Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009585.1 Hibiscus syriacus cultivar Beakdansim tig00116962_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: 8285662
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 24 of 35
Found at i:5429073 original size:20 final size:20
Alignment explanation
Indices: 5429011--5429164 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
5429001 CGATTTTCCA
* ** *
5429011 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
5429031 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
5429051 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
5429071 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
5429091 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
5429111 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
5429131 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
5429152 AAATCGCAACGCG
1 AAATCGCAACGCG
5429165 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 92 0.82
21 17 0.15
22 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:5429586 original size:33 final size:33
Alignment explanation
Indices: 5429547--5429617 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
5429537 TTCACTTAGA
*
5429547 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
5429580 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
5429613 TTTCA
1 TTTCA
5429618 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:5429741 original size:20 final size:20
Alignment explanation
Indices: 5429697--5429806 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
5429687 TGCAGAAGAG
*
5429697 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
5429718 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
5429738 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
5429759 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
5429773 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
5429792 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
5429807 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:5429754 original size:41 final size:38
Alignment explanation
Indices: 5429690--5429806 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
5429680 TTCAATTTGC
* *
5429690 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
5429728 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
5429769 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
5429802 AGAAT
1 AGAAT
5429807 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:5429776 original size:14 final size:14
Alignment explanation
Indices: 5429757--5429813 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
5429747 GAGAAATGAA
5429757 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
5429771 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
5429790 AATCGCAACGAGAG
1 AATCGCAACGAGAG
5429804 AATCGCAACG
1 AATCGCAACG
5429814 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:5429789 original size:33 final size:33
Alignment explanation
Indices: 5429749--5429829 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
5429739 CGCAACGAGA
5429749 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
5429782 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
5429815 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
5429830 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:5429852 original size:19 final size:19
Alignment explanation
Indices: 5429825--5429922 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
5429815 GAAACCAAAA
*
5429825 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
5429844 TCGTGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
5429858 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
5429877 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
**
5429891 TCTAGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
5429910 TCGCGTTGCGATT
1 TCGCGTTGCGATT
5429923 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 9, Indels: 20
0.67 0.10 0.22
Matches are distributed among these distances:
14 18 0.30
16 6 0.10
17 6 0.10
19 30 0.50
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:5429867 original size:14 final size:14
Alignment explanation
Indices: 5429848--5429936 Score: 61
Period size: 14 Copynumber: 5.6 Consensus size: 14
5429838 TTCATTTCGT
5429848 GTTGCGATTCTCTC
1 GTTGCGATTCTCTC
*
5429862 GTTGCGATTTTCATTTCGC
1 GTTGCGA--TTC---TCTC
*
5429881 GTTGCGATTCTCTA
1 GTTGCGATTCTCTC
*
5429895 GTTGCGATTTTCATTTCGC
1 GTTGCGA--TTC---TCTC
5429914 GTTGCGATTCTCTC
1 GTTGCGATTCTCTC
5429928 GTTGCGATT
1 GTTGCGATT
5429937 TTCATTTCAA
Statistics
Matches: 59, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 28 0.47
16 6 0.10
17 6 0.10
19 19 0.32
ACGTcount: A:0.10, C:0.22, G:0.22, T:0.45
Consensus pattern (14 bp):
GTTGCGATTCTCTC
Found at i:5429872 original size:33 final size:33
Alignment explanation
Indices: 5429830--5429944 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
5429820 CAAAATCGCA
*
5429830 TTGCGATTTTCATTTCGTGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
5429863 TTGCGATTTTCATTTCGCGTTGCGATTCTCTAG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
5429896 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
5429929 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
5429945 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.10, C:0.22, G:0.20, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:5431688 original size:17 final size:17
Alignment explanation
Indices: 5431666--5431718 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
5431656 GGTTGCTGCC
5431666 AATTCTGCTAAACTGTG
1 AATTCTGCTAAACTGTG
5431683 AATTCTGCTAAACTGTG
1 AATTCTGCTAAACTGTG
* *
5431700 TATTCT-TTAACACTGTG
1 AATTCTGCTAA-ACTGTG
5431717 AA
1 AA
5431719 ATAGTATTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
16 3 0.09
17 29 0.91
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (17 bp):
AATTCTGCTAAACTGTG
Found at i:5431842 original size:93 final size:93
Alignment explanation
Indices: 5431683--5432128 Score: 885
Period size: 93 Copynumber: 4.8 Consensus size: 93
5431673 CTAAACTGTG
5431683 AATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGG
1 AATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGG
5431748 TTGAAAGTAAATTTGTTCGGTTGCTGCC
66 TTGAAAGTAAATTTGTTCGGTTGCTGCC
5431776 AATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGG
1 AATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGG
5431841 TTGAAAGTAAATTTGTTCGGTTGCTGCC
66 TTGAAAGTAAATTTGTTCGGTTGCTGCC
5431869 AATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGG
1 AATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGG
5431934 TTGAAAGTAAATTTGTTCGGTTGCTGCC
66 TTGAAAGTAAATTTGTTCGGTTGCTGCC
5431962 AATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGG
1 AATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGG
5432027 TTGAAAGTAAATTTGTTCGGTTGCTGCC
66 TTGAAAGTAAATTTGTTCGGTTGCTGCC
5432055 AATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGG
1 AATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGG
5432120 TTG-AAGTAA
66 TTGAAAGTAA
5432129 TGCAATCCAT
Statistics
Matches: 353, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
92 6 0.02
93 347 0.98
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGG
TTGAAAGTAAATTTGTTCGGTTGCTGCC
Found at i:5432216 original size:19 final size:19
Alignment explanation
Indices: 5432176--5432304 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
5432166 TAGTTTACTT
* *
5432176 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
5432196 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
5432215 TCGCAACGCGAAATAAAAA
1 TCGCAACGCGAAACCAAAA
*
5432234 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
5432248 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
5432267 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
5432281 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
5432300 TCGCA
1 TCGCA
5432305 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:5432250 original size:33 final size:32
Alignment explanation
Indices: 5432212--5432304 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
5432202 CGCGAAACCA
**
5432212 AAATCGCAACGCGAAATAAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
5432244 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
5432277 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
5432305 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:5432302 original size:52 final size:52
Alignment explanation
Indices: 5432176--5432304 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 52
5432166 TAGTTTACTT
* **
5432176 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACGCGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
*** *
5432228 TAAAAATCGC--AACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAA-CGCGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
5432281 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACGCGAAACACAAAATCGCA
5432305 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 12
0.72 0.13 0.14
Matches are distributed among these distances:
51 3 0.05
52 47 0.78
53 7 0.12
54 3 0.05
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.09
Consensus pattern (52 bp):
TCGCAACGCGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:5432322 original size:19 final size:19
Alignment explanation
Indices: 5432300--5432418 Score: 123
Period size: 19 Copynumber: 6.8 Consensus size: 19
5432290 GAAACCAAAA
*
5432300 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
5432319 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
5432335 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
5432352 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
5432368 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
5432385 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
5432404 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
5432419 AAGTTTCATG
Statistics
Matches: 83, Mismatches: 7, Indels: 20
0.75 0.06 0.18
Matches are distributed among these distances:
14 15 0.18
16 11 0.13
17 11 0.13
19 46 0.55
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:5432341 original size:14 final size:14
Alignment explanation
Indices: 5432322--5432378 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
5432312 TTTCATTTCG
5432322 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
5432336 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
5432353 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
5432369 CGTTGCGATT
1 CGTTGCGATT
5432379 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:5432347 original size:33 final size:33
Alignment explanation
Indices: 5432305--5432397 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
5432295 CAAAATCGCA
*
5432305 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
5432338 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
5432371 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
5432398 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:5432432 original size:20 final size:19
Alignment explanation
Indices: 5432369--5432425 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
5432359 GCGATTCTGT
5432369 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTT-AGTTTCG
*
5432388 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTAGTTTCG
5432407 CGTTGCGATTTTAAGTTTC
1 CGTTGCGATTTT-AGTTTC
5432426 ATGTTGCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 29 0.85
20 5 0.15
ACGTcount: A:0.11, C:0.18, G:0.25, T:0.47
Consensus pattern (19 bp):
CGTTGCGATTTTAGTTTCG
Found at i:5434375 original size:14 final size:14
Alignment explanation
Indices: 5434356--5434391 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
5434346 ATTGTTTAAT
5434356 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
5434370 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
5434384 TGATTTGT
1 TGATTTGT
5434392 GTAATTGATG
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:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:5434522 original size:19 final size:19
Alignment explanation
Indices: 5434498--5434595 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
5434488 AAAATTGACT
5434498 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
5434517 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
5434536 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
5434550 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
5434569 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
5434589 ATCGCAA
1 ATCGCAA
5434596 CGGGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:5434627 original size:53 final size:53
Alignment explanation
Indices: 5434498--5434614 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
5434488 AAAATTGACT
5434498 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
*
5434550 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
5434603 ATCGCAATGCGA
1 ATCGCAATGCGA
5434615 TTTTAATTTC
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 29 0.46
53 34 0.54
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:5434632 original size:19 final size:19
Alignment explanation
Indices: 5434604--5434792 Score: 219
Period size: 19 Copynumber: 10.7 Consensus size: 19
5434594 AACGGGAGAA
* *
5434604 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
5434623 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
5434639 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
5434656 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
5434675 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
5434691 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
5434708 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
5434727 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
5434746 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
5434764 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
5434780 TCGCATTGCGATT
1 TCGCATTGCGATT
5434793 CTCTCGTTGC
Statistics
Matches: 146, Mismatches: 8, Indels: 32
0.78 0.04 0.17
Matches are distributed among these distances:
14 23 0.16
16 16 0.11
17 14 0.10
18 1 0.01
19 76 0.52
20 16 0.11
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:5434667 original size:52 final size:52
Alignment explanation
Indices: 5434604--5434806 Score: 281
Period size: 52 Copynumber: 3.9 Consensus size: 52
5434594 AACGGGAGAA
* *
5434604 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
5434656 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
5434708 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCA--
1 TCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--TTGCGATTTTCATT
*
5434764 T-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
5434807 GTAATTTCCG
Statistics
Matches: 140, Mismatches: 5, Indels: 17
0.86 0.03 0.10
Matches are distributed among these distances:
47 8 0.06
49 2 0.01
50 2 0.01
51 3 0.02
52 80 0.57
53 24 0.17
54 3 0.02
55 3 0.02
56 3 0.02
58 12 0.09
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:5434814 original size:33 final size:33
Alignment explanation
Indices: 5434661--5434806 Score: 195
Period size: 33 Copynumber: 4.2 Consensus size: 33
5434651 TCATTTCGCA
5434661 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
5434694 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
*
5434730 CATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 --TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
5434766 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
5434799 TTGCGATT
1 TTGCGATT
5434807 GTAATTTCCG
Statistics
Matches: 99, Mismatches: 6, Indels: 16
0.82 0.05 0.13
Matches are distributed among these distances:
32 1 0.01
33 47 0.47
34 14 0.14
35 3 0.03
36 6 0.06
37 3 0.03
38 15 0.15
39 10 0.10
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:5437272 original size:24 final size:24
Alignment explanation
Indices: 5437238--5437284 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5437228 CTGAAACATC
5437238 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
5437262 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
5437285 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:5437995 original size:20 final size:20
Alignment explanation
Indices: 5437967--5438236 Score: 281
Period size: 20 Copynumber: 13.5 Consensus size: 20
5437957 AAATTTCAGT
* * *
5437967 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
5437987 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
5438007 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
5438027 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
5438047 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
5438067 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
5438087 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
5438107 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
5438127 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
5438147 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
5438167 GTTACGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
5438187 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
5438207 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
5438227 GTTGCGATTT
1 GTTGCGATTT
5438237 TGGAAAATCG
Statistics
Matches: 218, Mismatches: 30, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
20 217 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:5438253 original size:21 final size:21
Alignment explanation
Indices: 5438223--5438305 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
5438213 ATTTTCATAT
*
5438223 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
5438244 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
5438265 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
5438286 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
5438306 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:5438296 original size:42 final size:43
Alignment explanation
Indices: 5438203--5438301 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
5438193 ATTTATGTGT
* *
5438203 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
5438244 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
5438286 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
5438302 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:5443128 original size:2 final size:2
Alignment explanation
Indices: 5443121--5443145 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5443111 TCATTTCTCC
5443121 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 A
5443146 ATTCATTGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5443143 original size:37 final size:37
Alignment explanation
Indices: 5443093--5443197 Score: 176
Period size: 37 Copynumber: 2.9 Consensus size: 37
5443083 ATTTAAAGGA
* *
5443093 ATAT-TATATATATAAAATTCATTTCTCCATATATAT
1 ATATATATATATATATAATTCATTGCTCCATATATAT
*
5443129 ATATATATATATATATAATTCATTGCTCCACATATAT
1 ATATATATATATATATAATTCATTGCTCCATATATAT
5443166 ATATATATATATATATAATTCATTGCTCCATA
1 ATATATATATATATATAATTCATTGCTCCATA
5443198 CTCTGTGATC
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
36 4 0.06
37 60 0.94
ACGTcount: A:0.41, C:0.12, G:0.02, T:0.45
Consensus pattern (37 bp):
ATATATATATATATATAATTCATTGCTCCATATATAT
Found at i:5443490 original size:16 final size:16
Alignment explanation
Indices: 5443469--5443505 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
5443459 TCAATGATGA
*
5443469 CGTGACATTATCTTAT
1 CGTGACATTACCTTAT
5443485 CGTGACATTACCTTAT
1 CGTGACATTACCTTAT
*
5443501 GGTGA
1 CGTGA
5443506 TATGTCAGCA
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:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (16 bp):
CGTGACATTACCTTAT
Found at i:5444558 original size:29 final size:29
Alignment explanation
Indices: 5444487--5444552 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 29
5444477 GTTAACCATA
* *
5444487 GGTTAATCTATAATCAAACCGTTAATAAT
1 GGTTAACCTATAATCAAACCGTTAATAAC
5444516 GGTTAACCTATAATCAAACCGTTAATAAC
1 GGTTAACCTATAATCAAACCGTTAATAAC
5444545 GGTTAACC
1 GGTTAACC
5444553 ATTAATGGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.30
Consensus pattern (29 bp):
GGTTAACCTATAATCAAACCGTTAATAAC
Found at i:5444756 original size:3 final size:3
Alignment explanation
Indices: 5444748--5444786 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
5444738 CGGCAACTAC
5444748 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5444787 GATAAAACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5454097 original size:18 final size:18
Alignment explanation
Indices: 5454072--5454113 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
5454062 TAATTTTAAA
5454072 AAAT-ATTTAA-ATTTCAT
1 AAATAATTTAATATTT-AT
5454089 AAATAATTTAATATTTAT
1 AAATAATTTAATATTTAT
*
5454107 ACATAAT
1 AAATAAT
5454114 ATCATTATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 4 0.18
18 14 0.64
19 4 0.18
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (18 bp):
AAATAATTTAATATTTAT
Found at i:5458443 original size:21 final size:21
Alignment explanation
Indices: 5458419--5458501 Score: 130
Period size: 21 Copynumber: 4.0 Consensus size: 21
5458409 CCCGGCTACC
* *
5458419 CCGATCACAACTCCAACAGCA
1 CCGACCACAACTCCAACAACA
*
5458440 CCGACCACAAATCCAACAACA
1 CCGACCACAACTCCAACAACA
5458461 CCGACCACAACTCCAACAACA
1 CCGACCACAACTCCAACAACA
*
5458482 CCGACCACAACTCCGACAAC
1 CCGACCACAACTCCAACAAC
5458502 CCAAAACCCA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.41, C:0.46, G:0.07, T:0.06
Consensus pattern (21 bp):
CCGACCACAACTCCAACAACA
Found at i:5472203 original size:12 final size:12
Alignment explanation
Indices: 5472188--5472230 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
5472178 GTTATTTAAA
5472188 CGGGTATTGGGT
1 CGGGTATTGGGT
*
5472200 CGGGTATTGGGC
1 CGGGTATTGGGT
* *
5472212 CGGGAATCGGGT
1 CGGGTATTGGGT
5472224 CGGGTAT
1 CGGGTAT
5472231 ATATATATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.12, C:0.14, G:0.49, T:0.26
Consensus pattern (12 bp):
CGGGTATTGGGT
Found at i:5472290 original size:24 final size:25
Alignment explanation
Indices: 5472228--5472290 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 25
5472218 TCGGGTCGGG
5472228 TATATA-TATATATATTTAAATTAAA
1 TATATATTATAT-TATTTAAATTAAA
*
5472253 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
5472277 T-T-TATTAATATTAT
1 TATATATT-ATATTAT
5472291 ATATATATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
22 4 0.12
23 1 0.03
24 19 0.58
25 8 0.24
26 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:5472377 original size:6 final size:6
Alignment explanation
Indices: 5472366--5472394 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
5472356 GATTACCAAA
5472366 CCCGTC CCCGTC CCCGTC CCCGTC CCCGT
1 CCCGTC CCCGTC CCCGTC CCCGTC CCCGT
5472395 TTATCATCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.66, G:0.17, T:0.17
Consensus pattern (6 bp):
CCCGTC
Found at i:5479942 original size:9 final size:9
Alignment explanation
Indices: 5479930--5479954 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5479920 GCAACAGCAA
5479930 CAGCAGCCC
1 CAGCAGCCC
5479939 CAGCAGCCC
1 CAGCAGCCC
5479948 CAGCAGC
1 CAGCAGC
5479955 AGCTTTTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.52, G:0.24, T:0.00
Consensus pattern (9 bp):
CAGCAGCCC
Found at i:5480064 original size:24 final size:24
Alignment explanation
Indices: 5480036--5480096 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
5480026 TCATTACCAT
*
5480036 ATCAGCAGCCACAGCTACTACAGA
1 ATCAGCAGCAACAGCTACTACAGA
5480060 ATCAGCAGCAACAGCTACTACAGA
1 ATCAGCAGCAACAGCTACTACAGA
5480084 ATCAGCAGCAACA
1 ATCAGCAGCAACA
5480097 ACAATTTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.41, C:0.31, G:0.16, T:0.11
Consensus pattern (24 bp):
ATCAGCAGCAACAGCTACTACAGA
Found at i:5483311 original size:2 final size:2
Alignment explanation
Indices: 5483304--5483328 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5483294 ATGTGCAGTT
5483304 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5483329 TCATTGCTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5493259 original size:2 final size:2
Alignment explanation
Indices: 5493252--5493278 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5493242 ATGACACAAA
5493252 TC 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 T
5493279 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5494439 original size:17 final size:16
Alignment explanation
Indices: 5494417--5494469 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
5494407 CTAATTACTA
5494417 ATGAACAAGATTCTTAC
1 ATGAACAA-ATTCTTAC
*
5494434 ATGAACTAATTAC-TA-
1 ATGAACAAATT-CTTAC
5494449 ATGAACAATATTCTTAC
1 ATGAACAA-ATTCTTAC
5494466 ATGA
1 ATGA
5494470 TGTTTCGAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
15 8 0.27
16 10 0.33
17 12 0.40
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.32
Consensus pattern (16 bp):
ATGAACAAATTCTTAC
Found at i:5494447 original size:32 final size:32
Alignment explanation
Indices: 5494406--5494469 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
5494396 TCGAGAAAAG
5494406 ACTAATTACTAATGAACAAGATTCTTACATGA
1 ACTAATTACTAATGAACAAGATTCTTACATGA
*
5494438 ACTAATTACTAATGAACAATATTCTTACATGA
1 ACTAATTACTAATGAACAAGATTCTTACATGA
5494470 TGTTTCGAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.33
Consensus pattern (32 bp):
ACTAATTACTAATGAACAAGATTCTTACATGA
Found at i:5494454 original size:15 final size:15
Alignment explanation
Indices: 5494406--5494454 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
5494396 TCGAGAAAAG
5494406 ACTAATTACTAATGA
1 ACTAATTACTAATGA
*
5494421 ACAAGATT-CTTACATGA
1 ACTA-ATTAC-TA-ATGA
5494438 ACTAATTACTAATGA
1 ACTAATTACTAATGA
5494453 AC
1 AC
5494455 AATATTCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 10 0.36
16 10 0.36
17 8 0.29
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.31
Consensus pattern (15 bp):
ACTAATTACTAATGA
Found at i:5504449 original size:23 final size:23
Alignment explanation
Indices: 5504423--5504476 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
5504413 GTGATAGTCT
* * *
5504423 AAGTTCGTGTTGCGATTTATTCC
1 AAGTTCGTATTACGATTTATTAC
*
5504446 AAGTTCGCATTACGATTTATTAC
1 AAGTTCGTATTACGATTTATTAC
*
5504469 AAATTCGT
1 AAGTTCGT
5504477 TGCGATAGTC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.41
Consensus pattern (23 bp):
AAGTTCGTATTACGATTTATTAC
Found at i:5505304 original size:21 final size:21
Alignment explanation
Indices: 5505275--5505535 Score: 138
Period size: 21 Copynumber: 12.5 Consensus size: 21
5505265 ATTTTGGATT
*
5505275 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* * *
5505296 ATCGTAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
5505317 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
5505338 ATCGCAACGCGAACTTCGG-CT--
1 ATCGCAA--CGAACTT-GGAATAA
5505359 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
5505380 ATCGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
5505401 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
5505422 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
** *
5505443 ATTACAACGAACTTGGACT--
1 ATCGCAACGAACTTGGAATAA
*
5505462 ATCGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAACTTGGAATAA
* * * *
5505483 ATCGAAACAAATTTGAAATAA
1 ATCGCAACGAACTTGGAATAA
*
5505504 ATCGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAACTTGGAATAA
5505525 ATCGCAACGAA
1 ATCGCAACGAA
5505536 TTTAGAAAAT
Statistics
Matches: 188, Mismatches: 30, Indels: 46
0.71 0.11 0.17
Matches are distributed among these distances:
18 2 0.01
19 56 0.30
21 83 0.44
23 45 0.24
24 2 0.01
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:5505538 original size:42 final size:42
Alignment explanation
Indices: 5505268--5505538 Score: 395
Period size: 42 Copynumber: 6.5 Consensus size: 42
5505258 CGTTACGATT
* *
5505268 TTGGATTATCGCAACGAATTTGGAATAAATCGTAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* *
5505310 TTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
*
5505352 TTCGG-CTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TT-GGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
5505394 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* ** * *
5505436 TTCGACTATTACAACGAACTTGGACT--ATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* * *
5505476 TTGGACTATCGAAACAAATTTGAAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
5505518 TTGGACTATCGCAACGAATTT
1 TTGGACTATCGCAACGAATTT
5505539 AGAAAATCGC
Statistics
Matches: 204, Mismatches: 21, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
40 32 0.16
41 2 0.01
42 169 0.83
43 1 0.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (42 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
Found at i:5505578 original size:21 final size:21
Alignment explanation
Indices: 5505545--5505597 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
5505535 ATTTAGAAAA
* *
5505545 TCGCATTGAGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
*
5505566 TCGCGTTGCGATAGTCGATGT
1 TCGCGTTGCGATAGTCGAAGT
5505587 TCGCGTTGCGA
1 TCGCGTTGCGA
5505598 ATCTGGAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.32, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:5506633 original size:27 final size:26
Alignment explanation
Indices: 5506575--5506634 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
5506565 TTAGACTTGA
* **
5506575 AATTAATTATATTATTTTTAAAAAAT
1 AATTAATTATAATATAATTAAAAAAT
*
5506601 ATATTAATTATAATATAAATTAAAAATT
1 A-ATTAATTATAATAT-AATTAAAAAAT
5506629 AATTAA
1 AATTAA
5506635 AAATAATTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 1 0.04
27 18 0.64
28 9 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
AATTAATTATAATATAATTAAAAAAT
Found at i:5507566 original size:22 final size:22
Alignment explanation
Indices: 5507541--5507588 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
5507531 CTTGTGAACC
5507541 GATAACCCAAAATCTATTTTTG
1 GATAACCCAAAATCTATTTTTG
5507563 GATAACCCAAAATCTATTTTTG
1 GATAACCCAAAATCTATTTTTG
5507585 GATA
1 GATA
5507589 TCAGTCATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (22 bp):
GATAACCCAAAATCTATTTTTG
Found at i:5509884 original size:22 final size:21
Alignment explanation
Indices: 5509848--5509898 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
5509838 AAGTAGGTGT
5509848 TATTTAAAAATTTGAA-ATCAA
1 TATTT-AAAATTTGAATATCAA
*
5509869 TATATTAAAATATTGAATATTAA
1 TAT-TTAAAAT-TTGAATATCAA
5509892 TATTTAA
1 TATTTAA
5509899 TTTAGAAGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 8 0.31
22 11 0.42
23 7 0.27
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (21 bp):
TATTTAAAATTTGAATATCAA
Found at i:5535526 original size:20 final size:20
Alignment explanation
Indices: 5535474--5535527 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
5535464 AATTTAATAT
*
5535474 TATTATTTTTAAAATATTAAAA
1 TATTATTTTT--ATTATTAAAA
*
5535496 TAATT-TATTTATTATTAAAA
1 T-ATTATTTTTATTATTAAAA
5535516 TATTATTTTTAT
1 TATTATTTTTAT
5535528 AATTTTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
19 3 0.11
20 16 0.59
22 5 0.19
23 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTATTTTTATTATTAAAA
Found at i:5535592 original size:31 final size:29
Alignment explanation
Indices: 5535484--5535654 Score: 77
Period size: 28 Copynumber: 5.8 Consensus size: 29
5535474 TATTATTTTT
*
5535484 AAAATATTAAAATAATT-TA-TTTATT-ATT
1 AAAATATT--AATAATTATATTTTATTAATA
**
5535512 AAAATATT-ATTTTTATAATTTTATTAATA
1 AAAATATTAATAATTAT-ATTTTATTAATA
*
5535541 AAAATATTAATATTGGTATATTTTATTGAAATA
1 AAAATATTAATAAT--TATATTTTATT--AATA
* *
5535574 AAAATATT-ATAAATTATATTAATTATTTATT
1 AAAATATTAAT-AATTATATT--TTATTAATA
* * * * * *
5535605 AAAGTAATAGT-GTTATATTATATT-TTA
1 AAAATATTAATAATTATATTTTATTAATA
* *
5535632 AAAATATTAATTAGTATATTTTA
1 AAAATATTAATAATTATATTTTA
5535655 AATATCTTTA
Statistics
Matches: 109, Mismatches: 20, Indels: 28
0.69 0.13 0.18
Matches are distributed among these distances:
25 4 0.04
26 1 0.01
27 10 0.09
28 26 0.24
29 10 0.09
30 11 0.10
31 22 0.20
32 6 0.06
33 19 0.17
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (29 bp):
AAAATATTAATAATTATATTTTATTAATA
Found at i:5535673 original size:23 final size:23
Alignment explanation
Indices: 5535624--5535674 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
5535614 GTGTTATATT
**
5535624 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
5535647 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
5535670 ATATT
1 ATATT
5535675 ATTAGATTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:5535867 original size:22 final size:23
Alignment explanation
Indices: 5535839--5535885 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
5535829 TTGATTATTT
5535839 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
5535861 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAAAAATATTAA
5535884 TA
1 TA
5535886 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:5535890 original size:22 final size:22
Alignment explanation
Indices: 5535847--5535890 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
5535837 TTTATTATAA
*
5535847 TATTAAAAATATAATATTATAT
1 TATTAAAAATATAATATAATAT
*
5535869 TATTAGAAATATTAATA-AATAT
1 TATTAAAAATA-TAATATAATAT
5535891 ATTTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TATTAAAAATATAATATAATAT
Found at i:5535975 original size:81 final size:82
Alignment explanation
Indices: 5535885--5536150 Score: 253
Period size: 81 Copynumber: 3.2 Consensus size: 82
5535875 AAATATTAAT
5535885 AAATATATTTTAAATATTTAAATAATTAGTATTTTGATTAAAATGATATTAAAATATTTATTAAT
1 AAATATATTTTAAATATTTAAATAATTAGTATTTTGATTAAAATGATATTAAAATATTTATTAAT
5535950 ATTAAATTCATAAAATA
66 ATTAAATTCATAAAATA
* * ** ** * * * * *
5535967 AAAT-TATTTTGAGTATTT--ATTTTTGAAGTGAAAAGTTCAGTATAAT-AT-TAAAAATATAAT
1 AAATATATTTTAAATATTTAAATAATT--AGT---ATTTTGATTAAAATGATATTAAAATAT-TT
* *
5536027 ATTATATTATTAAA--AATATTAAT-
60 ATTA-A-TATTAAATTCATA-AAATA
5536050 AAATATATTTTAAATATTTAAATAATTAGTATTTTGATTAAAATGATATTAAAATATTTATTAAT
1 AAATATATTTTAAATATTTAAATAATTAGTATTTTGATTAAAATGATATTAAAATATTTATTAAT
5536115 ATTAAATTCATAAAATA
66 ATTAAATTCATAAAATA
* *
5536132 AAAT-TATTTTGAGTATTTA
1 AAATATATTTTAAATATTTA
5536151 TTATTGAAGT
Statistics
Matches: 139, Mismatches: 28, Indels: 35
0.69 0.14 0.17
Matches are distributed among these distances:
79 4 0.03
80 7 0.05
81 41 0.29
82 26 0.19
83 22 0.16
84 28 0.20
85 7 0.05
86 4 0.03
ACGTcount: A:0.48, C:0.01, G:0.06, T:0.45
Consensus pattern (82 bp):
AAATATATTTTAAATATTTAAATAATTAGTATTTTGATTAAAATGATATTAAAATATTTATTAAT
ATTAAATTCATAAAATA
Found at i:5536017 original size:165 final size:165
Alignment explanation
Indices: 5535842--5536171 Score: 642
Period size: 165 Copynumber: 2.0 Consensus size: 165
5535832 ATTATTTTAT
*
5535842 TATAATATTAAAAATATAATATTATATTATTAGAAATATTAATAAATATATTTTAAATATTTAAA
1 TATAATATTAAAAATATAATATTATATTATTAAAAATATTAATAAATATATTTTAAATATTTAAA
5535907 TAATTAGTATTTTGATTAAAATGATATTAAAATATTTATTAATATTAAATTCATAAAATAAAATT
66 TAATTAGTATTTTGATTAAAATGATATTAAAATATTTATTAATATTAAATTCATAAAATAAAATT
*
5535972 ATTTTGAGTATTTATTTTTGAAGTGAAAAGTTCAG
131 ATTTTGAGTATTTATTATTGAAGTGAAAAGTTCAG
5536007 TATAATATTAAAAATATAATATTATATTATTAAAAATATTAATAAATATATTTTAAATATTTAAA
1 TATAATATTAAAAATATAATATTATATTATTAAAAATATTAATAAATATATTTTAAATATTTAAA
5536072 TAATTAGTATTTTGATTAAAATGATATTAAAATATTTATTAATATTAAATTCATAAAATAAAATT
66 TAATTAGTATTTTGATTAAAATGATATTAAAATATTTATTAATATTAAATTCATAAAATAAAATT
5536137 ATTTTGAGTATTTATTATTGAAGTGAAAAGTTCAG
131 ATTTTGAGTATTTATTATTGAAGTGAAAAGTTCAG
5536172 AAAATGACTT
Statistics
Matches: 163, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
165 163 1.00
ACGTcount: A:0.48, C:0.01, G:0.06, T:0.45
Consensus pattern (165 bp):
TATAATATTAAAAATATAATATTATATTATTAAAAATATTAATAAATATATTTTAAATATTTAAA
TAATTAGTATTTTGATTAAAATGATATTAAAATATTTATTAATATTAAATTCATAAAATAAAATT
ATTTTGAGTATTTATTATTGAAGTGAAAAGTTCAG
Found at i:5536032 original size:22 final size:23
Alignment explanation
Indices: 5536007--5536050 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
5535997 AAAAGTTCAG
5536007 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
*
5536029 TATATTATTAAAAATATTAATA
1 TATAATATTAAAAATATTAATA
5536051 AATATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:5536058 original size:21 final size:22
Alignment explanation
Indices: 5536011--5536075 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
5536001 GTTCAGTATA
*
5536011 ATATTAAAAATA-TAATATTAT
1 ATATTAAAAATATTAATATAAT
5536032 ATTATTAAAAATATTAATA-AAT
1 A-TATTAAAAATATTAATATAAT
**
5536054 ATATTTTAAATATTTAA-ATAAT
1 ATATTAAAAATA-TTAATATAAT
5536076 TAGTATTTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
21 11 0.30
22 21 0.57
23 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATTAAAAATATTAATATAAT
Found at i:5536074 original size:23 final size:23
Alignment explanation
Indices: 5536014--5536063 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
5536004 CAGTATAATA
*
5536014 TTAAAAATA-TAAT-ATTATATT
1 TTAAAAATATTAATAAATATATT
5536035 ATTAAAAATATTAATAAATATATT
1 -TTAAAAATATTAATAAATATATT
5536059 TTAAA
1 TTAAA
5536064 TATTTAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 9 0.36
23 9 0.36
24 7 0.28
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TTAAAAATATTAATAAATATATT
Found at i:5536099 original size:84 final size:84
Alignment explanation
Indices: 5535846--5536103 Score: 257
Period size: 84 Copynumber: 3.1 Consensus size: 84
5535836 TTTTATTATA
*
5535846 ATATTAAAAATATAATATTATATTATTAGAAATATTAATAAATATATTTTAAATATTTAAATAAT
1 ATATTAAAAATATAATATTATATTATTAAAAATATTAATAAATATATTTTAAATATTTAAATAAT
5535911 TAGTATTTTGATTAAAATG
66 TAGTATTTTGATTAAAATG
* * * * *
5535930 ATATT-AAAATAT-TTATTA-A-TATT-AAATTCATAAAATAAA-ATTATTTTGAGTATTT--AT
1 ATATTAAAAATATAATATTATATTATTAAAAAT-AT-TAATAAATA-TATTTTAAATATTTAAAT
** *** ** *
5535987 TTTTGAAGTGA-AAAG-TTCAGTATA
63 AATT--AGT-ATTTTGATT-AAAATG
5536011 ATATTAAAAATATAATATTATATTATTAAAAATATTAATAAATATATTTTAAATATTTAAATAAT
1 ATATTAAAAATATAATATTATATTATTAAAAATATTAATAAATATATTTTAAATATTTAAATAAT
5536076 TAGTATTTTGATTAAAATG
66 TAGTATTTTGATTAAAATG
5536095 ATATTAAAA
1 ATATTAAAA
5536104 TATTTATTAA
Statistics
Matches: 130, Mismatches: 27, Indels: 34
0.68 0.14 0.18
Matches are distributed among these distances:
79 7 0.05
80 9 0.07
81 31 0.24
82 13 0.10
83 13 0.10
84 40 0.31
85 9 0.07
86 8 0.06
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.45
Consensus pattern (84 bp):
ATATTAAAAATATAATATTATATTATTAAAAATATTAATAAATATATTTTAAATATTTAAATAAT
TAGTATTTTGATTAAAATG
Found at i:5539204 original size:7 final size:7
Alignment explanation
Indices: 5539192--5539223 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
5539182 GATGCTTAAA
*
5539192 GTTCCCT
1 GTTCCCC
5539199 GTTCCCC
1 GTTCCCC
5539206 GTTCCCC
1 GTTCCCC
5539213 GTTCCCC
1 GTTCCCC
5539220 GTTC
1 GTTC
5539224 AGAAATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.16, T:0.34
Consensus pattern (7 bp):
GTTCCCC
Found at i:5546943 original size:33 final size:33
Alignment explanation
Indices: 5546906--5546998 Score: 91
Period size: 33 Copynumber: 2.8 Consensus size: 33
5546896 AGAGAAAAAA
*
5546906 TATAATTGTATTAAATTTAAATTTAAATTTAAT
1 TATAATTCTATTAAATTTAAATTTAAATTTAAT
* * *
5546939 TATAATTCTATTTAA-TCAAAATTAAA-TTAAT
1 TATAATTCTATTAAATTTAAATTTAAATTTAAT
* * * *
5546970 TAGAGTCCTATTTAATTTTAAATTTAAAT
1 TATAATTCTA-TTAAATTTAAATTTAAAT
5546999 ACAATTTTAT
Statistics
Matches: 46, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
31 12 0.26
32 12 0.26
33 22 0.48
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.48
Consensus pattern (33 bp):
TATAATTCTATTAAATTTAAATTTAAATTTAAT
Found at i:5550978 original size:31 final size:31
Alignment explanation
Indices: 5550940--5551124 Score: 336
Period size: 31 Copynumber: 6.0 Consensus size: 31
5550930 GGGTCGAGGG
5550940 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
5550971 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
5551002 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
5551033 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
5551064 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
5551095 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
5551125 GTCCTTCGGG
Statistics
Matches: 151, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
31 150 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:5563611 original size:109 final size:108
Alignment explanation
Indices: 5563415--5563635 Score: 282
Period size: 109 Copynumber: 2.0 Consensus size: 108
5563405 ACTATGAAGC
* * * * * *
5563415 TTTTTTAGTCATGGAAATGTTGATGCTCGAGTTTTAATTCAAAAAATACAATTAGGTTTCAGGTT
1 TTTTTTAGTCATGGAAATGTTGA--CTCGAATTTGAAATCAAAAAATAAAAGTAGGTTCCAGGTT
* * *
5563480 TTGGTAACATCCCGTGGAGATAGAAAATTGCGGTAAAATATTGTT
64 CTGGTAACATCCCATGGAGATAGAAAATTGCGGTAAAAGATTGTT
*
5563525 TTTTTTTGTCATGGAAATGTTGA-TCGAATTTGAAATCAAAAGATATAAAAGTAGGTTCCAGGTT
1 TTTTTTAGTCATGGAAATGTTGACTCGAATTTGAAATCAAAA-A-ATAAAAGTAGGTTCCAGGTT
* **
5563589 CTGGTAACATCCCATGGGGATAGAAAATTGTTGTAAAAGATTGTT
64 CTGGTAACATCCCATGGAGATAGAAAATTGCGGTAAAAGATTGTT
5563634 TT
1 TT
5563636 CTCGATCTAA
Statistics
Matches: 96, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
107 15 0.16
108 1 0.01
109 58 0.60
110 22 0.23
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.37
Consensus pattern (108 bp):
TTTTTTAGTCATGGAAATGTTGACTCGAATTTGAAATCAAAAAATAAAAGTAGGTTCCAGGTTCT
GGTAACATCCCATGGAGATAGAAAATTGCGGTAAAAGATTGTT
Found at i:5563954 original size:13 final size:13
Alignment explanation
Indices: 5563936--5563962 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5563926 CACAGTTGAA
5563936 CAGTCTTCATATG
1 CAGTCTTCATATG
5563949 CAGTCTTCATATG
1 CAGTCTTCATATG
5563962 C
1 C
5563963 GCGTCTGTAA
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:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:5566779 original size:3 final size:3
Alignment explanation
Indices: 5566771--5566809 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
5566761 AAATAAGACC
5566771 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5566810 CCCACTTTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5573348 original size:59 final size:58
Alignment explanation
Indices: 5573216--5573385 Score: 157
Period size: 59 Copynumber: 2.8 Consensus size: 58
5573206 ATATACATAT
* * * * *
5573216 AGTTTGGGATGAAATTGGAATGTTCAAAAAGTTTGAAGATTAATTTAGAATGAAGGTCAT
1 AGTTTGGGATGAAATTGAAATGTTC-AAAAG-TTGAGGACTAATTTAAAATGAAGGTCAC
* *
5573276 AGTCTGGGGATGAAATTGAAATGTTCAAAAGTTGAGGACTAATTTAAAATGATA-TTCAC
1 AGT-TTGGGATGAAATTGAAATGTTCAAAAGTTGAGGACTAATTTAAAATGA-AGGTCAC
* * *
5573335 AGTTTAGGGATGAAATTAGAACAT-TT-AAAAATTTAGGGACCAATTTAAAAT
1 AGTTT-GGGATGAAATT-GAA-ATGTTCAAAAGTTGA-GGACTAATTTAAAAT
5573386 AAGCTTCATA
Statistics
Matches: 93, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
58 1 0.01
59 42 0.45
60 28 0.30
61 22 0.24
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.32
Consensus pattern (58 bp):
AGTTTGGGATGAAATTGAAATGTTCAAAAGTTGAGGACTAATTTAAAATGAAGGTCAC
Found at i:5576375 original size:17 final size:17
Alignment explanation
Indices: 5576353--5576391 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
5576343 TGAATCAAAT
5576353 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
5576370 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
5576387 -AATTA
1 TAATTA
5576392 ATTGTAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:5577809 original size:27 final size:29
Alignment explanation
Indices: 5577771--5577825 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 29
5577761 AATAGACCAT
*
5577771 GAAATCAACTTTTGC-CTTTCTT-TTTCG
1 GAAAGCAACTTTTGCTCTTTCTTCTTTCG
5577798 GAAAGCAACTTTTGCTCTTTCTTCTTTC
1 GAAAGCAACTTTTGCTCTTTCTTCTTTC
5577826 CGCATATATC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 14 0.56
28 7 0.28
29 4 0.16
ACGTcount: A:0.18, C:0.24, G:0.11, T:0.47
Consensus pattern (29 bp):
GAAAGCAACTTTTGCTCTTTCTTCTTTCG
Found at i:5583803 original size:33 final size:33
Alignment explanation
Indices: 5583766--5583831 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
5583756 CTAGGGGAGC
**
5583766 CGAGTCATCCA-AGGTGATGGATGAACCCATGAT
1 CGAGTCATCCATAGAAGAT-GATGAACCCATGAT
**
5583799 CGAGTTGTCCATAGAAGATGATGAACCCATGAT
1 CGAGTCATCCATAGAAGATGATGAACCCATGAT
5583832 AAAACTTGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 23 0.82
34 5 0.18
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.23
Consensus pattern (33 bp):
CGAGTCATCCATAGAAGATGATGAACCCATGAT
Found at i:5584312 original size:26 final size:26
Alignment explanation
Indices: 5584271--5584324 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
5584261 GAGTAAATGC
**
5584271 CACAAAATCAGTGGGAA-GCTACATCT
1 CACAAAATCAAAGGGAATG-TACATCT
5584297 CACAAAATCAAAGGGAATGTACATCT
1 CACAAAATCAAAGGGAATGTACATCT
5584323 CA
1 CA
5584325 ACACTATCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.43, C:0.22, G:0.17, T:0.19
Consensus pattern (26 bp):
CACAAAATCAAAGGGAATGTACATCT
Found at i:5586409 original size:21 final size:21
Alignment explanation
Indices: 5586383--5586424 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5586373 CCAGAATAGG
* *
5586383 GGGAATCGGTACCCTTTCATA
1 GGGAATCGATACCCCTTCATA
*
5586404 GGGAATTGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
5586425 ATATTCAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:5586555 original size:19 final size:19
Alignment explanation
Indices: 5586531--5586579 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
5586521 AGCCTCGGGG
*
5586531 TACTGTTCAAACAATGATT
1 TACTGTTCAAACAATAATT
* * *
5586550 TACTGTTTAAATAGTAATT
1 TACTGTTCAAACAATAATT
*
5586569 TACTTTTCAAA
1 TACTGTTCAAA
5586580 TAGTAAAGTA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.43
Consensus pattern (19 bp):
TACTGTTCAAACAATAATT
Found at i:5586580 original size:19 final size:19
Alignment explanation
Indices: 5586547--5586585 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
5586537 TCAAACAATG
5586547 ATTTACTGTTTAAATAGTA
1 ATTTACTGTTTAAATAGTA
5586566 ATTTACT-TTTCAAATAGTA
1 ATTTACTGTTT-AAATAGTA
5586585 A
1 A
5586586 AGTACTATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 3 0.16
19 16 0.84
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (19 bp):
ATTTACTGTTTAAATAGTA
Found at i:5586591 original size:19 final size:19
Alignment explanation
Indices: 5586558--5586596 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
5586548 TTTACTGTTT
** *
5586558 AAATAGTAATTTACTTTTC
1 AAATAGTAAAGTACTATTC
5586577 AAATAGTAAAGTACTATTC
1 AAATAGTAAAGTACTATTC
5586596 A
1 A
5586597 TAAAAACCAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (19 bp):
AAATAGTAAAGTACTATTC
Found at i:5586694 original size:29 final size:31
Alignment explanation
Indices: 5586662--5586721 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
5586652 AAATTTTGAA
*
5586662 TAAATTCAATT-AAGTCCAAATAC-ATTTTG
1 TAAATTCAATTCAAGTCCAAAAACTATTTTG
5586691 TAAATTCAATTCAAGTCCAAAAACTATTTTG
1 TAAATTCAATTCAAGTCCAAAAACTATTTTG
5586722 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.37
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACTATTTTG
Found at i:5590064 original size:14 final size:14
Alignment explanation
Indices: 5590045--5590071 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5590035 AATGATAAAT
5590045 GAACATAAATGAAC
1 GAACATAAATGAAC
5590059 GAACATAAATGAA
1 GAACATAAATGAA
5590072 TGGATGTAAA
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:0.59, C:0.11, G:0.15, T:0.15
Consensus pattern (14 bp):
GAACATAAATGAAC
Found at i:5590081 original size:14 final size:14
Alignment explanation
Indices: 5590064--5590110 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
5590054 TGAACGAACA
5590064 TAAATGAATGGATG
1 TAAATGAATGGATG
*
5590078 TAAATGAA--CA--
1 TAAATGAATGGATG
5590088 TAAATGAATGGATG
1 TAAATGAATGGATG
5590102 TAAATGAAT
1 TAAATGAAT
5590111 ATAAACGAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
10 8 0.30
12 2 0.07
14 17 0.63
ACGTcount: A:0.49, C:0.02, G:0.21, T:0.28
Consensus pattern (14 bp):
TAAATGAATGGATG
Found at i:5590086 original size:24 final size:24
Alignment explanation
Indices: 5590059--5590115 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
5590049 ATAAATGAAC
5590059 GAACATAAATGAATGGATGTAAAT
1 GAACATAAATGAATGGATGTAAAT
5590083 GAACATAAATGAATGGATGTAAAT
1 GAACATAAATGAATGGATGTAAAT
*
5590107 GAATATAAA
1 GAACATAAA
5590116 CGAACGTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.53, C:0.04, G:0.19, T:0.25
Consensus pattern (24 bp):
GAACATAAATGAATGGATGTAAAT
Found at i:5590126 original size:20 final size:20
Alignment explanation
Indices: 5590101--5590196 Score: 66
Period size: 20 Copynumber: 4.5 Consensus size: 20
5590091 ATGAATGGAT
* *
5590101 GTAAATGAATATAAACGAAC
1 GTAAATGAACACAAACGAAC
5590121 GTAAATGAACACAAACGAACGAAC
1 GTAAATGAACAC--A--AACGAAC
*
5590145 GTAAACGAACACAATAAACGAAC
1 GTAAATGAACAC---AAACGAAC
** *
5590168 GTAAATGAACGTAAACAAAC
1 GTAAATGAACACAAACGAAC
*
5590188 ATAAATGAA
1 GTAAATGAA
5590197 AATATTTTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
20 25 0.40
22 1 0.02
23 16 0.26
24 18 0.29
25 2 0.03
ACGTcount: A:0.56, C:0.16, G:0.15, T:0.14
Consensus pattern (20 bp):
GTAAATGAACACAAACGAAC
Found at i:5590146 original size:24 final size:23
Alignment explanation
Indices: 5590111--5590177 Score: 100
Period size: 24 Copynumber: 2.9 Consensus size: 23
5590101 GTAAATGAAT
5590111 ATAAACGAACGTAAATGAACACA
1 ATAAACGAACGTAAATGAACACA
*
5590134 A-ACGAACGAACGTAAACGAACACA
1 ATA--AACGAACGTAAATGAACACA
5590158 ATAAACGAACGTAAATGAAC
1 ATAAACGAACGTAAATGAAC
5590178 GTAAACAAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
22 1 0.03
23 17 0.44
24 20 0.51
25 1 0.03
ACGTcount: A:0.55, C:0.19, G:0.15, T:0.10
Consensus pattern (23 bp):
ATAAACGAACGTAAATGAACACA
Found at i:5590402 original size:19 final size:20
Alignment explanation
Indices: 5590363--5590403 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
5590353 GATATTGAGC
*
5590363 TAAACATAAATGAACGCACA
1 TAAACATAAATGAACGAACA
*
5590383 TAAACGTAAAT-AACGAACA
1 TAAACATAAATGAACGAACA
5590402 TA
1 TA
5590404 TTATCGAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.56, C:0.17, G:0.10, T:0.17
Consensus pattern (20 bp):
TAAACATAAATGAACGAACA
Found at i:5610727 original size:91 final size:95
Alignment explanation
Indices: 5610625--5610823 Score: 289
Period size: 99 Copynumber: 2.1 Consensus size: 95
5610615 TTTTCAAACG
*
5610625 TTTTCGCAATGCTAATTACCGATATAGGT-A-AAC-A-CGTAACTCAGTTTTCAAATTCGCAACG
1 TTTTCGCAATGCTAATTACCGATATAGGTAACAACTATCGCAACTCAGTTTTCAAATTCGCAACG
*
5610686 CGATTCTCCAAAATCGTAAAGCGAATTTCA
66 CGATTCTCCAAAATCGCAAAGCGAATTTCA
*
5610716 TTTTCGCAATGCTGATTACCGATATAGGTAAACACAACTATTCGCAACTCAGTTTTCAAATTCGC
1 TTTTCGCAATGCTAATTACCGATATAGGT--A-ACAACTA-TCGCAACTCAGTTTTCAAATTCGC
* *
5610781 AACGCGATTCTCCAAATTCGCAATGCGAATTTCA
62 AACGCGATTCTCCAAAATCGCAAAGCGAATTTCA
5610815 TTTTCGCAA
1 TTTTCGCAA
5610824 CTCGAATTTC
Statistics
Matches: 95, Mismatches: 5, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
91 28 0.29
95 1 0.01
96 3 0.03
97 1 0.01
99 62 0.65
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (95 bp):
TTTTCGCAATGCTAATTACCGATATAGGTAACAACTATCGCAACTCAGTTTTCAAATTCGCAACG
CGATTCTCCAAAATCGCAAAGCGAATTTCA
Found at i:5611012 original size:99 final size:99
Alignment explanation
Indices: 5610900--5611167 Score: 455
Period size: 99 Copynumber: 2.7 Consensus size: 99
5610890 AAAATGAAAT
*
5610900 TCGCGTTGCGAATTTGAAAACTGAGTTGCGAATAGTTGTGTTTACCTATATCGGTAATTAGCATT
1 TCGCGTTGCGAATTTGAAAACTGAGTTGCGAATAGTTGTGTTTACCTATATCGGTAATTAGCGTT
*
5610965 GCGAAAACGAAATTCGCGTTGCGATTTTAGAGAA
66 GCGAAAACGAAATTCGCGTTACGATTTTAGAGAA
* *
5610999 TCGCGTTGCGAATTTGAAAACTGAGTTGCGAATAATTGTGTTTACCTATATTGGTAATTAGCGTT
1 TCGCGTTGCGAATTTGAAAACTGAGTTGCGAATAGTTGTGTTTACCTATATCGGTAATTAGCGTT
*
5611064 GCGAAAACGAAATTCGCGTTACGATTTTGGAGAA
66 GCGAAAACGAAATTCGCGTTACGATTTTAGAGAA
* * * *
5611098 TCGCATTGTGAATTTGAAAACTGATTTGCGAATAGTTGTGTTTACCTATGTCGGTAATTAGCGTT
1 TCGCGTTGCGAATTTGAAAACTGAGTTGCGAATAGTTGTGTTTACCTATATCGGTAATTAGCGTT
5611163 GCGAA
66 GCGAA
5611168 TTTGTTGGTT
Statistics
Matches: 158, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
99 158 1.00
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.34
Consensus pattern (99 bp):
TCGCGTTGCGAATTTGAAAACTGAGTTGCGAATAGTTGTGTTTACCTATATCGGTAATTAGCGTT
GCGAAAACGAAATTCGCGTTACGATTTTAGAGAA
Found at i:5611295 original size:29 final size:29
Alignment explanation
Indices: 5611253--5611314 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
5611243 TTATTTTCTC
5611253 TAATAATGAATGTGTTTAGTAGTATAATG
1 TAATAATGAATGTGTTTAGTAGTATAATG
5611282 TAATAATGAATGTGTTTAGTAGTATAATG
1 TAATAATGAATGTGTTTAGTAGTATAATG
5611311 TAAT
1 TAAT
5611315 TTTATAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.39, C:0.00, G:0.19, T:0.42
Consensus pattern (29 bp):
TAATAATGAATGTGTTTAGTAGTATAATG
Found at i:5620250 original size:32 final size:32
Alignment explanation
Indices: 5620214--5620279 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 32
5620204 GATGTGATAA
* * * *
5620214 ATGTCACGTTATCATTTTAAGTGATATAATAC
1 ATGTCACATCATCATTTTAAATGACATAATAC
*
5620246 ATGTCACATCATCATTTTAAATGACATGATAC
1 ATGTCACATCATCATTTTAAATGACATAATAC
5620278 AT
1 AT
5620280 ATTACATTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (32 bp):
ATGTCACATCATCATTTTAAATGACATAATAC
Found at i:5620389 original size:27 final size:27
Alignment explanation
Indices: 5620357--5620417 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
5620347 GTTTTCATTT
5620357 AATATTATATGTTTTGATAAATATTAA
1 AATATTATATGTTTTGATAAATATTAA
5620384 AATATTATATGTTTTGATAAATATTAA
1 AATATTATATGTTTTGATAAATATTAA
5620411 AATATTA
1 AATATTA
5620418 AAAAAAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.48
Consensus pattern (27 bp):
AATATTATATGTTTTGATAAATATTAA
Found at i:5626815 original size:17 final size:16
Alignment explanation
Indices: 5626776--5626843 Score: 75
Period size: 17 Copynumber: 4.1 Consensus size: 16
5626766 CTGTAAAAAA
*
5626776 ATTAATTAAA-TATAAT
1 ATTAAATAAATTA-AAT
*
5626792 ATTAAATAATTTAAAT
1 ATTAAATAAATTAAAT
5626808 ACTTAAATAAATTAAAT
1 A-TTAAATAAATTAAAT
*
5626825 ATTAAATATAATAAAAT
1 ATTAAATA-AATTAAAT
5626842 AT
1 AT
5626844 ACCTTAAACA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
16 19 0.42
17 26 0.58
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTAAATAAATTAAAT
Found at i:5630288 original size:33 final size:32
Alignment explanation
Indices: 5630224--5630330 Score: 143
Period size: 32 Copynumber: 3.4 Consensus size: 32
5630214 GTCTGCATGT
5630224 GCCATGCACGTCCCCAACACCC-AACACAGGTC
1 GCCATGCAC-TCCCCAACACCCTAACACAGGTC
5630256 GCCATGCACGTCCCCAACACCCTAACACAGGTC
1 GCCATGCAC-TCCCCAACACCCTAACACAGGTC
*
5630289 GCCATGCACT-CCCAGCGA-CCT-ACA-AGGTC
1 GCCATGCACTCCCCAAC-ACCCTAACACAGGTC
5630318 GCCATGCACTCCC
1 GCCATGCACTCCC
5630331 AGCGACCTTG
Statistics
Matches: 71, Mismatches: 1, Indels: 8
0.89 0.01 0.10
Matches are distributed among these distances:
29 15 0.21
30 5 0.07
31 8 0.11
32 24 0.34
33 19 0.27
ACGTcount: A:0.25, C:0.46, G:0.17, T:0.12
Consensus pattern (32 bp):
GCCATGCACTCCCCAACACCCTAACACAGGTC
Found at i:5630326 original size:29 final size:31
Alignment explanation
Indices: 5630224--5630338 Score: 130
Period size: 29 Copynumber: 3.7 Consensus size: 31
5630214 GTCTGCATGT
* *
5630224 GCCATGCACGTCCCCAAC-ACCCAACACAGGTC
1 GCCATGCAC-T-CCCAGCGACCTAACACAGGTC
*
5630256 GCCATGCACGTCCCCAAC-ACCCTAACACAGGTC
1 GCCATGCAC-T-CCCAGCGA-CCTAACACAGGTC
5630289 GCCATGCACTCCCAGCGACCT-ACA-AGGTC
1 GCCATGCACTCCCAGCGACCTAACACAGGTC
5630318 GCCATGCACTCCCAGCGACCT
1 GCCATGCACTCCCAGCGACCT
5630339 TGTAGGTCGC
Statistics
Matches: 79, Mismatches: 2, Indels: 7
0.90 0.02 0.08
Matches are distributed among these distances:
29 26 0.33
30 3 0.04
31 8 0.10
32 21 0.27
33 21 0.27
ACGTcount: A:0.25, C:0.45, G:0.17, T:0.12
Consensus pattern (31 bp):
GCCATGCACTCCCAGCGACCTAACACAGGTC
Found at i:5630683 original size:26 final size:26
Alignment explanation
Indices: 5630650--5630707 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
5630640 ACATAAAAGA
*
5630650 AAGAAAGGGAGAAGAGATTGCAGCAG
1 AAGAAAGGGAGAAGAAATTGCAGCAG
*
5630676 AAGAAAGGGAGAAGAAATTGCAGCCG
1 AAGAAAGGGAGAAGAAATTGCAGCAG
5630702 -AGAAAG
1 AAGAAAG
5630708 AAAGAAAGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 6 0.20
26 24 0.80
ACGTcount: A:0.48, C:0.09, G:0.36, T:0.07
Consensus pattern (26 bp):
AAGAAAGGGAGAAGAAATTGCAGCAG
Found at i:5630878 original size:22 final size:21
Alignment explanation
Indices: 5630853--5630893 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
5630843 ATTAATTAGT
*
5630853 TTGTTAATTTAGGGTTATATGA
1 TTGTTAATTTA-AGTTATATGA
*
5630875 TTGTTAGTTTAAGTTATAT
1 TTGTTAATTTAAGTTATAT
5630894 TATACATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.54
Consensus pattern (21 bp):
TTGTTAATTTAAGTTATATGA
Found at i:5631222 original size:16 final size:16
Alignment explanation
Indices: 5631190--5631236 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
5631180 TTTAAAAAAT
*
5631190 TTAGTTTGTTAGT-TTA
1 TTAGTTTATTA-TATTA
5631206 TTAGTTTATTATATTA
1 TTAGTTTATTATATTA
*
5631222 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
5631237 AAGTTTAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:5631231 original size:15 final size:14
Alignment explanation
Indices: 5631211--5631241 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
5631201 GTTTATTAGT
5631211 TTATTATATTATAAG
1 TTATTATATTA-AAG
5631226 TTATTATATTAAAG
1 TTATTATATTAAAG
5631240 TT
1 TT
5631242 TAGTGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:5633421 original size:14 final size:14
Alignment explanation
Indices: 5633402--5633449 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
5633392 TTCAAGTCGT
5633402 AAATCATTACTATC
1 AAATCATTACTATC
5633416 AAATCATTAC--T-
1 AAATCATTACTATC
*
5633427 AAATCATTAATATC
1 AAATCATTACTATC
5633441 AAATCATTA
1 AAATCATTA
5633450 AATATTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 9 0.30
12 1 0.03
13 1 0.03
14 19 0.63
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:5633430 original size:25 final size:25
Alignment explanation
Indices: 5633401--5633449 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
5633391 GTTCAAGTCG
*
5633401 TAAATCATTACTATCAAATCATTAC
1 TAAATCATTAATATCAAATCATTAC
5633426 TAAATCATTAATATCAAATCATTA
1 TAAATCATTAATATCAAATCATTA
5633450 AATATTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (25 bp):
TAAATCATTAATATCAAATCATTAC
Found at i:5633689 original size:60 final size:60
Alignment explanation
Indices: 5633417--5633672 Score: 494
Period size: 60 Copynumber: 4.3 Consensus size: 60
5633407 ATTACTATCA
5633417 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
5633477 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
* *
5633537 AATCATTACTAAATTATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
5633597 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
5633657 AATCATTACTAAATCA
1 AATCATTACTAAATCA
5633673 ATATTATAAT
Statistics
Matches: 192, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 192 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (60 bp):
AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
Found at i:5633802 original size:15 final size:14
Alignment explanation
Indices: 5633748--5633845 Score: 58
Period size: 14 Copynumber: 6.8 Consensus size: 14
5633738 GTTCAAGTCG
*
5633748 TAAATCATTACTAT
1 TAAATCATTAATAT
* *
5633762 CAAATCA-T--TAC
1 TAAATCATTAATAT
5633773 TAAATCATTAATAT
1 TAAATCATTAATAT
5633787 TAAATCATTAAATAT
1 TAAATCATT-AATAT
* *
5633802 TAATAATAAATTATTAT
1 T-A-AAT-CATTAATAT
*
5633819 TACTAATCATTACTAT
1 TA--AATCATTAATAT
*
5633835 CAAATCATTAA
1 TAAATCATTAA
5633846 AAATTAATAA
Statistics
Matches: 66, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
11 8 0.12
12 1 0.02
13 1 0.02
14 25 0.38
15 6 0.09
16 10 0.15
17 12 0.18
18 3 0.05
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAATCATTAATAT
Found at i:5633804 original size:21 final size:22
Alignment explanation
Indices: 5633773--5633817 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
5633763 AAATCATTAC
*
5633773 TAAATCATTAATATTAAATCAT
1 TAAATCATTAATAATAAATCAT
*
5633795 TAAAT-ATTAATAATAAATTAT
1 TAAATCATTAATAATAAATCAT
5633816 TA
1 TA
5633818 TTACTAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAATCATTAATAATAAATCAT
Found at i:5633879 original size:48 final size:48
Alignment explanation
Indices: 5633766--5633881 Score: 164
Period size: 48 Copynumber: 2.4 Consensus size: 48
5633756 TACTATCAAA
* * * *
5633766 TCATTACTA-AATCATTAATATTAAATCATTAAATATTAATAATAAAT
1 TCATTATTATAATCATTACTATCAAATCATTAAAAATTAATAATAAAT
*
5633813 T-ATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATT
1 TCATTATTA-TAATCATTACTATCAAATCATTAAAAATTAATAATAAAT
5633861 TCATTATTATAATCATTACTA
1 TCATTATTATAATCATTACTA
5633882 AATCATTATT
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
46 6 0.10
47 1 0.02
48 47 0.77
49 7 0.11
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.42
Consensus pattern (48 bp):
TCATTATTATAATCATTACTATCAAATCATTAAAAATTAATAATAAAT
Found at i:5633888 original size:23 final size:24
Alignment explanation
Indices: 5633861--5633906 Score: 76
Period size: 23 Copynumber: 1.9 Consensus size: 24
5633851 AATAATAATT
5633861 TCATTATTATAA-TCATTACTAAA
1 TCATTATTATAATTCATTACTAAA
5633884 TCATTATTATAATTTCATTACTA
1 TCATTATTATAA-TTCATTACTA
5633907 GTTATGTAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 12 0.57
25 9 0.43
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (24 bp):
TCATTATTATAATTCATTACTAAA
Found at i:5633902 original size:73 final size:71
Alignment explanation
Indices: 5633750--5633906 Score: 167
Period size: 73 Copynumber: 2.2 Consensus size: 71
5633740 TCAAGTCGTA
* * *
5633750 AATCATTACTATCAAATCATTACTAAATCATTAATATTAAATCATTAAATATTAATAATAAATTA
1 AATCATTACTATCAAATCATTAC-AAA-CATTAATAATAAATCATTAAATATCAATAATAAATCA
5633815 TTATTACT
64 TTATTACT
* * * *
5633823 AATCATTACTATCAAATCATTA-AAA-ATTAATAATAATTTCATTATTATAATCATTACTAAATC
1 AATCATTACTATCAAATCATTACAAACATTAATAATAA-ATCATTA-AAT-ATCAATAATAAATC
5633886 ATTATTA-T
63 ATTATTACT
5633894 AATTTCATTACTA
1 AA--TCATTACTA
5633907 GTTATGTAAC
Statistics
Matches: 72, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
69 10 0.14
70 6 0.08
71 8 0.11
72 17 0.24
73 31 0.43
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.42
Consensus pattern (71 bp):
AATCATTACTATCAAATCATTACAAACATTAATAATAAATCATTAAATATCAATAATAAATCATT
ATTACT
Found at i:5633903 original size:14 final size:12
Alignment explanation
Indices: 5633861--5633896 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
5633851 AATAATAATT
5633861 TCATTATTATAA
1 TCATTATTATAA
*
5633873 TCATTACTA-AA
1 TCATTATTATAA
5633884 TCATTATTATAA
1 TCATTATTATAA
5633896 T
1 T
5633897 TTCATTACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (12 bp):
TCATTATTATAA
Found at i:5633915 original size:214 final size:201
Alignment explanation
Indices: 5633601--5634090 Score: 784
Period size: 200 Copynumber: 2.4 Consensus size: 201
5633591 ATTACTAATC
* *
5633601 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
* *
5633666 TAAATCAATATTATAATTTCATTACTAGTTATGTAACGAAAATATGGTTAATTGAACCAAACATT
65 TAAATCATTATTATAATTTCATTACTAGTTATGTAACGAAAATATAGTTAATTGAACCAAACATT
*
5633731 GTTCATTGTTCAAGTCGTAAATCATTACTATCAAATCATTACTAAATCATTAATATTAAATCATT
130 GTTCATTGTTCAAGTCG-------------T-AAATCATTACTAAATCATTAATATCAAATCATT
5633796 AAATATTAATAATAAATTATT
181 AAATATTAATAATAAATTATT
5633817 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTA-TAATCATTACT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
5633881 AAATCATTATTATAATTTCATTACTAGTTATGTAACGAAAATATAGTTAATTGAACCAAACATTG
66 AAATCATTATTATAATTTCATTACTAGTTATGTAACGAAAATATAGTTAATTGAACCAAACATTG
5633946 TTCATTGTTCAAGTCGTAAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAA
131 TTCATTGTTCAAGTCGTAAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAA
5634011 ATTATT
196 ATTATT
*
5634017 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTATTAATCATTACT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
5634082 AAATCATTA
66 AAATCATTA
5634091 ATATCAAATC
Statistics
Matches: 268, Mismatches: 5, Indels: 17
0.92 0.02 0.06
Matches are distributed among these distances:
200 106 0.40
201 21 0.08
214 90 0.34
215 45 0.17
216 6 0.02
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.40
Consensus pattern (201 bp):
ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
AAATCATTATTATAATTTCATTACTAGTTATGTAACGAAAATATAGTTAATTGAACCAAACATTG
TTCATTGTTCAAGTCGTAAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAA
ATTATT
Found at i:5634004 original size:21 final size:21
Alignment explanation
Indices: 5633973--5634174 Score: 84
Period size: 21 Copynumber: 9.6 Consensus size: 21
5633963 AAATCATTAC
5633973 TAAATCATTAATATCAAATCAT
1 TAAAT-ATTAATATCAAATCAT
* *
5633995 TAAATATTAATAATAAATTATTAT
1 TAAATATTAAT-ATCAA--ATCAT
*
5634019 TACTAATCATTACTATCAAATCAT
1 TA--AAT-ATTAATATCAAATCAT
* *
5634043 TAAAAATTAATAAT-AATTTCAT
1 TAAATATTAAT-ATCAA-ATCAT
* * *
5634065 T-ATTATT-A-ATC--ATTAC
1 TAAATATTAATATCAAATCAT
5634081 TAAATCATTAATATCAAATCAT
1 TAAAT-ATTAATATCAAATCAT
*
5634103 TAAATATTAATAAC-AAT--T
1 TAAATATTAATATCAAATCAT
* * * * *
5634121 TCATTATTACTAATC--ATTAC
1 TAAATATTAAT-ATCAAATCAT
*
5634141 TAAATCATTACTATCAAATCAT
1 TAAAT-ATTAATATCAAATCAT
5634163 TAAATATTAATA
1 TAAATATTAATA
5634175 ATAATTTCAT
Statistics
Matches: 132, Mismatches: 27, Indels: 43
0.65 0.13 0.21
Matches are distributed among these distances:
16 3 0.02
17 2 0.02
18 16 0.12
19 3 0.02
20 13 0.10
21 37 0.28
22 34 0.26
24 12 0.09
26 7 0.05
27 5 0.04
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAATATTAATATCAAATCAT
Found at i:5634030 original size:48 final size:49
Alignment explanation
Indices: 5633968--5634079 Score: 172
Period size: 48 Copynumber: 2.3 Consensus size: 49
5633958 GTCGTAAATC
*
5633968 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATT-ATT
1 ATTACT-AATCATTAATATCAAATCATTAAAAATTAATAATAAATTCATT
* *
5634017 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTAATATCAAATCATTAAAAATTAATAATAAATTCATT
*
5634066 ATTATTAATCATTA
1 ATTACTAATCATTA
5634080 CTAAATCATT
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
48 36 0.62
49 22 0.38
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (49 bp):
ATTACTAATCATTAATATCAAATCATTAAAAATTAATAATAAATTCATT
Found at i:5634096 original size:60 final size:60
Alignment explanation
Indices: 5634017--5634206 Score: 328
Period size: 60 Copynumber: 3.2 Consensus size: 60
5634007 ATAAATTATT
* *
5634017 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTATTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
* *
5634076 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
5634136 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
5634196 ATTACTAAATC
1 ATTACTAAATC
5634207 TTAGAAATAC
Statistics
Matches: 123, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
59 6 0.05
60 117 0.95
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.41
Consensus pattern (60 bp):
ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
Found at i:5634221 original size:10 final size:10
Alignment explanation
Indices: 5634208--5634239 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
5634198 TACTAAATCT
5634208 TAGAAATACA
1 TAGAAATACA
*
5634218 TAGAAATTCA
1 TAGAAATACA
5634228 TAGAAATACA
1 TAGAAATACA
5634238 TA
1 TA
5634240 TATCATTACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.25
Consensus pattern (10 bp):
TAGAAATACA
Found at i:5637055 original size:22 final size:23
Alignment explanation
Indices: 5637030--5637080 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
5637020 TTTGATTGAT
*
5637030 TGATTACTAATATTACTAA-TAA
1 TGATTAATAATATTACTAACTAA
*
5637052 TGATTAATAATATTATTAATCTAA
1 TGATTAATAATATTACTAA-CTAA
5637076 TGATT
1 TGATT
5637081 TGATATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 17 0.68
24 8 0.32
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (23 bp):
TGATTAATAATATTACTAACTAA
Found at i:5637723 original size:28 final size:30
Alignment explanation
Indices: 5637683--5637744 Score: 110
Period size: 28 Copynumber: 2.1 Consensus size: 30
5637673 ATTTTTTATA
5637683 TAATATAATATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
5637713 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
5637741 TAAT
1 TAAT
5637745 TAACTAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:5638288 original size:29 final size:29
Alignment explanation
Indices: 5638255--5638336 Score: 119
Period size: 29 Copynumber: 2.8 Consensus size: 29
5638245 TCCTAAGCTT
* *
5638255 GGTCGCTGGGACTGCTTGGCGACCTACAA
1 GGTCGCTGGGAGTGCATGGCGACCTACAA
***
5638284 GGTCGCTGGGAGTGCATGGCGACCTTGTA
1 GGTCGCTGGGAGTGCATGGCGACCTACAA
5638313 GGTCGCTGGGAGTGCATGGCGACC
1 GGTCGCTGGGAGTGCATGGCGACC
5638337 GCCGACCTGT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.15, C:0.24, G:0.40, T:0.21
Consensus pattern (29 bp):
GGTCGCTGGGAGTGCATGGCGACCTACAA
Found at i:5638392 original size:32 final size:33
Alignment explanation
Indices: 5638339--5638404 Score: 125
Period size: 32 Copynumber: 2.0 Consensus size: 33
5638329 TGGCGACCGC
5638339 CGACCTGTGTTGGGGTGTTGGGGACGTGCATGG
1 CGACCTGTGTTGGGGTGTTGGGGACGTGCATGG
5638372 CGACCTGTGTT-GGGTGTTGGGGACGTGCATGG
1 CGACCTGTGTTGGGGTGTTGGGGACGTGCATGG
5638404 C
1 C
5638405 ACATGCAGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 22 0.67
33 11 0.33
ACGTcount: A:0.09, C:0.17, G:0.47, T:0.27
Consensus pattern (33 bp):
CGACCTGTGTTGGGGTGTTGGGGACGTGCATGG
Found at i:5640860 original size:2 final size:2
Alignment explanation
Indices: 5640853--5640877 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5640843 AGTATTTTCT
5640853 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5640878 TAGGTGGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5644777 original size:30 final size:30
Alignment explanation
Indices: 5644699--5644780 Score: 119
Period size: 30 Copynumber: 2.7 Consensus size: 30
5644689 TTTTTAATAA
*
5644699 AATTAGAATTGTGGGATCAAATAAACTTTT
1 AATTAAAATTGTGGGATCAAATAAACTTTT
* * *
5644729 AATTAAAACTGCGAGATCAAATAAACTTTT
1 AATTAAAATTGTGGGATCAAATAAACTTTT
*
5644759 AATTACAATTGTGGGATCAAAT
1 AATTAAAATTGTGGGATCAAAT
5644781 GAATTATTAT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.33
Consensus pattern (30 bp):
AATTAAAATTGTGGGATCAAATAAACTTTT
Found at i:5650290 original size:29 final size:29
Alignment explanation
Indices: 5650248--5650332 Score: 145
Period size: 29 Copynumber: 2.9 Consensus size: 29
5650238 ATATTTTGAC
*
5650248 AAAATG-TTATATATGATATTTATATTTTT
1 AAAATGTTTA-ATATCATATTTATATTTTT
5650277 AAAATGTTTAATATCATATTTATATTTTT
1 AAAATGTTTAATATCATATTTATATTTTT
5650306 AAAATGTTTAATATCATATTTATATTT
1 AAAATGTTTAATATCATATTTATATTT
5650333 AATAAAAACA
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
29 51 0.94
30 3 0.06
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (29 bp):
AAAATGTTTAATATCATATTTATATTTTT
Found at i:5652344 original size:14 final size:14
Alignment explanation
Indices: 5652325--5652383 Score: 59
Period size: 14 Copynumber: 4.1 Consensus size: 14
5652315 GTAATTGATT
5652325 TTCTGAAAATTGAA
1 TTCTGAAAATTGAA
*
5652339 TTCTGAAAAATGAA
1 TTCTGAAAATTGAA
*
5652353 TTACT-AGAATTCGAA
1 TT-CTGAAAATT-GAA
5652368 TTCTAGAAAA-TGAA
1 TTCT-GAAAATTGAA
5652382 TT
1 TT
5652384 ACATTTCTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 26 0.70
15 8 0.22
16 3 0.08
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (14 bp):
TTCTGAAAATTGAA
Found at i:5652411 original size:14 final size:14
Alignment explanation
Indices: 5652394--5652427 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5652384 ACATTTCTAG
5652394 AAAATGTTTTCCGA
1 AAAATGTTTTCCGA
* *
5652408 AAAATATTTTCCGT
1 AAAATGTTTTCCGA
5652422 AAAATG
1 AAAATG
5652428 AATTACATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (14 bp):
AAAATGTTTTCCGA
Done.