Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 16 of 228
Found at i:5520528 original size:34 final size:34
Alignment explanation
Indices: 5520489--5520558 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
5520479 TGGATGGCAC
*
5520489 CAAATGTAAGTAAGAACCAACTCGCAATTGTACA
1 CAAATGTAAGTAAGAACCAACTCACAATTGTACA
5520523 CAAATGTAAGTAAGAACCAACTCACAATTGTACA
1 CAAATGTAAGTAAGAACCAACTCACAATTGTACA
5520557 CA
1 CA
5520559 TTTGCAACCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.46, C:0.21, G:0.13, T:0.20
Consensus pattern (34 bp):
CAAATGTAAGTAAGAACCAACTCACAATTGTACA
Found at i:5522110 original size:16 final size:16
Alignment explanation
Indices: 5522086--5522118 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5522076 GGGAATAACC
5522086 CAGAGCACAATCTAAA
1 CAGAGCACAATCTAAA
*
5522102 CAGATCACAATCTAAA
1 CAGAGCACAATCTAAA
5522118 C
1 C
5522119 TTCATGCTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.48, C:0.27, G:0.09, T:0.15
Consensus pattern (16 bp):
CAGAGCACAATCTAAA
Found at i:5524558 original size:14 final size:14
Alignment explanation
Indices: 5524506--5524559 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 14
5524496 ATTCTTAACA
5524506 AATATTTGAA-TTA-
1 AATATTT-AATTTAT
5524519 AATATTTAATATTA-
1 AATATTTAAT-TTAT
5524533 AAT-TTTAATTTAT
1 AATATTTAATTTAT
*
5524546 AATATTTACTTTAT
1 AATATTTAATTTAT
5524560 TCTTTTCAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
12 5 0.14
13 16 0.44
14 15 0.42
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (14 bp):
AATATTTAATTTAT
Found at i:5526854 original size:41 final size:41
Alignment explanation
Indices: 5526796--5526908 Score: 147
Period size: 41 Copynumber: 2.8 Consensus size: 41
5526786 TGATTCGGTA
* * *
5526796 CACCGGCTTTTAA-CCTGCTAGACATATAGTCCGAAATGTAT
1 CACCGGC-ATTAAGCCTGCTAGACATAAAGTCCGAAATATAT
* * *
5526837 CACCGGCATTAAGCCTGCTAGACATAAAGTCTGAATTATTT
1 CACCGGCATTAAGCCTGCTAGACATAAAGTCCGAAATATAT
*
5526878 CACCGGCATCAAGCCTGCTAGACATAAAGTC
1 CACCGGCATTAAGCCTGCTAGACATAAAGTC
5526909 TGTATTACAT
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
40 4 0.06
41 60 0.94
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACATAAAGTCCGAAATATAT
Found at i:5526909 original size:41 final size:41
Alignment explanation
Indices: 5526809--5526915 Score: 151
Period size: 41 Copynumber: 2.6 Consensus size: 41
5526799 CGGCTTTTAA
* * * * *
5526809 CCTGCTAGACATATAGTCCGAAATGTATCACCGGCATTAAG
1 CCTGCTAGACATAAAGTCTGAATTATATCACCGGCATCAAG
*
5526850 CCTGCTAGACATAAAGTCTGAATTATTTCACCGGCATCAAG
1 CCTGCTAGACATAAAGTCTGAATTATATCACCGGCATCAAG
*
5526891 CCTGCTAGACATAAAGTCTGTATTA
1 CCTGCTAGACATAAAGTCTGAATTA
5526916 CATTCGATCA
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (41 bp):
CCTGCTAGACATAAAGTCTGAATTATATCACCGGCATCAAG
Found at i:5527186 original size:12 final size:12
Alignment explanation
Indices: 5527169--5527222 Score: 63
Period size: 12 Copynumber: 4.2 Consensus size: 12
5527159 CTCAAAAACT
5527169 TATATATATACA
1 TATATATATACA
*
5527181 TATATATATTCGA
1 TATATATATAC-A
*
5527194 GTATTATACATACA
1 -TA-TATATATACA
5527208 TATATATATACA
1 TATATATATACA
5527220 TAT
1 TAT
5527223 CTTTGACTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
12 22 0.63
13 3 0.09
14 3 0.09
15 7 0.20
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (12 bp):
TATATATATACA
Found at i:5529392 original size:41 final size:41
Alignment explanation
Indices: 5529324--5529524 Score: 289
Period size: 41 Copynumber: 4.9 Consensus size: 41
5529314 TGACTTTTCG
* *
5529324 TGGGCTTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGTTC
1 TGGGATTTAGCGGCGTTTTTATTTAAGCGCCGCTAATGTTC
*
5529365 TGGGATTTAGCGGCGTTTTGT-TTTAAGCGCCACTAATGTTC
1 TGGGATTTAGCGGCGTTTT-TATTTAAGCGCCGCTAATGTTC
*
5529406 TGGGATTTAGCGGCGTTTTTATTTAAGCGCAGCTAATGTTC
1 TGGGATTTAGCGGCGTTTTTATTTAAGCGCCGCTAATGTTC
* *
5529447 TGGGATTTAGTGGCGTTTTTAATTAAGCGCCGCTAATGTTC
1 TGGGATTTAGCGGCGTTTTTATTTAAGCGCCGCTAATGTTC
* * *
5529488 TGGGCTTTAGCAGCGTTTTTATTGATA-CGCCGCTAAT
1 TGGGATTTAGCGGCGTTTTTATTTA-AGCGCCGCTAAT
5529525 TCGCAGGCCT
Statistics
Matches: 144, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
40 1 0.01
41 141 0.98
42 2 0.01
ACGTcount: A:0.18, C:0.17, G:0.27, T:0.38
Consensus pattern (41 bp):
TGGGATTTAGCGGCGTTTTTATTTAAGCGCCGCTAATGTTC
Found at i:5529538 original size:82 final size:82
Alignment explanation
Indices: 5529324--5529567 Score: 228
Period size: 82 Copynumber: 3.0 Consensus size: 82
5529314 TGACTTTTCG
* * * * * * *
5529324 TGGGCTTTAGCGGCGTTTTTA-TGTAAGCGCCGCTAATGTTCTGGGATTTAGCGGCGTTTTGT-T
1 TGGGATTTAGCAGCGTTTTTATTG-AAGCGCAGCTAATGTGCAGGCATTTAGCGGCGTTTT-TAA
*
5529387 TTAAGCGCCACTAATGTTC
64 TTAAGCGCCGCTAATGTTC
* * * * * *
5529406 TGGGATTTAGCGGCGTTTTTATTTAAGCGCAGCTAATGTTCTGGGATTTAGTGGCGTTTTTAATT
1 TGGGATTTAGCAGCGTTTTTATTGAAGCGCAGCTAATGTGCAGGCATTTAGCGGCGTTTTTAATT
5529471 AAGCGCCGCTAATGTTC
66 AAGCGCCGCTAATGTTC
* * *
5529488 TGGGCTTTAGCAGCGTTTTTATTGATA-CGCCGCTAAT-TCGCAGGCCTTTAGCGGCGCTTTTTT
1 TGGGATTTAGCAGCGTTTTTATTGA-AGCGCAGCTAATGT-GCAGGCATTTAGCGGCG--TTTTT
* *
5529551 AA-AAAACGCCGCTAATG
62 AATTAAGCGCCGCTAATG
5529568 CTCTTCATTT
Statistics
Matches: 139, Mismatches: 17, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
81 2 0.01
82 115 0.83
83 15 0.11
84 7 0.05
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.36
Consensus pattern (82 bp):
TGGGATTTAGCAGCGTTTTTATTGAAGCGCAGCTAATGTGCAGGCATTTAGCGGCGTTTTTAATT
AAGCGCCGCTAATGTTC
Found at i:5529578 original size:123 final size:123
Alignment explanation
Indices: 5529329--5529589 Score: 273
Period size: 123 Copynumber: 2.1 Consensus size: 123
5529319 TTTCGTGGGC
* * *
5529329 TTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGTTCTGGGATTTAGCGGCGTTTTGTTTTAAGCG
1 TTTAGTGGCGTTTTTATGTAAGCGCCGCTAATGTTCTGGGATTTAGCAGCGTTTTGTTTGAAGCG
* * * ** * * *
5529394 CCACTAATGTTCTGGGATTTAGCGGCGTTTTTATTTAAGCGCAGCTAATGTTCTGGGA
66 CCACTAATGTGCAGGCATTTAGCGGCGTTTTTATAAAAACGCAGCTAATGCTCTGGCA
*
5529452 TTTAGTGGCGTTTTTAAT-TAAGCGCCGCTAATGTTCTGGGCTTTAGCAGCGTTTT-TATTGATA
1 TTTAGTGGCGTTTTT-ATGTAAGCGCCGCTAATGTTCTGGGATTTAGCAGCGTTTTGT-TTGA-A
* * * *
5529515 -CGCCGCTAAT-TCGCAGGCCTTTAGCGGCGCTTTTT-TAAAAAACGCCGCTAATGCTCT-TCA
63 GCGCCACTAATGT-GCAGGCATTTAGCGGCG-TTTTTAT-AAAAACGCAGCTAATGCTCTGGCA
*
5529575 TTTAGTGGCATTTTT
1 TTTAGTGGCGTTTTT
5529590 GGAAAGAGCC
Statistics
Matches: 115, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
122 2 0.02
123 90 0.78
124 23 0.20
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (123 bp):
TTTAGTGGCGTTTTTATGTAAGCGCCGCTAATGTTCTGGGATTTAGCAGCGTTTTGTTTGAAGCG
CCACTAATGTGCAGGCATTTAGCGGCGTTTTTATAAAAACGCAGCTAATGCTCTGGCA
Found at i:5529981 original size:16 final size:16
Alignment explanation
Indices: 5529960--5530029 Score: 56
Period size: 16 Copynumber: 4.4 Consensus size: 16
5529950 CTATAGTATG
5529960 TAGTTTAAGGGTTTTA
1 TAGTTTAAGGGTTTTA
*
5529976 TAGTTTAA-GGTTTAA
1 TAGTTTAAGGGTTTTA
** * *
5529991 T-GTTTACTATAG-TATG
1 TAGTTTA--AGGGTTTTA
5530007 TAGTTTAAGGGTTTTA
1 TAGTTTAAGGGTTTTA
5530023 TAGTTTA
1 TAGTTTA
5530030 TGGTTTAGGG
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
14 5 0.12
15 9 0.22
16 20 0.50
17 6 0.15
ACGTcount: A:0.27, C:0.01, G:0.21, T:0.50
Consensus pattern (16 bp):
TAGTTTAAGGGTTTTA
Found at i:5529988 original size:23 final size:23
Alignment explanation
Indices: 5529962--5530042 Score: 80
Period size: 23 Copynumber: 3.5 Consensus size: 23
5529952 ATAGTATGTA
5529962 GTTTAAGGGTTTTATAGTTTAAG
1 GTTTAAGGGTTTTATAGTTTAAG
*
5529985 GTTTAA-TGTTTACTATAGTATGT-A-
1 GTTTAAGGGTTT--TATAGT-T-TAAG
*
5530009 GTTTAAGGGTTTTATAGTTTATG
1 GTTTAAGGGTTTTATAGTTTAAG
5530032 GTTT-AGGGTTT
1 GTTTAAGGGTTT
5530043 GTTATATTGG
Statistics
Matches: 48, Mismatches: 3, Indels: 15
0.73 0.05 0.23
Matches are distributed among these distances:
21 1 0.02
22 12 0.25
23 16 0.33
24 12 0.25
25 6 0.12
26 1 0.02
ACGTcount: A:0.23, C:0.01, G:0.25, T:0.51
Consensus pattern (23 bp):
GTTTAAGGGTTTTATAGTTTAAG
Found at i:5530078 original size:22 final size:21
Alignment explanation
Indices: 5530053--5530093 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
5530043 GTTATATTGG
5530053 GTTTGTGA-TTTAGTGTTTTAAA
1 GTTTG-GAGTTTAGT-TTTTAAA
5530075 GTTTGGAGTTTAGTTTTTA
1 GTTTGGAGTTTAGTTTTTA
5530094 TAGTCAGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.20, C:0.00, G:0.24, T:0.56
Consensus pattern (21 bp):
GTTTGGAGTTTAGTTTTTAAA
Found at i:5534767 original size:66 final size:66
Alignment explanation
Indices: 5534691--5534826 Score: 211
Period size: 66 Copynumber: 2.1 Consensus size: 66
5534681 GACCACAGTT
* * * *
5534691 GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAGAG-TAGATGCGGCAGCGAGAGAAG
1 GAGGTTCAAAAGAAATATGAAGAACTCCAGCGACAACTTAAAGCT-GATGCGACAGCCAGAGAAG
5534755 CA
65 CA
*
5534757 GAGGTTCAAAAGAAATATGAAGAACTCCAGCGACAACTTAAAGCTGATGCGACATCCAGAGAAGC
1 GAGGTTCAAAAGAAATATGAAGAACTCCAGCGACAACTTAAAGCTGATGCGACAGCCAGAGAAGC
5534822 A
66 A
5534823 GAGG
1 GAGG
5534827 CTGCAGCGAC
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
66 63 0.98
67 1 0.02
ACGTcount: A:0.41, C:0.18, G:0.26, T:0.15
Consensus pattern (66 bp):
GAGGTTCAAAAGAAATATGAAGAACTCCAGCGACAACTTAAAGCTGATGCGACAGCCAGAGAAGC
A
Found at i:5535223 original size:43 final size:43
Alignment explanation
Indices: 5535175--5535307 Score: 198
Period size: 43 Copynumber: 3.1 Consensus size: 43
5535165 AACAAAAAGT
* *
5535175 GGCGTTTGTGAAAAAAGCGCCACTAAAGAACAT-TAGCTTTAGC
1 GGCGTTTGTGAAAAAAGCGCCGCTAAAGAACATGT-TCTTTAGC
*
5535218 GGCGTTTGTGTAAAAAGCGCCGCTAAAGAACATGTTCTTTAGC
1 GGCGTTTGTGAAAAAAGCGCCGCTAAAGAACATGTTCTTTAGC
*
5535261 GGCGTTTGT-ATAAAATGCGCCGCTAAAGAACATGTTCTTTAGC
1 GGCGTTTGTGA-AAAAAGCGCCGCTAAAGAACATGTTCTTTAGC
5535304 GGCG
1 GGCG
5535308 CTTTTAAAAA
Statistics
Matches: 83, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
43 82 0.99
44 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (43 bp):
GGCGTTTGTGAAAAAAGCGCCGCTAAAGAACATGTTCTTTAGC
Found at i:5545631 original size:119 final size:119
Alignment explanation
Indices: 5545420--5545658 Score: 478
Period size: 119 Copynumber: 2.0 Consensus size: 119
5545410 AGAAAAAGAA
5545420 CCTTCTTTGATGCTTCTGAGTTCAACATTGATATCAACCAGGTTACTATATGCCAAAAGCCAATC
1 CCTTCTTTGATGCTTCTGAGTTCAACATTGATATCAACCAGGTTACTATATGCCAAAAGCCAATC
5545485 ATTACAACCAAAAGTCAGCCGTTCATTAGTTATTTAATTTAGTAAGTTGTTTAT
66 ATTACAACCAAAAGTCAGCCGTTCATTAGTTATTTAATTTAGTAAGTTGTTTAT
5545539 CCTTCTTTGATGCTTCTGAGTTCAACATTGATATCAACCAGGTTACTATATGCCAAAAGCCAATC
1 CCTTCTTTGATGCTTCTGAGTTCAACATTGATATCAACCAGGTTACTATATGCCAAAAGCCAATC
5545604 ATTACAACCAAAAGTCAGCCGTTCATTAGTTATTTAATTTAGTAAGTTGTTTAT
66 ATTACAACCAAAAGTCAGCCGTTCATTAGTTATTTAATTTAGTAAGTTGTTTAT
5545658 C
1 C
5545659 TGTTATTTGT
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
119 120 1.00
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (119 bp):
CCTTCTTTGATGCTTCTGAGTTCAACATTGATATCAACCAGGTTACTATATGCCAAAAGCCAATC
ATTACAACCAAAAGTCAGCCGTTCATTAGTTATTTAATTTAGTAAGTTGTTTAT
Found at i:5548775 original size:6 final size:6
Alignment explanation
Indices: 5548764--5548791 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
5548754 CTTAAAACTT
5548764 TTTTTG TTTTTG TTTTTG TTTTTG TTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTT
5548792 CTTCTGTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (6 bp):
TTTTTG
Found at i:5550978 original size:22 final size:21
Alignment explanation
Indices: 5550942--5550986 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
5550932 ATATATATTT
** *
5550942 TAAAATTTTTTATTAATTTTTA
1 TAAAATTTTAAATT-ATTTATA
5550964 TAAAATTTTAAATTATTTATA
1 TAAAATTTTAAATTATTTATA
5550985 TA
1 TA
5550987 CTTATTGTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TAAAATTTTAAATTATTTATA
Found at i:5550981 original size:21 final size:21
Alignment explanation
Indices: 5550925--5550986 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
5550915 GAACTAATTT
*
5550925 ATTTTTAATATATATTT-TAAA
1 ATTTTTAAT-TATTTTTATAAA
*
5550946 ATTTTTTATTAATTTTTATAAA
1 ATTTTTAATT-ATTTTTATAAA
* *
5550968 ATTTTAAATTATTTATATA
1 ATTTTTAATTATTTTTATA
5550987 CTTATTGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 1 0.03
21 21 0.62
22 12 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAATTATTTTTATAAA
Found at i:5557679 original size:27 final size:27
Alignment explanation
Indices: 5557631--5557689 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
5557621 AATAGCAGAA
*
5557631 ATATACATGAATCAAATAAATA-AAGAT
1 ATATACATGAATAAAATAAATAGAA-AT
*
5557658 ATATATATGAATTAAAAT-AATAGAAAT
1 ATATACATGAA-TAAAATAAATAGAAAT
5557685 ATATA
1 ATATA
5557690 AAAACATGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 21 0.75
28 7 0.25
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.31
Consensus pattern (27 bp):
ATATACATGAATAAAATAAATAGAAAT
Found at i:5557704 original size:16 final size:16
Alignment explanation
Indices: 5557683--5557721 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5557673 AATAATAGAA
5557683 ATATATAAAAACATGT
1 ATATATAAAAACATGT
* **
5557699 ATATATGAAAGTATGT
1 ATATATAAAAACATGT
5557715 ATATATA
1 ATATATA
5557722 TAGATGAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36
Consensus pattern (16 bp):
ATATATAAAAACATGT
Found at i:5557847 original size:3 final size:3
Alignment explanation
Indices: 5557810--5557834 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5557800 CAACAACAAC
5557810 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
5557835 GGTTAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5559491 original size:132 final size:132
Alignment explanation
Indices: 5559269--5559697 Score: 716
Period size: 132 Copynumber: 3.2 Consensus size: 132
5559259 TTCGTTATTG
* * * * * *
5559269 TTGATTTGCTCCATTACTGCTTAGGAG-GACAGAATCTACAGTCTTTGACCTACTCCACTACTGC
1 TTGATCTGCTCCACTACTGATTAGG-GTGACAGAATCTGCAATCTTCGACCTACTCCACTACTGC
*
5559333 TTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTATATTGGGAAGATAAGATTCACCA
65 TTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCA
5559398 TCT
130 TCT
* * * * *
5559401 TCGATCTGCTCCACTACTGCTTAGGGTGACAAAATCTGCAATCTTCAACCTACTCCACTACTGCC
1 TTGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCGACCTACTCCACTACTGCT
5559466 TAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCAT
66 TAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCAT
5559531 CT
131 CT
5559533 TTGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCGACCTACTCCACTACTGCT
1 TTGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCGACCTACTCCACTACTGCT
*
5559598 TAGGGTGATAGGACTAATGGCTTAAATATGCTTCTCCACTGTATTGGGAAGATAAGATTCACCAT
66 TAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCAT
5559663 CT
131 CT
5559665 TTGATCATGCTCCACTACTGATTAGGGTGACAG
1 TTGATC-TGCTCCACTACTGATTAGGGTGACAG
5559698 GACTAATGGC
Statistics
Matches: 279, Mismatches: 16, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
131 1 0.00
132 252 0.90
133 26 0.09
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (132 bp):
TTGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCGACCTACTCCACTACTGCT
TAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCAT
CT
Found at i:5559703 original size:221 final size:220
Alignment explanation
Indices: 5559453--5559917 Score: 833
Period size: 221 Copynumber: 2.1 Consensus size: 220
5559443 CTTCAACCTA
* *
5559453 CTCCACTACTGCCTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
1 CTCCACTACTGCTTAGGGTGACAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
*
5559518 TAAGATTCACCATCTTTGATCTGCTCCACTACTG-ATTAGGGTGACAGAATCTGCAATCTTCGAC
66 TAAGATTCACCATCTTTGATCTGCTCCACTACTGCA-TAGGGTGACAGAATCTGCAATCTTCAAC
*
5559582 CTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATATGCTTCTCCACTGTATTGGGA
130 CTACTCCACTACTGCTTAGGGTGATAGGACAAATGGCTTAAATATGCTTCTCCACTGTATTGGGA
*
5559647 AGATAAGATTCACCATCTTTGATCATG
195 AGATAAGATTCACCATCTTCGATC-TG
*
5559674 CTCCACTACTGATTAGGGTGACAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
1 CTCCACTACTGCTTAGGGTGACAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
*
5559739 TAAGATTCACCATCTTTGATCTGCTCCACTACTGCATAGGGTGACAGAATCTGCAATTTTCAACC
66 TAAGATTCACCATCTTTGATCTGCTCCACTACTGCATAGGGTGACAGAATCTGCAATCTTCAACC
*
5559804 TACTCCACTACTGCTTAGGGTGATAGGACAAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAA
131 TACTCCACTACTGCTTAGGGTGATAGGACAAATGGCTTAAATATGCTTCTCCACTGTATTGGGAA
5559869 GATAAGATTCACCATCTTCGATCTG
196 GATAAGATTCACCATCTTCGATCTG
5559894 CTCCACTACTGCTTAGGGTGACAG
1 CTCCACTACTGCTTAGGGTGACAG
5559918 AATCTGATTC
Statistics
Matches: 234, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
220 25 0.11
221 208 0.89
222 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (220 bp):
CTCCACTACTGCTTAGGGTGACAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
TAAGATTCACCATCTTTGATCTGCTCCACTACTGCATAGGGTGACAGAATCTGCAATCTTCAACC
TACTCCACTACTGCTTAGGGTGATAGGACAAATGGCTTAAATATGCTTCTCCACTGTATTGGGAA
GATAAGATTCACCATCTTCGATCTG
Found at i:5559736 original size:89 final size:88
Alignment explanation
Indices: 5559585--5559785 Score: 350
Period size: 89 Copynumber: 2.3 Consensus size: 88
5559575 CTTCGACCTA
* *
5559585 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATATGCTTCTCCACTGTATTGGGAAGA
1 CTCCACTACTGATTAGGGTGACAGGACTAATGGCTTAAATATGCTTCTCCACTGTATTGGGAAGA
5559650 TAAGATTCACCATCTTTGATCATG
66 TAAGATTCACCATCTTTGATC-TG
*
5559674 CTCCACTACTGATTAGGGTGACAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
1 CTCCACTACTGATTAGGGTGACAGGACTAATGGCTTAAATATGCTTCTCCACTGTATTGGGAAGA
5559739 TAAGATTCACCATCTTTGATCTG
66 TAAGATTCACCATCTTTGATCTG
5559762 CTCCACTACTGCA-TAGGGTGACAG
1 CTCCACTACTG-ATTAGGGTGACAG
5559786 AATCTGCAAT
Statistics
Matches: 108, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
88 24 0.22
89 84 0.78
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (88 bp):
CTCCACTACTGATTAGGGTGACAGGACTAATGGCTTAAATATGCTTCTCCACTGTATTGGGAAGA
TAAGATTCACCATCTTTGATCTG
Found at i:5559763 original size:45 final size:45
Alignment explanation
Indices: 5559626--5559763 Score: 124
Period size: 45 Copynumber: 3.1 Consensus size: 45
5559616 GGCTTAAATA
5559626 TGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTTGATC
1 TGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTTGATC
* * * * * * * **
5559671 ATGCTCCACTACTG-ATTAGGG-TGACAGGACT-A--ATGGCTTAAATC
1 -TGCTTCTCCACTGTATT-GGGAAGATAAGATTCACCAT--CTTTGATC
5559715 TGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTTGATC
1 TGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTTGATC
5559760 TGCT
1 TGCT
5559764 CCACTACTGC
Statistics
Matches: 66, Mismatches: 18, Indels: 17
0.65 0.18 0.17
Matches are distributed among these distances:
42 2 0.03
43 13 0.20
44 16 0.24
45 20 0.30
46 13 0.20
47 2 0.03
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (45 bp):
TGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTTGATC
Found at i:5559911 original size:132 final size:132
Alignment explanation
Indices: 5559674--5559923 Score: 455
Period size: 132 Copynumber: 1.9 Consensus size: 132
5559664 TTTGATCATG
*
5559674 CTCCACTACTGATTAGGGTGACAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
1 CTCCACTACTGATTAGGGTGACAGGACAAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
*
5559739 TAAGATTCACCATCTTTGATCTGCTCCACTACTGCATAGGGTGACAGAATCTGCAATTTTCAACC
66 TAAGATTCACCATCTTCGATCTGCTCCACTACTGCATAGGGTGACAGAATCTGCAATTTTCAACC
5559804 TA
131 TA
* *
5559806 CTCCACTACTGCTTAGGGTGATAGGACAAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
1 CTCCACTACTGATTAGGGTGACAGGACAAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
*
5559871 TAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTG
66 TAAGATTCACCATCTTCGATCTGCTCCACTACTGCATAGGGTGACAGAATCTG
5559924 ATTCGTAGCT
Statistics
Matches: 113, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
132 113 1.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (132 bp):
CTCCACTACTGATTAGGGTGACAGGACAAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
TAAGATTCACCATCTTCGATCTGCTCCACTACTGCATAGGGTGACAGAATCTGCAATTTTCAACC
TA
Found at i:5560725 original size:50 final size:49
Alignment explanation
Indices: 5560583--5561540 Score: 390
Period size: 50 Copynumber: 19.3 Consensus size: 49
5560573 TTCAATCGTC
* * * *
5560583 GTAGCTTCAATCTGTTCC-GTCGCATCGCCTGGGAGTAAGATTCGTCGTT
1 GTAGCTTCAATCTGTTCCACT-GCAACGCCTGGAAGTAAGATTCGCCGTT
* * ** * * * ** ** *
5560632 GTAGCCTCAATCTTTTAAATTGCTATGTCGGGGAAACAGGATTCGCCGTT
1 GTAGCTTCAATCTGTTCCACTGCAACG-CCTGGAAGTAAGATTCGCCGTT
* * * *
5560682 GTAGCTTCAATCTGTTCCGCTGCACCGCCTGAAAGGTAAGATTCACCGTT
1 GTAGCTTCAATCTGTTCCACTGCAACGCCTGGAA-GTAAGATTCGCCGTT
** * ** * * *
5560732 GTAGCTTCAATCT-TTGAAACTGCAATGTCGAGGAAGCAAGATTCGCTGTC
1 GTAGCTTCAATCTGTT-CCACTGCAACG-CCTGGAAGTAAGATTCGCCGTT
* * * * * * *
5560782 GTAGTTTTAATCTGTTCCGCTACATCGCCTGGAAGTAAGATTCACCATT
1 GTAGCTTCAATCTGTTCCACTGCAACGCCTGGAAGTAAGATTCGCCGTT
* ** * * ** * * * *
5560831 GTGGCTTCAATCT-TTTAATTGCAATGTCGGGGTAGTGAA-ATTTGCCATC
1 GTAGCTTCAATCTGTTCCACTGCAACG-CCTGGAAGT-AAGATTCGCCGTT
* * * *
5560880 GTAGCTTCAATCTATTCCGCTGCATCGCCTGGGAAGTAAGATTCACCGTT
1 GTAGCTTCAATCTGTTCCACTGCAACGCCT-GGAAGTAAGATTCGCCGTT
* ** * * * ** * * *
5560930 GTGGCTTCAATCT-TTTAATTGTAATGTCGGGGAAGTGAGATTCGCCATC
1 GTAGCTTCAATCTGTTCCACTGCAACG-CCTGGAAGTAAGATTCGCCGTT
* * * *
5560979 GTAGCTTCAATCTGTTCCGCTACATCGCCTGGGAAGTAAGATTCACCGTT
1 GTAGCTTCAATCTGTTCCACTGCAACGCCT-GGAAGTAAGATTCGCCGTT
* * * ** * * ** **
5561029 GTGGCTTCGATCTTTTTAATTGCAATGTCGAGGAAGGGAGATTCGCCGTT
1 GTAGCTTCAATCTGTTCCACTGCAACG-CCTGGAAGTAAGATTCGCCGTT
* * * *
5561079 GTAGTTTCAATCTATTCCACTGCATCGCCTGGGAAGTAAGATTTGCCGTT
1 GTAGCTTCAATCTGTTCCACTGCAACGCCT-GGAAGTAAGATTCGCCGTT
* * ** * * ** * * *
5561129 GTGGCTTCAATCTTTTGAATTGCAATGTCGGGGAAGTGAGATTCGCTGTC
1 GTAGCTTCAATCTGTTCCACTGCAACG-CCTGGAAGTAAGATTCGCCGTT
* * * * *
5561179 ATAGCTTTAATCTGTTCCGCTGCACCGCCTGAAAGGTAAGATTCGCCGTT
1 GTAGCTTCAATCTGTTCCACTGCAACGCCTGGAA-GTAAGATTCGCCGTT
* * ** * * ** * **
5561229 GTAGCTTCGATCTTTTTAATTGCAATGTCAGGGAAGTAAGATCCGTTGTT
1 GTAGCTTCAATCTGTTCCACTGCAACG-CCTGGAAGTAAGATTCGCCGTT
* * *
5561279 GTAGCTTCAATCTGTTACACTGCAACG-CTAGGAAAGTAAGATCCGCTGTT
1 GTAGCTTCAATCTGTTCCACTGCAACGCCT-GG-AAGTAAGATTCGCCGTT
** * * ** * * *
5561329 GTAGCTTCAATCT-TCTTAATTGCAATGTCAGGGAAGTAAGATCCACTGTT
1 GTAGCTTCAATCTGT-TCCACTGCAACG-CCTGGAAGTAAGATTCGCCGTT
* * * *
5561379 GTAGCTTCAATCTGTTCCACTGCAACG-CTAGGAAAATAAAATTTGCTGTT
1 GTAGCTTCAATCTGTTCCACTGCAACGCCT-GG-AAGTAAGATTCGCCGTT
** * * * * * *
5561429 GTAGCTTCAATCT-TTTAATTGCAATGTCAGGAAATTAAGA-TCTGCTGTT
1 GTAGCTTCAATCTGTTCCACTGCAACGCCTGG-AAGTAAGATTC-GCCGTT
* * * * *
5561478 GAAGCTTCAATCTGTTCTACTGCAACG-CTAAGAAAGTAAGATCCGCTGTT
1 GTAGCTTCAATCTGTTCCACTGCAACGCCT--GGAAGTAAGATTCGCCGTT
5561528 GTAGCTTCAATCT
1 GTAGCTTCAATCT
5561541 ATCATGTTGT
Statistics
Matches: 639, Mismatches: 237, Indels: 65
0.68 0.25 0.07
Matches are distributed among these distances:
48 7 0.01
49 157 0.25
50 458 0.72
51 17 0.03
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.33
Consensus pattern (49 bp):
GTAGCTTCAATCTGTTCCACTGCAACGCCTGGAAGTAAGATTCGCCGTT
Found at i:5560843 original size:49 final size:49
Alignment explanation
Indices: 5560790--5561041 Score: 158
Period size: 49 Copynumber: 5.1 Consensus size: 49
5560780 TCGTAGTTTT
5560790 AATCTGTTCCGCTACATCGCCTGGAAGTAAGATTCACCATTGTGGCTTC
1 AATCTGTTCCGCTACATCGCCTGGAAGTAAGATTCACCATTGTGGCTTC
* ** ** * ** * *
5560839 AATCTTTTAATTGC-A-AT-GTCGGGGTAGTGAA-ATTTGCCATCGTAGCTTC
1 AATCTGTT--CCGCTACATCG-CCTGGAAGT-AAGATTCACCATTGTGGCTTC
* * *
5560888 AATCTATTCCGCTGCATCGCCTGGGAAGTAAGATTCACCGTTGTGGCTTC
1 AATCTGTTCCGCTACATCGCCT-GGAAGTAAGATTCACCATTGTGGCTTC
* ** ** * * * *
5560938 AATCTTTTAATTG-TA-AT-GTCGGGGAAGTGAGATTCGCCATCGTAGCTTC
1 AATCTGTT--CCGCTACATCG-CCTGGAAGTAAGATTCACCATTGTGGCTTC
*
5560987 AATCTGTTCCGCTACATCGCCTGGGAAGTAAGATTCACCGTTGTGGCTTC
1 AATCTGTTCCGCTACATCGCCT-GGAAGTAAGATTCACCATTGTGGCTTC
*
5561037 GATCT
1 AATCT
5561042 TTTTAATTGC
Statistics
Matches: 143, Mismatches: 44, Indels: 31
0.66 0.20 0.14
Matches are distributed among these distances:
47 3 0.02
48 3 0.02
49 74 0.52
50 59 0.41
51 3 0.02
52 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.33
Consensus pattern (49 bp):
AATCTGTTCCGCTACATCGCCTGGAAGTAAGATTCACCATTGTGGCTTC
Found at i:5560924 original size:99 final size:99
Alignment explanation
Indices: 5560579--5561456 Score: 917
Period size: 100 Copynumber: 8.8 Consensus size: 99
5560569 TAGCTTCAAT
** * *
5560579 CGTCGTAGCTTCAATCTGTTCCG-TCGCATCGCCTGGG-AGTAAGATTCGTCGTTGTAGCCTCAA
1 CGTCGTAGCTTCAATCTGTTCCGCT-GCATCGCCTGGGAAGTAAGATTCACCGTTGTGGCTTCAA
* **
5560642 TCTTTTAAATTGCTATGTCGGGGAA-ACAGGATTCGC
65 TCTTTT-AATTGCAATGTCGGGGAAGTGA-GATTCGC
* * * *
5560678 CGTTGTAGCTTCAATCTGTTCCGCTGCACCGCCT-GAAAGGTAAGATTCACCGTTGTAGCTTCAA
1 CGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGGAA-GTAAGATTCACCGTTGTGGCTTCAA
* * * **
5560742 TCTTTGAAACTGCAATGTCGAGGAAGCAAGATTCGC
65 TCTTT-TAATTGCAATGTCGGGGAAGTGAGATTCGC
* * * * *
5560778 TGTCGTAGTTTTAATCTGTTCCGCTACATCGCCT-GGAAGTAAGATTCACCATTGTGGCTTCAAT
1 CGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGGAAGTAAGATTCACCGTTGTGGCTTCAAT
* * *
5560842 CTTTTAATTGCAATGTCGGGGTAGTGAAATTTGC
66 CTTTTAATTGCAATGTCGGGGAAGTGAGATTCGC
* *
5560876 CATCGTAGCTTCAATCTATTCCGCTGCATCGCCTGGGAAGTAAGATTCACCGTTGTGGCTTCAAT
1 CGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGGAAGTAAGATTCACCGTTGTGGCTTCAAT
*
5560941 CTTTTAATTGTAATGTCGGGGAAGTGAGATTCGC
66 CTTTTAATTGCAATGTCGGGGAAGTGAGATTCGC
* * *
5560975 CATCGTAGCTTCAATCTGTTCCGCTACATCGCCTGGGAAGTAAGATTCACCGTTGTGGCTTCGAT
1 CGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGGAAGTAAGATTCACCGTTGTGGCTTCAAT
* *
5561040 CTTTTTAATTGCAATGTCGAGGAAGGGAGATTCGC
66 C-TTTTAATTGCAATGTCGGGGAAGTGAGATTCGC
* * * * **
5561075 CGTTGTAGTTTCAATCTATTCCACTGCATCGCCTGGGAAGTAAGATTTGCCGTTGTGGCTTCAAT
1 CGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGGAAGTAAGATTCACCGTTGTGGCTTCAAT
5561140 CTTTTGAATTGCAATGTCGGGGAAGTGAGATTCGC
66 CTTTT-AATTGCAATGTCGGGGAAGTGAGATTCGC
* * * * * * * *
5561175 TGTCATAGCTTTAATCTGTTCCGCTGCACCGCCT-GAAAGGTAAGATTCGCCGTTGTAGCTTCGA
1 CGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGGAA-GTAAGATTCACCGTTGTGGCTTCAA
* * * *
5561239 TCTTTTTAATTGCAATGTCAGGGAAGTAAGATCCGT
65 TC-TTTTAATTGCAATGTCGGGGAAGTGAGATTCGC
* * * * * * * * * *
5561275 TGTTGTAGCTTCAATCTGTTACACTGCAACG-CTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAA
1 CGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCT-GGGAAGTAAGATTCACCGTTGTGGCTTCAA
* * * *
5561339 TCTTCTTAATTGCAATGTCAGGGAAGTAAGATCCAC
65 TCTT-TTAATTGCAATGTCGGGGAAGTGAGATTCGC
* * * * * * * ** * *
5561375 TGTTGTAGCTTCAATCTGTTCCACTGCAACG-CTAGGAAAATAAAATTTGCTGTTGTAGCTTCAA
1 CGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCT-GGGAAGTAAGATTCACCGTTGTGGCTTCAA
5561439 TCTTTTAATTGCAATGTC
65 TCTTTTAATTGCAATGTC
5561457 AGGAAATTAA
Statistics
Matches: 677, Mismatches: 89, Indels: 26
0.85 0.11 0.03
Matches are distributed among these distances:
98 51 0.08
99 206 0.30
100 411 0.61
101 9 0.01
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (99 bp):
CGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGGAAGTAAGATTCACCGTTGTGGCTTCAAT
CTTTTAATTGCAATGTCGGGGAAGTGAGATTCGC
Found at i:5561254 original size:200 final size:198
Alignment explanation
Indices: 5560580--5561540 Score: 981
Period size: 199 Copynumber: 4.8 Consensus size: 198
5560570 AGCTTCAATC
* * *
5560580 GTCGTAGCTTCAATCTGTTCCG-TCGCATCGCCTGGGAGTAAGATTCGTCGTTGTAGCCTCAATC
1 GTCGTAGCTTCAATCTGTTCCGCT-GCATCGCCTGGAAGTAAGATTCGCCGTTGTAGCTTCAATC
* * * ** * * *
5560644 TTTTAAATTGCTATGTCGGGGAA-ACAGGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCACC
65 TTTTTAATTGCAATGTCGAGGAAGTGA-GATTCGCCGTTGTAGCTTCAATCTATTCCACTGCATC
* * * *
5560708 GCCT-GAAAGGTAAGATTCACCGTTGTAGCTTCAATCTTTGAAACTGCAATGTCGAGGAAGCAAG
129 GCCTGGAAA-GTAAGATTCACCGTTGTAGCTTCAATCTTT-TAATTGCAATGTCGGGGAAGTAAG
5560772 ATTCGCT
192 ATTCGCT
* * * * * *
5560779 GTCGTAGTTTTAATCTGTTCCGCTACATCGCCTGGAAGTAAGATTCACCATTGTGGCTTCAATC-
1 GTCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAGTAAGATTCGCCGTTGTAGCTTCAATCT
* * * * * * *
5560843 TTTTAATTGCAATGTCGGGGTAGTGAAATTTGCCATCGTAGCTTCAATCTATTCCGCTGCATCGC
66 TTTTAATTGCAATGTCGAGGAAGTGAGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCATCGC
* * * *
5560908 CTGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTAATTGTAATGTCGGGGAAGTGAGATTC
131 CTGGAAAGTAAGATTCACCGTTGTAGCTTCAATCTTTTAATTGCAATGTCGGGGAAGTAAGATTC
*
5560973 GCC
196 GCT
* * * * *
5560976 ATCGTAGCTTCAATCTGTTCCGCTACATCGCCTGGGAAGTAAGATTCACCGTTGTGGCTTCGATC
1 GTCGTAGCTTCAATCTGTTCCGCTGCATCGCCT-GGAAGTAAGATTCGCCGTTGTAGCTTCAATC
* *
5561041 TTTTTAATTGCAATGTCGAGGAAGGGAGATTCGCCGTTGTAGTTTCAATCTATTCCACTGCATCG
65 TTTTTAATTGCAATGTCGAGGAAGTGAGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCATCG
* ** * *
5561106 CCTGGGAAGTAAGATTTGCCGTTGTGGCTTCAATCTTTTGAATTGCAATGTCGGGGAAGTGAGAT
130 CCTGGAAAGTAAGATTCACCGTTGTAGCTTCAATCTTTT-AATTGCAATGTCGGGGAAGTAAGAT
5561171 TCGCT
194 TCGCT
* * * * *
5561176 GTCATAGCTTTAATCTGTTCCGCTGCACCGCCTGAAAGGTAAGATTCGCCGTTGTAGCTTCGATC
1 GTCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAA-GTAAGATTCGCCGTTGTAGCTTCAATC
* * ** * * *
5561241 TTTTTAATTGCAATGTC-AGGGAAGTAAGATCCGTTGTTGTAGCTTCAATCTGTTACACTGCAAC
65 TTTTTAATTGCAATGTCGA-GGAAGTGAGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCATC
* * * *
5561305 G-CTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAG
129 GCCT-GGAAAGTAAGATTCACCGTTGTAGCTTCAATCTT-TTAATTGCAATGTCGGGGAAGTAAG
* *
5561369 ATCCACT
192 ATTCGCT
* * * * * * *
5561376 GTTGTAGCTTCAATCTGTTCCACTGCAACG-CTAGGAAAATAAAATTTGCTGTTGTAGCTTCAAT
1 GTCGTAGCTTCAATCTGTTCCGCTGCATCGCCT-GG-AAGTAAGATTCGCCGTTGTAGCTTCAAT
* * * * * *
5561440 C-TTTTAATTGCAATGTC-AGGAAATTAAGA-TCTGCTGTTGAAGCTTCAATCTGTTCTACTGCA
64 CTTTTTAATTGCAATGTCGAGG-AAGTGAGATTC-GCCGTTGTAGCTTCAATCTATTCCACTGCA
* * * * *
5561502 ACG-CTAAGAAAGTAAGATCCGCTGTTGTAGCTTCAATCT
127 TCGCCT-GGAAAGTAAGATTCACCGTTGTAGCTTCAATCT
5561541 ATCATGTTGT
Statistics
Matches: 657, Mismatches: 91, Indels: 28
0.85 0.12 0.04
Matches are distributed among these distances:
197 54 0.08
198 115 0.18
199 245 0.37
200 239 0.36
201 4 0.01
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.33
Consensus pattern (198 bp):
GTCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAGTAAGATTCGCCGTTGTAGCTTCAATCT
TTTTAATTGCAATGTCGAGGAAGTGAGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCATCGC
CTGGAAAGTAAGATTCACCGTTGTAGCTTCAATCTTTTAATTGCAATGTCGGGGAAGTAAGATTC
GCT
Found at i:5561806 original size:88 final size:88
Alignment explanation
Indices: 5561708--5562563 Score: 1433
Period size: 88 Copynumber: 9.7 Consensus size: 88
5561698 TTTCCACTTA
* * * * * * *
5561708 AACCGAGAGAGGTAAGGCTTGTGTCTTCGATCTACTTCGCTGTCAATGTAGGAAGGTAAGATCCT
1 AACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTT
5561773 TTGTCTTCAACCAGCTCCATCAC
66 TTGTCTTCAACCAGCTCCATCAC
*
5561796 AACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGTAAGATCTT
1 AACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTT
5561861 TTGTCTTCAACCAGCTCCATCAC
66 TTGTCTTCAACCAGCTCCATCAC
*
5561884 AACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTT
1 AACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTT
*
5561949 TTGTCTTCAACCAGCTCTATCAC
66 TTGTCTTCAACCAGCTCCATCAC
* *
5561972 AACTGAGAGAGGCAAGGTTTGTGTCTTCGACCTACTTCGCTGTCAATGCAGGAAGGCAAGATCTT
1 AACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTT
5562037 TTGTCTTCAACCAGCTCCATCAC
66 TTGTCTTCAACCAGCTCCATCAC
*
5562060 AACCGAGAGAGGTAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTT
1 AACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTT
*
5562125 TTGTCTTCAACCAGCTCTATCAC
66 TTGTCTTCAACCAGCTCCATCAC
* * *
5562148 AACCGAGAGAGGCAAGGTTTGTGTCTTCAACCTGCTTCGCTGTCAATCCAAGAAGGCAAGATCTT
1 AACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTT
5562213 TTGTCTTCAACCAGCTCCATCAC
66 TTGTCTTCAACCAGCTCCATCAC
* * * *
5562236 AACCGAGAGAAGCAAGGTTTGTGTCTTCGACATGCTTCGCTGTCAATACAGGAAGGCAAAATCTT
1 AACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTT
5562301 TTGTCTTCAACCAGCTCCATCAC
66 TTGTCTTCAACCAGCTCCATCAC
* * * *
5562324 AACCGAGAGAGGTAAGGTTTGTGTCTTCGACCTGCTTCGCTGTTAATACAGGAAGACAAGATCTT
1 AACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTT
* *
5562389 TTATCTTCAACCAGCTCTATCAC
66 TTGTCTTCAACCAGCTCCATCAC
* * *
5562412 AACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTACTTCGCTATCAATACAGGAAGGCAAGATCTT
1 AACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTT
5562477 TTGTCTTCAACCAGCTCCATCAC
66 TTGTCTTCAACCAGCTCCATCAC
*
5562500 AATCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
1 AACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
5562564 GCAACTTTAT
Statistics
Matches: 721, Mismatches: 47, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 721 1.00
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.27
Consensus pattern (88 bp):
AACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTT
TTGTCTTCAACCAGCTCCATCAC
Found at i:5563670 original size:21 final size:21
Alignment explanation
Indices: 5563644--5563687 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
5563634 GGTATAGCAA
5563644 GATCACCACATGCCCCAATCT
1 GATCACCACATGCCCCAATCT
** *
5563665 GATCACTTCATGCCCCATTCT
1 GATCACCACATGCCCCAATCT
5563686 GA
1 GA
5563688 ACAAATATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.25, C:0.39, G:0.11, T:0.25
Consensus pattern (21 bp):
GATCACCACATGCCCCAATCT
Found at i:5563790 original size:6 final size:7
Alignment explanation
Indices: 5563776--5563819 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
5563766 TTAGCCTCTC
5563776 CATTTTT
1 CATTTTT
5563783 CA-TTTT
1 CATTTTT
5563789 CATTTTT
1 CATTTTT
*
5563796 TATTTTT
1 CATTTTT
*
5563803 CA-TTCT
1 CATTTTT
5563809 CATTTTT
1 CATTTTT
5563816 CATT
1 CATT
5563820 CGTTTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
6 11 0.35
7 20 0.65
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (7 bp):
CATTTTT
Found at i:5563800 original size:20 final size:20
Alignment explanation
Indices: 5563777--5563815 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5563767 TAGCCTCTCC
*
5563777 ATTTTTCATTTTCATTTTTT
1 ATTTTTCATTCTCATTTTTT
5563797 ATTTTTCATTCTCATTTTT
1 ATTTTTCATTCTCATTTTT
5563816 CATTCGTTTT
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:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (20 bp):
ATTTTTCATTCTCATTTTTT
Found at i:5564699 original size:16 final size:16
Alignment explanation
Indices: 5564680--5564715 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
5564670 TTCTTTCTTC
* *
5564680 TTTTTGTTTTTTTTTA
1 TTTTTGATTTTTTTCA
5564696 TTTTTGATTTTTTTCA
1 TTTTTGATTTTTTTCA
5564712 TTTT
1 TTTT
5564716 CATTTTGACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.08, C:0.03, G:0.06, T:0.83
Consensus pattern (16 bp):
TTTTTGATTTTTTTCA
Found at i:5568781 original size:27 final size:27
Alignment explanation
Indices: 5568733--5568791 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
5568723 AATAGCAGAA
*
5568733 ATATACATGAATCAAATAAATA-AAGAT
1 ATATACATGAATAAAATAAATAGAA-AT
*
5568760 ATATATATGAATTAAAAT-AATAGAAAT
1 ATATACATGAA-TAAAATAAATAGAAAT
5568787 ATATA
1 ATATA
5568792 AAAACATGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 21 0.75
28 7 0.25
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.31
Consensus pattern (27 bp):
ATATACATGAATAAAATAAATAGAAAT
Found at i:5568806 original size:16 final size:16
Alignment explanation
Indices: 5568785--5568823 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5568775 AATAATAGAA
5568785 ATATATAAAAACATGT
1 ATATATAAAAACATGT
* **
5568801 ATATATGAAAGTATGT
1 ATATATAAAAACATGT
5568817 ATATATA
1 ATATATA
5568824 TAGATGAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36
Consensus pattern (16 bp):
ATATATAAAAACATGT
Found at i:5572567 original size:67 final size:67
Alignment explanation
Indices: 5572459--5572587 Score: 240
Period size: 67 Copynumber: 1.9 Consensus size: 67
5572449 TCAAATTCAG
*
5572459 AGAGCACACTCCCGCGAACCTCATTTCTTACAGCAGGATTACCAGTCCAGGTTAAATCCCCTACA
1 AGAGCACACTCCCGCGAACCTCATTTCTTACAGCAGGATTACCAGTCCAGGCTAAATCCCCTACA
5572524 AA
66 AA
*
5572526 AGAGCACACTCCCGCGAACCTCATTTCTTACAGCAGGATTACTAGTCCAGGCTAAATCCCCT
1 AGAGCACACTCCCGCGAACCTCATTTCTTACAGCAGGATTACCAGTCCAGGCTAAATCCCCT
5572588 GTAATATAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.29, C:0.33, G:0.16, T:0.22
Consensus pattern (67 bp):
AGAGCACACTCCCGCGAACCTCATTTCTTACAGCAGGATTACCAGTCCAGGCTAAATCCCCTACA
AA
Found at i:5575724 original size:30 final size:31
Alignment explanation
Indices: 5575667--5575730 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
5575657 AATATTACTT
* *
5575667 TTATTATTATCATATAATATTATTAATA-AA
1 TTATTATTATAATATAATATTAATAATATAA
*
5575697 TTATTATTATAATGTCAAT-TTAATAATATAA
1 TTATTATTATAATAT-AATATTAATAATATAA
5575728 TTA
1 TTA
5575731 ATAATAAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 21 0.72
31 8 0.28
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (31 bp):
TTATTATTATAATATAATATTAATAATATAA
Found at i:5576014 original size:26 final size:26
Alignment explanation
Indices: 5575978--5576028 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
5575968 ATGACATAAT
5575978 GTTCTTGCCATTGGGTCAAGAGGTTA
1 GTTCTTGCCATTGGGTCAAGAGGTTA
5576004 GTTCTTGCCATTGGGTCAAGAGGTT
1 GTTCTTGCCATTGGGTCAAGAGGTT
5576029 GTCGGCTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.18, C:0.16, G:0.31, T:0.35
Consensus pattern (26 bp):
GTTCTTGCCATTGGGTCAAGAGGTTA
Found at i:5581907 original size:20 final size:20
Alignment explanation
Indices: 5581866--5581907 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
5581856 TCTCTTAAAA
* *
5581866 TTTTTGTGTTAAAAGCATTT
1 TTTTTGTGTTAAAAACACTT
5581886 TTTTTGTCG-TAAAAACACTT
1 TTTTTGT-GTTAAAAACACTT
5581906 TT
1 TT
5581908 GAGAAACACG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.26, C:0.10, G:0.12, T:0.52
Consensus pattern (20 bp):
TTTTTGTGTTAAAAACACTT
Found at i:5581976 original size:21 final size:21
Alignment explanation
Indices: 5581950--5581992 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
5581940 GGTTCGCTGT
*
5581950 ATTGGATTAGAGGTGTATTGG
1 ATTGGATTAGAGGTGTAATGG
5581971 ATTGGATTAGAGGTGTAATGG
1 ATTGGATTAGAGGTGTAATGG
5581992 A
1 A
5581993 ATAGAGGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (21 bp):
ATTGGATTAGAGGTGTAATGG
Found at i:5581992 original size:16 final size:16
Alignment explanation
Indices: 5581973--5582005 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5581963 TGTATTGGAT
*
5581973 TGGATTAGAGGTGTAA
1 TGGAATAGAGGTGTAA
5581989 TGGAATAGAGGTGTAA
1 TGGAATAGAGGTGTAA
5582005 T
1 T
5582006 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (16 bp):
TGGAATAGAGGTGTAA
Found at i:5582050 original size:45 final size:44
Alignment explanation
Indices: 5581984--5582078 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
5581974 GGATTAGAGG
* *
5581984 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
5582029 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
5582073 TGTAAT
1 TGTAAT
5582079 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:5582260 original size:18 final size:17
Alignment explanation
Indices: 5582239--5582273 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5582229 TTATTATTTA
*
5582239 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
5582257 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
5582274 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:5582267 original size:28 final size:27
Alignment explanation
Indices: 5582197--5582269 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
5582187 ATTATTATCA
*
5582197 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
5582225 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
5582252 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
5582270 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:5582367 original size:144 final size:147
Alignment explanation
Indices: 5582159--5582429 Score: 494
Period size: 144 Copynumber: 1.9 Consensus size: 147
5582149 ATGATTATTG
5582159 TTATTGTTATTTAAATTTTAATAAGATTATTATTATCAAAAATAAATAATTTAATCATATTTAAA
1 TTATTGTTATTTAAATTTTAATAAGATTA-TATTATCAAAAATAAATAATTTAATCATATTTAAA
*
5582224 CATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCA
65 CATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCA
5582289 TAAATTTGTTTTGGTAAA
130 TAAATTTGTTTTGGTAAA
*
5582307 TTATT-TTATTTAAATTTTAATAAGATTA-A-TATCAATAATAAATAATTTAATCATATTTAAAC
1 TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
5582369 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
5582430 ATATTCTTAT
Statistics
Matches: 121, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
144 92 0.76
145 1 0.01
147 23 0.19
148 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAT
AAATTTGTTTTGGTAAA
Found at i:5582404 original size:18 final size:17
Alignment explanation
Indices: 5582383--5582417 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5582373 TTATTATTAA
*
5582383 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
5582401 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
5582418 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:5586330 original size:12 final size:12
Alignment explanation
Indices: 5586315--5586344 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5586305 GTGTACCTCC
5586315 TTTTCCTTTTTA
1 TTTTCCTTTTTA
*
5586327 TTTTCTTTTTTA
1 TTTTCCTTTTTA
5586339 TTTTCC
1 TTTTCC
5586345 CTCCTCTCCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTCCTTTTTA
Found at i:5591184 original size:25 final size:25
Alignment explanation
Indices: 5591151--5591223 Score: 92
Period size: 25 Copynumber: 2.9 Consensus size: 25
5591141 GCCCTCTCTC
*
5591151 GAGCTATATAACGGGAAGCTCATGT
1 GAGCTATATAACGGGAAGCTCATCT
* * *
5591176 GAGCCATATAACGGAAAGCTTATCT
1 GAGCTATATAACGGGAAGCTCATCT
* *
5591201 AAGCTATAGAACGGGAAGCTCAT
1 GAGCTATATAACGGGAAGCTCAT
5591224 AATAGCCAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.22
Consensus pattern (25 bp):
GAGCTATATAACGGGAAGCTCATCT
Found at i:5611882 original size:22 final size:21
Alignment explanation
Indices: 5611852--5611909 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
5611842 ATACAATCGT
*
5611852 AGATTTGATATGTAATCTTAG
1 AGATTTGATTTGTAATCTTAG
*
5611873 AAGATATGATTTTGTAATCTTAG
1 -AGATTTGA-TTTGTAATCTTAG
5611896 AGATTTGATTTGTA
1 AGATTTGATTTGTA
5611910 GATACCATTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.19
22 14 0.44
23 12 0.38
ACGTcount: A:0.33, C:0.03, G:0.19, T:0.45
Consensus pattern (21 bp):
AGATTTGATTTGTAATCTTAG
Found at i:5611892 original size:23 final size:22
Alignment explanation
Indices: 5611862--5611906 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
5611852 AGATTTGATA
5611862 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAG-AGATATGATTT
*
5611885 TGTAATCTTAGAGATTTGATTT
1 TGTAATCTTAGAGATATGATTT
5611907 GTAGATACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.31, C:0.04, G:0.18, T:0.47
Consensus pattern (22 bp):
TGTAATCTTAGAGATATGATTT
Found at i:5614948 original size:778 final size:777
Alignment explanation
Indices: 5613455--5615013 Score: 2893
Period size: 778 Copynumber: 2.0 Consensus size: 777
5613445 GGTGGTGTTG
5613455 AAGACAAGGCAAGTAATAGACTGATGTTTGTGGATATCATCGTGGCAGACAAGAAATTGAATGCC
1 AAGACAAGGCAAGTAATAGACTGATGTTTGTGGATATCATCGTGGCAGACAAGAAATTGAATGCC
* *
5613520 CTTGTTGATACTGGCGCATCCGATTTGTTCATATCTAAAGAGTTGGCAAACGAACTCGGTCTGAA
66 CTTGTTGATACTGGCGCATCCGATTTGGTCATATCTAAAGAGATGGCAAACGAACTCGGTCTGAA
*
5613585 AGTGGAGGAAGATGCGGGTCGACTCAAAACGGTAAACTCAGAAAGTATTCCCATAACGGGTGTGG
131 AGTGGAAGAAGATGCGGGTCGACTCAAAACGGTAAACTCAGAAAGTATTCCCATAACGGGTGTGG
*
5613650 CTAAAGGGGTGAACTCAAACTTGGCGAGTGGACAGGCAATGCAACCATTAAGGTAATCCCACTTG
196 CTAAAGGGGTGAACTCAAACTTGACGAGTGGACAGGCAATGCAACCATTAAGGTAATCCCACTTG
5613715 ATGATTATGATTTTGTGGTAGGATTGAGTTTGCTTGACCGACTTAATACGGATATTCACTCTTCC
261 ATGATTATGATTTTGTGGTAGGATTGAGTTTGCTTGACCGACTTAATACGGATATTCACTCTTCC
5613780 GAGAATTACATGACGATCTCTGATTCGAACCATCGATATATGGTGCGAATGAAAAGAAAGGGAAA
326 GAGAATTACATGACGATCTCTGATTCGAACCATCGATATATGGTGCGAATGAAAAGAAAGGGAAA
* *
5613845 CATGGAAGGCAAAACATTGTCGGCAATCCAATTTACCAAAAGAGTACGTAGAAACGATGTCTCTT
391 CATGGAAGGCAAAACATTGTCGGCAATCCAATTTACCAAAAGAGTACGTAGAAACGAAGTCTCCT
5613910 ATTTAGCCACCTTAAGGGACAATGTGGAGGAGAAATTCGAGGGGGAAATTCCAAAGGAAGTGAAG
456 ATTTAGCCACCTTAAGGGACAATGTGGAGGAGAAATTCGAGGGGGAAATTCCAAAGGAAGTGAAG
*
5613975 CAGCTGTTGCAGTCTTTTCAAGATGTAATGCCCACGGAGTTGCCCAAGACATTGTCACCAAAGAG
521 CAGCTGTTGCAGTCTTTTCAAGATGTAATGCCCACGGAGTTGCCCAAGACATTGCCACCAAAGAG
5614040 GGAGGTGGATCACAAGATTGAGTTGTTGCCTAATACTGAGCCGCCAGCAAGGGCACCATATCGAA
586 GGAGGTGGATCACAAGATTGAGTTGTTGCCTAATACTGAGCCGCCAGCAAGGGCACCATATCGAA
**
5614105 TGTCCCTGCCTGAGTTGGAGGAATTGCGGAAGCAGTTAAGGGAACTTCTAGATGCCGAGTTCATT
651 TGTCCCCACCTGAGTTGGAGGAATTGCGGAAGCAGTTAAGGGAACTTCTAGATGCCGAGTTCATT
* *
5614170 AAACCTTCCAAAGCCCCATTTGGTACGCCAGTGTTATTCTAAAGGAAGCATGATGGGTCCTT
716 AAACCTTCAAAAGCCCCATTTGGTACGCCAGTGTTATTCCAAAGGAAGCATGATGGGTCCTT
* *
5614232 AAGACAAGGCAAGTAATGGACTGATGTTTGTGGATATCATTGTGGCAGACAAGAAATTGAATGCC
1 AAGACAAGGCAAGTAATAGACTGATGTTTGTGGATATCATCGTGGCAGACAAGAAATTGAATGCC
*
5614297 CTTGTTGATACTGGCGCATCCGATTTGGTCATATCTAAAGAGATGGCAAAGGAACTCGGTCTGAA
66 CTTGTTGATACTGGCGCATCCGATTTGGTCATATCTAAAGAGATGGCAAACGAACTCGGTCTGAA
*
5614362 AGTGGAAGAAGATGCGGGTCGACTCAAAACGGTGAACTCAGAAAGTATTCCCATAACGGGTGTGG
131 AGTGGAAGAAGATGCGGGTCGACTCAAAACGGTAAACTCAGAAAGTATTCCCATAACGGGTGTGG
*
5614427 CTAAAGGGGTGGAACTCAAACTTGACGAGTGGACAGGCAATGCAACCTTTAAGGTAATCCCACTT
196 CTAAAGGGGT-GAACTCAAACTTGACGAGTGGACAGGCAATGCAACCATTAAGGTAATCCCACTT
*
5614492 GATGATTATGATTTTGTGGTAGGATTGAGTTTGCTTGACCGACTTAATGCGGATATTCACTCTTC
260 GATGATTATGATTTTGTGGTAGGATTGAGTTTGCTTGACCGACTTAATACGGATATTCACTCTTC
* *
5614557 CGAGAATTACATGACGATCTCTGATTTGAACCATTGATATATGGTGCGAATGAAAAGAAAGGGAA
325 CGAGAATTACATGACGATCTCTGATTCGAACCATCGATATATGGTGCGAATGAAAAGAAAGGGAA
* *
5614622 ACATGGAAGGCAAAACATTGTCGGCAATCCAATTTGCCAAAGGAGTACGTAGAAACGAAGTCTCC
390 ACATGGAAGGCAAAACATTGTCGGCAATCCAATTTACCAAAAGAGTACGTAGAAACGAAGTCTCC
5614687 TATTTAGCCACCTTAAGGGACAATGTGGAGGAGAAATTCGAGGGGGAAATTCCAAAGGAAGTGAA
455 TATTTAGCCACCTTAAGGGACAATGTGGAGGAGAAATTCGAGGGGGAAATTCCAAAGGAAGTGAA
5614752 GCAGCTGTTGCAGTCTTTTCAAGATGTAATGCCCACGGAGTTGCCCAAGACATTGCCACCAAAGA
520 GCAGCTGTTGCAGTCTTTTCAAGATGTAATGCCCACGGAGTTGCCCAAGACATTGCCACCAAAGA
*
5614817 GGGAGGTGGATCACAAGATTGAGTTGTTGCCTAATACTGAGCCGCCAGCAAGGGCACTATATCGA
585 GGGAGGTGGATCACAAGATTGAGTTGTTGCCTAATACTGAGCCGCCAGCAAGGGCACCATATCGA
*
5614882 ATGTCCCCACCTGAGTTGGAGGAATTGCGGAAGCAGTTAAGGGAACTTCTAGATGCCGGGTTCAT
650 ATGTCCCCACCTGAGTTGGAGGAATTGCGGAAGCAGTTAAGGGAACTTCTAGATGCCGAGTTCAT
*
5614947 TAAACCTTCAAAAGCCCCATTTGGTGCGCCAGTGTTATTCCAAAGGAAGCATGATGGGTCCTT
715 TAAACCTTCAAAAGCCCCATTTGGTACGCCAGTGTTATTCCAAAGGAAGCATGATGGGTCCTT
5615010 AAGA
1 AAGA
5615014 TTGTGCATTG
Statistics
Matches: 757, Mismatches: 24, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
777 198 0.26
778 559 0.74
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.24
Consensus pattern (777 bp):
AAGACAAGGCAAGTAATAGACTGATGTTTGTGGATATCATCGTGGCAGACAAGAAATTGAATGCC
CTTGTTGATACTGGCGCATCCGATTTGGTCATATCTAAAGAGATGGCAAACGAACTCGGTCTGAA
AGTGGAAGAAGATGCGGGTCGACTCAAAACGGTAAACTCAGAAAGTATTCCCATAACGGGTGTGG
CTAAAGGGGTGAACTCAAACTTGACGAGTGGACAGGCAATGCAACCATTAAGGTAATCCCACTTG
ATGATTATGATTTTGTGGTAGGATTGAGTTTGCTTGACCGACTTAATACGGATATTCACTCTTCC
GAGAATTACATGACGATCTCTGATTCGAACCATCGATATATGGTGCGAATGAAAAGAAAGGGAAA
CATGGAAGGCAAAACATTGTCGGCAATCCAATTTACCAAAAGAGTACGTAGAAACGAAGTCTCCT
ATTTAGCCACCTTAAGGGACAATGTGGAGGAGAAATTCGAGGGGGAAATTCCAAAGGAAGTGAAG
CAGCTGTTGCAGTCTTTTCAAGATGTAATGCCCACGGAGTTGCCCAAGACATTGCCACCAAAGAG
GGAGGTGGATCACAAGATTGAGTTGTTGCCTAATACTGAGCCGCCAGCAAGGGCACCATATCGAA
TGTCCCCACCTGAGTTGGAGGAATTGCGGAAGCAGTTAAGGGAACTTCTAGATGCCGAGTTCATT
AAACCTTCAAAAGCCCCATTTGGTACGCCAGTGTTATTCCAAAGGAAGCATGATGGGTCCTT
Found at i:5617804 original size:22 final size:21
Alignment explanation
Indices: 5617774--5617831 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
5617764 ATACAATCGT
*
5617774 AGATTTGATATGTAATCTTAG
1 AGATTTGATTTGTAATCTTAG
*
5617795 AAGATATGATTTTGTAATCTTAG
1 -AGATTTGA-TTTGTAATCTTAG
5617818 AGATTTGATTTGTA
1 AGATTTGATTTGTA
5617832 GATACTATTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.19
22 14 0.44
23 12 0.38
ACGTcount: A:0.33, C:0.03, G:0.19, T:0.45
Consensus pattern (21 bp):
AGATTTGATTTGTAATCTTAG
Found at i:5617814 original size:23 final size:22
Alignment explanation
Indices: 5617784--5617828 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
5617774 AGATTTGATA
5617784 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAG-AGATATGATTT
*
5617807 TGTAATCTTAGAGATTTGATTT
1 TGTAATCTTAGAGATATGATTT
5617829 GTAGATACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.31, C:0.04, G:0.18, T:0.47
Consensus pattern (22 bp):
TGTAATCTTAGAGATATGATTT
Found at i:5619222 original size:15 final size:15
Alignment explanation
Indices: 5619202--5619234 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
5619192 AATTGGACCT
5619202 AAATTTTAAAATCTA
1 AAATTTTAAAATCTA
5619217 AAATTTTAAAATCTA
1 AAATTTTAAAATCTA
5619232 AAA
1 AAA
5619235 AGTAGAGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (15 bp):
AAATTTTAAAATCTA
Found at i:5622383 original size:38 final size:38
Alignment explanation
Indices: 5622332--5622405 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
5622322 TTTTTTTAGG
*
5622332 TTAATATACTATTTAGCACATGAGTTTAGCTTTAATGT
1 TTAATATACTATTTAGCACATAAGTTTAGCTTTAATGT
*
5622370 TTAATATACTATTTAGTACATAAGTTTAGCTTTAAT
1 TTAATATACTATTTAGCACATAAGTTTAGCTTTAAT
5622406 ATTCGATTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (38 bp):
TTAATATACTATTTAGCACATAAGTTTAGCTTTAATGT
Found at i:5624009 original size:118 final size:118
Alignment explanation
Indices: 5623765--5624009 Score: 379
Period size: 118 Copynumber: 2.1 Consensus size: 118
5623755 AATCTTCTTC
*
5623765 TTGA-TTTTTGTGGAGAGGGAGCAATCATACGTACGTAACTAGCCATGCTTGTCTTTATGTCTAT
1 TTGACTTTTTGTGGAGAGGGAGCAATCATACGTACGTAACTAGCCATGCTTGTCTTTATGCCTAT
*
5623829 ATGCAGAGTCTAGAACTCAAACTAATTGATGCATTAATTGCCCAAAGCAGACA
66 AAGCAGAGTCTAGAACTCAAACTAATTGATGCATTAATTGCCCAAAGCAGACA
* * * *
5623882 TTGATTTTTTGTGGGGAGGGAGCAATCATACTTATGTAACTAGCCATGCTTGTCTTTATGCCTAT
1 TTGACTTTTTGTGGAGAGGGAGCAATCATACGTACGTAACTAGCCATGCTTGTCTTTATGCCTAT
* *
5623947 AAGCAGAG-CTTCGAACTC-AACTAATTGATGCATTAATTGGCCAAAGCAGACA
66 AAGCAGAGTC-TAGAACTCAAACTAATTGATGCATTAATTGCCCAAAGCAGACA
5623999 TTGACCTTTTT
1 TTGA-CTTTTT
5624010 TTCTTTTTCT
Statistics
Matches: 117, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
117 42 0.36
118 75 0.64
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (118 bp):
TTGACTTTTTGTGGAGAGGGAGCAATCATACGTACGTAACTAGCCATGCTTGTCTTTATGCCTAT
AAGCAGAGTCTAGAACTCAAACTAATTGATGCATTAATTGCCCAAAGCAGACA
Found at i:5627545 original size:16 final size:16
Alignment explanation
Indices: 5627524--5627555 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5627514 GTTCGCTGTT
5627524 TTGGATTAGAGGTGTA
1 TTGGATTAGAGGTGTA
5627540 TTGGATTAGAGGTGTA
1 TTGGATTAGAGGTGTA
5627556 ATAGCAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TTGGATTAGAGGTGTA
Found at i:5627596 original size:45 final size:44
Alignment explanation
Indices: 5627536--5627626 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 44
5627526 GGATTAGAGG
* * *
5627536 TGTATTGGATTAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
5627581 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
5627625 TG
1 TG
5627627 AAATAGAGGT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 18 0.46
45 21 0.54
ACGTcount: A:0.30, C:0.05, G:0.29, T:0.36
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:5627812 original size:18 final size:17
Alignment explanation
Indices: 5627791--5627825 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5627781 TTATTATTAA
*
5627791 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
5627809 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
5627826 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:5627879 original size:157 final size:157
Alignment explanation
Indices: 5627685--5627994 Score: 575
Period size: 157 Copynumber: 2.0 Consensus size: 157
5627675 CCCTTAGCAT
* *
5627685 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTATCAA
1 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAAATTATTAATATCAA
* *
5627750 TAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
5627815 TTTAATAAAATTCTTAATAATTACCAG
131 TTTAATAAAATTCTTAATAATTACCAG
*
5627842 AAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAAATTATTAATATCAA
1 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAAATTATTAATATCAA
5627907 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
5627972 TTTAATAAAATTCTTAATAATTA
131 TTTAATAAAATTCTTAATAATTA
5627995 ATATTCTTAT
Statistics
Matches: 148, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 148 1.00
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (157 bp):
AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAAATTATTAATATCAA
TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
TTTAATAAAATTCTTAATAATTACCAG
Found at i:5627965 original size:16 final size:16
Alignment explanation
Indices: 5627928--5627969 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
5627918 TTAATCATAT
*
5627928 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
5627944 TT-AAATATATTATAA
1 TTAAAATATATTATAA
5627959 TTAAAATATAT
1 TTAAAATATAT
5627970 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:5627976 original size:14 final size:15
Alignment explanation
Indices: 5627937--5627978 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
5627927 TTTAAACATA
*
5627937 ATTATTATTAAATAT
1 ATTATAATTAAATAT
5627952 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
5627966 A-TATAATTTAATA
1 ATTATAATTAAATA
5627979 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:5627991 original size:82 final size:82
Alignment explanation
Indices: 5627748--5627997 Score: 222
Period size: 82 Copynumber: 3.1 Consensus size: 82
5627738 TATTATTATC
* *
5627748 AATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATAT
1 AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATAT
5627813 AATTTAATAAAATTCTT
66 AATTTAATAAAATTCTT
* * * * ** **
5627830 AATAATTACCAGA-AATTT-GT--T-TTGGTAAATTATTATTGTTATT-GTTAT-TTA-AATTTT
1 AATAA-TA--A-ATAATTTAATCATATT--TAAA-CATAATTATTATTAAATATATTATAATTAA
* *
5627887 AATA-A-AA-TTATTAATA-TC--
59 AATATATAATTTAATAAAATTCTT
5627905 AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATAT
1 AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATAT
5627970 AATTTAATAAAATTCTT
66 AATTTAATAAAATTCTT
*
5627987 AATAATTAATA
1 AATAATAAATA
5627998 TTCTTATATG
Statistics
Matches: 124, Mismatches: 23, Indels: 42
0.66 0.12 0.22
Matches are distributed among these distances:
71 1 0.01
72 6 0.05
73 11 0.09
74 9 0.07
75 9 0.07
76 10 0.08
77 3 0.02
78 9 0.07
79 9 0.07
80 3 0.02
81 10 0.08
82 18 0.15
83 9 0.07
84 11 0.09
85 5 0.04
86 1 0.01
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (82 bp):
AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATAT
AATTTAATAAAATTCTT
Found at i:5628078 original size:157 final size:155
Alignment explanation
Indices: 5627749--5628079 Score: 348
Period size: 157 Copynumber: 2.1 Consensus size: 155
5627739 ATTATTATCA
*
5627749 ATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATA
1 ATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATA
* * * * * * * * * *
5627814 ATTTAATAAAATTCTTAATAATTACCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATT
66 ATTTAATAAAATTCTTAATAATTAACACAAATATGATTTAGTAAATCATTAATGATATTGATATA
*** *
5627879 TAAATTTTAATAAAATTATTAATAT
131 TAAAAGATAATAAAATAATTAATAT
*
5627904 CAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATA
1 --ATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATA
* ** *
5627969 TAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTATTCAAATCA-TAAT-ATA-T
64 TAATTTAATAAAATTCTTAATAATTAACA--CAAATATG-ATTTAGT-AAATCATTAATGATATT
*
5628031 GATACTATAAAAGATAATTTGAAATAATTAATAT
125 GATA-TATAAAAGATAA--TAAAATAATTAATAT
*
5628065 -TAA-ATATATTTTAAT
1 ATAATAAATATTTTAAT
5628080 TAAAATATAT
Statistics
Matches: 144, Mismatches: 23, Indels: 14
0.80 0.13 0.08
Matches are distributed among these distances:
157 98 0.68
158 7 0.05
159 14 0.10
160 7 0.05
161 18 0.12
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (155 bp):
ATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATA
ATTTAATAAAATTCTTAATAATTAACACAAATATGATTTAGTAAATCATTAATGATATTGATATA
TAAAAGATAATAAAATAATTAATAT
Found at i:5633505 original size:20 final size:19
Alignment explanation
Indices: 5633482--5633573 Score: 77
Period size: 20 Copynumber: 4.8 Consensus size: 19
5633472 ATAATTAAAT
5633482 ATAAAAATTATAAAAATTCA
1 ATAAAAATTATAAAAATT-A
*
5633502 ATAAAAAGTATAAAAAATTTA
1 ATAAAAATTAT-AAAAA-TTA
5633523 A-AAAAGA-TATAAATAATT-
1 ATAAAA-ATTATAAA-AATTA
*
5633541 ATAAAAATGATAAAAATT-
1 ATAAAAATTATAAAAATTA
5633559 ATAAGAAA-TATAAAA
1 ATAA-AAATTATAAAA
5633574 TACATAAAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
18 16 0.26
19 17 0.27
20 19 0.31
21 8 0.13
22 2 0.03
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.27
Consensus pattern (19 bp):
ATAAAAATTATAAAAATTA
Found at i:5633507 original size:11 final size:9
Alignment explanation
Indices: 5633481--5633600 Score: 86
Period size: 9 Copynumber: 12.9 Consensus size: 9
5633471 AATAATTAAA
5633481 TATAAAAAT
1 TATAAAAAT
5633490 TATAAAAAT
1 TATAAAAAT
*
5633499 TCAATAAAAAG
1 T--ATAAAAAT
5633510 TATAAAAAAT
1 TAT-AAAAAT
*
5633520 T-TAAAAAAGA
1 TAT-AAAAA-T
5633530 TATAAATAAT
1 TATAAA-AAT
5633540 TATAAAAAT
1 TATAAAAAT
*
5633549 GATAAAAAT
1 TATAAAAAT
5633558 TATAAGAAA-
1 TATAA-AAAT
5633567 TAT-AAAAT
1 TATAAAAAT
*
5633575 ACATAAAAA-
1 -TATAAAAAT
* *
5633584 AATGAAAAT
1 TATAAAAAT
5633593 TATAAAAA
1 TATAAAAA
5633601 ATAAATAAAT
Statistics
Matches: 89, Mismatches: 11, Indels: 22
0.73 0.09 0.18
Matches are distributed among these distances:
7 3 0.03
8 7 0.08
9 45 0.51
10 23 0.26
11 11 0.12
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.27
Consensus pattern (9 bp):
TATAAAAAT
Found at i:5633556 original size:38 final size:38
Alignment explanation
Indices: 5633514--5633601 Score: 96
Period size: 38 Copynumber: 2.4 Consensus size: 38
5633504 AAAAAGTATA
*
5633514 AAAAATT-TAAAAAAGATATAAATA-ATTATAAAAATGAT
1 AAAAATTATAAAAAAGATA-AAATACA-TAAAAAAATGAT
* *
5633552 AAAAATTATAAGAAATATAAAATACATAAAAAAATG--
1 AAAAATTATAAAAAAGATAAAATACATAAAAAAATGAT
5633588 -AAAATTATAAAAAA
1 AAAAATTATAAAAAA
5633602 TAAATAAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
35 13 0.30
38 21 0.48
39 10 0.23
ACGTcount: A:0.69, C:0.01, G:0.05, T:0.25
Consensus pattern (38 bp):
AAAAATTATAAAAAAGATAAAATACATAAAAAAATGAT
Found at i:5633585 original size:59 final size:58
Alignment explanation
Indices: 5633472--5633585 Score: 133
Period size: 59 Copynumber: 1.9 Consensus size: 58
5633462 ATAATAATTA
* * **
5633472 ATAATTAAATATAAAAATTATAAAAATTCAATAAAAAGTATAAAAAATTTAAAAAAGAT
1 ATAAATAAATATAAAAATGATAAAAATT-AATAAAAAGTATAAAAAATAAAAAAAAGAT
*
5633531 ATAAATAATTATAAAAATGATAAAAATT-ATAAGAAA-TATAAAATACATAAAAAAA
1 ATAAATAAATATAAAAATGATAAAAATTAATAA-AAAGTATAAAA-A-ATAAAAAAA
5633586 TGAAAATTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
57 11 0.23
58 4 0.09
59 32 0.68
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.27
Consensus pattern (58 bp):
ATAAATAAATATAAAAATGATAAAAATTAATAAAAAGTATAAAAAATAAAAAAAAGAT
Found at i:5634140 original size:21 final size:20
Alignment explanation
Indices: 5634114--5634157 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
5634104 ATATTTCTTT
5634114 ATTTTT-TTGTAATTTTATATA
1 ATTTTTATT-TAA-TTTATATA
5634135 ATTTTTAATTTAATTTATATA
1 ATTTTT-ATTTAATTTATATA
5634156 AT
1 AT
5634158 ATTCTTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 16 0.76
22 3 0.14
23 2 0.10
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
ATTTTTATTTAATTTATATA
Found at i:5634152 original size:37 final size:37
Alignment explanation
Indices: 5634076--5634152 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 37
5634066 TAATTTTCTA
* * *
5634076 TATTGTTTTGTAGTTTTTATCATTTTATATATTTCTT
1 TATTGTTTTGTAATTTTTATAATTTTATATATTTATT
*
5634113 TATTTTTTTGTAATTTTATATAATTTT-TA-ATTTAATT
1 TATTGTTTTGTAATTTT-TATAATTTTATATATTT-ATT
5634150 TAT
1 TAT
5634153 ATAATATTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
36 4 0.12
37 22 0.65
38 8 0.24
ACGTcount: A:0.25, C:0.03, G:0.05, T:0.68
Consensus pattern (37 bp):
TATTGTTTTGTAATTTTTATAATTTTATATATTTATT
Found at i:5634183 original size:23 final size:23
Alignment explanation
Indices: 5634128--5634177 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
5634118 TTTTGTAATT
* *
5634128 TTATATAAT-TT-TTAATTTAAT
1 TTATATAATATTCTTAATATAAA
5634149 TTATATAATATTCTTAATATAAA
1 TTATATAATATTCTTAATATAAA
5634172 TTATAT
1 TTATAT
5634178 TTTATTTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 9 0.36
22 2 0.08
23 14 0.56
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
TTATATAATATTCTTAATATAAA
Found at i:5649574 original size:138 final size:139
Alignment explanation
Indices: 5649326--5649603 Score: 540
Period size: 138 Copynumber: 2.0 Consensus size: 139
5649316 GACAAAAGGA
5649326 GAAATTGAGATGGATAAAGATATAAACTTTTAAGTGCTGAAGGAGCAAGACAAAACACAAAAATT
1 GAAATTGAGATGGATAAAGATATAAACTTTTAAGTGCTGAAGGAGCAAGACAAAACACAAAAATT
5649391 CCACATTGACACCATATGCCGATTACACATGCAAAGTAACAGAGGACACAATT-GGCAAGTATGC
66 CCACATTGACACCATATGCCGATTACACATGCAAAGTAACAGAGGACACAATTGGGCAAGTATGC
5649455 CTATGTAGG
131 CTATGTAGG
5649464 GAAATTGAGATGGATAAAGATATAAACTTTTAAGTGCTGAAGGAGCAAGACAAAACACAAAAATT
1 GAAATTGAGATGGATAAAGATATAAACTTTTAAGTGCTGAAGGAGCAAGACAAAACACAAAAATT
*
5649529 CCACATTGACACCATATGCCGATTACACATGCAAAGTTACAGAGGACACAATTGGGCAAGTATGC
66 CCACATTGACACCATATGCCGATTACACATGCAAAGTAACAGAGGACACAATTGGGCAAGTATGC
5649594 CTATGTAGG
131 CTATGTAGG
5649603 G
1 G
5649604 CTCATAGTCA
Statistics
Matches: 138, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
138 117 0.85
139 21 0.15
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.21
Consensus pattern (139 bp):
GAAATTGAGATGGATAAAGATATAAACTTTTAAGTGCTGAAGGAGCAAGACAAAACACAAAAATT
CCACATTGACACCATATGCCGATTACACATGCAAAGTAACAGAGGACACAATTGGGCAAGTATGC
CTATGTAGG
Found at i:5668741 original size:87 final size:86
Alignment explanation
Indices: 5668562--5668728 Score: 214
Period size: 87 Copynumber: 1.9 Consensus size: 86
5668552 AAAATGCTAT
* * *
5668562 ATATTTTAAAAAATTCATATAAATATTGATAATTTAATAGATATATGGGTAAAGTCTAAGATGTT
1 ATATTTTAAAAAATTCATATAAATATTGATAAATTAATAGATATATGGATAAAGTCTAAGATATT
5668627 TTGGTAAATCTAAAAGGTTAG
66 TTGGTAAATCTAAAAGGTTAG
* * *
5668648 ATATTTTAAGAAA-TC-TATAAAATATTGATAAATTGATAGAAATATATTGATAAAGTCTTAA-A
1 ATATTTTAAAAAATTCATAT-AAATATTGATAAATTAATAG--ATATATGGATAAAGTC-TAAGA
*
5668710 TATTTTGGTAAATTTAAAA
62 TATTTTGGTAAATCTAAAA
5668729 TTTTAGTTAT
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
84 3 0.04
85 20 0.29
86 12 0.17
87 32 0.46
88 3 0.04
ACGTcount: A:0.46, C:0.03, G:0.13, T:0.39
Consensus pattern (86 bp):
ATATTTTAAAAAATTCATATAAATATTGATAAATTAATAGATATATGGATAAAGTCTAAGATATT
TTGGTAAATCTAAAAGGTTAG
Found at i:5668748 original size:20 final size:20
Alignment explanation
Indices: 5668723--5668767 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
5668713 TTTGGTAAAT
* *
5668723 TTAAAATTTTAGTTATTTTG
1 TTAAAATATTAGATATTTTG
5668743 TTAAAATATTAGATATTTTG
1 TTAAAATATTAGATATTTTG
*
5668763 GTAAA
1 TTAAA
5668768 TCTATATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (20 bp):
TTAAAATATTAGATATTTTG
Found at i:5668817 original size:20 final size:20
Alignment explanation
Indices: 5668746--5668821 Score: 68
Period size: 22 Copynumber: 3.9 Consensus size: 20
5668736 TATTTTGTTA
* *
5668746 AAATAT-TAGATATTTTGGT
1 AAATATATATATATATTGGT
* * *
5668765 AAATCTATATAAATATTAGT
1 AAATATATATATATATTGGT
5668785 AAATCGATATATATATATTGGT
1 AAAT--ATATATATATATTGGT
5668807 AAA-ATAT-TATATATT
1 AAATATATATATATATT
5668822 TTGGTTAATC
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
18 8 0.17
19 9 0.20
20 13 0.28
22 16 0.35
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (20 bp):
AAATATATATATATATTGGT
Found at i:5668825 original size:20 final size:20
Alignment explanation
Indices: 5668736--5668826 Score: 69
Period size: 20 Copynumber: 4.5 Consensus size: 20
5668726 AAATTTTAGT
* *
5668736 TATTTTGTTAAA-ATATTAGA
1 TATTTTGGTAAATATA-TATA
*
5668756 TATTTTGGTAAATCTATATA
1 TATTTTGGTAAATATATATA
* * *
5668776 AATATTAGTAAATCGATATATA
1 TATTTTGGTAAAT--ATATATA
*
5668798 TATATTGGTAAA-ATATTATA
1 TATTTTGGTAAATATA-TATA
5668818 TATTTTGGT
1 TATTTTGGT
5668827 TAATCCAAAG
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
19 3 0.05
20 36 0.63
21 2 0.04
22 16 0.28
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.47
Consensus pattern (20 bp):
TATTTTGGTAAATATATATA
Found at i:5668867 original size:20 final size:20
Alignment explanation
Indices: 5668839--5668887 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
5668829 ATCCAAAGTG
*
5668839 TTTGGTAAAATATTAGATAT
1 TTTGATAAAATATTAGATAT
* *
5668859 TTTGATAAATTGTTAGATAT
1 TTTGATAAAATATTAGATAT
5668879 TTTGATAAA
1 TTTGATAAA
5668888 TCTTTAGCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.47
Consensus pattern (20 bp):
TTTGATAAAATATTAGATAT
Found at i:5668894 original size:20 final size:20
Alignment explanation
Indices: 5668851--5668945 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
5668841 TGGTAAAATA
5668851 TTAGATATTTTGATAAAT-T
1 TTAGATATTTTGATAAATCT
5668870 GTTAGATATTTTGATAAATCT
1 -TTAGATATTTTGATAAATCT
* * * *
5668891 TTAGCA-ATTTGGGTAAACCG
1 TTAG-ATATTTTGATAAATCT
*
5668911 TTAGAT-GTTTGAATAAATCT
1 TTAGATATTTTG-ATAAATCT
* *
5668931 TTAGAAATATTGATA
1 TTAGATATTTTGATA
5668946 TATCGCTAGA
Statistics
Matches: 58, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
19 4 0.07
20 49 0.84
21 5 0.09
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.43
Consensus pattern (20 bp):
TTAGATATTTTGATAAATCT
Found at i:5670950 original size:18 final size:18
Alignment explanation
Indices: 5670927--5670962 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5670917 GTAGGTTTCC
* *
5670927 AAAAATCGAAATGGAAAT
1 AAAAATAGAAATGAAAAT
5670945 AAAAATAGAAATGAAAAT
1 AAAAATAGAAATGAAAAT
5670963 TTGCAATCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.67, C:0.03, G:0.14, T:0.17
Consensus pattern (18 bp):
AAAAATAGAAATGAAAAT
Found at i:5686400 original size:44 final size:44
Alignment explanation
Indices: 5686339--5686425 Score: 174
Period size: 44 Copynumber: 2.0 Consensus size: 44
5686329 AGGTAAGTAC
5686339 AAAAAAATAAATAAATAAAAATAATGCAGAGACCGGTTTTTTCA
1 AAAAAAATAAATAAATAAAAATAATGCAGAGACCGGTTTTTTCA
5686383 AAAAAAATAAATAAATAAAAATAATGCAGAGACCGGTTTTTTC
1 AAAAAAATAAATAAATAAAAATAATGCAGAGACCGGTTTTTTC
5686426 TCTTTTATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.54, C:0.09, G:0.11, T:0.25
Consensus pattern (44 bp):
AAAAAAATAAATAAATAAAAATAATGCAGAGACCGGTTTTTTCA
Found at i:5691539 original size:19 final size:19
Alignment explanation
Indices: 5691515--5691680 Score: 75
Period size: 19 Copynumber: 8.7 Consensus size: 19
5691505 AGAGGCGCCA
5691515 ATGAATATTGTAATTTTGT
1 ATGAATATTGTAATTTTGT
*
5691534 ATGAATATTGTAATTATTTT
1 ATGAATATTGTAATT-TTGT
5691554 AT-AATTAAATTTGT-ATTTATAGTT
1 ATGAA-T--A-TTGTAATTT-T-G-T
* * *
5691578 TTGGAT-TAGT-ATTTTGT
1 ATGAATATTGTAATTTTGT
*
5691595 ATAAATATTGTAATTTTGT
1 ATGAATATTGTAATTTTGT
* *
5691614 ATGAACATTGTAA-TAT-T
1 ATGAATATTGTAATTTTGT
* *
5691631 AT-AATTTTGTATGAATATTG-
1 ATGAATATTG--T-AATTTTGT
5691651 -T-AATATTGTAA-TTTGT
1 ATGAATATTGTAATTTTGT
5691667 ATGAATATTGTAAT
1 ATGAATATTGTAAT
5691681 GTCGAGATAT
Statistics
Matches: 109, Mismatches: 18, Indels: 40
0.65 0.11 0.24
Matches are distributed among these distances:
15 3 0.03
16 7 0.06
17 9 0.08
18 17 0.16
19 45 0.41
20 14 0.13
21 1 0.01
22 5 0.05
23 4 0.04
24 3 0.03
25 1 0.01
ACGTcount: A:0.34, C:0.01, G:0.13, T:0.52
Consensus pattern (19 bp):
ATGAATATTGTAATTTTGT
Found at i:5691629 original size:27 final size:27
Alignment explanation
Indices: 5691598--5691680 Score: 141
Period size: 27 Copynumber: 3.1 Consensus size: 27
5691588 ATTTTGTATA
*
5691598 AATATTGTAATTTTGTATGAACATTGT
1 AATATTGTAATTTTGTATGAATATTGT
*
5691625 AATATTATAATTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGT
5691652 AATATTGTAA-TTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGT
5691678 AAT
1 AAT
5691681 GTCGAGATAT
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
26 19 0.36
27 34 0.64
ACGTcount: A:0.36, C:0.01, G:0.13, T:0.49
Consensus pattern (27 bp):
AATATTGTAATTTTGTATGAATATTGT
Found at i:5691909 original size:16 final size:16
Alignment explanation
Indices: 5691866--5691909 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
5691856 AAAATCAAAT
*
5691866 AAAATTTAATTATATA
1 AAAATTAAATTATATA
* *
5691882 AAAGTTACATTATATA
1 AAAATTAAATTATATA
5691898 AAAATTAAATTA
1 AAAATTAAATTA
5691910 GTTAACAACA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (16 bp):
AAAATTAAATTATATA
Found at i:5691985 original size:38 final size:38
Alignment explanation
Indices: 5691942--5692023 Score: 164
Period size: 38 Copynumber: 2.2 Consensus size: 38
5691932 AAAAAGTCAG
5691942 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
5691980 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
5692018 TTATAA
1 TTATAA
5692024 ACTTTATATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (38 bp):
TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
Found at i:5692197 original size:19 final size:19
Alignment explanation
Indices: 5692173--5692283 Score: 88
Period size: 19 Copynumber: 5.6 Consensus size: 19
5692163 ATAAAATAAC
5692173 TACAATATTCATACAAAAT
1 TACAATATTCATACAAAAT
5692192 TACAATATTCATACAAAA-
1 TACAATATTCATACAAAAT
*
5692210 TAC--TATTCCAAAACTATAAAT
1 TACAATATT-C-ATAC-A-AAAT
*
5692231 ATA-AATTTAATT-ATAAAATAAT
1 -TACAA--T-ATTCATACAA-AAT
5692253 TACAATATTCATACAAAAT
1 TACAATATTCATACAAAAT
5692272 TACAATATTCAT
1 TACAATATTCAT
5692284 TGGCGCCTCT
Statistics
Matches: 74, Mismatches: 4, Indels: 28
0.70 0.04 0.26
Matches are distributed among these distances:
16 4 0.05
17 1 0.01
18 6 0.08
19 37 0.50
20 9 0.12
21 3 0.04
22 8 0.11
23 2 0.03
25 1 0.01
26 3 0.04
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (19 bp):
TACAATATTCATACAAAAT
Found at i:5692317 original size:27 final size:27
Alignment explanation
Indices: 5692279--5692345 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
5692269 AATTACAATA
*
5692279 TTCATTGGCGCCTCTCTATGAGGCACC
1 TTCATTGGCGCCTCTCTATGAGACACC
*
5692306 TTCATTGGCGCCTCTCTGTGAGACACC
1 TTCATTGGCGCCTCTCTATGAGACACC
5692333 TTCATTGGCGCCT
1 TTCATTGGCGCCT
5692346 ACCTGATAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.13, C:0.33, G:0.22, T:0.31
Consensus pattern (27 bp):
TTCATTGGCGCCTCTCTATGAGACACC
Found at i:5697236 original size:31 final size:30
Alignment explanation
Indices: 5697201--5697277 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
5697191 AAAGCCCTAA
5697201 ATAAATATCTTCGAATAAACTTAAACC-TTAT
1 ATAAATATCTTCGAA-AAACTT-AACCTTTAT
**
5697232 ATAAATAT-TTTTAAAAACTTAACCTTTAT
1 ATAAATATCTTCGAAAAACTTAACCTTTAT
* *
5697261 ATAAATAACTTCTAAAA
1 ATAAATATCTTCGAAAA
5697278 TATTCCCCCA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 4 0.10
29 17 0.43
30 11 0.28
31 8 0.20
ACGTcount: A:0.48, C:0.13, G:0.01, T:0.38
Consensus pattern (30 bp):
ATAAATATCTTCGAAAAACTTAACCTTTAT
Found at i:5699984 original size:15 final size:14
Alignment explanation
Indices: 5699952--5699980 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5699942 GTAATAGCAT
5699952 AATG-AAAAAATTA
1 AATGAAAAAAATTA
5699965 AATGAAAAAAATTA
1 AATGAAAAAAATTA
5699979 AA
1 AA
5699981 ATGACTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (14 bp):
AATGAAAAAAATTA
Found at i:5700186 original size:37 final size:37
Alignment explanation
Indices: 5700124--5700432 Score: 139
Period size: 37 Copynumber: 7.9 Consensus size: 37
5700114 TTAATAAAAA
*
5700124 TATATAATTTAATAAAATTCTTAATAT-TAAATATTCT
1 TATATAATTTAATAAAATTCATAATATAT-AATATTCT
* *
5700161 TATATGAATTTACTAAAA-TCATAATATATAATATTAT
1 TATAT-AATTTAATAAAATTCATAATATATAATATTCT
* * ****
5700198 AAAATATAATTTAA-AATAATTATTATTAAATATAATTTAATAAAAA
1 --TATATAATTTAATAA-AA-T-TCA-T-AATAT-A--TAATATTCT
**
5700244 TATATAATTTAATAAAATTTTTAATAT-TAAATATTCT
1 TATATAATTTAATAAAATTCATAATATAT-AATATTCT
* **
5700281 TATATGAATTTACTAAAA-TCATAATATATAATACTGTAA
1 TATAT-AATTTAATAAAATTCATAATATATAATA-T-TCT
* ****
5700320 AATATAATTTAAAATAATAATT-ATTAAATATAATTTAATAAAAA
1 TATATAATTT--AATAA-AATTCA-T-AATAT-A--TAATATTCT
* *
5700364 TATATAATTTAATAAAATTCTTAATATA-ATTATTCT
1 TATATAATTTAATAAAATTCATAATATATAATATTCT
*
5700400 TATATGAATTTAGTAAAA-TCATAATATATAATA
1 TATAT-AATTTAATAAAATTCATAATATATAATA
5700433 CTATAAAAAT
Statistics
Matches: 207, Mismatches: 34, Indels: 62
0.68 0.11 0.20
Matches are distributed among these distances:
36 18 0.09
37 56 0.27
38 38 0.18
39 10 0.05
40 14 0.07
41 11 0.05
42 10 0.05
43 11 0.05
44 26 0.13
45 2 0.01
46 11 0.05
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (37 bp):
TATATAATTTAATAAAATTCATAATATATAATATTCT
Found at i:5700206 original size:22 final size:24
Alignment explanation
Indices: 5700161--5700207 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
5700151 TAAATATTCT
5700161 TATATGAATTTACTAAAATCATAA
1 TATATGAATTTACTAAAATCATAA
5700185 TATAT-AATATTA-TAAAAT-ATAA
1 TATATGAAT-TTACTAAAATCATAA
5700207 T
1 T
5700208 TTAAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.23
23 9 0.41
24 8 0.36
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (24 bp):
TATATGAATTTACTAAAATCATAA
Found at i:5700224 original size:120 final size:120
Alignment explanation
Indices: 5700087--5700445 Score: 641
Period size: 120 Copynumber: 3.0 Consensus size: 120
5700077 TTAATCATAT
*
5700087 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
*
5700152 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATATTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
*
5700207 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTTTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
*
5700272 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTGTAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
*
5700327 TTTAAAATAATAATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATA-T
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
* *
5700391 AATTATTCTTATATGAATTTAGTAAAATCATAATATATAATACTATAAAA-ATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
5700445 T
1 T
5700446 ATATAATCTA
Statistics
Matches: 230, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
118 5 0.02
119 48 0.21
120 177 0.77
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (120 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:5700228 original size:26 final size:25
Alignment explanation
Indices: 5700188--5700250 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 25
5700178 ATCATAATAT
5700188 ATAATATTATAAAATATAATTTAAA
1 ATAATATTATAAAATATAATTTAAA
*
5700213 ATAATTATTATTAAATATAATTTAATA
1 ATAA-TATTATAAAATATAATTTAA-A
*
5700240 AAAATA-TATAA
1 ATAATATTATAA
5700251 TTTAATAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 8 0.24
26 21 0.64
27 4 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
ATAATATTATAAAATATAATTTAAA
Found at i:5700341 original size:13 final size:12
Alignment explanation
Indices: 5700317--5700357 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
5700307 TATAATACTG
5700317 TAAAATATAATT
1 TAAAATATAATT
5700329 TAAAATAATAATT
1 TAAAAT-ATAATT
*
5700342 ATTAAATATAATT
1 -TAAAATATAATT
5700355 TAA
1 TAA
5700358 TAAAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 8 0.32
13 12 0.48
14 5 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAAATATAATT
Found at i:5704358 original size:12 final size:12
Alignment explanation
Indices: 5704341--5704382 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 12
5704331 AACTAATCAT
5704341 CTCTCAAAATTC
1 CTCTCAAAATTC
*
5704353 CTCTC-AATTTC
1 CTCTCAAAATTC
*
5704364 CT-TCAAAATTT
1 CTCTCAAAATTC
5704375 CTCTCAAA
1 CTCTCAAA
5704383 TCCATATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
10 2 0.08
11 13 0.52
12 10 0.40
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (12 bp):
CTCTCAAAATTC
Found at i:5704424 original size:29 final size:28
Alignment explanation
Indices: 5704370--5704426 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
5704360 TTTCCTTCAA
*
5704370 AATTTCTCTCAAATCCATATTTAATTTC
1 AATTTCTCTCAAATCCATATTAAATTTC
* * *
5704398 AATTTGCTCTCAAATTCTTCTTAAATTTC
1 AATTT-CTCTCAAATCCATATTAAATTTC
5704427 TCTTAAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.30, C:0.21, G:0.02, T:0.47
Consensus pattern (28 bp):
AATTTCTCTCAAATCCATATTAAATTTC
Found at i:5705414 original size:21 final size:20
Alignment explanation
Indices: 5705375--5705412 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5705365 TAACGAGGTA
5705375 AATTTTATATTAGATTTTAC
1 AATTTTATATTAGATTTTAC
5705395 AATTATTATA-TAGATTTT
1 AATT-TTATATTAGATTTT
5705413 TAAAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (20 bp):
AATTTTATATTAGATTTTAC
Found at i:5706780 original size:69 final size:70
Alignment explanation
Indices: 5706702--5706891 Score: 346
Period size: 70 Copynumber: 2.7 Consensus size: 70
5706692 ATATTTTAAA
* *
5706702 TATTTTGATATTATTTTATGTACTAAAATAGAAGTTTATTTGATGTAATAAAATA-AAATTTTTT
1 TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAAATTTTTT
5706766 TGAGT
66 TGAGT
5706771 TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAAATTTTTT
1 TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAAATTTTTT
5706836 TGAGT
66 TGAGT
*
5706841 TATTTTGATATTATTTGATATAATAAAATAGAAGTTTATTTGATGTAATAA
1 TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAA
5706892 CATGAGCTTA
Statistics
Matches: 117, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
69 53 0.45
70 64 0.55
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.48
Consensus pattern (70 bp):
TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAAATTTTTT
TGAGT
Found at i:5706809 original size:25 final size:25
Alignment explanation
Indices: 5706712--5706891 Score: 134
Period size: 25 Copynumber: 7.6 Consensus size: 25
5706702 TATTTTGATA
* *
5706712 TTATTTTATGTACTAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
*
5706737 TTATTTGATGTAATAAAATA-AAAT
1 TTATTTGATGTAATAAAATAGAAGT
* ** *
5706761 TTTTTTGA-GT--T-ATTTTG-A-T
1 TTATTTGATGTAATAAAATAGAAGT
5706780 ATTATTTGATGTAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
*
5706806 TTATTTGATGTAATAAAATAGAAAT
1 TTATTTGATGTAATAAAATAGAAGT
* ** *
5706831 TTTTTTGA-GT--T-ATTTTG-A-T
1 TTATTTGATGTAATAAAATAGAAGT
*
5706850 ATTATTTGATATAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
5706876 TTATTTGATGTAATAA
1 TTATTTGATGTAATAA
5706892 CATGAGCTTA
Statistics
Matches: 118, Mismatches: 22, Indels: 30
0.69 0.13 0.18
Matches are distributed among these distances:
19 2 0.02
20 18 0.15
21 7 0.06
22 1 0.01
23 4 0.03
24 18 0.15
25 66 0.56
26 2 0.02
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.47
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:5710003 original size:124 final size:124
Alignment explanation
Indices: 5709744--5710089 Score: 561
Period size: 124 Copynumber: 2.8 Consensus size: 124
5709734 CCCAAACATG
* *
5709744 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCGTCCTA-
1 CTACTGTAGCAAAAGCGTGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCC-AG
*
5709808 CTAGAAGCGA-TTTATACTATTTGCTCAGAAACGTTAAAAAAAATTATTTCTTCCATGAC
65 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
* * * * *
5709867 CAACAGTAGCAAAATCGTGACCACGAGGGCGCGATTTCACAAATTCTTCCCAAATAGCATCCAGC
1 CTACTGTAGCAAAAGCGTGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCAGC
* *
5709932 TAGATGCGATTTTATACTATTTCCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
*
5709991 CTACTGTAGCAAAAGCGTGTCCACGAGGGCGTGATTTCACAAATTCTTCTCAAATAGCATCCAGC
1 CTACTGTAGCAAAAGCGTGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCAGC
*
5710056 TAGAAGCGATTTTATACTATTTGATCAGAAACGT
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGT
5710090 TAACTCGAAA
Statistics
Matches: 202, Mismatches: 19, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
122 1 0.00
123 64 0.32
124 137 0.68
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGTGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCAGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
Found at i:5713269 original size:3 final size:3
Alignment explanation
Indices: 5713263--5713287 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5713253 TGGTGGAGGT
5713263 GGC GGC GGC GGC GGC GGC GGC GGC G
1 GGC GGC GGC GGC GGC GGC GGC GGC G
5713288 ATGGGGGTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.68, T:0.00
Consensus pattern (3 bp):
GGC
Found at i:5713480 original size:18 final size:18
Alignment explanation
Indices: 5713457--5713498 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
5713447 ACCCAGATAT
*
5713457 TGGAGGCGGCGGCGGAGG
1 TGGAGGCGGCGGAGGAGG
* *
5713475 TGGAGGCGGTGGATGAGG
1 TGGAGGCGGCGGAGGAGG
5713493 TGGAGG
1 TGGAGG
5713499 TGGAGGTGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.14, C:0.10, G:0.64, T:0.12
Consensus pattern (18 bp):
TGGAGGCGGCGGAGGAGG
Found at i:5713694 original size:21 final size:21
Alignment explanation
Indices: 5713660--5713699 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5713650 ACAGCCTTAG
*
5713660 GAGGCTGCGGTGGAGGCGACT
1 GAGGCGGCGGTGGAGGCGACT
*
5713681 GAGGCGGCGTTGGAGGCGA
1 GAGGCGGCGGTGGAGGCGA
5713700 TGCTGCGGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.17, G:0.55, T:0.12
Consensus pattern (21 bp):
GAGGCGGCGGTGGAGGCGACT
Found at i:5718065 original size:23 final size:23
Alignment explanation
Indices: 5718039--5718085 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
5718029 TAAGGTGGAG
*
5718039 TTAGAGTTAAGGTTTTATAGGTT
1 TTAGAGTTAAGGGTTTATAGGTT
* * *
5718062 TTAGTGTTTAGGGTTTATCGGTT
1 TTAGAGTTAAGGGTTTATAGGTT
5718085 T
1 T
5718086 AGGATTTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.19, C:0.02, G:0.28, T:0.51
Consensus pattern (23 bp):
TTAGAGTTAAGGGTTTATAGGTT
Found at i:5725883 original size:23 final size:22
Alignment explanation
Indices: 5725831--5725905 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
5725821 TGATACTACT
* *
5725831 ATAATGTAAACAAAAAAAATAAG
1 ATAAT-TAAATAAAAAAAATAAA
* *
5725854 ATGATTATATAAAAAAATATAAA
1 ATAATTAAATAAAAAAA-ATAAA
* **
5725877 ATTATTAAATATTAAAAATAAA
1 ATAATTAAATAAAAAAAATAAA
5725899 ATAATTA
1 ATAATTA
5725906 CAAATATAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
22 21 0.50
23 21 0.50
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.29
Consensus pattern (22 bp):
ATAATTAAATAAAAAAAATAAA
Found at i:5725910 original size:24 final size:24
Alignment explanation
Indices: 5725866--5725912 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5725856 GATTATATAA
* *
5725866 AAAAATATAAAATTATTAAATATT
1 AAAAATAAAAAATTATCAAATATT
5725890 AAAAATAAAATAATTA-CAAATAT
1 AAAAATAAAA-AATTATCAAATAT
5725913 AAATGTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (24 bp):
AAAAATAAAAAATTATCAAATATT
Found at i:5725914 original size:17 final size:16
Alignment explanation
Indices: 5725860--5725915 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
5725850 TAAGATGATT
*
5725860 ATATAAAAAAATATAAA
1 ATATAAAATAAT-TAAA
*
5725877 ATTATTAAAT-ATTAAA
1 A-TATAAAATAATTAAA
5725893 A-ATAAAATAATTACAA
1 ATATAAAATAATTA-AA
5725909 ATATAAA
1 ATATAAA
5725916 TGTATATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 6 0.19
15 4 0.12
16 8 0.25
17 8 0.25
18 6 0.19
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (16 bp):
ATATAAAATAATTAAA
Found at i:5732951 original size:6 final size:6
Alignment explanation
Indices: 5732940--5732969 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
5732930 AAATATATAT
5732940 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
5732970 AAATACTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:5732979 original size:12 final size:11
Alignment explanation
Indices: 5732962--5732991 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
5732952 TTTTTATTTT
5732962 TATTTTTAAAA
1 TATTTTTAAAA
*
5732973 TACTTTTAAAA
1 TATTTTTAAAA
5732984 TATTTTTA
1 TATTTTTA
5732992 TTTTTTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:5733024 original size:26 final size:24
Alignment explanation
Indices: 5732976--5733025 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
5732966 TTTAAAATAC
* *
5732976 TTTTAAAATATTTTTATTTTTTAT
1 TTTTAAAATATTTTTAATGTTTAT
5733000 TTTTAAAATAATTTTTTAATGTTTAT
1 TTTTAAAAT-A-TTTTTAATGTTTAT
5733026 AAAAATGGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 9 0.41
25 1 0.05
26 12 0.55
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (24 bp):
TTTTAAAATATTTTTAATGTTTAT
Found at i:5734349 original size:22 final size:22
Alignment explanation
Indices: 5734309--5734381 Score: 69
Period size: 22 Copynumber: 3.2 Consensus size: 22
5734299 TATATTCATC
*
5734309 TATATACATATATACATAT-TTT
1 TATATACATA-CTACATATATTT
* *
5734331 AATTTACATAC-ACATATATGTT
1 TATATACATACTACATATAT-TT
5734353 TATATACATACTTACATATATTTT
1 TATATACATAC-TACATATA-TTT
5734377 TATAT
1 TATAT
5734382 TGCATAATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
20 6 0.15
21 1 0.02
22 19 0.46
24 14 0.34
25 1 0.02
ACGTcount: A:0.40, C:0.11, G:0.01, T:0.48
Consensus pattern (22 bp):
TATATACATACTACATATATTT
Found at i:5734445 original size:43 final size:43
Alignment explanation
Indices: 5734397--5734479 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 43
5734387 AATTTTAAAA
* *
5734397 TATATATACATACATATAT-TCTCCATATTTTTATAATTTTATG
1 TATATATACATACACATATATAT-CATATTTTTATAATTTTATG
*
5734440 TATATATACATACACATATATATTATATTTTTATAATTTT
1 TATATATACATACACATATATATCATATTTTTATAATTTT
5734480 TATTTATTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 34 0.94
44 2 0.06
ACGTcount: A:0.37, C:0.10, G:0.01, T:0.52
Consensus pattern (43 bp):
TATATATACATACACATATATATCATATTTTTATAATTTTATG
Found at i:5747256 original size:113 final size:113
Alignment explanation
Indices: 5747028--5747233 Score: 279
Period size: 113 Copynumber: 1.8 Consensus size: 113
5747018 AAATGATCAT
* **
5747028 TTTTTATTGACTTATTATATAAAAAGATAAAAGCATTCTCATAAAAACATAACTTAATTTATATA
1 TTTTTATTGACTTATTATATAAAAAGATAAAAACACCCTCATAAAAACATAACTTAATTTATATA
** * * *
5747093 TGAGAATGTATTTTAATAATTTCAATTTCAAATCTCTTCAAATAAATA
66 TGAGAAAATATTTTAATAATTTAAAATTCAAATATCTTCAAATAAATA
* * * * *
5747141 TTTTTATTGATTTCTTATATAAAAGGATAAAAACACCCTCATAAAAATATAATTTAATTTATATA
1 TTTTTATTGACTTATTATATAAAAAGATAAAAACACCCTCATAAAAACATAACTTAATTTATATA
5747206 TGA-AAAATATTTTAATAATTCTAAAATT
66 TGAGAAAATATTTTAATAATT-TAAAATT
5747234 GAATTAATGT
Statistics
Matches: 80, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
112 15 0.19
113 65 0.81
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (113 bp):
TTTTTATTGACTTATTATATAAAAAGATAAAAACACCCTCATAAAAACATAACTTAATTTATATA
TGAGAAAATATTTTAATAATTTAAAATTCAAATATCTTCAAATAAATA
Found at i:5758095 original size:21 final size:21
Alignment explanation
Indices: 5758071--5758127 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 21
5758061 GAGGAAGTAC
*
5758071 AAAAAATTTTGAGAAAATAC-
1 AAAAAATTTTAAGAAAATACA
* * *
5758091 TAAAAATTTTAAGAGAATCCA
1 AAAAAATTTTAAGAAAATACA
*
5758112 AAAAAATTATAAGAAA
1 AAAAAATTTTAAGAAA
5758128 GCACCAAAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.61, C:0.05, G:0.09, T:0.25
Consensus pattern (21 bp):
AAAAAATTTTAAGAAAATACA
Found at i:5758447 original size:20 final size:21
Alignment explanation
Indices: 5758409--5758449 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
5758399 AAAAAATAAG
5758409 GAAGTATAAAAAATGTATGAA
1 GAAGTATAAAAAATGTATGAA
5758430 GAAGTATAAAAAAT-TATGAA
1 GAAGTATAAAAAATGTATGAA
5758450 TTAACACCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.59, C:0.00, G:0.17, T:0.24
Consensus pattern (21 bp):
GAAGTATAAAAAATGTATGAA
Found at i:5758480 original size:20 final size:21
Alignment explanation
Indices: 5758388--5758483 Score: 58
Period size: 21 Copynumber: 4.7 Consensus size: 21
5758378 AAAAATTTTG
*
5758388 AGGAAATACAAAAAA-AAT-A
1 AGGAAGTACAAAAAAGAATGA
* *
5758407 AGGAAGTATAAAAAATGTATGA
1 AGGAAGTACAAAAAA-GAATGA
* **
5758429 A-GAAGTATAAAAAATTATGA
1 AGGAAGTACAAAAAAGAATGA
** *
5758449 ATTAA-CACCAAAAAAGAATGA
1 AGGAAGTA-CAAAAAAGAATGA
5758470 A-GAAGTACAAAAAA
1 AGGAAGTACAAAAAA
5758484 ACTATAAGAG
Statistics
Matches: 60, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
19 13 0.22
20 16 0.27
21 29 0.48
22 2 0.03
ACGTcount: A:0.64, C:0.05, G:0.15, T:0.17
Consensus pattern (21 bp):
AGGAAGTACAAAAAAGAATGA
Found at i:5758524 original size:22 final size:22
Alignment explanation
Indices: 5758499--5758547 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
5758489 AAGAGAAGTC
5758499 CAAATAACACGAGGAGATACCA
1 CAAATAACACGAGGAGATACCA
5758521 CAAATAACACGAGGAGATACCA
1 CAAATAACACGAGGAGATACCA
*
5758543 AAAAT
1 CAAAT
5758548 TGTGAGGGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.53, C:0.20, G:0.16, T:0.10
Consensus pattern (22 bp):
CAAATAACACGAGGAGATACCA
Found at i:5758974 original size:39 final size:41
Alignment explanation
Indices: 5758893--5759069 Score: 118
Period size: 39 Copynumber: 4.5 Consensus size: 41
5758883 TAGATGTATC
* * * *
5758893 AAAAATCACGAGGGAATACCAAAAAAATATGAGGAAGTACA
1 AAAAATTATGAGGGAATACCAAAAAAATACGAGGAAGCACA
* *
5758934 AAAAATTATGAGGG-ATACC-AAAAACTACGAGGATGCACA
1 AAAAATTATGAGGGAATACCAAAAAAATACGAGGAAGCACA
* * * * * * *
5758973 AAAAATTATGA-AGATGTA-TAAAACATTATGAGAGAA-TACA
1 AAAAATTATGAGGGA-ATACCAAAAAAATACGAG-GAAGCACA
* * * *
5759013 AAAAA-TATGAGGGAATACTAAAAAAAT-TGA-GAAGTAAA
1 AAAAATTATGAGGGAATACCAAAAAAATACGAGGAAGCACA
*
5759051 AAAAATTATGAGAGAATAC
1 AAAAATTATGAGGGAATAC
5759070 TATAAAATCT
Statistics
Matches: 108, Mismatches: 20, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
37 3 0.03
38 9 0.08
39 49 0.45
40 33 0.31
41 14 0.13
ACGTcount: A:0.55, C:0.08, G:0.18, T:0.18
Consensus pattern (41 bp):
AAAAATTATGAGGGAATACCAAAAAAATACGAGGAAGCACA
Found at i:5759036 original size:59 final size:57
Alignment explanation
Indices: 5758905--5759393 Score: 244
Period size: 59 Copynumber: 8.2 Consensus size: 57
5758895 AAATCACGAG
* * * * * *
5758905 GGAATACCAAAAAAATATGAGGAAGTACAAAAAATTATGAG-GGATACCAAAAACTACGA
1 GGAATA-CTAAAAAA-ATGAAGAAGTACTAAAAATTATGAGAGAATA-CAAAAAATATGA
*
5758964 GG-ATGCAC-AAAAAATTATGAAGATGTA-TAAAACATTATGAGAGAATACAAAAAATATGA
1 GGAAT--ACTAAAAAA--ATGAAGAAGTACTAAAA-ATTATGAGAGAATACAAAAAATATGA
** * *
5759023 GGGAATACTAAAAAAATTG-AGAAGTAAAAAAAATTATGAGAGAATACTATAAAATCTGA
1 -GGAATACTAAAAAAA-TGAAGAAGTACTAAAAATTATGAGAGAATAC-AAAAAATATGA
* * * * * * *
5759082 GAAAGAATAAAAAAAATGAAGATGTACTAAAAATTA-GAAGGGTATATCAAAACATATGA
1 GGAATACT-AAAAAAATGAAGAAGTACTAAAAATTATG-AGAGAATA-CAAAAAATATGA
* ** * ** * * *
5759141 GGAAGTATCCAAAGATTATGAGAGAA-TACCAAAAACAAAGAGAAAGTATAAAAAAAATATGA
1 GGAA-TA-CTAAA-AAAATGA-AGAAGTACTAAAAATTATGAG--AGAATACAAAAAATATGA
* * * * * * * *
5759203 GG-AT-GTAAAAATATGATGATGTATTAAAAATTATGAGAAAATACCAAAAATTACGA
1 GGAATACTAAAAAAATGAAGAAGTACTAAAAATTATGAGAGAATA-CAAAAAATATGA
* * * * *
5759259 GGGAATATTAAAAAAAATAAGAGAAAGTACAAAAAATTATAAGAGAATACTATAAAATATGA
1 -GGAATACT-AAAAAAATGA-AG-AAGTACTAAAAATTATGAGAGAATAC-AAAAAATATGA
*
5759321 GGAAGTACTAAAAAAATG-AGAAAGTACCAAAAATTATGA-AGGAATACAAAAAAATATGA
1 GGAA-TACTAAAAAAATGAAG-AAGTACTAAAAATTATGAGA-GAATAC-AAAAAATATGA
*
5759380 GGAAGTACCAAAAA
1 GGAA-TACTAAAAA
5759394 TTGTAAGGGG
Statistics
Matches: 329, Mismatches: 68, Indels: 66
0.71 0.15 0.14
Matches are distributed among these distances:
55 4 0.01
56 11 0.03
57 19 0.06
58 48 0.15
59 135 0.41
60 27 0.08
61 33 0.10
62 47 0.14
63 5 0.02
ACGTcount: A:0.57, C:0.07, G:0.17, T:0.20
Consensus pattern (57 bp):
GGAATACTAAAAAAATGAAGAAGTACTAAAAATTATGAGAGAATACAAAAAATATGA
Done.