACTAAACCTTAAACACCAAACCCTAACCACAAATAATAAACTATACACATAAACACTAAAAC
* * *
6136470 TAGAATTAAAAACCCTAGAACCTAAACATAAACCCTCATTATATCATAAACCATAAACATAAACA
261 TAAAATTAAAAACCCTAAAACCTAAACATAAACCCTAATTATATCATAAACCATAAACATAAACA
6136535 CAAAACCTTAAACCCTAAAATAAAAACCTAAGATAAAACTAGAAACCCTAAAACCTATATATAAA
326 CAAAACCTTAAACCCTAAAATAAAAACCTAAGATAAAACTAGAAACCCTAAAACCTATATATAAA
* * *
6136600 CCATAAACTTAAACGCGAACACTAAACACTAAACCCT-AAACCCTAAACAC-AAACCCTAAACCC
391 CCATAAACCTAAACGCGAACACTAAACACTAAACCCTAAAACCCTAAAC-CTAAACCATAAACAC
* ** * * *
6136663 TAAACCCTATA-TTTATATCATAAACCCTAAA-T-A-T-AAACCTTAAACACTATA-A-TCATA-
455 -AAACCCTAAACACTAAATCATAAACCCTAAACTAACTAAAACCTTAAAC-C-ATACACACAAAC
* * *
6136720 TCATAAACCATAAATC-TAAACCCTAAACCCT-AAT-GAAAA-CTAAACCATAA-AGATAAACCC
517 T-ATAAACCATAAACCATAAACACTAAACCCTAAATAGAAAACCTAAACCATAATA-A-AAA-AC
* *
6136780 TAAAACATAAACATAAACCCTAATTATATCCTAAACCATAACCTCAAACACTAAACACTAAACCT
578 TAAAACATAAACATAAACCCTAACTATATCCAAAACCATAACCTCAAACACTAAACACTAAACCT
6136845 TAAATTATAAACCATAAACCCTAAACCTTAAAACCATAAAAATAAACCTTCAACCCTACAATT-A
643 TAAATTATAAACCATAAACCCTAAACCTTAAAACCATAAAAATAAACCTTCAACCCTACAATTAA
*
6136909 ACATAAACCCTAAAACTACCAT-TCTAAACCCTAAACCCTAAATCTTAAATATAAATAATAAATC
708 ACATAAACCCTAAAACTACCATGTC-AAACCCTAAA-CC-----C-TAAATATAAATAATAAACC
6136973 TAGAATTATAAACCCTAAATATAGAATCACAAAAACTAAAACTAAACATTAAACCCTATATTTAA
765 TAGAATTATAAACCCTAAATATAGAATCACAAAAACTAAAACTAAACATTAAACCCTATATTTAA
* *
6137038 ATCATAAATCATAAACCCCAAACTCTAATTCTAAACCCAAACTATAAACAACAAATCCTAAATAC
830 ATCATAAACCATAAACCCCAAACTCTAATTCTAAACCCAAAATATAAACAACAAATCCTAAATAC
*
6137103 T-AACATTAAACCCTAAAACCAAAATCACAAACCCTAAACATAAAAACTAAACCCTATACTTAAA
895 TAAACATTAAACCCTAAAACCAAAATCACAAACCATAAACATAAAAACTAAACCCTATACTTAAA
* * * *
6137167 TTATAAACCTTAAACTCTAACTATC
960 TTATAAACCCTAAACACCAACCATC
* *
6137192 AACCCTAAATCTCAAAACCTTAAAACTAAACTACCAAATCTAAAACTTTTAAACCTTACAACCCT
1 AACCCTAAATCTCAAAACCCTAAAACTAAACTACCAAATCTAAAACCTTTAAACCTT--AA----
* * *
6137257 AAACTCTAAACCCTAAAATTAAACTTTAAACCATAAACCTTAAAATCAAACACTAAAAACTAAAC
60 AAACT-TAAACCCTAAAAATAAACTTTAAACCACAAACCTTAAAATCAAACACCAAAAACTAAAC
* *
6137322 CCTAAATGATAAGCTATAAACCCTAAACTTAAACAATAAACCCAAAATATAAACCATAAATCCTA
124 CCTAAATAATAAACTATAAACCCTAAACTTAAACAATAAACCCAAAATATAAACCATAAATCCTA
*
6137387 AATCCTAAAAACTAAACCTTAAACACCAAACCTTAACCACAAATAATAAACTATACACATAAACA
189 AATCCTAAAAACTAAACCTTAAACACCAAACCCTAACCACAAATAATAAACTATACACATAAACA
6137452 CTAAAACTAAAATTAAAAACCCTAAAACCTAAACATAAACCCTAATTATATCATAAACCATAAAC
254 CTAAAACTAAAATTAAAAACCCTAAAACCTAAACATAAACCCTAATTATATCATAAACCATAAAC
*
6137517 ATAAACACAAAACCTTAAACCCTAAAATAAAAACCTAAGATAAAACTAGAAACCCTAAACCCTAT
319 ATAAACACAAAACCTTAAACCCTAAAATAAAAACCTAAGATAAAACTAGAAACCCTAAAACCTAT
*
6137582 ATATAAACCATAAACCTAAACTCGAACACTAAACACTAAACCCTAAACACAAACCCTAAACCTTA
384 ATATAAACCATAAACCTAAACGCGAACACTAAACACTAAACCCT----A-AAACCCTAAACC-TA
*
6137647 AACCATAAACACAAACCCTAAACACTAAATCATAAACCTTAAACGCTAAAACCCTAAAACCTTAA
443 AACCATAAACACAAACCCTAAACACTAAATCATAAACCCTAAA--CT--AA--CTAAAACCTTAA
* * *
6137712 ACCATACACACAAACTTTAAACCCTAAACCATAAACACTAAACCCTAAATCATAAAACCCTAAAC
502 ACCATACACACAAACTATAAACCATAAACCATAAACACTAAACCCTAAAT-AGAAAA-CCTAAAC
* *
6137777 CCTAATAAAAAACTAAACCATAAACATAAACCCTAACTATATCCAAAACCATAACCTCAAACACT
565 CATAATAAAAAACTAAAACATAAACATAAACCCTAACTATATCCAAAACCATAACCTCAAACACT
* *
6137842 AAACACTAAACCTTAAATTATAAACCTTAAACCCTAAACCTTAAAACCATAAAAATAAACTTTCA
630 AAACACTAAACCTTAAATTATAAACCATAAACCCTAAACCTTAAAACCATAAAAATAAACCTTCA
** *
6137907 ACCCTACAATTAAACATAAACCCTAAAACTATTATGTCAAACCCTAAACCCTAAATATAAGTAAT
695 ACCCTACAATTAAACATAAACCCTAAAACTACCATGTCAAACCCTAAACCCTAAATATAAATAAT
* *
6137972 AAACCTAGAATTATAAACCCTAAATATAGAATCATAAAAACTAAACCTAAACATTAAACCCTATA
760 AAACCTAGAATTATAAACCCTAAATATAGAATCACAAAAACTAAAACTAAACATTAAACCCTATA
* ** * * *
6138037 TTTAAATCATAAACCATAAGCCTTAAATTCTAATTCTAAACCCAAAATATAAACCACAAATCCTC
825 TTTAAATCATAAACCATAAACCCCAAACTCTAATTCTAAACCCAAAATATAAACAACAAATCCTA
6138102 AATACTAAACATTAAACCCTAAAACCAAAATCACAAACCATAAACATAAAAACTAAACCCTATAC
890 AATACTAAACATTAAACCCTAAAACCAAAATCACAAACCATAAACATAAAAACTAAACCCTATAC
*
6138167 TTAAATTATATACCCTAAACACCAACCATC
955 TTAAATTATAAACCCTAAACACCAACCATC
6138197 AACCCTAAA
1 AACCCTAAA
6138206 CAATAAATCC
Statistics
Matches: 910, Mismatches: 65, Indels: 55
0.88 0.06 0.05
Matches are distributed among these distances:
982 52 0.06
984 2 0.00
988 4 0.00
989 345 0.38
994 1 0.00
995 20 0.02
996 27 0.03
999 1 0.00
1002 1 0.00
1004 141 0.15
1005 95 0.10
1006 25 0.03
1007 15 0.02
1008 3 0.00
1010 130 0.14
1011 34 0.04
1012 13 0.01
1013 1 0.00
ACGTcount: A:0.52, C:0.26, G:0.01, T:0.21
Consensus pattern (984 bp):
AACCCTAAATCTCAAAACCCTAAAACTAAACTACCAAATCTAAAACCTTTAAACCTTAAAAACTT
AAACCCTAAAAATAAACTTTAAACCACAAACCTTAAAATCAAACACCAAAAACTAAACCCTAAAT
AATAAACTATAAACCCTAAACTTAAACAATAAACCCAAAATATAAACCATAAATCCTAAATCCTA
AAAACTAAACCTTAAACACCAAACCCTAACCACAAATAATAAACTATACACATAAACACTAAAAC
TAAAATTAAAAACCCTAAAACCTAAACATAAACCCTAATTATATCATAAACCATAAACATAAACA
CAAAACCTTAAACCCTAAAATAAAAACCTAAGATAAAACTAGAAACCCTAAAACCTATATATAAA
CCATAAACCTAAACGCGAACACTAAACACTAAACCCTAAAACCCTAAACCTAAACCATAAACACA
AACCCTAAACACTAAATCATAAACCCTAAACTAACTAAAACCTTAAACCATACACACAAACTATA
AACCATAAACCATAAACACTAAACCCTAAATAGAAAACCTAAACCATAATAAAAAACTAAAACAT
AAACATAAACCCTAACTATATCCAAAACCATAACCTCAAACACTAAACACTAAACCTTAAATTAT
AAACCATAAACCCTAAACCTTAAAACCATAAAAATAAACCTTCAACCCTACAATTAAACATAAAC
CCTAAAACTACCATGTCAAACCCTAAACCCTAAATATAAATAATAAACCTAGAATTATAAACCCT
AAATATAGAATCACAAAAACTAAAACTAAACATTAAACCCTATATTTAAATCATAAACCATAAAC
CCCAAACTCTAATTCTAAACCCAAAATATAAACAACAAATCCTAAATACTAAACATTAAACCCTA
AAACCAAAATCACAAACCATAAACATAAAAACTAAACCCTATACTTAAATTATAAACCCTAAACA
CCAACCATC
Found at i:6137281 original size:20 final size:20
Alignment explanation
Indices: 6137256--6137293 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6137246 CTTACAACCC
*
6137256 TAAACTCTAAACCCTAAAAT
1 TAAACTCTAAACCATAAAAT
*
6137276 TAAACTTTAAACCATAAA
1 TAAACTCTAAACCATAAA
6137294 CCTTAAAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (20 bp):
TAAACTCTAAACCATAAAAT
Found at i:6137286 original size:27 final size:26
Alignment explanation
Indices: 6137255--6137327 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 26
6137245 CCTTACAACC
* *
6137255 CTAAACTCTAAACCCTAAAATTAAACT
1 CTAAAC-CTAAACCCTAAAATCAAACA
* *
6137282 TTAAACCATAAACCTTAAAATCAAACA
1 CTAAACC-TAAACCCTAAAATCAAACA
*
6137309 CTAAAAACTAAACCCTAAA
1 CT-AAACCTAAACCCTAAA
6137328 TGATAAGCTA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
26 1 0.03
27 32 0.86
28 4 0.11
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.22
Consensus pattern (26 bp):
CTAAACCTAAACCCTAAAATCAAACA
Found at i:6137362 original size:20 final size:20
Alignment explanation
Indices: 6137337--6137410 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 20
6137327 ATGATAAGCT
6137337 ATAAACCCTAAACTTAAACA
1 ATAAACCCTAAACTTAAACA
* *
6137357 ATAAACCC-AAAATATAAACC
1 ATAAACCCTAAACT-TAAACA
* *
6137377 ATAAATCCTAAATCCTAAA-A
1 ATAAACCCTAAA-CTTAAACA
*
6137397 ACTAAACCTTAAAC
1 A-TAAACCCTAAAC
6137411 ACCAAACCTT
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
19 4 0.10
20 22 0.52
21 16 0.38
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.20
Consensus pattern (20 bp):
ATAAACCCTAAACTTAAACA
Found at i:6137493 original size:20 final size:20
Alignment explanation
Indices: 6137337--6137496 Score: 60
Period size: 20 Copynumber: 7.5 Consensus size: 20
6137327 ATGATAAGCT
*
6137337 ATAAACCCT-AAACTTAAAC
1 ATAAACCCTAAAACCTAAAC
**
6137356 AATAAACCC-AAAATATAAACC
1 -ATAAACCCTAAAACCTAAA-C
* * *
6137377 ATAAATCCTAAATCCTAAAA
1 ATAAACCCTAAAACCTAAAC
*
6137397 ACTAAACCTTAAACACC-AAAC
1 A-TAAACCCTAAA-ACCTAAAC
* * *
6137418 CTTAACCACAAATAATAAACTATACAC
1 ATAAACC-C---TAA-AACCTA-A-AC
*
6137445 ATAAACACTAAAA-CTAAA-
1 ATAAACCCTAAAACCTAAAC
6137463 ATTAAAAACCCTAAAACCTAAAC
1 A-T--AAACCCTAAAACCTAAAC
6137486 ATAAACCCTAA
1 ATAAACCCTAA
6137497 TTATATCATA
Statistics
Matches: 103, Mismatches: 19, Indels: 36
0.65 0.12 0.23
Matches are distributed among these distances:
18 1 0.01
19 2 0.02
20 38 0.37
21 33 0.32
22 10 0.10
23 4 0.04
24 5 0.05
25 2 0.02
26 2 0.02
27 6 0.06
ACGTcount: A:0.56, C:0.25, G:0.00, T:0.19
Consensus pattern (20 bp):
ATAAACCCTAAAACCTAAAC
Found at i:6137576 original size:7 final size:7
Alignment explanation
Indices: 6137566--6137781 Score: 120
Period size: 7 Copynumber: 31.3 Consensus size: 7
6137556 ATAAAACTAG
6137566 AAACCCT
1 AAACCCT
6137573 AAACCCT
1 AAACCCT
* **
6137580 ATA-TAT
1 AAACCCT
*
6137586 AAACCAT
1 AAACCCT
6137593 AAA-CCT
1 AAACCCT
*
6137599 AAACTC-
1 AAACCCT
* *
6137605 GAACACT
1 AAACCCT
*
6137612 AAACACT
1 AAACCCT
6137619 AAACCCT
1 AAACCCT
*
6137626 AAACAC-
1 AAACCCT
6137632 AAACCCT
1 AAACCCT
*
6137639 AAACCTT
1 AAACCCT
*
6137646 AAACCAT
1 AAACCCT
*
6137653 AAACAC-
1 AAACCCT
6137659 AAACCCT
1 AAACCCT
*
6137666 AAACACT
1 AAACCCT
* *
6137673 AAATCAT
1 AAACCCT
*
6137680 AAACCTT
1 AAACCCT
*
6137687 AAACGCT
1 AAACCCT
6137694 AAAACCCT
1 -AAACCCT
*
6137702 AAAACCTT
1 -AAACCCT
*
6137710 AAACCAT
1 AAACCCT
* *
6137717 ACACAC-
1 AAACCCT
**
6137723 AAACTTT
1 AAACCCT
6137730 AAACCCT
1 AAACCCT
*
6137737 AAACCAT
1 AAACCCT
*
6137744 AAACACT
1 AAACCCT
6137751 AAACCCT
1 AAACCCT
* *
6137758 AAATCAT
1 AAACCCT
6137765 AAAACCCT
1 -AAACCCT
6137773 AAACCCT
1 AAACCCT
6137780 AA
1 AA
6137782 TAAAAAACTA
Statistics
Matches: 156, Mismatches: 45, Indels: 16
0.72 0.21 0.07
Matches are distributed among these distances:
6 25 0.16
7 113 0.72
8 18 0.12
ACGTcount: A:0.50, C:0.31, G:0.01, T:0.17
Consensus pattern (7 bp):
AAACCCT
Found at i:6137680 original size:27 final size:27
Alignment explanation
Indices: 6137592--6137886 Score: 127
Period size: 27 Copynumber: 10.4 Consensus size: 27
6137582 ATATAAACCA
* * *
6137592 TAAACC-TAAACTCGAACACTAAACAC
1 TAAACCATAAACACAAACCCTAAACAC
*
6137618 TAAACCCTAAACACAAACCCTAAAC-C
1 TAAACCATAAACACAAACCCTAAACAC
6137644 TTAAACCATAAACACAAACCCTAAACAC
1 -TAAACCATAAACACAAACCCTAAACAC
*
6137672 TAAATCATAAACCTTAAACGCTAAAACCCTAAA-ACC
1 TAAACCATAAA-C----A--C--AAACCCTAAACA-C
* ** *
6137708 TTAAACCATACACACAAACTTTAAACCC
1 -TAAACCATAAACACAAACCCTAAACAC
6137736 TAAACCATAAACACTAAACCCTAAATCA-
1 TAAACCATAAACAC-AAACCCTAAA-CAC
* * * *
6137764 TAAAACCCTAAACCCTAA---TAAAAAAC
1 T-AAACCATAAACACAAACCCT-AAACAC
* *
6137790 TAAACCATAAACATAAACCCTAACTATATCC
1 TAAACCATAAACACAAACCCTAA--ACA--C
* * * *
6137821 AAAACCATAACCTCAAACACTAAACAC
1 TAAACCATAAACACAAACCCTAAACAC
* * * * *
6137848 TAAACCTTAAATTATAAACCTTAAACCC
1 TAAACCATAAA-CACAAACCCTAAACAC
*
6137876 TAAACCTTAAA
1 TAAACCATAAA
6137887 ACCATAAAAA
Statistics
Matches: 203, Mismatches: 38, Indels: 54
0.69 0.13 0.18
Matches are distributed among these distances:
25 14 0.07
26 11 0.05
27 73 0.36
28 44 0.22
29 16 0.08
30 1 0.00
31 19 0.09
32 2 0.01
34 1 0.00
35 1 0.00
36 12 0.06
37 9 0.04
ACGTcount: A:0.51, C:0.30, G:0.01, T:0.18
Consensus pattern (27 bp):
TAAACCATAAACACAAACCCTAAACAC
Found at i:6137792 original size:18 final size:22
Alignment explanation
Indices: 6137729--6137806 Score: 87
Period size: 21 Copynumber: 3.8 Consensus size: 22
6137719 ACACAAACTT
*
6137729 TAAACCCTAAACCAT-AAACAC
1 TAAACCCTAAATCATAAAACAC
*
6137750 TAAACCCTAAATCATAAAACCC
1 TAAACCCTAAATCATAAAACAC
6137772 TAAACCCT-AAT-A-AAAA-AC
1 TAAACCCTAAATCATAAAACAC
*
6137790 TAAACCATAAA-CATAAA
1 TAAACCCTAAATCATAAA
6137807 CCCTAACTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
18 8 0.16
19 7 0.14
20 4 0.08
21 17 0.35
22 13 0.27
ACGTcount: A:0.56, C:0.27, G:0.00, T:0.17
Consensus pattern (22 bp):
TAAACCCTAAATCATAAAACAC
Found at i:6137858 original size:14 final size:14
Alignment explanation
Indices: 6137841--6137886 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
6137831 CCTCAAACAC
6137841 TAAACACTAAACCT
1 TAAACACTAAACCT
*
6137855 TAAATTA-TAAACCT
1 TAAA-CACTAAACCT
*
6137869 TAAACCCTAAACCT
1 TAAACACTAAACCT
6137883 TAAA
1 TAAA
6137887 ACCATAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 26 0.96
15 1 0.04
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAACACTAAACCT
Found at i:6137995 original size:21 final size:21
Alignment explanation
Indices: 6137971--6138020 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
6137961 ATATAAGTAA
* **
6137971 TAAACCTAGAATTATAAACCC
1 TAAACCTAGAATCATAAAAAC
**
6137992 TAAATATAGAATCATAAAAAC
1 TAAACCTAGAATCATAAAAAC
6138013 TAAACCTA
1 TAAACCTA
6138021 AACATTAAAC
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.54, C:0.18, G:0.04, T:0.24
Consensus pattern (21 bp):
TAAACCTAGAATCATAAAAAC
Found at i:6138309 original size:20 final size:21
Alignment explanation
Indices: 6138286--6138336 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
6138276 ATTAAATTCT
6138286 AAACCCTAAACCTTAAAC-TA
1 AAACCCTAAACCTTAAACATA
*
6138306 AAACTAC-AAACCTTAAACATA
1 AAAC-CCTAAACCTTAAACATA
6138327 AAA-CCTAAAC
1 AAACCCTAAAC
6138337 ACTAAATCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 1 0.04
20 19 0.73
21 6 0.23
ACGTcount: A:0.55, C:0.27, G:0.00, T:0.18
Consensus pattern (21 bp):
AAACCCTAAACCTTAAACATA
Found at i:6138330 original size:14 final size:14
Alignment explanation
Indices: 6138284--6138342 Score: 54
Period size: 13 Copynumber: 4.4 Consensus size: 14
6138274 CAATTAAATT
*
6138284 CTAAACCCTAAAC-
1 CTAAAACCTAAACA
*
6138297 CTTAAA-CTAAA-A
1 CTAAAACCTAAACA
6138309 CTACAAACCTTAAACA
1 CTA-AAACC-TAAACA
6138325 -TAAAACCTAAACA
1 CTAAAACCTAAACA
6138338 CTAAA
1 CTAAA
6138343 TCTAAACTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
12 7 0.19
13 13 0.35
14 10 0.27
15 6 0.16
16 1 0.03
ACGTcount: A:0.54, C:0.27, G:0.00, T:0.19
Consensus pattern (14 bp):
CTAAAACCTAAACA
Found at i:6138371 original size:7 final size:7
Alignment explanation
Indices: 6138359--6138383 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6138349 CTTTTAACCC
6138359 TAAATTA
1 TAAATTA
6138366 TAAATTA
1 TAAATTA
6138373 TAAATTA
1 TAAATTA
6138380 TAAA
1 TAAA
6138384 CCTTAAACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
TAAATTA
Found at i:6138447 original size:27 final size:28
Alignment explanation
Indices: 6138373--6138450 Score: 74
Period size: 27 Copynumber: 2.9 Consensus size: 28
6138363 TTATAAATTA
* * *
6138373 TAAATTATAAACCTTAAACCTAAAACCC
1 TAAATCATAAACCTTAACCCTAAAACAC
*
6138401 TAAA-CATAAA-CTCAAACCCTAAAA-AC
1 TAAATCATAAACCT-TAACCCTAAAACAC
6138427 -AAATCATAAACCTTAATCCCTAAA
1 TAAATCATAAACCTTAA-CCCTAAA
6138451 TGTAAACCAT
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
25 3 0.07
26 11 0.27
27 23 0.56
28 4 0.10
ACGTcount: A:0.53, C:0.26, G:0.00, T:0.22
Consensus pattern (28 bp):
TAAATCATAAACCTTAACCCTAAAACAC
Found at i:6138644 original size:20 final size:20
Alignment explanation
Indices: 6138604--6138659 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
6138594 TAAAAACTAG
* *
6138604 ACCCTAAATGATAAACTATAA
1 ACCCTAAA-CATAAACAATAA
*
6138625 ACCCTAAACTTAAACAATAA
1 ACCCTAAACATAAACAATAA
*
6138645 ACTCTAAACATAAAC
1 ACCCTAAACATAAAC
6138660 CCTCATTATA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 22 0.73
21 8 0.27
ACGTcount: A:0.54, C:0.23, G:0.02, T:0.21
Consensus pattern (20 bp):
ACCCTAAACATAAACAATAA
Found at i:6138645 original size:13 final size:13
Alignment explanation
Indices: 6138614--6138697 Score: 55
Period size: 13 Copynumber: 6.1 Consensus size: 13
6138604 ACCCTAAATG
6138614 ATAAACTATAAACC
1 ATAAACTATAAA-C
*
6138628 CTAAACT-TAAAC
1 ATAAACTATAAAC
*
6138640 AATAAACTCTAAAC
1 -ATAAACTATAAAC
*
6138654 ATAAACCCTCATTATATC
1 ATAAA--CT-A-TA-AAC
*
6138672 ATAAACCATAAAC
1 ATAAACTATAAAC
6138685 ATAAAC-ATAAAC
1 ATAAACTATAAAC
6138697 A
1 A
6138698 CAAAACCTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 16
0.72 0.08 0.20
Matches are distributed among these distances:
12 8 0.14
13 23 0.40
14 13 0.23
15 3 0.05
16 1 0.02
17 2 0.04
18 7 0.12
ACGTcount: A:0.55, C:0.23, G:0.00, T:0.23
Consensus pattern (13 bp):
ATAAACTATAAAC
Found at i:6138822 original size:8 final size:7
Alignment explanation
Indices: 6138784--6138837 Score: 56
Period size: 7 Copynumber: 7.6 Consensus size: 7
6138774 AACTCAAATG
6138784 CTAAACC
1 CTAAACC
6138791 CTAAACC
1 CTAAACC
6138798 CT-AACC
1 CTAAACC
*
6138804 CTAAACT
1 CTAAACC
6138811 CTAAAACC
1 CT-AAACC
6138819 CTAAAACC
1 CT-AAACC
* *
6138827 ATAAATC
1 CTAAACC
6138834 CTAA
1 CTAA
6138838 TAAAAAACTA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
6 6 0.15
7 21 0.52
8 13 0.32
ACGTcount: A:0.46, C:0.35, G:0.00, T:0.19
Consensus pattern (7 bp):
CTAAACC
Found at i:6138864 original size:13 final size:14
Alignment explanation
Indices: 6138841--6138875 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
6138831 ATCCTAATAA
6138841 AAAAC-TAAACCAT
1 AAAACATAAACCAT
6138854 -AAACATAAACCAT
1 AAAACATAAACCAT
6138867 AAAACATAA
1 AAAACATAA
6138876 GCCTAAACCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.20
13 8 0.40
14 8 0.40
ACGTcount: A:0.66, C:0.20, G:0.00, T:0.14
Consensus pattern (14 bp):
AAAACATAAACCAT
Found at i:6139364 original size:7 final size:7
Alignment explanation
Indices: 6139352--6139386 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
6139342 AATTCTTAAT
6139352 CCTAAAC
1 CCTAAAC
6139359 CCTAAAC
1 CCTAAAC
6139366 CCTAAAC
1 CCTAAAC
6139373 CCTAAAC
1 CCTAAAC
6139380 CCTAAAC
1 CCTAAAC
6139387 TAAAACTACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.43, C:0.43, G:0.00, T:0.14
Consensus pattern (7 bp):
CCTAAAC
Found at i:6139413 original size:14 final size:14
Alignment explanation
Indices: 6139353--6139425 Score: 64
Period size: 14 Copynumber: 5.4 Consensus size: 14
6139343 ATTCTTAATC
* *
6139353 CTAAACCCTAAACC
1 CTAAAACCTAAACA
* *
6139367 CTAAACCCTAAACC
1 CTAAAACCTAAACA
6139381 CT-AAA-CTAAA-A
1 CTAAAACCTAAACA
6139392 CTACAAACCTTAAACA
1 CTA-AAACC-TAAACA
6139408 -TAAAACCTAAACA
1 CTAAAACCTAAACA
6139421 CTAAA
1 CTAAA
6139426 TCTAAACTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
11 2 0.04
12 5 0.10
13 11 0.22
14 26 0.51
15 6 0.12
16 1 0.02
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (14 bp):
CTAAAACCTAAACA
Found at i:6139431 original size:20 final size:19
Alignment explanation
Indices: 6139352--6139431 Score: 56
Period size: 21 Copynumber: 3.9 Consensus size: 19
6139342 AATTCTTAAT
* *
6139352 CCTAAACCCTAAACCCTAAAC
1 CCTAAACACTAAA--CTAAAA
*
6139373 CCTAAACCCTAAACTAAAA
1 CCTAAACACTAAACTAAAA
6139392 -CTACAA-ACCTTAAACATAAAA
1 CCTA-AACA-C-TAAAC-TAAAA
6139413 CCTAAACACTAAATCTAAA
1 CCTAAACACTAAA-CTAAA
6139432 CTTTAAACCC
Statistics
Matches: 50, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
18 3 0.06
19 8 0.16
20 13 0.26
21 22 0.44
22 4 0.08
ACGTcount: A:0.51, C:0.31, G:0.00, T:0.17
Consensus pattern (19 bp):
CCTAAACACTAAACTAAAA
Found at i:6139452 original size:7 final size:7
Alignment explanation
Indices: 6139442--6139473 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
6139432 CTTTAAACCC
6139442 TAAATTA
1 TAAATTA
6139449 TAAATTA
1 TAAATTA
6139456 TAAATTA
1 TAAATTA
*
6139463 TAAATCA
1 TAAATTA
6139470 TAAA
1 TAAA
6139474 CTTAAAACCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (7 bp):
TAAATTA
Found at i:6139459 original size:21 final size:22
Alignment explanation
Indices: 6139415--6139493 Score: 78
Period size: 21 Copynumber: 3.8 Consensus size: 22
6139405 ACATAAAACC
*
6139415 TAAACACTAAATC-TAAACTT-
1 TAAACCCTAAATCATAAACTTA
*
6139435 TAAACCCTAAATTATAAA-TTA
1 TAAACCCTAAATCATAAACTTA
***
6139456 TAAATTATAAATCATAAACTTA
1 TAAACCCTAAATCATAAACTTA
6139478 -AAACCCTAAA-CATAAA
1 TAAACCCTAAATCATAAA
6139494 GTTAAACCTT
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
20 19 0.40
21 25 0.53
22 3 0.06
ACGTcount: A:0.54, C:0.16, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAACCCTAAATCATAAACTTA
Found at i:6139491 original size:20 final size:20
Alignment explanation
Indices: 6139376--6139508 Score: 71
Period size: 20 Copynumber: 6.6 Consensus size: 20
6139366 CCTAAACCCT
6139376 AAACCCTAAAC-TAAAAC-TA
1 AAACCCTAAACAT-AAACTTA
* *
6139395 CAAACCTTAAACATAAAACCT-
1 -AAACCCTAAACAT-AAACTTA
* *
6139416 AAACACTAAATC-TAAACTTT
1 AAACCCTAAA-CATAAACTTA
*
6139436 AAACCCTAAATTATAAA-TTA
1 AAACCCTAAA-CATAAACTTA
***
6139456 TAAATTATAAATCATAAACTTA
1 -AAACCCTAAA-CATAAACTTA
*
6139478 AAACCCTAAACATAAAGTT-
1 AAACCCTAAACATAAACTTA
*
6139497 AAACCTTAAACA
1 AAACCCTAAACA
6139509 AAAATCAGAA
Statistics
Matches: 90, Mismatches: 16, Indels: 15
0.74 0.13 0.12
Matches are distributed among these distances:
19 16 0.18
20 39 0.43
21 31 0.34
22 4 0.04
ACGTcount: A:0.54, C:0.20, G:0.01, T:0.25
Consensus pattern (20 bp):
AAACCCTAAACATAAACTTA
Found at i:6139588 original size:40 final size:40
Alignment explanation
Indices: 6139539--6139647 Score: 146
Period size: 40 Copynumber: 2.7 Consensus size: 40
6139529 TTAAATATAA
* * *
6139539 ATCACAAACCCTAAATATAAACTTTAAATATTATAATTAT
1 ATCACAAACCCTAAATATAAACCTTAAACACTATAATTAT
*
6139579 ATCATAAACCCTAAATATAAACCTTAAACACTATAATTAT
1 ATCACAAACCCTAAATATAAACCTTAAACACTATAATTAT
* * * *
6139619 ATTAGAAACCATAAATATAAACCCTAAAC
1 ATCACAAACCCTAAATATAAACCTTAAAC
6139648 CTTAATAAGA
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 61 1.00
ACGTcount: A:0.51, C:0.18, G:0.01, T:0.29
Consensus pattern (40 bp):
ATCACAAACCCTAAATATAAACCTTAAACACTATAATTAT
Found at i:6139713 original size:18 final size:20
Alignment explanation
Indices: 6139667--6139717 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
6139657 AAACTATATC
*
6139667 ATAAACATAAACCCTAAAAT
1 ATAAGCATAAACCCTAAAAT
*
6139687 ATAAGCATAAACCC-AAATT
1 ATAAGCATAAACCCTAAAAT
*
6139706 AT-ATCATAAACC
1 ATAAGCATAAACC
6139718 ATAACCTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 9 0.32
19 6 0.21
20 13 0.46
ACGTcount: A:0.55, C:0.22, G:0.02, T:0.22
Consensus pattern (20 bp):
ATAAGCATAAACCCTAAAAT
Found at i:6140080 original size:14 final size:14
Alignment explanation
Indices: 6140061--6140094 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
6140051 AACCATCAAC
6140061 CCTAAACAATAAAT
1 CCTAAACAATAAAT
*
6140075 CCTAAACTATAAAT
1 CCTAAACAATAAAT
*
6140089 ACTAAA
1 CCTAAA
6140095 ACTTAAACCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.56, C:0.21, G:0.00, T:0.24
Consensus pattern (14 bp):
CCTAAACAATAAAT
Found at i:6140170 original size:20 final size:20
Alignment explanation
Indices: 6140147--6140223 Score: 54
Period size: 20 Copynumber: 3.9 Consensus size: 20
6140137 ATTAAATTCT
6140147 AAACCCTAAACCTTAAACTA
1 AAACCCTAAACCTTAAACTA
* *
6140167 AAACTAC-AAACTTTAAACATA
1 AAAC-CCTAAACCTTAAAC-TA
6140188 AAA-CCTAAACAC-TAAATCT-
1 AAACCCTAAAC-CTTAAA-CTA
**
6140207 AAACTTTAAACCTTAAA
1 AAACCCTAAACCTTAAA
6140224 TTAGAATTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
19 5 0.11
20 32 0.73
21 7 0.16
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.23
Consensus pattern (20 bp):
AAACCCTAAACCTTAAACTA
Found at i:6140636 original size:20 final size:20
Alignment explanation
Indices: 6140611--6140778 Score: 68
Period size: 20 Copynumber: 8.5 Consensus size: 20
6140601 CTAGAGTTAA
6140611 AAACCCTAAAACCTAAACAT
1 AAACCCTAAAACCTAAACAT
* *
6140631 AAACCCT---ACTTATATCAT
1 AAACCCTAAAACCTA-AACAT
* * *
6140649 AAACCAT-AAACATAAACACA
1 AAACCCTAAAACCTAAACA-T
** *
6140669 AAACTTTAAACCCTAAA-AT
1 AAACCCTAAAACCTAAACAT
* *
6140688 AAAACCCTAAGAA--AAAACTAA
1 -AAACCCTAA-AACCTAAAC-AT
* *
6140709 AAACCCTAAAACCTATATAT
1 AAACCCTAAAACCTAAACAT
*
6140729 AAACCAT-AAACCTAAAC-T
1 AAACCCTAAAACCTAAACAT
*
6140747 CAAACACT-AAACACTAAACACT
1 -AAACCCTAAAAC-CTAAACA-T
6140769 AAACCCTAAA
1 AAACCCTAAA
6140779 TATAAATTAC
Statistics
Matches: 106, Mismatches: 26, Indels: 30
0.65 0.16 0.19
Matches are distributed among these distances:
17 4 0.04
18 11 0.10
19 25 0.24
20 46 0.43
21 17 0.16
22 3 0.03
ACGTcount: A:0.55, C:0.26, G:0.01, T:0.18
Consensus pattern (20 bp):
AAACCCTAAAACCTAAACAT
Found at i:6140758 original size:7 final size:7
Alignment explanation
Indices: 6140735--6140778 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
6140725 ATATAAACCA
6140735 TAAAC-C
1 TAAACAC
*
6140741 TAAACTC
1 TAAACAC
6140748 -AAACAC
1 TAAACAC
6140754 TAAACAC
1 TAAACAC
6140761 TAAACAC
1 TAAACAC
*
6140768 TAAACCC
1 TAAACAC
6140775 TAAA
1 TAAA
6140779 TATAAATTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
6 10 0.29
7 24 0.71
ACGTcount: A:0.55, C:0.30, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAACAC
Found at i:6140784 original size:20 final size:20
Alignment explanation
Indices: 6140761--6140897 Score: 81
Period size: 20 Copynumber: 6.8 Consensus size: 20
6140751 CACTAAACAC
6140761 TAAACACTAAACCCTAAATA
1 TAAACACTAAACCCTAAATA
*
6140781 TAAATTAC-AAACCCTAAATA
1 TAAA-CACTAAACCCTAAATA
* *
6140801 AAAAC-CTTAAACACTATAAT-
1 TAAACAC-TAAACCCTA-AATA
* *
6140821 TATATCA-TAAACCATAAATA
1 TA-AACACTAAACCCTAAATA
*
6140841 TAAAC-CTTAAACACTATAAT-
1 TAAACAC-TAAACCCTA-AATA
* *
6140861 TGTATCA-TAAACCCTAAATA
1 T-AAACACTAAACCCTAAATA
*
6140881 TAAACCCTAAACCCTAA
1 TAAACACTAAACCCTAA
6140898 TGAAAAACTA
Statistics
Matches: 86, Mismatches: 17, Indels: 28
0.66 0.13 0.21
Matches are distributed among these distances:
18 1 0.01
19 10 0.12
20 63 0.73
21 12 0.14
ACGTcount: A:0.52, C:0.22, G:0.01, T:0.26
Consensus pattern (20 bp):
TAAACACTAAACCCTAAATA
Found at i:6140812 original size:40 final size:40
Alignment explanation
Indices: 6140789--6140892 Score: 172
Period size: 40 Copynumber: 2.6 Consensus size: 40
6140779 TATAAATTAC
*
6140789 AAACCCTAAATAAAAACCTTAAACACTATAATTATATCAT
1 AAACCCTAAATATAAACCTTAAACACTATAATTATATCAT
* *
6140829 AAACCATAAATATAAACCTTAAACACTATAATTGTATCAT
1 AAACCCTAAATATAAACCTTAAACACTATAATTATATCAT
*
6140869 AAACCCTAAATATAAACCCTAAAC
1 AAACCCTAAATATAAACCTTAAAC
6140893 CCTAATGAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.52, C:0.21, G:0.01, T:0.26
Consensus pattern (40 bp):
AAACCCTAAATATAAACCTTAAACACTATAATTATATCAT
Found at i:6140885 original size:13 final size:13
Alignment explanation
Indices: 6140867--6140891 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6140857 TAATTGTATC
6140867 ATAAACCCTAAAT
1 ATAAACCCTAAAT
6140880 ATAAACCCTAAA
1 ATAAACCCTAAA
6140892 CCCTAATGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.24, G:0.00, T:0.20
Consensus pattern (13 bp):
ATAAACCCTAAAT
Found at i:6140994 original size:14 final size:14
Alignment explanation
Indices: 6140977--6141022 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
6140967 CCTCAAACAC
6140977 TAAACTCTAAACCT
1 TAAACTCTAAACCT
* *
6140991 TAAATTATAAACCT
1 TAAACTCTAAACCT
*
6141005 TAAACCCTAAACCT
1 TAAACTCTAAACCT
6141019 TAAA
1 TAAA
6141023 ACCATAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (14 bp):
TAAACTCTAAACCT
Found at i:6141015 original size:35 final size:33
Alignment explanation
Indices: 6140939--6141048 Score: 93
Period size: 35 Copynumber: 3.3 Consensus size: 33
6140929 AACATAAGTA
*
6140939 TAAACCCTAAA-TCT-ATCCTAAACTAT-AACCT
1 TAAACCCTAAACTCTAAACCTAAA-TATAAACCT
* *
6140970 CAAACACTAAACTCTAAACCTTAAATTATAAACCT
1 TAAACCCTAAACTCTAAACC-TAAA-TATAAACCT
* *
6141005 TAAACCCTAAAC-CTTAAAACCATAAAAATAAAACT
1 TAAACCCTAAACTC-T-AAACC-TAAATATAAACCT
6141040 TAAACCCTA
1 TAAACCCTA
6141049 CAATTAAACA
Statistics
Matches: 64, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
31 9 0.14
32 3 0.05
33 3 0.05
34 8 0.12
35 32 0.50
36 9 0.14
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.25
Consensus pattern (33 bp):
TAAACCCTAAACTCTAAACCTAAATATAAACCT
Found at i:6141207 original size:40 final size:40
Alignment explanation
Indices: 6141111--6141208 Score: 103
Period size: 40 Copynumber: 2.4 Consensus size: 40
6141101 AAACCCTCAT
* *
6141111 TATATCATAAACCATAAATATAAACACAAAACCTTAAACCC
1 TATAT-ATAAACCCTAAATATAAACACAAAACCTTAAAACC
* *
6141152 TA-AAATAAAAACCTAAGATA-AAACTA-AAAACCTTAAAACC
1 TATATAT-AAACCCTAA-ATATAAAC-ACAAAACCTTAAAACC
6141192 TATATATAAACCCTAAA
1 TATATATAAACCCTAAA
6141209 CTTAAACTCG
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
39 3 0.06
40 35 0.74
41 9 0.19
ACGTcount: A:0.57, C:0.20, G:0.01, T:0.21
Consensus pattern (40 bp):
TATATATAAACCCTAAATATAAACACAAAACCTTAAAACC
Found at i:6141235 original size:7 final size:7
Alignment explanation
Indices: 6141223--6141274 Score: 88
Period size: 7 Copynumber: 7.6 Consensus size: 7
6141213 AACTCGAACA
6141223 CTAAACC
1 CTAAACC
6141230 CTAAACC
1 CTAAACC
*
6141237 CTAAACA
1 CTAAACC
6141244 C-AAACC
1 CTAAACC
6141250 CTAAACC
1 CTAAACC
6141257 CTAAACC
1 CTAAACC
6141264 CTAAACC
1 CTAAACC
6141271 CTAA
1 CTAA
6141275 TAGAAAACTA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
6 5 0.12
7 37 0.88
ACGTcount: A:0.46, C:0.40, G:0.00, T:0.13
Consensus pattern (7 bp):
CTAAACC
Found at i:6141253 original size:27 final size:27
Alignment explanation
Indices: 6141198--6141269 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 27
6141188 AACCTATATA
* * *
6141198 TAAACCCTAAA-CTTAAACTCGAACAC
1 TAAACCCTAAACCCTAAACACAAACAC
*
6141224 TAAACCCTAAACCCTAAACACAAACCC
1 TAAACCCTAAACCCTAAACACAAACAC
6141251 TAAACCCTAAACCCTAAAC
1 TAAACCCTAAACCCTAAAC
6141270 CCTAATAGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
26 11 0.27
27 30 0.73
ACGTcount: A:0.47, C:0.36, G:0.01, T:0.15
Consensus pattern (27 bp):
TAAACCCTAAACCCTAAACACAAACAC
Found at i:6141310 original size:14 final size:14
Alignment explanation
Indices: 6141197--6141312 Score: 51
Period size: 13 Copynumber: 8.3 Consensus size: 14
6141187 AAACCTATAT
6141197 ATAAACCCT-AAAC
1 ATAAACCCTAAAAC
* * * *
6141210 TTAAACTCGAACAC
1 ATAAACCCTAAAAC
*
6141224 -TAAACCCTAAACC
1 ATAAACCCTAAAAC
* * *
6141237 CTAAACAC-AAACC
1 ATAAACCCTAAAAC
* *
6141250 CTAAACCCTAAACC
1 ATAAACCCTAAAAC
* *
6141264 CTAAACCCTAATAGAAA
1 ATAAACCCT-A-A-AAC
*
6141281 ACTAAACCAT-AAAC
1 A-TAAACCCTAAAAC
6141295 ATAAACCCTAAAAC
1 ATAAACCCTAAAAC
6141309 ATAA
1 ATAA
6141313 GCATAAACCC
Statistics
Matches: 79, Mismatches: 16, Indels: 15
0.72 0.15 0.14
Matches are distributed among these distances:
13 34 0.43
14 34 0.43
15 2 0.03
16 1 0.01
17 1 0.01
18 7 0.09
ACGTcount: A:0.52, C:0.31, G:0.02, T:0.16
Consensus pattern (14 bp):
ATAAACCCTAAAAC
Found at i:6141311 original size:20 final size:20
Alignment explanation
Indices: 6141282--6141323 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
6141272 TAATAGAAAA
*
6141282 CTAAACCATAAACATAAACC
1 CTAAAACATAAACATAAACC
*
6141302 CTAAAACATAAGCATAAACC
1 CTAAAACATAAACATAAACC
6141322 CT
1 CT
6141324 TACTATATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.52, C:0.29, G:0.02, T:0.17
Consensus pattern (20 bp):
CTAAAACATAAACATAAACC
Found at i:6141468 original size:41 final size:42
Alignment explanation
Indices: 6141375--6141474 Score: 98
Period size: 41 Copynumber: 2.4 Consensus size: 42
6141365 CTTTAAATTA
* * *
6141375 TAAACCCTAAACCATAAACCTTAAAAAAATAAACCTTCAACCC
1 TAAACCTTAAA-CATAAACCCTAAAAAAATAAACCTTAAACCC
** *
6141418 TACAA--TTAAACATAAACCCTAAAACTATAATCC-TAAACCC
1 TA-AACCTTAAACATAAACCCTAAAAAAATAAACCTTAAACCC
*
6141458 TAAACCTTAAATATAAA
1 TAAACCTTAAACATAAA
6141475 AAATAAATCT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
39 2 0.04
40 8 0.17
41 29 0.62
42 4 0.09
43 2 0.04
44 2 0.04
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (42 bp):
TAAACCTTAAACATAAACCCTAAAAAAATAAACCTTAAACCC
Found at i:6141591 original size:20 final size:21
Alignment explanation
Indices: 6141568--6141610 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
6141558 CCTAAACTCC
*
6141568 AACCATCAACCCTAAA-TATA
1 AACCATAAACCCTAAATTATA
*
6141588 AACCATAAATCCTAAATTATA
1 AACCATAAACCCTAAATTATA
6141609 AA
1 AA
6141611 TACTAAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.23
Consensus pattern (21 bp):
AACCATAAACCCTAAATTATA
Found at i:6141678 original size:7 final size:7
Alignment explanation
Indices: 6141668--6141694 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
6141658 TAATTAAATT
6141668 CTAAACC
1 CTAAACC
6141675 CTAAACC
1 CTAAACC
6141682 CTAAACC
1 CTAAACC
6141689 CTAAAC
1 CTAAAC
6141695 TAAAACTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.41, G:0.00, T:0.15
Consensus pattern (7 bp):
CTAAACC
Found at i:6141814 original size:14 final size:14
Alignment explanation
Indices: 6141771--6141814 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
6141761 TATAAATTAT
*
6141771 AAACCTTAAACCTT
1 AAACCTTAAACCTA
6141785 AAACCTTAAACCTA
1 AAACCTTAAACCTA
* *
6141799 AAACCCTAAACATA
1 AAACCTTAAACCTA
6141813 AA
1 AA
6141815 TGCAAACCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.52, C:0.27, G:0.00, T:0.20
Consensus pattern (14 bp):
AAACCTTAAACCTA
Found at i:6141828 original size:7 final size:7
Alignment explanation
Indices: 6141770--6141809 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
6141760 TTATAAATTA
6141770 TAAACCT
1 TAAACCT
6141777 TAAACCT
1 TAAACCT
6141784 TAAACCT
1 TAAACCT
6141791 TAAACCT
1 TAAACCT
* *
6141798 AAAACCC
1 TAAACCT
6141805 TAAAC
1 TAAAC
6141810 ATAAATGCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (7 bp):
TAAACCT
Found at i:6141970 original size:7 final size:7
Alignment explanation
Indices: 6141923--6141986 Score: 58
Period size: 7 Copynumber: 9.0 Consensus size: 7
6141913 ACTACCAAAT
6141923 CTTAAAC
1 CTTAAAC
*
6141930 CTTTTAAC
1 C-TTAAAC
6141938 CTTAAAAC
1 CTT-AAAC
6141946 CTTAAAC
1 CTTAAAC
*
6141953 CCTAAA-
1 CTTAAAC
*
6141959 ATTAAAC
1 CTTAAAC
*
6141966 TTTAAAC
1 CTTAAAC
*
6141973 CATAAAC
1 CTTAAAC
6141980 CTTAAAC
1 CTTAAAC
6141987 TCAAACACCA
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
6 4 0.09
7 29 0.64
8 12 0.27
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.30
Consensus pattern (7 bp):
CTTAAAC
Found at i:6141972 original size:27 final size:27
Alignment explanation
Indices: 6141933--6141985 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
6141923 CTTAAACCTT
* *
6141933 TTAACCTTAAAACCTTAAACCCTAAAA
1 TTAAACTTAAAACCATAAACCCTAAAA
* *
6141960 TTAAACTTTAAACCATAAACCTTAAA
1 TTAAACTTAAAACCATAAACCCTAAA
6141986 CTCAAACACC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (27 bp):
TTAAACTTAAAACCATAAACCCTAAAA
Found at i:6142057 original size:48 final size:48
Alignment explanation
Indices: 6141968--6142060 Score: 123
Period size: 48 Copynumber: 1.9 Consensus size: 48
6141958 AATTAAACTT
* *
6141968 TAAACCATAAACCTTAAACTCAAACACCAAAAACTAGACCCTAAATGA
1 TAAACCATAAACCTTAAACTCAAACAACAAAAACTAAACCCTAAATGA
* * * * *
6142016 TAAACTATAAACCTTAAACTTAAACAATAAATATTAAACCCTAAA
1 TAAACCATAAACCTTAAACTCAAACAACAAAAACTAAACCCTAAA
6142061 ACCTAAACCT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.54, C:0.23, G:0.02, T:0.22
Consensus pattern (48 bp):
TAAACCATAAACCTTAAACTCAAACAACAAAAACTAAACCCTAAATGA
Found at i:6142068 original size:48 final size:48
Alignment explanation
Indices: 6141968--6142076 Score: 112
Period size: 48 Copynumber: 2.3 Consensus size: 48
6141958 AATTAAACTT
* * * **
6141968 TAAACCATAAACCTTAAACTCAAACACCAAAAACTAGACCCTAAATGA
1 TAAACTATAAACCTTAAACTCAAACAACAAAAACTAAACCCTAAAACA
* * * * *
6142016 TAAACTATAAACCTTAAACTTAAACAATAAATATTAAACCCTAAAACC
1 TAAACTATAAACCTTAAACTCAAACAACAAAAACTAAACCCTAAAACA
6142064 TAAACCT-TAAACC
1 TAAA-CTATAAACC
6142077 CTAATCACAA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
48 48 0.96
49 2 0.04
ACGTcount: A:0.52, C:0.25, G:0.02, T:0.21
Consensus pattern (48 bp):
TAAACTATAAACCTTAAACTCAAACAACAAAAACTAAACCCTAAAACA
Found at i:6142477 original size:13 final size:13
Alignment explanation
Indices: 6142436--6142483 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
6142426 AAACCATAAA
* *
6142436 CCTAAACTCGAAC
1 CCTAAACACAAAC
* *
6142449 ACTAAACATTAAAC
1 CCTAAACA-CAAAC
6142463 CCTAAACACAAAC
1 CCTAAACACAAAC
6142476 CCTAAACA
1 CCTAAACA
6142484 TTCTAATTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
13 18 0.64
14 10 0.36
ACGTcount: A:0.50, C:0.33, G:0.02, T:0.15
Consensus pattern (13 bp):
CCTAAACACAAAC
Found at i:6142480 original size:27 final size:26
Alignment explanation
Indices: 6142432--6142485 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
6142422 ATATAAACCA
* *
6142432 TAAACCTAAACTCGAACACTAAACAT
1 TAAACCTAAACACAAACACTAAACAT
*
6142458 TAAACCCTAAACACAAACCCTAAACAT
1 TAAA-CCTAAACACAAACACTAAACAT
6142485 T
1 T
6142486 CTAATTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.50, C:0.30, G:0.02, T:0.19
Consensus pattern (26 bp):
TAAACCTAAACACAAACACTAAACAT
Found at i:6142748 original size:13 final size:14
Alignment explanation
Indices: 6142664--6142742 Score: 53
Period size: 14 Copynumber: 5.9 Consensus size: 14
6142654 CCCCAACAAT
* *
6142664 TAAATTCTAAACCC
1 TAAATCCTAAACAC
6142678 TAAATCCTAAAC-C
1 TAAATCCTAAACAC
6142691 ATAAA--CTAAA-AC
1 -TAAATCCTAAACAC
* *
6142703 TACAAACCTTAAGCA-
1 TA-AATCC-TAAACAC
6142718 TAAATCCTAAACAC
1 TAAATCCTAAACAC
6142732 TAAAT-CTAAAC
1 TAAATCCTAAAC
6142743 TTTAAACCCC
Statistics
Matches: 53, Mismatches: 4, Indels: 17
0.72 0.05 0.23
Matches are distributed among these distances:
11 2 0.04
12 8 0.15
13 12 0.23
14 25 0.47
15 5 0.09
16 1 0.02
ACGTcount: A:0.51, C:0.25, G:0.01, T:0.23
Consensus pattern (14 bp):
TAAATCCTAAACAC
Found at i:6143016 original size:48 final size:48
Alignment explanation
Indices: 6142964--6143078 Score: 133
Period size: 48 Copynumber: 2.4 Consensus size: 48
6142954 AATTAAACTT
* * * *
6142964 TAAACCATAAACCTTAAACTCAAACACTAAAAACTAGACCTTAAATGA-
1 TAAACCATAAACCTTAAACTCAAACAATAAAAACTAAACCCTAAA-AAC
* * * *
6143012 TAAACTATAAACCCTAAACTTAAACAATAAATACTAAACCCTAAAAAC
1 TAAACCATAAACCTTAAACTCAAACAATAAAAACTAAACCCTAAAAAC
*
6143060 TAAACCTTAAACCTTAAAC
1 TAAACCATAAACCTTAAAC
6143079 CCTAATCATA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
47 1 0.02
48 54 0.98
ACGTcount: A:0.53, C:0.23, G:0.02, T:0.22
Consensus pattern (48 bp):
TAAACCATAAACCTTAAACTCAAACAATAAAAACTAAACCCTAAAAAC
Found at i:6143041 original size:20 final size:21
Alignment explanation
Indices: 6143012--6143078 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
6143002 CCTTAAATGA
*
6143012 TAAACTATAAACCCTAAA-CT
1 TAAACAATAAACCCTAAACCT
** *
6143032 TAAACAATAAATACTAAACCC
1 TAAACAATAAACCCTAAACCT
*
6143053 TAAA-AACTAAACCTTAAACCT
1 TAAACAA-TAAACCCTAAACCT
6143074 TAAAC
1 TAAAC
6143079 CCTAATCATA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
20 17 0.47
21 19 0.53
ACGTcount: A:0.54, C:0.24, G:0.00, T:0.22
Consensus pattern (21 bp):
TAAACAATAAACCCTAAACCT
Found at i:6143458 original size:7 final size:7
Alignment explanation
Indices: 6143448--6143487 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
6143438 CCTAAACTCG
6143448 AACACTA
1 AACACTA
6143455 AACACTA
1 AACACTA
*
6143462 AACCCTA
1 AACACTA
*
6143469 AACACAA
1 AACACTA
6143476 AAC-CTA
1 AACACTA
6143482 AACACT
1 AACACT
6143488 CTAAATATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.55, C:0.33, G:0.00, T:0.12
Consensus pattern (7 bp):
AACACTA
Found at i:6143483 original size:13 final size:14
Alignment explanation
Indices: 6143452--6143487 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
6143442 AACTCGAACA
*
6143452 CTAAACACTAAACC
1 CTAAACACTAAAAC
6143466 CTAAACAC-AAAAC
1 CTAAACACTAAAAC
6143479 CTAAACACT
1 CTAAACACT
6143488 CTAAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.53, C:0.33, G:0.00, T:0.14
Consensus pattern (14 bp):
CTAAACACTAAAAC
Found at i:6143688 original size:14 final size:14
Alignment explanation
Indices: 6143671--6143736 Score: 50
Period size: 14 Copynumber: 4.9 Consensus size: 14
6143661 CAATTAAATT
6143671 CTAAACACTAAACC
1 CTAAACACTAAACC
*
6143685 CTAAACCCTAAA--
1 CTAAACACTAAACC
6143697 CTAAA-ACTACAAACC
1 CTAAACACT--AAACC
* * *
6143712 TTAAGCA-TAAAAC
1 CTAAACACTAAACC
6143725 CTAAACACTAAA
1 CTAAACACTAAA
6143737 TCTAAACTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 12
0.67 0.12 0.21
Matches are distributed among these distances:
11 2 0.05
12 5 0.13
13 12 0.31
14 15 0.38
15 4 0.10
16 1 0.03
ACGTcount: A:0.53, C:0.29, G:0.02, T:0.17
Consensus pattern (14 bp):
CTAAACACTAAACC
Found at i:6144028 original size:83 final size:83
Alignment explanation
Indices: 6143925--6144107 Score: 341
Period size: 83 Copynumber: 2.2 Consensus size: 83
6143915 TAAACTTTTT
6143925 AACTCTAAAACCATAAACCCTAAAATTAAACTTTAAACCATAAACCTTAAACTCAAACAATAAAA
1 AACTCTAAAACCATAAACCCTAAAATTAAACTTTAAACCATAAACCTTAAACTCAAACAATAAAA
6143990 ACTAGACCCTAAATGATA
66 ACTAGACCCTAAATGATA
6144008 AACTCTAAAACCATAAACCCTAAAATTAAACTTTAAACCATAAACCTTAAACTCAAACAATAAAA
1 AACTCTAAAACCATAAACCCTAAAATTAAACTTTAAACCATAAACCTTAAACTCAAACAATAAAA
6144073 ACTAGACCCTAAATGATA
66 ACTAGACCCTAAATGATA
* *
6144091 AACTAT-AAACCCTAAAC
1 AACTCTAAAACCATAAAC
6144108 TTAAATAATA
Statistics
Matches: 98, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
82 10 0.10
83 88 0.90
ACGTcount: A:0.53, C:0.23, G:0.02, T:0.21
Consensus pattern (83 bp):
AACTCTAAAACCATAAACCCTAAAATTAAACTTTAAACCATAAACCTTAAACTCAAACAATAAAA
ACTAGACCCTAAATGATA
Found at i:6144065 original size:27 final size:27
Alignment explanation
Indices: 6143932--6144058 Score: 123
Period size: 27 Copynumber: 4.6 Consensus size: 27
6143922 TTTAACTCTA
6143932 AAACCATAAACCCTAAAATTAAACTTT
1 AAACCATAAACCCTAAAATTAAACTTT
* * * **
6143959 AAACCATAAACCTTAAACTCAAACAAT
1 AAACCATAAACCCTAAAATTAAACTTT
* * *
6143986 AAA-AACTAGACCCT-AAATGATAAACTCTA
1 AAACCA-TAAACCCTAAAAT--TAAACT-TT
6144015 AAACCATAAACCCTAAAATTAAACTTT
1 AAACCATAAACCCTAAAATTAAACTTT
*
6144042 AAACCATAAACCTTAAA
1 AAACCATAAACCCTAAA
6144059 CTCAAACAAT
Statistics
Matches: 77, Mismatches: 17, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
26 4 0.05
27 48 0.62
28 10 0.13
29 10 0.13
30 5 0.06
ACGTcount: A:0.54, C:0.23, G:0.02, T:0.22
Consensus pattern (27 bp):
AAACCATAAACCCTAAAATTAAACTTT
Found at i:6144071 original size:27 final size:27
Alignment explanation
Indices: 6143932--6144107 Score: 117
Period size: 27 Copynumber: 6.4 Consensus size: 27
6143922 TTTAACTCTA
*
6143932 AAACCATAAACCCTAAAATTAAACTTT
1 AAACCATAAACCCTAAAATTAAACTAT
* * * *
6143959 AAACCATAAACCTTAAACTCAAACAAT
1 AAACCATAAACCCTAAAATTAAACTAT
* * *
6143986 AAA-AACTAGACCCT-AAATGATAAACTCT
1 AAACCA-TAAACCCTAAAAT--TAAACTAT
*
6144014 AAAACCATAAACCCTAAAATTAAACTTT
1 -AAACCATAAACCCTAAAATTAAACTAT
* * * *
6144042 AAACCATAAACCTTAAACTCAAACAAT
1 AAACCATAAACCCTAAAATTAAACTAT
* *
6144069 AAA-AACTAGACCCT-AAATGATAAACTAT
1 AAACCA-TAAACCCTAAAAT--TAAACTAT
*
6144097 AAACCCTAAAC
1 AAACCATAAAC
6144108 TTAAATAATA
Statistics
Matches: 110, Mismatches: 29, Indels: 19
0.70 0.18 0.12
Matches are distributed among these distances:
26 8 0.07
27 62 0.56
28 25 0.23
29 10 0.09
30 5 0.05
ACGTcount: A:0.53, C:0.23, G:0.02, T:0.21
Consensus pattern (27 bp):
AAACCATAAACCCTAAAATTAAACTAT
Found at i:6144099 original size:48 final size:48
Alignment explanation
Indices: 6144041--6144155 Score: 135
Period size: 48 Copynumber: 2.4 Consensus size: 48
6144031 AATTAAACTT
* * *
6144041 TAAACCATAAACCTTAAACTCAAACAATAAAAACTAGACCCTAAATGA-
1 TAAACTATAAACCTTAAACTCAAACAATAAAAACTAAACCCTAAA-AAC
* * * *
6144089 TAAACTATAAACCCTAAACTTAAATAATAAATACTAAACCCTAAAAAC
1 TAAACTATAAACCTTAAACTCAAACAATAAAAACTAAACCCTAAAAAC
6144137 TAAACCT-TAAACCTTAAAC
1 TAAA-CTATAAACCTTAAAC
6144156 CCTAATCACA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
47 1 0.02
48 54 0.95
49 2 0.04
ACGTcount: A:0.54, C:0.23, G:0.02, T:0.22
Consensus pattern (48 bp):
TAAACTATAAACCTTAAACTCAAACAATAAAAACTAAACCCTAAAAAC
Found at i:6144118 original size:27 final size:27
Alignment explanation
Indices: 6144082--6144133 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
6144072 AACTAGACCC
*
6144082 TAAATGATAAACTA-TAAACCCTAAACT
1 TAAATAATAAA-TACTAAACCCTAAACT
6144109 TAAATAATAAATACTAAACCCTAAA
1 TAAATAATAAATACTAAACCCTAAA
6144134 AACTAAACCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.56, C:0.17, G:0.02, T:0.25
Consensus pattern (27 bp):
TAAATAATAAATACTAAACCCTAAACT
Found at i:6144412 original size:21 final size:21
Alignment explanation
Indices: 6144355--6144414 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
6144345 CACAAATAAT
*
6144355 AAACTATACACATAAA-CCCTA
1 AAACTAGA-ACATAAACCCCTA
*
6144376 AAACTAGAA-TTAAAACCCCTA
1 AAACTAGAACAT-AAACCCCTA
6144397 AAACCTA-AACATAAACCC
1 AAA-CTAGAACATAAACCC
6144415 TCATTATATC
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
19 1 0.03
20 4 0.12
21 23 0.72
22 4 0.12
ACGTcount: A:0.53, C:0.28, G:0.02, T:0.17
Consensus pattern (21 bp):
AAACTAGAACATAAACCCCTA
Found at i:6144537 original size:7 final size:7
Alignment explanation
Indices: 6144527--6144566 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
6144517 CCTAAACTCG
6144527 AACACTA
1 AACACTA
6144534 AACACTA
1 AACACTA
*
6144541 AACCCTA
1 AACACTA
6144548 AACAC-A
1 AACACTA
*
6144554 AACCCTA
1 AACACTA
6144561 AACACT
1 AACACT
6144567 CTAAATATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.53, C:0.35, G:0.00, T:0.12
Consensus pattern (7 bp):
AACACTA
Found at i:6144550 original size:14 final size:14
Alignment explanation
Indices: 6144531--6144566 Score: 65
Period size: 13 Copynumber: 2.6 Consensus size: 14
6144521 AACTCGAACA
6144531 CTAAACACTAAACC
1 CTAAACACTAAACC
6144545 CTAAACAC-AAACC
1 CTAAACACTAAACC
6144558 CTAAACACT
1 CTAAACACT
6144567 CTAAATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.50, C:0.36, G:0.00, T:0.14
Consensus pattern (14 bp):
CTAAACACTAAACC
Found at i:6144558 original size:13 final size:13
Alignment explanation
Indices: 6144517--6144565 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
6144507 AAACCATAAA
* *
6144517 CCTAAACTCGAAC
1 CCTAAACACAAAC
*
6144530 ACTAAACACTAAAC
1 CCTAAACAC-AAAC
6144544 CCTAAACACAAAC
1 CCTAAACACAAAC
6144557 CCTAAACAC
1 CCTAAACAC
6144566 TCTAAATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
13 20 0.65
14 11 0.35
ACGTcount: A:0.49, C:0.37, G:0.02, T:0.12
Consensus pattern (13 bp):
CCTAAACACAAAC
Found at i:6144561 original size:27 final size:26
Alignment explanation
Indices: 6144513--6144566 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
6144503 ATATAAACCA
* *
6144513 TAAACCTAAACTCGAACACTAAACAC
1 TAAACCTAAACACAAACACTAAACAC
*
6144539 TAAACCCTAAACACAAACCCTAAACAC
1 TAAA-CCTAAACACAAACACTAAACAC
6144566 T
1 T
6144567 CTAAATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.50, C:0.33, G:0.02, T:0.15
Consensus pattern (26 bp):
TAAACCTAAACACAAACACTAAACAC
Found at i:6145033 original size:21 final size:21
Alignment explanation
Indices: 6144976--6145035 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
6144966 CATAAATAAT
*
6144976 AAACTATACACATAAA-CCCTA
1 AAACTAGA-ACATAAACCCCTA
*
6144997 AAACTAGAA-TTAAAACCCCTA
1 AAACTAGAACAT-AAACCCCTA
6145018 AAACCTA-AACATAAACCC
1 AAA-CTAGAACATAAACCC
6145036 TCATTATATC
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
19 1 0.03
20 4 0.12
21 23 0.72
22 4 0.12
ACGTcount: A:0.53, C:0.28, G:0.02, T:0.17
Consensus pattern (21 bp):
AAACTAGAACATAAACCCCTA
Found at i:6145389 original size:14 final size:14
Alignment explanation
Indices: 6145372--6145457 Score: 56
Period size: 13 Copynumber: 6.4 Consensus size: 14
6145362 CAATTAAATT
6145372 CTAAACACTAAACC
1 CTAAACACTAAACC
*
6145386 CTAAACCCTAAA--
1 CTAAACACTAAACC
6145398 CTAAA-ACTACAAACC
1 CTAAACACT--AAACC
* * *
6145413 TTAAGCA-TAAAAC
1 CTAAACACTAAACC
*
6145426 CTAAACACTAAA-T
1 CTAAACACTAAACC
**
6145439 CTAAACTTTAAACC
1 CTAAACACTAAACC
6145453 CTAAA
1 CTAAA
6145458 TTAAAATTAT
Statistics
Matches: 54, Mismatches: 11, Indels: 14
0.68 0.14 0.18
Matches are distributed among these distances:
11 2 0.04
12 5 0.09
13 22 0.41
14 20 0.37
15 4 0.07
16 1 0.02
ACGTcount: A:0.51, C:0.28, G:0.01, T:0.20
Consensus pattern (14 bp):
CTAAACACTAAACC
Found at i:6145717 original size:48 final size:48
Alignment explanation
Indices: 6145659--6145751 Score: 114
Period size: 48 Copynumber: 1.9 Consensus size: 48
6145649 AATTAAACTT
* * * *
6145659 TAAACCATAAACCATAAACTCAAATACTAAAAACTAGACCCTAAATGA
1 TAAACCATAAACCATAAAATCAAACAATAAAAACTAAACCCTAAATGA
* * * *
6145707 TAAACTATAAACCTTAAAATTAAACAATAAATACTAAACCCTAAA
1 TAAACCATAAACCATAAAATCAAACAATAAAAACTAAACCCTAAA
6145752 AACTAAACAT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 37 1.00
ACGTcount: A:0.56, C:0.20, G:0.02, T:0.22
Consensus pattern (48 bp):
TAAACCATAAACCATAAAATCAAACAATAAAAACTAAACCCTAAATGA
Found at i:6145765 original size:28 final size:28
Alignment explanation
Indices: 6145708--6145778 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
6145698 CCTAAATGAT
* *
6145708 AAACTATAAA-CCTTAAAATTAAACAATA
1 AAACT-TAAACCCTAAAAACTAAACAATA
*
6145736 AATAC-TAAACCCTAAAAACTAAACATTA
1 AA-ACTTAAACCCTAAAAACTAAACAATA
*
6145764 AACCTTAAACCCTAA
1 AAACTTAAACCCTAA
6145779 TCACAAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
27 5 0.14
28 29 0.81
29 2 0.06
ACGTcount: A:0.56, C:0.21, G:0.00, T:0.23
Consensus pattern (28 bp):
AAACTTAAACCCTAAAAACTAAACAATA
Done.