Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 180 of 196
Found at i:52610018 original size:19 final size:20
Alignment explanation
Indices: 52609976--52610018 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
52609966 TCATGCTTTC
*
52609976 TATTCACATTTTCATATTCA
1 TATTCACATTTTCAAATTCA
52609996 -ATTCACATTTTCAAATT-A
1 TATTCACATTTTCAAATTCA
52610014 TATTC
1 TATTC
52610019 TACAATCACG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTCACATTTTCAAATTCA
Found at i:52610254 original size:45 final size:45
Alignment explanation
Indices: 52610190--52610384 Score: 186
Period size: 45 Copynumber: 4.3 Consensus size: 45
52610180 ACAGTAATCA
* * * *
52610190 GTAACGGTAGCAGTAACAGTATTCAACACACAAAGTGCTAAATTT
1 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCAAATTG
* * *
52610235 GTAACAGTAACGGTAACAGTATTCGACACACAAAGTGCCGAATCGGTAACG
1 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCAAAT---T---G
52610286 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCAAA---
1 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCAAATTG
* * * *
52610328 -T--CGGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCG
1 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCAAATTG
*
52610370 GTAACAGTAATAGTA
1 GTAACAGTAACAGTA
52610385 GTCAGAATAT
Statistics
Matches: 123, Mismatches: 15, Indels: 24
0.76 0.09 0.15
Matches are distributed among these distances:
39 35 0.28
41 1 0.01
43 1 0.01
45 46 0.37
48 1 0.01
51 39 0.32
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (45 bp):
GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCAAATTG
Found at i:52610255 original size:51 final size:49
Alignment explanation
Indices: 52610183--52610341 Score: 191
Period size: 51 Copynumber: 3.2 Consensus size: 49
52610173 TACCTAAACA
* **
52610183 GTAATCAGTAACGGTAGCAGTAACAGTATTCAACACACAAAGTGCTAAATTT
1 GTAA-CAGTAAC-GTA-CAGTAACAGTATTCAACACACAAAGTGCCAAATCG
* *
52610235 GTAACAGTAACG----GTAACAGTATTCGACACACAAAGTGCCGAATCG
1 GTAACAGTAACGTACAGTAACAGTATTCAACACACAAAGTGCCAAATCG
*
52610280 GTAACGGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCAAATCG
1 GTAACAGTAAC-GT-ACAGTAACAGTATTCAACACACAAAGTGCCAAATCG
52610331 GTAACAGTAAC
1 GTAACAGTAAC
52610342 AGTATTCGAC
Statistics
Matches: 92, Mismatches: 9, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
45 38 0.41
46 1 0.01
50 1 0.01
51 48 0.52
52 4 0.04
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (49 bp):
GTAACAGTAACGTACAGTAACAGTATTCAACACACAAAGTGCCAAATCG
Found at i:52610284 original size:39 final size:39
Alignment explanation
Indices: 52610241--52610384 Score: 144
Period size: 39 Copynumber: 3.4 Consensus size: 39
52610231 ATTTGTAACA
*
52610241 GTAACGGTAACAGTATTCGACACACAAAGTGCCGAATCGGTAACG
1 GTAACAGTAACAGTATTCGACACACAAAGTGCCGAA----T--CG
* *
52610286 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCAAATCG
1 GTAACAGT------AACAGTATTCGACACACAAAGTGCCGAATCG
52610331 GTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCG
1 GTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCG
*
52610370 GTAACAGTAATAGTA
1 GTAACAGTAACAGTA
52610385 GTCAGAATAT
Statistics
Matches: 87, Mismatches: 6, Indels: 18
0.78 0.05 0.16
Matches are distributed among these distances:
39 43 0.49
45 17 0.20
47 1 0.01
51 26 0.30
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.19
Consensus pattern (39 bp):
GTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCG
Found at i:52610299 original size:90 final size:84
Alignment explanation
Indices: 52610185--52610384 Score: 229
Period size: 90 Copynumber: 2.2 Consensus size: 84
52610175 CCTAAACAGT
* * * *
52610185 AATCAGTAACGGTAGCAGTAACAGTATTCAACACACAAAGTGCTAAATTTGTAACAGTAACGGTA
1 AATCGGTAACGGTAACAGTAACAGTATTCAACACACAAAGTGCCAAA----T--CAGTAACAGTA
52610250 ACAGTATTCGACACACAAAGTGCCG
60 ACAGTATTCGACACACAAAGTGCCG
*
52610275 AATCGGTAACGGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCAAATCGGTAACAGTA
1 AATCGGTAAC-G-----GTAACAGTAACAGTATTCAACACACAAAGTGCCAAATCAGTAACAGTA
52610340 ACAGTATTCGACACACAAAGTGCCG
60 ACAGTATTCGACACACAAAGTGCCG
* *
52610365 AATCGGTAACAGTAATAGTA
1 AATCGGTAACGGTAACAGTA
52610385 GTCAGAATAT
Statistics
Matches: 97, Mismatches: 7, Indels: 18
0.80 0.06 0.15
Matches are distributed among these distances:
84 8 0.08
90 53 0.55
91 1 0.01
92 1 0.01
96 34 0.35
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (84 bp):
AATCGGTAACGGTAACAGTAACAGTATTCAACACACAAAGTGCCAAATCAGTAACAGTAACAGTA
TTCGACACACAAAGTGCCG
Found at i:52615143 original size:17 final size:17
Alignment explanation
Indices: 52615117--52615169 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
52615107 TTTACAGAAT
*
52615117 CAAATTTTCTAAGATTA
1 CAAATCTTCTAAGATTA
*
52615134 CAAATCTTCTAAGATTG
1 CAAATCTTCTAAGATTA
*
52615151 CAAATCCTCTAAAGATTA
1 CAAATCTTCT-AAGATTA
52615169 C
1 C
52615170 TTCCCATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 24 0.77
18 7 0.23
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.34
Consensus pattern (17 bp):
CAAATCTTCTAAGATTA
Found at i:52618096 original size:28 final size:27
Alignment explanation
Indices: 52618053--52618112 Score: 63
Period size: 28 Copynumber: 2.2 Consensus size: 27
52618043 GTTGTGTGGT
52618053 TTTTTTTAGTAATTATATATTT-A-TATA
1 TTTTTTTAGTAATTAT-T-TTTCATTATA
52618080 TTTTTTTA-TAAATTTATTTTTCATTATA
1 TTTTTTTAGT-AA-TTATTTTTCATTATA
52618108 TTTTT
1 TTTTT
52618113 AATTGTGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
26 4 0.14
27 12 0.41
28 13 0.45
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (27 bp):
TTTTTTTAGTAATTATTTTTCATTATA
Found at i:52626357 original size:3 final size:3
Alignment explanation
Indices: 52626338--52626378 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
52626328 AATTTATTTC
* *
52626338 ATA AT- ATA ATA ACA ATA ATA TTA ATA ATA ATA A-A ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
52626379 AATGTCATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:52626362 original size:20 final size:20
Alignment explanation
Indices: 52626339--52626377 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
52626329 ATTTATTTCA
52626339 TAAT-ATAATAACAATAATAT
1 TAATAATAATAA-AATAATAT
52626359 TAATAATAATAAAATAATA
1 TAATAATAATAAAATAATA
52626378 AAATGTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (20 bp):
TAATAATAATAAAATAATAT
Found at i:52630817 original size:30 final size:28
Alignment explanation
Indices: 52630768--52630826 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 28
52630758 ATTATATATA
*
52630768 TTTTATAATTTTTAATTTTAAAAATTGT
1 TTTTATAATTTTTAATTTTAAAAAATGT
52630796 TTTTATAAATTTTTAAATTTTAAAAAATGT
1 TTTTAT-AATTTTT-AATTTTAAAAAATGT
52630826 T
1 T
52630827 GATACGACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 6 0.21
29 7 0.25
30 15 0.54
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (28 bp):
TTTTATAATTTTTAATTTTAAAAAATGT
Found at i:52642626 original size:34 final size:35
Alignment explanation
Indices: 52642586--52642660 Score: 109
Period size: 34 Copynumber: 2.2 Consensus size: 35
52642576 AATTTGTAAT
52642586 ATATAAAAATATTTATTT-AAATTTAATTATAAAA
1 ATATAAAAATATTTATTTAAAATTTAATTATAAAA
* *
52642620 ATAT-AAAATATTTATTTAAAATTTACTTTTAAAA
1 ATATAAAAATATTTATTTAAAATTTAATTATAAAA
*
52642654 ATGTAAA
1 ATATAAA
52642661 TCCCATTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
33 13 0.36
34 21 0.58
35 2 0.06
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (35 bp):
ATATAAAAATATTTATTTAAAATTTAATTATAAAA
Found at i:52648285 original size:76 final size:75
Alignment explanation
Indices: 52648135--52648287 Score: 202
Period size: 76 Copynumber: 2.0 Consensus size: 75
52648125 GCCACACAAC
*
52648135 CTAGACTTCTTAGATCACCAAATCCAAGAATCCAACCCCCCAACTGGACTCTTTCCCTGCACATC
1 CTAGACTTCTTAGATCACCAAATCCAAGAATCCAACCCCCCAACTGGACTCTTTCCCTGCACACC
52648200 GTCTCTGGAA
66 GTCTCTGGAA
* * ***
52648210 CTAGA-TTCCTTAGATCACCAAATTCAAGAGTCCAAAACCCCCC-ACTGGACTCTTTGTTTGCAC
1 CTAGACTT-CTTAGATCACCAAATCCAAGAATCC--AACCCCCCAACTGGACTCTTTCCCTGCAC
*
52648273 ACCGTTTCTGGAA
63 ACCGTCTCTGGAA
52648286 CT
1 CT
52648288 TGCGATTGCA
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
74 2 0.03
75 28 0.41
76 30 0.44
77 8 0.12
ACGTcount: A:0.27, C:0.33, G:0.13, T:0.26
Consensus pattern (75 bp):
CTAGACTTCTTAGATCACCAAATCCAAGAATCCAACCCCCCAACTGGACTCTTTCCCTGCACACC
GTCTCTGGAA
Found at i:52654524 original size:11 final size:11
Alignment explanation
Indices: 52654508--52654532 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
52654498 AATGTCAGAA
52654508 ATTAATCATAT
1 ATTAATCATAT
52654519 ATTAATCATAT
1 ATTAATCATAT
52654530 ATT
1 ATT
52654533 CCCTTATATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (11 bp):
ATTAATCATAT
Found at i:52658252 original size:25 final size:24
Alignment explanation
Indices: 52658224--52658271 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
52658214 ATCCAGGTAA
52658224 TATAACGGGAAGCTCACAAAGAGCC
1 TATAACGGGAAGCTC-CAAAGAGCC
* *
52658249 TATAACGGGTAGCTCCGAAGAGC
1 TATAACGGGAAGCTCCAAAGAGC
52658272 AATTAATCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.35, C:0.23, G:0.27, T:0.15
Consensus pattern (24 bp):
TATAACGGGAAGCTCCAAAGAGCC
Found at i:52660959 original size:25 final size:24
Alignment explanation
Indices: 52660930--52661017 Score: 76
Period size: 25 Copynumber: 3.6 Consensus size: 24
52660920 TTATTATGCA
52660930 CTAATGAACAGAGAGCACAGATGTG
1 CTAAT-AACAGAGAGCACAGATGTG
*
52660955 CTAAT--C-GAAGAGCACTA-ACGTG
1 CTAATAACAG-AGAGCAC-AGATGTG
*
52660977 CTAATAATCAGAGAGCACTGATGTG
1 CTAATAA-CAGAGAGCACAGATGTG
*
52661002 CTAATAATCAAAGAGC
1 CTAATAA-CAGAGAGC
52661018 GCACTAAGGT
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
21 1 0.02
22 17 0.33
23 1 0.02
25 32 0.62
26 1 0.02
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.19
Consensus pattern (24 bp):
CTAATAACAGAGAGCACAGATGTG
Found at i:52661649 original size:47 final size:48
Alignment explanation
Indices: 52661566--52661673 Score: 137
Period size: 47 Copynumber: 2.2 Consensus size: 48
52661556 TGCGCATAAT
52661566 CACATATCACACACCAAAGCCATAACCCAGCCATGGTCTTACACGG-AAG
1 CACATAT--CACACCAAAGCCATAACCCAGCCATGGTCTTACACGGAAAG
* * * * * *
52661615 CACATATCACACCAATGTCATAGCCCAGCTATGGTCTTATACGGAAAT
1 CACATATCACACCAAAGCCATAACCCAGCCATGGTCTTACACGGAAAG
52661663 CACATATCACA
1 CACATATCACA
52661674 TATTGCCATG
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
47 32 0.62
48 13 0.25
49 7 0.13
ACGTcount: A:0.36, C:0.31, G:0.13, T:0.19
Consensus pattern (48 bp):
CACATATCACACCAAAGCCATAACCCAGCCATGGTCTTACACGGAAAG
Found at i:52661696 original size:47 final size:47
Alignment explanation
Indices: 52661566--52661699 Score: 126
Period size: 47 Copynumber: 2.8 Consensus size: 47
52661556 TGCGCATAAT
* * *
52661566 CACATATCACACACCAAAGCCATAACCCAGCCATGGTCTTACACGGAAG
1 CACATAT--CACACCAATGCCATAGCCCAACCATGGTCTTACACGGAAG
* * * * *
52661615 CACATATCACACCAATGTCATAGCCCAGCTATGGTCTTATACGGAAAT
1 CACATATCACACCAATGCCATAGCCCAACCATGGTCTTACACGG-AAG
* * * *
52661663 CACATATCACA-TATTGCCATGGTCCAACCATGGTCTT
1 CACATATCACACCAATGCCATAGCCCAACCATGGTCTT
52661700 TTCTGTCAAT
Statistics
Matches: 71, Mismatches: 13, Indels: 4
0.81 0.15 0.05
Matches are distributed among these distances:
47 51 0.72
48 13 0.18
49 7 0.10
ACGTcount: A:0.33, C:0.31, G:0.14, T:0.22
Consensus pattern (47 bp):
CACATATCACACCAATGCCATAGCCCAACCATGGTCTTACACGGAAG
Found at i:52671474 original size:15 final size:15
Alignment explanation
Indices: 52671454--52671484 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
52671444 CAATGTCCGT
52671454 AAACAATAAACAAAC
1 AAACAATAAACAAAC
*
52671469 AAACAATAAATAAAC
1 AAACAATAAACAAAC
52671484 A
1 A
52671485 TGTATGTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.74, C:0.16, G:0.00, T:0.10
Consensus pattern (15 bp):
AAACAATAAACAAAC
Found at i:52672616 original size:11 final size:11
Alignment explanation
Indices: 52672580--52672649 Score: 72
Period size: 11 Copynumber: 6.4 Consensus size: 11
52672570 TAAATCATTT
*
52672580 CTCTC-AATTT
1 CTCTCAAATTC
52672590 CTCTCCAATATT-
1 CTCT-CAA-ATTC
52672602 CTCTCAAATTC
1 CTCTCAAATTC
52672613 CTCTCAAATTC
1 CTCTCAAATTC
* * *
52672624 TTTTCAATTTC
1 CTCTCAAATTC
52672635 CTCTCAAATTC
1 CTCTCAAATTC
52672646 CTCT
1 CTCT
52672650 TAAAATTTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
10 7 0.14
11 35 0.70
12 5 0.10
13 3 0.06
ACGTcount: A:0.23, C:0.33, G:0.00, T:0.44
Consensus pattern (11 bp):
CTCTCAAATTC
Found at i:52672617 original size:33 final size:33
Alignment explanation
Indices: 52672580--52672649 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
52672570 TAAATCATTT
*
52672580 CTCTCAATTTCTCTCCAATATT-CTCTCAAATTC
1 CTCTCAAATTCTCTCCAAT-TTCCTCTCAAATTC
* *
52672613 CTCTCAAATTCTTTTCAATTTCCTCTCAAATTC
1 CTCTCAAATTCTCTCCAATTTCCTCTCAAATTC
52672646 CTCT
1 CTCT
52672650 TAAAATTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 2 0.06
33 31 0.94
ACGTcount: A:0.23, C:0.33, G:0.00, T:0.44
Consensus pattern (33 bp):
CTCTCAAATTCTCTCCAATTTCCTCTCAAATTC
Found at i:52674521 original size:18 final size:18
Alignment explanation
Indices: 52674485--52674527 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
52674475 TGCCATGTGC
* * *
52674485 GTATCCTAGCCCTTTTAT
1 GTATCCTAACACTTATAT
52674503 GTATCCTAACACTTATAT
1 GTATCCTAACACTTATAT
*
52674521 GTTTCCT
1 GTATCCT
52674528 TTTTCTAGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.21, C:0.26, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACACTTATAT
Found at i:52675198 original size:114 final size:115
Alignment explanation
Indices: 52675004--52675214 Score: 309
Period size: 114 Copynumber: 1.8 Consensus size: 115
52674994 CATGTAATAA
* *
52675004 AATTGAAATTTACTTTTACATTTTTAATATAATAGAAATTCTTTTAAATAACACAATATTTTGAA
1 AATTGAAATTTACTTTAACATTTTTAATAAAATAG-AATTCTTTTAAATAACACAATATTTTGAA
*
52675069 TATTTCTATATTATTTCATTTAATAAA-ATAAAACGTTATTTTGAATAAAGT
65 TATTTCCATATTATTTCATTTAA-AAATATAAAACGTTATTTTGAATAAAGT
* * * **
52675120 AATTGTAATTTACTTTAATATTTTTAATAAAATAG-ATTTTTTTAAATAAGTCAATATTTTGAAT
1 AATTGAAATTTACTTTAACATTTTTAATAAAATAGAATTCTTTTAAATAACACAATATTTTGAAT
*
52675184 ATTTCCATATTATTTGATTTAAAAATATAAA
66 ATTTCCATATTATTTCATTTAAAAATATAAA
52675215 TAATACAATT
Statistics
Matches: 85, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
113 3 0.04
114 51 0.60
116 31 0.36
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.47
Consensus pattern (115 bp):
AATTGAAATTTACTTTAACATTTTTAATAAAATAGAATTCTTTTAAATAACACAATATTTTGAAT
ATTTCCATATTATTTCATTTAAAAATATAAAACGTTATTTTGAATAAAGT
Found at i:52678444 original size:126 final size:126
Alignment explanation
Indices: 52678218--52678509 Score: 408
Period size: 126 Copynumber: 2.3 Consensus size: 126
52678208 TCAGGCCAAA
* **
52678218 CAGGATCTATTGTAGCAAAAGCACGTCCACGTGAGAGCTTCTTTCAGTACTTTTGCTGTTAAAGC
1 CAGGAGCTATTGTAGCAAAAGCACGTCCACGTGAGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
* *
52678283 ATCCTGCTTAAAGCATTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTT
66 ATCCTGCTTAAAGCATTTTTGACACTATTTACTCAGAAACGTCTACTCAAAATTATTTTTT
* *
52678344 CAGGAGCTATTGTAGCAAAAGCGCGTCCACATTGA-AGCTTCTTTCAGTACTTTTGCTGACAAAG
1 CAGGAGCTATTGTAGCAAAAGCACGTCCAC-GTGAGAGCTTCTTTCAGTACTTTTGCTGACAAAG
** *
52678408 CATCAC-GCTTAAAGTGTTTTTGACACTATTTACTCAGAAACGTCTTCTCAAAATTATTTTTT
65 CATC-CTGCTTAAAGCATTTTTGACACTATTTACTCAGAAACGTCTACTCAAAATTATTTTTT
* * * * * *
52678470 CAAGAGCTACTGTAACAAAAGAACGTTCACGTGGGAGCTT
1 CAGGAGCTATTGTAGCAAAAGCACGTCCACGTGAGAGCTT
52678510 TTTTAAATTA
Statistics
Matches: 145, Mismatches: 18, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
125 2 0.01
126 139 0.96
127 4 0.03
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (126 bp):
CAGGAGCTATTGTAGCAAAAGCACGTCCACGTGAGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
ATCCTGCTTAAAGCATTTTTGACACTATTTACTCAGAAACGTCTACTCAAAATTATTTTTT
Found at i:52679040 original size:13 final size:13
Alignment explanation
Indices: 52679022--52679046 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52679012 AAAAAATATT
52679022 ATTTTTTAAAATA
1 ATTTTTTAAAATA
52679035 ATTTTTTAAAAT
1 ATTTTTTAAAAT
52679047 TAGAGAAATA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTTTTTAAAATA
Found at i:52681157 original size:5 final size:5
Alignment explanation
Indices: 52681147--52681174 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
52681137 CTTATGATCA
52681147 ATTTG ATTTG ATTTG ATTTG ATTTG ATT
1 ATTTG ATTTG ATTTG ATTTG ATTTG ATT
52681175 GCATTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.18, T:0.61
Consensus pattern (5 bp):
ATTTG
Found at i:52681916 original size:12 final size:12
Alignment explanation
Indices: 52681899--52681924 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
52681889 CCTGATTTTT
52681899 CTTCAGCTTCTC
1 CTTCAGCTTCTC
52681911 CTTCAGCTTCTC
1 CTTCAGCTTCTC
52681923 CT
1 CT
52681925 GGTTCAGTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.42, G:0.08, T:0.42
Consensus pattern (12 bp):
CTTCAGCTTCTC
Found at i:52701917 original size:47 final size:47
Alignment explanation
Indices: 52701845--52701974 Score: 136
Period size: 47 Copynumber: 2.8 Consensus size: 47
52701835 ATCTAAACAA
* * *
52701845 TACTATAGGATTTGAGATGAACATTTCTCGA-ACTACAGCATAAAAAG
1 TACTATAAGATTTCAGATGAACATTT-TCCACACTACAGCATAAAAAG
* * ** *
52701892 TACTATAAGATTTCAGATGAGCATTTTCCACACTATAGTGTAAACAG
1 TACTATAAGATTTCAGATGAACATTTTCCACACTACAGCATAAAAAG
* * * *
52701939 AACTATAAGATTTCAGATGAATATCTTCCAAACTAC
1 TACTATAAGATTTCAGATGAACATTTTCCACACTAC
52701975 TGTCTACAAC
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
46 3 0.04
47 65 0.96
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (47 bp):
TACTATAAGATTTCAGATGAACATTTTCCACACTACAGCATAAAAAG
Found at i:52712246 original size:15 final size:16
Alignment explanation
Indices: 52712219--52712254 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
52712209 CTGAACAATT
52712219 ATTTTATTTTTTAAAC
1 ATTTTATTTTTTAAAC
52712235 ATTTTA-TTTTTAAAC
1 ATTTTATTTTTTAAAC
52712250 -TTTTA
1 ATTTTA
52712255 ACAACGAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 5 0.25
15 9 0.45
16 6 0.30
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTTATTTTTTAAAC
Found at i:52716798 original size:43 final size:42
Alignment explanation
Indices: 52716744--52716883 Score: 165
Period size: 43 Copynumber: 3.3 Consensus size: 42
52716734 AGACTAAGAC
*
52716744 CTTTAGTGGCGTTTGTGGTCGAAGCGCCGCTATAGATCAGGGT
1 CTTTAGCGGCGTTTGTGG-CGAAGCGCCGCTATAGATCAGGGT
* * *
52716787 TTTTTGCGGCGTTTGTGGGGAAAGCGCCGCTATAGATCAGGGT
1 CTTTAGCGGCGTTTGTGGCG-AAGCGCCGCTATAGATCAGGGT
* * * *
52716830 CTTTAGCGGCATTT-TTGCGGCAAGCGCCGCTAAAGATTAGGGT
1 CTTTAGCGGCGTTTGTGGC-G-AAGCGCCGCTATAGATCAGGGT
52716873 CTTTAGCGGCG
1 CTTTAGCGGCG
52716884 CTTCTCCCTA
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
42 3 0.04
43 79 0.96
ACGTcount: A:0.17, C:0.19, G:0.34, T:0.29
Consensus pattern (42 bp):
CTTTAGCGGCGTTTGTGGCGAAGCGCCGCTATAGATCAGGGT
Found at i:52717079 original size:43 final size:43
Alignment explanation
Indices: 52716932--52717079 Score: 140
Period size: 43 Copynumber: 3.4 Consensus size: 43
52716922 CAGCGCTTCG
*
52716932 ACCACAAACGCCACTAAA-AAGCCTAATCTTTAGCGGCACTTTC
1 ACCACAAACGCCACTAAAGAA-CCTAATCTTTAGCGGCACTTTT
* * * * * **
52716975 CCCACAAACTCC-GTGAAAG-ACCATGATCTTTAGGGGGGCTTTT
1 ACCACAAACGCCACT-AAAGAACC-TAATCTTTAGCGGCACTTTT
* * *
52717018 TCCACAAACGCCGCTAAAGAACCTTATCTTTAGCGGCACTTTT
1 ACCACAAACGCCACTAAAGAACCTAATCTTTAGCGGCACTTTT
*
52717061 ACCAAAAACGCCACTAAAG
1 ACCACAAACGCCACTAAAG
52717080 GCTAACACCT
Statistics
Matches: 82, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
42 3 0.04
43 75 0.91
44 4 0.05
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (43 bp):
ACCACAAACGCCACTAAAGAACCTAATCTTTAGCGGCACTTTT
Found at i:52717455 original size:21 final size:21
Alignment explanation
Indices: 52717429--52717521 Score: 98
Period size: 21 Copynumber: 4.4 Consensus size: 21
52717419 TTTGACGCTG
*
52717429 CTCTGCTTCCCTCACTGTAGC
1 CTCTGCTTCCCTCGCTGTAGC
*
52717450 CTCTGCTTCCCTCGCTTTAGC
1 CTCTGCTTCCCTCGCTGTAGC
* *
52717471 CTCTGCTTCTCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGTAGC
* * **
52717492 CTGTACTTCTCC-CGCTGCCGC
1 CTCTGCTTC-CCTCGCTGTAGC
52717513 CTCTGCTTC
1 CTCTGCTTC
52717522 TCTTGCTGCC
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
21 59 0.98
22 1 0.02
ACGTcount: A:0.05, C:0.44, G:0.16, T:0.34
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGTAGC
Found at i:52717493 original size:42 final size:42
Alignment explanation
Indices: 52717429--52717541 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 42
52717419 TTTGACGCTG
* * * * **
52717429 CTCTGCTTCCCTCACTGTAGCCTCTGCTTC-CCTCGCTTTAGC
1 CTCTGCTTCTCTCGCTGCAGCCTCTACTTCTCC-CGCTGCAGC
* *
52717471 CTCTGCTTCTCTCGCTGCAGCCTGTACTTCTCCCGCTGCCGC
1 CTCTGCTTCTCTCGCTGCAGCCTCTACTTCTCCCGCTGCAGC
* * *
52717513 CTCTGCTTCTCTTGCTGCCGCATCTACTT
1 CTCTGCTTCTCTCGCTGCAGCCTCTACTT
52717542 TAAGCTGCTG
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
42 56 0.97
43 2 0.03
ACGTcount: A:0.06, C:0.42, G:0.16, T:0.35
Consensus pattern (42 bp):
CTCTGCTTCTCTCGCTGCAGCCTCTACTTCTCCCGCTGCAGC
Found at i:52717522 original size:21 final size:21
Alignment explanation
Indices: 52717429--52717533 Score: 93
Period size: 21 Copynumber: 5.0 Consensus size: 21
52717419 TTTGACGCTG
* * **
52717429 CTCTGCTTCCCTCACTGTAGC
1 CTCTGCTTCTCTCGCTGCCGC
* ***
52717450 CTCTGCTTCCCTCGCTTTAGC
1 CTCTGCTTCTCTCGCTGCCGC
*
52717471 CTCTGCTTCTCTCGCTGCAGC
1 CTCTGCTTCTCTCGCTGCCGC
* * *
52717492 CTGTACTTCTCCCGCTGCCGC
1 CTCTGCTTCTCTCGCTGCCGC
*
52717513 CTCTGCTTCTCTTGCTGCCGC
1 CTCTGCTTCTCTCGCTGCCGC
52717534 ATCTACTTTA
Statistics
Matches: 71, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 71 1.00
ACGTcount: A:0.05, C:0.44, G:0.17, T:0.34
Consensus pattern (21 bp):
CTCTGCTTCTCTCGCTGCCGC
Found at i:52717596 original size:66 final size:66
Alignment explanation
Indices: 52717512--52717658 Score: 199
Period size: 66 Copynumber: 2.2 Consensus size: 66
52717502 CCCGCTGCCG
* *
52717512 CCTCTGCTTCTCTTGCTGCCGCATCTACTTTAAGCTGCT-GCTGGAGTTCTTCATA-CTTTCGTT
1 CCTCAGCTTCTCTCGCTGCCGCATCTACTTTAAGCTG-TAGCTGGAGTTCTTCATATCTTT-GTT
52717575 GAA
64 GAA
* * * * *
52717578 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTCAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGA
1 CCTCAGCTTCTCTCGCTGCCGCATCTACTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA
52717643 A
66 A
52717644 CCTCAGCTTCTCTCG
1 CCTCAGCTTCTCTCG
52717659 ATGTTGCCTC
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
65 1 0.01
66 67 0.93
67 4 0.06
ACGTcount: A:0.13, C:0.29, G:0.18, T:0.40
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGCTGCCGCATCTACTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA
A
Found at i:52717674 original size:66 final size:66
Alignment explanation
Indices: 52717551--52717681 Score: 192
Period size: 66 Copynumber: 2.0 Consensus size: 66
52717541 TTAAGCTGCT
* * *
52717551 GCTGGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGCTGCTGCATCTGCTTTCAGTTGT
1 GCTGGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGT
52717616 A
66 A
* * *
52717617 GCTGGAGTTCTTCATATCTTT-TTTGAACCTCAGCTTCTCTCGATGTTGCCTCCGCTTTAAGTTG
1 GCTGGAGTTCTTCATA-CTTTCGTTGAACCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTG
52717681 T
65 T
52717682 GTAATTTGCT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
66 54 0.93
67 4 0.07
ACGTcount: A:0.14, C:0.26, G:0.19, T:0.41
Consensus pattern (66 bp):
GCTGGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGT
A
Found at i:52719832 original size:13 final size:15
Alignment explanation
Indices: 52719813--52719853 Score: 59
Period size: 13 Copynumber: 2.8 Consensus size: 15
52719803 CATATAAGTT
52719813 TATGTAAGTTATG-A
1 TATGTAAGTTATGTA
52719827 -ATGTAAGTTATGTA
1 TATGTAAGTTATGTA
52719841 TTATGTAAGTTAT
1 -TATGTAAGTTAT
52719854 TTAAATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.50
14 1 0.04
16 11 0.46
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (15 bp):
TATGTAAGTTATGTA
Found at i:52719848 original size:16 final size:16
Alignment explanation
Indices: 52719812--52719890 Score: 74
Period size: 16 Copynumber: 5.0 Consensus size: 16
52719802 ACATATAAGT
52719812 TTATGTAAGTTATG-A
1 TTATGTAAGTTATGTA
52719827 --ATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
*
52719841 TTATGTAAGTTATTTAAA
1 TTATGTAAGTTATGT--A
* *
52719859 TTATTTAAGTTGTGTA
1 TTATGTAAGTTATGTA
* *
52719875 TTATATAAGTCATGTA
1 TTATGTAAGTTATGTA
52719891 GGCTATGTGT
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
13 12 0.23
14 1 0.02
16 26 0.50
18 13 0.25
ACGTcount: A:0.34, C:0.01, G:0.16, T:0.48
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:52721361 original size:15 final size:15
Alignment explanation
Indices: 52721341--52721374 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
52721331 CATCAATTGC
*
52721341 AAGACAGCTAGAAAA
1 AAGACAACTAGAAAA
52721356 AAGACAACTAGAAAA
1 AAGACAACTAGAAAA
52721371 AAGA
1 AAGA
52721375 GGTATATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.65, C:0.12, G:0.18, T:0.06
Consensus pattern (15 bp):
AAGACAACTAGAAAA
Found at i:52721611 original size:11 final size:11
Alignment explanation
Indices: 52721597--52721633 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
52721587 TTGATACTAC
52721597 ATTATAATGAA
1 ATTATAATGAA
52721608 ATTATAATGAA
1 ATTATAATGAA
*
52721619 ATTATAATCAA
1 ATTATAATGAA
52721630 ATTA
1 ATTA
52721634 GAAAAGTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (11 bp):
ATTATAATGAA
Found at i:52722853 original size:27 final size:27
Alignment explanation
Indices: 52722821--52722872 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
52722811 TCTTACTTTT
* *
52722821 AAATAATTAATTACCAATTTATTTAAC
1 AAATAAATAATTACCAACTTATTTAAC
*
52722848 AAATAAATAATTACTAACTTATTTA
1 AAATAAATAATTACCAACTTATTTA
52722873 TTTGTTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (27 bp):
AAATAAATAATTACCAACTTATTTAAC
Found at i:52722963 original size:8 final size:10
Alignment explanation
Indices: 52722940--52722976 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
52722930 TAATAACTAT
52722940 ATATATATCC
1 ATATATATCC
*
52722950 ATATATATTC
1 ATATATATCC
52722960 ATATATATCC
1 ATATATATCC
52722970 ATATATA
1 ATATATA
52722977 AGTAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (10 bp):
ATATATATCC
Found at i:52724850 original size:14 final size:14
Alignment explanation
Indices: 52724831--52724898 Score: 52
Period size: 15 Copynumber: 4.9 Consensus size: 14
52724821 ATGACCCTTG
52724831 AAACCCTAAATCTC
1 AAACCCTAAATCTC
*
52724845 AAACCCCTAAACCTC
1 AAA-CCCTAAATCTC
*
52724860 TAACCCCTAAAT-T-
1 -AAACCCTAAATCTC
* *
52724873 -AACCTTAAATCCC
1 AAACCCTAAATCTC
*
52724886 AAACCTTAAATCT
1 AAACCCTAAATCT
52724899 ATACCCCGTA
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
11 8 0.19
14 15 0.36
15 17 0.40
16 2 0.05
ACGTcount: A:0.41, C:0.35, G:0.00, T:0.24
Consensus pattern (14 bp):
AAACCCTAAATCTC
Found at i:52724854 original size:15 final size:15
Alignment explanation
Indices: 52724834--52724871 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
52724824 ACCCTTGAAA
52724834 CCCTAAATCTCAAAC
1 CCCTAAATCTCAAAC
* *
52724849 CCCTAAACCTCTAAC
1 CCCTAAATCTCAAAC
52724864 CCCTAAAT
1 CCCTAAAT
52724872 TAACCTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.37, C:0.42, G:0.00, T:0.21
Consensus pattern (15 bp):
CCCTAAATCTCAAAC
Found at i:52725501 original size:41 final size:41
Alignment explanation
Indices: 52725439--52725659 Score: 266
Period size: 41 Copynumber: 5.4 Consensus size: 41
52725429 GCTTACCTAT
*
52725439 AAAACGCCGCTAAAAGACAGAGCATTAGTGGCGCTCAGATA
1 AAAACGCCGCTAAAGGACAGAGCATTAGTGGCGCTCAGATA
* * *
52725480 AAAACGCCACTAAAGGCCAGAGAATTAGTGGCGCTCAGATA
1 AAAACGCCGCTAAAGGACAGAGCATTAGTGGCGCTCAGATA
* * * * *
52725521 AAAACGCCACTAAA-GATACGAGCATTAGCGGCGCTTAGAGA
1 AAAACGCCGCTAAAGGACA-GAGCATTAGTGGCGCTCAGATA
*
52725562 AAAACGCCGCTAAAGGCCAGAGCATTAGTGGCGCTCAGATA
1 AAAACGCCGCTAAAGGACAGAGCATTAGTGGCGCTCAGATA
* * * * *
52725603 AAAACGCCGCTAAA-GATCGGACCATTAGCGGCGCTAAAATA
1 AAAACGCCGCTAAAGGA-CAGAGCATTAGTGGCGCTCAGATA
*
52725644 AAAATGCCGCTAAAGG
1 AAAACGCCGCTAAAGG
52725660 TTTAAAAATC
Statistics
Matches: 153, Mismatches: 23, Indels: 7
0.84 0.13 0.04
Matches are distributed among these distances:
40 3 0.02
41 147 0.96
42 3 0.02
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.14
Consensus pattern (41 bp):
AAAACGCCGCTAAAGGACAGAGCATTAGTGGCGCTCAGATA
Found at i:52725554 original size:82 final size:83
Alignment explanation
Indices: 52725439--52725659 Score: 313
Period size: 82 Copynumber: 2.7 Consensus size: 83
52725429 GCTTACCTAT
* * * *
52725439 AAAACGCCGCTAAA-AGACAGAGCATTAGTGGCGCTCAGATAAAAACGCCACTAAAGGCCAGAGA
1 AAAACGCCGCTAAAGATACAGAGCATTAGCGGCGCTAAGATAAAAACGCCGCTAAAGGCCAGAGA
52725503 ATTAGTGGCGCTCAGATA
66 ATTAGTGGCGCTCAGATA
* * * *
52725521 AAAACGCCACTAAAGATAC-GAGCATTAGCGGCGCTTAGAGAAAAACGCCGCTAAAGGCCAGAGC
1 AAAACGCCGCTAAAGATACAGAGCATTAGCGGCGCTAAGATAAAAACGCCGCTAAAGGCCAGAGA
52725585 ATTAGTGGCGCTCAGATA
66 ATTAGTGGCGCTCAGATA
* * * *
52725603 AAAACGCCGCTAAAGAT-CGGACCATTAGCGGCGCTAAAATAAAAATGCCGCTAAAGG
1 AAAACGCCGCTAAAGATACAGAGCATTAGCGGCGCTAAGATAAAAACGCCGCTAAAGG
52725660 TTTAAAAATC
Statistics
Matches: 124, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
81 1 0.01
82 120 0.97
83 3 0.02
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.14
Consensus pattern (83 bp):
AAAACGCCGCTAAAGATACAGAGCATTAGCGGCGCTAAGATAAAAACGCCGCTAAAGGCCAGAGA
ATTAGTGGCGCTCAGATA
Found at i:52725998 original size:18 final size:19
Alignment explanation
Indices: 52725977--52726013 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
52725967 TTTAGTTGGA
52725977 TTTGAA-TTTTTTCAAGAG
1 TTTGAATTTTTTTCAAGAG
52725995 TTTGAATTTTTTTCAAGAG
1 TTTGAATTTTTTTCAAGAG
52726014 AAAAAAGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.51
Consensus pattern (19 bp):
TTTGAATTTTTTTCAAGAG
Found at i:52731146 original size:15 final size:16
Alignment explanation
Indices: 52731126--52731158 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
52731116 TTCTATTTTG
*
52731126 ATAAAAAT-TTAAAAT
1 ATAAAAATGGTAAAAT
52731141 ATAAAAATGGTAAAAT
1 ATAAAAATGGTAAAAT
52731157 AT
1 AT
52731159 CGTGTTATGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (16 bp):
ATAAAAATGGTAAAAT
Found at i:52741017 original size:113 final size:114
Alignment explanation
Indices: 52740858--52741495 Score: 745
Period size: 114 Copynumber: 5.6 Consensus size: 114
52740848 AAAGTGCCGC
* ** * * *
52740858 AAAATACCTAAGCCCAACGACGCTATTTTCTGAGCTTTCGGTGATTTAGCGGCGATTTTAAGAAA
1 AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGTGGCGTTTTTAAGAAA
* * *
52740923 GCGCCGCTAATGCTCAAGGCTTTCGCGGCG-TTTCGAGAAAGCGCCACA
66 GCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCACA
* * * *
52740971 AAAAAACCAAAGCCCAACGACACCGTTTTTTGAGCTTTAGGGGATTTAGTGGCGTTTTTAAGTAA
1 AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGTGGCGTTTTTAAG-AA
* *
52741036 A-CGCCGCTAATGCTCAGGGCTTTAGCAGCGTTTTTGGGAAAGCGCCGA-A
65 AGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCC-ACA
* * * *
52741085 AAAATACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGAATTTAGTTGCGTTTTTAAGTAA
1 AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGTGGCGTTTTTAAGAAA
* * * *
52741150 GCGCCACTAATGTTTAGGGCTTTAGCAGCGTTTTTGAGAAAGCGCCACA
66 GCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCACA
* * * *
52741199 AAAAAACCAAAGCCCAATGACGCCGTTTT-TGAGCTTTCGGGGATTTAGTGGTGTTTTTAAGTAA
1 AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGTGGCGTTTTTAAGAAA
*
52741263 GCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCA
66 GCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCACA
* * * * *
52741312 ACAAAAA-CTAAGCCCAACTACACCGTTTTCTGA-CAATTCGTGGGCTTTAGCGGCG-TTTTAAG
1 A-AAAAACCTAAGCCCAACGACGCCGTTTTCTGAGC-TTTCG-GGGATTTAGTGGCGTTTTTAAG
* * * *
52741374 AATGCGCCGCTAATGCTTAGGGCTTTAGCGGCGTTTTTGTTG-AAGCGCCGCA
63 AAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTG-AGAAAGCGCCACA
* * * * *** * *
52741426 AAAAAACCTAAGCCCAACGGCGTCGTTTTCTAAACTTTTAAGGCTTTAGCGGCGTTTTTAA-AAA
1 AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGTGGCGTTTTTAAGAAA
52741490 GCGCCG
66 GCGCCG
52741496 TAAAAGCCTT
Statistics
Matches: 452, Mismatches: 60, Indels: 26
0.84 0.11 0.05
Matches are distributed among these distances:
113 203 0.45
114 235 0.52
115 14 0.03
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.27
Consensus pattern (114 bp):
AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGTGGCGTTTTTAAGAAA
GCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCACA
Found at i:52741257 original size:227 final size:227
Alignment explanation
Indices: 52740857--52741444 Score: 796
Period size: 227 Copynumber: 2.6 Consensus size: 227
52740847 TAAAGTGCCG
**
52740857 CAAAATACCTAAGCCCAACGACGCTATTTTCTGAGCTTTCGGTGATTTAGCGGCGATTTTAAGAA
1 CAAAATACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGG-GATTTAGCGGCG-TTTTAAG-A
* * * *
52740922 AGCGCCGCTAATGCTCAAGGCTTTCGCGGCG-TTTCGAGAAAGCGCCACAAAAAAACCAAAGCCC
63 AGCGCCGCTAATGCTTAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAAACCAAAGCCC
52740986 AACGACACCGTTTTTTGAGCTTTAGGGGATTTAGTGGCGTTTTTAAGTAAACGCCGCTAATGCTC
128 AACGACACCGTTTTTTGAGCTTTAGGGGATTTAGTGGCGTTTTTAAGTAAACGCCGCTAATGCTC
*
52741051 AGGGCTTTAGCAGCGTTTTTGGGAAAGCGCCG-AA
193 AGGGCTTTAGCAGCGTTTTTGAGAAAGCGCCGCAA
**
52741085 -AAAATACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGAATTTAGTTGCGTTTTTAAGTA
1 CAAAATACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGG-ATTTAGCGGCG-TTTTAAG-A
* * *
52741149 AGCGCCACTAATGTTTAGGGCTTTAGCAGCGTTTTTGAGAAAGCGCCACAAAAAAACCAAAGCCC
63 AGCGCCGCTAATGCTTAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAAACCAAAGCCC
* * * * *
52741214 AATGACGCCG-TTTTTGAGCTTTCGGGGATTTAGTGGTGTTTTTAAGTAAGCGCCGCTAATGCTC
128 AACGACACCGTTTTTTGAGCTTTAGGGGATTTAGTGGCGTTTTTAAGTAAACGCCGCTAATGCTC
*
52741278 AGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCAA
193 AGGGCTTTAGCAGCGTTTTTGAGAAAGCGCCGCAA
* * * *
52741313 CAAAA-A-CTAAGCCCAACTACACCGTTTTCTGA-CAATTCGTGGGCTTTAGCGGCGTTTTAAGA
1 CAAAATACCTAAGCCCAACGACGCCGTTTTCTGAGC-TTTC--GGGATTTAGCGGCGTTTTAAGA
* * *
52741375 ATGCGCCGCTAATGCTTAGGGCTTTAGCGGCGTTTTTGTTG-AAGCGCCGCAAAAAAACCTAAGC
63 A-GCGCCGCTAATGCTTAGGGCTTTAGCGGCGTTTTTG-AGAAAGCGCCACAAAAAAACCAAAGC
52741439 CCAACG
126 CCAACG
52741445 GCGTCGTTTT
Statistics
Matches: 318, Mismatches: 33, Indels: 19
0.86 0.09 0.05
Matches are distributed among these distances:
226 4 0.01
227 255 0.80
228 52 0.16
229 7 0.02
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (227 bp):
CAAAATACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGATTTAGCGGCGTTTTAAGAAGC
GCCGCTAATGCTTAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAAACCAAAGCCCAAC
GACACCGTTTTTTGAGCTTTAGGGGATTTAGTGGCGTTTTTAAGTAAACGCCGCTAATGCTCAGG
GCTTTAGCAGCGTTTTTGAGAAAGCGCCGCAA
Found at i:52741853 original size:14 final size:15
Alignment explanation
Indices: 52741825--52741857 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
52741815 AACGTTTATA
52741825 GATTATGGAATTAGG
1 GATTATGGAATTAGG
52741840 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
52741854 GATT
1 GATT
52741858 CTGGTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:52742091 original size:7 final size:7
Alignment explanation
Indices: 52742068--52742136 Score: 57
Period size: 7 Copynumber: 9.6 Consensus size: 7
52742058 TAAATAAGGT
52742068 TTAGGGG
1 TTAGGGG
**
52742075 TTAGTAG
1 TTAGGGG
52742082 TTAGGGG
1 TTAGGGG
*
52742089 TTAGTGGT
1 TTAG-GGG
*
52742097 TTTGGGG
1 TTAGGGG
52742104 TTAGGGG
1 TTAGGGG
*
52742111 TTAGTGGT
1 TTAG-GGG
*
52742119 TTTGGGG
1 TTAGGGG
*
52742126 TTAAGGG
1 TTAGGGG
52742133 TTAG
1 TTAG
52742137 AAGTTAAGAG
Statistics
Matches: 46, Mismatches: 14, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
7 36 0.78
8 10 0.22
ACGTcount: A:0.14, C:0.00, G:0.46, T:0.39
Consensus pattern (7 bp):
TTAGGGG
Found at i:52742106 original size:22 final size:22
Alignment explanation
Indices: 52742081--52742136 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
52742071 GGGGTTAGTA
52742081 GTTAGGGGTTAGTGGTTTTGGG
1 GTTAGGGGTTAGTGGTTTTGGG
52742103 GTTAGGGGTTAGTGGTTTTGGG
1 GTTAGGGGTTAGTGGTTTTGGG
*
52742125 GTTAAGGGTTAG
1 GTTAGGGGTTAG
52742137 AAGTTAAGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.12, C:0.00, G:0.48, T:0.39
Consensus pattern (22 bp):
GTTAGGGGTTAGTGGTTTTGGG
Found at i:52742538 original size:21 final size:20
Alignment explanation
Indices: 52742514--52742564 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
52742504 GGTTTTGACT
* *
52742514 TTTAGGGTTTGGGATTTGGGG
1 TTTAAGGTTT-GGATTTAGGG
*
52742535 TTTAAGGTTTGGTTTTAGGG
1 TTTAAGGTTTGGATTTAGGG
52742555 TTTAAGGTTT
1 TTTAAGGTTT
52742565 AGAATTTATG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 18 0.67
21 9 0.33
ACGTcount: A:0.14, C:0.00, G:0.37, T:0.49
Consensus pattern (20 bp):
TTTAAGGTTTGGATTTAGGG
Found at i:52743706 original size:146 final size:144
Alignment explanation
Indices: 52743509--52743920 Score: 391
Period size: 146 Copynumber: 2.8 Consensus size: 144
52743499 GAAATGTTAT
* * * * **
52743509 CGTTTTGTCTATGATATTAGTGGCGTTTTTAT-GAAAACGCCACAAGCTTGAGTTAACTGTTGGG
1 CGTTTTG--TATGTTATTAGTGGCGTTTTT-TCGAAAACGCCACAGGTTTGAGCTAACTGTTGAT
* *
52743573 GAAACAACTTCG-TTTGAGCTTATAGTTAGTGGCGCTTTACTCAAAACGCCGCAAATTGTTCTAA
63 GAAACGACTTCGTTTTGA-CTTATAGTTAGTGGCGCTTTATTCAAAACGCCGCAAATTGTTCTAA
**
52743637 CATTTATAGAAACGCTGC
127 CATTTATAGAAACGAGGC
* * * *
52743655 CGTTTTGTAAATGTTATTAGTGGCGTTTTTTCGAAAATGCCACGGGTTTGAGGTAAGTGTTGATG
1 CGTTTTGT--ATGTTATTAGTGGCGTTTTTTCGAAAACGCCACAGGTTTGAGCTAACTGTTGATG
* * * * ** * *
52743720 AAGCGACTGCGTTTTGATTTATAGTTAGTGGTGCTTCGGTTC-AAACGCCGCAAAAATGTTTTAA
64 AAACGACTTCGTTTTGACTTATAGTTAGTGGCGCTT-TATTCAAAACGCCGC-AAATTGTTCTAA
* **
52743784 CATTTATTGGTACGAGGC
127 CATTTATAGAAACGAGGC
* * * * * * **
52743802 CGTTTTGCTGTATTATTAGTGGCATTTATTCAAAAACGCCACAGGTGTGAGCTATTTGTTGATGA
1 CGTTTTG-TATGTTATTAGTGGCGTTTTTTCGAAAACGCCACAGGTTTGAGCTAACTGTTGATGA
* *
52743867 AACGGCTTCGTTTTGACTTATAGTTAGTGGCGC-TTATTTATAAACGCCGCAAAT
65 AACGACTTCGTTTTGACTTATAGTTAGTGGCGCTTTATTCA-AAACGCCGCAAAT
52743921 GGTTAATTTT
Statistics
Matches: 213, Mismatches: 44, Indels: 19
0.77 0.16 0.07
Matches are distributed among these distances:
144 3 0.01
145 5 0.02
146 167 0.78
147 37 0.17
148 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (144 bp):
CGTTTTGTATGTTATTAGTGGCGTTTTTTCGAAAACGCCACAGGTTTGAGCTAACTGTTGATGAA
ACGACTTCGTTTTGACTTATAGTTAGTGGCGCTTTATTCAAAACGCCGCAAATTGTTCTAACATT
TATAGAAACGAGGC
Found at i:52745247 original size:15 final size:15
Alignment explanation
Indices: 52745227--52745258 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
52745217 AGGGTTGAAG
52745227 TATTTGGTACTAATT
1 TATTTGGTACTAATT
52745242 TATTTGGTACTAATT
1 TATTTGGTACTAATT
52745257 TA
1 TA
52745259 CTGTTATCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.06, G:0.12, T:0.53
Consensus pattern (15 bp):
TATTTGGTACTAATT
Found at i:52745793 original size:7 final size:7
Alignment explanation
Indices: 52745781--52745813 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
52745771 TAAGTTATTG
52745781 ATTTTCA
1 ATTTTCA
52745788 ATTTTCA
1 ATTTTCA
52745795 ATTTTCA
1 ATTTTCA
52745802 ATTTTCA
1 ATTTTCA
52745809 ATTTT
1 ATTTT
52745814 ATGTCAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61
Consensus pattern (7 bp):
ATTTTCA
Found at i:52746079 original size:20 final size:19
Alignment explanation
Indices: 52746037--52746089 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
52746027 ACTTATTAAT
*
52746037 ATATATATTTTAA-AGTTA
1 ATATATATTTTAATATTTA
52746055 ATATATATTTTCAATATTTA
1 ATATATATTTT-AATATTTA
*
52746075 TTATAT-TTTTAATAT
1 ATATATATTTTAATAT
52746090 ATTTTTACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 16 0.52
19 6 0.19
20 9 0.29
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (19 bp):
ATATATATTTTAATATTTA
Found at i:52746256 original size:13 final size:13
Alignment explanation
Indices: 52746240--52746402 Score: 125
Period size: 13 Copynumber: 12.5 Consensus size: 13
52746230 TTACTAAAAT
*
52746240 TTACTTTAATATA
1 TTACTTAAATATA
*
52746253 TTACTTGAATATA
1 TTACTTAAATATA
*
52746266 TTACTTAAATAAA
1 TTACTTAAATATA
*
52746279 TTACTTAAATACA
1 TTACTTAAATATA
*
52746292 TTACTTACTAAAAT-
1 TTACTTA--AATATA
** *
52746306 TTGGTTAAATTTA
1 TTACTTAAATATA
*
52746319 TTACGTAAATAT-
1 TTACTTAAATATA
*
52746331 TTACTTAAATACA
1 TTACTTAAATATA
*
52746344 TTACTTACTAAAAT-
1 TTACTTA--AATATA
** *
52746358 TTGTTTAAATTTA
1 TTACTTAAATATA
*
52746371 TTACTTAAATATG
1 TTACTTAAATATA
*
52746384 TTACTTAAATACA
1 TTACTTAAATATA
52746397 TTACTT
1 TTACTT
52746403 GCTAAAATTT
Statistics
Matches: 115, Mismatches: 28, Indels: 14
0.73 0.18 0.09
Matches are distributed among these distances:
12 16 0.14
13 83 0.72
14 10 0.09
15 6 0.05
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46
Consensus pattern (13 bp):
TTACTTAAATATA
Found at i:52746321 original size:27 final size:27
Alignment explanation
Indices: 52746282--52746412 Score: 99
Period size: 27 Copynumber: 5.0 Consensus size: 27
52746272 AAATAAATTA
**
52746282 CTTAAATACATTACTTACTAAAATTTG
1 CTTAAATTTATTACTTACTAAAATTTG
* * * *
52746309 GTTAAATTTATTACGTA--AATATTTA
1 CTTAAATTTATTACTTACTAAAATTTG
**
52746334 CTTAAATACATTACTTACTAAAATTTG
1 CTTAAATTTATTACTTACTAAAATTTG
* * *
52746361 TTTAAATTTATTACTTA--AATATGTTA
1 CTTAAATTTATTACTTACTAAAAT-TTG
** *
52746387 CTTAAATACATTACTTGCTAAAATTT
1 CTTAAATTTATTACTTACTAAAATTT
52746413 AAGTATATAT
Statistics
Matches: 77, Mismatches: 22, Indels: 10
0.71 0.20 0.09
Matches are distributed among these distances:
25 23 0.30
26 15 0.19
27 35 0.45
28 4 0.05
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.45
Consensus pattern (27 bp):
CTTAAATTTATTACTTACTAAAATTTG
Found at i:52746380 original size:23 final size:23
Alignment explanation
Indices: 52746296--52746385 Score: 81
Period size: 23 Copynumber: 3.7 Consensus size: 23
52746286 AATACATTAC
*
52746296 TTACTAAAATTTGGTTAAATTTA
1 TTACTAAAATTTGTTTAAATTTA
**
52746319 TTACGTAAATATTTACTTAAATACATTA
1 TTAC-TAAA-ATTTGTTTAAAT---TTA
52746347 CTTACTAAAATTTGTTTAAATTTA
1 -TTACTAAAATTTGTTTAAATTTA
* *
52746371 TTACTTAAATATGTT
1 TTACTAAAATTTGTT
52746386 ACTTAAATAC
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
23 17 0.31
24 7 0.13
25 10 0.18
27 10 0.18
28 7 0.13
29 4 0.07
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.48
Consensus pattern (23 bp):
TTACTAAAATTTGTTTAAATTTA
Found at i:52746628 original size:16 final size:16
Alignment explanation
Indices: 52746607--52746656 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
52746597 CTTATATGTA
52746607 AACTTACATAATACAT
1 AACTTACATAATACAT
*
52746623 AACTTACAT-GT---T
1 AACTTACATAATACAT
52746635 AACTTACATAATACAT
1 AACTTACATAATACAT
52746651 AACTTA
1 AACTTA
52746657 TAATTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
12 10 0.36
13 1 0.04
15 1 0.04
16 16 0.57
ACGTcount: A:0.46, C:0.18, G:0.02, T:0.34
Consensus pattern (16 bp):
AACTTACATAATACAT
Found at i:52746633 original size:28 final size:28
Alignment explanation
Indices: 52746572--52746656 Score: 107
Period size: 28 Copynumber: 2.9 Consensus size: 28
52746562 AATATTTATA
*
52746572 TAAACTTACATAACTATCACATAAGCTTATATG
1 TAAACTTACAT-A--AT-ACATAA-CTTACATG
52746605 TAAACTTACATAATACATAACTTACATG
1 TAAACTTACATAATACATAACTTACATG
*
52746633 TTAACTTACATAATACATAACTTA
1 TAAACTTACATAATACATAACTTA
52746657 TAATTTTTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
28 30 0.60
29 6 0.12
30 2 0.04
32 1 0.02
33 11 0.22
ACGTcount: A:0.45, C:0.18, G:0.04, T:0.34
Consensus pattern (28 bp):
TAAACTTACATAATACATAACTTACATG
Found at i:52746780 original size:29 final size:28
Alignment explanation
Indices: 52746669--52746788 Score: 100
Period size: 28 Copynumber: 4.1 Consensus size: 28
52746659 ATTTTTTTTT
*
52746669 TATATAAACTTACATAATACATTACTTA
1 TATATAAACTTACATAATACATAACTTA
* * * *
52746697 CATATTAACTTACATAACTTA-TTAA-TATT
1 TATATAAACTTACATAA--TACATAACT-TA
52746726 TATATAAACTTACATAACTATCACATAAACTTA
1 TATATAAACTTACAT-A--AT-ACAT-AACTTA
*
52746759 TATGTAAACTTACATAATACATAACTTA
1 TATATAAACTTACATAATACATAACTTA
52746787 TA
1 TA
52746789 AAAATTTTTT
Statistics
Matches: 72, Mismatches: 10, Indels: 20
0.71 0.10 0.20
Matches are distributed among these distances:
28 24 0.33
29 20 0.28
30 6 0.08
31 1 0.01
32 3 0.04
33 17 0.24
34 1 0.01
ACGTcount: A:0.46, C:0.15, G:0.01, T:0.38
Consensus pattern (28 bp):
TATATAAACTTACATAATACATAACTTA
Found at i:52746820 original size:129 final size:125
Alignment explanation
Indices: 52746605--52746847 Score: 362
Period size: 129 Copynumber: 1.9 Consensus size: 125
52746595 AGCTTATATG
* ***
52746605 TAAACTTACATAATACATAACTTACATGTTAACTTACATAATACATAACTTATAATTTTTTTTTT
1 TAAACTTACATAATACATAACTTACATGTAAACTTACATAATACATAACTTATAATAAATTTTTT
* *
52746670 ATATAAACTTACATAATACATTACTTACATATTAACTTACATAACTTATTAATATTTATA
66 ATATAAACTTACATAACACATTACTTACATATGAACTTACATAACTTATTAATATTTATA
*
52746730 TAAACTTACATAACTATCACATAAACTTATATGTAAACTTACATAATACATAACTTATAA-AAAT
1 TAAACTTACAT-A--AT-ACAT-AACTTACATGTAAACTTACATAATACATAACTTATAATAAAT
*
52746794 TTTTTATATAAACTTACATAACACATTACTTACATATGAACTTACATAAGTTAT
61 TTTTTATATAAACTTACATAACACATTACTTACATATGAACTTACATAACTTAT
52746848 CTACAAGCTT
Statistics
Matches: 105, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
125 11 0.10
126 1 0.01
128 2 0.02
129 56 0.53
130 35 0.33
ACGTcount: A:0.44, C:0.14, G:0.02, T:0.40
Consensus pattern (125 bp):
TAAACTTACATAATACATAACTTACATGTAAACTTACATAATACATAACTTATAATAAATTTTTT
ATATAAACTTACATAACACATTACTTACATATGAACTTACATAACTTATTAATATTTATA
Found at i:52746898 original size:129 final size:130
Alignment explanation
Indices: 52746635--52746910 Score: 350
Period size: 129 Copynumber: 2.1 Consensus size: 130
52746625 CTTACATGTT
*** *
52746635 AACTTACATAATACATAACTTATAATTTTTTTTTTATATAAACTTACATAATACATTACTTACAT
1 AACTTACATAATACATAACTTATAATAAATTTTTTATATAAACTTACATAACACATTACTTACAT
* * * *
52746700 ATTAACTTACATAACTTATTAATATTTATATAAACTTACATAACTATCACATAAACTTATATGTA
66 ATGAACTTACATAACTTATTAATATTTATATAAACTTACATAACTATCACATAAACTAACATGAA
52746765 AACTTACATAATACATAACTTATAA-AAATTTTTTATATAAACTTACATAACACATTACTTACAT
1 AACTTACATAATACATAACTTATAATAAATTTTTTATATAAACTTACATAACACATTACTTACAT
* * *
52746829 ATGAACTTACATAAGTTATCTACA-AGCTTATATATAAACTTGCATAACT-T-ACGT-AA-TAAC
66 ATGAACTTACATAACTTAT-TA-ATA--TT-TATATAAACTTACATAACTATCACATAAACTAAC
52746889 AT-AA
126 ATGAA
52746893 CAACTTACATAATACATA
1 -AACTTACATAATACATA
52746911 GCATACATAA
Statistics
Matches: 129, Mismatches: 11, Indels: 13
0.84 0.07 0.08
Matches are distributed among these distances:
128 1 0.01
129 73 0.57
130 30 0.23
131 4 0.03
132 3 0.02
133 18 0.14
ACGTcount: A:0.45, C:0.15, G:0.02, T:0.38
Consensus pattern (130 bp):
AACTTACATAATACATAACTTATAATAAATTTTTTATATAAACTTACATAACACATTACTTACAT
ATGAACTTACATAACTTATTAATATTTATATAAACTTACATAACTATCACATAAACTAACATGAA
Found at i:52746926 original size:9 final size:9
Alignment explanation
Indices: 52746894--52747318 Score: 302
Period size: 9 Copynumber: 48.8 Consensus size: 9
52746884 ATAACATAAC
52746894 AACTTACAT
1 AACTTACAT
52746903 AA--TACAT
1 AACTTACAT
* *
52746910 AGCATACAT
1 AACTTACAT
52746919 AACTTACAT
1 AACTTACAT
52746928 AACTTACAT
1 AACTTACAT
*
52746937 AA--TACAA
1 AACTTACAT
52746944 AACTTACAT
1 AACTTACAT
*
52746953 AACTTAAAT
1 AACTTACAT
* *
52746962 ATCTTACAC
1 AACTTACAT
52746971 AACTTACAT
1 AACTTACAT
*
52746980 AACCTACAT
1 AACTTACAT
52746989 AA--TACATTT
1 AACTTACA--T
52746998 AACTTACAT
1 AACTTACAT
52747007 AACTTACAT
1 AACTTACAT
*
52747016 AA--TACAA
1 AACTTACAT
52747023 AACTTACAT
1 AACTTACAT
*
52747032 AACTTAAAT
1 AACTTACAT
* *
52747041 ATCTTACAC
1 AACTTACAT
52747050 AACTTACAT
1 AACTTACAT
*
52747059 AACCTACAT
1 AACTTACAT
52747068 AA--TACATTT
1 AACTTACA--T
52747077 AACTTACAT
1 AACTTACAT
52747086 AACTTACAT
1 AACTTACAT
* *
52747095 -A-GTACAA
1 AACTTACAT
*
52747102 AATTTACAT
1 AACTTACAT
*
52747111 AACTTAAAT
1 AACTTACAT
* * *
52747120 ATCTCACAC
1 AACTTACAT
52747129 AACTTACAT
1 AACTTACAT
*
52747138 AACCTACAT
1 AACTTACAT
52747147 AA--TACATTT
1 AACTTACA--T
52747156 AACTTACAT
1 AACTTACAT
52747165 AACTTACAT
1 AACTTACAT
52747174 AACTTACAT
1 AACTTACAT
*
52747183 AATACATA-AT
1 -A-ACTTACAT
52747193 AACTTAC--
1 AACTTACAT
*
52747200 AACTTAAAT
1 AACTTACAT
*
52747209 AACATACAT
1 AACTTACAT
* **
52747218 TACTTTGAT
1 AACTTACAT
* *
52747227 AATTTACCT
1 AACTTACAT
52747236 AACTTACAT
1 AACTTACAT
*
52747245 AA--TACAC
1 AACTTACAT
52747252 AACTTACAT
1 AACTTACAT
* *
52747261 AGCTTACTT
1 AACTTACAT
52747270 AA--TACAT
1 AACTTACAT
*
52747277 AACTTACGT
1 AACTTACAT
52747286 AACTT--AT
1 AACTTACAT
*
52747293 ACACGTACAT
1 A-ACTTACAT
52747303 AACTTACAT
1 AACTTACAT
*
52747312 AATTTAC
1 AACTTAC
52747319 TTAATACATA
Statistics
Matches: 322, Mismatches: 62, Indels: 64
0.72 0.14 0.14
Matches are distributed among these distances:
7 54 0.17
8 9 0.03
9 237 0.74
10 6 0.02
11 16 0.05
ACGTcount: A:0.45, C:0.21, G:0.01, T:0.32
Consensus pattern (9 bp):
AACTTACAT
Found at i:52747191 original size:79 final size:78
Alignment explanation
Indices: 52746892--52747175 Score: 477
Period size: 79 Copynumber: 3.6 Consensus size: 78
52746882 TAATAACATA
52746892 ACAACTTACATAA--TACATAGCATACA--TAACTTACATAACTTACATAATACAAAACTTACAT
1 ACAACTTACATAACCTACATA--ATACATTTAACTTACATAACTTACATAATACAAAA-TTACAT
52746953 AACTTAAATATCTTAC
63 AACTTAAATATCTTAC
52746969 ACAACTTACATAACCTACATAATACATTTAACTTACATAACTTACATAATACAAAACTTACATAA
1 ACAACTTACATAACCTACATAATACATTTAACTTACATAACTTACATAATACAAAA-TTACATAA
52747034 CTTAAATATCTTAC
65 CTTAAATATCTTAC
*
52747048 ACAACTTACATAACCTACATAATACATTTAACTTACATAACTTACATAGTACAAAATTTACATAA
1 ACAACTTACATAACCTACATAATACATTTAACTTACATAACTTACATAATACAAAA-TTACATAA
*
52747113 CTTAAATATCTCAC
65 CTTAAATATCTTAC
52747127 ACAACTTACATAACCTACATAATACATTTAACTTACATAACTTACATAA
1 ACAACTTACATAACCTACATAATACATTTAACTTACATAACTTACATAA
52747176 CTTACATAAT
Statistics
Matches: 199, Mismatches: 4, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
77 18 0.09
79 181 0.91
ACGTcount: A:0.47, C:0.21, G:0.01, T:0.31
Consensus pattern (78 bp):
ACAACTTACATAACCTACATAATACATTTAACTTACATAACTTACATAATACAAAATTACATAAC
TTAAATATCTTAC
Found at i:52752851 original size:21 final size:21
Alignment explanation
Indices: 52752827--52752892 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
52752817 CTACAACTTA
*
52752827 AAGCAGAGGCGGCAACGAGGG
1 AAGCAGAGGCGGCAACGAGAG
* *
52752848 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCGGCAACGAGAG
* * *
52752869 AAGCAGAGGCTGCAGCGCGAG
1 AAGCAGAGGCGGCAACGAGAG
52752890 AAG
1 AAG
52752893 TAGCGAGAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.33, C:0.20, G:0.44, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCGGCAACGAGAG
Found at i:52753372 original size:43 final size:42
Alignment explanation
Indices: 52753279--52753518 Score: 243
Period size: 42 Copynumber: 5.6 Consensus size: 42
52753269 AATCCCAAAA
* * * *
52753279 TTAGTGGCATTTTTTATAAAAGCGCCGCTAAAGAACATTA-CTT
1 TTAGCGGCGTTTTTT-TGAAAGCGCCGCTAAAGAACATGATC-T
* * ** *
52753322 TTCGCGGCGTTCGTGATGAAAGCGCCGCTGAAGAACATGATCT
1 TTAGCGGCGTT-TTTTTGAAAGCGCCGCTAAAGAACATGATCT
*
52753365 TTAGCGGCGTTTTTCTT-TAAGCGCCGCTAAAGAACATGATCT
1 TTAGCGGCGTTTTT-TTGAAAGCGCCGCTAAAGAACATGATCT
* * *
52753407 TCAGTGGCGTTTTTTTGAAATCGCCGCTAAAGAACATGATCT
1 TTAGCGGCGTTTTTTTGAAAGCGCCGCTAAAGAACATGATCT
* * * *
52753449 TTAGAGGCGTTTTTTTGTTAAGCGCCGCTAAAGAATATGATTT
1 TTAGCGGCGTTTTTTTG-AAAGCGCCGCTAAAGAACATGATCT
*
52753492 TTAGCGGCTTTTTTTTCG-AAGCGCCGC
1 TTAGCGGCGTTTTTTT-GAAAGCGCCGC
52753519 AAACACCTTT
Statistics
Matches: 164, Mismatches: 27, Indels: 13
0.80 0.13 0.06
Matches are distributed among these distances:
41 2 0.01
42 83 0.51
43 76 0.46
44 3 0.02
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (42 bp):
TTAGCGGCGTTTTTTTGAAAGCGCCGCTAAAGAACATGATCT
Found at i:52753470 original size:85 final size:84
Alignment explanation
Indices: 52753298--52753518 Score: 275
Period size: 85 Copynumber: 2.6 Consensus size: 84
52753288 TTTTTTATAA
* * ** *
52753298 AAGCGCCGCTAAAGAACATTACTTTTC-GCGGCGTTCGTGATGAAAGCGCCGCTGAAGAACATGA
1 AAGCGCCGCTAAAGAACATGA-TTTTCAGCGGCGTT-TTTTTGAAAGCGCCGCTAAAGAACATGA
*
52753362 TCTTTAGCGGCGTTTTTCTTT
64 TCTTTAGAGGCGTTTTTCTTT
* * *
52753383 AAGCGCCGCTAAAGAACATGATCTTCAGTGGCGTTTTTTTGAAATCGCCGCTAAAGAACATGATC
1 AAGCGCCGCTAAAGAACATGATTTTCAGCGGCGTTTTTTTGAAAGCGCCGCTAAAGAACATGATC
*
52753448 TTTAGAGGCGTTTTTTTGTT
66 TTTAGAGGCGTTTTTCT-TT
* * *
52753468 AAGCGCCGCTAAAGAATATGATTTTTAGCGGCTTTTTTTTCG-AAGCGCCGC
1 AAGCGCCGCTAAAGAACATGATTTTCAGCGGCGTTTTTTT-GAAAGCGCCGC
52753519 AAACACCTTT
Statistics
Matches: 117, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
84 44 0.38
85 72 0.62
86 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (84 bp):
AAGCGCCGCTAAAGAACATGATTTTCAGCGGCGTTTTTTTGAAAGCGCCGCTAAAGAACATGATC
TTTAGAGGCGTTTTTCTTT
Found at i:52753920 original size:23 final size:22
Alignment explanation
Indices: 52753865--52753926 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 22
52753855 AAAATAAATT
*
52753865 TTATTTTAT-AACTTTTGAATA
1 TTATTTTATAAAATTTTGAATA
*
52753886 TTATTTAATAAAATTTT-AATA
1 TTATTTTATAAAATTTTGAATA
52753907 TCTACTTTTATAAATATTTT
1 T-TA-TTTTATAAA-ATTTT
52753927 TAAAAAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 13 0.38
22 8 0.24
23 8 0.24
24 5 0.15
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (22 bp):
TTATTTTATAAAATTTTGAATA
Found at i:52766284 original size:15 final size:14
Alignment explanation
Indices: 52766259--52766303 Score: 51
Period size: 11 Copynumber: 3.3 Consensus size: 14
52766249 CAAATAAATT
52766259 TTAACAAATATTGTAA
1 TTAA-AAATA-TGTAA
52766275 TTAAAAATAT-T--
1 TTAAAAATATGTAA
52766286 TTAAAAATATGTAA
1 TTAAAAATATGTAA
52766300 TTAA
1 TTAA
52766304 GTTTATTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
11 10 0.38
12 1 0.04
13 1 0.04
14 5 0.19
15 5 0.19
16 4 0.15
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (14 bp):
TTAAAAATATGTAA
Found at i:52766808 original size:23 final size:24
Alignment explanation
Indices: 52766768--52766822 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
52766758 AATATAATAT
*
52766768 AGAAA-AAATAATTAAAACAAAAC
1 AGAAATAAATAAATAAAACAAAAC
*
52766791 AGAAATAAATAAAT-AAACACAAC
1 AGAAATAAATAAATAAAACAAAAC
*
52766814 ACAAATAAA
1 AGAAATAAA
52766823 AATAACTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 21 0.75
24 7 0.25
ACGTcount: A:0.73, C:0.11, G:0.04, T:0.13
Consensus pattern (24 bp):
AGAAATAAATAAATAAAACAAAAC
Found at i:52766825 original size:25 final size:24
Alignment explanation
Indices: 52766770--52766832 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 24
52766760 TATAATATAG
*
52766770 AAAAAATAATTAAAACAAAACAGA
1 AAAAAATAAATAAAACAAAACAGA
* *
52766794 AATAAATAAATAAACACAACACA-A
1 AAAAAATAAATAAA-ACAAAACAGA
*
52766818 ATAAAAATAACTAAA
1 A-AAAAATAAATAAA
52766833 TTTGGAAACT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
24 14 0.44
25 18 0.56
ACGTcount: A:0.73, C:0.11, G:0.02, T:0.14
Consensus pattern (24 bp):
AAAAAATAAATAAAACAAAACAGA
Found at i:52768017 original size:43 final size:42
Alignment explanation
Indices: 52767914--52768020 Score: 126
Period size: 42 Copynumber: 2.5 Consensus size: 42
52767904 TTATAGAAAT
* **
52767914 AAACGCCGCTAAAGGTCATGTTCTTTAGTGGCGCTTCCTCGA
1 AAACGCCGCTAAAGGTAATGTTCTTTAGCAGCGCTTCCTCGA
* * *
52767956 AAATGCCGCTAAAGGTAATGTTCTTTAGCAGCGTTTTCTTC-A
1 AAACGCCGCTAAAGGTAATGTTCTTTAGCAGCG-CTTCCTCGA
*
52767998 CAAACGCCGCTAAAAGTAATGTT
1 -AAACGCCGCTAAAGGTAATGTT
52768021 TTTTTTTTTC
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
42 30 0.55
43 25 0.45
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (42 bp):
AAACGCCGCTAAAGGTAATGTTCTTTAGCAGCGCTTCCTCGA
Found at i:52768785 original size:26 final size:26
Alignment explanation
Indices: 52768747--52768805 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
52768737 ATTACAATTT
*
52768747 AATTATTTTATAAGCTATAGAGTAAG
1 AATTATTTGATAAGCTATAGAGTAAG
52768773 AATTATTTGATAAGCTATAGAGTAAG
1 AATTATTTGATAAGCTATAGAGTAAG
52768799 AATTATT
1 AATTATT
52768806 ATGCAACGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.42, C:0.03, G:0.15, T:0.39
Consensus pattern (26 bp):
AATTATTTGATAAGCTATAGAGTAAG
Found at i:52769110 original size:18 final size:18
Alignment explanation
Indices: 52769087--52769129 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
52769077 ACCCAATCTA
**
52769087 AACCCAAGTATTCAACCC
1 AACCCAAGTACCCAACCC
*
52769105 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
52769123 AACCCAA
1 AACCCAA
52769130 TCATAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.44, G:0.02, T:0.12
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:52770501 original size:16 final size:16
Alignment explanation
Indices: 52770476--52770513 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
52770466 TTACCCTAGC
*
52770476 GACGGCAGAGGAGTGT
1 GACGGTAGAGGAGTGT
*
52770492 GACGGTAGAGGATTGT
1 GACGGTAGAGGAGTGT
52770508 GACGGT
1 GACGGT
52770514 CGACGAGCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.24, C:0.11, G:0.47, T:0.18
Consensus pattern (16 bp):
GACGGTAGAGGAGTGT
Found at i:52770630 original size:24 final size:24
Alignment explanation
Indices: 52770596--52770650 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
52770586 TCTAGATTTG
*
52770596 GGGGAATTTTGGGGAAAAATTAGA
1 GGGGAAATTTGGGGAAAAATTAGA
*
52770620 GGGGAAATTTGGGGAAAAATTTGA
1 GGGGAAATTTGGGGAAAAATTAGA
52770644 GGGGAAA
1 GGGGAAA
52770651 ACTGAGGGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.40, T:0.22
Consensus pattern (24 bp):
GGGGAAATTTGGGGAAAAATTAGA
Found at i:52770928 original size:20 final size:20
Alignment explanation
Indices: 52770903--52770940 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
52770893 AGTAATGCAT
*
52770903 TTTTAAAAAATAATTACACA
1 TTTTAAAAAATAAATACACA
52770923 TTTTAAAAAATAAATACA
1 TTTTAAAAAATAAATACA
52770941 TCAATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (20 bp):
TTTTAAAAAATAAATACACA
Found at i:52771166 original size:15 final size:16
Alignment explanation
Indices: 52771136--52771169 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
52771126 ATTTTTTTAA
*
52771136 ATATTAATTTATATTT
1 ATATTAATTTACATTT
52771152 ATATT-ATTTACATTT
1 ATATTAATTTACATTT
52771167 ATA
1 ATA
52771170 GTCTAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (16 bp):
ATATTAATTTACATTT
Found at i:52771318 original size:7 final size:7
Alignment explanation
Indices: 52771307--52771369 Score: 54
Period size: 7 Copynumber: 9.0 Consensus size: 7
52771297 CCGTAAATCT
52771307 TAAACCC
1 TAAACCC
* **
52771314 CAAACTA
1 TAAACCC
52771321 TAAACCC
1 TAAACCC
52771328 TAAACCC
1 TAAACCC
52771335 TAAACCC
1 TAAACCC
* * *
52771342 CAAATCA
1 TAAACCC
* *
52771349 TAAAACT
1 TAAACCC
52771356 TAAACCC
1 TAAACCC
52771363 TAAACCC
1 TAAACCC
52771370 GTCAATTAAC
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
7 42 1.00
ACGTcount: A:0.48, C:0.37, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAACCC
Found at i:52771338 original size:28 final size:28
Alignment explanation
Indices: 52771307--52771369 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
52771297 CCGTAAATCT
*
52771307 TAAACCCCAAA-CTATAAACCCTAAACCC
1 TAAACCCCAAATC-ATAAAACCTAAACCC
*
52771335 TAAACCCCAAATCATAAAACTTAAACCC
1 TAAACCCCAAATCATAAAACCTAAACCC
52771363 TAAACCC
1 TAAACCC
52771370 GTCAATTAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 31 0.97
29 1 0.03
ACGTcount: A:0.48, C:0.37, G:0.00, T:0.16
Consensus pattern (28 bp):
TAAACCCCAAATCATAAAACCTAAACCC
Found at i:52771466 original size:21 final size:22
Alignment explanation
Indices: 52771448--52771490 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
52771438 ACCGTAAATC
52771448 TTAAACCC-TAAACCATAAACA
1 TTAAACCCGTAAACCATAAACA
*
52771469 TTAAACCCGTAAACCACAAACA
1 TTAAACCCGTAAACCATAAACA
52771491 ACAACCACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.51, C:0.30, G:0.02, T:0.16
Consensus pattern (22 bp):
TTAAACCCGTAAACCATAAACA
Found at i:52772381 original size:114 final size:114
Alignment explanation
Indices: 52772236--52772954 Score: 1072
Period size: 114 Copynumber: 6.4 Consensus size: 114
52772226 CTATTGGCTT
* * *
52772236 TATACCTCAAGACCAAACGTTGCATTTTGGTTAAGATATTTTGCGGTGCTTTTTATAATGCGCCG
1 TATACCTCAAGACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTTATAATGCGCCG
52772301 CTAATGATGTGCTTTAGCGGCGTTTTCTCATAAGCGCCACTAATTCTAA
66 CTAATGATGTGCTTTAGCGGCGTTTTCTCATAAGCGCCACTAATTCTAA
* * *
52772350 TATACATCAAGACCAAACGTTGCATTTTGGTTAAGATATTTTGCGGCGCTTTTTATAATGCGCCG
1 TATACCTCAAGACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTTATAATGCGCCG
*
52772415 CTAATGATGTGCTTTAGCGGTGTTTTCTCATAAGCGCCACTAATTCTAA
66 CTAATGATGTGCTTTAGCGGCGTTTTCTCATAAGCGCCACTAATTCTAA
* * *
52772464 TATACATCAAGACCAAATGCTGCGTTTTGGTTAAGATATTTTGCGGTGCTTTTTATAATGCGCCG
1 TATACCTCAAGACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTTATAATGCGCCG
52772529 CTAATGATGTGCTTTAGCGGCGTTTTCTCATAAGCGCCACTAATTCTAAA
66 CTAATGATGTGCTTTAGCGGCGTTTTCTCATAAGCGCCACTAATTCT-AA
* *
52772579 TATACCTCAAGACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGACGCTTTTTATAATGCGCTG
1 TATACCTCAAGACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTTATAATGCGCCG
* * *
52772644 CTAATGCTGTTCTTTAGCGGCGTTTTTTCATAAGCGCCACTAATTCTAA
66 CTAATGATGTGCTTTAGCGGCGTTTTCTCATAAGCGCCACTAATTCTAA
*
52772693 TATACCTCAAGACCAAACGCTGC-----------G-T-TTTTGCGGCGCTTTTTATAATGCGCTG
1 TATACCTCAAGACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTTATAATGCGCCG
* * *
52772745 CTAAT-TTCGTGCTTTAGCGCCGTTTTTTCATAAGCGCCACTAATTCTAA
66 CTAATGAT-GTGCTTTAGCGGCGTTTTCTCATAAGCGCCACTAATTCTAA
* * * *
52772794 TATACCTCAAGACCAAGCGCTGCGTTTTGGTTAAGATATTTTACGGCGC-TTTTATAAAGGCGTC
1 TATACCTCAAGACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTTAT-AATGCGCC
* *
52772858 GCTAATTATGTGCTTTAGCGGCGTTTTTTCATAAGCGCCACTAATTCTAA
65 GCTAATGATGTGCTTTAGCGGCGTTTTCTCATAAGCGCCACTAATTCTAA
*
52772908 TATACCTCAAGACCAAACGCTGCGTTTTGGTTACGATATTTTGCGGC
1 TATACCTCAAGACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGGC
52772955 ACTTACAAGT
Statistics
Matches: 558, Mismatches: 30, Indels: 34
0.90 0.05 0.05
Matches are distributed among these distances:
100 1 0.00
101 92 0.16
102 1 0.00
103 1 0.00
112 1 0.00
113 7 0.01
114 348 0.62
115 107 0.19
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (114 bp):
TATACCTCAAGACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTTATAATGCGCCG
CTAATGATGTGCTTTAGCGGCGTTTTCTCATAAGCGCCACTAATTCTAA
Found at i:52772792 original size:101 final size:101
Alignment explanation
Indices: 52772617--52772935 Score: 403
Period size: 101 Copynumber: 3.0 Consensus size: 101
52772607 GGTTAAGATA
* * *
52772617 TTTTGCGACGCTTTTTATAATGCGCTGCTAA-TGCTGTTCTTTAGCGGCGTTTTTTCATAAGCGC
1 TTTTGCGGCGCTTTTTATAATGCGCTGCTAATTTC-GTGCTTTAGCGGCGTTTTTTCATAAGCGC
52772681 CACTAATTCTAATATACCTCAAGACCAAACGCTGCGT
65 CACTAATTCTAATATACCTCAAGACCAAACGCTGCGT
*
52772718 TTTTGCGGCGCTTTTTATAATGCGCTGCTAATTTCGTGCTTTAGCGCCGTTTTTTCATAAGCGCC
1 TTTTGCGGCGCTTTTTATAATGCGCTGCTAATTTCGTGCTTTAGCGGCGTTTTTTCATAAGCGCC
*
52772783 ACTAATTCTAATATACCTCAAGACCAAGCGCTGCGTT
66 ACTAATTCTAATATACCTCAAGACCAAACGCTGCG-T
*
52772820 TTGGTTAAGATATTTTACGGCGC-TTTTATAAAG-GCGTCGCTAATTAT-GTGCTTTAGCGGCGT
1 TT--TT--G--------CGGCGCTTTTTATAATGCGC-T-GCTAATT-TCGTGCTTTAGCGGCGT
52772882 TTTTTCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAACGCTGCGT
51 TTTTTCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAACGCTGCGT
52772933 TTT
1 TTT
52772936 GGTTACGATA
Statistics
Matches: 193, Mismatches: 8, Indels: 24
0.86 0.04 0.11
Matches are distributed among these distances:
101 92 0.48
102 5 0.03
104 2 0.01
106 1 0.01
111 1 0.01
112 2 0.01
113 13 0.07
114 76 0.39
115 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (101 bp):
TTTTGCGGCGCTTTTTATAATGCGCTGCTAATTTCGTGCTTTAGCGGCGTTTTTTCATAAGCGCC
ACTAATTCTAATATACCTCAAGACCAAACGCTGCGT
Found at i:52772878 original size:330 final size:335
Alignment explanation
Indices: 52772236--52772952 Score: 1063
Period size: 330 Copynumber: 2.1 Consensus size: 335
52772226 CTATTGGCTT
* * **
52772236 TATACCTCAAGACCAAACGTTGCATTTTGGTTAAGATATTTTGCGGTGCTTTTTATAATGCGCCG
1 TATACCTCAAGACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGACGCTTTTTATAATGCGCCG
52772301 CTAATGATGTGCTTTAGCGGCGTTTTCTCATAAGCGCCACTAATTCTAATATACATCAAGACCAA
66 CTAATGATGTGCTTTAGCGGCGTTTTCTCATAAGCGCCACTAATTCTAATATACATCAAGACCAA
52772366 ACGTTGCATTTTGGTTAAGATATTTTGCGGCGCTTTTTATAATGCGCCGCTAATGATGTGCTTTA
131 AC--TGC---TTGG-T-AGATATTTTGCGGCGCTTTTTATAATGCGCCGCTAATGATGTGCTTTA
** *
52772431 GCGGTGTTTTCTCATAAGCGCCACTAATTCTAATATACATCAAGACCAAATGCTGCGTTTTGGTT
189 GCGCCGTTTTCTCATAAGCGCCACTAATTCTAATATACATCAAGACCAAACGCTGCGTTTTGGTT
* * *
52772496 AAGATATTTTGCGGTGCTTTTTATAATGCGCCGCTAATGATGTGCTTTAGCGGCGTTTTCTCATA
254 AAGATATTTTACGGCGCTTTTTATAAGGCGCCGCTAATGATGTGCTTTAGCGGCGTTTTCTCATA
52772561 AGCGCCACTAATTCTAAA
319 AGCGCCACTAATTCT-AA
*
52772579 TATACCTCAAGACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGACGCTTTTTATAATGCGCTG
1 TATACCTCAAGACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGACGCTTTTTATAATGCGCCG
* * * *
52772644 CTAATGCTGTTCTTTAGCGGCGTTTTTTCATAAGCGCCACTAATTCTAATATACCTCAAGACCAA
66 CTAATGATGTGCTTTAGCGGCGTTTTCTCATAAGCGCCACTAATTCTAATATACATCAAGACCAA
* * *
52772709 AC-GC-T-G-CG-T-TTTTGCGGCGCTTTTTATAATGCGCTGCTAAT-TTCGTGCTTTAGCGCCG
131 ACTGCTTGGTAGATATTTTGCGGCGCTTTTTATAATGCGCCGCTAATGAT-GTGCTTTAGCGCCG
* * *
52772767 TTTTTTCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAGCGCTGCGTTTTGGTTAAGATA
195 TTTTCTCATAAGCGCCACTAATTCTAATATACATCAAGACCAAACGCTGCGTTTTGGTTAAGATA
* * *
52772832 TTTTACGGCGC-TTTTATAAAGGCGTCGCTAATTATGTGCTTTAGCGGCGTTTTTTCATAAGCGC
260 TTTTACGGCGCTTTTTAT-AAGGCGCCGCTAATGATGTGCTTTAGCGGCGTTTTCTCATAAGCGC
52772896 CACTAATTCTAA
324 CACTAATTCTAA
*
52772908 TATACCTCAAGACCAAACGCTGCGTTTTGGTTACGATATTTTGCG
1 TATACCTCAAGACCAAACGCTGCGTTTTGGTTAAGATATTTTGCG
52772953 GCACTTACAA
Statistics
Matches: 347, Mismatches: 25, Indels: 18
0.89 0.06 0.05
Matches are distributed among these distances:
329 53 0.15
330 165 0.48
331 1 0.00
332 1 0.00
335 1 0.00
336 1 0.00
340 2 0.01
343 123 0.35
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (335 bp):
TATACCTCAAGACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGACGCTTTTTATAATGCGCCG
CTAATGATGTGCTTTAGCGGCGTTTTCTCATAAGCGCCACTAATTCTAATATACATCAAGACCAA
ACTGCTTGGTAGATATTTTGCGGCGCTTTTTATAATGCGCCGCTAATGATGTGCTTTAGCGCCGT
TTTCTCATAAGCGCCACTAATTCTAATATACATCAAGACCAAACGCTGCGTTTTGGTTAAGATAT
TTTACGGCGCTTTTTATAAGGCGCCGCTAATGATGTGCTTTAGCGGCGTTTTCTCATAAGCGCCA
CTAATTCTAA
Found at i:52772995 original size:114 final size:113
Alignment explanation
Indices: 52772753--52772998 Score: 318
Period size: 114 Copynumber: 2.2 Consensus size: 113
52772743 TGCTAATTTC
* * *
52772753 GTGCTTTAGCGCCGTTTTTTCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAGCGCTGCG
1 GTGCTTTAACGGCGTTTTTTCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAACGCTGCG
* ** * *
52772818 TTTTGGTTAAGATATTTTACGGCGCTTTTATAAAGGCGTCGCTAATTAT
66 TTTTGGTTAAGATATTTTACGGCACTTCAATAAA-GCGCCGCTAAATAT
*
52772867 GTGCTTTAGCGGCGTTTTTTCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAACGCTGCG
1 GTGCTTTAACGGCGTTTTTTCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAACGCTGCG
* *
52772932 TTTTGGTTACGATATTTTGCGGCACTTACAAGTAAA-CGCCGC-AAAT-T
66 TTTTGGTTAAGATATTTTACGGCACTT-CAA-TAAAGCGCCGCTAAATAT
*
52772979 GTGCTATTTAATGGCGTTTT
1 GTGC--TTTAACGGCGTTTT
52772999 GTAGTGCGCT
Statistics
Matches: 117, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
112 5 0.04
113 3 0.03
114 104 0.89
115 1 0.01
116 4 0.03
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.35
Consensus pattern (113 bp):
GTGCTTTAACGGCGTTTTTTCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAACGCTGCG
TTTTGGTTAAGATATTTTACGGCACTTCAATAAAGCGCCGCTAAATAT
Found at i:52781117 original size:8 final size:8
Alignment explanation
Indices: 52781106--52781156 Score: 58
Period size: 7 Copynumber: 6.9 Consensus size: 8
52781096 GTGAAAAATG
52781106 TGAAAAAA
1 TGAAAAAA
52781114 TG--AAAA
1 TGAAAAAA
52781120 TG-AAAAA
1 TGAAAAAA
52781127 TGAAAAAA
1 TGAAAAAA
52781135 TG-AAAAA
1 TGAAAAAA
52781142 TGGAAAAAA
1 T-GAAAAAA
52781151 T-AAAAA
1 TGAAAAA
52781157 TGGAGAGGCT
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
6 6 0.15
7 17 0.44
8 10 0.26
9 6 0.15
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (8 bp):
TGAAAAAA
Found at i:52781126 original size:7 final size:7
Alignment explanation
Indices: 52781109--52781158 Score: 59
Period size: 6 Copynumber: 7.0 Consensus size: 7
52781099 AAAAATGTGA
52781109 AAAAATG
1 AAAAATG
52781116 -AAAATG
1 AAAAATG
52781122 AAAAATG
1 AAAAATG
52781129 AAAAAATG
1 -AAAAATG
52781137 AAAAATGG
1 AAAAAT-G
52781145 AAAAAAT-
1 -AAAAATG
52781152 AAAAATG
1 AAAAATG
52781159 GAGAGGCTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
6 12 0.32
7 12 0.32
8 8 0.21
9 6 0.16
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:52781159 original size:15 final size:16
Alignment explanation
Indices: 52781116--52781160 Score: 76
Period size: 15 Copynumber: 2.9 Consensus size: 16
52781106 TGAAAAAATG
52781116 AAAATGAAAAAT-GAA
1 AAAATGAAAAATGGAA
52781131 AAAATGAAAAATGGAA
1 AAAATGAAAAATGGAA
52781147 AAAAT-AAAAATGGA
1 AAAATGAAAAATGGA
52781161 GAGGCTAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 21 0.72
16 8 0.28
ACGTcount: A:0.71, C:0.00, G:0.16, T:0.13
Consensus pattern (16 bp):
AAAATGAAAAATGGAA
Found at i:52782718 original size:100 final size:100
Alignment explanation
Indices: 52782593--52783490 Score: 1332
Period size: 100 Copynumber: 9.0 Consensus size: 100
52782583 CTTTGACATT
* *
52782593 GCAATTAAAAAGATTAAAGCCACAACGGCGGATCTTACTTCCCTGGTGGTGCAGTGGAGCAGATT
1 GCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATT
*
52782658 GAAATCACAACGGCAGATCTGGTTTCCCCGACAGC
66 GAAGTCACAACGGCAGATCTGGTTTCCCCGACAGC
* * *
52782693 ACAATTAAAAAGATTGAGGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGCAGCAGATT
1 GCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATT
*
52782758 GAAGTCACAACGGCAGATTTGGTTTCCCCGACAGC
66 GAAGTCACAACGGCAGATCTGGTTTCCCCGACAGC
* * *
52782793 GCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGCAATGGAACAGATT
1 GCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATT
* *
52782858 GAAGTCACAACAGCAGATCTGGTTTCTCCGACAGC
66 GAAGTCACAACGGCAGATCTGGTTTCCCCGACAGC
* * * *
52782893 GTAATTAAAAAGATTGAAGCCACAACAGCAGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATC
1 GCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATT
52782958 GAAGTCACAACGGCAGATCTGGTTTCCCCGACAGC
66 GAAGTCACAACGGCAGATCTGGTTTCCCCGACAGC
* *
52782993 GCAATTAAAAAGATTGAAGCCACAACGACGGATCTTACTTCCCTGGCGGTGCAATGGAGCAGATT
1 GCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATT
* *
52783058 GAAGTCACAACGACAGATCTGGTTTCCCCGACAGG
66 GAAGTCACAACGGCAGATCTGGTTTCCCCGACAGC
* * *
52783093 GCAATTAAAAAGATTGAAGTCACAACAGCGGATCTTACTTCCCTGGCGATGCAGTGGAGCAGATT
1 GCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATT
*
52783158 GAAGTCACAACGGCAGATTTGGTTTCCCCGACAGC
66 GAAGTCACAACGGCAGATCTGGTTTCCCCGACAGC
**
52783193 GCAATTAAAAAGATTGAAGCCACAACGGTAGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATT
1 GCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATT
* *
52783258 GAAGTCACAACGGTAGATCTGGTTTCTCCGACAGC
66 GAAGTCACAACGGCAGATCTGGTTTCCCCGACAGC
* * * *
52783293 GCAATTAAAAAGATTGAAGCCACAACGGTGGATCTTACTTTCCTGGCGGCGCAGTGAAGCAGATT
1 GCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATT
* *
52783358 GAAGTCACAATGGCGGATCTGGTTTCCCCGACAGC
66 GAAGTCACAACGGCAGATCTGGTTTCCCCGACAGC
* * * * * * * * * *
52783393 GTAATT-AAAAGAATTGAAGCCACAACGACGAATTTTACCTCCTTAGCAGTGCAGTTGAACAGAT
1 GCAATTAAAAAG-ATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGAT
* * * *
52783457 TGAAG-CTACGACGGCGGATCTTGTTTCCTCGACA
65 TGAAGTC-ACAACGGCAGATCTGGTTTCCCCGACA
52783491 TTGTAATTGG
Statistics
Matches: 721, Mismatches: 75, Indels: 4
0.90 0.09 0.00
Matches are distributed among these distances:
99 6 0.01
100 715 0.99
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.22
Consensus pattern (100 bp):
GCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATT
GAAGTCACAACGGCAGATCTGGTTTCCCCGACAGC
Found at i:52784992 original size:3 final size:3
Alignment explanation
Indices: 52784984--52785014 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
52784974 AATCCTTAAT
52784984 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
52785015 ATACACGCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:52793121 original size:21 final size:23
Alignment explanation
Indices: 52793086--52793129 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
52793076 TTTTTGAACT
*
52793086 TTTTTCATCTTCTTCTTCCTTTC
1 TTTTTCATCTTCTTCTCCCTTTC
52793109 TTTTTC-T-TTCTTCTCCCTTTC
1 TTTTTCATCTTCTTCTCCCTTTC
52793130 ATAATTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 13 0.65
22 1 0.05
23 6 0.30
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTTTCATCTTCTTCTCCCTTTC
Found at i:52796062 original size:43 final size:43
Alignment explanation
Indices: 52795996--52796110 Score: 146
Period size: 43 Copynumber: 2.7 Consensus size: 43
52795986 AACTCGTATA
* * *
52795996 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATA-TCT
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACA-AGTCG
52796039 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGTAAACACAAGTCG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAAACACAAGTCG
*
52796082 ATGCCAACGTCCCTGACGTGGTCTTACAC
1 ATGCCAACGTCCCAGACGTGGTCTTACAC
52796111 AAAAAACACA
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
42 4 0.06
43 56 0.89
44 3 0.05
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.23
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACAAGTCG
Found at i:52825278 original size:2 final size:2
Alignment explanation
Indices: 52825271--52825297 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
52825261 AGATCTAAAA
52825271 AG AG AG 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 A
52825298 AAGAAAAACA
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:52832113 original size:20 final size:20
Alignment explanation
Indices: 52832059--52832110 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
52832049 GTTAATAAAT
** *
52832059 AATTCAAAAATAAAAAATAA
1 AATTCAAAAATAATTATTAA
52832079 AATTCAAAAATAATTATTAA
1 AATTCAAAAATAATTATTAA
52832099 AAGTTCATAAAA
1 AA-TTCA-AAAA
52832111 ATTCAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 19 0.70
21 4 0.15
22 4 0.15
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (20 bp):
AATTCAAAAATAATTATTAA
Found at i:52832655 original size:17 final size:17
Alignment explanation
Indices: 52832633--52832675 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
52832623 AGTATATTGA
*
52832633 ATATTAACTT-TTATATT
1 ATATTAAATTATT-TATT
52832650 ATATTAAATTATTTATT
1 ATATTAAATTATTTATT
*
52832667 ATAATAAAT
1 ATATTAAAT
52832676 AATATTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 21 0.91
18 2 0.09
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATTAAATTATTTATT
Found at i:52833328 original size:15 final size:15
Alignment explanation
Indices: 52833304--52833333 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52833294 TTAACTCGAT
52833304 ATTAAATTTTTTATA
1 ATTAAATTTTTTATA
*
52833319 ATTAATTTTTTTATA
1 ATTAAATTTTTTATA
52833334 TTGAAATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTAAATTTTTTATA
Found at i:52844527 original size:8 final size:8
Alignment explanation
Indices: 52844504--52844544 Score: 64
Period size: 8 Copynumber: 5.0 Consensus size: 8
52844494 AATAAATAAG
52844504 TATTATAT
1 TATTATAT
52844512 TAATTATAT
1 T-ATTATAT
*
52844521 TATTATAA
1 TATTATAT
52844529 TATTATAT
1 TATTATAT
52844537 TATTATAT
1 TATTATAT
52844545 ATATAACAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 22 0.73
9 8 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TATTATAT
Found at i:52845556 original size:22 final size:22
Alignment explanation
Indices: 52845528--52845585 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
52845518 ATTTAGCACA
52845528 TCAGTGTTCTCTGTATAACACT
1 TCAGTGTTCTCTGTATAACACT
*
52845550 TCAGTGTTCTCTGTATAGCACT
1 TCAGTGTTCTCTGTATAACACT
* *
52845572 TCTGTGCTCTCTGT
1 TCAGTGTTCTCTGT
52845586 TCATTAGTGC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.16, C:0.24, G:0.17, T:0.43
Consensus pattern (22 bp):
TCAGTGTTCTCTGTATAACACT
Found at i:52849588 original size:23 final size:23
Alignment explanation
Indices: 52849562--52849605 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
52849552 TGAAAAGGCA
*
52849562 AGTCATTTTTGTAAAAAAAAACG
1 AGTCATTTTTATAAAAAAAAACG
52849585 AGTCATTTTTATAAAAAAAAA
1 AGTCATTTTTATAAAAAAAAA
52849606 ACCAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.52, C:0.07, G:0.09, T:0.32
Consensus pattern (23 bp):
AGTCATTTTTATAAAAAAAAACG
Found at i:52851918 original size:23 final size:25
Alignment explanation
Indices: 52851892--52851954 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 25
52851882 AATTTTAATT
52851892 AATTTA-ATTTATGATA-TAT-TATA
1 AATTTATATTTAT-ATATTATATATA
*
52851915 AATTTATATTTGTATATTATATATA
1 AATTTATATTTATATATTATATATA
52851940 AATAATTATATTTAT
1 AAT--TTATATTTAT
52851955 TTAATAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 9 0.27
24 8 0.24
25 7 0.21
27 9 0.27
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (25 bp):
AATTTATATTTATATATTATATATA
Found at i:52852051 original size:31 final size:32
Alignment explanation
Indices: 52851982--52852061 Score: 101
Period size: 33 Copynumber: 2.5 Consensus size: 32
52851972 TTGATATATT
* *
52851982 TTTTA-ATGTATAATTGAATTAAAATAAAATTA
1 TTTTATATATATAATTGAATCAAAATAAAA-TA
* *
52852014 TTTTATATATATATTTGAATCAAAATTAAA-A
1 TTTTATATATATAATTGAATCAAAATAAAATA
52852045 TTTTATATATATAATTG
1 TTTTATATATATAATTG
52852062 TGTCAAATCA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
31 17 0.40
32 5 0.12
33 20 0.48
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.47
Consensus pattern (32 bp):
TTTTATATATATAATTGAATCAAAATAAAATA
Found at i:52852272 original size:17 final size:18
Alignment explanation
Indices: 52852252--52852286 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
52852242 ATTAAGTTAA
52852252 ATAT-TAAATTAAAATTT
1 ATATATAAATTAAAATTT
*
52852269 ATATATAATTTAAAATTT
1 ATATATAAATTAAAATTT
52852287 TACTACTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATATAAATTAAAATTT
Found at i:52875657 original size:17 final size:16
Alignment explanation
Indices: 52875636--52875720 Score: 52
Period size: 17 Copynumber: 5.1 Consensus size: 16
52875626 TGTAATATTT
52875636 TTAATTTTATTTTTAA
1 TTAATTTTATTTTTAA
*
52875652 TGTAATTTCA-TTTTAA
1 T-TAATTTTATTTTTAA
* *
52875668 TT-A-TTT-TTATGAA
1 TTAATTTTATTTTTAA
52875681 GTTAGATTTTATAATTATTAA
1 -TTA-ATTTTAT--TT-TTAA
52875702 TTAATTTTATATTTTAA
1 TTAATTTTAT-TTTTAA
52875719 TT
1 TT
52875721 TAGATATTGG
Statistics
Matches: 53, Mismatches: 6, Indels: 19
0.68 0.08 0.24
Matches are distributed among these distances:
13 6 0.11
14 3 0.06
15 1 0.02
16 9 0.17
17 16 0.30
18 4 0.08
19 7 0.13
20 4 0.08
21 3 0.06
ACGTcount: A:0.33, C:0.01, G:0.05, T:0.61
Consensus pattern (16 bp):
TTAATTTTATTTTTAA
Found at i:52875710 original size:19 final size:17
Alignment explanation
Indices: 52875636--52875720 Score: 58
Period size: 16 Copynumber: 5.1 Consensus size: 17
52875626 TGTAATATTT
52875636 TTAATTTTAT-TTTTAA
1 TTAATTTTATATTTTAA
*
52875652 TGTAA-TTT-CATTTTAA
1 T-TAATTTTATATTTTAA
*
52875668 TT-ATTTT-TA--TGAA
1 TTAATTTTATATTTTAA
52875681 GTTAGATTTTATAATTATTAA
1 -TTA-ATTTTAT-ATT-TTAA
52875702 TTAATTTTATATTTTAA
1 TTAATTTTATATTTTAA
52875719 TT
1 TT
52875721 TAGATATTGG
Statistics
Matches: 54, Mismatches: 4, Indels: 21
0.68 0.05 0.27
Matches are distributed among these distances:
13 3 0.06
14 3 0.06
15 5 0.09
16 16 0.30
17 10 0.19
18 4 0.07
19 7 0.13
20 3 0.06
21 3 0.06
ACGTcount: A:0.33, C:0.01, G:0.05, T:0.61
Consensus pattern (17 bp):
TTAATTTTATATTTTAA
Found at i:52887845 original size:3 final size:3
Alignment explanation
Indices: 52887837--52887880 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
52887827 TCATCTCCCT
*
52887837 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC CTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
52887881 GTTTTAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:52893988 original size:3 final size:3
Alignment explanation
Indices: 52893969--52894002 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
52893959 ATTAGCTTAA
* *
52893969 TAT TTT TAT TAT CAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
52894003 TTTAATGTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:52895869 original size:30 final size:30
Alignment explanation
Indices: 52895833--52895893 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
52895823 TGCCACCCCC
52895833 TAGAATCGCCTCTGTGGGTGGGGAAAGAAG
1 TAGAATCGCCTCTGTGGGTGGGGAAAGAAG
52895863 TAGAATCGCCTCTGTGGGTGGGGAAAGAAG
1 TAGAATCGCCTCTGTGGGTGGGGAAAGAAG
52895893 T
1 T
52895894 TGGAACTAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.13, G:0.39, T:0.21
Consensus pattern (30 bp):
TAGAATCGCCTCTGTGGGTGGGGAAAGAAG
Found at i:52897908 original size:33 final size:33
Alignment explanation
Indices: 52897861--52897928 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
52897851 CGTGGTTGTA
52897861 AGATTGAAAATTGTATGGTATTGTATGTGTAGG
1 AGATTGAAAATTGTATGGTATTGTATGTGTAGG
*
52897894 AGATTGAAACTTGTATGGTATTGTATGTGTAGG
1 AGATTGAAAATTGTATGGTATTGTATGTGTAGG
52897927 AG
1 AG
52897929 CCGCCCAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.31, T:0.38
Consensus pattern (33 bp):
AGATTGAAAATTGTATGGTATTGTATGTGTAGG
Found at i:52901325 original size:9 final size:9
Alignment explanation
Indices: 52901308--52901341 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
52901298 AACGGTTTGG
52901308 GCTGCTGTT
1 GCTGCTGTT
*
52901317 GCTGTTGTT
1 GCTGCTGTT
*
52901326 GCTGCTGCT
1 GCTGCTGTT
52901335 GCTGCTG
1 GCTGCTG
52901342 ATGACGCTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.00, C:0.24, G:0.35, T:0.41
Consensus pattern (9 bp):
GCTGCTGTT
Found at i:52905244 original size:33 final size:33
Alignment explanation
Indices: 52905206--52905272 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
52905196 TTCTGACTTC
*
52905206 GCCCCTAAATGTGACAAAAAGGGTAAATATTAA
1 GCCCCTAAATGTGACAAAAAGGATAAATATTAA
52905239 GCCCCTAAATGTGACAAAAAGGATAAATATTAA
1 GCCCCTAAATGTGACAAAAAGGATAAATATTAA
52905272 G
1 G
52905273 GGTTAGATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.46, C:0.15, G:0.18, T:0.21
Consensus pattern (33 bp):
GCCCCTAAATGTGACAAAAAGGATAAATATTAA
Found at i:52906925 original size:19 final size:17
Alignment explanation
Indices: 52906899--52906944 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 17
52906889 TAAACAAGAT
*
52906899 ATTTTTTAAAATTATATA
1 ATTTTTTAAAATGA-ATA
52906917 ATATTTTTACAAATGAATA
1 AT-TTTTTA-AAATGAATA
52906936 ATTTTTTAA
1 ATTTTTTAA
52906945 GGTGACCATC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 1 0.04
18 8 0.32
19 11 0.44
20 5 0.20
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
ATTTTTTAAAATGAATA
Found at i:52908078 original size:18 final size:18
Alignment explanation
Indices: 52908055--52908092 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
52908045 AGGGTGTCAC
*
52908055 TTTTTC-TGATGATTCAAG
1 TTTTTCGTGATCATT-AAG
52908073 TTTTTCGTGATCATTAAG
1 TTTTTCGTGATCATTAAG
52908091 TT
1 TT
52908093 ACTGTAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.21, C:0.11, G:0.16, T:0.53
Consensus pattern (18 bp):
TTTTTCGTGATCATTAAG
Found at i:52915139 original size:6 final size:6
Alignment explanation
Indices: 52915116--52915154 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
52915106 AAAAAGGAGA
* * *
52915116 AAAAGA AAAAGG AAAAGG AAAAGG AAACGG AAACGG AAA
1 AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAA
52915155 CTTCAGGACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.67, C:0.05, G:0.28, T:0.00
Consensus pattern (6 bp):
AAAAGG
Found at i:53096799 original size:3 final size:3
Alignment explanation
Indices: 53096793--53096828 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
53096783 GTGGTCCTCT
53096793 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
53096829 GAGAGTGCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.67, T:0.33
Consensus pattern (3 bp):
TGG
Found at i:53100069 original size:6 final size:6
Alignment explanation
Indices: 53100058--53100099 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
53100048 CTTCCTTGGC
53100058 TTATAT TTATAT TTATA- TT-TAT TTATAT TTATAT TTATAT TT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TT
53100100 GAAGGACTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 2 0.06
5 4 0.12
6 28 0.82
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTATAT
Found at i:53100082 original size:16 final size:16
Alignment explanation
Indices: 53100061--53100095 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
53100051 CCTTGGCTTA
53100061 TATTTATATTTATATT
1 TATTTATATTTATATT
53100077 TATTTATATTTATATT
1 TATTTATATTTATATT
53100093 TAT
1 TAT
53100096 ATTTGAAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TATTTATATTTATATT
Found at i:53100086 original size:22 final size:22
Alignment explanation
Indices: 53100058--53100099 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
53100048 CTTCCTTGGC
53100058 TTATATTTATATTTATATTTAT
1 TTATATTTATATTTATATTTAT
53100080 TTATATTTATATTTATATTT
1 TTATATTTATATTTATATTT
53100100 GAAGGACTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
TTATATTTATATTTATATTTAT
Done.