Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A01
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: 115637255
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5450143 characters in sequence are not A, C, G, or T
File 167 of 349
Found at i:54083247 original size:46 final size:46
Alignment explanation
Indices: 54083181--54083271 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
54083171 GAACATGTAT
* ** *
54083181 ATATGTGGTAAGGCTGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTATGAGATGG
* * *
54083227 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTATGAGATG
54083272 TGTATATATA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.33, C:0.08, G:0.32, T:0.27
Consensus pattern (46 bp):
ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTATGAGATGG
Found at i:54086906 original size:40 final size:40
Alignment explanation
Indices: 54086847--54087017 Score: 206
Period size: 40 Copynumber: 4.3 Consensus size: 40
54086837 CATTTGAATG
* * *
54086847 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATT
*
54086887 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGATT
*
54086927 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGATT
* * ** *
54086967 ATA-CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATT
54087006 ATATCC-GGCTAA
1 ATATCCGGGCTAA
54087018 ATTCGAAGAA
Statistics
Matches: 116, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
38 2 0.02
39 36 0.31
40 75 0.65
41 3 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATT
Found at i:54086985 original size:39 final size:40
Alignment explanation
Indices: 54086847--54086997 Score: 216
Period size: 40 Copynumber: 3.8 Consensus size: 40
54086837 CATTTGAATG
* * *
54086847 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
*
54086887 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
*
54086927 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
* *
54086967 ATA-CCGGGTTAAGACCCGAAGGCAATTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGC
54086998 TTGTGGTTAT
Statistics
Matches: 102, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
39 26 0.25
40 73 0.72
41 3 0.03
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
Found at i:54087009 original size:79 final size:80
Alignment explanation
Indices: 54086847--54087017 Score: 213
Period size: 79 Copynumber: 2.2 Consensus size: 80
54086837 CATTTGAATG
* * * *
54086847 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTGACTATATCCGGGCTAAGACCCGAAGGCA
* *
54086912 TTTGTGCGAGTTGAT
66 ATTGTGCGAGTGGAT
* *
54086927 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATA-CCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAG-TGACTATATCCGGGCTAAGACCCGAAGGC
** *
54086990 AATTGTGCTTGTGGTT
65 AATTGTGCGAGTGGAT
54087006 ATATCC-GGCTAA
1 ATATCCGGGCTAA
54087018 ATTCGAAGAA
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
78 6 0.08
79 36 0.46
80 35 0.44
81 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTGACTATATCCGGGCTAAGACCCGAAGGCA
ATTGTGCGAGTGGAT
Found at i:54098830 original size:40 final size:40
Alignment explanation
Indices: 54098786--54099048 Score: 314
Period size: 40 Copynumber: 6.8 Consensus size: 40
54098776 GAGAATTGAG
54098786 GTGATGTATCCGGGCTAAAGTCCCG-AGAGCATTCGTGCTA
1 GTGATGTATCCGGGCT-AAGTCCCGAAGAGCATTCGTGCTA
*
54098826 GTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCTA
1 GTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTA
*
54098866 GT-ATGTAT-CGGGCTAAGTCTCGAAGAGCATTCGTGCTA
1 GTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTA
* *
54098904 GTGATGTATCCGGGCTAAGT-CGGAGGAGCA-TCGTG-TA
1 GTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTA
* *
54098941 GTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTA
1 GTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTA
* * * *
54098981 GTGATATATCCGTGCTAA-ACCC--AGAGGC-TTCGTGCTG
1 GTGATGTATCCGGGCTAAGTCCCGAAGA-GCATTCGTGCTA
* *
54099018 GTG-TATATTCCGGGCTAGGTCCCGAAGAGCA
1 GTGATGTA-TCCGGGCTAAGTCCCGAAGAGCA
54099049 AATCATGCTG
Statistics
Matches: 195, Mismatches: 16, Indels: 24
0.83 0.07 0.10
Matches are distributed among these distances:
36 4 0.02
37 43 0.22
38 50 0.26
39 35 0.18
40 63 0.32
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (40 bp):
GTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTA
Found at i:54098979 original size:77 final size:80
Alignment explanation
Indices: 54098786--54098998 Score: 305
Period size: 77 Copynumber: 2.7 Consensus size: 80
54098776 GAGAATTGAG
*
54098786 GTGATGTATCCGGGCTAAAGTCCCG-AGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCTCG
1 GTGATGTATCCGGGCT-AAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCTCG
54098850 AAGAGCATTCGTGCTA
65 AAGAGCATTCGTGCTA
*
54098866 GT-ATGTAT-CGGGCTAAG-TCTCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTC-GG
1 GTGATGTATCCGGGCTAAGTTC-CGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCTCG
*
54098927 AGGAGCA-TCGTG-TA
65 AAGAGCATTCGTGCTA
* * *
54098941 GTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATCCGTGCTAA
1 GTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAA
54098999 ACCCAGAGGC
Statistics
Matches: 122, Mismatches: 6, Indels: 13
0.87 0.04 0.09
Matches are distributed among these distances:
75 4 0.03
76 12 0.10
77 54 0.44
78 44 0.36
79 6 0.05
80 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.27
Consensus pattern (80 bp):
GTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCTCGA
AGAGCATTCGTGCTA
Found at i:54099030 original size:77 final size:77
Alignment explanation
Indices: 54098794--54099048 Score: 263
Period size: 77 Copynumber: 3.3 Consensus size: 77
54098784 AGGTGATGTA
*
54098794 TCCGGGCTAAAGTCCCG-AGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCTCGAAGAGCAT
1 TCCGGGCT-AAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAA-ACTCG-AGAGC-T
* *
54098858 TCGTGCTAGTATGTA-
62 TCGTGCTAGTGTATAT
* * *
54098873 T-CGGGCTAAGTCTCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCT-AAGTCGGAGGAGCATC
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAACTC-GA-GAGCTTC
*
54098936 GTG-TAGTG-ATGT
64 GTGCTAGTGTATAT
* * * * *
54098948 ATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATCCGTGCTAAAC-CCAGAGGCTTC
1 -TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAACTCGAGA-GCTTC
*
54099012 GTGCTGGTGTATAT
64 GTGCTAGTGTATAT
*
54099026 TCCGGGCTAGGTCCCGAAGAGCA
1 TCCGGGCTAAGTCCCGAAGAGCA
54099049 AATCATGCTG
Statistics
Matches: 146, Mismatches: 20, Indels: 22
0.78 0.11 0.12
Matches are distributed among these distances:
74 1 0.01
75 6 0.04
76 17 0.12
77 79 0.54
78 42 0.29
79 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (77 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAACTCGAGAGCTTCGT
GCTAGTGTATAT
Found at i:54100538 original size:79 final size:81
Alignment explanation
Indices: 54100429--54100611 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
54100419 TACTCGTTCA
* *
54100429 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
54100492 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
54100509 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
54100572 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
54100588 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
54100612 CATCATTCGA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 59 0.66
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:54100611 original size:40 final size:40
Alignment explanation
Indices: 54100408--54100611 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
54100398 CGGAATTTAA
** *
54100408 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
54100448 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
54100488 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
54100527 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
54100567 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
54100607 CCGGA
1 CCGGA
54100612 CATCATTCGA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:54108613 original size:79 final size:81
Alignment explanation
Indices: 54108504--54108686 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
54108494 TACTCGTTCA
* *
54108504 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
54108567 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
54108584 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
54108647 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
54108663 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
54108687 CATCATTCGA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 59 0.66
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:54108686 original size:40 final size:40
Alignment explanation
Indices: 54108483--54108686 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
54108473 CGGAATTTAA
** *
54108483 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
54108523 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
54108563 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
54108602 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
54108642 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
54108682 CCGGA
1 CCGGA
54108687 CATCATTCGA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:54111390 original size:48 final size:48
Alignment explanation
Indices: 54111302--54111725 Score: 587
Period size: 48 Copynumber: 8.8 Consensus size: 48
54111292 ATGTCAGTGT
* * * * *
54111302 CGATGCTATGTCTCAGACATGGTCTTACACTAGCACACATATCAACGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCAACGC
* * * * * * * *
54111350 CCATGCCATGTTCCAGGCATGGTCATACACCGCCTCACATATCAACGA
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCAACGC
* * *
54111398 CAATGCCATGTCCCAGACATGGTCTTACACTGGTTCACATATCAACGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCAACGC
* *
54111446 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCAATGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCAACGC
* **
54111494 CGATGCCATGTCCCATACATGGTCTTACACTGGCTCTCATATCAATAC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCAACGC
*
54111542 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCCCATATCAACGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCAACGC
* * *
54111590 CGATGCCATGTCCAAAACATGGTCTTACACTGGCTCTCATATCAACAC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCAACGC
* *
54111638 CGATGCCATGTCCCAGACATGGTCTTATACTGGCTCTTATATCAACGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCAACGC
* *
54111686 TGATGTCATGTCCCAGACATGGTCTTACACTGGCTCTCAT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAT
54111726 TAACCAGGGT
Statistics
Matches: 332, Mismatches: 44, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 332 1.00
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.26
Consensus pattern (48 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCAACGC
Found at i:54119310 original size:48 final size:48
Alignment explanation
Indices: 54119249--54119413 Score: 147
Period size: 48 Copynumber: 3.5 Consensus size: 48
54119239 AAGTCTCATG
*
54119249 TCAATGCTGATGCCATGTCCCAGAAATGGTCTTACACTAGCACACATA
1 TCAAAGCTGATGCCATGTCCCAGAAATGGTCTTACACTAGCACACATA
* * * * *
54119297 TCAAAGCTTATGCCATGTCCCAGACATGGTCTTACATTGGCTCACATA
1 TCAAAGCTGATGCCATGTCCCAGAAATGGTCTTACACTAGCACACATA
** * * * * *
54119345 TCAACA-CCAATGCCATCT-CCA-AACATGGTCTTGCACTGGCTCTCATA
1 TCAA-AGCTGATGCCATGTCCCAGAA-ATGGTCTTACACTAGCACACATA
* * *
54119392 TTAATGCCGATGCCATGTCCCA
1 TCAAAGCTGATGCCATGTCCCA
54119414 TATACATTGG
Statistics
Matches: 96, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
46 1 0.01
47 36 0.38
48 58 0.60
49 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.27
Consensus pattern (48 bp):
TCAAAGCTGATGCCATGTCCCAGAAATGGTCTTACACTAGCACACATA
Found at i:54122218 original size:40 final size:40
Alignment explanation
Indices: 54122159--54122426 Score: 446
Period size: 40 Copynumber: 6.7 Consensus size: 40
54122149 GAGCATTGGA
* *
54122159 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
*
54122199 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
* *
54122239 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATA
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
*
54122279 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
* *
54122319 ATATATCCAGGCTAAAACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
*
54122359 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
*
54122399 ATATGTCCGGGCTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
54122427 ATGTGTTTGC
Statistics
Matches: 216, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 216 1.00
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
Found at i:54129937 original size:40 final size:40
Alignment explanation
Indices: 54129878--54130145 Score: 455
Period size: 40 Copynumber: 6.7 Consensus size: 40
54129868 GAGCATTGGA
* *
54129878 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
*
54129918 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
* *
54129958 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATA
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
*
54129998 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
*
54130038 ATATATCCGGGCTAAAACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
*
54130078 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
*
54130118 ATATGTCCGGGCTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
54130146 ATGTGTTTGC
Statistics
Matches: 218, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 218 1.00
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
Found at i:54133150 original size:48 final size:48
Alignment explanation
Indices: 54133094--54133313 Score: 305
Period size: 48 Copynumber: 4.6 Consensus size: 48
54133084 TATTAGCATA
* *
54133094 TCCCAGACATGGTCTTATACTGGCTCTCATTTCAACACCGATGCCATG
1 TCCCAGACATGGTCTTACACTGGCTCTCATATCAACACCGATGCCATG
* * * *
54133142 TCCCAGACATGGCCTTACACTGGCTCTTATATCGACGCCGATGCCATG
1 TCCCAGACATGGTCTTACACTGGCTCTCATATCAACACCGATGCCATG
* *
54133190 TCCTAAACATGGTCTTACACTGGCTCTCATATCAACACCGATGCCATG
1 TCCCAGACATGGTCTTACACTGGCTCTCATATCAACACCGATGCCATG
* * ***
54133238 TCCCAGACATGGTCTTACACTAGCTCACATATCAACGGTGATGCCATG
1 TCCCAGACATGGTCTTACACTGGCTCTCATATCAACACCGATGCCATG
* *
54133286 TCCCAGACAAGGTCTTACACTGACTCTC
1 TCCCAGACATGGTCTTACACTGGCTCTC
54133314 GTTAACCATG
Statistics
Matches: 149, Mismatches: 23, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 149 1.00
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.26
Consensus pattern (48 bp):
TCCCAGACATGGTCTTACACTGGCTCTCATATCAACACCGATGCCATG
Found at i:54136211 original size:43 final size:42
Alignment explanation
Indices: 54136162--54136311 Score: 133
Period size: 43 Copynumber: 3.5 Consensus size: 42
54136152 GATTAACGAG
54136162 ATGTGATTATGTGTAAGACCATGTCTGGGACATTGGCATCATT
1 ATGTGATTATGTGTAAGACCAT-TCTGGGACATTGGCATCATT
* * * * **
54136205 CTGTGATTACGTGCAAGACCTTATCTGCAACATTGGCATCATT
1 ATGTGATTATGTGTAAGACCAT-TCTGGGACATTGGCATCATT
* * * * *
54136248 ATTTAATTTTGTGTAAGACAATTGCTGGG-CTATTGGCATCAAT
1 ATGTGATTATGTGTAAGACCATT-CTGGGAC-ATTGGCATCATT
**
54136291 ATGTGA-TAAATGTAAGACCAT
1 ATGTGATTATGTGTAAGACCAT
54136312 ATCTCGGATA
Statistics
Matches: 81, Mismatches: 24, Indels: 5
0.74 0.22 0.05
Matches are distributed among these distances:
42 13 0.16
43 68 0.84
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (42 bp):
ATGTGATTATGTGTAAGACCATTCTGGGACATTGGCATCATT
Found at i:54140028 original size:11 final size:11
Alignment explanation
Indices: 54140012--54140048 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
54140002 TTTTGGGCTT
54140012 AACGGGCCGAA
1 AACGGGCCGAA
54140023 AACGGGCC---
1 AACGGGCCGAA
54140031 AACGGGCCGAA
1 AACGGGCCGAA
54140042 AACGGGC
1 AACGGGC
54140049 TAATGGGCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
8 8 0.35
11 15 0.65
ACGTcount: A:0.32, C:0.30, G:0.38, T:0.00
Consensus pattern (11 bp):
AACGGGCCGAA
Found at i:54140057 original size:19 final size:19
Alignment explanation
Indices: 54140012--54140048 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
54140002 TTTTGGGCTT
54140012 AACGGGCCGAAAACGGGCC
1 AACGGGCCGAAAACGGGCC
54140031 AACGGGCCGAAAACGGGC
1 AACGGGCCGAAAACGGGC
54140049 TAATGGGCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.30, G:0.38, T:0.00
Consensus pattern (19 bp):
AACGGGCCGAAAACGGGCC
Found at i:54142634 original size:47 final size:47
Alignment explanation
Indices: 54142563--54143015 Score: 719
Period size: 47 Copynumber: 9.6 Consensus size: 47
54142553 CCCTTCGGGA
* * * * *
54142563 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* *
54142610 CCTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
54142657 CTTATCACATATATACACTTTCACATTCATCACA-TGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* **
54142703 CTTATCAGATATATACACTTTCACATTCATCACATCAGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
54142750 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
54142797 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
54142846 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* *
54142893 CTTATCACATATATATACACTTTCACATTCATGACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
54142942 CTTATCACATATATACACTTTCGCATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
54142989 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
54143016 TATTCAAATA
Statistics
Matches: 382, Mismatches: 19, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
46 44 0.12
47 247 0.65
49 91 0.24
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
Found at i:54142641 original size:25 final size:25
Alignment explanation
Indices: 54142613--54142691 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
54142603 ACTCGGCCCT
54142613 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
** * * *
54142638 ATCACAT-T-GGC-CATTCGGCCTT-
1 ATCACATATATACACTTTC-ACATTC
54142660 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
54142685 ATCACAT
1 ATCACAT
54142692 GGCCATTAGG
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 11 0.28
23 5 0.13
24 5 0.13
25 18 0.46
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:54142845 original size:96 final size:95
Alignment explanation
Indices: 54142563--54143015 Score: 716
Period size: 96 Copynumber: 4.8 Consensus size: 95
54142553 CCCTTCGGGA
* * * * * * *
54142563 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTATCAC-ATATATACA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATACA
* *
54142627 CTTTCACATTCATCACATTGGCCATTCGGC
66 CTTTCACATTCATCACATCGGCCATTAGGC
*
54142657 CTTATCACATATATACACTTTCACATTCATCACAT-GGCCATTAGGCCTTATCA-GATATATACA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATACA
*
54142720 CTTTCACATTCATCACATCAGCCATTAGGC
66 CTTTCACATTCATCACATCGGCCATTAGGC
54142750 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA-ATATATAC
54142815 ACTTTCACATTCATCACATCGGCCATTAGGC
65 ACTTTCACATTCATCACATCGGCCATTAGGC
54142846 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA-ATATATAC
* * *
54142911 ACTTTCACATTCATGACATTGGCCATTCGGC
65 ACTTTCACATTCATCACATCGGCCATTAGGC
* *
54142942 CTTATCACATATATACACTTTCGCATTCATCACATTGGCCATTAGGCCTTATCAC-ATATATACA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATACA
54143006 CTTTCACATT
66 CTTTCACATT
54143016 TATTCAAATA
Statistics
Matches: 339, Mismatches: 16, Indels: 8
0.93 0.04 0.02
Matches are distributed among these distances:
93 86 0.25
94 69 0.20
96 184 0.54
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (95 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATACA
CTTTCACATTCATCACATCGGCCATTAGGC
Found at i:54142894 original size:143 final size:140
Alignment explanation
Indices: 54142563--54143015 Score: 735
Period size: 143 Copynumber: 3.2 Consensus size: 140
54142553 CCCTTCGGGA
* * * * * * *
54142563 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
54142628 TTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATG
66 TTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATG
54142693 GCCATTAGGC
131 GCCATTAGGC
* *
54142703 CTTATCAGATATATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
* *
54142768 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATATATACACTTTCACATTCATCACA
54142833 TCGGCCATTAGGC
129 T-GGCCATTAGGC
54142846 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
* *
54142911 ACTTTCACATTCATGACATTGGCCATTCGGCCTTATCACATATATACACTTTCGCATTCATCACA
64 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
54142976 TTGGCCATTAGGC
129 -TGGCCATTAGGC
54142989 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
54143016 TATTCAAATA
Statistics
Matches: 290, Mismatches: 17, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
140 91 0.31
142 27 0.09
143 127 0.44
144 1 0.00
145 44 0.15
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (140 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATG
GCCATTAGGC
Found at i:54142964 original size:25 final size:25
Alignment explanation
Indices: 54142936--54143010 Score: 68
Period size: 25 Copynumber: 3.1 Consensus size: 25
54142926 ACATTGGCCA
54142936 TTCGGCCTTATCACATATATACACT
1 TTCGGCCTTATCACATATATACACT
* ** *
54142961 TTC-GCATTCATCACAT-T-GGC-CA
1 TTCGGCCTT-ATCACATATATACACT
*
54142983 TTAGGCCTTATCACATATATACACT
1 TTCGGCCTTATCACATATATACACT
54143008 TTC
1 TTC
54143011 ACATTTATTC
Statistics
Matches: 35, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
22 10 0.29
23 6 0.17
24 6 0.17
25 13 0.37
ACGTcount: A:0.27, C:0.28, G:0.09, T:0.36
Consensus pattern (25 bp):
TTCGGCCTTATCACATATATACACT
Found at i:54147073 original size:40 final size:40
Alignment explanation
Indices: 54147041--54147311 Score: 418
Period size: 40 Copynumber: 6.8 Consensus size: 40
54147031 CCAGCATGAT
* * * *
54147041 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
** * *
54147081 TGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
54147121 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
54147161 TGCTC-TCGAGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
54147200 TGCTCTTCGAGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
54147240 TGCTCTTCGAGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
54147280 TGCTCTTCGGGACTTAGCCCGGATACATCACT
1 TGCTCTTCGGGACTTAGCCCGGATACATCACT
54147312 CTCAATTCTC
Statistics
Matches: 214, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
39 36 0.17
40 178 0.83
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.23
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:54147266 original size:119 final size:120
Alignment explanation
Indices: 54147041--54147311 Score: 420
Period size: 119 Copynumber: 2.3 Consensus size: 120
54147031 CCAGCATGAT
* * * * * **
54147041 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGGGTTTAGCACGGATA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGAGACTTAGCACGGATA
* *
54147106 TATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
66 CATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
* *
54147161 TGCTC-TCGAGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGAGACTTAGCCCGGATA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGAGACTTAGCACGGATA
54147225 CATCACTAGCACGAATGCTCTTC-GAGACTTAGCCCGGATACATCACTAGCACGAA
66 CATCACTAGCACGAATGCTCTTCGGA-ACTTAGCCCGGATACATCACTAGCACGAA
54147280 TGCTCTTCGGGACTTAGCCCGGATACATCACT
1 TGCTCTTCGGGACTTAGCCCGGATACATCACT
54147312 CTCAATTCTC
Statistics
Matches: 137, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
118 2 0.01
119 105 0.77
120 30 0.22
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.23
Consensus pattern (120 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGAGACTTAGCACGGATA
CATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
Found at i:54150096 original size:27 final size:27
Alignment explanation
Indices: 54150066--54150243 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
54150056 ATATTGAGTC
* * * *
54150066 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
54150093 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54150120 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
54150148 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
54150175 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
54150202 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54150229 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54150244 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:54150205 original size:82 final size:81
Alignment explanation
Indices: 54150087--54150242 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
54150077 TGCTATATAA
* *
54150087 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
54150152 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
54150169 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
54150233 CACTTAGTGC
65 CACTTAGTGC
54150243 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:54159428 original size:39 final size:38
Alignment explanation
Indices: 54159340--54159518 Score: 145
Period size: 39 Copynumber: 4.6 Consensus size: 38
54159330 TCGAATGATG
* * *
54159340 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTA-A
*
54159380 T-CGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAA
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAA
* * *
54159418 TCCGGGCTAAGCCCGAAAGGCATTGGTGCGAGCTACTAAA
1 TCCGGGCTAAGTCCG-AAGGCATTTGTGCGAGTTACT-AA
* *
54159458 TCCAGGTTAAGTCCCG-AGG-ATTTTGTGCGAGTTACTTAA
1 TCCGGGCTAAGT-CCGAAGGCA-TTTGTGCGAGTTAC-TAA
*
54159497 -CCGGGCTATGTCCG-AGGCATTT
1 TCCGGGCTAAGTCCGAAGGCATTT
54159519 TGAACGAGTA
Statistics
Matches: 114, Mismatches: 16, Indels: 21
0.75 0.11 0.14
Matches are distributed among these distances:
37 9 0.08
38 15 0.13
39 66 0.58
40 21 0.18
41 3 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (38 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAA
Found at i:54164209 original size:27 final size:27
Alignment explanation
Indices: 54164179--54164356 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
54164169 ATATTGAGTC
* * * *
54164179 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
54164206 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54164233 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
54164261 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
54164288 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
54164315 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54164342 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54164357 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:54164318 original size:82 final size:81
Alignment explanation
Indices: 54164200--54164355 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
54164190 TGCTATATAA
* *
54164200 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
54164265 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
54164282 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
54164346 CACTTAGTGC
65 CACTTAGTGC
54164356 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:54172388 original size:27 final size:27
Alignment explanation
Indices: 54172358--54172535 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
54172348 ATATTGAGTC
* * * *
54172358 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
54172385 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54172412 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
54172440 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
54172467 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
54172494 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54172521 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54172536 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:54172497 original size:82 final size:81
Alignment explanation
Indices: 54172379--54172534 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
54172369 TGCTATATAA
* *
54172379 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
54172444 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
54172461 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
54172525 CACTTAGTGC
65 CACTTAGTGC
54172535 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:54174466 original size:47 final size:47
Alignment explanation
Indices: 54174395--54174562 Score: 264
Period size: 47 Copynumber: 3.6 Consensus size: 47
54174385 CCCTTCGGGA
* * * * *
54174395 CTTATCACGTTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
54174442 CCTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
54174489 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
54174536 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
54174563 TATTCAAATA
Statistics
Matches: 112, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 112 1.00
ACGTcount: A:0.27, C:0.31, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:54174473 original size:25 final size:25
Alignment explanation
Indices: 54174445--54174523 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
54174435 ACTCGGCCCT
54174445 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
** * * *
54174470 ATCACAT-T-GGC-CATTCGGCCTT-
1 ATCACATATATACACTTTC-ACATTC
54174492 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
54174517 ATCACAT
1 ATCACAT
54174524 CGGCCATTAG
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 11 0.28
23 5 0.13
24 5 0.13
25 18 0.46
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:54183338 original size:27 final size:26
Alignment explanation
Indices: 54183294--54183345 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
54183284 CTCACTGCAA
*
54183294 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
54183321 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
54183346 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:54183422 original size:27 final size:26
Alignment explanation
Indices: 54183388--54183443 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
54183378 ATATATATAG
*
54183388 CTGTTCTGGTGGCCTAGCCACAATAT
1 CTGTTCTGGTGACCTAGCCACAATAT
* * *
54183414 CTGTATCTGGTGACTTCGTCACAATAT
1 CTGT-TCTGGTGACCTAGCCACAATAT
54183441 CTG
1 CTG
54183444 GCAGCCTCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.34
Consensus pattern (26 bp):
CTGTTCTGGTGACCTAGCCACAATAT
Found at i:54197968 original size:11 final size:11
Alignment explanation
Indices: 54197942--54198003 Score: 65
Period size: 11 Copynumber: 5.6 Consensus size: 11
54197932 CACATCAAAA
54197942 CACCACCATA-
1 CACCACCATAT
*
54197952 CAACCACTATAT
1 C-ACCACCATAT
*
54197964 CACCACCACCAT
1 CACCACCA-TAT
54197976 -ACCACCATAT
1 CACCACCATAT
*
54197986 CACCACCGTAT
1 CACCACCATAT
54197997 CACCACC
1 CACCACC
54198004 CTTGCACCAC
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
10 3 0.07
11 37 0.86
12 3 0.07
ACGTcount: A:0.35, C:0.48, G:0.02, T:0.15
Consensus pattern (11 bp):
CACCACCATAT
Found at i:54197992 original size:25 final size:25
Alignment explanation
Indices: 54197942--54197992 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
54197932 CACATCAAAA
*
54197942 CACCACCATACAACCACTATATCAC
1 CACCACCATACAACCACTATACCAC
*
54197967 CACCACCATACCACCA-TATCACCAC
1 CACCACCATACAACCACTAT-ACCAC
54197992 C
1 C
54197993 GTATCACCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 3 0.13
25 20 0.87
ACGTcount: A:0.37, C:0.49, G:0.00, T:0.14
Consensus pattern (25 bp):
CACCACCATACAACCACTATACCAC
Found at i:54200936 original size:42 final size:41
Alignment explanation
Indices: 54200861--54200959 Score: 110
Period size: 42 Copynumber: 2.4 Consensus size: 41
54200851 AGTACAGGGC
54200861 AGACACGGCCGTGTGAGGGTCTCAGGCACCTGTGTGCCCACT
1 AGACACGGCCGTGTGAGGGTCTCA-GCACCTGTGTGCCCACT
* * ** *
54200903 AGACATGGCCGTGTGAGGGTTTCA-CACGTCTGTGTGCCTGCC
1 AGACACGGCCGTGTGAGGGTCTCAGCAC--CTGTGTGCCCACT
*
54200945 AAACACGGCCGTGTG
1 AGACACGGCCGTGTG
54200960 TCCAAAACAC
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
40 3 0.06
42 45 0.94
ACGTcount: A:0.17, C:0.28, G:0.33, T:0.21
Consensus pattern (41 bp):
AGACACGGCCGTGTGAGGGTCTCAGCACCTGTGTGCCCACT
Found at i:54204398 original size:47 final size:47
Alignment explanation
Indices: 54204318--54204431 Score: 149
Period size: 47 Copynumber: 2.4 Consensus size: 47
54204308 AAGGTGGAAG
*
54204318 AAGTGACAGTTTTTTCTGA-AAAAGTGGTAGCTTGTCCACAATATTATA
1 AAGTGACAG-TTTATCT-ACAAAAGTGGTAGCTTGTCCACAATATTATA
* ** *
54204366 ATGTGGTAGTTTATCTACAAAAGTGGTGGCTTGTCCACAATATTATA
1 AAGTGACAGTTTATCTACAAAAGTGGTAGCTTGTCCACAATATTATA
*
54204413 AAGTTACAGTTTATCTACA
1 AAGTGACAGTTTATCTACA
54204432 TTATTGTGAC
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
46 1 0.02
47 49 0.88
48 6 0.11
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.36
Consensus pattern (47 bp):
AAGTGACAGTTTATCTACAAAAGTGGTAGCTTGTCCACAATATTATA
Found at i:54205578 original size:48 final size:47
Alignment explanation
Indices: 54205499--54205589 Score: 119
Period size: 48 Copynumber: 1.9 Consensus size: 47
54205489 AGCACACCAT
* ***
54205499 TTGTGGAGAAGCCACCACATAATTTTTGATAAACAGCCACATAACAAA
1 TTGTGGACAAGCCACCACATAATTGACGAT-AACAGCCACATAACAAA
* *
54205547 TTGTGGACAAGCCACCATATAATTGACGATAACGGCCACATAA
1 TTGTGGACAAGCCACCACATAATTGACGATAACAGCCACATAA
54205590 TCGCAAATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
47 12 0.32
48 25 0.68
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (47 bp):
TTGTGGACAAGCCACCACATAATTGACGATAACAGCCACATAACAAA
Found at i:54206864 original size:296 final size:295
Alignment explanation
Indices: 54206233--54207118 Score: 1373
Period size: 296 Copynumber: 3.0 Consensus size: 295
54206223 TATTGAAAAA
* * *
54206233 AATCTCACAAACTACTTACCCTTAGATCAAAACTTGGATTTGATGCCC-TCGTTGTCACATTAAT
1 AATCTCACCAACTACTTACCCTTAGATCAAAACTTGGATTTGATGCCCTTC-TTGTTACACTAAT
* * * *
54206297 GA-TTTTCTAGATTGGCGTCGTTTGGTCCTTCAAAGAACATAGGTACAAGATTTCAACACATGAA
65 -ATTTTTCTAGATTGGCATCATTTGGTCCTTTAAAGAACATAGGTACAAGATATCAACACATGAA
*
54206361 GAATGAAAGTATCTTAATACCA-TTGGACTATGAGGAAAAAATATAAAGAGAAAAAAATATTCTC
129 GAATGAAAGTATCTTAATACCATTTGG-CTATGAGGGAAAAATATAAAGAGAAAAAAATATTCTC
54206425 AATACTTCTCATGTACTTACACTACTCAATAACACAACAAAATCGATGATGAATCTCAGTGAAGG
193 AATACTTCTCATGTACTTACACTACTCAATAACACAACAAAATCGATGATGAATCTCAGTGAAGG
* * * * ** *
54206490 AGTACAAAGGTTTAACAATCTGGAAGGATTATATGATT
258 AGCAGAGAGGTTTAACGATCTACAAGGATTATATGATC
* * *
54206528 GATCTCACCAACTACTTTCCCTTAGATCAAAACTTGGATTTGGTGCCCTTCTTGTTACACTAATA
1 AATCTCACCAACTACTTACCCTTAGATCAAAACTTGGATTTGATGCCCTTCTTGTTACACTAATA
54206593 TTTTTCTAGATTGGCATCATTTGGTCCTTTAAAGAACATAGGTACAAGATATCAACACATGAAGA
66 TTTTTCTAGATTGGCATCATTTGGTCCTTTAAAGAACATAGGTACAAGATATCAACACATGAAGA
*
54206658 ATGAAAGTACCTTAATACCATTTGGCTATGAGGGAAAAATATAAAGAGAAAAAAAATATTCTCAA
131 ATGAAAGTATCTTAATACCATTTGGCTATGAGGGAAAAATATAAAGAG-AAAAAAATATTCTCAA
* * * *
54206723 TACTTCTCATGTACTTACACTACTCGATAACACAACAAAATCGATGATGAATCTCAATAAATGAG
195 TACTTCTCATGTACTTACACTACTCAATAACACAACAAAATCGATGATGAATCTCAGTGAAGGAG
*
54206788 CAGAGAGGCTTAACGATCTACAAGGATTATATGATC
260 CAGAGAGGTTTAACGATCTACAAGGATTATATGATC
* * *
54206824 AATCTCACCAACTACTTACCCTTAGACCAAAACCTGGATTTGATGCCCTTGTTGTTACACTAATA
1 AATCTCACCAACTACTTACCCTTAGATCAAAACTTGGATTTGATGCCCTTCTTGTTACACTAATA
* *
54206889 TTTTTCTAGATTGGCATCATTTGGTCCTTTAAAGAACATAGGTACAATATGTCAACACATGAAGA
66 TTTTTCTAGATTGGCATCATTTGGTCCTTTAAAGAACATAGGTACAAGATATCAACACATGAAGA
** *
54206954 ATGAAAGTATCTTAATACCATTCAGCTATGAGGGAAAAATATAAAGAGAAAAAAATATTCTTAAT
131 ATGAAAGTATCTTAATACCATTTGGCTATGAGGGAAAAATATAAAGAGAAAAAAATATTCTCAAT
* ** *
54207019 ATTTCTCATGTACTTACACTACTCAATAACACAATGAAATCGATGATGAATCTCGGTGAAGGAGC
196 ACTTCTCATGTACTTACACTACTCAATAACACAACAAAATCGATGATGAATCTCAGTGAAGGAGC
* *
54207084 AGAGAGATTTAATGATCTACAAGGATTATATGATC
261 AGAGAGGTTTAACGATCTACAAGGATTATATGATC
54207119 GATGAGTCTT
Statistics
Matches: 540, Mismatches: 47, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
294 1 0.00
295 261 0.48
296 278 0.51
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (295 bp):
AATCTCACCAACTACTTACCCTTAGATCAAAACTTGGATTTGATGCCCTTCTTGTTACACTAATA
TTTTTCTAGATTGGCATCATTTGGTCCTTTAAAGAACATAGGTACAAGATATCAACACATGAAGA
ATGAAAGTATCTTAATACCATTTGGCTATGAGGGAAAAATATAAAGAGAAAAAAATATTCTCAAT
ACTTCTCATGTACTTACACTACTCAATAACACAACAAAATCGATGATGAATCTCAGTGAAGGAGC
AGAGAGGTTTAACGATCTACAAGGATTATATGATC
Found at i:54207511 original size:50 final size:49
Alignment explanation
Indices: 54207419--54207521 Score: 127
Period size: 50 Copynumber: 2.1 Consensus size: 49
54207409 GAAGTATTTA
* * ***
54207419 GCAGTATATCTGCAATTTCTGGTGGCTTGACCAAAATATTTTG-TATCTG
1 GCAGTATATCTACAATTTCTGGTGACACAACCAAAATATTTTGCT-TCTG
*
54207468 GCAGTATATCTACAATTATCTGGTGACACAACCATAATATTTTGCTTCTG
1 GCAGTATATCTACAATT-TCTGGTGACACAACCAAAATATTTTGCTTCTG
54207518 GCAG
1 GCAG
54207522 CTCGATTGCA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
49 16 0.35
50 29 0.63
51 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (49 bp):
GCAGTATATCTACAATTTCTGGTGACACAACCAAAATATTTTGCTTCTG
Found at i:54209929 original size:51 final size:51
Alignment explanation
Indices: 54209842--54209966 Score: 128
Period size: 51 Copynumber: 2.5 Consensus size: 51
54209832 CGGATGCCCG
* * * * *
54209842 GTGGCCTGCACATAGTACCACCCTTGTAGTCAAAGCTACCTTCTT-CACAAA
1 GTGGCCTACACATAGTACCACACTTATAGCCAAAGCTACATT-TTACACAAA
* * * *
54209893 GTGGCCTTCACATAGTACCACACTTAT-GACCCAAGCTATATTTTACACATA
1 GTGGCCTACACATAGTACCACACTTATAG-CCAAAGCTACATTTTACACAAA
*
54209944 GTGGCCTACACTTAGTACCACAC
1 GTGGCCTACACATAGTACCACAC
54209967 ATGTGATCGA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
50 3 0.05
51 59 0.95
ACGTcount: A:0.29, C:0.30, G:0.14, T:0.26
Consensus pattern (51 bp):
GTGGCCTACACATAGTACCACACTTATAGCCAAAGCTACATTTTACACAAA
Found at i:54211947 original size:27 final size:27
Alignment explanation
Indices: 54211917--54212098 Score: 240
Period size: 27 Copynumber: 6.7 Consensus size: 27
54211907 TTAGTTTACC
*
54211917 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTATA
* *
54211944 AAA-TCCCTAAAATACCCTTGGTTTATA
1 AAATTACC-AAAATACCCCTGGTTTATA
* *
54211971 AAATCACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTATA
*
54211998 AAATTACCAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTATA
*
54212025 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTATA
* * *
54212052 AAATTACTAAAATACCCTTTGTTTATA
1 AAATTACCAAAATACCCCTGGTTTATA
* *
54212079 AAATTATCGAAATACCCCTG
1 AAATTACCAAAATACCCCTG
54212099 TAGGGTATAA
Statistics
Matches: 132, Mismatches: 21, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
26 3 0.02
27 127 0.96
28 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.31
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGGTTTATA
Found at i:54212110 original size:27 final size:27
Alignment explanation
Indices: 54212080--54212481 Score: 464
Period size: 27 Copynumber: 15.3 Consensus size: 27
54212070 TTGTTTATAA
* *
54212080 AATTATCGAAATACCCCTGTAGGGTAT
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
54212107 AATTACCGCAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* **
54212134 AATTACCGAAATACCCTTACAGGGTA-
1 AATTACCGAAATACCCCTGTAGGGTAG
*
54212160 AA-T-------TACCCCTGTAGCGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
54212179 AATTACCGGAATACCCTTGTAGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
54212206 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** * *
54212233 AATTATTGCAATACCCCTTTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
54212260 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
54212287 AATTAACGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
54212314 AATCACCGAAATACCCCTGTAGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
*
54212341 AATTACCGAAATACCCCTGTAGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
54212368 AATTATCGTAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
54212395 AATTATCGAAATACCCCTGTAGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
** *
54212422 AATTACTAAAATACCCCTGTAGGGTGG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
54212449 AATTACCGAGATA-CCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
54212475 AATTACC
1 AATTACC
54212482 ATTTTGCCCC
Statistics
Matches: 319, Mismatches: 47, Indels: 19
0.83 0.12 0.05
Matches are distributed among these distances:
18 11 0.03
19 2 0.01
20 1 0.00
25 1 0.00
26 18 0.06
27 286 0.90
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:54212112 original size:54 final size:54
Alignment explanation
Indices: 54211917--54212098 Score: 301
Period size: 54 Copynumber: 3.4 Consensus size: 54
54211907 TTAGTTTACC
**
54211917 AAATTACCAAAATACCCCTGGTTTGTAAAATCCCTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTGGTTTATA
* *
54211971 AAATCACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTGGTTTATA
*
54212025 AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTTGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTGGTTTATA
* *
54212079 AAATTATCGAAATACCCCTG
1 AAATTACCAAAATACCCCTG
54212099 TAGGGTATAA
Statistics
Matches: 119, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 119 1.00
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.31
Consensus pattern (54 bp):
AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTGGTTTATA
Found at i:54212182 original size:45 final size:46
Alignment explanation
Indices: 54212118--54212212 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 46
54212108 ATTACCGCAA
*
54212118 TACCCCTATAGGGTAGAATTACCGAAATACCCTTACAGGGT-AAAT
1 TACCCCTATAGCGTAGAATTACCGAAATACCCTTACAGGGTAAAAT
* * **
54212163 TACCCCTGTAGCGTAGAATTACCGGAATACCCTTGTAGGGTAAAAT
1 TACCCCTATAGCGTAGAATTACCGAAATACCCTTACAGGGTAAAAT
54212209 TACC
1 TACC
54212213 GAAATACCCC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 36 0.82
46 8 0.18
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (46 bp):
TACCCCTATAGCGTAGAATTACCGAAATACCCTTACAGGGTAAAAT
Found at i:54212959 original size:22 final size:22
Alignment explanation
Indices: 54212907--54212971 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
54212897 TTAAAGCCTT
* *
54212907 CTGATTATGGCTTTGTGTCAAC
1 CTGATTATGGCTCTGTGCCAAC
*
54212929 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
* *
54212951 CTGATTATGGCTGTGTACCAA
1 CTGATTATGGCTCTGTGCCAA
54212972 ACGTATTTGC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 1 0.03
22 33 0.94
23 1 0.03
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.34
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:54213160 original size:27 final size:27
Alignment explanation
Indices: 54213130--54213258 Score: 188
Period size: 27 Copynumber: 4.8 Consensus size: 27
54213120 ATTCTGTTAA
* * *
54213130 GTGGCTTTGCCACATTATCTGTTTCTG
1 GTGGCTCTGCCACAATATCTGTATCTG
*
54213157 GTGGCTATGCCACAAATATCTGT-TCTG
1 GTGGCTCTGCCAC-AATATCTGTATCTG
54213184 GTGGCTCTGCCACAATATCTGTATCTG
1 GTGGCTCTGCCACAATATCTGTATCTG
54213211 GTGGCTCTGCCACAATATCTGTATCTG
1 GTGGCTCTGCCACAATATCTGTATCTG
* *
54213238 GTGACTCTGTCACAATATCTG
1 GTGGCTCTGCCACAATATCTG
54213259 ATAATTGAGT
Statistics
Matches: 95, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
26 9 0.09
27 78 0.82
28 8 0.08
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.36
Consensus pattern (27 bp):
GTGGCTCTGCCACAATATCTGTATCTG
Found at i:54213446 original size:31 final size:31
Alignment explanation
Indices: 54213395--54213536 Score: 212
Period size: 31 Copynumber: 4.5 Consensus size: 31
54213385 TTGCATTCAC
* *
54213395 ATTCTGATTTTTTATTCTGTTACCTGATACTA
1 ATTCTGA-TTTTGATTCTGTTACCTGATACTG
*
54213427 ATTCTGATTTTGATTCTGTTACCTGATATTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
54213458 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
* * *
54213489 ATTCTGATTCTGATTCTGTCACCTGATTCTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
*
54213520 ATTTTGATTTTGATTCT
1 ATTCTGATTTTGATTCT
54213537 AGTTCTGATA
Statistics
Matches: 101, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
31 94 0.93
32 7 0.07
ACGTcount: A:0.19, C:0.15, G:0.14, T:0.51
Consensus pattern (31 bp):
ATTCTGATTTTGATTCTGTTACCTGATACTG
Found at i:54213458 original size:19 final size:19
Alignment explanation
Indices: 54213430--54213494 Score: 63
Period size: 19 Copynumber: 3.8 Consensus size: 19
54213420 GATACTAATT
*
54213430 CTGATTTTGATTCTGTTAC
1 CTGATATTGATTCTGTTAC
54213449 CTGATATTGATTCTG--A-
1 CTGATATTGATTCTGTTAC
54213465 -T--T-TTGATTCTGTTAC
1 CTGATATTGATTCTGTTAC
*
54213480 CTGATACTGATTCTG
1 CTGATATTGATTCTG
54213495 ATTCTGATTC
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
12 9 0.24
13 1 0.03
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 22 0.59
ACGTcount: A:0.18, C:0.15, G:0.17, T:0.49
Consensus pattern (19 bp):
CTGATATTGATTCTGTTAC
Found at i:54213465 original size:6 final size:6
Alignment explanation
Indices: 54213427--54213545 Score: 77
Period size: 6 Copynumber: 19.3 Consensus size: 6
54213417 CCTGATACTA
* *
54213427 ATTCTG ATTTTG ATTCTG -TTACCTG ATAT-TG ATTCTG ATTTTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG AT-TCTG ATTCTG ATTCTG ATTCTG
* * *
54213476 -TTACCTG ATACTG ATTCTG ATTCTG ATTCTG -TCACCTG ATTCTG ATTTTG
1 ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG
*
54213526 ATTTTG ATTCT- AGTTCTG AT
1 ATTCTG ATTCTG A-TTCTG AT
54213546 AATGTTTCTT
Statistics
Matches: 90, Mismatches: 10, Indels: 26
0.71 0.08 0.21
Matches are distributed among these distances:
5 7 0.08
6 69 0.77
7 10 0.11
8 3 0.03
9 1 0.01
ACGTcount: A:0.18, C:0.15, G:0.16, T:0.50
Consensus pattern (6 bp):
ATTCTG
Found at i:54222066 original size:34 final size:33
Alignment explanation
Indices: 54221986--54222082 Score: 117
Period size: 32 Copynumber: 3.0 Consensus size: 33
54221976 CTGATTGCAT
* *
54221986 ACTG-TACTGATTCTGTAATAGGCTTAGGCCCC
1 ACTGATACTGATTCTGTAATGGGCTAAGGCCCC
* *
54222018 ACTGATACT-ATTCTGAAATGGGCTCAGGCCCAC
1 ACTGATACTGATTCTGTAATGGGCTAAGGCCC-C
* *
54222051 ACTGTTTCTGATTCTGTAATGGGCTAAGGCCC
1 ACTGATACTGATTCTGTAATGGGCTAAGGCCC
54222083 TAACTGAAAC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
32 23 0.42
33 12 0.22
34 20 0.36
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.30
Consensus pattern (33 bp):
ACTGATACTGATTCTGTAATGGGCTAAGGCCCC
Found at i:54225994 original size:34 final size:35
Alignment explanation
Indices: 54225956--54226036 Score: 119
Period size: 34 Copynumber: 2.3 Consensus size: 35
54225946 ATACATTCTG
54225956 GGCCTAAGCCCATATTAGTAACAGT-AACAGTCTA
1 GGCCTAAGCCCATATTAGTAACAGTAAACAGTCTA
* * * *
54225990 GGCCTTAGCCTATTTTAGTATCAGTAAACAGTCTA
1 GGCCTAAGCCCATATTAGTAACAGTAAACAGTCTA
54226025 GGCCTAAGCCCA
1 GGCCTAAGCCCA
54226037 CCTCAATACA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
34 21 0.52
35 19 0.47
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.26
Consensus pattern (35 bp):
GGCCTAAGCCCATATTAGTAACAGTAAACAGTCTA
Found at i:54226586 original size:27 final size:27
Alignment explanation
Indices: 54226480--54226636 Score: 136
Period size: 27 Copynumber: 5.8 Consensus size: 27
54226470 GGGCAAAACA
* * * *
54226480 GTCATTTTGCCCTATAAGGGAATTATA
1 GTCATTTTACCCTATAAGGGTATTTTG
* * * *
54226507 GTCATTATACCTTATAAGGATATTTCG
1 GTCATTTTACCCTATAAGGGTATTTTG
*
54226534 ATCATTTTACCCTATAAGGGTATTTTG
1 GTCATTTTACCCTATAAGGGTATTTTG
*
54226561 GTCATTTTACCCTATAGGGGTATTTTG
1 GTCATTTTACCCTATAAGGGTATTTTG
* * * * *
54226588 GTTATTTTATCGTAT-GGGTGTATTTCG
1 GTCATTTTACCCTATAAGG-GTATTTTG
* *
54226615 GTTATTTTACCCGATTAAGGGT
1 GTCATTTTACCCTA-TAAGGGT
54226637 CTAAGTATGC
Statistics
Matches: 104, Mismatches: 23, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
26 3 0.03
27 96 0.92
28 3 0.03
29 2 0.02
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCTATAAGGGTATTTTG
Found at i:54230483 original size:27 final size:27
Alignment explanation
Indices: 54230460--54230579 Score: 138
Period size: 27 Copynumber: 4.4 Consensus size: 27
54230450 GGATATTTTA
54230460 GTCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* *
54230487 GTCAATTTACCCTAT-AGGGGCATTTCG
1 GTCATTTTACCCTATGA-GGGTATTTCG
* * * *
54230514 GTCTTTTTATCGTATG-GGTGTATTTTG
1 GTCATTTTACCCTATGAGG-GTATTTCG
54230541 GTCATTTTACCCTATG-GGTGTATTTCG
1 GTCATTTTACCCTATGAGG-GTATTTCG
54230568 GTCATTTTACCC
1 GTCATTTTACCC
54230580 GATAAAGGGT
Statistics
Matches: 78, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
26 3 0.04
27 75 0.96
ACGTcount: A:0.17, C:0.18, G:0.22, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCTATGAGGGTATTTCG
Found at i:54230505 original size:54 final size:54
Alignment explanation
Indices: 54230460--54230579 Score: 154
Period size: 54 Copynumber: 2.2 Consensus size: 54
54230450 GGATATTTTA
*
54230460 GTCATTTTACCCTATGAGG-GTATTTCGGTCAATTTACCCTATAGGGGCATTTCG
1 GTCATTTTACCCTATG-GGTGTATTTCGGTCAATTTACCCTATAGGGGTATTTCG
* * * * *
54230514 GTCTTTTTATCGTATGGGTGTATTTTGGTCATTTTACCCTAT-GGGTGTATTTCG
1 GTCATTTTACCCTATGGGTGTATTTCGGTCAATTTACCCTATAGGG-GTATTTCG
54230568 GTCATTTTACCC
1 GTCATTTTACCC
54230580 GATAAAGGGT
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
53 5 0.09
54 50 0.91
ACGTcount: A:0.17, C:0.18, G:0.22, T:0.43
Consensus pattern (54 bp):
GTCATTTTACCCTATGGGTGTATTTCGGTCAATTTACCCTATAGGGGTATTTCG
Found at i:54237365 original size:5 final size:5
Alignment explanation
Indices: 54237355--54237379 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
54237345 ACTCATCATG
54237355 TTTTC TTTTC TTTTC TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC
54237380 CCCTTCTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:54238593 original size:28 final size:28
Alignment explanation
Indices: 54238553--54238616 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 28
54238543 TGGGAAATAG
* * *
54238553 TTGGACCTGATGGGCCATATGAATGTGA
1 TTGGGCCTGATGGGCCATATGAACGAGA
*
54238581 TTGGGCCTGATGGGCCATGTGAACGAGA
1 TTGGGCCTGATGGGCCATATGAACGAGA
54238609 TTGGGCCT
1 TTGGGCCT
54238617 AAAGGGGCCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.20, C:0.17, G:0.36, T:0.27
Consensus pattern (28 bp):
TTGGGCCTGATGGGCCATATGAACGAGA
Found at i:54238963 original size:27 final size:27
Alignment explanation
Indices: 54238941--54239045 Score: 124
Period size: 27 Copynumber: 3.9 Consensus size: 27
54238931 AGAAATTATT
*
54238941 GAAATACCCTCAATTTGTAAAATTATC
1 GAAATACCCTCAATTTGTAAAATTACC
* * *
54238968 GAAATACCCCCGATTTTTAAAATTACC
1 GAAATACCCTCAATTTGTAAAATTACC
* * *
54238995 AAAATACCCTCGATTATG--AAATTACT
1 GAAATACCCTCAATT-TGTAAAATTACC
54239021 GAAATACCCTCAATTTGTAAAATTA
1 GAAATACCCTCAATTTGTAAAATTA
54239046 GAAAAATACC
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
25 2 0.03
26 20 0.31
27 42 0.65
28 1 0.02
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (27 bp):
GAAATACCCTCAATTTGTAAAATTACC
Found at i:54239042 original size:53 final size:53
Alignment explanation
Indices: 54238942--54239056 Score: 135
Period size: 53 Copynumber: 2.2 Consensus size: 53
54238932 GAAATTATTG
* * *
54238942 AAATACCCTCAATTTGTAAAATTATCGAAATACCCCCGATTTTTAAAATTACCA
1 AAATACCCTCAATTTG-AAAATTATCGAAATACCCCCAATTTGTAAAATTACAA
* * *
54238996 AAATACCCTCGATTATG-AAATTA-CTGAAATACCCTCAATTTGTAAAATTAGAA
1 AAATACCCTCAATT-TGAAAATTATC-GAAATACCCCCAATTTGTAAAATTACAA
54239049 AAATACCC
1 AAATACCC
54239057 ATTACGAGCA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
52 1 0.02
53 37 0.70
54 13 0.25
55 2 0.04
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.30
Consensus pattern (53 bp):
AAATACCCTCAATTTGAAAATTATCGAAATACCCCCAATTTGTAAAATTACAA
Found at i:54241174 original size:25 final size:28
Alignment explanation
Indices: 54241124--54241175 Score: 74
Period size: 25 Copynumber: 2.0 Consensus size: 28
54241114 CAATATTTTT
*
54241124 GTATGAAAATTGATATGATAGGAAAATC
1 GTATGAAAATTGATATGATAGAAAAATC
54241152 GTATGAAAA-T-AT-TGATAGAAAAAT
1 GTATGAAAATTGATATGATAGAAAAAT
54241176 TTTACCGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.48
26 2 0.09
27 1 0.04
28 9 0.39
ACGTcount: A:0.50, C:0.02, G:0.19, T:0.29
Consensus pattern (28 bp):
GTATGAAAATTGATATGATAGAAAAATC
Found at i:54244881 original size:40 final size:40
Alignment explanation
Indices: 54244837--54245062 Score: 241
Period size: 40 Copynumber: 5.7 Consensus size: 40
54244827 GCTCCTCGTT
* *
54244837 CAAATGCCTTCGGGACATAGCCCGG-TTGTAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAATTCGCA
* * *
54244877 CAAATGCCTTCGGGACTTAACCCGGACTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATTCGCA
54244917 CAAATGCCTTCGGGACTTAGCCCGGAATTAGT-ATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAAT-TCGCA
* *
54244957 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGT-ATCTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAATTAGTAAT-TCGCA
* * * *
54244997 CAAATGCCTTC-GGATCTTAGTCCGG-ATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAAT-TAGT-AATTCGCA
54245038 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
54245063 CATCATTCAA
Statistics
Matches: 164, Mismatches: 14, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
39 5 0.03
40 146 0.89
41 12 0.07
42 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATTCGCA
Found at i:54244938 original size:80 final size:79
Alignment explanation
Indices: 54244837--54245063 Score: 273
Period size: 80 Copynumber: 2.8 Consensus size: 79
54244827 GCTCCTCGTT
* * *
54244837 CAAATGCCTTCGGGACATAGCCCGGTTGTAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAT-TAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGG
54244902 ACTTAGTAACTCGCA
65 ACTTAGTAACTCGCA
*
54244917 CAAATGCCTTCGGGACTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACTTAGCCCGG-ATTAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAGCCC
* *
54244980 GGATTTAGTATCTCGCA
63 GGACTTAGTAACTCGCA
* * * *
54244997 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TAGT-AATTCGCACAAATGCCTTCGGGACTTAGCCC
54245060 GGAC
63 GGAC
54245064 ATCATTCAAA
Statistics
Matches: 127, Mismatches: 12, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
79 10 0.08
80 104 0.82
81 12 0.09
82 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGGA
CTTAGTAACTCGCA
Found at i:54245046 original size:120 final size:120
Alignment explanation
Indices: 54244837--54245062 Score: 293
Period size: 120 Copynumber: 1.9 Consensus size: 120
54244827 GCTCCTCGTT
54244837 CAAATGCCTTCGGGACATAGCCCGGTTGTAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGTTGTAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
*
54244902 ACTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
66 ACTTAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* * **
54244957 CAAATGCCTTC-GGATCTTAGTCCGGATT-TAGT-ATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CAAATGCCTTCGGGA-CATAGCCCGG-TTGTAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAAC
* *
54245018 CCGGA-TATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
62 CCGGACT-TAGTAAC-TAGCACAAATGCCTTCGGGACTTAGCCCGGA
54245063 CATCATTCAA
Statistics
Matches: 93, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
119 9 0.10
120 74 0.80
121 10 0.11
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.26
Consensus pattern (120 bp):
CAAATGCCTTCGGGACATAGCCCGGTTGTAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
ACTTAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:54256168 original size:27 final size:27
Alignment explanation
Indices: 54256110--54256168 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
54256100 GAGTACCTGA
* ***
54256110 ACCCTTATGTGATAAAATGACGATTTT
1 ACCCTTATGTGATAAAATGACCAAAAT
*
54256137 TCCCTTATGTGATAAAATGACCAAAAT
1 ACCCTTATGTGATAAAATGACCAAAAT
54256164 ACCCT
1 ACCCT
54256169 CATAGGGTGA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (27 bp):
ACCCTTATGTGATAAAATGACCAAAAT
Found at i:54256181 original size:27 final size:26
Alignment explanation
Indices: 54256151--54256248 Score: 99
Period size: 27 Copynumber: 3.7 Consensus size: 26
54256141 TTATGTGATA
54256151 AAATGACCAAAATACCCTCATAGGGT
1 AAATGACCAAAATACCCTCATAGGGT
* *
54256177 GAAATGATCGAAATACCCTCATAGGGT
1 -AAATGACCAAAATACCCTCATAGGGT
* * *
54256204 AGAATGACCGAAATACCCT-GTGGGGT
1 A-AATGACCAAAATACCCTCATAGGGT
* *
54256230 AAAATGACTATAATACCCT
1 -AAATGACCAAAATACCCT
54256249 GGTAAGGTAA
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
26 20 0.33
27 41 0.67
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.21
Consensus pattern (26 bp):
AAATGACCAAAATACCCTCATAGGGT
Found at i:54256263 original size:53 final size:54
Alignment explanation
Indices: 54256149--54256264 Score: 128
Period size: 53 Copynumber: 2.2 Consensus size: 54
54256139 CCTTATGTGA
* *
54256149 TAAAATGACCAAAATACCCTCATAGGGTGAAATGATCGAAATACCCTCATAGGG
1 TAAAATGACCAAAATACCCTCATAGGGTAAAATGATCGAAATACCCTCATAAGG
* * * * * **
54256203 TAGAATGACCGAAATACCCT-GTGGGGTAAAATGA-CTATAATACCCTGGTAAGG
1 TAAAATGACCAAAATACCCTCATAGGGTAAAATGATCGA-AATACCCTCATAAGG
54256256 TAAAATGAC
1 TAAAATGAC
54256265 AGATTTGTTC
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
52 2 0.04
53 31 0.61
54 18 0.35
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.22
Consensus pattern (54 bp):
TAAAATGACCAAAATACCCTCATAGGGTAAAATGATCGAAATACCCTCATAAGG
Found at i:54270575 original size:93 final size:93
Alignment explanation
Indices: 54270462--54270632 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
54270452 GCCCCTAAGT
* * *
54270462 GAACTTGGACTCAACTCAACGAGCTCGGGCATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACACAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
54270527 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
* *
54270555 GAACTCGGACTCAACACAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACACAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
54270620 CGAGTTCGGATGC
66 CGAGTTCGGATGC
54270633 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACACAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:54270629 original size:46 final size:46
Alignment explanation
Indices: 54270457--54270629 Score: 192
Period size: 46 Copynumber: 3.7 Consensus size: 46
54270447 AAACCGCCCC
* * *
54270457 TAAGTGAACTTGGACTCAACTCAACGAGCTCGGGCATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* * *
54270503 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* * *
54270551 TCA-CGAACTCGGACTCAACACAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
54270596 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
54270630 TGCTCAACCA
Statistics
Matches: 103, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 58 0.56
47 27 0.26
48 2 0.02
49 1 0.01
50 4 0.04
51 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:54271084 original size:30 final size:30
Alignment explanation
Indices: 54271050--54271109 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
54271040 ATTTAATACG
54271050 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
54271080 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
54271110 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:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:54272126 original size:19 final size:19
Alignment explanation
Indices: 54272086--54272129 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
54272076 AATTCATTCG
*
54272086 ATAACAGTAACTCATCCGT
1 ATAACAGTAACTCATCCAT
* *
54272105 ATAACAGTAATTCATCTAT
1 ATAACAGTAACTCATCCAT
54272124 ATAACA
1 ATAACA
54272130 CATAGCTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (19 bp):
ATAACAGTAACTCATCCAT
Found at i:54283223 original size:40 final size:40
Alignment explanation
Indices: 54283051--54283216 Score: 262
Period size: 40 Copynumber: 4.2 Consensus size: 40
54283041 AACCCAAGTA
* *
54283051 CCTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
54283090 CCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
54283130 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
54283170 CCTTCGAGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
54283210 CTTTCGG
1 CCTTCGG
54283217 ATCTTAGTCC
Statistics
Matches: 117, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 13 0.11
40 104 0.89
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:54291252 original size:77 final size:77
Alignment explanation
Indices: 54291094--54291260 Score: 250
Period size: 77 Copynumber: 2.2 Consensus size: 77
54291084 AACCCAAGTA
* *
54291094 CCTTGGGAT-TTAGCCGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGATATAGTAA
1 CCTTCGGATCTTAGCCGATATAGCAACTCGCACAAATGCCTTCGAGACTTAGCCCGATATAGTAA
*
54291158 CTCGCACAAATG
66 CTAGCACAAATG
*
54291170 CCTTCGGA-CTTAGCCCGATATAGTAACTCGCACAAATGCCTTCGAGACTTAGCCCGGATATAGT
1 CCTTCGGATCTTAG-CCGATATAGCAACTCGCACAAATGCCTTCGAGACTTAGCCC-GATATAGT
*
54291234 CACTAGCACAAATG
64 AACTAGCACAAATG
54291248 -CTTCGGATCTTAG
1 CCTTCGGATCTTAG
54291261 TCCGGTTATC
Statistics
Matches: 82, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
76 11 0.13
77 46 0.56
78 25 0.30
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (77 bp):
CCTTCGGATCTTAGCCGATATAGCAACTCGCACAAATGCCTTCGAGACTTAGCCCGATATAGTAA
CTAGCACAAATG
Found at i:54291260 original size:39 final size:38
Alignment explanation
Indices: 54291094--54291260 Score: 239
Period size: 38 Copynumber: 4.3 Consensus size: 38
54291084 AACCCAAGTA
* * *
54291094 CCTTGGGATTTAG-CCGATATAGCAACTCGCACAAATG
1 CCTTCGGACTTAGCCCGATATAGTAACTCGCACAAATG
54291131 CCTTCGGGACTTAGCCCGATATAGTAACTCGCACAAATG
1 CCTTC-GGACTTAGCCCGATATAGTAACTCGCACAAATG
54291170 CCTTCGGACTTAGCCCGATATAGTAACTCGCACAAATG
1 CCTTCGGACTTAGCCCGATATAGTAACTCGCACAAATG
* *
54291208 CCTTCGAGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCG-GACTTAGCCC-GATATAGTAACTCGCACAAATG
54291248 -CTTCGGATCTTAG
1 CCTTCGGA-CTTAG
54291261 TCCGGTTATC
Statistics
Matches: 120, Mismatches: 5, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
37 4 0.03
38 48 0.40
39 48 0.40
40 20 0.17
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (38 bp):
CCTTCGGACTTAGCCCGATATAGTAACTCGCACAAATG
Found at i:54296297 original size:45 final size:45
Alignment explanation
Indices: 54296246--54296331 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 45
54296236 ATGTGATCTA
* *
54296246 AACTCATTGAGTCGTGGTCCGAGTTCATGATATATGTGACATCCG
1 AACTCATTGAGTCGTGGTCCGAGTTCATGACACATGTGACATCCG
* * *
54296291 AACTCATTGAGTTGTGGTCTGAGTTCGTGACACATGTGACA
1 AACTCATTGAGTCGTGGTCCGAGTTCATGACACATGTGACA
54296332 CATGTTTTGG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (45 bp):
AACTCATTGAGTCGTGGTCCGAGTTCATGACACATGTGACATCCG
Found at i:54303302 original size:39 final size:39
Alignment explanation
Indices: 54303248--54303359 Score: 188
Period size: 39 Copynumber: 2.9 Consensus size: 39
54303238 TTTAGTGATG
*
54303248 TATATCCAGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
54303287 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
* * *
54303326 TATATCCGGACTTAAGGTCCACAGGCTACGTGCT
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCT
54303360 AGAAATATGT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 69 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (39 bp):
TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
Found at i:54305926 original size:43 final size:42
Alignment explanation
Indices: 54305878--54305962 Score: 100
Period size: 42 Copynumber: 2.0 Consensus size: 42
54305868 AGGATTTTCG
*
54305878 ATATCTG-TTTTGCGTGTAAGACCATGTCTAGGACATTGGCATC
1 ATATCTGATTTT--GTGTAAGACCATGTCTAGGACAGTGGCATC
* * * *
54305921 ATATCTGATTTTTTGTAAGACCCTGTTTGGGACAGTGGCATC
1 ATATCTGATTTTGTGTAAGACCATGTCTAGGACAGTGGCATC
54305963 GATGTTTGAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
42 25 0.69
43 7 0.19
44 4 0.11
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (42 bp):
ATATCTGATTTTGTGTAAGACCATGTCTAGGACAGTGGCATC
Found at i:54305995 original size:43 final size:42
Alignment explanation
Indices: 54305892--54305995 Score: 102
Period size: 42 Copynumber: 2.5 Consensus size: 42
54305882 CTGTTTTGCG
* * * ***
54305892 TGTAAGACCATGTCTAGGACATTGGCATCATATCTGATTTTT
1 TGTAAGACCACGTCTGGGACAGTGGCATCATATCTGATTACA
* * *
54305934 TGTAAGACC-CTGTTTGGGACAGTGGCATCGATGTTTGATTACA
1 TGTAAGACCAC-GTCTGGGACAGTGGCATC-ATATCTGATTACA
54305977 TGTAAGACCACGTCTGGGA
1 TGTAAGACCACGTCTGGGA
54305996 TGTCGACATT
Statistics
Matches: 49, Mismatches: 10, Indels: 5
0.77 0.16 0.08
Matches are distributed among these distances:
42 24 0.49
43 24 0.49
44 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (42 bp):
TGTAAGACCACGTCTGGGACAGTGGCATCATATCTGATTACA
Found at i:54311934 original size:269 final size:268
Alignment explanation
Indices: 54311549--54312085 Score: 1029
Period size: 269 Copynumber: 2.0 Consensus size: 268
54311539 ACAAATGTCG
54311549 TACACCTTTGTATTGGACGGAGCTTAACGAAAATAAGATTCATGGGATTGATTTGATTAAAGAAA
1 TACACCTTTGTATTGGACGGAGCTTAACGAAAATAAGATTCATGGGATTGATTTGATTAAAGAAA
54311614 CTGAATAGAAAGTGAAAGTGATCCGAGATAGTCTGAAAACAACTTCTGATCGTCAGAAATCATAT
66 CTGAATAGAAAGTGAAAGTGATCCGAGATAGTCTGAAAACAACTTCTGATCGTCAGAAATCATAT
54311679 GCAGATTTGAAAAGAAAAGATATTGAATTTTGAGATCGGCAACAAAGTATTTTTAAAGGTATCTC
131 GCAGATTTGAAAAGAAAAGATATTGAA-TTTGAGATCGGCAACAAAGTATTTTTAAAGGTATCTC
54311744 CGTGGAAGAAAGTGCTTCGATTCGGTAGAAAAGGAAAATTGAGTCTGAGGTTCATTGGACCGTAC
195 CGTGGAAGAAAGTGCTTCGATTCGGTAGAAAAGGAAAATTGAGTCTGAGGTTCATTGGACCGTAC
54311809 GAGATTACT
260 GAGATTACT
54311818 TACACCTTTGTATTGGACGGAGCTTAACGAAAATAAGATTCATGGGATTGATTTGATTAAAGAAA
1 TACACCTTTGTATTGGACGGAGCTTAACGAAAATAAGATTCATGGGATTGATTTGATTAAAGAAA
54311883 CTGAATAGAAAGTGAAAGTGATCCGAGATAGTCTGAAAACAACTTCTGATCGTCAGAAATCATAT
66 CTGAATAGAAAGTGAAAGTGATCCGAGATAGTCTGAAAACAACTTCTGATCGTCAGAAATCATAT
*
54311948 GCAGATTTGAAAAGAAAAGATATTGAATTTGAGATTGGCAACAAAGTATTTTTAAAGGTATCTCC
131 GCAGATTTGAAAAGAAAAGATATTGAATTTGAGATCGGCAACAAAGTATTTTTAAAGGTATCTCC
* * *
54312013 GTGGAAGAAAGTGTTTCGATTCGGTAGAAAATGCAAATTGAGTCTGAGGTTCATTGGACCGTACG
196 GTGGAAGAAAGTGCTTCGATTCGGTAGAAAAGGAAAATTGAGTCTGAGGTTCATTGGACCGTACG
54312078 AGATTACT
261 AGATTACT
54312086 GAGCGTATTG
Statistics
Matches: 264, Mismatches: 4, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
268 107 0.41
269 157 0.59
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (268 bp):
TACACCTTTGTATTGGACGGAGCTTAACGAAAATAAGATTCATGGGATTGATTTGATTAAAGAAA
CTGAATAGAAAGTGAAAGTGATCCGAGATAGTCTGAAAACAACTTCTGATCGTCAGAAATCATAT
GCAGATTTGAAAAGAAAAGATATTGAATTTGAGATCGGCAACAAAGTATTTTTAAAGGTATCTCC
GTGGAAGAAAGTGCTTCGATTCGGTAGAAAAGGAAAATTGAGTCTGAGGTTCATTGGACCGTACG
AGATTACT
Found at i:54316348 original size:48 final size:49
Alignment explanation
Indices: 54316137--54316375 Score: 232
Period size: 49 Copynumber: 4.9 Consensus size: 49
54316127 ATCATGTTTA
* * *
54316137 ATGAGATCCTGTGTAAGACCATGTCTGGGACATGGTATCGGCATTCGAG
1 ATGAGATCCTGTGTAAGACCATGTCTGGGACATGGCATCAGCATCCGAG
* * *
54316186 ATGAGATCCCGTGTAAGACCATGTCTGGGACATGGCATCAACATCTGAG
1 ATGAGATCCTGTGTAAGACCATGTCTGGGACATGGCATCAGCATCCGAG
* * * ** *
54316235 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAG-TTTTGAT
1 ATGAGATCCTGTGTAAGACCATGTCTGGGACATGGCATCAGCATCCGAG
* * * * *
54316283 ATGTG-TGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCA-CCAAT
1 ATGAGATCCT-GTGTAAGACCATGTCTGGGACATGGCATCAGCATCCGAG
* * * ** * *
54316331 ATGTGATCCTGTATAAGACCATATCAAGGATATGGCTTCAGCATC
1 ATGAGATCCTGTGTAAGACCATGTCTGGGACATGGCATCAGCATC
54316376 GTTAAGTCAT
Statistics
Matches: 157, Mismatches: 29, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
47 1 0.01
48 71 0.45
49 85 0.54
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (49 bp):
ATGAGATCCTGTGTAAGACCATGTCTGGGACATGGCATCAGCATCCGAG
Found at i:54318148 original size:48 final size:48
Alignment explanation
Indices: 54318045--54318149 Score: 124
Period size: 48 Copynumber: 2.2 Consensus size: 48
54318035 AGATCCCATG
** * *
54318045 TAAGACCATGTCTGGGACATGGCATTGGCGTTGATATGTGTGCTAGTG
1 TAAGACCATGTCTGGGACATGGCATTGGCCCTGATATGTGTCCTAGTA
* *
54318093 TAGGACCATGTCTGGGACATGGCGTTGGCACCT-ATATGTGATCCT-GTA
1 TAAGACCATGTCTGGGACATGGCATTGGC-CCTGATATGTG-TCCTAGTA
54318141 TAAGACCAT
1 TAAGACCAT
54318150 ATCAGGGATT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
48 44 0.92
49 4 0.08
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.30
Consensus pattern (48 bp):
TAAGACCATGTCTGGGACATGGCATTGGCCCTGATATGTGTCCTAGTA
Found at i:54318276 original size:42 final size:42
Alignment explanation
Indices: 54318187--54318291 Score: 131
Period size: 42 Copynumber: 2.5 Consensus size: 42
54318177 AGTCATTTCG
* ** * * *
54318187 TATAAGACCATGTCTGGG-CATGGCATCGATATGAGGTCCCG
1 TATAAGACCATGTCTGGGATATAACATAGATATGAGGACCCA
*
54318228 TATAAGACCATGTCTGGGATATAACATAGATATGTGGACCCA
1 TATAAGACCATGTCTGGGATATAACATAGATATGAGGACCCA
*
54318270 TGTAAGACCATGTCTGGGATAT
1 TATAAGACCATGTCTGGGATAT
54318292 GGCTTTGGCA
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 18 0.33
42 37 0.67
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.27
Consensus pattern (42 bp):
TATAAGACCATGTCTGGGATATAACATAGATATGAGGACCCA
Found at i:54321803 original size:54 final size:53
Alignment explanation
Indices: 54321736--54321885 Score: 237
Period size: 54 Copynumber: 2.8 Consensus size: 53
54321726 GGCCATGGCA
*
54321736 AGAAGACCGTATAGTGTAAGACCTAGTCTGGGACTATGGCATCATATGGGGAT
1 AGAAGACCATATAGTGTAAGACCTAGTCTGGGACTATGGCATCATATGGGGAT
***
54321789 GAGAAGACCATATAGTGTAAGACCTAGTCTAATACTATGGCATCATATGGGGAT
1 -AGAAGACCATATAGTGTAAGACCTAGTCTGGGACTATGGCATCATATGGGGAT
*
54321843 ACGAAGACCACATAGTGTAAGACCTAGTCTGGGACTATGGCAT
1 A-GAAGACCATATAGTGTAAGACCTAGTCTGGGACTATGGCAT
54321886 TGCTTGAGGA
Statistics
Matches: 87, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
53 1 0.01
54 86 0.99
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.24
Consensus pattern (53 bp):
AGAAGACCATATAGTGTAAGACCTAGTCTGGGACTATGGCATCATATGGGGAT
Found at i:54328396 original size:80 final size:79
Alignment explanation
Indices: 54328312--54328483 Score: 220
Period size: 79 Copynumber: 2.2 Consensus size: 79
54328302 GGACTAAGAT
*
54328312 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATATCAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACT
* *
54328376 AAATCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * * * * * *
54328392 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
54328457 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
54328471 CCGAAGGCATTTG
1 CCGAAGGCATTTG
54328484 AACGAGGAGC
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 38 0.48
80 38 0.48
81 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:54328463 original size:39 final size:39
Alignment explanation
Indices: 54328259--54328481 Score: 209
Period size: 40 Copynumber: 5.6 Consensus size: 39
54328249 TTGAATGCTG
* * * * *
54328259 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAA
**
54328299 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGATACTAAA
* *
54328338 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAA
* *
54328379 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAA
* * *
54328419 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
* * *
54328458 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
54328482 TGAACGAGGA
Statistics
Matches: 157, Mismatches: 18, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
39 40 0.25
40 103 0.66
41 13 0.08
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:54328501 original size:79 final size:80
Alignment explanation
Indices: 54328339--54328516 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
54328329 AGATACAAAT
* * * *
54328339 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
54328404 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * * *
54328419 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
54328483 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
54328498 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
54328517 TACGTGATTT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
78 15 0.19
79 48 0.59
80 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:54334775 original size:43 final size:43
Alignment explanation
Indices: 54334661--54334918 Score: 258
Period size: 43 Copynumber: 6.1 Consensus size: 43
54334651 GTATATGAGA
* *
54334661 CATCGATATGTGATTACATGTAAGACCACATTTGGGACATTGG
1 CATCGATATGTGATTACATGTAAGACCACATCTGGGACGTTGG
* * * *
54334704 CATC--TATAT-ATTACATGTAAGACAACGTCTGGGATGTTGG
1 CATCGATATGTGATTACATGTAAGACCACATCTGGGACGTTGG
** * *
54334744 CATCGATATGTGATTATGTGTAAGACCACGTCAGGGACGTTGG
1 CATCGATATGTGATTACATGTAAGACCACATCTGGGACGTTGG
* * ** * *
54334787 CATCTATATATGATTAGGTGTAAGACTACATCTGGGATGTTGG
1 CATCGATATGTGATTACATGTAAGACCACATCTGGGACGTTGG
* *
54334830 CATCGATATGTGTTTA-AGAGTAAGACC-CTATCTGGGACAG-TGG
1 CATCGATATGTGATTACA-TGTAAGACCAC-ATCTGGGAC-GTTGG
* * *
54334873 CATCGATATGAGATTACATGTAAAACCACATCAGGGACGTTGG
1 CATCGATATGTGATTACATGTAAGACCACATCTGGGACGTTGG
54334916 CAT
1 CAT
54334919 TATACAAAAT
Statistics
Matches: 175, Mismatches: 31, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
40 30 0.17
41 4 0.02
42 6 0.03
43 132 0.75
44 3 0.02
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (43 bp):
CATCGATATGTGATTACATGTAAGACCACATCTGGGACGTTGG
Found at i:54338815 original size:27 final size:27
Alignment explanation
Indices: 54338784--54338961 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
54338774 TAAATTGTAC
54338784 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
54338811 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
54338837 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
54338865 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
54338893 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
54338920 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
54338947 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
54338962 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:54338898 original size:82 final size:81
Alignment explanation
Indices: 54338785--54338940 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
54338775 AAATTGTACA
* *
54338785 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
54338849 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
54338866 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
54338931 TGCGAGTTGA
65 TGCGAATTGA
54338941 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:54338952 original size:82 final size:81
Alignment explanation
Indices: 54338781--54338961 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
54338771 GATTAAATTG
* *
54338781 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
54338846 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
54338862 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
54338926 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
54338944 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
54338962 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:54350570 original size:28 final size:28
Alignment explanation
Indices: 54350532--54350741 Score: 341
Period size: 28 Copynumber: 7.5 Consensus size: 28
54350522 TAAATTGTAC
54350532 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGCTTGATTATGT
54350560 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGCTTGATTATGT
54350588 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGCTTGATTATGT
**
54350616 AGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAAGTGTGCGAGCTTGATTATGT
* *
54350644 AGCACTAGGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGCTTGATTATGT
* *
54350672 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGCTTGATTATGT
*
54350700 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGCTTGATTATGT
*
54350727 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
54350742 GACTTAATAT
Statistics
Matches: 175, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
27 24 0.14
28 151 0.86
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGCTTGATTATGT
Found at i:54362142 original size:28 final size:27
Alignment explanation
Indices: 54362090--54362142 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
54362080 AACATAATTT
**
54362090 GGGCCTAAGCCCTTTCAGTCTCAGTTA
1 GGGCCTAAGCCCTTTCAGTAACAGTTA
*
54362117 GGGCCTTAGCCCATTTCAGTAACAGT
1 GGGCCTAAGCCC-TTTCAGTAACAGT
54362143 AGCAGTTTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 11 0.50
28 11 0.50
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.28
Consensus pattern (27 bp):
GGGCCTAAGCCCTTTCAGTAACAGTTA
Found at i:54362211 original size:33 final size:34
Alignment explanation
Indices: 54362105--54362211 Score: 117
Period size: 34 Copynumber: 3.2 Consensus size: 34
54362095 TAAGCCCTTT
* * *
54362105 CAGTCTCAGTTAGGGCCTTAGCCCATTTCAGTAA
1 CAGTATCAGTTGGGGCCTAAGCCCATTTCAGTAA
* * * *
54362139 CAGTAGCAGTTTGGGCCTGAGCCCATTTTAGTAA
1 CAGTATCAGTTGGGGCCTAAGCCCATTTCAGTAA
* * *
54362173 CAGTATCAG-TGGGGCCTAACCCCATTACAGTAT
1 CAGTATCAGTTGGGGCCTAAGCCCATTTCAGTAA
54362206 CAGTAT
1 CAGTAT
54362212 AGTATGCAAT
Statistics
Matches: 61, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
33 24 0.39
34 37 0.61
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.28
Consensus pattern (34 bp):
CAGTATCAGTTGGGGCCTAAGCCCATTTCAGTAA
Found at i:54371257 original size:13 final size:13
Alignment explanation
Indices: 54371239--54371267 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
54371229 TACGGTCCAA
54371239 TAAAACGTGGACT
1 TAAAACGTGGACT
54371252 TAAAACGTGGACT
1 TAAAACGTGGACT
54371265 TAA
1 TAA
54371268 CTTGCCCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (13 bp):
TAAAACGTGGACT
Found at i:54383305 original size:93 final size:93
Alignment explanation
Indices: 54383198--54383368 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
54383188 GCCCCTAAGT
* *
54383198 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54383263 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
*
54383291 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54383356 CGAGTTCGGATGC
66 CGAGTTCGGATGC
54383369 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:54383365 original size:46 final size:46
Alignment explanation
Indices: 54383193--54383365 Score: 210
Period size: 46 Copynumber: 3.7 Consensus size: 46
54383183 AACCCGCCCC
* * *
54383193 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
54383239 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
54383287 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
54383332 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
54383366 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 61 0.57
47 29 0.27
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:54388826 original size:93 final size:93
Alignment explanation
Indices: 54388718--54388888 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
54388708 GCCCCTAAGT
* * *
54388718 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTTGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54388783 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
* *
54388811 GAACTTGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54388876 CGAGTTCGGATGC
66 CGAGTTCGGATGC
54388889 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:54388885 original size:46 final size:46
Alignment explanation
Indices: 54388713--54388885 Score: 192
Period size: 46 Copynumber: 3.7 Consensus size: 46
54388703 AACCCGCCCC
* * *
54388713 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* * *
54388759 TAAGTGAACTTGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* * *
54388807 TCA-CGAACTTGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
54388852 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
54388886 TGCTCAACCA
Statistics
Matches: 105, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 59 0.56
47 29 0.28
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:54389886 original size:22 final size:22
Alignment explanation
Indices: 54389860--54389904 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
54389850 CCTTACTACT
54389860 AAACTTTCCAAAAATGCCATCC
1 AAACTTTCCAAAAATGCCATCC
*
54389882 AAACTTTCCAAAAATTCCATCC
1 AAACTTTCCAAAAATGCCATCC
54389904 A
1 A
54389905 TGTCCAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.42, C:0.31, G:0.02, T:0.24
Consensus pattern (22 bp):
AAACTTTCCAAAAATGCCATCC
Found at i:54397596 original size:15 final size:15
Alignment explanation
Indices: 54397576--54397606 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
54397566 AAATATTAAA
54397576 GATATGTTTTGGATT
1 GATATGTTTTGGATT
*
54397591 GATATGTTTTGTATT
1 GATATGTTTTGGATT
54397606 G
1 G
54397607 GAATTTTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.55
Consensus pattern (15 bp):
GATATGTTTTGGATT
Found at i:54407282 original size:30 final size:30
Alignment explanation
Indices: 54407246--54407306 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
54407236 TCCTTAACTC
54407246 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
54407276 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
54407306 A
1 A
54407307 GGCTCGGAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:54411671 original size:30 final size:30
Alignment explanation
Indices: 54411635--54411695 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
54411625 TCCTTAACTC
54411635 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
54411665 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
54411695 A
1 A
54411696 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:54417104 original size:43 final size:39
Alignment explanation
Indices: 54417055--54417209 Score: 171
Period size: 37 Copynumber: 4.0 Consensus size: 39
54417045 GGACTAAGAT
54417055 CCGAAGGCATTTGTGCGAGATACTATTCCGAATTCCGGGCTAA
1 CCGAAGGCATTTGTGCGAGATACTA-T---AATTCCGGGCTAA
54417098 CCGAAGGCATTTGTGCGAGATAC--TAATTCCGGGCTAA
1 CCGAAGGCATTTGTGCGAGATACTATAATTCCGGGCTAA
* *
54417135 CCGAAGGCATTTGTGCGAGTTACTA-AA-TCCGGGTTAA
1 CCGAAGGCATTTGTGCGAGATACTATAATTCCGGGCTAA
*
54417172 GTCCCGAAGGCATTTGTGCGA-TTACTATAA--CCGGGCTA
1 ---CCGAAGGCATTTGTGCGAGATACTATAATTCCGGGCTA
54417210 TGTCCCGAAG
Statistics
Matches: 103, Mismatches: 3, Indels: 16
0.84 0.02 0.13
Matches are distributed among these distances:
37 44 0.43
38 2 0.02
39 13 0.13
40 21 0.20
43 23 0.22
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTTGTGCGAGATACTATAATTCCGGGCTAA
Found at i:54417215 original size:39 final size:38
Alignment explanation
Indices: 54417098--54417226 Score: 156
Period size: 37 Copynumber: 3.3 Consensus size: 38
54417088 TCCGGGCTAA
* * *
54417098 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTA--A
1 CCGAAGGCATTTGTGCGAGTTACTAA-ACCGGGCTAGTC
*
54417135 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTAAA-CCGGGCT-AGTC
54417175 CCGAAGGCATTTGTGCGA-TTACTATAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGTTACTA-AACCGGGCTA-GTC
54417214 CCGAAGGCATTTG
1 CCGAAGGCATTTG
54417227 AACGAGGAGC
Statistics
Matches: 81, Mismatches: 5, Indels: 10
0.84 0.05 0.10
Matches are distributed among these distances:
37 31 0.38
38 2 0.02
39 28 0.35
40 20 0.25
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (38 bp):
CCGAAGGCATTTGTGCGAGTTACTAAACCGGGCTAGTC
Found at i:54425015 original size:39 final size:40
Alignment explanation
Indices: 54424920--54425142 Score: 248
Period size: 39 Copynumber: 5.7 Consensus size: 40
54424910 TTGAATGATG
*
54424920 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
54424958 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
* *
54424999 TCCGGGCTAAG-CCCGAAGGCATTTCTGCGAGACACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
54425038 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
54425077 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
54425116 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
54425143 AACGAGGAGC
Statistics
Matches: 160, Mismatches: 15, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
39 89 0.56
40 59 0.37
41 11 0.07
42 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:54425061 original size:78 final size:80
Alignment explanation
Indices: 54424920--54425142 Score: 244
Period size: 79 Copynumber: 2.8 Consensus size: 80
54424910 TTGAATGATG
* * * * * *
54424920 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGACAATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTCTGCGAA-TCACTATAACCGGGCTAAG-TCCCGAAGGCAT
*
54424982 TTGTGCGAGATACTAAT
64 TTGTGCGAGATACTAAA
*
54424999 TCCGGGCTAAG-CCCGAAGGCATTTCTGCGAGA-CACTA-ATTCCGGGCTAAG-CCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTCTGCGA-ATCACTATA-ACCGGGCTAAGTCCCGAAGGCAT
*
54425060 TTGTGCGAGTTACTAAA
64 TTGTGCGAGATACTAAA
* * * *
54425077 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTCTGCGAATCACTATAACCGGGCTAAGTCCCGAAGGCATTT
54425142 G
66 G
54425143 AACGAGGAGC
Statistics
Matches: 123, Mismatches: 12, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
78 46 0.37
79 55 0.45
80 21 0.17
81 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTCTGCGAATCACTATAACCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGATACTAAA
Found at i:54425164 original size:79 final size:78
Alignment explanation
Indices: 54424972--54425165 Score: 191
Period size: 78 Copynumber: 2.5 Consensus size: 78
54424962 GGACTAAGAT
** * *
54424972 CCGAAGGCATTTGTGCGAGAT-ACTAATTCCGGGCTAAGCCCGAAGGCATTTCTGCGAGACACTA
1 CCGAAGGCATTTGAACGAG-TGACTAAATCCGGGTTAAGCCCGAAGGCATTTCTGCGAGACACTA
*
54425036 ATTCCGGGCTAAGC
65 ATACCGGGCTAAGC
** * * *
54425050 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT
1 CCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAG-CCCGAAGGCATTTCTGCGAGA-CACT
*
54425114 -ATAACCGGGCTATGTC
64 AAT-ACCGGGCTAAG-C
*
54425130 CCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAA
1 CCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAA
54425166 ATTCGAAGGT
Statistics
Matches: 100, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
77 1 0.01
78 37 0.37
79 37 0.37
80 25 0.25
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (78 bp):
CCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAGCCCGAAGGCATTTCTGCGAGACACTAA
TACCGGGCTAAGC
Found at i:54430576 original size:16 final size:16
Alignment explanation
Indices: 54430555--54430597 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
54430545 GTAGATCAGC
* *
54430555 AAAAGCCGAAATGCCG
1 AAAAGCCAAAATGCCA
54430571 AAAAGCCAAAATGCCA
1 AAAAGCCAAAATGCCA
54430587 AAAAGCCAAAA
1 AAAAGCCAAAA
54430598 GTTTGACTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.56, C:0.23, G:0.16, T:0.05
Consensus pattern (16 bp):
AAAAGCCAAAATGCCA
Found at i:54430855 original size:28 final size:29
Alignment explanation
Indices: 54430802--54430862 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 29
54430792 TGAGTATGAT
* *
54430802 TATAAATGTGATTTGGGTCTAATGGGCCA
1 TATAAATGTGAATTGGGCCTAATGGGCCA
*
54430831 TATAAATGT-AATTGGGCCTAGTGGGCCA
1 TATAAATGTGAATTGGGCCTAATGGGCCA
54430859 TATA
1 TATA
54430863 CAAGTATGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 20 0.69
29 9 0.31
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.33
Consensus pattern (29 bp):
TATAAATGTGAATTGGGCCTAATGGGCCA
Found at i:54432957 original size:40 final size:40
Alignment explanation
Indices: 54432913--54433116 Score: 286
Period size: 40 Copynumber: 5.1 Consensus size: 40
54432903 CAGGATTTAA
* * *
54432913 CCGGATATAGCT-ACTCGCTCGAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
*
54432953 CCGGATATAGTAACTCGCACGAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
54432993 CCGGGTATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
54433033 CCGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * * *
54433073 CC-GAAACTAGTCACTAGCGCAAATGCCTTCGGGACTTAGC
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGC
54433113 CCGG
1 CCGG
54433117 TTATCATCCA
Statistics
Matches: 150, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
39 3 0.02
40 146 0.97
41 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.22
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:54440680 original size:40 final size:40
Alignment explanation
Indices: 54440618--54440795 Score: 218
Period size: 40 Copynumber: 4.5 Consensus size: 40
54440608 AAGCCACGTA
* * * *
54440618 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
54440657 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACGAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
54440697 CCTTCGGGACTTAGCTCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
54440737 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
*
54440777 CCTTCAGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
54440796 TTATCATCCA
Statistics
Matches: 124, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
39 13 0.10
40 111 0.90
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:54448809 original size:79 final size:78
Alignment explanation
Indices: 54448706--54448928 Score: 265
Period size: 79 Copynumber: 2.8 Consensus size: 78
54448696 GCTCCTCGTT
* *
54448706 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
54448771 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
*
54448786 CAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAAT-TCGCACAAATGCCTTCGGGACTTAGCCCGG
*
54448849 AATTAGTATCTCGCA
64 AATTAGTAACTCGCA
* * * * *
54448864 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGT-AATTCGCACAAATGCCTTCGGGACTTAGCCCG
54448927 GA
63 GA
54448929 CATCATTCAA
Statistics
Matches: 125, Mismatches: 11, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
78 47 0.38
79 57 0.46
80 20 0.16
81 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:54448823 original size:39 final size:40
Alignment explanation
Indices: 54448706--54448928 Score: 266
Period size: 39 Copynumber: 5.7 Consensus size: 40
54448696 GCTCCTCGTT
* *
54448706 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
54448746 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
54448786 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
54448825 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
54448864 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
54448905 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
54448929 CATCATTCAA
Statistics
Matches: 166, Mismatches: 9, Indels: 17
0.86 0.05 0.09
Matches are distributed among these distances:
38 2 0.01
39 89 0.54
40 64 0.39
41 11 0.07
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:54452748 original size:45 final size:46
Alignment explanation
Indices: 54452691--54452848 Score: 162
Period size: 45 Copynumber: 3.5 Consensus size: 46
54452681 CCTGAGTTGA
* * *
54452691 TGAATAGTAAGCTCTAT-TGAGCTAAAATGATAAGCTCTATCGAGC
1 TGAACAGTAAGCTCTATATGAGCTGAAACGATAAGCTCTATCGAGC
* * * *
54452736 TGAACTGTAAGCTC-ATACGAGCTGAAACGGTAAGCTCTATTGAGC
1 TGAACAGTAAGCTCTATATGAGCTGAAACGATAAGCTCTATCGAGC
* * * * *
54452781 TAAACAGTAAGC-CCATATGAGCTGAAACGATAAACTCTATCAAGA
1 TGAACAGTAAGCTCTATATGAGCTGAAACGATAAGCTCTATCGAGC
* *
54452826 TGAACAATAAGCTCT-TACGAGCT
1 TGAACAGTAAGCTCTATATGAGCT
54452849 AATATATCGG
Statistics
Matches: 91, Mismatches: 19, Indels: 6
0.78 0.16 0.05
Matches are distributed among these distances:
44 3 0.03
45 87 0.96
46 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.25
Consensus pattern (46 bp):
TGAACAGTAAGCTCTATATGAGCTGAAACGATAAGCTCTATCGAGC
Found at i:54452749 original size:22 final size:22
Alignment explanation
Indices: 54452697--54452806 Score: 98
Period size: 23 Copynumber: 4.9 Consensus size: 22
54452687 TTGATGAATA
* * *
54452697 GTAAGCTCTATTGAGCTAAAAT
1 GTAAGCTCTATCGAGCTGAACT
54452719 GATAAGCTCTATCGAGCTGAACT
1 G-TAAGCTCTATCGAGCTGAACT
*
54452742 GTAAGCTC-ATACGAGCTGAAACG
1 GTAAGCTCTAT-CGAGCTG-AACT
* * *
54452765 GTAAGCTCTATTGAGCTAAACA
1 GTAAGCTCTATCGAGCTGAACT
*
54452787 GTAAGCCCATAT-GAGCTGAA
1 GTAAGCTC-TATCGAGCTGAA
54452807 ACGATAAACT
Statistics
Matches: 74, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
21 2 0.03
22 32 0.43
23 38 0.51
24 2 0.03
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.25
Consensus pattern (22 bp):
GTAAGCTCTATCGAGCTGAACT
Found at i:54456049 original size:43 final size:42
Alignment explanation
Indices: 54456002--54456117 Score: 135
Period size: 43 Copynumber: 2.7 Consensus size: 42
54455992 ATCACATATC
* * *
54456002 GATGCCACTGTCCTAGACAGGGACTTACACGAAATCG-ATTAAT
1 GATGCCAATGTCC-AGACATGGTCTTACACGAAATCGTA-TAAT
* * *
54456045 GATGCTAATGTCCCAAACATGGTCTTACACGTAATCGTATAAT
1 GATGCCAATGT-CCAGACATGGTCTTACACGAAATCGTATAAT
54456088 GATGCCAATGTCACAGACATGGTCTTACAC
1 GATGCCAATGTC-CAGACATGGTCTTACAC
54456118 ATAATGACAA
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
42 1 0.02
43 58 0.94
44 3 0.05
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (42 bp):
GATGCCAATGTCCAGACATGGTCTTACACGAAATCGTATAAT
Found at i:54456473 original size:13 final size:13
Alignment explanation
Indices: 54456455--54456483 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
54456445 ATAATAACAA
54456455 AATTTCCTTATTT
1 AATTTCCTTATTT
54456468 AATTTCCTTATTT
1 AATTTCCTTATTT
54456481 AAT
1 AAT
54456484 CATTAATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.00, T:0.59
Consensus pattern (13 bp):
AATTTCCTTATTT
Done.