Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007716.1 Hibiscus syriacus cultivar Beakdansim tig00109945_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: 4364108
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 17
Found at i:593128 original size:249 final size:246
Alignment explanation
Indices: 592437--593132 Score: 853
Period size: 249 Copynumber: 2.8 Consensus size: 246
592427 CTGAATGTAA
** * * *** * * **
592437 TCGAACTCGGAGGTCTTCGG-TGACAGATAACCCTTCTATCCTTGAGTTATGCTGTAAATGATAT
1 TCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTACAAATGATAT
* *
592501 GCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
66 GCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGTAGATAACCCTTCTCGACTTAAGCT
* * * * * *
592566 ATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTTGAACTCAAAAGT-ATTTGGCAGCTAGCC
131 ATGCTGCAAATGATGTGCCTTGGAACTGAGCGTAGTCGAACTCGAAGGTCTTTTGGCAGATAGCC
* * *
592630 CTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
196 CTTCTCGACTTAAGCTATACTGCAAATGATATGCCTTAGAGCTGACCGTAG
* * *
592681 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATAATAT
1 TCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTACAAATGATAT
* * * * * * * *
592746 GCCTTAG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGTCTTG
66 GCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC-TTTGGT---AGATAACCCTTCTCGACTTA
* * * * * *
592810 AGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCG-AGGATC-TTTGGCAG
127 AGCTATGCTGCAAATGATGTGCCTTGGAA-CTGAGCGTAGTCGAACTCGAAGG-TCTTTTGGCAG
*
592873 ATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATATGCCTTAGAGCTGACCGTAG
190 ATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATATGCCTTAGAGCTGACCGTAG
* * * *
592930 TCGAACTCAAAGGTCTTTGTTTGGTATATAACCCTTCTCGACTTAAGTTATACTACAAATGATGT
1 TCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTACAAATGATAT
592995 GCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGTAGATAACCCTTCTCGACTTAAGCT
66 GCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGTAGATAACCCTTCTCGACTTAAGCT
* * *
593060 ATTCTGCAAATGATATGCCTTGGAACTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATA
131 ATGCTGCAAATGATGTGCCTTGGAACTGAGCGTAGTCGAACTCGAAGGTC--TT-TTGGCAGATA
593125 GCCCTTCT
193 GCCCTTCT
593133 TTCCTTGAGC
Statistics
Matches: 379, Mismatches: 59, Indels: 23
0.82 0.13 0.05
Matches are distributed among these distances:
244 42 0.11
245 65 0.17
246 43 0.11
248 43 0.11
249 162 0.43
250 24 0.06
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.30
Consensus pattern (246 bp):
TCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTACAAATGATAT
GCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGTAGATAACCCTTCTCGACTTAAGCT
ATGCTGCAAATGATGTGCCTTGGAACTGAGCGTAGTCGAACTCGAAGGTCTTTTGGCAGATAGCC
CTTCTCGACTTAAGCTATACTGCAAATGATATGCCTTAGAGCTGACCGTAG
Found at i:597203 original size:16 final size:16
Alignment explanation
Indices: 597182--597221 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
597172 AAAGATCCTA
597182 CCCACATGATATCTAC
1 CCCACATGATATCTAC
597198 CCCACATGATATCTAC
1 CCCACATGATATCTAC
597214 CCCACATG
1 CCCACATG
597222 CTTATTTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.30, C:0.40, G:0.07, T:0.23
Consensus pattern (16 bp):
CCCACATGATATCTAC
Found at i:599662 original size:25 final size:25
Alignment explanation
Indices: 599630--599683 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 25
599620 ATAAACAATA
599630 ATATATATATAAATATTTTCCAAAAGT
1 ATATATA-ATAAATATTTT-CAAAAGT
*
599657 ATATATAATATATATTTTCAAAAGT
1 ATATATAATAAATATTTTCAAAAGT
599682 AT
1 AT
599684 TTTAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 9 0.35
26 10 0.38
27 7 0.27
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.43
Consensus pattern (25 bp):
ATATATAATAAATATTTTCAAAAGT
Found at i:599695 original size:25 final size:26
Alignment explanation
Indices: 599642--599698 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
599632 ATATATATAA
*
599642 ATATTTTCCAAAAGTATATATAATAT
1 ATATTTTCCAAAAGTATATAAAATAT
*
599668 ATATTTT-CAAAAGTATTTTAAAATTAT
1 ATATTTTCCAAAAGTA-TATAAAA-TAT
599695 ATAT
1 ATAT
599699 ATATTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 8 0.30
26 12 0.44
27 7 0.26
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.46
Consensus pattern (26 bp):
ATATTTTCCAAAAGTATATAAAATAT
Found at i:599700 original size:29 final size:29
Alignment explanation
Indices: 599664--599760 Score: 88
Period size: 29 Copynumber: 3.2 Consensus size: 29
599654 AGTATATATA
*
599664 ATATATATTTTCAAAAGTATTTTAAAATTAT
1 ATATATATTTTCAAAAATATTTTAAAA-T-T
* *
599695 ATATATATTTTTTAAAAAATGTTTTCAAAATT
1 ATATATA--TTTTCAAAAATATTTT-AAAATT
* *
599727 ATATA-GTTTTCAAAAATATTTTTAAAACT
1 ATATATATTTTCAAAAATA-TTTTAAAATT
599756 ATATA
1 ATATA
599761 CTATATAATT
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
29 20 0.36
30 4 0.07
31 7 0.13
32 6 0.11
33 14 0.25
34 4 0.07
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.47
Consensus pattern (29 bp):
ATATATATTTTCAAAAATATTTTAAAATT
Found at i:599794 original size:65 final size:61
Alignment explanation
Indices: 599665--599796 Score: 176
Period size: 65 Copynumber: 2.1 Consensus size: 61
599655 GTATATATAA
* * *
599665 TATATATTTTCAAAAGTATTTTAAAATTATATATATATTTTTTAAAAAATGTTTTCAAAAT
1 TATATATTTTCAAAAATATTTTAAAATTATATATATAATTTTTAAAAAATGATTTCAAAAT
*
599726 TATATAGTTTTCAAAAATATTTTTAAAACTATATACTATATAATTTTT-CAAAATGATTTCAAAA
1 TATATA-TTTTCAAAAATA-TTTTAAAA-T-TATA-TATATAATTTTTAAAAAATGATTTCAAAA
599790 T
61 T
599791 TATATA
1 TATATA
599797 ATATATATAT
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
61 6 0.10
62 11 0.18
63 8 0.13
64 1 0.02
65 25 0.40
66 11 0.18
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (61 bp):
TATATATTTTCAAAAATATTTTAAAATTATATATATAATTTTTAAAAAATGATTTCAAAAT
Found at i:599813 original size:38 final size:37
Alignment explanation
Indices: 599726--599957 Score: 202
Period size: 36 Copynumber: 6.4 Consensus size: 37
599716 TTTTCAAAAT
* * *
599726 TATATAGTTTTCAAAAAT-ATTTTTAAAACTATATACTA
1 TATATATTTTTC-AAAATGA-TTTAAAAACTATATAATA
* *
599764 TATA-ATTTTTCAAAATGATTTCAAAATTATATAATA
1 TATATATTTTTCAAAATGATTTAAAAACTATATAATA
599800 TATATATGTTTTCAAAATGATTT------T-T-TAACTA
1 TATATAT-TTTTCAAAATGATTTAAAAACTATATAA-TA
*
599831 TATATA-TTTTCAAAATGTTTTAAAAAACTATATAATA
1 TATATATTTTTCAAAATGATTT-AAAAACTATATAATA
* * *
599868 TATATA-TTTTCAAAAATGTTTTAAAAAATATATATTA
1 TATATATTTTTC-AAAATGATTTAAAAACTATATAATA
* *
599905 TATTTATTTTT-AAAATGTTTTAAAAACTATATAATA
1 TATATATTTTTCAAAATGATTTAAAAACTATATAATA
*
599941 TATAAATGTTTTCAAAA
1 TATATAT-TTTTCAAAA
599958 CTATATATTA
Statistics
Matches: 165, Mismatches: 12, Indels: 34
0.78 0.06 0.16
Matches are distributed among these distances:
29 14 0.08
30 3 0.02
31 9 0.05
32 1 0.01
36 53 0.32
37 45 0.27
38 40 0.24
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.46
Consensus pattern (37 bp):
TATATATTTTTCAAAATGATTTAAAAACTATATAATA
Found at i:599974 original size:38 final size:37
Alignment explanation
Indices: 599932--600021 Score: 99
Period size: 38 Copynumber: 2.4 Consensus size: 37
599922 TTTTAAAAAC
**
599932 TATATAATATATAAATGTTTTCAAAACTATATATTATA
1 TATATAATATATAAATGTTTTC-AAACTATATACAATA
** * *
599970 TATATGTTTTTTTAAATGTTTTCAAACTATATACAATA
1 TATAT-AATATATAAATGTTTTCAAACTATATACAATA
600008 TATATATATATATA
1 TATATA-ATATATA
600022 TTTATATATA
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
38 27 0.68
39 13 0.32
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (37 bp):
TATATAATATATAAATGTTTTCAAACTATATACAATA
Found at i:599974 original size:141 final size:139
Alignment explanation
Indices: 599722--600014 Score: 344
Period size: 141 Copynumber: 2.1 Consensus size: 139
599712 AATGTTTTCA
* * *
599722 AAAT-TATATAGTTTTCAAAAATATTTTTAAAACTATATACTATATAATTTTTCAAAATGATTTC
1 AAATATATATA-TTTTCAAAAATATTTTAAAAAATATATACTATATAATTTTTCAAAATGATTTA
* * * *
599786 AAAATTATATAATATATATATGTTTTCAAAATGATTTTTTAACTATATATATTTTCAAAATGTTT
65 AAAACTATATAATATATAAATGTTTTCAAAATGATATATTAACTATATAT-TTTTCAAAATGTTT
599851 TAAAAAACTATAT
129 T--AAAACTATAT
* * * *
599864 -AATATATATATTTTCAAAAATGTTTTAAAAAATATATATTATATTTATTTTT-AAAATGTTTTA
1 AAATATATATATTTTCAAAAATATTTTAAAAAATATATACTATA-TAATTTTTCAAAATGATTTA
* **
599927 AAAACTATATAATATATAAATGTTTTCAAAACT-ATATATTATA-TATATGTTTTTTTAAATGTT
65 AAAACTATATAATATATAAATGTTTTCAAAA-TGATATATTA-ACTATATATTTTTCAAAATGTT
*
599990 TTCAAACTATAT
128 TTAAAACTATAT
600002 ACAATATATATAT
1 A-AATATATATAT
600015 ATATATATTT
Statistics
Matches: 130, Mismatches: 15, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
138 9 0.07
140 24 0.18
141 82 0.63
142 15 0.12
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.47
Consensus pattern (139 bp):
AAATATATATATTTTCAAAAATATTTTAAAAAATATATACTATATAATTTTTCAAAATGATTTAA
AAACTATATAATATATAAATGTTTTCAAAATGATATATTAACTATATATTTTTCAAAATGTTTTA
AAACTATAT
Found at i:599981 original size:29 final size:27
Alignment explanation
Indices: 599917--599979 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
599907 TTTATTTTTA
599917 AAATGTTTTAAAAACTATATAATATAT
1 AAATGTTTTAAAAACTATATAATATAT
* *
599944 AAATGTTTTCAAAACTATATATTATAT
1 AAATGTTTTAAAAACTATATAATATAT
*
599971 ATATGTTTT
1 AAATGTTTT
599980 TTTAAATGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (27 bp):
AAATGTTTTAAAAACTATATAATATAT
Found at i:602281 original size:27 final size:27
Alignment explanation
Indices: 602238--602292 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
602228 TTTTTATTTG
* *
602238 ATTTAAAAAATTTGATTCA-ATTTTTT
1 ATTTAAAAAATTCGATTCATAATTTTT
*
602264 ATTTAAATTAATTCGATTCATAATTTTT
1 ATTTAAA-AAATTCGATTCATAATTTTT
602292 A
1 A
602293 AAAGAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 7 0.29
27 10 0.42
28 7 0.29
ACGTcount: A:0.38, C:0.05, G:0.04, T:0.53
Consensus pattern (27 bp):
ATTTAAAAAATTCGATTCATAATTTTT
Found at i:606744 original size:20 final size:20
Alignment explanation
Indices: 606719--606814 Score: 147
Period size: 20 Copynumber: 4.8 Consensus size: 20
606709 ATAGTATAGG
* *
606719 TATTACATGAACAATACATA
1 TATTACAAGAACAATACAAA
*
606739 TATTACAAAAACAATACAAA
1 TATTACAAGAACAATACAAA
*
606759 TATTGCAAGAACAATACAAA
1 TATTACAAGAACAATACAAA
606779 TATTACAAGAACAATACAAA
1 TATTACAAGAACAATACAAA
*
606799 TATTGCAAGAACAATA
1 TATTACAAGAACAATA
606815 TTCATACTAC
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 69 1.00
ACGTcount: A:0.56, C:0.15, G:0.06, T:0.23
Consensus pattern (20 bp):
TATTACAAGAACAATACAAA
Found at i:606826 original size:40 final size:40
Alignment explanation
Indices: 606727--606829 Score: 143
Period size: 40 Copynumber: 2.6 Consensus size: 40
606717 GGTATTACAT
* * *
606727 GAACAATACATATATTACAAAAACAATACAAATATTGCAA
1 GAACAATACAAATACTACAAGAACAATACAAATATTGCAA
*
606767 GAACAATACAAATATTACAAGAACAATACAAATATTGCAA
1 GAACAATACAAATACTACAAGAACAATACAAATATTGCAA
***
606807 GAACAATATTCATACTACAAGAA
1 GAACAATACAAATACTACAAGAA
606830 AAGTAACAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 57 1.00
ACGTcount: A:0.56, C:0.16, G:0.07, T:0.21
Consensus pattern (40 bp):
GAACAATACAAATACTACAAGAACAATACAAATATTGCAA
Found at i:607858 original size:21 final size:21
Alignment explanation
Indices: 607832--607895 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
607822 AAACTGATCA
*
607832 ACCGTTAATCGTTGACCACTG
1 ACCGTTAACCGTTGACCACTG
* *
607853 ACCGTTGACCGTTGACCGCTG
1 ACCGTTAACCGTTGACCACTG
* *
607874 A--GGT-ACCGTTGACCATTG
1 ACCGTTAACCGTTGACCACTG
607892 ACCG
1 ACCG
607896 ACATTGAGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
18 13 0.37
19 2 0.06
20 1 0.03
21 19 0.54
ACGTcount: A:0.20, C:0.30, G:0.25, T:0.25
Consensus pattern (21 bp):
ACCGTTAACCGTTGACCACTG
Found at i:608707 original size:39 final size:39
Alignment explanation
Indices: 608650--608749 Score: 123
Period size: 39 Copynumber: 2.6 Consensus size: 39
608640 TCTATGACTT
* * *
608650 GTAAGACCTTACTA-CAGGCTCCTATGCTTTGTGCTCTGG
1 GTAAGTCCTTAC-AGCAGGCTCCTATACTTTGTGCTCAGG
* *
608689 GTAAGTCCTTACAGCAGGCTCCTCTATTTTGTGCTCAGG
1 GTAAGTCCTTACAGCAGGCTCCTATACTTTGTGCTCAGG
*
608728 GTAAGTCCTTACTGCAGG-TCCT
1 GTAAGTCCTTACAGCAGGCTCCT
608750 CATTGTTGGG
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
38 5 0.09
39 49 0.91
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (39 bp):
GTAAGTCCTTACAGCAGGCTCCTATACTTTGTGCTCAGG
Found at i:614438 original size:19 final size:19
Alignment explanation
Indices: 614414--614479 Score: 87
Period size: 19 Copynumber: 3.4 Consensus size: 19
614404 TTCTAGAACT
614414 GGTCCAGTCAGACCAAACC
1 GGTCCAGTCAGACCAAACC
*
614433 GGTCCATTCAGACCAAACC
1 GGTCCAGTCAGACCAAACC
* * *
614452 AGTCCAGTCAGATCAAATCG
1 GGTCCAGTCAGACCAAA-CC
614472 GGTCCAGT
1 GGTCCAGT
614480 TGAGTCAACT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 32 0.80
20 8 0.20
ACGTcount: A:0.30, C:0.32, G:0.21, T:0.17
Consensus pattern (19 bp):
GGTCCAGTCAGACCAAACC
Found at i:619417 original size:17 final size:17
Alignment explanation
Indices: 619395--619434 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
619385 GAGTCAACTT
619395 GTTGACTTTGACTGATC
1 GTTGACTTTGACTGATC
619412 GTTGACTTTGACTGATC
1 GTTGACTTTGACTGATC
*
619429 ATTGAC
1 GTTGAC
619435 CTAACCAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.40
Consensus pattern (17 bp):
GTTGACTTTGACTGATC
Found at i:627102 original size:16 final size:16
Alignment explanation
Indices: 627081--627120 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
627071 TTTTTTGTAT
*
627081 TTTTTTTCTTTCG-TTA
1 TTTTTTTATTT-GTTTA
627097 TTTTTTTATTTGTTTA
1 TTTTTTTATTTGTTTA
627113 TTTTTTTA
1 TTTTTTTA
627121 CTAACTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 1 0.05
16 21 0.95
ACGTcount: A:0.10, C:0.05, G:0.05, T:0.80
Consensus pattern (16 bp):
TTTTTTTATTTGTTTA
Found at i:629793 original size:39 final size:39
Alignment explanation
Indices: 629739--629818 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 39
629729 CACCCGGAGT
* *
629739 ATTACCCGAGGACTCATCCGCTACTAAAGGGAAAGTTGC
1 ATTACCCGAGGACTCATCCGCTACCAAAGGGAAAGCTGC
*
629778 ATTACCCG-GTGACTCATCCTCTACCAAAGGGAAAGCTGC
1 ATTACCCGAG-GACTCATCCGCTACCAAAGGGAAAGCTGC
629817 AT
1 AT
629819 CTACTGTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 1 0.03
39 36 0.97
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (39 bp):
ATTACCCGAGGACTCATCCGCTACCAAAGGGAAAGCTGC
Found at i:636549 original size:10 final size:10
Alignment explanation
Indices: 636517--636543 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
636507 GTCGAAAAAG
636517 AAAAAGAACA
1 AAAAAGAACA
636527 AAAAAGAACA
1 AAAAAGAACA
636537 AAAAAGA
1 AAAAAGA
636544 GAAAAATGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.81, C:0.07, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAAGAACA
Found at i:637692 original size:170 final size:169
Alignment explanation
Indices: 637410--637915 Score: 830
Period size: 170 Copynumber: 3.1 Consensus size: 169
637400 TTTACTGAAG
637410 ATTGGATTTCAACTTTACAGCGAAGGATATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTT
1 ATTGGATTTCAACTTTACAGCGAAGGATATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTT
* *
637475 CCCAGTTTCATTCAGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACATCCACGA
66 CCCAATTTCATTCAGAGCCAATTTCAACTTCATGACGAAGGATATTGGACTCGAAACATCCACGA
637540 TTTCAACTTCACGACGAAGGATATCGTGCTCACAAACAAC
131 TTTCAACTTCACGACGAAGGATAT-GTGCTCACAAACAAC
637580 ATTGGATTTCAACTTTACAGCGAAGGATATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTT
1 ATTGGATTTCAACTTTACAGCGAAGGATATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTT
*
637645 CCCAATTTCATTCAGAGCCAATTTCAACTTCATGATGAAGGATATTGGACTCGAAACATCCACGA
66 CCCAATTTCATTCAGAGCCAATTTCAACTTCATGACGAAGGATATTGGACTCGAAACATCCACGA
637710 TTTCAACTT-----C-------A-----TCACAAACAAC
131 TTTCAACTTCACGACGAAGGATATGTGCTCACAAACAAC
* *
637732 ATTGGATTTCAACTTTATAGCGAATGATATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTT
1 ATTGGATTTCAACTTTACAGCGAAGGATATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTT
637797 CCCAATTTCATTCAGAGCCAATTTCAACTTCATGACGAAGGATATTGGACTCGAAACATCCACGA
66 CCCAATTTCATTCAGAGCCAATTTCAACTTCATGACGAAGGATATTGGACTCGAAACATCCACGA
637862 TTTCAACTTCACGACGAAGGATATTGTGCTCACAAACAAC
131 TTTCAACTTCACGACGAAGGATA-TGTGCTCACAAACAAC
637902 ATTGGATTTCAACT
1 ATTGGATTTCAACT
637916 CTACGATAAA
Statistics
Matches: 312, Mismatches: 6, Indels: 36
0.88 0.02 0.10
Matches are distributed among these distances:
152 147 0.47
157 1 0.00
158 1 0.00
164 1 0.00
165 1 0.00
170 161 0.52
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25
Consensus pattern (169 bp):
ATTGGATTTCAACTTTACAGCGAAGGATATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTT
CCCAATTTCATTCAGAGCCAATTTCAACTTCATGACGAAGGATATTGGACTCGAAACATCCACGA
TTTCAACTTCACGACGAAGGATATGTGCTCACAAACAAC
Found at i:637845 original size:152 final size:152
Alignment explanation
Indices: 637569--637872 Score: 581
Period size: 152 Copynumber: 2.0 Consensus size: 152
637559 GATATCGTGC
637569 TCACAAACAACATTGGATTTCAACTTTACAGCGAAGGATATCCAATTCAAAGCTCAACTCCACAG
1 TCACAAACAACATTGGATTTCAACTTTACAGCGAAGGATATCCAATTCAAAGCTCAACTCCACAG
*
637634 CGAAGGGGCTTCCCAATTTCATTCAGAGCCAATTTCAACTTCATGATGAAGGATATTGGACTCGA
66 CGAAGGGGCTTCCCAATTTCATTCAGAGCCAATTTCAACTTCATGACGAAGGATATTGGACTCGA
637699 AACATCCACGATTTCAACTTCA
131 AACATCCACGATTTCAACTTCA
* *
637721 TCACAAACAACATTGGATTTCAACTTTATAGCGAATGATATCCAATTCAAAGCTCAACTCCACAG
1 TCACAAACAACATTGGATTTCAACTTTACAGCGAAGGATATCCAATTCAAAGCTCAACTCCACAG
637786 CGAAGGGGCTTCCCAATTTCATTCAGAGCCAATTTCAACTTCATGACGAAGGATATTGGACTCGA
66 CGAAGGGGCTTCCCAATTTCATTCAGAGCCAATTTCAACTTCATGACGAAGGATATTGGACTCGA
637851 AACATCCACGATTTCAACTTCA
131 AACATCCACGATTTCAACTTCA
637873 CGACGAAGGA
Statistics
Matches: 149, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
152 149 1.00
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (152 bp):
TCACAAACAACATTGGATTTCAACTTTACAGCGAAGGATATCCAATTCAAAGCTCAACTCCACAG
CGAAGGGGCTTCCCAATTTCATTCAGAGCCAATTTCAACTTCATGACGAAGGATATTGGACTCGA
AACATCCACGATTTCAACTTCA
Found at i:645130 original size:64 final size:66
Alignment explanation
Indices: 644982--645138 Score: 187
Period size: 64 Copynumber: 2.4 Consensus size: 66
644972 TATCAATATC
* * * *
644982 CTTTGAGT-TGTTTCTCTT-GAAACAAATTTTTTGGCTCTTTTGAGATAGTTTCTTTTGGAAAAA
1 CTTTGAGTCTGTTTCT-TTGGAAACAAA-TGTTTGGCTCTCTTGAGACAATTTCTTTTGGAAAAA
645045 AAT
64 AAT
* * * *
645048 CTTTGAGTCTATTTCTTTGGAAACAAA-GTTTGTCTCTCTTGAGACAATTTCTTTT-GAGAAAAT
1 CTTTGAGTCTGTTTCTTTGGAAACAAATGTTTGGCTCTCTTGAGACAATTTCTTTTGGAAAAAAA
645111 T
66 T
*
645112 TTTTGAGTCTGTTTCTTTGGAAACAAA
1 CTTTGAGTCTGTTTCTTTGGAAACAAA
645139 ATTTAACACC
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
64 32 0.41
65 23 0.29
66 10 0.13
67 14 0.18
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.45
Consensus pattern (66 bp):
CTTTGAGTCTGTTTCTTTGGAAACAAATGTTTGGCTCTCTTGAGACAATTTCTTTTGGAAAAAAA
T
Found at i:645153 original size:64 final size:65
Alignment explanation
Indices: 645021--645155 Score: 164
Period size: 64 Copynumber: 2.1 Consensus size: 65
645011 TTTGGCTCTT
* * * ** * *
645021 TTGAGATAGTTTCTTTTGGAAAAAAATCTTTGAGTCTATTTCTTTGGAAACAAAGTTTGTCTCTC
1 TTGAGACAATTTCTTTTGGAAAAAAATCTTTGAGTCTATTTCTTTGGAAACAAAATTTAACACCC
* * * *
645086 TTGAGACAATTTCTTTT-GAGAAAATTTTTTGAGTCTGTTTCTTTGGAAACAAAATTTAACACCC
1 TTGAGACAATTTCTTTTGGAAAAAAATCTTTGAGTCTATTTCTTTGGAAACAAAATTTAACACCC
645150 TTGAGA
1 TTGAGA
645156 TTGTTTCCCT
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
64 44 0.75
65 15 0.25
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.41
Consensus pattern (65 bp):
TTGAGACAATTTCTTTTGGAAAAAAATCTTTGAGTCTATTTCTTTGGAAACAAAATTTAACACCC
Found at i:645216 original size:30 final size:30
Alignment explanation
Indices: 645179--645510 Score: 168
Period size: 29 Copynumber: 11.0 Consensus size: 30
645169 AACAAAACCC
* *
645179 ATCTTTGAATCTGTTTCTCTTGAAACAAAA
1 ATCTTTGAGTCTGTTTCTTTTGAAACAAAA
* * *
645209 GTCTTTGAGTC-ATTTCTTTTGAAATAAAA
1 ATCTTTGAGTCTGTTTCTTTTGAAACAAAA
*
645238 ATCTTTGAGT-TGTTTCTTTTG-AA-AATA
1 ATCTTTGAGTCTGTTTCTTTTGAAACAAAA
* * *
645265 ATATTTAAGTATGTTTCTTTTGAAAC-AAA
1 ATCTTTGAGTCTGTTTCTTTTGAAACAAAA
* ** * *
645294 GT-TTTGTCTCTCTTAAGACAATTTCGTG-AA-AAAA
1 ATCTTTGAGTCTGTT---TC--TTT--TGAAACAAAA
* *
645328 ATCTTTGATTC-GTTTCTTTTGAAACCAAA
1 ATCTTTGAGTCTGTTTCTTTTGAAACAAAA
* *
645357 ATCTTTGAGTTTGTTTCTTTTGAAACAAAGTTTTGT
1 ATCTTTGAGTCTGTTTCTTTTGAAACAAA------A
* * * *
645393 CTCTCTTGAGACAGTTT-TTCATGAAA-AAAA
1 ATCT-TTGAGTCTGTTTCTT-TTGAAACAAAA
645423 ATCTTTGAGTC-GTTTCTTTTGAAACAAAA
1 ATCTTTGAGTCTGTTTCTTTTGAAACAAAA
* ***
645452 ATCTTTGATTC-GTTTCTTTTGAAACACTT
1 ATCTTTGAGTCTGTTTCTTTTGAAACAAAA
* * **
645481 ATCTTTGAGTTTGTTCCCATTGAAACAAAA
1 ATCTTTGAGTCTGTTTCTTTTGAAACAAAA
645511 CACCCAACTT
Statistics
Matches: 226, Mismatches: 49, Indels: 54
0.69 0.15 0.16
Matches are distributed among these distances:
27 13 0.06
28 31 0.14
29 99 0.44
30 40 0.18
31 2 0.01
33 3 0.01
34 8 0.04
35 8 0.04
36 8 0.04
37 14 0.06
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (30 bp):
ATCTTTGAGTCTGTTTCTTTTGAAACAAAA
Found at i:645287 original size:28 final size:27
Alignment explanation
Indices: 645221--645289 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 27
645211 CTTTGAGTCA
* *
645221 TTTCTTTTGAAATAAAAATCTTTGAGTTG
1 TTTCTTTTG-AA-AAAAATATTTAAGTTG
*
645250 TTTCTTTTGAAAATAATATTTAAGTATG
1 TTTCTTTTGAAAAAAATATTTAAGT-TG
645278 TTTCTTTTGAAA
1 TTTCTTTTGAAA
645290 CAAAGTTTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 11 0.31
28 16 0.44
29 9 0.25
ACGTcount: A:0.32, C:0.06, G:0.12, T:0.51
Consensus pattern (27 bp):
TTTCTTTTGAAAAAAATATTTAAGTTG
Found at i:645387 original size:92 final size:93
Alignment explanation
Indices: 645228--645477 Score: 339
Period size: 92 Copynumber: 2.7 Consensus size: 93
645218 TCATTTCTTT
* * * *
645228 TGAAATAAAAATCTTTGAGTT-GTTTCTTTTGAAA-ATAATATTTAAGTATGTTTCTTTTGAAAC
1 TGAAA-AAAAATCTTTGA-TTCGTTTCTTTTGAAACAAAATCTTTGAGTTTGTTTCTTTTGAAAC
*
645291 AAAGTTTTGTCTCTCTTAAGACA-ATTTCG
64 AAAGTTTTGTCTCTCTTAAGACAGATTTCA
645320 TG-AAAAAAATCTTTGATTCGTTTCTTTTGAAACCAAAATCTTTGAGTTTGTTTCTTTTGAAACA
1 TGAAAAAAAATCTTTGATTCGTTTCTTTTGAAA-CAAAATCTTTGAGTTTGTTTCTTTTGAAACA
* *
645384 AAGTTTTGTCTCTCTTGAGACAGTTTTTCA
65 AAGTTTTGTCTCTCTTAAGACAG-ATTTCA
* *
645414 TGAAAAAAAATCTTTGAGTCGTTTCTTTTGAAACAAAAATCTTTGA-TTCGTTTCTTTTGAAACA
1 TGAAAAAAAATCTTTGATTCGTTTCTTTTGAAAC-AAAATCTTTGAGTTTGTTTCTTTTGAAACA
645478 CTTATCTTTG
Statistics
Matches: 142, Mismatches: 9, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
89 2 0.01
90 25 0.18
91 2 0.01
92 49 0.35
94 24 0.17
95 40 0.28
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.44
Consensus pattern (93 bp):
TGAAAAAAAATCTTTGATTCGTTTCTTTTGAAACAAAATCTTTGAGTTTGTTTCTTTTGAAACAA
AGTTTTGTCTCTCTTAAGACAGATTTCA
Found at i:645592 original size:102 final size:96
Alignment explanation
Indices: 645463--645650 Score: 216
Period size: 102 Copynumber: 1.9 Consensus size: 96
645453 TCTTTGATTC
* ** *
645463 GTTTCTTTTGAAACACTTATCTTTGAGTTTG-TTCCCATTGAAACAAAACACCCAACTTTGAGAT
1 GTTTCTTTGGAAACACAAATCTTTGAGTATGTTTCCC-TTGAAACAAAA-A--CAACTTTGAG-T
645527 CCTTTCCATTGAAACAAATTTTGTCTCCCTTGAGGCA
61 CCTTTCC-TTGAAACAAATTTTGTCTCCCTTGAGGCA
** * *
645564 GTTTCTTTGGAAACACAAAATCTTTGAGTATGTTTTTCTTGAAACAAAAACATCTTTGAGTCGTT
1 GTTTCTTTGGAAACAC-AAATCTTTGAGTATGTTTCCCTTGAAACAAAAACAACTTTGAGTCCTT
**
645629 TCCTTGAAATGAATTTTGTCTC
65 TCCTTGAAACAAATTTTGTCTC
645651 TTTTGAGACA
Statistics
Matches: 75, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
97 17 0.23
98 7 0.09
99 9 0.12
101 16 0.21
102 23 0.31
103 3 0.04
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (96 bp):
GTTTCTTTGGAAACACAAATCTTTGAGTATGTTTCCCTTGAAACAAAAACAACTTTGAGTCCTTT
CCTTGAAACAAATTTTGTCTCCCTTGAGGCA
Found at i:645637 original size:30 final size:30
Alignment explanation
Indices: 645564--645637 Score: 78
Period size: 32 Copynumber: 2.4 Consensus size: 30
645554 CCTTGAGGCA
* * *
645564 GTTTCTTTGGAAACACAAAATCTTTGAGTAT
1 GTTTCCTT-GAAACAAAAAATCTTTGAGTAC
*
645595 GTTTTTCTTGAAACAAAAACATCTTTGAGT-C
1 G-TTTCCTTGAAACAAAAA-ATCTTTGAGTAC
645626 GTTTCCTTGAAA
1 GTTTCCTTGAAA
645638 TGAATTTTGT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
30 10 0.28
31 11 0.31
32 15 0.42
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (30 bp):
GTTTCCTTGAAACAAAAAATCTTTGAGTAC
Found at i:645950 original size:133 final size:130
Alignment explanation
Indices: 645732--646047 Score: 399
Period size: 133 Copynumber: 2.4 Consensus size: 130
645722 TCTGCCGTCC
* * *
645732 TCATCGCGTAGGAACCGTGTCATCCCTCGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCT
1 TCATCACGTACGAACCGTGTCATCCCTCGACCAGACCTCCTCATCACGTAGGAGCCATGTCACCT
*
645797 TAGATAACCAACCATCCTTATCACGTAGGAACTGTGTTATCACCCTTCCTAAAGATGGCCAGAAC
66 TAGATAACCAACCATCCTTATCACGTAGAAACTGTGTTATCA---TTCCTAAAGATGGCCAGAAC
645862 TCT
128 TCT
* * * *
645865 TCATCACGTACGAGCCGTGTCAT-CCTCCGACTAGACTTTCTCATCACGTAGGAGCCATGTCACC
1 TCATCACGTACGAACCGTGTCATCCCT-CGACCAGACCTCCTCATCACGTAGGAGCCATGTCA-C
*
645929 CTT-GATAACCAACCATCCTTATCATGTAGAAACTGTGTTATCATTCCTAAAGATGG-CATG-AC
64 CTTAGATAACCAACCATCCTTATCACGTAGAAACTGTGTTATCATTCCTAAAGATGGCCA-GAAC
*
645991 ATCA
128 -TCT
* * * * *
645995 TCATCGCATAGGAACCGTGTCAT-CCTCGACCAGATCTCCTAATCACGTAGGAG
1 TCATCACGTACGAACCGTGTCATCCCTCGACCAGACCTCCTCATCACGTAGGAG
646048 TCTCGTCACC
Statistics
Matches: 160, Mismatches: 19, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
129 26 0.16
130 38 0.24
132 3 0.02
133 89 0.56
134 4 0.03
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (130 bp):
TCATCACGTACGAACCGTGTCATCCCTCGACCAGACCTCCTCATCACGTAGGAGCCATGTCACCT
TAGATAACCAACCATCCTTATCACGTAGAAACTGTGTTATCATTCCTAAAGATGGCCAGAACTCT
Found at i:646278 original size:3 final size:3
Alignment explanation
Indices: 646270--646300 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
646260 TAAATATAAA
646270 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
646301 TTAAATTACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:647784 original size:30 final size:30
Alignment explanation
Indices: 647730--647830 Score: 98
Period size: 29 Copynumber: 3.4 Consensus size: 30
647720 TTGTTTAGTT
* *
647730 CATTTTAGTCC-CTACTTGTCTATTTTTTC
1 CATTTTAGTCCTTTACTTGTCTATTTTTAC
* *
647759 CATTTTAGTCCTTTATTTTTCTATTTTTAC
1 CATTTTAGTCCTTTACTTGTCTATTTTTAC
* * ** *
647789 TATTTTAGCCCTTTAAGTGT-TATTATTAC
1 CATTTTAGTCCTTTACTTGTCTATTTTTAC
*
647818 CATGTTAGTCCTT
1 CATTTTAGTCCTT
647831 GTAATTATAA
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
29 29 0.50
30 29 0.50
ACGTcount: A:0.18, C:0.19, G:0.08, T:0.55
Consensus pattern (30 bp):
CATTTTAGTCCTTTACTTGTCTATTTTTAC
Found at i:649117 original size:30 final size:30
Alignment explanation
Indices: 649060--649117 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
649050 TCACCGATCT
* * *
649060 TTTAATTTTATCAATCATACTATCTAACTA
1 TTTAATTGTATCAATCAGACCATCTAACTA
649090 TTTAATTGTATTCAATCAGACCA-CTAAC
1 TTTAATTGTA-TCAATCAGACCATCTAAC
649118 CATAAACATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.36, C:0.19, G:0.03, T:0.41
Consensus pattern (30 bp):
TTTAATTGTATCAATCAGACCATCTAACTA
Found at i:649617 original size:30 final size:30
Alignment explanation
Indices: 649566--649763 Score: 149
Period size: 30 Copynumber: 6.8 Consensus size: 30
649556 AATTCACATC
*
649566 TTAACATT-AAAAATATATTTTATTTTTATT
1 TTAAC-TTAAAAAATATATTTTAATTTTATT
* ** *
649596 TTAATTTAAAAAA-ATATTTTTAAACTTACT
1 TTAACTTAAAAAATATA-TTTTAATTTTATT
* *
649626 TTAACTTAAAAAATATATTTTAGTCTTATT
1 TTAACTTAAAAAATATATTTTAATTTTATT
* * *
649656 TTAGCTT--AATATATATTTTAATATTATT
1 TTAACTTAAAAAATATATTTTAATTTTATT
* * *
649684 TTAAC-TCAAAAA-ATATTTTATTTTTATC
1 TTAACTTAAAAAATATATTTTAATTTTATT
** * *
649712 TTAACTTATGAAATCTATTTTACTTTTATT
1 TTAACTTAAAAAATATATTTTAATTTTATT
* * *
649742 TTAATTTAAGATATAT-TTTTAA
1 TTAACTTAAAAAATATATTTTAA
649764 AAGTTAATAT
Statistics
Matches: 132, Mismatches: 29, Indels: 15
0.75 0.16 0.09
Matches are distributed among these distances:
27 1 0.01
28 40 0.30
29 17 0.13
30 71 0.54
31 3 0.02
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (30 bp):
TTAACTTAAAAAATATATTTTAATTTTATT
Found at i:649640 original size:60 final size:57
Alignment explanation
Indices: 649566--649719 Score: 168
Period size: 60 Copynumber: 2.6 Consensus size: 57
649556 AATTCACATC
*
649566 TTAACATTAAAAATATATTTTATTTTTATTTTAATTTAAAAAAATATTTTTAA-ACTTACT
1 TTAAC-TTAAAAATATATTTTATTTTTATTTTAACTT-AAAAAATA-TTTTAATA-TTACT
* * * * * *
649626 TTAACTTAAAAAATATATTTTAGTCTTATTTTAGCTTAATATATATTTTAATATTATT
1 TTAACTT-AAAAATATATTTTATTTTTATTTTAACTTAAAAAATATTTTAATATTACT
* *
649684 TTAACTCAAAAA-ATATTTTATTTTTATCTTAACTTA
1 TTAACTTAAAAATATATTTTATTTTTATTTTAACTTA
649720 TGAAATCTAT
Statistics
Matches: 80, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
56 20 0.25
57 5 0.06
58 16 0.20
59 9 0.11
60 30 0.38
ACGTcount: A:0.40, C:0.06, G:0.01, T:0.52
Consensus pattern (57 bp):
TTAACTTAAAAATATATTTTATTTTTATTTTAACTTAAAAAATATTTTAATATTACT
Found at i:649699 original size:28 final size:28
Alignment explanation
Indices: 649573--649717 Score: 103
Period size: 28 Copynumber: 5.0 Consensus size: 28
649563 ATCTTAACAT
* * * *
649573 TAAAAATATATTTTATTTTTATTTTAATT
1 TAAAAAAATATTTTAATATTATTTTAA-C
*
649602 TAAAAAAATATTTTTAA-ACTTACTTTAAC
1 TAAAAAAATA-TTTTAATA-TTATTTTAAC
* * *
649631 TTAAAAAATATATTTTAGTCTTATTTTAGC
1 -TAAAAAA-ATATTTTAATATTATTTTAAC
* * *
649661 TTAATATATATTTTAATATTATTTTAAC
1 TAAAAAAATATTTTAATATTATTTTAAC
* * * *
649689 TCAAAAAATATTTTATTTTTATCTTAAC
1 TAAAAAAATATTTTAATATTATTTTAAC
649717 T
1 T
649718 TATGAAATCT
Statistics
Matches: 90, Mismatches: 21, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
28 41 0.46
29 13 0.14
30 33 0.37
31 3 0.03
ACGTcount: A:0.40, C:0.06, G:0.01, T:0.52
Consensus pattern (28 bp):
TAAAAAAATATTTTAATATTATTTTAAC
Found at i:649731 original size:58 final size:58
Alignment explanation
Indices: 649566--649750 Score: 171
Period size: 58 Copynumber: 3.2 Consensus size: 58
649556 AATTCACATC
* * *
649566 TTAACATT-AAAAATATATTTTATTTTTATTTTAATTTAAAAAAATATTTTTAA-ACTTACT
1 TTAAC-TTAAAAAATATATTTTATTTTTATTTTAACTT-AAAATATA-TTTTAATA-TTATT
* * * *
649626 TTAACTTAAAAAATATATTTTAGTCTTATTTTAGCTTAATATATATTTTAATATTATT
1 TTAACTTAAAAAATATATTTTATTTTTATTTTAACTTAAAATATATTTTAATATTATT
* * * * *
649684 TTAAC-TCAAAAA-ATATTTTATTTTTATCTTAACTTATGAAATCTATTTTACTTTTATT
1 TTAACTTAAAAAATATATTTTATTTTTATTTTAACTTA--AAATATATTTTAATATTATT
*
649742 TTAATTTAA
1 TTAACTTAA
649751 GATATATTTT
Statistics
Matches: 102, Mismatches: 18, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
56 20 0.20
57 6 0.06
58 35 0.34
59 11 0.11
60 30 0.29
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (58 bp):
TTAACTTAAAAAATATATTTTATTTTTATTTTAACTTAAAATATATTTTAATATTATT
Found at i:650823 original size:34 final size:32
Alignment explanation
Indices: 650775--650934 Score: 114
Period size: 33 Copynumber: 4.9 Consensus size: 32
650765 AAATAAAAAT
*
650775 AAAACAAAACCAAAATAAAAAAATAAAAAAGAA
1 AAAATAAAA-CAAAATAAAAAAATAAAAAAGAA
650808 TAACAATAAAACAAAA-AATAAAAA-AGAAAAAGAA
1 -AA-AATAAAACAAAATAA-AAAAATA-AAAAAGAA
** * *
650842 AATAATGGAACTAAATAAAAAAA-ACAAAAA-CA
1 AA-AATAAAACAAAATAAAAAAATA-AAAAAGAA
* * * *
650874 AAAGTAAAACAACA-AAAAATATATAAAAGAAA
1 AAAATAAAACAAAATAAAAAAATAAAAAAG-AA
*
650906 AAAATAAAAGAAAATAAAAAGAATAAAAA
1 AAAATAAAACAAAATAAAAA-AATAAAAA
650935 TAATATATAC
Statistics
Matches: 97, Mismatches: 20, Indels: 18
0.72 0.15 0.13
Matches are distributed among these distances:
30 10 0.10
31 8 0.08
32 15 0.15
33 30 0.31
34 28 0.29
35 6 0.06
ACGTcount: A:0.78, C:0.06, G:0.06, T:0.10
Consensus pattern (32 bp):
AAAATAAAACAAAATAAAAAAATAAAAAAGAA
Found at i:650846 original size:36 final size:33
Alignment explanation
Indices: 650764--650937 Score: 97
Period size: 36 Copynumber: 5.1 Consensus size: 33
650754 ATGGTAATCG
*
650764 TAAATAAAAATAAAACAAAACCAAAATAAAAAAA
1 TAAA-AAAAATAAAACAAAACAAAAATAAAAAAA
*
650798 TAAAAAAGAATAACAATAAAACAAAAAATAAAAAAGA
1 TAAAAAA-AATAA-AACAAAAC-AAAAATAAAAAA-A
* * *
650835 -AAAAGAAAATAATGGAACTAAATAAAAA-AAACAAA
1 TAAAA-AAAATAA---AACAAAACAAAAATAAAAAAA
* * * *
650870 -AACAAAAGTAAAACAACA-AAAAATATATAAAA
1 TAAAAAAAATAAAACAAAACAAAAATA-AAAAAA
* * * *
650902 -GAAAAAAATAAAAGAAAATAAAAAGAATAAAAA
1 TAAAAAAAATAAAACAAAACAAAAATAA-AAAAA
650935 TAA
1 TAA
650938 TATATACATA
Statistics
Matches: 107, Mismatches: 21, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
30 5 0.05
31 6 0.06
32 18 0.17
33 13 0.12
34 16 0.15
35 11 0.10
36 25 0.23
37 8 0.07
38 5 0.05
ACGTcount: A:0.78, C:0.06, G:0.05, T:0.11
Consensus pattern (33 bp):
TAAAAAAAATAAAACAAAACAAAAATAAAAAAA
Found at i:650914 original size:13 final size:13
Alignment explanation
Indices: 650896--650937 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
650886 CAAAAAATAT
650896 ATAAAAGAAAAAA
1 ATAAAAGAAAAAA
*
650909 ATAAAAG-AAAAT
1 ATAAAAGAAAAAA
650921 A-AAAAGAATAAAA
1 ATAAAAGAA-AAAA
650934 ATAA
1 ATAA
650938 TATATACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
11 5 0.21
12 6 0.25
13 11 0.46
14 2 0.08
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.12
Consensus pattern (13 bp):
ATAAAAGAAAAAA
Found at i:650925 original size:87 final size:89
Alignment explanation
Indices: 650764--650928 Score: 205
Period size: 87 Copynumber: 1.9 Consensus size: 89
650754 ATGGTAATCG
* * *
650764 TAAATAAAAATAAAACAAAACCAAAATAAAAAAATAAAAAAGAATAACAATAAAACAAAAAATAA
1 TAAATAAAAATAAAACAAAAACAAAATAAAAAAACAAAAAAGAATAACAAGAAAACAAAAAATAA
650829 AAAAGAAAAAGAAAATAATGGAAC
66 AAAAGAAAAAGAAAATAATGGAAC
* *
650853 TAAAT-AAAA-AAAACAAAAACAAAAGTAAAACAACAAAAAATATATAA-AAGAAAA-AAATAAA
1 TAAATAAAAATAAAACAAAAACAAAA-TAAAAAAACAAAAAAGA-ATAACAAGAAAACAAA-AAA
* *
650914 -AGAAAATAAAAAGAA
63 TAAAAAAGAAAAAGAA
650929 TAAAAATAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
87 30 0.45
88 27 0.41
89 9 0.14
ACGTcount: A:0.78, C:0.06, G:0.05, T:0.11
Consensus pattern (89 bp):
TAAATAAAAATAAAACAAAAACAAAATAAAAAAACAAAAAAGAATAACAAGAAAACAAAAAATAA
AAAAGAAAAAGAAAATAATGGAAC
Found at i:650932 original size:9 final size:8
Alignment explanation
Indices: 650786--650939 Score: 55
Period size: 9 Copynumber: 17.8 Consensus size: 8
650776 AAACAAAACC
650786 AAAATAAA
1 AAAATAAA
650794 AAAATAAAA
1 AAAAT-AAA
650803 AAGAATAACA
1 AA-AATAA-A
650813 ATAAA-ACAA
1 A-AAATA-AA
650822 AAAATAAA
1 AAAATAAA
*
650830 AAAGAAAAA
1 AAA-ATAAA
*
650839 GAAAATAATG
1 -AAAATAA-A
* *
650849 GAACTAAA
1 AAAATAAA
650857 TAAAA-AAA
1 -AAAATAAA
650865 ACAAA-AACA
1 A-AAATAA-A
*
650874 AAAGTAAA
1 AAAATAAA
* *
650882 ACAA-CAA
1 AAAATAAA
*
650889 AAAATATAT
1 AAAATA-AA
*
650898 AAAAGAAA
1 AAAATAAA
650906 AAAATAAAA
1 AAAAT-AAA
650915 GAAAATAAA
1 -AAAATAAA
650924 AAGAATAAA
1 AA-AATAAA
650933 AATAATA
1 AA-AATA
650940 TATACATACT
Statistics
Matches: 109, Mismatches: 19, Indels: 35
0.67 0.12 0.21
Matches are distributed among these distances:
7 6 0.06
8 33 0.30
9 53 0.49
10 16 0.15
11 1 0.01
ACGTcount: A:0.78, C:0.05, G:0.06, T:0.12
Consensus pattern (8 bp):
AAAATAAA
Found at i:650992 original size:18 final size:16
Alignment explanation
Indices: 650964--650997 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 16
650954 TATAGTATTT
650964 AACAAAATAAGTAAAAA
1 AACAAAATAAG-AAAAA
650981 AACAATAATAAGAAAAA
1 AACAA-AATAAGAAAAA
650998 TAATAAAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.76, C:0.06, G:0.06, T:0.12
Consensus pattern (16 bp):
AACAAAATAAGAAAAA
Found at i:651027 original size:4 final size:4
Alignment explanation
Indices: 651018--651043 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
651008 ATATACATAT
651018 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
651044 ACAAGAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:651054 original size:11 final size:11
Alignment explanation
Indices: 651038--651079 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
651028 TAAATAAATA
*
651038 AATAAAACAAG
1 AATAAAATAAG
*
651049 AATAAAATAAA
1 AATAAAATAAG
651060 AAT-AAATAAG
1 AATAAAATAAG
651070 AATAAAATAA
1 AATAAAATAA
651080 ATATAAAGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (11 bp):
AATAAAATAAG
Found at i:651072 original size:21 final size:21
Alignment explanation
Indices: 651016--651086 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
651006 ATATATACAT
651016 ATAATAAATAAAT-A-AAT-AA
1 ATAA-AAATAAATAAGAATAAA
* *
651035 ATAAATA-AAACAAGAATAAA
1 ATAAAAATAAATAAGAATAAA
651055 ATAAAAATAAATAAGAATAAA
1 ATAAAAATAAATAAGAATAAA
*
651076 ATAAATATAAA
1 ATAAAAATAAA
651087 GGAAATAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
17 3 0.07
18 3 0.07
19 7 0.16
20 8 0.19
21 22 0.51
ACGTcount: A:0.75, C:0.01, G:0.03, T:0.21
Consensus pattern (21 bp):
ATAAAAATAAATAAGAATAAA
Found at i:651092 original size:26 final size:26
Alignment explanation
Indices: 651063--651123 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
651053 AAATAAAAAT
* *
651063 AAATAAGAATAAAATAAATATAAAGG
1 AAATAAAAATAAAATAAAGATAAAGG
* *
651089 AAATAAAAATAAAGTAAAGATAAAGA
1 AAATAAAAATAAAATAAAGATAAAGG
*
651115 AAAGAAAAA
1 AAATAAAAA
651124 AGAAAAGAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.15
Consensus pattern (26 bp):
AAATAAAAATAAAATAAAGATAAAGG
Found at i:651118 original size:11 final size:11
Alignment explanation
Indices: 651093--651139 Score: 53
Period size: 10 Copynumber: 4.4 Consensus size: 11
651083 TAAAGGAAAT
651093 AAAA-ATAAAG
1 AAAAGATAAAG
*
651103 TAAAGATAAAG
1 AAAAGATAAAG
*
651114 AAAAGAAAAAAG
1 AAAAG-ATAAAG
651126 AAAAGA-AAAG
1 AAAAGATAAAG
651136 AAAA
1 AAAA
651140 CAAATACAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 11 0.34
11 11 0.34
12 10 0.31
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (11 bp):
AAAAGATAAAG
Found at i:651127 original size:12 final size:12
Alignment explanation
Indices: 651110--651134 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
651100 AAGTAAAGAT
651110 AAAGAAAAGAAA
1 AAAGAAAAGAAA
651122 AAAGAAAAGAAA
1 AAAGAAAAGAAA
651134 A
1 A
651135 GAAAACAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAGAAAAGAAA
Found at i:651130 original size:17 final size:18
Alignment explanation
Indices: 651104--651139 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
651094 AAAATAAAGT
651104 AAAGATAAAGAAAAGAAA
1 AAAGATAAAGAAAAGAAA
651122 AAAGA-AAAGAAAAGAAA
1 AAAGATAAAGAAAAGAAA
651139 A
1 A
651140 CAAATACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.03
Consensus pattern (18 bp):
AAAGATAAAGAAAAGAAA
Found at i:653296 original size:124 final size:124
Alignment explanation
Indices: 653076--653426 Score: 524
Period size: 124 Copynumber: 2.8 Consensus size: 124
653066 GTCGATTTGT
* * *
653076 TGGGCACGATATCCTTCGTCGTGAAGTTGAAATCCTGGATGGCTCATTCGTTGTAAAGTTGAGCT
1 TGGGCACGATATCCTTCGTTGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCT
* * * * * *
653141 TGGAATTAGATATCCTTCGTTGTGAAGTTGAAATCTAATCTAGAGATGGGTACTTCTCG
66 TTGAATTGGATATCCTTCATTGTGAAGTTGAAATCCAATCTAGAGATGGATACTGCTCG
* *
653200 TGGGCACGATATCATTCGTTGTGAAGTTAAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCT
1 TGGGCACGATATCCTTCGTTGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCT
* * * *
653265 TTGAATTGGACATCCTTCATTGTGAAGTTGAAATCCAATCTAGAGGTGGATGCTGCTTG
66 TTGAATTGGATATCCTTCATTGTGAAGTTGAAATCCAATCTAGAGATGGATACTGCTCG
* *
653324 TGGTCACGATATCCTTC-TTCGTGAAGTTGAAATCGTGGATGGCTCATTTGTTGTGAAGTTGAGC
1 TGGGCACGATATCCTTCGTT-GTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGC
*
653388 TTTGAATTGGATATCTTTCATTGTGAAGTTGAAATCCAA
65 TTTGAATTGGATATCCTTCATTGTGAAGTTGAAATCCAA
653427 GGGTTGTTTT
Statistics
Matches: 205, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
123 2 0.01
124 203 0.99
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (124 bp):
TGGGCACGATATCCTTCGTTGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCT
TTGAATTGGATATCCTTCATTGTGAAGTTGAAATCCAATCTAGAGATGGATACTGCTCG
Found at i:653747 original size:15 final size:16
Alignment explanation
Indices: 653709--653749 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
653699 ACAGAGCAAC
* *
653709 TGAATCATTCATCATT
1 TGAATCATTCAGCACT
653725 TGAATCATTCAGCACT
1 TGAATCATTCAGCACT
653741 T-AATCATTC
1 TGAATCATTC
653750 TGAAGTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (16 bp):
TGAATCATTCAGCACT
Found at i:665121 original size:16 final size:16
Alignment explanation
Indices: 665102--665193 Score: 60
Period size: 16 Copynumber: 5.1 Consensus size: 16
665092 AACCAAAACC
665102 AAAAGAATAAAATAAA
1 AAAAGAATAAAATAAA
665118 AAAAGAATAAAAATAAAACAAAA
1 AAAAGAAT-AAAAT------AAA
*
665141 CCAAAAGAAAAAAATAAA
1 --AAAAGAATAAAATAAA
665159 AAAAGAATAAAAATAAA
1 AAAAGAAT-AAAATAAA
*
665176 ACAAA-AATAAAACAAA
1 A-AAAGAATAAAATAAA
665192 AA
1 AA
665194 TAAAAACAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 23
0.70 0.03 0.26
Matches are distributed among these distances:
15 1 0.02
16 23 0.37
17 17 0.27
18 6 0.10
23 3 0.05
24 5 0.08
25 7 0.11
ACGTcount: A:0.82, C:0.05, G:0.04, T:0.09
Consensus pattern (16 bp):
AAAAGAATAAAATAAA
Found at i:665128 original size:11 final size:10
Alignment explanation
Indices: 665110--665223 Score: 70
Period size: 11 Copynumber: 10.7 Consensus size: 10
665100 CCAAAAGAAT
665110 AAAATAAAAA
1 AAAATAAAAA
665120 AAGAATAAAAA
1 AA-AATAAAAA
* *
665131 TAAAACAAAAC
1 -AAAATAAAAA
* *
665142 CAAA-AGAAA
1 AAAATAAAAA
665151 AAAATAAAAA
1 AAAATAAAAA
665161 AAGAATAAAAA
1 AA-AATAAAAA
*
665172 TAAAACAAAAA
1 -AAAATAAAAA
*
665183 TAAAACAAAAA
1 -AAAATAAAAA
665194 TAAAA-ACAAAGA
1 -AAAATA-AAA-A
*
665206 AAAAGAAAAA
1 AAAATAAAAA
665216 GAAAATAA
1 -AAAATAA
665224 TGGAACTAAA
Statistics
Matches: 86, Mismatches: 9, Indels: 17
0.77 0.08 0.15
Matches are distributed among these distances:
9 6 0.07
10 13 0.15
11 61 0.71
12 6 0.07
ACGTcount: A:0.82, C:0.05, G:0.05, T:0.08
Consensus pattern (10 bp):
AAAATAAAAA
Found at i:665193 original size:17 final size:16
Alignment explanation
Indices: 665110--665314 Score: 92
Period size: 17 Copynumber: 11.9 Consensus size: 16
665100 CCAAAAGAAT
*
665110 AAAATAAAAAAAGAATA
1 AAAATAAAAAAA-AACA
*
665127 AAAATAAAACAAAACCA
1 AAAATAAAA-AAAAACA
*
665144 AAAGA-AAAAAATAAAAA
1 AAA-ATAAAAAA-AAACA
665161 AAGAATAAAAATAAAACA
1 AA-AATAAAAA-AAAACA
*
665179 AAAATAAAACAAAAATA
1 AAAATAAAA-AAAAACA
* * *
665196 AAAACAAAGAAAAAGA
1 AAAATAAAAAAAAACA
* *
665212 AAAAGAAAATAATGGAAC-
1 AAAATAAAA-AA--AAACA
* *
665230 TAAATAGAAAAAAACA
1 AAAATAAAAAAAAACA
*
665246 AAAACAAAAGTAAAATAACA
1 AAAA-TAAA--AAAA-AACA
*
665266 AAAACAAATAAAAGAA-A
1 AAAATAAA-AAAA-AACA
*
665283 ATAAATAAAAGAAAACA
1 A-AAATAAAAAAAAACA
*
665300 ATAATAAAAATAAAA
1 AAAATAAAAA-AAAA
665315 ATAATATATA
Statistics
Matches: 144, Mismatches: 26, Indels: 36
0.70 0.13 0.17
Matches are distributed among these distances:
15 3 0.02
16 27 0.19
17 60 0.42
18 36 0.25
19 10 0.07
20 8 0.06
ACGTcount: A:0.79, C:0.06, G:0.06, T:0.10
Consensus pattern (16 bp):
AAAATAAAAAAAAACA
Found at i:665193 original size:41 final size:41
Alignment explanation
Indices: 665082--665181 Score: 182
Period size: 41 Copynumber: 2.4 Consensus size: 41
665072 GGTAATCGTA
* *
665082 AATAAAAATAAACCAAAACCAAAAGAATAAAATAAAAAAAG
1 AATAAAAATAAAACAAAACCAAAAGAAAAAAATAAAAAAAG
665123 AATAAAAATAAAACAAAACCAAAAGAAAAAAATAAAAAAAG
1 AATAAAAATAAAACAAAACCAAAAGAAAAAAATAAAAAAAG
665164 AATAAAAATAAAACAAAA
1 AATAAAAATAAAACAAAA
665182 ATAAAACAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.79, C:0.08, G:0.04, T:0.09
Consensus pattern (41 bp):
AATAAAAATAAAACAAAACCAAAAGAAAAAAATAAAAAAAG
Found at i:665205 original size:41 final size:39
Alignment explanation
Indices: 665082--665206 Score: 160
Period size: 41 Copynumber: 3.1 Consensus size: 39
665072 GGTAATCGTA
*
665082 AATAAAAATAAACCAAAACCAAAAGAATAAAATAAAAAAAG
1 AATAAAAATAAAACAAAACCAAAAGAA-AAAA-AAAAAAAG
665123 AATAAAAATAAAACAAAACCAAAAGAAAAAAATAAAAAAAG
1 AATAAAAATAAAACAAAACCAAAAG-AAAAAA-AAAAAAAG
** *
665164 AATAAAAATAAAACAAAAATAAAACAAAAATAAAAACAAAG
1 AATAAAAATAAAACAAAACCAAAAGAAAAA-AAAAA-AAAG
665205 AA
1 AA
665207 AAAGAAAAAG
Statistics
Matches: 77, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
40 9 0.12
41 66 0.86
42 2 0.03
ACGTcount: A:0.79, C:0.08, G:0.04, T:0.09
Consensus pattern (39 bp):
AATAAAAATAAAACAAAACCAAAAGAAAAAAAAAAAAAG
Found at i:665372 original size:17 final size:15
Alignment explanation
Indices: 665345--665383 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
665335 TATAGTATTT
*
665345 AAAACAATAAGTAAAA
1 AAAATAATAAG-AAAA
665361 AACAATAATAAGAAAA
1 AA-AATAATAAGAAAA
665377 AAAATAA
1 AAAATAA
665384 AGATATATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 5 0.24
16 8 0.38
17 8 0.38
ACGTcount: A:0.77, C:0.05, G:0.05, T:0.13
Consensus pattern (15 bp):
AAAATAATAAGAAAA
Found at i:665443 original size:13 final size:14
Alignment explanation
Indices: 665427--665478 Score: 61
Period size: 15 Copynumber: 3.6 Consensus size: 14
665417 AAACAAGAAT
665427 AAAATAAATATAA-
1 AAAATAAATATAAG
665440 AAAATAAATATAAAG
1 AAAATAAATAT-AAG
*
665455 AAAATAAAAATAAG
1 AAAATAAATATAAG
665469 TAAAGATAAA
1 -AAA-ATAAA
665479 GAAAATAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
13 11 0.32
14 5 0.15
15 13 0.38
16 5 0.15
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (14 bp):
AAAATAAATATAAG
Found at i:665477 original size:16 final size:16
Alignment explanation
Indices: 665432--665499 Score: 63
Period size: 16 Copynumber: 4.4 Consensus size: 16
665422 AGAATAAAAT
665432 AAAT-ATAAAAAATAA
1 AAATAATAAAAAATAA
* *
665447 ATATAA-AGAAAATAA
1 AAATAATAAAAAATAA
*
665462 AAATAAGT-AAAGATAA
1 AAATAA-TAAAAAATAA
665478 AGAA-AATAAAAAATAA
1 A-AATAATAAAAAATAA
665494 AAATAA
1 AAATAA
665500 AGATATAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
15 19 0.46
16 20 0.49
17 2 0.05
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (16 bp):
AAATAATAAAAAATAA
Found at i:665493 original size:47 final size:45
Alignment explanation
Indices: 665436--665535 Score: 130
Period size: 47 Copynumber: 2.2 Consensus size: 45
665426 TAAAATAAAT
* *
665436 ATAAAAAATAAATATAAAGAAAATAAAAATA-AGTAAAGATAAAGAAA
1 ATAAAAAATAAAAATAAAG-AAATAAAAACACA-TAAAG-TAAAGAAA
* *
665483 ATAAAAAATAAAAATAAAGATATAAAAACACATAAAGTAAATAAA
1 ATAAAAAATAAAAATAAAGAAATAAAAACACATAAAGTAAAGAAA
665528 ATAAAAAA
1 ATAAAAAA
665536 ATCAAATCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
45 15 0.31
46 14 0.29
47 19 0.40
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.17
Consensus pattern (45 bp):
ATAAAAAATAAAAATAAAGAAATAAAAACACATAAAGTAAAGAAA
Found at i:665536 original size:47 final size:48
Alignment explanation
Indices: 665428--665537 Score: 131
Period size: 46 Copynumber: 2.4 Consensus size: 48
665418 AACAAGAATA
* *
665428 AAAT-AAATATAAAAAATAAATATAAAGAAAATAAAAATAAGTAAAGAT
1 AAATAAAATA-AAAAAATAAAAATAAAGAAAATAAAAACAAGTAAAGAT
* *
665476 AAAGAAAAT-AAAAAATAAAAATAAAG-ATATAAAAACACA-TAAAG-T
1 AAATAAAATAAAAAAATAAAAATAAAGAAAATAAAAACA-AGTAAAGAT
665521 AAATAAAATAAAAAAAT
1 AAATAAAATAAAAAAAT
665538 CAAATCAAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
45 9 0.17
46 21 0.39
47 17 0.31
48 3 0.06
49 4 0.07
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (48 bp):
AAATAAAATAAAAAAATAAAAATAAAGAAAATAAAAACAAGTAAAGAT
Found at i:667361 original size:77 final size:79
Alignment explanation
Indices: 667221--667365 Score: 188
Period size: 77 Copynumber: 1.9 Consensus size: 79
667211 ATATAGTAAG
* *
667221 TAAACATTAAAAGAATGTAATTCTGATTACAACTCTTTTAATGTATAATTAATTCAGAATAATTA
1 TAAACATTAAAAGAATGTAATTCGGATTACAACTCTTTTAATGGATAATTAATTCAGAATAATTA
667286 AATAAGAGTTTAAA
66 AATAAGAGTTTAAA
* * * * * *
667300 TAAACGTT-AAAGAGTGTAATTCGGATTATAAGT-TTTTAATGGATATTTAATT-TGAATTAATT
1 TAAACATTAAAAGAATGTAATTCGGATTACAACTCTTTTAATGGATAATTAATTCAGAA-TAATT
667362 AAAT
65 AAAT
667366 CAAAATAACC
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
76 3 0.05
77 26 0.46
78 21 0.37
79 7 0.12
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (79 bp):
TAAACATTAAAAGAATGTAATTCGGATTACAACTCTTTTAATGGATAATTAATTCAGAATAATTA
AATAAGAGTTTAAA
Found at i:667863 original size:18 final size:19
Alignment explanation
Indices: 667827--667868 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
667817 AAATATATTT
667827 TTTAATGTTAAGTTGTGAA
1 TTTAATGTTAAGTTGTGAA
667846 TTTAAT-TT-AGTATGTGAA
1 TTTAATGTTAAGT-TGTGAA
667864 TTTAA
1 TTTAA
667869 AGTAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 3 0.14
18 13 0.59
19 6 0.27
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (19 bp):
TTTAATGTTAAGTTGTGAA
Found at i:668618 original size:2 final size:2
Alignment explanation
Indices: 668611--668639 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
668601 ATCAAAAAGA
668611 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
668640 ATAGAGAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:669598 original size:18 final size:18
Alignment explanation
Indices: 669571--669605 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
669561 ATTAGTTTAA
669571 ATAATCAAAACTTAAAAG
1 ATAATCAAAACTTAAAAG
* *
669589 ATAATTAAAATTTAAAA
1 ATAATCAAAACTTAAAA
669606 TAAAAATATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.06, G:0.03, T:0.29
Consensus pattern (18 bp):
ATAATCAAAACTTAAAAG
Found at i:672527 original size:19 final size:19
Alignment explanation
Indices: 672503--672544 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
672493 GAACAAAATC
672503 TCTACAAGCTCAACTATAG
1 TCTACAAGCTCAACTATAG
672522 TCTACAAGCTCAACTATAG
1 TCTACAAGCTCAACTATAG
672541 TCTA
1 TCTA
672545 ATGCACAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.36, C:0.26, G:0.10, T:0.29
Consensus pattern (19 bp):
TCTACAAGCTCAACTATAG
Found at i:674669 original size:18 final size:19
Alignment explanation
Indices: 674646--674697 Score: 70
Period size: 18 Copynumber: 2.7 Consensus size: 19
674636 TGTAACCCTT
*
674646 TGAAAATACATGTTTTAA-
1 TGAAAATACATGCTTTAAG
674664 TGAAAATACATGGCTTTAAG
1 TGAAAATACAT-GCTTTAAG
*
674684 TGAAAAAACATGCT
1 TGAAAATACATGCT
674698 CTTGGATGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 11 0.37
19 9 0.30
20 10 0.33
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (19 bp):
TGAAAATACATGCTTTAAG
Found at i:689002 original size:22 final size:21
Alignment explanation
Indices: 688958--689005 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
688948 CACTTTTATT
*
688958 TTAATAATATATAATAATTTA
1 TTAATAAAATATAATAATTTA
688979 TTAATAAAAT-TAATATTATTTA
1 TTAATAAAATATAATA--ATTTA
689001 TTAAT
1 TTAAT
689006 TTCATTGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 5 0.21
21 9 0.38
22 10 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTAATAAAATATAATAATTTA
Found at i:689098 original size:15 final size:15
Alignment explanation
Indices: 689069--689107 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
689059 ATATAAAATT
*
689069 ATATTCTAA-TTTTA
1 ATATTATAATTTTTA
689083 ATATTATAATTTTTA
1 ATATTATAATTTTTA
*
689098 ATATTTTAAT
1 ATATTATAAT
689108 AATTTTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (15 bp):
ATATTATAATTTTTA
Found at i:689104 original size:8 final size:8
Alignment explanation
Indices: 689077--689125 Score: 64
Period size: 8 Copynumber: 6.1 Consensus size: 8
689067 TTATATTCTA
689077 ATTTTAAT
1 ATTTTAAT
*
689085 ATTATAAT
1 ATTTTAAT
689093 -TTTTAAT
1 ATTTTAAT
689100 ATTTTAAT
1 ATTTTAAT
*
689108 AATTTTATT
1 -ATTTTAAT
689117 ATTTTAAT
1 ATTTTAAT
689125 A
1 A
689126 AATAATTCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
7 6 0.17
8 22 0.63
9 7 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
ATTTTAAT
Found at i:689119 original size:17 final size:17
Alignment explanation
Indices: 689075--689126 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
689065 AATTATATTC
*
689075 TAATTTTAATATTATAA
1 TAATTTTAATATTTTAA
689092 T--TTTTAATATTTTAA
1 TAATTTTAATATTTTAA
*
689107 TAATTTTATTATTTTAA
1 TAATTTTAATATTTTAA
689124 TAA
1 TAA
689127 ATAATTCATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 14 0.45
17 17 0.55
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TAATTTTAATATTTTAA
Found at i:689220 original size:33 final size:32
Alignment explanation
Indices: 689168--689230 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
689158 CATTATAATG
689168 AATAATTTATAATAATTTTACTTTAATAAAATAT
1 AATAATTTATAATAATTTTA-TTTAA-AAAATAT
* *
689202 AATAA-TTGTAATACTTTTATTTAAAAAAT
1 AATAATTTATAATAATTTTATTTAAAAAAT
689231 TATAGATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 5 0.19
32 5 0.19
33 12 0.44
34 5 0.19
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (32 bp):
AATAATTTATAATAATTTTATTTAAAAAATAT
Found at i:705058 original size:18 final size:18
Alignment explanation
Indices: 705035--705073 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
705025 TTAATAAGTC
* *
705035 TATATAGTATTATTACGA
1 TATATACTATTATTAAGA
705053 TATATACTATTATTAAGA
1 TATATACTATTATTAAGA
705071 TAT
1 TAT
705074 TATTAAGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (18 bp):
TATATACTATTATTAAGA
Found at i:705117 original size:17 final size:15
Alignment explanation
Indices: 705086--705144 Score: 52
Period size: 14 Copynumber: 4.1 Consensus size: 15
705076 TTAAGAATAA
705086 TATTATATATTTTAT
1 TATTATATATTTTAT
* *
705101 TATTATATA-ATTCT
1 TATTATATATTTTAT
* *
705115 TATAATATATATTA-
1 TATTATATATTTTAT
705129 T-TTATATATTATTAT
1 TATTATATATT-TTAT
705144 T
1 T
705145 TAAATAATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
13 7 0.20
14 15 0.43
15 13 0.37
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTATATATTTTAT
Found at i:705204 original size:22 final size:22
Alignment explanation
Indices: 705179--705226 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
705169 TTTGAAAGAT
705179 TTAAAGTATTATTTATAATTTA
1 TTAAAGTATTATTTATAATTTA
705201 TTAAAGTATTATTTATAATTTA
1 TTAAAGTATTATTTATAATTTA
705223 TTAA
1 TTAA
705227 TAAATAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (22 bp):
TTAAAGTATTATTTATAATTTA
Found at i:705308 original size:17 final size:18
Alignment explanation
Indices: 705265--705331 Score: 54
Period size: 17 Copynumber: 3.9 Consensus size: 18
705255 TTAATTTATT
*
705265 TAATTA-AA-AATTAAAG
1 TAATTATAATAATTTAAG
*
705281 TTAAATATAATAATTTAAG
1 -TAATTATAATAATTTAAG
* *
705300 T-ATTATAAT-ATTTTAT
1 TAATTATAATAATTTAAG
705316 TAATT-TAATAATTTAA
1 TAATTATAATAATTTAA
705332 AATATCATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
16 10 0.25
17 20 0.50
18 3 0.08
19 7 0.17
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
TAATTATAATAATTTAAG
Found at i:707362 original size:49 final size:49
Alignment explanation
Indices: 707305--707406 Score: 186
Period size: 49 Copynumber: 2.1 Consensus size: 49
707295 ACATGATATT
*
707305 ATAAGCATATAAAAAGATATGAACTCAAAGGCATAAACAAATAAAATGC
1 ATAAGCATATAAAAAGATATGAACTCAAAGGAATAAACAAATAAAATGC
*
707354 ATAAGCATATAATAAGATATGAACTCAAAGGAATAAACAAATAAAATGC
1 ATAAGCATATAAAAAGATATGAACTCAAAGGAATAAACAAATAAAATGC
707403 ATAA
1 ATAA
707407 AGGATGTAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.58, C:0.11, G:0.12, T:0.20
Consensus pattern (49 bp):
ATAAGCATATAAAAAGATATGAACTCAAAGGAATAAACAAATAAAATGC
Found at i:713410 original size:25 final size:25
Alignment explanation
Indices: 713382--713444 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
713372 TAGTTGCAAG
*
713382 GTAACTTTTTTAACTTTATATTTGA
1 GTAACTTTTTTAAATTTATATTTGA
713407 GTAAAC--TTTTAAATTTATATTTGA
1 GT-AACTTTTTTAAATTTATATTTGA
*
713431 ATATA-TTTTTTAAA
1 GTA-ACTTTTTTAAA
713445 ATTTTTATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
23 1 0.03
24 19 0.59
25 9 0.28
26 3 0.09
ACGTcount: A:0.35, C:0.05, G:0.06, T:0.54
Consensus pattern (25 bp):
GTAACTTTTTTAAATTTATATTTGA
Found at i:713440 original size:24 final size:24
Alignment explanation
Indices: 713388--713440 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
713378 CAAGGTAACT
* *
713388 TTTTTAACTTTATATTTGAGTAAA
1 TTTTTAAATTTATATTTGAATAAA
* *
713412 CTTTTAAATTTATATTTGAATATA
1 TTTTTAAATTTATATTTGAATAAA
713436 TTTTT
1 TTTTT
713441 TAAAATTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.58
Consensus pattern (24 bp):
TTTTTAAATTTATATTTGAATAAA
Found at i:717944 original size:43 final size:43
Alignment explanation
Indices: 717883--718009 Score: 146
Period size: 44 Copynumber: 2.9 Consensus size: 43
717873 ACAATGAGCG
* *
717883 GCACATAGCAGAGGAGCCTGGGAAACGTTAAGGTCTTATCCTT
1 GCACATAGCAGAGGAGCCTGGGAAACGGTAAGGTCTTATCCTC
* * * * *
717926 GCACACAGCAAAGGAGCCTGTAGAAACGGTAAGTTCTTACCCTC
1 GCACATAGCAGAGGAGCCTG-GGAAACGGTAAGGTCTTATCCTC
* * *
717970 ACACATAGTAGAGGAGTCTGGGAAAACGGTAAGGTCTTAT
1 GCACATAGCAGAGGAGCCTGGG-AAACGGTAAGGTCTTAT
718010 AAGTCAAAGA
Statistics
Matches: 67, Mismatches: 15, Indels: 3
0.79 0.18 0.04
Matches are distributed among these distances:
43 19 0.28
44 48 0.72
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.21
Consensus pattern (43 bp):
GCACATAGCAGAGGAGCCTGGGAAACGGTAAGGTCTTATCCTC
Found at i:718111 original size:24 final size:24
Alignment explanation
Indices: 718084--718156 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 24
718074 GTAAACGAAG
*
718084 ATATCATAAATCAAAACAGAATTC
1 ATATCAAAAATCAAAACAGAATTC
* * * * *
718108 ATATCAGATATCATAATAGAATCC
1 ATATCAAAAATCAAAACAGAATTC
* * *
718132 AGATCAAAAATCAGAACATAATTC
1 ATATCAAAAATCAAAACAGAATTC
718156 A
1 A
718157 AATCGGAAAT
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.52, C:0.16, G:0.07, T:0.25
Consensus pattern (24 bp):
ATATCAAAAATCAAAACAGAATTC
Found at i:730305 original size:41 final size:41
Alignment explanation
Indices: 730242--730394 Score: 184
Period size: 41 Copynumber: 3.7 Consensus size: 41
730232 GGAAGTTCAA
* * *
730242 TGGATTCACCCTTTGGTG-TGAATTTCACTTTGGATTATCAG
1 TGGATTCACCCTTCGG-GATGAATTTCACTTTGAAATATCAG
*
730283 TGGATTCACCCTTCGGGATGAATTTCACTTTGAAATATTAG
1 TGGATTCACCCTTCGGGATGAATTTCACTTTGAAATATCAG
* * *
730324 TGGATTCACCATTCGGGATAAATTTCA-TTTCGAAAAATCAG
1 TGGATTCACCCTTCGGGATGAATTTCACTTT-GAAATATCAG
* **
730365 TGGATTTACCCTTCAAGATGAATTTCACTT
1 TGGATTCACCCTTCGGGATGAATTTCACTT
730395 CGGATTATCG
Statistics
Matches: 96, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
40 4 0.04
41 90 0.94
42 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (41 bp):
TGGATTCACCCTTCGGGATGAATTTCACTTTGAAATATCAG
Found at i:733162 original size:22 final size:20
Alignment explanation
Indices: 733131--733170 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
733121 TACTAGCTGA
733131 TGATTCAATTCATTTCTTTATC
1 TGATTCAATT-ATTT-TTTATC
*
733153 TGATTTAATTATTTTTTA
1 TGATTCAATTATTTTTTA
733171 ATTAAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 4 0.24
22 9 0.53
ACGTcount: A:0.25, C:0.10, G:0.05, T:0.60
Consensus pattern (20 bp):
TGATTCAATTATTTTTTATC
Found at i:733774 original size:2 final size:2
Alignment explanation
Indices: 733722--733756 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
733712 GAGAGGTGTC
733722 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
733757 TTTAGAGGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:740182 original size:91 final size:91
Alignment explanation
Indices: 740027--740209 Score: 366
Period size: 91 Copynumber: 2.0 Consensus size: 91
740017 AACACATCAC
740027 AACATGAAAAGTAAACAAATATCATGGAATGAGGAACACACTTATTTCAAGTATTTAATATCGGC
1 AACATGAAAAGTAAACAAATATCATGGAATGAGGAACACACTTATTTCAAGTATTTAATATCGGC
740092 TAAGTCGTATGCTTCCCATGGTCGTT
66 TAAGTCGTATGCTTCCCATGGTCGTT
740118 AACATGAAAAGTAAACAAATATCATGGAATGAGGAACACACTTATTTCAAGTATTTAATATCGGC
1 AACATGAAAAGTAAACAAATATCATGGAATGAGGAACACACTTATTTCAAGTATTTAATATCGGC
740183 TAAGTCGTATGCTTCCCATGGTCGTT
66 TAAGTCGTATGCTTCCCATGGTCGTT
740209 A
1 A
740210 GTACTAGGTA
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 92 1.00
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (91 bp):
AACATGAAAAGTAAACAAATATCATGGAATGAGGAACACACTTATTTCAAGTATTTAATATCGGC
TAAGTCGTATGCTTCCCATGGTCGTT
Found at i:745479 original size:120 final size:120
Alignment explanation
Indices: 745312--745527 Score: 344
Period size: 120 Copynumber: 1.8 Consensus size: 120
745302 GCAACTTACA
* * * *
745312 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCATAATGAA-GTGGCCA
1 TTGGATTTCAACTTCACGACGAAGGATATCCAAGTCAAAGCTAAACTTCACAACGAATG-GGCCA
*
745376 TCCACGGTTTCAACTTCACGACGGAGGGAATCGTGCTCACCAGCAACAATACAAGC
65 TCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACAATACAAGC
* * *
745432 TTGGATTTCAACTTCACGACGAAGGATTTTCAAGTCAAGGCTAAACTTCACAACGAATGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAAGTCAAAGCTAAACTTCACAACGAATGGGCCAT
745497 CCACGGTTTCAACTTCACGACGAAGGGAATC
66 CCACGGTTTCAACTTCACGACGAAGGGAATC
745528 ATACCTACCA
Statistics
Matches: 87, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
120 86 0.99
121 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (120 bp):
TTGGATTTCAACTTCACGACGAAGGATATCCAAGTCAAAGCTAAACTTCACAACGAATGGGCCAT
CCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACAATACAAGC
Found at i:745693 original size:36 final size:36
Alignment explanation
Indices: 745649--745732 Score: 127
Period size: 36 Copynumber: 2.3 Consensus size: 36
745639 AAGTTTTATC
*
745649 TCTCTTGAAACAAATTTTGTCTCTCTTGT-GATAGTT
1 TCTCTTGAAACAAATTTTGTCTCTCTT-TAGACAGTT
745685 T-TCTTTGAAACAAATTTTGTCTCTCTTTAGACAGTT
1 TCTC-TTGAAACAAATTTTGTCTCTCTTTAGACAGTT
745721 TCTCTTGAAACA
1 TCTCTTGAAACA
745733 CCAATCTTTG
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
35 3 0.07
36 39 0.89
37 2 0.05
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (36 bp):
TCTCTTGAAACAAATTTTGTCTCTCTTTAGACAGTT
Found at i:745851 original size:37 final size:36
Alignment explanation
Indices: 745785--745874 Score: 141
Period size: 37 Copynumber: 2.6 Consensus size: 36
745775 TCTTAAGATA
*
745785 GTTTCTCTTGAAATAC---AAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAACACAAAAAAAAACCTTTGAAAAT
745818 GTTTCTCTTGAAACACAAAAAAAAACCCTTTGAAAAT
1 GTTTCTCTTGAAACACAAAAAAAAA-CCTTTGAAAAT
745855 GTTTCTCTTGAAACACAAAA
1 GTTTCTCTTGAAACACAAAA
745875 GACCTTCGAG
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
33 15 0.29
36 6 0.12
37 31 0.60
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (36 bp):
GTTTCTCTTGAAACACAAAAAAAAACCTTTGAAAAT
Found at i:748259 original size:18 final size:18
Alignment explanation
Indices: 748232--748271 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
748222 ATAAATATGC
* * *
748232 ATATTTATTATATTGTAT
1 ATATTAATTATAATATAT
748250 ATATTAATTATAATATAT
1 ATATTAATTATAATATAT
748268 ATAT
1 ATAT
748272 CTACGTAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (18 bp):
ATATTAATTATAATATAT
Found at i:748586 original size:16 final size:16
Alignment explanation
Indices: 748565--748596 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
748555 CTCTAAAGCC
748565 CCTTCATTTTCCTTTT
1 CCTTCATTTTCCTTTT
*
748581 CCTTCATTTTTCTTTT
1 CCTTCATTTTCCTTTT
748597 TTCTTATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.28, G:0.00, T:0.66
Consensus pattern (16 bp):
CCTTCATTTTCCTTTT
Found at i:749024 original size:10 final size:9
Alignment explanation
Indices: 749010--749043 Score: 50
Period size: 10 Copynumber: 3.6 Consensus size: 9
749000 ACTCATTCTA
749010 TTTTTCTTT
1 TTTTTCTTT
749019 TCTTTTCTTT
1 T-TTTTCTTT
749029 TTTGTTCTTT
1 TTT-TTCTTT
749039 TTTTT
1 TTTTT
749044 TACTATGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 5 0.22
10 18 0.78
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:750233 original size:38 final size:37
Alignment explanation
Indices: 750185--750258 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 37
750175 TTCAAAGGTA
750185 AAATAACAAAC-ATAGCAAGAAATAAGGAATAGAAATAT
1 AAATAACAAACAATA-CAAGAAAT-AGGAATAGAAATAT
* * *
750223 AAATATCAAACAATACAAGCAATAGGAATGGAAATA
1 AAATAACAAACAATACAAGAAATAGGAATAGAAATA
750259 AACCAAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 12 0.38
38 17 0.53
39 3 0.09
ACGTcount: A:0.61, C:0.09, G:0.14, T:0.16
Consensus pattern (37 bp):
AAATAACAAACAATACAAGAAATAGGAATAGAAATAT
Found at i:751077 original size:6 final size:6
Alignment explanation
Indices: 751066--751098 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
751056 TCGATCATCT
751066 TTTCTC TTTCTC TTTCTC TTTCTC TTTCTC TTT
1 TTTCTC TTTCTC TTTCTC TTTCTC TTTCTC TTT
751099 TATGGTTGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTCTC
Found at i:752192 original size:19 final size:19
Alignment explanation
Indices: 752168--752204 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
752158 CATTTTCTGA
*
752168 AAATCAAGTAAGAAACTTC
1 AAATCAAATAAGAAACTTC
752187 AAATCAAATAAGAAACTT
1 AAATCAAATAAGAAACTT
752205 TGAAAATCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.57, C:0.14, G:0.08, T:0.22
Consensus pattern (19 bp):
AAATCAAATAAGAAACTTC
Found at i:752309 original size:41 final size:42
Alignment explanation
Indices: 752245--752345 Score: 105
Period size: 41 Copynumber: 2.4 Consensus size: 42
752235 CATATGACAA
* * * * *
752245 CATCATGGTCAGAGGTCTTACAGATGGCCCAAAGAACTT-AT
1 CATCATGCTCAGAAGACTCACAGATGACCCAAAGAACTTAAT
* * * *
752286 CATCTTGCTCAGAAGACTCACAGATGACCCGAAGCATTTAAT
1 CATCATGCTCAGAAGACTCACAGATGACCCAAAGAACTTAAT
*
752328 CATCATGCTCGGAAGACT
1 CATCATGCTCAGAAGACT
752346 TATTGATGGC
Statistics
Matches: 48, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
41 30 0.62
42 18 0.38
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.24
Consensus pattern (42 bp):
CATCATGCTCAGAAGACTCACAGATGACCCAAAGAACTTAAT
Found at i:756156 original size:12 final size:12
Alignment explanation
Indices: 756136--756165 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
756126 ACATGTAAGC
*
756136 ATTAATCATGAT
1 ATTATTCATGAT
756148 ATTATTCATGAT
1 ATTATTCATGAT
756160 ATTATT
1 ATTATT
756166 GTTATGGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (12 bp):
ATTATTCATGAT
Found at i:756280 original size:19 final size:20
Alignment explanation
Indices: 756247--756286 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
756237 ATTTATTTTG
*
756247 TATTGATAATTATTATTAAA
1 TATTGATAATAATTATTAAA
756267 TATT-ATAATAATTATTAAA
1 TATTGATAATAATTATTAAA
756286 T
1 T
756287 GGGTTTTGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TATTGATAATAATTATTAAA
Found at i:756495 original size:45 final size:43
Alignment explanation
Indices: 756406--756518 Score: 118
Period size: 45 Copynumber: 2.5 Consensus size: 43
756396 TGCCAGAAAG
* * *
756406 TAAAATCAAATGATTAGTTCCTTCCGATTATTGGGTTACGAAAAT
1 TAAAATCAAA-GATTAGTT-CTTTCGATTATTGGATTACAAAAAT
* **
756451 TAAAATCAAAGAGTTAGTTACTTTCGATTATTTGATTGTAAAAAT
1 TAAAATCAAAGA-TTAGTT-CTTTCGATTATTGGATTACAAAAAT
*
756496 TAAACTCAAAGAATTAGTTCTTT
1 TAAAATCAAAG-ATTAGTTCTTT
756519 TTAATTATCG
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
44 6 0.10
45 51 0.88
46 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (43 bp):
TAAAATCAAAGATTAGTTCTTTCGATTATTGGATTACAAAAAT
Found at i:756830 original size:39 final size:40
Alignment explanation
Indices: 756776--756876 Score: 127
Period size: 39 Copynumber: 2.5 Consensus size: 40
756766 ATGATTATGG
* * *
756776 TTTGTAAAAGTAAATAAATCGTTCTG-TTTATTTTT-CTAT
1 TTTGTAAAAGAAAATAAATC-ATCAGATTTATTTTTCCTAT
756815 TTTGTAAAATG-AAATAAATCATCAGATTTATTTTTCCTAT
1 TTTGTAAAA-GAAAATAAATCATCAGATTTATTTTTCCTAT
*
756855 TTAGTAAAAGAAAATAAATCAT
1 TTTGTAAAAGAAAATAAATCAT
756877 TGAATTTATT
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
38 3 0.05
39 28 0.51
40 24 0.44
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.44
Consensus pattern (40 bp):
TTTGTAAAAGAAAATAAATCATCAGATTTATTTTTCCTAT
Found at i:756884 original size:40 final size:38
Alignment explanation
Indices: 756779--756888 Score: 123
Period size: 40 Copynumber: 2.8 Consensus size: 38
756769 ATTATGGTTT
* ** *
756779 GTAAAAGTAAATAAATCGTTCTGTTTATTTTTCTATTTT
1 GTAAAAG-AAATAAATCATTCAATTTATTTTTCTATTTA
756818 GTAAAATGAAATAAATCA-TCAGATTTATTTTTCCTATTTA
1 GTAAAA-GAAATAAATCATTCA-ATTTATTTTT-CTATTTA
*
756858 GTAAAAGAAAATAAATCATTGAATTTATTTT
1 GTAAAAG-AAATAAATCATTCAATTTATTTT
756889 CCGAAGAATC
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
38 2 0.03
39 25 0.41
40 32 0.52
41 2 0.03
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.45
Consensus pattern (38 bp):
GTAAAAGAAATAAATCATTCAATTTATTTTTCTATTTA
Found at i:757004 original size:58 final size:57
Alignment explanation
Indices: 756860--757004 Score: 152
Period size: 58 Copynumber: 2.5 Consensus size: 57
756850 CCTATTTAGT
* *
756860 AAAAGAAAATAAATCATTGAATTTATTTTCCGAAGAATCTTATATGATTCTAGTTTAC
1 AAAAGAAAATAAATCGTTGAA-TTATTTTCCAAAGAATCTTATATGATTCTAGTTTAC
* * * *
756918 AAAAGAAAATAAATCGTTAAAATAATTTTCTAAAGAATCTTATATGATT-TTGTTTTGTA-
1 AAAAGAAAATAAATCGTT-GAATTATTTTCCAAAGAATCTTATATGATTCTAG--TT-TAC
*
756977 AAAAG-AAATAAATTGTTGTAATTATTTT
1 AAAAGAAAATAAATCGTTG-AATTATTTT
757005 TCTGTTCTGT
Statistics
Matches: 73, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
57 2 0.03
58 60 0.82
59 9 0.12
60 2 0.03
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.40
Consensus pattern (57 bp):
AAAAGAAAATAAATCGTTGAATTATTTTCCAAAGAATCTTATATGATTCTAGTTTAC
Found at i:759866 original size:20 final size:20
Alignment explanation
Indices: 759843--759889 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
759833 AAATATTGGC
*
759843 GGTTTTTCCGG-TTTTTTCT
1 GGTTTTCCCGGTTTTTTTCT
759862 AGGTTTTCCCGGTTTTTTTCT
1 -GGTTTTCCCGGTTTTTTTCT
759883 GGTTTTC
1 GGTTTTC
759890 AGTCGGTCCG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.02, C:0.17, G:0.21, T:0.60
Consensus pattern (20 bp):
GGTTTTCCCGGTTTTTTTCT
Found at i:763000 original size:16 final size:16
Alignment explanation
Indices: 762961--762992 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
762951 TTTGTAGTTC
762961 CAAAACCTGTATGAGA
1 CAAAACCTGTATGAGA
762977 CAAAACCTGTATGAGA
1 CAAAACCTGTATGAGA
762993 TTAAACCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.19
Consensus pattern (16 bp):
CAAAACCTGTATGAGA
Found at i:771256 original size:26 final size:26
Alignment explanation
Indices: 771207--771257 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
771197 TTTCGGTGGA
* * * *
771207 TTTAATTCCACCTTTCGGTGGATTTG
1 TTTAATGCCACATTTCGATAGATTTG
771233 TTTAATGCCACATTTCGATAGATTT
1 TTTAATGCCACATTTCGATAGATTT
771258 TAATTTTCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.22, C:0.18, G:0.16, T:0.45
Consensus pattern (26 bp):
TTTAATGCCACATTTCGATAGATTTG
Found at i:775911 original size:33 final size:33
Alignment explanation
Indices: 775864--775928 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
775854 GTGGTACATT
**
775864 ATCATCCATTTGAATAAATTATGTAAACAAAAA
1 ATCATCCAGCTGAATAAATTATGTAAACAAAAA
775897 ATCATCCAGCTGAATAAATTATGTAAACAAAA
1 ATCATCCAGCTGAATAAATTATGTAAACAAAA
775929 TTACCCCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.51, C:0.14, G:0.08, T:0.28
Consensus pattern (33 bp):
ATCATCCAGCTGAATAAATTATGTAAACAAAAA
Found at i:776428 original size:9 final size:9
Alignment explanation
Indices: 776380--776428 Score: 52
Period size: 9 Copynumber: 5.9 Consensus size: 9
776370 TTTTGAATCA
776380 AATTAA-TC
1 AATTAATTC
776388 AA-TAATTC
1 AATTAATTC
*
776396 AATTAATTA
1 AATTAATTC
*
776405 AATTAA-CC
1 AATTAATTC
776413 AA-TAATTC
1 AATTAATTC
776421 AATTAATT
1 AATTAATT
776429 GGGTTAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
7 6 0.18
8 11 0.33
9 16 0.48
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (9 bp):
AATTAATTC
Found at i:776435 original size:25 final size:25
Alignment explanation
Indices: 776379--776428 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
776369 ATTTTGAATC
*
776379 AAATTAATCAATAATTCAATTAATT
1 AAATTAACCAATAATTCAATTAATT
776404 AAATTAACCAATAATTCAATTAATT
1 AAATTAACCAATAATTCAATTAATT
776429 GGGTTAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (25 bp):
AAATTAACCAATAATTCAATTAATT
Found at i:776811 original size:15 final size:15
Alignment explanation
Indices: 776787--776844 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
776777 ATAAGGTTAT
*
776787 TTATTTTAAAATAAA
1 TTATTATAAAATAAA
*
776802 GTATTATAAAATAAA
1 TTATTATAAAATAAA
*
776817 TTATTTTAAAATAAA
1 TTATTATAAAATAAA
776832 TTATTATAAAATA
1 TTATTATAAAATA
776845 TAGATTGATT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (15 bp):
TTATTATAAAATAAA
Found at i:776823 original size:30 final size:30
Alignment explanation
Indices: 776787--776844 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
776777 ATAAGGTTAT
776787 TTATTTTAAAATAAAGTATTATAAAATAAA
1 TTATTTTAAAATAAAGTATTATAAAATAAA
*
776817 TTATTTTAAAATAAATTATTATAAAATA
1 TTATTTTAAAATAAAGTATTATAAAATA
776845 TAGATTGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (30 bp):
TTATTTTAAAATAAAGTATTATAAAATAAA
Found at i:776872 original size:15 final size:14
Alignment explanation
Indices: 776852--776887 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
776842 ATATAGATTG
776852 ATTTATTTTAAAATA
1 ATTTATTTT-AAATA
776867 ATTTATTTTAAATA
1 ATTTATTTTAAATA
776881 ATTTATT
1 ATTTATT
776888 AGTATGGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:776881 original size:14 final size:15
Alignment explanation
Indices: 776785--776887 Score: 82
Period size: 15 Copynumber: 6.5 Consensus size: 15
776775 TAATAAGGTT
776785 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
** *
776800 AAGTATTATAAAATA
1 ATTTATTTTAAAATA
*
776815 AATTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
776830 AATTATTATAAAATATAGA
1 ATTTATT-TTAAA-AT--A
776849 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
776867 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
776881 ATTTATT
1 ATTTATT
776888 AGTATGGATT
Statistics
Matches: 73, Mismatches: 8, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
14 12 0.16
15 41 0.56
16 4 0.05
17 2 0.03
18 1 0.01
19 1 0.01
20 2 0.03
21 4 0.05
22 6 0.08
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:776900 original size:47 final size:46
Alignment explanation
Indices: 776847--776967 Score: 142
Period size: 47 Copynumber: 2.6 Consensus size: 46
776837 ATAAAATATA
776847 GATTGATTTATTTTAAAATAATTTATTTTAAATAATT-TA-TTAGTATG
1 GATTGATTTATTTTAAAATAATTTATTTT--ATAATTGTAGTT-GTATG
* *
776894 GATTGATTTATTTTAAAATATGGATTGA-TTTATTATTGTAGTTGTATG
1 GATTGATTTATTTTAAAATA---ATTTATTTTATAATTGTAGTTGTATG
776942 GATTGATTTATTTT-AAATAATTTATT
1 GATTGATTTATTTTAAAATAATTTATT
776968 AGTATGAATT
Statistics
Matches: 65, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
44 4 0.06
45 1 0.02
47 30 0.46
48 21 0.32
49 5 0.08
50 4 0.06
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (46 bp):
GATTGATTTATTTTAAAATAATTTATTTTATAATTGTAGTTGTATG
Found at i:776906 original size:22 final size:23
Alignment explanation
Indices: 776881--776954 Score: 71
Period size: 22 Copynumber: 3.2 Consensus size: 23
776871 ATTTTAAATA
776881 ATTTAT-TAGTATGGATTGATTT
1 ATTTATATAGTATGGATTGATTT
* *
776903 ATTT-TAAAATATGGATTGATTT
1 ATTTATATAGTATGGATTGATTT
* *
776925 ATTATTGTAGTTGTATGGATTGATTT
1 A-T-TTATA-TAGTATGGATTGATTT
776951 ATTT
1 ATTT
776955 TAAATAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
21 1 0.02
22 19 0.45
23 1 0.02
24 4 0.10
25 3 0.07
26 14 0.33
ACGTcount: A:0.28, C:0.00, G:0.18, T:0.54
Consensus pattern (23 bp):
ATTTATATAGTATGGATTGATTT
Found at i:776966 original size:14 final size:14
Alignment explanation
Indices: 776947--776999 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
776937 GTATGGATTG
776947 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
776961 ATTTATTAGTATGAATTG
1 ATTTATT--T-T-AAATA
776979 ATTTATTTTAAATA
1 ATTTATTTTAAATA
776993 ATTTATT
1 ATTTATT
777000 AGTATGAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 17 0.55
15 1 0.03
16 2 0.06
17 1 0.03
18 10 0.32
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:776979 original size:32 final size:32
Alignment explanation
Indices: 776937--777724 Score: 339
Period size: 32 Copynumber: 26.8 Consensus size: 32
776927 TATTGTAGTT
*
776937 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGAATTGATTTATTTTAAATAATTTATTA
776969 GTATGAATTGATTTATTTTAAATAATTTATTA
1 GTATGAATTGATTTATTTTAAATAATTTATTA
777001 GTATGAATTGATTTATTTT-AA-AA--TA-T-
1 GTATGAATTGATTTATTTTAAATAATTTATTA
777027 G---G-ATTGATTTATTTTAAATAATTTATTA
1 GTATGAATTGATTTATTTTAAATAATTTATTA
777055 GTATGAATTGATTTATTTT-AA-AA--TA-T-
1 GTATGAATTGATTTATTTTAAATAATTTATTA
777081 G---G-ATTGATTTATTTTAAATAATTTATTA
1 GTATGAATTGATTTATTTTAAATAATTTATTA
*
777109 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGAATTGATTTATTTTAAATAATTTATTA
*
777141 GTATGAATTGATTTATTTTAAAATATGGATTAATTTA
1 GTATGAATTGATTTATTTT-AAATA---ATTTA-TTA
* * ** * *
777178 TTATTGTAGTTGTATGGA-TTT-ATTTATTT-TTAA
1 GTA-TG-AATTG-ATTTATTTTAAATAATTTATT-A
* *
777211 ATAT-AGATTGATTTATTATT--AT-A---GTT-
1 GTATGA-ATTGATTTATT-TTAAATAATTTATTA
*
777237 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGAATTGATTTATTTTAAATAATTTATTA
*
777269 GTATGTATTGGA-TTATTTT-AA-AA--TA-T-
1 GTATGAATT-GATTTATTTTAAATAATTTATTA
777295 G---G-ATTGATTTATTTTAAATAATTTATTA
1 GTATGAATTGATTTATTTTAAATAATTTATTA
777323 GTATGGAA-TGATTTATTTTAAATAATTTATTA
1 GTAT-GAATTGATTTATTTTAAATAATTTATTA
777355 GTAT-AGATTGATTTATTTT-AA-AA--TA-T-
1 GTATGA-ATTGATTTATTTTAAATAATTTATTA
*
777381 G---G-ATTGATTTATTTTAAAA----T-TT-
1 GTATGAATTGATTTATTTTAAATAATTTATTA
777403 G---G-ATTGATTTATTTTAAATAATTTATTA
1 GTATGAATTGATTTATTTTAAATAATTTATTA
**
777431 GTAT-ATATTGATTTATTTTAAA-ATATAGATT-
1 GTATGA-ATTGATTTATTTTAAATA-ATTTATTA
** * *
777462 G-ATTTATT-ATTGTAGTTGTATGAATTGATTTATTTTA
1 GTATGAATTGATT-TA-TT-T-T-AAATAATTTA--TTA
* * * * * *
777499 -AAT-AATTTATTAGTATGTATTGATTTATTT-TAAA
1 GTATGAATTGATT--TAT-T-TTAAATAATTTAT-TA
* *
777533 ATATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGAATTGATTTATTTTAAATAATTTATTA
*
777565 GTATGGATTGATTTATTTT-AA-AA--TA-T-
1 GTATGAATTGATTTATTTTAAATAATTTATTA
777591 G---G-ATTGATTTATTTTAAATAATTTATTA
1 GTATGAATTGATTTATTTTAAATAATTTATTA
*
777619 GTATGGATTGATTTATTTT-AA-AA--TA-T-
1 GTATGAATTGATTTATTTTAAATAATTTATTA
777645 G---G-ATTGATTTATTTTAAAT-A---ATT-
1 GTATGAATTGATTTATTTTAAATAATTTATTA
*
777668 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGAATTGATTTATTTTAAATAATTTATTA
* *
777700 GTATGTATTAATTTATTTTATAATA
1 GTATGAATTGATTTATTTTA-AATA
777725 TGGATTGATT
Statistics
Matches: 601, Mismatches: 42, Indels: 225
0.69 0.05 0.26
Matches are distributed among these distances:
21 2 0.00
22 96 0.16
23 20 0.03
24 8 0.01
25 2 0.00
26 30 0.05
27 31 0.05
28 21 0.03
29 3 0.00
30 25 0.04
31 30 0.05
32 247 0.41
33 19 0.03
34 12 0.02
35 2 0.00
36 22 0.04
37 14 0.02
38 7 0.01
39 7 0.01
40 3 0.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (32 bp):
GTATGAATTGATTTATTTTAAATAATTTATTA
Found at i:777027 original size:22 final size:22
Alignment explanation
Indices: 777002--777044 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
776992 AATTTATTAG
777002 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
777024 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
777045 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:777039 original size:54 final size:54
Alignment explanation
Indices: 776867--777753 Score: 515
Period size: 54 Copynumber: 16.4 Consensus size: 54
776857 TTTTAAAATA
776867 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
776921 ATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTT-AA-AA--TA-T-G---G-ATTG
*
776979 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
777033 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
777087 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAATA---ATTT
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * * * * * ** * * *
777137 A-TTAGTATGAATTGATTTATTTTAAAATATGGATTAATTTATTATTGTAGT-TGTATGG
1 ATTTA-TTTTAAATAATTTA--TT--AGTATGGATTGATTTATT-TTAAAATATGGATTG
* * * **
777195 ATTTA-TTT--AT--TTT-TAAATATAGATTGATTTATTATTATAGTTGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATT-TTA-A--AATATGGATTG
*
777247 ATTTATTTTAAATAATTTATTAGTATGTATTGGA-TTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATT-GATTTATTTTAAAATATGGATTG
* *
777301 ATTTATTTTAAATAATTTATTAGTATGGAATGATTTATTTT-AAATA---ATTT
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * * * * *
777351 A-TTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATTTGGATTG
1 ATTTATTTTA-AATAATTTA--TT--AGTATGGATTGATTTATTTTAAAATATGGATTG
** *
777409 ATTTATTTTAAATAATTTATTAGTATATATTGATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * **
777463 ATTTA--TT--AT--TGTAGTT-GTATGAATTGATTTATTTT-AAATAATTTATTAG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAAT-ATGGATT-G
* * ** * * * **
777512 TATGTA-TTGATTTATTTTA-AAATATGGATTGATTTATTTT-AAATAATTTATTAG
1 -ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAAT-ATGGATT-G
** * ** * * * **
777566 TATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTTT-AAATAATTTATTAG
1 -ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAAT-ATGGATT-G
** * ** * * *
777620 TATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTTTAAATAATTGTATGGATTG
1 -ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AA-AA---TATGGATTG
* * *
777678 ATTTATTTTAAATAATTTATTAGTATGTATTAATTTATTTTATAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
777732 ATTTATTTTAAATAATTTATTA
1 ATTTATTTTAAATAATTTATTA
777754 TTGTAGTTGT
Statistics
Matches: 686, Mismatches: 78, Indels: 138
0.76 0.09 0.15
Matches are distributed among these distances:
47 4 0.01
48 66 0.10
49 16 0.02
50 36 0.05
51 3 0.00
52 20 0.03
53 20 0.03
54 371 0.54
55 13 0.02
56 6 0.01
57 15 0.02
58 48 0.07
59 34 0.05
60 5 0.01
62 4 0.01
63 4 0.01
64 21 0.03
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:777053 original size:86 final size:86
Alignment explanation
Indices: 776938--777586 Score: 667
Period size: 86 Copynumber: 7.6 Consensus size: 86
776928 ATTGTAGTTG
776938 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAATAATTTATTAGT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAATAATTTATTAGT
777003 ATGAATTGATTTATTTTAAAA
66 ATGAATTGATTTATTTTAAAA
**
777024 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAA-ATATGGATT-G
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAATA-ATTTATTAG
* * * ** * * *
777087 -ATTTATTTTAAATAATTTATTAG
65 TA-TGAATTGATTTATTTTA-AAA
777110 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTAAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT---A-A---A-TAAT
* * *
777175 TTATTATTGTAGTTGTATGGATTTATTTATTTTTAAA
58 TTATTA--GTA--TGAATTGATTT----ATTTTAAAA
* * *
777212 TATAGATTGATTTATTATT--AT-A---GTT-GTATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATT-TTAAATAATTTATTAGTATGAATTGATTTATTTTAAATAATTTATTAG
*
777270 TATGTATTGGA-TTATTTTAAAA
65 TATGAATT-GATTTATTTTAAAA
777292 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGAA-TGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAGTAT-GAATTGATTTATTTTAAATAATTTATTAG
777356 TAT-AGATTGATTTATTTTAAAA
65 TATGA-ATTGATTTATTTTAAAA
777378 TATGGATTGATTTATTTT-AA-AA--T-TT-G---G-ATTGATTTATTTTAAATAATTTATTAGT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAATAATTTATTAGT
777433 AT-ATATTGATTTATTTTAAAA
66 ATGA-ATTGATTTATTTTAAAA
* *
777454 TATAGATTGATTTA--TT--AT--TGTAGTT-GTATGAATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTA-TTAGTATGAATTGATTTATTTTAAATAATTTATTAG
*
777512 TATGTATTGATTTATTTTAAAA
65 TATGAATTGATTTATTTTAAAA
*
777534 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAA
777587 ATATGGATTG
Statistics
Matches: 474, Mismatches: 38, Indels: 102
0.77 0.06 0.17
Matches are distributed among these distances:
73 1 0.00
74 3 0.01
75 1 0.00
76 63 0.13
79 3 0.01
80 84 0.18
81 4 0.01
82 4 0.01
84 12 0.03
85 23 0.05
86 200 0.42
87 2 0.00
88 10 0.02
89 2 0.00
90 1 0.00
92 1 0.00
93 2 0.00
94 5 0.01
95 1 0.00
96 18 0.04
97 3 0.01
98 1 0.00
99 5 0.01
100 1 0.00
101 2 0.00
102 16 0.03
103 6 0.01
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (86 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAATAATTTATTAGT
ATGAATTGATTTATTTTAAAA
Found at i:777081 original size:22 final size:22
Alignment explanation
Indices: 777056--777098 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
777046 AATTTATTAG
777056 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
777078 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
777099 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Done.