Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 138 of 190
Found at i:40705111 original size:29 final size:29
Alignment explanation
Indices: 40705021--40705119 Score: 94
Period size: 31 Copynumber: 3.2 Consensus size: 29
40705011 ACTTACATAT
* *
40705021 TTAATAATTTATATTTAGTCATATAATA-AA
1 TTAAT-ATTTATATTTAATTAT-TAATATAA
*
40705051 TTATATTAATTATATTCATAATTTATT-ATATAA
1 TTA-A-TATTTATATT--TAA-TTATTAATATAA
40705084 TTAATATTTATATTTAATTATTAATATAA
1 TTAATATTTATATTTAATTATTAATATAA
40705113 TTAATAT
1 TTAATAT
40705120 AATTATTTAT
Statistics
Matches: 58, Mismatches: 4, Indels: 15
0.75 0.05 0.19
Matches are distributed among these distances:
28 5 0.09
29 16 0.28
30 3 0.05
31 18 0.31
32 5 0.09
33 8 0.14
34 3 0.05
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (29 bp):
TTAATATTTATATTTAATTATTAATATAA
Found at i:40705126 original size:29 final size:28
Alignment explanation
Indices: 40705073--40705136 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
40705063 TATTCATAAT
*
40705073 TTATT-ATATAATTAATATTTATATTTAA
1 TTATTAATATAATTAATATATATATTT-A
40705101 TTATTAATATAATTAATATA-ATTATTTA
1 TTATTAATATAATTAATATATA-TATTTA
40705129 TT-TTAATA
1 TTATTAATA
40705137 AACTATTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
27 6 0.18
28 9 0.27
29 18 0.55
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
TTATTAATATAATTAATATATATATTTA
Found at i:40705130 original size:53 final size:51
Alignment explanation
Indices: 40705071--40705174 Score: 124
Period size: 53 Copynumber: 2.0 Consensus size: 51
40705061 TATATTCATA
*
40705071 ATTTATTATATAATTAA-TATTT-ATATTT-AATTATTAATATAATTAATATAATT
1 ATTTATT-T-TAATAAACTATTTAATATTTCAATT-TTAATATAA-TAATA-AATT
*
40705124 ATTTATTTTAATAAACTATTTAATATTTCAATTTTAATTTAATAATAAATT
1 ATTTATTTTAATAAACTATTTAATATTTCAATTTTAATATAATAATAAATT
40705175 TTAAAAATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
51 10 0.22
52 11 0.24
53 21 0.46
54 4 0.09
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (51 bp):
ATTTATTTTAATAAACTATTTAATATTTCAATTTTAATATAATAATAAATT
Found at i:40705185 original size:16 final size:16
Alignment explanation
Indices: 40705153--40705199 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
40705143 TTAATATTTC
*
40705153 AATTTTAATTTAATAAT
1 AATTTTAA-ATAATAAT
40705170 AAATTTTAAA-AATAAT
1 -AATTTTAAATAATAAT
40705186 AATTTTAAATAATA
1 AATTTTAAATAATA
40705200 TTCTTCACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 9 0.33
16 10 0.37
18 8 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTTTAAATAATAAT
Found at i:40705250 original size:15 final size:15
Alignment explanation
Indices: 40705232--40705288 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
40705222 ATTCAATATT
40705232 AATATTTTAACAATA
1 AATATTTTAACAATA
*
40705247 AATATTTATTACAATTATA
1 AATATTT-TAAC-A--ATA
* *
40705266 AATATATTAATAATA
1 AATATTTTAACAATA
40705281 AATATTTT
1 AATATTTT
40705289 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 17 0.52
16 3 0.09
17 2 0.06
18 2 0.06
19 9 0.27
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATTTTAACAATA
Found at i:40705748 original size:2 final size:2
Alignment explanation
Indices: 40705741--40705784 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
40705731 TGACTTTCAT
40705741 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40705783 TA
1 TA
40705785 CTACTACTNN
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40706753 original size:6 final size:6
Alignment explanation
Indices: 40706742--40706766 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
40706732 TGGCGACCCC
40706742 CGTTTT CGTTTT CGTTTT CGTTTT C
1 CGTTTT CGTTTT CGTTTT CGTTTT C
40706767 AAAATCCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.20, G:0.16, T:0.64
Consensus pattern (6 bp):
CGTTTT
Found at i:40709168 original size:33 final size:33
Alignment explanation
Indices: 40709086--40709168 Score: 78
Period size: 33 Copynumber: 2.5 Consensus size: 33
40709076 CATTCAAACC
* * ** *
40709086 ATGGTCTTACGTTCAAGGTGCCATAACCCAATT
1 ATGGTCTTACATTTAAAATGCCATAACCCAACT
* * *
40709119 ATGGTCTTTTCA-TTAAAATGCCATAGCCCAGCT
1 ATGGTC-TTACATTTAAAATGCCATAACCCAACT
40709152 ATGGTCTTACATTTAAA
1 ATGGTCTTACATTTAAA
40709169 CATTGTCATG
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
32 4 0.10
33 32 0.82
34 3 0.08
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.34
Consensus pattern (33 bp):
ATGGTCTTACATTTAAAATGCCATAACCCAACT
Found at i:40714380 original size:20 final size:21
Alignment explanation
Indices: 40714345--40714388 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
40714335 TTTTTTCTTT
*
40714345 CTAGTTGTACTTTTATTTTTTG
1 CTAGTTGTA-TTTTATTTTATG
40714367 CTAGTTGT-TTTTATTTTATG
1 CTAGTTGTATTTTATTTTATG
40714387 CT
1 CT
40714389 GAGACTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
22 8 0.38
ACGTcount: A:0.14, C:0.09, G:0.14, T:0.64
Consensus pattern (21 bp):
CTAGTTGTATTTTATTTTATG
Found at i:40727676 original size:5 final size:5
Alignment explanation
Indices: 40727657--40727689 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
40727647 CCAAATCGAC
40727657 AACAA AACTAA AACAA AACAA AACAA AACAA AA
1 AACAA AAC-AA AACAA AACAA AACAA AACAA AA
40727690 TTCAGTGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.79, C:0.18, G:0.00, T:0.03
Consensus pattern (5 bp):
AACAA
Found at i:40728789 original size:12 final size:12
Alignment explanation
Indices: 40728772--40728824 Score: 58
Period size: 11 Copynumber: 4.6 Consensus size: 12
40728762 TTTTCACAAA
40728772 CAAATTCTCTCT
1 CAAATTCTCTCT
40728784 CAAATT-TCCTCT
1 CAAATTCT-CTCT
* *
40728796 CAATTTC-CTTT
1 CAAATTCTCTCT
40728807 CAAATT-TCTCT
1 CAAATTCTCTCT
40728818 CAAATTC
1 CAAATTC
40728825 ATATTTAATC
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
11 18 0.55
12 15 0.45
ACGTcount: A:0.26, C:0.30, G:0.00, T:0.43
Consensus pattern (12 bp):
CAAATTCTCTCT
Found at i:40728802 original size:11 final size:12
Alignment explanation
Indices: 40728780--40728823 Score: 65
Period size: 11 Copynumber: 3.8 Consensus size: 12
40728770 AACAAATTCT
40728780 CTCTCAAATTTC
1 CTCTCAAATTTC
40728792 CTCTC-AATTTC
1 CTCTCAAATTTC
*
40728803 CTTTCAAATTT-
1 CTCTCAAATTTC
40728814 CTCTCAAATT
1 CTCTCAAATT
40728824 CATATTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.25, C:0.30, G:0.00, T:0.45
Consensus pattern (12 bp):
CTCTCAAATTTC
Found at i:40731423 original size:15 final size:15
Alignment explanation
Indices: 40731399--40731474 Score: 66
Period size: 15 Copynumber: 5.1 Consensus size: 15
40731389 TAAAAATTCC
*
40731399 AAACCCTAAACCTAA
1 AAACCATAAACCTAA
*
40731414 AAACCATAAACC-AT
1 AAACCATAAACCTAA
* *
40731428 AAACCTAAAAACC-AT
1 AAACC-ATAAACCTAA
* *
40731443 AAACCCTAAACATAA
1 AAACCATAAACCTAA
40731458 AAACCATAAACCCTAA
1 AAACCATAAA-CCTAA
40731474 A
1 A
40731475 CATAAAACTT
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
14 10 0.20
15 34 0.69
16 5 0.10
ACGTcount: A:0.58, C:0.29, G:0.00, T:0.13
Consensus pattern (15 bp):
AAACCATAAACCTAA
Found at i:40731424 original size:7 final size:7
Alignment explanation
Indices: 40731399--40731480 Score: 69
Period size: 7 Copynumber: 11.4 Consensus size: 7
40731389 TAAAAATTCC
*
40731399 AAACCCT
1 AAACCAT
*
40731406 AAACCTAA
1 AAACC-AT
40731414 AAACCAT
1 AAACCAT
40731421 AAACCAT
1 AAACCAT
*
40731428 AAACCTAA
1 AAACC-AT
40731436 AAACCAT
1 AAACCAT
*
40731443 AAACCCT
1 AAACCAT
40731450 AAA-CAT
1 AAACCAT
40731456 AAAAACCAT
1 --AAACCAT
*
40731465 AAACCCT
1 AAACCAT
40731472 AAA-CAT
1 AAACCAT
40731478 AAA
1 AAA
40731481 ACTTCAGACC
Statistics
Matches: 61, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
6 7 0.11
7 37 0.61
8 14 0.23
9 3 0.05
ACGTcount: A:0.59, C:0.28, G:0.00, T:0.13
Consensus pattern (7 bp):
AAACCAT
Found at i:40731448 original size:44 final size:44
Alignment explanation
Indices: 40731336--40731861 Score: 401
Period size: 44 Copynumber: 12.2 Consensus size: 44
40731326 CCCTAATCCT
* * * * *
40731336 AACCCTTAACTTAAAAACCCT-AACCCTTCAA-TTAAAAACGCT-
1 AACCCTAAACCTAAAAACCATAAACCC-TAAACTTAAAAACCCTA
* * * *
40731378 AACCCTTAACTTAAAAATTCC--AAACCCTAAACCTAAAAACCATA
1 AACCCTAAACCTAAAAA--CCATAAACCCTAAACTTAAAAACCCTA
* * *
40731422 AACCATAAACCTAAAAACCATAAACCCTAAACATAAAAACCATA
1 AACCCTAAACCTAAAAACCATAAACCCTAAACTTAAAAACCCTA
* * *
40731466 AACCCTAAACAT-AAAA-CTTCAGACCCTAAACTTAAAAA-CCTCA
1 AACCCTAAACCTAAAAACCAT-AAACCCTAAACTTAAAAACCCT-A
*
40731509 AACCCTAAACCTAAAAA-CAT-AACCCTTAACTT-AAAACCCTA
1 AACCCTAAACCTAAAAACCATAAACCCTAAACTTAAAAACCCTA
* ** * * ** **
40731550 AACCCTAAACTTAAAAACTTTAAACACTAAAATT-TTAACTTTAA
1 AACCCTAAACCTAAAAACCATAAACCCTAAACTTAAAAACCCT-A
* *
40731594 AACCCT-AACTCT--AATCC-T-AACCCTTAACTTAAAAA-CCTCA
1 AACCCTAAAC-CTAAAAACCATAAACCCTAAACTTAAAAACCCT-A
* * * * * *
40731634 AACCCTTAATCTAAAAACCATAGACCTTAAACTCAAAAATCCTA
1 AACCCTAAACCTAAAAACCATAAACCCTAAACTTAAAAACCCTA
* * *
40731678 AACTCTAAACCAAAAAACCATAAACCCTAAACTTAAAAACCCCA
1 AACCCTAAACCTAAAAACCATAAACCCTAAACTTAAAAACCCTA
* *
40731722 AACACTAAACCTAAAAA-CACT-AACCCTTAACTTAAAAACCCTA
1 AACCCTAAACCTAAAAACCA-TAAACCCTAAACTTAAAAACCCTA
* * * * *
40731765 AACCATAAACC-ATAAAACCTTAAACCTTAAACTTAAAAACCATG
1 AACCCTAAACCTA-AAAACCATAAACCCTAAACTTAAAAACCCTA
* *
40731809 AACCTTAAACCTAAAAACCCTAAACCCTAAACTTAAAAACCCTA
1 AACCCTAAACCTAAAAACCATAAACCCTAAACTTAAAAACCCTA
*
40731853 AACCTTAAA
1 AACCCTAAA
40731862 ACCTTAACTT
Statistics
Matches: 387, Mismatches: 70, Indels: 52
0.76 0.14 0.10
Matches are distributed among these distances:
40 19 0.05
41 26 0.07
42 48 0.12
43 98 0.25
44 192 0.50
45 4 0.01
ACGTcount: A:0.50, C:0.29, G:0.01, T:0.21
Consensus pattern (44 bp):
AACCCTAAACCTAAAAACCATAAACCCTAAACTTAAAAACCCTA
Found at i:40731775 original size:29 final size:29
Alignment explanation
Indices: 40731743--40731882 Score: 92
Period size: 29 Copynumber: 4.8 Consensus size: 29
40731733 TAAAAACACT
*
40731743 AACCCTTAACTTAAAAACCCTAAACCATA
1 AACCCTAAACTTAAAAACCCTAAACCATA
* * * *
40731772 AACCATAAAACCTT--AAACCTTAAACTTAAA
1 AACCCT-AAA-CTTAAAAACCCTAAAC-CATA
* * *
40731802 AACCATGAACCTT--AAA-CCTAAAAACCCTA
1 AACCCT-AAACTTAAAAACCCT--AAACCATA
*
40731831 AACCCTAAACTTAAAAACCCTAAACCTTA
1 AACCCTAAACTTAAAAACCCTAAACCATA
* *
40731860 AAACCTTAACTTAAAAACCCTAA
1 AACCCTAAACTTAAAAACCCTAA
40731883 CCCTTAAGTT
Statistics
Matches: 87, Mismatches: 16, Indels: 16
0.73 0.13 0.13
Matches are distributed among these distances:
28 7 0.08
29 55 0.63
30 19 0.22
31 6 0.07
ACGTcount: A:0.50, C:0.29, G:0.01, T:0.21
Consensus pattern (29 bp):
AACCCTAAACTTAAAAACCCTAAACCATA
Found at i:40731804 original size:15 final size:14
Alignment explanation
Indices: 40731786--40731875 Score: 51
Period size: 15 Copynumber: 6.2 Consensus size: 14
40731776 ATAAAACCTT
40731786 AAACCTTAAACTTAA
1 AAACCTTAAACTT-A
* *
40731801 AAACCATGAACCTT-
1 AAACC-TTAAACTTA
* *
40731815 AAACCTAAAAACCCT-
1 AAACCT-TAAA-CTTA
*
40731830 AAACCCTAAACTTAA
1 AAACCTTAAACTT-A
*
40731845 AAACCCTAAACCTTA
1 AAACCTTAAA-CTTA
40731860 AAACCTT-AACTTA
1 AAACCTTAAACTTA
40731873 AAA
1 AAA
40731876 ACCCTAACCC
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
13 10 0.17
14 12 0.20
15 29 0.48
16 9 0.15
ACGTcount: A:0.51, C:0.27, G:0.01, T:0.21
Consensus pattern (14 bp):
AAACCTTAAACTTA
Found at i:40731839 original size:16 final size:15
Alignment explanation
Indices: 40731830--40731882 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
40731820 TAAAAACCCT
*
40731830 AAACCCTAAACTTAA
1 AAACCCTAAACCTAA
*
40731845 AAACCCTAAACCTTA
1 AAACCCTAAACCTAA
* *
40731860 AAA-CCTTAACTTAA
1 AAACCCTAAACCTAA
40731874 AAACCCTAA
1 AAACCCTAA
40731883 CCCTTAAGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
14 11 0.35
15 20 0.65
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (15 bp):
AAACCCTAAACCTAA
Found at i:40731861 original size:7 final size:7
Alignment explanation
Indices: 40731757--40731868 Score: 66
Period size: 7 Copynumber: 15.3 Consensus size: 7
40731747 CTTAACTTAA
*
40731757 AAACCCT
1 AAACCTT
*
40731764 AAACCAT
1 AAACCTT
*
40731771 AAACCATA
1 AAACC-TT
40731779 AAACCTT
1 AAACCTT
40731786 AAACCTT
1 AAACCTT
40731793 AAA-CTT
1 AAACCTT
*
40731799 AAAAACCAT
1 --AAACCTT
*
40731808 GAACCTT
1 AAACCTT
*
40731815 AAACCTAA
1 AAACCT-T
*
40731823 AAACCCT
1 AAACCTT
*
40731830 AAACCCT
1 AAACCTT
40731837 AAA-CTT
1 AAACCTT
*
40731843 AAAAACCCT
1 --AAACCTT
40731852 AAACCTT
1 AAACCTT
40731859 AAAACCTT
1 -AAACCTT
40731867 AA
1 AA
40731869 CTTAAAAACC
Statistics
Matches: 82, Mismatches: 14, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
6 5 0.06
7 50 0.61
8 23 0.28
9 4 0.05
ACGTcount: A:0.51, C:0.29, G:0.01, T:0.20
Consensus pattern (7 bp):
AAACCTT
Found at i:40731861 original size:22 final size:22
Alignment explanation
Indices: 40731333--40731861 Score: 303
Period size: 22 Copynumber: 24.6 Consensus size: 22
40731323 TAACCCTAAT
*
40731333 CCTAACCCTT-AACTTAAAAAC
1 CCTAAACCTTAAACTTAAAAAC
* *
40731354 CCTAACCCTTCAA-TTAAAAAC
1 CCTAAACCTTAAACTTAAAAAC
* * *
40731375 GCTAACCCTT-AACTTAAAAATT
1 CCTAAACCTTAAACTTAAAAA-C
* *
40731397 CC-AAACCCTAAACCTAAAAAC
1 CCTAAACCTTAAACTTAAAAAC
* * *
40731418 CATAAACCATAAACCTAAAAAC
1 CCTAAACCTTAAACTTAAAAAC
* * *
40731440 CATAAACCCTAAACATAAAAAC
1 CCTAAACCTTAAACTTAAAAAC
* * *
40731462 CATAAACCCTAAACAT-AAAA-
1 CCTAAACCTTAAACTTAAAAAC
* * *
40731482 CTTCAGACCCTAAACTTAAAAA-
1 CCT-AAACCTTAAACTTAAAAAC
* *
40731504 CCTCAAACCCTAAACCTAAAAA-
1 CCT-AAACCTTAAACTTAAAAAC
* *
40731526 CATAACCCTT-AACTT-AAAAC
1 CCTAAACCTTAAACTTAAAAAC
*
40731546 CCTAAACCCTAAACTTAAAAAC
1 CCTAAACCTTAAACTTAAAAAC
** * **
40731568 TTTAAACAC-TAAAATT-TTAAC
1 CCTAAAC-CTTAAACTTAAAAAC
** * *
40731589 TTTAAAACCCT-AACTCT---AAT
1 CCT-AAACCTTAAACT-TAAAAAC
*
40731609 CCTAACCCTT-AACTTAAAAA-
1 CCTAAACCTTAAACTTAAAAAC
*
40731629 CCTCAAACCCTTAATC-TAAAAAC
1 CCT-AAA-CCTTAAACTTAAAAAC
* * * *
40731652 CATAGACCTTAAACTCAAAAAT
1 CCTAAACCTTAAACTTAAAAAC
**
40731674 CCTAAA-CTCTAAACCAAAAAAC
1 CCTAAACCT-TAAACTTAAAAAC
* *
40731696 CATAAACCCTAAACTTAAAAAC
1 CCTAAACCTTAAACTTAAAAAC
* *
40731718 CCCAAACAC-TAAACCTAAAAAC
1 CCTAAAC-CTTAAACTTAAAAAC
* *
40731740 ACTAACCCTT-AACTTAAAAAC
1 CCTAAACCTTAAACTTAAAAAC
* *
40731761 CCTAAACCATAAAC-CATAAAAC
1 CCTAAACCTTAAACTTA-AAAAC
*
40731783 CTTAAACCTTAAACTTAAAAAC
1 CCTAAACCTTAAACTTAAAAAC
* * *
40731805 CATGAACCTTAAACCTAAAAAC
1 CCTAAACCTTAAACTTAAAAAC
*
40731827 CCTAAACCCTAAACTTAAAAAC
1 CCTAAACCTTAAACTTAAAAAC
40731849 CCTAAACCTTAAA
1 CCTAAACCTTAAA
40731862 ACCTTAACTT
Statistics
Matches: 406, Mismatches: 73, Indels: 57
0.76 0.14 0.11
Matches are distributed among these distances:
18 1 0.00
19 13 0.03
20 21 0.05
21 107 0.26
22 256 0.63
23 8 0.02
ACGTcount: A:0.50, C:0.29, G:0.01, T:0.21
Consensus pattern (22 bp):
CCTAAACCTTAAACTTAAAAAC
Found at i:40731887 original size:29 final size:29
Alignment explanation
Indices: 40731824--40731889 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
40731814 TAAACCTAAA
*
40731824 AACCC-TAAACCCTAAACTTAAAAACCCT
1 AACCCTTAAAACCTAAACTTAAAAACCCT
* *
40731852 AAACCTTAAAACCTTAACTTAAAAACCCT
1 AACCCTTAAAACCTAAACTTAAAAACCCT
40731881 AACCCTTAA
1 AACCCTTAA
40731890 GTTAAATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
28 4 0.12
29 29 0.88
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.21
Consensus pattern (29 bp):
AACCCTTAAAACCTAAACTTAAAAACCCT
Found at i:40735277 original size:125 final size:125
Alignment explanation
Indices: 40735034--40735298 Score: 397
Period size: 125 Copynumber: 2.1 Consensus size: 125
40735024 CAAACATGCT
* * * *
40735034 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTATTCTCATAAAGCATCCTGGTA
1 ACTGTAGCAAAAGCGCGTCCACGAGAGCGCGATTTCACAAATTATTCGCATAAAGCATCCTGCTA
*
40735099 GAAGCAATTTTATACTATTTTCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCA
66 GAAGCAATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCA
* * * * * *
40735159 ATTGTAGCAAAAGCGCGTCCAGGAGAGCTCGATTTCACAAATTCTTCGCATATAGCATCCTGCTT
1 ACTGTAGCAAAAGCGCGTCCACGAGAGCGCGATTTCACAAATTATTCGCATAAAGCATCCTGCTA
* *
40735224 GAAGCATTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TTCCAGGACCT
66 GAAGCA-ATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCA
40735284 ACTGTAGCAAAAGCG
1 ACTGTAGCAAAAGCG
40735299 AGTACACGTG
Statistics
Matches: 125, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
125 85 0.68
126 40 0.32
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (125 bp):
ACTGTAGCAAAAGCGCGTCCACGAGAGCGCGATTTCACAAATTATTCGCATAAAGCATCCTGCTA
GAAGCAATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCA
Found at i:40737104 original size:2 final size:2
Alignment explanation
Indices: 40737097--40737146 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
40737087 ATAGCCACTT
40737097 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40737139 TA TA TA TA
1 TA TA TA TA
40737147 GTAGGGTGTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40739969 original size:12 final size:11
Alignment explanation
Indices: 40739954--40739996 Score: 56
Period size: 12 Copynumber: 4.1 Consensus size: 11
40739944 TAAAAAATAT
40739954 AAATATATAAA
1 AAATATATAAA
40739965 TAAATATATAAA
1 -AAATATATAAA
40739977 AAA-AT-T-AA
1 AAATATATAAA
40739985 AAATATATAAA
1 AAATATATAAA
40739996 A
1 A
40739997 TCTAGAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
8 5 0.18
9 3 0.11
10 3 0.11
11 6 0.21
12 11 0.39
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AAATATATAAA
Found at i:40740250 original size:21 final size:20
Alignment explanation
Indices: 40740221--40740271 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
40740211 ATATAAATAC
*
40740221 TTTT-ATTTTT-TTTATAAT
1 TTTTAATTTTTATATATAAT
*
40740239 TTTTCAATTTTTATATATTAT
1 TTTT-AATTTTTATATATAAT
40740260 TTTTAATTTTTA
1 TTTTAATTTTTA
40740272 AAATTTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 4 0.14
20 14 0.50
21 10 0.36
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTTAATTTTTATATATAAT
Found at i:40740345 original size:21 final size:21
Alignment explanation
Indices: 40740321--40740361 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
40740311 CTTTTCAAAA
40740321 ATATAT-TTATACATTATATAT
1 ATATATATT-TACATTATATAT
*
40740342 ATATATATTTACATTTTATA
1 ATATATATTTACATTATATA
40740362 ATCAATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (21 bp):
ATATATATTTACATTATATAT
Found at i:40741409 original size:79 final size:79
Alignment explanation
Indices: 40741275--40741422 Score: 217
Period size: 79 Copynumber: 1.9 Consensus size: 79
40741265 ACTTACCTTT
* * *
40741275 TATATTGACATATGCAATCATGAAGATATAAGTTGACTTTTATGATCTTTTGTATCTTTATATTA
1 TATATTAACATATGCAATCATGAAGATATAAGCTGACTTTTATGATCTTTGGTATCTTTATATTA
40741340 AGGATAATTGATGA
66 AGGATAATTGATGA
* * * *
40741354 TATATTAAGATATGCAATCCATGAATATATGAGCTGA-TTTTATTATCTTTGGTATCTTTATATT
1 TATATTAACATATGCAAT-CATGAAGATATAAGCTGACTTTTATGATCTTTGGTATCTTTATATT
40741418 AAGGA
65 AAGGA
40741423 CAATGAATTT
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
79 46 0.75
80 15 0.25
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (79 bp):
TATATTAACATATGCAATCATGAAGATATAAGCTGACTTTTATGATCTTTGGTATCTTTATATTA
AGGATAATTGATGA
Found at i:40750712 original size:18 final size:16
Alignment explanation
Indices: 40750681--40750722 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
40750671 TTGAGTAAAT
40750681 AAATATAT-TTTATACTA
1 AAATATATATTTATA--A
40750698 AAATATATATTTATAA
1 AAATATATATTTATAA
40750714 AAATATATA
1 AAATATATA
40750723 AAAAATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.42
17 8 0.33
18 6 0.25
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATATATATTTATAA
Found at i:40751100 original size:214 final size:213
Alignment explanation
Indices: 40750707--40751149 Score: 671
Period size: 214 Copynumber: 2.1 Consensus size: 213
40750697 AAAATATATA
* * * *
40750707 TTTATAAAAATATATAAAAAATTTATTATTAGTGGAATTAAGGGTAAAGCCAAAAAAATTTTTTG
1 TTTAT-AAATTATATAAAAAATTTATTATTAGTGAAATCAAGGGTAAAGCAAAAAAAATTTTTTG
* *
40750772 GGTAAAATTAATTTATGTATTTTTTACTATGTTAAAAATACAATTTCACCATTTTAATAGCCTAA
65 GGTAAAATTAATTTATGTATTTTTTACGATATTAAAAATACAATTTCACCATTTTAATAGCCTAA
** * *
40750837 ATTTTTATAATTTTTAAATAATTAAATTAAAATTTTATCATTCTTAAGGGTTAAAGTGTAATTTT
130 ATTTTTATAATTTAAAAAAAATTAAATTAAAATTTTATCATTCTTAAGGGTTAAAGTATAATTTT
40750902 ACCAATACAAATTTAAAAT
195 ACCAATACAAATTTAAAAT
* *
40750921 TTTATAAATTATATCAACAAA-TTATTCTTAGTGAAATCAAGGGTAAAGACAAAAAAATTATTTT
1 TTTATAAATTATAT-AAAAAATTTATTATTAGTGAAATCAAGGGTAAAG-CAAAAAAA--A-TTT
*
40750985 TTTGGGTAAAATTAATTTATGTA-TTTTTACGATATTAAAAATACAATTT-ATCATTTTAATAGC
61 TTTGGGTAAAATTAATTTATGTATTTTTTACGATATTAAAAATACAATTTCACCATTTTAATAGC
40751048 CTAAATTTTTATAA-TTAAAAAAAATTAAATTAAAATTTTATCA-TCTTTAAGGGTTAAAGTATA
126 CTAAATTTTTATAATTTAAAAAAAATTAAATTAAAATTTTATCATTC-TTAAGGGTTAAAGTATA
40751111 ATTTTACCAATACAAATTTAAAAT
190 ATTTTACCAATACAAATTTAAAAT
40751135 TTTATAAATTATATA
1 TTTATAAATTATATA
40751150 GGGACTTAAA
Statistics
Matches: 210, Mismatches: 13, Indels: 13
0.89 0.06 0.06
Matches are distributed among these distances:
213 35 0.17
214 97 0.46
215 27 0.13
216 25 0.12
217 26 0.12
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.42
Consensus pattern (213 bp):
TTTATAAATTATATAAAAAATTTATTATTAGTGAAATCAAGGGTAAAGCAAAAAAAATTTTTTGG
GTAAAATTAATTTATGTATTTTTTACGATATTAAAAATACAATTTCACCATTTTAATAGCCTAAA
TTTTTATAATTTAAAAAAAATTAAATTAAAATTTTATCATTCTTAAGGGTTAAAGTATAATTTTA
CCAATACAAATTTAAAAT
Found at i:40757038 original size:17 final size:17
Alignment explanation
Indices: 40757016--40757051 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
40757006 CTAAACCATG
40757016 CTTCAAAGTTGACTCTT
1 CTTCAAAGTTGACTCTT
40757033 CTTCAAAGTTGACTCTT
1 CTTCAAAGTTGACTCTT
40757050 CT
1 CT
40757052 AAACCCATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.25, G:0.11, T:0.42
Consensus pattern (17 bp):
CTTCAAAGTTGACTCTT
Found at i:40760405 original size:17 final size:17
Alignment explanation
Indices: 40760383--40760416 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
40760373 AAATAATAGT
40760383 AAAATAAAATTTTCAAC
1 AAAATAAAATTTTCAAC
40760400 AAAATAAAATTTTCAAC
1 AAAATAAAATTTTCAAC
40760417 CTCGAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATAAAATTTTCAAC
Found at i:40763422 original size:13 final size:14
Alignment explanation
Indices: 40763388--40763424 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
40763378 TATTTATAAA
*
40763388 AAATATATTATTTT
1 AAATATATTATATT
40763402 AAAT-TATT-TATT
1 AAATATATTATATT
40763414 AAATATATTAT
1 AAATATATTAT
40763425 TTTCTATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
12 7 0.35
13 8 0.40
14 5 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
AAATATATTATATT
Found at i:40763577 original size:31 final size:30
Alignment explanation
Indices: 40763542--40763626 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 30
40763532 TGATGCGCAA
*
40763542 ATCAACTACCTTTTTTAGCTGAAATAATTTT
1 ATCAACTA-CTTTTTTAGCTTAAATAATTTT
40763573 ATCAAACTA-TCTTTTTAGCTTAAATAATTTT
1 ATC-AACTACT-TTTTTAGCTTAAATAATTTT
*
40763604 -T-ATCTACTTTTTTAGCTTAAATA
1 ATCAACTACTTTTTTAGCTTAAATA
40763627 CCAATTTAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
28 19 0.39
29 1 0.02
30 2 0.04
31 22 0.45
32 5 0.10
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.48
Consensus pattern (30 bp):
ATCAACTACTTTTTTAGCTTAAATAATTTT
Found at i:40765461 original size:26 final size:26
Alignment explanation
Indices: 40765430--40765489 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
40765420 GTCTCGATAT
*
40765430 AAGGCTCTTTGTAAGCTTCCCGCTTA
1 AAGGCTCTTTGTAAGCTTCCCGATTA
*
40765456 AAGGCTCTTTGTAAGCTTCCTGATTA
1 AAGGCTCTTTGTAAGCTTCCCGATTA
*
40765482 ATGGCTCT
1 AAGGCTCT
40765490 CCTGAGCTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.37
Consensus pattern (26 bp):
AAGGCTCTTTGTAAGCTTCCCGATTA
Found at i:40768472 original size:18 final size:18
Alignment explanation
Indices: 40768444--40768504 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
40768434 TTGTTTCAAA
40768444 AAAAAATATAATAAAAATT
1 AAAAAA-ATAATAAAAATT
*
40768463 AAAAAAATAAT-TAAATT
1 AAAAAAATAATAAAAATT
*
40768480 ATGAAAAATAA-AAAGAATAT
1 A-AAAAAATAATAAA-AAT-T
40768500 AAAAA
1 AAAAA
40768505 TTTATTTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
17 6 0.18
18 14 0.41
19 12 0.35
20 2 0.06
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (18 bp):
AAAAAAATAATAAAAATT
Found at i:40768751 original size:25 final size:24
Alignment explanation
Indices: 40768723--40768776 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
40768713 TATATTATGT
40768723 TTTTATT-TTATAAATTATTTTTGAA
1 TTTTATTATTAT-AATTATTTTT-AA
* *
40768748 TTTTTTTATTATTATTATTTTTAA
1 TTTTATTATTATAATTATTTTTAA
40768772 TTTTA
1 TTTTA
40768777 GAATTTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 6 0.24
25 15 0.60
26 4 0.16
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (24 bp):
TTTTATTATTATAATTATTTTTAA
Found at i:40786033 original size:23 final size:21
Alignment explanation
Indices: 40786007--40786052 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
40785997 CATACTTTGT
*
40786007 TTATAGCATTTTATTATATATTA
1 TTATA-CATATTATT-TATATTA
40786030 TTATACATATTATTTATATTA
1 TTATACATATTATTTATATTA
40786051 TT
1 TT
40786053 GTTAGATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.41
22 8 0.36
23 5 0.23
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (21 bp):
TTATACATATTATTTATATTA
Found at i:40793039 original size:72 final size:71
Alignment explanation
Indices: 40792922--40793092 Score: 216
Period size: 72 Copynumber: 2.4 Consensus size: 71
40792912 AGATCGAGCA
* * * *
40792922 TTAGCGGCATTTTCTAAAAAGCGCTGCAATAAACATAAGCCCAACGATGCCGTTTTCTGAGCTTT
1 TTAGCGGCATTTT-TAGAAAGCGCCGCAAAAAACATAAGCCCAACGACGCCGTTTTCTGAGCTTT
40792987 CGAGGAT
65 CGAGGAT
* * * *
40792994 TTAGCGGCATTTTTGTGAAAGCGCCGCAAAAAACCTAAGCTCAACGACGCCGTTTTGTGAGCTTT
1 TTAGCGGCATTTTT-AGAAAGCGCCGCAAAAAACATAAGCCCAACGACGCCGTTTTCTGAGCTTT
* *
40793059 TGGGGAT
65 CGAGGAT
*
40793066 TTAGCGGCGTTTTTAAGAAAGCGCCGC
1 TTAGCGGCATTTTT-AGAAAGCGCCGC
40793093 TAATGCTCAG
Statistics
Matches: 85, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
71 1 0.01
72 84 0.99
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.27
Consensus pattern (71 bp):
TTAGCGGCATTTTTAGAAAGCGCCGCAAAAAACATAAGCCCAACGACGCCGTTTTCTGAGCTTTC
GAGGAT
Found at i:40793225 original size:73 final size:72
Alignment explanation
Indices: 40793106--40793281 Score: 253
Period size: 73 Copynumber: 2.4 Consensus size: 72
40793096 TGCTCAGGGC
* * *** *
40793106 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAGAACCTAAGCCAAAACGACGTGGTTTTGTGAGCT
1 TTTAGCGGCGTTTTT-AGGAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTATGAGCT
40793171 TTGGGGGA
65 TTGGGGGA
* *
40793179 TTTAGCGGCGTTTTTCAGGATGCGCCGCAAAAAACGTAAGCCAAAACGACACCGTTTTATGAGCT
1 TTTAGCGGCGTTTTT-AGGAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTATGAGCT
40793244 TTGGGGGA
65 TTGGGGGA
40793252 TTTAGCGGCGTTTTTAGGAAAGCGCCGCAA
1 TTTAGCGGCGTTTTTAGG-AAGCGCCGCAA
40793282 TGCTCAGGGC
Statistics
Matches: 92, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
72 3 0.03
73 89 0.97
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (72 bp):
TTTAGCGGCGTTTTTAGGAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTATGAGCTT
TGGGGGA
Found at i:40793249 original size:186 final size:185
Alignment explanation
Indices: 40792922--40793392 Score: 594
Period size: 186 Copynumber: 2.5 Consensus size: 185
40792912 AGATCGAGCA
* * * * *
40792922 TTAGCGGCATTTTCTAA-AAAGCGCTGCAATAAACATAAGCC-CAACGATGCCGTTTTCTGAGCT
1 TTAGCGGCGTTTT-TAAGAAAGCGCCGCAA-AAACCTAAGCCAAAACGATGCCGTTTTGTGAGCT
* * ** *
40792985 TTCGAGGATTTAGCGGCATTTTTGTGAAAGCGCCGCAAAAAACCTAAGCTCAACGACGCCGTTTT
64 TTCGGGGATTTAGCGGCGTTTTTCAGAAAGCGCCGCAAAAAACCTAAGCTCAACGACACCGTTTT
*
40793050 GTGAGCTTTT-GGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
129 ATGAGCTTTTGGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGC-AATGCTCAGGGCT
* **
40793107 TTAGCGGCGTTTTTAAGAAAGCGCCGCAAAGAACCTAAGCCAAAACGACGTGGTTTTGTGAGCTT
1 TTAGCGGCGTTTTTAAGAAAGCGCCGCAAA-AACCTAAGCCAAAACGATGCCGTTTTGTGAGCTT
* * * *
40793172 TGGGGGATTTAGCGGCGTTTTTCAGGATGCGCCGCAAAAAACGTAAGC-CAAAACGACACCGTTT
65 TCGGGGATTTAGCGGCGTTTTTCAGAAAGCGCCGCAAAAAACCTAAGCTC--AACGACACCGTTT
*
40793236 TATGAGC-TTTGGGGGATTTAGCGGCGTTTTTAGGAAAGCGCCGCAATGCTCAGGGCT
128 TATGAGCTTTTGGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCAATGCTCAGGGCT
* ** * * *
40793293 TTAGCAGCGTTTTCGAGAAAGCGCCACAAAAAACCTAAGCCAAAACAATGCCATTTTGTGAGCTT
1 TTAGCGGCGTTTTTAAGAAAGCGCCGC-AAAAACCTAAGCCAAAACGATGCCGTTTTGTGAGCTT
*
40793358 TCGGGGATTTAGCGGCGTTTTT-ATGTAAGCGCCGC
65 TCGGGGATTTAGCGGCGTTTTTCA-GAAAGCGCCGC
40793393 TAATGCTCAG
Statistics
Matches: 247, Mismatches: 31, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
184 4 0.02
185 34 0.14
186 156 0.63
187 53 0.21
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (185 bp):
TTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAACCTAAGCCAAAACGATGCCGTTTTGTGAGCTTT
CGGGGATTTAGCGGCGTTTTTCAGAAAGCGCCGCAAAAAACCTAAGCTCAACGACACCGTTTTAT
GAGCTTTTGGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCAATGCTCAGGGCT
Found at i:40793451 original size:114 final size:111
Alignment explanation
Indices: 40793179--40793506 Score: 442
Period size: 113 Copynumber: 2.9 Consensus size: 111
40793169 CTTTGGGGGA
* * * * *
40793179 TTTAGCGGCGTTTTTCAGGATGCGCCGCAAAAAACGTAAGCCAAAACGACACCGTTTTATGAGCT
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTATGAGCT
40793244 TTGGGGGATTTAGCGGCGTTTTTAGGAAAGCGCCGCAATGCTCAGGGC
66 TT-GGGGATTTAGCGGCGTTTTTA-GAAAGCGCCGCAATGCTCAGGGC
* ** * * * * *
40793292 TTTAGCAGCGTTTTCGAGAAAGCGCCACAAAAAACCTAAGCCAAAACAATGCCATTTTGTGAGCT
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTATGAGCT
*
40793357 TTCGGGGATTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGCTCAGGGC
66 TT-GGGGATTTAGCGGCGTTTTTA-GAAAGCGCCGC-AATGCTCAGGGC
* *
40793406 TTTAGCGGCGTTTTTAATAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGTCGTTTTATGAGCT
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTATGAGCT
*
40793471 TT-GGGATTTAGCGGCGTTTTTGAGGAAGCGCCGCAA
66 TTGGGGATTTAGCGGCGTTTTT-AGAAAGCGCCGCAA
40793507 AAAACCTAAG
Statistics
Matches: 187, Mismatches: 26, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
111 2 0.01
112 29 0.16
113 87 0.47
114 69 0.37
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26
Consensus pattern (111 bp):
TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGCCGTTTTATGAGCT
TTGGGGATTTAGCGGCGTTTTTAGAAAGCGCCGCAATGCTCAGGGC
Found at i:40793522 original size:71 final size:71
Alignment explanation
Indices: 40793406--40793577 Score: 256
Period size: 71 Copynumber: 2.4 Consensus size: 71
40793396 TGCTCAGGGC
** **
40793406 TTTAGCGGCGTTTTTAATAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGTCGTTTTATGAGCT
1 TTTAGCGGCGTTTTT-AGGAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTATGAGCT
40793471 TT-GGGA
65 TTCGGGA
40793477 TTTAGCGGCGTTTTTGAGGAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTATGAGCT
1 TTTAGCGGCGTTTTT-AGGAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTATGAGCT
40793542 TTCGGGGA
65 TTC-GGGA
*
40793550 TTTAGCGACGTTTTTAGGAAAGCGCCGC
1 TTTAGCGGCGTTTTTAGG-AAGCGCCGC
40793578 TAATGCTCAG
Statistics
Matches: 92, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
71 62 0.67
72 3 0.03
73 27 0.29
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (71 bp):
TTTAGCGGCGTTTTTAGGAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTATGAGCTT
TCGGGA
Found at i:40793542 original size:185 final size:186
Alignment explanation
Indices: 40793292--40793764 Score: 680
Period size: 185 Copynumber: 2.5 Consensus size: 186
40793282 TGCTCAGGGC
* * * * ** *
40793292 TTTAGCAGCGTTTTCGAGAAAGCGCCACAAAAAACCTAAGCCAAAACAATGCCATTTTGTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTGTGAGCT
* *
40793357 TTCGGGGATTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTA
66 TTCGGGGATTTAGCGGCGTTTTTAGGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTA
* * * *
40793422 ATAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGTCGTTTTATGAGCTTT-GGGA
131 AGAAAGCGCCACAAAAAACCTAAGCCAAAACAACGCCGTTTTATGAGCTTTCGGGA
* *
40793477 TTTAGCGGCGTTTTTGAGGAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTATGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTGTGAGCT
* *
40793542 TTCGGGGATTTAGCGACGTTTTTAGGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTG
66 TTCGGGGATTTAGCGGCGTTTTTAGGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTA
* * *
40793607 AGAAAGCGCCACAGAAAACCTAAGCCAAAACAATGCCGTTTTGTGAGCTTTCGGGGA
131 AGAAAGCGCCACAAAAAACCTAAGCCAAAACAACGCCGTTTTATGAGCTTTC-GGGA
* * * *
40793664 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAGAACCTAAGCCAAAACGACATCGCTTTGTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTGTGAGCT
* *
40793729 TTGGGGGATTTAGCGGCGTTTATGAGG-AAGCGCCGC
66 TTCGGGGATTTAGCGGCGTTT-TTAGGAAAGCGCCGC
40793765 AAAAAACCTA
Statistics
Matches: 256, Mismatches: 29, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
185 161 0.63
187 91 0.36
188 4 0.02
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.25
Consensus pattern (186 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTGTGAGCT
TTCGGGGATTTAGCGGCGTTTTTAGGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTA
AGAAAGCGCCACAAAAAACCTAAGCCAAAACAACGCCGTTTTATGAGCTTTCGGGA
Found at i:40793625 original size:114 final size:114
Alignment explanation
Indices: 40793477--40793691 Score: 349
Period size: 114 Copynumber: 1.9 Consensus size: 114
40793467 AGCTTTGGGA
* * *
40793477 TTTAGCGGCGTTTTTGAGGAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTATGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAACCTAAGCCAAAACAACACCGTTTTATGAGCT
*
40793542 TTCGGGGATTTAGCGACGTTTTTAGGAAAGCGCCGCTAATGCTCAGGGC
66 TTCGGGGATTTAGCGACGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
* ** *
40793591 TTTAGCGGCGTTTTTGAGAAAGCGCCACAGAAAACCTAAGCCAAAACAATGCCGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAACCTAAGCCAAAACAACACCGTTTTATGAGCT
*
40793656 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGC
66 TTCGGGGATTTAGCGACGTTTTTAAGAAAGCGCCGC
40793692 AAAGAACCTA
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 92 1.00
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (114 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAACCTAAGCCAAAACAACACCGTTTTATGAGCT
TTCGGGGATTTAGCGACGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
Found at i:40793689 original size:299 final size:299
Alignment explanation
Indices: 40792993--40793691 Score: 1161
Period size: 299 Copynumber: 2.3 Consensus size: 299
40792983 CTTTCGAGGA
* * * * *
40792993 TTTAGCGGCATTTTTGTGAAAGCGCCGCAAAAAACCTAAGCTC--AACGACGCCGTTTTGTGAGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAACCTAAGC-CAAAACAATGCCGTTTTGTGAGC
*
40793056 TTTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTT
65 TTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTT
* * *
40793121 AAGAAAGCGCCGCAAAGAACCTAAGCCAAAACGACGTGGTTTTGTGAGCTTTGGGGGATTTAGCG
130 AAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGTCGTTTTATGAGCTTT-GGGGATTTAGCG
* * *
40793186 GCGTTTTTCAGGATGCGCCGCAAAAAACGTAAGCCAAAACGACACCGTTTTATGAGCTTTGGGGG
194 GCGTTTTTCAGGAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTATGAGCTTTCGGGG
*
40793251 ATTTAGCGGCGTTTTTAGGAAAGCGCCGCAATGCTCAGGGC
259 ATTTAGCGACGTTTTTAGGAAAGCGCCGCAATGCTCAGGGC
* * *
40793292 TTTAGCAGCGTTTTCGAGAAAGCGCCACAAAAAACCTAAGCCAAAACAATGCCATTTTGTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAACCTAAGCCAAAACAATGCCGTTTTGTGAGCT
* *
40793357 TTCGGGGATTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTA
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTA
*
40793422 ATAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGTCGTTTTATGAGCTTT-GGGATTTAGCGGC
131 AGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGTCGTTTTATGAGCTTTGGGGATTTAGCGGC
*
40793486 GTTTTTGAGGAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTATGAGCTTTCGGGGAT
196 GTTTTTCAGGAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTATGAGCTTTCGGGGAT
40793551 TTAGCGACGTTTTTAGGAAAGCGCCGCTAATGCTCAGGGC
261 TTAGCGACGTTTTTAGGAAAGCGCCGC-AATGCTCAGGGC
*
40793591 TTTAGCGGCGTTTTTGAGAAAGCGCCACAGAAAACCTAAGCCAAAACAATGCCGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAACCTAAGCCAAAACAATGCCGTTTTGTGAGCT
40793656 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGC
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGC
40793692 AAAGAACCTA
Statistics
Matches: 371, Mismatches: 26, Indels: 6
0.92 0.06 0.01
Matches are distributed among these distances:
298 101 0.27
299 143 0.39
300 127 0.34
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (299 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAACCTAAGCCAAAACAATGCCGTTTTGTGAGCT
TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTA
AGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACGTCGTTTTATGAGCTTTGGGGATTTAGCGGC
GTTTTTCAGGAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTATGAGCTTTCGGGGAT
TTAGCGACGTTTTTAGGAAAGCGCCGCAATGCTCAGGGC
Found at i:40793710 original size:73 final size:69
Alignment explanation
Indices: 40793591--40793830 Score: 290
Period size: 73 Copynumber: 3.4 Consensus size: 69
40793581 TGCTCAGGGC
* *
40793591 TTTAGCGGCGTTTTTGAGAAAGCGCCACAGAAAACCTAAGCCAAAACAATGCCGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCA-AAAACCTAAGCCAAAACAAT--CG-TTTGTGAGCT
40793656 TTCGGGGA
62 TTCGGGGA
40793664 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAGAACCTAAGCCAAAACGACATCGCTTTGTGAGCT
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAA-AACCTAAGCCAAAAC-A-ATCG-TTTGTGAGCT
*
40793729 TTGGGGGA
62 TTCGGGGA
* * * * *
40793737 TTTAGCGGCGTTTATGAGGAAGCGCCGCAAAAAACCTAAGCC--AA-AA-CGATTATGAGCTTTC
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGC-AAAAACCTAAGCCAAAACAATCGTTTGTGAGCTTTC
40793798 GGGGA
65 GGGGA
*
40793803 TTTAGCGGCGTTTTTAGGAAAGCGCCGC
1 TTTAGCGGCGTTTTTAAGAAAGCGCCGC
40793831 TAATGCTTAG
Statistics
Matches: 149, Mismatches: 14, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
66 39 0.26
67 2 0.01
68 1 0.01
69 1 0.01
71 2 0.01
72 2 0.01
73 96 0.64
74 4 0.03
75 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (69 bp):
TTTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAACCTAAGCCAAAACAATCGTTTGTGAGCTTTCG
GGGA
Found at i:40794033 original size:14 final size:14
Alignment explanation
Indices: 40794014--40794053 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
40794004 TATCACTATA
*
40794014 GTTTAGGGTTTTTG
1 GTTTAGGGTTTATG
*
40794028 GTTTAGGGTATATG
1 GTTTAGGGTTTATG
*
40794042 GTTTAGAGTTTA
1 GTTTAGGGTTTA
40794054 AAGTTTAGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (14 bp):
GTTTAGGGTTTATG
Found at i:40795811 original size:20 final size:20
Alignment explanation
Indices: 40795772--40795813 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
40795762 ATGTTAGAGT
*
40795772 TAATATAGTCAAAGCAGTTG
1 TAATATAGTCAAAACAGTTG
*
40795792 TAATATAGTCAAAACTGTTG
1 TAATATAGTCAAAACAGTTG
40795812 TA
1 TA
40795814 CCGTTGTAAG
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:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (20 bp):
TAATATAGTCAAAACAGTTG
Found at i:40795842 original size:15 final size:15
Alignment explanation
Indices: 40795822--40795852 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
40795812 TACCGTTGTA
40795822 AGTCTGTTAGCAGTT
1 AGTCTGTTAGCAGTT
40795837 AGTCTGTTAGCAGTT
1 AGTCTGTTAGCAGTT
40795852 A
1 A
40795853 AAGATGATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.39
Consensus pattern (15 bp):
AGTCTGTTAGCAGTT
Found at i:40800509 original size:20 final size:20
Alignment explanation
Indices: 40800484--40800526 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
40800474 ATGTTAGAGT
*
40800484 TAATATAGTCAAAGCAGTTG
1 TAATATAGTCAAAACAGTTG
*
40800504 TAATATAGTCAAAACCGTTG
1 TAATATAGTCAAAACAGTTG
40800524 TAA
1 TAA
40800527 GTCTGTTAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (20 bp):
TAATATAGTCAAAACAGTTG
Found at i:40800546 original size:15 final size:15
Alignment explanation
Indices: 40800526--40800556 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
40800516 AACCGTTGTA
40800526 AGTCTGTTAGCAGTT
1 AGTCTGTTAGCAGTT
40800541 AGTCTGTTAGCAGTT
1 AGTCTGTTAGCAGTT
40800556 A
1 A
40800557 AAGATGATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.39
Consensus pattern (15 bp):
AGTCTGTTAGCAGTT
Found at i:40802686 original size:23 final size:23
Alignment explanation
Indices: 40802660--40802725 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
40802650 ATATGTTGTT
40802660 AATTGATA-TGTTAAAGTGCTGCA
1 AATTGA-AGTGTTAAAGTGCTGCA
*
40802683 AATTGAAGTGTTTAAA-TGCTGTA
1 AATTGAAGTG-TTAAAGTGCTGCA
*
40802706 ACTTGAAGTGTTAAAGTGCT
1 AATTGAAGTGTTAAAGTGCT
40802726 ACTTTCCATT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
22 6 0.16
23 27 0.71
24 5 0.13
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.36
Consensus pattern (23 bp):
AATTGAAGTGTTAAAGTGCTGCA
Found at i:40804831 original size:22 final size:23
Alignment explanation
Indices: 40804805--40804856 Score: 81
Period size: 22 Copynumber: 2.3 Consensus size: 23
40804795 TTTGGTTTAA
40804805 TTTATTTTTATAT-TATATCT-AT
1 TTTATTTTTATATATAT-TCTAAT
40804827 TTTATTTTTATATATATTCTAAT
1 TTTATTTTTATATATATTCTAAT
40804850 TTTATTT
1 TTTATTT
40804857 ATTTATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 16 0.57
23 12 0.43
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTATTTTTATATATATTCTAAT
Found at i:40804837 original size:17 final size:17
Alignment explanation
Indices: 40804817--40804877 Score: 65
Period size: 17 Copynumber: 3.8 Consensus size: 17
40804807 TATTTTTATA
40804817 TTATATCTATTTTATTT
1 TTATATCTATTTTATTT
* * *
40804834 TTATATATATTCTAATT
1 TTATATCTATTTTATTT
40804851 TTAT-T-TA-TTTATTT
1 TTATATCTATTTTATTT
*
40804865 TTATTTCTATTTT
1 TTATATCTATTTT
40804878 TTATACATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
14 9 0.25
15 3 0.08
16 3 0.08
17 21 0.58
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (17 bp):
TTATATCTATTTTATTT
Found at i:40804879 original size:14 final size:14
Alignment explanation
Indices: 40804827--40804870 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 14
40804817 TTATATCTAT
40804827 TTTATTTTTATATATA
1 TTTATTTTTAT-T-TA
*
40804843 TTCTAATTTTATTTA
1 TT-TATTTTTATTTA
40804858 TTTATTTTTATTT
1 TTTATTTTTATTT
40804871 CTATTTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 10 0.40
15 4 0.16
16 3 0.12
17 8 0.32
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTATTTTTATTTA
Found at i:40808000 original size:73 final size:72
Alignment explanation
Indices: 40807886--40808028 Score: 241
Period size: 73 Copynumber: 2.0 Consensus size: 72
40807876 TCTTTTCAAA
* * * *
40807886 CTCAAGTTTTAAACGATCTCAGGAATTAAGAAGAGATCGTGTCCTAACTTACTGGGCATGATCCC
1 CTCAAGTTTTAAACAATCTCAAGAATTAAGAAAAGACCGTGTCCTAACTTACT-GGCATGATCCC
40807951 TTTTTTTT
65 TTTTTTTT
40807959 CTCAAGTTTTAAACAATCTCAAGAATTAAGAAAAGACCGTGTCCTAACTTACTGGCATGATCCCT
1 CTCAAGTTTTAAACAATCTCAAGAATTAAGAAAAGACCGTGTCCTAACTTACTGGCATGATCCCT
40808024 TTTTT
66 TTTTT
40808029 AAATCTGAGA
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
72 17 0.26
73 49 0.74
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.34
Consensus pattern (72 bp):
CTCAAGTTTTAAACAATCTCAAGAATTAAGAAAAGACCGTGTCCTAACTTACTGGCATGATCCCT
TTTTTTT
Found at i:40814757 original size:40 final size:40
Alignment explanation
Indices: 40814699--40814775 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
40814689 TCGAGTGGAT
*
40814699 TATGTTAGATATTTGTCCCTATGAACCTGGAAGTGTTAGA
1 TATGTTAGATATTCGTCCCTATGAACCTGGAAGTGTTAGA
40814739 TATGTTAGATATTCGTCCCTATGAACCTGGAAGTGTT
1 TATGTTAGATATTCGTCCCTATGAACCTGGAAGTGTT
40814776 CTAAATAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (40 bp):
TATGTTAGATATTCGTCCCTATGAACCTGGAAGTGTTAGA
Found at i:40820254 original size:44 final size:44
Alignment explanation
Indices: 40819871--40820435 Score: 263
Period size: 44 Copynumber: 12.6 Consensus size: 44
40819861 AAGATAATAG
* * *
40819871 ATCTTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAGATAGCGA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-CCA
* * * *
40819916 ATCTTATTTTCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAGATTACA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG--AT--A--CCA
* * * * * *
40819966 GATTTTATCTCTCTGAAGTTGCAGTAGAGCAGA-T-CATAT-CAA
1 -ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACCA
* * * * * * *
40820008 ACCTTATCTCCCTAAAGTTGCAATGGAGCAGGTTAAAAATAAATCA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAT--ACCA
* * * *
40820054 ATTTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAAACGGGTTACAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTG--AA---GATACCA
* * * *
40820103 ATCTTATCTCCCTAAAGTTGCAGCGGAGAAGATGGAAGCCATA--A
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG--ATACCA
* * * * *
40820147 ACCTTATCCCCCTGAAGTTACAGTGGGGCAGGTTGAA-ATTA-CA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA-TACCA
* * *
40820190 AGTCTTATCCCCCTGAAGTTGCAATGGAGCAGGTTGAAGATACCA
1 A-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACCA
* * * * *
40820235 ATCTTATCTCTCTGAAGTTGCGGTGGAGCAAATTGAAGTTACTA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACCA
* * * * ** * ***
40820279 GTCCTATCTCTCTGAAGTTGCAGAGGAGTGGATT-AAAATGATGG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAT-ACCA
* * * * * *
40820323 ATCTTATTTCTCTAAAGTTGCAGTAGAGCAGA-T---CATATCA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACCA
* * * * * *
40820363 AACATTATCTTCTTGAAGTTGCGGTGGAGCAGATTGAAGTTACTA
1 ATC-TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACCA
* * *
40820408 GTCCTATCTCCCTGAAGTTGCAGAGGAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAG
40820436 TGGATCAAAA
Statistics
Matches: 381, Mismatches: 110, Indels: 59
0.69 0.20 0.11
Matches are distributed among these distances:
40 4 0.01
41 50 0.13
42 5 0.01
43 9 0.02
44 171 0.45
45 41 0.11
46 31 0.08
47 6 0.02
48 2 0.01
49 33 0.09
50 2 0.01
51 27 0.07
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACCA
Found at i:40820399 original size:129 final size:129
Alignment explanation
Indices: 40820238--40820500 Score: 431
Period size: 129 Copynumber: 2.0 Consensus size: 129
40820228 GATACCAATC
*
40820238 TTATCTCTCTGAAGTTGCGGTGGAGCAAATTGAAGTTACTAGTCCTATCTCTCTGAAGTTGCAGA
1 TTATCTCTCTGAAGTTGCGGTGGAGCAAATTGAAGTTACTAGTCCTATCTCCCTGAAGTTGCAGA
* *
40820303 GGAGTGGATTAAAATGATGGATCTTATTTCTCTAAAGTTGCA-GTAGAGCAGATCATATCAAACA
66 GGAGTGGATCAAAATGATGGATCTTATCTCTCTAAAGTTG-AGGTAGAGCAGATCATATCAAACA
*
40820367 TTATCT-TCTTGAAGTTGCGGTGGAGCAGATTGAAGTTACTAGTCCTATCTCCCTGAAGTTGCAG
1 TTATCTCTC-TGAAGTTGCGGTGGAGCAAATTGAAGTTACTAGTCCTATCTCCCTGAAGTTGCAG
* * *
40820431 AGGAGTGGATCAAAATTATGGATCTTATCTCTCTGAAGTTGAGGTAGAGCAGATCATATCAAACC
65 AGGAGTGGATCAAAATGATGGATCTTATCTCTCTAAAGTTGAGGTAGAGCAGATCATATCAAACA
40820496 TTATC
1 TTATC
40820501 CCCCAGAAGT
Statistics
Matches: 125, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
128 3 0.02
129 122 0.98
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (129 bp):
TTATCTCTCTGAAGTTGCGGTGGAGCAAATTGAAGTTACTAGTCCTATCTCCCTGAAGTTGCAGA
GGAGTGGATCAAAATGATGGATCTTATCTCTCTAAAGTTGAGGTAGAGCAGATCATATCAAACA
Found at i:40820552 original size:129 final size:129
Alignment explanation
Indices: 40820282--40820555 Score: 311
Period size: 129 Copynumber: 2.1 Consensus size: 129
40820272 GTTACTAGTC
* *
40820282 CTATCTCTCTGAAGTTGCAGAGGAGTGGATTAAAATGATGGATCTTATTTCTCTAAAGTTGCAGT
1 CTATCTCTCTGAAGTTGCAGAGGAGTGGATCAAAATGATGGATCTTATCTCTCTAAAGTTGCAGT
** ** * * * *** * * *
40820347 AGAGCAGATCATATCAAACATTATCTTCTTGAAGTTGCGGTGGAGCAGATTGAAGTTACTAGTC
66 AGAGCAGATCATATCAAACATTATCCCCCAGAAGTTGCAGCGGAGCAGATTAAAAACAATAATA
* * *
40820411 CTATCTCCCTGAAGTTGCAGAGGAGTGGATCAAAATTATGGATCTTATCTCTCTGAAGTTG-AGG
1 CTATCTCTCTGAAGTTGCAGAGGAGTGGATCAAAATGATGGATCTTATCTCTCTAAAGTTGCA-G
* * *
40820475 TAGAGCAGATCATATCAAACCTTATCCCCCAGAAGTTGTAGCGGAGCGGA-TAAAAACAATGAAT
65 TAGAGCAGATCATATCAAACATTATCCCCCAGAAGTTGCAGCGGAGCAGATTAAAAACAAT-AAT
40820539 A
129 A
40820540 CTATAC-CTCTGAAGTT
1 CTAT-CTCTCTGAAGTT
40820556 ACAGTAGGTT
Statistics
Matches: 120, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
128 6 0.05
129 113 0.94
130 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (129 bp):
CTATCTCTCTGAAGTTGCAGAGGAGTGGATCAAAATGATGGATCTTATCTCTCTAAAGTTGCAGT
AGAGCAGATCATATCAAACATTATCCCCCAGAAGTTGCAGCGGAGCAGATTAAAAACAATAATA
Found at i:40822241 original size:2 final size:2
Alignment explanation
Indices: 40822236--40822314 Score: 56
Period size: 2 Copynumber: 40.5 Consensus size: 2
40822226 TTTTATAATT
* * * *
40822236 TA TA TA TA TA CA TA CT- TA TA TA TA TA TT TA TT TA TA TC T- TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
40822277 TA -A TT TA TA TA TA TA TA TA TA TA TG TA CA TA AA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40822315 CTTTTTGCAT
Statistics
Matches: 58, Mismatches: 15, Indels: 8
0.72 0.19 0.10
Matches are distributed among these distances:
1 3 0.05
2 54 0.93
3 1 0.02
ACGTcount: A:0.43, C:0.05, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40822778 original size:73 final size:73
Alignment explanation
Indices: 40822697--40822840 Score: 270
Period size: 73 Copynumber: 2.0 Consensus size: 73
40822687 TCTTTTCAAA
*
40822697 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAGAGATCGTATCCTAACTTACTGGGCATGATCCC
1 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTATCCTAACTTACTGGGCATGATCCC
40822762 TTTTTTTT
66 TTTTTTTT
*
40822770 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCC
1 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTATCCTAACTTACTGGGCATGATCCC
40822835 TTTTTT
66 TTTTTT
40822841 AAATCTGAGA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (73 bp):
CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTATCCTAACTTACTGGGCATGATCCC
TTTTTTTT
Found at i:40823905 original size:22 final size:19
Alignment explanation
Indices: 40823865--40823908 Score: 52
Period size: 22 Copynumber: 2.2 Consensus size: 19
40823855 TGTTGTTTTA
*
40823865 TTGCTATTTTTCCATTGTT
1 TTGCTATTTTTCCACTGTT
40823884 TTGCTATTGCTTTCCCACTGTT
1 TTGCTATT--TTT-CCACTGTT
40823906 TTG
1 TTG
40823909 ATACCATTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 8 0.38
21 3 0.14
22 10 0.48
ACGTcount: A:0.09, C:0.20, G:0.14, T:0.57
Consensus pattern (19 bp):
TTGCTATTTTTCCACTGTT
Found at i:40825665 original size:41 final size:40
Alignment explanation
Indices: 40825620--40825787 Score: 161
Period size: 40 Copynumber: 4.2 Consensus size: 40
40825610 AAATAGGGTT
* * *
40825620 TTAGCGGCG-TTTGGACAAAAAACGCCACTAAAAATCGAGCA
1 TTAGCGGCGCTTT-GAC-AAAAACGCCGCTAAAGATCGAGTA
*
40825661 TTAGCGGCGCTTT-ACGTAAAACGCCGCTAAAGATCGAGTA
1 TTAGCGGCGCTTTGAC-AAAAACGCCGCTAAAGATCGAGTA
40825701 TTAGCGGCGCATTTTG--AAAAACGCCGCTAAAGATCGAGTA
1 TTAGCGGCGC--TTTGACAAAAACGCCGCTAAAGATCGAGTA
* * *
40825741 TTAGCGGTGCATTTTG--AAAAACGCCGCTAAAAAT-AAGTA
1 TTAGCGGCGC--TTTGACAAAAACGCCGCTAAAGATCGAGTA
40825780 TTAGCGGC
1 TTAGCGGC
40825788 ATTTTCCAAG
Statistics
Matches: 113, Mismatches: 10, Indels: 10
0.85 0.08 0.08
Matches are distributed among these distances:
39 11 0.10
40 87 0.77
41 9 0.08
42 6 0.05
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (40 bp):
TTAGCGGCGCTTTGACAAAAACGCCGCTAAAGATCGAGTA
Found at i:40825806 original size:39 final size:40
Alignment explanation
Indices: 40825637--40825787 Score: 207
Period size: 40 Copynumber: 3.8 Consensus size: 40
40825627 CGTTTGGACA
* * *
40825637 AAAAACGCCACTAAAAATCGAGCATTAGCGGCGC-TTTACG
1 AAAAACGCCGCTAAAAATCGAGTATTAGCGGCGCATTT-TG
* *
40825677 TAAAACGCCGCTAAAGATCGAGTATTAGCGGCGCATTTTG
1 AAAAACGCCGCTAAAAATCGAGTATTAGCGGCGCATTTTG
* *
40825717 AAAAACGCCGCTAAAGATCGAGTATTAGCGGTGCATTTTG
1 AAAAACGCCGCTAAAAATCGAGTATTAGCGGCGCATTTTG
*
40825757 AAAAACGCCGCTAAAAAT-AAGTATTAGCGGC
1 AAAAACGCCGCTAAAAATCGAGTATTAGCGGC
40825788 ATTTTCCAAG
Statistics
Matches: 100, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
39 11 0.11
40 86 0.86
41 3 0.03
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.21
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATCGAGTATTAGCGGCGCATTTTG
Found at i:40825812 original size:39 final size:39
Alignment explanation
Indices: 40825678--40825812 Score: 121
Period size: 40 Copynumber: 3.4 Consensus size: 39
40825668 CGCTTTACGT
* * * * *
40825678 AAAACGCCGCTAAAGATCGAGTATTAGCGGCGCATTTTGA
1 AAAACGCCGCAAAAAAT-AAGTATTAGCGGTGCATTTTCA
* * * *
40825718 AAAACGCCGCTAAAGATCGAGTATTAGCGGTGCATTTTGA
1 AAAACGCCGCAAAAAAT-AAGTATTAGCGGTGCATTTTCA
*
40825758 AAAACGCCGCTAAAAATAAGTATTAGC-G-GCATTTTCCA
1 AAAACGCCGCAAAAAATAAGTATTAGCGGTGCATTTT-CA
*
40825796 AGAAGCGCCGCAAAAAA
1 A-AAACGCCGCAAAAAA
40825813 AGGAAAGCGG
Statistics
Matches: 87, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
37 7 0.08
38 3 0.03
39 22 0.25
40 55 0.63
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.21
Consensus pattern (39 bp):
AAAACGCCGCAAAAAATAAGTATTAGCGGTGCATTTTCA
Found at i:40825910 original size:41 final size:41
Alignment explanation
Indices: 40825853--40826021 Score: 239
Period size: 41 Copynumber: 4.1 Consensus size: 41
40825843 TTTTGAGGCA
*
40825853 TTTAGCGGCGTTTTTGGGAAAGTGCCGCTAATGCTCGGGGC
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCGGGGC
40825894 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCGGGGC
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCGGGGC
* ** *
40825935 TTTAGCTGCGTTTTTGGGAAAGCGCCGCTAATGCTCAAGGA
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCGGGGC
** * * * *
40825976 TTTAGCGGCGTTTTTTAGAATGTGCCGCTAATGCTCGTGCC
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCGGGGC
40826017 TTTAG
1 TTTAG
40826022 TTCAAAAACG
Statistics
Matches: 114, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 114 1.00
ACGTcount: A:0.17, C:0.20, G:0.32, T:0.31
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCGGGGC
Found at i:40827713 original size:109 final size:109
Alignment explanation
Indices: 40827545--40827947 Score: 664
Period size: 109 Copynumber: 3.7 Consensus size: 109
40827535 GTCAATCGAG
* * * *
40827545 AAATCGAAACCCAGCACATTAGGGCACG-TTCCTCGAATTTCCAAACGCTAAACATTGCCTTATT
1 AAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
* *
40827609 TTGAAATTTTTAAAAGGATATTTAGCCATTTGGTTGAATGAGAA
66 TTAAAATTTTTAAAAGGATATTTAGCCATTTGGTTGAACGAGAA
40827653 AAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
1 AAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
* * *
40827718 TTAAAAATTTTAAAAGGACATTTAACCATTTGGTTGAACGAGAA
66 TTAAAATTTTTAAAAGGATATTTAGCCATTTGGTTGAACGAGAA
* *
40827762 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTTCAAACGCAAAACATTGCCTTATT
1 AAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
*
40827827 TTAAAATTTTTAAAAGGATATTAAGCCATTTGGTTGAACGAGAA
66 TTAAAATTTTTAAAAGGATATTTAGCCATTTGGTTGAACGAGAA
*
40827871 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCCAAACGCAAAACATTGCCTTAT
1 AAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTT-CCAAACGCAAAACATTGCCTTAT
*
40827936 TTGAAAATTTTT
65 TTTAAAATTTTT
40827948 CCTTTTTTGA
Statistics
Matches: 276, Mismatches: 17, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
108 26 0.09
109 217 0.79
110 33 0.12
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.30
Consensus pattern (109 bp):
AAATCGACACCCAGCACCTTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
TTAAAATTTTTAAAAGGATATTTAGCCATTTGGTTGAACGAGAA
Found at i:40828696 original size:21 final size:19
Alignment explanation
Indices: 40828595--40828700 Score: 99
Period size: 21 Copynumber: 5.4 Consensus size: 19
40828585 AAATGGAAAC
*
40828595 ATAATGATAATAATAACATAA
1 ATAATAATAATAAT-AC-TAA
* *
40828616 ATATTAATAATAATAACAAA
1 ATAATAATAATAAT-ACTAA
*
40828636 GATAATAATAATAATAAT-A
1 -ATAATAATAATAATACTAA
*
40828655 ATAATAATAATAATAAT-A
1 ATAATAATAATAATACTAA
40828673 ATAATAATAATAATTAGCTAA
1 ATAATAATAATAA-TA-CTAA
40828694 ATAATAA
1 ATAATAA
40828701 AGGAAACTAA
Statistics
Matches: 74, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
18 31 0.42
19 3 0.04
20 4 0.05
21 36 0.49
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (19 bp):
ATAATAATAATAATACTAA
Found at i:40828700 original size:3 final size:3
Alignment explanation
Indices: 40828595--40828686 Score: 116
Period size: 3 Copynumber: 30.7 Consensus size: 3
40828585 AAATGGAAAC
* * * *
40828595 ATA ATG ATA ATA ATA A-C ATAA ATA TTA ATA ATA ATA ACA A-A GATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA -ATA
40828640 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
40828687 TAGCTAAATA
Statistics
Matches: 78, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
2 2 0.03
3 73 0.94
4 3 0.04
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:40829083 original size:12 final size:12
Alignment explanation
Indices: 40829053--40829088 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
40829043 ACTGCTTTTA
* *
40829053 ATATATATATAT
1 ATATATGTATGT
40829065 ATATATGTATGT
1 ATATATGTATGT
40829077 ATATATGTATGT
1 ATATATGTATGT
40829089 GAAAAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (12 bp):
ATATATGTATGT
Found at i:40834555 original size:115 final size:115
Alignment explanation
Indices: 40834426--40834637 Score: 336
Period size: 114 Copynumber: 1.8 Consensus size: 115
40834416 ATAAAAATAA
* * * *
40834426 ATATTATTTTATTAAAATAATTTTTTTTAAAGGTTATGTTTTTAGTGGCGTTTTTGCTAGAAGCG
1 ATATTATTTGATTAAAATAA-TTTTTTTAAAGGTTATGCTTTTAGCGGCGTTTTTGCGAGAAGCG
* *
40834491 CCGCTAAA-GTTTGTTCTTTAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAG
65 ACGCTAAAGGTTTGCTCTTTAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAG
*
40834541 ATATTATTTGATTAAAATAATTTTTTTAAAGGTTATGCTTTTAGCGGCGTTTTTGCGAGAAGCTA
1 ATATTATTTGATTAAAATAATTTTTTTAAAGGTTATGCTTTTAGCGGCGTTTTTGCGAGAAGCGA
*
40834606 CGCTAAAGGTTTGCTCTTTAGCGGTGTTTGTA
66 CGCTAAAGGTTTGCTCTTTAGCGGCGTTTGTA
40834638 ATATGAAGGA
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
114 47 0.53
115 41 0.47
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.42
Consensus pattern (115 bp):
ATATTATTTGATTAAAATAATTTTTTTAAAGGTTATGCTTTTAGCGGCGTTTTTGCGAGAAGCGA
CGCTAAAGGTTTGCTCTTTAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAG
Found at i:40834991 original size:26 final size:26
Alignment explanation
Indices: 40834948--40835036 Score: 105
Period size: 25 Copynumber: 3.5 Consensus size: 26
40834938 AAACTTAGAG
*
40834948 TAATATATATAA-AC-TAAAACTGTT
1 TAATATAAATAATACATAAAACTGTT
* *
40834972 TAATATAAATAATACATAAAAATCTT
1 TAATATAAATAATACATAAAACTGTT
*
40834998 TAAAATAAATAATA-ATAAAACTGTT
1 TAATATAAATAATACATAAAACTGTT
40835023 TAA-ATGAAATAATA
1 TAATAT-AAATAATA
40835037 TAAAAAAAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
24 13 0.23
25 22 0.39
26 21 0.38
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.34
Consensus pattern (26 bp):
TAATATAAATAATACATAAAACTGTT
Found at i:40835024 original size:25 final size:25
Alignment explanation
Indices: 40834962--40835041 Score: 101
Period size: 26 Copynumber: 3.2 Consensus size: 25
40834952 ATATATAAAC
*
40834962 TAAAACTGTTTAATATAAATAATACA
1 TAAAACTGTTTAAAATAAATAATA-A
* *
40834988 TAAAAATCTTTAAAATAAATAATAA
1 TAAAACTGTTTAAAATAAATAATAA
40835013 TAAAACTGTTT-AAATGAAATAAT-A
1 TAAAACTGTTTAAAAT-AAATAATAA
40835037 TAAAA
1 TAAAA
40835042 AAAATCTAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
24 10 0.21
25 17 0.35
26 21 0.44
ACGTcount: A:0.59, C:0.05, G:0.04, T:0.33
Consensus pattern (25 bp):
TAAAACTGTTTAAAATAAATAATAA
Found at i:40835087 original size:17 final size:16
Alignment explanation
Indices: 40835065--40835115 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 16
40835055 TTTAAAAAGT
40835065 AAATAAAAATGAAATCA
1 AAATAAAAATGAAA-CA
*
40835082 AAATAAACATGAAA-A
1 AAATAAAAATGAAACA
*
40835097 CTAATAAAAAT-AAACA
1 -AAATAAAAATGAAACA
40835113 AAA
1 AAA
40835116 GCAAATTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 6 0.21
16 9 0.32
17 13 0.46
ACGTcount: A:0.73, C:0.08, G:0.04, T:0.16
Consensus pattern (16 bp):
AAATAAAAATGAAACA
Found at i:40835846 original size:26 final size:26
Alignment explanation
Indices: 40835817--40835869 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
40835807 ATAGCCATAT
*
40835817 TACAACCATTTATTTTCTATTCTTTG
1 TACAACCATTGATTTTCTATTCTTTG
40835843 TACAACCATTGATTTTCTATTCTTTG
1 TACAACCATTGATTTTCTATTCTTTG
40835869 T
1 T
40835870 CTTTTGTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.06, T:0.53
Consensus pattern (26 bp):
TACAACCATTGATTTTCTATTCTTTG
Found at i:40836435 original size:44 final size:44
Alignment explanation
Indices: 40836337--40836435 Score: 101
Period size: 44 Copynumber: 2.2 Consensus size: 44
40836327 TACATTGCGT
* * * *
40836337 CTTGTTGTTTCGATCCACTCTACTACAACTTCAGAGAGATACAA
1 CTTGTAGTTTCAATCCACTCTACTACAACTTCAGAGAGACAAAA
* * *
40836381 CTCGTAGTTTCAATCCACTCTGCTGCAACTTCAG-GAGGACAAAA
1 CTTGTAGTTTCAATCCACTCTACTACAACTTCAGAGA-GACAAAA
* *
40836425 TTTGTGGTTTC
1 CTTGTAGTTTC
40836436 TTTTGTCTAC
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
43 2 0.05
44 42 0.95
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.32
Consensus pattern (44 bp):
CTTGTAGTTTCAATCCACTCTACTACAACTTCAGAGAGACAAAA
Found at i:40836543 original size:44 final size:43
Alignment explanation
Indices: 40836445--40836674 Score: 166
Period size: 44 Copynumber: 5.4 Consensus size: 43
40836435 CTTTTGTCTA
* * * ***
40836445 CTCCACTGCAACTTCAGGGCGATAAGA-CTG-GATGCGATCTG
1 CTCCACTGCAACTTCAGAGAGATAAGATCTGTGTTTTAATCTG
* *
40836486 CTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCG
1 CTCCACTGCAACTTCAGAGAGATAAGATCTGT-GTTTTAATCTG
* * * * * **
40836530 CTCCATTGCAACTTCAGGGAGATAGGAT-TAATTTCTTTTGTCTG
1 CTCCACTGCAACTTCAGAGAGATAAGATCT-GTGT-TTTAATCTG
* ** * * **
40836574 CTCCACTACTGCTT-AGGGAGATAAGA-CT-TGATGGAATCTG
1 CTCCACTGCAACTTCAGAGAGATAAGATCTGTGTTTTAATCTG
* *
40836614 CTCTAGTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCTG
1 CTCCACTGCAACTTCAGAGAGATAAGATCTGT-GTTTTAATCTG
40836658 CTCCACTGCAACTTCAG
1 CTCCACTGCAACTTCAG
40836675 GAAGATAGGA
Statistics
Matches: 140, Mismatches: 39, Indels: 17
0.71 0.20 0.09
Matches are distributed among these distances:
40 14 0.10
41 36 0.26
42 5 0.04
43 15 0.11
44 70 0.50
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (43 bp):
CTCCACTGCAACTTCAGAGAGATAAGATCTGTGTTTTAATCTG
Found at i:40836638 original size:128 final size:129
Alignment explanation
Indices: 40836432--40836686 Score: 397
Period size: 128 Copynumber: 2.0 Consensus size: 129
40836422 AAATTTGTGG
* *
40836432 TTTCTTTTGTCTACTCCACTGCAACTTCAGGGCGATAAGACTGGATGCGATCTGCTCTACTGCAA
1 TTTCTTTTGTCTACTCCACTACAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAA
* *
40836497 CTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCATTGCAACTTCAGGGAGATAGGATTAA
66 CTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGAAGATAGGATTAA
* ** * *
40836561 TTTCTTTTGTCTGCTCCACTACTGCTT-AGGGAGATAAGACTTGATG-GAATCTGCTCTAGTGCA
1 TTTCTTTTGTCTACTCCACTACAACTTCAGGGAGATAAGACTGGATGCG-ATCTGCTCTACTGCA
*
40836624 ACTTCAGAGAGATAAGATCTGTGGTTTTAATCTGCTCCACTGCAACTTCAGGAAGATAGGATT
65 ACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGAAGATAGGATT
40836687 CGTCGTCTTC
Statistics
Matches: 115, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
127 1 0.01
128 91 0.79
129 23 0.20
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.32
Consensus pattern (129 bp):
TTTCTTTTGTCTACTCCACTACAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAA
CTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGAAGATAGGATTAA
Found at i:40836747 original size:50 final size:50
Alignment explanation
Indices: 40836704--40837199 Score: 172
Period size: 50 Copynumber: 10.0 Consensus size: 50
40836694 TTCATTTTAA
* *
40836704 TTAACTACAATGTCGGGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTT
1 TTAACTACAATATCGGGGAAGCAAGATTCACCGTTGCGGCTTCAATCTTT
* * * ** **
40836754 TTAATTGCAATATCGGGGAAGCAAGATTCACTGTTGTAGCTTCAATCTGC
1 TTAACTACAATATCGGGGAAGCAAGATTCACCGTTGCGGCTTCAATCTTT
** * **** * * * *
40836804 TCCACTGCACCGCCAGGGAAGTAAGATTCA-CTTTCGTGGCTTCAATCTTT
1 TTAACTACAATATCGGGGAAGCAAGATTCACCGTT-GCGGCTTCAATCTTT
* * * * * ** **
40836854 TAAATTACAATGTCGAGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGC
1 TTAACTACAATATCGGGGAAGCAAGATTCACCGTTGCGGCTTCAATCTTT
** * **** ** * *** *
40836904 TCCACTGCACCGCCAAGGAAGTAAGATTCGTAGTTGTGGCTTCAATCTTT
1 TTAACTACAATATCGGGGAAGCAAGATTCACCGTTGCGGCTTCAATCTTT
* * * * * ** *
40836954 TTAATTGCAATGTCGGGGAA-CAAGATTCGCCATTGTAGCTTCAATCTGT
1 TTAACTACAATATCGGGGAAGCAAGATTCACCGTTGCGGCTTCAATCTTT
** * ** * * *
40837003 TCCACTGC-ATCGCCAGGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTT
1 TTAACTACAAT-ATCGGGGAAGCAAGATTCACCGTTGCGGCTTCAATCTTT
* * * * * * ** *
40837053 TCAATTGCAATGTCGGGGAA-CAAGATTCGCCATTGTAGCTTCAATCTGT
1 TTAACTACAATATCGGGGAAGCAAGATTCACCGTTGCGGCTTCAATCTTT
** * ** * * * *
40837102 TCCACTGCACCACCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTT
1 TTAACTACAATATCGGGGAAGCAAGATTCACCGTTGCGGCTTCAATCTTT
* * * * * * * **
40837152 TAAATTACAATGTCCGTGAAGTAAGATTCACCGTCGTAGCTTCAATCT
1 TTAACTACAATATCGGGGAAGCAAGATTCACCGTTGCGGCTTCAATCT
40837200 GCTCCACTGT
Statistics
Matches: 329, Mismatches: 111, Indels: 12
0.73 0.25 0.03
Matches are distributed among these distances:
48 2 0.01
49 74 0.22
50 249 0.76
51 4 0.01
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (50 bp):
TTAACTACAATATCGGGGAAGCAAGATTCACCGTTGCGGCTTCAATCTTT
Found at i:40837023 original size:99 final size:100
Alignment explanation
Indices: 40836719--40837208 Score: 689
Period size: 99 Copynumber: 4.9 Consensus size: 100
40836709 TACAATGTCG
* * *
40836719 GGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATATCGGGGAAGCAAGATTCA
1 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGCAAGATTCA
*
40836784 CTGTTGTAGCTTCAATCTGCTCCACTGCACCGCCA
66 CCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCA
* * *
40836819 GGGAAGTAAGATTCA-CTTTCGTGGCTTCAATCTTTTAAATTACAATGTCGAGGAAGCAAGATTC
1 GGGAAGTAAGATTCACCGTT-GTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGCAAGATTC
*
40836883 ACCGTCGTAGCTTCAATCTGCTCCACTGCACCGCCA
65 ACCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCA
* *** * *
40836919 AGGAAGTAAGATTCGTAGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAA-CAAGATTCG
1 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGCAAGATTCA
* * *
40836983 CCATTGTAGCTTCAATCTGTTCCACTGCATCGCCA
66 CCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCA
* * * *
40837018 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTCAATTGCAATGTCGGGGAA-CAAGATTCG
1 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGCAAGATTCA
* * *
40837082 CCATTGTAGCTTCAATCTGTTCCACTGCACCACCA
66 CCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCA
* * * *
40837117 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTAAATTACAATGTCCGTGAAGTAAGATTCA
1 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGCAAGATTCA
*
40837182 CCGTCGTAGCTTCAATCTGCTCCACTG
66 CCGTTGTAGCTTCAATCTGCTCCACTG
40837209 TAATGCCAAA
Statistics
Matches: 349, Mismatches: 38, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
99 183 0.52
100 164 0.47
101 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (100 bp):
GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGCAAGATTCA
CCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCA
Found at i:40843914 original size:4 final size:4
Alignment explanation
Indices: 40843905--40843929 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
40843895 TCTTATCATG
40843905 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
40843930 TTTATAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:40844040 original size:26 final size:25
Alignment explanation
Indices: 40843995--40844085 Score: 103
Period size: 26 Copynumber: 3.4 Consensus size: 25
40843985 GGAAACTTAG
40843995 AATAATATATATACACTAAAACTGTTTA
1 AATAA-ATA-ATACA-TAAAACTGTTTA
* *
40844023 ATATAAATAATACATAAAAATCTTTAA
1 A-ATAAATAATACATAAAACTGTTT-A
40844050 AATAAATAATA-ATAAAACTGTTTA
1 AATAAATAATACATAAAACTGTTTA
40844074 AATGAAATAATA
1 AAT-AAATAATA
40844086 TAAAAAAATC
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
24 4 0.07
25 18 0.32
26 19 0.34
27 7 0.12
28 4 0.07
29 4 0.07
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (25 bp):
AATAAATAATACATAAAACTGTTTA
Found at i:40844091 original size:25 final size:24
Alignment explanation
Indices: 40844012--40844091 Score: 83
Period size: 25 Copynumber: 3.2 Consensus size: 24
40844002 TATATACACT
40844012 AAAACTGTTTAATATAAATAATACATA
1 AAAACTGTTTAA-ATAAATAAT--ATA
*
40844039 AAAATCT-TTAAAATAAATAATA-A
1 AAAA-CTGTTTAAATAAATAATATA
40844062 TAAAACTGTTTAAATGAAATAATATA
1 -AAAACTGTTTAAAT-AAATAATATA
40844088 AAAA
1 AAAA
40844092 AATCTAAACA
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
23 3 0.07
24 11 0.24
25 12 0.26
26 10 0.22
27 8 0.17
28 2 0.04
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.31
Consensus pattern (24 bp):
AAAACTGTTTAAATAAATAATATA
Found at i:40848196 original size:21 final size:21
Alignment explanation
Indices: 40848170--40848212 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
40848160 CTGAATGTCA
40848170 AGATCATTGTAGTCGAACTTT
1 AGATCATTGTAGTCGAACTTT
40848191 AGATCATTGTAGTCGAACTTT
1 AGATCATTGTAGTCGAACTTT
40848212 A
1 A
40848213 ATTAAAGTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (21 bp):
AGATCATTGTAGTCGAACTTT
Found at i:40848772 original size:30 final size:30
Alignment explanation
Indices: 40848736--40848795 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
40848726 TTGCATAAAT
40848736 GACCCAATATGTTTATACTTCTTCTCCATC
1 GACCCAATATGTTTATACTTCTTCTCCATC
40848766 GACCCAATATGTTTATACTTCTTCTCCATC
1 GACCCAATATGTTTATACTTCTTCTCCATC
40848796 CCAACAATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.30, G:0.07, T:0.40
Consensus pattern (30 bp):
GACCCAATATGTTTATACTTCTTCTCCATC
Found at i:40849578 original size:3 final size:3
Alignment explanation
Indices: 40849572--40849656 Score: 152
Period size: 3 Copynumber: 28.3 Consensus size: 3
40849562 CTCCTCCTCC
40849572 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* *
40849620 TCT TCT TCT TCT TCT ACT TCT TCT TCT TCT TTT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
40849657 TTATTGCCCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:40850802 original size:20 final size:20
Alignment explanation
Indices: 40850777--40850817 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
40850767 CTTCAAAACC
* *
40850777 ACACCTGAATTAAATTTAAT
1 ACACCTGAACTAAATTCAAT
40850797 ACACCTGAACTAAATTCAAT
1 ACACCTGAACTAAATTCAAT
40850817 A
1 A
40850818 ATATGAGGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.20, G:0.05, T:0.29
Consensus pattern (20 bp):
ACACCTGAACTAAATTCAAT
Found at i:40852133 original size:25 final size:26
Alignment explanation
Indices: 40852091--40852145 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
40852081 TGCATCACAA
*
40852091 TATTTTTATAAAGATTTT-AATTAAT
1 TATTTTTATAAACATTTTAAATTAAT
* * *
40852116 TATTTTTATAATCCTTTTAAATTATT
1 TATTTTTATAAACATTTTAAATTAAT
40852142 TATT
1 TATT
40852146 ATATCAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 15 0.60
26 10 0.40
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (26 bp):
TATTTTTATAAACATTTTAAATTAAT
Found at i:40861588 original size:16 final size:16
Alignment explanation
Indices: 40861567--40861606 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
40861557 TAATTTGATG
*
40861567 ATTTTACTAACAATTA
1 ATTTTAATAACAATTA
*
40861583 ATTTTAATAATAATTA
1 ATTTTAATAACAATTA
*
40861599 GTTTTAAT
1 ATTTTAAT
40861607 TTTATTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (16 bp):
ATTTTAATAACAATTA
Found at i:40861607 original size:22 final size:23
Alignment explanation
Indices: 40861580--40861641 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
40861570 TTACTAACAA
* *
40861580 TTAATTTTAATAATAAT-TAGTT
1 TTAATTTTAATAAAAATATAATT
*
40861602 TTAATTTTATTAAAAATATAATT
1 TTAATTTTAATAAAAATATAATT
40861625 TTAATTTTAATTAAAAA
1 TTAATTTTAA-TAAAAA
40861642 CGGGCTGGGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 15 0.44
23 13 0.38
24 6 0.18
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAATTTTAATAAAAATATAATT
Found at i:40862829 original size:5 final size:5
Alignment explanation
Indices: 40862819--40862844 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
40862809 AATTAAAAAA
40862819 TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
40862845 TAATCATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:40863470 original size:70 final size:71
Alignment explanation
Indices: 40863390--40863547 Score: 166
Period size: 69 Copynumber: 2.3 Consensus size: 71
40863380 AATTGTAAAA
* *
40863390 ATTTCATTTAAGATTTTAATTA-GA-GTTTTAAAATAGAATATTAGAATTTTTACA-TTAGTTAA
1 ATTTTATTTAAGATTTTAATTACCAGGTTTTAAAATAG-AT-TTAGAATTTTTACATTTAG-TAA
*
40863452 -AGTTTAGG
63 GAGTTTAAG
* * * * *
40863460 ATTTTATTTAA-ATTTT-TTTACCAGGTTTTAAATTAGATTTAGGATTTTTATATTTAGTAAGAT
1 ATTTTATTTAAGATTTTAATTACCAGGTTTTAAAATAGATTTAGAATTTTTACATTTAGTAAGAG
40863523 TTTAAG
66 TTTAAG
*
40863529 ATTTTATTTGAGATTTTAA
1 ATTTTATTTAAGATTTTAA
40863548 ACTTCGCCTT
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
68 18 0.25
69 28 0.39
70 26 0.36
ACGTcount: A:0.35, C:0.03, G:0.12, T:0.51
Consensus pattern (71 bp):
ATTTTATTTAAGATTTTAATTACCAGGTTTTAAAATAGATTTAGAATTTTTACATTTAGTAAGAG
TTTAAG
Found at i:40865087 original size:15 final size:15
Alignment explanation
Indices: 40865064--40865093 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40865054 AGCCAATAAA
*
40865064 TAAATAAATAAATAC
1 TAAACAAATAAATAC
40865079 TAAACAAATAAATAC
1 TAAACAAATAAATAC
40865094 ATACTAATGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (15 bp):
TAAACAAATAAATAC
Found at i:40865106 original size:19 final size:19
Alignment explanation
Indices: 40865060--40865100 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
40865050 AACAAGCCAA
*
40865060 TAAATAAATAAATAAATAC
1 TAAACAAATAAATAAATAC
*
40865079 TAAACAAATAAATACATAC
1 TAAACAAATAAATAAATAC
40865098 TAA
1 TAA
40865101 TGAAATGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.66, C:0.10, G:0.00, T:0.24
Consensus pattern (19 bp):
TAAACAAATAAATAAATAC
Found at i:40867531 original size:15 final size:15
Alignment explanation
Indices: 40867508--40867537 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40867498 AGCCAATAAA
*
40867508 TAAATAAATAAATAC
1 TAAACAAATAAATAC
40867523 TAAACAAATAAATAC
1 TAAACAAATAAATAC
40867538 ATACTAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (15 bp):
TAAACAAATAAATAC
Found at i:40867531 original size:19 final size:19
Alignment explanation
Indices: 40867504--40867544 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
40867494 AACAAGCCAA
*
40867504 TAAATAAATAAATAAATAC
1 TAAACAAATAAATAAATAC
*
40867523 TAAACAAATAAATACATAC
1 TAAACAAATAAATAAATAC
40867542 TAA
1 TAA
40867545 TATAAGTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.66, C:0.10, G:0.00, T:0.24
Consensus pattern (19 bp):
TAAACAAATAAATAAATAC
Found at i:40868417 original size:20 final size:19
Alignment explanation
Indices: 40868367--40868419 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
40868357 TTGTATATAT
* *
40868367 AAAAAGATAAAAAGAATGA
1 AAAAAGAAAAAAAGAATCA
40868386 AAAAA-ATCAAAAAATGAATCA
1 AAAAAGA--AAAAAA-GAATCA
40868407 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
40868420 ATCACCTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
18 1 0.04
19 5 0.18
20 11 0.39
21 10 0.36
22 1 0.04
ACGTcount: A:0.77, C:0.04, G:0.09, T:0.09
Consensus pattern (19 bp):
AAAAAGAAAAAAAGAATCA
Found at i:40872050 original size:17 final size:17
Alignment explanation
Indices: 40871999--40872050 Score: 86
Period size: 17 Copynumber: 3.0 Consensus size: 17
40871989 GGATCCAATG
*
40871999 GAAACACGAGAATTTTT
1 GAAACACGAAAATTTTT
40872016 GAAAACACGAAAATTTTT
1 G-AAACACGAAAATTTTT
40872034 GAAACACGAAAATTTTT
1 GAAACACGAAAATTTTT
40872051 ATAAATTACA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
17 17 0.52
18 16 0.48
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.29
Consensus pattern (17 bp):
GAAACACGAAAATTTTT
Found at i:40872460 original size:9 final size:8
Alignment explanation
Indices: 40872446--40872492 Score: 51
Period size: 8 Copynumber: 5.5 Consensus size: 8
40872436 AGAATGGGTC
40872446 TTTTTCTCT
1 TTTTTCT-T
40872455 TTTTTCTT
1 TTTTTCTT
40872463 TTTTTCTT
1 TTTTTCTT
40872471 CCTTTCTTCTT
1 --TTT-TTCTT
40872482 TTTTT-TT
1 TTTTTCTT
40872489 TTTT
1 TTTT
40872493 GCCTGGGCTG
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
7 6 0.17
8 11 0.31
9 10 0.29
10 3 0.09
11 5 0.14
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTCTT
Found at i:40872808 original size:7 final size:7
Alignment explanation
Indices: 40872798--40872876 Score: 90
Period size: 7 Copynumber: 11.0 Consensus size: 7
40872788 ATTTTTTTCC
40872798 TTTCTTT
1 TTTCTTT
40872805 TTTCTTT
1 TTTCTTT
40872812 TTTCTTT
1 TTTCTTT
40872819 TTTCTTT
1 TTTCTTT
40872826 TTTCTTT
1 TTTCTTT
40872833 CCTTT-TTT
1 --TTTCTTT
40872841 TCTTCTTT
1 T-TTCTTT
*
40872849 TTT-TTCC
1 TTTCTT-T
*
40872856 TTTCTTC
1 TTTCTTT
40872863 TTTCTTT
1 TTTCTTT
40872870 TTTCTTT
1 TTTCTTT
40872877 CCTTTTCCTT
Statistics
Matches: 64, Mismatches: 2, Indels: 12
0.82 0.03 0.15
Matches are distributed among these distances:
6 3 0.05
7 49 0.77
8 9 0.14
9 3 0.05
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTCTTT
Found at i:40872847 original size:37 final size:37
Alignment explanation
Indices: 40872780--40872901 Score: 112
Period size: 37 Copynumber: 3.3 Consensus size: 37
40872770 ACCCGATTTC
40872780 TCCTTT-TTATTTT-TTTCCTTTCTTTTTTCTTTTTTCT
1 TCCTTTCTT-TTTTCTTTCCTTTCTTTTTTCTTTTTT-T
*
40872817 T-TTTTCTTTTTTCTTTCCTTT-TTTTCTTCTTTTTTT
1 TCCTTTCTTTTTTCTTTCCTTTCTTTT-TTCTTTTTTT
* * *
40872853 TCCTTTCTTCTTTCTTT--TTTCTTTCCTTTTCCTTTTTC
1 TCCTTTCTTTTTTCTTTCCTTTC-TT--TTTTCTTTTTTT
40872891 TCCTTTCTTTT
1 TCCTTTCTTTT
40872902 CCGTTCAGCC
Statistics
Matches: 71, Mismatches: 6, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
35 3 0.04
36 13 0.18
37 35 0.49
38 18 0.25
39 2 0.03
ACGTcount: A:0.01, C:0.22, G:0.00, T:0.77
Consensus pattern (37 bp):
TCCTTTCTTTTTTCTTTCCTTTCTTTTTTCTTTTTTT
Found at i:40872848 original size:44 final size:46
Alignment explanation
Indices: 40872789--40872882 Score: 140
Period size: 44 Copynumber: 2.1 Consensus size: 46
40872779 CTCCTTTTTA
* *
40872789 TTTTTTTCCTTTCTTTTTTCTT-TTTTCTTTTTTCTTTTTTCTTTCC
1 TTTTTTTCCTTTCTTTTTT-TTCCTTTCTTCTTTCTTTTTTCTTTCC
40872835 TTTTTTT-C-TTCTTTTTTTTCCTTTCTTCTTTCTTTTTTCTTTCC
1 TTTTTTTCCTTTCTTTTTTTTCCTTTCTTCTTTCTTTTTTCTTTCC
40872879 TTTT
1 TTTT
40872883 CCTTTTTCTC
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
43 2 0.04
44 35 0.78
45 1 0.02
46 7 0.16
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (46 bp):
TTTTTTTCCTTTCTTTTTTTTCCTTTCTTCTTTCTTTTTTCTTTCC
Found at i:40872902 original size:19 final size:18
Alignment explanation
Indices: 40872790--40872903 Score: 74
Period size: 19 Copynumber: 6.0 Consensus size: 18
40872780 TCCTTTTTAT
*
40872790 TTTTTTCCTTTCTTTTTTC
1 TTTTTTCCTTTC-TTTTCC
*
40872809 TTTTTTCTTTTTTCTTTT--
1 TTTTTTC--CTTTCTTTTCC
*
40872827 TTCTTTCCTTT-TTTTCTTC
1 TTTTTTCCTTTCTTTTC--C
*
40872846 TTTTTTTTCCTTTCTTCTTTC
1 --TTTTTTCCTTTCTT-TTCC
40872867 TTTTTT-CTTTCCTTTTCC
1 TTTTTTCCTTT-CTTTTCC
40872885 TTTTTCTCCTTTCTTTTCC
1 TTTTT-TCCTTTCTTTTCC
40872904 GTTCAGCCAC
Statistics
Matches: 76, Mismatches: 6, Indels: 26
0.70 0.06 0.24
Matches are distributed among these distances:
15 4 0.05
16 3 0.04
18 18 0.24
19 24 0.32
20 8 0.11
21 15 0.20
22 2 0.03
23 2 0.03
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTTTCCTTTCTTTTCC
Found at i:40873504 original size:29 final size:29
Alignment explanation
Indices: 40873424--40873493 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
40873414 ATATGGGGCC
* *
40873424 AAAATGTAATTTATGGAAAGTTTAAGGGTT
1 AAAATATAA-TTATGAAAAGTTTAAGGGTT
* *
40873454 CAAATATAATTATGAAAAGTTTAGGGGTT
1 AAAATATAATTATGAAAAGTTTAAGGGTT
40873483 AAAATATAATT
1 AAAATATAATT
40873494 TTTTTAAGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 28 0.80
30 7 0.20
ACGTcount: A:0.44, C:0.01, G:0.19, T:0.36
Consensus pattern (29 bp):
AAAATATAATTATGAAAAGTTTAAGGGTT
Found at i:40874245 original size:76 final size:76
Alignment explanation
Indices: 40873853--40874663 Score: 1007
Period size: 75 Copynumber: 10.7 Consensus size: 76
40873843 GTGATTTAAA
* * * * * **
40873853 GCTCAATTCACCTCTCGGATTATGAGTTGATATTTG-AGAAACAGAAATTGAAAATACCTCAGTT
1 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAACAGAAATTGAAAATACCTCGGCG
*
40873917 TGTGACTCGAG
66 TGTGACCCGAG
* * * *
40873928 GCTCAACTCACCTCCCGGATTATGAGTTGATTTTTG-AAAAACATAAATTGAAAATACCTCAGCG
1 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAACAGAAATTGAAAATACCTCGGCG
*
40873992 TGTGACCCAAG
66 TGTGACCCGAG
* * **** * *
40874003 GCTCAACTCACCACTCGCATTATGAGTTAATTTTTTTTTAAA-TGAAATTGAAAAATACCTCAGC
1 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAACAGAAATTG-AAAATACCTCGGC
* *
40874067 ATGTG-TCCGAG
65 GTGTGACCCGAG
* *
40874078 GCTCGACTCACCTCTCGCATTATGAGTTGATTTTTG-AAAAACAGAAATTGAAAATACCTCAGCG
1 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAACAGAAATTGAAAATACCTCGGCG
40874142 TGTGACCCGAG
66 TGTGACCCGAG
* *
40874153 GCTCAACTCACCTCTCGCATTATGAGTTAATTTTTGAAAAAACAGAAATTGAAAAATACCACGGC
1 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAACAGAAATTG-AAAATACCTCGGC
* * *
40874218 GTGCG-CCTGTG
65 GTGTGACCCGAG
* * * * *
40874229 GATTAACTCACGTCTCGCATTATGAGTTGAGTTTTTTAAAAAAAATGAAATTGAAAAATACCTCG
1 GCTCAACTCACCTCTCGCATTATGAGTTGA-TTTTTGAAAAAACA-GAAATTG-AAAATACCTCG
* *
40874294 GCATGTG-TCCGAG
63 GCGTGTGACCCGAG
* * *
40874307 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTG-AAATACAGAAATTGAAAATACCTCAGCA
1 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAACAGAAATTGAAAATACCTCGGCG
*
40874371 TGTGACCTGAG
66 TGTGACCCGAG
* * * * *
40874382 GCTCAACTCACCTCTCCCATTATGAGTTGATTTTTAAAAAAATAGAAATTGAAAAATGCCTCGGT
1 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAACAGAAATTG-AAAATACCTCGGC
40874447 GTGTG-CCCGAG
65 GTGTGACCCGAG
* *
40874458 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTCAAAAAAATAGAAATTGAAAATACCTCGGC
1 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTT-GAAAAAACAGAAATTGAAAATACCTCGGC
40874523 GTGTG-CCCGAG
65 GTGTGACCCGAG
* *
40874534 GCTCAACTCATCTCTAGCATTATGAGTTGATTTTTG-AAAAACAGAAATTGAAAATACCTCGGCG
1 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAACAGAAATTGAAAATACCTCGGCG
40874598 TGTGACCCGAG
66 TGTGACCCGAG
*
40874609 ACTCAACTCACCTCTCGCATTATGAGTTGATTTTT-AAAAAGACAGAAATTGAAAA
1 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAA-ACAGAAATTGAAAA
40874664 ATAATTCTTG
Statistics
Matches: 644, Mismatches: 77, Indels: 29
0.86 0.10 0.04
Matches are distributed among these distances:
74 68 0.11
75 272 0.42
76 189 0.29
77 62 0.10
78 53 0.08
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (76 bp):
GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAACAGAAATTGAAAATACCTCGGCG
TGTGACCCGAG
Found at i:40874666 original size:151 final size:149
Alignment explanation
Indices: 40873853--40874663 Score: 1016
Period size: 151 Copynumber: 5.4 Consensus size: 149
40873843 GTGATTTAAA
* * * * * **
40873853 GCTCAATTCACCTCTCGGATTATGAGTTGATATTTGAGAAACAGAAATTGAAAATACCTCAGTTT
1 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTAAAAAACAGAAATTGAAAATACCTCAGCAT
* * * *
40873918 GTGACTCGAGGCTCAACTCACCTCCCGGATTATGAGTTGATTTTTGAAAAACATAAATTGAAAAT
66 GTG-CCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACAGAAATTGAAAAT
* *
40873983 ACCTCAGCGTGTGACCCAAG
130 ACCTCGGCGTGTGACCCGAG
* * *** *
40874003 GCTCAACTCACCACTCGCATTATGAGTTAATTTTTTTTTAAA-TGAAATTGAAAAATACCTCAGC
1 GCTCAACTCACCTCTCGCATTATGAGTTGA-TTTTTAAAAAACAGAAATTG-AAAATACCTCAGC
* *
40874067 ATGTGTCCGAGGCTCGACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACAGAAATTGAAAA
64 ATGTGCCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACAGAAATTGAAAA
*
40874132 TACCTCAGCGTGTGACCCGAG
129 TACCTCGGCGTGTGACCCGAG
* * *
40874153 GCTCAACTCACCTCTCGCATTATGAGTTAATTTTTGAAAAAACAGAAATTGAAAAATACCACGGC
1 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTT-AAAAAACAGAAATTG-AAAATACCTCAGC
* * * * * * * * *
40874218 GTGCGCCTGTGGATTAACTCACGTCTCGCATTATGAGTTGAGTTTTTTAAAAAAAATGAAATTGA
64 ATGTGCCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA--TTTTTGAAAAACA-GAAATTG-
* *
40874283 AAAATACCTCGGCATGTG-TCCGAG
125 AAAATACCTCGGCGTGTGACCCGAG
* *
40874307 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAATACAGAAATTGAAAATACCTCAGCAT
1 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTAAAAAACAGAAATTGAAAATACCTCAGCAT
* * * *
40874372 GTGACCTGAGGCTCAACTCACCTCTCCCATTATGAGTTGATTTTTAAAAAAATAGAAATTGAAAA
66 GTG-CCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTT-GAAAAACAGAAATTG-AAA
* *
40874437 ATGCCTCGGTGTGTG-CCCGAG
128 ATACCTCGGCGTGTGACCCGAG
* *
40874458 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTCAAAAAAATAGAAATTGAAAATACCTCGGC
1 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTT--AAAAAACAGAAATTGAAAATACCTCAGC
* * *
40874523 GTGTGCCCGAGGCTCAACTCATCTCTAGCATTATGAGTTGATTTTTGAAAAACAGAAATTGAAAA
64 ATGTGCCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACAGAAATTGAAAA
40874588 TACCTCGGCGTGTGACCCGAG
129 TACCTCGGCGTGTGACCCGAG
*
40874609 ACTCAACTCACCTCTCGCATTATGAGTTGATTTTTAAAAAGACAGAAATTGAAAA
1 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTAAAAA-ACAGAAATTGAAAA
40874664 ATAATTCTTG
Statistics
Matches: 576, Mismatches: 71, Indels: 28
0.85 0.11 0.04
Matches are distributed among these distances:
149 10 0.02
150 168 0.29
151 195 0.34
152 58 0.10
153 83 0.14
154 46 0.08
155 16 0.03
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (149 bp):
GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTAAAAAACAGAAATTGAAAATACCTCAGCAT
GTGCCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACAGAAATTGAAAATA
CCTCGGCGTGTGACCCGAG
Found at i:40886833 original size:19 final size:21
Alignment explanation
Indices: 40886803--40886845 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
40886793 AGAATGGGCA
40886803 TTTCTCTCCTTT-TTCTTTTT
1 TTTCTCTCCTTTCTTCTTTTT
40886823 TTTCT-TCCTTTCTTCTTTTT
1 TTTCTCTCCTTTCTTCTTTTT
40886843 TTT
1 TTT
40886846 TTCTGGCTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTCTCTCCTTTCTTCTTTTT
Found at i:40887160 original size:11 final size:11
Alignment explanation
Indices: 40887144--40887208 Score: 62
Period size: 11 Copynumber: 5.7 Consensus size: 11
40887134 CTCCTTTTTA
40887144 TTTTTTTTCCT
1 TTTTTTTTCCT
40887155 TTTTTTTT-CT
1 TTTTTTTTCCT
40887165 TCTTTTTTTCCT
1 T-TTTTTTTCCT
*
40887177 TTCTTCTTT-CT
1 TT-TTTTTTCCT
*
40887188 TCTTTCTTTCCT
1 T-TTTTTTTCCT
40887200 TTTTCTTTT
1 TTTT-TTTT
40887209 TCTCCTTTCT
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
10 3 0.07
11 28 0.61
12 15 0.33
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTTTTCCT
Found at i:40887186 original size:23 final size:22
Alignment explanation
Indices: 40887145--40887211 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 22
40887135 TCCTTTTTAT
*
40887145 TTTTTTTCCTTTTTTTTTCTTC
1 TTTTTTTCCTTTTTCTTTCTTC
40887167 TTTTTTTCCTTTCTTCTTTCTTC
1 TTTTTTTCCTTT-TTCTTTCTTC
*
40887190 TTTCTTTCCTTTTTCTTT-TTC
1 TTTTTTTCCTTTTTCTTTCTTC
40887211 T
1 T
40887212 CCTTTCTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
21 4 0.10
22 18 0.43
23 20 0.48
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTTTTTCCTTTTTCTTTCTTC
Found at i:40887789 original size:29 final size:29
Alignment explanation
Indices: 40887742--40887816 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
40887732 GAAAAATATA
* *
40887742 GGGCCAAAATACAATTTATGGAA-AGTTTAG
1 GGGCTAAAATATAA-TTAT-GAATAGTTTAG
* *
40887772 GGGCTCAAATGTAATTATGAATAGTTTAG
1 GGGCTAAAATATAATTATGAATAGTTTAG
40887801 GGGCTAAAATATAATT
1 GGGCTAAAATATAATT
40887817 TTTTTAAAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
28 3 0.08
29 25 0.66
30 10 0.26
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.31
Consensus pattern (29 bp):
GGGCTAAAATATAATTATGAATAGTTTAG
Found at i:40891349 original size:3 final size:3
Alignment explanation
Indices: 40891341--40891407 Score: 62
Period size: 3 Copynumber: 22.3 Consensus size: 3
40891331 CTCTTCTGGG
* * * * * * * *
40891341 TCA TCA TCA TCA CCA CCA CCA CCA TCA TCG TCG TCG TCG TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
40891389 TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA T
40891408 TGACTTGGCT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.27, C:0.39, G:0.06, T:0.28
Consensus pattern (3 bp):
TCA
Found at i:40905038 original size:21 final size:21
Alignment explanation
Indices: 40905013--40905176 Score: 68
Period size: 21 Copynumber: 7.9 Consensus size: 21
40905003 CGTGTTTGCT
*
40905013 TTTAGTTTAGCTCTTATGAGC
1 TTTAGTTTAACTCTTATGAGC
* *
40905034 TTTAG-CTAACTCATATGAG-
1 TTTAGTTTAACTCTTATGAGC
* *
40905053 TTTCAGTTTAAC-CCTACT-AGG
1 TTT-AGTTTAACTCTTA-TGAGC
* *
40905074 TTTCAGTTTAGCTCTTTTGAGC
1 TTT-AGTTTAACTCTTATGAGC
* * * *
40905096 TTCAGTTTAACCCTTGTG-GG
1 TTTAGTTTAACTCTTATGAGC
* * *
40905116 TTTCCGTTCAGCTCTTATGAGC
1 TTT-AGTTTAACTCTTATGAGC
* * * * *
40905138 TTTGGTTTAACCCTTACGGGT
1 TTTAGTTTAACTCTTATGAGC
* *
40905159 TTTCGTTTAACACTTATG
1 TTTAGTTTAACTCTTATG
40905177 TACTTCTATG
Statistics
Matches: 104, Mismatches: 31, Indels: 16
0.69 0.21 0.11
Matches are distributed among these distances:
19 3 0.03
20 21 0.20
21 70 0.67
22 10 0.10
ACGTcount: A:0.19, C:0.20, G:0.18, T:0.43
Consensus pattern (21 bp):
TTTAGTTTAACTCTTATGAGC
Found at i:40905159 original size:42 final size:42
Alignment explanation
Indices: 40905047--40905165 Score: 132
Period size: 42 Copynumber: 2.8 Consensus size: 42
40905037 AGCTAACTCA
* * * *
40905047 TATGAGTTTCAGTTTAACCC-TACTAGGTTTCAGTTTAGCTCT
1 TATGAGCTTCAGTTTAACCCTTAC-GGGTTTCCGTTCAGCTCT
* **
40905089 TTTGAGCTTCAGTTTAACCCTTGTGGGTTTCCGTTCAGCTCT
1 TATGAGCTTCAGTTTAACCCTTACGGGTTTCCGTTCAGCTCT
** *
40905131 TATGAGCTTTGGTTTAACCCTTACGGGTTTTCGTT
1 TATGAGCTTCAGTTTAACCCTTACGGGTTTCCGTT
40905166 TAACACTTAT
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
42 62 0.98
43 1 0.02
ACGTcount: A:0.16, C:0.20, G:0.20, T:0.44
Consensus pattern (42 bp):
TATGAGCTTCAGTTTAACCCTTACGGGTTTCCGTTCAGCTCT
Found at i:40913043 original size:44 final size:43
Alignment explanation
Indices: 40912954--40913047 Score: 145
Period size: 44 Copynumber: 2.2 Consensus size: 43
40912944 ACAGTCGCAC
40912954 ATTAGTAATTAACGATTCTTCCCTACTGTAAACTTCCTACAAT
1 ATTAGTAATTAACGATTCTTCCCTACTGTAAACTTCCTACAAT
* *
40912997 ATTAGTAATTAACGATTTTGTTCCC-ACTGTAAACTTCCTACCAT
1 ATTAGTAATTAACGA--TTCTTCCCTACTGTAAACTTCCTACAAT
40913041 ATTAGTA
1 ATTAGTA
40913048 CACCGTCAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
43 15 0.32
44 25 0.53
45 7 0.15
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.38
Consensus pattern (43 bp):
ATTAGTAATTAACGATTCTTCCCTACTGTAAACTTCCTACAAT
Found at i:40916004 original size:9 final size:9
Alignment explanation
Indices: 40915986--40916015 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
40915976 TTTTAAATCA
*
40915986 TTTTTGTTT
1 TTTTTATTT
40915995 TTTTTATTT
1 TTTTTATTT
40916004 TTTTTATTT
1 TTTTTATTT
40916013 TTT
1 TTT
40916016 AATGTTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.07, C:0.00, G:0.03, T:0.90
Consensus pattern (9 bp):
TTTTTATTT
Found at i:40924371 original size:24 final size:26
Alignment explanation
Indices: 40924318--40924384 Score: 77
Period size: 24 Copynumber: 2.7 Consensus size: 26
40924308 ACAATAGCAT
* *
40924318 TTTTACCAAAATAAAATAAATAAATA
1 TTTTATCAAAATAATATAAATAAATA
*
40924344 TTTT-TC-AAATAATATAAAT-AATCT
1 TTTTATCAAAATAATATAAATAAAT-A
40924368 TTTTATCAAAATAATAT
1 TTTTATCAAAATAATAT
40924385 GTTTAAAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
23 3 0.09
24 16 0.46
25 3 0.09
26 13 0.37
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.40
Consensus pattern (26 bp):
TTTTATCAAAATAATATAAATAAATA
Found at i:40925879 original size:28 final size:28
Alignment explanation
Indices: 40925847--40925944 Score: 133
Period size: 28 Copynumber: 3.5 Consensus size: 28
40925837 TGACTTTCGA
40925847 CACTAAGTGTGCGAGTTTAATTGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* * *
40925875 CACTAAGTGTGCGAGTTTAATGGCAAAA
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* * **
40925903 CACTAAGTGTGCGAGTTTGATTATTGAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
40925931 CACTAAGTGTGCGA
1 CACTAAGTGTGCGA
40925945 ACTTATTAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 60 1.00
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.30
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTAATTGTAAAG
Found at i:40926121 original size:2 final size:2
Alignment explanation
Indices: 40926114--40926145 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
40926104 TATTTGGAAT
40926114 TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40926146 GATTCTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:40926795 original size:23 final size:23
Alignment explanation
Indices: 40926768--40927387 Score: 390
Period size: 23 Copynumber: 26.6 Consensus size: 23
40926758 TTATGCTTAA
*
40926768 ATGCTGTCCAATTTGTTGTATTT
1 ATGCTGTCCAATTTGTTGTATAT
*
40926791 ATGCTG-CCAAAATTGTTGTATAT
1 ATGCTGTCC-AATTTGTTGTATAT
* *
40926814 ATGCTGTCCAATTTTGATGTA-AA
1 ATGCTGTCCAA-TTTGTTGTATAT
* *
40926837 ATGCTG-CTCAATTTGGTATATAT
1 ATGCTGTC-CAATTTGTTGTATAT
* * *
40926860 ATGCTG-CCTAAATTGTTGCACAT
1 ATGCTGTCC-AATTTGTTGTATAT
* * *
40926883 ATGCTGTCAAATTTTTATGCTA-AA
1 ATGCTGTCCAATTTGT-TG-TATAT
* *
40926907 ATGTTGTCCAATTTGTTGTATTT
1 ATGCTGTCCAATTTGTTGTATAT
* *
40926930 ATGCTGCCCAAATTGTTGTATAT
1 ATGCTGTCCAATTTGTTGTATAT
* * *
40926953 ATGTTGTCCAATTTTGATGTA-AA
1 ATGCTGTCCAA-TTTGTTGTATAT
* *
40926976 ATGCTG-CTCAATTTGGTATATAT
1 ATGCTGTC-CAATTTGTTGTATAT
* * *
40926999 ATGCTG-CTCAAATTGTTGCACAT
1 ATGCTGTC-CAATTTGTTGTATAT
* * *
40927022 ATGCTGTCAAATTTTTATGCTA-AA
1 ATGCTGTCCAATTTGT-TG-TATAT
*
40927046 ATGCTGTCCAATTTGTTGTATTT
1 ATGCTGTCCAATTTGTTGTATAT
* * * *
40927069 ATGCTGCCCAAATTGGTGCATAT
1 ATGCTGTCCAATTTGTTGTATAT
* * *
40927092 ATGCTGTCAAATTTTTATGCTA-AA
1 ATGCTGTCCAATTTGT-TG-TATAT
* *
40927116 ATGCTGCCCAATTTGTTGTATTT
1 ATGCTGTCCAATTTGTTGTATAT
* *
40927139 ATGCTG-CCTAAATTGTTGCATAT
1 ATGCTGTCC-AATTTGTTGTATAT
* *
40927162 ATGCTGTCCAATTTTTATGCT-TAA
1 ATGCTGTCCAATTTGT-TG-TATAT
* *
40927186 ATGATG-CTCAATTTGTTGTATTT
1 ATGCTGTC-CAATTTGTTGTATAT
* *
40927209 ATGCTGCCCAAATTGTTGTATAT
1 ATGCTGTCCAATTTGTTGTATAT
* * * *
40927232 ATGCTGTCTAATTTTGATGTAAAA
1 ATGCTGTCCAA-TTTGTTGTATAT
*
40927256 ATGCTG-CTCAATTTGGTATATATAT
1 ATGCTGTC-CAATTT-GT-TGTATAT
* * *
40927281 AGGCTGCCCAAATTGTTGTATAT
1 ATGCTGTCCAATTTGTTGTATAT
* *
40927304 ATGCTGTCCAATTTTTATGCTA-AA
1 ATGCTGTCCAATTTGT-TG-TATAT
*
40927328 ATGCTG-CTCAATTTGATGTATAT
1 ATGCTGTC-CAATTTGTTGTATAT
* *
40927351 ATGCTGCCCAAATTGTTGTATAT
1 ATGCTGTCCAATTTGTTGTATAT
40927374 ATGCTGTCCAATTT
1 ATGCTGTCCAATTT
40927388 TTGGTGTGAA
Statistics
Matches: 453, Mismatches: 107, Indels: 74
0.71 0.17 0.12
Matches are distributed among these distances:
22 30 0.07
23 282 0.62
24 121 0.27
25 19 0.04
26 1 0.00
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (23 bp):
ATGCTGTCCAATTTGTTGTATAT
Done.