Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr4
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: 30015117
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1306243 characters in sequence are not A, C, G, or T
File 64 of 85
Found at i:22350271 original size:12 final size:12
Alignment explanation
Indices: 22350256--22350288 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
22350246 ATCACCACCA
22350256 TCATCATCATCG
1 TCATCATCATCG
*
22350268 TCATCGTCATCG
1 TCATCATCATCG
22350280 TCATCATCA
1 TCATCATCA
22350289 GAGTAGTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.24, C:0.33, G:0.09, T:0.33
Consensus pattern (12 bp):
TCATCATCATCG
Found at i:22359049 original size:8 final size:8
Alignment explanation
Indices: 22359032--22359062 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
22359022 AGGGTTCTTT
*
22359032 GTTTTTGA
1 GTTTTCGA
22359040 GTTTTCGA
1 GTTTTCGA
22359048 GTTTTCGA
1 GTTTTCGA
22359056 GTTTTCG
1 GTTTTCG
22359063 GGGTTTTCGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.10, C:0.10, G:0.26, T:0.55
Consensus pattern (8 bp):
GTTTTCGA
Found at i:22359352 original size:11 final size:11
Alignment explanation
Indices: 22359336--22359370 Score: 70
Period size: 11 Copynumber: 3.2 Consensus size: 11
22359326 TTATATTACA
22359336 AAAAATCAAAT
1 AAAAATCAAAT
22359347 AAAAATCAAAT
1 AAAAATCAAAT
22359358 AAAAATCAAAT
1 AAAAATCAAAT
22359369 AA
1 AA
22359371 TCTAATTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAAATCAAAT
Found at i:22361841 original size:31 final size:31
Alignment explanation
Indices: 22361806--22361872 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 31
22361796 AAATAAACAC
22361806 ATTTCATA-AAAATCAAAAGTTGTTTAACATA
1 ATTTCA-ACAAAATCAAAAGTTGTTTAACATA
***
22361837 ATTTCAAGCTTCATCAAAAGTTGTTTAACATA
1 ATTTCAA-CAAAATCAAAAGTTGTTTAACATA
22361869 ATTT
1 ATTT
22361873 TAAGCTTCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 1 0.03
31 6 0.19
32 24 0.77
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (31 bp):
ATTTCAACAAAATCAAAAGTTGTTTAACATA
Found at i:22361854 original size:32 final size:32
Alignment explanation
Indices: 22361817--22361882 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
22361807 TTTCATAAAA
22361817 ATCAAAAGTTGTTTAACATAATTTCAAGCTTC
1 ATCAAAAGTTGTTTAACATAATTTCAAGCTTC
*
22361849 ATCAAAAGTTGTTTAACATAATTTTAAGCTTC
1 ATCAAAAGTTGTTTAACATAATTTCAAGCTTC
22361881 AT
1 AT
22361883 ACTCTACCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (32 bp):
ATCAAAAGTTGTTTAACATAATTTCAAGCTTC
Found at i:22364280 original size:219 final size:219
Alignment explanation
Indices: 22363901--22364340 Score: 799
Period size: 219 Copynumber: 2.0 Consensus size: 219
22363891 TGGCTTGCAA
*
22363901 AATAGCCCTTGAAGATTCCTTCAAATTTCATCCAAACCCTTCTACTATTTATGCCTTTATAGATT
1 AATAGCCCTTGAAGATTCCTTCAAATTTCATCCAAACCCGTCTACTATTTATGCCTTTATAGATT
22363966 TGCCCCTACCTTAAAATAGCAAGTTTGAAACCTTCAAACTTGCCACATGTGTGGCCAGTCATGGG
66 TGCCCCTACCTTAAAATAGCAAGTTTGAAACCTTCAAACTTGCCACATGTGTGGCCAGTCATGGG
22364031 GGGACTCCATGGCTGCTGATTTCTGCTAATTTTGGCGACCATCTCAACCTATAAATACCCCCAAT
131 GGGACTCCATGGCTGCTGATTTCTGCTAATTTTGGCGACCATCTCAACCTATAAATACCCCCAAT
*
22364096 GGCTGCTCACTTTAAACCCATCTC
196 GGCTGCTCACTTCAAACCCATCTC
* * *
22364120 AATAGCCTTTGAAGATTCCTTCAAATTTCATTCAAACCCGTCTACTATTTATGCCTTTCTAGATT
1 AATAGCCCTTGAAGATTCCTTCAAATTTCATCCAAACCCGTCTACTATTTATGCCTTTATAGATT
22364185 TGCCCCTACCTTAAAATAGCAAGTTTGAAACCTTCAAACTTGCCACATGTGTGGCCAGTCATGGG
66 TGCCCCTACCTTAAAATAGCAAGTTTGAAACCTTCAAACTTGCCACATGTGTGGCCAGTCATGGG
* * * *
22364250 GGGACTCTATGGCTGCTGATTTTTGCTAATTTTGGTGACCATCTCAACCTATAAATACCCCGAAT
131 GGGACTCCATGGCTGCTGATTTCTGCTAATTTTGGCGACCATCTCAACCTATAAATACCCCCAAT
22364315 GGCTGCTCACTTCAAACCCATCTC
196 GGCTGCTCACTTCAAACCCATCTC
22364339 AA
1 AA
22364341 CTCTTTTCAT
Statistics
Matches: 212, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
219 212 1.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.32
Consensus pattern (219 bp):
AATAGCCCTTGAAGATTCCTTCAAATTTCATCCAAACCCGTCTACTATTTATGCCTTTATAGATT
TGCCCCTACCTTAAAATAGCAAGTTTGAAACCTTCAAACTTGCCACATGTGTGGCCAGTCATGGG
GGGACTCCATGGCTGCTGATTTCTGCTAATTTTGGCGACCATCTCAACCTATAAATACCCCCAAT
GGCTGCTCACTTCAAACCCATCTC
Found at i:22372176 original size:25 final size:23
Alignment explanation
Indices: 22372143--22372202 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 23
22372133 AAATTTTCTC
* *
22372143 TTAAATTTTAATTTTATTTAATTA
1 TTAATTTTTAA-TTTATTGAATTA
22372167 TTTAATTTTTCAATTTATTGAATTA
1 -TTAATTTTT-AATTTATTGAATTA
22372192 TTAATATTTTA
1 TTAAT-TTTTA
22372203 TACTAATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 6 0.19
25 23 0.74
26 2 0.06
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (23 bp):
TTAATTTTTAATTTATTGAATTA
Found at i:22373964 original size:27 final size:28
Alignment explanation
Indices: 22373896--22373971 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 28
22373886 ATTTACTCTT
* *
22373896 AGGGGCATTACGGTCATTTTACCCTATA
1 AGGGGTATTATGGTCATTTTACCCTATA
* * * *
22373924 AGGGGTTTTTTGGTCATTTTAGCCTA-C
1 AGGGGTATTATGGTCATTTTACCCTATA
*
22373951 AGGGGTATTATGGTTATTTTA
1 AGGGGTATTATGGTCATTTTA
22373972 TAAATATTAA
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
27 18 0.46
28 21 0.54
ACGTcount: A:0.21, C:0.13, G:0.25, T:0.41
Consensus pattern (28 bp):
AGGGGTATTATGGTCATTTTACCCTATA
Found at i:22378374 original size:10 final size:10
Alignment explanation
Indices: 22378359--22378405 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
22378349 TAACATGCTG
22378359 AATTTTAATT
1 AATTTTAATT
22378369 AATTTTATAATT
1 AA-TTT-TAATT
*
22378381 AATTTTTATT
1 AATTTTAATT
*
22378391 AATTTTGATT
1 AATTTTAATT
22378401 AATTT
1 AATTT
22378406 CGACATATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
10 20 0.61
11 6 0.18
12 7 0.21
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (10 bp):
AATTTTAATT
Found at i:22378381 original size:12 final size:11
Alignment explanation
Indices: 22378361--22378405 Score: 58
Period size: 12 Copynumber: 4.2 Consensus size: 11
22378351 ACATGCTGAA
22378361 TTTTAATTAAT
1 TTTTAATTAAT
22378372 TTTATAATTAAT
1 TTT-TAATTAAT
22378384 TTTT-ATTAA-
1 TTTTAATTAAT
*
22378393 TTTTGATTAAT
1 TTTTAATTAAT
22378404 TT
1 TT
22378406 CGACATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
9 4 0.13
10 10 0.32
11 6 0.19
12 11 0.35
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (11 bp):
TTTTAATTAAT
Found at i:22385979 original size:18 final size:17
Alignment explanation
Indices: 22385958--22386000 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
22385948 AAATCAAAAT
*
22385958 AAAATAGAAAATTTTAGA
1 AAAATAGAAAATTTT-CA
*
22385976 AAAACATGAAAATTTTCA
1 AAAATA-GAAAATTTTCA
22385994 AAAATAG
1 AAAATAG
22386001 GGGTTACACG
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 1 0.05
18 11 0.52
19 9 0.43
ACGTcount: A:0.60, C:0.05, G:0.09, T:0.26
Consensus pattern (17 bp):
AAAATAGAAAATTTTCA
Found at i:22387814 original size:25 final size:25
Alignment explanation
Indices: 22387761--22387814 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
22387751 TACCGATGTC
* * *
22387761 AGCTCGTATGAGCTTATCGATACTC
1 AGCTCGCATGAGCTTACCGATACTA
* *
22387786 AGCTCGCATGAGCTTACCGTTATTA
1 AGCTCGCATGAGCTTACCGATACTA
22387811 AGCT
1 AGCT
22387815 TAGAGGAGCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.31
Consensus pattern (25 bp):
AGCTCGCATGAGCTTACCGATACTA
Found at i:22390641 original size:20 final size:20
Alignment explanation
Indices: 22390537--22390642 Score: 74
Period size: 20 Copynumber: 5.3 Consensus size: 20
22390527 GTAGATGCGT
*
22390537 AACAGAGGCACCAAAGTG-A
1 AACAGAGGCATCAAAGTGTA
* * **
22390556 AGATAGAGGCATGATTGTGTA
1 A-ACAGAGGCATCAAAGTGTA
* * * *
22390577 ATA-AGAAGCATCGAACTGCA
1 A-ACAGAGGCATCAAAGTGTA
* *
22390597 AACAGAGACACCAAAGTGT-
1 AACAGAGGCATCAAAGTGTA
22390616 AACAGAGGCATCAAAGTGTA
1 AACAGAGGCATCAAAGTGTA
22390636 AACAGAG
1 AACAGAG
22390643 ACACTCAAGT
Statistics
Matches: 62, Mismatches: 21, Indels: 7
0.69 0.23 0.08
Matches are distributed among these distances:
19 19 0.31
20 40 0.65
21 3 0.05
ACGTcount: A:0.44, C:0.16, G:0.25, T:0.14
Consensus pattern (20 bp):
AACAGAGGCATCAAAGTGTA
Found at i:22390653 original size:20 final size:21
Alignment explanation
Indices: 22390596--22390650 Score: 80
Period size: 19 Copynumber: 2.8 Consensus size: 21
22390586 ATCGAACTGC
22390596 AAACAGAGACAC-CAAAGTGT
1 AAACAGAGACACTCAAAGTGT
*
22390616 -AACAGAGGCA-TCAAAGTGT
1 AAACAGAGACACTCAAAGTGT
22390635 AAACAGAGACACTCAA
1 AAACAGAGACACTCAA
22390651 GTGGAATCCC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 17 0.57
20 9 0.30
21 4 0.13
ACGTcount: A:0.49, C:0.20, G:0.20, T:0.11
Consensus pattern (21 bp):
AAACAGAGACACTCAAAGTGT
Found at i:22393312 original size:13 final size:13
Alignment explanation
Indices: 22393294--22393318 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22393284 TAATTTATAT
22393294 GTGTGAAAATTTC
1 GTGTGAAAATTTC
22393307 GTGTGAAAATTT
1 GTGTGAAAATTT
22393319 TATCGTTTGT
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:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:22394465 original size:42 final size:43
Alignment explanation
Indices: 22394363--22394521 Score: 146
Period size: 43 Copynumber: 3.7 Consensus size: 43
22394353 AATGTGATAT
* * * *
22394363 CGTGTAAGACCAC-GTTTGGGACGTTGCCATCGATT-TAAGATTTA
1 CGTGTAAGACC-CTGTCTGGGACATTGGCATCG-TTATATGA-TTA
* *
22394407 CGTGTAAGACCATGTCTGGGACATTGGCGTCG-TATATGATTA
1 CGTGTAAGACCCTGTCTGGGACATTGGCATCGTTATATGATTA
* * *
22394449 CGTGTAAGACCCTGTCTGGGACAGTGGCATTGTTATTTGATTA
1 CGTGTAAGACCCTGTCTGGGACATTGGCATCGTTATATGATTA
* * *
22394492 CATGTAAGATCAC-GTCTGGGACGTTGGCAT
1 CGTGTAAGA-CCCTGTCTGGGACATTGGCAT
22394522 TGTATGAGTT
Statistics
Matches: 96, Mismatches: 15, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
42 32 0.33
43 36 0.38
44 28 0.29
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (43 bp):
CGTGTAAGACCCTGTCTGGGACATTGGCATCGTTATATGATTA
Found at i:22402248 original size:39 final size:39
Alignment explanation
Indices: 22402205--22402282 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
22402195 CTATTACATG
* *
22402205 TATAATCACCGAACACTCAAGCATATATCATAATACTCA
1 TATAATCACAGAACACTCAAGCATATATCACAATACTCA
* * *
22402244 TATAATCACATAACATTTAAGCATATATCACAATACTCA
1 TATAATCACAGAACACTCAAGCATATATCACAATACTCA
22402283 AAAACATCTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.45, C:0.23, G:0.04, T:0.28
Consensus pattern (39 bp):
TATAATCACAGAACACTCAAGCATATATCACAATACTCA
Found at i:22402912 original size:28 final size:29
Alignment explanation
Indices: 22402813--22402915 Score: 120
Period size: 30 Copynumber: 3.5 Consensus size: 29
22402803 AGAATTAGTC
* * * *
22402813 TGGGCCTGAGCCCTATACTGTAGCAGTGTG
1 TGGGCCTGAGCCCAATACAGTAACAG-ATG
22402843 TGGGCCAT-AGCCCAATACAGTAACAGAGTG
1 TGGGCC-TGAGCCCAATACAGTAACAGA-TG
*
22402873 TGGGCCTTAGCCCAATACAGTAACA-ATG
1 TGGGCCTGAGCCCAATACAGTAACAGATG
22402901 TGGGCCTGAGCCCAA
1 TGGGCCTGAGCCCAA
22402916 AACAATATTC
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
28 16 0.25
29 2 0.03
30 46 0.71
31 1 0.02
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.20
Consensus pattern (29 bp):
TGGGCCTGAGCCCAATACAGTAACAGATG
Found at i:22403100 original size:26 final size:26
Alignment explanation
Indices: 22403040--22403103 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
22403030 AATATAGCAG
* *
22403040 CAAAGCTGCCAGTAATAATAACACAG
1 CAAAGCTGCTAGTAATAATAACACAA
*
22403066 CAAAACTGCTAGTAATAATAACACAA
1 CAAAGCTGCTAGTAATAATAACACAA
*
22403092 CAGAGCTGCTAG
1 CAAAGCTGCTAG
22403104 AATCAGTAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.45, C:0.22, G:0.16, T:0.17
Consensus pattern (26 bp):
CAAAGCTGCTAGTAATAATAACACAA
Found at i:22403542 original size:27 final size:27
Alignment explanation
Indices: 22403298--22403545 Score: 205
Period size: 27 Copynumber: 9.2 Consensus size: 27
22403288 TATAACAGTC
*
22403298 ATTTTACCCTAT--AGGTGTATTTCGGTC
1 ATTTTACCCT-TCGAGG-GTATTTCGGTA
* * ** *
22403325 ATTTTACCCTTAGGGGGTATTTTAGTC
1 ATTTTACCCTTCGAGGGTATTTCGGTA
* *
22403352 ATTTTACCCTTCGAGGGTATTTCGATC
1 ATTTTACCCTTCGAGGGTATTTCGGTA
* * * *
22403379 ATTGTACCTTTTGAGGGTAATTT-AGTA
1 ATTTTACCCTTCGAGGGT-ATTTCGGTA
* ** **
22403406 AATTTACCCTTCGAAAGTATTTTAGTA
1 ATTTTACCCTTCGAGGGTATTTCGGTA
* *
22403433 ATTTTTCCCTTCGAGGGTATTTTGGTA
1 ATTTTACCCTTCGAGGGTATTTCGGTA
* **
22403460 ATTTTACCCTTCGTGGGTATTTCAATA
1 ATTTTACCCTTCGAGGGTATTTCGGTA
* * *
22403487 ATTTAACCCTTCAAGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGGTA
* *
22403514 ATTTTACCCTTTGAGGGTATCTCGGTA
1 ATTTTACCCTTCGAGGGTATTTCGGTA
22403541 ATTTT
1 ATTTT
22403546 CTCAGGAATC
Statistics
Matches: 178, Mismatches: 39, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
26 5 0.03
27 167 0.94
28 6 0.03
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTCGGTA
Found at i:22405612 original size:28 final size:29
Alignment explanation
Indices: 22405511--22405631 Score: 109
Period size: 30 Copynumber: 4.1 Consensus size: 29
22405501 CATGCAGAAT
* * * *
22405511 CAGTCTGGGCCTGATCCCTATACAGTAGTA
1 CAGTGTGGGCCTTAGCCCAATACAGTA-TA
** * *
22405541 GTGTGTGGGCCATAGCCTAATACAGTAATA
1 CAGTGTGGGCCTTAGCCCAATACAGT-ATA
* *
22405571 GAGTGTAGGCCTTAGCCCAATACAGTA-A
1 CAGTGTGGGCCTTAGCCCAATACAGTATA
* *
22405599 CAGTGTGGGCCTTAGCCCAAAACAGTATT
1 CAGTGTGGGCCTTAGCCCAATACAGTATA
22405628 CAGT
1 CAGT
22405632 ACAAATGCAG
Statistics
Matches: 73, Mismatches: 16, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
28 25 0.34
29 5 0.07
30 42 0.58
31 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (29 bp):
CAGTGTGGGCCTTAGCCCAATACAGTATA
Found at i:22405839 original size:26 final size:26
Alignment explanation
Indices: 22405741--22405840 Score: 121
Period size: 26 Copynumber: 3.8 Consensus size: 26
22405731 CCAATATCGT
* *
22405741 AGCAAAGCTGCCAGTAATAATAACGC
1 AGCAAAGCTGCCAGTAACAGTAACGC
*
22405767 AGCAAAGCTGCCAGTAACAGTAACAC
1 AGCAAAGCTGCCAGTAACAGTAACGC
* *
22405793 AGCAGAGCTGCCA-AAATCAGTAACGC
1 AGCAAAGCTGCCAGTAA-CAGTAACGC
* *
22405819 AGCAAAGCTACTAGTAACAGTA
1 AGCAAAGCTGCCAGTAACAGTA
22405841 TTTGTGGCAA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
25 2 0.03
26 58 0.94
27 2 0.03
ACGTcount: A:0.42, C:0.24, G:0.20, T:0.14
Consensus pattern (26 bp):
AGCAAAGCTGCCAGTAACAGTAACGC
Found at i:22406167 original size:27 final size:27
Alignment explanation
Indices: 22406011--22406253 Score: 271
Period size: 27 Copynumber: 9.0 Consensus size: 27
22406001 AGGGGTATAA
22406011 CAGTCATTTTACCCTAT-G-GGAGTATTT
1 CAGTCATTTTACCCT-TCGAGG-GTATTT
22406038 CTA-TCATTTTACCCTTCG-GAGGTATTT
1 C-AGTCATTTTACCCTTCGAG-GGTATTT
22406065 CAGTCATTTTACCCTTCGAGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
* *
22406092 CAGTCATTTTACCTTTCAAGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
* *
22406119 CGGTCATTTTACCCGTCGAGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
* *
22406146 CAATCATTTTACCCTTCAAGGGTATGTT
1 CAGTCATTTTACCCTTCGAGGGTAT-TT
* *
22406174 -AGTAATTTTACCCTTCAAGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
* * * *
22406200 CGGTAATTTTACCTTTTGAGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
* * *
22406227 TAGTAATTTTACCCTTCGAGGATATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
22406254 TGGTAATTTA
Statistics
Matches: 188, Mismatches: 21, Indels: 14
0.84 0.09 0.06
Matches are distributed among these distances:
26 4 0.02
27 179 0.95
28 5 0.03
ACGTcount: A:0.21, C:0.19, G:0.18, T:0.42
Consensus pattern (27 bp):
CAGTCATTTTACCCTTCGAGGGTATTT
Found at i:22425163 original size:27 final size:27
Alignment explanation
Indices: 22425129--22425413 Score: 381
Period size: 27 Copynumber: 10.6 Consensus size: 27
22425119 AGACCCCAAA
* *
22425129 ATAGGGTAAAATGACTGAAATACCCTC
1 ATAGGGTAAAATGACCGAAATACCCCC
* *
22425156 ATAAGGTAAAATGACCGAAATACCCTC
1 ATAGGGTAAAATGACCGAAATACCCCC
* *
22425183 ATAGGGCAAAATAACCGAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
* * *
22425210 ATAGGCTAGAATGACCGAAATACCCTC
1 ATAGGGTAAAATGACCGAAATACCCCC
*
22425237 ATAGGGTAAAATGAGCGAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
* *
22425264 ATAGGATAAAATGATCGAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
* * * *
22425291 ATAGGGTAAAATGTCTGGAATACCCCT
1 ATAGGGTAAAATGACCGAAATACCCCC
*
22425318 ATAGGGTAAAATGACCGAAATACCCCT
1 ATAGGGTAAAATGACCGAAATACCCCC
* **
22425345 ATAGGGTAAAATGACCAAAATACCCTT
1 ATAGGGTAAAATGACCGAAATACCCCC
22425372 ATAGGGTAAAATGACCGAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCCC
*
22425399 ATAAGGTAAAATGAC
1 ATAGGGTAAAATGAC
22425414 ATGTATGATA
Statistics
Matches: 226, Mismatches: 32, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 226 1.00
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.19
Consensus pattern (27 bp):
ATAGGGTAAAATGACCGAAATACCCCC
Found at i:22438458 original size:17 final size:17
Alignment explanation
Indices: 22438432--22438467 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
22438422 GGAAATGGAT
*
22438432 TTCCAGTTCTAAAATAG
1 TTCCACTTCTAAAATAG
22438449 TTCCACTTCTAAAATAG
1 TTCCACTTCTAAAATAG
22438466 TT
1 TT
22438468 TGCAAGGGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.39
Consensus pattern (17 bp):
TTCCACTTCTAAAATAG
Found at i:22443348 original size:25 final size:25
Alignment explanation
Indices: 22443313--22443371 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
22443303 TTTTAGAATT
*
22443313 AAATCAAATCTAACAAAAT-ACCAT
1 AAATCAAATCTAACAAAATAACCAC
22443337 ACAATCAAATCTAACAAAATAACCAC
1 A-AATCAAATCTAACAAAATAACCAC
22443363 AAATCAAAT
1 AAATCAAAT
22443372 GAAACAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 1 0.03
25 26 0.81
26 5 0.16
ACGTcount: A:0.59, C:0.22, G:0.00, T:0.19
Consensus pattern (25 bp):
AAATCAAATCTAACAAAATAACCAC
Found at i:22446588 original size:147 final size:148
Alignment explanation
Indices: 22446214--22446610 Score: 523
Period size: 147 Copynumber: 2.6 Consensus size: 148
22446204 TTTTGGTTTT
*
22446214 TTTTAAAAGGAGAAAGTTTAAATTTTTAAAACAAAGTTTTGATTTTTTTGTCAACTATTTCGAAA
1 TTTTAAAA-GA-AAAGTTTAAAATTTTAAAACAAAGTTTTGA-TTTTTT-TCAACTATTTC-AAA
* * * *
22446279 TAAAAGTTTTGATCTTTAAGAAAAATAGTAATTTTTTAAAAGAAAAAAAGAGAAAGTTTAGATTT
61 AAAAAGATTTGATCTTTAAGAAAAATAGTGA---TTT--AAGAAAAAAACAGAAAGTTTAGATTT
* *
22446344 TTAAAAATAACAATTTGTTTTTTTGTCA
121 TTAAAAATAAAAATATGTTTTTTTGTCA
* ** *
22446372 TTTT-AAAGAAAAGTTT-AAATTTTAAAACAAATTTTTGATTTTTTTCAACTATTTTGAAATAAA
1 TTTTAAAAGAAAAGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTCAACTATTTCAAAAAAAA
*
22446435 GCTTTGATCTTTAAGAAAAATAGTGATTT-A-AAAAAAACAGAAAGTTTAGATTTTTAAAAATAA
66 GATTTGATCTTTAAGAAAAATAGTGATTTAAGAAAAAAACAGAAAGTTTAGATTTTTAAAAATAA
22446498 AAATATGTTTTTTTAGTCA
131 AAATATGTTTTTTT-GTCA
*
22446517 TTTTAAAAGAAAAGTTTAAAATTTTAAAACAAAGTTTTGATCTTTTTCAACTATTTCAAAAAAAA
1 TTTTAAAAGAAAAGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTCAACTATTTCAAAAAAAA
* * *
22446582 GATTTGATTTTTAAGAAAAGTAATGATTT
66 GATTTGATCTTTAAGAAAAATAGTGATTT
22446611 TTTTAAAAGA
Statistics
Matches: 216, Mismatches: 20, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
144 44 0.20
145 9 0.04
146 12 0.06
147 67 0.31
148 3 0.01
151 29 0.13
152 10 0.05
153 6 0.03
154 20 0.09
155 7 0.03
156 2 0.01
157 3 0.01
158 4 0.02
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.41
Consensus pattern (148 bp):
TTTTAAAAGAAAAGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTCAACTATTTCAAAAAAAA
GATTTGATCTTTAAGAAAAATAGTGATTTAAGAAAAAAACAGAAAGTTTAGATTTTTAAAAATAA
AAATATGTTTTTTTGTCA
Found at i:22448703 original size:20 final size:21
Alignment explanation
Indices: 22448672--22448711 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
22448662 TGTTTGTACA
*
22448672 TATTAGATTTATTTATTTGTG
1 TATTAGATTTATTTAATTGTG
22448693 TATTA-ATTTATTTAATTGT
1 TATTAGATTTATTTAATTGT
22448712 CTAATGTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (21 bp):
TATTAGATTTATTTAATTGTG
Found at i:22450717 original size:29 final size:29
Alignment explanation
Indices: 22450662--22450717 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
22450652 TGTGTCAGTG
* **
22450662 CAATTCAAGGGAAAGAGGAAGGTCCCAAA
1 CAATTCAAGGGAAAGAGAAAGAACCCAAA
*
22450691 CAATTCAAGGGAAAGATAAAGAACCCA
1 CAATTCAAGGGAAAGAGAAAGAACCCA
22450718 GATGATGTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (29 bp):
CAATTCAAGGGAAAGAGAAAGAACCCAAA
Found at i:22451625 original size:19 final size:20
Alignment explanation
Indices: 22451601--22451638 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
22451591 GTTTATTTAG
22451601 AAACATTATTT-TGAAAAAA
1 AAACATTATTTATGAAAAAA
*
22451620 AAACATTTTTTATGAAAAA
1 AAACATTATTTATGAAAAA
22451639 TCCAAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (20 bp):
AAACATTATTTATGAAAAAA
Found at i:22455510 original size:19 final size:21
Alignment explanation
Indices: 22455479--22455521 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
22455469 TTTAAAAATC
22455479 AATAAATAATA-TTTCAGAAA
1 AATAAATAATATTTTCAGAAA
*
22455499 AATAAA-AATATTTTTAGAAA
1 AATAAATAATATTTTCAGAAA
22455519 AAT
1 AAT
22455522 TAATTGTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (21 bp):
AATAAATAATATTTTCAGAAA
Found at i:22456768 original size:20 final size:20
Alignment explanation
Indices: 22456722--22456770 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
22456712 ATCACGGTCT
22456722 TTGCTT-CTTCTTTACTTAC
1 TTGCTTACTTCTTTACTTAC
* *
22456741 TCT-ATTACTTGTTTACTTAC
1 T-TGCTTACTTCTTTACTTAC
22456761 TTGCTTACTT
1 TTGCTTACTT
22456771 AAATAACTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.14, C:0.22, G:0.06, T:0.57
Consensus pattern (20 bp):
TTGCTTACTTCTTTACTTAC
Found at i:22457097 original size:50 final size:50
Alignment explanation
Indices: 22456973--22457158 Score: 216
Period size: 50 Copynumber: 3.7 Consensus size: 50
22456963 GATAATAACA
* * *
22456973 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTT-TCCTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATAT-CGG
* * *
22457022 TGCCAATGCCATATCCCAAATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
* ** ** *
22457072 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
*
22457122 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
22457159 TCTCATTCCC
Statistics
Matches: 115, Mismatches: 19, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
48 4 0.03
49 37 0.32
50 74 0.64
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
Found at i:22478767 original size:136 final size:136
Alignment explanation
Indices: 22478515--22478768 Score: 332
Period size: 136 Copynumber: 1.9 Consensus size: 136
22478505 GTTTACCGTA
* * * * * *
22478515 TTTCAGGTGGTGGTCTTGAATGTCCTACTAGTGGCTGAGTTCTGACATTTGTTACGGATACTCGA
1 TTTCAAGTGCTGGTCTTGAATGTCCTACCAATGGCTGAGTTCTAACATTTCTTACGGATACTCGA
**
22478580 TAGCTTGAGGAGCAGCACCATGTAGCTACGTTCTGACCGACAGCTTGTGTGAGCAGACCCAGGTT
66 TAGCTTGAGGAGCAGCACCATGTAGCTACGTTCTGACCGACAGCTCATGTGAGCAGACCCAGGTT
22478645 ATCATG
131 ATCATG
* * *
22478651 TTTCAAGTGCTGGTCTTGAATGTCCTACCAATGGCTGAGTT-TCAACGTTTCTTTCGGATACTGG
1 TTTCAAGTGCTGGTCTTGAATGTCCTACCAATGGCTGAGTTCT-AACATTTCTTACGGATACTCG
* * * * *
22478715 ATAGCTTGTGGAGCAGCATCGTGTAGTTACGTT-TCGACCGATAGCTCATGTGAG
65 ATAGCTTGAGGAGCAGCACCATGTAGCTACGTTCT-GACCGACAGCTCATGTGAG
22478769 TAGGCTCATT
Statistics
Matches: 100, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
135 2 0.02
136 98 0.98
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (136 bp):
TTTCAAGTGCTGGTCTTGAATGTCCTACCAATGGCTGAGTTCTAACATTTCTTACGGATACTCGA
TAGCTTGAGGAGCAGCACCATGTAGCTACGTTCTGACCGACAGCTCATGTGAGCAGACCCAGGTT
ATCATG
Found at i:22482189 original size:21 final size:21
Alignment explanation
Indices: 22482165--22482205 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
22482155 GAAATCCATT
* *
22482165 TCATCATCTCCTTCTTCTTCG
1 TCATCACCTCCTTCCTCTTCG
*
22482186 TCATCCCCTCCTTCCTCTTC
1 TCATCACCTCCTTCCTCTTC
22482206 ATTTTCACGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.07, C:0.46, G:0.02, T:0.44
Consensus pattern (21 bp):
TCATCACCTCCTTCCTCTTCG
Found at i:22483442 original size:23 final size:22
Alignment explanation
Indices: 22483416--22483463 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
22483406 AAATAAGGGG
22483416 ATAATATGTATTTA-GGTTAGAAA
1 ATAA-ATGTATTTATGGTTA-AAA
* *
22483439 ATAAGTGTTTTTATGGTTAAAA
1 ATAAATGTATTTATGGTTAAAA
22483461 ATA
1 ATA
22483464 GGGTAAAGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.42, C:0.00, G:0.17, T:0.42
Consensus pattern (22 bp):
ATAAATGTATTTATGGTTAAAA
Found at i:22500838 original size:32 final size:32
Alignment explanation
Indices: 22500797--22500858 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
22500787 CTTGCACTAG
*
22500797 TGTATATTCATATACAATGCATTAATTAAATA
1 TGTATATTCATATACAACGCATTAATTAAATA
22500829 TGTATATTCATATACAACGCATTAATTAAA
1 TGTATATTCATATACAACGCATTAATTAAA
22500859 AATATTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.39
Consensus pattern (32 bp):
TGTATATTCATATACAACGCATTAATTAAATA
Found at i:22501046 original size:63 final size:64
Alignment explanation
Indices: 22500974--22501155 Score: 271
Period size: 64 Copynumber: 2.9 Consensus size: 64
22500964 AAATAAAATA
*
22500974 AAAATTGGATCATTAGATATAATCAAGTAAACAAGTTGATTAAAAAA-ATATT-TAT-AACATAT
1 AAAATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACA-ATTAT-TGAACATAT
*
22501036 T
64 G
* * *
22501037 AAAATTGGATCATTAGATATAATCAAGTAAATAACTTGATTAAAAAACAATTATTGGATATATG
1 AAAATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACAATTATTGAACATATG
*
22501101 AAAATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACAAATATT
1 AAAATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACAATTATT
22501156 CATTGTTAAT
Statistics
Matches: 109, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
63 49 0.45
64 60 0.55
ACGTcount: A:0.51, C:0.07, G:0.10, T:0.32
Consensus pattern (64 bp):
AAAATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACAATTATTGAACATATG
Found at i:22502745 original size:49 final size:49
Alignment explanation
Indices: 22502688--22502791 Score: 147
Period size: 49 Copynumber: 2.1 Consensus size: 49
22502678 TCATGTGTTA
* * * *
22502688 TAATTTTATACAGTGTTGA-GTTTGTGATTCATGATATTGAACTCAATTT
1 TAATTTTATAAAGTGTTCACCTTT-TGATTCATGATATTAAACTCAATTT
*
22502737 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTCAATTT
22502786 TAATTT
1 TAATTT
22502792 CTTTTTTTTC
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
49 46 0.94
50 3 0.06
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.49
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTCAATTT
Found at i:22504510 original size:44 final size:44
Alignment explanation
Indices: 22504447--22504583 Score: 238
Period size: 44 Copynumber: 3.1 Consensus size: 44
22504437 TTACACCTCT
22504447 ATTCCATTCAACCAAACACAAGAATACCATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACACAAGAATACCATTACGCCTCTATTCC
22504491 ATTCCATTCAACCAAACACAAGAATACCATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACACAAGAATACCATTACGCCTCTATTCC
* *
22504535 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTTTATTCC
1 ATTCCATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTATTCC
22504581 ATT
1 ATT
22504584 ACAGCGAACC
Statistics
Matches: 89, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
44 67 0.75
45 4 0.04
46 18 0.20
ACGTcount: A:0.36, C:0.31, G:0.04, T:0.28
Consensus pattern (44 bp):
ATTCCATTCAACCAAACACAAGAATACCATTACGCCTCTATTCC
Found at i:22505166 original size:41 final size:39
Alignment explanation
Indices: 22505115--22505354 Score: 159
Period size: 41 Copynumber: 6.0 Consensus size: 39
22505105 GAAGACTATC
* * *
22505115 AGGCTCAAAGCCTGATATAACGCACCGGCATAAAGCCTACT
1 AGGCACAAAGCCTGATATAA-GCACCGGCA-GAAGCCTGCT
* * **
22505156 AGGCAGAAAGCCTGATATAATACACCAACACGAAGCCTGCT
1 AGGCACAAAGCCTGATATAA-GCACCGGCA-GAAGCCTGCT
* *
22505197 AGGAACAAAGCCTGATATAAGACATCGGCAGAAGCCTGCT
1 AGGCACAAAGCCTGATATAAG-CACCGGCAGAAGCCTGCT
* * * * *
22505237 AGGCACAGAG-CTAGA-AT-ATCACTGGCACAAAGCCAGCT
1 AGGCACAAAGCCT-GATATAAGCACCGGCA-GAAGCCTGCT
* * * *
22505275 AGGCACAAAGCCTGAT-T-ATCACTGGCACCAATCCTGCT
1 AGGCACAAAGCCTGATATAAGCACCGGCA-GAAGCCTGCT
* *
22505313 AGGCACAAAGTC-GAATATAATACACCGGCACGAAGCCTGCT
1 AGGCACAAAGCCTG-ATATAA-GCACCGGCA-GAAGCCTGCT
22505354 A
1 A
22505355 CACACAGAGC
Statistics
Matches: 159, Mismatches: 31, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
37 7 0.04
38 52 0.33
39 7 0.04
40 21 0.13
41 72 0.45
ACGTcount: A:0.36, C:0.27, G:0.21, T:0.16
Consensus pattern (39 bp):
AGGCACAAAGCCTGATATAAGCACCGGCAGAAGCCTGCT
Found at i:22505279 original size:38 final size:38
Alignment explanation
Indices: 22505141--22505330 Score: 143
Period size: 38 Copynumber: 4.9 Consensus size: 38
22505131 ATAACGCACC
* * * *
22505141 GGCATAAAGCCTACTAGGCAGAAAGCCTGATATAATACACC
1 GGCACAAAGCCTGCTAGGCACAAAGCCTGA-AT-AT-CACT
** * * **
22505182 AACACGAAGCCTGCTAGGAACAAAGCCTGATATAAGACAT
1 GGCACAAAGCCTGCTAGGCACAAAGCCTGA-ATATCAC-T
* *
22505222 CGGCA-GAAGCCTGCTAGGCACAGAG-CTAGAATATCACT
1 -GGCACAAAGCCTGCTAGGCACAAAGCCT-GAATATCACT
* *
22505260 GGCACAAAGCCAGCTAGGCACAAAGCCTGATTATCACT
1 GGCACAAAGCCTGCTAGGCACAAAGCCTGAATATCACT
* * *
22505298 GGCACCAATCCTGCTAGGCACAAAGTC-GAATAT
1 GGCACAAAGCCTGCTAGGCACAAAGCCTGAATAT
22505331 AATACACCGG
Statistics
Matches: 119, Mismatches: 25, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
37 9 0.08
38 50 0.42
39 11 0.09
40 21 0.18
41 28 0.24
ACGTcount: A:0.36, C:0.26, G:0.22, T:0.16
Consensus pattern (38 bp):
GGCACAAAGCCTGCTAGGCACAAAGCCTGAATATCACT
Found at i:22511748 original size:21 final size:21
Alignment explanation
Indices: 22511723--22511763 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
22511713 TAGTGTACTT
*
22511723 ATCCATAACCTAGATAAATTC
1 ATCCATAACCTAAATAAATTC
*
22511744 ATCCATAACTTAAATAAATT
1 ATCCATAACCTAAATAAATT
22511764 TTGCACATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.32
Consensus pattern (21 bp):
ATCCATAACCTAAATAAATTC
Found at i:22512263 original size:41 final size:41
Alignment explanation
Indices: 22512186--22512535 Score: 306
Period size: 41 Copynumber: 8.8 Consensus size: 41
22512176 ACTTACTTGG
** * * * *
22512186 TATAATACATTGGCACGAAGACTGCCAGGCTCAAAGCTTGA
1 TATAATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGA
* ** ** * *
22512227 TATAACACATTGGCATAAAGCCTGCTAGGCAGAAAGCCTAA
1 TATAATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGA
* * *
22512268 TATAATACACTGGCACGAA-CCTTGGTAGGCACAAAACCTGA
1 TATAATACACCGGCACGAAGCC-TGCTAGGCACAAAGCCTGA
** * * *
22512309 TATAATACACCAACACAAAGCCTACTAGGCACAAATCCTGA
1 TATAATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGA
*
22512350 TATAATACACCGGCACGAAGTCTGCTAGGCACAAAGCCTGA
1 TATAATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGA
* * *
22512391 TATAATACACCGGCACGAAGCCTGCTAGGCATAGAGCC-CA
1 TATAATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGA
* * * * *
22512431 AAT-AT-CACCAGCACAAAGCCTGCTAGGCACAGAGCCCGA
1 TATAATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGA
* * *
22512470 -AT-AT-CACCAGCACAAAGCCTGCTAGGCACAAAGCTTGA
1 TATAATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGA
* *
22512508 T-T-AT-CACCGGCACAAAGCCTGTTAGGCA
1 TATAATACACCGGCACGAAGCCTGCTAGGCA
22512536 TAGAGCCCGA
Statistics
Matches: 261, Mismatches: 44, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
38 88 0.34
39 3 0.01
40 5 0.02
41 163 0.62
42 2 0.01
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.17
Consensus pattern (41 bp):
TATAATACACCGGCACGAAGCCTGCTAGGCACAAAGCCTGA
Found at i:22512455 original size:38 final size:38
Alignment explanation
Indices: 22512312--22512548 Score: 224
Period size: 38 Copynumber: 6.1 Consensus size: 38
22512302 AACCTGATAT
* * * * *
22512312 AATA-CACCAACACAAAGCCTACTAGGCACAAATCCTG
1 AATATCACCAGCACAAAGCCTGCTAGGCACAGAGCCCG
* * * * *
22512349 ATATAATACACCGGCACGAAGTCTGCTAGGCACAAAGCCTG
1 A-AT-AT-CACCAGCACAAAGCCTGCTAGGCACAGAGCCCG
* * * *
22512390 ATATAATACACCGGCACGAAGCCTGCTAGGCATAGAGCCCA
1 A-AT-AT-CACCAGCACAAAGCCTGCTAGGCACAGAGCCCG
22512431 AATATCACCAGCACAAAGCCTGCTAGGCACAGAGCCCG
1 AATATCACCAGCACAAAGCCTGCTAGGCACAGAGCCCG
* **
22512469 AATATCACCAGCACAAAGCCTGCTAGGCACAAAGCTTG
1 AATATCACCAGCACAAAGCCTGCTAGGCACAGAGCCCG
* * * *
22512507 ATTATCACCGGCACAAAGCCTGTTAGGCATAGAGCCCG
1 AATATCACCAGCACAAAGCCTGCTAGGCACAGAGCCCG
22512545 AATA
1 AATA
22512549 ACGTTACATT
Statistics
Matches: 170, Mismatches: 26, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
37 1 0.01
38 100 0.59
39 3 0.02
40 2 0.01
41 64 0.38
ACGTcount: A:0.36, C:0.30, G:0.19, T:0.15
Consensus pattern (38 bp):
AATATCACCAGCACAAAGCCTGCTAGGCACAGAGCCCG
Found at i:22513562 original size:14 final size:14
Alignment explanation
Indices: 22513543--22513582 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
22513533 TTGATTGCCA
22513543 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
22513557 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
22513571 GGAAAATGTTTT
1 GTAAAATGTTTT
22513583 ACTTTTCTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:22519382 original size:30 final size:30
Alignment explanation
Indices: 22519346--22519402 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
22519336 CACATTTAAC
* *
22519346 ATAGAACAGCCATAAAGGCTTCTACATATA
1 ATAGAACAGCCACAAAGGCTTCCACATATA
*
22519376 ATAGAACAGTCACAAAGGCTTCCACAT
1 ATAGAACAGCCACAAAGGCTTCCACAT
22519403 TTTGGTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.42, C:0.23, G:0.14, T:0.21
Consensus pattern (30 bp):
ATAGAACAGCCACAAAGGCTTCCACATATA
Found at i:22525554 original size:20 final size:20
Alignment explanation
Indices: 22525531--22525570 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
22525521 GTAGTGTTAT
*
22525531 ACAGAGGCACCGAATTGCAA
1 ACAGAGGCACCGAAGTGCAA
*
22525551 ACAGAGGCATCGAAGTGCAA
1 ACAGAGGCACCGAAGTGCAA
22525571 TCCTGTACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.23, G:0.28, T:0.10
Consensus pattern (20 bp):
ACAGAGGCACCGAAGTGCAA
Found at i:22528437 original size:14 final size:14
Alignment explanation
Indices: 22528418--22528452 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
22528408 ATAATTAAAC
*
22528418 TTTAATTAAGTTAA
1 TTTAATTAACTTAA
22528432 TTTAATTAACTTAA
1 TTTAATTAACTTAA
22528446 -TTAATTA
1 TTTAATTA
22528453 CTAACCCCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (14 bp):
TTTAATTAACTTAA
Found at i:22532387 original size:16 final size:16
Alignment explanation
Indices: 22532366--22532397 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
22532356 CTCTCTTTAA
22532366 CATGAAACACATATAT
1 CATGAAACACATATAT
*
22532382 CATGAATCACATATAT
1 CATGAAACACATATAT
22532398 GTACACATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.19, G:0.06, T:0.28
Consensus pattern (16 bp):
CATGAAACACATATAT
Found at i:22534386 original size:19 final size:20
Alignment explanation
Indices: 22534349--22534393 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
22534339 TGTTATCTAT
*
22534349 ATCTTAATTAATATAGTTTA
1 ATCTTAAATAATATAGTTTA
22534369 ATCTTAAATAAT-TAGTTTA
1 ATCTTAAATAATATAGTTTA
22534388 ATCTTA
1 ATCTTA
22534394 GTTTAGTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (20 bp):
ATCTTAAATAATATAGTTTA
Found at i:22552538 original size:259 final size:255
Alignment explanation
Indices: 22552071--22552538 Score: 645
Period size: 259 Copynumber: 1.8 Consensus size: 255
22552061 AAAAGTATTC
* * *
22552071 TTCCGTATTTAGAATAAGTTATGTTATTAAATGGTACTTTAACTTTTTATTCTTTTTAAAAAATA
1 TTCCGTATTTAGAATAAGTTATATTATTAAACGGTACTTTAACGTTTTATTCTTTTTAAAAAATA
* * * **
22552136 AAAACTTTGCTTATTGAGATACTTGAACCCATACCATTTGCATCAATAAATTTTAACTTTACCAC
66 AAAAC-TTGCTTATTAAGATA-TTAAACCCATACCAATTGCATCAATAAACCTTAACTTTACCAC
* * *
22552201 TCAACCAAAATTTTATTTTACTATATTTTATACATTTTAATATTATTATGCATACTTTATTACCT
129 TCAAACAAAATTTTATTTTAATATATTTTATACATTTTAATATTATTATGCACACTTTATTACCT
*
22552266 CCGTCAATTGTATATCTATATTTATTTCTATTTAAACCCCTAACTAAGTTACGGAAATGTCT
194 CCATCAATTGTATATCTATATTTATTTCTATTTAAACCCCTAACTAAGTTACGGAAATGTCT
** *
22552328 TTCCGTATTTAGAATAAGTTATATTATTTGACGGTACTTTAGTCGTTTTATTCTTTTTAAAAATC
1 TTCCGTATTTAGAATAAGTTATATTATTAAACGGTACTTTA-ACGTTTTATTCTTTTT-AAAA--
* **
22552393 AATAAAAA-TTGCTTATGATAAGAT-TTAAACTCATGTCAATTGCATCAATAAAACCTTAACTTT
62 AATAAAAACTTGCTTAT--TAAGATATTAAACCCATACCAATTGCATCAAT-AAACCTTAACTTT
* *
22552456 ACCACTCAAACAAAATTTTATTTTAATAT-TTTTATACATTTTAATTTTATTGTGCACACTTTAT
124 ACCACTCAAACAAAATTTTATTTTAATATATTTTATACATTTTAATATTATTATGCACACTTTAT
*
22552520 TACCTCCATCATTTGTATA
189 TACCTCCATCAATTGTATA
22552539 CATTGATAAT
Statistics
Matches: 183, Mismatches: 21, Indels: 12
0.85 0.10 0.06
Matches are distributed among these distances:
257 37 0.20
258 14 0.08
259 81 0.44
260 38 0.21
261 13 0.07
ACGTcount: A:0.34, C:0.15, G:0.07, T:0.44
Consensus pattern (255 bp):
TTCCGTATTTAGAATAAGTTATATTATTAAACGGTACTTTAACGTTTTATTCTTTTTAAAAAATA
AAAACTTGCTTATTAAGATATTAAACCCATACCAATTGCATCAATAAACCTTAACTTTACCACTC
AAACAAAATTTTATTTTAATATATTTTATACATTTTAATATTATTATGCACACTTTATTACCTCC
ATCAATTGTATATCTATATTTATTTCTATTTAAACCCCTAACTAAGTTACGGAAATGTCT
Found at i:22558177 original size:14 final size:14
Alignment explanation
Indices: 22558158--22558194 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
22558148 GTTTGGTTTA
22558158 GAGGAAAATTCGAG
1 GAGGAAAATTCGAG
* *
22558172 GAGGAAATTTTGAG
1 GAGGAAAATTCGAG
22558186 GAGGAAAAT
1 GAGGAAAAT
22558195 AAATAATCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.43, C:0.03, G:0.35, T:0.19
Consensus pattern (14 bp):
GAGGAAAATTCGAG
Found at i:22559558 original size:26 final size:26
Alignment explanation
Indices: 22559514--22559567 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
22559504 GTTCACTCTA
*
22559514 TTTAAGATGAGGCACCAAATTAATTG
1 TTTAAGATGAGGCACCAAACTAATTG
* *
22559540 TTTAAGGTGAGGCGA-CAAACTGATTG
1 TTTAAGATGAGGC-ACCAAACTAATTG
22559566 TT
1 TT
22559568 CTAGTGGTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.31
Consensus pattern (26 bp):
TTTAAGATGAGGCACCAAACTAATTG
Found at i:22560342 original size:94 final size:94
Alignment explanation
Indices: 22560141--22560454 Score: 285
Period size: 94 Copynumber: 3.4 Consensus size: 94
22560131 AATATCCATT
* * * * * * * *
22560141 TTGGGGTGTCTACTTTGTAACTTTACAAAATTAAGTTAAGTACCTTAAAAGAGTCTAGAAGTAG-
1 TTGGGGTGTCTGCTTTATAACTTTGCAAAATAAAGCTAAGTGCC-T-GAAGAGACTAGAAGTAGT
* * *
22560205 --TTCTATTAAACATAGCGAGCAA-TTTCCTC
64 TCTTCTATTAAACTTAGCAAG-AAGTCTCCTC
* *** ** **
22560234 TTGGGGTGCCTGCTTTATAACTTTGTTGAATTTATTTAAGTGCCTGAAGAGACTAGAAGTAGTTC
1 TTGGGGTGTCTGCTTTATAACTTTGCAAAATAAAGCTAAGTGCCTGAAGAGACTAGAAGTAGTTC
* *
22560299 TTCTTTTAAACTTAGCAAGTAGTCTCCTC
66 TTCTATTAAACTTAGCAAGAAGTCTCCTC
* * * * * * * *
22560328 TTGAGGTGTTTGCTTTGTAACTTTGCAAAATAAAGCTAAGTGCCTTATGAGGCTATAAGTGGTTC
1 TTGGGGTGTCTGCTTTATAACTTTGCAAAATAAAGCTAAGTGCCTGAAGAGACTAGAAGTAGTTC
**
22560393 TTCTATTAAACTTAGTGAGAAGTCTCCTC
66 TTCTATTAAACTTAGCAAGAAGTCTCCTC
*
22560422 TCGGGGTGTCTGCTTTATAACTTTGCAAAATAA
1 TTGGGGTGTCTGCTTTATAACTTTGCAAAATAA
22560455 CATGCTATAA
Statistics
Matches: 176, Mismatches: 41, Indels: 7
0.79 0.18 0.03
Matches are distributed among these distances:
91 15 0.09
92 1 0.01
93 35 0.20
94 125 0.71
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (94 bp):
TTGGGGTGTCTGCTTTATAACTTTGCAAAATAAAGCTAAGTGCCTGAAGAGACTAGAAGTAGTTC
TTCTATTAAACTTAGCAAGAAGTCTCCTC
Found at i:22562803 original size:19 final size:19
Alignment explanation
Indices: 22562779--22562816 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
22562769 CAATCAAGGG
22562779 TAATTAGCGACTTAATTGA
1 TAATTAGCGACTTAATTGA
* *
22562798 TAATTAGTGATTTAATTGA
1 TAATTAGCGACTTAATTGA
22562817 AAATAGGCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (19 bp):
TAATTAGCGACTTAATTGA
Found at i:22563127 original size:2 final size:2
Alignment explanation
Indices: 22563122--22563148 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
22563112 ACTTAATTTC
22563122 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
22563149 TNNNNNNNNN
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:22565811 original size:23 final size:23
Alignment explanation
Indices: 22565780--22565828 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
22565770 ACCTACTTTC
* *
22565780 TTACTGTAGTAATTTTCGGGGTA
1 TTACAGTAGTAATTTTCGGGATA
22565803 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
22565826 TTA
1 TTA
22565829 TACCGGTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.08, G:0.22, T:0.43
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:22581876 original size:33 final size:33
Alignment explanation
Indices: 22581834--22581899 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
22581824 ATAAACAAGA
22581834 ATCGAATGAAATAGTGACTTTAATCAAAATTAT
1 ATCGAATGAAATAGTGACTTTAATCAAAATTAT
22581867 ATCGAATGAAATAGTGACTTTAATCAAAATTAT
1 ATCGAATGAAATAGTGACTTTAATCAAAATTAT
22581900 CTCATGGGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.33
Consensus pattern (33 bp):
ATCGAATGAAATAGTGACTTTAATCAAAATTAT
Found at i:22582522 original size:14 final size:15
Alignment explanation
Indices: 22582486--22582522 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
22582476 AATGTTTCAC
*
22582486 TTCCTTCATTCTCTT
1 TTCCTTCTTTCTCTT
22582501 TTCC-TCTTTCTC-T
1 TTCCTTCTTTCTCTT
22582514 TTCCTTCTT
1 TTCCTTCTT
22582523 CTTGCCTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 5 0.25
14 11 0.55
15 4 0.20
ACGTcount: A:0.03, C:0.35, G:0.00, T:0.62
Consensus pattern (15 bp):
TTCCTTCTTTCTCTT
Found at i:22584242 original size:18 final size:19
Alignment explanation
Indices: 22584219--22584267 Score: 82
Period size: 18 Copynumber: 2.6 Consensus size: 19
22584209 GATGACAAAG
22584219 ATGAGAAATGG-ATATGAA
1 ATGAGAAATGGAATATGAA
22584237 ATGAGAAATGGAATATGAA
1 ATGAGAAATGGAATATGAA
22584256 ATGATGAAATGG
1 ATGA-GAAATGG
22584268 GATGAGTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.38
19 11 0.38
20 7 0.24
ACGTcount: A:0.49, C:0.00, G:0.29, T:0.22
Consensus pattern (19 bp):
ATGAGAAATGGAATATGAA
Found at i:22591660 original size:21 final size:21
Alignment explanation
Indices: 22591634--22591674 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
22591624 AAGTTATACC
22591634 TTTTTTTACCAATCGATAGCT
1 TTTTTTTACCAATCGATAGCT
22591655 TTTTTTTACCAATCGATAGC
1 TTTTTTTACCAATCGATAGC
22591675 CGAAGCTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (21 bp):
TTTTTTTACCAATCGATAGCT
Found at i:22591703 original size:30 final size:30
Alignment explanation
Indices: 22591669--22591813 Score: 96
Period size: 30 Copynumber: 4.8 Consensus size: 30
22591659 TTTACCAATC
**
22591669 GATAGCCGAAGCTAACTGATTTCATAATTT
1 GATAGCCGAAGCTAACCCATTTCATAATTT
* *
22591699 GATAGCCGAAGCTATCCCTTTTCATAATTT
1 GATAGCCGAAGCTAACCCATTTCATAATTT
** * * * * *
22591729 GACGGTCG--TCTCCATCCATTTTCACAATTT
1 GATAGCCGAAGCT-AACCCA-TTTCATAATTT
* * * *
22591759 GATAGTCGAAGCTATCCCTTTTCATAATTC
1 GATAGCCGAAGCTAACCCATTTCATAATTT
* * *
22591789 GATAGCAGAAGCTATCCCTTTTCAT
1 GATAGCCGAAGCTAACCCATTTCAT
22591814 TGTTCGATGG
Statistics
Matches: 87, Mismatches: 24, Indels: 8
0.73 0.20 0.07
Matches are distributed among these distances:
28 2 0.02
29 2 0.02
30 79 0.91
31 2 0.02
32 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.35
Consensus pattern (30 bp):
GATAGCCGAAGCTAACCCATTTCATAATTT
Found at i:22591811 original size:60 final size:60
Alignment explanation
Indices: 22591688--22591812 Score: 144
Period size: 60 Copynumber: 2.1 Consensus size: 60
22591678 AGCTAACTGA
* * * ***
22591688 TTTCATAATTTGATAGCCGAAGCTATCCCTTTTCATAATTTGACGGTCGTCTCCATCCAT
1 TTTCACAATTTGATAGCCGAAGCTATCCCTTTTCATAATTCGACAGTCGAAGCCATCCAT
* * * *
22591748 TTTCACAATTTGATAGTCGAAGCTATCCCTTTTCATAATTCGATAG-CAGAAGCTATCCCT
1 TTTCACAATTTGATAGCCGAAGCTATCCCTTTTCATAATTCGACAGTC-GAAGCCATCCAT
22591808 TTTCA
1 TTTCA
22591813 TTGTTCGATG
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
59 1 0.02
60 53 0.98
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.38
Consensus pattern (60 bp):
TTTCACAATTTGATAGCCGAAGCTATCCCTTTTCATAATTCGACAGTCGAAGCCATCCAT
Found at i:22591836 original size:30 final size:29
Alignment explanation
Indices: 22591802--22591869 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
22591792 AGCAGAAGCT
*
22591802 ATCCCTTTTCATTGTTCGATGGTCATCATC
1 ATCCCTTTTCATTGTT-GATGGTCATCACC
* *
22591832 ATCCCTTGTCATTGTTGATGGTCGTCACC
1 ATCCCTTTTCATTGTTGATGGTCATCACC
22591861 ATCCCTTTT
1 ATCCCTTTT
22591870 ATTAACTTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 19 0.56
30 15 0.44
ACGTcount: A:0.15, C:0.28, G:0.15, T:0.43
Consensus pattern (29 bp):
ATCCCTTTTCATTGTTGATGGTCATCACC
Found at i:22591895 original size:30 final size:31
Alignment explanation
Indices: 22591861--22591935 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
22591851 GGTCGTCACC
* *
22591861 ATCCCTTTT-ATTAACTTGATAGCCGAGGCT
1 ATCCCTTTTCATTAACTTGATAGCCAAAGCT
*
22591891 ATCCCTTTTCATTAATTTGATAGCCAAAGCT
1 ATCCCTTTTCATTAACTTGATAGCCAAAGCT
*
22591922 ATCCCTTTCCATTA
1 ATCCCTTTTCATTA
22591936 GTTGATAATC
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 9 0.22
31 31 0.77
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.39
Consensus pattern (31 bp):
ATCCCTTTTCATTAACTTGATAGCCAAAGCT
Found at i:22598560 original size:51 final size:50
Alignment explanation
Indices: 22598475--22598674 Score: 183
Period size: 51 Copynumber: 4.0 Consensus size: 50
22598465 TTAATGATAC
* * * * *
22598475 CGGTTCACATAGTAGCATGCACCTAGTACTACACATGTGACCATCACTAT
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACTAT
* * *
22598525 ACGATACACGTAGTAGCCTGCACATAGTACTACACACCTGATCGA--AGCTATT
1 -CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTA-T
* * * *
22598577 CGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-T
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTAT
* * *
22598626 CTGGTACACGTAGTAGCCTACACATAATACTACACACGTGGCCATCACT
1 C-GGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
22598675 TTCACTTTCA
Statistics
Matches: 119, Mismatches: 22, Indels: 17
0.75 0.14 0.11
Matches are distributed among these distances:
49 6 0.05
50 37 0.31
51 72 0.61
52 3 0.03
53 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (50 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACTAT
Found at i:22598690 original size:101 final size:101
Alignment explanation
Indices: 22598477--22598662 Score: 243
Period size: 102 Copynumber: 1.8 Consensus size: 101
22598467 AATGATACCG
* * *
22598477 GTTCACATAGTAGCATGCACCTAGTACTACACATGTGACCATCACTATACGATACACGTAGTAGC
1 GTTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATACGATACACGTAGTAGC
* * *
22598542 CTGCACATAGTACTACACACCTGATCGAAGCTATTCG
66 CTACACATAATACTACACACCTGATC-AAGCTATTCC
* * *
22598579 GTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-T-CTGGTACACGTAGTA
1 GTTCACATAGTAGCCTGCACATAGTACTACACATGCGACC-ATCACTATAC-GATACACGTAGTA
22598641 GCCTACACATAATACTACACAC
64 GCCTACACATAATACTACACAC
22598663 GTGGCCATCA
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
100 1 0.01
101 33 0.45
102 36 0.49
103 4 0.05
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (101 bp):
GTTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATACGATACACGTAGTAGC
CTACACATAATACTACACACCTGATCAAGCTATTCC
Found at i:22603954 original size:51 final size:51
Alignment explanation
Indices: 22603868--22604068 Score: 212
Period size: 51 Copynumber: 4.0 Consensus size: 51
22603858 ATTAATGATA
* * * * *
22603868 CCGGTTCACATAGTAGCATGCACCTAGTACTACACATGTGACCATCACTAT
1 CCGGTACACGTAGTAGCCTACACATAGTACTACACATGTGACCATCACTAT
* * * *
22603919 CCGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGA--AGCTAT
1 CCGGTACACGTAGTAGCCTACACATAGTACTACACATGTGA-CCATCA-CTAT
* * *
22603970 CCGGTACGCATAGTAGCCTACACATAGTACTACACATGCGACCTATCA-T-T
1 CCGGTACACGTAGTAGCCTACACATAGTACTACACATGTGACC-ATCACTAT
* * *
22604020 CTGGTACATGTAGTAGCCTACACATAATACTACACATGTGACCATCACT
1 CCGGTACACGTAGTAGCCTACACATAGTACTACACATGTGACCATCACT
22604069 TTCACTTTCA
Statistics
Matches: 124, Mismatches: 20, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
49 4 0.03
50 41 0.33
51 76 0.61
52 2 0.02
53 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.24
Consensus pattern (51 bp):
CCGGTACACGTAGTAGCCTACACATAGTACTACACATGTGACCATCACTAT
Found at i:22604084 original size:101 final size:102
Alignment explanation
Indices: 22603868--22604060 Score: 246
Period size: 102 Copynumber: 1.9 Consensus size: 102
22603858 ATTAATGATA
* * * *
22603868 CCGGTTCACATAGTAGCATGCACCTAGTACTACACATGTGACCATCACTATCCGATACACGTAGT
1 CCGGTTCACATAGTAGCCTACACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGT
* * *
22603933 AGCCTGCACATAGTACTACACACGTGATCGAAGCTAT
66 AGCCTACACATAATACTACACACGTGATCCAAGCTAT
* * * * *
22603970 CCGGTACGCATAGTAGCCTACACATAGTACTACACATGCGACCTATCA-T-TCTGGTACATGTAG
1 CCGGTTCACATAGTAGCCTACACATAGTACTACACATGCGACC-ATCACTATCCGATACACGTAG
*
22604033 TAGCCTACACATAATACTACACATGTGA
65 TAGCCTACACATAATACTACACACGTGA
22604061 CCATCACTTT
Statistics
Matches: 78, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
101 36 0.46
102 38 0.49
103 4 0.05
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.24
Consensus pattern (102 bp):
CCGGTTCACATAGTAGCCTACACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGT
AGCCTACACATAATACTACACACGTGATCCAAGCTAT
Found at i:22614117 original size:12 final size:12
Alignment explanation
Indices: 22614100--22614124 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
22614090 ATAAAAAGCA
22614100 TTTTTTCTCTCT
1 TTTTTTCTCTCT
22614112 TTTTTTCTCTCT
1 TTTTTTCTCTCT
22614124 T
1 T
22614125 CGATCCTCTT
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:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTTCTCTCT
Found at i:22619126 original size:70 final size:67
Alignment explanation
Indices: 22619042--22619173 Score: 165
Period size: 70 Copynumber: 1.9 Consensus size: 67
22619032 TCAGAATAAG
* * *
22619042 AAAAGACAAAACTACGCCGTTTTAATAAGCGTTTACCTTTTCTAAAGTTAAAAGTCAAAACCATT
1 AAAAGACAAAACTACGCCGTTGTAATAAACGTTTA-CTTAT-T-AAGTTAAAAGTCAAAACCATT
22619107 GAGTT
63 GAGTT
* ** * *
22619112 AAAAGGCAAAACTACGTTGTTGTGATAAATGTTTACTTATTAAGTTAAAAGTCAAAACCATT
1 AAAAGACAAAACTACGCCGTTGTAATAAACGTTTACTTATTAAGTTAAAAGTCAAAACCATT
22619174 ATATTGTGTA
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
67 21 0.39
68 1 0.02
69 4 0.07
70 28 0.52
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (67 bp):
AAAAGACAAAACTACGCCGTTGTAATAAACGTTTACTTATTAAGTTAAAAGTCAAAACCATTGAG
TT
Found at i:22621689 original size:18 final size:18
Alignment explanation
Indices: 22621636--22621700 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 18
22621626 ATATTAAAAA
*
22621636 ATATTTTGTTATGATTTTT
1 ATATTTT-TAATGATTTTT
*
22621655 ATACTTTTTAATGATTTTA
1 ATA-TTTTTAATGATTTTT
22621674 ATATTTTTAACT-ATTTTTT
1 ATATTTTTAA-TGA-TTTTT
22621693 ATATTTTT
1 ATATTTTT
22621701 TGAATTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
18 8 0.20
19 28 0.70
20 4 0.10
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (18 bp):
ATATTTTTAATGATTTTT
Found at i:22622115 original size:26 final size:26
Alignment explanation
Indices: 22622076--22622143 Score: 84
Period size: 26 Copynumber: 2.5 Consensus size: 26
22622066 GAATATATAA
22622076 TAAATATATATTTTTTATTTTTTTAATTT
1 TAAA-ATA-ATTTTTTA-TTTTTTAATTT
* *
22622105 T-AAATACTTTTTTATTTTTTATTTT
1 TAAAATAATTTTTTATTTTTTAATTT
22622130 TAAAATAATTTTTT
1 TAAAATAATTTTTT
22622144 GGTGTTTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 11 0.31
26 18 0.51
27 3 0.09
28 2 0.06
29 1 0.03
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (26 bp):
TAAAATAATTTTTTATTTTTTAATTT
Found at i:22626180 original size:3 final size:3
Alignment explanation
Indices: 22626172--22626221 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
22626162 GGAGACAAGA
*
22626172 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
22626220 AA
1 AA
22626222 AAGTGATAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:22631447 original size:21 final size:21
Alignment explanation
Indices: 22631422--22631463 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
22631412 TTCCCTCTTC
22631422 TTTTTCTTCCTTT-CTTTATTTG
1 TTTTTCTT--TTTCCTTTATTTG
22631444 TTTTTCTTTTTCCTTTATTT
1 TTTTTCTTTTTCCTTTATTT
22631464 ATTTATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.16
21 8 0.42
22 8 0.42
ACGTcount: A:0.05, C:0.17, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTTTCTTTTTCCTTTATTTG
Found at i:22631500 original size:13 final size:13
Alignment explanation
Indices: 22631482--22631509 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
22631472 ATTTATTTTG
22631482 TTTCTTATTATTA
1 TTTCTTATTATTA
22631495 TTTCTTATTATTA
1 TTTCTTATTATTA
22631508 TT
1 TT
22631510 ATTACCATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTCTTATTATTA
Found at i:22631728 original size:20 final size:19
Alignment explanation
Indices: 22631663--22631722 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
22631653 GGCTTTGTTG
22631663 ATTTTTATT-TGTATTTAAT
1 ATTTTTATTATGT-TTTAAT
*
22631682 -TCTATTATTATGTTTTTAAT
1 AT-TTTTATTATG-TTTTAAT
22631702 ATTTTTATTATG-TTTAAT
1 ATTTTTATTATGTTTTAAT
22631720 ATT
1 ATT
22631723 AGTTTAGTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
18 10 0.29
19 6 0.17
20 17 0.49
21 2 0.06
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.67
Consensus pattern (19 bp):
ATTTTTATTATGTTTTAAT
Found at i:22634201 original size:29 final size:29
Alignment explanation
Indices: 22634158--22634298 Score: 113
Period size: 29 Copynumber: 4.8 Consensus size: 29
22634148 TATCGACAAT
* * ***
22634158 CATCGACCAATGAAAAGGGATGGTTTTGAC
1 CATCGA-CTATGAAAAGGGATAGTGACGAC
* * **
22634188 CATCGATTATGAAAAAGAGATAGTTTCGAC
1 CATCGACTATG-AAAAGGGATAGTGACGAC
* * * *
22634218 TATCGACTGTGAAAAGGGATGGTGACGGC
1 CATCGACTATGAAAAGGGATAGTGACGAC
*
22634247 CATCAACTATGAAAAGGGATAGTGACGAC
1 CATCGACTATGAAAAGGGATAGTGACGAC
*
22634276 CATC-ATATATGAAAAGGGATAGT
1 CATCGA-CTATGAAAAGGGATAGT
22634299 TCACGGAGCA
Statistics
Matches: 90, Mismatches: 19, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
28 1 0.01
29 60 0.67
30 29 0.32
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (29 bp):
CATCGACTATGAAAAGGGATAGTGACGAC
Found at i:22648520 original size:25 final size:25
Alignment explanation
Indices: 22648489--22648587 Score: 101
Period size: 25 Copynumber: 4.0 Consensus size: 25
22648479 AGCTCTCTCT
* *
22648489 TGAGCCATATAACGGGAAGCTCATG
1 TGAGCCATATAATGGGAAGCTCATA
* * *
22648514 TGAGCCATGTAATGGGAAGCTTATT
1 TGAGCCATATAATGGGAAGCTCATA
* **
22648539 TGGGCTGTATAATGGGAAGCTCATA
1 TGAGCCATATAATGGGAAGCTCATA
* *
22648564 AGAGCCATA-ATTGGGAAGCTCATA
1 TGAGCCATATAATGGGAAGCTCATA
22648588 CTAGCCAATA
Statistics
Matches: 59, Mismatches: 15, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
24 14 0.24
25 45 0.76
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.25
Consensus pattern (25 bp):
TGAGCCATATAATGGGAAGCTCATA
Found at i:22648715 original size:26 final size:26
Alignment explanation
Indices: 22648685--22648744 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
22648675 GGAGCTCTAG
* *
22648685 AGAGCCATTAATTATGAAGCTCACAA
1 AGAGCCATTAATCAGGAAGCTCACAA
* * *
22648711 AGAGCCTTTAATCGGGAAGCTCACGA
1 AGAGCCATTAATCAGGAAGCTCACAA
22648737 AGAGCCAT
1 AGAGCCAT
22648745 ATATTAGGAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.20
Consensus pattern (26 bp):
AGAGCCATTAATCAGGAAGCTCACAA
Found at i:22656883 original size:29 final size:27
Alignment explanation
Indices: 22656838--22656893 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
22656828 TAATATATAA
22656838 TTTATAAATAATATAATTATATATTAAAG
1 TTTATAAATAATATAA-TA-ATATTAAAG
*
22656867 TTTATCAAATTAT-TAATAATATTAAAG
1 TTTAT-AAATAATATAATAATATTAAAG
22656894 ATATTTATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 9 0.36
28 2 0.08
29 8 0.32
30 6 0.24
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.45
Consensus pattern (27 bp):
TTTATAAATAATATAATAATATTAAAG
Found at i:22657272 original size:130 final size:130
Alignment explanation
Indices: 22657033--22657291 Score: 437
Period size: 130 Copynumber: 2.0 Consensus size: 130
22657023 ATCGAGTTGC
* *
22657033 AAATTAAAACTTGGATCAAAATTGACCCTTTTATTTGAAACTAAAAATTTATTTTTCCATTTAGG
1 AAATTAAAACTTAGATCAAAATTGACCCTTTTATTTGAAACTAAAAATTTAATTTTCCATTTAGG
* * * *
22657098 GGATATTTTATTGGAAAATTATGTCAAAATAAATTTCCAGGAAAGATTGGAGGGGTCACAAACGG
66 GGATAATTTATTGGAAAATCATGTCAAAATAAATTCCCAAGAAAGATTGGAGGGGTCACAAACGG
*
22657163 AAATTAAAACTTAGATCAAACTTGACCCTTTTATTTGAAACTAAAAATTTAATTTTCCATTTAGG
1 AAATTAAAACTTAGATCAAAATTGACCCTTTTATTTGAAACTAAAAATTTAATTTTCCATTTAGG
* *
22657228 GGATAATTTCTTGGAAAATCATGTCAAAATAAATTCCCAAGAAAGATTGGATGGGTCACAAACG
66 GGATAATTTATTGGAAAATCATGTCAAAATAAATTCCCAAGAAAGATTGGAGGGGTCACAAACG
22657292 ATCCCGCTTA
Statistics
Matches: 120, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 120 1.00
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.33
Consensus pattern (130 bp):
AAATTAAAACTTAGATCAAAATTGACCCTTTTATTTGAAACTAAAAATTTAATTTTCCATTTAGG
GGATAATTTATTGGAAAATCATGTCAAAATAAATTCCCAAGAAAGATTGGAGGGGTCACAAACGG
Found at i:22659358 original size:51 final size:48
Alignment explanation
Indices: 22659298--22659479 Score: 204
Period size: 51 Copynumber: 3.6 Consensus size: 48
22659288 AAAGGTTGCA
22659298 TGTGTAGTACTATGTGCAGGCTACTATGCGTGCCGGATAGCTTTGATCACG
1 TGTGTAGTACTATGTGCAGGCTACTA--CGTGCCGGATAG-TTTGATCACG
* ** *
22659349 TGTGTAGTACTATGTGCAGGCTAGTACATGTATCGGATA-TTAATGGTCACG
1 TGTGTAGTACTATGTGCAGGCTACTAC--GTGCCGGATAGTT--TGATCACG
* * *
22659400 TGTGTAGTACTATGTGCAGGCTACTACTTGAACCGGAAAGTTTGATCACA
1 TGTGTAGTACTATGTGCAGGCTACTACGTG--CCGGATAGTTTGATCACG
*
22659450 TGTGTAGTACTATGTGAAGGCTACTACGTG
1 TGTGTAGTACTATGTGCAGGCTACTACGTG
22659480 TATCGAATGA
Statistics
Matches: 111, Mismatches: 13, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
49 4 0.04
50 34 0.31
51 71 0.64
52 2 0.02
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (48 bp):
TGTGTAGTACTATGTGCAGGCTACTACGTGCCGGATAGTTTGATCACG
Found at i:22659482 original size:101 final size:101
Alignment explanation
Indices: 22659298--22659484 Score: 279
Period size: 101 Copynumber: 1.8 Consensus size: 101
22659288 AAAGGTTGCA
* *
22659298 TGTGTAGTACTATGTGCAGGCTACTATGCGTGCCGGATAGCTTTGATCACGTGTGTAGTACTATG
1 TGTGTAGTACTATGTGCAGGCTACTA-GCGTGCCGGAAAGCTTTGATCACATGTGTAGTACTATG
* *
22659363 TGCAGGCTAGTACATGTATCGGATATTAATGGTCACG
65 TGAAGGCTACTACATGTATCGGATATTAATGGTCACG
*
22659400 TGTGTAGTACTATGTGCAGGCTACTA-CTTGAACCGGAAAG-TTTGATCACATGTGTAGTACTAT
1 TGTGTAGTACTATGTGCAGGCTACTAGCGTG--CCGGAAAGCTTTGATCACATGTGTAGTACTAT
*
22659463 GTGAAGGCTACTACGTGTATCG
64 GTGAAGGCTACTACATGTATCG
22659485 AATGATAATA
Statistics
Matches: 77, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
100 3 0.04
101 41 0.53
102 33 0.43
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (101 bp):
TGTGTAGTACTATGTGCAGGCTACTAGCGTGCCGGAAAGCTTTGATCACATGTGTAGTACTATGT
GAAGGCTACTACATGTATCGGATATTAATGGTCACG
Found at i:22659511 original size:101 final size:101
Alignment explanation
Indices: 22659301--22659518 Score: 262
Period size: 101 Copynumber: 2.1 Consensus size: 101
22659291 GGTTGCATGT
* * *
22659301 GTAGTACTATGTGCAGGCTACTATGCGTGCCGGATAGCTTTGATCACGTGTGTAGTACTATGTGC
1 GTAGTACTATGTGCAGGCTACTA-GCGTGCCGGAAAGCTTTGATCACATGTGTAGTACTATGTGA
* * * ** *
22659366 AGGCTAGTACATGTATCGGATATTAATGGTCACGTGT
65 AGGCTACTACATGTATCGAATATTAATAGTCAAATGA
*
22659403 GTAGTACTATGTGCAGGCTACTA-CTTGAACCGGAAAG-TTTGATCACATGTGTAGTACTATGTG
1 GTAGTACTATGTGCAGGCTACTAGCGTG--CCGGAAAGCTTTGATCACATGTGTAGTACTATGTG
* *
22659466 AAGGCTACTACGTGTATCGAATGA-TAATAGTTAAATGA
64 AAGGCTACTACATGTATCGAAT-ATTAATAGTCAAATGA
*
22659504 GTGGTACTATGTGCA
1 GTAGTACTATGTGCA
22659519 AACCATTGAA
Statistics
Matches: 100, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
100 3 0.03
101 66 0.66
102 31 0.31
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.32
Consensus pattern (101 bp):
GTAGTACTATGTGCAGGCTACTAGCGTGCCGGAAAGCTTTGATCACATGTGTAGTACTATGTGAA
GGCTACTACATGTATCGAATATTAATAGTCAAATGA
Found at i:22672284 original size:41 final size:41
Alignment explanation
Indices: 22672224--22672310 Score: 104
Period size: 41 Copynumber: 2.1 Consensus size: 41
22672214 TACAATACAT
* * *
22672224 CGGCACGAAGACTGCTAAGCTCAAAGC-CTGATTTAAAACAC
1 CGGCACGAAGACTGATAAGCACAAAGCTC-GATATAAAACAC
* * *
22672265 CGGCACGAAGCCTGATAAGCACAGAGCTCGATATAATACAC
1 CGGCACGAAGACTGATAAGCACAAAGCTCGATATAAAACAC
22672306 CGGCA
1 CGGCA
22672311 TAACGCCTAC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 38 0.97
42 1 0.03
ACGTcount: A:0.36, C:0.28, G:0.22, T:0.15
Consensus pattern (41 bp):
CGGCACGAAGACTGATAAGCACAAAGCTCGATATAAAACAC
Found at i:22672362 original size:38 final size:38
Alignment explanation
Indices: 22672320--22672496 Score: 203
Period size: 38 Copynumber: 4.7 Consensus size: 38
22672310 ATAACGCCTA
* *
22672320 CTAGGCACGGGGCCTGAATATCACCGACACAAAGCTTG
1 CTAGGCACAGAGCCTGAATATCACCGACACAAAGCTTG
***
22672358 CTAGGCACAGAGCCTGAATATCACCGGTTCAAAGCCTT-
1 CTAGGCACAGAGCCTGAATATCACCGACACAAAG-CTTG
* * * * *
22672396 TTGGGAACGGAGCCCGAATATCACCGACACAAAGCTTG
1 CTAGGCACAGAGCCTGAATATCACCGACACAAAGCTTG
* * * *
22672434 TTAGGCACAGAGCCTGAATATCACCGGCATAAAGCCTG
1 CTAGGCACAGAGCCTGAATATCACCGACACAAAGCTTG
*
22672472 CTAGGCACAGAGCCCGAATATCACC
1 CTAGGCACAGAGCCTGAATATCACC
22672497 ACATTTTAAT
Statistics
Matches: 115, Mismatches: 22, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
37 3 0.03
38 109 0.95
39 3 0.03
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.17
Consensus pattern (38 bp):
CTAGGCACAGAGCCTGAATATCACCGACACAAAGCTTG
Found at i:22672418 original size:76 final size:76
Alignment explanation
Indices: 22672299--22672496 Score: 265
Period size: 76 Copynumber: 2.6 Consensus size: 76
22672289 AGCTCGATAT
* * * * *
22672299 AATA-CACCGGCATAACGCCTACTAGGCACGGGGCCTGAATATCACCGACACAAAGCTTGCTAGG
1 AATATCACCGGCATAAAGCCTGCTAGGAACGGAGCCCGAATATCACCGACACAAAGCTTGCTAGG
22672363 CACAGAGCCTG
66 CACAGAGCCTG
* ** * *
22672374 AATATCACCGG-TTCAAAGCCTTTTGGGAACGGAGCCCGAATATCACCGACACAAAGCTTGTTAG
1 AATATCACCGGCAT-AAAGCCTGCTAGGAACGGAGCCCGAATATCACCGACACAAAGCTTGCTAG
22672438 GCACAGAGCCTG
65 GCACAGAGCCTG
* *
22672450 AATATCACCGGCATAAAGCCTGCTAGGCACAGAGCCCGAATATCACC
1 AATATCACCGGCATAAAGCCTGCTAGGAACGGAGCCCGAATATCACC
22672497 ACATTTTAAT
Statistics
Matches: 105, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
75 5 0.05
76 99 0.94
77 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.23, T:0.17
Consensus pattern (76 bp):
AATATCACCGGCATAAAGCCTGCTAGGAACGGAGCCCGAATATCACCGACACAAAGCTTGCTAGG
CACAGAGCCTG
Found at i:22679233 original size:27 final size:27
Alignment explanation
Indices: 22679197--22679470 Score: 343
Period size: 27 Copynumber: 10.1 Consensus size: 27
22679187 AGAGGTCAAT
22679197 AAATGATCGAAATACCCCCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
* *
22679224 AAATGATCGAAATTCCTCCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
22679251 AAATGATCGAAATACCCCCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
* * *
22679278 AAATGACCAAAATGCCCCCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
** *
22679305 AGCTGATCGAAATACCCTCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
22679332 AAATGATCGAAATACCCCCATAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
* * * *
22679359 AAATGACCAAAATACCCCTATAGGTTA
1 AAATGATCGAAATACCCCCATAGGGTA
* *
22679386 AAATGATCGAAATACCCTCATAGGATA
1 AAATGATCGAAATACCCCCATAGGGTA
* * *
22679413 AAATTA-CTGAAATACCCTCATAGCGTA
1 AAATGATC-GAAATACCCCCATAGGGTA
* * * *
22679440 AAATGACCGAAACACCTCCACAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
22679467 AAAT
1 AAAT
22679471 TACTATTATA
Statistics
Matches: 211, Mismatches: 34, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
26 1 0.00
27 209 0.99
28 1 0.00
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (27 bp):
AAATGATCGAAATACCCCCATAGGGTA
Found at i:22679744 original size:26 final size:26
Alignment explanation
Indices: 22679636--22679742 Score: 126
Period size: 26 Copynumber: 4.1 Consensus size: 26
22679626 TAGAGGAAGT
* *
22679636 ATACTATTACTGGTAGCTTTACTGCG
1 ATACTATTACTGGCAGCTTTGCTGCG
* * *
22679662 ATACTGTTATTGGTAGCTTTGCTGCG
1 ATACTATTACTGGCAGCTTTGCTGCG
*
22679688 ATACTGTTA-TGAGCAGCTTTGCTGCG
1 ATACTATTACTG-GCAGCTTTGCTGCG
* *
22679714 ATATTATTACTGGCAGTTTTGCTGCG
1 ATACTATTACTGGCAGCTTTGCTGCG
22679740 ATA
1 ATA
22679743 TTGGTGTGTT
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
25 2 0.03
26 68 0.94
27 2 0.03
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.39
Consensus pattern (26 bp):
ATACTATTACTGGCAGCTTTGCTGCG
Found at i:22705172 original size:31 final size:33
Alignment explanation
Indices: 22705137--22705226 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 33
22705127 AGCATGCAAG
*
22705137 CTAAATGAAGA-T-TCACT-AGGATACCACATGC
1 CTAAATTAAGAGTGTCACTAAGG-TACCACATGC
*
22705168 CTAAATTAAGAGTGTCTCTAAGGTACCACATGC
1 CTAAATTAAGAGTGTCACTAAGGTACCACATGC
*
22705201 CTAAATTAAGAGTGTCTCTAAGGTAC
1 CTAAATTAAGAGTGTCACTAAGGTAC
22705227 ATAAAAATTT
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
31 10 0.19
32 1 0.02
33 40 0.74
34 3 0.06
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (33 bp):
CTAAATTAAGAGTGTCACTAAGGTACCACATGC
Found at i:22705196 original size:33 final size:33
Alignment explanation
Indices: 22705158--22705226 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
22705148 TTCACTAGGA
22705158 TACCACATGCCTAAATTAAGAGTGTCTCTAAGG
1 TACCACATGCCTAAATTAAGAGTGTCTCTAAGG
22705191 TACCACATGCCTAAATTAAGAGTGTCTCTAAGG
1 TACCACATGCCTAAATTAAGAGTGTCTCTAAGG
22705224 TAC
1 TAC
22705227 ATAAAAATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (33 bp):
TACCACATGCCTAAATTAAGAGTGTCTCTAAGG
Found at i:22706467 original size:14 final size:14
Alignment explanation
Indices: 22706448--22706480 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
22706438 ATTGTCACAT
22706448 GTGTAGGCTACTAC
1 GTGTAGGCTACTAC
22706462 GTGTAGGCTACTAC
1 GTGTAGGCTACTAC
22706476 GTGTA
1 GTGTA
22706481 CTGGGTACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.30
Consensus pattern (14 bp):
GTGTAGGCTACTAC
Found at i:22706547 original size:45 final size:45
Alignment explanation
Indices: 22706483--22706642 Score: 241
Period size: 45 Copynumber: 3.6 Consensus size: 45
22706473 TACGTGTACT
*
22706483 GGGTACCATTGATTATAAAGGTGGTTGCTGTGTGCTGATTCCACC
1 GGGTATCATTGATTATAAAGGTGGTTGCTGTGTGCTGATTCCACC
*
22706528 GGGTATCATTGATTATAAAGGTGGTTGATGTGTGCTGATTCCACC
1 GGGTATCATTGATTATAAAGGTGGTTGCTGTGTGCTGATTCCACC
* *
22706573 GGGTA-CTATTGATTATGAAGGTGGTTGCTATGTGCTGATTCCACC
1 GGGTATC-ATTGATTATAAAGGTGGTTGCTGTGTGCTGATTCCACC
* * *
22706618 GAGTATCATTGACTATAAGGGTGGT
1 GGGTATCATTGATTATAAAGGTGGT
22706643 GCTATGAGTT
Statistics
Matches: 104, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
44 1 0.01
45 102 0.98
46 1 0.01
ACGTcount: A:0.22, C:0.14, G:0.29, T:0.34
Consensus pattern (45 bp):
GGGTATCATTGATTATAAAGGTGGTTGCTGTGTGCTGATTCCACC
Found at i:22719858 original size:12 final size:13
Alignment explanation
Indices: 22719834--22719862 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
22719824 GGGCTATAAC
22719834 TATTGCATTTATT
1 TATTGCATTTATT
22719847 TATTGC-TTTATT
1 TATTGCATTTATT
22719859 TATT
1 TATT
22719863 TTAGTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:22729440 original size:54 final size:54
Alignment explanation
Indices: 22729309--22729486 Score: 223
Period size: 54 Copynumber: 3.3 Consensus size: 54
22729299 ACATTAAAAG
* * * * * *
22729309 TTTAATCCAGCAAC-TAAGTGAACTAAGTTGAACTTAATTAACTAAAATGAGTGAT
1 TTTATTCCAGCAACTTAA-TTAACTAAGATGAACTCAATTAACTAAGATGAGT-AA
* * *
22729364 TTTATTCCAGTAACTTAATTAACTAAGATGAACTCAAGTAACGAAGATGAGTAA
1 TTTATTCCAGCAACTTAATTAACTAAGATGAACTCAATTAACTAAGATGAGTAA
* *
22729418 TTTATTCAAGCAACTTAATTAACTAAGATGAGCTCAATTAACTAAGATGAGTAA
1 TTTATTCCAGCAACTTAATTAACTAAGATGAACTCAATTAACTAAGATGAGTAA
*
22729472 CTTATTCCAGCAACT
1 TTTATTCCAGCAACT
22729487 AAATACTTAT
Statistics
Matches: 106, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
54 63 0.59
55 40 0.38
56 3 0.03
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (54 bp):
TTTATTCCAGCAACTTAATTAACTAAGATGAACTCAATTAACTAAGATGAGTAA
Found at i:22729458 original size:19 final size:19
Alignment explanation
Indices: 22729380--22729468 Score: 71
Period size: 19 Copynumber: 4.8 Consensus size: 19
22729370 CCAGTAACTT
*
22729380 AATTAACTAAGATGAACTC
1 AATTAACTAAGATGAGCTC
* *
22729399 AAGTAACGAAGATGAG-T-
1 AATTAACTAAGATGAGCTC
* * *
22729416 AATTTATTCAAGCA--A-CTT
1 AATTAACT-AAG-ATGAGCTC
22729434 AATTAACTAAGATGAGCTC
1 AATTAACTAAGATGAGCTC
22729453 AATTAACTAAGATGAG
1 AATTAACTAAGATGAG
22729469 TAACTTATTC
Statistics
Matches: 53, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
16 1 0.02
17 9 0.17
18 11 0.21
19 32 0.60
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (19 bp):
AATTAACTAAGATGAGCTC
Found at i:22733821 original size:54 final size:54
Alignment explanation
Indices: 22733755--22733891 Score: 195
Period size: 54 Copynumber: 2.5 Consensus size: 54
22733745 ACATTAAAAT
* * * * *
22733755 TTTAATCCAGCAACTAAGTGAACTAAGTTGAACTTAATTAACTAATATGAGTAA
1 TTTATTCCAGCAACTAAGTTAACTAAGATGAACTCAATTAACTAAGATGAGTAA
22733809 TTTATTCCAGCAACTTAA-TTAACTAAGATGAACTCAATTAACTAAGATGAGTAA
1 TTTATTCCAGCAAC-TAAGTTAACTAAGATGAACTCAATTAACTAAGATGAGTAA
* *
22733863 TTTATTCAAGCAACTTAGTTAACTAAGAT
1 TTTATTCCAGCAACTAAGTTAACTAAGAT
22733892 TATTAATTTA
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
53 2 0.03
54 69 0.93
55 3 0.04
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.33
Consensus pattern (54 bp):
TTTATTCCAGCAACTAAGTTAACTAAGATGAACTCAATTAACTAAGATGAGTAA
Found at i:22733847 original size:19 final size:19
Alignment explanation
Indices: 22733820--22733858 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
22733810 TTATTCCAGC
*
22733820 AACTTAATTAACTAAGATG
1 AACTCAATTAACTAAGATG
22733839 AACTCAATTAACTAAGATG
1 AACTCAATTAACTAAGATG
22733858 A
1 A
22733859 GTAATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.28
Consensus pattern (19 bp):
AACTCAATTAACTAAGATG
Found at i:22733885 original size:35 final size:35
Alignment explanation
Indices: 22733846--22733912 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
22733836 ATGAACTCAA
22733846 TTAACTAAGATGAGTAATTTATTCAAGCAACTTAG
1 TTAACTAAGATGAGTAATTTATTCAAGCAACTTAG
* * *
22733881 TTAACTAAGATTATTAATTTATTCCAGCAACT
1 TTAACTAAGATGAGTAATTTATTCAAGCAACT
22733913 AAATACTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.37
Consensus pattern (35 bp):
TTAACTAAGATGAGTAATTTATTCAAGCAACTTAG
Found at i:22736581 original size:3 final size:3
Alignment explanation
Indices: 22736573--22736597 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
22736563 CTCTGTGGGA
22736573 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
22736598 TGGGATCCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:22737413 original size:25 final size:25
Alignment explanation
Indices: 22737385--22737440 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
22737375 TAATTAGTAT
*
22737385 AAAATATT-AATAATTCAATAAATTG
1 AAAAT-TTAAATAATTAAATAAATTG
*
22737410 AAAATTTAAATAATTAAATAAATTT
1 AAAATTTAAATAATTAAATAAATTG
22737435 AAAATT
1 AAAATT
22737441 GAGGAGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 2 0.07
25 26 0.93
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (25 bp):
AAAATTTAAATAATTAAATAAATTG
Found at i:22738169 original size:16 final size:15
Alignment explanation
Indices: 22738144--22738177 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
22738134 AAAGTTGATA
*
22738144 ATAATTAATATATATT
1 ATAATAAATATA-ATT
22738160 ATAATAAATATAATT
1 ATAATAAATATAATT
22738175 ATA
1 ATA
22738178 TACTAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:22748456 original size:26 final size:26
Alignment explanation
Indices: 22748407--22748467 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
22748397 AAAGGTTTTT
* * *
22748407 AAATGACCGAAATACCCTCGAAGGGTA
1 AAATTACCAAAATACCCTCGAA-GGCA
*
22748434 AAATTACCAAAATACCC-CTAAGGCA
1 AAATTACCAAAATACCCTCGAAGGCA
22748459 AAATTACCA
1 AAATTACCA
22748468 TTTTACCCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 12 0.40
26 3 0.10
27 15 0.50
ACGTcount: A:0.46, C:0.25, G:0.13, T:0.16
Consensus pattern (26 bp):
AAATTACCAAAATACCCTCGAAGGCA
Found at i:22754338 original size:26 final size:27
Alignment explanation
Indices: 22754293--22754343 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
22754283 TAATTGAATG
22754293 AAATACCCTTAAAGGATAAAATTACTA
1 AAATACCCTTAAAGGATAAAATTACTA
* *
22754320 AAATA-CCTTATAGGGTAAAATTAC
1 AAATACCCTTAAAGGATAAAATTAC
22754344 CATTTTACCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.49, C:0.14, G:0.10, T:0.27
Consensus pattern (27 bp):
AAATACCCTTAAAGGATAAAATTACTA
Found at i:22755815 original size:11 final size:11
Alignment explanation
Indices: 22755799--22755827 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
22755789 AGGGAATGAA
22755799 GAGAGAAAAGT
1 GAGAGAAAAGT
22755810 GAGAGAAAAGT
1 GAGAGAAAAGT
22755821 GA-AGAAA
1 GAGAGAAA
22755828 TGAATGCGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.59, C:0.00, G:0.34, T:0.07
Consensus pattern (11 bp):
GAGAGAAAAGT
Found at i:22759945 original size:5 final size:5
Alignment explanation
Indices: 22759935--22759973 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
22759925 TACTGAAAAT
22759935 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTA
22759974 TAAAATATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTAA
Found at i:22760394 original size:29 final size:30
Alignment explanation
Indices: 22760362--22760428 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 30
22760352 ATTGGGAAAC
22760362 ATTTTTATATTAATTA-ATAATGAGAAAAA
1 ATTTTTATATTAATTATATAATGAGAAAAA
* * * *
22760391 A-TTTTACATTAGTTATATTATGAGAAAAT
1 ATTTTTATATTAATTATATAATGAGAAAAA
*
22760420 TTTTTTATA
1 ATTTTTATA
22760429 AGGAAGTGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
28 12 0.40
29 12 0.40
30 6 0.20
ACGTcount: A:0.43, C:0.01, G:0.07, T:0.48
Consensus pattern (30 bp):
ATTTTTATATTAATTATATAATGAGAAAAA
Found at i:22760395 original size:28 final size:29
Alignment explanation
Indices: 22760364--22760418 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
22760354 TGGGAAACAT
*
22760364 TTTTATATTAATTA-ATAATGAGAAAAAA
1 TTTTACATTAATTATATAATGAGAAAAAA
* *
22760392 TTTTACATTAGTTATATTATGAGAAAA
1 TTTTACATTAATTATATAATGAGAAAA
22760419 TTTTTTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (29 bp):
TTTTACATTAATTATATAATGAGAAAAAA
Found at i:22762780 original size:29 final size:29
Alignment explanation
Indices: 22762738--22762798 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
22762728 AGGTCTACAT
22762738 CAAGATCAGAATTTAGAAACCAAGAAAAA
1 CAAGATCAGAATTTAGAAACCAAGAAAAA
*
22762767 CAAGATCAGAATTTAGAAACTAAGAAAAA
1 CAAGATCAGAATTTAGAAACCAAGAAAAA
22762796 CAA
1 CAA
22762799 TCTGGCTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.59, C:0.13, G:0.13, T:0.15
Consensus pattern (29 bp):
CAAGATCAGAATTTAGAAACCAAGAAAAA
Found at i:22767431 original size:29 final size:29
Alignment explanation
Indices: 22767349--22767439 Score: 87
Period size: 29 Copynumber: 3.1 Consensus size: 29
22767339 TCATTAGGAT
* * *
22767349 TTATCAGGCACTATGTGCTAGAGATTACAG
1 TTATCAGGCACTTTGTGCTAGTG-TTATAG
* * *
22767379 TTATCAGGTACTTTGT-ATCCGTGTTATAG
1 TTATCAGGCACTTTGTGCT-AGTGTTATAG
*
22767408 TTATCAGGCACTTTGTGCTGGTGTTATA-
1 TTATCAGGCACTTTGTGCTAGTGTTATAG
22767436 TTAT
1 TTAT
22767440 TGGGTACTAT
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
28 4 0.08
29 29 0.58
30 17 0.34
ACGTcount: A:0.23, C:0.14, G:0.22, T:0.41
Consensus pattern (29 bp):
TTATCAGGCACTTTGTGCTAGTGTTATAG
Found at i:22770408 original size:28 final size:27
Alignment explanation
Indices: 22770351--22770433 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
22770341 CGAAAGCTGT
* * *
22770351 GAATAGCCTTTTTGGTGAACTCTGAAA
1 GAATAGCCTTTGTGGCGAACTATGAAA
22770378 GAATAGCCTTTGTGGCGAAACTAT-ATAA
1 GAATAGCCTTTGTGGCG-AACTATGA-AA
* ** *
22770406 GAATAACCTTTGTGATGAACTCTGAAA
1 GAATAGCCTTTGTGGCGAACTATGAAA
22770433 G
1 G
22770434 GGATGCCTTG
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
27 24 0.52
28 22 0.48
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (27 bp):
GAATAGCCTTTGTGGCGAACTATGAAA
Found at i:22773896 original size:20 final size:20
Alignment explanation
Indices: 22773871--22773917 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 20
22773861 AAAAATGAAC
22773871 TTTTAAACATTTTTTTTT-AT
1 TTTTAAA-ATTTTTTTTTAAT
*
22773891 TTTTAAAGTTTTTTTTTCAAT
1 TTTTAAAATTTTTTTTT-AAT
22773912 TTTTAA
1 TTTTAA
22773918 GAAATAAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 9 0.38
20 7 0.29
21 8 0.33
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (20 bp):
TTTTAAAATTTTTTTTTAAT
Found at i:22774006 original size:59 final size:62
Alignment explanation
Indices: 22773909--22774028 Score: 149
Period size: 59 Copynumber: 2.0 Consensus size: 62
22773899 TTTTTTTTTC
* * *
22773909 AATTTTTAAGAAATAAACCTAAATTGACAAAATGTGT-AACGTT-GATGG-CTAAATTTGTTG
1 AATTTTTAAGAAATAAAACTAAATTGACAAAATATGTAAACATTGGA-GGTCTAAATTTGTTG
* * *
22773969 AATTTTT-AGAATTAAAACTAAATTGATAGAATATGTAAACATTGGAGGTCTAAATTTGTT
1 AATTTTTAAGAAATAAAACTAAATTGACAAAATATGTAAACATTGGAGGTCTAAATTTGTT
22774029 ATTATGTCAA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
59 24 0.47
60 14 0.27
61 13 0.25
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.37
Consensus pattern (62 bp):
AATTTTTAAGAAATAAAACTAAATTGACAAAATATGTAAACATTGGAGGTCTAAATTTGTTG
Found at i:22776701 original size:21 final size:20
Alignment explanation
Indices: 22776685--22776721 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
22776675 TGTTTTTAAT
*
22776685 AAATAAATA-AAAATTTTTA
1 AAATAAAAATAAAATTTTTA
22776704 AAATAAAAATAAAATTTT
1 AAATAAAAATAAAATTTT
22776722 ATGTTTTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
AAATAAAAATAAAATTTTTA
Found at i:22779954 original size:29 final size:28
Alignment explanation
Indices: 22779920--22780096 Score: 133
Period size: 29 Copynumber: 6.1 Consensus size: 28
22779910 CAAAGTCTTT
22779920 CCACAAAGGTGTCCTTTTAACAGAGATAG
1 CCACAAAGGT-TCCTTTTAACAGAGATAG
*
22779949 CCACAAAGGCATCCTTTTAACAGAGATAG
1 CCACAAAGG-TTCCTTTTAACAGAGATAG
* * * * *
22779978 CCACAAAAGCTTCCTTATAACAAATATGG
1 CCAC-AAAGGTTCCTTTTAACAGAGATAG
* *
22780007 CGACATAGGCGTT-CTTTTAACAGAGATAG
1 CCACA-AAG-GTTCCTTTTAACAGAGATAG
* * * *
22780036 CCACATAGGCTTCCTTATAGCAGAGATTG
1 CCACAAAGG-TTCCTTTTAACAGAGATAG
* **
22780065 CCACAAGGGCATT-CTTTTAATTGAGATAG
1 CCACAAAGG--TTCCTTTTAACAGAGATAG
22780094 CCA
1 CCA
22780097 TAAATACATC
Statistics
Matches: 113, Mismatches: 28, Indels: 14
0.73 0.18 0.09
Matches are distributed among these distances:
27 1 0.01
28 4 0.04
29 100 0.88
30 8 0.07
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (28 bp):
CCACAAAGGTTCCTTTTAACAGAGATAG
Found at i:22779993 original size:58 final size:58
Alignment explanation
Indices: 22779931--22780096 Score: 197
Period size: 58 Copynumber: 2.9 Consensus size: 58
22779921 CACAAAGGTG
* *
22779931 TCCTTTTAACAGAGATAGCCACAAAGGCATCCTTTTAACAGAGATAGCCACAAAAGCT
1 TCCTTATAACAGAGATAGCCACAAAGGCATTCTTTTAACAGAGATAGCCACAAAAGCT
* * * * * * * *
22779989 TCCTTATAACAAATATGGCGACATAGGCGTTCTTTTAACAGAGATAGCCACATAGGCT
1 TCCTTATAACAGAGATAGCCACAAAGGCATTCTTTTAACAGAGATAGCCACAAAAGCT
* * * **
22780047 TCCTTATAGCAGAGATTGCCACAAGGGCATTCTTTTAATTGAGATAGCCA
1 TCCTTATAACAGAGATAGCCACAAAGGCATTCTTTTAACAGAGATAGCCA
22780097 TAAATACATC
Statistics
Matches: 88, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
58 88 1.00
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.27
Consensus pattern (58 bp):
TCCTTATAACAGAGATAGCCACAAAGGCATTCTTTTAACAGAGATAGCCACAAAAGCT
Found at i:22792516 original size:43 final size:41
Alignment explanation
Indices: 22792403--22792523 Score: 127
Period size: 43 Copynumber: 2.9 Consensus size: 41
22792393 AAAATGCAAT
* * *
22792403 GCACCAAGGTTGCCGATTGTGTCCGAGGCTCCCGTACATCCAA
1 GCACCAAGGTT-CCGATAGTGT-CGAGGCTCCTGCACATCCAA
* * *
22792446 GCACC-AGGTGCCGATAGTGTTTGAGGCTCCTGCACATCCGA
1 GCACCAAGGTTCCGATAGTG-TCGAGGCTCCTGCACATCCAA
*
22792487 GCCACCAAGGTTCCGATGGTGCTCGAGGCTCCTGCAC
1 G-CACCAAGGTTCCGATAGTG-TCGAGGCTCCTGCAC
22792524 GACTGAGGGC
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
41 25 0.38
42 9 0.14
43 31 0.48
ACGTcount: A:0.19, C:0.32, G:0.28, T:0.21
Consensus pattern (41 bp):
GCACCAAGGTTCCGATAGTGTCGAGGCTCCTGCACATCCAA
Found at i:22797413 original size:11 final size:11
Alignment explanation
Indices: 22797386--22797423 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
22797376 ACAATTGAAT
22797386 ATTTCATTTCAC
1 ATTTCATTTC-C
22797398 ATTTCATTTCC
1 ATTTCATTTCC
22797409 ATTTC-TTATCC
1 ATTTCATT-TCC
22797420 ATTT
1 ATTT
22797424 TCCATTTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 2 0.08
11 13 0.52
12 10 0.40
ACGTcount: A:0.21, C:0.24, G:0.00, T:0.55
Consensus pattern (11 bp):
ATTTCATTTCC
Done.