Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 96 of 325
Found at i:28167064 original size:30 final size:30
Alignment explanation
Indices: 28167030--28167089 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
28167020 ATTTAATACG
28167030 AACTTTTAAAAAATTACACTTTTGCCCCTA
1 AACTTTTAAAAAATTACACTTTTGCCCCTA
** *
28167060 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTTAAAAAATTACACTTTTGCCCCTA
28167090 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (30 bp):
AACTTTTAAAAAATTACACTTTTGCCCCTA
Found at i:28174932 original size:24 final size:26
Alignment explanation
Indices: 28174877--28174932 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
28174867 GAGTCCTGGT
*
28174877 CAGTAAGCTCCTCCTGAGCTGATAAA
1 CAGTAAGCTCCTACTGAGCTGATAAA
* *
28174903 CAGTAAGCT-CTATTGAGTTGA-AAA
1 CAGTAAGCTCCTACTGAGCTGATAAA
28174927 CAGTAA
1 CAGTAA
28174933 TGTAACGCCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 9 0.33
25 9 0.33
26 9 0.33
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.25
Consensus pattern (26 bp):
CAGTAAGCTCCTACTGAGCTGATAAA
Found at i:28175360 original size:24 final size:24
Alignment explanation
Indices: 28175328--28175418 Score: 146
Period size: 24 Copynumber: 3.8 Consensus size: 24
28175318 TCAAGAGAGA
*
28175328 ATTTAGGAGTTGATAAGGGATAGG
1 ATTTAGGAGCTGATAAGGGATAGG
*
28175352 ATTTAGGAGTTGATAAGGGATAGG
1 ATTTAGGAGCTGATAAGGGATAGG
*
28175376 ATTTAGGAGCTGATAAGGGAGAGG
1 ATTTAGGAGCTGATAAGGGATAGG
28175400 ATTTAGGAGCTGATTAAGG
1 ATTTAGGAGCTGA-TAAGG
28175419 AGAACAATGT
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
24 59 0.92
25 5 0.08
ACGTcount: A:0.33, C:0.02, G:0.37, T:0.27
Consensus pattern (24 bp):
ATTTAGGAGCTGATAAGGGATAGG
Found at i:28176859 original size:27 final size:27
Alignment explanation
Indices: 28176819--28176929 Score: 143
Period size: 27 Copynumber: 4.1 Consensus size: 27
28176809 AGGAAGCGTC
* *
28176819 CTGGTGGCTATGCCACATTTATCTGAT
1 CTGGTGGCTCTGCCACATTTATCTGTT
* *
28176846 CTGGTGGCTCTGCCACATATATTTGTT
1 CTGGTGGCTCTGCCACATTTATCTGTT
* *
28176873 CTGGTGGCTCTGCCACAATTATTTGTT
1 CTGGTGGCTCTGCCACATTTATCTGTT
* *
28176900 CTGGTGACTCTGTCACA-TTATCTGTT
1 CTGGTGGCTCTGCCACATTTATCTGTT
28176926 CTGG
1 CTGG
28176930 CAGCAATGCT
Statistics
Matches: 75, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
26 12 0.16
27 63 0.84
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.40
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACATTTATCTGTT
Found at i:28177872 original size:22 final size:22
Alignment explanation
Indices: 28177847--28177922 Score: 73
Period size: 22 Copynumber: 3.4 Consensus size: 22
28177837 GGTGTTACAG
28177847 GTAAGCTCTATTGAGCTGAACA
1 GTAAGCTCTATTGAGCTGAACA
* * *
28177869 GTAAGCTAT-TTCGAGCTAAACG
1 GTAAGCTCTATT-GAGCTGAACA
* * *
28177891 GTAAGCTCCAATGAGCTGAAATA
1 GTAAGCTCTATTGAGCTG-AACA
28177914 GTAAGCTCT
1 GTAAGCTCT
28177923 TACGAGTTGA
Statistics
Matches: 41, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
21 2 0.05
22 28 0.68
23 11 0.27
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.26
Consensus pattern (22 bp):
GTAAGCTCTATTGAGCTGAACA
Found at i:28179323 original size:137 final size:138
Alignment explanation
Indices: 28179032--28179855 Score: 1140
Period size: 138 Copynumber: 6.1 Consensus size: 138
28179022 TATTTTCATC
*
28179032 ATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGATCGAAATTAATTAAT
1 ATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAAT
* *
28179097 ATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATAAAATTC
66 ATAACTATTTATATTAATAAATTCGATAAAATATATACAATTAATATTTTGTATGAATCAAATTC
28179162 ATATATTA
131 ATATATTA
* * * *
28179170 ATTATATT-TTTTCAAAAGAATATTAATTTTCATATCTGTTATATTTTGACCGATATTAATTAAT
1 ATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAAT
* * * * *
28179234 ATATCTGTTTATATTAGTAAATTCGATAAAATATATACAATCAA-AATTTGTATGAATCAAATT-
66 ATAACTATTTATATTAATAAATTCGATAAAATATATACAATTAATATTTTGTATGAATCAAATTC
28179297 ACTATATTA
131 A-TATATTA
* *
28179306 ATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAAC
1 ATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAAT
* * * *
28179371 ATAACTGTTTATATTAATGAATTC-AGTAAAATATATTCAATTAATATTTTTTATGAATCAAATT
66 ATAACTATTTATATTAATAAATTCGA-TAAAATATATACAATTAATATTTTGTATGAATCAAATT
28179435 CATATATTA
130 CATATATTA
* * *
28179444 ATTATATTCTTTCCAAAAGAAAATTAA-TTTCTATGTATTTTATATTTTGATCGAAATTAATTAA
1 ATTATATTCTTTCCAAAAGAATATTAATTTTC-ATGTCTTTTATATTTTGACCGAAATTAATTAA
* ** * *
28179508 TATAACTATTTATATTCATAAA-T---T----T-GGT-CAATTAATATTTTATATAAATCAAATT
65 TATAACTATTTATATTAATAAATTCGATAAAATATATACAATTAATATTTTGTATGAATCAAATT
28179563 CATATATTA
130 CATATATTA
* *
28179572 ATTATATTCTTTCTAGAAGAATATTAATTTTCATGTCTTTTATATTTTGACC-AGAATTAATTAA
1 ATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGA-AATTAATTAA
* * *
28179636 TATAACTGTTTATATTAATAAGTTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
65 TATAACTATTTATATTAATAAATTCGATAAAATATATACAATTAATATTTTGTATGAATCAAATT
28179701 CATATATTA
130 CATATATTA
* * * * *
28179710 ATCATATTCTTTCCAAAAGAATATTACTTTCCATGTATTTTATATTTTGACCAAAATTAATTAAT
1 ATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAAT
* * * *
28179775 ATAACTATTTATATTAATAAATTCGACAAAATATATTCAATTAATATTTTGTATGAATCAATTTT
66 ATAACTATTTATATTAATAAATTCGATAAAATATATACAATTAATATTTTGTATGAATCAAATTC
28179840 ATATATTA
131 ATATATTA
28179848 ATTATATT
1 ATTATATT
28179856 TATGTTCTCT
Statistics
Matches: 604, Mismatches: 63, Indels: 38
0.86 0.09 0.05
Matches are distributed among these distances:
127 1 0.00
128 105 0.17
129 6 0.01
130 1 0.00
132 1 0.00
134 1 0.00
135 1 0.00
136 34 0.06
137 182 0.30
138 270 0.45
139 2 0.00
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (138 bp):
ATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAAT
ATAACTATTTATATTAATAAATTCGATAAAATATATACAATTAATATTTTGTATGAATCAAATTC
ATATATTA
Found at i:28179643 original size:266 final size:269
Alignment explanation
Indices: 28179032--28179855 Score: 1101
Period size: 266 Copynumber: 3.0 Consensus size: 269
28179022 TATTTTCATC
*
28179032 ATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGATCGAAATTAATTAAT
1 ATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAAT
* *
28179097 ATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATAAAATTC
66 ATAACTGTTTATATTAAT-AATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATTC
* * * * *
28179162 ATATATTAATTATATT-TTTTCAAAAGAATATTAATTT-TCATATCTGTTATATTTTGACCGATA
130 ATATATTAATTATATTCTTTCCAAAAGAATATTAATTTCT-ATGTATTTTATATTTTGACCGAAA
* * * *
28179225 TTAATTAATATATCTGTTTATATTAGTAAATTCGATAAAATATATACAATCAAAATTTGTATGAA
194 TTAATTAATATAACTATTTATATTA-TAAATTCGAT-AAATATATA-AAT--AAATTTATATAAA
28179290 TCAAATTACTATATTA
254 TCAAATTACTATATTA
* *
28179306 ATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAAC
1 ATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAAT
* * *
28179371 ATAACTGTTTATATTAATGAATTCAGTAAAATATATTCAATTAATATTTTTTATGAATCAAATTC
66 ATAACTGTTTATATTAAT-AATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATTC
* *
28179436 ATATATTAATTATATTCTTTCCAAAAGAAAATTAATTTCTATGTATTTTATATTTTGATCGAAAT
130 ATATATTAATTATATTCTTTCCAAAAGAATATTAATTTCTATGTATTTTATATTTTGACCGAAAT
* * * *
28179501 TAATTAATATAACTATTTATATTCATAAATTTGGT-CA-AT-T-AAT-ATTTTATATAAATCAAA
195 TAATTAATATAACTATTTATATT-ATAAATTCGATAAATATATAAATAAATTTATATAAATCAAA
28179561 TT-CATATATTA
259 TTAC-TATATTA
* *
28179572 ATTATATTCTTTCTAGAAGAATATTAATTTTCATGTCTTTTATATTTTGACC-AGAATTAATTAA
1 ATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGA-AATTAATTAA
28179636 TATAACTGTTTATATTAATAAGTTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
65 TATAACTGTTTATATTAATAA-TTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
* * * *
28179701 CATATATTAATCATATTCTTTCCAAAAGAATATTACTTTCCATGTATTTTATATTTTGACCAAAA
129 CATATATTAATTATATTCTTTCCAAAAGAATATTAATTTCTATGTATTTTATATTTTGACCGAAA
* * * *
28179766 TTAATTAATATAACTATTTATATTAATAAATTCGACAAAATATATTCAATTAATATTTTGTATGA
194 TTAATTAATATAACTATTTATATT-ATAAATTCGA-TAAATATA-T-AAATAA-A-TTTATATAA
*
28179831 ATCAATTTTA-TATATTA
253 ATCAA-ATTACTATATTA
28179848 ATTATATT
1 ATTATATT
28179856 TATGTTCTCT
Statistics
Matches: 485, Mismatches: 47, Indels: 34
0.86 0.08 0.06
Matches are distributed among these distances:
265 4 0.01
266 231 0.48
268 1 0.00
269 5 0.01
271 2 0.00
272 2 0.00
273 3 0.01
274 138 0.28
275 68 0.14
276 29 0.06
277 2 0.00
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (269 bp):
ATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAAT
ATAACTGTTTATATTAATAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATTCA
TATATTAATTATATTCTTTCCAAAAGAATATTAATTTCTATGTATTTTATATTTTGACCGAAATT
AATTAATATAACTATTTATATTATAAATTCGATAAATATATAAATAAATTTATATAAATCAAATT
ACTATATTA
Found at i:28186522 original size:29 final size:29
Alignment explanation
Indices: 28186489--28186581 Score: 123
Period size: 29 Copynumber: 3.2 Consensus size: 29
28186479 TGACGAGATT
* *
28186489 GGCACTAAGTGTGCGTGCTGGAAATATAA
1 GGCACTAAGTGTGCATGCTGGAAAAATAA
*
28186518 GGCACTAAGTGTGCATGCTGGAAAAATAT
1 GGCACTAAGTGTGCATGCTGGAAAAATAA
* * * *
28186547 GACACTATGTGTGCAAGCTGGAAAAATAC
1 GGCACTAAGTGTGCATGCTGGAAAAATAA
28186576 GGCACT
1 GGCACT
28186582 GGGTGTGCGA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (29 bp):
GGCACTAAGTGTGCATGCTGGAAAAATAA
Found at i:28186594 original size:29 final size:29
Alignment explanation
Indices: 28186489--28186594 Score: 115
Period size: 29 Copynumber: 3.7 Consensus size: 29
28186479 TGACGAGATT
* *
28186489 GGCACTAAGTGTGCGTGCTGGAAATATAA
1 GGCACTAAGTGTGCGAGCTGGAAAAATAA
*
28186518 GGCACTAAGTGTGC-ATGCTGGAAAAATAT
1 GGCACTAAGTGTGCGA-GCTGGAAAAATAA
* * * *
28186547 GACACTATGTGTGCAAGCTGGAAAAATAC
1 GGCACTAAGTGTGCGAGCTGGAAAAATAA
**
28186576 GGCACTGGGTGTGCGAGCT
1 GGCACTAAGTGTGCGAGCT
28186595 CGGAGGGTAT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
29 64 0.98
30 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.31, T:0.23
Consensus pattern (29 bp):
GGCACTAAGTGTGCGAGCTGGAAAAATAA
Found at i:28194605 original size:29 final size:29
Alignment explanation
Indices: 28194511--28194605 Score: 100
Period size: 29 Copynumber: 3.2 Consensus size: 29
28194501 TGACGAGATT
** * *
28194511 GGCACTAAGTGTGCGTGCTGGAAATATAAGT
1 GGCACTAAGTGTGCAAGCTGGAAAAAT-A-C
* *
28194542 GGCACTAAGTGTGCATGCTGGAAAAATAT
1 GGCACTAAGTGTGCAAGCTGGAAAAATAC
* *
28194571 GACACTATGTGTGCAAGCTGGAAAAATAC
1 GGCACTAAGTGTGCAAGCTGGAAAAATAC
28194600 GGCACT
1 GGCACT
28194606 GGGTGTGCGA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
29 31 0.54
30 1 0.02
31 25 0.44
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (29 bp):
GGCACTAAGTGTGCAAGCTGGAAAAATAC
Found at i:28194611 original size:29 final size:29
Alignment explanation
Indices: 28194544--28194618 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
28194534 ATATAAGTGG
* * *
28194544 CACTAAGTGTGCATGCTGGAAAAATATGA
1 CACTAGGTGTGCAAGCTGGAAAAATACGA
* *
28194573 CACTATGTGTGCAAGCTGGAAAAATACGG
1 CACTAGGTGTGCAAGCTGGAAAAATACGA
* *
28194602 CACTGGGTGTGCGAGCT
1 CACTAGGTGTGCAAGCT
28194619 CGGAGGGTAT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (29 bp):
CACTAGGTGTGCAAGCTGGAAAAATACGA
Found at i:28199300 original size:71 final size:71
Alignment explanation
Indices: 28199214--28199377 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
28199204 CGATTTGTCT
28199214 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
28199279 CTTTCA
66 CTTTCA
28199285 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
28199350 CTTTCA
66 CTTTCA
28199356 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
28199378 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:28199415 original size:71 final size:70
Alignment explanation
Indices: 28199214--28199411 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
28199204 CGATTTGTCT
* * * *
28199214 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
28199279 CTTTCA
65 CTTTCA
* * * *
28199285 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
28199350 CTTTCA
65 CTTTCA
* *
28199356 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
28199412 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 22 0.18
69 1 0.01
70 1 0.01
71 96 0.80
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:28203581 original size:30 final size:30
Alignment explanation
Indices: 28203547--28203607 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
28203537 ATGGATGCTC
* *
28203547 TTTTGGACAGTT-ATATGTTGTGGTATTATT
1 TTTTGGA-AGTTGATATATTGTGGTATGATT
*
28203577 TTTTGGAAGTTGATATATTTTGGTATGATT
1 TTTTGGAAGTTGATATATTGTGGTATGATT
28203607 T
1 T
28203608 GGGATGATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.21, C:0.02, G:0.23, T:0.54
Consensus pattern (30 bp):
TTTTGGAAGTTGATATATTGTGGTATGATT
Found at i:28213051 original size:40 final size:40
Alignment explanation
Indices: 28212901--28213087 Score: 218
Period size: 40 Copynumber: 4.7 Consensus size: 40
28212891 TTCGAATGAT
* * * *
28212901 ATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA
* *
28212942 ATTCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAA
1 ATCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA
* *
28212982 ATCTGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
*
28213021 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-A
* * *
28213062 A-CCGGGCTATGGCCAGAAGGCATTTG
1 ATCCGGGCTAAGTCCCGAAGGCATTTG
28213088 AACGAGTAGC
Statistics
Matches: 125, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
39 35 0.28
40 62 0.50
41 27 0.22
42 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.26
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
Found at i:28213109 original size:79 final size:77
Alignment explanation
Indices: 28212937--28213120 Score: 192
Period size: 79 Copynumber: 2.3 Consensus size: 77
28212927 GTGCTAAGTG
* * *
28212937 ACTATATTCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAATCTGGGCTAAGCCCGAAGG
1 ACTATATTCGG-TTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGCCAGAAGG
**
28213002 CATTGGTGCGAGTT
64 CATTGGAACGAGTT
* * *
28213016 ACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGGCCAGAA
1 ACTATATTC-GGTTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTA-AGCCAGAA
*
28213080 GGCATTTGAACGAG-T
62 GGCATTGGAACGAGTT
*
28213095 AGCTATATTCGGTTAAATTCCGAAGG
1 A-CTATATTCGGTT-AAGTCCGAAGG
28213121 TACGTGATTC
Statistics
Matches: 87, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
78 1 0.01
79 56 0.64
80 30 0.34
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (77 bp):
ACTATATTCGGTTAAGTCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGCCAGAAGGCA
TTGGAACGAGTT
Found at i:28220802 original size:40 final size:40
Alignment explanation
Indices: 28220609--28220795 Score: 209
Period size: 40 Copynumber: 4.7 Consensus size: 40
28220599 ATTCAATGAT
* * * * *
28220609 ATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAAGTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA
* *
28220650 ATCTGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAA
1 ATCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA
*
28220690 ATCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
* * *
28220729 ATCCGGGTTAAATCCCAAAGGCATTTGTGCGAGTTACTATA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-A
**
28220770 A-CCGGGCTGTGTCCCGAAGGCATTTG
1 ATCCGGGCTAAGTCCCGAAGGCATTTG
28220796 AACGAGTAGC
Statistics
Matches: 123, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
39 35 0.28
40 61 0.50
41 26 0.21
42 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
Found at i:28222200 original size:26 final size:27
Alignment explanation
Indices: 28222167--28222222 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
28222157 AGTTTAGTTA
* *
28222167 ATTAGTTAGTTAAAAC-AAACCCCATT
1 ATTAGTTAATTAAAACAAAACCCCACT
28222193 ATTAGTTAATTAAAACAAAACCCCACT
1 ATTAGTTAATTAAAACAAAACCCCACT
28222220 ATT
1 ATT
28222223 CTTAGGCTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (27 bp):
ATTAGTTAATTAAAACAAAACCCCACT
Found at i:28231171 original size:45 final size:45
Alignment explanation
Indices: 28231120--28231211 Score: 166
Period size: 45 Copynumber: 2.0 Consensus size: 45
28231110 TAAGGCCTTT
* *
28231120 TATGGATTTAAGTTTTAATTGGGCATTTGCTTGTTTACTTTAAAC
1 TATGGATTTAAATTTTAATTGGGCATTTGCTTGCTTACTTTAAAC
28231165 TATGGATTTAAATTTTAATTGGGCATTTGCTTGCTTACTTTAAAC
1 TATGGATTTAAATTTTAATTGGGCATTTGCTTGCTTACTTTAAAC
28231210 TA
1 TA
28231212 CTAGTCTAGG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.26, C:0.10, G:0.16, T:0.48
Consensus pattern (45 bp):
TATGGATTTAAATTTTAATTGGGCATTTGCTTGCTTACTTTAAAC
Found at i:28235812 original size:30 final size:30
Alignment explanation
Indices: 28235773--28235829 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
28235763 ATTGATTTAC
* *
28235773 AAGCTTAGGGATAAAATAGTAATTTTGTGA
1 AAGCCTAGGGACAAAATAGTAATTTTGTGA
* *
28235803 AAGCCTAGGGGCAAAATGGTAATTTTG
1 AAGCCTAGGGACAAAATAGTAATTTTG
28235830 CCAAAATATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (30 bp):
AAGCCTAGGGACAAAATAGTAATTTTGTGA
Found at i:28236216 original size:48 final size:48
Alignment explanation
Indices: 28236144--28236416 Score: 318
Period size: 48 Copynumber: 5.7 Consensus size: 48
28236134 TATGTGTGCT
28236144 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGACATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGACATGAGAGCC
* * ****** * * *
28236192 AGTGTAAGACCATGTCTGGAACATGGTATCAATGTTGATATGTGCA-CT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGACATGAG-AGCC
*
28236240 AGTGTAAGACCATGTCTGGGACATGGCATCGACCAC-ATCATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGA-CATGAGAGCC
* * *
28236288 AGTGTAAGACCATGTCTGGGACATGGCATCGG-CAGTGAGATGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCA-CGACATGAGAGCC
* * * * *
28236336 AGTATAAGACCATGTCTGGGACATGGCATCGGGCTCGACGTGTGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGACATGAGAGCC
28236384 AGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC
28236417 AATTTACCCT
Statistics
Matches: 185, Mismatches: 34, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
47 4 0.02
48 178 0.96
49 3 0.02
ACGTcount: A:0.27, C:0.21, G:0.31, T:0.22
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGACATGAGAGCC
Found at i:28236404 original size:144 final size:144
Alignment explanation
Indices: 28236144--28236414 Score: 386
Period size: 144 Copynumber: 1.9 Consensus size: 144
28236134 TATGTGTGCT
*
28236144 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGACATGAGAGCCAGTGTAAGACCATGTCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGACATGAGAGCCAGTATAAGACCATGTCT
* * * * *
28236209 GGAACATGGTATCAATGTTGATATGTGCACTAGTGTAAGACCATGTCTGGGACATGGCATCGACC
66 GGAACATGGCATCAAGGTCGACATGTGCACCAGTGTAAGACCATGTCTGGGACATGGCATCGACC
28236274 ACATCATGAGAGCC
131 ACATCATGAGAGCC
* * *
28236288 AGTGTAAGACCATGTCTGGGACATGGCATCGG-CAGTGAGATGAGAGCTAGTATAAGACCATGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCA-CGACATGAGAGCCAGTATAAGACCATGTC
* * *
28236352 TGGGACATGGCATC-GGGCTCGACGTGTG-AGCCAGTGTAAGACCATGTCTGGGACATGGCATCG
65 TGGAACATGGCATCAAGG-TCGACATGTGCA-CCAGTGTAAGACCATGTCTGGGACATGGCATCG
28236415 GCAATTTACC
Statistics
Matches: 112, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
143 4 0.04
144 108 0.96
ACGTcount: A:0.27, C:0.21, G:0.31, T:0.22
Consensus pattern (144 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGACATGAGAGCCAGTATAAGACCATGTCT
GGAACATGGCATCAAGGTCGACATGTGCACCAGTGTAAGACCATGTCTGGGACATGGCATCGACC
ACATCATGAGAGCC
Found at i:28236415 original size:96 final size:99
Alignment explanation
Indices: 28236141--28236417 Score: 397
Period size: 96 Copynumber: 2.9 Consensus size: 99
28236131 TGATATGTGT
28236141 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGACATGAGAGCCAGTGTAAGACCATG
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGACATGAGAGCCAGTGTAAGACCATG
* * * * *
28236206 TCTGGAACATGGTATC--AATGTTGATATGTGCA
66 TCTGGGACATGGCATCGGCATGTTGAGATGAGCA
*
28236238 -CTAGTGTAAGACCATGTCTGGGACATGGCATCGACCAC-ATCATGAGAGCCAGTGTAAGACCAT
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGA-CATGAGAGCCAGTGTAAGACCAT
28236301 GTCTGGGACATGGCATCGGCA-G-TGAGATGAG-A
65 GTCTGGGACATGGCATCGGCATGTTGAGATGAGCA
* * * * *
28236333 GCTAGTATAAGACCATGTCTGGGACATGGCATCGGGCTCGACGTGTGAGCCAGTGTAAGACCATG
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGACATGAGAGCCAGTGTAAGACCATG
28236398 TCTGGGACATGGCATCGGCA
66 TCTGGGACATGGCATCGGCA
28236418 ATTTACCCTC
Statistics
Matches: 163, Mismatches: 12, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
95 2 0.01
96 158 0.97
97 2 0.01
98 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.31, T:0.22
Consensus pattern (99 bp):
GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGACATGAGAGCCAGTGTAAGACCATG
TCTGGGACATGGCATCGGCATGTTGAGATGAGCA
Found at i:28239072 original size:55 final size:53
Alignment explanation
Indices: 28238990--28239293 Score: 274
Period size: 55 Copynumber: 5.8 Consensus size: 53
28238980 ATTAGGGTTT
28238990 AAGGATACCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGA
1 AAGGATACCATGTAAGACCATGCCAAGGCATGG-AATTGGTAA-GTTTCTAAGGA
*
28239045 AAGGATACCATGTAAGACCATGTCAAGGCATGGCAATTGGTAAGATTTCTAAGGA
1 AAGGATACCATGTAAGACCATGCCAAGGCATGG-AATTGGTAAG-TTTCTAAGGA
* * * * * *
28239100 AAGGATACCATGTAAGATCATGCCAAGACATCGCATTGATAAGTTACTATAAGGCA
1 AAGGATACCATGTAAGACCATGCCAAGGCATGGAATTGGTAAGTT--TCTAAGG-A
* * * *
28239156 AAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATT-GTCA-----TAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGGCATGGAATTGGTAAGTTTCTAAGGA
* * *
28239202 AAGGATACCATGTAAGACCATGTCGAGACATGGCAA-TGGTAAGTTTC--A--A
1 AAGGATACCATGTAAGACCATGCCAAGGCATGG-AATTGGTAAGTTTCTAAGGA
** * *
28239251 AAGGATACCACATAAGACCATGACAAGTCATGGTAA-TGGTAAG
1 AAGGATACCATGTAAGACCATGCCAAGGCATGG-AATTGGTAAG
28239294 GTACCCGTGT
Statistics
Matches: 208, Mismatches: 29, Indels: 30
0.78 0.11 0.11
Matches are distributed among these distances:
46 4 0.02
47 30 0.14
48 4 0.02
49 37 0.18
51 1 0.00
53 2 0.01
54 11 0.05
55 114 0.55
56 5 0.02
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGGCATGGAATTGGTAAGTTTCTAAGGA
Found at i:28239450 original size:14 final size:14
Alignment explanation
Indices: 28239431--28239459 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
28239421 GTATGTAATG
28239431 TTCATGTATGCTTA
1 TTCATGTATGCTTA
28239445 TTCATGTATGCTTA
1 TTCATGTATGCTTA
28239459 T
1 T
28239460 AAAAAAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.52
Consensus pattern (14 bp):
TTCATGTATGCTTA
Found at i:28239518 original size:20 final size:20
Alignment explanation
Indices: 28239490--28239529 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
28239480 GTATTAATAA
*
28239490 ATTTGATTAAGTAAGTAAGT
1 ATTTAATTAAGTAAGTAAGT
*
28239510 ATTTAATTAAGTGAGTAAGT
1 ATTTAATTAAGTAAGTAAGT
28239530 GAAGAAGTTT
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:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (20 bp):
ATTTAATTAAGTAAGTAAGT
Found at i:28243885 original size:26 final size:27
Alignment explanation
Indices: 28243856--28243910 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
28243846 GCGAAGTGCC
28243856 AAAT-TTTCACTGA-TCACAAAAG-TTTG
1 AAATATTTCA-TGACTCA-AAAAGATTTG
*
28243882 AAATATTTGATGACTCAAAAAGATTTG
1 AAATATTTCATGACTCAAAAAGATTTG
28243909 AA
1 AA
28243911 CTTGAGACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
26 12 0.48
27 13 0.52
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.33
Consensus pattern (27 bp):
AAATATTTCATGACTCAAAAAGATTTG
Found at i:28246876 original size:55 final size:53
Alignment explanation
Indices: 28246768--28246952 Score: 212
Period size: 55 Copynumber: 3.4 Consensus size: 53
28246758 ATTAGGGTTT
* *
28246768 AAGGATACCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTT-TCTAAGGC
1 AAGG-TACCATGTAAGACCATGCCAAGGCATGG-CATTGGTAA-GTTCTATAAGGC
* * * *
28246823 AAGTGTACCATGTAAGACCATGTCAAGACATCGCATTGATAAGTTACTATAAGGC
1 AAG-GTACCATGTAAGACCATGCCAAGGCATGGCATTGGTAAGTT-CTATAAGGC
* * *
28246878 AAAGGTCCCATGTAAGACCATGCCAAGGCGTGGCATTGGTGAGTTC-ATAAGGC
1 -AAGGTACCATGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTCTATAAGGC
28246931 AAGGATACCATGTAAGACCATG
1 AAGG-TACCATGTAAGACCATG
28246953 TTGAGACATG
Statistics
Matches: 111, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
52 4 0.04
53 26 0.23
54 8 0.07
55 69 0.62
56 4 0.04
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.22
Consensus pattern (53 bp):
AAGGTACCATGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTCTATAAGGC
Found at i:28246974 original size:108 final size:110
Alignment explanation
Indices: 28246775--28246975 Score: 275
Period size: 108 Copynumber: 1.8 Consensus size: 110
28246765 TTTAAGGATA
28246775 CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGTGTACCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGTGTACCATGTAAGA
* *
28246840 CCATGTCAAGACATCGCATTGATAAGTTACTATAAGGCAAAGGTC
66 CCATGTCAAGACATCGAAATGATAAGTTACTATAAGGCAAAGGTC
* * *
28246885 CCATGTAAGACCATGCCAAGGCGTGG-CATTGGTGA-G-TTCATAAGGCAAG-GATACCATGTAA
1 CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTC-TAAGGCAAGTG-TACCATGTAA
** * *
28246946 GACCATGTTGAGACATGGAAATGGTAAGTT
64 GACCATGTCAAGACATCGAAATGATAAGTT
28246976 TCAAAAGGAT
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
107 4 0.05
108 44 0.55
109 7 0.09
110 25 0.31
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.23
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGTGTACCATGTAAGA
CCATGTCAAGACATCGAAATGATAAGTTACTATAAGGCAAAGGTC
Found at i:28249721 original size:17 final size:16
Alignment explanation
Indices: 28249687--28249732 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
28249677 AAATTATAAG
28249687 TAAATTTT-TTAT-TT
1 TAAATTTTATTATGTT
28249701 TAAATTTTATTATGATT
1 TAAATTTTATTATG-TT
*
28249718 TAAATTTCATTATGT
1 TAAATTTTATTATGT
28249733 GAGCTCTGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 8 0.29
15 4 0.14
16 1 0.04
17 15 0.54
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (16 bp):
TAAATTTTATTATGTT
Found at i:28250132 original size:26 final size:28
Alignment explanation
Indices: 28250103--28250156 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
28250093 TAGATATTAT
*
28250103 AGAATA-AAATTTATTTTTAA-ATTTTA
1 AGAATATAAATTTATTTTGAATATTTTA
*
28250129 AGAATATATATTTATTTTGAATATTTTA
1 AGAATATAAATTTATTTTGAATATTTTA
28250157 GATTTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 6 0.25
27 12 0.50
28 6 0.25
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.52
Consensus pattern (28 bp):
AGAATATAAATTTATTTTGAATATTTTA
Found at i:28251876 original size:31 final size:31
Alignment explanation
Indices: 28251838--28251901 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
28251828 TTATTTGAGA
*
28251838 AAGAAATTTAGCCCTCGAGGGGGTTTAGTTC
1 AAGAAATTTAGCCCTCGAGGAGGTTTAGTTC
*
28251869 AAGAAATTTAGCCCTCGAGTAGGTTTAGTTC
1 AAGAAATTTAGCCCTCGAGGAGGTTTAGTTC
28251900 AA
1 AA
28251902 AATGGTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (31 bp):
AAGAAATTTAGCCCTCGAGGAGGTTTAGTTC
Found at i:28259664 original size:40 final size:40
Alignment explanation
Indices: 28259579--28259729 Score: 141
Period size: 40 Copynumber: 3.8 Consensus size: 40
28259569 AATTGAATGA
* * * *
28259579 TATCCGGGCTAAGCCCCGAAGACAATTATGCTG-GAAATTA-
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC-GAGACA-TAC
* * *
28259619 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGACATAC
*
28259660 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGACATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGACATAC
*
28259699 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
28259730 ACGTGGTTAT
Statistics
Matches: 92, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
38 3 0.03
39 5 0.05
40 80 0.87
41 3 0.03
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.22
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGACATAC
Found at i:28259743 original size:40 final size:40
Alignment explanation
Indices: 28259616--28259745 Score: 154
Period size: 40 Copynumber: 3.2 Consensus size: 40
28259606 ATGCTGGAAA
* * *
28259616 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* * * ***
28259656 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGACA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
*
28259696 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGG
28259736 TTATATCCGG
1 TTATATCCGG
28259746 TTATATTCCG
Statistics
Matches: 72, Mismatches: 17, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
39 1 0.01
40 71 0.99
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
Found at i:28259744 original size:80 final size:80
Alignment explanation
Indices: 28259578--28259745 Score: 207
Period size: 80 Copynumber: 2.1 Consensus size: 80
28259568 AAATTGAATG
* *
28259578 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATTATATCCGGGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTGGAAATTATATCCGGGCTAAGACCCGAAGGCA
28259643 ATTGTGCTAGTGGCT
66 ATTGTGCTAGTGGCT
* * * * *
28259658 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGACATTCTATCCGGGCTAAGACCCGAAGG
1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTG-GAAATTATATCCGGGCTAAGACCCGAAGG
* *
28259721 CATTTGTGC-ACGTGGTT
64 CAATTGTGCTA-GTGGCT
28259738 ATATCCGG
1 ATATCCGG
28259746 TTATATTCCG
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
79 5 0.07
80 70 0.93
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTGGAAATTATATCCGGGCTAAGACCCGAAGGCA
ATTGTGCTAGTGGCT
Found at i:28267632 original size:40 final size:40
Alignment explanation
Indices: 28267566--28267716 Score: 155
Period size: 40 Copynumber: 3.8 Consensus size: 40
28267556 AAATTGAATG
* *
28267566 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGAAATT
* * ****
28267605 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGAAATT
* *
28267645 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGACATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GAAATT
* *
28267685 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
28267717 ACGTGGTTAT
Statistics
Matches: 90, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
39 16 0.18
40 72 0.80
41 2 0.02
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGAAATT
Found at i:28267730 original size:40 final size:40
Alignment explanation
Indices: 28267603--28267732 Score: 154
Period size: 40 Copynumber: 3.2 Consensus size: 40
28267593 ATGCTGGAAA
* * *
28267603 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* * * ***
28267643 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGACA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
*
28267683 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGG
28267723 TTATATCCGG
1 TTATATCCGG
28267733 TTATATTCCG
Statistics
Matches: 72, Mismatches: 17, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
39 1 0.01
40 71 0.99
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
Found at i:28267731 original size:80 final size:79
Alignment explanation
Indices: 28267566--28267732 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
28267556 AAATTGAATG
*
28267566 ATATCCGGGCTAAGCCCGAAGACAATTATGCTGGAAATTATATCCGGGTTAAGACCCGAAGGCAA
1 ATATCCGGGCTAAGCCCGAAGACAATTATGCTGGAAATTATATCCGGGCTAAGACCCGAAGGCAA
28267631 TTGTGCTAGTGGCT
66 TTGTGCTAGTGGCT
* * * * *
28267645 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGACATTCTATCCGGGCTAAGACCCGAAGG
1 ATATCCGGGCTAAG-CCCGAAGACAATT-ATGCTG-GAAATTATATCCGGGCTAAGACCCGAAGG
* *
28267708 CATTTGTGC-ACGTGGTT
63 CAATTGTGCTA-GTGGCT
28267725 ATATCCGG
1 ATATCCGG
28267733 TTATATTCCG
Statistics
Matches: 75, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
79 18 0.24
80 57 0.76
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (79 bp):
ATATCCGGGCTAAGCCCGAAGACAATTATGCTGGAAATTATATCCGGGCTAAGACCCGAAGGCAA
TTGTGCTAGTGGCT
Found at i:28270003 original size:29 final size:29
Alignment explanation
Indices: 28269970--28270052 Score: 109
Period size: 29 Copynumber: 3.0 Consensus size: 29
28269960 CAAATATAAG
28269970 ATAGCCACAAAGGCGTCTACATAATAAAT
1 ATAGCCACAAAGGCGTCTACATAATAAAT
* * * *
28269999 ATAGCCACAAGGGCGTCCACTTAATAGAT
1 ATAGCCACAAAGGCGTCTACATAATAAAT
28270028 ATAGCCACAAAGGC-TCT-CAT-ATAAA
1 ATAGCCACAAAGGCGTCTACATAATAAA
28270053 ATTAGATAGT
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
26 4 0.09
27 2 0.04
28 2 0.04
29 38 0.83
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.20
Consensus pattern (29 bp):
ATAGCCACAAAGGCGTCTACATAATAAAT
Found at i:28276830 original size:21 final size:22
Alignment explanation
Indices: 28276804--28276849 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
28276794 AGCATGGGCA
28276804 TGTCCCAAGG-TCACACAGGCG
1 TGTCCCAAGGATCACACAGGCG
**
28276825 TGTCCCTTGGATCACACAGGCG
1 TGTCCCAAGGATCACACAGGCG
28276847 TGT
1 TGT
28276850 GAGCCCTGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.20, C:0.30, G:0.28, T:0.22
Consensus pattern (22 bp):
TGTCCCAAGGATCACACAGGCG
Found at i:28284400 original size:189 final size:189
Alignment explanation
Indices: 28284080--28284457 Score: 657
Period size: 189 Copynumber: 2.0 Consensus size: 189
28284070 CTTTGAAAAT
28284080 TTAAGAACAATTGGGAGTTGAGTCCGTAAGCTTTCAGATCATATGAGAAATTAAAGACATGTATT
1 TTAAGAACAATTGGGAGTTGAGTCCGTAAGCTTTCAGATCATATGAGAAATTAAAGACATGTATT
* *
28284145 GGAGGCACCGCCTGAGCGAAGGTACTTTGGTATCGAGAATGAGATTGAGGAATCTAAGTGAAGAC
66 GGAGGCACCGCCTGAGCGAAGGTACTTTGGTATCAAGAATGAGACTGAGGAATCTAAGTGAAGAC
* *
28284210 CACTTTTCCGATAAGATTTTCGGAGACAAAAATCCCTAAAGGGGGGAGGGTTGTAACAC
131 CACTTTTCCGATAAGATTTTCGGAGACAAAAATCCCTAAAGGGGGGAGAGTTATAACAC
*
28284269 TTAAGAACAATTGGGAGTTGAGTCCGTAAGCTTTCAGATCATATGAGAAATTAAAGAGATGTATT
1 TTAAGAACAATTGGGAGTTGAGTCCGTAAGCTTTCAGATCATATGAGAAATTAAAGACATGTATT
*
28284334 GGAGGCACCGCCTGAGCGAAGGTACTTTGGTATCAAGTATGAGACTGAGGAATCTAAGTGAAGAC
66 GGAGGCACCGCCTGAGCGAAGGTACTTTGGTATCAAGAATGAGACTGAGGAATCTAAGTGAAGAC
* * ** *
28284399 CACTTTTCCGGTAAGATTTTCGGGGATGAAAATCCCTAAAGGGTGGAGAGTTATAACAC
131 CACTTTTCCGATAAGATTTTCGGAGACAAAAATCCCTAAAGGGGGGAGAGTTATAACAC
28284458 CCAGATTTTG
Statistics
Matches: 178, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
189 178 1.00
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (189 bp):
TTAAGAACAATTGGGAGTTGAGTCCGTAAGCTTTCAGATCATATGAGAAATTAAAGACATGTATT
GGAGGCACCGCCTGAGCGAAGGTACTTTGGTATCAAGAATGAGACTGAGGAATCTAAGTGAAGAC
CACTTTTCCGATAAGATTTTCGGAGACAAAAATCCCTAAAGGGGGGAGAGTTATAACAC
Found at i:28289859 original size:26 final size:26
Alignment explanation
Indices: 28289823--28289875 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
28289813 TGATGAGCTT
*
28289823 ATGTGTCCTTTGATTTTTAATGGTGA
1 ATGTGTCCTTTGATGTTTAATGGTGA
28289849 ATGTGTCCTTTGATGTTTAATGGTGA
1 ATGTGTCCTTTGATGTTTAATGGTGA
28289875 A
1 A
28289876 ATATGAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.21, C:0.08, G:0.25, T:0.47
Consensus pattern (26 bp):
ATGTGTCCTTTGATGTTTAATGGTGA
Found at i:28290514 original size:42 final size:42
Alignment explanation
Indices: 28290467--28290570 Score: 172
Period size: 42 Copynumber: 2.5 Consensus size: 42
28290457 TATCGGGATG
* *
28290467 TGAGATTCATGTAAGACCATGACTGGGACATTTGCATCGATA
1 TGAGATTCGTGTAAGACCATGACTGGGACATTGGCATCGATA
*
28290509 TGAGATTCGTGTAAGACCATGTCTGGGACATTGGCATCGATA
1 TGAGATTCGTGTAAGACCATGACTGGGACATTGGCATCGATA
*
28290551 TGAGATTTGTGTAAGACCAT
1 TGAGATTCGTGTAAGACCAT
28290571 AGCTAGGCTA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (42 bp):
TGAGATTCGTGTAAGACCATGACTGGGACATTGGCATCGATA
Found at i:28290584 original size:42 final size:42
Alignment explanation
Indices: 28290467--28290592 Score: 159
Period size: 42 Copynumber: 3.0 Consensus size: 42
28290457 TATCGGGATG
* * * *
28290467 TGAGATTCATGTAAGACCATGACTGGGACATTTGCATCGATA
1 TGAGATTCGTGTAAGACCATGTCTAGGACATTGGCATCGATA
*
28290509 TGAGATTCGTGTAAGACCATGTCTGGGACATTGGCATCGATA
1 TGAGATTCGTGTAAGACCATGTCTAGGACATTGGCATCGATA
*
28290551 TGAGATTTGTGTAAGACCATAG-CTAGG-CTATTGG-ATCGATA
1 TGAGATTCGTGTAAGACCAT-GTCTAGGAC-ATTGGCATCGATA
28290592 T
1 T
28290593 ACTATAACAT
Statistics
Matches: 77, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
41 9 0.12
42 67 0.87
43 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (42 bp):
TGAGATTCGTGTAAGACCATGTCTAGGACATTGGCATCGATA
Found at i:28291506 original size:21 final size:21
Alignment explanation
Indices: 28291480--28291536 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 21
28291470 ATGGTATAAG
28291480 GTTGATGAATTGGTACATTTT
1 GTTGATGAATTGGTACATTTT
*
28291501 GTTGATGATGAATTGGTATATTTT
1 G-T--TGATGAATTGGTACATTTT
*
28291525 GTGGCATGAATT
1 GTTG-ATGAATT
28291537 ATATGATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
21 2 0.07
22 8 0.27
23 1 0.03
24 19 0.63
ACGTcount: A:0.25, C:0.04, G:0.26, T:0.46
Consensus pattern (21 bp):
GTTGATGAATTGGTACATTTT
Found at i:28298313 original size:29 final size:28
Alignment explanation
Indices: 28298281--28298383 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
28298271 GGGACGAGAT
* *
28298281 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTG-AATATA
* *
28298310 TGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTT-GAATATA
* * *
28298339 TGGCACTATGTGTGCGGGCTTGAATCACA
1 TGGCACTAAGTGTGCGAGCTTGAAT-ATA
28298368 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
28298384 TGATTGAGTA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 3 0.05
29 58 0.94
30 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (28 bp):
TGGCACTAAGTGTGCGAGCTTGAATATA
Found at i:28306354 original size:29 final size:28
Alignment explanation
Indices: 28306322--28306424 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
28306312 GGGACGAGAT
* *
28306322 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTG-AATATA
* *
28306351 TGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTT-GAATATA
* * *
28306380 TGGCACTATGTGTGCGGGCTTGAATCACA
1 TGGCACTAAGTGTGCGAGCTTGAAT-ATA
28306409 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
28306425 TGATTGAGTA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 3 0.05
29 58 0.94
30 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (28 bp):
TGGCACTAAGTGTGCGAGCTTGAATATA
Found at i:28325505 original size:45 final size:45
Alignment explanation
Indices: 28325402--28325578 Score: 249
Period size: 45 Copynumber: 4.0 Consensus size: 45
28325392 CCGAATTCAT
* * *
28325402 TCACCGGCATT-TCA-CCTGCTAGGCTC-GAGGCCCG-ATA-TCCTT
1 TCACCGGCATTAT-AGCCTGCTAGGCTCAAAGGCCCGAATAGT-ATC
28325444 TCACCGGCATTATAGCCTGCTAGGCTCGAAA-GCCCGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTC-AAAGGCCCGAATAGTATC
*
28325489 TCACCGGCATTGTAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
28325534 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
28325579 GTACGATAAT
Statistics
Matches: 123, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
42 12 0.10
43 13 0.11
44 8 0.07
45 89 0.72
46 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.23, T:0.23
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
Found at i:28337772 original size:26 final size:25
Alignment explanation
Indices: 28337743--28337888 Score: 168
Period size: 26 Copynumber: 5.6 Consensus size: 25
28337733 TAAATCACCG
28337743 GCTCAAAGCCTACTAACTAATCATCA
1 GCTCAAAGCCTACTAACTAATCA-CA
*
28337769 GCTCAAAGCCTACTAACTAATCATCG
1 GCTCAAAGCCTACTAACTAATCA-CA
* *
28337795 GCTCAACGCCTACTAACTAATCACCG
1 GCTCAAAGCCTACTAACTAATCA-CA
* *
28337821 GCTCAAAGCCTGCTAA-TCAGTCACAA
1 GCTCAAAGCCTACTAACT-AATCAC-A
*
28337847 GCTCAAAGCCTGCTAACTAATCACTA
1 GCTCAAAGCCTACTAACTAATCAC-A
*
28337873 GCTCAAAGCCTGCTAA
1 GCTCAAAGCCTACTAA
28337889 TCAGTAACAT
Statistics
Matches: 108, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
25 2 0.02
26 105 0.97
27 1 0.01
ACGTcount: A:0.34, C:0.32, G:0.12, T:0.21
Consensus pattern (25 bp):
GCTCAAAGCCTACTAACTAATCACA
Found at i:28337877 original size:78 final size:78
Alignment explanation
Indices: 28337735--28337888 Score: 206
Period size: 78 Copynumber: 2.0 Consensus size: 78
28337725 ATGTTATATA
*
28337735 AATCACCGGCTCAAAGCCTACTAACTAATCATCAGCTCAAAGCCTACTAACTAATCATCGGCTCA
1 AATCACCGGCTCAAAGCCTACTAACTAATCATCAGCTCAAAGCCTACTAACTAATCATCAGCTCA
*
28337800 ACGCCTACTAACT
66 AAGCCTACTAACT
* * *
28337813 AATCACCGGCTCAAAGCCTGCTAA-TCAGTCA-CAAGCTCAAAGCCTGCTAACTAATCA-CTAGC
1 AATCACCGGCTCAAAGCCTACTAACT-AATCATC-AGCTCAAAGCCTACTAACTAATCATC-AGC
*
28337875 TCAAAGCCTGCTAA
63 TCAAAGCCTACTAA
28337889 TCAGTAACAT
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
77 3 0.04
78 64 0.96
ACGTcount: A:0.34, C:0.32, G:0.12, T:0.21
Consensus pattern (78 bp):
AATCACCGGCTCAAAGCCTACTAACTAATCATCAGCTCAAAGCCTACTAACTAATCATCAGCTCA
AAGCCTACTAACT
Found at i:28337892 original size:52 final size:52
Alignment explanation
Indices: 28337743--28337893 Score: 191
Period size: 52 Copynumber: 2.9 Consensus size: 52
28337733 TAAATCACCG
* * *
28337743 GCTCAAAGCCTACTAACTAATCA-TCAGCTCAAAGCCTACTAA-CTAATCATCG
1 GCTCAAAGCCTACTAACTAATCACT-AGCTCAAAGCCTGCTAATC-AGTCATCA
* **
28337795 GCTCAACGCCTACTAACTAATCACCGGCTCAAAGCCTGCTAATCAGTCA-CAA
1 GCTCAAAGCCTACTAACTAATCACTAGCTCAAAGCCTGCTAATCAGTCATC-A
*
28337847 GCTCAAAGCCTGCTAACTAATCACTAGCTCAAAGCCTGCTAATCAGT
1 GCTCAAAGCCTACTAACTAATCACTAGCTCAAAGCCTGCTAATCAGT
28337894 AACATACTCA
Statistics
Matches: 86, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
51 1 0.01
52 84 0.98
53 1 0.01
ACGTcount: A:0.34, C:0.32, G:0.13, T:0.22
Consensus pattern (52 bp):
GCTCAAAGCCTACTAACTAATCACTAGCTCAAAGCCTGCTAATCAGTCATCA
Found at i:28337903 original size:26 final size:27
Alignment explanation
Indices: 28337821--28337903 Score: 104
Period size: 26 Copynumber: 3.2 Consensus size: 27
28337811 CTAATCACCG
*
28337821 GCTCAAAGCCTGCTAATCAGTCACA-A
1 GCTCAAAGCCTGCTAATCAGTAACATA
28337847 GCTCAAAGCCTGCTAA-C--TAATCACTA
1 GCTCAAAGCCTGCTAATCAGTAA-CA-TA
28337873 GCTCAAAGCCTGCTAATCAGTAACATA
1 GCTCAAAGCCTGCTAATCAGTAACATA
28337900 -CTCA
1 GCTCA
28337904 CTATATCTAT
Statistics
Matches: 50, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
23 2 0.04
24 2 0.04
25 1 0.02
26 37 0.74
27 3 0.06
28 2 0.04
29 3 0.06
ACGTcount: A:0.35, C:0.30, G:0.13, T:0.22
Consensus pattern (27 bp):
GCTCAAAGCCTGCTAATCAGTAACATA
Found at i:28343894 original size:21 final size:21
Alignment explanation
Indices: 28343870--28343936 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
28343860 ACGGTTTGCA
* *
28343870 CACACGGCCGTGTGACCTATC
1 CACAAGGCCGTGTGACCCATC
28343891 CACAAGGCCGTGTGACCCATC
1 CACAAGGCCGTGTGACCCATC
* *
28343912 CACAAGGCTGTGTGACCCATG
1 CACAAGGCCGTGTGACCCATC
28343933 CACA
1 CACA
28343937 TGACCATGTG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (21 bp):
CACAAGGCCGTGTGACCCATC
Found at i:28346514 original size:13 final size:13
Alignment explanation
Indices: 28346496--28346520 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28346486 TATTACATAA
28346496 AAGAAAAAGGAAG
1 AAGAAAAAGGAAG
28346509 AAGAAAAAGGAA
1 AAGAAAAAGGAA
28346521 CTGATGGAGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (13 bp):
AAGAAAAAGGAAG
Found at i:28355968 original size:117 final size:118
Alignment explanation
Indices: 28355761--28355991 Score: 367
Period size: 117 Copynumber: 2.0 Consensus size: 118
28355751 CATGTGGATA
*
28355761 TAACATCTGTTAATTGAAATTGGATTGAAGCATACATCACTAGCAAAACTTTGGTACCATAATTA
1 TAACATCTGTTAATTGAAATTGGATTGAAGCATACACCACTAGCAAAACTTTGGTACCATAATTA
* * *
28355826 AGTTTCTGTTCATATTGCCTCGAAATGAAACTATCATGAAAGAATCAAACTAT
66 AGTTGCTCTTCATATTGCCTCGAAATCAAACTATCATGAAAGAATCAAACTAT
* *
28355879 TAACATCTGTTAATTG-AATTGGATTGGAGCATACACCACTAGCAAAA-TTTGGGTGCCATAATT
1 TAACATCTGTTAATTGAAATTGGATTGAAGCATACACCACTAGCAAAACTTT-GGTACCATAATT
* *
28355942 AAGTTGCTCTTCATATTGCCTCGAAATCAATCTATCATGAACGAATCAAA
65 AAGTTGCTCTTCATATTGCCTCGAAATCAAACTATCATGAAAGAATCAAA
28355992 GCATCAAGGT
Statistics
Matches: 104, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
116 3 0.03
117 85 0.82
118 16 0.15
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (118 bp):
TAACATCTGTTAATTGAAATTGGATTGAAGCATACACCACTAGCAAAACTTTGGTACCATAATTA
AGTTGCTCTTCATATTGCCTCGAAATCAAACTATCATGAAAGAATCAAACTAT
Found at i:28361781 original size:21 final size:21
Alignment explanation
Indices: 28361739--28361781 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
28361729 TTGAGTCAAA
* * **
28361739 TATTTTCAAATATGTTTTAAT
1 TATTTTCAAACAAGTTAGAAT
28361760 TATTTTCAAACAAGTTAGAAT
1 TATTTTCAAACAAGTTAGAAT
28361781 T
1 T
28361782 GCTCCATGAC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (21 bp):
TATTTTCAAACAAGTTAGAAT
Found at i:28365224 original size:19 final size:19
Alignment explanation
Indices: 28365200--28365238 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
28365190 TTCTTATCTC
28365200 TAAGGATAGTATGTACTGT
1 TAAGGATAGTATGTACTGT
28365219 TAAGGATAGTATGTACTGT
1 TAAGGATAGTATGTACTGT
28365238 T
1 T
28365239 GTATTGCCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.05, G:0.26, T:0.38
Consensus pattern (19 bp):
TAAGGATAGTATGTACTGT
Found at i:28367331 original size:7 final size:7
Alignment explanation
Indices: 28367319--28367352 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
28367309 CATATTCGAA
28367319 TATATAT
1 TATATAT
28367326 TATATAT
1 TATATAT
*
28367333 TACATA-
1 TATATAT
28367339 TATATAT
1 TATATAT
28367346 TATATAT
1 TATATAT
28367353 ACATAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (7 bp):
TATATAT
Found at i:28367343 original size:20 final size:19
Alignment explanation
Indices: 28367318--28367357 Score: 71
Period size: 20 Copynumber: 2.1 Consensus size: 19
28367308 TCATATTCGA
28367318 ATATATATTATATATTACAT
1 ATATATATTATATA-TACAT
28367338 ATATATATTATATATACAT
1 ATATATATTATATATACAT
28367357 A
1 A
28367358 ATTATTTAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (19 bp):
ATATATATTATATATACAT
Found at i:28368334 original size:26 final size:26
Alignment explanation
Indices: 28368305--28368359 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
28368295 TCTCAAAAGA
28368305 AAACCATTCAATTCATGCAATTACTT
1 AAACCATTCAATTCATGCAATTACTT
*
28368331 AAACCATTCAATTCATGCAATTATTT
1 AAACCATTCAATTCATGCAATTACTT
28368357 AAA
1 AAA
28368360 AAATTTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.42, C:0.20, G:0.04, T:0.35
Consensus pattern (26 bp):
AAACCATTCAATTCATGCAATTACTT
Found at i:28368973 original size:3 final size:3
Alignment explanation
Indices: 28368965--28368990 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
28368955 TTAGTCTTTG
28368965 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
28368991 TTTTACTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:28374570 original size:33 final size:33
Alignment explanation
Indices: 28374533--28374639 Score: 124
Period size: 33 Copynumber: 3.2 Consensus size: 33
28374523 ATCCCATCAA
* *
28374533 CACACTAATGCTCAGAAGAGCTAATCCAAGCAG
1 CACACCAATGCTCAGAAGAGCTAATCCAACCAG
* *
28374566 CACACCAATGCTCATAAGAGCTAATCCAACCAT
1 CACACCAATGCTCAGAAGAGCTAATCCAACCAG
* * * * * *
28374599 CACACCGATGCTTATAAGAGATAGTCCAACCAA
1 CACACCAATGCTCAGAAGAGCTAATCCAACCAG
28374632 CACACCAA
1 CACACCAA
28374640 ACAAAGAGTA
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 64 1.00
ACGTcount: A:0.40, C:0.31, G:0.13, T:0.16
Consensus pattern (33 bp):
CACACCAATGCTCAGAAGAGCTAATCCAACCAG
Found at i:28378489 original size:27 final size:27
Alignment explanation
Indices: 28378445--28378899 Score: 615
Period size: 27 Copynumber: 16.9 Consensus size: 27
28378435 AATACTTTAA
* * *
28378445 TTTATCAAATTACTAAAATACCCCTGG
1 TTTATAAAATTACCAAAATACCCTTGG
* * * *
28378472 TTTGTAAAATCACCAAAATGCACTTGG
1 TTTATAAAATTACCAAAATACCCTTGG
*
28378499 TTTGTAAAATT-CCAAAATACCCTTGG
1 TTTATAAAATTACCAAAATACCCTTGG
*
28378525 TTTATAAAATTACCAAAATACCCCTGG
1 TTTATAAAATTACCAAAATACCCTTGG
* *
28378552 TTTGTAAAATTACCAAAATATCCTTGG
1 TTTATAAAATTACCAAAATACCCTTGG
*
28378579 TTTACAAAATTACCAAAATACCCTTGG
1 TTTATAAAATTACCAAAATACCCTTGG
*
28378606 TTTACAAAATTACCAAAATACCCTTGG
1 TTTATAAAATTACCAAAATACCCTTGG
* *
28378633 TTTACAAAATTACCAAAATACCCCTGG
1 TTTATAAAATTACCAAAATACCCTTGG
*
28378660 TTTGTAAAATTACCAAAATACCCTTGG
1 TTTATAAAATTACCAAAATACCCTTGG
* *
28378687 TTTACAAAATTACCAAAATACCCCTGG
1 TTTATAAAATTACCAAAATACCCTTGG
* *
28378714 TTTGTAAAATTACCAAAATACCCTTAG
1 TTTATAAAATTACCAAAATACCCTTGG
* *
28378741 TTTACAAAATTACCAAAATACCCCTGG
1 TTTATAAAATTACCAAAATACCCTTGG
*
28378768 TTTATAAAATTACCAAAATACCCTTAG
1 TTTATAAAATTACCAAAATACCCTTGG
* *
28378795 TTTACAAAATTACCAAAATACCCTTAG
1 TTTATAAAATTACCAAAATACCCTTGG
* *
28378822 TTTGTAAAATTACCAAAATACCCCTGG
1 TTTATAAAATTACCAAAATACCCTTGG
* * * *
28378849 TTTGTAAAATTATCAAAATACTCTTAG
1 TTTATAAAATTACCAAAATACCCTTGG
*
28378876 TTTGTAAAATTACCAAAATACCCT
1 TTTATAAAATTACCAAAATACCCT
28378900 CGACTTGTAA
Statistics
Matches: 380, Mismatches: 47, Indels: 2
0.89 0.11 0.00
Matches are distributed among these distances:
26 23 0.06
27 357 0.94
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (27 bp):
TTTATAAAATTACCAAAATACCCTTGG
Found at i:28378907 original size:27 final size:27
Alignment explanation
Indices: 28378451--28378952 Score: 496
Period size: 27 Copynumber: 18.6 Consensus size: 27
28378441 TTAATTTATC
*
28378451 AAATTACTAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GGTTTGTA
* * * *
28378478 AAATCACCAAAATGCACTTGGTTTGTA
1 AAATTACCAAAATACCCTCGGTTTGTA
* *
28378505 AAATT-CCAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCTCGGTTTGTA
28378531 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GGTTTGTA
* * **
28378558 AAATTACCAAAATATCCTTGGTTTACA
1 AAATTACCAAAATACCCTCGGTTTGTA
* **
28378585 AAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCTCGGTTTGTA
* **
28378612 AAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCTCGGTTTGTA
28378639 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GGTTTGTA
* **
28378666 AAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCTCGGTTTGTA
28378693 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GGTTTGTA
** **
28378720 AAATTACCAAAATACCCTTAGTTTACA
1 AAATTACCAAAATACCCTCGGTTTGTA
*
28378747 AAATTACCAAAATACCC-CTGGTTTATA
1 AAATTACCAAAATACCCTC-GGTTTGTA
** **
28378774 AAATTACCAAAATACCCTTAGTTTACA
1 AAATTACCAAAATACCCTCGGTTTGTA
**
28378801 AAATTACCAAAATACCCTTAGTTTGTA
1 AAATTACCAAAATACCCTCGGTTTGTA
28378828 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GGTTTGTA
* * **
28378855 AAATTATCAAAATACTCTTAGTTTGTA
1 AAATTACCAAAATACCCTCGGTTTGTA
**
28378882 AAATTACCAAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCTCGGTTTGTA
*** * ** *
28378909 AAATTATTGAAACACCCTCGACTTGCA
1 AAATTACCAAAATACCCTCGGTTTGTA
*
28378936 AAATTACCAAAGTACCC
1 AAATTACCAAAATACCC
28378953 CTAATTTACA
Statistics
Matches: 404, Mismatches: 59, Indels: 24
0.83 0.12 0.05
Matches are distributed among these distances:
26 23 0.06
27 381 0.94
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGGTTTGTA
Found at i:28379027 original size:27 final size:27
Alignment explanation
Indices: 28378997--28379236 Score: 313
Period size: 27 Copynumber: 8.9 Consensus size: 27
28378987 ACAAAATTAT
28378997 CGAAATACCCTTGTAGGGTAGAAATAC
1 CGAAATACCCTTGTAGGGTAGAAATAC
28379024 CGAAATACCCTTGTAGGGTAGAAATAC
1 CGAAATACCCTTGTAGGGTAGAAATAC
*
28379051 CGAAATACCCCTGTAGGGTAGAAATAC
1 CGAAATACCCTTGTAGGGTAGAAATAC
* * * *
28379078 CGAAATACCCCTATAGGGTAGAATTAT
1 CGAAATACCCTTGTAGGGTAGAAATAC
** *
28379105 TAAAATACCCTTGTAGGGTAGAATTAC
1 CGAAATACCCTTGTAGGGTAGAAATAC
*
28379132 CGAAATACCCTTGTAGGGTAGAAATAT
1 CGAAATACCCTTGTAGGGTAGAAATAC
* *
28379159 CGAAATACCCCTATAGGGTA-AAATTAC
1 CGAAATACCCTTGTAGGGTAGAAA-TAC
* * *
28379186 TGAAATACCCCTGTAGGGTAGAATTAC
1 CGAAATACCCTTGTAGGGTAGAAATAC
* *
28379213 CGAGATACCCTTGTGGGGTA-AAAT
1 CGAAATACCCTTGTAGGGTAGAAAT
28379237 TACCATTTTA
Statistics
Matches: 187, Mismatches: 24, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
26 6 0.03
27 179 0.96
28 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.24
Consensus pattern (27 bp):
CGAAATACCCTTGTAGGGTAGAAATAC
Found at i:28379099 original size:81 final size:81
Alignment explanation
Indices: 28378997--28379236 Score: 349
Period size: 81 Copynumber: 3.0 Consensus size: 81
28378987 ACAAAATTAT
* * * * *
28378997 CGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCC
1 CGAAATACCCCTATAGGGTAGAAATACTGAAATACCCTTGTAGGGTAGAATTACCGAAATACCCT
28379062 TGTAGGGTAGAAATAC
66 TGTAGGGTAGAAATAC
* * *
28379078 CGAAATACCCCTATAGGGTAGAATTATTAAAATACCCTTGTAGGGTAGAATTACCGAAATACCCT
1 CGAAATACCCCTATAGGGTAGAAATACTGAAATACCCTTGTAGGGTAGAATTACCGAAATACCCT
*
28379143 TGTAGGGTAGAAATAT
66 TGTAGGGTAGAAATAC
* *
28379159 CGAAATACCCCTATAGGGTA-AAATTACTGAAATACCCCTGTAGGGTAGAATTACCGAGATACCC
1 CGAAATACCCCTATAGGGTAGAAA-TACTGAAATACCCTTGTAGGGTAGAATTACCGAAATACCC
*
28379223 TTGTGGGGTA-AAAT
65 TTGTAGGGTAGAAAT
28379237 TACCATTTTA
Statistics
Matches: 143, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
80 6 0.04
81 137 0.96
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.24
Consensus pattern (81 bp):
CGAAATACCCCTATAGGGTAGAAATACTGAAATACCCTTGTAGGGTAGAATTACCGAAATACCCT
TGTAGGGTAGAAATAC
Found at i:28379762 original size:6 final size:6
Alignment explanation
Indices: 28379753--28379894 Score: 105
Period size: 6 Copynumber: 23.0 Consensus size: 6
28379743 TTGCATTCAC
* *
28379753 ATTCTG ATTCTG ATTCTG -TTACCTG ATACTG ATTCTG ATTCTG -TTACCTA
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATT--CTG
* * *
28379803 ATTTTG ATTCTG GTTCTG ATTCTG ATTCTG -TTACCTG ATACTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG
* *
28379852 ATTCTG -TTACCTA ATTCTG ATTCTG ATT-TGG ATTTTG ATTCTG
1 ATTCTG ATT--CTG ATTCTG ATTCTG ATTCT-G ATTCTG ATTCTG
28379895 TCGCCTGATT
Statistics
Matches: 109, Mismatches: 13, Indels: 28
0.73 0.09 0.19
Matches are distributed among these distances:
5 9 0.08
6 83 0.76
7 11 0.10
8 6 0.06
ACGTcount: A:0.18, C:0.17, G:0.16, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:28379784 original size:25 final size:25
Alignment explanation
Indices: 28379756--28379820 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 25
28379746 CATTCACATT
*
28379756 CTGATTCTGATTCTGTTACCTGATA
1 CTGATTCTGATTCTGTTACCTAATA
*
28379781 CTGATTCTGATTCTGTTACCTAATT
1 CTGATTCTGATTCTGTTACCTAATA
* *
28379806 TTGATTCTGGTTCTG
1 CTGATTCTGATTCTG
28379821 ATTCTGATTC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.17, C:0.18, G:0.17, T:0.48
Consensus pattern (25 bp):
CTGATTCTGATTCTGTTACCTAATA
Found at i:28379822 original size:37 final size:37
Alignment explanation
Indices: 28379775--28379857 Score: 121
Period size: 37 Copynumber: 2.2 Consensus size: 37
28379765 ATTCTGTTAC
* **
28379775 CTGATACTGATTCTGATTCTGTTACCTAATTTTGATT
1 CTGATTCTGATTCTGATTCTGTTACCTAATACTGATT
* *
28379812 CTGGTTCTGATTCTGATTCTGTTACCTGATACTGATT
1 CTGATTCTGATTCTGATTCTGTTACCTAATACTGATT
28379849 CTGATTCTG
1 CTGATTCTG
28379858 TTACCTAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.18, C:0.18, G:0.17, T:0.47
Consensus pattern (37 bp):
CTGATTCTGATTCTGATTCTGTTACCTAATACTGATT
Found at i:28379852 original size:25 final size:25
Alignment explanation
Indices: 28379818--28379879 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
28379808 GATTCTGGTT
*
28379818 CTGATTCTGATTCTGTTACCTGATA
1 CTGATTCTGATTCTGTTACCTAATA
*
28379843 CTGATTCTGATTCTGTTACCTAATT
1 CTGATTCTGATTCTGTTACCTAATA
28379868 CTGATTCTGATT
1 CTGATTCTGATT
28379880 TGGATTTTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.47
Consensus pattern (25 bp):
CTGATTCTGATTCTGTTACCTAATA
Found at i:28379868 original size:19 final size:19
Alignment explanation
Indices: 28379784--28379876 Score: 91
Period size: 19 Copynumber: 4.6 Consensus size: 19
28379774 CCTGATACTG
28379784 ATTCTGATTCTGTTACCTA
1 ATTCTGATTCTGTTACCTA
* *
28379803 ATTTTGATTCTGGTT--CTG
1 ATTCTGATTCT-GTTACCTA
28379821 ATTCTGATTCTGTTACCTGATA
1 ATTCTGATTCTGTTACC---TA
28379843 CTGATTCTGATTCTGTTACCTA
1 ---ATTCTGATTCTGTTACCTA
28379865 ATTCTGATTCTG
1 ATTCTGATTCTG
28379877 ATTTGGATTT
Statistics
Matches: 61, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
17 3 0.05
18 12 0.20
19 23 0.38
20 3 0.05
22 3 0.05
25 17 0.28
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.48
Consensus pattern (19 bp):
ATTCTGATTCTGTTACCTA
Found at i:28379918 original size:62 final size:62
Alignment explanation
Indices: 28379753--28379895 Score: 243
Period size: 62 Copynumber: 2.3 Consensus size: 62
28379743 TTGCATTCAC
*
28379753 ATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTTACCTAATTTTGATTCTG
1 ATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTTACCTAATTCTGATTCTG
*
28379815 GTTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTTACCTAATTCTGATTCTG
1 ATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTTACCTAATTCTGATTCTG
*
28379877 ATT-TGGATTTTGATTCTGT
1 ATTCT-GATTCTGATTCTGT
28379896 CGCCTGATTC
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
61 1 0.01
62 75 0.99
ACGTcount: A:0.18, C:0.17, G:0.16, T:0.49
Consensus pattern (62 bp):
ATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTTACCTAATTCTGATTCTG
Found at i:28382267 original size:27 final size:27
Alignment explanation
Indices: 28382230--28382496 Score: 363
Period size: 27 Copynumber: 9.9 Consensus size: 27
28382220 GAATACTTTA
*
28382230 GTTTATCAAATTACCAAAATACCCCTG
1 GTTTATAAAATTACCAAAATACCCCTG
* *
28382257 GTTTGTAAAATCACCAAAATACCCCTG
1 GTTTATAAAATTACCAAAATACCCCTG
* * *
28382284 GTTTACAAAATTACCAAAATACTCTTG
1 GTTTATAAAATTACCAAAATACCCCTG
* *
28382311 GTTTACAAAATTACCAAAATACCCTTG
1 GTTTATAAAATTACCAAAATACCCCTG
* *
28382338 GTTTACAAAATTACCAAAATACCCTTG
1 GTTTATAAAATTACCAAAATACCCCTG
* *
28382365 GTTTATAAAATTACTAAAATACCCTTG
1 GTTTATAAAATTACCAAAATACCCCTG
*
28382392 GTTTACAAAATTACCAAAATACCCCTG
1 GTTTATAAAATTACCAAAATACCCCTG
28382419 GTTTATAAAATTACCAAAATACCCCTG
1 GTTTATAAAATTACCAAAATACCCCTG
*
28382446 GTTTGTAAAATTACCAAAATACCCCTG
1 GTTTATAAAATTACCAAAATACCCCTG
* * * **
28382473 ATTTGTGAAATTACTGAAATACCC
1 GTTTATAAAATTACCAAAATACCC
28382497 TCGACCTGTA
Statistics
Matches: 220, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 220 1.00
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (27 bp):
GTTTATAAAATTACCAAAATACCCCTG
Found at i:28382509 original size:81 final size:81
Alignment explanation
Indices: 28382237--28382604 Score: 328
Period size: 81 Copynumber: 4.5 Consensus size: 81
28382227 TTAGTTTATC
* *
28382237 AAATTACCAAAATACCC-CTGGTTTGTAAAATCACCAAAATACCCCTGGTTTACAAAATTACCAA
1 AAATTACCAAAATACCCTC-GGTTTATAAAATTACCAAAATACCCCTGGTTTACAAAATTACCAA
* * *
28382301 AATACTCTTGGTTTACA
65 AATACCCCTGATTTACA
* * * * *
28382318 AAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCTTGGTTTATAAAATTACTAAA
1 AAATTACCAAAATACCCTCGGTTTATAAAATTACCAAAATACCCCTGGTTTACAAAATTACCAAA
* *
28382383 ATACCCTTGGTTTACA
66 ATACCCCTGATTTACA
**
28382399 AAATTACCAAAATACCC-CTGGTTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAA
1 AAATTACCAAAATACCCTC-GGTTTATAAAATTACCAAAATACCCCTGGTTTACAAAATTACCAA
***
28382463 AATACCCCTGATTTGTG
65 AATACCCCTGATTTACA
** *** * *** ** *
28382480 AAATTACTGAAATACCCTCGACCTGTAAAATTATTGAAATA-CCCTCGACTTGCAAAATTACCAA
1 AAATTACCAAAATACCCTCGGTTTATAAAATTACCAAAATACCCCT-GGTTTACAAAATTACCAA
* *
28382544 AGTACCCCTGATTTATA
65 AATACCCCTGATTTACA
* **** * * * *
28382561 GAATTACCGTTTTACCCTTGATTTATAAAATTATCGAAATACCC
1 AAATTACCAAAATACCCTCGGTTTATAAAATTACCAAAATACCC
28382605 TTGTAGGGTA
Statistics
Matches: 239, Mismatches: 43, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
80 4 0.02
81 232 0.97
82 3 0.01
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (81 bp):
AAATTACCAAAATACCCTCGGTTTATAAAATTACCAAAATACCCCTGGTTTACAAAATTACCAAA
ATACCCCTGATTTACA
Found at i:28382510 original size:27 final size:27
Alignment explanation
Indices: 28382448--28382540 Score: 107
Period size: 27 Copynumber: 3.4 Consensus size: 27
28382438 TACCCCTGGT
** *
28382448 TTGTAAAATTACCAAAATACCC-CTGAT
1 TTGTAAAATTACTGAAATACCCTC-GAC
*
28382475 TTGTGAAATTACTGAAATACCCTCGAC
1 TTGTAAAATTACTGAAATACCCTCGAC
* *
28382502 CTGTAAAATTATTGAAATACCCTCGAC
1 TTGTAAAATTACTGAAATACCCTCGAC
*
28382529 TTGCAAAATTAC
1 TTGTAAAATTAC
28382541 CAAAGTACCC
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
27 54 0.98
28 1 0.02
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.30
Consensus pattern (27 bp):
TTGTAAAATTACTGAAATACCCTCGAC
Found at i:28382603 original size:27 final size:27
Alignment explanation
Indices: 28382533--28382607 Score: 51
Period size: 27 Copynumber: 2.8 Consensus size: 27
28382523 CTCGACTTGC
* * *
28382533 AAAATTACCAAAGTACCCCTGATTTAT
1 AAAATTACCAAAATACCCTTGGTTTAT
* **** *
28382560 AGAATTACCGTTTTACCCTTGATTTAT
1 AAAATTACCAAAATACCCTTGGTTTAT
* *
28382587 AAAATTATCGAAATACCCTTG
1 AAAATTACCAAAATACCCTTG
28382608 TAGGGTAGAA
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (27 bp):
AAAATTACCAAAATACCCTTGGTTTAT
Found at i:28382627 original size:27 final size:26
Alignment explanation
Indices: 28382595--28382831 Score: 255
Period size: 27 Copynumber: 8.9 Consensus size: 26
28382585 ATAAAATTAT
28382595 CGAAATACCCTTGTAGGGTAGAAATAC
1 CGAAATACCC-TGTAGGGTAGAAATAC
* * *
28382622 CAAAATATCCTTGTAGTGTAGAAATAC
1 CGAAATA-CCCTGTAGGGTAGAAATAC
* *
28382649 CTAAATACTCCTGTAGGGTAGAAATAT
1 CGAAATAC-CCTGTAGGGTAGAAATAC
*
28382676 CGAAATACTCCTGTAGGGTAGAATTAC
1 CGAAATAC-CCTGTAGGGTAGAAATAC
**
28382703 TAAAATACCCCTGTAGGGTAGAAATAC
1 CGAAATA-CCCTGTAGGGTAGAAATAC
*
28382730 CGAAATACCC-CT-GGGTAGAAATAC
1 CGAAATACCCTGTAGGGTAGAAATAC
*
28382754 CGAAATACCCATGTAGGGTAGAATTAC
1 CGAAATACCC-TGTAGGGTAGAAATAC
* *
28382781 TGAAATACCCCTGTAGGGTAGAATTAC
1 CGAAATA-CCCTGTAGGGTAGAAATAC
* *
28382808 CGAGATACCCTTGTGGGGTA-AAAT
1 CGAAATACCC-TGTAGGGTAGAAAT
28382832 TACCATTTTA
Statistics
Matches: 179, Mismatches: 23, Indels: 17
0.82 0.11 0.08
Matches are distributed among these distances:
24 22 0.12
25 1 0.01
26 11 0.06
27 139 0.78
28 6 0.03
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.24
Consensus pattern (26 bp):
CGAAATACCCTGTAGGGTAGAAATAC
Found at i:28382779 original size:78 final size:79
Alignment explanation
Indices: 28382595--28382818 Score: 299
Period size: 78 Copynumber: 2.8 Consensus size: 79
28382585 ATAAAATTAT
* * * * * *
28382595 CGAAATACCCTTGTAGGGTAGAAATACCAAAATATCCTTGTAGTGTAGAAATACCTAAATACTCC
1 CGAAATACCC-TGTAGGGTAGAATTACTAAAATACCCCTGTAGGGTAGAAATACCGAAATAC-CC
* *
28382660 TGTAGGGTAGAAATAT
64 TCTAGGGTAGAAATAC
28382676 CGAAATACTCCTGTAGGGTAGAATTACTAAAATACCCCTGTAGGGTAGAAATACCGAAATACCC-
1 CGAAATAC-CCTGTAGGGTAGAATTACTAAAATACCCCTGTAGGGTAGAAATACCGAAATACCCT
28382740 CT-GGGTAGAAATAC
65 CTAGGGTAGAAATAC
* * *
28382754 CGAAATACCCATGTAGGGTAGAATTACTGAAATACCCCTGTAGGGTAGAATTACCGAGATACCCT
1 CGAAATACCC-TGTAGGGTAGAATTACTAAAATACCCCTGTAGGGTAGAAATACCGAAATACCCT
28382819 TGTGGGGTAA
Statistics
Matches: 129, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
77 2 0.02
78 69 0.53
79 1 0.01
80 2 0.02
81 53 0.41
82 2 0.02
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (79 bp):
CGAAATACCCTGTAGGGTAGAATTACTAAAATACCCCTGTAGGGTAGAAATACCGAAATACCCTC
TAGGGTAGAAATAC
Found at i:28382846 original size:105 final size:105
Alignment explanation
Indices: 28382597--28382831 Score: 296
Period size: 105 Copynumber: 2.2 Consensus size: 105
28382587 AAAATTATCG
* * * * *
28382597 AAATACCCTTGTAGGGTAGAAATACCAAAATATCCTTGTAGTGTAGAAATACCTAAATACTCCTG
1 AAATACCCCTGTAGGGTAGAAATACCGAAATACCCCTG--G-GTAGAAATACCGAAATACTCCTG
* *
28382662 TAGGGTAGAAATATCGAAATACTCCTGTAGGGTAGAATTACTA
63 TAGGGTAGAAATATCGAAATACCCCTGTAGGGTAGAATTACCA
28382705 AAATACCCCTGTAGGGTAGAAATACCGAAATACCCCTGGGTAGAAATACCGAAATAC-CCATGTA
1 AAATACCCCTGTAGGGTAGAAATACCGAAATACCCCTGGGTAGAAATACCGAAATACTCC-TGTA
* *
28382769 GGGTAGAATTA-CTGAAATACCCCTGTAGGGTAGAATTACCG
65 GGGTAGAAATATC-GAAATACCCCTGTAGGGTAGAATTACCA
* * *
28382810 AGATACCCTTGTGGGGTA-AAAT
1 AAATACCCCTGTAGGGTAGAAAT
28382832 TACCATTTTA
Statistics
Matches: 113, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
104 7 0.06
105 71 0.63
106 1 0.01
108 34 0.30
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.25
Consensus pattern (105 bp):
AAATACCCCTGTAGGGTAGAAATACCGAAATACCCCTGGGTAGAAATACCGAAATACTCCTGTAG
GGTAGAAATATCGAAATACCCCTGTAGGGTAGAATTACCA
Found at i:28383357 original size:6 final size:6
Alignment explanation
Indices: 28383348--28383546 Score: 131
Period size: 6 Copynumber: 32.3 Consensus size: 6
28383338 TTGCATTCAC
* *
28383348 ATTCTG ATTCTG ATTCTG -TTACCTG ATACTG ATTCTG ATTCTG -TTACCTA
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATT--CTG
* * * *
28383398 ACTCTG ATTCTG GTTCTG ATTCTA ATTCTG -TTACCTG ATACTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG
* * * * *
28383447 ATTCTG -TTACCTA ATTCTA ATTCTG ATTTTG ATTTTG ATTCTG -TCACCTG
1 ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG
* * *
28383497 ATTCTG ATTCTG ATTCTG ATTTTG ATTCTC ATTTTG ATTCT- AGTTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG
28383545 AT
1 AT
28383547 AATGTTTCTT
Statistics
Matches: 152, Mismatches: 24, Indels: 34
0.72 0.11 0.16
Matches are distributed among these distances:
5 10 0.07
6 122 0.80
7 14 0.09
8 6 0.04
ACGTcount: A:0.19, C:0.18, G:0.14, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:28383379 original size:25 final size:25
Alignment explanation
Indices: 28383350--28383415 Score: 98
Period size: 25 Copynumber: 2.6 Consensus size: 25
28383340 GCATTCACAT
*
28383350 TCTGATTCTGATTCTGTTACCTGA-
1 TCTGATTCTGATTCTGTTACCTAAC
28383374 TACTGATTCTGATTCTGTTACCTAAC
1 T-CTGATTCTGATTCTGTTACCTAAC
*
28383400 TCTGATTCTGGTTCTG
1 TCTGATTCTGATTCTG
28383416 ATTCTAATTC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
24 1 0.03
25 36 0.95
26 1 0.03
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.45
Consensus pattern (25 bp):
TCTGATTCTGATTCTGTTACCTAAC
Found at i:28383417 original size:37 final size:37
Alignment explanation
Indices: 28383370--28383452 Score: 114
Period size: 37 Copynumber: 2.2 Consensus size: 37
28383360 ATTCTGTTAC
* *
28383370 CTGATACTGATTCTGATTCTGTTACCTAACT-CTGATT
1 CTGATTCTGATTCTAATTCTGTTACCTAA-TACTGATT
* *
28383407 CTGGTTCTGATTCTAATTCTGTTACCTGATACTGATT
1 CTGATTCTGATTCTAATTCTGTTACCTAATACTGATT
28383444 CTGATTCTG
1 CTGATTCTG
28383453 TTACCTAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
36 1 0.03
37 39 0.98
ACGTcount: A:0.19, C:0.20, G:0.16, T:0.45
Consensus pattern (37 bp):
CTGATTCTGATTCTAATTCTGTTACCTAATACTGATT
Found at i:28383446 original size:62 final size:62
Alignment explanation
Indices: 28383348--28383514 Score: 262
Period size: 62 Copynumber: 2.7 Consensus size: 62
28383338 TTGCATTCAC
*
28383348 ATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTTACCTAACTCTGATTCTG
1 ATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTTACCTAACTCTAATTCTG
* * *
28383410 GTTCTGATTCTAATTCTGTTACCTGATACTGATTCTGATTCTGTTACCTAATTCTAATTCTG
1 ATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTTACCTAACTCTAATTCTG
* * * *
28383472 ATTTTGATTTTGATTCTGTCACCTGATTCTGATTCTGATTCTG
1 ATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTG
28383515 ATTTTGATTC
Statistics
Matches: 95, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
62 95 1.00
ACGTcount: A:0.19, C:0.19, G:0.14, T:0.47
Consensus pattern (62 bp):
ATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTTACCTAACTCTAATTCTG
Found at i:28383469 original size:25 final size:25
Alignment explanation
Indices: 28383411--28383474 Score: 92
Period size: 25 Copynumber: 2.6 Consensus size: 25
28383401 CTGATTCTGG
* *
28383411 TTCTGATTCTAATTCTGTTACCTGA
1 TTCTGATTCTGATTCTGTTACCTAA
*
28383436 TACTGATTCTGATTCTGTTACCTAA
1 TTCTGATTCTGATTCTGTTACCTAA
*
28383461 TTCTAATTCTGATT
1 TTCTGATTCTGATT
28383475 TTGATTTTGA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.22, C:0.19, G:0.11, T:0.48
Consensus pattern (25 bp):
TTCTGATTCTGATTCTGTTACCTAA
Found at i:28383486 original size:43 final size:37
Alignment explanation
Indices: 28383432--28383525 Score: 134
Period size: 37 Copynumber: 2.5 Consensus size: 37
28383422 ATTCTGTTAC
* * *
28383432 CTGATACTGATTCTGATTCTGTTACCTAATTCTAATT
1 CTGATTCTGATTTTGATTCTGTCACCTAATTCTAATT
* * *
28383469 CTGATTTTGATTTTGATTCTGTCACCTGATTCTGATT
1 CTGATTCTGATTTTGATTCTGTCACCTAATTCTAATT
28383506 CTGATTCTGATTTTGATTCT
1 CTGATTCTGATTTTGATTCT
28383526 CATTTTGATT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.19, C:0.17, G:0.14, T:0.50
Consensus pattern (37 bp):
CTGATTCTGATTTTGATTCTGTCACCTAATTCTAATT
Found at i:28383489 original size:18 final size:18
Alignment explanation
Indices: 28383348--28383546 Score: 77
Period size: 19 Copynumber: 10.8 Consensus size: 18
28383338 TTGCATTCAC
*
28383348 ATTCTGATTCTGATTCTG
1 ATTCTGATTCTGATTTTG
* *
28383366 -TTACCTGATACTGATTCTG
1 ATT--CTGATTCTGATTTTG
* * *
28383385 ATTCTG-TTACCTAACTCTG
1 ATTCTGATT--CTGATTTTG
* * *
28383404 ATTCTGGTTCTGATTCTA
1 ATTCTGATTCTGATTTTG
**
28383422 ATTCTG-TTACCTGATACTG
1 ATTCTGATT--CTGATTTTG
* *
28383441 ATTCTGATTCTG-TTACCTA
1 ATTCTGATTCTGATT--TTG
*
28383460 ATTCTAATTCTGATTTTG
1 ATTCTGATTCTGATTTTG
* **
28383478 ATTTTGATTCTG-TCACCTG
1 ATTCTGATTCTGAT--TTTG
*
28383497 ATTCTGATTCTGATTCTG
1 ATTCTGATTCTGATTTTG
* *
28383515 ATTTTGATTCTCATTTTG
1 ATTCTGATTCTGATTTTG
28383533 ATTCT-AGTTCTGAT
1 ATTCTGA-TTCTGAT
28383547 AATGTTTCTT
Statistics
Matches: 140, Mismatches: 25, Indels: 32
0.71 0.13 0.16
Matches are distributed among these distances:
17 8 0.06
18 57 0.41
19 66 0.47
20 9 0.06
ACGTcount: A:0.19, C:0.18, G:0.14, T:0.49
Consensus pattern (18 bp):
ATTCTGATTCTGATTTTG
Found at i:28387815 original size:70 final size:71
Alignment explanation
Indices: 28387664--28387826 Score: 310
Period size: 70 Copynumber: 2.3 Consensus size: 71
28387654 GAGATGTATC
28387664 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
28387729 AGGACA
66 AGGACA
28387735 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCT-GGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
*
28387799 CGGACA
66 AGGACA
28387805 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
28387827 AGACAAATCG
Statistics
Matches: 91, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
70 51 0.56
71 40 0.44
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:28395345 original size:70 final size:71
Alignment explanation
Indices: 28395194--28395356 Score: 310
Period size: 70 Copynumber: 2.3 Consensus size: 71
28395184 GAGATGTATC
28395194 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
28395259 AGGACA
66 AGGACA
28395265 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCT-GGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
*
28395329 CGGACA
66 AGGACA
28395335 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
28395357 AGACAAATCG
Statistics
Matches: 91, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
70 51 0.56
71 40 0.44
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:28403493 original size:27 final size:26
Alignment explanation
Indices: 28403420--28403574 Score: 122
Period size: 26 Copynumber: 6.0 Consensus size: 26
28403410 TAAAAAGGTC
28403420 TAAAATAAATAATATATAT-ATAATAT
1 TAAAATAAATAATATATATAATAAT-T
* *
28403446 TAAAGTAAATAATATACATAATAATT
1 TAAAATAAATAATATATATAATAATT
* *
28403472 TAAAATACAAAAATGTATATAA-AAGTT
1 TAAAATA-AATAATATATATAATAA-TT
* * *
28403499 TCAAAATAAACAATATGTATAATAGTT
1 T-AAAATAAATAATATATATAATAATT
* * *
28403526 TAAAAGAAATAACATATGTAA-AA--
1 TAAAATAAATAATATATATAATAATT
* *
28403549 TAAAATAATATAAAATATATGATAAT
1 TAAAATAA-ATAATATATATAATAAT
28403575 AATAATGGTA
Statistics
Matches: 101, Mismatches: 20, Indels: 16
0.74 0.15 0.12
Matches are distributed among these distances:
23 7 0.07
24 10 0.10
25 3 0.03
26 41 0.41
27 33 0.33
28 7 0.07
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.32
Consensus pattern (26 bp):
TAAAATAAATAATATATATAATAATT
Found at i:28403744 original size:60 final size:60
Alignment explanation
Indices: 28403677--28403800 Score: 221
Period size: 60 Copynumber: 2.1 Consensus size: 60
28403667 AATAGTAATA
* *
28403677 ATATAATAATAATAAAATAGAGACTAATGATGACAATACATTAATGAGAATAATTATAGC
1 ATATAATAATAATAAAATAGAAACTAATGATGACAATACATTAATGAGAATAATGATAGC
*
28403737 ATATAATAATAATAAAATAGAAACTAATGATGACAATACATTGATGAGAATAATGATAGC
1 ATATAATAATAATAAAATAGAAACTAATGATGACAATACATTAATGAGAATAATGATAGC
28403797 ATAT
1 ATAT
28403801 TGATAATGAC
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.28
Consensus pattern (60 bp):
ATATAATAATAATAAAATAGAAACTAATGATGACAATACATTAATGAGAATAATGATAGC
Found at i:28406075 original size:205 final size:204
Alignment explanation
Indices: 28405707--28406420 Score: 1072
Period size: 205 Copynumber: 3.5 Consensus size: 204
28405697 TGGGAACATC
* * * * *
28405707 TGAAAGTCAAATCTGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTG
1 TGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAACACAAGGATGCCAAACCATCTTG
* * * * * *
28405772 GATCTTGCTTCAGTATAAACATCTGAAGATCAGATCTGCTATGTATCTGCTCTCCATTGAAA-TG
66 GATC-CGCTTCAGCATAAACATCCGAAG-GCAGATCTGCTATGTGTCTGCTCTCCA-TCAAAGTG
* * * * * *
28405836 GAGATGCCAGACTTCGATTTGTTCTCTAACAATACAGAGACGACAAATCATCTTAGATTTGTTTC
128 AAGATGCCAAACTTCGATTCGTTCTCTGACAATACAGAGATGACAAATCATCTTAGATTTGCTTC
* *
28405901 AACGTAAACACG
193 ATCGTAATCACG
* * * * *
28405913 TGAAACCCAAATTAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATTCTAAACCATCTTG
1 TGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAACACAAGGATGCCAAACCATCTTG
* *
28405978 GATCCGCTTCAGCAGAAACATCCGAAGGCGAGATCTGCTGTGTGTCTGCTCTCCATCAAAGTGAA
66 GATCCGCTTCAGCATAAACATCCGAAGGC-AGATCTGCTATGTGTCTGCTCTCCATCAAAGTGAA
* *
28406043 GATGCCAAACTTCGATTCATTCTTTGACAATACAGAGATGACAAATCATCTTAGATTTGCTTCAT
130 GATGCCAAACTTCGATTCGTTCTCTGACAATACAGAGATGACAAATCATCTTAGATTTGCTTCAT
28406108 CGTAATCACG
195 CGTAATCACG
*
28406118 TGAAAGCCAAATCAACTATGTCTTCGATTTGCTCCTTGTAAACACAAGGATGCCAAACCATCTTG
1 TGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAACACAAGGATGCCAAACCATCTTG
28406183 GATCCGCTTCAGCATAAACATCCGAAGGCAAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGAA
66 GATCCGCTTCAGCATAAACATCCGAAGGC-AGATCTGCTATGTGTCTGCTCTCCATCAAAGTGAA
28406248 GATGCCAAACTTCGATTCGTTCTCTGACAATACAGAGATGACAAATCATCTTAGATTTGCTTCAT
130 GATGCCAAACTTCGATTCGTTCTCTGACAATACAGAGATGACAAATCATCTTAGATTTGCTTCAT
28406313 CGTAATCACG
195 CGTAATCACG
28406323 TGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAACACAAGGATGCCAAACCATCTTG
1 TGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAACACAAGGATGCCAAACCATCTTG
* * *
28406388 GATCAGCTTCAGTAT-AACATCTGAAGGCCAGAT
66 GATCCGCTTCAGCATAAACATCCGAAGG-CAGAT
28406421 TTGTTATGCT
Statistics
Matches: 464, Mismatches: 41, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
204 20 0.04
205 383 0.83
206 61 0.13
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (204 bp):
TGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAACACAAGGATGCCAAACCATCTTG
GATCCGCTTCAGCATAAACATCCGAAGGCAGATCTGCTATGTGTCTGCTCTCCATCAAAGTGAAG
ATGCCAAACTTCGATTCGTTCTCTGACAATACAGAGATGACAAATCATCTTAGATTTGCTTCATC
GTAATCACG
Found at i:28416355 original size:80 final size:80
Alignment explanation
Indices: 28416271--28416419 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
28416261 TATGGTAACC
* * * *
28416271 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
28416335 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
28416351 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
28416416 CCGG
66 CCGG
28416420 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:28416361 original size:40 final size:38
Alignment explanation
Indices: 28416312--28416419 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
28416302 ATCACGATTT
*
28416312 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
28416352 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
28416392 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
28416420 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:28424470 original size:80 final size:80
Alignment explanation
Indices: 28424386--28424534 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
28424376 TATGGTAACC
* * * *
28424386 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
28424450 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
28424466 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
28424531 CCGG
66 CCGG
28424535 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:28424476 original size:40 final size:38
Alignment explanation
Indices: 28424427--28424534 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
28424417 ATCACGATTT
*
28424427 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
28424467 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
28424507 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
28424535 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:28428195 original size:27 final size:26
Alignment explanation
Indices: 28428160--28428304 Score: 116
Period size: 26 Copynumber: 5.5 Consensus size: 26
28428150 GACAATTTAA
*
28428160 AATA-ATATAAAAGGTCTAAAATAAAT
1 AATATATATAAAA-GTTTAAAATAAAT
* *
28428186 AATATATATATAA-TATTAAAGTAAAT
1 AATATATATAAAAGT-TTAAAATAAAT
* *
28428212 AATATACATAATAA-TTTAAAATACAAA
1 AATATATATAA-AAGTTTAAAATA-AAT
* *
28428239 AATGTATATAAAAGTTTCAAAATAAAC
1 AATATATATAAAAGTTT-AAAATAAAT
* * *
28428266 AATATGTATAATAGTTTAAAAGAAAT
1 AATATATATAAAAGTTTAAAATAAAT
* *
28428292 AACATATGTAAAA
1 AATATATATAAAA
28428305 AATAATATAA
Statistics
Matches: 94, Mismatches: 19, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
25 1 0.01
26 47 0.50
27 40 0.43
28 6 0.06
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.31
Consensus pattern (26 bp):
AATATATATAAAAGTTTAAAATAAAT
Found at i:28428205 original size:26 final size:26
Alignment explanation
Indices: 28428176--28428332 Score: 115
Period size: 26 Copynumber: 6.0 Consensus size: 26
28428166 ATAAAAGGTC
28428176 TAAAATAAATAATATATAT-ATAATAT
1 TAAAATAAATAATATATATAATAAT-T
* *
28428202 TAAAGTAAATAATATACATAATAATT
1 TAAAATAAATAATATATATAATAATT
* *
28428228 TAAAATACAAAAATGTATATAA-AAGTT
1 TAAAATA-AATAATATATATAATAA-TT
* * *
28428255 TCAAAATAAACAATATGTATAATAGTT
1 T-AAAATAAATAATATATATAATAATT
* * * **
28428282 TAAAAGAAATAACATATGTAA-AAAA
1 TAAAATAAATAATATATATAATAATT
*
28428307 TAATATAAAATAATGATA-ATAATAAT
1 TAAAAT-AAATAAT-ATATATAATAAT
28428333 GGTAATAATA
Statistics
Matches: 100, Mismatches: 23, Indels: 15
0.72 0.17 0.11
Matches are distributed among these distances:
25 5 0.05
26 50 0.50
27 38 0.38
28 7 0.07
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.32
Consensus pattern (26 bp):
TAAAATAAATAATATATATAATAATT
Found at i:28428352 original size:12 final size:12
Alignment explanation
Indices: 28428305--28428348 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
28428295 ATATGTAAAA
28428305 AATAAT-ATAA-
1 AATAATGATAAT
28428315 AATAATGATAAT
1 AATAATGATAAT
*
28428327 AATAATGGTAAT
1 AATAATGATAAT
28428339 AATAAT-ATAA
1 AATAATGATAA
28428349 ATAAATGCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
10 6 0.20
11 7 0.23
12 17 0.57
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (12 bp):
AATAATGATAAT
Found at i:28428531 original size:56 final size:57
Alignment explanation
Indices: 28428428--28428541 Score: 169
Period size: 56 Copynumber: 2.0 Consensus size: 57
28428418 TAGTAATAAT
*
28428428 ATAATAATAATAAATAGAGACTAATGATGAACATACATTAATGAGAATAATGATAGCA
1 ATAATAATAATAAATAGAAACTAATGA-GAACATACATTAATGAGAATAATGATAGCA
* *
28428486 ATAATAATAATAAAATAGAAACTAATGA-CA-ATACATTGATGAGAATAATGATAGCA
1 ATAATAATAAT-AAATAGAAACTAATGAGAACATACATTAATGAGAATAATGATAGCA
28428542 TATTGATAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
56 25 0.48
57 1 0.02
58 11 0.21
59 15 0.29
ACGTcount: A:0.54, C:0.07, G:0.13, T:0.25
Consensus pattern (57 bp):
ATAATAATAATAAATAGAAACTAATGAGAACATACATTAATGAGAATAATGATAGCA
Found at i:28435752 original size:40 final size:40
Alignment explanation
Indices: 28435667--28435817 Score: 134
Period size: 40 Copynumber: 3.8 Consensus size: 40
28435657 AATTGAATGA
* * *
28435667 TATCCGGGCTAA-ATCCCGAAGACAATTATGCTG-GAAATTA-
1 TATCCGGGCTAAGA-CCCGAAGGCAATTGTGC-GAGACA-TAC
* * *
28435707 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGACATAC
*
28435748 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGACATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGACATAC
*
28435787 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
28435818 ACATGGTTAT
Statistics
Matches: 92, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
38 3 0.03
39 5 0.05
40 79 0.86
41 4 0.04
42 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGACATAC
Found at i:28435831 original size:40 final size:40
Alignment explanation
Indices: 28435704--28435833 Score: 138
Period size: 40 Copynumber: 3.2 Consensus size: 40
28435694 ATGCTGGAAA
* * * *
28435704 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
* * * **
28435744 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGA-CA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
*
28435784 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
28435824 TTATATCCGG
1 TTATATCCGG
28435834 TTATATTCCG
Statistics
Matches: 71, Mismatches: 17, Indels: 4
0.77 0.18 0.04
Matches are distributed among these distances:
39 2 0.03
40 69 0.97
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
Found at i:28439074 original size:27 final size:27
Alignment explanation
Indices: 28439036--28439335 Score: 194
Period size: 27 Copynumber: 10.7 Consensus size: 27
28439026 GTAGTTTACC
* *
28439036 AAATTACTAAAATGCCCTCAATTTGTA
1 AAATTACTAAAATACCCTCGATTTGTA
* * *
28439063 AAATTACTAAAATACCGTTGGTTTGTA
1 AAATTACTAAAATACCCTCGATTTGTA
* * *
28439090 AAATTACCAAAATACCC-CTAGTTTGTG
1 AAATTACTAAAATACCCTCGA-TTTGTA
* *
28439117 AAATTACCAAAATACCC-CTGATTTGTG
1 AAATTACTAAAATACCCTC-GATTTGTA
* * *
28439144 AAATTACTGAAATACCCTTGACTTGTA
1 AAATTACTAAAATACCCTCGATTTGTA
* *
28439171 AAATGTTTACAAAATTACCAAAATACCCCCGGTTTGTA
1 AAA---TTAC-----T---AAAATACCCTCGATTTGTA
*
28439209 AAATTACCAAAATACCC-CTGATTTGTA
1 AAATTACTAAAATACCCTC-GATTTGTA
* **
28439236 AAATTACTGAAATACCCTC-AGTTTACA
1 AAATTACTAAAATACCCTCGA-TTTGTA
* *
28439263 AAATTACTGAAATACCCTCAATTTGTA
1 AAATTACTAAAATACCCTCGATTTGTA
* * *
28439290 AAATTACTGAAATACTCTCGACTTGTAA
1 AAATTACTAAAATACCCTCGATTTGT-A
* *
28439318 AAATTACCAAAGTACCCT
1 AAATTACTAAAATACCCT
28439336 GAATTTACAA
Statistics
Matches: 217, Mismatches: 37, Indels: 37
0.75 0.13 0.13
Matches are distributed among these distances:
26 2 0.01
27 171 0.79
28 18 0.08
30 4 0.02
35 5 0.02
38 17 0.08
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.31
Consensus pattern (27 bp):
AAATTACTAAAATACCCTCGATTTGTA
Found at i:28439222 original size:65 final size:65
Alignment explanation
Indices: 28439117--28439239 Score: 183
Period size: 65 Copynumber: 1.9 Consensus size: 65
28439107 CTAGTTTGTG
* * ** *
28439117 AAATTACCAAAATACCCCTGATTTGTGAAATTACTGAAATACCCTTGACTTGTAAAATGTTTACA
1 AAATTACCAAAATACCCCCGATTTGTAAAATTACCAAAATACCCCTGACTTGTAAAATGTTTACA
* *
28439182 AAATTACCAAAATACCCCCGGTTTGTAAAATTACCAAAATACCCCTGATTTGTAAAAT
1 AAATTACCAAAATACCCCCGATTTGTAAAATTACCAAAATACCCCTGACTTGTAAAAT
28439240 TACTGAAATA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
65 51 1.00
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (65 bp):
AAATTACCAAAATACCCCCGATTTGTAAAATTACCAAAATACCCCTGACTTGTAAAATGTTTACA
Found at i:28439273 original size:119 final size:119
Alignment explanation
Indices: 28439062--28439280 Score: 307
Period size: 119 Copynumber: 1.8 Consensus size: 119
28439052 CTCAATTTGT
* *** *
28439062 AAAATTACTAAAATACCGTTGGTTTGTAAAATTACCAAAATACCCCTAGTTTGTGAAATTACCAA
1 AAAATTACCAAAATACCCCCGGTTTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAA
* ***
28439127 AATACCCCTGATTTGTGAAATTACTGAAATACCCTTGACTTGTAAAATGTTTAC
66 AATACCCCAGATTTACAAAATTACTGAAATACCCTTGACTTGTAAAATGTTTAC
**
28439181 AAAATTACCAAAATACCCCCGGTTTGTAAAATTACCAAAATACCCCT-GATTTGTAAAATTACTG
1 AAAATTACCAAAATACCCCCGGTTTGTAAAATTACCAAAATACCCCTAG-TTTGTAAAATTACCA
28439245 AAATACCCTCAG-TTTACAAAATTACTGAAATACCCT
65 AAATACCC-CAGATTTACAAAATTACTGAAATACCCT
28439281 CAATTTGTAA
Statistics
Matches: 87, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
118 1 0.01
119 84 0.97
120 2 0.02
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.31
Consensus pattern (119 bp):
AAAATTACCAAAATACCCCCGGTTTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAA
AATACCCCAGATTTACAAAATTACTGAAATACCCTTGACTTGTAAAATGTTTAC
Found at i:28439294 original size:146 final size:146
Alignment explanation
Indices: 28439029--28439319 Score: 361
Period size: 146 Copynumber: 2.0 Consensus size: 146
28439019 GAATACTGTA
* * * * * ** *
28439029 GTTTACCAAATTACTAAAATGCCCTCAATTTGTAAAATTACTAAAATACCGTTGGTTTGTAAAAT
1 GTTTACAAAATTACCAAAATACCCCCAATTTGTAAAATTACCAAAATACCCCTGATTTGTAAAAT
*** * *
28439094 TACCAAAATACCCCTAGTTTGTGAAATTACCAAAATACCCCTGATTTGTGAAATTACTGAAATAC
66 TACCAAAATACCCCTAGTTTACAAAATTACCAAAATACCCCTAATTTGTAAAATTACTGAAATAC
*
28439159 CCTTGACTTGTAAAAT
131 CCTCGACTTGTAAAAT
**
28439175 GTTTACAAAATTACCAAAATACCCCCGGTTTGTAAAATTACCAAAATACCCCTGATTTGTAAAAT
1 GTTTACAAAATTACCAAAATACCCCCAATTTGTAAAATTACCAAAATACCCCTGATTTGTAAAAT
** **
28439240 TACTGAAATA-CCCTCAGTTTACAAAATTACTGAAATA-CCCTCAATTTGTAAAATTACTGAAAT
66 TACCAAAATACCCCT-AGTTTACAAAATTACCAAAATACCCCT-AATTTGTAAAATTACTGAAAT
*
28439303 ACTCTCGACTTGTAAAA
129 ACCCTCGACTTGTAAAA
28439320 ATTACCAAAG
Statistics
Matches: 122, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
145 8 0.07
146 114 0.93
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.32
Consensus pattern (146 bp):
GTTTACAAAATTACCAAAATACCCCCAATTTGTAAAATTACCAAAATACCCCTGATTTGTAAAAT
TACCAAAATACCCCTAGTTTACAAAATTACCAAAATACCCCTAATTTGTAAAATTACTGAAATAC
CCTCGACTTGTAAAAT
Found at i:28439316 original size:81 final size:82
Alignment explanation
Indices: 28439175--28439387 Score: 227
Period size: 81 Copynumber: 2.6 Consensus size: 82
28439165 CTTGTAAAAT
* * ** ** *
28439175 GTTTACAAAATTACCAAAATACCCCCGGTTTGTAAAATTACCAAAATACCCCTGATTTGT-AAAA
1 GTTTACAAAATTACCGAAATACCCTCAATTTGTAAAATTACTGAAATACCCCTGACTTGTAAAAA
*
28439239 TTACTGAAA-TACCCTCA
66 TTAC-CAAAGTACCCTCA
* *
28439256 GTTTACAAAATTACTGAAATACCCTCAATTTGTAAAATTACTGAAATA-CTCTCGACTTGTAAAA
1 GTTTACAAAATTACCGAAATACCCTCAATTTGTAAAATTACTGAAATACCCCT-GACTTGTAAAA
*
28439320 ATTACCAAAGTACCCTGA
65 ATTACCAAAGTACCCTCA
* ** ** *
28439338 ATTTACAAAATTACCG-TTTACCCTCAATTTACAAAATTATTGAAATACCC
1 GTTTACAAAATTACCGAAATACCCTCAATTTGTAAAATTACTGAAATACCC
28439388 TTGTAGGGTA
Statistics
Matches: 109, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
80 3 0.03
81 76 0.70
82 30 0.28
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.31
Consensus pattern (82 bp):
GTTTACAAAATTACCGAAATACCCTCAATTTGTAAAATTACTGAAATACCCCTGACTTGTAAAAA
TTACCAAAGTACCCTCA
Found at i:28439513 original size:27 final size:27
Alignment explanation
Indices: 28439372--28439511 Score: 192
Period size: 27 Copynumber: 5.2 Consensus size: 27
28439362 CAATTTACAA
*
28439372 AATTATTGAAATACCCTTGTAGGGTAG
1 AATTATCGAAATACCCTTGTAGGGTAG
*
28439399 AATTATCGAAATACCCCTGTAGGGTAG
1 AATTATCGAAATACCCTTGTAGGGTAG
* *
28439426 AATTATTGAAATATCCC-TGTAGGGTAA
1 AATTATCGAAATA-CCCTTGTAGGGTAG
28439453 AATTATCGAAATACCCTTGTAGGGTAG
1 AATTATCGAAATACCCTTGTAGGGTAG
* * * *
28439480 AATTACCGAGATACCCTTGTGGGGTAA
1 AATTATCGAAATACCCTTGTAGGGTAG
28439507 AATTA
1 AATTA
28439512 CCATTTTGCC
Statistics
Matches: 101, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
26 3 0.03
27 95 0.94
28 3 0.03
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.30
Consensus pattern (27 bp):
AATTATCGAAATACCCTTGTAGGGTAG
Found at i:28439789 original size:24 final size:25
Alignment explanation
Indices: 28439718--28439787 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
28439708 AGGAAGTGCT
* *
28439718 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTATCA
28439743 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
* *
28439768 AAAAGGACTTTGCCCTAGTT
1 AAAAGGGCTTTGCCCCAGTT
28439788 ATTAAAAGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.27
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:28442972 original size:7 final size:7
Alignment explanation
Indices: 28442960--28442984 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28442950 ATTATTTTTA
28442960 TTTTATT
1 TTTTATT
28442967 TTTTATT
1 TTTTATT
28442974 TTTTATT
1 TTTTATT
28442981 TTTT
1 TTTT
28442985 CTCTTTTTCT
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTATT
Found at i:28453053 original size:85 final size:85
Alignment explanation
Indices: 28452890--28453060 Score: 227
Period size: 85 Copynumber: 2.0 Consensus size: 85
28452880 TTGGATTCGC
28452890 TTTCACCATAGGTAAGACAATATCAGAGATAAGGTCAAAATCCAATTTCGGATAATCTTGTGAAA
1 TTTCACCATAGGTAAGACAATATCAGAGATAAGGTCAAAATCCAATTTCGGATAATCTTGTGAAA
* * *
28452955 TGCCTATAGCAACACAAGTA
66 TACCTACAACAACACAAGTA
* * * * * **
28452975 TTTCACCATAGGTAAG-CAATGTTAGAGATAATGTCAAAATCCAATTTCTGGATGATTTTGTGGC
1 TTTCACCATAGGTAAGACAATATCAGAGATAAGGTCAAAATCCAATTTC-GGATAATCTTGTGAA
*
28453039 ATACCTCCAACAACACAAGTA
65 ATACCTACAACAACACAAGTA
28453060 T
1 T
28453061 GTGGAATGTC
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
84 29 0.39
85 45 0.61
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.28
Consensus pattern (85 bp):
TTTCACCATAGGTAAGACAATATCAGAGATAAGGTCAAAATCCAATTTCGGATAATCTTGTGAAA
TACCTACAACAACACAAGTA
Found at i:28455411 original size:28 final size:25
Alignment explanation
Indices: 28455353--28455412 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 25
28455343 ATTATAATGT
* *
28455353 ATGATTTGAATTGAAATGGTATAAA
1 ATGATGTGAATTGAAATAGTATAAA
28455378 AT--TGTGAATTGATAATAGTATATGAA
1 ATGATGTGAATTGA-AATAGTATA--AA
28455404 ATGATGTGA
1 ATGATGTGA
28455413 TAATATGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
23 9 0.32
24 8 0.29
25 2 0.07
26 4 0.14
28 5 0.18
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.37
Consensus pattern (25 bp):
ATGATGTGAATTGAAATAGTATAAA
Found at i:28458736 original size:44 final size:44
Alignment explanation
Indices: 28458687--28458771 Score: 170
Period size: 44 Copynumber: 1.9 Consensus size: 44
28458677 TAGGTTTGCA
28458687 GATCAATATGAGTTATGTTATGATATGTTAATTGCTTAAATGCG
1 GATCAATATGAGTTATGTTATGATATGTTAATTGCTTAAATGCG
28458731 GATCAATATGAGTTATGTTATGATATGTTAATTGCTTAAAT
1 GATCAATATGAGTTATGTTATGATATGTTAATTGCTTAAAT
28458772 TGTGTATATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (44 bp):
GATCAATATGAGTTATGTTATGATATGTTAATTGCTTAAATGCG
Found at i:28459582 original size:12 final size:12
Alignment explanation
Indices: 28459567--28459599 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
28459557 GCTTGTGATA
28459567 TGGGCGTGTCTT
1 TGGGCGTGTCTT
28459579 TGGGCGTGTCTT
1 TGGGCGTGTCTT
28459591 TGGGCGTGT
1 TGGGCGTGT
28459600 GAGACCCACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.45, T:0.39
Consensus pattern (12 bp):
TGGGCGTGTCTT
Found at i:28460989 original size:42 final size:44
Alignment explanation
Indices: 28460925--28461037 Score: 108
Period size: 43 Copynumber: 2.6 Consensus size: 44
28460915 ATTGATTTGA
* * *
28460925 GATTTATGTGTAATACTATGTCTAGGACATTAGCATCG-TATTT
1 GATTTATGTGTAAGACCATGTCTAGGACAGTAGCATCGATATTT
* * * *
28460968 GATTT-TGTGTAAGACCCTGTCTGGGATAGTGGCATCGATATTT
1 GATTTATGTGTAAGACCATGTCTAGGACAGTAGCATCGATATTT
* *
28461011 GATTACAT-T-TAAGACCACGTCTAGGAC
1 GATT-TATGTGTAAGACCATGTCTAGGAC
28461038 GTTGGCATTG
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
42 25 0.45
43 28 0.51
44 1 0.02
45 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (44 bp):
GATTTATGTGTAAGACCATGTCTAGGACAGTAGCATCGATATTT
Found at i:28468634 original size:40 final size:39
Alignment explanation
Indices: 28468598--28468704 Score: 142
Period size: 39 Copynumber: 2.7 Consensus size: 39
28468588 ATATCCGGAC
*
28468598 TAAGATCCGAAGGCGTTCGTGCGAGTTAATAAATCCGGGT
1 TAAG-TCCGAAGGCATTCGTGCGAGTTAATAAATCCGGGT
* * * * *
28468638 TAAGCCCGAAGGCATTTGTGCTAGTTACTAAACCCGGGT
1 TAAGTCCGAAGGCATTCGTGCGAGTTAATAAATCCGGGT
28468677 TAAGTCCCGAAGGCATTCGTGCGAGTTA
1 TAAGT-CCGAAGGCATTCGTGCGAGTTA
28468705 CTATAACCGG
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
39 33 0.58
40 24 0.42
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (39 bp):
TAAGTCCGAAGGCATTCGTGCGAGTTAATAAATCCGGGT
Found at i:28468705 original size:40 final size:40
Alignment explanation
Indices: 28468604--28468730 Score: 168
Period size: 40 Copynumber: 3.2 Consensus size: 40
28468594 GGACTAAGAT
* * *
28468604 CCGAAGGCGTTCGTGCGAGTTAATAAATCCGGGTTAAG-C
1 CCGAAGGCATTCGTGCGAGTTACTAAACCCGGGTTAAGTC
* *
28468643 CCGAAGGCATTTGTGCTAGTTACTAAACCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAACCCGGGTTAAGTC
* *
28468683 CCGAAGGCATTCGTGCGAGTTACTATAACCGGGGTT-TGTC
1 CCGAAGGCATTCGTGCGAGTTACTA-AACCCGGGTTAAGTC
28468723 CCGAAGGC
1 CCGAAGGC
28468731 CTTTGAGCGA
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
39 33 0.43
40 35 0.45
41 9 0.12
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.24
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTACTAAACCCGGGTTAAGTC
Found at i:28478795 original size:8 final size:8
Alignment explanation
Indices: 28478769--28478802 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
28478759 GAAAAAGGAA
28478769 ATTTTGTG
1 ATTTTGTG
*
28478777 TATTTTTTG
1 -ATTTTGTG
28478786 ATTTTGTG
1 ATTTTGTG
28478794 ATTTTGTG
1 ATTTTGTG
28478802 A
1 A
28478803 ATTAGGGACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.15, C:0.00, G:0.21, T:0.65
Consensus pattern (8 bp):
ATTTTGTG
Found at i:28483782 original size:37 final size:37
Alignment explanation
Indices: 28483732--28483817 Score: 111
Period size: 37 Copynumber: 2.4 Consensus size: 37
28483722 TAAATAGGTG
* ** *
28483732 TGTTATCGGTTGGATTAGCTTTTATGAGTGTTTGGCA
1 TGTTATCGGTTGGATTACCACTTATGAGCGTTTGGCA
* *
28483769 TGTTATTGGTTGGATTACCACTTATGAGCGTTTGGCG
1 TGTTATCGGTTGGATTACCACTTATGAGCGTTTGGCA
28483806 TGTT-TCGGTTGG
1 TGTTATCGGTTGG
28483818 CCTACTTGTG
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 7 0.17
37 35 0.83
ACGTcount: A:0.14, C:0.10, G:0.31, T:0.44
Consensus pattern (37 bp):
TGTTATCGGTTGGATTACCACTTATGAGCGTTTGGCA
Found at i:28485713 original size:21 final size:20
Alignment explanation
Indices: 28485689--28485758 Score: 52
Period size: 21 Copynumber: 3.3 Consensus size: 20
28485679 GGGCACACAG
28485689 CGTGTGGCTGAGGCACATGCC
1 CGTGTGGCTGAGGCACAT-CC
* * * *
28485710 CGTGTGAAG-AGAAGCATATCGT
1 CGTGTG--GCTGAGGCACATC-C
28485732 CGTGTGGCTGAGGCACATACC
1 CGTGTGGCTGAGGCACAT-CC
28485753 CGTGTG
1 CGTGTG
28485759 AAGAGAGGTA
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
20 1 0.03
21 20 0.56
22 14 0.39
23 1 0.03
ACGTcount: A:0.20, C:0.23, G:0.36, T:0.21
Consensus pattern (20 bp):
CGTGTGGCTGAGGCACATCC
Found at i:28485717 original size:42 final size:42
Alignment explanation
Indices: 28485669--28485800 Score: 158
Period size: 42 Copynumber: 3.1 Consensus size: 42
28485659 TCAAAAGCTT
*
28485669 GTGTGAAGAGGGGCACACAGCGTGTGGCTGAGGCACATGCCC
1 GTGTGAAGAGAGGCACACAGCGTGTGGCTGAGGCACATGCCC
* * *
28485711 GTGTGAAGAGAAGCATATC-GTCGTGTGGCTGAGGCACATACCC
1 GTGTGAAGAGAGGCACA-CAG-CGTGTGGCTGAGGCACATGCCC
* * * * *
28485754 GTGTGAAGAGAGGTACACACCGTGTGACTGAGGCATACGCCC
1 GTGTGAAGAGAGGCACACAGCGTGTGGCTGAGGCACATGCCC
28485796 GTGTG
1 GTGTG
28485801 GATTAGGGAC
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
42 39 0.52
43 36 0.48
ACGTcount: A:0.23, C:0.22, G:0.36, T:0.18
Consensus pattern (42 bp):
GTGTGAAGAGAGGCACACAGCGTGTGGCTGAGGCACATGCCC
Done.