Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007981.1 Hibiscus syriacus cultivar Beakdansim tig00110422_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: 1405786
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 8
Found at i:620157 original size:24 final size:25
Alignment explanation
Indices: 620108--620158 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
620098 CCATATCCAT
*
620108 TTTTAACTTTAAAATCTTTTCTTTA
1 TTTTAACTTTAAAATCTTTTCATTA
*
620133 TTTT-ACTTTAAATTACTTTT-ATTA
1 TTTTAACTTTAAAAT-CTTTTCATTA
620157 TT
1 TT
620159 ATTTAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.63
Consensus pattern (25 bp):
TTTTAACTTTAAAATCTTTTCATTA
Found at i:622119 original size:19 final size:21
Alignment explanation
Indices: 622087--622140 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
622077 TACAAAAATG
* *
622087 GTATCGGTATCATA-ATAG-A
1 GTATCGATACCATAGATAGTA
622106 GTATCGATACCATAGTATAGTA
1 GTATCGATACCATAG-ATAGTA
622128 GTATCGATACCAT
1 GTATCGATACCAT
622141 GGTGGGGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 12 0.40
21 4 0.13
22 14 0.47
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (21 bp):
GTATCGATACCATAGATAGTA
Found at i:623082 original size:81 final size:81
Alignment explanation
Indices: 622934--623445 Score: 751
Period size: 81 Copynumber: 6.3 Consensus size: 81
622924 TGAGGTCTAA
* * *
622934 CTGTGCAATT-GACAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGAACGTTGAGTA
1 CTGTGCATTTGGA-AGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTA
622998 AAAGATAAATGGCCTAG
65 AAAGATAAATGGCCTAG
* * *
623015 CTTTGCATTTGGAAGAAAGATGTCAATTATGCCAGTTAGATGAATGGTTAAAGACCGTTGAGTAA
1 CTGTGCATTTGGAAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAA
623080 AAGATAAATGGCCTAG
66 AAGATAAATGGCCTAG
* * * *
623096 TTGTGCATTTGGTAGAAAGGTGTCAGTTATGCCAGTTAGATGAATGGTTAAAGACCGTTGAGTAA
1 CTGTGCATTTGGAAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAA
623161 AAGATAAATGGCCTAG
66 AAGATAAATGGCCTAG
* *
623177 CTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACAGTTAAAGACCGTTGAGTAA
1 CTGTGCATTTGGAAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAA
*
623242 AAGATAAATAGCCTAG
66 AAGATAAATGGCCTAG
* * * * * **
623258 TTGTGCATTTGGTAGAAAGGTGTTAATTATGTCAATTAGATGAATAGTT-AAGACCGTTGAGTAA
1 CTGTGCATTTGGAAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAA
* *
623322 CAGATAAATGGCCTAA
66 AAGATAAATGGCCTAG
*
623338 CTGTGCATTTGGACGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAA
1 CTGTGCATTTGGAAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAA
* *
623403 AAGATAAATGTCCTAA
66 AAGATAAATGGCCTAG
*
623419 CTGTGCATTTGGCAGAAAAGG-GTCAAT
1 CTGTGCATTTGGAAG-AAAGGTGTCAAT
623446 CTTATTCCTT
Statistics
Matches: 390, Mismatches: 38, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
80 69 0.18
81 314 0.81
82 7 0.02
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (81 bp):
CTGTGCATTTGGAAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAA
AAGATAAATGGCCTAG
Found at i:623399 original size:242 final size:243
Alignment explanation
Indices: 622930--623445 Score: 806
Period size: 242 Copynumber: 2.1 Consensus size: 243
622920 ACTTTGAGGT
* * * *
622930 CTAACTGTGCAATTGACAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGAACGTTGA
1 CTAACTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACAGTTAAAGAACGTTGA
* *
622995 GTAAAAGATAAATGGCCTAGCTTTGCATTTGGAAGAAAGATGTCAATTATGCCAGTTAGATGAAT
66 GTAAAAGATAAATAGCCTAGCTTTGCATTTGGAAGAAAGATGTCAATTATGCCAATTAGATGAAT
* ** *
623060 GGTTAAAGACCGTTGAGTAAAAGATAAATGGCCTAGTTGTGCATTTGGTAGAAAGGTGTCAGTTA
131 AGTTAAAGACCGTTGAGTAAAAGATAAATGGCCTAACTGTGCATTTGGTAGAAAGGTGTCAATTA
*
623125 TGCCAGTTAGATGAATGGTTAAAGACCGTTGAGTAAAAGATAAATGGC
196 TGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGATAAATGGC
* *
623173 CTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACAGTTAAAGACCGTTGA
1 CTAACTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACAGTTAAAGAACGTTGA
* * * *
623238 GTAAAAGATAAATAGCCTAG-TTGTGCATTTGGTAGAAAGGTGTTAATTATGTCAATTAGATGAA
66 GTAAAAGATAAATAGCCTAGCTT-TGCATTTGGAAGAAAGATGTCAATTATGCCAATTAGATGAA
*
623302 TAGTT-AAGACCGTTGAGTAACAGATAAATGGCCTAACTGTGCATTTGG-ACGAAAGGTGTCAAT
130 TAGTTAAAGACCGTTGAGTAAAAGATAAATGGCCTAACTGTGCATTTGGTA-GAAAGGTGTCAAT
*
623365 TATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGATAAATGTC
194 TATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGATAAATGGC
623415 CTAACTGTGCATTTGGCAGAAAAGG-GTCAAT
1 CTAACTGTGCATTTGGCAG-AAAGGTGTCAAT
623446 CTTATTCCTT
Statistics
Matches: 250, Mismatches: 20, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
241 1 0.00
242 126 0.50
243 123 0.49
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (243 bp):
CTAACTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACAGTTAAAGAACGTTGA
GTAAAAGATAAATAGCCTAGCTTTGCATTTGGAAGAAAGATGTCAATTATGCCAATTAGATGAAT
AGTTAAAGACCGTTGAGTAAAAGATAAATGGCCTAACTGTGCATTTGGTAGAAAGGTGTCAATTA
TGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGATAAATGGC
Found at i:626497 original size:21 final size:21
Alignment explanation
Indices: 626473--626522 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
626463 TCGAGGGTTC
626473 TATGTGGTCCTTC-GAGACATA
1 TATGTGGTCCTTCGGA-ACATA
** *
626494 TATGTAATCCTTTGGAACATA
1 TATGTGGTCCTTCGGAACATA
626515 TATGTGGT
1 TATGTGGT
626523 ATTTCGATAC
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (21 bp):
TATGTGGTCCTTCGGAACATA
Found at i:632690 original size:19 final size:19
Alignment explanation
Indices: 632666--632702 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
632656 ATGACCAACA
*
632666 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
632685 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
632703 CAGTATCGCA
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:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:632832 original size:20 final size:20
Alignment explanation
Indices: 632809--632853 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
632799 GAATATGTAA
632809 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
632829 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
632849 ATCGC
1 ATCGC
632854 GTTACGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:633050 original size:22 final size:22
Alignment explanation
Indices: 633025--633067 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
633015 ACGGCGACAT
633025 CCGTCCCCATCTCCGACGAAAA
1 CCGTCCCCATCTCCGACGAAAA
* *
633047 CCGTCCTCATCTCCGGCGAAA
1 CCGTCCCCATCTCCGACGAAA
633068 TCCATCTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.44, G:0.16, T:0.16
Consensus pattern (22 bp):
CCGTCCCCATCTCCGACGAAAA
Found at i:633564 original size:20 final size:20
Alignment explanation
Indices: 633462--633567 Score: 90
Period size: 20 Copynumber: 5.4 Consensus size: 20
633452 AAATTGCAAC
*
633462 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
633481 GCGATTTTCA-TTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
** ** *
633500 GCGATAGTCAAATTCACGTT
1 GCGATTTTCATTTTCGCGTT
** * *
633520 GCGATAGTCATTTTCGTGAT
1 GCGATTTTCATTTTCGCGTT
* *
633540 ACGATTTTCATTTTCGTGTT
1 GCGATTTTCATTTTCGCGTT
633560 GCGATTTT
1 GCGATTTT
633568 AAGTTTCAGA
Statistics
Matches: 71, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
19 25 0.35
20 46 0.65
ACGTcount: A:0.17, C:0.17, G:0.22, T:0.44
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Found at i:633574 original size:20 final size:20
Alignment explanation
Indices: 633531--633574 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
633521 CGATAGTCAT
* *
633531 TTTCGTGATACGATTTTCAT
1 TTTCGTGATACGATTTTAAG
* *
633551 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGATACGATTTTAAG
633571 TTTC
1 TTTC
633575 AGAAACTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.16, C:0.14, G:0.18, T:0.52
Consensus pattern (20 bp):
TTTCGTGATACGATTTTAAG
Found at i:633768 original size:25 final size:26
Alignment explanation
Indices: 633714--633768 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
633704 TGTTTATTAT
**
633714 TGTTTTTGGTATATCTTCACATTGTA
1 TGTTTTTGGTATATCTAAACATTGTA
633740 -GTTTTTGGTATATC-AAAC-TTGGTA
1 TGTTTTTGGTATATCTAAACATT-GTA
633764 TGTTT
1 TGTTT
633769 ATTGTTTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 2 0.08
24 5 0.20
25 18 0.72
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (26 bp):
TGTTTTTGGTATATCTAAACATTGTA
Found at i:635588 original size:19 final size:19
Alignment explanation
Indices: 635564--635600 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
635554 CACGAATTTA
*
635564 GTTTCGCGTTGCGATTTTG
1 GTTTCGCATTGCGATTTTG
635583 GTTTCGCATTGCGATTTT
1 GTTTCGCATTGCGATTTT
635601 TTCGTTGCGA
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:0.08, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
GTTTCGCATTGCGATTTTG
Found at i:635674 original size:20 final size:20
Alignment explanation
Indices: 635651--635694 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
635641 TGATAGTCAT
635651 TTTCGCGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
*
635671 TTTCGTGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
635691 TTTC
1 TTTC
635695 AGAAACTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.14, G:0.23, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTAAG
Found at i:636236 original size:21 final size:21
Alignment explanation
Indices: 636166--636243 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
636156 CCGACTCACT
*
636166 TGTCATCGTTCAAGAGGCCCC
1 TGTCATCGTTCAAGAGTCCCC
* **
636187 TATCATCCCTCAAGAGTCCCC
1 TGTCATCGTTCAAGAGTCCCC
**
636208 TCCCATCGTTCAAGAGTCCCC
1 TGTCATCGTTCAAGAGTCCCC
*
636229 TGTCATCGTTGAAGA
1 TGTCATCGTTCAAGA
636244 TGTCTCTCCC
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.22, C:0.35, G:0.18, T:0.26
Consensus pattern (21 bp):
TGTCATCGTTCAAGAGTCCCC
Found at i:637831 original size:40 final size:40
Alignment explanation
Indices: 637787--637864 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
637777 AGGTACACTT
* * *
637787 TCGCAACGCTAAA-CTCAAAATCGCAATGCGAAAGTCAAAA
1 TCGCAACGCGAAAGC-CAAAATCGCAACGCAAAAGTCAAAA
*
637827 TCGCAATGCGAAAGCCAAAATCGCAACGCAAAAGTCAA
1 TCGCAACGCGAAAGCCAAAATCGCAACGCAAAAGTCAA
637865 TTCGCGTTGC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 32 0.97
41 1 0.03
ACGTcount: A:0.45, C:0.26, G:0.17, T:0.13
Consensus pattern (40 bp):
TCGCAACGCGAAAGCCAAAATCGCAACGCAAAAGTCAAAA
Found at i:637860 original size:20 final size:20
Alignment explanation
Indices: 637787--637860 Score: 87
Period size: 20 Copynumber: 3.7 Consensus size: 20
637777 AGGTACACTT
*
637787 TCGCAACGCTAAA-CTCAAAA
1 TCGCAACGCGAAAGC-CAAAA
* *
637807 TCGCAATGCGAAAGTCAAAA
1 TCGCAACGCGAAAGCCAAAA
*
637827 TCGCAATGCGAAAGCCAAAA
1 TCGCAACGCGAAAGCCAAAA
*
637847 TCGCAACGCAAAAG
1 TCGCAACGCGAAAG
637861 TCAATTCGCG
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.45, C:0.26, G:0.18, T:0.12
Consensus pattern (20 bp):
TCGCAACGCGAAAGCCAAAA
Found at i:637928 original size:20 final size:20
Alignment explanation
Indices: 637859--638053 Score: 182
Period size: 20 Copynumber: 10.4 Consensus size: 20
637849 GCAACGCAAA
637859 AGTC-AATTCGCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
* * *
637878 AGTCTAATACGCTTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
*
637898 --T----TTCTCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
*
637912 AGTCAAATTCCCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
* * *
637932 AATCAAATTCACGTTACGAT
1 AGTCAAATTCGCGTTGCGAT
637952 AGTCAAATTCGCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
637972 AGTCAAATTCGCGTTGC-A-
1 AGTCAAATTCGCGTTGCGAT
* *
637990 A-T---TTTTGCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
*
638006 AGTCAAATTCGCATTGCGAT
1 AGTCAAATTCGCGTTGCGAT
*
638026 AGTCAAATTCGTGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
*
638046 ATTCAAAT
1 AGTCAAAT
638054 GAATGTGTAA
Statistics
Matches: 143, Mismatches: 20, Indels: 25
0.76 0.11 0.13
Matches are distributed among these distances:
14 19 0.13
15 1 0.01
16 2 0.01
17 2 0.01
18 2 0.01
19 5 0.03
20 112 0.78
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (20 bp):
AGTCAAATTCGCGTTGCGAT
Found at i:637974 original size:94 final size:94
Alignment explanation
Indices: 637859--638053 Score: 268
Period size: 94 Copynumber: 2.1 Consensus size: 94
637849 GCAACGCAAA
* * *
637859 AGTC-AATTCGCGTTGCGATAGTCTAATACGCTTTGCGATTTTCT-CGTTGCGATAGTCAAATTC
1 AGTCAAATTCGCGTTGCGATAGTCAAATACGCGTTGCAATTTT-TGCGTTGCGATAGTCAAATTC
*
637922 CCGTTGCGATAATCAAATTCACGTTACGAT
65 CCATTGCGATAATCAAATTCACGTTACGAT
* *
637952 AGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCAATTTTTGCGTTGCGATAGTCAAATTCG
1 AGTCAAATTCGCGTTGCGATAGTCAAATACGCGTTGCAATTTTTGCGTTGCGATAGTCAAATTCC
* ** *
638017 CATTGCGATAGTCAAATTCGTGTTGCGAT
66 CATTGCGATAATCAAATTCACGTTACGAT
*
638046 ATTCAAAT
1 AGTCAAAT
638054 GAATGTGTAA
Statistics
Matches: 89, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
93 5 0.06
94 84 0.94
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (94 bp):
AGTCAAATTCGCGTTGCGATAGTCAAATACGCGTTGCAATTTTTGCGTTGCGATAGTCAAATTCC
CATTGCGATAATCAAATTCACGTTACGAT
Found at i:638276 original size:140 final size:140
Alignment explanation
Indices: 638024--638306 Score: 539
Period size: 140 Copynumber: 2.0 Consensus size: 140
638014 TCGCATTGCG
*
638024 ATAGTCAAATTCGTGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCATGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
638089 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
638154 AATACACATA
131 AATACACATA
*
638164 ATAGTCAAATTCATGTTGCGATATTCAAATGAATTTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCATGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
*
638229 TAGCAATGTTCAAACTCAAGTTACTAATACATGTCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
638294 AATACACATA
131 AATACACATA
638304 ATA
1 ATA
638307 CAACGTTTGC
Statistics
Matches: 140, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 140 1.00
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCATGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:640415 original size:14 final size:14
Alignment explanation
Indices: 640396--640422 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
640386 TCCCGTGGCA
640396 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
640410 TTTTCTTCGGGGA
1 TTTTCTTCGGGGA
640423 TTTCTTCTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.19, G:0.30, T:0.44
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:640428 original size:12 final size:13
Alignment explanation
Indices: 640397--640429 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
640387 CCCGTGGCAT
640397 TTTCTTCGGGGAC
1 TTTCTTCGGGGAC
640410 TTTTCTTCGGGGA-
1 -TTTCTTCGGGGAC
640423 TTTCTTC
1 TTTCTTC
640430 TTATTCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
14 12 0.63
ACGTcount: A:0.06, C:0.21, G:0.24, T:0.48
Consensus pattern (13 bp):
TTTCTTCGGGGAC
Found at i:640656 original size:24 final size:24
Alignment explanation
Indices: 640622--640675 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
640612 CTGAAACATC
640622 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
640646 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
640670 ATCAAA
1 ATCAAA
640676 TTTCGAATAC
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:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:640689 original size:24 final size:24
Alignment explanation
Indices: 640622--640689 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
640612 CTGAAACATC
* * *
640622 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
640646 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
640670 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
640690 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:641520 original size:20 final size:20
Alignment explanation
Indices: 641495--641563 Score: 104
Period size: 20 Copynumber: 3.5 Consensus size: 20
641485 TGAAATTCAG
*
641495 CGTTGCGACAGTCAGAATCA
1 CGTTGCGATAGTCAGAATCA
*
641515 CGTTGCGATAGTCAGAATCG
1 CGTTGCGATAGTCAGAATCA
641535 CGTTGCGATAGTCAGAATCGA
1 CGTTGCGATAGTCAGAATC-A
641556 -GTTGCGAT
1 CGTTGCGAT
641564 TATGTATTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (20 bp):
CGTTGCGATAGTCAGAATCA
Found at i:641580 original size:21 final size:21
Alignment explanation
Indices: 641551--641606 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
641541 GATAGTCAGA
641551 ATCGAGTTGCGATTATGTATT
1 ATCGAGTTGCGATTATGTATT
*
641572 ATCGCGTTGCGATTATGTATT
1 ATCGAGTTGCGATTATGTATT
* *
641593 ATCGTGTTGTGATT
1 ATCGAGTTGCGATT
641607 TACATATTCG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.20, C:0.11, G:0.25, T:0.45
Consensus pattern (21 bp):
ATCGAGTTGCGATTATGTATT
Found at i:642439 original size:23 final size:23
Alignment explanation
Indices: 642396--642439 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
642386 CATAGAAGAG
* *
642396 ATTAATGATTTTTTATTATTAAA
1 ATTAATAATTTTTTATAATTAAA
642419 ATTAATAATTATTTTA-AATTA
1 ATTAATAATT-TTTTATAATTA
642440 TTTTAAAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
ATTAATAATTTTTTATAATTAAA
Found at i:642899 original size:28 final size:27
Alignment explanation
Indices: 642868--642920 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
642858 AATTTAACTT
642868 GAAACTTT-TTGAGTTGAGTCGAGTTTGA
1 GAAA-TTTATTGAGTT-AGTCGAGTTTGA
*
642896 GAAATTTATTGAGTTATTCGAGTTT
1 GAAATTTATTGAGTTAGTCGAGTTT
642921 ATATGCTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.26, C:0.06, G:0.25, T:0.43
Consensus pattern (27 bp):
GAAATTTATTGAGTTAGTCGAGTTTGA
Found at i:646353 original size:21 final size:21
Alignment explanation
Indices: 646327--646383 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
646317 CATATGAAAT
*
646327 TTGTCCCGAATGACCACTGTA
1 TTGTCCCGAAGGACCACTGTA
646348 TTGTCCCGAAGGACCACTGTA
1 TTGTCCCGAAGGACCACTGTA
* *
646369 TTATCCTGAAGGACC
1 TTGTCCCGAAGGACC
646384 TATGAAACCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (21 bp):
TTGTCCCGAAGGACCACTGTA
Found at i:647120 original size:18 final size:19
Alignment explanation
Indices: 647085--647121 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
647075 TTTTCTTTAG
647085 GGGGGAATCGATACCCCCA
1 GGGGGAATCGATACCCCCA
647104 GGGGGAATCTG-TACCCCC
1 GGGGGAATC-GATACCCCC
647122 TGCATAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.22, C:0.32, G:0.32, T:0.14
Consensus pattern (19 bp):
GGGGGAATCGATACCCCCA
Found at i:652401 original size:21 final size:21
Alignment explanation
Indices: 652372--652417 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
652362 GAAATTTTCT
*
652372 CGAATGACCACTGTATTATCC
1 CGAAGGACCACTGTATTATCC
652393 CGAAGGACCACTGTATTATCC
1 CGAAGGACCACTGTATTATCC
652414 CGAA
1 CGAA
652418 TATGAAACCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (21 bp):
CGAAGGACCACTGTATTATCC
Found at i:670720 original size:29 final size:29
Alignment explanation
Indices: 670685--670764 Score: 119
Period size: 29 Copynumber: 2.8 Consensus size: 29
670675 AAACTAAATT
*
670685 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
670714 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
670743 GA--TCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
670765 GTTAGGTGAG
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
27 14 0.29
28 5 0.10
29 29 0.60
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.42
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:675418 original size:29 final size:29
Alignment explanation
Indices: 675383--675464 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
675373 AAACTAAATT
*
675383 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
675412 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
675441 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
675465 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:682317 original size:19 final size:18
Alignment explanation
Indices: 682293--682328 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
682283 ATTTTTATTA
682293 AATAAAAATAATTATTTTT
1 AATAAAAAT-ATTATTTTT
*
682312 AATAAATATATTATTTT
1 AATAAAAATATTATTTT
682329 GGGTCGAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AATAAAAATATTATTTTT
Found at i:683664 original size:2 final size:2
Alignment explanation
Indices: 683652--683682 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
683642 CTAAATTGTT
*
683652 TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
683683 GATATACTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:683905 original size:19 final size:19
Alignment explanation
Indices: 683881--683924 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
683871 AGATCTAAAT
*
683881 TGTTTCCCTCTCTTATTTC
1 TGTTTCCCTCTCTTATTTA
683900 TGTTTCCCTCTCTTATTTA
1 TGTTTCCCTCTCTTATTTA
683919 TGTTTC
1 TGTTTC
683925 TGTCGGAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.07, C:0.27, G:0.07, T:0.59
Consensus pattern (19 bp):
TGTTTCCCTCTCTTATTTA
Found at i:688589 original size:12 final size:13
Alignment explanation
Indices: 688553--688596 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
688543 GCCCCGATTA
688553 CCCGATTACCCGC
1 CCCGATTACCCGC
688566 CCCGATTACCCGC
1 CCCGATTACCCGC
*
688579 CCCGA-TACCCGA
1 CCCGATTACCCGC
688591 CCCGAT
1 CCCGAT
688597 AAATATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.18, C:0.52, G:0.16, T:0.14
Consensus pattern (13 bp):
CCCGATTACCCGC
Found at i:688673 original size:8 final size:8
Alignment explanation
Indices: 688660--688685 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
688650 AAATAAAAAA
688660 TATATATT
1 TATATATT
688668 TATATATT
1 TATATATT
688676 TATATATT
1 TATATATT
688684 TA
1 TA
688686 ATTTAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATATT
Found at i:688686 original size:40 final size:41
Alignment explanation
Indices: 688618--688708 Score: 123
Period size: 40 Copynumber: 2.3 Consensus size: 41
688608 ATAATTATTT
688618 ATATATATATATAATATTAATAAATTTAATTTAAATAAAAA
1 ATATATATATATAATATTAATAAATTTAATTTAAATAAAAA
* * * * *
688659 ATATATATTTAT-ATATTTATATATTTAATTTAAAT-ATAT
1 ATATATATATATAATATTAATAAATTTAATTTAAATAAAAA
688698 ATATATATATA
1 ATATATATATA
688709 CCCGGCCCGA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
39 12 0.27
40 21 0.48
41 11 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (41 bp):
ATATATATATATAATATTAATAAATTTAATTTAAATAAAAA
Found at i:688740 original size:12 final size:12
Alignment explanation
Indices: 688723--688748 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
688713 GCCCGATTCT
688723 CGACCCAATACC
1 CGACCCAATACC
688735 CGACCCAATACC
1 CGACCCAATACC
688747 CG
1 CG
688749 TTTAAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.50, G:0.12, T:0.08
Consensus pattern (12 bp):
CGACCCAATACC
Found at i:689059 original size:64 final size:65
Alignment explanation
Indices: 688927--689063 Score: 179
Period size: 64 Copynumber: 2.1 Consensus size: 65
688917 GCCATCCCTA
* * * * *
688927 GATACACTCATGGCTTTATTAAAACATCGAATGCATTTTGTGTACCAATACACATCCTATGCATC
1 GATACACTCATGGCTTTATTAAAACATCGAATGCAATTAGTGTACCAATACACACCCAATGCACC
** *
688992 GATACACTC-TGGCTTTATTAAAACATCGAATGCAATTAGTGTACTGATACAC-CCCAAGTGTAC
1 GATACACTCATGGCTTTATTAAAACATCGAATGCAATTAGTGTACCAATACACACCCAA-TGCAC
689055 C
65 C
689056 GATACACT
1 GATACACT
689064 AAGTCATATA
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
63 3 0.05
64 51 0.81
65 9 0.14
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (65 bp):
GATACACTCATGGCTTTATTAAAACATCGAATGCAATTAGTGTACCAATACACACCCAATGCACC
Found at i:693548 original size:17 final size:18
Alignment explanation
Indices: 693494--693540 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
693484 GATTGTCAAA
*
693494 TTTTTTAAAAGAAAAAGG
1 TTTTTCAAAAGAAAAAGG
693512 TTTTTCAAAAGAAAAAGG
1 TTTTTCAAAAGAAAAAGG
693530 TTTTTCAAAAG
1 TTTTTCAAAAG
693541 GGAAGGTTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.47, C:0.04, G:0.15, T:0.34
Consensus pattern (18 bp):
TTTTTCAAAAGAAAAAGG
Found at i:695441 original size:13 final size:13
Alignment explanation
Indices: 695409--695444 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
695399 ATTATAATTG
*
695409 TTCAAACATTGTT
1 TTCAAAAATTGTT
695422 TTC-AAAATTGTT
1 TTCAAAAATTGTT
695434 TTCAAAAATTG
1 TTCAAAAATTG
695445 CCCATTAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.44
Consensus pattern (13 bp):
TTCAAAAATTGTT
Found at i:696947 original size:19 final size:20
Alignment explanation
Indices: 696906--696947 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
696896 TTATTTATAT
* * *
696906 ATTTGGTTTTGACTGTTTGA
1 ATTTGGTTTTGAATATTTAA
696926 ATTTGG-TTTGAATATTTAA
1 ATTTGGTTTTGAATATTTAA
696945 ATT
1 ATT
696948 AAGCTTCATG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.24, C:0.02, G:0.19, T:0.55
Consensus pattern (20 bp):
ATTTGGTTTTGAATATTTAA
Found at i:698922 original size:26 final size:26
Alignment explanation
Indices: 698893--698949 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
698883 TCATGAATAC
*
698893 GGTGGATGAAGAATAAGTTAAAATTT
1 GGTGGATGAAGAACAAGTTAAAATTT
*
698919 GGTGGATGAAGAACAAGTTGAAATTT
1 GGTGGATGAAGAACAAGTTAAAATTT
698945 GGTGG
1 GGTGG
698950 TTTGAAGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.37, C:0.02, G:0.33, T:0.28
Consensus pattern (26 bp):
GGTGGATGAAGAACAAGTTAAAATTT
Found at i:700115 original size:26 final size:26
Alignment explanation
Indices: 700086--700139 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
700076 ACTTAATATG
* *
700086 TATGGTGGGCACGACCTTATGTCTAT
1 TATGATGGGCACAACCTTATGTCTAT
*
700112 TATGATGGGCACAACCTTATGTGTAT
1 TATGATGGGCACAACCTTATGTCTAT
700138 TA
1 TA
700140 GTACTTCAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (26 bp):
TATGATGGGCACAACCTTATGTCTAT
Found at i:701444 original size:21 final size:22
Alignment explanation
Indices: 701418--701458 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
701408 CCAGGACAAG
701418 GAGTATCGGTAC-TCTTTTAAT
1 GAGTATCGGTACTTCTTTTAAT
*
701439 GAGTATTGGTACTTCTTTTA
1 GAGTATCGGTACTTCTTTTA
701459 TAATTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.22, C:0.12, G:0.20, T:0.46
Consensus pattern (22 bp):
GAGTATCGGTACTTCTTTTAAT
Found at i:702743 original size:24 final size:24
Alignment explanation
Indices: 702716--702778 Score: 92
Period size: 24 Copynumber: 2.7 Consensus size: 24
702706 CACCATAGCT
* *
702716 CGTATAAATTGTACCGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
*
702740 CGTAGAATTTGCACCGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
702764 CGTAGAAA-TGCACCG
1 CGTAGAAATTGCACCG
702779 TAGTACCATA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
23 7 0.20
24 28 0.80
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.21
Consensus pattern (24 bp):
CGTAGAAATTGCACCGAAGTGCCA
Found at i:703204 original size:13 final size:13
Alignment explanation
Indices: 703186--703212 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
703176 ATACACATAA
703186 TCTCATAGCTCAT
1 TCTCATAGCTCAT
703199 TCTCATAGCTCAT
1 TCTCATAGCTCAT
703212 T
1 T
703213 ATCAATATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.30, G:0.07, T:0.41
Consensus pattern (13 bp):
TCTCATAGCTCAT
Found at i:706982 original size:21 final size:24
Alignment explanation
Indices: 706941--706985 Score: 69
Period size: 21 Copynumber: 2.0 Consensus size: 24
706931 AAAACATACT
706941 AAATGGTTTACATATAACTATTCA
1 AAATGGTTTACATATAACTATTCA
706965 AAAT-GTTTACA-A-AACTATTCA
1 AAATGGTTTACATATAACTATTCA
706986 GAGCTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 9 0.43
22 1 0.05
23 7 0.33
24 4 0.19
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (24 bp):
AAATGGTTTACATATAACTATTCA
Found at i:710055 original size:2 final size:2
Alignment explanation
Indices: 710048--710074 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
710038 CAAAAGGGCA
710048 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 A
710075 AGCAATGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:712266 original size:15 final size:15
Alignment explanation
Indices: 712246--712282 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
712236 GTTTTGCATC
*
712246 AATATTTTTACTAGA
1 AATATTCTTACTAGA
*
712261 AATATTCTTACTAGC
1 AATATTCTTACTAGA
712276 AATATTC
1 AATATTC
712283 ACGATGGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (15 bp):
AATATTCTTACTAGA
Found at i:715738 original size:19 final size:20
Alignment explanation
Indices: 715709--715770 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 20
715699 AATGTTAGAT
715709 AAATCAAAGAA-AAACATAAA
1 AAATCAAAGAATAAA-ATAAA
715729 AAAT-AAAGAATAAAATAAAA
1 AAATCAAAGAATAAAAT-AAA
*
715749 TAAATCAAAAGGA-AAAATAAA
1 -AAATC-AAAGAATAAAATAAA
715770 A
1 A
715771 TTTTAAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
19 8 0.22
20 11 0.31
21 7 0.19
22 5 0.14
23 5 0.14
ACGTcount: A:0.76, C:0.05, G:0.06, T:0.13
Consensus pattern (20 bp):
AAATCAAAGAATAAAATAAA
Found at i:716023 original size:29 final size:27
Alignment explanation
Indices: 715989--716048 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 27
715979 AAAACAAATA
* *
715989 AAAATAATGAATAT-ATATATAAAATAATG
1 AAAATAAAGAAAATAATA-ATAAAA-AA-G
716018 AAAATAAAGAAAATAATAATAAAAAAG
1 AAAATAAAGAAAATAATAATAAAAAAG
716045 AAAA
1 AAAA
716049 ATTAAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 5 0.18
28 2 0.07
29 18 0.64
30 3 0.11
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.22
Consensus pattern (27 bp):
AAAATAAAGAAAATAATAATAAAAAAG
Found at i:716032 original size:18 final size:19
Alignment explanation
Indices: 715989--716048 Score: 70
Period size: 18 Copynumber: 3.2 Consensus size: 19
715979 AAAACAAATA
* *
715989 AAAATAATGAATATATATAT
1 AAAATAATGAATA-ATAAAG
716009 AAAATAATGAA-AATAAAG
1 AAAATAATGAATAATAAAG
*
716027 AAAATAAT-AATAAAAAAG
1 AAAATAATGAATAATAAAG
716045 AAAA
1 AAAA
716049 ATTAAATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
17 2 0.06
18 22 0.61
19 1 0.03
20 11 0.31
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.22
Consensus pattern (19 bp):
AAAATAATGAATAATAAAG
Found at i:716040 original size:15 final size:17
Alignment explanation
Indices: 716019--716066 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
716009 AAAATAATGA
*
716019 AAATAAAGAAAATAA-T
1 AAATAAAGAAAAAAATT
*
716035 -AATAAAAAAGAAAAATT
1 AAATAAAGAA-AAAAATT
716052 AAATAAAGAAAAAAA
1 AAATAAAGAAAAAAA
716067 CAAGAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 8 0.31
16 4 0.15
17 6 0.23
18 8 0.31
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (17 bp):
AAATAAAGAAAAAAATT
Found at i:716144 original size:17 final size:17
Alignment explanation
Indices: 716109--716159 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
716099 AAAACAAAAG
*
716109 AAATCAAAG-AAAATGAA
1 AAATAAAAGAAAAAT-AA
716126 AAATAAAAGAAAAAT-A
1 AAATAAAAGAAAAATAA
*
716142 AAATAAAATAGAAAATAA
1 AAATAAAAGA-AAAATAA
716160 TTAATAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 10 0.34
17 13 0.45
18 6 0.21
ACGTcount: A:0.76, C:0.02, G:0.08, T:0.14
Consensus pattern (17 bp):
AAATAAAAGAAAAATAA
Found at i:716146 original size:16 final size:17
Alignment explanation
Indices: 716125--716159 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
716115 AAGAAAATGA
716125 AAAATAAAAGA-AAAAT
1 AAAATAAAAGAGAAAAT
*
716141 AAAATAAAATAGAAAAT
1 AAAATAAAAGAGAAAAT
716158 AA
1 AA
716160 TTAATAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (17 bp):
AAAATAAAAGAGAAAAT
Found at i:716218 original size:17 final size:19
Alignment explanation
Indices: 716188--716231 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
716178 GTTAAATTTT
716188 AAAAAGTAATAAAATAAAG
1 AAAAAGTAATAAAATAAAG
716207 AAAAA-TAA-AAAATAAA-
1 AAAAAGTAATAAAATAAAG
*
716223 ATAAAGTAA
1 AAAAAGTAA
716232 CAACTTAGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 4 0.17
17 11 0.48
18 3 0.13
19 5 0.22
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (19 bp):
AAAAAGTAATAAAATAAAG
Found at i:717424 original size:18 final size:17
Alignment explanation
Indices: 717401--717451 Score: 70
Period size: 16 Copynumber: 3.0 Consensus size: 17
717391 AAGAAAATTG
717401 AAATGAATTAAAATAATA
1 AAATGAA-TAAAATAATA
717419 AAATGAATAAAATAA-A
1 AAATGAATAAAATAATA
717435 AAAT-AATAATAATAATA
1 AAATGAATAA-AATAATA
717452 TACTAAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
15 5 0.16
16 10 0.32
17 9 0.29
18 7 0.23
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (17 bp):
AAATGAATAAAATAATA
Found at i:717429 original size:9 final size:8
Alignment explanation
Indices: 717409--717451 Score: 61
Period size: 9 Copynumber: 5.2 Consensus size: 8
717399 TGAAATGAAT
717409 TAAAATAA
1 TAAAATAA
717417 TAAAATGAA
1 TAAAAT-AA
717426 TAAAATAA
1 TAAAATAA
717434 -AAAATAA
1 TAAAATAA
717441 TAATAATAA
1 TAA-AATAA
717450 TA
1 TA
717452 TACTAAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
7 7 0.22
8 10 0.31
9 15 0.47
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (8 bp):
TAAAATAA
Found at i:717711 original size:104 final size:101
Alignment explanation
Indices: 717467--717925 Score: 317
Period size: 98 Copynumber: 4.5 Consensus size: 101
717457 AATATAATTT
* *
717467 ATATAATATATATATTTC-AAAATATTTTTTTAAACTATATA-T-TATATTTTAAAAAGTTTTCA
1 ATAT-ATATATATTTTTCAAAAATA-TTTTTAAAACTATATATTATATATTTTAAAAAGTTTTCA
* *
717529 AAACTATATGTTATATAGTTTTCAAAATGTTTTAAAAA
64 AAACTATATGATATATAGTTTTCAAAATATTTTAAAAA
*
717567 ATAT-TATATAAGTTTTCAAAAACTATTTTTAAAACTATATATTATATATTTTTTCAAAAATGTT
1 ATATATATAT-ATTTTTCAAAAA-TATTTTTAAAACTATATATTATATA--TTTT-AAAAA-GTT
* * **
717631 TTTAAAACTATACT-ATATA-ATTTTTCAAAATATTTTTTAAA
60 TTCAAAACTATA-TGATATATAGTTTTCAAAATATTTTAAAAA
* * *
717672 CTATATATATATTTTTCAAAAATATTTTTAAAACTATATA-T-TATA-TTTAAAAACATTTTAAA
1 ATATATATATATTTTTCAAAAATATTTTTAAAACTATATATTATATATTTTAAAAA-GTTTTCAA
*
717734 AACTATAT-ACTATATAAGTTTTCAAAATGTTTTAAAAA
65 AACTATATGA-TATAT-AGTTTTCAAAATATTTTAAAAA
** * * * *
717772 CCATACAGTATA----T---AAATGTTTTCAAAACTATATA-T-TATATTTTAAAAATATTTTCA
1 ATATATA-TATATTTTTCAAAAATATTTTTAAAACTATATATTATATATTTTAAAAA-GTTTTC-
* * * *
717828 AAAAAAATATATAATATATAAATTTTCGAAAATCATTTTCTGAAAA
63 --AAAACTATATGATATAT-AGTTTTC-AAAAT-A-TTT-TAAAAA
* * *
717874 TTATATATTATATTTTGTCAAAAACATTTTCACAAACTATATATATATATAT
1 ATATATA-TATATTTT-TCAAAAATATTTTTA-AAACTATATAT-TATATAT
717926 AATAAGATGA
Statistics
Matches: 289, Mismatches: 34, Indels: 58
0.76 0.09 0.15
Matches are distributed among these distances:
94 24 0.08
95 13 0.04
97 3 0.01
98 48 0.17
99 14 0.05
100 46 0.16
101 10 0.03
102 21 0.07
103 1 0.00
104 22 0.08
105 37 0.13
106 23 0.08
107 2 0.01
110 9 0.03
111 10 0.03
113 1 0.00
114 5 0.02
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (101 bp):
ATATATATATATTTTTCAAAAATATTTTTAAAACTATATATTATATATTTTAAAAAGTTTTCAAA
ACTATATGATATATAGTTTTCAAAATATTTTAAAAA
Found at i:717767 original size:36 final size:35
Alignment explanation
Indices: 717481--717798 Score: 247
Period size: 33 Copynumber: 9.2 Consensus size: 35
717471 AATATATATA
*
717481 TTTCAAAATATTTTTTTAAACTATATAT-TAT-A-T
1 TTTCAAAATA-TTTTTAAAACTATATATATATAAGT
* *
717514 TTT-AAAA-AGTTTTCAAAACTATATGT-TATATAGT
1 TTTCAAAATA-TTTTTAAAACTATATATATATA-AGT
* *
717548 TTTCAAAAT-GTTTTAAAA-AATAT-TATATAAGT
1 TTTCAAAATATTTTTAAAACTATATATATATAAGT
**
717580 TTTCAAAAACTATTTTTAAAACTATATATTATATATTT
1 TTTC-AAAA-TATTTTTAAAACTATATA-TATATAAGT
* * *
717618 TTTCAAAAATGTTTTTAAAACTATA-CTATATAATT
1 TTTC-AAAATATTTTTAAAACTATATATATATAAGT
*
717653 TTTCAAAATATTTTTTAAACTATATATATAT---T
1 TTTCAAAATATTTTTAAAACTATATATATATAAGT
717685 TTTCAAAAATATTTTTAAAACTATATAT-TAT-A--
1 TTTC-AAAATATTTTTAAAACTATATATATATAAGT
* * *
717717 TTTAAAAACATTTTAAAAACTATATACTATATAAGT
1 TTTCAAAATATTTTTAAAACTATATA-TATATAAGT
* * * *
717753 TTTCAAAATGTTTTAAAAACCATACAGTATATAAATGT
1 TTTCAAAATATTTTTAAAACTATATA-TATAT-AA-GT
717791 TTTCAAAA
1 TTTCAAAA
717799 CTATATATTA
Statistics
Matches: 236, Mismatches: 27, Indels: 39
0.78 0.09 0.13
Matches are distributed among these distances:
31 38 0.16
32 24 0.10
33 41 0.17
34 31 0.13
35 29 0.12
36 30 0.13
37 17 0.07
38 26 0.11
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (35 bp):
TTTCAAAATATTTTTAAAACTATATATATATAAGT
Found at i:717918 original size:2 final size:2
Alignment explanation
Indices: 717911--717951 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
717901 TTTCACAAAC
*
717911 TA TA TA TA TA TA TA TA -A TA -A GA TGA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA
717952 AACAAAATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
1 2 0.06
2 31 0.89
3 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (2 bp):
TA
Found at i:718619 original size:84 final size:83
Alignment explanation
Indices: 718512--719389 Score: 713
Period size: 84 Copynumber: 10.5 Consensus size: 83
718502 ACAATTTTAT
* * * * * *
718512 TGACAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATAATGTGCATTGGAGCTGAGCATAGTC
1 TGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
*
718577 GAACTCAAAGGTCTTCTGG
66 GAACTCGAAGGTCTT-TGG
* * * * * * * ** **
718596 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGTCCTCGAAGCTGAATGTAAC
1 TGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGT
*
718661 CGAACTCGAGGGTCTTT-G
65 CGAACTCGAAGGTCTTTGG
* *
718679 -G-CAGATAACCCATCTCGACTTAAGCTATGCTGCATATGATGTGCCTTGGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
*
718742 GAACTCAAAGGTCTTTGG
66 GAACTCGAAGGTCTTTGG
* * * * * ** * * * * * *
718760 TGACAGATAATCCTTCTAGCCTTGAGTTATATTGTAAATGATGTGCCCTCGAAGTTGAGTGTAAT
1 TGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGT
718825 CGAACTC-AAGGGTCTTT-G
65 CGAACTCGAA-GGTCTTTGG
* * *
718843 -G-CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTTAGCGTAGTT
1 TGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
718906 GAACTCGAAGGTCTTTGG
66 GAACTCGAAGGTCTTTGG
* * * * * * * * ** *
718924 TGGA-AAATAACCCTTCTAGCCTTGAGTTATGCTTCAAATGATGTGCCCTCGAAGCTGAGTATAA
1 T-GACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAG
**
718988 TCGAACTCGGGGGTCTTT-G
64 TCGAACTCGAAGGTCTTTGG
* *
719007 -G-CAGATAGCCCTTCTCGACTTAAGCTATGGTGCAAATGATGAGCCTTGGAGCTAGCCTTGGAG
1 TGACAGATAACCCTTCTCGACTTAAGCTATGCTGC-AA--ATGA----T---G-T-GCCTTGGAG
719070 CTGAGCGTAGTCGAACTCGAAGGTCTTTGG
54 CTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* * * * *
719100 TTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTAAGCGTAGT
1 -TGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
*
719165 CGAACTCGAAGGACTTTTGG
65 CGAACTCGAAGGTC-TTTGG
* * * * * * * * * * * *
719185 TGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCCCTCGAAGTTGAGTGTAAT
1 TGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGT
*
719250 CGAACTCGAGGGTCTTT-G
65 CGAACTCGAAGGTCTTTGG
* * ** *
719268 -GA-AAATATCCCTTCTCGACTTAAGCTATGCTGCAAATGATGCACATTGGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
*
719331 AAACTCGAAGGTCTTTGG
66 GAACTCGAAGGTCTTTGG
* * * * *
719349 TTGGCAGATAACCCTTCTCGATTTAAGTTATACTGTAAATG
1 -TGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATG
719390 TTGTCTTAAA
Statistics
Matches: 620, Mismatches: 139, Indels: 70
0.75 0.17 0.08
Matches are distributed among these distances:
80 82 0.13
81 127 0.20
82 7 0.01
83 74 0.12
84 204 0.33
85 56 0.09
88 1 0.00
89 1 0.00
91 1 0.00
92 30 0.05
93 6 0.01
95 3 0.00
96 28 0.05
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (83 bp):
TGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
GAACTCGAAGGTCTTTGG
Found at i:718831 original size:164 final size:164
Alignment explanation
Indices: 718515--719059 Score: 797
Period size: 164 Copynumber: 3.3 Consensus size: 164
718505 ATTTTATTGA
* * * * * *
718515 CAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATAATGTGCATTGGAGCTGAGCATAGTCGAA
1 CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
** *
718580 CTCAAAGGTCTTCTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGTCCT
66 CTCAAAGGTCTT-TGGTGACAGATAACCCTTCTAGCCTTGAGTTATATTGTAAATGATGTGCCCT
* *
718645 CGAAGCTGAATGTAACCGAACTCGAGGGTCTTTGG
130 CGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
* *
718680 CAGATAACCCATCTCGACTTAAGCTATGCTGCATATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
*
718745 CTCAAAGGTCTTTGGTGACAGATAATCCTTCTAGCCTTGAGTTATATTGTAAATGATGTGCCCTC
66 CTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATATTGTAAATGATGTGCCCTC
* *
718810 GAAGTTGAGTGTAATCGAACTCAAGGGTCTTTGG
131 GAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
* * *
718844 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTTAGCGTAGTTGAA
1 CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* * * *
718909 CTCGAAGGTCTTTGGTGGA-AAATAACCCTTCTAGCCTTGAGTTATGCTT-CAAATGATGTGCCC
66 CTCAAAGGTCTTTGGT-GACAGATAACCCTTCTAGCCTTGAGTTAT-ATTGTAAATGATGTGCCC
* *
718972 TCGAAGCTGAGTATAATCGAACTCGGGGGTCTTTGG
129 TCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
* * *
719008 CAGATAGCCCTTCTCGACTTAAGCTATGGTGCAAATGATGAGCCTTGGAGCT
1 CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCT
719060 AGCCTTGGAG
Statistics
Matches: 346, Mismatches: 32, Indels: 5
0.90 0.08 0.01
Matches are distributed among these distances:
164 273 0.79
165 73 0.21
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (164 bp):
CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
CTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATATTGTAAATGATGTGCCCTC
GAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG
Found at i:724698 original size:14 final size:14
Alignment explanation
Indices: 724661--724698 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
724651 AAAAATAAAA
724661 AATAAA-AATATTT
1 AATAAATAATATTT
724674 ATATAACATAATATTT
1 A-ATAA-ATAATATTT
724690 AATAAATAA
1 AATAAATAA
724699 AAAAAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 1 0.05
14 8 0.36
15 5 0.23
16 8 0.36
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (14 bp):
AATAAATAATATTT
Found at i:724868 original size:13 final size:13
Alignment explanation
Indices: 724852--724928 Score: 59
Period size: 13 Copynumber: 5.7 Consensus size: 13
724842 AAAGTCAAAG
724852 AAAAAAATAAATA
1 AAAAAAATAAATA
*
724865 AAAAGAATAAAT-
1 AAAAAAATAAATA
*
724877 AAAAAAAGAAATCA
1 AAAAAAATAAAT-A
*
724891 AAGAAAATGAAA-A
1 AAAAAAAT-AAATA
*
724904 AAAAAGAGAAAAATA
1 AAAAA-A-ATAAATA
724919 AAATAAAATA
1 AAA-AAAATA
724929 GAAAATAATT
Statistics
Matches: 49, Mismatches: 8, Indels: 13
0.70 0.11 0.19
Matches are distributed among these distances:
12 10 0.20
13 16 0.33
14 12 0.24
15 9 0.18
16 2 0.04
ACGTcount: A:0.79, C:0.01, G:0.08, T:0.12
Consensus pattern (13 bp):
AAAAAAATAAATA
Found at i:724905 original size:25 final size:25
Alignment explanation
Indices: 724852--724910 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
724842 AAAGTCAAAG
*
724852 AAAAAAATAAATAAAAAGAATAAAT
1 AAAAAAAGAAATAAAAAGAATAAAT
*
724877 AAAAAAAGAAATCAAAGAA-AATGAA-
1 AAAAAAAGAAAT-AAA-AAGAATAAAT
724902 AAAAAAAGA
1 AAAAAAAGA
724911 GAAAAATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 20 0.67
26 8 0.27
27 2 0.07
ACGTcount: A:0.80, C:0.02, G:0.08, T:0.10
Consensus pattern (25 bp):
AAAAAAAGAAATAAAAAGAATAAAT
Found at i:724921 original size:24 final size:23
Alignment explanation
Indices: 724877--724926 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 23
724867 AAGAATAAAT
724877 AAAAAAAGAAATCAAAGAAAATGAA
1 AAAAAAAGAAA-CAAAGAAAAT-AA
*
724902 AAAAAAAGAGAA-AAATAAAATAA
1 AAAAAAAGA-AACAAAGAAAATAA
724925 AA
1 AA
724927 TAGAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 4 0.17
24 8 0.35
25 9 0.39
26 2 0.09
ACGTcount: A:0.80, C:0.02, G:0.10, T:0.08
Consensus pattern (23 bp):
AAAAAAAGAAACAAAGAAAATAA
Found at i:726164 original size:5 final size:5
Alignment explanation
Indices: 726150--726190 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
726140 TGAAATGTAT
726150 TAAAA T-AAA TAAAA T-AAA TAAAA T-AAA TAAAA TAATAA TAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAA-AA TAA
726191 TATACTAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
4 12 0.38
5 15 0.47
6 5 0.16
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (5 bp):
TAAAA
Found at i:726192 original size:9 final size:9
Alignment explanation
Indices: 726150--726184 Score: 70
Period size: 9 Copynumber: 3.9 Consensus size: 9
726140 TGAAATGTAT
726150 TAAAATAAA
1 TAAAATAAA
726159 TAAAATAAA
1 TAAAATAAA
726168 TAAAATAAA
1 TAAAATAAA
726177 TAAAATAA
1 TAAAATAA
726185 TAATAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
TAAAATAAA
Found at i:726378 original size:31 final size:32
Alignment explanation
Indices: 726343--726410 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 32
726333 AAAACTATAT
* *
726343 TATATAATT-T-TTCAAAAATGTTTTTTAAAAC
1 TATATAATTATATTCAAAAACG-TTTTAAAAAC
*
726374 TATAT-ATTATATTTAAAAACGTTTTAAAAAC
1 TATATAATTATATTCAAAAACGTTTTAAAAAC
726405 TATATA
1 TATATA
726411 CTATATAAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
30 3 0.10
31 20 0.65
32 8 0.26
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (32 bp):
TATATAATTATATTCAAAAACGTTTTAAAAAC
Found at i:726416 original size:69 final size:64
Alignment explanation
Indices: 726207--726444 Score: 232
Period size: 68 Copynumber: 3.6 Consensus size: 64
726197 AAATATAATT
* * ** *
726207 TATATAATAT-ATATTTCAAAATATTTTTTAAACTATATATTATATTTAAAAA-GTTTTCAAAAC
1 TATATTATATAAT-TTTCAAAATGTTTTAAAAACTATATATTATATTTAAAAACGTTTTAAAAAC
* * * * *
726270 TATATGT-TATATAGTTTCAAAATGTTTTAAAAAATATTATATAAGT-TTTCAAAAACTATTTTT
1 TATAT-TATATA-ATTTTCAAAATGTTTTAAAAACTA-TATATTA-TATTT-AAAAAC-GTTTTA
726333 AAAAC
60 AAAAC
*
726338 TATATTATATAATTTTTCAAAAATGTTTTTTAAAACTATATATTATATTTAAAAACGTTTTAAAA
1 TATATTATATAA-TTTTC-AAAATG-TTTTAAAAACTATATATTATATTTAAAAACGTTTTAAAA
726403 AC
63 AC
726405 TATATACTATATAAGTTTTCAAAATGTTTTAAAAACTATA
1 TATAT--TATATAA-TTTTCAAAATGTTTTAAAAACTATA
726445 CAGTATATAA
Statistics
Matches: 143, Mismatches: 17, Indels: 26
0.77 0.09 0.14
Matches are distributed among these distances:
63 8 0.06
64 18 0.13
65 10 0.07
66 6 0.04
67 29 0.20
68 35 0.24
69 27 0.19
70 10 0.07
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (64 bp):
TATATTATATAATTTTCAAAATGTTTTAAAAACTATATATTATATTTAAAAACGTTTTAAAAAC
Found at i:726513 original size:34 final size:32
Alignment explanation
Indices: 726207--726513 Score: 184
Period size: 36 Copynumber: 9.4 Consensus size: 32
726197 AAATATAATT
* * **
726207 TATATAATATATATTTCAAAATATTTTTTAAAC
1 TATATAATATAT-TTTAAAAATGTTTTAAAAAC
* *
726240 TATATATTATA-TTTAAAAA-GTTTTCAAAAC
1 TATATAATATATTTTAAAAATGTTTTAAAAAC
* * *
726270 TATATGTTATATAGTTTCAAAATGTTTTAAAAA-
1 TATA--TAATATATTTTAAAAATGTTTTAAAAAC
* * *
726303 -ATATTATATAAGTTTTCAAAAACTATTTTTAAAAC
1 TATATAATAT-A-TTTT-AAAAA-TGTTTTAAAAAC
* *
726338 TATATTATATAATTTTTCAAAAATGTTTTTTAAAAC
1 TATATAATAT-A-TTTT-AAAAATG-TTTTAAAAAC
* *
726374 TATATATTATA-TTTAAAAACGTTTTAAAAAC
1 TATATAATATATTTTAAAAATGTTTTAAAAAC
*
726405 TATATACTATATAAGTTTTCAAAATGTTTTAAAAAC
1 TATATA--ATAT-A-TTTTAAAAATGTTTTAAAAAC
* * * *
726441 TATACAGTATA---T--AAATGTTTTCAAAAT
1 TATATAATATATTTTAAAAATGTTTTAAAAAC
* *
726468 TATATATTATATTTTAAAAATATTTTCAAAAAAC
1 TATATAATATATTTTAAAAATGTTTT--AAAAAC
726502 TATATAATATAT
1 TATATAATATAT
726514 AAATTTTTCA
Statistics
Matches: 219, Mismatches: 32, Indels: 45
0.74 0.11 0.15
Matches are distributed among these distances:
27 22 0.10
29 1 0.00
30 19 0.09
31 23 0.11
32 25 0.11
33 28 0.13
34 37 0.17
35 2 0.01
36 62 0.28
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.45
Consensus pattern (32 bp):
TATATAATATATTTTAAAAATGTTTTAAAAAC
Found at i:733048 original size:15 final size:15
Alignment explanation
Indices: 733028--733066 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
733018 ACCAGGAGAG
733028 ATAATAGAAGTTTTC
1 ATAATAGAAGTTTTC
733043 ATAATAGAAGTTTTC
1 ATAATAGAAGTTTTC
*
733058 ATAACAGAA
1 ATAATAGAA
733067 ATGCAAGCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (15 bp):
ATAATAGAAGTTTTC
Found at i:754858 original size:7 final size:7
Alignment explanation
Indices: 754848--754879 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
754838 GTGGAAATAA
754848 GAAATTT
1 GAAATTT
754855 GAAATTT
1 GAAATTT
754862 GAAATTT
1 GAAATTT
754869 GAAATTT
1 GAAATTT
754876 GAAA
1 GAAA
754880 CACCTAGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.38
Consensus pattern (7 bp):
GAAATTT
Found at i:772398 original size:22 final size:23
Alignment explanation
Indices: 772368--772417 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
772358 TCCATATATT
*
772368 TATTTTTAAT-TTATGAATAAAAA
1 TATTTTAAATATTAT-AATAAAAA
*
772391 TATTTTAAATATTATATTAAAAA
1 TATTTTAAATATTATAATAAAAA
772414 TATT
1 TATT
772418 ATTTGTAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TATTTTAAATATTATAATAAAAA
Found at i:776878 original size:2 final size:2
Alignment explanation
Indices: 776871--776896 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
776861 TTGTAAAATG
776871 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
776897 TGTGCTCTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:780883 original size:76 final size:74
Alignment explanation
Indices: 780792--781013 Score: 216
Period size: 76 Copynumber: 3.1 Consensus size: 74
780782 TAAACTCAAA
780792 TTTAAGATAATATTTTAAACATTATAT-TTTATATTTGTATTTTAGTTTAAATAGGTTTTTAGTA
1 TTTAAGATAATATTTT-AACATTATATCTTTATATTTGTATTTTAGTTTAAATA--TTTTTAGTA
780856 TTTTAATTAAGT
63 TTTTAATTAAGT
* * * * *
780868 TTTAAGATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTAAATATTTTTAGTATTT
1 TTTAAGATAATATTTTAACATTATATCTTTATATTTGTATTTTAGTTTAAATATTTTTAGTATTT
* *
780933 TAATTAGGA
66 TAATTAAGT
* * *
780942 TTT-AG--AATA--TT-ATATTAT-T-TTT-TA--GGTATTTTAGTTTAAATAGTTTTAAGTATT
1 TTTAAGATAATATTTTAACATTATATCTTTATATTTGTATTTTAGTTTAAATA-TTTTTAGTATT
* *
780996 TTAATTAGGA
65 TTAATTAAGT
781006 TTTAAGAT
1 TTTAAGAT
781014 GTTTTAGCTT
Statistics
Matches: 129, Mismatches: 12, Indels: 19
0.81 0.08 0.12
Matches are distributed among these distances:
63 17 0.13
64 23 0.18
65 3 0.02
66 3 0.02
67 1 0.01
68 6 0.05
69 2 0.02
71 3 0.02
73 2 0.02
74 22 0.17
75 7 0.05
76 40 0.31
ACGTcount: A:0.32, C:0.01, G:0.10, T:0.57
Consensus pattern (74 bp):
TTTAAGATAATATTTTAACATTATATCTTTATATTTGTATTTTAGTTTAAATATTTTTAGTATTT
TAATTAAGT
Found at i:781722 original size:9 final size:9
Alignment explanation
Indices: 781708--781733 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
781698 TTTATTATTA
781708 TATTTTTTT
1 TATTTTTTT
781717 TATTTTTTT
1 TATTTTTTT
781726 TATTTTTT
1 TATTTTTT
781734 ATTTTAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TATTTTTTT
Found at i:785060 original size:16 final size:15
Alignment explanation
Indices: 785030--785067 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
785020 TTAGGATAAA
785030 TTAAT-TTTTAATAT
1 TTAATATTTTAATAT
785044 TTAATATTTTAATTAT
1 TTAATATTTTAA-TAT
*
785060 TAAATATT
1 TTAATATT
785068 AATTACACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.24
15 6 0.29
16 10 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTAATATTTTAATAT
Found at i:786050 original size:4 final size:4
Alignment explanation
Indices: 785831--786112 Score: 339
Period size: 4 Copynumber: 70.5 Consensus size: 4
785821 TATCTATCTA
* * * *
785831 TCTG TCTA TCTG TCTG TCTA TCTG TCTG TCTA TCTA TCTG TCTG TCTG
1 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG
* * * * *
785879 TCTA TCTA TCTG TCTG TCTA TCTA TCTG TCTG TCTA TCTG TCTG TCTG
1 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG
* * *
785927 TCTG TTTG TCTG TCTG TCTG TCTA TCTG TCTG TCTG TCTG TCTA TCTG
1 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG
* * * * * *
785975 TGTG TCTG TCTG TCTG TCTA TCTG TCTA TCTG TCTA TCTA TCTG TCTA
1 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG
* * * * * *
786023 TCTC TCTG TCGG TCTG TCTC TCTG TCTG TCTG TATG TCTG TCTA TCTA
1 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG
*
786071 TCTG TCTG TCTG TCTG TCTA TCTG TCTG TCTG TCTG TCTG TC
1 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TC
786113 AGTTTGTCAG
Statistics
Matches: 239, Mismatches: 39, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 239 1.00
ACGTcount: A:0.07, C:0.25, G:0.18, T:0.50
Consensus pattern (4 bp):
TCTG
Found at i:786120 original size:12 final size:12
Alignment explanation
Indices: 785839--786183 Score: 184
Period size: 12 Copynumber: 28.6 Consensus size: 12
785829 TATCTGTCTA
785839 TCTGTCTGTCTA-
1 TCTGTCTGTC-AG
785851 TCTGTCTGTCTA-
1 TCTGTCTGTC-AG
* *
785863 TCTATCTGTCTG
1 TCTGTCTGTCAG
*
785875 TCTGTCTATCTA-
1 TCTGTCTGTC-AG
785887 TCTGTCTGTCTA-
1 TCTGTCTGTC-AG
* *
785899 TCTATCTGTCTG
1 TCTGTCTGTCAG
* *
785911 TCTATCTGTCTG
1 TCTGTCTGTCAG
**
785923 TCTGTCTGTTTG
1 TCTGTCTGTCAG
*
785935 TCTGTCTGTCTG
1 TCTGTCTGTCAG
* *
785947 TCTATCTGTCTG
1 TCTGTCTGTCAG
785959 TCTGTCTGTCTA-
1 TCTGTCTGTC-AG
* *
785971 TCTGTGTGTCTG
1 TCTGTCTGTCAG
785983 TCTGTCTGTCTA-
1 TCTGTCTGTC-AG
* *
785995 TCTGTCTATCTG
1 TCTGTCTGTCAG
* * *
786007 TCTATCTATCTG
1 TCTGTCTGTCAG
* * *
786019 TCTATCTCTCTG
1 TCTGTCTGTCAG
* **
786031 TCGGTCTGTCTC
1 TCTGTCTGTCAG
*
786043 TCTGTCTGTCTG
1 TCTGTCTGTCAG
*
786055 TATGTCTGTCTA-
1 TCTGTCTGTC-AG
* *
786067 TCTATCTGTCTG
1 TCTGTCTGTCAG
786079 TCTGTCTGTCTA-
1 TCTGTCTGTC-AG
*
786091 TCTGTCTGTCTG
1 TCTGTCTGTCAG
786103 TCTGTCTGTCAG
1 TCTGTCTGTCAG
* *
786115 TTTGTCAGTCAG
1 TCTGTCTGTCAG
* *
786127 TCAGTCAGTCAG
1 TCTGTCTGTCAG
* *
786139 TCAGTCAGTCAG
1 TCTGTCTGTCAG
*
786151 TCAGTCTGTGTCAG
1 TCTGTC--TGTCAG
* *
786165 TCAGTCAGTCAG
1 TCTGTCTGTCAG
*
786177 TCAGTCT
1 TCTGTCT
786184 CTCTCTCTCT
Statistics
Matches: 276, Mismatches: 44, Indels: 26
0.80 0.13 0.08
Matches are distributed among these distances:
12 265 0.96
14 11 0.04
ACGTcount: A:0.10, C:0.24, G:0.20, T:0.46
Consensus pattern (12 bp):
TCTGTCTGTCAG
Found at i:786120 original size:16 final size:16
Alignment explanation
Indices: 785831--786183 Score: 226
Period size: 16 Copynumber: 21.9 Consensus size: 16
785821 TATCTATCTA
* *
785831 TCTGTCTATCTGTCTG
1 TCTGTCTGTCAGTCTG
* * *
785847 TCTATCTGTCTGTCTA
1 TCTGTCTGTCAGTCTG
* *
785863 TCTATCTGTCTGTCTG
1 TCTGTCTGTCAGTCTG
* * *
785879 TCTATCTATCTGTCTG
1 TCTGTCTGTCAGTCTG
* * *
785895 TCTATCTATCTGTCTG
1 TCTGTCTGTCAGTCTG
* *
785911 TCTATCTGTCTGTCTG
1 TCTGTCTGTCAGTCTG
* *
785927 TCTGTTTGTCTGTCTG
1 TCTGTCTGTCAGTCTG
* *
785943 TCTGTCTATCTGTCTG
1 TCTGTCTGTCAGTCTG
785959 TCTGTCTGTCTA-TCTG
1 TCTGTCTGTC-AGTCTG
* *
785975 TGTGTCTGTCTGTCTG
1 TCTGTCTGTCAGTCTG
*
785991 TCTATCTGTCTA-TCTG
1 TCTGTCTGTC-AGTCTG
* * * *
786007 TCTATCTATCTGTCTA
1 TCTGTCTGTCAGTCTG
* *
786023 TCTCTCTGTCGGTCTG
1 TCTGTCTGTCAGTCTG
* *
786039 TCTCTCTGTCTGTCTG
1 TCTGTCTGTCAGTCTG
* *
786055 TATGTCTGTCTA-TCTA
1 TCTGTCTGTC-AGTCTG
*
786071 TCTGTCTGTCTGTCTG
1 TCTGTCTGTCAGTCTG
* *
786087 TCTATCTGTCTGTCTG
1 TCTGTCTGTCAGTCTG
*
786103 TCTGTCTGTCAGTTTG
1 TCTGTCTGTCAGTCTG
* * *
786119 TCAGTCAGTCAGTCAG
1 TCTGTCTGTCAGTCTG
* * *
786135 TCAGTCAGTCAGTCAG
1 TCTGTCTGTCAGTCTG
* *
786151 TCAGTCTGTGTCAGTCAG
1 TCTGTC--TGTCAGTCTG
* *
786169 TCAGTCAGTCAGTCT
1 TCTGTCTGTCAGTCT
786184 CTCTCTCTCT
Statistics
Matches: 286, Mismatches: 43, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
16 271 0.95
18 15 0.05
ACGTcount: A:0.10, C:0.24, G:0.20, T:0.46
Consensus pattern (16 bp):
TCTGTCTGTCAGTCTG
Found at i:786120 original size:20 final size:20
Alignment explanation
Indices: 785834--786159 Score: 253
Period size: 20 Copynumber: 16.3 Consensus size: 20
785824 CTATCTATCT
* * *
785834 GTCTATCTGTCTGTCTATCT
1 GTCTGTCTGTCTGTCTGTCA
* * *
785854 GTCTGTCTATCTATCTGTCT
1 GTCTGTCTGTCTGTCTGTCA
* * *
785874 GTCTGTCTATCTATCTGTCT
1 GTCTGTCTGTCTGTCTGTCA
* *
785894 GTCTATCTATCTGTCTGTCTA
1 GTCTGTCTGTCTGTCTGTC-A
**
785915 -TCTGTCTGTCTGTCTGTTT
1 GTCTGTCTGTCTGTCTGTCA
* *
785934 GTCTGTCTGTCTGTCTATCT
1 GTCTGTCTGTCTGTCTGTCA
* *
785954 GTCTGTCTGTCTGTCTATCT
1 GTCTGTCTGTCTGTCTGTCA
*
785974 GTGTGTCTGTCTGTCTGTCTA
1 GTCTGTCTGTCTGTCTGTC-A
* *
785995 -TCTGTCTATCTGTCTATCTA
1 GTCTGTCTGTCTGTCTGTC-A
* * *
786015 -TCTGTCTATCTCTCTGTCG
1 GTCTGTCTGTCTGTCTGTCA
* *
786034 GTCTGTCTCTCTGTCTGTCT
1 GTCTGTCTGTCTGTCTGTCA
* * * *
786054 GTATGTCTGTCTATCTATCT
1 GTCTGTCTGTCTGTCTGTCA
* *
786074 GTCTGTCTGTCTGTCTATCT
1 GTCTGTCTGTCTGTCTGTCA
786094 GTCTGTCTGTCTGTCTGTCA
1 GTCTGTCTGTCTGTCTGTCA
* * * *
786114 GTTTGTCAGTCAGTCAGTCA
1 GTCTGTCTGTCTGTCTGTCA
* * * *
786134 GTCAGTCAGTCAGTCAGTCA
1 GTCTGTCTGTCTGTCTGTCA
786154 GTCTGT
1 GTCTGT
786160 GTCAGTCAGT
Statistics
Matches: 262, Mismatches: 40, Indels: 8
0.85 0.13 0.03
Matches are distributed among these distances:
20 262 1.00
ACGTcount: A:0.09, C:0.24, G:0.19, T:0.47
Consensus pattern (20 bp):
GTCTGTCTGTCTGTCTGTCA
Found at i:786125 original size:4 final size:4
Alignment explanation
Indices: 786118--786182 Score: 107
Period size: 4 Copynumber: 16.8 Consensus size: 4
786108 CTGTCAGTTT
*
786118 GTCA GTCA GTCA GTCA GTCA GTCA GTCA GTCA GTCA GTCT GT-- GTCA
1 GTCA GTCA GTCA GTCA GTCA GTCA GTCA GTCA GTCA GTCA GTCA GTCA
786164 GTCA GTCA GTCA GTCA GTC
1 GTCA GTCA GTCA GTCA GTC
786183 TCTCTCTCTC
Statistics
Matches: 58, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
2 2 0.03
4 56 0.97
ACGTcount: A:0.22, C:0.25, G:0.26, T:0.28
Consensus pattern (4 bp):
GTCA
Found at i:786188 original size:2 final size:2
Alignment explanation
Indices: 786181--786317 Score: 274
Period size: 2 Copynumber: 68.5 Consensus size: 2
786171 AGTCAGTCAG
786181 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
786223 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
786265 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
786307 TC TC TC TC TC T
1 TC TC TC TC TC T
786318 AATCTCAGTT
Statistics
Matches: 135, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 135 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:797400 original size:2 final size:2
Alignment explanation
Indices: 797393--797423 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
797383 AATAAAAATG
797393 AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
797424 TAAATCGAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:803134 original size:21 final size:21
Alignment explanation
Indices: 803108--803206 Score: 103
Period size: 21 Copynumber: 4.7 Consensus size: 21
803098 AGAGTGTCAA
*
803108 AGTGCATCCATGTACCCCTAC
1 AGTGCATCCATGCACCCCTAC
* *
803129 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCACCCCTAC
*
803150 AGTGCATCCATGCACCTAC-AC
1 AGTGCATCCATGCACC-CCTAC
* * *
803171 TAGTGCATCGATGCA-CCATGC
1 -AGTGCATCCATGCACCCCTAC
803192 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
803207 TCCATTTCGA
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
20 13 0.21
21 36 0.57
22 14 0.22
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.22
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTAC
Found at i:803193 original size:42 final size:42
Alignment explanation
Indices: 803108--803206 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 42
803098 AGAGTGTCAA
* * *
803108 AGTGCATCCATGTACCCCTACAGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCACCACTACAGTGCATCCATGCATCCATGC
*
803150 AGTGCATCCATGCACCTAC-ACTAGTGCATCGATGCA-CCATGC
1 AGTGCATCCATGCACC-ACTAC-AGTGCATCCATGCATCCATGC
803192 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
803207 TCCATTTCGA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
42 37 0.73
43 14 0.27
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.22
Consensus pattern (42 bp):
AGTGCATCCATGCACCACTACAGTGCATCCATGCATCCATGC
Found at i:803197 original size:20 final size:19
Alignment explanation
Indices: 803128--803299 Score: 104
Period size: 20 Copynumber: 8.8 Consensus size: 19
803118 TGTACCCCTA
*
803128 CAGTGCATCCATGCATCCCTG
1 CAGTGCATCGATGCA--CCTG
* *
803149 CAGTGCATCCATGCACCTACA
1 CAGTGCATCGATGCACCT--G
803170 CTAGTGCATCGATGCACCATG
1 C-AGTGCATCGATGCACC-TG
* *
803191 CAGTGCATCCATGCA-CTC
1 CAGTGCATCGATGCACCTG
*
803209 CA-T--TTCGAATGCA-CT-
1 CAGTGCATCG-ATGCACCTG
* *
803224 TAGTGCATCGATGCATCCTT
1 CAGTGCATCGATGCA-CCTG
*
803244 CTGTGCATCGATGCATCCTG
1 CAGTGCATCGATGCA-CCTG
*
803264 CTGTGCATCGATGCATCCTG
1 CAGTGCATCGATGCA-CCTG
* *
803284 CTGTGCATCCATGCAC
1 CAGTGCATCGATGCAC
803300 GAAGGCTGCA
Statistics
Matches: 127, Mismatches: 13, Indels: 24
0.77 0.08 0.15
Matches are distributed among these distances:
15 3 0.02
16 8 0.06
17 6 0.05
18 6 0.05
19 7 0.06
20 64 0.50
21 17 0.13
22 15 0.12
23 1 0.01
ACGTcount: A:0.21, C:0.33, G:0.20, T:0.27
Consensus pattern (19 bp):
CAGTGCATCGATGCACCTG
Found at i:806712 original size:16 final size:17
Alignment explanation
Indices: 806691--806733 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 17
806681 TCCCTGCACC
806691 TGCACT-AGTGCATCCA
1 TGCACTCAGTGCATCCA
806707 TGCACTATGCAGTGCATCCA
1 TGCAC--T-CAGTGCATCCA
806727 TGCACTC
1 TGCACTC
806734 CATTTCGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
16 5 0.22
17 1 0.04
18 2 0.09
20 15 0.65
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.26
Consensus pattern (17 bp):
TGCACTCAGTGCATCCA
Found at i:806722 original size:20 final size:20
Alignment explanation
Indices: 806633--806733 Score: 96
Period size: 21 Copynumber: 4.8 Consensus size: 20
806623 AGGGTGTCAA
* *
806633 AGTGCATCCATGAACCCCTGC
1 AGTGCATCCATGCA-CTCTGC
* *
806654 AGTGCATCCATCCATCCCTGC
1 AGTGCATCCATGCA-CTCTGC
*
806675 AGTGCATCCCTGCAC-CTGCAC
1 AGTGCATCCATGCACTCTG--C
*
806696 TAGTGCATCCATGCACTATGC
1 -AGTGCATCCATGCACTCTGC
806717 AGTGCATCCATGCACTC
1 AGTGCATCCATGCACTC
806734 CATTTCGAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
19 3 0.04
20 17 0.25
21 32 0.47
22 14 0.21
23 2 0.03
ACGTcount: A:0.22, C:0.38, G:0.18, T:0.23
Consensus pattern (20 bp):
AGTGCATCCATGCACTCTGC
Found at i:806934 original size:20 final size:22
Alignment explanation
Indices: 806896--806935 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
806886 TTCGAGTAGA
806896 AAAATCATCCCCAAACGGCTCT
1 AAAATCATCCCCAAACGGCTCT
806918 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
806936 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCT
Found at i:809043 original size:27 final size:27
Alignment explanation
Indices: 809002--809053 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
808992 CAGACTTTAA
*
809002 CTTCTTTTTGCTTGCTGAATTATCATC
1 CTTCTTTTTGATTGCTGAATTATCATC
*
809029 CTTCTTTTTGATTGCTGTATTATCA
1 CTTCTTTTTGATTGCTGAATTATCA
809054 CACTCTAGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.15, C:0.19, G:0.12, T:0.54
Consensus pattern (27 bp):
CTTCTTTTTGATTGCTGAATTATCATC
Found at i:811564 original size:31 final size:31
Alignment explanation
Indices: 811529--811594 Score: 116
Period size: 31 Copynumber: 2.1 Consensus size: 31
811519 GTGTGTGTAT
811529 AAGGTTACTTG-GGGAAGAGTTTTCATGATAA
1 AAGGTTAC-TGAGGGAAGAGTTTTCATGATAA
811560 AAGGTTACTGAGGGAAGAGTTTTCATGATAA
1 AAGGTTACTGAGGGAAGAGTTTTCATGATAA
811591 AAGG
1 AAGG
811595 AAAGGCACTC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 2 0.06
31 32 0.94
ACGTcount: A:0.35, C:0.06, G:0.30, T:0.29
Consensus pattern (31 bp):
AAGGTTACTGAGGGAAGAGTTTTCATGATAA
Found at i:814208 original size:17 final size:17
Alignment explanation
Indices: 814178--814219 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
814168 ATTTAGATTC
*
814178 AATTGTAATCGAAA-TG
1 AATTGAAATCGAAATTG
*
814194 AAATTGAAATTGAAATTG
1 -AATTGAAATCGAAATTG
814212 AATTGAAA
1 AATTGAAA
814220 AGATTGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 20 0.91
18 2 0.09
ACGTcount: A:0.50, C:0.02, G:0.17, T:0.31
Consensus pattern (17 bp):
AATTGAAATCGAAATTG
Found at i:814215 original size:5 final size:6
Alignment explanation
Indices: 814178--814219 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
814168 ATTTAGATTC
* *
814178 AATTGT AATCGA AA-TGA AATTGA AATTGA AATTG- AATTGA AA
1 AATTGA AATTGA AATTGA AATTGA AATTGA AATTGA AATTGA AA
814220 AGATTGAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
5 9 0.29
6 22 0.71
ACGTcount: A:0.50, C:0.02, G:0.17, T:0.31
Consensus pattern (6 bp):
AATTGA
Found at i:816751 original size:6 final size:6
Alignment explanation
Indices: 816740--816773 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
816730 AATGTGCCAT
816740 ATCATA ATCATA ATCATA ATCATA ATCATA ATCA
1 ATCATA ATCATA ATCATA ATCATA ATCATA ATCA
816774 ATCCATCTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (6 bp):
ATCATA
Found at i:832000 original size:19 final size:20
Alignment explanation
Indices: 831962--832001 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
831952 CTCAAGCTGA
831962 TTGTTTCTTTCATTTTTAAG
1 TTGTTTCTTTCATTTTTAAG
831982 TTGTTT-TTT-ATTGTTTAAG
1 TTGTTTCTTTCATT-TTTAAG
832001 T
1 T
832002 GTTAGGAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.16
19 10 0.53
20 6 0.32
ACGTcount: A:0.15, C:0.05, G:0.12, T:0.68
Consensus pattern (20 bp):
TTGTTTCTTTCATTTTTAAG
Found at i:833591 original size:22 final size:22
Alignment explanation
Indices: 833514--833593 Score: 81
Period size: 23 Copynumber: 3.5 Consensus size: 22
833504 CTTCAAGATA
* *
833514 ATTCTACGTGATCTTTCGGGAC
1 ATTCTATGTGGTCTTTCGGGAC
*
833536 ATT-TATACGCGGTCTTTCGGGAC
1 ATTCTAT--GTGGTCTTTCGGGAC
* *
833559 AATACTATGTGGTCCTTCGGGAC
1 -ATTCTATGTGGTCTTTCGGGAC
833582 ATTCTATGTGGT
1 ATTCTATGTGGT
833594 ATTTTGGTGT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
21 2 0.04
22 14 0.30
23 26 0.55
24 2 0.04
25 3 0.06
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (22 bp):
ATTCTATGTGGTCTTTCGGGAC
Found at i:836257 original size:25 final size:25
Alignment explanation
Indices: 836225--836280 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
836215 TTGGTTGTGT
*
836225 TTTGTATTGTTGTTTTTTGTTTTAG
1 TTTGTATTGTTGTTTTTGGTTTTAG
836250 TTTGTATTGTTGTTTTTGGTTTTAG
1 TTTGTATTGTTGTTTTTGGTTTTAG
836275 TTTGTA
1 TTTGTA
836281 GCAGTGTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.09, C:0.00, G:0.21, T:0.70
Consensus pattern (25 bp):
TTTGTATTGTTGTTTTTGGTTTTAG
Found at i:836467 original size:63 final size:63
Alignment explanation
Indices: 836400--836588 Score: 207
Period size: 69 Copynumber: 2.9 Consensus size: 63
836390 TAAAGTTGAT
*
836400 TTTAATCATGTTATATAACTTAAATTACGCATTTTGAAGTATCCAATCAACTTTAAAGTCAAC
1 TTTAATCATGTTATATAACTTAAATTACGCATTTTGAACTATCCAATCAACTTTAAAGTCAAC
* * * *
836463 TTTAATCATGTTATAGAACTTAAATTATGCATTTTGAACAACCCAATCCTAATTGACTTTAAAGT
1 TTTAATCATGTTATATAACTTAAATTACGCATTTTGAACTATCCAAT-C--A---ACTTTAAAGT
** *
836528 TGAT
60 CAAC
* * * * *
836532 TTTAATTATATTATATAACTTAAATTACGCATTTTAAATTATCCAATCAAATTTAAA
1 TTTAATCATGTTATATAACTTAAATTACGCATTTTGAACTATCCAATCAACTTTAAA
836589 ATTGACTTTA
Statistics
Matches: 103, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
63 49 0.48
64 1 0.01
66 2 0.02
68 1 0.01
69 50 0.49
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.40
Consensus pattern (63 bp):
TTTAATCATGTTATATAACTTAAATTACGCATTTTGAACTATCCAATCAACTTTAAAGTCAAC
Found at i:836552 original size:69 final size:63
Alignment explanation
Indices: 836388--836599 Score: 217
Period size: 63 Copynumber: 3.3 Consensus size: 63
836378 CCAAATGTAA
** *
836388 TTTAAAGTTGATTTTAATCATGTTATATAACTTAAATTACGCATTTTGAAGTATCCAATCAAC
1 TTTAAAGTTGATTTTAATCATGTTATATAACTTAAATTACGCATTTTGAACAACCCAATCAAC
** * * *
836451 TTTAAAGTCAACTTTAATCATGTTATAGAACTTAAATTATGCATTTTGAACAACCCAATCCTAAT
1 TTTAAAGTTGATTTTAATCATGTTATATAACTTAAATTACGCATTTTGAACAACCCAAT-C--A-
836516 TGAC
62 --AC
* * * ** * *
836520 TTTAAAGTTGATTTTAATTATATTATATAACTTAAATTACGCATTTTAAATTATCCAATCAAA
1 TTTAAAGTTGATTTTAATCATGTTATATAACTTAAATTACGCATTTTGAACAACCCAATCAAC
* *
836583 TTTAAAATTGACTTTAA
1 TTTAAAGTTGATTTTAA
836600 ATTACACATT
Statistics
Matches: 121, Mismatches: 22, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
63 67 0.55
64 1 0.01
66 2 0.02
68 1 0.01
69 50 0.41
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.41
Consensus pattern (63 bp):
TTTAAAGTTGATTTTAATCATGTTATATAACTTAAATTACGCATTTTGAACAACCCAATCAAC
Found at i:837457 original size:35 final size:35
Alignment explanation
Indices: 837418--837628 Score: 308
Period size: 35 Copynumber: 6.2 Consensus size: 35
837408 TTAGGAACCT
837418 ACTTGTTTTAGGTTGCAACCATATTTTAGGTTGGA
1 ACTTGTTTTAGGTTGCAACCATATTTTAGGTTGGA
* *
837453 ACTTGTATTAGGTTACAACCATATTTTAGGTTGGA
1 ACTTGTTTTAGGTTGCAACCATATTTTAGGTTGGA
* *
837488 ACTTGTCTTAGGTTACAACCATATTTTAGGTTGGA
1 ACTTGTTTTAGGTTGCAACCATATTTTAGGTTGGA
837523 ACTTG-TTTA-G-TGCAACCATATTTTAGGTTGGA
1 ACTTGTTTTAGGTTGCAACCATATTTTAGGTTGGA
* *
837555 ATTTGTTTTAGGTTGCAACCATATTTTCGGTTGGA
1 ACTTGTTTTAGGTTGCAACCATATTTTAGGTTGGA
* *
837590 ACTAG-TTTA-G-TGCAACCATATTTCAGGTTGGA
1 ACTTGTTTTAGGTTGCAACCATATTTTAGGTTGGA
837622 ACTTGTT
1 ACTTGTT
837629 GCAAGAAAGT
Statistics
Matches: 160, Mismatches: 12, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
32 49 0.31
33 7 0.04
34 8 0.05
35 96 0.60
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.41
Consensus pattern (35 bp):
ACTTGTTTTAGGTTGCAACCATATTTTAGGTTGGA
Found at i:837465 original size:17 final size:17
Alignment explanation
Indices: 837418--837597 Score: 96
Period size: 18 Copynumber: 10.5 Consensus size: 17
837408 TTAGGAACCT
*
837418 ACTTGTTTTAGGTTGCA
1 ACTTGTTTTAGGTTGGA
* *
837435 ACCATATTTTAGGTTGGA
1 A-CTTGTTTTAGGTTGGA
* **
837453 ACTTGTATTAGGTTACA
1 ACTTGTTTTAGGTTGGA
* *
837470 ACCATATTTTAGGTTGGA
1 A-CTTGTTTTAGGTTGGA
* **
837488 ACTTGTCTTAGGTTACA
1 ACTTGTTTTAGGTTGGA
* *
837505 ACCATATTTTAGGTTGGA
1 A-CTTGTTTTAGGTTGGA
*
837523 ACTTG-TTTA-G-TGCA
1 ACTTGTTTTAGGTTGGA
* *
837537 ACCATATTTTAGGTTGGA
1 A-CTTGTTTTAGGTTGGA
* *
837555 ATTTGTTTTAGGTTGCA
1 ACTTGTTTTAGGTTGGA
* * *
837572 ACCATATTTTCGGTTGGA
1 A-CTTGTTTTAGGTTGGA
*
837590 ACTAGTTT
1 ACTTGTTT
837598 AGTGCAACCA
Statistics
Matches: 114, Mismatches: 41, Indels: 16
0.67 0.24 0.09
Matches are distributed among these distances:
14 4 0.04
15 3 0.03
16 8 0.07
17 45 0.39
18 54 0.47
ACGTcount: A:0.24, C:0.12, G:0.21, T:0.42
Consensus pattern (17 bp):
ACTTGTTTTAGGTTGGA
Found at i:837549 original size:102 final size:99
Alignment explanation
Indices: 837431--837628 Score: 306
Period size: 102 Copynumber: 2.0 Consensus size: 99
837421 TGTTTTAGGT
*
837431 TGCAACCATATTTTAGGTTGGAACTTGTATTAGGTTACAACCATATTTTAGGTTGGAACTTGTCT
1 TGCAACCATATTTTAGGTTGGAACTTGTATTAGGTTACAACCATATTTTAGGTTGGAACTAGT-T
*
837496 TAGGTTACAACCATATTTTAGGTTGGAACTTGTTTAG
65 TA-G-TACAACCATATTTCAGGTTGGAACTTGTTTAG
* * * *
837533 TGCAACCATATTTTAGGTTGGAATTTGTTTTAGGTTGCAACCATATTTTCGGTTGGAACTAGTTT
1 TGCAACCATATTTTAGGTTGGAACTTGTATTAGGTTACAACCATATTTTAGGTTGGAACTAGTTT
*
837598 AGTGCAACCATATTTCAGGTTGGAACTTGTT
66 AGTACAACCATATTTCAGGTTGGAACTTGTT
837629 GCAAGAAAGT
Statistics
Matches: 89, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
99 27 0.30
100 1 0.01
101 3 0.03
102 58 0.65
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.40
Consensus pattern (99 bp):
TGCAACCATATTTTAGGTTGGAACTTGTATTAGGTTACAACCATATTTTAGGTTGGAACTAGTTT
AGTACAACCATATTTCAGGTTGGAACTTGTTTAG
Found at i:837574 original size:67 final size:67
Alignment explanation
Indices: 837418--837628 Score: 332
Period size: 67 Copynumber: 3.1 Consensus size: 67
837408 TTAGGAACCT
*
837418 ACTTGTTTTAGGTTGCAACCATATTTTAGGTTGGAACTTGTATTAGGTTACAACCATATTTTAGG
1 ACTTGTTTTAGGTTGCAACCATATTTTAGGTTGGAACTTGT-TTA-G-TGCAACCATATTTTAGG
837483 TTGGA
63 TTGGA
* *
837488 ACTTGTCTTAGGTTACAACCATATTTTAGGTTGGAACTTGTTTAGTGCAACCATATTTTAGGTTG
1 ACTTGTTTTAGGTTGCAACCATATTTTAGGTTGGAACTTGTTTAGTGCAACCATATTTTAGGTTG
837553 GA
66 GA
* * * *
837555 ATTTGTTTTAGGTTGCAACCATATTTTCGGTTGGAACTAGTTTAGTGCAACCATATTTCAGGTTG
1 ACTTGTTTTAGGTTGCAACCATATTTTAGGTTGGAACTTGTTTAGTGCAACCATATTTTAGGTTG
837620 GA
66 GA
837622 ACTTGTT
1 ACTTGTT
837629 GCAAGAAAGT
Statistics
Matches: 131, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
67 88 0.67
68 1 0.01
69 3 0.02
70 39 0.30
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.41
Consensus pattern (67 bp):
ACTTGTTTTAGGTTGCAACCATATTTTAGGTTGGAACTTGTTTAGTGCAACCATATTTTAGGTTG
GA
Found at i:838041 original size:40 final size:39
Alignment explanation
Indices: 837837--838045 Score: 140
Period size: 40 Copynumber: 5.3 Consensus size: 39
837827 ATATGAAGGT
* *
837837 GGTGATGTATTGTACGGGATACACACCCAACTAT-AGCAA
1 GGTGATGTATTGTACAGGATACACA-TCAACTATAAGCAA
* * * * * **
837876 GATGATATATCGTACAGGGTACACATCTAAATATAAAG-GT
1 GGTGATGTATTGTACAGGATACACATC-AACTAT-AAGCAA
* * *
837916 GGTGATGTATTGTGCGGGATACACATCCAACTACAAGCAA
1 GGTGATGTATTGTACAGGATACACAT-CAACTATAAGCAA
* * * *
837956 GATGATGTATCGTAC-GGAGTACACATCTAA--ATATGAAA
1 GGTGATGTATTGTACAGGA-TACACATC-AACTATAAGCAA
* *
837994 GTTGTGATGTATTGTACATGATACACACTCAATTATAAGCAA
1 G--GTGATGTATTGTACAGGATACACA-TCAACTATAAGCAA
838036 GGTGATGTAT
1 GGTGATGTAT
838046 CATATGTGGT
Statistics
Matches: 127, Mismatches: 30, Indels: 25
0.70 0.16 0.14
Matches are distributed among these distances:
38 7 0.06
39 32 0.25
40 74 0.58
41 7 0.06
42 7 0.06
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.27
Consensus pattern (39 bp):
GGTGATGTATTGTACAGGATACACATCAACTATAAGCAA
Found at i:838058 original size:80 final size:79
Alignment explanation
Indices: 837824--838067 Score: 296
Period size: 80 Copynumber: 3.1 Consensus size: 79
837814 CTAGAATTTA
* * *
837824 TAAATATGAAGGTGGTGATGTATTGTACGGGATACACACCCAACTAT-AGCAAGATGATATATCG
1 TAAATATGAAAGTGGTGATGTATTGTACGGGATACACACTCAACTATAAGCAAGATGATGTATCG
837888 TACAGGGTACACATC
66 TA-AGGGTACACATC
* *
837903 TAAATAT-AAAGGTGGTGATGTATTGTGCGGGATACACA-TCCAACTACAAGCAAGATGATGTAT
1 TAAATATGAAA-GTGGTGATGTATTGTACGGGATACACACT-CAACTATAAGCAAGATGATGTAT
*
837966 CGTACGGAGTACACATC
64 CGTAAGG-GTACACATC
* ** * * *
837983 TAAATATGAAAGTTGTGATGTATTGTACATGATACACACTCAATTATAAGCAAGGTGATGTATCA
1 TAAATATGAAAGTGGTGATGTATTGTACGGGATACACACTCAACTATAAGCAAGATGATGTATCG
* *
838048 TATGTGGTACACACC
66 TAAG-GGTACACATC
838063 TAAAT
1 TAAAT
838068 TTATGAGTAG
Statistics
Matches: 142, Mismatches: 16, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
78 2 0.01
79 41 0.29
80 94 0.66
81 5 0.04
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.27
Consensus pattern (79 bp):
TAAATATGAAAGTGGTGATGTATTGTACGGGATACACACTCAACTATAAGCAAGATGATGTATCG
TAAGGGTACACATC
Found at i:842363 original size:21 final size:21
Alignment explanation
Indices: 842312--842364 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
842302 ATTATGACTA
842312 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
842333 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
842354 TCGCAATGCGA
1 TCGCAATGCGA
842365 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:842448 original size:21 final size:21
Alignment explanation
Indices: 842414--842486 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
842404 ATACTGACTA
* *
842414 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
842435 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
842455 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
842476 TCGCAATGCGA
1 TCGCAATGCGA
842487 ATTAGGAAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:842500 original size:21 final size:21
Alignment explanation
Indices: 842476--842529 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
842466 TTTTCATAAT
*
842476 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
842497 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
842517 TCGCAATGCGAAT
1 TCGCAATGCGAAT
842530 CTTACTATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:843103 original size:19 final size:19
Alignment explanation
Indices: 843065--843131 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
843055 TTCGAGAATG
843065 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
843085 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
843104 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
843123 AAAATCGCA
1 AAAATCGCA
843132 TTGTGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.73
20 11 0.27
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:843149 original size:19 final size:19
Alignment explanation
Indices: 843136--843279 Score: 120
Period size: 20 Copynumber: 7.6 Consensus size: 19
843126 ATCGCATTGT
843136 GATTTTCATTTCGCGTTGC
1 GATTTTCATTTCGCGTTGC
* *
843155 GATTCTCTCGTTGCGACGTTGC
1 GATT-T-TCATTTCG-CGTTGC
843177 GATTTTCATTTCGCGTTGC
1 GATTTTCATTTCGCGTTGC
**
843196 GATAGTCATTTCGCGTTGC
1 GATTTTCATTTCGCGTTGC
*
843215 GA--TTC---TCTCGTTGC
1 GATTTTCATTTCGCGTTGC
**
843229 GATAGTCATTTCCGCGTTGC
1 GATTTTCATTT-CGCGTTGC
* *
843249 GATTCTCATTATCTCGTTGC
1 GATTTTCATT-TCGCGTTGC
843269 GATTTT-ATTTC
1 GATTTTCATTTC
843280 AACCAAAAGA
Statistics
Matches: 101, Mismatches: 14, Indels: 21
0.74 0.10 0.15
Matches are distributed among these distances:
14 10 0.10
16 2 0.02
17 2 0.02
18 2 0.02
19 33 0.33
20 34 0.34
21 8 0.08
22 10 0.10
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (19 bp):
GATTTTCATTTCGCGTTGC
Found at i:843232 original size:33 final size:34
Alignment explanation
Indices: 843190--843255 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 34
843180 TTTCATTTCG
843190 CGTTGCGATAGTCATTT-CGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTCT
843223 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
843256 ATTATCTCGT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 17 0.53
34 15 0.47
ACGTcount: A:0.12, C:0.26, G:0.24, T:0.38
Consensus pattern (34 bp):
CGTTGCGATAGTCATTTCCGCGTTGCGATTCTCT
Found at i:843257 original size:20 final size:19
Alignment explanation
Indices: 843136--843272 Score: 115
Period size: 19 Copynumber: 7.2 Consensus size: 19
843126 ATCGCATTGT
*
843136 GATTTTCATTTCGCGTTGC
1 GATTCTCATTTCGCGTTGC
843155 GATTCTC-TCGTTGCGACGTTGC
1 GATTCTCAT--TT-CG-CGTTGC
*
843177 GATTTTCATTTCGCGTTGC
1 GATTCTCATTTCGCGTTGC
**
843196 GATAGTCATTTCGCGTTGC
1 GATTCTCATTTCGCGTTGC
843215 GATTCTC---T--CGTTGC
1 GATTCTCATTTCGCGTTGC
**
843229 GATAGTCATTTCCGCGTTGC
1 GATTCTCATTT-CGCGTTGC
*
843249 GATTCTCATTATCTCGTTGC
1 GATTCTCATT-TCGCGTTGC
843269 GATT
1 GATT
843273 TTATTTCAAC
Statistics
Matches: 95, Mismatches: 11, Indels: 23
0.74 0.09 0.18
Matches are distributed among these distances:
14 11 0.12
16 1 0.01
17 1 0.01
18 1 0.01
19 34 0.36
20 29 0.31
21 5 0.05
22 12 0.13
23 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.42
Consensus pattern (19 bp):
GATTCTCATTTCGCGTTGC
Found at i:845448 original size:21 final size:21
Alignment explanation
Indices: 845424--845490 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
845414 TCATTCCTCG
845424 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
845445 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
845466 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
845487 AGAG
1 AGAG
845491 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:845448 original size:42 final size:42
Alignment explanation
Indices: 845372--845490 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
845362 GACTCGCCTG
* * *
845372 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCTTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCTTA
* * * *
845414 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCAC-TG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC-CTTA
** * *
845456 TCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 TCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
845491 CCCGATTCAC
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
42 57 0.92
43 5 0.08
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.24
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCTTA
Found at i:846868 original size:14 final size:14
Alignment explanation
Indices: 846849--846884 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
846839 ATTGTTTAAT
846849 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
846863 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
846877 TGATTTGT
1 TGATTTGT
846885 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Done.