Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 156 of 208
Found at i:47538787 original size:18 final size:19
Alignment explanation
Indices: 47538745--47538793 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
47538735 CAGAAAATAA
* *
47538745 AGAAACATAAAAATGGTAT
1 AGAAACATAAAAATGCTAG
*
47538764 AGAAACAT-AACATGCTAG
1 AGAAACATAAAAATGCTAG
*
47538782 AGAAACAGAAAA
1 AGAAACATAAAA
47538794 TTTTGTGTCC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.59, C:0.10, G:0.16, T:0.14
Consensus pattern (19 bp):
AGAAACATAAAAATGCTAG
Found at i:47539573 original size:6 final size:6
Alignment explanation
Indices: 47539562--47539590 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
47539552 TCAATTCTGT
47539562 ATATAC ATATAC ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATA
47539591 TATACATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:47539990 original size:18 final size:18
Alignment explanation
Indices: 47539944--47539995 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
47539934 GTATTATGTC
*
47539944 GGGTTTGGGGAACTGTTAG
1 GGGTTT-GGGAAATGTTAG
* * *
47539963 GGATTAGGGAAATTTTAG
1 GGGTTTGGGAAATGTTAG
47539981 GGGTTTGGGAGAATG
1 GGGTTTGGGA-AATG
47539996 AGAGGTTGGG
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.23, C:0.02, G:0.44, T:0.31
Consensus pattern (18 bp):
GGGTTTGGGAAATGTTAG
Found at i:47541091 original size:47 final size:48
Alignment explanation
Indices: 47541004--47541102 Score: 110
Period size: 47 Copynumber: 2.1 Consensus size: 48
47540994 GTTTTGTTAA
* * * **
47541004 TTTAGGTAATATTTAAAAAAAGTATATAAAATTATCAATTTCAGT-TT
1 TTTAAGTAATATTTAAAAAAAGTAGATAAAAATAAAAATTTCAGTGTT
* * * *
47541051 TTTAAGTAATATTTATAAAAATTAGGTAAAAATAAAAATTTTAGTGTT
1 TTTAAGTAATATTTAAAAAAAGTAGATAAAAATAAAAATTTCAGTGTT
47541099 TTTA
1 TTTA
47541103 TTTCTTTTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
47 36 0.86
48 6 0.14
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.43
Consensus pattern (48 bp):
TTTAAGTAATATTTAAAAAAAGTAGATAAAAATAAAAATTTCAGTGTT
Found at i:47541124 original size:12 final size:11
Alignment explanation
Indices: 47541097--47541136 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
47541087 AATTTTAGTG
*
47541097 TTTTTATTTCT
1 TTTTTATTTTT
47541108 TTTTTATTTTT
1 TTTTTATTTTT
47541119 TATTTTATTTTAT
1 T-TTTTATTTT-T
47541132 TTTTT
1 TTTTT
47541137 GTAATTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 11 0.42
12 13 0.50
13 2 0.08
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTATTTTT
Found at i:47541129 original size:17 final size:18
Alignment explanation
Indices: 47541097--47541136 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
47541087 AATTTTAGTG
*
47541097 TTTTTATTTCTTTTTTAT
1 TTTTTATTTCTATTTTAT
47541115 TTTTTATTT-TATTTTAT
1 TTTTTATTTCTATTTTAT
47541132 TTTTT
1 TTTTT
47541137 GTAATTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTTTATTTCTATTTTAT
Found at i:47541373 original size:89 final size:88
Alignment explanation
Indices: 47541267--47541499 Score: 333
Period size: 89 Copynumber: 2.6 Consensus size: 88
47541257 ATATAAAGAA
* * * * *
47541267 CTTATTTAATATATAAATTAAAAAGTACTAATTAATCCAAATCTTAAACCCTAACCCGACCCCAA
1 CTTATTTAATATATAAATTAAAAA-CACTAATTAATCTAAACCCTAAACCCTAACCCAACCCCAA
*
47541332 ATCCCTAACCCCTAACCCCTAAAC
65 ACCCCTAACCCCTAACCCCTAAAC
* * * *
47541356 TTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCATAACCCAATCCCTA
1 CTTATTTAATATATAAATT-AAAAACACTAATTAATCTAAACCCTAAACCCTAACCCAACCCCAA
47541421 ACCCCTAACCCCTAACCCCTAAAC
65 ACCCCTAACCCCTAACCCCTAAAC
*
47541445 CTTATTTAATATAT-AATTAAAACACACTAATTAATCTAAACCCTAAACTCTAACC
1 CTTATTTAATATATAAATTAAAA-ACACTAATTAATCTAAACCCTAAACCCTAACC
47541500 TAACACCGAA
Statistics
Matches: 129, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
87 4 0.03
88 34 0.26
89 86 0.67
90 5 0.04
ACGTcount: A:0.43, C:0.28, G:0.01, T:0.27
Consensus pattern (88 bp):
CTTATTTAATATATAAATTAAAAACACTAATTAATCTAAACCCTAAACCCTAACCCAACCCCAAA
CCCCTAACCCCTAACCCCTAAAC
Found at i:47541435 original size:14 final size:14
Alignment explanation
Indices: 47541416--47541442 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
47541406 ATAACCCAAT
47541416 CCCTAACCCCTAAC
1 CCCTAACCCCTAAC
47541430 CCCTAACCCCTAA
1 CCCTAACCCCTAA
47541443 ACCTTATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.56, G:0.00, T:0.15
Consensus pattern (14 bp):
CCCTAACCCCTAAC
Found at i:47541559 original size:7 final size:7
Alignment explanation
Indices: 47541549--47541593 Score: 53
Period size: 7 Copynumber: 7.0 Consensus size: 7
47541539 CATCTAACAT
47541549 CTAACCC
1 CTAACCC
47541556 CTAA--C
1 CTAACCC
47541561 CTAACCC
1 CTAACCC
47541568 CTAA--C
1 CTAACCC
47541573 CTAACCC
1 CTAACCC
*
47541580 CTAATCC
1 CTAACCC
47541587 CTAACCC
1 CTAACCC
47541594 ATAAACCTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
5 10 0.31
7 22 0.69
ACGTcount: A:0.31, C:0.51, G:0.00, T:0.18
Consensus pattern (7 bp):
CTAACCC
Found at i:47541566 original size:12 final size:12
Alignment explanation
Indices: 47541549--47541593 Score: 72
Period size: 12 Copynumber: 3.6 Consensus size: 12
47541539 CATCTAACAT
47541549 CTAACCCCTAAC
1 CTAACCCCTAAC
47541561 CTAACCCCTAAC
1 CTAACCCCTAAC
47541573 CTAACCCCTAATCC
1 CTAACCCCTAA--C
47541587 CTAACCC
1 CTAACCC
47541594 ATAAACCTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 23 0.74
14 8 0.26
ACGTcount: A:0.31, C:0.51, G:0.00, T:0.18
Consensus pattern (12 bp):
CTAACCCCTAAC
Found at i:47541649 original size:14 final size:15
Alignment explanation
Indices: 47541627--47541660 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
47541617 CTTAAACTAG
*
47541627 AATCCCTAA-TCCAT
1 AATCTCTAATTCCAT
47541641 AATCTCTAATTCCAT
1 AATCTCTAATTCCAT
47541656 AATCT
1 AATCT
47541661 ATAAAACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.35
Consensus pattern (15 bp):
AATCTCTAATTCCAT
Found at i:47542449 original size:81 final size:81
Alignment explanation
Indices: 47542314--47542473 Score: 302
Period size: 81 Copynumber: 2.0 Consensus size: 81
47542304 GATAAAGCCC
* *
47542314 TGAGCATTAGCGGCGCCTACTTAAAAACGCCACTAAATCCCCGAAAGCTTAGAAAACGGCGTCGT
1 TGAGCATTAGCGGCGCATACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAACGGCGTCGT
47542379 TGGGCTTAGGTATTTT
66 TGGGCTTAGGTATTTT
47542395 TGAGCATTAGCGGCGCATACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAACGGCGTCGT
1 TGAGCATTAGCGGCGCATACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAACGGCGTCGT
47542460 TGGGCTTAGGTATT
66 TGGGCTTAGGTATT
47542474 CTGCGGCGCT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
81 77 1.00
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23
Consensus pattern (81 bp):
TGAGCATTAGCGGCGCATACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAACGGCGTCGT
TGGGCTTAGGTATTTT
Found at i:47543739 original size:101 final size:99
Alignment explanation
Indices: 47543473--47543769 Score: 366
Period size: 100 Copynumber: 3.0 Consensus size: 99
47543463 ATAGCTAGTA
* * * *
47543473 GTGCCGCCACATTTAGAGTTGACACCAAGAGAAATTTTTTTTACTGATTTTGGTGCCTCCACATG
1 GTGCCGCCACATTTAGAGTTGGCA-CTAGGGAATTTTTTTTTACTGATTTTGGTGCCTCCACATG
* *
47543538 AAGAGGCGACACCAAAAAATTCCAAAAAAAATTATAG
65 AAGAGGCGACACCGAAAAATT--AAAAAAATTTATAG
* * * *
47543575 GTGTCGTCACATTTGGAGTTGGCATTA-GGAATTTTTTTTTA-TAGATTTTGGTGCCTCCACATG
1 GTGCCGCCACATTTAGAGTTGGCACTAGGGAATTTTTTTTTACT-GATTTTGGTGCCTCCACATG
* **
47543638 ATGAGGCGACACCGAAAAGGTAAAAAAATTTACT-G
65 AAGAGGCGACACCGAAAAATTAAAAAAATTTA-TAG
* *
47543673 GTGCCGCCACATCTAAAGTTGGCACTAGGGGAATTTCTTTTTTACTGATTTTGGTGCCTCCACAT
1 GTGCCGCCACATTTAGAGTTGGCACTA-GGGAATTT-TTTTTTACTGATTTTGGTGCCTCCACAT
*
47543738 GAAGAGGCGGCACCGAAAAATTAAAAAAATTT
64 GAAGAGGCGACACCGAAAAATTAAAAAAATTT
47543770 TAAAAAAATT
Statistics
Matches: 166, Mismatches: 23, Indels: 13
0.82 0.11 0.06
Matches are distributed among these distances:
98 32 0.19
99 2 0.01
100 56 0.34
101 55 0.33
102 21 0.13
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.30
Consensus pattern (99 bp):
GTGCCGCCACATTTAGAGTTGGCACTAGGGAATTTTTTTTTACTGATTTTGGTGCCTCCACATGA
AGAGGCGACACCGAAAAATTAAAAAAATTTATAG
Found at i:47543868 original size:111 final size:112
Alignment explanation
Indices: 47543658--47543863 Score: 272
Period size: 111 Copynumber: 1.8 Consensus size: 112
47543648 ACCGAAAAGG
*
47543658 TAAAAAAATTTACTGGTGCCGCCACATCTAAAGTTGGCACTAGGGGAATTTCTTTTTTACTGATT
1 TAAAAAAATTTACTGGTGCCGCCACATCTAAAGTTGGCACCAGGGGAATTTCTTTTTTACTGATT
* **
47543723 TTGGTGCCTCCACATGAAGAGGCGGCACCGAAAAATTAAAAAAATTT
66 TTGGTGACTCCACATGAAGAGGCAACACCGAAAAATTAAAAAAATTT
* * * ** *
47543770 TAAAAAAA-TTATTGGTGTCGGCACATCTTGAGTTGGCACCAGGGGAATTT-TTTTAAATTATTG
1 TAAAAAAATTTACTGGTGCCGCCACATCTAAAGTTGGCACCAGGGGAATTTCTTTT---TTACTG
*
47543833 ATTTTGGTGACTCCACTTGAAGAGGCAACAC
63 ATTTTGGTGACTCCACATGAAGAGGCAACAC
47543864 AAAAAAAAAG
Statistics
Matches: 80, Mismatches: 11, Indels: 5
0.83 0.11 0.05
Matches are distributed among these distances:
110 4 0.05
111 36 0.45
112 8 0.10
113 32 0.40
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.31
Consensus pattern (112 bp):
TAAAAAAATTTACTGGTGCCGCCACATCTAAAGTTGGCACCAGGGGAATTTCTTTTTTACTGATT
TTGGTGACTCCACATGAAGAGGCAACACCGAAAAATTAAAAAAATTT
Found at i:47543878 original size:113 final size:112
Alignment explanation
Indices: 47543658--47543882 Score: 265
Period size: 113 Copynumber: 2.0 Consensus size: 112
47543648 ACCGAAAAGG
*
47543658 TAAAAAAATTTACTGGTGCCGCCACATCTAAAGTTGGCACTAGGGGAATTTCTTTTTTACTGATT
1 TAAAAAAATTTACTGGTGCCGCCACATCTAAAGTTGGCACCAGGGGAATTTCTTTTTTACTGATT
* ** * **
47543723 TTGGTGCCTCCACATGAAGAGGCGGCACCGAAAAATTAAAAAAATTT
66 TTGGTGACTCCACATGAAGAGGCAACACCAAAAAAAAAAAAAAATTT
* * * ** *
47543770 TAAAAAAA-TTATTGGTGTCGGCACATCTTGAGTTGGCACCAGGGGAATTT-TTTTAAATTATTG
1 TAAAAAAATTTACTGGTGCCGCCACATCTAAAGTTGGCACCAGGGGAATTTCTTTT---TTACTG
* *
47543833 ATTTTGGTGACTCCACTTGAAGAGGCAACACAAAAAAAAAGAAAAAAATT
63 ATTTTGGTGACTCCACATGAAGAGGCAACACCAAAAAAAA-AAAAAAATT
47543883 ACACCGGTGC
Statistics
Matches: 94, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
110 4 0.04
111 36 0.38
112 8 0.09
113 37 0.39
114 9 0.10
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (112 bp):
TAAAAAAATTTACTGGTGCCGCCACATCTAAAGTTGGCACCAGGGGAATTTCTTTTTTACTGATT
TTGGTGACTCCACATGAAGAGGCAACACCAAAAAAAAAAAAAAATTT
Found at i:47546179 original size:12 final size:12
Alignment explanation
Indices: 47546164--47546203 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
47546154 TTGCATATAT
47546164 TACATAATAATA
1 TACATAATAATA
47546176 TACATAATAATA
1 TACATAATAATA
47546188 TACATATATATATA
1 TACATA-ATA-ATA
47546202 TA
1 TA
47546204 TATATAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 18 0.69
13 3 0.12
14 5 0.19
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (12 bp):
TACATAATAATA
Found at i:47549583 original size:36 final size:38
Alignment explanation
Indices: 47549491--47549586 Score: 106
Period size: 40 Copynumber: 2.5 Consensus size: 38
47549481 GGGCGCAACT
* *
47549491 TTCGTCAGCTTATCTGACTAGTGCTAGGCACATCATTATA
1 TTCGTCAGTTTATCTGACTAGCGCTAGGCACA-CA-TATA
* * * *
47549531 TTTGCCAGTTTATCTGACTAGCGTTAGGCACA-A-ATC
1 TTCGTCAGTTTATCTGACTAGCGCTAGGCACACATATA
47549567 TTCGTCAGTTTATCTGACTA
1 TTCGTCAGTTTATCTGACTA
47549587 ATATTGGCAC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
36 20 0.42
38 1 0.02
40 27 0.56
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (38 bp):
TTCGTCAGTTTATCTGACTAGCGCTAGGCACACATATA
Found at i:47552981 original size:28 final size:27
Alignment explanation
Indices: 47552942--47553120 Score: 187
Period size: 28 Copynumber: 6.4 Consensus size: 27
47552932 ACATGTCATA
* *
47552942 AAAAGGAAGCCTTTGTGGTGATTTATG
1 AAAAGGAAGCCTTTGTGGCGATCTATG
*
47552969 AAAAGAGAAGCCTTTGTGGCGATCTATA
1 AAAAG-GAAGCCTTTGTGGCGATCTATG
*
47552997 AAAAGGGAAGCCTTTGTGGCGATCTATA
1 AAAA-GGAAGCCTTTGTGGCGATCTATG
* *
47553025 AAAAGGAAAGCCTTTATGGCGATCAATG
1 AAAAGG-AAGCCTTTGTGGCGATCTATG
* **
47553053 AAAATGGAGGCCTTTGTCCCGATCTATG
1 AAAA-GGAAGCCTTTGTGGCGATCTATG
* * **
47553081 AAAAGAGAGGTCTTTGTGGTAATCTATG
1 AAAAG-GAAGCCTTTGTGGCGATCTATG
*
47553109 AAATGGAAGCCT
1 AAAAGGAAGCCT
47553121 GCATGGAATA
Statistics
Matches: 128, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
27 13 0.10
28 112 0.88
29 3 0.02
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (27 bp):
AAAAGGAAGCCTTTGTGGCGATCTATG
Found at i:47557069 original size:16 final size:19
Alignment explanation
Indices: 47557048--47557088 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
47557038 GAGTCTTGTG
47557048 TTTAT-ATTATAA-A-ATA
1 TTTATAATTATAATATATA
47557064 TTTATAAATTATAATATATA
1 TTTAT-AATTATAATATATA
47557084 TTTAT
1 TTTAT
47557089 TATTGGACAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 5 0.24
18 7 0.33
19 1 0.05
20 8 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTATAATTATAATATATA
Found at i:47558838 original size:21 final size:21
Alignment explanation
Indices: 47558814--47558856 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
47558804 ATTAATGTTC
* *
47558814 ACTCTTTTGTATAGGGTAATA
1 ACTCTTTTGTATAAGCTAATA
47558835 ACTCTTTTGTATAAGCTAATA
1 ACTCTTTTGTATAAGCTAATA
47558856 A
1 A
47558857 TTGTCAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.42
Consensus pattern (21 bp):
ACTCTTTTGTATAAGCTAATA
Found at i:47560531 original size:13 final size:13
Alignment explanation
Indices: 47560513--47560538 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
47560503 CATGCAAATT
47560513 AAAGAAAGAAAAG
1 AAAGAAAGAAAAG
47560526 AAAGAAAGAAAAG
1 AAAGAAAGAAAAG
47560539 GAGAAGAAGC
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:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAAAG
Found at i:47563814 original size:18 final size:20
Alignment explanation
Indices: 47563791--47563828 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
47563781 TTTAAGTGAT
47563791 TTTTGA-AAA-AAAAATTAA
1 TTTTGATAAAGAAAAATTAA
*
47563809 TTTTGATAAAGTAAAATTAA
1 TTTTGATAAAGAAAAATTAA
47563829 ATTAATCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 3 0.18
20 8 0.47
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (20 bp):
TTTTGATAAAGAAAAATTAA
Found at i:47564329 original size:37 final size:37
Alignment explanation
Indices: 47564266--47564357 Score: 98
Period size: 37 Copynumber: 2.4 Consensus size: 37
47564256 ATTCCAAAAA
*
47564266 TAATATTATTTTAATAGTTTAATATTAAATTAA-ATT
1 TAATATTATCTTAATAGTTTAATATTAAATTAATATT
* *
47564302 TAATACTTATCTTAATAGTATT-TTATTAATTTAATATT
1 TAATA-TTATCTTAATAGT-TTAATATTAAATTAATATT
*
47564340 AAAGTGATTATCTTAATA
1 TAA-T-ATTATCTTAATA
47564358 TGAAATTTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
36 5 0.11
37 22 0.47
38 7 0.15
39 12 0.26
40 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.51
Consensus pattern (37 bp):
TAATATTATCTTAATAGTTTAATATTAAATTAATATT
Found at i:47565888 original size:13 final size:13
Alignment explanation
Indices: 47565870--47565895 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
47565860 GGTTTTCTCC
47565870 AAAATGAAAATGA
1 AAAATGAAAATGA
47565883 AAAATGAAAATGA
1 AAAATGAAAATGA
47565896 CCTGAAAAAT
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:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
AAAATGAAAATGA
Found at i:47567370 original size:23 final size:23
Alignment explanation
Indices: 47567344--47567387 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
47567334 TTTGAGACTA
47567344 AAATTGAAATTAACCAATGGTCT
1 AAATTGAAATTAACCAATGGTCT
*
47567367 AAATTGCAATTAACCAATGGT
1 AAATTGAAATTAACCAATGGT
47567388 ACAAAACAAC
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:0.43, C:0.14, G:0.14, T:0.30
Consensus pattern (23 bp):
AAATTGAAATTAACCAATGGTCT
Found at i:47571774 original size:78 final size:78
Alignment explanation
Indices: 47571692--47571886 Score: 309
Period size: 78 Copynumber: 2.5 Consensus size: 78
47571682 AAAATATATA
*
47571692 AATTGAATTCAAGGTATGAATTTTATATATGTATATGTGACGTTCGAATATATATGTATATACAT
1 AATTGAATTAAAGGTATGAATTTTATATATGTATATGTGACGTTCGAATATATATGTATATACAT
47571757 GTATAAGTTTTTG
66 GTATAAGTTTTTG
* * *
47571770 AATTGAATTAAAGGTATGAATTGTATATATGTATAAGTGAGGTTCGAATATATATGTATATACAT
1 AATTGAATTAAAGGTATGAATTTTATATATGTATATGTGACGTTCGAATATATATGTATATACAT
*
47571835 GTATAATTTTTTG
66 GTATAAGTTTTTG
* * * *
47571848 AATTGTATTAAAGGTATGAATCTTACATATGTATGTGTG
1 AATTGAATTAAAGGTATGAATTTTATATATGTATATGTG
47571887 TGATTCGAAT
Statistics
Matches: 106, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
78 106 1.00
ACGTcount: A:0.35, C:0.04, G:0.18, T:0.43
Consensus pattern (78 bp):
AATTGAATTAAAGGTATGAATTTTATATATGTATATGTGACGTTCGAATATATATGTATATACAT
GTATAAGTTTTTG
Found at i:47571894 original size:78 final size:76
Alignment explanation
Indices: 47571692--47571945 Score: 296
Period size: 78 Copynumber: 3.3 Consensus size: 76
47571682 AAAATATATA
*
47571692 AATTGAATTCAAGGTATGAATTTTATATATGTATATGTGACGTTCGAATATATATGTATATACAT
1 AATTGAATTAAAGGTATGAA-TTTATATATGTATATGTGA-GTTCGAATATATATGTATATACAT
47571757 GTATAAGTTTTTG
64 GTATAAGTTTTTG
*
47571770 AATTGAATTAAAGGTATGAATTGTATATATGTATAAGTGAGGTTCGAATATATATGTATATACAT
1 AATTGAATTAAAGGTATGAATT-TATATATGTATATGTGA-GTTCGAATATATATGTATATACAT
*
47571835 GTATAATTTTTTG
64 GTATAAGTTTTTG
* * * * * *
47571848 AATTGTATTAAAGGTATGAATCTTACATATGTATGTGTGTGATTCG-A-ATAGATGTATATTCAT
1 AATTGAATTAAAGGTATGAAT-TTATATATGTATATGTGAG-TTCGAATATATATGTATATACAT
* * * **
47571911 ATACAGGTACTTG
64 GTATAAGTTTTTG
* *
47571924 AGTTGAATTAAAAGTATGAATT
1 AATTGAATTAAAGGTATGAATT
47571946 GTAAATACTT
Statistics
Matches: 153, Mismatches: 20, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
75 1 0.01
76 39 0.25
77 4 0.03
78 108 0.71
79 1 0.01
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (76 bp):
AATTGAATTAAAGGTATGAATTTATATATGTATATGTGAGTTCGAATATATATGTATATACATGT
ATAAGTTTTTG
Found at i:47572344 original size:31 final size:30
Alignment explanation
Indices: 47572306--47572479 Score: 145
Period size: 31 Copynumber: 5.5 Consensus size: 30
47572296 GATAAGTATA
47572306 TATATGCATTCGGTTTTATACCTTTGATGTG
1 TATATGCATTCGGTTTTATA-CTTTGATGTG
* * *
47572337 TATATGCATTCGATTATAAGTA-TTTGATAGGTA
1 TATATGCATTCGGTT-TTA-TACTTTGAT--GTG
* *
47572370 TATATGCATTCGGTTGTACACATTTGATGTG
1 TATATGCATTCGGTTTTATAC-TTTGATGTG
* * *
47572401 TATATGCATTCGATTATAAGTA-TTTGATAGGTA
1 TATATGCATTCGGTT-TTA-TACTTTGAT--GTG
* *
47572434 TATATGCATTCGGTTGTATACATTTCATGTG
1 TATATGCATTCGGTTTTATAC-TTTGATGTG
47572465 TATATGCATTCGGTT
1 TATATGCATTCGGTT
47572480 ATAAGTAGTT
Statistics
Matches: 113, Mismatches: 18, Indels: 24
0.73 0.12 0.15
Matches are distributed among these distances:
31 62 0.55
32 5 0.04
33 46 0.41
ACGTcount: A:0.26, C:0.10, G:0.20, T:0.44
Consensus pattern (30 bp):
TATATGCATTCGGTTTTATACTTTGATGTG
Found at i:47572379 original size:33 final size:32
Alignment explanation
Indices: 47572304--47572534 Score: 224
Period size: 33 Copynumber: 7.2 Consensus size: 32
47572294 TTGATAAGTA
*
47572304 TATATATGCATTCGGTT-TTA-TACCTTTGAT-G
1 TATATATGCATTCGGTTATAAGTA--TTTGATAG
* *
47572335 TGTATATGCATTCGATTATAAGTATTTGATAGG
1 TATATATGCATTCGGTTATAAGTATTTGATA-G
* *
47572368 TATATATGCATTCGGTTGTACA-CATTTGAT-G
1 TATATATGCATTCGGTTATA-AGTATTTGATAG
* *
47572399 TGTATATGCATTCGATTATAAGTATTTGATAGG
1 TATATATGCATTCGGTTATAAGTATTTGATA-G
* * *
47572432 TATATATGCATTCGGTTGTATA-CATTTCAT-G
1 TATATATGCATTCGGTTATA-AGTATTTGATAG
* *
47572463 TGTATATGCATTCGGTTATAAGTAGTTGATAAG
1 TATATATGCATTCGGTTATAAGTATTTGAT-AG
*
47572496 TATATATGCATTCGGTTATAAGTATTTGATGAA
1 TATATATGCATTCGGTTATAAGTATTTGAT-AG
47572529 TATATA
1 TATATA
47572535 CATACATTTG
Statistics
Matches: 163, Mismatches: 25, Indels: 22
0.78 0.12 0.10
Matches are distributed among these distances:
30 2 0.01
31 70 0.43
32 2 0.01
33 87 0.53
34 2 0.01
ACGTcount: A:0.29, C:0.09, G:0.19, T:0.43
Consensus pattern (32 bp):
TATATATGCATTCGGTTATAAGTATTTGATAG
Found at i:47572384 original size:64 final size:64
Alignment explanation
Indices: 47572304--47572512 Score: 355
Period size: 64 Copynumber: 3.3 Consensus size: 64
47572294 TTGATAAGTA
* *
47572304 TATATATGCATTCGGTTTTATACCTTTGATGTGTATATGCATTCGATTATAAGTATTTGATAGG
1 TATATATGCATTCGGTTGTATACATTTGATGTGTATATGCATTCGATTATAAGTATTTGATAGG
*
47572368 TATATATGCATTCGGTTGTACACATTTGATGTGTATATGCATTCGATTATAAGTATTTGATAGG
1 TATATATGCATTCGGTTGTATACATTTGATGTGTATATGCATTCGATTATAAGTATTTGATAGG
* * * *
47572432 TATATATGCATTCGGTTGTATACATTTCATGTGTATATGCATTCGGTTATAAGTAGTTGATAAG
1 TATATATGCATTCGGTTGTATACATTTGATGTGTATATGCATTCGATTATAAGTATTTGATAGG
47572496 TATATATGCATTCGGTT
1 TATATATGCATTCGGTT
47572513 ATAAGTATTT
Statistics
Matches: 137, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 137 1.00
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.44
Consensus pattern (64 bp):
TATATATGCATTCGGTTGTATACATTTGATGTGTATATGCATTCGATTATAAGTATTTGATAGG
Found at i:47590970 original size:19 final size:20
Alignment explanation
Indices: 47590935--47590973 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
47590925 TTCCAAAAAT
*
47590935 CTTAGAAAATGTTTTGAACA
1 CTTAGAAAATATTTTGAACA
47590955 CTTAGAAAA-ATTTTGAACA
1 CTTAGAAAATATTTTGAACA
47590974 AAATTCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (20 bp):
CTTAGAAAATATTTTGAACA
Found at i:47591016 original size:20 final size:20
Alignment explanation
Indices: 47590991--47591033 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
47590981 AAAACAGTTT
*
47590991 AAACATTTTTAACTCAATTG
1 AAACATTTTTAAATCAATTG
*
47591011 AAACATTTTTAAATCGATTG
1 AAACATTTTTAAATCAATTG
47591031 AAA
1 AAA
47591034 AATTGTAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (20 bp):
AAACATTTTTAAATCAATTG
Found at i:47591703 original size:22 final size:23
Alignment explanation
Indices: 47591678--47591720 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
47591668 TGGTTATGCG
47591678 AATGC-AATATTTCAGAAAACGA
1 AATGCAAATATTTCAGAAAACGA
*
47591700 AATGCAAATTTTTCAGAAAAC
1 AATGCAAATATTTCAGAAAAC
47591721 TTTCTACCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.26
Consensus pattern (23 bp):
AATGCAAATATTTCAGAAAACGA
Found at i:47593697 original size:16 final size:16
Alignment explanation
Indices: 47593673--47593724 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
47593663 TGGTTCACTA
*
47593673 TAATGGAATAGAGCTG
1 TAATGGAATAGAGTTG
*
47593689 TAATTGAATAGAGTTG
1 TAATGGAATAGAGTTG
47593705 TAATGGAATAGAGTTG
1 TAATGGAATAGAGTTG
47593721 TAAT
1 TAAT
47593725 TAGTAATTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.38, C:0.02, G:0.27, T:0.33
Consensus pattern (16 bp):
TAATGGAATAGAGTTG
Found at i:47593963 original size:58 final size:57
Alignment explanation
Indices: 47593891--47594025 Score: 180
Period size: 58 Copynumber: 2.3 Consensus size: 57
47593881 TTGTTATTAA
* * * * * *
47593891 ATTTTAATAAAATTATTTTTAAATATATTTTAATAAAAATAATAAATAATTTAATCAT
1 ATTTTAATATAATTATTATTAAATACAATTTAAT-AAAATAATAAATAATTTAATAAC
* *
47593949 ATTTTAACATAATTATTATTAAATACAATTTAATAAAATAATATATAATTTAATAAC
1 ATTTTAATATAATTATTATTAAATACAATTTAATAAAATAATAAATAATTTAATAAC
47594006 ATTCTTAATATAATTATTAT
1 ATT-TTAATATAATTATTAT
47594026 AATATGAATT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
57 23 0.34
58 44 0.66
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (57 bp):
ATTTTAATATAATTATTATTAAATACAATTTAATAAAATAATAAATAATTTAATAAC
Found at i:47594048 original size:58 final size:57
Alignment explanation
Indices: 47593891--47594055 Score: 165
Period size: 58 Copynumber: 2.9 Consensus size: 57
47593881 TTGTTATTAA
* * * * * * * *
47593891 ATTTTAATAAAATTATTTTTAAATATATTTTAATAAAAATAATAAATAATTTAATCAT
1 ATTTTAACATAATTATTATTAAATACAATTTAA-AAAAATAATATATAATTTAATAAC
*
47593949 ATTTTAACATAATTATTATTAAATACAATTTAATAAAATAATATATAATTTAATAAC
1 ATTTTAACATAATTATTATTAAATACAATTTAAAAAAATAATATATAATTTAATAAC
* *
47594006 ATTCTTAATATAATTATTA-T-AATATGAA-TTAAAAAATCATAATATATAAT
1 ATT-TTAACATAATTATTATTAAATA-CAATTTAAAAAA--ATAATATATAAT
47594056 ATTATAAAAA
Statistics
Matches: 91, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
56 11 0.12
57 26 0.29
58 54 0.59
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.44
Consensus pattern (57 bp):
ATTTTAACATAATTATTATTAAATACAATTTAAAAAAATAATATATAATTTAATAAC
Found at i:47594064 original size:23 final size:21
Alignment explanation
Indices: 47594033--47594075 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
47594023 TATAATATGA
47594033 ATTAAAAAATCATAATATATAAT
1 ATTAAAAAA--ATAATATATAAT
*
47594056 ATTATAAAAATAATATATAA
1 ATTAAAAAAATAATATATAA
47594076 CCTACTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
23 8 0.42
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
ATTAAAAAAATAATATATAAT
Found at i:47607592 original size:21 final size:22
Alignment explanation
Indices: 47607560--47607602 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
47607550 GAAAATAAAA
*
47607560 TTTTATATATAGTTTGTAACTT
1 TTTTATATATAGTTTCTAACTT
47607582 TTTTATA-ATAGTTTCTAACTT
1 TTTTATATATAGTTTCTAACTT
47607603 AAATTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.58
Consensus pattern (22 bp):
TTTTATATATAGTTTCTAACTT
Found at i:47608457 original size:17 final size:16
Alignment explanation
Indices: 47608430--47608463 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
47608420 TAATAATTTT
47608430 TTTGAGTTTTTACATA
1 TTTGAGTTTTTACATA
*
47608446 TTTGATGTTTTTATATA
1 TTTGA-GTTTTTACATA
47608463 T
1 T
47608464 GCTTTAGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.24, C:0.03, G:0.12, T:0.62
Consensus pattern (16 bp):
TTTGAGTTTTTACATA
Found at i:47612258 original size:37 final size:36
Alignment explanation
Indices: 47612207--47612314 Score: 107
Period size: 37 Copynumber: 2.9 Consensus size: 36
47612197 ATTTCAAAAA
*
47612207 TAATATTATTTTAATAGTTTAATATTAAATTTAAT-T
1 TAATATTATCTTAATAGTTTAATATT-AATTTAATAT
*
47612243 TAATACTTATCTTAATAGTATT-TTATTAATTTAATAT
1 TAATA-TTATCTTAATAGT-TTAATATTAATTTAATAT
*
47612280 TAAAGTGATTATCTTAATA-TTAAAT-TTAATTTAAT
1 T-AA-T-ATTATCTTAATAGTTTAATATTAATTTAAT
47612315 GTTTATCTTG
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
36 13 0.21
37 29 0.48
38 6 0.10
39 12 0.20
40 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.53
Consensus pattern (36 bp):
TAATATTATCTTAATAGTTTAATATTAATTTAATAT
Found at i:47614445 original size:26 final size:26
Alignment explanation
Indices: 47614416--47614498 Score: 66
Period size: 26 Copynumber: 3.3 Consensus size: 26
47614406 TGATGGTCAC
47614416 ATGTGTAGTACTATGTGAAGGCTACT
1 ATGTGTAGTACTATGTGAAGGCTACT
* * ** *
47614442 ATGTGTA--CCGAAATGATAGG-T-CGC
1 ATGTGTAGTACTATGTGA-AGGCTAC-T
*
47614466 ATGTGTAGTACTATGTGCAGGCTACT
1 ATGTGTAGTACTATGTGAAGGCTACT
47614492 ATGTGTA
1 ATGTGTA
47614499 TCGGATGTTA
Statistics
Matches: 40, Mismatches: 11, Indels: 12
0.63 0.17 0.19
Matches are distributed among these distances:
23 1 0.03
24 13 0.32
25 6 0.15
26 19 0.47
27 1 0.03
ACGTcount: A:0.27, C:0.13, G:0.28, T:0.33
Consensus pattern (26 bp):
ATGTGTAGTACTATGTGAAGGCTACT
Found at i:47614474 original size:50 final size:50
Alignment explanation
Indices: 47614401--47614547 Score: 172
Period size: 50 Copynumber: 2.9 Consensus size: 50
47614391 ATGTAAAAGT
47614401 GAAAGTGAT-GGTCACATGTGTAGTACTATGTGAAGGCTACTATGTGTACC
1 GAAA-TGATAGGTCACATGTGTAGTACTATGTGAAGGCTACTATGTGTACC
* * *
47614451 GAAATGATAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGTGTATC
1 GAAATGATAGGTCACATGTGTAGTACTATGTGAAGGCTACTATGTGTACC
* * * * * *
47614501 G-GATGTTAATGATCACATGTGTATTAGTATGTGTAGGCTACTATGTG
1 GAAATGAT-A-GGTCACATGTGTAGTACTATGTGAAGGCTACTATGTG
47614548 AATCGAACAT
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
49 8 0.10
50 44 0.52
51 32 0.38
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.33
Consensus pattern (50 bp):
GAAATGATAGGTCACATGTGTAGTACTATGTGAAGGCTACTATGTGTACC
Found at i:47614546 original size:26 final size:25
Alignment explanation
Indices: 47614466--47614547 Score: 60
Period size: 26 Copynumber: 3.2 Consensus size: 25
47614456 GATAGGTCGC
* *
47614466 ATGTGTAGTACTATGTGCAGGCTACT
1 ATGTGTA-TAGTATGTGTAGGCTACT
* * * *
47614492 ATGTGTATCGGATGT-TAATGATCAC-
1 ATGTGTATAGTATGTGT-AGGCT-ACT
47614517 ATGTGTATTAGTATGTGTAGGCTACT
1 ATGTGTA-TAGTATGTGTAGGCTACT
47614543 ATGTG
1 ATGTG
47614548 AATCGAACAT
Statistics
Matches: 41, Mismatches: 10, Indels: 10
0.67 0.16 0.16
Matches are distributed among these distances:
25 17 0.41
26 23 0.56
27 1 0.02
ACGTcount: A:0.24, C:0.11, G:0.27, T:0.38
Consensus pattern (25 bp):
ATGTGTATAGTATGTGTAGGCTACT
Found at i:47614618 original size:45 final size:45
Alignment explanation
Indices: 47614554--47614642 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
47614544 TGTGAATCGA
* *
47614554 ACATCATTGATTAGTAAGGTGGCTGCTATGTGCTGATTCCACCGG
1 ACATCATTGATTAATAAGGTGGCTGCTATGTGCTGAATCCACCGG
*
47614599 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCG
1 ACATCATTGATTAATAAGGTGGCTGCTATGTGCTGAATCCACCG
47614643 AGTATCTGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGCTGCTATGTGCTGAATCCACCGG
Found at i:47620288 original size:22 final size:22
Alignment explanation
Indices: 47620263--47620304 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
47620253 GCAAATGTTA
47620263 TTTCATTCTTTACGATTTTTTC
1 TTTCATTCTTTACGATTTTTTC
**
47620285 TTTCATTCTTTTGGATTTTT
1 TTTCATTCTTTACGATTTTT
47620305 CTGCCAAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.14, G:0.07, T:0.67
Consensus pattern (22 bp):
TTTCATTCTTTACGATTTTTTC
Found at i:47622658 original size:50 final size:50
Alignment explanation
Indices: 47622601--47622859 Score: 252
Period size: 50 Copynumber: 5.2 Consensus size: 50
47622591 AAGTTACGAT
47622601 GGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAGCCACAAC
1 GGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAGCCACAAC
* *** * * * * ** * * *
47622651 GGTGGATCTTACTT-CCTTAGCAGTGCAGTGGAATAGATTGAAGCTACGAC
1 GGCGGATCTGGTTTCCCTGA-TATTGCAATTAAAAAGATTGAAGCCACAAC
*
47622701 GGCGGATCTGGTTTCCCTGATATTGTAATTAAAAAGATTGAAGCCACAAC
1 GGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAGCCACAAC
*** * * * ** * * *
47622751 GGCGGATCTTACTT-CCTTAGTAGTACAATGGAACAGATTGAAGCTACGAC
1 GGCGGATCTGGTTTCCCTGA-TATTGCAATTAAAAAGATTGAAGCCACAAC
*
47622801 GGCAGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAGCCACAAC
1 GGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAGCCACAAC
47622851 GGCGGATCT
1 GGCGGATCT
47622860 TACTTCTCTG
Statistics
Matches: 153, Mismatches: 52, Indels: 8
0.72 0.24 0.04
Matches are distributed among these distances:
49 8 0.05
50 137 0.90
51 8 0.05
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (50 bp):
GGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAGCCACAAC
Found at i:47622935 original size:50 final size:50
Alignment explanation
Indices: 47622574--47622943 Score: 233
Period size: 50 Copynumber: 7.4 Consensus size: 50
47622564 TCCTTAGCAG
* * * *
47622574 TGCAG-TGAAACAGATTGAAGTTACGATGGCGGATCTGGTTTCCCTGATAT
1 TGCAGTTG-AACAGATTGAAGCTACGACGGCGGATCTTGTTTCCCTGACAT
* * * * * * ** * *
47622624 TGCAATTAAAAAGATTGAAGCCACAACGGTGGATCTTACTT-CCTTAGCAG
1 TGCAGTTGAACAGATTGAAGCTACGACGGCGGATCTTGTTTCCCTGA-CAT
* * * *
47622674 TGCAGTGGAATAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
1 TGCAGTTGAACAGATTGAAGCTACGACGGCGGATCTTGTTTCCCTGACAT
* * * * * * ** * * *
47622724 TGTAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTT-CCTTAGTAG
1 TGCAGTTGAACAGATTGAAGCTACGACGGCGGATCTTGTTTCCCTGA-CAT
* * * * * *
47622774 TACAATGGAACAGATTGAAGCTACGACGGCAGATCTGGTTTCCCTGATAT
1 TGCAGTTGAACAGATTGAAGCTACGACGGCGGATCTTGTTTCCCTGACAT
* * * * * ** * *
47622824 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCTCTGACAG
1 TGCAGTTGAACAGATTGAAGCTACGACGGCGGATCTTGTTTCCCTGACAT
* * * * **
47622874 TGCGGTGGAACAGATTGAAGGTACGACAGCGGATCTTGTTTCCCCAACAT
1 TGCAGTTGAACAGATTGAAGCTACGACGGCGGATCTTGTTTCCCTGACAT
*
47622924 TGCAGTTGAACAAATTGAAG
1 TGCAGTTGAACAGATTGAAG
47622944 ATAACAGATC
Statistics
Matches: 232, Mismatches: 83, Indels: 10
0.71 0.26 0.03
Matches are distributed among these distances:
49 8 0.03
50 215 0.93
51 9 0.04
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCAGTTGAACAGATTGAAGCTACGACGGCGGATCTTGTTTCCCTGACAT
Found at i:47622943 original size:100 final size:100
Alignment explanation
Indices: 47622555--47622917 Score: 575
Period size: 100 Copynumber: 3.6 Consensus size: 100
47622545 CGAAACCATA
* * *
47622555 GATCTTACTTCCTTAGCAGTGCAGTGAAACAGATTGAAGTTACGATGGCGGATCTGGTTTCCCTG
1 GATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTG
*
47622620 ATATTGCAATTAAAAAGATTGAAGCCACAACGGTG
66 ATATTGCAATTAAAAAGATTGAAGCCACAACGGCG
*
47622655 GATCTTACTTCCTTAGCAGTGCAGTGGAATAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTG
1 GATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTG
*
47622720 ATATTGTAATTAAAAAGATTGAAGCCACAACGGCG
66 ATATTGCAATTAAAAAGATTGAAGCCACAACGGCG
* * * *
47622755 GATCTTACTTCCTTAGTAGTACAATGGAACAGATTGAAGCTACGACGGCAGATCTGGTTTCCCTG
1 GATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTG
47622820 ATATTGCAATTAAAAAGATTGAAGCCACAACGGCG
66 ATATTGCAATTAAAAAGATTGAAGCCACAACGGCG
* * * * *
47622855 GATCTTACTTCTCTGA-CAGTGCGGTGGAACAGATTGAAGGTACGACAGCGGATCTTGTTTCCC
1 GATCTTACTTC-CTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCC
47622918 CAACATTGCA
Statistics
Matches: 241, Mismatches: 21, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
100 238 0.99
101 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (100 bp):
GATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTG
ATATTGCAATTAAAAAGATTGAAGCCACAACGGCG
Found at i:47623174 original size:132 final size:132
Alignment explanation
Indices: 47622937--47623893 Score: 1621
Period size: 132 Copynumber: 7.2 Consensus size: 132
47622927 AGTTGAACAA
*
47622937 ATTGAAGATAACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTAC
1 ATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTAC
47623002 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGGAAT
66 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGGAAT
47623067 AG
131 AG
* **
47623069 ATTGAAGATTACAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCAAAGATGGCAGATTTTAC
1 ATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTAC
** * *
47623134 CTCCCTGAGGTTACAGTACAGTATATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAAT
66 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGGAAT
47623199 AG
131 AG
*
47623201 ATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGGTGGTGGATTTTAC
1 ATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTAC
* * * *
47623266 CTCCTTGAAGTTACAGTGGAGTACATTAAAGCTAGTAATTCTATCTCCCTGGGCAACAGTGGAAT
66 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGGAAT
47623331 AG
131 AG
*
47623333 ATTGAAGATTACAGATTTTATCTCCCTAAGCAGTAGTGGAGCAGATC-AAGATGGTGGATTTTAC
1 ATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTAC
*
47623397 CTCCCTGAGGTTACAGT-GAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAAT
66 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGGAAT
47623461 AG
131 AG
* **
47623463 ATTAAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTAC
1 ATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTAC
* *
47623528 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCTCTGAGCAACAGTGGAAT
66 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGGAAT
47623593 AG
131 AG
* *
47623595 ATTGAAGATTACATATTTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTAC
1 ATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTAC
* * *
47623660 CTCTCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGCCAGCAGTGGAAT
66 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGGAAT
47623725 AG
131 AG
* *
47623727 ATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAATGATGGCGGATTTTAC
1 ATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTAC
*
47623792 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAACTCTATCTCCCTAGGGGCAACAGTGGA
66 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT--GGGCAACAGTGGA
47623857 ATAG
129 ATAG
*
47623861 ATTGAAGATTACAGATCTTATCTCCCTAGGCAG
1 ATTGAAGATTACAGATCTTATCTCCCTAAGCAG
47623894 CGAAGTAGAT
Statistics
Matches: 768, Mismatches: 53, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
130 91 0.12
131 63 0.08
132 567 0.74
134 47 0.06
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (132 bp):
ATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTAC
CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGGAAT
AG
Found at i:47623327 original size:43 final size:43
Alignment explanation
Indices: 47623278--47623729 Score: 124
Period size: 44 Copynumber: 10.3 Consensus size: 43
47623268 CCTTGAAGTT
*
47623278 ACAGTGGAGTACATTAAAGCTAGTAATTCTATCTCCCTGGGCA
1 ACAGTGGAGTAGATTAAAGCTAGTAATTCTATCTCCCTGGGCA
* * * * * **
47623321 ACAGTGGAATAGATTGAAGATTA-CAGATTTTATCTCCCTAAGCA
1 ACAGTGGAGTAGATTAAAG-CTAGTA-ATTCTATCTCCCTGGGCA
** * * * * * * * **
47623365 GTAGTGGAGCAGA-TCAAGATGGTGGATTTTACCTCCCTGAGGTT
1 ACAGTGGAGTAGATTAAAGCTAGT-AATTCTATCTCCCTG-GGCA
* * *
47623409 ACAGT-GAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCA
1 ACAGTGGAGTAGATTAAAGCTAGTAATTCTATCTCCCTGGGCA
* * * * **
47623451 GCAGTGGAATAGATTAAAG--ATTACAGATCTTATCTCCCTAAGCA
1 ACAGTGGAGTAGATTAAAGCTAGTA-A-TTC-TATCTCCCTGGGCA
** * * * * * * * **
47623495 GTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTT
1 ACAGTGGAGTAGATTAAAGCTAGTA-ATTCTATCTCCCTG-GGCA
* * * * *
47623540 ACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCTCTGAGCA
1 ACAGTGGAGTAGATTAAAGCTAGTAATTCTATCTCCCTGGGCA
* * * * * **
47623583 ACAGTGGAATAGATTGAAGATTA-CATATTTTATCTCCCTAAGCA
1 ACAGTGGAGTAGATTAAAG-CTAGTA-ATTCTATCTCCCTGGGCA
** * * * * * * * * **
47623627 GTAGTGGAGCAGATCAAAGATGGTGGATTTTACCTCTCTGAGGTT
1 ACAGTGGAGTAGATTAAAGCTAGT-AATTCTATCTCCCTG-GGCA
* * * *
47623672 ACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGCCA
1 ACAGTGGAGTAGATTAAAGCTAGTAATTCTATCTCCCTGGGCA
* *
47623715 GCAGTGGAATAGATT
1 ACAGTGGAGTAGATT
47623730 GAAGATTACA
Statistics
Matches: 274, Mismatches: 117, Indels: 36
0.64 0.27 0.08
Matches are distributed among these distances:
41 3 0.01
42 8 0.03
43 95 0.35
44 133 0.49
45 33 0.12
46 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.28
Consensus pattern (43 bp):
ACAGTGGAGTAGATTAAAGCTAGTAATTCTATCTCCCTGGGCA
Found at i:47623750 original size:394 final size:395
Alignment explanation
Indices: 47622937--47623893 Score: 1657
Period size: 394 Copynumber: 2.4 Consensus size: 395
47622927 AGTTGAACAA
*
47622937 ATTGAAGATAACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTAC
1 ATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-AAGATGGTGGATTTTAC
47623002 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGGAAT
65 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGGAAT
*
47623067 AGATTGAAGATTACAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCAAAGATGGCAGATTTT
130 AGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTT
* * *
47623132 ACCTCCCTGAGGTTACAGTACAGTATATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGA
195 ACCTCCCTGAGGTTACAGTACAGTACATTGAAGCCAGTAATTCTATCTCCCTGAGCAACAGTGGA
*
47623197 ATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGGTGGTGGATT
260 ATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATT
* *
47623262 TTACCTCCTTGAAGTTACAGTGGAGTACATTAAAGCTAGTAATTCTATCTCCCTGGGCAACAGTG
325 TTACCTCCTTGAAGTTACAGTGGAGTACATTAAAGCCAGTAATTCTATCTCCCTGGCCAACAGTG
47623327 GAATAG
390 GAATAG
*
47623333 ATTGAAGATTACAGATTTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAGATGGTGGATTTTACC
1 ATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAGATGGTGGATTTTACC
*
47623398 TCCCTGAGGTTACAGT-GAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATA
66 TCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGGAATA
*
47623462 GATTAAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTA
131 GATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTA
** *
47623527 CCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCTCTGAGCAACAGTGGAA
196 CCTCCCTGAGGTTACAGTACAGTACATTGAAGCCAGTAATTCTATCTCCCTGAGCAACAGTGGAA
* *
47623592 TAGATTGAAGATTACATATTTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTT
261 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTT
* * *
47623657 TACCT-CTCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGCCAGCAGTG
326 TACCTCCT-TGAAGTTACAGTGGAGTACATTAAAGCCAGTAATTCTATCTCCCTGGCCAACAGTG
47623721 GAATAG
390 GAATAG
*
47623727 ATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAATGATGGCGGATTTTAC
1 ATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAA-GATGGTGGATTTTAC
*
47623792 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAACTCTATCTCCCTAGGGGCAACAGTGGA
65 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT--GGGCAACAGTGGA
*
47623857 ATAGATTGAAGATTACAGATCTTATCTCCCTAGGCAG
128 ATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAG
47623894 CGAAGTAGAT
Statistics
Matches: 531, Mismatches: 25, Indels: 8
0.94 0.04 0.01
Matches are distributed among these distances:
393 2 0.00
394 341 0.64
395 65 0.12
396 76 0.14
398 47 0.09
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (395 bp):
ATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAGATGGTGGATTTTACC
TCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGGAATA
GATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTA
CCTCCCTGAGGTTACAGTACAGTACATTGAAGCCAGTAATTCTATCTCCCTGAGCAACAGTGGAA
TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTT
TACCTCCTTGAAGTTACAGTGGAGTACATTAAAGCCAGTAATTCTATCTCCCTGGCCAACAGTGG
AATAG
Found at i:47623969 original size:44 final size:45
Alignment explanation
Indices: 47623906--47624011 Score: 139
Period size: 45 Copynumber: 2.4 Consensus size: 45
47623896 AAGTAGATCA
47623906 AAGTTGCAGTGGGGCAGACT-AAGGA-A-GCAAGTCTTATC-CTCCTG
1 AAGTTGCAGTGGGGCAGACTGAAGGAGACG-AA-TCTTATCTC-CCTG
*
47623950 AAGTTGCAGTGGGGCAGACTGAAGGTGACGAATCTTATCTCCCTG
1 AAGTTGCAGTGGGGCAGACTGAAGGAGACGAATCTTATCTCCCTG
*
47623995 AAGTTGCAGTGGAGCAG
1 AAGTTGCAGTGGGGCAG
47624012 GTTAAAGCCA
Statistics
Matches: 56, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
44 20 0.36
45 31 0.55
46 4 0.07
47 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.23
Consensus pattern (45 bp):
AAGTTGCAGTGGGGCAGACTGAAGGAGACGAATCTTATCTCCCTG
Found at i:47624085 original size:44 final size:44
Alignment explanation
Indices: 47623980--47624088 Score: 132
Period size: 44 Copynumber: 2.5 Consensus size: 44
47623970 GAAGGTGACG
*
47623980 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAACCAAT
* *
47624024 AATCCTATTTCCCTGAAGTTGCAGTGGAGC-GGATTAAAACCACA-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGG-TTAAAACCA-AT
* **
47624068 GATCTTATCTCTTTGAAGTTG
1 AATCTTATCTCCCTGAAGTTG
47624089 TAGAGGGCGG
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
43 2 0.04
44 52 0.95
45 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.30
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAACCAAT
Found at i:47634912 original size:9 final size:9
Alignment explanation
Indices: 47634900--47634943 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
47634890 AACGAGAAAG
47634900 TTGAGAGAC
1 TTGAGAGAC
47634909 TTGAGAGAC
1 TTGAGAGAC
**
47634918 TTGAGAGGT
1 TTGAGAGAC
*
47634927 TTGAGAGAG
1 TTGAGAGAC
47634936 TTGAGAGA
1 TTGAGAGA
47634944 AGGATGTGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.32, C:0.05, G:0.39, T:0.25
Consensus pattern (9 bp):
TTGAGAGAC
Found at i:47635585 original size:15 final size:15
Alignment explanation
Indices: 47635553--47635609 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
47635543 AAATATAACA
*
47635553 TATTTTT-ATATTATT
1 TATTTTTAATA-TAAT
47635568 TATTTTTAATATAAT
1 TATTTTTAATATAAT
**
47635583 TATTCTTCTTTTATAAT
1 TATT-TT-TAATATAAT
47635600 TATTTTTAAT
1 TATTTTTAAT
47635610 TTGTAAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
15 16 0.47
16 7 0.21
17 11 0.32
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTTTTAATATAAT
Found at i:47640309 original size:18 final size:19
Alignment explanation
Indices: 47640286--47640334 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
47640276 AAGTTTTATT
*
47640286 TTTATTTTTATTTATTTA-
1 TTTATTTTTATTTACTTAG
47640304 TTTATTTATT-TTTACTTAG
1 TTTATTT-TTATTTACTTAG
47640323 TTTAATTTTTAT
1 TTT-ATTTTTAT
47640335 GTAAATATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.54
19 7 0.27
20 5 0.19
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTATTTTTATTTACTTAG
Found at i:47640314 original size:22 final size:22
Alignment explanation
Indices: 47640277--47640334 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
47640267 CAAGTTGTAA
* *
47640277 AGTTTTATTTTTATTTTTATTT
1 AGTTTAATTTTTATTTTTACTT
*
47640299 A-TTTATTTATTTATTTTTACTT
1 AGTTTAATT-TTTATTTTTACTT
47640321 AGTTTAATTTTTAT
1 AGTTTAATTTTTAT
47640335 GTAAATATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 5 0.17
22 19 0.63
23 6 0.20
ACGTcount: A:0.22, C:0.02, G:0.03, T:0.72
Consensus pattern (22 bp):
AGTTTAATTTTTATTTTTACTT
Found at i:47647448 original size:24 final size:24
Alignment explanation
Indices: 47647391--47647463 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
47647381 GGCTACTCAT
* *
47647391 CTGGAAGAAACAGTTATGTCAGCA
1 CTGGAAGAAGCAGTCATGTCAGCA
*
47647415 CTGGAAGAAGCAGTCATGTCAGCG
1 CTGGAAGAAGCAGTCATGTCAGCA
* * *
47647439 CTGGAAGAAGTAGCCATGGCAGCA
1 CTGGAAGAAGCAGTCATGTCAGCA
47647463 C
1 C
47647464 AATTACCCTT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.33, C:0.21, G:0.30, T:0.16
Consensus pattern (24 bp):
CTGGAAGAAGCAGTCATGTCAGCA
Found at i:47650292 original size:23 final size:22
Alignment explanation
Indices: 47650266--47650311 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
47650256 TCTTTTTCAT
*
47650266 TCAATCTTATTATATCAATTCTC
1 TCAATCGTATTA-ATCAATTCTC
* *
47650289 TCAATCGTGTTAATCTATTCTC
1 TCAATCGTATTAATCAATTCTC
47650311 T
1 T
47650312 AAACTATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.26, C:0.22, G:0.04, T:0.48
Consensus pattern (22 bp):
TCAATCGTATTAATCAATTCTC
Found at i:47652664 original size:5 final size:5
Alignment explanation
Indices: 47652654--47652696 Score: 86
Period size: 5 Copynumber: 8.6 Consensus size: 5
47652644 AAATAAATCA
47652654 ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATT
1 ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATT
47652697 TTACATCAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.21, C:0.00, G:0.19, T:0.60
Consensus pattern (5 bp):
ATTGT
Found at i:47653662 original size:17 final size:17
Alignment explanation
Indices: 47653608--47653662 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
47653598 TCCTGATTGG
* *
47653608 TTTATTGATTTTTGTCA
1 TTTATTTATTTTTGTTA
* * *
47653625 TTTGTTTATTTTTCTTG
1 TTTATTTATTTTTGTTA
*
47653642 TTTATTTATTTTAGTTA
1 TTTATTTATTTTTGTTA
47653659 TTTA
1 TTTA
47653663 AATTCTCTCA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.16, C:0.04, G:0.09, T:0.71
Consensus pattern (17 bp):
TTTATTTATTTTTGTTA
Found at i:47658010 original size:19 final size:19
Alignment explanation
Indices: 47657972--47658010 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
47657962 GTGCGATCTT
*
47657972 TTAGTGTATAGGCGATCCC
1 TTAGTGTATAGGCGAACCC
*
47657991 TTAGTGTATAGGTGAACCC
1 TTAGTGTATAGGCGAACCC
47658010 T
1 T
47658011 GCATGTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (19 bp):
TTAGTGTATAGGCGAACCC
Found at i:47658129 original size:29 final size:27
Alignment explanation
Indices: 47658047--47658149 Score: 80
Period size: 28 Copynumber: 3.6 Consensus size: 27
47658037 GTATGCAAAC
* *
47658047 CCCCTATATGCGAACACCTATATGTGAA
1 CCCCTATAAGCGAAC-CCTGTATGTGAA
* * *
47658075 CCCCAATAAGCGAACCCCCAGAATGTGAA
1 CCCCTATAAGCGAA--CCCTGTATGTGAA
*
47658104 CTCCCTATAAGCGAACCCTTGTATGTGAG
1 C-CCCTATAAGCGAACCC-TGTATGTGAA
* * *
47658133 CCCATATATGTGAACCC
1 CCCCTATAAGCGAACCC
47658150 GCCCATATGT
Statistics
Matches: 59, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
28 28 0.47
29 18 0.31
30 13 0.22
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (27 bp):
CCCCTATAAGCGAACCCTGTATGTGAA
Found at i:47658155 original size:18 final size:18
Alignment explanation
Indices: 47658132--47658167 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
47658122 TTGTATGTGA
47658132 GCCCATATATGTGAACCC
1 GCCCATATATGTGAACCC
*
47658150 GCCCATATGTGTGAACCC
1 GCCCATATATGTGAACCC
47658168 TTATATAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.22
Consensus pattern (18 bp):
GCCCATATATGTGAACCC
Found at i:47658546 original size:111 final size:112
Alignment explanation
Indices: 47658400--47658624 Score: 362
Period size: 111 Copynumber: 2.0 Consensus size: 112
47658390 TGTGAATATG
*
47658400 CAAACCCTACATATTGTAGCATGTGAATCCTATCTATTTCCACTAAGCAAACCTTACATGTTTTA
1 CAAACCCTACATATTGTAGCATGCGAATCCTATCTATTTCCACTAAGCAAACCTTACATGTTTTA
*
47658465 TATGTGAA-CCTATATGTATATTCATGTGAACCCTAGGATGAATGTA
66 TATGTGAACCCTATATGTATATTCATGTGAACCCTAGGAGGAATGTA
* ** * *
47658511 CAAACCCTACATATTGTAGTATGCGAATCCTATCTATTTCTGCTATGTAAACCTTACATGTTTTA
1 CAAACCCTACATATTGTAGCATGCGAATCCTATCTATTTCCACTAAGCAAACCTTACATGTTTTA
* *
47658576 TATGTGAACCCTATATGTATATTCATGTGAGCCTTAGGAGGAATGTA
66 TATGTGAACCCTATATGTATATTCATGTGAACCCTAGGAGGAATGTA
47658623 CA
1 CA
47658625 TGCGATCCTT
Statistics
Matches: 104, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
111 67 0.64
112 37 0.36
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (112 bp):
CAAACCCTACATATTGTAGCATGCGAATCCTATCTATTTCCACTAAGCAAACCTTACATGTTTTA
TATGTGAACCCTATATGTATATTCATGTGAACCCTAGGAGGAATGTA
Found at i:47658810 original size:15 final size:15
Alignment explanation
Indices: 47658734--47658804 Score: 97
Period size: 15 Copynumber: 4.7 Consensus size: 15
47658724 TACTGTAATA
*
47658734 TGCGAACCTTATATG
1 TGCGAACCCTATATG
*
47658749 TGCGAACCCTATTTG
1 TGCGAACCCTATATG
*
47658764 TACGAACCCTATATG
1 TGCGAACCCTATATG
*
47658779 TGTGAACCCTATATG
1 TGCGAACCCTATATG
*
47658794 TGTGAACCCTA
1 TGCGAACCCTA
47658805 CTTGTGAACC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 50 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (15 bp):
TGCGAACCCTATATG
Found at i:47672079 original size:80 final size:81
Alignment explanation
Indices: 47671932--47672095 Score: 294
Period size: 80 Copynumber: 2.0 Consensus size: 81
47671922 AATATATGGA
* *
47671932 TATAGTCTTTGAAAATGCGTTCTAATATTCCCTTTTTTATACCATGTTGTAAAACATTACGTCGA
1 TATAGTCTTTGAAAACGCATTCTAATATTCCCTTTTTTATACCATGTTGTAAAACATTACGTCGA
47671997 AAGAAAACTTACTTAT
66 AAGAAAACTTACTTAT
*
47672013 TATAGTCTTTGAAAACGCATTCTAATATTCCC-TTTTTATACCATGTTGTAAAACATTACGTTGA
1 TATAGTCTTTGAAAACGCATTCTAATATTCCCTTTTTTATACCATGTTGTAAAACATTACGTCGA
47672077 AAGAAAACTTACTTAT
66 AAGAAAACTTACTTAT
47672093 TAT
1 TAT
47672096 TTGTAAAACA
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
80 50 0.62
81 30 0.38
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (81 bp):
TATAGTCTTTGAAAACGCATTCTAATATTCCCTTTTTTATACCATGTTGTAAAACATTACGTCGA
AAGAAAACTTACTTAT
Found at i:47672735 original size:48 final size:47
Alignment explanation
Indices: 47672675--47672765 Score: 155
Period size: 48 Copynumber: 1.9 Consensus size: 47
47672665 AACACATTAT
47672675 TTGTGGACAAGCCACCACATAAATCCCGATAAACGACCACATAACACA
1 TTGTGGACAAGCCACCACATAAATCCCGAT-AACGACCACATAACACA
* *
47672723 TTGTGGACAAGCCACCACATAATTGCCGATAACGACCACATAA
1 TTGTGGACAAGCCACCACATAAATCCCGATAACGACCACATAA
47672766 TCGCAGATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
47 13 0.32
48 28 0.68
ACGTcount: A:0.40, C:0.30, G:0.14, T:0.16
Consensus pattern (47 bp):
TTGTGGACAAGCCACCACATAAATCCCGATAACGACCACATAACACA
Found at i:47672761 original size:21 final size:21
Alignment explanation
Indices: 47672736--47672775 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
47672726 TGGACAAGCC
* *
47672736 ACCACATAATTGCCGATAACG
1 ACCACATAATCGCAGATAACG
47672757 ACCACATAATCGCAGATAA
1 ACCACATAATCGCAGATAA
47672776 ACTGCAACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.28, G:0.12, T:0.17
Consensus pattern (21 bp):
ACCACATAATCGCAGATAACG
Found at i:47672945 original size:7 final size:7
Alignment explanation
Indices: 47672933--47672961 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
47672923 GTAAACATGC
47672933 TCACATA
1 TCACATA
47672940 TCACATA
1 TCACATA
47672947 TCACATA
1 TCACATA
47672954 TCACATA
1 TCACATA
47672961 T
1 T
47672962 TATTCACTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.41, C:0.28, G:0.00, T:0.31
Consensus pattern (7 bp):
TCACATA
Found at i:47693623 original size:45 final size:44
Alignment explanation
Indices: 47693573--47693665 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 44
47693563 GGTTCGCTGT
*
47693573 AATGGAATAGAGCTGTAATAGTAACTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGT-ACTC-ATGTGTTTGGTTGAATGG
* * *
47693618 AATGGAATAGAACTGTAATGGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGTACTCATGTGTTTGGTTGAATGG
47693662 AATG
1 AATG
47693666 ATGTTGTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
43 1 0.02
44 22 0.51
45 20 0.47
ACGTcount: A:0.31, C:0.05, G:0.28, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAGTACTCATGTGTTTGGTTGAATGG
Found at i:47696818 original size:13 final size:13
Alignment explanation
Indices: 47696800--47696829 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
47696790 TGAAGGGGTT
*
47696800 AACAAGGAAATCA
1 AACAAGAAAATCA
47696813 AACAAGAAAATCA
1 AACAAGAAAATCA
47696826 AACA
1 AACA
47696830 TGCAATACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.17, G:0.10, T:0.07
Consensus pattern (13 bp):
AACAAGAAAATCA
Found at i:47701006 original size:3 final size:3
Alignment explanation
Indices: 47700998--47701032 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
47700988 CATATTCCTA
47700998 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
47701033 GAATACTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:47706763 original size:18 final size:19
Alignment explanation
Indices: 47706727--47706764 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
47706717 CAAAAATAAA
47706727 TAAATATTTGTATTATATT
1 TAAATATTTGTATTATATT
*
47706746 TAAATATTT-TATTTTATT
1 TAAATATTTGTATTATATT
47706764 T
1 T
47706765 TCGTATTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (19 bp):
TAAATATTTGTATTATATT
Found at i:47707111 original size:61 final size:59
Alignment explanation
Indices: 47706994--47707180 Score: 155
Period size: 61 Copynumber: 3.0 Consensus size: 59
47706984 ACCTAATGAC
* * * * * *
47706994 AAATTTAGCCCTCCAATATTTACATATTGTATCAATTT-GATCCTAAATCTAAAAATTCAACA
1 AAATTTAGCCCT-CAATATTTAAAAATTTTTTC-ATTTAG-TTCTAATTCTAAAAATTCAA-A
*
47707056 AAATTTAGCCCTCAATATTTAAAAATTTTTTCATTTAGTTCTAATTCTAATAAATTCAAT
1 AAATTTAGCCCTCAATATTTAAAAATTTTTTCATTTAGTTCTAATTCTAA-AAATTCAAA
* * * *
47707116 AAATTTAAG-CCTGAACATTTACAAAATTTGTTGAT-ATTTAATTCTAATTCTAAAAGTTTCAAA
1 AAATTT-AGCCCTCAATATTTA-AAAATTT-TT--TCATTTAGTTCTAATTCTAAAA-ATTCAAA
47707179 AA
1 AA
47707181 TGAAAAATAT
Statistics
Matches: 105, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
60 30 0.29
61 34 0.32
62 16 0.15
63 24 0.23
64 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.40
Consensus pattern (59 bp):
AAATTTAGCCCTCAATATTTAAAAATTTTTTCATTTAGTTCTAATTCTAAAAATTCAAA
Found at i:47707136 original size:60 final size:62
Alignment explanation
Indices: 47706994--47707170 Score: 154
Period size: 60 Copynumber: 2.9 Consensus size: 62
47706984 ACCTAATGAC
* * * * *
47706994 AAATTTAGCCCTCCAATATTTAC-ATA-TTG-TATCAATTTGATCCTAAATCTAAAAATTCAACA
1 AAATTTAGCCCT-CAACATTTACAAAATTTGTTAT--ATTTAATTCTAATTCTAAAAATTCAACA
* * *
47707056 AAATTTAGCCCTCAATATTTA-AAAATTT-TT-TCATTTAGTTCTAATTCTAATAAATTCAA-T
1 AAATTTAGCCCTCAACATTTACAAAATTTGTTAT-ATTTAATTCTAATTCTAA-AAATTCAACA
*
47707116 AAATTTAAG-CCTGAACATTTACAAAATTTGTTGATATTTAATTCTAATTCTAAAA
1 AAATTT-AGCCCTCAACATTTACAAAATTTGTT-ATATTTAATTCTAATTCTAAAA
47707171 GTTTCAAAAA
Statistics
Matches: 96, Mismatches: 10, Indels: 18
0.77 0.08 0.15
Matches are distributed among these distances:
60 30 0.31
61 29 0.30
62 19 0.20
63 17 0.18
64 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.40
Consensus pattern (62 bp):
AAATTTAGCCCTCAACATTTACAAAATTTGTTATATTTAATTCTAATTCTAAAAATTCAACA
Found at i:47708140 original size:26 final size:26
Alignment explanation
Indices: 47708104--47708155 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
47708094 TTGAACTTAG
47708104 TTTGACCAATCCCTATAGCATAGACC
1 TTTGACCAATCCCTATAGCATAGACC
47708130 TTTGACCAATCCCTATAGCATAGACC
1 TTTGACCAATCCCTATAGCATAGACC
47708156 CTTCACCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.31, G:0.12, T:0.27
Consensus pattern (26 bp):
TTTGACCAATCCCTATAGCATAGACC
Found at i:47710729 original size:30 final size:28
Alignment explanation
Indices: 47710693--47710751 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 28
47710683 AAATTTAAAT
47710693 TTTTTTTAAATGAATATTTTTCTATATTTA
1 TTTTTTTAAATGAATA-TTTT-TATATTTA
47710723 TTTTTTTAAATGAATATTTTTATATTTA
1 TTTTTTTAAATGAATATTTTTATATTTA
47710751 T
1 T
47710752 ACGTATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 9 0.31
29 4 0.14
30 16 0.55
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (28 bp):
TTTTTTTAAATGAATATTTTTATATTTA
Found at i:47710740 original size:16 final size:16
Alignment explanation
Indices: 47710693--47710743 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
47710683 AAATTTAAAT
47710693 TTTTTTTAAATGAATA
1 TTTTTTTAAATGAATA
* * *
47710709 TTTTTCTATAT--TTA
1 TTTTTTTAAATGAATA
47710723 TTTTTTTAAATGAATA
1 TTTTTTTAAATGAATA
47710739 TTTTT
1 TTTTT
47710744 ATATTTATAC
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
14 11 0.41
16 16 0.59
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (16 bp):
TTTTTTTAAATGAATA
Found at i:47722963 original size:44 final size:44
Alignment explanation
Indices: 47722907--47723492 Score: 420
Period size: 44 Copynumber: 13.4 Consensus size: 44
47722897 TCAAATATAA
* ** *
47722907 CAGATCCTGTCTTCCTATATTGGTAACGAAGTGGATCGAAGATG
1 CAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATCGAAGATG
* * * * * *
47722951 CAAATATTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAAAAAG
1 CAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATCG-AAGATG
** * * * * * *
47722996 CAGATCTTGTCCACATGTATTGG-CGTGAAGTAGATCAAAGATAA
1 CAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATCGAAGAT-G
* * * *
47723040 CAGATCCTGTCTTCCT-TATTGGTAGTGAAGTGGATCGAAGATG
1 CAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATCGAAGATG
* * * * *
47723083 AAAATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAAGAAAG
1 CAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATCGAAG-ATG
* * * * *
47723128 GAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATAG
1 CAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATCGAAGAT-G
* * ** *
47723172 CAGATCCTGTTTTCCTATATTGGT-AAGAAGTGGATCGAAGA--
1 CAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATCGAAGATG
* * *
47723213 CTAAATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAG
1 C-AGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATCGAAG-ATG
* * * * * *
47723259 CAAATCTTGTCTTCATGTATTAG-CGCGAAGTAGATTGAAG-TAG
1 CAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATCGAAGAT-G
* * * *
47723302 CAGATCCTGTCTTCCTATATTGGTAG-GAAATGGATCGAAGATG
1 CAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATCGAAGATG
* * * *
47723345 CAGATCATGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAG
1 CAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATCGAAG-ATG
* * * * * *
47723390 CAGATTTTGTCTTCATGTATTAG-CGTGAAGTAGATCGAAGATAG
1 CAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATCGAAGAT-G
* * * * *
47723434 CAGATCCTATCTTCCTATATTGGTAG-GAAGTGGATCGAAGAAG
1 CAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATCGAAGATG
*
47723477 CAGATCTTGCCTTCCT
1 CAGATCTTGTCTTCCT
47723493 GCACCGACAA
Statistics
Matches: 413, Mismatches: 110, Indels: 39
0.73 0.20 0.07
Matches are distributed among these distances:
41 1 0.00
42 19 0.05
43 103 0.25
44 213 0.52
45 76 0.18
46 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (44 bp):
CAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATCGAAGATG
Found at i:47723402 original size:262 final size:263
Alignment explanation
Indices: 47722861--47723474 Score: 901
Period size: 262 Copynumber: 2.3 Consensus size: 263
47722851 GCTAAAAAAC
* * * * * * *
47722861 AGCAAATCTTGCCTTCATGTATTGGCATGAAATAGATCAAATATAACAGATCCTGTCTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
47722926 TTGGTAACGAAGTGGATCGAAGATGCAAATATTGTCTTCCCATACTGGTGGCGAAGTAGATCGAA
66 TTGGTAA-GAAGTGGATCGAAGAT-CAAATATTGTCTTCCCATACTGGTGGCGAAGTAGATCGAA
* * *
47722991 AAAAGCAGATCTTGTCCACATGTATTGGCGTGAAGTAGATCAAAGATAACAGATCCTGTCTTCCT
129 AAAAGCAAATCTTGTCCACATGTATTAGCGCGAAGTAGATCAAAGATAACAGATCCTGTCTTCCT
* * *
47723056 TATTGGTAGTGAAGTGGATCGAAGATGAAAATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCA
194 TATTGGTAGTGAAATGGATCGAAGATGAAAATCATGTCTTCCCATACTGGTGGCGAAGTAGATCA
47723121 AAGAA
259 AAGAA
* *
47723126 AGGAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTTTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
* * *
47723191 TTGGTAAGAAGTGGATCGAAGA-CTAAATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAG
66 TTGGTAAGAAGTGGATCGAAGATC-AAATATTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAA
** ** *
47723255 AAAGCAAATCTTGTCTTCATGTATTAGCGCGAAGTAGATTGAAG-TAGCAGATCCTGTCTTCCTA
130 AAAGCAAATCTTGTCCACATGTATTAGCGCGAAGTAGATCAAAGATAACAGATCCTGTCTTCCT-
* * *
47723319 TATTGGTAG-GAAATGGATCGAAGATGCAGATCATGTCTTCCCATACTGGTGGCGAAGTAGATCG
194 TATTGGTAGTGAAATGGATCGAAGATGAAAATCATGTCTTCCCATACTGGTGGCGAAGTAGATCA
47723383 AAGAA
259 AAGAA
* * *
47723388 AGCAGATTTTGTCTTCATGTATTAGCGTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
*
47723453 TTGGTAGGAAGTGGATCGAAGA
66 TTGGTAAGAAGTGGATCGAAGA
47723475 AGCAGATCTT
Statistics
Matches: 315, Mismatches: 32, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
262 154 0.49
263 83 0.26
264 15 0.05
265 63 0.20
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (263 bp):
AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
TTGGTAAGAAGTGGATCGAAGATCAAATATTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAAA
AAGCAAATCTTGTCCACATGTATTAGCGCGAAGTAGATCAAAGATAACAGATCCTGTCTTCCTTA
TTGGTAGTGAAATGGATCGAAGATGAAAATCATGTCTTCCCATACTGGTGGCGAAGTAGATCAAA
GAA
Found at i:47723518 original size:132 final size:132
Alignment explanation
Indices: 47722861--47723491 Score: 901
Period size: 132 Copynumber: 4.8 Consensus size: 132
47722851 GCTAAAAAAC
* * * * * * *
47722861 AGCAAATCTTGCCTTCATGTATTGGCATGAAATAGATCAAATATAACAGATCCTGTCTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
* *
47722926 TTGGTAACGAAGTGGATCGAAGATGCAAATATTGTCTTCCCATACTGGTGGCGAAGTAGATCGAA
66 TTGGT-AGGAAGTGGATCGAAGATGCAAATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAA
*
47722991 AAA
130 GAA
** * *
47722994 AGCAGATCTTGTCCACATGTATTGGCGTGAAGTAGATCAAAGATAACAGATCCTGTCTTCCT-TA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
* * *
47723058 TTGGTAGTGAAGTGGATCGAAGATGAAAATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCAAA
66 TTGGTAG-GAAGTGGATCGAAGATGCAAATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAA
47723123 GAA
130 GAA
* *
47723126 AGGAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTTTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
* *
47723191 TTGGTAAGAAGTGGATCGAAGA--CTAAATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAA
66 TTGGTAGGAAGTGGATCGAAGATGC-AAATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAA
47723254 GAA
130 GAA
* * * *
47723257 AGCAAATCTTGTCTTCATGTATTAGCGCGAAGTAGATTGAAG-TAGCAGATCCTGTCTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
* * *
47723321 TTGGTAGGAAATGGATCGAAGATGCAGATCATGTCTTCCCATACTGGTGGCGAAGTAGATCGAAG
66 TTGGTAGGAAGTGGATCGAAGATGCAAATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAG
47723386 AA
131 AA
* * *
47723388 AGCAGATTTTGTCTTCATGTATTAGCGTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
* * *
47723453 TTGGTAGGAAGTGGATCGAAGAAGCAGATCTTGCCTTCC
66 TTGGTAGGAAGTGGATCGAAGATGCAAATCTTGTCTTCC
47723492 TGCACCGACA
Statistics
Matches: 450, Mismatches: 42, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
130 41 0.09
131 156 0.35
132 190 0.42
133 63 0.14
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.29
Consensus pattern (132 bp):
AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
TTGGTAGGAAGTGGATCGAAGATGCAAATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAG
AA
Found at i:47723582 original size:88 final size:88
Alignment explanation
Indices: 47723475--47723872 Score: 625
Period size: 88 Copynumber: 4.5 Consensus size: 88
47723465 GGATCGAAGA
** *
47723475 AGCAGATCTTGCCTTCCTGCACCGACAATGAAGCAGATCGAAGACACCAGCCTTGTCTCCCTGGG
1 AGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGG
47723540 TTGCAGCGGAGCAGGTTAAAAAT
66 TTGCAGCGGAGCAGGTTAAAAAT
* * *
47723563 TGCAGATCTTGCATTCCTGCACCGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGG
1 AGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGG
*
47723628 TTGTAGCGGAGCAGGTTAAAAAT
66 TTGCAGCGGAGCAGGTTAAAAAT
* * *
47723651 AGTAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTGGG
1 AGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGG
* *
47723716 TTGTAGCGGAGTAGGTTAAAAAT
66 TTGCAGCGGAGCAGGTTAAAAAT
* * *
47723739 AGTAGTTCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACTAGCCTTGCCTCCCTGGG
1 AGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGG
*
47723804 TTGCAGCAGAGCAGGTTAAAAAT
66 TTGCAGCGGAGCAGGTTAAAAAT
* * *
47723827 AGCAGATCTTGTCTTCCTGTACCGATAGCGAAGCAGATCGAAGACA
1 AGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACA
47723873 TCAGTCTTAT
Statistics
Matches: 286, Mismatches: 24, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 286 1.00
ACGTcount: A:0.27, C:0.26, G:0.25, T:0.22
Consensus pattern (88 bp):
AGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGG
TTGCAGCGGAGCAGGTTAAAAAT
Found at i:47723641 original size:43 final size:43
Alignment explanation
Indices: 47723594--47723726 Score: 104
Period size: 44 Copynumber: 3.0 Consensus size: 43
47723584 CCGACAGTGA
47723594 AGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGTAGCGG
1 AGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGTAGCGG
* ** * * ** * * **** * *
47723637 AGCAGGTTAAAAATAGTAGATCTTGCCTTCCTGTACCGACAGCGA
1 AGCAGATCGAAGACACCAG-CCTTGCCTCCCTGGGTTG-TAGCGG
*
47723682 AGCAGATCGAAGACACCAACCTTGCCTCCCTGGGTTGTAGCGG
1 AGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGTAGCGG
47723725 AG
1 AG
47723727 TAGGTTAAAA
Statistics
Matches: 57, Mismatches: 31, Indels: 4
0.62 0.34 0.04
Matches are distributed among these distances:
43 18 0.32
44 24 0.42
45 15 0.26
ACGTcount: A:0.26, C:0.27, G:0.27, T:0.20
Consensus pattern (43 bp):
AGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGTAGCGG
Found at i:47723664 original size:44 final size:44
Alignment explanation
Indices: 47723614--47723837 Score: 119
Period size: 44 Copynumber: 5.1 Consensus size: 44
47723604 AGACACCAGC
*
47723614 CTTGCCTCCCTGGGTTGTAGCGGAGCAGGTTAAAAATAGTAGAT
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGTAGAT
* **** * * ** * * ** *
47723658 CTTGCCTTCCTGTACCGACAGCGAAGCAGATCGAAGACACCA-AC
1 CTTGCCTCCCTGGGTTG-CAGCGGAGCAGGTTAAAAATAGTAGAT
* * *
47723702 CTTGCCTCCCTGGGTTGTAGCGGAGTAGGTTAAAAATAGTAGTT
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGTAGAT
* **** * * ** * * * *
47723746 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACTAG-C
1 CTTGCCTCCCTGGGTTG-CAGCGGAGCAGGTTAAAAATAGTAGAT
* *
47723790 CTTGCCTCCCTGGGTTGCAGCAGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGTAGAT
47723834 CTTG
1 CTTG
47723838 TCTTCCTGTA
Statistics
Matches: 114, Mismatches: 62, Indels: 8
0.62 0.34 0.04
Matches are distributed among these distances:
43 30 0.26
44 53 0.46
45 31 0.27
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (44 bp):
CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGTAGAT
Found at i:47731156 original size:12 final size:12
Alignment explanation
Indices: 47731093--47731150 Score: 89
Period size: 12 Copynumber: 4.8 Consensus size: 12
47731083 CTTTAGGGTT
47731093 ATTTCGATTTCA
1 ATTTCGATTTCA
*
47731105 ATTTTGATTTCA
1 ATTTCGATTTCA
47731117 ATTTCGATTTCA
1 ATTTCGATTTCA
*
47731129 ATGTCGATTTCA
1 ATTTCGATTTCA
*
47731141 ATTTCAATTT
1 ATTTCGATTT
47731151 AGATTTAGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 41 1.00
ACGTcount: A:0.26, C:0.14, G:0.09, T:0.52
Consensus pattern (12 bp):
ATTTCGATTTCA
Found at i:47731202 original size:6 final size:6
Alignment explanation
Indices: 47731093--47731186 Score: 71
Period size: 6 Copynumber: 15.7 Consensus size: 6
47731083 CTTTAGGGTT
* * * * * *
47731093 ATTTCG ATTTCA ATTTTG ATTTCA ATTTCG ATTTCA ATGTCG ATTTCA
1 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG
* * * * * * *
47731141 ATTTCA ATTTAG ATTTAG ATTTTG ATTTGG ATTTGG ATTTTG ATTT
1 ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTTCG ATTT
47731187 AGGGTTATTT
Statistics
Matches: 72, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 72 1.00
ACGTcount: A:0.24, C:0.09, G:0.14, T:0.53
Consensus pattern (6 bp):
ATTTCG
Found at i:47731644 original size:15 final size:15
Alignment explanation
Indices: 47731620--47731649 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
47731610 GAAGAAGAAA
*
47731620 TGTCTGGTAGTGATG
1 TGTCTAGTAGTGATG
47731635 TGTCTAGTAGTGATG
1 TGTCTAGTAGTGATG
47731650 CATATGAAAG
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:0.17, C:0.07, G:0.37, T:0.40
Consensus pattern (15 bp):
TGTCTAGTAGTGATG
Found at i:47733451 original size:29 final size:29
Alignment explanation
Indices: 47733413--47733469 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
47733403 GACTATTTTT
47733413 TAATATGCATGCAGTGAGTT-TTTTTTTAA
1 TAATATGCATGCAGTGA-TTGTTTTTTTAA
*
47733442 TAATATGCATGTAGTGATTGTTTTTTTA
1 TAATATGCATGCAGTGATTGTTTTTTTA
47733470 GGTGTGTGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 2 0.08
29 24 0.92
ACGTcount: A:0.26, C:0.05, G:0.18, T:0.51
Consensus pattern (29 bp):
TAATATGCATGCAGTGATTGTTTTTTTAA
Found at i:47734164 original size:21 final size:21
Alignment explanation
Indices: 47734140--47734191 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
47734130 CAAGTGGTTG
47734140 CCCCAACTCAGCAACA-AGCTA
1 CCCCAACTCAGCAACAGAG-TA
* *
47734161 CCCCAAATCAGCAAGAGAGTA
1 CCCCAACTCAGCAACAGAGTA
*
47734182 CTCCAACTCA
1 CCCCAACTCA
47734192 ATAGGCTGCC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.38, C:0.38, G:0.12, T:0.12
Consensus pattern (21 bp):
CCCCAACTCAGCAACAGAGTA
Found at i:47734981 original size:33 final size:31
Alignment explanation
Indices: 47734910--47734981 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
47734900 CAACAGTATT
* *
47734910 ACAA-AACATAAGCTGTTTTCAATGTTAACA
1 ACAACAACATAAGCTGTTTTCAAGGTTAAAA
47734940 ACAACAACATAAGCTGATTTT-AAGGTTTAAAAA
1 ACAACAACATAAGCTG-TTTTCAAGG-TT-AAAA
47734973 ACAACAACA
1 ACAACAACA
47734982 CAGTTACAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
30 4 0.11
31 14 0.39
32 6 0.17
33 12 0.33
ACGTcount: A:0.49, C:0.17, G:0.10, T:0.25
Consensus pattern (31 bp):
ACAACAACATAAGCTGTTTTCAAGGTTAAAA
Found at i:47735525 original size:10 final size:10
Alignment explanation
Indices: 47735498--47735535 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
47735488 TTTACCCTTA
*
47735498 TAAAAATT-G
1 TAAAAATTAT
47735507 TAAATAATTAT
1 TAAA-AATTAT
47735518 TAAAAATTAT
1 TAAAAATTAT
47735528 TAAAAATT
1 TAAAAATT
47735536 CTAAATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
9 4 0.15
10 18 0.69
11 4 0.15
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:47743876 original size:12 final size:11
Alignment explanation
Indices: 47743848--47743887 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
47743838 ATTTTTTTAA
47743848 TTTTAAAATAC
1 TTTTAAAATAC
47743859 TTTTAAAATAC
1 TTTTAAAATAC
*
47743870 TTTTTAAA-A-
1 TTTTAAAATAC
47743879 TTTTAAAAT
1 TTTTAAAAT
47743888 TTTAAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
9 7 0.27
10 1 0.04
11 18 0.69
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:47743884 original size:8 final size:8
Alignment explanation
Indices: 47743871--47743917 Score: 58
Period size: 8 Copynumber: 5.8 Consensus size: 8
47743861 TTAAAATACT
47743871 TTTTAAAA
1 TTTTAAAA
47743879 TTTTAAAA
1 TTTTAAAA
*
47743887 TTTTAAAT
1 TTTTAAAA
47743895 TTTTAAATA
1 TTTTAAA-A
* *
47743904 TTTTTAAT
1 TTTTAAAA
47743912 TTTTAA
1 TTTTAA
47743918 TTTAAATATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
8 27 0.82
9 6 0.18
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TTTTAAAA
Found at i:47743906 original size:17 final size:16
Alignment explanation
Indices: 47743871--47743917 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
47743861 TTAAAATACT
*
47743871 TTTTAAAATTTTAAAA
1 TTTTAAATTTTTAAAA
47743887 TTTTAAATTTTTAAATA
1 TTTTAAATTTTTAAA-A
*
47743904 TTTTTAATTTTTAA
1 TTTTAAATTTTTAA
47743918 TTTAAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
16 14 0.50
17 14 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTTAAATTTTTAAAA
Found at i:47743930 original size:31 final size:33
Alignment explanation
Indices: 47743827--47743947 Score: 124
Period size: 31 Copynumber: 3.5 Consensus size: 33
47743817 CCGAATATAA
*
47743827 TAAATA-TTTTTATTTTTTTAATTTTAAAATACTTT
1 TAAATACTTTTTA-ATTTTTAATTTT-AAATA-TTT
*
47743862 TAAAATACTTTTTAAAATTTTAAAATTTTAAAT-TTT
1 T-AAATACTTTTT--AATTTT-TAATTTTAAATATTT
47743898 TAAATA-TTTTTAATTTTTAA-TTTAAATATTT
1 TAAATACTTTTTAATTTTTAATTTTAAATATTT
47743929 TAAATACTTTTTTAATTTT
1 TAAATAC-TTTTTAATTTT
47743948 GTTTAATTTT
Statistics
Matches: 75, Mismatches: 3, Indels: 18
0.78 0.03 0.19
Matches are distributed among these distances:
30 7 0.09
31 11 0.15
32 6 0.08
33 11 0.15
34 5 0.07
35 6 0.08
36 9 0.12
37 5 0.07
38 8 0.11
39 7 0.09
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (33 bp):
TAAATACTTTTTAATTTTTAATTTTAAATATTT
Found at i:47746377 original size:29 final size:29
Alignment explanation
Indices: 47746322--47746378 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
47746312 CAACGGTCTC
* **
47746322 TTCGAACCAATAACTCAGATATTACTTGG
1 TTCGAACCAACAACTCAGATACCACTTGG
*
47746351 TTCGAACCAACAGCTCAGATACCACTTG
1 TTCGAACCAACAACTCAGATACCACTTG
47746379 ACACGGGGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.26
Consensus pattern (29 bp):
TTCGAACCAACAACTCAGATACCACTTGG
Found at i:47749547 original size:23 final size:23
Alignment explanation
Indices: 47749520--47749563 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
47749510 TTCTTTGTAA
*
47749520 ATGATGAAATTATAAATTAATAT
1 ATGATAAAATTATAAATTAATAT
*
47749543 ATGATAAAATTATAATTTAAT
1 ATGATAAAATTATAAATTAAT
47749564 TTTCTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (23 bp):
ATGATAAAATTATAAATTAATAT
Found at i:47751361 original size:31 final size:31
Alignment explanation
Indices: 47751298--47751363 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
47751288 GTAATCATAT
*
47751298 ACATGAAACTTGAATTGTGGTTTATATTTAC
1 ACATGAAACTTGAATTGTGATTTATATTTAC
*
47751329 ACATGAAACTTTG-ATTTTGATTTA-ATTGTAC
1 ACATGAAAC-TTGAATTGTGATTTATATT-TAC
47751360 ACAT
1 ACAT
47751364 TTAAATAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 3 0.10
31 25 0.81
32 3 0.10
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (31 bp):
ACATGAAACTTGAATTGTGATTTATATTTAC
Found at i:47751988 original size:3 final size:3
Alignment explanation
Indices: 47751980--47752007 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
47751970 AAAATCTTAG
47751980 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
47752008 AGATTTTGAT
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:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:47755162 original size:20 final size:19
Alignment explanation
Indices: 47755119--47755163 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
47755109 TTCGAAAATG
*
47755119 ATTTTTAAAAAATGAATTT
1 ATTTTTAAAAAATGAATAT
*
47755138 ATTTTTAAAAAAATTAATAT
1 ATTTTT-AAAAAATGAATAT
*
47755158 CTTTTT
1 ATTTTT
47755164 TTGTGTTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (19 bp):
ATTTTTAAAAAATGAATAT
Found at i:47755423 original size:11 final size:11
Alignment explanation
Indices: 47755407--47755442 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
47755397 AACTATTTTT
47755407 TTAATTTTTAA
1 TTAATTTTTAA
47755418 TTAATTTTTAA
1 TTAATTTTTAA
*
47755429 -TGATTTTTAA
1 TTAATTTTTAA
47755439 TTAA
1 TTAA
47755443 ACTAGTTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (11 bp):
TTAATTTTTAA
Found at i:47757285 original size:112 final size:111
Alignment explanation
Indices: 47757085--47757413 Score: 441
Period size: 108 Copynumber: 3.0 Consensus size: 111
47757075 TGGATTAAGA
* * ** *
47757085 TTTAAGAGAATATTTGGCTATTTGGTTAAACGAAAAAAATCGAAACCCAGCGCATTAGGGCACGT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACG-AAAAAATCGAAACCCAGCACATTAGGGCACGT
* *
47757150 TTTCTCAAATTTCCAAACGCAAAATATTGTCTTATTTTGAAAAAAAT
65 TTTCTCGAATTTCCAAACGCAAAATATTGCCTTATTTTGAAAAAAAT
* * *
47757197 TTTAAAAGGGATATTTGACTATTTGGTCGAACGAAAAAATCGAAACCCAGCACATTAGGACACAT
1 TTTAAAA-GGATATTTGGCTATTTGGTCGAACGAAAAAATCGAAACCCAGCACATTAGGGCACGT
* * * *
47757262 TTTTTCGAATTTCCAAACACAAAACATTGCCTTATTTTG----TAAT
65 TTTCTCGAATTTCCAAACGCAAAATATTGCCTTATTTTGAAAAAAAT
** *
47757305 TTTTTAAGGATATTTGGCTATTTGGTCGAACGAGAAATATCGAAACCCAGCACATTAGGGCACGT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGA-AAAAATCGAAACCCAGCACATTAGGGCACGT
*
47757370 TTTCTCGAATTTCCAAACGCAAAATATTGCCTTATTTAGAAAAA
65 TTTCTCGAATTTCCAAACGCAAAATATTGCCTTATTTTGAAAAA
47757414 TTTTCCTTTT
Statistics
Matches: 186, Mismatches: 25, Indels: 12
0.83 0.11 0.05
Matches are distributed among these distances:
107 25 0.13
108 71 0.38
112 69 0.37
113 21 0.11
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (111 bp):
TTTAAAAGGATATTTGGCTATTTGGTCGAACGAAAAAATCGAAACCCAGCACATTAGGGCACGTT
TTCTCGAATTTCCAAACGCAAAATATTGCCTTATTTTGAAAAAAAT
Found at i:47757817 original size:36 final size:35
Alignment explanation
Indices: 47757777--47757907 Score: 93
Period size: 38 Copynumber: 3.6 Consensus size: 35
47757767 ATGTATATAC
47757777 ATGTATATGTATATAAAATATATAAAACATATAAGT
1 ATGTATATGTATATAAAATATATAAAA-ATATAAGT
* * * * * *
47757813 ATGTATATATTTTCATAAAAAATGTATATATATATAGTT
1 ATGTATAT-GTAT-ATAAAATATATAAAAATATA-AG-T
* ** *
47757852 ATGTACATAAATTATAAAATATATAAAAATATGAGT
1 ATGTATATGTA-TATAAAATATATAAAAATATAAGT
*
47757888 ATGTA-AGTGTATATTAAATA
1 ATGTATA-TGTATATAAAATA
47757908 AGTTAAAAAA
Statistics
Matches: 71, Mismatches: 18, Indels: 13
0.70 0.18 0.13
Matches are distributed among these distances:
35 9 0.13
36 16 0.23
37 9 0.13
38 28 0.39
39 9 0.13
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.39
Consensus pattern (35 bp):
ATGTATATGTATATAAAATATATAAAAATATAAGT
Found at i:47758736 original size:22 final size:21
Alignment explanation
Indices: 47758683--47758736 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
47758673 ACAGAAGAAA
47758683 AAATAA-AAAAATAAAAAAAG
1 AAATAAGAAAAATAAAAAAAG
* *
47758703 -ATTAATGAAAAATAAAAAACG
1 AAATAA-GAAAAATAAAAAAAG
47758724 AAATAAGATAAAA
1 AAATAAGA-AAAA
47758737 AGGTTACTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
19 4 0.15
21 15 0.56
22 8 0.30
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (21 bp):
AAATAAGAAAAATAAAAAAAG
Found at i:47759927 original size:44 final size:44
Alignment explanation
Indices: 47759480--47759929 Score: 186
Period size: 44 Copynumber: 10.2 Consensus size: 44
47759470 TACCTTGGGA
* * ** *
47759480 AGATAAGATTCACCATATTTGATCTGCTCCACTACTGCTTAAGG
1 AGATAAGATTCACAATCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * *
47759524 AGA-CAGAATCTGCAATCTTCAA-CTTACTCCACTACTGATTAGGG
1 AGATAAGATTC-ACAATCTTCAATC-TGCTCCACTACTGCTTAGGG
* *
47759568 AGATAGGATT---AATGGCTTAAATCTGCTTCTCCACTA-T-CTT-GGG
1 AGATAAGATTCACAAT--CTTCAATCTG---CTCCACTACTGCTTAGGG
* * *
47759611 AAGATAAGATTCACCATCTCCGATCTGCTCCACTACTGCTTAGGG
1 -AGATAAGATTCACAATCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * *
47759656 AGA-CAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGG
1 AGATAAGATTC-ACAATCTTCAATCTGCTCCACTACTGCTTAGGG
* *
47759700 AGATAGGA--CA-AATGGCTTAAATCTGCTTCTCCACTA-T-CTT-GGG
1 AGATAAGATTCACAAT--CTTCAATCTG---CTCCACTACTGCTTAGGG
* * * * * *
47759743 AAGATAAGATTCACCATCTTCGATCTACTCTATTACTGCTCAGGG
1 -AGATAAGATTCACAATCTTCAATCTGCTCCACTACTGCTTAGGG
* ** * * * *
47759788 AGA-CAGAACCTGCAATCTTCAACCTACTCCACTACTACTTAGGG
1 AGATAAGATTC-ACAATCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * *
47759832 AGATAGGA--C-TAATGGCTTAAATCTGCTTCTCCACTA-T-CTTCGGA
1 AGATAAGATTCACAAT--CTTCAATCTG---CTCCACTACTGCTTAGGG
* *
47759876 AGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTCACAATCTTCAATCTGCTCCACTACTGCTTAGGG
47759920 AGATAAGATT
1 AGATAAGATT
47759930 TGCTATCTTT
Statistics
Matches: 295, Mismatches: 69, Indels: 84
0.66 0.15 0.19
Matches are distributed among these distances:
41 9 0.03
42 22 0.07
43 46 0.16
44 147 0.50
45 38 0.13
46 27 0.09
47 6 0.02
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (44 bp):
AGATAAGATTCACAATCTTCAATCTGCTCCACTACTGCTTAGGG
Found at i:47759938 original size:132 final size:132
Alignment explanation
Indices: 47759468--47759922 Score: 759
Period size: 132 Copynumber: 3.4 Consensus size: 132
47759458 TTACTTCCCT
* * * *
47759468 ACTACCTTGGGAAGATAAGATTCACCATATTTGATCTGCTCCACTACTGCTTAAGGAGACAGAAT
1 ACTATCTTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGAAT
* *
47759533 CTGCAATCTTCAACTTACTCCACTACTGA-TTAGGGAGATAGGATTAATGGCTTAAATCTGCTTC
66 CTGCAATCTTCAACCTACTCCACTACT-ACTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTC
47759597 TCC
130 TCC
*
47759600 ACTATCTTGGGAAGATAAGATTCACCATCTCCGATCTGCTCCACTACTGCTTAGGGAGACAGAAT
1 ACTATCTTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGAAT
* *
47759665 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACAAATGGCTTAAATCTGCTTCT
66 CTGCAATCTTCAACCTACTCCACTACTACTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCT
47759730 CC
131 CC
* * * * *
47759732 ACTATCTTGGGAAGATAAGATTCACCATCTTCGATCTACTCTATTACTGCTCAGGGAGACAGAAC
1 ACTATCTTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGAAT
47759797 CTGCAATCTTCAACCTACTCCACTACTACTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCT
66 CTGCAATCTTCAACCTACTCCACTACTACTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCT
47759862 CC
131 CC
*
47759864 ACTATCTTCGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGA
1 ACTATCTTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGA
47759923 TAAGATTTGC
Statistics
Matches: 300, Mismatches: 22, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
132 300 1.00
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.29
Consensus pattern (132 bp):
ACTATCTTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGAAT
CTGCAATCTTCAACCTACTCCACTACTACTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCT
CC
Found at i:47760121 original size:89 final size:89
Alignment explanation
Indices: 47759961--47761529 Score: 1452
Period size: 89 Copynumber: 17.6 Consensus size: 89
47759951 CTGTAAACTA
* * * * *
47759961 TGGTGTCTTTGATCTGCTTCGCTGTCAGTACAAGAAGGCAAGATCTGCTATCTTCAGTCTGCTCT
1 TGGTGTCTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCAAGATCTGTTATCTTCAGTCTGCTCC
* *
47760026 GTTGTCAGTATAGGAAGGCAAGGT
66 GCTGTCAGTACAGGAAGGCAAGGT
* * * *
47760050 TGGTGTCTTCGATCTGCTTCACCGTCAGTACAGGAAGGCAATATCTGCTATCTTCAGTCTGCCCC
1 TGGTGTCTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCAAGATCTGTTATCTTCAGTCTGCTCC
* *
47760115 GCTGTCAGTACAAGAAGGCAAGGC
66 GCTGTCAGTACAGGAAGGCAAGGT
* ** * *
47760139 TGGTGTCTTCGATCTGCTTCGCCGTTAGTACAAAAAGGCAAGATCTGCTATCTTTAGTCTGCTCC
1 TGGTGTCTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCAAGATCTGTTATCTTCAGTCTGCTCC
* *
47760204 ACTGTCAGTACAGGAAGGCAAGAT
66 GCTGTCAGTACAGGAAGGCAAGGT
* * * * * * * *
47760228 CTGCTATCTTC-AGTCTGCTCCGCTGTCAGTACAGGAAGGCAAGGT-TGGTGTCTTC-GATCTAC
1 -TGGTGTCTTCGA-TCTGCTTCGCCGTCAGTACAGGAAGGCAAGATCTGTTATCTTCAG-TCTGC
* * * *
47760290 TTCGCCGTCAGTATAGGAAGGCAAGAT
63 TCCGCTGTCAGTACAGGAAGGCAAGGT
* * * * * ** * * * * *
47760317 CTGTTATCTTC-AGTTTGCTCCACTATCAGTACAGGAAGGTAAG-GCTGATGTCTTCATTCTGCT
1 -TGGTGTCTTCGA-TCTGCTTCGCCGTCAGTACAGGAAGGCAAGATCTGTTATCTTCAGTCTGCT
* * * *
47760380 TCGCTGTCAGTATAGGAAAGCAAGAT
64 CCGCTGTCAGTACAGGAAGGCAAGGT
* * * * * * * * *
47760406 CTGTTATCTTC-AGTCTGCTCCGCTGTTAGTACAGGAAGGCAA-AGT-TGGTGTCTTCAATTTGC
1 -TGGTGTCTTCGA-TCTGCTTCGCCGTCAGTACAGGAAGGCAAGA-TCTGTTATCTTCAGTCTGC
* * * * *
47760468 TTCACCGTCAGTATAGGAAGGCAAGAT
63 TCCGCTGTCAGTACAGGAAGGCAAGGT
* * * * * * *
47760495 CTGTTATCTTC-AGTCTGCTCCGCTGTCAGTACAGGAAGGCAAG-GCTGGTGTCTTC-GATCTGC
1 -TGGTGTCTTCGA-TCTGCTTCGCCGTCAGTACAGGAAGGCAAGATCTGTTATCTTCAG-TCTGC
* *
47760557 TTCC-CCGTCAGTACAGGAAGGCAAGAT
63 -TCCGCTGTCAGTACAGGAAGGCAAGGT
* * * * * * *
47760584 CTGTTATCTTC-AGTTTGCTTCGCTGTCAGTACAGGAAGGCAAG-GCTGGTGTCTTC-GCTCTGC
1 -TGGTGTCTTCGA-TCTGCTTCGCCGTCAGTACAGGAAGGCAAGATCTGTTATCTTCAG-TCTGC
** * **
47760646 TTTGCCGTCAGTACAGGAAGGCAATAT
63 TCCGCTGTCAGTACAGGAAGGCAAGGT
* * * * * * *
47760673 CTGCTATCTTC-AGTCTGCTTCACCATCAGTACAGAAAGGCAAGATCTGGTATCTTCAGTTTGCT
1 -TGGTGTCTTCGA-TCTGCTTCGCCGTCAGTACAGGAAGGCAAGATCTGTTATCTTCAGTCTGCT
* * * *
47760737 CCACTGTCACTACAGGAAGGCAATGC
64 CCGCTGTCAGTACAGGAAGGCAAGGT
* * * * *
47760763 TGGTGTCCTCGATCTGCTTCACCGTCAGTACAAGAAGGCAGGATCTGCTATCTAT-AGTCTGCTC
1 TGGTGTCTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCAAGATCTGTTATCT-TCAGTCTGCTC
47760827 CGCTGTCAGTACAGGAAGGCAAGGT
65 CGCTGTCAGTACAGGAAGGCAAGGT
* * *
47760852 TGGTGTCTTCGATCTACTTCGCCGTCAGTATAGGAAGGCAAGATCTGTTATCTTCAGTTTGCTCC
1 TGGTGTCTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCAAGATCTGTTATCTTCAGTCTGCTCC
* * *
47760917 ACTATCAGTACAGGAAGGTAAGGT
66 GCTGTCAGTACAGGAAGGCAAGGT
* * * * *
47760941 TGATGTCTTCGTTCTGCTTCACTGTCAGTACAGGAAAGCAAGATCTGTTATCTTCAGTCTGCTCC
1 TGGTGTCTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCAAGATCTGTTATCTTCAGTCTGCTCC
* *
47761006 GCTGTTAGTACAGGAAGGCAAAGT
66 GCTGTCAGTACAGGAAGGCAAGGT
* * * *
47761030 TGGTGTCTTCAATTTGCTTCACCGTCAGTATAGGAAGGCAAGATCTGTTATCTTCAGTCTGCTCC
1 TGGTGTCTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCAAGATCTGTTATCTTCAGTCTGCTCC
*
47761095 GCTGTCAGTACAGGAAGGCAAGGC
66 GCTGTCAGTACAGGAAGGCAAGGT
* * * *
47761119 TGGTGTCTTCGATTTGCTTCCCCGTCAGTACAGGAAGGCAAGATCTGTTATCTTCAGTTTGCTTC
1 TGGTGTCTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCAAGATCTGTTATCTTCAGTCTGCTCC
*
47761184 GCTGTCAGTACAGGAAGGCAAGGC
66 GCTGTCAGTACAGGAAGGCAAGGT
* * *
47761208 TGGTGTCTTCGATCTACTTCGCCGTTAGTACAGGAAGGCAAGATTTGTTATCTTCAGTCTGCTCC
1 TGGTGTCTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCAAGATCTGTTATCTTCAGTCTGCTCC
* * *
47761273 ACTGTCAGTACAGGAAGACAAGGC
66 GCTGTCAGTACAGGAAGGCAAGGT
* * *
47761297 TGGTGTCTTCGATCTGCTTCACCGTCAGTACAGGAAGGCAAGATCTGTTATCTTCACTCTACTCC
1 TGGTGTCTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCAAGATCTGTTATCTTCAGTCTGCTCC
* ** *
47761362 GCTGTCAATACAGGAAGGTGAGGC
66 GCTGTCAGTACAGGAAGGCAAGGT
* * * * * * *
47761386 TGGTGTCTTCGATCTGCTTCGCTGTCAGTATAGGAAGGTAAGGTC-GGTGTCTTC-GATCTG-TT
1 TGGTGTCTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCAAGATCTGTTATCTTCAG-TCTGCTC
* * *
47761448 CGCCGTCAGTACAGGAAGACAAGAT
65 CGCTGTCAGTACAGGAAGGCAAGGT
* * * * *
47761473 CTGTTATCTTC-AGTCTGCTCCGCTGTCAGTACAGGAAGGCAATATCTGTTATCTTCA
1 -TGGTGTCTTCGA-TCTGCTTCGCCGTCAGTACAGGAAGGCAAGATCTGTTATCTTCA
47761530 CTGATCTGTT
Statistics
Matches: 1271, Mismatches: 187, Indels: 43
0.85 0.12 0.03
Matches are distributed among these distances:
87 20 0.02
88 49 0.04
89 1129 0.89
90 72 0.06
91 1 0.00
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (89 bp):
TGGTGTCTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCAAGATCTGTTATCTTCAGTCTGCTCC
GCTGTCAGTACAGGAAGGCAAGGT
Found at i:47762721 original size:8 final size:8
Alignment explanation
Indices: 47762708--47762737 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
47762698 GGCCTCTCCT
47762708 TTTTTTTC
1 TTTTTTTC
47762716 TTTTTTTC
1 TTTTTTTC
47762724 -TTTTTTC
1 TTTTTTTC
47762731 TTTTTTT
1 TTTTTTT
47762738 TTAACAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTTC
Found at i:47762729 original size:15 final size:15
Alignment explanation
Indices: 47762709--47762737 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
47762699 GCCTCTCCTT
47762709 TTTTTTCTTTTTTTC
1 TTTTTTCTTTTTTTC
47762724 TTTTTTCTTTTTTT
1 TTTTTTCTTTTTTT
47762738 TTAACAATTT
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:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTTTCTTTTTTTC
Found at i:47766653 original size:113 final size:110
Alignment explanation
Indices: 47766441--47766774 Score: 483
Period size: 108 Copynumber: 3.0 Consensus size: 110
47766431 TGGATTAAGA
* * * *
47766441 TTTAAGAGAATATTTGGCTATTTGGTCAAACGAAAAAAATCGAAACCCAGCGCATTAGGGCACGT
1 TTTAAG-G-ATATTTGGCTATTTGGTCGAACGAGAAAAATCAAAACCCAGCACATTAGGGCACGT
* * *
47766506 TTCCTCAAATTTCCAAACGCAAAATATTGTCTTATTTTGAAAAATTT
64 TTTCTCGAATTTCCAAACGCAAAATATTGCCTTATTTTGAAAAATTT
* * *
47766553 TTTAAAAGGGATATTTAGCTATTTGGTCGAACGAGAAAAATTAAAACCCAGCACATTAGGGCACA
1 TTT--AA-GGATATTTGGCTATTTGGTCGAACGAGAAAAATCAAAACCCAGCACATTAGGGCACG
*
47766618 TTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTG--AAATTT
63 TTTTCTCGAATTTCCAAACGCAAAATATTGCCTTATTTTGAAAAATTT
* *
47766664 TTTAAGGATATTTGGCTATTTGGTCGAACGAGAAATATCAAAACCCAACACATTAGGGCACGTTT
1 TTTAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCAAAACCCAGCACATTAGGGCACGTTT
*
47766729 TCTCGAATTTCCAAACGCAAAATATTGCCTTATTTAGAAAAATTT
66 TCTCGAATTTCCAAACGCAAAATATTGCCTTATTTTGAAAAATTT
47766774 T
1 T
47766775 CCTTTTTGAA
Statistics
Matches: 199, Mismatches: 18, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
108 90 0.45
109 2 0.01
110 7 0.04
111 9 0.05
112 3 0.02
113 84 0.42
114 3 0.02
115 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (110 bp):
TTTAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCAAAACCCAGCACATTAGGGCACGTTT
TCTCGAATTTCCAAACGCAAAATATTGCCTTATTTTGAAAAATTT
Found at i:47766871 original size:21 final size:20
Alignment explanation
Indices: 47766833--47766871 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
47766823 TAATATGAAT
* *
47766833 AAAAATAAAATGAGCAAAAA
1 AAAAATAAAAAGAACAAAAA
47766853 AAAAATGAAAAAGAACAAA
1 AAAAAT-AAAAAGAACAAA
47766872 TCAATCATGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.77, C:0.05, G:0.10, T:0.08
Consensus pattern (20 bp):
AAAAATAAAAAGAACAAAAA
Found at i:47767115 original size:38 final size:39
Alignment explanation
Indices: 47767046--47767120 Score: 91
Period size: 40 Copynumber: 1.9 Consensus size: 39
47767036 AGGAAATATT
*
47767046 TATGTATGTATATACATAAAATTATGAAAATATGAAAAAA
1 TATGTATATATATACATAAAATTATGAAAATAT-AAAAAA
* * *
47767086 TATGTATATATATA-TTAAAGTTAT-TAAATATAAAA
1 TATGTATATATATACATAAAATTATGAAAATATAAAA
47767121 GTTTATGTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
37 4 0.13
38 6 0.19
39 8 0.26
40 13 0.42
ACGTcount: A:0.53, C:0.01, G:0.08, T:0.37
Consensus pattern (39 bp):
TATGTATATATATACATAAAATTATGAAAATATAAAAAA
Found at i:47769646 original size:100 final size:100
Alignment explanation
Indices: 47769509--47769800 Score: 372
Period size: 100 Copynumber: 2.9 Consensus size: 100
47769499 TCTGCTTAAC
* * * * * * *
47769509 TGCAATGTCGGGGAGACAAGATTCACTGTCGTAGCTTCAATCTGTTCCACTACACCACCAGGGAA
1 TGCAATGTCAGGGAAACCAGATCCACCGTCGTAGCTTCAATCTATTCCACTACACCGCCAGGGAA
** *
47769574 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTT-ATT
66 ACAAGATTCGCCGTTGTGGCTTCAATCTTTTTGA-T
* * *
47769609 TGTAATGTCAGGGAAACCAGATCCACCGTCGTAGCTTCAATCTAAAT-AACTACACCGCCAGGGA
1 TGCAATGTCAGGGAAACCAGATCCACCGTCGTAGCTTCAATCT-ATTCCACTACACCGCCAGGGA
*
47769673 AACAAGATTCACCGTTGTGGCTTCAATCTTTTTGAT
65 AACAAGATTCGCCGTTGTGGCTTCAATCTTTTTGAT
* * * * *
47769709 TGCAATGTTAGGGAAACCAGATCCGCCGTCATGGCTTCAATCTATTCCAATACACCGCCAGGGAA
1 TGCAATGTCAGGGAAACCAGATCCACCGTCGTAGCTTCAATCTATTCCACTACACCGCCAGGGAA
*
47769774 ACAAGATTTGCCGTTGTGGCTTCAATC
66 ACAAGATTCGCCGTTGTGGCTTCAATC
47769801 CATTCCACTG
Statistics
Matches: 165, Mismatches: 24, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
99 2 0.01
100 161 0.98
101 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (100 bp):
TGCAATGTCAGGGAAACCAGATCCACCGTCGTAGCTTCAATCTATTCCACTACACCGCCAGGGAA
ACAAGATTCGCCGTTGTGGCTTCAATCTTTTTGAT
Found at i:47769772 original size:50 final size:50
Alignment explanation
Indices: 47769519--47769807 Score: 161
Period size: 50 Copynumber: 5.8 Consensus size: 50
47769509 TGCAATGTCG
* * * * * * *
47769519 GGGAGACAAGATTCACTGTCGTAGCTTCAATCTGTTCCACTACACCACCA
1 GGGAAACAAGATCCACCGTCGTGGCTTCAATCTATTCCAATACACCGCCA
** * * ** * ** ** *
47769569 GGGAAGTAAGATCCGCCGTTGTGGCTTCAATCT-TTTTATTTGTAATGTCA
1 GGGAAACAAGATCCACCGTCGTGGCTTCAATCTATTCCA-ATACACCGCCA
* * *
47769619 GGGAAACCAGATCCACCGTCGTAGCTTCAATCTAAAT--AACTACACCGCCA
1 GGGAAACAAGATCCACCGTCGTGGCTTCAATCT-ATTCCAA-TACACCGCCA
* * * ** * * ** **
47769669 GGGAAACAAGATTCACCGTTGTGGCTTCAATCTTTTTGATTGCAATGTTA
1 GGGAAACAAGATCCACCGTCGTGGCTTCAATCTATTCCAATACACCGCCA
* * *
47769719 GGGAAACCAGATCCGCCGTCATGGCTTCAATCTATTCCAATACACCGCCA
1 GGGAAACAAGATCCACCGTCGTGGCTTCAATCTATTCCAATACACCGCCA
*** * *
47769769 GGGAAACAAGATTTGCCGTTGTGGCTTCAATCCATTCCA
1 GGGAAACAAGATCCACCGTCGTGGCTTCAATCTATTCCA
47769808 CTGTAATGCC
Statistics
Matches: 171, Mismatches: 62, Indels: 12
0.70 0.25 0.05
Matches are distributed among these distances:
49 4 0.02
50 165 0.96
51 1 0.01
52 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (50 bp):
GGGAAACAAGATCCACCGTCGTGGCTTCAATCTATTCCAATACACCGCCA
Found at i:47771251 original size:6 final size:6
Alignment explanation
Indices: 47771228--47771269 Score: 57
Period size: 6 Copynumber: 6.7 Consensus size: 6
47771218 TGGCCTCTCA
*
47771228 TTTTCC TTTTCT TCTTTCT TTTTCTT TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT T-TTTCT TTTTC-T TTTTCT TTTTCT TTTT
47771270 TTTCCATCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
6 21 0.64
7 12 0.36
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTCT
Found at i:47771267 original size:13 final size:13
Alignment explanation
Indices: 47771228--47771270 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
47771218 TGGCCTCTCA
*
47771228 TTTTCCTTTTCTT
1 TTTTCTTTTTCTT
*
47771241 CTTTCTTTTTCTT
1 TTTTCTTTTTCTT
47771254 TTTTCTTTTTCTT
1 TTTTCTTTTTCTT
47771267 TTTT
1 TTTT
47771271 TTCCATCATC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTCTTTTTCTT
Found at i:47771270 original size:7 final size:7
Alignment explanation
Indices: 47771234--47771270 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
47771224 CTCATTTTCC
47771234 TTTTCTT
1 TTTTCTT
*
47771241 CTTTC-T
1 TTTTCTT
47771247 TTTTCTT
1 TTTTCTT
47771254 TTTTC-T
1 TTTTCTT
47771260 TTTTCTT
1 TTTTCTT
47771267 TTTT
1 TTTT
47771271 TTCCATCATC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
6 11 0.42
7 15 0.58
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTCTT
Found at i:47779185 original size:11 final size:11
Alignment explanation
Indices: 47779169--47779194 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
47779159 CTTCAATCAT
47779169 CATCCATCAAG
1 CATCCATCAAG
47779180 CATCCATCAAG
1 CATCCATCAAG
47779191 CATC
1 CATC
47779195 ATTCTCTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.38, G:0.08, T:0.19
Consensus pattern (11 bp):
CATCCATCAAG
Found at i:47783303 original size:30 final size:30
Alignment explanation
Indices: 47783257--47783345 Score: 116
Period size: 25 Copynumber: 3.1 Consensus size: 30
47783247 ATTTCTTATG
*
47783257 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
47783288 CCAATATTTGATACCCATATCTTTGAC-TT
1 CCAATATTTGATACCCATATCTTTGACTTT
*
47783317 ----TATTTGATACCCATATCTTTGAATTT
1 CCAATATTTGATACCCATATCTTTGACTTT
47783343 CCA
1 CCA
47783346 TAAATATGGA
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
25 22 0.42
26 2 0.04
29 2 0.04
30 19 0.37
31 7 0.13
ACGTcount: A:0.27, C:0.25, G:0.07, T:0.42
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Done.