Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A04
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: 82679320
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4050000 characters in sequence are not A, C, G, or T
File 160 of 255
Found at i:52363683 original size:19 final size:19
Alignment explanation
Indices: 52363661--52363697 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
52363651 ATGAGGGAAT
* *
52363661 TGAGAGATATTTGAGATTG
1 TGAGAGAGAGTTGAGATTG
52363680 TGAGAGAGAGTTGAGATT
1 TGAGAGAGAGTTGAGATT
52363698 AAATTAAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (19 bp):
TGAGAGAGAGTTGAGATTG
Found at i:52368286 original size:18 final size:18
Alignment explanation
Indices: 52368263--52368298 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
52368253 TTCTCGGGAG
52368263 ATAGTCGATTATCAACTC
1 ATAGTCGATTATCAACTC
**
52368281 ATAGTCTTTTATCAACTC
1 ATAGTCGATTATCAACTC
52368299 TAATCATCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (18 bp):
ATAGTCGATTATCAACTC
Found at i:52370334 original size:40 final size:40
Alignment explanation
Indices: 52370287--52370490 Score: 293
Period size: 40 Copynumber: 5.1 Consensus size: 40
52370277 CGGGCTTTAA
** *
52370287 CCGGATATAGCCACTCGCTCAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
**
52370327 CCGGATATAGTAGTTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
52370367 CCGGATATAGTAACTCACACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
52370407 CCGGATATAGTAACTTGCACAAATGCCTTCGAGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
52370447 CC-GAAATTAGTCACTAGCACAAATGCCTTCGGGACTTAGC
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGC
52370487 CCGG
1 CCGG
52370491 TTATCATCTG
Statistics
Matches: 147, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
39 3 0.02
40 143 0.97
41 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:52389196 original size:35 final size:35
Alignment explanation
Indices: 52389156--52389332 Score: 151
Period size: 35 Copynumber: 5.0 Consensus size: 35
52389146 GTGTGTACAT
52389156 ATGTGATGATATATTGAACTTGTATATTTGGCCAC
1 ATGTGATGATATATTGAACTTGTATATTTGGCCAC
* * * * *
52389191 ATGTGATGTTATATTAAACTTGAATATTTGACTAC
1 ATGTGATGATATATTGAACTTGTATATTTGGCCAC
* * * * * *
52389226 ATGTGATGTTTTATTGAGCTTGTATATCCT-GTCAT
1 ATGTGATGATATATTGAACTTGTATAT-TTGGCCAC
* * * *
52389261 ATATGATGATATATTGTACTTGTATAGTTGGCCAT
1 ATGTGATGATATATTGAACTTGTATATTTGGCCAC
* * *
52389296 ATCTGATGATATAATGAACCTTG-AGTATTCGGCCAC
1 ATGTGATGATATATTGAA-CTTGTA-TATTTGGCCAC
52389332 A
1 A
52389333 CAAGTAAGTA
Statistics
Matches: 110, Mismatches: 28, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
34 1 0.01
35 95 0.86
36 14 0.13
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.41
Consensus pattern (35 bp):
ATGTGATGATATATTGAACTTGTATATTTGGCCAC
Found at i:52394284 original size:46 final size:46
Alignment explanation
Indices: 52394223--52394356 Score: 162
Period size: 46 Copynumber: 2.9 Consensus size: 46
52394213 AGGATATTTG
* *
52394223 GGCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGA-ACGA
* *** * *
52394270 -GCGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGAACGA
*
52394316 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
52394357 GCGGGTTACA
Statistics
Matches: 71, Mismatches: 14, Indels: 5
0.79 0.16 0.06
Matches are distributed among these distances:
46 36 0.51
47 35 0.49
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.28
Consensus pattern (46 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGAACGA
Found at i:52397318 original size:15 final size:15
Alignment explanation
Indices: 52397279--52397358 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
52397269 ATATCTTGGG
*
52397279 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
52397294 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
* *
52397309 TTTCTTTATTCCGGG
1 TTTCTTTATTCTGGA
*
52397324 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
52397339 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
52397353 TTTCTT
1 TTTCTT
52397359 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
14 10 0.19
15 41 0.77
16 2 0.04
ACGTcount: A:0.10, C:0.19, G:0.14, T:0.57
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:52397348 original size:30 final size:30
Alignment explanation
Indices: 52397270--52397357 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
52397260 CATAGTATCA
* * *
52397270 TATCTTGGGTTTCTTTA-TCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCC-GGATTTCTC
*
52397300 TAT-TCTGGATTTCTTTATTCCGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCCGGATTTCTC
*
52397330 TATCTTGGATTTCTTTATT-CGGTTTTCT
1 TATCTTGGATTTCTTTATTCCGGATTTCT
52397358 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
29 9 0.18
30 37 0.74
31 4 0.08
ACGTcount: A:0.10, C:0.18, G:0.16, T:0.56
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCCGGATTTCTC
Found at i:52399085 original size:25 final size:25
Alignment explanation
Indices: 52399057--52399107 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
52399047 TTTTGGTATT
52399057 TTATGATAGAATATGAAGTTTTAAA
1 TTATGATAGAATATGAAGTTTTAAA
52399082 TTATGATAGAATATGAAGTTTTAAA
1 TTATGATAGAATATGAAGTTTTAAA
52399107 T
1 T
52399108 AATTATTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.00, G:0.16, T:0.41
Consensus pattern (25 bp):
TTATGATAGAATATGAAGTTTTAAA
Found at i:52401067 original size:47 final size:43
Alignment explanation
Indices: 52400985--52401117 Score: 131
Period size: 46 Copynumber: 2.9 Consensus size: 43
52400975 GTAACCCGCC
* * *
52400985 CATAAGTGAACTCGGACTCAACTCAATGAGCTCGGATGCCTAGTTA
1 CATAACTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A--TA
** * *
52401031 CATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATC
1 CATAACT-GAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CATA
*
52401078 CATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC
1 CATAACTGAACTCGGACTCAACTCAACGAGTTCGGATGCC
52401118 CAAATATCCT
Statistics
Matches: 72, Mismatches: 11, Indels: 11
0.77 0.12 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.04
46 32 0.44
47 31 0.43
49 4 0.06
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.23
Consensus pattern (43 bp):
CATAACTGAACTCGGACTCAACTCAACGAGTTCGGATGCCATA
Found at i:52401132 original size:46 final size:44
Alignment explanation
Indices: 52400989--52401132 Score: 107
Period size: 46 Copynumber: 3.1 Consensus size: 44
52400979 CCCGCCCATA
* * *
52400989 AGTGAACTCGGACTCAACTCAATGAGCTCGGATGCCTAGTTACATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA---A-ATC-CT
* * *
52401038 --CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGC--ATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCCCAAATCC-T
52401081 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCC-AA-ATCCT
52401128 AGTGA
1 AGTGA
52401133 CATGTCACTT
Statistics
Matches: 76, Mismatches: 9, Indels: 23
0.70 0.08 0.21
Matches are distributed among these distances:
42 1 0.01
43 4 0.05
44 4 0.05
46 33 0.43
47 27 0.36
48 4 0.05
49 3 0.04
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATCCT
Found at i:52403349 original size:40 final size:40
Alignment explanation
Indices: 52403305--52403495 Score: 176
Period size: 40 Copynumber: 4.8 Consensus size: 40
52403295 GGATATAGCT
* * *
52403305 ACTCGCTCGAATGCCTTCGGGACATAGCCTGGATATAGTA
1 ACTCGCACGAATGCCTTCGGGACATAGCCCGGATATAATA
* * * *
52403345 ACTCGCACCAATGCCTTCGGCACTTAGCCCGGACATAATA
1 ACTCGCACGAATGCCTTCGGGACATAGCCCGGATATAATA
*
52403385 ACTCAG-ACGAATGCCTTCGGGA-ATTAGCCCGGGTATAATA
1 ACTC-GCACGAATGCCTTCGGGACA-TAGCCCGGATATAATA
* * *
52403425 ACTCGCAC-AATTGCCTTCGGG-CTTAGCCCGGA-ATTAGTC
1 ACTCGCACGAA-TGCCTTCGGGACATAGCCCGGATA-TAATA
* * * *
52403464 ACTAGCACAAATGCCTTTGGGACTTAGCCCGG
1 ACTCGCACGAATGCCTTCGGGACATAGCCCGG
52403496 TTATCATCCG
Statistics
Matches: 125, Mismatches: 18, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
38 1 0.01
39 30 0.24
40 93 0.74
41 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
ACTCGCACGAATGCCTTCGGGACATAGCCCGGATATAATA
Found at i:52403427 original size:80 final size:79
Alignment explanation
Indices: 52403312--52403495 Score: 214
Period size: 79 Copynumber: 2.3 Consensus size: 79
52403302 GCTACTCGCT
* *
52403312 CGAATGCCTTCGGGACA-TAGCCTGGATATAGTAACTCGCACCAA-TGCCTTCGGCACTTAGCCC
1 CGAATGCCTTCGGGA-ATTAGCCCGGATATAATAACTCGCA-CAATTGCCTTCGG-ACTTAGCCC
52403375 GGACA-TAATAACTCAG-A
63 GGA-ATTAATAACT-AGCA
* *
52403392 CGAATGCCTTCGGGAATTAGCCCGGGTATAATAACTCGCACAATTGCCTTCGGGCTTAGCCCGGA
1 CGAATGCCTTCGGGAATTAGCCCGGATATAATAACTCGCACAATTGCCTTCGGACTTAGCCCGGA
* *
52403457 ATTAGTCACTAGCA
66 ATTAATAACTAGCA
* * *
52403471 CAAATGCCTTTGGGACTTAGCCCGG
1 CGAATGCCTTCGGGAATTAGCCCGG
52403496 TTATCATCCG
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
78 3 0.03
79 44 0.48
80 44 0.48
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (79 bp):
CGAATGCCTTCGGGAATTAGCCCGGATATAATAACTCGCACAATTGCCTTCGGACTTAGCCCGGA
ATTAATAACTAGCA
Found at i:52411456 original size:40 final size:40
Alignment explanation
Indices: 52411394--52411610 Score: 228
Period size: 40 Copynumber: 5.5 Consensus size: 40
52411384 AAGCCAAGTA
* * *
52411394 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACGAATG
* *
52411433 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACGAATG
* * * *
52411473 CCTTCGGCACTTAGCCCGGACATAATAACTCGCCCGAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACGAATG
* * * *
52411513 CCTTCAGGAATTAGCCCGGGTATAATAACTCGCAC-AATTG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACGAA-TG
* * *
52411553 CCTTCGGG-CTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACGAATG
52411592 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
52411611 TTATCATCCG
Statistics
Matches: 149, Mismatches: 23, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
38 1 0.01
39 43 0.29
40 105 0.70
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACGAATG
Found at i:52415771 original size:29 final size:30
Alignment explanation
Indices: 52415718--52415775 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
52415708 CAGAAGTTTT
52415718 GGCACTAAGTGTGCGATTTAAACTAGCTTG
1 GGCACTAAGTGTGCGATTTAAACTAGCTTG
52415748 GGCACTAAGTGTGCGATTT-AACTAGCTT
1 GGCACTAAGTGTGCGATTTAAACTAGCTT
52415776 CGGCTATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 9 0.32
30 19 0.68
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (30 bp):
GGCACTAAGTGTGCGATTTAAACTAGCTTG
Found at i:52418531 original size:39 final size:40
Alignment explanation
Indices: 52418458--52418627 Score: 189
Period size: 40 Copynumber: 4.3 Consensus size: 40
52418448 TCCTCGTTCA
* * * * * *
52418458 AATGCCTTCGGGACATAGCCCTGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
52418497 CATGCCTTCGGGACGTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
52418537 AATGCCTTCAGGACTTAACCCGGCTTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * *
52418577 AATGCCCTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
52418617 AAGGCCTTCGG
1 AATGCCTTCGG
52418628 ATCTTAGTCC
Statistics
Matches: 109, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
39 31 0.28
40 78 0.72
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:52418570 original size:79 final size:80
Alignment explanation
Indices: 52418458--52418604 Score: 197
Period size: 79 Copynumber: 1.9 Consensus size: 80
52418448 TCCTCGTTCA
* * * * * * *
52418458 AATGCCTTCGGGACATAGCCCTGTTTTAGTAACTCACAC-CATGCCTTCGGGACGTAACCCGGAT
1 AATGCCTTCAGGACATAACCCGGCTTTAATAACTCACACGAATGCCCTCGGGACGTAACCCGGAT
52418522 TTAACAACTCGCACG
66 TTAACAACTCGCACG
* * *
52418537 AATGCCTTCAGGACTTAACCCGGCTTTAATAACTCGCACGAATGCCCTCGGGACTTAACCCGGAT
1 AATGCCTTCAGGACATAACCCGGCTTTAATAACTCACACGAATGCCCTCGGGACGTAACCCGGAT
52418602 TTA
66 TTA
52418605 GTATCTCGCA
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
79 32 0.56
80 25 0.44
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (80 bp):
AATGCCTTCAGGACATAACCCGGCTTTAATAACTCACACGAATGCCCTCGGGACGTAACCCGGAT
TTAACAACTCGCACG
Found at i:52426954 original size:37 final size:38
Alignment explanation
Indices: 52426872--52426954 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 38
52426862 GCAGAGGATA
* * *
52426872 GCTCAACCCTTTGAAGCATCCCAATGGTGGGAAGATTT
1 GCTCAACCCTGTGAAGCATCCAAATGATGGGAAGATTT
*
52426910 GCTCAACCCTGTGGAGCAT-CAAGATGATGGG-AGATTT
1 GCTCAACCCTGTGAAGCATCCAA-ATGATGGGAAGATTT
52426947 GCTCAACC
1 GCTCAACC
52426955 TTTCGGAGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
37 16 0.40
38 24 0.60
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (38 bp):
GCTCAACCCTGTGAAGCATCCAAATGATGGGAAGATTT
Found at i:52428598 original size:19 final size:19
Alignment explanation
Indices: 52428570--52428606 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
52428560 AGTTGTGATA
*
52428570 TTAAAATTTATAATTCGAG
1 TTAAAATTTACAATTCGAG
*
52428589 TTAAATTTTACAATTCGA
1 TTAAAATTTACAATTCGA
52428607 ATAACTCGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (19 bp):
TTAAAATTTACAATTCGAG
Found at i:52429880 original size:32 final size:31
Alignment explanation
Indices: 52429811--52429880 Score: 76
Period size: 32 Copynumber: 2.3 Consensus size: 31
52429801 CTCCCTTTTC
52429811 TCTCTT-TTGCTACCGATTTCCCTTCGCCTA
1 TCTCTTGTTGCTACCGATTTCCCTTCGCCTA
*
52429841 T-TTTTGTTGCTACCGAAATTTCCCTT-GCCT-
1 TCTCTTGTTGCTACCG--ATTTCCCTTCGCCTA
52429871 TCCTCTTGTT
1 T-CTCTTGTT
52429881 TGTTTTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
29 3 0.09
30 11 0.33
31 4 0.12
32 15 0.45
ACGTcount: A:0.10, C:0.31, G:0.11, T:0.47
Consensus pattern (31 bp):
TCTCTTGTTGCTACCGATTTCCCTTCGCCTA
Found at i:52433031 original size:21 final size:21
Alignment explanation
Indices: 52433007--52433071 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 21
52432997 CACATAAGTG
52433007 CCCCTATTTGTACTTCGATAC
1 CCCCTATTTGTACTTCGATAC
* * * *
52433028 CCCCGAATTGCACATAC-ATA-
1 CCCCTATTTGTAC-TTCGATAC
* *
52433048 CCCCTATTTGTACTTTGGTAC
1 CCCCTATTTGTACTTCGATAC
52433069 CCC
1 CCC
52433072 TGAATAGCAC
Statistics
Matches: 31, Mismatches: 10, Indels: 6
0.66 0.21 0.13
Matches are distributed among these distances:
19 1 0.03
20 12 0.39
21 16 0.52
22 2 0.06
ACGTcount: A:0.22, C:0.35, G:0.11, T:0.32
Consensus pattern (21 bp):
CCCCTATTTGTACTTCGATAC
Found at i:52433040 original size:41 final size:41
Alignment explanation
Indices: 52432992--52433087 Score: 131
Period size: 41 Copynumber: 2.3 Consensus size: 41
52432982 TTATACCCTA
*
52432992 AATTGCACATA-AGTGCCCCTATTTGTACTTCGATACCCCCG
1 AATTGCACATACA-TACCCCTATTTGTACTTCGATACCCCCG
* * *
52433033 AATTGCACATACATACCCCTATTTGTACTTTGGTACCCCTG
1 AATTGCACATACATACCCCTATTTGTACTTCGATACCCCCG
*
52433074 AATAGCACATACAT
1 AATTGCACATACAT
52433088 GCACTATTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
41 48 0.98
42 1 0.02
ACGTcount: A:0.28, C:0.29, G:0.12, T:0.30
Consensus pattern (41 bp):
AATTGCACATACATACCCCTATTTGTACTTCGATACCCCCG
Found at i:52445462 original size:40 final size:40
Alignment explanation
Indices: 52445384--52445463 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
52445374 TGGATAGTAC
** *
52445384 TTGAGTAAGGGACGAGATGTATAAAGTATGTATGAATGAA
1 TTGAGTAAGGGACGAGATGTATAAAGTATACATAAATGAA
52445424 TTGAGTAAGGGACGAGATGTATAAAGTATACATAAATGAA
1 TTGAGTAAGGGACGAGATGTATAAAGTATACATAAATGAA
52445464 AGGAAGAGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.42, C:0.04, G:0.28, T:0.26
Consensus pattern (40 bp):
TTGAGTAAGGGACGAGATGTATAAAGTATACATAAATGAA
Found at i:52446459 original size:22 final size:21
Alignment explanation
Indices: 52446434--52446475 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 21
52446424 GCCTAAATGG
52446434 TCACACAGGCGTGTTGCCCCTC
1 TCACACAGGCGTG-TGCCCCTC
52446456 TCACACAGGCGTGTGCCCCT
1 TCACACAGGCGTGTGCCCCT
52446476 ATGTTAAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.14, C:0.40, G:0.24, T:0.21
Consensus pattern (21 bp):
TCACACAGGCGTGTGCCCCTC
Found at i:52447390 original size:20 final size:20
Alignment explanation
Indices: 52447367--52447414 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
52447357 TGATAAAAGT
52447367 TGCATTGGAAGAACAAAAAC
1 TGCATTGGAAGAACAAAAAC
52447387 TGCATTGGAAGAACAAAAAC
1 TGCATTGGAAGAACAAAAAC
52447407 TGCATTGG
1 TGCATTGG
52447415 TGATAAACGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.44, C:0.15, G:0.23, T:0.19
Consensus pattern (20 bp):
TGCATTGGAAGAACAAAAAC
Found at i:52448539 original size:31 final size:31
Alignment explanation
Indices: 52448504--52448563 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
52448494 AACAGCCTAT
52448504 TGACTTAAATAG-AAACGTTT-GAATAGTTTGG
1 TGACTT-AATAGAAAAC-TTTCGAATAGTTTGG
*
52448535 TGACTTAATTGAAAACTTTCGAATAGTTT
1 TGACTTAATAGAAAACTTTCGAATAGTTT
52448564 AATGATAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 7 0.27
31 19 0.73
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (31 bp):
TGACTTAATAGAAAACTTTCGAATAGTTTGG
Found at i:52453180 original size:41 final size:40
Alignment explanation
Indices: 52453053--52453197 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
52453043 CTCGCACAAG
* * * * *
52453053 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
52453093 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
52453133 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
52453174 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
52453198 CATTCGAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.64
41 27 0.29
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:52454426 original size:38 final size:38
Alignment explanation
Indices: 52454384--52454459 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
52454374 CAAGAACTCC
52454384 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
*
52454422 TTCCTCCTTCCTTAGAATTTTTGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
52454460 AAAGGATGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (38 bp):
TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
Found at i:52457049 original size:51 final size:51
Alignment explanation
Indices: 52456963--52457078 Score: 119
Period size: 51 Copynumber: 2.3 Consensus size: 51
52456953 CGGTGCCCTA
* * * * *
52456963 CACATAGTACCACCCTTGTAGTCAAAGCTACCTTTTTCACAAATTGGCCTT-
1 CACATAGTACCACACTTGTAGCCAAAGATACCTTTTACACAAAGTGG-CTTG
* * *
52457014 CACATAGTACCACACTTGT-GACCCAAGATATCTTTTACACATAGTGGCTTG
1 CACATAGTACCACACTTGTAG-CCAAAGATACCTTTTACACAAAGTGGCTTG
*
52457065 CACTTAGTACCACA
1 CACATAGTACCACA
52457079 TATGTGATCG
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
50 4 0.07
51 50 0.93
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.29
Consensus pattern (51 bp):
CACATAGTACCACACTTGTAGCCAAAGATACCTTTTACACAAAGTGGCTTG
Found at i:52457085 original size:51 final size:51
Alignment explanation
Indices: 52457018--52457130 Score: 129
Period size: 51 Copynumber: 2.2 Consensus size: 51
52457008 GGCCTTCACA
*** *
52457018 TAGTACCACACTTGTGACCCAAGATATCTTTTACACATAGTGGCTTGCACT
1 TAGTACCACACTTGTGACCCAAGATATCGGGTACACATAGTAGCTTGCACT
* * * *
52457069 TAGTACCACA-TATGTGATCGAAGCTATCGGGTACACATCGTAGCTTGCACT
1 TAGTACCACACT-TGTGACCCAAGATATCGGGTACACATAGTAGCTTGCACT
*
52457120 TAGTACTACAC
1 TAGTACCACAC
52457131 ATGCGACCTA
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
50 1 0.02
51 50 0.98
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (51 bp):
TAGTACCACACTTGTGACCCAAGATATCGGGTACACATAGTAGCTTGCACT
Found at i:52463854 original size:28 final size:24
Alignment explanation
Indices: 52463827--52463873 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
52463817 CTTAATAAGT
52463827 AAGTACGTAAATAATTATCAATAA
1 AAGTACGTAAATAATTATCAATAA
52463851 AAGTACGTAAATAATTATCAATA
1 AAGTACGTAAATAATTATCAATA
52463874 TATTAACAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.30
Consensus pattern (24 bp):
AAGTACGTAAATAATTATCAATAA
Found at i:52464715 original size:51 final size:50
Alignment explanation
Indices: 52464660--52464833 Score: 161
Period size: 50 Copynumber: 3.4 Consensus size: 50
52464650 ATAGTGGTTA
* * * * *
52464660 GCACTTAGTACCACACATGTGATCGAAGCTATCGGGTACGCATAGTAGCCT
1 GCACTTAGTACTACACATGTGACCGAA-CCATCGAGTACACATAGTAGCCT
* * * * *
52464711 GCACTTAGTATTACACATGCGACCTAACCATCTAGTACACGTAGTAGCCT
1 GCACTTAGTACTACACATGTGACCGAACCATCGAGTACACATAGTAGCCT
* ** *
52464761 ACACTTAGTACTACACATGTGACCGAAAACCATTTTA-AACACATAGTAGCCT
1 GCACTTAGTACTACACATGTGACCG--AACCA-TCGAGTACACATAGTAGCCT
* *
52464813 GCACATAGTACTACCCATGTG
1 GCACTTAGTACTACACATGTG
52464834 TTCTCACAAT
Statistics
Matches: 100, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
50 39 0.39
51 22 0.22
52 36 0.36
53 3 0.03
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (50 bp):
GCACTTAGTACTACACATGTGACCGAACCATCGAGTACACATAGTAGCCT
Found at i:52464822 original size:52 final size:50
Alignment explanation
Indices: 52464700--52464833 Score: 153
Period size: 52 Copynumber: 2.6 Consensus size: 50
52464690 ATCGGGTACG
* * * *
52464700 CATAGTAGCCTGCACTTAGTATTACACATGCGACCTAACCATCTAGTACA
1 CATAGTAGCCTGCACTTAGTACTACACATGTGACCAAACCATCTAGAACA
* * *
52464750 CGTAGTAGCCTACACTTAGTACTACACATGTGACCGAAAACCATTTTA-AACA
1 CATAGTAGCCTGCACTTAGTACTACACATGTGACC--AAACCA-TCTAGAACA
* *
52464802 CATAGTAGCCTGCACATAGTACTACCCATGTG
1 CATAGTAGCCTGCACTTAGTACTACACATGTG
52464834 TTCTCACAAT
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
50 31 0.44
52 36 0.51
53 3 0.04
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (50 bp):
CATAGTAGCCTGCACTTAGTACTACACATGTGACCAAACCATCTAGAACA
Found at i:52467748 original size:6 final size:6
Alignment explanation
Indices: 52467739--52467797 Score: 72
Period size: 6 Copynumber: 10.5 Consensus size: 6
52467729 TTGAAATTGA
* *
52467739 TATATG TATATA TATATG TATA-- TATATG TATATA TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
52467785 --TATG TATATG TAT
1 TATATG TATATG TAT
52467798 GTTTGAGTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 8 0.18
6 37 0.82
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:52467753 original size:10 final size:10
Alignment explanation
Indices: 52467747--52467797 Score: 70
Period size: 10 Copynumber: 5.3 Consensus size: 10
52467737 GATATATGTA
52467747 TATATATATG
1 TATATATATG
52467757 TATATATATG
1 TATATATATG
52467767 TATATATA--
1 TATATATATG
*
52467775 TATGTATATG
1 TATATATATG
*
52467785 TATGTATATG
1 TATATATATG
52467795 TAT
1 TAT
52467798 GTTTGAGTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
8 7 0.18
10 31 0.82
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (10 bp):
TATATATATG
Found at i:52467763 original size:22 final size:22
Alignment explanation
Indices: 52467738--52467793 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
52467728 ATTGAAATTG
52467738 ATATATGTATATATATATGTAT
1 ATATATGTATATATATATGTAT
52467760 ATATATGTATATATATATGTAT
1 ATATATGTATATATATATGTAT
*
52467782 ATGTATGTATAT
1 ATATATGTATAT
52467794 GTATGTTTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (22 bp):
ATATATGTATATATATATGTAT
Found at i:52469471 original size:25 final size:25
Alignment explanation
Indices: 52469443--52469625 Score: 123
Period size: 25 Copynumber: 7.3 Consensus size: 25
52469433 ATCTAGGAAA
*
52469443 CCTTTATGGCTAATCTTGTGAAAAG
1 CCTTTGTGGCTAATCTTGTGAAAAG
* *
52469468 CCTTTGTGACGTATTATCTAG-G--AAG
1 CCTTTGTGGC-TA--ATCTTGTGAAAAG
52469493 CCTTTGTGGCTAATCTTGTGAAAAG
1 CCTTTGTGGCTAATCTTGTGAAAAG
*
52469518 CCCTTGTTGTG-TATTATCTTG-G--AAG
1 CCTTTG-TG-GCTA--ATCTTGTGAAAAG
* *
52469543 CCATTGTGGCTAATCTTGT-AAGAAA
1 CCTTTGTGGCTAATCTTGTGAA-AAG
* **
52469568 CCTTTGTGGCGTATTCTT-TGGCAAG
1 CCTTTGTGGC-TAATCTTGTGAAAAG
* *
52469593 CCTTTGTGGCTAATGTTGTGGAAAG
1 CCTTTGTGGCTAATCTTGTGAAAAG
52469618 CCTTTGTG
1 CCTTTGTG
52469626 CCATATTATT
Statistics
Matches: 124, Mismatches: 16, Indels: 36
0.70 0.09 0.20
Matches are distributed among these distances:
22 11 0.09
23 2 0.02
24 11 0.09
25 74 0.60
26 12 0.10
27 3 0.02
28 11 0.09
ACGTcount: A:0.21, C:0.16, G:0.25, T:0.38
Consensus pattern (25 bp):
CCTTTGTGGCTAATCTTGTGAAAAG
Found at i:52469490 original size:50 final size:50
Alignment explanation
Indices: 52469432--52469706 Score: 252
Period size: 50 Copynumber: 5.5 Consensus size: 50
52469422 AACATGACAC
* *
52469432 TATCTAGGAAACCTTTATGGCTAATCTTGTGAAAAGCCTTTGTGACGTAT
1 TATCTAGGAAACCTTTGTGGCTAATCTTGTGAAAAGCCTTTGTGGCGTAT
* * * *
52469482 TATCTAGGAAGCCTTTGTGGCTAATCTTGTGAAAAGCCCTTGTTGTGTAT
1 TATCTAGGAAACCTTTGTGGCTAATCTTGTGAAAAGCCTTTGTGGCGTAT
* * * *
52469532 TATCTTGGAAGCCATTGTGGCTAATCTTGT-AAGAAACCTTTGTGGCGTAT
1 TATCTAGGAAACCTTTGTGGCTAATCTTGTGAA-AAGCCTTTGTGGCGTAT
* * * * * * *
52469582 TCT-TTGGCAAGCCTTTGTGGCTAATGTTGTGGAAAGCCTTTGTGCCATAT
1 TATCTAGG-AAACCTTTGTGGCTAATCTTGTGAAAAGCCTTTGTGGCGTAT
* * * * * * **
52469632 TAT-T-TGACAATTCTTTGTGACTTATCTTATGAAAAGCCCTTGTGGTATAT
1 TATCTAGGA-AA-CCTTTGTGGCTAATCTTGTGAAAAGCCTTTGTGGCGTAT
*
52469682 TATCTAGGAAACCTTTGTGTCTAAT
1 TATCTAGGAAACCTTTGTGGCTAAT
52469707 TTTTTAAGAA
Statistics
Matches: 183, Mismatches: 35, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
48 1 0.01
49 8 0.04
50 168 0.92
51 4 0.02
52 2 0.01
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (50 bp):
TATCTAGGAAACCTTTGTGGCTAATCTTGTGAAAAGCCTTTGTGGCGTAT
Found at i:52471343 original size:18 final size:18
Alignment explanation
Indices: 52471306--52471345 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
52471296 TTGGAAATCA
*
52471306 AAATTATTAAAAGATGAT
1 AAATTATTAAAAGATAAT
52471324 AAATTATTAAATAGA-AAT
1 AAATTATTAAA-AGATAAT
52471342 AAAT
1 AAAT
52471346 ATCATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (18 bp):
AAATTATTAAAAGATAAT
Found at i:52473171 original size:18 final size:18
Alignment explanation
Indices: 52473148--52473183 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
52473138 ACCTCAAAAT
52473148 AGAATGAATGGTAAGTTA
1 AGAATGAATGGTAAGTTA
52473166 AGAATGAATGGTAAGTTA
1 AGAATGAATGGTAAGTTA
52473184 CGTACCATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.28, T:0.28
Consensus pattern (18 bp):
AGAATGAATGGTAAGTTA
Found at i:52479421 original size:28 final size:28
Alignment explanation
Indices: 52479381--52479444 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
52479371 TGTACTAAAG
*
52479381 TACCCCTATGTATGCAAAATTACCAT-TA
1 TACCCCTATGTATGCAAAATGACC-TCTA
*
52479409 TACCCCTCTGTATGCAAAATGACCTCTA
1 TACCCCTATGTATGCAAAATGACCTCTA
52479437 TACCCCTA
1 TACCCCTA
52479445 GGGGTAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
27 1 0.03
28 31 0.97
ACGTcount: A:0.31, C:0.31, G:0.08, T:0.30
Consensus pattern (28 bp):
TACCCCTATGTATGCAAAATGACCTCTA
Found at i:52479611 original size:27 final size:28
Alignment explanation
Indices: 52479550--52479639 Score: 94
Period size: 27 Copynumber: 3.2 Consensus size: 28
52479540 AGGAAGCGTC
* *
52479550 CTGGTGGCTA-TGCCACACATTATCTGTT
1 CTGGTGGC-ACTGCCACAAAATATCTGTT
* * **
52479578 CTAGTGGCCCTGCCAC-GTATATCTGTT
1 CTGGTGGCACTGCCACAAAATATCTGTT
52479605 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAAATATCTGT-T
52479634 CTGGTG
1 CTGGTG
52479640 ACTCTGTCAC
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
27 22 0.44
28 21 0.42
29 7 0.14
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.32
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAAATATCTGTT
Found at i:52479650 original size:29 final size:28
Alignment explanation
Indices: 52479560--52479650 Score: 76
Period size: 27 Copynumber: 3.2 Consensus size: 28
52479550 CTGGTGGCTA
* * * * *
52479560 TGCCACACATTATCTGTTCTAGTGGCCC
1 TGCCACAAAATATCTGTTCTGGTGACAC
** *
52479588 TGCCAC-GTATATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
52479615 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
52479644 TGTCACA
1 TGCCACA
52479651 TTTTCTGTAT
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
27 22 0.43
28 14 0.27
29 15 0.29
ACGTcount: A:0.21, C:0.27, G:0.20, T:0.32
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:52480127 original size:19 final size:19
Alignment explanation
Indices: 52480103--52480141 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
52480093 TTTTAATTAT
* *
52480103 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
52480122 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
52480141 T
1 T
52480142 ATGATGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:52480565 original size:38 final size:38
Alignment explanation
Indices: 52480514--52480589 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
52480504 CTAAGTAATA
*
52480514 CGGAATGTTTTGTACGCATCAATGTGGCGCACCGGATC
1 CGGAATGTTTTGTACGCATCAATGTGGCACACCGGATC
*
52480552 CGGAATGTTTTGTACGCATCAATGTGGCATACCGGATC
1 CGGAATGTTTTGTACGCATCAATGTGGCACACCGGATC
52480590 TGGTCGTAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (38 bp):
CGGAATGTTTTGTACGCATCAATGTGGCACACCGGATC
Found at i:52487352 original size:28 final size:28
Alignment explanation
Indices: 52487294--52487357 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
52487284 TGTACTAGAG
* *
52487294 TACCCCTATGTATGCAAAATTACCATTA
1 TACCCCTATGTATGCAAAATGACCATCA
*
52487322 TACCCCTCTGTATGCAAAATGACC-TCCA
1 TACCCCTATGTATGCAAAATGACCAT-CA
52487350 TACCCCTA
1 TACCCCTA
52487358 GGGTTAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 1 0.03
28 30 0.97
ACGTcount: A:0.31, C:0.33, G:0.08, T:0.28
Consensus pattern (28 bp):
TACCCCTATGTATGCAAAATGACCATCA
Found at i:52487506 original size:28 final size:27
Alignment explanation
Indices: 52487473--52487544 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
52487463 CTGGTGGCTA
*
52487473 TGCCACAAATTATCTGTTCTAGTGGCCC
1 TGCCACAAA-TATCTGTTCTAGTGGCAC
** * *
52487501 TGCCACGTATATTTGTTCTGGTGGCAC
1 TGCCACAAATATCTGTTCTAGTGGCAC
52487528 TGCCACAAAATATCTGT
1 TGCCAC-AAATATCTGT
52487545 ATCTGGTGAC
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
27 21 0.60
28 14 0.40
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.33
Consensus pattern (27 bp):
TGCCACAAATATCTGTTCTAGTGGCAC
Found at i:52487563 original size:29 final size:28
Alignment explanation
Indices: 52487473--52487563 Score: 76
Period size: 27 Copynumber: 3.2 Consensus size: 28
52487463 CTGGTGGCTA
* * * *
52487473 TGCCACAAATTATCTGTTCTAGTGGCCC
1 TGCCACAAAATATCTGTTCTGGTGACAC
** * *
52487501 TGCCAC-GTATATTTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
52487528 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
52487557 TGTCACA
1 TGCCACA
52487564 TTTTCTGTAT
Statistics
Matches: 49, Mismatches: 12, Indels: 3
0.77 0.19 0.05
Matches are distributed among these distances:
27 21 0.43
28 13 0.27
29 15 0.31
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:52490988 original size:47 final size:48
Alignment explanation
Indices: 52490642--52490997 Score: 172
Period size: 47 Copynumber: 7.8 Consensus size: 48
52490632 CACATTATGG
* * * **
52490642 GAGCCAGTGTAAGATCATGTCTAGGACATGGCATCGGTA-T-GAGACGA-
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATC-G-ACTCGATTCGAT
* * *
52490689 GAGCTAGTGTAAGA-CATGTCTGGGATAT-G-ATCGCCTCGCAAT-G-T
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACTCG-ATTCGAT
* **
52490733 AAGCTAGTG-AAGA-CATGTC-GGGACAT-GCATC-AGCT--ATGAGAT
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGA-CTCGATTCGAT
* * * *
52490775 GTG-TAGTGTAAGACCATGTCTGGGACATGGCATCGACAC-ATATAGAG
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACTCGAT-TCGAT
* * * * * *
52490822 GTG-TCAGTGT-ATA-CATG--TGGGACATCGC-TCGGCACGGATATGTGA-
1 GAGCT-AGTGTAAGACCATGTCTGGGACATGGCATCGACTC-GAT-T-CGAT
* *
52490867 GAGCT-GTGTAAGACCATGTCTGGGACATGGCGTCGGCCTCGATTTCGAT
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATC-GACTCGA-TTCGAT
* * *
52490916 -AGTTAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGA-TGGAT
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACTCGATTCGAT
* *
52490962 GAGCTAGTGTAAGACCATGTTTGGGACATGACATCG
1 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCG
52490998 GCATCATACT
Statistics
Matches: 245, Mismatches: 34, Indels: 60
0.72 0.10 0.18
Matches are distributed among these distances:
40 1 0.00
41 6 0.02
42 13 0.05
43 29 0.12
44 34 0.14
45 16 0.07
46 30 0.12
47 54 0.22
48 25 0.10
49 33 0.13
50 4 0.02
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (48 bp):
GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACTCGATTCGAT
Found at i:52501659 original size:1 final size:1
Alignment explanation
Indices: 52501653--52501706 Score: 108
Period size: 1 Copynumber: 54.0 Consensus size: 1
52501643 TTTGAAAATA
52501653 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
52501707 AAAATAGGAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:52501882 original size:17 final size:18
Alignment explanation
Indices: 52501850--52501884 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
52501840 AACAAATACC
52501850 AAAATTAAATTAAAAAGT
1 AAAATTAAATTAAAAAGT
*
52501868 AAAATTTAA-TAAAAAGT
1 AAAATTAAATTAAAAAGT
52501885 CCATGCAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.29
Consensus pattern (18 bp):
AAAATTAAATTAAAAAGT
Found at i:52505626 original size:39 final size:39
Alignment explanation
Indices: 52505572--52505840 Score: 486
Period size: 39 Copynumber: 6.9 Consensus size: 39
52505562 TAATGGAGAA
52505572 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
52505611 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
*
52505650 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTA
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
52505689 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
*
52505728 TTATATTCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
52505767 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* *
52505806 TTATATCCGGGCTAAAGTCCCGCAGGC-TTTGTGCT
1 TTATATCCGGGCT-AAGTCCCGAAGGCATTCGTGCT
52505841 AGTATTATGT
Statistics
Matches: 223, Mismatches: 6, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
39 211 0.95
40 12 0.05
ACGTcount: A:0.18, C:0.23, G:0.30, T:0.29
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
Found at i:52510272 original size:46 final size:46
Alignment explanation
Indices: 52510222--52510397 Score: 201
Period size: 46 Copynumber: 3.8 Consensus size: 46
52510212 TGTTTGGGCA
*
52510222 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
*** * * ** *
52510268 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGC-AAACG
* *
52510315 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
52510361 CCCGAGCTCGTTGAGTTGAGTCCAAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
52510398 GCGAGTTACA
Statistics
Matches: 106, Mismatches: 21, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
46 71 0.67
47 35 0.33
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:52510377 original size:93 final size:93
Alignment explanation
Indices: 52510218--52510389 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
52510208 AGGATGTTTG
* *
52510218 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAG
*
52510283 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCAAGTTCGAGAGATGTAACTA
* * *
52510311 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAG
52510376 TTGAGTCCAAGTTC
66 TTGAGTCCAAGTTC
52510390 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAG
TTGAGTCCAAGTTCGAGAGATGTAACTA
Found at i:52513398 original size:14 final size:15
Alignment explanation
Indices: 52513349--52513398 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
52513339 GTATCTCGGG
52513349 TTTCTTTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
52513364 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
52513379 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
52513393 TTTCTT
1 TTTCTT
52513399 GTTATCTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
14 8 0.26
15 21 0.68
16 2 0.06
ACGTcount: A:0.10, C:0.16, G:0.12, T:0.62
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:52515846 original size:46 final size:48
Alignment explanation
Indices: 52515795--52515925 Score: 148
Period size: 46 Copynumber: 2.8 Consensus size: 48
52515785 ATGTTTGGGC
*
52515795 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA-ATG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACAGG
* * *
52515842 -TCCGAACTCGTTGAGTTGAGTTCGAGTT--C-GA-GAGATGTAACTAGG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCAAC-AGG
*
52515887 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 -ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
52515926 GCGGGTTACA
Statistics
Matches: 68, Mismatches: 7, Indels: 15
0.76 0.08 0.17
Matches are distributed among these distances:
42 1 0.01
43 7 0.10
44 1 0.01
45 2 0.03
46 27 0.40
47 26 0.38
49 1 0.01
50 2 0.03
51 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (48 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACAGG
Found at i:52518403 original size:17 final size:17
Alignment explanation
Indices: 52518381--52518417 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
52518371 CTTAGGCGGA
52518381 TTCCAACCCAGAACAGC
1 TTCCAACCCAGAACAGC
52518398 TTCCAACCCAGAACAGC
1 TTCCAACCCAGAACAGC
52518415 TTC
1 TTC
52518418 AATTTTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.41, G:0.11, T:0.16
Consensus pattern (17 bp):
TTCCAACCCAGAACAGC
Found at i:52522220 original size:262 final size:258
Alignment explanation
Indices: 52521755--52522275 Score: 873
Period size: 262 Copynumber: 2.0 Consensus size: 258
52521745 TGCATAGAAA
* * *
52521755 ATAGAAGGGTGAGTTTGTGAAAACTCAGTGTGTAATCCCTTAACAACAATCAGTCATATAGTAGG
1 ATAGAAGGGTGAGTTTGCGAAAACTCAATGTGTAATCCCTTAACAACAATCAGTCATACAGTAGG
* *
52521820 CATTTATAGTCTAGGCCTAAGCCCGCTTCAGTATCAGTTTAATTTCAGTTAGGGCCTTAGCCCAT
66 CATTTATAGTCTAGGCCTAAGCCCACTTCAGTAACAGTTTAATTTCAGTTAGGGCCTTAGCCCAT
* *
52521885 TACAGTAGCAGACACAGTACATATATGTAATCGAAAATCCTACCCAAGCAGCCTCTACACACAAC
131 TACAGTAGCAGACACAGTACATATATGTAATCAAAAATCCTACCCAACCAGCCTCTACACACAAC
52521950 TCTGTCCAGCCCTACACACCATGTGGGGATAAAATCAACCCA-CCTATCCCTACACACTAGAAAT
196 TCTGTCCAGCCCT--ACA-CA-GTGGGGATAAAATCAACCCATCC-ATCCCTACACACTAGAAAT
52522014 AGC
256 AGC
*
52522017 ATAGAAGGGTGAGTTTGCGAAAACTCAATGTGTAATCCTTTAACAACAATCAGTCATACAGTAGG
1 ATAGAAGGGTGAGTTTGCGAAAACTCAATGTGTAATCCCTTAACAACAATCAGTCATACAGTAGG
* * *
52522082 CATTTATAGTCTAGGCCTAAGCCTACTTCAGTAACAGTTTAATTTTAGTTAGGGCCTTAGCTCAT
66 CATTTATAGTCTAGGCCTAAGCCCACTTCAGTAACAGTTTAATTTCAGTTAGGGCCTTAGCCCAT
* *
52522147 TACAGTAGCAGATAGAGTACATATATGTAATCAAAAATCCTACCCAACCAGCCTCTACACACAAC
131 TACAGTAGCAGACACAGTACATATATGTAATCAAAAATCCTACCCAACCAGCCTCTACACACAAC
52522212 TCTGTCCAGCCCTACACAGTGGGGATAAAATCAACCCATCCATCCCTACACACTAGAAATAGC
196 TCTGTCCAGCCCTACACAGTGGGGATAAAATCAACCCATCCATCCCTACACACTAGAAATAGC
52522275 A
1 A
52522276 CCGGTTGTGG
Statistics
Matches: 245, Mismatches: 13, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
258 43 0.18
259 4 0.02
260 3 0.01
262 195 0.80
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (258 bp):
ATAGAAGGGTGAGTTTGCGAAAACTCAATGTGTAATCCCTTAACAACAATCAGTCATACAGTAGG
CATTTATAGTCTAGGCCTAAGCCCACTTCAGTAACAGTTTAATTTCAGTTAGGGCCTTAGCCCAT
TACAGTAGCAGACACAGTACATATATGTAATCAAAAATCCTACCCAACCAGCCTCTACACACAAC
TCTGTCCAGCCCTACACAGTGGGGATAAAATCAACCCATCCATCCCTACACACTAGAAATAGC
Found at i:52524476 original size:38 final size:38
Alignment explanation
Indices: 52524382--52524476 Score: 104
Period size: 39 Copynumber: 2.5 Consensus size: 38
52524372 AAGTTGTTTT
*
52524382 TAATA-TTTTAATAAAATAAACGTTCTTTTAAATTAGC
1 TAATATTTTTAATAAAATAAACGTTATTTTAAATTAGC
* * * * *
52524419 CAATATTTTTTATTAAAATAAATGTTATTTTGAA-TACGG
1 TAATA-TTTTTAATAAAATAAACGTTATTTTAAATTA-GC
52524458 TAATATTTTTAATAAAATA
1 TAATATTTTTAATAAAATA
52524477 TAAATAATGC
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
37 4 0.09
38 15 0.32
39 28 0.60
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.45
Consensus pattern (38 bp):
TAATATTTTTAATAAAATAAACGTTATTTTAAATTAGC
Found at i:52527738 original size:125 final size:123
Alignment explanation
Indices: 52527515--52527750 Score: 364
Period size: 125 Copynumber: 1.9 Consensus size: 123
52527505 GTAACTATTA
* **
52527515 TAGCAAAAGAGCGTCCATGTGGGAGTTTTTTCCATAATTTTGCTGACAATGCATCCTCCTTGAAG
1 TAGCAAAAGAGCGTCCACGTAAGAGTTTTTTCCATAATTTTGCTGACAATGCATCCTCCTTGAAG
* *
52527580 CGTTTTGGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTAGATACTACTG
66 CGTTTTGGACACTATTTATTCAGAAACACCTTCTCAAAATTATTTTTAGATACTACTG
* * *
52527638 TAGCAAAAGAGCGTCCACGTAAGAGTTTTTTTTCCGTAATTTTGCTGTCAATGCATCCTGCTTGA
1 TAGCAAAAGAGCGTCCACGTAAGAG--TTTTTTCCATAATTTTGCTGACAATGCATCCTCCTTGA
* *
52527703 AGCGTTTTTGACACTATTTATTCAGAAACGCCTTCTCAAAATTATTTT
64 AGCGTTTTGGACACTATTTATTCAGAAACACCTTCTCAAAATTATTTT
52527751 CTCTAATACT
Statistics
Matches: 101, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
123 22 0.22
125 79 0.78
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (123 bp):
TAGCAAAAGAGCGTCCACGTAAGAGTTTTTTCCATAATTTTGCTGACAATGCATCCTCCTTGAAG
CGTTTTGGACACTATTTATTCAGAAACACCTTCTCAAAATTATTTTTAGATACTACTG
Found at i:52527793 original size:125 final size:124
Alignment explanation
Indices: 52527540--52527777 Score: 309
Period size: 125 Copynumber: 1.9 Consensus size: 124
52527530 CATGTGGGAG
*
52527540 TTTTTTCCATAATTTTGCTGACAATGCATCCTCCTTGAAGCGTTTTGGACACTATTTGTTCAGAA
1 TTTTTTCCATAATTTTGCTGACAATGCATCCTCCTTGAAGCGTTTTGGACACTATTTATTCAGAA
* * *** *
52527605 ACATCTTCTCAAAATTATTTTTAGATACTACTGTAGCAAAAGAGCGTCCACGTAAGAGTT
66 ACACCTTCTCAAAATTATTTTTAGATACTACTGCAGCAAAAGAAAATCCAC-TAAGAATT
* * * *
52527665 TTTTTTCCGTAATTTTGCTGTCAATGCATCCTGCTTGAAGCGTTTTTGACACTATTTATTCAGAA
1 TTTTTTCCATAATTTTGCTGACAATGCATCCTCCTTGAAGCGTTTTGGACACTATTTATTCAGAA
* *
52527730 ACGCCTTCTCAAAATTATTTTCTCTA-ATACTACTGCAGTAAAA-AAAAT
66 ACACCTTCTCAAAATTA-TTT-T-TAGATACTACTGCAGCAAAAGAAAAT
52527778 TTATATATAA
Statistics
Matches: 98, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
125 75 0.77
126 5 0.05
127 16 0.16
128 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38
Consensus pattern (124 bp):
TTTTTTCCATAATTTTGCTGACAATGCATCCTCCTTGAAGCGTTTTGGACACTATTTATTCAGAA
ACACCTTCTCAAAATTATTTTTAGATACTACTGCAGCAAAAGAAAATCCACTAAGAATT
Found at i:52527952 original size:64 final size:63
Alignment explanation
Indices: 52527775--52527953 Score: 225
Period size: 64 Copynumber: 2.8 Consensus size: 63
52527765 CAGTAAAAAA
** **
52527775 AATTTATATATAATTTTTTAAAATTAATAGTTAATTTAATTAATTAACATTAATTACCCAAACCC
1 AATTTA-AT-TAA-TTTTTAAAATTAATAGTTAATTTAATTAATTAACCCTAAAAACCCAAACCC
52527840 T
63 T
* * * *
52527841 AATTTAATTAATTCTTTTAAATTAATAATTAATTTAATTAATAAACCCTAAAAATCCTAAACCCT
1 AATTTAATTAATT-TTTAAAATTAATAGTTAATTTAATTAATTAACCCTAAAAA-CCCAAACCCT
52527906 AATTTAATT-ATTTTTAAAAATTAATAGTTAATTTAATTAATTAACCCT
1 AATTTAATTAATTTTT-AAAATTAATAGTTAATTTAATTAATTAACCCT
52527954 CAACCCTAAT
Statistics
Matches: 99, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
63 5 0.05
64 68 0.69
65 20 0.20
66 6 0.06
ACGTcount: A:0.45, C:0.11, G:0.01, T:0.44
Consensus pattern (63 bp):
AATTTAATTAATTTTTAAAATTAATAGTTAATTTAATTAATTAACCCTAAAAACCCAAACCCT
Found at i:52528010 original size:16 final size:15
Alignment explanation
Indices: 52527989--52528029 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
52527979 CTTAAAAATA
52527989 TTAAAACCCTAAACTC
1 TTAAAACCCTAAAC-C
52528005 TTAAAACCCTAAACC
1 TTAAAACCCTAAACC
52528020 -T-AAACCCTAA
1 TTAAAACCCTAA
52528030 TCCTAAACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.36
14 1 0.04
15 1 0.04
16 14 0.56
ACGTcount: A:0.46, C:0.32, G:0.00, T:0.22
Consensus pattern (15 bp):
TTAAAACCCTAAACC
Found at i:52528026 original size:13 final size:13
Alignment explanation
Indices: 52527992--52528038 Score: 58
Period size: 13 Copynumber: 3.4 Consensus size: 13
52527982 AAAAATATTA
52527992 AAACCCTAAACTCTT
1 AAACCCTAAAC-C-T
52528007 AAAACCCTAAACCT
1 -AAACCCTAAACCT
*
52528021 AAACCCTAATCCT
1 AAACCCTAAACCT
52528034 AAACC
1 AAACC
52528039 AATCAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 17 0.57
14 1 0.03
15 1 0.03
16 11 0.37
ACGTcount: A:0.45, C:0.36, G:0.00, T:0.19
Consensus pattern (13 bp):
AAACCCTAAACCT
Found at i:52531200 original size:48 final size:47
Alignment explanation
Indices: 52531129--52531289 Score: 161
Period size: 44 Copynumber: 3.5 Consensus size: 47
52531119 AGCTAACGCT
* *
52531129 ATGTCCCAGACAGGTCTTACACTAGCTTGTATATCCCGAGGCCGATGC
1 ATGTCCCAGACATGTCTTACACTAGCTTG-ATATCACGAGGCCGATGC
* * *
52531177 ATGTCCCAGACATGTTTTACACTAGCTTG-TCTCA--ATGCCGATGC
1 ATGTCCCAGACATGTCTTACACTAGCTTGATATCACGAGGCCGATGC
* * * * * *
52531221 ATGTCCCAGGCATGTCTAACAATGGCTCTCATA--ACGTGGCCGATGC
1 ATGTCCCAGACATGTCTTACACTAGCT-TGATATCACGAGGCCGATGC
*
52531267 ATGTCCCAGACATGTATTACACT
1 ATGTCCCAGACATGTCTTACACT
52531290 GGCTCACATA
Statistics
Matches: 91, Mismatches: 18, Indels: 10
0.76 0.15 0.08
Matches are distributed among these distances:
44 32 0.35
45 1 0.01
46 31 0.34
48 27 0.30
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.27
Consensus pattern (47 bp):
ATGTCCCAGACATGTCTTACACTAGCTTGATATCACGAGGCCGATGC
Found at i:52538859 original size:49 final size:48
Alignment explanation
Indices: 52538798--52538961 Score: 144
Period size: 49 Copynumber: 3.5 Consensus size: 48
52538788 GTTGATGCCC
52538798 TGTCCCAAACAGGTCTTACACTGACTTTCATATATCAAGGCTAATTCCA
1 TGTCCCAAACAGGTCTTACACTGAC-TTCATATATCAAGGCTAATTCCA
* * * * *
52538847 TGTCCCAGACAGGTCTTACAATGTCTCTCATGTATC-AGTG-TCGATGT-CA
1 TGTCCCAAACAGGTCTTACACTGACT-TCATATATCAAG-GCT-AAT-TCCA
* * *
52538896 TGTCCCAAACAGGTCTTACACTGAC-ACACA-A-CAA-GCTAATGCCA
1 TGTCCCAAACAGGTCTTACACTGACTTCATATATCAAGGCTAATTCCA
* *
52538940 TGTCCCAGACAGGTTTTACACT
1 TGTCCCAAACAGGTCTTACACT
52538962 AGCTTGTATA
Statistics
Matches: 93, Mismatches: 15, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
44 25 0.27
45 2 0.02
46 2 0.02
47 2 0.02
48 4 0.04
49 57 0.61
50 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (48 bp):
TGTCCCAAACAGGTCTTACACTGACTTCATATATCAAGGCTAATTCCA
Found at i:52540842 original size:36 final size:36
Alignment explanation
Indices: 52540793--52540865 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
52540783 TCAGAGTCTA
52540793 TATATATACACCTGATGATCTCTAACTGATTAGACC
1 TATATATACACCTGATGATCTCTAACTGATTAGACC
*
52540829 TATATATATACCTGATGATCTCTAACTGATTAGACC
1 TATATATACACCTGATGATCTCTAACTGATTAGACC
52540865 T
1 T
52540866 CTGATATGTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.36
Consensus pattern (36 bp):
TATATATACACCTGATGATCTCTAACTGATTAGACC
Found at i:52552973 original size:25 final size:25
Alignment explanation
Indices: 52552944--52552994 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
52552934 TTTATGGTAG
52552944 AAAATGAAAGTTTATTCATAGATAA
1 AAAATGAAAGTTTATTCATAGATAA
52552969 AAAATGAAAGTTTATTCATAGATAA
1 AAAATGAAAGTTTATTCATAGATAA
52552994 A
1 A
52552995 TAACTTTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.53, C:0.04, G:0.12, T:0.31
Consensus pattern (25 bp):
AAAATGAAAGTTTATTCATAGATAA
Found at i:52556381 original size:54 final size:54
Alignment explanation
Indices: 52556309--52556597 Score: 346
Period size: 54 Copynumber: 5.4 Consensus size: 54
52556299 TACTAAAATG
* * *** * *
52556309 CCCTCAATTTGTAAAATTACCAAAGTACCCTCGATTTACAGAATTACCATTTTA
1 CCCTCGATTTATAAAATTACCATTTTACCCTCGATTTATAGAATTACCGTTTTA
* * *
52556363 CCCTCGATTGATAGAATTACCATTTTACCCTCGATTTATAAAATTACCGTTTTA
1 CCCTCGATTTATAAAATTACCATTTTACCCTCGATTTATAGAATTACCGTTTTA
** ***
52556417 CCCTTTATTTATAAAATTACCATTTTACCCTCGATTTATAGAATTATTATTTTA
1 CCCTCGATTTATAAAATTACCATTTTACCCTCGATTTATAGAATTACCGTTTTA
* *
52556471 CCCTCGATTTATAGAATTACCATTTTACCCTCGATTTATAGAATTATCGTTTTA
1 CCCTCGATTTATAAAATTACCATTTTACCCTCGATTTATAGAATTACCGTTTTA
* * * ** *
52556525 CCCTCGATTTACAAAATTATC-GTTTACCCTTAATTTACAGAATTACCGTTTTA
1 CCCTCGATTTATAAAATTACCATTTTACCCTCGATTTATAGAATTACCGTTTTA
**
52556578 CCCTCGATTTCCAAAATTAC
1 CCCTCGATTTATAAAATTAC
52556598 TAAAATACCA
Statistics
Matches: 202, Mismatches: 33, Indels: 1
0.86 0.14 0.00
Matches are distributed among these distances:
53 45 0.22
54 157 0.78
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (54 bp):
CCCTCGATTTATAAAATTACCATTTTACCCTCGATTTATAGAATTACCGTTTTA
Found at i:52556597 original size:27 final size:27
Alignment explanation
Indices: 52556334--52556587 Score: 330
Period size: 27 Copynumber: 9.4 Consensus size: 27
52556324 ATTACCAAAG
*
52556334 TACCCTCGATTTACAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCATTT
*
52556361 TACCCTCGATTGATAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCATTT
* *
52556388 TACCCTCGATTTATAAAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCATTT
** *
52556415 TACCCTTTATTTATAAAATTACCATTT
1 TACCCTCGATTTATAGAATTACCATTT
**
52556442 TACCCTCGATTTATAGAATTATTATTT
1 TACCCTCGATTTATAGAATTACCATTT
52556469 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCATTT
* *
52556496 TACCCTCGATTTATAGAATTATCGTTT
1 TACCCTCGATTTATAGAATTACCATTT
* * * *
52556523 TACCCTCGATTTACAAAATTATC-GTT
1 TACCCTCGATTTATAGAATTACCATTT
** * *
52556549 TACCCTTAATTTACAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCATTT
52556576 TACCCTCGATTT
1 TACCCTCGATTT
52556588 CCAAAATTAC
Statistics
Matches: 199, Mismatches: 27, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
26 21 0.11
27 178 0.89
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.42
Consensus pattern (27 bp):
TACCCTCGATTTATAGAATTACCATTT
Found at i:52556606 original size:27 final size:27
Alignment explanation
Indices: 52556289--52556689 Score: 142
Period size: 27 Copynumber: 14.9 Consensus size: 27
52556279 AATACTTTAG
* * * *
52556289 TTTACCAAATTACTAAAATGCCCTCAA
1 TTTACAAAATTACCAAAATACCCTCGA
** *
52556316 TTTGTAAAATTACCAAAGTACCCTCGA
1 TTTACAAAATTACCAAAATACCCTCGA
* ***
52556343 TTTACAGAATTACCATTTTACCCTCGA
1 TTTACAAAATTACCAAAATACCCTCGA
* * * ***
52556370 TTGATAGAATTACCATTTTACCCTCGA
1 TTTACAAAATTACCAAAATACCCTCGA
* **** **
52556397 TTTATAAAATTACCGTTTTACCCTTTA
1 TTTACAAAATTACCAAAATACCCTCGA
* ***
52556424 TTTATAAAATTACCATTTTACCCTCGA
1 TTTACAAAATTACCAAAATACCCTCGA
* * ** ***
52556451 TTTATAGAATTATTATTTTACCCTCGA
1 TTTACAAAATTACCAAAATACCCTCGA
* * ***
52556478 TTTATAGAATTACCATTTTACCCTCGA
1 TTTACAAAATTACCAAAATACCCTCGA
* * * ****
52556505 TTTATAGAATTATCGTTTTACCCTCGA
1 TTTACAAAATTACCAAAATACCCTCGA
* *** **
52556532 TTTACAAAATTATC-GTTTACCCTTAA
1 TTTACAAAATTACCAAAATACCCTCGA
* ****
52556558 TTTACAGAATTACCGTTTTACCCTCGA
1 TTTACAAAATTACCAAAATACCCTCGA
* * * * *
52556585 TTTCCAAAATTACTAAAATACCATTGG
1 TTTACAAAATTACCAAAATACCCTCGA
52556612 TTTACAAAATTACCAAAATACCCTCGA
1 TTTACAAAATTACCAAAATACCCTCGA
* ** *
52556639 -TCAGTTAAATTACCAAAATACCCT-TA
1 TTTA-CAAAATTACCAAAATACCCTCGA
**
52556665 GTTTGTAAAATTACCAAAATACCCT
1 -TTTACAAAATTACCAAAATACCCT
52556690 TTGCTAGTTA
Statistics
Matches: 308, Mismatches: 62, Indels: 8
0.81 0.16 0.02
Matches are distributed among these distances:
26 24 0.08
27 283 0.92
28 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (27 bp):
TTTACAAAATTACCAAAATACCCTCGA
Found at i:52557915 original size:42 final size:42
Alignment explanation
Indices: 52557809--52557922 Score: 113
Period size: 42 Copynumber: 2.7 Consensus size: 42
52557799 AGTACTGTAT
* ** ** * *
52557809 CAATGCCATATCCCGGATATGGAATTATATGAAATATTATAT
1 CAATGCCATATCCCAGATATGGTCTTATACAAAATATCATAC
* * * *
52557851 CAACGCCATCTCCCTGACATGGTCTTATACAAAATCA-CATAC
1 CAATGCCATATCCCAGATATGGTCTTATACAAAAT-ATCATAC
52557893 CAATGCCATATCCCAGATATGGTCTTATAC
1 CAATGCCATATCCCAGATATGGTCTTATAC
52557923 GGAATCTCGG
Statistics
Matches: 57, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
42 56 0.98
43 1 0.02
ACGTcount: A:0.34, C:0.25, G:0.12, T:0.29
Consensus pattern (42 bp):
CAATGCCATATCCCAGATATGGTCTTATACAAAATATCATAC
Found at i:52561464 original size:36 final size:37
Alignment explanation
Indices: 52561424--52561507 Score: 109
Period size: 37 Copynumber: 2.3 Consensus size: 37
52561414 CAAAATCCAA
52561424 CTATGGTCTTAC-TCAT-ATCACAATGCCATAGCCCAG
1 CTATGGTCTTACAT-ATCATCACAATGCCATAGCCCAG
* * * *
52561460 CTATGGTCTTACATGTCGTCACGATGTCATAGCCCAG
1 CTATGGTCTTACATATCATCACAATGCCATAGCCCAG
52561497 CTATGGTCTTA
1 CTATGGTCTTA
52561508 GACGAAGTCT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 13 0.31
37 29 0.69
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (37 bp):
CTATGGTCTTACATATCATCACAATGCCATAGCCCAG
Found at i:52561571 original size:42 final size:42
Alignment explanation
Indices: 52561481--52561614 Score: 108
Period size: 42 Copynumber: 3.2 Consensus size: 42
52561471 CATGTCGTCA
* * * * * * *
52561481 CGATGTCATAGCCCAG-CTATGGTCTTAGACGAAGTCTCATAT
1 CGATGCCATATCCCAGAC-ATGGTCTTACACAAAATCACATAC
* * * *
52561523 CAATGCCATGTCCTAGACATGGTCTTACACAAAATCACATGC
1 CGATGCCATATCCCAGACATGGTCTTACACAAAATCACATAC
* * * * *
52561565 CGATGCCATATCCCAGATATGGTCTTATACGAGATCACATAT
1 CGATGCCATATCCCAGACATGGTCTTACACAAAATCACATAC
52561607 CGATGCCA
1 CGATGCCA
52561615 ATGCCATGTC
Statistics
Matches: 71, Mismatches: 20, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
42 70 0.99
43 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (42 bp):
CGATGCCATATCCCAGACATGGTCTTACACAAAATCACATAC
Found at i:52561619 original size:48 final size:48
Alignment explanation
Indices: 52561561--52561748 Score: 261
Period size: 48 Copynumber: 3.9 Consensus size: 48
52561551 ACAAAATCAC
* * * *
52561561 ATGCCGATGCCATATCCCAGATATGGTCTTATACGAGATCACATATCG
1 ATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCACATATCG
* * *
52561609 ATGCCAATGCCATGTCCCAAACATGGTCTTACATGGGATCACATATTC-
1 ATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCACATA-TCG
* * *
52561657 ATGCCAATGCCATATCCTAGATATGGTCTCACATGGGATCACATATTG
1 ATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCACATATCG
*
52561705 ATGCCAATGCCATATCCTAGATATGGTCTTACATGGGATCACAT
1 ATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCACAT
52561749 CTATTGCCAT
Statistics
Matches: 124, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
47 1 0.01
48 121 0.98
49 2 0.02
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.28
Consensus pattern (48 bp):
ATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCACATATCG
Found at i:52561651 original size:90 final size:90
Alignment explanation
Indices: 52561523--52561748 Score: 263
Period size: 96 Copynumber: 2.4 Consensus size: 90
52561513 AGTCTCATAT
**** *
52561523 CAATGCCATGTCCTAGACATGGTCTTACACAAAATCACATGCCGATGCCATATCCCAGATATGGT
1 CAATGCCATGTCCTAGACATGGTCTTACATGGGATCACATGCCAATGCCATATCCCAGATATGGT
* *
52561588 CTTATACGAGATCACATATCGATGC
66 CTCACACGAGATCACATATCGATGC
* * *
52561613 CAATGCCATGTCCCAAACATGGTCTTACATGGGATCACATATTCATGCCAATGCCATATCCTAGA
1 CAATGCCATGTCCTAGACATGGTCTTACATGGGAT--C--A--CATGCCAATGCCATATCCCAGA
* * *
52561678 TATGGTCTCACATGGGATCACATATTGATGC
60 TATGGTCTCACACGAGATCACATATCGATGC
* *
52561709 CAATGCCATATCCTAGATATGGTCTTACATGGGATCACAT
1 CAATGCCATGTCCTAGACATGGTCTTACATGGGATCACAT
52561749 CTATTGCCAT
Statistics
Matches: 113, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
90 32 0.28
92 2 0.02
94 2 0.02
96 77 0.68
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.27
Consensus pattern (90 bp):
CAATGCCATGTCCTAGACATGGTCTTACATGGGATCACATGCCAATGCCATATCCCAGATATGGT
CTCACACGAGATCACATATCGATGC
Found at i:52569975 original size:13 final size:13
Alignment explanation
Indices: 52569957--52569990 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
52569947 TAATTTGGGG
52569957 ACATAACTCTAAT
1 ACATAACTCTAAT
52569970 ACATAACTCTAAT
1 ACATAACTCTAAT
*
52569983 ATATAACT
1 ACATAACT
52569991 TTGGCACATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (13 bp):
ACATAACTCTAAT
Found at i:52570521 original size:18 final size:17
Alignment explanation
Indices: 52570498--52570536 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
52570488 TAAAACATTT
*
52570498 TAAAATAATTTAATTTAA
1 TAAAATAA-TAAATTTAA
*
52570516 TAAAATCATAAATTTAA
1 TAAAATAATAAATTTAA
52570533 TAAA
1 TAAA
52570537 TTTTAATTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAATAATAAATTTAA
Found at i:52570818 original size:21 final size:21
Alignment explanation
Indices: 52570783--52570823 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
52570773 TATTATAATT
* *
52570783 TTTAATTTTATTGCTACAATG
1 TTTAATTTCACTGCTACAATG
*
52570804 TTTAATTTCACTGCTGCAAT
1 TTTAATTTCACTGCTACAAT
52570824 AATTAATCTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.49
Consensus pattern (21 bp):
TTTAATTTCACTGCTACAATG
Found at i:52572954 original size:46 final size:46
Alignment explanation
Indices: 52572810--52573112 Score: 217
Period size: 46 Copynumber: 6.5 Consensus size: 46
52572800 TTTGGGCGCT
* * *
52572810 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGA-GATGAGAGCC
* * * **
52572856 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGAAGAGAGAT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGAGAGCC
* *
52572904 AGTGTAAGAAATGTTTGGGACATGCATCGGCCTCGAGATGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATG-AGAGCC
* *
52572950 AGTGTAAGACATGTCTGGGACATGCATCGG-CTACGAGAT--GTGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGAGAGCC
* * * * *
52572994 AGTGTAAGGCCATGTTTGGGACATGGCATCGACAT--A-AAGAGAGCC
1 AGTGTAA-GACATGTCTGGGACAT-GCATCGGCCTCGAGATGAGAGCC
* * ** * ** * *
52573039 AGTGTAAGGCCATGTCTAGGACATGGTGTTGGCCTCGATTTCGACAGTC
1 AGTGTAA-GACATGTCTGGGACAT-GCATCGGCCTCGAGAT-GAGAGCC
52573088 AGTGTAAGACCATGTCTGGGACATG
1 AGTGTAAGA-CATGTCTGGGACATG
52573113 GGATCGACTT
Statistics
Matches: 204, Mismatches: 37, Indels: 30
0.75 0.14 0.11
Matches are distributed among these distances:
43 1 0.00
44 10 0.05
45 47 0.23
46 65 0.32
47 29 0.14
48 26 0.13
49 26 0.13
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGAGAGCC
Found at i:52573091 original size:138 final size:140
Alignment explanation
Indices: 52572810--52573163 Score: 341
Period size: 138 Copynumber: 2.5 Consensus size: 140
52572800 TTTGGGCGCT
*
52572810 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCTAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATGATGAGAGCTAGTGTAAGACCATGTCTGG
* * * *
52572875 GACATGGCATCGGCATTGAGAAGAGAGATAGTGTAAGAAATGTTTGGGACATGCATCGGCCTCGA
66 GACATGGCATCGACATTGAGAAGAGAGACAGTGTAAGAAATGTCTAGGACATGCATCGGCCTCGA
52572940 GATGTAAGCC
131 GATGTAAGCC
* * * * *
52572950 AGTGTAAGACATGTCTGGGACATGCATCGGCTACGA-GATGTG-TC-AGTGTAAGGCCATGTTTG
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATGATGAGAGCTAGTGTAAGACCATGTCTG
* ** ** *
52573012 GGACATGGCATCGACA-T-A-AAGAGAGCCAGTGTAAGGCCATGTCTAGGACATGGTGTTGGCCT
65 GGACATGGCATCGACATTGAGAAGAGAGACAGTGTAA-GAAATGTCTAGGACAT-GCATCGGCCT
** *
52573074 CGATTTCG-ACAGTC
128 CGAGAT-GTA-AGCC
* * * * *
52573088 AGTGTAAGACCATGTCTGGGACATGGGATC-G--ACTTGATGGACGAGCCAGTGTAGGACCTTGT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACATGAT-GA-GAGCTAGTGTAAGACCATGT
52573150 CTGGGACATGGCAT
62 CTGGGACATGGCAT
52573164 TGGCATTACA
Statistics
Matches: 175, Mismatches: 27, Indels: 23
0.78 0.12 0.10
Matches are distributed among these distances:
135 14 0.08
136 13 0.07
137 18 0.10
138 45 0.26
139 17 0.10
140 42 0.24
141 26 0.15
ACGTcount: A:0.27, C:0.18, G:0.32, T:0.24
Consensus pattern (140 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCACATGATGAGAGCTAGTGTAAGACCATGTCTGG
GACATGGCATCGACATTGAGAAGAGAGACAGTGTAAGAAATGTCTAGGACATGCATCGGCCTCGA
GATGTAAGCC
Found at i:52580325 original size:40 final size:40
Alignment explanation
Indices: 52580281--52580504 Score: 239
Period size: 40 Copynumber: 5.7 Consensus size: 40
52580271 GCTCCTCGTT
* *
52580281 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAATTCGCA
* * *
52580321 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAATTCGCA
52580361 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGT-ATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAAT-TCGCA
*
52580400 CAAATGCCTTCGGG-CTTAGCCC-GAAATTAGT-ATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAAT-TCGCA
* * * * *
52580439 CAAATGCCTTC-GGATCTTGGTCCGGATATTGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGT-AATTCGCA
52580480 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
52580505 CATCATTCAA
Statistics
Matches: 159, Mismatches: 16, Indels: 18
0.82 0.08 0.09
Matches are distributed among these distances:
38 5 0.03
39 66 0.42
40 73 0.46
41 14 0.09
42 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAATTCGCA
Found at i:52580383 original size:79 final size:78
Alignment explanation
Indices: 52580281--52580504 Score: 256
Period size: 79 Copynumber: 2.8 Consensus size: 78
52580271 GCTCCTCGTT
* *
52580281 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
52580346 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
* *
52580361 CAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCCGA
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAAT-TCGCACAAATGCCTTCGGGACTTAGCCCGG
*
52580424 AATTAGTATCTCGCA
64 AATTAGTAACTCGCA
* * * * * *
52580439 CAAATGCCTTCGGATCTTGGTCCGGATATTGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGT-AATTCGCACAAATGCCTTCGGGACTTAGCCCG
52580503 GA
63 GA
52580505 CATCATTCAA
Statistics
Matches: 123, Mismatches: 14, Indels: 14
0.81 0.09 0.09
Matches are distributed among these distances:
78 37 0.30
79 52 0.42
80 33 0.27
81 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:52580398 original size:39 final size:40
Alignment explanation
Indices: 52580281--52580504 Score: 257
Period size: 39 Copynumber: 5.7 Consensus size: 40
52580271 GCTCCTCGTT
* *
52580281 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
52580321 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
52580361 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
*
52580400 CAAATGCCTTCGGG-CTTAGCCCGAAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* * *
52580439 CAAATGCCTTC-GGATCTTGGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
52580480 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
52580505 CATCATTCAA
Statistics
Matches: 163, Mismatches: 13, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
38 2 0.01
39 72 0.44
40 72 0.44
41 17 0.10
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:52597657 original size:23 final size:22
Alignment explanation
Indices: 52597605--52597657 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
52597595 TCCACGTCTT
*
52597605 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
52597627 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
52597650 TTTCTTTT
1 TTTCTTTT
52597658 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:52600818 original size:20 final size:20
Alignment explanation
Indices: 52600795--52600848 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
52600785 AGTTTTTCCC
*
52600795 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
52600815 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
52600835 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
52600849 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:52600830 original size:30 final size:31
Alignment explanation
Indices: 52600795--52600868 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 31
52600785 AGTTTTTCCC
52600795 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCGATTTGAGCTCA-ATTGAGCTTAATTT
* *
52600825 AGCTCG-TTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTTGAGCTCAATTGAGCTTAATTT
52600855 AGCTC-ATTTGAGCT
1 AGCTCGATTTGAGCT
52600869 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
29 4 0.10
30 35 0.90
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (31 bp):
AGCTCGATTTGAGCTCAATTGAGCTTAATTT
Found at i:52600858 original size:20 final size:20
Alignment explanation
Indices: 52600795--52600869 Score: 57
Period size: 20 Copynumber: 3.8 Consensus size: 20
52600785 AGTTTTTCCC
* * * *
52600795 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
52600815 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
52600834 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
52600855 AGCTC-ATTTGAGCTT
1 AGCTCAATTT-AGCTT
52600870 GGCTTAAGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
18 1 0.02
19 5 0.11
20 33 0.75
21 4 0.09
22 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:52602391 original size:10 final size:11
Alignment explanation
Indices: 52602369--52602404 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
52602359 AAAAGAGAAG
52602369 AAATTCAAAAA
1 AAATTCAAAAA
52602380 AAATTCAAAAA
1 AAATTCAAAAA
52602391 AAA-TCGAAAAA
1 AAATTC-AAAAA
52602402 AAA
1 AAA
52602405 GAAAAAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 2 0.08
11 22 0.92
ACGTcount: A:0.75, C:0.08, G:0.03, T:0.14
Consensus pattern (11 bp):
AAATTCAAAAA
Found at i:52603459 original size:12 final size:12
Alignment explanation
Indices: 52603428--52603564 Score: 52
Period size: 12 Copynumber: 11.4 Consensus size: 12
52603418 CCATTGAGCG
* *
52603428 AGAAATGGAGAA
1 AGAAATAGAAAA
* *
52603440 AGAGATTGAAAA
1 AGAAATAGAAAA
*
52603452 AGAAATTG--AA
1 AGAAATAGAAAA
*
52603462 AGAAA-ACAAAA
1 AGAAATAGAAAA
52603473 AGAAA-ACGAAAA
1 AGAAATA-GAAAA
* *
52603485 AGAAAAAGAAAT
1 AGAAATAGAAAA
*
52603497 TGCAAA-AGAAAA
1 AG-AAATAGAAAA
*
52603509 AGAAATCGAAAA
1 AGAAATAGAAAA
** *
52603521 AGTGAGAGAAAA
1 AGAAATAGAAAA
52603533 AGAAA-ATGAAGAAA
1 AGAAATA-G-A-AAA
*
52603547 AGAAAATTGAAAA
1 AG-AAATAGAAAA
52603560 AGAAA
1 AGAAA
52603565 AAGCGAAAAA
Statistics
Matches: 95, Mismatches: 19, Indels: 22
0.70 0.14 0.16
Matches are distributed among these distances:
10 7 0.07
11 12 0.13
12 56 0.59
13 10 0.11
14 6 0.06
15 4 0.04
ACGTcount: A:0.68, C:0.03, G:0.20, T:0.09
Consensus pattern (12 bp):
AGAAATAGAAAA
Found at i:52603490 original size:18 final size:18
Alignment explanation
Indices: 52603464--52603567 Score: 82
Period size: 18 Copynumber: 5.6 Consensus size: 18
52603454 AAATTGAAAG
*
52603464 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
52603482 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
*
52603500 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAAACGA
** * *
52603518 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAACGA
* *
52603536 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-CGA
52603557 AAAAGAAAAAG
1 AAAAGAAAAAG
52603568 CGAAAAAAGA
Statistics
Matches: 66, Mismatches: 17, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
18 47 0.71
19 5 0.08
20 8 0.12
21 6 0.09
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:52603492 original size:6 final size:6
Alignment explanation
Indices: 52603460--52603567 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
52603450 AAAGAAATTG
* * ** *
52603460 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
52603507 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
52603558 AAAGAA AAAG
1 AAAGAA AAAG
52603568 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 24, Indels: 7
0.71 0.23 0.07
Matches are distributed among these distances:
5 3 0.04
6 61 0.81
7 7 0.09
8 4 0.05
ACGTcount: A:0.71, C:0.04, G:0.19, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:52603549 original size:14 final size:13
Alignment explanation
Indices: 52603528--52603565 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
52603518 AAAAGTGAGA
52603528 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
52603540 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
52603555 GAAAAAGAAAA
1 GAAAAAGAAAA
52603566 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:52603579 original size:21 final size:21
Alignment explanation
Indices: 52603529--52603579 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
52603519 AAAGTGAGAG
*
52603529 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
52603550 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
52603571 AAAAAGAAA
1 AAAAAGAAA
52603580 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:52612801 original size:23 final size:22
Alignment explanation
Indices: 52612749--52612801 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
52612739 TCCACGTCTT
*
52612749 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
52612771 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
52612794 TTTCTTTT
1 TTTCTTTT
52612802 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:52616498 original size:27 final size:27
Alignment explanation
Indices: 52616447--52616498 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
52616437 TCATCTTAGT
* *
52616447 TTTAATTAATAAGTGTTTTTGTTAAAC
1 TTTAATTAATAAGTGTTGTTCTTAAAC
*
52616474 TTTATTTAATAAGTGTTGTTCTTAA
1 TTTAATTAATAAGTGTTGTTCTTAA
52616499 TTGATCTAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.31, C:0.04, G:0.12, T:0.54
Consensus pattern (27 bp):
TTTAATTAATAAGTGTTGTTCTTAAAC
Found at i:52617136 original size:20 final size:20
Alignment explanation
Indices: 52617113--52617158 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
52617103 CCAGCTCGAA
*
52617113 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
52617133 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
52617153 TTAGCT
1 TTAGCT
52617159 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:52617140 original size:30 final size:30
Alignment explanation
Indices: 52617105--52617178 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
52617095 AGTTTTTCCC
52617105 AGCTCGAATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-ATTGAGCTCA-ATTGAGCTTAATTT
* * *
52617135 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTGAGCTCAATTGAGCTTAATTT
*
52617165 AGCTCGTTTGAGCT
1 AGCTCGATTGAGCT
52617179 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 36 0.92
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGATTGAGCTCAATTGAGCTTAATTT
Found at i:52618779 original size:11 final size:10
Alignment explanation
Indices: 52618762--52618792 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
52618752 ATAGGAGTAA
52618762 CAAAAAAAAT
1 CAAAAAAAAT
52618772 CAAAAAAAAT
1 CAAAAAAAAT
52618782 CGAAAAAAAAT
1 C-AAAAAAAAT
52618793 TTGATTGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.55
11 9 0.45
ACGTcount: A:0.77, C:0.10, G:0.03, T:0.10
Consensus pattern (10 bp):
CAAAAAAAAT
Found at i:52618788 original size:12 final size:12
Alignment explanation
Indices: 52618763--52618845 Score: 50
Period size: 12 Copynumber: 6.7 Consensus size: 12
52618753 TAGGAGTAAC
52618763 AAAAAAAATC--
1 AAAAAAAATCGA
52618773 AAAAAAAATCGA
1 AAAAAAAATCGA
*
52618785 AAAAAAATTTGATTGA
1 AAAAAAA----ATCGA
52618801 AAAAAAAATTC-A
1 AAAAAAAA-TCGA
52618813 AAAAAAAAGT-G-
1 AAAAAAAA-TCGA
52618824 AAAAAAAATCGA
1 AAAAAAAATCGA
52618836 GCAAAAAAAA
1 --AAAAAAAA
52618846 AAGAAAATAA
Statistics
Matches: 58, Mismatches: 3, Indels: 20
0.72 0.04 0.25
Matches are distributed among these distances:
10 11 0.19
11 9 0.16
12 18 0.31
13 1 0.02
14 8 0.14
16 11 0.19
ACGTcount: A:0.72, C:0.06, G:0.08, T:0.13
Consensus pattern (12 bp):
AAAAAAAATCGA
Found at i:52619940 original size:39 final size:38
Alignment explanation
Indices: 52619897--52620037 Score: 124
Period size: 42 Copynumber: 3.5 Consensus size: 38
52619887 GAAAGAGATT
*
52619897 GAAAAAGAAATTGAAAGAAAACAAAAAGAAAACGAAGAA
1 GAAAAAGAAATTGAAAGAAAA-AAAAAGAAAAAGAAGAA
*
52619936 GAAAAAGAAATTGCAAAAGAAAAAAAAATCGAAAAAG-TGAGA
1 GAAAAAGAAATTG--AAAGAAAAAAAAA--GAAAAAGAAGA-A
* * *
52619978 GAAAAAGAAAATG-AAGAAAAGAAAATTGAAAAAGAAAAA
1 GAAAAAGAAATTGAAAGAAAA-AAAA-AGAAAAAGAAGAA
52620017 GCGAAAAAAGAAATTGAAAGA
1 --G-AAAAAGAAATTGAAAGA
52620038 GAGCTTGAAA
Statistics
Matches: 83, Mismatches: 7, Indels: 20
0.75 0.06 0.18
Matches are distributed among these distances:
39 28 0.34
40 10 0.12
41 11 0.13
42 30 0.36
43 4 0.05
ACGTcount: A:0.70, C:0.04, G:0.19, T:0.08
Consensus pattern (38 bp):
GAAAAAGAAATTGAAAGAAAAAAAAAGAAAAAGAAGAA
Found at i:52619943 original size:6 final size:6
Alignment explanation
Indices: 52619910--52620017 Score: 58
Period size: 6 Copynumber: 17.7 Consensus size: 6
52619900 AAAGAAATTG
* * * ** *
52619910 AAAG-A AAACAA AAAGAA AACGAA GAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* ** * * *
52619957 AAA-AA AATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AA-AGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
52620008 AAAGAA AAAG
1 AAAGAA AAAG
52620018 CGAAAAAAGA
Statistics
Matches: 73, Mismatches: 24, Indels: 11
0.68 0.22 0.10
Matches are distributed among these distances:
5 7 0.10
6 51 0.70
7 11 0.15
8 4 0.05
ACGTcount: A:0.71, C:0.04, G:0.19, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:52619999 original size:14 final size:13
Alignment explanation
Indices: 52619978--52620015 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
52619968 AAAAGTGAGA
52619978 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
52619990 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
52620005 GAAAAAGAAAA
1 GAAAAAGAAAA
52620016 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:52620012 original size:13 final size:12
Alignment explanation
Indices: 52619877--52620015 Score: 65
Period size: 12 Copynumber: 11.6 Consensus size: 12
52619867 TCCATTGAGC
* *
52619877 AAGAAAAGGAGA
1 AAGAAAATGAAA
* *
52619889 AAGAGATTGAAA
1 AAGAAAATGAAA
*
52619901 AAGAAATTG--A
1 AAGAAAATGAAA
*
52619911 AAGAAAA-CAAA
1 AAGAAAATGAAA
* *
52619922 AAGAAAACGAAG
1 AAGAAAATGAAA
*
52619934 AAGAAAAAGAAA
1 AAGAAAATGAAA
**
52619946 TTGCAAAA-GAAA
1 AAG-AAAATGAAA
52619958 AA-AAAATCGAAA
1 AAGAAAAT-GAAA
* *
52619970 AAGTGAGA-GAAA
1 AAG-AAAATGAAA
52619982 AAGAAAATGAAGAA
1 AAGAAAATG-A-AA
52619996 AAGAAAATTGAAA
1 AAGAAAA-TGAAA
52620009 AAGAAAA
1 AAGAAAA
52620016 AGCGAAAAAA
Statistics
Matches: 96, Mismatches: 19, Indels: 23
0.70 0.14 0.17
Matches are distributed among these distances:
10 11 0.11
11 10 0.10
12 47 0.49
13 14 0.15
14 12 0.12
15 2 0.02
ACGTcount: A:0.69, C:0.03, G:0.20, T:0.08
Consensus pattern (12 bp):
AAGAAAATGAAA
Found at i:52620029 original size:21 final size:21
Alignment explanation
Indices: 52619979--52620029 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
52619969 AAAGTGAGAG
*
52619979 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
52620000 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
52620021 AAAAAGAAA
1 AAAAAGAAA
52620030 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:52620069 original size:33 final size:33
Alignment explanation
Indices: 52620032--52620094 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
52620022 AAAAGAAATT
52620032 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
52620065 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
52620095 GGGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:52621414 original size:22 final size:22
Alignment explanation
Indices: 52621384--52621430 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
52621374 TTTGGTATTT
52621384 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
52621406 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
52621428 GGG
1 GGG
52621431 TTCAAAAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.32, C:0.04, G:0.40, T:0.23
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:52622619 original size:4 final size:4
Alignment explanation
Indices: 52622610--52622636 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
52622600 AAGTTTTATT
52622610 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
52622637 TACTTAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:52632468 original size:11 final size:11
Alignment explanation
Indices: 52632452--52632506 Score: 51
Period size: 10 Copynumber: 5.0 Consensus size: 11
52632442 AGACCGTATA
52632452 CAATTTTTTTT
1 CAATTTTTTTT
*
52632463 CAATTTCTTTT
1 CAATTTTTTTT
**
52632474 CTTTGATTTTTTT
1 CAAT--TTTTTTT
52632487 CAA-TTTTTTT
1 CAATTTTTTTT
52632497 -AATTTTTTTT
1 CAATTTTTTTT
52632507 TCACGAATCT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
9 2 0.06
10 14 0.40
11 12 0.34
13 7 0.20
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.73
Consensus pattern (11 bp):
CAATTTTTTTT
Found at i:52632507 original size:24 final size:24
Alignment explanation
Indices: 52632455--52632507 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
52632445 CCGTATACAA
*
52632455 TTTTTTTTCAATTTCTTTTCTTTG
1 TTTTTTTTCAATTTCTTTTATTTG
* *
52632479 ATTTTTTTCAATTT-TTTTAATT-
1 TTTTTTTTCAATTTCTTTTATTTG
52632501 TTTTTTT
1 TTTTTTT
52632508 CACGAATCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 6 0.24
23 6 0.24
24 13 0.52
ACGTcount: A:0.13, C:0.08, G:0.02, T:0.77
Consensus pattern (24 bp):
TTTTTTTTCAATTTCTTTTATTTG
Found at i:52632668 original size:19 final size:18
Alignment explanation
Indices: 52632646--52632682 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
52632636 ACGATGAAGT
*
52632646 TTCGTTCTCCTTGAGTCAA
1 TTCGTTCTACTTGA-TCAA
52632665 TTCGTTCTACTTGATCAA
1 TTCGTTCTACTTGATCAA
52632683 CGAAGTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.19, C:0.24, G:0.14, T:0.43
Consensus pattern (18 bp):
TTCGTTCTACTTGATCAA
Found at i:52635474 original size:21 final size:23
Alignment explanation
Indices: 52635429--52635475 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
52635419 TCACCTGCAA
* *
52635429 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
52635452 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
52635473 TAA
1 TAA
52635476 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:52639486 original size:23 final size:22
Alignment explanation
Indices: 52639456--52639501 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 22
52639446 AGTAGTTTCT
52639456 TCAAAAAAAATTCGAAAAAAAAA
1 TCAAAAAAAATTC-AAAAAAAAA
52639479 TCAAAAAAAATTCAAAAAAAAA
1 TCAAAAAAAATTCAAAAAAAAA
52639501 T
1 T
52639502 TGGTTTCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.74, C:0.09, G:0.02, T:0.15
Consensus pattern (22 bp):
TCAAAAAAAATTCAAAAAAAAA
Found at i:52639499 original size:11 final size:11
Alignment explanation
Indices: 52639455--52639499 Score: 72
Period size: 11 Copynumber: 4.0 Consensus size: 11
52639445 TAGTAGTTTC
52639455 TTCAAAAAAAA
1 TTCAAAAAAAA
52639466 TTCGAAAAAAAA
1 TTC-AAAAAAAA
*
52639478 ATCAAAAAAAA
1 TTCAAAAAAAA
52639489 TTCAAAAAAAA
1 TTCAAAAAAAA
52639500 ATTGGTTTCC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
11 21 0.68
12 10 0.32
ACGTcount: A:0.73, C:0.09, G:0.02, T:0.16
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:52639500 original size:12 final size:12
Alignment explanation
Indices: 52639458--52639502 Score: 67
Period size: 12 Copynumber: 3.8 Consensus size: 12
52639448 TAGTTTCTTC
52639458 AAAAAAAATTCGA
1 AAAAAAAATTC-A
52639471 AAAAAAAA-TC-
1 AAAAAAAATTCA
52639481 AAAAAAAATTCA
1 AAAAAAAATTCA
52639493 AAAAAAAATT
1 AAAAAAAATT
52639503 GGTTTCCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
10 8 0.27
11 2 0.07
12 12 0.40
13 8 0.27
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.16
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:52641902 original size:22 final size:22
Alignment explanation
Indices: 52641874--52641917 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
52641864 TTTTGAACCA
52641874 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
52641896 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
52641918 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:52659340 original size:21 final size:19
Alignment explanation
Indices: 52659316--52659356 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
52659306 TTAAAATATT
52659316 AATGATCAAATTTAACTAAAA
1 AATGATCAAA-TTAA-TAAAA
*
52659337 AATGGTCAAATTAATAAAA
1 AATGATCAAATTAATAAAA
52659356 A
1 A
52659357 TTCTAAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 4 0.21
21 9 0.47
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.27
Consensus pattern (19 bp):
AATGATCAAATTAATAAAA
Found at i:52669583 original size:68 final size:68
Alignment explanation
Indices: 52669511--52669641 Score: 226
Period size: 68 Copynumber: 1.9 Consensus size: 68
52669501 GTATTGGTGG
*
52669511 ACTTCATTTGTTATCATAGCCTAGCTATGGTCTTACACAATATAATCTCATGTTTATTGTCCTAC
1 ACTTCATTTATTATCATAGCCTAGCTATGGTCTTACACAATATAATCTCATGTTTATTGTCCTAC
52669576 CGA
66 CGA
* * *
52669579 ACTTCATTTATTGTCATAGCCTAGTTATGGTCTTACACAGTATAATCTCATGTTTATTGTCCT
1 ACTTCATTTATTATCATAGCCTAGCTATGGTCTTACACAATATAATCTCATGTTTATTGTCCT
52669642 GACGGACTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 59 1.00
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (68 bp):
ACTTCATTTATTATCATAGCCTAGCTATGGTCTTACACAATATAATCTCATGTTTATTGTCCTAC
CGA
Found at i:52669651 original size:68 final size:68
Alignment explanation
Indices: 52669474--52669651 Score: 225
Period size: 68 Copynumber: 2.6 Consensus size: 68
52669464 TTTTCCAACA
* * ** ** *
52669474 CTTACATC-GTATAATGTCATATTTATTGTATTGGTGGACTTCATTTGTTATCATAGCCTAGCTA
1 CTTACA-CAGTATAATCTCATGTTTATTGTCCTGACGGACTTCATTTATTATCATAGCCTAGCTA
52669538 TGGT
65 TGGT
* * * *
52669542 CTTACACAATATAATCTCATGTTTATTGTCCT-ACCGAACTTCATTTATTGTCATAGCCTAGTTA
1 CTTACACAGTATAATCTCATGTTTATTGTCCTGA-CGGACTTCATTTATTATCATAGCCTAGCTA
52669606 TGGT
65 TGGT
52669610 CTTACACAGTATAATCTCATGTTTATTGTCCTGACGGACTTC
1 CTTACACAGTATAATCTCATGTTTATTGTCCTGACGGACTTC
52669652 CAATTCTAAG
Statistics
Matches: 94, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
67 1 0.01
68 92 0.98
69 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.42
Consensus pattern (68 bp):
CTTACACAGTATAATCTCATGTTTATTGTCCTGACGGACTTCATTTATTATCATAGCCTAGCTAT
GGT
Found at i:52682961 original size:57 final size:57
Alignment explanation
Indices: 52682889--52683002 Score: 201
Period size: 57 Copynumber: 2.0 Consensus size: 57
52682879 ATGCTGCCTA
* *
52682889 AGAATTAATTTCTTCTGAGTGATGAAGTACTTGAGCTCTTATGATCAATGTAGATAG
1 AGAATTAATTCCTTCTGAGTGATGAAGTACTTAAGCTCTTATGATCAATGTAGATAG
*
52682946 AGAATTAATTCCTTCTGAGTGATGAGGTACTTAAGCTCTTATGATCAATGTAGATAG
1 AGAATTAATTCCTTCTGAGTGATGAAGTACTTAAGCTCTTATGATCAATGTAGATAG
52683003 TACACTTCTC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (57 bp):
AGAATTAATTCCTTCTGAGTGATGAAGTACTTAAGCTCTTATGATCAATGTAGATAG
Found at i:52686005 original size:17 final size:18
Alignment explanation
Indices: 52685980--52686026 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
52685970 TCATAAATCG
*
52685980 CAGTGTCACTACAG-TTT
1 CAGTTTCACTACAGTTTT
*
52685997 CAGTTTCACTACCGTTTT
1 CAGTTTCACTACAGTTTT
52686015 CAGTTTACACTA
1 CAGTTT-CACTA
52686027 ACTAAAGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 12 0.46
18 9 0.35
19 5 0.19
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (18 bp):
CAGTTTCACTACAGTTTT
Done.