Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 184 of 230
Found at i:55170722 original size:7 final size:7
Alignment explanation
Indices: 55170712--55170785 Score: 80
Period size: 7 Copynumber: 10.7 Consensus size: 7
55170702 TATGTTTTAT
55170712 ATTTTGA
1 ATTTTGA
55170719 ATTTTGA
1 ATTTTGA
55170726 ATTTTGA
1 ATTTTGA
*
55170733 AATTTGA
1 ATTTTGA
*
55170740 AATTTGA
1 ATTTTGA
*
55170747 AATTTGA
1 ATTTTGA
*
55170754 AATTTGA
1 ATTTTGA
*
55170761 AATTTGAA
1 ATTTTG-A
55170769 ATTTT-A
1 ATTTTGA
55170775 ATTTT-A
1 ATTTTGA
55170781 ATTTT
1 ATTTT
55170786 ATATTAATTA
Statistics
Matches: 64, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
6 12 0.19
7 47 0.73
8 5 0.08
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (7 bp):
ATTTTGA
Found at i:55170729 original size:14 final size:14
Alignment explanation
Indices: 55170712--55170785 Score: 89
Period size: 14 Copynumber: 5.4 Consensus size: 14
55170702 TATGTTTTAT
*
55170712 ATTTTGAATTTTGA
1 ATTTTGAAATTTGA
55170726 ATTTTGAAATTTGA
1 ATTTTGAAATTTGA
*
55170740 AATTTGAAATTTGA
1 ATTTTGAAATTTGA
*
55170754 AATTTGAAATTTGAA
1 ATTTTGAAATTTG-A
*
55170769 ATTTT--AATTTTA
1 ATTTTGAAATTTGA
55170781 ATTTT
1 ATTTT
55170786 ATATTAATTA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
12 6 0.11
13 5 0.09
14 39 0.71
15 5 0.09
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (14 bp):
ATTTTGAAATTTGA
Found at i:55170730 original size:21 final size:20
Alignment explanation
Indices: 55170683--55170785 Score: 73
Period size: 21 Copynumber: 4.9 Consensus size: 20
55170673 TAATTTGTTT
* *
55170683 ATTTTAATTTTTATATTTTTA
1 ATTTTAATTTTGA-ATTTTGA
*
55170704 TGTTTTATATTTTGAATTTTGA
1 -ATTTTA-ATTTTGAATTTTGA
* *
55170726 ATTTTGAAATTTGAAATTTGAA
1 ATTTT-AATTTTGAATTTTG-A
* * *
55170748 ATTTGAAATTTGAAATTTGAA
1 ATTTTAATTTTGAATTTTG-A
55170769 ATTTTAATTTT-AATTTT
1 ATTTTAATTTTGAATTTT
55170786 ATATTAATTA
Statistics
Matches: 68, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
20 5 0.07
21 40 0.59
22 17 0.25
23 6 0.09
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (20 bp):
ATTTTAATTTTGAATTTTGA
Found at i:55171963 original size:8 final size:8
Alignment explanation
Indices: 55171950--55171978 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
55171940 AGTTTATTGG
55171950 AAAATTAT
1 AAAATTAT
55171958 AAAATTAT
1 AAAATTAT
55171966 AAAATTAT
1 AAAATTAT
55171974 AAAAT
1 AAAAT
55171979 AGTATAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
AAAATTAT
Found at i:55176784 original size:48 final size:48
Alignment explanation
Indices: 55176730--55176829 Score: 182
Period size: 48 Copynumber: 2.1 Consensus size: 48
55176720 CTGGTCATGA
*
55176730 AGGAAGTTGGGGAGGATTTGATGGAGAAAATCAAGGAGTTTGTGGAAG
1 AGGAAGTTAGGGAGGATTTGATGGAGAAAATCAAGGAGTTTGTGGAAG
*
55176778 AGGAAGTTAGGGAGGATTTGATGGAGAAAATCAAGGAGTTTGTGGGAG
1 AGGAAGTTAGGGAGGATTTGATGGAGAAAATCAAGGAGTTTGTGGAAG
55176826 AGGA
1 AGGA
55176830 GGAGAGTGTG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.34, C:0.02, G:0.42, T:0.22
Consensus pattern (48 bp):
AGGAAGTTAGGGAGGATTTGATGGAGAAAATCAAGGAGTTTGTGGAAG
Found at i:55177897 original size:27 final size:27
Alignment explanation
Indices: 55177859--55178377 Score: 523
Period size: 27 Copynumber: 19.2 Consensus size: 27
55177849 ATTCTTAGGA
* *
55177859 AAAATTACCGAAATACTCTCGAAGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
**
55177886 AAAATTATCGAAATACCCTTAAAGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
* *
55177913 AAAATTATCGAAATACCTTCGATGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
*
55177940 AAAATTACCGAAATACCCTCGAAGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
* *
55177967 AAAATTA-CTGAAACACCCTAGAAGGGT
1 AAAATTATC-GAAATACCCTCGAAGGGT
**
55177994 AAAATTA-CTGAAATACCCTTAAAGGGT
1 AAAATTATC-GAAATACCCTCGAAGGGT
* * *
55178021 AAAATTATCGAAACACCTTTGAAGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
* *
55178048 AAAATTACCAAAATACCCTC-AATGGGT
1 AAAATTATCGAAATACCCTCGAA-GGGT
* * *
55178075 AAAATTA-CTAAAATACCCTCAAAAGGT
1 AAAATTATC-GAAATACCCTCGAAGGGT
* ** *
55178102 AAAATTACCGAAATAATCTCGAATGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
*
55178129 AAAATTA-CTGAAATACCCCCGAAGGGT
1 AAAATTATC-GAAATACCCTCGAAGGGT
**
55178156 AAAATTATCGAAATACCCTTAAAGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
* *
55178183 AAAATTA-CTGAAACACCC-CTAAAGGGT
1 AAAATTATC-GAAATACCCTC-GAAGGGT
* *
55178210 AAAATTA-CTAAAATTCCCTCGAAGGGT
1 AAAATTATC-GAAATACCCTCGAAGGGT
* *
55178237 AAAATTATCGAAACACCCTCAAAGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
* * *
55178264 AAAAATTATTGAAATACCCTTGAAGGGA
1 -AAAATTATCGAAATACCCTCGAAGGGT
* *
55178292 AAAATTACCAAAATACCCTCGAAGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
* *
55178319 AAAATTATTGAAATGCCCTCGAAGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
* * *
55178346 AAAATTATCAAAATACCCCCGAGGGGT
1 AAAATTATCGAAATACCCTCGAAGGGT
55178373 AAAAT
1 AAAAT
55178378 GACCGTTTAC
Statistics
Matches: 413, Mismatches: 66, Indels: 26
0.82 0.13 0.05
Matches are distributed among these distances:
26 6 0.01
27 378 0.92
28 29 0.07
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.23
Consensus pattern (27 bp):
AAAATTATCGAAATACCCTCGAAGGGT
Found at i:55178600 original size:26 final size:26
Alignment explanation
Indices: 55178571--55178673 Score: 111
Period size: 26 Copynumber: 4.0 Consensus size: 26
55178561 TTTGCCACAA
55178571 ATACTG-TCACTGGCAGCTTTGCTGCT
1 ATACTGAT-ACTGGCAGCTTTGCTGCT
** * * *
55178597 ATACTGATACAAGCAGCTCTACTGCG
1 ATACTGATACTGGCAGCTTTGCTGCT
* *
55178623 ATACTGTTACTGGCAGCTTTGCTACGT
1 ATACTGATACTGGCAGCTTTGCTGC-T
55178650 -TACTGATACTGGCAGCTTTGCTGC
1 ATACTGATACTGGCAGCTTTGCTGC
55178674 GATATTGGTG
Statistics
Matches: 61, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
26 60 0.98
27 1 0.02
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.32
Consensus pattern (26 bp):
ATACTGATACTGGCAGCTTTGCTGCT
Found at i:55178635 original size:52 final size:52
Alignment explanation
Indices: 55178571--55178677 Score: 144
Period size: 52 Copynumber: 2.1 Consensus size: 52
55178561 TTTGCCACAA
*
55178571 ATACTGTCACTGGCAGCTTTGCTGC-TATACTGATACAAGCAGCTCTACTGCG
1 ATACTGTCACTGGCAGCTTTGCTACGT-TACTGATACAAGCAGCTCTACTGCG
* ** * *
55178623 ATACTGTTACTGGCAGCTTTGCTACGTTACTGATACTGGCAGCTTTGCTGCG
1 ATACTGTCACTGGCAGCTTTGCTACGTTACTGATACAAGCAGCTCTACTGCG
55178675 ATA
1 ATA
55178678 TTGGTGTGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
52 47 0.98
53 1 0.02
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.32
Consensus pattern (52 bp):
ATACTGTCACTGGCAGCTTTGCTACGTTACTGATACAAGCAGCTCTACTGCG
Found at i:55178851 original size:30 final size:28
Alignment explanation
Indices: 55178794--55178896 Score: 100
Period size: 30 Copynumber: 3.5 Consensus size: 28
55178784 GATTACTATT
55178794 TTGGGCTAAGGCCCACACTGTTACTGTA
1 TTGGGCTAAGGCCCACACTGTTACTGTA
55178822 TTGGGCTAAGGCCCACA-TGTTGATACTGTA
1 TTGGGCTAAGGCCCACACTG-T--TACTGTA
* * * *
55178852 TTGGGTTATGACCCACACACTGCTACTGTA
1 TTGGGCTAAG-GCC-CACACTGTTACTGTA
* *
55178882 TAGGGCTATGGCCCA
1 TTGGGCTAAGGCCCA
55178897 GACTAATTCT
Statistics
Matches: 62, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
27 2 0.03
28 20 0.32
29 2 0.03
30 30 0.48
31 2 0.03
32 4 0.06
33 2 0.03
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.28
Consensus pattern (28 bp):
TTGGGCTAAGGCCCACACTGTTACTGTA
Found at i:55182593 original size:17 final size:18
Alignment explanation
Indices: 55182571--55182617 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
55182561 GTTTTAATTT
55182571 TTTATTTCAATTTTAA-G
1 TTTATTTCAATTTTAATG
* *
55182588 TTTATTTTAATTTTAATT
1 TTTATTTCAATTTTAATG
55182606 TTTATGTTCAAT
1 TTTAT-TTCAAT
55182618 AGGAGGGTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 15 0.60
18 5 0.20
19 5 0.20
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (18 bp):
TTTATTTCAATTTTAATG
Found at i:55184984 original size:71 final size:71
Alignment explanation
Indices: 55184896--55185034 Score: 278
Period size: 71 Copynumber: 2.0 Consensus size: 71
55184886 TCTTAGAGAT
55184896 GAGGAAACTCGAAGACCACATAGTGTTATGTGGAAAATAGTGACAGTGAGAGGTAATGATGGACC
1 GAGGAAACTCGAAGACCACATAGTGTTATGTGGAAAATAGTGACAGTGAGAGGTAATGATGGACC
55184961 ATTGAC
66 ATTGAC
55184967 GAGGAAACTCGAAGACCACATAGTGTTATGTGGAAAATAGTGACAGTGAGAGGTAATGATGGACC
1 GAGGAAACTCGAAGACCACATAGTGTTATGTGGAAAATAGTGACAGTGAGAGGTAATGATGGACC
55185032 ATT
66 ATT
55185035 CTCTCCGAAA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.37, C:0.12, G:0.29, T:0.22
Consensus pattern (71 bp):
GAGGAAACTCGAAGACCACATAGTGTTATGTGGAAAATAGTGACAGTGAGAGGTAATGATGGACC
ATTGAC
Found at i:55186495 original size:27 final size:27
Alignment explanation
Indices: 55186465--55186525 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
55186455 TCATCTCCTA
* *
55186465 GGGGTATAACAACCATTTTACTTTATT
1 GGGGTATAACAACCATTTTACTCTATG
** * *
55186492 GGGGTATTTCGATCATTTTACTCTATG
1 GGGGTATAACAACCATTTTACTCTATG
55186519 GGGGTAT
1 GGGGTAT
55186526 TTCGTCATTC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.41
Consensus pattern (27 bp):
GGGGTATAACAACCATTTTACTCTATG
Found at i:55186526 original size:27 final size:27
Alignment explanation
Indices: 55186478--55186849 Score: 423
Period size: 27 Copynumber: 13.9 Consensus size: 27
55186468 GTATAACAAC
** *
55186478 CATTTTACTTTATTGGGGTATTTCGAT
1 CATTTTACCCTATGGGGGTATTTCGAT
*
55186505 CATTTTACTCTATGGGGGTATTTCG-T
1 CATTTTACCCTATGGGGGTATTTCGAT
*
55186531 CATTCTA-CCT-TGTGGGGTATTTCGAT
1 CATTTTACCCTATG-GGGGTATTTCGAT
* * *
55186557 CATTTTACCCTATGAGGGTATTTTGGT
1 CATTTTACCCTATGGGGGTATTTCGAT
* * **
55186584 CATTTTACCCTATAGGAGTATTTTTAT
1 CATTTTACCCTATGGGGGTATTTCGAT
* *
55186611 CATTTTACCCTCTGGGGGTATTTCTAT
1 CATTTTACCCTATGGGGGTATTTCGAT
* *
55186638 TATTTTACCCTATGGGGGTATTTCGGT
1 CATTTTACCCTATGGGGGTATTTCGAT
55186665 CATTTTACCCTATGGGGGTATTTCGAT
1 CATTTTACCCTATGGGGGTATTTCGAT
*
55186692 CATTTTACCTTATGGGGGTATTTCGAT
1 CATTTTACCCTATGGGGGTATTTCGAT
*
55186719 CATTTTACCCTAT-GGGGTATTTCGGT
1 CATTTTACCCTATGGGGGTATTTCGAT
* * *
55186745 CATTCTACCTTATAGGGGTATTTC-AGT
1 CATTTTACCCTATGGGGGTATTTCGA-T
* * *
55186772 CATTTTACCTTATGAGGGTATTT-TAGT
1 CATTTTACCCTATGGGGGTATTTCGA-T
*
55186799 CATTTTACCCTATGGGGGTATTTCGGT
1 CATTTTACCCTATGGGGGTATTTCGAT
* * *
55186826 TATTTTACCTTATGAGGGTATTTC
1 CATTTTACCCTATGGGGGTATTTC
55186850 ATTCATTCTA
Statistics
Matches: 298, Mismatches: 39, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
24 2 0.01
25 13 0.04
26 37 0.12
27 244 0.82
28 2 0.01
ACGTcount: A:0.18, C:0.16, G:0.21, T:0.45
Consensus pattern (27 bp):
CATTTTACCCTATGGGGGTATTTCGAT
Found at i:55186878 original size:134 final size:133
Alignment explanation
Indices: 55186478--55186861 Score: 409
Period size: 134 Copynumber: 2.9 Consensus size: 133
55186468 GTATAACAAC
* * * * * * *
55186478 CATTTTACTTTATTGGGGTATTTCGATCATTTTACTCTATGGGGGTATTTC-GTCATTCTA-CCT
1 CATTCTACCTTATAGGGGTATTTCTATCATTTTACCCTATGAGGGTATTTCAGTCATTTTACCCT
* * * * *
55186541 -TGTGGGGTATTTCGATCATTTTACCCTATGAGGGTATTTTGGTCATTTTACCCTATAGGAGTAT
66 ATG-GGGGTATTTCGATCATTTTACCTTATGAGGGTATTTCGATCATTCTACCCTAT-GG-GGAT
* ***
55186605 TTTTAT
128 CTCGGT
* * * * * * *
55186611 CATTTTACCCTCTGGGGGTATTTCTATTATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCT
1 CATTCTACCTTATAGGGGTATTTCTATCATTTTACCCTATGAGGGTATTTCAGTCATTTTACCCT
* * *
55186676 ATGGGGGTATTTCGATCATTTTACCTTATGGGGGTATTTCGATCATTTTACCCTATGGGGTATTT
66 ATGGGGGTATTTCGATCATTTTACCTTATGAGGGTATTTCGATCATTCTACCCTATGGGG-ATCT
55186741 CGGT
130 CGGT
* *
55186745 CATTCTACCTTATAGGGGTATTTC-AGTCATTTTACCTTATGAGGGTATTTTAGTCATTTTACCC
1 CATTCTACCTTATAGGGGTATTTCTA-TCATTTTACCCTATGAGGGTATTTCAGTCATTTTACCC
* *
55186809 TATGGGGGTATTTCGGTTATTTTACCTTATGAGGGTATTTC-ATTCATTCTACC
65 TATGGGGGTATTTCGATCATTTTACCTTATGAGGGTATTTCGA-TCATTCTACC
55186862 TATTTTTGGG
Statistics
Matches: 216, Mismatches: 29, Indels: 11
0.84 0.11 0.04
Matches are distributed among these distances:
133 47 0.22
134 115 0.53
135 52 0.24
136 2 0.01
ACGTcount: A:0.18, C:0.17, G:0.20, T:0.45
Consensus pattern (133 bp):
CATTCTACCTTATAGGGGTATTTCTATCATTTTACCCTATGAGGGTATTTCAGTCATTTTACCCT
ATGGGGGTATTTCGATCATTTTACCTTATGAGGGTATTTCGATCATTCTACCCTATGGGGATCTC
GGT
Found at i:55201494 original size:18 final size:19
Alignment explanation
Indices: 55201471--55201515 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
55201461 TAGTTTTATA
55201471 ATTTATTTTCATTAT-TGAT
1 ATTTATTTTC-TTATCTGAT
*
55201490 A-TTATTGTCTTATCTGAT
1 ATTTATTTTCTTATCTGAT
55201508 ATTTATTT
1 ATTTATTT
55201516 ATTTATGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 4 0.18
18 12 0.55
19 6 0.27
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (19 bp):
ATTTATTTTCTTATCTGAT
Found at i:55209762 original size:22 final size:22
Alignment explanation
Indices: 55209734--55209778 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
55209724 CTATGGACGT
55209734 TAGTACATCTGAGTTAGTCAAA
1 TAGTACATCTGAGTTAGTCAAA
55209756 TAGTACATCTGAGTTAGTCAAA
1 TAGTACATCTGAGTTAGTCAAA
55209778 T
1 T
55209779 CCTTAAGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (22 bp):
TAGTACATCTGAGTTAGTCAAA
Found at i:55211852 original size:6 final size:6
Alignment explanation
Indices: 55211841--55211868 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
55211831 CAAATGGATT
55211841 ATTTCC ATTTCC ATTTCC ATTTCC ATTT
1 ATTTCC ATTTCC ATTTCC ATTTCC ATTT
55211869 TTTGAAACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.29, G:0.00, T:0.54
Consensus pattern (6 bp):
ATTTCC
Found at i:55236003 original size:13 final size:13
Alignment explanation
Indices: 55235985--55236012 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
55235975 AACAAGGCTC
55235985 CTTTGTTCCTTTG
1 CTTTGTTCCTTTG
55235998 CTTTGTTCCTTTG
1 CTTTGTTCCTTTG
55236011 CT
1 CT
55236013 GATGGCTCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.25, G:0.14, T:0.61
Consensus pattern (13 bp):
CTTTGTTCCTTTG
Found at i:55242842 original size:18 final size:18
Alignment explanation
Indices: 55242815--55242853 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
55242805 TTTTTCTATC
*
55242815 TTTATTTCA-TTGTTTCT
1 TTTATTTCATTTCTTTCT
55242832 TTTATTTTCATTTCTTTCT
1 TTTA-TTTCATTTCTTTCT
55242851 TTT
1 TTT
55242854 GTTTAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 5 0.26
19 10 0.53
ACGTcount: A:0.10, C:0.13, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTATTTCATTTCTTTCT
Found at i:55247870 original size:12 final size:12
Alignment explanation
Indices: 55247849--55247893 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
55247839 AAAACCCTAT
*
55247849 TTTTCCTTTTTC
1 TTTTCTTTTTTC
*
55247861 TTTTCTTTTTCC
1 TTTTCTTTTTTC
55247873 TTTTCTTTCTTTCC
1 TTTTCTTT-TTT-C
55247887 TTTTCTT
1 TTTTCTT
55247894 GATCTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 18 0.64
13 2 0.07
14 8 0.29
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:55247887 original size:14 final size:13
Alignment explanation
Indices: 55247849--55247893 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 13
55247839 AAAACCCTAT
*
55247849 TTTTCCTTTTT-C
1 TTTTCTTTTTTCC
55247861 TTTTC-TTTTTCC
1 TTTTCTTTTTTCC
55247873 TTTTCTTTCTTTCC
1 TTTTCTTT-TTTCC
55247887 TTTTCTT
1 TTTTCTT
55247894 GATCTTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 5 0.17
12 11 0.37
13 2 0.07
14 12 0.40
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTCTTTTTTCC
Found at i:55247945 original size:18 final size:18
Alignment explanation
Indices: 55247918--55247956 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
55247908 TTTTTCTATC
*
55247918 TTTATTTCA-TTGTTTCT
1 TTTATTTCATTTCTTTCT
55247935 TTTATTTTCATTTCTTTCT
1 TTTA-TTTCATTTCTTTCT
55247954 TTT
1 TTT
55247957 GTTTAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 5 0.26
19 10 0.53
ACGTcount: A:0.10, C:0.13, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTATTTCATTTCTTTCT
Found at i:55257607 original size:41 final size:40
Alignment explanation
Indices: 55257469--55257607 Score: 106
Period size: 41 Copynumber: 3.5 Consensus size: 40
55257459 AACACACCAG
* * * * *
55257469 TTTGGCACCCAGTGACTTATCGATTTAATTCGAAGCAATAA
1 TTTGACACCCAGTGTCTCATCGATTT-ATCCGAAGTAATAA
* ** *
55257510 GTTGACACCCAGTGTCTCATCGA-CCATGCCAAAGT-A-AA
1 TTTGACACCCAGTGTCTCATCGATTTAT-CCGAAGTAATAA
** **
55257548 -TTGGTACCCAGTACCTCATCGAATTTATCCGAAGTAATAA
1 TTTGACACCCAGTGTCTCATCG-ATTTATCCGAAGTAATAA
55257588 TTTGACACCCAGTGTCTCAT
1 TTTGACACCCAGTGTCTCAT
55257608 TAACTTGAAG
Statistics
Matches: 72, Mismatches: 20, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
37 17 0.24
38 9 0.12
39 6 0.08
40 6 0.08
41 34 0.47
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (40 bp):
TTTGACACCCAGTGTCTCATCGATTTATCCGAAGTAATAA
Found at i:55260663 original size:14 final size:14
Alignment explanation
Indices: 55260629--55260679 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
55260619 AATCCTAATT
*
55260629 TTTTTCTCCTTTT-
1 TTTTTCTTCTTTTC
*
55260642 TCTTTCTTCTTTTC
1 TTTTTCTTCTTTTC
*
55260656 TTTTTCTT-TCTCTC
1 TTTTTCTTCT-TTTC
55260670 TTTTTCTTCT
1 TTTTTCTTCT
55260680 CTGTTTCGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
13 12 0.39
14 18 0.58
15 1 0.03
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTTCTTCTTTTC
Found at i:55260664 original size:11 final size:11
Alignment explanation
Indices: 55260639--55260723 Score: 57
Period size: 11 Copynumber: 7.3 Consensus size: 11
55260629 TTTTTCTCCT
55260639 TTTTCTTTCTTC
1 TTTTCTTT-TTC
55260651 TTTTCTTTTTC
1 TTTTCTTTTTC
55260662 TTTCTCTCTTTTTC
1 -TT-T-TCTTTTTC
* *
55260676 TTCTCTGTTTC
1 TTTTCTTTTTC
*
55260687 GTTCTACTTTGTTC
1 -TT-TTCTTT-TTC
55260701 --TTCTTTTTC
1 TTTTCTTTTTC
*
55260710 TATTCTTTTTC
1 TTTTCTTTTTC
55260721 TTT
1 TTT
55260724 CATTTATTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 17
0.71 0.09 0.21
Matches are distributed among these distances:
9 3 0.05
10 5 0.09
11 21 0.36
12 12 0.21
13 6 0.10
14 11 0.19
ACGTcount: A:0.02, C:0.22, G:0.04, T:0.72
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:55260686 original size:25 final size:26
Alignment explanation
Indices: 55260642--55260704 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 26
55260632 TTCTCCTTTT
* * *
55260642 TCTTTCTTCTTTTCTTTTTCTTTCT-C
1 TCTTT-TTCTTCTCTGTTTCGTTCTAC
55260668 TCTTTTTCTTCTCTGTTTCGTTCTAC
1 TCTTTTTCTTCTCTGTTTCGTTCTAC
*
55260694 T-TTGTTCTTCT
1 TCTTTTTCTTCT
55260705 TTTTCTATTC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
25 25 0.78
26 7 0.22
ACGTcount: A:0.02, C:0.25, G:0.05, T:0.68
Consensus pattern (26 bp):
TCTTTTTCTTCTCTGTTTCGTTCTAC
Found at i:55261037 original size:17 final size:17
Alignment explanation
Indices: 55261015--55261049 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
55261005 CACAACTAAC
55261015 TTCGTAAATATTTTTAA
1 TTCGTAAATATTTTTAA
55261032 TTCGTAAATATTTTTAA
1 TTCGTAAATATTTTTAA
55261049 T
1 T
55261050 AAATATTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.54
Consensus pattern (17 bp):
TTCGTAAATATTTTTAA
Found at i:55262882 original size:12 final size:12
Alignment explanation
Indices: 55262867--55262893 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
55262857 AAATAATCGA
55262867 TAAAAAATAAAT
1 TAAAAAATAAAT
55262879 TAAAAAATAAAT
1 TAAAAAATAAAT
55262891 TAA
1 TAA
55262894 GGTAAGGAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
TAAAAAATAAAT
Found at i:55268476 original size:95 final size:95
Alignment explanation
Indices: 55268313--55268488 Score: 334
Period size: 95 Copynumber: 1.9 Consensus size: 95
55268303 ATATGAATTC
*
55268313 TAAGAAACTCATTGCTATCTCTTTGTGGGCCCTTTGGTATAAGCAAAATAAGCTTGTTAATGAAG
1 TAAGAAACTCATTGCTATCTCTTTGTGGGCCCTTTGGTATAAGCAAAATAAGCTGGTTAATGAAG
55268378 GCCTAAAATTTAAGTTGCCGCAAGACGAAA
66 GCCTAAAATTTAAGTTGCCGCAAGACGAAA
*
55268408 TAAGAAACTCATTGCTATCTCTTTGTGGGCCCTTTGGTATAAGCGAAATAAGCTGGTTAATGAAG
1 TAAGAAACTCATTGCTATCTCTTTGTGGGCCCTTTGGTATAAGCAAAATAAGCTGGTTAATGAAG
55268473 GCCTAAAATTTAAGTT
66 GCCTAAAATTTAAGTT
55268489 CCATGAAACT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
95 79 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.31
Consensus pattern (95 bp):
TAAGAAACTCATTGCTATCTCTTTGTGGGCCCTTTGGTATAAGCAAAATAAGCTGGTTAATGAAG
GCCTAAAATTTAAGTTGCCGCAAGACGAAA
Found at i:55269750 original size:83 final size:83
Alignment explanation
Indices: 55269651--55269810 Score: 302
Period size: 83 Copynumber: 1.9 Consensus size: 83
55269641 TTAACGGATA
55269651 TATGTTTAACGCATGAACCACTAAAAAACAATAGTATTAGTAAATCATAATATTACTGTATATTA
1 TATGTTTAACGCATGAACCACTAAAAAACAATAGTATTAGTAAATCATAATATTACTGTATATTA
*
55269716 TAAAATTGTATACAATTG
66 TAAAACTGTATACAATTG
*
55269734 TATGTTTAACGCATGAACCACTAAAAACCAATAGTATTAGTAAATCATAATATTACTGTATATTA
1 TATGTTTAACGCATGAACCACTAAAAAACAATAGTATTAGTAAATCATAATATTACTGTATATTA
55269799 TAAAACTGTATA
66 TAAAACTGTATA
55269811 TTATAATATT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 75 1.00
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.34
Consensus pattern (83 bp):
TATGTTTAACGCATGAACCACTAAAAAACAATAGTATTAGTAAATCATAATATTACTGTATATTA
TAAAACTGTATACAATTG
Found at i:55269808 original size:15 final size:15
Alignment explanation
Indices: 55269788--55269816 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
55269778 TCATAATATT
55269788 ACTGTATATTATAAA
1 ACTGTATATTATAAA
55269803 ACTGTATATTATAA
1 ACTGTATATTATAA
55269817 TATTATGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (15 bp):
ACTGTATATTATAAA
Found at i:55273215 original size:45 final size:45
Alignment explanation
Indices: 55273131--55273237 Score: 110
Period size: 45 Copynumber: 2.4 Consensus size: 45
55273121 TAGTACTCGG
* *
55273131 TGAAATCAGCACATAGCAACCACTTTTATACTCAATGGTA-CCAGA
1 TGAAATCAGCACATAGCAACAACTTATATACTCAATGGTATCC-GA
* * * *
55273176 TGAATTCAGGACATAGCAATAACTTATATAAC-CATTGGTATCCGA
1 TGAAATCAGCACATAGCAACAACTTATAT-ACTCAATGGTATCCGA
* *
55273221 TGAAATCAACATATAGC
1 TGAAATCAGCACATAGC
55273238 GATCACCTTT
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
45 46 0.92
46 4 0.08
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.26
Consensus pattern (45 bp):
TGAAATCAGCACATAGCAACAACTTATATACTCAATGGTATCCGA
Found at i:55280161 original size:44 final size:44
Alignment explanation
Indices: 55280055--55280661 Score: 170
Period size: 44 Copynumber: 13.2 Consensus size: 44
55280045 TTCGGTCTAT
* * * * *
55280055 TCCACTGTAATCTCAAGGAGATAAGA--CTTGA-TGCGATCTAC
1 TCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTCAATCTGC
* ** * *
55280096 TCTACTGTAA-CTTCAAAGAGATAAGATCCTTTATTTTAATCCGC
1 TCCACTGTAATC-TCAGGGAGATAAGATCCTTTATTTCAATCTGC
* * *
55280140 TCCACTGTAATCTCAGGGAGATAGGA--CTACTAGCTTCAATCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATCCT-TTA-TTTCAATCTGC
** * * *
55280184 TCTGCTATAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGATGCAATCTAC
1 TCCACTGTAATCTCAGGGAGATAAGA--TC---CTT-TAT-T--T-CAATCTGC
* * * * *
55280238 TCTACTATAA-CTTCAGAGAGATAAGATCCTTTATTTTAATCCGC
1 TCCACTGTAATC-TCAGGGAGATAAGATCCTTTATTTCAATCTGC
* * *
55280282 TCCACTGTAATCTCAGGGAGATAGGAT--TACTAGCTTCAATCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATCCT-TTA-TTTCAATCTGC
* * *
55280326 TCCGCTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAATCTGATGCAATCTAC
1 TCCACTGTAATCTCAGGGAGATAAGA--TC---CTT-TAT-T--T-CAATCTGC
* * * * *
55280380 TCTACTGTAA-CTTCAGAGAGATAAAATCCTTTATTTTAATCTAC
1 TCCACTGTAATC-TCAGGGAGATAAGATCCTTTATTTCAATCTGC
* * *
55280424 TCCACTGTAATCTCAGGGAGATAGGAT--TACTAGCTTCAATCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATCCT-TTA-TTTCAATCTGC
*** * * *
55280468 -CTTGTTGTAATCTCAGTGAGATAAGATTTCTGGCTTCAATCTGATGCAATCTAC
1 TC-CACTGTAATCTCAGGGAGATAAGA--TC---CTT-TAT-T--T-CAATCTGC
* * * * * *
55280522 TCTACAGTAA-CTTCAGAGAGATAAGATCATTTATTTTAATCAGC
1 TCCACTGTAATC-TCAGGGAGATAAGATCCTTTATTTCAATCTGC
* ** * *
55280566 TCCACTGTAACCTCAGGGAGATCGGAT--TACTAGCTTCAATCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATCCT-TTA-TTTCAATCTGC
* **
55280610 TCCGCTGTAATCTCAGGGAGATAAGAT--TTCTGGCTTCAATCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATCCTT-T-ATTTCAATCTGC
55280654 TCCACTGT
1 TCCACTGT
55280662 TGCTTAGGGA
Statistics
Matches: 415, Mismatches: 92, Indels: 115
0.67 0.15 0.18
Matches are distributed among these distances:
40 1 0.00
41 22 0.05
42 5 0.01
43 13 0.03
44 244 0.59
45 7 0.02
46 2 0.00
47 3 0.01
48 6 0.01
49 8 0.02
51 10 0.02
52 6 0.01
53 6 0.01
54 81 0.20
55 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (44 bp):
TCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTCAATCTGC
Found at i:55280339 original size:142 final size:142
Alignment explanation
Indices: 55280083--55280652 Score: 946
Period size: 142 Copynumber: 4.0 Consensus size: 142
55280073 AGATAAGACT
* * *
55280083 TGATGCGATCTACTCTACTGTAACTTCAAAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGT
1 TGATGCAATCTACTCTACTATAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGT
* * *
55280148 AATCTCAGGGAGATAGGACTACTAGCTTCAATCTGCTCTGCTATAATCTCAGGGAGATAAGATTT
66 AATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTT
55280213 CTGGCTTCAATC
131 CTGGCTTCAATC
55280225 TGATGCAATCTACTCTACTATAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGT
1 TGATGCAATCTACTCTACTATAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGT
55280290 AATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTT
66 AATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTT
*
55280355 CTAGCTTCAATC
131 CTGGCTTCAATC
* * **
55280367 TGATGCAATCTACTCTACTGTAACTTCAGAGAGATAAAATCCTTTATTTTAATCTACTCCACTGT
1 TGATGCAATCTACTCTACTATAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGT
* * *
55280432 AATCTCAGGGAGATAGGATTACTAGCTTCAATCTGC-CTTGTTGTAATCTCAGTGAGATAAGATT
66 AATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTC-CGCTGTAATCTCAGGGAGATAAGATT
55280496 TCTGGCTTCAATC
130 TCTGGCTTCAATC
* *
55280509 TGATGCAATCTACTCTAC-AGTAACTTCAGAGAGATAAGATCATTTATTTTAATCAGCTCCACTG
1 TGATGCAATCTACTCTACTA-TAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* *
55280573 TAACCTCAGGGAGATCGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
65 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
55280638 TCTGGCTTCAATC
130 TCTGGCTTCAATC
55280651 TG
1 TG
55280653 CTCCACTGTT
Statistics
Matches: 400, Mismatches: 25, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
141 1 0.00
142 398 1.00
143 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (142 bp):
TGATGCAATCTACTCTACTATAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGT
AATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTT
CTGGCTTCAATC
Found at i:55298996 original size:25 final size:28
Alignment explanation
Indices: 55298962--55299034 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 28
55298952 TTTCAAAGGT
*
55298962 TTTAGCAGAAA-G-AAT-CACAAATTAG
1 TTTAGAAGAAACGAAATGCACAAATTAG
55298987 TTTAGAAGAAAACGAAATGCACAAATTAG
1 TTTAGAAG-AAACGAAATGCACAAATTAG
55299016 TTTAGAAGAAAACGAAATG
1 TTTAGAAG-AAACGAAATG
55299035 ACATTAATCC
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
25 7 0.16
26 3 0.07
27 1 0.02
28 3 0.07
29 29 0.67
ACGTcount: A:0.51, C:0.10, G:0.18, T:0.22
Consensus pattern (28 bp):
TTTAGAAGAAACGAAATGCACAAATTAG
Found at i:55299010 original size:29 final size:29
Alignment explanation
Indices: 55298977--55299034 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
55298967 CAGAAAGAAT
55298977 CACAAATTAGTTTAGAAGAAAACGAAATG
1 CACAAATTAGTTTAGAAGAAAACGAAATG
55299006 CACAAATTAGTTTAGAAGAAAACGAAATG
1 CACAAATTAGTTTAGAAGAAAACGAAATG
55299035 ACATTAATCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.52, C:0.10, G:0.17, T:0.21
Consensus pattern (29 bp):
CACAAATTAGTTTAGAAGAAAACGAAATG
Found at i:55301938 original size:13 final size:13
Alignment explanation
Indices: 55301920--55301944 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55301910 GTTTGCGATA
55301920 ATTTCTTTGTTTC
1 ATTTCTTTGTTTC
55301933 ATTTCTTTGTTT
1 ATTTCTTTGTTT
55301945 TTCTTTTCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.12, G:0.08, T:0.72
Consensus pattern (13 bp):
ATTTCTTTGTTTC
Found at i:55313497 original size:16 final size:16
Alignment explanation
Indices: 55313476--55313506 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
55313466 TTTCTAGTAT
55313476 TTTATTTACTAGCGTG
1 TTTATTTACTAGCGTG
55313492 TTTATTTACTAGCGT
1 TTTATTTACTAGCGT
55313507 ATTTGCTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.13, G:0.16, T:0.52
Consensus pattern (16 bp):
TTTATTTACTAGCGTG
Found at i:55322821 original size:17 final size:17
Alignment explanation
Indices: 55322799--55322840 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
55322789 AAAGACTGTT
55322799 GAACAAAACA-AGTTAGC
1 GAACAAAACACA-TTAGC
*
55322816 GAACAAAATACATTAGC
1 GAACAAAACACATTAGC
55322833 GAACAAAA
1 GAACAAAA
55322841 TATATAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 22 0.96
18 1 0.04
ACGTcount: A:0.57, C:0.17, G:0.14, T:0.12
Consensus pattern (17 bp):
GAACAAAACACATTAGC
Found at i:55322865 original size:16 final size:17
Alignment explanation
Indices: 55322844--55322891 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
55322834 AACAAAATAT
55322844 ATAAATATATAAATAAA
1 ATAAATATATAAATAAA
*
55322861 A-AAATATTTATATATAAA
1 ATAAATA--TATAAATAAA
55322879 ATAAA-ATATAAAT
1 ATAAATATATAAAT
55322892 TGAATAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
16 11 0.42
17 1 0.04
18 11 0.42
19 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAAATATATAAATAAA
Found at i:55322867 original size:22 final size:20
Alignment explanation
Indices: 55322837--55322891 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 20
55322827 ATTAGCGAAC
*
55322837 AAAATATATAAATATATAAATA
1 AAAAAATATAAATATAT-AA-A
**
55322859 AAAAAATATTTATATATAAA
1 AAAAAATATAAATATATAAA
*
55322879 ATAAAATATAAAT
1 AAAAAATATAAAT
55322892 TGAATAGTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 11 0.41
21 2 0.07
22 14 0.52
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAAATATAAATATATAAA
Found at i:55322874 original size:20 final size:20
Alignment explanation
Indices: 55322848--55322887 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
55322838 AAATATATAA
55322848 ATATATAAATAAAAAAATATTT
1 ATATAT-AA-AAAAAAATATTT
*
55322870 ATATATAAAATAAAATAT
1 ATATATAAAAAAAAATAT
55322888 AAATTGAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 2 0.12
22 6 0.35
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
ATATATAAAAAAAAATATTT
Found at i:55323356 original size:20 final size:20
Alignment explanation
Indices: 55323331--55323399 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
55323321 AGTGGCTATT
* * *
55323331 AAATCAATTTGATAAAAATC
1 AAATCAAATTGATTAGAATC
55323351 AAATCAAATTGATTAGAATC
1 AAATCAAATTGATTAGAATC
*
55323371 AAATAAAATTGATTAGAATC
1 AAATCAAATTGATTAGAATC
*
55323391 AAATAAAAT
1 AAATCAAAT
55323400 AAGGATATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (20 bp):
AAATCAAATTGATTAGAATC
Found at i:55327051 original size:24 final size:23
Alignment explanation
Indices: 55327022--55327067 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
55327012 TTAGTGAACA
55327022 AAATATATAAATATATAAATAAAC
1 AAATATATAAATATA-AAATAAAC
* *
55327046 AAATATTTATATATAAAATAAA
1 AAATATATAAATATAAAATAAA
55327068 ATATAAATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
AAATATATAAATATAAAATAAAC
Found at i:55327545 original size:20 final size:20
Alignment explanation
Indices: 55327522--55327562 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
55327512 TTAAATCAAT
*
55327522 TTGATTAAAATCAAATTAAA
1 TTGATTAAAATCAAATAAAA
*
55327542 TTGATTAGAATCAAATAAAA
1 TTGATTAAAATCAAATAAAA
55327562 T
1 T
55327563 CAGGATATAT
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:0.54, C:0.05, G:0.07, T:0.34
Consensus pattern (20 bp):
TTGATTAAAATCAAATAAAA
Found at i:55329102 original size:12 final size:14
Alignment explanation
Indices: 55329072--55329103 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
55329062 ATCAAATAAA
55329072 AAAAATTAGAATGT
1 AAAAATTAGAATGT
55329086 AAAAATTA-AAT-T
1 AAAAATTAGAATGT
55329098 AAAAAT
1 AAAAAT
55329104 AAAAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 3 0.17
14 8 0.44
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (14 bp):
AAAAATTAGAATGT
Found at i:55329130 original size:12 final size:12
Alignment explanation
Indices: 55329113--55329159 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
55329103 TAAAAAATAT
*
55329113 TAAAACGAAAAC
1 TAAAACTAAAAC
55329125 TAAAACTAAAAC
1 TAAAACTAAAAC
*
55329137 TAAAACTAAAAA
1 TAAAACTAAAAC
*
55329149 TAAAAATAAAA
1 TAAAACTAAAA
55329160 AATGGCTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.72, C:0.11, G:0.02, T:0.15
Consensus pattern (12 bp):
TAAAACTAAAAC
Found at i:55329135 original size:34 final size:35
Alignment explanation
Indices: 55329065--55329141 Score: 84
Period size: 34 Copynumber: 2.2 Consensus size: 35
55329055 TGTAAGAATC
* * * *
55329065 AAATAAAAAAAATTAGAATGTAAAAATTAAATTAA
1 AAATAAAAAAAATTAAAACGTAAAAATAAAACTAA
* *
55329100 AAATAAAAAATATTAAAACG-AAAACTAAAACTAA
1 AAATAAAAAAAATTAAAACGTAAAAATAAAACTAA
*
55329134 AACTAAAA
1 AAATAAAA
55329142 CTAAAAATAA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
34 18 0.51
35 17 0.49
ACGTcount: A:0.70, C:0.05, G:0.04, T:0.21
Consensus pattern (35 bp):
AAATAAAAAAAATTAAAACGTAAAAATAAAACTAA
Found at i:55329136 original size:18 final size:18
Alignment explanation
Indices: 55329113--55329153 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
55329103 TAAAAAATAT
*
55329113 TAAAACGAAAACTAAAAC
1 TAAAACGAAAACTAAAAA
*
55329131 TAAAACTAAAACTAAAAA
1 TAAAACGAAAACTAAAAA
55329149 TAAAA
1 TAAAA
55329154 ATAAAAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.71, C:0.12, G:0.02, T:0.15
Consensus pattern (18 bp):
TAAAACGAAAACTAAAAA
Found at i:55329158 original size:18 final size:18
Alignment explanation
Indices: 55329120--55329159 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
55329110 TATTAAAACG
* *
55329120 AAAACTAAAACTAAAACT
1 AAAACTAAAAATAAAAAT
55329138 AAAACTAAAAATAAAAAT
1 AAAACTAAAAATAAAAAT
55329156 AAAA
1 AAAA
55329160 AATGGCTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.75, C:0.10, G:0.00, T:0.15
Consensus pattern (18 bp):
AAAACTAAAAATAAAAAT
Found at i:55329162 original size:7 final size:6
Alignment explanation
Indices: 55329085--55329160 Score: 53
Period size: 6 Copynumber: 12.0 Consensus size: 6
55329075 AATTAGAATG
* * * * * *
55329085 TAAAAA TTAAAT TAAAAA TAAAAAA TATTAAAA CGAAAAC TAAAAC TAAAAC
1 TAAAAA TAAAAA TAAAAA T-AAAAA TA--AAAA -TAAAAA TAAAAA TAAAAA
*
55329137 TAAAAC TAAAAA TAAAAA TAAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA
55329161 ATGGCTAAAT
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
6 44 0.76
7 9 0.16
8 4 0.07
9 1 0.02
ACGTcount: A:0.72, C:0.07, G:0.01, T:0.20
Consensus pattern (6 bp):
TAAAAA
Found at i:55331046 original size:16 final size:17
Alignment explanation
Indices: 55331006--55331056 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 17
55330996 TTATTTTTAA
55331006 TATATTA-TAAATATAT
1 TATATTATTAAATATAT
55331022 TATATTATTAAAT-TAT
1 TATATTATTAAATATAT
* *
55331038 TTTATTATTTATATATAT
1 TATATTA-TTAAATATAT
55331056 T
1 T
55331057 TAACTCTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 16 0.53
17 10 0.33
18 4 0.13
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATATTATTAAATATAT
Found at i:55333418 original size:2 final size:2
Alignment explanation
Indices: 55333411--55333440 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
55333401 CCTACAAAGT
55333411 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
55333441 TCTAACTACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:55339375 original size:25 final size:24
Alignment explanation
Indices: 55339306--55339375 Score: 59
Period size: 24 Copynumber: 2.8 Consensus size: 24
55339296 CACAACTCTT
* * **
55339306 ATGAGCGTCCTGATATTTGGCTCTT
1 ATGAGC-TCCTGTTATATGGCTCAA
* * *
55339331 ATGAGCGCCCGTTACATGGCTCAA
1 ATGAGCTCCTGTTATATGGCTCAA
55339355 ATGAGCTTCCTGTTATATGGC
1 ATGAGC-TCCTGTTATATGGC
55339376 ACGAGAGAGA
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
24 17 0.50
25 17 0.50
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.33
Consensus pattern (24 bp):
ATGAGCTCCTGTTATATGGCTCAA
Found at i:55346745 original size:24 final size:25
Alignment explanation
Indices: 55346718--55346765 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
55346708 GGATGCTTTG
*
55346718 AAGAACTAT-TAACGGGAAGCTCGC
1 AAGAACCATATAACGGGAAGCTCGC
55346742 AAGAACCATATAACGGGAAGCTCG
1 AAGAACCATATAACGGGAAGCTCG
55346766 TGAGAGCCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.40, C:0.21, G:0.25, T:0.15
Consensus pattern (25 bp):
AAGAACCATATAACGGGAAGCTCGC
Found at i:55356374 original size:17 final size:17
Alignment explanation
Indices: 55356348--55356388 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
55356338 CTCAATACAC
*
55356348 TGAC-ATGAATATGTAA
1 TGACAATGAATATGCAA
55356364 TGACAATGAATATGCAA
1 TGACAATGAATATGCAA
*
55356381 TAACAATG
1 TGACAATG
55356389 TATACTTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.27
Consensus pattern (17 bp):
TGACAATGAATATGCAA
Found at i:55372672 original size:42 final size:42
Alignment explanation
Indices: 55372559--55372672 Score: 115
Period size: 42 Copynumber: 2.8 Consensus size: 42
55372549 AAGTACTAAC
* * *
55372559 AGCTTATTTGCAACATTGGTGGCTTGT-C-CATATTACTGGC
1 AGCTTGTTTGCAACACTGGTGGCTTGTCCACATATTACTGGA
** * * * *
55372599 ATTTTGTTTGCGACACTGGTGGCTAGACCACATATTAGTGGA
1 AGCTTGTTTGCAACACTGGTGGCTTGTCCACATATTACTGGA
* *
55372641 AGCTTGTTTGCAATACTGGTGGATTGTCCACA
1 AGCTTGTTTGCAACACTGGTGGCTTGTCCACA
55372673 ATACTGATAT
Statistics
Matches: 56, Mismatches: 16, Indels: 2
0.76 0.22 0.03
Matches are distributed among these distances:
40 20 0.36
41 1 0.02
42 35 0.62
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (42 bp):
AGCTTGTTTGCAACACTGGTGGCTTGTCCACATATTACTGGA
Found at i:55385584 original size:27 final size:27
Alignment explanation
Indices: 55385553--55385639 Score: 113
Period size: 27 Copynumber: 3.2 Consensus size: 27
55385543 ATATGTGCAA
*
55385553 AGGGTAAAATGACTGAAATACCCTCG-
1 AGGGTAAAATGACTAAAATACCCTCGT
* * *
55385579 ATGGGTAAAATGGCTAAAATGCCCCCGT
1 A-GGGTAAAATGACTAAAATACCCTCGT
*
55385607 AGGGTAAAATGACCAAAATACCCTCGT
1 AGGGTAAAATGACTAAAATACCCTCGT
55385634 AGGGTA
1 AGGGTA
55385640 GAATATCGAA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
26 1 0.02
27 49 0.96
28 1 0.02
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.20
Consensus pattern (27 bp):
AGGGTAAAATGACTAAAATACCCTCGT
Found at i:55385694 original size:27 final size:26
Alignment explanation
Indices: 55385633--55385867 Score: 184
Period size: 27 Copynumber: 8.7 Consensus size: 26
55385623 AATACCCTCG
* * *
55385633 TAGGGTAGAATATCGAAATACCTCC-A
1 TAGGGTAAAATAACGTAATACC-CCTA
* *
55385659 TAGGATAAAATAACAGTAATACCCTTA
1 TAGGGTAAAATAAC-GTAATACCCCTA
* *
55385686 TGGGGTAAAATAACCGTAATGCCCCTA
1 TAGGGTAAAATAA-CGTAATACCCCTA
* *
55385713 TAGGGTAAAATAATCGTAATACCCTTG
1 TAGGGTAAAATAA-CGTAATACCCCTA
* * * *
55385740 TAGGATAAAATGACCGTAATGCCCCTG
1 TAGGGTAAAAT-AACGTAATACCCCTA
*
55385767 TAGGGTAAAATGATCGTAATACCCCTA
1 TAGGGTAAAAT-AACGTAATACCCCTA
* * * *
55385794 TAGGGTAAATTGACCGTAATGCCCCTG
1 TAGGGTAAAAT-AACGTAATACCCCTA
* * *
55385821 TAGGGTAAAATGAATGTAATGCCCCTG
1 TAGGGTAAAAT-AACGTAATACCCCTA
*
55385848 TAGGGTAAAATGATCGTAAT
1 TAGGGTAAAAT-AACGTAAT
55385868 GTCCTTGTAA
Statistics
Matches: 174, Mismatches: 31, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
26 12 0.07
27 160 0.92
28 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (26 bp):
TAGGGTAAAATAACGTAATACCCCTA
Found at i:55385868 original size:27 final size:27
Alignment explanation
Indices: 55385688--55385897 Score: 253
Period size: 27 Copynumber: 7.8 Consensus size: 27
55385678 TACCCTTATG
* * *
55385688 GGGTAAAATAACCGTAATGCCCCTATA
1 GGGTAAAATGATCGTAATGCCCCTGTA
* * *
55385715 GGGTAAAATAATCGTAATACCCTTGTA
1 GGGTAAAATGATCGTAATGCCCCTGTA
* *
55385742 GGATAAAATGACCGTAATGCCCCTGTA
1 GGGTAAAATGATCGTAATGCCCCTGTA
* *
55385769 GGGTAAAATGATCGTAATACCCCTATA
1 GGGTAAAATGATCGTAATGCCCCTGTA
* *
55385796 GGGTAAATTGACCGTAATGCCCCTGTA
1 GGGTAAAATGATCGTAATGCCCCTGTA
55385823 GGGTAAAATGAAT-GTAATGCCCCTGTA
1 GGGTAAAATG-ATCGTAATGCCCCTGTA
* *
55385850 GGGTAAAATGATCGTAATGTCCTTGTA
1 GGGTAAAATGATCGTAATGCCCCTGTA
*
55385877 AGGTAAAATGA-CAGTAATGCC
1 GGGTAAAATGATC-GTAATGCC
55385898 TTAGTGGGTA
Statistics
Matches: 157, Mismatches: 23, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
26 3 0.02
27 153 0.97
28 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (27 bp):
GGGTAAAATGATCGTAATGCCCCTGTA
Found at i:55385882 original size:81 final size:81
Alignment explanation
Indices: 55385659--55385897 Score: 264
Period size: 81 Copynumber: 3.0 Consensus size: 81
55385649 AATACCTCCA
* * * * * * * *
55385659 TAGGATAAAAT-AACAGTAATACCCTTATGGGGTAAAATAACCGTAATGCCCCTATAGGGTAAAA
1 TAGGATAAAATGAAC-GTAATGCCCCTGTAGGGTAAAATGATCGTAATACCCCTATAAGGTAAAA
* * * *
55385723 TAATCGTAATACCCTTG
65 TGACCGTAATGCCCCTG
* * *
55385740 TAGGATAAAATGACCGTAATGCCCCTGTAGGGTAAAATGATCGTAATACCCCTATAGGGTAAATT
1 TAGGATAAAATGAACGTAATGCCCCTGTAGGGTAAAATGATCGTAATACCCCTATAAGGTAAAAT
55385805 GACCGTAATGCCCCTG
66 GACCGTAATGCCCCTG
* * ** * *
55385821 TAGGGTAAAATGAATGTAATGCCCCTGTAGGGTAAAATGATCGTAATGTCCTTGTAAGGTAAAAT
1 TAGGATAAAATGAACGTAATGCCCCTGTAGGGTAAAATGATCGTAATACCCCTATAAGGTAAAAT
*
55385886 GACAGTAATGCC
66 GACCGTAATGCC
55385898 TTAGTGGGTA
Statistics
Matches: 134, Mismatches: 23, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
81 132 0.99
82 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (81 bp):
TAGGATAAAATGAACGTAATGCCCCTGTAGGGTAAAATGATCGTAATACCCCTATAAGGTAAAAT
GACCGTAATGCCCCTG
Found at i:55385897 original size:54 final size:54
Alignment explanation
Indices: 55385553--55385894 Score: 277
Period size: 54 Copynumber: 6.4 Consensus size: 54
55385543 ATATGTGCAA
* * * * *** *
55385553 AGGGTAAAATGACTGAAATACCCTCGAT-GGGTAAAATGGCTAAAATGCCCCCGT
1 AGGGTAAAATGACAGTAATACCC-CTATAGGGTAAAATGACCGTAATGCCCCTGT
* * * * * * *
55385607 AGGGTAAAATGACCA-AAATA-CCCTCGTAGGGTAGAAT-ATCGAAATACCTCC-AT
1 AGGGTAAAATGA-CAGTAATACCCCT-ATAGGGTAAAATGACCGTAATGCC-CCTGT
* * * * * *
55385660 AGGATAAAATAACAGTAATACCCTTATGGGGTAAAATAACCGTAATGCCCCTAT
1 AGGGTAAAATGACAGTAATACCCCTATAGGGTAAAATGACCGTAATGCCCCTGT
* * * *
55385714 AGGGTAAAATAATC-GTAATACCCTTGTAGGATAAAATGACCGTAATGCCCCTGT
1 AGGGTAAAATGA-CAGTAATACCCCTATAGGGTAAAATGACCGTAATGCCCCTGT
*
55385768 AGGGTAAAATGATC-GTAATACCCCTATAGGGTAAATTGACCGTAATGCCCCTGT
1 AGGGTAAAATGA-CAGTAATACCCCTATAGGGTAAAATGACCGTAATGCCCCTGT
* * * * *
55385822 AGGGTAAAATGA-ATGTAATGCCCCTGTAGGGTAAAATGATCGTAATGTCCTTGT
1 AGGGTAAAATGACA-GTAATACCCCTATAGGGTAAAATGACCGTAATGCCCCTGT
*
55385876 AAGGTAAAATGACAGTAAT
1 AGGGTAAAATGACAGTAAT
55385895 GCCTTAGTGG
Statistics
Matches: 238, Mismatches: 38, Indels: 24
0.79 0.13 0.08
Matches are distributed among these distances:
52 3 0.01
53 35 0.15
54 197 0.83
55 3 0.01
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (54 bp):
AGGGTAAAATGACAGTAATACCCCTATAGGGTAAAATGACCGTAATGCCCCTGT
Found at i:55386013 original size:24 final size:24
Alignment explanation
Indices: 55385958--55386016 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
55385948 TCTATGGTTA
*
55385958 AATGACTGATTTGTTTGTGTTTGG
1 AATGACTGATTTGTCTGTGTTTGG
* *
55385982 TATAACTGATTTGTCTGTGATTT-G
1 AATGACTGATTTGTCTGTG-TTTGG
55386006 AATGACTGATT
1 AATGACTGATT
55386017 CTGAGCATGG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
24 26 0.90
25 3 0.10
ACGTcount: A:0.22, C:0.07, G:0.24, T:0.47
Consensus pattern (24 bp):
AATGACTGATTTGTCTGTGTTTGG
Found at i:55386170 original size:26 final size:26
Alignment explanation
Indices: 55386115--55386170 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
55386105 ATACTATTAC
* * ** *
55386115 TGGCATCTTTGCTGCGATATTGTTGC
1 TGGCAGCTTTGCTGCGATACTACTGA
55386141 TGGCAGCTTTGCTGCGATACTACTGA
1 TGGCAGCTTTGCTGCGATACTACTGA
55386167 TGGC
1 TGGC
55386171 TTTGTGCCGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.14, C:0.21, G:0.29, T:0.36
Consensus pattern (26 bp):
TGGCAGCTTTGCTGCGATACTACTGA
Found at i:55386202 original size:32 final size:32
Alignment explanation
Indices: 55386161--55386381 Score: 221
Period size: 32 Copynumber: 6.9 Consensus size: 32
55386151 GCTGCGATAC
55386161 TACTGATGGCTTTGTGCCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* *
55386193 TACTGATGGCTTTGTGCTGATCATAGTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* *
55386225 TACTGATGGCTTTGTGCCGATCATATTACTGC
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * * **
55386257 TACCGATGGCTGTGTGTCGATCAT-TTCACTAT
1 TACTGATGGCTTTGTGCCGATCATATT-ACCGT
* * * *
55386289 CACTGATGTCTGTGTGCCGATCATGTTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * * * * *
55386321 TACTAATGGCTGTGT-CCCAGTCATATCACTGC
1 TACTGATGGCTTTGTGCCGA-TCATATTACCGT
* *
55386353 TACTGATGGCTTTGTGCCAATCACATTAC
1 TACTGATGGCTTTGTGCCGATCATATTAC
55386382 TATACTTATG
Statistics
Matches: 155, Mismatches: 30, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
31 5 0.03
32 145 0.94
33 5 0.03
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTACCGT
Found at i:55386384 original size:96 final size:95
Alignment explanation
Indices: 55386160--55386394 Score: 260
Period size: 96 Copynumber: 2.5 Consensus size: 95
55386150 TGCTGCGATA
** * * *
55386160 CTACTGATGGCTTTGTGCCGATCATATTACCGTTACTGATGGCTTTGTGCTGATCATAGTACCGT
1 CTACTGATGGCTTTGTGCCGATCA-ATTACTATCACTGATGGCTGTGTGCCGATCATAGTACCGT
* * * *
55386225 TACTGATGGCTTTGTGCCGATCATATTACTG
65 TACTAATGGCTGTGTCCCGATCATATCACTG
* * * * *
55386256 CTACCGATGGCTGTGTGTCGATCATTTCACTATCACTGATGTCTGTGTGCCGATCAT-GTTACCG
1 CTACTGATGGCTTTGTGCCGATCAATT-ACTATCACTGATGGCTGTGTGCCGATCATAG-TACCG
55386320 TTACTAATGGCTGTGTCCC-AGTCATATCACTG
64 TTACTAATGGCTGTGTCCCGA-TCATATCACTG
* *
55386352 CTACTGATGGCTTTGTGCCAATCACATTACTAT-ACTTATGGCT
1 CTACTGATGGCTTTGTGCCGATCA-ATTACTATCACTGATGGCT
55386395 TATAGCCATT
Statistics
Matches: 114, Mismatches: 21, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
95 12 0.11
96 100 0.88
97 2 0.02
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (95 bp):
CTACTGATGGCTTTGTGCCGATCAATTACTATCACTGATGGCTGTGTGCCGATCATAGTACCGTT
ACTAATGGCTGTGTCCCGATCATATCACTG
Found at i:55386412 original size:22 final size:22
Alignment explanation
Indices: 55386387--55386451 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
55386377 ATTACTATAC
55386387 TTATGGCTTATAGCCATTCTGT
1 TTATGGCTTATAGCCATTCTGT
** * * *
55386409 TTATAACTTATAACTATACTGT
1 TTATGGCTTATAGCCATTCTGT
*
55386431 TTAAGGCTCT-TAGCCATTCTG
1 TTATGGCT-TATAGCCATTCTG
55386452 ACTACTGGCA
Statistics
Matches: 31, Mismatches: 11, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
22 30 0.97
23 1 0.03
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (22 bp):
TTATGGCTTATAGCCATTCTGT
Found at i:55387718 original size:34 final size:34
Alignment explanation
Indices: 55387675--55387799 Score: 162
Period size: 34 Copynumber: 3.7 Consensus size: 34
55387665 AGGTGGATGG
* *
55387675 ATTTGGTGTGCTGGATGGATTAACTCATACGAGC
1 ATTTGATGTGCTAGATGGATTAACTCATACGAGC
* * *
55387709 ATTTGGTGTGCTAGATGGATTAGCTCATATGAGC
1 ATTTGATGTGCTAGATGGATTAACTCATACGAGC
* * *
55387743 ATTTGATGTGCTGGATGGATTAGCTCTTACGAGC
1 ATTTGATGTGCTAGATGGATTAACTCATACGAGC
*
55387777 ATCTGATGTGCTAGATGG-TTAAC
1 ATTTGATGTGCTAGATGGATTAAC
55387800 CGTGTACTCG
Statistics
Matches: 81, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 4 0.05
34 77 0.95
ACGTcount: A:0.23, C:0.14, G:0.29, T:0.34
Consensus pattern (34 bp):
ATTTGATGTGCTAGATGGATTAACTCATACGAGC
Found at i:55389681 original size:23 final size:23
Alignment explanation
Indices: 55389655--55389710 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
55389645 CTAGCCATTT
*
55389655 AGGCGCCACAGAATATGCCACAA
1 AGGCGCCAAAGAATATGCCACAA
** *
55389678 AGGCTTCAAAGATTATGCCACAA
1 AGGCGCCAAAGAATATGCCACAA
*
55389701 AGGCTCCAAA
1 AGGCGCCAAA
55389711 AAGTGCGCTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.39, C:0.27, G:0.20, T:0.14
Consensus pattern (23 bp):
AGGCGCCAAAGAATATGCCACAA
Found at i:55389746 original size:23 final size:23
Alignment explanation
Indices: 55389668--55389803 Score: 116
Period size: 23 Copynumber: 5.9 Consensus size: 23
55389658 CGCCACAGAA
*
55389668 TATGCCACAAAGGCTTCAAAGAT
1 TATGCCACAAAGGCTTCATAGAT
* * * *
55389691 TATGCCACAAAGGCTCCAAAAAG
1 TATGCCACAAAGGCTTCATAGAT
** *
55389714 TGCGCTACAAAGGCTTCATAGAT
1 TATGCCACAAAGGCTTCATAGAT
* *
55389737 TATACCACAAAGCCTTCATTA-AT
1 TATGCCACAAAGGCTTCA-TAGAT
*
55389760 TCTGCCACAAAGGC-TCTATAGAAT
1 TATGCCACAAAGGCTTC-ATAG-AT
*
55389784 GA-GCCACAAAGGCTTCATAG
1 TATGCCACAAAGGCTTCATAG
55389804 GTAACTTTCC
Statistics
Matches: 88, Mismatches: 20, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
22 4 0.05
23 78 0.89
24 6 0.07
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (23 bp):
TATGCCACAAAGGCTTCATAGAT
Found at i:55397285 original size:39 final size:40
Alignment explanation
Indices: 55397230--55397358 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 40
55397220 TACAACACCA
* * * * *
55397230 GCACAATGCATGCTAGGTACAAAACCTGATAAACACACTG
1 GCACAAAGCCTGCTAGGCACAAAACCCGATAAATACACTG
* *
55397270 GCACAAA-CCTGCTAGGCACAAACCCCGATAAATACACTA
1 GCACAAAGCCTGCTAGGCACAAAACCCGATAAATACACTG
* * * *
55397309 GCATAAAGCCTACTAGGCACAAAGCCCGATAAATACACCG
1 GCACAAAGCCTGCTAGGCACAAAACCCGATAAATACACTG
55397349 GCACAAAGCC
1 GCACAAAGCC
55397359 ACTAACTCGT
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
39 32 0.43
40 43 0.57
ACGTcount: A:0.40, C:0.30, G:0.16, T:0.13
Consensus pattern (40 bp):
GCACAAAGCCTGCTAGGCACAAAACCCGATAAATACACTG
Found at i:55401826 original size:4 final size:4
Alignment explanation
Indices: 55401817--55401854 Score: 58
Period size: 4 Copynumber: 9.0 Consensus size: 4
55401807 CTAGTTTCTC
55401817 CTTT CTTT CTTT CTTT CTTTT CTTT CTTT CCTTT CTTT
1 CTTT CTTT CTTT CTTT C-TTT CTTT CTTT -CTTT CTTT
55401855 TTCTCCCTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 24 0.75
5 8 0.25
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
CTTT
Found at i:55401840 original size:9 final size:9
Alignment explanation
Indices: 55401818--55401855 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
55401808 TAGTTTCTCC
55401818 TTTCTTTC-
1 TTTCTTTCT
55401826 TTTCTTTCT
1 TTTCTTTCT
55401835 TTTCTTTCT
1 TTTCTTTCT
*
55401844 TTCCTTTCT
1 TTTCTTTCT
55401853 TTT
1 TTT
55401856 TCTCCCTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 8 0.30
9 19 0.70
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTCTTTCT
Found at i:55401840 original size:13 final size:12
Alignment explanation
Indices: 55401817--55401854 Score: 58
Period size: 13 Copynumber: 3.0 Consensus size: 12
55401807 CTAGTTTCTC
55401817 CTTTCTTTCTTT
1 CTTTCTTTCTTT
55401829 CTTTCTTTTCTTT
1 CTTTC-TTTCTTT
55401842 CTTTCCTTTCTTT
1 CTTT-CTTTCTTT
55401855 TTCTCCCTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.21
13 18 0.75
14 1 0.04
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
CTTTCTTTCTTT
Found at i:55401921 original size:22 final size:23
Alignment explanation
Indices: 55401884--55401941 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
55401874 ACTTTTGTTC
55401884 TTTA-TTTATT-TCATTTA-CTTA
1 TTTATTTTATTAT-ATTTACCTTA
55401905 TTTATTTTATTATATTTACCTTA
1 TTTATTTTATTATATTTACCTTA
*
55401928 -TTATATTATTATAT
1 TTTATTTTATTATAT
55401942 ATATATTTAC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
21 4 0.12
22 24 0.73
23 5 0.15
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTATTTTATTATATTTACCTTA
Found at i:55401922 original size:14 final size:14
Alignment explanation
Indices: 55401903--55401950 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
55401893 TTCATTTACT
55401903 TATTTATTTTATTA
1 TATTTATTTTATTA
**
55401917 TATTTACCTTATTA
1 TATTTATTTTATTA
*
55401931 TA-TTATTATATATA
1 TATTTATTTTAT-TA
55401945 TATTTA
1 TATTTA
55401951 CTTAAATATT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
13 6 0.22
14 18 0.67
15 3 0.11
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (14 bp):
TATTTATTTTATTA
Found at i:55409747 original size:17 final size:17
Alignment explanation
Indices: 55409727--55409787 Score: 65
Period size: 17 Copynumber: 3.8 Consensus size: 17
55409717 TAGAATTGGG
55409727 TTGAAAAAATAATTTAA
1 TTGAAAAAATAATTTAA
* *
55409744 TTGAAAAATTAATCTAA
1 TTGAAAAAATAATTTAA
* *
55409761 TT---AATATAAATTAA
1 TTGAAAAAATAATTTAA
55409775 TTGAAAAAATAAT
1 TTGAAAAAATAAT
55409788 ATTTTAGGAA
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
14 10 0.30
17 23 0.70
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (17 bp):
TTGAAAAAATAATTTAA
Found at i:55410695 original size:29 final size:29
Alignment explanation
Indices: 55410663--55410718 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
55410653 AAATGCATCA
* * *
55410663 ATTTATTTTTATATTAAATAAATATAATT
1 ATTTATATATATAATAAATAAATATAATT
*
55410692 ATTTATATATATAATATATAAATATAA
1 ATTTATATATATAATAAATAAATATAA
55410719 AATGACGTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
ATTTATATATATAATAAATAAATATAATT
Found at i:55414345 original size:11 final size:11
Alignment explanation
Indices: 55414329--55414358 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
55414319 ATGTAGCTAT
55414329 TGGATGGTGGA
1 TGGATGGTGGA
55414340 TGGATGGTGGA
1 TGGATGGTGGA
55414351 TGGATGGT
1 TGGATGGT
55414359 CGGTCTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.17, C:0.00, G:0.53, T:0.30
Consensus pattern (11 bp):
TGGATGGTGGA
Found at i:55416725 original size:3 final size:3
Alignment explanation
Indices: 55416717--55416758 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
55416707 AGCAAAAGAA
55416717 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
55416759 AGTAAGATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.67, T:0.33
Consensus pattern (3 bp):
TGG
Found at i:55431399 original size:34 final size:34
Alignment explanation
Indices: 55431355--55431534 Score: 225
Period size: 34 Copynumber: 5.3 Consensus size: 34
55431345 AACCAGCCAA
* * * * *
55431355 CACACTAAATGCTCATATGAGCTAGTCCATCCAA
1 CACACCAAATGCTCGTATGAGCCAATCCATCCAG
* * *
55431389 CACACCAAATGCTCGTCTGAGCTAGTCCATCCAG
1 CACACCAAATGCTCGTATGAGCCAATCCATCCAG
*
55431423 CACACCAAATGCTCGTATGAGCCAATCCATCTAG
1 CACACCAAATGCTCGTATGAGCCAATCCATCCAG
*
55431457 CACACTAAATGCTCGTATGAGCCAATCCATCCAG
1 CACACCAAATGCTCGTATGAGCCAATCCATCCAG
* *** *
55431491 CACACCAGATGCTCGTATGAAAAAATCCATCCAT
1 CACACCAAATGCTCGTATGAGCCAATCCATCCAG
55431525 CACACCAAAT
1 CACACCAAAT
55431535 AATACGGTAA
Statistics
Matches: 129, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 129 1.00
ACGTcount: A:0.34, C:0.32, G:0.13, T:0.21
Consensus pattern (34 bp):
CACACCAAATGCTCGTATGAGCCAATCCATCCAG
Found at i:55435078 original size:21 final size:22
Alignment explanation
Indices: 55435048--55435092 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
55435038 GAGCAAATTG
55435048 TTGATTCTATTTCCTTTTTG-AT
1 TTGATTCTA-TTCCTTTTTGTAT
*
55435070 TTGA-TCTATTCTTTTTTGTAT
1 TTGATTCTATTCCTTTTTGTAT
55435091 TT
1 TT
55435093 CTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 8 0.38
22 4 0.19
ACGTcount: A:0.13, C:0.11, G:0.09, T:0.67
Consensus pattern (22 bp):
TTGATTCTATTCCTTTTTGTAT
Found at i:55440750 original size:35 final size:34
Alignment explanation
Indices: 55440663--55440936 Score: 335
Period size: 35 Copynumber: 8.1 Consensus size: 34
55440653 GTCCAAAAAG
* *
55440663 AAATAATACATGAACAGGAGAGATTCCCTGCAA-G
1 AAATAAT-CGTGAACAGGAGAGATTCCCTGCAACA
*
55440697 AAATGAT-GTGAACAGGAGAGATTCCCTGCAACA
1 AAATAATCGTGAACAGGAGAGATTCCCTGCAACA
*
55440730 AAATAATCCGTGAACAGGAGAGATTCCCTGCAA-G
1 AAATAAT-CGTGAACAGGAGAGATTCCCTGCAACA
* *
55440764 AAATGAT-GTGAACAGGAAAGATTCCCTGCAACA
1 AAATAATCGTGAACAGGAGAGATTCCCTGCAACA
*
55440797 AAATAATGTGTGAACAGGAGAGATTCCCTGCAACA
1 AAATAAT-CGTGAACAGGAGAGATTCCCTGCAACA
*
55440832 AAATAATGCGTGAACAGGAGAGATTCCCTGCAA-G
1 AAATAAT-CGTGAACAGGAGAGATTCCCTGCAACA
* *
55440866 AAATGAT-GTGAACAGGAAAGATTCCCTGCAACA
1 AAATAATCGTGAACAGGAGAGATTCCCTGCAACA
* * * *
55440899 GAATAATGCGTGAACAGGAAATATTCCCTGCAAGA
1 AAATAAT-CGTGAACAGGAGAGATTCCCTGCAACA
55440934 AAA
1 AAA
55440937 GACAAGTGAA
Statistics
Matches: 211, Mismatches: 20, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
32 69 0.33
33 17 0.08
34 18 0.09
35 107 0.51
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (34 bp):
AAATAATCGTGAACAGGAGAGATTCCCTGCAACA
Found at i:55440771 original size:67 final size:67
Alignment explanation
Indices: 55440663--55440936 Score: 340
Period size: 67 Copynumber: 4.0 Consensus size: 67
55440653 GTCCAAAAAG
* * *
55440663 AAATAATACATGAACAGGAGAGATTCCCTGCAAGAAATGAT-GTGAACAGGAGAGATTCCCTGCA
1 AAATAAT-CGTGAACAGGAGAGATTCCCTGCAAGAAATAATCGTGAACAGGAAAGATTCCCTGCA
55440727 ACA
65 ACA
*
55440730 AAATAATCCGTGAACAGGAGAGATTCCCTGCAAGAAATGAT-GTGAACAGGAAAGATTCCCTGCA
1 AAATAAT-CGTGAACAGGAGAGATTCCCTGCAAGAAATAATCGTGAACAGGAAAGATTCCCTGCA
55440794 ACA
65 ACA
* * *
55440797 AAATAATGTGTGAACAGGAGAGATTCCCTGCAACAAAATAATGCGTGAACAGGAGAGATTCCCTG
1 AAATAAT-CGTGAACAGGAGAGATTCCCTGCAA-GAAATAAT-CGTGAACAGGAAAGATTCCCTG
*
55440862 CAA-G
63 CAACA
* * * *
55440866 AAATGAT-GTGAACAGGAAAGATTCCCTGCAACAGAATAATGCGTGAACAGGAAATATTCCCTGC
1 AAATAATCGTGAACAGGAGAGATTCCCTGCAAGA-AATAAT-CGTGAACAGGAAAGATTCCCTGC
*
55440930 AAGA
64 AACA
55440934 AAA
1 AAA
55440937 GACAAGTGAA
Statistics
Matches: 187, Mismatches: 15, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
66 1 0.01
67 148 0.79
68 9 0.05
69 6 0.03
70 23 0.12
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (67 bp):
AAATAATCGTGAACAGGAGAGATTCCCTGCAAGAAATAATCGTGAACAGGAAAGATTCCCTGCAA
CA
Found at i:55440846 original size:102 final size:102
Alignment explanation
Indices: 55440673--55440936 Score: 426
Period size: 102 Copynumber: 2.6 Consensus size: 102
55440663 AAATAATACA
* * *
55440673 TGAACAGGAGAGATTCCCTGCAA-GAAATGA--TGTGAACAGGAGAGATTCCCTGCAACAAAATA
1 TGAACAGGAAAGATTCCCTGCAACAAAATAATGTGTGAACAGGAGAGATTCCCTGCAACAAAATA
55440735 ATCCGTGAACAGGAGAGATTCCCTGCAAGAAATGATG
66 ATCCGTGAACAGGAGAGATTCCCTGCAAGAAATGATG
55440772 TGAACAGGAAAGATTCCCTGCAACAAAATAATGTGTGAACAGGAGAGATTCCCTGCAACAAAATA
1 TGAACAGGAAAGATTCCCTGCAACAAAATAATGTGTGAACAGGAGAGATTCCCTGCAACAAAATA
*
55440837 ATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATG
66 ATCCGTGAACAGGAGAGATTCCCTGCAAGAAATGATG
* * * * *
55440874 TGAACAGGAAAGATTCCCTGCAACAGAATAATGCGTGAACAGGAAATATTCCCTGCAAGAAAA
1 TGAACAGGAAAGATTCCCTGCAACAAAATAATGTGTGAACAGGAGAGATTCCCTGCAACAAAA
55440937 GACAAGTGAA
Statistics
Matches: 153, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
99 22 0.14
100 5 0.03
102 126 0.82
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.18
Consensus pattern (102 bp):
TGAACAGGAAAGATTCCCTGCAACAAAATAATGTGTGAACAGGAGAGATTCCCTGCAACAAAATA
ATCCGTGAACAGGAGAGATTCCCTGCAAGAAATGATG
Found at i:55445889 original size:11 final size:12
Alignment explanation
Indices: 55445873--55445901 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
55445863 TTATTAACGG
55445873 TGAATG-ATATT
1 TGAATGAATATT
55445884 TGAATGAATATT
1 TGAATGAATATT
55445896 TGAATG
1 TGAATG
55445902 TTCTTATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (12 bp):
TGAATGAATATT
Found at i:55453232 original size:44 final size:43
Alignment explanation
Indices: 55453125--55453243 Score: 134
Period size: 44 Copynumber: 2.7 Consensus size: 43
55453115 TCGTACAACA
* *
55453125 CCAACATCCCAGACGTGGTCTTACATGTAACCACATATCGATG
1 CCAACATCCCAGACGTGGTCTTACACGTAACCACAAATCGATG
* *
55453168 CC-ACTATCCTAGACAG-GGTCTTACACGTAAGTCACAAATCGATG
1 CCAAC-ATCCCAGAC-GTGGTCTTACACGTAA-CCACAAATCGATG
* *
55453212 CCAACGTCCCAGACGTGGTCTTAGACGATAAC
1 CCAACATCCCAGACGTGGTCTTACACG-TAAC
55453244 ACATAATGAA
Statistics
Matches: 62, Mismatches: 8, Indels: 11
0.77 0.10 0.14
Matches are distributed among these distances:
42 2 0.03
43 24 0.39
44 31 0.50
45 5 0.08
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.22
Consensus pattern (43 bp):
CCAACATCCCAGACGTGGTCTTACACGTAACCACAAATCGATG
Found at i:55460520 original size:44 final size:43
Alignment explanation
Indices: 55460425--55460531 Score: 110
Period size: 44 Copynumber: 2.4 Consensus size: 43
55460415 AACATCTCAA
* * *
55460425 ACGTGGTCTTACATGTAACCACATATCGATGCCACTATCCTAG
1 ACGTGGTCTTACACGTAACCACAAATCGATGCCACTATCCCAG
* *
55460468 ACAG-GGTCTTACACGTAAGTCACAAATCGATGCCAAC-GTCCCAG
1 AC-GTGGTCTTACACGTAA-CCACAAATCGATGCC-ACTATCCCAG
*
55460512 ACGTGGTCTTAGACGATAAC
1 ACGTGGTCTTACACG-TAAC
55460532 ACATAATGAA
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
43 16 0.31
44 31 0.60
45 5 0.10
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (43 bp):
ACGTGGTCTTACACGTAACCACAAATCGATGCCACTATCCCAG
Found at i:55466335 original size:13 final size:13
Alignment explanation
Indices: 55466296--55466343 Score: 55
Period size: 12 Copynumber: 3.8 Consensus size: 13
55466286 TTAAAAGAGT
55466296 ATAAATAAAATAA
1 ATAAATAAAATAA
* *
55466309 TTAACT-AAATAA
1 ATAAATAAAATAA
*
55466321 ATAAATAAAACAA
1 ATAAATAAAATAA
55466334 ATAAA-AAAAT
1 ATAAATAAAAT
55466344 TTAATAATTG
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
12 14 0.50
13 14 0.50
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.23
Consensus pattern (13 bp):
ATAAATAAAATAA
Found at i:55466335 original size:17 final size:19
Alignment explanation
Indices: 55466296--55466343 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 19
55466286 TTAAAAGAGT
55466296 ATAAATAAAATAATTAACTAA
1 ATAAAT-AAATAA-TAACTAA
55466317 ATAAATAAATAA-AAC-AA
1 ATAAATAAATAATAACTAA
*
55466334 ATAAAAAAAT
1 ATAAATAAAT
55466344 TTAATAATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 11 0.42
18 3 0.12
20 6 0.23
21 6 0.23
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.23
Consensus pattern (19 bp):
ATAAATAAATAATAACTAA
Found at i:55466343 original size:25 final size:25
Alignment explanation
Indices: 55466296--55466343 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
55466286 TTAAAAGAGT
* * **
55466296 ATAAATAAAATAATTAACTAAATAA
1 ATAAATAAAACAAATAAAAAAATAA
55466321 ATAAATAAAACAAATAAAAAAAT
1 ATAAATAAAACAAATAAAAAAAT
55466344 TTAATAATTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.23
Consensus pattern (25 bp):
ATAAATAAAACAAATAAAAAAATAA
Found at i:55473161 original size:18 final size:18
Alignment explanation
Indices: 55473128--55473202 Score: 59
Period size: 18 Copynumber: 4.3 Consensus size: 18
55473118 ATACATACAT
55473128 ATATATAC-TA-AAATAA
1 ATATATACATATAAATAA
*
55473144 ATATATACATATAGATAA
1 ATATATACATATAAATAA
*
55473162 A-AAATTACATATAAATAA
1 ATATA-TACATATAAATAA
* * *
55473180 AAATA-AAATAAAAATAA
1 ATATATACATATAAATAA
*
55473197 TTATAT
1 ATATAT
55473203 TATACTACAA
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
16 8 0.17
17 17 0.37
18 19 0.41
19 2 0.04
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.31
Consensus pattern (18 bp):
ATATATACATATAAATAA
Found at i:55475081 original size:173 final size:173
Alignment explanation
Indices: 55474770--55475081 Score: 425
Period size: 173 Copynumber: 1.8 Consensus size: 173
55474760 AATTTGCTAT
* *
55474770 CTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATACGATCTGCTCTCTGCAACTTCA
1 CTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATACGATCTGCTATCTACAACTTCA
* * * * *
55474835 GAGAGATAAGATCTAAGGTTTTAATCCGCCTCACTACAACTTCAGGGACGTAGGATTTGCCATCT
66 GAGAGATAAGATCCAAAGTTGTAATCCGCCTCACTACAACTTCAGAGACGTAGGATTTGCCAGCT
*
55474900 TCAATCTGCCTCGCTGCAACTTCAGGAGGATAAGACTTGCTTA
131 TAAATCTGCCTCGCTGCAACTTCAGGAGGATAAGACTTGCTTA
*
55474943 CTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTA-A-ACGGGATTTGCTATCTACAACTT
1 CTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATAC--GATCTGCTATCTACAACTT
* * * **
55475006 CAGAGAGATAAGTTCCAAAGTTGTAATCCG-CTCCGCTGCAACTTCAGAGA-GATAGGATTTGGT
64 CAGAGAGATAAGATCCAAAGTTGTAATCCGCCT-CACTACAACTTCAGAGACG-TAGGATTTGCC
*
55475069 GGCTTAAATCTGC
127 AGCTTAAATCTGC
55475082 TTCCCACTAT
Statistics
Matches: 120, Mismatches: 15, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
171 2 0.02
172 4 0.03
173 114 0.95
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (173 bp):
CTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATACGATCTGCTATCTACAACTTCA
GAGAGATAAGATCCAAAGTTGTAATCCGCCTCACTACAACTTCAGAGACGTAGGATTTGCCAGCT
TAAATCTGCCTCGCTGCAACTTCAGGAGGATAAGACTTGCTTA
Found at i:55475147 original size:44 final size:44
Alignment explanation
Indices: 55475099--55475540 Score: 117
Period size: 44 Copynumber: 10.2 Consensus size: 44
55475089 TATCTTGGAA
*
55475099 AGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** * * * * *
55475143 AGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGG
1 AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* ** ** * * * *
55475187 AGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTA-T--TTTGGAA
1 AGATAAGATTTGCCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
** *
55475231 AGATAAGATTTGCCGTCTTTGATCTGATCCACTACTGCTTAGGG
1 AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * *** *
55475275 AGAT-AG----G--ATCTACAACCTCCTCCGCCGTTGCTCAGGG
1 AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** * * *
55475312 AGACAAGGCTTTGTAG-CTTAAATTTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTTGCCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
* * **
55475356 AGATAAGACTTGTCGTCTTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** * * * ** * *
55475400 AGATAAGATCTACAATCTTTAACCTACTCTGCTGCTGCTCAGGG
1 AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* ** ** * * *
55475444 AGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTTGCCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
*
55475488 AGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
55475532 AGATAAGAT
1 AGATAAGAT
55475541 CTACAATCTT
Statistics
Matches: 262, Mismatches: 109, Indels: 54
0.62 0.26 0.13
Matches are distributed among these distances:
37 21 0.08
38 1 0.00
39 2 0.01
42 18 0.07
43 22 0.08
44 174 0.66
45 14 0.05
46 10 0.04
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (44 bp):
AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
Found at i:55475204 original size:132 final size:132
Alignment explanation
Indices: 55475064--55475590 Score: 852
Period size: 132 Copynumber: 4.0 Consensus size: 132
55475054 GAGATAGGAT
55475064 TTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCC
1 TTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCC
55475129 ACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAG
66 ACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAG
55475194 GC
131 GC
* * *
55475196 TTGGTGGCTTAAATCTGCTTCCCACTATTTTGGAAAGATAAGATTTGCCGTCTTTGATCTGATCC
1 TTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCC
* * * *
55475261 ACTACTGCTTAGGGAGATAGGATCT---A----CAACCTCCTCCGCCGTTGCTCAGGGAGACAAG
66 ACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAG
55475319 GC
131 GC
* * * * * *
55475321 TTTGTAGCTTAAATTTGCTTCCCACTATCTTGGAAAGATAAGACTTGTCGTCTTTGATCTGCTCC
1 TTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCC
* * *
55475386 ACTACTGCTTAGGGAGATAAGATCTACAATCTTTAACCTACTCTGCTGCTGCTCAGGGAGACAAG
66 ACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAG
55475451 GC
131 GC
55475453 TTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCC
1 TTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCC
*
55475518 ACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGAGAGACAAG
66 ACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAG
55475583 GC
131 GC
55475585 TTGGTG
1 TTGGTG
55475591 TTTCACCGGT
Statistics
Matches: 358, Mismatches: 30, Indels: 14
0.89 0.07 0.03
Matches are distributed among these distances:
125 113 0.32
128 1 0.00
129 1 0.00
132 243 0.68
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (132 bp):
TTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCC
ACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAG
GC
Found at i:55475526 original size:257 final size:257
Alignment explanation
Indices: 55475070--55475546 Score: 855
Period size: 257 Copynumber: 1.9 Consensus size: 257
55475060 GGATTTGGTG
*
55475070 GCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACT
1 GCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGACTTGCCGTCTTCGATCTGCTCCACTACT
*
55475135 GCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGG
66 GCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGG
* *
55475200 TGGCTTAAATCTGCTTCCCACTATTTTGGAAAGATAAGATTTGCCGTCTTTGATCTGATCCACTA
131 TGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGATCCACTA
*
55475265 CTGCTTAGGGAGATAGGATCTACAACCTCCTCCGCCGTTGCTCAGGGAGACAAGGCTTTGTA
196 CTGCTTAGGGAGATAAGATCTACAACCTCCTCCGCCGTTGCTCAGGGAGACAAGGCTTTGTA
* * *
55475327 GCTTAAATTTGCTTCCCACTATCTTGGAAAGATAAGACTTGTCGTCTTTGATCTGCTCCACTACT
1 GCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGACTTGCCGTCTTCGATCTGCTCCACTACT
* *
55475392 GCTTAGGGAGATAAGATCTACAATCTTTAACCTACTCTGCTGCTGCTCAGGGAGACAAGGCTTGG
66 GCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGG
*
55475457 TGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTA
131 TGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGATCCACTA
55475522 CTGCTTAGGGAGATAAGATCTACAA
196 CTGCTTAGGGAGATAAGATCTACAA
55475547 TCTTCAACCT
Statistics
Matches: 209, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
257 209 1.00
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.31
Consensus pattern (257 bp):
GCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGACTTGCCGTCTTCGATCTGCTCCACTACT
GCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGG
TGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGATCCACTA
CTGCTTAGGGAGATAAGATCTACAACCTCCTCCGCCGTTGCTCAGGGAGACAAGGCTTTGTA
Found at i:55477828 original size:39 final size:39
Alignment explanation
Indices: 55477733--55477954 Score: 244
Period size: 40 Copynumber: 5.7 Consensus size: 39
55477723 TTGAATGATG
*
55477733 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAA-T-ACTAAT
*
55477771 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGATATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGA-ATACTAAT
55477812 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGA-ACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGA-ATACTAAT
* *
55477850 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGA-ATACTAAT
*
55477889 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAA-TACTAAT
* *
55477928 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
55477955 AACGAGGAGC
Statistics
Matches: 161, Mismatches: 12, Indels: 19
0.84 0.06 0.10
Matches are distributed among these distances:
38 37 0.23
39 53 0.33
40 59 0.37
41 11 0.07
42 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAATACTAAT
Found at i:55477972 original size:80 final size:78
Alignment explanation
Indices: 55477733--55477987 Score: 195
Period size: 79 Copynumber: 3.3 Consensus size: 78
55477723 TTGAATGATG
* * * * *
55477733 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAG-AACTAATA-CCGGGCTAAG-CCCGAAGGCAT
** * *
55477795 TTGTGCGA-TATACTAAT
62 TTGAACGAGT-GACTAAA
* * *
55477812 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGAACTAATTCCGGGCTAAGCCCGAAGGCATTTGT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGAACTAATACCGGGCTAAGCCCGAAGGCATTTGA
* *
55477876 GCGAGTTACTAAA
66 ACGAGTGACTAAA
*
55477889 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA--ACTAAT-ACCGGGCTAAG-CCCGAAGGCAT
*
55477952 TTGAACGAG-GAGCTATA
62 TTGAACGAGTGA-CTAAA
* *
55477969 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
55477988 TACGTGATTT
Statistics
Matches: 151, Mismatches: 15, Indels: 20
0.81 0.08 0.11
Matches are distributed among these distances:
77 35 0.23
78 42 0.28
79 43 0.28
80 31 0.21
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (78 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGAACTAATACCGGGCTAAGCCCGAAGGCATTTGA
ACGAGTGACTAAA
Found at i:55486525 original size:24 final size:24
Alignment explanation
Indices: 55486497--55486542 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
55486487 ATCATTTTTT
* *
55486497 GCTGCTCATTCATTTGCTTTTGAA
1 GCTGCTCATGCATTTCCTTTTGAA
*
55486521 GCTGCTCCTGCATTTCCTTTTG
1 GCTGCTCATGCATTTCCTTTTG
55486543 GGACTGTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (24 bp):
GCTGCTCATGCATTTCCTTTTGAA
Found at i:55492789 original size:10 final size:10
Alignment explanation
Indices: 55492776--55492826 Score: 52
Period size: 10 Copynumber: 5.2 Consensus size: 10
55492766 AAAATGTTTC
55492776 AAAAATATAA
1 AAAAATATAA
* *
55492786 AAAAATCTTA
1 AAAAATATAA
55492796 AAAAATA-AA
1 AAAAATATAA
55492805 TAAAAATATAA
1 -AAAAATATAA
*
55492816 AATAAT-TAA
1 AAAAATATAA
55492825 AA
1 AA
55492827 TTAATAAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
9 6 0.18
10 26 0.76
11 2 0.06
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAAATATAA
Found at i:55492833 original size:30 final size:29
Alignment explanation
Indices: 55492776--55492836 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 29
55492766 AAAATGTTTC
55492776 AAAAATATAAAAAAATCTTAAAAAATAAAT
1 AAAAATATAAAAAAA-CTTAAAAAATAAAT
*
55492806 AAAAATATAAAATAA-TTAAAATTAATAAAT
1 AAAAATATAAAAAAACTTAAAA--AATAAAT
55492836 A
1 A
55492837 TTATAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 6 0.21
30 22 0.79
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (29 bp):
AAAAATATAAAAAAACTTAAAAAATAAAT
Found at i:55492870 original size:17 final size:16
Alignment explanation
Indices: 55492782--55492870 Score: 52
Period size: 17 Copynumber: 5.1 Consensus size: 16
55492772 TTTCAAAAAT
*
55492782 ATAAAAAAATCTTAAAAA
1 ATAAAAAAA--TTATAAA
*
55492800 ATAAATAAAAATATAAA
1 ATAAA-AAAATTATAAA
*
55492817 ATAATTAAAATTAATAAA
1 ATAA-AAAAATT-ATAAA
* **
55492835 TATTATAAAAATTCCAAA
1 -A-TAAAAAAATTATAAA
55492853 ATAAAAAAATTATTAAA
1 ATAAAAAAATTA-TAAA
55492870 A
1 A
55492871 AACATTATAA
Statistics
Matches: 54, Mismatches: 11, Indels: 13
0.69 0.14 0.17
Matches are distributed among these distances:
16 9 0.17
17 19 0.35
18 13 0.24
19 11 0.20
20 2 0.04
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (16 bp):
ATAAAAAAATTATAAA
Found at i:55493485 original size:16 final size:16
Alignment explanation
Indices: 55493464--55493531 Score: 102
Period size: 16 Copynumber: 4.2 Consensus size: 16
55493454 TTTGGTTCGC
55493464 TGTATTGGATTAGAGA
1 TGTATTGGATTAGAGA
55493480 TGTATTGGATTAGA-A
1 TGTATTGGATTAGAGA
*
55493495 GTGTATTGGATTAGAGG
1 -TGTATTGGATTAGAGA
*
55493512 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGA
55493528 TGTA
1 TGTA
55493532 ATAGCAAATC
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
15 1 0.02
16 48 0.98
ACGTcount: A:0.28, C:0.00, G:0.34, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGA
Found at i:55493500 original size:32 final size:32
Alignment explanation
Indices: 55493464--55493531 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
55493454 TTTGGTTCGC
55493464 TGTATTGGATTAGAGATGTATTGGATTAGAAG
1 TGTATTGGATTAGAGATGTATTGGATTAGAAG
* *
55493496 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGATTAGAGATGTATTGGATTAGAAG
55493528 TGTA
1 TGTA
55493532 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.28, C:0.00, G:0.34, T:0.38
Consensus pattern (32 bp):
TGTATTGGATTAGAGATGTATTGGATTAGAAG
Found at i:55493857 original size:157 final size:157
Alignment explanation
Indices: 55493661--55493970 Score: 530
Period size: 157 Copynumber: 2.0 Consensus size: 157
55493651 CCCTTAGCAT
*
55493661 AAATTTATTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTATCAA
1 AAATTTATTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
* *
55493726 TAATAAATATTTTAATCATATTTAAACATAATTATTATTAAACATATTTTAATTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATATTATAATTAAAATATATAA
55493791 TTTAATAAAATTCTTAATAATTACCAG
131 TTTAATAAAATTCTTAATAATTACCAG
* * * * *
55493818 AAATTTGTTTTGGTTAATTATTATTGTTATTGTTATTTAAATTTTGATAAGATTATTAATATGAA
1 AAATTTATTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
* *
55493883 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATACTTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATATTATAATTAAAATATATAA
55493948 TTTAATAAAATTCTTAATAATTA
131 TTTAATAAAATTCTTAATAATTA
55493971 ATATTCTTAT
Statistics
Matches: 143, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
157 143 1.00
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.48
Consensus pattern (157 bp):
AAATTTATTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATATTATAATTAAAATATATAA
TTTAATAAAATTCTTAATAATTACCAG
Found at i:55494868 original size:13 final size:13
Alignment explanation
Indices: 55494850--55494879 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
55494840 CAATCAGCTA
55494850 AATTCAGAAAAAC
1 AATTCAGAAAAAC
55494863 AATTCAGAAAAAC
1 AATTCAGAAAAAC
55494876 AATT
1 AATT
55494880 ACATGACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.60, C:0.13, G:0.07, T:0.20
Consensus pattern (13 bp):
AATTCAGAAAAAC
Found at i:55509010 original size:38 final size:38
Alignment explanation
Indices: 55508959--55509031 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
55508949 AAGTCAACCT
* *
55508959 AACTCGTACAAAGTGAAAATTTTCTATAGAAATTCTCA
1 AACTCGTACAAAGTAAAAATTCTCTATAGAAATTCTCA
*
55508997 AACTCGTGCAAAGTAAAAATTCTCTATAGAAATTC
1 AACTCGTACAAAGTAAAAATTCTCTATAGAAATTC
55509032 CCATAAGGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.30
Consensus pattern (38 bp):
AACTCGTACAAAGTAAAAATTCTCTATAGAAATTCTCA
Found at i:55510101 original size:34 final size:35
Alignment explanation
Indices: 55510061--55510140 Score: 130
Period size: 34 Copynumber: 2.4 Consensus size: 35
55510051 ATATGTTCAT
55510061 ACAACCAAT-ATGCCCAAAGGGCATCTCAATCACA
1 ACAACCAATCATGCCCAAAGGGCATCTCAATCACA
55510095 ACAACC-ATCATGCCCAAAGGGCATCTCAATCACA
1 ACAACCAATCATGCCCAAAGGGCATCTCAATCACA
*
55510129 AAAACCAA-CATG
1 ACAACCAATCATG
55510141 TACTACCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
33 2 0.05
34 40 0.93
35 1 0.02
ACGTcount: A:0.42, C:0.33, G:0.11, T:0.14
Consensus pattern (35 bp):
ACAACCAATCATGCCCAAAGGGCATCTCAATCACA
Found at i:55510800 original size:15 final size:16
Alignment explanation
Indices: 55510771--55510800 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55510761 CAAACATGCT
55510771 TTAACACATTATCAAA
1 TTAACACATTATCAAA
55510787 TTAACACA-TATCAA
1 TTAACACATTATCAA
55510801 CAAGGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:55528287 original size:22 final size:22
Alignment explanation
Indices: 55528238--55528292 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
55528228 CCTGTTTTTA
* * **
55528238 ATTAAAATTAAAATTATTTTTT
1 ATTAAAATTAAAACTAATAGTT
*
55528260 AATAAAATTAAAACTAATAGTT
1 ATTAAAATTAAAACTAATAGTT
55528282 ATTAAAATTAA
1 ATTAAAATTAA
55528293 TTGTTAGTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
ATTAAAATTAAAACTAATAGTT
Found at i:55528305 original size:16 final size:16
Alignment explanation
Indices: 55528268--55528307 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
55528258 TTAATAAAAT
* *
55528268 TAAAACTAATAGTTAT
1 TAAAATTAATAGTTAG
*
55528284 TAAAATTAATTGTTAG
1 TAAAATTAATAGTTAG
55528300 TAAAATTA
1 TAAAATTA
55528308 TCAAATTATT
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:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (16 bp):
TAAAATTAATAGTTAG
Found at i:55528346 original size:68 final size:66
Alignment explanation
Indices: 55528296--55528501 Score: 333
Period size: 68 Copynumber: 3.1 Consensus size: 66
55528286 AAATTAATTG
*
55528296 TTAGTAAAATTATCAAATTATTAATTG-TTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
1 TTAGTAAATTTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAATAAAAT-TAACATTT
55528360 GA
65 GA
55528362 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATTTAACATT
1 TTAGTAAATTTATCAAATTATTAATTG-ATTAATTGTATTAATTGTTGTAATAAAA-TTAACATT
55528427 TGA
64 TGA
* *
55528430 TTAGTAAATTTATCAAATTATTGATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTG-ATTAATTGTATTAATTGTTGTAATAAAAT-TAACATT
55528495 TGA
64 TGA
55528498 TTAG
1 TTAG
55528502 GAAAACAAAC
Statistics
Matches: 133, Mismatches: 3, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
66 26 0.20
67 1 0.01
68 105 0.79
69 1 0.01
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.47
Consensus pattern (66 bp):
TTAGTAAATTTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAATAAAATTAACATTTG
A
Found at i:55528413 original size:9 final size:9
Alignment explanation
Indices: 55528380--55528407 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
55528370 TTTATCAAAT
55528380 TATTAATTG
1 TATTAATTG
55528389 TATTAATTG
1 TATTAATTG
55528398 TATTAATTG
1 TATTAATTG
55528407 T
1 T
55528408 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:55530511 original size:90 final size:90
Alignment explanation
Indices: 55530396--55530567 Score: 247
Period size: 90 Copynumber: 1.9 Consensus size: 90
55530386 TTTTCTTTTT
* *
55530396 TTTTTTTGCACTCAATTGAGCACTTGAACTTTCAAAATGCACCAAAAAGGCCCTCAAAATGCACC
1 TTTTTTTGCACTCAATTGAGCACTTGAACTTTCAAAATGAACCAAAAAGACCCTCAAAATGCACC
55530461 AAAAAAAGCAATTAAGCCTCTGCTTA
66 -AAAAAAGCAATTAAGCCTCTGCTTA
* * * ****
55530487 TTTTTTT-CACTCAATTGGGTACTTGAACTTTCAAAATGAATCAAAAAGACCCTCAAAATTTTTC
1 TTTTTTTGCACTCAATTGAGCACTTGAACTTTCAAAATGAACCAAAAAGACCCTCAAAATGCACC
55530551 AAAAAAGCAATTAAGCC
66 AAAAAAGCAATTAAGCC
55530568 CCTGGTCTTA
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
89 17 0.24
90 48 0.67
91 7 0.10
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (90 bp):
TTTTTTTGCACTCAATTGAGCACTTGAACTTTCAAAATGAACCAAAAAGACCCTCAAAATGCACC
AAAAAAGCAATTAAGCCTCTGCTTA
Found at i:55530604 original size:10 final size:9
Alignment explanation
Indices: 55530591--55530705 Score: 83
Period size: 9 Copynumber: 12.4 Consensus size: 9
55530581 AAAATTAGAA
55530591 AAAAAGTTAT
1 AAAAA-TTAT
55530601 AAAAATTATT
1 AAAAATTA-T
**
55530611 AAATTTTAAT
1 AAAAATT-AT
55530621 AAAAA-TAT
1 AAAAATTAT
55530629 AAAAAATTAT
1 -AAAAATTAT
55530639 --AAATTAT
1 AAAAATTAT
*
55530646 AAAAATTGT
1 AAAAATTAT
* *
55530655 AAAAAATAA
1 AAAAATTAT
*
55530664 AAAAATTGT
1 AAAAATTAT
*
55530673 AAAATTTTAT
1 AAAA-ATTAT
*
55530683 AAAAATCAT
1 AAAAATTAT
55530692 AAAAAATTAT
1 -AAAAATTAT
55530702 AAAA
1 AAAA
55530706 TGTATCAAAA
Statistics
Matches: 81, Mismatches: 16, Indels: 17
0.71 0.14 0.15
Matches are distributed among these distances:
7 7 0.09
8 2 0.02
9 38 0.47
10 33 0.41
11 1 0.01
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:55530657 original size:26 final size:28
Alignment explanation
Indices: 55530601--55530661 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 28
55530591 AAAAAGTTAT
55530601 AAAAATTATTAAATTTTAATAAAAATATA
1 AAAAATTATTAAA-TTTAATAAAAATATA
*
55530630 AAAAATTA-TAAA-TT-ATAAAAATTGTA
1 AAAAATTATTAAATTTAATAAAAA-TATA
55530656 AAAAAT
1 AAAAAT
55530662 AAAAAAATTG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 7 0.23
26 11 0.37
28 4 0.13
29 8 0.27
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (28 bp):
AAAAATTATTAAATTTAATAAAAATATA
Found at i:55530845 original size:18 final size:18
Alignment explanation
Indices: 55530801--55530881 Score: 69
Period size: 17 Copynumber: 4.4 Consensus size: 18
55530791 TTTTATAGTT
*
55530801 TTTTTTACGATTTTTATAA
1 TTTTTTACAATTTTTAT-A
**
55530820 AATTTTACAACTTTTTAT-
1 TTTTTTACAA-TTTTTATA
55530838 TTTTTTACAATTTTTATA
1 TTTTTTACAATTTTTATA
55530856 -TTTTT-CTAATTTTTAATAA
1 TTTTTTAC-AATTTTT-AT-A
55530875 TTTTTTA
1 TTTTTTA
55530882 ATATTTGAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
16 1 0.02
17 19 0.38
18 10 0.20
19 8 0.16
20 12 0.24
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.64
Consensus pattern (18 bp):
TTTTTTACAATTTTTATA
Found at i:55530883 original size:8 final size:8
Alignment explanation
Indices: 55530831--55530898 Score: 55
Period size: 8 Copynumber: 7.9 Consensus size: 8
55530821 ATTTTACAAC
*
55530831 TTTTTATT
1 TTTTTAAT
*
55530839 TTTTTACAA
1 TTTTTA-AT
55530848 TTTTTATAT
1 TTTTTA-AT
55530857 TTTTCTAAT
1 TTTT-TAAT
55530866 TTTTAATAAT
1 TTTT--TAAT
55530876 TTTTTAAT
1 TTTTTAAT
* *
55530884 ATTTGAAT
1 TTTTTAAT
55530892 TTTTTAA
1 TTTTTAA
55530899 ATTAAAATTT
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
8 21 0.44
9 17 0.35
10 10 0.21
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (8 bp):
TTTTTAAT
Found at i:55531081 original size:88 final size:88
Alignment explanation
Indices: 55530975--55531167 Score: 257
Period size: 89 Copynumber: 2.2 Consensus size: 88
55530965 TAATAAAATC
* * * * *
55530975 AGGGACTTAATTACTTTTTTTGGAAAA-TTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAG
1 AGGGACTTAATTACTTTTTTTGGAAAAGATTTGAGGGCCTTTTTGATACATTTTAAAAGTTCAAA
* * *
55531039 TATCCAATTGAGTGCAAAAAAAG
66 TACCCAAATGAATGCAAAAAAAG
* * *
55531062 TAGGGGCTTAATTACTTTTTTTTGAAAAGATTTGAGGGCCTTTTTGATATATTTTAAAAGTTCAA
1 -AGGGACTTAATTACTTTTTTTGGAAAAGATTTGAGGGCCTTTTTGATACATTTTAAAAGTTCAA
55531127 ATACCCAAATGAATGCAAAAAAAG
65 ATACCCAAATGAATGCAAAAAAAG
55531151 A--GACTTAATTACTTTTT
1 AGGGACTTAATTACTTTTT
55531168 CTTTTTTGAA
Statistics
Matches: 92, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
86 15 0.16
88 26 0.28
89 51 0.55
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (88 bp):
AGGGACTTAATTACTTTTTTTGGAAAAGATTTGAGGGCCTTTTTGATACATTTTAAAAGTTCAAA
TACCCAAATGAATGCAAAAAAAG
Found at i:55531194 original size:89 final size:88
Alignment explanation
Indices: 55530977--55531195 Score: 248
Period size: 89 Copynumber: 2.5 Consensus size: 88
55530967 ATAAAATCAG
* * * * * *
55530977 GGACTTAATTAC-TTTTTTTGGAAAATTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTA
1 GGACTTAATTACTTTTTTTTGAAAAAATTTGAGGGACTTTTTGATACATTTTAAAAGTTCAAATA
* * *
55531041 TCCAATTGAGTGCAAAAAAAGTA
66 CCCAAATGAATGCAAAAAAAGTA
* * * *
55531064 GGGGCTTAATTACTTTTTTTTGAAAAGATTTGAGGGCCTTTTTGATATATTTTAAAAGTTCAAAT
1 -GGACTTAATTACTTTTTTTTGAAAAAATTTGAGGGACTTTTTGATACATTTTAAAAGTTCAAAT
55531129 ACCCAAATGAATGCAAAAAAAG-A
65 ACCCAAATGAATGCAAAAAAAGTA
55531152 -GACTTAATTACTTTTTCTTTTTTGAAAAAATTTGA-GGACTTTTT
1 GGACTTAATTAC---TT-TTTTTTGAAAAAATTTGAGGGACTTTTT
55531196 ACATCTTTAA
Statistics
Matches: 111, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
86 10 0.09
88 12 0.11
89 72 0.65
90 17 0.15
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (88 bp):
GGACTTAATTACTTTTTTTTGAAAAAATTTGAGGGACTTTTTGATACATTTTAAAAGTTCAAATA
CCCAAATGAATGCAAAAAAAGTA
Done.