Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 166 of 322
Found at i:54270808 original size:18 final size:17
Alignment explanation
Indices: 54270759--54270809 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
54270749 TGAAAACGCG
54270759 AAAATTCGAAAATTTCT
1 AAAATTCGAAAATTTCT
* * *
54270776 AAAATACGAGTAATTTTT
1 AAAATTCGA-AAATTTCT
54270794 AAAGATTCGAAAATTT
1 AAA-ATTCGAAAATTT
54270810 GAAACAAGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
17 8 0.30
18 14 0.52
19 5 0.19
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.35
Consensus pattern (17 bp):
AAAATTCGAAAATTTCT
Found at i:54271332 original size:26 final size:26
Alignment explanation
Indices: 54271293--54271349 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
54271283 CTTTTTTTTT
* *
54271293 CTGCTGCAGGATTCGGGCCGGGGGGC
1 CTGCTGCAGAATTCGGGCCAGGGGGC
*
54271319 CTGCTGCCGAATTCGGGCCAGGGGGC
1 CTGCTGCAGAATTCGGGCCAGGGGGC
54271345 CTGCT
1 CTGCT
54271350 TGGTCTGCTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.09, C:0.30, G:0.44, T:0.18
Consensus pattern (26 bp):
CTGCTGCAGAATTCGGGCCAGGGGGC
Found at i:54271481 original size:20 final size:19
Alignment explanation
Indices: 54271456--54271499 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
54271446 TCGCTGTGGC
54271456 CTGCTTCTATTTTATTTTTT
1 CTGCTT-TATTTTATTTTTT
* *
54271476 CTGCTTTGTTTTGTTTTTT
1 CTGCTTTATTTTATTTTTT
*
54271495 TTGCT
1 CTGCT
54271500 GCTTTGTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.05, C:0.14, G:0.11, T:0.70
Consensus pattern (19 bp):
CTGCTTTATTTTATTTTTT
Found at i:54271501 original size:22 final size:20
Alignment explanation
Indices: 54271465--54271513 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 20
54271455 CCTGCTTCTA
*
54271465 TTTTATTTTTTCTGCTTTGT
1 TTTTTTTTTTTCTGCTTTGT
54271485 TTTGTTTTTTTTGCTGCTTTGT
1 TTT-TTTTTTTT-CTGCTTTGT
54271507 TTTTTTT
1 TTTTTTT
54271514 CAAAAACCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 3 0.12
21 11 0.42
22 12 0.46
ACGTcount: A:0.02, C:0.08, G:0.12, T:0.78
Consensus pattern (20 bp):
TTTTTTTTTTTCTGCTTTGT
Found at i:54271707 original size:29 final size:29
Alignment explanation
Indices: 54271674--54271790 Score: 94
Period size: 30 Copynumber: 3.9 Consensus size: 29
54271664 TGTAATTTTT
*
54271674 AGAAAATTTAGGATTAAAATGAAATTTAA
1 AGAAAATTTAGGGTTAAAATGAAATTTAA
* * *
54271703 TGAAAGTTTAGGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTA-GGGT-TAAAATGAAATTTAA
* *
54271733 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTT-AGGGTTAAAATGAAATTTAA
* * *
54271762 GGAAAAGTTTAGGGGTCAAAATGCAATTT
1 AGAAAA-TTTA-GGGTTAAAATGAAATTT
54271791 TTATTTTTTA
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
29 14 0.19
30 56 0.78
31 2 0.03
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.30
Consensus pattern (29 bp):
AGAAAATTTAGGGTTAAAATGAAATTTAA
Found at i:54271729 original size:30 final size:30
Alignment explanation
Indices: 54271689--54271790 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
54271679 ATTTAGGATT
*
54271689 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * *
54271719 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
*
54271749 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
*
54271779 AAAATGCAATTT
1 AAAATGAAATTT
54271791 TTATTTTTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 2 0.03
30 60 0.97
ACGTcount: A:0.44, C:0.04, G:0.23, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:54271806 original size:15 final size:15
Alignment explanation
Indices: 54271786--54271814 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
54271776 GTCAAAATGC
54271786 AATTTTTATTTTTTA
1 AATTTTTATTTTTTA
54271801 AATTTTTATTTTTT
1 AATTTTTATTTTTT
54271815 TTTTGAAATT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
AATTTTTATTTTTTA
Found at i:54271812 original size:20 final size:20
Alignment explanation
Indices: 54271787--54271826 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
54271777 TCAAAATGCA
*
54271787 ATTTTTATTTTTTAAATTTTT
1 ATTTTT-TTTTTGAAATTTTT
54271808 ATTTTTTTTTTGAAATTTT
1 ATTTTTTTTTTGAAATTTT
54271827 GAAAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.75
Consensus pattern (20 bp):
ATTTTTTTTTTGAAATTTTT
Found at i:54273695 original size:91 final size:91
Alignment explanation
Indices: 54273540--54273724 Score: 370
Period size: 91 Copynumber: 2.0 Consensus size: 91
54273530 GAATAGAAGT
54273540 TATATTCATAACATTTTGCATCACAACATGTCTAATAAGGAGCATTTGACTCACTTCGATTATAA
1 TATATTCATAACATTTTGCATCACAACATGTCTAATAAGGAGCATTTGACTCACTTCGATTATAA
54273605 CATCCTGATCATCAGGCATGAGCACA
66 CATCCTGATCATCAGGCATGAGCACA
54273631 TATATTCATAACATTTTGCATCACAACATGTCTAATAAGGAGCATTTGACTCACTTCGATTATAA
1 TATATTCATAACATTTTGCATCACAACATGTCTAATAAGGAGCATTTGACTCACTTCGATTATAA
54273696 CATCCTGATCATCAGGCATGAGCACA
66 CATCCTGATCATCAGGCATGAGCACA
54273722 TAT
1 TAT
54273725 GCATTCTACA
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 94 1.00
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.31
Consensus pattern (91 bp):
TATATTCATAACATTTTGCATCACAACATGTCTAATAAGGAGCATTTGACTCACTTCGATTATAA
CATCCTGATCATCAGGCATGAGCACA
Found at i:54276950 original size:16 final size:15
Alignment explanation
Indices: 54276925--54276979 Score: 65
Period size: 16 Copynumber: 3.5 Consensus size: 15
54276915 NTTCTATTTT
54276925 AAAAAAAAAGAAAAA
1 AAAAAAAAAGAAAAA
54276940 AAAAGAAAAAGAGAAAA
1 AAAA-AAAAAGA-AAAA
* *
54276957 AAATAAAGAGAAAAA
1 AAAAAAAAAGAAAAA
54276972 ATAAAAAA
1 A-AAAAAA
54276980 TGGAGAGGCC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
15 9 0.26
16 18 0.53
17 7 0.21
ACGTcount: A:0.85, C:0.00, G:0.11, T:0.04
Consensus pattern (15 bp):
AAAAAAAAAGAAAAA
Found at i:54276956 original size:14 final size:14
Alignment explanation
Indices: 54276925--54276976 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
54276915 NTTCTATTTT
*
54276925 AAAAAA-AAAGAAAA
1 AAAAAATAAAG-AGA
*
54276939 AAAAAGAAAAAGAGA
1 AAAAA-ATAAAGAGA
54276954 AAAAAATAAAGAG-
1 AAAAAATAAAGAGA
54276967 AAAAAATAAA
1 AAAAAATAAA
54276977 AAATGGAGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
13 10 0.29
14 12 0.35
15 8 0.24
16 4 0.12
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.04
Consensus pattern (14 bp):
AAAAAATAAAGAGA
Found at i:54277990 original size:44 final size:44
Alignment explanation
Indices: 54277851--54278025 Score: 158
Period size: 44 Copynumber: 4.0 Consensus size: 44
54277841 AAGAAACAAG
* * *
54277851 ATTTGGCATCCCTATGTTTATAGGGAACAGATCAAAGATAGTAG
1 ATTTGGCATCCCTATGTTTATAGGGAACAGATCGAAGATAGCAA
* * * * * * * * ** *
54277895 ATCTGACATTCCTGTGCTTACAGCGAAGCAGATTGAAGATTTCAGC
1 ATTTGGCATCCCTATGTTTATAGGGAA-CAGATCGAAGATAGCA-A
* *
54277941 A--TGGCATCCCTGTGTTTATAGGGAACAAGTTC-AAGATAGCAA
1 ATTTGGCATCCCTATGTTTATAGGGAAC-AGATCGAAGATAGCAA
54277983 ATTTGGCATCCCTATGTTTATAGGGAACAGATCGAAGATAGCA
1 ATTTGGCATCCCTATGTTTATAGGGAACAGATCGAAGATAGCA
54278026 GATCTGACCT
Statistics
Matches: 100, Mismatches: 25, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
42 1 0.01
43 12 0.12
44 75 0.75
45 11 0.11
46 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (44 bp):
ATTTGGCATCCCTATGTTTATAGGGAACAGATCGAAGATAGCAA
Found at i:54278228 original size:119 final size:119
Alignment explanation
Indices: 54278017--54278239 Score: 428
Period size: 119 Copynumber: 1.9 Consensus size: 119
54278007 GAACAGATCG
*
54278017 AAGATAGCAGATCTGACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATTCTTG
1 AAGATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATTCTTG
*
54278082 TGTTTACAAGGAACAAATCGAGGACATAGTAGATTTGACTCTCAGACGTTCTCA
66 TGTTTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCA
54278136 AAGATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATTCTTG
1 AAGATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATTCTTG
54278201 TGTTTACAAGGAACAAATCGAGGACATAGCAGATTTGAC
66 TGTTTACAAGGAACAAATCGAGGACATAGCAGATTTGAC
54278240 AAAGATATCA
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
119 102 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (119 bp):
AAGATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATTCTTG
TGTTTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCA
Found at i:54279553 original size:46 final size:46
Alignment explanation
Indices: 54279491--54279759 Score: 378
Period size: 46 Copynumber: 5.8 Consensus size: 46
54279481 TTTGACATGA
* * * * * *
54279491 TGCCATAGTGTCTTTCAACTATGATCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATGTCAGGT
* * *
54279537 TGCCATGGTATTTTTCAACCATGGTCTTACACATTTCATGTCACGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCAGGT
** ** *
54279583 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCAGGT
*
54279629 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCAGGT
*
54279675 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCAGGT
54279721 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
54279760 ATTAGAGAGC
Statistics
Matches: 201, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 4 0.02
46 197 0.98
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCAGGT
Found at i:54283222 original size:12 final size:12
Alignment explanation
Indices: 54283205--54283288 Score: 72
Period size: 12 Copynumber: 7.2 Consensus size: 12
54283195 TAAAAAATAG
54283205 TATATATTATTT
1 TATATATTATTT
54283217 TATATATTA-TT
1 TATATATTATTT
54283228 TATTATATTATTT
1 TA-TATATTATTT
**
54283241 T-TACT-TATAAAT
1 TATA-TAT-TATTT
54283253 TATAT-TTA-TT
1 TATATATTATTT
*
54283263 TATATATT-TTA
1 TATATATTATTT
54283274 TATATATTATTT
1 TATATATTATTT
54283286 TAT
1 TAT
54283289 CACTCATTAG
Statistics
Matches: 59, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
10 6 0.10
11 20 0.34
12 28 0.47
13 5 0.08
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (12 bp):
TATATATTATTT
Found at i:54283233 original size:19 final size:19
Alignment explanation
Indices: 54283209--54283278 Score: 65
Period size: 19 Copynumber: 3.8 Consensus size: 19
54283199 AAATAGTATA
*
54283209 TATTATTTTATATATTATT
1 TATTATATTATATATTATT
* *
54283228 TATTATATTAT-TTTTACT
1 TATTATATTATATATTATT
*
54283246 TA-TAAATTATAT-TTATT
1 TATTATATTATATATTATT
*
54283263 TATATATTTTATATAT
1 TAT-TATATTATATAT
54283279 ATTATTTTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
17 13 0.32
18 8 0.20
19 18 0.45
20 1 0.03
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (19 bp):
TATTATATTATATATTATT
Found at i:54286726 original size:26 final size:26
Alignment explanation
Indices: 54286697--54286761 Score: 67
Period size: 27 Copynumber: 2.5 Consensus size: 26
54286687 AGATCAACAT
*
54286697 AAATTGTCCATCAAAATACAACCATC
1 AAATTGTCCATCAAAATAAAACCATC
* * *
54286723 AAATTGATCTAACAAAATAAAACTATC
1 AAATTG-TCCATCAAAATAAAACCATC
* *
54286750 AAACTATCCATC
1 AAATTGTCCATC
54286762 GTATGTTAAC
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
26 10 0.33
27 20 0.67
ACGTcount: A:0.49, C:0.23, G:0.03, T:0.25
Consensus pattern (26 bp):
AAATTGTCCATCAAAATAAAACCATC
Found at i:54292640 original size:19 final size:18
Alignment explanation
Indices: 54292613--54292651 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
54292603 AGCCCCACCA
54292613 TTAACTCTTTCATTACAAT
1 TTAACTC-TTCATTACAAT
* *
54292632 TTAATTCTTCATTATAAT
1 TTAACTCTTCATTACAAT
54292650 TT
1 TT
54292652 GGTTCCCCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (18 bp):
TTAACTCTTCATTACAAT
Found at i:54301542 original size:19 final size:19
Alignment explanation
Indices: 54301518--54301565 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
54301508 CACCAACAAT
54301518 TTTTTTAAAGGTA-AATTTA
1 TTTTTTAAA-GTATAATTTA
*
54301537 TTTTTTATAATTATAATTTA
1 TTTTTTA-AAGTATAATTTA
54301557 TTTGTTTAA
1 TTT-TTTAA
54301566 TATTTTTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 9 0.36
20 12 0.48
21 4 0.16
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.60
Consensus pattern (19 bp):
TTTTTTAAAGTATAATTTA
Found at i:54305808 original size:18 final size:17
Alignment explanation
Indices: 54305782--54305815 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
54305772 AAGATATTCA
54305782 AAACAAAATTATAATTAT
1 AAACAAAATT-TAATTAT
*
54305800 AAACTAAATTTAATTA
1 AAACAAAATTTAATTA
54305816 ATTAACCAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (17 bp):
AAACAAAATTTAATTAT
Found at i:54307509 original size:20 final size:20
Alignment explanation
Indices: 54307475--54307512 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
54307465 TATAAACAAA
**
54307475 TTTTTATAATGTTTTAAATT
1 TTTTTATAAAATTTTAAATT
54307495 TTTTTATAAAATTTTAAA
1 TTTTTATAAAATTTTAAA
54307513 AAGTCAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (20 bp):
TTTTTATAAAATTTTAAATT
Found at i:54307670 original size:18 final size:19
Alignment explanation
Indices: 54307647--54307686 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
54307637 CTTTTTTAAA
54307647 TTACAATTTTT-TATAATT
1 TTACAATTTTTATATAATT
*
54307665 TTACAATTTTTATATATTT
1 TTACAATTTTTATATAATT
54307684 TTA
1 TTA
54307687 ATAATATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
TTACAATTTTTATATAATT
Found at i:54309909 original size:27 final size:27
Alignment explanation
Indices: 54309871--54309992 Score: 149
Period size: 27 Copynumber: 4.5 Consensus size: 27
54309861 NNNNNNNNAT
* *
54309871 TATCTGATCTGGTGGTTCTGCCACATA
1 TATCTGATCTGGTGGCTATGCCACATA
*
54309898 TATCTGTTCTGGTGGCTATGCCACGAT-
1 TATCTGATCTGGTGGCTATGCCAC-ATA
* *
54309925 TATCTGATCTGGTGGCTCTGCCACACA
1 TATCTGATCTGGTGGCTATGCCACATA
* *
54309952 TATCTGTTCTGGTGGCGATGCCACA-A
1 TATCTGATCTGGTGGCTATGCCACATA
54309978 TTATCTGATCTGGTG
1 -TATCTGATCTGGTG
54309993 ACTTCGTCAC
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
26 2 0.02
27 78 0.95
28 2 0.02
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.35
Consensus pattern (27 bp):
TATCTGATCTGGTGGCTATGCCACATA
Found at i:54309955 original size:54 final size:54
Alignment explanation
Indices: 54309869--54309992 Score: 212
Period size: 54 Copynumber: 2.3 Consensus size: 54
54309859 NNNNNNNNNN
* * * *
54309869 ATTATCTGATCTGGTGGTTCTGCCACATATATCTGTTCTGGTGGCTATGCCACG
1 ATTATCTGATCTGGTGGCTCTGCCACACATATCTGTTCTGGTGGCGATGCCACA
54309923 ATTATCTGATCTGGTGGCTCTGCCACACATATCTGTTCTGGTGGCGATGCCACA
1 ATTATCTGATCTGGTGGCTCTGCCACACATATCTGTTCTGGTGGCGATGCCACA
54309977 ATTATCTGATCTGGTG
1 ATTATCTGATCTGGTG
54309993 ACTTCGTCAC
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 66 1.00
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.35
Consensus pattern (54 bp):
ATTATCTGATCTGGTGGCTCTGCCACACATATCTGTTCTGGTGGCGATGCCACA
Found at i:54310003 original size:27 final size:27
Alignment explanation
Indices: 54309869--54310010 Score: 127
Period size: 27 Copynumber: 5.3 Consensus size: 27
54309859 NNNNNNNNNN
54309869 ATTATCTGATCTGGTGG-TTCTGCCAC-
1 ATTATCTGATCTGGTGGCTTC-GCCACA
* *
54309895 ATATATCTGTTCTGGTGGCTAT-GCCACG
1 AT-TATCTGATCTGGTGGCT-TCGCCACA
54309923 ATTATCTGATCTGGTGGC-TCTGCCACA
1 ATTATCTGATCTGGTGGCTTC-GCCACA
* *
54309950 CA-TATCTGTTCTGGTGGCGAT-GCCACA
1 -ATTATCTGATCTGGTGGC-TTCGCCACA
* *
54309977 ATTATCTGATCTGGTGACTTCGTCACA
1 ATTATCTGATCTGGTGGCTTCGCCACA
54310004 A-TATCTG
1 ATTATCTG
54310011 GCAGCCTCGC
Statistics
Matches: 97, Mismatches: 8, Indels: 22
0.76 0.06 0.17
Matches are distributed among these distances:
25 1 0.01
26 10 0.10
27 80 0.82
28 4 0.04
29 2 0.02
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (27 bp):
ATTATCTGATCTGGTGGCTTCGCCACA
Found at i:54311748 original size:35 final size:35
Alignment explanation
Indices: 54311664--54311748 Score: 84
Period size: 35 Copynumber: 2.4 Consensus size: 35
54311654 GTTTGGCAAA
* * *
54311664 ATAAATTA-TCTACAGTCTTTACGGAGTGACACCGT
1 ATAAA-TAGTCTACAGACTTTACGGAGCGACACCAT
* *
54311699 ATAATTAGTATACAGACTTTACGGAGCGACACCAT
1 ATAAATAGTCTACAGACTTTACGGAGCGACACCAT
*
54311734 GA-AAATGGTCTACAG
1 -ATAAATAGTCTACAG
54311749 GCTCTACAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
34 2 0.05
35 37 0.93
36 1 0.03
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (35 bp):
ATAAATAGTCTACAGACTTTACGGAGCGACACCAT
Found at i:54313738 original size:26 final size:26
Alignment explanation
Indices: 54313709--54313759 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
54313699 ATAGGGAAAA
54313709 ATCATTTTATCTTTTTAATTTCATTT
1 ATCATTTTATCTTTTTAATTTCATTT
54313735 ATCATTTTATCTTTTTAATTTCATT
1 ATCATTTTATCTTTTTAATTTCATT
54313760 CTTTCCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (26 bp):
ATCATTTTATCTTTTTAATTTCATTT
Found at i:54315235 original size:25 final size:26
Alignment explanation
Indices: 54315207--54315257 Score: 95
Period size: 25 Copynumber: 2.0 Consensus size: 26
54315197 ATATTAACAT
54315207 TTATATTTATATTAAA-AAAATAAAA
1 TTATATTTATATTAAACAAAATAAAA
54315232 TTATATTTATATTAAACAAAATAAAA
1 TTATATTTATATTAAACAAAATAAAA
54315258 ATCCCCTACC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 16 0.64
26 9 0.36
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (26 bp):
TTATATTTATATTAAACAAAATAAAA
Found at i:54315509 original size:15 final size:15
Alignment explanation
Indices: 54315489--54315521 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
54315479 AAGGAAGTGA
54315489 AAAAAGAAAAAAAAG
1 AAAAAGAAAAAAAAG
*
54315504 AAAAAGAAAAAGAAG
1 AAAAAGAAAAAAAAG
54315519 AAA
1 AAA
54315522 GGCACCAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAAAG
Found at i:54315664 original size:33 final size:34
Alignment explanation
Indices: 54315617--54315684 Score: 111
Period size: 33 Copynumber: 2.0 Consensus size: 34
54315607 ATAGTACTTG
*
54315617 TCTGAAAACTCAAAGGGAGAACA-TTTTGGCTCA
1 TCTGAAAACCCAAAGGGAGAACATTTTTGGCTCA
*
54315650 TCTGAAAACCCAAAGGGAGGACATTTTTGGCTCA
1 TCTGAAAACCCAAAGGGAGAACATTTTTGGCTCA
54315684 T
1 T
54315685 ACTTTGATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 21 0.66
34 11 0.34
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (34 bp):
TCTGAAAACCCAAAGGGAGAACATTTTTGGCTCA
Found at i:54317323 original size:63 final size:63
Alignment explanation
Indices: 54317246--54317394 Score: 183
Period size: 63 Copynumber: 2.4 Consensus size: 63
54317236 TCGTGTGCCT
* * * *
54317246 CAAAATAGTGAGTTACACGGTCTGGACACACACTCATGTCTCTGGCCCATGTGTCC-CTAGTTC
1 CAAAATAGTGAGTTACACGGCCTGGACACACACCCATGTCTCTAGCCCATGTG-CCTCTAATTC
* * * *** *
54317309 CAAAACAGTGAGTTACACTGCCTGGACACACGCCCATGTCTCTATTTCGTGTGCCTCTAATTC
1 CAAAATAGTGAGTTACACGGCCTGGACACACACCCATGTCTCTAGCCCATGTGCCTCTAATTC
54317372 CAAAATAGTGAGTTACACGGCCT
1 CAAAATAGTGAGTTACACGGCCT
54317395 ACCACACGGC
Statistics
Matches: 72, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
62 2 0.03
63 70 0.97
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (63 bp):
CAAAATAGTGAGTTACACGGCCTGGACACACACCCATGTCTCTAGCCCATGTGCCTCTAATTC
Found at i:54323388 original size:30 final size:30
Alignment explanation
Indices: 54323313--54323388 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
54323303 TGATTGATGA
* *
54323313 TATTTTATAATTATTTAATTAGAAAATTAT
1 TATTTTATTATTATTTAATAAGAAAATTAT
* * *
54323343 TATTTTATTAATATTTAATAAGATATTTAT
1 TATTTTATTATTATTTAATAAGAAAATTAT
54323373 TATTATT-TTATTATTT
1 TATT-TTATTATTATTT
54323389 TATTTAGTAC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 37 0.95
31 2 0.05
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (30 bp):
TATTTTATTATTATTTAATAAGAAAATTAT
Found at i:54333712 original size:10 final size:10
Alignment explanation
Indices: 54333691--54333734 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
54333681 AAATTTTAAC
54333691 TTTTATATATT
1 TTTTATA-ATT
54333702 TTTTATAATT
1 TTTTATAATT
*
54333712 TTTCATAA--
1 TTTTATAATT
54333720 TTTTATAATT
1 TTTTATAATT
54333730 TTTTA
1 TTTTA
54333735 AAAATATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
8 7 0.24
10 15 0.52
11 7 0.24
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTATAATT
Found at i:54333732 original size:9 final size:9
Alignment explanation
Indices: 54333673--54333732 Score: 54
Period size: 9 Copynumber: 6.8 Consensus size: 9
54333663 TATTTTAGAA
54333673 AATTTTTA-
1 AATTTTTAT
*
54333681 AAATTTTA-
1 AATTTTTAT
*
54333689 ACTTTTATAT
1 AATTTT-TAT
*
54333699 ATTTTTTAT
1 AATTTTTAT
54333708 AATTTTTCAT
1 AATTTTT-AT
54333718 AA-TTTTAT
1 AATTTTTAT
54333726 AATTTTT
1 AATTTTT
54333733 TAAAAATATA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
8 15 0.35
9 19 0.44
10 9 0.21
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (9 bp):
AATTTTTAT
Found at i:54333775 original size:18 final size:18
Alignment explanation
Indices: 54333744--54333794 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 18
54333734 AAAAATATAA
54333744 ATTTTGAGATTTTTATAAA-T
1 ATTTTGA-A-TTTTA-AAATT
54333764 ATTTTGAATTTTAAAATTT
1 ATTTTGAATTTTAAAA-TT
*
54333783 ATTTTAAATTTT
1 ATTTTGAATTTT
54333795 TGAAAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 3 0.11
18 5 0.18
19 13 0.46
20 7 0.25
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (18 bp):
ATTTTGAATTTTAAAATT
Found at i:54334123 original size:48 final size:48
Alignment explanation
Indices: 54334045--54334136 Score: 123
Period size: 48 Copynumber: 1.9 Consensus size: 48
54334035 ACAATAATTT
* * * *
54334045 TATCTCAAGCTTATTATGATTAGATTCACCT-GAAGTTGCAAGATCTTC
1 TATCTAAAGCTTATTATGATCAAATGCACCTAG-AGTTGCAAGATCTTC
*
54334093 TATCTAAAGCTTTTTATGATCAAATGCACCTAGAGTTGCAAGAT
1 TATCTAAAGCTTATTATGATCAAATGCACCTAGAGTTGCAAGAT
54334137 TTTGAAATTG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
48 37 0.97
49 1 0.03
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (48 bp):
TATCTAAAGCTTATTATGATCAAATGCACCTAGAGTTGCAAGATCTTC
Found at i:54336755 original size:48 final size:48
Alignment explanation
Indices: 54336665--54336760 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
54336655 TGGCCACAGT
* *
54336665 ACTGATAGCATAAGTGGCAATGAAAAACCACGAGATGCGAAGCAGGGA
1 ACTGATAGCACAAGTGGCAATGAAAAACCACGAGATACGAAGCAGGGA
* * * *
54336713 ACTGATAGCACAAGTGGCAATGAGAGACCACGAGATATGAAGCGGGGA
1 ACTGATAGCACAAGTGGCAATGAAAAACCACGAGATACGAAGCAGGGA
54336761 TCCAACAACC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.40, C:0.17, G:0.31, T:0.12
Consensus pattern (48 bp):
ACTGATAGCACAAGTGGCAATGAAAAACCACGAGATACGAAGCAGGGA
Found at i:54342317 original size:74 final size:74
Alignment explanation
Indices: 54342196--54342349 Score: 308
Period size: 74 Copynumber: 2.1 Consensus size: 74
54342186 TTAGCTAAAT
54342196 CATTTTACTGCAATTTTAGAAACTGCAACAATTGTAAAGTTATAAGATCAAATCAACCTTGCCGC
1 CATTTTACTGCAATTTTAGAAACTGCAACAATTGTAAAGTTATAAGATCAAATCAACCTTGCCGC
54342261 CTTCTCCAG
66 CTTCTCCAG
54342270 CATTTTACTGCAATTTTAGAAACTGCAACAATTGTAAAGTTATAAGATCAAATCAACCTTGCCGC
1 CATTTTACTGCAATTTTAGAAACTGCAACAATTGTAAAGTTATAAGATCAAATCAACCTTGCCGC
54342335 CTTCTCCAG
66 CTTCTCCAG
54342344 CATTTT
1 CATTTT
54342350 TCAAATATTG
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 80 1.00
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.32
Consensus pattern (74 bp):
CATTTTACTGCAATTTTAGAAACTGCAACAATTGTAAAGTTATAAGATCAAATCAACCTTGCCGC
CTTCTCCAG
Found at i:54343193 original size:21 final size:21
Alignment explanation
Indices: 54343143--54343209 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
54343133 GACTGCGGGT
*
54343143 TGTAACTTGGAGAGGTAGGG-C
1 TGTAACTTGGTGAGGT-GGGAC
* * *
54343164 TATAGCTTGGTGATGTGGGAC
1 TGTAACTTGGTGAGGTGGGAC
*
54343185 TGTAACTTGGTGAGGTTGGAC
1 TGTAACTTGGTGAGGTGGGAC
54343206 TGTA
1 TGTA
54343210 CCCAGGAGAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 3 0.08
21 34 0.92
ACGTcount: A:0.21, C:0.09, G:0.39, T:0.31
Consensus pattern (21 bp):
TGTAACTTGGTGAGGTGGGAC
Found at i:54343239 original size:42 final size:42
Alignment explanation
Indices: 54343193--54343311 Score: 114
Period size: 42 Copynumber: 2.8 Consensus size: 42
54343183 ACTGTAACTT
* * * *
54343193 GGTGAGGTTGGACTGTACCCAGGAGATGTGGGGCTATAAGCA
1 GGTGAAGTAGGACTATACCAAGGAGATGTGGGGCTATAAGCA
* ** *
54343235 GGTGAAGTAGGGCTATATGAAGGAGATGTGGGGCTAT-AGGA
1 GGTGAAGTAGGACTATACCAAGGAGATGTGGGGCTATAAGCA
* * * *
54343276 CGGTGAAGTAGGGCTGTACGAAGGAGATGTCGGGCT
1 -GGTGAAGTAGGACTATACCAAGGAGATGTGGGGCT
54343312 GTACGATGGA
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 3 0.05
42 62 0.95
ACGTcount: A:0.25, C:0.11, G:0.43, T:0.21
Consensus pattern (42 bp):
GGTGAAGTAGGACTATACCAAGGAGATGTGGGGCTATAAGCA
Found at i:54343247 original size:21 final size:21
Alignment explanation
Indices: 54343223--54343416 Score: 106
Period size: 21 Copynumber: 9.2 Consensus size: 21
54343213 AGGAGATGTG
*
54343223 GGGCTATAAGCAGGTGAAGTA
1 GGGCTATATGCAGGTGAAGTA
* * * *
54343244 GGGCTATATGAAGGAGATGTG
1 GGGCTATATGCAGGTGAAGTA
*
54343265 GGGCTATA-GGACGGTGAAGTA
1 GGGCTATATGCA-GGTGAAGTA
* * * * * *
54343286 GGGCTGTACGAAGGAGATGTC
1 GGGCTATATGCAGGTGAAGTA
* * * *
54343307 GGGCTGTACG-ATGGAGATGTA
1 GGGCTATATGCA-GGTGAAGTA
* * *
54343328 GGGCTGTATG-ATGGAGAAGTG
1 GGGCTATATGCA-GGTGAAGTA
* *
54343349 GGGCTGTATGCAGGTGAAGTG
1 GGGCTATATGCAGGTGAAGTA
* *
54343370 GGGCTATATGCTGGTGAGGTA
1 GGGCTATATGCAGGTGAAGTA
* * *
54343391 GGGCTATATACGGGTGAAGTG
1 GGGCTATATGCAGGTGAAGTA
54343412 GGGCT
1 GGGCT
54343417 GTAGCTGGGT
Statistics
Matches: 142, Mismatches: 27, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
20 3 0.02
21 136 0.96
22 3 0.02
ACGTcount: A:0.24, C:0.09, G:0.44, T:0.23
Consensus pattern (21 bp):
GGGCTATATGCAGGTGAAGTA
Found at i:54343281 original size:84 final size:84
Alignment explanation
Indices: 54343193--54343353 Score: 189
Period size: 84 Copynumber: 1.9 Consensus size: 84
54343183 ACTGTAACTT
* * * * *
54343193 GGTGAGGTTGGACTGTACCCAGGAGATGTGGGGCTATAAGCA-GGTGAAGTAGGGCTATATGAAG
1 GGTGAAGTAGGACTGTACCAAGGAGATGTCGGGCTATAAG-ATGGAGAAGTAGGGCTATATGAAG
*
54343257 GAGATGTGGGGCTATAGGAC
65 GAGAAGTGGGGCTATAGGAC
* * * * * * *
54343277 GGTGAAGTAGGGCTGTACGAAGGAGATGTCGGGCTGTACGATGGAGATGTAGGGCTGTATGATGG
1 GGTGAAGTAGGACTGTACCAAGGAGATGTCGGGCTATAAGATGGAGAAGTAGGGCTATATGAAGG
54343342 AGAAGTGGGGCT
66 AGAAGTGGGGCT
54343354 GTATGCAGGT
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
83 1 0.02
84 62 0.98
ACGTcount: A:0.25, C:0.10, G:0.43, T:0.22
Consensus pattern (84 bp):
GGTGAAGTAGGACTGTACCAAGGAGATGTCGGGCTATAAGATGGAGAAGTAGGGCTATATGAAGG
AGAAGTGGGGCTATAGGAC
Found at i:54343332 original size:63 final size:62
Alignment explanation
Indices: 54343220--54343419 Score: 166
Period size: 63 Copynumber: 3.2 Consensus size: 62
54343210 CCCAGGAGAT
* * * * * * * *
54343220 GTGGGGCTATAAGCAGGTGAAGTAGGGCTATATGAAGGAGATGTGGGGCTATAGGACGGTGAA
1 GTGGGGCTGTACGAAGGAGAAGTCGGGCTATACGATGGAGATGTAGGGCTATA-GACGGTGAA
* * * * * *
54343283 GTAGGGCTGTACGAAGGAGATGTCGGGCTGTACGATGGAGATGTAGGGCTGTATGATGGAGAA
1 GTGGGGCTGTACGAAGGAGAAGTCGGGCTATACGATGGAGATGTAGGGCTATA-GACGGTGAA
* * * * * * * * *
54343346 GTGGGGCTGTATGCAGGTGAAGTGGGGCTATATGCTGGTGAGGTAGGGCTATATACGGGTGAA
1 GTGGGGCTGTACGAAGGAGAAGTCGGGCTATACGATGGAGATGTAGGGCTATAGAC-GGTGAA
54343409 GTGGGGCTGTA
1 GTGGGGCTGTA
54343420 GCTGGGTGAA
Statistics
Matches: 106, Mismatches: 30, Indels: 2
0.77 0.22 0.01
Matches are distributed among these distances:
62 1 0.01
63 105 0.99
ACGTcount: A:0.24, C:0.09, G:0.44, T:0.23
Consensus pattern (62 bp):
GTGGGGCTGTACGAAGGAGAAGTCGGGCTATACGATGGAGATGTAGGGCTATAGACGGTGAA
Found at i:54343374 original size:42 final size:42
Alignment explanation
Indices: 54343213--54343419 Score: 184
Period size: 42 Copynumber: 4.9 Consensus size: 42
54343203 GACTGTACCC
* *
54343213 AGGAGATGTGGGGCTATAAGCAGGTGAAGTAGGGCTATATGA
1 AGGAGATGTGGGGCTATATGCAGGTGAAGTAGGGCTGTATGA
* *
54343255 AGGAGATGTGGGGCTATA-GGACGGTGAAGTAGGGCTGTACGA
1 AGGAGATGTGGGGCTATATGCA-GGTGAAGTAGGGCTGTATGA
* * * * *
54343297 AGGAGATGTCGGGCTGTACG-ATGGAGATGTAGGGCTGTATGA
1 AGGAGATGTGGGGCTATATGCA-GGTGAAGTAGGGCTGTATGA
* * * * * *
54343339 TGGAGAAGTGGGGCTGTATGCAGGTGAAGTGGGGCTATATGC
1 AGGAGATGTGGGGCTATATGCAGGTGAAGTAGGGCTGTATGA
* * * * * * *
54343381 TGGTGAGGTAGGGCTATATACGGGTGAAGTGGGGCTGTA
1 AGGAGATGTGGGGCTATATGCAGGTGAAGTAGGGCTGTA
54343420 GCTGGGTGAA
Statistics
Matches: 137, Mismatches: 25, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
41 2 0.01
42 133 0.97
43 2 0.01
ACGTcount: A:0.25, C:0.09, G:0.44, T:0.23
Consensus pattern (42 bp):
AGGAGATGTGGGGCTATATGCAGGTGAAGTAGGGCTGTATGA
Found at i:54343426 original size:21 final size:22
Alignment explanation
Indices: 54343343--54343446 Score: 110
Period size: 21 Copynumber: 5.0 Consensus size: 22
54343333 GTATGATGGA
* *
54343343 GAAGTGGGGCTGTATGC-AGGT
1 GAAGTGGGGCTATATGCTGGGT
54343364 GAAGTGGGGCTATATGCT-GGT
1 GAAGTGGGGCTATATGCTGGGT
* * *
54343385 GAGGTAGGGCTATATAC-GGGT
1 GAAGTGGGGCTATATGCTGGGT
*
54343406 GAAGTGGGGCTGTA-GCTGGGT
1 GAAGTGGGGCTATATGCTGGGT
*
54343427 GAAGTGGGACTATA-GCTGGG
1 GAAGTGGGGCTATATGCTGGG
54343447 GGATCTGGGA
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
20 1 0.01
21 69 0.99
ACGTcount: A:0.20, C:0.10, G:0.46, T:0.24
Consensus pattern (22 bp):
GAAGTGGGGCTATATGCTGGGT
Found at i:54343440 original size:42 final size:41
Alignment explanation
Indices: 54343328--54343440 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 41
54343318 TGGAGATGTA
* * * * *
54343328 GGGCTGTATGATGGAGAAGTGGGGCTGTATGCAGGTGAAGTG
1 GGGCTATATGCTGGTGAAGT-GGGCTATATACAGGTGAAGTG
* *
54343370 GGGCTATATGCTGGTGAGGTAGGGCTATATACGGGTGAAGTG
1 GGGCTATATGCTGGTGAAGT-GGGCTATATACAGGTGAAGTG
*
54343412 GGGCTGTA-GCTGGGTGAAGTGGGACTATA
1 GGGCTATATGCT-GGTGAAGTGGG-CTATA
54343441 GCTGGGGGAT
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 6 0.10
42 53 0.90
ACGTcount: A:0.21, C:0.09, G:0.45, T:0.25
Consensus pattern (41 bp):
GGGCTATATGCTGGTGAAGTGGGCTATATACAGGTGAAGTG
Found at i:54343473 original size:63 final size:63
Alignment explanation
Indices: 54343325--54343445 Score: 158
Period size: 63 Copynumber: 1.9 Consensus size: 63
54343315 CGATGGAGAT
* *
54343325 GTAGGGCTGTATGA-TGGAGAAGTGGGGCTGTATGCAGGTGAAGTGGGGCTATATGCTGGTGAG
1 GTAGGGCTATAT-ACTGGAGAAGTGGGGCTGTATGCAGGTGAAGTGGGACTATATGCTGGTGAG
* * *
54343388 GTAGGGCTATATACGGGTGAAGTGGGGCTGTA-GCTGGGTGAAGTGGGACTATA-GCTGG
1 GTAGGGCTATATACTGGAGAAGTGGGGCTGTATGC-AGGTGAAGTGGGACTATATGCTGG
54343446 GGGATCTGGG
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
62 8 0.16
63 43 0.84
ACGTcount: A:0.21, C:0.09, G:0.45, T:0.25
Consensus pattern (63 bp):
GTAGGGCTATATACTGGAGAAGTGGGGCTGTATGCAGGTGAAGTGGGACTATATGCTGGTGAG
Found at i:54343519 original size:21 final size:21
Alignment explanation
Indices: 54343457--54343536 Score: 106
Period size: 21 Copynumber: 3.8 Consensus size: 21
54343447 GGATCTGGGA
* *
54343457 CTGTAACTTGGAGAAGTAGGA
1 CTGTAACTTGGAGAGGTAGGG
*
54343478 CTGTAACTTGGAGATGTAGGG
1 CTGTAACTTGGAGAGGTAGGG
54343499 CTGTAACTTGGAGAGGTAGGG
1 CTGTAACTTGGAGAGGTAGGG
* * *
54343520 CTATAGCTTGGTGAGGT
1 CTGTAACTTGGAGAGGT
54343537 TGGAGAATAT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.25, C:0.10, G:0.38, T:0.28
Consensus pattern (21 bp):
CTGTAACTTGGAGAGGTAGGG
Found at i:54343643 original size:21 final size:21
Alignment explanation
Indices: 54343580--54343740 Score: 128
Period size: 21 Copynumber: 7.7 Consensus size: 21
54343570 TGGACTTGTC
* * * *
54343580 GGACTGTATCCTGGTGAGCTA
1 GGACTGTAACCAGGAGAGGTA
** * * *
54343601 GGACTGTAAGTAGGTGATGTG
1 GGACTGTAACCAGGAGAGGTA
* *
54343622 GGGCTGTAACCAGGAGAGGTG
1 GGACTGTAACCAGGAGAGGTA
* *
54343643 GGACTGTACCCAGGAGATGTA
1 GGACTGTAACCAGGAGAGGTA
54343664 GGACTGTAACCAGGAGAGGTA
1 GGACTGTAACCAGGAGAGGTA
* *
54343685 GGACTGTAACCAGGTGATG-A
1 GGACTGTAACCAGGAGAGGTA
* *
54343705 CGGACTGTATCCAGGAGATG-A
1 -GGACTGTAACCAGGAGAGGTA
*
54343726 TGGGCTGTAACCAGG
1 -GGACTGTAACCAGG
54343741 GGATGACGTA
Statistics
Matches: 114, Mismatches: 25, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
20 1 0.01
21 113 0.99
ACGTcount: A:0.26, C:0.16, G:0.38, T:0.20
Consensus pattern (21 bp):
GGACTGTAACCAGGAGAGGTA
Found at i:54343647 original size:42 final size:42
Alignment explanation
Indices: 54343601--54343745 Score: 168
Period size: 42 Copynumber: 3.5 Consensus size: 42
54343591 TGGTGAGCTA
** * *
54343601 GGACTGTAAGTAGGTGATGTGGGGCTGTAACCAGGAGAGGTG
1 GGACTGTAACCAGGTGATGTAGGACTGTAACCAGGAGAGGTG
* * *
54343643 GGACTGTACCCAGGAGATGTAGGACTGTAACCAGGAGAGGTA
1 GGACTGTAACCAGGTGATGTAGGACTGTAACCAGGAGAGGTG
* *
54343685 GGACTGTAACCAGGTGATG-ACGGACTGTATCCAGGAGATGATG
1 GGACTGTAACCAGGTGATGTA-GGACTGTAACCAGGAGA-GGTG
*
54343728 GG-CTGTAACCAGGGGATG
1 GGACTGTAACCAGGTGATG
54343746 ACGTAGGAGA
Statistics
Matches: 88, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
41 1 0.01
42 83 0.94
43 4 0.05
ACGTcount: A:0.27, C:0.14, G:0.39, T:0.19
Consensus pattern (42 bp):
GGACTGTAACCAGGTGATGTAGGACTGTAACCAGGAGAGGTG
Found at i:54348664 original size:14 final size:14
Alignment explanation
Indices: 54348618--54348653 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
54348608 AAAAAAAAAG
*
54348618 ATTAACAAAGCCAA
1 ATTAACAAAACCAA
54348632 ATTAACAAAACCAA
1 ATTAACAAAACCAA
54348646 ATTAACAA
1 ATTAACAA
54348654 CACAAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.61, C:0.19, G:0.03, T:0.17
Consensus pattern (14 bp):
ATTAACAAAACCAA
Found at i:54349968 original size:15 final size:16
Alignment explanation
Indices: 54349950--54349982 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
54349940 AAAAGACTGC
54349950 AAGAAAAA-TGGAGAA
1 AAGAAAAAGTGGAGAA
54349965 AAGAAAAAGTTGGAGAA
1 AAGAAAAAG-TGGAGAA
54349982 A
1 A
54349983 TTGAAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.64, C:0.00, G:0.27, T:0.09
Consensus pattern (16 bp):
AAGAAAAAGTGGAGAA
Found at i:54355987 original size:35 final size:35
Alignment explanation
Indices: 54355948--54356022 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 35
54355938 TGTCGCCCCT
*
54355948 AAGGAATCGTATACCATTTACACAATGTCACCTCA
1 AAGGAATCATATACCATTTACACAATGTCACCTCA
* * * ** *
54355983 AAGGACTTATATACCATTTAGACGGTGTTACCTCA
1 AAGGAATCATATACCATTTACACAATGTCACCTCA
54356018 AAGGA
1 AAGGA
54356023 CCAATAAATA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (35 bp):
AAGGAATCATATACCATTTACACAATGTCACCTCA
Found at i:54356023 original size:35 final size:35
Alignment explanation
Indices: 54355957--54356023 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
54355947 TAAGGAATCG
54355957 TATACCATTTACACAATGTCACCTCAAAGGACTTA
1 TATACCATTTACACAATGTCACCTCAAAGGACTTA
* ** *
54355992 TATACCATTTAGACGGTGTTACCTCAAAGGAC
1 TATACCATTTACACAATGTCACCTCAAAGGAC
54356024 CAATAAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.28
Consensus pattern (35 bp):
TATACCATTTACACAATGTCACCTCAAAGGACTTA
Found at i:54359451 original size:21 final size:21
Alignment explanation
Indices: 54359426--54359483 Score: 116
Period size: 21 Copynumber: 2.8 Consensus size: 21
54359416 TACACGACCT
54359426 AACCACACGGGCGTGTCCCTA
1 AACCACACGGGCGTGTCCCTA
54359447 AACCACACGGGCGTGTCCCTA
1 AACCACACGGGCGTGTCCCTA
54359468 AACCACACGGGCGTGT
1 AACCACACGGGCGTGT
54359484 GAGCCTTGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.24, C:0.36, G:0.26, T:0.14
Consensus pattern (21 bp):
AACCACACGGGCGTGTCCCTA
Found at i:54359673 original size:22 final size:22
Alignment explanation
Indices: 54359639--54359682 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
54359629 TTTTGATTCG
54359639 ATTTTTCTATAATTAATCTGTAA
1 ATTTTTCTATAA-TAATCTGTAA
* *
54359662 ATTTTT-TGTAATACTCTGTAA
1 ATTTTTCTATAATAATCTGTAA
54359683 CCCTATTTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
22 4 0.21
23 6 0.32
ACGTcount: A:0.32, C:0.09, G:0.07, T:0.52
Consensus pattern (22 bp):
ATTTTTCTATAATAATCTGTAA
Found at i:54373532 original size:20 final size:20
Alignment explanation
Indices: 54373504--54373542 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
54373494 CCCTTACAAT
*
54373504 TTTGCAAGAGTTTTAGTAAA
1 TTTGCAAGAATTTTAGTAAA
*
54373524 TTTGTAAGAATTTTAGTAA
1 TTTGCAAGAATTTTAGTAA
54373543 TATCATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.03, G:0.18, T:0.44
Consensus pattern (20 bp):
TTTGCAAGAATTTTAGTAAA
Found at i:54373629 original size:19 final size:20
Alignment explanation
Indices: 54373605--54373653 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
54373595 ACAAAGTCAT
54373605 AAGCAATTCAATAA-TTTGC
1 AAGCAATTCAATAATTTTGC
*
54373624 AAGCAATTCAATAATTTTGT
1 AAGCAATTCAATAATTTTGC
54373644 AAG-AATTCAA
1 AAGCAATTCAA
54373654 GGAATTAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 21 0.75
20 7 0.25
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (20 bp):
AAGCAATTCAATAATTTTGC
Found at i:54374661 original size:22 final size:22
Alignment explanation
Indices: 54374636--54374732 Score: 72
Period size: 22 Copynumber: 4.4 Consensus size: 22
54374626 TGCACCATGA
*
54374636 TGCCTACTGATTTGCACTACAG
1 TGCCTACTAATTTGCACTACAG
** *
54374658 TGCCTACTAATTCACACTTC-G
1 TGCCTACTAATTTGCACTACAG
*
54374679 ATACCTAC-AATTTTGCACTACAG
1 -TGCCTACTAA-TTTGCACTACAG
* ** * *
54374702 TGCCTATTGTTTTGCACTTCGG
1 TGCCTACTAATTTGCACTACAG
54374724 TGCCTACTA
1 TGCCTACTA
54374733 TTAAAATACT
Statistics
Matches: 55, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
21 3 0.05
22 51 0.93
23 1 0.02
ACGTcount: A:0.23, C:0.28, G:0.14, T:0.35
Consensus pattern (22 bp):
TGCCTACTAATTTGCACTACAG
Found at i:54377436 original size:30 final size:30
Alignment explanation
Indices: 54377401--54377458 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 30
54377391 TTGGCACTTC
54377401 CACACGGGT-GATCCACACGCCCATGTGTGA
1 CACACGGGTAGA-CCACACGCCCATGTGTGA
54377431 CACACGGGTAGACCACACGCCCATGTGT
1 CACACGGGTAGACCACACGCCCATGTGT
54377459 CATGGCCGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 25 0.93
31 2 0.07
ACGTcount: A:0.24, C:0.34, G:0.26, T:0.16
Consensus pattern (30 bp):
CACACGGGTAGACCACACGCCCATGTGTGA
Found at i:54383934 original size:39 final size:39
Alignment explanation
Indices: 54383881--54384162 Score: 492
Period size: 39 Copynumber: 7.2 Consensus size: 39
54383871 CCGGCAATTA
* *
54383881 GCCTACTAGATATAAACCTGAACTTATCACCGGCACGAG
1 GCCTGCTAGGTATAAACCTGAACTTATCACCGGCACGAG
* *
54383920 GCCTGCTAGGTATAAACCTGAGCTTATCACCGGCACTAG
1 GCCTGCTAGGTATAAACCTGAACTTATCACCGGCACGAG
54383959 GCCTGCTAGGTATAAACCTGAACTTATCACCGGCACGAG
1 GCCTGCTAGGTATAAACCTGAACTTATCACCGGCACGAG
* *
54383998 GCCTGCTAGGTATAAACCTGAGCTTATCACCGGCACTAG
1 GCCTGCTAGGTATAAACCTGAACTTATCACCGGCACGAG
54384037 GCCTGCTAGGTATAAACCTGAACTTATCACCGGCACGAG
1 GCCTGCTAGGTATAAACCTGAACTTATCACCGGCACGAG
* *
54384076 GCCTGCTAGGTATAAACCTGAGCTTATCACCGGCACTAG
1 GCCTGCTAGGTATAAACCTGAACTTATCACCGGCACGAG
54384115 GCCTGCTAGGTATAAACCTGAACTTATCACCGGCACGAG
1 GCCTGCTAGGTATAAACCTGAACTTATCACCGGCACGAG
54384154 GCCTGCTAG
1 GCCTGCTAG
54384163 ACATTAAGTC
Statistics
Matches: 229, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 229 1.00
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.22
Consensus pattern (39 bp):
GCCTGCTAGGTATAAACCTGAACTTATCACCGGCACGAG
Found at i:54383997 original size:78 final size:78
Alignment explanation
Indices: 54383868--54384162 Score: 547
Period size: 78 Copynumber: 3.8 Consensus size: 78
54383858 TTTTATTATT
* * *
54383868 TCACCGGCAATTA-GCCTACTAGATATAAACCTGAACTTATCACCGGCACGAGGCCTGCTAGGTA
1 TCACCGGC-ACTAGGCCTGCTAGGTATAAACCTGAACTTATCACCGGCACGAGGCCTGCTAGGTA
54383932 TAAACCTGAGCTTA
65 TAAACCTGAGCTTA
54383946 TCACCGGCACTAGGCCTGCTAGGTATAAACCTGAACTTATCACCGGCACGAGGCCTGCTAGGTAT
1 TCACCGGCACTAGGCCTGCTAGGTATAAACCTGAACTTATCACCGGCACGAGGCCTGCTAGGTAT
54384011 AAACCTGAGCTTA
66 AAACCTGAGCTTA
54384024 TCACCGGCACTAGGCCTGCTAGGTATAAACCTGAACTTATCACCGGCACGAGGCCTGCTAGGTAT
1 TCACCGGCACTAGGCCTGCTAGGTATAAACCTGAACTTATCACCGGCACGAGGCCTGCTAGGTAT
54384089 AAACCTGAGCTTA
66 AAACCTGAGCTTA
54384102 TCACCGGCACTAGGCCTGCTAGGTATAAACCTGAACTTATCACCGGCACGAGGCCTGCTAG
1 TCACCGGCACTAGGCCTGCTAGGTATAAACCTGAACTTATCACCGGCACGAGGCCTGCTAG
54384163 ACATTAAGTC
Statistics
Matches: 213, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
77 3 0.01
78 210 0.99
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.22
Consensus pattern (78 bp):
TCACCGGCACTAGGCCTGCTAGGTATAAACCTGAACTTATCACCGGCACGAGGCCTGCTAGGTAT
AAACCTGAGCTTA
Found at i:54389569 original size:48 final size:47
Alignment explanation
Indices: 54389514--54389688 Score: 208
Period size: 48 Copynumber: 3.7 Consensus size: 47
54389504 GGTGAATTTT
* *
54389514 CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATGTTGAGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTC-CATGTTGAGGC
* * * * *
54389562 CGATGCCATGTCCCAGTCATGGTCTTACACTAGCT-CTTGTCTCATTGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCCATGT-TGA-GGC
* * * *
54389610 TGATGCCATGTCCCAGACATGGCCTTACACTGGCTCTCATGATGTGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTC-CATGTTGAGGC
54389658 CGATGCCATGTCCCAGACATGGTCTTACACT
1 CGATGCCATGTCCCAGACATGGTCTTACACT
54389689 AGTACACATA
Statistics
Matches: 105, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
46 4 0.04
47 2 0.02
48 95 0.90
49 1 0.01
50 3 0.03
ACGTcount: A:0.20, C:0.30, G:0.22, T:0.29
Consensus pattern (47 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCCATGTTGAGGC
Found at i:54389679 original size:96 final size:96
Alignment explanation
Indices: 54389515--54389690 Score: 289
Period size: 96 Copynumber: 1.8 Consensus size: 96
54389505 GTGAATTTTC
* * * *
54389515 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATGTTGAGGCCGATGCCATGTCCCAGTC
1 GATGCCATGTCCCAAACATGGCCTTACACTGGCTCACATGATGAGGCCGATGCCATGTCCCAGAC
54389580 ATGGTCTTACACTAGCTCTTGTCTCATTGCT
66 ATGGTCTTACACTAGCTCTTGTCTCATTGCT
* * *
54389611 GATGCCATGTCCCAGACATGGCCTTACACTGGCTCTCATGATGTGGCCGATGCCATGTCCCAGAC
1 GATGCCATGTCCCAAACATGGCCTTACACTGGCTCACATGATGAGGCCGATGCCATGTCCCAGAC
54389676 ATGGTCTTACACTAG
66 ATGGTCTTACACTAG
54389691 TACACATATC
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
96 73 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.28
Consensus pattern (96 bp):
GATGCCATGTCCCAAACATGGCCTTACACTGGCTCACATGATGAGGCCGATGCCATGTCCCAGAC
ATGGTCTTACACTAGCTCTTGTCTCATTGCT
Found at i:54397578 original size:35 final size:35
Alignment explanation
Indices: 54397539--54397606 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
54397529 CCATGGTTGT
54397539 TCCATGGAAAAG-TGTGAAATGTAGGTATGGTATCA
1 TCCAT-GAAAAGTTGTGAAATGTAGGTATGGTATCA
***
54397574 TCCATGCTGAGTTGTGAAATGTAGGTATGGTAT
1 TCCATGAAAAGTTGTGAAATGTAGGTATGGTAT
54397607 TATCAAATCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 3 0.10
35 26 0.90
ACGTcount: A:0.29, C:0.09, G:0.29, T:0.32
Consensus pattern (35 bp):
TCCATGAAAAGTTGTGAAATGTAGGTATGGTATCA
Found at i:54397617 original size:40 final size:35
Alignment explanation
Indices: 54397551--54397681 Score: 111
Period size: 35 Copynumber: 3.6 Consensus size: 35
54397541 CATGGAAAAG
*
54397551 TGTGAAATGTAGGTATGGTATCATCCATGCTGAGT
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
54397586 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGT
** ** * * *
54397626 TAAGAAATGTAGGTACAGCAT-TTCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATCAT-CCATACTGAGT
* *
54397661 TGTAAAATGTAGGTATAGTAT
1 TGTGAAATGTAGGTATGGTAT
54397682 TTCAATGAGA
Statistics
Matches: 77, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
34 1 0.01
35 44 0.57
37 2 0.03
38 4 0.05
40 26 0.34
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
Found at i:54399471 original size:48 final size:47
Alignment explanation
Indices: 54399416--54399685 Score: 218
Period size: 48 Copynumber: 5.6 Consensus size: 47
54399406 GTGAATTACC
* * * * *
54399416 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATGTCGAGGCT
1 GATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATC-ATGCT
** * * * *
54399464 GATGCCATGTCCCAGTCATGGTATTACACTAGCTCTCGTTTCATTGTT
1 GATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATCA-TGCT
* *
54399512 GATGCCATGTCCCAAACATGGTCTTACACTAGCGT-ACATATCAATGCC
1 GATGCCATGTCCCAAACATGGTCTTACACTAGC-TCTCATATC-ATGCT
* * * * * * *
54399560 GATGTCATGTCTCAGACATGGTTTTACACTAGCTCTCACAACATTGTT
1 GATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATCA-TGCT
* * * * * *
54399608 GATGCCATGTTCCAAACATTGTCTTACATTGGCTCTCATATCGTGGCC
1 GATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATCAT-GCT
* * *
54399656 GATTCCATGTCCCAGACATAGTCTTACACT
1 GATGCCATGTCCCAAACATGGTCTTACACT
54399686 GGCACATATT
Statistics
Matches: 171, Mismatches: 45, Indels: 12
0.75 0.20 0.05
Matches are distributed among these distances:
47 4 0.02
48 165 0.96
49 2 0.01
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (47 bp):
GATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATCATGCT
Found at i:54399580 original size:96 final size:96
Alignment explanation
Indices: 54399416--54399685 Score: 317
Period size: 96 Copynumber: 2.8 Consensus size: 96
54399406 GTGAATTACC
* * * * *
54399416 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATGTCGAGGCTGATGCCATGTCCCAGTC
1 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATATCAAGGCCGATGCCATGTCCCAGAC
****
54399481 ATGGTATTACACTAGCTCTCGTTTCATTGTT
66 ATGGTATTACACTAGCTCTCACAACATTGTT
* * * *
54399512 GATGCCATGTCCCAAACATGGTCTTACACTAGCGT-ACATATCAATGCCGATGTCATGTCTCAGA
1 GATGCCATGTTCCAAACATGGTCTTACACTAGC-TCACATATCAAGGCCGATGCCATGTCCCAGA
*
54399576 CATGGTTTTACACTAGCTCTCACAACATTGTT
65 CATGGTATTACACTAGCTCTCACAACATTGTT
* * * * ** *
54399608 GATGCCATGTTCCAAACATTGTCTTACATTGGCTCTCATATCGTGGCCGATTCCATGTCCCAGAC
1 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATATCAAGGCCGATGCCATGTCCCAGAC
* *
54399673 ATAGTCTTACACT
66 ATGGTATTACACT
54399686 GGCACATATT
Statistics
Matches: 145, Mismatches: 27, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
95 1 0.01
96 143 0.99
97 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (96 bp):
GATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATATCAAGGCCGATGCCATGTCCCAGAC
ATGGTATTACACTAGCTCTCACAACATTGTT
Found at i:54412655 original size:17 final size:17
Alignment explanation
Indices: 54412600--54412655 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
54412590 TAATTTTTAA
*
54412600 TAATTTATAAATTATAT
1 TAATTTAAAAATTATAT
54412617 TAATTT---AATTAT-T
1 TAATTTAAAAATTATAT
*
54412630 CACATTTAAAAATTATAT
1 TA-ATTTAAAAATTATAT
54412648 TAATTTAA
1 TAATTTAA
54412656 TCTTCAAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
13 2 0.06
14 10 0.31
17 18 0.56
18 2 0.06
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATTTAAAAATTATAT
Found at i:54426750 original size:9 final size:9
Alignment explanation
Indices: 54426722--54426758 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
54426712 TGATTAAAAC
54426722 AATATTTAA
1 AATATTTAA
54426731 AA-A-TTATA
1 AATATTTA-A
54426739 AATATTTAA
1 AATATTTAA
54426748 AATATTTAA
1 AATATTTAA
54426757 AA
1 AA
54426759 AAATAGTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
7 3 0.12
8 4 0.16
9 15 0.60
10 3 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
AATATTTAA
Found at i:54429908 original size:20 final size:19
Alignment explanation
Indices: 54429880--54429925 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
54429870 AATCACCTAA
* *
54429880 TTCTCCTTTTTTTCTTTTCT
1 TTCTTCTTTCTTTC-TTTCT
54429900 TTCTTCTTTCTTTCTTTCT
1 TTCTTCTTTCTTTCTTTCT
54429919 TTGCTTC
1 TT-CTTC
54429926 CCCTGCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.00, C:0.26, G:0.02, T:0.72
Consensus pattern (19 bp):
TTCTTCTTTCTTTCTTTCT
Found at i:54429915 original size:15 final size:16
Alignment explanation
Indices: 54429890--54429919 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
54429880 TTCTCCTTTT
54429890 TTTCTTTTCTTTCTTC
1 TTTCTTTTCTTTCTTC
54429906 TTTC-TTTCTTTCTT
1 TTTCTTTTCTTTCTT
54429920 TGCTTCCCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTCTTTTCTTTCTTC
Found at i:54429983 original size:14 final size:14
Alignment explanation
Indices: 54429951--54429992 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
54429941 GCCTATTCTG
54429951 TTTCTTTTATTTGTTC
1 TTTCTTTTA-TT-TTC
54429967 TTTAC-TTTATTTTC
1 TTT-CTTTTATTTTC
54429981 TTTCTTTTATTT
1 TTTCTTTTATTT
54429993 GTTTTAGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 1 0.04
14 13 0.54
15 2 0.08
16 7 0.29
17 1 0.04
ACGTcount: A:0.10, C:0.12, G:0.02, T:0.76
Consensus pattern (14 bp):
TTTCTTTTATTTTC
Found at i:54431611 original size:29 final size:31
Alignment explanation
Indices: 54431579--54431638 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
54431569 TTAAAAATTA
54431579 GAAATTTAGTC-TCTATATTTTC-ATTTCAT
1 GAAATTTAGTCTTCTATATTTTCAATTTCAT
*
54431608 GAAATTTAGTCTTTCTATTTTTTCAATTTCA
1 GAAATTTAGTC-TTCTATATTTTCAATTTCA
54431639 AAATTCAGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 11 0.41
31 10 0.37
32 6 0.22
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (31 bp):
GAAATTTAGTCTTCTATATTTTCAATTTCAT
Found at i:54436119 original size:6 final size:6
Alignment explanation
Indices: 54436105--54436143 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
54436095 CACTAATCTC
*
54436105 TCTCCT TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT TCT
1 TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT TCT
54436144 TTGGCTGCCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (6 bp):
TCTCTT
Found at i:54441966 original size:18 final size:18
Alignment explanation
Indices: 54441928--54441960 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54441918 ACTTGTAAGA
54441928 AATTGTAACCTATCTCAC
1 AATTGTAACCTATCTCAC
54441946 AATTGT-ACCT-TCTCA
1 AATTGTAACCTATCTCA
54441961 TCCAATCACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 4 0.27
18 6 0.40
ACGTcount: A:0.30, C:0.27, G:0.06, T:0.36
Consensus pattern (18 bp):
AATTGTAACCTATCTCAC
Found at i:54453854 original size:30 final size:31
Alignment explanation
Indices: 54453782--54453860 Score: 81
Period size: 30 Copynumber: 2.6 Consensus size: 31
54453772 TACTATTCAT
* * *
54453782 TTCAGGTTATTTATGTACATAATAAAAAAAA
1 TTCAAGTTATTTTTGTAAATAATAAAAAAAA
* * *
54453813 GT-GAGTCATTTTTGTAAATAAT-AAAAAAA
1 TTCAAGTTATTTTTGTAAATAATAAAAAAAA
*
54453842 TTCAAGTTATTTTTATAAA
1 TTCAAGTTATTTTTGTAAA
54453861 AAAAACACAT
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
29 8 0.22
30 28 0.76
31 1 0.03
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (31 bp):
TTCAAGTTATTTTTGTAAATAATAAAAAAAA
Found at i:54461355 original size:19 final size:19
Alignment explanation
Indices: 54461319--54461356 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
54461309 ATTCCATCAA
*
54461319 TTATAAAATTTTTATTAAT
1 TTATAAAATTATTATTAAT
54461338 TTATAAAAGTTATT-TTAAT
1 TTATAAAA-TTATTATTAAT
54461357 ATCTATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
TTATAAAATTATTATTAAT
Found at i:54462133 original size:30 final size:30
Alignment explanation
Indices: 54462094--54462150 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
54462084 GAGTTGCTGT
54462094 AATTAATATTT-AT-TACTTAAAAATATTTAA
1 AATTAATATTTCATATA-TT-AAAATATTTAA
*
54462124 AATTTATATTTCATATATTAAAATATT
1 AATTAATATTTCATATATTAAAATATT
54462151 AACGACAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 18 0.75
31 4 0.17
32 2 0.08
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (30 bp):
AATTAATATTTCATATATTAAAATATTTAA
Found at i:54471119 original size:27 final size:27
Alignment explanation
Indices: 54471086--54471167 Score: 85
Period size: 27 Copynumber: 3.0 Consensus size: 27
54471076 TTTAAAATTG
54471086 TTTAAAATTTTTAAAAAATCATAAAAT
1 TTTAAAATTTTTAAAAAATCATAAAAT
* * * *
54471113 TTTAAAAATTATACTAAAATC-TAGAAT
1 TTTAAAATTTTTA-AAAAATCATAAAAT
* * *
54471140 TTTGAAATTTTAAAAAAATTATAAAAT
1 TTTAAAATTTTTAAAAAATCATAAAAT
54471167 T
1 T
54471168 ATAAGAGAAT
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
26 5 0.12
27 31 0.74
28 6 0.14
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (27 bp):
TTTAAAATTTTTAAAAAATCATAAAAT
Found at i:54472740 original size:46 final size:47
Alignment explanation
Indices: 54472665--54472766 Score: 129
Period size: 46 Copynumber: 2.2 Consensus size: 47
54472655 TAAATTTATA
* *
54472665 TAAT-TTTTTACAATTCTTATAATAATTTTAATAGT-TTTTATATTTT
1 TAATATTTTTACAATTCTTATAATAATTTTAATA-TATTTAATATATT
* * *
54472711 TAATATTTTTGCAATT-TTATATTATTTTTAATATATTTAATATATT
1 TAATATTTTTACAATTCTTATAATAATTTTAATATATTTAATATATT
54472757 TAATATTTTT
1 TAATATTTTT
54472767 TATAACTTCT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
45 1 0.02
46 38 0.78
47 10 0.20
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (47 bp):
TAATATTTTTACAATTCTTATAATAATTTTAATATATTTAATATATT
Found at i:54479820 original size:8 final size:8
Alignment explanation
Indices: 54479807--54479840 Score: 68
Period size: 8 Copynumber: 4.2 Consensus size: 8
54479797 TTGTTTTAGT
54479807 TATAATAA
1 TATAATAA
54479815 TATAATAA
1 TATAATAA
54479823 TATAATAA
1 TATAATAA
54479831 TATAATAA
1 TATAATAA
54479839 TA
1 TA
54479841 ATTTCTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
TATAATAA
Found at i:54480888 original size:50 final size:50
Alignment explanation
Indices: 54480626--54480885 Score: 292
Period size: 50 Copynumber: 5.2 Consensus size: 50
54480616 CCTAAATGAC
* * * * * *
54480626 CTTGTATATTCGGCCACATAGGTATGTACATATGTGATGTTGTATTGGAT
1 CTTGTATATTCGGCCATATAGGTAAGCACATATGTGATATTATATTTGAT
* * * *
54480676 CTTGAATATTCGACCATGAAAGTGT--GCACAAATGTGATATTATATTTGAAT
1 CTTGTATATTCGGCCAT-ATAG-GTAAGCACATATGTGATATTATATTTG-AT
* * * *
54480727 -TTGTATATTCGGCCATATAAGTAAGTACATATGTGATGTTAAATTTGAT
1 CTTGTATATTCGGCCATATAGGTAAGCACATATGTGATATTATATTTGAT
* * *
54480776 CTTGCATATTCGGCCATATAGGTAAGCACATATGTGATATTAAATTTGTT
1 CTTGTATATTCGGCCATATAGGTAAGCACATATGTGATATTATATTTGAT
* * *
54480826 CTTGCATATTTGGCCATATAGGTAAGCACATATGTGATATTATATCTGAT
1 CTTGTATATTCGGCCATATAGGTAAGCACATATGTGATATTATATTTGAT
54480876 CTTGTATATT
1 CTTGTATATT
54480886 TGGTCAAATG
Statistics
Matches: 177, Mismatches: 27, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
48 2 0.01
49 4 0.02
50 164 0.93
51 5 0.03
52 2 0.01
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (50 bp):
CTTGTATATTCGGCCATATAGGTAAGCACATATGTGATATTATATTTGAT
Found at i:54484723 original size:48 final size:50
Alignment explanation
Indices: 54484634--54484728 Score: 124
Period size: 48 Copynumber: 1.9 Consensus size: 50
54484624 AGTAAAAGAG
* *
54484634 TATTAATTAAAAAGATAAATTAAAAATAAATAATTTGAAAACAATATATT
1 TATTAATTAAAAAGATAAATTAAAAATAAAAAACTTGAAAACAATATATT
* *
54484684 TATTAATTAAAAA-A-CAGTTAAAAATAAAAAAGCTT-AAAACAATAT
1 TATTAATTAAAAAGATAAATTAAAAATAAAAAA-CTTGAAAACAATAT
54484729 CAAATAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
48 24 0.60
49 3 0.08
50 13 0.32
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (50 bp):
TATTAATTAAAAAGATAAATTAAAAATAAAAAACTTGAAAACAATATATT
Found at i:54491268 original size:55 final size:54
Alignment explanation
Indices: 54491188--54491298 Score: 204
Period size: 55 Copynumber: 2.0 Consensus size: 54
54491178 TTGAAAATAC
*
54491188 ATTTTATTTTCAAAAACTTTGAAAATTTAAATTTAAACTTTAAAGATGAAAGAA
1 ATTTTATTTTCAAAAACTTTAAAAATTTAAATTTAAACTTTAAAGATGAAAGAA
54491242 ATTTCTATTTTCAAAAACTTTAAAAATTTAAATTTAAACTTTAAAGATGAAAGAA
1 ATTT-TATTTTCAAAAACTTTAAAAATTTAAATTTAAACTTTAAAGATGAAAGAA
54491297 AT
1 AT
54491299 AATCATGAAC
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
54 4 0.07
55 51 0.93
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.39
Consensus pattern (54 bp):
ATTTTATTTTCAAAAACTTTAAAAATTTAAATTTAAACTTTAAAGATGAAAGAA
Found at i:54491933 original size:40 final size:40
Alignment explanation
Indices: 54491889--54492002 Score: 174
Period size: 40 Copynumber: 2.8 Consensus size: 40
54491879 TAAATTTATA
54491889 ATTATATTTTGGTACAAATAAATAATAAAAAAATATTTTT
1 ATTATATTTTGGTACAAATAAATAATAAAAAAATATTTTT
54491929 ATTATATTTTGGTACAAATAAATAATAAAAAAATATTTTT
1 ATTATATTTTGGTACAAATAAATAATAAAAAAATATTTTT
** * *
54491969 AAAATTAGTTTTTGTACAAATATATAATAAAAAA
1 ATTA-TA-TTTTGGTACAAATAAATAATAAAAAA
54492003 TTAAATTTAA
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
40 42 0.62
41 2 0.03
42 24 0.35
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.40
Consensus pattern (40 bp):
ATTATATTTTGGTACAAATAAATAATAAAAAAATATTTTT
Found at i:54491987 original size:42 final size:40
Alignment explanation
Indices: 54491892--54492017 Score: 171
Period size: 40 Copynumber: 3.1 Consensus size: 40
54491882 ATTTATAATT
**
54491892 ATATTTTGGTACAAATAAATAATAAAAAAATATTTTTATT
1 ATATTTTGGTACAAATAAATAATAAAAAAATATTTTTAAA
54491932 ATATTTTGGTACAAATAAATAATAAAAAAATATTTTTAAA
1 ATATTTTGGTACAAATAAATAATAAAAAAATATTTTTAAA
* * * **
54491972 ATTAGTTTTTGTACAAATATATAATAAAAAATTAAATTTAAA
1 A-TA-TTTTGGTACAAATAAATAATAAAAAAATATTTTTAAA
54492014 ATAT
1 ATAT
54492018 ATTTTAAGAT
Statistics
Matches: 77, Mismatches: 7, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
40 40 0.52
41 4 0.05
42 33 0.43
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.40
Consensus pattern (40 bp):
ATATTTTGGTACAAATAAATAATAAAAAAATATTTTTAAA
Found at i:54496823 original size:16 final size:16
Alignment explanation
Indices: 54496802--54496868 Score: 84
Period size: 16 Copynumber: 4.2 Consensus size: 16
54496792 AATCTTTCTT
54496802 TTTATTTTTAT-TTTTA
1 TTTATTTTT-TCTTTTA
54496818 TTTATTTTTTCTTTTA
1 TTTATTTTTTCTTTTA
*
54496834 TTTATTTTTTCTTTTC
1 TTTATTTTTTCTTTTA
* *
54496850 TTT-TCTTTTATTTTA
1 TTTATTTTTTCTTTTA
54496865 TTTA
1 TTTA
54496869 AATATTAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
15 13 0.29
16 32 0.71
ACGTcount: A:0.13, C:0.06, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTATTTTTTCTTTTA
Found at i:54496842 original size:26 final size:27
Alignment explanation
Indices: 54496796--54496867 Score: 87
Period size: 26 Copynumber: 2.6 Consensus size: 27
54496786 CAACCCAATC
54496796 TTTCTTTTTATTTTTATTTTTAT-TTATT-T
1 TTTC-TTTTA-TTTTATTTTT-TCTT-TTCT
54496825 TTTCTTTTA-TTTATTTTTTCTTTTCT
1 TTTCTTTTATTTTATTTTTTCTTTTCT
54496851 TTTCTTTTATTTTATTT
1 TTTCTTTTATTTTATTT
54496868 AAATATTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
25 3 0.08
26 21 0.52
27 7 0.17
28 5 0.12
29 4 0.10
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.82
Consensus pattern (27 bp):
TTTCTTTTATTTTATTTTTTCTTTTCT
Found at i:54497048 original size:42 final size:42
Alignment explanation
Indices: 54496946--54497050 Score: 156
Period size: 42 Copynumber: 2.5 Consensus size: 42
54496936 ATCCATGGTA
* *
54496946 CCAAACAGTTCTATTCCAACCCAAAATGCCATATCCCTGCTG
1 CCAAACAGTTCTATTCCAGCCCAAAATGCCATATCCCTGCAG
** *
54496988 CCAAACAGTTCTATTCCAGCCCAGGATGCCATATCTCTGCAG
1 CCAAACAGTTCTATTCCAGCCCAAAATGCCATATCCCTGCAG
*
54497030 CCAAACAGTCCTATTCCAGCC
1 CCAAACAGTTCTATTCCAGCC
54497051 GTAGAATCCC
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.29, C:0.36, G:0.12, T:0.23
Consensus pattern (42 bp):
CCAAACAGTTCTATTCCAGCCCAAAATGCCATATCCCTGCAG
Found at i:54501558 original size:41 final size:40
Alignment explanation
Indices: 54501503--54501620 Score: 96
Period size: 41 Copynumber: 2.9 Consensus size: 40
54501493 AAGCCTTGTG
* *
54501503 CTGGTGAATTAAATCGGGCTTTATGCCTAGCAGGCTTATTA
1 CTGGTGTATAAAATCGGGCTTTATGCCTAGCAGGCTTA-TA
* * * * *
54501544 CTGGTGTATAAAATCAGACTTTGA-GTCTAGCAGGCCTCATG
1 CTGGTGTATAAAATCGGGCTTT-ATGCCTAGCAGG-CTTATA
* * * *
54501585 CCGGTGTGTGATA-CGGGCTTTATGCCTAGCAGGCTT
1 CTGGTGTATAAAATCGGGCTTTATGCCTAGCAGGCTT
54501621 TATGCCGGTG
Statistics
Matches: 59, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
39 3 0.05
40 15 0.25
41 37 0.63
42 4 0.07
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.31
Consensus pattern (40 bp):
CTGGTGTATAAAATCGGGCTTTATGCCTAGCAGGCTTATA
Found at i:54504341 original size:33 final size:33
Alignment explanation
Indices: 54504298--54504466 Score: 196
Period size: 33 Copynumber: 5.1 Consensus size: 33
54504288 TGTACGTTTC
* *
54504298 TTTCTGAGTGGTACATACAAAGTATACCTTTCCT
1 TTTCT-AGTGGTATACACAAAGTATACCTTTCCT
**
54504332 TTTCTAGTGGTATACACAAAGTATACCTAACCT
1 TTTCTAGTGGTATACACAAAGTATACCTTTCCT
* * * * * **
54504365 TTCCAAGT-GTACACACAAAGTGTACATAACCT
1 TTTCTAGTGGTATACACAAAGTATACCTTTCCT
* *
54504397 TTTCAAATGGTATACACAAAGTATACCTTTCCT
1 TTTCTAGTGGTATACACAAAGTATACCTTTCCT
*
54504430 TTTCTAGTGGTATGCACAAAGTATACCTTTCCT
1 TTTCTAGTGGTATACACAAAGTATACCTTTCCT
54504463 TTTC
1 TTTC
54504467 ACATTTGATA
Statistics
Matches: 115, Mismatches: 19, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
32 27 0.23
33 83 0.72
34 5 0.04
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (33 bp):
TTTCTAGTGGTATACACAAAGTATACCTTTCCT
Found at i:54504377 original size:65 final size:66
Alignment explanation
Indices: 54504304--54504467 Score: 204
Period size: 65 Copynumber: 2.5 Consensus size: 66
54504294 TTTCTTTCTG
* * *
54504304 AGTGGTACATACAAAGTATACCTTTCCTTTTCTAGTGGTATACACAAAGTATACCTAACCTTTCC
1 AGTGGTACACACAAAGTATACCTTTCCTTTTCAAATGGTATACACAAAGTATACCTAACCTTTCC
54504369 A
66 A
* * ** ** *
54504370 AGT-GTACACACAAAGTGTACATAACCTTTTCAAATGGTATACACAAAGTATACCTTTCCTTTTC
1 AGTGGTACACACAAAGTATACCTTTCCTTTTCAAATGGTATACACAAAGTATACCTAACCTTTCC
*
54504434 T
66 A
**
54504435 AGTGGTATGCACAAAGTATACCTTTCCTTTTCA
1 AGTGGTACACACAAAGTATACCTTTCCTTTTCA
54504468 CATTTGATAA
Statistics
Matches: 80, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
65 54 0.68
66 26 0.32
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (66 bp):
AGTGGTACACACAAAGTATACCTTTCCTTTTCAAATGGTATACACAAAGTATACCTAACCTTTCC
A
Found at i:54504516 original size:29 final size:29
Alignment explanation
Indices: 54504460--54504587 Score: 184
Period size: 29 Copynumber: 4.4 Consensus size: 29
54504450 GTATACCTTT
** * * *
54504460 CCTTTTCACATTTGATAACTGAAACTATC
1 CCTTTTCACATTCAATAGCCGAAGCTATC
54504489 CCTTTTCACATTCAATAGCCGAAGCTATC
1 CCTTTTCACATTCAATAGCCGAAGCTATC
* * *
54504518 CCTTTTCACATTCGATAGCTGAAGGTATC
1 CCTTTTCACATTCAATAGCCGAAGCTATC
54504547 CCTTTTCACATTCAATAGCCGAAGCTATC
1 CCTTTTCACATTCAATAGCCGAAGCTATC
54504576 CCTTTTCACATT
1 CCTTTTCACATT
54504588 GTACACACAA
Statistics
Matches: 88, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 88 1.00
ACGTcount: A:0.27, C:0.28, G:0.10, T:0.35
Consensus pattern (29 bp):
CCTTTTCACATTCAATAGCCGAAGCTATC
Found at i:54504524 original size:58 final size:58
Alignment explanation
Indices: 54504460--54504587 Score: 220
Period size: 58 Copynumber: 2.2 Consensus size: 58
54504450 GTATACCTTT
*
54504460 CCTTTTCACATTTGATAACTGAAACTATCCCTTTTCACATTCAATAGCCGAAGCTATC
1 CCTTTTCACATTCGATAACTGAAACTATCCCTTTTCACATTCAATAGCCGAAGCTATC
* **
54504518 CCTTTTCACATTCGATAGCTGAAGGTATCCCTTTTCACATTCAATAGCCGAAGCTATC
1 CCTTTTCACATTCGATAACTGAAACTATCCCTTTTCACATTCAATAGCCGAAGCTATC
54504576 CCTTTTCACATT
1 CCTTTTCACATT
54504588 GTACACACAA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 66 1.00
ACGTcount: A:0.27, C:0.28, G:0.10, T:0.35
Consensus pattern (58 bp):
CCTTTTCACATTCGATAACTGAAACTATCCCTTTTCACATTCAATAGCCGAAGCTATC
Found at i:54512923 original size:10 final size:10
Alignment explanation
Indices: 54512905--54512935 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
54512895 AATTTTCTTG
*
54512905 CTTTAAAAAT
1 CTTTGAAAAT
54512915 CTTTGAAAAT
1 CTTTGAAAAT
54512925 CTTTGAAAAT
1 CTTTGAAAAT
54512935 C
1 C
54512936 AGGGTGGTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (10 bp):
CTTTGAAAAT
Found at i:54514757 original size:33 final size:33
Alignment explanation
Indices: 54514719--54514784 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
54514709 GAGGTGTACG
* *
54514719 TTTCTTTCCGAGTGGTACACACAAAGTATACCT
1 TTTCTTTCCAAATGGTACACACAAAGTATACCT
* *
54514752 TTTCTTTTCAAATGGTATACACAAAGTATACCT
1 TTTCTTTCCAAATGGTACACACAAAGTATACCT
54514785 AACCTTTCCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.36
Consensus pattern (33 bp):
TTTCTTTCCAAATGGTACACACAAAGTATACCT
Found at i:54514853 original size:84 final size:85
Alignment explanation
Indices: 54514731--54514886 Score: 260
Period size: 84 Copynumber: 1.8 Consensus size: 85
54514721 TCTTTCCGAG
* *
54514731 TGGTACACACAAAGTATACCTTTTCTTTTCAAATGGTATACACAAAGTATACCTAACCTTTCCAA
1 TGGTACACACAAAGTATACCTTTCCTTTTCAAATGGTATACACAAAGTATAACTAACCTTTCCAA
54514796 GTGTACATAACCTTTTTAAA
66 GTGTACATAACCTTTTTAAA
* * *
54514816 TGGTATAC-CAAAGTATACCTTTCCTTTTCTAGTGGTATACACAAAGTATAACTAACCTTTCCAA
1 TGGTACACACAAAGTATACCTTTCCTTTTCAAATGGTATACACAAAGTATAACTAACCTTTCCAA
54514880 GTGTACA
66 GTGTACA
54514887 CACAAAGTGT
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
84 59 0.89
85 7 0.11
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (85 bp):
TGGTACACACAAAGTATACCTTTCCTTTTCAAATGGTATACACAAAGTATAACTAACCTTTCCAA
GTGTACATAACCTTTTTAAA
Found at i:54514964 original size:33 final size:33
Alignment explanation
Indices: 54514806--54514976 Score: 184
Period size: 33 Copynumber: 5.2 Consensus size: 33
54514796 GTGTACATAA
* *
54514806 CCTTTTTAAATGGTATAC-CAAAGTATACCTTT
1 CCTTTTCAAGTGGTATACACAAAGTATACCTTT
* * **
54514838 CCTTTTCTAGTGGTATACACAAAGTATAACTAA
1 CCTTTTCAAGTGGTATACACAAAGTATACCTTT
* * * * **
54514871 CCTTTCCAAGT-GTACACACAAAGTGTACATAA
1 CCTTTTCAAGTGGTATACACAAAGTATACCTTT
* * *
54514903 CCTTTGCAAATGGTATATACAAAGTATACCTTT
1 CCTTTTCAAGTGGTATACACAAAGTATACCTTT
*
54514936 CCTTTTCTAGTGGTATACACAAAGTATACCTTT
1 CCTTTTCAAGTGGTATACACAAAGTATACCTTT
54514969 CCTTTTCA
1 CCTTTTCA
54514977 CATTCGATAG
Statistics
Matches: 112, Mismatches: 25, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
32 41 0.37
33 71 0.63
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (33 bp):
CCTTTTCAAGTGGTATACACAAAGTATACCTTT
Found at i:54515015 original size:29 final size:29
Alignment explanation
Indices: 54514969--54515096 Score: 202
Period size: 29 Copynumber: 4.4 Consensus size: 29
54514959 GTATACCTTT
* *
54514969 CCTTTTCACATTCGATAGCTGAAGGTATC
1 CCTTTTCACATTCGATAGCCGAAGCTATC
*
54514998 CCTTTTCACATTCAATAGCCGAAGCTATC
1 CCTTTTCACATTCGATAGCCGAAGCTATC
* * *
54515027 CCTTTTTATATTCGATAGCTGAAGCTATC
1 CCTTTTCACATTCGATAGCCGAAGCTATC
54515056 CCTTTTCACATTCGATAGCCGAAGCTATC
1 CCTTTTCACATTCGATAGCCGAAGCTATC
54515085 CCTTTTCACATT
1 CCTTTTCACATT
54515097 GTACACACAA
Statistics
Matches: 89, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 89 1.00
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.36
Consensus pattern (29 bp):
CCTTTTCACATTCGATAGCCGAAGCTATC
Found at i:54523447 original size:10 final size:10
Alignment explanation
Indices: 54523429--54523459 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
54523419 AATTTTCTTG
*
54523429 CTTTAAAAAT
1 CTTTGAAAAT
54523439 CTTTGAAAAT
1 CTTTGAAAAT
54523449 CTTTGAAAAT
1 CTTTGAAAAT
54523459 C
1 C
54523460 AGGGTGGTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (10 bp):
CTTTGAAAAT
Found at i:54525281 original size:33 final size:33
Alignment explanation
Indices: 54525243--54525308 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
54525233 GAGGTGTACG
* *
54525243 TTTCTTTCCGAGTGGTACACACAAAGTATACCT
1 TTTCTTTCCAAATGGTACACACAAAGTATACCT
* *
54525276 TTTCTTTTCAAATGGTATACACAAAGTATACCT
1 TTTCTTTCCAAATGGTACACACAAAGTATACCT
54525309 AACCTTTCCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.36
Consensus pattern (33 bp):
TTTCTTTCCAAATGGTACACACAAAGTATACCT
Found at i:54525377 original size:84 final size:85
Alignment explanation
Indices: 54525255--54525410 Score: 260
Period size: 84 Copynumber: 1.8 Consensus size: 85
54525245 TCTTTCCGAG
* *
54525255 TGGTACACACAAAGTATACCTTTTCTTTTCAAATGGTATACACAAAGTATACCTAACCTTTCCAA
1 TGGTACACACAAAGTATACCTTTCCTTTTCAAATGGTATACACAAAGTATAACTAACCTTTCCAA
54525320 GTGTACATAACCTTTTTAAA
66 GTGTACATAACCTTTTTAAA
* * *
54525340 TGGTATAC-CAAAGTATACCTTTCCTTTTCTAGTGGTATACACAAAGTATAACTAACCTTTCCAA
1 TGGTACACACAAAGTATACCTTTCCTTTTCAAATGGTATACACAAAGTATAACTAACCTTTCCAA
54525404 GTGTACA
66 GTGTACA
54525411 CACAAAGTGT
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
84 59 0.89
85 7 0.11
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (85 bp):
TGGTACACACAAAGTATACCTTTCCTTTTCAAATGGTATACACAAAGTATAACTAACCTTTCCAA
GTGTACATAACCTTTTTAAA
Found at i:54525488 original size:33 final size:33
Alignment explanation
Indices: 54525330--54525500 Score: 184
Period size: 33 Copynumber: 5.2 Consensus size: 33
54525320 GTGTACATAA
* *
54525330 CCTTTTTAAATGGTATAC-CAAAGTATACCTTT
1 CCTTTTCAAGTGGTATACACAAAGTATACCTTT
* * **
54525362 CCTTTTCTAGTGGTATACACAAAGTATAACTAA
1 CCTTTTCAAGTGGTATACACAAAGTATACCTTT
* * * * **
54525395 CCTTTCCAAGT-GTACACACAAAGTGTACATAA
1 CCTTTTCAAGTGGTATACACAAAGTATACCTTT
* * *
54525427 CCTTTGCAAATGGTATATACAAAGTATACCTTT
1 CCTTTTCAAGTGGTATACACAAAGTATACCTTT
*
54525460 CCTTTTCTAGTGGTATACACAAAGTATACCTTT
1 CCTTTTCAAGTGGTATACACAAAGTATACCTTT
54525493 CCTTTTCA
1 CCTTTTCA
54525501 CATTCGATAG
Statistics
Matches: 112, Mismatches: 25, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
32 41 0.37
33 71 0.63
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (33 bp):
CCTTTTCAAGTGGTATACACAAAGTATACCTTT
Found at i:54525539 original size:29 final size:29
Alignment explanation
Indices: 54525493--54525620 Score: 202
Period size: 29 Copynumber: 4.4 Consensus size: 29
54525483 GTATACCTTT
* *
54525493 CCTTTTCACATTCGATAGCTGAAGGTATC
1 CCTTTTCACATTCGATAGCCGAAGCTATC
*
54525522 CCTTTTCACATTCAATAGCCGAAGCTATC
1 CCTTTTCACATTCGATAGCCGAAGCTATC
* * *
54525551 CCTTTTTATATTCGATAGCTGAAGCTATC
1 CCTTTTCACATTCGATAGCCGAAGCTATC
54525580 CCTTTTCACATTCGATAGCCGAAGCTATC
1 CCTTTTCACATTCGATAGCCGAAGCTATC
54525609 CCTTTTCACATT
1 CCTTTTCACATT
54525621 GTACACACAA
Statistics
Matches: 89, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 89 1.00
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.36
Consensus pattern (29 bp):
CCTTTTCACATTCGATAGCCGAAGCTATC
Found at i:54528546 original size:40 final size:40
Alignment explanation
Indices: 54528491--54528696 Score: 333
Period size: 40 Copynumber: 5.2 Consensus size: 40
54528481 GGACTAATAT
* *
54528491 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
54528531 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
* * *
54528571 CTGAAGGCATTTGTACGAGTTACTATATCCGAGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
54528611 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
** *
54528651 CCGAAGGCATTTGTGCGAGTTGTTATATCC-GGCTAAATC
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
54528690 CCGAAGG
1 CCGAAGG
54528697 TACTTGGGTT
Statistics
Matches: 155, Mismatches: 11, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
39 15 0.10
40 140 0.90
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.28
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
Found at i:54530736 original size:179 final size:179
Alignment explanation
Indices: 54530431--54530793 Score: 663
Period size: 179 Copynumber: 2.0 Consensus size: 179
54530421 ATTTATACCC
*
54530431 TTTTTGTGAATGCCTATGAGATTTAGGGTTTTGTTTACAAGTGTTCTCTTTGGGATTTTGAGCTT
1 TTTTTGTGAATGCCTATGAGATTTAGAGTTTTGTTTACAAGTGTTCTCTTTGGGATTTTGAGCTT
* *
54530496 CGTATTCGAGGTTTTGGGTAATGTACATTTGGTACATTTATGTTAATTTTCTCCATATTTTACTC
66 CGTATTCGAGGTTTTAGGTAATGTACATTTAGTACATTTATGTTAATTTTCTCCATATTTTACTC
*
54530561 TCATTTGTTTGCTCATTTAGTTAAAAGCTGAAGCCTCCTTTACCTATGG
131 TCATTTGTTTGCTCATTTAGTTAAAAGCCGAAGCCTCCTTTACCTATGG
* *
54530610 TTTTTGTGAATGCCTATGAGATTTAGAGTTTTGTTTACCAGTTTTCTCTTTGGGATTTTGAGCTT
1 TTTTTGTGAATGCCTATGAGATTTAGAGTTTTGTTTACAAGTGTTCTCTTTGGGATTTTGAGCTT
*
54530675 CGTATTCGAGGTTTTAGGTAATGTACATTTAGTACATTTATGTTAATTTTCTCCTTATTTTACTC
66 CGTATTCGAGGTTTTAGGTAATGTACATTTAGTACATTTATGTTAATTTTCTCCATATTTTACTC
54530740 TCATTTGTTTGCTCATTTAGTTAAAAGCCGAAGCCTCCTTTACCTATGG
131 TCATTTGTTTGCTCATTTAGTTAAAAGCCGAAGCCTCCTTTACCTATGG
54530789 TTTTT
1 TTTTT
54530794 CCTTCTTTGA
Statistics
Matches: 177, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
179 177 1.00
ACGTcount: A:0.20, C:0.14, G:0.18, T:0.47
Consensus pattern (179 bp):
TTTTTGTGAATGCCTATGAGATTTAGAGTTTTGTTTACAAGTGTTCTCTTTGGGATTTTGAGCTT
CGTATTCGAGGTTTTAGGTAATGTACATTTAGTACATTTATGTTAATTTTCTCCATATTTTACTC
TCATTTGTTTGCTCATTTAGTTAAAAGCCGAAGCCTCCTTTACCTATGG
Found at i:54537004 original size:20 final size:20
Alignment explanation
Indices: 54536979--54537030 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
54536969 CACCATTGTT
* *
54536979 TCTAATATCACTCTACAGTA
1 TCTAATCTCACGCTACAGTA
54536999 TCTAATCTCACCGCTACAGTA
1 TCTAATCTCA-CGCTACAGTA
*
54537020 ACTAATCTCAC
1 TCTAATCTCAC
54537031 CGCCACCGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.33, C:0.31, G:0.06, T:0.31
Consensus pattern (20 bp):
TCTAATCTCACGCTACAGTA
Found at i:54537017 original size:21 final size:21
Alignment explanation
Indices: 54536991--54537033 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
54536981 TAATATCACT
*
54536991 CTACAGTATCTAATCTCACCG
1 CTACAGTAACTAATCTCACCG
54537012 CTACAGTAACTAATCTCACCG
1 CTACAGTAACTAATCTCACCG
54537033 C
1 C
54537034 CACCGCTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.35, G:0.09, T:0.26
Consensus pattern (21 bp):
CTACAGTAACTAATCTCACCG
Found at i:54537613 original size:29 final size:27
Alignment explanation
Indices: 54537579--54537675 Score: 81
Period size: 27 Copynumber: 3.4 Consensus size: 27
54537569 AATTTTAGAA
54537579 ATTTTTTTATATTTTAAAAATAGTTTTT
1 ATTTTTTTATATTTTAAAAATA-TTTTT
* *
54537607 A-TTTTTTAAATTTTAAAGAGTTATTTTT
1 ATTTTTTTATATTTTAAA-A-ATATTTTT
*
54537635 CATAATTTTTAT-TTTTAAAAATAAATTTTT
1 -AT-TTTTTTATATTTTAAAAAT--ATTTTT
54537665 ATGTTTTTTAT
1 AT-TTTTTTAT
54537676 TTAAAATATA
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
27 15 0.27
28 8 0.15
29 13 0.24
30 13 0.24
31 6 0.11
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.62
Consensus pattern (27 bp):
ATTTTTTTATATTTTAAAAATATTTTT
Found at i:54537676 original size:29 final size:27
Alignment explanation
Indices: 54537579--54537677 Score: 90
Period size: 30 Copynumber: 3.4 Consensus size: 27
54537569 AATTTTAGAA
*
54537579 ATTTTTTTATATTTTAAAAATAGTTTTT
1 ATTTTTTTAT-TTTTAAAAATAATTTTT
* * * *
54537607 ATTTTTTAAATTTTAAAGAGTTATTTTT
1 ATTTTTTTATTTTTAAA-AATAATTTTT
*
54537635 CATAATTTTTATTTTTAAAAATAAATTTTT
1 -AT-TTTTTTATTTTTAAAAAT-AATTTTT
54537665 ATGTTTTTTATTT
1 AT-TTTTTTATTT
54537678 AAAATATAAA
Statistics
Matches: 55, Mismatches: 12, Indels: 7
0.74 0.16 0.09
Matches are distributed among these distances:
27 7 0.13
28 15 0.27
29 15 0.27
30 18 0.33
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.63
Consensus pattern (27 bp):
ATTTTTTTATTTTTAAAAATAATTTTT
Found at i:54537869 original size:35 final size:35
Alignment explanation
Indices: 54537811--54537884 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
54537801 CATTTTAACC
54537811 TACTAAATTACATAGTATATATTATAAATTATTTA
1 TACTAAATTACATAGTATATATTATAAATTATTTA
* * *
54537846 TACTAAATTAGAT-GATATTTATTATTAATTATTTA
1 TACTAAATTACATAG-TATATATTATAAATTATTTA
54537881 TACT
1 TACT
54537885 TAATCAATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
34 1 0.03
35 34 0.97
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (35 bp):
TACTAAATTACATAGTATATATTATAAATTATTTA
Found at i:54540349 original size:15 final size:15
Alignment explanation
Indices: 54540329--54540358 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
54540319 AGGACTATAA
54540329 GTATGTTATAACCAT
1 GTATGTTATAACCAT
54540344 GTATGTTATAACCAT
1 GTATGTTATAACCAT
54540359 ATTTAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (15 bp):
GTATGTTATAACCAT
Found at i:54544552 original size:626 final size:626
Alignment explanation
Indices: 54543361--54544608 Score: 2406
Period size: 626 Copynumber: 2.0 Consensus size: 626
54543351 GAAAACGATC
* * *
54543361 AAGAGAACCACATTTATAACATGCTCCAGTTCTCAAATAGCATTCCCTAAAATAAAATTTATTAT
1 AAGAGAACCACATTTATAACATGCTCCAGTTCTCAAACAGCATTCCCCAAAATAAAATTTATTAC
*
54543426 AGTGTTTACACCTCAATTTGGGGTTACCGACACTTCCCATACTTGTTACAAATAGAGACCAAGAT
66 AGTGTTTACACCTCAATTTGGGGTTACCGACACTTCCCACACTTGTTACAAATAGAGACCAAGAT
*
54543491 CTCGGGTTAGAACGTTGAGAGCTTCGCTTTTTCCCAAAATATCCCGTAAAGGTGGTAGAACGATC
131 CTCGGGTTAGAACGTTGAGAGCCTCGCTTTTTCCCAAAATATCCCGTAAAGGTGGTAGAACGATC
54543556 ATGGTACTTCTTTGATTTCTTTGAAATAGATGATTGTGACTTATCCATAAATCTTTTACTAGAAA
196 ATGGTACTTCTTTGATTTCTTTGAAATAGATGATTGTGACTTATCCATAAATCTTTTACTAGAAA
54543621 TCCGGGCTTCTCTCTCTGCTTGTTTCTTTTCTTTCCTTAATTCTTCAGCTTTGTGTGCTCGATTA
261 TCCGGGCTTCTCTCTCTGCTTGTTTCTTTTCTTTCCTTAATTCTTCAGCTTTGTGTGCTCGATTA
54543686 TCTAGTACCAAAAATTCCATTAATTCAAGGATTCCAATCAACAACTTAATATCTTCATTTAATCC
326 TCTAGTACCAAAAATTCCATTAATTCAAGGATTCCAATCAACAACTTAATATCTTCATTTAATCC
54543751 TTCTTCAAAATGTTTACAAATGTCAGCCTCGGTCGGAACCCATTCTCTAGCATACTTGCTCAATC
391 TTCTTCAAAATGTTTACAAATGTCAGCCTCGGTCGGAACCCATTCTCTAGCATACTTGCTCAATC
54543816 TAATGAATTCTCATTCATATTCAGATACAATCATGTTTCCCTGTTTGAGCTCTAGAAATACTTTA
456 TAATGAATTCTCATTCATATTCAGATACAATCATGTTTCCCTGTTTGAGCTCTAGAAATACTTTA
54543881 TTTTTCTGATCCAGAAATCTTTGACCAATGTACTTCTTTCTAAATTCAGTCTGGAAGAATTATCA
521 TTTTTCTGATCCAGAAATCTTTGACCAATGTACTTCTTTCTAAATTCAGTCTGGAAGAATTATCA
54543946 TGTAACATTTCTCTCGGTACAACTAAAATCAGGGTATGATT
586 TGTAACATTTCTCTCGGTACAACTAAAATCAGGGTATGATT
*
54543987 AAGAGAACCACATTTATAACATGCTCCAGTTCTCAAACAGCATTCCCCAAAATAAAATTTATTGC
1 AAGAGAACCACATTTATAACATGCTCCAGTTCTCAAACAGCATTCCCCAAAATAAAATTTATTAC
** * *
54544052 AGTGTTTACACCTCAATTTGGGGTTACCGACACTTCTTACACTTGTTACAAATGGAGACGAAGAT
66 AGTGTTTACACCTCAATTTGGGGTTACCGACACTTCCCACACTTGTTACAAATAGAGACCAAGAT
54544117 CTCGGGTTAGAACGTTGAGAGCCTCGCTTTTTCCCAAAATATCCCGTAAAGGTGGTAGAACGATC
131 CTCGGGTTAGAACGTTGAGAGCCTCGCTTTTTCCCAAAATATCCCGTAAAGGTGGTAGAACGATC
54544182 ATGGTACTTCTTTGATTTCTTTGAAATAGATGATTGTGACTTATCCATAAATCTTTTACTAGAAA
196 ATGGTACTTCTTTGATTTCTTTGAAATAGATGATTGTGACTTATCCATAAATCTTTTACTAGAAA
54544247 TCCGGGCTTCTCTCTCTGCTTGTTTCTTTTCTTTCCTTAATTCTTCAGCTTTGTGTGCTCGATTA
261 TCCGGGCTTCTCTCTCTGCTTGTTTCTTTTCTTTCCTTAATTCTTCAGCTTTGTGTGCTCGATTA
54544312 TCTAGTACCAAAAATTCCATTAATTCAAGGATTCCAATCAACAACTTAATATCTTCATTTAATCC
326 TCTAGTACCAAAAATTCCATTAATTCAAGGATTCCAATCAACAACTTAATATCTTCATTTAATCC
54544377 TTCTTCAAAATGTTTACAAATGTCAGCCTCGGTCGGAACCCATTCTCTAGCATACTTGCTCAATC
391 TTCTTCAAAATGTTTACAAATGTCAGCCTCGGTCGGAACCCATTCTCTAGCATACTTGCTCAATC
54544442 TAATGAATTCTCATTCATATTCAGATACAATCATGTTTCCCTGTTTGAGCTCTAGAAATACTTTA
456 TAATGAATTCTCATTCATATTCAGATACAATCATGTTTCCCTGTTTGAGCTCTAGAAATACTTTA
54544507 TTTTTCTGATCCAGAAATCTTTGACCAATGTACTTCTTTCTAAATTCAGTCTGGAAGAATTATCA
521 TTTTTCTGATCCAGAAATCTTTGACCAATGTACTTCTTTCTAAATTCAGTCTGGAAGAATTATCA
54544572 TGTAACATTTCTCTCGGTACAACTAAAATCAGGGTAT
586 TGTAACATTTCTCTCGGTACAACTAAAATCAGGGTAT
54544609 TCCACCAATG
Statistics
Matches: 612, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
626 612 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (626 bp):
AAGAGAACCACATTTATAACATGCTCCAGTTCTCAAACAGCATTCCCCAAAATAAAATTTATTAC
AGTGTTTACACCTCAATTTGGGGTTACCGACACTTCCCACACTTGTTACAAATAGAGACCAAGAT
CTCGGGTTAGAACGTTGAGAGCCTCGCTTTTTCCCAAAATATCCCGTAAAGGTGGTAGAACGATC
ATGGTACTTCTTTGATTTCTTTGAAATAGATGATTGTGACTTATCCATAAATCTTTTACTAGAAA
TCCGGGCTTCTCTCTCTGCTTGTTTCTTTTCTTTCCTTAATTCTTCAGCTTTGTGTGCTCGATTA
TCTAGTACCAAAAATTCCATTAATTCAAGGATTCCAATCAACAACTTAATATCTTCATTTAATCC
TTCTTCAAAATGTTTACAAATGTCAGCCTCGGTCGGAACCCATTCTCTAGCATACTTGCTCAATC
TAATGAATTCTCATTCATATTCAGATACAATCATGTTTCCCTGTTTGAGCTCTAGAAATACTTTA
TTTTTCTGATCCAGAAATCTTTGACCAATGTACTTCTTTCTAAATTCAGTCTGGAAGAATTATCA
TGTAACATTTCTCTCGGTACAACTAAAATCAGGGTATGATT
Found at i:54553296 original size:13 final size:13
Alignment explanation
Indices: 54553278--54553302 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54553268 ATAACAGTAC
54553278 ATATAAAATACCT
1 ATATAAAATACCT
54553291 ATATAAAATACC
1 ATATAAAATACC
54553303 AGAAGAGATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (13 bp):
ATATAAAATACCT
Found at i:54555819 original size:57 final size:57
Alignment explanation
Indices: 54555726--54555882 Score: 190
Period size: 57 Copynumber: 2.8 Consensus size: 57
54555716 ATCAAATAAC
* ** * *
54555726 AGGATTACCAGTCCAGGCTAAATCCTGTCTCCAACATATGCTCACAAGAGCTTAATT
1 AGGATTACCAGTCCAGGCTAAATCCTATCTGTAACATATGCTCACAAAAGCTCAATT
* * * * *
54555783 AGGATTACCAATCCAAGCTGAATCCTTTCTGTAACATATGCTCAGAAAAGCTCAATT
1 AGGATTACCAGTCCAGGCTAAATCCTATCTGTAACATATGCTCACAAAAGCTCAATT
* *
54555840 AGGATTACTAGTCCAGGCTAAATCCTAAT-TGTAGCATATGCTC
1 AGGATTACCAGTCCAGGCTAAATCCT-ATCTGTAACATATGCTC
54555883 GAGAGGGATT
Statistics
Matches: 84, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
57 83 0.99
58 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (57 bp):
AGGATTACCAGTCCAGGCTAAATCCTATCTGTAACATATGCTCACAAAAGCTCAATT
Found at i:54559937 original size:21 final size:21
Alignment explanation
Indices: 54559911--54559954 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
54559901 CTTAGAGCGA
*
54559911 AGGCAGCAGCGAGGGAGGCGG
1 AGGCAGCAGAGAGGGAGGCGG
54559932 AGGCAGCAGAGAGGGAGGCGG
1 AGGCAGCAGAGAGGGAGGCGG
54559953 AG
1 AG
54559955 CAGAACAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.16, G:0.57, T:0.00
Consensus pattern (21 bp):
AGGCAGCAGAGAGGGAGGCGG
Found at i:54569006 original size:130 final size:129
Alignment explanation
Indices: 54568594--54569057 Score: 417
Period size: 131 Copynumber: 3.6 Consensus size: 129
54568584 AGAAAATCGA
* * * **
54568594 AACCCAGCAC-AGTAGGGCACGACTCCTTGAATTTCTAAACATTCG-ACATTGCCTT-ATTTTAG
1 AACCCAGCACGA-TAGGGCACGATTCC-CGAATTTCCAAACA-TCGAACATCACCTTCATTTTAG
* * * * *
54568656 -G-A-TTTGAAGAACAT-GAGTGAAATTCTAAAGGAATATTCGATTATTTTGAACAAA-CAGGAG
63 AGAATTTTTAAAAACATGGA-TGAAATTCTAAAGGAATATTCGATTA-TTTGAGCAAATGA-GAA
*
54568716 ATCGC
125 ATTGC
* * *
54568721 AACCCAGCACGATAGGGCACGATTCCCCGAATTGCTAAACATCGAACATTACCTTCATTTTAGAG
1 AACCCAGCACGATAGGGCACGATT-CCCGAATTTCCAAACATCGAACATCACCTTCATTTTAGAG
* * * * * * * *
54568786 AATTTTTAAAGACATGGGTGAAATTCCAAAGGAATACTCAATTGTTTAGAGCGAATGGGAAATTG
65 AATTTTTAAAAACATGGATGAAATTCTAAAGGAATATTCGATTATTT-GAGCAAATGAGAAATTG
*
54568851 A
129 C
* * ** * *
54568852 AACCCAGCACGATAGGGCACGATTCCCTAATTTCCAAACATTGAGTATCACTTTCGTTTT-GAAG
1 AACCCAGCACGATAGGGCACGATTCCCGAATTTCCAAACATCGAACATCACCTTCATTTTAG-AG
* *
54568916 AATTTTTAGAAAACATGGATGAAATTCTAAAGGGACATTCGATTATTTGAGCAAATGAGAAATTG
65 AATTTTTA-AAAACATGGATGAAATTCTAAAGGAATATTCGATTATTTGAGCAAATGAGAAATTG
54568981 C
129 C
* ** ** *
54568982 AACCCAGCAC-ATTAGGGCACGATTCCGCGAATTTCCAAATATCGAACATCGTCTTTGTTTTAAA
1 AACCCAGCACGA-TAGGGCACGATTCC-CGAATTTCCAAACATCGAACATCACCTTCATTTTAGA
54569046 GAATTTTTAAAA
64 GAATTTTTAAAA
54569058 GAATGATTAT
Statistics
Matches: 273, Mismatches: 49, Indels: 27
0.78 0.14 0.08
Matches are distributed among these distances:
126 3 0.01
127 42 0.15
128 10 0.04
129 3 0.01
130 83 0.30
131 131 0.48
132 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (129 bp):
AACCCAGCACGATAGGGCACGATTCCCGAATTTCCAAACATCGAACATCACCTTCATTTTAGAGA
ATTTTTAAAAACATGGATGAAATTCTAAAGGAATATTCGATTATTTGAGCAAATGAGAAATTGC
Found at i:54571456 original size:4 final size:4
Alignment explanation
Indices: 54571447--54571472 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
54571437 GGACTGTGGG
54571447 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
54571473 TATATTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:54578065 original size:131 final size:129
Alignment explanation
Indices: 54577848--54578241 Score: 477
Period size: 131 Copynumber: 3.0 Consensus size: 129
54577838 ATAATCATTC
* ** * * * *
54577848 TTTTAAAAATTCTTTAAAACGAAGACGATGTTTGATATTTGGCAATTCGTAGAATCGTGCCCTAA
1 TTTTAAAAATTCTTCAAAACGAAGGTGATGTTCGATGTTTGGCAATTCG-GGAATCGTGCCCTAT
* * * * * *
54577913 CGTGCTAGGTTGCAATTTCTCATTTGCTCAAAATAATCGAATGTCCCTTTAGAATTTCATCCATG
65 CGTGCTGGGTTGCGATTTCTCATTT-TTCAAAATAATCGAATATTCCTTTAGAATTTCACCCATG
54577978 T
129 T
** *
54577979 TTTCTAAAAATTCTTCAAAACGAAGGTGATACTCGATGTTTGTCAATTCGGGAATCGTGCCCTAT
1 TTT-TAAAAATTCTTCAAAACGAAGGTGATGTTCGATGTTTGGCAATTCGGGAATCGTGCCCTAT
* *
54578044 CGTGTTGGGTTGCGATTTCTCATTCTTTCAAAACAATCGAATATTCCTTT-GAAATTTCACCCAT
65 CGTGCTGGGTTGCGATTTCTCATT-TTTCAAAATAATCGAATATTCCTTTAG-AATTTCACCCAT
54578108 GT
128 GT
* *
54578110 CTTTAAAAATTC-TCTAAAACGAAGGTAATGTTCGATGTTTGGCAATTCGGGGAATCGTGCCCTA
1 TTTTAAAAATTCTTC-AAAACGAAGGTGATGTTCGATGTTTGGCAATTC-GGGAATCGTGCCCTA
* * ** *
54578174 TCGTGCTGGATTGCGATCTCTTGTTTATTTAAAATAATCGAATATTCCTTTAGAATTTCACCCAT
64 TCGTGCTGGGTTGCGATTTCTCATTT-TTCAAAATAATCGAATATTCCTTTAGAATTTCACCCAT
54578239 GT
128 GT
54578241 T
1 T
54578242 CTTCAAATCC
Statistics
Matches: 225, Mismatches: 31, Indels: 14
0.83 0.11 0.05
Matches are distributed among these distances:
129 2 0.01
130 40 0.18
131 143 0.64
132 40 0.18
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (129 bp):
TTTTAAAAATTCTTCAAAACGAAGGTGATGTTCGATGTTTGGCAATTCGGGAATCGTGCCCTATC
GTGCTGGGTTGCGATTTCTCATTTTTCAAAATAATCGAATATTCCTTTAGAATTTCACCCATGT
Done.