Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 128 of 204
Found at i:39038814 original size:32 final size:28
Alignment explanation
Indices: 39038758--39038838 Score: 81
Period size: 32 Copynumber: 2.7 Consensus size: 28
39038748 TACCAAAACT
* **
39038758 TAAATTATATTTTATTTTTTATTAAAAATAG
1 TAAATTA-ATTTTATATTAAATT-AAAA-AG
39038789 ATAAATTAATTTATATATTAAATTAAAAAG
1 -TAAATTAATTT-TATATTAAATTAAAAAG
*
39038819 TAAATTAATTTTTTATTAAA
1 TAAATTAATTTTATATTAAA
39038839 ATTTTTATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
28 8 0.18
29 11 0.25
30 2 0.05
31 8 0.18
32 15 0.34
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.49
Consensus pattern (28 bp):
TAAATTAATTTTATATTAAATTAAAAAG
Found at i:39038849 original size:16 final size:17
Alignment explanation
Indices: 39038830--39038862 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
39038820 AAATTAATTT
39038830 TTTATTAAAATT-TTTA
1 TTTATTAAAATTGTTTA
*
39038846 TTTATTTAAATTGTTTA
1 TTTATTAAAATTGTTTA
39038863 GTTGATAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
TTTATTAAAATTGTTTA
Found at i:39039193 original size:9 final size:9
Alignment explanation
Indices: 39039179--39039225 Score: 67
Period size: 9 Copynumber: 5.2 Consensus size: 9
39039169 ATTCAGTCGG
39039179 TTAACCGAA
1 TTAACCGAA
39039188 TTAACCGAA
1 TTAACCGAA
* *
39039197 TTACCCAAA
1 TTAACCGAA
*
39039206 TTAACAGAA
1 TTAACCGAA
39039215 TTAACCGAA
1 TTAACCGAA
39039224 TT
1 TT
39039226 GAATCACTAC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.45, C:0.21, G:0.09, T:0.26
Consensus pattern (9 bp):
TTAACCGAA
Found at i:39039282 original size:6 final size:7
Alignment explanation
Indices: 39039249--39039295 Score: 62
Period size: 7 Copynumber: 6.7 Consensus size: 7
39039239 ATTAAATTAT
39039249 TTTTAGA
1 TTTTAGA
39039256 CTTTTAGA
1 -TTTTAGA
39039264 TTTTAGA
1 TTTTAGA
39039271 TTTTAG-
1 TTTTAGA
39039277 TTTTAG-
1 TTTTAGA
39039283 TTTTAGAA
1 TTTTAG-A
39039291 TTTTA
1 TTTTA
39039296 TTTTTATTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
6 12 0.32
7 13 0.35
8 12 0.32
ACGTcount: A:0.26, C:0.02, G:0.13, T:0.60
Consensus pattern (7 bp):
TTTTAGA
Found at i:39039312 original size:20 final size:20
Alignment explanation
Indices: 39039257--39039301 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
39039247 ATTTTTAGAC
39039257 TTTTAGATTTTAG-ATTTTAG
1 TTTTAG-TTTTAGAATTTTAG
*
39039277 TTTTAGTTTTAGAATTTTAT
1 TTTTAGTTTTAGAATTTTAG
39039297 TTTTA
1 TTTTA
39039302 TTTATTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.24, C:0.00, G:0.11, T:0.64
Consensus pattern (20 bp):
TTTTAGTTTTAGAATTTTAG
Found at i:39040899 original size:2 final size:2
Alignment explanation
Indices: 39040894--39040933 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
39040884 GTTACAAATA
39040894 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39040934 ACATGAATCA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:39041868 original size:16 final size:16
Alignment explanation
Indices: 39041847--39041877 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39041837 TATGTTAAAG
39041847 CATATAAATTTGAAAC
1 CATATAAATTTGAAAC
*
39041863 CATATATATTTGAAA
1 CATATAAATTTGAAA
39041878 ACTCTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.35
Consensus pattern (16 bp):
CATATAAATTTGAAAC
Found at i:39042080 original size:18 final size:19
Alignment explanation
Indices: 39042059--39042095 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
39042049 TTAAAAAATA
39042059 TATAAAT-TTTGGAATTTT
1 TATAAATATTTGGAATTTT
*
39042077 TATAAATATTTTGAATTTT
1 TATAAATATTTGGAATTTT
39042096 AAAAATTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (19 bp):
TATAAATATTTGGAATTTT
Found at i:39042094 original size:19 final size:20
Alignment explanation
Indices: 39042064--39042132 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
39042054 AAATATATAA
39042064 ATTTTGGAATTTTTATAAA-T
1 ATTTT-GAATTTTTATAAATT
*
39042084 ATTTTGAA-TTTTAAAAATT
1 ATTTTGAATTTTTATAAATT
*
39042103 AGTTTGAATTTTTGA-AAATT
1 ATTTTGAATTTTT-ATAAATT
39042123 ATTTTGAATT
1 ATTTTGAATT
39042133 ATTTTGTAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
18 8 0.19
19 11 0.26
20 23 0.53
21 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (20 bp):
ATTTTGAATTTTTATAAATT
Found at i:39050330 original size:131 final size:130
Alignment explanation
Indices: 39050080--39050350 Score: 380
Period size: 131 Copynumber: 2.1 Consensus size: 130
39050070 CTTTTAATTC
* * * * *
39050080 AATTGTGGCGCATCAATAAATTGTATGGACAATGATAATAAAATGATAATAGTAATTGTGATGCA
1 AATTGTGGTGCATCAATAAATTGCATGGACAATGACAATAAAATGATAACAGTAATTGTGATGAA
* * *
39050145 TCAATTAAATCGAATGAGTAATTACAATAAATATTAATTAATGAAAAATCTTTTAATTAATGCAA
66 TCAATTAAATCGAATGAGTAATCAAAATAAAAATTAATTAATGAAAAATCTTTTAATTAATGCAA
** * *
39050210 AATTGTGGTGCATCAATTAAATTGCATGGGTAATTACAATAAAATGATAACAGTAATTGTGGTGA
1 AATTGTGGTGCATCAA-TAAATTGCATGGACAATGACAATAAAATGATAACAGTAATTGTGATGA
* * * * *
39050275 ATTAATTAAATTGCATGAGTAATCAAAATAAAAATTAATTAATGGAAAATCTTTTAATTGATGCA
65 ATCAATTAAATCGAATGAGTAATCAAAATAAAAATTAATTAATGAAAAATCTTTTAATTAATGCA
39050340 A
130 A
39050341 AATTGTGGTG
1 AATTGTGGTG
39050351 TAAAATCTTG
Statistics
Matches: 123, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
130 15 0.12
131 108 0.88
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.34
Consensus pattern (130 bp):
AATTGTGGTGCATCAATAAATTGCATGGACAATGACAATAAAATGATAACAGTAATTGTGATGAA
TCAATTAAATCGAATGAGTAATCAAAATAAAAATTAATTAATGAAAAATCTTTTAATTAATGCAA
Found at i:39057806 original size:10 final size:10
Alignment explanation
Indices: 39057771--39057808 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
39057761 CCTCGACAAA
39057771 TATTAAAAAT
1 TATTAAAAAT
* *
39057781 TCTTTAAAAT
1 TATTAAAAAT
39057791 TA-TAAAAAT
1 TATTAAAAAT
39057800 TATTAAAAA
1 TATTAAAAA
39057809 GGTGGTTTGG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (10 bp):
TATTAAAAAT
Found at i:39060016 original size:2 final size:2
Alignment explanation
Indices: 39060011--39060036 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39060001 TTGCTAGAAT
39060011 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
39060037 AATTTATTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39065419 original size:76 final size:76
Alignment explanation
Indices: 39065303--39065470 Score: 203
Period size: 76 Copynumber: 2.2 Consensus size: 76
39065293 AGTTTACCCT
* ** * ** *
39065303 ACTAGTGCTAGGCACATCATTATATTCGTCGATTTATCCGACTAGTGCTGGGCGTAAATCTTCGT
1 ACTAGTACTAGGCACATCATTATATTCAACGATTTATCCGACTAGTGCTAGGCACAAATCTTCAT
*
39065368 CAGCTTGCCTG
66 CAGCTTACCTG
*
39065379 ACTAGTACTAGGCACATCATTATATTCAAC-AGTTTCTCCGACTAGTGCTAGGCACAAATCTTCA
1 ACTAGTACTAGGCACATCATTATATTCAACGA-TTTATCCGACTAGTGCTAGGCACAAATCTTCA
* *
39065443 TCAGTTTATCTG
65 TCAGCTTACCTG
**
39065455 ACTAGTTTTAGGCACA
1 ACTAGTACTAGGCACA
39065471 ACCTCTATAA
Statistics
Matches: 78, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
75 1 0.01
76 77 0.99
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (76 bp):
ACTAGTACTAGGCACATCATTATATTCAACGATTTATCCGACTAGTGCTAGGCACAAATCTTCAT
CAGCTTACCTG
Found at i:39065458 original size:36 final size:36
Alignment explanation
Indices: 39065335--39065471 Score: 105
Period size: 36 Copynumber: 3.7 Consensus size: 36
39065325 TATTCGTCGA
* ** *
39065335 TTTATCCGACTAGTGCTGGGCGTAAATCTTCGTCAG
1 TTTATCCGACTAGTGCTAGGCACAAATCTTCATCAG
* * * * *
39065371 CTT-GCCTGACTAGTACTAGGCACATCATTATATTCAACAG
1 TTTATCC-GACTAGTGCTAGGCACA--A--ATCTTCATCAG
*
39065411 TTTCTCCGACTAGTGCTAGGCACAAATCTTCATCAG
1 TTTATCCGACTAGTGCTAGGCACAAATCTTCATCAG
* **
39065447 TTTATCTGACTAGTTTTAGGCACAA
1 TTTATCCGACTAGTGCTAGGCACAA
39065472 CCTCTATAAC
Statistics
Matches: 77, Mismatches: 18, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
35 2 0.03
36 45 0.58
38 2 0.03
40 26 0.34
41 2 0.03
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (36 bp):
TTTATCCGACTAGTGCTAGGCACAAATCTTCATCAG
Found at i:39072327 original size:40 final size:40
Alignment explanation
Indices: 39072267--39072385 Score: 106
Period size: 40 Copynumber: 3.1 Consensus size: 40
39072257 TTAGCAAATC
* *
39072267 TTCGTTAGTTTACCTTACTAGTGTTGGGCACATCAATATA
1 TTCGTCAGTTTACCTAACTAGTGTTGGGCACATCAATATA
* * * *
39072307 TTCGTC-GATTTATCTAACTAGCGTT--G-A-GTGCAA-ATC
1 TTCGTCAG-TTTACCTAACTAGTGTTGGGCACAT-CAATATA
* *
39072343 TTCGTCAGTTTACCTAACTAGTGCTGGGCACATCATTATA
1 TTCGTCAGTTTACCTAACTAGTGTTGGGCACATCAATATA
39072383 TTC
1 TTC
39072386 ATTGGTTTAT
Statistics
Matches: 59, Mismatches: 12, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
36 23 0.39
37 5 0.08
38 2 0.03
39 4 0.07
40 25 0.42
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (40 bp):
TTCGTCAGTTTACCTAACTAGTGTTGGGCACATCAATATA
Found at i:39072395 original size:76 final size:74
Alignment explanation
Indices: 39072260--39072526 Score: 243
Period size: 76 Copynumber: 3.5 Consensus size: 74
39072250 TTTGTGGTTA
* * * * * * *
39072260 GCAAATCTTCGTTAGTTTACCTTACTAGTGTTGGGCACATCAATATATTCGTCGATTTATCTAAC
1 GCAAATCTTCGTCAGTTTACCTGACTAGTGCTGGGCACATCATTATATTC-TTGGTTTATCCAAC
*
39072325 TAGCGTTGAG
65 TAGCGCTGAG
* *
39072335 TGCAAATCTTCGTCAGTTTACCTAACTAGTGCTGGGCACATCATTATATTCATTGGTTTATCCGA
1 -GCAAATCTTCGTCAGTTTACCTGACTAGTGCTGGGCACATCATTATATTC-TTGGTTTATCCAA
*
39072400 CTAGAGCTG-G
64 CTAGCGCTGAG
* * * * * * *
39072410 GCACAAATCTTCGTTAGTGTACCTGACTAGTACTAGGCACGTCATTATAATT-TTCAGTTTCTCC
1 G--CAAATCTTCGTCAGTTTACCTGACTAGTGCTGGGCACATCATTAT-ATTCTT-GGTTTATCC
*
39072474 AACTAGCACT-AG
62 AACTAGCGCTGAG
* *
39072486 GCACAAATCTTCATCAGTTTATCTGACTAGTGCTGGGCACA
1 G--CAAATCTTCGTCAGTTTACCTGACTAGTGCTGGGCACA
39072527 ACCTCTATAA
Statistics
Matches: 157, Mismatches: 29, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
74 1 0.01
75 3 0.02
76 150 0.96
77 3 0.02
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (74 bp):
GCAAATCTTCGTCAGTTTACCTGACTAGTGCTGGGCACATCATTATATTCTTGGTTTATCCAACT
AGCGCTGAG
Found at i:39072525 original size:36 final size:36
Alignment explanation
Indices: 39072337--39072527 Score: 87
Period size: 36 Copynumber: 5.1 Consensus size: 36
39072327 GCGTTGAGTG
* * *
39072337 CAAATCTTCGTCAGTTTACCTAACTAGTGCTGGGCA
1 CAAATCTTCATCAGTTTATCTGACTAGTGCTGGGCA
* ** * *
39072373 CATCATTATATTCATTGGTTTATCCGACTAGAGCTGGGCA
1 CA--A--ATCTTCATCAGTTTATCTGACTAGTGCTGGGCA
* * * * * *
39072413 CAAATCTTCGTTAGTGTACCTGACTAGTACTAGGCA
1 CAAATCTTCATCAGTTTATCTGACTAGTGCTGGGCA
* * * * ** ** *
39072449 CGTCATTATAATT-TTCAGTTTCTCCAACTAGCACTAGGCA
1 ---CA-AAT-CTTCATCAGTTTATCTGACTAGTGCTGGGCA
39072489 CAAATCTTCATCAGTTTATCTGACTAGTGCTGGGCA
1 CAAATCTTCATCAGTTTATCTGACTAGTGCTGGGCA
39072525 CAA
1 CAA
39072528 CCTCTATAAC
Statistics
Matches: 109, Mismatches: 36, Indels: 20
0.66 0.22 0.12
Matches are distributed among these distances:
35 2 0.02
36 51 0.47
37 2 0.02
38 2 0.02
39 2 0.02
40 48 0.44
41 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (36 bp):
CAAATCTTCATCAGTTTATCTGACTAGTGCTGGGCA
Found at i:39075611 original size:5 final size:6
Alignment explanation
Indices: 39075592--39075621 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
39075582 TAATGATAAT
39075592 AAAGAA AAAGAA AAAGAA AAAG-A AAAGAA A
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA A
39075622 GGAACACGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:39083185 original size:19 final size:19
Alignment explanation
Indices: 39083144--39083188 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
39083134 AAAAATTGCA
39083144 AAAAATCTAAAATAAATTTT
1 AAAAATCTAAAAT-AATTTT
*
39083164 AAAAATTTAAAAT-ATTTAT
1 AAAAATCTAAAATAATTT-T
39083183 AAAAAT
1 AAAAAT
39083189 ACCAAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 7 0.30
20 12 0.52
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAAATCTAAAATAATTTT
Found at i:39083222 original size:9 final size:9
Alignment explanation
Indices: 39083206--39083268 Score: 56
Period size: 10 Copynumber: 6.6 Consensus size: 9
39083196 TTTATATATT
39083206 TTAAAAAAA
1 TTAAAAAAA
*
39083215 TTATAAAAAT
1 TTA-AAAAAA
39083225 TTCAAAAAAA
1 TT-AAAAAAA
*
39083235 TTCTAAAAACA
1 -T-TAAAAAAA
39083246 TATAAAAAAA
1 T-TAAAAAAA
39083256 TT-AAAAAA
1 TTAAAAAAA
39083264 TTAAA
1 TTAAA
39083269 TTTTTCTTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
8 8 0.18
9 6 0.14
10 21 0.48
11 8 0.18
12 1 0.02
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:39083223 original size:11 final size:11
Alignment explanation
Indices: 39083207--39083263 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
39083197 TTATATATTT
39083207 TAAAAAAATTA
1 TAAAAAAATTA
39083218 T--AAAAATT-
1 TAAAAAAATTA
*
39083226 TCAAAAAAATTC
1 T-AAAAAAATTA
*
39083238 TAAAAACA-TA
1 TAAAAAAATTA
39083248 TAAAAAAATTA
1 TAAAAAAATTA
39083259 -AAAAA
1 TAAAAA
39083264 TTAAATTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
8 1 0.03
9 7 0.18
10 13 0.34
11 16 0.42
12 1 0.03
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (11 bp):
TAAAAAAATTA
Found at i:39083231 original size:20 final size:19
Alignment explanation
Indices: 39083144--39083265 Score: 81
Period size: 19 Copynumber: 6.4 Consensus size: 19
39083134 AAAAATTGCA
* *
39083144 AAAAATCTAAAATAAATTTT
1 AAAAATTTAAAA-AAATTAT
* *
39083164 AAAAATTTAAAATATTTAT
1 AAAAATTTAAAAAAATTAT
**
39083183 AAAAA--TACCAAAATT-T
1 AAAAATTTAAAAAAATTAT
* *
39083199 ATATATTTTAAAAAAATTAT
1 A-AAAATTTAAAAAAATTAT
*
39083219 AAAAATTTCAAAAAAATTCT
1 AAAAATTT-AAAAAAATTAT
*
39083239 AAAAACATATAAAAAAATTA-
1 -AAAA-ATTTAAAAAAATTAT
39083259 AAAAATT
1 AAAAATT
39083266 AAATTTTTCT
Statistics
Matches: 77, Mismatches: 18, Indels: 16
0.69 0.16 0.14
Matches are distributed among these distances:
16 2 0.03
17 8 0.10
18 2 0.03
19 26 0.34
20 23 0.30
21 13 0.17
22 3 0.04
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAAATTTAAAAAAATTAT
Found at i:39083232 original size:10 final size:9
Alignment explanation
Indices: 39083143--39083265 Score: 61
Period size: 9 Copynumber: 12.9 Consensus size: 9
39083133 CAAAAATTGC
*
39083143 AAAAAATCTA
1 AAAAAAT-TT
39083153 AAATAAATTT
1 AAA-AAATTT
*
39083163 TAAAAATTT
1 AAAAAATTT
*
39083172 AAAATATTT
1 AAAAAATTT
39083181 ATAAAAA--T
1 A-AAAAATTT
*
39083189 ACCAAAATTT
1 A-AAAAATTT
* * *
39083199 ATATATTTT
1 AAAAAATTT
*
39083208 AAAAAAATT
1 AAAAAATTT
39083217 ATAAAAATTT
1 A-AAAAATTT
39083227 CAAAAAAATTCT
1 --AAAAAATT-T
*
39083239 AAAAACATAT
1 AAAAA-ATTT
*
39083249 AAAAAAATT
1 AAAAAATTT
39083258 AAAAAATT
1 AAAAAATT
39083266 AAATTTTTCT
Statistics
Matches: 85, Mismatches: 19, Indels: 19
0.69 0.15 0.15
Matches are distributed among these distances:
8 6 0.07
9 34 0.40
10 30 0.35
11 13 0.15
12 2 0.02
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (9 bp):
AAAAAATTT
Found at i:39084392 original size:26 final size:26
Alignment explanation
Indices: 39084330--39084404 Score: 78
Period size: 31 Copynumber: 2.7 Consensus size: 26
39084320 ACAAAGAATA
*
39084330 CTTTCAATACTCAATACATTTTCATT
1 CTTTCAATACTCAATACAATTTCATT
*
39084356 CTATTCCTTCAATACTCAGTACAATTTCATT
1 C---T--TTCAATACTCAATACAATTTCATT
*
39084387 CTTTCAATACACAATACA
1 CTTTCAATACTCAATACA
39084405 TTAACAAATC
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
26 15 0.38
28 1 0.03
29 1 0.03
31 23 0.57
ACGTcount: A:0.33, C:0.25, G:0.01, T:0.40
Consensus pattern (26 bp):
CTTTCAATACTCAATACAATTTCATT
Found at i:39089422 original size:31 final size:31
Alignment explanation
Indices: 39089387--39089448 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
39089377 AATACAAAGA
* *
39089387 ATTCTTTCAATACTCAATACATTTTCATTCT
1 ATTCTTTCAATACCCAATACAGTTTCATTCT
* * *
39089418 ATTCTTTTAATACCCAGTATAGTTTCATTCT
1 ATTCTTTCAATACCCAATACAGTTTCATTCT
39089449 TTCAATACAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.27, C:0.21, G:0.03, T:0.48
Consensus pattern (31 bp):
ATTCTTTCAATACCCAATACAGTTTCATTCT
Found at i:39092391 original size:30 final size:30
Alignment explanation
Indices: 39092331--39092392 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
39092321 AAACCATGAA
* * *
39092331 AATATTTACAAAAAGAGGCATCTAATTTTT
1 AATATTTACAAAAAGAGGCACCAAAATTTT
39092361 AATATTTACAAAAAGA-GCAACCAAAATTTT
1 AATATTTACAAAAAGAGGC-ACCAAAATTTT
39092391 AA
1 AA
39092393 AAATAATTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 2 0.07
30 26 0.93
ACGTcount: A:0.50, C:0.11, G:0.08, T:0.31
Consensus pattern (30 bp):
AATATTTACAAAAAGAGGCACCAAAATTTT
Found at i:39104018 original size:14 final size:14
Alignment explanation
Indices: 39103999--39104026 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
39103989 ACCCTGAATT
39103999 TTGGGAAAATGATG
1 TTGGGAAAATGATG
39104013 TTGGGAAAATGATG
1 TTGGGAAAATGATG
39104027 AACTCAAGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.29
Consensus pattern (14 bp):
TTGGGAAAATGATG
Found at i:39118064 original size:18 final size:18
Alignment explanation
Indices: 39118036--39118078 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
39118026 CCTCATTGAC
39118036 ACCACAATTCA-ATTACAAA
1 ACCA-AATTCATATT-CAAA
*
39118055 ACCAAATTCATATTCCAA
1 ACCAAATTCATATTCAAA
39118073 ACCAAA
1 ACCAAA
39118079 GTAATTGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (18 bp):
ACCAAATTCATATTCAAA
Found at i:39139692 original size:10 final size:10
Alignment explanation
Indices: 39139673--39139720 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
39139663 GAATCTGTCG
*
39139673 AAAATAAATC
1 AAAATTAATC
39139683 AAAATTAATC
1 AAAATTAATC
*
39139693 AAAATTTAATAT
1 AAAA-TTAAT-C
*
39139705 AAAATTAATT
1 AAAATTAATC
39139715 AAAATT
1 AAAATT
39139721 CAACATGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
10 20 0.59
11 10 0.29
12 4 0.12
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAATTAATC
Found at i:39142477 original size:30 final size:30
Alignment explanation
Indices: 39142420--39142478 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
39142410 TGCCTTTGAA
* *
39142420 AATATTTACAAAAAGAGACATCTAATTTTT
1 AATATTTACAAAAAGAGACACCAAATTTTT
*
39142450 AATATTTACATAAAGAG-CAACCAAATTTT
1 AATATTTACAAAAAGAGAC-ACCAAATTTT
39142479 GAAAAGAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.34
Consensus pattern (30 bp):
AATATTTACAAAAAGAGACACCAAATTTTT
Found at i:39151149 original size:49 final size:50
Alignment explanation
Indices: 39151054--39151149 Score: 113
Period size: 49 Copynumber: 1.9 Consensus size: 50
39151044 CAAACGAACT
* * * * **
39151054 ATCCATCTGAAAACACACCTGGGTACTAAGTGTCAAGGCCGTAGGCTAAC
1 ATCCATCTGAAAACACACCTCGGCACTAAGTGCCAAGCCCAAAGGCTAAC
* *
39151104 ATCCCTCTG-AAACACACCTCGGCACTGAGTGCCAAGCCCAAAGGCT
1 ATCCATCTGAAAACACACCTCGGCACTAAGTGCCAAGCCCAAAGGCT
39151150 TTACATTCGC
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
49 30 0.79
50 8 0.21
ACGTcount: A:0.30, C:0.31, G:0.21, T:0.18
Consensus pattern (50 bp):
ATCCATCTGAAAACACACCTCGGCACTAAGTGCCAAGCCCAAAGGCTAAC
Found at i:39152402 original size:54 final size:54
Alignment explanation
Indices: 39152290--39152409 Score: 132
Period size: 54 Copynumber: 2.2 Consensus size: 54
39152280 CATGGCCTTG
* * ** * * *
39152290 TGACCCGATTTCGAATTGCACACAGTTTGTCACACGATCTGTGACACGGCTATG
1 TGACCCTATTTCAAATCACACACAGTTTGGCACACGATCTGTGACACGGCCATA
* ** *
39152344 TGACCCTATTTCAAATCACACACGGTTTGGCACACGATCTGTGACATTGCCGTA
1 TGACCCTATTTCAAATCACACACAGTTTGGCACACGATCTGTGACACGGCCATA
39152398 TGACCCTTATTT
1 TGACCC-TATTT
39152410 TTTTATTTTC
Statistics
Matches: 54, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
54 49 0.91
55 5 0.09
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (54 bp):
TGACCCTATTTCAAATCACACACAGTTTGGCACACGATCTGTGACACGGCCATA
Found at i:39158031 original size:102 final size:103
Alignment explanation
Indices: 39157865--39158058 Score: 327
Period size: 102 Copynumber: 1.9 Consensus size: 103
39157855 CGATACAACA
*
39157865 TCCCAAACTTGTATAAAACGAGTTTAAAACACTTAAAAACATTTTAGATTGACTCAAAAATATTT
1 TCCCAAACTTGTATAAAACGAGTTTAAAACACTCAAAAACATTTTAGATTGACTCAAAAATATTT
39157930 AGATAAATTAAAATACATTTAAAATATGTTATATAACT
66 AGATAAATTAAAATACATTTAAAATATGTTATATAACT
* * * * *
39157968 TCCCATACTTGTATAAAATGAGTTTAAAACAC-CAAAATCATTTTGGATTGGCTCAAAAATATTT
1 TCCCAAACTTGTATAAAACGAGTTTAAAACACTCAAAAACATTTTAGATTGACTCAAAAATATTT
39158032 AGATAAATTAAAATACATTTAAAATAT
66 AGATAAATTAAAATACATTTAAAATAT
39158059 ATTTTTGAGT
Statistics
Matches: 85, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
102 55 0.65
103 30 0.35
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.34
Consensus pattern (103 bp):
TCCCAAACTTGTATAAAACGAGTTTAAAACACTCAAAAACATTTTAGATTGACTCAAAAATATTT
AGATAAATTAAAATACATTTAAAATATGTTATATAACT
Found at i:39158795 original size:23 final size:23
Alignment explanation
Indices: 39158731--39158794 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 23
39158721 AAGTAATATT
*
39158731 AAATATCAAATAATAAAAGCGTC
1 AAATATCAAATAATAAAATCGTC
*
39158754 AAAAATCAAATAATAAAATC-TC
1 AAATATCAAATAATAAAATCGTC
39158776 AACATATCAAATAAATAAA
1 AA-ATATCAAAT-AATAAA
39158795 TAAATTTCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
22 4 0.11
23 26 0.72
24 6 0.17
ACGTcount: A:0.62, C:0.12, G:0.03, T:0.22
Consensus pattern (23 bp):
AAATATCAAATAATAAAATCGTC
Found at i:39167221 original size:11 final size:11
Alignment explanation
Indices: 39167205--39167234 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
39167195 ATGAGATTTC
39167205 TACTTCTTTTA
1 TACTTCTTTTA
39167216 TACTTCTTTTA
1 TACTTCTTTTA
39167227 TACTTCTT
1 TACTTCTT
39167235 ATGTCTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.17, C:0.20, G:0.00, T:0.63
Consensus pattern (11 bp):
TACTTCTTTTA
Found at i:39170729 original size:20 final size:18
Alignment explanation
Indices: 39170681--39170729 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 18
39170671 AAAATAAAAT
*
39170681 AAAATAAAAATATATTTG
1 AAAATAAAAATAAATTTG
39170699 AAAATGCAAAAATAAATTTAAG
1 AAAAT--AAAAATAAATTT--G
39170721 AAAATAAAA
1 AAAATAAAA
39170730 TATTTTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 5 0.19
20 15 0.58
22 6 0.23
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.24
Consensus pattern (18 bp):
AAAATAAAAATAAATTTG
Found at i:39177831 original size:172 final size:172
Alignment explanation
Indices: 39177545--39177889 Score: 690
Period size: 172 Copynumber: 2.0 Consensus size: 172
39177535 GCGTCTGCGG
39177545 AACACACGCTAATGTTTCACAATGGCCAGGCAAATCATGAGATTTGGATATTATTGGTCCACCAT
1 AACACACGCTAATGTTTCACAATGGCCAGGCAAATCATGAGATTTGGATATTATTGGTCCACCAT
39177610 GTGAAAGCAATGATGCATCCAATTAAATAGATCAATTCAGTCCCTATCCTATAAAAAGAATCAAA
66 GTGAAAGCAATGATGCATCCAATTAAATAGATCAATTCAGTCCCTATCCTATAAAAAGAATCAAA
39177675 TAGTCCATTTTCCAATTTGGCCATATTTTGATTCTTTTTAAT
131 TAGTCCATTTTCCAATTTGGCCATATTTTGATTCTTTTTAAT
39177717 AACACACGCTAATGTTTCACAATGGCCAGGCAAATCATGAGATTTGGATATTATTGGTCCACCAT
1 AACACACGCTAATGTTTCACAATGGCCAGGCAAATCATGAGATTTGGATATTATTGGTCCACCAT
39177782 GTGAAAGCAATGATGCATCCAATTAAATAGATCAATTCAGTCCCTATCCTATAAAAAGAATCAAA
66 GTGAAAGCAATGATGCATCCAATTAAATAGATCAATTCAGTCCCTATCCTATAAAAAGAATCAAA
39177847 TAGTCCATTTTCCAATTTGGCCATATTTTGATTCTTTTTAAT
131 TAGTCCATTTTCCAATTTGGCCATATTTTGATTCTTTTTAAT
39177889 A
1 A
39177890 CGATAGGAAC
Statistics
Matches: 173, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
172 173 1.00
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.32
Consensus pattern (172 bp):
AACACACGCTAATGTTTCACAATGGCCAGGCAAATCATGAGATTTGGATATTATTGGTCCACCAT
GTGAAAGCAATGATGCATCCAATTAAATAGATCAATTCAGTCCCTATCCTATAAAAAGAATCAAA
TAGTCCATTTTCCAATTTGGCCATATTTTGATTCTTTTTAAT
Found at i:39178336 original size:40 final size:40
Alignment explanation
Indices: 39178273--39178357 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
39178263 TAGCTTGAAT
* * *
39178273 ATCAACACTTCAATATTTAATATGTAAGGAATTATCAAAA
1 ATCAACACTTCAATATTTAATATGCAAGAAATTAACAAAA
*
39178313 ATCAACATTTCAATAATTT-ATATGCAAGAAATTAACAAAA
1 ATCAACACTTCAAT-ATTTAATATGCAAGAAATTAACAAAA
39178353 ATCAA
1 ATCAA
39178358 TCTTACAACA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 36 0.90
41 4 0.10
ACGTcount: A:0.51, C:0.13, G:0.06, T:0.31
Consensus pattern (40 bp):
ATCAACACTTCAATATTTAATATGCAAGAAATTAACAAAA
Found at i:39178373 original size:40 final size:40
Alignment explanation
Indices: 39178287--39178398 Score: 109
Period size: 40 Copynumber: 2.8 Consensus size: 40
39178277 ACACTTCAAT
* * * * *
39178287 ATTTAATATGTAAGGAATTATCAAAAATCAACATTTCAATA
1 ATTT-ATATGAAAGAAATTAACAAAAATCAACATTACAACA
*
39178328 ATTTATATGCAAGAAATTAACAAAAATCAATC-TTACAACA
1 ATTTATATGAAAGAAATTAACAAAAATCAA-CATTACAACA
* * * *
39178368 GTTTATGTGAAACAAATTAGCAAAAATCAAC
1 ATTTATATGAAAGAAATTAACAAAAATCAAC
39178399 TATTCATAGT
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
39 1 0.02
40 54 0.90
41 5 0.08
ACGTcount: A:0.50, C:0.12, G:0.08, T:0.29
Consensus pattern (40 bp):
ATTTATATGAAAGAAATTAACAAAAATCAACATTACAACA
Found at i:39178547 original size:86 final size:86
Alignment explanation
Indices: 39178457--39178710 Score: 339
Period size: 86 Copynumber: 3.0 Consensus size: 86
39178447 CTATAATGAT
* ** *
39178457 TTATATGCAACAAATTAGCAAAAATCAATGGTTCAAGTTCATGTATTTATGAAAAATCAGACTAA
1 TTATATGCAACAAATTAGCAAAAATCAATGGTTCAAGTTCATGCATTTACCAAAAACCAGACTAA
*
39178522 TTTTTCAATATTTATAACAAC
66 ATTTTCAATATTTATAACAAC
* *
39178543 TTATATGCAACAAATTAGCAAAAATAAATGGTTCAAGTTCATGCATTTACCAATAACCAGACTAA
1 TTATATGCAACAAATTAGCAAAAATCAATGGTTCAAGTTCATGCATTTACCAAAAACCAGACTAA
*
39178608 ATTTTCAATTTTTATAACAAC
66 ATTTTCAATATTTATAACAAC
* * ** * * * * *
39178629 TTATGTGCAACAAATTAGAAAAAATCAACAGTTCAAGTTCATGCATTCACTAACAGCCAGACCAA
1 TTATATGCAACAAATTAGCAAAAATCAATGGTTCAAGTTCATGCATTTACCAAAAACCAGACTAA
39178694 ATTTTCAA-ATTTTATAA
66 ATTTTCAATA-TTTATAA
39178711 AGTAGAAGGA
Statistics
Matches: 148, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
86 148 1.00
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (86 bp):
TTATATGCAACAAATTAGCAAAAATCAATGGTTCAAGTTCATGCATTTACCAAAAACCAGACTAA
ATTTTCAATATTTATAACAAC
Found at i:39180472 original size:15 final size:14
Alignment explanation
Indices: 39180444--39180481 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
39180434 ATCTCTTAAA
39180444 CCATAAACCATAAT
1 CCATAAACCATAAT
*
39180458 CCCTAAACTCATAAT
1 CCATAAAC-CATAAT
39180473 CCATAAACC
1 CCATAAACC
39180482 TTAAGATAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (14 bp):
CCATAAACCATAAT
Found at i:39181090 original size:40 final size:39
Alignment explanation
Indices: 39180975--39181090 Score: 108
Period size: 40 Copynumber: 2.9 Consensus size: 39
39180965 ATTTTTTTAG
* * * * *
39180975 AAAAA-CGGCGCTAATGCTTATTTTCAGCGGCGTGTTCT
1 AAAAAGCGCCGCTAATGCTGATTTTTAGCGGCGTTTTCC
* * * *
39181013 AAAAATCGCCGCAAATGCTAGATCTTTAGCGGTGTTTTCC
1 AAAAAGCGCCGCTAATGCT-GATTTTTAGCGGCGTTTTCC
* *
39181053 ATAAAGCGCCGCTAATGCTCGATTTTTAGCTGCGTTTT
1 AAAAAGCGCCGCTAATGCT-GATTTTTAGCGGCGTTTT
39181091 TTGTCCAAAC
Statistics
Matches: 61, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
38 5 0.08
39 11 0.18
40 45 0.74
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.33
Consensus pattern (39 bp):
AAAAAGCGCCGCTAATGCTGATTTTTAGCGGCGTTTTCC
Found at i:39185175 original size:31 final size:33
Alignment explanation
Indices: 39185104--39185179 Score: 86
Period size: 33 Copynumber: 2.3 Consensus size: 33
39185094 TTAATTTTAT
39185104 CAATTTTAGCTTTTGTGATTTTTTAAAAAATTGA
1 CAATTTTAG-TTTTGTGATTTTTTAAAAAATTGA
**
39185138 TCAATTTTAGTTTT-T-ATATTTTTAAAATTTTGA
1 -CAATTTTAGTTTTGTGAT-TTTTTAAAAAATTGA
39185171 -AATTTTAGT
1 CAATTTTAGT
39185180 CCTGATCCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
31 9 0.24
32 2 0.05
33 14 0.37
34 4 0.11
35 9 0.24
ACGTcount: A:0.32, C:0.04, G:0.09, T:0.55
Consensus pattern (33 bp):
CAATTTTAGTTTTGTGATTTTTTAAAAAATTGA
Found at i:39185239 original size:37 final size:37
Alignment explanation
Indices: 39185198--39185268 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
39185188 AAAACATATA
*
39185198 GTTAAATCGATTTGGTTCAGTTTAATTACTAGTTTGT
1 GTTAAATCGATTTGGTTAAGTTTAATTACTAGTTTGT
39185235 GTTAAATCGATTTGGTTAAGTTTAATTACTAGTT
1 GTTAAATCGATTTGGTTAAGTTTAATTACTAGTT
39185269 ATGTACTATG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.27, C:0.07, G:0.18, T:0.48
Consensus pattern (37 bp):
GTTAAATCGATTTGGTTAAGTTTAATTACTAGTTTGT
Found at i:39187132 original size:116 final size:117
Alignment explanation
Indices: 39186927--39187161 Score: 445
Period size: 116 Copynumber: 2.0 Consensus size: 117
39186917 TGACCTTGCG
39186927 AACAATATCCTGCACTTGAACAATAGCATTTGGATGTACATGCTGATTTCGAGCATGCCAAATAT
1 AACAATATCCTGCACTTGAACAATAGCATTTGGATGTACATGCTGATTTCGAGCATGCCAAATAT
*
39186992 ACCAAAGTGCACACACAATTTGCCTAAAAACAGTAGGCTTAGAGACAACCAA
66 ACCAAAGTGCACACACAATTTGCCTAAAAACAGTAGGCTTAGAAACAACCAA
39187044 AACAATATCCTGCACTTGAACAATAGCA-TTGGATGTACATGCTGATTTCGAGCATGCCAAATAT
1 AACAATATCCTGCACTTGAACAATAGCATTTGGATGTACATGCTGATTTCGAGCATGCCAAATAT
*
39187108 ACCAAAGTGCACACATAATTTGCCTAAAAACAGTAGGCTTAGAAACAACCAA
66 ACCAAAGTGCACACACAATTTGCCTAAAAACAGTAGGCTTAGAAACAACCAA
39187160 AA
1 AA
39187162 GAAAAAAAAC
Statistics
Matches: 116, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
116 88 0.76
117 28 0.24
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.23
Consensus pattern (117 bp):
AACAATATCCTGCACTTGAACAATAGCATTTGGATGTACATGCTGATTTCGAGCATGCCAAATAT
ACCAAAGTGCACACACAATTTGCCTAAAAACAGTAGGCTTAGAAACAACCAA
Found at i:39190219 original size:32 final size:32
Alignment explanation
Indices: 39190178--39190244 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
39190168 CTTGTCATCG
39190178 AGATGTACAAACGAGTAGGACGGTTCGAGTGA
1 AGATGTACAAACGAGTAGGACGGTTCGAGTGA
39190210 AGATGTACAAACGAGTAGGACGGTTCGAGTGA
1 AGATGTACAAACGAGTAGGACGGTTCGAGTGA
39190242 AGA
1 AGA
39190245 AGCGACGTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.36, C:0.12, G:0.34, T:0.18
Consensus pattern (32 bp):
AGATGTACAAACGAGTAGGACGGTTCGAGTGA
Found at i:39190516 original size:15 final size:15
Alignment explanation
Indices: 39190496--39190532 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
39190486 GTTACTTGAT
39190496 AAGCCTGTCAGATTG
1 AAGCCTGTCAGATTG
39190511 AAGCCTGTCAGATTG
1 AAGCCTGTCAGATTG
39190526 AAGCCTG
1 AAGCCTG
39190533 GTTGGCCCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (15 bp):
AAGCCTGTCAGATTG
Found at i:39195915 original size:71 final size:73
Alignment explanation
Indices: 39195840--39195989 Score: 191
Period size: 72 Copynumber: 2.1 Consensus size: 73
39195830 TGTCAAATGT
* * * *
39195840 TTTTTTTACATATATT-TGGGTATGGT-GACTTCTAATATTGA-AAAATCAAATAATCATTT-CA
1 TTTTTTCACATACATTGTGGGTATGGTAGA-TTCTAATA-TCATAAAATCAAATAATCATTTAAA
39195901 AATATCATTA
64 AATATCATTA
* *
39195911 TTTTTTCACCTACATTGTGGGTATGGTAGATTCTAATATCATAAAATCAAATAATTATTTAAAAA
1 TTTTTTCACATACATTGTGGGTATGGTAGATTCTAATATCATAAAATCAAATAATCATTT-AAAA
39195976 ATATCATTA
65 ATATCATTA
39195985 TTTTT
1 TTTTT
39195990 ATATGTGAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
71 15 0.22
72 35 0.51
73 2 0.03
74 16 0.24
ACGTcount: A:0.37, C:0.10, G:0.09, T:0.44
Consensus pattern (73 bp):
TTTTTTCACATACATTGTGGGTATGGTAGATTCTAATATCATAAAATCAAATAATCATTTAAAAA
TATCATTA
Found at i:39200064 original size:4 final size:4
Alignment explanation
Indices: 39200055--39200109 Score: 110
Period size: 4 Copynumber: 13.8 Consensus size: 4
39200045 TTCCATTTAT
39200055 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
39200103 ATAC ATA
1 ATAC ATA
39200110 TGTTTGTTTC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:39203631 original size:17 final size:17
Alignment explanation
Indices: 39203609--39203642 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
39203599 AGATAGTTGC
39203609 AATTAA-AATAATAACAA
1 AATTAACAATAA-AACAA
39203626 AATTAACAATAAAACAA
1 AATTAACAATAAAACAA
39203643 GAGTTGTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.21
Consensus pattern (17 bp):
AATTAACAATAAAACAA
Found at i:39207380 original size:40 final size:39
Alignment explanation
Indices: 39207325--39207423 Score: 108
Period size: 40 Copynumber: 2.5 Consensus size: 39
39207315 GAAGTCAGAG
* * *
39207325 GACGTGTCAGCAAATCGCTTCCACGTCAGAGCGCTTTGTT
1 GACGTGTCAACAAATCGCTT-CACGTAAGAGCGATTTGTT
* *
39207365 GACGTGGCAACAAATCGCGTTCACGTAAGCGCGATTTGTT
1 GACGTGTCAACAAATCGC-TTCACGTAAGAGCGATTTGTT
* * *
39207405 GCCATGTCAACAAAGCGCT
1 GACGTGTCAACAAATCGCT
39207424 CTGACATGGA
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
39 1 0.02
40 46 0.94
41 2 0.04
ACGTcount: A:0.24, C:0.26, G:0.25, T:0.24
Consensus pattern (39 bp):
GACGTGTCAACAAATCGCTTCACGTAAGAGCGATTTGTT
Found at i:39207973 original size:127 final size:127
Alignment explanation
Indices: 39207664--39208360 Score: 1017
Period size: 127 Copynumber: 5.5 Consensus size: 127
39207654 ATAAAAATCA
* * * * * *
39207664 AAGCAGGATGCTTTATTAGAAGAATTTCTGAAGTTGCGCCCACGTGTACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
* * *
39207729 AGGTCCTGGAAGAAATAATTTTGACTTGACGTTTCTGAGCAAAT-A-GTATAAAAACGCTTC
66 AGGTCCTGGAAGAAATAATTTCGACTTGACGTTTCTGAGCAAATAATTTAAAAAAACGCTTC
* * ** * *
39207789 AAGCAAGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTAGACATGTTTTTGCTACAAT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
* *
39207854 AGTTCCTGGAAGAAATAATTTCGACTTGACGTTTCTGAGTAAATAATTTAAAAAAACGCTTC
66 AGGTCCTGGAAGAAATAATTTCGACTTGACGTTTCTGAGCAAATAATTTAAAAAAACGCTTC
*
39207916 AAGCAGGATACTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
* * * * **
39207981 AGGTCCTGGAAGAAATAATTTCAACTTAACGTTTCTGAGCAAATAGTTTTAAAAAACTTTTC
66 AGGTCCTGGAAGAAATAATTTCGACTTGACGTTTCTGAGCAAATAATTTAAAAAAACGCTTC
39208043 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
* *
39208108 AGGTCCTGGAAGAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTTT-AAAAAATGCTTC
66 AGGTCCTGGAAGAAATAATTTCGACTTGACGTTTCTGAGCAAATAATTTAAAAAAACGCTTC
* **
39208169 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCACCCTTATGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
* * * *
39208234 AGGTCCTGGAAAAAATAATTTCGACTTGACGTTTCTGAGCAAAT-A-GTATAAAAACGTTTC
66 AGGTCCTGGAAGAAATAATTTCGACTTGACGTTTCTGAGCAAATAATTTAAAAAAACGCTTC
* ** * *
39208294 AAGCAGGATACTTTATGAGAAGAATTTGTGAAATCATGCCCACGTGGACGCACTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
39208359 AG
66 AG
39208361 CATGTTTGGA
Statistics
Matches: 514, Mismatches: 55, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
124 1 0.00
125 162 0.32
126 115 0.22
127 236 0.46
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (127 bp):
AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
AGGTCCTGGAAGAAATAATTTCGACTTGACGTTTCTGAGCAAATAATTTAAAAAAACGCTTC
Found at i:39211095 original size:54 final size:54
Alignment explanation
Indices: 39211017--39211125 Score: 182
Period size: 54 Copynumber: 2.0 Consensus size: 54
39211007 TTATCTATGC
*
39211017 GCTCATGTTATTACAACTTCTCAGAATCTCTGTCTGGATCCGATGAGTTATGTG
1 GCTCATGTTATTACAACTTCTCAGAATCTCTGTCTGGATCCGATGAGCTATGTG
* * *
39211071 GCTCATGTTATTGCAACTTGTCAGAATCTCTGTCTGGATCTGATGAGCTATGTG
1 GCTCATGTTATTACAACTTCTCAGAATCTCTGTCTGGATCCGATGAGCTATGTG
39211125 G
1 G
39211126 ACGAAGTGTA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (54 bp):
GCTCATGTTATTACAACTTCTCAGAATCTCTGTCTGGATCCGATGAGCTATGTG
Found at i:39211540 original size:27 final size:28
Alignment explanation
Indices: 39211501--39211632 Score: 148
Period size: 28 Copynumber: 4.8 Consensus size: 28
39211491 AGTACCAGTC
*
39211501 AAGGGTT-AGGGTTAGGGTTTTTAAGTT
1 AAGGGTTAAGGTTTAGGGTTTTTAAGTT
**
39211528 AAGGGTTAAGGTTTAGGGTTTACAA-TT
1 AAGGGTTAAGGTTTAGGGTTTTTAAGTT
*
39211555 AAGGGTTTAAGG-TTAGAGGATTTTTAAATT
1 AAGGG-TTAAGGTTTAG-GG-TTTTTAAGTT
39211585 AA--GTTAAGGGTTTAGGGTTTTTAAGTT
1 AAGGGTTAA-GGTTTAGGGTTTTTAAGTT
*
39211612 AAGGGTTAGGGTTTAGGGTTT
1 AAGGGTTAAGGTTTAGGGTTT
39211633 GTCAATTATA
Statistics
Matches: 89, Mismatches: 7, Indels: 17
0.79 0.06 0.15
Matches are distributed among these distances:
27 33 0.37
28 39 0.44
29 13 0.15
30 4 0.04
ACGTcount: A:0.27, C:0.01, G:0.33, T:0.40
Consensus pattern (28 bp):
AAGGGTTAAGGTTTAGGGTTTTTAAGTT
Found at i:39211622 original size:21 final size:22
Alignment explanation
Indices: 39211583--39211625 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
39211573 GATTTTTAAA
39211583 TTAAGTTAAGGGTTTAGGGTTT
1 TTAAGTTAAGGGTTTAGGGTTT
39211605 TTAAGTTAAGGG-TTAGGGTTT
1 TTAAGTTAAGGGTTTAGGGTTT
39211626 AGGGTTTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.44
Consensus pattern (22 bp):
TTAAGTTAAGGGTTTAGGGTTT
Found at i:39212182 original size:18 final size:18
Alignment explanation
Indices: 39212156--39212198 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
39212146 GACTTGGAAA
* *
39212156 AGGAAACATATAAGGGTT
1 AGGAAACATAAAAGGGCT
*
39212174 AGGATACATAAAAGGGCT
1 AGGAAACATAAAAGGGCT
39212192 AGGAAAC
1 AGGAAAC
39212199 GCACCTGCAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.47, C:0.09, G:0.28, T:0.16
Consensus pattern (18 bp):
AGGAAACATAAAAGGGCT
Found at i:39213069 original size:20 final size:20
Alignment explanation
Indices: 39213032--39213069 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
39213022 ATTATTTTTA
*
39213032 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
39213052 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
39213070 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:39214055 original size:51 final size:51
Alignment explanation
Indices: 39214011--39214110 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
39214001 AATTATTTAA
39214011 AAATAAGGATTTAAGAGAAATTTA-AGAGGAAATTGAGAGCAAATTGAGATT
1 AAATAAGGATTTAAGAGAAATTTAGA-AGGAAATTGAGAGCAAATTGAGATT
* * *
39214062 AAATATGGATTTAAGAGAAATTTGGAAGGAATTTGAGAGCAAATTGAGA
1 AAATAAGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAGA
39214111 GGAAATTTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 44 0.98
52 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.25, T:0.26
Consensus pattern (51 bp):
AAATAAGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAGATT
Found at i:39214120 original size:12 final size:12
Alignment explanation
Indices: 39214078--39214122 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
39214068 GGATTTAAGA
39214078 GAAATTTG-GAAG
1 GAAATTTGAG-AG
39214090 G-AATTTGAGAG
1 GAAATTTGAGAG
*
39214101 CAAA-TTGAGAG
1 GAAATTTGAGAG
39214112 GAAATTTGAGA
1 GAAATTTGAGA
39214123 AAGAATTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.42, C:0.02, G:0.31, T:0.24
Consensus pattern (12 bp):
GAAATTTGAGAG
Found at i:39217436 original size:21 final size:21
Alignment explanation
Indices: 39217410--39217462 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
39217400 CGACACATAA
39217410 GTGCCTGAAATGACACACGAG
1 GTGCCTGAAATGACACACGAG
* *
39217431 GTGCCTGATACGACACACGAG
1 GTGCCTGAAATGACACACGAG
39217452 GTGCCTGAAAT
1 GTGCCTGAAAT
39217463 ACAACACATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.30, C:0.25, G:0.28, T:0.17
Consensus pattern (21 bp):
GTGCCTGAAATGACACACGAG
Found at i:39217469 original size:21 final size:21
Alignment explanation
Indices: 39217410--39217469 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
39217400 CGACACATAA
39217410 GTGCCTGAAATGAC-ACACGAG
1 GTGCCTGAAAT-ACAACACGAG
39217431 GTGCCTG--ATACGACACACGAG
1 GTGCCTGAAATAC-A-ACACGAG
39217452 GTGCCTGAAATACAACAC
1 GTGCCTGAAATACAACAC
39217470 ATAAAGTGCC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
18 2 0.06
19 2 0.06
21 25 0.74
22 1 0.03
23 4 0.12
ACGTcount: A:0.33, C:0.27, G:0.25, T:0.15
Consensus pattern (21 bp):
GTGCCTGAAATACAACACGAG
Found at i:39218587 original size:54 final size:54
Alignment explanation
Indices: 39218523--39218629 Score: 214
Period size: 54 Copynumber: 2.0 Consensus size: 54
39218513 TTGTTTCGAA
39218523 ATGCTCTCTGCTTCTTTCTCCTTTCTTTTTCTTTTGTTTCGTTTTTATTTCTTG
1 ATGCTCTCTGCTTCTTTCTCCTTTCTTTTTCTTTTGTTTCGTTTTTATTTCTTG
39218577 ATGCTCTCTGCTTCTTTCTCCTTTCTTTTTCTTTTGTTTCGTTTTTATTTCTT
1 ATGCTCTCTGCTTCTTTCTCCTTTCTTTTTCTTTTGTTTCGTTTTTATTTCTT
39218630 TACTTTCTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.04, C:0.22, G:0.08, T:0.65
Consensus pattern (54 bp):
ATGCTCTCTGCTTCTTTCTCCTTTCTTTTTCTTTTGTTTCGTTTTTATTTCTTG
Found at i:39222350 original size:30 final size:30
Alignment explanation
Indices: 39222316--39222397 Score: 137
Period size: 30 Copynumber: 2.7 Consensus size: 30
39222306 TTGGCACATG
*
39222316 GGCGTGTGTCCAGCCCATGTGGCTTACACA
1 GGCGTGTGTCCAGCCCATGTGGCTCACACA
39222346 GGCGTGTGTCCAGCCCATGTGGCTCACACA
1 GGCGTGTGTCCAGCCCATGTGGCTCACACA
* *
39222376 GGCATGTATCCAGCCCATGTGG
1 GGCGTGTGTCCAGCCCATGTGG
39222398 AAATGCTCAG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.22
Consensus pattern (30 bp):
GGCGTGTGTCCAGCCCATGTGGCTCACACA
Found at i:39223354 original size:17 final size:17
Alignment explanation
Indices: 39223332--39223367 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
39223322 AGTATTATAA
39223332 TATTTATCATAA-AATTT
1 TATTTATCA-AATAATTT
39223349 TATTTATCAAATAATTT
1 TATTTATCAAATAATTT
39223366 TA
1 TA
39223368 AAAACAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 2 0.11
17 16 0.89
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (17 bp):
TATTTATCAAATAATTT
Found at i:39223754 original size:16 final size:16
Alignment explanation
Indices: 39223730--39223783 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
39223720 TTTGGTTCGC
* *
39223730 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
39223746 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
39223762 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
39223778 TGTAAT
1 TGTAAT
39223784 AGCAAATCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.31
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:39223867 original size:39 final size:43
Alignment explanation
Indices: 39223762--39223871 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
39223752 GGAATAGAGG
39223762 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
* * ***
39223807 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
39223847 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
39223872 TAATGGAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
39 20 0.35
40 2 0.04
43 1 0.02
44 11 0.19
45 23 0.40
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:39224025 original size:25 final size:25
Alignment explanation
Indices: 39223993--39224047 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
39223983 TAATTTAATC
*
39223993 ATAT-TTAAACATAATTATTATT-AA
1 ATATATTAAACAT-ATTATAATTAAA
*
39224017 ATATATTAAATATATTATAATTAAA
1 ATATATTAAACATATTATAATTAAA
39224042 ATATAT
1 ATATAT
39224048 AATTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATATTAAACATATTATAATTAAA
Found at i:39228836 original size:2 final size:2
Alignment explanation
Indices: 39228829--39228877 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
39228819 TGTGTATGAC
39228829 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39228871 AT AT AT A
1 AT AT AT A
39228878 AACTTAATAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39232381 original size:14 final size:14
Alignment explanation
Indices: 39232362--39232388 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39232352 CCGTTTGCAT
39232362 ATAAAATATTTTTC
1 ATAAAATATTTTTC
39232376 ATAAAATATTTTT
1 ATAAAATATTTTT
39232389 ATTATTGTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAAAATATTTTTC
Found at i:39233316 original size:21 final size:22
Alignment explanation
Indices: 39233263--39233316 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
39233253 CTTAATTAAG
39233263 TAAATTAAGATTAATTAAAACTA
1 TAAA-TAAGATTAATTAAAACTA
* *
39233286 -AAACATGATTAATTAAAA-TA
1 TAAATAAGATTAATTAAAACTA
39233306 TAAATAAGATT
1 TAAATAAGATT
39233317 TATGAAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 2 0.08
21 21 0.81
22 3 0.12
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (22 bp):
TAAATAAGATTAATTAAAACTA
Found at i:39234743 original size:19 final size:19
Alignment explanation
Indices: 39234719--39234758 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
39234709 TAAATGGCTC
39234719 TTCAATTTGTTTTTTCATT
1 TTCAATTTGTTTTTTCATT
39234738 TTCAATTTGTTTTTTCATT
1 TTCAATTTGTTTTTTCATT
39234757 TT
1 TT
39234759 GCTTCAGCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.70
Consensus pattern (19 bp):
TTCAATTTGTTTTTTCATT
Found at i:39237491 original size:13 final size:13
Alignment explanation
Indices: 39237470--39237520 Score: 66
Period size: 13 Copynumber: 3.9 Consensus size: 13
39237460 ATACTCAAAT
39237470 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
* *
39237483 TTCTCAAAAGCAT
1 TTTTCAAAAGCAC
* *
39237496 TTTTCCACAGCAC
1 TTTTCAAAAGCAC
39237509 TTTTCAAAAGCA
1 TTTTCAAAAGCA
39237521 ATGAAGAACT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.35, C:0.25, G:0.08, T:0.31
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:39237507 original size:26 final size:26
Alignment explanation
Indices: 39237468--39237520 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
39237458 AAATACTCAA
39237468 ATTTTTCAAAAGCACTTCTCAAAAGC
1 ATTTTTCAAAAGCACTTCTCAAAAGC
* * *
39237494 ATTTTTCCACAGCACTTTTCAAAAGC
1 ATTTTTCAAAAGCACTTCTCAAAAGC
39237520 A
1 A
39237521 ATGAAGAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.36, C:0.25, G:0.08, T:0.32
Consensus pattern (26 bp):
ATTTTTCAAAAGCACTTCTCAAAAGC
Found at i:39243813 original size:43 final size:43
Alignment explanation
Indices: 39243764--39244293 Score: 697
Period size: 43 Copynumber: 12.4 Consensus size: 43
39243754 TTTTTATAAT
* *
39243764 AAACGCCGCTATAGACCATGGTATTTAGCGGCGCTTATCCATT
1 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTATCCATC
* * *
39243807 AAACGCCGTTATAGACCATGGTCTTTAGCGGCGCTTTTGCATC
1 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTATCCATC
* * ** * *
39243850 AAACACCGCTAAAGACCATGGTCTTTAGAAGCGCTTTTGCATC
1 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTATCCATC
* * *
39243893 AAACGCCGCTATAGATCATGGTCTTTAGCGGCACTTACCCATC
1 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTATCCATC
* * *
39243936 AAACGCCGCTATAGCCCATGGTCTTTAGTGGCGCTTACCCATC
1 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTATCCATC
*
39243979 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTATCCATA
1 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTATCCATC
* * *
39244022 AAACGCCGCTATAGACCATGGTCTTTAGCGGCACTTTTGCATC
1 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTATCCATC
* * * *
39244065 AAACGCCGCTATGGACCATGGTCTTTAGCGGCACTTTTGCATC
1 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTATCCATC
* ** * *
39244108 AAACGCCGCTATGGACCATGGTCTTTAGAAGCGCTTTTGCATC
1 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTATCCATC
*
39244151 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCATC
1 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTATCCATC
* *
39244194 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCATA
1 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTATCCATC
* * * * *
39244237 AAATGCCGC--T-GACTATGATCTTTCGCGGCGCTTACCCATC
1 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTATCCATC
39244277 AAACGCCGCTATAGACC
1 AAACGCCGCTATAGACC
39244294 TTGGCGCTTT
Statistics
Matches: 435, Mismatches: 49, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
40 34 0.08
41 1 0.00
42 1 0.00
43 399 0.92
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTATCCATC
Found at i:39244651 original size:21 final size:21
Alignment explanation
Indices: 39244625--39244678 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
39244615 AGCTGTTCTG
39244625 CTTCCCTCGCTGCAGCCTCTA
1 CTTCCCTCGCTGCAGCCTCTA
* *
39244646 CTTCCCTTGCTGCAGCCTCTG
1 CTTCCCTCGCTGCAGCCTCTA
*
39244667 CTTCTCTCGCTG
1 CTTCCCTCGCTG
39244679 TCGCATCTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.06, C:0.44, G:0.17, T:0.33
Consensus pattern (21 bp):
CTTCCCTCGCTGCAGCCTCTA
Found at i:39244773 original size:87 final size:87
Alignment explanation
Indices: 39244654--39244838 Score: 257
Period size: 87 Copynumber: 2.1 Consensus size: 87
39244644 TACTTCCCTT
* * * * *
39244654 GCTGCAGCCTCTGCTTCTCTCGCTGTCGCATCTGCTTTAAGTTGCT-GCTAGAGTTGTTCATA-C
1 GCTGCTGCCTCTACTTCTCTCGCTGCCACATCTGCTTTAAGTTG-TAGCTAGAGTTCTTCATATC
39244717 TTTCGTTGAACCTCAGCTTCTCTC
65 TTT-GTTGAACCTCAGCTTCTCTC
*
39244741 GCTGCTGCCTCTACTTCTCTCGCTGCCACATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCT
1 GCTGCTGCCTCTACTTCTCTCGCTGCCACATCTGCTTTAAGTTGTAGCTAGAGTTCTTCATATCT
*
39244806 TTTTTGAACCTCAGCTTCTCTC
66 TTGTTGAACCTCAGCTTCTCTC
* *
39244828 GATGTTGCCTC
1 GCTGCTGCCTC
39244839 CCCTTTAAGT
Statistics
Matches: 87, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
86 1 0.01
87 82 0.94
88 4 0.05
ACGTcount: A:0.13, C:0.30, G:0.18, T:0.39
Consensus pattern (87 bp):
GCTGCTGCCTCTACTTCTCTCGCTGCCACATCTGCTTTAAGTTGTAGCTAGAGTTCTTCATATCT
TTGTTGAACCTCAGCTTCTCTC
Found at i:39251217 original size:16 final size:16
Alignment explanation
Indices: 39251196--39251226 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39251186 CGTTTATGAG
39251196 TTAGGGATTTCAGAAC
1 TTAGGGATTTCAGAAC
*
39251212 TTAGGGATTTTAGAA
1 TTAGGGATTTCAGAA
39251227 TAGGGAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.35
Consensus pattern (16 bp):
TTAGGGATTTCAGAAC
Found at i:39252814 original size:23 final size:23
Alignment explanation
Indices: 39252771--39252815 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
39252761 TGCTTTTGTA
*
39252771 CCCTAAAACCCGAAGCTATTAAT
1 CCCTAAAACCCGAAACTATTAAT
*
39252794 CCCTATAACCCGTAAAC-ATTAA
1 CCCTAAAACCCG-AAACTATTAA
39252816 AATTAAAGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.40, C:0.31, G:0.07, T:0.22
Consensus pattern (23 bp):
CCCTAAAACCCGAAACTATTAAT
Found at i:39253741 original size:41 final size:41
Alignment explanation
Indices: 39253696--39253858 Score: 141
Period size: 41 Copynumber: 4.0 Consensus size: 41
39253686 TAGATTTTCT
* *
39253696 AATTAGCGGCGTTTTTACACAAACGTCGCTATAGACC-GAA
1 AATTAGCGGCGCTTTTACACAAACGCCGCTATAGACCGGAA
* *
39253736 GAATTACCGGCGCTTTTACACAAATGCCGCTATAGACCGGAA
1 -AATTAGCGGCGCTTTTACACAAACGCCGCTATAGACCGGAA
* * * * * * * *
39253778 CATTAGCGGCGATTCTCCATAAACGCCGCTTTAGAGCGGAG
1 AATTAGCGGCGCTTTTACACAAACGCCGCTATAGACCGGAA
* * * * *
39253819 CATCAGCGGCGGTTTATA-AAAAACGCCGCTATAGATCGGA
1 AATTAGCGGCGCTTT-TACACAAACGCCGCTATAGACCGGA
39253859 TTATTTGCGG
Statistics
Matches: 99, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
41 95 0.96
42 4 0.04
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (41 bp):
AATTAGCGGCGCTTTTACACAAACGCCGCTATAGACCGGAA
Found at i:39253908 original size:39 final size:39
Alignment explanation
Indices: 39253836--39253911 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
39253826 GGCGGTTTAT
* ** ** *
39253836 AAAAAACGCCGCTATAGATCGGATTATTTGCGGCGCATA
1 AAAAAACGCCGCTAAAGATAAGACCATTAGCGGCGCATA
39253875 AAAAAACGCCGCTAAAGATAAGACCATTAGCGGCGCA
1 AAAAAACGCCGCTAAAGATAAGACCATTAGCGGCGCA
39253912 GACACAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (39 bp):
AAAAAACGCCGCTAAAGATAAGACCATTAGCGGCGCATA
Found at i:39254149 original size:40 final size:40
Alignment explanation
Indices: 39254059--39254190 Score: 115
Period size: 40 Copynumber: 3.3 Consensus size: 40
39254049 TTACTCTATT
* * * *
39254059 GCGGCGCTTTTT-GTAAAACGCCGCTAATGCTTGGTTTTA
1 GCGGCGATTTTTCATAAAACGCCGCTAATGCTCGATTTTA
* * ** *
39254098 GCGGCGTTTTTTTATGTAACGCCGCTAATGCTCGATATTTT
1 GCGGCGATTTTTCATAAAACGCCGCTAATGCTCGAT-TTTA
* *
39254139 GCGGC-ATTTTTCGTAAAATGCCGCTAATGCTCGATTGTTA
1 GCGGCGATTTTTCATAAAACGCCGCTAATGCTCGATT-TTA
* *
39254179 GTGGCGTTTTTT
1 GCGGCGATTTTT
39254191 GTCCAAACGC
Statistics
Matches: 73, Mismatches: 16, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
39 12 0.16
40 48 0.66
41 13 0.18
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.39
Consensus pattern (40 bp):
GCGGCGATTTTTCATAAAACGCCGCTAATGCTCGATTTTA
Found at i:39273306 original size:26 final size:26
Alignment explanation
Indices: 39273271--39273324 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
39273261 ACTGAGATTC
*
39273271 AGATTTTGAGGACTCGAAAGA-GGTA
1 AGATTTTGAGAACTCGAAAGAGGGTA
39273296 AGATATTTGAGAACTCGAAAGAGGGTA
1 AGAT-TTTGAGAACTCGAAAGAGGGTA
39273323 AG
1 AG
39273325 GATGCCAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 4 0.15
26 16 0.62
27 6 0.23
ACGTcount: A:0.39, C:0.07, G:0.31, T:0.22
Consensus pattern (26 bp):
AGATTTTGAGAACTCGAAAGAGGGTA
Found at i:39275280 original size:22 final size:22
Alignment explanation
Indices: 39275252--39275298 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
39275242 GCATTAATAT
39275252 AACAGTAGGCATCAAAGTGCAA
1 AACAGTAGGCATCAAAGTGCAA
**
39275274 AACAGTAGGCATTGAAGTGCAA
1 AACAGTAGGCATCAAAGTGCAA
39275296 AAC
1 AAC
39275299 GATAAGCACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (22 bp):
AACAGTAGGCATCAAAGTGCAA
Found at i:39276707 original size:22 final size:22
Alignment explanation
Indices: 39276682--39276727 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
39276672 AAGGACCAAG
39276682 TTGTAAAGAAATTTTTTTTCTT
1 TTGTAAAGAAATTTTTTTTCTT
*
39276704 TTGTAAAGAATTTTTTTTTCTT
1 TTGTAAAGAAATTTTTTTTCTT
39276726 TT
1 TT
39276728 TTCTCACGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.24, C:0.04, G:0.09, T:0.63
Consensus pattern (22 bp):
TTGTAAAGAAATTTTTTTTCTT
Found at i:39281058 original size:50 final size:50
Alignment explanation
Indices: 39280983--39281170 Score: 250
Period size: 50 Copynumber: 3.6 Consensus size: 50
39280973 GATAATAACA
* *
39280983 TGCCAAAGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
39281033 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
39281083 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTTATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTC---TCATC-T-CGG
39281138 ATGCCAATGCCATGTCCCAGACATGGTCTTACA
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACA
39281171 TGAGATCTCT
Statistics
Matches: 121, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
50 84 0.69
53 3 0.02
54 1 0.01
55 2 0.02
56 31 0.26
ACGTcount: A:0.21, C:0.31, G:0.23, T:0.24
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:39281196 original size:106 final size:100
Alignment explanation
Indices: 39280990--39281180 Score: 247
Period size: 106 Copynumber: 1.9 Consensus size: 100
39280980 ACATGCCAAA
* *
39280990 GCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACA
1 GCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTAGGTGCCAACGCCATGTCCCAGACA
* * **
39281055 TGGTCTTACATGGGACCTCTCGTCTCGGTGCCCAT
66 TGGTCTTACATGAGACCTCTCGTCCCAATGCCCAT
* *
39281090 GCCATGTCCCAGACATGGTCTTACAGGGGACCTCTTATGATCTTAAGGATGCCAATGCCATGTCC
1 GCCATGTCCCAGACATGGTCTTACAGGGGACCTC---TCATC-T-AGG-TGCCAACGCCATGTCC
*
39281155 CAGACATGGTCTTACATGAGATCTCT
60 CAGACATGGTCTTACATGAGACCTCT
39281181 TTACCCAAAT
Statistics
Matches: 79, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
100 33 0.42
103 4 0.05
104 1 0.01
105 2 0.03
106 39 0.49
ACGTcount: A:0.20, C:0.30, G:0.24, T:0.26
Consensus pattern (100 bp):
GCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTAGGTGCCAACGCCATGTCCCAGACA
TGGTCTTACATGAGACCTCTCGTCCCAATGCCCAT
Found at i:39281296 original size:13 final size:13
Alignment explanation
Indices: 39281275--39281306 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
39281265 GCTTGGATCA
*
39281275 TCATCAAATAAAT
1 TCATAAAATAAAT
39281288 TCATAAAATAAAT
1 TCATAAAATAAAT
39281301 TCATAA
1 TCATAA
39281307 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:39284809 original size:31 final size:31
Alignment explanation
Indices: 39284774--39284835 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
39284764 AAAAGAATAA
*
39284774 GATTGAATCGTGCTAGCATGTTGCATATTTC
1 GATTGAATCGTGCTAGCATATTGCATATTTC
*
39284805 GATTGAATTGTGCTAGCATATTGCATATTTC
1 GATTGAATCGTGCTAGCATATTGCATATTTC
39284836 ATAACTTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (31 bp):
GATTGAATCGTGCTAGCATATTGCATATTTC
Found at i:39285590 original size:24 final size:26
Alignment explanation
Indices: 39285563--39285610 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
39285553 GGAAAATAGC
*
39285563 AGAAAAGAGCAGAAG-GAA-AGAAAA
1 AGAAAAGAACAGAAGAGAAGAGAAAA
*
39285587 AGAAGAGAACAGAAGAGAAGAGAA
1 AGAAAAGAACAGAAGAGAAGAGAA
39285611 GAAAACTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 13 0.65
25 3 0.15
26 4 0.20
ACGTcount: A:0.65, C:0.04, G:0.31, T:0.00
Consensus pattern (26 bp):
AGAAAAGAACAGAAGAGAAGAGAAAA
Found at i:39285640 original size:18 final size:18
Alignment explanation
Indices: 39285617--39285653 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
39285607 AGAAGAAAAC
39285617 TTTTACTGGAATTTTCTT
1 TTTTACTGGAATTTTCTT
39285635 TTTTACTGGAATTTTCTT
1 TTTTACTGGAATTTTCTT
39285653 T
1 T
39285654 GTTCAAATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.11, G:0.11, T:0.62
Consensus pattern (18 bp):
TTTTACTGGAATTTTCTT
Found at i:39296517 original size:13 final size:13
Alignment explanation
Indices: 39296501--39296540 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
39296491 TTTAAACCAA
39296501 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
39296514 ACTTTTCCACAGC
1 ACTTTTCAAAAGC
39296527 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
39296540 A
1 A
39296541 ATGAAGAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.35, C:0.28, G:0.07, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:39299659 original size:42 final size:42
Alignment explanation
Indices: 39299599--39299678 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
39299589 GAAACAGTCA
* * * *
39299599 AGAAAAGCTGTCAGCCATCTATGAT-AGATTTTCCTAACTAAC
1 AGAAAAGATGCCAACCATCTATCATCAG-TTTTCCTAACTAAC
39299641 AGAAAAGATGCCAACCATCTATCATCAGTTTTCCTAAC
1 AGAAAAGATGCCAACCATCTATCATCAGTTTTCCTAAC
39299679 AAACTTTTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 31 0.94
43 2 0.06
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (42 bp):
AGAAAAGATGCCAACCATCTATCATCAGTTTTCCTAACTAAC
Found at i:39300769 original size:5 final size:5
Alignment explanation
Indices: 39300759--39300785 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
39300749 TTGTACTGAA
39300759 AAAAT AAAAT AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AA
39300786 TTGGAGAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:39311164 original size:30 final size:30
Alignment explanation
Indices: 39311114--39311170 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
39311104 CTGGCAAATG
*
39311114 GCCATGTGGTAGCCCTTGTGG-ATCACACA
1 GCCATGTGCTAGCCCTTGTGGAATCACACA
39311143 GCCATGTGCCTAG-CCTGTGTGGAATCAC
1 GCCATGTG-CTAGCCCT-TGTGGAATCAC
39311171 CCAACCTGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 11 0.46
30 8 0.33
31 5 0.21
ACGTcount: A:0.19, C:0.28, G:0.28, T:0.25
Consensus pattern (30 bp):
GCCATGTGCTAGCCCTTGTGGAATCACACA
Found at i:39316931 original size:68 final size:68
Alignment explanation
Indices: 39316792--39316946 Score: 154
Period size: 68 Copynumber: 2.3 Consensus size: 68
39316782 AGTGAAGCCC
** * **
39316792 CAACTCTCTTT-ATGTGGTTTTTTAGGTACAACTATTGTGATATTTGTTGGTTTATTTTTGTGAA
1 CAACTCT-TTTCATGTTATTTTTTAGGTACAACTATTATGATATTTGTTGGTTTATTTTTGCAAA
**
39316856 GTTT
65 ACTT
* * * * *
39316860 CAACT-TCTTTCATTTTATTTTTT-GGTACAACTATTATGTTGTTTGTTAGTTTTGTTTTTGCAA
1 CAACTCT-TTTCATGTTATTTTTTAGGTACAACTATTATGATATTTGTT-GGTTTATTTTTGCAA
39316923 AACTT
64 AACTT
39316928 CAACTCTTTTCATGTTATT
1 CAACTCTTTTCATGTTATT
39316947 GTGGGTGCAA
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
67 26 0.37
68 44 0.62
69 1 0.01
ACGTcount: A:0.20, C:0.12, G:0.14, T:0.54
Consensus pattern (68 bp):
CAACTCTTTTCATGTTATTTTTTAGGTACAACTATTATGATATTTGTTGGTTTATTTTTGCAAAA
CTT
Found at i:39316936 original size:67 final size:69
Alignment explanation
Indices: 39316809--39316946 Score: 156
Period size: 68 Copynumber: 2.0 Consensus size: 69
39316799 CTTTATGTGG
* ** **
39316809 TTTTTTAGGTACAACTATTGTGATATTTGTTGGTTTATTTTTGTGAAGTTTCAACTTC-TTTCAT
1 TTTTTTAGGTACAACTATTATGATATTTGTTGGTTTATTTTTGCAAAACTTCAACTTCTTTTCAT
*
39316873 TTTA
66 GTTA
* * * *
39316877 TTTTTT-GGTACAACTATTATGTTGTTTGTTAGTTTTGTTTTTGCAAAACTTCAAC-TCTTTTCA
1 TTTTTTAGGTACAACTATTATGATATTTGTT-GGTTTATTTTTGCAAAACTTCAACTTCTTTTCA
39316940 TGTTA
65 TGTTA
39316945 TT
1 TT
39316947 GTGGGTGCAA
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
67 23 0.40
68 35 0.60
ACGTcount: A:0.20, C:0.10, G:0.14, T:0.56
Consensus pattern (69 bp):
TTTTTTAGGTACAACTATTATGATATTTGTTGGTTTATTTTTGCAAAACTTCAACTTCTTTTCAT
GTTA
Found at i:39334340 original size:22 final size:22
Alignment explanation
Indices: 39334312--39334376 Score: 103
Period size: 22 Copynumber: 3.0 Consensus size: 22
39334302 TTTATTGTTC
39334312 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
*
39334334 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTG
**
39334356 AGCCATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
39334377 CAGAGGTTCG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.25
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:39336102 original size:29 final size:31
Alignment explanation
Indices: 39336056--39336120 Score: 107
Period size: 29 Copynumber: 2.2 Consensus size: 31
39336046 GTTTAGCCTT
*
39336056 GGAAGAAAATTTTGAGATTTGGTC-AAAAAG
1 GGAAGAAAATTTTAAGATTTGGTCAAAAAAG
39336086 GGAA-AAAATTTTAAGATTTGGTCAAAAAAG
1 GGAAGAAAATTTTAAGATTTGGTCAAAAAAG
39336116 GGAAG
1 GGAAG
39336121 TTGAGTCCTC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 18 0.56
30 14 0.44
ACGTcount: A:0.46, C:0.03, G:0.26, T:0.25
Consensus pattern (31 bp):
GGAAGAAAATTTTAAGATTTGGTCAAAAAAG
Found at i:39336824 original size:35 final size:36
Alignment explanation
Indices: 39336766--39336846 Score: 94
Period size: 35 Copynumber: 2.2 Consensus size: 36
39336756 TGTGTGAATT
39336766 TATTATATATATATTATAATAATTA-AAGTTAAA-ATA
1 TATTATA-ATATATTATAATAATTATAAG-TAAATATA
* **
39336802 TATTATAATATGTTATCTTAATTATTAAGTAAATATA
1 TATTATAATATATTATAATAATTA-TAAGTAAATATA
39336839 TATTATAA
1 TATTATAA
39336847 AATAATAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
35 14 0.36
36 11 0.28
37 14 0.36
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TATTATAATATATTATAATAATTATAAGTAAATATA
Found at i:39341498 original size:28 final size:28
Alignment explanation
Indices: 39341465--39341520 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
39341455 ATGGTCGGAG
39341465 ATAGTGTGTAGAAGATGGGGGTAGGATT
1 ATAGTGTGTAGAAGATGGGGGTAGGATT
39341493 ATAGTGTGTAGAAGATGGGGGTAGGATT
1 ATAGTGTGTAGAAGATGGGGGTAGGATT
39341521 CTTTACATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.43, T:0.29
Consensus pattern (28 bp):
ATAGTGTGTAGAAGATGGGGGTAGGATT
Found at i:39344834 original size:20 final size:21
Alignment explanation
Indices: 39344774--39344841 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
39344764 AATCAATAGT
*
39344774 TCAAATACTAACTACGAAAAA
1 TCAAATACTAACTAAGAAAAA
* * * *
39344795 TC-TATAGTCAGTAAGAAAAA
1 TCAAATACTAACTAAGAAAAA
39344815 TCAAATACTAACTAAGAAAAA
1 TCAAATACTAACTAAGAAAAA
39344836 TCAAAT
1 TCAAAT
39344842 TGGTGTGAAA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 15 0.41
21 22 0.59
ACGTcount: A:0.56, C:0.15, G:0.07, T:0.22
Consensus pattern (21 bp):
TCAAATACTAACTAAGAAAAA
Found at i:39347076 original size:18 final size:18
Alignment explanation
Indices: 39347042--39347076 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39347032 ATAAATAATT
* *
39347042 TTTTTAATATTTTAAAAC
1 TTTTAAATATTTAAAAAC
39347060 TTTTAAATATTTAAAAA
1 TTTTAAATATTTAAAAA
39347077 AATTTAGAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTTAAATATTTAAAAAC
Found at i:39347082 original size:18 final size:19
Alignment explanation
Indices: 39347047--39347097 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
39347037 TAATTTTTTT
* **
39347047 AATATTTTAAAACTTTTA-
1 AATATTTAAAAAAATTTAG
39347065 AATATTTAAAAAAATTTAG
1 AATATTTAAAAAAATTTAG
* *
39347084 AAAATCTAAAAAAA
1 AATATTTAAAAAAA
39347098 AAAAAGTTAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (19 bp):
AATATTTAAAAAAATTTAG
Found at i:39348227 original size:20 final size:19
Alignment explanation
Indices: 39348190--39348228 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
39348180 TATTTACAGC
* *
39348190 TTTTAATATTTTTTTATTT
1 TTTTAATATTTATGTATTT
39348209 TTTTAAATATTTATGTATTT
1 TTTT-AATATTTATGTATTT
39348229 ATATATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (19 bp):
TTTTAATATTTATGTATTT
Found at i:39348556 original size:14 final size:14
Alignment explanation
Indices: 39348505--39348557 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
39348495 TATAATTTAT
* *
39348505 AAAATGTAAAAAAA
1 AAAATGTAAATAAC
*
39348519 AAAAAGTGAAATAAC
1 AAAATGT-AAATAAC
* *
39348534 AAGACGTAAATAAC
1 AAAATGTAAATAAC
39348548 AAAATGTAAA
1 AAAATGTAAA
39348558 AGCTTAGATG
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
14 21 0.68
15 10 0.32
ACGTcount: A:0.68, C:0.06, G:0.11, T:0.15
Consensus pattern (14 bp):
AAAATGTAAATAAC
Found at i:39348878 original size:16 final size:16
Alignment explanation
Indices: 39348857--39348889 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
39348847 ATATATATAT
39348857 ATTTTTA-AAGATTTTA
1 ATTTTTATAA-ATTTTA
39348873 ATTTTTATAAATTTTA
1 ATTTTTATAAATTTTA
39348889 A
1 A
39348890 ATCATATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (16 bp):
ATTTTTATAAATTTTA
Found at i:39360736 original size:31 final size:31
Alignment explanation
Indices: 39360658--39360736 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 31
39360648 ATTTATAAAC
* * *
39360658 AAAATAATTAA-ATTGTATAAATGCATTGAT
1 AAAAGAATTAATATTTTATAAATGCAATGAT
* *
39360688 AAAAGAATTAATTTTTTATAAATGTAATGAT
1 AAAAGAATTAATATTTTATAAATGCAATGAT
*
39360719 AAAA-ATTATAATATTTTA
1 AAAAGAAT-TAATATTTTA
39360737 AATAAAATAT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
30 12 0.30
31 28 0.70
ACGTcount: A:0.51, C:0.01, G:0.08, T:0.41
Consensus pattern (31 bp):
AAAAGAATTAATATTTTATAAATGCAATGAT
Found at i:39361062 original size:32 final size:28
Alignment explanation
Indices: 39361043--39361113 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
39361033 ATTAATTTAT
39361043 AATTTATTATCTAAAATATTAAAATTGA
1 AATTTATTATCTAAAATATTAAAATTGA
* * *
39361071 AATTTATTATCTAAATTA-TACAATTTA
1 AATTTATTATCTAAAATATTAAAATTGA
*
39361098 AACATTATTATCTAAA
1 AA-TTTATTATCTAAA
39361114 GATTAATTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 9 0.24
28 29 0.76
ACGTcount: A:0.48, C:0.07, G:0.01, T:0.44
Consensus pattern (28 bp):
AATTTATTATCTAAAATATTAAAATTGA
Found at i:39362948 original size:21 final size:21
Alignment explanation
Indices: 39362922--39362962 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
39362912 ATAGTATCCC
39362922 CCATGTG-CAACATGATGAGCT
1 CCATGTGACAA-ATGATGAGCT
*
39362943 CCATGTGACAAATGGTGAGC
1 CCATGTGACAAATGATGAGC
39362963 CCCGTAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (21 bp):
CCATGTGACAAATGATGAGCT
Found at i:39363195 original size:18 final size:18
Alignment explanation
Indices: 39363169--39363229 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
39363159 TGAGGTGGAT
*
39363169 GAGGGTATCCTCCATGAG
1 GAGGATATCCTCCATGAG
*
39363187 GAGGATATCCTGCA-G-G
1 GAGGATATCCTCCATGAG
*
39363203 TG-GG-TATCCGCCATGAG
1 -GAGGATATCCTCCATGAG
39363220 GAGGATATCC
1 GAGGATATCC
39363230 CGCTGGTGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
15 7 0.21
16 5 0.15
17 5 0.15
18 17 0.50
ACGTcount: A:0.23, C:0.21, G:0.34, T:0.21
Consensus pattern (18 bp):
GAGGATATCCTCCATGAG
Found at i:39363217 original size:33 final size:33
Alignment explanation
Indices: 39363171--39363238 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
39363161 AGGTGGATGA
* *
39363171 GGGTATCCTCCATGAGGAGGATATCCTGCAGGT
1 GGGTATCCGCCATGAGGAGGATATCCCGCAGGT
*
39363204 GGGTATCCGCCATGAGGAGGATATCCCGCTGGT
1 GGGTATCCGCCATGAGGAGGATATCCCGCAGGT
39363237 GG
1 GG
39363239 AGGATATCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.19, C:0.22, G:0.37, T:0.22
Consensus pattern (33 bp):
GGGTATCCGCCATGAGGAGGATATCCCGCAGGT
Found at i:39363255 original size:18 final size:18
Alignment explanation
Indices: 39363219--39363256 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
39363209 TCCGCCATGA
* *
39363219 GGAGGATATCCCGCTGGT
1 GGAGGATATCCAGCCGGT
39363237 GGAGGATATCCAGCCGGT
1 GGAGGATATCCAGCCGGT
39363255 GG
1 GG
39363257 GTATCCTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.42, T:0.18
Consensus pattern (18 bp):
GGAGGATATCCAGCCGGT
Found at i:39363276 original size:15 final size:15
Alignment explanation
Indices: 39363258--39363301 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
39363248 AGCCGGTGGG
*
39363258 TATCCTTGTGGGGGA
1 TATCCTTGTGGAGGA
*
39363273 TATCCTTGAGGAGGA
1 TATCCTTGTGGAGGA
39363288 TATCCTTGTGGAGG
1 TATCCTTGTGGAGG
39363302 GTAGGATCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.18, C:0.14, G:0.36, T:0.32
Consensus pattern (15 bp):
TATCCTTGTGGAGGA
Found at i:39364737 original size:2 final size:2
Alignment explanation
Indices: 39364730--39364760 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39364720 GAAATGGGGA
39364730 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39364761 AGATTTTCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39388030 original size:2 final size:2
Alignment explanation
Indices: 39388023--39388049 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39388013 TTTAGTTTTA
39388023 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
39388050 CACAATGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39400842 original size:13 final size:13
Alignment explanation
Indices: 39400824--39400853 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
39400814 TTTAAAATAC
*
39400824 TTTTAATGGTCCA
1 TTTTAATGGTACA
39400837 TTTTAATGGTACA
1 TTTTAATGGTACA
39400850 TTTT
1 TTTT
39400854 CCCCTATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.10, G:0.13, T:0.53
Consensus pattern (13 bp):
TTTTAATGGTACA
Found at i:39401990 original size:9 final size:9
Alignment explanation
Indices: 39401973--39402016 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
39401963 TGATGATATC
*
39401973 GATATTGAT
1 GATAGTGAT
39401982 GATAGTGAT
1 GATAGTGAT
39401991 GATAGTGAT
1 GATAGTGAT
*
39402000 GATATTGAT
1 GATAGTGAT
*
39402009 GCTAGTGA
1 GATAGTGA
39402017 CGCTATTGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.32, C:0.02, G:0.30, T:0.36
Consensus pattern (9 bp):
GATAGTGAT
Found at i:39401994 original size:18 final size:18
Alignment explanation
Indices: 39401973--39402026 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
39401963 TGATGATATC
* *
39401973 GATATTGATGATAGTGAT
1 GATAGTGATGATATTGAT
39401991 GATAGTGATGATATTGAT
1 GATAGTGATGATATTGAT
* * *
39402009 GCTAGTGACGCTATTGAT
1 GATAGTGATGATATTGAT
39402027 CGTGACTTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.30, C:0.06, G:0.28, T:0.37
Consensus pattern (18 bp):
GATAGTGATGATATTGAT
Found at i:39403997 original size:15 final size:15
Alignment explanation
Indices: 39403977--39404009 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
39403967 ATTAAAATTC
39403977 AAAACC-AAATTTTAT
1 AAAACCAAAATTTT-T
39403992 AAAACCAAAATTTTT
1 AAAACCAAAATTTTT
39404007 AAA
1 AAA
39404010 CACGTATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAACCAAAATTTTT
Found at i:39404216 original size:2 final size:2
Alignment explanation
Indices: 39404161--39404203 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
39404151 AGCAAAATTC
39404161 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39404203 T
1 T
39404204 TCAAAATATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.