Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 154 of 185
Found at i:47496040 original size:107 final size:108
Alignment explanation
Indices: 47495922--47496129 Score: 391
Period size: 107 Copynumber: 1.9 Consensus size: 108
47495912 ATATTTAAAT
*
47495922 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
1 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
*
47495987 TCTTATATGAATTTACTCAAATCATAATATA-GATAATTTAAC
66 TCTTATATGAATTTACTAAAATCATAATATATGATAATTTAAC
47496029 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
1 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
47496094 TCTTATATGAATTTACTAAAATCATAATATATGATA
66 TCTTATATGAATTTACTAAAATCATAATATATGATA
47496130 CTATAAAATA
Statistics
Matches: 98, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
107 94 0.96
108 4 0.04
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (108 bp):
ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
TCTTATATGAATTTACTAAAATCATAATATATGATAATTTAAC
Found at i:47496062 original size:16 final size:16
Alignment explanation
Indices: 47496019--47496064 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
47496009 CATAATATAG
*
47496019 ATAATTTAACATA-ATT
1 ATAA-TTAAAATATATT
*
47496035 ATTATT-AAATATATT
1 ATAATTAAAATATATT
47496050 ATAATTAAAATATAT
1 ATAATTAAAATATAT
47496065 AATTTAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 4 0.16
15 10 0.40
16 11 0.44
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
ATAATTAAAATATATT
Found at i:47496071 original size:14 final size:15
Alignment explanation
Indices: 47496019--47496073 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
47496009 CATAATATAG
47496019 ATAATTTAACATA-ATT
1 ATAA-TTAA-ATATATT
*
47496035 ATTATTAAATATATT
1 ATAATTAAATATATT
47496050 ATAATTAAA-ATA-T
1 ATAATTAAATATATT
*
47496063 ATAATTTAATA
1 ATAATTAAATA
47496074 AAATTCTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 9 0.26
14 7 0.21
15 15 0.44
16 3 0.09
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATTAAATATATT
Found at i:47496122 original size:37 final size:35
Alignment explanation
Indices: 47495953--47496122 Score: 100
Period size: 37 Copynumber: 4.7 Consensus size: 35
47495943 ATAATTAAAA
*
47495953 TATATAATTTAATAAAATTCTTAATAATTAATATTCT
1 TATATAATTTAATAAAA-TCATAATAATTAATATT-T
* *
47495990 TATATGAATTTACTCAAATCATAAT-A-TAGATAATTT
1 TATAT-AATTTAATAAAATCATAATAATTA-AT-ATTT
* * * * *
47496026 AACATAATTATTATTAAATAT-ATTATAATTAA-A--A
1 TATATAA-T-TTAATAAA-ATCATAATAATTAATATTT
* *
47496060 TATATAATTTAATAAAATTCTTAATAATCAATATTCT
1 TATATAATTTAATAAAA-TCATAATAATTAATATT-T
*
47496097 TATATGAATTTACTAAAATCATAATA
1 TATAT-AATTTAATAAAATCATAATA
47496123 TATGATACTA
Statistics
Matches: 100, Mismatches: 18, Indels: 30
0.68 0.12 0.20
Matches are distributed among these distances:
31 1 0.01
32 8 0.08
33 9 0.09
34 6 0.06
35 4 0.04
36 9 0.09
37 36 0.36
38 25 0.25
39 2 0.02
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (35 bp):
TATATAATTTAATAAAATCATAATAATTAATATTT
Found at i:47496175 original size:107 final size:107
Alignment explanation
Indices: 47495943--47496168 Score: 336
Period size: 107 Copynumber: 2.1 Consensus size: 107
47495933 TAAATATATT
* *
47495943 ATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAA
1 ATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAA
* * * *
47496008 TCATAATATAGATAATTTAACATAATTATTATTAAATATATT
66 TCATAATATAGATAATATAAAATAATAATTATGAAATATATT
47496050 ATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAA
1 ATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAA
*
47496115 TCATAATATATGATACTATAAAAT-ATAATT-TGAAATA-ATT
66 TCATAATATA-GATAATATAAAATAATAATTATGAAATATATT
47496155 A-ATATT-AAATATAT
1 ATA-ATTAAAATATAT
47496169 TTTAATTAAT
Statistics
Matches: 110, Mismatches: 7, Indels: 7
0.89 0.06 0.06
Matches are distributed among these distances:
104 9 0.08
105 7 0.06
106 6 0.05
107 78 0.71
108 10 0.09
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.42
Consensus pattern (107 bp):
ATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAA
TCATAATATAGATAATATAAAATAATAATTATGAAATATATT
Found at i:47496211 original size:28 final size:27
Alignment explanation
Indices: 47496135--47496211 Score: 68
Period size: 29 Copynumber: 2.9 Consensus size: 27
47496125 TGATACTATA
* *
47496135 AAATATAATTTGAAATAATTA-ATATT
1 AAATAAAATTTAAAATAATTATATATT
* * *
47496161 AAAT-ATATTTTAATTAATATATATGATT
1 AAATAAAATTTAAAATAAT-TATAT-ATT
*
47496189 TAATAAAATTTAAAATAATTATA
1 AAATAAAATTTAAAATAATTATA
47496212 CCTAATGAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
25 10 0.26
26 6 0.15
27 2 0.05
28 10 0.26
29 11 0.28
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (27 bp):
AAATAAAATTTAAAATAATTATATATT
Found at i:47496317 original size:91 final size:91
Alignment explanation
Indices: 47496222--47496472 Score: 457
Period size: 91 Copynumber: 2.8 Consensus size: 91
47496212 CCTAATGAAT
* * *
47496222 TTTCTTATATGAATTTGTATAATTTAAAATAATTATTATTAAATATAATTTAATAATAATATATA
1 TTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAATGATATATA
47496287 ATTTCATAAAATTCTTGATAATAAAA
66 ATTTCATAAAATTCTTGATAATAAAA
47496313 TTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAATGATATATA
1 TTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAATGATATATA
*
47496378 ATTTCATAAAATTCTTGATAATAAAT
66 ATTTCATAAAATTCTTGATAATAAAA
*
47496404 TTTCTTATATGAATTTATATAATTTAAAATAAATAATATTAAATATAATTTAATAATGATATATA
1 TTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAATGATATATA
47496469 ATTT
66 ATTT
47496473 ATACATTTAA
Statistics
Matches: 155, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
91 155 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (91 bp):
TTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAATGATATATA
ATTTCATAAAATTCTTGATAATAAAA
Found at i:47496320 original size:221 final size:226
Alignment explanation
Indices: 47495922--47496329 Score: 559
Period size: 221 Copynumber: 1.8 Consensus size: 226
47495912 ATATTTAAAT
*
47495922 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
1 ATAATTAATATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
* * *
47495987 TCTTATATGAATTTACTCAAATCATAATATAGATAATTTAACATAATTATTATTAAATATATTAT
66 ACCTATATGAATTTA-TCAAATCATAATATAGATAATTTAAAATAATTATTATTAAATATATTAT
*
47496052 AATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATC
130 AATTAAAATATATAATTTAATAAAATTCTTAATAATAAATATTCTTATATGAATTTACTAAAATC
47496117 ATAATATATGATACTATAAAATATAATTTGAA
195 ATAATATATGATACTATAAAATATAATTTGAA
* * *
47496149 ATAATTAATATTAAATATATTTTAATTAATATATATGATTTAATAAAA-T-TTAA-AA-TAATTA
1 ATAATTAATATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA-TA
** *
47496210 TACCTA-ATGAATTT-TCTTAT-ATGAAT-TTGTATAATTTAAAATAATTATTATTAAATATAAT
65 TACCTATATGAATTTATCAAATCAT-AATATAG-ATAATTTAAAATAATTATTATTAAATAT-AT
* *
47496271 T-TAA-TAATAATATATAATTTCATAAAATTCTTGATAATAAA-ATTTCTTATATGAATTTA
127 TATAATTAA-AATATATAATTTAATAAAATTCTTAATAATAAATA-TTCTTATATGAATTTA
47496330 TATAATTTAA
Statistics
Matches: 162, Mismatches: 13, Indels: 18
0.84 0.07 0.09
Matches are distributed among these distances:
220 8 0.05
221 83 0.51
222 3 0.02
223 11 0.07
224 8 0.05
225 4 0.02
226 1 0.01
227 44 0.27
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (226 bp):
ATAATTAATATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
ACCTATATGAATTTATCAAATCATAATATAGATAATTTAAAATAATTATTATTAAATATATTATA
ATTAAAATATATAATTTAATAAAATTCTTAATAATAAATATTCTTATATGAATTTACTAAAATCA
TAATATATGATACTATAAAATATAATTTGAA
Found at i:47497984 original size:16 final size:17
Alignment explanation
Indices: 47497958--47497990 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
47497948 TAAATTTTTA
*
47497958 GATATAAGTGATAAAGT
1 GATATAAGTGAGAAAGT
47497975 GATA-AAGTGAGAAAGT
1 GATATAAGTGAGAAAGT
47497991 AGGGGGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.48, C:0.00, G:0.27, T:0.24
Consensus pattern (17 bp):
GATATAAGTGAGAAAGT
Found at i:47502069 original size:20 final size:20
Alignment explanation
Indices: 47502044--47502084 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
47502034 TAGGACTAAA
* *
47502044 TAGGAAACATTTGAAAATTT
1 TAGGAAAAAGTTGAAAATTT
47502064 TAGGAAAAAGTTGAAAATTT
1 TAGGAAAAAGTTGAAAATTT
47502084 T
1 T
47502085 GGACTGTAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.02, G:0.17, T:0.34
Consensus pattern (20 bp):
TAGGAAAAAGTTGAAAATTT
Found at i:47502997 original size:40 final size:40
Alignment explanation
Indices: 47502953--47503156 Score: 237
Period size: 40 Copynumber: 5.1 Consensus size: 40
47502943 CACACTAGAT
* * * * *
47502953 AGAAGCTCATAAGAGCTGATCCACCCGAAGCACACCAGAC
1 AGAAGCTCATAAGAGTTGATCCAACCGAAACACGCCAAAC
* *
47502993 AGAAGCTCATAAGAGTTGATCCAACCGTAACATGCCAAAC
1 AGAAGCTCATAAGAGTTGATCCAACCGAAACACGCCAAAC
* * **
47503033 AGAAGATCATAAGAGTTGATTCAATAGAAACACGCCAAAC
1 AGAAGCTCATAAGAGTTGATCCAACCGAAACACGCCAAAC
* * * * *
47503073 AGTAGCTCAGAAGAGCTGATCCAACTGAAACATGCCAAAC
1 AGAAGCTCATAAGAGTTGATCCAACCGAAACACGCCAAAC
* * *
47503113 AAAAGCTCATAAGAGTTGATCCAACCGTAACACGCCTAAC
1 AGAAGCTCATAAGAGTTGATCCAACCGAAACACGCCAAAC
47503153 AGAA
1 AGAA
47503157 AGTATAACAC
Statistics
Matches: 134, Mismatches: 30, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 134 1.00
ACGTcount: A:0.42, C:0.25, G:0.18, T:0.15
Consensus pattern (40 bp):
AGAAGCTCATAAGAGTTGATCCAACCGAAACACGCCAAAC
Found at i:47511982 original size:19 final size:20
Alignment explanation
Indices: 47511955--47511994 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
47511945 GTAAATACAC
* *
47511955 ATATGTTTATAAT-TGATCA
1 ATATATTTAAAATATGATCA
47511974 ATATATTTAAAATATGATCA
1 ATATATTTAAAATATGATCA
47511994 A
1 A
47511995 CATCATATCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (20 bp):
ATATATTTAAAATATGATCA
Found at i:47514160 original size:26 final size:27
Alignment explanation
Indices: 47514101--47514172 Score: 92
Period size: 26 Copynumber: 2.7 Consensus size: 27
47514091 TCATAGTATA
*
47514101 GTAAAAATAAAAATAAAATAATTTTCT
1 GTAAAAATAAAAATAAAATAATTTCCT
47514128 GTAAAAAT-AAAATAAAATAATTTCCT
1 GTAAAAATAAAAATAAAATAATTTCCT
* * *
47514154 TTGAAAAACAAAAAAAAAA
1 GT-AAAAATAAAAATAAAA
47514173 CTAAGATTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
26 18 0.46
27 13 0.33
28 8 0.21
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (27 bp):
GTAAAAATAAAAATAAAATAATTTCCT
Found at i:47514435 original size:26 final size:27
Alignment explanation
Indices: 47514379--47514449 Score: 81
Period size: 26 Copynumber: 2.6 Consensus size: 27
47514369 TTATAATAGT
* *
47514379 AAAAATAAAATAAAACAATTTTCTGT-
1 AAAAATAAAATAAAATAATTTCCTGTA
*
47514405 AAAAATAAAATAAAATAATTTCCTTTGA
1 AAAAATAAAATAAAATAATTTCCTGT-A
* *
47514433 AAAACTAAAAAAAAATA
1 AAAAATAAAATAAAATA
47514450 CTAAGATTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
26 23 0.61
28 15 0.39
ACGTcount: A:0.63, C:0.07, G:0.03, T:0.27
Consensus pattern (27 bp):
AAAAATAAAATAAAATAATTTCCTGTA
Found at i:47515291 original size:43 final size:43
Alignment explanation
Indices: 47515202--47515293 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 43
47515192 CTTGTGGTTG
* * * *
47515202 CTTCCTTTTTTGTTGTTTCTTGGTTGTGGTTGCTTCCATGTTA
1 CTTCCTTTTTTGTCGTTTCTTGGTAGTGGTTGCTTCCACGTAA
** **
47515245 CTTCCTTTTTTGTCGTTTCTTGGTAGTGGTTTTTTTTACGTAA
1 CTTCCTTTTTTGTCGTTTCTTGGTAGTGGTTGCTTCCACGTAA
47515288 CTTCCT
1 CTTCCT
47515294 CTGTCTTTTA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.07, C:0.17, G:0.18, T:0.58
Consensus pattern (43 bp):
CTTCCTTTTTTGTCGTTTCTTGGTAGTGGTTGCTTCCACGTAA
Found at i:47515908 original size:21 final size:22
Alignment explanation
Indices: 47515870--47515911 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
47515860 AATAAATGAA
**
47515870 AAGAAAAATTTTATCCACAACC
1 AAGAAAAATTACATCCACAACC
47515892 AAGAAAAATTACA-CCACAAC
1 AAGAAAAATTACATCCACAAC
47515912 TGGCAAGTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.55, C:0.24, G:0.05, T:0.17
Consensus pattern (22 bp):
AAGAAAAATTACATCCACAACC
Found at i:47523225 original size:106 final size:106
Alignment explanation
Indices: 47523087--47523298 Score: 361
Period size: 106 Copynumber: 2.0 Consensus size: 106
47523077 CATATCAAAT
* * ** **
47523087 GACACGAAACATAACCAATTGGTCACAAACATACATTTACCAAAACCTTATTTACGTGCCACTTA
1 GACACGAAACATAACCAATTGATCACAAACATAAATACACCAAAACCCAATTTACGTGCCACTTA
47523152 AAATTGAGCCAAAATAAACAAATAGATACCAAAAGAGTTGA
66 AAATTGAGCCAAAATAAACAAATAGATACCAAAAGAGTTGA
*
47523193 GACACGAAACATAACCAATTGATCACAAACATAAATACACCAAAACCCAATTTACGTGTCACTTA
1 GACACGAAACATAACCAATTGATCACAAACATAAATACACCAAAACCCAATTTACGTGCCACTTA
47523258 AAATTGAGCCAAAATAAACAAATAGATACCAAAAGAGTTGA
66 AAATTGAGCCAAAATAAACAAATAGATACCAAAAGAGTTGA
47523299 CGGATAGTGC
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
106 99 1.00
ACGTcount: A:0.48, C:0.21, G:0.11, T:0.20
Consensus pattern (106 bp):
GACACGAAACATAACCAATTGATCACAAACATAAATACACCAAAACCCAATTTACGTGCCACTTA
AAATTGAGCCAAAATAAACAAATAGATACCAAAAGAGTTGA
Found at i:47531343 original size:75 final size:74
Alignment explanation
Indices: 47531260--47531399 Score: 174
Period size: 75 Copynumber: 1.9 Consensus size: 74
47531250 AATATACATA
* * * * *
47531260 CATAATCAAAACTTTCACAT-ACATATATAAATTTCATACTTAAATTCATTACAAGAACATATAC
1 CATAATC-AAAC-CTCACATAACATATATAAATGTCATACCTAAATTCAATAAAAGAACATATAC
47531324 ACATAATCTTG
64 ACATAATCTTG
* * *
47531335 CATAATCAAACCTCATATAAACTTATATAAATGTCCTACCTAAATTCAATAAAAGAACATATACA
1 CATAATCAAACCTCACAT-AACATATATAAATGTCATACCTAAATTCAATAAAAGAACATATACA
47531400 TATATGTAAG
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
73 5 0.09
74 4 0.07
75 46 0.84
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.31
Consensus pattern (74 bp):
CATAATCAAACCTCACATAACATATATAAATGTCATACCTAAATTCAATAAAAGAACATATACAC
ATAATCTTG
Found at i:47531675 original size:12 final size:12
Alignment explanation
Indices: 47531658--47531711 Score: 63
Period size: 12 Copynumber: 4.2 Consensus size: 12
47531648 CTCAAAAACT
47531658 TATATATATACA
1 TATATATATACA
*
47531670 TATATATATTCGAA
1 TATATATATAC--A
*
47531684 TATTATACATACA
1 TA-TATATATACA
47531697 TATATATATACA
1 TATATATATACA
47531709 TAT
1 TAT
47531712 CTTTGTCTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
12 22 0.63
13 3 0.09
14 3 0.09
15 7 0.20
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (12 bp):
TATATATATACA
Found at i:47532186 original size:15 final size:15
Alignment explanation
Indices: 47532166--47532197 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
47532156 CAAAATAAGC
47532166 TAGTTTAAATATAAT
1 TAGTTTAAATATAAT
47532181 TAGTTTAAATATAAT
1 TAGTTTAAATATAAT
47532196 TA
1 TA
47532198 CATTCAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (15 bp):
TAGTTTAAATATAAT
Found at i:47536152 original size:30 final size:30
Alignment explanation
Indices: 47536093--47536172 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
47536083 ACACAAAGTG
*
47536093 CTTGGAAACTATAA-CACTAGTACATAGTA
1 CTTGGAAACTATAATCACCAGTACATAGTA
* * *
47536122 CTTGGAAACTGTAATCACCGGTATATAGTA
1 CTTGGAAACTATAATCACCAGTACATAGTA
* *
47536152 CCTGGAAACTAAAATCACCAG
1 CTTGGAAACTATAATCACCAG
47536173 CACCTAGTGC
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 13 0.31
30 29 0.69
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (30 bp):
CTTGGAAACTATAATCACCAGTACATAGTA
Found at i:47539906 original size:6 final size:6
Alignment explanation
Indices: 47539891--47539965 Score: 87
Period size: 6 Copynumber: 12.5 Consensus size: 6
47539881 GCAAATGAAT
* * * * * *
47539891 CATTTA CATTTC CATTTT CATTTT CATTTC CATTTC CGTTTT CATTTT
1 CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC
*
47539939 CATTTC CATTTC CATTTT CATTTC CAT
1 CATTTC CATTTC CATTTC CATTTC CAT
47539966 ATCTAATTTT
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 60 1.00
ACGTcount: A:0.17, C:0.25, G:0.01, T:0.56
Consensus pattern (6 bp):
CATTTC
Found at i:47539913 original size:18 final size:18
Alignment explanation
Indices: 47539891--47539965 Score: 96
Period size: 18 Copynumber: 4.2 Consensus size: 18
47539881 GCAAATGAAT
* *
47539891 CATTTACATTTCCATTTT
1 CATTTTCATTTCCATTTC
47539909 CATTTTCATTTCCATTTC
1 CATTTTCATTTCCATTTC
* *
47539927 CGTTTTCATTTTCATTTC
1 CATTTTCATTTCCATTTC
* *
47539945 CATTTCCATTTTCATTTC
1 CATTTTCATTTCCATTTC
47539963 CAT
1 CAT
47539966 ATCTAATTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 51 1.00
ACGTcount: A:0.17, C:0.25, G:0.01, T:0.56
Consensus pattern (18 bp):
CATTTTCATTTCCATTTC
Found at i:47539918 original size:24 final size:24
Alignment explanation
Indices: 47539890--47539961 Score: 126
Period size: 24 Copynumber: 3.0 Consensus size: 24
47539880 TGCAAATGAA
*
47539890 TCATTTACATTTCCATTTTCATTT
1 TCATTTCCATTTCCATTTTCATTT
*
47539914 TCATTTCCATTTCCGTTTTCATTT
1 TCATTTCCATTTCCATTTTCATTT
47539938 TCATTTCCATTTCCATTTTCATTT
1 TCATTTCCATTTCCATTTTCATTT
47539962 CCATATCTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.17, C:0.24, G:0.01, T:0.58
Consensus pattern (24 bp):
TCATTTCCATTTCCATTTTCATTT
Found at i:47551337 original size:21 final size:21
Alignment explanation
Indices: 47551311--47551367 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
47551301 TTATCGCTTT
*
47551311 CCACACGGGCGTGTGCCTTAGA
1 CCACACGGGCGTGTGCCTCA-A
* *
47551333 -CACACGGTCGTGTTCCTCAA
1 CCACACGGGCGTGTGCCTCAA
*
47551353 CCACATGGGCGTGTG
1 CCACACGGGCGTGTG
47551368 AGTTAGCCAC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.18, C:0.32, G:0.30, T:0.21
Consensus pattern (21 bp):
CCACACGGGCGTGTGCCTCAA
Found at i:47551496 original size:21 final size:21
Alignment explanation
Indices: 47551472--47551519 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
47551462 CACATGGGCG
47551472 TGTGTCTCAGCCACACGGCCA
1 TGTGTCTCAGCCACACGGCCA
* **
47551493 TGTGCCTTTGCCACACGGCCA
1 TGTGTCTCAGCCACACGGCCA
47551514 TGTGTC
1 TGTGTC
47551520 ACTCTCCGCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.15, C:0.35, G:0.25, T:0.25
Consensus pattern (21 bp):
TGTGTCTCAGCCACACGGCCA
Found at i:47554772 original size:3 final size:3
Alignment explanation
Indices: 47554766--47554793 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
47554756 GACCACCACA
47554766 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
47554794 CGACAATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:47569293 original size:54 final size:51
Alignment explanation
Indices: 47569157--47569314 Score: 183
Period size: 51 Copynumber: 3.0 Consensus size: 51
47569147 ATTTTTTTTG
* * * * * *
47569157 GGTGTTGGCACACTAATGGCTGGCACCCTTGTACCAGATTTTAAAAAAATT
1 GGTGCTGGGACACTAATAGCCGGCACTCTTGTACCAGATTTAAAAAAAATT
* *
47569208 GGTGCTGGGACACTAATGGCCGACA-TCCTTGTACCAGAATTTAAAAAAAAATT
1 GGTGCTGGGACACTAATAGCCGGCACT-CTTGTACCAG-ATTT-AAAAAAAATT
* *
47569261 GGATGCTGGGACACTGATAGCCGGCACTCTTGTATCAGATTTAAAAAAAATT
1 GG-TGCTGGGACACTAATAGCCGGCACTCTTGTACCAGATTTAAAAAAAATT
47569313 GG
1 GG
47569315 GGTGTCGAGA
Statistics
Matches: 92, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
51 31 0.34
52 16 0.17
53 15 0.16
54 29 0.32
55 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (51 bp):
GGTGCTGGGACACTAATAGCCGGCACTCTTGTACCAGATTTAAAAAAAATT
Found at i:47569327 original size:53 final size:52
Alignment explanation
Indices: 47569154--47569339 Score: 207
Period size: 53 Copynumber: 3.5 Consensus size: 52
47569144 AAAATTTTTT
* * * * *
47569154 TTGGGTGTTGGCACACTAATGGCTGGCACCCTTGTACCAGATTTTAAAAAAA
1 TTGGGTGCTGGGACACTAATGGCCGGCACTCTTGTACCAGATTTAAAAAAAA
*
47569206 TT-GGTGCTGGGACACTAATGGCCGACA-TCCTTGTACCAGAATTTAAAAAAAAA
1 TTGGGTGCTGGGACACTAATGGCCGGCACT-CTTGTACCAG-ATTT-AAAAAAAA
* * * *
47569259 TTGGATGCTGGGACACTGATAGCCGGCACTCTTGTATCAGATTTAAAAAAAA
1 TTGGGTGCTGGGACACTAATGGCCGGCACTCTTGTACCAGATTTAAAAAAAA
*
47569311 TTGGGGTG-TCGAGACACTAATGGCCGGCA
1 TT-GGGTGCT-GGGACACTAATGGCCGGCA
47569340 ACCACTTAGT
Statistics
Matches: 112, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
51 31 0.28
52 17 0.15
53 33 0.29
54 30 0.27
55 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.26
Consensus pattern (52 bp):
TTGGGTGCTGGGACACTAATGGCCGGCACTCTTGTACCAGATTTAAAAAAAA
Found at i:47572604 original size:28 final size:29
Alignment explanation
Indices: 47572580--47572640 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 29
47572570 CATTTTTATT
47572580 TTTTATTAC-TTTATTT-ATTTATTTTAAC
1 TTTTA-TACTTTTATTTAATTTATTTTAAC
*
47572608 TTTTATACTTTTATTTAATTTAATTTACAC
1 TTTTATACTTTTATTTAATTTATTTTA-AC
47572638 TTT
1 TTT
47572641 ATTTATTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 3 0.10
28 12 0.41
29 9 0.31
30 5 0.17
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66
Consensus pattern (29 bp):
TTTTATACTTTTATTTAATTTATTTTAAC
Found at i:47572651 original size:16 final size:15
Alignment explanation
Indices: 47572593--47572664 Score: 53
Period size: 14 Copynumber: 4.8 Consensus size: 15
47572583 TATTACTTTA
47572593 TTTATTTATTTTAAC
1 TTTATTTATTTTAAC
*
47572608 TTT-TATACTTTT-A-
1 TTTATTTA-TTTTAAC
*
47572621 TTTAATTTAATTTACAC
1 TTT-ATTTATTTTA-AC
47572638 TTTATTTATTTT-AC
1 TTTATTTATTTTAAC
*
47572652 TCTATTTCATTTT
1 TTTATTT-ATTTT
47572665 GTAATAAATG
Statistics
Matches: 45, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
13 3 0.07
14 15 0.33
15 15 0.33
16 9 0.20
17 3 0.07
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTATTTATTTTAAC
Found at i:47577683 original size:9 final size:9
Alignment explanation
Indices: 47577669--47577699 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
47577659 GTTAAACGAA
47577669 TCGAGTTAT
1 TCGAGTTAT
*
47577678 TCGAGTTAA
1 TCGAGTTAT
47577687 TCGAGTTAT
1 TCGAGTTAT
47577696 TCGA
1 TCGA
47577700 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:47578017 original size:30 final size:31
Alignment explanation
Indices: 47577983--47578042 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
47577973 AAACCTTTTA
*
47577983 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
47578013 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
47578043 TCCCACCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:47583304 original size:20 final size:20
Alignment explanation
Indices: 47583262--47583308 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
47583252 CTACCCACAT
*
47583262 TAGGGCTCTAAATCTAGTGC
1 TAGGGCTCTAAATCTACTGC
47583282 TAGGGCTCTAAATCTGACT-C
1 TAGGGCTCTAAATCT-ACTGC
47583302 TAGGGCT
1 TAGGGCT
47583309 TGGCCTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (20 bp):
TAGGGCTCTAAATCTACTGC
Found at i:47585003 original size:25 final size:24
Alignment explanation
Indices: 47584972--47585030 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
47584962 TTTGTTTATG
47584972 TTTTAATT-TTATGTGATTTAATAA
1 TTTTAATTATTATGTG-TTTAATAA
* *
47584996 TTATTAATTAATTTTGTGTTTCATAA
1 TT-TTAATT-ATTATGTGTTTAATAA
47585022 TTTTAATTA
1 TTTTAATTA
47585031 GGTACAGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
25 12 0.40
26 9 0.30
27 6 0.20
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.59
Consensus pattern (24 bp):
TTTTAATTATTATGTGTTTAATAA
Found at i:47585006 original size:29 final size:25
Alignment explanation
Indices: 47584974--47585030 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 25
47584964 TGTTTATGTT
47584974 TTAATTTTATGTGATTTAATAATTATTAA
1 TTAA-TTT-TGTG-TTTAATAATT-TTAA
*
47585003 TTAATTTTGTGTTTCATAATTTTAA
1 TTAATTTTGTGTTTAATAATTTTAA
47585028 TTA
1 TTA
47585031 GGTACAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 7 0.26
26 9 0.33
27 4 0.15
28 3 0.11
29 4 0.15
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (25 bp):
TTAATTTTGTGTTTAATAATTTTAA
Found at i:47585174 original size:20 final size:20
Alignment explanation
Indices: 47585149--47585198 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
47585139 AAAAAGGCCA
47585149 AGCCCTAG-AGCCAGATTTGG
1 AGCCCTAGCA-CCAGATTTGG
*
47585169 AGCCCTAGCACTAGATTTGG
1 AGCCCTAGCACCAGATTTGG
*
47585189 AGCCCCAGCA
1 AGCCCTAGCA
47585199 TGGGTAGCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.26, C:0.30, G:0.26, T:0.18
Consensus pattern (20 bp):
AGCCCTAGCACCAGATTTGG
Found at i:47590959 original size:20 final size:20
Alignment explanation
Indices: 47590934--47590971 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
47590924 CGTAAAATAA
*
47590934 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
47590954 TTTCTGTAAAATGATTTA
1 TTTCTGGAAAATGATTTA
47590972 TTGGAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.08, G:0.13, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:47590963 original size:34 final size:35
Alignment explanation
Indices: 47590919--47590985 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
47590909 CAGTAAAATA
*
47590919 TTTTCCGTAAAATAATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATAATTTACTGGAAAATATTTTAC
* * *
47590953 TTTTCTGTAAAATGATTTATTGGAAAATATTTT
1 TTTTCCGTAAAATAATTTACTGGAAAATATTTT
47590986 CTGGTGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.48
Consensus pattern (35 bp):
TTTTCCGTAAAATAATTTACTGGAAAATATTTTAC
Found at i:47593543 original size:29 final size:30
Alignment explanation
Indices: 47593511--47593587 Score: 93
Period size: 31 Copynumber: 2.6 Consensus size: 30
47593501 AAGTTGTAGA
*
47593511 TTTAGTCCTTATACTTT-AATTTGATCAAT
1 TTTAGTCCTTGTACTTTCAATTTGATCAAT
* * *
47593540 TTTAGTCCTTGTAGTTTTCAATTTGGTTAAT
1 TTTAGTCCTTGTA-CTTTCAATTTGATCAAT
*
47593571 GTTAGTCCTTGTACTTT
1 TTTAGTCCTTGTACTTT
47593588 TCAAAATTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 12 0.30
30 6 0.15
31 22 0.55
ACGTcount: A:0.21, C:0.13, G:0.13, T:0.53
Consensus pattern (30 bp):
TTTAGTCCTTGTACTTTCAATTTGATCAAT
Found at i:47596850 original size:18 final size:18
Alignment explanation
Indices: 47596823--47596857 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
47596813 TAATATTATA
47596823 AAATAAAATTATTATTTC
1 AAATAAAATTATTATTTC
*
47596841 AAATATAATTATTATTT
1 AAATAAAATTATTATTT
47596858 TTATATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
AAATAAAATTATTATTTC
Found at i:47600573 original size:14 final size:14
Alignment explanation
Indices: 47600554--47600593 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
47600544 TTGATTGCCA
47600554 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
47600568 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
47600582 GGAAAATGTTTT
1 GTAAAATGTTTT
47600594 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:47600602 original size:20 final size:20
Alignment explanation
Indices: 47600577--47600616 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
47600567 CGTAAAATGA
*
47600577 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
47600597 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
47600617 AAAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:47600948 original size:49 final size:49
Alignment explanation
Indices: 47600880--47600979 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
47600870 TTTCTTAATA
47600880 TTTTAGCAACATTTTCCCATAATTATAAGTATTCCTAGTAATCACATTT
1 TTTTAGCAACATTTTCCCATAATTATAAGTATTCCTAGTAATCACATTT
47600929 TTTTAGCAACATTTTCCCATAATTATAAGTATTCCTAGTAATCACATTT
1 TTTTAGCAACATTTTCCCATAATTATAAGTATTCCTAGTAATCACATTT
47600978 TT
1 TT
47600980 AACTATCTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (49 bp):
TTTTAGCAACATTTTCCCATAATTATAAGTATTCCTAGTAATCACATTT
Found at i:47603525 original size:16 final size:16
Alignment explanation
Indices: 47603504--47603534 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
47603494 TGACGGTTCT
47603504 AAATTTAGCAAAGATG
1 AAATTTAGCAAAGATG
47603520 AAATTTAGCAAAGAT
1 AAATTTAGCAAAGAT
47603535 TGCAGAAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.06, G:0.16, T:0.26
Consensus pattern (16 bp):
AAATTTAGCAAAGATG
Found at i:47603980 original size:24 final size:24
Alignment explanation
Indices: 47603953--47604005 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
47603943 TGCAATCGAT
*
47603953 AGGGTGAAGAGAGGAGCTGTGGAA
1 AGGGTGAAGAAAGGAGCTGTGGAA
47603977 AGGGTGAAGAAAGGAGCTGTGGAA
1 AGGGTGAAGAAAGGAGCTGTGGAA
47604001 AGGGT
1 AGGGT
47604006 TTCAAAGGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.34, C:0.04, G:0.49, T:0.13
Consensus pattern (24 bp):
AGGGTGAAGAAAGGAGCTGTGGAA
Found at i:47610175 original size:31 final size:32
Alignment explanation
Indices: 47610133--47610223 Score: 139
Period size: 31 Copynumber: 2.8 Consensus size: 32
47610123 GTTCAGATTC
47610133 AAAAAAAATCAAAATCAAAGTCAAAAAGAAG-
1 AAAAAAAATCAAAATCAAAGTCAAAAAGAAGA
*
47610164 AAAAAAGATCAAAATCAAAGTCAAAAAGAAGAA
1 AAAAAAAATCAAAATCAAAGTCAAAAAGAAG-A
*
47610197 AAAGAAAAACCAAAATCAAAGTCAAAA
1 AAA-AAAAATCAAAATCAAAGTCAAAA
47610224 TGAAAATGAA
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
31 30 0.56
33 3 0.06
34 21 0.39
ACGTcount: A:0.70, C:0.11, G:0.10, T:0.09
Consensus pattern (32 bp):
AAAAAAAATCAAAATCAAAGTCAAAAAGAAGA
Found at i:47610229 original size:31 final size:31
Alignment explanation
Indices: 47610136--47610236 Score: 123
Period size: 31 Copynumber: 3.2 Consensus size: 31
47610126 CAGATTCAAA
47610136 AAAAATCAAAATCAAAGTCAAAAAGAAGAAA-
1 AAAAATCAAAATCAAAGTCAAAAAGAA-AAAG
*
47610167 AAAGATCAAAATCAAAGTCAAAAAGAAGAAAAAG
1 AAAAATCAAAATCAAAGTC--AAA-AAGAAAAAG
* * *
47610201 AAAAACCAAAATCAAAGTCAAAATGAAAATG
1 AAAAATCAAAATCAAAGTCAAAAAGAAAAAG
47610232 AAAAA
1 AAAAA
47610237 GAGAGAAGAA
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
31 30 0.49
32 3 0.05
33 6 0.10
34 22 0.36
ACGTcount: A:0.69, C:0.10, G:0.11, T:0.10
Consensus pattern (31 bp):
AAAAATCAAAATCAAAGTCAAAAAGAAAAAG
Found at i:47611157 original size:13 final size:14
Alignment explanation
Indices: 47611139--47611172 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
47611129 TTTGAGTCAA
*
47611139 AAAAATGAAAATG-
1 AAAAATGAAAAAGT
47611152 AAAAATGAAAAAGT
1 AAAAATGAAAAAGT
47611166 AAAAATG
1 AAAAATG
47611173 GAGACGCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (14 bp):
AAAAATGAAAAAGT
Found at i:47612562 original size:87 final size:87
Alignment explanation
Indices: 47612407--47612702 Score: 403
Period size: 87 Copynumber: 3.4 Consensus size: 87
47612397 AACAGATCAG
*
47612407 TAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGTGAAGCAGATCAAAAACAAAGCCTTGCCTC
1 TAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCAAAAACAAAGCCTTGCCTC
47612472 CATCGGTTGCAGTGGAGCGGGT
66 CATCGGTTGCAGTGGAGCGGGT
* * * * * *
47612494 TAAAAATATCAGATCTTGCCTTCCTGCATTAACAGCAAAGCATATCAAAAACAAAGACTTGCCTC
1 TAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCAAAAACAAAGCCTTGCCTC
47612559 CATCGGTTGCAGTGGAGCGGGT
66 CATCGGTTGCAGTGGAGCGGGT
* * ** * *
47612581 TAAAGATAGCAGATCTTGCCTTCCTGCACTGACAGCGAAGTAGATTGAAGACACCAGCCTTGCCT
1 TAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCAAAAACA-AAGCCTTGCCT
* **
47612646 CCCTCGGTTGCAGTGGAGTAGGT
65 CCATCGGTTGCAGTGGAGCGGGT
* * * *
47612669 TGAATATAGCAGATCTTGCCTTCCCGCATCGACA
1 TAAAGATAGCAGATCTTGCCTTCCTGCATTGACA
47612703 ATGAAGTAGA
Statistics
Matches: 181, Mismatches: 27, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
87 123 0.68
88 58 0.32
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (87 bp):
TAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCAAAAACAAAGCCTTGCCTC
CATCGGTTGCAGTGGAGCGGGT
Found at i:47612687 original size:44 final size:44
Alignment explanation
Indices: 47612551--47612689 Score: 120
Period size: 44 Copynumber: 3.2 Consensus size: 44
47612541 AAAACAAAGA
* ** *
47612551 CTTGCCTCCATCGGTTGCAGTGGAGCGGGTTAAAGATAGCAGAT
1 CTTGCCTCCCTCGGTTGCAGTGGAGTAGGTTGAAGATAGCAGAT
* ** * * * * * *
47612595 CTTGCCTTCCT-GCACTGACAGCGAAGTAGATTGAAGACACCAG-C
1 CTTGCCTCCCTCG-GTTG-CAGTGGAGTAGGTTGAAGATAGCAGAT
*
47612639 CTTGCCTCCCTCGGTTGCAGTGGAGTAGGTTGAATATAGCAGAT
1 CTTGCCTCCCTCGGTTGCAGTGGAGTAGGTTGAAGATAGCAGAT
47612683 CTTGCCT
1 CTTGCCT
47612690 TCCCGCATCG
Statistics
Matches: 68, Mismatches: 23, Indels: 8
0.69 0.23 0.08
Matches are distributed among these distances:
43 20 0.29
44 30 0.44
45 18 0.26
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.26
Consensus pattern (44 bp):
CTTGCCTCCCTCGGTTGCAGTGGAGTAGGTTGAAGATAGCAGAT
Found at i:47613090 original size:44 final size:44
Alignment explanation
Indices: 47612970--47613109 Score: 136
Period size: 44 Copynumber: 3.1 Consensus size: 44
47612960 TGTAAGGAAA
* * *
47612970 CAGATTGAAGCCGGTAATCCTATCTCCCTGAGATTACAGTGGAA
1 CAGATTGAAGCCAGTAATCCTATCTACCTGAGATTACAGTGGAG
* ** ** * * * *
47613014 TAGACCGAAGATATTCAAATCTTATCTACCTGAGATTATAGCGGAG
1 CAGATTGAAGCCAGT--AATCCTATCTACCTGAGATTACAGTGGAG
*
47613060 CAGATTGAAGCCAGTAATCCTATCTTCCTGAGATTACAGTGGAG
1 CAGATTGAAGCCAGTAATCCTATCTACCTGAGATTACAGTGGAG
*
47613104 CGGATT
1 CAGATT
47613110 AAAAGGATCT
Statistics
Matches: 71, Mismatches: 23, Indels: 4
0.72 0.23 0.04
Matches are distributed among these distances:
44 38 0.54
46 33 0.46
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (44 bp):
CAGATTGAAGCCAGTAATCCTATCTACCTGAGATTACAGTGGAG
Found at i:47618094 original size:16 final size:17
Alignment explanation
Indices: 47618058--47618098 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
47618048 TTTGCTAAGG
*
47618058 GAAATAAATGGAAAGAA
1 GAAAAAAATGGAAAGAA
*
47618075 GAAAAAAATGTAAA-AA
1 GAAAAAAATGGAAAGAA
47618091 GAAAAAAA
1 GAAAAAAA
47618099 GTAGGGTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.73, C:0.00, G:0.17, T:0.10
Consensus pattern (17 bp):
GAAAAAAATGGAAAGAA
Found at i:47622291 original size:18 final size:19
Alignment explanation
Indices: 47622270--47622311 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
47622260 TGGTTAATTT
47622270 TTAATTAAGCTA-GTTTAA
1 TTAATTAAGCTAGGTTTAA
*
47622288 TTAATTTAGCTATGGTTTAA
1 TTAATTAAGCTA-GGTTTAA
47622308 TTAA
1 TTAA
47622312 GCTAATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.52
20 10 0.48
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.48
Consensus pattern (19 bp):
TTAATTAAGCTAGGTTTAA
Found at i:47622974 original size:19 final size:19
Alignment explanation
Indices: 47622948--47622997 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
47622938 AAACTTAAAA
*
47622948 AATA-TTTTTTGTAATTTT
1 AATACTTTTTTATAATTTT
* *
47622966 TATACTTTTTAATAATTTT
1 AATACTTTTTTATAATTTT
47622985 AATACTTTTTTAT
1 AATACTTTTTTAT
47622998 TTTTAAATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 3 0.12
19 23 0.88
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (19 bp):
AATACTTTTTTATAATTTT
Found at i:47623020 original size:27 final size:27
Alignment explanation
Indices: 47622947--47623036 Score: 78
Period size: 27 Copynumber: 3.3 Consensus size: 27
47622937 AAAACTTAAA
47622947 AAAT-ATTTTTTGTAATTTTTATACTTTTT
1 AAATAATTTTTTG-AATTTTT-TA-TTTTT
* *
47622976 -AATAATTTTAAT-ACTTTTTTATTTTT
1 AAATAATTTT-TTGAATTTTTTATTTTT
* *
47623002 AAATAATTTTTTGAATTTTTAAATTTT
1 AAATAATTTTTTGAATTTTTTATTTTT
*
47623029 AAAAAATT
1 AAATAATT
47623037 AATTACTGAT
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
26 6 0.12
27 29 0.58
28 9 0.18
29 5 0.10
30 1 0.02
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (27 bp):
AAATAATTTTTTGAATTTTTTATTTTT
Found at i:47623597 original size:22 final size:21
Alignment explanation
Indices: 47623566--47623610 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
47623556 TACACCAAAA
*
47623566 TAGGCTTTTAGCGGCGCTTTTT
1 TAGGCCTTTAGCGGCG-TTTTT
47623588 TAGGCCTTTAGCGGCGTTTTT
1 TAGGCCTTTAGCGGCGTTTTT
47623609 TA
1 TA
47623611 ACGCCACTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.11, C:0.18, G:0.27, T:0.44
Consensus pattern (21 bp):
TAGGCCTTTAGCGGCGTTTTT
Found at i:47623729 original size:43 final size:43
Alignment explanation
Indices: 47623681--47623885 Score: 256
Period size: 42 Copynumber: 4.8 Consensus size: 43
47623671 GCGTCGCTAA
* * *
47623681 CTTTAGCGGCGCTTTTCCCATAAACGCCGCTAAAGACCATGAT
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
* *
47623724 CTTTAGCGGCGC--TTCCCTACAAATGCCACTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCC-ACAAACGCCGCTAAAGACCAAGAC
* *
47623766 CTTTAGCGGCGC-TTCCCCACAAACGTCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
* * * *
47623808 CTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGA-TATTGAG
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCA-AGAC
47623851 CTTTAGCGGCGCTTTTTCCCACAAACGCCGCTAAA
1 CTTTAGCGGCGC-TTTTCCCACAAACGCCGCTAAA
47623886 AATATATCGT
Statistics
Matches: 141, Mismatches: 16, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
41 5 0.04
42 64 0.45
43 50 0.35
44 22 0.16
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.22
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
Found at i:47624224 original size:43 final size:43
Alignment explanation
Indices: 47624158--47624248 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
47624148 ATATATGCAA
* * * *
47624158 GGTAATAAAATATACAATGCATTTTCTTAATCAAGTAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
*
47624201 GGTAATAAAAGATATAATACATTTACTTAATCAAGGAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
47624244 -GTAAT
1 GGTAAT
47624249 GAACTCAAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 5 0.12
43 38 0.88
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (43 bp):
GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
Found at i:47629120 original size:41 final size:41
Alignment explanation
Indices: 47629074--47629276 Score: 334
Period size: 41 Copynumber: 5.0 Consensus size: 41
47629064 TCAAAAGCGG
* * *
47629074 GCATTAGCGGCGCTTTTTCAAAAATGCCGCTAAAGGCCCAA
1 GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGA
* *
47629115 GCATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGA
47629156 GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGA
* *
47629197 GCATTAGCGGCGCTTCTTCACAAACGCCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGA
*
47629238 GCATTAGTGGCGCTTATTCAAAAACGCCGCTAAAGGCCC
1 GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCC
47629277 CAAAACTCAG
Statistics
Matches: 152, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 152 1.00
ACGTcount: A:0.28, C:0.29, G:0.24, T:0.19
Consensus pattern (41 bp):
GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGA
Found at i:47629458 original size:41 final size:41
Alignment explanation
Indices: 47629330--47629462 Score: 141
Period size: 40 Copynumber: 3.3 Consensus size: 41
47629320 CACTTTTTGG
* **
47629330 AAAA-CGCCGGTAATGCTT-ATTTTTAGCGGCGTTTTCCA-
1 AAAAGCGCCGCTAATGCTTGATTTTTAGCGGCGTTTTTTAT
* ** *
47629368 AAAAGCGCCGCTAATGCTCGACCTTTAGCAGCG-TTTTTAT
1 AAAAGCGCCGCTAATGCTTGATTTTTAGCGGCGTTTTTTAT
*
47629408 AAAAGCGCCGCTAATGCTTGATTTTTAGTGGCGTTTTTTAT
1 AAAAGCGCCGCTAATGCTTGATTTTTAGCGGCGTTTTTTAT
*
47629449 CCAAA-CGCCGCTAA
1 -AAAAGCGCCGCTAA
47629463 AAGCCTATTT
Statistics
Matches: 77, Mismatches: 13, Indels: 7
0.79 0.13 0.07
Matches are distributed among these distances:
38 4 0.05
39 16 0.21
40 38 0.49
41 16 0.21
42 3 0.04
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (41 bp):
AAAAGCGCCGCTAATGCTTGATTTTTAGCGGCGTTTTTTAT
Found at i:47634549 original size:2 final size:2
Alignment explanation
Indices: 47634542--47634577 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
47634532 CTGTTTCTTT
* *
47634542 TC TC TC TC CC TC TC AC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
47634578 GGGATTGGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.03, C:0.53, G:0.00, T:0.44
Consensus pattern (2 bp):
TC
Found at i:47647575 original size:16 final size:16
Alignment explanation
Indices: 47647554--47647584 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
47647544 TTCAATGTGG
*
47647554 TTCTATTACTTGTTTA
1 TTCTATTACATGTTTA
47647570 TTCTATTACATGTTT
1 TTCTATTACATGTTT
47647585 GACTGATTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.13, G:0.06, T:0.61
Consensus pattern (16 bp):
TTCTATTACATGTTTA
Found at i:47650351 original size:15 final size:15
Alignment explanation
Indices: 47650321--47650354 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
47650311 TAACTCATCA
47650321 TTTAATTTTAATTTT
1 TTTAATTTTAATTTT
47650336 TTTAACTTTTAATTTT
1 TTTAA-TTTTAATTTT
47650352 TTT
1 TTT
47650355 TCAAATATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTAATTTTAATTTT
Found at i:47652207 original size:59 final size:60
Alignment explanation
Indices: 47652134--47652261 Score: 213
Period size: 60 Copynumber: 2.1 Consensus size: 60
47652124 ATCTAGTAGA
*
47652134 CAAGTTCAGGTACCAAAGTGAACG-AAAAAAAGTACAGGTACCAAAGTAGACTTAGTTGC
1 CAAGTTCAGATACCAAAGTGAACGAAAAAAAAGTACAGGTACCAAAGTAGACTTAGTTGC
* *
47652193 CAAGTTCAGATACCAAAGTGAACGAAAAAAAAGTATAGGTACCAAAGTGGACTTAGTTGC
1 CAAGTTCAGATACCAAAGTGAACGAAAAAAAAGTACAGGTACCAAAGTAGACTTAGTTGC
*
47652253 TAAGTTCAG
1 CAAGTTCAG
47652262 GGGCTAAAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
59 23 0.36
60 41 0.64
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.20
Consensus pattern (60 bp):
CAAGTTCAGATACCAAAGTGAACGAAAAAAAAGTACAGGTACCAAAGTAGACTTAGTTGC
Found at i:47653986 original size:95 final size:95
Alignment explanation
Indices: 47653823--47654014 Score: 323
Period size: 95 Copynumber: 2.0 Consensus size: 95
47653813 AATATAATGC
* *
47653823 TTAGACCCAACCCACACCCTACCCGGTCCATTAACATCTCATAATAATACAGTCACCGAAAGGTG
1 TTAGACCCAACCCACACCCGACCCGGTCCATCAACATCTCATAATAATACAGTCACCGAAAGGTG
*
47653888 AAATGTTGTGATAGTGCTTGGACTTTTCTT
66 AAATGTTGTGATAATGCTTGGACTTTTCTT
* *
47653918 TTAGACCCAGCCCACACCCGACCCGGTCCATCAACATCTCATAATAATACAGTCACTGATAA-GT
1 TTAGACCCAACCCACACCCGACCCGGTCCATCAACATCTCATAATAATACAGTCACCGA-AAGGT
47653982 GAAATGTTGTGATAATGCTTGGACTTTTCTT
65 GAAATGTTGTGATAATGCTTGGACTTTTCTT
47654013 TT
1 TT
47654015 TCTTTTATAG
Statistics
Matches: 91, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
95 89 0.98
96 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (95 bp):
TTAGACCCAACCCACACCCGACCCGGTCCATCAACATCTCATAATAATACAGTCACCGAAAGGTG
AAATGTTGTGATAATGCTTGGACTTTTCTT
Found at i:47679901 original size:10 final size:10
Alignment explanation
Indices: 47679888--47679921 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
47679878 GAAAAATTCT
*
47679888 TTAAAAATTG
1 TTAAAAATTA
47679898 TTAAAAATTA
1 TTAAAAATTA
*
47679908 TTAAGAATTA
1 TTAAAAATTA
47679918 TTAA
1 TTAA
47679922 TTTCTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:47680472 original size:20 final size:20
Alignment explanation
Indices: 47680433--47680476 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
47680423 CAAAACAAAA
*
47680433 TTTTAAATTTTTTTACTAAT
1 TTTTAAATTTATTTACTAAT
47680453 TTTTATAATTTATTTA-TAAT
1 TTTTA-AATTTATTTACTAAT
47680473 TTTT
1 TTTT
47680477 GCAGTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTAAATTTATTTACTAAT
Found at i:47680488 original size:20 final size:21
Alignment explanation
Indices: 47680433--47680488 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 21
47680423 CAAAACAAAA
47680433 TTTTA-AATTTTTTTACTAAT
1 TTTTACAATTTTTTTACTAAT
* *
47680453 TTTTATAATTTATTTA-TAAT
1 TTTTACAATTTTTTTACTAAT
* *
47680473 TTTTGCAGTTTTTTTA
1 TTTTACAATTTTTTTA
47680489 AAAAAATAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 21 0.70
21 9 0.30
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.66
Consensus pattern (21 bp):
TTTTACAATTTTTTTACTAAT
Found at i:47680615 original size:40 final size:40
Alignment explanation
Indices: 47680544--47680619 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
47680534 AAGCGCAATT
* * *
47680544 AATATACCATGTCACTAGTCACCTTGTCATGTCATCGGTC
1 AATACACCATGTCACTAGTCAACTTGCCATGTCATCGGTC
*
47680584 AATACACCATGTCACTTGTCAACTTGCCATGTCATC
1 AATACACCATGTCACTAGTCAACTTGCCATGTCATC
47680620 AATGATGTGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.32
Consensus pattern (40 bp):
AATACACCATGTCACTAGTCAACTTGCCATGTCATCGGTC
Found at i:47696471 original size:15 final size:15
Alignment explanation
Indices: 47696453--47696501 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 15
47696443 CTATAAAACC
47696453 TTTATTATTAAAATA
1 TTTATTATTAAAATA
*
47696468 TTTATAATTGTAATAAATA
1 TTTATTA-T-T-A-AAATA
47696487 TTTATTATTAAAATA
1 TTTATTATTAAAATA
47696502 ATATTAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 11 0.39
16 2 0.07
17 2 0.07
18 2 0.07
19 11 0.39
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
TTTATTATTAAAATA
Found at i:47696501 original size:19 final size:19
Alignment explanation
Indices: 47696463--47696506 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
47696453 TTTATTATTA
**
47696463 AAATATTTATAATTGTAAT
1 AAATATTTATAATTAAAAT
*
47696482 AAATATTTATTATTAAAAT
1 AAATATTTATAATTAAAAT
47696501 -AATATT
1 AAATATT
47696507 AAATATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
AAATATTTATAATTAAAAT
Found at i:47696572 original size:13 final size:14
Alignment explanation
Indices: 47696534--47696575 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
47696524 ATATGAAGAA
47696534 ATATTATTTAAAATT
1 ATATTA-TTAAAATT
*
47696549 ATCATTTTTAAAATT
1 AT-ATTATTAAAATT
47696564 -TATTATTAAAAT
1 ATATTATTAAAAT
47696576 AAAATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 10 0.42
16 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (14 bp):
ATATTATTAAAATT
Found at i:47697998 original size:18 final size:18
Alignment explanation
Indices: 47697950--47698009 Score: 50
Period size: 17 Copynumber: 3.3 Consensus size: 18
47697940 GAAAAATTAT
* * *
47697950 AAAATATTTAAAACATTA
1 AAAATATTAAAAAAAATA
* *
47697968 TAAAT-TTATAAAAAATA
1 AAAATATTAAAAAAAATA
47697985 AAAATATTAAAAAAACTATA
1 AAAATATTAAAAAAA--ATA
47698005 AAAAT
1 AAAAT
47698010 TCAAGAAATA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
17 12 0.38
18 12 0.38
20 8 0.25
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAATATTAAAAAAAATA
Found at i:47700326 original size:125 final size:125
Alignment explanation
Indices: 47700104--47700474 Score: 627
Period size: 125 Copynumber: 3.0 Consensus size: 125
47700094 TTTTAGGGCT
**** *
47700104 TGGAAGAAATAATTTCGAGTTGACGTTTCTGATCAAATAGTATAAAATCGCTTCTAGCAGGATGC
1 TGGAAGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGC
* *
47700169 TATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCA
66 TATTTGAGAAGAATTTATAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCA
*
47700229 TGGAAGAAATAATTTTTTTTTGACGTTTCTGAGAAAATAGTATAAAATCGCTTCTAGCAGGATGC
1 TGGAAGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGC
*
47700294 TATTTGAGAAGAATTTATAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTTGGTCA
66 TATTTGAGAAGAATTTATAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCA
47700354 TGGAAGAAATAA-TTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGC
1 TGGAAGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGC
* *
47700418 TATTTGAGAAGAATTTATGAAAATCGCGCCCTTGTGGACGCACTTTTGCTACAGTAG
66 TATTTGAGAAGAATTTAT-AAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
47700475 CATGTTTGGG
Statistics
Matches: 232, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
124 69 0.30
125 163 0.70
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (125 bp):
TGGAAGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGC
TATTTGAGAAGAATTTATAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCA
Found at i:47703631 original size:17 final size:17
Alignment explanation
Indices: 47703564--47703631 Score: 57
Period size: 17 Copynumber: 3.8 Consensus size: 17
47703554 TATGTGAATG
*
47703564 TAAAATTATTAATT-GA
1 TAAAATTATTAATTATA
* *
47703580 TAAATTGTATTAATGATTA
1 TAAAAT-TATTAATTA-TA
*
47703599 GTAAAATTATCAAATTATA
1 -TAAAATTAT-TAATTATA
47703618 TAAAATTATTAATT
1 TAAAATTATTAATT
47703632 GTTAGTACCA
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
16 5 0.12
17 11 0.28
18 9 0.22
19 6 0.15
20 9 0.22
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (17 bp):
TAAAATTATTAATTATA
Found at i:47703654 original size:116 final size:116
Alignment explanation
Indices: 47703450--47703693 Score: 427
Period size: 116 Copynumber: 2.1 Consensus size: 116
47703440 TAAGTTTGTG
*
47703450 AAATTATTAATTGATAAATTGTATTAATGGTTAGTAAAAATTATCAAATTATATAAAATTATTAA
1 AAATTATTAATTGATAAATTGTATTAATGATTAGTAAAAATTATCAAATTATATAAAATTATTAA
** * *
47703515 TTGTTAGTACCAGTCAAAACATTTTTCCAAATCTAGCATTATGTGAATGTA
66 TTGTTAGTACCAGAAAAAACATTTTTCCAAATCTAACATTATGTGAAAGTA
47703566 AAATTATTAATTGATAAATTGTATTAATGATTAGT-AAAATTATCAAATTATATAAAATTATTAA
1 AAATTATTAATTGATAAATTGTATTAATGATTAGTAAAAATTATCAAATTATATAAAATTATTAA
47703630 TTGTTAGTACCAGGAAAAAACATTTTTCCAAATCTAACATTATGTGAAAGTA
66 TTGTTAGTACCA-GAAAAAACATTTTTCCAAATCTAACATTATGTGAAAGTA
47703682 AAATTATTAATT
1 AAATTATTAATT
47703694 TAGTTTAGGG
Statistics
Matches: 122, Mismatches: 5, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
115 41 0.34
116 81 0.66
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.39
Consensus pattern (116 bp):
AAATTATTAATTGATAAATTGTATTAATGATTAGTAAAAATTATCAAATTATATAAAATTATTAA
TTGTTAGTACCAGAAAAAACATTTTTCCAAATCTAACATTATGTGAAAGTA
Found at i:47703808 original size:68 final size:67
Alignment explanation
Indices: 47703719--47704600 Score: 637
Period size: 68 Copynumber: 13.0 Consensus size: 67
47703709 AATTAAATTA
* * *
47703719 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAAAGGAGTTAGGATTTTTAAGCTT
1 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAA-TTAAATGAGTTAGGGTTTTTAAGTTT
47703784 -AG
65 AAG
*
47703786 GGTTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTT-AATTAGGTTAGGGTTTTTAAG-
1 GG-TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAA-TTAAATGA-GTTAGGGTTTTTAAGT
47703849 TTAAGGG
63 TTAA--G
* * * *
47703856 GGTTAGGGTTTTTAAGTTT-A--GGGTTTAAGGATTTTAATTAAATTAGGTTAGGGTTTTTAAGT
1 GGTTAGGGTTTTTAA-TTTAATTAGG-TTAGGGTTTTTAATTAAATGA-GTTAGGGTTTTTAAGT
47703918 TTAAG
63 TTAAG
* * *
47703923 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAG-TT
1 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTAAATGA-GTTAGGGTTTTTAAGTTT
*
47703987 AATTA
65 AA--G
* *** *
47703992 GGTTAGGGTTTTTAAGTTAAGGGGGTTAGGGTTTTTAAGTTTAA-G-GTTTAGGGTTTTTAA-TT
1 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAA-TTAAATGAG-TTAGGGTTTTTAAGTT
*
47704054 TAATTA
64 TAA--G
** * * *
47704060 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTTA-GGGTTTA-GGATTTTAA-TTA
1 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTAAATGAG-TTAGGGTTTTTAAGTTT
*
47704122 AATTA
65 AA--G
* *
47704127 GGTTAGGGTTTTTAAGTTTAGA-T---TTAGGGTTTTTAATTAAATTAGGTTAGGGGTTTTAAG-
1 GGTTAGGGTTTTTAA-TTTA-ATTAGGTTAGGGTTTTTAATTAAATGA-GTTAGGGTTTTTAAGT
47704187 TTAAGGG
63 TTAA--G
* * * * * * *
47704194 GGTTAGGGTTTTTAATTAAATTAGGTTAGGATTTTTAAGTT-TAGGATTTAGAGTTTTTAA-TTA
1 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAA-TTAAATGAGTTAGGGTTTTTAAGTTT
*
47704257 AATTA
65 AA--G
* * *
47704262 GGTTAGGGTTTTTAA-GT--TTAGGTTTAGGGTTTTTAATTAAATTAGGTTAGTGTTTTTAAGTT
1 GGTTAGGGTTTTTAATTTAATTAGG-TTAGGGTTTTTAATTAAATGA-GTTAGGGTTTTTAAGTT
47704324 T-AG
64 TAAG
** * * * *
47704327 GGTTTAATGTTTTTAATTAAATTAGGTTAGAGTTTTTAATTTAATTAGGTTAGGGTTTTTAA-TT
1 GG-TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTAAATGA-GTTAGGGTTTTTAAGTT
*
47704391 TAATTA
64 TAA--G
* * *
47704397 GGTTAGGGTTTTTAAGTTT-A--GGGTTTAGGGTTTTTAATTAAATTAGGTTGGGGTTTTTAAGT
1 GGTTAGGGTTTTTAA-TTTAATTAGG-TTAGGGTTTTTAATTAAATGA-GTTAGGGTTTTTAAGT
47704459 TT-AG
63 TTAAG
* * *
47704463 TGTTTAGGGTTTTAAATTTAATTAGGTTAGGGTTTTTAAGTT-AATTAGGTTAGGGTTTTTAAGT
1 -GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAA-TTAAATGA-GTTAGGGTTTTTAAGT
*
47704527 TAAGAG
63 TTA-AG
* * * *
47704533 GGTCAGGGTTTTTAAGTTT-A--AGGTTTAAGG-TTTTAATTTAATTAGGTTAGGGTTTTTAA-T
1 GGTTAGGGTTTTTAA-TTTAATTAGG-TTAGGGTTTTTAATTAAATGA-GTTAGGGTTTTTAAGT
47704593 TTAAG
63 TTAAG
47704598 GGT
1 GGT
47704601 ATTAATGGTT
Statistics
Matches: 677, Mismatches: 84, Indels: 110
0.78 0.10 0.13
Matches are distributed among these distances:
65 31 0.05
66 42 0.06
67 155 0.23
68 324 0.48
69 104 0.15
70 21 0.03
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (67 bp):
GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTAAATGAGTTAGGGTTTTTAAGTTTA
AG
Found at i:47703851 original size:91 final size:91
Alignment explanation
Indices: 47703696--47704600 Score: 966
Period size: 91 Copynumber: 10.0 Consensus size: 91
47703686 TATTAATTTA
*
47703696 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTA
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAA-TTA
* * *
47703761 AAGGA-GTTAGGATTTTTAAGCTTAGG
65 AATGAGGTTAGGGTTTTTAAGTTTAGG
*
47703787 GTTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTT-
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAA-TTA
* *
47703851 AAGGGGGTTAGGGTTTTTAAGTTTAGG
65 AATGAGGTTAGGGTTTTTAAGTTTAGG
* * *
47703878 GTTTAAGGATTTTAATTAAATTAGGTTAGGGTTTTTAAGTT--TAAGGTTTAGGGTTTTTAATTA
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAATTAGG-TTAGGGTTTTTAATTA
* *
47703941 AATTAGGTTAGGGTTTTTAATTAAATTA-G
65 AATGAGGTTAGGGTTTTTAAGT---TTAGG
***
47703970 G-TTAGGGTTTTTAAGTT-AATTAGGTTAGGGTTTTTAAGTTAAGGGGGTTAGGGTTTTTAAGTT
1 GTTTAGGGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAA-TT
* * *
47704033 TAA-G-GTTTAGGGTTTTTAA-TTTAATTAG
64 AAATGAGGTTAGGGTTTTTAAGTTT-A--GG
* *
47704061 G-TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAA-TT--TTAGGGTTTA-GGATTTTAATT
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAATTA-GG-TTAGGGTTTTTAATT
*
47704121 AAATTAGGTTAGGGTTTTTAAGTTTA-G
64 AAATGAGGTTAGGGTTTTTAAGTTTAGG
* * ***
47704148 ATTTAGGGTTTTTAATTAAATTAGGTTAGGGGTTTTAAGTTAAGGGGGTTAGGGTTTTTAATTAA
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAATTAA
* *
47704213 ATTAGGTTAGGATTTTTAAGTTTAGG
66 ATGAGGTTAGGGTTTTTAAGTTTAGG
* *
47704239 ATTTAGAGTTTTTAATTAAATTAGGTTAGGGTTTTTAAG-T--TTAGGTTTAGGGTTTTTAATTA
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAATTAGG-TTAGGGTTTTTAATTA
* *
47704301 AATTAGGTTAGTGTTTTTAAGTTTAGG
65 AATGAGGTTAGGGTTTTTAAGTTTAGG
** * * *
47704328 GTTTAATGTTTTTAATTAAATTAGGTTAGAGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTA
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAATTAA
*
47704393 ATTAGGTTAGGGTTTTTAAGTTTAGG
66 ATGAGGTTAGGGTTTTTAAGTTTAGG
* * * * * *
47704419 GTTTAGGGTTTTTAATTAAATTAGGTTGGGGTTTTTAAGTTTAGT-GTTTAGGGTTTTAAATTTA
1 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAATTAA
*
47704483 ATTAGGTTAGGGTTTTTAAGTTAATTA-G
66 ATGAGGTTAGGGTTTTTAAG-T--TTAGG
* * * *
47704511 G-TTAGGGTTTTTAAGTTAAGA--GGGTCAGGGTTTTTAAGTT--TAAGGTTTAAGG-TTTTAAT
1 GTTTAGGGTTTTTAA-TTAA-ATTAGGTTAGGGTTTTTAAGTTAATTAGG-TTAGGGTTTTTAAT
* *
47704570 TTAATTAGGTTAGGGTTTTTAA-TTTAAGG
63 TAAATGAGGTTAGGGTTTTTAAGTTT-AGG
47704599 GT
1 GT
47704601 ATTAATGGTT
Statistics
Matches: 707, Mismatches: 67, Indels: 82
0.83 0.08 0.10
Matches are distributed among these distances:
86 2 0.00
87 4 0.01
88 44 0.06
89 96 0.14
90 163 0.23
91 357 0.50
92 28 0.04
93 13 0.02
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.48
Consensus pattern (91 bp):
GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAATTAA
ATGAGGTTAGGGTTTTTAAGTTTAGG
Found at i:47704594 original size:23 final size:23
Alignment explanation
Indices: 47703688--47704596 Score: 811
Period size: 23 Copynumber: 40.2 Consensus size: 23
47703678 AGTAAAATTA
*
47703688 TTAATTTAGTTTAGGGTTTTTAAT
1 TTAA-TTAGGTTAGGGTTTTTAAT
*
47703712 TAAATTAGGTTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
*
47703735 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAT
* *
47703758 TTAA--AGGAGTTAGGATTTTTAAGC
1 TTAATTA-G-GTTAGGGTTTTTAA-T
*
47703782 TT-A--GGGTTTAGGGTTTTTAAT
1 TTAATTAGG-TTAGGGTTTTTAAT
*
47703803 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAT
*
47703826 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAT
***
47703849 TTAAGGGGGTTAGGGTTTTTAAGT
1 TTAATTAGGTTAGGGTTTTTAA-T
* * *
47703873 TT-A--GGGTTTAAGGATTTTAAT
1 TTAATTAGG-TTAGGGTTTTTAAT
*
47703894 TAAATTAGGTTAGGGTTTTTAAGT
1 TTAATTAGGTTAGGGTTTTTAA-T
47703918 TT-A--AGGTTTAGGGTTTTTAAT
1 TTAATTAGG-TTAGGGTTTTTAAT
*
47703939 TAAATTAGGTTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
* *
47703962 TAAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAT
*
47703985 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAT
***
47704008 TTAAGGGGGTTAGGGTTTTTAAGT
1 TTAATTAGGTTAGGGTTTTTAA-T
47704032 TT-A--AGGTTTAGGGTTTTTAAT
1 TTAATTAGG-TTAGGGTTTTTAAT
47704053 TTAATTAGGTTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
47704076 TTAATTAGGTTAGGGTTTTTAA-
1 TTAATTAGGTTAGGGTTTTTAAT
*
47704098 TT--TTAGGGTTTA-GGATTTTAAT
1 TTAATTA-GG-TTAGGGTTTTTAAT
*
47704120 TAAATTAGGTTAGGGTTTTTAAGT
1 TTAATTAGGTTAGGGTTTTTAA-T
47704144 TTAGA-T---TTAGGGTTTTTAAT
1 TTA-ATTAGGTTAGGGTTTTTAAT
* * *
47704164 TAAATTAGGTTAGGGGTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAT
***
47704187 TTAAGGGGGTTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
* *
47704210 TAAATTAGGTTAGGATTTTTAA-
1 TTAATTAGGTTAGGGTTTTTAAT
* *
47704232 GT--TTAGGATTTAGAGTTTTTAAT
1 TTAATTAGG--TTAGGGTTTTTAAT
*
47704255 TAAATTAGGTTAGGGTTTTTAA-
1 TTAATTAGGTTAGGGTTTTTAAT
*
47704277 GT--TTAGGTTTAGGGTTTTTAAT
1 TTAATTAGG-TTAGGGTTTTTAAT
* *
47704299 TAAATTAGGTTAGTGTTTTTAAGT
1 TTAATTAGGTTAGGGTTTTTAA-T
* **
47704323 TT-A--GGGTTTAATGTTTTTAAT
1 TTAATTAGG-TTAGGGTTTTTAAT
* *
47704344 TAAATTAGGTTAGAGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
47704367 TTAATTAGGTTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
47704390 TTAATTAGGTTAGGGTTTTTAAGT
1 TTAATTAGGTTAGGGTTTTTAA-T
*
47704414 TT-A--GGGTTTAGGGTTTTTAAT
1 TTAATTAGG-TTAGGGTTTTTAAT
* *
47704435 TAAATTAGGTTGGGGTTTTTAAGT
1 TTAATTAGGTTAGGGTTTTTAA-T
* * *
47704459 TT-AGT-GTTTAGGGTTTTAAAT
1 TTAATTAGGTTAGGGTTTTTAAT
*
47704480 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAT
*
47704503 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAT
* *
47704526 TTAA-GAGGGTCAGGGTTTTTAAGT
1 TTAATTA-GGTTAGGGTTTTTAA-T
*
47704550 TT-A--AGGTTTAAGG-TTTTAAT
1 TTAATTAGG-TTAGGGTTTTTAAT
47704570 TTAATTAGGTTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT
47704593 TTAA
1 TTAA
47704597 GGGTATTAAT
Statistics
Matches: 734, Mismatches: 88, Indels: 127
0.77 0.09 0.13
Matches are distributed among these distances:
19 1 0.00
20 20 0.03
21 75 0.10
22 127 0.17
23 459 0.63
24 46 0.06
25 6 0.01
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.48
Consensus pattern (23 bp):
TTAATTAGGTTAGGGTTTTTAAT
Found at i:47704669 original size:25 final size:25
Alignment explanation
Indices: 47704639--47704686 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
47704629 TATCAAAAAT
47704639 TTTTATTTTATTACATCAAATAAAC
1 TTTTATTTTATTACATCAAATAAAC
47704664 TTTTATTTTATTACATCAAATAA
1 TTTTATTTTATTACATCAAATAA
47704687 TATCAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (25 bp):
TTTTATTTTATTACATCAAATAAAC
Found at i:47705039 original size:18 final size:18
Alignment explanation
Indices: 47705016--47705051 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
47705006 CGGAAAAGGG
*
47705016 TACATACAAGGGTTAGGA
1 TACATACAAGGGCTAGGA
*
47705034 TACATATAAGGGCTAGGA
1 TACATACAAGGGCTAGGA
47705052 AACGCACCTG
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:0.39, C:0.11, G:0.28, T:0.22
Consensus pattern (18 bp):
TACATACAAGGGCTAGGA
Found at i:47705704 original size:7 final size:7
Alignment explanation
Indices: 47705694--47705718 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
47705684 TTATATACAT
47705694 AATACTA
1 AATACTA
47705701 AATACTA
1 AATACTA
47705708 AATACTA
1 AATACTA
47705715 AATA
1 AATA
47705719 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:47705926 original size:20 final size:20
Alignment explanation
Indices: 47705889--47705926 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
47705879 TTTATTTTTA
*
47705889 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
47705909 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
47705927 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:47706859 original size:12 final size:11
Alignment explanation
Indices: 47706817--47706859 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
47706807 ATTTTTATGG
*
47706817 TTTAAAAAAAA
1 TTTAAAAAATA
47706828 TTTAAAAAATA
1 TTTAAAAAATA
* *
47706839 TTTTTAAAATTA
1 -TTTAAAAAATA
47706851 TTTAAAAAA
1 TTTAAAAAA
47706860 GGGAGTTAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TTTAAAAAATA
Found at i:47706881 original size:11 final size:11
Alignment explanation
Indices: 47706865--47706906 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
47706855 AAAAAGGGAG
47706865 TTAAGAGAAAC
1 TTAAGAGAAAC
* *
47706876 TTAAGAGGAGC
1 TTAAGAGAAAC
*
47706887 TTAAGAGGAAC
1 TTAAGAGAAAC
47706898 TTAAGAGAA
1 TTAAGAGAA
47706907 TTTTTGAAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.48, C:0.07, G:0.26, T:0.19
Consensus pattern (11 bp):
TTAAGAGAAAC
Found at i:47706890 original size:22 final size:21
Alignment explanation
Indices: 47706861--47706904 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
47706851 TTTAAAAAAG
47706861 GGAGTTAAGAGAAACTTAAGA
1 GGAGTTAAGAGAAACTTAAGA
*
47706882 GGAGCTTAAGAGGAACTTAAGA
1 GGAG-TTAAGAGAAACTTAAGA
47706904 G
1 G
47706905 AATTTTTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.43, C:0.07, G:0.32, T:0.18
Consensus pattern (21 bp):
GGAGTTAAGAGAAACTTAAGA
Found at i:47711450 original size:15 final size:15
Alignment explanation
Indices: 47711427--47711458 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
47711417 GATTGATTGA
47711427 GAAAAAAAATAAGAG
1 GAAAAAAAATAAGAG
*
47711442 GAAAGAAAATAAGAG
1 GAAAAAAAATAAGAG
47711457 GA
1 GA
47711459 TACCATTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.06
Consensus pattern (15 bp):
GAAAAAAAATAAGAG
Found at i:47711915 original size:20 final size:20
Alignment explanation
Indices: 47711890--47711943 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
47711880 TCTTTCTTAA
47711890 CAAAAATTAAAAATAATTTT
1 CAAAAATTAAAAATAATTTT
* *
47711910 CAAAAATTCAAAATGATTTT
1 CAAAAATTAAAAATAATTTT
*
47711930 -TAAAATTAAAAATA
1 CAAAAATTAAAAATA
47711944 TTTATAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 11 0.38
20 18 0.62
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (20 bp):
CAAAAATTAAAAATAATTTT
Found at i:47731940 original size:10 final size:10
Alignment explanation
Indices: 47731925--47731949 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
47731915 TTTTTTAATT
47731925 TAAAACTATA
1 TAAAACTATA
47731935 TAAAACTATA
1 TAAAACTATA
47731945 TAAAA
1 TAAAA
47731950 TTATTAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (10 bp):
TAAAACTATA
Found at i:47732208 original size:20 final size:20
Alignment explanation
Indices: 47732185--47732253 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
47732175 GTTAGATATT
*
47732185 TTGATAAATCTTTAAAAATA
1 TTGATAAATCTTTAGAAATA
*
47732205 TTGATAAAT-TATTAGATATA
1 TTGATAAATCT-TTAGAAATA
* * *
47732225 TTGATAAATCCTTCGAAATT
1 TTGATAAATCTTTAGAAATA
47732245 TTGATAAAT
1 TTGATAAAT
47732254 TGTTATATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
19 1 0.02
20 40 0.98
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (20 bp):
TTGATAAATCTTTAGAAATA
Found at i:47732229 original size:40 final size:40
Alignment explanation
Indices: 47732169--47732254 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
47732159 ATTATCTTGG
* * *
47732169 TAAATTGTTAGATATTTTGATAAATCTTTAAAAATATTGA
1 TAAATTATTAGATATATTGATAAATCCTTAAAAATATTGA
** *
47732209 TAAATTATTAGATATATTGATAAATCCTTCGAAATTTTGA
1 TAAATTATTAGATATATTGATAAATCCTTAAAAATATTGA
47732249 TAAATT
1 TAAATT
47732255 GTTATATTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (40 bp):
TAAATTATTAGATATATTGATAAATCCTTAAAAATATTGA
Found at i:47732884 original size:16 final size:16
Alignment explanation
Indices: 47732851--47732884 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
47732841 TCAAAATGTT
* *
47732851 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
47732867 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
47732883 AA
1 AA
47732885 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:47737650 original size:16 final size:16
Alignment explanation
Indices: 47737617--47737650 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
47737607 GGAGATTGTT
* *
47737617 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
47737633 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
47737649 AA
1 AA
47737651 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:47739077 original size:30 final size:29
Alignment explanation
Indices: 47739013--47739068 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
47739003 CCCAAATCGA
* *
47739013 TTAAAAATAATTTTTCTAATAAAAATTAC
1 TTAAAAATAAATTTTCTAACAAAAATTAC
47739042 TTAAAAATAAATTTTC-AACAAACAATT
1 TTAAAAATAAATTTTCTAACAAA-AATT
47739069 GATATAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.38
Consensus pattern (29 bp):
TTAAAAATAAATTTTCTAACAAAAATTAC
Found at i:47740814 original size:18 final size:19
Alignment explanation
Indices: 47740791--47740829 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
47740781 GAAACTCTAT
47740791 ATCCTTC-AGGGATTTT-AA
1 ATCCTTCTA-GGATTTTCAA
47740809 ATCCTTCTAGGATTTTCAA
1 ATCCTTCTAGGATTTTCAA
47740828 AT
1 AT
47740830 AAATTTAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (19 bp):
ATCCTTCTAGGATTTTCAA
Found at i:47748265 original size:2 final size:2
Alignment explanation
Indices: 47748258--47748302 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
47748248 TCTTATAATT
47748258 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
47748300 TC T
1 TC T
47748303 AAATATATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:47752196 original size:17 final size:18
Alignment explanation
Indices: 47752176--47752222 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
47752166 ATTTTTCGAA
47752176 AAATAA-ATTTTTTGTTC
1 AAATAATATTTTTTGTTC
*
47752193 AAATAATTTTTTTTGTTC
1 AAATAATATTTTTTGTTC
47752211 AAAT--TATTTTTT
1 AAATAATATTTTTT
47752223 TCCAGTTGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 7 0.26
17 6 0.22
18 14 0.52
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (18 bp):
AAATAATATTTTTTGTTC
Found at i:47752204 original size:18 final size:18
Alignment explanation
Indices: 47752183--47752223 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
47752173 GAAAAATAAA
47752183 TTTTTTGTTCAAATAATT
1 TTTTTTGTTCAAATAATT
*
47752201 TTTTTTGTTCAAATTATT
1 TTTTTTGTTCAAATAATT
47752219 TTTTT
1 TTTTT
47752224 CCAGTTGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTTTTGTTCAAATAATT
Found at i:47760507 original size:25 final size:23
Alignment explanation
Indices: 47760464--47760510 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
47760454 GGAATTTTTT
*
47760464 TTATTTTTTTAATATTAATATAG
1 TTATTTTTTTAATAATAATATAG
47760487 TTATTTTTAATTAATAATAATATA
1 TTATTTTT--TTAATAATAATATA
47760511 AAATTATAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.38
25 13 0.62
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TTATTTTTTTAATAATAATATAG
Found at i:47778034 original size:16 final size:17
Alignment explanation
Indices: 47778013--47778047 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
47778003 AATTGAAATT
*
47778013 AATTAATTAA-TTTCTC
1 AATTAAATAATTTTCTC
47778029 AATTAAATAATTTTCTC
1 AATTAAATAATTTTCTC
47778046 AA
1 AA
47778048 CCTGATTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTAAATAATTTTCTC
Found at i:47780987 original size:49 final size:49
Alignment explanation
Indices: 47780930--47781029 Score: 173
Period size: 49 Copynumber: 2.0 Consensus size: 49
47780920 TCCTTTACAT
* *
47780930 CACCAAGCCCAAATCCTAGTAAACCCAACTAGCCTGAAGTTTTAAGACC
1 CACCAAGCCCAAATCCTAGTAAACCCAACTAACCTAAAGTTTTAAGACC
*
47780979 CACCAAGCCCAAATCCTAGTAAACCCAACTAACCTAAAGTTTTAATACC
1 CACCAAGCCCAAATCCTAGTAAACCCAACTAACCTAAAGTTTTAAGACC
47781028 CA
1 CA
47781030 GCCCAAGCAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.39, C:0.33, G:0.09, T:0.19
Consensus pattern (49 bp):
CACCAAGCCCAAATCCTAGTAAACCCAACTAACCTAAAGTTTTAAGACC
Found at i:47781004 original size:25 final size:25
Alignment explanation
Indices: 47780930--47781005 Score: 68
Period size: 25 Copynumber: 3.1 Consensus size: 25
47780920 TCCTTTACAT
47780930 CACCAAGCCCAAATCCTAGTAAACC
1 CACCAAGCCCAAATCCTAGTAAACC
* * * * *
47780955 CAACTAGCCTGAAGT--T-TTAAGACC
1 CACCAAGCC-CAAATCCTAGTAA-ACC
47780979 CACCAAGCCCAAATCCTAGTAAACC
1 CACCAAGCCCAAATCCTAGTAAACC
47781004 CA
1 CA
47781006 ACTAACCTAA
Statistics
Matches: 36, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
23 6 0.17
24 11 0.31
25 13 0.36
26 6 0.17
ACGTcount: A:0.38, C:0.36, G:0.11, T:0.16
Consensus pattern (25 bp):
CACCAAGCCCAAATCCTAGTAAACC
Found at i:47786112 original size:11 final size:11
Alignment explanation
Indices: 47786096--47786127 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
47786086 TGGCGAACTT
*
47786096 TGTCAAATTAC
1 TGTCAAATTAA
47786107 TGTCAAATTAA
1 TGTCAAATTAA
47786118 TGTCAAATTA
1 TGTCAAATTA
47786128 TTGTGATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (11 bp):
TGTCAAATTAA
Found at i:47788999 original size:43 final size:43
Alignment explanation
Indices: 47788931--47789034 Score: 131
Period size: 43 Copynumber: 2.4 Consensus size: 43
47788921 AGATCGTACA
* * *
47788931 ATGCCTAC-GTCCCAGACGAGGTCTTACATGT-AATCAAATATCG
1 ATGCC-ACTGTCCCAGACAAGATCTTACACGTAAATCAAATA-CG
*
47788974 ATGCCACTGTCCCAGACAAGATCTTACACGTAAATCATATACG
1 ATGCCACTGTCCCAGACAAGATCTTACACGTAAATCAAATACG
*
47789017 ATGCCAATGTCCCAGACA
1 ATGCCACTGTCCCAGACA
47789035 TGGTCTTTCT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
42 2 0.04
43 44 0.81
44 8 0.15
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (43 bp):
ATGCCACTGTCCCAGACAAGATCTTACACGTAAATCAAATACG
Found at i:47790251 original size:16 final size:17
Alignment explanation
Indices: 47790230--47790261 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
47790220 TGTTCATACT
47790230 AAAAAGAAAA-GAAAAC
1 AAAAAGAAAAGGAAAAC
47790246 AAAAAGAAAAGGAAAA
1 AAAAAGAAAAGGAAAA
47790262 GTCTTACCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAGGAAAAC
Found at i:47791055 original size:3 final size:3
Alignment explanation
Indices: 47791005--47791083 Score: 59
Period size: 3 Copynumber: 25.7 Consensus size: 3
47790995 TAATGTGTGC
* * * * * *
47791005 TAT TATT TAT TAC TAT TAT ATAT TAT TCT TAA CAC TAT TAT AAT TAT
1 TAT TA-T TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
47791052 TAT TAT TAG CAT TAT TAT TAT TAA TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
47791084 AATACCTTTT
Statistics
Matches: 57, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
3 51 0.89
4 6 0.11
ACGTcount: A:0.37, C:0.06, G:0.01, T:0.56
Consensus pattern (3 bp):
TAT
Found at i:47791067 original size:24 final size:23
Alignment explanation
Indices: 47791016--47791084 Score: 77
Period size: 24 Copynumber: 3.0 Consensus size: 23
47791006 ATTATTTATT
*
47791016 ACTATTATA-TATTATTCTTAAC
1 ACTATTATATTATTATTATTAAC
*
47791038 ACTATTATAATTATTATTATTAGC
1 ACTATTAT-ATTATTATTATTAAC
* *
47791062 ATTATTATTATTAATATTATTAA
1 ACTATTA-TATTATTATTATTAA
47791085 ATACCTTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
22 8 0.21
23 1 0.03
24 29 0.74
25 1 0.03
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.52
Consensus pattern (23 bp):
ACTATTATATTATTATTATTAAC
Found at i:47796005 original size:6 final size:6
Alignment explanation
Indices: 47795976--47796028 Score: 52
Period size: 6 Copynumber: 8.5 Consensus size: 6
47795966 AATCAAAGTC
* * * *
47795976 AAAATG AAAATG AAAAAG AGAAAAG AAAAATG AAAAGG AAAAAG AAAAGG
1 AAAAAG AAAAAG AAAAAG A-AAAAG AAAAA-G AAAAAG AAAAAG AAAAAG
47796026 AAA
1 AAA
47796029 GGCCAAGGCG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
6 30 0.73
7 11 0.27
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.06
Consensus pattern (6 bp):
AAAAAG
Found at i:47796010 original size:26 final size:25
Alignment explanation
Indices: 47795976--47796028 Score: 79
Period size: 26 Copynumber: 2.1 Consensus size: 25
47795966 AATCAAAGTC
*
47795976 AAAATGAAAATGAAAAAGAGAAAAGA
1 AAAATGAAAAGGAAAAAGA-AAAAGA
*
47796002 AAAATGAAAAGGAAAAAGAAAAGGA
1 AAAATGAAAAGGAAAAAGAAAAAGA
47796027 AA
1 AA
47796029 GGCCAAGGCG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.06
Consensus pattern (25 bp):
AAAATGAAAAGGAAAAAGAAAAAGA
Found at i:47796011 original size:19 final size:20
Alignment explanation
Indices: 47795982--47796023 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
47795972 AGTCAAAATG
47795982 AAAATGAAAAA-GAGAAAAGA
1 AAAATGAAAAAGGA-AAAAGA
47796002 AAAATG-AAAAGGAAAAAGA
1 AAAATGAAAAAGGAAAAAGA
47796021 AAA
1 AAA
47796024 GGAAAGGCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (20 bp):
AAAATGAAAAAGGAAAAAGA
Found at i:47796025 original size:12 final size:12
Alignment explanation
Indices: 47795976--47796028 Score: 61
Period size: 13 Copynumber: 4.2 Consensus size: 12
47795966 AATCAAAGTC
* *
47795976 AAAATGAAAATG
1 AAAAAGAAAAGG
*
47795988 AAAAAGAGAAAAG
1 AAAAAGA-AAAGG
47796001 AAAAATGAAAAGG
1 AAAAA-GAAAAGG
47796014 AAAAAGAAAAGG
1 AAAAAGAAAAGG
47796026 AAA
1 AAA
47796029 GGCCAAGGCG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
12 16 0.44
13 18 0.50
14 2 0.06
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.06
Consensus pattern (12 bp):
AAAAAGAAAAGG
Found at i:47796413 original size:21 final size:22
Alignment explanation
Indices: 47796373--47796417 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
47796363 GGATTTCAAG
*
47796373 AACAAAAAAGAAAGAGATGAAA
1 AACAAAAAAGAAAGAAATGAAA
*
47796395 AACAAAAATGAAA-AAATGAAA
1 AACAAAAAAGAAAGAAATGAAA
47796416 AA
1 AA
47796418 TGAAAGAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.76, C:0.04, G:0.13, T:0.07
Consensus pattern (22 bp):
AACAAAAAAGAAAGAAATGAAA
Found at i:47798387 original size:43 final size:43
Alignment explanation
Indices: 47798251--47798387 Score: 104
Period size: 43 Copynumber: 3.2 Consensus size: 43
47798241 GATAACAGAT
*
47798251 CTTGCCTTTCTGTTTTAACAGCGAAGCAGACCGAAAACAAAGC
1 CTTGCCTTTCTGTGTTAACAGCGAAGCAGACCGAAAACAAAGC
* * * *** * *
47798294 CTTGCC-TCCATCG-GTT-ACAG-TAGAGCTG-GTTAAAGATAACAGAT
1 CTTGCCTTTC-T-GTGTTAACAGCGA-AGCAGACCGAAA-ACAA-AG-C
47798338 CTTGCCTTTCTGTGTTAACAGCGAAGCAGACCGAAAACAAAGC
1 CTTGCCTTTCTGTGTTAACAGCGAAGCAGACCGAAAACAAAGC
47798381 CTTGCCT
1 CTTGCCT
47798388 CCATCGGTTA
Statistics
Matches: 66, Mismatches: 17, Indels: 22
0.63 0.16 0.21
Matches are distributed among these distances:
41 4 0.06
42 13 0.20
43 19 0.29
44 13 0.20
45 13 0.20
46 4 0.06
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (43 bp):
CTTGCCTTTCTGTGTTAACAGCGAAGCAGACCGAAAACAAAGC
Found at i:47798523 original size:87 final size:87
Alignment explanation
Indices: 47797672--47798522 Score: 1308
Period size: 87 Copynumber: 9.8 Consensus size: 87
47797662 ATCAGTGAAT
* *
47797672 ATCGAAAACAAAGCCTTGCCTCCATCGATTGCAGTGGAGCTGGTTAAAGATAGCAGATATTGCCT
1 ATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCT
47797737 TCCTGCGTTAACAGCGAAGCAG
66 TCCTGCGTTAACAGCGAAGCAG
* * * * * *
47797759 ATCGAAAACAAAACCTTGCCTCCATCGGTTGTAGTGGAACTGGTTAAAGATAGAAGATATTGCAT
1 ATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCT
47797824 TCCTGCGTTAACAGCGAAGCAG
66 TCCTGCGTTAACAGCGAAGCAG
* * **
47797846 ATCGAAAACAAAGCCTTGCCTCCATCGATTGCAGTGGAGCTGATTAAAGATAATAGATCTTGCC-
1 ATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCT
*
47797910 TCCTGCGTTAACAGCGAAGCAT
66 TCCTGCGTTAACAGCGAAGCAG
* * *
47797932 ACCGAAAACAAAGCCTTGCCTCCATCGATTACAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCT
1 ATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCT
* *
47797997 TCTTGCGTTAACAGCGAAGCAA
66 TCCTGCGTTAACAGCGAAGCAG
* * ** *
47798019 ACCGAAAACAAAGCTTTGCCTCCATCAATTGCAGTGGAGCTGGTTAAATATAGCAGATCTTGCCT
1 ATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCT
* *
47798084 TACTGCGTTAACAACGAAGCAG
66 TCCTGCGTTAACAGCGAAGCAG
* *
47798106 ATCGAAAATAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCT
1 ATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCT
*
47798171 TCCTGCGTTAACAGCGAAACAG
66 TCCTGCGTTAACAGCGAAGCAG
*
47798193 ATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAACAGATCTTGCCT
1 ATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCT
* **
47798258 TTCTGTTTTAACAGCGAAGCAG
66 TCCTGCGTTAACAGCGAAGCAG
* * * *
47798280 ACCGAAAACAAAGCCTTGCCTCCATCGGTTACAGTAGAGCTGGTTAAAGATAACAGATCTTGCCT
1 ATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCT
* *
47798345 TTCTGTGTTAACAGCGAAGCAG
66 TCCTGCGTTAACAGCGAAGCAG
* * *
47798367 ACCGAAAACAAAGCCTTGCCTCCATCGGTTACAGTGGAGCTGGTTAAAGATAACAGATCTTGCCT
1 ATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCT
* *
47798432 TCCTACGTTAATAGCGAAGCAG
66 TCCTGCGTTAACAGCGAAGCAG
47798454 ATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCT
1 ATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCT
47798519 TCCT
66 TCCT
47798523 AAGCACTAGC
Statistics
Matches: 703, Mismatches: 60, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
86 80 0.11
87 623 0.89
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.24
Consensus pattern (87 bp):
ATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCT
TCCTGCGTTAACAGCGAAGCAG
Found at i:47798860 original size:44 final size:44
Alignment explanation
Indices: 47798768--47798862 Score: 102
Period size: 44 Copynumber: 2.2 Consensus size: 44
47798758 TCGCATCAGG
* ** *
47798768 TCTTATCTCTCTGAAGTTGCAGCGGAGCAGACTGAGAAAACAAG
1 TCTTATCCCTCTGAAGTCACAGCGGAGCAGACTGAGAAAACAAA
* * * *
47798812 TCTTATCCCTCTGAAGTCACAGTGGGGCAGATTGA-AGAAGCAAA
1 TCTTATCCCTCTGAAGTCACAGCGGAGCAGACTGAGA-AAACAAA
47798856 TCTTATC
1 TCTTATC
47798863 TCCTTGAGGT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
43 1 0.02
44 41 0.98
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (44 bp):
TCTTATCCCTCTGAAGTCACAGCGGAGCAGACTGAGAAAACAAA
Found at i:47799834 original size:16 final size:17
Alignment explanation
Indices: 47799813--47799845 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
47799803 TTGTTCATAC
47799813 TAAAAAGAAAA-GAAAA
1 TAAAAAGAAAAGGAAAA
47799829 TAAAAAGAAAAGGAAAA
1 TAAAAAGAAAAGGAAAA
47799846 GCCTTACCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (17 bp):
TAAAAAGAAAAGGAAAA
Found at i:47800576 original size:3 final size:3
Alignment explanation
Indices: 47800564--47800629 Score: 51
Period size: 3 Copynumber: 21.7 Consensus size: 3
47800554 TAATGTGTGC
* * * * * * *
47800564 TAT TATT TAT TAT TAT TAT TAA CAC TAT TAT AAT CAT TAT TAG CAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
47800610 TAT TAT TAT TAA TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
47800630 AATACCTTTT
Statistics
Matches: 48, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.55
Consensus pattern (3 bp):
TAT
Found at i:47821650 original size:6 final size:6
Alignment explanation
Indices: 47821639--47821667 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
47821629 ATGTTTGGAC
47821639 GAAAAG GAAAAG GAAAAG GAAAAG GAAAA
1 GAAAAG GAAAAG GAAAAG GAAAAG GAAAA
47821668 TACAAGGGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (6 bp):
GAAAAG
Found at i:47822978 original size:11 final size:11
Alignment explanation
Indices: 47822951--47822994 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
47822941 TTTGATCACT
*
47822951 TAATTATTTAA
1 TAATTATTAAA
47822962 -AATTATTAAA
1 TAATTATTAAA
47822972 TAATTATTAAA
1 TAATTATTAAA
* *
47822983 TTATTAATAAA
1 TAATTATTAAA
47822994 T
1 T
47822995 TTTCATTTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 9 0.31
11 20 0.69
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TAATTATTAAA
Done.