Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 165 of 235
Found at i:55682157 original size:25 final size:24
Alignment explanation
Indices: 55681966--55682143 Score: 284
Period size: 24 Copynumber: 7.4 Consensus size: 24
55681956 GAGGAAGTGC
*
55681966 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
* *
55681990 AAAAAGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
* *
55682014 AAAAAGGCTTATGCCCCAGTTATA
1 AAAAGGGCTTATGCCCCAGTTATT
*
55682038 AAAAGGGCTTATGCCCCAGTTACT
1 AAAAGGGCTTATGCCCCAGTTATT
55682062 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
55682086 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
55682110 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
55682134 AAAAGAGGCT
1 AAAAG-GGCT
55682144 AGGCCTCCAA
Statistics
Matches: 146, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
24 142 0.97
25 4 0.03
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:55690133 original size:25 final size:25
Alignment explanation
Indices: 55690104--55690151 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
55690094 TTATAACATG
* * *
55690104 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
55690129 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
55690152 GTTTATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:55690235 original size:11 final size:11
Alignment explanation
Indices: 55690199--55690254 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
55690189 CATGGTATGT
55690199 ATGATATGCAC
1 ATGATATGCAC
* *
55690210 ATGACATG--T
1 ATGATATGCAC
55690219 ATGATATGCAC
1 ATGATATGCAC
*
55690230 ATGATATG--T
1 ATGATATGCAC
55690239 ATGATATGCAC
1 ATGATATGCAC
55690250 ATGAT
1 ATGAT
55690255 GTATTCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:55690254 original size:20 final size:20
Alignment explanation
Indices: 55690188--55690254 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
55690178 ATTTTCATAA
*
55690188 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
55690208 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
55690228 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
55690248 ACATGAT
1 ACATGAT
55690255 GTATTCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:55690451 original size:24 final size:24
Alignment explanation
Indices: 55690304--55690470 Score: 230
Period size: 24 Copynumber: 7.0 Consensus size: 24
55690294 GAGGAAGTGC
*
55690304 AAAAGGGCTTATG-CCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
* *
55690327 AAAAAGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
* *
55690351 AAAAGGGCTTATGCCCTAGTTATA
1 AAAAGGGCTTATGCCCCAGTTATT
*
55690375 AAAAGGGCTTATGCCCCAGTTACT
1 AAAAGGGCTTATGCCCCAGTTATT
55690399 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
55690423 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
55690447 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
55690471 ATGATAAAGC
Statistics
Matches: 130, Mismatches: 11, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
23 12 0.09
24 107 0.82
25 11 0.08
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:55695953 original size:49 final size:50
Alignment explanation
Indices: 55695881--55696011 Score: 169
Period size: 49 Copynumber: 2.7 Consensus size: 50
55695871 GATAAGATGT
55695881 CGATGCCATGTCCTAGACAGGTCTTACACTGACTT-TCATATATCGAG-GC
1 CGATGCCATGTCCTAGACAGGTCTTACACTGACTTCTCATATATC-AGTGC
* * * *
55695930 CGATGCCGTGTCCTAGATAGGTCTTACACTG-TTTCTCATTTATCAGTGC
1 CGATGCCATGTCCTAGACAGGTCTTACACTGACTTCTCATATATCAGTGC
* * *
55695979 CGATGCCATGTCCCAGGCAGGTTTTACACTGAC
1 CGATGCCATGTCCTAGACAGGTCTTACACTGAC
55696012 ACACTAGAAG
Statistics
Matches: 69, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
48 4 0.06
49 65 0.94
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.31
Consensus pattern (50 bp):
CGATGCCATGTCCTAGACAGGTCTTACACTGACTTCTCATATATCAGTGC
Found at i:55696088 original size:48 final size:48
Alignment explanation
Indices: 55696029--55696198 Score: 218
Period size: 48 Copynumber: 3.6 Consensus size: 48
55696019 AAGCTGACGC
* * *
55696029 CATGTCCCAGACAGGTCTTACACTAGCTTGTCTATCTCAAGGCTGATG
1 CATGTCCCAGACATGTCTTACACTGGCTTGTCTATCTCAAGGCCGATG
* * * *
55696077 CATGTCCCAGACATGTCTTACACTGGC-TCTC-GTCTCAATGCCGATA
1 CATGTCCCAGACATGTCTTACACTGGCTTGTCTATCTCAAGGCCGATG
* * ** *
55696123 CATGTCCCAGACATGACTTACACTGGCTTGTATATCTTGAGGCCCATG
1 CATGTCCCAGACATGTCTTACACTGGCTTGTCTATCTCAAGGCCGATG
55696171 CATGTCCCAGACATGTCTTACACTGGCT
1 CATGTCCCAGACATGTCTTACACTGGCT
55696199 CTCATAATGT
Statistics
Matches: 103, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
46 37 0.36
47 5 0.05
48 61 0.59
ACGTcount: A:0.22, C:0.29, G:0.19, T:0.29
Consensus pattern (48 bp):
CATGTCCCAGACATGTCTTACACTGGCTTGTCTATCTCAAGGCCGATG
Found at i:55696130 original size:46 final size:47
Alignment explanation
Indices: 55696029--55696240 Score: 209
Period size: 46 Copynumber: 4.5 Consensus size: 47
55696019 AAGCTGACGC
* * * *
55696029 CATGTCCCAGACAGGTCTTACACTAGCTTGTCTATCTCAAGGCTGATG
1 CATGTCCCAGACATGTCTTACACTGGCTTCTC-ATCTCAAGGCCGATG
* * *
55696077 CATGTCCCAGACATGTCTTACACTGGC-TCTCGTCTCAATGCCGATA
1 CATGTCCCAGACATGTCTTACACTGGCTTCTCATCTCAAGGCCGATG
* * * ** *
55696123 CATGTCCCAGACATGACTTACACTGGCTTGTATATCTTGAGGCCCATG
1 CATGTCCCAGACATGTCTTACACTGGCTTCT-CATCTCAAGGCCGATG
*
55696171 CATGTCCCAGACATGTCTTACACTGGC-TCTCA--T-AATGTGTCCGATC
1 CATGTCCCAGACATGTCTTACACTGGCTTCTCATCTCAA-G-G-CCGATG
*
55696217 CATGTCCCAAACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
55696241 AGCACACATA
Statistics
Matches: 136, Mismatches: 23, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
43 1 0.01
44 2 0.01
45 1 0.01
46 65 0.48
47 7 0.05
48 60 0.44
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.29
Consensus pattern (47 bp):
CATGTCCCAGACATGTCTTACACTGGCTTCTCATCTCAAGGCCGATG
Found at i:55696143 original size:94 final size:93
Alignment explanation
Indices: 55696029--55696243 Score: 281
Period size: 94 Copynumber: 2.3 Consensus size: 93
55696019 AAGCTGACGC
* * **
55696029 CATGTCCCAGACAGGTCTTACACTAGCTTGTCTATCTCAAGGCTGATGCATGTCCCAGACATGTC
1 CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTCAAGGCCCATGCATGTCCCAGACATGTC
*
55696094 TTACACTGGCTCTCGTCTCAA-TG-CCGATA
66 TTACACTGGCTCTC--AT-AAGTGTCCGATA
* * **
55696123 CATGTCCCAGACATGACTTACACTGGCTTGTATATCTTGAGGCCCATGCATGTCCCAGACATGTC
1 CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTCAAGGCCCATGCATGTCCCAGACATGTC
*
55696188 TTACACTGGCTCTCATAATGTGTCCGATC
66 TTACACTGGCTCTCATAA-GTGTCCGATA
*
55696217 CATGTCCCAAACATGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
55696244 ACACATATCC
Statistics
Matches: 105, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
91 2 0.02
92 1 0.01
93 2 0.02
94 100 0.95
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.29
Consensus pattern (93 bp):
CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTCAAGGCCCATGCATGTCCCAGACATGTC
TTACACTGGCTCTCATAAGTGTCCGATA
Found at i:55698768 original size:39 final size:39
Alignment explanation
Indices: 55698710--55698791 Score: 155
Period size: 39 Copynumber: 2.1 Consensus size: 39
55698700 AAACTCCCAC
55698710 AAACTTAATTCATTACTTGTCCTCAAGCAACACAAATAA
1 AAACTTAATTCATTACTTGTCCTCAAGCAACACAAATAA
*
55698749 AAACTTAATTCATTTCTTGTCCTCAAGCAACACAAATAA
1 AAACTTAATTCATTACTTGTCCTCAAGCAACACAAATAA
55698788 AAAC
1 AAAC
55698792 AATAAACAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.44, C:0.23, G:0.05, T:0.28
Consensus pattern (39 bp):
AAACTTAATTCATTACTTGTCCTCAAGCAACACAAATAA
Found at i:55702001 original size:63 final size:63
Alignment explanation
Indices: 55701902--55702024 Score: 237
Period size: 63 Copynumber: 2.0 Consensus size: 63
55701892 TCCAAGCTCC
*
55701902 ATAGTAAGTGATTCCAAGCCCCGTTTTTAATGTTCTTTACGTTTTTGGAATCCCGGTAGCACG
1 ATAGTAAGTGATTCCAAGCCCCGTTTTTAATGTTCTTTACGTTTTTGGAATCCCAGTAGCACG
55701965 ATAGTAAGTGATTCCAAGCCCCGTTTTTAATGTTCTTTACGTTTTTGGAATCCCAGTAGC
1 ATAGTAAGTGATTCCAAGCCCCGTTTTTAATGTTCTTTACGTTTTTGGAATCCCAGTAGC
55702025 TCAATTAAGC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (63 bp):
ATAGTAAGTGATTCCAAGCCCCGTTTTTAATGTTCTTTACGTTTTTGGAATCCCAGTAGCACG
Found at i:55702406 original size:109 final size:109
Alignment explanation
Indices: 55702270--55702486 Score: 416
Period size: 109 Copynumber: 2.0 Consensus size: 109
55702260 AAAGTGATCA
55702270 GCATGTTATAGAACATAAGAATAAGGAATAAAGTTTAATTCCCGAGCCTAGGGGCAAAAGTGTAA
1 GCATGTTATAGAACATAAGAATAAGGAATAAAGTTTAATTCCCGAGCCTAGGGGCAAAAGTGTAA
*
55702335 TTATGCAAAAGTTTAGGGGCAAAAGTGTAATTTTTCTAAAGTTT
66 TTATGCAAAAGTTTAGGGGCAAAAGTGTAATTTTTCCAAAGTTT
*
55702379 GCATGTTATAGAACATAAGAATAAGGAATAAAGTTTAATTCCCGAGCCTAGGGGTAAAAGTGTAA
1 GCATGTTATAGAACATAAGAATAAGGAATAAAGTTTAATTCCCGAGCCTAGGGGCAAAAGTGTAA
55702444 TTATGCAAAAGTTTAGGGGCAAAAGTGTAATTTTTCCAAAGTT
66 TTATGCAAAAGTTTAGGGGCAAAAGTGTAATTTTTCCAAAGTT
55702487 CGTATTAAAT
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
109 106 1.00
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (109 bp):
GCATGTTATAGAACATAAGAATAAGGAATAAAGTTTAATTCCCGAGCCTAGGGGCAAAAGTGTAA
TTATGCAAAAGTTTAGGGGCAAAAGTGTAATTTTTCCAAAGTTT
Found at i:55702782 original size:109 final size:109
Alignment explanation
Indices: 55702591--55702807 Score: 407
Period size: 109 Copynumber: 2.0 Consensus size: 109
55702581 AAAGAAAAGA
55702591 TTGTGGACTAAATTGCAAAATCTTTATATTTTGGTACCAAGGTAAGTTCATGTGCAAAAAATGTA
1 TTGTGGACTAAATTGCAAAATCTTTATATTTTGGTACCAAGGTAAGTTCATGTGCAAAAAATGTA
*
55702656 GCATAATTGTTATTTTTAAGTTATTGATGTTAATTATATGATAT
66 GCATAATTGTTATTTTTAAGTTATAGATGTTAATTATATGATAT
* *
55702700 TTGTGGACTAAATTGCAAAATCTTTATATTTTGGTACCAAGGTAAGTTCATGTGTAAATAATGTA
1 TTGTGGACTAAATTGCAAAATCTTTATATTTTGGTACCAAGGTAAGTTCATGTGCAAAAAATGTA
55702765 GCATAATTGTTATTTTTAAGTTATAGATGTTAATTATATGATA
66 GCATAATTGTTATTTTTAAGTTATAGATGTTAATTATATGATA
55702808 CCCAAAGTTC
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
109 105 1.00
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.42
Consensus pattern (109 bp):
TTGTGGACTAAATTGCAAAATCTTTATATTTTGGTACCAAGGTAAGTTCATGTGCAAAAAATGTA
GCATAATTGTTATTTTTAAGTTATAGATGTTAATTATATGATAT
Found at i:55703295 original size:46 final size:46
Alignment explanation
Indices: 55703239--55703601 Score: 280
Period size: 46 Copynumber: 7.7 Consensus size: 46
55703229 TGGTTGAGCA
55703239 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
* *
55703285 TCCGAACTCGTTGAGTTGAGTCCGAGTT---C-GTGAGATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATG-GATGCGAA-T--G
*
55703330 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCTAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
* * * *
55703378 TCCAAACTCGTTGAGTTGAGTCCGAG--C-TC-GTGAGATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATG-GATGCGAA-T--G
* *
55703423 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
* * * * * *
55703471 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTAGGGGCGTGATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTA-TGG-ATG-CG-AA-T--G
* * *
55703524 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATAC-CATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
* *
55703571 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCAC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCAC
55703602 TTAGGGGCAG
Statistics
Matches: 259, Mismatches: 27, Indels: 63
0.74 0.08 0.18
Matches are distributed among these distances:
42 9 0.03
43 12 0.05
44 1 0.00
45 31 0.12
46 85 0.33
47 56 0.22
48 4 0.02
49 3 0.01
50 13 0.05
51 9 0.03
53 2 0.01
54 2 0.01
55 32 0.12
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
Found at i:55703354 original size:47 final size:47
Alignment explanation
Indices: 55703285--55703554 Score: 229
Period size: 47 Copynumber: 5.6 Consensus size: 47
55703275 GATGCGAATG
55703285 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
*
55703332 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCT-ATGGATGCTAA-T--G--
1 TCCGAACTCGTTGAGTTGAGTCCGAGTT--CGTGA--GATG-TAACTAGGCA
* *
55703378 TCCAAACTCGTTGAGTTGAGTCCGAGCTCGTGAGATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
* * *
55703425 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---GC-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCA
* * *
55703472 -CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTAGGGGCGTGATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTT--C------GTGAGATGTAACTAGGCA
55703526 TCCGAACTCGTTGAGTTGAGTCCGAGTTC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC
55703555 ACTTATGGAT
Statistics
Matches: 179, Mismatches: 17, Indels: 48
0.73 0.07 0.20
Matches are distributed among these distances:
42 3 0.02
43 5 0.03
44 2 0.01
45 2 0.01
46 52 0.29
47 55 0.31
48 7 0.04
49 2 0.01
50 12 0.07
51 10 0.06
53 3 0.02
55 26 0.15
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (47 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
Found at i:55703395 original size:93 final size:93
Alignment explanation
Indices: 55703236--55703599 Score: 523
Period size: 93 Copynumber: 3.8 Consensus size: 93
55703226 GGATGGTTGA
*
55703236 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGCCCGAACTCGTTGAGT
55703301 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
55703329 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCTAATGTCCAAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGCCCGAACTCGTTGAGT
*
55703394 TGAGTCCGAGCTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
55703422 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGCCCGAACTCGTTGAGT
* *
55703487 TGAGTCCGAGTTCACTTAGGGGCGTGATGTAACTAG
66 TGAGTCCGAGTT--C------GTGAGATGTAACTAG
* * * *
55703523 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATAC-CATGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGCCCGAACTCGTTGAGT
55703587 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
55703600 ACTTAGGGGC
Statistics
Matches: 248, Mismatches: 15, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
93 160 0.65
95 1 0.00
98 1 0.00
100 30 0.12
101 56 0.23
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:55703525 original size:101 final size:100
Alignment explanation
Indices: 55703411--55703609 Score: 362
Period size: 101 Copynumber: 2.0 Consensus size: 100
55703401 GAGCTCGTGA
*
55703411 GATGTAACTAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGA
1 GATGTAACTAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATAC-AACGCCCGA
55703476 GCTCGTTGAGTTGAGTCCGAGTTCACTTAGGGGCGT
65 GCTCGTTGAGTTGAGTCCGAGTTCACTTAGGGGCGT
* *
55703512 GATGTAACTAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACCATGCCCGAG
1 GATGTAACTAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAACGCCCGAG
55703577 CTCGTTGAGTTGAGTCCGAGTTCACTTAGGGGC
66 CTCGTTGAGTTGAGTCCGAGTTCACTTAGGGGC
55703610 AGGTTACATG
Statistics
Matches: 95, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
100 41 0.43
101 54 0.57
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (100 bp):
GATGTAACTAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAACGCCCGAG
CTCGTTGAGTTGAGTCCGAGTTCACTTAGGGGCGT
Found at i:55703901 original size:137 final size:137
Alignment explanation
Indices: 55703655--55703927 Score: 528
Period size: 137 Copynumber: 2.0 Consensus size: 137
55703645 TATGTGCAAA
55703655 TTATCCGTGTATCCGAGTTGTATTCCGATGTGTTCAACGGGTGAAATTTCTAGTAAAATGGAAGA
1 TTATCCGTGTATCCGAGTTGTATTCCGATGTGTTCAACGGGTGAAATTTCTAGTAAAATGGAAGA
*
55703720 ACACTTAAGATGCAAGTGACGTTTTGGTAAGTGTTGTGAAATGGACACTTTGGACAGGTATGTTC
66 ACACTTAAGATGCAAGTGACGTTTTGGTAAGTGTTGTGAAATGGACACTTTGGACAGGTATGCTC
55703785 TTAACCT
131 TTAACCT
*
55703792 TTATCCGTGTATCCGAGTTGTATTCCGATGTGTTCAACGGGTGAAATTTCTAGTGAAATGGAAGA
1 TTATCCGTGTATCCGAGTTGTATTCCGATGTGTTCAACGGGTGAAATTTCTAGTAAAATGGAAGA
55703857 ACACTTAAGATGCAAGTGACGTTTTGGTAAGTGTTGTGAAATGGACACTTTGGACAGGTATGCTC
66 ACACTTAAGATGCAAGTGACGTTTTGGTAAGTGTTGTGAAATGGACACTTTGGACAGGTATGCTC
55703922 TTAACC
131 TTAACC
55703928 CTCGGGTTGA
Statistics
Matches: 134, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
137 134 1.00
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.33
Consensus pattern (137 bp):
TTATCCGTGTATCCGAGTTGTATTCCGATGTGTTCAACGGGTGAAATTTCTAGTAAAATGGAAGA
ACACTTAAGATGCAAGTGACGTTTTGGTAAGTGTTGTGAAATGGACACTTTGGACAGGTATGCTC
TTAACCT
Found at i:55706159 original size:11 final size:11
Alignment explanation
Indices: 55706143--55706172 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
55706133 GTTTAATAAA
55706143 TATTTAATAGT
1 TATTTAATAGT
*
55706154 TGTTTAATAGT
1 TATTTAATAGT
55706165 TATTTAAT
1 TATTTAAT
55706173 GTGTCTAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (11 bp):
TATTTAATAGT
Found at i:55712279 original size:17 final size:17
Alignment explanation
Indices: 55712257--55712311 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
55712247 AAAAGAAAAT
** *
55712257 AATAAAATTGAAATGAA
1 AATAAAATAAAAATAAA
55712274 AATAAAATAAAAATAAA
1 AATAAAATAAAAATAAA
55712291 AATAAAAATAAAAAATAAA
1 AAT-AAAAT-AAAAATAAA
55712310 AA
1 AA
55712312 GATAAGAGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
17 17 0.52
18 5 0.15
19 11 0.33
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (17 bp):
AATAAAATAAAAATAAA
Found at i:55712298 original size:7 final size:6
Alignment explanation
Indices: 55712267--55712311 Score: 65
Period size: 6 Copynumber: 7.5 Consensus size: 6
55712257 AATAAAATTG
*
55712267 AAATGA AAAT-A AAATAA AAATAA AAATAA AAATAAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAAT-AA AAATAA AAA
55712312 GATAAGAGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.14
6 26 0.70
7 6 0.16
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:55717358 original size:9 final size:9
Alignment explanation
Indices: 55717333--55717364 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
55717323 AAGAAAAAGT
55717333 AAATTAAT-
1 AAATTAATA
55717341 AAA-TAATA
1 AAATTAATA
55717349 AAATTAATA
1 AAATTAATA
55717358 AAATTAA
1 AAATTAA
55717365 ATTAAATTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 4 0.18
8 6 0.27
9 12 0.55
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
AAATTAATA
Found at i:55733760 original size:23 final size:22
Alignment explanation
Indices: 55733734--55733786 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
55733724 TTGAGGGTGA
*
55733734 AAAAGAAATT-GAAGAAAGAAGAG
1 AAAAGAAATTAGAA-AAAGAA-AC
55733757 AAAATG-AATTAGAAAAAGAAAC
1 AAAA-GAAATTAGAAAAAGAAAC
55733779 AAAAGAAA
1 AAAAGAAA
55733787 AAGACGTGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 1 0.04
22 7 0.27
23 14 0.54
24 4 0.15
ACGTcount: A:0.70, C:0.02, G:0.19, T:0.09
Consensus pattern (22 bp):
AAAAGAAATTAGAAAAAGAAAC
Found at i:55739735 original size:46 final size:46
Alignment explanation
Indices: 55739686--55739848 Score: 179
Period size: 47 Copynumber: 3.5 Consensus size: 46
55739676 TAGTGCAAAA
55739686 CATGTCTGGGACATGCATCGACCATGAGACGTAAGCCAGTGTAAGA-
1 CATGTCTGGGACATGCATCGACCATGAGA-GTAAGCCAGTGTAAGAC
* * ** * *
55739732 CATGTCTGGGACATGCATCGGCTACAAGAGGATAGTCAGTGTAAGAC
1 CATGTCTGGGACATGCATCGACCATGAGAGTA-AGCCAGTGTAAGAC
*
55739779 CATGTCTGGGACATGACATCGA-CTTGAGA-TATGAGCCAGTGTAAGAC
1 CATGTCTGGGACATG-CATCGACCATGAGAGTA--AGCCAGTGTAAGAC
*
55739826 CATGTCTAGGACATGGCATCGAC
1 CATGTCTGGGACAT-GCATCGAC
55739849 ACCTTACCCT
Statistics
Matches: 96, Mismatches: 15, Indels: 10
0.79 0.12 0.08
Matches are distributed among these distances:
45 2 0.02
46 38 0.40
47 50 0.52
48 6 0.06
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.21
Consensus pattern (46 bp):
CATGTCTGGGACATGCATCGACCATGAGAGTAAGCCAGTGTAAGAC
Found at i:55739838 original size:140 final size:141
Alignment explanation
Indices: 55739583--55739848 Score: 315
Period size: 140 Copynumber: 1.9 Consensus size: 141
55739573 TGTGTGAGCT
** * *
55739583 AGTGTAAGACATGTCTGAGACATGCATCGGCCACATTATGAGAGCCAATGTAAGACCATGTTTAG
1 AGTGTAAGACATGTCTGAGACATGCATCGGCCACAAGAGGAGAGCCAATGTAAGACCATGTCTAG
* * * * *
55739648 GACATAGCATTGGCATTGAGACGAGGGCTAGTGCAAAACATGTCTGGGACAT-GCATCGACCATG
66 GACATAGCATCGACATTGAGACGAGAGCCAGTGCAAAACATGTCTAGGACATGGCATCGACCATG
55739712 AGACGTAAGCC
131 AGACGTAAGCC
* * * * * *
55739723 AGTGTAAGACATGTCTGGGACATGCATCGGCTACAAGAGGATAGTCAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCTGAGACATGCATCGGCCACAAGAGGAGAGCCAATGTAAGACCATGTCTAG
* * *
55739788 GACAT-GACATCGAC-TTGAGA-TATGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGAC
66 GACATAG-CATCGACATTGAGACGA-GAGCCAGTGCAA-AACATGTCTAGGACATGGCATCGAC
55739849 ACCTTACCCT
Statistics
Matches: 104, Mismatches: 18, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
138 1 0.01
139 16 0.15
140 79 0.76
141 8 0.08
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.22
Consensus pattern (141 bp):
AGTGTAAGACATGTCTGAGACATGCATCGGCCACAAGAGGAGAGCCAATGTAAGACCATGTCTAG
GACATAGCATCGACATTGAGACGAGAGCCAGTGCAAAACATGTCTAGGACATGGCATCGACCATG
AGACGTAAGCC
Found at i:55743371 original size:48 final size:48
Alignment explanation
Indices: 55743299--55743566 Score: 271
Period size: 48 Copynumber: 5.6 Consensus size: 48
55743289 TATGTGTGCT
* *
55743299 AGTGTAAGACCATGTTTGACACATGGCATCAGCAATATTATAAGAGCC
1 AGTGTAAGACCATGTCTGAGACATGGCATCAGCAATATTATAAGAGCC
* * * *
55743347 AGTGTAAGACCATGTTTGGGACATGGCATCGGCAATATTATGAGAGCC
1 AGTGTAAGACCATGTCTGAGACATGGCATCAGCAATATTATAAGAGCC
* * * *
55743395 AGTGTAATACCATGTCTGAGACATGGCAT-TGACAATGTTATGAGAGCC
1 AGTGTAAGACCATGTCTGAGACATGGCATCAG-CAATATTATAAGAGCC
* * *
55743443 AGTGTAAGACCATGTCTGGGACATGGCATC-G-AA-ATTGAAACGAGAGCT
1 AGTGTAAGACCATGTCTGAGACATGGCATCAGCAATATT-ATA--AGAGCC
* * * * *
55743491 AGTGTAAGACCATTTCTGGGACATGGCATCAGC-CTCGA-CATATGAGCC
1 AGTGTAAGACCATGTCTGAGACATGGCATCAGCAAT--ATTATAAGAGCC
55743539 AGTGTAAGA-CATGTCTGAGACATGGCAT
1 AGTGTAAGACCATGTCTGAGACATGGCAT
55743567 TGGTAATTTG
Statistics
Matches: 187, Mismatches: 23, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
45 2 0.01
46 3 0.02
47 18 0.10
48 160 0.86
49 1 0.01
50 2 0.01
52 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGAGACATGGCATCAGCAATATTATAAGAGCC
Found at i:55747058 original size:30 final size:30
Alignment explanation
Indices: 55746997--55747073 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 30
55746987 GTCATTTGAG
* * **
55746997 TTTATCAGGCACTATGTGCAGGTGATTATA
1 TTTATCAGGTACTATGTACAGGTGACCATA
55747027 TTTATCAGGTACTATGTACTA-GTGACCATA
1 TTTATCAGGTACTATGTAC-AGGTGACCATA
* *
55747057 -TTATTAGGTACTTTGTA
1 TTTATCAGGTACTATGTA
55747074 TCGGTGTTCA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 15 0.38
30 24 0.60
31 1 0.03
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.40
Consensus pattern (30 bp):
TTTATCAGGTACTATGTACAGGTGACCATA
Found at i:55749701 original size:64 final size:64
Alignment explanation
Indices: 55749552--55749803 Score: 197
Period size: 68 Copynumber: 3.8 Consensus size: 64
55749542 TACAGATGGT
* ** * * * *
55749552 ATGTAGCTAGGTCACATGTATGGTGCTGAGTGCACATCATGT-GTACAAGAGAGCTACGAGACAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTAAGTGTACACCATGTAG-ACAAGAGAGCTACGAG--A-
*
55749616 TATG
62 TA-A
* * * * *
55749620 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGTGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTAAGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
55749684 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAAGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTAAGTG---TACACCATGTAGACAAGAGAGCTACGAGAT
55749749 AA
63 AA
* * *
55749751 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATCT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGGTACTAAGTGTACACCATGTAG-ACAAGAGAGC
55749804 CAAAATTATG
Statistics
Matches: 149, Mismatches: 29, Indels: 17
0.76 0.15 0.09
Matches are distributed among these distances:
62 1 0.01
63 17 0.11
64 27 0.18
65 2 0.01
66 23 0.15
67 29 0.19
68 49 0.33
69 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.24
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTAAGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:55753141 original size:23 final size:22
Alignment explanation
Indices: 55753102--55753228 Score: 101
Period size: 23 Copynumber: 5.3 Consensus size: 22
55753092 AGCTCCTGTT
55753102 GAGCTGATGAACAGTAAGCTCTAC
1 GAGCTGA--AACAGTAAGCTCTAC
*
55753126 TAAGCTGAAACAGTAAGCTCTGAC
1 -GAGCTGAAACAGTAAGCTCT-AC
* *
55753150 GAGTTGAATCAGTAAGCTCATAC
1 GAGCTGAAACAGTAAGCTC-TAC
* *
55753173 GAGCTGAGAATAGTAAGCTCCAAC
1 GAGCTGA-AACAGTAAGCT-CTAC
*
55753197 GAGCTGATATATCGGTAAGCTCATAC
1 GAGCTGA-A-A-CAGTAAGCTC-TAC
55753223 GAGCTG
1 GAGCTG
55753229 TGGTAAGTCG
Statistics
Matches: 83, Mismatches: 12, Indels: 13
0.77 0.11 0.12
Matches are distributed among these distances:
23 37 0.45
24 22 0.27
25 9 0.11
26 15 0.18
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (22 bp):
GAGCTGAAACAGTAAGCTCTAC
Found at i:55761662 original size:39 final size:40
Alignment explanation
Indices: 55761562--55761746 Score: 200
Period size: 40 Copynumber: 4.7 Consensus size: 40
55761552 TTGAATGATG
* * *
55761562 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* * *
55761601 ATCTGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
*
55761642 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
55761681 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
55761720 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
55761747 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
39 36 0.30
40 76 0.62
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:55761702 original size:79 final size:81
Alignment explanation
Indices: 55761562--55761746 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 81
55761552 TTGAATGATG
* * *
55761562 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCTGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
55761626 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
55761641 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
55761703 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
55761721 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
55761747 AACGAGTAGC
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 1 0.01
79 56 0.62
80 33 0.37
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:55761768 original size:79 final size:79
Alignment explanation
Indices: 55761615--55761779 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
55761605 GGACTAAGAT
* * **
55761615 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
55761680 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
55761694 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
55761757 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
55761773 CCGAAGG
1 CCGAAGG
55761780 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:55763724 original size:93 final size:93
Alignment explanation
Indices: 55763616--55763787 Score: 274
Period size: 93 Copynumber: 1.8 Consensus size: 93
55763606 GCCCATAAGT
* *
55763616 GAACTCGAACTCAACTCAACGAGCTCAGG-CGTTTGCATCCATAAGTGAACTCAGACTCAACTCA
1 GAACTCGAACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
55763680 ACGAGCTCGGATGCCTAGTTACATCTCTC
65 ACGAGCTCGGATGCCTAGTTACATCTCTC
* * *
55763709 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
*
55763774 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
55763788 CAAATATCCT
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 2 0.03
93 70 0.97
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:55763783 original size:46 final size:45
Alignment explanation
Indices: 55763608--55763782 Score: 183
Period size: 46 Copynumber: 3.8 Consensus size: 45
55763598 TGTAACCCGC
* * *
55763608 CCATAAGTGAACTCGAACTCAACTCAACGAGCTCAGGCGTTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-GGCATTCGCAT
* *
55763654 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGG-ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGC-A--T
* *** *
55763700 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCAT
*
55763747 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
55763783 ATGCCCAAAT
Statistics
Matches: 106, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
43 1 0.01
44 2 0.02
45 2 0.02
46 65 0.61
47 31 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCAT
Found at i:55763802 original size:46 final size:44
Alignment explanation
Indices: 55763659--55763802 Score: 107
Period size: 46 Copynumber: 3.1 Consensus size: 44
55763649 TGCATCCATA
* * *
55763659 AGTGAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA---A-ATC-CT
* * *
55763708 --CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGC--ATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCCCAAATCC-T
55763751 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCC-AA-ATCCT
55763798 AGTGA
1 AGTGA
55763803 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:0.30, C:0.28, G:0.19, T:0.22
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATCCT
Found at i:55763909 original size:47 final size:47
Alignment explanation
Indices: 55763840--55763934 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 47
55763830 TAAGGTTCAA
* *
55763840 CGGGACCTTTTTCCCAATCATGTGTCTCAACCATCTTCTACGGAATG
1 CGGGACCTTTCTCCCAATCATGTGTCTCAACCATCTTCTACAGAATG
55763887 CGGGACCTTTCTCCCAATCATGTGTCTCAACCATCTTCTACAGAATG
1 CGGGACCTTTCTCCCAATCATGTGTCTCAACCATCTTCTACAGAATG
55763934 C
1 C
55763935 CGATACCGAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.22, C:0.32, G:0.16, T:0.31
Consensus pattern (47 bp):
CGGGACCTTTCTCCCAATCATGTGTCTCAACCATCTTCTACAGAATG
Found at i:55769574 original size:47 final size:47
Alignment explanation
Indices: 55769523--55769619 Score: 158
Period size: 47 Copynumber: 2.1 Consensus size: 47
55769513 TTTTCAATCA
* *
55769523 TATAAACAATAATTTATTTCAAAACCGTAACTCATATGTATAAACAG
1 TATAAACAATAATTCATTTCAAAACCATAACTCATATGTATAAACAG
* *
55769570 TATAAACAATAATTCATTTGAAAACCATAACTCATCTGTATAAACAG
1 TATAAACAATAATTCATTTCAAAACCATAACTCATATGTATAAACAG
55769617 TAT
1 TAT
55769620 CTATGCCCGT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.46, C:0.15, G:0.06, T:0.32
Consensus pattern (47 bp):
TATAAACAATAATTCATTTCAAAACCATAACTCATATGTATAAACAG
Found at i:55772014 original size:43 final size:43
Alignment explanation
Indices: 55771960--55772045 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
55771950 GATATATGTG
* * *
55771960 GCATCCTAGCTCGTTGAGTGGTCTGAGTTCATTATGGATGCGA
1 GCATCCGAGCTCGTTGAGTGGTCCGAGTTCATAATGGATGCGA
*
55772003 GCATCCGAGCTCGTTGAGTGGTCCGAGTTCATAATTGATGCGA
1 GCATCCGAGCTCGTTGAGTGGTCCGAGTTCATAATGGATGCGA
55772046 TACATGTGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (43 bp):
GCATCCGAGCTCGTTGAGTGGTCCGAGTTCATAATGGATGCGA
Found at i:55776840 original size:42 final size:43
Alignment explanation
Indices: 55776781--55776896 Score: 126
Period size: 43 Copynumber: 2.7 Consensus size: 43
55776771 GTCCGGACTT
* * * *
55776781 GTTGAGTGGTCCAAGTTCGTGATATATGTG-GCATCCGAGCTC
1 GTTGAGTGGTCCAAGTTCATGATAGATGCGAGCATCCAAGCTC
** * *
55776823 GTTGAGTGGTCTGAGTTCATTATGGATGCGAGCATCCAAGCTC
1 GTTGAGTGGTCCAAGTTCATGATAGATGCGAGCATCCAAGCTC
* * *
55776866 GTTGAGTGGTCCAAGTACATAATGGATGCGA
1 GTTGAGTGGTCCAAGTTCATGATAGATGCGA
55776897 TACATGTGAT
Statistics
Matches: 61, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
42 23 0.38
43 38 0.62
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.29
Consensus pattern (43 bp):
GTTGAGTGGTCCAAGTTCATGATAGATGCGAGCATCCAAGCTC
Found at i:55776870 original size:43 final size:43
Alignment explanation
Indices: 55776811--55776896 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
55776801 GATATATGTG
* ** * *
55776811 GCATCCGAGCTCGTTGAGTGGTCTGAGTTCATTATGGATGCGA
1 GCATCCAAGCTCGTTGAGTGGTCCAAGTACATAATGGATGCGA
55776854 GCATCCAAGCTCGTTGAGTGGTCCAAGTACATAATGGATGCGA
1 GCATCCAAGCTCGTTGAGTGGTCCAAGTACATAATGGATGCGA
55776897 TACATGTGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (43 bp):
GCATCCAAGCTCGTTGAGTGGTCCAAGTACATAATGGATGCGA
Found at i:55784887 original size:44 final size:42
Alignment explanation
Indices: 55784841--55784994 Score: 152
Period size: 42 Copynumber: 3.6 Consensus size: 42
55784831 TGAGTTGTCG
* *
55784841 TGTAAGACCACGTCTGGGACATTGGCGTCGATTTGAGATTTACG
1 TGTAAGACCACGTCTGGGACATTGGCATCGATTT--GATTTACA
* *
55784885 TGTAAGACCATGTCTGGGACATAGGCATCGTATTTGATTT-CA
1 TGTAAGACCACGTCTGGGACATTGGCATCG-ATTTGATTTACA
* * * *
55784927 TGTAAAACC-CTGTCTAGGATAGTGGCATCGATATTGA-TTACA
1 TGTAAGACCAC-GTCTGGGACATTGGCATCGAT-TTGATTTACA
* *
55784969 TATAAGACCACGTCTGGGACGTTGGC
1 TGTAAGACCACGTCTGGGACATTGGC
55784995 GTTGTACTAG
Statistics
Matches: 89, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
41 4 0.04
42 48 0.54
43 6 0.07
44 27 0.30
45 4 0.04
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (42 bp):
TGTAAGACCACGTCTGGGACATTGGCATCGATTTGATTTACA
Found at i:55789392 original size:47 final size:47
Alignment explanation
Indices: 55789323--55789487 Score: 230
Period size: 47 Copynumber: 3.5 Consensus size: 47
55789313 TCCCCTAAGT
55789323 GAACTCGGACTCAACTCAACGAGTTTGGATGCCTCGTTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGTTTGGATGCCTCGTTACATCTCAC
* * * * *
55789370 GAACTCGGACTCAACTCAACGAGTTCGGA--CAT--TTGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTTGGATGCCTCGTTACAT-C-TCA-C
55789416 GAACTCGGACTCAACTCAACGAGTTTGGATGCCTCGTTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGTTTGGATGCCTCGTTACATCTCAC
55789463 GAACTCGGACTCAACTCAACGAGTT
1 GAACTCGGACTCAACTCAACGAGTT
55789488 CGGACATTTG
Statistics
Matches: 101, Mismatches: 10, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
43 5 0.05
44 1 0.01
45 4 0.04
46 28 0.28
47 53 0.52
48 4 0.04
49 1 0.01
50 5 0.05
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.24
Consensus pattern (47 bp):
GAACTCGGACTCAACTCAACGAGTTTGGATGCCTCGTTACATCTCAC
Found at i:55789437 original size:46 final size:46
Alignment explanation
Indices: 55789317--55789537 Score: 238
Period size: 46 Copynumber: 4.8 Consensus size: 46
55789307 TAACCCTCCC
* *
55789317 CTAAGTGAACTCGGACTCAACTCAACGAGTTTGGATGCCTCGTTACAT
1 CTAAGTGAACTCGGACTCAACTCAACGAGTTCGGA-GCATC-TTACAT
* * *
55789365 CTCA-CGAACTCGGACTCAACTCAACGAGTTCGGA-CAT-TTGCAT
1 CTAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATCTTACAT
* *
55789408 CCATAAGTGAACTCGGACTCAACTCAACGAGTTTGGATGCCTCGTTACAT
1 -C-TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA-GCATC-TTACAT
* * *
55789458 CTCA-CGAACTCGGACTCAACTCAACGAGTTCGGA-CAT-TTGCAT
1 CTAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATCTTACAT
55789501 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 -C-TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
55789538 TGCTCAACCA
Statistics
Matches: 146, Mismatches: 17, Indels: 22
0.79 0.09 0.12
Matches are distributed among these distances:
43 10 0.07
44 2 0.01
45 8 0.05
46 57 0.39
47 56 0.38
48 7 0.05
49 1 0.01
50 5 0.03
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.24
Consensus pattern (46 bp):
CTAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATCTTACAT
Found at i:55789477 original size:93 final size:93
Alignment explanation
Indices: 55789318--55789540 Score: 437
Period size: 93 Copynumber: 2.4 Consensus size: 93
55789308 AACCCTCCCC
55789318 TAAGTGAACTCGGACTCAACTCAACGAGTTTGGATGCCTCGTTACATCTCACGAACTCGGACTCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTTGGATGCCTCGTTACATCTCACGAACTCGGACTCA
55789383 ACTCAACGAGTTCGGACATTTGCATCCA
66 ACTCAACGAGTTCGGACATTTGCATCCA
55789411 TAAGTGAACTCGGACTCAACTCAACGAGTTTGGATGCCTCGTTACATCTCACGAACTCGGACTCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTTGGATGCCTCGTTACATCTCACGAACTCGGACTCA
55789476 ACTCAACGAGTTCGGACATTTGCATCCA
66 ACTCAACGAGTTCGGACATTTGCATCCA
*
55789504 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTTGGATGC
55789541 TCAACCATCC
Statistics
Matches: 129, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 129 1.00
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.24
Consensus pattern (93 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTTGGATGCCTCGTTACATCTCACGAACTCGGACTCA
ACTCAACGAGTTCGGACATTTGCATCCA
Found at i:55790612 original size:74 final size:74
Alignment explanation
Indices: 55790524--55790676 Score: 281
Period size: 74 Copynumber: 2.1 Consensus size: 74
55790514 CTTTCCAAAA
*
55790524 ATTCC-TTCCATGTCCTAATTTTGTCCATGAACTTAAAATTGGTCAAATTGCTATTTAAGACCTC
1 ATTCCATTCCATGTCCTAAATTTGTCCATGAACTTAAAATTGGTCAAATTGCTATTTAAGACCTC
55790588 CTCATTAAT
66 CTCATTAAT
55790597 ATTCCATTCCATGTCCTAAATTTGTCCATGAACTTAAAATTGGTCAAATTGCTATTTAAGACCTC
1 ATTCCATTCCATGTCCTAAATTTGTCCATGAACTTAAAATTGGTCAAATTGCTATTTAAGACCTC
*
55790662 CTCGTTAAT
66 CTCATTAAT
55790671 ATTCCA
1 ATTCCA
55790677 AAACAATTTC
Statistics
Matches: 77, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
73 5 0.06
74 72 0.94
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (74 bp):
ATTCCATTCCATGTCCTAAATTTGTCCATGAACTTAAAATTGGTCAAATTGCTATTTAAGACCTC
CTCATTAAT
Found at i:55796832 original size:69 final size:68
Alignment explanation
Indices: 55796721--55796858 Score: 258
Period size: 69 Copynumber: 2.0 Consensus size: 68
55796711 ATACTTCATC
55796721 TCTTTCCCTCATTCTATTTTGTTCGATTTTGACAATTAATCTTCAATCAATTGGTAGGGGAACAG
1 TCTTTCCCTCATTCTATTTTGTTCGATTTTGACAATTAATCTTCAATCAATTGGTAGGGGAACAG
55796786 TTT
66 TTT
*
55796789 NTCTTTCCCTCTTTCTATTTTGTTCGATTTTGACAATTAATCTTCAATCAATTGGTAGGGGAACA
1 -TCTTTCCCTCATTCTATTTTGTTCGATTTTGACAATTAATCTTCAATCAATTGGTAGGGGAACA
55796854 GTTT
65 GTTT
55796858 T
1 T
55796859 TCCAAGGTTT
Statistics
Matches: 68, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
68 1 0.01
69 67 0.99
ACGTcount: A:0.22, C:0.17, G:0.14, T:0.45
Consensus pattern (68 bp):
TCTTTCCCTCATTCTATTTTGTTCGATTTTGACAATTAATCTTCAATCAATTGGTAGGGGAACAG
TTT
Found at i:55799062 original size:42 final size:42
Alignment explanation
Indices: 55799014--55799113 Score: 105
Period size: 42 Copynumber: 2.4 Consensus size: 42
55799004 TGAGATTTAC
* *
55799014 GTGTAAGACCATGTTTGGGACA-TAGGCATCG-TATTTGATTTT
1 GTGTAAGACCATGTCTAGGACAGT-GGCATCGATA-TTGATTTT
* **
55799056 GTGTAAGACCCTGTCTAGGACAGTGGCATCGATATTGATTAC
1 GTGTAAGACCATGTCTAGGACAGTGGCATCGATATTGATTTT
* *
55799098 ATGTAAGACCACGTCT
1 GTGTAAGACCATGTCT
55799114 GAGACGTTGG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
42 45 0.94
43 3 0.06
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (42 bp):
GTGTAAGACCATGTCTAGGACAGTGGCATCGATATTGATTTT
Found at i:55806770 original size:27 final size:28
Alignment explanation
Indices: 55806735--55806790 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
55806725 TGAAATTCAC
* *
55806735 ACTTTAATTA-TAAAATAATTAATTTTA
1 ACTTAAATTATTAAAATAATGAATTTTA
* *
55806762 ACTTAAATTATTAACATACTGAATTTTA
1 ACTTAAATTATTAAAATAATGAATTTTA
55806790 A
1 A
55806791 TTATTTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 9 0.38
28 15 0.62
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (28 bp):
ACTTAAATTATTAAAATAATGAATTTTA
Found at i:55811707 original size:23 final size:24
Alignment explanation
Indices: 55811662--55811707 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
55811652 CCTGTTACAT
55811662 GGCTCTTTGTGAGAATTCCTGATA
1 GGCTCTTTGTGAGAATTCCTGATA
*
55811686 GGCTCTTTGTGAG-CTTCCTGAT
1 GGCTCTTTGTGAGAATTCCTGAT
55811708 TAAAAGTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.15, C:0.20, G:0.26, T:0.39
Consensus pattern (24 bp):
GGCTCTTTGTGAGAATTCCTGATA
Found at i:55815905 original size:43 final size:43
Alignment explanation
Indices: 55815839--55815946 Score: 137
Period size: 43 Copynumber: 2.5 Consensus size: 43
55815829 GATCAACGAG
* *
55815839 ATGTGTTTATGTGTAAGACCATGTCTGGGACATTGGCATCATT
1 ATGTGATTATATGTAAGACCATGTCTGGGACATTGGCATCATT
* * *
55815882 ATGTGATTATATGTACGATCATGTCTGGGACATTTGCATCATT
1 ATGTGATTATATGTAAGACCATGTCTGGGACATTGGCATCATT
* *
55815925 ATTTGATT-TCGTGTAAGACCAT
1 ATGTGATTAT-ATGTAAGACCAT
55815947 AGTTGGGCTA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 1 0.02
43 54 0.98
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (43 bp):
ATGTGATTATATGTAAGACCATGTCTGGGACATTGGCATCATT
Found at i:55819388 original size:35 final size:35
Alignment explanation
Indices: 55819361--55819445 Score: 98
Period size: 35 Copynumber: 2.4 Consensus size: 35
55819351 ATTAATATTC
* *
55819361 TGATTCACATGTTAATCATGCTATTATTCTGATTA
1 TGATTCACATGTTAAGCATGCTATTATTATGATTA
** *
55819396 TGATTTGCATGTTAAGCATGCTATTATTTTGATTA
1 TGATTCACATGTTAAGCATGCTATTATTATGATTA
* * *
55819431 GGACTCACAAGTTAA
1 TGATTCACATGTTAA
55819446 ACATATCATC
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.42
Consensus pattern (35 bp):
TGATTCACATGTTAAGCATGCTATTATTATGATTA
Found at i:55822028 original size:44 final size:44
Alignment explanation
Indices: 55821966--55822059 Score: 170
Period size: 44 Copynumber: 2.1 Consensus size: 44
55821956 GATAACTTGT
*
55821966 TTGTGGCTGATTTGGTTGTATATATATGCTTGGATTGGTGTTGC
1 TTGTTGCTGATTTGGTTGTATATATATGCTTGGATTGGTGTTGC
*
55822010 TTGTTGCTGATTTGGTTGTATGTATATGCTTGGATTGGTGTTGC
1 TTGTTGCTGATTTGGTTGTATATATATGCTTGGATTGGTGTTGC
55822054 TTGTTG
1 TTGTTG
55822060 TTGAGTAGGT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.12, C:0.06, G:0.32, T:0.50
Consensus pattern (44 bp):
TTGTTGCTGATTTGGTTGTATATATATGCTTGGATTGGTGTTGC
Found at i:55822071 original size:44 final size:44
Alignment explanation
Indices: 55821979--55822071 Score: 150
Period size: 44 Copynumber: 2.1 Consensus size: 44
55821969 TGGCTGATTT
* *
55821979 GGTTGTATATATATGCTTGGATTGGTGTTGCTTGTTGCTGATTT
1 GGTTGTATATATATGCTTGGATTGGTGTTGCTTGTTGCTGAGTA
* *
55822023 GGTTGTATGTATATGCTTGGATTGGTGTTGCTTGTTGTTGAGTA
1 GGTTGTATATATATGCTTGGATTGGTGTTGCTTGTTGCTGAGTA
55822067 GGTTG
1 GGTTG
55822072 GTGCAAGTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.13, C:0.05, G:0.33, T:0.48
Consensus pattern (44 bp):
GGTTGTATATATATGCTTGGATTGGTGTTGCTTGTTGCTGAGTA
Found at i:55829186 original size:34 final size:34
Alignment explanation
Indices: 55829116--55829187 Score: 81
Period size: 34 Copynumber: 2.1 Consensus size: 34
55829106 TTAGTTATTA
* * *
55829116 AATTAAGTTGTTGGAATCAATATTCAACTTAGTT
1 AATTAAGTTGTTAGAATAAATATTCAACTTAATT
* * * *
55829150 AATTGAGTTGTTAGAATAAATCTTTATCTTAATT
1 AATTAAGTTGTTAGAATAAATATTCAACTTAATT
55829184 AATT
1 AATT
55829188 TAATTACTGG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.44
Consensus pattern (34 bp):
AATTAAGTTGTTAGAATAAATATTCAACTTAATT
Found at i:55829281 original size:9 final size:9
Alignment explanation
Indices: 55829267--55829322 Score: 85
Period size: 9 Copynumber: 6.2 Consensus size: 9
55829257 TTTATAGTAA
55829267 TTAATGTGT
1 TTAATGTGT
55829276 TTAATGTGT
1 TTAATGTGT
* *
55829285 TTAGTGTGC
1 TTAATGTGT
55829294 TTAATGTGT
1 TTAATGTGT
*
55829303 TTAGTGTGT
1 TTAATGTGT
55829312 TTAATGTGT
1 TTAATGTGT
55829321 TT
1 TT
55829323 TTAAAGTGTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.18, C:0.02, G:0.25, T:0.55
Consensus pattern (9 bp):
TTAATGTGT
Found at i:55829282 original size:27 final size:27
Alignment explanation
Indices: 55829247--55829314 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
55829237 AGTTAATTAA
*
55829247 GTTTCATGTGTTTA-TAGTAATTAATGT
1 GTTTAATGTGTTTAGT-GTAATTAATGT
**
55829274 GTTTAATGTGTTTAGTGTGCTTAATGT
1 GTTTAATGTGTTTAGTGTAATTAATGT
*
55829301 GTTTAGTGTGTTTA
1 GTTTAATGTGTTTA
55829315 ATGTGTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
27 35 0.97
28 1 0.03
ACGTcount: A:0.21, C:0.03, G:0.24, T:0.53
Consensus pattern (27 bp):
GTTTAATGTGTTTAGTGTAATTAATGT
Found at i:55829292 original size:18 final size:18
Alignment explanation
Indices: 55829271--55829322 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
55829261 TAGTAATTAA
55829271 TGTGTTTAATGTGTTTAG
1 TGTGTTTAATGTGTTTAG
*
55829289 TGTGCTTAATGTGTTTAG
1 TGTGTTTAATGTGTTTAG
55829307 TGTGTTTAATGTGTTT
1 TGTGTTTAATGTGTTT
55829323 TTAAAGTGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.15, C:0.02, G:0.27, T:0.56
Consensus pattern (18 bp):
TGTGTTTAATGTGTTTAG
Found at i:55841535 original size:16 final size:16
Alignment explanation
Indices: 55841514--55841550 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
55841504 GAACTTTCGG
55841514 CTTTTCGGCATTTAGA
1 CTTTTCGGCATTTAGA
* *
55841530 CTTTTCGGTATTTCGA
1 CTTTTCGGCATTTAGA
55841546 CTTTT
1 CTTTT
55841551 GCCGATACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.14, C:0.19, G:0.16, T:0.51
Consensus pattern (16 bp):
CTTTTCGGCATTTAGA
Found at i:55845410 original size:24 final size:24
Alignment explanation
Indices: 55845378--55845430 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
55845368 AGAGAGTAAT
* *
55845378 GCGCCAGCTCTGGGTGAAGGGGCA
1 GCGCCAGCTCCGGCTGAAGGGGCA
55845402 GCGCCAGCTCCGGCTGAAGGGGCA
1 GCGCCAGCTCCGGCTGAAGGGGCA
55845426 GCGCC
1 GCGCC
55845431 GACTGAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.15, C:0.32, G:0.43, T:0.09
Consensus pattern (24 bp):
GCGCCAGCTCCGGCTGAAGGGGCA
Found at i:55851405 original size:46 final size:44
Alignment explanation
Indices: 55851352--55851524 Score: 161
Period size: 46 Copynumber: 3.8 Consensus size: 44
55851342 TGGTTGAGCA
*
55851352 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATCGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAT-GATGCGAA-G
* * *
55851398 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GATGTGACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGATGCGA--A-G
* *
55851443 AATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAT-GATGCGAAG
* * * *
55851490 ACCCAAGCTCATTGAGTTGAGTTCGAGTTCACTTA
1 TCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTA
55851525 GGGGCGGGTT
Statistics
Matches: 104, Mismatches: 15, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
43 6 0.06
45 7 0.07
46 54 0.52
47 28 0.27
48 3 0.03
50 6 0.06
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (44 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGATGCGAAG
Found at i:55851428 original size:20 final size:20
Alignment explanation
Indices: 55851405--55851473 Score: 50
Period size: 20 Copynumber: 3.1 Consensus size: 20
55851395 ATGTCCGAAC
55851405 TCGTTGAGTTGAGTCCGAGT
1 TCGTTGAGTTGAGTCCGAGT
*
55851425 TCG-TGAGATGTGACTAGGAATCCGAGC
1 TCGTTGAG-T-TG---A-G--TCCGAGT
55851452 TCGTTGAGTTGAGTCCGAGT
1 TCGTTGAGTTGAGTCCGAGT
55851472 TC
1 TC
55851474 ACTTATGGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 18
0.66 0.03 0.31
Matches are distributed among these distances:
19 4 0.11
20 12 0.32
21 2 0.05
22 1 0.03
23 1 0.03
24 1 0.03
25 1 0.03
26 2 0.05
27 10 0.26
28 4 0.11
ACGTcount: A:0.19, C:0.17, G:0.33, T:0.30
Consensus pattern (20 bp):
TCGTTGAGTTGAGTCCGAGT
Found at i:55851510 original size:93 final size:93
Alignment explanation
Indices: 55851351--55851519 Score: 250
Period size: 93 Copynumber: 1.8 Consensus size: 93
55851341 ATGGTTGAGC
* ** * *
55851351 ATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATCGATGCGAATGTCCGAACTCGTTGAGTTG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATCGATGCGAATCACCCAACTCATTGAGTTG
55851416 AGTCCGAGTTCGTGAGATGTGACTAGGA
66 AGTCCGAGTTCGTGAGATGTGACTAGGA
* *
55851444 ATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-CACCCAAGCTCATTGAGTT
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATCGATGCGAATCACCCAA-CTCATTGAGTT
*
55851508 GAGTTCGAGTTC
65 GAGTCCGAGTTC
55851520 ACTTAGGGGC
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
92 4 0.06
93 63 0.94
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (93 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATCGATGCGAATCACCCAACTCATTGAGTTG
AGTCCGAGTTCGTGAGATGTGACTAGGA
Found at i:55853902 original size:16 final size:16
Alignment explanation
Indices: 55853881--55853927 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
55853871 GAAAATTCGG
55853881 GATTTCAGGATTTTTA
1 GATTTCAGGATTTTTA
*
55853897 GATTTC-GAGATTTTTG
1 GATTTCAG-GATTTTTA
*
55853913 GATTTTAGGATTTTT
1 GATTTCAGGATTTTT
55853928 GGGGAGTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 1 0.04
16 25 0.93
17 1 0.04
ACGTcount: A:0.21, C:0.04, G:0.21, T:0.53
Consensus pattern (16 bp):
GATTTCAGGATTTTTA
Found at i:55854571 original size:24 final size:24
Alignment explanation
Indices: 55854539--55854587 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
55854529 AATACCAGGG
55854539 AAAGATAGAGCAATGTCGATCATA
1 AAAGATAGAGCAATGTCGATCATA
55854563 AAAGATAGAGCAATGTCGATCATA
1 AAAGATAGAGCAATGTCGATCATA
55854587 A
1 A
55854588 CCTAAATAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.12, G:0.20, T:0.20
Consensus pattern (24 bp):
AAAGATAGAGCAATGTCGATCATA
Found at i:55857248 original size:43 final size:43
Alignment explanation
Indices: 55857200--55857299 Score: 155
Period size: 43 Copynumber: 2.3 Consensus size: 43
55857190 ATGTCCCCGA
* * * * *
55857200 TATGGTCATACATGTAATTTCATATCGATGCCAATAGCCCAGC
1 TATGGTCTTACACGAAATCTCATAGCGATGCCAATAGCCCAGC
55857243 TATGGTCTTACACGAAATCTCATAGCGATGCCAATAGCCCAGC
1 TATGGTCTTACACGAAATCTCATAGCGATGCCAATAGCCCAGC
55857286 TATGGTCTTACACG
1 TATGGTCTTACACG
55857300 TATTATAATC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (43 bp):
TATGGTCTTACACGAAATCTCATAGCGATGCCAATAGCCCAGC
Found at i:55857375 original size:41 final size:41
Alignment explanation
Indices: 55857312--55857414 Score: 134
Period size: 41 Copynumber: 2.5 Consensus size: 41
55857302 TTATAATCTT
* * ** *
55857312 GCACACTAAGTGCCATACATAGCTGAAGCTATCTCATTCTC
1 GCACACTAAGTGTCATATATAGCCAAAGCTATCTCAGTCTC
* * *
55857353 GCACACTAAGTATCGTATATAGCCAAAGCTATCTCGGTCTC
1 GCACACTAAGTGTCATATATAGCCAAAGCTATCTCAGTCTC
55857394 GCACACTAAGTGTCATATATA
1 GCACACTAAGTGTCATATATA
55857415 TATTCGAATC
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (41 bp):
GCACACTAAGTGTCATATATAGCCAAAGCTATCTCAGTCTC
Found at i:55861333 original size:14 final size:14
Alignment explanation
Indices: 55861314--55861347 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
55861304 TTCAGTGGAG
55861314 AGATGAGCTAATGA
1 AGATGAGCTAATGA
55861328 AGATGAGCTAATGA
1 AGATGAGCTAATGA
55861342 AGATGA
1 AGATGA
55861348 TACATTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.44, C:0.06, G:0.29, T:0.21
Consensus pattern (14 bp):
AGATGAGCTAATGA
Found at i:55862742 original size:40 final size:40
Alignment explanation
Indices: 55862698--55862796 Score: 135
Period size: 40 Copynumber: 2.4 Consensus size: 40
55862688 CGACTATTTG
* *
55862698 TGGCACTTAGTGTGCGATTCGACTTAGCTTCGGCTATATA
1 TGGCACTTAGTGTGCGATTCGACATAGCTTCAGCTATATA
* * *
55862738 TGGCACTTAGTGTGCGATTTGAGATAGCTTCAGCTATGTA
1 TGGCACTTAGTGTGCGATTCGACATAGCTTCAGCTATATA
55862778 TGGCACACTTAGTGTGCGA
1 TGG--CACTTAGTGTGCGA
55862797 GATATTGAGT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
40 38 0.73
42 14 0.27
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.33
Consensus pattern (40 bp):
TGGCACTTAGTGTGCGATTCGACATAGCTTCAGCTATATA
Found at i:55862820 original size:28 final size:28
Alignment explanation
Indices: 55862783--55862864 Score: 103
Period size: 28 Copynumber: 2.9 Consensus size: 28
55862773 ATGTATGGCA
* *
55862783 CACTTAGTGTGCGAGATATTGAGTGTGG
1 CACTTAGTGTGCGAGATATTGAGTATGC
* * *
55862811 CACTTAGTGTGCAAGATATCGCGTATGC
1 CACTTAGTGTGCGAGATATTGAGTATGC
55862839 CACTTAGTGTGCGAGGA-ATTGAGTAT
1 CACTTAGTGTGCGA-GATATTGAGTAT
55862865 TCAACGGCAT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
28 43 0.96
29 2 0.04
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.30
Consensus pattern (28 bp):
CACTTAGTGTGCGAGATATTGAGTATGC
Found at i:55869076 original size:43 final size:43
Alignment explanation
Indices: 55868978--55869100 Score: 160
Period size: 43 Copynumber: 2.9 Consensus size: 43
55868968 TGATGCCACT
* * * *
55868978 GTCCCAGACAGGGTCTTACACG-AATCAAATA-CGATGCTGAT
1 GTCCCAGACATGGTCTTACACGTAATCACATATCGATGCTAAC
*
55869019 GTTCCAGACATGGTCTTACACGTAATCACATATCGATGCTAAC
1 GTCCCAGACATGGTCTTACACGTAATCACATATCGATGCTAAC
* * *
55869062 GTCCCAGGCGTGGTCTTACACGTAATCACATATCAATGC
1 GTCCCAGACATGGTCTTACACGTAATCACATATCGATGC
55869101 ACAAGAACAC
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
41 20 0.28
42 8 0.11
43 43 0.61
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACACGTAATCACATATCGATGCTAAC
Found at i:55880129 original size:22 final size:22
Alignment explanation
Indices: 55880090--55880132 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
55880080 ATCACTCTTC
* *
55880090 CTCTCCTTTTATTTTTCTTTTT
1 CTCTCCATTTATTATTCTTTTT
*
55880112 CTCTCCATTTGTTATTCTTTT
1 CTCTCCATTTATTATTCTTTT
55880133 CTTCTTCTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.07, C:0.23, G:0.02, T:0.67
Consensus pattern (22 bp):
CTCTCCATTTATTATTCTTTTT
Found at i:55881414 original size:27 final size:27
Alignment explanation
Indices: 55881374--55881485 Score: 129
Period size: 27 Copynumber: 4.1 Consensus size: 27
55881364 AGGAAGCGTC
*
55881374 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
55881401 CTGGTGGCTCTGCCACATATT-TCTGTT
1 CTGGTGGCTCTGCCACA-ATTATCTGAT
* *
55881428 ATGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* * *
55881456 CTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
55881482 CTGG
1 CTGG
55881486 CAGCCATGCT
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
26 8 0.11
27 48 0.66
28 17 0.23
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:55881480 original size:54 final size:54
Alignment explanation
Indices: 55881375--55881481 Score: 153
Period size: 54 Copynumber: 2.0 Consensus size: 54
55881365 GGAAGCGTCC
* *
55881375 TGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATTTCTGTTA
1 TGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTTA
* * *
55881429 TGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 TGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
55881482 CTGGCAGCCA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
54 29 0.62
55 18 0.38
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (54 bp):
TGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTTA
Found at i:55883509 original size:42 final size:43
Alignment explanation
Indices: 55883401--55883562 Score: 136
Period size: 43 Copynumber: 3.8 Consensus size: 43
55883391 AGCATATACA
* * *
55883401 ATGCCAAC-GTCCCAGACGTGGTATTACATGCAATCAAACATCG
1 ATGCC-ACTGTCCCAGACATGGTCTTACATGAAATCAAACATCG
* * *
55883444 ATGCCACTGTCCCAGACAGGGTCTTACATGAAATCAGATAT-G
1 ATGCCACTGTCCCAGACATGGTCTTACATGAAATCAAACATCG
* * *
55883486 ATGTCGA-TGTCCCAGACATGGTCTTACACGTAAAACAAA-AGTCG
1 ATG-CCACTGTCCCAGACATGGTCTTACATG-AAATCAAACA-TCG
** *
55883530 ATGCCAAC-GTCCCAGATGTGGTCTTACACGAAA
1 ATGCC-ACTGTCCCAGACATGGTCTTACATGAAA
55883563 ACACATATCG
Statistics
Matches: 98, Mismatches: 14, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
42 28 0.29
43 45 0.46
44 25 0.26
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.22
Consensus pattern (43 bp):
ATGCCACTGTCCCAGACATGGTCTTACATGAAATCAAACATCG
Found at i:55888948 original size:43 final size:44
Alignment explanation
Indices: 55888820--55888987 Score: 136
Period size: 43 Copynumber: 4.0 Consensus size: 44
55888810 ATATCGTACA
* ** *
55888820 ATGCCAACGTCCCAGACGTGGTCTTACA-TACTATCTCATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACTAGAATCACATATCG
* * * * * * *
55888863 ATGCC-ACTATTCTAGAGAGGGT-GTACAC--GAATCAAATA-CG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACTAGAATCACATATCG
* * * *
55888903 ATGCCGATGTCCTAGACATGGTCTTACA-TATAATCACATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACTAGAATCACATATCG
55888946 ATGCCAACGTCCCAGACATGGTCTTACACTAGAA-CACATATC
1 ATGCCAACGTCCCAGACATGGTCTTACACTAGAATCACATATC
55888988 AGAAACCCTA
Statistics
Matches: 94, Mismatches: 23, Indels: 16
0.71 0.17 0.12
Matches are distributed among these distances:
40 17 0.18
41 11 0.12
42 14 0.15
43 48 0.51
44 4 0.04
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (44 bp):
ATGCCAACGTCCCAGACATGGTCTTACACTAGAATCACATATCG
Found at i:55889678 original size:25 final size:24
Alignment explanation
Indices: 55889624--55889678 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
55889614 ATAGCATCAC
*
55889624 AAAAATCAAATATTCATCAATAGT
1 AAAAATCAAATATTCATCAAAAGT
* *
55889648 ATAAATCAAAATATTCATTAAAA-T
1 AAAAATC-AAATATTCATCAAAAGT
55889672 GAAAAAT
1 -AAAAAT
55889679 TCATGCATGG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.58, C:0.09, G:0.04, T:0.29
Consensus pattern (24 bp):
AAAAATCAAATATTCATCAAAAGT
Found at i:55893083 original size:43 final size:43
Alignment explanation
Indices: 55893018--55893283 Score: 347
Period size: 43 Copynumber: 6.2 Consensus size: 43
55893008 TCCCAGACAG
* * * * *
55893018 GGTCTTACTCATAAACACATATCGATGCCAACGTCTCAGACAT
1 GGTCTTACACGTAATCATATATCGATGCCAACGTCTCAGACGT
*
55893061 GGTCTTACACGTAATCATATATCGATGCCAACGTCCCAGACGT
1 GGTCTTACACGTAATCATATATCGATGCCAACGTCTCAGACGT
* * * *
55893104 GGTCTTACACGTAATTACATATCGATGCCAACCTCTCAGGCGT
1 GGTCTTACACGTAATCATATATCGATGCCAACGTCTCAGACGT
*
55893147 GGTCTTATACGTAATCATATATCGATGCCAACGTCTCAGACGT
1 GGTCTTACACGTAATCATATATCGATGCCAACGTCTCAGACGT
*
55893190 GGTCTTACACGCAATCATATATC-AGTGCCAACGTC-CTAGACGT
1 GGTCTTACACGTAATCATATATCGA-TGCCAACGTCTC-AGACGT
* * * * *
55893233 GGTCTTACATGTAATCATATATCAATGCCAACGTATTAAACGT
1 GGTCTTACACGTAATCATATATCGATGCCAACGTCTCAGACGT
55893276 GGTCTTAC
1 GGTCTTAC
55893284 TCGCATACAC
Statistics
Matches: 196, Mismatches: 23, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
42 2 0.01
43 193 0.98
44 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (43 bp):
GGTCTTACACGTAATCATATATCGATGCCAACGTCTCAGACGT
Found at i:55894588 original size:21 final size:22
Alignment explanation
Indices: 55894564--55894604 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
55894554 ATTTCGATAA
*
55894564 AATTATTGTAAAA-AATTATAT
1 AATTATTATAAAATAATTATAT
55894585 AATTATTATAAAATAATTAT
1 AATTATTATAAAATAATTAT
55894605 TTTGGACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
AATTATTATAAAATAATTATAT
Found at i:55894656 original size:22 final size:22
Alignment explanation
Indices: 55894625--55894668 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
55894615 AATTATTAAC
*
55894625 ATAATGAATTTTAAATAATTTT
1 ATAATAAATTTTAAATAATTTT
*
55894647 ATAATAAATTTTGAATAATTTT
1 ATAATAAATTTTAAATAATTTT
55894669 GATCATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (22 bp):
ATAATAAATTTTAAATAATTTT
Found at i:55904000 original size:30 final size:30
Alignment explanation
Indices: 55903965--55904044 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
55903955 CAAGAAAACT
*
55903965 GAATAAAGAAATCCAAGATAGAGAAACCCA
1 GAATAAAGAAATCCAAGATAAAGAAACCCA
* *
55903995 GAATAAAGAAATCC-AGAATAAAGAGATCCA
1 GAATAAAGAAATCCAAG-ATAAAGAAACCCA
* *
55904025 GGATAAAGAAACCCAAGATA
1 GAATAAAGAAATCCAAGATA
55904045 CAATACTATG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
29 2 0.05
30 39 0.91
31 2 0.05
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.11
Consensus pattern (30 bp):
GAATAAAGAAATCCAAGATAAAGAAACCCA
Found at i:55904004 original size:15 final size:15
Alignment explanation
Indices: 55903965--55904035 Score: 90
Period size: 15 Copynumber: 4.7 Consensus size: 15
55903955 CAAGAAAACT
55903965 GAATAAAGAAATCCA
1 GAATAAAGAAATCCA
* *
55903980 -AGATAGAGAAACCCA
1 GA-ATAAAGAAATCCA
55903995 GAATAAAGAAATCCA
1 GAATAAAGAAATCCA
*
55904010 GAATAAAGAGATCCA
1 GAATAAAGAAATCCA
*
55904025 GGATAAAGAAA
1 GAATAAAGAAA
55904036 CCCAAGATAC
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
14 1 0.02
15 45 0.96
16 1 0.02
ACGTcount: A:0.58, C:0.13, G:0.18, T:0.11
Consensus pattern (15 bp):
GAATAAAGAAATCCA
Found at i:55904044 original size:15 final size:15
Alignment explanation
Indices: 55903967--55904044 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
55903957 AGAAAACTGA
55903967 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
55903982 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
55903996 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
55904011 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
55904027 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
55904042 ATA
1 ATA
55904045 CAATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:55910298 original size:14 final size:14
Alignment explanation
Indices: 55910279--55910308 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
55910269 AAATCAAAGG
55910279 GATGGAGATTTAGA
1 GATGGAGATTTAGA
*
55910293 GATGGAGCTTTAGA
1 GATGGAGATTTAGA
55910307 GA
1 GA
55910309 AGCAAGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.03, G:0.37, T:0.27
Consensus pattern (14 bp):
GATGGAGATTTAGA
Found at i:55910395 original size:14 final size:14
Alignment explanation
Indices: 55910376--55910405 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
55910366 AATGGTGGAA
*
55910376 GGATTTTGATTTGG
1 GGATTTCGATTTGG
55910390 GGATTTCGATTTGG
1 GGATTTCGATTTGG
55910404 GG
1 GG
55910406 GAAAAATTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.03, G:0.40, T:0.43
Consensus pattern (14 bp):
GGATTTCGATTTGG
Found at i:55911573 original size:30 final size:30
Alignment explanation
Indices: 55911537--55911597 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
55911527 AATTGTAGTT
55911537 CATGTTTCAAAGGTTTAGACATTTTTCTTC
1 CATGTTTCAAAGGTTTAGACATTTTTCTTC
55911567 CATGTTTCAAAGGTTTAGACATTTTTCTTC
1 CATGTTTCAAAGGTTTAGACATTTTTCTTC
55911597 C
1 C
55911598 CTTTCAAACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.46
Consensus pattern (30 bp):
CATGTTTCAAAGGTTTAGACATTTTTCTTC
Found at i:55911836 original size:16 final size:15
Alignment explanation
Indices: 55911793--55911839 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
55911783 AGGGGTTATA
*
55911793 GTTTAGTGTTTAAGG
1 GTTTAGTGTTTTAGG
*
55911808 GTTTTAG-GATTTAGAG
1 G-TTTAGTGTTTTAG-G
55911824 GTTTAGTGTTTTAGG
1 GTTTAGTGTTTTAGG
55911839 G
1 G
55911840 GTTATAGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.19, C:0.00, G:0.34, T:0.47
Consensus pattern (15 bp):
GTTTAGTGTTTTAGG
Found at i:55911842 original size:16 final size:16
Alignment explanation
Indices: 55911793--55911842 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
55911783 AGGGGTTATA
*
55911793 GTTTAGTGTTTAAGGG
1 GTTTAGTGTTTTAGGG
* * *
55911809 TTTTAG-GATTTAGAG
1 GTTTAGTGTTTTAGGG
55911824 GTTTAGTGTTTTAGGG
1 GTTTAGTGTTTTAGGG
55911840 GTT
1 GTT
55911843 ATAGATTAGT
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
15 11 0.42
16 15 0.58
ACGTcount: A:0.18, C:0.00, G:0.34, T:0.48
Consensus pattern (16 bp):
GTTTAGTGTTTTAGGG
Found at i:55911993 original size:40 final size:41
Alignment explanation
Indices: 55911943--55912046 Score: 138
Period size: 41 Copynumber: 2.5 Consensus size: 41
55911933 CTGGTTTTTA
* * ***
55911943 GCTCTAGTTTTTAGCGGCGTTTT-ACCAAAAGCGTTGCTAAT
1 GCTCT-GTTTTTAGCGGCGTTTTAACAAAAAACCCCGCTAAT
*
55911984 GCTCTGTTTTTAGCGGCGTTTTAACAAAAAACCCCGCTATT
1 GCTCTGTTTTTAGCGGCGTTTTAACAAAAAACCCCGCTAAT
55912025 GCTCTGTTTTTAGCGGCGTTTT
1 GCTCTGTTTTTAGCGGCGTTTT
55912047 TGGTAAAACG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
40 17 0.30
41 39 0.70
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
GCTCTGTTTTTAGCGGCGTTTTAACAAAAAACCCCGCTAAT
Found at i:55912066 original size:40 final size:40
Alignment explanation
Indices: 55911943--55912077 Score: 119
Period size: 41 Copynumber: 3.3 Consensus size: 40
55911933 CTGGTTTTTA
* * ** *
55911943 GCTCTAGTTTTTAGCGGCG-TTTTACCAAAAGCGTTGCTAAT
1 GCTCT-GTTTTTAGCGGCGTTTTTA-AAAAAACGCAGCTATT
* * *
55911984 GCTCTGTTTTTAGCGGCGTTTTAACAAAAAACCCCGCTATT
1 GCTCTGTTTTTAGCGGCGTTTTTA-AAAAAACGCAGCTATT
***
55912025 GCTCTGTTTTTAGCGGCGTTTTTGGTAAAACGCAGCTATT
1 GCTCTGTTTTTAGCGGCGTTTTTAAAAAAACGCAGCTATT
*
55912065 GCTCCGTGTTTTA
1 GCTCTGT-TTTTA
55912078 TAATTTTTAC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 31 0.40
41 47 0.60
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (40 bp):
GCTCTGTTTTTAGCGGCGTTTTTAAAAAAACGCAGCTATT
Found at i:55912116 original size:12 final size:12
Alignment explanation
Indices: 55912101--55912126 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
55912091 GTTTTTTGAT
55912101 AAAACGCCGCTA
1 AAAACGCCGCTA
55912113 AAAACGCCGCTA
1 AAAACGCCGCTA
55912125 AA
1 AA
55912127 GCCCTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAAACGCCGCTA
Found at i:55913986 original size:24 final size:24
Alignment explanation
Indices: 55913941--55913986 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
55913931 AAAGAATAAT
* *
55913941 TTAAATACTACTTACAATAAAAAA
1 TTAAATACAACTTACAAAAAAAAA
55913965 TTAAATACCAACTTA-AAAAAAA
1 TTAAATA-CAACTTACAAAAAAA
55913987 TTGGTATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.61, C:0.13, G:0.00, T:0.26
Consensus pattern (24 bp):
TTAAATACAACTTACAAAAAAAAA
Found at i:55937774 original size:53 final size:53
Alignment explanation
Indices: 55937711--55937821 Score: 168
Period size: 53 Copynumber: 2.1 Consensus size: 53
55937701 TTTTTGTCAT
* *
55937711 GGGCGACCACAGGGGCATGTCTAGGCCGTGTGAAGGACACGGGCCAGGGACAC
1 GGGCGACCACAGAGGCATGTCTAAGCCGTGTGAAGGACACGGGCCAGGGACAC
* * * *
55937764 GGGCGACCACATAGTCGTGTCTAAGCCGTGTGAAGGGCACGGGCCAGGGACAC
1 GGGCGACCACAGAGGCATGTCTAAGCCGTGTGAAGGACACGGGCCAGGGACAC
55937817 GGGCG
1 GGGCG
55937822 TGTGCTTGGC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.22, C:0.26, G:0.41, T:0.11
Consensus pattern (53 bp):
GGGCGACCACAGAGGCATGTCTAAGCCGTGTGAAGGACACGGGCCAGGGACAC
Found at i:55953443 original size:70 final size:70
Alignment explanation
Indices: 55953330--55953471 Score: 275
Period size: 70 Copynumber: 2.0 Consensus size: 70
55953320 TGAATTAAAA
*
55953330 AGCCAAATTAAAAGCCAATTTTTGCTCATCTTTTACCCCATGGAATGTGCCAAGAAGAAACCATG
1 AGCCAAATTAAAAGCCAATTTTTGCTCATCTTTTACCCCATGGAATGTACCAAGAAGAAACCATG
55953395 GCTAG
66 GCTAG
55953400 AGCCAAATTAAAAGCCAATTTTTGCTCATCTTTTACCCCATGGAATGTACCAAGAAGAAACCATG
1 AGCCAAATTAAAAGCCAATTTTTGCTCATCTTTTACCCCATGGAATGTACCAAGAAGAAACCATG
55953465 GCTAG
66 GCTAG
55953470 AG
1 AG
55953472 TTTTTCAAGC
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (70 bp):
AGCCAAATTAAAAGCCAATTTTTGCTCATCTTTTACCCCATGGAATGTACCAAGAAGAAACCATG
GCTAG
Found at i:55954318 original size:42 final size:41
Alignment explanation
Indices: 55954243--55954396 Score: 193
Period size: 42 Copynumber: 3.7 Consensus size: 41
55954233 CGAGGATTAT
**
55954243 GTGTAAGACCATATCT-GGATATGGCATTAATATGAGACTTC
1 GTGTAAGACCATATCTGGGATATGGCATCGATATGAGA-TTC
*
55954284 GTGTAAGACCATATCTGGGATATGACATCGATATGAGATTTC
1 GTGTAAGACCATATCTGGGATATGGCATCGATATGAGA-TTC
* * * *
55954326 GTGTAAGACCATAGCTAGGCTATTGGCATCGATACGAGATTAC
1 GTGTAAGACCATATCTGGGATA-TGGCATCGATATGAGATT-C
*
55954369 ATGTAAGACCATATCTGGGATATGGCAT
1 GTGTAAGACCATATCTGGGATATGGCAT
55954397 TGGTATGGTA
Statistics
Matches: 97, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
41 16 0.16
42 48 0.49
43 33 0.34
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (41 bp):
GTGTAAGACCATATCTGGGATATGGCATCGATATGAGATTC
Found at i:55954415 original size:85 final size:83
Alignment explanation
Indices: 55954243--55954415 Score: 188
Period size: 85 Copynumber: 2.1 Consensus size: 83
55954233 CGAGGATTAT
* * * *
55954243 GTGTAAGACCATATCTGGATATGGCATTAATATGAGACTTCGTGTAAGACCATATCTGGGATATG
1 GTGTAAGACCATAGCTGGATATGGCATCAATACGAGACTTCATGTAAGACCATATCTGGGATATG
* **
55954308 ACATCGATATGAGATTTC
66 ACATCGATATGAGACTGA
* *
55954326 GTGTAAGACCATAGCTAGGCTATTGGCATCGATACGAGA-TTACATGTAAGACCATATCTGGGAT
1 GTGTAAGACCATAGCT-GGATA-TGGCATCAATACGAGACTT-CATGTAAGACCATATCTGGGAT
* * *
55954390 ATGGCATTGGTATG-GTACTGA
63 ATGACATCGATATGAG-ACTGA
55954411 GTGTA
1 GTGTA
55954416 CGGGGCTCCT
Statistics
Matches: 74, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
83 15 0.20
84 7 0.09
85 52 0.70
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (83 bp):
GTGTAAGACCATAGCTGGATATGGCATCAATACGAGACTTCATGTAAGACCATATCTGGGATATG
ACATCGATATGAGACTGA
Found at i:55954449 original size:22 final size:22
Alignment explanation
Indices: 55954421--55954465 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
55954411 GTGTACGGGG
55954421 CTCCTAAATATCCTTTAGTATT
1 CTCCTAAATATCCTTTAGTATT
55954443 CTCCTAAATATCCTTTAGTATT
1 CTCCTAAATATCCTTTAGTATT
55954465 C
1 C
55954466 CAAGTGGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.24, G:0.04, T:0.44
Consensus pattern (22 bp):
CTCCTAAATATCCTTTAGTATT
Found at i:55958726 original size:71 final size:71
Alignment explanation
Indices: 55958638--55958804 Score: 298
Period size: 71 Copynumber: 2.4 Consensus size: 71
55958628 ATGAATTTTC
55958638 ATCCAATTAATACGTGAACCTAATTCCTTAGGTATTCACACGTACTAATAATCGCTTCACGTTTG
1 ATCCAATTAATACGTGAACCTAATTCCTTAGGTATTCACACGTACTAATAATCGCTTCACGTTTG
55958703 GTCATA
66 GTCATA
* * *
55958709 ATCCAATTAATATGTGAACCTGATTCCTTAGGTATTCACACGTACTAATGATCGCTTCACGTTTG
1 ATCCAATTAATACGTGAACCTAATTCCTTAGGTATTCACACGTACTAATAATCGCTTCACGTTTG
55958774 GTCATA
66 GTCATA
*
55958780 ATCCAATTAATACATGAACCTAATT
1 ATCCAATTAATACGTGAACCTAATT
55958805 TATGCTTGAT
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 90 1.00
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.34
Consensus pattern (71 bp):
ATCCAATTAATACGTGAACCTAATTCCTTAGGTATTCACACGTACTAATAATCGCTTCACGTTTG
GTCATA
Found at i:55969993 original size:18 final size:18
Alignment explanation
Indices: 55969970--55970044 Score: 73
Period size: 18 Copynumber: 4.2 Consensus size: 18
55969960 ATATAGTTTA
55969970 GATATGAAGTTTTGTTAT
1 GATATGAAGTTTTGTTAT
* * *
55969988 GATATGAAGATCTGTTCT
1 GATATGAAGTTTTGTTAT
*
55970006 GATATTG-AGTTTTGATAT
1 GATA-TGAAGTTTTGTTAT
*
55970024 GATATGGAA-TTTTGTTGT
1 GATAT-GAAGTTTTGTTAT
55970042 GAT
1 GAT
55970045 TTAGAGTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
17 1 0.02
18 41 0.91
19 3 0.07
ACGTcount: A:0.27, C:0.03, G:0.24, T:0.47
Consensus pattern (18 bp):
GATATGAAGTTTTGTTAT
Found at i:55970052 original size:36 final size:36
Alignment explanation
Indices: 55969977--55970076 Score: 89
Period size: 36 Copynumber: 2.8 Consensus size: 36
55969967 TTAGATATGA
* * * *
55969977 AGTTTTGTTATGATAT-GAAGATCTGTTCTGATATTG
1 AGTTTTGATATGATATGGAA-TTTTGTTGTGATATTG
55970013 AGTTTTGATATGATATGGAATTTTGTTGTGAT-TTAG
1 AGTTTTGATATGATATGGAATTTTGTTGTGATATT-G
* * *
55970049 AGTTCT-ATTATCATCTGGAATTTTGTTG
1 AGTTTTGA-TATGATATGGAATTTTGTTG
55970077 CCTTCGGGCT
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
35 3 0.06
36 48 0.89
37 3 0.06
ACGTcount: A:0.24, C:0.05, G:0.22, T:0.49
Consensus pattern (36 bp):
AGTTTTGATATGATATGGAATTTTGTTGTGATATTG
Found at i:55970167 original size:34 final size:34
Alignment explanation
Indices: 55970118--55970182 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
55970108 GATACCTTAG
* *
55970118 CACTTACGTGTTCTCTGGTGTTTTGGA-GGATTAA
1 CACTTACGTGCTCTCTAGTG-TTTGGATGGATTAA
*
55970152 CACTTATGTGCTCTCTAGTGTTTGGATGGAT
1 CACTTACGTGCTCTCTAGTGTTTGGATGGAT
55970183 CCTATACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 6 0.22
34 21 0.78
ACGTcount: A:0.17, C:0.15, G:0.26, T:0.42
Consensus pattern (34 bp):
CACTTACGTGCTCTCTAGTGTTTGGATGGATTAA
Found at i:55975761 original size:47 final size:47
Alignment explanation
Indices: 55975705--55975798 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
55975695 GGTAAAAGAA
55975705 TGAATTATATTGATAGACTAAGCACTAAAAGGTTATGTTGAGATTAC
1 TGAATTATATTGATAGACTAAGCACTAAAAGGTTATGTTGAGATTAC
*
55975752 TGAATTATATTGATAGACTAAGCACTAATAGGTTATGTTGAGATTAC
1 TGAATTATATTGATAGACTAAGCACTAAAAGGTTATGTTGAGATTAC
55975799 CTTGACTCTT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (47 bp):
TGAATTATATTGATAGACTAAGCACTAAAAGGTTATGTTGAGATTAC
Found at i:55979356 original size:25 final size:24
Alignment explanation
Indices: 55979328--55979374 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
55979318 TTTTGTTAAA
55979328 AAAAAGGTT-AAAAATAAAAAAAACT
1 AAAAA-GTTGAAAAA-AAAAAAAACT
*
55979353 AAAAATTTGAAAAAAAAAAAAA
1 AAAAAGTTGAAAAAAAAAAAAA
55979375 TTTGCCTGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (24 bp):
AAAAAGTTGAAAAAAAAAAAAACT
Found at i:55979365 original size:18 final size:17
Alignment explanation
Indices: 55979343--55979378 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 17
55979333 GGTTAAAAAT
55979343 AAAAAAAACTAAAAATTTG
1 AAAAAAAA--AAAAATTTG
55979362 AAAAAAAAAAAAATTTG
1 AAAAAAAAAAAAATTTG
55979379 CCTGACAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
19 8 0.47
ACGTcount: A:0.72, C:0.03, G:0.06, T:0.19
Consensus pattern (17 bp):
AAAAAAAAAAAAATTTG
Found at i:55979513 original size:36 final size:34
Alignment explanation
Indices: 55979470--55979554 Score: 91
Period size: 34 Copynumber: 2.4 Consensus size: 34
55979460 GAAGAAGAAG
* * *
55979470 AAGAAAAAGAA-GAAGAGGACGGCGGGAAAGGAAAGA
1 AAGAAAAAAAAGGAAGAAGACGGAGGG-AAGG-AA-A
*
55979506 AAGAAAAAAAAGGAAGAAGAGGGAGGGAAGGAAA
1 AAGAAAAAAAAGGAAGAAGACGGAGGGAAGGAAA
*
55979540 AAGAAAAATAAGGAA
1 AAGAAAAAAAAGGAA
55979555 AAAAATAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
34 15 0.35
35 2 0.05
36 14 0.33
37 12 0.28
ACGTcount: A:0.61, C:0.02, G:0.35, T:0.01
Consensus pattern (34 bp):
AAGAAAAAAAAGGAAGAAGACGGAGGGAAGGAAA
Found at i:55979699 original size:21 final size:22
Alignment explanation
Indices: 55979662--55979705 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
55979652 ATAATTAAAG
55979662 TGTTAAAAATATAAATTT-TTT
1 TGTTAAAAATATAAATTTGTTT
*
55979683 TGTTATAAAAT-TTAATTTGTTT
1 TGTTA-AAAATATAAATTTGTTT
55979705 T
1 T
55979706 TATTATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (22 bp):
TGTTAAAAATATAAATTTGTTT
Found at i:55979705 original size:23 final size:22
Alignment explanation
Indices: 55979662--55979711 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
55979652 ATAATTAAAG
55979662 TGTTA-AAAATATAAATTTTTT
1 TGTTATAAAATATAAATTTTTT
* *
55979683 TGTTATAAAATTTAATTTGTTTT
1 TGTTATAAAATATAAATT-TTTT
*
55979706 TATTAT
1 TGTTAT
55979712 TATTGTTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 5 0.21
22 10 0.42
23 9 0.38
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (22 bp):
TGTTATAAAATATAAATTTTTT
Found at i:55979744 original size:7 final size:7
Alignment explanation
Indices: 55979732--55979775 Score: 88
Period size: 7 Copynumber: 6.3 Consensus size: 7
55979722 TTAATTTGAA
55979732 TTTAATT
1 TTTAATT
55979739 TTTAATT
1 TTTAATT
55979746 TTTAATT
1 TTTAATT
55979753 TTTAATT
1 TTTAATT
55979760 TTTAATT
1 TTTAATT
55979767 TTTAATT
1 TTTAATT
55979774 TT
1 TT
55979776 ATTTTTATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTAATT
Found at i:55979758 original size:21 final size:20
Alignment explanation
Indices: 55979732--55979782 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 20
55979722 TTAATTTGAA
55979732 TTTAATTTTTAATTTTTAATT
1 TTTAATTTTTAATTTTTAA-T
55979753 TTTAATTTTTAATTTTTAAT
1 TTTAATTTTTAATTTTTAAT
55979773 TTT-ATTTTTA
1 TTTAATTTTTA
55979783 TAAGGTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 7 0.23
20 4 0.13
21 19 0.63
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTAATTTTTAATTTTTAAT
Found at i:55979851 original size:21 final size:19
Alignment explanation
Indices: 55979825--55979873 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
55979815 GGTATGTTTG
*
55979825 TATTTATTTTATATTTTTAT
1 TATTTATTTT-TATTTTTAA
*
55979845 TGATTTATAATTTATTTTTAA
1 T-ATTTAT-TTTTATTTTTAA
55979866 TATTTATT
1 TATTTATT
55979874 GGAGTAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
20 7 0.29
21 15 0.62
22 2 0.08
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (19 bp):
TATTTATTTTTATTTTTAA
Found at i:55980125 original size:31 final size:31
Alignment explanation
Indices: 55980087--55980146 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
55980077 ATTATGAGTT
* *
55980087 AAAAAATTATATCAACTTTTAAAATAACATA
1 AAAAAATTATACCAACATTTAAAATAACATA
*
55980118 AAAAAATTATACCGACATTTAAAATAACA
1 AAAAAATTATACCAACATTTAAAATAACA
55980147 ATACATACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (31 bp):
AAAAAATTATACCAACATTTAAAATAACATA
Found at i:55980471 original size:13 final size:13
Alignment explanation
Indices: 55980443--55980483 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
55980433 TTCCCTATCG
*
55980443 CTTCTTTCTTTTTT
1 CTTCTTT-TCTTTT
*
55980457 CTTTTTTTCTTTT
1 CTTCTTTTCTTTT
55980470 CTTCTTTTCTTTT
1 CTTCTTTTCTTTT
55980483 C
1 C
55980484 CGCTGCCCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
13 18 0.75
14 6 0.25
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (13 bp):
CTTCTTTTCTTTT
Found at i:55980478 original size:8 final size:8
Alignment explanation
Indices: 55980448--55980480 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
55980438 TATCGCTTCT
55980448 TTCTTTT-
1 TTCTTTTC
*
55980455 TTCTTTTT
1 TTCTTTTC
55980463 TTCTTTTC
1 TTCTTTTC
55980471 TTCTTTTC
1 TTCTTTTC
55980479 TT
1 TT
55980481 TTCCGCTGCC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
7 7 0.29
8 17 0.71
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (8 bp):
TTCTTTTC
Found at i:55981181 original size:33 final size:30
Alignment explanation
Indices: 55981097--55981158 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
55981087 TTTATAGGCA
55981097 TTTACTTGTTAAGTTGCACCTATCTTAATG
1 TTTACTTGTTAAGTTGCACCTATCTTAATG
55981127 TTTACTTGTTAAGTTGCACCTATCTTAATG
1 TTTACTTGTTAAGTTGCACCTATCTTAATG
55981157 TT
1 TT
55981159 ATTTAAGTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.23, C:0.16, G:0.13, T:0.48
Consensus pattern (30 bp):
TTTACTTGTTAAGTTGCACCTATCTTAATG
Found at i:55982786 original size:47 final size:47
Alignment explanation
Indices: 55982729--55982942 Score: 190
Period size: 47 Copynumber: 4.6 Consensus size: 47
55982719 AGAGCTAATT
*
55982729 TAAGACCATGTCTGGGACATGGCATCGACATTGAGACGAAAGCTAGTG
1 TAAGACCATGTCTGGGACATGGCATCGAC-TCGAGACGAAAGCTAGTG
* * * *
55982777 TAAGA-CATGTTTGGGACAT-GCATCGGCCTCGAGACGTAAGCCAGTG
1 TAAGACCATGTCTGGGACATGGCATC-GACTCGAGACGAAAGCTAGTG
* * * * *
55982823 TAAGA-CATGTCTGGGATAT-GCATTGGCTACGAGATGATAG-TCAGTG
1 TAAGACCATGTCTGGGACATGGCATCGACT-CGAGACGAAAGCT-AGTG
* * * *
55982869 TAAGACCATGTCTGGGACATGGCATC-AGCTTGAGA-TATGAGCTTGTG
1 TAAGACCATGTCTGGGACATGGCATCGA-CTCGAGACGA-AAGCTAGTG
*
55982916 TAAGACCGTGTCTGGGACATGGCATCG
1 TAAGACCATGTCTGGGACATGGCATCG
55982943 GTACCTTACC
Statistics
Matches: 136, Mismatches: 21, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
45 3 0.02
46 59 0.43
47 62 0.46
48 12 0.09
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.24
Consensus pattern (47 bp):
TAAGACCATGTCTGGGACATGGCATCGACTCGAGACGAAAGCTAGTG
Found at i:55982823 original size:46 final size:47
Alignment explanation
Indices: 55982729--55982943 Score: 192
Period size: 46 Copynumber: 4.6 Consensus size: 47
55982719 AGAGCTAATT
* * * *
55982729 TAAGACCATGTCTGGGACATGGCATCGACATTGAGACGAAAGCTAGTG
1 TAAGACCATGTCTGGGACATGGCATCGGCCTCGAGACG-AAGCCAGTG
*
55982777 TAAGA-CATGTTTGGGACAT-GCATCGGCCTCGAGACGTAAGCCAGTG
1 TAAGACCATGTCTGGGACATGGCATCGGCCTCGAGACG-AAGCCAGTG
* * * *
55982823 TAAGA-CATGTCTGGGATAT-GCATTGG-CTACGAGATGATAGTCAGTG
1 TAAGACCATGTCTGGGACATGGCATCGGCCT-CGAGACGA-AGCCAGTG
* * * **
55982869 TAAGACCATGTCTGGGACATGGCATCAG-CTTGAGA-TATGAGCTTGTG
1 TAAGACCATGTCTGGGACATGGCATCGGCCTCGAGACGA--AGCCAGTG
*
55982916 TAAGACCGTGTCTGGGACATGGCATCGG
1 TAAGACCATGTCTGGGACATGGCATCGG
55982944 TACCTTACCC
Statistics
Matches: 140, Mismatches: 22, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
45 3 0.02
46 64 0.46
47 61 0.44
48 12 0.09
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (47 bp):
TAAGACCATGTCTGGGACATGGCATCGGCCTCGAGACGAAGCCAGTG
Found at i:55990821 original size:25 final size:25
Alignment explanation
Indices: 55990793--55990842 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
55990783 CATTGAGTTG
55990793 GTATCAATCAATATCGTTCAATTTC
1 GTATCAATCAATATCGTTCAATTTC
*
55990818 GTATCAATCAATATTGTTCAATTTC
1 GTATCAATCAATATCGTTCAATTTC
55990843 ACATACTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.32, C:0.18, G:0.08, T:0.42
Consensus pattern (25 bp):
GTATCAATCAATATCGTTCAATTTC
Found at i:55993398 original size:17 final size:19
Alignment explanation
Indices: 55993356--55993399 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
55993346 AAGAAATTTT
*
55993356 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
55993375 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
55993393 AA-TATTA
1 AATTATTA
55993400 CTGCATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:56002281 original size:11 final size:11
Alignment explanation
Indices: 56002261--56002297 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
56002251 CGGTCGACAG
56002261 TGGT-TGGCGA
1 TGGTCTGGCGA
56002271 TGGTCTGGCGA
1 TGGTCTGGCGA
*
56002282 TGGTCTGACGA
1 TGGTCTGGCGA
56002293 TGGTC
1 TGGTC
56002298 GAAGGCAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 4 0.16
11 21 0.84
ACGTcount: A:0.11, C:0.16, G:0.43, T:0.30
Consensus pattern (11 bp):
TGGTCTGGCGA
Found at i:56005987 original size:37 final size:37
Alignment explanation
Indices: 56005932--56006034 Score: 161
Period size: 37 Copynumber: 2.8 Consensus size: 37
56005922 GGAAATATAT
56005932 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* * *
56005969 TCCGGGTAAGACCTGATGACTATGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* *
56006006 TCTGGGTAAGACCCGATAACTACGTGTGG
1 TCCGGGTAAGACCCGATGACTACGTGTGG
56006035 GGACTATTCG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:56008003 original size:11 final size:11
Alignment explanation
Indices: 56007973--56008006 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
56007963 AATATTGTAT
56007973 TTATTAATTT-
1 TTATTAATTTA
56007983 TTATTAATTTA
1 TTATTAATTTA
*
56007994 TTATTTATTTA
1 TTATTAATTTA
56008005 TT
1 TT
56008007 CCAAATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 10 0.45
11 12 0.55
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTAATTTA
Done.