Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009330.1 Hibiscus syriacus cultivar Beakdansim tig00113096_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: 1820295
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 8
Found at i:496 original size:21 final size:21
Alignment explanation
Indices: 433--540 Score: 101
Period size: 21 Copynumber: 5.1 Consensus size: 21
423 GCTGATATAT
* * *
433 TTCTCTCTGTTCTACCGCTGC
1 TTCTCTCTCTGCTTCCGCTGC
* * *
454 CTCTCTCTGTGCTGCCGCTGC
1 TTCTCTCTCTGCTTCCGCTGC
475 TTCTCTCTCTGCTTCCGCTGC
1 TTCTCTCTCTGCTTCCGCTGC
* **
496 TGCTCTAGCTGCTTCCGCTGC
1 TTCTCTCTCTGCTTCCGCTGC
* *
517 TGCTCTCTCTGTTTCC-CTTGC
1 TTCTCTCTCTGCTTCCGC-TGC
538 TTC
1 TTC
541 ATTTTCCGCT
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
20 1 0.01
21 72 0.99
ACGTcount: A:0.02, C:0.40, G:0.18, T:0.41
Consensus pattern (21 bp):
TTCTCTCTCTGCTTCCGCTGC
Found at i:10283 original size:41 final size:41
Alignment explanation
Indices: 10217--10377 Score: 213
Period size: 41 Copynumber: 4.0 Consensus size: 41
10207 CGTTTATACA
10217 AAAAAACGCCACTATTGATTA-CACTATT-CTGGCGTTTGTT
1 AAAAAACGCCACTATTGATTATCACTATTGC-GGCGTTTGTT
10257 AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTT-TT
1 AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTTGTT
* * * **
10297 CTAAAAACGCCATTATTGATTAACACTATTATGGCGTTTGTCT
1 -AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTTGT-T
*
10340 -AAAAACACCACTATTGATTATCACTATTGCGGCGTTTG
1 AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTTG
10378 AGGAATAAAC
Statistics
Matches: 106, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
40 23 0.22
41 80 0.75
42 2 0.02
43 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (41 bp):
AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTTGTT
Found at i:10335 original size:82 final size:81
Alignment explanation
Indices: 10218--10376 Score: 266
Period size: 82 Copynumber: 2.0 Consensus size: 81
10208 GTTTATACAA
* *
10218 AAAAACGCCACTATTGATTACACTATTCTGGCGTTTGT-TAAAAAACGCCACTATTGATTATCAC
1 AAAAACGCCACTATTGATTACACTATTATGGCGTTTGTCT-AAAAACACCACTATTGATTATCAC
10282 TATTGCGGCGTTTTTCT
65 TATTGCGGCGTTTTTCT
*
10299 AAAAACGCCATTATTGATTAACACTATTATGGCGTTTGTCTAAAAACACCACTATTGATTATCAC
1 AAAAACGCCACTATTGATT-ACACTATTATGGCGTTTGTCTAAAAACACCACTATTGATTATCAC
10364 TATTGCGGCGTTT
65 TATTGCGGCGTTT
10377 GAGGAATAAA
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
81 18 0.25
82 54 0.74
83 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.35
Consensus pattern (81 bp):
AAAAACGCCACTATTGATTACACTATTATGGCGTTTGTCTAAAAACACCACTATTGATTATCACT
ATTGCGGCGTTTTTCT
Found at i:10533 original size:41 final size:42
Alignment explanation
Indices: 10406--10599 Score: 157
Period size: 41 Copynumber: 4.7 Consensus size: 42
10396 ATGTGTAATA
* *
10406 TATTGCGGCGTTTGTGGTATAAACGCCACGAATTTACCACTC
1 TATTGCGGCGTTTGTGGTATAAACGCCGCAAATTTACCACTC
* * *
10448 TATTGCGGCGTTT-TGGCT-CAATCGCCGCAAAATTTA-TACTC
1 TATTGCGGCGTTTGTGG-TATAAACGCCGC-AAATTTACCACTC
* * *
10489 TATTGTGGCGTTTGTGGTATAAAC-CCGCTAATTTACCACCC
1 TATTGCGGCGTTTGTGGTATAAACGCCGCAAATTTACCACTC
* * * * * * *
10530 TATTGCGGCATTTTTTGTAAAAACGCCGCTATATGT-CAACTC
1 TATTGCGGCGTTTGTGGTATAAACGCCGC-AAATTTACCACTC
* **
10572 TATTGCAGCGTTTGTACTA-AAACGCCGC
1 TATTGCGGCGTTTGTGGTATAAACGCCGC
10600 TAAAGTATCA
Statistics
Matches: 119, Mismatches: 26, Indels: 15
0.74 0.16 0.09
Matches are distributed among these distances:
40 6 0.05
41 62 0.52
42 48 0.40
43 3 0.03
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (42 bp):
TATTGCGGCGTTTGTGGTATAAACGCCGCAAATTTACCACTC
Found at i:10557 original size:83 final size:83
Alignment explanation
Indices: 10406--10586 Score: 206
Period size: 83 Copynumber: 2.2 Consensus size: 83
10396 ATGTGTAATA
* * *
10406 TATTGCGGCGTTTGTGGTATAAACGCCACGAATTTACCACTCTATTGCGGCGTTTTGGCTCAATC
1 TATTGCGGCGTTTGTGGTATAAACGCCACGAATTTACCACCCTATTGCGGCGTTTTGGCTAAAAC
10471 GCCGCAAAATTTATACTC
66 GCCGCAAAATTTATACTC
* * * * *
10489 TATTGTGGCGTTTGTGGTATAAAC-CCGCTAATTTACCACCCTATTGCGGCATTTTTTG-TAAAA
1 TATTGCGGCGTTTGTGGTATAAACGCCACGAATTTACCACCCTATTGCGGC-GTTTTGGCT-AAA
* * *
10552 ACGCCGCTATATGTCA-ACTC
64 ACGCCGCAAAAT-TTATACTC
*
10572 TATTGCAGCGTTTGT
1 TATTGCGGCGTTTGT
10587 ACTAAAACGC
Statistics
Matches: 82, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
82 24 0.29
83 56 0.68
84 2 0.02
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.35
Consensus pattern (83 bp):
TATTGCGGCGTTTGTGGTATAAACGCCACGAATTTACCACCCTATTGCGGCGTTTTGGCTAAAAC
GCCGCAAAATTTATACTC
Found at i:10868 original size:25 final size:25
Alignment explanation
Indices: 10834--10885 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
10824 AAGAAAAACA
10834 ATCTGCCGCTAATATTAGTAATATC
1 ATCTGCCGCTAATATTAGTAATATC
10859 ATCTGCCGCTAATATTAGTAATATC
1 ATCTGCCGCTAATATTAGTAATATC
10884 AT
1 AT
10886 GCCCACTGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (25 bp):
ATCTGCCGCTAATATTAGTAATATC
Found at i:11176 original size:128 final size:131
Alignment explanation
Indices: 10938--11198 Score: 501
Period size: 128 Copynumber: 2.0 Consensus size: 131
10928 ATACTTTATG
10938 TAGATAATATGAATTTATCAAAGCCAAATGCCCCTTATAATAAAATAACTGATTTTTTTATTATA
1 TAGATAATATGAATTTATCAAAGCCAAATGCCCCTTATAATAAAATAACTGATTTTTTTATTATA
11003 ATGTTGAATGATGATTTTAAAAGTTGAAATAATAATGATGAGATT-A-ATATATGAGGGTAAAGT
66 ATGTTGAATGATGATTTTAAAAGTTGAAATAATAATGATGAGATTAATATATATGAGGGTAAAGT
11066 A
131 A
11067 TAGATAATATGAATTTATCAAAGCCAAATGCCCCTTATAATAAAATAACTGA-TTTTTTATTATA
1 TAGATAATATGAATTTATCAAAGCCAAATGCCCCTTATAATAAAATAACTGATTTTTTTATTATA
11131 ATGTTGAATGATGATTTTAAAAGTTGAAATAATAATGATGAGATTAATATATATGAGGGTAAAGT
66 ATGTTGAATGATGATTTTAAAAGTTGAAATAATAATGATGAGATTAATATATATGAGGGTAAAGT
11196 A
131 A
11197 TA
1 TA
11199 ATGGTATTAT
Statistics
Matches: 130, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
128 57 0.44
129 53 0.41
130 20 0.15
ACGTcount: A:0.43, C:0.06, G:0.15, T:0.36
Consensus pattern (131 bp):
TAGATAATATGAATTTATCAAAGCCAAATGCCCCTTATAATAAAATAACTGATTTTTTTATTATA
ATGTTGAATGATGATTTTAAAAGTTGAAATAATAATGATGAGATTAATATATATGAGGGTAAAGT
A
Found at i:19696 original size:20 final size:20
Alignment explanation
Indices: 19671--19751 Score: 65
Period size: 20 Copynumber: 3.9 Consensus size: 20
19661 TTTTGGTGCA
*
19671 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
* *
19691 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATACCCCC-AT
* *
19712 GAAGCGGAACCGATTCCCCCCT
1 G-AG-GGAACCGATACCCCCAT
*
19734 -AGGGGAATCGATACCCCC
1 GA-GGGAACCGATACCCCC
19752 TAGGGTTCTG
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
20 30 0.59
21 3 0.06
22 3 0.06
23 15 0.29
ACGTcount: A:0.25, C:0.35, G:0.25, T:0.16
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:21778 original size:33 final size:31
Alignment explanation
Indices: 21725--21789 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 31
21715 TTTTAACATT
*
21725 TTGATTATTTTGGAATGTTTGAATTTGTGGA
1 TTGATTATTTTGGAATGTTTGAATTTATGGA
*
21756 TTGATTGATTTT-GAATTTGTTTGGATTTATGGA
1 TTGATT-ATTTTGGAA--TGTTTGAATTTATGGA
21789 T
1 T
21790 GGTGAGAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 9 0.31
32 5 0.17
33 15 0.52
ACGTcount: A:0.22, C:0.00, G:0.25, T:0.54
Consensus pattern (31 bp):
TTGATTATTTTGGAATGTTTGAATTTATGGA
Found at i:36467 original size:20 final size:20
Alignment explanation
Indices: 36430--36472 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
36420 ATTCCACCAC
36430 ATGCAACTAAATGCTTCTAA
1 ATGCAACTAAATGCTTCTAA
* * *
36450 ATGCACCTACATGGTTCTAA
1 ATGCAACTAAATGCTTCTAA
36470 ATG
1 ATG
36473 AGCTCTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTTCTAA
Found at i:45445 original size:32 final size:31
Alignment explanation
Indices: 45408--45487 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 31
45398 TCCATATATC
45408 CTGAAGGACATAGGTAAACATGTCCATAGGT
1 CTGAAGGACATAGGTAAACATGTCCATAGGT
* * * *
45439 CTTGAAGGACATAGATAATCCTGTCCATATGT
1 C-TGAAGGACATAGGTAAACATGTCCATAGGT
**
45471 CCCAAGGACATAGGTAA
1 CTGAAGGACATAGGTAA
45488 CCTCTCGACT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 14 0.34
32 27 0.66
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.24
Consensus pattern (31 bp):
CTGAAGGACATAGGTAAACATGTCCATAGGT
Found at i:51577 original size:18 final size:18
Alignment explanation
Indices: 51554--51594 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
51544 AATCATTCGG
51554 ATAACTATAAATTTTCTC
1 ATAACTATAAATTTTCTC
51572 ATAACTATAAATTTTCTC
1 ATAACTATAAATTTTCTC
51590 ATAAC
1 ATAAC
51595 CAAAACCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (18 bp):
ATAACTATAAATTTTCTC
Found at i:51756 original size:42 final size:42
Alignment explanation
Indices: 51686--51780 Score: 102
Period size: 42 Copynumber: 2.3 Consensus size: 42
51676 AATCGCGATG
* * *
51686 TTTA-TAATAAAAATGCCACTAAGGTACATCACTATTGCATCA
1 TTTATTAA-AAAAAAGCCACTAAAGTACATCACTATTGCAGCA
* * * * *
51728 TTTATTAAAAAAAAGCCACTAAATTACATGATTATTGCGGCG
1 TTTATTAAAAAAAAGCCACTAAAGTACATCACTATTGCAGCA
51770 TTTATTAAAAA
1 TTTATTAAAAA
51781 CGCAGTTAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 41 0.93
43 3 0.07
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.33
Consensus pattern (42 bp):
TTTATTAAAAAAAAGCCACTAAAGTACATCACTATTGCAGCA
Found at i:51978 original size:135 final size:133
Alignment explanation
Indices: 51810--52102 Score: 408
Period size: 133 Copynumber: 2.2 Consensus size: 133
51800 TATTACGGTT
*
51810 TTTGTATACAAACACCACTAAAGTAAGAGTATTTTGCGACATTTGATCAAAAAACACCGCTAAAA
1 TTTGTATACAAACACCACTAAAGTAAGAGTATTTTACGACATTTGATC-AAAAACACCGCTAAAA
* * * * *
51875 ATGACATTATACATCTCTATTGTGGCGTTTGTTGAAAAAAACACCACTAAAGTACTACTCTGTTG
65 AAGACACTATACATCTCTATTGCGGCATTTATTG-AAAAAACACCACTAAAGTACTACTCTGTTG
51940 CGGCA
129 CGGCA
* * *
51945 TTTGTATACAAACACCACTAAAGTCAA-AGTATTTTACGGCGTTTGATCAAAAATACCGCTAAAA
1 TTTGTATACAAACACCACTAAAGT-AAGAGTATTTTACGACATTTGATCAAAAACACCGCTAAAA
* * * * *
52009 AAGGCGCTATACATCTCTATTGCGGCATTTATTGAAAAAACGCTACTAAAGTACTACTCTGTTGT
65 AAGACACTATACATCTCTATTGCGGCATTTATTGAAAAAACACCACTAAAGTACTACTCTGTTGC
*
52074 GGCG
130 GGCA
*
52078 TTTGTATACAAACACCGCTAAAGTA
1 TTTGTATACAAACACCACTAAAGTA
52103 CTTATATGTT
Statistics
Matches: 141, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
132 1 0.01
133 54 0.38
134 42 0.30
135 42 0.30
136 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.29
Consensus pattern (133 bp):
TTTGTATACAAACACCACTAAAGTAAGAGTATTTTACGACATTTGATCAAAAACACCGCTAAAAA
AGACACTATACATCTCTATTGCGGCATTTATTGAAAAAACACCACTAAAGTACTACTCTGTTGCG
GCA
Found at i:52551 original size:23 final size:23
Alignment explanation
Indices: 52520--52577 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
52510 AGTTTTTATG
*
52520 TATGACACATTTTCCTCTGCCTT
1 TATGGCACATTTTCCTCTGCCTT
* *
52543 TATGGCACATTTTCTTCTGTCTT
1 TATGGCACATTTTCCTCTGCCTT
*
52566 T-TCGCACATTTT
1 TATGGCACATTTT
52578 TCGGCCGTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 10 0.32
23 21 0.68
ACGTcount: A:0.16, C:0.26, G:0.10, T:0.48
Consensus pattern (23 bp):
TATGGCACATTTTCCTCTGCCTT
Found at i:54020 original size:14 final size:14
Alignment explanation
Indices: 54001--54050 Score: 63
Period size: 15 Copynumber: 3.8 Consensus size: 14
53991 ATGATAAATG
54001 ATTATAAATATATT
1 ATTATAAATATATT
54015 ATTATAAAATATATT
1 ATTAT-AAATATATT
54030 ATT-TAAAT-TATT
1 ATTATAAATATATT
54042 -TTA-AAATAT
1 ATTATAAATAT
54051 TAATATATTC
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 6 0.18
12 5 0.15
13 4 0.12
14 6 0.18
15 12 0.36
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTATAAATATATT
Found at i:54732 original size:101 final size:100
Alignment explanation
Indices: 54551--54739 Score: 247
Period size: 101 Copynumber: 1.9 Consensus size: 100
54541 TTCGCGTTAT
* * *
54551 GAATTTGACTTTTGTGTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGCGAATT
1 GAATTTGACTTTTGTATTGCGAATTTGACTTCTGCGTTGCGATTTAC-AATTCGCGTTGCGAAGT
* *
54616 TGACTTTCGCATTGCGAATTTGAAATTTCGTATTGC
65 TAACTATCGCATTGCGAATTTGAAATTTCGTATTGC
* * *
54652 GAATTTGACTTTTGTATTGCGAATTTGACTAT-TGCGTTGCGAATTTGAC-TTTTGTGTTGCGAA
1 GAATTTGACTTTTGTATTGCGAATTTGACT-TCTGCGTTGCG-ATTT-ACAATTCGCGTTGCGAA
*
54715 GTTAACTATCGCGTTGCGAATTTGA
63 GTTAACTATCGCATTGCGAATTTGA
54740 CTTCTGTGTT
Statistics
Matches: 76, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
101 69 0.91
102 5 0.07
103 2 0.03
ACGTcount: A:0.21, C:0.14, G:0.23, T:0.42
Consensus pattern (100 bp):
GAATTTGACTTTTGTATTGCGAATTTGACTTCTGCGTTGCGATTTACAATTCGCGTTGCGAAGTT
AACTATCGCATTGCGAATTTGAAATTTCGTATTGC
Found at i:54750 original size:20 final size:19
Alignment explanation
Indices: 54528--54753 Score: 177
Period size: 20 Copynumber: 11.3 Consensus size: 19
54518 TCTTTGATAA
*
54528 TGCGAATTTGACTTTCGCGT
1 TGCGAATTTGACTTT-GTGT
**
54548 TATGAATTTGACTTTTGTGT
1 TGCGAATTTGAC-TTTGTGT
54568 TGCGAATTTGACTTCTGTGT
1 TGCGAATTTGACTT-TGTGT
* *
54588 TGCG-ATTT-ACAAATTCGCGT
1 TGCGAATTTGAC---TTTGTGT
**
54608 TGCGAATTTGACTTTCGCAT
1 TGCGAATTTGACTTT-GTGT
* *
54628 TGCGAATTTGAAATTTCGTAT
1 TGCGAATTTG-ACTTT-GTGT
*
54649 TGCGAATTTGACTTTTGTAT
1 TGCGAATTTGAC-TTTGTGT
*
54669 TGCGAATTTGACTATTGCGT
1 TGCGAATTTGACT-TTGTGT
54689 TGCGAATTTGACTTTTGTGT
1 TGCGAATTTGAC-TTTGTGT
* * * *
54709 TGCGAAGTTAACTATCGCGT
1 TGCGAATTTGACT-TTGTGT
54729 TGCGAATTTGACTTCTGTGT
1 TGCGAATTTGACTT-TGTGT
54749 TGCGA
1 TGCGA
54754 TTTACAGATT
Statistics
Matches: 169, Mismatches: 23, Indels: 28
0.77 0.10 0.13
Matches are distributed among these distances:
18 2 0.01
19 11 0.07
20 123 0.73
21 31 0.18
22 2 0.01
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.42
Consensus pattern (19 bp):
TGCGAATTTGACTTTGTGT
Found at i:54770 original size:20 final size:20
Alignment explanation
Indices: 54747--54813 Score: 125
Period size: 20 Copynumber: 3.4 Consensus size: 20
54737 TGACTTCTGT
*
54747 GTTGCGATTTACAGATTCAC
1 GTTGCGATTTACAGATTCGC
54767 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAGATTCGC
54787 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAGATTCGC
54807 GTTGCGA
1 GTTGCGA
54814 AATTGGAAAC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACAGATTCGC
Found at i:54770 original size:40 final size:40
Alignment explanation
Indices: 54566--54858 Score: 221
Period size: 40 Copynumber: 7.3 Consensus size: 40
54556 TGACTTTTGT
54566 GTTGCGAATTTGACTTCTGTGTTGCG-ATTTACAAATTCGC
1 GTTGCGAATTTGACTTCTGTGTTGCGAATTTAC-AATTCGC
** *
54606 GTTGCGAATTTGACTT-TCGCATTGCGAATTTGA-AATTTCGT
1 GTTGCGAATTTGACTTCT-GTGTTGCGAATTT-ACAA-TTCGC
* * * *
54647 ATTGCGAATTTGACTTTTGTATTGCGAATTTGACTATT-GC
1 GTTGCGAATTTGACTTCTGTGTTGCGAATTT-ACAATTCGC
* * *
54687 GTTGCGAATTTGACTTTTGTGTTGCGAAGTTA-ACTATCGC
1 GTTGCGAATTTGACTTCTGTGTTGCGAATTTACAAT-TCGC
*
54727 GTTGCGAATTTGACTTCTGTGTTGCG-ATTTACAGATTCAC
1 GTTGCGAATTTGACTTCTGTGTTGCGAATTTACA-ATTCGC
*
54767 GTTGCG-ATTT-ACAGATTC-GCGTTGCG-ATTTACAGATTCGC
1 GTTGCGAATTTGAC---TTCTGTGTTGCGAATTTACA-ATTCGC
* ** * * ** *
54807 GTTGCGAAATTGGA-AACTGAGTTGCGAAATTGGAGTTCGC
1 GTTGCG-AATTTGACTTCTGTGTTGCGAATTTACAATTCGC
54847 GTTGCGAATTTG
1 GTTGCGAATTTG
54859 TTGGTCATTT
Statistics
Matches: 208, Mismatches: 27, Indels: 37
0.76 0.10 0.14
Matches are distributed among these distances:
38 3 0.01
39 17 0.08
40 134 0.64
41 47 0.23
42 6 0.03
43 1 0.00
ACGTcount: A:0.22, C:0.15, G:0.25, T:0.39
Consensus pattern (40 bp):
GTTGCGAATTTGACTTCTGTGTTGCGAATTTACAATTCGC
Found at i:54850 original size:20 final size:19
Alignment explanation
Indices: 54800--54854 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
54790 GCGATTTACA
54800 GATTCGCGTTGCGAAATTG
1 GATTCGCGTTGCGAAATTG
** *
54819 GAAACTGAGTTGCGAAATTG
1 GATTC-GCGTTGCGAAATTG
54839 GAGTTCGCGTTGCGAA
1 GA-TTCGCGTTGCGAA
54855 TTTGTTGGTC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 3 0.11
20 24 0.86
21 1 0.04
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.27
Consensus pattern (19 bp):
GATTCGCGTTGCGAAATTG
Found at i:55437 original size:10 final size:9
Alignment explanation
Indices: 55409--55450 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
55399 TTTTACCTAG
55409 TTTTATAAT
1 TTTTATAAT
*
55418 TTCTATAAT
1 TTTTATAAT
55427 TTTTCATAA-
1 TTTT-ATAAT
55436 TTTTATATAT
1 TTTTATA-AT
55446 TTTTA
1 TTTTA
55451 AAATATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
8 3 0.11
9 16 0.57
10 9 0.32
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (9 bp):
TTTTATAAT
Found at i:55437 original size:19 final size:18
Alignment explanation
Indices: 55409--55450 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
55399 TTTTACCTAG
55409 TTTTATAATTTCTATA-AT
1 TTTTATAATTT-TATATAT
55427 TTTTCATAATTTTATATAT
1 TTTT-ATAATTTTATATAT
55446 TTTTA
1 TTTTA
55451 AAATATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTATAATTTTATATAT
Found at i:55965 original size:59 final size:59
Alignment explanation
Indices: 55903--56019 Score: 144
Period size: 59 Copynumber: 2.0 Consensus size: 59
55893 GAATAGTCAG
* * * * * *
55903 AAAACCATTTTATAATTTTTAATAGTCGAGGGACTCAATGAAATAACATCATATAATCGA
1 AAAACCA-TTTATAACTTTTAATAATCAAGAGACTCAATAAAATAACACCATATAATCGA
* * *
55963 AAAATCATTTATAACTTTTAATAATTAAGATACTCAATAAAATAACACCATATAATC
1 AAAACCATTTATAACTTTTAATAATCAAGAGACTCAATAAAATAACACCATATAATC
56020 AAGGGATCAT
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
59 42 0.88
60 6 0.12
ACGTcount: A:0.47, C:0.14, G:0.07, T:0.32
Consensus pattern (59 bp):
AAAACCATTTATAACTTTTAATAATCAAGAGACTCAATAAAATAACACCATATAATCGA
Found at i:63412 original size:20 final size:19
Alignment explanation
Indices: 63387--63441 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 19
63377 CTCAACAAAG
63387 TTATAAAATAATATTATAAT
1 TTAT-AAATAATATTATAAT
* *
63407 TTATAAAT-AT-TAAAAAT
1 TTATAAATAATATTATAAT
*
63424 TTATAATTAATATTATAA
1 TTATAAATAATATTATAA
63442 ACATAAGAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
17 12 0.43
18 4 0.14
19 8 0.29
20 4 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTATAAATAATATTATAAT
Found at i:63627 original size:30 final size:30
Alignment explanation
Indices: 63580--63684 Score: 90
Period size: 30 Copynumber: 3.5 Consensus size: 30
63570 TCTAAGCTAA
*
63580 ATTTTGAT-CAAATTTAAGAGTTAAATTGAT
1 ATTTT-ATCCAAAGTTAAGAGTTAAATTGAT
*
63610 ATTTTATCCAAAGTTAAG-GTTCAAAATGAT
1 ATTTTATCCAAAGTTAAGAGTT-AAATTGAT
** * *
63640 ATTTTATTTAAAGTTATAGA-TCAAATTGGT
1 ATTTTATCCAAAGTTA-AGAGTTAAATTGAT
* *
63670 ATTCTATCTAAAGTT
1 ATTTTATCCAAAGTT
63685 TAGGGTCAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
29 5 0.08
30 54 0.87
31 3 0.05
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.43
Consensus pattern (30 bp):
ATTTTATCCAAAGTTAAGAGTTAAATTGAT
Found at i:63694 original size:30 final size:30
Alignment explanation
Indices: 63602--63696 Score: 102
Period size: 30 Copynumber: 3.2 Consensus size: 30
63592 TTTAAGAGTT
* * *
63602 AAATTGATATTTTATCCAAAGTTAAGGTTC
1 AAATTGATATTTTATCTAAAGTTTAGGATC
* *
63632 AAAATGATATTTTATTTAAAGTTATA-GATC
1 AAATTGATATTTTATCTAAAGTT-TAGGATC
* * *
63662 AAATTGGTATTCTATCTAAAGTTTAGGGTC
1 AAATTGATATTTTATCTAAAGTTTAGGATC
63692 AAATT
1 AAATT
63697 AAAGAACAGA
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
29 2 0.04
30 50 0.94
31 1 0.02
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (30 bp):
AAATTGATATTTTATCTAAAGTTTAGGATC
Found at i:65260 original size:3 final size:3
Alignment explanation
Indices: 65252--65283 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
65242 ATATATAAAT
65252 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
65284 TATTCTATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:68295 original size:38 final size:39
Alignment explanation
Indices: 68253--68373 Score: 90
Period size: 38 Copynumber: 2.9 Consensus size: 39
68243 GAAAATAGAT
68253 AAAAAAAATATAAAAAAAAATAATAATAACAAAAGGT-G
1 AAAAAAAATATAAAAAAAAATAATAATAACAAAAGGTAG
* *
68291 AAAAAATATTAGTATAATAATAATAATAATATAATTAA-AGAAA-ATAG
1 AAAAAA-A--A-TATAA-AA-AAAAAT-A-ATAA-TAACA-AAAGGTAG
68338 ATAAAAAAATAT--AAAAAAATAATAATAACAAAAGGT
1 A-AAAAAAATATAAAAAAAAATAATAATAACAAAAGGT
68374 TAGATTCTAA
Statistics
Matches: 65, Mismatches: 4, Indels: 28
0.67 0.04 0.29
Matches are distributed among these distances:
37 6 0.09
38 12 0.18
39 2 0.03
40 5 0.08
41 3 0.05
42 5 0.08
43 2 0.03
44 8 0.12
45 2 0.03
46 6 0.09
47 9 0.14
48 5 0.08
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.22
Consensus pattern (39 bp):
AAAAAAAATATAAAAAAAAATAATAATAACAAAAGGTAG
Found at i:68307 original size:84 final size:83
Alignment explanation
Indices: 68208--68373 Score: 282
Period size: 84 Copynumber: 2.0 Consensus size: 83
68198 AAAAGAAAGG
68208 AAAAATATTAG-T-ATAATAATAATAATATAATTAAAGAAAATAGATAAAAAAAATATAAAAAAA
1 AAAAATATTAGATAATAATAATAATAATATAATTAAAGAAAATAGAT-AAAAAAATAT--AAAAA
68271 AATAATAATAACAAAAGGTGA
63 AATAATAATAACAAAAGGTGA
68292 AAAAATATTAGTATAATAATAATAATAATATAATTAAAGAAAATAGATAAAAAAATATAAAAAAA
1 AAAAATATTAG-ATAATAATAATAATAATATAATTAAAGAAAATAGATAAAAAAATATAAAAAAA
68357 TAATAATAACAAAAGGT
65 TAATAATAACAAAAGGT
68374 TAGATTCTAA
Statistics
Matches: 79, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
84 35 0.44
86 11 0.14
87 33 0.42
ACGTcount: A:0.67, C:0.01, G:0.07, T:0.25
Consensus pattern (83 bp):
AAAAATATTAGATAATAATAATAATAATATAATTAAAGAAAATAGATAAAAAAATATAAAAAAAT
AATAATAACAAAAGGTGA
Found at i:69845 original size:24 final size:25
Alignment explanation
Indices: 69813--69870 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
69803 GATCCTGTAA
*
69813 ATAAAATAAT-AA-ATAAATTAGTAT
1 ATAATATAATCAACATAAATTA-TAT
*
69837 ATAATATAATCAATCATATATTATAT
1 ATAATATAATCAA-CATAAATTATAT
69863 ATAATATA
1 ATAATATA
69871 TTTTATAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 9 0.31
25 2 0.07
26 11 0.38
27 7 0.24
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (25 bp):
ATAATATAATCAACATAAATTATAT
Found at i:71013 original size:164 final size:164
Alignment explanation
Indices: 70438--71738 Score: 1955
Period size: 164 Copynumber: 7.9 Consensus size: 164
70428 CGACAAATAG
* * * * * * * ***
70438 CCCTTCTTGCCTTGAGCTATGTTGTAAATGATATGACCTCGAAGTTGAGTGTAATCGAACTCGGG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAG
* * *
70503 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGT
66 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGC
* * ** *
70568 GTAATCGAACTCAAAGGTCTTTTGTTGGCAGACAA
131 GTAGTCGAACTCAAAGGTC-TTTGCTAACAGATAA
* * * * * * * * *
70603 CCCTTCTAGACTTAAGTTGTGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCAAA
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAG
* * * * * * * *
70668 GGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATGTGCCCTCGAAGC
66 GGTC---T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTG-CCTTGGAGC
* * * * *
70733 TGAGTGTAATCGAACTCGAAGGTCTTTG---GCAGATAG
126 TGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAA
* * * * * * * * * ***
70769 CCCTTCTCGACTT-AGGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGG
1 CCCTTCTAGCCTTGA-GTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAA
*
70832 GGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAG
65 GGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAG
70897 CGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAA
130 CGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAA
70932 CCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAG
* * *
70997 GGTCTTCGGCAGATAGCCCTTCTTGACTTAAGCTATTCTACAAATGATGTGCCTTGGAGCTGAGC
66 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGC
71062 GTAGTCGAACTCAAAGGTCTTTGCTAACAGATAA
131 GTAGTCGAACTCAAAGGTCTTTGCTAACAGATAA
71096 CCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAG
71161 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGC
66 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGC
71226 GTAGTCGAACTCAAAGGTCTTTGCTAACAGATAA
131 GTAGTCGAACTCAAAGGTCTTTGCTAACAGATAA
71260 CCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAG
* * *
71325 GGTCTTCGGCAGATAGCCCTTCTTGACTTAAGCTATTCTACAAATGATGTGCCTTGGAGCTGAGC
66 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGC
71390 GTAGTCGAACTCAAAGGTCTTTGCTAACAGATAA
131 GTAGTCGAACTCAAAGGTCTTTGCTAACAGATAA
71424 CCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAG
71489 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGC
66 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGC
71554 GTAGTCGAACTCAAAGGTCTTTGCTAACAGATAA
131 GTAGTCGAACTCAAAGGTCTTTGCTAACAGATAA
71588 CCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAG
*
71653 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCATGGAGCTGAGC
66 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGC
*
71718 GTAGTCGAACTCGAAGGTCTT
131 GTAGTCGAACTCAAAGGTCTT
71739 GGTGGCAGGT
Statistics
Matches: 1053, Mismatches: 72, Indels: 23
0.92 0.06 0.02
Matches are distributed among these distances:
160 32 0.03
161 40 0.04
162 1 0.00
163 33 0.03
164 753 0.72
165 83 0.08
166 36 0.03
168 1 0.00
169 44 0.04
170 30 0.03
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.31
Consensus pattern (164 bp):
CCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAG
GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGC
GTAGTCGAACTCAAAGGTCTTTGCTAACAGATAA
Found at i:75179 original size:18 final size:19
Alignment explanation
Indices: 75138--75182 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
75128 AGTTAATGTG
75138 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
75157 AATGCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
75175 AATGCAAA
1 AATGCAAA
75183 ATATCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.67, C:0.09, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:76986 original size:14 final size:14
Alignment explanation
Indices: 76919--76986 Score: 50
Period size: 14 Copynumber: 4.8 Consensus size: 14
76909 AAATATTAGT
*
76919 ATAATAATAATAAT-
1 ATAATAA-AAAAATA
* *
76933 ATAATTAAAGAA-A
1 ATAATAAAAAAATA
76946 ATAGATAAAAAAATA
1 ATA-ATAAAAAAATA
* *
76961 TTAAAAAAAAAATA
1 ATAATAAAAAAATA
76975 ATAATAACAAAA
1 ATAATAA-AAAA
76987 GGTGGAAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
13 7 0.17
14 28 0.67
15 7 0.17
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (14 bp):
ATAATAAAAAAATA
Found at i:77005 original size:85 final size:83
Alignment explanation
Indices: 76905--77073 Score: 279
Period size: 88 Copynumber: 2.0 Consensus size: 83
76895 AAAAAAGAAA
76905 GGAAAAATATTAG-T-ATAATAATAATAATATAATTAAAGAAAATAGATAAAAAAATATTAAAAA
1 GGAAAAATATTAGATAATAATAATAATAATATAATTAAAGAAAATAGATAAAAAAATA-T---AA
76968 AAAAATAATAATAACAAAAGGT
62 AAAAATAATAATAACAAAAGGT
76990 GGAAAAATATTAGTATAATAATAATAATAATATAATTAAAGAAAATAGATAAAAAAATATAAAAA
1 GGAAAAATATTAG-ATAATAATAATAATAATATAATTAAAGAAAATAGATAAAAAAATATAAAAA
77055 AATAATAATAACAAAAGGT
65 AATAATAATAACAAAAGGT
77074 TAGATTCTAA
Statistics
Matches: 81, Mismatches: 0, Indels: 7
0.92 0.00 0.08
Matches are distributed among these distances:
84 24 0.30
85 13 0.16
87 2 0.02
88 42 0.52
ACGTcount: A:0.66, C:0.01, G:0.08, T:0.25
Consensus pattern (83 bp):
GGAAAAATATTAGATAATAATAATAATAATATAATTAAAGAAAATAGATAAAAAAATATAAAAAA
ATAATAATAACAAAAGGT
Found at i:78541 original size:24 final size:25
Alignment explanation
Indices: 78509--78566 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
78499 GATCCTGTAA
*
78509 ATAAAATAAT-AA-ATAAATTAGTAT
1 ATAATATAATCAACATAAATTA-TAT
*
78533 ATAATATAATCAATCATATATTATAT
1 ATAATATAATCAA-CATAAATTATAT
78559 ATAATATA
1 ATAATATA
78567 TTTTATAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 9 0.31
25 2 0.07
26 11 0.38
27 7 0.24
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (25 bp):
ATAATATAATCAACATAAATTATAT
Found at i:79651 original size:2 final size:2
Alignment explanation
Indices: 79644--79678 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
79634 CAATACATAC
79644 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
79679 TTAAACTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:80204 original size:31 final size:31
Alignment explanation
Indices: 80163--80225 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
80153 GATCAAACTG
*
80163 ATATTGTATCTAAAATTTATTAGTT-AAATTA
1 ATATTGTATCTAAAATTTAATA-TTCAAATTA
* *
80194 ATATTTTATCTAAATTTTAATATTCAAATTA
1 ATATTGTATCTAAAATTTAATATTCAAATTA
80225 A
1 A
80226 AAATCATTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 2 0.07
31 26 0.93
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (31 bp):
ATATTGTATCTAAAATTTAATATTCAAATTA
Found at i:80860 original size:29 final size:30
Alignment explanation
Indices: 80805--80865 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
80795 GCCACTTAAT
80805 TATAAATAAGTTTCTTTTTGATCATTCGAC
1 TATAAATAAGTTTCTTTTTGATCATTCGAC
* *
80835 TATAAAT-A-TTTCTTTTTTGGTTATTCGAC
1 TATAAATAAGTTTC-TTTTTGATCATTCGAC
80864 TA
1 TA
80866 CTGTATTAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 4 0.14
29 17 0.61
30 7 0.25
ACGTcount: A:0.28, C:0.11, G:0.10, T:0.51
Consensus pattern (30 bp):
TATAAATAAGTTTCTTTTTGATCATTCGAC
Found at i:83087 original size:13 final size:14
Alignment explanation
Indices: 83063--83092 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
83053 TTTAGTAATT
83063 TTAAGATTTTGAAA
1 TTAAGATTTTGAAA
83077 TTAAG-TTTTGAAA
1 TTAAGATTTTGAAA
83090 TTA
1 TTA
83093 CTCCCCCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (14 bp):
TTAAGATTTTGAAA
Found at i:91714 original size:18 final size:19
Alignment explanation
Indices: 91668--91719 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
91658 TTGAACTGGT
91668 CTGACCCGTTGACCTTGACC
1 CTGA-CCGTTGACCTTGACC
** *
91688 CAAACCGTTGACTTTGA-C
1 CTGACCGTTGACCTTGACC
91706 CTGACCGTTGACCT
1 CTGACCGTTGACCT
91720 ATATTGACTT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
18 12 0.46
19 12 0.46
20 2 0.08
ACGTcount: A:0.19, C:0.35, G:0.19, T:0.27
Consensus pattern (19 bp):
CTGACCGTTGACCTTGACC
Found at i:93051 original size:22 final size:21
Alignment explanation
Indices: 92991--93288 Score: 153
Period size: 22 Copynumber: 13.5 Consensus size: 21
92981 ATAGGATAAT
*
92991 ATATAGTATATAGTTTGGTAAAA
1 ATATA-TATATAGTTTTG-AAAA
* *
93014 A-AAATATATGGTTTTTGAAAA
1 ATATATATATAG-TTTTGAAAA
*
93035 ATATATAGTATAGTTTTTAAAA
1 ATATATA-TATAGTTTTGAAAA
* * * *
93057 ACATATGACATAATTTTCAAAA
1 ATATAT-ATATAGTTTTGAAAA
* **
93079 GCATGT-TATATAGTTTAAAAAA
1 --ATATATATATAGTTTTGAAAA
93101 ATATAATATATAGTTTTTG-AAA
1 ATAT-ATATATAG-TTTTGAAAA
*
93123 ATATATAGTATAATTTT-AAAA
1 ATATATA-TATAGTTTTGAAAA
* * *
93144 ACATATGGTGGA-ATTTTTGAAAA
1 ATATAT-AT--ATAGTTTTGAAAA
**
93167 CATAT-TATATAGTTTAAAAAA
1 -ATATATATATAGTTTTGAAAA
93188 CATATAATATATAGTTTTTG-AAA
1 -ATAT-ATATATAG-TTTTGAAAA
*
93211 ATATATAATATAGTTTTTAAAA
1 ATATAT-ATATAGTTTTGAAAA
93233 CATAGTATTATATAGTTTTG-AAA
1 -ATA-TA-TATATAGTTTTGAAAA
*
93256 ACATATATATAGTTTTTGAAAA
1 ATATATATATAG-TTTTGAAAA
* *
93278 ACATATGTATA
1 ATATATATATA
93289 TATATATATA
Statistics
Matches: 214, Mismatches: 34, Indels: 55
0.71 0.11 0.18
Matches are distributed among these distances:
20 11 0.05
21 53 0.25
22 97 0.45
23 32 0.15
24 20 0.09
25 1 0.00
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.40
Consensus pattern (21 bp):
ATATATATATAGTTTTGAAAA
Found at i:93124 original size:88 final size:89
Alignment explanation
Indices: 93016--93236 Score: 315
Period size: 88 Copynumber: 2.5 Consensus size: 89
93006 TGGTAAAAAA
* *
93016 AATATATGGTTTTTGAAAAATATATAGTATAGTTTTTAAAAACATATGACATAA-TTTTCAAAAG
1 AATATATAGTTTTTG-AAAATATATAGTATAGTTTTTAAAAACATATGACAGAATTTTTCAAAA-
*
93080 CATGTTATATAGTTTAAAAAA-ATAT
64 CATATTATATAGTTTAAAAAACATAT
* *** *
93105 AATATATAGTTTTTGAAAATATATAGTATA-ATTTTAAAAACATATGGTGGAATTTTTGAAAACA
1 AATATATAGTTTTTGAAAATATATAGTATAGTTTTTAAAAACATATGACAGAATTTTTCAAAACA
93169 TATTATATAGTTTAAAAAACATAT
66 TATTATATAGTTTAAAAAACATAT
*
93193 AATATATAGTTTTTGAAAATATATAATATAGTTTTT-AAAACATA
1 AATATATAGTTTTTGAAAATATATAGTATAGTTTTTAAAAACATA
93237 GTATTATATA
Statistics
Matches: 119, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
87 37 0.31
88 64 0.54
89 18 0.15
ACGTcount: A:0.47, C:0.04, G:0.10, T:0.40
Consensus pattern (89 bp):
AATATATAGTTTTTGAAAATATATAGTATAGTTTTTAAAAACATATGACAGAATTTTTCAAAACA
TATTATATAGTTTAAAAAACATAT
Found at i:93141 original size:45 final size:46
Alignment explanation
Indices: 92988--93292 Score: 200
Period size: 45 Copynumber: 6.8 Consensus size: 46
92978 AATATAGGAT
*
92988 AATATATAGTATATAGTTTGGT-AAAA-A-A-AATATATGGTTTTTGAAA
1 AATATATAGTATATA-TTT--TAAAAACATATAATATATAGTTTTTG-AA
* * *
93034 AATATATAGTATAGT-TTTTAAAAACATATGACATA-A--TTTTCAA
1 AATATATAGTATA-TATTTTAAAAACATATAATATATAGTTTTTGAA
** * *
93077 AA-GCAT-GTTATATAGTTTAAAAAAATATAATATATAGTTTTTGAA
1 AATATATAG-TATATATTTTAAAAACATATAATATATAGTTTTTGAA
** **
93122 AATATATAGTATA-ATTTTAAAAACATATGGTGGA-A-TTTTTGAA
1 AATATATAGTATATATTTTAAAAACATATAATATATAGTTTTTGAA
* *
93165 AACATAT--TATATAGTTTAAAAAACATATAATATATAGTTTTTGAA
1 AATATATAGTATATA-TTTTAAAAACATATAATATATAGTTTTTGAA
* *
93210 AATATATA--ATATAGTTTTTAAAACATAGTATTATATAG-TTTTGAA
1 AATATATAGTATATA-TTTTAAAAACATA-TAATATATAGTTTTTGAA
* *
93255 AACATATA-TATAGT-TTTTGAAAAACATATGTATATATA
1 AATATATAGTATA-TATTTT-AAAAACATAT-AATATATA
93293 TATATATATA
Statistics
Matches: 204, Mismatches: 33, Indels: 44
0.73 0.12 0.16
Matches are distributed among these distances:
41 6 0.03
42 23 0.11
43 35 0.17
44 10 0.05
45 77 0.38
46 46 0.23
47 7 0.03
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.40
Consensus pattern (46 bp):
AATATATAGTATATATTTTAAAAACATATAATATATAGTTTTTGAA
Found at i:93161 original size:43 final size:44
Alignment explanation
Indices: 93024--93283 Score: 201
Period size: 45 Copynumber: 5.8 Consensus size: 44
93014 AAAATATATG
* *
93024 GTTTTTGAAAAATATATAGTATAGTTTTTAAAAACATAT--GACATA
1 GTTTTTG-AAAATATATA-TATAG-TTTTAAAAACATATAATAGATA
* * * * * *
93069 -ATTTTCAAAAGCATGTTATATAG-TTTAAAAAAATATAATATATA
1 GTTTTTGAAAA-TAT-ATATATAGTTTTAAAAACATATAATAGATA
* ** *
93113 GTTTTTGAAAATATATAGTATAATTTTAAAAACATATGGTGGA-A
1 GTTTTTGAAAATATATA-TATAGTTTTAAAAACATATAATAGATA
* * *
93157 -TTTTTGAAAACATATTATATAGTTTAAAAAACATATAATATATA
1 GTTTTTGAAAATATA-TATATAGTTTTAAAAACATATAATAGATA
* * *
93201 GTTTTTGAAAATATATAATATAGTTTTTAAAACATAGTATTATATA
1 GTTTTTGAAAATATAT-ATATAGTTTTAAAAACATA-TAATAGATA
*
93247 G-TTTTGAAAACATATATATAGTTTTTGAAAAACATAT
1 GTTTTTGAAAATATATATATAG-TTTT-AAAAACATAT
93284 GTATATATAT
Statistics
Matches: 171, Mismatches: 30, Indels: 28
0.75 0.13 0.12
Matches are distributed among these distances:
42 12 0.07
43 38 0.22
44 32 0.19
45 72 0.42
46 17 0.10
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.41
Consensus pattern (44 bp):
GTTTTTGAAAATATATATATAGTTTTAAAAACATATAATAGATA
Found at i:93292 original size:2 final size:2
Alignment explanation
Indices: 93280--93329 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
93270 TTTGAAAAAC
*
93280 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
93322 AT AT AT AT
1 AT AT AT AT
93330 TGAAATCATT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:93372 original size:28 final size:31
Alignment explanation
Indices: 93341--93403 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 31
93331 GAAATCATTT
93341 TATATG-ATTTTGAAAATATA-ATATAT-TA
1 TATATGTATTTTGAAAATATATATATATATA
* * *
93369 TATA-GTTTTTTTAAAGTATATATATATATA
1 TATATGTATTTTGAAAATATATATATATATA
93399 TATAT
1 TATAT
93404 TAAGCTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
27 1 0.04
28 15 0.54
29 6 0.21
30 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (31 bp):
TATATGTATTTTGAAAATATATATATATATA
Found at i:95652 original size:29 final size:29
Alignment explanation
Indices: 95594--95654 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
95584 TCACCTTTAT
* * *
95594 AAAATTTAAAACTTTATATATATTTTTTA
1 AAAACTTAAAACTTTATATATATATATTA
*
95623 AAAACTTAAAA-TTATATATGTATATATTA
1 AAAACTTAAAACTT-TATATATATATATTA
95652 AAA
1 AAA
95655 GAAAACCCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 2 0.07
29 25 0.93
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (29 bp):
AAAACTTAAAACTTTATATATATATATTA
Found at i:98372 original size:2 final size:2
Alignment explanation
Indices: 98365--98398 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
98355 AGTGCCAAGC
98365 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
98399 CCCCACAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:101630 original size:31 final size:31
Alignment explanation
Indices: 101595--101658 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
101585 TTGCATCAAT
101595 TCAATTATACCTATTAGTTTTTCAACAAATC
1 TCAATTATACCTATTAGTTTTTCAACAAATC
*
101626 TCAATTATACTTATTAGTTTTTCAACAAATC
1 TCAATTATACCTATTAGTTTTTCAACAAATC
101657 TC
1 TC
101659 TTCATCAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.34, C:0.19, G:0.03, T:0.44
Consensus pattern (31 bp):
TCAATTATACCTATTAGTTTTTCAACAAATC
Found at i:101754 original size:13 final size:13
Alignment explanation
Indices: 101730--101776 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
101720 GCACAATCTT
*
101730 AGAAATAACTTTG
1 AGAAACAACTTTG
*
101743 ATAAACAACTTTG
1 AGAAACAACTTTG
*
101756 AGAGACAACTTTG
1 AGAAACAACTTTG
*
101769 AGACACAA
1 AGAAACAA
101777 TTCACAAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.23
Consensus pattern (13 bp):
AGAAACAACTTTG
Found at i:109515 original size:135 final size:135
Alignment explanation
Indices: 109268--109543 Score: 462
Period size: 135 Copynumber: 2.0 Consensus size: 135
109258 CTGACATGTG
* *
109268 TCCAAGTTTCTGATAACATAACATTGCAGAATCTGAACTACATGTGGCAACAGAGGCTTCTGCTT
1 TCCACGTTTCTGATAACATAACATTGCAGAATCTGAACTACATGAGGCAACAGAGGCTTCTGCTT
* * * *
109333 CTAGCAAAGTTTCTCCCTTCAGCATGTACAAGTTTGTTGTTATCTTTTCGCCTTTCAACACCACA
66 CTAGCAAAATTTCTCCCTTCAGCATGTACAAGTTTGCTATTATCTTTTCACCTTTCAACACCACA
109398 AGCGC
131 AGCGC
** *
109403 TCCACGTTTCTGATGCCATAACATTGTAGAATCTGAACTACATGAGGCAACAGAGGCTTCTGCTT
1 TCCACGTTTCTGATAACATAACATTGCAGAATCTGAACTACATGAGGCAACAGAGGCTTCTGCTT
*
109468 CTAGCAAAATTTCTCCCTTCAGCATGTACAAGTTTGCTATTATCTTTTCACCTTTCAACACCGCA
66 CTAGCAAAATTTCTCCCTTCAGCATGTACAAGTTTGCTATTATCTTTTCACCTTTCAACACCACA
109533 AGCGC
131 AGCGC
109538 TCCACG
1 TCCACG
109544 AAAAACCTTC
Statistics
Matches: 131, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
135 131 1.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.31
Consensus pattern (135 bp):
TCCACGTTTCTGATAACATAACATTGCAGAATCTGAACTACATGAGGCAACAGAGGCTTCTGCTT
CTAGCAAAATTTCTCCCTTCAGCATGTACAAGTTTGCTATTATCTTTTCACCTTTCAACACCACA
AGCGC
Found at i:117588 original size:22 final size:22
Alignment explanation
Indices: 117561--117615 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
117551 AGACAAGTTG
117561 ATAAACGAACTTGTTCATAAAT
1 ATAAACGAACTTGTTCATAAAT
117583 ATAAACGAACTTGTTCATAAAT
1 ATAAACGAACTTGTTCATAAAT
117605 ATAAACGAACT
1 ATAAACGAACT
117616 AAACACAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.29
Consensus pattern (22 bp):
ATAAACGAACTTGTTCATAAAT
Found at i:127554 original size:43 final size:44
Alignment explanation
Indices: 127486--127685 Score: 246
Period size: 44 Copynumber: 4.6 Consensus size: 44
127476 GCAAAAATGA
* * * *
127486 TAAGGTCTTATCCTTGCACATAGCAAA-AGAGCCT-AGGGAAACTG
1 TAAGG-CTTACCCTTGCACACAACAAAGAGA-CCTGGGGGAAACTG
* * *
127530 TAAGGCTTACCCTTGCACACAGC-AAGGGAAACT-GGGGAAACTG
1 TAAGGCTTACCCTTGCACACAACAAAGAG-ACCTGGGGGAAACTG
* * * *
127573 TAAGGCTTACCCTTGTACACAACAAAGGGATCTGGGGGAAACTA
1 TAAGGCTTACCCTTGCACACAACAAAGAGACCTGGGGGAAACTG
127617 TAAGGCTTACCCTTGCACACAACAAAGAGACCTGGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAACAAAGAGACCTGGGGGAAACTG
127661 TAAGGCTTACCCTTGCACACAACAA
1 TAAGGCTTACCCTTGCACACAACAA
127686 GGGAGCCTGC
Statistics
Matches: 139, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
42 2 0.01
43 52 0.37
44 85 0.61
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.19
Consensus pattern (44 bp):
TAAGGCTTACCCTTGCACACAACAAAGAGACCTGGGGGAAACTG
Found at i:127621 original size:44 final size:43
Alignment explanation
Indices: 127521--127689 Score: 250
Period size: 44 Copynumber: 3.9 Consensus size: 43
127511 AAAGAGCCTA
*
127521 GGGAAACTGTAAGGCTTACCCTTGCACACAGCAAGGGAAACT-G
1 GGGAAACTGTAAGGCTTACCCTTGCACACAACAAGGG-AACTGG
* *
127564 GGGAAACTGTAAGGCTTACCCTTGTACACAACAAAGGGATCTGG
1 GGGAAACTGTAAGGCTTACCCTTGCACACAAC-AAGGGAACTGG
* * *
127608 GGGAAACTATAAGGCTTACCCTTGCACACAACAAAGAGACCTGG
1 GGGAAACTGTAAGGCTTACCCTTGCACACAAC-AAGGGAACTGG
127652 GGGAAACTGTAAGGCTTACCCTTGCACACAACAAGGGA
1 GGGAAACTGTAAGGCTTACCCTTGCACACAACAAGGGA
127690 GCCTGCTGTA
Statistics
Matches: 115, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
43 38 0.33
44 77 0.67
ACGTcount: A:0.34, C:0.23, G:0.26, T:0.17
Consensus pattern (43 bp):
GGGAAACTGTAAGGCTTACCCTTGCACACAACAAGGGAACTGG
Found at i:127621 original size:87 final size:87
Alignment explanation
Indices: 127521--127689 Score: 261
Period size: 87 Copynumber: 1.9 Consensus size: 87
127511 AAAGAGCCTA
* * *
127521 GGGAAACTGTAAGGCTTACCCTTGCACACAGC-AAGGGAAACT-GGGGAAACTGTAAGGCTTACC
1 GGGAAACTATAAGGCTTACCCTTGCACACAACAAAGAG-AACTGGGGGAAACTGTAAGGCTTACC
*
127584 CTTGTACACAACAAAGGGATCTGG
65 CTTGCACACAAC-AAGGGATCTGG
*
127608 GGGAAACTATAAGGCTTACCCTTGCACACAACAAAGAGACCTGGGGGAAACTGTAAGGCTTACCC
1 GGGAAACTATAAGGCTTACCCTTGCACACAACAAAGAGAACTGGGGGAAACTGTAAGGCTTACCC
127673 TTGCACACAACAAGGGA
66 TTGCACACAACAAGGGA
127690 GCCTGCTGTA
Statistics
Matches: 75, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
87 39 0.52
88 36 0.48
ACGTcount: A:0.34, C:0.23, G:0.26, T:0.17
Consensus pattern (87 bp):
GGGAAACTATAAGGCTTACCCTTGCACACAACAAAGAGAACTGGGGGAAACTGTAAGGCTTACCC
TTGCACACAACAAGGGATCTGG
Found at i:132393 original size:43 final size:43
Alignment explanation
Indices: 132325--132465 Score: 176
Period size: 43 Copynumber: 3.2 Consensus size: 43
132315 GCAAAAACGA
* * *
132325 TAAGGTCTTATCCTTGCACATAGCAAAAGAGCCTAGGGAAACTG
1 TAAGG-CTTACCCTTGCACACAGCAAAAGAGCCTGGGGAAACTG
* * *
132369 TAAGGCTTACCCTTGTACACAGCAAGAGAACCTGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAAGAGCCTGGGGAAACTG
* *
132412 TAAGGCTTGCCCTTGCACACAGC-AAAGGGACCTGGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAAGAG-CCT-GGGGAAACTG
132456 TAAGGCTTAC
1 TAAGGCTTAC
132466 TCTAACCCGA
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
42 3 0.04
43 56 0.67
44 24 0.29
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.20
Consensus pattern (43 bp):
TAAGGCTTACCCTTGCACACAGCAAAAGAGCCTGGGGAAACTG
Found at i:133521 original size:30 final size:30
Alignment explanation
Indices: 133481--133583 Score: 170
Period size: 30 Copynumber: 3.4 Consensus size: 30
133471 GGACCTGGAC
* *
133481 CTATCTAGAGGTCATAAAGATCCTCGATAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
133511 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
133541 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
133571 CTGTCCATAGGTC
1 CTATCCAGAGGTC
133584 CCGAAGAACC
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 69 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:133600 original size:60 final size:59
Alignment explanation
Indices: 133463--133600 Score: 161
Period size: 60 Copynumber: 2.3 Consensus size: 59
133453 TTGTATAAAT
* * *
133463 GTCCCGAAGGACCTGG-ACCTATCTAGAGGTCATAAAGATCCTCGATAACTATCCAGAG
1 GTCCCGAAGAACCTGGTAACTATCCAGAGGTCATAAAGATCCTCGATAACTATCCAGAG
*** * * * *
133521 GTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCCATAG
1 GTCCCGAAGAACCT-GGTAACTATCCAGAGGTCATAAAGATCCTCGATAACTATCCAGAG
133581 GTCCCGAAGAACCTAGGTAA
1 GTCCCGAAGAACCT-GGTAA
133601 ACTGTCCATA
Statistics
Matches: 63, Mismatches: 15, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
58 9 0.14
59 2 0.03
60 52 0.83
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.22
Consensus pattern (59 bp):
GTCCCGAAGAACCTGGTAACTATCCAGAGGTCATAAAGATCCTCGATAACTATCCAGAG
Found at i:133607 original size:31 final size:31
Alignment explanation
Indices: 133569--133633 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
133559 GATCCTCGGT
*
133569 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACATAGGTA
* * **
133600 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATAGGTCCCGAAGAACATAGGTA
133631 AAC
1 AAC
133634 CCTCGACTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAGAACATAGGTA
Found at i:133966 original size:48 final size:48
Alignment explanation
Indices: 133907--134003 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
133897 TTCATGGGTA
133907 TATCCCATAGCATATAAAGTAACATATAAACTTGTACATGTATTCATG
1 TATCCCATAGCATATAAAGTAACATATAAACTTGTACATGTATTCATG
133955 TATCCCATAGCATATAAAGTAACATATAAACTTGTACATGTATTCATG
1 TATCCCATAGCATATAAAGTAACATATAAACTTGTACATGTATTCATG
134003 T
1 T
134004 GTATACTTTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.34
Consensus pattern (48 bp):
TATCCCATAGCATATAAAGTAACATATAAACTTGTACATGTATTCATG
Found at i:134617 original size:24 final size:20
Alignment explanation
Indices: 134564--134621 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
134554 TTCCCCTTGA
*
134564 AGTGCATCAATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
134584 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
134607 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
134622 CTACTCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:134684 original size:64 final size:63
Alignment explanation
Indices: 134609--134749 Score: 185
Period size: 64 Copynumber: 2.2 Consensus size: 63
134599 TCTTTAACAT
* *
134609 GTGCATCGATGCACTACTCATGCATCGATACACAAATTACCTTCGATGTTTTCAT-TTTAAAGG
1 GTGCATCGATGCACTACTCATGCATCGATACACAAATTACATTCGATG-TTTCATCTTTAAAGA
* * * * * *
134672 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTACTCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
134736 GTGCATCGATGCAC
1 GTGCATCGATGCAC
134750 ATTCAATATG
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
63 19 0.28
64 49 0.72
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTACTCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
Found at i:135232 original size:3 final size:3
Alignment explanation
Indices: 135224--135326 Score: 199
Period size: 3 Copynumber: 34.7 Consensus size: 3
135214 GCTTACGAGG
135224 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A-A AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
135271 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
135319 AGA AGA AG
1 AGA AGA AG
135327 GAAATAAGCT
Statistics
Matches: 99, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 97 0.98
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:136097 original size:87 final size:88
Alignment explanation
Indices: 135981--136209 Score: 340
Period size: 88 Copynumber: 2.6 Consensus size: 88
135971 AATGTCTTAT
* *
135981 CCTTGCATATAACAAA-AGAGCCT-AGGGAAACTGTAAGGCTTACCCTTGCACACAAC-AAGGGA
1 CCTTGCACACAACAAAGAGA-CCTGAGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGG-
*
136043 ACCT-GGGGAAACTGTAAGCCTCAC
64 ACCTGGGGGAAACTATAAGCCTCAC
* *
136067 CCTTGCACACAACAAAGTGACCTGAGGGAAACTGTATGGCTTACCCTTGCACACAACAAAGGGAC
1 CCTTGCACACAACAAAGAGACCTGAGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGAC
* *
136132 CTGGGGGAAACTATAAGGCTTAC
66 CTGGGGGAAACTATAAGCCTCAC
*
136155 CCTTGCACACAACAAAGAGACCTGGGGGAAACTGTAAGGCTTACCCTTGCACACA
1 CCTTGCACACAACAAAGAGACCTGAGGGAAACTGTAAGGCTTACCCTTGCACACA
136210 GTAAGGGAGC
Statistics
Matches: 129, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
86 17 0.13
87 38 0.29
88 74 0.57
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.17
Consensus pattern (88 bp):
CCTTGCACACAACAAAGAGACCTGAGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGAC
CTGGGGGAAACTATAAGCCTCAC
Found at i:136113 original size:44 final size:44
Alignment explanation
Indices: 136004--136209 Score: 317
Period size: 44 Copynumber: 4.7 Consensus size: 44
135994 AAAAGAGCCT
136004 AGGGAAACTGTAAGGCTTACCCTTGCACACAAC-AAGGGAACCTG
1 AGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGG-ACCTG
* * *
136048 -GGGAAACTGTAAGCCTCACCCTTGCACACAACAAAGTGACCTG
1 AGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTG
*
136091 AGGGAAACTGTATGGCTTACCCTTGCACACAACAAAGGGACCTG
1 AGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTG
* * *
136135 GGGGAAACTATAAGGCTTACCCTTGCACACAACAAAGAGACCTG
1 AGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTG
*
136179 GGGGAAACTGTAAGGCTTACCCTTGCACACA
1 AGGGAAACTGTAAGGCTTACCCTTGCACACA
136210 GTAAGGGAGC
Statistics
Matches: 148, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
43 35 0.24
44 113 0.76
ACGTcount: A:0.33, C:0.26, G:0.24, T:0.17
Consensus pattern (44 bp):
AGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTG
Found at i:138923 original size:17 final size:17
Alignment explanation
Indices: 138892--138925 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
138882 GGTCAACAGT
*
138892 GGTCAACGTAAGTCAAC
1 GGTCAACGCAAGTCAAC
*
138909 GGTCAACGCAGGTCAAC
1 GGTCAACGCAAGTCAAC
138926 AGTTGACCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.26, G:0.26, T:0.15
Consensus pattern (17 bp):
GGTCAACGCAAGTCAAC
Found at i:141988 original size:64 final size:63
Alignment explanation
Indices: 141915--142093 Score: 207
Period size: 64 Copynumber: 2.8 Consensus size: 63
141905 TGGAACACTT
* * * * * **
141915 AGTGCATCGGTGCACCAAGTGTGAATTGATGCATAAAATGCATTCGATGTTTGAA-AATAGCCTG
1 AGTGCATCGGTGCA-TAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAA-AACCCA
** *
141979 AGTGCATCGGTGCATTACTTGTGCATCGATGCATGAAATGCATTCGATGTTTTAATAAAACCCA
1 AGTGCATCGGTGCA-TAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCA
* *
142043 AGTGCATCGATGCATAGAGAGTGCATCGATGCATGAAATGCATTCGATGTT
1 AGTGCATCGGTGCATA-AGTGTGCATCGATGCATGAAATGCATTCGATGTT
142094 CAATTTATTC
Statistics
Matches: 98, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
63 2 0.02
64 94 0.96
65 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (63 bp):
AGTGCATCGGTGCATAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCA
Found at i:145545 original size:20 final size:21
Alignment explanation
Indices: 145520--145559 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
145510 TTTGAAAACC
145520 AGGAAATCAACATAT-TTCCA
1 AGGAAATCAACATATGTTCCA
145540 AGGAAATCAACATATGTTCC
1 AGGAAATCAACATATGTTCC
145560 TTCATAATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.25
Consensus pattern (21 bp):
AGGAAATCAACATATGTTCCA
Found at i:148717 original size:22 final size:21
Alignment explanation
Indices: 148675--148714 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
148665 AAGACTATTT
148675 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
148696 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
148715 ATAGAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:150794 original size:19 final size:19
Alignment explanation
Indices: 150745--150797 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
150735 ATAAAACCCA
* *
150745 AGTGCATTGATCCATAGAG
1 AGTGCATCGATGCATAGAG
150764 AGTGCATCGATGCATAGAG
1 AGTGCATCGATGCATAGAG
150783 AGTGCATCGATGCAT
1 AGTGCATCGATGCAT
150798 GAAATGCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (19 bp):
AGTGCATCGATGCATAGAG
Found at i:151669 original size:49 final size:49
Alignment explanation
Indices: 151597--151736 Score: 169
Period size: 49 Copynumber: 2.9 Consensus size: 49
151587 ATTTTCAAAG
* *
151597 TTGTAGACTTCTGATTTACCATGACATGTGATTCAATCTCATTTAAAAC
1 TTGTAAACTTCTGATTTACCATGACATGTGATTCAATCTCATTCAAAAC
* * *
151646 TTGTAAACTTCT-AGTTTACCATGACATATGATTTAATTTCATTCAAAAC
1 TTGTAAACTTCTGA-TTTACCATGACATGTGATTCAATCTCATTCAAAAC
* * * *
151695 TTGTGAACATATGATTTATCA--ACATGTGATTCAATCTCATTC
1 TTGTAAACTTCTGATTTACCATGACATGTGATTCAATCTCATTC
151737 GTACGTGTGT
Statistics
Matches: 77, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
47 18 0.23
48 1 0.01
49 57 0.74
50 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (49 bp):
TTGTAAACTTCTGATTTACCATGACATGTGATTCAATCTCATTCAAAAC
Found at i:153138 original size:21 final size:20
Alignment explanation
Indices: 153101--153139 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
153091 CGTAATTCAA
* *
153101 TTTTTTTTGTTCTTTTTATC
1 TTTTTTTTATTATTTTTATC
153121 TTTTTTTTATTATGTTTTA
1 TTTTTTTTATTAT-TTTTA
153140 CATAAGTGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.10, C:0.05, G:0.05, T:0.79
Consensus pattern (20 bp):
TTTTTTTTATTATTTTTATC
Found at i:153422 original size:29 final size:30
Alignment explanation
Indices: 153354--153434 Score: 103
Period size: 29 Copynumber: 2.7 Consensus size: 30
153344 GGATGAGATT
153354 GGTCGCCATGCAGTCGAGGCGAAGCATGAA
1 GGTCGCCATGCAGTCGAGGCGAAGCATGAA
* *
153384 GGTCGCCATGCAGTCG-GAGCGTA-CTTGAA
1 GGTCGCCATGCAGTCGAG-GCGAAGCATGAA
* *
153413 GGTCGCCATGCAGCCGGGGCGA
1 GGTCGCCATGCAGTCGAGGCGA
153435 TCTTGTAGTG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
29 24 0.53
30 21 0.47
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (30 bp):
GGTCGCCATGCAGTCGAGGCGAAGCATGAA
Found at i:154739 original size:10 final size:10
Alignment explanation
Indices: 154697--154748 Score: 72
Period size: 9 Copynumber: 5.3 Consensus size: 10
154687 GTTGGAAACT
154697 GGTTTTGACC
1 GGTTTTGACC
*
154707 GG-TTTAACC
1 GGTTTTGACC
154716 GGTTTTGAACC
1 GGTTTTG-ACC
154727 GGTTTTGACC
1 GGTTTTGACC
154737 GG-TTTGACC
1 GGTTTTGACC
154746 GGT
1 GGT
154749 CACGACCCGT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
9 17 0.46
10 10 0.27
11 10 0.27
ACGTcount: A:0.13, C:0.19, G:0.31, T:0.37
Consensus pattern (10 bp):
GGTTTTGACC
Found at i:154778 original size:18 final size:18
Alignment explanation
Indices: 154751--154804 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
154741 TGACCGGTCA
154751 CGACCCGTTTACCCGACC
1 CGACCCGTTTACCCGACC
*
154769 CGACCAGTTTACCCGACC
1 CGACCCGTTTACCCGACC
154787 CGACCCGTTTACCCGACC
1 CGACCCGTTTACCCGACC
154805 GTTGACCCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.19, C:0.48, G:0.17, T:0.17
Consensus pattern (18 bp):
CGACCCGTTTACCCGACC
Found at i:154800 original size:13 final size:13
Alignment explanation
Indices: 154783--154824 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
154773 CAGTTTACCC
154783 GACCCGACCCGTT
1 GACCCGACCCGTT
*
154796 TACCCGA-CCGTT
1 GACCCGACCCGTT
154808 GACCCGACCCGTT
1 GACCCGACCCGTT
154821 GACC
1 GACC
154825 GTTGACCGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.17, C:0.45, G:0.21, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:154826 original size:7 final size:7
Alignment explanation
Indices: 154816--154846 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
154806 TTGACCCGAC
154816 CCGTTGA
1 CCGTTGA
154823 CCGTTGA
1 CCGTTGA
154830 CCGTTGA
1 CCGTTGA
154837 CCGTTGA
1 CCGTTGA
154844 CCG
1 CCG
154847 GTGCTATTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.13, C:0.32, G:0.29, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:154907 original size:29 final size:29
Alignment explanation
Indices: 154846--154912 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
154836 ACCGTTGACC
* ** *
154846 GGTGCTATTCTGGGAATTAATTCAGTTTT
1 GGTGCTATTCTGAGAATTAATTCAGAATG
154875 GGTGCTATTCTGAGAATTAATTC-GAAATG
1 GGTGCTATTCTGAGAATTAATTCAG-AATG
154904 GGTGCTATT
1 GGTGCTATT
154913 TTAGTAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 1 0.03
29 32 0.97
ACGTcount: A:0.24, C:0.10, G:0.25, T:0.40
Consensus pattern (29 bp):
GGTGCTATTCTGAGAATTAATTCAGAATG
Found at i:162530 original size:13 final size:13
Alignment explanation
Indices: 162512--162553 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
162502 AACGGTCAAC
162512 GGTCAACGGGTCG
1 GGTCAACGGGTCG
162525 GGTCAAC-GGTCG
1 GGTCAACGGGTCG
*
162537 GGTAAACGGGTCG
1 GGTCAACGGGTCG
162550 GGTC
1 GGTC
162554 GGGTAAACTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.17, C:0.21, G:0.45, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:162555 original size:18 final size:18
Alignment explanation
Indices: 162532--162585 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
162522 TCGGGTCAAC
162532 GGTCGGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
*
162550 GGTCGGGTAAACTGGTCG
1 GGTCGGGTAAACGGGTCG
162568 GGTCGGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
162586 TGACCGGTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.17, C:0.17, G:0.48, T:0.19
Consensus pattern (18 bp):
GGTCGGGTAAACGGGTCG
Found at i:162585 original size:13 final size:13
Alignment explanation
Indices: 162516--162552 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
162506 GTCAACGGTC
*
162516 AACGGGTCGGGTC
1 AACGGGTCGGGTA
162529 AAC-GGTCGGGTA
1 AACGGGTCGGGTA
162541 AACGGGTCGGGT
1 AACGGGTCGGGT
162553 CGGGTAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.19, C:0.19, G:0.46, T:0.16
Consensus pattern (13 bp):
AACGGGTCGGGTA
Found at i:162618 original size:11 final size:10
Alignment explanation
Indices: 162588--162630 Score: 70
Period size: 10 Copynumber: 4.3 Consensus size: 10
162578 ACGGGTCGTG
162588 ACCGGTC-AA
1 ACCGGTCAAA
162597 ACCGGTCAAA
1 ACCGGTCAAA
162607 ACCGGTTCAAA
1 ACCGG-TCAAA
162618 ACCGGTCAAA
1 ACCGGTCAAA
162628 ACC
1 ACC
162631 AGTTTCCAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
9 7 0.22
10 15 0.47
11 10 0.31
ACGTcount: A:0.37, C:0.33, G:0.19, T:0.12
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:162621 original size:21 final size:19
Alignment explanation
Indices: 162588--162630 Score: 68
Period size: 21 Copynumber: 2.2 Consensus size: 19
162578 ACGGGTCGTG
162588 ACCGGTCAAACCGGTCAAA
1 ACCGGTCAAACCGGTCAAA
162607 ACCGGTTCAAAACCGGTCAAA
1 ACCGG-TC-AAACCGGTCAAA
162628 ACC
1 ACC
162631 AGTTTCCAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 5 0.23
20 2 0.09
21 15 0.68
ACGTcount: A:0.37, C:0.33, G:0.19, T:0.12
Consensus pattern (19 bp):
ACCGGTCAAACCGGTCAAA
Found at i:168973 original size:10 final size:10
Alignment explanation
Indices: 168931--168982 Score: 72
Period size: 9 Copynumber: 5.3 Consensus size: 10
168921 GTTGGAAACT
168931 GGTTTTGACC
1 GGTTTTGACC
*
168941 GG-TTTAACC
1 GGTTTTGACC
168950 GGTTTTGAACC
1 GGTTTTG-ACC
168961 GGTTTTGACC
1 GGTTTTGACC
168971 GG-TTTGACC
1 GGTTTTGACC
168980 GGT
1 GGT
168983 CACGACCCGT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
9 17 0.46
10 10 0.27
11 10 0.27
ACGTcount: A:0.13, C:0.19, G:0.31, T:0.37
Consensus pattern (10 bp):
GGTTTTGACC
Found at i:169012 original size:18 final size:18
Alignment explanation
Indices: 168985--169038 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
168975 TGACCGGTCA
168985 CGACCCGTTTACCCGACC
1 CGACCCGTTTACCCGACC
*
169003 CGACCAGTTTACCCGACC
1 CGACCCGTTTACCCGACC
169021 CGACCCGTTTACCCGACC
1 CGACCCGTTTACCCGACC
169039 GTTGACCCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.19, C:0.48, G:0.17, T:0.17
Consensus pattern (18 bp):
CGACCCGTTTACCCGACC
Found at i:169034 original size:13 final size:13
Alignment explanation
Indices: 169017--169058 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
169007 CAGTTTACCC
169017 GACCCGACCCGTT
1 GACCCGACCCGTT
*
169030 TACCCGA-CCGTT
1 GACCCGACCCGTT
169042 GACCCGACCCGTT
1 GACCCGACCCGTT
169055 GACC
1 GACC
169059 GTTGACCGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.17, C:0.45, G:0.21, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:169060 original size:7 final size:7
Alignment explanation
Indices: 169050--169087 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
169040 TTGACCCGAC
169050 CCGTTGA
1 CCGTTGA
169057 CCGTTGA
1 CCGTTGA
169064 CCGTTGA
1 CCGTTGA
169071 CCGTTGA
1 CCGTTGA
169078 CCGTTGA
1 CCGTTGA
169085 CCG
1 CCG
169088 GTGCTATTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.13, C:0.32, G:0.29, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:169148 original size:29 final size:29
Alignment explanation
Indices: 169087--169153 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
169077 ACCGTTGACC
* *** *
169087 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCTGAGAATTAATTCGAAATG
169116 GGTGCTATTCTGAGAATTAATTCGAAATG
1 GGTGCTATTCTGAGAATTAATTCGAAATG
169145 GGTGCTATT
1 GGTGCTATT
169154 TTAGTAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.22, C:0.10, G:0.27, T:0.40
Consensus pattern (29 bp):
GGTGCTATTCTGAGAATTAATTCGAAATG
Found at i:170984 original size:13 final size:13
Alignment explanation
Indices: 170966--171007 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
170956 AACGGTCAAC
170966 GGTCAACGGGTCG
1 GGTCAACGGGTCG
170979 GGTCAAC-GGTCG
1 GGTCAACGGGTCG
*
170991 GGTAAACGGGTCG
1 GGTCAACGGGTCG
171004 GGTC
1 GGTC
171008 GGGTAAACTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.17, C:0.21, G:0.45, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:170989 original size:7 final size:7
Alignment explanation
Indices: 170944--170974 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
170934 AGAATAGCAC
170944 CGGTCAA
1 CGGTCAA
170951 CGGTCAA
1 CGGTCAA
170958 CGGTCAA
1 CGGTCAA
170965 CGGTCAA
1 CGGTCAA
170972 CGG
1 CGG
170975 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.32, T:0.13
Consensus pattern (7 bp):
CGGTCAA
Found at i:171009 original size:18 final size:18
Alignment explanation
Indices: 170986--171037 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
170976 TCGGGTCAAC
170986 GGTCGGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
*
171004 GGTCGGGTAAACTGGTCG
1 GGTCGGGTAAACGGGTCG
171022 GGTCGGGTAAACGGGT
1 GGTCGGGTAAACGGGT
171038 AAACGGGTCG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.17, C:0.15, G:0.48, T:0.19
Consensus pattern (18 bp):
GGTCGGGTAAACGGGTCG
Found at i:171037 original size:13 final size:13
Alignment explanation
Indices: 170970--171006 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
170960 GTCAACGGTC
*
170970 AACGGGTCGGGTC
1 AACGGGTCGGGTA
170983 AAC-GGTCGGGTA
1 AACGGGTCGGGTA
170995 AACGGGTCGGGT
1 AACGGGTCGGGT
171007 CGGGTAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.19, C:0.19, G:0.46, T:0.16
Consensus pattern (13 bp):
AACGGGTCGGGTA
Found at i:171080 original size:11 final size:10
Alignment explanation
Indices: 171050--171101 Score: 72
Period size: 9 Copynumber: 5.3 Consensus size: 10
171040 ACGGGTCGTG
171050 ACCGGTC-AA
1 ACCGGTCAAA
171059 ACCGGTCAAA
1 ACCGGTCAAA
171069 ACCGGTTCAAA
1 ACCGG-TCAAA
*
171080 ACCGGT-TAA
1 ACCGGTCAAA
171089 ACCGGTCAAA
1 ACCGGTCAAA
171099 ACC
1 ACC
171102 AGTTTCCAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
9 15 0.39
10 13 0.34
11 10 0.26
ACGTcount: A:0.37, C:0.31, G:0.19, T:0.13
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:171923 original size:23 final size:23
Alignment explanation
Indices: 171897--171941 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
171887 ACTGAAGAAG
*
171897 AAAGAAATGTGAAGGAAAGGAAT
1 AAAGAAAGGTGAAGGAAAGGAAT
*
171920 AAAGAAAGGTGATGGAAAGGAA
1 AAAGAAAGGTGAAGGAAAGGAA
171942 GAGAAAGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.33, T:0.11
Consensus pattern (23 bp):
AAAGAAAGGTGAAGGAAAGGAAT
Found at i:177901 original size:15 final size:15
Alignment explanation
Indices: 177875--177924 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
177865 ACCTAGTCTC
*
177875 TTCTTC-TCCTTTTT
1 TTCTTCTTCCTTTCT
*
177889 TTCTTCTTCCTTTCC
1 TTCTTCTTCCTTTCT
*
177904 TTCTTCTCCCTTTCT
1 TTCTTCTTCCTTTCT
177919 TTCTTC
1 TTCTTC
177925 ATAACCGTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 6 0.19
15 25 0.81
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (15 bp):
TTCTTCTTCCTTTCT
Found at i:178849 original size:30 final size:30
Alignment explanation
Indices: 178815--178896 Score: 119
Period size: 30 Copynumber: 2.7 Consensus size: 30
178805 CACTACAAGA
*
178815 TCGCCCCGACTGCATGGCGACCTTCAAGCT
1 TCGCCCCGACTACATGGCGACCTTCAAGCT
*
178845 TCGCCTCGACTACATGGCGACCTTCAAGCT
1 TCGCCCCGACTACATGGCGACCTTCAAGCT
* * *
178875 TTGCCCCAACTACATGGTGACC
1 TCGCCCCGACTACATGGCGACC
178897 AATCTCATCC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.20, C:0.38, G:0.21, T:0.22
Consensus pattern (30 bp):
TCGCCCCGACTACATGGCGACCTTCAAGCT
Found at i:184061 original size:3 final size:3
Alignment explanation
Indices: 184055--184101 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
184045 AATAATAATA
184055 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
184102 AAATATAGCC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:184513 original size:80 final size:80
Alignment explanation
Indices: 184395--184563 Score: 250
Period size: 80 Copynumber: 2.1 Consensus size: 80
184385 CAACTCCTTA
* * *
184395 TGTGATGGAATCGAGCGAAATGCTGATCAAGTTCTTCTCATTATGAACTTCTTCATTGTAAATGT
1 TGTGATGGAATCGAGCGAAATGCTGAACAAGTTCTTCTCATTAAGAACTTCTTCATTGGAAATGT
184460 TGATCAACCT-CATTC
66 TGATCAACCTGCA-TC
* * * *
184475 TGTGATGGAATCGAGTGAAATGTTTAACAAGTTCTTCTCATTAAGAACTTTTTCATTGGAAATGT
1 TGTGATGGAATCGAGCGAAATGCTGAACAAGTTCTTCTCATTAAGAACTTCTTCATTGGAAATGT
*
184540 TGATCCACCTGCATC
66 TGATCAACCTGCATC
184555 TGTGATGGA
1 TGTGATGGA
184564 TTCTAACGAA
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
80 78 0.98
81 2 0.03
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.36
Consensus pattern (80 bp):
TGTGATGGAATCGAGCGAAATGCTGAACAAGTTCTTCTCATTAAGAACTTCTTCATTGGAAATGT
TGATCAACCTGCATC
Found at i:186313 original size:54 final size:54
Alignment explanation
Indices: 186207--186668 Score: 445
Period size: 54 Copynumber: 8.5 Consensus size: 54
186197 CAAACTTGGT
* * * *
186207 TTCTTCAAAAATTCATTTACAGTTATCATAAAGAAACCCCTAAAAATTAGGCTTAGC
1 TTCTTTAAAAATTCATTTAAAG--A-CATCAAGAAACCCCTAAAAATCAGGCTTAGC
* * *
186264 TTCTTTAAAAATTCATTTAAAGACATTAACAAACCCCTGAAAATCAGGCTTAGC
1 TTCTTTAAAAATTCATTTAAAGACATCAAGAAACCCCTAAAAATCAGGCTTAGC
* * * * *
186318 -TCATTTCTAAAATTCATTTGAAGATATCAAGAAAGCCCTGAAAATCAGGCTTAGC
1 TTC-TTT-AAAAATTCATTTAAAGACATCAAGAAACCCCTAAAAATCAGGCTTAGC
* * *
186373 -TCATTTAAAAATTCATTTAAAAACATCAAG-AACCACTAAAAATTAGGCTTAGC
1 TTC-TTTAAAAATTCATTTAAAGACATCAAGAAACCCCTAAAAATCAGGCTTAGC
* * *
186426 TTCTTTCAAAATTCATTTAAAAACATCAAGAAACCCCTAAAAATCAGGCTTATC
1 TTCTTTAAAAATTCATTTAAAGACATCAAGAAACCCCTAAAAATCAGGCTTAGC
* * * * * * *
186480 TCCTTTAAAAATTCATTTGAAGACATCAAGAAACGCTTGAAAATCATG-TATAAC
1 TTCTTTAAAAATTCATTTAAAGACATCAAGAAACCCCTAAAAATCAGGCT-TAGC
* * *
186534 TCCTTTAAAAATTCATTTGAAA-ACATCAAG-AACCTCTAAAAAGT-AGGCTTAGA
1 TTCTTTAAAAATTCATTT-AAAGACATCAAGAAACCCCTAAAAA-TCAGGCTTAGC
* ** * * *
186587 TTCTTTCAAAATTCATTTGAAA-ACATCAAGAAACCTTTGAAAATTAGTCTTAGC
1 TTCTTTAAAAATTCATTT-AAAGACATCAAGAAACCCCTAAAAATCAGGCTTAGC
** *
186641 TTCTTTCTAAATTCATTTAAAGATATCA
1 TTCTTTAAAAATTCATTTAAAGACATCA
186669 TAATATTTGG
Statistics
Matches: 345, Mismatches: 49, Indels: 25
0.82 0.12 0.06
Matches are distributed among these distances:
53 92 0.27
54 182 0.53
55 51 0.15
57 20 0.06
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.31
Consensus pattern (54 bp):
TTCTTTAAAAATTCATTTAAAGACATCAAGAAACCCCTAAAAATCAGGCTTAGC
Found at i:186472 original size:107 final size:106
Alignment explanation
Indices: 186237--186661 Score: 444
Period size: 107 Copynumber: 3.9 Consensus size: 106
186227 AGTTATCATA
* * * * *
186237 AAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTAAAGACATTAACAAACCCCT
1 AAGAAACCCCTAAAAATCAGGCTTAGC-TCTTTAAAAATTCATTTAAAAACATCAA-GAACCACT
* * *
186302 GAAAATCAGGCTTAGC-TCATTTCTAAAATTCATTTGAAGATATC
64 GAAAATCAGGCTTAGCTTC-TTTC-AAAATTCATTTAAAAACATC
* * *
186346 AAGAAAGCCCTGAAAATCAGGCTTAGCTCATTTAAAAATTCATTTAAAAACATCAAGAACCACTA
1 AAGAAACCCCTAAAAATCAGGCTTAGCTC-TTTAAAAATTCATTTAAAAACATCAAGAACCACTG
*
186411 AAAATTAGGCTTAGCTTCTTTCAAAATTCATTTAAAAACATC
65 AAAATCAGGCTTAGCTTCTTTCAAAATTCATTTAAAAACATC
* * * * *
186453 AAGAAACCCCTAAAAATCAGGCTTATCTCCTTTAAAAATTCATTTGAAGACATCAAGAAACGCTT
1 AAGAAACCCCTAAAAATCAGGCTTAGCT-CTTTAAAAATTCATTTAAAAACATCAAGAACCAC-T
* * * * *
186518 GAAAATCATG-TATAACTCCTTTAAAAATTCATTTGAAAACATC
64 GAAAATCAGGCT-TAGCTTCTTTCAAAATTCATTTAAAAACATC
* * * * **
186561 AAG-AACCTCTAAAAAGT-AGGCTTAGATTCTTTCAAAATTCATTTGAAAACATCAAGAAACCTT
1 AAGAAACCCCTAAAAA-TCAGGCTTAG-CTCTTTAAAAATTCATTTAAAAACATCAAG-AACCAC
* * *
186624 TGAAAATTAGTCTTAGCTTCTTTCTAAATTCATTTAAA
63 TGAAAATCAGGCTTAGCTTCTTTCAAAATTCATTTAAA
186662 GATATCATAA
Statistics
Matches: 265, Mismatches: 42, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
107 144 0.54
108 71 0.27
109 50 0.19
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.30
Consensus pattern (106 bp):
AAGAAACCCCTAAAAATCAGGCTTAGCTCTTTAAAAATTCATTTAAAAACATCAAGAACCACTGA
AAATCAGGCTTAGCTTCTTTCAAAATTCATTTAAAAACATC
Found at i:186655 original size:161 final size:160
Alignment explanation
Indices: 186241--186668 Score: 565
Period size: 161 Copynumber: 2.6 Consensus size: 160
186231 ATCATAAAGA
* * * *
186241 AACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTTAAAGACATTAACAAACCCCTGAAA
1 AACCACTAAAAATTAGGCTTAGCTTCTTTCAAAATTCATTTAAA-ACATCAAGAAACCCCTGAAA
186306 ATCAGGCTTAGC-TCATTTCTAAAATTCATTTGAAGATATCAAGAAAGCCCTGAAAATCAGGCTT
65 ATCAGGCTTAGCTTC-TTTCT-AAATTCATTTGAAGATATCAAGAAAGCCCTGAAAATCAGGCTT
*
186370 AGCTCATTTAAAAATTCATTTAAAAACATCAAG
128 AACTCATTTAAAAATTCATTTAAAAACATCAAG
*
186403 AACCACTAAAAATTAGGCTTAGCTTCTTTCAAAATTCATTTAAAAACATCAAGAAACCCCTAAAA
1 AACCACTAAAAATTAGGCTTAGCTTCTTTCAAAATTCATTT-AAAACATCAAGAAACCCCTGAAA
* * ** * * *
186468 ATCAGGCTTATCTCCTTTAAAAATTCATTTGAAGACATCAAGAAA-CGCTTGAAAATCATG-TAT
65 ATCAGGCTTAGCTTCTTTCTAAATTCATTTGAAGATATCAAGAAAGC-CCTGAAAATCAGGCT-T
* *
186531 AACTCCTTTAAAAATTCATTTGAAAACATCAAG
128 AACTCATTTAAAAATTCATTTAAAAACATCAAG
* * * **
186564 AACCTCTAAAAAGTAGGCTTAGATTCTTTCAAAATTCATTTGAAAACATCAAGAAACCTTTGAAA
1 AACCACTAAAAATTAGGCTTAGCTTCTTTCAAAATTCATTT-AAAACATCAAGAAACCCCTGAAA
* * *
186629 ATTAGTCTTAGCTTCTTTCTAAATTCATTTAAAGATATCA
65 ATCAGGCTTAGCTTCTTTCTAAATTCATTTGAAGATATCA
186669 TAATATTTGG
Statistics
Matches: 232, Mismatches: 30, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
160 2 0.01
161 156 0.67
162 70 0.30
163 4 0.02
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (160 bp):
AACCACTAAAAATTAGGCTTAGCTTCTTTCAAAATTCATTTAAAACATCAAGAAACCCCTGAAAA
TCAGGCTTAGCTTCTTTCTAAATTCATTTGAAGATATCAAGAAAGCCCTGAAAATCAGGCTTAAC
TCATTTAAAAATTCATTTAAAAACATCAAG
Found at i:187992 original size:28 final size:28
Alignment explanation
Indices: 187960--188019 Score: 95
Period size: 28 Copynumber: 2.1 Consensus size: 28
187950 TTAAGCTGAC
187960 TTGGGAAGGTAGA-GTGTTTCAGGTTAAT
1 TTGGGAAGGTA-ATGTGTTTCAGGTTAAT
*
187988 TTGGGGAGGTAATGTGTTTCAGGTTAAT
1 TTGGGAAGGTAATGTGTTTCAGGTTAAT
188016 TTGG
1 TTGG
188020 TTAAGGTCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 1 0.03
28 29 0.97
ACGTcount: A:0.22, C:0.03, G:0.37, T:0.38
Consensus pattern (28 bp):
TTGGGAAGGTAATGTGTTTCAGGTTAAT
Found at i:188718 original size:10 final size:10
Alignment explanation
Indices: 188703--188727 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
188693 TGCACAACAT
188703 TTTAGTTGTA
1 TTTAGTTGTA
188713 TTTAGTTGTA
1 TTTAGTTGTA
188723 TTTAG
1 TTTAG
188728 GTTATATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (10 bp):
TTTAGTTGTA
Found at i:190851 original size:17 final size:18
Alignment explanation
Indices: 190829--190874 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
190819 ATTATCAGTA
190829 GTCCTTCGGG-CA-TAGTG
1 GTCCTTCGGGACAGT-GTG
*
190846 GTCCTTTGGGACAGTGTG
1 GTCCTTCGGGACAGTGTG
*
190864 GTTCTTCGGGA
1 GTCCTTCGGGA
190875 AAAATATTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 9 0.38
18 14 0.58
19 1 0.04
ACGTcount: A:0.11, C:0.20, G:0.37, T:0.33
Consensus pattern (18 bp):
GTCCTTCGGGACAGTGTG
Found at i:197719 original size:18 final size:18
Alignment explanation
Indices: 197678--197730 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
197668 AGGGATTATC
**
197678 AGTGGTCCTTTAGGACAT
1 AGTGGTCCTTCGGGACAT
* *
197696 ATTGGTCCTTCGGGATAT
1 AGTGGTCCTTCGGGACAT
197714 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
197731 AATATTTAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.32
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:211084 original size:15 final size:16
Alignment explanation
Indices: 211064--211096 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
211054 ACTCTCCTTA
*
211064 TGGTATCGGTAC-CCT
1 TGGTATCGATACTCCT
211079 TGGTATCGATACTCCT
1 TGGTATCGATACTCCT
211095 TG
1 TG
211097 AATATCTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.36
Consensus pattern (16 bp):
TGGTATCGATACTCCT
Found at i:214985 original size:21 final size:21
Alignment explanation
Indices: 214961--215038 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
214951 CCTTCAGGAT
*
214961 ATATATGTAATCCTTTGGAAC
1 ATATATGTGATCCTTTGGAAC
* * * *
214982 ATATATGCGGTTCTTTGGGAC
1 ATATATGTGATCCTTTGGAAC
* * * *
215003 ACATATTTGGTCCTTTGGAAT
1 ATATATGTGATCCTTTGGAAC
215024 ATATATGTGATCCTT
1 ATATATGTGATCCTT
215039 AAGGAGTGGT
Statistics
Matches: 43, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.41
Consensus pattern (21 bp):
ATATATGTGATCCTTTGGAAC
Found at i:215095 original size:23 final size:21
Alignment explanation
Indices: 215044--215103 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
215034 TCCTTAAGGA
*
215044 GTGGTCCTTCGAGACATATAT
1 GTGGTCCTTCGAGACATATAC
215065 GTGGTCCTTCTG-GACATATCTAC
1 GTGGTCCTTC-GAGACATA--TAC
*
215088 GTGGTCCTTCGCGACA
1 GTGGTCCTTCGAGACA
215104 AAATCTATGT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
21 16 0.47
22 2 0.06
23 16 0.47
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (21 bp):
GTGGTCCTTCGAGACATATAC
Found at i:217421 original size:18 final size:18
Alignment explanation
Indices: 217371--217423 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
217361 TAAGACTACT
* *
217371 ATGTCCCGAAGGAACACT
1 ATGTCCCGAAGGACCACA
* *
217389 TTGTCTCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
*
217407 ATGTCCCGAATGACCAC
1 ATGTCCCGAAGGACCAC
217424 TGATATTCCC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACA
Found at i:219745 original size:31 final size:31
Alignment explanation
Indices: 219707--219776 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
219697 ACAAATCGTA
219707 TCTTTCCTTTCATGTTCACATATTCTTTTTT
1 TCTTTCCTTTCATGTTCACATATTCTTTTTT
*
219738 TCTTTCCTTTCTTGTTCACATATTCTTTTTT
1 TCTTTCCTTTCATGTTCACATATTCTTTTTT
219769 TCTTTCCT
1 TCTTTCCT
219777 ATCACTTATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.10, C:0.24, G:0.03, T:0.63
Consensus pattern (31 bp):
TCTTTCCTTTCATGTTCACATATTCTTTTTT
Found at i:221591 original size:18 final size:18
Alignment explanation
Indices: 221512--221600 Score: 88
Period size: 18 Copynumber: 4.9 Consensus size: 18
221502 GCGTAAAATT
*
221512 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
**
221530 TGTCCTAAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* * * *
221548 TCTCCAGAAAGACCACTT
1 TGTCCCGAAGGACCACTA
* *
221566 TATACCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
221584 TGTCCCGAAAGACCACT
1 TGTCCCGAAGGACCACT
221601 GATAATCCCT
Statistics
Matches: 55, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 55 1.00
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:225685 original size:18 final size:17
Alignment explanation
Indices: 225664--225724 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 17
225654 TGTCCCGTAT
*
225664 GACCACTATGTCTTGAAG
1 GACCACTATGTC-CGAAG
*
225682 GACCACTTTGTACCGAAG
1 GACCACTATGT-CCGAAG
*
225700 GACCACCATGTCCCGAAG
1 GACCACTATGT-CCGAAG
225718 GACCACT
1 GACCACT
225725 GATAATCCCT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
18 35 0.97
19 1 0.03
ACGTcount: A:0.28, C:0.31, G:0.21, T:0.20
Consensus pattern (17 bp):
GACCACTATGTCCGAAG
Found at i:226157 original size:12 final size:13
Alignment explanation
Indices: 226133--226161 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
226123 GCTCCAATAG
226133 CATACTATTATTA
1 CATACTATTATTA
226146 CATACT-TTATTA
1 CATACTATTATTA
226158 CATA
1 CATA
226162 ACCATATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.45
Consensus pattern (13 bp):
CATACTATTATTA
Found at i:232634 original size:2 final size:2
Alignment explanation
Indices: 232627--232667 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
232617 CATTCAAATC
232627 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
232668 GTACCTTTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:239186 original size:17 final size:18
Alignment explanation
Indices: 239142--239186 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
239132 TTGATATTGA
*
239142 TAAAT-ATTAATTTAAAT
1 TAAATAATTATTTTAAAT
239159 TAAATAA-TATTTTAAA-
1 TAAATAATTATTTTAAAT
*
239175 TAATTAATTATT
1 TAAATAATTATT
239187 AAATTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 6 0.25
17 17 0.71
18 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAAATAATTATTTTAAAT
Found at i:240721 original size:21 final size:21
Alignment explanation
Indices: 240680--240723 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
240670 ATTGGGCTTG
* *
240680 TATATATTTTTTATTATTATT
1 TATATATTATTTAATATTATT
240701 TATATATGTATTTAATA-TATT
1 TATATAT-TATTTAATATTATT
240722 TA
1 TA
240724 ATAATAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TATATATTATTTAATATTATT
Found at i:240730 original size:3 final size:3
Alignment explanation
Indices: 240722--240787 Score: 123
Period size: 3 Copynumber: 22.0 Consensus size: 3
240712 TTAATATATT
*
240722 TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
240770 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
240788 ATCAATATGG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:241237 original size:113 final size:113
Alignment explanation
Indices: 241040--241657 Score: 1075
Period size: 113 Copynumber: 5.5 Consensus size: 113
241030 ATAAGCTCTT
* * *
241040 GATGAGTTCTTCTCATTATGAACTTC--TCTGGAAAA-ATTGA-CCAATCAAGTGATGGATTTGA
1 GATGAGTTCTTCTCATTATGAAC-TCGAACTGGAAAAGA-TAATCC-ATCAAGTGATAGATTTGA
*
241101 GCAAAA-ATCTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCA
63 GCAAAAGGT-TGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCA
* * *
241152 GATGAGTTCTTCTTATTATGAACTCGAACTGGAAAAGCTAATCTATCAAGTGATAGATTTGAGCA
1 GATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAGCA
241217 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCA
66 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCA
241265 GATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAGCA
1 GATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAGCA
*
241330 AAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCATCCTTCTTCA
66 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCA
241378 GATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAGCA
1 GATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAGCA
241443 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCA
66 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCA
241491 GATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAGCA
1 GATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAGCA
*
241556 AAAGGTTGAACAAATTCTTCTCATTATAAACTTCTTCATCCTTCTTCA
66 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCA
*
241604 GATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCACCAAGTGAT
1 GATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGAT
241658 GAATTTAAAT
Statistics
Matches: 487, Mismatches: 14, Indels: 9
0.95 0.03 0.02
Matches are distributed among these distances:
111 2 0.00
112 22 0.05
113 461 0.95
114 2 0.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (113 bp):
GATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAGCA
AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCA
Found at i:242660 original size:167 final size:166
Alignment explanation
Indices: 242382--243182 Score: 1325
Period size: 167 Copynumber: 4.8 Consensus size: 166
242372 CCTACCGAAT
* * *
242382 CAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATGAGTACATTGCATTTGTTCC-ATTT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT-CA--TCTTCCAATTT
* * *
242446 TAAGGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGATC
63 CAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGC
* *
242511 ACATTCATCTTTCAATTTCAATGATTTGATTCTGCCAAAC
128 ACATTCATCTTCCAAATTCAATGA-TTGATTCTGCCAAAC
* * *
242551 CAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCGTCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATTTCAA
*
242616 TGATTGGTTCTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACA
66 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACA
* *
242681 TTCGTCTTCCAAATTCAATGATTGGTTCTGCCAAAC
131 TTCATCTTCCAAATTCAATGATTGATTCTGCCAAAC
* *
242717 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCGTCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATTTCAA
242782 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACA
66 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACA
* * *
242847 TTCATCTTTCAATTTCAATGATTTGATTTTGCCAAAC
131 TTCATCTTCCAAATTCAATGA-TTGATTCTGCCAAAC
*
242884 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAATTTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATTTCAA
*
242949 TGATTTGATTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAC
66 TGA-TTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAC
*
243014 ATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAAC
130 ATTCATCTTCCAAATTCAATGATTGATTCTGCCAAAC
*
243051 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCAATTTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATTTCAA
*
243116 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGTACA
66 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACA
243181 TT
131 TT
243183 GCATTTGTTC
Statistics
Matches: 596, Mismatches: 33, Indels: 9
0.93 0.05 0.01
Matches are distributed among these distances:
166 227 0.38
167 242 0.41
168 81 0.14
169 46 0.08
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (166 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAATTTCAA
TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACA
TTCATCTTCCAAATTCAATGATTGATTCTGCCAAAC
Done.