Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008150.1 Hibiscus syriacus cultivar Beakdansim tig00110716_pilon, whole genome shotgun sequence
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: 3012591
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 14
Found at i:1480506 original size:40 final size:40
Alignment explanation
Indices: 1480449--1480570 Score: 235
Period size: 40 Copynumber: 3.0 Consensus size: 40
1480439 TGCAGGTTTA
*
1480449 TAATACACTTCGATGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1480489 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1480529 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1480569 TA
1 TA
1480571 GCACTACGGT
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 81 1.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:1480745 original size:47 final size:45
Alignment explanation
Indices: 1480674--1480795 Score: 127
Period size: 48 Copynumber: 2.6 Consensus size: 45
1480664 GTAACCATGC
* *
1480674 AAATAATCTTATGAGCTTACGGAATAATGGCAAGTATATTGAAAAAA
1 AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTG--AAAA
* * * **
1480721 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTAA
1 AAATAAGCTTATGAGCTTATGGAA--T-AATGGCAAGTATATTGAAAA
*
1480769 AAATAAGCTTATGAGCTTATGGGATAA
1 AAATAAGCTTATGAGCTTATGGAATAA
1480796 GAGGTAAGAA
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
45 2 0.03
46 1 0.02
47 21 0.33
48 24 0.38
49 1 0.02
50 14 0.22
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGAAAA
Found at i:1486883 original size:19 final size:19
Alignment explanation
Indices: 1486859--1486905 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1486849 ATGATTTTCA
* *
1486859 TTTGAAAGAAAATTTGGAT
1 TTTGAAAAAAAAATTGGAT
1486878 TTTGAAAAAAAAAATTGGAT
1 TTTG-AAAAAAAAATTGGAT
1486898 TTTGAAAA
1 TTTGAAAA
1486906 GCAAAATGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (19 bp):
TTTGAAAAAAAAATTGGAT
Found at i:1486895 original size:20 final size:20
Alignment explanation
Indices: 1486867--1486905 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1486857 CATTTGAAAG
*
1486867 AAAATTTGGATTTTGAAAAA
1 AAAAATTGGATTTTGAAAAA
1486887 AAAAATTGGATTTTGAAAA
1 AAAAATTGGATTTTGAAAA
1486906 GCAAAATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.33
Consensus pattern (20 bp):
AAAAATTGGATTTTGAAAAA
Found at i:1486911 original size:20 final size:19
Alignment explanation
Indices: 1486859--1486912 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
1486849 ATGATTTTCA
1486859 TTTG-AAAGAAAATTTGGAT
1 TTTGAAAAGAAAA-TTGGAT
*
1486878 TTTGAAAAAAAAAATTGGAT
1 TTTG-AAAAGAAAATTGGAT
1486898 TTTGAAAAGCAAAAT
1 TTTGAAAAG-AAAAT
1486913 GTAACATTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 8 0.27
20 15 0.50
21 7 0.23
ACGTcount: A:0.50, C:0.02, G:0.17, T:0.31
Consensus pattern (19 bp):
TTTGAAAAGAAAATTGGAT
Found at i:1488541 original size:21 final size:22
Alignment explanation
Indices: 1488502--1488544 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1488492 ATTTAAATAT
1488502 ATTAAAGGAAGTACTGATACTC
1 ATTAAAGGAAGTACTGATACTC
1488524 ATTAAAGG-AGTA-TCGATACTC
1 ATTAAAGGAAGTACT-GATACTC
1488545 CTTGTACTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 1 0.05
21 11 0.55
22 8 0.40
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.28
Consensus pattern (22 bp):
ATTAAAGGAAGTACTGATACTC
Found at i:1491651 original size:120 final size:120
Alignment explanation
Indices: 1491407--1491645 Score: 290
Period size: 120 Copynumber: 2.0 Consensus size: 120
1491397 AAAAATATAT
* * * *
1491407 ATTAATTTATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAGG
1 ATTAATATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGG
*
1491472 TACCTTAAGATAGCTCTTTTCCTTGATATTAAAAAATAAATAAACAATTAAAACA
66 TACCTTAAGATAGCTCTTTTCCTTAATATTAAAAAATAAATAAACAATTAAAACA
** * *
1491527 ATTAATATATA-ATTTATAAAATAGGATATTTATTTATTTAAAAATATTAGAAAATGGGCATCCA
1 ATTAATATATATATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAA-GGACATCCA
* *** *
1491591 GTTGTTTTAAGACT-GCTC-TTT-CTTAATATTAAAAAATAAATAAA-TATTAAAACA
64 GGTACCTTAAGA-TAGCTCTTTTCCTTAATATTAAAAAATAAATAAACAATTAAAACA
1491645 A
1 A
1491646 GATTAAAATA
Statistics
Matches: 102, Mismatches: 14, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
118 10 0.10
119 28 0.27
120 45 0.44
121 18 0.18
122 1 0.01
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (120 bp):
ATTAATATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGG
TACCTTAAGATAGCTCTTTTCCTTAATATTAAAAAATAAATAAACAATTAAAACA
Found at i:1493051 original size:3 final size:3
Alignment explanation
Indices: 1493043--1493097 Score: 87
Period size: 3 Copynumber: 18.7 Consensus size: 3
1493033 AATTATTTTT
1493043 TAA TAA TAA TAA TAA T-A TATA TAA TAA T-A TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
1493087 TAA TAA TAA TA
1 TAA TAA TAA TA
1493098 TTATTATTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.08
3 42 0.86
4 3 0.06
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1493081 original size:26 final size:26
Alignment explanation
Indices: 1493045--1493098 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
1493035 TTATTTTTTA
1493045 ATAATAATAATAAT-ATATATAATAAT
1 ATAATAATAATAATAATA-ATAATAAT
1493071 ATAATAATAATAATAATAATAATAAT
1 ATAATAATAATAATAATAATAATAAT
1493097 AT
1 AT
1493099 TATTATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 24 0.89
27 3 0.11
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
ATAATAATAATAATAATAATAATAAT
Found at i:1493514 original size:120 final size:121
Alignment explanation
Indices: 1493327--1493555 Score: 306
Period size: 124 Copynumber: 1.9 Consensus size: 121
1493317 GATGACAATT
* * *
1493327 TATCTCCTTCTGTGATGTAATCTAGCAAAGGTTGAACAAGCTATTCTCATTGTGAACATC-TTC-
1 TATCTCCTTCTGTGATGTAATCTAGCAAAGGTCGAACAACCTATTCTCATTATGAACATCGTTCT
*
1493390 TTCTTCAGATGAGTTCTTCTCATTGTGAACT-TCTTCTGGAAATGCTGATGATGATA
66 TTCTTCAGATGAGTTCTTCTCATTATGAACTCTC-TCTGGAAATGCTGATGATGATA
* * *
1493446 TATCTCCTTCTGTGATAG-AGTC-ATGCAAAAGGTCGAACAACCTCTTCTCATTATGAACTTCGT
1 TATCTCCTTCTGTGAT-GTAATCTA-GC-AAAGGTCGAACAACCTATTCTCATTATGAACATCG-
1493509 CTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAA
62 -TTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAA
1493556 AGTTGATCCA
Statistics
Matches: 95, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
118 1 0.01
119 21 0.22
120 30 0.32
123 3 0.03
124 38 0.40
125 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (121 bp):
TATCTCCTTCTGTGATGTAATCTAGCAAAGGTCGAACAACCTATTCTCATTATGAACATCGTTCT
TTCTTCAGATGAGTTCTTCTCATTATGAACTCTCTCTGGAAATGCTGATGATGATA
Found at i:1493609 original size:113 final size:113
Alignment explanation
Indices: 1493470--1494600 Score: 1865
Period size: 113 Copynumber: 10.0 Consensus size: 113
1493460 ATAGAGTCAT
* ** * * *
1493470 GCAAAAGGTCGAACAACCTCTTCTCATTATGAACTTCGTCTTCTTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * * *
1493535 ATTATGAACTCTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTTGA
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
* *
1493583 GCGAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 GC-AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* ** ** * **
1493647 CATTATGAACTCTTTCACTGGGGATCCTGATCCATCAAATGATGAATTCAA
65 CATTATGAACT-TTT-TCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
* * *
1493698 ACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTTTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * **
1493763 ATTATGAACTTTTTCTGGAAAAGCTGATCTATCAAGTGATGAATTCAA
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
*
1493811 ACAAAAGGTTGAAC-AATTACTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 GCAAAAGGTTGAACAAATT-CTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1493875 CATTATGAAC-TTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
65 CATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
1493923 GCAAAAGGTTGAACAAATT-TTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
1493987 ATTATGAACTTTTTTCTGGAAAAGCTGATCCATCAAATGATGAATTTGA
66 ATTATGAAC-TTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
*
1494036 GCAAAAGGTTGGACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1494101 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
*
1494149 GCAAAATGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1494214 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
*
1494262 GCAAAAGGTTGAACAATTTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
1494327 ATTATGAACTTTTTCTGGAAAAGCTGATTCATCAAATGATGGATTTGA
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
1494375 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1494440 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
1494488 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1494553 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
66 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
1494601 ATCTTTGCTA
Statistics
Matches: 964, Mismatches: 45, Indels: 18
0.94 0.04 0.02
Matches are distributed among these distances:
111 54 0.06
112 50 0.05
113 702 0.73
114 66 0.07
115 92 0.10
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
Found at i:1495034 original size:22 final size:22
Alignment explanation
Indices: 1495000--1495051 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
1494990 CATGAAGCTT
* * *
1495000 TCATTTTTGAAAAGAGAATTTA
1 TCATCTTTAAAAAGAGAATCTA
1495022 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
1495044 TCATCTTT
1 TCATCTTT
1495052 GAAGAGTGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (22 bp):
TCATCTTTAAAAAGAGAATCTA
Found at i:1497775 original size:115 final size:114
Alignment explanation
Indices: 1497574--1497800 Score: 364
Period size: 115 Copynumber: 2.0 Consensus size: 114
1497564 GATCATGCAG
* * * *
1497574 TTCATCTTTCAATTCCAATGATTAGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTAGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAAA
* *
1497639 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTACAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
* *
1497688 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAA
1 TTCATCTTTCAAATCCAATGATTAG-TTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAA
*
1497753 AACACTTACAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCA
65 AACACTTACAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCA
1497801 CATGGCACTT
Statistics
Matches: 103, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
114 23 0.22
115 80 0.78
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTAGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAAA
ACACTTACAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
Found at i:1499928 original size:15 final size:16
Alignment explanation
Indices: 1499908--1499939 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1499898 ATTCAATTTC
1499908 TCCCC-TTTTTCTTTT
1 TCCCCTTTTTTCTTTT
1499923 TCCCCTTTTTTCTTTT
1 TCCCCTTTTTTCTTTT
1499939 T
1 T
1499940 TCGTATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (16 bp):
TCCCCTTTTTTCTTTT
Found at i:1505641 original size:120 final size:118
Alignment explanation
Indices: 1505435--1505673 Score: 275
Period size: 120 Copynumber: 2.0 Consensus size: 118
1505425 AAAAATATAT
* * ** *
1505435 ATTAATTTATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAGG
1 ATTAATATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGAAGTCCAGG
* *
1505500 TACCTTAAGACAGCTCTTTTCTTTGATATTAAAAAATAAATAAAGAATTAAAACA
66 TACCTTAAGACAGCTCCTTTC-TTAATATTAAAAAATAAATAAA-AATTAAAACA
** *
1505555 ATTAATATATA-ATTTATAAAATAGGATATTTATTTATTTAAAAATATTAGAAAATGGAAGTCCA
1 ATTAATATATATATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAA-GGAAGTCCA
* *** * * *
1505619 GTTGTTTTAAGACTGC-CCTTTCTTAATATTGAAAAATAAATAAATATTAAAACA
64 GGTACCTTAAGACAGCTCCTTTCTTAATATTAAAAAATAAATAAAAATTAAAACA
1505673 A
1 A
1505674 GATTCAAATA
Statistics
Matches: 100, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
118 10 0.10
119 26 0.26
120 47 0.47
121 17 0.17
ACGTcount: A:0.46, C:0.08, G:0.09, T:0.38
Consensus pattern (118 bp):
ATTAATATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGAAGTCCAGG
TACCTTAAGACAGCTCCTTTCTTAATATTAAAAAATAAATAAAAATTAAAACA
Found at i:1507133 original size:3 final size:3
Alignment explanation
Indices: 1507125--1507164 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
1507115 AATTATTTTT
1507125 TAA TAA TAA TAA TAA T-A TATA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA T
1507165 TATTATTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1508748 original size:29 final size:30
Alignment explanation
Indices: 1508695--1508764 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
1508685 TTGGTATTAT
* *
1508695 ATATTAATAAAATATACCATGTCATA-ATA
1 ATATTAATAAAATATACCATATCATAGAAA
***
1508724 ATATTAATAAAATATGTTATATCATATGAAA
1 ATATTAATAAAATATACCATATCATA-GAAA
1508755 ATATTAATAA
1 ATATTAATAA
1508765 GTCATGTCAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 22 0.65
31 12 0.35
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.37
Consensus pattern (30 bp):
ATATTAATAAAATATACCATATCATAGAAA
Found at i:1510684 original size:3 final size:3
Alignment explanation
Indices: 1510676--1510815 Score: 55
Period size: 3 Copynumber: 47.3 Consensus size: 3
1510666 TTGGACCTAA
* *
1510676 AAT AAT AAT TA- AAT AAT AAAT AAT -AT AAT -AT AA- GAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT -AAT
* * * *
1510719 AAT ATT ATT AAT -AT AAT AAT AAT AAC ATAT ATT ATAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT A-AT AAT AAT AAT
* * * * *
1510764 AAT -AT AAT TAT -AT AAT TAT -AT AAA AAT ATAT ACT CTAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT -AAT AAT AAT
1510808 ATAT AAT A
1 A-AT AAT A
1510816 TTATATATTG
Statistics
Matches: 103, Mismatches: 18, Indels: 32
0.67 0.12 0.21
Matches are distributed among these distances:
2 16 0.16
3 70 0.68
4 17 0.17
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:1510699 original size:15 final size:14
Alignment explanation
Indices: 1510679--1510767 Score: 58
Period size: 14 Copynumber: 6.0 Consensus size: 14
1510669 GACCTAAAAT
1510679 AATAATTAAATAATA
1 AATAA-TAAATAATA
1510694 AATAATATAAT-ATA
1 AATAATA-AATAATA
1510708 AGATAATAAATAAT-
1 A-ATAATAAATAATA
* *
1510722 ATTATTAATATAAT-
1 AATAATAA-ATAATA
1510736 AATAATAACATATATTA
1 AATAATAA-ATA-A-TA
*
1510753 TATAATATAATAATA
1 AATAATA-AATAATA
1510768 TAATTATATA
Statistics
Matches: 60, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
13 5 0.08
14 24 0.40
15 19 0.32
16 2 0.03
17 9 0.15
18 1 0.02
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (14 bp):
AATAATAAATAATA
Found at i:1510705 original size:5 final size:5
Alignment explanation
Indices: 1510691--1510909 Score: 89
Period size: 5 Copynumber: 45.2 Consensus size: 5
1510681 TAATTAAATA
* *
1510691 ATAA- ATAAT ATAAT ATAAG ATAAT A-AAT AATATT ATTAAT ATAAT AATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT A-TAAT ATAAT -ATAAT
1510742 A-ACAT ATATTAT ATAAT AT-A- ATAAT ATAAT -T-AT ATAAT -T-AT
1 ATA-AT ATA--AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
* * * *
1510783 ATAA- A-AAT AT-AT ACT-CT ATAAT A-ATAT ATAAT ATTAT ATATT GT-AT
1 ATAAT ATAAT ATAAT A-TAAT ATAAT ATA-AT ATAAT ATAAT ATAAT ATAAT
* ** *
1510829 A-AAT ATTAT A-ATAT ATAAT ACCAT ATCAT ATAAT ATAAT ATAA- ACT-AT
1 ATAAT ATAAT ATA-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A-TAAT
* *
1510877 ATAAA ATAAT ATATATT ATAAT ATGAT ATAAT A
1 ATAAT ATAAT ATA-A-T ATAAT ATAAT ATAAT A
1510910 AAAAGGAACT
Statistics
Matches: 163, Mismatches: 23, Indels: 57
0.67 0.09 0.23
Matches are distributed among these distances:
3 8 0.05
4 28 0.17
5 102 0.63
6 16 0.10
7 9 0.06
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:1510767 original size:36 final size:35
Alignment explanation
Indices: 1510688--1510910 Score: 106
Period size: 36 Copynumber: 6.2 Consensus size: 35
1510678 TAATAATTAA
* * *
1510688 ATAATAA-ATAAT-ATAATATAAGATAATAAATAAT
1 ATAATAATATAATAATAATA-AATATATTATATAAT
*
1510722 ATTATTAATATAATAATAATAACATATATTATATAAT
1 A-TAATAATATAATAATAATAA-ATATATTATATAAT
* * *
1510759 ATAATAATATAATTAT-ATAATTATA-TA-AAAAT
1 ATAATAATATAATAATAATAAATATATTATATAAT
* * * *
1510791 AT-ATACTCT-ATAATAATATATAATATTATATATTGT
1 ATAATAATATAATAATAATAAAT-ATATTATATA--AT
* *
1510827 ATAAATATTATAATATATAATACCATATCATATAATATAAT
1 AT-AATAATATAATA-ATAATA--A-AT-ATATTATATAAT
*
1510868 ATAA-ACTAT-ATAA-AATAATATATATTATAATATGAT
1 ATAATAATATAATAATAATAA-ATATATTAT-ATA--AT
1510904 ATAATAA
1 ATAATAA
1510911 AAAGGAACTC
Statistics
Matches: 144, Mismatches: 24, Indels: 39
0.70 0.12 0.19
Matches are distributed among these distances:
30 4 0.03
31 9 0.06
32 9 0.06
33 10 0.07
34 14 0.10
35 9 0.06
36 32 0.22
37 20 0.14
38 8 0.06
39 7 0.05
40 8 0.06
41 3 0.02
43 11 0.08
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (35 bp):
ATAATAATATAATAATAATAAATATATTATATAAT
Found at i:1510865 original size:53 final size:51
Alignment explanation
Indices: 1510695--1510899 Score: 143
Period size: 53 Copynumber: 3.9 Consensus size: 51
1510685 TAAATAATAA
* * * * *
1510695 ATAATATAATATAAGATAATAAATAATATTATTAATATAATAATAATA-ACAT
1 ATAATATAATATAATATTAT-AATTATATAAAT-ATATAATAATAATACACAT
* * * *
1510747 ATATTATATAATATAATAATATAATTATATAATTATATAAAAATATATACTC-T
1 ATA--ATATAATATAATATTATAATTATATAAATATATAATAATA-ATACACAT
*
1510800 ATAATA-ATATATAATATTATATATTGTATAAATATTATAATATATAATAC-CAT
1 ATAATATA-ATATAATATTATA-ATTATATAAATA-TATAATA-ATAATACACAT
* * *
1510853 ATCATATAATATAATA-TA-AACTATATAAAATAATATATATTATAATA
1 ATAATATAATATAATATTATAATTATAT-AAAT-ATATA-ATAATAATA
1510900 TGATATAATA
Statistics
Matches: 125, Mismatches: 15, Indels: 27
0.75 0.09 0.16
Matches are distributed among these distances:
50 6 0.05
51 30 0.24
52 29 0.23
53 41 0.33
54 19 0.15
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.40
Consensus pattern (51 bp):
ATAATATAATATAATATTATAATTATATAAATATATAATAATAATACACAT
Found at i:1510906 original size:46 final size:46
Alignment explanation
Indices: 1510686--1510909 Score: 124
Period size: 48 Copynumber: 4.6 Consensus size: 46
1510676 AATAATAATT
* * * *
1510686 AAATAATAAATAATATAATATAAGATAATA-AATAATATTATTAATATA
1 AAATAATATATATTATAATAT-ATATAATATAAT-ATATAATT-ATATA
*
1510734 ATAATAATA-ACA-TAT-AT-TATATAATATAATAATATAATTATATA
1 A-AATAATATATATTATAATATATATAATATAAT-ATATAATTATATA
*
1510778 ATTATATAAAAATATATACTCTATAATAATATATAATAT--TATAT-ATTGTATA
1 A--A-AT---AATATATA-T-TATAAT-ATATATAATATAATATATAATTATATA
* * *
1510830 AATATTATAATATATAATACCATATCATATAATATAATATA-AACTATATA
1 AA-ATAAT-ATATATTATA--ATAT-ATATAATATAATATATAATTATATA
1510880 AAATAATATATATTATAATATGATATAATA
1 AAATAATATATATTATAATAT-ATATAATA
1510910 AAAAGGAACT
Statistics
Matches: 143, Mismatches: 12, Indels: 44
0.72 0.06 0.22
Matches are distributed among these distances:
44 13 0.09
45 14 0.10
46 19 0.13
47 8 0.06
48 28 0.20
49 15 0.10
50 18 0.13
52 8 0.06
53 7 0.05
54 3 0.02
56 10 0.07
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (46 bp):
AAATAATATATATTATAATATATATAATATAATATATAATTATATA
Found at i:1511914 original size:199 final size:200
Alignment explanation
Indices: 1511561--1511950 Score: 525
Period size: 199 Copynumber: 1.9 Consensus size: 200
1511551 GTAGTTCCTC
* * *
1511561 GCTGCTACAATGCGATTGATATGCCCTTGAGCTGAATGGAATTGAACTTGACAGTTTTTGTTGAC
1 GCTGCTACAATGCGATTGATACGCCCTTGAGCTGAATGGAATCGAACTTGACAGTTTTCGTTGAC
* * ** **
1511626 ATATAACTTTTCTTGACTTAAACTATGTTGTAAATTAGGCTTAGATTTAGTTCTTTGTTGCTAAA
66 AGATAACTTTTC-TGACTTAAACTATGTTGTAAATTAGGCTGAGAGATAGTTCACTGTTGCTAAA
* **
1511691 TCTCAGCCAACCTAGGTCTTCTTCTTGTCTTAAAGACCTCGGTTTAAAATTCAATAGGAAAGTAG
130 TCGCAGCCAACCTAGGTCTTCTTCTTGGATTAAAGACCTCGGTTTAAAATTCAATAGGAAAGTAG
1511756 TGCTTT
195 TGCTTT
* *
1511762 GCTGCTACCATGC-AGTTGATACGCCCTTGAGGTGAATGGAATCGAACTTGA-AGTTTTCGTTGA
1 GCTGCTACAATGCGA-TTGATACGCCCTTGAGCTGAATGGAATCGAACTTGACAGTTTTCGTTGA
* * * *
1511825 TAGATAGCTTTATC-GACTTAAGCTATGTTGTAAATTAGGCTGGGAGATAGTTCACTGTTGCTAA
65 CAGATAACTTT-TCTGACTTAAACTATGTTGTAAATTAGGCTGAGAGATAGTTCACTGTTGCTAA
* * * * *
1511889 ATCGCATCCAACCTAGGTTTTCTTCTTGGATTAAATACCTCGGTTTCAAATTCAATCGGAAA
129 ATCGCAGCCAACCTAGGTCTTCTTCTTGGATTAAAGACCTCGGTTTAAAATTCAATAGGAAA
1511951 TTAGATCACT
Statistics
Matches: 164, Mismatches: 23, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
199 97 0.59
200 20 0.12
201 47 0.29
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (200 bp):
GCTGCTACAATGCGATTGATACGCCCTTGAGCTGAATGGAATCGAACTTGACAGTTTTCGTTGAC
AGATAACTTTTCTGACTTAAACTATGTTGTAAATTAGGCTGAGAGATAGTTCACTGTTGCTAAAT
CGCAGCCAACCTAGGTCTTCTTCTTGGATTAAAGACCTCGGTTTAAAATTCAATAGGAAAGTAGT
GCTTT
Found at i:1517859 original size:14 final size:15
Alignment explanation
Indices: 1517835--1517864 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1517825 TGCAAATGAT
1517835 AAAAATGGAAAAGAA
1 AAAAATGGAAAAGAA
1517850 AAAAAT-GAAAAGAA
1 AAAAATGGAAAAGAA
1517864 A
1 A
1517865 TAAGTTAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.07
Consensus pattern (15 bp):
AAAAATGGAAAAGAA
Found at i:1518024 original size:20 final size:20
Alignment explanation
Indices: 1517995--1518038 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1517985 CAAATCCTAA
1517995 ACAT-ATACATTTCTAATTC
1 ACATGATACATTTCTAATTC
*
1518014 ACATGATACATTTTTAATTC
1 ACATGATACATTTCTAATTC
1518034 ACATG
1 ACATG
1518039 CTTTGAACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (20 bp):
ACATGATACATTTCTAATTC
Found at i:1518971 original size:5 final size:5
Alignment explanation
Indices: 1518961--1519019 Score: 56
Period size: 5 Copynumber: 12.8 Consensus size: 5
1518951 GTTAAATAAA
* * *
1518961 AAAAT AAAAT -AAAT AAAAC AAAAT -AAA- AAAAT TAAAT TAAAT -AAA-
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
1519006 AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAA
1519020 ATTAAAGAGG
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
4 16 0.35
5 30 0.65
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:1518972 original size:13 final size:13
Alignment explanation
Indices: 1518954--1519020 Score: 71
Period size: 13 Copynumber: 4.7 Consensus size: 13
1518944 AATTAATGTT
1518954 AAATAAAAAAATA
1 AAATAAAAAAATA
*
1518967 AAATAAATAAAACA
1 AAATAAA-AAAATA
1518981 AAATAAAAAAATTAAA
1 AAATAAAAAAA-T--A
1518997 TTAAATAAAAAAATA
1 --AAATAAAAAAATA
1519012 AAATAAAAA
1 AAATAAAAA
1519021 TTAAAGAGGG
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
13 20 0.43
14 12 0.26
15 1 0.02
16 1 0.02
17 1 0.02
18 11 0.24
ACGTcount: A:0.81, C:0.01, G:0.00, T:0.18
Consensus pattern (13 bp):
AAATAAAAAAATA
Found at i:1518986 original size:10 final size:9
Alignment explanation
Indices: 1518954--1519019 Score: 64
Period size: 9 Copynumber: 7.3 Consensus size: 9
1518944 AATTAATGTT
1518954 AAAT-AAAA
1 AAATAAAAA
*
1518962 AAATAAAAT
1 AAATAAAAA
1518971 AAATAAAACA
1 AAATAAAA-A
1518981 AAATAAAAA
1 AAATAAAAA
* **
1518990 AATTAAATT
1 AAATAAAAA
1518999 AAAT-AAAA
1 AAATAAAAA
1519007 AAATAAAATA
1 AAATAAAA-A
1519017 AAA
1 AAA
1519020 ATTAAAGAGG
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
8 10 0.22
9 24 0.52
10 12 0.26
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (9 bp):
AAATAAAAA
Found at i:1519002 original size:18 final size:18
Alignment explanation
Indices: 1518961--1519019 Score: 82
Period size: 18 Copynumber: 3.2 Consensus size: 18
1518951 GTTAAATAAA
*
1518961 AAAATAAAATAAATAAAAC
1 AAAATAAAA-AAATAAAAT
*
1518980 AAAATAAAAAAATTAAAT
1 AAAATAAAAAAATAAAAT
*
1518998 TAAATAAAAAAATAAAAT
1 AAAATAAAAAAATAAAAT
1519016 AAAA
1 AAAA
1519020 ATTAAAGAGG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
18 26 0.74
19 9 0.26
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.19
Consensus pattern (18 bp):
AAAATAAAAAAATAAAAT
Found at i:1519958 original size:5 final size:5
Alignment explanation
Indices: 1519948--1520444 Score: 662
Period size: 5 Copynumber: 100.8 Consensus size: 5
1519938 TTGCTAGGTC
1519948 AATAT AATAT AATAT AATAT AATAT AATAAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AAT-AT AATAT AATAT AATAT AATAT
1519999 AATAT AATAT -ATAT AATAT AATAT AATAT -ATAT -ATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1520046 -A-AT AATAT AATAT AATAT AATAAT AATAT AATAT AATAT AATATAT
1 AATAT AATAT AATAT AATAT AAT-AT AATAT AATAT AATAT -A-ATAT
1520092 AATAT AATAT AATAT AATA- AATAT AATAT AATAT -A-AT AATAT ATATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT A-ATAT
1520140 AATAT AATATAT AATAT AATAT -ATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT -A-ATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1520191 AATAT AATAT AATATAT AATAT AATAT -ATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT -A-ATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1520242 AATATAT AATAT AATAT AATAT -ATAT AATAT AATAT AATAT -ATAT -ATAT
1 -A-ATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1520291 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1520341 AATAT AATAT AATAT AATAT -A-AT AATAT ACTATAT AAT-T -ATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT A--ATAT AATAT AATAT AATAT
* *
1520389 -ATACT -ATAT AATACT -ATAT ACTAT -ATA- AATACT -ATAT AAAAT
1 AATA-T AATAT AATA-T AATAT AATAT AATAT AATA-T AATAT AATAT
*
1520431 AATAT GATAT AATA
1 AATAT AATAT AATA
1520445 AAAAGGAACC
Statistics
Matches: 450, Mismatches: 6, Indels: 72
0.85 0.01 0.14
Matches are distributed among these distances:
3 8 0.02
4 55 0.12
5 342 0.76
6 24 0.05
7 21 0.05
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:1531947 original size:144 final size:144
Alignment explanation
Indices: 1531668--1531948 Score: 309
Period size: 144 Copynumber: 1.9 Consensus size: 144
1531658 CTAATTCCAA
* *
1531668 TTCCTAATTCCTTCGATTCCTCTTTCATTTTAAGTCTATACTTTTACAAAAATTTGAACCACATG
1 TTCCTAATTCCTTCGATTCCTCCTTCATTTTAAGTCTATA-TTTTACAAAAATTTAAACCACATG
* * * ** * ****
1531733 TTTCTAAACCATCATAGAATACCGATGTACTTTCAATTCCTCTTTTGTTAGCATTTTTAATTTTT
65 CTCCTAAACCATCATAGAATACAGATGTACTTTCAATTAATCTTTTGATA-CATTTTTAAAAAAT
*
1531798 TAATTTAGTCTCTAAT
129 CAATTTAGTCTCTAAT
* *
1531814 TTCCTAATTCCTTC-AGTTCCTCCTTCATTTTAAGTCTAT-TTGTTAC-CAAATTTAAATCACAT
1 TTCCTAATTCCTTCGA-TTCCTCCTTCATTTTAAGTCTATATT-TTACAAAAATTTAAACCACAT
* * * *
1531876 GCTCCTAAACCATCGTAGAATACATATGTGCTTTCGATTAATCTTTTTGATA-ATTTTTAAAAAA
64 GCTCCTAAACCATCATAGAATACAGATGTACTTTCAATTAATC-TTTTGATACATTTTT-AAAAA
1531940 ATCAATTTA
127 ATCAATTTA
1531949 ATCCCTAAAC
Statistics
Matches: 112, Mismatches: 19, Indels: 10
0.79 0.13 0.07
Matches are distributed among these distances:
143 6 0.05
144 58 0.52
145 12 0.11
146 36 0.32
ACGTcount: A:0.29, C:0.20, G:0.07, T:0.44
Consensus pattern (144 bp):
TTCCTAATTCCTTCGATTCCTCCTTCATTTTAAGTCTATATTTTACAAAAATTTAAACCACATGC
TCCTAAACCATCATAGAATACAGATGTACTTTCAATTAATCTTTTGATACATTTTTAAAAAATCA
ATTTAGTCTCTAAT
Found at i:1534025 original size:15 final size:15
Alignment explanation
Indices: 1534005--1534177 Score: 208
Period size: 15 Copynumber: 11.5 Consensus size: 15
1533995 TAATAAGGTT
1534005 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
1534020 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
1534035 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
1534050 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
1534065 A-TTATTATAAAATA
1 ATTTATTTTAAAATA
1534079 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
1534094 A-TTATTATAAAATAA
1 ATTTATTTTAAAAT-A
1534109 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* * *
1534124 AATTATTATAAATATGG
1 ATTTATTTTAAA-AT-A
*
1534141 ATTGTTTTTTAAAATA
1 ATT-TATTTTAAAATA
1534157 A-TTATTTTAAAATA
1 ATTTATTTTAAAATA
*
1534171 AATTATT
1 ATTTATT
1534178 AGTATGGATT
Statistics
Matches: 139, Mismatches: 12, Indels: 14
0.84 0.07 0.08
Matches are distributed among these distances:
14 37 0.27
15 77 0.55
16 14 0.10
17 4 0.03
18 7 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:1534079 original size:29 final size:29
Alignment explanation
Indices: 1534007--1534177 Score: 234
Period size: 30 Copynumber: 5.7 Consensus size: 29
1533997 ATAAGGTTAT
*
1534007 TTATTTTAAAATAATTTATTTTAAAATAA
1 TTATTATAAAATAATTTATTTTAAAATAA
*
1534036 TTTATTATAAAATAATTTATTATAAAATAA
1 -TTATTATAAAATAATTTATTTTAAAATAA
1534066 TTATTATAAAATAATTTATTTTAAAATAA
1 TTATTATAAAATAATTTATTTTAAAATAA
1534095 TTATTATAAAATAAATTTATTTTAAAATAAA
1 TTATTATAAAAT-AATTTATTTTAAAAT-AA
* *
1534126 TTATTATAAATATGGATTGTTTTTTAAAATAA
1 TTATTATAAA-AT-AATT-TATTTTAAAATAA
* *
1534158 TTATTTTAAAATAAATTATT
1 TTATTATAAAATAATTTATT
1534178 AGTATGGATT
Statistics
Matches: 127, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
29 43 0.34
30 44 0.35
31 14 0.11
32 16 0.13
33 10 0.08
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (29 bp):
TTATTATAAAATAATTTATTTTAAAATAA
Found at i:1534157 original size:63 final size:59
Alignment explanation
Indices: 1534007--1534178 Score: 240
Period size: 59 Copynumber: 2.9 Consensus size: 59
1533997 ATAAGGTTAT
*
1534007 TTATTTTAAAATAATTTATTTTAAAATAATTTATTATAAAAT-AATTTATTATAAAATAA
1 TTATTATAAAATAATTTATTTTAAAATAA-TTATTATAAAATAAATTTATTATAAAATAA
*
1534066 TTATTATAAAATAATTTATTTTAAAATAATTATTATAAAATAAATTTATTTTAAAATAAA
1 TTATTATAAAATAATTTATTTTAAAATAATTATTATAAAATAAATTTATTATAAAAT-AA
* * *
1534126 TTATTATAAATATGGATTGTTTTTTAAAATAATTATTTTAAAATAAA-TTATTA
1 TTATTATAAA-AT-AATT-TATTTTAAAATAATTATTATAAAATAAATTTATTA
1534179 GTATGGATTG
Statistics
Matches: 102, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
58 12 0.12
59 42 0.41
60 12 0.12
61 2 0.02
62 8 0.08
63 26 0.25
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (59 bp):
TTATTATAAAATAATTTATTTTAAAATAATTATTATAAAATAAATTTATTATAAAATAA
Found at i:1534243 original size:31 final size:30
Alignment explanation
Indices: 1534208--1534571 Score: 121
Period size: 31 Copynumber: 13.2 Consensus size: 30
1534198 AAACATATGG
* *
1534208 ATTTTATTATTGTAGTT-GTATGGATTGATTT
1 ATTTTATAATT-TA-TTAGTATGGATTAATTT
1534239 ATTTTAATAATTTATTAGTATGGATTAATTT
1 ATTTT-ATAATTTATTAGTATGGATTAATTT
* *
1534270 A-CTT-TAA---A--A-TATGGA-TGATTT
1 ATTTTATAATTTATTAGTATGGATTAATTT
*
1534291 ATTTTAAATAATTTATTAGTATGGATTGA-TT
1 ATTTT--ATAATTTATTAGTATGGATTAATTT
*
1534322 A-TTT-TAA---A--A-TATGGATTGA-TT
1 ATTTTATAATTTATTAGTATGGATTAATTT
* *
1534343 ATTTTAAATATTTATTAGTATGGATTGATTT
1 ATTTTATA-ATTTATTAGTATGGATTAATTT
* *
1534374 ATTTTAAATAATTTATTTGTATGGATTGATTT
1 ATTTT--ATAATTTATTAGTATGGATTAATTT
* *
1534406 A--TTAT--TGTAGTT-GTATGGATTGA-TT
1 ATTTTATAATTTA-TTAGTATGGATTAATTT
*
1534431 ATTTTAAATAATTTATTAGTATGGATTGA-TT
1 ATTTT--ATAATTTATTAGTATGGATTAATTT
* *
1534462 ATTTTA-AA-ATA-T-GTAT-GATTTA-TT
1 ATTTTATAATTTATTAGTATGGATTAATTT
** *
1534486 -TTAAATAA-TTATTAGTATGGATTGATTT
1 ATTTTATAATTTATTAGTATGGATTAATTT
* *
1534514 ATTTTA-AA---A-TAG-ATTGATTTA-TT
1 ATTTTATAATTTATTAGTATGGATTAATTT
** *
1534537 -TTAAATAATTTATTAGTATGGATTGATTT
1 ATTTTATAATTTATTAGTATGGATTAATTT
1534566 ATTTTA
1 ATTTTA
1534572 AAATATCGAT
Statistics
Matches: 260, Mismatches: 26, Indels: 95
0.68 0.07 0.25
Matches are distributed among these distances:
21 19 0.07
22 15 0.06
23 9 0.03
24 20 0.08
25 15 0.06
26 21 0.08
27 18 0.07
28 19 0.07
29 9 0.03
30 25 0.10
31 58 0.22
32 30 0.12
33 2 0.01
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (30 bp):
ATTTTATAATTTATTAGTATGGATTAATTT
Found at i:1534296 original size:21 final size:22
Alignment explanation
Indices: 1534257--1534298 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1534247 AATTTATTAG
1534257 TATGGATTAATTTACTTTAAAA
1 TATGGATTAATTTACTTTAAAA
* *
1534279 TATGGA-TGATTTATTTTAAA
1 TATGGATTAATTTACTTTAAA
1534299 TAATTTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (22 bp):
TATGGATTAATTTACTTTAAAA
Found at i:1534302 original size:53 final size:54
Alignment explanation
Indices: 1534226--1534381 Score: 259
Period size: 52 Copynumber: 3.0 Consensus size: 54
1534216 ATTGTAGTTG
* *
1534226 TATGGATTGATTTATTTT-AATAATTTATTAGTATGGATTAATTTACTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1534279 TATGGA-TGATTTATTTTAAATAATTTATTAGTATGGATTGA-TTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1534331 TATGGATTGA-TTATTTTAAAT-ATTTATTAGTATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
1534382 TAATTTATTT
Statistics
Matches: 98, Mismatches: 2, Indels: 7
0.92 0.02 0.07
Matches are distributed among these distances:
51 19 0.19
52 48 0.49
53 31 0.32
ACGTcount: A:0.35, C:0.01, G:0.13, T:0.51
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
Found at i:1534353 original size:20 final size:21
Alignment explanation
Indices: 1534310--1534350 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1534300 AATTTATTAG
1534310 TATGGATTGATTATTTTAAAA
1 TATGGATTGATTATTTTAAAA
1534331 TATGGATTGATTATTTTAAA
1 TATGGATTGATTATTTTAAA
1534351 TATTTATTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.49
Consensus pattern (21 bp):
TATGGATTGATTATTTTAAAA
Found at i:1534375 original size:18 final size:18
Alignment explanation
Indices: 1534352--1534409 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
1534342 TATTTTAAAT
1534352 ATTTATTAGTATGGATTG
1 ATTTATTAGTATGGATTG
* * *
1534370 ATTTATT--T-T-AAATA
1 ATTTATTAGTATGGATTG
*
1534384 ATTTATTTGTATGGATTG
1 ATTTATTAGTATGGATTG
1534402 ATTTATTA
1 ATTTATTA
1534410 TTGTAGTTGT
Statistics
Matches: 29, Mismatches: 7, Indels: 8
0.66 0.16 0.18
Matches are distributed among these distances:
14 9 0.31
15 1 0.03
16 2 0.07
17 1 0.03
18 16 0.55
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (18 bp):
ATTTATTAGTATGGATTG
Found at i:1534396 original size:32 final size:32
Alignment explanation
Indices: 1534331--1534839 Score: 269
Period size: 32 Copynumber: 15.4 Consensus size: 32
1534321 TATTTTAAAA
*
1534331 TATGGATTGA-TTATTTTAAAT-ATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTTG
1534361 TATGGATTGATTTATTTTAAATAATTTATTTG
1 TATGGATTGATTTATTTTAAATAATTTATTTG
* *
1534393 TATGGATTGATTTA--TT--AT--TGTAGTTG
1 TATGGATTGATTTATTTTAAATAATTTATTTG
*
1534419 TATGGATTGA-TTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTTG
*
1534450 TATGGATTGA-TTATTTTAAA-ATATGTATGATTTA
1 TATGGATTGATTTATTTTAAATA-AT-T-T-ATTTG
* ** * * * * *
1534484 TTTTAAAT-AATTATTAGTATGGATTGATTTATTT-
1 TATGGATTGATTTATT--T-T-AAATAATTTATTTG
* *
1534518 TAAAATAGATTGATTTATTTTAAATAATTTATTAG
1 T---ATGGATTGATTTATTTTAAATAATTTATTTG
*
1534553 TATGGATTGATTTATTTTAAAATATCGATTGATTT-
1 TATGGATTGATTTATTTT-AAATA---ATTTATTTG
** * * * ** * * *
1534588 T-TTAAATAATATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGAT-TTA-TTTTAAATAATTTA-TTT---G
*
1534625 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTTG
*
1534657 TATAGATTGA-TTATTTTAAATAATTTATTTG
1 TATGGATTGATTTATTTTAAATAATTTATTTG
** *
1534688 TATCCA-TGATTTATTTTAAAATATGGATGATTTATTTTAA
1 TATGGATTGATTTATTTT--AA-AT--A--ATTTA-TTT-G
* *
1534728 TATGGATTGATTAATTTTAAAAATAATTTATTAG
1 TATGGATTGATTTATTTT--AAATAATTTATTTG
* * *
1534762 TATAGATTGATTTATTTTTAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTTG
*
1534794 TATAGATTGATTTATTTTAAATAATTTATTTG
1 TATGGATTGATTTATTTTAAATAATTTATTTG
1534826 TATTGGATTGATTT
1 TA-TGGATTGATTT
1534840 TTAAAATATG
Statistics
Matches: 368, Mismatches: 64, Indels: 91
0.70 0.12 0.17
Matches are distributed among these distances:
25 3 0.01
26 16 0.04
27 2 0.01
28 2 0.01
29 2 0.01
30 16 0.04
31 69 0.19
32 97 0.26
33 22 0.06
34 45 0.12
35 16 0.04
36 26 0.07
37 9 0.02
38 20 0.05
39 3 0.01
40 6 0.02
41 14 0.04
ACGTcount: A:0.35, C:0.01, G:0.12, T:0.52
Consensus pattern (32 bp):
TATGGATTGATTTATTTTAAATAATTTATTTG
Found at i:1534455 original size:140 final size:135
Alignment explanation
Indices: 1534157--1534521 Score: 462
Period size: 140 Copynumber: 2.7 Consensus size: 135
1534147 TTTTAAAATA
* *
1534157 ATTATTTTAAAATAAATTATTAGTATGGATTGATTTATTTAAAACATATGGATT--TTA--TT--
1 ATTATTTT-AAATAATTTATTAGTATGGATTGA-TTATTTTAAA-ATATGGATTGATTATTTTAA
* *
1534216 AT-TGTAGTT-GTATGGATTGATTTATTTT-AATAATTTATTAGTATGGATTAATTTACTTTAAA
63 ATATTTA-TTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTAATTTAATTTAAA
1534278 ATATGGATG
127 ATATGGATG
1534287 ATTTATTTTAAATAATTTATTAGTATGGATTGATTATTTTAAAATATGGATTGATTATTTTAAAT
1 A-TTATTTTAAATAATTTATTAGTATGGATTGATTATTTTAAAATATGGATTGATTATTTTAAAT
* * *
1534352 ATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTATTGTAGT
65 ATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTAATTTA--ATT-TA-A
**
1534417 TGTATGGATTG
126 AATATGGA-TG
*
1534428 ATTATTTTAAATAATTTATTAGTATGGATTGATTATTTTAAAATATGTA-TGATTTATTTTAAAT
1 ATTATTTTAAATAATTTATTAGTATGGATTGATTATTTTAAAATATGGATTGA-TTATTTTAAAT
*
1534492 AATTATTAGTATGGATTGATTTATTTTAAA
65 ATTTATTAGTATGGATTGATTTATTTTAAA
1534522 ATAGATTGAT
Statistics
Matches: 208, Mismatches: 11, Indels: 22
0.86 0.05 0.09
Matches are distributed among these distances:
128 9 0.04
129 9 0.04
130 27 0.13
131 7 0.03
132 2 0.01
134 4 0.02
135 22 0.11
136 25 0.12
138 2 0.01
139 5 0.02
140 93 0.45
141 3 0.01
ACGTcount: A:0.35, C:0.01, G:0.13, T:0.52
Consensus pattern (135 bp):
ATTATTTTAAATAATTTATTAGTATGGATTGATTATTTTAAAATATGGATTGATTATTTTAAATA
TTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTAATTTAATTTAAAATAT
GGATG
Found at i:1534474 original size:21 final size:21
Alignment explanation
Indices: 1534450--1534490 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1534440 AATTTATTAG
1534450 TATGGATTGA-TTATTTTAAAA
1 TATGGA-TGATTTATTTTAAAA
*
1534471 TATGTATGATTTATTTTAAA
1 TATGGATGATTTATTTTAAA
1534491 TAATTATTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (21 bp):
TATGGATGATTTATTTTAAAA
Found at i:1534516 original size:52 final size:53
Alignment explanation
Indices: 1534365--1534857 Score: 459
Period size: 52 Copynumber: 9.2 Consensus size: 53
1534355 TATTAGTATG
* ***
1534365 GATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTATTGTAGTTGTAT
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-T-TT-TA-AAATAT
1534422 GGATTGA-TTATTTTAAATAATTTATTAGTATGGATTGA-TTATTTTAAAATAT
1 -GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATAT
1534474 G-TATGATTTATTTTAAATAA-TTATTAGTATGGATTGATTTATTTTAAAATA-
1 GAT-TGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATAT
1534525 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATAT
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATAT
1534578 CGATTGA-TT-TTTTAAATAA--TATTAGTATGGATTGATTTATTTTAAAATAT
1 -GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATAT
*
1534628 GGATTGATTTATTTTAAATAATTTATTAGTATAGATTGA-TTATTTT-AAATA-
1 -GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATAT
* * * ** * *
1534679 -ATTTATTT-GTATCCATGATTTATTTTAAAATATGGA-TGATTTATTTT--AATAT
1 GATTGATTTATTTTAAATAATTTA--TT--AGTATGGATTGATTTATTTTAAAATAT
* *
1534731 GGATTGATTAATTTTAAAAATAATTTATTAGTATAGATTGATTTATTTTTAATAATTTATTAGTA
1 -GATTGATTTATTTT--AAATAATTTATTAGTATGGATTGATTTA--TTT--TAA---A--A-TA
1534796 T
53 T
*
1534797 AGATTGATTTATTTTAAATAATTTATTTGTATTGGATTGA--T-TTTTAAAATAT
1 -GATTGATTTATTTTAAATAATTTATTAGTA-TGGATTGATTTATTTTAAAATAT
1534849 GGATTGATT
1 -GATTGATT
1534858 ATTATTGTAG
Statistics
Matches: 371, Mismatches: 28, Indels: 78
0.78 0.06 0.16
Matches are distributed among these distances:
48 9 0.02
49 7 0.02
50 40 0.11
51 48 0.13
52 110 0.30
53 18 0.05
54 36 0.10
55 6 0.02
56 6 0.02
57 37 0.10
58 10 0.03
60 3 0.01
63 2 0.01
64 15 0.04
65 8 0.02
66 16 0.04
ACGTcount: A:0.35, C:0.01, G:0.12, T:0.52
Consensus pattern (53 bp):
GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATAT
Found at i:1534520 original size:192 final size:193
Alignment explanation
Indices: 1534210--1534573 Score: 630
Period size: 192 Copynumber: 1.9 Consensus size: 193
1534200 ACATATGGAT
1534210 TTTATTATTGTAGTTGTATGGATTGATTTATTTTAATAATTTATTAGTATGGATTAATTTACTTT
1 TTTATTATTGTAGTTGTATGGATTGATTTATTTTAATAATTTATTAGTATGGATTAATTTACTTT
1534275 AAAATATGGATGATTTATTTTAAATAATTTATTAGTATGGATTGATTATTTTAAAATATGGATTG
66 AAAATATGGATGATTTATTTTAAATAATTTATTAGTATGGATTGATTATTTTAAAATA--GATTG
1534340 A-TTATTTTAAAT-ATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGA
129 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGA
* *
1534403 TTTATTATTGTAGTTGTATGGATTGA-TTATTTTAAATAATTTATTAGTATGGATTGA-TTATTT
1 TTTATTATTGTAGTTGTATGGATTGATTTATTTT-AATAATTTATTAGTATGGATTAATTTACTT
*
1534466 TAAAATATGTATGATTTATTTTAAATAA-TTATTAGTATGGATTGATTTATTTTAAAATAGATTG
65 TAAAATATGGATGATTTATTTTAAATAATTTATTAGTATGGATTGA-TTATTTTAAAATAGATTG
1534530 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
129 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
1534574 ATATCGATTG
Statistics
Matches: 164, Mismatches: 3, Indels: 9
0.93 0.02 0.05
Matches are distributed among these distances:
190 6 0.04
191 28 0.17
192 82 0.50
193 48 0.29
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.52
Consensus pattern (193 bp):
TTTATTATTGTAGTTGTATGGATTGATTTATTTTAATAATTTATTAGTATGGATTAATTTACTTT
AAAATATGGATGATTTATTTTAAATAATTTATTAGTATGGATTGATTATTTTAAAATAGATTGAT
TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGA
Found at i:1534582 original size:22 final size:22
Alignment explanation
Indices: 1534553--1534645 Score: 107
Period size: 22 Copynumber: 4.0 Consensus size: 22
1534543 AATTTATTAG
1534553 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
*
1534575 TATCGATTGATTT-TTTAAATAATATTA
1 TATGGATTGATTTATTT---TAA-A--A
1534602 GTATGGATTGATTTATTTTAAAA
1 -TATGGATTGATTTATTTTAAAA
1534625 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1534646 TAATTTATTA
Statistics
Matches: 61, Mismatches: 2, Indels: 16
0.77 0.03 0.20
Matches are distributed among these distances:
21 3 0.05
22 33 0.54
23 1 0.02
24 3 0.05
25 2 0.03
26 3 0.05
27 1 0.02
28 12 0.20
29 3 0.05
ACGTcount: A:0.35, C:0.01, G:0.13, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1534717 original size:21 final size:21
Alignment explanation
Indices: 1534693--1534749 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
1534683 ATTTGTATCC
1534693 ATGATTTATTTTAAAATATGG
1 ATGATTTATTTTAAAATATGG
1534714 ATGATTTATTTT--AATATGG
1 ATGATTTATTTTAAAATATGG
*
1534733 ATTGATTAATTTTAAAA
1 A-TGATTTATTTTAAAA
1534750 ATAATTTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
19 8 0.25
20 10 0.31
21 12 0.38
22 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (21 bp):
ATGATTTATTTTAAAATATGG
Found at i:1534744 original size:20 final size:19
Alignment explanation
Indices: 1534693--1534747 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
1534683 ATTTGTATCC
*
1534693 ATGATTTATTTTAAAATATGG
1 ATGATTAATTTT--AATATGG
*
1534714 ATGATTTATTTTAATATGG
1 ATGATTAATTTTAATATGG
1534733 ATTGATTAATTTTAA
1 A-TGATTAATTTTAA
1534748 AAATAATTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 8 0.25
20 12 0.38
21 12 0.38
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (19 bp):
ATGATTAATTTTAATATGG
Found at i:1534766 original size:105 final size:107
Alignment explanation
Indices: 1534603--1534944 Score: 372
Period size: 105 Copynumber: 3.2 Consensus size: 107
1534593 ATAATATTAG
*
1534603 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGA-
1 TATGGATTGATTTATTTT-AAATATGGATTGATTAATTTTAAATAATTTATTAGTATAGATTGAT
* *
1534667 TTATTTTAAATAATTTATTTGTATCCA-TGATTTATTTTAAAA
65 TTATTTTAAATAATTTATTAGTATACATTGATTTATTTTAAAA
1534709 TATGGA-TGATTTATTTT-AATATGGATTGATTAATTTTAAAAATAATTTATTAGTATAGATTGA
1 TATGGATTGATTTATTTTAAATATGGATTGATTAATTTT--AAATAATTTATTAGTATAGATTGA
* *
1534772 TTTATTTTTAATAATTTATTAGTATAGATTGATTTATTTTAAATAA
64 TTTATTTTAAATAATTTATTAGTATACATTGATTTATTTT-AA-AA
* * *
1534818 TTTATTTGTATTGGATTGATTTTTAAAATATGGATTGATT-A--TT--AT--TGTAGTT-GTATA
1 --TA--TGGATT-GATTTA-TTTT-AAATATGGATTGATTAATTTTAAATAATTTA-TTAGTATA
**
1534875 GATTGATTTATTTTAAATAA-TT-TTAGTATGGATTGATTTATTTTAAAA
58 GATTGATTTATTTTAAATAATTTATTAGTATACATTGATTTATTTTAAAA
1534923 TATGGATTGA-TTATTTTAAATA
1 TATGGATTGATTTATTTTAAATA
1534945 ATTTATTATT
Statistics
Matches: 208, Mismatches: 12, Indels: 41
0.80 0.05 0.16
Matches are distributed among these distances:
97 5 0.02
98 4 0.02
99 2 0.01
100 2 0.01
101 5 0.02
103 21 0.10
105 37 0.18
106 31 0.15
107 32 0.15
108 4 0.02
109 29 0.14
110 2 0.01
111 4 0.02
113 3 0.01
114 1 0.00
115 7 0.03
116 4 0.02
117 1 0.00
118 14 0.07
ACGTcount: A:0.35, C:0.01, G:0.12, T:0.52
Consensus pattern (107 bp):
TATGGATTGATTTATTTTAAATATGGATTGATTAATTTTAAATAATTTATTAGTATAGATTGATT
TATTTTAAATAATTTATTAGTATACATTGATTTATTTTAAAA
Found at i:1534776 original size:18 final size:18
Alignment explanation
Indices: 1534753--1534809 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 18
1534743 TTTAAAAATA
1534753 ATTTATTAGTATAGATTG
1 ATTTATTAGTATAGATTG
* *
1534771 ATTTATT--TTTA-A-TA
1 ATTTATTAGTATAGATTG
1534785 ATTTATTAGTATAGATTG
1 ATTTATTAGTATAGATTG
1534803 ATTTATT
1 ATTTATT
1534810 TTAAATAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 8 0.26
15 1 0.03
16 6 0.19
17 1 0.03
18 15 0.48
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (18 bp):
ATTTATTAGTATAGATTG
Found at i:1534786 original size:137 final size:138
Alignment explanation
Indices: 1534522--1534921 Score: 418
Period size: 137 Copynumber: 2.9 Consensus size: 138
1534512 TTATTTTAAA
* *
1534522 ATAGATTGATTTATTTTAAATAATTTATTAGTA-TGGATTGATTTATTTTAAAATATCGATTGAT
1 ATAGATTGATTTATTTTAAATAATTTATTTGTATTGGATTGA--T-TTTTAAAATATGGATTGAT
** * * * * *
1534586 T-TT-TTAAATAATATTAGTATGGATTGA-TTT--AT--TTTAAAATATGGATTGATTTATTTTA
63 TATTATTGTATAATA-TAG-ATTGATTAATTTTAAATAATTT-TAGTATAGATTGATTTATTTTA
1534644 AATAATTTATTAGT
125 AATAATTTATTAGT
*
1534658 ATAGATTGA-TTATTTTAAATAATTTATTTGTATCCAT-GATTTA-TTTTAAAATATGGA-TGA-
1 ATAGATTGATTTATTTTAAATAATTTATTTGTAT---TGGATTGATTTTTAAAATATGGATTGAT
*
1534718 T-TTATT-T-TAATATGGATTGATTAATTTTAAAAATAATTTATTAGTATAGATTGATTTATTTT
63 TATTATTGTATAATATAGATTGATTAATTTT--AAATAA-TT-TTAGTATAGATTGATTTATTTT
*
1534780 TAATAATTTATTAGT
124 AAATAATTTATTAGT
1534795 ATAGATTGATTTATTTTAAATAATTTATTTGTATTGGATTGATTTTTAAAATATGGATTGATTAT
1 ATAGATTGATTTATTTTAAATAATTTATTTGTATTGGATTGATTTTTAAAATATGGATTGATTAT
** * *
1534860 TATTGTAGTTGTATAGATTGATTTATTTTAAATAATTTTAGTATGGATTGATTTATTTTAAA
66 TATTGTA-TAATATAGATTGATTAATTTTAAATAATTTTAGTATAGATTGATTTATTTTAAA
1534922 ATATGGATTG
Statistics
Matches: 223, Mismatches: 18, Indels: 43
0.79 0.06 0.15
Matches are distributed among these distances:
129 7 0.03
130 5 0.02
131 5 0.02
132 3 0.01
133 5 0.02
134 15 0.07
135 23 0.10
136 14 0.06
137 57 0.26
138 33 0.15
139 25 0.11
140 7 0.03
141 7 0.03
143 17 0.08
ACGTcount: A:0.35, C:0.01, G:0.12, T:0.52
Consensus pattern (138 bp):
ATAGATTGATTTATTTTAAATAATTTATTTGTATTGGATTGATTTTTAAAATATGGATTGATTAT
TATTGTATAATATAGATTGATTAATTTTAAATAATTTTAGTATAGATTGATTTATTTTAAATAAT
TTATTAGT
Found at i:1534885 original size:77 final size:76
Alignment explanation
Indices: 1534793--1534937 Score: 231
Period size: 77 Copynumber: 1.9 Consensus size: 76
1534783 TAATTTATTA
*
1534793 GTATAGATTGATTTATTTTAAATAATTTATTTGTATTGGATTGA-T-TTTTAAAATATGGATTGA
1 GTATAGATTGATTTATTTTAAATAA-TT-TTAGTA-TGGATTGATTATTTTAAAATATGGATTGA
1534856 TTATTATTGTAGTT
63 TTATTATTGTAGTT
1534870 GTATAGATTGATTTATTTTAAATAATTTTAGTATGGATTGATTTATTTTAAAATATGGATTGATT
1 GTATAGATTGATTTATTTTAAATAATTTTAGTATGGATTGA-TTATTTTAAAATATGGATTGATT
1534935 ATT
65 ATT
1534938 TTAAATAATT
Statistics
Matches: 64, Mismatches: 1, Indels: 6
0.90 0.01 0.08
Matches are distributed among these distances:
74 8 0.12
75 5 0.08
76 3 0.05
77 48 0.75
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.52
Consensus pattern (76 bp):
GTATAGATTGATTTATTTTAAATAATTTTAGTATGGATTGATTATTTTAAAATATGGATTGATTA
TTATTGTAGTT
Found at i:1534938 original size:21 final size:22
Alignment explanation
Indices: 1534901--1534942 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
1534891 ATAATTTTAG
1534901 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
1534923 TATGGATTGA-TTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1534943 TAATTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1535002 original size:31 final size:31
Alignment explanation
Indices: 1534967--1535025 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1534957 AGTTGTATGG
* *
1534967 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
1534998 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
1535026 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:1536294 original size:171 final size:172
Alignment explanation
Indices: 1536001--1536344 Score: 599
Period size: 171 Copynumber: 2.0 Consensus size: 172
1535991 GGGAACCAAC
1536001 TCCAACATCCCATTAGTTTGTTGTCAGGCGGGTCTATATGGGTATGTGCTAGTGGATAGTGGGTG
1 TCCAACATCCCATTAG-TTGTTGTCAGGCGGGTCTATATGGGTATGTGCTAGTGGATAGTGGGTG
1536066 TGGTGATGGATTTGAAAATGTACCGCGTGGGTGTGTGATTTGAAAATTTGTACCCATCATGGGTG
65 TGGTGATGGATTTGAAAATGTACCGCGTGGGTGTGTGATTTGAAAATTTGTACCCATCATGGGTG
1536131 GGGGCGGG-GGTGGATTGAAAAATATTAGG-GGGTATGGGGAT
130 GGGGCGGGTGGTGGATTGAAAAATATTAGGTGGGTATGGGGAT
1536172 TCCAACATCCCATTAG-T-TTGTCAGGCGGGTCTATATGGGTATGTCGCTAGTGGATAGTGGGTG
1 TCCAACATCCCATTAGTTGTTGTCAGGCGGGTCTATATGGGTATGT-GCTAGTGGATAGTGGGTG
1536235 TGG-GATGGATTTGAAAATGTACCCGCGTGGGTGGGTGTGATTTGAAAATTTGTACCCATCATGG
65 TGGTGATGGATTTGAAAATGTA-CCGCGTGGGT--GTGTGATTTGAAAATTTGTACCCATCATGG
*
1536299 GTGTGGGCGGGTGGTGGATTGAAAAATATTAGGTGGGTATGGGGAT
127 GTGGGGGCGGGTGGTGGATTGAAAAATATTAGGTGGGTATGGGGAT
1536345 GGGGGAGGGG
Statistics
Matches: 166, Mismatches: 1, Indels: 10
0.94 0.01 0.06
Matches are distributed among these distances:
168 45 0.27
169 32 0.19
171 56 0.34
172 21 0.13
173 12 0.07
ACGTcount: A:0.22, C:0.11, G:0.37, T:0.31
Consensus pattern (172 bp):
TCCAACATCCCATTAGTTGTTGTCAGGCGGGTCTATATGGGTATGTGCTAGTGGATAGTGGGTGT
GGTGATGGATTTGAAAATGTACCGCGTGGGTGTGTGATTTGAAAATTTGTACCCATCATGGGTGG
GGGCGGGTGGTGGATTGAAAAATATTAGGTGGGTATGGGGAT
Found at i:1541491 original size:16 final size:15
Alignment explanation
Indices: 1541472--1541524 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
1541462 ACCGAAACAA
1541472 AAAAATAGTATAAAAT
1 AAAAATA-TATAAAAT
*
1541488 AAAAATAATATATAAT
1 AAAAAT-ATATAAAAT
*
1541504 AATAATATAATAACAAT
1 AAAAATAT-ATAA-AAT
1541521 AAAA
1 AAAA
1541525 CAAAAGGGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
15 2 0.07
16 21 0.70
17 7 0.23
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (15 bp):
AAAAATATATAAAAT
Found at i:1541502 original size:13 final size:14
Alignment explanation
Indices: 1541485--1541522 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
1541475 AATAGTATAA
1541485 AATAAAAATAATAT
1 AATAAAAATAATAT
*
1541499 -ATAATAATAATAT
1 AATAAAAATAATAT
*
1541512 AATAACAATAA
1 AATAAAAATAA
1541523 AACAAAAGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (14 bp):
AATAAAAATAATAT
Found at i:1544204 original size:19 final size:19
Alignment explanation
Indices: 1544177--1544243 Score: 116
Period size: 19 Copynumber: 3.5 Consensus size: 19
1544167 AATGTAACAC
*
1544177 CTCGGATCGGATCGAGTCA
1 CTCGCATCGGATCGAGTCA
1544196 CTCGCATCGGATCGAGTCA
1 CTCGCATCGGATCGAGTCA
1544215 CTCGCATCGGATCGAGTCA
1 CTCGCATCGGATCGAGTCA
*
1544234 CTCACATCGG
1 CTCGCATCGG
1544244 TCTGTGGGTG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 46 1.00
ACGTcount: A:0.21, C:0.31, G:0.27, T:0.21
Consensus pattern (19 bp):
CTCGCATCGGATCGAGTCA
Found at i:1544721 original size:21 final size:20
Alignment explanation
Indices: 1544697--1544763 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
1544687 ACTTCGACTA
*
1544697 TCGCATTGCGATAGTCCAAGT
1 TCGC-TTGCGATAGTCCAAAT
*
1544718 TCGCGTTGCGATTTATTCCAAAT
1 TCGC-TTGCGA--TAGTCCAAAT
*
1544741 TCG-TTGCGATAGTCCAAAA
1 TCGCTTGCGATAGTCCAAAT
1544760 TCGC
1 TCGC
1544764 AACGACTGGT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
19 11 0.29
21 16 0.42
23 11 0.29
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (20 bp):
TCGCTTGCGATAGTCCAAAT
Found at i:1545492 original size:6 final size:6
Alignment explanation
Indices: 1545472--1545518 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
1545462 CCGTCTCGTC
* * *
1545472 TCGT-G TCGT-G TCGTGG TCGTGC TTGTGG TCGTGG TAGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1545518 T
1 T
1545519 AATACGTGTC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
5 9 0.26
6 26 0.74
ACGTcount: A:0.02, C:0.15, G:0.45, T:0.38
Consensus pattern (6 bp):
TCGTGG
Found at i:1545645 original size:19 final size:19
Alignment explanation
Indices: 1545618--1545707 Score: 99
Period size: 19 Copynumber: 4.5 Consensus size: 19
1545608 AATCGCAACG
*
1545618 CGAACTTGGACTATCGCAA
1 CGAATTTGGACTATCGCAA
*
1545637 CGAATTTGGAATAAATCGCAA
1 CGAATTTGGACT--ATCGCAA
*
1545658 CGCGAATTTCGACTATCGCAA
1 --CGAATTTGGACTATCGCAA
* *
1545679 CGAACTTAGACTATCGCAA
1 CGAATTTGGACTATCGCAA
1545698 CGAATTTGGA
1 CGAATTTGGA
1545708 AAATCGCATT
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
19 35 0.59
21 14 0.24
23 10 0.17
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.23
Consensus pattern (19 bp):
CGAATTTGGACTATCGCAA
Found at i:1545659 original size:42 final size:42
Alignment explanation
Indices: 1545600--1545682 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
1545590 CCACCAGTCG
*
1545600 TTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAAT
1 TTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAAT
*
1545642 TTGGAATAAATCGCAACGCGAATTTCGACTATCGCAACGAA
1 TTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAA
1545683 CTTAGACTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (42 bp):
TTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAAT
Found at i:1545713 original size:19 final size:19
Alignment explanation
Indices: 1545607--1545715 Score: 74
Period size: 19 Copynumber: 5.4 Consensus size: 19
1545597 TCGTTGGAAT
*
1545607 AAATCGCAACGCGAACTTGGA
1 AAATCGCAA--CGAATTTGGA
**
1545628 CTATCGCAACGAATTTGGAA
1 AAATCGCAACGAATTTGG-A
*
1545648 TAAATCGCAACGCGAATTTCGA
1 -AAATCGCAA--CGAATTTGGA
** * *
1545670 CTATCGCAACGAACTTAGA
1 AAATCGCAACGAATTTGGA
**
1545689 CTATCGCAACGAATTTGGA
1 AAATCGCAACGAATTTGGA
1545708 AAATCGCA
1 AAATCGCA
1545716 TTGCGATAGT
Statistics
Matches: 70, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
19 39 0.56
20 1 0.01
21 21 0.30
22 1 0.01
23 8 0.11
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (19 bp):
AAATCGCAACGAATTTGGA
Found at i:1545740 original size:21 final size:21
Alignment explanation
Indices: 1545711--1545763 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
1545701 ATTTGGAAAA
*
1545711 TCGCATTGCGATAGTCG-TAGT
1 TCGCGTTGCGATAGTCGAT-GT
1545732 TCGCGTTGCGATAGTCGATGT
1 TCGCGTTGCGATAGTCGATGT
1545753 TCGCGTTGCGA
1 TCGCGTTGCGA
1545764 ATCTAGAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 29 0.97
22 1 0.03
ACGTcount: A:0.15, C:0.21, G:0.32, T:0.32
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGATGT
Found at i:1546692 original size:178 final size:184
Alignment explanation
Indices: 1546484--1546845 Score: 682
Period size: 178 Copynumber: 2.0 Consensus size: 184
1546474 TGTAATTTGA
1546484 GTGTAATGATTTCCTTGGATAACTTTCAGTTTTCAGTAGAAGTTGTGAATCGTGCTAATATTATC
1 GTGTAATGATTTCCTTGGATAACTTTCAGTTTTCAGTAGAAGTTGTGAATCGTGCTAATATTATC
1546549 ATTGTTTATTTGGTCTA-TTTCTTTCTTG-AAATATA-TGAAAATTAAATTTAAACCAATTTTTA
66 ATTGTTTATTTGGTCTATTTTCTTTCTTGAAAATATATTGAAAATTAAATTTAAACCAATTTTTA
1546611 C-AATTTCAAACATCGTTT-GAATTGAGATAAAC-ACGCTTGTAAGAATTCATC
131 CAAATTTCAAACATCGTTTGGAATTGAGATAAACAACGCTTGTAAGAATTCATC
1546662 GTGTAATGATTTCCTTGGATAACTTTCAGTTTTCAGTAGAAGTTGTGAATCGTGCTAATATTATC
1 GTGTAATGATTTCCTTGGATAACTTTCAGTTTTCAGTAGAAGTTGTGAATCGTGCTAATATTATC
1546727 ATTGTTTATTTGGTCTATTTTCTTTCTTGAAAATATATTGAAAATTAAATTTAAACCAATTTTTA
66 ATTGTTTATTTGGTCTATTTTCTTTCTTGAAAATATATTGAAAATTAAATTTAAACCAATTTTTA
1546792 CAAATTTCAAACATCGTTTGGAATTGAGATAAACAACGCTTGTAAGAATTCATC
131 CAAATTTCAAACATCGTTTGGAATTGAGATAAACAACGCTTGTAAGAATTCATC
1546846 TCTAATGGCA
Statistics
Matches: 178, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
178 82 0.46
179 11 0.06
180 7 0.04
181 28 0.16
182 17 0.10
183 14 0.08
184 19 0.11
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.41
Consensus pattern (184 bp):
GTGTAATGATTTCCTTGGATAACTTTCAGTTTTCAGTAGAAGTTGTGAATCGTGCTAATATTATC
ATTGTTTATTTGGTCTATTTTCTTTCTTGAAAATATATTGAAAATTAAATTTAAACCAATTTTTA
CAAATTTCAAACATCGTTTGGAATTGAGATAAACAACGCTTGTAAGAATTCATC
Found at i:1550592 original size:11 final size:14
Alignment explanation
Indices: 1550563--1550600 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
1550553 ACCTCTTCCC
1550563 GGAGGTACCAAAGA
1 GGAGGTACCAAAGA
1550577 GGAGGTACCAAAGA
1 GGAGGTACCAAAGA
*
1550591 GGAGGCACCA
1 GGAGGTACCA
1550601 CAAGGTGGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.39, C:0.18, G:0.37, T:0.05
Consensus pattern (14 bp):
GGAGGTACCAAAGA
Found at i:1553171 original size:24 final size:24
Alignment explanation
Indices: 1553144--1553243 Score: 87
Period size: 24 Copynumber: 4.2 Consensus size: 24
1553134 GATATCAAAA
*
1553144 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
1553168 ATCAGAAA-AGAATCCAGGTTAGGA-
1 ATCA-AAACAGAATTCAGATCA-GAT
* *
1553192 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
1553216 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
1553240 ATCA
1 ATCA
1553244 GATAAAATAT
Statistics
Matches: 57, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
23 4 0.07
24 48 0.84
25 5 0.09
ACGTcount: A:0.48, C:0.16, G:0.15, T:0.21
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:1553243 original size:48 final size:48
Alignment explanation
Indices: 1553137--1553245 Score: 112
Period size: 48 Copynumber: 2.3 Consensus size: 48
1553127 AAACGGAGAT
* * * *
1553137 ATCAAAAATCAAAACATAATTCAGATCAGATATCAGAAAAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAGAAAAGAATCCAA
* * * * * *
1553185 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCA-AAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAGAAA-AGAATCCAA
1553233 ATCAGAAATCAGA
1 ATCAGAAATCAGA
1553246 TAAAATATTC
Statistics
Matches: 47, Mismatches: 13, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
47 3 0.06
48 44 0.94
ACGTcount: A:0.50, C:0.16, G:0.15, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAGAAAAGAATCCAA
Found at i:1555523 original size:27 final size:27
Alignment explanation
Indices: 1555487--1555599 Score: 136
Period size: 27 Copynumber: 4.1 Consensus size: 27
1555477 TCTCAATTGT
*
1555487 TTTTTTACTTTTTCTATTTCTCTTTCA
1 TTTTTAACTTTTTCTATTTCTCTTTCA
** * *
1555514 TTTTTAACTTTACCCATTTCTCTCTCA
1 TTTTTAACTTTTTCTATTTCTCTTTCA
*
1555541 TTTTTTTAACTTTTTCTTTTTCTCTTTCA
1 --TTTTTAACTTTTTCTATTTCTCTTTCA
* *
1555570 TTTGTAACTTTTTCTTTTTCTCTTTCA
1 TTTTTAACTTTTTCTATTTCTCTTTCA
1555597 TTT
1 TTT
1555600 CTTCATCTTC
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
27 51 0.70
29 22 0.30
ACGTcount: A:0.12, C:0.20, G:0.01, T:0.66
Consensus pattern (27 bp):
TTTTTAACTTTTTCTATTTCTCTTTCA
Found at i:1558439 original size:17 final size:18
Alignment explanation
Indices: 1558406--1558439 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1558396 ATTAACTTAA
*
1558406 TCAATTTTAACTAATTAT
1 TCAATTTGAACTAATTAT
1558424 TCAATTTGAA-TAATTA
1 TCAATTTGAACTAATTA
1558440 AAATGAAACC
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:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (18 bp):
TCAATTTGAACTAATTAT
Found at i:1558835 original size:137 final size:137
Alignment explanation
Indices: 1558239--1558980 Score: 755
Period size: 137 Copynumber: 5.4 Consensus size: 137
1558229 GAAACTAAAA
* * * * * * * * * *
1558239 AAAATGTAGGCTCTAAGATTAATCCTAGTTATTTTTTAGTAAATTAT-TGAATCGAATAGTCAAA
1 AAAATGGAGACTCTAATATTAATCCTAATTA-ATTTTAATCAATTATGTGATTCGAATAATTAAA
* * * * ** * *
1558303 ATGGAACCTCAAGCATAAGCGAGGACCAAATCAAAAATTCTCCTAGATAAAAGGACTAGGTGTGA
65 ATGGAACCTCGAGCAAAAGCGAGGATCAAATTAAAAATTC-CCTA-ATTTAAGGACTAAGTTTGA
1558368 AATTGAA-CCT
128 AATT-AAGCCT
* * * * * * *
1558378 ATAATGGA-ATCTTTAAAAATTAA-CTTAATCAATTTTAA-CTAATTAT-TCAATTTGAATAATT
1 AAAATGGAGA-CTCT-AATATTAATCCTAATTAATTTTAATC-AATTATGT-GATTCGAATAATT
* * * * * *
1558439 AAAATGAAACCTCGATCGAAAGCGATGACCAAATTAAAAATTTCCCTAATTTAAGGACTAAGTTA
62 AAAATGGAACCTCGAGCAAAAGCGAGGATCAAATTAAAAA-TTCCCTAATTTAAGGACTAAGTTT
1558504 GAAATTAAGCCT
126 GAAATTAAGCCT
* * *
1558516 AAAATGGA-AGCTCTAATATTAATCCTGATTAATTTTAGTCAATTATGTGATTCGAATAATGAAA
1 AAAATGGAGA-CTCTAATATTAATCCTAATTAATTTTAATCAATTATGTGATTCGAATAATTAAA
* * * *
1558580 ATGGAACCTTGATCAAAAGCGAGGATCGAATTAAAAATTCATCTAAATTTAAGGACTAAGTTTGA
65 ATGGAACCTCGAGCAAAAGCGAGGATCAAATTAAAAATTC-CCT-AATTTAAGGACTAAGTTTGA
*
1558645 AATTAAACCT
128 AATTAAGCCT
**
1558655 AAAATGGAGGTTCTAATATTAATCCTAATTAATTTTAATCAATTATGTGATTCGAATAATTAAAA
1 AAAATGGAGACTCTAATATTAATCCTAATTAATTTTAATCAATTATGTGATTCGAATAATTAAAA
* *** * * *
1558720 TAGAACCTCGAGCAAAAATAAGGATTAAATTAAAAACT-CCTAATTTTAAGGACTAAATTTGAAA
66 TGGAACCTCGAGCAAAAGCGAGGATCAAATTAAAAATTCCCTAA-TTTAAGGACTAAGTTTGAAA
1558784 TTAAGCCT
130 TTAAGCCT
* * * *
1558792 AAAATGGAGACTCTAATTATTAA-CCTAGTCAATTTTAACCAATTATTTGATTCGAATAATTAAA
1 AAAATGGAGACTCTAA-TATTAATCCTAATTAATTTTAATCAATTATGTGATTCGAATAATTAAA
* *
1558856 ATGGAACCTCGAGCAAAAGCGAGGACCAAATTAAAAATTCCCTAATATAAGGACTAAGTTTGAAA
65 ATGGAACCTCGAGCAAAAGCGAGGATCAAATTAAAAATTCCCTAATTTAAGGACTAAGTTTGAAA
* *
1558921 CTAGGCCT
130 TTAAGCCT
* * * *
1558929 AAAGTGAAGGCTCTAATATCAATCCTAATTAATTTTAATCAATTATGTGATT
1 AAAATGGAGACTCTAATATTAATCCTAATTAATTTTAATCAATTATGTGATT
1558981 ATTCATCTAA
Statistics
Matches: 497, Mismatches: 90, Indels: 34
0.80 0.14 0.05
Matches are distributed among these distances:
136 7 0.01
137 185 0.37
138 118 0.24
139 177 0.36
140 10 0.02
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (137 bp):
AAAATGGAGACTCTAATATTAATCCTAATTAATTTTAATCAATTATGTGATTCGAATAATTAAAA
TGGAACCTCGAGCAAAAGCGAGGATCAAATTAAAAATTCCCTAATTTAAGGACTAAGTTTGAAAT
TAAGCCT
Found at i:1559370 original size:14 final size:14
Alignment explanation
Indices: 1559344--1559386 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1559334 TAATTTAAGG
*
1559344 AAAAAAA-TGAAAT
1 AAAAAAATTTAAAT
1559357 AAAAAAATTTAAAT
1 AAAAAAATTTAAAT
**
1559371 GGAAAAATTTAAAT
1 AAAAAAATTTAAAT
1559385 AA
1 AA
1559387 TGAAAAAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 7 0.29
14 17 0.71
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (14 bp):
AAAAAAATTTAAAT
Found at i:1559396 original size:18 final size:19
Alignment explanation
Indices: 1559373--1559415 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
1559363 ATTTAAATGG
1559373 AAAAATTTAAATAAT-GAA
1 AAAAATTTAAATAATCGAA
*
1559391 AAAAA-TTAATTAATCGAA
1 AAAAATTTAAATAATCGAA
*
1559409 TAAAATT
1 AAAAATT
1559416 ATGAGTTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 8 0.38
18 12 0.57
19 1 0.05
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (19 bp):
AAAAATTTAAATAATCGAA
Found at i:1559416 original size:18 final size:17
Alignment explanation
Indices: 1559368--1559416 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
1559358 AAAAAATTTA
* *
1559368 AATGGAAAAATTTAAAT
1 AATGAAAAAAATTAAAT
*
1559385 AATGAAAAAAATTAATT
1 AATGAAAAAAATTAAAT
*
1559402 AATCGAATAAAATTA
1 AAT-GAAAAAAATTA
1559417 TGAGTTAGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 17 0.63
18 10 0.37
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.29
Consensus pattern (17 bp):
AATGAAAAAAATTAAAT
Found at i:1561420 original size:17 final size:17
Alignment explanation
Indices: 1561398--1561430 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1561388 AACCCTTCTG
1561398 TTGGAAATGATGATCTA
1 TTGGAAATGATGATCTA
1561415 TTGGAAATGATGATCT
1 TTGGAAATGATGATCT
1561431 GCTTTCTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.36
Consensus pattern (17 bp):
TTGGAAATGATGATCTA
Found at i:1561616 original size:17 final size:17
Alignment explanation
Indices: 1561590--1561622 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1561580 GTTGAACAAG
*
1561590 TTCTTTTCATTATGAAT
1 TTCTTCTCATTATGAAT
1561607 TTCTTCTCATTATGAA
1 TTCTTCTCATTATGAA
1561623 CCCTTCAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.15, G:0.06, T:0.55
Consensus pattern (17 bp):
TTCTTCTCATTATGAAT
Found at i:1561676 original size:97 final size:97
Alignment explanation
Indices: 1561510--1561699 Score: 240
Period size: 97 Copynumber: 2.0 Consensus size: 97
1561500 TTCGGACGAG
* * * *
1561510 TTCTTCTCATTATGAACTCCTCCATTGAAAATGTTGATCCAACTCCTTTTATGATGAATTTGAGC
1 TTCTTCTCATTATGAACTCCTCAATTGAAAATGTCGATCCAACTCATTCTATGATGAATTTGAGC
** * *
1561575 AAAAGGTTGAACAAGTTCTTTTCATTATGAAT
66 AAAAGGTCAAAAAAGTTCTTCTCATTATGAAT
* * *
1561607 TTCTTCTCATTATGAAC-CCTTCAATTGGAAATGTCGATCC-ACATCATTCTGTGATGGATTTGA
1 TTCTTCTCATTATGAACTCC-TCAATTGAAAATGTCGATCCAAC-TCATTCTATGATGAATTTGA
*
1561670 GTAAAAGGTCAAAAAAGTTCTTCTCATTAT
64 GCAAAAGGTCAAAAAAGTTCTTCTCATTAT
1561700 AAACTTATTC
Statistics
Matches: 79, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
96 4 0.05
97 75 0.95
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (97 bp):
TTCTTCTCATTATGAACTCCTCAATTGAAAATGTCGATCCAACTCATTCTATGATGAATTTGAGC
AAAAGGTCAAAAAAGTTCTTCTCATTATGAAT
Found at i:1561789 original size:216 final size:216
Alignment explanation
Indices: 1561437--1561830 Score: 533
Period size: 216 Copynumber: 1.8 Consensus size: 216
1561427 ATCTGCTTTC
* * * *
1561437 TTCTGTGATTGATTTGAACAAAAAGTCGAATAAGTTCTTCTCATTATGAAATTTCTCTCTCTCTT
1 TTCTGTGATGGATTTGAACAAAAAGTCAAAAAAGTTCTTCTCATTATGAAATTTCTCTCCCTCTT
** * *
1561502 CGGACGAGTTCTTCTCATTATGAACTCCTCCATTGAAAATGTTGATCCAACTCCTTTTATGATGA
66 CGGACGAGTTCTTCTCATTATGAACTCCTCCATTGAAAATGTCAATCCAACTCATTCTATGATGA
** * *
1561567 ATTTGAGCAAAAGGTTGAACAAGTTCTTTTCATTATGAATTTCTTCTCATTATGAACCCTTCAAT
131 ATTTGAGCAAAAGGTCAAACAAGTTCTTCTCATTATGAACTTCTTCTCATTATGAACCCTTCAAT
1561632 TGGAAATGTCGATCCACATCA
196 TGGAAATGTCGATCCACATCA
** *
1561653 TTCTGTGATGGATTTGAGTAAAAGGTCAAAAAAGTTCTTCTCATTAT-AAACTTAT-TCTCCCTC
1 TTCTGTGATGGATTTGAACAAAAAGTCAAAAAAGTTCTTCTCATTATGAAA-TT-TCTCTCCCTC
* * * * * *
1561716 TTCGGATGAGTTCTTCTCATTATGAAC-CTTTCTATTGGAAATGTCAATCCACCTCATTCTGTGA
64 TTCGGACGAGTTCTTCTCATTATGAACTC-CTCCATTGAAAATGTCAATCCAACTCATTCTATGA
* *
1561780 TGGATTTGAGCAAAAGGTCAAACATGTTCTTCTCATTATGAACTTCTTCTC
128 TGAATTTGAGCAAAAGGTCAAACAAGTTCTTCTCATTATGAACTTCTTCTC
1561831 CCTCTTCGAA
Statistics
Matches: 152, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
215 4 0.03
216 147 0.97
217 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (216 bp):
TTCTGTGATGGATTTGAACAAAAAGTCAAAAAAGTTCTTCTCATTATGAAATTTCTCTCCCTCTT
CGGACGAGTTCTTCTCATTATGAACTCCTCCATTGAAAATGTCAATCCAACTCATTCTATGATGA
ATTTGAGCAAAAGGTCAAACAAGTTCTTCTCATTATGAACTTCTTCTCATTATGAACCCTTCAAT
TGGAAATGTCGATCCACATCA
Found at i:1561818 original size:119 final size:119
Alignment explanation
Indices: 1561607--1561904 Score: 440
Period size: 119 Copynumber: 2.5 Consensus size: 119
1561597 CATTATGAAT
* * *
1561607 TTCTTCTCATTATGAACCCTTCAATTGGAAATGTCGATCCACATCATTCTGTGATGGATTTGAGT
1 TTCTTCTCATTATGAACCCTTCTATTGGAAATGTCGATCCACCTCATTCTGTGATGGATTTGAGC
* *
1561672 AAAAGGTCAAAAAAGTTCTTCTCATTATAAACTTATTCTCCCTCTTCGGATGAG
66 AAAAGGTCAAAAAAGTTCTTCTCATTATAAACTTATTCTCCCTCTTCGAACGAG
* *
1561726 TTCTTCTCATTATGAACCTTTCTATTGGAAATGTCAATCCACCTCATTCTGTGATGGATTTGAGC
1 TTCTTCTCATTATGAACCCTTCTATTGGAAATGTCGATCCACCTCATTCTGTGATGGATTTGAGC
* * * *
1561791 AAAAGGTCAAACATGTTCTTCTCATTATGAACTTCTTCTCCCTCTTCGAACGAG
66 AAAAGGTCAAAAAAGTTCTTCTCATTATAAACTTATTCTCCCTCTTCGAACGAG
* * * *
1561845 TTC-T-T-ATTATGAACCCTTCTATTGTAAATGTCGGTCCACCTCCTTCTGTGATAGATTTGA
1 TTCTTCTCATTATGAACCCTTCTATTGGAAATGTCGATCCACCTCATTCTGTGATGGATTTGA
1561905 ATCTGTAAAA
Statistics
Matches: 162, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
116 49 0.30
117 1 0.01
118 1 0.01
119 111 0.69
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.38
Consensus pattern (119 bp):
TTCTTCTCATTATGAACCCTTCTATTGGAAATGTCGATCCACCTCATTCTGTGATGGATTTGAGC
AAAAGGTCAAAAAAGTTCTTCTCATTATAAACTTATTCTCCCTCTTCGAACGAG
Found at i:1566427 original size:23 final size:23
Alignment explanation
Indices: 1566375--1566435 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
1566365 AAATTTATGA
*
1566375 AATGAATGTAAAGAATGAAGAAT
1 AATGAATGTAAAGAATGAAAAAT
*
1566398 AACGAATGTAAAGAATGTAAAAAT
1 AATGAATGTAAAGAATG-AAAAAT
*
1566422 -ATGAATGCAAAGAA
1 AATGAATGTAAAGAA
1566436 CGATTTCCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 28 0.85
24 5 0.15
ACGTcount: A:0.57, C:0.03, G:0.20, T:0.20
Consensus pattern (23 bp):
AATGAATGTAAAGAATGAAAAAT
Found at i:1578805 original size:136 final size:138
Alignment explanation
Indices: 1578447--1578843 Score: 415
Period size: 139 Copynumber: 2.9 Consensus size: 138
1578437 TAGCGAGGAT
* * * ** * * * * *
1578447 CAAATAAAAAATTCTCCTAGATAAAAGGACTAGGTGTGAAACTAAACCTACAATGGAGGCTCTAA
1 CAAATTAAAAATTCCCCTAAATTTAAGGACTAAGTTTGAAATTAAACATAAAATGGAGGCTCT-A
* * * * * *
1578512 AAATTAACTTAATCAATTTTAACCAATTATTTAATTCAAATAATTAAAATGGACCCTCGAGCAAA
65 ATATTAACCTAATCAATTTTAACCAATTATTTGATTCGAATAATTAAAATGGAACCTCAAGCAAA
* *
1578577 AATGAGGAC
130 AACGAGAAC
** ** * **
1578586 TTAATTAAAAATTTGCCTAAATTTAAGGACTAAGTTTGAAATTAAACCTAAAATTAAGGCTCTAA
1 CAAATTAAAAATTCCCCTAAATTTAAGGACTAAGTTTGAAATTAAACATAAAATGGAGGCTCTAA
* * * * *
1578651 TATTAATCCTAATTAATTTTAATCATTTATGTGATTCGAATAATTAAAATAGAACCTCAAGCAAA
66 TATTAA-CCTAATCAATTTTAACCAATTATTTGATTCGAATAATTAAAATGGAACCTCAAGCAAA
** *
1578716 CGCGATAAC
130 AACGAGAAC
* *
1578725 CAAATTAAAAA-TCCCCT-AA-TTAAGGATTAAGTTTGAAATTAAGCATAAAATGGAGGCTCTAA
1 CAAATTAAAAATTCCCCTAAATTTAAGGACTAAGTTTGAAATTAAACATAAAATGGAGGCTCTAA
*
1578787 TTATTAACCTAGTCAATTTTAACCAATTATTTGATTCG-ATAATTAAAATGGAACCTC
66 -TATTAACCTAATCAATTTTAACCAATTATTTGATTCGAATAATTAAAATGGAACCTC
1578844 TACTAGATCC
Statistics
Matches: 211, Mismatches: 45, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
135 18 0.09
136 64 0.30
137 8 0.04
138 11 0.05
139 110 0.52
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (138 bp):
CAAATTAAAAATTCCCCTAAATTTAAGGACTAAGTTTGAAATTAAACATAAAATGGAGGCTCTAA
TATTAACCTAATCAATTTTAACCAATTATTTGATTCGAATAATTAAAATGGAACCTCAAGCAAAA
ACGAGAAC
Found at i:1579772 original size:15 final size:15
Alignment explanation
Indices: 1579752--1579802 Score: 75
Period size: 15 Copynumber: 3.3 Consensus size: 15
1579742 TATTTAAGGA
1579752 AAAAATTTAAATAAC
1 AAAAATTTAAATAAC
**
1579767 AAAAATTTAAATGGC
1 AAAAATTTAAATAAC
1579782 AAAAATTTAAATAAC
1 AAAAATTTAAATAAC
1579797 GAAAAA
1 -AAAAA
1579803 ATAAATCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
15 26 0.84
16 5 0.16
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (15 bp):
AAAAATTTAAATAAC
Found at i:1579808 original size:30 final size:30
Alignment explanation
Indices: 1579752--1579808 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1579742 TATTTAAGGA
*
1579752 AAAAATTTAAATAACAAAAATTTAAATGGC
1 AAAAATTTAAATAACAAAAATATAAATGGC
1579782 AAAAATTTAAATAACGAAAAA-ATAAAT
1 AAAAATTTAAATAAC-AAAAATATAAAT
1579809 CAAACGAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.25
Consensus pattern (30 bp):
AAAAATTTAAATAACAAAAATATAAATGGC
Found at i:1579964 original size:23 final size:22
Alignment explanation
Indices: 1579929--1579981 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
1579919 AATATATTTT
*
1579929 AAAAGTTAGATGTTAGAAGTTA
1 AAAAATTAGATGTTAGAAGTTA
* **
1579951 GAAAATTAGCATGTTAGCGGTTA
1 AAAAATTAG-ATGTTAGAAGTTA
1579974 AAAAATTA
1 AAAAATTA
1579982 AAATTTTACT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.45, C:0.04, G:0.21, T:0.30
Consensus pattern (22 bp):
AAAAATTAGATGTTAGAAGTTA
Found at i:1582024 original size:10 final size:10
Alignment explanation
Indices: 1581997--1582209 Score: 50
Period size: 11 Copynumber: 18.4 Consensus size: 10
1581987 ATTAATAAAC
*
1581997 TAAAGAAAAA
1 TAAAAAAAAA
1582007 TAAAAAAAGGAAA
1 T-AAAAAA--AAA
1582020 TAAAAAAAAA
1 TAAAAAAAAA
1582030 TAAAAAAGGAAAA
1 T-AAAAA--AAAA
1582043 TAAGATAAAGAAA
1 TAA-A-AAA-AAA
1582056 -AGACATAAAAAA
1 TA-A-A-AAAAAA
*
1582068 TAAAATAAAGA
1 TAAAA-AAAAA
1582079 TAAAAAATAAA
1 TAAAAAA-AAA
1582090 TAAAATAAAGAACA
1 T-AAA-AAA-AA-A
1582104 TAAAAAACAAAA
1 T-AAAAA-AAAA
*
1582116 GAAATAAAAAAA
1 -TAA-AAAAAAA
* *
1582128 TGAAGAAAAA
1 TAAAAAAAAA
1582138 TAAATAAAATAA
1 TAAA-AAAA-AA
*
1582150 TCAAAATAAAGA
1 T-AAAA-AAAAA
**
1582162 TAACGAGCAAAA
1 TAA--AAAAAAA
*
1582174 TAAAATAAAA
1 TAAAAAAAAA
*
1582184 TAAATAAATAA
1 TAAA-AAAAAA
*
1582195 TAAATAATAAA
1 TAAA-AAAAAA
1582206 TAAA
1 TAAA
1582210 TGAAAATACT
Statistics
Matches: 156, Mismatches: 21, Indels: 51
0.68 0.09 0.22
Matches are distributed among these distances:
10 26 0.17
11 46 0.29
12 36 0.23
13 39 0.25
14 9 0.06
ACGTcount: A:0.75, C:0.03, G:0.08, T:0.15
Consensus pattern (10 bp):
TAAAAAAAAA
Found at i:1582036 original size:9 final size:9
Alignment explanation
Indices: 1582017--1582368 Score: 63
Period size: 9 Copynumber: 37.0 Consensus size: 9
1582007 TAAAAAAAGG
1582017 AAATAAAAAA
1 AAAT-AAAAA
1582027 AAATAAAAA
1 AAATAAAAA
* *
1582036 AGGA-AAATA
1 A-AATAAAAA
*
1582045 AGATAAAGAA
1 AAATAAA-AA
* *
1582055 AAGACATAAA
1 AA-ATAAAAA
*
1582065 AAATAAAAT
1 AAATAAAAA
* *
1582074 AAAGATAAA
1 AAATAAAAA
*
1582083 AAATAAATA
1 AAATAAAAA
*
1582092 AAATAAAGA
1 AAATAAAAA
*
1582101 ACAT--AAA
1 AAATAAAAA
* *
1582108 AAACAAAAG
1 AAATAAAAA
1582117 AAAT-AAAA
1 AAATAAAAA
*
1582125 AAATGAAGAA
1 AAAT-AAAAA
*
1582135 AAATAAATA
1 AAATAAAAA
**
1582144 AAATAATCA
1 AAATAAAAA
1582153 AAATAAAGATA
1 AAATAAA-A-A
**
1582164 ACGAGCAAAATA
1 A--AATAAAA-A
*
1582176 AAATAAAAT
1 AAATAAAAA
1582185 AAATAAATAA
1 AAATAAA-AA
1582195 TAAATAATAAA
1 -AAATAA-AAA
1582206 TAAATGAAAATA
1 -AAAT-AAAA-A
* **
1582218 CTAATAATAGT
1 -AAATAA-AAA
*
1582229 ATATAAATAA
1 AAATAAA-AA
1582239 TAAATAAAAA
1 -AAATAAAAA
*
1582249 AACA-AGAGAA
1 AA-ATA-AAAA
1582259 AAATACAAATGA
1 AAATA-AAA--A
* *
1582271 AAATTAAAT
1 AAATAAAAA
*
1582280 ATATAAATAA
1 AAATAAA-AA
* * *
1582290 AACTAATAT
1 AAATAAAAA
*
1582299 AAA-AAATA
1 AAATAAAAA
1582307 AAATAAGAAA
1 AAATAA-AAA
*
1582317 AGA-AAAAA
1 AAATAAAAA
* *
1582325 AATTAAAGA
1 AAATAAAAA
*
1582334 AAA-GAAAA
1 AAATAAAAA
*
1582342 AAATAAATA
1 AAATAAAAA
*
1582351 AAATAAGAA
1 AAATAAAAA
1582360 AAATAAAAA
1 AAATAAAAA
1582369 GTAAATATAT
Statistics
Matches: 238, Mismatches: 74, Indels: 61
0.64 0.20 0.16
Matches are distributed among these distances:
7 4 0.02
8 24 0.10
9 110 0.46
10 48 0.20
11 31 0.13
12 17 0.07
13 4 0.02
ACGTcount: A:0.74, C:0.03, G:0.07, T:0.17
Consensus pattern (9 bp):
AAATAAAAA
Found at i:1582042 original size:13 final size:13
Alignment explanation
Indices: 1581998--1582045 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
1581988 TTAATAAACT
*
1581998 AAAGAAAAATAAAA
1 AAAGGAAAAT-AAA
1582012 AAAGG-AAAT-AA
1 AAAGGAAAATAAA
1582023 AAA--AAAATAAA
1 AAAGGAAAATAAA
1582034 AAAGGAAAATAA
1 AAAGGAAAATAA
1582046 GATAAAGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
10 4 0.14
11 10 0.34
13 11 0.38
14 4 0.14
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.08
Consensus pattern (13 bp):
AAAGGAAAATAAA
Found at i:1582045 original size:23 final size:23
Alignment explanation
Indices: 1581997--1582041 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
1581987 ATTAATAAAC
*
1581997 TAAAGAAAAATAAAAAAAGGAAA
1 TAAAAAAAAATAAAAAAAGGAAA
1582020 TAAAAAAAAAT-AAAAAAGGAAA
1 TAAAAAAAAATAAAAAAAGGAAA
1582042 ATAAGATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (23 bp):
TAAAAAAAAATAAAAAAAGGAAA
Found at i:1582075 original size:25 final size:22
Alignment explanation
Indices: 1582008--1582215 Score: 84
Period size: 22 Copynumber: 9.2 Consensus size: 22
1581998 AAAGAAAAAT
**
1582008 AAAAAAAGGAAATAAAA-AAA-
1 AAAAAAAAAAAATAAAATAAAG
*
1582028 AATAAAAAAGGAAAATAAGATAAAG
1 AA-AAAAAA--AAAATAAAATAAAG
1582053 AAAAGACATAAAAAATAAAATAAAG
1 AAAA-A-A-AAAAAATAAAATAAAG
* *
1582078 ATAAAAAATAAATAAAATAAAG
1 AAAAAAAAAAAATAAAATAAAG
* * * * *
1582100 -AACATAAAAAACAAAAGAAAT
1 AAAAAAAAAAAATAAAATAAAG
* * *
1582121 AAAAAAATGAAGA-AAAATAAAT
1 AAAAAAA-AAAAATAAAATAAAG
** *
1582143 AAAATAATCAAAATAAAGATAACG
1 AAAA-AAAAAAAATAAA-ATAAAG
** * *
1582167 AGCAAAATAAAATAAAATAAAT
1 AAAAAAAAAAAATAAAATAAAG
* *
1582189 AAATAATAAATAAT-AAATAAATG
1 AAA-AAAAAAAAATAAAATAAA-G
1582212 AAAA
1 AAAA
1582216 TACTAATAAT
Statistics
Matches: 138, Mismatches: 35, Indels: 28
0.69 0.17 0.14
Matches are distributed among these distances:
20 2 0.01
21 19 0.14
22 47 0.34
23 36 0.26
24 12 0.09
25 19 0.14
26 1 0.01
27 2 0.01
ACGTcount: A:0.75, C:0.03, G:0.08, T:0.14
Consensus pattern (22 bp):
AAAAAAAAAAAATAAAATAAAG
Found at i:1582081 original size:18 final size:17
Alignment explanation
Indices: 1582060--1582373 Score: 102
Period size: 18 Copynumber: 17.7 Consensus size: 17
1582050 AAGAAAAGAC
1582060 ATAAAAAATAAAATAAA
1 ATAAAAAATAAAATAAA
1582077 GATAAAAAAT-AAATAAA
1 -ATAAAAAATAAAATAAA
1582094 ATAAAGAACATAAAA-AACA
1 ATAAA-AA-ATAAAATAA-A
*
1582113 A-AAGAAAT-AAA-AAA
1 ATAAAAAATAAAATAAA
1582127 ATGAAGAAAA-ATAAATAAA
1 AT-AA-AAAATA-AAATAAA
*
1582146 ATAATCAAAATAAAGATAACG
1 ATAA--AAAATAAA-ATAA-A
**
1582167 A-GCAAAATAAAATAAA
1 ATAAAAAATAAAATAAA
1582183 ATAAATAAAT--AAT-AA
1 ATAAA-AAATAAAATAAA
*
1582198 ATAATAAAT-AAATGAAA
1 ATAAAAAATAAAAT-AAA
* **
1582215 ATACTAATAATAGTATATAA
1 ATA--AAAAATAAAATA-AA
* *
1582235 ATAATAAATAAAAAAACA
1 ATAAAAAATAAAATAA-A
*
1582253 AGAGAAAAATACAAATGAAA
1 ATA-AAAAATA-AAAT-AAA
* *
1582273 ATTAAATATATAAATAAA
1 ATAAAAAATA-AAATAAA
*
1582291 ACTAATATAA-AAAATAAA
1 A-TAA-AAAATAAAATAAA
*
1582309 ATAAGAAAAGAAAA-AAA
1 ATAA-AAAATAAAATAAA
1582326 ATTAAAGAAA-AGAAA-AAA
1 A-TAAA-AAATA-AAATAAA
*
1582344 ATAAATAAAATAAGA-AAA
1 AT-AA-AAAATAAAATAAA
*
1582362 ATAAAAAGTAAA
1 ATAAAAAATAAA
1582374 TATATGGAAA
Statistics
Matches: 226, Mismatches: 34, Indels: 74
0.68 0.10 0.22
Matches are distributed among these distances:
14 6 0.03
15 14 0.06
16 19 0.08
17 40 0.18
18 83 0.37
19 42 0.19
20 19 0.08
21 3 0.01
ACGTcount: A:0.73, C:0.03, G:0.06, T:0.18
Consensus pattern (17 bp):
ATAAAAAATAAAATAAA
Found at i:1582086 original size:43 final size:42
Alignment explanation
Indices: 1582006--1582164 Score: 122
Period size: 43 Copynumber: 3.8 Consensus size: 42
1581996 CTAAAGAAAA
*
1582006 ATAAAAAAAGGAAAT-AAAAA-AAAATAAA-A-AAGGAAAATAAG
1 ATAAAAAAA-GACATAAAAAATAAAATAAAGATAA--AAAATAAG
1582047 ATAAAGAAAAGACATAAAAAATAAAATAAAGATAAAAAATAA-
1 ATAAA-AAAAGACATAAAAAATAAAATAAAGATAAAAAATAAG
* * *
1582089 ATAAAATAAAGAACATAAAAAACAAAAGAAATA-AAAAAATGAAG
1 ATAAAA-AAAG-ACATAAAAAATAAAATAAAGATAAAAAAT-AAG
*
1582133 --AAAAATA-A-ATAAAATAATCAAAATAAAGATAA
1 ATAAAAAAAGACATAAAA-AAT-AAAATAAAGATAA
1582165 CGAGCAAAAT
Statistics
Matches: 98, Mismatches: 8, Indels: 24
0.75 0.06 0.18
Matches are distributed among these distances:
38 6 0.06
39 3 0.03
40 8 0.08
41 14 0.14
42 29 0.30
43 35 0.36
44 1 0.01
45 2 0.02
ACGTcount: A:0.76, C:0.03, G:0.08, T:0.13
Consensus pattern (42 bp):
ATAAAAAAAGACATAAAAAATAAAATAAAGATAAAAAATAAG
Found at i:1582190 original size:4 final size:4
Alignment explanation
Indices: 1582171--1582246 Score: 50
Period size: 4 Copynumber: 17.8 Consensus size: 4
1582161 ATAACGAGCA
1582171 AAAT AAAAT AAAAT AAAT AAAT -AAT AAAT -AAT AAAT AAAT GAAAAT
1 AAAT -AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT --AAAT
*
1582217 ACTAAT AATAGT ATAT AAAT -AAT AAAT AAA
1 A--AAT AA-A-T AAAT AAAT AAAT AAAT AAA
1582247 AAAACAAGAG
Statistics
Matches: 60, Mismatches: 2, Indels: 19
0.74 0.02 0.23
Matches are distributed among these distances:
3 9 0.15
4 30 0.50
5 11 0.18
6 10 0.17
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:1582198 original size:7 final size:7
Alignment explanation
Indices: 1582181--1582245 Score: 53
Period size: 7 Copynumber: 8.9 Consensus size: 7
1582171 AAATAAAATA
1582181 AAATAAAT
1 AAAT-AAT
1582189 AAATAAT
1 AAATAAT
1582196 AAATAAT
1 AAATAAT
1582203 AAATAAAT
1 AAAT-AAT
*
1582211 GAA-AAT
1 AAATAAT
1582217 ACTAATAAT
1 A--AATAAT
*
1582226 -AGTATAT
1 AAATA-AT
1582233 AAATAAT
1 AAATAAT
1582240 AAATAA
1 AAATAA
1582246 AAAAACAAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
6 6 0.13
7 24 0.51
8 14 0.30
9 3 0.06
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.28
Consensus pattern (7 bp):
AAATAAT
Found at i:1582198 original size:11 final size:11
Alignment explanation
Indices: 1582182--1582246 Score: 55
Period size: 11 Copynumber: 5.9 Consensus size: 11
1582172 AATAAAATAA
1582182 AATAAATAAAT
1 AATAAATAAAT
1582193 AATAAAT-AAT
1 AATAAATAAAT
*
1582203 AAATAAATGAA-
1 -AATAAATAAAT
1582214 AATACTAAT-AAT
1 AATA--AATAAAT
* *
1582226 AGTATATAAAT
1 AATAAATAAAT
1582237 AATAAATAAA
1 AATAAATAAA
1582247 AAAACAAGAG
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
10 9 0.20
11 27 0.61
12 8 0.18
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.28
Consensus pattern (11 bp):
AATAAATAAAT
Found at i:1582216 original size:37 final size:36
Alignment explanation
Indices: 1582171--1582250 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 36
1582161 ATAACGAGCA
1582171 AAATAAAATA-AAATAAATAA-ATAATAAATAATAAAT
1 AAATAAAATACAAAT-AATAATAT-ATAAATAATAAAT
* *
1582207 AAATGAAAATACTAATAATAGTATATAAATAATAAAT
1 AAAT-AAAATACAAATAATAATATATAAATAATAAAT
1582244 AAA-AAAA
1 AAATAAAA
1582251 CAAGAGAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
35 4 0.10
36 4 0.10
37 26 0.67
38 5 0.13
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.25
Consensus pattern (36 bp):
AAATAAAATACAAATAATAATATATAAATAATAAAT
Found at i:1582322 original size:13 final size:12
Alignment explanation
Indices: 1582297--1582368 Score: 56
Period size: 14 Copynumber: 5.6 Consensus size: 12
1582287 TAAAACTAAT
*
1582297 ATAAAAAATAAA
1 ATAAAAAAGAAA
1582309 ATAAGAAAAGAAA
1 ATAA-AAAAGAAA
*
1582322 AAAAATTAAAGAAA
1 ATAAA--AAAGAAA
*
1582336 AGAAAAAA-ATAA
1 ATAAAAAAGA-AA
1582348 ATAAAATAAGAAAA
1 ATAAAA-AAG-AAA
1582362 ATAAAAA
1 ATAAAAA
1582369 GTAAATATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
11 1 0.02
12 15 0.31
13 13 0.27
14 19 0.39
15 1 0.02
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.12
Consensus pattern (12 bp):
ATAAAAAAGAAA
Found at i:1582843 original size:3 final size:3
Alignment explanation
Indices: 1582835--1582904 Score: 106
Period size: 3 Copynumber: 23.7 Consensus size: 3
1582825 TATATATTGA
*
1582835 AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
1582882 AAT AAT AAT AAT GCT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
1582905 AAAATGGTGA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
2 2 0.03
3 58 0.97
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1583837 original size:20 final size:20
Alignment explanation
Indices: 1583808--1583846 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1583798 AGAGCCCATG
*
1583808 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
1583828 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
1583847 GTGGTGGAAA
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:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:1585144 original size:15 final size:15
Alignment explanation
Indices: 1585126--1585169 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1585116 TTAAGATAAA
*
1585126 TAAACTAAAGAAAAT
1 TAAAATAAAGAAAAT
*
1585141 TAAAATAAAGGAAAT
1 TAAAATAAAGAAAAT
* *
1585156 AAAAATAAATAAAA
1 TAAAATAAAGAAAA
1585170 AAGGAAAATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (15 bp):
TAAAATAAAGAAAAT
Found at i:1585185 original size:22 final size:22
Alignment explanation
Indices: 1585147--1585191 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1585137 AAATTAAAAT
*
1585147 AAAGGAAATAAAAATAAATAAA
1 AAAGGAAATAAAAATAAAGAAA
*
1585169 AAAGGAAA-ATAAGATAAAGAAA
1 AAAGGAAATA-AAAATAAAGAAA
1585191 A
1 A
1585192 GACATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (22 bp):
AAAGGAAATAAAAATAAAGAAA
Found at i:1585230 original size:31 final size:30
Alignment explanation
Indices: 1585118--1585231 Score: 99
Period size: 31 Copynumber: 3.7 Consensus size: 30
1585108 AGAGGCAATT
* * *
1585118 AAGATAAATAAACTAAA-GAAAATTAAAATA
1 AAGATAAA-AAAATAAATAAAAAATAAAATA
*
1585148 AAGGA-AATAAAAATAAATAAAAAAGGAAAAT-
1 AA-GATAA-AAAAATAAATAAAAAA-TAAAATA
* *
1585179 AAGATAAAGAAAAGACATAAAAAATAAAATA
1 AAGATAAA-AAAATAAATAAAAAATAAAATA
1585210 AAGATAAAAAAACTAAATAAAA
1 AAGATAAAAAAA-TAAATAAAA
1585232 TAAAGAACAT
Statistics
Matches: 67, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
30 23 0.34
31 39 0.58
32 5 0.07
ACGTcount: A:0.74, C:0.03, G:0.09, T:0.15
Consensus pattern (30 bp):
AAGATAAAAAAATAAATAAAAAATAAAATA
Found at i:1585231 original size:24 final size:25
Alignment explanation
Indices: 1585175--1585285 Score: 79
Period size: 25 Copynumber: 4.4 Consensus size: 25
1585165 TAAAAAAGGA
* *
1585175 AAATAAGATAAAGAAAAGACATAAA--
1 AAATAAAATAAAGATAAGA-A-AAACT
1585200 AAATAAAATAAAGATAA-AAAAACT
1 AAATAAAATAAAGATAAGAAAAACT
* *
1585224 AAATAAAATAAAGA-ACATAAAAACA
1 AAATAAAATAAAGATA-AGAAAAACT
* * *
1585249 AAAGAAATAAAAAAATGAAGAAAAA-T
1 AAATAAA-ATAAAGAT-AAGAAAAACT
1585275 AAATAAAATAA
1 AAATAAAATAA
1585286 TCAAAATAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
22 3 0.04
23 2 0.03
24 16 0.23
25 30 0.43
26 11 0.16
27 6 0.09
28 1 0.01
ACGTcount: A:0.76, C:0.04, G:0.07, T:0.14
Consensus pattern (25 bp):
AAATAAAATAAAGATAAGAAAAACT
Found at i:1585234 original size:5 final size:5
Alignment explanation
Indices: 1585199--1585338 Score: 52
Period size: 5 Copynumber: 28.6 Consensus size: 5
1585189 AAAGACATAA
* * *
1585199 AAAAT AAAAT AAAGAT AAAA- AAACT -AAAT AAAAT -AAAG AACAT AAAA-
1 AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
*
1585246 ACAAA- AGAAAT -AAA- AAAAT GAAGA- AAAAT -AAAT AAAAT --AAT
1 A-AAAT A-AAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT
* * *
1585287 CAAAAT AAAGAT AACAAGC AACAT AAAAT AAAAT AAAA- AATAAG AAAAT
1 -AAAAT AAA-AT AA-AA-T AAAAT AAAAT AAAAT AAAAT AA-AAT AAAAT
1585336 AAA
1 AAA
1585339 TGAAAATACT
Statistics
Matches: 102, Mismatches: 14, Indels: 38
0.66 0.09 0.25
Matches are distributed among these distances:
3 3 0.03
4 25 0.25
5 52 0.51
6 19 0.19
7 3 0.03
ACGTcount: A:0.75, C:0.05, G:0.06, T:0.14
Consensus pattern (5 bp):
AAAAT
Found at i:1585452 original size:16 final size:18
Alignment explanation
Indices: 1585413--1585471 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 18
1585403 TAAATATATA
* *
1585413 AATAAAACTAATATAAAA-
1 AATAAAATTAA-AGAAAAG
1585431 AATAAAA-T-AAGAAAAG
1 AATAAAATTAAAGAAAAG
1585447 AATAAAAATTAAAGAAAAG
1 AAT-AAAATTAAAGAAAAG
1585466 AA-AAAA
1 AATAAAA
1585472 ACAAATAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
15 5 0.14
16 4 0.11
17 9 0.25
18 8 0.22
19 10 0.28
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (18 bp):
AATAAAATTAAAGAAAAG
Found at i:1585489 original size:19 final size:21
Alignment explanation
Indices: 1585428--1585501 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 21
1585418 AACTAATATA
1585428 AAAAATAAAATAAGAAAAGAAT
1 AAAAATAAAATAAGAAAA-AAT
*
1585450 AAAAATTAAAGAAAAGAAAAAA-
1 AAAAA-TAAA-ATAAGAAAAAAT
*
1585472 ACAAATAAAATAAG-AAAAAT
1 AAAAATAAAATAAGAAAAAAT
1585492 AAAAAGTAAA
1 AAAAA-TAAA
1585502 TATATGGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
19 5 0.11
20 8 0.18
21 8 0.18
22 9 0.20
23 6 0.14
24 8 0.18
ACGTcount: A:0.78, C:0.01, G:0.08, T:0.12
Consensus pattern (21 bp):
AAAAATAAAATAAGAAAAAAT
Found at i:1585975 original size:3 final size:3
Alignment explanation
Indices: 1585967--1586029 Score: 94
Period size: 3 Copynumber: 21.7 Consensus size: 3
1585957 TATATATTGA
* *
1585967 AAT AAT AAT AAT AAC AAT AAT AA- AAT AA- AAC AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1586013 AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
1586030 ATGGTGATTA
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
2 4 0.07
3 51 0.93
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:1586959 original size:20 final size:20
Alignment explanation
Indices: 1586930--1586968 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1586920 AGAGCCCATG
*
1586930 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
1586950 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
1586969 GTGGTGGAAA
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:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:1590589 original size:16 final size:16
Alignment explanation
Indices: 1590564--1590602 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1590554 TTATGGAATG
1590564 AATG-AAAGAATAGAA-
1 AATGTAAAGAATA-AAT
1590579 AATGTAAAGAATAAAT
1 AATGTAAAGAATAAAT
1590595 AATGTAAA
1 AATGTAAA
1590603 AATGATAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.64, C:0.00, G:0.15, T:0.21
Consensus pattern (16 bp):
AATGTAAAGAATAAAT
Found at i:1590590 original size:24 final size:25
Alignment explanation
Indices: 1590563--1590624 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 25
1590553 GTTATGGAAT
1590563 GAATGAAAGAAT-AGAAAATG-TAAA
1 GAATGAAAGAATGA-AAAATGATAAA
*
1590587 GAAT-AAATAATGTAAAAATGATAAA
1 GAATGAAAGAATG-AAAAATGATAAA
1590612 GAATGTAAA-AATG
1 GAATG-AAAGAATG
1590625 TATAGAATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
23 6 0.19
24 10 0.31
25 9 0.28
26 4 0.12
27 3 0.09
ACGTcount: A:0.61, C:0.00, G:0.18, T:0.21
Consensus pattern (25 bp):
GAATGAAAGAATGAAAAATGATAAA
Found at i:1590624 original size:8 final size:9
Alignment explanation
Indices: 1590579--1590633 Score: 55
Period size: 9 Copynumber: 6.4 Consensus size: 9
1590569 AAGAATAGAA
1590579 AATGTAAAG
1 AATGTAAAG
*
1590588 AA--TAAAT
1 AATGTAAAG
1590595 AATGTAAA-
1 AATGTAAAG
1590603 AATGATAAAG
1 AATG-TAAAG
1590613 AATGTAAA-
1 AATGTAAAG
*
1590621 AATGTATAG
1 AATGTAAAG
1590630 AATG
1 AATG
1590634 ATTGCCACTT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
7 6 0.15
8 11 0.28
9 18 0.46
10 4 0.10
ACGTcount: A:0.58, C:0.00, G:0.16, T:0.25
Consensus pattern (9 bp):
AATGTAAAG
Found at i:1590631 original size:17 final size:18
Alignment explanation
Indices: 1590589--1590633 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
1590579 AATGTAAAGA
*
1590589 ATAAATAATGTAAAAATG
1 ATAAAGAATGTAAAAATG
1590607 ATAAAGAATGTAAAAATG
1 ATAAAGAATGTAAAAATG
*
1590625 -TATAGAATG
1 ATAAAGAATG
1590634 ATTGCCACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.58, C:0.00, G:0.16, T:0.27
Consensus pattern (18 bp):
ATAAAGAATGTAAAAATG
Found at i:1593025 original size:46 final size:47
Alignment explanation
Indices: 1592951--1593099 Score: 124
Period size: 47 Copynumber: 3.2 Consensus size: 47
1592941 ATCTCTACTC
* * * *
1592951 TCATGCTTTGTTCACAAAACA-AATCCTAACCTCA-TGTTATCTAGTTCT
1 TCATGC-TTGTTCAGAAAA-ATAAACCTAACATCATTATTATCTAGTT-T
* * *
1592999 T-ATTCTTGTTCAGAAAAATAAACCTAATATCATTATTTTCTAGTTT
1 TCATGCTTGTTCAGAAAAATAAACCTAACATCATTATTATCTAGTTT
* * * * * * *
1593045 TCATGCTTATTCAGAAAAATAAACTTAATAACATCATTTTCTAGTTC
1 TCATGCTTGTTCAGAAAAATAAACCTAACATCATTATTATCTAGTTT
1593092 TCATGCTT
1 TCATGCTT
1593100 TATTTGATAA
Statistics
Matches: 85, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
45 1 0.01
46 23 0.27
47 60 0.71
48 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.41
Consensus pattern (47 bp):
TCATGCTTGTTCAGAAAAATAAACCTAACATCATTATTATCTAGTTT
Found at i:1593058 original size:47 final size:47
Alignment explanation
Indices: 1592990--1593099 Score: 150
Period size: 47 Copynumber: 2.3 Consensus size: 47
1592980 CCTCATGTTA
* * * *
1592990 TCTAGTTCTT-ATTCTTGTTCAGAAAAATAAACCTAATATCATTATTT
1 TCTAGTT-TTCATGCTTATTCAGAAAAATAAACCTAATAACATCATTT
*
1593037 TCTAGTTTTCATGCTTATTCAGAAAAATAAACTTAATAACATCATTT
1 TCTAGTTTTCATGCTTATTCAGAAAAATAAACCTAATAACATCATTT
*
1593084 TCTAGTTCTCATGCTT
1 TCTAGTTTTCATGCTT
1593100 TATTTGATAA
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
46 2 0.04
47 54 0.96
ACGTcount: A:0.33, C:0.16, G:0.07, T:0.44
Consensus pattern (47 bp):
TCTAGTTTTCATGCTTATTCAGAAAAATAAACCTAATAACATCATTT
Found at i:1595620 original size:13 final size:13
Alignment explanation
Indices: 1595602--1595626 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1595592 ATTTTTGGTA
1595602 ATAATAATAATAT
1 ATAATAATAATAT
1595615 ATAATAATAATA
1 ATAATAATAATA
1595627 ATTATTATAT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATAATAATAATAT
Found at i:1604694 original size:18 final size:18
Alignment explanation
Indices: 1604671--1604707 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1604661 CGTGTTTCTG
1604671 CGTACGCGTGAGCTTCCT
1 CGTACGCGTGAGCTTCCT
1604689 CGTACGCGTGAGCTTCCT
1 CGTACGCGTGAGCTTCCT
1604707 C
1 C
1604708 TCTTTCCCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.35, G:0.27, T:0.27
Consensus pattern (18 bp):
CGTACGCGTGAGCTTCCT
Found at i:1606173 original size:2 final size:2
Alignment explanation
Indices: 1606166--1606196 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1606156 GATTAATTCC
1606166 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1606197 TAATTAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1608298 original size:135 final size:134
Alignment explanation
Indices: 1608052--1608379 Score: 462
Period size: 135 Copynumber: 2.4 Consensus size: 134
1608042 GATCAAGAAA
* ** * * *
1608052 TTTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGGTAGACTTG-TTC-CACTGTTACC
1 TTTGATTCATTCCACTATTCTTCAGGGAAGATTGAACCGAATTCGATTTGCTTCTC-TTGTTACC
* * *
1608115 ATAGAATATCAAATCTTGAAAGAGAAGGATCTGTTCCACTTCTTCTTAAGGGAAAATCAGATCTA
65 AGAGAATATCAAATCTTGAAAGAAAAGGATCTATTCCACTTCTTCTTAAGGGAAAATCAGATCTA
1608180 GGGAC
130 GGGAC
* *
1608185 TTTGATTCATTCCACTGTTCTTCAAGGAAGATTGAACCGAATTCGATTTGCTTCTCTTGTTACTC
1 TTTGATTCATTCCACTATTCTTCAGGGAAGATTGAACCGAATTCGATTTGCTTCTCTTGTTAC-C
* * * *** *
1608250 AGGGAATATCAAATCTTGAAATAAAATGATCTATTTTGCTTCTTCTTAAGGGAAAATCAGATCTG
65 AGAGAATATCAAATCTTGAAAGAAAAGGATCTATTCCACTTCTTCTTAAGGGAAAATCAGATCTA
1608315 GGGAC
130 GGGAC
1608320 TTTGATTCATTCCACTATTCTTCAGGGAAGATTGAACCGAATTCGATTTGCTTCTCTTGT
1 TTTGATTCATTCCACTATTCTTCAGGGAAGATTGAACCGAATTCGATTTGCTTCTCTTGT
1608380 CTTTAAGAAT
Statistics
Matches: 172, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
133 43 0.25
134 9 0.05
135 120 0.70
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (134 bp):
TTTGATTCATTCCACTATTCTTCAGGGAAGATTGAACCGAATTCGATTTGCTTCTCTTGTTACCA
GAGAATATCAAATCTTGAAAGAAAAGGATCTATTCCACTTCTTCTTAAGGGAAAATCAGATCTAG
GGAC
Found at i:1609008 original size:41 final size:42
Alignment explanation
Indices: 1608963--1609064 Score: 107
Period size: 42 Copynumber: 2.5 Consensus size: 42
1608953 AAGGTCTTAT
* * * *
1608963 AGATGGCCCAAAGGACTT-GTTATCTTGCTCAAAAGACTGAC
1 AGATGGCCCAAAGGACTTAATCATCATGCTCAAAAGACTCAC
* * * *
1609004 AGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTCAC
1 AGATGGCCCAAAGGACTTAATCATCATGCTCAAAAGACTCAC
* *
1609046 TGATGGCCCAAATGACTTA
1 AGATGGCCCAAAGGACTTA
1609065 CTAATTTTGG
Statistics
Matches: 47, Mismatches: 13, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
41 15 0.32
42 32 0.68
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.24
Consensus pattern (42 bp):
AGATGGCCCAAAGGACTTAATCATCATGCTCAAAAGACTCAC
Found at i:1609218 original size:260 final size:257
Alignment explanation
Indices: 1608675--1609444 Score: 1100
Period size: 260 Copynumber: 3.0 Consensus size: 257
1608665 GAGAAAAAAC
* *
1608675 ATGTGAAAACATCCT-CTATGAAGGTCTTATGGATAGCCAAAGGACTTATCATCTTGCTCGAAAT
1 ATGTGAAAACATCCTGC--TGAAGGTCTTATAGATGGCCAAAGGACTTATCATCTTGCTCGAAAT
* * * * * *
1608739 ACTTACAGATTACCTGAAGGATTTACTCATCATGCTTGAAAGACTTACTGATGGCTCAAAGGACT
64 ACTAACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACT
* * * * * *
1608804 TACCAATTTTGGAATTAGTTTATTGGT-AAGAAACTTTGAAAAATCGCTTTTTTACTTTTCAAAA
129 TACAAATTTTGGAAATAGTTTACTGGTAAAAAAACTTTG-GAAATCGCTTTCTTACTTTTCAAAA
*
1608868 ATTTCATTTTCTGAAAAGATTTAAATGAGAAACTTTGGAAATTGCTTTCTCATTTTTTGAAAATA
193 ATTTCATTTTCTGAAAAGATTTAAATGAGAAACTTTGGAAATTGCTTTCTCATTTTTTAAAAATA
* * * * *
1608933 ATGTGGAAACATCCTGCTCGAAGGTCTTATAGATGGCCCAAAGGACTTGTTATCTTGCTCAAAAG
1 ATGTGAAAACATCCTGCT-GAAGGTCTTATAGATGG-CCAAAGGACTTATCATCTTGCTCGAAAT
* * *
1608998 ACTGACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTCACTGATGGCCCAAATGACT
64 ACTAACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACT
* *
1609063 TACTAATTTTGGAAATAGTTTACTAGGTAAAAAAACCTTGGAAATCGCTTTCTTACTTTTCAAAA
129 TACAAATTTTGGAAATAGTTTACT-GGTAAAAAAACTTTGGAAATCGCTTTCTTACTTTTCAAAA
*
1609128 ATTTCATTTTCTGAAAAGATTTAAATGAGAAACTTTGGAAATTTCTTTCTC-TTTTTTCAAAAAT
193 ATTTCATTTTCTGAAAAGATTTAAATGAGAAACTTTGGAAATTGCTTTCTCATTTTTT-AAAAAT
*
1609192 C
257 A
* * *
1609193 ATTTGAAAACATCTTGCCTGAAGGTCTTATAGATGGCCATAAGGACTTATCATATTGCTCGAAAT
1 ATGTGAAAACATCCTG-CTGAAGGTCTTATAGATGGCCA-AAGGACTTATCATCTTGCTCGAAAT
*
1609258 ACTAACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTAATGGCCCAAAGGACT
64 ACTAACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACT
* *
1609323 TACAAATTTTGGAAATAATTTACTGGATAAGAAAA-TTTGGAAATCGCTTTCTTACTTTTCAAAA
129 TACAAATTTTGGAAATAGTTTACTGG-TAAAAAAACTTTGGAAATCGCTTTCTTACTTTTCAAAA
*
1609387 ATTTCATTTTCT-AAAATGATTTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTT
193 ATTTCATTTTCTGAAAA-GATTTAAATGAGAAACTTTGGAAATTGCTTTCTCATTTTTT
1609445 TGGAAATCAA
Statistics
Matches: 458, Mismatches: 43, Indels: 20
0.88 0.08 0.04
Matches are distributed among these distances:
257 1 0.00
258 33 0.07
259 186 0.41
260 227 0.50
261 11 0.02
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (257 bp):
ATGTGAAAACATCCTGCTGAAGGTCTTATAGATGGCCAAAGGACTTATCATCTTGCTCGAAATAC
TAACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTA
CAAATTTTGGAAATAGTTTACTGGTAAAAAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATT
TCATTTTCTGAAAAGATTTAAATGAGAAACTTTGGAAATTGCTTTCTCATTTTTTAAAAATA
Found at i:1611207 original size:3 final size:3
Alignment explanation
Indices: 1611188--1611234 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
1611178 GCCTGCAAAG
* * *
1611188 ATA ATA A-A AAA ATTA ATA ATA ACA ATA ATA ATA ATA ATG ATA ATA
1 ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1611233 AT
1 AT
1611235 TGGTTTCGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.89
4 2 0.05
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
ATA
Done.