Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 53 of 141
Found at i:15963711 original size:13 final size:13
Alignment explanation
Indices: 15963690--15963719 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
15963680 GCTTGGACCA
15963690 TCATCAAATAAAT
1 TCATCAAATAAAT
*
15963703 TCATGAAATAAAT
1 TCATCAAATAAAT
15963716 TCAT
1 TCAT
15963720 AGTTGCTGGA
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:0.50, C:0.13, G:0.03, T:0.33
Consensus pattern (13 bp):
TCATCAAATAAAT
Found at i:15966898 original size:69 final size:69
Alignment explanation
Indices: 15966786--15966950 Score: 163
Period size: 69 Copynumber: 2.4 Consensus size: 69
15966776 GTCCAGATGG
* * * * *
15966786 ACTCTATTGGTTGCCAAAGCCGAGCTATGTTTTTAAATATTGAAAT-CTC-TATGTTTACTATCC
1 ACTCTATTGGTTGTCATAGCCGAGCTATGGTCTTAAACATTGAAATACTCGTA--TTTACTATCC
*
15966849 TAACAA
64 CAACAA
* * * * *
15966855 ACTCTATTGGTTGTCATAGCTGAGCTATGGTCTTACACCTTGAAATATTCGTATTTACTGTCCCA
1 ACTCTATTGGTTGTCATAGCCGAGCTATGGTCTTAAACATTGAAATACTCGTATTTACTATCCCA
* *
15966920 ATAG
66 ACAA
* *
15966924 ACTCTATTGGTTTTCATAGCCAAGCTA
1 ACTCTATTGGTTGTCATAGCCGAGCTA
15966951 ACCTTCAAAT
Statistics
Matches: 78, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
69 74 0.95
70 2 0.03
71 2 0.03
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (69 bp):
ACTCTATTGGTTGTCATAGCCGAGCTATGGTCTTAAACATTGAAATACTCGTATTTACTATCCCA
ACAA
Found at i:15974246 original size:18 final size:18
Alignment explanation
Indices: 15974223--15974258 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
15974213 GCGGAGGGTT
*
15974223 GTTGGCCGATTCGATTTG
1 GTTGGCCAATTCGATTTG
15974241 GTTGGCCAATTCGATTTG
1 GTTGGCCAATTCGATTTG
15974259 TTTCAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.17, G:0.31, T:0.39
Consensus pattern (18 bp):
GTTGGCCAATTCGATTTG
Found at i:15976923 original size:41 final size:41
Alignment explanation
Indices: 15976862--15976942 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 41
15976852 ACCTAATTGA
*
15976862 GAAAATAATTCCCTTGTTCTAATAAACTACTAAAAGATAAG
1 GAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAAG
*
15976903 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAA
1 GAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAA
15976943 AATAAAATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.30
Consensus pattern (41 bp):
GAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAAG
Found at i:15977007 original size:19 final size:19
Alignment explanation
Indices: 15976980--15977020 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
15976970 TGATTTATTC
15976980 TAAGATTTATCTACCTAAA
1 TAAGATTTATCTACCTAAA
*
15976999 TAAGTTTTATCTACCTAAA
1 TAAGATTTATCTACCTAAA
15977018 TAA
1 TAA
15977021 CTTTAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.39
Consensus pattern (19 bp):
TAAGATTTATCTACCTAAA
Found at i:15980767 original size:41 final size:41
Alignment explanation
Indices: 15980712--15980790 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
15980702 CTAATTGGGA
15980712 AAATAATTCCCTTATTCTAATAAACTACTAAAAGATAAGGG
1 AAATAATTCCCTTATTCTAATAAACTACTAAAAGATAAGGG
*
15980753 AAATAATTCTCTTATTCTAATAAACTACTAAAAGATAA
1 AAATAATTCCCTTATTCTAATAAACTACTAAAAGATAA
15980791 AATAAAATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.32
Consensus pattern (41 bp):
AAATAATTCCCTTATTCTAATAAACTACTAAAAGATAAGGG
Found at i:15982771 original size:30 final size:30
Alignment explanation
Indices: 15982747--15982970 Score: 286
Period size: 30 Copynumber: 7.4 Consensus size: 30
15982737 TATATTGCTA
* * *
15982747 AATTAATTTGTATATGGATATATATATTGTCG
1 AATTGATTTGTATATGG--ATATACATTGCCG
* * * * *
15982779 AATTGATTTATATATAGATATATATAGACG
1 AATTGATTTGTATATGGATATACATTGCCG
*
15982809 AATTGATTTGTATATGGATATACATTACCG
1 AATTGATTTGTATATGGATATACATTGCCG
* *
15982839 AATTGATTTGTATATGGATATACATAGTCG
1 AATTGATTTGTATATGGATATACATTGCCG
*
15982869 AATTGATTTATATATGGATATACATTGCCG
1 AATTGATTTGTATATGGATATACATTGCCG
* *
15982899 AATTGATTTATATATAGATATACATTGCCG
1 AATTGATTTGTATATGGATATACATTGCCG
* *
15982929 AATTGATTTGTATATGTATATATATTGCCG
1 AATTGATTTGTATATGGATATACATTGCCG
15982959 AATTGATTTGTA
1 AATTGATTTGTA
15982971 ATGTATACAT
Statistics
Matches: 170, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
30 156 0.92
32 14 0.08
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.42
Consensus pattern (30 bp):
AATTGATTTGTATATGGATATACATTGCCG
Found at i:15982871 original size:90 final size:90
Alignment explanation
Indices: 15982747--15982967 Score: 316
Period size: 90 Copynumber: 2.4 Consensus size: 90
15982737 TATATTGCTA
* *
15982747 AATTAATTTGTATATGGATATATATATTGTCGAATTGATTTATATATAGATATATATAGACGAAT
1 AATTGATTTGTATATGGATATATATA--GTCGAATTGATTTATATATAGATATACATAGACGAAT
* *
15982812 TGATTTGTATATGGATATACATTACCG
64 TGATTTATATATAGATATACATTACCG
* * * *
15982839 AATTGATTTGTATATGGATATACATAGTCGAATTGATTTATATATGGATATACATTGCCGAATTG
1 AATTGATTTGTATATGGATATATATAGTCGAATTGATTTATATATAGATATACATAGACGAATTG
*
15982904 ATTTATATATAGATATACATTGCCG
66 ATTTATATATAGATATACATTACCG
* * *
15982929 AATTGATTTGTATATGTATATATATTGCCGAATTGATTT
1 AATTGATTTGTATATGGATATATATAGTCGAATTGATTT
15982968 GTAATGTATA
Statistics
Matches: 116, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
90 92 0.79
92 24 0.21
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.43
Consensus pattern (90 bp):
AATTGATTTGTATATGGATATATATAGTCGAATTGATTTATATATAGATATACATAGACGAATTG
ATTTATATATAGATATACATTACCG
Found at i:15982984 original size:35 final size:30
Alignment explanation
Indices: 15982735--15982999 Score: 233
Period size: 30 Copynumber: 8.7 Consensus size: 30
15982725 GTATATGTTT
** *
15982735 TATATATTGCTAAATTAATTTGTATATGGATA
1 TATATATTGCCGAATTGATTTGTATAT--ATA
* * *
15982767 TATATATTGTCGAATTGATTTATATATAGA
1 TATATATTGCCGAATTGATTTGTATATATA
* * **
15982797 TATATATAGACGAATTGATTTGTATATGGA
1 TATATATTGCCGAATTGATTTGTATATATA
* * **
15982827 TATACATTACCGAATTGATTTGTATATGGA
1 TATATATTGCCGAATTGATTTGTATATATA
* * * * **
15982857 TATACATAGTCGAATTGATTTATATATGGA
1 TATATATTGCCGAATTGATTTGTATATATA
* * *
15982887 TATACATTGCCGAATTGATTTATATATAGA
1 TATATATTGCCGAATTGATTTGTATATATA
* *
15982917 TATACATTGCCGAATTGATTTGTATATGTA
1 TATATATTGCCGAATTGATTTGTATATATA
*
15982947 TATATATTGCCGAATTGATTTGTAATGTATACA
1 TATATATTGCCGAATTGATTTGT-A--TATATA
* *
15982980 TATATATTGTCAAATTGATT
1 TATATATTGCCGAATTGATT
15983000 GAGCATTGGA
Statistics
Matches: 201, Mismatches: 29, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
30 156 0.78
31 1 0.00
32 22 0.11
33 22 0.11
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (30 bp):
TATATATTGCCGAATTGATTTGTATATATA
Found at i:15992554 original size:12 final size:12
Alignment explanation
Indices: 15992520--15992556 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
15992510 GGTTCAGCCA
15992520 ATTTTAATAACC
1 ATTTTAATAACC
*
15992532 ATATT--TAACC
1 ATTTTAATAACC
15992542 ATTTTAATAACC
1 ATTTTAATAACC
15992554 ATT
1 ATT
15992557 CATCATCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
10 9 0.43
12 12 0.57
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.43
Consensus pattern (12 bp):
ATTTTAATAACC
Found at i:15993208 original size:50 final size:50
Alignment explanation
Indices: 15993094--15993336 Score: 351
Period size: 50 Copynumber: 4.8 Consensus size: 50
15993084 GATAATAACA
* * ** *
15993094 TGCCAAAGCCATGCCCCAGACATGGTCTTACATGGGATGTTCTCATGTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* **
15993145 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
15993195 TGCCAATGCCATGTCCCAGGCATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
15993245 TGCCAATGACATGTCCCAGACATGGTCTTACGTGGGACCTCTCATCTCGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
15993295 TTCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
15993337 TTACCCAAAT
Statistics
Matches: 172, Mismatches: 20, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 140 0.81
51 32 0.19
ACGTcount: A:0.20, C:0.31, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:15993452 original size:13 final size:13
Alignment explanation
Indices: 15993431--15993460 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
15993421 GCTTGGACCA
15993431 TCATCAAATAAAT
1 TCATCAAATAAAT
*
15993444 TCATGAAATAAAT
1 TCATCAAATAAAT
15993457 TCAT
1 TCAT
15993461 AGTTGCTGGA
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:0.50, C:0.13, G:0.03, T:0.33
Consensus pattern (13 bp):
TCATCAAATAAAT
Found at i:16002400 original size:18 final size:18
Alignment explanation
Indices: 16002377--16002411 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
16002367 CCGAAAATCT
16002377 ATAAAGAAAAATAAAGGC
1 ATAAAGAAAAATAAAGGC
*
16002395 ATAAAGAAAATTAAAGG
1 ATAAAGAAAAATAAAGG
16002412 AGAAAAGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.66, C:0.03, G:0.17, T:0.14
Consensus pattern (18 bp):
ATAAAGAAAAATAAAGGC
Found at i:16002418 original size:18 final size:18
Alignment explanation
Indices: 16002379--16002420 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
16002369 GAAAATCTAT
*
16002379 AAAGAAAAATAAAGGCAT
1 AAAGAAAAATAAAGGCAA
*
16002397 AAAGAAAATTAAAGG-AGA
1 AAAGAAAAATAAAGGCA-A
16002415 AAAGAA
1 AAAGAA
16002421 CCCCTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 1 0.05
18 20 0.95
ACGTcount: A:0.69, C:0.02, G:0.19, T:0.10
Consensus pattern (18 bp):
AAAGAAAAATAAAGGCAA
Found at i:16006834 original size:13 final size:13
Alignment explanation
Indices: 16006816--16006842 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
16006806 CAAAATTGGC
16006816 AAGATGATAAATA
1 AAGATGATAAATA
16006829 AAGATGATAAATA
1 AAGATGATAAATA
16006842 A
1 A
16006843 TAAAAGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.15, T:0.22
Consensus pattern (13 bp):
AAGATGATAAATA
Found at i:16007346 original size:5 final size:5
Alignment explanation
Indices: 16007329--16007377 Score: 53
Period size: 5 Copynumber: 9.6 Consensus size: 5
16007319 TCCTAAGATG
* * * *
16007329 TGAAT TGATT TGAAT TGAAT TGAAT TGAAT ATAAAT TGTAT TAAAT TGA
1 TGAAT TGAAT TGAAT TGAAT TGAAT TGAAT -TGAAT TGAAT TGAAT TGA
16007378 GTTAAATTAC
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
5 31 0.89
6 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.43
Consensus pattern (5 bp):
TGAAT
Found at i:16007375 original size:21 final size:20
Alignment explanation
Indices: 16007331--16007385 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 20
16007321 CTAAGATGTG
* * *
16007331 AATTGATTTGAATTGAATTG
1 AATTGAATTAAATTGAATTA
*
16007351 AATTGAATATAAATTGTATTA
1 AATTGAAT-TAAATTGAATTA
*
16007372 AATTGAGTTAAATT
1 AATTGAATTAAATT
16007386 ACTCGTATAG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.44
Consensus pattern (20 bp):
AATTGAATTAAATTGAATTA
Found at i:16007382 original size:10 final size:10
Alignment explanation
Indices: 16007331--16007385 Score: 56
Period size: 10 Copynumber: 5.4 Consensus size: 10
16007321 CTAAGATGTG
* *
16007331 AATTGATTTG
1 AATTGAATTA
*
16007341 AATTGAATTG
1 AATTGAATTA
16007351 AATTGAATATA
1 AATTGAAT-TA
*
16007362 AATTGTATTA
1 AATTGAATTA
*
16007372 AATTGAGTTA
1 AATTGAATTA
16007382 AATT
1 AATT
16007386 ACTCGTATAG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
10 31 0.79
11 8 0.21
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.44
Consensus pattern (10 bp):
AATTGAATTA
Found at i:16007857 original size:26 final size:25
Alignment explanation
Indices: 16007822--16007908 Score: 77
Period size: 26 Copynumber: 3.4 Consensus size: 25
16007812 ACAGCTCTTA
*
16007822 TGAGCGTCCCGTTATATGGCTCTTTG
1 TGAGCTTCCCGTTA-ATGGCTCTTTG
* *
16007848 TGAGCTTCCCGATTAAAGGCTCTTTC
1 TGAGCTTCCCG-TTAATGGCTCTTTG
* ** *
16007874 TAAGCTTCCTAATTAATGGCTCTCTG
1 TGAGCTTCC-CGTTAATGGCTCTTTG
16007900 -GAGCTTCCC
1 TGAGCTTCCC
16007909 AATATGACTC
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
25 7 0.15
26 38 0.79
27 3 0.06
ACGTcount: A:0.17, C:0.26, G:0.21, T:0.36
Consensus pattern (25 bp):
TGAGCTTCCCGTTAATGGCTCTTTG
Found at i:16010386 original size:21 final size:21
Alignment explanation
Indices: 16010360--16010511 Score: 106
Period size: 21 Copynumber: 7.1 Consensus size: 21
16010350 CCGACGGCTG
* *
16010360 AACAGAAGCACATAAGTGCTA
1 AACAGAAGCTCATAAGAGCTA
* * * * *
16010381 AACAGAAACCCATAAGGGTTG
1 AACAGAAGCTCATAAGAGCTA
*
16010402 AACGGAAGCTCATAAGAGCTA
1 AACAGAAGCTCATAAGAGCTA
* *
16010423 AACAGAAACTCATAAGAGTTA
1 AACAGAAGCTCATAAGAGCTA
* * *
16010444 AACAGAAGCCCAAAAGAGAGCTG
1 AACAGAAGCTC-ATA-AGAGCTA
** * * *
16010467 AATGGAAACTCATATGAGTTA
1 AACAGAAGCTCATAAGAGCTA
* *
16010488 AACAGAAGCTCGTGAGAGCTA
1 AACAGAAGCTCATAAGAGCTA
16010509 AAC
1 AAC
16010512 GGAAAGTAAA
Statistics
Matches: 95, Mismatches: 34, Indels: 4
0.71 0.26 0.03
Matches are distributed among these distances:
21 79 0.83
22 4 0.04
23 12 0.13
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTA
Found at i:16010410 original size:42 final size:42
Alignment explanation
Indices: 16010358--16010516 Score: 138
Period size: 42 Copynumber: 3.7 Consensus size: 42
16010348 GCCCGACGGC
* *
16010358 TGAACAGAAGCACATAAGTGCTAAACAGAAACCCATAAGGGT
1 TGAACAGAAGCACATAAGAGCTAAACAGAAACCCATAAGAGT
* * *
16010400 TGAACGGAAGCTCATAAGAGCTAAACAGAAACTCATAAGAGT
1 TGAACAGAAGCACATAAGAGCTAAACAGAAACCCATAAGAGT
* * * * ** * *
16010442 TAAACAGAAGCCCAAAAGAGAGCTGAATGGAAACTCATATGAGT
1 TGAACAGAAGCAC-ATA-AGAGCTAAACAGAAACCCATAAGAGT
* * * * *
16010486 TAAACAGAAGCTCGTGAGAGCTAAACGGAAA
1 TGAACAGAAGCACATAAGAGCTAAACAGAAA
16010517 GTAAACACGA
Statistics
Matches: 96, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
42 60 0.62
43 2 0.02
44 34 0.35
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (42 bp):
TGAACAGAAGCACATAAGAGCTAAACAGAAACCCATAAGAGT
Found at i:16018362 original size:31 final size:32
Alignment explanation
Indices: 16018303--16018367 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
16018293 GGCAAATTAC
16018303 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
16018335 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
16018366 AA
1 AA
16018368 ATTATCTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:16032200 original size:12 final size:13
Alignment explanation
Indices: 16032183--16032211 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
16032173 CTCATACATG
16032183 AATAAATAAA-GC
1 AATAAATAAATGC
16032195 AATAAATAAATGC
1 AATAAATAAATGC
16032208 AATA
1 AATA
16032212 GTTATAGCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (13 bp):
AATAAATAAATGC
Found at i:16039147 original size:6 final size:6
Alignment explanation
Indices: 16039136--16039174 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
16039126 TATTAGGAAT
16039136 CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG CTC
1 CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG CTCCTG CTC
16039175 ATGGCTTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.15, T:0.33
Consensus pattern (6 bp):
CTCCTG
Found at i:16052075 original size:41 final size:41
Alignment explanation
Indices: 16052025--16052127 Score: 109
Period size: 41 Copynumber: 2.5 Consensus size: 41
16052015 CCTTATTCAG
* * * * *
16052025 TTCACCGGCAATT-AGCCTGTTAGACTTAAAGTCTGAATTAT
1 TTCACCGGC-ATTAAGCATGCTAGACATAAAGTCCGAATTAC
*
16052066 TTCACCGGCATTAAGCATGCTGGACATAAAGTCCGAATTAC
1 TTCACCGGCATTAAGCATGCTAGACATAAAGTCCGAATTAC
* * *
16052107 ATCACCGGCCTTAAGCTTGCT
1 TTCACCGGCATTAAGCATGCT
16052128 GGACTTTAAG
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 3 0.06
41 49 0.94
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.29
Consensus pattern (41 bp):
TTCACCGGCATTAAGCATGCTAGACATAAAGTCCGAATTAC
Found at i:16052128 original size:41 final size:41
Alignment explanation
Indices: 16052051--16052131 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 41
16052041 CTGTTAGACT
* **
16052051 TAAAGTCTGAATTATTTCACCGGCATTAAGCATGCTGGACA
1 TAAAGTCCGAATTACATCACCGGCATTAAGCATGCTGGACA
* *
16052092 TAAAGTCCGAATTACATCACCGGCCTTAAGCTTGCTGGAC
1 TAAAGTCCGAATTACATCACCGGCATTAAGCATGCTGGAC
16052132 TTTAAGCTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (41 bp):
TAAAGTCCGAATTACATCACCGGCATTAAGCATGCTGGACA
Found at i:16055303 original size:14 final size:14
Alignment explanation
Indices: 16055237--16055304 Score: 50
Period size: 14 Copynumber: 4.8 Consensus size: 14
16055227 CCTACTATGG
*
16055237 TTAGGGTTTTGGGT
1 TTAGGGTTTTAGGT
**
16055251 TTTTGGTTTTAGGT
1 TTAGGGTTTTAGGT
*
16055265 TTAAGG--TTAGGGTT
1 TTAGGGTTTTA-GG-T
*
16055279 TTGGGGTTTTTAGGT
1 TTAGGG-TTTTAGGT
16055294 TTAGGGTTTTA
1 TTAGGGTTTTA
16055305 AAGAAAAATT
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
12 3 0.07
13 2 0.05
14 25 0.61
15 6 0.15
16 2 0.05
17 3 0.07
ACGTcount: A:0.12, C:0.00, G:0.35, T:0.53
Consensus pattern (14 bp):
TTAGGGTTTTAGGT
Found at i:16055695 original size:126 final size:126
Alignment explanation
Indices: 16055496--16055788 Score: 372
Period size: 126 Copynumber: 2.3 Consensus size: 126
16055486 GTGTTAATTT
* * * * * * *
16055496 AAAAAAGCTCTCACGTGGATGTGGTTTTGCTACAGTAGCTCCTGCAAAAATAATTTCGAATAGAT
1 AAAAAAGCTCCCAAGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAATAGAC
* * *
16055561 ATTCCTGAGCAAATAGTGTCAAAGACGCTTTAAGCAGGATGCTTTGTCAAAAAAAGTACTG
66 ATTCCTGAGCAAATAGTGTCAAAAACGCTTTAAACAGGATGCTTTATCAAAAAAAGTACTG
* * * * *
16055622 AAAGAAGCTCCCACA-TGGACGCGTTTTTGTTACAGTAGCTCTTGAAAAAATAATTTCGAGTAGA
1 AAAAAAGCTCCCA-AGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAATAGA
* * **
16055686 CGTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAACAGGATGCTTTATCAGCAAAAGTACTG
65 CATTCCTGAGCAAATAGTGTCAAAAACGCTTTAAACAGGATGCTTTATCAAAAAAAGTACTG
* * *
16055748 AAAAAAGCTTCTAAGTGGATGCGCTTTTGCTACAGTAGCTC
1 AAAAAAGCTCCCAAGTGGACGCGCTTTTGCTACAGTAGCTC
16055789 ATGTTTGGCC
Statistics
Matches: 141, Mismatches: 24, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
125 1 0.01
126 140 0.99
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.28
Consensus pattern (126 bp):
AAAAAAGCTCCCAAGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAATAGAC
ATTCCTGAGCAAATAGTGTCAAAAACGCTTTAAACAGGATGCTTTATCAAAAAAAGTACTG
Found at i:16058957 original size:34 final size:33
Alignment explanation
Indices: 16058905--16059066 Score: 107
Period size: 34 Copynumber: 4.7 Consensus size: 33
16058895 AACAATGTTT
* * *
16058905 TATTTTAATAAATGAAATAATATAGAAGAATTTC
1 TATTTTATTACATCAAATAATAT-GAAGAATTTC
*
16058939 TATTTTATTACATCAAATAATATCAA-AATATTC
1 TATTTTATTACATCAAATAATATGAAGAAT-TTC
* * * *
16058972 AAAATGTTT-GTACA--AATATAGATGTAAAAGTAAATTTC
1 --TAT-TTTATTACATCAA-ATA-ATAT-GAAG--AATTTC
* *
16059010 TATTTTATTACATGAAATAATATGTCAGAATTTC
1 TATTTTATTACATCAAATAATATG-AAGAATTTC
16059044 TATTTTATTACATCAAATAATAT
1 TATTTTATTACATCAAATAATAT
16059067 CAAAATATTC
Statistics
Matches: 100, Mismatches: 14, Indels: 28
0.70 0.10 0.20
Matches are distributed among these distances:
32 3 0.03
33 7 0.07
34 51 0.51
35 12 0.12
36 16 0.16
37 3 0.03
38 5 0.05
39 3 0.03
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (33 bp):
TATTTTATTACATCAAATAATATGAAGAATTTC
Found at i:16058986 original size:105 final size:104
Alignment explanation
Indices: 16058905--16059096 Score: 323
Period size: 105 Copynumber: 1.8 Consensus size: 104
16058895 AACAATGTTT
16058905 TATTTTAATAAATGAAATAATATAG-AAGAATTTCTATTTTATTACATCAAATAATATCAAAATA
1 TATTTTAATAAATGAAATAATAT-GTAAGAATTTCTATTTTATTACATCAAATAATATCAAAATA
*
16058969 TTCAAAATGTTTGTACAAATATAGATGTAAAAGTAAATTTC
65 TTCAAAATGTTGGTACAAATATAGATGTAAAAG-AAATTTC
* * *
16059010 TATTTTATTACATGAAATAATATGTCAGAATTTCTATTTTATTACATCAAATAATATCAAAATAT
1 TATTTTAATAAATGAAATAATATGTAAGAATTTCTATTTTATTACATCAAATAATATCAAAATAT
16059075 TCAAAATGTTGGTACAAATATA
66 TCAAAATGTTGGTACAAATATA
16059097 TTAAAATAAA
Statistics
Matches: 82, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 1 0.01
105 81 0.99
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (104 bp):
TATTTTAATAAATGAAATAATATGTAAGAATTTCTATTTTATTACATCAAATAATATCAAAATAT
TCAAAATGTTGGTACAAATATAGATGTAAAAGAAATTTC
Found at i:16061288 original size:11 final size:11
Alignment explanation
Indices: 16061272--16061319 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
16061262 GCTTTTTTTA
16061272 AGAGGAATTTG
1 AGAGGAATTTG
16061283 AGAGGAATTTG
1 AGAGGAATTTG
16061294 AGA-GAATATTG
1 AGAGGAAT-TTG
*
16061305 -GAGAGAAATTG
1 AGAG-GAATTTG
16061316 AGAG
1 AGAG
16061320 AAAGGATTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
10 6 0.19
11 20 0.62
12 6 0.19
ACGTcount: A:0.42, C:0.00, G:0.35, T:0.23
Consensus pattern (11 bp):
AGAGGAATTTG
Found at i:16061318 original size:10 final size:10
Alignment explanation
Indices: 16061280--16061322 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
16061270 TAAGAGGAAT
*
16061280 TTGAGAGGAAT
1 TTGAGA-GAAA
16061291 TTGAGAGAATA
1 TTGAGAGAA-A
16061302 TTGGAGAGAAA
1 TT-GAGAGAAA
16061313 TTGAGAGAAA
1 TTGAGAGAAA
16061323 GGATTTAGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 11 0.38
11 11 0.38
12 7 0.24
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.23
Consensus pattern (10 bp):
TTGAGAGAAA
Found at i:16067269 original size:17 final size:16
Alignment explanation
Indices: 16067237--16067279 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
16067227 CTAGCTCGGG
16067237 TATTAAATTGTGAAAC
1 TATTAAATTGTGAAAC
*
16067253 TATTAAAGTTTTGAAAC
1 TATTAAA-TTGTGAAAC
16067270 -ATTACAATTG
1 TATTA-AATTG
16067280 ATGATTCTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.40
Consensus pattern (16 bp):
TATTAAATTGTGAAAC
Found at i:16069311 original size:38 final size:37
Alignment explanation
Indices: 16069229--16069311 Score: 87
Period size: 38 Copynumber: 2.2 Consensus size: 37
16069219 TACAGTACAG
* * * *
16069229 AAACAGTAGAATGCTTAACATGTATTCAGTTCAACAG
1 AAACAGTAGAATGCTTAACATGCAATCAGTTAAACAA
* *
16069266 TAGCAGTAGACATGCTTAACATGCAATCAG-TAAGACAA
1 AAACAGTAGA-ATGCTTAACATGCAATCAGTTAA-ACAA
16069304 AAACAGTA
1 AAACAGTA
16069312 ATAACAGTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
37 10 0.28
38 26 0.72
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (37 bp):
AAACAGTAGAATGCTTAACATGCAATCAGTTAAACAA
Found at i:16072856 original size:45 final size:47
Alignment explanation
Indices: 16072786--16072882 Score: 137
Period size: 46 Copynumber: 2.1 Consensus size: 47
16072776 TAACGATGAC
* *
16072786 TTTTACTACAATAACTTACCATCCCGGTTG-CCC-GATTTTGATGGCT
1 TTTTACTACAATAACTTACCATCCCGGTCGACCCAG-TTTTAATGGCT
*
16072832 TTTTACTACAATAAC-TATCATCCCGGTCGACCCAGTTTTAATGGCT
1 TTTTACTACAATAACTTACCATCCCGGTCGACCCAGTTTTAATGGCT
16072878 TTTTA
1 TTTTA
16072883 AATTACCATC
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
45 12 0.26
46 33 0.72
47 1 0.02
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.38
Consensus pattern (47 bp):
TTTTACTACAATAACTTACCATCCCGGTCGACCCAGTTTTAATGGCT
Found at i:16073270 original size:15 final size:15
Alignment explanation
Indices: 16073231--16073274 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
16073221 TTAACACATA
16073231 TATAGAGGTTCGCATC
1 TATAG-GGTTCGCATC
* *
16073247 TA-GGGGTTCGCATG
1 TATAGGGTTCGCATC
16073261 TATAGGGTTCGCAT
1 TATAGGGTTCGCAT
16073275 ATTATCATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 11 0.46
15 11 0.46
16 2 0.08
ACGTcount: A:0.20, C:0.16, G:0.32, T:0.32
Consensus pattern (15 bp):
TATAGGGTTCGCATC
Found at i:16074700 original size:23 final size:23
Alignment explanation
Indices: 16074667--16074710 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
16074657 AAATCATTAT
16074667 AAAAAAATATAA-AAATTATAAA
1 AAAAAAATATAAGAAATTATAAA
16074689 AAAAAAACTATAAGAAATTATA
1 AAAAAAA-TATAAGAAATTATA
16074711 TAAATTGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 5 0.25
24 8 0.40
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (23 bp):
AAAAAAATATAAGAAATTATAAA
Found at i:16076898 original size:20 final size:18
Alignment explanation
Indices: 16076861--16076904 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 18
16076851 ATAGTTAATT
16076861 TAAAAAAATTAAAATTCA
1 TAAAAAAATTAAAATTCA
16076879 -AAAAAAATATAAAAAGTTCA
1 TAAAAAAAT-T-AAAA-TTCA
16076899 TAAAAA
1 TAAAAA
16076905 TTCAAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 8 0.36
18 1 0.05
19 4 0.18
20 4 0.18
21 5 0.23
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (18 bp):
TAAAAAAATTAAAATTCA
Found at i:16077478 original size:13 final size:13
Alignment explanation
Indices: 16077447--16077496 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
16077437 GTCATGATTC
*
16077447 TAAAAAATTATCTA
1 TAAAAAA-TATATA
*
16077461 GAAAAAATATATA
1 TAAAAAATATATA
*
16077474 TAAAAAATTTATA
1 TAAAAAATATATA
16077487 TAACAAAATA
1 TAA-AAAATA
16077497 GCTTTCTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
13 19 0.63
14 11 0.37
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (13 bp):
TAAAAAATATATA
Found at i:16081095 original size:21 final size:20
Alignment explanation
Indices: 16081038--16081096 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 20
16081028 TGTAAAACAG
* *
16081038 GGGTCATACGGCCATGTAGAA
1 GGGTCATA-GGTCATGTGGAA
* *
16081059 GGCT-ATAGGTCGTGTGGAA
1 GGGTCATAGGTCATGTGGAA
16081078 GGGTCATATGGTCATGTGG
1 GGGTCATA-GGTCATGTGG
16081097 CTAGGCCTTG
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
19 12 0.40
20 6 0.20
21 12 0.40
ACGTcount: A:0.22, C:0.14, G:0.39, T:0.25
Consensus pattern (20 bp):
GGGTCATAGGTCATGTGGAA
Found at i:16098573 original size:39 final size:40
Alignment explanation
Indices: 16098497--16098658 Score: 227
Period size: 40 Copynumber: 4.1 Consensus size: 40
16098487 GTAAGAGTAG
* * * *
16098497 TCAGAGGTACCGAAGTAGAAACAAGGGCATGCATGTGCAT
1 TCAGGGGTACCGAAGTACAAACAGGGGCACGCATGTGCAT
* *
16098537 TCAGGGGTACTGAAGTAC-AACAGGGGCACGTATGTGCAT
1 TCAGGGGTACCGAAGTACAAACAGGGGCACGCATGTGCAT
* *
16098576 TCAGGGGTACTGAAGTACAAACAGGGGCACGCATGTGCCT
1 TCAGGGGTACCGAAGTACAAACAGGGGCACGCATGTGCAT
* *
16098616 TTAGGGGTACCGAAGTACAAACAGGGGTACGCATGTGCAT
1 TCAGGGGTACCGAAGTACAAACAGGGGCACGCATGTGCAT
16098656 TCA
1 TCA
16098659 TACAATAATT
Statistics
Matches: 108, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
39 36 0.33
40 72 0.67
ACGTcount: A:0.30, C:0.19, G:0.31, T:0.19
Consensus pattern (40 bp):
TCAGGGGTACCGAAGTACAAACAGGGGCACGCATGTGCAT
Found at i:16098600 original size:20 final size:20
Alignment explanation
Indices: 16098538--16098602 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
16098528 CATGTGCATT
16098538 CAGGGGTACTGAAGTAC-AA
1 CAGGGGTACTGAAGTACAAA
* * * **
16098557 CAGGGGCAC-GTATGTGCATT
1 CAGGGGTACTG-AAGTACAAA
16098577 CAGGGGTACTGAAGTACAAA
1 CAGGGGTACTGAAGTACAAA
16098597 CAGGGG
1 CAGGGG
16098603 CACGCATGTG
Statistics
Matches: 33, Mismatches: 10, Indels: 5
0.69 0.21 0.10
Matches are distributed among these distances:
18 1 0.03
19 12 0.36
20 19 0.58
21 1 0.03
ACGTcount: A:0.31, C:0.17, G:0.35, T:0.17
Consensus pattern (20 bp):
CAGGGGTACTGAAGTACAAA
Found at i:16098633 original size:79 final size:80
Alignment explanation
Indices: 16098497--16098658 Score: 227
Period size: 79 Copynumber: 2.0 Consensus size: 80
16098487 GTAAGAGTAG
* * *
16098497 TCAGAGGTACCGAAGTAGAAACAAGGGCATGCATGTGCATTCAGGGGTACTGAAGTAC-AACAGG
1 TCAGAGGTACCGAAGTACAAACAAGGGCACGCATGTGCATTCAGGGGTACCGAAGTACAAACAGG
*
16098561 GGCACGTATGTGCAT
66 GGCACGCATGTGCAT
* * * * *
16098576 TCAGGGGTACTGAAGTACAAACAGGGGCACGCATGTGCCTTTAGGGGTACCGAAGTACAAACAGG
1 TCAGAGGTACCGAAGTACAAACAAGGGCACGCATGTGCATTCAGGGGTACCGAAGTACAAACAGG
*
16098641 GGTACGCATGTGCAT
66 GGCACGCATGTGCAT
16098656 TCA
1 TCA
16098659 TACAATAATT
Statistics
Matches: 72, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
79 50 0.69
80 22 0.31
ACGTcount: A:0.30, C:0.19, G:0.31, T:0.19
Consensus pattern (80 bp):
TCAGAGGTACCGAAGTACAAACAAGGGCACGCATGTGCATTCAGGGGTACCGAAGTACAAACAGG
GGCACGCATGTGCAT
Found at i:16099820 original size:40 final size:40
Alignment explanation
Indices: 16099739--16099981 Score: 278
Period size: 40 Copynumber: 6.1 Consensus size: 40
16099729 ATACTACATA
* * * * * *
16099739 ATTCAGAGTTACCGGAGTATAAACAA-GGCACATAAGTGC
1 ATTCAGGGGTACCGAAGTACAAACAAGGGCACGTATGTGC
* *
16099778 ATTCAAGGGTACGGAAGTACAAACAAGGGCACGTATGTGC
1 ATTCAGGGGTACCGAAGTACAAACAAGGGCACGTATGTGC
* *
16099818 ATTCAGGGGTACCGAAGTACAAATAAGGGCACGCATGTGC
1 ATTCAGGGGTACCGAAGTACAAACAAGGGCACGTATGTGC
* * * *
16099858 ATTCAGGGATACCAAAGTAC-AACATGGGCACGTATGTCC
1 ATTCAGGGGTACCGAAGTACAAACAAGGGCACGTATGTGC
*
16099897 ATTCAGGGGTACTC-AAGTACAAAC-AGAGGCACGCATGTGC
1 ATTCAGGGGTAC-CGAAGTACAAACAAG-GGCACGTATGTGC
* * *
16099937 ATTCAGGGGTATCGAAGTACAAACAAAGGCACATATGTGC
1 ATTCAGGGGTACCGAAGTACAAACAAGGGCACGTATGTGC
16099977 ATTCA
1 ATTCA
16099982 TACAATAATT
Statistics
Matches: 172, Mismatches: 26, Indels: 11
0.82 0.12 0.05
Matches are distributed among these distances:
39 54 0.31
40 117 0.68
41 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.19
Consensus pattern (40 bp):
ATTCAGGGGTACCGAAGTACAAACAAGGGCACGTATGTGC
Found at i:16099893 original size:79 final size:79
Alignment explanation
Indices: 16099774--16099981 Score: 278
Period size: 79 Copynumber: 2.6 Consensus size: 79
16099764 AGGCACATAA
*
16099774 GTGCATTCAAGGGTACGGAAGTACAAACAAGGGCACGTATGTGCATTCAGGGGTAC-CGAAGTAC
1 GTGCATTC-AGGGTACCGAAGTACAAACAAGGGCACGTATGTGCATTCAGGGGTACTC-AAGTAC
16099838 AAATAAG-GGCACGCAT
64 AAA-AAGAGGCACGCAT
* * *
16099854 GTGCATTCAGGGATACCAAAGTAC-AACATGGGCACGTATGTCCATTCAGGGGTACTCAAGTACA
1 GTGCATTCAGGG-TACCGAAGTACAAACAAGGGCACGTATGTGCATTCAGGGGTACTCAAGTACA
*
16099918 AACAGAGGCACGCAT
65 AAAAGAGGCACGCAT
* * *
16099933 GTGCATTCAGGGGTATCGAAGTACAAACAAAGGCACATATGTGCATTCA
1 GTGCATTCA-GGGTACCGAAGTACAAACAAGGGCACGTATGTGCATTCA
16099982 TACAATAATT
Statistics
Matches: 112, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
78 2 0.02
79 69 0.62
80 41 0.37
ACGTcount: A:0.34, C:0.20, G:0.27, T:0.19
Consensus pattern (79 bp):
GTGCATTCAGGGTACCGAAGTACAAACAAGGGCACGTATGTGCATTCAGGGGTACTCAAGTACAA
AAAGAGGCACGCAT
Found at i:16107516 original size:63 final size:63
Alignment explanation
Indices: 16107432--16107675 Score: 320
Period size: 63 Copynumber: 4.0 Consensus size: 63
16107422 ATATATATAT
* ** * * * *
16107432 GTTCTATAAGCTGAATTTAATTTTATGAATTATATAAATATGTTAGCTGAATGTATGCTTTAA
1 GTTCTATAAGTTGAAACTAATTGTATGAATTATATAAATATGTTAGCCGAATGTATGTTTTGA
16107495 GTT-TGATAAGTTGAAACTAATTGTATGAA-T-TATAAATATGTTAGCC-AATGTATGTTTTGA
1 GTTCT-ATAAGTTGAAACTAATTGTATGAATTATATAAATATGTTAGCCGAATGTATGTTTTGA
* * *
16107555 GTTCTATGAGTTGAAACTAATTGTATAAATTATATATATATGTTAGCCGAATGTATGTTTTGA
1 GTTCTATAAGTTGAAACTAATTGTATGAATTATATAAATATGTTAGCCGAATGTATGTTTTGA
** *
16107618 GTTCTATAAGTTGAATTTAATTGTATGAATTATAT--ATATGTTATCCGAATGTATGTTT
1 GTTCTATAAGTTGAAACTAATTGTATGAATTATATAAATATGTTAGCCGAATGTATGTTT
16107676 GCTACGAAGA
Statistics
Matches: 161, Mismatches: 15, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
60 37 0.23
61 39 0.24
62 17 0.11
63 68 0.42
ACGTcount: A:0.34, C:0.06, G:0.16, T:0.44
Consensus pattern (63 bp):
GTTCTATAAGTTGAAACTAATTGTATGAATTATATAAATATGTTAGCCGAATGTATGTTTTGA
Found at i:16107651 original size:123 final size:124
Alignment explanation
Indices: 16107449--16107675 Score: 341
Period size: 123 Copynumber: 1.8 Consensus size: 124
16107439 AAGCTGAATT
* * *
16107449 TAATTTTATGAATTATATAAATATGTTAGCTGAATGTATGCTTTAAGTTTGATAAGTTGAAACTA
1 TAATTGTATAAATTATATAAATATGTTAGCCGAATGTATGCTTTAAGTTTGATAAGTTGAAACTA
16107514 ATTGTATGAATTATAAATATGTTAGCC-AATGTATGTTTTGAGTTCTATGAGTTGAAAC
66 ATTGTATGAATTATAAATATGTTAGCCGAATGTATGTTTTGAGTTCTATGAGTTGAAAC
* * * **
16107572 TAATTGTATAAATTATATATATATGTTAGCCGAATGTATGTTTTGAGTTCT-ATAAGTTGAATTT
1 TAATTGTATAAATTATATAAATATGTTAGCCGAATGTATGCTTTAAGTT-TGATAAGTTGAAACT
* *
16107636 AATTGTATGAATTATATATATGTTATCCGAATGTATGTTT
65 AATTGTATGAATTATAAATATGTTAGCCGAATGTATGTTT
16107676 GCTACGAAGA
Statistics
Matches: 92, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
123 80 0.87
124 12 0.13
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.44
Consensus pattern (124 bp):
TAATTGTATAAATTATATAAATATGTTAGCCGAATGTATGCTTTAAGTTTGATAAGTTGAAACTA
ATTGTATGAATTATAAATATGTTAGCCGAATGTATGTTTTGAGTTCTATGAGTTGAAAC
Found at i:16124142 original size:22 final size:21
Alignment explanation
Indices: 16124105--16124188 Score: 73
Period size: 22 Copynumber: 3.9 Consensus size: 21
16124095 ATTAGCAGAT
*
16124105 TTTATCTATACG-ATTAGTGG
1 TTTATCCATACGTATTAGTGG
*
16124125 TTTATCCATAGCGTATTAGTAGTT
1 TTTATCCATA-CGTATTAGT-G-G
*
16124149 TTTATCTATAC-TAATTAGTGG
1 TTTATCCATACGT-ATTAGTGG
*
16124170 TTTATCCACACTGTATTAG
1 TTTATCCATAC-GTATTAG
16124189 CAGCTTTTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
20 9 0.18
21 11 0.22
22 13 0.25
23 9 0.18
24 9 0.18
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.45
Consensus pattern (21 bp):
TTTATCCATACGTATTAGTGG
Found at i:16124186 original size:45 final size:44
Alignment explanation
Indices: 16124074--16124200 Score: 150
Period size: 44 Copynumber: 2.9 Consensus size: 44
16124064 TCTTCACCGT
* * *
16124074 TTAGTGGTTAATCCAC-GTCGTATTAGCAGATTTTATCTATACGA
1 TTAGTGGTTTATCCACACT-GTATTAGCAGATTTTATCTATACAA
* * *
16124118 TTAGTGGTTTATCCATAGC-GTATTAGTAGTTTTTATCTATACTAA
1 TTAGTGGTTTATCCACA-CTGTATTAGCAGATTTTATCTATAC-AA
*
16124163 TTAGTGGTTTATCCACACTGTATTAGCAGCTTTTATCT
1 TTAGTGGTTTATCCACACTGTATTAGCAGATTTTATCT
16124201 GCAACATTTA
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
44 36 0.51
45 34 0.49
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.43
Consensus pattern (44 bp):
TTAGTGGTTTATCCACACTGTATTAGCAGATTTTATCTATACAA
Found at i:16124212 original size:45 final size:45
Alignment explanation
Indices: 16124073--16124225 Score: 145
Period size: 45 Copynumber: 3.4 Consensus size: 45
16124063 GTCTTCACCG
* *
16124073 TTTAGTGGTTAATCCAC-GTCGTATTAGCAGATTTTATCTATACGA
1 TTTAGTGGTTTATCCACACT-GTATTAGCAGATTTTATCTATACGA
* * * *
16124118 -TTAGTGGTTTATCCATAGC-GTATTAGTAGTTTTTATCTATACTA
1 TTTAGTGGTTTATCCACA-CTGTATTAGCAGATTTTATCTATACGA
* *
16124162 ATTAGTGGTTTATCCACACTGTATTAGCAGCTTTTATCTGCA-AC-A
1 TTTAGTGGTTTATCCACACTGTATTAGCAGATTTTATCT--ATACGA
* *
16124207 TTTAGTGGTTCATCTACAC
1 TTTAGTGGTTTATCCACAC
16124226 CGTGGTGTAA
Statistics
Matches: 90, Mismatches: 12, Indels: 12
0.79 0.11 0.11
Matches are distributed among these distances:
44 37 0.41
45 50 0.56
46 2 0.02
47 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.42
Consensus pattern (45 bp):
TTTAGTGGTTTATCCACACTGTATTAGCAGATTTTATCTATACGA
Found at i:16128349 original size:4 final size:4
Alignment explanation
Indices: 16128342--16128369 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
16128332 AGTAATTCTA
16128342 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
16128370 CAGTGGTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:16129665 original size:14 final size:13
Alignment explanation
Indices: 16129641--16129670 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
16129631 TATTTATAGA
16129641 TTTAAAATTTAAT
1 TTTAAAATTTAAT
16129654 TTTAAGAATTTAAT
1 TTTAA-AATTTAAT
16129668 TTT
1 TTT
16129671 TGTATTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (13 bp):
TTTAAAATTTAAT
Found at i:16135369 original size:23 final size:23
Alignment explanation
Indices: 16135343--16135387 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
16135333 TATTAGTTAA
*
16135343 AAGGCTTATA-TGGTAAATTAACC
1 AAGGCTTAAAGTGG-AAATTAACC
*
16135366 AAGGTTTAAAGTGGAAATTAAC
1 AAGGCTTAAAGTGGAAATTAAC
16135388 TACTTTTTAA
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:0.42, C:0.09, G:0.20, T:0.29
Consensus pattern (23 bp):
AAGGCTTAAAGTGGAAATTAACC
Found at i:16136570 original size:22 final size:22
Alignment explanation
Indices: 16136545--16136638 Score: 86
Period size: 22 Copynumber: 4.3 Consensus size: 22
16136535 GGATCTCTGA
16136545 TTAGCACTTCAGTGCTCTCTAT
1 TTAGCACTTCAGTGCTCTCTAT
* * *
16136567 TTAGCACTTTTA-TGCTTTCTAA
1 TTAGCAC-TTCAGTGCTCTCTAT
*
16136589 TTATCACTTCTAG-GCTCTCTAAT
1 TTAGCACTTC-AGTGCTCTCT-AT
**
16136612 TT-GCACTTTTGTGCTCTCTAT
1 TTAGCACTTCAGTGCTCTCTAT
16136633 TTAGCA
1 TTAGCA
16136639 TTTATGTACT
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
21 7 0.12
22 43 0.77
23 6 0.11
ACGTcount: A:0.19, C:0.23, G:0.12, T:0.46
Consensus pattern (22 bp):
TTAGCACTTCAGTGCTCTCTAT
Found at i:16136606 original size:44 final size:44
Alignment explanation
Indices: 16136538--16136663 Score: 125
Period size: 44 Copynumber: 2.9 Consensus size: 44
16136528 TGAAATTGGA
*
16136538 TCTCTGATTAGCACTTCAGTGCTCTCT-ATTTAGCACTTTTATGC
1 TCTCTAATTAGCACTTCAGTGCTCTCTAATTT-GCACTTTTATGC
* * *
16136582 TTTCTAATTATCACTTCTAG-GCTCTCTAATTTGCACTTTTGTGC
1 TCTCTAATTAGCACTTC-AGTGCTCTCTAATTTGCACTTTTATGC
* * * *
16136626 TCTCTATTTAGCA-TTTATGTACTCTCTGA-TTGCACTTT
1 TCTCTAATTAGCACTTCA-GTGCTCTCTAATTTGCACTTT
16136664 GGTGCCTTTG
Statistics
Matches: 68, Mismatches: 10, Indels: 9
0.78 0.11 0.10
Matches are distributed among these distances:
42 1 0.01
43 12 0.18
44 49 0.72
45 6 0.09
ACGTcount: A:0.18, C:0.23, G:0.12, T:0.47
Consensus pattern (44 bp):
TCTCTAATTAGCACTTCAGTGCTCTCTAATTTGCACTTTTATGC
Found at i:16136650 original size:22 final size:22
Alignment explanation
Indices: 16136603--16136663 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
16136593 CACTTCTAGG
*
16136603 CTCTCTAATTTGCACTTTTGTG
1 CTCTCTAATTTGCACTTTTGTA
16136625 CTCTCT-ATTTAGCA-TTTATGTA
1 CTCTCTAATTT-GCACTTT-TGTA
*
16136647 CTCTCTGA-TTGCACTTT
1 CTCTCTAATTTGCACTTT
16136664 GGTGCCTTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
21 10 0.29
22 23 0.68
23 1 0.03
ACGTcount: A:0.16, C:0.23, G:0.11, T:0.49
Consensus pattern (22 bp):
CTCTCTAATTTGCACTTTTGTA
Found at i:16136677 original size:20 final size:20
Alignment explanation
Indices: 16136649--16136753 Score: 129
Period size: 20 Copynumber: 5.2 Consensus size: 20
16136639 TTTATGTACT
* *
16136649 CTCTGATTGCACTTTGGTGC
1 CTCTGATTGCACTTCGATGC
* * *
16136669 CTTTGATTGTACTTCGACGC
1 CTCTGATTGCACTTCGATGC
16136689 CTCTGATTGCACTTCGATGC
1 CTCTGATTGCACTTCGATGC
* * *
16136709 CTTTGATTGTACTTCGCTGC
1 CTCTGATTGCACTTCGATGC
*
16136729 CTCTGATTGCACTTCGGTGC
1 CTCTGATTGCACTTCGATGC
16136749 CTCTG
1 CTCTG
16136754 TTCAGCAATA
Statistics
Matches: 71, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 71 1.00
ACGTcount: A:0.11, C:0.28, G:0.22, T:0.39
Consensus pattern (20 bp):
CTCTGATTGCACTTCGATGC
Found at i:16136697 original size:40 final size:40
Alignment explanation
Indices: 16136649--16136750 Score: 170
Period size: 40 Copynumber: 2.5 Consensus size: 40
16136639 TTTATGTACT
*
16136649 CTCTGATTGCACTTTGGTGCCTTTGATTGTACTTCGAC-GC
1 CTCTGATTGCACTTCGGTGCCTTTGATTGTACTTCG-CTGC
*
16136689 CTCTGATTGCACTTCGATGCCTTTGATTGTACTTCGCTGC
1 CTCTGATTGCACTTCGGTGCCTTTGATTGTACTTCGCTGC
16136729 CTCTGATTGCACTTCGGTGCCT
1 CTCTGATTGCACTTCGGTGCCT
16136751 CTGTTCAGCA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
39 1 0.02
40 57 0.98
ACGTcount: A:0.12, C:0.27, G:0.22, T:0.39
Consensus pattern (40 bp):
CTCTGATTGCACTTCGGTGCCTTTGATTGTACTTCGCTGC
Found at i:16142584 original size:22 final size:21
Alignment explanation
Indices: 16142558--16142608 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
16142548 ACAATTTCAA
16142558 ATATTCAATCAATTCAAAACAT
1 ATATTCAATCAATTCAAAA-AT
* *
16142580 ATATT-ATTTCAATTCACAAAT
1 ATATTCA-ATCAATTCAAAAAT
16142601 A-ATTCAAT
1 ATATTCAAT
16142609 ATCATTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
20 4 0.17
21 5 0.21
22 15 0.62
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (21 bp):
ATATTCAATCAATTCAAAAAT
Found at i:16143411 original size:35 final size:34
Alignment explanation
Indices: 16143363--16143429 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 34
16143353 CGTGGTTCTC
* *
16143363 TTTCTTTTTCTTCTTTCTCTT-TTTCTTTCTCAAA
1 TTTCTTTTGCTTCTCTCT-TTCTTTCTTTCTCAAA
*
16143397 TTTCGTTTTGCTTCTCTGTTTCTTTCTTTCTCA
1 TTTC-TTTTGCTTCTCTCTTTCTTTCTTTCTCA
16143430 TTTCTATTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 6 0.21
35 22 0.79
ACGTcount: A:0.06, C:0.24, G:0.04, T:0.66
Consensus pattern (34 bp):
TTTCTTTTGCTTCTCTCTTTCTTTCTTTCTCAAA
Found at i:16143482 original size:24 final size:24
Alignment explanation
Indices: 16143452--16143502 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 24
16143442 CTTTTGTTAT
*
16143452 ATATATATATATAATAATATAGTATA
1 ATATAT-TA-ATAATAATATAATATA
16143478 ATATATTAATAATAATATAATATA
1 ATATATTAATAATAATATAATATA
16143502 A
1 A
16143503 AAACATACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 2 0.08
26 6 0.25
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (24 bp):
ATATATTAATAATAATATAATATA
Found at i:16143540 original size:10 final size:10
Alignment explanation
Indices: 16143450--16143540 Score: 50
Period size: 10 Copynumber: 9.0 Consensus size: 10
16143440 TTCTTTTGTT
16143450 ATATATATATA
1 ATATA-ATATA
16143461 TATAATAATATA
1 -AT-ATAATATA
*
16143473 GTATAATAT-
1 ATATAATATA
16143482 AT-TAATAATA
1 ATATAAT-ATA
16143492 ATATAATATA
1 ATATAATATA
*
16143502 A-A-AACATA
1 ATATAATATA
*
16143510 CTTATTAAT-TA
1 -ATA-TAATATA
16143521 AGTA-AATATA
1 A-TATAATATA
16143531 ATATAATATA
1 ATATAATATA
16143541 TATTTTAAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 24
0.67 0.07 0.26
Matches are distributed among these distances:
8 9 0.15
9 9 0.15
10 23 0.37
11 9 0.15
12 9 0.15
13 3 0.05
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (10 bp):
ATATAATATA
Found at i:16148239 original size:68 final size:66
Alignment explanation
Indices: 16148140--16148363 Score: 215
Period size: 68 Copynumber: 3.3 Consensus size: 66
16148130 ATAGCCGAGC
* *
16148140 CATGGTCTTACACAGTCTG-AA-CCCATGTTTAACCTCATAGCAGACTCTATTGGTTGCCATAG-
1 CATGGTCTTACAC-CT-TGTAACCCCATGTTTAACATCAT-GCAGACTCTATTGGTTGCCATAGC
*
16148202 TCGAG
63 T-AAG
** * * *
16148207 TTGTGGTCTTACACCTTGTAACCCCATATTTAACATCATGTCTGACTCTATTGGTTACCATAGCT
1 -CATGGTCTTACACCTTGTAACCCCATGTTTAACATCATG-CAGACTCTATTGGTTGCCATAGCT
16148272 AAG
64 AAG
* * * *
16148275 CATGGTCTTACACCTTGTAACCCCATGTTTAACATCCTTGCGGACTTTATTGGTTG-CATTAGCC
1 CATGGTCTTACACCTTGTAACCCCATGTTTAACAT-CATGCAGACTCTATTGGTTGCCA-TAGCT
16148339 AAG
64 AAG
*
16148342 CTAAGGTCTTACACCTTG-AACC
1 C-ATGGTCTTACACCTTGTAACC
16148364 TTTTTTGAGG
Statistics
Matches: 132, Mismatches: 17, Indels: 15
0.80 0.10 0.09
Matches are distributed among these distances:
66 4 0.03
67 61 0.46
68 66 0.50
69 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (66 bp):
CATGGTCTTACACCTTGTAACCCCATGTTTAACATCATGCAGACTCTATTGGTTGCCATAGCTAA
G
Found at i:16151552 original size:27 final size:28
Alignment explanation
Indices: 16151522--16151576 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
16151512 TCGAAATTCA
*
16151522 CACTTTAATTA-TAAAATAATTAATTTT
1 CACTTAAATTATTAAAATAATTAATTTT
* *
16151549 CACTTAAATTATTAACATATTTAATTTT
1 CACTTAAATTATTAAAATAATTAATTTT
16151577 AATTAGTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 10 0.42
28 14 0.58
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (28 bp):
CACTTAAATTATTAAAATAATTAATTTT
Found at i:16154172 original size:59 final size:59
Alignment explanation
Indices: 16154080--16154193 Score: 192
Period size: 59 Copynumber: 1.9 Consensus size: 59
16154070 CATTGAGTCA
16154080 AATGGCTTAAAAGTTTCTCATAGGGTTCTTGTTGTAATGAGAGGACAAAAAAGGGTAGT
1 AATGGCTTAAAAGTTTCTCATAGGGTTCTTGTTGTAATGAGAGGACAAAAAAGGGTAGT
* * * *
16154139 AATGGCTTAAGAGTTTCTCGTAGGGTTCTTGTTGTGATGAGAGGGCAAAAAAGGG
1 AATGGCTTAAAAGTTTCTCATAGGGTTCTTGTTGTAATGAGAGGACAAAAAAGGG
16154194 CACTCTACAC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 51 1.00
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.30
Consensus pattern (59 bp):
AATGGCTTAAAAGTTTCTCATAGGGTTCTTGTTGTAATGAGAGGACAAAAAAGGGTAGT
Found at i:16165600 original size:21 final size:20
Alignment explanation
Indices: 16165557--16165600 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
16165547 ACTTAAGTAA
16165557 ATTTTGTTACATTTTTAGGAT
1 ATTTTGTTACATTTTTA-GAT
16165578 ATTTTGGTTAGCATTTTTA-AT
1 ATTTT-GTTA-CATTTTTAGAT
16165599 AT
1 AT
16165601 GGCATTAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 9 0.43
22 4 0.19
23 8 0.38
ACGTcount: A:0.25, C:0.05, G:0.14, T:0.57
Consensus pattern (20 bp):
ATTTTGTTACATTTTTAGAT
Found at i:16165817 original size:6 final size:6
Alignment explanation
Indices: 16165806--16165831 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
16165796 TAGCAGTCCC
16165806 AATTCA AATTCA AATTCA AATTCA AA
1 AATTCA AATTCA AATTCA AATTCA AA
16165832 CTTGTACCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (6 bp):
AATTCA
Found at i:16175194 original size:3 final size:3
Alignment explanation
Indices: 16175186--16175217 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
16175176 CATAGTTATA
16175186 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
16175218 GGAAAAGCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:16189522 original size:39 final size:39
Alignment explanation
Indices: 16189461--16189538 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
16189451 GTTGGTTTGC
** * *
16189461 CATATGTTCTTACTTATATAATGATTTGCTACTTTTTTT
1 CATATGTTCTTAAATATATAATGATTTACTACTGTTTTT
* *
16189500 CATATGTTCTTAAATATCTAATGTTTTACTACTGTTTTT
1 CATATGTTCTTAAATATATAATGATTTACTACTGTTTTT
16189539 AAGTGTAGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.24, C:0.13, G:0.08, T:0.55
Consensus pattern (39 bp):
CATATGTTCTTAAATATATAATGATTTACTACTGTTTTT
Found at i:16189586 original size:108 final size:109
Alignment explanation
Indices: 16189396--16189600 Score: 306
Period size: 108 Copynumber: 1.9 Consensus size: 109
16189386 CTCATTTTAA
* * * * *
16189396 GTTCTTAAATATCTACTGTTTGGCTAGTTTTTTATAAGTGTTGTTTTGGTCAAGTGTTGGTTTGC
1 GTTCTTAAATATCTAATGTTTGACTACTGTTTTATAAGTGTAGTTTTGGTCAAGTGTTGGTTTGC
*
16189461 CATATGTTCTTACTTATATAATGATTTGCTACTTTTTTTCATAT
66 CATATGTCCTTACTTATATAATGATTTGCTACTTTTTTTCATAT
* * *
16189505 GTTCTTAAATATCTAATGTTTTACTACTGTTTT-TAAGTGTAGTTTTGGTTATA-TGTTGGTTTT
1 GTTCTTAAATATCTAATGTTTGACTACTGTTTTATAAGTGTAGTTTTGGTCA-AGTGTTGGTTTG
16189568 CCATATGTCCTTACTTATATAATGATTTGCTAC
65 CCATATGTCCTTACTTATATAATGATTTGCTAC
16189601 CATTTTAAAT
Statistics
Matches: 86, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
108 57 0.66
109 29 0.34
ACGTcount: A:0.21, C:0.11, G:0.16, T:0.52
Consensus pattern (109 bp):
GTTCTTAAATATCTAATGTTTGACTACTGTTTTATAAGTGTAGTTTTGGTCAAGTGTTGGTTTGC
CATATGTCCTTACTTATATAATGATTTGCTACTTTTTTTCATAT
Found at i:16189725 original size:69 final size:69
Alignment explanation
Indices: 16189646--16189890 Score: 264
Period size: 69 Copynumber: 3.6 Consensus size: 69
16189636 AAAATTTCAC
*
16189646 ATGTTCTTAAATATCTAATATTTTGCTATTGTTTTTAAGTCTTGTTTTAGTTAAGTGTTAGTTTG
1 ATGTTCTTAAATATCTAATATTTTGCTACTGTTTTTAAGTCTTGTTTTAGTTAAGTGTTAGTTTG
16189711 TCAT
66 TCAT
* * * * ** * *** *
16189715 ATGTTCTTAAATATCTACT-TTTTGGCTACTGTTTGTAA-AC-TGTTGTAACATATGTCAAAATT
1 ATGTTCTTAAATATCTAATATTTT-GCTACTGTTTTTAAGTCTTGTT-TTAGTTAAGTGTTAGTT
*
16189777 T-TCTT
64 TGTCAT
* * * * *
16189782 ATGTTCTCAAATATCTAATGTTTTGCTACTGTTTCTAAGTCTTGTTTTAGTTGAGTGTTGGTTTG
1 ATGTTCTTAAATATCTAATATTTTGCTACTGTTTTTAAGTCTTGTTTTAGTTAAGTGTTAGTTTG
*
16189847 CCAT
66 TCAT
*
16189851 ATGTTCTTAAATATCTAAGATTTTGCTACTGTTTTTAAGT
1 ATGTTCTTAAATATCTAATATTTTGCTACTGTTTTTAAGT
16189891 GTAACATACT
Statistics
Matches: 137, Mismatches: 33, Indels: 12
0.75 0.18 0.07
Matches are distributed among these distances:
67 37 0.27
68 28 0.20
69 72 0.53
ACGTcount: A:0.24, C:0.11, G:0.15, T:0.51
Consensus pattern (69 bp):
ATGTTCTTAAATATCTAATATTTTGCTACTGTTTTTAAGTCTTGTTTTAGTTAAGTGTTAGTTTG
TCAT
Found at i:16189807 original size:136 final size:136
Alignment explanation
Indices: 16189622--16189884 Score: 393
Period size: 136 Copynumber: 1.9 Consensus size: 136
16189612 TGTTTTAAAG
* * *
16189622 TGTAACATATGCCAAAAATTTCACATGTTCTTAAATATCTAATATTTTGCTATTGTTTTTAAGTC
1 TGTAACATATGCCAAAAATTTCACATGTTCTCAAATATCTAATATTTTGCTACTGTTTCTAAGTC
* *
16189687 TTGTTTTAGTTAAGTGTTAGTTTGTCATATGTTCTTAAATATCT-ACTTTTTGGCTACTGTTTGT
66 TTGTTTTAGTTAAGTGTTAGTTTGCCATATGTTCTTAAATATCTAACATTTT-GCTACTGTTTGT
16189751 AAACTGT
130 AAACTGT
* * ** *
16189758 TGTAACATATGTCAAAATTTTCTTATGTTCTCAAATATCTAATGTTTTGCTACTGTTTCTAAGTC
1 TGTAACATATGCCAAAAATTTCACATGTTCTCAAATATCTAATATTTTGCTACTGTTTCTAAGTC
* * *
16189823 TTGTTTTAGTTGAGTGTTGGTTTGCCATATGTTCTTAAATATCTAAGATTTTGCTACTGTTT
66 TTGTTTTAGTTAAGTGTTAGTTTGCCATATGTTCTTAAATATCTAACATTTTGCTACTGTTT
16189885 TTAAGTGTAA
Statistics
Matches: 113, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
136 108 0.96
137 5 0.04
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (136 bp):
TGTAACATATGCCAAAAATTTCACATGTTCTCAAATATCTAATATTTTGCTACTGTTTCTAAGTC
TTGTTTTAGTTAAGTGTTAGTTTGCCATATGTTCTTAAATATCTAACATTTTGCTACTGTTTGTA
AACTGT
Found at i:16195737 original size:9 final size:9
Alignment explanation
Indices: 16195723--16195753 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
16195713 GTTAAATGAA
16195723 TCGAGTTAT
1 TCGAGTTAT
*
16195732 TCGAGTTAA
1 TCGAGTTAT
16195741 TCGAGTTAT
1 TCGAGTTAT
16195750 TCGA
1 TCGA
16195754 ATCAACTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:16195823 original size:9 final size:9
Alignment explanation
Indices: 16195809--16195833 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
16195799 GTTTTCGAAT
16195809 TCGAATAAC
1 TCGAATAAC
16195818 TCGAATAAC
1 TCGAATAAC
16195827 TCGAATA
1 TCGAATA
16195834 TCAAACTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.20, G:0.12, T:0.24
Consensus pattern (9 bp):
TCGAATAAC
Found at i:16197423 original size:15 final size:15
Alignment explanation
Indices: 16197403--16197440 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
16197393 TATATACTTG
16197403 TATATATATTTTATA
1 TATATATATTTTATA
16197418 TATATAGT-TTTTATA
1 TATATA-TATTTTATA
*
16197433 TACATATA
1 TATATATA
16197441 CGTATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
14 1 0.05
15 18 0.90
16 1 0.05
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (15 bp):
TATATATATTTTATA
Found at i:16202366 original size:6 final size:5
Alignment explanation
Indices: 16202281--16202364 Score: 100
Period size: 5 Copynumber: 16.8 Consensus size: 5
16202271 AAAGAATGTT
* * *
16202281 AAAA- AAAAC AAAAA AAAAT AAAAG AAAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG
*
16202331 AAAAG AAAAG AAGA- AAAAG AAAAG AAAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG -AAAAG AAAA
16202365 AGTAGAGGCC
Statistics
Matches: 71, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
4 7 0.10
5 54 0.76
6 10 0.14
ACGTcount: A:0.83, C:0.01, G:0.14, T:0.01
Consensus pattern (5 bp):
AAAAG
Found at i:16203899 original size:44 final size:43
Alignment explanation
Indices: 16203794--16203941 Score: 136
Period size: 44 Copynumber: 3.4 Consensus size: 43
16203784 TATCAAACAT
* * * * * *
16203794 TATCTCTCTGAAGTTGTAGTAGAGTAGGTTGAA-ATAACAAACC
1 TATCTCTCTAAAGTTGCAGTGGAGCAGGTTGAAGAT-ATAATCC
* * *
16203837 TTATCCCTCTAAAATTGCAGTGGGGCAGGTTGAAGATATAATTCC
1 -TATCTCTCTAAAGTTGCAGTGGAGCAGGTTGAAGATATAA-TCC
* * *
16203882 TATCTCTCTGAAGTTGCAGTGGAGCAGGCTGAAGCTACTAATCC
1 TATCTCTCTAAAGTTGCAGTGGAGCAGGTTGAAGATA-TAATCC
*
16203926 TATCTCCCTAAAGTTG
1 TATCTCTCTAAAGTTG
16203942 TATTGAAGCG
Statistics
Matches: 84, Mismatches: 17, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
44 77 0.92
45 7 0.08
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (43 bp):
TATCTCTCTAAAGTTGCAGTGGAGCAGGTTGAAGATATAATCC
Found at i:16204143 original size:45 final size:45
Alignment explanation
Indices: 16204059--16204144 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
16204049 TTGAAGCAAT
*
16204059 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACATCA
1 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAACATCA
* * *
16204104 AAGTCTTATTTCCCTGACGTTGCAGTGGAGCAGGCTAAAAC
1 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAAC
16204145 CACAAATCTC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (45 bp):
AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAACATCA
Found at i:16206276 original size:19 final size:19
Alignment explanation
Indices: 16206247--16206283 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
16206237 TACATAATTG
16206247 TTTTGTTTTATTT-TTTTA
1 TTTTGTTTTATTTGTTTTA
16206265 TTTTGTTTTTATTTGTTTT
1 TTTTG-TTTTATTTGTTTT
16206284 TGCTCGTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 8 0.47
20 4 0.24
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.84
Consensus pattern (19 bp):
TTTTGTTTTATTTGTTTTA
Found at i:16209445 original size:16 final size:17
Alignment explanation
Indices: 16209410--16209446 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
16209400 CTAATCCCCT
16209410 TTTC-TTCTTCTTCTTC
1 TTTCATTCTTCTTCTTC
16209426 -TTCATTCTTCTT-TTC
1 TTTCATTCTTCTTCTTC
16209441 TTTCAT
1 TTTCAT
16209447 CAATTTATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.05, C:0.27, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTCATTCTTCTTCTTC
Found at i:16211917 original size:30 final size:30
Alignment explanation
Indices: 16211883--16211975 Score: 159
Period size: 30 Copynumber: 3.1 Consensus size: 30
16211873 ACTTATTTTA
* *
16211883 TTGTTAATTTTGTTATAATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
16211913 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
*
16211943 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
16211973 TTG
1 TTG
16211976 CTTGTTAAGT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.27, C:0.03, G:0.14, T:0.56
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:16217636 original size:28 final size:27
Alignment explanation
Indices: 16217575--16217636 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 27
16217565 AGAAAATCGA
*
16217575 TTAAT-TTTAGTTTTGATATTTTTATT
1 TTAATATTTAGTTTTGATATTTTAATT
*
16217601 ATAGATATTTAAGTTTT-ATATTTTAATTT
1 TTA-ATATTT-AGTTTTGATATTTTAA-TT
16217630 TTAATAT
1 TTAATAT
16217637 AGCTTTACCT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
26 2 0.07
27 2 0.07
28 15 0.52
29 10 0.34
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (27 bp):
TTAATATTTAGTTTTGATATTTTAATT
Found at i:16219582 original size:28 final size:27
Alignment explanation
Indices: 16219521--16219582 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 27
16219511 AGAAAATCGA
*
16219521 TTAAT-TTTAGTTTTGATATTTTTATT
1 TTAATATTTAGTTTTGATATTTTAATT
*
16219547 ATAGATATTTAAGTTTT-ATATTTTAATTT
1 TTA-ATATTT-AGTTTTGATATTTTAA-TT
16219576 TTAATAT
1 TTAATAT
16219583 AGCTTTACCT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
26 2 0.07
27 2 0.07
28 15 0.52
29 10 0.34
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (27 bp):
TTAATATTTAGTTTTGATATTTTAATT
Found at i:16222538 original size:33 final size:33
Alignment explanation
Indices: 16222494--16222564 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
16222484 CATGATGGAG
*
16222494 GACTGTTGTGGGGCAGGTGAA-GAGGACATATGT
1 GACTGTAGTGGGGCAGGTGAAGGA-GACATATGT
* *
16222527 GACTGTAGTGGGGCAGGTTAAGGAGACCTATGT
1 GACTGTAGTGGGGCAGGTGAAGGAGACATATGT
16222560 GACTG
1 GACTG
16222565 AGATACAGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 32 0.94
34 2 0.06
ACGTcount: A:0.24, C:0.11, G:0.41, T:0.24
Consensus pattern (33 bp):
GACTGTAGTGGGGCAGGTGAAGGAGACATATGT
Found at i:16225143 original size:2 final size:2
Alignment explanation
Indices: 16225136--16225162 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16225126 TATAGGTTCT
16225136 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
16225163 TGTTTCTTTT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:16229957 original size:55 final size:53
Alignment explanation
Indices: 16229882--16230021 Score: 163
Period size: 55 Copynumber: 2.6 Consensus size: 53
16229872 ACACGAAAAA
* ** * *
16229882 TTTTTAAAACACGAGGATTTTAGAAACACGAAAATTCTTAAAAACACAAGGATTT
1 TTTTTGAAACACGAAAATTTTTGAAACACGAAAATT-TTAAAAACAC-AGGAATT
* * *
16229937 TTTTTGAAACACGAAAATTTTTGAAAACACGGAAATTTTTAAAACACGGGAATT
1 TTTTTGAAACACGAAAATTTTTG-AAACACGAAAATTTTAAAAACACAGGAATT
* *
16229991 TTTTGGAAACATGAAAATTTTTGAAACACGA
1 TTTTTGAAACACGAAAATTTTTGAAACACGA
16230022 TTAGTTTTTT
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
53 7 0.10
54 26 0.36
55 28 0.38
56 12 0.16
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (53 bp):
TTTTTGAAACACGAAAATTTTTGAAACACGAAAATTTTAAAAACACAGGAATT
Found at i:16229994 original size:18 final size:18
Alignment explanation
Indices: 16229936--16229994 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
16229926 CACAAGGATT
* **
16229936 TTTTTTGAAACACGAAAA
1 TTTTTTAAAACACGGGAA
*
16229954 TTTTTGAAAACAC-GGAA
1 TTTTTTAAAACACGGGAA
*
16229971 ATTTTTAAAACACGGGAA
1 TTTTTTAAAACACGGGAA
16229989 TTTTTT
1 TTTTTT
16229995 GGAAACATGA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
17 13 0.39
18 20 0.61
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (18 bp):
TTTTTTAAAACACGGGAA
Found at i:16230011 original size:18 final size:17
Alignment explanation
Indices: 16229822--16230021 Score: 114
Period size: 17 Copynumber: 11.2 Consensus size: 17
16229812 CGATCAAAAT
* *
16229822 ACGAAATTTTTTTAAAC
1 ACGAAAATTTTTGAAAC
* *
16229839 ACGAAGATTTTTGAAAT
1 ACGAAAATTTTTGAAAC
*** **
16229856 AATTATTTTTTTGAGAAC
1 ACGAAAATTTTTGA-AAC
*
16229874 ACGAAAAATTTTTAAAAC
1 ACG-AAAATTTTTGAAAC
** *
16229892 ACGAGGATTTTAGAAAC
1 ACGAAAATTTTTGAAAC
**
16229909 ACGAAAATTCTTAAAAAC
1 ACGAAAATT-TTTGAAAC
*
16229927 AC-AAGGATTTTTTTTGAAAC
1 ACGAA--A--ATTTTTGAAAC
16229947 ACGAAAATTTTTGAAAAC
1 ACGAAAATTTTTG-AAAC
* *
16229965 ACGGAAATTTTTAAAAC
1 ACGAAAATTTTTGAAAC
* *
16229982 ACGGGAATTTTTTGGAAAC
1 AC-GAAAATTTTT-GAAAC
*
16230001 ATGAAAATTTTTGAAAC
1 ACGAAAATTTTTGAAAC
16230018 ACGA
1 ACGA
16230022 TTAGTTTTTT
Statistics
Matches: 137, Mismatches: 35, Indels: 22
0.71 0.18 0.11
Matches are distributed among these distances:
17 61 0.45
18 50 0.36
19 14 0.10
20 8 0.06
21 4 0.03
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (17 bp):
ACGAAAATTTTTGAAAC
Found at i:16230030 original size:36 final size:35
Alignment explanation
Indices: 16229863--16230021 Score: 133
Period size: 36 Copynumber: 4.4 Consensus size: 35
16229853 AATAATTATT
**
16229863 TTTTTGAGAACACGAAAAATTTTT-AAAACACGAGGA
1 TTTTTGA-AACACG-AAAATTTTTGAAAACACGAAAA
* * * *
16229899 TTTTAGAAACACGAAAATTCTTAAAAACAC-AAGGATTT
1 TTTTTGAAACACGAAAATTTTTGAAAACACGAA--A--A
*
16229937 TTTTTGAAACACGAAAATTTTTGAAAACACGGAAA
1 TTTTTGAAACACGAAAATTTTTGAAAACACGAAAA
* * * * *
16229972 TTTTTAAAACACGGGAATTTTTTGGAAACATGAAAA
1 TTTTTGAAACAC-GAAAATTTTTGAAAACACGAAAA
16230008 TTTTTGAAACACGA
1 TTTTTGAAACACGA
16230022 TTAGTTTTTT
Statistics
Matches: 98, Mismatches: 18, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
34 9 0.09
35 25 0.26
36 35 0.36
37 1 0.01
38 27 0.28
39 1 0.01
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.30
Consensus pattern (35 bp):
TTTTTGAAACACGAAAATTTTTGAAAACACGAAAA
Found at i:16230337 original size:5 final size:5
Alignment explanation
Indices: 16230327--16230371 Score: 54
Period size: 5 Copynumber: 8.4 Consensus size: 5
16230317 AATTTTAACG
*
16230327 AATAA AATAA AATAA AATTAA AAAAA ACATAA ATATAA AATAA AA
1 AATAA AATAA AATAA AA-TAA AATAA A-ATAA A-ATAA AATAA AA
16230372 AGATTTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
5 21 0.60
6 14 0.40
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:16230507 original size:18 final size:17
Alignment explanation
Indices: 16230486--16230549 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 17
16230476 GATTTTGGGC
*
16230486 CTTTTCGTTT-TTTTTT
1 CTTTTCTTTTCTTTTTT
16230502 CTCTTTCTTTTCTCTTTTTT
1 CT-TTTC-TTT-TCTTTTTT
16230522 CTTTTTCTTTTCTTTTTT
1 C-TTTTCTTTTCTTTTTT
16230540 CTTTT-TTTTC
1 CTTTTCTTTTC
16230550 AGGTTGGGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
16 7 0.17
17 8 0.19
18 11 0.26
19 4 0.10
20 11 0.26
21 1 0.02
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.80
Consensus pattern (17 bp):
CTTTTCTTTTCTTTTTT
Found at i:16230519 original size:7 final size:6
Alignment explanation
Indices: 16230487--16230545 Score: 59
Period size: 6 Copynumber: 9.7 Consensus size: 6
16230477 ATTTTGGGCC
* *
16230487 TTTTCG TTTT-T TTTTCT CTTTCT TTTCTCTT TTTTCT TTTTC- TTTTCTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTT-TC-T TTTTCT TTTTCT TTTTC-T
16230536 TTTTCT TTTT
1 TTTTCT TTTT
16230546 TTTCAGGTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
5 9 0.20
6 23 0.51
7 9 0.20
8 4 0.09
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (6 bp):
TTTTCT
Found at i:16230519 original size:20 final size:19
Alignment explanation
Indices: 16230495--16230539 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 19
16230485 CCTTTTCGTT
16230495 TTTTTTTCTCTTTCTTTTC
1 TTTTTTTCTCTTTCTTTTC
*
16230514 TCTTTTTTCTTTTTCTTTTC
1 T-TTTTTTCTCTTTCTTTTC
16230534 TTTTTT
1 TTTTTT
16230540 CTTTTTTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTTTCTCTTTCTTTTC
Found at i:16230533 original size:25 final size:25
Alignment explanation
Indices: 16230493--16230548 Score: 87
Period size: 25 Copynumber: 2.2 Consensus size: 25
16230483 GGCCTTTTCG
16230493 TTTTTTTTTCTCTTTCTTTTCTCTT
1 TTTTTTTTTCTCTTTCTTTTCTCTT
*
16230518 TTTTCTTTTTCT-TTTCTTTTTTCTT
1 TTTT-TTTTTCTCTTTCTTTTCTCTT
16230543 TTTTTT
1 TTTTTT
16230549 CAGGTTGGGC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 2 0.07
25 20 0.69
26 7 0.24
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (25 bp):
TTTTTTTTTCTCTTTCTTTTCTCTT
Found at i:16230546 original size:7 final size:7
Alignment explanation
Indices: 16230496--16230546 Score: 56
Period size: 7 Copynumber: 7.9 Consensus size: 7
16230486 CTTTTCGTTT
16230496 TTTTTTC
1 TTTTTTC
*
16230503 -TCTTTC
1 TTTTTTC
*
16230509 TTTTCTC
1 TTTTTTC
16230516 TTTTTTC
1 TTTTTTC
16230523 -TTTTTC
1 TTTTTTC
16230529 --TTTTC
1 TTTTTTC
16230534 TTTTTTC
1 TTTTTTC
16230541 TTTTTT
1 TTTTTT
16230547 TTCAGGTTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
5 5 0.14
6 11 0.30
7 21 0.57
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTTC
Found at i:16230546 original size:20 final size:19
Alignment explanation
Indices: 16230486--16230547 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 19
16230476 GATTTTGGGC
16230486 CTTTTCGTTTTTTTTTCTCTTT
1 CTTTTC-TTTTTTTTT-T-TTT
*
16230508 CTTTTCTCTTTTTTCTTTTT
1 CTTTTCT-TTTTTTTTTTTT
16230528 CTTTTCTTTTTTCTTTTTTT
1 CTTTTCTTTTTT-TTTTTTT
16230548 TCAGGTTGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
19 5 0.14
20 16 0.44
21 2 0.06
22 13 0.36
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.81
Consensus pattern (19 bp):
CTTTTCTTTTTTTTTTTTT
Found at i:16230752 original size:18 final size:18
Alignment explanation
Indices: 16230726--16230767 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
16230716 CCTAATCTGC
* *
16230726 TGGGCCTGCTGGGTGTTG
1 TGGGTCTGCTGGCTGTTG
*
16230744 TGGGTCTGCTGGCTGTTT
1 TGGGTCTGCTGGCTGTTG
16230762 TGGGTC
1 TGGGTC
16230768 GGGTTGCTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.00, C:0.17, G:0.45, T:0.38
Consensus pattern (18 bp):
TGGGTCTGCTGGCTGTTG
Found at i:16230880 original size:10 final size:10
Alignment explanation
Indices: 16230865--16230892 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
16230855 TTTCCCCCCT
16230865 TTCTTCTTCC
1 TTCTTCTTCC
16230875 TTCTTCTTCC
1 TTCTTCTTCC
16230885 TTCTTCTT
1 TTCTTCTT
16230893 TTTTTTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (10 bp):
TTCTTCTTCC
Found at i:16230904 original size:10 final size:10
Alignment explanation
Indices: 16230891--16230920 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
16230881 TTCCTTCTTC
16230891 TTTTTTTTCT
1 TTTTTTTTCT
16230901 TTTTTTTTCT
1 TTTTTTTTCT
*
16230911 TTTTTCTTCT
1 TTTTTTTTCT
16230921 CCTTCGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:16231031 original size:15 final size:16
Alignment explanation
Indices: 16231007--16231050 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
16230997 TCTTCTCCCC
*
16231007 TTTTCCTTTTCTT-CT
1 TTTTCTTTTTCTTCCT
16231022 TTTTCTTTTTCTTCCT
1 TTTTCTTTTTCTTCCT
* *
16231038 TTGTCTTTCTCTT
1 TTTTCTTTTTCTT
16231051 TTATTTTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.00, C:0.25, G:0.02, T:0.73
Consensus pattern (16 bp):
TTTTCTTTTTCTTCCT
Found at i:16231986 original size:74 final size:73
Alignment explanation
Indices: 16231422--16232682 Score: 1302
Period size: 74 Copynumber: 16.6 Consensus size: 73
16231412 GGGCTTAACT
* * * *
16231422 CGAGGCTTAACTCGCCTCTCGCAATATGAGTTGATTTTTGAAAAGCAGAAATTTAAAATACCTCA
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAATACCTCA
16231487 GCGTGCGACC
66 GCGT--GACC
* * * *
16231497 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAGTA-AAAAATGAAAAATACA
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAA--ACAGAAATTAAAAATACC
* *
16231561 TC-GATGTGACT
63 TCAG-CGTGACC
* * *
16231572 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGGAAAACAAAAATTTAAAATACCTCA
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAATACCTCA
16231637 GCGTGCGACC
66 GCGT--GACC
*
16231647 CGAGACTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAAATAC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA-TT--AA-AAATAC
* * *
16231712 ATCGGCATGTG-TC
62 CTCAGC--GTGACC
* * *
16231725 CAAGGCTCAACTCACCTCTCTCATTATGAGTTGATTTTTTGAAAAACAGAAATTGAAAAGAATAC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATT--AAA-AATAC
* * *
16231790 CTCGGCATGCGATC
62 CTCAGC--GTGACC
*
16231804 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAAGAC-GAAATTTAAAAGAAAT
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAA-ACAGAAA-TT--AA-AAAT
*
16231868 ACCTCGGCATGTGACC
60 ACCTCAGC--GTGACC
* * * * *
16231884 TGAGGCTCAACTCACCCCTTGCAGTATGAGTTGATTTTTGAAAAACAGGAATTGAAAAATACCTC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT-AAAAATACCTC
*
16231949 GGCGTGACC
65 AGCGTGACC
*
16231958 CGATGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAAATAC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA-TT--AA-AAATAC
* * **
16232023 CTCGGCATGGTC
62 CTCAGCGTGACC
* *
16232035 CAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGGAAAACAGAAATTTAAAAGAAATAC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA-TT--AA-AAATAC
* * **
16232100 CTCGGCATGGTC
62 CTCAGCGTGACC
*
16232112 CGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTTGAAAAACAGAAATTTAAAAGAAATA
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAA-TT--AA-AAATA
16232177 CCTCAGCGTGACC
61 CCTCAGCGTGACC
* * * *
16232190 CGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTAAAAAAAGACATAAATTAAAAATACC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT--GAAAA-ACAGAAATTAAAAATACC
16232254 TCAGCGTGACC
63 TCAGCGTGACC
* *
16232265 CGAGGCTCAACTCACCTCT-GTACTATGAGTTGATTTTTTGAAAAAAGCAGAAATTTAAAAATAC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTG-AAAAA-CAGAAA-TTAAAAATAC
16232329 CTCAGCGTGACC
62 CTCAGCGTGACC
* * *** * *
16232341 CGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTGAAAAAAAAGACATAAATTACAAATACC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT--TTGAAAA-ACAGAAATTAAAAATACC
16232405 TCAGCGTGACC
63 TCAGCGTGACC
* * * *
16232416 CAAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTAAAAAAGACAGAAATTAAAAATACCT
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-GAAAA-ACAGAAATTAAAAATACCT
16232480 CAGCGTGACC
64 CAGCGTGACC
* * *
16232490 CGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTAAAAAAGACAGAAATTAAAAATACCT
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-GAAAA-ACAGAAATTAAAAATACCT
16232554 CAGCGTGACC
64 CAGCGTGACC
* * *
16232564 CGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTAAAAAAGACAGAAATTAAAAATACCT
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-GAAAA-ACAGAAATTAAAAATACCT
16232628 CAGCGTGACC
64 CAGCGTGACC
* *
16232638 CGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTGTGAAAAA
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT-TGAAAAA
16232683 AAACAGAATT
Statistics
Matches: 1064, Mismatches: 85, Indels: 76
0.87 0.07 0.06
Matches are distributed among these distances:
72 1 0.00
73 18 0.02
74 283 0.27
75 239 0.22
76 102 0.10
77 153 0.14
78 118 0.11
79 93 0.09
80 54 0.05
81 3 0.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (73 bp):
CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAATACCTCA
GCGTGACC
Found at i:16232080 original size:151 final size:148
Alignment explanation
Indices: 16231422--16232682 Score: 1344
Period size: 151 Copynumber: 8.3 Consensus size: 148
16231412 GGGCTTAACT
* * * * *
16231422 CGAGGCTTAACTCGCCTCTCGCAATATGAGTTGATTTTTGAAAAGCAGAAATTTAAAATACCTCA
1 CGAGGCTCAACTCACCTCT-GCATTATGAGTTGATTTTTGAAAAACAGAAATTAAAAATACCTCA
* ** **
16231487 GCGTGCGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAGTA-AAAAAT
65 GCGT--GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTT
* * *
16231551 GAAAAATACATC-G-ATGTGACT
128 AAAAAATACCTCAGCA--TGACC
* * * *
16231572 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGGAAAACAAAAATTTAAAATACCTCA
1 CGAGGCTCAACTCACCTCT-GCATTATGAGTTGATTTTTGAAAAACAGAAATTAAAAATACCTCA
*
16231637 GCGTGCGACCCGAGACTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTT
65 GCGT--GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTT
* * **
16231701 AAAAGAAATACATCGGCATGTGTC
128 -AAA-AAATACCTCAGCATG-ACC
* *
16231725 CAAGGCTCAACTCACCTCTCTCATTATGAGTTGATTTTTTGAAAAACAGAAATTGAAAAGAATAC
1 CGAGGCTCAACTCACCTCT-GCATTATGAGTTGA-TTTTTGAAAAACAGAAATT--AAA-AATAC
* * * *
16231790 CTCGGCATGCGATCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAAGAC-GA
61 CTCAGC--GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAA-ACAGA
*
16231854 AATTTAAAAGAAATACCTCGGCATGTGACC
123 AATTT-AAA-AAATACCTCAGCA--TGACC
* * * *
16231884 TGAGGCTCAACTCACCCCTTGCAGTATGAGTTGATTTTTGAAAAACAGGAATTGAAAAATACCTC
1 CGAGGCTCAACTCACCTC-TGCATTATGAGTTGATTTTTGAAAAACAGAAATT-AAAAATACCTC
* *
16231949 GGCGTGACCCGATGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTTA
64 AGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTT-
* **
16232013 AAAGAAATACCTCGGCATGGTC
128 AAA-AAATACCTCAGCATGACC
* * *
16232035 CAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGGAAAACAGAAATTTAAAAGAAATAC
1 CGAGGCTCAACTCACCTCT-GCATTATGAGTTGATTTTTGAAAAACAGAAA-TT--AA-AAATAC
* * ** *
16232100 CTCGGCATGGTCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTTGAAAAACAGAAAT
61 CTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAAT
*
16232165 TTAAAAGAAATACCTCAGCGTGACC
126 TT-AAA-AAATACCTCAGCATGACC
* * *
16232190 CGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAAGACATAAATTAAAAATACCT
1 CGAGGCTCAACTCACCTCTGCATTATGAGTTGATTTTT--GAAAA-ACAGAAATTAAAAATACCT
* *
16232255 CAGCGTGACCCGAGGCTCAACTCACCTCT-GTACTATGAGTTGATTTTTTGAAAAAAGCAGAAAT
63 CAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG-AAAAA-CAGAAAT
*
16232319 TT-AAAAATACCTCAGCGTGACC
126 TTAAAAAATACCTCAGCATGACC
* *** * *
16232341 CGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTGAAAAAAAAGACATAAATTACAAATACCT
1 CGAGGCTCAACTCACCTCTGCATTATGAGTTGATTT--TTGAAAA-ACAGAAATTAAAAATACCT
* * * **
16232406 CAGCGTGACCCAAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTAAAAAAGACAGAAA-T
63 CAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAA-ACAGAAATT
*
16232469 T-AAAAATACCTCAGCGTGACC
127 TAAAAAATACCTCAGCATGACC
* *
16232490 CGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTAAAAAAGACAGAAATTAAAAATACCTC
1 CGAGGCTCAACTCACCTCTGCATTATGAGTTGATTTTT-GAAAA-ACAGAAATTAAAAATACCTC
* * **
16232555 AGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTAAAAAAGACAGAAA-TT
64 AGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAA-ACAGAAATTT
*
16232618 -AAAAATACCTCAGCGTGACC
128 AAAAAATACCTCAGCATGACC
*
16232638 CGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTGTGAAAAA
1 CGAGGCTCAACTCACCTCTGCATTATGAGTTGATTTT-TGAAAAA
16232683 AAACAGAATT
Statistics
Matches: 995, Mismatches: 83, Indels: 69
0.87 0.07 0.06
Matches are distributed among these distances:
147 1 0.00
148 147 0.15
149 70 0.07
150 117 0.12
151 173 0.17
152 36 0.04
153 106 0.11
154 130 0.13
155 57 0.06
156 18 0.02
157 55 0.06
158 51 0.05
159 31 0.03
160 3 0.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (148 bp):
CGAGGCTCAACTCACCTCTGCATTATGAGTTGATTTTTGAAAAACAGAAATTAAAAATACCTCAG
CGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTTAAA
AAATACCTCAGCATGACC
Found at i:16233568 original size:1 final size:1
Alignment explanation
Indices: 16233558--16233624 Score: 53
Period size: 1 Copynumber: 67.0 Consensus size: 1
16233548 TTCATCTTGA
* * * * * * * * *
16233558 TTTTTCTTTTTCTTTTCTTTTTTGTTTGTTTTTTTGTTTTTTTGTTTTTGTTTTTTTTTGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
16233623 TT
1 TT
16233625 AGGCATAATA
Statistics
Matches: 48, Mismatches: 18, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.87
Consensus pattern (1 bp):
T
Found at i:16233589 original size:16 final size:15
Alignment explanation
Indices: 16233558--16233624 Score: 80
Period size: 16 Copynumber: 4.3 Consensus size: 15
16233548 TTCATCTTGA
* *
16233558 TTTTTCTTTTTCTTT
1 TTTTTTTTTTTGTTT
*
16233573 TCTTTTTTGTTTGTTT
1 T-TTTTTTTTTTGTTT
16233589 TTTTGTTTTTTTGTTT
1 TTTT-TTTTTTTGTTT
16233605 TTGTTTTTTTTTGTTT
1 TT-TTTTTTTTTGTTT
16233621 TTTT
1 TTTT
16233625 AGGCATAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
15 6 0.13
16 37 0.82
17 2 0.04
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.87
Consensus pattern (15 bp):
TTTTTTTTTTTGTTT
Found at i:16233595 original size:8 final size:8
Alignment explanation
Indices: 16233564--16233624 Score: 72
Period size: 8 Copynumber: 7.6 Consensus size: 8
16233554 TTGATTTTTC
*
16233564 TTTTTCTT
1 TTTTTGTT
16233572 TTCTTT-TT
1 TT-TTTGTT
*
16233580 TGTTTGTT
1 TTTTTGTT
16233588 TTTTTGTT
1 TTTTTGTT
16233596 TTTTTGTT
1 TTTTTGTT
16233604 TTTGTT-TT
1 TTT-TTGTT
16233612 TTTTTGTT
1 TTTTTGTT
16233620 TTTTT
1 TTTTT
16233625 AGGCATAATA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
7 5 0.11
8 37 0.79
9 5 0.11
ACGTcount: A:0.00, C:0.03, G:0.10, T:0.87
Consensus pattern (8 bp):
TTTTTGTT
Found at i:16237193 original size:4 final size:4
Alignment explanation
Indices: 16237184--16237214 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
16237174 ATGTACATGT
16237184 AATG AATG AATG AATG AATG AATG -ATG AATG
1 AATG AATG AATG AATG AATG AATG AATG AATG
16237215 TCAGTCATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (4 bp):
AATG
Found at i:16239534 original size:9 final size:9
Alignment explanation
Indices: 16239518--16239566 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
16239508 TTTTCACTTT
16239518 TAATTATAA
1 TAATTATAA
*
16239527 TCATTATAA
1 TAATTATAA
*
16239536 TAATAATAA
1 TAATTATAA
*
16239545 TAATTATAT
1 TAATTATAA
**
16239554 TAACAATAA
1 TAATTATAA
16239563 TAAT
1 TAAT
16239567 AAAATTTTTA
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (9 bp):
TAATTATAA
Found at i:16239544 original size:18 final size:18
Alignment explanation
Indices: 16239518--16239566 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
16239508 TTTTCACTTT
* *
16239518 TAATTATAATCATTATAA
1 TAATAATAATAATTATAA
*
16239536 TAATAATAATAATTATAT
1 TAATAATAATAATTATAA
*
16239554 TAACAATAATAAT
1 TAATAATAATAAT
16239567 AAAATTTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (18 bp):
TAATAATAATAATTATAA
Found at i:16240388 original size:5 final size:5
Alignment explanation
Indices: 16240380--16240422 Score: 86
Period size: 5 Copynumber: 8.6 Consensus size: 5
16240370 TTTTTTTTTT
16240380 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAA
16240423 AGCATAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:16246346 original size:3 final size:3
Alignment explanation
Indices: 16246338--16246378 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
16246328 TAATCATTAA
* * *
16246338 AAT AAT AAT AAT AAT AAT TAT ATT AAC AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
16246379 AATTTTTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:16246351 original size:21 final size:20
Alignment explanation
Indices: 16246322--16246381 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
16246312 TTTTCACTTT
*
16246322 TAATTATAATCATTAAAATAA
1 TAATAATAAT-ATTAAAATAA
* *
16246343 TAATAATAATAATTATATTAA
1 TAATAATAAT-ATTAAAATAA
* *
16246364 CAATAATAATAATAAAAT
1 TAATAATAATATTAAAAT
16246382 TTTTATTCAA
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
20 5 0.16
21 26 0.84
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (20 bp):
TAATAATAATATTAAAATAA
Found at i:16247201 original size:5 final size:5
Alignment explanation
Indices: 16247193--16247237 Score: 81
Period size: 5 Copynumber: 9.0 Consensus size: 5
16247183 TTTTTTACTT
*
16247193 ATATA ATATA ATACA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
16247238 TAAAGCATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:16248262 original size:18 final size:17
Alignment explanation
Indices: 16248120--16248319 Score: 123
Period size: 17 Copynumber: 11.2 Consensus size: 17
16248110 CGATCAAAAT
* *
16248120 ACGAAATTTTTTTAAAC
1 ACGAAAATTTTTGAAAC
* *
16248137 ACGAAGATTTTTGAAAT
1 ACGAAAATTTTTGAAAC
*** **
16248154 AATTATTTTTTTGAGAAC
1 ACGAAAATTTTTGA-AAC
*
16248172 ACGAAAAATTTTTAAAAC
1 ACG-AAAATTTTTGAAAC
** *
16248190 ACGAGGATTTTAGAAAC
1 ACGAAAATTTTTGAAAC
**
16248207 ACGAAAATTCTTAAAAAC
1 ACGAAAATT-TTTGAAAC
*
16248225 AC-AAGGATTTTTTTTGAAAC
1 ACGAA--A--ATTTTTGAAAC
16248245 ACGAAAATTTTTGAAAAC
1 ACGAAAATTTTTG-AAAC
*
16248263 ATGAAAATTTTTGAAAC
1 ACGAAAATTTTTGAAAC
* *
16248280 ACGGGAATTTTTTGGAAAC
1 AC-GAAAATTTTT-GAAAC
*
16248299 ATGAAAATTTTTGAAAC
1 ACGAAAATTTTTGAAAC
16248316 ACGA
1 ACGA
16248320 TTAGTTTTTT
Statistics
Matches: 137, Mismatches: 35, Indels: 22
0.71 0.18 0.11
Matches are distributed among these distances:
17 60 0.44
18 50 0.36
19 15 0.11
20 8 0.06
21 4 0.03
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (17 bp):
ACGAAAATTTTTGAAAC
Found at i:16248328 original size:36 final size:35
Alignment explanation
Indices: 16248122--16248319 Score: 143
Period size: 36 Copynumber: 5.5 Consensus size: 35
16248112 ATCAAAATAC
* * *
16248122 GAAATTTTTTTAAACACGAAGATTTTTGAAATA-AT
1 GAAAATTTTTGAAACACGAAAATTTTTGAAA-ACAT
* ** *
16248157 -TATTTTTTTGAGAACACGAAAAATTTTT-AAAACAC
1 GAAAATTTTTGA-AACACG-AAAATTTTTGAAAACAT
** * * *
16248192 GAGGATTTTAGAAACACGAAAATTCTTAAAAACA-
1 GAAAATTTTTGAAACACGAAAATTTTTGAAAACAT
* *
16248226 CAAGGATTTTTTTTGAAACACGAAAATTTTTGAAAACAT
1 GAA--A--ATTTTTGAAACACGAAAATTTTTGAAAACAT
* * *
16248265 GAAAATTTTTGAAACACGGGAATTTTTTGGAAACAT
1 GAAAATTTTTGAAACAC-GAAAATTTTTGAAAACAT
16248301 GAAAATTTTTGAAACACGA
1 GAAAATTTTTGAAACACGA
16248320 TTAGTTTTTT
Statistics
Matches: 128, Mismatches: 24, Indels: 22
0.74 0.14 0.13
Matches are distributed among these distances:
34 18 0.14
35 35 0.27
36 46 0.36
37 1 0.01
38 26 0.20
39 2 0.02
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (35 bp):
GAAAATTTTTGAAACACGAAAATTTTTGAAAACAT
Found at i:16248635 original size:5 final size:5
Alignment explanation
Indices: 16248625--16248663 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
16248615 GAATTTAATG
*
16248625 AATAA AATAA AATAA AAAAA ACATAA ATATAA AATAA AA
1 AATAA AATAA AATAA AATAA A-ATAA A-ATAA AATAA AA
16248664 ATATTTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
5 21 0.70
6 9 0.30
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (5 bp):
AATAA
Found at i:16248808 original size:7 final size:6
Alignment explanation
Indices: 16248788--16248842 Score: 60
Period size: 6 Copynumber: 9.0 Consensus size: 6
16248778 CTTTTCCTTT
*
16248788 TTTTTC TCTTTC TTTTCTC TTTTTTC TTTTTC -TTTTC TTTTTTC TTTTT-
1 TTTTTC TTTTTC TTTT-TC -TTTTTC TTTTTC TTTTTC -TTTTTC TTTTTC
16248837 TTTTTC
1 TTTTTC
16248843 AGGTTGGGCC
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
5 10 0.24
6 19 0.45
7 9 0.21
8 4 0.10
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:16248810 original size:18 final size:19
Alignment explanation
Indices: 16248788--16248842 Score: 76
Period size: 20 Copynumber: 2.9 Consensus size: 19
16248778 CTTTTCCTTT
*
16248788 TTTTTCTCTTTCTTTTCTC
1 TTTTTCTTTTTCTTTTCTC
16248807 TTTTTTCTTTTTCTTTTCT-
1 -TTTTTCTTTTTCTTTTCTC
*
16248826 TTTTTCTTTTTTTTTTC
1 TTTTTCTTTTTCTTTTC
16248843 AGGTTGGGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
18 16 0.48
20 17 0.52
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTCTTTTTCTTTTCTC
Found at i:16248837 original size:20 final size:19
Alignment explanation
Indices: 16248778--16248842 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 19
16248768 AATTTTGGGC
*
16248778 CTTTTCCTTTTTTTTCTCTTT
1 CTTTT-CTTTTTTTT-TTTTT
*
16248799 CTTTTCTCTTTTTTCTTTTT
1 CTTTTCT-TTTTTTTTTTTT
*
16248819 CTTTTCTTTTTTCTTTTTT
1 CTTTTCTTTTTTTTTTTTT
16248838 -TTTTC
1 CTTTTC
16248843 AGGTTGGGCC
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
18 5 0.13
19 10 0.26
20 13 0.33
21 11 0.28
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (19 bp):
CTTTTCTTTTTTTTTTTTT
Found at i:16248839 original size:11 final size:11
Alignment explanation
Indices: 16248779--16248842 Score: 65
Period size: 11 Copynumber: 5.5 Consensus size: 11
16248769 ATTTTGGGCC
*
16248779 TTTTCCTTTTT
1 TTTTTCTTTTT
* *
16248790 TTTCTCTTTCT
1 TTTTTCTTTTT
*
16248801 TTTCTCTTTTTT
1 TTTTTC-TTTTT
16248813 CTTTTTCTTTTCT
1 -TTTTTCTTTT-T
16248826 TTTTTCTTTTT
1 TTTTTCTTTTT
16248837 TTTTTC
1 TTTTTC
16248843 AGGTTGGGCC
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
11 21 0.47
12 18 0.40
13 6 0.13
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:16249137 original size:13 final size:12
Alignment explanation
Indices: 16249113--16249152 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
16249103 GATTTAATTG
*
16249113 TTTTTTTATTCT
1 TTTTTTTTTTCT
16249125 TTATTTTTTTTCT
1 TT-TTTTTTTTCT
16249138 TTTTTCTTTTTCT
1 TTTTT-TTTTTCT
16249151 TT
1 TT
16249153 CCCCCCTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 5 0.20
13 20 0.80
ACGTcount: A:0.05, C:0.10, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTTTTTCT
Done.