Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002273.1 Hibiscus syriacus cultivar Beakdansim tig00004620_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: 802197
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:549792 original size:61 final size:61
Alignment explanation
Indices: 549671--549798 Score: 193
Period size: 61 Copynumber: 2.1 Consensus size: 61
549661 GAATATGTAA
* *
549671 ATCGCAACGCGATAACACGTGATCGCAACGCGATTCTGACTATCACAACGAGATTTTGACT
1 ATCGCAACGCGATAACACGTAATCGCAACGCGATTCTGACTATCACAACGAGATTCTGACT
* * * *
549732 ATCGCAACGCGATAATATGTAATCGCAACGCGATTCTGACTATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAACACGTAATCGCAACGCGATTCTGACTATCACAACGAGATTCTGACT
*
549793 AACGCA
1 ATCGCA
549799 TCACTGAATT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.23
Consensus pattern (61 bp):
ATCGCAACGCGATAACACGTAATCGCAACGCGATTCTGACTATCACAACGAGATTCTGACT
Found at i:549819 original size:61 final size:60
Alignment explanation
Indices: 549692--549821 Score: 145
Period size: 61 Copynumber: 2.1 Consensus size: 60
549682 ATAACACGTG
* * * **
549692 ATCGCAACGCGATTCTGACTATCACAACGAGATTTTGACTATCGCAACGCGATAATATGTA
1 ATCGCAACGCGATTCTGACTATCACAACGAGATTCTGACTAACGCAACACGA-AATATCAA
* * * *
549753 ATCGCAACGCGATTCTGACTATCGCAACGCGATTCTGACTAACGCATCACTG-AATTTCAA
1 ATCGCAACGCGATTCTGACTATCACAACGAGATTCTGACTAACGCAACAC-GAAATATCAA
549813 ATTCGCAAC
1 A-TCGCAAC
549822 AGGTTTTAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
60 6 0.10
61 51 0.88
62 1 0.02
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (60 bp):
ATCGCAACGCGATTCTGACTATCACAACGAGATTCTGACTAACGCAACACGAAATATCAA
Found at i:550650 original size:24 final size:24
Alignment explanation
Indices: 550618--550671 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
550608 GTATTCGAAA
550618 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
550642 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
550666 TTTGAT
1 TTTGAT
550672 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:550890 original size:14 final size:14
Alignment explanation
Indices: 550861--550897 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
550851 AGAAAAAGAA
550861 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
550876 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
550890 GAAGAAAA
1 GAAGAAAA
550898 TGCCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:552948 original size:12 final size:12
Alignment explanation
Indices: 552931--552961 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
552921 CAAGCAAAAG
552931 GCAATCAAAATC
1 GCAATCAAAATC
552943 GCAATCAAAATC
1 GCAATCAAAATC
*
552955 CCAATCA
1 GCAATCA
552962 CAACCGGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.48, C:0.29, G:0.06, T:0.16
Consensus pattern (12 bp):
GCAATCAAAATC
Found at i:553164 original size:20 final size:20
Alignment explanation
Indices: 553139--553360 Score: 198
Period size: 20 Copynumber: 11.7 Consensus size: 20
553129 CACATTCATT
553139 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAATA
*
553159 TGACTATCGCAACACGAATA
1 TGACTATCGCAACGCGAATA
553179 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAATA
*** *
553199 TGACTATCGCAACATAAATT
1 TGACTATCGCAACGCGAATA
* *
553219 TGAATATCGCAACG-G--GA
1 TGACTATCGCAACGCGAATA
* * *
553236 T-A--ATCGCAATGCAAAAA
1 TGACTATCGCAACGCGAATA
*
553253 TGACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
* *
553273 TGACTATCACAACG-G--GA
1 TGACTATCGCAACGCGAATA
*
553290 T-A--ATCGCAACGCGAAAA
1 TGACTATCGCAACGCGAATA
* * *
553307 TGACAATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
*
553327 TGACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
553347 TGACTATCGCAACG
1 TGACTATCGCAACG
553361 AGAAAATCGC
Statistics
Matches: 162, Mismatches: 28, Indels: 24
0.76 0.13 0.11
Matches are distributed among these distances:
14 16 0.10
15 1 0.01
16 2 0.01
17 6 0.04
18 2 0.01
19 1 0.01
20 134 0.83
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (20 bp):
TGACTATCGCAACGCGAATA
Found at i:553273 original size:54 final size:54
Alignment explanation
Indices: 553139--553340 Score: 215
Period size: 54 Copynumber: 3.6 Consensus size: 54
553129 CACATTCATT
** *
553139 TGACTATCGCAACGCGAATATGACTATCGCAACACGAATATGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAATATGACTATCGC-A-ACG-GGAT-A--ATCGCAACGCGAAAA
*** * * * *
553199 TGACTATCGCAACATAAATTTGAATATCGCAACGGGATAATCGCAATGCAAAAA
1 TGACTATCGCAACGCGAATATGACTATCGCAACGGGATAATCGCAACGCGAAAA
* *
553253 TGACTATCGCAACGCGAATTTGACTATCACAACGGGATAATCGCAACGCGAAAA
1 TGACTATCGCAACGCGAATATGACTATCGCAACGGGATAATCGCAACGCGAAAA
* * *
553307 TGACAATCGCAATGCGAAAATGACTATCGCAACG
1 TGACTATCGCAACGCGAATATGACTATCGCAACG
553341 CGAATTTGAC
Statistics
Matches: 120, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
54 88 0.73
56 1 0.01
57 2 0.02
58 3 0.03
59 1 0.01
60 25 0.21
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.20
Consensus pattern (54 bp):
TGACTATCGCAACGCGAATATGACTATCGCAACGGGATAATCGCAACGCGAAAA
Found at i:553296 original size:34 final size:34
Alignment explanation
Indices: 553258--553394 Score: 121
Period size: 34 Copynumber: 3.9 Consensus size: 34
553248 AAAAATGACT
* *
553258 ATCGCAACGCGAATTTGACTATCACAACGGGATA
1 ATCGCAACGCGAATTTGACTATCGCAACGAGATA
** * *
553292 ATCGCAACGCGAAAATGACAATCGCAATGCGAAAATGA
1 ATCGCAACGCGAATTTGACTATCGCAA--CG-AGAT-A
*
553330 CTATCGCAACGCGAATTTGACTATCGCAACGAGAAA
1 --ATCGCAACGCGAATTTGACTATCGCAACGAGATA
* * * *
553366 ATCGCAAAGTGTATTAGACTATCGCAACG
1 ATCGCAACGCGAATTTGACTATCGCAACG
553395 CGAATATGAT
Statistics
Matches: 82, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
34 48 0.59
36 3 0.04
37 4 0.05
38 3 0.04
40 24 0.29
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (34 bp):
ATCGCAACGCGAATTTGACTATCGCAACGAGATA
Found at i:553369 original size:74 final size:74
Alignment explanation
Indices: 553144--553372 Score: 264
Period size: 74 Copynumber: 3.1 Consensus size: 74
553134 TCATTTGACT
* * ** * *
553144 ATCGCAACGCGAATATGACTATCGCAACACGAATATGACTATCGCAACGCGAATATGACTATCGC
1 ATCGCAACGCGAAAATGACAATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGC
*
553209 AAC-ATAAA
66 AACGAGAAA
* * * *** * *
553217 TTTGAATATCGC-AACGGGATAATCGCAATGCAAAAATGACTATCGCAACGCGAATTTGACTATC
1 ATCGCA-A-CGCGAAAATGACAATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATC
* * *
553281 ACAACGGGATA
64 GCAACGAGAAA
553292 ATCGCAACGCGAAAATGACAATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGC
1 ATCGCAACGCGAAAATGACAATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGC
553357 AACGAGAAA
66 AACGAGAAA
553366 ATCGCAA
1 ATCGCAA
553373 AGTGTATTAG
Statistics
Matches: 124, Mismatches: 28, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
73 6 0.05
74 110 0.89
75 8 0.06
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (74 bp):
ATCGCAACGCGAAAATGACAATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGC
AACGAGAAA
Found at i:553535 original size:36 final size:34
Alignment explanation
Indices: 553495--553574 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 34
553485 TAAACTTTTA
*
553495 ATCAATTAAACAAGCACAAATAATAATTATTTACAC
1 ATCAATTAAACAA--ACAAATAAGAATTATTTACAC
*
553531 ATCAATT----AAACAAATAAGAATTATTTATAC
1 ATCAATTAAACAAACAAATAAGAATTATTTACAC
553561 ATCAATTAAACAAA
1 ATCAATTAAACAAA
553575 TCAACTCTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
30 26 0.68
32 2 0.05
34 3 0.08
36 7 0.18
ACGTcount: A:0.55, C:0.14, G:0.03, T:0.29
Consensus pattern (34 bp):
ATCAATTAAACAAACAAATAAGAATTATTTACAC
Found at i:553544 original size:30 final size:30
Alignment explanation
Indices: 553510--553575 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
553500 TTAAACAAGC
*
553510 ACAAATAATAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
*
553540 ACAAATAAGAATTATTTATACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
553570 ACAAAT
1 ACAAAT
553576 CAACTCTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.55, C:0.12, G:0.02, T:0.32
Consensus pattern (30 bp):
ACAAATAAGAATTATTTACACATCAATTAA
Found at i:554768 original size:14 final size:14
Alignment explanation
Indices: 554749--554777 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
554739 CGCTCATGTA
554749 GATAAAAATCAACT
1 GATAAAAATCAACT
554763 GATAAAAATCAACT
1 GATAAAAATCAACT
554777 G
1 G
554778 CGGTGTTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.14, G:0.10, T:0.21
Consensus pattern (14 bp):
GATAAAAATCAACT
Found at i:555013 original size:21 final size:21
Alignment explanation
Indices: 554964--555070 Score: 106
Period size: 21 Copynumber: 5.1 Consensus size: 21
554954 TCTAGAATGT
* *
554964 TGGGAGGGACCTCTTCAACGA
1 TGGGAGGGGCCTCTTGAACGA
** *
554985 TGACAGGGGCCTCTTGAACGG
1 TGGGAGGGGCCTCTTGAACGA
* **
555006 TGGGAGGGGACTCTTGAGGGA
1 TGGGAGGGGCCTCTTGAACGA
**
555027 TGATAGGGGCCTCTTGAACGA
1 TGGGAGGGGCCTCTTGAACGA
* *
555048 TAGGAGAGGCCTCTTGAACGA
1 TGGGAGGGGCCTCTTGAACGA
555069 TG
1 TG
555071 ACAGGTGATT
Statistics
Matches: 65, Mismatches: 21, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 65 1.00
ACGTcount: A:0.22, C:0.19, G:0.38, T:0.21
Consensus pattern (21 bp):
TGGGAGGGGCCTCTTGAACGA
Found at i:555029 original size:42 final size:42
Alignment explanation
Indices: 554966--555075 Score: 132
Period size: 42 Copynumber: 2.6 Consensus size: 42
554956 TAGAATGTTG
* * *
554966 GGAG-GGACCTCTTCAACGATGACAGGGGCCTCTTGAACGGTG
1 GGAGAGGA-CTCTTGAACGATGACAGGGGCCTCTTGAACGATA
* ** *
555008 GGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGATA
1 GGAGAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGATA
*
555050 GGAGAGGCCTCTTGAACGATGACAGG
1 GGAGAGGACTCTTGAACGATGACAGG
555076 TGATTCGAGC
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 53 0.95
43 3 0.05
ACGTcount: A:0.24, C:0.19, G:0.38, T:0.19
Consensus pattern (42 bp):
GGAGAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGATA
Found at i:555578 original size:20 final size:20
Alignment explanation
Indices: 555553--555590 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
555543 ATAGCTTCTG
555553 AAACTTAAAATCGCAACACA
1 AAACTTAAAATCGCAACACA
555573 AAACTTAAAATCGCAACA
1 AAACTTAAAATCGCAACA
555591 TGAAAATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.24, G:0.05, T:0.16
Consensus pattern (20 bp):
AAACTTAAAATCGCAACACA
Found at i:555712 original size:20 final size:19
Alignment explanation
Indices: 555687--555794 Score: 117
Period size: 20 Copynumber: 5.4 Consensus size: 19
555677 GTGATTATCC
555687 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
*
555707 CGTTGCGATAGTCGTTTTCG
1 CGTTGCGATAGTC-ATTTCG
* *
555727 CATTGCGATAGTCAAATTCG
1 CGTTGCGATAGTC-ATTTCG
*
555747 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTC-ATTTCG
*
555767 CGTTGCGATAATCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
*
555787 TGTTGCGA
1 CGTTGCGA
555795 CTATTCTTCT
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
19 1 0.01
20 73 0.95
21 3 0.04
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.35
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:555785 original size:60 final size:54
Alignment explanation
Indices: 555646--555786 Score: 158
Period size: 60 Copynumber: 2.5 Consensus size: 54
555636 ATGCGAAACT
* *
555646 AAATTCGTGTTGCGATAGTCATTTTCGCATTGTGATTATCCCGTTGCGATAGTC
1 AAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCGTTGCGATAGTC
* * *
555700 -ATTTCCGCGTTGCGATAGTCGTTTTCGCATTGCGATAGTCAAATTCGCGTTGCGATAGTC
1 AAATT-CGCGTTGCGATAGTCATTTTCGCATTGCGAT--T---A-TCCCGTTGCGATAGTC
*
555760 AAATTCGCGTTGCGATAATCATTTTCG
1 AAATTCGCGTTGCGATAGTCATTTTCG
555787 TGTTGCGACT
Statistics
Matches: 71, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
53 3 0.04
54 28 0.39
56 1 0.01
59 1 0.01
60 35 0.49
61 3 0.04
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.37
Consensus pattern (54 bp):
AAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCGTTGCGATAGTC
Found at i:555970 original size:29 final size:31
Alignment explanation
Indices: 555913--555973 Score: 99
Period size: 29 Copynumber: 2.0 Consensus size: 31
555903 CTACTACCGA
555913 ATGAATTTACTAAGCAATCCAAAAGACAAAT
1 ATGAATTTACTAAGCAATCCAAAAGACAAAT
*
555944 ATGAATTTACTGA-CAA-CCAAAAGACAAAT
1 ATGAATTTACTAAGCAATCCAAAAGACAAAT
555973 A
1 A
555974 CTAAGTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 14 0.48
30 3 0.10
31 12 0.41
ACGTcount: A:0.52, C:0.16, G:0.10, T:0.21
Consensus pattern (31 bp):
ATGAATTTACTAAGCAATCCAAAAGACAAAT
Found at i:557785 original size:20 final size:20
Alignment explanation
Indices: 557762--557817 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
557752 TCTGAAACTT
557762 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
557782 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
557802 ATTATCGCAACGCGAA
1 AAAATCGCAACACGAA
557818 TTTAACTATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:558441 original size:20 final size:20
Alignment explanation
Indices: 558416--558485 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
558406 GCAACGAGCT
558416 CGTTGCGATAGTCAAAATCA
1 CGTTGCGATAGTCAAAATCA
** *
558436 CGTTGCGATCACGT-ATTATCG
1 CGTTGCGAT-A-GTCAAAATCA
* *
558457 CGTTGCGATAGTCAGAATCT
1 CGTTGCGATAGTCAAAATCA
*
558477 CATTGCGAT
1 CGTTGCGAT
558486 CATGTGTTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
19 2 0.05
20 22 0.55
21 14 0.35
22 2 0.05
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (20 bp):
CGTTGCGATAGTCAAAATCA
Found at i:558462 original size:21 final size:20
Alignment explanation
Indices: 558436--558506 Score: 63
Period size: 21 Copynumber: 3.5 Consensus size: 20
558426 GTCAAAATCA
558436 CGTTGCGATCACGTATTATCG
1 CGTTGCGATCA-GTATTATCG
** *
558457 CGTTGCGAT-AGTCAGAATCT
1 CGTTGCGATCAGT-ATTATCG
* *
558477 CATTGCGATCATGTGTTATCG
1 CGTTGCGATCA-GTATTATCG
558498 CGTTGCGAT
1 CGTTGCGAT
558507 TTACATATTC
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 2 0.05
20 13 0.34
21 21 0.55
22 2 0.05
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.34
Consensus pattern (20 bp):
CGTTGCGATCAGTATTATCG
Found at i:558483 original size:41 final size:41
Alignment explanation
Indices: 558416--558506 Score: 137
Period size: 41 Copynumber: 2.2 Consensus size: 41
558406 GCAACGAGCT
*
558416 CGTTGCGATAGTCAAAATCACGTTGCGATCACGTATTATCG
1 CGTTGCGATAGTCAAAATCACATTGCGATCACGTATTATCG
* * * *
558457 CGTTGCGATAGTCAGAATCTCATTGCGATCATGTGTTATCG
1 CGTTGCGATAGTCAAAATCACATTGCGATCACGTATTATCG
558498 CGTTGCGAT
1 CGTTGCGAT
558507 TTACATATTC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (41 bp):
CGTTGCGATAGTCAAAATCACATTGCGATCACGTATTATCG
Found at i:558638 original size:19 final size:19
Alignment explanation
Indices: 558614--558668 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
558604 GCGATAATGG
*
558614 AGATCGCGTTGCGATTTAA
1 AGATCGCATTGCGATTTAA
558633 AGATCGCATTGCGATTTAA
1 AGATCGCATTGCGATTTAA
558652 AGATCGCATTGCGATTT
1 AGATCGCATTGCGATTT
558669 TGTTGGTCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (19 bp):
AGATCGCATTGCGATTTAA
Found at i:566141 original size:103 final size:103
Alignment explanation
Indices: 565962--566174 Score: 381
Period size: 103 Copynumber: 2.1 Consensus size: 103
565952 GGGTCTACGC
*
565962 GGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
** *
566027 CTTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
566065 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
*
566130 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
566168 GGTCCTT
1 GGTCCTT
566175 ATGGACATTA
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
Found at i:566258 original size:23 final size:23
Alignment explanation
Indices: 566193--566258 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
566183 TATTATATGC
*
566193 CACTACGGTGCAATTCTACACGG
1 CACTACGGTGCAATTCTACGCGG
* *
566216 CACTCCGGTGCAATTCTACGTGG
1 CACTACGGTGCAATTCTACGCGG
* *
566239 CACTTCGGTGCAATTATACG
1 CACTACGGTGCAATTCTACG
566259 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.26
Consensus pattern (23 bp):
CACTACGGTGCAATTCTACGCGG
Found at i:566482 original size:16 final size:16
Alignment explanation
Indices: 566431--566483 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
566421 TGTATGTGAT
566431 ATATGTATATGATGTGTG
1 ATATG-ATAT-ATGTGTG
* * **
566449 ATATGATGTGTGCATG
1 ATATGATATATGTGTG
566465 ATATGATATATGTGTG
1 ATATGATATATGTGTG
566481 ATA
1 ATA
566484 GGGGTTATGG
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
16 19 0.70
17 3 0.11
18 5 0.19
ACGTcount: A:0.30, C:0.02, G:0.26, T:0.42
Consensus pattern (16 bp):
ATATGATATATGTGTG
Found at i:574121 original size:57 final size:57
Alignment explanation
Indices: 574033--574146 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
574023 TATGGCGTTG
574033 CACTTTTAGCATCAGGGCAAAGGTCAACCATTACAGGCATTTATGTAGGACAATCTA
1 CACTTTTAGCATCAGGGCAAAGGTCAACCATTACAGGCATTTATGTAGGACAATCTA
574090 CACTTTTAGCATCAGGGCAAAGGTCAACCATTACAGGCATTTATGTAGGACAATCTA
1 CACTTTTAGCATCAGGGCAAAGGTCAACCATTACAGGCATTTATGTAGGACAATCTA
574147 TCATACAGGT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.26
Consensus pattern (57 bp):
CACTTTTAGCATCAGGGCAAAGGTCAACCATTACAGGCATTTATGTAGGACAATCTA
Found at i:579272 original size:24 final size:25
Alignment explanation
Indices: 579240--579286 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
579230 TGCATAATTT
*
579240 AAAACAAAAAG-AGAGAAAATTAAA
1 AAAAAAAAAAGAAGAGAAAATTAAA
*
579264 AAAAAAAAAAGAAGATAAAATTA
1 AAAAAAAAAAGAAGAGAAAATTA
579287 CATTGGCGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.77, C:0.02, G:0.11, T:0.11
Consensus pattern (25 bp):
AAAAAAAAAAGAAGAGAAAATTAAA
Found at i:585477 original size:4 final size:4
Alignment explanation
Indices: 585470--585498 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
585460 ACTCTCTCTC
585470 TCTA TCTA TCTA TCTA TCTA TCTA TCTA T
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA T
585499 ATATTATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (4 bp):
TCTA
Found at i:592148 original size:9 final size:9
Alignment explanation
Indices: 592134--592185 Score: 54
Period size: 9 Copynumber: 5.9 Consensus size: 9
592124 ATAAATCATG
592134 GAAAAAAAT
1 GAAAAAAAT
592143 GAAAAAAAT
1 GAAAAAAAT
*
592152 GAATCAAAA-
1 GAA-AAAAAT
592161 GAAAAAAAT
1 GAAAAAAAT
* *
592170 TAAATAAA-
1 GAAAAAAAT
592178 GAAAAAAA
1 GAAAAAAA
592186 GAGTTAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
8 10 0.29
9 21 0.60
10 4 0.11
ACGTcount: A:0.77, C:0.02, G:0.10, T:0.12
Consensus pattern (9 bp):
GAAAAAAAT
Found at i:592222 original size:28 final size:28
Alignment explanation
Indices: 592163--592224 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
592153 AATCAAAAGA
**
592163 AAAAAATTAAATAAAGAAAAAAAGAGTT
1 AAAAAATTAAATAAAGAAAAAAAGAGAG
* *
592191 AAAAAATTAAATAAA-ATTAAAGAGAGAG
1 AAAAAATTAAATAAAGA-AAAAAAGAGAG
592219 AAAAAA
1 AAAAAA
592225 GAAAAGAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 1 0.03
28 28 0.97
ACGTcount: A:0.73, C:0.00, G:0.11, T:0.16
Consensus pattern (28 bp):
AAAAAATTAAATAAAGAAAAAAAGAGAG
Found at i:592301 original size:35 final size:35
Alignment explanation
Indices: 592224--592315 Score: 86
Period size: 35 Copynumber: 2.6 Consensus size: 35
592214 GAGAGAAAAA
592224 AGAAAAGAAG-ATAA-AAAAAACATAAAATACAATTT
1 AGAAAA-AAGAATAATAAAAAA-ATAAAATACAATTT
*
592259 A-ATAAAAAGAATAATAAAAAAATAAATTA-AATATT
1 AGA-AAAAAGAATAATAAAAAAATAAAATACAAT-TT
*
592294 AGAAAAAATGAA-AATGAAAAAA
1 AGAAAAAA-GAATAATAAAAAAA
592316 GGTTAAAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
34 7 0.14
35 32 0.65
36 10 0.20
ACGTcount: A:0.72, C:0.02, G:0.08, T:0.18
Consensus pattern (35 bp):
AGAAAAAAGAATAATAAAAAAATAAAATACAATTT
Found at i:593487 original size:12 final size:13
Alignment explanation
Indices: 593462--593486 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
593452 TATTTGACCC
593462 TAAAAAATGAAAA
1 TAAAAAATGAAAA
593475 TAAAAAATGAAA
1 TAAAAAATGAAA
593487 TTAATAATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (13 bp):
TAAAAAATGAAAA
Found at i:593563 original size:25 final size:25
Alignment explanation
Indices: 593535--593584 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
593525 AATAAATAAT
593535 ATATATAAAAAAT-TATTTTCCAAAA
1 ATATATAAAAAATATATTTT-CAAAA
* *
593560 ATATATATAATATATATTTTCAAAA
1 ATATATAAAAAATATATTTTCAAAA
593585 GTATTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (25 bp):
ATATATAAAAAATATATTTTCAAAA
Found at i:593601 original size:36 final size:37
Alignment explanation
Indices: 593543--593639 Score: 117
Period size: 36 Copynumber: 2.6 Consensus size: 37
593533 ATATATATAA
*
593543 AAAATTATTTTCCAAAAATATATATAATAT-ATATTTTC
1 AAAA-TATTTT-CAAAATTATATATAATATAATATTTTC
* * *
593581 AAAAGTATTTT-AAAATTATATATATTATAATTTTTTT
1 AAAA-TATTTTCAAAATTATATATAATATAATATTTTC
593618 AAAATATTTTCAAAATTATATA
1 AAAATATTTTCAAAATTATATA
593640 GTTTTAAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
36 21 0.40
37 21 0.40
38 10 0.19
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
AAAATATTTTCAAAATTATATATAATATAATATTTTC
Found at i:593682 original size:102 final size:98
Alignment explanation
Indices: 593556--593831 Score: 243
Period size: 102 Copynumber: 2.7 Consensus size: 98
593546 ATTATTTTCC
* *
593556 AAAAATATATATAATATATATTTTCAAAAGTATTTTAAAATTATATATATTATAATTTTTTTAAA
1 AAAAATATATATTATATA-ATTTTCAAAA-TATTTTAAAAATATATATATTATAATTTTTTTAAA
* * *
593621 ATATTTTCAAAATTATATAGTTTTAAAAAATGTTTTT
64 ATATTTTAAAAACTACATA-TTTTAAAAAATG-TTTT
* * * * *
593658 AAAACTATATATTATATAAGTTTTCAAAATGATTTCAAAACTATATA-A-TATATATGTTTTCAA
1 AAAAATATATATTATATAA-TTTTCAAAAT-ATTTTAAAAATATATATATTATA-ATTTTTTTAA
* **
593721 AATGTTTTTAAAAACTACATATTTTTCAAAATGTTTT
63 AAT-ATTTTAAAAACTACATATTTTAAAAAATGTTTT
* * * * *
593758 AAAAATATACAATATATATTTTTTCAAAAATGTTTTAAAAAAACTATATATTAT-ATTTATTTTC
1 AAAAATATATATTATATA-ATTTTC-AAAATATTTTAAAAATA-TATATATTATAATTT-TTTT-
*
593822 AAAATGTTTT
61 AAAATATTTT
593832 TTAAAAAAAA
Statistics
Matches: 140, Mismatches: 23, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
100 36 0.26
101 36 0.26
102 60 0.43
103 8 0.06
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (98 bp):
AAAAATATATATTATATAATTTTCAAAATATTTTAAAAATATATATATTATAATTTTTTTAAAAT
ATTTTAAAAACTACATATTTTAAAAAATGTTTT
Found at i:593687 original size:36 final size:36
Alignment explanation
Indices: 593632--593893 Score: 186
Period size: 36 Copynumber: 7.2 Consensus size: 36
593622 TATTTTCAAA
*
593632 ATTATAT-AGTTTTAAAAAATGTTTTTAAAACTATAT
1 ATTATATAAGTTTT-CAAAATGTTTTTAAAACTATAT
* *
593668 ATTATATAAGTTTTCAAAATGATTTCAAAACTATAT
1 ATTATATAAGTTTTCAAAATGTTTTTAAAACTATAT
* * *
593704 AATATATATGTTTTCAAAATGTTTTTAAAA--A-CT
1 ATTATATAAGTTTTCAAAATGTTTTTAAAACTATAT
* * *
593737 A-CATAT---TTTTCAAAATG-TTTTAAAAATATAC
1 ATTATATAAGTTTTCAAAATGTTTTTAAAACTATAT
* ** *
593768 AATATATATTTTTTCAAAAATGTTTTAAAAAAACTATAT
1 ATTATATAAGTTTTC-AAAATGTTTT--TAAAACTATAT
*
593807 ATTATATTTA-TTTTCAAAATGTTTTTTAAAAAAAACTATAT
1 ATTATA-TAAGTTTTCAAAATG-TTTTT----AAAACTATAT
* *
593848 AATATATAAATGTTTTCAAACATG-TTTCAAAACTATAT
1 ATTATAT-AA-GTTTTCAAA-ATGTTTTTAAAACTATAT
593886 ATTATATA
1 ATTATATA
593894 TATATTTTCA
Statistics
Matches: 181, Mismatches: 23, Indels: 43
0.73 0.09 0.17
Matches are distributed among these distances:
28 8 0.04
29 11 0.06
30 1 0.01
31 1 0.01
32 8 0.04
33 2 0.01
34 1 0.01
35 5 0.03
36 58 0.32
37 10 0.06
38 22 0.12
39 22 0.12
40 2 0.01
41 16 0.09
42 3 0.02
43 8 0.04
44 3 0.02
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.44
Consensus pattern (36 bp):
ATTATATAAGTTTTCAAAATGTTTTTAAAACTATAT
Found at i:593768 original size:29 final size:30
Alignment explanation
Indices: 593704--593768 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
593694 AAAACTATAT
*
593704 AATATATATGTTTTCAAAATGTTTTTAAAA
1 AATACATATGTTTTCAAAATGTTTTTAAAA
*
593734 ACTACATAT-TTTTCAAAATG-TTTTAAAA
1 AATACATATGTTTTCAAAATGTTTTTAAAA
593762 ATATACA
1 A-ATACA
593769 ATATATATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 9 0.29
29 15 0.48
30 7 0.23
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.43
Consensus pattern (30 bp):
AATACATATGTTTTCAAAATGTTTTTAAAA
Found at i:593782 original size:64 final size:67
Alignment explanation
Indices: 593678--593809 Score: 189
Period size: 64 Copynumber: 2.0 Consensus size: 67
593668 ATTATATAAG
* * *
593678 TTTTCAAAATGATTTCAAAACTATATAATATATATGTTTTC-AAAATGTTTT-TAAAAACTACAT
1 TTTTCAAAATGATTTCAAAAATATACAATATATATGTTTTCAAAAATGTTTTAAAAAAACTACAT
593741 AT
66 AT
* * *
593743 TTTTCAAAATG-TTTTAAAAATATACAATATATATTTTTTCAAAAATGTTTTAAAAAAACTATAT
1 TTTTCAAAATGATTTCAAAAATATACAATATATATGTTTTCAAAAATGTTTTAAAAAAACTACAT
593807 AT
66 AT
593809 T
1 T
593810 ATATTTATTT
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
64 25 0.42
65 21 0.36
66 13 0.22
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.44
Consensus pattern (67 bp):
TTTTCAAAATGATTTCAAAAATATACAATATATATGTTTTCAAAAATGTTTTAAAAAAACTACAT
AT
Found at i:593826 original size:38 final size:38
Alignment explanation
Indices: 593743--593906 Score: 137
Period size: 38 Copynumber: 4.2 Consensus size: 38
593733 AACTACATAT
593743 TTTTCAAAATGTTTTAAAAATATAC-A-ATA-TATA-TT-
1 TTTTCAAAATGTTTTAAAAA-A-ACTATATATTATATTTA
593778 TTTTCAAAAATGTTTTAAAAAAACTATATATTATATTTA
1 TTTTC-AAAATGTTTTAAAAAAACTATATATTATATTTA
** *
593817 TTTTCAAAATGTTTTTTAAAAAAAACTATATAATATATAAATG
1 TTTTCAAAATG--TTTT-AAAAAAACTATAT-AT-TATATTTA
*
593860 TTTTCAAACATG-TTT--CAAAACTATATATTATATATATA
1 TTTTCAAA-ATGTTTTAAAAAAACTATATATTATAT-T-TA
593898 TTTTCAAAA
1 TTTTCAAAA
593907 ACCATTTGCA
Statistics
Matches: 108, Mismatches: 7, Indels: 26
0.77 0.05 0.18
Matches are distributed among these distances:
34 2 0.02
35 7 0.06
36 22 0.20
37 7 0.06
38 27 0.25
39 5 0.05
40 4 0.04
41 16 0.15
42 2 0.02
43 13 0.12
44 3 0.03
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.45
Consensus pattern (38 bp):
TTTTCAAAATGTTTTAAAAAAACTATATATTATATTTA
Found at i:593931 original size:39 final size:38
Alignment explanation
Indices: 593838--593932 Score: 113
Period size: 38 Copynumber: 2.5 Consensus size: 38
593828 TTTTTTAAAA
* *
593838 AAAACTATATAATATATAAATGTTTTCAAACATGTTTC
1 AAAACTATATAATATATAAATATTTTCAAACATGTTGC
* *
593876 AAAACTATATATTATATATATATTTTCAAAAACCAT-TTGC
1 AAAACTATATAATATATAAATATTTTC--AAA-CATGTTGC
593916 -AAACTATATAATATATA
1 AAAACTATATAATATATA
593933 GACGTATATG
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
38 24 0.49
39 16 0.33
40 6 0.12
41 3 0.06
ACGTcount: A:0.47, C:0.11, G:0.03, T:0.39
Consensus pattern (38 bp):
AAAACTATATAATATATAAATATTTTCAAACATGTTGC
Found at i:594877 original size:165 final size:162
Alignment explanation
Indices: 594513--595759 Score: 1349
Period size: 165 Copynumber: 7.6 Consensus size: 162
594503 TTTTTCCTTG
** * ** * *
594513 AGTTATGCTATAAATGATGTGCCTTGGAGTTGAGCGTAGTTAAACTCGAAGGTTTTTAGT---AG
1 AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAG
* * ** * *
594575 ACAACCCTTCTAGCCTTGAGCTATATTGCAAATGATATGCCGTTGAGCTGAGTGTAATCGAACTC
66 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCCTCGAGCTGAGTGTAATCGAACTC
*
594640 AAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTA
131 -GAGGTC--T-TTGGCAGATAACCCTTCTCGACTTA
* * * *
594676 AGTTATACTGCAAATGATATGCCTGGGAGTTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACA
1 AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACA
*
594741 GATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGATGCTGAGTGTAATCGAAC
65 GATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCCTCGA-GCTGAGTGTAATCGAAC
*
594806 TCGAGTGTCTTTGGCAGATAACCCTTCTCAACTTA
129 TCGAG-GTCTTTGGCAGATAACCCTTCTCGACTTA
* * * * * * *
594841 AGTTATGCTGTAAATGACGTGCATCGTAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCA
1 AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACA
* * * * * * *
594906 GATAACCATTCTTGACTTAAGTTACGCTGCAAATGATGTGCCCTCGAAGTTGAGTGTAATCGAAC
65 GATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCCTCG-AGCTGAGTGTAATCGAAC
* *
594971 TCAAAGGTCTTTGGCAGATAGCCC-TCTCGACTTA
129 TC-GAGGTCTTTGGCAGATAACCCTTCTCGACTTA
* * * *
595005 AGTTATGTTGCAAATGATGTACCTTAGAGCTGAGCGTAATCGAACTCGAAGGTCTTT-G-GA-AG
1 AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAG
* * * * * * * * * * * *
595067 ATAGCCCTTCTCGACTTAAGCTATGGTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTAGAACTC
66 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCCTCGAGCTGAGTGTAATCGAACTC
* *
595132 GAAGGTCTTTGGTGACAGATAACCCTTCTAG-CATTG
131 G-AGGTCTTT-G-G-CAGATAACCCTTCTCGAC-TTA
* * *
595168 AGTTATGATGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAATTCGAAGGTCTTTGGTGACAG
1 AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAG
* * * *
595233 AAAACCCTTCTAGCCTTGAGTTATGCTGTAAATGGTATGCCCTCGAAGCTGAGTGTAATCGAACA
66 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCCTCG-AGCTGAGTGTAATCGAACT
* * * * *
595298 CGAGAGTCTTTCGCATATAGCACTTCTCGACTTT
130 CGAG-GTCTTTGGCAGATAACCCTTCTCGACTTA
* * * *** * *
595332 AGCTATGCTGCAAATGATGTACCTAGGAGCTGAATATAGTCGAACTCGAAGGTCTTTGTTGGCAG
1 AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAG
* * *
595397 ATAACCCTTCTAGCCTTGAGTTATACTGAAAATGTTATGCCCTCGGAGCTGAGTGTAATCGAACT
66 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCCTC-GAGCTGAGTGTAATCGAACT
* * *
595462 CGGGGGTCTTTGGCAAATAGCCCTTCTCGACTTA
130 C-GAGGTCTTTGGCAGATAACCCTTCTCGACTTA
* * * *
595496 AGCTATGCTGCAAATGATGTTCATTGGAGCTGAGCGTAGTTGAACTCGAAGGTCTTTGGTTGACA
1 AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGACA
* * * * * *
595561 GATAACCATTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGTTGAGTGTAATCGAAC
65 GATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCCTCG-AGCTGAGTGTAATCGAAC
* * * *
595626 TCGGGGGACTTTGGCAGATAACCCTTCTCGCCTTG
129 TC-GAGGTCTTTGGCAGATAACCCTTCTCGACTTA
* * * *
595661 AGCTATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCGAACTCGAAGGTCTTTGTTGGCAG
1 AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAG
*
595726 ATAACCCTTCTAGCCTTGAGTTATACTGCAAATG
66 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
595760 TTATCTTAAA
Statistics
Matches: 911, Mismatches: 149, Indels: 47
0.82 0.13 0.04
Matches are distributed among these distances:
159 24 0.03
160 40 0.04
161 2 0.00
162 10 0.01
163 106 0.12
164 298 0.33
165 302 0.33
166 41 0.05
167 66 0.07
168 22 0.02
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (162 bp):
AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAG
ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCCTCGAGCTGAGTGTAATCGAACTC
GAGGTCTTTGGCAGATAACCCTTCTCGACTTA
Found at i:595374 original size:164 final size:164
Alignment explanation
Indices: 594513--595759 Score: 1350
Period size: 164 Copynumber: 7.6 Consensus size: 164
594503 TTTTTCCTTG
** * ** * *
594513 AGTTATGCTATAAATGATGTGCCTTGGAGTTGAGCGTAGTTAAACTCGAAGGTTTTTAGT---AG
1 AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAG
* * ** * *
594575 ACAACCCTTCTAGCCTTGAGCTATATTGCAAATGATATGCCGTTG-AGCTGAGTGTAATCGAACT
66 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACT
*
594639 C-AAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTA
131 CGAGA-GTC--T-TTGGCAGATAACCCTTCTCGACTTA
* * * *
594676 AGTTATACTGCAAATGATATGCCTGGGAGTTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACA
1 AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACA
* *
594741 GATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGATGCTGAGTGTAATCGAAC
65 GATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCGAAC
* *
594806 TCGAGTGTCTTTGGCAGATAACCCTTCTCAACTTA
130 TCGAGAGTCTTTGGCAGATAACCCTTCTCGACTTA
* * * * * * *
594841 AGTTATGCTGTAAATGACGTGCATCGTAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCA
1 AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACA
* * * * * * *
594906 GATAACCATTCTTGACTTAAGTTACGCTGCAAATGATGTGCCCTCGAAGTTGAGTGTAATCGAAC
65 GATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCGAAC
* *
594971 TC-AAAGGTCTTTGGCAGATAGCCC-TCTCGACTTA
130 TCGAGA-GTCTTTGGCAGATAACCCTTCTCGACTTA
* * * *
595005 AGTTATGTTGCAAATGATGTACCTTAGAGCTGAGCGTAATCGAACTCGAAGGTCTTT-G-GA-AG
1 AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAG
* * * * * * * * * * * *
595067 ATAGCCCTTCTCGACTTAAGCTATGGTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTAGAACT
66 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACT
* *
595131 CGA-AGGTCTTTGGTGACAGATAACCCTTCTAG-CATTG
131 CGAGA-GTCTTT-G-G-CAGATAACCCTTCTCGAC-TTA
* * *
595168 AGTTATGATGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAATTCGAAGGTCTTTGGTGACAG
1 AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAG
* * * *
595233 AAAACCCTTCTAGCCTTGAGTTATGCTGTAAATGGTATGCCCTCGAAGCTGAGTGTAATCGAACA
66 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACT
* * * * *
595298 CGAGAGTCTTTCGCATATAGCACTTCTCGACTTT
131 CGAGAGTCTTTGGCAGATAACCCTTCTCGACTTA
* * * *** * *
595332 AGCTATGCTGCAAATGATGTACCTAGGAGCTGAATATAGTCGAACTCGAAGGTCTTTGTTGGCAG
1 AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAG
* * * *
595397 ATAACCCTTCTAGCCTTGAGTTATACTGAAAATGTTATGCCCTCGGAGCTGAGTGTAATCGAACT
66 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACT
* * * *
595462 CGGGGGTCTTTGGCAAATAGCCCTTCTCGACTTA
131 CGAGAGTCTTTGGCAGATAACCCTTCTCGACTTA
* * * *
595496 AGCTATGCTGCAAATGATGTTCATTGGAGCTGAGCGTAGTTGAACTCGAAGGTCTTTGGTTGACA
1 AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGACA
* * * * * *
595561 GATAACCATTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGTTGAGTGTAATCGAAC
65 GATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCGAAC
* * * * *
595626 TCGGGGGACTTTGGCAGATAACCCTTCTCGCCTTG
130 TCGAGAGTCTTTGGCAGATAACCCTTCTCGACTTA
* * * *
595661 AGCTATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCGAACTCGAAGGTCTTTGTTGGCAG
1 AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAG
*
595726 ATAACCCTTCTAGCCTTGAGTTATACTGCAAATG
66 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
595760 TTATCTTAAA
Statistics
Matches: 909, Mismatches: 155, Indels: 39
0.82 0.14 0.04
Matches are distributed among these distances:
159 28 0.03
160 37 0.04
161 2 0.00
162 10 0.01
163 106 0.12
164 301 0.33
165 301 0.33
166 32 0.04
167 68 0.07
168 23 0.03
169 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (164 bp):
AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAG
ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACT
CGAGAGTCTTTGGCAGATAACCCTTCTCGACTTA
Found at i:599196 original size:19 final size:19
Alignment explanation
Indices: 599172--599217 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
599162 AGTTAATGTG
599172 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
599191 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
599210 AATGCAAA
1 AATGCAAA
599218 ATGTCTAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.67, C:0.11, G:0.11, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:602368 original size:38 final size:35
Alignment explanation
Indices: 602326--602439 Score: 95
Period size: 38 Copynumber: 3.1 Consensus size: 35
602316 AAATAAACAA
*
602326 ATAATATATATATAAAAAATTATTTTCCAAAAATCTAT
1 ATAATATATATATAAAAAAGTATTTT--AAAAAT-TAT
* **
602364 ATAATATATATTTTCAAAAGTATTTTAAAAATTAT
1 ATAATATATATATAAAAAAGTATTTTAAAAATTAT
* * *
602399 ATATATTATATATTTTTTAAAAA-TATTTTCAAAATTAT
1 ATA-A-TATATA--TATAAAAAAGTATTTTAAAAATTAT
602437 ATA
1 ATA
602440 GTTTTAAAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
35 6 0.09
36 7 0.11
37 6 0.09
38 39 0.59
39 8 0.12
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (35 bp):
ATAATATATATATAAAAAAGTATTTTAAAAATTAT
Found at i:602449 original size:29 final size:29
Alignment explanation
Indices: 602403--602468 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 29
602393 AATTATATAT
* *
602403 ATTATATATTTTTTAAAAATATTTTCAAA
1 ATTATATAGTTTTAAAAAATATTTTCAAA
* *
602432 ATTATATAGTTTTAAAAAATGTTTTTAAA
1 ATTATATAGTTTTAAAAAATATTTTCAAA
*
602461 ACTATATA
1 ATTATATA
602469 TTATATAAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (29 bp):
ATTATATAGTTTTAAAAAATATTTTCAAA
Found at i:602498 original size:35 final size:36
Alignment explanation
Indices: 602432--602540 Score: 109
Period size: 35 Copynumber: 3.1 Consensus size: 36
602422 TATTTTCAAA
* * *
602432 ATTATAT-AGTTTTAAAAAATGTTTTTAAAACTATAT
1 ATTATATAAGTTTT-CAAAATGTATTCAAAACTATAT
602468 ATTATATAAGTTTTCAAAATG-ATTCAAAACTATAT
1 ATTATATAAGTTTTCAAAATGTATTCAAAACTATAT
* * * *
602503 A--ATATATGTTTTCAAAATGTTTTTAAAAACTACAT
1 ATTATATAAGTTTTCAAAATG-TATTCAAAACTATAT
602538 ATT
1 ATT
602541 TTTCAAAATG
Statistics
Matches: 61, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
33 17 0.28
35 25 0.41
36 13 0.21
37 6 0.10
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (36 bp):
ATTATATAAGTTTTCAAAATGTATTCAAAACTATAT
Found at i:602614 original size:37 final size:36
Alignment explanation
Indices: 602536--602649 Score: 111
Period size: 36 Copynumber: 3.0 Consensus size: 36
602526 TAAAAACTAC
* * *
602536 ATATTTTTCAAAATGTTTTAAAAATATATAATATAT
1 ATATTTTTAAAAAGGTTTAAAAAATATATAATATAT
*
602572 ATATTTTTAAAAAGGTTTAAAAAACTATATATTATAT
1 ATATTTTTAAAAAGGTTTAAAAAA-TATATAATATAT
* * **
602609 TTATTTTCAAAATATTTTTAAAAAAAATTATATAATATAT
1 ATATTTTTAAAA-AGGTTT--AAAAAA-TATATAATATAT
602649 A
1 A
602650 AATGTTTTCA
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
36 21 0.33
37 21 0.33
38 4 0.06
40 17 0.27
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (36 bp):
ATATTTTTAAAAAGGTTTAAAAAATATATAATATAT
Found at i:602667 original size:26 final size:26
Alignment explanation
Indices: 602637--602687 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
602627 TAAAAAAAAT
602637 TATATAATATATAAATGTTTTCAAAC
1 TATATAATATATAAATGTTTTCAAAC
* * *
602663 TATATATTATATATATTTTTTCAAA
1 TATATAATATATAAATGTTTTCAAA
602688 AATCATTTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (26 bp):
TATATAATATATAAATGTTTTCAAAC
Found at i:602706 original size:103 final size:99
Alignment explanation
Indices: 602447--602713 Score: 258
Period size: 103 Copynumber: 2.6 Consensus size: 99
602437 ATAGTTTTAA
*
602447 AAAATGTTTTTAAAACTATATATTATATA-AGTTTTC-AAAATGA-TTCAAAACTATATAATATA
1 AAAATG-TTTTAAAACTATATATTATATATATTTTTCAAAAATGATTTC-AAACTATATAATATA
* * ** * *
602509 TGTTTTCAAAATGTTTTTAAAAACTACATATTTTTC
64 TATTTTCAAAATATTTTTAAAAAAAACATATATATC
* * * *
602545 AAAATGTTTTAAAAATATATAATATATATATTTTT-AAAAA-GGTTTAAAAAACTATATATTATA
1 AAAATGTTTTAAAACTATATATTATATATATTTTTCAAAAATGATTT--CAAACTATATA--ATA
* *
602608 TTTATTTTCAAAATATTTTTAAAAAAAATTATATAATAT-
62 TATATTTTCAAAATATTTTTAAAAAAAA-CATAT-ATATC
* *
602647 ATAAATGTTTTCAAACTATATATTATATATATTTTTTCAAAAATCATTTGCAAACTATATAATAT
1 A-AAATGTTTTAAAACTATATATTATATATA-TTTTTCAAAAATGATTT-CAAACTATATAATAT
602712 AT
63 AT
602714 GGACGTGTAT
Statistics
Matches: 135, Mismatches: 21, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
97 21 0.16
98 17 0.13
99 10 0.07
101 26 0.19
102 5 0.04
103 33 0.24
104 5 0.04
105 15 0.11
106 3 0.02
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (99 bp):
AAAATGTTTTAAAACTATATATTATATATATTTTTCAAAAATGATTTCAAACTATATAATATATA
TTTTCAAAATATTTTTAAAAAAAACATATATATC
Found at i:605750 original size:2 final size:2
Alignment explanation
Indices: 605743--605829 Score: 106
Period size: 2 Copynumber: 44.5 Consensus size: 2
605733 ACCATTGGGA
* * * * * *
605743 CT CT CT CT CT CT CT C- CC CC CT CT CC CT CT CC CT CT CC CT CC
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
605784 CT CT C- CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
605825 CT CT C
1 CT CT C
605830 ACACACACAC
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
1 2 0.03
2 72 0.97
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (2 bp):
CT
Found at i:605777 original size:21 final size:23
Alignment explanation
Indices: 605745--605825 Score: 112
Period size: 23 Copynumber: 3.6 Consensus size: 23
605735 CATTGGGACT
605745 CTCTCTCTCTCTCCC-CCCTCTC
1 CTCTCTCTCTCTCCCTCCCTCTC
*
605767 C-CTCTCCCTCTCCCTCCCTCTC
1 CTCTCTCTCTCTCCCTCCCTCTC
* *
605789 CTCTCTCTCTCTCTCTCTCTCTC
1 CTCTCTCTCTCTCCCTCCCTCTC
605812 TCTCTCTCTCTCTC
1 -CTCTCTCTCTCTC
605826 TCTCACACAC
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
21 12 0.23
22 9 0.17
23 18 0.35
24 13 0.25
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (23 bp):
CTCTCTCTCTCTCCCTCCCTCTC
Found at i:605834 original size:2 final size:2
Alignment explanation
Indices: 605829--605864 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
605819 CTCTCTCTCT
*
605829 CA CA CA CA CA CA CA CA CA CA CA CA CA AA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
605865 TATTGAGACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:606326 original size:2 final size:2
Alignment explanation
Indices: 606319--606396 Score: 156
Period size: 2 Copynumber: 39.0 Consensus size: 2
606309 TAATAATTTA
606319 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
606361 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
606397 GCAAAATAAT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:612251 original size:192 final size:191
Alignment explanation
Indices: 611803--612252 Score: 561
Period size: 192 Copynumber: 2.3 Consensus size: 191
611793 GTTTTTGTGG
* * *
611803 TTACTCCAATTATCAGGAACTTCTTGAACAATTTCAGTATTTAGTGCTGGAATTAGTCAGAACAG
1 TTACTCCAATTATCAGTAACTTCTTGAACGATTTCAGTATTTAGTGCTGGAATTAGTCAGAAGA-
* * ** *
611868 GGGGTATTTTAATGATGTAGAATATAGACATTTATAACCCTCAATTTTACATCCTTTAATTATTT
65 GGGGTATTTTAATGATGCAGAATATAAACATTTATAACCCTCAAGGTTACATCCTTGAATTATTT
*
611933 CAATTATTGGGATCTTATTGAGTTGATTCAATTTAAGTCTTGTTTTGTTGCTGCTGCATTGA
130 CAATTATTGGGATCTTATTGAGTTGATTCAATTTAAGTCATGTTTTGTTGCTGCTGCATTGA
* *
611995 TTACTCCAATTATCA-TGAACTTCTTGAGCGATTTCAGTATTTAGTGCTGGAACTAGTCAGAAGA
1 TTACTCCAATTATCAGT-AACTTCTTGAACGATTTCAGTATTTAGTGCTGGAATTAGTCAGAAGA
* * * *
612059 GGGG-ATGTTT-GTGATGCAGAATATAAACATTTATAGA-CCTGAAGGTTACATGCTTGAATTGT
65 GGGGTAT-TTTAATGATGCAGAATATAAACATTTATA-ACCCTCAAGGTTACATCCTTGAATTAT
* * * * * *
612121 TTCATTTATTAGGG-TGTTATTTGAGTTGGTTCAA-TTAAGTCATGTTTGTTTTTGGTGGTGCAT
128 TTCAATTATT-GGGATCTTA-TTGAGTTGATTCAATTTAAGTCATG-TT-TTGTTGCTGCTGCAT
612184 TGA
189 TGA
* * * *
612187 TTACTGCAATTAGCAGTAACTTCTTGAATGATTTCAGTATTTAGTGCTGGAATTAGTTAGAAGAG
1 TTACTCCAATTATCAGTAACTTCTTGAACGATTTCAGTATTTAGTGCTGGAATTAGTCAGAAGAG
612252 G
66 G
612253 TGTGTATGTT
Statistics
Matches: 223, Mismatches: 27, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
190 65 0.29
191 26 0.12
192 131 0.59
193 1 0.00
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (191 bp):
TTACTCCAATTATCAGTAACTTCTTGAACGATTTCAGTATTTAGTGCTGGAATTAGTCAGAAGAG
GGGTATTTTAATGATGCAGAATATAAACATTTATAACCCTCAAGGTTACATCCTTGAATTATTTC
AATTATTGGGATCTTATTGAGTTGATTCAATTTAAGTCATGTTTTGTTGCTGCTGCATTGA
Found at i:618841 original size:16 final size:16
Alignment explanation
Indices: 618816--618852 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
618806 GTTTATGAAC
* *
618816 ATAAATGAACTAGTCG
1 ATAAACGAACAAGTCG
618832 ATAAACGAACAAGTCG
1 ATAAACGAACAAGTCG
618848 ATAAA
1 ATAAA
618853 TAATCTTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.14, G:0.16, T:0.19
Consensus pattern (16 bp):
ATAAACGAACAAGTCG
Found at i:629254 original size:16 final size:16
Alignment explanation
Indices: 629229--629265 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
629219 GTTTATGAAC
* *
629229 ATAAATGAACTAGTCG
1 ATAAACGAACAAGTCG
629245 ATAAACGAACAAGTCG
1 ATAAACGAACAAGTCG
629261 ATAAA
1 ATAAA
629266 TAATCTTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.14, G:0.16, T:0.19
Consensus pattern (16 bp):
ATAAACGAACAAGTCG
Found at i:655169 original size:12 final size:12
Alignment explanation
Indices: 655152--655176 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
655142 AGGAAGGATC
655152 AGCAATAAGACA
1 AGCAATAAGACA
655164 AGCAATAAGACA
1 AGCAATAAGACA
655176 A
1 A
655177 TCCTTAGAGA
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:0.60, C:0.16, G:0.16, T:0.08
Consensus pattern (12 bp):
AGCAATAAGACA
Found at i:659498 original size:463 final size:463
Alignment explanation
Indices: 658633--659561 Score: 1858
Period size: 463 Copynumber: 2.0 Consensus size: 463
658623 ATAAAAGAGA
658633 AAAATGCAAACTGAAAACCTCTACCAGCATCACCTTAATTAACCCCATTCAAACTTTTCTCTAAA
1 AAAATGCAAACTGAAAACCTCTACCAGCATCACCTTAATTAACCCCATTCAAACTTTTCTCTAAA
658698 GCCATGATTTTCTCCAGAAATGCTTCTTTCCCTTCCTTAAAAGACACCCCCAGAAGCTCACTCAC
66 GCCATGATTTTCTCCAGAAATGCTTCTTTCCCTTCCTTAAAAGACACCCCCAGAAGCTCACTCAC
658763 CTGTCAAGTAGCCAGAGCTTCTTCCATTAAAATCGAGAAGTCTGAAGAGGAGGTTGTATCAATGC
131 CTGTCAAGTAGCCAGAGCTTCTTCCATTAAAATCGAGAAGTCTGAAGAGGAGGTTGTATCAATGC
658828 TAACTTGTTCAAGGGCATCCCGTAACAAATTCCTTTTTGTCCTTCTAATTAACAAGCCAGATTTG
196 TAACTTGTTCAAGGGCATCCCGTAACAAATTCCTTTTTGTCCTTCTAATTAACAAGCCAGATTTG
658893 AATCTTAAACAGTCTCCTTCTGAAAAATAGCCATCAAACTCCCTCTCCTCACTCCCATCCACTGT
261 AATCTTAAACAGTCTCCTTCTGAAAAATAGCCATCAAACTCCCTCTCCTCACTCCCATCCACTGT
658958 GCGCTGTCAAAATTAGAAACTTTGCTCCCATTTGCAATCAAAACTGGTGGTAAACAAAGATGTTT
326 GCGCTGTCAAAATTAGAAACTTTGCTCCCATTTGCAATCAAAACTGGTGGTAAACAAAGATGTTT
659023 ATTAGCACTAAAAATCGCATCAATCTTTCCCTGACTAACTCTGACCCCATCAGCTACAGGCGTTA
391 ATTAGCACTAAAAATCGCATCAATCTTTCCCTGACTAACTCTGACCCCATCAGCTACAGGCGTTA
659088 ACTTCAGC
456 ACTTCAGC
659096 AAAATGCAAACTGAAAACCTCTACCAGCATCACCTTAATTAACCCCATTCAAACTTTTCTCTAAA
1 AAAATGCAAACTGAAAACCTCTACCAGCATCACCTTAATTAACCCCATTCAAACTTTTCTCTAAA
659161 GCCATGATTTTCTCCAGAAATGCTTCTTTCCCTTCCTTAAAAGACACCCCCAGAAGCTCACTCAC
66 GCCATGATTTTCTCCAGAAATGCTTCTTTCCCTTCCTTAAAAGACACCCCCAGAAGCTCACTCAC
659226 CTGTCAAGTAGCCAGAGCTTCTTCCATTAAAATCGAGAAGTCTGAAGAGGAGGTTGTATCAATGC
131 CTGTCAAGTAGCCAGAGCTTCTTCCATTAAAATCGAGAAGTCTGAAGAGGAGGTTGTATCAATGC
659291 TAACTTGTTCAAGGGCATCCCGTAACAAATTCCTTTTTGTCCTTCTAATTAACAAGCCAGATTTG
196 TAACTTGTTCAAGGGCATCCCGTAACAAATTCCTTTTTGTCCTTCTAATTAACAAGCCAGATTTG
659356 AATCTTAAACAGTCTCCTTCTGAAAAATAGCCATCAAACTCCCTCTCCTCACTCCCATCCACTGT
261 AATCTTAAACAGTCTCCTTCTGAAAAATAGCCATCAAACTCCCTCTCCTCACTCCCATCCACTGT
659421 GCGCTGTCAAAATTAGAAACTTTGCTCCCATTTGCAATCAAAACTGGTGGTAAACAAAGATGTTT
326 GCGCTGTCAAAATTAGAAACTTTGCTCCCATTTGCAATCAAAACTGGTGGTAAACAAAGATGTTT
659486 ATTAGCACTAAAAATCGCATCAATCTTTCCCTGACTAACTCTGACCCCATCAGCTACAGGCGTTA
391 ATTAGCACTAAAAATCGCATCAATCTTTCCCTGACTAACTCTGACCCCATCAGCTACAGGCGTTA
659551 ACTTCAGC
456 ACTTCAGC
659559 AAA
1 AAA
659562 TCCCCATGCC
Statistics
Matches: 466, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
463 466 1.00
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (463 bp):
AAAATGCAAACTGAAAACCTCTACCAGCATCACCTTAATTAACCCCATTCAAACTTTTCTCTAAA
GCCATGATTTTCTCCAGAAATGCTTCTTTCCCTTCCTTAAAAGACACCCCCAGAAGCTCACTCAC
CTGTCAAGTAGCCAGAGCTTCTTCCATTAAAATCGAGAAGTCTGAAGAGGAGGTTGTATCAATGC
TAACTTGTTCAAGGGCATCCCGTAACAAATTCCTTTTTGTCCTTCTAATTAACAAGCCAGATTTG
AATCTTAAACAGTCTCCTTCTGAAAAATAGCCATCAAACTCCCTCTCCTCACTCCCATCCACTGT
GCGCTGTCAAAATTAGAAACTTTGCTCCCATTTGCAATCAAAACTGGTGGTAAACAAAGATGTTT
ATTAGCACTAAAAATCGCATCAATCTTTCCCTGACTAACTCTGACCCCATCAGCTACAGGCGTTA
ACTTCAGC
Found at i:674051 original size:43 final size:43
Alignment explanation
Indices: 673985--674071 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
673975 CGTTGCACGC
673985 ATGCATGCGTTGGGTAGGGACTCACTCCTCTTCTTATTCTTTT
1 ATGCATGCGTTGGGTAGGGACTCACTCCTCTTCTTATTCTTTT
*
674028 ATGCATGCGTTGGGTAGGTACTCACTCCTCTTCTTATTCTTTT
1 ATGCATGCGTTGGGTAGGGACTCACTCCTCTTCTTATTCTTTT
674071 A
1 A
674072 ATTATCAGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (43 bp):
ATGCATGCGTTGGGTAGGGACTCACTCCTCTTCTTATTCTTTT
Found at i:675587 original size:566 final size:558
Alignment explanation
Indices: 674499--675895 Score: 2116
Period size: 566 Copynumber: 2.5 Consensus size: 558
674489 TTGGCCCGAT
* *
674499 CCCTAAACCCTAAACCATATATAAACAAAATTAAATCGAATGTAATCTAGACACAAACTAAATTG
1 CCCTAAATCCTAAACCCTATATAAACAAAATTAAATCGAATGTAATCTAGACACAAACTAAATTG
* * * *
674564 ATATGAAATGTTCCAACTTAAATCTAATACGAATCATCCGTTTGTTGCCCCTACTTCTACTTA-A
66 ATCTGAAATG-TCCAACTTAAATCTAATTCGAATGATCCGTTTGTTACCCCTACTTCTACTTATA
* **** * * * * *** * *
674628 ACCTAAAAGC-AT-TTTA-TAACA-TATACTCTTAATAAATAAAGAAAATA-ATTATACGTAGAA
130 A-TTATTTTCTTTATTTATTAAGAGTATA-TGTT-AT-AA-AATGATTTTAGGTT-TAAGTAGAA
*
674688 GTAGGGGTGACAAACGGATCATTCGAATTAGATTTAAGTTGGATCATTTCAGATCAATTTAGTTT
189 GTAGGGGTGACAAACGGATCATTCGTATTAGATTTAAGTTGGATCATTTCAGATCAATTTAGTTT
* *
674753 GTGTCTAGATTACATTCGATTTAATTTTGTTCATATAAGGTTTATGATTTAGGATTTAAGGTTTA
254 GTGTCTAGATTACATTCGATTTAATTTTATTCATATAAGGTTTAAGATTTAGGATTTAAGGTTTA
674818 ACCATAGGCTTTTAAAGTATAACTATTAACACATTATATTTTATATAGATATAAAAAATAAACAC
319 ACCATAGGCTTTTAAAGTATAACTATTAACACATTATATTTTATATAGATATAAAAAATAAACAC
*
674883 GAAGAAACACAGAATTACTGAAATGTCGATATCACCAAATCTGCTAATACGTTATACTTTACCCA
384 GAAGAAACACAGAATTACTGAAATGTCGATATCACCAAATCTGCTAATACGTTATAATTTACCCA
*
674948 TAGGCTACCGAGTAGTGACCCACTTAATTGCTGAAAGTTTTCAACCCTTAAAAAATTAACCTATT
449 TAGGCTACCGAGTAGTGACCCACTTAATTGCTGAAAGTTTTCAACCCTTAAAAAATTAACCGATT
*
675013 CGTATTGACCCGAACAAAAAATTAACCGATCTAATATTGACTTAA
514 CATATTGACCCGAACAAAAAATTAACCGATCTAATATTGACTTAA
* *
675058 CCCTAAATCCTAAACCCTATATGAACAAAACTAAATCGAATGTAATCTAGACACAAACTAAATTG
1 CCCTAAATCCTAAACCCTATATAAACAAAATTAAATCGAATGTAATCTAGACACAAACTAAATTG
675123 ATCTGAAATGATCCAACTTAAATCTAATTCGAATGATCCGTTTGTTACCCCTACTTCTACTTATA
66 ATCTGAAATG-TCCAACTTAAATCTAATTCGAATGATCCGTTTGTTACCCCTACTTCTACTTATA
675188 ATTATTTTCTTTATTTATTAAGAGTATATGTTATAAAATGATTTTAGGTTTAAGTAGAAGTAGGG
130 ATTATTTTCTTTATTTATTAAGAGTATATGTTATAAAATGATTTTAGGTTTAAGTAGAAGTAGGG
* *
675253 GTGACAAACGGATGATTCGTATTAGATTTAAGTTGGAACATTTCAGATCAATTTAGTTTGTGTCT
195 GTGACAAACGGATCATTCGTATTAGATTTAAGTTGGATCATTTCAGATCAATTTAGTTTGTGTCT
* *
675318 AGATTACATTCGATTTAATTTTATTCATATAATGTTTAAGATTTAGGGTTTAGGGTTTAGGATTT
260 AGATTACATTCGATTTAATTTTATTCATATAAGGTTTAAGATTTAGGATTTA------AGG-TTT
* *
675383 AACCATAGGCTTTTAAAGTATAACTATTAGCACGTTATATTTTATATAGATATAAAAAATAAACA
318 AACCATAGGCTTTTAAAGTATAACTATTAACACATTATATTTTATATAGATATAAAAAATAAACA
*
675448 TGAAGAAACACAGAATTACTGAAATGTCGATATCACCAAATCTGCTAATACGTTATAATTTACCC
383 CGAAGAAACACAGAATTACTGAAATGTCGATATCACCAAATCTGCTAATACGTTATAATTTACCC
*
675513 ATAGGCTACCGAGTAGTGACCCACTTAATTGTTGAAAGTTTTCAACCCTTAAAAAATTAACCGAT
448 ATAGGCTACCGAGTAGTGACCCACTTAATTGCTGAAAGTTTTCAACCCTTAAAAAATTAACCGAT
* *
675578 TCATATTGACCCGAACAAAAAATTAATCGATTTAATATTGACTTAA
513 TCATATTGACCCGAACAAAAAATTAACCGATCTAATATTGACTTAA
*
675624 CCTTAAATCCTAAACCCTATATAAACAAAATTAAATCGAATGTAATCTAGACACAAACTAAATTG
1 CCCTAAATCCTAAACCCTATATAAACAAAATTAAATCGAATGTAATCTAGACACAAACTAAATTG
* * *
675689 ATCTGAAATG---------------ATTCGAATGATCCGTTTGTCACCCTTACTTCTACGTATAA
66 ATCTGAAATGTCCAACTTAAATCTAATTCGAATGATCCGTTTGTTACCCCTACTTCTACTTATAA
*
675739 TTATTTTCTTTATTTATTAAGAGTATATGTTATAAAATGATTTTAGGTTTAAGTAGAAGTAGGAG
131 TTATTTTCTTTATTTATTAAGAGTATATGTTATAAAATGATTTTAGGTTTAAGTAGAAGTAGGGG
*
675804 TGACAAACAGATCATTCGTATTAGATTTAAGTTGGATCATTTCAGATCAATTTAGTTTGTGTCTA
196 TGACAAACGGATCATTCGTATTAGATTTAAGTTGGATCATTTCAGATCAATTTAGTTTGTGTCTA
675869 GATTACATTCGATTTAATTTTATTCAT
261 GATTACATTCGATTTAATTTTATTCAT
675896 TCAGGGTTTA
Statistics
Matches: 776, Mismatches: 49, Indels: 35
0.90 0.06 0.04
Matches are distributed among these distances:
550 190 0.24
559 252 0.32
560 7 0.01
561 6 0.01
562 7 0.01
563 4 0.01
565 3 0.00
566 307 0.40
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (558 bp):
CCCTAAATCCTAAACCCTATATAAACAAAATTAAATCGAATGTAATCTAGACACAAACTAAATTG
ATCTGAAATGTCCAACTTAAATCTAATTCGAATGATCCGTTTGTTACCCCTACTTCTACTTATAA
TTATTTTCTTTATTTATTAAGAGTATATGTTATAAAATGATTTTAGGTTTAAGTAGAAGTAGGGG
TGACAAACGGATCATTCGTATTAGATTTAAGTTGGATCATTTCAGATCAATTTAGTTTGTGTCTA
GATTACATTCGATTTAATTTTATTCATATAAGGTTTAAGATTTAGGATTTAAGGTTTAACCATAG
GCTTTTAAAGTATAACTATTAACACATTATATTTTATATAGATATAAAAAATAAACACGAAGAAA
CACAGAATTACTGAAATGTCGATATCACCAAATCTGCTAATACGTTATAATTTACCCATAGGCTA
CCGAGTAGTGACCCACTTAATTGCTGAAAGTTTTCAACCCTTAAAAAATTAACCGATTCATATTG
ACCCGAACAAAAAATTAACCGATCTAATATTGACTTAA
Found at i:675933 original size:23 final size:23
Alignment explanation
Indices: 675903--675948 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
675893 CATTCAGGGT
675903 TTAGGGCTTAGGGTTTAGCCATA
1 TTAGGGCTTAGGGTTTAGCCATA
675926 TTAGGGCTTAGGGTTTAGCCATA
1 TTAGGGCTTAGGGTTTAGCCATA
675949 GGATTTAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.13, G:0.30, T:0.35
Consensus pattern (23 bp):
TTAGGGCTTAGGGTTTAGCCATA
Found at i:677905 original size:19 final size:17
Alignment explanation
Indices: 677883--677921 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
677873 ATTTTTAAAC
*
677883 TATTAAATAATTTATTTAT
1 TATTAAA-AAATTATTT-T
677902 TATTAAAAAATTATTTT
1 TATTAAAAAATTATTTT
677919 TAT
1 TAT
677922 AATTTTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 8 0.42
19 7 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTAAAAAATTATTTT
Found at i:677939 original size:12 final size:12
Alignment explanation
Indices: 677920--677959 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
677910 AATTATTTTT
677920 ATAATTTTATTA
1 ATAATTTTATTA
* * *
677932 ATATTTTTTTTT
1 ATAATTTTATTA
677944 ATAATTTTATTA
1 ATAATTTTATTA
677956 ATAA
1 ATAA
677960 AAATATTAAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
ATAATTTTATTA
Found at i:685951 original size:26 final size:26
Alignment explanation
Indices: 685911--685974 Score: 101
Period size: 26 Copynumber: 2.5 Consensus size: 26
685901 TAAGGAAGTG
685911 AATTTATAAAATTTTAAAAGATAATA
1 AATTTATAAAATTTTAAAAGATAATA
* * *
685937 AATTTATAAAGTTTTAAGAGATGATA
1 AATTTATAAAATTTTAAAAGATAATA
685963 AATTTATAAAAT
1 AATTTATAAAAT
685975 GTTCGCCGAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (26 bp):
AATTTATAAAATTTTAAAAGATAATA
Found at i:686245 original size:21 final size:21
Alignment explanation
Indices: 686194--686246 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
686184 ATTATTACTA
686194 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
686215 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
686236 TCGCAATGCGA
1 TCGCAATGCGA
686247 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:686301 original size:20 final size:20
Alignment explanation
Indices: 686276--686390 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
686266 AATTTGGAAA
*
686276 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
686296 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
686317 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
686337 TTCGCAACGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* **
686357 TTCGCAACGATATACTGACT
1 ATCGCAACGCGATACTGACT
* *
686377 TTCGCAACGAGATA
1 ATCGCAACGCGATA
686391 ATACATAATC
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.03
20 61 0.77
21 14 0.18
22 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:686318 original size:41 final size:41
Alignment explanation
Indices: 686273--686406 Score: 164
Period size: 41 Copynumber: 3.3 Consensus size: 41
686263 ACGAATTTGG
*
686273 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAATGCGATACTGACTTTCGCAACGCGATAATAC
*
686314 AAAATCGCAATGCGATACTGACTTTCGCAACGCGATACTTAC
1 AAAATCGCAATGCGATACTGACTTTCGCAACGCGATA-ATAC
** * ** *
686356 --TTTCGCAACGATATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAATGCGATACTGACTTTCGCAACGCGATAATAC
*
686395 ATAATCGCAATG
1 AAAATCGCAATG
686407 TGATTTTCAA
Statistics
Matches: 78, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
39 3 0.04
40 29 0.37
41 43 0.55
42 3 0.04
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (41 bp):
AAAATCGCAATGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:686604 original size:22 final size:22
Alignment explanation
Indices: 686577--686620 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
686567 CACTCTCTCA
686577 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
686599 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
686621 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:686922 original size:20 final size:20
Alignment explanation
Indices: 686883--686941 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
686873 TTTATTCTCT
* **
686883 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
*
686903 CGTTGCGGTTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
686923 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
686942 AGAAACTGTT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.14, C:0.19, G:0.24, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:688282 original size:18 final size:18
Alignment explanation
Indices: 688261--688308 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
688251 TCCACTTCGG
688261 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
688279 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
688297 GAGCCATCACCT
1 GAGCCATCACCT
688309 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:688903 original size:19 final size:20
Alignment explanation
Indices: 688849--688915 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
688839 TAGTTTACTT
* *
688849 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
688869 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
688889 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
688908 TCGCAACG
1 TCGCAACG
688916 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:688942 original size:19 final size:19
Alignment explanation
Indices: 688849--688951 Score: 72
Period size: 19 Copynumber: 5.6 Consensus size: 19
688839 TAGTTTACTT
* **
688849 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
688869 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
688889 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
688908 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
688922 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
688941 TCGCAATGCGA
1 TCGCAACGCGA
688952 TTTGTGTTTC
Statistics
Matches: 68, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
14 10 0.15
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 27 0.40
20 24 0.35
21 1 0.01
ACGTcount: A:0.42, C:0.23, G:0.21, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:689009 original size:20 final size:20
Alignment explanation
Indices: 688963--689049 Score: 122
Period size: 20 Copynumber: 4.4 Consensus size: 20
688953 TTGTGTTTCA
**
688963 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
* *
688982 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTTCCG
689002 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
689022 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
689042 CGTTGCGA
1 CGTTGCGA
689050 AAGTAAGTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
19 13 0.22
20 47 0.78
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:689489 original size:41 final size:42
Alignment explanation
Indices: 689421--689504 Score: 116
Period size: 41 Copynumber: 2.0 Consensus size: 42
689411 CACCTGTCAG
* *
689421 CCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTATCAT
1 CCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTATCAT
* * *
689463 CCCTCAATAGT-CCCTCCCACCGTTCAAGAGGCCACTGTCAT
1 CCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTATCAT
689504 C
1 C
689505 GTTGAAGAGG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 27 0.73
42 10 0.27
ACGTcount: A:0.23, C:0.42, G:0.14, T:0.21
Consensus pattern (42 bp):
CCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTATCAT
Found at i:690949 original size:14 final size:14
Alignment explanation
Indices: 690915--690953 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
690905 TTAATTGTTT
690915 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
690929 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
690943 TGTTGATTTGT
1 AATTGATTTGT
690954 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:691117 original size:19 final size:19
Alignment explanation
Indices: 691093--691157 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
691083 GCAACGAGAG
691093 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
691112 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
691131 AATCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
691145 AATCGCAATGCGA
1 AATCGCAATGCGA
691158 TTTTCATTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
14 11 0.26
15 1 0.02
16 2 0.05
17 2 0.05
19 27 0.63
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:691189 original size:20 final size:20
Alignment explanation
Indices: 691164--691217 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
691154 GCGATTTTCA
691164 TTTCGCGTTGCGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
*
691184 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGCCAT
691204 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
691218 TTCCCCGTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.13, C:0.22, G:0.26, T:0.39
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGCCAT
Found at i:692099 original size:21 final size:21
Alignment explanation
Indices: 692055--692099 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
692045 GATTTCTGGG
* * *
692055 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
692076 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
692097 CAA
1 CAA
692100 ACGAACATAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:693064 original size:31 final size:31
Alignment explanation
Indices: 693011--693096 Score: 154
Period size: 31 Copynumber: 2.7 Consensus size: 31
693001 GTTCTACGGA
*
693011 ACATATGGACAGTTTTACCTATGTCTTTCGAG
1 ACATATGGACAG-TATACCTATGTCTTTCGAG
693043 ACATATGGACAGTATACCTATGTCTTTCGAG
1 ACATATGGACAGTATACCTATGTCTTTCGAG
693074 ACATATGGACAGTATACCTATGT
1 ACATATGGACAGTATACCTATGT
693097 TCTAAGGAAC
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
31 41 0.77
32 12 0.23
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (31 bp):
ACATATGGACAGTATACCTATGTCTTTCGAG
Found at i:693109 original size:31 final size:31
Alignment explanation
Indices: 692994--693115 Score: 142
Period size: 31 Copynumber: 3.9 Consensus size: 31
692984 GTCGAGGGTT
*
692994 TACCTATGTTCTA-CG-GAACATATGGACAGTTT
1 TACCTATG-TCTATCGAG-ACATATGGACAG-TA
*
693026 TACCTATGTCTTTCGAGACATATGGACAGTA
1 TACCTATGTCTATCGAGACATATGGACAGTA
*
693057 TACCTATGTCTTTCGAGACATATGGACAGTA
1 TACCTATGTCTATCGAGACATATGGACAGTA
**
693088 TACCTATGTTCTAAGGA-ACATATGGACA
1 TACCTATG-TCTATCGAGACATATGGACA
693116 ATTACCGAGG
Statistics
Matches: 82, Mismatches: 5, Indels: 7
0.87 0.05 0.07
Matches are distributed among these distances:
31 54 0.66
32 27 0.33
33 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (31 bp):
TACCTATGTCTATCGAGACATATGGACAGTA
Found at i:693131 original size:62 final size:63
Alignment explanation
Indices: 693011--693131 Score: 140
Period size: 62 Copynumber: 1.9 Consensus size: 63
693001 GTTCTACGGA
* ** * * *
693011 ACATATGGACAGTTTTACCTATGTCTTTCGAGACATATGGACAGTATACCTATGTCTTTCGAG
1 ACATATGGACAGTTATACCTATGTCTAACGAGACATATGGACAATATACCGAGGTCTTTCGAG
*
693074 ACATATGGACAG-TATACCTATGTTCTAAGGA-ACATATGGACAAT-TACCGAGGATCTTT
1 ACATATGGACAGTTATACCTATG-TCTAACGAGACATATGGACAATATACCGAGG-TCTTT
693132 ATGACCTCTG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
61 6 0.12
62 26 0.53
63 17 0.35
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (63 bp):
ACATATGGACAGTTATACCTATGTCTAACGAGACATATGGACAATATACCGAGGTCTTTCGAG
Found at i:693151 original size:30 final size:30
Alignment explanation
Indices: 693110--693292 Score: 323
Period size: 30 Copynumber: 6.1 Consensus size: 30
693100 AAGGAACATA
*
693110 TGGACAATTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
693140 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
693170 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
693200 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
693230 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
693260 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
693289 TGGA
1 TGGA
693293 TAGGTCCTTC
Statistics
Matches: 149, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
29 18 0.12
30 131 0.88
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:694479 original size:20 final size:20
Alignment explanation
Indices: 694458--694526 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
694448 TGTAATATCT
*
694458 CGTTGCGATAGTCAGAATCT
1 CGTTGCGATAGTCAGAATCG
*
694478 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGATAGTCAGAATCG
*
694498 CGTTGCGATAGTCAGTATCG
1 CGTTGCGATAGTCAGAATCG
*
694518 CATTGCGAT
1 CGTTGCGAT
694527 TTTCCAAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.28
Consensus pattern (20 bp):
CGTTGCGATAGTCAGAATCG
Found at i:694559 original size:20 final size:21
Alignment explanation
Indices: 694515--694563 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
694505 ATAGTCAGTA
*
694515 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
694536 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
694556 TCGCATTG
1 TCGCATTG
694564 TGAATTGGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:697157 original size:2 final size:2
Alignment explanation
Indices: 697152--697185 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
697142 TTTTTCAATA
697152 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
697186 GTGTGTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:702974 original size:2 final size:2
Alignment explanation
Indices: 702967--703000 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
702957 ATCCAAATTA
702967 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
703001 GTATGTATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:705670 original size:16 final size:16
Alignment explanation
Indices: 705649--705679 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
705639 AATATGTATT
705649 TAATATATATAATATA
1 TAATATATATAATATA
*
705665 TAATATATTTAATAT
1 TAATATATATAATAT
705680 TTTTGATTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TAATATATATAATATA
Found at i:710562 original size:22 final size:22
Alignment explanation
Indices: 710521--710562 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
710511 AAGTTATTAT
*
710521 TTTCATAAAAAAAAGGAAATAA
1 TTTCATAAAAAAAAGCAAATAA
* *
710543 TTTCATATAAACAAGCAAAT
1 TTTCATAAAAAAAAGCAAAT
710563 TTCAGAGATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.26
Consensus pattern (22 bp):
TTTCATAAAAAAAAGCAAATAA
Found at i:715262 original size:6 final size:6
Alignment explanation
Indices: 715251--715361 Score: 222
Period size: 6 Copynumber: 18.5 Consensus size: 6
715241 CTCTTTCCTT
715251 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC
1 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC
715299 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC
1 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC
715347 TCTTCC TCTTCC TCT
1 TCTTCC TCTTCC TCT
715362 CTCGGCTCTT
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 105 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (6 bp):
TCTTCC
Found at i:716266 original size:24 final size:24
Alignment explanation
Indices: 716234--716290 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
716224 GCTTTTTTTG
**
716234 CAGCTTCAGGCGTTGCCATATGTT
1 CAGCTTCAGGCACTGCCATATGTT
*
716258 CAGCTTCAGGCACTGCCATGTGTT
1 CAGCTTCAGGCACTGCCATATGTT
716282 CAGCTTCAG
1 CAGCTTCAG
716291 TTGTAGATAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.18, C:0.28, G:0.25, T:0.30
Consensus pattern (24 bp):
CAGCTTCAGGCACTGCCATATGTT
Found at i:723055 original size:14 final size:14
Alignment explanation
Indices: 723036--723063 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
723026 CTATCACATC
723036 TCTTTTTCTTTTTT
1 TCTTTTTCTTTTTT
723050 TCTTTTTCTTTTTT
1 TCTTTTTCTTTTTT
723064 GAAGACGAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
TCTTTTTCTTTTTT
Found at i:732031 original size:20 final size:21
Alignment explanation
Indices: 732006--732064 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 21
731996 GGCTGCTGGA
732006 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
* *
732026 AACCGGTTCTGACTGG-TTTC
1 AACCGGTTCTAACCGGTTTTC
* *
732046 GACCGGTTCAAACCGGTTT
1 AACCGGTTCTAACCGGTTT
732065 GACCGATCTG
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 24 0.77
21 7 0.23
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.32
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:732078 original size:19 final size:19
Alignment explanation
Indices: 732056--732094 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
732046 GACCGGTTCA
*
732056 AACCGGTTTGACCGATCTG
1 AACCAGTTTGACCGATCTG
*
732075 AACCAGTTTGACCGGTCTG
1 AACCAGTTTGACCGATCTG
732094 A
1 A
732095 CCCAACCGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.26
Consensus pattern (19 bp):
AACCAGTTTGACCGATCTG
Found at i:732134 original size:18 final size:18
Alignment explanation
Indices: 732093--732136 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
732083 TGACCGGTCT
*
732093 GACCCAACCGACCGACCC
1 GACCCGACCGACCGACCC
*
732111 GACCCGACCGTCCGACCC
1 GACCCGACCGACCGACCC
732129 GACCCGAC
1 GACCCGAC
732137 TGGACCGTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.23, C:0.55, G:0.20, T:0.02
Consensus pattern (18 bp):
GACCCGACCGACCGACCC
Found at i:738878 original size:15 final size:15
Alignment explanation
Indices: 738855--738902 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
738845 ATATTTGGCT
*
738855 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
*
738870 GGGCAGGCGGATGCG
1 GGGCGGGCGGATGCG
*
738885 GGGCGGGTGGATGCG
1 GGGCGGGCGGATGCG
738900 GGG
1 GGG
738903 TAGGTAATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.08, C:0.15, G:0.67, T:0.10
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:740997 original size:46 final size:46
Alignment explanation
Indices: 740940--741033 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
740930 AAAACTTCCA
740940 AGATCAAAATAGACCACATTTATAATTATGAAAAGTGAAAACTTTG
1 AGATCAAAATAGACCACATTTATAATTATGAAAAGTGAAAACTTTG
740986 AGATCAAAATAGACCACATTTATAATTATGAAAAGTGAAAACTTTG
1 AGATCAAAATAGACCACATTTATAATTATGAAAAGTGAAAACTTTG
741032 AG
1 AG
741034 GTGGAAAACC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.28
Consensus pattern (46 bp):
AGATCAAAATAGACCACATTTATAATTATGAAAAGTGAAAACTTTG
Found at i:745954 original size:26 final size:25
Alignment explanation
Indices: 745925--745985 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
745915 AAATAATAAT
* * *
745925 TTTAAATATTAATATAATACAATACA
1 TTTAAACAATAAT-TAACACAATACA
*
745951 TTTAAACAATAATTAACACAATATA
1 TTTAAACAATAATTAACACAATACA
*
745976 TTGAAACAAT
1 TTTAAACAAT
745986 TAAAATACCC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 19 0.63
26 11 0.37
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (25 bp):
TTTAAACAATAATTAACACAATACA
Found at i:745961 original size:13 final size:12
Alignment explanation
Indices: 745912--745985 Score: 51
Period size: 13 Copynumber: 5.8 Consensus size: 12
745902 TTTTGATATT
*
745912 TTTAAATAATAA
1 TTTAAACAATAA
* *
745924 TTTTAAATATTAA
1 -TTTAAACAATAA
*
745937 TATAATACAATACA
1 TTTAA-ACAATA-A
745951 TTTAAACAATAA
1 TTTAAACAATAA
745963 -TTAACACAATATA
1 TTTAA-ACAATA-A
*
745976 TTGAAACAAT
1 TTTAAACAAT
745986 TAAAATACCC
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
11 4 0.08
12 11 0.22
13 27 0.54
14 8 0.16
ACGTcount: A:0.54, C:0.08, G:0.01, T:0.36
Consensus pattern (12 bp):
TTTAAACAATAA
Found at i:745982 original size:25 final size:26
Alignment explanation
Indices: 745934--745985 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
745924 TTTTAAATAT
* *
745934 TAATATAATACAATACATTTAAACAA
1 TAATATAACACAATACATTGAAACAA
*
745960 TAAT-TAACACAATATATTGAAACAA
1 TAATATAACACAATACATTGAAACAA
745985 T
1 T
745986 TAAAATACCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.31
Consensus pattern (26 bp):
TAATATAACACAATACATTGAAACAA
Found at i:750489 original size:16 final size:16
Alignment explanation
Indices: 750470--750545 Score: 71
Period size: 16 Copynumber: 4.8 Consensus size: 16
750460 AATCAACTAT
750470 AACCGAAATTAACCCG
1 AACCGAAATTAACCCG
* ** *
750486 AACCAAAAGCAACTCG
1 AACCGAAATTAACCCG
*
750502 AACCGAAATTAACGCG
1 AACCGAAATTAACCCG
** *
750518 AACCGAAAGCAAACCG
1 AACCGAAATTAACCCG
*
750534 AACTGAAATTAA
1 AACCGAAATTAA
750546 TTCAAACCTA
Statistics
Matches: 45, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.49, C:0.26, G:0.14, T:0.11
Consensus pattern (16 bp):
AACCGAAATTAACCCG
Found at i:750506 original size:32 final size:32
Alignment explanation
Indices: 750470--750545 Score: 109
Period size: 32 Copynumber: 2.4 Consensus size: 32
750460 AATCAACTAT
750470 AACCGAAATTAACCCGAACCAAAAGC-AACTCG
1 AACCGAAATTAACCCGAACCAAAAGCAAAC-CG
* *
750502 AACCGAAATTAACGCGAACCGAAAGCAAACCG
1 AACCGAAATTAACCCGAACCAAAAGCAAACCG
*
750534 AACTGAAATTAA
1 AACCGAAATTAA
750546 TTCAAACCTA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 37 0.93
33 3 0.08
ACGTcount: A:0.49, C:0.26, G:0.14, T:0.11
Consensus pattern (32 bp):
AACCGAAATTAACCCGAACCAAAAGCAAACCG
Found at i:750637 original size:17 final size:16
Alignment explanation
Indices: 750611--750651 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
750601 AGTTATTAAA
*
750611 CAATAAAAATTATTTT
1 CAATAAAAATTAATTT
750627 CAATAATAAATTAATTT
1 CAATAA-AAATTAATTT
*
750644 AAATAAAA
1 CAATAAAA
750652 TTGATAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (16 bp):
CAATAAAAATTAATTT
Found at i:753516 original size:62 final size:62
Alignment explanation
Indices: 753417--753539 Score: 219
Period size: 62 Copynumber: 2.0 Consensus size: 62
753407 TCAGCTACCT
**
753417 CTCCCAAAAGCAACTAGACAATAAAAAACAATGCAGTATCCCACATCTAATGCACATATTCA
1 CTCCCAAAAGCAACTAGACAATAAAAAACAAAACAGTATCCCACATCTAATGCACATATTCA
*
753479 CTCCCAAAAGCAACTAGACAATAAAAAACAAAACAGTATCCCACATCTCATGCACATATTC
1 CTCCCAAAAGCAACTAGACAATAAAAAACAAAACAGTATCCCACATCTAATGCACATATTC
753540 CATTACTCTT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.46, C:0.28, G:0.07, T:0.19
Consensus pattern (62 bp):
CTCCCAAAAGCAACTAGACAATAAAAAACAAAACAGTATCCCACATCTAATGCACATATTCA
Found at i:756226 original size:128 final size:128
Alignment explanation
Indices: 756055--756310 Score: 485
Period size: 128 Copynumber: 2.0 Consensus size: 128
756045 ATATCAACCA
756055 ATGTACCTCTTTGTTGGTCGCTACATCCACCTTCTTGAAATTTTACCCATTGACTTCATCTACTC
1 ATGTACCTCTTTGTTGGTCGCTACATCCACCTTCTTGAAATTTTACCCATTGACTTCATCTACTC
*
756120 AGCACATGGATTAGGATCGTAGCATTCAATGATTTCATTTGTGAATGCTGCATGAACTGAGCC
66 AGCACATGGATTAGGATCGTAGCATTCAATGATTTCATTTCTGAATGCTGCATGAACTGAGCC
* *
756183 ATGTACCTCTTTGTTGGTCGTTACATCCACCTTCTTGAAATTTTACCCATTGATTTCATCTACTC
1 ATGTACCTCTTTGTTGGTCGCTACATCCACCTTCTTGAAATTTTACCCATTGACTTCATCTACTC
756248 AGCACATGGATTAGGATCGTAGCATTCAATGATTTCATTTCTGAATGCTGCATGAACTGAGCC
66 AGCACATGGATTAGGATCGTAGCATTCAATGATTTCATTTCTGAATGCTGCATGAACTGAGCC
756311 CAGATTCTCA
Statistics
Matches: 125, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 125 1.00
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (128 bp):
ATGTACCTCTTTGTTGGTCGCTACATCCACCTTCTTGAAATTTTACCCATTGACTTCATCTACTC
AGCACATGGATTAGGATCGTAGCATTCAATGATTTCATTTCTGAATGCTGCATGAACTGAGCC
Found at i:757559 original size:66 final size:63
Alignment explanation
Indices: 757452--757574 Score: 158
Period size: 66 Copynumber: 1.9 Consensus size: 63
757442 TTTGTTGAAG
* *
757452 GTGCATCGATGCACATGGAGTGTATCGATGCACTCATTTAAAATAAATGAACATCGAATGCCATT
1 GTGCATCGATGCACAAGGAGTGCATCGATGCACTCA-TTAAAATAAA--AACATCGAATGCCATT
757517 A
63 A
* *
757518 GTGCATCGATGCATAAGGAGTGCATCGATGCACCTGC-TTAAAATACAAACATCGAAT
1 GTGCATCGATGCACAAGGAGTGCATCGATGCA-CT-CATTAAAATAAAAACATCGAAT
757575 AGGATTTATG
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
64 10 0.20
66 38 0.75
67 2 0.04
68 1 0.02
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (63 bp):
GTGCATCGATGCACAAGGAGTGCATCGATGCACTCATTAAAATAAAAACATCGAATGCCATTA
Found at i:758191 original size:22 final size:22
Alignment explanation
Indices: 758166--758265 Score: 164
Period size: 22 Copynumber: 4.5 Consensus size: 22
758156 GGGTATATTA
*
758166 GTCCTTCAGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
758188 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
758210 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
*
758232 GTCCTTCGGGACGTATCTAGTG
1 GTCCTTCGGGACGTATCCAGTG
* *
758254 GTTCTTCAGGAC
1 GTCCTTCGGGAC
758266 ATAGTGGTCA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 74 1.00
ACGTcount: A:0.15, C:0.26, G:0.30, T:0.29
Consensus pattern (22 bp):
GTCCTTCGGGACGTATCCAGTG
Found at i:761051 original size:50 final size:50
Alignment explanation
Indices: 760988--761142 Score: 204
Period size: 50 Copynumber: 3.1 Consensus size: 50
760978 TTAGCAGTAA
* **
760988 AGCGCG-CCCCTGCACCGCGCTATACGATGATTTGGCGCCACGTGGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGGTGAGCTGGCGCCACGTGGGTAT
* * *
761037 AACGCGCCCCCTGCACCGCGCTATACGGTGAGCTGGCGTCACGTGGATAT
1 AGCGCGCCCCCTGCACCGCGCTATACGGTGAGCTGGCGCCACGTGGGTAT
* ** * *
761087 AGCGCGGCCCCAACAGCACGCTATACGGTGAGCTGGCGCCACGTGGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGGTGAGCTGGCGCCACGTGGGTAT
761137 AGCGCG
1 AGCGCG
761143 GATCAGGTAC
Statistics
Matches: 91, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
49 5 0.05
50 86 0.95
ACGTcount: A:0.18, C:0.33, G:0.32, T:0.17
Consensus pattern (50 bp):
AGCGCGCCCCCTGCACCGCGCTATACGGTGAGCTGGCGCCACGTGGGTAT
Found at i:761993 original size:2 final size:2
Alignment explanation
Indices: 761986--762013 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
761976 GTCACCAGTG
761986 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
762014 GGAAAATCGT
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:762872 original size:20 final size:19
Alignment explanation
Indices: 762843--762882 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
762833 AGTAATCATA
*
762843 TTCCCTGATAATCTTACAT
1 TTCCCTGATAATATTACAT
762862 TTCCACTGATAATATTACAT
1 TTCC-CTGATAATATTACAT
762882 T
1 T
762883 CCGTGAACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.30, C:0.23, G:0.05, T:0.42
Consensus pattern (19 bp):
TTCCCTGATAATATTACAT
Found at i:766802 original size:21 final size:21
Alignment explanation
Indices: 766776--766856 Score: 69
Period size: 21 Copynumber: 3.8 Consensus size: 21
766766 CAGAACCCCA
*
766776 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
766797 GGGGGGAATCGGTTCCCCT-T
1 GGGGGGAATCGATTCCCCTGT
* *
766817 GAAAGGGGGAATCGGTT-CCCTCAT
1 G---GGGGGAATCGATTCCCCT-GT
766841 GGGGGG-ATCGATTCCC
1 GGGGGGAATCGATTCCC
766857 TCTGCACCAA
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
20 8 0.16
21 24 0.47
22 4 0.08
23 13 0.25
24 2 0.04
ACGTcount: A:0.15, C:0.23, G:0.38, T:0.23
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:766850 original size:20 final size:20
Alignment explanation
Indices: 766821--766858 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
766811 CCCCTTGAAA
*
766821 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
766841 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
766859 TGCACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:770712 original size:22 final size:21
Alignment explanation
Indices: 770670--770709 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
770660 GAGTTTGTTT
*
770670 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
770691 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
770710 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:777679 original size:15 final size:15
Alignment explanation
Indices: 777659--777690 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
777649 ATTGTCTTTT
777659 ATAAAATTAAATTAA
1 ATAAAATTAAATTAA
*
777674 ATAAAATTATATTAA
1 ATAAAATTAAATTAA
777689 AT
1 AT
777691 CTTATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAAAATTAAATTAA
Found at i:789763 original size:15 final size:15
Alignment explanation
Indices: 789739--789774 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
789729 ACACCATTAA
*
789739 ATTAATTTATAAAAT
1 ATTAAATTATAAAAT
789754 ATTAAATTATAAAAT
1 ATTAAATTATAAAAT
*
789769 ACTAAA
1 ATTAAA
789775 CGTATAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (15 bp):
ATTAAATTATAAAAT
Found at i:791944 original size:31 final size:31
Alignment explanation
Indices: 791901--791973 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 31
791891 TTGGTTTGTC
*
791901 AAACTGTTGCTGCTGAAATACCCCTCAACAT
1 AAACTGTAGCTGCTGAAATACCCCTCAACAT
* **
791932 AAACTGTAGCTGCTGCAATACCCCTCAATGT
1 AAACTGTAGCTGCTGAAATACCCCTCAACAT
791963 AAACTGTAGCT
1 AAACTGTAGCT
791974 TTTCGCCTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.26
Consensus pattern (31 bp):
AAACTGTAGCTGCTGAAATACCCCTCAACAT
Found at i:793574 original size:20 final size:19
Alignment explanation
Indices: 793535--793576 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
793525 CTTTTCTTCT
793535 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
793554 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
793574 ATT
1 ATT
793577 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:794999 original size:3 final size:3
Alignment explanation
Indices: 794986--795032 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
794976 AAATATATAA
794986 TAT TAAT TAT TAT TAT TAT TA- TAT TA- TAT TAT TAT TAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
795030 TAT
1 TAT
795033 AATTTTAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.10
3 34 0.83
4 3 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:795019 original size:22 final size:21
Alignment explanation
Indices: 794985--795029 Score: 81
Period size: 22 Copynumber: 2.1 Consensus size: 21
794975 TAAATATATA
794985 ATATTAATTATTATTATTATT
1 ATATTAATTATTATTATTATT
795006 ATATTATATTATTATTATTATT
1 ATATTA-ATTATTATTATTATT
795028 AT
1 AT
795030 TATAATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATATTAATTATTATTATTATT
Found at i:795293 original size:46 final size:45
Alignment explanation
Indices: 795183--795330 Score: 242
Period size: 45 Copynumber: 3.3 Consensus size: 45
795173 GATGGAAATG
*
795183 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
*
795228 TTGAAAACATCATGCACTGAAGGACTTACAGATGACTCGAAGGTTT
1 TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-TT
* * *
795274 TTGAAAACATCATGCACTGAAGGACTTATAGATGACCCTAAGGCT
1 TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
795319 TTGAAAACATCA
1 TTGAAAACATCA
795331 AAAAGCTCCC
Statistics
Matches: 96, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
45 54 0.56
46 42 0.44
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (45 bp):
TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
Done.