Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 196 of 204
Found at i:57781855 original size:16 final size:15
Alignment explanation
Indices: 57781836--57781870 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
57781826 TTTATATTAT
*
57781836 TTTTGTTTTCTTTTTC
1 TTTTGTTTTC-CTTTC
57781852 TTTTGTTTTCCTTTC
1 TTTTGTTTTCCTTTC
57781867 TTTT
1 TTTT
57781871 TTCATGGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (15 bp):
TTTTGTTTTCCTTTC
Found at i:57782529 original size:9 final size:9
Alignment explanation
Indices: 57782505--57782539 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
57782495 TTAATTATAA
*
57782505 TACTATTAT
1 TACTATTAC
*
57782514 TATTATTAC
1 TACTATTAC
57782523 TACTATTAC
1 TACTATTAC
57782532 TACTATTA
1 TACTATTA
57782540 TTATAGGTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.51
Consensus pattern (9 bp):
TACTATTAC
Found at i:57782727 original size:25 final size:23
Alignment explanation
Indices: 57782698--57782768 Score: 56
Period size: 25 Copynumber: 3.0 Consensus size: 23
57782688 ACATTTTTTA
57782698 TAATTTTATTTTACAATATATTC
1 TAATTTTATTTTACAATATATTC
** *
57782721 ATAAATTCCATTTT--TATATATTTC
1 -T-AATTTTATTTTACAATATA-TTC
57782745 TAATTTTATTTATACAATAATATT
1 TAATTTTATTT-TACAAT-ATATT
57782769 TTCATAATTC
Statistics
Matches: 35, Mismatches: 6, Indels: 11
0.67 0.12 0.21
Matches are distributed among these distances:
22 8 0.23
23 7 0.20
24 4 0.11
25 13 0.37
26 3 0.09
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (23 bp):
TAATTTTATTTTACAATATATTC
Found at i:57785514 original size:19 final size:18
Alignment explanation
Indices: 57785464--57785514 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
57785454 AAATTGTGTC
*
57785464 ATTCATTTTCAAAATATT
1 ATTCAATTTCAAAATATT
*
57785482 ATTC-ATTT-ATAAATCGTT
1 ATTCAATTTCA-AAAT-ATT
57785500 ATTCAATTTCAAAAT
1 ATTCAATTTCAAAAT
57785515 GTTTTTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
16 1 0.04
17 7 0.26
18 10 0.37
19 8 0.30
20 1 0.04
ACGTcount: A:0.39, C:0.12, G:0.02, T:0.47
Consensus pattern (18 bp):
ATTCAATTTCAAAATATT
Found at i:57787637 original size:21 final size:21
Alignment explanation
Indices: 57787611--57787653 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
57787601 GAAAAAGGAA
57787611 AAAAATGATCAGATTTTGGAT
1 AAAAATGATCAGATTTTGGAT
57787632 AAAAATGATCAGATTTTGGAT
1 AAAAATGATCAGATTTTGGAT
57787653 A
1 A
57787654 TATTCCCCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.33
Consensus pattern (21 bp):
AAAAATGATCAGATTTTGGAT
Found at i:57790348 original size:21 final size:20
Alignment explanation
Indices: 57790322--57790360 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
57790312 TAAAACTTCA
57790322 TAAAAATTATAAAAATATTTT
1 TAAAAATTAT-AAAATATTTT
57790343 TAAAAATTATAAAATATT
1 TAAAAATTATAAAATATT
57790361 AAAAATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAAAATTATAAAATATTTT
Found at i:57790356 original size:29 final size:31
Alignment explanation
Indices: 57790310--57790372 Score: 87
Period size: 29 Copynumber: 2.1 Consensus size: 31
57790300 ATTTTTTAAA
*
57790310 TTTAAAACTTCATAAAAAT-TATAAAAATATT
1 TTTAAAAATTCATAAAAATAT-TAAAAATATT
57790341 TTTAAAAATT-AT-AAAATATTAAAAATATT
1 TTTAAAAATTCATAAAAATATTAAAAATATT
57790370 TTT
1 TTT
57790373 TAATATACCA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 18 0.60
30 3 0.10
31 9 0.30
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (31 bp):
TTTAAAAATTCATAAAAATATTAAAAATATT
Found at i:57790898 original size:26 final size:26
Alignment explanation
Indices: 57790867--57790923 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
57790857 GCCCGTTTTT
* **
57790867 AATAAACACAAAAATTGTATTTTAAA
1 AATAAAAACAAAAAAAGTATTTTAAA
*
57790893 AATAAAAAATAAAAAAAGTATTTTAAA
1 AAT-AAAAACAAAAAAAGTATTTTAAA
57790920 AATA
1 AATA
57790924 TTTTAAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.28
Consensus pattern (26 bp):
AATAAAAACAAAAAAAGTATTTTAAA
Found at i:57798352 original size:15 final size:15
Alignment explanation
Indices: 57798332--57798360 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
57798322 AACATCACTT
57798332 ATAGCAACTTTATTC
1 ATAGCAACTTTATTC
57798347 ATAGCAACTTTATT
1 ATAGCAACTTTATT
57798361 TAACACGACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.41
Consensus pattern (15 bp):
ATAGCAACTTTATTC
Found at i:57799447 original size:21 final size:21
Alignment explanation
Indices: 57799398--57799451 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
57799388 CCATCAGCAC
*
57799398 AATAATTTTGACCAATTTCAA
1 AATAATTTTGACCAATTCCAA
*
57799419 AACT-ATTTTGACC-ATATCCAT
1 AA-TAATTTTGACCAAT-TCCAA
57799440 AATAATTTTGAC
1 AATAATTTTGAC
57799452 TAGAAGCCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 3 0.11
21 24 0.86
22 1 0.04
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.39
Consensus pattern (21 bp):
AATAATTTTGACCAATTCCAA
Found at i:57802542 original size:15 final size:15
Alignment explanation
Indices: 57802522--57802552 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
57802512 AAAAATTATT
*
57802522 TTTTAAATAATAAAA
1 TTTTAAAAAATAAAA
57802537 TTTTAAAAAATAAAA
1 TTTTAAAAAATAAAA
57802552 T
1 T
57802553 AAAATATTAA
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TTTTAAAAAATAAAA
Found at i:57804246 original size:44 final size:44
Alignment explanation
Indices: 57804146--57804253 Score: 132
Period size: 44 Copynumber: 2.5 Consensus size: 44
57804136 AGCTAAGTCT
** **
57804146 TATCTCC-CTGAAGTTGCAGTGGAGCAGATTGAAGTTACAAATC
1 TATCTCCTCTGAAGTTATAGTGGAGCAGATTGAAGCGACAAATC
57804189 TCATCTCCT-TGAAGTTATAGTGGAGCAGATTGAAGCGACAAATC
1 T-ATCTCCTCTGAAGTTATAGTGGAGCAGATTGAAGCGACAAATC
*
57804233 T-TGTACCTCTGAAGTTATAGT
1 TATCT-CCTCTGAAGTTATAGT
57804254 AGGTCGGATT
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
42 2 0.04
43 4 0.07
44 50 0.89
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.31
Consensus pattern (44 bp):
TATCTCCTCTGAAGTTATAGTGGAGCAGATTGAAGCGACAAATC
Found at i:57807149 original size:46 final size:46
Alignment explanation
Indices: 57807082--57807403 Score: 531
Period size: 46 Copynumber: 7.0 Consensus size: 46
57807072 CATGGCAAAG
* *
57807082 TGTGAAACA-TAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAA-AGTAGGTATGGTATTTCGGTAAAGAAAACCATACTGAGT
57807128 TGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCATACTGAGT
*
57807174 TGTGAAAAGTAGGTATGGTATTCCGGTAAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCATACTGAGT
*
57807220 TGTGAAAAATAGGTATGGTATTTCGGTAAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCATACTGAGT
* *
57807266 TGTGAAAAGTATGTATGGTATTTTGGT-AAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCATACTGAGT
* *
57807311 TGTGAAAAGTAGGTATGGTGTTTCGGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCATACTGAGT
* *
57807357 TGTGAAAAGTAGGTATGGTATTTCCGTTAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCATACTGAGT
57807403 T
1 T
57807404 ATAGCAATGT
Statistics
Matches: 260, Mismatches: 14, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
45 43 0.17
46 217 0.83
ACGTcount: A:0.36, C:0.09, G:0.25, T:0.29
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCATACTGAGT
Found at i:57808055 original size:11 final size:11
Alignment explanation
Indices: 57808039--57808063 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
57808029 GTATTAGAAA
57808039 TTTCTTTTATT
1 TTTCTTTTATT
57808050 TTTCTTTTATT
1 TTTCTTTTATT
57808061 TTT
1 TTT
57808064 AAACTATATA
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:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTCTTTTATT
Found at i:57808688 original size:3 final size:3
Alignment explanation
Indices: 57808671--57808768 Score: 74
Period size: 3 Copynumber: 33.0 Consensus size: 3
57808661 CGTTATTTTC
* * * *
57808671 ATT ATT AGT AGT ATT ATT ATT -TAT ATT ATT AAT ATT AAT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT
* * * * * * *
57808716 ATT AAT GTT ATC ATT ACT A-T ACT ATT ATT ACT ATT ATT GTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
57808763 ATT ATT
1 ATT ATT
57808769 CACTTATTTA
Statistics
Matches: 74, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
2 3 0.04
3 70 0.95
4 1 0.01
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:57808866 original size:18 final size:18
Alignment explanation
Indices: 57808826--57808866 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
57808816 ACACTTGTAT
*
57808826 ATATA-TTTTTATAATAT
1 ATATACTTTTTATAATAC
*
57808843 ACATACTTTTTATAATAC
1 ATATACTTTTTATAATAC
57808861 ATATAC
1 ATATAC
57808867 ACGTACATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATACTTTTTATAATAC
Found at i:57808917 original size:10 final size:10
Alignment explanation
Indices: 57808904--57808967 Score: 51
Period size: 10 Copynumber: 6.3 Consensus size: 10
57808894 ATATATACAC
57808904 ATATTTTTAT
1 ATATTTTTAT
57808914 ATATATATTTAT
1 ATAT-T-TTTAT
*
57808926 TTATTTATT-T
1 ATATTT-TTAT
* *
57808936 TTATTTTCAT
1 ATATTTTTAT
57808946 A-ATTTTTAT
1 ATATTTTTAT
*
57808955 ATATATTTAT
1 ATATTTTTAT
57808965 ATA
1 ATA
57808968 CATATATACA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
9 9 0.20
10 23 0.52
11 4 0.09
12 8 0.18
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (10 bp):
ATATTTTTAT
Found at i:57810999 original size:19 final size:19
Alignment explanation
Indices: 57810977--57811019 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
57810967 AATTAACCAT
57810977 TTTAACAAAGATTACAAAC
1 TTTAACAAAGATTACAAAC
57810996 TTTAACAAAGATTACAAAC
1 TTTAACAAAGATTACAAAC
57811015 TTTAA
1 TTTAA
57811020 ACCTTACCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (19 bp):
TTTAACAAAGATTACAAAC
Found at i:57812566 original size:150 final size:154
Alignment explanation
Indices: 57812277--57812566 Score: 410
Period size: 150 Copynumber: 1.9 Consensus size: 154
57812267 CTCAGGTCTG
* * * *
57812277 CTCACACAAGCTGTCAGTCTTTTGTTACTACTCAGTGCTGCACTATTGCTTACATAAGCTGTCAG
1 CTCACACAAGCTGTCAGTCATTCGTTACTACTCAGTGCTG-AC--TTGC-TACACAAGCTATCAG
* *
57812342 GTATCTGCAACATATGCCGGTATACCCAGCCACTGGTAGAACTTAAGACCAACACCCGAGTTCAC
62 GTATCCGCAACATATGCCGGTATACCCAGCCACTGGTAGAACTTAAGACCAACACCCGAGTCCAC
57812407 ATTAATCACAGTTTCGCATCACGACCTA
127 ATTAATCACAGTTTCGCATCACGACCTA
57812435 CTCACACAAGCTGTCAGTCATTCGTTACTACTCAGTGCTG-C-T-C-ACACAAGCTATCAGGTAT
1 CTCACACAAGCTGTCAGTCATTCGTTACTACTCAGTGCTGACTTGCTACACAAGCTATCAGGTAT
* * *
57812496 CCGCAACATATGCCGGTATACCCAGCCACTGGTAGAACTTATGACCAACGCCC-AGATCCACTTT
66 CCGCAACATATGCCGGTATACCCAGCCACTGGTAGAACTTAAGACCAACACCCGAG-TCCACATT
*
57812560 ATTCACA
130 AATCACA
57812567 ATTCCACATA
Statistics
Matches: 121, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
149 2 0.02
150 78 0.64
152 1 0.01
153 1 0.01
156 1 0.01
158 38 0.31
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (154 bp):
CTCACACAAGCTGTCAGTCATTCGTTACTACTCAGTGCTGACTTGCTACACAAGCTATCAGGTAT
CCGCAACATATGCCGGTATACCCAGCCACTGGTAGAACTTAAGACCAACACCCGAGTCCACATTA
ATCACAGTTTCGCATCACGACCTA
Found at i:57817649 original size:16 final size:16
Alignment explanation
Indices: 57817630--57817665 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
57817620 TTATTTAGTT
57817630 ATTTATTTA-TTCTTGC
1 ATTTATTTATTTCTT-C
57817646 ATTTATTTATTTCTTC
1 ATTTATTTATTTCTTC
57817662 ATTT
1 ATTT
57817666 CCCTTGTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.19, C:0.11, G:0.03, T:0.67
Consensus pattern (16 bp):
ATTTATTTATTTCTTC
Found at i:57819444 original size:2 final size:2
Alignment explanation
Indices: 57819431--57819464 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
57819421 GAATTTAATC
*
57819431 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57819465 TTGAGTGAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:57835212 original size:21 final size:21
Alignment explanation
Indices: 57835186--57835226 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
57835176 AGACGAGCAA
* *
57835186 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
57835207 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
57835227 TTGAGCAGAT
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:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:57841025 original size:21 final size:20
Alignment explanation
Indices: 57840999--57841037 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
57840989 TAAAACTTCA
57840999 TAAAAATTATAAAAATATTTT
1 TAAAAATTAT-AAAATATTTT
57841020 TAAAAATTATAAAATATT
1 TAAAAATTATAAAATATT
57841038 AAAAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAAAATTATAAAATATTTT
Found at i:57841053 original size:31 final size:31
Alignment explanation
Indices: 57840987--57841050 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
57840977 TTTTTTAAAA
*
57840987 TTTAAAACTTCATAAAAATTATAAAAATATT
1 TTTAAAAATTCATAAAAATTATAAAAATATT
57841018 TTTAAAAATT-ATAAAATATTA-AAAAATATT
1 TTTAAAAATTCATAAAA-ATTATAAAAATATT
57841048 TTT
1 TTT
57841051 TAATATACCA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
30 18 0.58
31 13 0.42
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTAAAAATTCATAAAAATTATAAAAATATT
Found at i:57842649 original size:4 final size:4
Alignment explanation
Indices: 57842635--57842664 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
57842625 CCACAAACTT
57842635 TTTA TTTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA T
57842665 CATTATTTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:57843017 original size:27 final size:26
Alignment explanation
Indices: 57842962--57843017 Score: 60
Period size: 25 Copynumber: 2.1 Consensus size: 26
57842952 CAGAAATTAA
**
57842962 ATAATATAATAAAAAATTTGAGATTC
1 ATAATATAATAAAAAATTTGAGAAAC
*
57842988 ATAA-ATAATAACAAATTTGGAAGAAAC
1 ATAATATAATAAAAAATTT-G-AGAAAC
57843015 ATA
1 ATA
57843018 TTTGGTGGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
25 13 0.52
26 5 0.20
27 7 0.28
ACGTcount: A:0.57, C:0.05, G:0.09, T:0.29
Consensus pattern (26 bp):
ATAATATAATAAAAAATTTGAGAAAC
Found at i:57844058 original size:30 final size:28
Alignment explanation
Indices: 57844024--57844080 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
57844014 ATATTTTTAT
57844024 ATTTTTAATAATTTTAATT-TTTTTAAAAAG
1 ATTTTT-ATAATTTT--TTATTTTTAAAAAG
57844054 ATTTTTATAATTTTTTATTTTTAAAAA
1 ATTTTTATAATTTTTTATTTTTAAAAA
57844081 AGTTAATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 2 0.08
28 10 0.38
29 8 0.31
30 6 0.23
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (28 bp):
ATTTTTATAATTTTTTATTTTTAAAAAG
Found at i:57844067 original size:20 final size:19
Alignment explanation
Indices: 57843997--57844067 Score: 56
Period size: 20 Copynumber: 3.7 Consensus size: 19
57843987 TTAATTAATT
57843997 TTTTTA-AATTTTAAAAAA
1 TTTTTATAATTTTAAAAAA
* *
57844015 TATTTT-TATATTTTTAATAA
1 T-TTTTATA-ATTTTAAAAAA
* **
57844035 TTTTAATTTTTTTAAAAAGA
1 TTTTTATAATTTTAAAAA-A
57844055 TTTTTATAATTTT
1 TTTTTATAATTTT
57844068 TTATTTTTAA
Statistics
Matches: 38, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
18 1 0.03
19 15 0.39
20 22 0.58
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (19 bp):
TTTTTATAATTTTAAAAAA
Found at i:57845324 original size:26 final size:25
Alignment explanation
Indices: 57845293--57845348 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
57845283 CCCATTTTTT
*
57845293 AATAAACACTAAAAAATTATTTTAAA
1 AATAAAAACTAAAAAA-TATTTTAAA
* *
57845319 AATAAAAAATTAAAAAATATTTTTAA
1 AAT-AAAAACTAAAAAATATTTTAAA
57845345 AATA
1 AATA
57845349 TTTTAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 1 0.04
26 14 0.54
27 11 0.42
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (25 bp):
AATAAAAACTAAAAAATATTTTAAA
Found at i:57845355 original size:37 final size:38
Alignment explanation
Indices: 57845305--57845380 Score: 102
Period size: 36 Copynumber: 2.0 Consensus size: 38
57845295 TAAACACTAA
*
57845305 AAAATTATTTTAAAAATAAAAAATTAAAAA-ATATTTTT
1 AAAATTATTTT-AAAATAAAAAATTAAAAATATATATTT
* *
57845343 AAAA-TATTTTAAAATTAAGAATTAAAAATATATATTT
1 AAAATTATTTTAAAATAAAAAATTAAAAATATATATTT
57845380 A
1 A
57845381 TTATATTCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 16 0.47
37 14 0.41
38 4 0.12
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (38 bp):
AAAATTATTTTAAAATAAAAAATTAAAAATATATATTT
Found at i:57845871 original size:16 final size:16
Alignment explanation
Indices: 57845850--57845880 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
57845840 CATGTGAGAG
57845850 CATATAAATTTGAAAC
1 CATATAAATTTGAAAC
*
57845866 CATATATATTTGAAA
1 CATATAAATTTGAAA
57845881 ACTCTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.35
Consensus pattern (16 bp):
CATATAAATTTGAAAC
Found at i:57846074 original size:40 final size:42
Alignment explanation
Indices: 57846012--57846089 Score: 108
Period size: 40 Copynumber: 1.9 Consensus size: 42
57846002 TATATATTTT
* *
57846012 TAAAAATATAACTTTTGGAATTTTTATAAAT-ATTTTGAATTC
1 TAAAAATATAACTTTTGAAATTTTGA-AAATCATTTTGAATTC
57846054 TAAAAAT-TAA-TTTTGAAATTTTGAAAATCATTTTGA
1 TAAAAATATAACTTTTGAAATTTTGAAAATCATTTTGA
57846090 TTTTTTGTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 4 0.12
40 19 0.58
41 3 0.09
42 7 0.21
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (42 bp):
TAAAAATATAACTTTTGAAATTTTGAAAATCATTTTGAATTC
Found at i:57846086 original size:20 final size:19
Alignment explanation
Indices: 57846033--57846089 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 19
57846023 CTTTTGGAAT
*
57846033 TTTTATAAATATTTTG-AA
1 TTTTAAAAATATTTTGAAA
*
57846051 TTCTAAAAATTAATTTTGAAA
1 TTTTAAAAA-T-ATTTTGAAA
*
57846072 TTTTGAAAATCATTTTGA
1 TTTTAAAAAT-ATTTTGA
57846090 TTTTTTGTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
18 7 0.23
19 1 0.03
20 14 0.45
21 9 0.29
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (19 bp):
TTTTAAAAATATTTTGAAA
Found at i:57847064 original size:32 final size:31
Alignment explanation
Indices: 57847007--57847068 Score: 74
Period size: 33 Copynumber: 2.0 Consensus size: 31
57846997 AACTTTGGTT
*
57847007 TTCTGAATTTTTTGAATTAATTATTTTATTTA
1 TTCTGAATTTTTTGAACTAATTA-TTTATTTA
57847039 TTCTCGAATTTTTT-ATACTAA-TATTTATTT
1 TTCT-GAATTTTTTGA-ACTAATTATTTATTT
57847069 TTCGTTGGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
31 7 0.26
32 7 0.26
33 13 0.48
ACGTcount: A:0.27, C:0.06, G:0.05, T:0.61
Consensus pattern (31 bp):
TTCTGAATTTTTTGAACTAATTATTTATTTA
Found at i:57849426 original size:20 final size:20
Alignment explanation
Indices: 57849390--57849428 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
57849380 TTAGATTACG
57849390 ATAAAATAATTATTTAAAAA
1 ATAAAATAATTATTTAAAAA
*
57849410 ATAAATATATTTA-TTAAAA
1 ATAAA-ATAATTATTTAAAA
57849429 GATTATGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATAAAATAATTATTTAAAAA
Found at i:57852624 original size:20 final size:21
Alignment explanation
Indices: 57852585--57852624 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
57852575 AAATATTTTG
*
57852585 AATTTTAAAAATTATTTTTCA
1 AATTTTAAAAATTATCTTTCA
57852606 AATTTTAAAAATTA-CTTTC
1 AATTTTAAAAATTATCTTTC
57852625 TTTTTGTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.50
Consensus pattern (21 bp):
AATTTTAAAAATTATCTTTCA
Found at i:57857013 original size:17 final size:17
Alignment explanation
Indices: 57856991--57857024 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
57856981 ATCCACTAAT
*
57856991 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
57857008 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
57857025 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:57861642 original size:17 final size:17
Alignment explanation
Indices: 57861620--57861653 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
57861610 ATCCACTAAT
*
57861620 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
57861637 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
57861654 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:57864605 original size:11 final size:11
Alignment explanation
Indices: 57864589--57864616 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
57864579 GCTCAAGTAG
57864589 AAAGAGATACA
1 AAAGAGATACA
57864600 AAAGAGATACA
1 AAAGAGATACA
57864611 AAAGAG
1 AAAGAG
57864617 TACCAAGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.64, C:0.07, G:0.21, T:0.07
Consensus pattern (11 bp):
AAAGAGATACA
Found at i:57868105 original size:2 final size:2
Alignment explanation
Indices: 57868100--57868135 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
57868090 CCCCCTTCTG
*
57868100 TC TC TC TG TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
57868136 AGACACAGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
TC
Found at i:57878652 original size:37 final size:37
Alignment explanation
Indices: 57878610--57878683 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
57878600 TCCTCACACC
*
57878610 ATTTTTGCTCTTACTCTTTCTTCTAACAAGTTCCATG
1 ATTTTTGCTCCTACTCTTTCTTCTAACAAGTTCCATG
*
57878647 ATTTTTGCTCCTACTCTTTCTTCTAACAAGTTTCATG
1 ATTTTTGCTCCTACTCTTTCTTCTAACAAGTTCCATG
57878684 GTATACTCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.19, C:0.24, G:0.08, T:0.49
Consensus pattern (37 bp):
ATTTTTGCTCCTACTCTTTCTTCTAACAAGTTCCATG
Found at i:57878969 original size:22 final size:22
Alignment explanation
Indices: 57878943--57879013 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
57878933 CATTTCTATT
57878943 GTTAAAAAACTAATCCTCGTAC
1 GTTAAAAAACTAATCCTCGTAC
** * *
57878965 GTTAACAAATGTACA-CAT--TATT
1 GTTAA-AAAACTA-ATCCTCGTA-C
57878987 GTTAAAAAACTAATCCTCGTAC
1 GTTAAAAAACTAATCCTCGTAC
57879009 GTTAA
1 GTTAA
57879014 CAAATGTACA
Statistics
Matches: 35, Mismatches: 8, Indels: 12
0.64 0.15 0.22
Matches are distributed among these distances:
20 1 0.03
21 9 0.26
22 15 0.43
23 9 0.26
24 1 0.03
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (22 bp):
GTTAAAAAACTAATCCTCGTAC
Found at i:57878989 original size:44 final size:44
Alignment explanation
Indices: 57878939--57879026 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
57878929 TATTCATTTC
57878939 TATTGTTAAAAAACTAATCCTCGTACGTTAACAAATGTACACAT
1 TATTGTTAAAAAACTAATCCTCGTACGTTAACAAATGTACACAT
57878983 TATTGTTAAAAAACTAATCCTCGTACGTTAACAAATGTACACAT
1 TATTGTTAAAAAACTAATCCTCGTACGTTAACAAATGTACACAT
57879027 ACATATCACT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (44 bp):
TATTGTTAAAAAACTAATCCTCGTACGTTAACAAATGTACACAT
Found at i:57883519 original size:23 final size:23
Alignment explanation
Indices: 57883488--57883531 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
57883478 TTTTTAATAT
*
57883488 ATTATGTAATTTATAA-ATTAAA
1 ATTATGTAATATATAATATTAAA
57883510 ATTATTGTAATATATAATATTA
1 ATTA-TGTAATATATAATATTA
57883532 TAATGTAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 11 0.58
24 4 0.21
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (23 bp):
ATTATGTAATATATAATATTAAA
Found at i:57883814 original size:20 final size:20
Alignment explanation
Indices: 57883789--57883830 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
57883779 CTATTTCATA
*
57883789 TTTAGTAAATTATATTAAAT
1 TTTAGTAAATTACATTAAAT
**
57883809 TTTAGTGTATTACATTAAAT
1 TTTAGTAAATTACATTAAAT
57883829 TT
1 TT
57883831 CAAACTGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.52
Consensus pattern (20 bp):
TTTAGTAAATTACATTAAAT
Found at i:57897657 original size:72 final size:73
Alignment explanation
Indices: 57897479--57897663 Score: 338
Period size: 72 Copynumber: 2.5 Consensus size: 73
57897469 ACAACTTGAC
57897479 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
57897544 CACTAACA
66 CACTAACA
57897552 AACTTAGTTGGAATACAACTAAGTTTCATCATTAACATCCACTTAAAATAAATCACCA-CTACTA
1 AACTTAGTTGGAATACAACTAAGTTTCATCATT-ACATCCACTTAAAATAAATCACCACCTACTA
57897616 -CACTAACA
65 CCACTAACA
*
57897624 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCA
57897664 TAATAATAAT
Statistics
Matches: 110, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
71 7 0.06
72 40 0.36
73 39 0.35
74 24 0.22
ACGTcount: A:0.42, C:0.24, G:0.06, T:0.28
Consensus pattern (73 bp):
AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
CACTAACA
Found at i:57897671 original size:3 final size:3
Alignment explanation
Indices: 57897663--57897703 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
57897653 CATTACATCC
57897663 ATA ATA ATA ATA TATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA A
57897704 ACATGTGATT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:57901997 original size:73 final size:73
Alignment explanation
Indices: 57901915--57902100 Score: 363
Period size: 73 Copynumber: 2.5 Consensus size: 73
57901905 ACAACTTGAC
57901915 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
57901980 CACTAACA
66 CACTAACA
57901988 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
57902053 CACTAACA
66 CACTAACA
*
57902061 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCA
57902101 AATAATAATA
Statistics
Matches: 112, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 112 1.00
ACGTcount: A:0.41, C:0.25, G:0.06, T:0.28
Consensus pattern (73 bp):
AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
CACTAACA
Found at i:57902109 original size:3 final size:3
Alignment explanation
Indices: 57902101--57902129 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
57902091 ATTACATCCA
57902101 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
57902130 AACATGTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:57908868 original size:32 final size:32
Alignment explanation
Indices: 57908831--57908907 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
57908821 ATGCATGTGT
* * **
57908831 GTAACTTTTCATCTTCAAGTCTCTTTGCATTA
1 GTAACTTTTCATATTCAAGCCTCTTCACATTA
* * *
57908863 TTAACTCTTCATATTCAAGCCTCTTCACATTC
1 GTAACTTTTCATATTCAAGCCTCTTCACATTA
57908895 GTAACTTTTCATA
1 GTAACTTTTCATA
57908908 ATTTATTTTG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.25, C:0.25, G:0.06, T:0.44
Consensus pattern (32 bp):
GTAACTTTTCATATTCAAGCCTCTTCACATTA
Found at i:57913375 original size:32 final size:32
Alignment explanation
Indices: 57913338--57913414 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
57913328 ATGCATGTGT
* * **
57913338 GTAACTTTTCATCTTCAAGTCTCTTTGCATTA
1 GTAACTTTTCATATTCAAGCCTCTTCACATTA
* * *
57913370 TTAACTCTTCATATTCAAGCCTCTTCACATTC
1 GTAACTTTTCATATTCAAGCCTCTTCACATTA
57913402 GTAACTTTTCATA
1 GTAACTTTTCATA
57913415 ATTTATTTTG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.25, C:0.25, G:0.06, T:0.44
Consensus pattern (32 bp):
GTAACTTTTCATATTCAAGCCTCTTCACATTA
Found at i:57919839 original size:21 final size:21
Alignment explanation
Indices: 57919813--57919853 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
57919803 AGACGAGCAA
* *
57919813 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
57919834 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
57919854 TTGAGCAGAT
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:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:57942674 original size:42 final size:42
Alignment explanation
Indices: 57942567--57942674 Score: 105
Period size: 42 Copynumber: 2.6 Consensus size: 42
57942557 CTGAACGAGT
* * ** * *
57942567 TTTCCTGCTAACTGTGCAGAAAGCTTGCTTAGCTAGACAAGC
1 TTTCCTGATAACTGTGCAGAAAGCTCGCCCAACTAGACAAGA
*
57942609 TTTCCTGATAATTGTGC-GAAAAGCTCGCCCAACTAGACAA-A
1 TTTCCTGATAACTGTGCAG-AAAGCTCGCCCAACTAGACAAGA
57942650 TTTCCCTG-TCAACTGTGCAGAAAGC
1 TTT-CCTGAT-AACTGTGCAGAAAGC
57942675 GCACCCATTG
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
41 5 0.09
42 48 0.89
43 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (42 bp):
TTTCCTGATAACTGTGCAGAAAGCTCGCCCAACTAGACAAGA
Found at i:57957670 original size:22 final size:23
Alignment explanation
Indices: 57957618--57957660 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
57957608 AAAATTTGTA
57957618 TAAA-TAAAAATAGATTAAATAT
1 TAAATTAAAAATAGATTAAATAT
57957640 TAAATTAAAAATA-ATATAAAT
1 TAAATTAAAAATAGAT-TAAAT
57957661 TTATTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
TAAATTAAAAATAGATTAAATAT
Found at i:57957981 original size:6 final size:6
Alignment explanation
Indices: 57957970--57958009 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
57957960 ATGCATGTAC
* *
57957970 GTATAT GTATAT GTATAT GTATAT GTATAT ATGTAT GTAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTAT
57958010 GAAATTCTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
GTATAT
Found at i:57965673 original size:3 final size:3
Alignment explanation
Indices: 57965667--57965694 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
57965657 AGAAGAAGAA
57965667 GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT G
57965695 GGAGAAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:57966491 original size:18 final size:18
Alignment explanation
Indices: 57966464--57966508 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
57966454 AATATTTAAA
57966464 TTTTATTTTAA-AAATAT
1 TTTTATTTTAATAAATAT
*
57966481 TTTTCATTTTAATAATTA-
1 TTTT-ATTTTAATAAATAT
57966499 TTTTATTTTA
1 TTTTATTTTA
57966509 CTATTTGCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 10 0.40
18 11 0.44
19 4 0.16
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTATTTTAATAAATAT
Found at i:57967825 original size:18 final size:19
Alignment explanation
Indices: 57967804--57967851 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
57967794 AATAAATCAT
57967804 TAAAAATTCAT-AAAAAAA
1 TAAAAATTCATAAAAAAAA
*
57967822 TAAAAAAT-ATTAAAAAAAA
1 TAAAAATTCA-TAAAAAAAA
57967841 TAAAAATTCAT
1 TAAAAATTCAT
57967852 GAGGTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 1 0.04
18 8 0.32
19 15 0.60
20 1 0.04
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (19 bp):
TAAAAATTCATAAAAAAAA
Found at i:57968548 original size:27 final size:26
Alignment explanation
Indices: 57968497--57968557 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
57968487 ATCAGGTTTG
*
57968497 TTTAAAATAAAAATTTTACATTTAAA
1 TTTAAAATAAAAATTATACATTTAAA
*
57968523 TTTAAAACTGAAAATTATA-ATATTAAA
1 TTTAAAA-TAAAAATTATACAT-TTAAA
57968550 TATTAAAA
1 T-TTAAAA
57968558 ATTATTTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 9 0.30
27 15 0.50
28 6 0.20
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (26 bp):
TTTAAAATAAAAATTATACATTTAAA
Found at i:57968931 original size:21 final size:22
Alignment explanation
Indices: 57968893--57968941 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
57968883 ATTTAAACCT
57968893 TTTTTTAAAA-TTTCTTTTACA
1 TTTTTTAAAATTTTCTTTTACA
** *
57968914 TTTTTTACAGTTTTTTTTTTACA
1 TTTTTTA-AAATTTTCTTTTACA
57968937 TTTTT
1 TTTTT
57968942 AATAATATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 7 0.30
22 1 0.04
23 15 0.65
ACGTcount: A:0.20, C:0.08, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTTTTAAAATTTTCTTTTACA
Found at i:57969225 original size:21 final size:21
Alignment explanation
Indices: 57969191--57969231 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
57969181 TTTGTTATTA
*
57969191 TTTATGAAAAATA-TTAAAAT
1 TTTATCAAAAATATTTAAAAT
57969211 TTTATCAAATAATATTTAAAA
1 TTTATCAAA-AATATTTAAAA
57969232 ACTATAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 4 0.22
22 6 0.33
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
TTTATCAAAAATATTTAAAAT
Found at i:57970565 original size:18 final size:18
Alignment explanation
Indices: 57970538--57970574 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
57970528 TATAGTTTGA
57970538 TATTCAAGTTATTCGAAT
1 TATTCAAGTTATTCGAAT
*
57970556 TATTCGAGTTATTCGAAT
1 TATTCAAGTTATTCGAAT
57970574 T
1 T
57970575 CGAAAACTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (18 bp):
TATTCAAGTTATTCGAAT
Found at i:57972403 original size:50 final size:50
Alignment explanation
Indices: 57972320--57972481 Score: 187
Period size: 50 Copynumber: 3.4 Consensus size: 50
57972310 TACACGAAAT
* * *
57972320 CACTTATC-CTTTATCTCTTGTCACTAATAAGATAAGTGTAGTTAAGCTAC
1 CACTTATCAC-TTATCACTTGTCACTGATCAGATAAGTGTAGTTAAGCTAC
57972370 CACTTATCACTTATCACTTGTCACTGATCAGATAA--GT-G-T-AGCTA-
1 CACTTATCACTTATCACTTGTCACTGATCAGATAAGTGTAGTTAAGCTAC
* * * *
57972414 AAC-TACCACTTATCACTTGTCACTGATCAGATAAGTGCAGCTAAAGCTAC
1 CACTTATCACTTATCACTTGTCACTGATCAGATAAGTGTAG-TTAAGCTAC
57972464 CACTTATCACTTATCACT
1 CACTTATCACTTATCACT
57972482 GATCAGAAGT
Statistics
Matches: 94, Mismatches: 9, Indels: 17
0.78 0.08 0.14
Matches are distributed among these distances:
43 30 0.32
44 2 0.02
45 6 0.06
46 2 0.02
47 1 0.01
48 2 0.02
49 5 0.05
50 32 0.34
51 14 0.15
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (50 bp):
CACTTATCACTTATCACTTGTCACTGATCAGATAAGTGTAGTTAAGCTAC
Found at i:57972424 original size:43 final size:44
Alignment explanation
Indices: 57972377--57972488 Score: 199
Period size: 43 Copynumber: 2.6 Consensus size: 44
57972367 TACCACTTAT
*
57972377 CACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAA-CTAC
1 CACTTATCACTTGTCACTGATCAGATAAGTGCAGCTAAAGCTAC
57972420 CACTTATCACTTGTCACTGATCAGATAAGTGCAGCTAAAGCTAC
1 CACTTATCACTTGTCACTGATCAGATAAGTGCAGCTAAAGCTAC
*
57972464 CACTTATCACTTATCACTGATCAGA
1 CACTTATCACTTGTCACTGATCAGA
57972489 AGTACTCAAA
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
43 38 0.58
44 28 0.42
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.29
Consensus pattern (44 bp):
CACTTATCACTTGTCACTGATCAGATAAGTGCAGCTAAAGCTAC
Found at i:57975404 original size:50 final size:50
Alignment explanation
Indices: 57975329--57975621 Score: 397
Period size: 50 Copynumber: 5.8 Consensus size: 50
57975319 ATTTGGGTAA
* *
57975329 AGAGGTCCTATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
57975379 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
57975429 AGAGGTCCCATATAAGACCATGTCCGGGACATGGCATTGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * *
57975479 AGAGGTCCCATGTGAGACCATGTTTGGGACATGGCGTTGGTATCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
57975529 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
57975579 AGAACATCCCATGTAAAACCATGTCTGGGACATAGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
57975622 TGTTATTATC
Statistics
Matches: 210, Mismatches: 32, Indels: 1
0.86 0.13 0.00
Matches are distributed among these distances:
50 178 0.85
51 32 0.15
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:57977788 original size:81 final size:81
Alignment explanation
Indices: 57977653--57977816 Score: 328
Period size: 81 Copynumber: 2.0 Consensus size: 81
57977643 CCCTCGTTCT
57977653 TTTTCTTGTCATTCCCGCGTGGAAAATTCGTGTGAATGAATGAAATGTCCTTTGATTTTTAAGAG
1 TTTTCTTGTCATTCCCGCGTGGAAAATTCGTGTGAATGAATGAAATGTCCTTTGATTTTTAAGAG
57977718 AAAGACAAATTATTTA
66 AAAGACAAATTATTTA
57977734 TTTTCTTGTCATTCCCGCGTGGAAAATTCGTGTGAATGAATGAAATGTCCTTTGATTTTTAAGAG
1 TTTTCTTGTCATTCCCGCGTGGAAAATTCGTGTGAATGAATGAAATGTCCTTTGATTTTTAAGAG
57977799 AAAGACAAATTATTTA
66 AAAGACAAATTATTTA
57977815 TT
1 TT
57977817 CTAAGTATTA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 83 1.00
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.39
Consensus pattern (81 bp):
TTTTCTTGTCATTCCCGCGTGGAAAATTCGTGTGAATGAATGAAATGTCCTTTGATTTTTAAGAG
AAAGACAAATTATTTA
Found at i:57988298 original size:24 final size:24
Alignment explanation
Indices: 57988266--57988313 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
57988256 AATTGAAAAA
57988266 GATTAAAAAGTTGTCCTTGCTCTT
1 GATTAAAAAGTTGTCCTTGCTCTT
57988290 GATTAAAAAGTTGTCCTTGCTCTT
1 GATTAAAAAGTTGTCCTTGCTCTT
57988314 TCTCCGCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.42
Consensus pattern (24 bp):
GATTAAAAAGTTGTCCTTGCTCTT
Found at i:58004664 original size:29 final size:28
Alignment explanation
Indices: 58004606--58004666 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
58004596 TTTTGGGATT
* *
58004606 AAATTTTAGGGTTTAATATAAGTTTTAA
1 AAATTTTAGAGTTTAATAGAAGTTTTAA
*
58004634 AAATTTTACGAGTTTAATGGAA-TTTTAA
1 AAATTTTA-GAGTTTAATAGAAGTTTTAA
58004662 AAATT
1 AAATT
58004667 AGGGGTCTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 19 0.66
29 10 0.34
ACGTcount: A:0.41, C:0.02, G:0.13, T:0.44
Consensus pattern (28 bp):
AAATTTTAGAGTTTAATAGAAGTTTTAA
Found at i:58005811 original size:48 final size:48
Alignment explanation
Indices: 58005739--58005832 Score: 136
Period size: 48 Copynumber: 2.0 Consensus size: 48
58005729 TGCTTTTATA
* * * *
58005739 TATATTAGTTATAATGTTATATGCGTTGTACGTGATTTTATGTGTATT
1 TATATTAGTTATAATGTTACATGCGTCGTACATGATTTTATCTGTATT
58005787 TATATTAGTT-TCAATGTTACATGCGTCGTACATGATTTTATCTGTA
1 TATATTAGTTAT-AATGTTACATGCGTCGTACATGATTTTATCTGTA
58005833 ACTTTTAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
47 1 0.02
48 40 0.98
ACGTcount: A:0.26, C:0.09, G:0.17, T:0.49
Consensus pattern (48 bp):
TATATTAGTTATAATGTTACATGCGTCGTACATGATTTTATCTGTATT
Found at i:58009286 original size:19 final size:19
Alignment explanation
Indices: 58009254--58009305 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
58009244 CATTTCTTCA
*
58009254 CAAATATATATATATAAATT
1 CAAA-ATATTTATATAAATT
*
58009274 CAAAATATTTATAAAAATT
1 CAAAATATTTATATAAATT
*
58009293 C-TAATATTTATAT
1 CAAAATATTTATAT
58009306 TTTAAAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 10 0.36
19 14 0.50
20 4 0.14
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (19 bp):
CAAAATATTTATATAAATT
Found at i:58021745 original size:13 final size:13
Alignment explanation
Indices: 58021727--58021751 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58021717 TGAAATTCAG
58021727 ATTAAAAAATTTA
1 ATTAAAAAATTTA
58021740 ATTAAAAAATTT
1 ATTAAAAAATTT
58021752 CTCAAATTCC
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATTAAAAAATTTA
Found at i:58032625 original size:3 final size:3
Alignment explanation
Indices: 58032617--58032658 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
58032607 CACCGGCCTT
*
58032617 TCC TCC TCC TTCC TCC T-C TCC CCC TCC TCC TCC TCC TCC TCC
1 TCC TCC TCC -TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC
58032659 AAAAAATTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (3 bp):
TCC
Found at i:58034697 original size:16 final size:16
Alignment explanation
Indices: 58034676--58034709 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
58034666 GGCCATGCTA
58034676 TATAATGGGTTACTAT
1 TATAATGGGTTACTAT
58034692 TATAATGGGTTACTAT
1 TATAATGGGTTACTAT
58034708 TA
1 TA
58034710 ACTTATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (16 bp):
TATAATGGGTTACTAT
Found at i:58042314 original size:30 final size:31
Alignment explanation
Indices: 58042258--58042319 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 31
58042248 TCTTGATAAC
58042258 TTAAATAAATTTTTTAAAATAATTTAATGAT
1 TTAAATAAATTTTTTAAAATAATTTAATGAT
* *
58042289 TTAAAT-AATTTGTTT-TAATAGTTTAATGAT
1 TTAAATAAATTT-TTTAAAATAATTTAATGAT
58042319 T
1 T
58042320 AATTTATAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 19 0.68
31 9 0.32
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (31 bp):
TTAAATAAATTTTTTAAAATAATTTAATGAT
Found at i:58050423 original size:3 final size:3
Alignment explanation
Indices: 58050415--58050445 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
58050405 TAGTTGAGCT
58050415 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
58050446 TAGATACGAA
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:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:58071947 original size:13 final size:13
Alignment explanation
Indices: 58071929--58071954 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
58071919 TTTAAGAAGC
58071929 GGACAAATCGATT
1 GGACAAATCGATT
58071942 GGACAAATCGATT
1 GGACAAATCGATT
58071955 TGATTCTGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
GGACAAATCGATT
Found at i:58072603 original size:61 final size:62
Alignment explanation
Indices: 58072476--58072611 Score: 152
Period size: 60 Copynumber: 2.2 Consensus size: 62
58072466 GGACCTAAAA
* * * *
58072476 TTTTTTTTGATCCAAGTTTAAGCCCTGAATTTGGTAATTCTTCTCACATTTGGGGCATGAAC
1 TTTTTTTTGATCCAAGTTTAAGCCATAAACTTGGCAATTCTTCTCACATTTGGGGCATGAAC
* * * * **
58072538 TTTTTTGT-ATCCAAG-TTAGGCCATAAACTTGGCAATTCTTTTTACA-TTGGGGTTTGAAC
1 TTTTTTTTGATCCAAGTTTAAGCCATAAACTTGGCAATTCTTCTCACATTTGGGGCATGAAC
*
58072597 TTTTTTTTGGTCCAA
1 TTTTTTTTGATCCAA
58072612 ATTAGTCCTT
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
59 18 0.30
60 29 0.48
61 7 0.11
62 7 0.11
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (62 bp):
TTTTTTTTGATCCAAGTTTAAGCCATAAACTTGGCAATTCTTCTCACATTTGGGGCATGAAC
Found at i:58073274 original size:30 final size:29
Alignment explanation
Indices: 58073240--58073311 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
58073230 GTCTTTGTAC
*
58073240 CTTTTATAGATTTGGAATTTAGTCTCTATA
1 CTTTTATAGATTT-GAATTTAGTCCCTATA
** *
58073270 CTTTTATTTATATGAATTTAGTCCCTATA
1 CTTTTATAGATTTGAATTTAGTCCCTATA
58073299 CATTTT-TAGATTT
1 C-TTTTATAGATTT
58073312 TAAAATTTAG
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
29 20 0.59
30 14 0.41
ACGTcount: A:0.26, C:0.11, G:0.10, T:0.53
Consensus pattern (29 bp):
CTTTTATAGATTTGAATTTAGTCCCTATA
Found at i:58081692 original size:31 final size:32
Alignment explanation
Indices: 58081646--58081712 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
58081636 GTAATCACAT
* * *
58081646 GGACCAAAATTGAGAAAAGTTGTAAAGTTTAG
1 GGACCAAAATTGAGAAAACTTATAAAGTTCAG
* *
58081678 GGACC-AAGTTGAGAAAACTTATCAAGTTCAG
1 GGACCAAAATTGAGAAAACTTATAAAGTTCAG
58081709 GGAC
1 GGAC
58081713 TAAATGTTGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 25 0.83
32 5 0.17
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.22
Consensus pattern (32 bp):
GGACCAAAATTGAGAAAACTTATAAAGTTCAG
Found at i:58098297 original size:49 final size:49
Alignment explanation
Indices: 58098215--58098308 Score: 120
Period size: 49 Copynumber: 1.9 Consensus size: 49
58098205 CCTGAGGCTC
* * *
58098215 AACTCACCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAGGTT
1 AACTCACCTCGCAATATGAGTTCAATTTGAAAACAAAAACTAAAAGGTT
*
58098264 AACTCACCTCTCGCAATATGAG-TCAATTT-AAAACATAAACTAAAA
1 AACTCA-C-CTCGCAATATGAGTTCAATTTGAAAACAAAAACTAAAA
58098309 ATACCTCGCG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
49 20 0.51
50 6 0.15
51 13 0.33
ACGTcount: A:0.45, C:0.18, G:0.11, T:0.27
Consensus pattern (49 bp):
AACTCACCTCGCAATATGAGTTCAATTTGAAAACAAAAACTAAAAGGTT
Found at i:58098419 original size:70 final size:67
Alignment explanation
Indices: 58098264--58098428 Score: 208
Period size: 67 Copynumber: 2.4 Consensus size: 67
58098254 TTAAAAGGTT
* * * *
58098264 AACTCACCTCTCGCAATATGAG-TCAATTTAAAACATAAACTAAAAATACCTCGCGTGCCCGAGG
1 AACTCA-CTCTCGCAATATGAGTTGATTTTAAAACAAAAACTAAAAATACCTCACGTGCCCGAGG
58098328 CTC
65 CTC
* **
58098331 AACTCACTCTCGCAATATGAGTTGATTTTGAAAA-AAAAATTAAAAATACCTCAACGTGTCTTGA
1 AACTCACTCTCGCAATATGAGTTGATTTT-AAAACAAAAACTAAAAATACCTC-ACGTG-CCCGA
58098395 GGCTC
63 GGCTC
58098400 AACTCATCTCTCGCAATATGAGTTGATTT
1 AACTCA-CTCTCGCAATATGAGTTGATTT
58098429 CCTTGGAAAG
Statistics
Matches: 86, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
66 15 0.17
67 27 0.31
68 8 0.09
69 14 0.16
70 22 0.26
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (67 bp):
AACTCACTCTCGCAATATGAGTTGATTTTAAAACAAAAACTAAAAATACCTCACGTGCCCGAGGC
TC
Found at i:58106685 original size:16 final size:15
Alignment explanation
Indices: 58106664--58106711 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
58106654 GATGTGAATA
58106664 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
58106680 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
* *
58106695 ATCAAAACATTAGAAT
1 AT-AAAATATTAAAAT
58106711 A
1 A
58106712 ATAATAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 8 0.28
16 21 0.72
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:58106694 original size:8 final size:8
Alignment explanation
Indices: 58106660--58106711 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
58106650 TAATGATGTG
*
58106660 AATAATAA
1 AATATTAA
58106668 AATATATAA
1 AATAT-TAA
58106677 AATA-TAA
1 AATATTAA
58106684 AATATTAA
1 AATATTAA
*
58106692 AATATCAA
1 AATATTAA
* *
58106700 AACATTAG
1 AATATTAA
58106708 AATA
1 AATA
58106712 ATAATAATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
7 7 0.19
8 22 0.61
9 7 0.19
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (8 bp):
AATATTAA
Found at i:58106711 original size:24 final size:24
Alignment explanation
Indices: 58106659--58106715 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
58106649 ATAATGATGT
58106659 GAATAATAAAATATATAAAATATA
1 GAATAATAAAATATATAAAATATA
* *
58106683 AAATATTAAAATATCA-AAACAT-TA
1 GAATAATAAAATAT-ATAAA-ATATA
58106707 GAATAATAA
1 GAATAATAA
58106716 TAATTAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
24 24 0.89
25 3 0.11
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.28
Consensus pattern (24 bp):
GAATAATAAAATATATAAAATATA
Found at i:58106894 original size:25 final size:23
Alignment explanation
Indices: 58106866--58106928 Score: 76
Period size: 22 Copynumber: 2.7 Consensus size: 23
58106856 CGTGATAATA
58106866 TTAAAAATATGTACATAATATAGTG
1 TTAAAAATA--TACATAATATAGTG
58106891 TTAAAAATATACATAATATA--G
1 TTAAAAATATACATAATATAGTG
*
58106912 TTAAGATATATACATAA
1 TTAA-AAATATACATAA
58106929 GATAACATGT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
21 5 0.14
22 11 0.31
23 11 0.31
25 9 0.25
ACGTcount: A:0.52, C:0.05, G:0.08, T:0.35
Consensus pattern (23 bp):
TTAAAAATATACATAATATAGTG
Found at i:58106950 original size:2 final size:2
Alignment explanation
Indices: 58106943--58107007 Score: 57
Period size: 2 Copynumber: 34.5 Consensus size: 2
58106933 ACATGTAAAA
* * *
58106943 AT AT AT AT AT AT AT AT AT AT AA AT A- AT AT A- AT AT -T AA AG
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
58106982 AT AT AT AC AT A- AA AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
58107008 CGTAATCTAG
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
1 4 0.08
2 47 0.92
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (2 bp):
AT
Found at i:58106963 original size:40 final size:40
Alignment explanation
Indices: 58106917--58107003 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 40
58106907 TATAGTTAAG
* * *
58106917 ATATATACATAAGATAACATGTAAAAATATATATAT-ATAT
1 ATATATAAATAAGATAACAT-TAAAAATATATACATAAAAT
* * *
58106957 ATATATAAATAATATAATATTAAAGATATATACATAAAAT
1 ATATATAAATAAGATAACATTAAAAATATATACATAAAAT
58106997 ATATATA
1 ATATATA
58107004 TATACGTAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
39 13 0.32
40 27 0.68
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.36
Consensus pattern (40 bp):
ATATATAAATAAGATAACATTAAAAATATATACATAAAAT
Found at i:58107080 original size:23 final size:25
Alignment explanation
Indices: 58107037--58107082 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
58107027 TATACCTAAT
58107037 ATATTAAAAGAATATATATAATATA
1 ATATTAAAAGAATATATATAATATA
*
58107062 ATATTAAGA-AATATA-ATAATA
1 ATATTAAAAGAATATATATAATA
58107083 ACAAAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (25 bp):
ATATTAAAAGAATATATATAATATA
Found at i:58107644 original size:30 final size:30
Alignment explanation
Indices: 58107566--58107710 Score: 170
Period size: 30 Copynumber: 4.8 Consensus size: 30
58107556 TAGGTACAAG
* *
58107566 TGGTGGTGGAGCAA-GTGTGGTTAGTGGAGT
1 TGGTGGTGGA-AAAGGTGTGGCTAGTGGAGT
* ** * *
58107596 AGGTAATGGAGCAA-GTGTGGCTAGTGGATT
1 TGGTGGTGGA-AAAGGTGTGGCTAGTGGAGT
58107626 TGGTGGT-GAAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAA-AAGGTGTGGCTAGTGGAGT
58107656 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
*
58107686 TGGTGGTGGAAAAGGTGTAGCTAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGT
58107711 TGAGAAAAGT
Statistics
Matches: 101, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
29 4 0.04
30 94 0.93
31 3 0.03
ACGTcount: A:0.21, C:0.04, G:0.47, T:0.28
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
Found at i:58111286 original size:14 final size:14
Alignment explanation
Indices: 58111263--58111293 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
58111253 TATTGCGTTC
*
58111263 TTAGTTAATTTAGA
1 TTAGTAAATTTAGA
58111277 TTAGTAAATTTAGA
1 TTAGTAAATTTAGA
58111291 TTA
1 TTA
58111294 AAACAATTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (14 bp):
TTAGTAAATTTAGA
Found at i:58123645 original size:22 final size:23
Alignment explanation
Indices: 58123607--58123649 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
58123597 TCATAAAATT
58123607 AAAAATGAAAAACGAATCAATCC
1 AAAAATGAAAAACGAATCAATCC
58123630 AAAAAT-AATAAA-GAATCAAT
1 AAAAATGAA-AAACGAATCAAT
58123650 TTATTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.65, C:0.12, G:0.07, T:0.16
Consensus pattern (23 bp):
AAAAATGAAAAACGAATCAATCC
Found at i:58129603 original size:38 final size:38
Alignment explanation
Indices: 58129547--58129622 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
58129537 AGAGAAAAGC
*
58129547 AAGAGAAGCAGAGAAAGAAAAACAGGGATTGATGAAGA
1 AAGAGAAGCAGAGAAAGAAAAACAAGGATTGATGAAGA
*
58129585 AAGATAAGCAGAGAAAGAAAAACAAGGATTGATGAAGA
1 AAGAGAAGCAGAGAAAGAAAAACAAGGATTGATGAAGA
58129623 TGAGAGAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.57, C:0.05, G:0.29, T:0.09
Consensus pattern (38 bp):
AAGAGAAGCAGAGAAAGAAAAACAAGGATTGATGAAGA
Found at i:58129980 original size:38 final size:38
Alignment explanation
Indices: 58129927--58129999 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
58129917 TACCCATTGC
* *
58129927 AAGAGAAGCAGAGAAAGAAAAATAGGGATTGATGAAGA
1 AAGAGAAGCAGAGAAAGAAAAACAGGGATCGATGAAGA
*
58129965 AAGAGAAGCATAGAAAGAAAAACAGGGATCGATGA
1 AAGAGAAGCAGAGAAAGAAAAACAGGGATCGATGA
58130000 TGAGAGAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.55, C:0.05, G:0.30, T:0.10
Consensus pattern (38 bp):
AAGAGAAGCAGAGAAAGAAAAACAGGGATCGATGAAGA
Found at i:58134024 original size:23 final size:24
Alignment explanation
Indices: 58133975--58134026 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
58133965 AAATATTCTC
* * **
58133975 ATTTTAACTAAAAAAATTATCTAA
1 ATTTAAACTAAAAAAATCAAATAA
58133999 ATTTAAACTAAAAAAATCAAAT-A
1 ATTTAAACTAAAAAAATCAAATAA
58134022 ATTTA
1 ATTTA
58134027 TAATTTATGG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (24 bp):
ATTTAAACTAAAAAAATCAAATAA
Found at i:58144518 original size:24 final size:25
Alignment explanation
Indices: 58144479--58144534 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
58144469 CATAGATCAG
* *
58144479 TTTTTAATAGTAAAAATGGATGAAA
1 TTTTTAACAGTAAAAATGAATGAAA
58144504 TTTTTAACAGTAAAAATGAATGAAA
1 TTTTTAACAGTAAAAATGAATGAAA
58144529 TTTTTA
1 TTTTTA
58144535 GGAGAATGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.39
Consensus pattern (25 bp):
TTTTTAACAGTAAAAATGAATGAAA
Found at i:58151092 original size:27 final size:27
Alignment explanation
Indices: 58151062--58151113 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
58151052 TGACTAAAAC
58151062 AGAAAAA-TTCAAATAGCTGGGTGACAA
1 AGAAAAAGTT-AAATAGCTGGGTGACAA
* *
58151089 AGAAAAAGTTTAATAGTTGGGTGAC
1 AGAAAAAGTTAAATAGCTGGGTGAC
58151114 TATTTTGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.44, C:0.08, G:0.25, T:0.23
Consensus pattern (27 bp):
AGAAAAAGTTAAATAGCTGGGTGACAA
Found at i:58159903 original size:96 final size:96
Alignment explanation
Indices: 58159739--58159936 Score: 360
Period size: 96 Copynumber: 2.1 Consensus size: 96
58159729 CAATTCAACC
* *
58159739 GATTTCAATACTAAAGAAGGAGAAACTGATATCTAGAGAAAAATAACATTTTCGGTAGCTGATTT
1 GATTTCAATACTAAAGAAGGAGAAACTGATATCTAGAGAAAAATAACATTTCCAGTAGCTGATTT
*
58159804 AATAGGTTCTAAGTCCCCAACATAATTTATT
66 AATAGGTTCCAAGTCCCCAACATAATTTATT
*
58159835 GATTTCAATACTAAAGAAGGAGAAACTGATATCTAGAGAAAAATAATATTTCCAGTAGCTGATTT
1 GATTTCAATACTAAAGAAGGAGAAACTGATATCTAGAGAAAAATAACATTTCCAGTAGCTGATTT
58159900 AATAGGTTCCAAGTCCCCAACATAATTTATT
66 AATAGGTTCCAAGTCCCCAACATAATTTATT
58159931 GATTTC
1 GATTTC
58159937 TAACGTGGCT
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
96 98 1.00
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.31
Consensus pattern (96 bp):
GATTTCAATACTAAAGAAGGAGAAACTGATATCTAGAGAAAAATAACATTTCCAGTAGCTGATTT
AATAGGTTCCAAGTCCCCAACATAATTTATT
Found at i:58165745 original size:5 final size:5
Alignment explanation
Indices: 58165735--58165759 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
58165725 TTACTATCAG
58165735 CTGTA CTGTA CTGTA CTGTA CTGTA
1 CTGTA CTGTA CTGTA CTGTA CTGTA
58165760 ATGGTATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (5 bp):
CTGTA
Found at i:58167843 original size:19 final size:18
Alignment explanation
Indices: 58167807--58167849 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
58167797 TTTATTTTAC
*
58167807 ATATGATATAAATTACATA
1 ATAT-ATATAAATAACATA
58167826 ATATATATAAAGTAACATA
1 ATATATATAAA-TAACATA
*
58167845 TTATA
1 ATATA
58167850 AATTTGAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (18 bp):
ATATATATAAATAACATA
Found at i:58169059 original size:29 final size:29
Alignment explanation
Indices: 58168992--58169059 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
58168982 CTTTTTTGTT
* *
58168992 ACTCGACTATGAAAAGTTAAAAAATAGTC
1 ACTCAACTATAAAAAGTTAAAAAATAGTC
* * *
58169021 ACTCAGCTATAAAAAGTTACAAAATGGTC
1 ACTCAACTATAAAAAGTTAAAAAATAGTC
58169050 A-TCGAACTAT
1 ACTC-AACTAT
58169060 TCAATTTTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 2 0.06
29 30 0.94
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.25
Consensus pattern (29 bp):
ACTCAACTATAAAAAGTTAAAAAATAGTC
Found at i:58170782 original size:11 final size:11
Alignment explanation
Indices: 58170768--58170797 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
58170758 TTTTATTATT
58170768 TATTTTTAAAA
1 TATTTTTAAAA
58170779 TATTTTTAAAA
1 TATTTTTAAAA
58170790 TACTTTTT
1 TA-TTTTT
58170798 TTTATTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:58175913 original size:16 final size:16
Alignment explanation
Indices: 58175892--58175922 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
58175882 TGAATTGCTA
*
58175892 AAAATTTAAAAAATAC
1 AAAATTCAAAAAATAC
58175908 AAAATTCAAAAAATA
1 AAAATTCAAAAAATA
58175923 TTTTATAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAATTCAAAAAATAC
Found at i:58180164 original size:26 final size:26
Alignment explanation
Indices: 58180105--58180170 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
58180095 TTTAATATTT
* * *
58180105 AAAAA-ATTAAAAATATAAAATTATT
1 AAAAATATTAAAAATAAAAAAATATA
* *
58180130 AACATTATTAAAAATAAAAAAATATA
1 AAAAATATTAAAAATAAAAAAATATA
58180156 AAAAATATTTAAAAA
1 AAAAATA-TTAAAAA
58180171 AATTAGATCC
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
25 3 0.09
26 22 0.69
27 7 0.22
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.29
Consensus pattern (26 bp):
AAAAATATTAAAAATAAAAAAATATA
Found at i:58180169 original size:9 final size:9
Alignment explanation
Indices: 58180098--58180175 Score: 63
Period size: 9 Copynumber: 8.8 Consensus size: 9
58180088 TTAATTTTTT
58180098 AATATTTAAA
1 AATA-TTAAA
58180108 AA-ATTAAA
1 AATATTAAA
58180116 AATA-TAAA
1 AATATTAAA
* *
58180124 ATTATTAAC
1 AATATTAAA
*
58180133 ATTATTAAA
1 AATATTAAA
*
58180142 AATA-AAAA
1 AATATTAAA
*
58180150 AATATAAAA
1 AATATTAAA
58180159 AATATTTAAA
1 AATA-TTAAA
*
58180169 AAAATTA
1 AATATTA
58180176 GATCCACTTC
Statistics
Matches: 57, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
8 21 0.37
9 27 0.47
10 9 0.16
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (9 bp):
AATATTAAA
Found at i:58180200 original size:3 final size:3
Alignment explanation
Indices: 58180192--58180234 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
58180182 CTTCATGTGC
58180192 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
58180235 ATGTAATATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:58180485 original size:14 final size:15
Alignment explanation
Indices: 58180466--58180501 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
58180456 ATAATATAAT
58180466 ATTAAAATTAAT-TA
1 ATTAAAATTAATATA
*
58180480 ATTAAAATTGATATA
1 ATTAAAATTAATATA
58180495 ATTAAAA
1 ATTAAAA
58180502 ATATTCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (15 bp):
ATTAAAATTAATATA
Found at i:58185966 original size:6 final size:6
Alignment explanation
Indices: 58185955--58185984 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
58185945 AATAATTATA
58185955 TATATT TATATT TATATT TATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT
58185985 AAATCACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATATT
Found at i:58196099 original size:31 final size:29
Alignment explanation
Indices: 58196029--58196102 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
58196019 GGCTCAAGTT
* *
58196029 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTCAAATGTA
* **
58196058 ACGTTTTAGTCACTTATGTTATCACGTTGTA
1 ACATTTTAGTCACTTATGTT-TCA-AATGTA
58196089 ACATTTTAGTCACT
1 ACATTTTAGTCACT
58196103 GAGCCGTTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 19 0.51
30 2 0.05
31 16 0.43
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.46
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTCAAATGTA
Found at i:58201729 original size:22 final size:20
Alignment explanation
Indices: 58201704--58201754 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 20
58201694 AATAAATATC
58201704 AAAAATTTATTTTAAAAATTAA
1 AAAAATTTATTTT-AAAA-TAA
**
58201726 AAAAAAGTATTTTAAAATAA
1 AAAAATTTATTTTAAAATAA
*
58201746 AAAATTTTA
1 AAAAATTTA
58201755 AAAAGTATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 9 0.38
21 4 0.17
22 11 0.46
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAAATTTATTTTAAAATAA
Found at i:58201742 original size:15 final size:15
Alignment explanation
Indices: 58201722--58201770 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
58201712 ATTTTAAAAA
58201722 TTAAAAAAAAGTATT
1 TTAAAAAAAAGTATT
*
58201737 TTAAAATAAAA-AATT
1 TTAAAA-AAAAGTATT
58201752 TT---AAAAAGTATT
1 TTAAAAAAAAGTATT
58201764 TTAAAAA
1 TTAAAAA
58201771 TATTTTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 10
0.69 0.05 0.26
Matches are distributed among these distances:
11 4 0.15
12 6 0.22
15 13 0.48
16 4 0.15
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (15 bp):
TTAAAAAAAAGTATT
Found at i:58201757 original size:28 final size:27
Alignment explanation
Indices: 58201717--58201769 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
58201707 AATTTATTTT
58201717 AAAAATTAAAAAAAAGTATTTTAAAATA
1 AAAAATT-AAAAAAAGTATTTTAAAATA
**
58201745 AAAAATTTTAAAAAGTATTTTAAAA
1 AAAAATTAAAAAAAGTATTTTAAAA
58201770 ATATTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (27 bp):
AAAAATTAAAAAAAGTATTTTAAAATA
Found at i:58201770 original size:40 final size:38
Alignment explanation
Indices: 58201727--58201839 Score: 145
Period size: 40 Copynumber: 2.9 Consensus size: 38
58201717 AAAAATTAAA
*
58201727 AAAAAGTATTTTAAAATAAAAAATTTTAAAAAGTATTTT
1 AAAAA-TATTTTAAAATAAAAAATTTTAAAAAATATTTT
* *
58201766 AAAAATATTTTAAAATTAAAAAATAATAAAAAAATATTTT
1 AAAAATATTTTAAAA-TAAAAAAT-TTTAAAAAATATTTT
* * *
58201806 AAAAATATTTTAAATTAAAAAAATTTAAATAATA
1 AAAAATATTTTAAAATAAAAAATTTTAAAAAATA
58201840 AATATATTTA
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
38 18 0.28
39 20 0.31
40 26 0.41
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (38 bp):
AAAAATATTTTAAAATAAAAAATTTTAAAAAATATTTT
Found at i:58201786 original size:39 final size:39
Alignment explanation
Indices: 58201727--58201839 Score: 149
Period size: 39 Copynumber: 2.9 Consensus size: 39
58201717 AAAAATTAAA
*
58201727 AAAAAGTATTTTAAAA-TAAAAAATTTTAAAAAGTATTTT
1 AAAAA-TATTTTAAAATTAAAAAATTTTAAAAAATATTTT
* *
58201766 AAAAATATTTTAAAATTAAAAAATAATAAAAAAATATTTT
1 AAAAATATTTTAAAATTAAAAAAT-TTTAAAAAATATTTT
* *
58201806 AAAAATATTTT-AAATTAAAAAAATTTAAATAATA
1 AAAAATATTTTAAAATTAAAAAATTTTAAAAAATA
58201840 AATATATTTA
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
38 18 0.28
39 24 0.37
40 23 0.35
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (39 bp):
AAAAATATTTTAAAATTAAAAAATTTTAAAAAATATTTT
Found at i:58201809 original size:10 final size:11
Alignment explanation
Indices: 58201743--58201819 Score: 74
Period size: 11 Copynumber: 7.4 Consensus size: 11
58201733 TATTTTAAAA
58201743 TAAAAA-ATTT
1 TAAAAATATTT
58201753 TAAAAAGTATTT
1 TAAAAA-TATTT
58201765 TAAAAATATTT
1 TAAAAATATTT
58201776 T--AAA-A-TT
1 TAAAAATATTT
* * *
58201783 AAAAAATAATA
1 TAAAAATATTT
*
58201794 AAAAAATATTT
1 TAAAAATATTT
58201805 TAAAAATATTT
1 TAAAAATATTT
58201816 TAAA
1 TAAA
58201820 TTAAAAAAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
7 2 0.04
8 1 0.02
9 6 0.11
10 7 0.12
11 30 0.54
12 10 0.18
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (11 bp):
TAAAAATATTT
Found at i:58201848 original size:17 final size:17
Alignment explanation
Indices: 58201804--58201849 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
58201794 AAAAAATATT
58201804 TTAAAAATAT-TTTAAA
1 TTAAAAATATATTTAAA
58201820 TTAAAAA-A-ATTTAAA
1 TTAAAAATATATTTAAA
58201835 -TAATAAATATATTTA
1 TTAA-AAATATATTTA
58201850 TTATATCGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 3 0.12
15 10 0.38
16 8 0.31
17 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAAAATATATTTAAA
Found at i:58202275 original size:21 final size:22
Alignment explanation
Indices: 58202235--58202280 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
58202225 ACTTCTCAAC
*
58202235 ACAAAAATGAAATTTATAATTAA
1 ACAAAAAT-AAATTTATAATAAA
*
58202258 ACAAAAAT-AATTTCTAATAAA
1 ACAAAAATAAATTTATAATAAA
58202279 AC
1 AC
58202281 TTTAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 13 0.62
23 8 0.38
ACGTcount: A:0.61, C:0.09, G:0.02, T:0.28
Consensus pattern (22 bp):
ACAAAAATAAATTTATAATAAA
Found at i:58204762 original size:13 final size:12
Alignment explanation
Indices: 58204745--58204790 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
58204735 TAGTATAGTA
58204745 AAAAGAAGAAAG
1 AAAAGAAGAAAG
58204757 AAAAAGGAAGAAAG
1 -AAAA-GAAGAAAG
58204771 AAAAGAA-AGAAG
1 AAAAGAAGA-AAG
58204783 AAAAGAAG
1 AAAAGAAG
58204791 GAGAACGCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 1 0.03
12 13 0.43
13 8 0.27
14 8 0.27
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AAAAGAAGAAAG
Found at i:58207350 original size:14 final size:14
Alignment explanation
Indices: 58207333--58207360 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
58207323 ACTTAGCCTT
58207333 GGGGTCTTAACTTG
1 GGGGTCTTAACTTG
58207347 GGGGTCTTAACTTG
1 GGGGTCTTAACTTG
58207361 TCCAAAATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.36, T:0.36
Consensus pattern (14 bp):
GGGGTCTTAACTTG
Found at i:58208898 original size:19 final size:20
Alignment explanation
Indices: 58208871--58208908 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
58208861 TTTTATCACA
58208871 CACAAAAAAAAATT-AATAT
1 CACAAAAAAAAATTCAATAT
*
58208890 CACATAAAAAAATTCAATA
1 CACAAAAAAAAATTCAATA
58208909 AAATACATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.66, C:0.13, G:0.00, T:0.21
Consensus pattern (20 bp):
CACAAAAAAAAATTCAATAT
Found at i:58212172 original size:4 final size:4
Alignment explanation
Indices: 58212163--58212217 Score: 110
Period size: 4 Copynumber: 13.8 Consensus size: 4
58212153 GTTGATAGAT
58212163 GTAA GTAA GTAA GTAA GTAA GTAA GTAA GTAA GTAA GTAA GTAA GTAA
1 GTAA GTAA GTAA GTAA GTAA GTAA GTAA GTAA GTAA GTAA GTAA GTAA
58212211 GTAA GTA
1 GTAA GTA
58212218 TGTATGTATG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
GTAA
Done.