Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 49 of 106
Found at i:18312597 original size:25 final size:25
Alignment explanation
Indices: 18312564--18312617 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
18312554 GATTAATAAT
*
18312564 ATTAATCTTCATGCAATAAATAAAC
1 ATTAATCTTCATACAATAAATAAAC
* **
18312589 ATTAATCTTTATATGATAAATAAAC
1 ATTAATCTTCATACAATAAATAAAC
18312614 ATTA
1 ATTA
18312618 GTTTCAAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.11, G:0.04, T:0.37
Consensus pattern (25 bp):
ATTAATCTTCATACAATAAATAAAC
Found at i:18315366 original size:85 final size:85
Alignment explanation
Indices: 18315232--18315610 Score: 620
Period size: 85 Copynumber: 4.5 Consensus size: 85
18315222 ATTTCCAATA
* * * *
18315232 TTTAATTATAACATATTGCCAATCATTTTAATTAAAAAT-TCAAATAATAATTGTAAACATTAAT
1 TTTAATTCTAACATATTACCAATCATTTTAATTAAAAATCT-AAACAATAATTCTAAACATTAAT
18315296 TCTCAAATATAATATTTAATG
65 TCTCAAATATAATATTTAATG
* *
18315317 TTTAATTCCAACATATTACCAATAATTTTAATTAAAAATCTAAACAATAATTCTAAACATTAATT
1 TTTAATTCTAACATATTACCAATCATTTTAATTAAAAATCTAAACAATAATTCTAAACATTAATT
18315382 CTCAAATATAATATTTAATAG
66 CTCAAATATAATATTTAAT-G
* *
18315403 -TTAATTCTAACATATTACCAATCATTTTACTTAAAAATCTTAACAATAATTCTAAACATTAATT
1 TTTAATTCTAACATATTACCAATCATTTTAATTAAAAATCTAAACAATAATTCTAAACATTAATT
*
18315467 CTCAAATATAATATTTAATA
66 CTCAAATATAATATTTAATG
18315487 TTTAATTCTAACATATTACCAATCATTTTAATTAAAAATCTAAACAATAATTCTAAACATTAATT
1 TTTAATTCTAACATATTACCAATCATTTTAATTAAAAATCTAAACAATAATTCTAAACATTAATT
18315552 CTCAAATATAAT-TCTTAATG
66 CTCAAATATAATAT-TTAATG
*
18315572 TTTAATTCTAACATATTACCAATTATTTTAATTAAAAAT
1 TTTAATTCTAACATATTACCAATCATTTTAATTAAAAAT
18315611 AAACCCAGAT
Statistics
Matches: 275, Mismatches: 15, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
84 1 0.00
85 272 0.99
86 2 0.01
ACGTcount: A:0.46, C:0.12, G:0.01, T:0.41
Consensus pattern (85 bp):
TTTAATTCTAACATATTACCAATCATTTTAATTAAAAATCTAAACAATAATTCTAAACATTAATT
CTCAAATATAATATTTAATG
Found at i:18315543 original size:13 final size:13
Alignment explanation
Indices: 18315525--18315566 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
18315515 TAATTAAAAA
18315525 TCTAAACAATAAT
1 TCTAAACAATAAT
*
18315538 TCTAAACATTAAT
1 TCTAAACAATAAT
*
18315551 TCTCAAA-TATAAT
1 TCT-AAACAATAAT
18315564 TCT
1 TCT
18315567 TAATGTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 22 0.88
14 3 0.12
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (13 bp):
TCTAAACAATAAT
Found at i:18316150 original size:23 final size:23
Alignment explanation
Indices: 18316124--18316176 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
18316114 CAGTGGTAGC
18316124 AATTTTGACTGAGAAGCACCAAT
1 AATTTTGACTGAGAAGCACCAAT
*
18316147 AATTTTGACTGAGAAGCACCAGT
1 AATTTTGACTGAGAAGCACCAAT
18316170 AATTTTG
1 AATTTTG
18316177 GCTGTTGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (23 bp):
AATTTTGACTGAGAAGCACCAAT
Found at i:18316747 original size:15 final size:14
Alignment explanation
Indices: 18316722--18316753 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
18316712 TGTCTTTCTA
18316722 CCTCTTCTCTCTCT
1 CCTCTTCTCTCTCT
18316736 CCTCTCTCTCTCTCT
1 CCTCT-TCTCTCTCT
18316751 CCT
1 CCT
18316754 ATATTTAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (14 bp):
CCTCTTCTCTCTCT
Found at i:18320433 original size:17 final size:16
Alignment explanation
Indices: 18320396--18320439 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
18320386 GATGAAAGAT
*
18320396 AAAATAATAATAAAAAT
1 AAAATAA-AATAAAAAG
18320413 AAAATAAAATAAATAAG
1 AAAATAAAATAAA-AAG
18320430 AAAATGAAAA
1 AAAAT-AAAA
18320440 CTCATATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 6 0.25
17 14 0.58
18 4 0.17
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (16 bp):
AAAATAAAATAAAAAG
Found at i:18320434 original size:22 final size:23
Alignment explanation
Indices: 18320382--18320439 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 23
18320372 ATAAGTAAAC
18320382 AAAAGATGAAAGATAAAATAATAAT
1 AAAA-ATGAAA-ATAAAATAATAAT
18320407 AAAAAT-AAAATAAAATAAATAA-
1 AAAAATGAAAATAAAAT-AATAAT
*
18320429 GAAAATGAAAA
1 AAAAATGAAAA
18320440 CTCATATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 12 0.40
23 12 0.40
24 2 0.07
25 4 0.13
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (23 bp):
AAAAATGAAAATAAAATAATAAT
Found at i:18320861 original size:90 final size:90
Alignment explanation
Indices: 18320754--18320936 Score: 321
Period size: 90 Copynumber: 2.0 Consensus size: 90
18320744 TCATAACTGT
*
18320754 TCAACAAGAAGAAAAACATAGCATGCAGCCTGAACACTAACCCGTACTTACATAACTGATCAGAA
1 TCAACAAGAAGAAAAACATAGCATGCAGCCTGAACACTAACCAGTACTTACATAACTGATCAGAA
18320819 TACTCCTGGCAGCGGTACTGGGTCA
66 TACTCCTGGCAGCGGTACTGGGTCA
*
18320844 TCAACAAGAAGAAAAACATAGCATGCAGCCTGAACACTAACCAGTACTTACATAACTGGTCAGAA
1 TCAACAAGAAGAAAAACATAGCATGCAGCCTGAACACTAACCAGTACTTACATAACTGATCAGAA
* **
18320909 TACTCTTGGTGGCGGTACTGGGTCA
66 TACTCCTGGCAGCGGTACTGGGTCA
18320934 TCA
1 TCA
18320937 TCAGGAAAAG
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 88 1.00
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (90 bp):
TCAACAAGAAGAAAAACATAGCATGCAGCCTGAACACTAACCAGTACTTACATAACTGATCAGAA
TACTCCTGGCAGCGGTACTGGGTCA
Found at i:18323867 original size:23 final size:23
Alignment explanation
Indices: 18323841--18323886 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
18323831 ATACAATAAC
*
18323841 CTTATCCTAATATAATTAGGAAT
1 CTTATCCTAATAGAATTAGGAAT
18323864 CTTATCCTAATAGAATTAGGAAT
1 CTTATCCTAATAGAATTAGGAAT
18323887 TTTTATTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (23 bp):
CTTATCCTAATAGAATTAGGAAT
Found at i:18326343 original size:4 final size:4
Alignment explanation
Indices: 18326320--18326385 Score: 66
Period size: 4 Copynumber: 16.0 Consensus size: 4
18326310 AAAAAATATT
18326320 TAAA TTAAA TTAAA TAAAA TAAA T-AA TAAA TAAAA TAAA T-AA TAAA
1 TAAA -TAAA -TAAA T-AAA TAAA TAAA TAAA T-AAA TAAA TAAA TAAA
18326366 TAAAA TAAA T-AA TAAA TAAA
1 T-AAA TAAA TAAA TAAA TAAA
18326386 AATAATAATA
Statistics
Matches: 55, Mismatches: 0, Indels: 13
0.81 0.00 0.19
Matches are distributed among these distances:
3 9 0.16
4 25 0.45
5 21 0.38
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:18326349 original size:12 final size:11
Alignment explanation
Indices: 18326336--18326390 Score: 64
Period size: 11 Copynumber: 5.2 Consensus size: 11
18326326 AAATTAAATA
18326336 AAATAAATAAT
1 AAATAAATAAT
18326347 AAAT-AA-AAT
1 AAATAAATAAT
18326356 AAAT-AATAAAT
1 AAATAAAT-AAT
18326367 AAAATAAATAAT
1 -AAATAAATAAT
18326379 AAATAAA-AAT
1 AAATAAATAAT
18326389 AA
1 AA
18326391 TAATAAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
9 9 0.22
10 7 0.17
11 14 0.35
12 7 0.17
13 3 0.08
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:18326351 original size:16 final size:16
Alignment explanation
Indices: 18326330--18326402 Score: 123
Period size: 16 Copynumber: 4.6 Consensus size: 16
18326320 TAAATTAAAT
18326330 TAAATAAAATAAATAA
1 TAAATAAAATAAATAA
18326346 TAAATAAAATAAATAA
1 TAAATAAAATAAATAA
18326362 TAAATAAAATAAATAA
1 TAAATAAAATAAATAA
18326378 TAAATAAAA-ATAATAA
1 TAAATAAAATA-AATAA
18326394 TAAA-AAAAT
1 TAAATAAAAT
18326403 TGGGGATGGC
Statistics
Matches: 55, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.09
16 50 0.91
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (16 bp):
TAAATAAAATAAATAA
Found at i:18326395 original size:12 final size:12
Alignment explanation
Indices: 18326341--18326399 Score: 59
Period size: 12 Copynumber: 4.7 Consensus size: 12
18326331 AAATAAAATA
18326341 AATAATAAATAA-
1 AATAA-AAATAAT
18326353 AATAAATAATAAAT
1 AATAAA-AAT-AAT
18326367 AA-AATAAATAAT
1 AATAA-AAATAAT
18326379 AAATAAAAATAAT
1 -AATAAAAATAAT
18326392 AATAAAAA
1 AATAAAAA
18326400 AATTGGGGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
11 1 0.02
12 19 0.46
13 16 0.39
14 5 0.12
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AATAAAAATAAT
Found at i:18334012 original size:23 final size:23
Alignment explanation
Indices: 18333986--18334031 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
18333976 ATATACTAAC
*
18333986 CTTATCATAATATAATTAGGAAT
1 CTTATCATAATAGAATTAGGAAT
*
18334009 CTTATCCTAATAGAATTAGGAAT
1 CTTATCATAATAGAATTAGGAAT
18334032 TGTTATTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (23 bp):
CTTATCATAATAGAATTAGGAAT
Found at i:18335891 original size:21 final size:22
Alignment explanation
Indices: 18335866--18335908 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
18335856 AATATATGTT
*
18335866 ATTAAAATGTTTAAT-TTTTAA
1 ATTAAAATATTTAATATTTTAA
*
18335887 ATTAAAATATTTATTATTTTAA
1 ATTAAAATATTTAATATTTTAA
18335909 TAATTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
ATTAAAATATTTAATATTTTAA
Found at i:18335949 original size:53 final size:51
Alignment explanation
Indices: 18335882--18335982 Score: 123
Period size: 53 Copynumber: 1.9 Consensus size: 51
18335872 ATGTTTAATT
*
18335882 TTTAAATTAAAATATTTATTATTT-TAATAATTTATTAAATATATTAATAAATA
1 TTTAAATTAAAATA-TGATTATTTATAATAATTTA-TAAA-ATATTAATAAATA
** **
18335935 TTTAAATTTTAATATGATTATTTATTTTAATTTATAAAATATTAATAA
1 TTTAAATTAAAATATGATTATTTATAATAATTTATAAAATATTAATAA
18335983 TTTATATTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
51 10 0.24
52 12 0.29
53 20 0.48
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (51 bp):
TTTAAATTAAAATATGATTATTTATAATAATTTATAAAATATTAATAAATA
Found at i:18335978 original size:24 final size:24
Alignment explanation
Indices: 18335933--18335978 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
18335923 TATTAATAAA
*
18335933 TATTTAAATTTTAATATGATTATT
1 TATTTAAATTTTAAAATGATTATT
*
18335957 TATTTTAATTTATAAAAT-ATTA
1 TATTTAAATTT-TAAAATGATTA
18335979 ATAATTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
TATTTAAATTTTAAAATGATTATT
Found at i:18336099 original size:20 final size:22
Alignment explanation
Indices: 18336054--18336115 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 22
18336044 TTATTTTATT
*
18336054 TTTAAAATATTAAAATATTACAAA
1 TTTAAAATATT-AAAT-TTTCAAA
*
18336078 TTTATAAT-TT-AATTTTCAAA
1 TTTAAAATATTAAATTTTCAAA
18336098 TTTAAAATATTAAATTTT
1 TTTAAAATATTAAATTTT
18336116 ATTAATTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 13 0.39
21 5 0.15
22 6 0.18
23 2 0.06
24 7 0.21
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTAAAATATTAAATTTTCAAA
Found at i:18336104 original size:36 final size:37
Alignment explanation
Indices: 18336048--18336123 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 37
18336038 CTTATTTTAT
*
18336048 TTTATTTTTAAAATATTAAAATATTACAAATTTA-TAA
1 TTTAATTTTAAAATATTAAAATATTA-AAATTTATTAA
* *
18336085 TTTAATTTTCAAAT-TTAAAATATTAAATTTTATTAA
1 TTTAATTTTAAAATATTAAAATATTAAAATTTATTAA
18336121 TTT
1 TTT
18336124 TGAATTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 6 0.17
36 17 0.49
37 12 0.34
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (37 bp):
TTTAATTTTAAAATATTAAAATATTAAAATTTATTAA
Found at i:18339385 original size:86 final size:86
Alignment explanation
Indices: 18339232--18339404 Score: 283
Period size: 86 Copynumber: 2.0 Consensus size: 86
18339222 AAAAAACTCT
* *
18339232 TAACGCTTCAAAATAACTAAATAACATGGTTAGTATTTTTGTATAAAGGATGATCTATCTTGAAT
1 TAACACTTCAAAATAACTAAATAACATGGTTAGCATTTTTGTATAAAGGATGATCTATCTTGAAT
18339297 AGCTCCATTTAATATAATCAC
66 AGCTCCATTTAATATAATCAC
* * * * *
18339318 TAACACTTCAAAATAACTAAATAACGTGGTTAGCATTTTTGTATATAGGTTGGTCTATCTTGGAT
1 TAACACTTCAAAATAACTAAATAACATGGTTAGCATTTTTGTATAAAGGATGATCTATCTTGAAT
18339383 AGCTCCATTTAATATAATCAC
66 AGCTCCATTTAATATAATCAC
18339404 T
1 T
18339405 TTGAATCTTC
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
86 80 1.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (86 bp):
TAACACTTCAAAATAACTAAATAACATGGTTAGCATTTTTGTATAAAGGATGATCTATCTTGAAT
AGCTCCATTTAATATAATCAC
Found at i:18346525 original size:35 final size:34
Alignment explanation
Indices: 18346419--18346688 Score: 180
Period size: 34 Copynumber: 7.8 Consensus size: 34
18346409 GCAGAGGAAT
*
18346419 AGTGAAATCTGGGGTTGTTTGCCGCCGGTTAGGAGG
1 AGTGAAATCT-GGGTGGTTTGCCGCCGG-TAGGAGG
* * * * * * ** *
18346455 AG-CAACAGCTTGGAGGTTGGTCGCCTCTTGGAGG
1 AGTGAA-ATCTGGGTGGTTTGCCGCCGGTAGGAGG
18346489 AGTGAAATCTGGGTTGGTTTGCCGCCGGTAGGAGG
1 AGTGAAATCTGGG-TGGTTTGCCGCCGGTAGGAGG
* * * * *
18346524 AG-CAACAGCTTGGTTGTTTGCTGCCGGTAGGAGG
1 AGTGAA-ATCTGGGTGGTTTGCCGCCGGTAGGAGG
*
18346558 AGTGAAATCTGGGGTGGTTTGCCGCCGGTATGAGG
1 AGTGAAATCT-GGGTGGTTTGCCGCCGGTAGGAGG
*
18346593 AGTGAAATCTGGAGT-GTTTGCTGCCGG-AGAGAGG
1 AGTGAAATCTGG-GTGGTTTGCCGCCGGTAG-GAGG
*
18346627 AGT-AACAGCCTGGG-GGTTTGCCGCCGGT-GAGAGG
1 AGTGAA-A-TCTGGGTGGTTTGCCGCCGGTAG-GAGG
* *
18346661 AGT-AATAGCTGGAGT-GTTAGCCGCCGGT
1 AGTGAA-ATCTGG-GTGGTTTGCCGCCGGT
18346689 GGGGGATGAT
Statistics
Matches: 183, Mismatches: 37, Indels: 30
0.73 0.15 0.12
Matches are distributed among these distances:
33 7 0.04
34 97 0.53
35 74 0.40
36 5 0.03
ACGTcount: A:0.19, C:0.16, G:0.41, T:0.24
Consensus pattern (34 bp):
AGTGAAATCTGGGTGGTTTGCCGCCGGTAGGAGG
Found at i:18346611 original size:69 final size:70
Alignment explanation
Indices: 18346419--18346688 Score: 265
Period size: 69 Copynumber: 3.9 Consensus size: 70
18346409 GCAGAGGAAT
* * **
18346419 AGTGAAATCTGGGGTTGTTTGCCGCCGGTTAGGAGGAGCAACAGCTTGGAG-G-TTGGTCGCCTC
1 AGTGAAATCTGGGGTGGTTTGCCGCCGG-TAGGAGGAGCAACAGCTTGGAGTGTTTGCT-GCCGG
*
18346482 TTGGAGG
64 TAGGAGG
* *
18346489 AGTGAAATCTGGGTTGGTTTGCCGCCGGTAGGAGGAGCAACAGCTTGG-TTGTTTGCTGCCGGTA
1 AGTGAAATCTGGGGTGGTTTGCCGCCGGTAGGAGGAGCAACAGCTTGGAGTGTTTGCTGCCGGTA
18346553 GGAGG
66 GGAGG
* * *
18346558 AGTGAAATCTGGGGTGGTTTGCCGCCGGTATGAGGAGTGAA-ATC-TGGAGTGTTTGCTGCCGG-
1 AGTGAAATCTGGGGTGGTTTGCCGCCGGTAGGAGGAG-CAACAGCTTGGAGTGTTTGCTGCCGGT
18346620 AGAGAGG
65 AG-GAGG
* * * * *
18346627 AGT-AACAGCCT-GGG-GGTTTGCCGCCGGT-GAGAGGAGTAATAGC-TGGAGTGTTAGCCGCCG
1 AGTGAA-A-TCTGGGGTGGTTTGCCGCCGGTAG-GAGGAGCAACAGCTTGGAGTGTTTGCTGCCG
18346687 GT
63 GT
18346689 GGGGGATGAT
Statistics
Matches: 172, Mismatches: 18, Indels: 21
0.82 0.09 0.10
Matches are distributed among these distances:
67 2 0.01
68 45 0.26
69 91 0.53
70 34 0.20
ACGTcount: A:0.19, C:0.16, G:0.41, T:0.24
Consensus pattern (70 bp):
AGTGAAATCTGGGGTGGTTTGCCGCCGGTAGGAGGAGCAACAGCTTGGAGTGTTTGCTGCCGGTA
GGAGG
Found at i:18346635 original size:103 final size:103
Alignment explanation
Indices: 18346485--18346688 Score: 247
Period size: 103 Copynumber: 2.0 Consensus size: 103
18346475 TCGCCTCTTG
* ** *
18346485 GAGGAGTGAAATCTGGGTTGGTTTGCCGCCGGTAGGAGGAGCAACAGCTTGGTTGTTTGCTGCCG
1 GAGGAGTGAAATCTGGGTTGGTTTGCCGCCGGTAGGAGGAGCAACAGCCTGGGGGTTTGCCGCCG
* * *
18346550 GT-AGGAGGAGTGAA-ATCTGGGGTGGTTTGCCGCCGGTAT
66 GTGA-GAGGAGT-AATAGCTGGAGT-GTTAGCCGCCGGTAT
* *
18346589 GAGGAGTGAAATCTGGAG-T-GTTTGCTGCCGG-AGAGAGGAGTAACAGCCTGGGGGTTTGCCGC
1 GAGGAGTGAAATCTGG-GTTGGTTTGCCGCCGGTAG-GAGGAGCAACAGCCTGGGGGTTTGCCGC
18346651 CGGTGAGAGGAGTAATAGCTGGAGTGTTAGCCGCCGGT
64 CGGTGAGAGGAGTAATAGCTGGAGTGTTAGCCGCCGGT
18346689 GGGGGATGAT
Statistics
Matches: 87, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
102 16 0.18
103 52 0.60
104 18 0.21
105 1 0.01
ACGTcount: A:0.19, C:0.16, G:0.42, T:0.24
Consensus pattern (103 bp):
GAGGAGTGAAATCTGGGTTGGTTTGCCGCCGGTAGGAGGAGCAACAGCCTGGGGGTTTGCCGCCG
GTGAGAGGAGTAATAGCTGGAGTGTTAGCCGCCGGTAT
Found at i:18351703 original size:2 final size:2
Alignment explanation
Indices: 18351696--18351720 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18351686 GGTTCAAATT
18351696 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
18351721 GAACTTTTTT
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:18352719 original size:20 final size:21
Alignment explanation
Indices: 18352696--18352743 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
18352686 TCCTTCAGTT
*
18352696 TTTTTTTTCTGA-AAA-GACCA
1 TTTTTTTTCT-ATAAATCACCA
*
18352716 TTTTATTTCTATAAATCACCA
1 TTTTTTTTCTATAAATCACCA
18352737 TTTTTTT
1 TTTTTTT
18352744 ACCCATGTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 12 0.52
21 10 0.43
ACGTcount: A:0.27, C:0.15, G:0.04, T:0.54
Consensus pattern (21 bp):
TTTTTTTTCTATAAATCACCA
Found at i:18354002 original size:70 final size:75
Alignment explanation
Indices: 18353888--18354034 Score: 205
Period size: 70 Copynumber: 2.0 Consensus size: 75
18353878 CTTTATCTAA
*
18353888 TGTTAACAATTAAATAGTTCCTATAGACGGTAATTATAA-TTTAA-ATATA-T-AT-AATTTACT
1 TGTTAACAATTAAATAGTTCCTATAGACGGTAATTATAACTTAAACATATATTAATAAATTTACT
18353948 AGATTAGATT
66 AGATTAGATT
* **
18353958 TGTTAAGAATTAAATAGTTCCTATAGTTGGTAATTATAACTTAAAACATATATTAATACAATTTA
1 TGTTAACAATTAAATAGTTCCTATAGACGGTAATTATAACTT-AAACATATATTAATA-AATTTA
18354023 CTAGATTAGATT
64 CTAGATTAGATT
18354035 ATGTATACAA
Statistics
Matches: 66, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
70 36 0.55
71 2 0.03
72 2 0.03
73 5 0.08
74 1 0.02
75 2 0.03
77 18 0.27
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (75 bp):
TGTTAACAATTAAATAGTTCCTATAGACGGTAATTATAACTTAAACATATATTAATAAATTTACT
AGATTAGATT
Found at i:18376341 original size:13 final size:13
Alignment explanation
Indices: 18376325--18376350 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18376315 TAAAAAGAAA
18376325 AATTAAAACTAAT
1 AATTAAAACTAAT
18376338 AATTAAAACTAAT
1 AATTAAAACTAAT
18376351 CTAAAATCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
AATTAAAACTAAT
Found at i:18381865 original size:2 final size:2
Alignment explanation
Indices: 18381858--18381887 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
18381848 ATTTTGATTA
18381858 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
18381888 GCATTCTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:18383676 original size:34 final size:34
Alignment explanation
Indices: 18383554--18383677 Score: 103
Period size: 33 Copynumber: 3.7 Consensus size: 34
18383544 TTGTTGGTGA
*
18383554 GTTTCGCTTTATCTCGTGAAAAAGCT-TGTA--AGG
1 GTTTCGCTTGATCTCGT-AAAAAGCTAT-TATGAGG
* * * * *
18383587 GTTTTGCTTGGTCGCGTAAAAAAC-ATTATGGGG
1 GTTTCGCTTGATCTCGTAAAAAGCTATTATGAGG
* * * * *
18383620 GTTTCACTTGATCCCATTAAAAGCTATTATGAAG
1 GTTTCGCTTGATCTCGTAAAAAGCTATTATGAGG
18383654 GTTTCGCTTGATCTCGTAAAAAGC
1 GTTTCGCTTGATCTCGTAAAAAGC
18383678 ACATTTCTTT
Statistics
Matches: 68, Mismatches: 19, Indels: 7
0.72 0.20 0.07
Matches are distributed among these distances:
31 2 0.03
32 7 0.10
33 32 0.47
34 27 0.40
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.35
Consensus pattern (34 bp):
GTTTCGCTTGATCTCGTAAAAAGCTATTATGAGG
Found at i:18391566 original size:2 final size:2
Alignment explanation
Indices: 18391559--18391587 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18391549 TTGTATTGAT
18391559 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18391588 TGGATATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18394397 original size:2 final size:2
Alignment explanation
Indices: 18394390--18394420 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
18394380 GCGTAACTTT
*
18394390 AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
18394421 TTCCTTCGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:18414113 original size:211 final size:210
Alignment explanation
Indices: 18413748--18414167 Score: 804
Period size: 211 Copynumber: 2.0 Consensus size: 210
18413738 GAGAAGTATT
*
18413748 GCATAGACACTTGAGTGAGGTACCAAATGCACTTCTCATGGCTGGTCATGTTCAGTGAACTCGCT
1 GCATAGACACTTGAGTGAGGTACCAAATGCACTTCTAATGGCTGGTCATGTTCAGTGAACTCGCT
18413813 TTCCCATGGCAAATATCCACATGCTAGTTTCAAGTATCTCTATACTTCAACCTATGAGAACGATT
66 TTCCCATGGCAAATATCCACATGCTAGTTTCAAGTATCTCTATACTTCAACCTATGAGAACGATT
18413878 GCTTACTTCACAAGTAAGGAACATAACATGTGCCAATCTTTGAGCATTATTGATGCCCTGTCTCA
131 GCTTACTTCACAAGTAAGGAACATAACATGTGCCAATCTTTGAGCATTATTGATGCCCTGTCTCA
18413943 ATAATACAATGATCC
196 ATAATACAATGATCC
*
18413958 GNCATAGACACTTGAGTGAGGTACCAAGTGCACTTCTAATGGCTGGTCATGTTCAGTGAACTCGC
1 G-CATAGACACTTGAGTGAGGTACCAAATGCACTTCTAATGGCTGGTCATGTTCAGTGAACTCGC
18414023 TTTCCCATGGCAAATATCCACATGCTAGTTTCAAGTATCTCTATACTTCAACCTATGAGAACGAT
65 TTTCCCATGGCAAATATCCACATGCTAGTTTCAAGTATCTCTATACTTCAACCTATGAGAACGAT
*
18414088 TGCTTACTTCACAAGTAAGGAACATAACATGTGCCAATCTTTGAGTATTATTGATGCCCTGTCTC
130 TGCTTACTTCACAAGTAAGGAACATAACATGTGCCAATCTTTGAGCATTATTGATGCCCTGTCTC
18414153 AATAATACAATGATC
195 AATAATACAATGATC
18414168 AGGAACTTTA
Statistics
Matches: 206, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
210 1 0.00
211 205 1.00
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (210 bp):
GCATAGACACTTGAGTGAGGTACCAAATGCACTTCTAATGGCTGGTCATGTTCAGTGAACTCGCT
TTCCCATGGCAAATATCCACATGCTAGTTTCAAGTATCTCTATACTTCAACCTATGAGAACGATT
GCTTACTTCACAAGTAAGGAACATAACATGTGCCAATCTTTGAGCATTATTGATGCCCTGTCTCA
ATAATACAATGATCC
Found at i:18418616 original size:7 final size:7
Alignment explanation
Indices: 18418600--18418666 Score: 59
Period size: 7 Copynumber: 9.4 Consensus size: 7
18418590 AACCTTTTTT
18418600 TTTCTT-
1 TTTCTTC
18418606 TTTCTTC
1 TTTCTTC
*
18418613 TTTCTCC
1 TTTCTTC
18418620 TTTCTTCC
1 TTTCTT-C
18418628 TTTC-TC
1 TTTCTTC
18418634 TTCTTCTTC
1 -T-TTCTTC
*
18418643 TTTCTCC
1 TTTCTTC
18418650 TTTCTTCC
1 TTTCTT-C
18418658 TTTC-TC
1 TTTCTTC
18418664 TTT
1 TTT
18418667 TTACTTTGTT
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
6 11 0.22
7 24 0.47
8 14 0.27
9 2 0.04
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (7 bp):
TTTCTTC
Found at i:18418630 original size:8 final size:8
Alignment explanation
Indices: 18418606--18418662 Score: 61
Period size: 7 Copynumber: 7.6 Consensus size: 8
18418596 TTTTTTTCTT
18418606 TTTCTT-C
1 TTTCTTCC
18418613 TTTC-TCC
1 TTTCTTCC
18418620 TTTCTTCC
1 TTTCTTCC
*
18418628 TTTC-TCT
1 TTTCTTCC
18418635 TCTTCTT-C
1 T-TTCTTCC
18418643 TTTC-TCC
1 TTTCTTCC
18418650 TTTCTTCC
1 TTTCTTCC
18418658 TTTCT
1 TTTCT
18418663 CTTTTTACTT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
6 2 0.05
7 20 0.48
8 19 0.45
9 1 0.02
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (8 bp):
TTTCTTCC
Found at i:18418632 original size:15 final size:14
Alignment explanation
Indices: 18418606--18418663 Score: 80
Period size: 15 Copynumber: 3.9 Consensus size: 14
18418596 TTTTTTTCTT
18418606 TTTCTTCTTTCTCC
1 TTTCTTCTTTCTCC
*
18418620 TTTCTTCCTTTCTCT
1 TTTCTT-CTTTCTCC
18418635 TCTTCTTCTTTCTCC
1 T-TTCTTCTTTCTCC
18418650 TTTCTTCCTTTCTC
1 TTTCTT-CTTTCTC
18418664 TTTTTACTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
14 11 0.28
15 23 0.59
16 5 0.13
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTCTTCTTTCTCC
Found at i:18418643 original size:30 final size:30
Alignment explanation
Indices: 18418602--18418665 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
18418592 CCTTTTTTTT
*
18418602 TCTTTTTCTTCTTTCTCCTTTCTTCCTTTC
1 TCTTCTTCTTCTTTCTCCTTTCTTCCTTTC
18418632 TCTTCTTCTTCTTTCTCCTTTCTTCCTTTC
1 TCTTCTTCTTCTTTCTCCTTTCTTCCTTTC
18418662 TCTT
1 TCTT
18418666 TTTACTTTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (30 bp):
TCTTCTTCTTCTTTCTCCTTTCTTCCTTTC
Found at i:18419916 original size:2 final size:2
Alignment explanation
Indices: 18419909--18419934 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18419899 AATCAACACA
18419909 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
18419935 TTGTCACATT
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):
AT
Found at i:18427191 original size:15 final size:15
Alignment explanation
Indices: 18427157--18427189 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
18427147 AAATTTTTTA
18427157 TTTTATTATATTATT
1 TTTTATTATATTATT
18427172 TTTTATTAT-TTATT
1 TTTTATTATATTATT
18427186 TTTT
1 TTTT
18427190 TACATATTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTATTATATTATT
Found at i:18431430 original size:21 final size:22
Alignment explanation
Indices: 18431406--18431452 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
18431396 TTGAATGGAG
*
18431406 GCATCAGTCTTTGTTATGAA-T
1 GCATCAGTCTTTGTCATGAATT
*
18431427 GCATTAGTCTTTGTCATGAATT
1 GCATCAGTCTTTGTCATGAATT
18431449 GCAT
1 GCAT
18431453 GAACATATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (22 bp):
GCATCAGTCTTTGTCATGAATT
Found at i:18444645 original size:18 final size:18
Alignment explanation
Indices: 18444622--18444661 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
18444612 TGATCACAAC
18444622 AGTTTACATTTTGAATAG
1 AGTTTACATTTTGAATAG
18444640 AGTTTACATTTTGAATAG
1 AGTTTACATTTTGAATAG
18444658 AGTT
1 AGTT
18444662 GCCATTAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.45
Consensus pattern (18 bp):
AGTTTACATTTTGAATAG
Found at i:18444667 original size:18 final size:18
Alignment explanation
Indices: 18444622--18444667 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
18444612 TGATCACAAC
*
18444622 AGTTTACATTTTGAATAG
1 AGTTGACATTTTGAATAG
*
18444640 AGTTTACATTTTGAATAG
1 AGTTGACATTTTGAATAG
*
18444658 AGTTGCCATT
1 AGTTGACATT
18444668 AGAGTCATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.43
Consensus pattern (18 bp):
AGTTGACATTTTGAATAG
Found at i:18451514 original size:2 final size:2
Alignment explanation
Indices: 18451476--18451504 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18451466 ATCATGTTGT
18451476 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18451505 GAACATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18451591 original size:42 final size:42
Alignment explanation
Indices: 18451528--18451641 Score: 122
Period size: 42 Copynumber: 2.7 Consensus size: 42
18451518 GTAATGATAT
* * *
18451528 TGACTCGACTATGTGCAAGTGGGAGTGCGCATAAGACGATGC
1 TGACTCGACTATGTGCAAGTGGGAGTGCACACAAGACGATGA
* * *
18451570 TGACTCGGCTATGTGCGAGTGGGAGTGCACACAAGTCGATGA
1 TGACTCGACTATGTGCAAGTGGGAGTGCACACAAGACGATGA
* * *
18451612 TGACACAGAC-ATGCGCTAGTGGGGAGTGCA
1 TGACTC-GACTATGTGCAAGT-GGGAGTGCA
18451642 TATGAGCTGA
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
42 49 0.82
43 11 0.18
ACGTcount: A:0.25, C:0.19, G:0.35, T:0.20
Consensus pattern (42 bp):
TGACTCGACTATGTGCAAGTGGGAGTGCACACAAGACGATGA
Found at i:18453893 original size:46 final size:46
Alignment explanation
Indices: 18453826--18453963 Score: 249
Period size: 46 Copynumber: 3.0 Consensus size: 46
18453816 TAGCAGAATG
*
18453826 AATCTCACTGCAGCAGAAAGGCGCTGTAGAGAGAATGAATTTTCGC
1 AATCTCACTGCAGCAGAAAGGCGCTGTAGCGAGAATGAATTTTCGC
* *
18453872 AATCTCACTGCAGCAGAAAGGCGTTGTAGCGAGAATGAATTTTTGC
1 AATCTCACTGCAGCAGAAAGGCGCTGTAGCGAGAATGAATTTTCGC
18453918 AATCTCACTGCAGCAGAAAGGCGCTGTAGCGAGAATGAATTTTCGC
1 AATCTCACTGCAGCAGAAAGGCGCTGTAGCGAGAATGAATTTTCGC
18453964 TGTAGCAAAC
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 87 1.00
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (46 bp):
AATCTCACTGCAGCAGAAAGGCGCTGTAGCGAGAATGAATTTTCGC
Found at i:18454368 original size:36 final size:35
Alignment explanation
Indices: 18454336--18454415 Score: 88
Period size: 36 Copynumber: 2.3 Consensus size: 35
18454326 TCGTGTGCAG
* *
18454336 CCCCACATCACGCACAATTAATGCCATGGTGTGGTC
1 CCCCACATCACGCACAACTAATGCCATGGTGT-GAC
* * ** *
18454372 CCCCACATCGCGCATAACTAATGCCATTATGTGAT
1 CCCCACATCACGCACAACTAATGCCATGGTGTGAC
18454407 CCCCACATC
1 CCCCACATC
18454416 GTGCACAGGC
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
35 10 0.27
36 27 0.73
ACGTcount: A:0.26, C:0.36, G:0.15, T:0.23
Consensus pattern (35 bp):
CCCCACATCACGCACAACTAATGCCATGGTGTGAC
Found at i:18458347 original size:42 final size:42
Alignment explanation
Indices: 18458300--18458403 Score: 156
Period size: 42 Copynumber: 2.5 Consensus size: 42
18458290 CATCTCACAT
* *
18458300 GCAACGGCTTATGCGCACTCCCACCCA-CACATTGTCGGGTCA
1 GCAACGGCTTATGTGCACTCCCA-CCAGCACATAGTCGGGTCA
*
18458342 GCAACGGCTTATGTGCACTCCCACTAGCACATAGTCGGGTCA
1 GCAACGGCTTATGTGCACTCCCACCAGCACATAGTCGGGTCA
*
18458384 GCAACGGCTCATGTGCACTC
1 GCAACGGCTTATGTGCACTC
18458404 TTACTCGCAG
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
41 2 0.04
42 55 0.96
ACGTcount: A:0.22, C:0.35, G:0.23, T:0.20
Consensus pattern (42 bp):
GCAACGGCTTATGTGCACTCCCACCAGCACATAGTCGGGTCA
Found at i:18460172 original size:2 final size:2
Alignment explanation
Indices: 18460165--18460207 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
18460155 NNNNNNNNNN
18460165 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18460207 A
1 A
18460208 GAATATTGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18460800 original size:24 final size:25
Alignment explanation
Indices: 18460745--18460803 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
18460735 TTTGTGATAT
* * *
18460745 ATATACATGGCAAGGCCATAGGATG
1 ATATACGTGGCAAGGCCACAAGATG
*
18460770 ATATACGTGGCTAGGCCACAAG-TG
1 ATATACGTGGCAAGGCCACAAGATG
18460794 ATATACGTGG
1 ATATACGTGG
18460804 TTACGACCAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 12 0.40
25 18 0.60
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (25 bp):
ATATACGTGGCAAGGCCACAAGATG
Found at i:18462615 original size:14 final size:14
Alignment explanation
Indices: 18462597--18462631 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
18462587 TCCAAATAAT
18462597 CAAAATTAATTAAC
1 CAAAATTAATTAAC
* *
18462611 TAAAACTAATTAAC
1 CAAAATTAATTAAC
18462625 CAAAATT
1 CAAAATT
18462632 TAAACTGAAA
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (14 bp):
CAAAATTAATTAAC
Found at i:18464592 original size:19 final size:20
Alignment explanation
Indices: 18464568--18464605 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
18464558 AAAATTTTAG
*
18464568 AATAAAATATTATT-TTATT
1 AATAAAATAATATTATTATT
18464587 AATAAAATAATATTATTAT
1 AATAAAATAATATTATTAT
18464606 ATTAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATAAAATAATATTATTATT
Found at i:18465982 original size:52 final size:52
Alignment explanation
Indices: 18465903--18466058 Score: 267
Period size: 52 Copynumber: 3.0 Consensus size: 52
18465893 GCACATGATA
*
18465903 GTGATAGTGGTGTGTTGTGTGAATGCACACACTGATGATATATGCCATGTGC
1 GTGATAGTGGTGTGTTGTGTGAGTGCACACACTGATGATATATGCCATGTGC
* *
18465955 GTGATAGTGGTGTGTTATGTGAGTGCACACACTGATGATATATGCCATGTGA
1 GTGATAGTGGTGTGTTGTGTGAGTGCACACACTGATGATATATGCCATGTGC
* *
18466007 GTGATAGTGGTGTGCTGTGTGAGTACACACACTGATGATATATGCCATGTGC
1 GTGATAGTGGTGTGTTGTGTGAGTGCACACACTGATGATATATGCCATGTGC
18466059 AAGGGGGAAT
Statistics
Matches: 97, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 97 1.00
ACGTcount: A:0.24, C:0.13, G:0.31, T:0.32
Consensus pattern (52 bp):
GTGATAGTGGTGTGTTGTGTGAGTGCACACACTGATGATATATGCCATGTGC
Found at i:18466078 original size:35 final size:35
Alignment explanation
Indices: 18466034--18466115 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 35
18466024 TGTGAGTACA
18466034 CACACTGATGATATATGCCATGTGCAAG-GGGGAA-TG
1 CACA-TGATGATAT-TGCCATGTGC-AGTGGGGAAGTG
* *
18466070 CACATGATGATATTGCCTTGTGCAGTGTGGAAGTG
1 CACATGATGATATTGCCATGTGCAGTGGGGAAGTG
*
18466105 CACAGGATGAT
1 CACATGATGAT
18466116 TCTAGCTGTG
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
33 2 0.05
34 14 0.34
35 21 0.51
36 4 0.10
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.26
Consensus pattern (35 bp):
CACATGATGATATTGCCATGTGCAGTGGGGAAGTG
Found at i:18471903 original size:19 final size:20
Alignment explanation
Indices: 18471879--18471916 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
18471869 AAAATTTTAA
18471879 AATAAAATAATATT-TTATT
1 AATAAAATAATATTATTATT
18471898 AATAAAATAATATTATTAT
1 AATAAAATAATATTATTAT
18471917 ATTAATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AATAAAATAATATTATTATT
Found at i:18478525 original size:19 final size:19
Alignment explanation
Indices: 18478501--18478538 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
18478491 CTGCCAAACC
*
18478501 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
18478520 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
18478539 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:18479421 original size:2 final size:2
Alignment explanation
Indices: 18479414--18479441 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
18479404 AAATAAAATA
18479414 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18479442 TAGAAGACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18480025 original size:34 final size:36
Alignment explanation
Indices: 18479981--18480053 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 36
18479971 TGGCTGCTAA
* *
18479981 TTTTTGGAGGA-AAA-AGTGCGGCTTAGCTACTGAT
1 TTTTTGGAGGACAAATAGAGCAGCTTAGCTACTGAT
*
18480015 TTTTTTGAGGACAAATAGAGCAGCTTAGCTACTGAT
1 TTTTTGGAGGACAAATAGAGCAGCTTAGCTACTGAT
18480051 TTT
1 TTT
18480054 GAAGCCAGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 10 0.29
35 3 0.09
36 21 0.62
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.36
Consensus pattern (36 bp):
TTTTTGGAGGACAAATAGAGCAGCTTAGCTACTGAT
Found at i:18480334 original size:27 final size:27
Alignment explanation
Indices: 18480244--18480327 Score: 132
Period size: 27 Copynumber: 3.1 Consensus size: 27
18480234 AAAAGAAAGT
*
18480244 AACAAGAAAGAAAAAATGGGCATGACCC
1 AACAAGAAAG-AAAAATGGGCATGGCCC
*
18480272 AACAAGAAAGAAAAATGGGTATGGCCC
1 AACAAGAAAGAAAAATGGGCATGGCCC
*
18480299 AACAAGAAAGAAAACTGGGCATGGCCC
1 AACAAGAAAGAAAAATGGGCATGGCCC
18480326 AA
1 AA
18480328 TTAGAAATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 42 0.81
28 10 0.19
ACGTcount: A:0.50, C:0.18, G:0.24, T:0.08
Consensus pattern (27 bp):
AACAAGAAAGAAAAATGGGCATGGCCC
Found at i:18486156 original size:17 final size:17
Alignment explanation
Indices: 18486131--18486165 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
18486121 GGAGGTTTTC
* *
18486131 CTCCTCCTTGGTGTGTG
1 CTCCCCCTTAGTGTGTG
18486148 CTCCCCCTTAGTGTGTG
1 CTCCCCCTTAGTGTGTG
18486165 C
1 C
18486166 ATATTTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.03, C:0.34, G:0.26, T:0.37
Consensus pattern (17 bp):
CTCCCCCTTAGTGTGTG
Found at i:18501473 original size:38 final size:39
Alignment explanation
Indices: 18501375--18501480 Score: 135
Period size: 38 Copynumber: 2.7 Consensus size: 39
18501365 CACTCCCGGC
*
18501375 TCATGTACATCCCCCCACATCGTGCACATAGCCGGCACCA
1 TCATGTACATCCCCCCACATCGTGCACATAGCAGG-ACCA
* * *
18501415 TCATGTGCATCCCCCCACATCGTGCACA-ATCAGTG-CTA
1 TCATGTACATCCCCCCACATCGTGCACATAGCAG-GACCA
*
18501453 TCGTGTACATCCCCCCACATCGTGCACA
1 TCATGTACATCCCCCCACATCGTGCACA
18501481 CGGGCACTAT
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
38 28 0.47
39 3 0.05
40 28 0.47
ACGTcount: A:0.24, C:0.41, G:0.15, T:0.21
Consensus pattern (39 bp):
TCATGTACATCCCCCCACATCGTGCACATAGCAGGACCA
Found at i:18502865 original size:27 final size:28
Alignment explanation
Indices: 18502835--18502888 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
18502825 ACAAGTGCTG
*
18502835 GGACG-AAAAATTTATTGA-TTTGCCCCC
1 GGACGAAAAAAATTA-TGATTTTGCCCCC
18502862 GGACGAAAAAAATTATGATTTTGCCCC
1 GGACGAAAAAAATTATGATTTTGCCCC
18502889 TATATTCCGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (28 bp):
GGACGAAAAAAATTATGATTTTGCCCCC
Found at i:18507125 original size:13 final size:15
Alignment explanation
Indices: 18507094--18507125 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
18507084 GGGTGCATAA
18507094 ACACTATGGTTTTTC
1 ACACTATGGTTTTTC
18507109 ACACT-TGGTTTTT-
1 ACACTATGGTTTTTC
18507122 ACAC
1 ACAC
18507126 CATAAATCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 4 0.24
14 8 0.47
15 5 0.29
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (15 bp):
ACACTATGGTTTTTC
Found at i:18508083 original size:25 final size:25
Alignment explanation
Indices: 18508055--18508139 Score: 71
Period size: 25 Copynumber: 3.2 Consensus size: 25
18508045 ATCTCACCCA
18508055 GCACATGTGCATCCCACCACATCGT
1 GCACATGTGCATCCCACCACATCGT
* * * * **
18508080 GCACATAGCCGGACATCCCATCTCACCCA
1 GCACAT-G--TG-CATCCCACCACATCGT
*
18508109 GCTCATGTGCATCCCACCACATCGT
1 GCACATGTGCATCCCACCACATCGT
18508134 GCACAT
1 GCACAT
18508140 AGCCGGACAT
Statistics
Matches: 42, Mismatches: 14, Indels: 8
0.66 0.22 0.12
Matches are distributed among these distances:
25 22 0.52
26 2 0.05
28 2 0.05
29 16 0.38
ACGTcount: A:0.25, C:0.41, G:0.15, T:0.19
Consensus pattern (25 bp):
GCACATGTGCATCCCACCACATCGT
Found at i:18508101 original size:54 final size:54
Alignment explanation
Indices: 18508037--18508155 Score: 229
Period size: 54 Copynumber: 2.2 Consensus size: 54
18508027 AGTTGGGCTT
18508037 GACATCCCATCTCACCCAGCACATGTGCATCCCACCACATCGTGCACATAGCCG
1 GACATCCCATCTCACCCAGCACATGTGCATCCCACCACATCGTGCACATAGCCG
*
18508091 GACATCCCATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCG
1 GACATCCCATCTCACCCAGCACATGTGCATCCCACCACATCGTGCACATAGCCG
18508145 GACATCCCATC
1 GACATCCCATC
18508156 CATCTCCCTC
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 64 1.00
ACGTcount: A:0.25, C:0.43, G:0.14, T:0.18
Consensus pattern (54 bp):
GACATCCCATCTCACCCAGCACATGTGCATCCCACCACATCGTGCACATAGCCG
Found at i:18511787 original size:14 final size:14
Alignment explanation
Indices: 18511770--18511799 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
18511760 TGGTATTAGA
*
18511770 ATATATGTATGTAT
1 ATATATGTATATAT
18511784 ATATATGTATATAT
1 ATATATGTATATAT
18511798 AT
1 AT
18511800 GATTGCCTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (14 bp):
ATATATGTATATAT
Found at i:18511790 original size:10 final size:10
Alignment explanation
Indices: 18511771--18511800 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
18511761 GGTATTAGAA
*
18511771 TATATGTATG
1 TATATATATG
18511781 TATATATATG
1 TATATATATG
18511791 TATATATATG
1 TATATATATG
18511801 ATTGCCTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (10 bp):
TATATATATG
Found at i:18516817 original size:2 final size:2
Alignment explanation
Indices: 18516810--18516844 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
18516800 TATAATTTTG
* *
18516810 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18516845 GTACATTGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:18526876 original size:106 final size:103
Alignment explanation
Indices: 18526701--18526920 Score: 309
Period size: 106 Copynumber: 2.1 Consensus size: 103
18526691 TCTCAAGCAC
*
18526701 TTGATTAAAATTGTTTAATTAAGTTGTGCCTAATTAATTAAATTATTTAATTAAATCATTGGGCC
1 TTGATTAAATTTGTTTAATTAAGTTGTGCCTAATTAATTAAATTATTTAATTAAATCATTGGGCC
18526766 TAATTAATTAAATTAAACAATTAAGTTATTGGGCTTAA
66 TAATTAATTAAATTAAACAATTAAGTTATTGGGCTTAA
* **
18526804 TTGATTAAATTTGTTTAATTAAGTCAT-TAGGCCTAATTGATTAAAATTATTTAA-TAAATTGTT
1 TTGATTAAATTTGTTTAATTAAGT--TGT--GCCTAATTAATT-AAATTATTTAATTAAATCATT
*** *
18526867 GGGCCTAATTAATTAAATTATTTAATTAATTTATTGGGCTTAA
61 GGGCCTAATTAATTAAATTAAACAATTAAGTTATTGGGCTTAA
18526910 TTGATTAAATT
1 TTGATTAAATT
18526921 AAACAATTAA
Statistics
Matches: 104, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
103 23 0.22
104 1 0.01
105 1 0.01
106 68 0.65
107 11 0.11
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.45
Consensus pattern (103 bp):
TTGATTAAATTTGTTTAATTAAGTTGTGCCTAATTAATTAAATTATTTAATTAAATCATTGGGCC
TAATTAATTAAATTAAACAATTAAGTTATTGGGCTTAA
Found at i:18526930 original size:35 final size:35
Alignment explanation
Indices: 18526728--18526921 Score: 219
Period size: 35 Copynumber: 5.5 Consensus size: 35
18526718 ATTAAGTTGT
*
18526728 GCCTAATTAATTAAATTATTTAATTAAATCATTGG
1 GCCTAATTAATTAAATTATTTAATTAAATTATTGG
*** *
18526763 GCCTAATTAATTAAATTAAACAATTAAGTTATTGG
1 GCCTAATTAATTAAATTATTTAATTAAATTATTGG
* * * * * *
18526798 GCTTAATTGATTAAATTTGTTTAATTAAGTCATTAG
1 GCCTAATTAATTAAA-TTATTTAATTAAATTATTGG
* *
18526834 GCCTAATTGATTAAAATTATTTAA-TAAATTGTTGG
1 GCCTAATTAATT-AAATTATTTAATTAAATTATTGG
*
18526869 GCCTAATTAATTAAATTATTTAATTAATTTATTGG
1 GCCTAATTAATTAAATTATTTAATTAAATTATTGG
* *
18526904 GCTTAATTGATTAAATTA
1 GCCTAATTAATTAAATTA
18526922 AACAATTAAG
Statistics
Matches: 132, Mismatches: 24, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
34 11 0.08
35 86 0.65
36 32 0.24
37 3 0.02
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.44
Consensus pattern (35 bp):
GCCTAATTAATTAAATTATTTAATTAAATTATTGG
Found at i:18534795 original size:20 final size:21
Alignment explanation
Indices: 18534765--18534814 Score: 84
Period size: 20 Copynumber: 2.4 Consensus size: 21
18534755 TTTTAGCATA
*
18534765 AAAATTATTTCCAATTTTCTC
1 AAAATTTTTTCCAATTTTCTC
18534786 -AAATTTTTTCCAATTTTCTC
1 AAAATTTTTTCCAATTTTCTC
18534806 AAAATTTTT
1 AAAATTTTT
18534815 AAATATTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 19 0.70
21 8 0.30
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (21 bp):
AAAATTTTTTCCAATTTTCTC
Found at i:18535134 original size:15 final size:15
Alignment explanation
Indices: 18535113--18535225 Score: 69
Period size: 15 Copynumber: 7.8 Consensus size: 15
18535103 GATAGTATAA
18535113 ATTTAAATTTAATTT
1 ATTTAAATTTAATTT
* *
18535128 GTTTAAATTTAAATT
1 ATTTAAATTTAATTT
* **
18535143 ATCT--A-TCCATTGT
1 ATTTAAATTTAATT-T
18535156 ATTTAAATTTAATTT
1 ATTTAAATTTAATTT
* **
18535171 GTTTAAATTTAAATAA
1 ATTTAAATTT-AATTT
*
18535187 AGATT--ATTT-ATTT
1 A-TTTAAATTTAATTT
18535200 -TTTAAATTTAATTT
1 ATTTAAATTTAATTT
18535214 ATTTAAATTTAA
1 ATTTAAATTTAA
18535226 AATATCATAT
Statistics
Matches: 70, Mismatches: 18, Indels: 20
0.65 0.17 0.19
Matches are distributed among these distances:
11 2 0.03
12 3 0.04
13 11 0.16
14 4 0.06
15 41 0.59
16 7 0.10
17 2 0.03
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.55
Consensus pattern (15 bp):
ATTTAAATTTAATTT
Found at i:18535160 original size:43 final size:42
Alignment explanation
Indices: 18535113--18535236 Score: 144
Period size: 43 Copynumber: 2.9 Consensus size: 42
18535103 GATAGTATAA
18535113 ATTTAAATTTAATTTGTTTAAATTTAAATTATCTATCCATTGT
1 ATTTAAATTTAATTTGTTTAAATTTAAATTATCTATCCATT-T
* **
18535156 ATTTAAATTTAATTTGTTTAAATTTAAATAAAGAT-TATTTATTT
1 ATTTAAATTTAATTTGTTTAAATTTAAAT---TATCTATCCATTT
* *
18535200 -TTTAAATTTAATTTATTTAAATTTAAAATATCATATC
1 ATTTAAATTTAATTTGTTTAAATTTAAATTATC-TATC
18535237 TCTATATCCC
Statistics
Matches: 69, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
40 2 0.03
42 3 0.04
43 55 0.80
44 1 0.01
45 6 0.09
46 2 0.03
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.53
Consensus pattern (42 bp):
ATTTAAATTTAATTTGTTTAAATTTAAATTATCTATCCATTT
Found at i:18543912 original size:22 final size:20
Alignment explanation
Indices: 18543882--18543934 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
18543872 GCTGGCAGAT
* *
18543882 GGAAGAAGAAAGGAAAGAGGG
1 GGAAAAAGAAA-GAAAAAGGG
18543903 AGGAAAAAGACAAGAAAAAGGG
1 -GGAAAAAGA-AAGAAAAAGGG
18543925 GG-AAAAGAAA
1 GGAAAAAGAAA
18543935 ATCAGGGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 2 0.07
20 6 0.21
21 2 0.07
22 16 0.57
23 2 0.07
ACGTcount: A:0.60, C:0.02, G:0.38, T:0.00
Consensus pattern (20 bp):
GGAAAAAGAAAGAAAAAGGG
Found at i:18559250 original size:38 final size:39
Alignment explanation
Indices: 18559161--18559267 Score: 146
Period size: 38 Copynumber: 2.7 Consensus size: 39
18559151 CACACCCGGC
*
18559161 TCATGTACATCCCCCCACATCGTGCACATATCCGGCACCA
1 TCATGTACATCCCCCCACATCGTGCACATATCAGG-ACCA
* *
18559201 TCATGTGCATCCCCCCACATCGTGCATA-ATCAGTG-CCA
1 TCATGTACATCCCCCCACATCGTGCACATATCAG-GACCA
*
18559239 TCATGTACATCCCCCCACATCATGCACAT
1 TCATGTACATCCCCCCACATCGTGCACAT
18559268 GAGCACTATC
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
38 28 0.47
39 4 0.07
40 27 0.46
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.22
Consensus pattern (39 bp):
TCATGTACATCCCCCCACATCGTGCACATATCAGGACCA
Found at i:18560702 original size:19 final size:19
Alignment explanation
Indices: 18560680--18560720 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
18560670 TTAATATTTT
*
18560680 AATATTATTTTATTAATAA
1 AATATTATTTTATTAAAAA
18560699 AATATTATTTTATTAAAAA
1 AATATTATTTTATTAAAAA
18560718 AAT
1 AAT
18560721 TTTCTCTTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AATATTATTTTATTAAAAA
Found at i:18566620 original size:38 final size:40
Alignment explanation
Indices: 18566531--18566636 Score: 153
Period size: 38 Copynumber: 2.7 Consensus size: 40
18566521 CACACCCGGC
*
18566531 TCATGTACATCCCCCCACATCGTGCACATAGCCGGTGCCA
1 TCATGTACATCCCCCCACATCGTGCACATAGCCAGTGCCA
* * *
18566571 TCATGTGCATCCCGCCACATCGTGCACA-A-TCAGTGCCA
1 TCATGTACATCCCCCCACATCGTGCACATAGCCAGTGCCA
*
18566609 TCGTGTACATCCCCCCACATCGTGCACA
1 TCATGTACATCCCCCCACATCGTGCACA
18566637 CGAGCACTAT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
38 32 0.54
39 1 0.02
40 26 0.44
ACGTcount: A:0.23, C:0.40, G:0.17, T:0.21
Consensus pattern (40 bp):
TCATGTACATCCCCCCACATCGTGCACATAGCCAGTGCCA
Found at i:18572528 original size:26 final size:23
Alignment explanation
Indices: 18572494--18572553 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
18572484 TGAGCTGGTG
* *
18572494 ATGATGATGATGTGATGGTGTGT
1 ATGATGATGATGGGATGGTGTGC
18572517 ATGATGATGATGGGATGGTGTGC
1 ATGATGATGATGGGATGGTGTGC
18572540 ATGATGATGATGGG
1 ATGATGATGATGGG
18572554 TATACGTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.23, C:0.02, G:0.42, T:0.33
Consensus pattern (23 bp):
ATGATGATGATGGGATGGTGTGC
Found at i:18574603 original size:21 final size:21
Alignment explanation
Indices: 18574574--18574615 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
18574564 AAAGGACAGT
*
18574574 AGGCACTTAGTCGACTAAGAG
1 AGGCACTTAGTCAACTAAGAG
*
18574595 AGGCTCTTAGTCAACTAAGAG
1 AGGCACTTAGTCAACTAAGAG
18574616 CATTCTGTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.21
Consensus pattern (21 bp):
AGGCACTTAGTCAACTAAGAG
Found at i:18576606 original size:56 final size:55
Alignment explanation
Indices: 18576535--18576843 Score: 417
Period size: 54 Copynumber: 5.6 Consensus size: 55
18576525 CATCGCATCT
** * *
18576535 AGCTCATGTGCATCCCCTTACATCGTGCACATAGCCAGAGTCATCGTGTCTCACCC
1 AGCTCATGTGCATCCCCCCACATCGTGCACATAGCCAG-GACATCCTGTCTCACCC
* * *
18576591 AGCTCATGTGCATCCCCCCATATCGTGCACATAGCC-GGACATCCCGTCTCACCT
1 AGCTCATGTGCATCCCCCCACATCGTGCACATAGCCAGGACATCCTGTCTCACCC
* ** *
18576645 AGCTCATGTGCAGCCCCCCACATCGTGCACATAGCC-GGACATCCCATCTCACCT
1 AGCTCATGTGCATCCCCCCACATCGTGCACATAGCCAGGACATCCTGTCTCACCC
* * * * *
18576699 AGCTCATGTGCATTCCCCCACATTGTGCACATAG-TAGGACATCCTATCTCACTC
1 AGCTCATGTGCATCCCCCCACATCGTGCACATAGCCAGGACATCCTGTCTCACCC
* *
18576753 AGCTCATGTGCATCCCCCCACATCGTGCACATAGCCAGAGTCATCGTGTCTCACCC
1 AGCTCATGTGCATCCCCCCACATCGTGCACATAGCCAG-GACATCCTGTCTCACCC
18576809 AGCTCATGTGCATCCCCCCACATCGTGCACATAGC
1 AGCTCATGTGCATCCCCCCACATCGTGCACATAGC
18576844 TGGAGTCATC
Statistics
Matches: 226, Mismatches: 24, Indels: 6
0.88 0.09 0.02
Matches are distributed among these distances:
54 142 0.63
55 3 0.01
56 81 0.36
ACGTcount: A:0.22, C:0.39, G:0.17, T:0.23
Consensus pattern (55 bp):
AGCTCATGTGCATCCCCCCACATCGTGCACATAGCCAGGACATCCTGTCTCACCC
Found at i:18576870 original size:40 final size:39
Alignment explanation
Indices: 18576815--18576917 Score: 120
Period size: 38 Copynumber: 2.6 Consensus size: 39
18576805 ACCCAGCTCA
* * *
18576815 TGTGCATCCCCCCACATCGTGCACATAGCTGGA-GTCATCG
1 TGTGCATCCCCCCACATCGTGCACA-AGAT-AATGCCATCG
*
18576855 TGTGCATCCCCCCACATCGTGTAC-AGATAATGCCATCG
1 TGTGCATCCCCCCACATCGTGCACAAGATAATGCCATCG
* *
18576893 TATACATCCCCCCACATCGTGCACA
1 TGTGCATCCCCCCACATCGTGCACA
18576918 CGGGCAGTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
37 1 0.02
38 30 0.56
40 23 0.43
ACGTcount: A:0.23, C:0.37, G:0.17, T:0.22
Consensus pattern (39 bp):
TGTGCATCCCCCCACATCGTGCACAAGATAATGCCATCG
Found at i:18580318 original size:17 final size:17
Alignment explanation
Indices: 18580296--18580330 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
18580286 ATAAAACTAT
18580296 GCACACACTAAGGGGGA
1 GCACACACTAAGGGGGA
*
18580313 GCACACACTTAGGGGGA
1 GCACACACTAAGGGGGA
18580330 G
1 G
18580331 GAAAACCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.23, G:0.37, T:0.09
Consensus pattern (17 bp):
GCACACACTAAGGGGGA
Found at i:18585223 original size:17 final size:17
Alignment explanation
Indices: 18585201--18585233 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
18585191 GTTCATAGGG
18585201 CACATATTTAGGGGGAA
1 CACATATTTAGGGGGAA
18585218 CACATATTTAGGGGGA
1 CACATATTTAGGGGGA
18585234 GAAATCCCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.33, C:0.12, G:0.30, T:0.24
Consensus pattern (17 bp):
CACATATTTAGGGGGAA
Found at i:18595382 original size:38 final size:39
Alignment explanation
Indices: 18595284--18595389 Score: 126
Period size: 38 Copynumber: 2.7 Consensus size: 39
18595274 CACTCCTAGC
*
18595284 TCATGTACATCCCCCCACATCGTGCACATAGCCGGCACAA
1 TCATGTACATCCCCCCACATCGTGCACATAGCAGG-ACAA
* * * *
18595324 TCACGTGCATCCCCCCACATCGTGCACA-ATCAGTG-CTA
1 TCATGTACATCCCCCCACATCGTGCACATAGCAG-GACAA
*
18595362 TCGTGTACATCCCCCCACATCGTGCACA
1 TCATGTACATCCCCCCACATCGTGCACA
18595390 CGGGTACTAT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
38 27 0.47
39 3 0.05
40 27 0.47
ACGTcount: A:0.25, C:0.41, G:0.15, T:0.20
Consensus pattern (39 bp):
TCATGTACATCCCCCCACATCGTGCACATAGCAGGACAA
Found at i:18595511 original size:2 final size:2
Alignment explanation
Indices: 18595500--18595536 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
18595490 ATTCATTATG
*
18595500 CA CA -A CA CA CA CA CA CA CA CA CA CA CG CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
18595537 TATATATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.49, G:0.03, T:0.00
Consensus pattern (2 bp):
CA
Found at i:18596817 original size:29 final size:28
Alignment explanation
Indices: 18596761--18596815 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
18596751 TGACAAGTGC
18596761 TGGGATGAAAAATTTACCGATTTGCCCT
1 TGGGATGAAAAATTTACCGATTTGCCCT
18596789 TGGGACTGAAAAA-TTA-CGATTTTGCCC
1 TGGGA-TGAAAAATTTACCGA-TTTGCCC
18596816 CTATACTCCG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 3 0.12
28 15 0.60
29 7 0.28
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (28 bp):
TGGGATGAAAAATTTACCGATTTGCCCT
Found at i:18597906 original size:10 final size:10
Alignment explanation
Indices: 18597893--18597934 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
18597883 TTTCTTTCAT
18597893 TTTCTTTTCC
1 TTTCTTTTCC
*
18597903 TTTCCTTTCC
1 TTTCTTTTCC
18597913 TTTCTTTT-C
1 TTTCTTTTCC
*
18597922 TTACTTTTTCC
1 TTTC-TTTTCC
18597933 TT
1 TT
18597935 CTCCTACCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
9 4 0.15
10 20 0.74
11 3 0.11
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTCTTTTCC
Found at i:18601536 original size:11 final size:11
Alignment explanation
Indices: 18601520--18601549 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
18601510 GCACGAGAAG
18601520 AAATAATAAAA
1 AAATAATAAAA
*
18601531 AAATAATAATA
1 AAATAATAAAA
18601542 AAATAATA
1 AAATAATA
18601550 GTATTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AAATAATAAAA
Found at i:18608172 original size:76 final size:75
Alignment explanation
Indices: 18608059--18608252 Score: 192
Period size: 76 Copynumber: 2.6 Consensus size: 75
18608049 AAAGTTTAAC
* ** * * * * * *
18608059 CACACCCTTTACAAGAAACGACTTTTAAGGATCAAGCACGAGC-TCTACAAAAGTCAGTGCCTTT
1 CACAACCTTTACAACCAACTACTTTTAAGGATCAAGCAC-AACAACTACAAAACTCACTACCTTT
18608123 TTAAGAACAAG
65 TTAAGAACAAG
*
18608134 CACAACCTTTACAACCAACTACTTTTTAAAGATCAAGCACAACAACTACAAAACTCACTACCTTT
1 CACAACCTTTACAACCAACTAC-TTTTAAGGATCAAGCACAACAACTACAAAACTCACTACCTTT
* **
18608199 TTAGGGTCAAG
65 TTAAGAACAAG
* ** * *
18608210 AACAACCTTTGTAGCCAACTTCCTTTTAAGGATCAAGCACAAC
1 CACAACCTTTACAACCAAC-TACTTTTAAGGATCAAGCACAAC
18608253 TTCTCTACCT
Statistics
Matches: 97, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
75 20 0.21
76 75 0.77
77 2 0.02
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.24
Consensus pattern (75 bp):
CACAACCTTTACAACCAACTACTTTTAAGGATCAAGCACAACAACTACAAAACTCACTACCTTTT
TAAGAACAAG
Found at i:18610169 original size:53 final size:53
Alignment explanation
Indices: 18610069--18610169 Score: 139
Period size: 53 Copynumber: 1.9 Consensus size: 53
18610059 GAAAAGAAAA
* * * * * *
18610069 AATCCTTTTGTGGATTGTGTAAGGGTTATTGCTAGATCTCGTTAAAAATTTAG
1 AATCCTTTTGTGGAGTGTGTAAAGGTTATCGCTAGATCCCATGAAAAATTTAG
*
18610122 AATCCTTTTGTGGAGTGTGTAAAGGTTATCGCTTGATCCCATGAAAAA
1 AATCCTTTTGTGGAGTGTGTAAAGGTTATCGCTAGATCCCATGAAAAA
18610170 GCCATTGTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
53 41 1.00
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.38
Consensus pattern (53 bp):
AATCCTTTTGTGGAGTGTGTAAAGGTTATCGCTAGATCCCATGAAAAATTTAG
Found at i:18610574 original size:18 final size:18
Alignment explanation
Indices: 18610535--18610580 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
18610525 TTATCATTGG
*
18610535 AAAATTGTTTTTGAAGGTA
1 AAAAATGTTTTTG-AGGTA
*
18610554 AAAAATGTTTTTG-GGTG
1 AAAAATGTTTTTGAGGTA
18610571 AAAAA-GTTTT
1 AAAAATGTTTT
18610581 AATATTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 5 0.20
17 8 0.32
19 12 0.48
ACGTcount: A:0.37, C:0.00, G:0.22, T:0.41
Consensus pattern (18 bp):
AAAAATGTTTTTGAGGTA
Found at i:18620808 original size:35 final size:35
Alignment explanation
Indices: 18620769--18621089 Score: 229
Period size: 35 Copynumber: 9.1 Consensus size: 35
18620759 TTGTAATTGC
* * *
18620769 CAATTAATCCAATAATTTGAA-TAAACAATTTTAAT
1 CAATTAAGCCAATAACTT-AATTAAACAAATTTAAT
* *
18620804 CAATTAGGCCAATGACTTAATTAAACAAATTTAAT
1 CAATTAAGCCAATAACTTAATTAAACAAATTTAAT
* ****
18620839 CAATTAGGCCCAATAACTTAATT-GTTTAATTTAAT
1 CAATTAAG-CCAATAACTTAATTAAACAAATTTAAT
* *
18620874 TAATTAGGCCCAATAACTTAATTAAA-AAATTTAAT
1 CAATTAAG-CCAATAACTTAATTAAACAAATTTAAT
* * * * * *
18620909 TAATTAAGCCCAACAATTTACTGAAACAATTTTAAT
1 CAATTAAG-CCAATAACTTAATTAAACAAATTTAAT
* *
18620945 CAATTAGGCTCAATAACTTAACTAAACAAATTTAAT
1 CAATTAAGC-CAATAACTTAATTAAACAAATTTAAT
* ****
18620981 CAATTAGGCCCAATAACTTAATT-GTTTAATTTAAT
1 CAATTAAG-CCAATAACTTAATTAAACAAATTTAAT
** * *
18621016 TTATTAGGCCCAATGACTTAATTAAAC-AATTTAAT
1 CAATTAAG-CCAATAACTTAATTAAACAAATTTAAT
* * * * *
18621051 TAATTAGGCCCAATGATTTAATTAAACAATTTTAAT
1 CAATTAAG-CCAATAACTTAATTAAACAAATTTAAT
18621087 CAA
1 CAA
18621090 GTGCTTGAGA
Statistics
Matches: 235, Mismatches: 43, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
34 2 0.01
35 156 0.66
36 76 0.32
37 1 0.00
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.36
Consensus pattern (35 bp):
CAATTAAGCCAATAACTTAATTAAACAAATTTAAT
Found at i:18620987 original size:142 final size:141
Alignment explanation
Indices: 18620777--18621089 Score: 502
Period size: 142 Copynumber: 2.2 Consensus size: 141
18620767 GCCAATTAAT
* * *
18620777 CCAATAATTTGAAT-AAACAATTTTAATCAATTAGGCCAATGACTTAATTAAACAAATTTAATCA
1 CCAACAATTT-AATGAAACAATTTTAATCAATTAGGCCAATAACTTAACTAAACAAATTTAATCA
18620841 ATTAGGCCCAATAACTTAATTGTTTAATTTAATTAATTAGGCCCAATAACTTAATTAAAAAATTT
65 ATTAGGCCCAATAACTTAATTGTTTAATTTAATTAATTAGGCCCAATAACTTAATTAAAAAATTT
18620906 AATTAATTAAGC
130 AATTAATTAAGC
*
18620918 CCAACAATTTACTGAAACAATTTTAATCAATTAGGCTCAATAACTTAACTAAACAAATTTAATCA
1 CCAACAATTTAATGAAACAATTTTAATCAATTAGGC-CAATAACTTAACTAAACAAATTTAATCA
* * *
18620983 ATTAGGCCCAATAACTTAATTGTTTAATTTAATTTATTAGGCCCAATGACTTAATTAAACAATTT
65 ATTAGGCCCAATAACTTAATTGTTTAATTTAATTAATTAGGCCCAATAACTTAATTAAAAAATTT
*
18621048 AATTAATTAGGC
130 AATTAATTAAGC
** *
18621060 CCAATGATTTAATTAAACAATTTTAATCAA
1 CCAACAATTTAATGAAACAATTTTAATCAA
18621090 GTGCTTGAGA
Statistics
Matches: 158, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
140 2 0.01
141 31 0.20
142 125 0.79
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.35
Consensus pattern (141 bp):
CCAACAATTTAATGAAACAATTTTAATCAATTAGGCCAATAACTTAACTAAACAAATTTAATCAA
TTAGGCCCAATAACTTAATTGTTTAATTTAATTAATTAGGCCCAATAACTTAATTAAAAAATTTA
ATTAATTAAGC
Found at i:18623420 original size:2 final size:2
Alignment explanation
Indices: 18623407--18623450 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
18623397 CATGCACAAC
*
18623407 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18623449 AT
1 AT
18623451 CAACATAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18630204 original size:42 final size:43
Alignment explanation
Indices: 18630145--18630334 Score: 176
Period size: 42 Copynumber: 4.4 Consensus size: 43
18630135 TTATGTGATA
* * *
18630145 ATGATGACCCAGTTATGTGCGTGT-GGGAGTGCACATGAGCTG
1 ATGATGACCCAGCTATGTGCGAGTAGGGAGTGCACATAAGCTG
* *
18630187 ATGATGACCCAGCTATGTGC--GTATGAGAGTGCACATGAGCTG
1 ATGATGACCCAGCTATGTGCGAGTA-GGGAGTGCACATAAGCTG
*** *
18630229 ATGATGACTTGGCTATGTGCGAGTAGGGAGTGCGCATAAG-TCG
1 ATGATGACCCAGCTATGTGCGAGTAGGGAGTGCACATAAGCT-G
*
18630272 ATGATGACCC-GACTATGTACGAGTAGGGAGTG-AGCATAAGTCGATG
1 ATGATGACCCAG-CTATGTGCGAGTAGGGAGTGCA-CATAAG-C--TG
*
18630318 ATGATGACCCAACTATG
1 ATGATGACCCAGCTATG
18630335 ACGATGAATG
Statistics
Matches: 123, Mismatches: 13, Indels: 20
0.79 0.08 0.13
Matches are distributed among these distances:
40 2 0.02
42 55 0.45
43 46 0.37
44 3 0.02
46 16 0.13
47 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.33, T:0.24
Consensus pattern (43 bp):
ATGATGACCCAGCTATGTGCGAGTAGGGAGTGCACATAAGCTG
Found at i:18630323 original size:46 final size:44
Alignment explanation
Indices: 18630226--18630338 Score: 140
Period size: 43 Copynumber: 2.6 Consensus size: 44
18630216 TGCACATGAG
** * * *
18630226 CTGATGATGACTTGGCTATGTGCGAGTAGGGAGTGCGCATAAGT
1 CTGATGATGACCCGACTATGTACGAGTAGGGAGTGAGCATAAGT
18630270 C-GATGATGACCCGACTATGTACGAGTAGGGAGTGAGCATAAGT
1 CTGATGATGACCCGACTATGTACGAGTAGGGAGTGAGCATAAGT
*
18630313 CGATGATGATGACCCAACTATG-ACGA
1 C--TGATGATGACCCGACTATGTACGA
18630339 TGAATGAAGT
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
43 38 0.63
44 1 0.02
45 4 0.07
46 17 0.28
ACGTcount: A:0.28, C:0.17, G:0.32, T:0.23
Consensus pattern (44 bp):
CTGATGATGACCCGACTATGTACGAGTAGGGAGTGAGCATAAGT
Found at i:18648008 original size:289 final size:288
Alignment explanation
Indices: 18647489--18648065 Score: 1100
Period size: 289 Copynumber: 2.0 Consensus size: 288
18647479 ATTTATAGGC
* *
18647489 AAATATCACTATTCAAAATATTGGTTAAGATATAACATTTTAATATAAAACAATATTTATAGAAA
1 AAATATCACTATTCAAAATATTGATTAAAATATAACATTTTAATATAAAACAATATTTATAGAAA
*
18647554 CATGTGTAAGAAATCTTTTGTAATGTGTAAGTAAAATAAATTCATACATACAAAAATTTACTAAG
66 CACGTGTAAGAAATCTTTTGTAATGTGTAAGTAAAATAAATTCATACATACAAAAATTTACTAAG
18647619 TTATAATGTACAATAATGGTTACAATGACAAGTGGTCCAAAATACACCCAGTGTTGGTGCTAGAA
131 TTATAATGTACAATAATGGTTACAATGACAAGTGGTCCAAAATACACCCAGTGTTGGTGCTAGAA
18647684 ACCTACTGTCTGTATGGTAGAGATGTTAACTGGAATCCTCGATAAAATAGGGTATCTACAAGCTA
196 ACCTACTGTCTGTATGGTAGAGATGTTAACTGGAATCCTCGATAAAATAGGGTATCTACAAGCTA
18647749 CCACAGACCTGAAATGTTTGGAAATGAG
261 CCACAGACCTGAAATGTTTGGAAATGAG
* *
18647777 NAAATATCACTATTCAAAATATTGATTAAAATATAGCATTTTTATATAAAACAATATTTATAGAA
1 -AAATATCACTATTCAAAATATTGATTAAAATATAACATTTTAATATAAAACAATATTTATAGAA
18647842 ACACGTGTAAGAAATCTTTTGTAATGTGTAAGTAAAATAAATTCATACATACAAAAATTTACTAA
65 ACACGTGTAAGAAATCTTTTGTAATGTGTAAGTAAAATAAATTCATACATACAAAAATTTACTAA
18647907 GTTATAATGTACAATAATGGTTACAATGACAAGTGGTCCAAAATACACCCAGTGTTGGTGCTAGA
130 GTTATAATGTACAATAATGGTTACAATGACAAGTGGTCCAAAATACACCCAGTGTTGGTGCTAGA
18647972 AACCTACTGTCTGTATGGTAGAGATGTTAACTGGAATCCTCGATAAAATAGGGTATCTACAAGCT
195 AACCTACTGTCTGTATGGTAGAGATGTTAACTGGAATCCTCGATAAAATAGGGTATCTACAAGCT
18648037 ACCACAGACCTGAAATGTTTGGAAATGAG
260 ACCACAGACCTGAAATGTTTGGAAATGAG
18648066 GTGGGTGAGA
Statistics
Matches: 283, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
289 283 1.00
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.31
Consensus pattern (288 bp):
AAATATCACTATTCAAAATATTGATTAAAATATAACATTTTAATATAAAACAATATTTATAGAAA
CACGTGTAAGAAATCTTTTGTAATGTGTAAGTAAAATAAATTCATACATACAAAAATTTACTAAG
TTATAATGTACAATAATGGTTACAATGACAAGTGGTCCAAAATACACCCAGTGTTGGTGCTAGAA
ACCTACTGTCTGTATGGTAGAGATGTTAACTGGAATCCTCGATAAAATAGGGTATCTACAAGCTA
CCACAGACCTGAAATGTTTGGAAATGAG
Found at i:18654380 original size:42 final size:42
Alignment explanation
Indices: 18654325--18654443 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
18654315 TTGTGATAAC
* * *
18654325 GATGACCTAGCTATGTCCGTGTGCGAGTGCACATGAGCCGAT
1 GATGACCCAGCTATGTGCGTGTGGGAGTGCACATGAGCCGAT
* *
18654367 GATGACCCAGCTATGTGCGTATGGGAGTGCACATGAGCTGAT
1 GATGACCCAGCTATGTGCGTGTGGGAGTGCACATGAGCCGAT
*
18654409 GATGACCCAGCTATGTGCGTGTGGGAGTACACATG
1 GATGACCCAGCTATGTGCGTGTGGGAGTGCACATG
18654444 TGTCAAGCCC
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.24
Consensus pattern (42 bp):
GATGACCCAGCTATGTGCGTGTGGGAGTGCACATGAGCCGAT
Found at i:18655163 original size:21 final size:22
Alignment explanation
Indices: 18655138--18655178 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
18655128 CTTAGGTGGA
* *
18655138 AAAATTCAAGGGAA-AAGTGTG
1 AAAATCCAAGGAAACAAGTGTG
18655159 AAAATCCAAGGAAACAAGTG
1 AAAATCCAAGGAAACAAGTG
18655179 ACAAAAGGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.51, C:0.10, G:0.24, T:0.15
Consensus pattern (22 bp):
AAAATCCAAGGAAACAAGTGTG
Found at i:18663750 original size:20 final size:20
Alignment explanation
Indices: 18663724--18663769 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
18663714 TTCTTACCCT
* *
18663724 TTTTTCACTTGTTTCCTTGAA
1 TTTTACACTT-TTCCCTTGAA
18663745 TTTTCACACTTTTCCCTTGAA
1 TTTT-ACACTTTTCCCTTGAA
18663766 TTTT
1 TTTT
18663770 TCCACCTTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.15, C:0.22, G:0.07, T:0.57
Consensus pattern (20 bp):
TTTTACACTTTTCCCTTGAA
Found at i:18663771 original size:22 final size:22
Alignment explanation
Indices: 18663729--18663769 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
18663719 ACCCTTTTTT
*
18663729 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
18663751 CACTT-TTCCCTTGAATTTT
1 CACTTGTTCCCTTGAATTTT
18663770 TCCACCTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.51
Consensus pattern (22 bp):
CACTTGTTCCCTTGAATTTTCA
Found at i:18669681 original size:2 final size:2
Alignment explanation
Indices: 18669674--18669710 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
18669664 ACTTAATGTA
18669674 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18669711 TGAAAATTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18683043 original size:44 final size:43
Alignment explanation
Indices: 18682986--18683075 Score: 153
Period size: 44 Copynumber: 2.1 Consensus size: 43
18682976 AAAACATAAA
*
18682986 AATCTACGGTTTAAGTTCATTATTCTTTAAAATCATAAAAACG
1 AATCTACGATTTAAGTTCATTATTCTTTAAAATCATAAAAACG
*
18683029 AANTCTACGATTTAAGTTCATTATTCTTTAAAATCATAGAAACG
1 AA-TCTACGATTTAAGTTCATTATTCTTTAAAATCATAAAAACG
18683073 AAT
1 AAT
18683076 ATAAACTACT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
43 3 0.07
44 41 0.93
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.37
Consensus pattern (43 bp):
AATCTACGATTTAAGTTCATTATTCTTTAAAATCATAAAAACG
Found at i:18700550 original size:21 final size:21
Alignment explanation
Indices: 18700526--18700568 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
18700516 AATACTTAAA
*
18700526 TTAAGTTGTTTTAGTTTAATT
1 TTAAGTTATTTTAGTTTAATT
* *
18700547 TTAATTTATTTTGGTTTAATT
1 TTAAGTTATTTTAGTTTAATT
18700568 T
1 T
18700569 ACTTTAAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.12, T:0.65
Consensus pattern (21 bp):
TTAAGTTATTTTAGTTTAATT
Found at i:18709351 original size:21 final size:20
Alignment explanation
Indices: 18709322--18709362 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
18709312 GATTAAGTTG
18709322 TTTTAGTTTAATTTTACTTTA
1 TTTTAGTTTAA-TTTACTTTA
*
18709343 TTTTGGTTTAATTTACTTTA
1 TTTTAGTTTAATTTACTTTA
18709363 AGAAGTGCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.22, C:0.05, G:0.07, T:0.66
Consensus pattern (20 bp):
TTTTAGTTTAATTTACTTTA
Found at i:18710153 original size:19 final size:19
Alignment explanation
Indices: 18710129--18710166 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
18710119 CCATTTGACT
18710129 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
18710148 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
18710167 GTTTAGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:18710248 original size:28 final size:28
Alignment explanation
Indices: 18710211--18710269 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
18710201 TTTGGAGCAT
*
18710211 AGGGGTAAAATGGTAATTTTACCACC-CC
1 AGGGGCAAAATGGTAATTTT-CCACCACC
*
18710239 AGGGGCAAAATTGTAATTTTCCACCACC
1 AGGGGCAAAATGGTAATTTTCCACCACC
18710267 AGG
1 AGG
18710270 ACATTTGTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 5 0.18
28 23 0.82
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (28 bp):
AGGGGCAAAATGGTAATTTTCCACCACC
Found at i:18711411 original size:13 final size:13
Alignment explanation
Indices: 18711393--18711418 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18711383 AGGAGAAATT
18711393 ATGATTTTATAAA
1 ATGATTTTATAAA
18711406 ATGATTTTATAAA
1 ATGATTTTATAAA
18711419 TTTTCTGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
ATGATTTTATAAA
Found at i:18713155 original size:22 final size:20
Alignment explanation
Indices: 18713112--18713153 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
18713102 AAGCCAATTC
18713112 TTCATATATTATGAATCATT
1 TTCATATATTATGAATCATT
18713132 TTCATATATTATGAATCATT
1 TTCATATATTATGAATCATT
18713152 TT
1 TT
18713154 TTTCTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.52
Consensus pattern (20 bp):
TTCATATATTATGAATCATT
Found at i:18718949 original size:60 final size:60
Alignment explanation
Indices: 18718876--18719005 Score: 251
Period size: 60 Copynumber: 2.2 Consensus size: 60
18718866 CCAAACAGCT
18718876 ACTCACACCCAAATCCCAGCAATTCAATTCGCAGCAAACCAGCAGAACCCTGTGTCGTTG
1 ACTCACACCCAAATCCCAGCAATTCAATTCGCAGCAAACCAGCAGAACCCTGTGTCGTTG
*
18718936 ACTCACACCCAAATCCCAGCAATTCAATTCGCAGCAAGCCAGCAGAACCCTGTGTCGTTG
1 ACTCACACCCAAATCCCAGCAATTCAATTCGCAGCAAACCAGCAGAACCCTGTGTCGTTG
18718996 ACTCACACCC
1 ACTCACACCC
18719006 CTAACCCAAC
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
60 69 1.00
ACGTcount: A:0.31, C:0.37, G:0.15, T:0.18
Consensus pattern (60 bp):
ACTCACACCCAAATCCCAGCAATTCAATTCGCAGCAAACCAGCAGAACCCTGTGTCGTTG
Found at i:18728327 original size:76 final size:76
Alignment explanation
Indices: 18728144--18728355 Score: 267
Period size: 76 Copynumber: 2.9 Consensus size: 76
18728134 AAGTACCATC
*
18728144 TATTTTAATTTTGGGTAATTCATAAAAAAATAGAAAATTGTTTCCTACTTTAAAAGCAATTCCTA
1 TATTTTAATTTTGGGTAATTCAT--AAAAATAGAAAATTGTTTCCTACTTTAAAAGAAATTCCTA
18728209 AAATTAAGGATAA
64 AAATTAAGGATAA
* * *
18728222 AATTTTAATTTTGGGTGATTCATAAAAATAGGAAATTGTTTCCTACTTTAAAAGAAATTCCTAAA
1 TATTTTAATTTTGGGTAATTCATAAAAATAGAAAATTGTTTCCTACTTTAAAAGAAATTCCTAAA
*
18728287 ATTAAGGATAG
66 ATTAAGGATAA
** * * *
18728298 TATTTTAA-TTTGGAAAATTC------ATAGGAAATAGTTTCCTACTTTAGAAGAAATTCCTAAA
1 TATTTTAATTTTGGGTAATTCATAAAAATAGAAAATTGTTTCCTACTTTAAAAGAAATTCCTAAA
18728356 GTTATGTGAT
Statistics
Matches: 123, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
69 36 0.29
75 9 0.07
76 57 0.46
78 21 0.17
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (76 bp):
TATTTTAATTTTGGGTAATTCATAAAAATAGAAAATTGTTTCCTACTTTAAAAGAAATTCCTAAA
ATTAAGGATAA
Found at i:18732126 original size:2 final size:2
Alignment explanation
Indices: 18732113--18732159 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
18732103 TATCATGAAA
* * * *
18732113 TC TC TC TT TC TC TC TT TT TC TC TC TC TT TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
18732155 TC TC T
1 TC TC T
18732160 ACACAGTTCA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (2 bp):
TC
Found at i:18732132 original size:10 final size:10
Alignment explanation
Indices: 18732113--18732159 Score: 76
Period size: 10 Copynumber: 4.7 Consensus size: 10
18732103 TATCATGAAA
18732113 TCTCTCTTTC
1 TCTCTCTTTC
*
18732123 TCTCTTTTTC
1 TCTCTCTTTC
18732133 TCTCTCTTTC
1 TCTCTCTTTC
*
18732143 TCTCTCTCTC
1 TCTCTCTTTC
18732153 TCTCTCT
1 TCTCTCT
18732160 ACACAGTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 34 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (10 bp):
TCTCTCTTTC
Found at i:18736299 original size:20 final size:20
Alignment explanation
Indices: 18736241--18736300 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
18736231 ATACCCATCT
*
18736241 TCATCATC-TCACCAACCCA
1 TCATCATCATCACCAACTCA
* * *
18736260 TTATCATCATCACTAGCTCA
1 TCATCATCATCACCAACTCA
18736280 TCATCATCATCACCAACTCA
1 TCATCATCATCACCAACTCA
18736300 T
1 T
18736301 GCGCACTCCC
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
19 7 0.21
20 26 0.79
ACGTcount: A:0.32, C:0.38, G:0.02, T:0.28
Consensus pattern (20 bp):
TCATCATCATCACCAACTCA
Found at i:18736347 original size:43 final size:43
Alignment explanation
Indices: 18736299--18736408 Score: 177
Period size: 43 Copynumber: 2.6 Consensus size: 43
18736289 TCACCAACTC
** *
18736299 ATGCGCACTCCCTACTCGCACATGGCTGGGTCATCAC-CGGGTT
1 ATGCGCACTCCCTACTCGCACATAACTGGGTCATC-CTCGGCTT
18736342 ATGCGCACTCCCTACTCGCACATAACTGGGTCATCCTCGGCTT
1 ATGCGCACTCCCTACTCGCACATAACTGGGTCATCCTCGGCTT
18736385 ATGCGCACTCCCTACTCGCACATA
1 ATGCGCACTCCCTACTCGCACATA
18736409 GTCGAGTCAA
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
42 1 0.02
43 62 0.98
ACGTcount: A:0.19, C:0.37, G:0.20, T:0.24
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACTGGGTCATCCTCGGCTT
Found at i:18748327 original size:32 final size:32
Alignment explanation
Indices: 18748289--18748354 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
18748279 CTTCTCCATT
* *
18748289 TTTCCTATTTGGGCTAAGCCCATTTATTTT-TA
1 TTTCCTA-TTGGGCCAAGCCCACTTATTTTCTA
*
18748321 TTTCCTATTGGGCCATGCCCACTTATTTTCTA
1 TTTCCTATTGGGCCAAGCCCACTTATTTTCTA
18748353 TT
1 TT
18748355 GGGCCATGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 19 0.63
32 11 0.37
ACGTcount: A:0.17, C:0.23, G:0.12, T:0.48
Consensus pattern (32 bp):
TTTCCTATTGGGCCAAGCCCACTTATTTTCTA
Found at i:18748341 original size:31 final size:30
Alignment explanation
Indices: 18748287--18748377 Score: 102
Period size: 25 Copynumber: 3.1 Consensus size: 30
18748277 GACTTCTCCA
* *
18748287 TTTTTCCTATTTGGGCTAAGCCCATTTATTT
1 TTTTTCCTA-TTGGGCCATGCCCATTTATTT
*
18748318 TTATTTCCTATTGGGCCATGCCCACTTA---
1 TT-TTTCCTATTGGGCCATGCCCATTTATTT
18748346 -TTTT-CTATTGGGCCATGCCCATTTATTT
1 TTTTTCCTATTGGGCCATGCCCATTTATTT
18748374 TTTT
1 TTTT
18748378 ATCTATTTTC
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
25 20 0.39
26 3 0.06
27 1 0.02
29 3 0.06
31 17 0.33
32 7 0.14
ACGTcount: A:0.15, C:0.22, G:0.13, T:0.49
Consensus pattern (30 bp):
TTTTTCCTATTGGGCCATGCCCATTTATTT
Found at i:18748578 original size:34 final size:34
Alignment explanation
Indices: 18748540--18748652 Score: 138
Period size: 34 Copynumber: 3.3 Consensus size: 34
18748530 CTCAATGCTA
* * *
18748540 TCCAATTTTCCTGCACAAACTATCAGAAAACAGC
1 TCCAATTTTTCTGCACAAATTAGCAGAAAACAGC
* * *
18748574 TCCAATTTTTCTGCACAAATTGGCAGCAAACAAC
1 TCCAATTTTTCTGCACAAATTAGCAGAAAACAGC
*
18748608 TCCAATTTTTTTGCACAAATTAGCA-ACAAACAGC
1 TCCAATTTTTCTGCACAAATTAGCAGA-AAACAGC
*
18748642 TCAAATTTTTC
1 TCCAATTTTTC
18748653 AGCATCCAAA
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
34 66 1.00
ACGTcount: A:0.36, C:0.26, G:0.09, T:0.29
Consensus pattern (34 bp):
TCCAATTTTTCTGCACAAATTAGCAGAAAACAGC
Found at i:18752537 original size:27 final size:28
Alignment explanation
Indices: 18752480--18752537 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
18752470 GGAAAAATGT
*
18752480 CCTGGTGGTGGAAAATTACAATTTTGCC
1 CCTGGTGGTGGAAAATTACAATTTTGAC
*
18752508 CCTGG-GGTGGCAAAATTACCATTTT-AC
1 CCTGGTGGTGG-AAAATTACAATTTTGAC
18752535 CCT
1 CCT
18752538 TTTACTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 9 0.33
28 18 0.67
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (28 bp):
CCTGGTGGTGGAAAATTACAATTTTGAC
Found at i:18752608 original size:20 final size:20
Alignment explanation
Indices: 18752591--18752628 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
18752581 CCTCAAATCT
18752591 TACTCCAATAAGTCAAATTA
1 TACTCCAATAAGTCAAATTA
18752611 TACTCCAATAAGTCAAAT
1 TACTCCAATAAGTCAAAT
18752629 GGGGCCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (20 bp):
TACTCCAATAAGTCAAATTA
Found at i:18756786 original size:5 final size:5
Alignment explanation
Indices: 18756779--18756817 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
18756769 CTATTCAATC
* *
18756779 TAACC TAACT TAACT TAACT TAACT TATCT TAACT TAAC
1 TAACT TAACT TAACT TAACT TAACT TAACT TAACT TAAC
18756818 CAGACTTGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38
Consensus pattern (5 bp):
TAACT
Found at i:18759571 original size:20 final size:20
Alignment explanation
Indices: 18759554--18759591 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
18759544 CCTCAAATCT
18759554 TACTCCAATAAGTCAAATTA
1 TACTCCAATAAGTCAAATTA
18759574 TACTCCAATAAGTCAAAT
1 TACTCCAATAAGTCAAAT
18759592 GGGGCCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (20 bp):
TACTCCAATAAGTCAAATTA
Done.