Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 72 of 213
Found at i:19460758 original size:102 final size:102
Alignment explanation
Indices: 19460628--19460826 Score: 362
Period size: 102 Copynumber: 2.0 Consensus size: 102
19460618 GTCTCTTTAT
19460628 TTTTCTTGAAAATGTCCTCTTTTCGACATTCCACCCAAATCCAAGTAACATAAATACCAAGGATC
1 TTTTCTTGAAAATGTCCTCTTTTCGACATTCCACCCAAATCCAAGTAACATAAATACCAAGGATC
*
19460693 AGAGTACTTTTGGCCCTCAAATTGAGCAATAATAACA
66 AGAGAACTTTTGGCCCTCAAATTGAGCAATAATAACA
* * *
19460730 TTTTCTTGAAAATGTCCTTTTTTTGACATTCCACCCAAATCCAAGTAACATAAATGCCAAGGATC
1 TTTTCTTGAAAATGTCCTCTTTTCGACATTCCACCCAAATCCAAGTAACATAAATACCAAGGATC
19460795 AGAGAACTTTTGGCCCTCAAATTGAGCAATAA
66 AGAGAACTTTTGGCCCTCAAATTGAGCAATAA
19460827 CAGCATCAAG
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
102 93 1.00
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.30
Consensus pattern (102 bp):
TTTTCTTGAAAATGTCCTCTTTTCGACATTCCACCCAAATCCAAGTAACATAAATACCAAGGATC
AGAGAACTTTTGGCCCTCAAATTGAGCAATAATAACA
Found at i:19463051 original size:26 final size:26
Alignment explanation
Indices: 19463022--19463087 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
19463012 AGTTTGGTAA
*
19463022 TGCTTTTAAAAAGTGA-TTTTGAA-AAG
1 TGCTTTTGAAAAGT-ACTTTT-AAGAAG
* *
19463048 TGCTGTGGAAAAGTACTTTTAAGAAG
1 TGCTTTTGAAAAGTACTTTTAAGAAG
19463074 TGCTTTTGAAAAGT
1 TGCTTTTGAAAAGT
19463088 TTGGTTTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
25 3 0.09
26 30 0.91
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.36
Consensus pattern (26 bp):
TGCTTTTGAAAAGTACTTTTAAGAAG
Found at i:19463316 original size:24 final size:24
Alignment explanation
Indices: 19463282--19463327 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
19463272 CATATGAAAT
* *
19463282 ATAAATTTTAAATATTTTTAAACA
1 ATAAATATTAAATATTTATAAACA
*
19463306 ATAAATATTAATTATTTATAAA
1 ATAAATATTAAATATTTATAAA
19463328 ATGTAATTAG
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:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
ATAAATATTAAATATTTATAAACA
Found at i:19464155 original size:15 final size:16
Alignment explanation
Indices: 19464120--19464160 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
19464110 TTGATAAACT
*
19464120 AAAAAATTAAGTGTTG
1 AAAAAATTAAGTGCTG
19464136 AAAAAATTAAGTGCTG
1 AAAAAATTAAGTGCTG
19464152 -AAAAATTAA
1 AAAAAATTAA
19464161 TTATTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 9 0.38
16 15 0.62
ACGTcount: A:0.56, C:0.02, G:0.15, T:0.27
Consensus pattern (16 bp):
AAAAAATTAAGTGCTG
Found at i:19464170 original size:15 final size:15
Alignment explanation
Indices: 19464119--19464177 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
19464109 TTTGATAAAC
19464119 TAAAAAATTAAGTGT
1 TAAAAAATTAAGTGT
*
19464134 TGAAAAAATTAAGTGC
1 T-AAAAAATTAAGTGT
* * *
19464150 TGAAAAATTAATTAT
1 TAAAAAATTAAGTGT
*
19464165 TAAAAATTTAAGT
1 TAAAAAATTAAGT
19464178 ACTGAATTAA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
15 21 0.60
16 14 0.40
ACGTcount: A:0.53, C:0.02, G:0.12, T:0.34
Consensus pattern (15 bp):
TAAAAAATTAAGTGT
Found at i:19464176 original size:30 final size:31
Alignment explanation
Indices: 19464121--19464183 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 31
19464111 TGATAAACTA
* *
19464121 AAAAATTAAGTGTTGAAAAAATTAAGTGCTG
1 AAAAATTAAGTATTGAAAAAATTAAGTACTG
* *
19464152 AAAAATTAATTATT-AAAAATTTAAGTACTG
1 AAAAATTAAGTATTGAAAAAATTAAGTACTG
19464182 AA
1 AA
19464184 TTAAAATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 16 0.57
31 12 0.43
ACGTcount: A:0.52, C:0.03, G:0.13, T:0.32
Consensus pattern (31 bp):
AAAAATTAAGTATTGAAAAAATTAAGTACTG
Found at i:19464640 original size:14 final size:15
Alignment explanation
Indices: 19464618--19464658 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
19464608 ATGCTTTTTG
*
19464618 TATATTTTTA-ATTA
1 TATAATTTTATATTA
*
19464632 TATAATTTTATATTT
1 TATAATTTTATATTA
19464647 TAT-ATTTTATAT
1 TATAATTTTATAT
19464659 ATCTTTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 18 0.75
15 6 0.25
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TATAATTTTATATTA
Found at i:19466073 original size:16 final size:15
Alignment explanation
Indices: 19466052--19466081 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
19466042 GTTAGGGTTA
19466052 AGGTTTTGGGGTTTTT
1 AGGTTTT-GGGTTTTT
19466068 AGGTTTTGGGTTTT
1 AGGTTTTGGGTTTT
19466082 AGAGAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.07, C:0.00, G:0.37, T:0.57
Consensus pattern (15 bp):
AGGTTTTGGGTTTTT
Found at i:19467907 original size:535 final size:535
Alignment explanation
Indices: 19466898--19467972 Score: 1920
Period size: 535 Copynumber: 2.0 Consensus size: 535
19466888 AATGGTGTAG
* *
19466898 ACTCATCTCGCTAGTGGAGCACCCTATATTGAGTTATATGTACAATTTATATCGCCAAATGATGT
1 ACTCATCTCGCTAGTGGAGCACCCTATATTGAGTTATATGTACAATTTACATCGCCAAATAATGT
19466963 ACTTGCAACTGCGGTTCGAGAGGTATACACAACCCCTGCCCGACATTCGGTTAGTGGGTTATAAA
66 ACTTGCAACTGCGGTTCGAGAGGTATACACAACCCCTGCCCGACATTCGGTTAGTGGGTTATAAA
*
19467028 ACACAGAACAGCCCATGTTTGGTAGCAGTATGGAATGCACATCCCCTGCAGGACACTCTGTCGGT
131 ACACAGAACAGCCCATGTTTGGTAGCAGTATGGAATGCACATCCCCTGCAAGACACTCTGTCGGT
* * *
19467093 GGATGGGACATGTACCTTGGTGGGTCGATGTTTGATGCTAGAAATACGTACTGGGGAACGGCATC
196 GGATGGGACATGTACCTCGGTGGGTCGATGTTTGACGCTAGAAATACGTACTGGGGAACGACATC
* *
19467158 AACTTCTAGTGGTTGGCAATCTACATTCAATTGGGGACGTTATAAAATGCCTAGAAGAAGGGATA
261 AACTTCTAGTGGTTGGCAATCTACATTCAATTGGGGACGTTATAAAACGCCTAGAAGAAAGGATA
* *
19467223 ATGTACTCCCTACGACGTCCACCGGTGAGGGGACCTCGTACATTACAGATAATGGTATGTTAGAA
326 ATGTACTCCCTACGACATCCACCGGTGAGGGGACCTCGTACATTACAGATAATGGTAGGTTAGAA
*
19467288 GATGACTTCGATGTGGATCTACCTCGAGAGCCCAGGCCCGATGGTACAGAAGTTGCATTATTTTT
391 GATGACTTCAATGTGGATCTACCTCGAGAGCCCAGGCCCGATGGTACAGAAGTTGCATTATTTTT
19467353 TGAACCGAAGCCTATTCCAACCGAACCTGAAGATGTTGAAGAAGGTTTAGATGACAAAGAAAATC
456 TGAACCGAAGCCTATTCCAACCGAACCTGAAGATGTTGAAGAAGGTTTAGATGACAAAGAAAATC
19467418 CACGATTCAGGGCAT
521 CACGATTCAGGGCAT
*
19467433 ACTCATCTCGCTAGTGGAGCACCCTATATTGAGTTATATGTACAATTTACATCGCCAAATAATTT
1 ACTCATCTCGCTAGTGGAGCACCCTATATTGAGTTATATGTACAATTTACATCGCCAAATAATGT
* *
19467498 ACTTGCGACTGTGGTTCGAGAGGTATACACAACCCCTGCCCGACATTCGGTTAGTGGGTTATAAA
66 ACTTGCAACTGCGGTTCGAGAGGTATACACAACCCCTGCCCGACATTCGGTTAGTGGGTTATAAA
*
19467563 ACACAGAACAGCCCATGTTTGGTAGCGGTATGGAATGCACATCCCCTGCAAGACACTCTGTCGGT
131 ACACAGAACAGCCCATGTTTGGTAGCAGTATGGAATGCACATCCCCTGCAAGACACTCTGTCGGT
19467628 GGATGGGACATGTACCTCGGTGGGTCGATGTTTGACGCT-GAAAATACGTACTGGGGAACGACAT
196 GGATGGGACATGTACCTCGGTGGGTCGATGTTTGACGCTAG-AAATACGTACTGGGGAACGACAT
19467692 CAACTTCTAGTGGTTGGCAATCTACATTCAATTGGGGACGTTATAAAACGCCTAGAAGAAAGGAT
260 CAACTTCTAGTGGTTGGCAATCTACATTCAATTGGGGACGTTATAAAACGCCTAGAAGAAAGGAT
* * *
19467757 GATGTACTCCCTACGACATCCACCGG-GAAGGGGACCTCGTACATTGCAGATGATGGTAGGTTAG
325 AATGTACTCCCTACGACATCCACCGGTG-AGGGGACCTCGTACATTACAGATAATGGTAGGTTAG
* *
19467821 AAGATGACTTCAATGTGGATCTACCTCGAGAGCCCAGGCCTGATGGTGCAGAAGTTGCATTATTT
389 AAGATGACTTCAATGTGGATCTACCTCGAGAGCCCAGGCCCGATGGTACAGAAGTTGCATTATTT
* *
19467886 TTTGAACCGAAGTCTATTCCAACCGAACCTGAAGATGTTGAAGAGGGTTTAGATGACAAAGAAAA
454 TTTGAACCGAAGCCTATTCCAACCGAACCTGAAGATGTTGAAGAAGGTTTAGATGACAAAGAAAA
19467951 TCCACGATTCAGGGCAT
519 TCCACGATTCAGGGCAT
19467968 ACTCA
1 ACTCA
19467973 CCTCCAGCCC
Statistics
Matches: 516, Mismatches: 22, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
534 2 0.00
535 514 1.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.26
Consensus pattern (535 bp):
ACTCATCTCGCTAGTGGAGCACCCTATATTGAGTTATATGTACAATTTACATCGCCAAATAATGT
ACTTGCAACTGCGGTTCGAGAGGTATACACAACCCCTGCCCGACATTCGGTTAGTGGGTTATAAA
ACACAGAACAGCCCATGTTTGGTAGCAGTATGGAATGCACATCCCCTGCAAGACACTCTGTCGGT
GGATGGGACATGTACCTCGGTGGGTCGATGTTTGACGCTAGAAATACGTACTGGGGAACGACATC
AACTTCTAGTGGTTGGCAATCTACATTCAATTGGGGACGTTATAAAACGCCTAGAAGAAAGGATA
ATGTACTCCCTACGACATCCACCGGTGAGGGGACCTCGTACATTACAGATAATGGTAGGTTAGAA
GATGACTTCAATGTGGATCTACCTCGAGAGCCCAGGCCCGATGGTACAGAAGTTGCATTATTTTT
TGAACCGAAGCCTATTCCAACCGAACCTGAAGATGTTGAAGAAGGTTTAGATGACAAAGAAAATC
CACGATTCAGGGCAT
Found at i:19470486 original size:21 final size:21
Alignment explanation
Indices: 19470462--19470501 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19470452 TTCTAGTTGT
* *
19470462 TCCGGTGGGGATTCTGGTTCC
1 TCCGGTAGGGAATCTGGTTCC
19470483 TCCGGTAGGGAATCTGGTT
1 TCCGGTAGGGAATCTGGTT
19470502 GTCGGTGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.20, G:0.38, T:0.33
Consensus pattern (21 bp):
TCCGGTAGGGAATCTGGTTCC
Found at i:19470742 original size:18 final size:18
Alignment explanation
Indices: 19470715--19470752 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
19470705 TAAAAAAGAA
* *
19470715 ACATATAAGGGTTAGGAT
1 ACATAAAAGGGCTAGGAT
19470733 ACATAAAAGGGCTAGGAT
1 ACATAAAAGGGCTAGGAT
19470751 AC
1 AC
19470753 GCACTTGGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.26, T:0.21
Consensus pattern (18 bp):
ACATAAAAGGGCTAGGAT
Found at i:19471415 original size:7 final size:7
Alignment explanation
Indices: 19471405--19471437 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
19471395 CATAATGCAT
*
19471405 AATACTG
1 AATACTA
19471412 AATACTA
1 AATACTA
19471419 AATACTA
1 AATACTA
19471426 AATACTA
1 AATACTA
19471433 AATAC
1 AATAC
19471438 CAATTGACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.55, C:0.15, G:0.03, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:19472623 original size:22 final size:24
Alignment explanation
Indices: 19472595--19472657 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 24
19472585 TTAAAATAGG
19472595 AATTTGAGAGGAA-ATT-GAGACA
1 AATTTGAGAGGAATATTAGAGACA
*
19472617 AATTTGAGA-GAATATTAGAGAGA
1 AATTTGAGAGGAATATTAGAGACA
*
19472640 AA-TTGAGAGAAAGTATTA
1 AATTTGAGAGGAA-TATTA
19472658 AGTTGTGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 3 0.09
22 18 0.51
23 9 0.26
24 5 0.14
ACGTcount: A:0.48, C:0.02, G:0.25, T:0.25
Consensus pattern (24 bp):
AATTTGAGAGGAATATTAGAGACA
Found at i:19472647 original size:10 final size:10
Alignment explanation
Indices: 19472598--19472651 Score: 63
Period size: 11 Copynumber: 5.0 Consensus size: 10
19472588 AAATAGGAAT
19472598 TTGAGAGGAAA
1 TTGAGA-GAAA
*
19472609 TTGAGACAAA
1 TTGAGAGAAA
19472619 TTTGAGAGAATA
1 -TTGAGAGAA-A
19472631 TTAGAGAGAAA
1 TT-GAGAGAAA
19472642 TTGAGAGAAA
1 TTGAGAGAAA
19472652 GTATTAAGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
10 11 0.29
11 19 0.50
12 8 0.21
ACGTcount: A:0.48, C:0.02, G:0.28, T:0.22
Consensus pattern (10 bp):
TTGAGAGAAA
Found at i:19474088 original size:52 final size:52
Alignment explanation
Indices: 19474031--19474136 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
19474021 CGAGCATGTG
19474031 AGTTGAACTCTCTCCTTGGAGAAAGATAAAACTAGTTTTGGGTTTGATGTAA
1 AGTTGAACTCTCTCCTTGGAGAAAGATAAAACTAGTTTTGGGTTTGATGTAA
19474083 AGTTGAACTCTCTCCTTGGAGAAAGATAAAACTAGTTTTGGGTTTGATGTAA
1 AGTTGAACTCTCTCCTTGGAGAAAGATAAAACTAGTTTTGGGTTTGATGTAA
19474135 AG
1 AG
19474137 ATTGGTGATG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.31, C:0.11, G:0.24, T:0.34
Consensus pattern (52 bp):
AGTTGAACTCTCTCCTTGGAGAAAGATAAAACTAGTTTTGGGTTTGATGTAA
Found at i:19488188 original size:24 final size:24
Alignment explanation
Indices: 19488156--19488201 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
19488146 TGCCACAAAT
19488156 CCTGAAGGTTACAAACTTTATCAA
1 CCTGAAGGTTACAAACTTTATCAA
19488180 CCTGAAGGTTACAAACTTTATC
1 CCTGAAGGTTACAAACTTTATC
19488202 TTCCATACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (24 bp):
CCTGAAGGTTACAAACTTTATCAA
Found at i:19492461 original size:20 final size:19
Alignment explanation
Indices: 19492425--19492463 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
19492415 AATTTCAAAA
*
19492425 TTATAAAATTTGGAATTTT
1 TTATAAAATTTGAAATTTT
*
19492444 TTATAAATATTTTAAATTTT
1 TTATAAA-ATTTGAAATTTT
19492464 AAAAATTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (19 bp):
TTATAAAATTTGAAATTTT
Found at i:19492503 original size:20 final size:20
Alignment explanation
Indices: 19492442--19492495 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
19492432 ATTTGGAATT
*
19492442 TTTTATAAA-TATTTT-AAA
1 TTTTAAAAATTATTTTAAAA
19492460 TTTTAAAAATTATTTTAAAA
1 TTTTAAAAATTATTTTAAAA
*
19492480 TTTTGAAAATTATTTT
1 TTTTAAAAATTATTTT
19492496 GTAATTTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.25
19 6 0.19
20 18 0.56
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTAAAAATTATTTTAAAA
Found at i:19499255 original size:22 final size:22
Alignment explanation
Indices: 19499210--19499272 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 22
19499200 TATGTATATG
19499210 TTTATAAAATGTATTATAATTTATAA
1 TTTATAAAAT-T-TTAT-ATTTAT-A
*
19499236 TTTATAAAATTTTAT-TTTATG
1 TTTATAAAATTTTATATTTATA
19499257 TTT-TAAAATTTT-TATT
1 TTTATAAAATTTTATATT
19499273 CATTTCGATT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
19 1 0.03
20 11 0.31
21 3 0.09
22 5 0.14
24 4 0.11
25 1 0.03
26 10 0.29
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (22 bp):
TTTATAAAATTTTATATTTATA
Found at i:19502036 original size:38 final size:36
Alignment explanation
Indices: 19501991--19502087 Score: 115
Period size: 38 Copynumber: 2.6 Consensus size: 36
19501981 GAAATCCTTG
*
19501991 TTATAATTATTGTAATTATAATTTAT-GATCGAATATTA
1 TTATAATTATTGTAATTATAATTTATCGATC-AA-A-CA
* *
19502029 TTATAATTATTGTAATTGTAATTTTTCGATCAAACA
1 TTATAATTATTGTAATTATAATTTATCGATCAAACA
* *
19502065 TTCTAATTATGGTAATTATAATT
1 TTATAATTATTGTAATTATAATT
19502088 ATTATATTTG
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
36 21 0.40
37 1 0.02
38 26 0.50
39 4 0.08
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.49
Consensus pattern (36 bp):
TTATAATTATTGTAATTATAATTTATCGATCAAACA
Found at i:19505367 original size:18 final size:18
Alignment explanation
Indices: 19505344--19505387 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
19505334 AGTTAATGAC
*
19505344 TTGAAATGGCAAATGATA
1 TTGAAATGACAAATGATA
* *
19505362 TTGAAATAACAAATGTTA
1 TTGAAATGACAAATGATA
19505380 -TGAAATGA
1 TTGAAATGA
19505388 AATTAAATGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.30
Consensus pattern (18 bp):
TTGAAATGACAAATGATA
Found at i:19514726 original size:9 final size:9
Alignment explanation
Indices: 19514712--19514737 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
19514702 GGGGAGGCAA
19514712 GAAGAAAGG
1 GAAGAAAGG
19514721 GAAGAAAGG
1 GAAGAAAGG
19514730 GAAGAAAG
1 GAAGAAAG
19514738 TTAGTCCAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (9 bp):
GAAGAAAGG
Found at i:19515643 original size:21 final size:22
Alignment explanation
Indices: 19515613--19515653 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
19515603 CCGGTTTGAT
*
19515613 TAAATAAATATTAAATAATTTA
1 TAAATAAATATTAAAAAATTTA
19515635 TAAA-AAATATTAAAAAATT
1 TAAATAAATATTAAAAAATT
19515654 AGTTCAACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAATAAATATTAAAAAATTTA
Found at i:19516628 original size:18 final size:16
Alignment explanation
Indices: 19516576--19516621 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 16
19516566 AAAGCTTATA
*
19516576 AAAAATAAAAAAATAG
1 AAAATTAAAAAAATAG
19516592 AAAATATTAAAAAAATAG
1 -AAA-ATTAAAAAAATAG
19516610 AAAATTAAAAAA
1 AAAATTAAAAAA
19516622 TGATAGATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 9 0.33
17 6 0.22
18 12 0.44
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.17
Consensus pattern (16 bp):
AAAATTAAAAAAATAG
Found at i:19517211 original size:15 final size:15
Alignment explanation
Indices: 19517188--19517217 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19517178 TGTTTTCAGC
*
19517188 TTCTTTTTTCTCTCA
1 TTCTATTTTCTCTCA
19517203 TTCTATTTTCTCTCA
1 TTCTATTTTCTCTCA
19517218 GTTTTCTCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.27, G:0.00, T:0.63
Consensus pattern (15 bp):
TTCTATTTTCTCTCA
Found at i:19522164 original size:15 final size:15
Alignment explanation
Indices: 19522141--19522170 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19522131 TGTTTTCAGC
*
19522141 TTCTTTTTTCTCTCA
1 TTCTGTTTTCTCTCA
19522156 TTCTGTTTTCTCTCA
1 TTCTGTTTTCTCTCA
19522171 GTTTTCTCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.27, G:0.03, T:0.63
Consensus pattern (15 bp):
TTCTGTTTTCTCTCA
Found at i:19522477 original size:18 final size:20
Alignment explanation
Indices: 19522451--19522493 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
19522441 AGATATTCTA
*
19522451 TTTTGTTTT-TTAGCTT-TG
1 TTTTCTTTTATTAGCTTGTG
*
19522469 TTTTCTTTTATTTGCTTGTG
1 TTTTCTTTTATTAGCTTGTG
19522489 TTTTC
1 TTTTC
19522494 ACAGTTTGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 8 0.38
19 6 0.29
20 7 0.33
ACGTcount: A:0.05, C:0.09, G:0.14, T:0.72
Consensus pattern (20 bp):
TTTTCTTTTATTAGCTTGTG
Found at i:19522907 original size:73 final size:73
Alignment explanation
Indices: 19522820--19522965 Score: 265
Period size: 73 Copynumber: 2.0 Consensus size: 73
19522810 GACGATATGT
* *
19522820 GTGCTTGGTAGGAGAGACGGAAAAATGGTAAGAAAATCACTTTTTCTTTCCATGCATTGCTTGTT
1 GTGCTTGGTAGGAGAGACAGAAAAATGGTAAGAAAATAACTTTTTCTTTCCATGCATTGCTTGTT
19522885 AGAGTTGA
66 AGAGTTGA
*
19522893 GTGCTTGGTAGGAGAGACAGAAAATTGGTAAGAAAATAACTTTTTCTTTCCATGCATTGCTTGTT
1 GTGCTTGGTAGGAGAGACAGAAAAATGGTAAGAAAATAACTTTTTCTTTCCATGCATTGCTTGTT
19522958 AGAGTTGA
66 AGAGTTGA
19522966 AAATTAGAAG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 70 1.00
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (73 bp):
GTGCTTGGTAGGAGAGACAGAAAAATGGTAAGAAAATAACTTTTTCTTTCCATGCATTGCTTGTT
AGAGTTGA
Found at i:19522990 original size:73 final size:73
Alignment explanation
Indices: 19522839--19522983 Score: 193
Period size: 73 Copynumber: 2.0 Consensus size: 73
19522829 AGGAGAGACG
* * *** * *
19522839 GAAAAATGGTAAGAAAATCACTTTTTCTTTCCATGCATTGCTTGTTAGAGTTGAGTGCTTGGTAG
1 GAAAATTGGTAAGAAAATAACTTTTTCTTTCCATGCATTGCTTGTTAGAGTTGAGAAATTAGAAG
* *
19522904 GAGAGACA
66 GAAAGAAA
19522912 GAAAATTGGTAAGAAAATAACTTTTTCTTTCCATGCATTGCTTGTTAGAGTTGA-AAATTAGAAG
1 GAAAATTGGTAAGAAAATAACTTTTTCTTTCCATGCATTGCTTGTTAGAGTTGAGAAATTAGAAG
*
19522976 TAAAGAAA
66 GAAAGAAA
19522984 ATAAAATATT
Statistics
Matches: 62, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
72 10 0.16
73 52 0.84
ACGTcount: A:0.35, C:0.10, G:0.21, T:0.33
Consensus pattern (73 bp):
GAAAATTGGTAAGAAAATAACTTTTTCTTTCCATGCATTGCTTGTTAGAGTTGAGAAATTAGAAG
GAAAGAAA
Found at i:19526755 original size:19 final size:20
Alignment explanation
Indices: 19526722--19526764 Score: 79
Period size: 19 Copynumber: 2.2 Consensus size: 20
19526712 TGATTTAAGT
19526722 CATATAAGAAAAAACATTAA
1 CATATAAGAAAAAACATTAA
19526742 CATATAAG-AAAAACATTAA
1 CATATAAGAAAAAACATTAA
19526761 CATA
1 CATA
19526765 CATACATACA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.63, C:0.12, G:0.05, T:0.21
Consensus pattern (20 bp):
CATATAAGAAAAAACATTAA
Found at i:19526769 original size:4 final size:4
Alignment explanation
Indices: 19526760--19527637 Score: 1232
Period size: 4 Copynumber: 219.0 Consensus size: 4
19526750 AAAAACATTA
* * *
19526760 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AAAA ACATT AACAT ACAA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA-T -ACAT ACAT
19526810 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * * *
19526858 ACAT ACAC ACAC ACAC ACAT ACAC ACAC ACAT ACAT ACAT AC-- ACAC
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
19526904 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
19526952 ACAT ACAT ACAT ACAT ACAT ACAT ATAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * *
19527000 ACAT ACAT ACAT ACAT ACAT ACAT ACAC ACAC ACAT ACAC ACAC ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * * *
19527048 ACAC AGAC ACAT ACAC ATAC ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
19527096 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AAAA ACATT AACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA-T -ACAT
* *
19527146 ACAT ACAT ACAT ACAT ACAT ACAT ACAC ACAC ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
19527194 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAC ACAC
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
19527242 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * *
19527290 ACAT ACAT ACAT ACAT ACAT ACAT ACAC ACAT ACAC ACAC ACAT ACAC
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * *
19527338 ACAC ACAT AC-- ACAC ACAT ACAT ACAT ACAT ACAT ACAT ATAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
19527384 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AAAA ACATT AACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA-T -ACAT
* *
19527434 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AAAA ACATT AACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA-T -ACAT ACAT
*
19527484 ACAA ACAT ACAT ACAT ACAT ACATT AACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACA-T -ACAT ACAT ACAT ACAT ACAT ACAT
19527534 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC--
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * *
19527580 ACAC ACAT ACAC ACAT ACAT AC-- ACAC ACAC ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
19527626 ACAT ACAT ACAT
1 ACAT ACAT ACAT
19527638 TGAACTCGAA
Statistics
Matches: 800, Mismatches: 56, Indels: 36
0.90 0.06 0.04
Matches are distributed among these distances:
2 8 0.01
4 771 0.96
5 6 0.01
6 15 0.02
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (4 bp):
ACAT
Found at i:19528331 original size:27 final size:26
Alignment explanation
Indices: 19528295--19528348 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
19528285 CTCCTTCCAC
*
19528295 TAGTTTATTA-TATATAGTATGATTAA
1 TAGTTTATTAGTATA-AGTATAATTAA
*
19528321 TAGTTTAATTAGTTTAAGTATAATTAA
1 TAGTTT-ATTAGTATAAGTATAATTAA
19528348 T
1 T
19528349 TAATAAGACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 6 0.25
27 15 0.62
28 3 0.12
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (26 bp):
TAGTTTATTAGTATAAGTATAATTAA
Found at i:19535209 original size:16 final size:16
Alignment explanation
Indices: 19535188--19535220 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19535178 GAACTTAATT
19535188 ATAATT-CATATGATCC
1 ATAATTACATATG-TCC
19535204 ATAATTACATATGTCC
1 ATAATTACATATGTCC
19535220 A
1 A
19535221 ATCGGTCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.36
Consensus pattern (16 bp):
ATAATTACATATGTCC
Found at i:19538898 original size:28 final size:27
Alignment explanation
Indices: 19538867--19538949 Score: 112
Period size: 27 Copynumber: 3.0 Consensus size: 27
19538857 ATTCAGATGA
* *
19538867 TTGCCACAAAGGCTAATCTTTTTATTTT
1 TTGCCACAAAGGCT-TTCTTTTTATTGT
* *
19538895 TTGCCACAAAGGCTTTCTTTTCATGGT
1 TTGCCACAAAGGCTTTCTTTTTATTGT
*
19538922 TTGCCACCAAGGCTTTCTTTTTATTGT
1 TTGCCACAAAGGCTTTCTTTTTATTGT
19538949 T
1 T
19538950 CACCCCAAAG
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 34 0.71
28 14 0.29
ACGTcount: A:0.19, C:0.20, G:0.14, T:0.46
Consensus pattern (27 bp):
TTGCCACAAAGGCTTTCTTTTTATTGT
Found at i:19553893 original size:169 final size:169
Alignment explanation
Indices: 19553614--19553952 Score: 570
Period size: 169 Copynumber: 2.0 Consensus size: 169
19553604 GGACCCCACC
* *
19553614 AGGTGGAGTCATTAGGGGGATCGCGAGCCCAGTTCACACATCCTTGGATGTCCACGAGCATAGGA
1 AGGTGGAGTAATTAGGGGGATCGCGAGCCCAGTTCACACATCCCTGGATGTCCACGAGCATAGGA
19553679 TACAAGGTCAAACGAATAAACCGATGAGCACCTGGACCAGTGAACACGTGTTGAGTTTAGGGTAA
66 TACAAGGTCAAACGAATAAACCGATGAGCACCTGGACCAGTGAACACGTGTTGAGTTTAGGGTAA
* *
19553744 CATACGTGTTGACATGCATGGAGCCTACCTAGAACGTCA
131 CATACATGTCGACATGCATGGAGCCTACCTAGAACGTCA
* * *
19553783 AGGTGGAGTAATTAGGGGGCTCGCGAGCCCAGTTCGCACATCCCTGGATGTCCACGAGCATAGGG
1 AGGTGGAGTAATTAGGGGGATCGCGAGCCCAGTTCACACATCCCTGGATGTCCACGAGCATAGGA
* * * * *
19553848 TACGAGGTCAAACGAATGAACTGATGAGCACCTGGACTAGTGAACATGTGTTGAGTTTAGGGTAA
66 TACAAGGTCAAACGAATAAACCGATGAGCACCTGGACCAGTGAACACGTGTTGAGTTTAGGGTAA
19553913 CATACATGTCGACATGCATGGAGCCTACCTAGAACGTCA
131 CATACATGTCGACATGCATGGAGCCTACCTAGAACGTCA
19553952 A
1 A
19553953 TTCCATGAAC
Statistics
Matches: 158, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
169 158 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.21
Consensus pattern (169 bp):
AGGTGGAGTAATTAGGGGGATCGCGAGCCCAGTTCACACATCCCTGGATGTCCACGAGCATAGGA
TACAAGGTCAAACGAATAAACCGATGAGCACCTGGACCAGTGAACACGTGTTGAGTTTAGGGTAA
CATACATGTCGACATGCATGGAGCCTACCTAGAACGTCA
Found at i:19559797 original size:16 final size:16
Alignment explanation
Indices: 19559760--19559801 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
19559750 TTAATCATAT
*
19559760 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
19559776 TT-AAATATATTATAA
1 TTAAAATATATTATAA
19559791 TTAAAATATAT
1 TTAAAATATAT
19559802 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:19559808 original size:14 final size:15
Alignment explanation
Indices: 19559769--19559810 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
19559759 TTTAAACATA
*
19559769 ATTATTATTAAATAT
1 ATTATAATTAAATAT
19559784 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
19559798 A-TATAATTTAATA
1 ATTATAATTAAATA
19559811 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:19559927 original size:14 final size:15
Alignment explanation
Indices: 19559875--19559929 Score: 62
Period size: 15 Copynumber: 3.8 Consensus size: 15
19559865 TACTATAAAA
19559875 TATAATTAACATA-AT
1 TATAATTAA-ATATAT
*
19559890 TATTATTAAATATAT
1 TATAATTAAATATAT
19559905 TATAATTAAA-ATA-
1 TATAATTAAATATAT
*
19559918 TATAATTTAATA
1 TATAATTAAATA
19559930 AAATTCTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
13 9 0.26
14 7 0.20
15 19 0.54
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
TATAATTAAATATAT
Found at i:19560026 original size:15 final size:15
Alignment explanation
Indices: 19559998--19560062 Score: 64
Period size: 15 Copynumber: 4.3 Consensus size: 15
19559988 ATAAAATATA
19559998 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
19560013 TATTAAATATATTAT
1 AATTAAATATATTAT
19560028 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
19560041 AATTTAATAATATTAAT
1 AATTAAAT-ATATT-AT
19560058 AATTA
1 AATTA
19560063 TTAATACTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
13 9 0.22
14 6 0.15
15 19 0.46
16 1 0.02
17 6 0.15
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:19560091 original size:120 final size:120
Alignment explanation
Indices: 19559763--19560174 Score: 684
Period size: 120 Copynumber: 3.4 Consensus size: 120
19559753 ATCATATTTA
19559763 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
19559828 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATAT-AATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
19559882 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
19559947 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
* ** * *
19560002 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAATATTAATAATTATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
* * * *
19560067 TACTCTTATATGAATTTATTCAAATCATAATATATGATACTATAAAAGATAATTT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
* * * *
19560122 GAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGACTTAATAAAATT
1 -AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
19560175 TAAAATAATT
Statistics
Matches: 277, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
119 115 0.42
120 160 0.58
121 2 0.01
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
Found at i:19560245 original size:27 final size:28
Alignment explanation
Indices: 19560215--19560276 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
19560205 TATGAATTTG
*
19560215 TATAATTTAAAAATAAT-TATTATTACA
1 TATAATTTAAAAATAATATATAATTACA
* *
19560242 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAAAAATAATATATAATTACA
*
19560270 TAAAATT
1 TATAATT
19560277 CTTGATAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 16 0.53
28 14 0.47
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (28 bp):
TATAATTTAAAAATAATATATAATTACA
Found at i:19560352 original size:91 final size:92
Alignment explanation
Indices: 19560190--19560398 Score: 314
Period size: 91 Copynumber: 2.3 Consensus size: 92
19560180 TAATTATAAC
* * * *
19560190 TAAT-AATTTATCTTATATGAATTTGTATAATTTAAAAATAATTATTATTACATATAATTTAATA
1 TAATAAATTT-TCTTATATGAATTTATACAATTTAAAAATAATTAATATTAAATATAATTTAATA
*
19560254 ATAATATATAATTTCATAAAATTCTTGA
65 ATAATATATAATTTCATAAAATTCTTAA
*
19560282 TAATAAATTTTCTTATATTAATTTATACAATTT-AAAATAATTAATATTAAATATAATTTAATAA
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAAATAATTAATATTAAATATAATTTAATAA
*
19560346 TGATATATAATTTCATAAAATTCTTAA
66 TAATATATAATTTCATAAAATTCTTAA
*
19560373 TAATAAAATGTTCTTATATGAATTTA
1 TAAT-AAATTTTCTTATATGAATTTA
19560399 CTAAAATCAA
Statistics
Matches: 106, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
91 58 0.55
92 43 0.41
93 5 0.05
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (92 bp):
TAATAAATTTTCTTATATGAATTTATACAATTTAAAAATAATTAATATTAAATATAATTTAATAA
TAATATATAATTTCATAAAATTCTTAA
Found at i:19563733 original size:6 final size:6
Alignment explanation
Indices: 19563722--19563747 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
19563712 TAGTTTGAAC
19563722 ATTTAA ATTTAA ATTTAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA AT
19563748 ATAGTTTCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTTAA
Found at i:19564203 original size:13 final size:13
Alignment explanation
Indices: 19564185--19564209 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19564175 ATCAAATTTG
19564185 TATGTACTCTTTA
1 TATGTACTCTTTA
19564198 TATGTACTCTTT
1 TATGTACTCTTT
19564210 CACTAATAAA
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:0.20, C:0.16, G:0.08, T:0.56
Consensus pattern (13 bp):
TATGTACTCTTTA
Found at i:19564229 original size:51 final size:51
Alignment explanation
Indices: 19564174--19564278 Score: 156
Period size: 51 Copynumber: 2.1 Consensus size: 51
19564164 TATATATTAG
** *
19564174 TATCAAATTTGTATGTACTCTTTATATGTACTCTTTCACTAATAAATTATA
1 TATCAAATTTGTATCAACTCTTTATATGTACGCTTTCACTAATAAATTATA
* * *
19564225 TATCAAATTTGTATCAATTTTTTTTATGTACGCTTTCACTAATAAATTATA
1 TATCAAATTTGTATCAACTCTTTATATGTACGCTTTCACTAATAAATTATA
19564276 TAT
1 TAT
19564279 TAGTAAAAAG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.49
Consensus pattern (51 bp):
TATCAAATTTGTATCAACTCTTTATATGTACGCTTTCACTAATAAATTATA
Found at i:19564710 original size:3 final size:3
Alignment explanation
Indices: 19564702--19564733 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
19564692 TAATTAGTGG
19564702 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
19564734 GCTTTCCTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:19567658 original size:3 final size:3
Alignment explanation
Indices: 19567650--19567677 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
19567640 CAAGGTATGT
19567650 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
19567678 CTTTTTCCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:19573676 original size:51 final size:50
Alignment explanation
Indices: 19573615--19573765 Score: 277
Period size: 50 Copynumber: 3.0 Consensus size: 50
19573605 AAATTAAAAG
19573615 ATTATACATACACCAACAATGTTTTTTAGGGTAAATAACATTAAACCAACA
1 ATTATACATACACCAACAATG-TTTTTAGGGTAAATAACATTAAACCAACA
*
19573666 ATTATACATACACCAACAATGTTTTTAAGGTAAATAACATTAAACCAACA
1 ATTATACATACACCAACAATGTTTTTAGGGTAAATAACATTAAACCAACA
19573716 ATTATACATACACCAACAATGTTTTTAGGG-AAATAACATTAAACCAACA
1 ATTATACATACACCAACAATGTTTTTAGGGTAAATAACATTAAACCAACA
19573765 A
1 A
19573766 GTAATTTAGG
Statistics
Matches: 98, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
49 20 0.20
50 57 0.58
51 21 0.21
ACGTcount: A:0.47, C:0.18, G:0.07, T:0.28
Consensus pattern (50 bp):
ATTATACATACACCAACAATGTTTTTAGGGTAAATAACATTAAACCAACA
Found at i:19573812 original size:33 final size:33
Alignment explanation
Indices: 19573714--19573820 Score: 125
Period size: 33 Copynumber: 3.3 Consensus size: 33
19573704 ATTAAACCAA
19573714 CAATTATACATACACCAACAATGT--TTTTAGG-
1 CAATTATACATACACCAACAAT-TAATTTTAGGT
* * * *
19573745 GAAATA-ACATTAAACCAACAAGTAA-TTTAGGT
1 CAATTATACA-TACACCAACAATTAATTTTAGGT
19573777 CAATTATACATACACCAACAATTAATTTTAGGT
1 CAATTATACATACACCAACAATTAATTTTAGGT
19573810 CAATTATACAT
1 CAATTATACAT
19573821 GCTTTATAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
30 4 0.06
31 20 0.32
32 17 0.27
33 21 0.34
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (33 bp):
CAATTATACATACACCAACAATTAATTTTAGGT
Found at i:19577152 original size:18 final size:17
Alignment explanation
Indices: 19577124--19577158 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
19577114 AATTATAAGA
*
19577124 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
19577141 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
19577159 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:19577195 original size:137 final size:138
Alignment explanation
Indices: 19576978--19577397 Score: 458
Period size: 156 Copynumber: 2.9 Consensus size: 138
19576968 TAAGAATATG
* * *
19576978 AATTATTAAGAATTTTATTAAATTATATACCA--AATTATAATGTATTTAATATAATTATGTTTA
1 AATTA-TAAGAATTTTATTAAATTATATA-TATTAATTAAAATATATTTAATATAATTATGTTTA
* * * *
19577041 AATACGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAAA
64 AATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAAA
*
19577106 T-TTCT-GC-T
129 TATT-TACCAT
*
19577114 AATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAA
1 AATTATAAGAATTTTATTAAATTATATATATTAATTAAAATATATTTAAT-ATAATTATGTTTAA
*
19577179 ATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACATTAACAATA
65 ATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAAC-A-A
19577244 ATCATTTACCAAAATAATTTTCTGCT
128 AT-ATTTACC------A--------T
* *
19577270 AATTATAAGAATTTTATTAAA--TTATATATTTTAATTAAAATATATTTAATTATAATTATGTTT
1 AATTATAAGAATTTTATTAAATTATATATATTA--ATTAAAATATATTTAA-TATAATTATGTTT
*
19577333 AAATATGATTAAAATATTTATTACTAATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
63 AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
19577398 TAATCATTTA
Statistics
Matches: 243, Mismatches: 15, Indels: 34
0.83 0.05 0.12
Matches are distributed among these distances:
135 23 0.09
136 21 0.09
137 70 0.29
138 1 0.00
139 3 0.01
140 1 0.00
141 3 0.01
154 8 0.03
155 1 0.00
156 111 0.46
157 1 0.00
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (138 bp):
AATTATAAGAATTTTATTAAATTATATATATTAATTAAAATATATTTAATATAATTATGTTTAAA
TATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAAATA
TTTACCAT
Found at i:19577277 original size:156 final size:156
Alignment explanation
Indices: 19577100--19577427 Score: 602
Period size: 156 Copynumber: 2.1 Consensus size: 156
19577090 AAATAACAAT
*
19577100 AACAAATTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATA
1 AACAATTTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATA
*
19577165 ATAATTATGTTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAA
66 ATAATTATGTTTAAATATGATTAAAATATTTATTACTAATAATAATAATCTTATTAAAATTTAAA
*
19577230 TAACATTAACAATAATCATTTACCAA
131 TAACAATAACAATAATCATTTACCAA
* *
19577256 AATAATTTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATT
1 AACAATTTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATA
19577321 ATAATTATGTTTAAATATGATTAAAATATTTATTACTAATAATAATAATCTTATTAAAATTTAAA
66 ATAATTATGTTTAAATATGATTAAAATATTTATTACTAATAATAATAATCTTATTAAAATTTAAA
19577386 TAACAATAACAATAATCATTTACCAA
131 TAACAATAACAATAATCATTTACCAA
*
19577412 AACAATTTTATGCTAA
1 AACAATTTTCTGCTAA
19577428 GGGTATTCTA
Statistics
Matches: 165, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
156 165 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.43
Consensus pattern (156 bp):
AACAATTTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATA
ATAATTATGTTTAAATATGATTAAAATATTTATTACTAATAATAATAATCTTATTAAAATTTAAA
TAACAATAACAATAATCATTTACCAA
Found at i:19577308 original size:18 final size:18
Alignment explanation
Indices: 19577280--19577328 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 18
19577270 AATTATAAGA
19577280 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAATTATAT
19577297 ATTTTAATTAAA--ATAT
1 ATTTTAATTAAATTATAT
19577313 A-TTTAATTATAATTAT
1 ATTTTAATTA-AATTAT
19577329 GTTTAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 8 0.29
16 7 0.25
17 5 0.18
18 8 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTTAATTAAATTATAT
Found at i:19577314 original size:16 final size:16
Alignment explanation
Indices: 19577280--19577334 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
19577270 AATTATAAGA
19577280 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA--ATAT
19577297 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
*
19577313 A-TTTAATTATAAT-T
1 ATTTTAATTAAAATAT
19577327 ATGTTTAA
1 AT-TTTAA
19577335 ATATGATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 2 0.06
15 11 0.32
16 10 0.29
17 5 0.15
18 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:19577385 original size:50 final size:51
Alignment explanation
Indices: 19577174--19577387 Score: 131
Period size: 50 Copynumber: 4.2 Consensus size: 51
19577164 AATAATTATG
*
19577174 TTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTT-ATTAAAA
1 TTTAAATATGATTAAAATATTTATTACTAATAATAATAATCTTAATTAAAA
** * * * ** *
19577224 TTTAAATAACATTAACAATAATCATTTACCAA-AATAATTTTCTGCTAATTATAA
1 TTTAAATATGATTAA-AATATTTA-TTACTAATAATAATAATCT--TAATTAAAA
* * * * * *
19577278 ---GAATTTTATTAAATTATATATT-TTAATTAA-AATATAT-TTAATTATAATTA
1 TTTAAATATGATTAAAATATTTATTACTAA-TAATAATA-ATCTTAATTA-AA--A
19577328 TGTTTAAATATGATTAAAATATTTATTACTAATAATAATAATCTT-ATTAAAA
1 --TTTAAATATGATTAAAATATTTATTACTAATAATAATAATCTTAATTAAAA
19577380 TTTAAATA
1 TTTAAATA
19577388 ACAATAACAA
Statistics
Matches: 117, Mismatches: 28, Indels: 38
0.64 0.15 0.21
Matches are distributed among these distances:
47 6 0.05
48 3 0.03
49 6 0.05
50 29 0.25
51 23 0.20
52 6 0.05
53 1 0.01
54 8 0.07
55 26 0.22
56 9 0.08
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (51 bp):
TTTAAATATGATTAAAATATTTATTACTAATAATAATAATCTTAATTAAAA
Found at i:19577549 original size:44 final size:44
Alignment explanation
Indices: 19577479--19577568 Score: 119
Period size: 44 Copynumber: 2.0 Consensus size: 44
19577469 ACCTCTATTC
* * *
19577479 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACACCTCTAATCCAATA
**
19577523 CATTCAACCAAACA-TGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTA-CTATTACACCTCTAATCCAATA
19577567 CA
1 CA
19577569 CATCTAATCC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 5 0.12
44 35 0.88
ACGTcount: A:0.38, C:0.29, G:0.06, T:0.28
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACACCTCTAATCCAATA
Found at i:19577574 original size:16 final size:16
Alignment explanation
Indices: 19577549--19577600 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
19577539 GATTAGCTAT
19577549 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
19577565 TACACATCTAATCCAA
1 TACACCTCTAATCCAA
19577581 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
19577597 TACA
1 TACA
19577601 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.40, C:0.35, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:19584759 original size:101 final size:101
Alignment explanation
Indices: 19584584--19584806 Score: 295
Period size: 101 Copynumber: 2.2 Consensus size: 101
19584574 CATGCATTTC
* * ** * *
19584584 CATGGCCCAGCCATGGTCTTACATTCGTAGTGTCATAACCCAGTTATGGTCTTATCATCAGAATG
1 CATGGTCCAACCATGGTCTTACATTCAAAGTGCCATAACCCAGTTATGGTCTTATCATCAAAATG
* * *
19584649 CCACAGCCCAGCTGTGGTATTACTTATAAATACTGT
66 CCACAGCCCAGCTATGGTATTACATATAAACACTGT
* * *
19584685 CATGGTCCAACCATGGTCTTACGTTCAAAGTGCCATAACTCAGTTATGGTCTTTTCA-CTAAAAT
1 CATGGTCCAACCATGGTCTTACATTCAAAGTGCCATAACCCAGTTATGGTCTTATCATC-AAAAT
* * *
19584749 GCCATAGCCCAGCTATGGTCTTACATATAAACATTGT
65 GCCACAGCCCAGCTATGGTATTACATATAAACACTGT
19584786 CATGGTCCAACCATGGTCTTA
1 CATGGTCCAACCATGGTCTTA
19584807 TCCGTCAATT
Statistics
Matches: 106, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
100 1 0.01
101 105 0.99
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (101 bp):
CATGGTCCAACCATGGTCTTACATTCAAAGTGCCATAACCCAGTTATGGTCTTATCATCAAAATG
CCACAGCCCAGCTATGGTATTACATATAAACACTGT
Found at i:19602502 original size:50 final size:49
Alignment explanation
Indices: 19602378--19602570 Score: 221
Period size: 50 Copynumber: 3.9 Consensus size: 49
19602368 GATAATAACA
* * ** * *
19602378 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATGTAC-
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCT-CG
* * * * *
19602427 TGCCAATGCCATATCCCAGATATGGTTTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTC-G
19602477 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCAG
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTC-G
* *
19602527 TGTCAACGCCATGTTCCAAACATGGTCTTACATGGGA--TCTCATC
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATC
19602571 CTCTTAATGT
Statistics
Matches: 126, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
48 8 0.06
49 39 0.31
50 79 0.63
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (49 bp):
TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCG
Found at i:19607607 original size:21 final size:21
Alignment explanation
Indices: 19607576--19607637 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
19607566 GAAAAGGCTA
*
19607576 CAGAATTCTACTGGTAGAACT
1 CAGACTTCTACTGGTAGAACT
* * * *
19607597 GAGAGTTCTACCGGTACAACT
1 CAGACTTCTACTGGTAGAACT
19607618 CAGACTTCTA-TCGGTAGAAC
1 CAGACTTCTACT-GGTAGAAC
19607638 GCACTCTAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.26
Consensus pattern (21 bp):
CAGACTTCTACTGGTAGAACT
Found at i:19615685 original size:7 final size:8
Alignment explanation
Indices: 19615670--19615694 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
19615660 ATAATAAATA
19615670 TTTATTTT
1 TTTATTTT
19615678 TTTATTTT
1 TTTATTTT
19615686 TTTATTTT
1 TTTATTTT
19615694 T
1 T
19615695 AAAATATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTATTTT
Found at i:19615716 original size:12 final size:11
Alignment explanation
Indices: 19615688--19615717 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
19615678 TTTATTTTTT
19615688 TATTTTTAAAA
1 TATTTTTAAAA
19615699 TATTTTTAAAA
1 TATTTTTAAAA
19615710 TACTTTTT
1 TA-TTTTT
19615718 TTTATTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:19615738 original size:21 final size:21
Alignment explanation
Indices: 19615699--19615739 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
19615689 ATTTTTAAAA
* **
19615699 TATTTTTAAAATACTTTTTTT
1 TATTTTAAAAATAAATTTTTT
19615720 TATTTTAAAAATAAATTTTT
1 TATTTTAAAAATAAATTTTT
19615740 AGTGTTTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TATTTTAAAAATAAATTTTTT
Found at i:19619232 original size:13 final size:13
Alignment explanation
Indices: 19619214--19619244 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
19619204 ACTCACTACT
19619214 AACAACCCAACCA
1 AACAACCCAACCA
19619227 AACAACCCAACCA
1 AACAACCCAACCA
19619240 AACAA
1 AACAA
19619245 AAGTTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.58, C:0.42, G:0.00, T:0.00
Consensus pattern (13 bp):
AACAACCCAACCA
Found at i:19620737 original size:31 final size:31
Alignment explanation
Indices: 19620688--19620750 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
19620678 TTTTAAAAAT
*
19620688 AATAATTGCTTATAATTTTTAATAATT-TTTA
1 AATAATTGCCTATAATTTTT-ATAATTATTTA
* *
19620719 AATAATTTCCTATCATTTTTATAATTATTTA
1 AATAATTGCCTATAATTTTTATAATTATTTA
19620750 A
1 A
19620751 GAAACCACTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 6 0.21
31 22 0.79
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (31 bp):
AATAATTGCCTATAATTTTTATAATTATTTA
Found at i:19622669 original size:21 final size:22
Alignment explanation
Indices: 19622630--19622670 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
19622620 GCAAATCTGG
19622630 GATTAAAATTAACTTTTTAAGA
1 GATTAAAATTAACTTTTTAAGA
19622652 GATTAAAATTAA-TTTTTAA
1 GATTAAAATTAACTTTTTAA
19622671 TAAAAATAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.44
Consensus pattern (22 bp):
GATTAAAATTAACTTTTTAAGA
Found at i:19622820 original size:71 final size:69
Alignment explanation
Indices: 19622651--19622828 Score: 191
Period size: 71 Copynumber: 2.5 Consensus size: 69
19622641 ACTTTTTAAG
* **
19622651 AGATTAAAATT--AATTTTTAATAAAAATAGTAAAGAAGTGAGTTATGGAAGTACTCTCTAGTCA
1 AGATTAAAATTAAAATTTTTAAT-AAAATAGTGAAGAAGTGAACTATGGAAGTACTCTCTAGTCA
19622714 ATGTA
65 ATGTA
* * * * * *
19622719 GGATTTAAATTAAATTTTTTCAATTAAAATAGTGAAGAAGTGAACTA-GGAGAGTATTTTCTTTG
1 AGATTAAAATTAAAATTTTT-AA-TAAAATAGTGAAGAAGTGAACTATGGA-AGTA--CTCTCTA
19622783 GTCAATGTA
61 GTCAATGTA
*
19622792 AGATTAAAATTAAAATTTTTAATGAAATAGTGAAGAA
1 AGATTAAAATTAAAATTTTTAATAAAATAGTGAAGAA
19622829 ATTGTCACTT
Statistics
Matches: 90, Mismatches: 13, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
68 9 0.10
70 9 0.10
71 39 0.43
72 3 0.03
73 30 0.33
ACGTcount: A:0.43, C:0.04, G:0.17, T:0.35
Consensus pattern (69 bp):
AGATTAAAATTAAAATTTTTAATAAAATAGTGAAGAAGTGAACTATGGAAGTACTCTCTAGTCAA
TGTA
Found at i:19622978 original size:87 final size:86
Alignment explanation
Indices: 19622807--19622979 Score: 215
Period size: 87 Copynumber: 2.0 Consensus size: 86
19622797 AAAATTAAAA
* * * *
19622807 TTTTTAATGAAATAGTGAAGAAATTGTCACTTATTTATAAGGTTAGTGTGAGATATGATAGTGTT
1 TTTTTAATGAAATAGTGAAGAAATTGACACTTATTTATAAGGTAACTGCGAGATATGA-AGTGTT
* **
19622872 CTCTAGTCAATGTGGGATTAAC
65 CTCTAGCCAATGTAAGATTAAC
* *
19622894 TTTTTAATGAAAATAGTGAAGAAATTGACACTTCTTTAT-AGAGTAACTGCGAGCATGTG-AGTG
1 TTTTTAATG-AAATAGTGAAGAAATTGACACTTATTTATAAG-GTAACTGCGAG-ATATGAAGTG
19622957 TTCTCTAGCCAATGTAAGATTAA
63 TTCTCTAGCCAATGTAAGATTAA
19622980 AATTAACCTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
87 35 0.47
88 35 0.47
89 4 0.05
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (86 bp):
TTTTTAATGAAATAGTGAAGAAATTGACACTTATTTATAAGGTAACTGCGAGATATGAAGTGTTC
TCTAGCCAATGTAAGATTAAC
Found at i:19623000 original size:19 final size:20
Alignment explanation
Indices: 19622971--19623026 Score: 78
Period size: 19 Copynumber: 2.8 Consensus size: 20
19622961 CTAGCCAATG
19622971 TAAGATTAAAATTAACCTTT
1 TAAGATTAAAATTAACCTTT
*
19622991 TAAG-TTAAAATTAACTTTT
1 TAAGATTAAAATTAACCTTT
19623010 TAAAGGATTAAAATTAA
1 T-AA-GATTAAAATTAA
19623027 TTTTTAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 15 0.47
20 6 0.19
21 1 0.03
22 10 0.31
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.39
Consensus pattern (20 bp):
TAAGATTAAAATTAACCTTT
Found at i:19629612 original size:43 final size:42
Alignment explanation
Indices: 19629552--19629708 Score: 187
Period size: 43 Copynumber: 3.7 Consensus size: 42
19629542 TATGTATTTT
19629552 CGTGTAAGACCACGTCTGGGACGTTGGCATCGAATTGTGTATA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGAATTGTG-ATA
* * * *
19629595 CGTGTAAGACCATGTCTGGGACATTGGCATCGTATT-TGATT
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGAATTGTGATA
*
19629636 TGTGTAAGACC-CTGTCTGGGACAG-TGGCATC-AATATGTGATTA
1 CGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGAAT-TGTGA-TA
*
19629679 CATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACGTTGGCAT
19629709 TGTACGAGCC
Statistics
Matches: 96, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
40 2 0.02
41 29 0.30
42 6 0.06
43 58 0.60
44 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (42 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCGAATTGTGATA
Found at i:19629654 original size:84 final size:84
Alignment explanation
Indices: 19629553--19629708 Score: 221
Period size: 84 Copynumber: 1.9 Consensus size: 84
19629543 ATGTATTTTC
* *
19629553 GTGTAAGACCACGTCTGGGAC-GTTGGCATCGAAT-TGTG-TATACGTGTAAGACCATGTCTGGG
1 GTGTAAGACCACGTCTGGGACAG-TGGCATC-AATATGTGAT-TACATGTAAGACCACGTCTGGG
19629615 ACATTGGCATCGTATTTGATTT
63 ACATTGGCATCGTATTTGATTT
19629637 GTGTAAGACC-CTGTCTGGGACAGTGGCATCAATATGTGATTACATGTAAGACCACGTCTGGGAC
1 GTGTAAGACCAC-GTCTGGGACAGTGGCATCAATATGTGATTACATGTAAGACCACGTCTGGGAC
*
19629701 GTTGGCAT
65 ATTGGCAT
19629709 TGTACGAGCC
Statistics
Matches: 65, Mismatches: 3, Indels: 8
0.86 0.04 0.11
Matches are distributed among these distances:
83 4 0.06
84 59 0.91
85 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (84 bp):
GTGTAAGACCACGTCTGGGACAGTGGCATCAATATGTGATTACATGTAAGACCACGTCTGGGACA
TTGGCATCGTATTTGATTT
Found at i:19633001 original size:67 final size:68
Alignment explanation
Indices: 19632922--19633098 Score: 207
Period size: 67 Copynumber: 2.6 Consensus size: 68
19632912 TTCTCTAGCT
* * *
19632922 AATGTGGGATTAAAAATAA-TTTTTAATGAAATAGTGAAGAAGTGAACTATGAGAGTATTCTCAA
1 AATGTGAGATTAAAATTAACTTTTTAATGAAATAGTGAAGAAGTGAACTATGAGAGTATTATCAA
19632986 GTC
66 GTC
* * * *
19632989 AATGTGAGATTAAAATTAACTTTTCAATGAAAATAGTG-A-AAGTTAGCTATGAGAGTATTATCT
1 AATGTGAGATTAAAATTAACTTTTTAATG-AAATAGTGAAGAAGTGAACTATGAGAGTATTATCA
19633052 AGTC
65 AGTC
** * * *
19633056 GGTGTGTGACTAAAATTAACTTTTTAATAAAAATAGTGAAGAA
1 AATGTGAGATTAAAATTAACTTTTTAAT-GAAATAGTGAAGAA
19633099 ATTGTTACTT
Statistics
Matches: 92, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
67 72 0.78
68 10 0.11
69 10 0.11
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (68 bp):
AATGTGAGATTAAAATTAACTTTTTAATGAAATAGTGAAGAAGTGAACTATGAGAGTATTATCAA
GTC
Found at i:19635051 original size:8 final size:8
Alignment explanation
Indices: 19635038--19635075 Score: 76
Period size: 8 Copynumber: 4.8 Consensus size: 8
19635028 ATATAATAAA
19635038 TTATTATT
1 TTATTATT
19635046 TTATTATT
1 TTATTATT
19635054 TTATTATT
1 TTATTATT
19635062 TTATTATT
1 TTATTATT
19635070 TTATTA
1 TTATTA
19635076 AAACTATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
TTATTATT
Found at i:19639677 original size:4 final size:4
Alignment explanation
Indices: 19639668--19639694 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
19639658 CACTACTGCA
19639668 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
19639695 AATATATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:19648380 original size:22 final size:22
Alignment explanation
Indices: 19648337--19648397 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
19648327 TTTAAAAAAT
19648337 AAATATAGAAATAAATATATAA
1 AAATATAGAAATAAATATATAA
* *
19648359 AAATTTAG-AATATATATAATAATA
1 AAATATAGAAATAAATAT-AT-A-A
*
19648383 AAATATAAAAATAAA
1 AAATATAGAAATAAA
19648398 AATTCATTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
21 8 0.27
22 9 0.30
23 1 0.03
24 7 0.23
25 5 0.17
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (22 bp):
AAATATAGAAATAAATATATAA
Found at i:19648390 original size:13 final size:13
Alignment explanation
Indices: 19648331--19648398 Score: 57
Period size: 14 Copynumber: 4.8 Consensus size: 13
19648321 TATCAATTTA
19648331 AAAAAT-AAATAT
1 AAAAATAAAATAT
*
19648343 AGAAATAAATATAT
1 AAAAATAAA-ATAT
19648357 AAAAATTTAGAATATAT
1 AAAAA--TA-AA-ATAT
19648374 ATAATAATAAAATAT
1 A-AA-AATAAAATAT
19648389 AAAAATAAAA
1 AAAAATAAAA
19648399 ATTCATTAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
12 5 0.11
13 9 0.19
14 10 0.21
15 5 0.11
16 4 0.09
17 10 0.21
18 2 0.04
19 2 0.04
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (13 bp):
AAAAATAAAATAT
Found at i:19649033 original size:22 final size:22
Alignment explanation
Indices: 19649005--19649048 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
19648995 ATTTTCTAAC
19649005 AGATTTAATGAATAAATTCAAG
1 AGATTTAATGAATAAATTCAAG
19649027 AGATTTAATGAATAAATTCAAG
1 AGATTTAATGAATAAATTCAAG
19649049 GTTTCAATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.05, G:0.14, T:0.32
Consensus pattern (22 bp):
AGATTTAATGAATAAATTCAAG
Found at i:19649510 original size:29 final size:29
Alignment explanation
Indices: 19649456--19649513 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
19649446 AAGTTTCAAA
**
19649456 CCAAAACCCAAACTAAAGGAAGAAAATTT
1 CCAAAACCCAAACTAAACCAAGAAAATTT
*
19649485 CCAAATCCCAAACTAAAACCAA-AAAATTT
1 CCAAAACCCAAACT-AAACCAAGAAAATTT
19649514 TCCAGATTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.55, C:0.24, G:0.05, T:0.16
Consensus pattern (29 bp):
CCAAAACCCAAACTAAACCAAGAAAATTT
Found at i:19662417 original size:20 final size:20
Alignment explanation
Indices: 19662376--19662417 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
19662366 CTATAGTTTA
*
19662376 AAAAATATTAAAAAATCTAT
1 AAAAATATTAAAAAAACTAT
19662396 AAAAATAATTAAAAAAAC-AT
1 AAAAAT-ATTAAAAAAACTAT
19662416 AA
1 AA
19662418 TTCTTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAAATATTAAAAAAACTAT
Found at i:19664466 original size:8 final size:8
Alignment explanation
Indices: 19664453--19664485 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
19664443 AAATAGCGGA
19664453 AGAAATTG
1 AGAAATTG
19664461 AGAAATTG
1 AGAAATTG
19664469 AGAAATTG
1 AGAAATTG
19664477 AGAAATTG
1 AGAAATTG
19664485 A
1 A
19664486 ACACAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (8 bp):
AGAAATTG
Found at i:19667085 original size:30 final size:31
Alignment explanation
Indices: 19667046--19667110 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
19667036 GTAATTATAC
* *
19667046 ACATTAAACTTTTATTTTG-TTCAAATGTAT
1 ACATAAAACTTTAATTTTGATTCAAATGTAT
**
19667076 ACATAAAACTTTAATTTTGATTCAGTTGTAT
1 ACATAAAACTTTAATTTTGATTCAAATGTAT
19667107 ACAT
1 ACAT
19667111 TTAAATAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 17 0.57
31 13 0.43
ACGTcount: A:0.35, C:0.11, G:0.08, T:0.46
Consensus pattern (31 bp):
ACATAAAACTTTAATTTTGATTCAAATGTAT
Found at i:19667453 original size:25 final size:26
Alignment explanation
Indices: 19667405--19667453 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
19667395 GATTAAATCT
*
19667405 AAATATAAAATAAATAATTAAAATTC
1 AAATATAAAATAAATAACTAAAATTC
19667431 AAATA-AAAATAAAT-ACTAGAAAT
1 AAATATAAAATAAATAACTA-AAAT
19667454 AAATTGAACG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 13 0.62
26 5 0.24
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (26 bp):
AAATATAAAATAAATAACTAAAATTC
Found at i:19673601 original size:21 final size:21
Alignment explanation
Indices: 19673575--19673682 Score: 153
Period size: 21 Copynumber: 5.1 Consensus size: 21
19673565 GCTCGAAATT
19673575 TGAACAGAAGCTCGTAAGAGC
1 TGAACAGAAGCTCGTAAGAGC
* *
19673596 TGAACAGAAACTCATAAGAGC
1 TGAACAGAAGCTCGTAAGAGC
* *
19673617 TGAACAAAAGCTCATAAGAGC
1 TGAACAGAAGCTCGTAAGAGC
* *
19673638 TTAATAGAAGCTCGTAAGAGC
1 TGAACAGAAGCTCGTAAGAGC
*
19673659 TGAACAGAAGCTCGTGAGAGC
1 TGAACAGAAGCTCGTAAGAGC
19673680 TGA
1 TGA
19673683 TCCACCCAAT
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 76 1.00
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TGAACAGAAGCTCGTAAGAGC
Found at i:19677649 original size:37 final size:37
Alignment explanation
Indices: 19677565--19677693 Score: 154
Period size: 37 Copynumber: 3.5 Consensus size: 37
19677555 TATCTACTAA
* * * * *
19677565 TATACGGAAAGAAGCTCAATCGAGCAAATCCTA-CGT
1 TATACTGAATGAAGCTCAATCAAGTAAATCCTATTGT
*
19677601 TATGCTGAATGAAGCTCAATCAAGTAAATCCTATTGT
1 TATACTGAATGAAGCTCAATCAAGTAAATCCTATTGT
*
19677638 TATATTGAATGAAGCTCAATCAA-TCAAATCCTATTGT
1 TATACTGAATGAAGCTCAATCAAGT-AAATCCTATTGT
* *
19677675 TATACAGAGTGAAGCTCAA
1 TATACTGAATGAAGCTCAA
19677694 ACGAGTAGAA
Statistics
Matches: 80, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
36 29 0.36
37 51 0.64
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (37 bp):
TATACTGAATGAAGCTCAATCAAGTAAATCCTATTGT
Found at i:19681033 original size:18 final size:19
Alignment explanation
Indices: 19681006--19681047 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
19680996 TGTAGAAGGG
*
19681006 TGAAACTGA-GATCAATTT
1 TGAAACTGAGGATCAAATT
* *
19681024 TGAAATTGAGGCTCAAATT
1 TGAAACTGAGGATCAAATT
19681043 TGAAA
1 TGAAA
19681048 GTTATAACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (19 bp):
TGAAACTGAGGATCAAATT
Found at i:19683847 original size:18 final size:19
Alignment explanation
Indices: 19683820--19683861 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
19683810 AAATATTGTG
19683820 AAAATCATTAAAAATT-TA
1 AAAATCATTAAAAATTATA
*
19683838 AAAATGATTAAAAATTATA
1 AAAATCATTAAAAATTATA
19683857 AAAAT
1 AAAAT
19683862 AATAAGATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAATCATTAAAAATTATA
Found at i:19683850 original size:27 final size:28
Alignment explanation
Indices: 19683792--19683843 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
19683782 AAAATGTAAA
*
19683792 AAAAACATTAAATAATTTAAATATTGTG
1 AAAAACATTAAATAATTTAAATAATGTG
*
19683820 AAAATCATTAAA-AATTTAAA-AATG
1 AAAAACATTAAATAATTTAAATAATG
19683844 ATTAAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 3 0.14
27 8 0.36
28 11 0.50
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.33
Consensus pattern (28 bp):
AAAAACATTAAATAATTTAAATAATGTG
Found at i:19684123 original size:16 final size:15
Alignment explanation
Indices: 19684092--19684120 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
19684082 AAATTGTAAA
19684092 AAAAAATTATAATTT
1 AAAAAATTATAATTT
19684107 AAAAAA-TATAATTT
1 AAAAAATTATAATTT
19684121 TTACAATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAAAATTATAATTT
Found at i:19684196 original size:19 final size:19
Alignment explanation
Indices: 19684174--19684220 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
19684164 AATGATTGCA
19684174 ATTTTTAAAATTTTTAATG
1 ATTTTTAAAATTTTTAATG
* * **
19684193 ATTTTCACAATTTTTTGTG
1 ATTTTTAAAATTTTTAATG
19684212 -TTTTTAAAA
1 ATTTTTAAAA
19684221 AAATTGCAAT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.57
Consensus pattern (19 bp):
ATTTTTAAAATTTTTAATG
Found at i:19684565 original size:20 final size:20
Alignment explanation
Indices: 19684495--19684565 Score: 53
Period size: 20 Copynumber: 3.6 Consensus size: 20
19684485 TATATATATA
* *
19684495 AAATAAT-TTTTAAAATTTCT
1 AAATAATATTTT-ATATTTTT
*
19684515 AAATAATGTTTTACTAATTTTT
1 AAATAATATTTTA-T-ATTTTT
19684537 --AT-A-ATTTTATATTTTT
1 AAATAATATTTTATATTTTT
19684553 AAATAATATTTTA
1 AAATAATATTTTA
19684566 CGATTTTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
16 6 0.15
17 1 0.02
18 7 0.17
19 2 0.05
20 16 0.39
21 4 0.10
22 5 0.12
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (20 bp):
AAATAATATTTTATATTTTT
Found at i:19684583 original size:38 final size:38
Alignment explanation
Indices: 19684500--19684584 Score: 91
Period size: 38 Copynumber: 2.2 Consensus size: 38
19684490 ATATAAAATA
* *
19684500 ATTTTTAAAATTTCTAAATAATGTTTTACTAATTTTTAT
1 ATTTTT-AAATTTCTAAATAATATTTTACTAATTTTAAT
* * * *
19684539 AATTTTATATTTTTAAATAATATTTTAC-GATTTTAAT
1 ATTTTTAAATTTCTAAATAATATTTTACTAATTTTAAT
19684576 CATTTTTAA
1 -ATTTTTAA
19684585 TGATTTGTTG
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
37 7 0.19
38 25 0.68
39 5 0.14
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.56
Consensus pattern (38 bp):
ATTTTTAAATTTCTAAATAATATTTTACTAATTTTAAT
Found at i:19685046 original size:20 final size:19
Alignment explanation
Indices: 19685021--19685098 Score: 77
Period size: 20 Copynumber: 4.1 Consensus size: 19
19685011 AGTTGGAGCA
19685021 TAAATAATTTTATATATTTT
1 TAAATAATTTTATA-ATTTT
* * *
19685041 TAAATAAATTTAAAATTTC
1 TAAATAATTTTATAATTTT
19685060 TAAATAATTATTATAATTTT
1 TAAATAATT-TTATAATTTT
* * *
19685080 T-TATATTTTTACAATTTT
1 TAAATAATTTTATAATTTT
19685098 T
1 T
19685099 TTTCATTTCT
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
18 10 0.21
19 17 0.35
20 21 0.44
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (19 bp):
TAAATAATTTTATAATTTT
Found at i:19685063 original size:19 final size:20
Alignment explanation
Indices: 19685021--19685066 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
19685011 AGTTGGAGCA
* * *
19685021 TAAATAATTTTATATATTTT
1 TAAATAAATTTATAAATTTC
19685041 TAAATAAATTTA-AAATTTC
1 TAAATAAATTTATAAATTTC
19685060 TAAATAA
1 TAAATAA
19685067 TTATTATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
TAAATAAATTTATAAATTTC
Found at i:19689159 original size:9 final size:9
Alignment explanation
Indices: 19689145--19689185 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
19689135 AAAATATTTT
*
19689145 TTTTTTATA
1 TTTTTTAAA
19689154 TTTTTTATAA
1 TTTTTTA-AA
19689164 TTTTTTAAA
1 TTTTTTAAA
*
19689173 ATTTTTAAA
1 TTTTTTAAA
19689182 TTTT
1 TTTT
19689186 GCTATGTGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
9 20 0.71
10 8 0.29
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:19689234 original size:31 final size:31
Alignment explanation
Indices: 19689194--19689259 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
19689184 TTGCTATGTG
* ** *
19689194 GTATGCCACATCAGTGTCGTTTGCCATGTCA
1 GTATACCACATCAGCATCATTTGCCATGTCA
19689225 GTATACCACATCAGCATCATTTGCCATGTCA
1 GTATACCACATCAGCATCATTTGCCATGTCA
19689256 GTAT
1 GTAT
19689260 CATTAACGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (31 bp):
GTATACCACATCAGCATCATTTGCCATGTCA
Found at i:19689925 original size:29 final size:30
Alignment explanation
Indices: 19689884--19689956 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 30
19689874 ATTTAATTAT
* * *
19689884 AAATTTAATTATACATGAAAT-GTTTTTAA
1 AAATTTAAATATACATGAAATAATATTTAA
*
19689913 AAATTTAAATATAATATGAAATAATATTTAA
1 AAATTTAAATAT-ACATGAAATAATATTTAA
19689944 ATAATTT-AATATA
1 A-AATTTAAATATA
19689957 ATTATACATA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 11 0.30
30 9 0.24
31 12 0.32
32 5 0.14
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.42
Consensus pattern (30 bp):
AAATTTAAATATACATGAAATAATATTTAA
Found at i:19700447 original size:6 final size:6
Alignment explanation
Indices: 19700436--19700463 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
19700426 ATTTTGATCC
19700436 AAATAT AAATAT AAATAT AAATAT AAAT
1 AAATAT AAATAT AAATAT AAATAT AAAT
19700464 TTATTCAGTT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATAT
Found at i:19714117 original size:14 final size:15
Alignment explanation
Indices: 19714098--19714126 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
19714088 CCTTAGTTGC
19714098 TGAAAAAT-AAAAGA
1 TGAAAAATGAAAAGA
19714112 TGAAAAATGAAAAGA
1 TGAAAAATGAAAAGA
19714127 ATGGGGCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (15 bp):
TGAAAAATGAAAAGA
Found at i:19730349 original size:20 final size:21
Alignment explanation
Indices: 19730312--19730350 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
19730302 TTTTGGAATT
19730312 TTTTTCATATTCTTAAAATCA
1 TTTTTCATATTCTTAAAATCA
19730333 TTTTT-ATATT-TTGAAAAT
1 TTTTTCATATTCTT-AAAAT
19730351 TATAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.12
20 10 0.59
21 5 0.29
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (21 bp):
TTTTTCATATTCTTAAAATCA
Found at i:19742081 original size:52 final size:52
Alignment explanation
Indices: 19741998--19742104 Score: 178
Period size: 52 Copynumber: 2.1 Consensus size: 52
19741988 GTAGGTAAAA
* *
19741998 CTTACTTTTTGGCTATAGATTCTACAACATAAACTTCGCCGTTGGAATCGGC
1 CTTACTTTTTGGCTATAGATTCTACAACATAAACTTCGCCATTGGAATCAGC
* *
19742050 CTTACTTTTTGGCTATAGATTCTATAGCATAAACTTCGCCATTGGAATCAGC
1 CTTACTTTTTGGCTATAGATTCTACAACATAAACTTCGCCATTGGAATCAGC
19742102 CTT
1 CTT
19742105 TAGCTGTGGA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.36
Consensus pattern (52 bp):
CTTACTTTTTGGCTATAGATTCTACAACATAAACTTCGCCATTGGAATCAGC
Found at i:19752579 original size:20 final size:20
Alignment explanation
Indices: 19752550--19752587 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
19752540 TTTTGGAATT
19752550 TTTTTCATATTCTTAAAATCA
1 TTTTTCATATT-TTAAAATCA
19752571 TTTTT-ATATTTTAAAAT
1 TTTTTCATATTTTAAAAT
19752588 TATAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 5 0.29
21 5 0.29
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTTCATATTTTAAAATCA
Found at i:19753031 original size:22 final size:20
Alignment explanation
Indices: 19752983--19753031 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
19752973 TTAGCATGCT
19752983 TGCAT-ACAGATATCATATA
1 TGCATAACAGATATCATATA
**
19753002 TGTTTAACAGAATAATCATATA
1 TGCATAACAG-AT-ATCATATA
19753024 TGCATAAC
1 TGCATAAC
19753032 GATGTCCTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 3 0.13
20 4 0.17
21 2 0.09
22 14 0.61
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (20 bp):
TGCATAACAGATATCATATA
Found at i:19755743 original size:3 final size:3
Alignment explanation
Indices: 19755735--19755765 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
19755725 AGTGAATGGA
19755735 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
19755766 TTGTGAAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:19755897 original size:21 final size:21
Alignment explanation
Indices: 19755873--19755921 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
19755863 TTTTTTATTT
19755873 ATTTTAAAGATT-TT-TTAAAA
1 ATTTTAAA-ATTATTGTTAAAA
* *
19755893 AATTTACAATTATTGTTAAAA
1 ATTTTAAAATTATTGTTAAAA
19755914 ATTTTAAA
1 ATTTTAAA
19755922 TGTCAAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 3 0.13
20 8 0.35
21 12 0.52
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (21 bp):
ATTTTAAAATTATTGTTAAAA
Found at i:19758558 original size:5 final size:6
Alignment explanation
Indices: 19758540--19758574 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
19758530 TCAAAAGTTA
19758540 TAAAAT TAAAAT T-AAAT TAAAAT TAAAAT ATAAAA
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT -TAAAA
19758575 GAATAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.19
6 17 0.63
7 5 0.19
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
TAAAAT
Found at i:19758558 original size:11 final size:11
Alignment explanation
Indices: 19758542--19758566 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19758532 AAAAGTTATA
19758542 AAATTAAAATT
1 AAATTAAAATT
19758553 AAATTAAAATT
1 AAATTAAAATT
19758564 AAA
1 AAA
19758567 ATATAAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATTAAAATT
Found at i:19758562 original size:17 final size:18
Alignment explanation
Indices: 19758540--19758573 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
19758530 TCAAAAGTTA
19758540 TAAAATTAAAAT-TAAAT
1 TAAAATTAAAATATAAAT
19758557 TAAAATTAAAATATAAA
1 TAAAATTAAAATATAAA
19758574 AGAATAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAAATTAAAATATAAAT
Found at i:19762889 original size:18 final size:20
Alignment explanation
Indices: 19762841--19762889 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
19762831 CGGCCTAAAT
19762841 ATTATATTATTTATATGTTAG
1 ATTATATTA-TTATATGTTAG
*
19762862 ATAATAATTA-TATAT-TTAG
1 ATTAT-ATTATTATATGTTAG
19762881 ATTATATTA
1 ATTATATTA
19762890 AGGGTCCGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 4 0.16
19 8 0.32
20 5 0.20
21 4 0.16
22 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (20 bp):
ATTATATTATTATATGTTAG
Found at i:19763175 original size:21 final size:21
Alignment explanation
Indices: 19763149--19763189 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
19763139 AAAATATTAA
19763149 ATATATATAAA-AAATATATTC
1 ATATAT-TAAACAAATATATTC
*
19763170 ATATATTAAACATATATATT
1 ATATATTAAACAAATATATT
19763190 TTTATACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (21 bp):
ATATATTAAACAAATATATTC
Found at i:19763240 original size:25 final size:23
Alignment explanation
Indices: 19763201--19763257 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
19763191 TTATACTATA
19763201 TTAATAAA-TA-TTAATAAATTAT
1 TTAATAAATTATTTAATAAA-TAT
*
19763223 TTATATCAATTATTTAATAAATAT
1 TTA-ATAAATTATTTAATAAATAT
19763247 TTAATAAATTA
1 TTAATAAATTA
19763258 AATATTTCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 3 0.10
23 11 0.37
24 8 0.27
25 8 0.27
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TTAATAAATTATTTAATAAATAT
Found at i:19763249 original size:11 final size:11
Alignment explanation
Indices: 19763201--19763255 Score: 67
Period size: 11 Copynumber: 4.8 Consensus size: 11
19763191 TTATACTATA
19763201 TTAATAAATA-
1 TTAATAAATAT
19763211 TTAATAAATTAT
1 TTAATAAA-TAT
*
19763223 TTATATCAATTAT
1 TTA-AT-AAATAT
19763236 TTAATAAATAT
1 TTAATAAATAT
19763247 TTAATAAAT
1 TTAATAAAT
19763256 TAAATATTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
10 8 0.21
11 16 0.41
12 5 0.13
13 8 0.21
14 2 0.05
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (11 bp):
TTAATAAATAT
Found at i:19765843 original size:20 final size:20
Alignment explanation
Indices: 19765795--19765843 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
19765785 AAATTTGAAT
*
19765795 CTATCGATACTTAACAAAAT
1 CTATCGATACTTAACAAAAA
*
19765815 CTATTGATACTTGAA-AAAAA
1 CTATCGATACTT-AACAAAAA
*
19765835 GTATCGATA
1 CTATCGATA
19765844 TAGGATCGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 22 0.92
21 2 0.08
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (20 bp):
CTATCGATACTTAACAAAAA
Found at i:19766425 original size:28 final size:30
Alignment explanation
Indices: 19766361--19766425 Score: 73
Period size: 28 Copynumber: 2.2 Consensus size: 30
19766351 ATGTTGCTAC
19766361 TATTTTGTTGTTATTGTTTAGATATTGTAT
1 TATTTTGTTGTTATTGTTTAGATATTGTAT
* *
19766391 AACTTTTGTT-TTATT-TTTA-ATTTTGTTAT
1 TA-TTTTGTTGTTATTGTTTAGATATTG-TAT
19766420 TATTTT
1 TATTTT
19766426 AAAGGCATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
28 9 0.30
29 8 0.27
30 6 0.20
31 7 0.23
ACGTcount: A:0.20, C:0.02, G:0.11, T:0.68
Consensus pattern (30 bp):
TATTTTGTTGTTATTGTTTAGATATTGTAT
Found at i:19770601 original size:3 final size:3
Alignment explanation
Indices: 19770595--19770638 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
19770585 TAAGTAAAAT
19770595 ATA ATA ATA ATA ACTA A-A AT- ATA ATA ATA AT- ATA AT- ATA ATA
1 ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
19770637 AT
1 AT
19770639 TAAAAGTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
2 8 0.22
3 25 0.69
4 3 0.08
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:19770614 original size:20 final size:20
Alignment explanation
Indices: 19770589--19770626 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
19770579 ATTATTTAAG
19770589 TAAAATATAATAATAATAAC
1 TAAAATATAATAATAATAAC
19770609 TAAAATATAATAATAATA
1 TAAAATATAATAATAATA
19770627 TAATATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (20 bp):
TAAAATATAATAATAATAAC
Found at i:19770652 original size:10 final size:9
Alignment explanation
Indices: 19770589--19770671 Score: 60
Period size: 10 Copynumber: 8.4 Consensus size: 9
19770579 ATTATTTAAG
19770589 TAAAATATAA
1 TAAAATA-AA
*
19770599 TAATAATAAC
1 TAA-AATAAA
19770609 TAAAATATAA
1 TAAAATA-AA
19770619 TAATAATATAA
1 TAA-AATA-AA
* *
19770630 TATAATAAT
1 TAAAATAAA
19770639 TAAAAGTAAA
1 TAAAA-TAAA
19770649 TAAAATAAA
1 TAAAATAAA
19770658 -AGAAATAGAA
1 TA-AAATA-AA
19770668 TAAA
1 TAAA
19770672 GAAAGAAAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
8 1 0.02
9 18 0.30
10 27 0.45
11 14 0.23
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (9 bp):
TAAAATAAA
Found at i:19774254 original size:27 final size:28
Alignment explanation
Indices: 19774202--19774256 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
19774192 TTTACAGTCC
19774202 GGGCCTGAGCCCCTTACAGAATCAATTT
1 GGGCCTGAGCCCCTTACAGAATCAATTT
19774230 GGGCCTGAG-CCCTTACAG-ATACAATTT
1 GGGCCTGAGCCCCTTACAGAAT-CAATTT
19774257 CAAAATTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 2 0.08
27 15 0.58
28 9 0.35
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (28 bp):
GGGCCTGAGCCCCTTACAGAATCAATTT
Found at i:19774744 original size:16 final size:17
Alignment explanation
Indices: 19774709--19774747 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
19774699 AAAATGGGCG
19774709 CACACGCCCATGTAGGC
1 CACACGCCCATGTAGGC
* *
19774726 CACAGGCCCGTGT-GGC
1 CACACGCCCATGTAGGC
19774742 CACACG
1 CACACG
19774748 GCACAAATTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.21, C:0.41, G:0.28, T:0.10
Consensus pattern (17 bp):
CACACGCCCATGTAGGC
Found at i:19774851 original size:31 final size:32
Alignment explanation
Indices: 19774813--19774881 Score: 97
Period size: 31 Copynumber: 2.2 Consensus size: 32
19774803 GCTAGAATCT
*
19774813 CACACGCCCGTGTGGTTTAC-CTATGTGGG-CC
1 CACACGCCCATGTGGTTTACTC-ATGTGGGACC
*
19774844 CACACGCCCATGTGGTTTACTCGTGTGGGACC
1 CACACGCCCATGTGGTTTACTCATGTGGGACC
19774876 CACACG
1 CACACG
19774882 ACCAAATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 25 0.74
32 9 0.26
ACGTcount: A:0.16, C:0.33, G:0.28, T:0.23
Consensus pattern (32 bp):
CACACGCCCATGTGGTTTACTCATGTGGGACC
Found at i:19806634 original size:8 final size:9
Alignment explanation
Indices: 19806611--19806637 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
19806601 GAAAATCAAA
19806611 ATAAAAATT
1 ATAAAAATT
19806620 ATAAAAATT
1 ATAAAAATT
19806629 ATAAAAATT
1 ATAAAAATT
19806638 GGTTCAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
ATAAAAATT
Done.