Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167949.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_21, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 19848060
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Warning! 113000 characters in sequence are not A, C, G, or T
File 21 of 138
Found at i:5684531 original size:57 final size:57
Alignment explanation
Indices: 5684436--5684546 Score: 159
Period size: 57 Copynumber: 1.9 Consensus size: 57
5684426 GATATCCGAG
* * * *
5684436 TTTTCTTTGATTGTGATATCTACACTCATTTGTATTTTCTCAATGATGATATTTAAA
1 TTTTCTTTGATAGCGATATCTAAACTCATTTGCATTTTCTCAATGATGATATTTAAA
* * *
5684493 TTTTCTTTTATAGCGATATCTAAACTCATTTGCATTTTCTTAGTGATGATATTT
1 TTTTCTTTGATAGCGATATCTAAACTCATTTGCATTTTCTCAATGATGATATTT
5684547 GAGTTCCCTT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 47 1.00
ACGTcount: A:0.25, C:0.13, G:0.11, T:0.51
Consensus pattern (57 bp):
TTTTCTTTGATAGCGATATCTAAACTCATTTGCATTTTCTCAATGATGATATTTAAA
Found at i:5684634 original size:33 final size:33
Alignment explanation
Indices: 5684563--5684635 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
5684553 CCTTCAGTGA
* *
5684563 TGATATCCAAAATCATTTGCATCTTTTTGATAG
1 TGATATCCAAAATCATTTGCATATTCTTGATAG
* * * *
5684596 CGATATCCAAAATTATTTGCATATTCTTGGTGG
1 TGATATCCAAAATCATTTGCATATTCTTGATAG
5684629 TGATATC
1 TGATATC
5684636 TAAGTTTCCT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (33 bp):
TGATATCCAAAATCATTTGCATATTCTTGATAG
Found at i:5684657 original size:24 final size:23
Alignment explanation
Indices: 5684625--5684683 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 23
5684615 CATATTCTTG
5684625 GTGGTGATATCTAAGTTTCCTTCA
1 GTGGTGATATC-AAGTTTCCTTCA
* **
5684649 GTGGTGATAGTCGAGTTTCCTTTG
1 GTGGTGATA-TCAAGTTTCCTTCA
5684673 GTGGTGATATC
1 GTGGTGATATC
5684684 CGAAGTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 2 0.06
24 27 0.87
25 2 0.06
ACGTcount: A:0.17, C:0.14, G:0.29, T:0.41
Consensus pattern (23 bp):
GTGGTGATATCAAGTTTCCTTCA
Found at i:5686328 original size:20 final size:21
Alignment explanation
Indices: 5686305--5686352 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
5686295 AGTATTTCAA
5686305 TCATAATTTT-TT-AATTTTTT
1 TCAT-ATTTTGTTCAATTTTTT
*
5686325 TCATTTTTTGTTCAATTTTTT
1 TCATATTTTGTTCAATTTTTT
5686346 T-ATATTT
1 TCATATTT
5686353 CTATTACTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 4 0.17
20 11 0.46
21 9 0.38
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.71
Consensus pattern (21 bp):
TCATATTTTGTTCAATTTTTT
Found at i:5686562 original size:25 final size:25
Alignment explanation
Indices: 5686534--5686582 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
5686524 ACTTAAAAAA
5686534 TAAT-AATAAATAATGAAA-AAAAATT
1 TAATGAATAAA-AAT-AAAGAAAAATT
5686559 TAATGAATAAAAATAAAGAAAAAT
1 TAATGAATAAAAATAAAGAAAAAT
5686583 ATAAAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 3 0.14
25 13 0.59
26 6 0.27
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.24
Consensus pattern (25 bp):
TAATGAATAAAAATAAAGAAAAATT
Found at i:5686599 original size:11 final size:10
Alignment explanation
Indices: 5686567--5686609 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
5686557 TTTAATGAAT
*
5686567 AAAAATAAAG
1 AAAAATAAAA
5686577 AAAAATATAAA
1 AAAAATA-AAA
*
5686588 AAAGATAAAA
1 AAAAATAAAA
5686598 AAATAATAAAA
1 AAA-AATAAAA
5686609 A
1 A
5686610 TACCAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 13 0.46
11 15 0.54
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:5687430 original size:7 final size:6
Alignment explanation
Indices: 5687411--5687440 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
5687401 ATTTACAAGT
*
5687411 AATAAA AATAAA AATGAA AATAAA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA
5687441 TGATAACGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (6 bp):
AATAAA
Found at i:5688005 original size:23 final size:23
Alignment explanation
Indices: 5687974--5688018 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
5687964 TTAATTGATT
*
5687974 TAATACATT-TCAAATATAAAATG
1 TAATACATTCTAAAATA-AAAATG
*
5687997 TAATGCATTCTAAAATAAAAAT
1 TAATACATTCTAAAATAAAAAT
5688019 AAAATTCGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.33
Consensus pattern (23 bp):
TAATACATTCTAAAATAAAAATG
Found at i:5688785 original size:19 final size:19
Alignment explanation
Indices: 5688761--5688800 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
5688751 CGTGCTTAAG
5688761 TAGTGCTTGTTTTAATTAC
1 TAGTGCTTGTTTTAATTAC
5688780 TAGTGCTTGTTTTAATTAC
1 TAGTGCTTGTTTTAATTAC
5688799 TA
1 TA
5688801 AGGATTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.23, C:0.10, G:0.15, T:0.53
Consensus pattern (19 bp):
TAGTGCTTGTTTTAATTAC
Found at i:5689059 original size:2 final size:2
Alignment explanation
Indices: 5689052--5689077 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5689042 ACCGCCTGTG
5689052 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
5689078 AGTCAAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5690158 original size:19 final size:18
Alignment explanation
Indices: 5690123--5690167 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
5690113 AATAAAAACT
5690123 TATAATATTTGAAAATTA
1 TATAATATTTGAAAATTA
5690141 TATAATCATTT-AAGAATTA
1 TATAAT-ATTTGAA-AATTA
5690160 -A-AATATTT
1 TATAATATTT
5690168 TTTATAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.16
17 3 0.12
18 9 0.36
19 9 0.36
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (18 bp):
TATAATATTTGAAAATTA
Found at i:5690267 original size:17 final size:16
Alignment explanation
Indices: 5690247--5690278 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
5690237 ATTAATTTGA
5690247 TTTTTATATTATATAAT
1 TTTTTATATT-TATAAT
5690264 TTTTTATATTTATAA
1 TTTTTATATTTATAA
5690279 AAATATAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTTATATTTATAAT
Found at i:5690941 original size:5 final size:6
Alignment explanation
Indices: 5690914--5690939 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
5690904 TAGTTGAAAC
5690914 AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AA
5690940 TATGCTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:5704700 original size:2 final size:2
Alignment explanation
Indices: 5704693--5704736 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
5704683 AACTTATTAG
5704693 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5704735 CT
1 CT
5704737 GAGTGTGTGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5711382 original size:25 final size:25
Alignment explanation
Indices: 5711354--5711401 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
5711344 ATTAAGCTGC
5711354 ACTAATGTAGAAGAATAAGATTTGT
1 ACTAATGTAGAAGAATAAGATTTGT
*
5711379 ACTAATGTAGGAGAATAAGATTT
1 ACTAATGTAGAAGAATAAGATTT
5711402 TTACACTCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.44, C:0.04, G:0.21, T:0.31
Consensus pattern (25 bp):
ACTAATGTAGAAGAATAAGATTTGT
Found at i:5713178 original size:8 final size:8
Alignment explanation
Indices: 5713161--5713196 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
5713151 GTCAACTTTG
*
5713161 AAAATTAA
1 AAAATAAA
5713169 AAAATAAA
1 AAAATAAA
5713177 AAAATAAA
1 AAAATAAA
*
5713185 AAAACAAA
1 AAAATAAA
5713193 AAAA
1 AAAA
5713197 ATGTTTGAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.86, C:0.03, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAATAAA
Found at i:5713970 original size:17 final size:18
Alignment explanation
Indices: 5713936--5713987 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 18
5713926 ATTTATTTTC
*
5713936 AAACA-AAAAA-AATTAA
1 AAACATAAAAATAATAAA
*
5713952 AAA-TTAAAAATAATAAA
1 AAACATAAAAATAATAAA
5713969 AAACATAAAAAT-ATAAA
1 AAACATAAAAATAATAAA
5713986 AA
1 AA
5713988 TATAAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 8 0.27
17 15 0.50
18 7 0.23
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.17
Consensus pattern (18 bp):
AAACATAAAAATAATAAA
Found at i:5713977 original size:25 final size:26
Alignment explanation
Indices: 5713940--5713994 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
5713930 ATTTTCAAAC
5713940 AAAAAAAATTAAAAAT-TAAAAATAAT
1 AAAAAAAATTAAAAATATAAAAAT-AT
*
5713966 AAAAAACA-TAAAAATATAAAAATAT
1 AAAAAAAATTAAAAATATAAAAATAT
5713991 AAAA
1 AAAA
5713995 TTTTTGGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 13 0.48
26 14 0.52
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (26 bp):
AAAAAAAATTAAAAATATAAAAATAT
Found at i:5713995 original size:7 final size:8
Alignment explanation
Indices: 5713943--5713994 Score: 63
Period size: 8 Copynumber: 6.5 Consensus size: 8
5713933 TTCAAACAAA
5713943 AAAAAT-T
1 AAAAATAT
5713950 AAAAAT-T
1 AAAAATAT
5713957 AAAAATAAT
1 AAAAAT-AT
*
5713966 AAAAAACAT
1 -AAAAATAT
5713975 AAAAATAT
1 AAAAATAT
5713983 AAAAATAT
1 AAAAATAT
5713991 AAAA
1 AAAA
5713995 TTTTTGGAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
7 13 0.32
8 19 0.47
9 3 0.08
10 5 0.12
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (8 bp):
AAAAATAT
Found at i:5714057 original size:219 final size:215
Alignment explanation
Indices: 5713759--5714162 Score: 528
Period size: 219 Copynumber: 1.9 Consensus size: 215
5713749 AATTTAATAA
** * *
5713759 AAAAATAAAAAATAAAAATTTTGGGAATAAATATTAATCATCCAATGATGAAATTTATAAAAATT
1 AAAAATAAAAAATAAAAATTTTGGGAATAAATACAAATCACCCAAGGATGAAATTTATAAAAATT
* * * * *
5713824 TCAAATGGTAAATTTTTATGAAATTCCTAGGTGAGAAATTTTGTTTAAATTTA-TCTCAAATGGT
66 TCAAATGGTAAATTTTAAAGAAATTCCTAGGTGAGAAATTTTCTCTAAATTTAGCCT-AAATGGT
*
5713888 GGAATAATTTAGATAAAATTTCAATAACAA-TAATTAATATTTATTTTC-AAACAAAAAAAATTA
130 AGAATAATTTAGATAAAATTTCAAT-ACAAGTAATT-ATATTT-TTTTCTAAACAAAAAAAATTA
5713951 AAAATTAAAAATAATAAAAAACAT
192 AAAATTAAAAATAATAAAAAACAT
* * *
5713975 AAAAATATAAAAATATAAAATTTTTGGAATTAAATACAAATTACCCAAGGATGAGATTCT-TAAA
1 AAAAATA-AAAAATA-AAAATTTTGGGAA-TAAATACAAATCACCCAAGGATGAAATT-TATAAA
* * *
5714039 AATTTCAAATGGTAAATTTTAAAGAAATTTCTAGGTGATAAATTTTCTCTAAATTTGGCCTAAAT
62 AATTTCAAATGGTAAATTTTAAAGAAATTCCTAGGTGAGAAATTTTCTCTAAATTTAGCCTAAAT
* * * *
5714104 GGTAGAATGATTTAGATGAAATTTCAATACAAGTAATTGTATTTTTTTCTAAATAAAAA
127 GGTAGAATAATTTAGATAAAATTTCAATACAAGTAATTATATTTTTTTCTAAACAAAAA
5714163 TTTGGATTGA
Statistics
Matches: 161, Mismatches: 20, Indels: 12
0.83 0.10 0.06
Matches are distributed among these distances:
216 7 0.04
217 12 0.07
218 29 0.18
219 110 0.68
220 3 0.02
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.35
Consensus pattern (215 bp):
AAAAATAAAAAATAAAAATTTTGGGAATAAATACAAATCACCCAAGGATGAAATTTATAAAAATT
TCAAATGGTAAATTTTAAAGAAATTCCTAGGTGAGAAATTTTCTCTAAATTTAGCCTAAATGGTA
GAATAATTTAGATAAAATTTCAATACAAGTAATTATATTTTTTTCTAAACAAAAAAAATTAAAAA
TTAAAAATAATAAAAAACAT
Found at i:5720434 original size:18 final size:18
Alignment explanation
Indices: 5720402--5720461 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
5720392 GTGAAATGTG
5720402 AAAGGTGAAAAAAAAAAA
1 AAAGGTGAAAAAAAAAAA
*
5720420 AAAGG-GAAAATAAAAATA
1 AAAGGTGAAAA-AAAAAAA
* *
5720438 AAAGATGAAAGGAGAAAAAA
1 AAAGGTGAAA--AAAAAAAA
5720458 AAAG
1 AAAG
5720462 ACTCAAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 5 0.15
18 15 0.44
19 4 0.12
20 9 0.26
21 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAGGTGAAAAAAAAAAA
Found at i:5721893 original size:43 final size:43
Alignment explanation
Indices: 5721845--5721948 Score: 122
Period size: 43 Copynumber: 2.4 Consensus size: 43
5721835 CTTTGAACTT
*
5721845 AAATGAGAAGCTTTGAATTTTTGGATGTGAATCTCCAAAATT-C
1 AAATGAGAAGCTTTGAATTTTTGGATATGAAT-TCCAAAATTCC
* **
5721888 AAATGAAAAGCTTT-AGATTTTTGGATATGAATTCCAAGTTTGCC
1 AAATGAGAAGCTTTGA-ATTTTTGGATATGAATTCCAAAATT-CC
*
5721932 AAATGAGAACCTTTGAA
1 AAATGAGAAGCTTTGAA
5721949 AAGCCTTGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
42 8 0.16
43 28 0.55
44 14 0.27
45 1 0.02
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.34
Consensus pattern (43 bp):
AAATGAGAAGCTTTGAATTTTTGGATATGAATTCCAAAATTCC
Found at i:5722269 original size:41 final size:41
Alignment explanation
Indices: 5722223--5722924 Score: 651
Period size: 42 Copynumber: 17.1 Consensus size: 41
5722213 ATGATTGTTA
* * * *
5722223 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCTTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTTGTGGTGCCTCTATTTAG
* **
5722264 AGGAGCAATTTATTTTTCAAAGTCATGGTTGCCTCTATTTAG
1 AGGAGCAATTTACTTTTCAAAGTTGTGG-TGCCTCTATTTAG
5722306 AGGAGCAATTTAC-TTTCAAAAGTTGTGGTGCCTCTATTTAG
1 AGGAGCAATTTACTTTTC-AAAGTTGTGGTGCCTCTATTTAG
* * * *
5722347 AGGAGCAATTTACTTTCCAAAAGTTGAGGCGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTC-AAAGTTGTGGTGCCTCTATTTAG
5722389 AGGAGCAATTTAC-TTTCAAAGTTGTGGTGCCTCTATTTAG
1 AGGAGCAATTTACTTTTCAAAGTTGTGGTGCCTCTATTTAG
* * *
5722429 AGAAGCAATTTACTTTTCAAAGTTGTAGTACCTCTATTTAG
1 AGGAGCAATTTACTTTTCAAAGTTGTGGTGCCTCTATTTAG
*
5722470 AGGAGCAATTTACTTTCCAAAAGTTGTGGTGCCTCTATTTAG
1 AGGAGCAATTTACTTTTC-AAAGTTGTGGTGCCTCTATTTAG
**
5722512 AGGAGCAATTTACTTTTCAAAAGTTGCAGTGCCTCTATTT-G
1 AGGAGCAATTTACTTTTC-AAAGTTGTGGTGCCTCTATTTAG
* * * *
5722553 AATGAGCAATTTAC-TTTCAAAATT-TACGGTGCCTTTGTTT-G
1 -AGGAGCAATTTACTTTTCAAAGTTGT--GGTGCCTCTATTTAG
*
5722594 AAGGAGCAATTTAC-TTTCAAAGTTGCGGTGCCTCTATTTAG
1 -AGGAGCAATTTACTTTTCAAAGTTGTGGTGCCTCTATTTAG
* * *
5722635 AGGAGCAATTTACTTTTTAAAATTGTGATGCCTCTATTTAG
1 AGGAGCAATTTACTTTTCAAAGTTGTGGTGCCTCTATTTAG
** *
5722676 AGGAGCAATTTACTTTTCAAAAGTTACGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTC-AAAGTTGTGGTGCCTCTATTTAG
* * * * **
5722718 AAGAGTAATTT-C----AAAAGTTGTGGTGCCTCTGTTCGG
1 AGGAGCAATTTACTTTTCAAAGTTGTGGTGCCTCTATTTAG
* * * *
5722754 AGGAGCAATTTAC-TTTCAAAGTTGTAGTACCTTTATTTAA
1 AGGAGCAATTTACTTTTCAAAGTTGTGGTGCCTCTATTTAG
* * * *** * *
5722794 AGGAGCAATTTGCTTTCCAAAGTTATTAAGCCTTTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTTGTGGTGCCTCTATTTAG
** * * * * *
5722835 AGGAGCTTTGTTTA-TTTTCAAAGTCGTTGAGCCTATGTTTAG
1 AGGAGC--AATTTACTTTTCAAAGTTGTGGTGCCTCTATTTAG
* * * *
5722877 AGGAGCTTTATTTA-TTTTCAAAGTCGTTGAGCCTCTATTTAG
1 AGGAGC--AATTTACTTTTCAAAGTTGTGGTGCCTCTATTTAG
*
5722919 AAGAGC
1 AGGAGC
5722925 TCTGTTTATT
Statistics
Matches: 559, Mismatches: 83, Indels: 37
0.82 0.12 0.05
Matches are distributed among these distances:
36 28 0.05
37 1 0.00
40 89 0.16
41 206 0.37
42 232 0.42
43 3 0.01
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.38
Consensus pattern (41 bp):
AGGAGCAATTTACTTTTCAAAGTTGTGGTGCCTCTATTTAG
Found at i:5722381 original size:83 final size:82
Alignment explanation
Indices: 5722223--5722817 Score: 666
Period size: 83 Copynumber: 7.3 Consensus size: 82
5722213 ATGATTGTTA
* * * * *
5722223 AGGAGCAATTTATTTTTC-AAAGTCGTGGTGCTTCTGTTTAGAGGAGCAATTTATTTTTCAAAGT
1 AGGAGCAATTTA-CTTTCAAAAGTTGTGGTGCCTCTATTTAGAGGAGCAATTTACTTTTCAAAGT
*
5722287 CATG-GTTGCCTCTATTTAG
65 --TGAGGTGCCTCTATTTAG
*
5722306 AGGAGCAATTTACTTTCAAAAGTTGTGGTGCCTCTATTTAGAGGAGCAATTTACTTTCCAAAAGT
1 AGGAGCAATTTACTTTCAAAAGTTGTGGTGCCTCTATTTAGAGGAGCAATTTACTTTTC-AAAGT
* *
5722371 TGAGGCGCCTCTGTTTAG
65 TGAGGTGCCTCTATTTAG
*
5722389 AGGAGCAATTTACTTTC-AAAGTTGTGGTGCCTCTATTTAGAGAAGCAATTTACTTTTCAAAGTT
1 AGGAGCAATTTACTTTCAAAAGTTGTGGTGCCTCTATTTAGAGGAGCAATTTACTTTTCAAAGTT
*
5722453 GTA-GTACCTCTATTTAG
66 G-AGGTGCCTCTATTTAG
5722470 AGGAGCAATTTACTTTCCAAAAGTTGTGGTGCCTCTATTTAGAGGAGCAATTTACTTTTCAAAAG
1 AGGAGCAATTTACTTT-CAAAAGTTGTGGTGCCTCTATTTAGAGGAGCAATTTACTTTTC-AAAG
5722535 TTGCA-GTGCCTCTATTT-G
64 TTG-AGGTGCCTCTATTTAG
* * ** * *
5722553 AATGAGCAATTTACTTTCAAAATTTACGGTGCCTTTGTTT-GAAGGAGCAATTTAC-TTTCAAAG
1 -AGGAGCAATTTACTTTCAAAAGTTGTGGTGCCTCTATTTAG-AGGAGCAATTTACTTTTCAAAG
*
5722616 TTGCGGTGCCTCTATTTAG
64 TTGAGGTGCCTCTATTTAG
* *
5722635 AGGAGCAATTTACTTTTTAAAA-TTGTGATGCCTCTATTTAGAGGAGCAATTTACTTTTCAAAAG
1 AGGAGCAATTTAC-TTTCAAAAGTTGTGGTGCCTCTATTTAGAGGAGCAATTTACTTTTC-AAAG
*
5722699 TT-ACGGTGCCTCTGTTTAG
64 TTGA-GGTGCCTCTATTTAG
* * * **
5722718 A--AG--A-GTAATTTCAAAAGTTGTGGTGCCTCTGTTCGGAGGAGCAATTTAC-TTTCAAAGTT
1 AGGAGCAATTTACTTTCAAAAGTTGTGGTGCCTCTATTTAGAGGAGCAATTTACTTTTCAAAGTT
* * *
5722777 GTA-GTACCTTTATTTAA
66 G-AGGTGCCTCTATTTAG
* *
5722794 AGGAGCAATTTGCTTTCCAAAGTT
1 AGGAGCAATTTACTTTCAAAAGTT
5722818 ATTAAGCCTT
Statistics
Matches: 440, Mismatches: 48, Indels: 50
0.82 0.09 0.09
Matches are distributed among these distances:
76 17 0.04
77 11 0.03
78 33 0.08
79 1 0.00
80 1 0.00
81 103 0.23
82 65 0.15
83 170 0.39
84 39 0.09
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (82 bp):
AGGAGCAATTTACTTTCAAAAGTTGTGGTGCCTCTATTTAGAGGAGCAATTTACTTTTCAAAGTT
GAGGTGCCTCTATTTAG
Found at i:5722601 original size:206 final size:202
Alignment explanation
Indices: 5722226--5722817 Score: 732
Period size: 206 Copynumber: 2.9 Consensus size: 202
5722216 ATTGTTAAGG
* * * * * *
5722226 AGCAATTTATTTTTCAAAGTCGTGGTGCTTCTGTTTAGAGGAGCAATTTATTTTTC-AAAGTCAT
1 AGCAATTTACTTTTCAAAGTTGT-GTGCCTCTATTTAGAGGAGCAATTTACTTTTCAAAAGTTAT
5722290 GGTTGCCTCTATTTAGAGGAGCAATTTACTTTCAAAAGTTGTGGTGCCTCTATTT-AGAGGAGCA
65 GG-TGCCTCTATTTAGAGGAGCAATTTACTTTCAAAAGTTGTGGTGCCTCTATTTGA-AGGAGCA
* * * *
5722354 ATTTACTTTCCAAAAGTTGAGGCGCCTCTGTTTAGAGGAGCAATTTACTTTCAAAGTTGTGGTGC
128 ATTTACTTT-CAAAA-TTTAGGTGCCTTTGTTTA-AGGAGCAATTTACTTTCAAAGTTGCGGTGC
5722419 CTCTATTTAGAGA
190 CTCTATTTAGAGA
* * *
5722432 AGCAATTTACTTTTCAAAGTTGTAGTACCTCTATTTAGAGGAGCAATTTACTTTCCAAAAGTTGT
1 AGCAATTTACTTTTCAAAGTTGT-GTGCCTCTATTTAGAGGAGCAATTTACTTTTCAAAAGTTAT
** *
5722497 GGTGCCTCTATTTAGAGGAGCAATTTACTTTTCAAAAGTTGCAGTGCCTCTATTTGAATGAGCAA
65 GGTGCCTCTATTTAGAGGAGCAATTTAC-TTTCAAAAGTTGTGGTGCCTCTATTTGAAGGAGCAA
5722562 TTTACTTTCAAAATTTACGGTGCCTTTGTTTGAAGGAGCAATTTACTTTCAAAGTTGCGGTGCCT
129 TTTACTTTCAAAATTTA-GGTGCCTTTGTTT-AAGGAGCAATTTACTTTCAAAGTTGCGGTGCCT
*
5722627 CTATTTAGAGG
192 CTATTTAGAGA
* * *
5722638 AGCAATTTACTTTTTAAAATTGTGATGCCTCTATTTAGAGGAGCAATTTACTTTTCAAAAGTTAC
1 AGCAATTTACTTTTCAAAGTTGTG-TGCCTCTATTTAGAGGAGCAATTTACTTTTCAAAAGTTAT
* * * * * *
5722703 GGTGCCTCTGTTTAGA--AG--A-GTAATTTCAAAAGTTGTGGTGCCTCTGTTCGGAGGAGCAAT
65 GGTGCCTCTATTTAGAGGAGCAATTTACTTTCAAAAGTTGTGGTGCCTCTATTTGAAGGAGCAAT
* * * *
5722763 TTACTTTCAAAGTTGTA-GTACCTTTATTTAAAGGAGCAATTTGCTTTCCAAAGTT
130 TTACTTTCAAAATT-TAGGTGCCTTTGTTT-AAGGAGCAATTTACTTT-CAAAGTT
5722818 ATTAAGCCTT
Statistics
Matches: 340, Mismatches: 38, Indels: 22
0.85 0.09 0.05
Matches are distributed among these distances:
199 26 0.08
200 51 0.15
201 4 0.01
202 1 0.00
204 2 0.01
205 4 0.01
206 203 0.60
207 48 0.14
208 1 0.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (202 bp):
AGCAATTTACTTTTCAAAGTTGTGTGCCTCTATTTAGAGGAGCAATTTACTTTTCAAAAGTTATG
GTGCCTCTATTTAGAGGAGCAATTTACTTTCAAAAGTTGTGGTGCCTCTATTTGAAGGAGCAATT
TACTTTCAAAATTTAGGTGCCTTTGTTTAAGGAGCAATTTACTTTCAAAGTTGCGGTGCCTCTAT
TTAGAGA
Found at i:5722764 original size:36 final size:36
Alignment explanation
Indices: 5722690--5722764 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 36
5722680 GCAATTTACT
* *
5722690 TTTCAAAAGTTACGGTGCCTCTGTTTAGAAGAGTAA
1 TTTCAAAAGTTACGGTGCCTCTGTTCAGAAGAGCAA
** * *
5722726 TTTCAAAAGTTGTGGTGCCTCTGTTCGGAGGAGCAA
1 TTTCAAAAGTTACGGTGCCTCTGTTCAGAAGAGCAA
5722762 TTT
1 TTT
5722765 ACTTTCAAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (36 bp):
TTTCAAAAGTTACGGTGCCTCTGTTCAGAAGAGCAA
Found at i:5722874 original size:42 final size:42
Alignment explanation
Indices: 5722830--5722978 Score: 210
Period size: 42 Copynumber: 3.5 Consensus size: 42
5722820 TAAGCCTTTG
* *
5722830 TTTAGAGGAGCTTTGTTTATTTTCAAAGTCGTTGAGCCTATG
1 TTTAGAGGAGCTTTGTTTATTTTCAAAGTCGTTGAGCCTCTA
*
5722872 TTTAGAGGAGCTTTATTTATTTTCAAAGTCGTTGAGCCTCTA
1 TTTAGAGGAGCTTTGTTTATTTTCAAAGTCGTTGAGCCTCTA
* * * *
5722914 TTTAGAAGAGCTCTGTTTATTTTCAAAAGTCATTGAGTCTCTA
1 TTTAGAGGAGCTTTGTTTATTTTC-AAAGTCGTTGAGCCTCTA
*
5722957 TTTAGAGAAGCTTTG-TTATTTT
1 TTTAGAGGAGCTTTGTTTATTTT
5722979 TTCTTTTAAA
Statistics
Matches: 95, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
42 67 0.71
43 28 0.29
ACGTcount: A:0.24, C:0.12, G:0.19, T:0.44
Consensus pattern (42 bp):
TTTAGAGGAGCTTTGTTTATTTTCAAAGTCGTTGAGCCTCTA
Found at i:5723158 original size:18 final size:18
Alignment explanation
Indices: 5723118--5723158 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
5723108 TTTGACAATT
* *
5723118 AAAAAATTAAAAAAATAA
1 AAAAAATGAAAAAAACAA
*
5723136 TAAAAATGAAAAAAACAA
1 AAAAAATGAAAAAAACAA
5723154 AAAAA
1 AAAAA
5723159 GGTGTTTGAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.12
Consensus pattern (18 bp):
AAAAAATGAAAAAAACAA
Found at i:5723940 original size:9 final size:8
Alignment explanation
Indices: 5723903--5723950 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
5723893 TTTTCAAACC
5723903 ATAAAAAA
1 ATAAAAAA
*
5723911 TTAAAAAA
1 ATAAAAAA
*
5723919 TTAAAAATA
1 ATAAAAA-A
5723928 ATAAAAAA
1 ATAAAAAA
*
5723936 CATAAAAAT
1 -ATAAAAAA
5723945 ATAAAA
1 ATAAAA
5723951 TTTTTGGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
8 21 0.60
9 14 0.40
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (8 bp):
ATAAAAAA
Found at i:5723941 original size:18 final size:18
Alignment explanation
Indices: 5723902--5723950 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 18
5723892 ATTTTCAAAC
*
5723902 CATAAAAA-ATTAAAAAA
1 CATAAAAATAATAAAAAA
*
5723919 -TTAAAAATAATAAAAAA
1 CATAAAAATAATAAAAAA
5723936 CATAAAAAT-ATAAAA
1 CATAAAAATAATAAAA
5723951 TTTTTGGAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 6 0.22
17 14 0.52
18 7 0.26
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (18 bp):
CATAAAAATAATAAAAAA
Found at i:5733390 original size:29 final size:30
Alignment explanation
Indices: 5733336--5733407 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
5733326 TTAAAAAATT
*
5733336 AATTAAATTTTTACTTGTTTTCTTATAATC
1 AATTAAATTTTTAATTGTTTTCTTATAATC
* * *
5733366 AATTAATTTTTTAATT-TTTAT-TTATATTT
1 AATTAAATTTTTAATTGTTT-TCTTATAATC
5733395 AATTAAATTTTTA
1 AATTAAATTTTTA
5733408 TTTGAATGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 21 0.58
30 15 0.42
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.61
Consensus pattern (30 bp):
AATTAAATTTTTAATTGTTTTCTTATAATC
Found at i:5733404 original size:30 final size:31
Alignment explanation
Indices: 5733332--5733406 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 31
5733322 ATAATTAAAA
*
5733332 AATTAATTAAA-TTTTTACTTGTTTTCTTAT
1 AATTAATTAAATTTTTTAATTGTTTTCTTAT
*
5733362 AATCAATT-AATTTTTTAATT-TTTAT-TTAT
1 AATTAATTAAATTTTTTAATTGTTT-TCTTAT
*
5733391 ATTTAATTAAATTTTT
1 AATTAATTAAATTTTT
5733407 ATTTGAATGA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
29 15 0.39
30 23 0.61
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.61
Consensus pattern (31 bp):
AATTAATTAAATTTTTTAATTGTTTTCTTAT
Found at i:5733834 original size:3 final size:3
Alignment explanation
Indices: 5733826--5733869 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
5733816 CAACTATTTG
5733826 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5733870 CTTTTCTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5734212 original size:23 final size:22
Alignment explanation
Indices: 5734186--5734235 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
5734176 TAGGTTTAAA
* *
5734186 GATTTTAGGTTTGGAGTTTTTGG
1 GATTTTAGGTTTGAAGTTTCT-G
* *
5734209 GATTCTGGGTTTGAAGTTTCTG
1 GATTTTAGGTTTGAAGTTTCTG
5734231 GATTT
1 GATTT
5734236 GAAATTTCTG
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.14, C:0.04, G:0.32, T:0.50
Consensus pattern (22 bp):
GATTTTAGGTTTGAAGTTTCTG
Found at i:5734231 original size:15 final size:15
Alignment explanation
Indices: 5734211--5734256 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
5734201 GTTTTTGGGA
*
5734211 TTCTGGGTTTGAAGT
1 TTCTGGGTTTGAAAT
*
5734226 TTCTGGATTTGAAAT
1 TTCTGGGTTTGAAAT
*
5734241 TTCTGGGTTTGGAAT
1 TTCTGGGTTTGAAAT
5734256 T
1 T
5734257 GAATTTCTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.17, C:0.07, G:0.28, T:0.48
Consensus pattern (15 bp):
TTCTGGGTTTGAAAT
Found at i:5734342 original size:86 final size:87
Alignment explanation
Indices: 5734248--5734422 Score: 273
Period size: 86 Copynumber: 2.0 Consensus size: 87
5734238 AATTTCTGGG
*
5734248 TTTGGAATTGAATTTCTAGGAAATTTTTGAAAAATCT-AGAAAAATCTAGTTTTG-GTTTGAATG
1 TTTGGAATTGAATTTCTAGGAAACTTTTGAAAAATCTGA-AAAAATCTAGTTTTGAGTTTGAATG
* *
5734311 TTTAAATTTTTCAGTTGAATTTT
65 TTTAAATTTTTCAATTAAATTTT
* *
5734334 TTTGGAATTGAATTTTTGGGAAACTTTTGAAAAATCTGAAAAAATCTAGTTTTGAGTTTGAATGT
1 TTTGGAATTGAATTTCTAGGAAACTTTTGAAAAATCTGAAAAAATCTAGTTTTGAGTTTGAATGT
*
5734399 TTGAATTTTTCAATTAAATTTT
66 TTAAATTTTTCAATTAAATTTT
5734421 TT
1 TT
5734423 GGCAGAGTTT
Statistics
Matches: 81, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
86 49 0.60
87 32 0.40
ACGTcount: A:0.33, C:0.05, G:0.16, T:0.47
Consensus pattern (87 bp):
TTTGGAATTGAATTTCTAGGAAACTTTTGAAAAATCTGAAAAAATCTAGTTTTGAGTTTGAATGT
TTAAATTTTTCAATTAAATTTT
Found at i:5734780 original size:36 final size:35
Alignment explanation
Indices: 5734695--5734780 Score: 84
Period size: 36 Copynumber: 2.4 Consensus size: 35
5734685 CGATTACAAG
* * * *
5734695 TTTTCTTTTATTTTCATTTGTTGATTTTATTTTTA
1 TTTTTTTTTATTTTCATTTGTTAACTTTATTCTTA
* *
5734730 TTTTTTTATGATTTTCATTTTTTAAGCTTT-TTCTTA
1 TTTTTTT-TTATTTTCATTTGTTAA-CTTTATTCTTA
5734766 TTTTATTTTTATTTT
1 TTTT-TTTTTATTTT
5734781 TTATTTTATT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
35 6 0.15
36 29 0.71
37 6 0.15
ACGTcount: A:0.15, C:0.06, G:0.05, T:0.74
Consensus pattern (35 bp):
TTTTTTTTTATTTTCATTTGTTAACTTTATTCTTA
Found at i:5734802 original size:18 final size:18
Alignment explanation
Indices: 5734763--5734806 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
5734753 AAGCTTTTTC
* *
5734763 TTATTTTATTTTTATTTT
1 TTATTTTATTTTCATTTA
5734781 TTATTTTATTTATCA-TTA
1 TTATTTTATTT-TCATTTA
5734799 TTATTTTA
1 TTATTTTA
5734807 CTAATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 21 0.91
19 2 0.09
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (18 bp):
TTATTTTATTTTCATTTA
Found at i:5745339 original size:12 final size:12
Alignment explanation
Indices: 5745322--5745346 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5745312 TACTTTGCTT
5745322 AAATAACAAAAA
1 AAATAACAAAAA
5745334 AAATAACAAAAA
1 AAATAACAAAAA
5745346 A
1 A
5745347 GAGTTTAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (12 bp):
AAATAACAAAAA
Found at i:5746154 original size:60 final size:59
Alignment explanation
Indices: 5746072--5746195 Score: 140
Period size: 60 Copynumber: 2.1 Consensus size: 59
5746062 TATCTGATCG
* * * * * *
5746072 ATCCAGATCATCTTTTTGACTCATAATTCAATCCCGATCACTTATTTTGATCTCGACTCA
1 ATCCAAATTATCTTTTTAACTCACAATTCAATCCCGATCACTAATTTTAATCTCG-CTCA
* ** * *
5746132 GTCCAAATTATCTTTTTAACTCACGGTTCAATCTCGGTCACTAATTTTAATCTCGCTCA
1 ATCCAAATTATCTTTTTAACTCACAATTCAATCCCGATCACTAATTTTAATCTCGCTCA
5746191 ATCCA
1 ATCCA
5746196 GATCATTTTT
Statistics
Matches: 52, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
59 8 0.15
60 44 0.85
ACGTcount: A:0.27, C:0.27, G:0.09, T:0.38
Consensus pattern (59 bp):
ATCCAAATTATCTTTTTAACTCACAATTCAATCCCGATCACTAATTTTAATCTCGCTCA
Found at i:5746922 original size:3 final size:3
Alignment explanation
Indices: 5746910--5746960 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
5746900 TCCAATCAAC
5746910 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5746957 TAT T
1 TAT T
5746961 CCTTTCTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:5747271 original size:15 final size:15
Alignment explanation
Indices: 5747251--5747293 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
5747241 TTAAAGATTT
5747251 TAGGTTTGAAGTTTC
1 TAGGTTTGAAGTTTC
*
5747266 TAGGTTTGAAATTTC
1 TAGGTTTGAAGTTTC
*
5747281 TATGTTT-AAGTTT
1 TAGGTTTGAAGTTT
5747294 GAATTTCTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 5 0.20
15 20 0.80
ACGTcount: A:0.23, C:0.05, G:0.21, T:0.51
Consensus pattern (15 bp):
TAGGTTTGAAGTTTC
Found at i:5747300 original size:20 final size:21
Alignment explanation
Indices: 5747269--5747322 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
5747259 AAGTTTCTAG
*
5747269 GTTTGAAATTTCTATGTTT-AA
1 GTTTG-AATTTCTAGGTTTGAA
*
5747290 GTTTGAATTTCTAGGTTTGGA
1 GTTTGAATTTCTAGGTTTGAA
5747311 G-TTGAATTTCTA
1 GTTTGAATTTCTA
5747323 AAAAATTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 23 0.77
21 7 0.23
ACGTcount: A:0.24, C:0.06, G:0.20, T:0.50
Consensus pattern (21 bp):
GTTTGAATTTCTAGGTTTGAA
Found at i:5747670 original size:14 final size:14
Alignment explanation
Indices: 5747651--5747693 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
5747641 ATCGCAGGTT
5747651 TTTTTTTATTTTCA
1 TTTTTTTATTTTCA
5747665 TTTTTTTA---T-A
1 TTTTTTTATTTTCA
5747675 TTTTTTTATTTTCA
1 TTTTTTTATTTTCA
5747689 TTTTT
1 TTTTT
5747694 AAGCTTTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
10 9 0.36
11 1 0.04
13 1 0.04
14 14 0.56
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTTTATTTTCA
Found at i:5747686 original size:6 final size:6
Alignment explanation
Indices: 5747649--5747731 Score: 52
Period size: 6 Copynumber: 14.3 Consensus size: 6
5747639 CAATCGCAGG
* * *
5747649 TTTT-T TTTTAT TTTCAT TTTT-T TATATT-T TTTTAT TTTCAT TTTTAAG
1 TTTTAT TTTTAT TTTTAT TTTTAT T-T-TTAT TTTTAT TTTTAT TTTT-AT
* *
5747697 CTTT-T TCTTA- TTTTAT TTTTAT TTTTA- TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT
5747732 ATCATTATTG
Statistics
Matches: 60, Mismatches: 10, Indels: 15
0.71 0.12 0.18
Matches are distributed among these distances:
5 19 0.32
6 33 0.55
7 8 0.13
ACGTcount: A:0.16, C:0.05, G:0.01, T:0.78
Consensus pattern (6 bp):
TTTTAT
Found at i:5747702 original size:24 final size:22
Alignment explanation
Indices: 5747650--5747737 Score: 88
Period size: 24 Copynumber: 3.8 Consensus size: 22
5747640 AATCGCAGGT
*
5747650 TTTTTTTTATTTTCATTTTTTTA
1 TTTTTTTTATTTTCA-TTTTTAA
5747673 TATTTTTTTATTTTCATTTTTAA
1 T-TTTTTTTATTTTCATTTTTAA
* *
5747696 GCTTTTTCTTATTTT-ATTTTTAT
1 --TTTTTTTTATTTTCATTTTTAA
5747719 TTTTATTTTATTTATCATT
1 TTTT-TTTTATTT-TCATT
5747738 ATTGTTTTAC
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
21 4 0.07
22 7 0.13
23 15 0.27
24 28 0.51
25 1 0.02
ACGTcount: A:0.17, C:0.06, G:0.01, T:0.76
Consensus pattern (22 bp):
TTTTTTTTATTTTCATTTTTAA
Found at i:5749220 original size:30 final size:30
Alignment explanation
Indices: 5749180--5749240 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
5749170 GAGCGTGAAG
* *
5749180 AGTTTAATTGAATCGAAATAAAATATTAAA
1 AGTTTAATTGAATAGAAAAAAAATATTAAA
* * *
5749210 AGTTTGATTGATTATAAAAAAAATATTAAA
1 AGTTTAATTGAATAGAAAAAAAATATTAAA
5749240 A
1 A
5749241 ACAAATGATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.54, C:0.02, G:0.10, T:0.34
Consensus pattern (30 bp):
AGTTTAATTGAATAGAAAAAAAATATTAAA
Found at i:5756742 original size:24 final size:24
Alignment explanation
Indices: 5756699--5756797 Score: 71
Period size: 24 Copynumber: 4.1 Consensus size: 24
5756689 ACTTTTAGAT
*
5756699 TTATTTATTTA-TTTATTAAAAATA
1 TTATATATTTATTTTA-TAAAAATA
*
5756723 TTATATATTTATTTTAT-AAACTA
1 TTATATATTTATTTTATAAAAATA
* *
5756746 TTA-ATAATATTATTATATACAAAT-
1 TTATAT-AT-TTATTTTATAAAAATA
* * *
5756770 TCATATATATATATTTATAAATATA
1 TTATATATTTAT-TTTATAAAAATA
5756795 TTA
1 TTA
5756798 GTATTAAATC
Statistics
Matches: 57, Mismatches: 11, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
22 2 0.04
23 13 0.23
24 31 0.54
25 11 0.19
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (24 bp):
TTATATATTTATTTTATAAAAATA
Found at i:5759661 original size:12 final size:12
Alignment explanation
Indices: 5759640--5759673 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5759630 TAAGCATTCA
*
5759640 TAAAATTAAATT
1 TAAAAATAAATT
*
5759652 TAAAAGTAAATT
1 TAAAAATAAATT
5759664 TAAAAATAAA
1 TAAAAATAAA
5759674 CCTATCTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (12 bp):
TAAAAATAAATT
Found at i:5761760 original size:6 final size:6
Alignment explanation
Indices: 5761751--5761787 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
5761741 TAACAATAAT
* *
5761751 ATATTA ATATTA ATATTA ATAATA ATATTA TTATTA A
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA A
5761788 AACTATCATC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (6 bp):
ATATTA
Found at i:5762346 original size:2 final size:2
Alignment explanation
Indices: 5762339--5762363 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5762329 GACCAAATCC
5762339 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5762364 TGAAGAGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5773373 original size:2 final size:2
Alignment explanation
Indices: 5773362--5773390 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5773352 GATGATATGG
5773362 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5773391 GATCTAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5775694 original size:22 final size:21
Alignment explanation
Indices: 5775666--5775715 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 21
5775656 ATGAGTTTTT
5775666 TAGTGTGCTCCCATAGGCTCTC
1 TAGTGTGCTCCCATAGGCTC-C
*
5775688 TAGTGTGCTCTCATAGGCTCC
1 TAGTGTGCTCCCATAGGCTCC
*
5775709 AAGTGTG
1 TAGTGTG
5775716 ATTTATCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 7 0.27
22 19 0.73
ACGTcount: A:0.16, C:0.26, G:0.26, T:0.32
Consensus pattern (21 bp):
TAGTGTGCTCCCATAGGCTCC
Found at i:5780071 original size:21 final size:22
Alignment explanation
Indices: 5780019--5780065 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
5780009 GTGGTGTCGC
*
5780019 AAAA-CCAAGAAAAGAAAGAAG
1 AAAAGCCAAAAAAAGAAAGAAG
*
5780040 AAAAGCCAAAAAAATAAAG-AG
1 AAAAGCCAAAAAAAGAAAGAAG
5780061 AAAAG
1 AAAAG
5780066 GGAAAAGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.72, C:0.09, G:0.17, T:0.02
Consensus pattern (22 bp):
AAAAGCCAAAAAAAGAAAGAAG
Found at i:5783598 original size:12 final size:12
Alignment explanation
Indices: 5783583--5783626 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
5783573 ATATACATAA
5783583 ATATATATGTAT
1 ATATATATGTAT
*
5783595 ATATGTATGTAT
1 ATATATATGTAT
*
5783607 ATATATGTGTAT
1 ATATATATGTAT
5783619 ATATATAT
1 ATATATAT
5783627 AAAGCAAAGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (12 bp):
ATATATATGTAT
Found at i:5783625 original size:14 final size:14
Alignment explanation
Indices: 5783586--5783626 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
5783576 TACATAAATA
*
5783586 TATATGTATATATG
1 TATATATATATATG
*
5783600 TATGTATATATATG
1 TATATATATATATG
*
5783614 TGTATATATATAT
1 TATATATATATAT
5783627 AAAGCAAAGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (14 bp):
TATATATATATATG
Found at i:5784062 original size:13 final size:13
Alignment explanation
Indices: 5784044--5784070 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5784034 TATGGTCCTT
5784044 TCTAGCTTGATGA
1 TCTAGCTTGATGA
5784057 TCTAGCTTGATGA
1 TCTAGCTTGATGA
5784070 T
1 T
5784071 AATTTCTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (13 bp):
TCTAGCTTGATGA
Found at i:5785943 original size:2 final size:2
Alignment explanation
Indices: 5785936--5785965 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5785926 GCCATGAATA
*
5785936 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5785966 TCATGATCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5789030 original size:23 final size:23
Alignment explanation
Indices: 5788981--5789026 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
5788971 TAATTTTATA
*
5788981 TTAAATTTTATTGATTTATCAAT
1 TTAAATTTTATTGATTTATAAAT
5789004 TTAAATTTT-TT-ATTTATAAAT
1 TTAAATTTTATTGATTTATAAAT
5789025 TT
1 TT
5789027 TTAATAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.50
22 2 0.09
23 9 0.41
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (23 bp):
TTAAATTTTATTGATTTATAAAT
Found at i:5790573 original size:24 final size:22
Alignment explanation
Indices: 5790546--5790623 Score: 68
Period size: 24 Copynumber: 3.4 Consensus size: 22
5790536 ATAAGTTAAA
5790546 TAAATATAAATATTATGAAAATAT
1 TAAATA-AAATATTAT-AAAATAT
* * **
5790570 TAAATAAATTAATTATTTATGTAT
1 TAAATAAAAT-ATTA-TAAAATAT
5790594 TAAATAAATATATTA-AAAATAT
1 TAAATAAA-ATATTATAAAATAT
5790616 TAAATAAA
1 TAAATAAA
5790624 TAATTTTATA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
22 12 0.28
23 3 0.07
24 26 0.60
25 2 0.05
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.40
Consensus pattern (22 bp):
TAAATAAAATATTATAAAATAT
Found at i:5790573 original size:28 final size:25
Alignment explanation
Indices: 5790541--5790605 Score: 71
Period size: 28 Copynumber: 2.5 Consensus size: 25
5790531 CATTTATAAG
5790541 TTAAATAAATATAAATA-TTATGAAAATA
1 TTAAATAAATATAAATATTTATG----TA
*
5790569 TTAAATAAAT-TAATTATTTATGTA
1 TTAAATAAATATAAATATTTATGTA
5790593 TTAAATAAATATA
1 TTAAATAAATATA
5790606 TTAAAAATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
24 12 0.35
25 2 0.06
27 5 0.15
28 15 0.44
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (25 bp):
TTAAATAAATATAAATATTTATGTA
Found at i:5792867 original size:97 final size:97
Alignment explanation
Indices: 5792756--5792936 Score: 240
Period size: 97 Copynumber: 1.9 Consensus size: 97
5792746 TATAAAAAAC
* * * ***
5792756 TTCAATCCTACTAAATGATT-GAAGAATTTTAATTTTAAATTATGAATTTTGTTAAACGATT-GA
1 TTCAATCCTACTAAATGATTAG-AGAATTTAAATTTCAAATTATGAATTATACCAAACGATTAG-
* *
5792819 AGAATTTTATGATAAATTTTTAAAAAGATAATTT
64 AGAATTTCATAATAAATTTTTAAAAAGATAATTT
* *
5792853 TTCATTCCTACTAAATGATTAGAGGATTTAAATTTCAAATTATGAATTATACCAAACGATTAGAG
1 TTCAATCCTACTAAATGATTAGAGAATTTAAATTTCAAATTATGAATTATACCAAACGATTAGAG
5792918 AATTTCATAATAAATTTTT
66 AATTTCATAATAAATTTTT
5792937 TTAAAAATAA
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
97 70 0.97
98 2 0.03
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (97 bp):
TTCAATCCTACTAAATGATTAGAGAATTTAAATTTCAAATTATGAATTATACCAAACGATTAGAG
AATTTCATAATAAATTTTTAAAAAGATAATTT
Found at i:5792947 original size:16 final size:17
Alignment explanation
Indices: 5792926--5792957 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5792916 AGAATTTCAT
5792926 AATAAATT-TTTTTAAA
1 AATAAATTATTTTTAAA
5792942 AATAAATTATTTTTAA
1 AATAAATTATTTTTAA
5792958 TTAACCAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AATAAATTATTTTTAAA
Found at i:5797012 original size:95 final size:96
Alignment explanation
Indices: 5796875--5797100 Score: 341
Period size: 95 Copynumber: 2.4 Consensus size: 96
5796865 TAAAATCTTT
* *
5796875 CAATAGTTTGGTAAGATTT-ATTTCAATGTAAATCTCCTAATAGTTTGGTGAGATTTTATTGTGA
1 CAATAGTTTGGTAAGATTTAATTTCAATATAAATCTCCTAATAGTTTGGTGAGATTTTATTGTAA
5796939 AATTTATTTTAAAAAAATTTATTAAACCTTC
66 AATTTATTTTAAAAAAATTTATTAAACCTTC
*
5796970 CAATAGTTTGGTAAGATTTAATTT-AATATAGATCTTCC-AATAGTTTGGTGAGATTTTATTGTA
1 CAATAGTTTGGTAAGATTTAATTTCAATATAAATC-TCCTAATAGTTTGGTGAGATTTTATTGTA
* **
5797033 AAATTTATTTTAAGAAAATTTATTAAATTTTC
65 AAATTTATTTTAAAAAAATTTATTAAACCTTC
* *
5797065 CAATAGTTTGATAAGATTTAATTTCAAATACAAATC
1 CAATAGTTTGGTAAGATTTAATTTC-AATATAAATC
5797101 CTTCACTAGT
Statistics
Matches: 118, Mismatches: 9, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
95 103 0.87
96 7 0.06
97 8 0.07
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.44
Consensus pattern (96 bp):
CAATAGTTTGGTAAGATTTAATTTCAATATAAATCTCCTAATAGTTTGGTGAGATTTTATTGTAA
AATTTATTTTAAAAAAATTTATTAAACCTTC
Found at i:5797267 original size:20 final size:19
Alignment explanation
Indices: 5797219--5797288 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 19
5797209 TTATCTTCTA
* *
5797219 AATAATATAAATATAATGC
1 AATAATATAATTATCATGC
5797238 AATAATATAATATATTAATCATGC
1 AAT-A-AT-ATA-ATT-ATCATGC
5797262 AAATAATATGAATTATCATGC
1 -AATAATAT-AATTATCATGC
5797283 AATAAT
1 AATAAT
5797289 GCGAATAATG
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
19 3 0.07
20 7 0.17
21 9 0.21
22 8 0.19
23 5 0.12
24 7 0.17
25 3 0.07
ACGTcount: A:0.53, C:0.07, G:0.06, T:0.34
Consensus pattern (19 bp):
AATAATATAATTATCATGC
Found at i:5797294 original size:20 final size:21
Alignment explanation
Indices: 5797255--5797294 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
5797245 TAATATATTA
*
5797255 ATCATGCAAATAATATGAATT
1 ATCATGCAAATAATACGAATT
*
5797276 ATCATGC-AATAATGCGAAT
1 ATCATGCAAATAATACGAAT
5797295 AATGAATCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (21 bp):
ATCATGCAAATAATACGAATT
Found at i:5797303 original size:45 final size:44
Alignment explanation
Indices: 5797218--5797312 Score: 111
Period size: 45 Copynumber: 2.1 Consensus size: 44
5797208 ATTATCTTCT
* *
5797218 AAATAATATAAATATAATGCAATAATATAATATATTAATCATGC
1 AAATAATATAAATATAATGCAATAATAGAATATATGAATCATGC
* * * *
5797262 AAATAATATGAATTATCATGCAATAATGCGAATA-ATGAATCATGT
1 AAATAATAT-AAATATAATGCAATAAT-AGAATATATGAATCATGC
5797307 AAATAA
1 AAATAA
5797313 ATATCACATG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
44 9 0.21
45 30 0.70
46 4 0.09
ACGTcount: A:0.53, C:0.07, G:0.08, T:0.32
Consensus pattern (44 bp):
AAATAATATAAATATAATGCAATAATAGAATATATGAATCATGC
Found at i:5797377 original size:21 final size:20
Alignment explanation
Indices: 5797354--5797423 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 20
5797344 AATCATGCCA
5797354 AAAAAAAATA-ATAAAAGAAT
1 AAAAAAAATAGATAAAA-AAT
*
5797374 AAAATAAATAGATAAATAAAT
1 AAAAAAAATAGATAAA-AAAT
* *
5797395 AATAAAAATATG-TAAAAATT
1 AAAAAAAATA-GATAAAAAAT
5797415 AAATAAAAA
1 AAA-AAAAA
5797424 ATAAAAGCAG
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
20 14 0.34
21 25 0.61
22 2 0.05
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.21
Consensus pattern (20 bp):
AAAAAAAATAGATAAAAAAT
Found at i:5800522 original size:19 final size:19
Alignment explanation
Indices: 5800498--5800540 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
5800488 AAGTTTCCAT
*
5800498 TTTTTTCTCTT-TTTTTTTA
1 TTTTTTCT-TTCTTTTTTCA
*
5800517 TTTTTTGTTTCTTTTTTCA
1 TTTTTTCTTTCTTTTTTCA
5800536 TTTTT
1 TTTTT
5800541 CATTTTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.05, C:0.09, G:0.02, T:0.84
Consensus pattern (19 bp):
TTTTTTCTTTCTTTTTTCA
Found at i:5800887 original size:24 final size:24
Alignment explanation
Indices: 5800854--5800903 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
5800844 TCTCCTTAAT
* *
5800854 ATTTTTTCTTTTTTTTTTCCTTTC
1 ATTTTCTCTTTCTTTTTTCCTTTC
*
5800878 ATTTTCTCTTTCTTTTTTCTTTTC
1 ATTTTCTCTTTCTTTTTTCCTTTC
5800902 AT
1 AT
5800904 CATTTTTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (24 bp):
ATTTTCTCTTTCTTTTTTCCTTTC
Found at i:5800901 original size:12 final size:12
Alignment explanation
Indices: 5800855--5800901 Score: 53
Period size: 11 Copynumber: 4.0 Consensus size: 12
5800845 CTCCTTAATA
5800855 TTTTTTCTTTT-
1 TTTTTTCTTTTC
*
5800866 TTTTTTCCTTTC
1 TTTTTTCTTTTC
*
5800878 -ATTTTCTCTTTC
1 TTTTTTCT-TTTC
5800890 TTTTTTCTTTTC
1 TTTTTTCTTTTC
5800902 ATCATTTTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
11 15 0.52
12 8 0.28
13 6 0.21
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTTTCTTTTC
Found at i:5806668 original size:94 final size:94
Alignment explanation
Indices: 5806547--5806761 Score: 335
Period size: 95 Copynumber: 2.3 Consensus size: 94
5806537 ATTAATATTT
* * *
5806547 TTTAATAGTTTGGTATGATTTATTTTAATGCAGATCTCCCAATAG-TTTG-GAAGATTTTATTGT
1 TTTAATAGTTTGGTAAGATTTAATTTAATGCAGATCTCCCAATAGTTTTGTG-AGATTTTATTAT
5806610 AAAATTTATTTTAAGAAAATTTATTAAACC
65 AAAATTTATTTTAAGAAAATTTATTAAACC
**
5806640 TTGTAATAGTTTGGTAAGATTTAATTTAATGCAGATCTTTCAATAGTTTTGTGAGATTTTATTAT
1 TT-TAATAGTTTGGTAAGATTTAATTTAATGCAGATCTCCCAATAGTTTTGTGAGATTTTATTAT
*
5806705 GAAATTTATTTTAAGAAAATTTATTAAACC
65 AAAATTTATTTTAAGAAAATTTATTAAACC
5806735 TTTCAATAGTTTGGTAAGATTTAATTT
1 TTT-AATAGTTTGGTAAGATTTAATTT
5806762 CATATACAAA
Statistics
Matches: 112, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
93 2 0.02
94 40 0.36
95 69 0.62
96 1 0.01
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.47
Consensus pattern (94 bp):
TTTAATAGTTTGGTAAGATTTAATTTAATGCAGATCTCCCAATAGTTTTGTGAGATTTTATTATA
AAATTTATTTTAAGAAAATTTATTAAACC
Found at i:5806806 original size:95 final size:94
Alignment explanation
Indices: 5806611--5806803 Score: 239
Period size: 95 Copynumber: 2.0 Consensus size: 94
5806601 TTTTATTGTA
* *
5806611 AAATTTATTTTAAGAAAATTTATTAAACCTTGTAATAGTTTGGTAAGATTTAATTTAATGCAGAT
1 AAATTTATTTTAAGAAAATTTATTAAACCTTGTAATAGTTTGGTAAGATTTAATTTAATACAAAT
* ** **
5806676 CTTTCAATAGTTTTGTGAGATTTTATTAT
66 CATTCAATAGTTTTGTGAGATTAAAAAAT
5806705 GAAATTTATTTTAAGAAAATTTATTAAACCTT-TCAATAGTTTGGTAAGATTTAATTTCATATAC
1 -AAATTTATTTTAAGAAAATTTATTAAACCTTGT-AATAGTTTGGTAAGATTTAATTT-A-ATAC
*
5806769 AAATCATTCAATTG-TTTGAT-AGGATTAAAAAAT
62 AAATCATTCAATAGTTTTG-TGA-GATTAAAAAAT
5806802 AA
1 AA
5806804 TTTTTTGAAA
Statistics
Matches: 85, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
94 1 0.01
95 54 0.64
96 8 0.09
97 22 0.26
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44
Consensus pattern (94 bp):
AAATTTATTTTAAGAAAATTTATTAAACCTTGTAATAGTTTGGTAAGATTTAATTTAATACAAAT
CATTCAATAGTTTTGTGAGATTAAAAAAT
Found at i:5806924 original size:20 final size:20
Alignment explanation
Indices: 5806893--5806944 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
5806883 ATCTTGTAAG
*
5806893 TAATATAA-ATATCATATAA
1 TAATATAATATATCATACAA
5806912 TAATATAATATATCATACAA
1 TAATATAATATATCATACAA
5806932 TAATATAATATAT
1 TAATATAATATAT
5806945 TAATCATGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 8 0.26
20 23 0.74
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (20 bp):
TAATATAATATATCATACAA
Found at i:5806943 original size:25 final size:25
Alignment explanation
Indices: 5806911--5806962 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
5806901 ATATCATATA
5806911 ATAATATAATATATCATAC-AATAAT
1 ATAATATAATA-ATCATACAAATAAT
* *
5806936 ATAATATATTAATCATGCAAATAAT
1 ATAATATAATAATCATACAAATAAT
5806961 AT
1 AT
5806963 GAATTACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.37
Consensus pattern (25 bp):
ATAATATAATAATCATACAAATAAT
Found at i:5807053 original size:3 final size:3
Alignment explanation
Indices: 5807045--5807088 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
5807035 AAATCATGCC
5807045 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5807089 AAAGAATAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5813736 original size:10 final size:10
Alignment explanation
Indices: 5813672--5813735 Score: 56
Period size: 10 Copynumber: 5.8 Consensus size: 10
5813662 CTTTTTCTTT
5813672 TTTTATTTAA
1 TTTTATTTAA
5813682 TTTTATTTAA
1 TTTTATTTAA
5813692 TTATTAATTTAA
1 TT-TT-ATTTAA
*
5813704 TTCTTTATTATTTA
1 -T-TTTA-T-TTAA
*
5813718 TTTTATTTTA
1 TTTTATTTAA
5813728 TTTTATTT
1 TTTTATTT
5813736 TTGAAAAGCC
Statistics
Matches: 47, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
10 24 0.51
11 3 0.06
12 11 0.23
13 5 0.11
14 4 0.09
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTTATTTAA
Found at i:5814229 original size:62 final size:65
Alignment explanation
Indices: 5814158--5814281 Score: 166
Period size: 65 Copynumber: 2.0 Consensus size: 65
5814148 TAAATTACAT
5814158 AAATTTAAATTGCAAGAAAGTTAAATA-A-A-A-AAATCAAAATGCTTAAACATAAATTGCAAAT
1 AAATTTAAATTGCAAGAAAGTTAAA-ACATATATAAATCAAAATGCTTAAACATAAATTGCAAAT
5814219 A
65 A
* * * * *
5814220 AAATTTAAATTGCTAGAAATTTAAAACATATATAAATTATAGTGCTTAAACATAAATTGCAA
1 AAATTTAAATTGCAAGAAAGTTAAAACATATATAAATCAAAATGCTTAAACATAAATTGCAA
5814282 GAAAATTAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
61 1 0.02
62 24 0.45
63 1 0.02
64 1 0.02
65 26 0.49
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.30
Consensus pattern (65 bp):
AAATTTAAATTGCAAGAAAGTTAAAACATATATAAATCAAAATGCTTAAACATAAATTGCAAATA
Found at i:5819680 original size:4 final size:4
Alignment explanation
Indices: 5819673--5819711 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
5819663 TTTAAACTAT
* *
5819673 TTTA TTTA TTTA TTTA CTTA TTTA TTCA TTTA TTT- TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
5819712 AAATATATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
3 3 0.10
4 27 0.90
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:5821078 original size:16 final size:16
Alignment explanation
Indices: 5821050--5821089 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
5821040 CCTTTTATGC
5821050 TATTTTTTGTATATAT
1 TATTTTTTGTATATAT
5821066 TATTCTTTT-TATATAT
1 TATT-TTTTGTATATAT
*
5821082 CATTTTTT
1 TATTTTTT
5821090 ACTTTTCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 4 0.18
16 14 0.64
17 4 0.18
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.70
Consensus pattern (16 bp):
TATTTTTTGTATATAT
Found at i:5823880 original size:18 final size:16
Alignment explanation
Indices: 5823857--5823896 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 16
5823847 GAAAAATGTG
5823857 CAAAAAAGAATGAAAAAA
1 CAAAAAAGAAT--AAAAA
5823875 CAAAAAAAGAATAAAAA
1 C-AAAAAAGAATAAAAA
5823892 CAAAA
1 CAAAA
5823897 GCAAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 4 0.19
17 6 0.29
18 1 0.05
19 10 0.48
ACGTcount: A:0.80, C:0.07, G:0.07, T:0.05
Consensus pattern (16 bp):
CAAAAAAGAATAAAAA
Found at i:5823890 original size:17 final size:18
Alignment explanation
Indices: 5823858--5823896 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
5823848 AAAAATGTGC
5823858 AAAAAAGAATGAAAAAACA
1 AAAAAAGAAT-AAAAAACA
5823877 AAAAAAGAAT-AAAAACA
1 AAAAAAGAATAAAAAACA
5823894 AAA
1 AAA
5823897 GCAAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 10 0.50
19 10 0.50
ACGTcount: A:0.82, C:0.05, G:0.08, T:0.05
Consensus pattern (18 bp):
AAAAAAGAATAAAAAACA
Found at i:5824401 original size:13 final size:13
Alignment explanation
Indices: 5824383--5824407 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5824373 AAATGGCAAA
5824383 TAAGGAAACCCAG
1 TAAGGAAACCCAG
5824396 TAAGGAAACCCA
1 TAAGGAAACCCA
5824408 ATGATGAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.24, G:0.20, T:0.08
Consensus pattern (13 bp):
TAAGGAAACCCAG
Found at i:5825238 original size:53 final size:55
Alignment explanation
Indices: 5825173--5825304 Score: 148
Period size: 53 Copynumber: 2.5 Consensus size: 55
5825163 ATATTTTAAA
*
5825173 TGCGAATATTTGAATTTCTTATGAACTTAAATTTCTTAC-AAACC-TG-AATCTCT
1 TGCGAATCTTTGAATTTCTTATGAACTTAAATTTCTTACGAAACCTTGAAAT-TCT
* * * * *
5825226 TGCGAATCTTTGAAGTTCTTGTCAATTTAAATTTCTTACGAATCCTTGAAATTCT
1 TGCGAATCTTTGAATTTCTTATGAACTTAAATTTCTTACGAAACCTTGAAATTCT
**
5825281 TATGAATC--TGAATTTCTTATGAAC
1 TGCGAATCTTTGAATTTCTTATGAAC
5825305 CTGAATCTCT
Statistics
Matches: 64, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
53 46 0.72
54 4 0.06
55 11 0.17
56 3 0.05
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.42
Consensus pattern (55 bp):
TGCGAATCTTTGAATTTCTTATGAACTTAAATTTCTTACGAAACCTTGAAATTCT
Found at i:5825268 original size:36 final size:36
Alignment explanation
Indices: 5825223--5825299 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
5825213 AACCTGAATC
* * * * *
5825223 TCTTGCGAATCTTTGAAGTTCTTGTCAATTTAAATT
1 TCTTACGAATCCTTGAAATTCTTATCAATCTAAATT
* *
5825259 TCTTACGAATCCTTGAAATTCTTATGAATCTGAATT
1 TCTTACGAATCCTTGAAATTCTTATCAATCTAAATT
5825295 TCTTA
1 TCTTA
5825300 TGAACCTGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.45
Consensus pattern (36 bp):
TCTTACGAATCCTTGAAATTCTTATCAATCTAAATT
Found at i:5825297 original size:17 final size:17
Alignment explanation
Indices: 5825183--5825323 Score: 70
Period size: 17 Copynumber: 8.1 Consensus size: 17
5825173 TGCGAATATT
5825183 TGAATTTCTTATGAA-C
1 TGAATTTCTTATGAATC
* ** *
5825199 TTAAATTTCTTACAAACC
1 -TGAATTTCTTATGAATC
* **
5825217 TGAATCTCTTGCGAATC
1 TGAATTTCTTATGAATC
* * * *
5825234 TTTGAAGTTCTTGTCAATT
1 --TGAATTTCTTATGAATC
* *
5825253 TAAATTTCTTACGAATCC
1 TGAATTTCTTATGAAT-C
*
5825271 TTGAAATTCTTATGAATC
1 -TGAATTTCTTATGAATC
*
5825289 TGAATTTCTTATGAACC
1 TGAATTTCTTATGAATC
*
5825306 TGAATCTC-TAGTGAATC
1 TGAATTTCTTA-TGAATC
5825323 T
1 T
5825324 TTGAAACATT
Statistics
Matches: 92, Mismatches: 26, Indels: 12
0.71 0.20 0.09
Matches are distributed among these distances:
16 2 0.02
17 63 0.68
18 2 0.02
19 25 0.27
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.42
Consensus pattern (17 bp):
TGAATTTCTTATGAATC
Found at i:5825453 original size:18 final size:20
Alignment explanation
Indices: 5825424--5825472 Score: 66
Period size: 18 Copynumber: 2.5 Consensus size: 20
5825414 AAGAATCTTT
*
5825424 CATTCTACGAAATCTAAAT-
1 CATTCTATGAAATCTAAATC
*
5825443 C-TTCTATGAAATCTAGATC
1 CATTCTATGAAATCTAAATC
5825462 CATTCTATGAA
1 CATTCTATGAA
5825473 TCTTTGGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 15 0.58
19 2 0.08
20 9 0.35
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.35
Consensus pattern (20 bp):
CATTCTATGAAATCTAAATC
Found at i:5831440 original size:17 final size:17
Alignment explanation
Indices: 5831420--5831463 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
5831410 AAAAAAAAAC
5831420 TATTATAT-CTATATTTT
1 TATTATATACTATA-TTT
*
5831437 TATTATGATAGTATATTT
1 TATTAT-ATACTATATTT
5831455 TATTATATA
1 TATTATATA
5831464 ACTAACAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 9 0.38
18 11 0.46
19 4 0.17
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (17 bp):
TATTATATACTATATTT
Found at i:5831922 original size:14 final size:15
Alignment explanation
Indices: 5831903--5831940 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
5831893 TTTAAAAAAA
5831903 CTTTTCTTT-CCCCT
1 CTTTTCTTTGCCCCT
**
5831917 CTTTTCTTTGCCTTT
1 CTTTTCTTTGCCCCT
5831932 CTTTTCTTT
1 CTTTTCTTT
5831941 TATTAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.00, C:0.32, G:0.03, T:0.66
Consensus pattern (15 bp):
CTTTTCTTTGCCCCT
Found at i:5833759 original size:22 final size:23
Alignment explanation
Indices: 5833734--5833786 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
5833724 TTTCTTTTAT
5833734 TTTTATATAT-TATTT-AATAGAA
1 TTTTATATATATATTTAAATAG-A
5833756 TTTT-TA-ATATATTTAAATAGA
1 TTTTATATATATATTTAAATAGA
5833777 -TTTATATATA
1 TTTTATATATA
5833787 AAATAATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
20 5 0.19
21 10 0.37
22 12 0.44
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (23 bp):
TTTTATATATATATTTAAATAGA
Found at i:5833779 original size:21 final size:23
Alignment explanation
Indices: 5833732--5833786 Score: 71
Period size: 21 Copynumber: 2.5 Consensus size: 23
5833722 AATTTCTTTT
5833732 ATTTTTATATATTATTTAATAGA
1 ATTTTTATATATTATTTAATAGA
5833755 ATTTTTA-ATA-TATTTAAATAG-
1 ATTTTTATATATTATTT-AATAGA
*
5833776 ATTTATATATA
1 ATTTTTATATA
5833787 AAATAATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 11 0.38
22 11 0.38
23 7 0.24
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (23 bp):
ATTTTTATATATTATTTAATAGA
Found at i:5834084 original size:17 final size:19
Alignment explanation
Indices: 5834052--5834086 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
5834042 CAAGTTGAAT
5834052 AATTTCAATAAATTTAAAG
1 AATTTCAATAAATTTAAAG
5834071 AATTTC-AT-AATTTAAA
1 AATTTCAATAAATTTAAA
5834087 TTTTAATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 2 0.12
19 6 0.38
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (19 bp):
AATTTCAATAAATTTAAAG
Found at i:5834229 original size:2 final size:2
Alignment explanation
Indices: 5834222--5834248 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5834212 CATGTGGCTT
5834222 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5834249 TACTACTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5835642 original size:17 final size:17
Alignment explanation
Indices: 5835620--5835652 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5835610 TTAGTATGCA
*
5835620 TTGTTTTATGTGTTGTT
1 TTGTTTTATGTATTGTT
5835637 TTGTTTTATGTATTGT
1 TTGTTTTATGTATTGT
5835653 GTAATTGGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.00, G:0.21, T:0.70
Consensus pattern (17 bp):
TTGTTTTATGTATTGTT
Found at i:5839442 original size:24 final size:24
Alignment explanation
Indices: 5839415--5839474 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
5839405 TGATAATAAG
* *
5839415 TTTTCATAAAAAA-AAAGAACTTT
1 TTTTTATAAAAAACAAAGAACGTT
*
5839438 TTTTTTTAAAAAACAAAGAACGTT
1 TTTTTATAAAAAACAAAGAACGTT
* *
5839462 TTTATAAAAAAAA
1 TTTTTATAAAAAA
5839475 TTTATGTTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 11 0.37
24 19 0.63
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.35
Consensus pattern (24 bp):
TTTTTATAAAAAACAAAGAACGTT
Found at i:5841798 original size:20 final size:19
Alignment explanation
Indices: 5841753--5841803 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 19
5841743 ATAGACTAAA
5841753 AAGATAAAATAACTAAACAAT
1 AAGAT-AAAT-ACTAAACAAT
5841774 AAGATAAATACT-AACATAT
1 AAGATAAATACTAAACA-AT
5841793 ACAGATAAATA
1 A-AGATAAATA
5841804 AAATTAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.14
19 6 0.21
20 13 0.46
21 5 0.18
ACGTcount: A:0.63, C:0.10, G:0.06, T:0.22
Consensus pattern (19 bp):
AAGATAAATACTAAACAAT
Found at i:5843786 original size:13 final size:13
Alignment explanation
Indices: 5843768--5843792 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5843758 ATAAATTAAA
5843768 ATTTTTAAAAATG
1 ATTTTTAAAAATG
5843781 ATTTTTAAAAAT
1 ATTTTTAAAAAT
5843793 TTTAAATATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
ATTTTTAAAAATG
Found at i:5843941 original size:14 final size:14
Alignment explanation
Indices: 5843907--5843940 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
5843897 ATTTGTTTTA
5843907 TGAAAAATGACTTT
1 TGAAAAATGACTTT
5843921 TGAAAAATGA-TTT
1 TGAAAAATGACTTT
5843934 TGAAAAA
1 TGAAAAA
5843941 AAATAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.50, C:0.03, G:0.15, T:0.32
Consensus pattern (14 bp):
TGAAAAATGACTTT
Found at i:5846660 original size:22 final size:22
Alignment explanation
Indices: 5846635--5846686 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
5846625 GAATTTAATG
*
5846635 AATTAAAT-TAATAAATTAATAA
1 AATTAAATATAA-AAATCAATAA
*
5846657 AATTTAATATAAAAATCAATAA
1 AATTAAATATAAAAATCAATAA
5846679 AATATAAA
1 AAT-TAAA
5846687 AAATATTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
AATTAAATATAAAAATCAATAA
Found at i:5846858 original size:21 final size:23
Alignment explanation
Indices: 5846820--5846868 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 23
5846810 TATAATAATT
*
5846820 TTTTTAATTTATTGATTT-TA-A
1 TTTTTAATTTAATGATTTGTATA
5846841 TTTTTAATTCTAAT-ATTTGTATA
1 TTTTTAATT-TAATGATTTGTATA
5846864 TTTTT
1 TTTTT
5846869 TTTAAATTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 13 0.54
22 5 0.21
23 6 0.25
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (23 bp):
TTTTTAATTTAATGATTTGTATA
Found at i:5847885 original size:6 final size:6
Alignment explanation
Indices: 5847874--5847905 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
5847864 AAACACAGAG
5847874 AGAGAC AGAGAC AGAGAC AGAGAC AGAGAC AG
1 AGAGAC AGAGAC AGAGAC AGAGAC AGAGAC AG
5847906 GGAATAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.16, G:0.34, T:0.00
Consensus pattern (6 bp):
AGAGAC
Found at i:5851804 original size:144 final size:144
Alignment explanation
Indices: 5851544--5851835 Score: 377
Period size: 144 Copynumber: 2.0 Consensus size: 144
5851534 CAATTAAGAA
* * * * *
5851544 TATGAGAATTAGTGAAGATCGATTACAACCGATCACCACAATATTAGTGGGATTCAAGAATGAAC
1 TATGAGAATAAGTAAAGATAGATTACAACCGATCACCACAACATTAGTAGGATTCAAGAATGAAC
** * * *
5851609 AGGTGCCTATGAAAGGAACAATCAAACTACCGATTTCCTTGGGGATAGAACCAAGGACAACCACC
66 AGGTGCCTATGAAAAAAACAATCAAACTACCGATTTCCTTAGGGACAGAACCAAAGACAACCACC
5851674 TCGATTATAGAATT
131 TCGATTATAGAATT
* * * * * *
5851688 TATGAGAATAAGTAAAGGTAGATTGCAATCGATCACTATAACATTAGTAGGATTCAAGAATGAAT
1 TATGAGAATAAGTAAAGATAGATTACAACCGATCACCACAACATTAGTAGGATTCAAGAATGAAC
* * * ** *
5851753 AGGTGCTTGTGAAAAAAATAATCAAACTATTGATTTTCTTAGGGACAGAACCAAAGACAACCACC
66 AGGTGCCTATGAAAAAAACAATCAAACTACCGATTTCCTTAGGGACAGAACCAAAGACAACCACC
*
5851818 TTGATTATAGAATT
131 TCGATTATAGAATT
5851832 TATG
1 TATG
5851836 GTGGTGGACC
Statistics
Matches: 125, Mismatches: 23, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
144 125 1.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (144 bp):
TATGAGAATAAGTAAAGATAGATTACAACCGATCACCACAACATTAGTAGGATTCAAGAATGAAC
AGGTGCCTATGAAAAAAACAATCAAACTACCGATTTCCTTAGGGACAGAACCAAAGACAACCACC
TCGATTATAGAATT
Found at i:5863509 original size:19 final size:19
Alignment explanation
Indices: 5863485--5863525 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
5863475 AAGGTACGTG
5863485 ATCTAGCATATGTTCTGGA
1 ATCTAGCATATGTTCTGGA
5863504 ATCTAGCATATGTTCTGGA
1 ATCTAGCATATGTTCTGGA
5863523 ATC
1 ATC
5863526 AGATAAGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.37
Consensus pattern (19 bp):
ATCTAGCATATGTTCTGGA
Found at i:5864217 original size:28 final size:28
Alignment explanation
Indices: 5864176--5864230 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
5864166 ATATTTTTAT
* *
5864176 ATTTACATCTAAATTAA-ATTTATAATTA
1 ATTTAAATC-AAAATAATATTTATAATTA
*
5864204 ATTTAAATCAAAATAATATTTTTAATT
1 ATTTAAATCAAAATAATATTTATAATT
5864231 TTAGTCATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (28 bp):
ATTTAAATCAAAATAATATTTATAATTA
Found at i:5868420 original size:23 final size:23
Alignment explanation
Indices: 5868370--5868420 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
5868360 TATTTTTATT
5868370 ATTTTTACTTCTATTTTTTAAGA
1 ATTTTTACTTCTATTTTTTAAGA
* * *
5868393 TTTTTTA-TTTTATTTTTATATGA
1 ATTTTTACTTCTATTTTT-TAAGA
5868416 ATTTT
1 ATTTT
5868421 GTTAGGAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.69
Consensus pattern (23 bp):
ATTTTTACTTCTATTTTTTAAGA
Found at i:5881993 original size:11 final size:11
Alignment explanation
Indices: 5881977--5882008 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
5881967 CACCCATCAG
5881977 CAGCCACCTTA
1 CAGCCACCTTA
5881988 CAGCCACCTTA
1 CAGCCACCTTA
5881999 CAGCCACCTT
1 CAGCCACCTT
5882009 TGTAGCTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.25, C:0.47, G:0.09, T:0.19
Consensus pattern (11 bp):
CAGCCACCTTA
Found at i:5883446 original size:18 final size:20
Alignment explanation
Indices: 5883405--5883446 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
5883395 TCTAATTTAT
* *
5883405 TAATCTTAAATAAAATAGAT
1 TAATCTTAAATAAAATAAAG
5883425 TAATCTT-AA-AAAATAAAG
1 TAATCTTAAATAAAATAAAG
5883443 TAAT
1 TAAT
5883447 AAAAAAAGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 11 0.55
19 2 0.10
20 7 0.35
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (20 bp):
TAATCTTAAATAAAATAAAG
Found at i:5884567 original size:42 final size:41
Alignment explanation
Indices: 5884498--5884578 Score: 99
Period size: 42 Copynumber: 2.0 Consensus size: 41
5884488 GAATCCATAT
* * *
5884498 TTATATAATATAAAATATTAATAATTTATGTATTTATATTA
1 TTATATAAAATAAAAAATTAATAATTTATGTATATATATTA
* * *
5884539 TTATCATAAAATAAAAAATTATTTATTTATTTATATATAT
1 TTAT-ATAAAATAAAAAATTAATAATTTATGTATATATAT
5884579 ATAATTTTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
41 4 0.12
42 29 0.88
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (41 bp):
TTATATAAAATAAAAAATTAATAATTTATGTATATATATTA
Found at i:5884929 original size:17 final size:17
Alignment explanation
Indices: 5884900--5884932 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5884890 ATATCAGAAC
5884900 TTATGCATGTATTTTTT
1 TTATGCATGTATTTTTT
5884917 TTAT-CATGTTATTTTT
1 TTATGCATG-TATTTTT
5884933 ATTTTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.18, C:0.06, G:0.09, T:0.67
Consensus pattern (17 bp):
TTATGCATGTATTTTTT
Found at i:5887564 original size:13 final size:12
Alignment explanation
Indices: 5887531--5887570 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
5887521 ATATTGATAT
5887531 TATATAAAAATA
1 TATATAAAAATA
5887543 TATATAAAAATA
1 TATATAAAAATA
* *
5887555 TATTTGAAAAT-
1 TATATAAAAATA
5887566 TATAT
1 TATAT
5887571 GATTTTTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
11 4 0.16
12 21 0.84
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (12 bp):
TATATAAAAATA
Found at i:5887597 original size:27 final size:27
Alignment explanation
Indices: 5887578--5887640 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
5887568 TATGATTTTT
5887578 AATAAT-TATATGATTAATATATATAA
1 AATAATATATATGATTAATATATATAA
* * *
5887604 AATAATATATATGTTTAATA-AAATTCA
1 AATAATATATATGATTAATATATA-TAA
5887631 AATAATATAT
1 AATAATATAT
5887641 TTTATATTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 8 0.25
27 24 0.75
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (27 bp):
AATAATATATATGATTAATATATATAA
Found at i:5890282 original size:9 final size:9
Alignment explanation
Indices: 5890268--5890551 Score: 110
Period size: 9 Copynumber: 29.7 Consensus size: 9
5890258 AATTCAAATA
5890268 AAAAATTTT
1 AAAAATTTT
*
5890277 AAAAATTAT
1 AAAAATTTT
*
5890286 AAAAATTAT
1 AAAAATTTT
*
5890295 AAAAAATTT
1 AAAAATTTT
*
5890304 AGAAAATTCTA
1 A-AAAATT-TT
*
5890315 AAAAATTCT
1 AAAAATTTT
5890324 AAAAATTTTTT
1 AAAAA--TTTT
* *
5890335 AGAAATTCTA
1 AAAAATT-TT
**
5890345 AAATAATATCA
1 AAA-AAT-TTT
5890356 AAAAATTCTT
1 AAAAATT-TT
* *
5890366 AGCAAA-TTA
1 A-AAAATTTT
5890375 AAAAATTTT
1 AAAAATTTT
5890384 --AAATTTT
1 AAAAATTTT
* *
5890391 -CAATTTTT
1 AAAAATTTT
5890399 CAATAAATTTT
1 -AA-AAATTTT
*
5890410 AAAAATTTA
1 AAAAATTTT
5890419 AAAAACTTTT
1 AAAAA-TTTT
* *
5890429 CAAACTTTT
1 AAAAATTTT
5890438 CAAAAATTATAAAT
1 -AAAAATT-T---T
*
5890452 AAAAA-TTC
1 AAAAATTTT
5890460 AAAAATTTT
1 AAAAATTTT
*
5890469 AAAAATTCT
1 AAAAATTTT
* *
5890478 AACGACTTTT
1 AA-AAATTTT
5890488 AAAAAATTTT
1 -AAAAATTTT
5890498 AAAAAATTTAT
1 -AAAAATTT-T
* *
5890509 AACAATCTT
1 AAAAATTTT
*
5890518 AAAAATTAT
1 AAAAATTTT
5890527 AGAAAATTTT
1 A-AAAATTTT
* *
5890537 AAAAAATTC
1 AAAAATTTT
5890546 AAAAAT
1 AAAAAT
5890552 AATTAAGGAA
Statistics
Matches: 206, Mismatches: 44, Indels: 50
0.69 0.15 0.17
Matches are distributed among these distances:
7 7 0.03
8 14 0.07
9 83 0.40
10 64 0.31
11 30 0.15
12 2 0.01
13 5 0.02
14 1 0.00
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.37
Consensus pattern (9 bp):
AAAAATTTT
Found at i:5890430 original size:30 final size:31
Alignment explanation
Indices: 5890395--5890510 Score: 91
Period size: 30 Copynumber: 3.8 Consensus size: 31
5890385 AATTTTCAAT
5890395 TTTTCAATAAATTTT-AAAAATT-TAAAAAAC
1 TTTTCAA-AAATTTTAAAAAATTATAAAAAAC
* *
5890425 TTTTC-AAACTTTTCAAAAATTATAAATAAA-
1 TTTTCAAAAATTTTAAAAAATTATAAA-AAAC
** * **
5890455 AATTCAAAAATTTT-AAAAATTCT-AACGAC
1 TTTTCAAAAATTTTAAAAAATTATAAAAAAC
*
5890484 TTTTAAAAAATTTTAAAAAATTTATAA
1 TTTTCAAAAATTTTAAAAAA-TTATAA
5890511 CAATCTTAAA
Statistics
Matches: 67, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
28 7 0.10
29 21 0.31
30 25 0.37
31 13 0.19
32 1 0.01
ACGTcount: A:0.53, C:0.08, G:0.01, T:0.39
Consensus pattern (31 bp):
TTTTCAAAAATTTTAAAAAATTATAAAAAAC
Found at i:5890507 original size:19 final size:19
Alignment explanation
Indices: 5890105--5890550 Score: 118
Period size: 19 Copynumber: 22.2 Consensus size: 19
5890095 AGTATAAAAT
*
5890105 AAAATTTTAAAAAATTT-C
1 AAAATTTTAAAAAATTTAA
5890123 AAAATTTTCAAAAAATTTCAAAAAA
1 AAAATTTT-AAAAAATTT-----AA
** * *
5890148 ACAAAAGTTAAAAAGTTAAA
1 A-AAATTTTAAAAAATTTAA
* * *
5890168 AAAAATCTAAAAAATTCAA
1 AAAATTTTAAAAAATTTAA
* *
5890187 AAAATTCTAAAAAA-TTGA
1 AAAATTTTAAAAAATTTAA
*
5890205 AAATTTTCTAAAATAATTTTAA
1 AAAATTT-TAAAA-AA-TTTAA
*** *
5890227 AAAATTTTGTTAAATTCAA
1 AAAATTTTAAAAAATTTAA
*
5890246 AAATATTTTTAAAATTCAA-ATAA
1 AAA-A-TTTTAAAA---AATTTAA
5890269 AAAATTTT-AAAAA-TTATA
1 AAAATTTTAAAAAATTTA-A
* *
5890287 AAAATTATAAAAAATTTAG
1 AAAATTTTAAAAAATTTAA
*
5890306 AAAATTCTAAAAAATTCTAA
1 AAAATTTTAAAAAATT-TAA
* * *
5890326 AAATTTTTTAGAAATTCTAA
1 AAAATTTTAAAAAATT-TAA
* * *
5890346 AATAATATCAAAAAATTCTTAG
1 AA-AATTTTAAAAAA-T-TTAA
*
5890368 CAAA--TTAAAAAATTTTAA
1 AAAATTTTAAAAAA-TTTAA
* * *
5890386 ATTTTCAATTTTTCAATAAATTTTA
1 A-----AAATTTT-AAAAAATTTAA
**
5890411 AAAA-TTTAAAAAACTTTTC
1 AAAATTTTAAAAAA-TTTAA
* *
5890430 AAACTTTTCAAAAATTATAA
1 AAAATTTTAAAAAATT-TAA
** * *
5890450 ATAAAAATTCAAAAATTTTA
1 A-AAATTTTAAAAAATTTAA
* * **
5890470 AAAATTCTAACGACTTTTAA
1 AAAATTTTAA-AAAATTTAA
5890490 AAAATTTTAAAAAATTTATA
1 AAAATTTTAAAAAATTTA-A
* * *
5890510 ACAATCTT-AAAAATTATAG
1 AAAATTTTAAAAAATT-TAA
*
5890529 AAAATTTTAAAAAATTCAA
1 AAAATTTTAAAAAATTTAA
5890548 AAA
1 AAA
5890551 TAATTAAGGA
Statistics
Matches: 311, Mismatches: 77, Indels: 79
0.67 0.16 0.17
Matches are distributed among these distances:
17 4 0.01
18 31 0.10
19 116 0.37
20 79 0.25
21 32 0.10
22 14 0.05
23 8 0.03
24 2 0.01
25 15 0.05
26 10 0.03
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (19 bp):
AAAATTTTAAAAAATTTAA
Found at i:5890596 original size:11 final size:11
Alignment explanation
Indices: 5890567--5890605 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
5890557 AGGAAACTTG
*
5890567 AAATTTTTCAA
1 AAATTTTTCAT
*
5890578 AAAATTTTCAT
1 AAATTTTTCAT
*
5890589 AAATTTTTTAT
1 AAATTTTTCAT
5890600 AAATTT
1 AAATTT
5890606 AAGGAAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (11 bp):
AAATTTTTCAT
Found at i:5890632 original size:16 final size:16
Alignment explanation
Indices: 5890611--5890665 Score: 65
Period size: 16 Copynumber: 3.3 Consensus size: 16
5890601 AATTTAAGGA
5890611 AATTTATTTTTTAATT
1 AATTTATTTTTTAATT
5890627 AATTTAAATTTTTTAATT
1 AATTT--ATTTTTTAATT
** *
5890645 TTTTTATTTTTTAATA
1 AATTTATTTTTTAATT
5890661 AATTT
1 AATTT
5890666 TCAAAATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
16 18 0.56
18 14 0.44
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
AATTTATTTTTTAATT
Found at i:5890639 original size:18 final size:18
Alignment explanation
Indices: 5890616--5890665 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
5890606 AAGGAAATTT
5890616 ATTTTTTAATTAATTTAA
1 ATTTTTTAATTAATTTAA
**
5890634 ATTTTTTAATT--TTTTT
1 ATTTTTTAATTAATTTAA
*
5890650 ATTTTTTAATAAATTT
1 ATTTTTTAATTAATTT
5890666 TCAAAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 13 0.48
18 14 0.52
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
ATTTTTTAATTAATTTAA
Found at i:5890646 original size:8 final size:8
Alignment explanation
Indices: 5890616--5890659 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
5890606 AAGGAAATTT
5890616 ATTTTTTA
1 ATTTTTTA
*
5890624 ATTAATTTAA
1 ATT--TTTTA
5890634 ATTTTTTA
1 ATTTTTTA
*
5890642 ATTTTTTT
1 ATTTTTTA
5890650 ATTTTTTA
1 ATTTTTTA
5890658 AT
1 AT
5890660 AAATTTTCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
8 23 0.77
10 7 0.23
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (8 bp):
ATTTTTTA
Found at i:5890748 original size:20 final size:19
Alignment explanation
Indices: 5890723--5890789 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 19
5890713 ATAGTTTTAG
*
5890723 TTTTTTTATAAATTTAGAAC
1 TTTTTTTAGAAATTTA-AAC
* *
5890743 TTTTTTTCGAATATTTAAAA
1 TTTTTTTAGAA-ATTTAAAC
*
5890763 TTTTTTAAAGAAATTTATAAC
1 TTTTTT-TAGAAATTTA-AAC
5890784 TTTTTT
1 TTTTTT
5890790 ATAATTTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.57
Consensus pattern (19 bp):
TTTTTTTAGAAATTTAAAC
Found at i:5890787 original size:21 final size:20
Alignment explanation
Indices: 5890732--5890790 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
5890722 GTTTTTTTAT
**
5890732 AAATTTAGAACTTTTTT-TCG
1 AAATTTA-AACTTTTTTAAAG
*
5890752 AATATTTAAAATTTTTTAAAG
1 AA-ATTTAAACTTTTTTAAAG
5890773 AAATTTATAACTTTTTTA
1 AAATTTA-AACTTTTTTA
5890791 TAATTTTTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (20 bp):
AAATTTAAACTTTTTTAAAG
Done.