Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008724.1 Hibiscus syriacus cultivar Beakdansim tig00111783_pilon, whole genome shotgun sequence
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: 5289199
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 23
Found at i:266681 original size:2 final size:2
Alignment explanation
Indices: 266656--266723 Score: 77
Period size: 2 Copynumber: 34.5 Consensus size: 2
266646 TTATGTAGTT
* * * *
266656 TA TA -A TA TA AA TA TA GTT TA TA TA TA -A TT TA AA 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
266697 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
266724 TATTTTTCAA
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
1 2 0.04
2 52 0.95
3 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:271588 original size:14 final size:14
Alignment explanation
Indices: 271569--271598 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
271559 AACCTGTATA
271569 AAGAACATAAAAAT
1 AAGAACATAAAAAT
*
271583 AAGAACTTAAAAAT
1 AAGAACATAAAAAT
271597 AA
1 AA
271599 ATGACAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.17
Consensus pattern (14 bp):
AAGAACATAAAAAT
Found at i:272649 original size:19 final size:19
Alignment explanation
Indices: 272591--272652 Score: 115
Period size: 19 Copynumber: 3.3 Consensus size: 19
272581 ACAAATTCAT
272591 TGGCATCTTTAAAAAGCAA
1 TGGCATCTTTAAAAAGCAA
*
272610 TAGCATCTTTAAAAAGCAA
1 TGGCATCTTTAAAAAGCAA
272629 TGGCATCTTTAAAAAGCAA
1 TGGCATCTTTAAAAAGCAA
272648 TGGCA
1 TGGCA
272653 AAAAATATCC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (19 bp):
TGGCATCTTTAAAAAGCAA
Found at i:273062 original size:107 final size:107
Alignment explanation
Indices: 272876--273073 Score: 342
Period size: 107 Copynumber: 1.9 Consensus size: 107
272866 TCATATTAGG
* * *
272876 TGGCATTATTACACTAACTAGATAGTTTGCAAATTTTGCATACCATGGTAATGTTGTAGCATCAA
1 TGGCATCATTACACTAACTAGATAGTTTGCAAAATTTGCATACCATGGTAATGTTGTAGCAACAA
272941 GTAGTCGTTTGTCTAGAAAATCATTTAGAATTACTAAAATGA
66 GTAGTCGTTTGTCTAGAAAATCATTTAGAATTACTAAAATGA
* * *
272983 TGGCATCATTCCACTAACTTGATAGTTTGCAAAATTTGCATACTATGGTAATGTTGTAGCAACAA
1 TGGCATCATTACACTAACTAGATAGTTTGCAAAATTTGCATACCATGGTAATGTTGTAGCAACAA
273048 GTAGTCGTTTGTCTAGAAAATCATTT
66 GTAGTCGTTTGTCTAGAAAATCATTT
273074 TAAGATCCCT
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
107 85 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (107 bp):
TGGCATCATTACACTAACTAGATAGTTTGCAAAATTTGCATACCATGGTAATGTTGTAGCAACAA
GTAGTCGTTTGTCTAGAAAATCATTTAGAATTACTAAAATGA
Found at i:283207 original size:20 final size:20
Alignment explanation
Indices: 283182--283221 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
283172 AACGATGAAG
283182 AACTAAAAAAAGACATTCTT
1 AACTAAAAAAAGACATTCTT
*
283202 AACTAAAGAAAGACATTCTT
1 AACTAAAAAAAGACATTCTT
283222 TTTGAGGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.15, G:0.07, T:0.25
Consensus pattern (20 bp):
AACTAAAAAAAGACATTCTT
Found at i:290465 original size:10 final size:11
Alignment explanation
Indices: 290446--290484 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
290436 AATAAAAGCT
290446 AAATTAACAT-A
1 AAATT-ACATGA
290457 AAATTACATGA
1 AAATTACATGA
*
290468 AAATTTCATGA
1 AAATTACATGA
290479 AAATTA
1 AAATTA
290485 GGCCATTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 4 0.16
11 21 0.84
ACGTcount: A:0.56, C:0.08, G:0.05, T:0.31
Consensus pattern (11 bp):
AAATTACATGA
Found at i:293100 original size:3 final size:3
Alignment explanation
Indices: 293085--293139 Score: 74
Period size: 3 Copynumber: 18.3 Consensus size: 3
293075 TACATCTTAT
* * * *
293085 TTA TTA ATA TTA TTA TTG TTA TTA TTA TTA TTA TTA CTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
293133 TTA TTA T
1 TTA TTA T
293140 CAAATTACAA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:294907 original size:15 final size:17
Alignment explanation
Indices: 294887--294919 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
294877 ATATTATTCA
294887 TTTT-AAATA-AAATAT
1 TTTTAAAATATAAATAT
294902 TTTTAAAATATAAATAT
1 TTTTAAAATATAAATAT
294919 T
1 T
294920 GGGTGTTGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 5 0.31
17 7 0.44
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTAAAATATAAATAT
Found at i:296867 original size:25 final size:24
Alignment explanation
Indices: 296819--296886 Score: 91
Period size: 25 Copynumber: 2.8 Consensus size: 24
296809 ATTAAGGGAC
296819 AACATTTTTCAAAATTCTTCATCA
1 AACATTTTTCAAAATTCTTCATCA
* * *
296843 AACTTTTTTCAAAATATTTTTATCA
1 AACATTTTTCAAAAT-TCTTCATCA
*
296868 AACATTTTTAAAAATTCTT
1 AACATTTTTCAAAATTCTT
296887 TAATTATTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
24 17 0.46
25 20 0.54
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.47
Consensus pattern (24 bp):
AACATTTTTCAAAATTCTTCATCA
Found at i:300871 original size:122 final size:121
Alignment explanation
Indices: 300511--301408 Score: 895
Period size: 122 Copynumber: 7.4 Consensus size: 121
300501 ATCTGACAGT
* * * * * *
300511 AAACAATTTACCTGAAAGCAGCCATATCTCTTCAATGTGGATGAGCAGAGTCGTATTCAACACCA
1 AAACAATTTACCCGAAAGCGGCCAGATCTCTTCAATGTGGATGAGCAGTGTCTTCTTCAACACCA
* * * * * *
300576 AATTATTTCTAGATTGACTCGACTTCATCAATTAGAAAGAACAACGTCATCTTCAAC
66 AATTATCTCCAGATTGAC-CAACTTCCTCAATGAGAAGGAACAACGTCATCTTCAAC
* * ** * *
300633 AAACAATTTACCCGAAAGCGACTAGATCTCTTCAATGTGGATGAATAG-GT-TGTCTTTAATACC
1 AAACAATTTACCCGAAAGCGGCCAGATCTCTTCAATGTGGATGAGCAGTGTCT-TCTTCAACACC
* * * *
300696 AAATTATCTCAAGATTGACACGACTTCCTAAATGAGAAGGAACAGCGTCATCTTCAAC
65 AAATTATCTCCAGATTGAC-CAACTTCCTCAATGAGAAGGAACAACGTCATCTTCAAC
* * * *
300754 AAACAATTGACCCCAAAGCGGCCATATCTCTTCAATGTGGATGAGCAGTGTCTTCTTCAGCACCA
1 AAACAATTTACCCGAAAGCGGCCAGATCTCTTCAATGTGGATGAGCAGTGTCTTCTTCAACACCA
*
300819 AATTATCTCCAGATTGATCCAACTTCCTCAATTAGAAGGAACAACGTCATCTTCAAC
66 AATTATCTCCAGATTGA-CCAACTTCCTCAATGAGAAGGAACAACGTCATCTTCAAC
* * * * * * *
300876 AAACAATTTACCCGAAAGTGGTCAGATCTCTTAAATATGGATGAGTAGTGT-TGTCTTTAACACT
1 AAACAATTTACCCGAAAGCGGCCAGATCTCTTCAATGTGGATGAGCAGTGTCT-TCTTCAACACC
*
300940 AAATTATCTCCAGATTGACCTGAA-TTCCTCAATGAGAAGGAACAATGTCATCTT-AA-
65 AAATTATCTCCAGATTGACC--AACTTCCTCAATGAGAAGGAACAACGTCATCTTCAAC
* * ** ** * * *
300996 AAA-AAATTACCCAAAAATGGTAAGATCTCTTCAATGTGGATGACCAGT-TCCGTCTTTAACACC
1 AAACAATTTACCCGAAAGCGGCCAGATCTCTTCAATGTGGATGAGCAGTGT-CTTCTTCAACACC
* * * *
301059 AAATTATCTCCAGATTGGCCTAACTTCCTCAATAAGAAGGAAC-ACTATTATCTTCAAC
65 AAATTATCTCCAGATTGACC-AACTTCCTCAATGAGAAGGAACAAC-GTCATCTTCAAC
* * * * *
301117 AAACAATTTACCTGAAAACGGCTAGATCTCTTCAATATGGATGAGCAGTGTCGTCTTCAACACCA
1 AAACAATTTACCCGAAAGCGGCCAGATCTCTTCAATGTGGATGAGCAGTGTCTTCTTCAACACCA
* * * * *
301182 AATTATCTCTAGATTGACCCGATTTCCTCAATGAGAAGGAATAGCGTCATCTTCAAC
66 AATTATCTCCAGATTGA-CCAACTTCCTCAATGAGAAGGAACAACGTCATCTTCAAC
* ** * * * * *
301239 AAACAATTCACTTGAAAGCGGCTAGATATTTTAAATGTGGGTGAGCAGTGTCTTCTTCAACACCA
1 AAACAATTTACCCGAAAGCGGCCAGATCTCTTCAATGTGGATGAGCAGTGTCTTCTTCAACACCA
* * * * * * * *
301304 ATTTATCTCCATATTAACCCAACTTCCTCAAAGAGCAGGAACGATGTCATCTACAAC
66 AATTATCTCCAGATTGA-CCAACTTCCTCAATGAGAAGGAACAACGTCATCTTCAAC
* * * *
301361 AAACTATTTACCCG-AA---GCCAAATCTCTTCAATATTGATGAGCAGTGTC
1 AAACAATTTACCCGAAAGCGGCCAGATCTCTTCAATGTGGATGAGCAGTGTC
301409 ATTTCCAATA
Statistics
Matches: 644, Mismatches: 115, Indels: 38
0.81 0.14 0.05
Matches are distributed among these distances:
118 28 0.04
119 90 0.14
120 5 0.01
121 111 0.17
122 402 0.62
123 8 0.01
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.28
Consensus pattern (121 bp):
AAACAATTTACCCGAAAGCGGCCAGATCTCTTCAATGTGGATGAGCAGTGTCTTCTTCAACACCA
AATTATCTCCAGATTGACCAACTTCCTCAATGAGAAGGAACAACGTCATCTTCAAC
Found at i:301099 original size:241 final size:241
Alignment explanation
Indices: 300536--301407 Score: 902
Period size: 241 Copynumber: 3.6 Consensus size: 241
300526 AAGCAGCCAT
* * * * * *
300536 ATCTCTTCAATGTGGATGAGCAGAGTCGTATTCAACACCAAATTATTTCTAGATT-GACTCGACT
1 ATCTCTTCAATGTGGATGAGCAG-TTCGTCTTCAACACCAAATTATCTCCAGATTGGCCT-AACT
* * *
300600 TCATCAATTAGAAAGAACAACGTCATCTTCAACAAACAATTTACCCGAAAGCGACTAGATCTCTT
64 TCCTCAATTAGAAGGAACAACGTCATCTTCAACAAACAATTTACCCGAAAG-GGCTAGATCTCTT
* * * * *
300665 CAATGTGGATGAATAG-GTTGTCTTTAATACCAAATTATCTCAAGATTGACACGACTTCCTAAAT
128 CAATATGGATGAGTAGTGTTGTCTTTAACACCAAATTATCTCAAGATTGAC-CGAATTCCTCAAT
* * * * * *
300729 GAGAAGGAACAGCGTCATCTTCAACAAACAATTGACCCCAAAGCGGCCAT
192 GAGAAGGAACAACGTCATCTTCAACAAAAAATTGACCCAAAAACGGCAAG
* * *
300779 ATCTCTTCAATGTGGATGAGCAGTGTCTTCTTCAGCACCAAATTATCTCCAGATTGATCC-AACT
1 ATCTCTTCAATGTGGATGAGCAGT-TCGTCTTCAACACCAAATTATCTCCAGATTG-GCCTAACT
300843 TCCTCAATTAGAAGGAACAACGTCATCTTCAACAAACAATTTACCCGAAAGTGG-TCAGATCTCT
64 TCCTCAATTAGAAGGAACAACGTCATCTTCAACAAACAATTTACCCGAAAG-GGCT-AGATCTCT
* * *
300907 TAAATATGGATGAGTAGTGTTGTCTTTAACACTAAATTATCTCCAGATTGACCTGAATTCCTCAA
127 TCAATATGGATGAGTAGTGTTGTCTTTAACACCAAATTATCTCAAGATTGACC-GAATTCCTCAA
* * *
300972 TGAGAAGGAACAATGTCATCTT-AA-AAAAAATT-ACCCAAAAATGGTAAG
191 TGAGAAGGAACAACGTCATCTTCAACAAAAAATTGACCCAAAAACGGCAAG
* *
301020 ATCTCTTCAATGTGGATGACCAGTTCCGTCTTTAACACCAAATTATCTCCAGATTGGCCTAACTT
1 ATCTCTTCAATGTGGATGAGCAGTT-CGTCTTCAACACCAAATTATCTCCAGATTGGCCTAACTT
* * * * *
301085 CCTCAATAAGAAGGAAC-ACTATTATCTTCAACAAACAATTTACCTGAAAACGGCTAGATCTCTT
65 CCTCAATTAGAAGGAACAAC-GTCATCTTCAACAAACAATTTACCCG-AAAGGGCTAGATCTCTT
* * * * *
301149 CAATATGGATGAGCAGTGTCGTCTTCAACACCAAATTATCTCTAGATTGACCCGATTTCCTCAAT
128 CAATATGGATGAGTAGTGTTGTCTTTAACACCAAATTATCTCAAGATTGA-CCGAATTCCTCAAT
* * * * *** * *
301214 GAGAAGGAATAGCGTCATCTTCAACAAACAATTCACTTGAAAGCGGCTAG
192 GAGAAGGAACAACGTCATCTTCAACAAAAAATTGACCCAAAAACGGCAAG
* * * * * * * ** *
301264 ATATTTTAAATGTGGGTGAGCAGTGTCTTCTTCAACACCAATTTATCTCCATATTAACCCAACTT
1 ATCTCTTCAATGTGGATGAGCAGT-TCGTCTTCAACACCAAATTATCTCCAGATTGGCCTAACTT
** * * * * * * *
301329 CCTCAAAGAGCAGGAACGATGTCATCTACAACAAACTATTTACCCG-AA--GCCAAATCTCTTCA
65 CCTCAATTAGAAGGAACAACGTCATCTTCAACAAACAATTTACCCGAAAGGGCTAGATCTCTTCA
* *
301391 ATATTGATGAGCAGTGT
130 ATATGGATGAGTAGTGT
301408 CATTTCCAAT
Statistics
Matches: 530, Mismatches: 82, Indels: 37
0.82 0.13 0.06
Matches are distributed among these distances:
240 33 0.06
241 188 0.35
242 18 0.03
243 133 0.25
244 155 0.29
245 3 0.01
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.28
Consensus pattern (241 bp):
ATCTCTTCAATGTGGATGAGCAGTTCGTCTTCAACACCAAATTATCTCCAGATTGGCCTAACTTC
CTCAATTAGAAGGAACAACGTCATCTTCAACAAACAATTTACCCGAAAGGGCTAGATCTCTTCAA
TATGGATGAGTAGTGTTGTCTTTAACACCAAATTATCTCAAGATTGACCGAATTCCTCAATGAGA
AGGAACAACGTCATCTTCAACAAAAAATTGACCCAAAAACGGCAAG
Found at i:301183 original size:363 final size:364
Alignment explanation
Indices: 300511--301373 Score: 972
Period size: 363 Copynumber: 2.4 Consensus size: 364
300501 ATCTGACAGT
* * * * * *
300511 AAACAATTTACCTGAAAGCAGCCATATCTCTTCAATGTGGATGAGCAGAGTCGTATTCAACACCA
1 AAACAATTTACCTGAAAGC-GGCAGATCTCTTAAATGTGGATGAGCAGTGTTGTCTTCAACACCA
* * * * * * * *
300576 AATTATTTCTAGATTGA-CTCGACTTCATCAATTAGAAAGAACAACGTCATCTTCAACAAACAAT
65 AATTATCTCCAGATTGACCT-GAATTCCTCAATGAGAAGGAACAATGTCATCTTCAACAAACAAA
* * * *
300640 TTACCCGAAAGCGACTAGATCTCTTCAATGTGGATGAATAGGTTGTCTTTAATACCAAATTATCT
129 TTACCCAAAAACGACTAGATCTCTTCAATGTGGATGAACAGGTTGTCTTTAACACCAAATTATCT
* * *
300705 CAAGATTGACACGACTTCCTAAATGAGAAGGAACAGCGTCATCTTCAACAAACAATTGACCCCAA
194 CAAGATTGACACAACTTCCTAAATAAGAAGGAACAGCATCATCTTCAACAAACAATTGACCCCAA
* * * * *
300770 AGCGGCCATATCTCTTCAATGTGGATGAGCAGTGTCTTCTTCAGCACCAAATTATCTCCAGATTG
259 AACGGCCAGATCTCTTCAATATGGATGAGCAGTGTCGTCTTCAACACCAAATTATCTCCAGATTG
* *
300835 ATCCAACTTCCTCAATTAGAAGGAACAACGTCATCTTCAAC
324 ACCCAACTTCCTCAATGAGAAGGAACAACGTCATCTTCAAC
* * * * * *
300876 AAACAATTTACCCGAAAGTGGTCAGATCTCTTAAATATGGATGAGTAGTGTTGTCTTTAACACTA
1 AAACAATTTACCTGAAAGCGG-CAGATCTCTTAAATGTGGATGAGCAGTGTTGTCTTCAACACCA
300941 AATTATCTCCAGATTGACCTGAATTCCTCAATGAGAAGGAACAATGTCATCTT-AA-AAA-AAAT
65 AATTATCTCCAGATTGACCTGAATTCCTCAATGAGAAGGAACAATGTCATCTTCAACAAACAAAT
* * *
301003 TACCCAAAAATG-GTAAGATCTCTTCAATGTGGATGACCA-GTTCCGTCTTTAACACCAAATTAT
130 TACCCAAAAACGACT-AGATCTCTTCAATGTGGATGAACAGGTT--GTCTTTAACACCAAATTAT
* * * * *
301066 CTCCAGATTGGC-CTAACTTCCTCAATAAGAAGGAACA-CTATTATCTTCAACAAACAATTTACC
192 CTCAAGATTGACAC-AACTTCCTAAATAAGAAGGAACAGC-ATCATCTTCAACAAACAATTGACC
** * *
301129 TGAAAACGGCTAGATCTCTTCAATATGGATGAGCAGTGTCGTCTTCAACACCAAATTATCTCTAG
255 CCAAAACGGCCAGATCTCTTCAATATGGATGAGCAGTGTCGTCTTCAACACCAAATTATCTCCAG
* * * *
301194 ATTGACCCGATTTCCTCAATGAGAAGGAATAGCGTCATCTTCAAC
320 ATTGACCCAACTTCCTCAATGAGAAGGAACAACGTCATCTTCAAC
* * * * *
301239 AAACAATTCACTTGAAAGCGGCTAGATATTTTAAATGTGGGTGAGCAGTGTCT-TCTTCAACACC
1 AAACAATTTACCTGAAAGCGGC-AGATCTCTTAAATGTGGATGAGCAGTGT-TGTCTTCAACACC
* * * * * * * * *
301303 AATTTATCTCCATATTAACC-CAACTTCCTCAAAGAGCAGGAACGATGTCATCTACAACAAACTA
64 AAATTATCTCCAGATTGACCTGAA-TTCCTCAATGAGAAGGAACAATGTCATCTTCAACAAACAA
*
301367 TTTACCC
128 ATTACCC
301374 GAAGCCAAAT
Statistics
Matches: 414, Mismatches: 71, Indels: 25
0.81 0.14 0.05
Matches are distributed among these distances:
361 4 0.01
362 39 0.09
363 259 0.63
364 6 0.01
365 97 0.23
366 9 0.02
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (364 bp):
AAACAATTTACCTGAAAGCGGCAGATCTCTTAAATGTGGATGAGCAGTGTTGTCTTCAACACCAA
ATTATCTCCAGATTGACCTGAATTCCTCAATGAGAAGGAACAATGTCATCTTCAACAAACAAATT
ACCCAAAAACGACTAGATCTCTTCAATGTGGATGAACAGGTTGTCTTTAACACCAAATTATCTCA
AGATTGACACAACTTCCTAAATAAGAAGGAACAGCATCATCTTCAACAAACAATTGACCCCAAAA
CGGCCAGATCTCTTCAATATGGATGAGCAGTGTCGTCTTCAACACCAAATTATCTCCAGATTGAC
CCAACTTCCTCAATGAGAAGGAACAACGTCATCTTCAAC
Found at i:303724 original size:16 final size:16
Alignment explanation
Indices: 303703--303757 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
303693 AAAATATAAT
303703 TATATTTTTAGTTAGA
1 TATATTTTTAGTTAGA
*
303719 TATATTTTTACATT-G-
1 TATATTTTTA-GTTAGA
303734 T-TA-TTTTAGTTAGA
1 TATATTTTTAGTTAGA
303748 TATATTTTTA
1 TATATTTTTA
303758 CATAGTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
12 2 0.06
13 6 0.19
14 3 0.09
15 3 0.09
16 16 0.50
17 2 0.06
ACGTcount: A:0.29, C:0.02, G:0.09, T:0.60
Consensus pattern (16 bp):
TATATTTTTAGTTAGA
Found at i:303748 original size:29 final size:29
Alignment explanation
Indices: 303708--303770 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
303698 ATAATTATAT
*
303708 TTTTAGTTAGATATATTTTTACATTGTTA
1 TTTTAGTTAGATATATTTTTACATAGTTA
303737 TTTTAGTTAGATATATTTTTACATAGTTA
1 TTTTAGTTAGATATATTTTTACATAGTTA
303766 TTTTA
1 TTTTA
303771 TTTCAAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.29, C:0.03, G:0.10, T:0.59
Consensus pattern (29 bp):
TTTTAGTTAGATATATTTTTACATAGTTA
Found at i:304051 original size:23 final size:23
Alignment explanation
Indices: 303988--304038 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
303978 AGAATAATTT
303988 TGCCTATGTTGCACATTTATCTC
1 TGCCTATGTTGCACATTTATCTC
*
304011 TGCCTGTGTTGCACATTTATCTC
1 TGCCTATGTTGCACATTTATCTC
304034 TGCCT
1 TGCCT
304039 TTGTGGCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.14, C:0.27, G:0.16, T:0.43
Consensus pattern (23 bp):
TGCCTATGTTGCACATTTATCTC
Found at i:304550 original size:18 final size:18
Alignment explanation
Indices: 304518--304566 Score: 68
Period size: 17 Copynumber: 2.8 Consensus size: 18
304508 AAAAAAGTTC
304518 ATTTTTATTTA-TTTCAT
1 ATTTTTATTTATTTTCAT
304535 ATTTTTATTTATTTTCAT
1 ATTTTTATTTATTTTCAT
304553 -TTATTTATTT-TTTT
1 ATT-TTTATTTATTTT
304567 ACATTTGGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 17 0.57
18 13 0.43
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (18 bp):
ATTTTTATTTATTTTCAT
Found at i:304571 original size:18 final size:16
Alignment explanation
Indices: 304515--304572 Score: 64
Period size: 18 Copynumber: 3.4 Consensus size: 16
304505 TTAAAAAAAG
*
304515 TTCA-TTTTTATTTAT
1 TTCATTTTTTATTTTT
304530 TTCATATTTTTATTTATT
1 TTCAT-TTTTTATTT-TT
304548 TTCATTTATTTATTTTT
1 TTCATTT-TTTATTTTT
304565 TTACATTT
1 TT-CATTT
304573 GGTTAGTTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
15 4 0.11
17 15 0.41
18 18 0.49
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (16 bp):
TTCATTTTTTATTTTT
Found at i:318104 original size:31 final size:30
Alignment explanation
Indices: 318036--318107 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
318026 TTTACAAGCC
* * * *
318036 TTAGAAAAATTTGGGGATCATTTTGTAATT
1 TTAGAAAAGTTAGGGGACCAATTTGTAATT
*
318066 TTTGAAAAGTTAGGGGACCAATTTGTTAATT
1 TTAGAAAAGTTAGGGGACCAATTTG-TAATT
318097 TTAGAAAAGTT
1 TTAGAAAAGTT
318108 GTGAATGGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
30 20 0.57
31 15 0.43
ACGTcount: A:0.35, C:0.04, G:0.21, T:0.40
Consensus pattern (30 bp):
TTAGAAAAGTTAGGGGACCAATTTGTAATT
Found at i:319507 original size:80 final size:80
Alignment explanation
Indices: 319363--319673 Score: 444
Period size: 80 Copynumber: 3.9 Consensus size: 80
319353 CGGCAAAAAG
* * * * * *
319363 GGGAGCCAACCTAAGGATATACCTT-GGGTCTACCCAAGGACATCCTTAGATCCCTAGGGATACC
1 GGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAA-GATATCCTTAGGTCCGTAGGGTTACC
* * **
319427 TTAAGCATACAGTTAA
65 TTATGCACACAGCAAA
* * *
319443 GAGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGCTCCGTAGCGTTACCT
1 GGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
319508 TATGCACACAGCAAA
66 TATGCACACAGCAAA
* *
319523 GGGAACTAACCTAAGGATATGCCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
1 GGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
*
319588 TATGCACACAACAAA
66 TATGCACACAGCAAA
* *
319603 GGGAACCAACCTAAGGATATGCCTTGGTGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
1 GGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
319668 TATGCA
66 TATGCA
319674 AGTATATTCG
Statistics
Matches: 210, Mismatches: 20, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
80 199 0.95
81 11 0.05
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.23
Consensus pattern (80 bp):
GGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
TATGCACACAGCAAA
Found at i:329144 original size:19 final size:20
Alignment explanation
Indices: 329122--329164 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
329112 TCGAGGGATT
329122 ATATA-AGATCCTTCGGGAC
1 ATATACAGATCCTTCGGGAC
*
329141 ATATACGAGGTCCTTCGGGAC
1 ATATAC-AGATCCTTCGGGAC
329162 ATA
1 ATA
329165 CATGAGGTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
21 16 0.76
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (20 bp):
ATATACAGATCCTTCGGGAC
Found at i:329154 original size:21 final size:21
Alignment explanation
Indices: 329130--329181 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
329120 TTATATAAGA
*
329130 TCCTTCGGGACATATACGAGG
1 TCCTTCGGGACATACACGAGG
*
329151 TCCTTCGGGACATACATGAGG
1 TCCTTCGGGACATACACGAGG
329172 TCCTTCGGGA
1 TCCTTCGGGA
329182 TAAAATTCAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.21, C:0.25, G:0.29, T:0.25
Consensus pattern (21 bp):
TCCTTCGGGACATACACGAGG
Found at i:329350 original size:18 final size:19
Alignment explanation
Indices: 329306--329350 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
329296 TGATATAAAA
329306 ATTGTTTA-CATTATTATT
1 ATTGTTTATCATTATTATT
*
329324 ATATG-TTATCA-TGTTATT
1 AT-TGTTTATCATTATTATT
329342 ATTGTTTAT
1 ATTGTTTAT
329351 AATGGATCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
17 2 0.09
18 17 0.74
19 4 0.17
ACGTcount: A:0.27, C:0.04, G:0.09, T:0.60
Consensus pattern (19 bp):
ATTGTTTATCATTATTATT
Found at i:341288 original size:17 final size:17
Alignment explanation
Indices: 341241--341411 Score: 87
Period size: 17 Copynumber: 9.8 Consensus size: 17
341231 ATTCTAAATG
* *
341241 TTTACAGTTATCATACA
1 TTTACAATTATCATATA
**
341258 TTTCACTTTTATCATATA
1 TTT-ACAATTATCATATA
*
341276 TTTACAATTATCAGATGA
1 TTTACAATTATCATAT-A
* * *
341294 TTTTCAGTTATCAAATA
1 TTTACAATTATCATATA
* *
341311 TTTACAATTATTAGATGA
1 TTTACAATTATCATAT-A
* * *
341329 TTTTCAGTTATCAAATA
1 TTTACAATTATCATATA
* *
341346 TTTA-AAGATATCAGATGA
1 TTTACAA-TTATCATAT-A
*
341364 -TTACAGTTATCATATA
1 TTTACAATTATCATATA
* *
341380 TTTAAAAATATCAT-TA
1 TTTACAATTATCATATA
*
341396 GTTTTACATTTATCAT
1 --TTTACAATTATCAT
341412 GTAATACCCC
Statistics
Matches: 115, Mismatches: 30, Indels: 17
0.71 0.19 0.10
Matches are distributed among these distances:
16 4 0.03
17 57 0.50
18 54 0.47
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.45
Consensus pattern (17 bp):
TTTACAATTATCATATA
Found at i:341305 original size:35 final size:35
Alignment explanation
Indices: 341266--341392 Score: 168
Period size: 35 Copynumber: 3.7 Consensus size: 35
341256 CATTTCACTT
* *
341266 TTATCATATATTTACAATTATCAGATGATTTTCAG
1 TTATCAAATATTTACAAATATCAGATGATTTTCAG
* *
341301 TTATCAAATATTTACAATTATTAGATGATTTTCAG
1 TTATCAAATATTTACAAATATCAGATGATTTTCAG
*
341336 TTATCAAATATTTA-AAGATATCAGATGA-TTACAG
1 TTATCAAATATTTACAA-ATATCAGATGATTTTCAG
* *
341370 TTATCATATATTTAAAAATATCA
1 TTATCAAATATTTACAAATATCA
341393 TTAGTTTTAC
Statistics
Matches: 84, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
34 26 0.31
35 58 0.69
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (35 bp):
TTATCAAATATTTACAAATATCAGATGATTTTCAG
Found at i:341503 original size:31 final size:30
Alignment explanation
Indices: 341431--341520 Score: 94
Period size: 29 Copynumber: 3.0 Consensus size: 30
341421 CAAATTTTGG
* *
341431 TTAGCGACCAAAATATAAA-TTTTAAAAGT
1 TTAGGGACCAAAGTATAAATTTTTAAAAGT
* *
341460 TTAGTGAACAAAGTATAAATTTTGTAAAAGT
1 TTAGGGACCAAAGTATAAATTTT-TAAAAGT
* * *
341491 TTTGGGACCAAAGTGT-AATTTTAAAAAGT
1 TTAGGGACCAAAGTATAAATTTTTAAAAGT
341520 T
1 T
341521 ATGTAATTTG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
29 23 0.45
30 9 0.18
31 19 0.37
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.34
Consensus pattern (30 bp):
TTAGGGACCAAAGTATAAATTTTTAAAAGT
Found at i:342009 original size:10 final size:10
Alignment explanation
Indices: 341988--342022 Score: 52
Period size: 11 Copynumber: 3.3 Consensus size: 10
341978 AATAAAGGTT
341988 AAATTAACATG
1 AAATT-ACATG
341999 AAATTACATG
1 AAATTACATG
342009 AAAATTACATG
1 -AAATTACATG
342020 AAA
1 AAA
342023 CTTAGGTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.26
Consensus pattern (10 bp):
AAATTACATG
Found at i:345368 original size:27 final size:28
Alignment explanation
Indices: 345337--345393 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
345327 ATTACGATGG
345337 AAGTAT-GA-TTTAGTTTTATATC-AATTT
1 AAGTATCGATTTTA-TTTT-TATCGAATTT
345364 AAGTATCGATTTTATTTTTATCGAATTT
1 AAGTATCGATTTTATTTTTATCGAATTT
345392 AA
1 AA
345394 TATTTAGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
27 10 0.37
28 13 0.48
29 4 0.15
ACGTcount: A:0.33, C:0.05, G:0.11, T:0.51
Consensus pattern (28 bp):
AAGTATCGATTTTATTTTTATCGAATTT
Found at i:346040 original size:2 final size:2
Alignment explanation
Indices: 346033--346076 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
346023 TAATTTTTCA
346033 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
346075 AT
1 AT
346077 TAATACAGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:346390 original size:17 final size:17
Alignment explanation
Indices: 346300--346446 Score: 109
Period size: 17 Copynumber: 8.5 Consensus size: 17
346290 TGAATTCTAA
346300 ATATTTACAGTTATCAG
1 ATATTTACAGTTATCAG
* *
346317 ACATTTCACCGTTATCAG
1 ATATTT-ACAGTTATCAG
* *
346335 ATATTTGCAATTATCAG
1 ATATTTACAGTTATCAG
* * *
346352 ATGACTTT-TAGTTGTCAA
1 AT-A-TTTACAGTTATCAG
346370 ATATTTACAGTTATCAG
1 ATATTTACAGTTATCAG
** *
346387 ATATTTTTAGTTATCAT
1 ATATTTACAGTTATCAG
* * *
346404 ATTTTTACA-TATATTAT
1 ATATTTACAGT-TATCAG
**
346421 ATGGTTACAGTTATCAG
1 ATATTTACAGTTATCAG
346438 ATATTTACA
1 ATATTTACA
346447 AATATTAGAT
Statistics
Matches: 98, Mismatches: 26, Indels: 12
0.72 0.19 0.09
Matches are distributed among these distances:
16 4 0.04
17 66 0.67
18 25 0.26
19 3 0.03
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (17 bp):
ATATTTACAGTTATCAG
Found at i:349984 original size:18 final size:18
Alignment explanation
Indices: 349961--350026 Score: 105
Period size: 18 Copynumber: 3.7 Consensus size: 18
349951 ATACAATTAA
349961 TATCGATACTAATGTGAG
1 TATCGATACTAATGTGAG
*
349979 TATCGATACTGATGTGAG
1 TATCGATACTAATGTGAG
* *
349997 TATCGATACTGATGTCAG
1 TATCGATACTAATGTGAG
350015 TATCGATACTAA
1 TATCGATACTAA
350027 GAGAAAGGTA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (18 bp):
TATCGATACTAATGTGAG
Found at i:350640 original size:81 final size:81
Alignment explanation
Indices: 350534--350694 Score: 234
Period size: 81 Copynumber: 2.0 Consensus size: 81
350524 CTGTTCTAAA
* * * * *
350534 ATGAAAGACTAAATGTCTAATTGTGCATTTGGTA-AAACGTTGTCAATTATGCAAGTTAGATGAA
1 ATGAAAGACTAAATGCCTAACTGTGCATTTGGCAGAAACGTT-CCAATAATGCAAGTTAGATGAA
350598 AGGTTAAATGCCTTTAT
65 AGGTTAAATGCCTTTAT
* * *
350615 ATGAAAGACTAAATGCCTAACTGTGCGTTTGGCAGAAAGGTTCCAATAATGCAAGTTAGATGAAG
1 ATGAAAGACTAAATGCCTAACTGTGCATTTGGCAGAAACGTTCCAATAATGCAAGTTAGATGAAA
350680 GGTTAAATGCCTTTA
66 GGTTAAATGCCTTTA
350695 GAAGAAAGGT
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
81 65 0.92
82 6 0.08
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (81 bp):
ATGAAAGACTAAATGCCTAACTGTGCATTTGGCAGAAACGTTCCAATAATGCAAGTTAGATGAAA
GGTTAAATGCCTTTAT
Found at i:350721 original size:81 final size:81
Alignment explanation
Indices: 350536--350723 Score: 209
Period size: 81 Copynumber: 2.3 Consensus size: 81
350526 GTTCTAAAAT
* * * *
350536 GAAAGACTAAATGTC-TAATTGTGCATTTGGTAAAACGTTGTCAATTATGCAAGTTAGATGAAAG
1 GAAAGACTAAAT-ACATAATTGTGCATTTGGCAAAACGTTGCCAATAATGCAAGTTAGATGAAAG
* *
350600 GTTAAATGCCTTTATAT
65 GTTAAATGCCTTTAGAA
* * * * * *
350617 GAAAGACTAAATGCCTAACTGTGCGTTTGGCAGAAAGGTT-CCAATAATGCAAGTTAGATGAAGG
1 GAAAGACTAAATACATAATTGTGCATTTGGCA-AAACGTTGCCAATAATGCAAGTTAGATGAAAG
350681 GTTAAATGCCTTTAGAA
65 GTTAAATGCCTTTAGAA
** *
350698 GAAAGGTTAAATATATAATTGTGCAT
1 GAAAGACTAAATACATAATTGTGCAT
350724 AATTGGCATG
Statistics
Matches: 88, Mismatches: 17, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
80 1 0.01
81 81 0.92
82 6 0.07
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.31
Consensus pattern (81 bp):
GAAAGACTAAATACATAATTGTGCATTTGGCAAAACGTTGCCAATAATGCAAGTTAGATGAAAGG
TTAAATGCCTTTAGAA
Found at i:350779 original size:46 final size:46
Alignment explanation
Indices: 350718--351031 Score: 457
Period size: 46 Copynumber: 6.8 Consensus size: 46
350708 ATATATAATT
* *
350718 GTGCATAATTGGCATGAAAGGATGCCATAAATGAAAATGCATAATG
1 GTGCATAATTGGCATGAAAGGATGTCATAAATGAAAATGCATAACG
* *
350764 GTGCATAATTGGCATGAAAGGATGTCATAAATAAAAATGTATAACG
1 GTGCATAATTGGCATGAAAGGATGTCATAAATGAAAATGCATAACG
* *
350810 GTGCACAATTGGCATGAAAGGATGTCATAAATGAAAATGCATAATG
1 GTGCATAATTGGCATGAAAGGATGTCATAAATGAAAATGCATAACG
* *
350856 GTTCATAATTGGCATGAAAGGATATCATAAATGAAAATGCATAACG
1 GTGCATAATTGGCATGAAAGGATGTCATAAATGAAAATGCATAACG
* * *
350902 GTGCATAATTGGCATGAAAGGATATCATAAATAAAAATGAATAACG
1 GTGCATAATTGGCATGAAAGGATGTCATAAATGAAAATGCATAACG
* ** * *
350948 GTGCATAATTGGAATGAAAGGATACCATAAATGAAAATGAATAACA
1 GTGCATAATTGGCATGAAAGGATGTCATAAATGAAAATGCATAACG
* * *
350994 ATGCATAATTGGCATGAAAGGATGTAAAAAATGAAAAT
1 GTGCATAATTGGCATGAAAGGATGTCATAAATGAAAAT
351032 ACATTACTTT
Statistics
Matches: 243, Mismatches: 25, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 243 1.00
ACGTcount: A:0.45, C:0.09, G:0.21, T:0.24
Consensus pattern (46 bp):
GTGCATAATTGGCATGAAAGGATGTCATAAATGAAAATGCATAACG
Found at i:356137 original size:182 final size:182
Alignment explanation
Indices: 355830--356193 Score: 638
Period size: 182 Copynumber: 2.0 Consensus size: 182
355820 TCAGGTGACA
* *
355830 GCATATATTGTTATTATATGAGATGAGGGAGACTCACACAGAGTCAACCTCTAATGTTTTGATTT
1 GCATATATTGTTATTATATGAGATAAAGGAGACTCACACAGAGTCAACCTCTAATGTTTTGATTT
355895 AATGTATGGTTTATCGTATTTGATATATGTTTATAATGTGTATGGAATTGATATTATGAATAATT
66 AATGTATGGTTTATCGTATTTGATATATGTTTATAATGTGTATGGAATTGATATTATGAATAATT
*
355960 ATTAGAGTAGGAACTGTTCTAAATTAAAAGACTAAATGTCTAACTGTGCATT
131 ATTAGAGTAGGAACTGTTCTAAAATAAAAGACTAAATGTCTAACTGTGCATT
* * *
356012 GCATATATTGTTATTATATGGGATAAAGGAGGCTCACATAGAGTCAACCTCTAATGTTTTGATTT
1 GCATATATTGTTATTATATGAGATAAAGGAGACTCACACAGAGTCAACCTCTAATGTTTTGATTT
356077 AATGTATGGTTTATCGTATTTGATATATGTTTATAATGTGTATGGAATTGATATTATGAATAATT
66 AATGTATGGTTTATCGTATTTGATATATGTTTATAATGTGTATGGAATTGATATTATGAATAATT
* * * *
356142 ATTATAGTATGAATTGTTCTAAAATGAAAGACTAAATGTCTAACTGTGCATT
131 ATTAGAGTAGGAACTGTTCTAAAATAAAAGACTAAATGTCTAACTGTGCATT
356194 TGGTAGAAAG
Statistics
Matches: 172, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
182 172 1.00
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.40
Consensus pattern (182 bp):
GCATATATTGTTATTATATGAGATAAAGGAGACTCACACAGAGTCAACCTCTAATGTTTTGATTT
AATGTATGGTTTATCGTATTTGATATATGTTTATAATGTGTATGGAATTGATATTATGAATAATT
ATTAGAGTAGGAACTGTTCTAAAATAAAAGACTAAATGTCTAACTGTGCATT
Found at i:356301 original size:81 final size:81
Alignment explanation
Indices: 356163--356347 Score: 239
Period size: 81 Copynumber: 2.3 Consensus size: 81
356153 AATTGTTCTA
* * * * *
356163 AAATGAAAGACTAAATGTCTAACTGTGCATTTGGTAGAAAGGTGACAATCATGCAAGTTAGATGA
1 AAATGAAAGACTAAATGCCTAACTATGCATTTGGCAGAAAGGTGACAATAATACAAGTTAGATGA
*
356228 AATGTTAAATGCCTTT
66 AAGGTTAAATGCCTTT
*
356244 AAATGAAAGACTAAATGCCTAACTATGCATTTGGCATAAAGGT-ATCAATAATACAAGTTAGATG
1 AAATGAAAGACTAAATGCCTAACTATGCATTTGGCAGAAAGGTGA-CAATAATACAAGTTAGATG
*
356308 AAGGGTTAAATGCCTTT
65 AAAGGTTAAATGCCTTT
** *
356325 AGAA-GAAAGGTTAAATGCATAAC
1 A-AATGAAAGACTAAATGCCTAAC
356348 GGTGCATAAT
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
80 1 0.01
81 88 0.97
82 2 0.02
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.28
Consensus pattern (81 bp):
AAATGAAAGACTAAATGCCTAACTATGCATTTGGCAGAAAGGTGACAATAATACAAGTTAGATGA
AAGGTTAAATGCCTTT
Found at i:356336 original size:22 final size:22
Alignment explanation
Indices: 356301--356342 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
356291 ATAATACAAG
* *
356301 TTAGATGAAGGGTTAAATGCCT
1 TTAGAAGAAAGGTTAAATGCCT
356323 TTAGAAGAAAGGTTAAATGC
1 TTAGAAGAAAGGTTAAATGC
356343 ATAACGGTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.38, C:0.07, G:0.26, T:0.29
Consensus pattern (22 bp):
TTAGAAGAAAGGTTAAATGCCT
Found at i:356390 original size:46 final size:46
Alignment explanation
Indices: 356337--356485 Score: 228
Period size: 46 Copynumber: 3.2 Consensus size: 46
356327 AAGAAAGGTT
* * *
356337 AAATGCATAACGGTGCATAATAGGTATGAAATGATGCCATAAATGA
1 AAATGCATAACGGTGCATAATTGGCATGAAAGGATGCCATAAATGA
356383 AAATGCATAACGGTGCATAATTGGCATGAAAGGATGCCATAAAT-A
1 AAATGCATAACGGTGCATAATTGGCATGAAAGGATGCCATAAATGA
* *
356428 AAAGTGCATAACGGTGCATAGTTGGCATGAAAGGATTCCATAAATGA
1 AAA-TGCATAACGGTGCATAATTGGCATGAAAGGATGCCATAAATGA
*
356475 AAATGTATAAC
1 AAATGCATAAC
356486 TGTAATACCC
Statistics
Matches: 95, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
45 4 0.04
46 87 0.92
47 4 0.04
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.23
Consensus pattern (46 bp):
AAATGCATAACGGTGCATAATTGGCATGAAAGGATGCCATAAATGA
Found at i:357215 original size:22 final size:22
Alignment explanation
Indices: 357188--357238 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
357178 GGAGTTATGT
357188 CGTGAAATAGGAAAGTGATCTA
1 CGTGAAATAGGAAAGTGATCTA
*
357210 CTTGAAATAGGAAAGTGATCTA
1 CGTGAAATAGGAAAGTGATCTA
357232 CGTGAAA
1 CGTGAAA
357239 AACGCTATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.41, C:0.10, G:0.25, T:0.24
Consensus pattern (22 bp):
CGTGAAATAGGAAAGTGATCTA
Found at i:357721 original size:28 final size:31
Alignment explanation
Indices: 357689--357745 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
357679 GAAAAACTCA
*
357689 GGGACC-ATTTTGTAA-TTT-AAAAAGTTAG
1 GGGACCAATTTGGTAACTTTGAAAAAGTTAG
357717 GGGACCAATTTGGTAACTTTGAAAAAGTT
1 GGGACCAATTTGGTAACTTTGAAAAAGTT
357746 GTGAATGGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 6 0.24
29 8 0.32
30 3 0.12
31 8 0.32
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.33
Consensus pattern (31 bp):
GGGACCAATTTGGTAACTTTGAAAAAGTTAG
Found at i:358877 original size:45 final size:45
Alignment explanation
Indices: 358827--358958 Score: 228
Period size: 45 Copynumber: 2.9 Consensus size: 45
358817 GTAACCATGC
358827 AAATAAGCTTACGAGCTTATGGGTTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGTTAAATGGTAAGTATATTGGTA
358872 AAATAAGCTTACGAGCTTATGGGTTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGTTAAATGGTAAGTATATTGGTA
* ** *
358917 AAATAAGCTTACGAGCTTATGAGAAAAATGGTAAATATATTG
1 AAATAAGCTTACGAGCTTATGGGTTAAATGGTAAGTATATTG
358959 ATAAGAAATT
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 83 1.00
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.32
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGGTTAAATGGTAAGTATATTGGTA
Found at i:359407 original size:21 final size:21
Alignment explanation
Indices: 359373--359413 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
359363 GTAGTAGTAT
* *
359373 TGTAGTAGTGCATCGATACAA
1 TGTAGCAGTACATCGATACAA
359394 TGTAGCAGTACATCGATACA
1 TGTAGCAGTACATCGATACA
359414 CATTTTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (21 bp):
TGTAGCAGTACATCGATACAA
Found at i:359794 original size:46 final size:46
Alignment explanation
Indices: 359725--359839 Score: 167
Period size: 46 Copynumber: 2.5 Consensus size: 46
359715 ACAACAACGA
* * **
359725 TGCATAATTGGCATGAAAGGATGTCATAAATGAAAATGAATAATGG
1 TGCATAATTGGCATGAAATGATGTCATAAATGAAAATAAATAACAG
* * *
359771 TGCATAATTGGCATGACATGATGTCATGAATGGAAATAAATAACAG
1 TGCATAATTGGCATGAAATGATGTCATAAATGAAAATAAATAACAG
359817 TGCATAATTGGCATGAAATGATG
1 TGCATAATTGGCATGAAATGATG
359840 CTGCAAATGA
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 61 1.00
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.27
Consensus pattern (46 bp):
TGCATAATTGGCATGAAATGATGTCATAAATGAAAATAAATAACAG
Found at i:359854 original size:46 final size:44
Alignment explanation
Indices: 359725--359854 Score: 152
Period size: 46 Copynumber: 2.8 Consensus size: 44
359715 ACAACAACGA
* * **
359725 TGCATAATTGGCATGAAAGGATGTCATAAATGAAAATGAATAATGG
1 TGCATAATTGGCATGAAATGATGTC--AAATGAAAATAAATAACAG
* *
359771 TGCATAATTGGCATGACATGATGTCATGAATGGAAATAAATAACAG
1 TGCATAATTGGCATGAAATGATGTCA--AATGAAAATAAATAACAG
359817 TGCATAATTGGCATGAAATGATGCTGCAAATGAAAATA
1 TGCATAATTGGCATGAAATGATG-T-CAAATGAAAATA
359855 CATTACTTTC
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
44 1 0.01
46 68 0.94
47 1 0.01
48 2 0.03
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.26
Consensus pattern (44 bp):
TGCATAATTGGCATGAAATGATGTCAAATGAAAATAAATAACAG
Found at i:362435 original size:30 final size:30
Alignment explanation
Indices: 362379--362437 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
362369 CAAAATTTTT
* *
362379 GGGACAATTTTCTAATTTTGTGAAAGTTGA
1 GGGACAATTTGCTAATTTTGTAAAAGTTGA
362409 GGGACATATTTGCTAATTTTG-AAAAGTTG
1 GGGACA-ATTTGCTAATTTTGTAAAAGTTG
362438 TGGGGTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.31, C:0.07, G:0.24, T:0.39
Consensus pattern (30 bp):
GGGACAATTTGCTAATTTTGTAAAAGTTGA
Found at i:367376 original size:20 final size:20
Alignment explanation
Indices: 367304--367378 Score: 80
Period size: 20 Copynumber: 3.7 Consensus size: 20
367294 AAAACATCTT
* *
367304 GCCCGAAGGTCTTATGGATG
1 GCCCGAAGGACTTATTGATG
*
367324 GCCCGAAGGACTTA-TGATCAT
1 GCCCGAAGGACTTATTGAT--G
* *
367345 GCTCGAAAGACTTATTGATG
1 GCCCGAAGGACTTATTGATG
367365 GCCCGAAGGACTTA
1 GCCCGAAGGACTTA
367379 CTAAGTGTGA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
19 3 0.07
20 25 0.57
21 12 0.27
22 4 0.09
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (20 bp):
GCCCGAAGGACTTATTGATG
Found at i:367630 original size:34 final size:34
Alignment explanation
Indices: 367584--367787 Score: 219
Period size: 36 Copynumber: 5.9 Consensus size: 34
367574 CTGATGGATT
*
367584 TGCTTCAATACTCTTCGGTGAAGGCTTAAGATAG
1 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATAG
* * *
367618 TGCTTCACTACTCTTCTGTGAAGGCTTAAAATTG
1 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATAG
* * *
367652 TTTGCTTTACTACTCTTTGGTGAAGGCTTAAGATGG
1 --TGCTTCACTACTCTTCGGTGAAGGCTTAAGATAG
* * * * *
367688 TGCTTCAATACTCTTCTGTGAGGGCTTAAAATTATT
1 TGCTTCACTACTCTTCGGTGAAGGCTTAAGA-TA-G
* * *
367724 TGATTCAGTACTCTTCGGTGAAGGCTTAAGATGAT
1 TGCTTCACTACTCTTCGGTGAAGGCTTAAGAT-AG
*
367759 TGCTTCGCTACTCTTCGGTGAAGGCTTAA
1 TGCTTCACTACTCTTCGGTGAAGGCTTAA
367788 AATTGACTTG
Statistics
Matches: 140, Mismatches: 25, Indels: 9
0.80 0.14 0.05
Matches are distributed among these distances:
34 55 0.39
35 29 0.21
36 56 0.40
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (34 bp):
TGCTTCACTACTCTTCGGTGAAGGCTTAAGATAG
Found at i:367665 original size:36 final size:36
Alignment explanation
Indices: 367582--367792 Score: 234
Period size: 34 Copynumber: 6.0 Consensus size: 36
367572 TACTGATGGA
* * *
367582 TTTGCTTCAATACTCTTCGGTGAAGGCTTAAGATAG
1 TTTGCTTCACTACTCTTCGGTGAAGGCTTAAAATTG
*
367618 --TGCTTCACTACTCTTCTGTGAAGGCTTAAAATTG
1 TTTGCTTCACTACTCTTCGGTGAAGGCTTAAAATTG
* * *
367652 TTTGCTTTACTACTCTTTGGTGAAGGCTTAAGA-TG
1 TTTGCTTCACTACTCTTCGGTGAAGGCTTAAAATTG
* * * * *
367687 -GTGCTTCAATACTCTTCTGTGAGGGCTTAAAATTA
1 TTTGCTTCACTACTCTTCGGTGAAGGCTTAAAATTG
* * *
367722 TTTGATTCAGTACTCTTCGGTGAAGGCTTAAGA-TG
1 TTTGCTTCACTACTCTTCGGTGAAGGCTTAAAATTG
* *
367757 ATTGCTTCGCTACTCTTCGGTGAAGGCTTAAAATTG
1 TTTGCTTCACTACTCTTCGGTGAAGGCTTAAAATTG
367793 ACTTGCCCCA
Statistics
Matches: 142, Mismatches: 28, Indels: 10
0.79 0.16 0.06
Matches are distributed among these distances:
34 55 0.39
35 32 0.23
36 55 0.39
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (36 bp):
TTTGCTTCACTACTCTTCGGTGAAGGCTTAAAATTG
Found at i:367700 original size:70 final size:70
Alignment explanation
Indices: 367582--367792 Score: 305
Period size: 70 Copynumber: 3.0 Consensus size: 70
367572 TACTGATGGA
*
367582 TTTGCTTCAATACTCTTCGGTGAAGGCTTAAGATAGTGCTTCACTACTCTTCTGTGAAGGCTTAA
1 TTTGCTTCAATACTCTTCGGTGAAGGCTTAAGATGGTGCTTCACTACTCTTCTGTGAAGGCTTAA
367647 AATTG
66 AATTG
* * * * *
367652 TTTGCTTTACTACTCTTTGGTGAAGGCTTAAGATGGTGCTTCAATACTCTTCTGTGAGGGCTTAA
1 TTTGCTTCAATACTCTTCGGTGAAGGCTTAAGATGGTGCTTCACTACTCTTCTGTGAAGGCTTAA
*
367717 AATTA
66 AATTG
* * * * *
367722 TTTGATTCAGTACTCTTCGGTGAAGGCTTAAGATGATTGCTTCGCTACTCTTCGGTGAAGGCTTA
1 TTTGCTTCAATACTCTTCGGTGAAGGCTTAAGATG-GTGCTTCACTACTCTTCTGTGAAGGCTTA
367787 AAATTG
65 AAATTG
367793 ACTTGCCCCA
Statistics
Matches: 123, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
70 94 0.76
71 29 0.24
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (70 bp):
TTTGCTTCAATACTCTTCGGTGAAGGCTTAAGATGGTGCTTCACTACTCTTCTGTGAAGGCTTAA
AATTG
Found at i:369326 original size:114 final size:117
Alignment explanation
Indices: 369110--369465 Score: 459
Period size: 125 Copynumber: 3.0 Consensus size: 117
369100 CATTATCTTA
* * * * * *
369110 TACTGGTACGGGGCCCTCAAAATACCCCAACACCTCAAATTGTAAGGCTCATTCTTAATACCTTC
1 TACTGGTAC-AGGCCATCAAAATGCCCCATCACCTCAAATTGTAAGGCTCATTCTTCATGCCTTC
* *
369175 TTGGTCTGAATCTTATCATCTCAACATGATGTGGGTTCAATCGTGCCCCAA-C
65 TTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCCCCAATC
* * *
369227 -A-TGGTAC-GAGCCTTCAAAATGCCCCATCACCTCAAATTATAAGGCTCATTCTTCATGCCTCC
1 TACTGGTACAG-GCCATCAAAATGCCCCATCACCTCAAATTGTAAGGCTCATTCTTCATGCCTTC
*
369289 TTGGTCTGAATCTCGTCATCTCAACATGATGTGGGTTCAGTCGTGCCCCAACATTATC
65 TTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTG-CCC--CA--ATC
* *
369347 TTATACTGGTACAGGCCATCAAAATGCCCCATCACCTCAAATTGTAAGGCTCATTCTTCAGGCTT
1 ---TACTGGTACAGGCCATCAAAATGCCCCATCACCTCAAATTGTAAGGCTCATTCTTCATGCCT
*
369412 TCTTGGTTTGAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCCCCAAT
63 TCTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCCCCAAT
369466 ATATCCTAAC
Statistics
Matches: 209, Mismatches: 17, Indels: 23
0.84 0.07 0.09
Matches are distributed among these distances:
113 1 0.00
114 88 0.42
115 9 0.04
116 1 0.00
117 2 0.01
119 1 0.00
120 3 0.01
122 2 0.01
124 4 0.02
125 97 0.46
126 1 0.00
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.31
Consensus pattern (117 bp):
TACTGGTACAGGCCATCAAAATGCCCCATCACCTCAAATTGTAAGGCTCATTCTTCATGCCTTCT
TGGTCTGAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCCCCAATC
Found at i:375933 original size:16 final size:16
Alignment explanation
Indices: 375912--375942 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
375902 ACCACCCCTC
375912 TTCTATTATTATTTTT
1 TTCTATTATTATTTTT
*
375928 TTCTATTTTTATTTT
1 TTCTATTATTATTTT
375943 AGAAATCCCG
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:0.16, C:0.06, G:0.00, T:0.77
Consensus pattern (16 bp):
TTCTATTATTATTTTT
Found at i:377100 original size:22 final size:22
Alignment explanation
Indices: 377070--377112 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
377060 TCATTGAGCA
* *
377070 CGATTGTCTCCAAATTAATTCC
1 CGATCGTCTCCAAATGAATTCC
*
377092 CGATCGTCTTCAAATGAATTC
1 CGATCGTCTCCAAATGAATTC
377113 AAATGGTCCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.35
Consensus pattern (22 bp):
CGATCGTCTCCAAATGAATTCC
Found at i:381773 original size:19 final size:19
Alignment explanation
Indices: 381749--381791 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
381739 TTCATTGCGA
*
381749 AAATTTGAAA-TTTAAATTG
1 AAATTT-AAAGTTTAAATTC
*
381768 AAATTTAAAGTTTCAATTC
1 AAATTTAAAGTTTAAATTC
381787 AAATT
1 AAATT
381792 ATTCATCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.42
Consensus pattern (19 bp):
AAATTTAAAGTTTAAATTC
Found at i:381930 original size:12 final size:13
Alignment explanation
Indices: 381913--381943 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
381903 ATGTTAAAAT
381913 AAAAAAT-GAAAG
1 AAAAAATAGAAAG
381925 AAAAAATAGAAAG
1 AAAAAATAGAAAG
381938 AAAAAA
1 AAAAAA
381944 ATTTAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (13 bp):
AAAAAATAGAAAG
Found at i:381989 original size:15 final size:15
Alignment explanation
Indices: 381971--382001 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
381961 AAAAATTAAA
381971 AAATGTTAAGAAAAT
1 AAATGTTAAGAAAAT
*
381986 AAATGTTAATAAAAT
1 AAATGTTAAGAAAAT
382001 A
1 A
382002 CAAAACCCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (15 bp):
AAATGTTAAGAAAAT
Found at i:383295 original size:32 final size:33
Alignment explanation
Indices: 383213--383344 Score: 117
Period size: 34 Copynumber: 3.9 Consensus size: 33
383203 ATATTTTTTT
* * *
383213 AAAAATATTTTCAAAACCATGTAATATATTTTCA
1 AAAAATATTTTCAAAACTATATAATATA-TATCA
* * *
383247 AAAATTGTTTTTAAAACTATATAATATATAT-A
1 AAAAATATTTTCAAAACTATATAATATATATCA
*
383279 AAAAATATTTTCAAAACTATATATATATATTTTTTTC-
1 AAAAATATTTTCAAAACTATATA-ATATA----TATCA
*
383316 AAAAATATTTT-AAAACTATATATTATATA
1 AAAAATATTTTCAAAACTATATAATATATA
383345 GTTTTTTAAA
Statistics
Matches: 80, Mismatches: 12, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
31 1 0.01
32 21 0.26
33 7 0.09
34 23 0.29
35 4 0.05
36 11 0.14
37 13 0.16
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (33 bp):
AAAAATATTTTCAAAACTATATAATATATATCA
Found at i:383304 original size:36 final size:36
Alignment explanation
Indices: 383264--383381 Score: 109
Period size: 36 Copynumber: 3.3 Consensus size: 36
383254 TTTTTAAAAC
383264 TATATA-ATATATATAAAAAATATTTTCAAAACTATA
1 TATATATATATATATAAAAAATATTTT-AAAACTATA
* * * *
383300 TATATATATTTTTTTCAAAAATATTTTAAAACTATA
1 TATATATATATATATAAAAAATATTTTAAAACTATA
* ** *
383336 TAT-TATATAGT-TTTTTAAAATGTTTTTAAAACTATA
1 TATATATATA-TATATAAAAAAT-ATTTTAAAACTATA
383372 TAT-TATATAT
1 TATATATATAT
383382 GTTTTCAATA
Statistics
Matches: 71, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
35 14 0.20
36 41 0.58
37 16 0.23
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (36 bp):
TATATATATATATATAAAAAATATTTTAAAACTATA
Found at i:383368 original size:104 final size:103
Alignment explanation
Indices: 383188--383381 Score: 286
Period size: 104 Copynumber: 1.9 Consensus size: 103
383178 TTTTTAAAAA
*
383188 AAAACTATATAATATATATTTTTTTAAAAATATTTTCAAAACCATGTAATATATTTTCAAAAATT
1 AAAACTATATAATATATATTTTTTTAAAAATATTTTCAAAACCATATAATATATTTTCAAAAATT
383253 GTTTTTAAAACTATATAATATATATAAAAAATATTTTC
66 GTTTTTAAAACTATATAATATATATAAAAAATATTTTC
* **
383291 AAAACTATAT-ATATATATTTTTTTCAAAAATATTTT-AAAACTATATATTATATAGTTTTTTAA
1 AAAACTATATAATATATATTTTTTT-AAAAATATTTTCAAAACCATATA--ATATA-TTTTCAAA
*
383354 AA-TGTTTTTAAAACTATATATTATATAT
62 AATTGTTTTTAAAACTATATAATATATAT
383382 GTTTTCAATA
Statistics
Matches: 82, Mismatches: 5, Indels: 7
0.87 0.05 0.07
Matches are distributed among these distances:
102 23 0.28
103 21 0.26
104 30 0.37
105 8 0.10
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (103 bp):
AAAACTATATAATATATATTTTTTTAAAAATATTTTCAAAACCATATAATATATTTTCAAAAATT
GTTTTTAAAACTATATAATATATATAAAAAATATTTTC
Found at i:383394 original size:54 final size:56
Alignment explanation
Indices: 383335--383445 Score: 199
Period size: 56 Copynumber: 2.0 Consensus size: 56
383325 TTAAAACTAT
*
383335 ATATTATAT-AGTTTTTTAAAATGTTTTT-AAAACTATATATTATATATGTTTTCA
1 ATATTATATAAGTTTTTTAAAATGTTTTTAAAAACTATATATTATATAAGTTTTCA
383389 ATATTATATAAGTTTTTTAAAATGTTTTTAAAAACTATATATTATATAAGTTTTCA
1 ATATTATATAAGTTTTTTAAAATGTTTTTAAAAACTATATATTATATAAGTTTTCA
383445 A
1 A
383446 AATGTTTTCA
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
54 9 0.17
55 19 0.35
56 26 0.48
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (56 bp):
ATATTATATAAGTTTTTTAAAATGTTTTTAAAAACTATATATTATATAAGTTTTCA
Found at i:383459 original size:37 final size:38
Alignment explanation
Indices: 383389--383472 Score: 143
Period size: 37 Copynumber: 2.2 Consensus size: 38
383379 TATGTTTTCA
* *
383389 ATATTATATAAGTTTTTTAAAATGTTTTTAAAAACTAT
1 ATATTATATAAGTTTTTCAAAATGTTTTCAAAAACTAT
383427 ATATTATATAAG-TTTTCAAAATGTTTTCAAAAACTAT
1 ATATTATATAAGTTTTTCAAAATGTTTTCAAAAACTAT
383464 ATATTATAT
1 ATATTATAT
383473 TTCAAAAACT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
37 32 0.73
38 12 0.27
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (38 bp):
ATATTATATAAGTTTTTCAAAATGTTTTCAAAAACTAT
Found at i:384441 original size:83 final size:84
Alignment explanation
Indices: 384146--384637 Score: 621
Period size: 83 Copynumber: 5.8 Consensus size: 84
384136 ATATGTCATC
* * *
384146 GAGCTGAATGGAATTGAACTCGATAGTTTTTTGTTGAAAGATAGCCCTTCTCGCCTTGAGCTATG
1 GAGCTGAATGGAATCGAACTCGA-AGATTTTTGTTGATAGATAGCCCTTCTCGCCTTGAGCTATG
* *
384211 CTATAAATTTGATATGC-CTTT
65 CTGTAAATTTG-GATGCAC-TT
* * * ** *
384232 GAGCAGAATGGAATCAAACTCGAAGGTTTTTGTTGGCAGATATCCCTTCTCGCCTTTGAGCTATG
1 GAGCTGAATGGAATCGAACTCGAAGATTTTTGTTGATAGATAGCCCTTCTCGCC-TTGAGCTATG
* * *
384297 CTTTAAATTTGATATGCCCTT
65 CTGTAAATTTG-GATGCACTT
* *
384318 GAGCTGAATGGAATCGAACTCGGAGGTTTTTGTTGATAGATAGCCCTTCTCGCCTTGAGCTATGC
1 GAGCTGAATGGAATCGAACTCGAAGATTTTTGTTGATAGATAGCCCTTCTCGCCTTGAGCTATGC
384383 TGTAAATTTGGATGCACTT
66 TGTAAATTTGGATGCACTT
* * * *
384402 GAGCTGAATGGAAT-AAACTCTAAGATTTTTGTTGATAGATAGCCATTCTCGCCTTGAGTTATGC
1 GAGCTGAATGGAATCGAACTCGAAGATTTTTGTTGATAGATAGCCCTTCTCGCCTTGAGCTATGC
*
384466 TGTAAATTTGGCTGCACTT
66 TGTAAATTTGGATGCACTT
* * * **
384485 GAGCTTAATGGAATCGAACTCGAAGATTTTTGTTGATAGATAACCCTTCTCGCCTTGAACTATAA
1 GAGCTGAATGGAATCGAACTCGAAGATTTTTGTTGATAGATAGCCCTTCTCGCCTTGAGCTATGC
* * *
384550 TCTAAATTTGGCTGCCCTT
66 TGTAAATTTGGATGCACTT
* ** *
384569 GAGCTGAATGGAATCGAACTCGAAG-GTTTTGTTGATAGATAATCCTTCTCGCCTTGAGCTATAC
1 GAGCTGAATGGAATCGAACTCGAAGATTTTTGTTGATAGATAGCCCTTCTCGCCTTGAGCTATGC
384633 TGTAA
66 TGTAA
384638 TAGGTTGGGA
Statistics
Matches: 362, Mismatches: 41, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
83 114 0.31
84 104 0.29
85 47 0.13
86 96 0.27
87 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.35
Consensus pattern (84 bp):
GAGCTGAATGGAATCGAACTCGAAGATTTTTGTTGATAGATAGCCCTTCTCGCCTTGAGCTATGC
TGTAAATTTGGATGCACTT
Found at i:384524 original size:167 final size:166
Alignment explanation
Indices: 384146--384637 Score: 628
Period size: 167 Copynumber: 2.9 Consensus size: 166
384136 ATATGTCATC
* * *
384146 GAGCTGAATGGAATTGAACTCGATAGTTTTTTGTTGAAAGATAGCCCTTCTCGCCTTGAGCTATG
1 GAGCTGAATGGAATCGAACTCGA-AGATTTTTGTTGATAGATAGCCCTTCTCGCCTTGAGCTATG
* * **
384211 CTATAAATTTGATATGCCTTTGAGCAGAATGGAATCAAACTCGAAGGTTTTTGTTGGCAGATATC
65 CTATAAATTTG-GATGCC-TTGAGCTGAATGGAATCAAACTCGAA-GTTTTTGTTGATAGATAT-
* * *
384276 CCTTCTCGCCTTTGAGCTATGCTTTAAATTTGATATGCCCTT
126 CCTTCTCGCC-TTGAGCTATGCTGTAAATTTGAGATGCACTT
* *
384318 GAGCTGAATGGAATCGAACTCGGAGGTTTTTGTTGATAGATAGCCCTTCTCGCCTTGAGCTATGC
1 GAGCTGAATGGAATCGAACTCGAAGATTTTTGTTGATAGATAGCCCTTCTCGCCTTGAGCTATGC
* * *
384383 TGTAAATTTGGATGCACTTGAGCTGAATGGAAT-AAACTCTAAGATTTTTGTTGATAGATAGCCA
66 TATAAATTTGGATGC-CTTGAGCTGAATGGAATCAAACTCGAAG-TTTTTGTTGATAGATATCC-
* *
384447 TTCTCGCCTTGAGTTATGCTGTAAATTTG-GCTGCACTT
128 TTCTCGCCTTGAGCTATGCTGTAAATTTGAGATGCACTT
* * * **
384485 GAGCTTAATGGAATCGAACTCGAAGATTTTTGTTGATAGATAACCCTTCTCGCCTTGAACTATAA
1 GAGCTGAATGGAATCGAACTCGAAGATTTTTGTTGATAGATAGCCCTTCTCGCCTTGAGCTATGC
* * * *
384550 TCTAAATTTGGCTGCCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTGTTGATAGATAATCCT
66 TATAAATTTGGATG-CCTTGAGCTGAATGGAATCAAACTCGAAGTTTTTGTTGATAGAT-ATCCT
*
384615 TCTCGCCTTGAGCTATACTGTAA
129 TCTCGCCTTGAGCTATGCTGTAA
384638 TAGGTTGGGA
Statistics
Matches: 283, Mismatches: 31, Indels: 17
0.85 0.09 0.05
Matches are distributed among these distances:
167 129 0.46
168 34 0.12
169 30 0.11
170 19 0.07
171 50 0.18
172 21 0.07
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.35
Consensus pattern (166 bp):
GAGCTGAATGGAATCGAACTCGAAGATTTTTGTTGATAGATAGCCCTTCTCGCCTTGAGCTATGC
TATAAATTTGGATGCCTTGAGCTGAATGGAATCAAACTCGAAGTTTTTGTTGATAGATATCCTTC
TCGCCTTGAGCTATGCTGTAAATTTGAGATGCACTT
Found at i:390463 original size:5 final size:5
Alignment explanation
Indices: 390455--390597 Score: 68
Period size: 5 Copynumber: 27.8 Consensus size: 5
390445 ACAAAAAGAA
*
390455 AAAAT AAAAT AAAAT AAAAT AATAAC AAAAT -AAAT AAAAT -AAAT -AAAT
1 AAAAT AAAAT AAAAT AAAAT AA-AAT AAAAT AAAAT AAAAT AAAAT AAAAT
* * * *
390503 AAAATT GAGAAG AATATT AAAAT -AAA- AAAAT GAAAT -AAA- AAAAT
1 AAAA-T -AAAAT AA-AAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
*
390547 AGAAAT AAAA- AAAAGTT AAAATTT GAAAAT AAAAT AATAAA AAAATT AAAA
1 A-AAAT AAAAT AAAA--T AAAA--T -AAAAT AAAAT AA-AAT AAAA-T AAAA
390598 ATGTTAAGAA
Statistics
Matches: 109, Mismatches: 12, Indels: 33
0.71 0.08 0.21
Matches are distributed among these distances:
4 28 0.26
5 46 0.42
6 22 0.20
7 9 0.08
8 4 0.04
ACGTcount: A:0.73, C:0.01, G:0.05, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:390478 original size:13 final size:13
Alignment explanation
Indices: 390453--390588 Score: 60
Period size: 13 Copynumber: 10.9 Consensus size: 13
390443 ATACAAAAAG
390453 AAAA-AATAAAAT
1 AAAATAATAAAAT
390465 AAAATAA-AATAAT
1 AAAATAATAA-AAT
390478 AACAA-AAT-AAAT
1 AA-AATAATAAAAT
390490 AAAATAA-ATAAAT
1 AAAATAATA-AAAT
* *
390503 AAAAT--TGAGA-
1 AAAATAATAAAAT
* *
390513 AGAATATTAAAAT
1 AAAATAATAAAAT
* *
390526 AAAAAAATGAAAT
1 AAAATAATAAAAT
*
390539 AAAAAAATAGAAAT
1 AAAATAATA-AAAT
**
390553 AAAA-AA-AAGTT
1 AAAATAATAAAAT
*
390564 AAAAT-TTGAAAAT
1 AAAATAAT-AAAAT
390577 AAAATAATAAAA
1 AAAATAATAAAA
390589 AAATTAAAAA
Statistics
Matches: 92, Mismatches: 16, Indels: 31
0.66 0.12 0.22
Matches are distributed among these distances:
10 4 0.04
11 10 0.11
12 17 0.18
13 50 0.54
14 11 0.12
ACGTcount: A:0.74, C:0.01, G:0.05, T:0.21
Consensus pattern (13 bp):
AAAATAATAAAAT
Found at i:390545 original size:14 final size:14
Alignment explanation
Indices: 390522--390559 Score: 69
Period size: 13 Copynumber: 2.8 Consensus size: 14
390512 AAGAATATTA
390522 AAATAAAAAAAT-G
1 AAATAAAAAAATAG
390535 AAATAAAAAAATAG
1 AAATAAAAAAATAG
390549 AAATAAAAAAA
1 AAATAAAAAAA
390560 AGTTAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.13
Consensus pattern (14 bp):
AAATAAAAAAATAG
Found at i:390616 original size:15 final size:15
Alignment explanation
Indices: 390596--390626 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
390586 AAAAAATTAA
390596 AAATGTTAAGAAAAT
1 AAATGTTAAGAAAAT
*
390611 AAATGTTAATAAAAT
1 AAATGTTAAGAAAAT
390626 A
1 A
390627 CAAAAAAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (15 bp):
AAATGTTAAGAAAAT
Found at i:391911 original size:36 final size:35
Alignment explanation
Indices: 391871--392162 Score: 228
Period size: 36 Copynumber: 8.3 Consensus size: 35
391861 GTTCAAAACG
*
391871 TTTTCAAAAATGTTTTTTAAAATTATATAATATATA
1 TTTTCAAAAAT-TTTTTCAAAATTATATAATATATA
**
391907 TTTTCAAAAATTATTTTCAAAACCATATAATATAT-
1 TTTTCAAAAATT-TTTTCAAAATTATATAATATATA
* *
391942 TTTT-AAAAATTGTTTTTAAAACTATAT-A-ATATA
1 TTTTCAAAAATT-TTTTCAAAATTATATAATATATA
* *
391975 -TTTCAAAAATATTTTCAAAACTATATAATATATA
1 TTTTCAAAAATTTTTTCAAAATTATATAATATATA
* *
392009 TTTTTTTC-AAAATTATTTTCAAACTATATATTATATATA
1 ---TTTTCAAAAATT-TTTTCAAAAT-TATATAATATATA
* * * *
392048 TTTT---TAATTTTTTAAAAACTATATATTATATATG
1 TTTTCAAAAATTTTTTCAAAA-T-TATATAATATATA
* *
392082 TTTTC-AAAATATTTTCAAAATTATATATTATATATG
1 TTTTCAAAAATTTTTTCAAAATTATATA--ATATATA
* *
392118 TTTTC-AAAATGTTTTCAAAATTATATATTATATATG
1 TTTTCAAAAATTTTTTCAAAATTATATA--ATATATA
392154 TTTTCAAAA
1 TTTTCAAAA
392163 CTATATATTA
Statistics
Matches: 218, Mismatches: 21, Indels: 33
0.80 0.08 0.12
Matches are distributed among these distances:
32 21 0.10
33 15 0.07
34 52 0.24
35 6 0.03
36 92 0.42
37 8 0.04
38 12 0.06
39 12 0.06
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (35 bp):
TTTTCAAAAATTTTTTCAAAATTATATAATATATA
Found at i:392155 original size:25 final size:25
Alignment explanation
Indices: 392126--392188 Score: 99
Period size: 25 Copynumber: 2.5 Consensus size: 25
392116 TGTTTTCAAA
392126 ATGTTTTCAAAATTATATATTATAT
1 ATGTTTTCAAAATTATATATTATAT
*
392151 ATGTTTTCAAAACTATATATTATAT
1 ATGTTTTCAAAATTATATATTATAT
* *
392176 AAGTTTTTAAAAT
1 ATGTTTTCAAAAT
392189 GTTTTCAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (25 bp):
ATGTTTTCAAAATTATATATTATAT
Found at i:392159 original size:61 final size:62
Alignment explanation
Indices: 392093--392225 Score: 223
Period size: 61 Copynumber: 2.2 Consensus size: 62
392083 TTTCAAAATA
* *
392093 TTTTCAAAATTATATATTATATATGTTTTCAAAATGTTTTC-AAAATTATATATTATATATG
1 TTTTCAAAATTATATATTATATAAGTTTTCAAAATGTTTTCAAAAATTATATATTATATAGG
* *
392154 TTTTCAAAACTATATATTATATAAGTTTTTAAAATGTTTTCAAAAATTATATATTATATAGG
1 TTTTCAAAATTATATATTATATAAGTTTTCAAAATGTTTTCAAAAATTATATATTATATAGG
392216 TTTTCAAAAT
1 TTTTCAAAAT
392226 GTTTTCAAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
61 38 0.58
62 28 0.42
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (62 bp):
TTTTCAAAATTATATATTATATAAGTTTTCAAAATGTTTTCAAAAATTATATATTATATAGG
Found at i:392207 original size:134 final size:132
Alignment explanation
Indices: 392024--392288 Score: 374
Period size: 134 Copynumber: 2.0 Consensus size: 132
392014 TTCAAAATTA
* *
392024 TTTTCAAACTATATATTATATATATTTTTAATTTTTTAAAAACTATATATTATATATGTTTTCAA
1 TTTTCAAACTATATATTATATATATTTTTAATTTTTCAAAAACTATATATTATATAGGTTTTCAA
* * * * *
392089 AATATTTTCAAAATTATATATTATATATG-TTTTCAAAATG-TTTTCAAAATTATATATTATATA
66 AATATTTTCAAAACTATATATTATATAAGTTTTTCAAAATGTTTTTAAAAACTATAGATTATATA
392152 TG
131 TG
*
392154 TTTTCAAAACTATATATTATATA-AGTTTTTAAAATGTTTTCAAAAATTATATATTATATAGGTT
1 TTTTC-AAACTATATATTATATATA-TTTTT--AAT-TTTTCAAAAACTATATATTATATAGGTT
* *
392218 TTCAAAATGTTTTCAAAACTATATATTATATAAGTTTTTTAAAATGTTTTTAAAAACTATAGATT
61 TTCAAAATATTTTCAAAACTATATATTATATAAGTTTTTCAAAATGTTTTTAAAAACTATAGATT
392283 ATATAT
126 ATATAT
392289 TATATTTCAA
Statistics
Matches: 118, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
130 6 0.05
131 22 0.19
133 3 0.03
134 56 0.47
135 10 0.08
136 21 0.18
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (132 bp):
TTTTCAAACTATATATTATATATATTTTTAATTTTTCAAAAACTATATATTATATAGGTTTTCAA
AATATTTTCAAAACTATATATTATATAAGTTTTTCAAAATGTTTTTAAAAACTATAGATTATATA
TG
Found at i:392212 original size:37 final size:36
Alignment explanation
Indices: 392151--392287 Score: 202
Period size: 37 Copynumber: 3.7 Consensus size: 36
392141 TATATTATAT
392151 ATGTTTTCAAAACTATATATTATATAAGTTTTTAAA
1 ATGTTTTCAAAACTATATATTATATAAGTTTTTAAA
* * *
392187 ATGTTTTCAAAAATTATATATTATATAGGTTTTCAAA
1 ATGTTTTC-AAAACTATATATTATATAAGTTTTTAAA
392224 ATGTTTTCAAAACTATATATTATATAAGTTTTTTAAA
1 ATGTTTTCAAAACTATATATTATATAAG-TTTTTAAA
* *
392261 ATGTTTTTAAAAACTATAGATTATATA
1 ATG-TTTTCAAAACTATATATTATATA
392288 TTATATTTCA
Statistics
Matches: 90, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
36 26 0.29
37 43 0.48
38 21 0.23
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (36 bp):
ATGTTTTCAAAACTATATATTATATAAGTTTTTAAA
Found at i:392234 original size:73 final size:74
Alignment explanation
Indices: 392151--392287 Score: 240
Period size: 74 Copynumber: 1.9 Consensus size: 74
392141 TATATTATAT
* *
392151 ATGTTTTCAAAACTATATATTATATAAG-TTTTTAAAATGTTTTCAAAAATTATATATTATATAG
1 ATGTTTTCAAAACTATATATTATATAAGTTTTTTAAAATGTTTTCAAAAACTATAGATTATATAG
392215 GTTTTCAAA
66 GTTTTCAAA
*
392224 ATGTTTTCAAAACTATATATTATATAAGTTTTTTAAAATGTTTTTAAAAACTATAGATTATATA
1 ATGTTTTCAAAACTATATATTATATAAGTTTTTTAAAATGTTTTCAAAAACTATAGATTATATA
392288 TTATATTTCA
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
73 28 0.47
74 32 0.53
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (74 bp):
ATGTTTTCAAAACTATATATTATATAAGTTTTTTAAAATGTTTTCAAAAACTATAGATTATATAG
GTTTTCAAA
Found at i:392242 original size:98 final size:97
Alignment explanation
Indices: 392057--392255 Score: 326
Period size: 98 Copynumber: 2.0 Consensus size: 97
392047 ATTTTTAATT
* *
392057 TTTTAAAAACTATATATTATATATGTTTTCAAAATATTTTCAAAATTATATATTATATATGTTTT
1 TTTTAAAAACTATATATTATATAAGTTTTCAAAATATTTTCAAAATTATATATTATATAGGTTTT
* *
392122 CAAAATGTTTTCAAAATTATATATTATATATG
66 CAAAATGTTTTCAAAACTATATATTATATAAG
* * *
392154 TTTTCAAAACTATATATTATATAAGTTTTTAAAATGTTTTCAAAAATTATATATTATATAGGTTT
1 TTTTAAAAACTATATATTATATAAGTTTTCAAAATATTTTC-AAAATTATATATTATATAGGTTT
392219 TCAAAATGTTTTCAAAACTATATATTATATAAG
65 TCAAAATGTTTTCAAAACTATATATTATATAAG
392252 TTTT
1 TTTT
392256 TTAAAATGTT
Statistics
Matches: 94, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
97 37 0.39
98 57 0.61
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.49
Consensus pattern (97 bp):
TTTTAAAAACTATATATTATATAAGTTTTCAAAATATTTTCAAAATTATATATTATATAGGTTTT
CAAAATGTTTTCAAAACTATATATTATATAAG
Found at i:394103 original size:34 final size:37
Alignment explanation
Indices: 394040--394113 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 37
394030 TCTAATAAAT
394040 ATTTTAAAAAAATACATAAAATATATTTA-TTAATAA
1 ATTTTAAAAAAATACATAAAATATATTTATTTAATAA
* * *
394076 ATTTT-AAAATATA-ATATAATATTTTTATTTTAATAA
1 ATTTTAAAAAAATACATAAAATATATTTA-TTTAATAA
394112 AT
1 AT
394114 AGTTAATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
34 12 0.36
35 7 0.21
36 14 0.42
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (37 bp):
ATTTTAAAAAAATACATAAAATATATTTATTTAATAA
Found at i:394580 original size:60 final size:60
Alignment explanation
Indices: 394491--394645 Score: 170
Period size: 60 Copynumber: 2.6 Consensus size: 60
394481 TTTGGATGAA
* * * * ** *
394491 TTTGAGGATAAAATT-GAATATGGAAAAGTTTAGGAACTAATTTAGAATGCTATTCATAG
1 TTTGGGGATGAAATTAGAATGTTGAAAAGTTTAGGAACTAATTTAGAATGAGAGTCATAG
* * *
394550 TTTGGGGGTGAAATTGGAATGTTGAAAAGTTTAAGG-ACTAATTTAGAATGAGAGTCTTAG
1 TTTGGGGATGAAATTAGAATGTTGAAAAGTTT-AGGAACTAATTTAGAATGAGAGTCATAG
* * *
394610 TTTTGGGATGAAATTAGAATGTTTAAAAATTTAGGA
1 TTTGGGGATGAAATTAGAATGTTGAAAAGTTTAGGA
394646 CGTCTAGTTT
Statistics
Matches: 79, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
59 15 0.19
60 61 0.77
61 3 0.04
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (60 bp):
TTTGGGGATGAAATTAGAATGTTGAAAAGTTTAGGAACTAATTTAGAATGAGAGTCATAG
Found at i:394755 original size:14 final size:14
Alignment explanation
Indices: 394703--394747 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
394693 AAAGTTGTAG
*
394703 AAATAAT-TTTAAT
1 AAATAATATTAAAT
394716 -AATAATATTGAAAT
1 AAATAATATT-AAAT
394730 AAATAATATTAAAT
1 AAATAATATTAAAT
394744 AAAT
1 AAAT
394748 TATTTTAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 6 0.21
13 2 0.07
14 11 0.39
15 9 0.32
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (14 bp):
AAATAATATTAAAT
Found at i:394769 original size:21 final size:20
Alignment explanation
Indices: 394733--394808 Score: 64
Period size: 21 Copynumber: 3.5 Consensus size: 20
394723 TTGAAATAAA
*
394733 TAATATTAAATAAATTATTT
1 TAATATTAAATAAATTATAT
394753 TAATATTTAAA-ATAATTATAT
1 TAATA-TTAAATA-AATTATAT
*
394774 TAAGTTATTATAATAAATAATAT
1 TAA--TATTA-AATAAATTATAT
*
394797 TATTTATTAAAT
1 TA-ATATTAAAT
394809 TTATATTTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
20 6 0.13
21 18 0.39
22 8 0.17
23 13 0.28
24 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (20 bp):
TAATATTAAATAAATTATAT
Found at i:396368 original size:87 final size:84
Alignment explanation
Indices: 396211--396370 Score: 248
Period size: 87 Copynumber: 1.9 Consensus size: 84
396201 TATGTTATAT
* *
396211 TATTTAACCGAAAATATTATTAAACATAACATATTAGGTAACGCTTATATAATGTAATAGATAGT
1 TATTTAACCGAAAATATTATAAAACATAACATATTAGGTAACGCTTATATAATGTAATAGATAGC
396276 ACTTATATAATAAAATAGG
66 ACTTATATAATAAAATAGG
* *
396295 TATTTAACCGAAAATATTATCAAATACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 TATTTAACCGAAAATATTAT-AAA-AC-ATAACATATTAGGTAACGCTTATATAATGTAATAGAT
*
396360 AGCGCTTATAT
63 AGCACTTATAT
396371 TGACCTTTTA
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
84 20 0.29
85 2 0.03
86 2 0.03
87 44 0.65
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (84 bp):
TATTTAACCGAAAATATTATAAAACATAACATATTAGGTAACGCTTATATAATGTAATAGATAGC
ACTTATATAATAAAATAGG
Found at i:396795 original size:154 final size:159
Alignment explanation
Indices: 396522--396843 Score: 489
Period size: 155 Copynumber: 2.1 Consensus size: 159
396512 TATAGACCGA
*
396522 TTTTATCATATTTTACATGTTATATTATTATGGATCGATACATTTTTATAAAGTATCGACACTTA
1 TTTTGTCATATTTTACATGTTATATTATTATGGATCGATACATTTTTATAAAGTATCGACACTTA
* * *
396587 TTGTCGCTATAACATCTTCTCTTATTAATTCCAAAAGTGTCGATACTTATATAAATTATCGACAC
66 TTGGCGCTATAACATCTTCTCTTATAAATTCCAAAAGTGTCGACACTTATATAAATTATCGACAC
*
396652 TTTC-ACATATCCGGTAGCGCTTTACCTG
131 TTTCAACATAACCGGTAGCGCTTTACCTG
* *
396680 -TTTGTCATATTTTTAC-TG-T-TATTGTTATGGATCGATACATTTTTAT-AAGTATCGACATTT
1 TTTTGTCATA-TTTTACATGTTATATTATTATGGATCGATACATTTTTATAAAGTATCGACA-CT
*
396740 TATTGGCGCTATAACTTCTT-TCATT-TAAATTCCAAAAGTGTCGACACTTATATAAATTATCGA
64 TATTGGCGCTATAACATCTTCTC-TTATAAATTCCAAAAGTGTCGACACTTATATAAATTATCGA
396803 CACTTTCAACATAACCGGTAGCGCTTTACCTG
128 CACTTTCAACATAACCGGTAGCGCTTTACCTG
396835 TTTTGTCAT
1 TTTTGTCAT
396844 TTCGAGACCG
Statistics
Matches: 151, Mismatches: 8, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
154 56 0.37
155 70 0.46
156 9 0.06
157 10 0.07
158 6 0.04
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (159 bp):
TTTTGTCATATTTTACATGTTATATTATTATGGATCGATACATTTTTATAAAGTATCGACACTTA
TTGGCGCTATAACATCTTCTCTTATAAATTCCAAAAGTGTCGACACTTATATAAATTATCGACAC
TTTCAACATAACCGGTAGCGCTTTACCTG
Found at i:397028 original size:181 final size:181
Alignment explanation
Indices: 396680--397566 Score: 1447
Period size: 179 Copynumber: 4.9 Consensus size: 181
396670 GCTTTACCTG
*
396680 TTTGTCATATTTTTA-CTG-T-TATTGTTATGGATCGATACATTTTTAT-AAGTATCGACATTTT
1 TTTGTCATA-TTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
* *
396741 ATTGGCGCTATAACTTCTT-TCATTTAAATTCCAAAAGTGTCGACACTTAT-ATAAATTATCGAC
65 ATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAATTATCGAC
396804 ACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCGAGACCGGT
130 ACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCGAGACCGGT
*
396856 TTTGTCATATTATTACCTGTTATATTGTTATGGATCGATACA-TTTTATCAAGTATCGACACTTT
1 TTTGTCATATT-TTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
*
396920 ATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACGTATAATAAATTATCGAC
65 ATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAATTATCGAC
396985 ACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCGAGACCGGT
130 ACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCGAGACCGGT
* **
397037 TTTGTCATATTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACAAGTTA
1 TTTGTCATATTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTA
397102 TTGGCGCTATAACTTCTTCTCTTATT-AATTCCAAAA--GTCGATACTTATAATAAATTATCGAC
66 TTGGCGCTATAACTTCTTCTCTT-TTAAATTCCAAAAGTGTCGATACTTATAATAAATTATCGAC
* * * *
397164 ACTTTCAATATAACCAGTAGCGCTTTACCTGTTTTGTCATTTTGAGACCGTT
130 ACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCGAGACCGGT
**
397216 TTTGTCATATTTTATATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTA
1 TTTGTCATATTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTA
* *
397281 TTGGCGCTATAAC-TCTTCTCTTTTAAATTCCAAAAGTGTTGATACGTATAATAAATTATCGACA
66 TTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAATTATCGACA
* *
397345 CTTTCAACATAACTGGTAGTGCTTTACCTGTTTTGTCATTTCGAGACCGGT
131 CTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCGAGACCGGT
*
397396 TTTGTCGTATTTTTTACCTGTTATATTGGTTATGGATCGATACATTTTTATAAAGTATCGACACT
1 TTTGTC--ATATTTTACCTGTTATATT-GTTATGGATCGATACATTTTTATAAAGTATCGACACT
*
397461 TTATTGGCGCTAT-ACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAATTATCA
63 TTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAATTATCG
*
397525 ACACTTTCAACATATCCGGTAGCGCTTTACCTGTTTTGTCAT
128 ACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCAT
397567 ATTTTTACCT
Statistics
Matches: 662, Mismatches: 33, Indels: 25
0.92 0.05 0.03
Matches are distributed among these distances:
175 2 0.00
176 12 0.02
177 5 0.01
178 26 0.04
179 201 0.30
180 133 0.20
181 129 0.19
182 20 0.03
183 134 0.20
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (181 bp):
TTTGTCATATTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTA
TTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAATTATCGACA
CTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCGAGACCGGT
Found at i:397371 original size:359 final size:358
Alignment explanation
Indices: 396680--397829 Score: 1755
Period size: 359 Copynumber: 3.3 Consensus size: 358
396670 GCTTTACCTG
*
396680 TTTGTCATATTTTTA-CTG-T-TATTGTTATGGATCGATACATTTTTAT-AAGTATCGACATTTT
1 TTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
* *
396741 ATTGGCGCTATAACTTCTT-TCATTTAAATTCCAAAAGTGTCGACACTTAT-ATAAATTATCGAC
66 ATTGGCGCTATAACTTCTTCTC-TTTTAATTCCAAAAG-GTCGATACTTATAATAAATTATCGAC
*
396804 ACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCGAGACCGGTTTTGTCATATTAT
129 ACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTTGAGACC-GTTTTGTCATATT-T
** *
396869 TACCTGTTATATTGTTATGGATCGATACATTTTATCAAGTATCGACACTTTATTGGCGCTATAAC
192 TATATGTTATATTGTTATGGATCGATACATTTTATAAAGTATCGACACTTTATTGGCGCTATAAC
396934 TTCTTCTCTTTTAAATTCCAAAAGTGTCGATACGTATAATAAATTATCGACACTTTCAACATAAC
257 -TCTTCTCTTTTAAATTCCAAAAGTGTCGATACGTATAATAAATTATCGACACTTTCAACATAAC
396999 CGGTAGCGCTTTACCTGTTTTGTCATTTCGAGACCGGT
321 CGGTAGCGCTTTACCTGTTTTGTCATTTCGAGACCGGT
* **
397037 TTTGTCATA-TTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACAAGTT
1 TTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
397101 ATTGGCGCTATAACTTCTTCTCTTATTAATTCCAAAA-GTCGATACTTATAATAAATTATCGACA
66 ATTGGCGCTATAACTTCTTCTCTT-TTAATTCCAAAAGGTCGATACTTATAATAAATTATCGACA
* *
397165 CTTTCAATATAACCAGTAGCGCTTTACCTGTTTTGTCATTTTGAGACCGTTTTTGTCATATTTTA
130 CTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTTGAGACCG-TTTTGTCATATTTTA
397230 TATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACT
194 TATGTTATATTGTTATGGATCGATACA-TTTTATAAAGTATCGACACTTTATTGGCGCTATAACT
* *
397295 CTTCTCTTTTAAATTCCAAAAGTGTTGATACGTATAATAAATTATCGACACTTTCAACATAACTG
258 CTTCTCTTTTAAATTCCAAAAGTGTCGATACGTATAATAAATTATCGACACTTTCAACATAACCG
*
397360 GTAGTGCTTTACCTGTTTTGTCATTTCGAGACCGGT
323 GTAGCGCTTTACCTGTTTTGTCATTTCGAGACCGGT
*
397396 TTTGTCGTATTTTTTACCTGTTATATTGGTTATGGATCGATACATTTTTATAAAGTATCGACACT
1 TTTGTCATA-TTTTTACCTGTTATATT-GTTATGGATCGATACATTTTTATAAAGTATCGACACT
*
397461 TTATTGGCGCTAT-ACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAATTATCA
64 TTATTGGCGCTATAACTTCTTCTCTTTT-AATTCCAAAAG-GTCGATACTTATAATAAATTATCG
*
397525 ACACTTTCAACATATCCGGTAGCGCTTTACCTGTTTTGTCA---T---A----TTT-T--TA---
127 ACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTTGAGACCGTTTTGTCATATTT
** * * *
397574 CCTA--TTATATTGTTATGGATCGATACATTTTATAAAGTATCGACACTTTATTGACGATATAGC
192 TATATGTTATATTGTTATGGATCGATACATTTTATAAAGTATCGACACTTTATTGGCGCTATAAC
397637 TCTTCTCTTTTAAATTCCAAAAGTGTCGATACGTATAATAAA-TATCGACACTTTCAACATAACC
257 TCTTCTCTTTTAAATTCCAAAAGTGTCGATACGTATAATAAATTATCGACACTTTCAACATAACC
397701 GGTAGCGCTTTACCTGTTTTGTCATTTCGAGACCGGT
322 GGTAGCGCTTTACCTGTTTTGTCATTTCGAGACCGGT
397738 TTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCG-CACTTT
1 TTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
** *
397802 ATTGATGATATAACTTCTTCTCTTTTAA
66 ATTGGCGCTATAACTTCTTCTCTTTTAA
397830 AAAGGTAAAA
Statistics
Matches: 743, Mismatches: 34, Indels: 50
0.90 0.04 0.06
Matches are distributed among these distances:
339 16 0.02
340 46 0.06
341 17 0.02
342 65 0.09
343 74 0.10
344 23 0.03
346 2 0.00
349 2 0.00
351 1 0.00
352 3 0.00
356 5 0.01
357 12 0.02
358 1 0.00
359 174 0.23
360 143 0.19
361 50 0.07
362 48 0.06
363 61 0.08
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.42
Consensus pattern (358 bp):
TTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
ATTGGCGCTATAACTTCTTCTCTTTTAATTCCAAAAGGTCGATACTTATAATAAATTATCGACAC
TTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTTGAGACCGTTTTGTCATATTTTATA
TGTTATATTGTTATGGATCGATACATTTTATAAAGTATCGACACTTTATTGGCGCTATAACTCTT
CTCTTTTAAATTCCAAAAGTGTCGATACGTATAATAAATTATCGACACTTTCAACATAACCGGTA
GCGCTTTACCTGTTTTGTCATTTCGAGACCGGT
Found at i:397643 original size:160 final size:162
Alignment explanation
Indices: 397394--397725 Score: 555
Period size: 160 Copynumber: 2.1 Consensus size: 162
397384 TTCGAGACCG
* *
397394 GTTTTGTCGTATTTTTTACCTGTTATATTGGTTATGGATCGATACATTTTTATAAAGTATCGACA
1 GTTTTGTCATATTTTTTACCTATTATATTGGTTATGGATCGATACATTTTTATAAAGTATCGACA
* * *
397459 CTTTATTGGCGCTATACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAATTATC
66 CTTTATTGACGATATACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACGTATAATAAA-TATC
*
397524 AACACTTTCAACATATCCGGTAGCGCTTTACCT
130 AACACTTTCAACATAACCGGTAGCGCTTTACCT
397557 GTTTTGTCATA-TTTTTACCTATTATATT-GTTATGGATCGATACA-TTTTATAAAGTATCGACA
1 GTTTTGTCATATTTTTTACCTATTATATTGGTTATGGATCGATACATTTTTATAAAGTATCGACA
397619 CTTTATTGACGATATAGC-TCTTCTCTTTTAAATTCCAAAAGTGTCGATACGTATAATAAATATC
66 CTTTATTGACGATATA-CTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACGTATAATAAATATC
*
397683 GACACTTTCAACATAACCGGTAGCGCTTTACCT
130 AACACTTTCAACATAACCGGTAGCGCTTTACCT
397716 GTTTTGTCAT
1 GTTTTGTCAT
397726 TTCGAGACCG
Statistics
Matches: 161, Mismatches: 7, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
159 45 0.28
160 73 0.45
161 17 0.11
162 16 0.10
163 10 0.06
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (162 bp):
GTTTTGTCATATTTTTTACCTATTATATTGGTTATGGATCGATACATTTTTATAAAGTATCGACA
CTTTATTGACGATATACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACGTATAATAAATATCA
ACACTTTCAACATAACCGGTAGCGCTTTACCT
Found at i:399756 original size:19 final size:19
Alignment explanation
Indices: 399711--399756 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
399701 TCCGATATCA
399711 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
399730 TTGATACCGG-TTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
399750 TTTTACC
1 TTTTACC
399757 TATTATATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.20, C:0.17, G:0.11, T:0.52
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:400004 original size:177 final size:180
Alignment explanation
Indices: 399678--400144 Score: 638
Period size: 178 Copynumber: 2.6 Consensus size: 180
399668 ACGTACTACG
* * * * *
399678 AAAGTATCGAAACTTTTAATATATCCGATATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTACCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
*
399743 ATCATATTTTTACCTATTATATCG-TGTTTGATCGATACATTTTTTAAAGTATCGACATTTTATA
66 ATCATATTTTTACCTGTTATATCGTTG-TTGATCGATACATTTTTTAAAGTATCGACATTTTATA
* *
399807 GACGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGT-GATCCTTATA-T
130 GACGCTAAAACTGCTTCTCTTTTAAATTAACAAAGTATCGATCCTTATATT
* * * * *
399856 AAAGTTTCGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTCATCATTTTGATACCAGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTACCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
*
399921 -T-ATATTTTTACCTGTTATATCGTTGTTGATCGATATATTTTTTGAAAGTATCGACATTTTATA
66 ATCATATTTTTACCTGTTATATCGTTGTTGATCGATACATTTTTT-AAAGTATCGACATTTTATA
* * *
399984 GGCGCTAAAACTGGTTCTCTTTTAAATTAACGAAGTATCGATCCTTATATT
130 GACGCTAAAACTGCTTCTCTTTTAAATTAACAAAGTATCGATCCTTATATT
* * * ** *
400035 AAAGTACCGACACTTTAAATATATTCGGTACCGCTTTACCGGTTTTATCATTTCAATACTGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTACCGTTTTACCGGTTTTATCATTTTGATACCGG-TT
* * *
400100 TGTCATAGTTTTACCTGTTATATCGTTGTGGATCGATACATTTTT
65 TATCATATTTTTACCTGTTATATCGTTGTTGATCGATACATTTTT
400145 AATTTGGATC
Statistics
Matches: 253, Mismatches: 29, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
176 37 0.15
177 55 0.22
178 67 0.26
179 52 0.21
180 3 0.01
181 1 0.00
182 38 0.15
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.43
Consensus pattern (180 bp):
AAAGTATCGACACTTTAAATATATCCGGTACCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
ATCATATTTTTACCTGTTATATCGTTGTTGATCGATACATTTTTTAAAGTATCGACATTTTATAG
ACGCTAAAACTGCTTCTCTTTTAAATTAACAAAGTATCGATCCTTATATT
Found at i:405471 original size:21 final size:21
Alignment explanation
Indices: 405354--405491 Score: 68
Period size: 21 Copynumber: 6.7 Consensus size: 21
405344 ACGCGAAATA
**
405354 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
405374 ATAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
*
405394 AAAATCGCAACGCGATTCTT-G
1 AAAATCGCAACGCGATT-TTCC
* * ** *
405415 AAAATCGCGATGCGATAGTAC
1 AAAATCGCAACGCGATTTTCC
* **
405436 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTTCC
* * * *
405457 ATAATCGCAACGCGAATAT-G
1 AAAATCGCAACGCGATTTTCC
405477 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
405492 ACACATAAAT
Statistics
Matches: 85, Mismatches: 29, Indels: 8
0.70 0.24 0.07
Matches are distributed among these distances:
19 1 0.01
20 38 0.45
21 44 0.52
22 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (21 bp):
AAAATCGCAACGCGATTTTCC
Found at i:405484 original size:20 final size:20
Alignment explanation
Indices: 405459--405652 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
405449 GATTTTCCAT
* *
405459 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
405479 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
405499 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
405519 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
405539 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
405559 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
405579 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
405599 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
405620 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
405640 AATCGCAACGCGA
1 AATCGCAACGCGA
405653 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:405504 original size:40 final size:39
Alignment explanation
Indices: 405455--405652 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
405445 TTGCGATTTT
* ** *
405455 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
405493 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
405534 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
405574 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
405613 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
405653 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:405542 original size:60 final size:60
Alignment explanation
Indices: 405459--405651 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
405449 GATTTTCCAT
* ** * *
405459 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
405519 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
405579 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
405640 AATCGCAACGCG
1 AATCGCAACGCG
405652 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:406139 original size:20 final size:20
Alignment explanation
Indices: 406111--406500 Score: 457
Period size: 20 Copynumber: 19.4 Consensus size: 20
406101 AAATTTCAGT
* * * *
406111 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
406131 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
406151 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
406171 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
406191 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
406211 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
406231 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
406251 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
406271 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
406291 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
406311 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* * *
406331 GTTGCGATTTTATGTATTA-TC
1 GTTGCGA-TTTACGGA-TACGC
406352 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
406372 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
406392 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
406412 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
406432 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
406452 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
406472 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
406492 GTTGCGATT
1 GTTGCGATT
406501 ATGGAAAATC
Statistics
Matches: 323, Mismatches: 36, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
19 7 0.02
20 295 0.91
21 19 0.06
22 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:412250 original size:51 final size:53
Alignment explanation
Indices: 412109--412250 Score: 127
Period size: 51 Copynumber: 2.7 Consensus size: 53
412099 ATTTCTTCTA
* *
412109 ATATCCTAAAGAACCCACTGATAGATTTAAGTTTCAATAAGATCTGTAATCTTTT
1 ATATCCTAAAGAACCCATTGATAGATTTAAGTTTC-A-AAGATCTATAATCTTTT
* * * *
412164 ATTTCTTCTAACA-ATA-CGATT-ATAG-TTGAA-ATTCAAA-ATCTATAATCTTTT
1 ATATC--CTAA-AGA-ACCCATTGATAGATTTAAGTTTCAAAGATCTATAATCTTTT
412215 A-ATCCTAAAGAACCCATTGATAGATTTAAGTTTCAA
1 ATATCCTAAAGAACCCATTGATAGATTTAAGTTTCAA
412251 TAAGATAATT
Statistics
Matches: 68, Mismatches: 10, Indels: 22
0.68 0.10 0.22
Matches are distributed among these distances:
47 2 0.03
48 9 0.13
49 4 0.06
50 6 0.09
51 19 0.28
52 2 0.03
53 1 0.01
54 3 0.04
55 8 0.12
56 4 0.06
57 8 0.12
58 2 0.03
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.37
Consensus pattern (53 bp):
ATATCCTAAAGAACCCATTGATAGATTTAAGTTTCAAAGATCTATAATCTTTT
Found at i:413340 original size:16 final size:16
Alignment explanation
Indices: 413319--413349 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
413309 ATCTTAGCTC
413319 GATAAATACTCGGATT
1 GATAAATACTCGGATT
413335 GATAAATACTCGGAT
1 GATAAATACTCGGAT
413350 CGAATGGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (16 bp):
GATAAATACTCGGATT
Found at i:413837 original size:19 final size:19
Alignment explanation
Indices: 413813--413856 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
413803 GATTCAATTT
413813 AAATATTAATAATTTTAAA
1 AAATATTAATAATTTTAAA
413832 AAATATTAATAATTTTAAA
1 AAATATTAATAATTTTAAA
413851 AAATAT
1 AAATAT
413857 CAAAACAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AAATATTAATAATTTTAAA
Found at i:413973 original size:21 final size:22
Alignment explanation
Indices: 413949--414015 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 22
413939 TTTGATATGA
413949 TTTAAGATTTAAGAT-TTAGGG
1 TTTAAGATTTAAGATATTAGGG
* *
413970 TTT-AGAGTTTATG-TGA-TAGGA
1 TTTAAGA-TTTAAGAT-ATTAGGG
*
413991 TTTAAGGTTT-AGATATTAGGG
1 TTTAAGATTTAAGATATTAGGG
414012 TTTA
1 TTTA
414016 GTGTTTATGT
Statistics
Matches: 35, Mismatches: 5, Indels: 12
0.67 0.10 0.23
Matches are distributed among these distances:
20 6 0.17
21 27 0.77
22 2 0.06
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.45
Consensus pattern (22 bp):
TTTAAGATTTAAGATATTAGGG
Found at i:413974 original size:42 final size:42
Alignment explanation
Indices: 413915--414113 Score: 170
Period size: 42 Copynumber: 4.6 Consensus size: 42
413905 TAATTATGTG
* * * *
413915 TTAAGGTTTAGAGTTTAGGGTTTATTTGATATGATTTAAGAT
1 TTAAGATTTAGGGTTTAGAGTTTATGTGATATGATTTAAGAT
* *
413957 TTAAGATTTAGGGTTTAGAGTTTATGTGATAGGATTTAAGGT
1 TTAAGATTTAGGGTTTAGAGTTTATGTGATATGATTTAAGAT
* *
413999 TT-AGATATTAGGGTTTAGTGTTTATGTGTTATGGGTTAGAGTTT-AGAGT
1 TTAAGAT-TTAGGGTTTAGAGTTTATGTG--AT---AT-GA-TTTAAGA-T
* * *
414048 TTAAGGTTTAAGGTTTAGAGTTTATGTGATATGATTTAAGGT
1 TTAAGATTTAGGGTTTAGAGTTTATGTGATATGATTTAAGAT
* *
414090 TTATAG-TTTAGGATTTAGGGTTTA
1 TTA-AGATTTAGGGTTTAGAGTTTA
414114 GGGTTATGCA
Statistics
Matches: 127, Mismatches: 18, Indels: 24
0.75 0.11 0.14
Matches are distributed among these distances:
41 4 0.03
42 80 0.63
43 6 0.05
44 3 0.02
47 2 0.02
48 4 0.03
49 25 0.20
50 3 0.02
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (42 bp):
TTAAGATTTAGGGTTTAGAGTTTATGTGATATGATTTAAGAT
Found at i:414021 original size:21 final size:20
Alignment explanation
Indices: 413960--414066 Score: 55
Period size: 21 Copynumber: 5.2 Consensus size: 20
413950 TTAAGATTTA
413960 AGAT-TTAGGGTTTAGAGTTT
1 AGATATTAGGGTTTAG-GTTT
*
413980 ATG-TGA-TAGGATTTAAGGTTT
1 A-GAT-ATTAGGGTTT-AGGTTT
414001 AGATATTAGGGTTTAGTGTTT
1 AGATATTAGGGTTTAG-GTTT
*
414022 ATG-TGTTATGGG-TTAGAGTTT
1 A-GATATTA-GGGTTTAG-GTTT
*
414043 AGAGT-TTAAGGTTTAAGGTTT
1 AGA-TATTAGGGTTT-AGGTTT
414064 AGA
1 AGA
414067 GTTTATGTGA
Statistics
Matches: 69, Mismatches: 5, Indels: 25
0.70 0.05 0.25
Matches are distributed among these distances:
20 9 0.13
21 51 0.74
22 9 0.13
ACGTcount: A:0.26, C:0.00, G:0.30, T:0.44
Consensus pattern (20 bp):
AGATATTAGGGTTTAGGTTT
Found at i:414065 original size:28 final size:28
Alignment explanation
Indices: 413991--414071 Score: 76
Period size: 28 Copynumber: 2.9 Consensus size: 28
413981 TGTGATAGGA
* * *
413991 TTTAAGGTTT-AGATATTAGGGTTTAGTG
1 TTTAAGGTTTAAGGT-TTAGAGTTTAGAG
* * *
414019 TTT-ATGTGTTATGGGTTAGAGTTTAGAG
1 TTTAAGGT-TTAAGGTTTAGAGTTTAGAG
414047 TTTAAGGTTTAAGGTTTAGAGTTTA
1 TTTAAGGTTTAAGGTTTAGAGTTTA
414072 TGTGATATGA
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
27 3 0.07
28 34 0.83
29 4 0.10
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (28 bp):
TTTAAGGTTTAAGGTTTAGAGTTTAGAG
Found at i:415340 original size:23 final size:23
Alignment explanation
Indices: 415313--415371 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
415303 ACCCTTCGAT
415313 CTTGAATCGAGCTAAAAAACGAG
1 CTTGAATCGAGCTAAAAAACGAG
* *
415336 CTTGAATCGAGCTTAAAAACTAG
1 CTTGAATCGAGCTAAAAAACGAG
*
415359 CTTCAATCGAGCT
1 CTTGAATCGAGCT
415372 CTTGAATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (23 bp):
CTTGAATCGAGCTAAAAAACGAG
Found at i:416873 original size:15 final size:16
Alignment explanation
Indices: 416843--416875 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
416833 CGGGTAAAAT
416843 TTAAAAAAAAATTAAA
1 TTAAAAAAAAATTAAA
*
416859 TTAAAGAAAAA-TAAA
1 TTAAAAAAAAATTAAA
416874 TT
1 TT
416876 TATTATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (16 bp):
TTAAAAAAAAATTAAA
Found at i:418012 original size:16 final size:19
Alignment explanation
Indices: 417991--418030 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
417981 GATGCCATTT
417991 AAAATATT-T-AA-AAATA
1 AAAATATTATAAACAAATA
418007 AAAATATTATAAACAAATA
1 AAAATATTATAAACAAATA
418026 AAAAT
1 AAAAT
418031 TAAATTTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.38
17 1 0.05
18 2 0.10
19 10 0.48
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAATATTATAAACAAATA
Found at i:454639 original size:67 final size:67
Alignment explanation
Indices: 454522--454650 Score: 177
Period size: 67 Copynumber: 1.9 Consensus size: 67
454512 CAGCTGCAGG
*** * * *
454522 TTTGATTCAACACTATAGTGTTTGAGGACACTTAGTGTAGGTAGTGGGCACGACCTTATGTGTAA
1 TTTGATTCAACACTATAGTGTGCAAGGAAACTTAGTGCAGGTAGTAGGCACGACCTTATGTGTAA
454587 TA
66 TA
** *
454589 TTTGATTCAGTACTATAGTGTGCAAGGAAACTTAGTGCAGGTGGTAGGCACGACCTTATGTG
1 TTTGATTCAACACTATAGTGTGCAAGGAAACTTAGTGCAGGTAGTAGGCACGACCTTATGTG
454651 CAAGCACATA
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
67 53 1.00
ACGTcount: A:0.26, C:0.14, G:0.27, T:0.33
Consensus pattern (67 bp):
TTTGATTCAACACTATAGTGTGCAAGGAAACTTAGTGCAGGTAGTAGGCACGACCTTATGTGTAA
TA
Found at i:460040 original size:32 final size:32
Alignment explanation
Indices: 459972--460052 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
459962 GTGACACTGG
* * *
459972 GTTTGTATTCTGATAATGCATAGTATATGCAG
1 GTTTGAATTCAGATAATGCATAGTATATGCAA
*
460004 GTTTGAATTCAGATAGTGCATAGTATAAT-CAA
1 GTTTGAATTCAGATAATGCATAGTAT-ATGCAA
* *
460036 GTTTGCATTCAAATAAT
1 GTTTGAATTCAGATAAT
460053 TGACATTACA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
32 39 0.95
33 2 0.05
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (32 bp):
GTTTGAATTCAGATAATGCATAGTATATGCAA
Found at i:463616 original size:20 final size:21
Alignment explanation
Indices: 463579--463617 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
463569 TTTAATACCT
*
463579 TGTATATTTTTATTGTATTCA
1 TGTATATTTTTATAGTATTCA
*
463600 TGTA-ATTTTTGTAGTATT
1 TGTATATTTTTATAGTATT
463618 TTATTCATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.23, C:0.03, G:0.13, T:0.62
Consensus pattern (21 bp):
TGTATATTTTTATAGTATTCA
Found at i:467272 original size:2 final size:2
Alignment explanation
Indices: 467260--467300 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
467250 TTCCATGTTA
467260 AT AT A- 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
467301 CCTTTATTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:470346 original size:17 final size:20
Alignment explanation
Indices: 470307--470345 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
470297 TAAGTAAAAT
470307 AATAATAATAAAATAAGAAA
1 AATAATAATAAAATAAGAAA
470327 AATAAT-ATAAAAT-AGAAA
1 AATAATAATAAAATAAGAAA
470345 A
1 A
470346 TCAAAAGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.32
19 7 0.37
20 6 0.32
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (20 bp):
AATAATAATAAAATAAGAAA
Found at i:485736 original size:23 final size:23
Alignment explanation
Indices: 485710--485755 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
485700 TCAAAAACTG
485710 AAAGAAAAAAAAAGAAAAGAAAA
1 AAAGAAAAAAAAAGAAAAGAAAA
* * *
485733 AAAGAAATAAAAAGGAAATAAAA
1 AAAGAAAAAAAAAGAAAAGAAAA
485756 CCGATCAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (23 bp):
AAAGAAAAAAAAAGAAAAGAAAA
Found at i:488011 original size:151 final size:152
Alignment explanation
Indices: 487731--488134 Score: 693
Period size: 151 Copynumber: 2.7 Consensus size: 152
487721 GTAAAAAATG
** * *
487731 AAATGAGAAAGGTTTCTCATTCCAATATGAAAATTGAAATTTTTGAAAAGTAAGAAATGTTTCTT
1 AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTT
487796 ACCTAGTAAAATATTTCCAAAATTTATAAGTCCTTCGGGCCATCCATAAGACCTTCAAGCAGGAT
66 ACCTAGTAAAATATTTCCAAAATTTATAAGTCCTTCGGGCCATCCATAAGACCTTCAAGCAGGAT
487861 GTTTTCACATGTCTATC-AAAA
131 GTTTTCACATGTCTATCAAAAA
*
487882 AAATGAGAAAGGCTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTT
1 AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTT
* * ** *
487947 ACCTAGTAAAATATTTTCAAAATTTATAAGTCCTTCGGGTCATCCATAAGACCTTCGGGTAGGAT
66 ACCTAGTAAAATATTTCCAAAATTTATAAGTCCTTCGGGCCATCCATAAGACCTTCAAGCAGGAT
488012 GTTTTCACATGTCTATCAAAAA
131 GTTTTCACATGTCTATCAAAAA
* *
488034 AAATGAGAAAGGTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAAGTAAGAAAGGGTTCTT
1 AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTT
488099 ACCTAGTAAAATATTTCCAAAATTTATAAGTCCTTC
66 ACCTAGTAAAATATTTCCAAAATTTATAAGTCCTTC
488135 AAGCCATCAG
Statistics
Matches: 238, Mismatches: 14, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
151 137 0.58
152 101 0.42
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (152 bp):
AAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTT
ACCTAGTAAAATATTTCCAAAATTTATAAGTCCTTCGGGCCATCCATAAGACCTTCAAGCAGGAT
GTTTTCACATGTCTATCAAAAA
Found at i:488448 original size:234 final size:234
Alignment explanation
Indices: 487972--488459 Score: 737
Period size: 233 Copynumber: 2.1 Consensus size: 234
487962 TTCAAAATTT
* *
487972 ATAAGTCCTTCGGGTCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGTCTATCAAAAAAAA
1 ATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGAAGGATGTTTTCACATGTCTATC-AAAAAAA
*
488037 TGAGAAAGGTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAAGTAAGAAAGGGTTCTTACC
65 TGAGAAACGTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAAGTAAGAAAGGGTTCTTACC
* *
488102 TAGTAAAATATTTCCAAAATTTATAAGTCCTTCAAGCCATCAGTAAGTCTTCCGAGCATGATGCT
130 TAGTAAAATATTTCCAAAATTTATAAGTCCTTCAAGCCATCAGTAAGTCCTCCGAGCATGAGGCT
* * * *
488167 TAAATCCTTTAGGTCATCTGTAAGTCTTTCGAGCAAGATG
195 TAAATCCTTCAGGTCATCTGTAAGCCTTACAAGCAAGATG
*
488207 ATAAGTCCTTCGGGCCATCCATAAGTCCTTCGGGAAGGATGTTTTTCACATGTCTATC-AAAAAA
1 ATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGAAGGATG-TTTTCACATGTCTATCAAAAAAA
* *
488271 TGAGAAACGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTACC
65 TGAGAAACGTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAAGTAAGAAAGGGTTCTTACC
* * ***
488336 -AGTAAACTATTTCCAAAATTTATAAGTCTTTTGGGCCATCAGTAAGTCCTCCGAGCATGAGGCT
130 TAGTAAAATATTTCCAAAATTTATAAGTCCTTCAAGCCATCAGTAAGTCCTCCGAGCATGAGGCT
* * * *
488400 TAAATCGTTCGGGTCATTTGTAAGCCTTACAAGCATGATG
195 TAAATCCTTCAGGTCATCTGTAAGCCTTACAAGCAAGATG
*
488440 ATTAAGTCCTCCGGGCCATC
1 A-TAAGTCCTTCGGGCCATC
488460 TTAAGCCTTC
Statistics
Matches: 229, Mismatches: 22, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
233 90 0.39
234 85 0.37
235 38 0.17
236 16 0.07
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (234 bp):
ATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGAAGGATGTTTTCACATGTCTATCAAAAAAAT
GAGAAACGTTTCTCATTTAAATCTAAAAATTGAAATTTTTGAAAAGTAAGAAAGGGTTCTTACCT
AGTAAAATATTTCCAAAATTTATAAGTCCTTCAAGCCATCAGTAAGTCCTCCGAGCATGAGGCTT
AAATCCTTCAGGTCATCTGTAAGCCTTACAAGCAAGATG
Found at i:488501 original size:37 final size:37
Alignment explanation
Indices: 488457--488544 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 37
488447 CCTCCGGGCC
*
488457 ATCTTAAGCCTTCACTAAAGAGTAGAGAAGCAAATCA
1 ATCTTAAGCCTTCACCAAAGAGTAGAGAAGCAAATCA
* * *
488494 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC
1 ATCTTAAGCCTTCACCAAAGAGTAGAGAAGCAAATCA
*
488531 ATCAGTAAGCCTTC
1 ATC-TTAAGCCTTC
488545 CAAGCATGAT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
37 36 0.80
38 9 0.20
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.23
Consensus pattern (37 bp):
ATCTTAAGCCTTCACCAAAGAGTAGAGAAGCAAATCA
Found at i:488623 original size:116 final size:115
Alignment explanation
Indices: 488419--488724 Score: 459
Period size: 116 Copynumber: 2.6 Consensus size: 115
488409 CGGGTCATTT
*
488419 GTAAGCCTTACAAGCATGATGATTAAGTCCTCCGGGCCATCTTAAGCCTTCACTAAAGAGTAGAG
1 GTAAGCCTTACAAGCATGATGATTAAGTCCTCCGGGCCATCTTAAGCCTTCAC-AAAGAGTAGTG
* **
488484 AAGCAAATCAATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCA
65 AAGCAAATCAATCATAAGCCTTCACCGAAGAGTAGTGAAAAAAATCCATCA
* * *
488535 GTAAGCCTTCCAAGCATGATGATTAAGTCCTTCGGGCCATCTAAAGCCTTCACAGAAGAGTAGTG
1 GTAAGCCTTACAAGCATGATGATTAAGTCCTCCGGGCCATCTTAAGCCTTCACA-AAGAGTAGTG
* * *
488600 AAGCAAATCTATCATACGCCTTCACGGAAGAGTAGTGAAAAAAATCCATCA
65 AAGCAAATCAATCATAAGCCTTCACCGAAGAGTAGTGAAAAAAATCCATCA
* * * *
488651 GTAAGCCTTTCGAGCATGACGATTAAGTCCTCCGGGCCATCTTAAGCCTTCACCAAAGATTAGTG
1 GTAAGCCTTACAAGCATGATGATTAAGTCCTCCGGGCCATCTTAAGCCTTCA-CAAAGAGTAGTG
488716 AAGCAAATC
65 AAGCAAATC
488725 CAAGATTTGA
Statistics
Matches: 172, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
115 1 0.01
116 169 0.98
117 2 0.01
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.23
Consensus pattern (115 bp):
GTAAGCCTTACAAGCATGATGATTAAGTCCTCCGGGCCATCTTAAGCCTTCACAAAGAGTAGTGA
AGCAAATCAATCATAAGCCTTCACCGAAGAGTAGTGAAAAAAATCCATCA
Found at i:488645 original size:37 final size:38
Alignment explanation
Indices: 488578--488659 Score: 112
Period size: 37 Copynumber: 2.2 Consensus size: 38
488568 GGGCCATCTA
** *
488578 AAGCCTTCACAGAAGAGTAGTGAAGCAAATCTATCA-T
1 AAGCCTTCACAGAAGAGTAGTGAAAAAAATCCATCAGT
* *
488615 ACGCCTTCACGGAAGAGTAGTGAAAAAAATCCATCAGT
1 AAGCCTTCACAGAAGAGTAGTGAAAAAAATCCATCAGT
488653 AAGCCTT
1 AAGCCTT
488660 TCGAGCATGA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
37 31 0.82
38 7 0.18
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.21
Consensus pattern (38 bp):
AAGCCTTCACAGAAGAGTAGTGAAAAAAATCCATCAGT
Found at i:490652 original size:2 final size:2
Alignment explanation
Indices: 490645--490671 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
490635 ATATGGCATG
490645 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
490672 CCTTTTGTAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:492447 original size:33 final size:33
Alignment explanation
Indices: 492410--492485 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
492400 ACTAAATAAT
* **
492410 TTTGTTACAATTTGTTATAGTGAAAAAATATTA
1 TTTGTTACAATTTGTTATAATGAAAAAATAACA
* * * *
492443 TTTGTCACAATTTTTTATAATGAGAAATTAACA
1 TTTGTTACAATTTGTTATAATGAAAAAATAACA
492476 TTTGTTACAA
1 TTTGTTACAA
492486 ATTATTATTT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.45
Consensus pattern (33 bp):
TTTGTTACAATTTGTTATAATGAAAAAATAACA
Found at i:492727 original size:189 final size:189
Alignment explanation
Indices: 492453--492797 Score: 467
Period size: 189 Copynumber: 1.8 Consensus size: 189
492443 TTTGTCACAA
* * * *
492453 TTTTTTATAATGAGAAATTAACATTTGTTACAAATTATTATTTTAATTAAATAAATTTGTCAAAA
1 TTTTTTATAATGAGAAATTAACATTTATTACAAATTATTACTATAACTAAATAAATTTGTCAAAA
*
492518 GTTGTTATTTTGAGAAAATA-TTGACCAAATAAATTTAACATAAATTTTTATTTTGACTAAATTT
66 GTTGTTATTTTGAGAAAATATTTGACCAAATAAATTTAACATAAATTTTTATTTTAACTAAATTT
492582 AATATGTTATTGTGACTAAATAAATTTGTTATAATTGATTATTGTGAAAAAAATCATACT
131 AAT-TGTTATTGTGACTAAATAAATTTGTTATAATTGATTATTGTGAAAAAAATCATACT
* * * * * ** *
492642 TTTTTTATATTGAGAAATTAATATTTATTATAATTTGTTACTATAACTATTTAAATTTGTCATAA
1 TTTTTTATAATGAGAAATTAACATTTATTACAAATTATTACTATAACTAAATAAATTTGTCAAAA
* * * * *
492707 TTTGTTATTTTGATAAAATATTTTGACTAAATAAATTTGACATAATTTTTTATTTTAACTAAATT
66 GTTGTTATTTTGAGAAAATA-TTTGACCAAATAAATTTAACATAAATTTTTATTTTAACTAAATT
* * * *
492772 TAATTTTTATTTTGCCTATATAAATT
130 TAATTGTTATTGTGACTAAATAAATT
492798 ATCATAATTT
Statistics
Matches: 132, Mismatches: 22, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
189 71 0.54
190 18 0.14
191 43 0.33
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (189 bp):
TTTTTTATAATGAGAAATTAACATTTATTACAAATTATTACTATAACTAAATAAATTTGTCAAAA
GTTGTTATTTTGAGAAAATATTTGACCAAATAAATTTAACATAAATTTTTATTTTAACTAAATTT
AATTGTTATTGTGACTAAATAAATTTGTTATAATTGATTATTGTGAAAAAAATCATACT
Found at i:492814 original size:31 final size:30
Alignment explanation
Indices: 492772--492835 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 30
492762 TAACTAAATT
* *
492772 TAATTTTTATTTTGCCTATATAAATTATCA
1 TAATTTTTATTTTGCCTAAATAAATTACCA
*
492802 TAATTTGTTATTTTGTCTAAATAAATTACCA
1 TAATTT-TTATTTTGCCTAAATAAATTACCA
492833 TAA
1 TAA
492836 ATTATCTCTC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 6 0.20
31 24 0.80
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (30 bp):
TAATTTTTATTTTGCCTAAATAAATTACCA
Found at i:496291 original size:21 final size:21
Alignment explanation
Indices: 496267--496315 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
496257 TCAGAACTCT
*
496267 CTGGTTCTTGTTCATCATGTG
1 CTGGTTCTTGTTCATCATGTA
496288 CTGGTTCTTGTTCATCATGTA
1 CTGGTTCTTGTTCATCATGTA
496309 CTGGTTC
1 CTGGTTC
496316 CGCTTCAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.10, C:0.20, G:0.22, T:0.47
Consensus pattern (21 bp):
CTGGTTCTTGTTCATCATGTA
Found at i:500640 original size:64 final size:61
Alignment explanation
Indices: 500464--500644 Score: 190
Period size: 64 Copynumber: 2.9 Consensus size: 61
500454 ATGGAATAAA
*
500464 TTGAAA-ATCGAATACATTTCATGCATCGATGCACACTA-TGCATCGATGCACTCAGAGTTT
1 TTGAAACATCGAATGCATTTCATGCATCGATGCAC-CTAGTGCATCGATGCACTCAGAGTTT
* *
500524 TATGAAAACATCGAATGCATTTGATGCATCGATGTACC-AGCCATGCATCGATGCACTCAG-GCT
1 T-TG-AAACATCGAATGCATTTCATGCATCGATGCACCTAG---TGCATCGATGCACTCAGAG-T
500587 ATT
60 -TT
* * *
500590 TTGAAACATCAAATGCATTTTATGCATCGATGCACTCTTAGTGCACCGATGCACT
1 TTGAAACATCGAATGCATTTCATGCATCGATGCAC-C-TAGTGCATCGATGCACT
500645 AAGGTTCCAA
Statistics
Matches: 102, Mismatches: 7, Indels: 20
0.79 0.05 0.16
Matches are distributed among these distances:
60 1 0.01
61 3 0.03
62 4 0.04
63 25 0.25
64 43 0.42
65 21 0.21
66 3 0.03
67 2 0.02
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (61 bp):
TTGAAACATCGAATGCATTTCATGCATCGATGCACCTAGTGCATCGATGCACTCAGAGTTT
Found at i:507210 original size:32 final size:31
Alignment explanation
Indices: 507174--507249 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
507164 TGGGGCCATG
*
507174 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
507206 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
507237 GAGCCTA-CTAAGA
1 GGGCCTACCTAAGA
507250 GTCATAGGTC
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
30 4 0.11
31 19 0.53
32 13 0.36
ACGTcount: A:0.28, C:0.30, G:0.28, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:515929 original size:44 final size:44
Alignment explanation
Indices: 515844--515945 Score: 122
Period size: 44 Copynumber: 2.3 Consensus size: 44
515834 TTGTGCTTCA
*
515844 TGCATCGATACACTTAACAGTGCATCGATGCATCCCTTTGAATG
1 TGCATCGATACACATAACAGTGCATCGATGCATCCCTTTGAATG
515888 TGCATCGATACACCATAA-AGGTGCA-CTGATGCA-CGCC-TTGAATG
1 TGCATCGATACA-CATAACA-GTGCATC-GATGCATC-CCTTTGAATG
*
515932 TGCATCGATGCACA
1 TGCATCGATACACA
515946 AGGCCATGCA
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
43 2 0.04
44 33 0.63
45 17 0.33
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.25
Consensus pattern (44 bp):
TGCATCGATACACATAACAGTGCATCGATGCATCCCTTTGAATG
Found at i:515941 original size:23 final size:22
Alignment explanation
Indices: 515863--515944 Score: 78
Period size: 23 Copynumber: 3.6 Consensus size: 22
515853 ACACTTAACA
515863 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCA-CCC-TTGAAT
* * * *
515887 GTGCATCGATACA-CCATAAAG
1 GTGCATCGATGCACCCTTGAAT
515908 GTGCA-CTGATGCACGCCTTGAAT
1 GTGCATC-GATGCAC-CCTTGAAT
515931 GTGCATCGATGCAC
1 GTGCATCGATGCAC
515945 AAGGCCATGC
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
20 1 0.02
21 13 0.28
22 2 0.04
23 17 0.37
24 13 0.28
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACCCTTGAAT
Found at i:518757 original size:45 final size:45
Alignment explanation
Indices: 518661--518768 Score: 150
Period size: 45 Copynumber: 2.4 Consensus size: 45
518651 ATGCATACAC
518661 TATGCATCGATGCACTCAGAGTTTTATGAAAACATCGAATGCATT
1 TATGCATCGATGCACTCAGAGTTTTATGAAAACATCGAATGCATT
*
518706 TGATGCATCGATGCACTCAG-GCTATTT-TG-AAACATCTAATGCAATT
1 T-ATGCATCGATGCACTCAGAG-T-TTTATGAAAACATCGAATGC-ATT
518752 TATGCATCGATGCACTC
1 TATGCATCGATGCACTC
518769 TTAGTGCACC
Statistics
Matches: 58, Mismatches: 1, Indels: 8
0.87 0.01 0.12
Matches are distributed among these distances:
45 30 0.52
46 25 0.43
47 3 0.05
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (45 bp):
TATGCATCGATGCACTCAGAGTTTTATGAAAACATCGAATGCATT
Found at i:519833 original size:27 final size:27
Alignment explanation
Indices: 519781--519831 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
519771 TATTTTTCTC
519781 GAATACTCTAAAATTTTCTCGTAAACT
1 GAATACTCTAAAATTTTCTCGTAAACT
* *
519808 GAATTCTCTTAAATTTTCTC-TAAA
1 GAATACTCTAAAATTTTCTCGTAAA
519832 ACATTCATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (27 bp):
GAATACTCTAAAATTTTCTCGTAAACT
Done.