Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005203.1 Hibiscus syriacus cultivar Beakdansim tig00011761_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: 1490345
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 8
Found at i:323886 original size:20 final size:20
Alignment explanation
Indices: 323857--323894 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
323847 TTTCAAAGTG
323857 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
323877 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
323895 TAATTTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:323961 original size:45 final size:46
Alignment explanation
Indices: 323912--324003 Score: 159
Period size: 45 Copynumber: 2.0 Consensus size: 46
323902 TCAAACATCG
* *
323912 AATGCATTTTATGCATCGATGCAC-AGACCATGTATCGATGCACTC
1 AATGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTC
323957 AATGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTC
1 AATGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTC
324003 A
1 A
324004 GGCTTTTTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 23 0.52
46 21 0.48
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.26
Consensus pattern (46 bp):
AATGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTC
Found at i:325898 original size:14 final size:14
Alignment explanation
Indices: 325879--325905 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
325869 TAACTTTTCG
325879 GTCAAAGTCAACGA
1 GTCAAAGTCAACGA
325893 GTCAAAGTCAACG
1 GTCAAAGTCAACG
325906 GGTTAACTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.15
Consensus pattern (14 bp):
GTCAAAGTCAACGA
Found at i:328353 original size:71 final size:71
Alignment explanation
Indices: 328232--328365 Score: 205
Period size: 71 Copynumber: 1.9 Consensus size: 71
328222 TTAGATCCGT
* *
328232 AAGGAATTACCAGTTCGATTGGTCTGAACCCATATAAGGAATTACCAGTTTGATCGAGCTGAATT
1 AAGGAATTACCAATTCGATCGGTCTGAACCCATATAAGGAATTACCAGTTTGATCGAGCTGAATT
328297 TGCCGA
66 TGCCGA
* * * * *
328303 AAGGAATTATCAATTTGATCGGTCTGAACCTATATAAGGAATTACTAGTTTGATTGAGCTGAA
1 AAGGAATTACCAATTCGATCGGTCTGAACCCATATAAGGAATTACCAGTTTGATCGAGCTGAA
328366 CCTATAGAGA
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
71 56 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.31
Consensus pattern (71 bp):
AAGGAATTACCAATTCGATCGGTCTGAACCCATATAAGGAATTACCAGTTTGATCGAGCTGAATT
TGCCGA
Found at i:328368 original size:35 final size:35
Alignment explanation
Indices: 328231--328371 Score: 126
Period size: 35 Copynumber: 4.0 Consensus size: 35
328221 CTTAGATCCG
* * *
328231 TAAGGAATTACCAGTTCGATTGGTCTGAACCCATA
1 TAAGGAATTACCAGTTTGATCGGTCTGAACCTATA
** **
328266 TAAGGAATTACCAGTTTGATCGAG-CTGAATTTGCCGA
1 TAAGGAATTACCAGTTTGATCG-GTCTGAACCT--ATA
* *
328303 -AAGGAATTATCAATTTGATCGGTCTGAACCTATA
1 TAAGGAATTACCAGTTTGATCGGTCTGAACCTATA
* *
328337 TAAGGAATTACTAGTTTGATTGAG-CTGAACCTATA
1 TAAGGAATTACCAGTTTGATCG-GTCTGAACCTATA
328372 GAGACTTCAT
Statistics
Matches: 83, Mismatches: 17, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
34 1 0.01
35 54 0.65
36 27 0.33
37 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31
Consensus pattern (35 bp):
TAAGGAATTACCAGTTTGATCGGTCTGAACCTATA
Found at i:332862 original size:2 final size:2
Alignment explanation
Indices: 332855--332896 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
332845 ATTACTATTT
332855 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
332897 ATTAAATTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:333496 original size:25 final size:25
Alignment explanation
Indices: 333468--333539 Score: 94
Period size: 25 Copynumber: 2.9 Consensus size: 25
333458 TTAAATTCAT
333468 AATATTTTTATATATTAACTTAAAA
1 AATATTTTTATATATTAACTTAAAA
* **
333493 AATATTTTT-TACATTAACTTATTA
1 AATATTTTTATATATTAACTTAAAA
333517 AATATATTTTAT-TATTAACTTAA
1 AATAT-TTTTATATATTAACTTAA
333540 TTTAAAAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
24 17 0.43
25 22 0.55
26 1 0.03
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (25 bp):
AATATTTTTATATATTAACTTAAAA
Found at i:333544 original size:27 final size:26
Alignment explanation
Indices: 333468--333556 Score: 96
Period size: 24 Copynumber: 3.5 Consensus size: 26
333458 TTAAATTCAT
*
333468 AATAT-TTTTATATATTAACTTAA-AA
1 AATATATTTTAT-TATTAACTTAATTA
* *
333493 AATATTTTTTA-CATTAACTT-ATTA
1 AATATATTTTATTATTAACTTAATTA
333517 AATATATTTTATTATTAACTTAATTTA
1 AATATATTTTATTATTAACTTAA-TTA
*
333544 AAAATATTTTATT
1 AATATATTTTATT
333557 TTTTTCATTT
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
23 1 0.02
24 19 0.35
25 13 0.24
26 6 0.11
27 15 0.28
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (26 bp):
AATATATTTTATTATTAACTTAATTA
Found at i:333566 original size:24 final size:23
Alignment explanation
Indices: 333539--333583 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
333529 TATTAACTTA
*
333539 ATTTAAAAATATTTTATTTTTTTC
1 ATTTAAAAATA-TATATTTTTTTC
333563 ATTTAAAAATATATATTTTTT
1 ATTTAAAAATATATATTTTTT
333584 GTAAATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (23 bp):
ATTTAAAAATATATATTTTTTTC
Found at i:333751 original size:31 final size:31
Alignment explanation
Indices: 333713--333779 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
333703 TAATGACCAC
* *
333713 ATCTTAATCAAATAAAAACGAAATTGATCAT
1 ATCTTAATCAAATAAAAACAAAAGTGATCAT
*
333744 ATCTTAATTAAATAAAAACAAAAGTGATCAT
1 ATCTTAATCAAATAAAAACAAAAGTGATCAT
333775 ATCTT
1 ATCTT
333780 TTTTTTAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.51, C:0.12, G:0.06, T:0.31
Consensus pattern (31 bp):
ATCTTAATCAAATAAAAACAAAAGTGATCAT
Found at i:337382 original size:21 final size:21
Alignment explanation
Indices: 337356--337400 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
337346 GATTTCTGGG
* *
337356 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
337377 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
337398 CAA
1 CAA
337401 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:339054 original size:149 final size:149
Alignment explanation
Indices: 338867--339181 Score: 569
Period size: 149 Copynumber: 2.1 Consensus size: 149
338857 GAGTCGAGGG
* * *
338867 TCTACGCGGTCCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
338932 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
338997 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
339016 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
339081 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTGTTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
339146 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
339165 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
339182 TGCAATTATA
Statistics
Matches: 160, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
148 1 0.01
149 159 0.99
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:339182 original size:23 final size:23
Alignment explanation
Indices: 339149--339193 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
339139 ATTGTTATAT
*
339149 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
339172 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
339194 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:347016 original size:13 final size:13
Alignment explanation
Indices: 347000--347036 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
346990 TTCGGTTTTA
347000 ACCGAATTAACCG
1 ACCGAATTAACCG
347013 ACCGAATTAACCG
1 ACCGAATTAACCG
*
347026 ACTGAATTAAC
1 ACCGAATTAAC
347037 TGAAGCAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.41, C:0.27, G:0.14, T:0.19
Consensus pattern (13 bp):
ACCGAATTAACCG
Found at i:349101 original size:64 final size:64
Alignment explanation
Indices: 348948--349102 Score: 177
Period size: 64 Copynumber: 2.4 Consensus size: 64
348938 TACACTTAGG
* * * * * **
348948 GTGCATCGGTACACTAATTACATTCAATGTTTCAAAAAAGCAAAAGTGTATCGATGCATGGTCT
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAAAGCAAAAGTGCATCGATGCATGGAAT
* * * **
349012 GTGCATCGGTACATAAAATGCATTCGATGTTTTAATAAAATCAGGAGTGCATCGATGCAT-GAAT
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAA-AAAAGCAAAAGTGCATCGATGCATGGAAT
*
349076 GTGCATTGGTACACAAAATGCATTCGA
1 GTGCATCGGTACACAAAATGCATTCGA
349103 ATTAGGGTGT
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
64 56 0.74
65 20 0.26
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (64 bp):
GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAAAGCAAAAGTGCATCGATGCATGGAAT
Found at i:351266 original size:13 final size:13
Alignment explanation
Indices: 351231--351268 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
351221 TCCTAATGGG
351231 CAATGTTTGAAAA
1 CAATGTTTGAAAA
*
351244 TAAT-TTTGAAAA
1 CAATGTTTGAAAA
351256 CAATGTTTGAAAA
1 CAATGTTTGAAAA
351269 ATTATGGTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.47, C:0.05, G:0.13, T:0.34
Consensus pattern (13 bp):
CAATGTTTGAAAA
Found at i:351326 original size:18 final size:16
Alignment explanation
Indices: 351303--351340 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 16
351293 AAAACAACAT
351303 AATTAAATCAACAACAAC
1 AATTAAATCAA-AA-AAC
351321 AATTAAATCAAAAAAC
1 AATTAAATCAAAAAAC
351337 AATT
1 AATT
351341 TTTTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 7 0.35
17 2 0.10
18 11 0.55
ACGTcount: A:0.63, C:0.16, G:0.00, T:0.21
Consensus pattern (16 bp):
AATTAAATCAAAAAAC
Found at i:351808 original size:44 final size:44
Alignment explanation
Indices: 351746--351863 Score: 168
Period size: 44 Copynumber: 2.7 Consensus size: 44
351736 CGACGAGTGT
*
351746 ATCGGTACAC-TGCATAGTGTATCGATGCACATTCAAGGAATGC
1 ATCGGTACACTTTCATAGTGTATCGATGCACATTCAAGGAATGC
** *
351789 ATCGGTGTA-TCTTCATAGTGTATCGATGCATATTCAAGGAATGC
1 ATCGGTACACT-TTCATAGTGTATCGATGCACATTCAAGGAATGC
*
351833 ATTGGTACACTTTCATAGTGTATCGATGCAC
1 ATCGGTACACTTTCATAGTGTATCGATGCAC
351864 GATGCATAGT
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
43 7 0.11
44 56 0.88
45 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (44 bp):
ATCGGTACACTTTCATAGTGTATCGATGCACATTCAAGGAATGC
Found at i:354209 original size:21 final size:21
Alignment explanation
Indices: 354183--354224 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
354173 CCAGAATGGG
*
354183 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
354204 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
354225 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:354332 original size:29 final size:31
Alignment explanation
Indices: 354300--354359 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
354290 AAATTTTGAA
*
354300 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
354329 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
354360 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:356391 original size:20 final size:21
Alignment explanation
Indices: 356352--356391 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
356342 GAAGCTTTAA
* *
356352 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTTACTCTTGAT
356373 GATCATC-ATTTACTCTTGA
1 GATCATCAATTTACTCTTGA
356392 AAGTAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (21 bp):
GATCATCAATTTACTCTTGAT
Found at i:368135 original size:26 final size:25
Alignment explanation
Indices: 368089--368138 Score: 55
Period size: 26 Copynumber: 1.9 Consensus size: 25
368079 AATATATTAA
*
368089 ATATTAAAAATATAAACTAATTTTAA
1 ATATTAAAAATATTAA-TAATTTTAA
**
368115 ATACTTAAATTTATTAATAATTTT
1 ATA-TTAAAAATATTAATAATTTT
368139 GTATATTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
26 10 0.50
27 10 0.50
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (25 bp):
ATATTAAAAATATTAATAATTTTAA
Found at i:372564 original size:14 final size:14
Alignment explanation
Indices: 372545--372578 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
372535 TTAAATGATA
372545 AACGAATACAAATG
1 AACGAATACAAATG
372559 AACGAATACAAATG
1 AACGAATACAAATG
372573 AACGAA
1 AACGAA
372579 CGTAAATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.59, C:0.15, G:0.15, T:0.12
Consensus pattern (14 bp):
AACGAATACAAATG
Found at i:372585 original size:14 final size:14
Alignment explanation
Indices: 372545--372589 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
372535 TTAAATGATA
*
372545 AACGAATACAAATG
1 AACGAACACAAATG
*
372559 AACGAATACAAATG
1 AACGAACACAAATG
**
372573 AACGAACGTAAATG
1 AACGAACACAAATG
372587 AAC
1 AAC
372590 ATAAACGAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.56, C:0.16, G:0.16, T:0.13
Consensus pattern (14 bp):
AACGAACACAAATG
Found at i:373581 original size:17 final size:17
Alignment explanation
Indices: 373559--373594 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
373549 AAGCACCTCC
373559 AACTAAATTCATATTCA
1 AACTAAATTCATATTCA
*
373576 AACTAAATTTATATTCA
1 AACTAAATTCATATTCA
373593 AA
1 AA
373595 AAGAGAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (17 bp):
AACTAAATTCATATTCA
Found at i:389949 original size:8 final size:8
Alignment explanation
Indices: 389930--389958 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
389920 ACCCTAAAGC
389930 AAAAGT-A
1 AAAAGTAA
389937 AAAAGTAA
1 AAAAGTAA
389945 AAAAGTAA
1 AAAAGTAA
389953 AAAAGT
1 AAAAGT
389959 TTTCCCTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 6 0.29
8 15 0.71
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (8 bp):
AAAAGTAA
Found at i:393831 original size:15 final size:15
Alignment explanation
Indices: 393811--393844 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
393801 CCTTTCTTTT
393811 CTTGGTAACAATTTC
1 CTTGGTAACAATTTC
393826 CTTGGTAACAATTTC
1 CTTGGTAACAATTTC
393841 CTTG
1 CTTG
393845 AGGAGCTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.41
Consensus pattern (15 bp):
CTTGGTAACAATTTC
Found at i:397621 original size:20 final size:20
Alignment explanation
Indices: 397592--397634 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
397582 ATTCCACTAC
397592 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGCTCCTAA
* * *
397612 ATGCATCTATATGGTTCTAA
1 ATGCAACTATATGCTCCTAA
397632 ATG
1 ATG
397635 AGCTCCTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (20 bp):
ATGCAACTATATGCTCCTAA
Found at i:400044 original size:21 final size:21
Alignment explanation
Indices: 400009--400120 Score: 138
Period size: 21 Copynumber: 5.4 Consensus size: 21
399999 GTTGAGGGTT
* * *
400009 TTATGTTGTCATTCGGGATAA
1 TTATGTGGTCCTTCGGGACAA
*
400030 TTATATGGTCCTTCGGGACAA
1 TTATGTGGTCCTTCGGGACAA
*
400051 TTATGTGGTCTTTCGGGACAA
1 TTATGTGGTCCTTCGGGACAA
*
400072 --ATGTGGTCTTTCGGGACAA
1 TTATGTGGTCCTTCGGGACAA
*
400091 ATATGTGGTCCTTCGGGACAA
1 TTATGTGGTCCTTCGGGACAA
*
400112 ATATGTGGT
1 TTATGTGGT
400121 ACTTTAGTGC
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
19 19 0.23
21 63 0.77
ACGTcount: A:0.22, C:0.14, G:0.28, T:0.36
Consensus pattern (21 bp):
TTATGTGGTCCTTCGGGACAA
Found at i:400088 original size:40 final size:40
Alignment explanation
Indices: 400035--400113 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
400025 GATAATTATA
* *
400035 TGGTCCTTCGGGACAATTATGTGGTCTTTCGGGACAAATG
1 TGGTCCTTCGGGACAAATATGTGGTCCTTCGGGACAAATG
*
400075 TGGTCTTTCGGGACAAATATGTGGTCCTTCGGGACAAAT
1 TGGTCCTTCGGGACAAATATGTGGTCCTTCGGGACAAAT
400114 ATGTGGTACT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.32
Consensus pattern (40 bp):
TGGTCCTTCGGGACAAATATGTGGTCCTTCGGGACAAATG
Found at i:400134 original size:61 final size:61
Alignment explanation
Indices: 400011--400127 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
400001 TGAGGGTTTT
* * * * *
400011 ATGTTGTCATTCGGGATAATTATATGGTCCTTCGGGACAATTATGTGGTCTTTCGGGACAA
1 ATGTGGTCATTCGGGACAAATATATGGTCCTTCGGGACAAATATGTGGTCTTTAGGGACAA
* *
400072 ATGTGGTCTTTCGGGACAAATATGTGGTCCTTCGGGACAAATATGTGGTACTTTAG
1 ATGTGGTCATTCGGGACAAATATATGGTCCTTCGGGACAAATATGTGGT-CTTTAG
400128 TGCAAATTAC
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
61 43 0.90
62 5 0.10
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.35
Consensus pattern (61 bp):
ATGTGGTCATTCGGGACAAATATATGGTCCTTCGGGACAAATATGTGGTCTTTAGGGACAA
Found at i:401640 original size:16 final size:15
Alignment explanation
Indices: 401619--401667 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
401609 TATTAGTTTT
401619 TTAATTATTTATATTA
1 TTAATTA-TTATATTA
401635 TTAATTATTATATT-
1 TTAATTATTATATTA
* * *
401649 TTGATCACTATATTA
1 TTAATTATTATATTA
401664 TTAA
1 TTAA
401668 CTCTAGTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 11 0.39
15 10 0.36
16 7 0.25
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (15 bp):
TTAATTATTATATTA
Found at i:401800 original size:30 final size:31
Alignment explanation
Indices: 401750--401814 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
401740 GAATATTATT
* * *
401750 TTAAATTTTAGATAAAATATCATTTTGACCC
1 TTAAAATTTAGATAAAATATCAATTTGACCA
401781 TTAAAATTTAGAT-AAATATCAATTTGACCA
1 TTAAAATTTAGATAAAATATCAATTTGACCA
401811 TTAA
1 TTAA
401815 TTCAACCAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 19 0.61
31 12 0.39
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (31 bp):
TTAAAATTTAGATAAAATATCAATTTGACCA
Found at i:403908 original size:20 final size:19
Alignment explanation
Indices: 403883--403921 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
403873 TTCAATTAAG
403883 GGGTATCGATACCAACGGGT
1 GGGTATCGATACCAA-GGGT
403903 GGGTATCGATACCAAGGGT
1 GGGTATCGATACCAAGGGT
403922 CTTATATCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.26, C:0.18, G:0.36, T:0.21
Consensus pattern (19 bp):
GGGTATCGATACCAAGGGT
Found at i:415668 original size:30 final size:31
Alignment explanation
Indices: 415628--415690 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 31
415618 GTGTCTTTCA
* * *
415628 TCCACATAGAATACTTTCACATAGAGCA-TT
1 TCCACATAGAACACATTCACATAAAGCACTT
*
415658 TCCACGTAGAACACATTCACATAAAGCACTT
1 TCCACATAGAACACATTCACATAAAGCACTT
415689 TC
1 TC
415691 ATATGTTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.37, C:0.27, G:0.10, T:0.27
Consensus pattern (31 bp):
TCCACATAGAACACATTCACATAAAGCACTT
Found at i:422360 original size:24 final size:24
Alignment explanation
Indices: 422333--422390 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
422323 CACCACTGCT
*
422333 CATATAATTTGCAGT-GAAGTGCCA
1 CATAGAATTTGCA-TCGAAGTGCCA
*
422357 CATAGAATTTGTATCGAAGTGCCA
1 CATAGAATTTGCATCGAAGTGCCA
422381 CATAG-ATTTG
1 CATAGAATTTG
422391 TCCCGAAGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
23 6 0.19
24 25 0.81
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31
Consensus pattern (24 bp):
CATAGAATTTGCATCGAAGTGCCA
Found at i:422397 original size:23 final size:23
Alignment explanation
Indices: 422348--422420 Score: 85
Period size: 22 Copynumber: 3.2 Consensus size: 23
422338 AATTTGCAGT
**
422348 GAAGTGCCACATAGAATTTGTATC
1 GAAGTGCCACATAG-ATTTGTCCC
422372 GAAGTGCCACATAGATTTGTCCC
1 GAAGTGCCACATAGATTTGTCCC
* * *
422395 GAAG-GACGCATAAATTTGTCCC
1 GAAGTGCCACATAGATTTGTCCC
422417 GAAG
1 GAAG
422421 GACCTCGTAG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
22 19 0.43
23 11 0.25
24 14 0.32
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.25
Consensus pattern (23 bp):
GAAGTGCCACATAGATTTGTCCC
Found at i:422456 original size:25 final size:25
Alignment explanation
Indices: 422386--422457 Score: 96
Period size: 25 Copynumber: 3.0 Consensus size: 25
422376 TGCCACATAG
422386 ATTTGTCCCGAAGGA-CGCAT--AA
1 ATTTGTCCCGAAGGACCGCATAGAA
* *
422408 ATTTGTCCCGAAGGACCTCGTAGAA
1 ATTTGTCCCGAAGGACCGCATAGAA
*
422433 ATTTGTCTCGAAGGACCGCATAGAA
1 ATTTGTCCCGAAGGACCGCATAGAA
422458 CCCTCGACTC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
22 15 0.36
23 3 0.07
25 24 0.57
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.24
Consensus pattern (25 bp):
ATTTGTCCCGAAGGACCGCATAGAA
Found at i:422608 original size:15 final size:15
Alignment explanation
Indices: 422599--422636 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
422589 TTTCACGTAG
422599 AACACATTCACATAA
1 AACACATTCACATAA
*
422614 AACACATTCACATAT
1 AACACATTCACATAA
422629 AACACATT
1 AACACATT
422637 TATATGTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (15 bp):
AACACATTCACATAA
Found at i:436593 original size:21 final size:21
Alignment explanation
Indices: 436541--436593 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
436531 AGTTCCTACA
* *
436541 CAACCAACTCCTAGTGCCGAG
1 CAACCAACTCTTACTGCCGAG
**
436562 CAACCAACTCTTACTGTTGAG
1 CAACCAACTCTTACTGCCGAG
436583 CAACCAACTCT
1 CAACCAACTCT
436594 AGCACGAGCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (21 bp):
CAACCAACTCTTACTGCCGAG
Found at i:438619 original size:15 final size:15
Alignment explanation
Indices: 438599--438637 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
438589 TGATGAATTA
438599 TGTTTTGCTCATAAC
1 TGTTTTGCTCATAAC
*
438614 TGTTTTGCTCATAAT
1 TGTTTTGCTCATAAC
*
438629 TATTTTGCT
1 TGTTTTGCT
438638 AATTATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.18, C:0.15, G:0.13, T:0.54
Consensus pattern (15 bp):
TGTTTTGCTCATAAC
Found at i:439996 original size:20 final size:20
Alignment explanation
Indices: 439971--440025 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
439961 TGATTCAATC
*
439971 AGTATCGATACCTA-TGAGG
1 AGTATCGATACCTAGTAAGG
439990 TAGTATCGATACCATAGTAAGG
1 -AGTATCGATACC-TAGTAAGG
440012 -GTATCGATACCTAG
1 AGTATCGATACCTAG
440026 AAACATCGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
19 3 0.09
20 23 0.72
21 2 0.06
22 4 0.12
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (20 bp):
AGTATCGATACCTAGTAAGG
Found at i:440629 original size:55 final size:55
Alignment explanation
Indices: 440545--441031 Score: 687
Period size: 55 Copynumber: 8.9 Consensus size: 55
440535 TGTGTACTAT
*
440545 AAGCACTTTGTGTGCATAATCACGGAATTCATCATAAGTTGATGAATCACCGTAC
1 AAGCACTTTGTGTGCATAATCACGAAATTCATCATAAGTTGATGAATCACCGTAC
* * *
440600 AAGCACTTCGTGTGCATAATCACGAAATTCATCACAAGTTGATGAATCACCGTAT
1 AAGCACTTTGTGTGCATAATCACGAAATTCATCATAAGTTGATGAATCACCGTAC
*
440655 AGGCACTTTGTGTGCATAATCACGAAATTCATCATAAGTTGATGAATCACCGTAC
1 AAGCACTTTGTGTGCATAATCACGAAATTCATCATAAGTTGATGAATCACCGTAC
* * * *
440710 ATGCACTTTGTGTGCATAATTACGGAATTCATTATAAGTTGATGAATCACCGTAC
1 AAGCACTTTGTGTGCATAATCACGAAATTCATCATAAGTTGATGAATCACCGTAC
* * *
440765 AGGCACTTCGTGTGCATAATCAC-AGAATTCATCATAAGTTAATGAATCACCGTAC
1 AAGCACTTTGTGTGCATAATCACGA-AATTCATCATAAGTTGATGAATCACCGTAC
440820 AAGCACTTTGTGTGCATAATCACGAAATTCATCATAAGTTGATGAATCACCGTAC
1 AAGCACTTTGTGTGCATAATCACGAAATTCATCATAAGTTGATGAATCACCGTAC
*
440875 -AGACACTTTGTGTGCATAATCAC-AGAATTCATCATAAGTTGATGAATCACCATAC
1 AAG-CACTTTGTGTGCATAATCACGA-AATTCATCATAAGTTGATGAATCACCGTAC
* * * * *
440930 AGGAACTTCGTGTGCATAATCA-TAGAATTCATCATAAGTTGATGAATCACAGTAC
1 AAGCACTTTGTGTGCATAATCACGA-AATTCATCATAAGTTGATGAATCACCGTAC
** * * *
440985 ATA-CACTTTGTGTGCATTTTCACGGAATTTATCATGAGTTGATGAAT
1 A-AGCACTTTGTGTGCATAATCACGAAATTCATCATAAGTTGATGAAT
441032 TTATGTATAG
Statistics
Matches: 388, Mismatches: 36, Indels: 16
0.88 0.08 0.04
Matches are distributed among these distances:
54 3 0.01
55 383 0.99
56 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (55 bp):
AAGCACTTTGTGTGCATAATCACGAAATTCATCATAAGTTGATGAATCACCGTAC
Found at i:440704 original size:27 final size:27
Alignment explanation
Indices: 440562--440704 Score: 66
Period size: 27 Copynumber: 5.2 Consensus size: 27
440552 TTGTGTGCAT
*
440562 AATCACGGAATTCATCATAAGTTGATG
1 AATCACGAAATTCATCATAAGTTGATG
* **
440589 AATCACCGTACAA-GCA-C-TTCGTGTGCAT-
1 AATCA-CG-A-AATTCATCATAAGT-TG-ATG
*
440617 AATCACGAAATTCATCACAAGTTGATG
1 AATCACGAAATTCATCATAAGTTGATG
* ** **
440644 AATCACCGTATAGGCA-C-TTTGTGTGCAT-
1 AATCA-CG-AAATTCATCATAAGT-TG-ATG
440672 AATCACGAAATTCATCATAAGTTGATG
1 AATCACGAAATTCATCATAAGTTGATG
440699 AATCAC
1 AATCAC
440705 CGTACATGCA
Statistics
Matches: 81, Mismatches: 19, Indels: 32
0.61 0.14 0.24
Matches are distributed among these distances:
25 2 0.02
26 11 0.14
27 31 0.38
28 25 0.31
29 10 0.12
30 2 0.02
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (27 bp):
AATCACGAAATTCATCATAAGTTGATG
Found at i:440828 original size:165 final size:164
Alignment explanation
Indices: 440546--441031 Score: 769
Period size: 165 Copynumber: 3.0 Consensus size: 164
440536 GTGTACTATA
*
440546 AGCACTTTGTGTGCATAATCACGGAATTCATCATAAGTTGATGAATCACCGTACAAGCACTTCGT
1 AGCACTTTGTGTGCATAATCACGGAATTCATCATAAGTTGATGAATCACCGTACAGGCACTTCGT
* * *
440611 GTGCATAATCAC-GAAATTCATCACAAGTTGATGAATCACCGTATAGGCACTTTGTGTGCATAAT
66 GTGCATAATCACAG-AATTCATCATAAGTTGATGAATCACCGTACAAGCACTTTGTGTGCATAAT
440675 CACGAAATTCATCATAAGTTGATGAATCACCGTAC
130 CACGAAATTCATCATAAGTTGATGAATCACCGTAC
* *
440710 ATGCACTTTGTGTGCATAATTACGGAATTCATTATAAGTTGATGAATCACCGTACAGGCACTTCG
1 A-GCACTTTGTGTGCATAATCACGGAATTCATCATAAGTTGATGAATCACCGTACAGGCACTTCG
*
440775 TGTGCATAATCACAGAATTCATCATAAGTTAATGAATCACCGTACAAGCACTTTGTGTGCATAAT
65 TGTGCATAATCACAGAATTCATCATAAGTTGATGAATCACCGTACAAGCACTTTGTGTGCATAAT
440840 CACGAAATTCATCATAAGTTGATGAATCACCGTAC
130 CACGAAATTCATCATAAGTTGATGAATCACCGTAC
* * *
440875 AGACACTTTGTGTGCATAATCACAGAATTCATCATAAGTTGATGAATCACCATACAGGAACTTCG
1 AG-CACTTTGTGTGCATAATCACGGAATTCATCATAAGTTGATGAATCACCGTACAGGCACTTCG
* * **
440940 TGTGCATAATCATAGAATTCATCATAAGTTGATGAATCACAGTACATA-CACTTTGTGTGCATTT
65 TGTGCATAATCACAGAATTCATCATAAGTTGATGAATCACCGTACA-AGCACTTTGTGTGCATAA
* * *
441004 TCACGGAATTTATCATGAGTTGATGAAT
129 TCACGAAATTCATCATAAGTTGATGAAT
441032 TTATGTATAG
Statistics
Matches: 298, Mismatches: 20, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
164 2 0.01
165 294 0.99
166 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (164 bp):
AGCACTTTGTGTGCATAATCACGGAATTCATCATAAGTTGATGAATCACCGTACAGGCACTTCGT
GTGCATAATCACAGAATTCATCATAAGTTGATGAATCACCGTACAAGCACTTTGTGTGCATAATC
ACGAAATTCATCATAAGTTGATGAATCACCGTAC
Found at i:449952 original size:66 final size:65
Alignment explanation
Indices: 449798--450008 Score: 189
Period size: 64 Copynumber: 3.2 Consensus size: 65
449788 AATTTCAAAG
* * * * * ** *
449798 TGATGCACCGATGCACCA-ATCTATGCATCGATGCACCATGGAATAAATTG-AGCATCGAATGCA
1 TGATGCATCGATGCACCATA-CCATGCATCAATGCACTAAGG-ATATTTTGAAACATCGAATGCA
449861 TT
64 TT
* * * *
449863 TCATGCATTGATCCA-CATACCATGCATCGATGCACTAAGGAT-TTTATGAAAACATCGAATGGC
1 TGATGCATCGATGCACCATACCATGCATCAATGCACTAAGGATATTT-TG-AAACATCGAAT-GC
449926 ATT
63 ATT
* ** * *
449929 TGATGCATCGATGCACCA-GCCATGCATCAATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCACCATACCATGCATCAATGCACTAAGGATATTTTGAAACATCGAATGCATT
449993 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
450009 TCTTAGTGCA
Statistics
Matches: 120, Mismatches: 19, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 40 0.33
65 32 0.27
66 38 0.32
67 5 0.04
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.27
Consensus pattern (65 bp):
TGATGCATCGATGCACCATACCATGCATCAATGCACTAAGGATATTTTGAAACATCGAATGCATT
Found at i:450008 original size:17 final size:19
Alignment explanation
Indices: 449980--450028 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
449970 TATTTTGAAA
449980 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
449998 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
450017 CACCGATGCACT
1 CATCGATGCACT
450029 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:450785 original size:13 final size:13
Alignment explanation
Indices: 450767--450792 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
450757 TCTAAAAAAA
450767 TATTTTTTGTTTT
1 TATTTTTTGTTTT
450780 TATTTTTTGTTTT
1 TATTTTTTGTTTT
450793 CAGAAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.85
Consensus pattern (13 bp):
TATTTTTTGTTTT
Found at i:452005 original size:20 final size:21
Alignment explanation
Indices: 451969--452016 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
451959 CTAGTATTTT
* *
451969 ATTATAAT-ATTATATTAT-A
1 ATTATATTAATTAAATTATAA
451988 ATTATATTAATTAAATTATCAA
1 ATTATATTAATTAAATTAT-AA
452010 ATTATAT
1 ATTATAT
452017 AAATAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 7 0.29
20 9 0.38
22 8 0.33
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTATATTAATTAAATTATAA
Found at i:453333 original size:8 final size:8
Alignment explanation
Indices: 453322--453377 Score: 53
Period size: 8 Copynumber: 6.6 Consensus size: 8
453312 GGGCTTTGTA
453322 AATAATAT
1 AATAATAT
453330 AATAATAT
1 AATAATAT
453338 AAT-ATAT
1 AATAATAT
453345 ATATATATAT
1 A-ATA-ATAT
453355 ATATAATA-
1 A-ATAATAT
453363 ACATATATAT
1 A-ATA-ATAT
453373 AATAA
1 AATAA
453378 ACGTCACTCG
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
7 5 0.12
8 18 0.43
9 9 0.21
10 10 0.24
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (8 bp):
AATAATAT
Found at i:453346 original size:2 final size:2
Alignment explanation
Indices: 453326--453373 Score: 52
Period size: 2 Copynumber: 26.5 Consensus size: 2
453316 TTTGTAAATA
453326 AT AT A- AT A- AT AT A- AT AT AT AT AT AT AT AT AT AT A- AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
453363 AC AT AT AT AT A
1 AT AT AT AT AT A
453374 ATAAACGTCA
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
1 5 0.12
2 35 0.88
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:453374 original size:14 final size:14
Alignment explanation
Indices: 453326--453377 Score: 70
Period size: 14 Copynumber: 3.6 Consensus size: 14
453316 TTTGTAAATA
453326 ATATAATAATATA-
1 ATATAATAATATAT
453339 ATATATATATATATAT
1 ATATA-ATA-ATATAT
*
453355 ATATAATAACATAT
1 ATATAATAATATAT
453369 ATATAATAA
1 ATATAATAA
453378 ACGTCACTCG
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
13 5 0.14
14 17 0.49
15 8 0.23
16 5 0.14
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (14 bp):
ATATAATAATATAT
Found at i:454847 original size:19 final size:20
Alignment explanation
Indices: 454817--454860 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
454807 ATTTAGTTTT
454817 TTATTATATATATAAAAATA
1 TTATTATATATATAAAAATA
* *
454837 TTATT-TATATATAATAGTA
1 TTATTATATATATAAAAATA
454856 TTATT
1 TTATT
454861 GTAATTGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TTATTATATATATAAAAATA
Found at i:456847 original size:16 final size:15
Alignment explanation
Indices: 456820--456865 Score: 74
Period size: 15 Copynumber: 3.0 Consensus size: 15
456810 TATTTTTTTC
456820 TAAAAATAAAAATAT
1 TAAAAATAAAAATAT
*
456835 TTAAAATATAAAATAT
1 TAAAAATA-AAAATAT
456851 TAAAAATAAAAATAT
1 TAAAAATAAAAATAT
456866 GATTAATTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 14 0.50
16 14 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAAAATAAAAATAT
Found at i:459193 original size:22 final size:22
Alignment explanation
Indices: 459166--459224 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 22
459156 TTAATGGTAT
* *
459166 TTTTATATTTAATTTTTAAATA
1 TTTTATATTTAAATTTAAAATA
459188 TTTTATATTTAAAATTTAAAATA
1 TTTTATATTT-AAATTTAAAATA
*
459211 TTTGTATTTTTAAA
1 TTT-TATATTTAAA
459225 AAAATAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.31
23 16 0.50
24 6 0.19
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
TTTTATATTTAAATTTAAAATA
Found at i:460319 original size:22 final size:19
Alignment explanation
Indices: 460294--460338 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 19
460284 ATATTAAATT
460294 ATATTACAAATAATCAATAAAA
1 ATATTA-AAA-AATC-ATAAAA
*
460316 ATATTAAAAATTCATAAAA
1 ATATTAAAAAATCATAAAA
460335 ATAT
1 ATAT
460339 CATATTAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 10 0.45
20 3 0.14
21 3 0.14
22 6 0.27
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (19 bp):
ATATTAAAAAATCATAAAA
Found at i:461524 original size:19 final size:19
Alignment explanation
Indices: 461482--461518 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
461472 AAATGGTTTG
461482 ACTCGATTAACACGGCTCA
1 ACTCGATTAACACGGCTCA
*
461501 ACTCGATTAACATGGCTC
1 ACTCGATTAACACGGCTC
461519 GGCTCGGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (19 bp):
ACTCGATTAACACGGCTCA
Found at i:463158 original size:21 final size:22
Alignment explanation
Indices: 463134--463175 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
463124 GCTCTGTTAG
463134 TATT-TGTTTATATTTTTTTAA
1 TATTATGTTTATATTTTTTTAA
* *
463155 TATTATGTTTGTGTTTTTTTA
1 TATTATGTTTATATTTTTTTA
463176 TTTATTTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.19, C:0.00, G:0.10, T:0.71
Consensus pattern (22 bp):
TATTATGTTTATATTTTTTTAA
Found at i:470161 original size:55 final size:55
Alignment explanation
Indices: 469831--470626 Score: 489
Period size: 55 Copynumber: 14.7 Consensus size: 55
469821 CGTGTCTGCC
* * * * * *
469831 CCCTATATCTTCAGAGAGTATA-AGAC-C-TACAATCTTCATCAATCGCG-TCTGCC
1 CCCTATTTCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAACGGGTTC-GCT
* * * * *
469884 CCCTATTTCTTCAGAGAGTATA-AGAC-C-TACAATCTTCATCAATCGCG-TCTGCC
1 CCCTATTTCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAACGGGTTC-GCT
* * *
469937 CCCTATTTCTTCAGAGAGTATA-AGACTCGAACAATCTTCAACAATCGTG-TCTACT
1 CCCTATTTCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAACGGGTTC-GCT
* * *
469992 CCCTA-TTCTTTCAGAGAGTAT-GAGACTCGAATAATCTTCAACAATCGTG-TCAGCT
1 CCCTATTTC-TTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAACGGGTTC-GCT
* * * * *
470047 CCCTA-TTCTTTCAGAGAGTATA-AGACTC-AATATATCTTCAACGATCGCG-TCTGCC
1 CCCTATTTC-TTCAGAGAGTATAGA-ACTCGAACA-ATCTTCAACAAACGGGTTC-GCT
* *
470102 CCCTATTTCTTCAGAGAGTATA-AGACTCGAACAATCTTCAACAAATGGGTTCACT
1 CCCTATTTCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAACGGGTTCGCT
* * * **
470157 CCCTATTTC-TCTAGGGAGTATGGAACTC-AGAC-ATATTCTTCAAACGGGTTCGCT
1 CCCTATTTCTTC-AGAGAGTATAGAACTCGA-ACAATCTTCAACAAACGGGTTCGCT
** * **
470211 CCCCCTTTC-TCTAGGGAGTATAGAACTCGAAC-ATC-TCTTCAAACGGGTTCGCT
1 CCCTATTTCTTC-AGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTTCGCT
* ** *
470264 CCTTCCTTCTTTA-AGGAGTATAGAACTCGAAC-ATCTT---CAAACGGGTTCGCT
1 CCCTATTTCTTCAGA-GAGTATAGAACTCGAACAATCTTCAACAAACGGGTTCGCT
* * * * *
470315 CCTTCTTTCTTTA-AGGAGTATAGAACTCGAACAATCTTCAACAAACAGGTTCCCT
1 CCCTATTTCTTCAGA-GAGTATAGAACTCGAACAATCTTCAACAAACGGGTTCGCT
* * * * **
470370 CCCTCTTTC-TCTAGGGAGTATAGAACTTGAAC-ATTTTCTTCAAACGGGTTCGCT
1 CCCTATTTCTTC-AGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTTCGCT
* **
470424 CCCTCTTTCTTCA-AGGAGTATAGAACTCGAAC-ATCTTCTTCAAACGGGTTCGCT
1 CCCTATTTCTTCAGA-GAGTATAGAACTCGAACAATCTTCAACAAACGGGTTCGCT
** * **
470478 CCCCCTTTC-TCTAGGGAGTATAGAACTCGAACAATCTTCAACAAACATGTTCGCT
1 CCCTATTTCTTC-AGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTTCGCT
* * * * **
470533 CCCTCTTTC-TCTAGGGAGTATAGAACTTGAAC-ATTTTCTTCAAACGGGTTCGCT
1 CCCTATTTCTTC-AGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTTCGCT
* * * * * *
470587 CCCTCTCTC-TCTAGGGAGTATGGAACTCAAATAATCTTCA
1 CCCTATTTCTTC-AGAGAGTATAGAACTCGAACAATCTTCA
470627 TTTGCTTCAC
Statistics
Matches: 644, Mismatches: 71, Indels: 54
0.84 0.09 0.07
Matches are distributed among these distances:
51 45 0.07
52 5 0.01
53 125 0.19
54 194 0.30
55 266 0.41
56 9 0.01
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.31
Consensus pattern (55 bp):
CCCTATTTCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTTCGCT
Found at i:470220 original size:54 final size:54
Alignment explanation
Indices: 470117--470614 Score: 614
Period size: 54 Copynumber: 9.2 Consensus size: 54
470107 TTTCTTCAGA
** * * *
470117 GAGTATA-AGACTCGAACAATCTTCAACAAATGGGTTCACTCCCTATTTCTCTAGG
1 GAGTATAGA-ACTCGAAC-ATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
* * *
470172 GAGTATGGAACTC-AGACATATTCTTCAAACGGGTTCGCTCCCCCTTTCTCTAGG
1 GAGTATAGAACTCGA-ACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
* * * *
470226 GAGTATAGAACTCGAACATC-TCTTCAAACGGGTTCGCTCCTTCCTTCTTTAAG
1 GAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
* * *
470279 GAGTATAGAACTCGAACA---TCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
1 GAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
** * *
470330 GAGTATAGAACTCGAACAATCTTCAACAAACAGGTTCCCTCCCTCTTTCTCTAGG
1 GAGTATAGAACTCGAAC-ATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
* * *
470385 GAGTATAGAACTTGAACATTTTCTTCAAACGGGTTCGCTCCCTCTTTCT-TCAAG
1 GAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGG
*
470439 GAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCCCTTTCTCTAGG
1 GAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
** **
470493 GAGTATAGAACTCGAACAATCTTCAACAAACATGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATAGAACTCGAAC-ATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
* * *
470548 GAGTATAGAACTTGAACATTTTCTTCAAACGGGTTCGCTCCCTCTCTCTCTAGG
1 GAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
*
470602 GAGTATGGAACTC
1 GAGTATAGAACTC
470615 AAATAATCTT
Statistics
Matches: 385, Mismatches: 48, Indels: 21
0.85 0.11 0.05
Matches are distributed among these distances:
51 49 0.13
52 1 0.00
53 47 0.12
54 183 0.48
55 104 0.27
56 1 0.00
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (54 bp):
GAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
Found at i:470440 original size:109 final size:107
Alignment explanation
Indices: 470102--470614 Score: 601
Period size: 109 Copynumber: 4.8 Consensus size: 107
470092 CGCGTCTGCC
* ** * * *
470102 CCCTATTTCTTC-AGAGAGTATA-AGACTCGAACAATCTTCAACAAATGGGTTCACTCCCTATTT
1 CCCTCTTTCTTCAAG-GAGTATAGA-ACTCGAAC-ATCTTCTTCAAACGGGTTCGCTCCCTCTTT
*
470165 CTCTAGGGAGTATGGAACTC-AGACATATTCTTCAAACGGGTTCGCT
63 CTCTAGGGAGTATAGAACTCGA-ACAT-TTCTTCAAACGGGTTCGCT
* * * *
470211 CCCCCTTTC-TCTAGGGAGTATAGAACTCGAACATC-TCTTCAAACGGGTTCGCTCCTTCCTTCT
1 CCCTCTTTCTTC-AAGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCT
* *
470274 TTAAGGAGTATAGAACTCGAACA--TCTTCAAACGGGTTCGCT
65 CTAGGGAGTATAGAACTCGAACATTTCTTCAAACGGGTTCGCT
* * ** * *
470315 CCTTCTTTCTTTAAGGAGTATAGAACTCGAACAATCTTCAACAAACAGGTTCCCTCCCTCTTTCT
1 CCCTCTTTCTTCAAGGAGTATAGAACTCGAAC-ATCTTCTTCAAACGGGTTCGCTCCCTCTTTCT
*
470380 CTAGGGAGTATAGAACTTGAACATTTTCTTCAAACGGGTTCGCT
65 CTAGGGAGTATAGAACTCGAACA-TTTCTTCAAACGGGTTCGCT
*
470424 CCCTCTTTCTTCAAGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCCCTTTCTC
1 CCCTCTTTCTTCAAGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTC
** **
470489 TAGGGAGTATAGAACTCGAACAATCTTCAACAAACATGTTCGCT
66 TAGGGAGTATAGAACTCGAAC-AT-TTCTTCAAACGGGTTCGCT
* * * *
470533 CCCTCTTTC-TCTAGGGAGTATAGAACTTGAACATTTTCTTCAAACGGGTTCGCTCCCTCTCTCT
1 CCCTCTTTCTTC-AAGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCT
*
470597 CTAGGGAGTATGGAACTC
65 CTAGGGAGTATAGAACTC
470615 AAATAATCTT
Statistics
Matches: 347, Mismatches: 44, Indels: 26
0.83 0.11 0.06
Matches are distributed among these distances:
104 44 0.13
105 4 0.01
106 42 0.12
107 39 0.11
108 57 0.16
109 159 0.46
110 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (107 bp):
CCCTCTTTCTTCAAGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTC
TAGGGAGTATAGAACTCGAACATTTCTTCAAACGGGTTCGCT
Found at i:470517 original size:163 final size:163
Alignment explanation
Indices: 470102--470614 Score: 684
Period size: 163 Copynumber: 3.2 Consensus size: 163
470092 CGCGTCTGCC
* ** * * *
470102 CCCTATTTCTTC-AGAGAGTATA-AGACTCGAACAATCTTCAACAAATGGGTTCACTCCCTATTT
1 CCCTCTTTCTTCAAG-GAGTATAGA-ACTCGAAC-ATCTTCTTCAAACGGGTTCGCTCCCTCTTT
* * ** * *
470165 CTCTAGGGAGTATGGAACTC-AGAC-ATATTCTTCAAACGGGTTCGCTCCCCCTTTCTCTAGGGA
63 CTCTAGGGAGTATAGAACTCGA-ACAATCTTCAACAAACAGGTTCGCTCCCTCTTTCTCTAGGGA
* *
470228 GTATAGAACTCGAACA-TCTCTTCAAACGGGTTCGCT
127 GTATAGAACTTGAACATTTTCTTCAAACGGGTTCGCT
* * * * *
470264 CCTTCCTTCTTTAAGGAGTATAGAACTCGAACA---TCTTCAAACGGGTTCGCTCCTTCTTTCTT
1 CCCTCTTTCTTCAAGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTC
* *
470326 TAAGGAGTATAGAACTCGAACAATCTTCAACAAACAGGTTCCCTCCCTCTTTCTCTAGGGAGTAT
66 TAGGGAGTATAGAACTCGAACAATCTTCAACAAACAGGTTCGCTCCCTCTTTCTCTAGGGAGTAT
470391 AGAACTTGAACATTTTCTTCAAACGGGTTCGCT
131 AGAACTTGAACATTTTCTTCAAACGGGTTCGCT
*
470424 CCCTCTTTCTTCAAGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCCCTTTCTC
1 CCCTCTTTCTTCAAGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTC
*
470489 TAGGGAGTATAGAACTCGAACAATCTTCAACAAACATGTTCGCTCCCTCTTTCTCTAGGGAGTAT
66 TAGGGAGTATAGAACTCGAACAATCTTCAACAAACAGGTTCGCTCCCTCTTTCTCTAGGGAGTAT
470554 AGAACTTGAACATTTTCTTCAAACGGGTTCGCT
131 AGAACTTGAACATTTTCTTCAAACGGGTTCGCT
* * *
470587 CCCTCTCTC-TCTAGGGAGTATGGAACTC
1 CCCTCTTTCTTC-AAGGAGTATAGAACTC
470615 AAATAATCTT
Statistics
Matches: 309, Mismatches: 33, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
158 39 0.13
159 49 0.16
160 49 0.16
161 1 0.00
162 25 0.08
163 146 0.47
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (163 bp):
CCCTCTTTCTTCAAGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTC
TAGGGAGTATAGAACTCGAACAATCTTCAACAAACAGGTTCGCTCCCTCTTTCTCTAGGGAGTAT
AGAACTTGAACATTTTCTTCAAACGGGTTCGCT
Found at i:471069 original size:36 final size:36
Alignment explanation
Indices: 470997--471194 Score: 238
Period size: 36 Copynumber: 5.5 Consensus size: 36
470987 ACTCTTCTGA
* * *
470997 GAAGGCTTAAAATGGATCTGCTTCACTACTT-T-TGGT
1 GAAGGCTTAAGATGG-TTTGCTTCACTA-TTCTCCGGT
* * * *
471033 GAAGACTTAAGATGCTTTGCTTCACTACTCTCTGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* *
471069 GAAGACTTATGATGGTTTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* * *
471105 GAAGGCTTCAGATTGATTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
*
471141 GAAGGCTTCAGATGGTTTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
*
471177 GAAGGCTTAGGATGGTTT
1 GAAGGCTTAAGATGGTTT
471195 TTCTCCAATC
Statistics
Matches: 142, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
34 1 0.01
35 12 0.08
36 129 0.91
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (36 bp):
GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
Found at i:475979 original size:20 final size:21
Alignment explanation
Indices: 475954--476090 Score: 83
Period size: 21 Copynumber: 6.6 Consensus size: 21
475944 AATGTGAAGT
475954 GGTCTTCAT-GTCGTTATG-AA
1 GGTCTTC-TCGTCGTTATGAAA
*
475974 GGTCTTCTCGTTGTTATGAAA
1 GGTCTTCTCGTCGTTATGAAA
*
475995 GGTCTTCTCGTC-TTGATGAAT
1 GGTCTTCTCGTCGTT-ATGAAA
* *
476016 GGCCTTCTCGTC-TTGATGAAT
1 GGTCTTCTCGTCGTT-ATGAAA
476037 GG-CATTCTCGTC-TTGATG-AA
1 GGTC-TTCTCGTCGTT-ATGAAA
* * *
476057 TGACATTCTCGTC-TTGATGAAT
1 GGTC-TTCTCGTCGTT-ATGAAA
*
476079 GCTCTTCTCGTC
1 GGTCTTCTCGTC
476091 CTTGGTACAA
Statistics
Matches: 101, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
19 1 0.01
20 20 0.20
21 78 0.77
22 2 0.02
ACGTcount: A:0.17, C:0.20, G:0.23, T:0.40
Consensus pattern (21 bp):
GGTCTTCTCGTCGTTATGAAA
Found at i:476013 original size:21 final size:21
Alignment explanation
Indices: 475972--476090 Score: 118
Period size: 21 Copynumber: 5.7 Consensus size: 21
475962 TGTCGTTATG
*
475972 AAGGTCTTCTCGT-TGTTATGA
1 AAGGTCTTCTCGTCT-TGATGA
475993 AAGGTCTTCTCGTCTTGATGA
1 AAGGTCTTCTCGTCTTGATGA
* *
476014 ATGGCCTTCTCGTCTTGATGA
1 AAGGTCTTCTCGTCTTGATGA
*
476035 ATGG-CATTCTCGTCTTGATG-
1 AAGGTC-TTCTCGTCTTGATGA
* *
476055 AATGACATTCTCGTCTTGATGA
1 AAGGTC-TTCTCGTCTTGATGA
* *
476077 ATGCTCTTCTCGTC
1 AAGGTCTTCTCGTC
476091 CTTGGTACAA
Statistics
Matches: 85, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
20 3 0.04
21 79 0.93
22 3 0.04
ACGTcount: A:0.18, C:0.21, G:0.22, T:0.39
Consensus pattern (21 bp):
AAGGTCTTCTCGTCTTGATGA
Found at i:476035 original size:42 final size:42
Alignment explanation
Indices: 475989--476090 Score: 152
Period size: 42 Copynumber: 2.4 Consensus size: 42
475979 TCTCGTTGTT
* * *
475989 ATGAAAGGTCTTCTCGTCTTGATGAATGGCCTTCTCGTCTTG
1 ATGAATGGTCTTCTCGTCTTGATGAATGACATTCTCGTCTTG
476031 ATGAATGG-CATTCTCGTCTTGATGAATGACATTCTCGTCTTG
1 ATGAATGGTC-TTCTCGTCTTGATGAATGACATTCTCGTCTTG
*
476073 ATGAATGCTCTTCTCGTC
1 ATGAATGGTCTTCTCGTC
476091 CTTGGTACAA
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
41 1 0.02
42 52 0.96
43 1 0.02
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.38
Consensus pattern (42 bp):
ATGAATGGTCTTCTCGTCTTGATGAATGACATTCTCGTCTTG
Found at i:480839 original size:23 final size:23
Alignment explanation
Indices: 480813--480863 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 23
480803 ATAATTTTGT
** *
480813 CTTTGTGGTACGTTTTTTATATG
1 CTTTGTGACACGTTTTTCATATG
*
480836 CTTTTGTGACACGTTTTTCATATT
1 C-TTTGTGACACGTTTTTCATATG
480860 CTTT
1 CTTT
480864 CTAAGTCATT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.14, C:0.14, G:0.16, T:0.57
Consensus pattern (23 bp):
CTTTGTGACACGTTTTTCATATG
Found at i:482065 original size:14 final size:14
Alignment explanation
Indices: 482028--482058 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
482018 AGGGTTTTAA
*
482028 GTTAGAATTTAGGG
1 GTTAGAGTTTAGGG
482042 GTTAGAGTTTAGGG
1 GTTAGAGTTTAGGG
482056 GTT
1 GTT
482059 TAAGTTTGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.39, T:0.39
Consensus pattern (14 bp):
GTTAGAGTTTAGGG
Found at i:482087 original size:14 final size:14
Alignment explanation
Indices: 482068--482099 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
482058 TTAAGTTTGG
482068 TTTAGGATTTAAGA
1 TTTAGGATTTAAGA
*
482082 TTTAGGGTTTAAGA
1 TTTAGGATTTAAGA
482096 TTTA
1 TTTA
482100 AGATGATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TTTAGGATTTAAGA
Found at i:483501 original size:2 final size:2
Alignment explanation
Indices: 483494--483519 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
483484 ACGTTAGAGG
483494 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
483520 GTTAAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:483641 original size:18 final size:17
Alignment explanation
Indices: 483618--483686 Score: 59
Period size: 17 Copynumber: 3.8 Consensus size: 17
483608 AAAGGGAAAG
483618 AAAAAAATAAGAAT-AAT
1 AAAAAAATAA-AATAAAT
483635 AAAAAAATAAAATGAAAT
1 AAAAAAATAAAAT-AAAT
*
483653 AAAATAAAATAAAAGAAAAAT
1 -AAA-AAAAT-AAA-ATAAAT
*
483674 AAAACAATAAAAT
1 AAAAAAATAAAAT
483687 TGTTAGATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
16 3 0.07
17 11 0.26
18 6 0.14
19 7 0.16
20 8 0.19
21 7 0.16
22 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.04, T:0.16
Consensus pattern (17 bp):
AAAAAAATAAAATAAAT
Found at i:483652 original size:5 final size:5
Alignment explanation
Indices: 483621--483677 Score: 60
Period size: 5 Copynumber: 10.8 Consensus size: 5
483611 GGGAAAGAAA
* * *
483621 AAAAT AAGAAT AATAAA AAAAT AAAAT GAAAT AAAAT AAAAT AAAAGA
1 AAAAT AA-AAT AA-AAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T
483669 AAAAT AAAA
1 AAAAT AAAA
483678 CAATAAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
5 30 0.70
6 13 0.30
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:483672 original size:31 final size:31
Alignment explanation
Indices: 483617--483677 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
483607 CAAAGGGAAA
483617 GAAAAAAATAAGAATAATAAAAAAATAAAAT
1 GAAAAAAATAAGAATAATAAAAAAATAAAAT
483648 GAAATAAAATAA-AATAA-AAGAAAAATAAAA
1 GAAA-AAAATAAGAATAATAA-AAAAATAAAA
483678 CAATAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 2 0.07
31 19 0.68
32 7 0.25
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.15
Consensus pattern (31 bp):
GAAAAAAATAAGAATAATAAAAAAATAAAAT
Found at i:483676 original size:72 final size:72
Alignment explanation
Indices: 483542--483676 Score: 159
Period size: 72 Copynumber: 1.9 Consensus size: 72
483532 AGAGGAATGA
* * * * *
483542 AAAGGAAAAAATAATAATAAAATAAAATAATAAGACAATGAAGAAAATAAAACATTAAATAAATC
1 AAAGAAAAAAATAAGAATAAAAAAAAATAATAAGACAATAAAGAAAATAAAACATAAAATAAATC
483607 CAAAGGG
66 CAAAGGG
* *
483614 AAAGAAAAAAATAAGAATAATAAAAAAATAA-AATGA-AATAAAATAAAATAAAAGA-AAAATAA
1 AAAGAAAAAAATAAGAATAA-AAAAAAATAATAA-GACAAT-AAAGAAAATAAAACATAAAATAA
483676 A
63 A
483677 ACAATAAAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
72 30 0.57
73 23 0.43
ACGTcount: A:0.73, C:0.03, G:0.09, T:0.16
Consensus pattern (72 bp):
AAAGAAAAAAATAAGAATAAAAAAAAATAATAAGACAATAAAGAAAATAAAACATAAAATAAATC
CAAAGGG
Found at i:485231 original size:39 final size:38
Alignment explanation
Indices: 484959--485245 Score: 214
Period size: 38 Copynumber: 7.5 Consensus size: 38
484949 ATAAATAAAT
*
484959 ATATTTTAAAAAATTATAT-A-ATATAAATTTT-AAAA
1 ATATTTTCAAAAATTATATAATATATAAATTTTCAAAA
* * * *
484994 ATGTTTTTTAAAAACATATATTATATATAAATTTTCAAAA
1 AT-ATTTTCAAAAA-TTATATAATATATAAATTTTCAAAA
* ** * * * *
485034 CTATTTT-TTAAACTATACATTATATAATTTTTCAAAA
1 ATATTTTCAAAAATTATATAATATATAAATTTTCAAAA
* * *
485071 ATGCTTTT-AAAAATTATATATTATATAAGTTTTC-AAA
1 AT-ATTTTCAAAAATTATATAATATATAAATTTTCAAAA
* * *
485108 ATGTTTT-AAAAACTATATAACATATAAATGTTTTC-AAA
1 ATATTTTCAAAAATTATATAATATATAAA--TTTTCAAAA
* * *
485146 ATATTTTCAAAACTATATATTAAT-TATATATTTTTTAAAA
1 ATATTTTCAAAAAT-TATA-TAATATATA-AATTTTCAAAA
*
485186 ATATTTTCAAAATTTATATAATATATAAATTTTCAAAA
1 ATATTTTCAAAAATTATATAATATATAAATTTTCAAAA
*
485224 ATCATTTTCTGAAAATTATATA
1 AT-ATTTTC-AAAAATTATATA
485246 TTACATTTTG
Statistics
Matches: 201, Mismatches: 35, Indels: 27
0.76 0.13 0.10
Matches are distributed among these distances:
35 2 0.01
36 30 0.15
37 31 0.15
38 58 0.29
39 37 0.18
40 39 0.19
41 4 0.02
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (38 bp):
ATATTTTCAAAAATTATATAATATATAAATTTTCAAAA
Found at i:485326 original size:25 final size:25
Alignment explanation
Indices: 485293--485343 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
485283 CTATATACAT
* *
485293 ATATGTATACATATATAATAAAATA
1 ATATATATACATATATAACAAAATA
*
485318 ATATATATATATATATAACAAAATA
1 ATATATATACATATATAACAAAATA
485343 A
1 A
485344 CTCCGGACGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (25 bp):
ATATATATACATATATAACAAAATA
Found at i:485848 original size:2 final size:2
Alignment explanation
Indices: 485836--485887 Score: 74
Period size: 2 Copynumber: 27.0 Consensus size: 2
485826 ACACTTGATG
485836 TA TA GTA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T- 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
485877 TA TA TA -A TA TA
1 TA TA TA TA TA TA
485888 CTTTTAAATT
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.07
2 41 0.89
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:486507 original size:21 final size:19
Alignment explanation
Indices: 486468--486537 Score: 50
Period size: 21 Copynumber: 3.4 Consensus size: 19
486458 CATATAATCA
*
486468 TAAAATATATCAATTTAATTT
1 TAAAATAAATCAA--TAATTT
*
486489 TAAAATAAACTCACATAATATA
1 TAAAATAAA-TCA-ATAAT-TT
* *
486511 TAAATTTAATCAATAAATTT
1 TAAAATAAATCAAT-AATTT
486531 TAAAATA
1 TAAAATA
486538 TATATATATA
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
20 8 0.21
21 18 0.47
22 11 0.29
23 1 0.03
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (19 bp):
TAAAATAAATCAATAATTT
Found at i:486846 original size:2 final size:2
Alignment explanation
Indices: 486839--486873 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
486829 AAATAATTAT
486839 TA TA TA TA 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 TA TA TA TA T
486874 TGTAAAGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:489087 original size:22 final size:22
Alignment explanation
Indices: 489059--489122 Score: 128
Period size: 22 Copynumber: 2.9 Consensus size: 22
489049 ATGTGAAATT
489059 TGTCCCGAAGGACCTATGTATA
1 TGTCCCGAAGGACCTATGTATA
489081 TGTCCCGAAGGACCTATGTATA
1 TGTCCCGAAGGACCTATGTATA
489103 TGTCCCGAAGGACCTATGTA
1 TGTCCCGAAGGACCTATGTA
489123 ACCCTCGACT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (22 bp):
TGTCCCGAAGGACCTATGTATA
Found at i:491120 original size:32 final size:32
Alignment explanation
Indices: 491084--491156 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 32
491074 TAATTGCTAC
* *
491084 GCATTATCTAAATATAGACCTGAACATACTAT
1 GCATTATCTAAATACACACCTGAACATACTAT
* * *
491116 GCATTATCTGAATGCACACGTGAACATACTAT
1 GCATTATCTAAATACACACCTGAACATACTAT
*
491148 GCATCATCT
1 GCATTATCT
491157 GAATGCAAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (32 bp):
GCATTATCTAAATACACACCTGAACATACTAT
Found at i:492340 original size:20 final size:20
Alignment explanation
Indices: 492317--492388 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
492307 TGAGCATCGG
492317 GTATCGATACTAAACCCTCA
1 GTATCGATACTAAACCCTCA
* ****
492337 GTATCGATACCAAGGGGTCA
1 GTATCGATACTAAACCCTCA
* * *
492357 GTATCGAAACTCCAACCCTTA
1 GTATCGATACT-AAACCCTCA
492378 GTATCGATACT
1 GTATCGATACT
492389 CTCTACATGA
Statistics
Matches: 37, Mismatches: 14, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
20 24 0.65
21 13 0.35
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (20 bp):
GTATCGATACTAAACCCTCA
Found at i:500046 original size:23 final size:23
Alignment explanation
Indices: 500003--500046 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
499993 TAATAAATCA
*
500003 TGTAAATTAATAATTATTCAAAT
1 TGTAAATTAATAATTAGTCAAAT
*
500026 TGTAACTTAA-AATGTAGTCAA
1 TGTAAATTAATAAT-TAGTCAA
500047 TACATTCTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.17
23 15 0.83
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (23 bp):
TGTAAATTAATAATTAGTCAAAT
Found at i:505240 original size:16 final size:17
Alignment explanation
Indices: 505215--505248 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
505205 TTGAGGTGTC
505215 ACATTGACTTTT-CAAA
1 ACATTGACTTTTACAAA
*
505231 ACATTTACTTTTACAAA
1 ACATTGACTTTTACAAA
505248 A
1 A
505249 TACCCAAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.41, C:0.18, G:0.03, T:0.38
Consensus pattern (17 bp):
ACATTGACTTTTACAAA
Found at i:509295 original size:18 final size:19
Alignment explanation
Indices: 509258--509295 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
509248 CTTTTGAAGC
* *
509258 TATCACATCATACTTCTAT
1 TATCACATAATACATCTAT
509277 TATCACATAATA-ATCTAT
1 TATCACATAATACATCTAT
509295 T
1 T
509296 TCTATTAGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (19 bp):
TATCACATAATACATCTAT
Found at i:509509 original size:16 final size:17
Alignment explanation
Indices: 509484--509517 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
509474 CTGAGGTGTC
509484 ACATTGACTTTT-CAAA
1 ACATTGACTTTTACAAA
*
509500 ACATTTACTTTTACAAA
1 ACATTGACTTTTACAAA
509517 A
1 A
509518 TACCCAAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.41, C:0.18, G:0.03, T:0.38
Consensus pattern (17 bp):
ACATTGACTTTTACAAA
Found at i:509980 original size:15 final size:16
Alignment explanation
Indices: 509952--509981 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
509942 TCTATCTCTT
509952 ATCTCTTGTTCATATG
1 ATCTCTTGTTCATATG
509968 ATCTCTT-TTCATAT
1 ATCTCTTGTTCATAT
509982 TCTATATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.53
Consensus pattern (16 bp):
ATCTCTTGTTCATATG
Found at i:511416 original size:64 final size:65
Alignment explanation
Indices: 511334--511489 Score: 192
Period size: 65 Copynumber: 2.4 Consensus size: 65
511324 CTAAGAGTGT
* * * *
511334 ATCGATGCATCAAGTGCATTCGATGTTTT-A-AAGTAGCCAGAGTGCATTGATGCATGGCT-GGT
1 ATCGATGCATCAAATGCATTCGATGTTTTCATAA-AAGCCACAGTGCATCGATGCATGG-TAGGT
511396 GC
64 GC
* * * *
511398 ATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTATGTGC
1 ATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCACAGTGCATCGATGCATGGTAGGTGC
*
511463 ATCGATGCATGAAATGCATTCGATGTT
1 ATCGATGCATCAAATGCATTCGATGTT
511490 CAATTTAATT
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 29 0.36
65 49 0.61
66 2 0.03
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.31
Consensus pattern (65 bp):
ATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCACAGTGCATCGATGCATGGTAGGTGC
Found at i:511528 original size:65 final size:63
Alignment explanation
Indices: 511334--511539 Score: 190
Period size: 65 Copynumber: 3.2 Consensus size: 63
511324 CTAAGAGTGT
* * * *
511334 ATCGATGCATCAAGTGCATTCGATGTTT--TAAAGTAGC-CAGAGTGCATTGATGCATGGCTGGT
1 ATCGATGCATCAAATGCATTCGATGTTTCATAAA--ATCTC--AGTGCATCGATGCATGGTTGGT
511396 GC
62 GC
*
511398 ATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT-GTG
1 ATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGT-TGGTG
511462 C
63 C
* **
511463 ATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGATTGGT
1 ATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-TTGGT
511526 GC
62 GC
*
511528 ATCGGTGCATCA
1 ATCGATGCATCA
511540 CTCTAAAAAA
Statistics
Matches: 120, Mismatches: 11, Indels: 21
0.79 0.07 0.14
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 45 0.38
65 62 0.52
66 2 0.02
67 5 0.04
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.32
Consensus pattern (63 bp):
ATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTGGTGC
Found at i:512013 original size:2 final size:2
Alignment explanation
Indices: 512006--512050 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
511996 AATTGATGAA
512006 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
512048 AT A
1 AT A
512051 GCTTAAGCTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:512192 original size:2 final size:2
Alignment explanation
Indices: 512185--512233 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
512175 TAACAAACCA
512185 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
512227 AT A- AT AT
1 AT AT AT AT
512234 CAAATAGTCA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:518137 original size:22 final size:21
Alignment explanation
Indices: 518095--518134 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
518085 GAGTTTATTT
*
518095 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
518116 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
518135 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:520121 original size:64 final size:62
Alignment explanation
Indices: 520039--520243 Score: 202
Period size: 65 Copynumber: 3.2 Consensus size: 62
520029 CTAAGAGTGT
*
520039 ATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTGGTGC
1 ATCGATGCATCAAATGCATTCGATGTTTCAAAATA-CCAGAGTGCATCGATGCATGG-TGGTGC
** * *
520103 ATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGGTATGTG
1 ATCGATGCATCAAATGCATTCGATG-TTTCA-AAATA-CCAGAGTGCATCGATGCATGGT-GGTG
520167 C
62 C
* * *
520168 ATCGATGCATGAAATGCATTTGATG-TTCAATTAAT-TCATG-GTGCATCGATGCATGGATTGGT
1 ATCGATGCATCAAATGCATTCGATGTTTCAA--AATACCA-GAGTGCATCGATGCATGG--TGGT
520230 GC
61 GC
*
520232 ATCGGTGCATCA
1 ATCGATGCATCA
520244 CTTTGAAAAA
Statistics
Matches: 117, Mismatches: 15, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
62 1 0.01
63 20 0.17
64 41 0.35
65 52 0.44
66 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (62 bp):
ATCGATGCATCAAATGCATTCGATGTTTCAAAATACCAGAGTGCATCGATGCATGGTGGTGC
Found at i:524932 original size:18 final size:18
Alignment explanation
Indices: 524906--524950 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
524896 ATCATTTACA
*
524906 TTATCATTATTAATCTTC
1 TTATCATTATCAATCTTC
* *
524924 TTATAATTATCAATCTTG
1 TTATCATTATCAATCTTC
524942 TTATCATTA
1 TTATCATTA
524951 ATCTCTCTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.31, C:0.13, G:0.02, T:0.53
Consensus pattern (18 bp):
TTATCATTATCAATCTTC
Found at i:525798 original size:23 final size:24
Alignment explanation
Indices: 525754--525799 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
525744 ACTAGGGGCA
**
525754 CGTAGAAATTGTCCCGGTGGACCG
1 CGTAGAAATTGTCCCGAAGGACCG
525778 CGTAGAAA-TGTCCCGAAGGACC
1 CGTAGAAATTGTCCCGAAGGACC
525800 ACATATAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.26, C:0.26, G:0.30, T:0.17
Consensus pattern (24 bp):
CGTAGAAATTGTCCCGAAGGACCG
Found at i:525898 original size:21 final size:20
Alignment explanation
Indices: 525874--525927 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
525864 AATAAGTGTA
*
525874 CCAAAGTACCACATATATGTT
1 CCAAAG-ACCACATATATGTC
**
525895 CCAAAGGATTACATATATGTC
1 CCAAA-GACCACATATATGTC
525916 CCGAAAGACCAC
1 CC-AAAGACCAC
525928 GTAGAACCCT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.39, C:0.26, G:0.13, T:0.22
Consensus pattern (20 bp):
CCAAAGACCACATATATGTC
Found at i:530789 original size:23 final size:24
Alignment explanation
Indices: 530742--530790 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
530732 CCACTAGGGG
530742 CACGTAGAAATTATCCCGAAAGAC
1 CACGTAGAAATTATCCCGAAAGAC
* *
530766 CACGTAGAAA-TGTCCCGAAGGAC
1 CACGTAGAAATTATCCCGAAAGAC
530789 CA
1 CA
530791 TATATAACAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.39, C:0.27, G:0.20, T:0.14
Consensus pattern (24 bp):
CACGTAGAAATTATCCCGAAAGAC
Found at i:531578 original size:24 final size:24
Alignment explanation
Indices: 531545--531606 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
531535 ACACTCTATA
*
531545 GTGTATCGATACATTCCTTAACGT
1 GTGTATCGATACATTCCTTAACAT
*
531569 TTGTATCGATACATTCCTTAACAT
1 GTGTATCGATACATTCCTTAACAT
*
531593 GTGTAACGATACAT
1 GTGTATCGATACAT
531607 AAATTACATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (24 bp):
GTGTATCGATACATTCCTTAACAT
Found at i:541530 original size:345 final size:340
Alignment explanation
Indices: 540906--541732 Score: 1256
Period size: 345 Copynumber: 2.5 Consensus size: 340
540896 TTTATTATTT
* **
540906 ATAATAATAAAAATTTTATAATTTAAAAAATTATAAATTTCATATA-TTTTGAAAAAAAAATT--
1 ATAATAATAAATATTTTATAATTTAAAAAATTATAAATTTCATATATTTTTGAAAAAATTATTAC
*
540968 C-TTTAAAATTAATTGTTAAAAAATAT-AAAAATATTAAAATAAACTTTTAATTACAATTAAGGG
66 CTTTTAAAATTAATTGTTTAAAAATATAAAAAATATTAAAATAAACTTTTAATTACAATTAAGGG
* **
541031 ATCAAATGAATTATTATTCATTAATTTTTATTTTTTAACCCCAGTTAATAATGTTTATTCATTTT
131 ATCAAATGAATTATTATTCATTAATTTTTAATTTTTAACAACAGTTAATAATGTTTATTCATTTT
** * * * *
541096 TAATAAAATTATTTTGATTTTTGCTTTAAAATTACACAATACGTATAATCTAGTATAGGAAAACT
196 TAATAAAATTATTTAAATTTTTACATTAAAATTACACAATACATATAATCTAGTATAGAAAAACT
* *
541161 TTGAGGGTAAGTATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACTAGTATTTCTTTTAC
261 TTAAGGGTAAGTATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACTAGTATTTATTTT--
541226 ATAATGATGATGATGATG
324 AT-ATGATGATGATGATG
*
541244 ATAATAATAAATATTTTATAATTTTAAAAATTATAAATTTCATATATTTTTGAAAAAATTATTAC
1 ATAATAATAAATATTTTATAATTTAAAAAATTATAAATTTCATATATTTTTGAAAAAATTATTAC
* *
541309 CTTTTAAAATTAATTGTTTAAAAATATAAAAAAAATATAAAAATAAACTTTTAATTACAATTGAG
66 CTTTTAAAATTAATTGTTTAAAAATAT--AAAAAATATTAAAATAAACTTTTAATTACAATTAAG
541374 GGATCAAATGAATTATTATTCATTAATTTTTAATTTTTAACAACAGTTAATAATGTTTATTCATT
129 GGATCAAATGAATTATTATTCATTAATTTTTAATTTTTAACAACAGTTAATAATGTTTATTCATT
*
541439 TTTAATAAAATTATTTAAATTTTTACATTAAAATTACACAATACATATAATCTAGTATATAAAAA
194 TTTAATAAAATTATTTAAATTTTTACATTAAAATTACACAATACATATAATCTAGTATAGAAAAA
*
541504 CTTTAAGGGTAAGTATTTTGAAATATGAATAATTTTATAAAAGTTTTATAACTAGTATTTATTTT
259 CTTTAAGGGTAAGTATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACTAGTATTTATTTT
541569 ATATGATGATGATGATG
324 ATATGATGATGATGATG
*
541586 ------ATAAATATTTTATAATTTAAAAAATTATAAATTTCATATATTTTTGAAAATATTATTAC
1 ATAATAATAAATATTTTATAATTTAAAAAATTATAAATTTCATATATTTTTGAAAAAATTATTAC
* * *
541645 CTTTTAAAATT--GT-TTTAAAAATAT---AAATATTAAAATAAACTTTTAATTACAATTAAAGA
66 CTTTTAAAATTAATTGTTTAAAAATATAAAAAATATTAAAATAAACTTTTAATTACAATTAAGGG
* *
541704 AACAAATGAATTATTATTCAATAATTTTT
131 ATCAAATGAATTATTATTCATTAATTTTT
541733 TCAAAATATA
Statistics
Matches: 453, Mismatches: 29, Indels: 24
0.90 0.06 0.05
Matches are distributed among these distances:
328 58 0.13
333 11 0.02
334 1 0.00
336 68 0.15
338 44 0.10
339 14 0.03
341 1 0.00
342 39 0.09
343 2 0.00
345 215 0.47
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (340 bp):
ATAATAATAAATATTTTATAATTTAAAAAATTATAAATTTCATATATTTTTGAAAAAATTATTAC
CTTTTAAAATTAATTGTTTAAAAATATAAAAAATATTAAAATAAACTTTTAATTACAATTAAGGG
ATCAAATGAATTATTATTCATTAATTTTTAATTTTTAACAACAGTTAATAATGTTTATTCATTTT
TAATAAAATTATTTAAATTTTTACATTAAAATTACACAATACATATAATCTAGTATAGAAAAACT
TTAAGGGTAAGTATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACTAGTATTTATTTTAT
ATGATGATGATGATG
Found at i:541768 original size:26 final size:27
Alignment explanation
Indices: 541724--541778 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
541714 TTATTATTCA
**
541724 ATAATTTTTTCAAAATATATGAAATTT
1 ATAATTTTTTCAAAATATAAAAAATTT
541751 ATAA-TTTTT-AAAATTATAAAAAATTT
1 ATAATTTTTTCAAAA-TATAAAAAATTT
541777 AT
1 AT
541779 TATTATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 4 0.16
26 17 0.68
27 4 0.16
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (27 bp):
ATAATTTTTTCAAAATATAAAAAATTT
Found at i:545280 original size:15 final size:16
Alignment explanation
Indices: 545262--545293 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
545252 AAATTTGATC
545262 AAATAATTA-AATATA
1 AAATAATTATAATATA
545277 AAATAATTATAATATA
1 AAATAATTATAATATA
545293 A
1 A
545294 TAAAAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AAATAATTATAATATA
Found at i:547321 original size:18 final size:18
Alignment explanation
Indices: 547298--547362 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
547288 ATGATAAACA
*
547298 ATATCATACATAATAGTC
1 ATATCATACATAATAGAC
* * *
547316 ATATCAAAGCCATGATAAAC
1 ATATCATA--CATAATAGAC
*
547336 AATATCATACATAATAGGC
1 -ATATCATACATAATAGAC
547355 ATATCATA
1 ATATCATA
547363 TTCTTTTTCA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
18 15 0.42
19 7 0.19
20 7 0.19
21 7 0.19
ACGTcount: A:0.48, C:0.17, G:0.08, T:0.28
Consensus pattern (18 bp):
ATATCATACATAATAGAC
Found at i:547329 original size:39 final size:39
Alignment explanation
Indices: 547286--547360 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
547276 TTTATTAAAA
*
547286 CCATGATAAACAATATCATACATAATAGTCATATCAAAG
1 CCATGATAAACAATATCATACATAATAGGCATATCAAAG
547325 CCATGATAAACAATATCATACATAATAGGCATATCA
1 CCATGATAAACAATATCATACATAATAGGCATATCA
547361 TATTCTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.48, C:0.19, G:0.08, T:0.25
Consensus pattern (39 bp):
CCATGATAAACAATATCATACATAATAGGCATATCAAAG
Found at i:547410 original size:13 final size:13
Alignment explanation
Indices: 547390--547449 Score: 68
Period size: 13 Copynumber: 4.7 Consensus size: 13
547380 ACAATACAAA
*
547390 ACTTTCATATCTC
1 ACTTTCATATTTC
* *
547403 ATTTTCATCTTTC
1 ACTTTCATATTTC
547416 ACTTTCATA-TTC
1 ACTTTCATATTTC
*
547428 ACTTTCACATTTC
1 ACTTTCATATTTC
*
547441 ATTTTCATA
1 ACTTTCATA
547450 ATACATACTT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
12 11 0.29
13 27 0.71
ACGTcount: A:0.23, C:0.25, G:0.00, T:0.52
Consensus pattern (13 bp):
ACTTTCATATTTC
Found at i:555230 original size:21 final size:22
Alignment explanation
Indices: 555187--555254 Score: 77
Period size: 21 Copynumber: 3.1 Consensus size: 22
555177 ATAAATTGCA
*
555187 CCGAAGTACCACATAGAATGTC
1 CCGAAGGACCACATAGAATGTC
*
555209 CCGAAGGACCACGTAG-ATGTC
1 CCGAAGGACCACATAGAATGTC
*
555230 CC-AATGGACCGCATAGAAATGTC
1 CCGAA-GGACCACATAG-AATGTC
555253 CC
1 CC
555255 AAAGAACCGC
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
20 2 0.05
21 16 0.41
22 14 0.36
23 7 0.18
ACGTcount: A:0.32, C:0.29, G:0.22, T:0.16
Consensus pattern (22 bp):
CCGAAGGACCACATAGAATGTC
Found at i:555255 original size:23 final size:23
Alignment explanation
Indices: 555225--555270 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
555215 GACCACGTAG
* *
555225 ATGTCCCAATGGACCGCATAGAA
1 ATGTCCCAAAGAACCGCATAGAA
*
555248 ATGTCCCAAAGAACCGCGTAGAA
1 ATGTCCCAAAGAACCGCATAGAA
555271 CCCTCTACTC
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:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (23 bp):
ATGTCCCAAAGAACCGCATAGAA
Found at i:559236 original size:18 final size:18
Alignment explanation
Indices: 559213--559260 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
559203 GCACATATAT
559213 CATCATTATCATCATCAA
1 CATCATTATCATCATCAA
* *
559231 CATCATTATCGTTATCAA
1 CATCATTATCATCATCAA
* *
559249 TATTATTATCAT
1 CATCATTATCAT
559261 TAATCCCTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.35, C:0.21, G:0.02, T:0.42
Consensus pattern (18 bp):
CATCATTATCATCATCAA
Found at i:559535 original size:43 final size:42
Alignment explanation
Indices: 559463--559544 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 42
559453 ATAAATTACA
***
559463 CCGAAGTGCCACATAAAATGTCTTGAAGGACCACATAGATGT
1 CCGAAGTGCCACATAAAATGTCCCAAAGGACCACATAGATGT
*
559505 CCGAA-TGACCACATAGAAATGTCCCAAAGGACCACGTAGA
1 CCGAAGTG-CCACATA-AAATGTCCCAAAGGACCACATAGA
559545 ATTGTCCCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 2 0.06
42 12 0.35
43 20 0.59
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (42 bp):
CCGAAGTGCCACATAAAATGTCCCAAAGGACCACATAGATGT
Found at i:559544 original size:23 final size:23
Alignment explanation
Indices: 559471--559555 Score: 79
Period size: 23 Copynumber: 3.9 Consensus size: 23
559461 CACCGAAGTG
***
559471 CCACATA-AAATGTCTTGAAGGA
1 CCACATAGAAATGTCCCAAAGGA
* *
559493 CCACATAG--ATGT-CCGAATGA
1 CCACATAGAAATGTCCCAAAGGA
559513 CCACATAGAAATGTCCCAAAGGA
1 CCACATAGAAATGTCCCAAAGGA
* *
559536 CCACGTAGAATTGTCCCAAA
1 CCACATAGAAATGTCCCAAA
559556 AAACTGCGTA
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
20 13 0.25
21 4 0.08
22 11 0.21
23 24 0.46
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.19
Consensus pattern (23 bp):
CCACATAGAAATGTCCCAAAGGA
Found at i:570242 original size:30 final size:31
Alignment explanation
Indices: 570186--570244 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
570176 AATTTTAGAT
*
570186 ATAAAATTTTTAAAATAAATTCAAATTATTC
1 ATAAAATTTATAAAATAAATTCAAATTATTC
*
570217 ATAAAA-TTATAAAA-AAATATGAAATTAT
1 ATAAAATTTATAAAATAAAT-TCAAATTAT
570245 GTGATAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 4 0.16
30 15 0.60
31 6 0.24
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (31 bp):
ATAAAATTTATAAAATAAATTCAAATTATTC
Found at i:571556 original size:40 final size:40
Alignment explanation
Indices: 571509--571760 Score: 162
Period size: 40 Copynumber: 6.3 Consensus size: 40
571499 TTGAGATTTT
*
571509 TCAAATTCGCAACGAGAATCTGT-AAA-TCGCAACACAGAAG
1 TCAAATTCGCAACGAGAAT-T-TCAAATTCGCAACACAAAAG
* * *
571549 TCAAATTCGCAACGA-TA-GTCAAATCCGCAACACAAAAG
1 TCAAATTCGCAACGAGAATTTCAAATTCGCAACACAAAAG
* * * * * ***
571587 TCAAATCCGCAATGCG-ATAGTCAAATTCGCAACGCGGTAG
1 TCAAATTCGCAACGAGAAT-TTCAAATTCGCAACACAAAAG
*
571627 TTAAATTCGCAAC-ACTGAATTTCAAATTCGCAACACAAAAG
1 TCAAATTCGCAACGA--GAATTTCAAATTCGCAACACAAAAG
* * * *
571668 TCAAATTCGCAACGCG-ATAGTCAAATTCGCAACGCGATAA-
1 TCAAATTCGCAACGAGAAT-TTCAAATTCGCAACAC-AAAAG
* ** * * *
571708 TCAAATTCGCAAC-ATAAAAGTCAAATTCGCAACGCGATAG
1 TCAAATTCGCAACGA-GAATTTCAAATTCGCAACACAAAAG
571748 TCAAATTCGCAAC
1 TCAAATTCGCAAC
571761 ACGAAACACA
Statistics
Matches: 166, Mismatches: 32, Indels: 28
0.73 0.14 0.12
Matches are distributed among these distances:
36 1 0.01
37 3 0.02
38 25 0.15
39 4 0.02
40 98 0.59
41 33 0.20
42 2 0.01
ACGTcount: A:0.40, C:0.24, G:0.15, T:0.20
Consensus pattern (40 bp):
TCAAATTCGCAACGAGAATTTCAAATTCGCAACACAAAAG
Found at i:571558 original size:20 final size:19
Alignment explanation
Indices: 571535--571765 Score: 196
Period size: 20 Copynumber: 11.6 Consensus size: 19
571525 AATCTGTAAA
571535 TCGCAACACAGAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
571555 TCGC-A-ACGATAGTCAAAT
1 TCGCAACACGA-AGTCAAAT
* *
571573 CCGCAACACAAAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
* **
571593 CCGCAATGCGATAGTCAAAT
1 TCGCAACACGA-AGTCAAAT
* * *
571613 TCGCAACGCGGTAGTTAAAT
1 TCGCAACAC-GAAGTCAAAT
*
571633 TCGCAACACTGAATTTCAAAT
1 TCGCAACAC-GAA-GTCAAAT
*
571654 TCGCAACACAAAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
*
571674 TCGCAACGCGATAGTCAAAT
1 TCGCAACACGA-AGTCAAAT
* *
571694 TCGCAACGCGATAATCAAAT
1 TCGCAACACGA-AGTCAAAT
**
571714 TCGCAACATAAAAGTCAAAT
1 TCGCAACA-CGAAGTCAAAT
*
571734 TCGCAACGCGATAGTCAAAT
1 TCGCAACACGA-AGTCAAAT
571754 TCGCAACACGAA
1 TCGCAACACGAA
571766 ACACAATATT
Statistics
Matches: 173, Mismatches: 28, Indels: 21
0.78 0.13 0.09
Matches are distributed among these distances:
17 2 0.01
18 13 0.08
19 6 0.03
20 133 0.77
21 19 0.11
ACGTcount: A:0.41, C:0.25, G:0.16, T:0.19
Consensus pattern (19 bp):
TCGCAACACGAAGTCAAAT
Found at i:571671 original size:81 final size:80
Alignment explanation
Indices: 571549--571760 Score: 277
Period size: 81 Copynumber: 2.7 Consensus size: 80
571539 AACACAGAAG
* * *
571549 TCAAATTCGCAACGAT---AGTCAAATCCGCAACACAAAAGTCAAATCCGCAATGCGATAGTCAA
1 TCAAATTCGCAAC-ATAAAAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAA
* *
571611 ATTCGCAACGCGGTAG
65 ATTCGCAACGCGATAA
* * **
571627 TTAAATTCGCAACACTGAATTTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAA
1 TCAAATTCGCAACA-TAAAAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAA
571692 ATTCGCAACGCGATAA
65 ATTCGCAACGCGATAA
* * *
571708 TCAAATTCGCAACATAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAAC
1 TCAAATTCGCAACATAAAAGTCAAATTCGCAACACAAAAGTCAAATTCGCAAC
571761 ACGAAACACA
Statistics
Matches: 115, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
77 1 0.01
78 13 0.11
80 33 0.29
81 68 0.59
ACGTcount: A:0.40, C:0.25, G:0.15, T:0.20
Consensus pattern (80 bp):
TCAAATTCGCAACATAAAAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAA
TTCGCAACGCGATAA
Found at i:571737 original size:60 final size:59
Alignment explanation
Indices: 571535--571766 Score: 297
Period size: 60 Copynumber: 3.9 Consensus size: 59
571525 AATCTGTAAA
* * *
571535 TCGCAACACAGAAGTCAAATTCGCAA--CGATAGTCAAATCCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACGAAA-TCAAAT
* ** * * * * *
571593 CCGCAATGCGATAGTCAAATTCGCAACGCGGTAGTTAAATTCGCAACACTGAATTTCAAAT
1 TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACAC-GAA-ATCAAAT
*
571654 TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACGCGATAATCAAAT
1 TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACGA-AATCAAAT
*
571714 TCGCAACATAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACGAAA
1 TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACGAAA
571767 CACAATATTA
Statistics
Matches: 147, Mismatches: 22, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
58 20 0.14
59 2 0.01
60 75 0.51
61 50 0.34
ACGTcount: A:0.41, C:0.25, G:0.16, T:0.19
Consensus pattern (59 bp):
TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACGAAATCAAAT
Found at i:571907 original size:22 final size:22
Alignment explanation
Indices: 571882--571925 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
571872 GACATTGTCA
571882 CCATCTCCGACGAAATCCGTCT
1 CCATCTCCGACGAAATCCGTCT
*
571904 CCATCTCCGGCGAAATCCGTCT
1 CCATCTCCGACGAAATCCGTCT
571926 ATCTCCATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.41, G:0.16, T:0.23
Consensus pattern (22 bp):
CCATCTCCGACGAAATCCGTCT
Found at i:572353 original size:19 final size:19
Alignment explanation
Indices: 572331--572377 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
572321 AAATCGCAAC
572331 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCA-TTTCGCGTT
572350 GCGATTTTCATTTCGCGTT
1 GCGATTTTCATTTCGCGTT
572369 GCGATTTTC
1 GCGATTTTC
572378 TCGTTGCTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 26 0.96
20 1 0.04
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (19 bp):
GCGATTTTCATTTCGCGTT
Found at i:572358 original size:14 final size:14
Alignment explanation
Indices: 572359--572405 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
572349 TGCGATTTTC
572359 ATTT-CGCGTTGCG
1 ATTTTCGCGTTGCG
* *
572372 ATTTTCTCGTTGCT
1 ATTTTCGCGTTGCG
* *
572386 ATTTTGGTGTTGCG
1 ATTTTCGCGTTGCG
572400 ATTTTC
1 ATTTTC
572406 ATTTTCGTGT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
13 4 0.15
14 22 0.85
ACGTcount: A:0.09, C:0.17, G:0.23, T:0.51
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:572431 original size:20 final size:20
Alignment explanation
Indices: 572392--572431 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
572382 TGCTATTTTG
* * *
572392 GTGTTGCGATTTTCATTTTC
1 GTGTTGCGAATTTAAGTTTC
572412 GTGTTGCGAATTTAAGTTTC
1 GTGTTGCGAATTTAAGTTTC
572432 AAAAACTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.12, G:0.23, T:0.50
Consensus pattern (20 bp):
GTGTTGCGAATTTAAGTTTC
Found at i:574412 original size:12 final size:12
Alignment explanation
Indices: 574395--574436 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
574385 TTTTTTGGCA
*
574395 TTATTTATTTAT
1 TTATTTATTAAT
*
574407 TTATTTACTAAT
1 TTATTTATTAAT
*
574419 TTATGTATTAAT
1 TTATTTATTAAT
574431 TTATTT
1 TTATTT
574437 TCAGCGGCCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (12 bp):
TTATTTATTAAT
Found at i:574616 original size:21 final size:21
Alignment explanation
Indices: 574586--574636 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
574576 CCTATCATCA
* *
574586 TTCAAAAGGCGCCTCCT-ATCG
1 TTCAAGAGGCCCCT-CTGATCG
*
574607 TTCAAGAGGCCCCTGTGATCG
1 TTCAAGAGGCCCCTCTGATCG
574628 TTCAAGAGG
1 TTCAAGAGG
574637 TCCCGCCGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.24, C:0.27, G:0.25, T:0.24
Consensus pattern (21 bp):
TTCAAGAGGCCCCTCTGATCG
Done.