Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008466.1 Hibiscus syriacus cultivar Beakdansim tig00111280_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: 685270
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:362726 original size:343 final size:342
Alignment explanation
Indices: 362073--362748 Score: 879
Period size: 343 Copynumber: 2.0 Consensus size: 342
362063 ATAATTTAGT
* * ** *
362073 TTTTAAGAGGTTTAATTAAGTGAATAGAATTGTTTTCCACATGTCTAGTGTGGTCATAGATGAAG
1 TTTTAAGAGGTTTAATTAAGTAAATAGAATTGTTTCCCACATGTCTACCGTGGTCATAAATGAAG
*
362138 GGTTTTGTTTAGTGTGTATATGTAGTGGCGTGTTTATAGTTTTAGAGTTTTCAAGTTGTCGGATG
66 GGTTTTGTTTAGTGTGTATATGTAGTGGCGTGTTTATAGTTTTAGAGTTTTCAAGTTGTCAGATG
* *
362203 TGAGCATGTTTACCGGAGAAGGCCTTGCTCATAACTTCGTTGCCGTGAAATGTTGGCGATGGCTA
131 TGAGCATGTTTACCAGAGAAGGCATTGCTCATAACTTCGTTGCCGTGAAATGTTGGCGATGG--A
* * * * *
362268 ATTATTGTAATCTTGAATGTATCTTTTGTAATTGGAAGTTAGCAGAGCAAGATTCAAATGGCGTT
194 ATTATTGTAA--TTGAATGTAACGTTTGTAATTGGAAGTTAACAAAGCAAGATTCAAATGGCATT
*
362333 CTTTGCAACTTTTGTTTTAATGTAAGCTCGATGATGTTTTATTGTGGTAATTTTTT-ATATAACT
257 CTTTGCAACTTTTGTTTTAATGTAAGCTCGATGATGTTTTATTGTGGTAATTTTTTAATATAACC
362397 TTGGGGATCCAGAGAAACTAG
322 TTGGGGATCCAGAGAAACTAG
* *
362418 TTTTAAGAGGTTTAGTTAAGTAAATAGAATTGTTCTCCACAACATGTCTACCGTGGTCATAAATT
1 TTTTAAGAGGTTTAATTAAGTAAATAGAATTGTT-TCC-C-ACATGTCTACCGTGGTCATAAATG
* * *
362483 AAGGGTTTTGTTTAGTGTGTGTATGTAGTGGTGTGTTTATAG-TTTAGGGTTTTTCAAGTTGTCA
63 AAGGGTTTTGTTTAGTGTGTATATGTAGTGGCGTGTTTATAGTTTTAGAG-TTTTCAAGTTGTCA
**
362547 GATGTGAGTTAGAGACATGTTTACCAGAGAAGGCATTGCTCATAACTTCGTTGCCGTTCAATGTT
127 GA--T--G-T-GAG-CATGTTTACCAGAGAAGGCATTGCTCATAACTTCGTTGCCGTGAAATGTT
* * **
362612 -G-G-T-G-A-TGTT-TAA-TGAATGTAACGTTTGTAATTGGAAGTTAACAAAGTAAGATTCATT
185 GGCGATGGAATTATTGTAATTGAATGTAACGTTTGTAATTGGAAGTTAACAAAGCAAGATTCAAA
* * *
362669 TGGCATTCTTTTG-AACTTTTGTTTTAATGTAAGGTTGGTGATGTTTTATTGTGGTAATTTTTTA
250 TGGCATTC-TTTGCAACTTTTGTTTTAATGTAAGCTCGATGATGTTTTATTGTGGTAATTTTTTA
362733 ATATAACCTTGGGGAT
314 ATATAACCTTGGGGAT
362749 TTGATAGTTG
Statistics
Matches: 290, Mismatches: 28, Indels: 27
0.84 0.08 0.08
Matches are distributed among these distances:
343 92 0.32
344 19 0.07
345 32 0.11
346 5 0.02
347 10 0.03
348 76 0.26
350 1 0.00
351 1 0.00
352 2 0.01
353 2 0.01
354 4 0.01
355 46 0.16
ACGTcount: A:0.26, C:0.10, G:0.24, T:0.41
Consensus pattern (342 bp):
TTTTAAGAGGTTTAATTAAGTAAATAGAATTGTTTCCCACATGTCTACCGTGGTCATAAATGAAG
GGTTTTGTTTAGTGTGTATATGTAGTGGCGTGTTTATAGTTTTAGAGTTTTCAAGTTGTCAGATG
TGAGCATGTTTACCAGAGAAGGCATTGCTCATAACTTCGTTGCCGTGAAATGTTGGCGATGGAAT
TATTGTAATTGAATGTAACGTTTGTAATTGGAAGTTAACAAAGCAAGATTCAAATGGCATTCTTT
GCAACTTTTGTTTTAATGTAAGCTCGATGATGTTTTATTGTGGTAATTTTTTAATATAACCTTGG
GGATCCAGAGAAACTAG
Found at i:368457 original size:10 final size:10
Alignment explanation
Indices: 368439--368479 Score: 64
Period size: 10 Copynumber: 4.1 Consensus size: 10
368429 TCAAGCTTGA
* *
368439 TTTTATCTTC
1 TTTTTTCTTT
368449 TTTTTTCTTT
1 TTTTTTCTTT
368459 TTTTTTCTTT
1 TTTTTTCTTT
368469 TTTTTTCTTT
1 TTTTTTCTTT
368479 T
1 T
368480 GAAAATTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:368994 original size:11 final size:11
Alignment explanation
Indices: 368978--369012 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
368968 GATTAGTGAG
368978 AATGCGAAATA
1 AATGCGAAATA
368989 AATGCGAAATA
1 AATGCGAAATA
*
369000 AAAGCGAAA-A
1 AATGCGAAATA
369010 AAT
1 AAT
369013 AATACTCGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 3 0.14
11 19 0.86
ACGTcount: A:0.60, C:0.09, G:0.17, T:0.14
Consensus pattern (11 bp):
AATGCGAAATA
Found at i:378633 original size:165 final size:167
Alignment explanation
Indices: 378361--378661 Score: 588
Period size: 165 Copynumber: 1.8 Consensus size: 167
378351 CGGCTCTGAG
378361 CATCACGAAATTAACCAAAGAAGAGGAAGAAGAAGAAAGAAGGCGGCTCAGAAGGATCCATTGGT
1 CATCACGAAATTAACCAAAGAAGAGGAAGAAGAAGAAAGAAGGCGGCTCAGAAGGATCCATTGGT
378426 GAATTTCTAATCACGAAAAATGGTGAAAACCCATTCATAAAATAGGTAGTTTTC-A-ATCATCGC
66 GAATTTCTAATCACGAAAAATGGTGAAAACCCATTCATAAAATAGGTAGTTTTCAACATCATCGC
378489 CCCCTTATAGAAAAGAAAGAGAAAATTGAGATAGAGC
131 CCCCTTATAGAAAAGAAAGAGAAAATTGAGATAGAGC
378526 CATCACGAAATTAACCAAAGAAGAGGAAGAAGAAGAAAGAAGGCGGCTCAGAAGGATCCATTGGT
1 CATCACGAAATTAACCAAAGAAGAGGAAGAAGAAGAAAGAAGGCGGCTCAGAAGGATCCATTGGT
378591 GAATTTCTAATCACGAAAAATGGTGAAAACCCATTCATAAAATAGGTAGTTTTCAACATCATCGC
66 GAATTTCTAATCACGAAAAATGGTGAAAACCCATTCATAAAATAGGTAGTTTTCAACATCATCGC
378656 CCCCTT
131 CCCCTT
378662 CATCCATTTT
Statistics
Matches: 134, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
165 119 0.89
166 1 0.01
167 14 0.10
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.20
Consensus pattern (167 bp):
CATCACGAAATTAACCAAAGAAGAGGAAGAAGAAGAAAGAAGGCGGCTCAGAAGGATCCATTGGT
GAATTTCTAATCACGAAAAATGGTGAAAACCCATTCATAAAATAGGTAGTTTTCAACATCATCGC
CCCCTTATAGAAAAGAAAGAGAAAATTGAGATAGAGC
Found at i:381573 original size:21 final size:21
Alignment explanation
Indices: 381549--381588 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
381539 TTTATTTTAT
381549 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
381570 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
381589 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:381676 original size:33 final size:33
Alignment explanation
Indices: 381583--381682 Score: 157
Period size: 34 Copynumber: 3.0 Consensus size: 33
381573 TTTGTTTCAA
381583 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
381615 TTATCGAACTTGGAAGTTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAG-TTTTTAAGTATTTGAAT
* * *
381649 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
381682 T
1 T
381683 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
32 11 0.17
33 20 0.32
34 32 0.51
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.46
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:381711 original size:13 final size:13
Alignment explanation
Indices: 381668--381722 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
381658 TTGGAAGTAT
381668 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
381681 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
381695 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
381708 TTAAGTATTTAAA
1 TTAAGTATTTCAA
381721 TT
1 TT
381723 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:381944 original size:21 final size:21
Alignment explanation
Indices: 381918--381974 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
381908 TGGAGCGTGG
*
381918 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
* *
381939 GGGAATCAGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
381960 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
381975 AAGTGTAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.21, C:0.26, G:0.25, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:382193 original size:15 final size:15
Alignment explanation
Indices: 382141--382193 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
382131 ATCTGGAATA
382141 TTAAAATCGGTTTTT
1 TTAAAATCGGTTTTT
* *
382156 TTATAACCGGTTTTT
1 TTAAAATCGGTTTTT
*
382171 TAAAAAAATCGGTTTTT
1 T--TAAAATCGGTTTTT
382188 TTAAAA
1 TTAAAA
382194 CCGAAACCGG
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
15 18 0.60
17 12 0.40
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.47
Consensus pattern (15 bp):
TTAAAATCGGTTTTT
Found at i:383736 original size:109 final size:109
Alignment explanation
Indices: 383586--383793 Score: 344
Period size: 109 Copynumber: 1.9 Consensus size: 109
383576 GGCCCCAAAC
* * * *
383586 CGTCCCTATGAGTTTATCTTAGAGAGATATCGTACCATCCACTTGATCTCATTGTCCACACACTT
1 CGTCCCTATGAATTTATCCTAGAGAGATATCGTACCATCCACTTGATCTCAATGCCCACACACTT
383651 AGACTTCACATGAATCTAGGAAAAGGTCACTTACGGTCCTAAAT
66 AGACTTCACATGAATCTAGGAAAAGGTCACTTACGGTCCTAAAT
* *
383695 CGTCCCTATGAATTTATCCTAGAGAGGTATCGTACCATCCACTTGATCTCAATGCCCACGCACTT
1 CGTCCCTATGAATTTATCCTAGAGAGATATCGTACCATCCACTTGATCTCAATGCCCACACACTT
* *
383760 AGATTTCACATGAATCTAGGGAAAGGTCACTTAC
66 AGACTTCACATGAATCTAGGAAAAGGTCACTTAC
383794 ACCATAATAA
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
109 91 1.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (109 bp):
CGTCCCTATGAATTTATCCTAGAGAGATATCGTACCATCCACTTGATCTCAATGCCCACACACTT
AGACTTCACATGAATCTAGGAAAAGGTCACTTACGGTCCTAAAT
Found at i:388323 original size:24 final size:25
Alignment explanation
Indices: 388272--388323 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
388262 TATGATTTTG
* *
388272 AAAAAATTGAAAGCTTAGATATTAA
1 AAAAAATTAAAAACTTAGATATTAA
388297 AAAAAATTAAAAACTTAGATATTAA
1 AAAAAATTAAAAACTTAGATATTAA
388322 AA
1 AA
388324 CGGATCGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.62, C:0.04, G:0.08, T:0.27
Consensus pattern (25 bp):
AAAAAATTAAAAACTTAGATATTAA
Found at i:389354 original size:18 final size:19
Alignment explanation
Indices: 389312--389351 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
389302 AAGAATACTA
389312 TTTCTCCAGACCCTTTTTT
1 TTTCTCCAGACCCTTTTTT
389331 TTTCTCCAGACCCTTTTTT
1 TTTCTCCAGACCCTTTTTT
389350 TT
1 TT
389352 CTCTGAACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.10, C:0.30, G:0.05, T:0.55
Consensus pattern (19 bp):
TTTCTCCAGACCCTTTTTT
Found at i:403204 original size:26 final size:26
Alignment explanation
Indices: 403164--403223 Score: 97
Period size: 26 Copynumber: 2.3 Consensus size: 26
403154 AATTATTTGC
403164 GAAA-AAATATATATTATT-ATTGTAT
1 GAAACAAATATATATTATTAATT-TAT
403189 GAAACAAATATATATTATTAATTTAT
1 GAAACAAATATATATTATTAATTTAT
403215 GAAACAAAT
1 GAAACAAAT
403224 TACCCTTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
25 4 0.12
26 26 0.79
27 3 0.09
ACGTcount: A:0.52, C:0.03, G:0.07, T:0.38
Consensus pattern (26 bp):
GAAACAAATATATATTATTAATTTAT
Found at i:405050 original size:149 final size:153
Alignment explanation
Indices: 404768--405069 Score: 567
Period size: 149 Copynumber: 2.0 Consensus size: 153
404758 CCTGTTATAC
404768 AATGTAAAACTGTTGGGATTTTCGAAGCTCAATTTGTGACAACCAAAAATTGCTTAAGGGGGTGA
1 AATGTAAAACTGTTGGGATTTTCGAAGCTCAATTTGTGACAACCAAAAATTGCTTAAGGGGGTGA
*
404833 ATTGACAAAACCTGTTTAGGGAGTAAGGATAGTAAAAGATAGAAAATTTTGTATAAAGATTTATA
66 ATTGACAAAACCTGTTTAGGGAGTAAGGATAGTAAAAGATAGAAAATTTGGTATAAAGATTTATA
404898 GTAGTTCGAC-T-TCAACTAAGT
131 GTAGTTCGACTTCTCAACTAAGT
404919 AATGTAAAACTGTTGGGA-TTTCGAAGCTCAATTTGTGACAACCAAAAATTGCTTAAGGGGGTGA
1 AATGTAAAACTGTTGGGATTTTCGAAGCTCAATTTGTGACAACCAAAAATTGCTTAAGGGGGTGA
404983 ATTGACAAAA-CTGTTTAGGGAGTAAGGATAGTAAAAGATAGAAAATTTGGTATAAAGATTTATA
66 ATTGACAAAACCTGTTTAGGGAGTAAGGATAGTAAAAGATAGAAAATTTGGTATAAAGATTTATA
405047 GTAGTTCGACTTCTCAACTAAGT
131 GTAGTTCGACTTCTCAACTAAGT
405070 CTATCTTCAA
Statistics
Matches: 148, Mismatches: 1, Indels: 4
0.97 0.01 0.03
Matches are distributed among these distances:
149 63 0.43
150 57 0.39
151 28 0.19
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (153 bp):
AATGTAAAACTGTTGGGATTTTCGAAGCTCAATTTGTGACAACCAAAAATTGCTTAAGGGGGTGA
ATTGACAAAACCTGTTTAGGGAGTAAGGATAGTAAAAGATAGAAAATTTGGTATAAAGATTTATA
GTAGTTCGACTTCTCAACTAAGT
Found at i:407715 original size:9 final size:9
Alignment explanation
Indices: 407689--407745 Score: 57
Period size: 9 Copynumber: 6.7 Consensus size: 9
407679 TAAATTTTTT
*
407689 TTATTAATT
1 TTATTAATA
407698 TTATTAATA
1 TTATTAATA
407707 TTATTAATA
1 TTATTAATA
*
407716 TTACT-ATA
1 TTATTAATA
407724 -T-TTAATA
1 TTATTAATA
* *
407731 TTAATAAAA
1 TTATTAATA
407740 TTATTA
1 TTATTA
407746 CAGCTTGCAG
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
6 1 0.03
7 4 0.10
8 4 0.10
9 30 0.77
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (9 bp):
TTATTAATA
Found at i:407717 original size:15 final size:15
Alignment explanation
Indices: 407699--407736 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
407689 TTATTAATTT
407699 TATTAATAT-TATTAA
1 TATTAATATAT-TTAA
*
407714 TATTACTATATTTAA
1 TATTAATATATTTAA
407729 TATTAATA
1 TATTAATA
407737 AAATTATTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 19 0.95
16 1 0.05
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTAATATATTTAA
Found at i:408599 original size:12 final size:12
Alignment explanation
Indices: 408582--408608 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
408572 CGGTCCCTAC
408582 GCCGCCGCGCCG
1 GCCGCCGCGCCG
408594 GCCGCCGCGCCG
1 GCCGCCGCGCCG
408606 GCC
1 GCC
408609 ACCGTGGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.59, G:0.41, T:0.00
Consensus pattern (12 bp):
GCCGCCGCGCCG
Found at i:410002 original size:2 final size:2
Alignment explanation
Indices: 409995--410022 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
409985 ATAAATTTAA
409995 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
410023 TGCTATTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:411703 original size:21 final size:21
Alignment explanation
Indices: 411674--411726 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
411664 ATTCTGACTA
411674 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* **
411695 TCGCGTTGCGATTTTCTTAAT
1 TCGCATTGCGATTTTCCAAAT
*
411716 TCGCAATGCGA
1 TCGCATTGCGA
411727 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:411741 original size:20 final size:20
Alignment explanation
Indices: 411716--411768 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
411706 TTTTCTTAAT
411716 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
411736 TCGCAACGCGAATACTTAAA
1 TCGCAATGCGAATACGTAAA
411756 TCGCAATGCGAAT
1 TCGCAATGCGAAT
411769 CTGACTATCG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:411778 original size:20 final size:20
Alignment explanation
Indices: 411755--411821 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
411745 GAATACTTAA
411755 ATCGCAATGCGAATCTGACT
1 ATCGCAATGCGAATCTGACT
411775 ATCGCAATGCGAATCTGACT
1 ATCGCAATGCGAATCTGACT
* *
411795 ATCGCAATGAGATTCTGACT
1 ATCGCAATGCGAATCTGACT
411815 ATCGCAA
1 ATCGCAA
411822 CGAGATTCTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGAATCTGACT
Found at i:411779 original size:40 final size:39
Alignment explanation
Indices: 411709--411823 Score: 117
Period size: 40 Copynumber: 2.9 Consensus size: 39
411699 GTTGCGATTT
* *
411709 TCTTAATTCGCAATGCGAATAC-GTA-AATCGCAACGCGAA
1 TCTTAAATCGCAATGCGAAT-CTG-ACTATCGCAACGCGAA
*
411748 TACTTAAATCGCAATGCGAATCTGACTATCGCAATGCGAA
1 T-CTTAAATCGCAATGCGAATCTGACTATCGCAACGCGAA
* * * *
411788 TCTGACTATCGCAATGAGATTCTGACTATCGCAACG
1 TCTTA-AATCGCAATGCGAATCTGACTATCGCAACG
411824 AGATTCTAAC
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
39 6 0.09
40 58 0.91
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.25
Consensus pattern (39 bp):
TCTTAAATCGCAATGCGAATCTGACTATCGCAACGCGAA
Found at i:411826 original size:20 final size:20
Alignment explanation
Indices: 411755--411842 Score: 113
Period size: 20 Copynumber: 4.4 Consensus size: 20
411745 GAATACTTAA
* *
411755 ATCGCAATGCGAATCTGACT
1 ATCGCAATGAGATTCTGACT
* *
411775 ATCGCAATGCGAATCTGACT
1 ATCGCAATGAGATTCTGACT
411795 ATCGCAATGAGATTCTGACT
1 ATCGCAATGAGATTCTGACT
* *
411815 ATCGCAACGAGATTCTAACT
1 ATCGCAATGAGATTCTGACT
*
411835 ATCACAAT
1 ATCGCAAT
411843 ACTGAATTTC
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (20 bp):
ATCGCAATGAGATTCTGACT
Found at i:415125 original size:151 final size:151
Alignment explanation
Indices: 414853--415154 Score: 556
Period size: 151 Copynumber: 2.0 Consensus size: 151
414843 AAGTGGTCAT
414853 ACAAGGTTGACATGTGGATCACCATGCCATCACAATCATCATTTTCCTACCAAAATATGGATCCT
1 ACAAGGTTGACATGTGGATCACCATGCCATCACAATCATCATTTTCCTACCAAAATATGGATCCT
414918 CATCAAAATCCCAATCACAACCGGCTTCACCTTTGGGACTGTTAACTTAGGTGA-TTTTAAATGC
66 CATCAAAATCCCAATCACAACCGGCTTCACCTTTGGGACTGTTAACTTAGGTGATTTTTAAATGC
414982 AAACGTTGTATTA-GTGTATA
131 AAACGTTGTATTATGTGTATA
415002 ACAAGGTTGACATGTGGATCACCAGTGCCATCACAATCATC-TTTTCCTCTACCAAAATATGGAT
1 ACAAGGTTGACATGTGGATCACCA-TGCCATCACAATCATCATTTT-C-CTACCAAAATATGGAT
415066 CCTCATCAAAATCCCAATCACAACCGGCTTCACCTTTGGGACTGTTAACTTAGGTGATTTTTAAA
63 CCTCATCAAAATCCCAATCACAACCGGCTTCACCTTTGGGACTGTTAACTTAGGTGATTTTTAAA
415131 TGCAAACGTTGTATTATGTGTATA
128 TGCAAACGTTGTATTATGTGTATA
415155 TTATGTGTGA
Statistics
Matches: 148, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
149 28 0.19
150 17 0.11
151 73 0.49
152 23 0.16
153 7 0.05
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.31
Consensus pattern (151 bp):
ACAAGGTTGACATGTGGATCACCATGCCATCACAATCATCATTTTCCTACCAAAATATGGATCCT
CATCAAAATCCCAATCACAACCGGCTTCACCTTTGGGACTGTTAACTTAGGTGATTTTTAAATGC
AAACGTTGTATTATGTGTATA
Found at i:415295 original size:20 final size:18
Alignment explanation
Indices: 415270--415318 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 18
415260 TATCAGCGCA
*
415270 ATCGCAACGTGAATTTGACT
1 ATCGCAACG-GAA-ATGACT
415290 ATCGCAACACGGAAATGACT
1 ATCGC-A-ACGGAAATGACT
415310 ATCGCAACG
1 ATCGCAACG
415319 AGAGAATCGC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 3 0.12
19 1 0.04
20 15 0.58
21 4 0.15
22 3 0.12
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (18 bp):
ATCGCAACGGAAATGACT
Found at i:415378 original size:34 final size:33
Alignment explanation
Indices: 415301--415384 Score: 132
Period size: 33 Copynumber: 2.5 Consensus size: 33
415291 TCGCAACACG
**
415301 GAAATGACTATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
*
415334 GAAATGAAAATCGCAACGAGTGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
415367 GAAAATGAAAATCGCAAC
1 G-AAATGAAAATCGCAAC
415385 ATGAATTTAG
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 31 0.66
34 16 0.34
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAATGC
Found at i:415428 original size:20 final size:20
Alignment explanation
Indices: 415395--415462 Score: 60
Period size: 20 Copynumber: 3.8 Consensus size: 20
415385 ATGAATTTAG
* *
415395 TTTCGCGTTACGATTTTCAT
1 TTTCGCATTGCGATTTTCAT
415415 TTTCGCATTGCGA--TTC-T
1 TTTCGCATTGCGATTTTCAT
*
415432 CTT-G--TTGCGATTTTCA-
1 TTTCGCATTGCGATTTTCAT
415448 TTTCGCATTGCGATT
1 TTTCGCATTGCGATT
415463 CTCTCGTTGC
Statistics
Matches: 38, Mismatches: 4, Indels: 13
0.69 0.07 0.24
Matches are distributed among these distances:
14 6 0.16
16 6 0.16
17 4 0.11
18 3 0.08
19 8 0.21
20 11 0.29
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.49
Consensus pattern (20 bp):
TTTCGCATTGCGATTTTCAT
Found at i:415457 original size:33 final size:33
Alignment explanation
Indices: 415400--415495 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
415390 TTTAGTTTCG
*
415400 CGTTACGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
*
415434 TGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
** *
415467 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
415496 AGTCTGTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 33 0.60
34 22 0.40
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:415620 original size:14 final size:14
Alignment explanation
Indices: 415601--415637 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
415591 CATCAATTAA
415601 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
415615 ACAAATCATCTTTT
1 ACAAATCAACATTT
415629 ACAAATCAA
1 ACAAATCAA
415638 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:417069 original size:21 final size:21
Alignment explanation
Indices: 417014--417120 Score: 99
Period size: 21 Copynumber: 5.1 Consensus size: 21
417004 TCTAGAATGT
* *
417014 TGGGAGGGACCTCTTCAACGA
1 TGGGAGGGGCCTCTTGAACGA
** *
417035 TGACAGTGGCCTCTTGAACGA
1 TGGGAGGGGCCTCTTGAACGA
* **
417056 TGGGAGGGGACTCTTGAGGGA
1 TGGGAGGGGCCTCTTGAACGA
**
417077 TGATAGGGGCCTCTTGAACGA
1 TGGGAGGGGCCTCTTGAACGA
*
417098 TAGGG-GAGGCCTCTTGAACGA
1 T-GGGAGGGGCCTCTTGAACGA
417119 TG
1 TG
417121 ACAGGTGAGT
Statistics
Matches: 66, Mismatches: 19, Indels: 3
0.75 0.22 0.03
Matches are distributed among these distances:
20 1 0.02
21 64 0.97
22 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.37, T:0.21
Consensus pattern (21 bp):
TGGGAGGGGCCTCTTGAACGA
Found at i:417079 original size:42 final size:42
Alignment explanation
Indices: 417015--417125 Score: 125
Period size: 42 Copynumber: 2.6 Consensus size: 42
417005 CTAGAATGTT
* *
417015 GGGAGGGACCTCTTCAACGATGACAGTGGCCTCTTGAACGAT-G
1 GGGA-GGA-CTCTTGAACGATGACAGGGGCCTCTTGAACGATAG
* ** *
417058 GGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGATAG
1 GG-GAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGATAG
*
417101 GGGAGGCCTCTTGAACGATGACAGG
1 GGGAGGACTCTTGAACGATGACAGG
417126 TGAGTCGGGC
Statistics
Matches: 55, Mismatches: 11, Indels: 5
0.77 0.15 0.07
Matches are distributed among these distances:
42 46 0.84
43 8 0.15
44 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.38, T:0.20
Consensus pattern (42 bp):
GGGAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGATAG
Found at i:417629 original size:20 final size:20
Alignment explanation
Indices: 417606--417714 Score: 137
Period size: 20 Copynumber: 5.5 Consensus size: 20
417596 GAAACTTAAA
417606 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
417626 ATCGCAACGCAAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
417646 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
417666 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
* ** *
417686 ATCGCAATGCGAATTTAACT
1 ATCGCAACGCGAAAATGACT
417706 ATCGCAACG
1 ATCGCAACG
417715 AGAGAATCGT
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 82 1.00
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:417796 original size:53 final size:53
Alignment explanation
Indices: 417738--417917 Score: 184
Period size: 53 Copynumber: 3.3 Consensus size: 53
417728 GCGATTTTCA
* *
417738 TTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGTGATAATCAA
1 TTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGTGATAGTCAT
* ** * *
417791 ATTCGCATTGCGATAGTCATTTTCGCATTACGATAGTCATTTTCTCATTGTGATAGTCAT
1 TTTCGCATTGCGATTTTCA-TTTCGCATTGCGAT--TC---TT-TCGTTGTGATAGTCAT
*
417851 TTTCG-AGTTGCGATTTTCATTTCGCATTGCGATTCTCTT-GTTGCGATAGTCAT
1 TTTCGCA-TTGCGATTTTCATTTCGCATTGCGATTCT-TTCGTTGTGATAGTCAT
*
417904 TTTCGTATTGCGAT
1 TTTCGCATTGCGAT
417918 AATAAACTAT
Statistics
Matches: 104, Mismatches: 13, Indels: 20
0.76 0.09 0.15
Matches are distributed among these distances:
53 40 0.38
54 16 0.15
55 1 0.01
56 2 0.02
57 2 0.02
59 16 0.15
60 27 0.26
ACGTcount: A:0.19, C:0.18, G:0.18, T:0.44
Consensus pattern (53 bp):
TTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGTGATAGTCAT
Found at i:417815 original size:20 final size:20
Alignment explanation
Indices: 417738--417918 Score: 131
Period size: 20 Copynumber: 9.8 Consensus size: 20
417728 GCGATTTTCA
**
417738 TTTCGCATTGCGATTTTCA-
1 TTTCGCATTGCGATAGTCAT
417757 TTTCGCATTGCGAT--TC--
1 TTTCGCATTGCGATAGTCAT
* * *
417773 TTTCG--TTGTGATAATCAA
1 TTTCGCATTGCGATAGTCAT
*
417791 ATTCGCATTGCGATAGTCAT
1 TTTCGCATTGCGATAGTCAT
*
417811 TTTCGCATTACGATAGTCAT
1 TTTCGCATTGCGATAGTCAT
* *
417831 TTTCTCATTGTGATAGTCAT
1 TTTCGCATTGCGATAGTCAT
**
417851 TTTCG-AGTTGCGATTTTCA-
1 TTTCGCA-TTGCGATAGTCAT
417870 TTTCGCATTGCGAT--TC-T
1 TTTCGCATTGCGATAGTCAT
*
417887 CTT-G--TTGCGATAGTCAT
1 TTTCGCATTGCGATAGTCAT
*
417904 TTTCGTATTGCGATA
1 TTTCGCATTGCGATA
417919 ATAAACTATT
Statistics
Matches: 131, Mismatches: 16, Indels: 29
0.74 0.09 0.16
Matches are distributed among these distances:
14 13 0.10
16 10 0.08
17 9 0.07
18 5 0.04
19 27 0.21
20 67 0.51
ACGTcount: A:0.19, C:0.18, G:0.18, T:0.44
Consensus pattern (20 bp):
TTTCGCATTGCGATAGTCAT
Found at i:419815 original size:21 final size:20
Alignment explanation
Indices: 419779--419834 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 20
419769 TTGAAACTTT
419779 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
419799 AAATCGCAACAACGAAAATGA
1 AAATCGCAAC-ACGAAAATGA
** *
419820 CTATCGCAACGCGAA
1 AAATCGCAACACGAA
419835 TTTGACTATC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.50, C:0.23, G:0.16, T:0.11
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:419890 original size:33 final size:34
Alignment explanation
Indices: 419822--419894 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 34
419812 GAAAATGACT
* **
419822 ATCGCAACGCGAATTTGACTATCGCAACGCAAGA
1 ATCGCAACGCGAATATGAAAATCGCAACGCAAGA
419856 ATCGCAACGCGAA-ATGAAAATCGCAACG-ACAGA
1 ATCGCAACGCGAATATGAAAATCGCAACGCA-AGA
419889 ATCGCA
1 ATCGCA
419895 TTGCGATAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 1 0.03
33 21 0.60
34 13 0.37
ACGTcount: A:0.40, C:0.26, G:0.21, T:0.14
Consensus pattern (34 bp):
ATCGCAACGCGAATATGAAAATCGCAACGCAAGA
Found at i:420231 original size:22 final size:22
Alignment explanation
Indices: 420169--420234 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
420159 TGACCGTGAA
* *
420169 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
*
420191 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
420213 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
420235 GGATGTCGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.21, C:0.15, G:0.39, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:420436 original size:20 final size:20
Alignment explanation
Indices: 420411--420459 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
420401 ATGTAAATCG
*
420411 CATTGCGATAGTCAGATTCA
1 CATTGCGATAGTCAAATTCA
**
420431 CATTGCGATAGTCAAATTTG
1 CATTGCGATAGTCAAATTCA
420451 CATTGCGAT
1 CATTGCGAT
420460 TTACATATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (20 bp):
CATTGCGATAGTCAAATTCA
Found at i:420473 original size:20 final size:20
Alignment explanation
Indices: 420450--420559 Score: 157
Period size: 20 Copynumber: 5.5 Consensus size: 20
420440 AGTCAAATTT
*
420450 GCATTGCGATTTACATATTC
1 GCATTGCGATTTACGTATTC
*
420470 GCATTGTGATTTACGTATTC
1 GCATTGCGATTTACGTATTC
420490 GCATTGCGATTTACGTATTC
1 GCATTGCGATTTACGTATTC
* **
420510 GCATTGCGATTTTCCAAATTC
1 GCATTGCGA-TTTACGTATTC
*
420531 GCGTTGCGATTTACGTATTC
1 GCATTGCGATTTACGTATTC
420551 GCATTGCGA
1 GCATTGCGA
420560 ATTAGGAAAA
Statistics
Matches: 78, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
20 62 0.79
21 16 0.21
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (20 bp):
GCATTGCGATTTACGTATTC
Found at i:420543 original size:41 final size:40
Alignment explanation
Indices: 420426--420559 Score: 169
Period size: 40 Copynumber: 3.3 Consensus size: 40
420416 CGATAGTCAG
* ** * *
420426 ATTCACATTGCGATAGTCAAATTTGCATTGCGATTTACAT
1 ATTCGCATTGCGATTTTCAAATTCGCATTGCGATTTACGT
* * **
420466 ATTCGCATTGTGATTTACGTATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTTCAAATTCGCATTGCGATTTACGT
*
420506 ATTCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTT-CAAATTCGCATTGCGATTTACGT
420547 ATTCGCATTGCGA
1 ATTCGCATTGCGA
420560 ATTAGGAAAA
Statistics
Matches: 79, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
40 46 0.58
41 33 0.42
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (40 bp):
ATTCGCATTGCGATTTTCAAATTCGCATTGCGATTTACGT
Found at i:421472 original size:12 final size:13
Alignment explanation
Indices: 421455--421512 Score: 55
Period size: 15 Copynumber: 4.1 Consensus size: 13
421445 TATCAAGAAC
421455 TTATTATTAT-TA
1 TTATTATTATATA
421467 TTATTATATATATA
1 TTATTAT-TATATA
421481 TATATATATTATATA
1 T-TAT-TATTATATA
421496 TATATATATATATATA
1 T-TAT-TAT-TATATA
421512 T
1 T
421513 ATGCAAATAG
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
12 7 0.17
13 3 0.07
14 3 0.07
15 18 0.44
16 10 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTATTATTATATA
Found at i:421478 original size:2 final size:2
Alignment explanation
Indices: 421471--421514 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
421461 TTATTATTAT
421471 TA TA TA TA TA TA TA TA TA T- 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
421512 TA T
1 TA T
421515 GCAAATAGAG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:421909 original size:3 final size:3
Alignment explanation
Indices: 421901--421928 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
421891 TACTTTACCC
421901 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
421929 GGTAAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:422906 original size:31 final size:31
Alignment explanation
Indices: 422843--422935 Score: 159
Period size: 31 Copynumber: 3.0 Consensus size: 31
422833 AATTGATCTA
* *
422843 TAATGTTATCGATTTGTAACAAAAATGATCAT
1 TAATATTATCGATTTGTAAC-AAAATGGTCAT
422875 TAATATTATCGATTTGTAACAAAATGGTCAT
1 TAATATTATCGATTTGTAACAAAATGGTCAT
422906 TAATATTATCGATTTGTAACAAAATGGTCA
1 TAATATTATCGATTTGTAACAAAATGGTCA
422936 CTCCACTGTA
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
31 40 0.68
32 19 0.32
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.38
Consensus pattern (31 bp):
TAATATTATCGATTTGTAACAAAATGGTCAT
Found at i:423530 original size:17 final size:16
Alignment explanation
Indices: 423501--423552 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
423491 AACTCATCAC
*
423501 TTTTTAATATTTTTAA
1 TTTTTAATTTTTTTAA
*
423517 TTTTTAATTTTTTTAG
1 TTTTTAATTTTTTTAA
*
423533 TGTTTTAATTTTTTAAA
1 T-TTTTAATTTTTTTAA
423550 TTT
1 TTT
423553 AATTAAATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
16 17 0.55
17 14 0.45
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (16 bp):
TTTTTAATTTTTTTAA
Found at i:425415 original size:146 final size:148
Alignment explanation
Indices: 425013--425666 Score: 708
Period size: 146 Copynumber: 4.4 Consensus size: 148
425003 ATTGACATTG
* * * * *
425013 ACATTGACATTGTTCTTCTCGGCCAGCATGCAGTCCCCTGGTGACATATCACCTTGCAACTCGGC
1 ACATCGACATTGTTATTCTCCGTCAGCATGCAGTCCCCTGGTGACATATCACCATGCAACTCGGC
* * * * * *
425078 ACCACTCGATTGAAGTAAAA---CGTTGTCG--CTCTTGTCGATTTCGAGATGGATCGAGGTTTC
66 ACCACTCGATTGAACTAAAACCTCGATGTCGTAGTC-T-TCGATTTCAAGAGGGACCGAGGTTTC
425138 CG-ATGACTTCTTGATGTTC
129 CGAATGACTTCTTGATGTTC
* * * * *
425157 ATATCGACATT-TTCATTCTCTGTCAGCAAGCAGT-CCCTGGTGACATATCATCATGTAACTCGG
1 ACATCGACATTGTT-ATTCTCCGTCAGCATGCAGTCCCCTGGTGACATATCACCATGCAACTCGG
* * * * * *
425220 CACCACTCAATTGAAGTAAAACCT-GACGTCGAAGCCTTCGATTTCAAGAGGGACCAAGGTTTCC
65 CACCACTCGATTGAACTAAAACCTCGATGTCGTAGTCTTCGATTTCAAGAGGGACCGAGGTTTCC
425284 -AATGACTTCTTGATGTTC
130 GAATGACTTCTTGATGTTC
* * * **
425302 ACATCGACATTGTTATTCTCTGTCAGCAGGCACTCCCCTGGTGACATATCACCATGCAACTCAAC
1 ACATCGACATTGTTATTCTCCGTCAGCATGCAGTCCCCTGGTGACATATCACCATGCAACTCGGC
* * *
425367 ACCAATTGATTTAACTAAAACCTCGATGTCGTA-TCTTCGATTTCAAGAGGGACCGAGGTTTCCG
66 ACCACTCGATTGAACTAAAACCTCGATGTCGTAGTCTTCGATTTCAAGAGGGACCGAGGTTTCCG
*
425431 ACT-ACTTCTTGATGTTC
131 AATGACTTCTTGATGTTC
*
425448 ACATCGACATTGTCATTCTCCGTCAGCATGCAGTCCCCTGGTGACATATCACCATGCAACTCGGC
1 ACATCGACATTGTTATTCTCCGTCAGCATGCAGTCCCCTGGTGACATATCACCATGCAACTCGGC
* * * * * *
425513 ACCACTCGATTGAAGC-ACAACCTTGATGTCTTAGTCATCAATTTCAAGAGGGACTGAGGTTTCC
66 ACCACTCGATTGAA-CTAAAACCTCGATGTCGTAGTCTTCGATTTCAAGAGGGACCGAGGTTTCC
*
425577 GAGTTCGACGACTTCTTGATGTTC
130 GA-----ATGACTTCTTGATGTTC
* * * * *
425601 ACATCCACATTGTTATTCTCCGTCACCGTGTAGTTCCCTGGTGACATAAT-ACC-TCGCAACTCG
1 ACATCGACATTGTTATTCTCCGTCAGCATGCAGTCCCCTGGTGACAT-ATCACCAT-GCAACTCG
425664 GCA
64 GCA
425667 TCAGTTGAAA
Statistics
Matches: 431, Mismatches: 58, Indels: 33
0.83 0.11 0.06
Matches are distributed among these distances:
143 48 0.11
144 25 0.06
145 73 0.17
146 173 0.40
147 40 0.09
152 1 0.00
153 69 0.16
154 2 0.00
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (148 bp):
ACATCGACATTGTTATTCTCCGTCAGCATGCAGTCCCCTGGTGACATATCACCATGCAACTCGGC
ACCACTCGATTGAACTAAAACCTCGATGTCGTAGTCTTCGATTTCAAGAGGGACCGAGGTTTCCG
AATGACTTCTTGATGTTC
Found at i:429612 original size:21 final size:21
Alignment explanation
Indices: 429587--429636 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
429577 CAGAGGGAAT
429587 CGATTCCCTATGAGGGGGTAC
1 CGATTCCCTATGAGGGGGTAC
*
429608 CGATTCTCTATGAGGGGGTAC
1 CGATTCCCTATGAGGGGGTAC
429629 CGATTCCC
1 CGATTCCC
429637 CCCACGCTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.18, C:0.26, G:0.30, T:0.26
Consensus pattern (21 bp):
CGATTCCCTATGAGGGGGTAC
Found at i:430404 original size:97 final size:98
Alignment explanation
Indices: 430227--430422 Score: 369
Period size: 97 Copynumber: 2.0 Consensus size: 98
430217 TAACAATTGG
430227 TATCAGAGCCTAACTCATTAAGAAGGTTTAACCACCTTGAGACGATCCTCAAAGAAGCTCTACTA
1 TATCAGAGCCTAACTCATTAAGAAGGTTTAACCACCTTGAGACGATCCTCAAAGAAGCTCTACTA
430292 TTTCTGACGCAAACCGACAAAG-AATGACTTTT
66 TTTCTGACGCAAACCGACAAAGAAATGACTTTT
430324 TATCAGAGCCTAACTCATTAAGAAGGTTTAACCACCTTGAGACGATCCTCAAAGAAGCTCTACTA
1 TATCAGAGCCTAACTCATTAAGAAGGTTTAACCACCTTGAGACGATCCTCAAAGAAGCTCTACT-
430389 ATTTCTGACGC-AACCGACAAAGAAATGACTTTT
65 ATTTCTGACGCAAACCGACAAAGAAATGACTTTT
430422 T
1 T
430423 CCTCCGGTGC
Statistics
Matches: 97, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
97 75 0.77
98 22 0.23
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.26
Consensus pattern (98 bp):
TATCAGAGCCTAACTCATTAAGAAGGTTTAACCACCTTGAGACGATCCTCAAAGAAGCTCTACTA
TTTCTGACGCAAACCGACAAAGAAATGACTTTT
Found at i:432488 original size:15 final size:15
Alignment explanation
Indices: 432468--432497 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
432458 GAGTAAGGGG
432468 GAGTAATTTTTCAAA
1 GAGTAATTTTTCAAA
432483 GAGTAATTTTTCAAA
1 GAGTAATTTTTCAAA
432498 CTTGGTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (15 bp):
GAGTAATTTTTCAAA
Found at i:438993 original size:94 final size:92
Alignment explanation
Indices: 438823--439002 Score: 281
Period size: 93 Copynumber: 1.9 Consensus size: 92
438813 TATAATATTA
438823 TATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAACGCCCCGACTTTATGGAT
1 TATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAACGCCCCGACTTTATGGAT
* * *
438888 AATATTCAGCTAGCTTGATAAGGTGAT
66 AAGATTCAGCTAACCTGATAAGGTGAT
* *
438915 TATACTATACAATAAAGTTTGAGTTGTCCCTCTA-AGGCAATTGGTTAAACGCCCCGGCTTTATG
1 TATA-TATACAATAAAGCTTGAGTTGTCCCTCTAGA-GCAATTGGTT-AACGCCCCGACTTTATG
438979 GATAAGATTCAGCTAACCTGATAA
63 GATAAGATTCAGCTAACCTGATAA
439003 AGATATTATA
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
92 5 0.06
93 38 0.47
94 37 0.46
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (92 bp):
TATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAACGCCCCGACTTTATGGAT
AAGATTCAGCTAACCTGATAAGGTGAT
Found at i:439011 original size:94 final size:93
Alignment explanation
Indices: 438817--439013 Score: 281
Period size: 94 Copynumber: 2.1 Consensus size: 93
438807 CCACATTATA
438817 ATATTATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAACGCCCCGACTTT
1 ATATTATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAACGCCCCGACTTT
* * *
438882 ATGGATAATATTCAGCTAGCTTGATAAG
66 ATGGATAAGATTCAGCTAACCTGATAAG
* * * *
438910 GTGATTATA-CTATACAATAAAGTTTGAGTTGTCCCTCTA-AGGCAATTGGTTAAACGCCCCGGC
1 AT-ATTATATATATACAATAAAGCTTGAGTTGTCCCTCTAGA-GCAATTGGTT-AACGCCCCGAC
438973 TTTATGGATAAGATTCAGCTAACCTGATAAAG
63 TTTATGGATAAGATTCAGCTAACCTGAT-AAG
439005 ATATTATAT
1 ATATTATAT
439014 GTTGAGATGT
Statistics
Matches: 91, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
92 1 0.01
93 39 0.43
94 47 0.52
95 4 0.04
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (93 bp):
ATATTATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAACGCCCCGACTTT
ATGGATAAGATTCAGCTAACCTGATAAG
Found at i:440381 original size:36 final size:36
Alignment explanation
Indices: 440332--440447 Score: 137
Period size: 35 Copynumber: 3.2 Consensus size: 36
440322 TAATTTACTC
*
440332 AAAATAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTT
1 AAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTT
*
440369 AAAACAAATTTTGTCTCTC-TGAAAC-GATTTCTCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAG-TTTCTCTT
* * * *
440404 AAAATAAATTTTGTTTCTCTCGAGACAGTTTCCCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
*
440440 GAAACAAA
1 AAAACAAA
440448 ATCTTTGAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
34 1 0.01
35 30 0.45
36 28 0.42
37 8 0.12
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
Found at i:440550 original size:137 final size:136
Alignment explanation
Indices: 440345--440639 Score: 441
Period size: 137 Copynumber: 2.2 Consensus size: 136
440335 ATAAAGTTTT
* * *
440345 GTCTCTCTTGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTCTGAAACGATTTCTCTTAAAATA
1 GTCTCTCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTGAAACGATTTCTCGTAAAACA
* * *
440410 AATTTTGTTTCTCTCGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTCCTT-TAACA
66 AATTTTGTCTCTCTCGAGACAGTTTCCCTTGAAACAAAATCTCTGAATCTGTTTTCCTTGAAACA
*
440474 AATTTC
131 AATGTC
* *
440480 GTCTCTCTTGAGACAGTTTCTTTTAGAAATAAATTTTGTCTCTCTTGAGAC-ATTTTCTCGTAAA
1 GTCTCTCTTGAGACAGTTTCTTTTA-AAACAAATTTTGTCTCTC-TGAAACGA-TTTCTCGTAAA
* * *
440544 ACAAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATCTCTGAATCTGTTTTCCTTGAA
63 ACAAATTTTGTCTCTCTCGAGACAGTTTCCCTTGAAACAAAATCTCTGAATCTGTTTTCCTTGAA
440609 ACAAATGTC
128 ACAAATGTC
440618 GTCTCTCTTGAGACAGTTTCTT
1 GTCTCTCTTGAGACAGTTTCTT
440640 ATTTTTAACT
Statistics
Matches: 144, Mismatches: 12, Indels: 5
0.89 0.07 0.03
Matches are distributed among these distances:
135 24 0.17
136 18 0.12
137 71 0.49
138 31 0.22
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (136 bp):
GTCTCTCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTGAAACGATTTCTCGTAAAACA
AATTTTGTCTCTCTCGAGACAGTTTCCCTTGAAACAAAATCTCTGAATCTGTTTTCCTTGAAACA
AATGTC
Found at i:440557 original size:36 final size:36
Alignment explanation
Indices: 440470--440584 Score: 158
Period size: 36 Copynumber: 3.2 Consensus size: 36
440460 GTTTTCCTTT
* *
440470 AACAAATTTCGTCTCTCTTGAGACAGTTTCTTTTAGA
1 AACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTA-A
* * *
440507 AATAAATTTTGTCTCTCTTGAGACATTTTCTCGTAA
1 AACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTAA
* *
440543 AACAAATTTTGTCTCTCTTGAGATAGTTTCTCTTGA
1 AACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTAA
440579 AACAAA
1 AACAAA
440585 ATCTCTGAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
36 38 0.56
37 30 0.44
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (36 bp):
AACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTAA
Found at i:440963 original size:34 final size:35
Alignment explanation
Indices: 440910--441005 Score: 106
Period size: 35 Copynumber: 2.7 Consensus size: 35
440900 CTAATTTACC
* * *
440910 AAAATAAAGTGTTGTCTCTCTTGAGA-TAGTTCTCTT
1 AAAATAAA-T-TTGTCTCTCTCGAGACGACTTCTCTT
440946 AAAATAAATTTGTCTCTCTCGAGACGACTTCTCTT
1 AAAATAAATTTGTCTCTCTCGAGACGACTTCTCTT
* *
440981 AAAACAAA-TTGTTTTCTCTCGAGAC
1 AAAATAAATTTG-TCTCTCTCGAGAC
441006 AGTTTCCCTT
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
34 17 0.32
35 28 0.53
36 8 0.15
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (35 bp):
AAAATAAATTTGTCTCTCTCGAGACGACTTCTCTT
Found at i:441146 original size:33 final size:35
Alignment explanation
Indices: 441044--441156 Score: 140
Period size: 36 Copynumber: 3.2 Consensus size: 35
441034 CTATTTTCCT
* *
441044 TTAAACAAATTTTGTTTCTCTTGAGACAGTTTCTT
1 TTAAACAAATTTTGTCTCTCTTGAGACAGTTTCTC
* *
441079 TTAGACTAAATTTTGTCTCTCTTGAGACATTTTCTC
1 TTAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTC
* *
441115 GTAAACAAA-TTT-TCTCTCTTGAGACCGTTTCTC
1 TTAAACAAATTTTGTCTCTCTTGAGACAGTTTCTC
441148 TTGAAACAA
1 TT-AAACAA
441157 TCTCTGAATC
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
33 20 0.30
34 9 0.13
35 8 0.12
36 30 0.45
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.43
Consensus pattern (35 bp):
TTAAACAAATTTTGTCTCTCTTGAGACAGTTTCTC
Found at i:441215 original size:121 final size:124
Alignment explanation
Indices: 440954--441324 Score: 421
Period size: 121 Copynumber: 2.9 Consensus size: 124
440944 TTAAAATAAA
* * * * *
440954 TTTGTCTCTCTCGAGACGACTTCTCTTAAAACAAATTGTTTTCTCTC-GAGACAGTTTCCCTTGA
1 TTTGTCTCTCTTGAGAC-ATTTCTCGTAAAACAAATT-TTCTCTCTCTGAGACAGTTTCTCTTGA
* * * * **
441018 AACAAAATCTTTGAATCTATTTTCCTTTAAACAAATTTTGTTTCTCTTGAGACAGTTTCTTTTAG
64 AAC-AAATCTCTGAATCTGTTTTCCTTGAAACAAA-TTCGCCTCTCTTGAGACA-----TTTT--
*
441083 ACTAAAT
120 -CT-ATT
*
441090 TTTGTCTCTCTTGAGACATTTTCTCGT-AAACAAATTTTCTCTCT-TGAGACCGTTTCTCTTGAA
1 TTTGTCTCTCTTGAGACA-TTTCTCGTAAAACAAATTTTCTCTCTCTGAGACAGTTTCTCTTGAA
441153 AC-AATCTCTGAATCTG-TTTCCTTG-AACAAATGTCGCCTCTCTTGAGACATTTTCTATT
65 ACAAATCTCTGAATCTGTTTTCCTTGAAACAAAT-TCGCCTCTCTTGAGACATTTTCTATT
*
441211 TTTGTCTCTCTTGAGACATTTCTCGTAAAACAAATTTTGTCTCTCTGAGACAGTTTCTCTTGAAA
1 TTTGTCTCTCTTGAGACATTTCTCGTAAAACAAATTTTCTCTCTCTGAGACAGTTTCTCTTGAAA
*
441276 CAAAATCTCTGAATCTGTTTTCCTTGAAACAAATTCGTCTCTCTTGAGA
66 C-AAATCTCTGAATCTGTTTTCCTTGAAACAAATTCGCCTCTCTTGAGA
441325 TAGTTTCTTT
Statistics
Matches: 210, Mismatches: 16, Indels: 29
0.82 0.06 0.11
Matches are distributed among these distances:
120 8 0.04
121 36 0.17
122 22 0.10
124 14 0.07
125 26 0.12
126 7 0.03
129 1 0.00
130 20 0.10
131 7 0.03
132 12 0.06
134 25 0.12
135 10 0.05
136 22 0.10
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.41
Consensus pattern (124 bp):
TTTGTCTCTCTTGAGACATTTCTCGTAAAACAAATTTTCTCTCTCTGAGACAGTTTCTCTTGAAA
CAAATCTCTGAATCTGTTTTCCTTGAAACAAATTCGCCTCTCTTGAGACATTTTCTATT
Found at i:441255 original size:35 final size:35
Alignment explanation
Indices: 441210--441279 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
441200 CATTTTCTAT
441210 TTTTGTCTCTCTTGAGACA-TTTCTCGTAAAACAAA
1 TTTTGTCTCTC-TGAGACAGTTTCTCGTAAAACAAA
* *
441245 TTTTGTCTCTCTGAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTGAGACAGTTTCTCGTAAAACAAA
441280 ATCTCTGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 7 0.22
35 25 0.78
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (35 bp):
TTTTGTCTCTCTGAGACAGTTTCTCGTAAAACAAA
Found at i:441390 original size:101 final size:99
Alignment explanation
Indices: 441214--441434 Score: 311
Period size: 101 Copynumber: 2.2 Consensus size: 99
441204 TTCTATTTTT
*
441214 GTCTCTCTTGAGACA-TTTCTCGTAAAACAAATTTTGTCTCTCTGAGACAGTTTCTCTTGAAACA
1 GTCTCTCTTGAGACAGTTTCTCGTAAAACAAATTTTGTCTCTCTGAGACAGTTTCCCTTGAAACA
*
441278 AAATCTCTGAATCTGTTTTCC-TTGAAACAAATTC
66 AAATATCTGAATCTGTTTTCCATT-AAACAAATTC
* ** *
441312 GTCTCTCTTGAGATAGTTTCTTTTAGAACTAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA
1 GTCTCTCTTGAGACAGTTTCTCGTAAAAC-AAATTTTGTCTCTC-TGAGACAGTTTCCCTTGAAA
* *
441377 CAAAATATTTGAATCTGTTTTCCATTAAACAATTTC
64 CAAAATATCTGAATCTGTTTTCCATTAAACAAATTC
* *
441413 ATCTCTCTCGAGACAGTTTCTC
1 GTCTCTCTTGAGACAGTTTCTC
441435 TTGAAACACA
Statistics
Matches: 107, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
98 14 0.13
99 10 0.09
100 14 0.13
101 67 0.63
102 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (99 bp):
GTCTCTCTTGAGACAGTTTCTCGTAAAACAAATTTTGTCTCTCTGAGACAGTTTCCCTTGAAACA
AAATATCTGAATCTGTTTTCCATTAAACAAATTC
Found at i:442214 original size:18 final size:19
Alignment explanation
Indices: 442180--442216 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
442170 CACGGAATGT
442180 AAGATTACCAGAGGGAATAA
1 AAGATTACCA-AGGGAATAA
442200 AAGATTACC-AGGGAATA
1 AAGATTACCAAGGGAATA
442217 GGATTAATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
20 9 0.53
ACGTcount: A:0.49, C:0.11, G:0.24, T:0.16
Consensus pattern (19 bp):
AAGATTACCAAGGGAATAA
Found at i:444953 original size:2 final size:2
Alignment explanation
Indices: 444888--444935 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
444878 AAAGTGGAAC
444888 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
444930 AT AT AT
1 AT AT AT
444936 TTATTTAATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:450267 original size:38 final size:38
Alignment explanation
Indices: 450223--450362 Score: 181
Period size: 38 Copynumber: 3.7 Consensus size: 38
450213 TGTTCGTTCA
* *
450223 TTTATGTTCACGTACAAGCTCCTTTATCAGGTCATTCG
1 TTTATGTTCACGAACAAGCTCGTTTATCAGGTCATTCG
450261 TTTATGTTCACGAACAAGCTCGTTTATCAGGTCATTCG
1 TTTATGTTCACGAACAAGCTCGTTTATCAGGTCATTCG
* * * *
450299 TTTATGTTCATGGACAAGCTCGTTTATCGGGTCGTTCG
1 TTTATGTTCACGAACAAGCTCGTTTATCAGGTCATTCG
* * ** *
450337 TTTGTGTTTATTAACAAACTCGTTTA
1 TTTATGTTCACGAACAAGCTCGTTTA
450363 CTTTTTTATT
Statistics
Matches: 91, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 91 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (38 bp):
TTTATGTTCACGAACAAGCTCGTTTATCAGGTCATTCG
Found at i:453491 original size:59 final size:58
Alignment explanation
Indices: 453397--453576 Score: 153
Period size: 59 Copynumber: 3.0 Consensus size: 58
453387 CATCATATGT
* * * * * *
453397 CCCAAATTATAACCCTCATTTTAAATTGGTCTTTAAACTTTTGAGTATTTAATTTCATC
1 CCCAAACTATGACCATCATTCTAAACTAGTCTTTAAACTTTTGA-TATTTAATTTCATC
* * * *
453456 CCCAAACTTTGACTATCATTCTAAACTAGTCTTTAAACATTTGACATTTCAATTTCATC
1 CCCAAACTATGACCATCATTCTAAACTAGTCTTTAAACTTTTGATATTT-AATTTCATC
* * * * * ** *
453515 CCTACACTATGACCCTCTTTCTAAATTAGTCCCTAAACTTTTTGAATATTCCAATTTCATC
1 CCCAAACTATGACCATCATTCTAAACTAGTCTTTAAAC-TTTTG-ATATT-TAATTTCATC
453576 C
1 C
453577 TAATTTCATC
Statistics
Matches: 95, Mismatches: 22, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
58 4 0.04
59 73 0.77
60 4 0.04
61 14 0.15
ACGTcount: A:0.30, C:0.24, G:0.06, T:0.41
Consensus pattern (58 bp):
CCCAAACTATGACCATCATTCTAAACTAGTCTTTAAACTTTTGATATTTAATTTCATC
Found at i:453867 original size:60 final size:59
Alignment explanation
Indices: 453703--453875 Score: 190
Period size: 60 Copynumber: 2.9 Consensus size: 59
453693 TATACGTATG
* * * *
453703 GTTTGGGATGAAATTGGAATGTTTAAAAAGTTTGGGGACTAATTTAGAATGAAAGTTATA
1 GTTTGGGATGAAATT-GAATATTTAAAAAGTTTAGGGACTAATTTAGAATGATAGTAATA
* *
453763 GTTTGGGGATGAAATTGAA-ATGTTCAAAAA-TTTAAGGAATAATTTAGAATGATAGTAATA
1 GTTT-GGGATGAAATTGAATAT-TT-AAAAAGTTTAGGGACTAATTTAGAATGATAGTAATA
* * *
453823 GTTTGGAGATAAAATTAGAATATTT-AAAAGTTTAGGGACCAATTTAAAATGAT
1 GTTTGG-GATGAAATT-GAATATTTAAAAAGTTTAGGGACTAATTTAGAATGAT
453876 GGGCATACTT
Statistics
Matches: 95, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
59 7 0.07
60 65 0.68
61 21 0.22
62 2 0.02
ACGTcount: A:0.41, C:0.02, G:0.23, T:0.34
Consensus pattern (59 bp):
GTTTGGGATGAAATTGAATATTTAAAAAGTTTAGGGACTAATTTAGAATGATAGTAATA
Found at i:462180 original size:220 final size:220
Alignment explanation
Indices: 461798--462242 Score: 836
Period size: 220 Copynumber: 2.0 Consensus size: 220
461788 TTTATTTAAT
461798 TTTTGACTTATATCTAAATAATTATATTCAGTGTTTTAATTTTATTCTTTTTACATATCATTTAA
1 TTTTGACTTATATCTAAATAATTATATTCAGTGTTTTAATTTTATTCTTTTTACATATCATTTAA
461863 GAGTTTGTTTTTGTCTGCTTCTATGACATATTTATTCCTTGGATTTTATGACACAATTTTTTCTA
66 GAGTTTGTTTTTGTCTGCTTCTATGACATATTTATTCCTTGGATTTTATGACACAATTTTTTCTA
*
461928 TCATTGTAGTAGTTTGACATTTCATGTTACATTTATCACAATACATCTTCTGATCAAGAAATGTC
131 TCATTATAGTAGTTTGACATTTCATGTTACATTTATCACAATACATCTTCTGATCAAGAAATGTC
461993 GACGATGTTTCATAATTAGATCTCA
196 GACGATGTTTCATAATTAGATCTCA
462018 TTTTGACTTATATCTAAATAATTATATTCAGTGTTTTAATTTTATTCTTTTTACATATCATTTAA
1 TTTTGACTTATATCTAAATAATTATATTCAGTGTTTTAATTTTATTCTTTTTACATATCATTTAA
* *
462083 GAGTTTGTTTTTGTCTGCTTCTATTACATATTTATTCCTTTGATTTTATGACACAATTTTTTCTA
66 GAGTTTGTTTTTGTCTGCTTCTATGACATATTTATTCCTTGGATTTTATGACACAATTTTTTCTA
* *
462148 TCATTATAGTAGTTTGACGTTTCATGTTACATTTATCACAATACATTTTCTGATCAAGAAATGTC
131 TCATTATAGTAGTTTGACATTTCATGTTACATTTATCACAATACATCTTCTGATCAAGAAATGTC
*
462213 GACGATGTTTCATAATTGGATCTCA
196 GACGATGTTTCATAATTAGATCTCA
462238 TTTTG
1 TTTTG
462243 CAATAGTTTA
Statistics
Matches: 219, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
220 219 1.00
ACGTcount: A:0.27, C:0.13, G:0.11, T:0.49
Consensus pattern (220 bp):
TTTTGACTTATATCTAAATAATTATATTCAGTGTTTTAATTTTATTCTTTTTACATATCATTTAA
GAGTTTGTTTTTGTCTGCTTCTATGACATATTTATTCCTTGGATTTTATGACACAATTTTTTCTA
TCATTATAGTAGTTTGACATTTCATGTTACATTTATCACAATACATCTTCTGATCAAGAAATGTC
GACGATGTTTCATAATTAGATCTCA
Found at i:466927 original size:12 final size:12
Alignment explanation
Indices: 466912--466950 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
466902 TTTTTTTCCT
466912 AATTTTAAAATA
1 AATTTTAAAATA
466924 AATTTTAAATATA
1 AATTTTAAA-ATA
* *
466937 TATTTAAAAATA
1 AATTTTAAAATA
466949 AA
1 AA
466951 AAAATAGTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
AATTTTAAAATA
Found at i:469532 original size:59 final size:59
Alignment explanation
Indices: 469379--469670 Score: 220
Period size: 59 Copynumber: 4.9 Consensus size: 59
469369 TGAGCCATAG
* * * * * *
469379 ACTATTAAAAGTTATAAAATAGTTTTTAAATTATATAGG-GTTGCATTGTTGATTTTCTCA
1 ACTATTAAAAGTTCTAAAATAGTCTTCAAATTATAT-GGTGTTGCTTTGTTGA-GTACTCA
* * * * * *
469439 ACTATTAATAGTTAC-AAAATTGTCTCCAAGTTATACGGTGTTGTTTTGTTGAGTACT-A
1 ACTATTAAAAGTT-CTAAAATAGTCTTCAAATTATATGGTGTTGCTTTGTTGAGTACTCA
* * *
469497 TACTATTAAAAGTTCTAAAATAGTCTTCAAATTATATAGTGTTGCATTGTTGA-TTCTCCCA
1 -ACTATTAAAAGTTCTAAAATAGTCTTCAAATTATATGGTGTTGCTTTGTTGAGTACT--CA
* * * * *
469558 ACTATTAATAGTTAC-AAAATAGTCTCCAAATTATATGGTATTGTTTTGTTGAGTCAC-CG
1 ACTATTAAAAGTT-CTAAAATAGTCTTCAAATTATATGGTGTTGCTTTGTTGAGT-ACTCA
* * * * * *
469617 ACTATTAAAAATTATAAAATAATC-TCTAAATTATAGGGTGATGCTTTATTGAGT
1 ACTATTAAAAGTTCTAAAATAGTCTTC-AAATTATATGGTGTTGCTTTGTTGAGT
469671 CCCACGACTA
Statistics
Matches: 181, Mismatches: 39, Indels: 25
0.74 0.16 0.10
Matches are distributed among these distances:
58 6 0.03
59 89 0.49
60 82 0.45
61 3 0.02
62 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (59 bp):
ACTATTAAAAGTTCTAAAATAGTCTTCAAATTATATGGTGTTGCTTTGTTGAGTACTCA
Found at i:469575 original size:119 final size:119
Alignment explanation
Indices: 469364--469651 Score: 400
Period size: 119 Copynumber: 2.4 Consensus size: 119
469354 AGCACGTTGC
* * * *
469364 TTTGTTGAGCCATAGACTATTAAAAGTTATAAAATAGTTTTTAAATTATATAGGGTTGCATTGTT
1 TTTGTTGAGTCACAGACTATTAAAAGTTATAAAATAGTCTTCAAATTATATAGGGTTGCATTGTT
* * * * *
469429 GATTTTCTCAACTATTAATAGTTACAAAATTGTCTCCAAGTTATACGGTGTTGT
66 GATTCTCCCAACTATTAATAGTTACAAAATAGTCTCCAAATTATACGGTATTGT
* * *
469483 TTTGTTGAGT-ACTATACTATTAAAAGTTCTAAAATAGTCTTCAAATTATATAGTGTTGCATTGT
1 TTTGTTGAGTCAC-AGACTATTAAAAGTTATAAAATAGTCTTCAAATTATATAGGGTTGCATTGT
*
469547 TGATTCTCCCAACTATTAATAGTTACAAAATAGTCTCCAAATTATATGGTATTGT
65 TGATTCTCCCAACTATTAATAGTTACAAAATAGTCTCCAAATTATACGGTATTGT
* * *
469602 TTTGTTGAGTCACCGACTATTAAAAATTATAAAATAATC-TCTAAATTATA
1 TTTGTTGAGTCACAGACTATTAAAAGTTATAAAATAGTCTTC-AAATTATA
469652 GGGTGATGCT
Statistics
Matches: 148, Mismatches: 18, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
118 3 0.02
119 143 0.97
120 2 0.01
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.41
Consensus pattern (119 bp):
TTTGTTGAGTCACAGACTATTAAAAGTTATAAAATAGTCTTCAAATTATATAGGGTTGCATTGTT
GATTCTCCCAACTATTAATAGTTACAAAATAGTCTCCAAATTATACGGTATTGT
Found at i:469607 original size:60 final size:60
Alignment explanation
Indices: 469379--469696 Score: 245
Period size: 60 Copynumber: 5.3 Consensus size: 60
469369 TGAGCCATAG
* * ** * *
469379 ACTATTAAAAGTTATAAAATAGTTTTTAAATTATATAGG-GTTGCATTGTTGATTTTCTCA
1 ACTATTAAAAGTTACAAAATAGTCTCCAAATTATAT-GGTGTTGCATTGTTGATTCTCCCA
* * * * ** *
469439 ACTATTAATAGTTACAAAATTGTCTCCAAGTTATACGGTGTTGTTTTGTTGAGTACT---A
1 ACTATTAAAAGTTACAAAATAGTCTCCAAATTATATGGTGTTGCATTGTTGA-TTCTCCCA
* *
469497 TACTATTAAAAGTT-CTAAAATAGTCTTCAAATTATATAGTGTTGCATTGTTGATTCTCCCA
1 -ACTATTAAAAGTTAC-AAAATAGTCTCCAAATTATATGGTGTTGCATTGTTGATTCTCCCA
* * ** * * *
469558 ACTATTAATAGTTACAAAATAGTCTCCAAATTATATGGTATTGTTTTGTTGAGTC-ACCG
1 ACTATTAAAAGTTACAAAATAGTCTCCAAATTATATGGTGTTGCATTGTTGATTCTCCCA
* * * * * * * * * *
469617 ACTATTAAAAATTATAAAATAATCTCTAAATTATAGGGTGATGCTTTATTGAGTC-CCACG
1 ACTATTAAAAGTTACAAAATAGTCTCCAAATTATATGGTGTTGCATTGTTGATTCTCC-CA
*
469677 ACTATTGAAAGTTACAAAAT
1 ACTATTAAAAGTTACAAAAT
469697 GGTCACTTAG
Statistics
Matches: 205, Mismatches: 44, Indels: 18
0.77 0.16 0.07
Matches are distributed among these distances:
58 5 0.02
59 92 0.45
60 104 0.51
61 4 0.02
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.40
Consensus pattern (60 bp):
ACTATTAAAAGTTACAAAATAGTCTCCAAATTATATGGTGTTGCATTGTTGATTCTCCCA
Found at i:469671 original size:59 final size:60
Alignment explanation
Indices: 469439--469696 Score: 184
Period size: 59 Copynumber: 4.3 Consensus size: 60
469429 GATTTTCTCA
* ** * * * * * *
469439 ACTATTAATAGTTACAAAATTGTCTCCAAGTTATACGGTGTTGTTTTGTTGAGT-ACTA-T
1 ACTATTAAAAGTTACAAAATAATCTCCAAATTATAGGGTATTGCTTTATTGAGTCAC-ACG
* * ** * * * * * * *
469498 ACTATTAAAAGTT-CTAAAATAGTCTTCAAATTATATAGTGTTGCATTGTTGATTCTCCCA
1 ACTATTAAAAGTTAC-AAAATAATCTCCAAATTATAGGGTATTGCTTTATTGAGTCACACG
* * * * *
469558 ACTATTAATAGTTACAAAATAGTCTCCAAATTATATGGTATTGTTTTGTTGAGTCAC-CG
1 ACTATTAAAAGTTACAAAATAATCTCCAAATTATAGGGTATTGCTTTATTGAGTCACACG
* * * *
469617 ACTATTAAAAATTATAAAATAATCTCTAAATTATAGGGTGA-TGCTTTATTGAGTCCCACG
1 ACTATTAAAAGTTACAAAATAATCTCCAAATTATAGGGT-ATTGCTTTATTGAGTCACACG
*
469677 ACTATTGAAAGTTACAAAAT
1 ACTATTAAAAGTTACAAAAT
469697 GGTCACTTAG
Statistics
Matches: 160, Mismatches: 33, Indels: 11
0.78 0.16 0.05
Matches are distributed among these distances:
58 1 0.01
59 90 0.56
60 68 0.43
61 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.38
Consensus pattern (60 bp):
ACTATTAAAAGTTACAAAATAATCTCCAAATTATAGGGTATTGCTTTATTGAGTCACACG
Found at i:469681 original size:119 final size:119
Alignment explanation
Indices: 469376--469696 Score: 335
Period size: 119 Copynumber: 2.7 Consensus size: 119
469366 TGTTGAGCCA
* * * * * * * * * * *
469376 TAGACTATTAAAAGTTATAAAATAGTTTTTAAATTATATAGGGTTGCATTGTTGATTTTCTCAAC
1 TAGACTATTAAAAATTATAAAATAATCTTCAAATTATAGAGTGATGCATTATTGAGTCTCCCAAC
* * *
469441 TATTAATAGTTACAAAATTGTCTCCAAGTTATACGGTGTTGTTTTGTTGAGTAC
66 TATTAATAGTTACAAAATAGTCTCCAAATTATACGGTATTGTTTTGTTGAGTAC
* * * * * * * *
469495 TATACTATTAAAAGTTCTAAAATAGTCTTCAAATTATATAGTGTTGCATTGTTGATTCTCCCAAC
1 TAGACTATTAAAAATTATAAAATAATCTTCAAATTATAGAGTGATGCATTATTGAGTCTCCCAAC
*
469560 TATTAATAGTTACAAAATAGTCTCCAAATTATATGGTATTGTTTTGTTGAGTCAC
66 TATTAATAGTTACAAAATAGTCTCCAAATTATACGGTATTGTTTTGTTGAGT-AC
* * * *
469615 -CGACTATTAAAAATTATAAAATAATC-TCTAAATTATAGGGTGATGCTTTATTGAGTC-CCACG
1 TAGACTATTAAAAATTATAAAATAATCTTC-AAATTATAGAGTGATGCATTATTGAGTCTCC-CA
469677 ACTATTGAA-AGTTACAAAAT
64 ACTATT-AATAGTTACAAAAT
469697 GGTCACTTAG
Statistics
Matches: 175, Mismatches: 23, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
118 4 0.02
119 167 0.95
120 4 0.02
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.40
Consensus pattern (119 bp):
TAGACTATTAAAAATTATAAAATAATCTTCAAATTATAGAGTGATGCATTATTGAGTCTCCCAAC
TATTAATAGTTACAAAATAGTCTCCAAATTATACGGTATTGTTTTGTTGAGTAC
Found at i:472816 original size:23 final size:23
Alignment explanation
Indices: 472697--472816 Score: 118
Period size: 23 Copynumber: 5.3 Consensus size: 23
472687 AAAGTGCCAT
* * *
472697 ATAGAAATATCTCGAAGGACCAC
1 ATAGAATTATCCCGAAGGACCGC
* *
472720 ATAGTATTGTCCCGAAGGA-C-C
1 ATAGAATTATCCCGAAGGACCGC
* *
472741 ACAGTATTATCCCGAAGGACCGC
1 ATAGAATTATCCCGAAGGACCGC
* *
472764 GTAGAAATATCCCGAAGGACCGC
1 ATAGAATTATCCCGAAGGACCGC
* * *
472787 GTAGAATTGTCCCGAAAGACCGC
1 ATAGAATTATCCCGAAGGACCGC
472810 ATAGAAT
1 ATAGAAT
472817 CCTCGACTCT
Statistics
Matches: 81, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
21 18 0.22
22 2 0.02
23 61 0.75
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.18
Consensus pattern (23 bp):
ATAGAATTATCCCGAAGGACCGC
Found at i:480155 original size:20 final size:22
Alignment explanation
Indices: 480132--480180 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
480122 CCTTTCTGTT
480132 TTTTTATTATC-TATTAT-TAA
1 TTTTTATTATCTTATTATATAA
* *
480152 TTTTTAGTATCTTATTATATAT
1 TTTTTATTATCTTATTATATAA
480174 TTTTTAT
1 TTTTTAT
480181 ATTATATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 10 0.42
21 6 0.25
22 8 0.33
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTTTATTATCTTATTATATAA
Found at i:480167 original size:21 final size:21
Alignment explanation
Indices: 480132--480192 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
480122 CCTTTCTGTT
*
480132 TTTTTATTATCTATTAT-TAA
1 TTTTTAGTATCTATTATATAA
*
480152 TTTTTAGTATCTTATTATATAT
1 TTTTTAGTATC-TATTATATAA
480174 TTTTTA-TAT-TATATATATA
1 TTTTTAGTATCTAT-TATATA
480193 TATATATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
19 3 0.08
20 16 0.44
21 9 0.25
22 8 0.22
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTTAGTATCTATTATATAA
Found at i:480215 original size:47 final size:48
Alignment explanation
Indices: 480130--480247 Score: 124
Period size: 49 Copynumber: 2.5 Consensus size: 48
480120 ATCCTTTCTG
* *
480130 TTTTTT-TATTATCTAT-TAT-TA-ATTTTTAGTATCTTATTATATA-
1 TTTTTTATATTATATATATATATATATTATTAGTATCTTATTATATAC
*
480173 TTTTTTATATTATATATATATATATATTATTAGTTAT-TTATTATTTAC
1 TTTTTTATATTATATATATATATATATTATTAG-TATCTTATTATATAC
*
480221 TATTATTA-ATGTATATATATATATATA
1 T-TTTTTATAT-TATATATATATATATA
480248 GTTTTCTCTT
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
43 6 0.10
44 9 0.14
45 3 0.05
46 2 0.03
47 16 0.25
48 6 0.10
49 21 0.33
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (48 bp):
TTTTTTATATTATATATATATATATATTATTAGTATCTTATTATATAC
Found at i:483435 original size:20 final size:20
Alignment explanation
Indices: 483406--483449 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
483396 TAAATAAATT
483406 TTGA-AGGTGCATCGATGCA
1 TTGAGAGGTGCATCGATGCA
483425 TTGAGAGGTGCATCGATGCA
1 TTGAGAGGTGCATCGATGCA
483445 -TGAGA
1 TTGAGA
483450 ATTTCAAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.27, C:0.14, G:0.34, T:0.25
Consensus pattern (20 bp):
TTGAGAGGTGCATCGATGCA
Found at i:484123 original size:18 final size:18
Alignment explanation
Indices: 484100--484152 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
484090 GTTCTTAAGG
*
484100 AGTGGTCCTTCAGGACAT
1 AGTGGTCCTTCGGGACAT
*
484118 AGTGGTCCTTTGGGACAT
1 AGTGGTCCTTCGGGACAT
484136 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
484153 AATATACAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.19, C:0.21, G:0.32, T:0.28
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:484519 original size:40 final size:40
Alignment explanation
Indices: 484464--484542 Score: 158
Period size: 40 Copynumber: 2.0 Consensus size: 40
484454 ACGCTATGTA
484464 TATATATATATATACATAAATAATGAAGTGGTGAATTATG
1 TATATATATATATACATAAATAATGAAGTGGTGAATTATG
484504 TATATATATATATACATAAATAATGAAGTGGTGAATTAT
1 TATATATATATATACATAAATAATGAAGTGGTGAATTAT
484543 ATGATTAATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.46, C:0.03, G:0.14, T:0.38
Consensus pattern (40 bp):
TATATATATATATACATAAATAATGAAGTGGTGAATTATG
Found at i:486345 original size:7 final size:7
Alignment explanation
Indices: 486328--486356 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
486318 ACATCATGCA
486328 TTGCA-T
1 TTGCATT
486334 TTGCATT
1 TTGCATT
486341 TTGCATT
1 TTGCATT
486348 TTGCATT
1 TTGCATT
486355 TT
1 TT
486357 ATTTATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.23
7 17 0.77
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (7 bp):
TTGCATT
Found at i:486924 original size:21 final size:21
Alignment explanation
Indices: 486891--486930 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
486881 GCAAATAAGA
*
486891 TGGAAGAGAAGATTAAGATAT
1 TGGAAGAGAAGATGAAGATAT
**
486912 TGGAAGATCAGATGAAGAT
1 TGGAAGAGAAGATGAAGAT
486931 GGTCAAGGGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.30, T:0.23
Consensus pattern (21 bp):
TGGAAGAGAAGATGAAGATAT
Found at i:493392 original size:22 final size:22
Alignment explanation
Indices: 493364--493407 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
493354 GCCCTAAATT
*
493364 AAAAAAACATTAA-AAAAGAGAA
1 AAAAAAACA-AAAGAAAAGAGAA
493386 AAAAAAACAAAAGAAAAGAGAA
1 AAAAAAACAAAAGAAAAGAGAA
493408 GAGAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.80, C:0.05, G:0.11, T:0.05
Consensus pattern (22 bp):
AAAAAAACAAAAGAAAAGAGAA
Found at i:503699 original size:14 final size:14
Alignment explanation
Indices: 503680--503706 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
503670 AATCAGAACT
503680 TCAAGATTCCAGAA
1 TCAAGATTCCAGAA
503694 TCAAGATTCCAGA
1 TCAAGATTCCAGA
503707 CAAGCAACCA
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:0.15, T:0.22
Consensus pattern (14 bp):
TCAAGATTCCAGAA
Found at i:506268 original size:21 final size:20
Alignment explanation
Indices: 506244--506413 Score: 74
Period size: 20 Copynumber: 8.6 Consensus size: 20
506234 ATCCTTTCTG
506244 TTTTTTATTATC-TATTACTA
1 TTTTTTATTATCTTATTA-TA
* *
506264 CTTTTTAGTATCTTATTATA
1 TTTTTTATTATCTTATTATA
506284 TTTTTTA-TAT-TATATATATA
1 TTTTTTATTATCT-TAT-TATA
*
506304 TATATATATATATAT-TTAATTATA
1 T-T-T-TTTAT-TATCTT-ATTATA
*
506328 TCTTTTATTAT-TT-TT-T-
1 TTTTTTATTATCTTATTATA
** * * *
506344 TTCCTT-TTATCCT-TTCTG
1 TTTTTTATTATCTTATTATA
506362 TTTTTTATTATC-TATTACTA
1 TTTTTTATTATCTTATTA-TA
* *
506382 CTTTTTAGTATCTTATTATA
1 TTTTTTATTATCTTATTATA
506402 TTTTTATATTAT
1 TTTTT-TATTAT
506414 ATATATATAT
Statistics
Matches: 115, Mismatches: 18, Indels: 33
0.69 0.11 0.20
Matches are distributed among these distances:
15 4 0.03
16 6 0.05
17 2 0.02
18 8 0.07
19 13 0.11
20 45 0.39
21 20 0.17
22 2 0.02
23 3 0.03
24 6 0.05
25 6 0.05
ACGTcount: A:0.26, C:0.08, G:0.02, T:0.64
Consensus pattern (20 bp):
TTTTTTATTATCTTATTATA
Found at i:506296 original size:14 final size:15
Alignment explanation
Indices: 506277--506328 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 15
506267 TTTAGTATCT
*
506277 TATTATAT-TTTTTA
1 TATTATATATATTTA
*
506291 TATTATATATATATA
1 TATTATATATATTTA
506306 TATATATATATATTTA
1 TAT-TATATATATTTA
506322 -ATTATAT
1 TATTATAT
506329 CTTTTATTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 13 0.39
15 9 0.27
16 11 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTATATATATTTA
Found at i:506299 original size:2 final size:2
Alignment explanation
Indices: 506289--506318 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
506279 TTATATTTTT
506289 TA TA T- 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 T
506319 TTAATTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:506324 original size:118 final size:117
Alignment explanation
Indices: 506192--506431 Score: 453
Period size: 118 Copynumber: 2.0 Consensus size: 117
506182 TAGTCCGTAT
*
506192 TATATATATTTAATTATATCTTTTATTATTATTTTTCTTTTTATCCTTTCTGTTTTTTATTATCT
1 TATATATATTTAATTATATCTTTTATTATTATTTTTCCTTTTATCCTTTCTGTTTTTTATTATCT
506257 ATTACTACTTTTTAGTATCTTATTATATTTTTTATATTATATATATATATATA
66 ATTACTACTTTTTAGTATCTTATTATA-TTTTTATATTATATATATATATATA
*
506310 TATATATATTTAATTATATCTTTTATTATTTTTTTTCCTTTTATCCTTTCTGTTTTTTATTATCT
1 TATATATATTTAATTATATCTTTTATTATTATTTTTCCTTTTATCCTTTCTGTTTTTTATTATCT
506375 ATTACTACTTTTTAGTATCTTATTATATTTTTATATTATATATATATATATA
66 ATTACTACTTTTTAGTATCTTATTATATTTTTATATTATATATATATATATA
506427 TATAT
1 TATAT
506432 TAGTTATTTA
Statistics
Matches: 120, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
117 30 0.25
118 90 0.75
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.63
Consensus pattern (117 bp):
TATATATATTTAATTATATCTTTTATTATTATTTTTCCTTTTATCCTTTCTGTTTTTTATTATCT
ATTACTACTTTTTAGTATCTTATTATATTTTTATATTATATATATATATATA
Found at i:507230 original size:34 final size:32
Alignment explanation
Indices: 507168--507237 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
507158 TCTTACAAAC
* * *
507168 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACATT
*
507200 TCCCTAGCTTTTACACGGGATAAGCTAGAACATT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACATT
507234 TCCC
1 TCCC
507238 CTTTATAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 5 0.16
34 20 0.62
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACATT
Found at i:510735 original size:38 final size:38
Alignment explanation
Indices: 510666--510876 Score: 205
Period size: 38 Copynumber: 5.8 Consensus size: 38
510656 AATAATATAG
**
510666 TATAGTTTTT-GAAAA-TATTTTTGAAAACATATAATA
1 TATAGTTTTTAGAAAACGGTTTTTGAAAACATATAATA
*
510702 TATAGTTTTTAGAAAACGGTTTTTGAAAGCATATAATA
1 TATAGTTTTTAGAAAACGGTTTTTGAAAACATATAATA
*
510740 TATAGTTTTTAGAAAACGGTTTTTGAAAGCATAT-A-A
1 TATAGTTTTTAGAAAACGGTTTTTGAAAACATATAATA
* ** *
510776 TAT-GGTTTT-GAAAACACATTTTTGAAAACGTATAATA
1 TATAGTTTTTAGAAAAC-GGTTTTTGAAAACATATAATA
* *
510813 TATAG--TTTA-AAAACAGTTTTTGAAAATATAT-ATAA
1 TATAGTTTTTAGAAAACGGTTTTTGAAAACATATAAT-A
*
510848 TATAG-TTTT-GAAAAC-ATATTTTGAAAACA
1 TATAGTTTTTAGAAAACGGT-TTTTGAAAACA
510877 CACACATATA
Statistics
Matches: 150, Mismatches: 14, Indels: 22
0.81 0.08 0.12
Matches are distributed among these distances:
34 8 0.05
35 38 0.25
36 41 0.27
37 10 0.07
38 53 0.35
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.40
Consensus pattern (38 bp):
TATAGTTTTTAGAAAACGGTTTTTGAAAACATATAATA
Found at i:513328 original size:11 final size:12
Alignment explanation
Indices: 513312--513341 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
513302 AATTAACCCC
513312 TTCTTTTC-TTT
1 TTCTTTTCTTTT
513323 TTCTTTTCTTTT
1 TTCTTTTCTTTT
513335 TTCTTTT
1 TTCTTTT
513342 TGCTGTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (12 bp):
TTCTTTTCTTTT
Found at i:513850 original size:2 final size:2
Alignment explanation
Indices: 513843--513874 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
513833 AACTGCTTTA
513843 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
513875 TCATATCCGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:523752 original size:6 final size:6
Alignment explanation
Indices: 523743--523769 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
523733 CCATATATAT
523743 AATTTA AATTTA AATTTA AATTTA AAT
1 AATTTA AATTTA AATTTA AATTTA AAT
523770 GATTAGGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTTA
Found at i:524903 original size:160 final size:161
Alignment explanation
Indices: 524629--524964 Score: 512
Period size: 160 Copynumber: 2.1 Consensus size: 161
524619 CGGTATTGAA
* * * * *
524629 ATGATAAAACCGGTAAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGA
1 ATGATAAAACCGGTAAAACACTACCGGATACATTGAAAGTGTCGATACTTTAATACAAGGATCGA
* * **
524694 CACTTCGTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTAAAAATGT
66 CACTTCGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAAAAAAAAT
*
524759 ATCGATCCAAAACGATATACCAGGTAAAAAT
131 ATCGATCCAAAACGATATAACAGGTAAAAAT
* *
524790 ATGATAAAACCGGTAAAACATTACCGGATATATTGAAAGTGTCGATACTTT-ATACAAGGATCGA
1 ATGATAAAACCGGTAAAACACTACCGGATACATTGAAAGTGTCGATACTTTAATACAAGGATCGA
* ** *
524854 CACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATACTTTAAAAAAAAT
66 CACTTCGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAAAAAAAAT
*
524919 ATCGATCCACAACGATATAACAGGTAAAAAT
131 ATCGATCCAAAACGATATAACAGGTAAAAAT
524950 ATGATAAAACCGGTA
1 ATGATAAAACCGGTA
524965 TCAAAATGAT
Statistics
Matches: 158, Mismatches: 17, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
160 113 0.72
161 45 0.28
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (161 bp):
ATGATAAAACCGGTAAAACACTACCGGATACATTGAAAGTGTCGATACTTTAATACAAGGATCGA
CACTTCGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAAAAAAAAT
ATCGATCCAAAACGATATAACAGGTAAAAAT
Found at i:524964 original size:20 final size:19
Alignment explanation
Indices: 524941--524987 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
524931 CGATATAACA
524941 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
524961 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
*
524981 AGTAAAA
1 GGTAAAA
524988 CGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.55, C:0.11, G:0.15, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:527239 original size:21 final size:21
Alignment explanation
Indices: 527213--527277 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
527203 AAGACAATCA
527213 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAT
*
527234 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAT
* *
527255 AGAGTCGAAGATACACTTGAT
1 AGAGTCGAAGAGAAACTTGAT
527276 AG
1 AG
527278 GCATAAGGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.42, C:0.11, G:0.29, T:0.18
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAT
Found at i:529181 original size:19 final size:19
Alignment explanation
Indices: 529157--529205 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
529147 AATGTAGGGT
529157 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
529176 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
529195 TAATTTTGTAT
1 TAATTTTGTAT
529206 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:529793 original size:200 final size:200
Alignment explanation
Indices: 529439--531195 Score: 3141
Period size: 200 Copynumber: 8.8 Consensus size: 200
529429 AATTTACAAT
* * *
529439 ATGGCAAATAGTGTGCAACCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* * ** *
529503 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGAAACAAGTATATCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
529568 ATGAGAGAATAGGTCTAAATAATGTATCGACAATTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
529633 AATGA
196 AATGA
* * * *
529638 ATGGAAAACAGGGTGCAACCATAAAGTGTTGATCCATATATAAAAAGTGTCGATCTCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
529703 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCAGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
529768 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
529833 AATGA
196 AATGA
529838 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
529903 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
529968 ATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
530033 AATGA
196 AATGA
*
530038 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCTATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
530103 C-AAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
530167 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
530232 AATGA
196 AATGA
*
530237 ATGGCAAACAGGGTGCAACAGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
530302 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
530367 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
530432 AATGA
196 AATGA
*
530437 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCGATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
530501 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* * *
530566 ATGAGA-TATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCTAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
530630 AATGA
196 AATGA
* *
530635 ATGGCAAACAGGGTGCAACAATAAAGTGTCTATCCATATATAAAAAGTGTCGATCCGATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
530700 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* *
530765 ATAAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCAAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
530830 AATGA
196 AATGA
530835 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* *
530900 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCTGTACAAGTATATCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* *
530965 ATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAT
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
531030 AATGA
196 AATGA
531035 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* * *
531100 CGAAACCCAAAAGTATAATGTATTAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* * *
531165 ATGGGAGAATTGG--TATAT-ATGTATCGACACT
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACT
531196 GTTTAATGTT
Statistics
Matches: 1503, Mismatches: 51, Indels: 10
0.96 0.03 0.01
Matches are distributed among these distances:
197 12 0.01
198 104 0.07
199 418 0.28
200 969 0.64
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
AATGA
Found at i:530200 original size:399 final size:400
Alignment explanation
Indices: 529439--531195 Score: 3141
Period size: 399 Copynumber: 4.4 Consensus size: 400
529429 AATTTACAAT
* * *
529439 ATGGCAAATAGTGTGCAACCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* * ** *
529503 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGAAACAAGTATATCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
529568 ATGAGAGAATAGGTCTAAATAATGTATCGACAATTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
* * * *
529633 AATGAATGGAAAACAGGGTGCAACCATAAAGTGTTGATCCATATATAAAAAGTGTCGATCTCATA
196 AATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATA
*
529698 AACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCA
261 AACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCG
529763 GTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGG
326 GTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGG
529828 TCCAGAATGA
391 TCCAGAATGA
529838 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
529903 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
529968 ATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
*
530033 AATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCTATATATAAAAAGTGTCGATCCCATA
196 AATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATA
530098 AACATC-AAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCG
261 AACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCG
530162 GTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGG
326 GTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGG
530227 TCCAGAATGA
391 TCCAGAATGA
*
530237 ATGGCAAACAGGGTGCAACAGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
530302 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
530367 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
*
530432 AATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCGATA
196 AATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATA
530496 AACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCG
261 AACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCG
* *
530561 GTTTTATGAGA-TATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGG
326 GTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGG
*
530625 TCTAGAATGA
391 TCCAGAATGA
* *
530635 ATGGCAAACAGGGTGCAACAATAAAGTGTCTATCCATATATAAAAAGTGTCGATCCGATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
530700 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* *
530765 ATAAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCAAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
530830 AATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATA
196 AATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATA
* *
530895 AACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCTGTACAAGTATATCG
261 AACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCG
*
530960 GTTTTATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGG
326 GTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGG
*
531025 TCCATAATGA
391 TCCAGAATGA
531035 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* * *
531100 CGAAACCCAAAAGTATAATGTATTAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* * *
531165 ATGGGAGAATTGG--TATAT-ATGTATCGACACT
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACT
531196 GTTTAATGTT
Statistics
Matches: 1309, Mismatches: 45, Indels: 10
0.96 0.03 0.01
Matches are distributed among these distances:
397 13 0.01
398 322 0.25
399 568 0.43
400 406 0.31
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (400 bp):
ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
AATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATA
AACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCG
GTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGG
TCCAGAATGA
Found at i:531738 original size:23 final size:23
Alignment explanation
Indices: 531707--531779 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
531697 ATAAGTAAAA
*
531707 ATATGATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGTTT
531730 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGTTT
* * *
531753 ATATAATGTAATAAGTAGTGCTT
1 ATATAATGTAATAGGTAGCGTTT
531776 ATAT
1 ATAT
531780 TGTAAAGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGTTT
Found at i:532227 original size:23 final size:22
Alignment explanation
Indices: 532196--532267 Score: 99
Period size: 23 Copynumber: 3.2 Consensus size: 22
532186 ATAGGTAAAA
*
532196 ATATGATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAG-GTTT
*
532219 ATATAATGTAATAGGTAGTTTT
1 ATATAATGTAATAGGTAGGTTT
*
532241 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAG-GTTT
532264 ATAT
1 ATAT
532268 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 21 0.48
23 23 0.52
ACGTcount: A:0.35, C:0.03, G:0.21, T:0.42
Consensus pattern (22 bp):
ATATAATGTAATAGGTAGGTTT
Found at i:532244 original size:22 final size:22
Alignment explanation
Indices: 532196--532259 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
532186 ATAGGTAAAA
* *
532196 ATATGATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAG-TTTT
532219 ATATAATGTAATAGGTAGTTTT
1 ATATAATGTAATAGGTAGTTTT
532241 ATATAATGTAATAGGTAGT
1 ATATAATGTAATAGGTAGT
532260 GCTTATATTG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 22 0.56
23 17 0.44
ACGTcount: A:0.36, C:0.02, G:0.22, T:0.41
Consensus pattern (22 bp):
ATATAATGTAATAGGTAGTTTT
Found at i:532715 original size:23 final size:23
Alignment explanation
Indices: 532684--532756 Score: 128
Period size: 23 Copynumber: 3.2 Consensus size: 23
532674 ATAGGTAAAA
*
532684 ATATGATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGTTT
532707 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGTTT
*
532730 ATATAATGTAATAGGTAGTGTTT
1 ATATAATGTAATAGGTAGCGTTT
532753 ATAT
1 ATAT
532757 TGTAAATTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.34, C:0.03, G:0.22, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGTTT
Found at i:532885 original size:489 final size:488
Alignment explanation
Indices: 531583--533154 Score: 2838
Period size: 488 Copynumber: 3.2 Consensus size: 488
531573 CAGACGAGTT
*
531583 TTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTT
1 TTAATATTATAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTT
* *
531648 AAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAAGTAAAAATATGA
66 AAAAAAAGTATCGATCTTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGA
*
531713 TGTAATAGGTAGCGTTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAAGTAGTGCTTAT
131 TGTAATAGGTAGCGTTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTAT
*
531778 ATTGTAAAGTATATATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATT
196 ATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATT
531843 TAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTAT
261 TAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTAT
531908 TTTTTACGTTACGGTATATATTATTATTAAATTAAAAAAATAAACATATATATTACATATTTTTT
326 TTTTTACGTTACGGTATATATTATTATTAAATTAAAAAAATAAACATATATATTACATATTTTTT
531973 ATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAAT
391 ATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAAT
532038 CAAATAATTTTTTGTGTAAATGAAATTATTAAA
456 CAAATAATTTTTTGTGTAAATGAAATTATTAAA
*
532071 TTAATATTATAGGTGGAAAACATGAAACACTGTTAAAAAAATTGAAACATAAATTACATAACTTT
1 TTAATATTATAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTT
532136 AAAAAAAGTATCGATCATTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATG
66 AAAAAAAGTATCGATC-TTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATG
*
532201 ATGTAATAGGTAGCGTTTATATAATGTAATAGGTAG-TTTTATATAATGTAATAGGTAGTGCTTA
130 ATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTA
532265 TATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAAT
195 TATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAAT
*
532330 TTAAGGTTATCTTTTAAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTA
260 TTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTA
532395 TTTTTTACGTTACGGTATATATTATTATTAAATTAAAAAAATAAACATATATATTACATATTTTT
325 TTTTTTACGTTACGGTATATATTATTATTAAATTAAAAAAATAAACATATATATTACATA-TTTT
532460 TTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAAT-TTTTATAAAATATCAAAACA
389 TTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACA
532524 ATC-AATAATTTTTTGTGTAAATGAAATTATTAAA
454 ATCAAATAATTTTTTGTGTAAATGAAATTATTAAA
*
532558 TTAATATTATAGGTGGAAAACATGAAACACTGTTAAAAAAAATTGAAACATAAATTACATAACTT
1 TTAATATTATAGGTGGAAAACATGAAACACTATT-AAAAAAATTGAAACATAAATTACATAACTT
532623 TAAAAAAAGTATCGATCATTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATAT
65 TAAAAAAAGTATCGATC-TTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATAT
*
532688 GATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGTTT
129 GATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTT
* * *
532753 ATATTGTAAATTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCATTGTGAAAAACATTAA
194 ATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAA
*
532818 TTTAAGGTTATCTTTTGAGTGAGTTTTAATATATTAATTTAGTAATTATAGGCGTCTAATGATTT
259 TTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTT
532883 ATTTTTTACGTTAC-G-ATATATTATTATTAAATTAAAAACAA-AAACATATATATTACATATTT
324 ATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAA-AATAAACATATATATTACATATTT
* *
532945 ATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAAC
388 TTTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAAC
* *
533010 AATCAAATAATTGTTTGTGCAAATGAAATTATTAAA
453 AATCAAATAATTTTTTGTGTAAATGAAATTATTAAA
* *
533046 TTAATATTGTAGGTGGAAAATATGAAACACTATT-AAAAAATTGAAACATAAATTACATAACTTT
1 TTAATATTATAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTT
533110 -AAAAAAGTATCGAT-TCTTTTTATAAAAAAGTATGGACACTTTCAA
66 AAAAAAAGTATCGATCT-TTTTTAT-AAAAAGTATGGACACTTTCAA
533155 CATATTATAA
Statistics
Matches: 1053, Mismatches: 22, Indels: 21
0.96 0.02 0.02
Matches are distributed among these distances:
483 1 0.00
484 7 0.01
485 35 0.03
486 76 0.07
487 129 0.12
488 511 0.49
489 294 0.28
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.40
Consensus pattern (488 bp):
TTAATATTATAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTT
AAAAAAAGTATCGATCTTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGA
TGTAATAGGTAGCGTTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTAT
ATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATT
TAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTAT
TTTTTACGTTACGGTATATATTATTATTAAATTAAAAAAATAAACATATATATTACATATTTTTT
ATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAAT
CAAATAATTTTTTGTGTAAATGAAATTATTAAA
Found at i:541673 original size:66 final size:66
Alignment explanation
Indices: 541562--541690 Score: 161
Period size: 66 Copynumber: 2.0 Consensus size: 66
541552 TGTCTGTCTG
* * * *
541562 TTCATGTATATAATATTTATCACATTTCACATTATCATACGTGGATATTATTTTGA-ATAAAATT
1 TTCATGCATATAATATTAATCACATGTCACATTATCATACATGGATATTATTTT-ATATAAAATT
541626 TA
65 TA
** * **
541628 TTCATGCATATAATATTAATCACATGTCATGTTATTATTTATGGATATTATTTTATATAAAAT
1 TTCATGCATATAATATTAATCACATGTCACATTATCATACATGGATATTATTTTATATAAAAT
541691 AAAAGATTGG
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
65 1 0.02
66 52 0.98
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.47
Consensus pattern (66 bp):
TTCATGCATATAATATTAATCACATGTCACATTATCATACATGGATATTATTTTATATAAAATTT
A
Found at i:541845 original size:60 final size:59
Alignment explanation
Indices: 541716--541846 Score: 147
Period size: 60 Copynumber: 2.2 Consensus size: 59
541706 ACAAATTAGT
* * * * *
541716 TCCTCAATTATAGGACGTTGATTTGTTAAGTCATTTGATTATTAAAAGTTATAAAATGA
1 TCCTCAACTATAGGACGCTCATTTGTTAAGTCATTTGACTATTAAAAGTTACAAAATGA
* * * *
541775 TCCTTGAACTATAGGACGCTCCTTTGTTGAGTC-TTTCGACTATTAAAAGTTACAAAATGG
1 TCC-TCAACTATAGGACGCTCATTTGTTAAGTCATTT-GACTATTAAAAGTTACAAAATGA
541835 TCACTCAACTAT
1 TC-CTCAACTAT
541847 TCATATAGTC
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
59 6 0.10
60 52 0.88
61 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (59 bp):
TCCTCAACTATAGGACGCTCATTTGTTAAGTCATTTGACTATTAAAAGTTACAAAATGA
Found at i:542028 original size:28 final size:28
Alignment explanation
Indices: 541985--542039 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
541975 GTCCGTTTAT
* * *
541985 ATTATGTTGTCGAGCTAGTGCTTAAAAC
1 ATTATGTTGTCAAGCTAATCCTTAAAAC
542013 ATTATGTTGTCAAGCTAATCCTTAAAA
1 ATTATGTTGTCAAGCTAATCCTTAAAA
542040 GGAATGGCGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (28 bp):
ATTATGTTGTCAAGCTAATCCTTAAAAC
Found at i:545677 original size:17 final size:16
Alignment explanation
Indices: 545655--545700 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
545645 TTTAAGAATC
*
545655 TTTAATCTTTTTTTATT
1 TTTAAT-TTTTTTTATA
*
545672 TTTAATATTTTATTATA
1 TTTAAT-TTTTTTTATA
545689 TTTAATTTTTTT
1 TTTAATTTTTTT
545701 CACAAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTAATTTTTTTTATA
Found at i:554582 original size:6 final size:6
Alignment explanation
Indices: 554571--554608 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
554561 ATGAGAGCCT
* *
554571 GATGAG GATGAG GATGAG GATGAG GAAGAG GAAGAG GA
1 GATGAG GATGAG GATGAG GATGAG GATGAG GATGAG GA
554609 AGGCATGTGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.39, C:0.00, G:0.50, T:0.11
Consensus pattern (6 bp):
GATGAG
Found at i:557642 original size:2 final size:2
Alignment explanation
Indices: 557635--557698 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
557625 CAATTTAGTT
557635 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
557677 TA -A TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
557699 CATTTATTAA
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:560868 original size:58 final size:56
Alignment explanation
Indices: 560774--560896 Score: 158
Period size: 58 Copynumber: 2.2 Consensus size: 56
560764 GTTGTGTAAT
* *
560774 CTTTGTTTCGAATGACAACATGCAGTGCAGAAAACTTCTTTGTGTTCGGTTTTAGACG
1 CTTTGTTTCGAATGACAACATGCAGTGCAGAAAAC-T-TATGTGTTCAGTTTTAGACG
** **
560832 CTTTGTTTCGAATGAC-ACTATGCAGTGCAGGGAACTTATGTGTTCAGTTTTAGGTG
1 CTTTGTTTCGAATGACAAC-ATGCAGTGCAGAAAACTTATGTGTTCAGTTTTAGACG
560888 CTTTGTTTC
1 CTTTGTTTC
560897 AGGGTCACGC
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
56 25 0.43
57 3 0.05
58 30 0.52
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.39
Consensus pattern (56 bp):
CTTTGTTTCGAATGACAACATGCAGTGCAGAAAACTTATGTGTTCAGTTTTAGACG
Found at i:562136 original size:59 final size:59
Alignment explanation
Indices: 562044--562165 Score: 244
Period size: 59 Copynumber: 2.1 Consensus size: 59
562034 CAGAAAATGA
562044 TTCAATGTATTCTTGACTCTCCCACAGTAGGATCTGGTAATCTCTATCTATATCCTTAT
1 TTCAATGTATTCTTGACTCTCCCACAGTAGGATCTGGTAATCTCTATCTATATCCTTAT
562103 TTCAATGTATTCTTGACTCTCCCACAGTAGGATCTGGTAATCTCTATCTATATCCTTAT
1 TTCAATGTATTCTTGACTCTCCCACAGTAGGATCTGGTAATCTCTATCTATATCCTTAT
562162 TTCA
1 TTCA
562166 GTTAAATTAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 63 1.00
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.41
Consensus pattern (59 bp):
TTCAATGTATTCTTGACTCTCCCACAGTAGGATCTGGTAATCTCTATCTATATCCTTAT
Found at i:562690 original size:34 final size:34
Alignment explanation
Indices: 562644--562708 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
562634 GGTGTCTGCA
562644 AGTTAAAAAAAGAATTACTTGAAGAAAGCTATTC
1 AGTTAAAAAAAGAATTACTTGAAGAAAGCTATTC
*
562678 AGTTAAAGAAAGAATTACTTGAAGAAAGCTA
1 AGTTAAAAAAAGAATTACTTGAAGAAAGCTA
562709 GTTGAATAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.51, C:0.08, G:0.17, T:0.25
Consensus pattern (34 bp):
AGTTAAAAAAAGAATTACTTGAAGAAAGCTATTC
Found at i:565477 original size:19 final size:20
Alignment explanation
Indices: 565439--565506 Score: 59
Period size: 19 Copynumber: 3.5 Consensus size: 20
565429 AAAGTTTCAT
*
565439 AATATATATATATTTGTAGA
1 AATATATATATATTTATAGA
*
565459 AATAT-TATTTATTTATAGA
1 AATATATATATATTTATAGA
*** * *
565478 TGCAT-TTTATTTTTATAGA
1 AATATATATATATTTATAGA
565497 AATATATATA
1 AATATATATA
565507 ATAGAAGGTA
Statistics
Matches: 35, Mismatches: 12, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
19 27 0.77
20 8 0.23
ACGTcount: A:0.41, C:0.01, G:0.07, T:0.50
Consensus pattern (20 bp):
AATATATATATATTTATAGA
Found at i:570818 original size:20 final size:20
Alignment explanation
Indices: 570767--570819 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
570757 AACTTAATAT
*
570767 TATTATTTTTAAATATTAAAA
1 TATTATTTTT-ATTATTAAAA
*
570788 TAATT-TATTTATTATTAAAA
1 T-ATTATTTTTATTATTAAAA
570808 TATTATTTTTAT
1 TATTATTTTTAT
570820 AATTTTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
19 3 0.11
20 16 0.59
21 5 0.19
22 3 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TATTATTTTTATTATTAAAA
Found at i:571005 original size:30 final size:33
Alignment explanation
Indices: 570945--571026 Score: 89
Period size: 32 Copynumber: 2.5 Consensus size: 33
570935 AGTATATCTT
* * *
570945 ATATTATTATAATATAATTGATTATTTTATTA-TA
1 ATATTAATA-AATATAA-TGATTATATTATTAGAA
570979 ATATTAA-AAATATAAT-ATTATATTATTAGAA
1 ATATTAATAAATATAATGATTATATTATTAGAA
*
571010 ATATTAATTAATATAAT
1 ATATTAATAAATATAAT
571027 TTTAAATATT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
30 11 0.26
31 9 0.21
32 15 0.36
33 1 0.02
34 6 0.14
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (33 bp):
ATATTAATAAATATAATGATTATATTATTAGAA
Found at i:571043 original size:24 final size:24
Alignment explanation
Indices: 570975--571071 Score: 78
Period size: 24 Copynumber: 4.1 Consensus size: 24
570965 ATTATTTTAT
**
570975 TATAATATTAAAAATATAATATT-A
1 TATAATATT-AAAATATTTTATTAA
*
570999 TAT--TATTAGAAATA-TTAATTAA
1 TATAATATTA-AAATATTTTATTAA
*
571021 TATAAT-TTTAAATATTTTGATTAA
1 TATAATATTAAAATATTTT-ATTAA
* *
571045 AATTATATTAAAATATTTTATTAA
1 TATAATATTAAAATATTTTATTAA
571069 TAT
1 TAT
571072 TAAATTCATA
Statistics
Matches: 57, Mismatches: 9, Indels: 14
0.71 0.11 0.17
Matches are distributed among these distances:
21 4 0.07
22 18 0.32
23 4 0.07
24 20 0.35
25 11 0.19
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.48
Consensus pattern (24 bp):
TATAATATTAAAATATTTTATTAA
Found at i:571073 original size:24 final size:24
Alignment explanation
Indices: 570967--571073 Score: 77
Period size: 22 Copynumber: 4.7 Consensus size: 24
570957 TATAATTGAT
570967 TATTTTATT-ATA--ATATTAAAAA
1 TATTTTATTAATATTATATT-AAAA
**
570989 TATAATATT-ATA-T-TATTAGAAA
1 TATTTTATTAATATTATATTA-AAA
* * *
571011 TA-TTAATTAATATAAT-TTTAAA
1 TATTTTATTAATATTATATTAAAA
*
571033 TATTTTGATTAAAATTATATTAAAA
1 TATTTT-ATTAATATTATATTAAAA
571058 TATTTTATTAATATTA
1 TATTTTATTAATATTA
571074 AATTCATAAA
Statistics
Matches: 65, Mismatches: 12, Indels: 14
0.71 0.13 0.15
Matches are distributed among these distances:
21 4 0.06
22 27 0.42
23 4 0.06
24 19 0.29
25 11 0.17
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
TATTTTATTAATATTATATTAAAA
Found at i:579273 original size:27 final size:25
Alignment explanation
Indices: 579220--579305 Score: 97
Period size: 27 Copynumber: 3.5 Consensus size: 25
579210 CCGGTTTAAA
*
579220 AAAAAAACCGGATTTTT-T-CGGTT
1 AAAAAAACCGGTTTTTTATCCGGTT
579243 -AAAAAACCGGTTTTTTATCCGGTTT
1 AAAAAAACCGGTTTTTTATCCGG-TT
* * *
579268 GAAAAAATCCGGTTTTTAATCCGGTA
1 -AAAAAAACCGGTTTTTTATCCGGTT
579294 AAAAAAACCGGT
1 AAAAAAACCGGT
579306 CATTCAATTT
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
22 15 0.28
23 1 0.02
24 3 0.06
25 13 0.25
26 1 0.02
27 20 0.38
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.31
Consensus pattern (25 bp):
AAAAAAACCGGTTTTTTATCCGGTT
Found at i:579950 original size:15 final size:15
Alignment explanation
Indices: 579932--579967 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
579922 TCTGAAAATT
579932 GTTCTATGTGAAAAC
1 GTTCTATGTGAAAAC
*
579947 GTTCTATGTGAAAAT
1 GTTCTATGTGAAAAC
579962 GTTCTA
1 GTTCTA
579968 CACAAATGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (15 bp):
GTTCTATGTGAAAAC
Found at i:580159 original size:24 final size:23
Alignment explanation
Indices: 580123--580167 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
580113 TTTCTACGTG
*
580123 GTCCTCCGGGACAAATTCTATGCA
1 GTCCTCCGAGACAAA-TCTATGCA
* *
580147 GTCCTTCGAGACATATCTATG
1 GTCCTCCGAGACAAATCTATG
580168 TGGCACTTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 6 0.33
24 12 0.67
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (23 bp):
GTCCTCCGAGACAAATCTATGCA
Found at i:586012 original size:23 final size:23
Alignment explanation
Indices: 585982--586037 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
585972 ACTAAATGGT
585982 TGTTATTTAATTTTATAATTAGA
1 TGTTATTTAATTTTATAATTAGA
*
586005 TGTTATTTAATTTTATAATTATA
1 TGTTATTTAATTTTATAATTAGA
*
586028 TATTATTTAA
1 TGTTATTTAA
586038 ATTAATTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (23 bp):
TGTTATTTAATTTTATAATTAGA
Done.