Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007905.1 Hibiscus syriacus cultivar Beakdansim tig00110299_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: 2946335
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 14
Found at i:5224 original size:23 final size:23
Alignment explanation
Indices: 5168--5232 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 23
5158 CAGCGACCGA
*
5168 AGAAAGAA-AAAGGAGGAAGAAAG
1 AGAAA-AAGAAAGCAGGAAGAAAG
*
5191 ATAAAAAGAAAGCAGGAAGAAAG
1 AGAAAAAGAAAGCAGGAAGAAAG
5214 AGGAAATGAA-AAAGCAGGA
1 A-GAAA--AAGAAAGCAGGA
5233 TCCCTTTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
22 2 0.06
23 19 0.54
24 3 0.09
25 9 0.26
26 2 0.06
ACGTcount: A:0.63, C:0.03, G:0.31, T:0.03
Consensus pattern (23 bp):
AGAAAAAGAAAGCAGGAAGAAAG
Found at i:5573 original size:7 final size:7
Alignment explanation
Indices: 5561--5602 Score: 84
Period size: 7 Copynumber: 6.0 Consensus size: 7
5551 CATGTCCATG
5561 CTTCACA
1 CTTCACA
5568 CTTCACA
1 CTTCACA
5575 CTTCACA
1 CTTCACA
5582 CTTCACA
1 CTTCACA
5589 CTTCACA
1 CTTCACA
5596 CTTCACA
1 CTTCACA
5603 GGTCATCAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.29, C:0.43, G:0.00, T:0.29
Consensus pattern (7 bp):
CTTCACA
Found at i:8811 original size:2 final size:2
Alignment explanation
Indices: 8806--8830 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8796 ACACACACAC
8806 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
8831 CCCCCATCCC
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:9071 original size:24 final size:24
Alignment explanation
Indices: 9016--9083 Score: 77
Period size: 24 Copynumber: 2.8 Consensus size: 24
9006 AATTCAAAAT
9016 AGATATCAGAACAGAA-TCTAGATC
1 AGATATCAGAACAGAATTC-AGATC
* *
9040 AGAAATCAGAACAGAATTCAGGTC
1 AGATATCAGAACAGAATTCAGATC
*
9064 ATG-TATCAGAACATAATTCA
1 A-GATATCAGAACAGAATTCA
9084 AGTCGGAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
24 35 0.92
25 3 0.08
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.22
Consensus pattern (24 bp):
AGATATCAGAACAGAATTCAGATC
Found at i:9095 original size:24 final size:25
Alignment explanation
Indices: 9020--9097 Score: 74
Period size: 24 Copynumber: 3.2 Consensus size: 25
9010 CAAAATAGAT
*
9020 ATCAGAACAGAA-TCTAGATCA-GAA
1 ATCAGAACAGAATTCAAG-TCAGGAA
* * *
9044 ATCAGAACAGAATTCAGGTCATG-T
1 ATCAGAACAGAATTCAAGTCAGGAA
*
9068 ATCAGAACATAATTCAAGTC-GGAA
1 ATCAGAACAGAATTCAAGTCAGGAA
9092 ATCAGA
1 ATCAGA
9098 TAAAATATTT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
23 1 0.02
24 39 0.89
25 4 0.09
ACGTcount: A:0.45, C:0.17, G:0.18, T:0.21
Consensus pattern (25 bp):
ATCAGAACAGAATTCAAGTCAGGAA
Found at i:17496 original size:18 final size:18
Alignment explanation
Indices: 17470--17504 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
17460 CCTATTTGAT
*
17470 TGTTTATCTTCTTTGAGG
1 TGTTCATCTTCTTTGAGG
17488 TGTTCATCTTCTTTGAG
1 TGTTCATCTTCTTTGAG
17505 TTGATGAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.54
Consensus pattern (18 bp):
TGTTCATCTTCTTTGAGG
Found at i:18569 original size:16 final size:16
Alignment explanation
Indices: 18548--18581 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
18538 TTACTATTCA
*
18548 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
18564 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
18580 CG
1 CG
18582 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:19349 original size:15 final size:16
Alignment explanation
Indices: 19331--19363 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
19321 GTGGCAGATC
19331 AAAATCCAG-ACGGGA
1 AAAATCCAGAACGGGA
*
19346 AAAATCTAGAACGGGA
1 AAAATCCAGAACGGGA
19362 AA
1 AA
19364 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.15, G:0.24, T:0.09
Consensus pattern (16 bp):
AAAATCCAGAACGGGA
Found at i:28153 original size:17 final size:17
Alignment explanation
Indices: 28124--28165 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
28114 CTTTTAAGGG
*
28124 GCATGGACTTATATGTA
1 GCATGGACATATATGTA
*
28141 GCTTGGACATATATGTA
1 GCATGGACATATATGTA
28158 GCATGGAC
1 GCATGGAC
28166 GAACCAGGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (17 bp):
GCATGGACATATATGTA
Found at i:38309 original size:60 final size:60
Alignment explanation
Indices: 38206--38323 Score: 141
Period size: 60 Copynumber: 2.0 Consensus size: 60
38196 CTGATGATAT
* *
38206 GATGTTGCTTTGTTGAGTTTCCTGACTATTAAAAATTACAAAATGATC-CTCTGACTATAG
1 GATGTTACTTTGTTGAGTTCCCTGACTATTAAAAATTACAAAATGATCAC-CTGACTATAG
* * * * *
38266 GATGTTACTTTTTTGAG-TCCCTCGACTATTGAAAGTTATAAAATGGTCACCTGACTAT
1 GATGTTACTTTGTTGAGTTCCCT-GACTATTAAAAATTACAAAATGATCACCTGACTAT
38324 TCATATGTTC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
59 4 0.08
60 44 0.90
61 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (60 bp):
GATGTTACTTTGTTGAGTTCCCTGACTATTAAAAATTACAAAATGATCACCTGACTATAG
Found at i:42644 original size:64 final size:63
Alignment explanation
Indices: 42543--42706 Score: 183
Period size: 64 Copynumber: 2.5 Consensus size: 63
42533 TCCCTTAACG
* * *
42543 GGTGCATCGATGCACTACC-CATGCATCGGTGCATAAAT-CCTATTCGATGTT-TGTATTTTAAG
1 GGTGCATCGATGCACT-CCTTATGCATCGATGCATAAATGCC-ATTCGATGTTAT-TAATTTAA-
42605 CA-
62 -AT
* *
42607 GGTGCATCGATGCACTCCTTATGCATCGATGGATAAATGGCATTCGATGTTCAATTAATTTAAAT
1 GGTGCATCGATGCACTCCTTATGCATCGATGCATAAATGCCATTCGATGTT--ATTAATTTAAAT
42672 GAGTGCATCGATGCACTCCTTATGCATCGATGCAT
1 G-GTGCATCGATGCACTCCTTATGCATCGATGCAT
42707 CTTCAACAAA
Statistics
Matches: 87, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
63 2 0.02
64 43 0.49
65 2 0.02
66 39 0.45
67 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (63 bp):
GGTGCATCGATGCACTCCTTATGCATCGATGCATAAATGCCATTCGATGTTATTAATTTAAAT
Found at i:52832 original size:24 final size:24
Alignment explanation
Indices: 52805--52850 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
52795 ACAAACATCT
*
52805 TAAAAAAAATAAATGAACACGATA
1 TAAAAAAAATAAACGAACACGATA
**
52829 TAAAAAATTTAAACGAACACGA
1 TAAAAAAAATAAACGAACACGA
52851 ACCAATCATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.63, C:0.11, G:0.09, T:0.17
Consensus pattern (24 bp):
TAAAAAAAATAAACGAACACGATA
Found at i:66930 original size:23 final size:23
Alignment explanation
Indices: 66884--66930 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
66874 GGCCATTTTG
* * *
66884 ACACACAAAAATTAAGGGCTAAA
1 ACACACAAAAAATAAGGACCAAA
*
66907 ACACTCAAAAAATAAGGACCAAA
1 ACACACAAAAAATAAGGACCAAA
66930 A
1 A
66931 TAATCATTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.60, C:0.19, G:0.11, T:0.11
Consensus pattern (23 bp):
ACACACAAAAAATAAGGACCAAA
Found at i:67507 original size:12 final size:12
Alignment explanation
Indices: 67490--67517 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
67480 CAAATATGTA
67490 CAATTAATAGTG
1 CAATTAATAGTG
67502 CAATTAATAGTG
1 CAATTAATAGTG
67514 CAAT
1 CAAT
67518 CTGGGATCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (12 bp):
CAATTAATAGTG
Found at i:67710 original size:63 final size:63
Alignment explanation
Indices: 67611--67738 Score: 229
Period size: 63 Copynumber: 2.0 Consensus size: 63
67601 GGTGACATTC
* * *
67611 CACCCCACTCAATCTCGTCACATTCGTTTTGATATCAAATGTCGCTAGTCATTATTCTTTTCT
1 CACCCCACTCAATATCGTCACATTAGTTTTGATATCAAATGTCGCTAGTCATTATCCTTTTCT
67674 CACCCCACTCAATATCGTCACATTAGTTTTGATATCAAATGTCGCTAGTCATTATCCTTTTCT
1 CACCCCACTCAATATCGTCACATTAGTTTTGATATCAAATGTCGCTAGTCATTATCCTTTTCT
67737 CA
1 CA
67739 AAAACACATC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.24, C:0.28, G:0.09, T:0.38
Consensus pattern (63 bp):
CACCCCACTCAATATCGTCACATTAGTTTTGATATCAAATGTCGCTAGTCATTATCCTTTTCT
Found at i:72709 original size:19 final size:20
Alignment explanation
Indices: 72685--72735 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
72675 AATGACCAAT
72685 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
72704 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
72724 AAAATCGCAACG
1 AAAATCGCAACG
72736 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:72729 original size:20 final size:20
Alignment explanation
Indices: 72685--72982 Score: 170
Period size: 20 Copynumber: 14.6 Consensus size: 20
72675 AATGACCAAT
* *
72685 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
72704 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
72724 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
72744 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
72764 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
72785 AAGTTCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* *
72805 AAGAGAATCGCAATGCGATTTAT
1 -A-A-AATCGCAACGCGATTTAG
* * * *
72828 AGAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
72848 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
72868 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* * *
72888 AGAGTCGCAACGCGTTTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
72911 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
72931 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
72951 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
72971 AAAATCGCAACG
1 AAAATCGCAACG
72983 GTCAAAAGAA
Statistics
Matches: 224, Mismatches: 43, Indels: 23
0.77 0.15 0.08
Matches are distributed among these distances:
19 17 0.08
20 162 0.72
21 15 0.07
22 2 0.01
23 28 0.12
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:72859 original size:40 final size:40
Alignment explanation
Indices: 72806--72980 Score: 224
Period size: 40 Copynumber: 4.3 Consensus size: 40
72796 GCGATTTAGA
72806 AGAGAATCGCAATGCGATTTATAGAATCGCAATGCGATTG
1 AGAGAATCGCAATGCGATTTATAGAATCGCAATGCGATTG
*
72846 ATAGAATCGCAATGCGATTTATAGAATCGCAATGCGATTG
1 AGAGAATCGCAATGCGATTTATAGAATCGCAATGCGATTG
* * * * *
72886 AGAGAGTCGCAACGCGTTTTAGAAGAAAATCGCAATGCGACTG
1 AGAGAATCGCAATGCGATTTA-TAG--AATCGCAATGCGATTG
* * * *
72929 AGAGAATCGCAATGCGATTGAGAGAATCGCAACGCGATTT
1 AGAGAATCGCAATGCGATTTATAGAATCGCAATGCGATTG
*
72969 AGAAAATCGCAA
1 AGAGAATCGCAA
72981 CGGTCAAAAG
Statistics
Matches: 116, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
40 80 0.69
41 2 0.02
42 2 0.02
43 32 0.28
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.22
Consensus pattern (40 bp):
AGAGAATCGCAATGCGATTTATAGAATCGCAATGCGATTG
Found at i:72917 original size:83 final size:83
Alignment explanation
Indices: 72830--72982 Score: 234
Period size: 83 Copynumber: 1.8 Consensus size: 83
72820 CGATTTATAG
* * * * * * *
72830 AATCGCAATGCGATTGATAGAATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAGTCG
1 AATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATCGCAACGCGATTGAGAAAATCG
72895 CAACGCGTTTTAGAAGAA
66 CAACGCGTTTTAGAAGAA
*
72913 AATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATCGCAACGCGATTTAGAAAATCG
1 AATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATCGCAACGCGATTGAGAAAATCG
72978 CAACG
66 CAACG
72983 GTCAAAAGAA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
83 62 1.00
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (83 bp):
AATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATCGCAACGCGATTGAGAAAATCG
CAACGCGTTTTAGAAGAA
Found at i:72925 original size:103 final size:103
Alignment explanation
Indices: 72789--72980 Score: 303
Period size: 103 Copynumber: 1.9 Consensus size: 103
72779 GCTTCCAAGT
* * * * *
72789 TCGCAACGCGATTTAGAAGAGAATCGCAATGCGATTTATAGAATCGCAATGCGATTGATAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATC
* * *
72854 GCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAG
66 GCAACGCGATTTAGAAAATCGCAATGCGATTGAGAGAG
*
72892 TCGCAACGCGTTTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATC
72957 GCAACGCGATTTAGAAAATCGCAA
66 GCAACGCGATTTAGAAAATCGCAA
72981 CGGTCAAAAG
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
103 80 1.00
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (103 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATC
GCAACGCGATTTAGAAAATCGCAATGCGATTGAGAGAG
Found at i:73081 original size:6 final size:6
Alignment explanation
Indices: 73070--73211 Score: 275
Period size: 6 Copynumber: 23.5 Consensus size: 6
73060 GACACGTATT
73070 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A-CCACG ACCACG
73119 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
73167 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
73212 GACCGACCGA
Statistics
Matches: 135, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
6 129 0.96
7 6 0.04
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:73931 original size:6 final size:6
Alignment explanation
Indices: 73915--73970 Score: 105
Period size: 6 Copynumber: 9.5 Consensus size: 6
73905 TCTCGTCTCG
73915 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
73962 GGTCGT GGT
1 GGTCGT GGT
73971 AATACGTGTC
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.10
6 45 0.90
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:74073 original size:20 final size:20
Alignment explanation
Indices: 74048--74091 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
74038 TTTTTAACTA
*
74048 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
74068 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
74088 TTCT
1 TTCT
74092 AAATCGCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:74103 original size:20 final size:20
Alignment explanation
Indices: 74080--74391 Score: 264
Period size: 20 Copynumber: 15.3 Consensus size: 20
74070 CTTTTTAACG
*
74080 TTGCGATTTTCTAAATCGCA
1 TTGCGATTCTCTAAATCGCA
*
74100 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTAAATCGCA
* *
74120 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCA
* *** ** *
74140 TTGCGATTTTCTTTTTAACG
1 TTGCGATTCTCTAAATCGCA
* *** ** *
74160 TTGCGATTTTCTTTTTAACG
1 TTGCGATTCTCTAAATCGCA
* *
74180 TTGCGATTTTCTAAATCGCG
1 TTGCGATTCTCTAAATCGCA
*
74200 TTGCGATTCTCTCAATCGCA
1 TTGCGATTCTCTAAATCGCA
*
74220 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTAAATCGCA
* *
74240 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCA
* *
74260 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCA
* *
74280 TTGCGATTTTCTTCTAAATCACG
1 TTGCGA--TTC-TCTAAATCGCA
* *
74303 TTGCGACTCTCTCAATCGCA
1 TTGCGATTCTCTAAATCGCA
*
74323 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTAAATCGCA
* *
74343 TTGCGATTCTTTCAATCGCA
1 TTGCGATTCTCTAAATCGCA
*
74363 TTGCGATTTTCTTCTAAATCGCG
1 TTGCGA--TTC-TCTAAATCGCA
74386 TTGCGA
1 TTGCGA
74392 ACTTGGAAGC
Statistics
Matches: 245, Mismatches: 41, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
20 210 0.86
21 2 0.01
22 6 0.02
23 27 0.11
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.39
Consensus pattern (20 bp):
TTGCGATTCTCTAAATCGCA
Found at i:74195 original size:80 final size:80
Alignment explanation
Indices: 74060--74227 Score: 246
Period size: 80 Copynumber: 2.1 Consensus size: 80
74050 CTTTTGACCG
**
74060 TTGCGATTTTCTTTTTAACGTTGCGATTTTCTAAATCGCATTGCGATTCTATAAATCGCATTGCG
1 TTGCGATTTTCTTTTTAACGTTGCGATTTTCTAAATAACATTGCGATTCTATAAATCGCATTGCG
*
74125 ATTCTCTCAGTCGCA
66 ATTCTCTCAATCGCA
*** * * * *
74140 TTGCGATTTTCTTTTTAACGTTGCGATTTTCTTTTTAACGTTGCGATTTTCTAAATCGCGTTGCG
1 TTGCGATTTTCTTTTTAACGTTGCGATTTTCTAAATAACATTGCGATTCTATAAATCGCATTGCG
74205 ATTCTCTCAATCGCA
66 ATTCTCTCAATCGCA
74220 TTGCGATT
1 TTGCGATT
74228 CTATAAATCG
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
80 78 1.00
ACGTcount: A:0.19, C:0.20, G:0.17, T:0.44
Consensus pattern (80 bp):
TTGCGATTTTCTTTTTAACGTTGCGATTTTCTAAATAACATTGCGATTCTATAAATCGCATTGCG
ATTCTCTCAATCGCA
Found at i:74221 original size:100 final size:100
Alignment explanation
Indices: 74048--74350 Score: 363
Period size: 100 Copynumber: 3.0 Consensus size: 100
74038 TTTTTAACTA
* * * * *
74048 TTCTTTTGACCGTTGCGATTTTCTTTTTAACGTTGCGATTTTCTAAATCGCATTGCGATTCTATA
1 TTCTTTTTAACGTTGCGATTTTCTTTTTAACGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTC
* * *
74113 AATCGCATTGCGATTCTCTCAGTCGCATTGCGATT
66 AATCGCATTGCGATTCTATAAATCGCATTGCGATT
74148 TTCTTTTTAACGTTGCGATTTTCTTTTTAACGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTC
1 TTCTTTTTAACGTTGCGATTTTCTTTTTAACGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTC
74213 AATCGCATTGCGATTCTATAAATCGCATTGCGATT
66 AATCGCATTGCGATTCTATAAATCGCATTGCGATT
* *** ** * * *** ** * * *
74248 CTCTCAGTCGCATTGCGATTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCACGTTGCGACTCT
1 TTCTTTTTAACGTTGCGATTTTCTTTTTAACGTTGCGA--TT-TTCTAAATCGCGTTGCGATTCT
74313 CTCAATCGCATTGCGATTCTATAAATCGCATTGCGATT
63 CTCAATCGCATTGCGATTCTATAAATCGCATTGCGATT
74351 CTTTCAATCG
Statistics
Matches: 176, Mismatches: 24, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
100 116 0.66
102 2 0.01
103 58 0.33
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.41
Consensus pattern (100 bp):
TTCTTTTTAACGTTGCGATTTTCTTTTTAACGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTC
AATCGCATTGCGATTCTATAAATCGCATTGCGATT
Found at i:74327 original size:83 final size:83
Alignment explanation
Indices: 74180--74391 Score: 268
Period size: 83 Copynumber: 2.6 Consensus size: 83
74170 CTTTTTAACG
* * * * * * * * *
74180 TTGCGATTTTCTAAATCGCGTTGCGA--TTC-TCTCAATCGCATTGCGATTCTATAAATCGCATT
1 TTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCACGTTGCGACTCTCTCAATCGCATT
* * *
74242 GCGATTCTCTCAGTCGCA
66 GCGATTCTATAAATCGCA
*
74260 TTGCGATTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCACGTTGCGACTCTCTCAATCGCATT
1 TTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCACGTTGCGACTCTCTCAATCGCATT
74325 GCGATTCTATAAATCGCA
66 GCGATTCTATAAATCGCA
* *
74343 TTGCGATTCTTTCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCACGTTGCGA
74392 ACTTGGAAGC
Statistics
Matches: 113, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
80 22 0.19
82 3 0.03
83 88 0.78
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37
Consensus pattern (83 bp):
TTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCACGTTGCGACTCTCTCAATCGCATT
GCGATTCTATAAATCGCA
Found at i:74430 original size:20 final size:20
Alignment explanation
Indices: 74405--74458 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
74395 TGGAAGCTCG
*
74405 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTGAA
*
74425 CGTTGCGATTTTCTTTTTAA
1 CGTTGCGATTTTCTTTTGAA
74445 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
74459 AAATCGCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.19, G:0.19, T:0.52
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTGAA
Found at i:74489 original size:19 final size:20
Alignment explanation
Indices: 74445--74495 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
74435 TTCTTTTTAA
*
74445 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
* *
74465 CATTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
74484 CGTTGCGATTTT
1 CGTTGCGATTTT
74496 ATTGGTCATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:80298 original size:11 final size:11
Alignment explanation
Indices: 80282--80307 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
80272 TAGCAAGTTG
80282 AATTTTACTAT
1 AATTTTACTAT
80293 AATTTTACTAT
1 AATTTTACTAT
80304 AATT
1 AATT
80308 AATTTATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
AATTTTACTAT
Found at i:90330 original size:24 final size:24
Alignment explanation
Indices: 90298--90354 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
90288 GTATTGTAGA
*
90298 ATTCTCATGGGGTGGGAATCCTAC
1 ATTCTCATGGGGTGGGAATCATAC
90322 ATTCTCATGGGGTGGGAATCATAC
1 ATTCTCATGGGGTGGGAATCATAC
90346 ATTCTCATG
1 ATTCTCATG
90355 TTTGATTGGT
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:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (24 bp):
ATTCTCATGGGGTGGGAATCATAC
Found at i:90752 original size:37 final size:37
Alignment explanation
Indices: 90676--90752 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
90666 TTTTTATATT
* *
90676 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATACAAATATTATCAA
* * *
90713 TTTAATTTTTTTAAAAAAA-TATACAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATACAAATATTAT-CAA
90750 TTT
1 TTT
90753 GTAATATTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
36 12 0.35
37 22 0.65
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATACAAATATTATCAA
Found at i:90917 original size:20 final size:20
Alignment explanation
Indices: 90892--90946 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
90882 AGTAATCCTA
90892 TTCACTGATAATCTTTTATT
1 TTCACTGATAATCTTTTATT
90912 TTCACTGATAATCTTTTATT
1 TTCACTGATAATCTTTTATT
* *
90932 CTCACTGGTAATCTT
1 TTCACTGATAATCTT
90947 ACATTCCGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.24, C:0.18, G:0.07, T:0.51
Consensus pattern (20 bp):
TTCACTGATAATCTTTTATT
Found at i:92528 original size:2 final size:2
Alignment explanation
Indices: 92521--92547 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
92511 ACCGCTTTAT
92521 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
92548 TACATATGAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:92835 original size:18 final size:18
Alignment explanation
Indices: 92796--92840 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
92786 ACCCACCAGA
*
92796 TGAACTGGATGAAGAGGC
1 TGAACTTGATGAAGAGGC
92814 TGAACTTGATGAAGA-GC
1 TGAACTTGATGAAGAGGC
92831 TTGAACTTGA
1 -TGAACTTGA
92841 ACCCCACGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 2 0.08
18 23 0.92
ACGTcount: A:0.33, C:0.11, G:0.31, T:0.24
Consensus pattern (18 bp):
TGAACTTGATGAAGAGGC
Found at i:92865 original size:6 final size:6
Alignment explanation
Indices: 92854--92878 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
92844 CCACGATCCC
92854 GAACCA GAACCA GAACCA GAACCA G
1 GAACCA GAACCA GAACCA GAACCA G
92879 CCCCAGCTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.32, G:0.20, T:0.00
Consensus pattern (6 bp):
GAACCA
Found at i:93806 original size:36 final size:36
Alignment explanation
Indices: 93766--93840 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 36
93756 AAAATTGATG
* *
93766 TTATTTATAATAAGTCACATCACTTAGTGAATGGAC
1 TTATTAATAATAAGTCACATCACTTAGTGAATAGAC
* * *
93802 TTATTAATAATACGTCATATCACTTGGTGAATAGAC
1 TTATTAATAATAAGTCACATCACTTAGTGAATAGAC
93838 TTA
1 TTA
93841 ATTTTTTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.37
Consensus pattern (36 bp):
TTATTAATAATAAGTCACATCACTTAGTGAATAGAC
Found at i:104441 original size:63 final size:63
Alignment explanation
Indices: 104374--104650 Score: 317
Period size: 63 Copynumber: 4.4 Consensus size: 63
104364 TACTTCATCT
* * * * *
104374 ATGAAGGAGATGAATTTGCAGTGCCACCGGA-ATCCGATTACGACTTAGTCCTTGACTACTATC
1 ATGAAGAAGATGAATTTGCAGTGCCACCGGAGAT-GGATTACGACTTAGGCCTTGACTACAACC
* * * *
104437 ATGAAGGAGATGAATTTGCGGTGCCACCGGAGGTGGATTACGACTCAGGCCTTGACTACAACC
1 ATGAAGAAGATGAATTTGCAGTGCCACCGGAGATGGATTACGACTTAGGCCTTGACTACAACC
* *
104500 ATGAAGAAGATGAATTTGCGGTGCCACCGGAGGTGGATTACGACTTAGGCCTTGACTACAACC
1 ATGAAGAAGATGAATTTGCAGTGCCACCGGAGATGGATTACGACTTAGGCCTTGACTACAACC
* * * * * * *
104563 ATGAAGAAGATGAATTTGCACTCCCACCAGA-ATCTGATTACGACTTAAGACTTTGAATACAACC
1 ATGAAGAAGATGAATTTGCAGTGCCACCGGAGAT-GGATTACGACTT-AGGCCTTGACTACAACC
*
104627 ATGAA-ATATTATGAATTTGCAGTG
1 ATGAAGA-A-GATGAATTTGCAGTG
104651 GCGGATATTC
Statistics
Matches: 188, Mismatches: 21, Indels: 8
0.87 0.10 0.04
Matches are distributed among these distances:
62 1 0.01
63 154 0.82
64 21 0.11
65 12 0.06
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (63 bp):
ATGAAGAAGATGAATTTGCAGTGCCACCGGAGATGGATTACGACTTAGGCCTTGACTACAACC
Found at i:104602 original size:126 final size:126
Alignment explanation
Indices: 104325--104650 Score: 329
Period size: 126 Copynumber: 2.6 Consensus size: 126
104315 GGAGGCGAAT
* * * * * * *
104325 TTTGAACTTCCACCGGAACCTGATTACGAC-CATGGCCCTT-ACTTCATCTATGAAGGAGATGAA
1 TTTGCACTCCCACCGGAATCTGATTACGACTCA-GG-CCTTGACTACAACCATGAAGAAGATGAA
* * * *
104388 TTTGCAGTGCCACCGGAATCCGATTACGACTTAGTCCTTGACTACTATCATGAAGGAGATGAA
64 TTTGCAGTGCCACCGGAATCCGATTACGACTTAGGCCTTGACTACAACCATGAAGAAGATGAA
** * * *
104451 TTTGCGGTGCCACCGGAGGT-GGATTACGACTCAGGCCTTGACTACAACCATGAAGAAGATGAAT
1 TTTGCACTCCCACCGGA-ATCTGATTACGACTCAGGCCTTGACTACAACCATGAAGAAGATGAAT
* * *
104515 TTGCGGTGCCACCGGAGGT-GGATTACGACTTAGGCCTTGACTACAACCATGAAGAAGATGAA
65 TTGCAGTGCCACCGGA-ATCCGATTACGACTTAGGCCTTGACTACAACCATGAAGAAGATGAA
* * * * * *
104577 TTTGCACTCCCACCAGAATCTGATTACGACTTAAGACTTTGAATACAACCATGAA-ATATTATGA
1 TTTGCACTCCCACCGGAATCTGATTACGAC-TCAGGCCTTGACTACAACCATGAAGA-A-GATGA
104641 ATTTGCAGTG
63 ATTTGCAGTG
104651 GCGGATATTC
Statistics
Matches: 162, Mismatches: 30, Indels: 14
0.79 0.15 0.07
Matches are distributed among these distances:
125 5 0.03
126 120 0.74
127 24 0.15
128 13 0.08
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (126 bp):
TTTGCACTCCCACCGGAATCTGATTACGACTCAGGCCTTGACTACAACCATGAAGAAGATGAATT
TGCAGTGCCACCGGAATCCGATTACGACTTAGGCCTTGACTACAACCATGAAGAAGATGAA
Found at i:105774 original size:69 final size:69
Alignment explanation
Indices: 105663--105871 Score: 307
Period size: 69 Copynumber: 3.1 Consensus size: 69
105653 GATGTAGGAC
* * * * *
105663 CTGACTACGACGGTGAAGGAGATGAATTCGTAGTGCCAACGGAGGCGGATTTTGCTCTTCCACCA
1 CTGACTACTACCGTGAAGTAGAAGAATTTGTAGTGCCAACGGAGGCGGATTTTGCTCTTCCACCA
105728 GACT
66 GACT
105732 CTGACTACTACCGTGAAGTAGAAGAATTTGTAGTGCCAACGGAGGCGGATTTTGCTCTTCCACCA
1 CTGACTACTACCGTGAAGTAGAAGAATTTGTAGTGCCAACGGAGGCGGATTTTGCTCTTCCACCA
105797 GA--
66 GACT
* * *
105799 CTGACTACTACCGTGAAGTAGAAGAATTTGTAGTGCC-ACTAGAGGCGGATTTCGCACTTCCACC
1 CTGACTACTACCGTGAAGTAGAAGAATTTGTAGTGCCAAC-GGAGGCGGATTTTGCTCTTCCACC
*
105863 GGACT
65 AGACT
105868 CTGA
1 CTGA
105872 TTACAACTTA
Statistics
Matches: 128, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
66 2 0.02
67 60 0.47
69 66 0.52
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.24
Consensus pattern (69 bp):
CTGACTACTACCGTGAAGTAGAAGAATTTGTAGTGCCAACGGAGGCGGATTTTGCTCTTCCACCA
GACT
Found at i:105844 original size:67 final size:67
Alignment explanation
Indices: 105663--105867 Score: 295
Period size: 67 Copynumber: 3.0 Consensus size: 67
105653 GATGTAGGAC
* * * * *
105663 CTGACTACGACGGTGAAGGAGATGAATTCGTAGTGCCAACGGAGGCGGATTTTGCTCTTCCACCA
1 CTGACTACTACCGTGAAGTAGAAGAATTTGTAGTGCCAACGGAGGCGGATTTTGCTCTTCCACCA
105728 GA
66 GA
105730 CTCTGACTACTACCGTGAAGTAGAAGAATTTGTAGTGCCAACGGAGGCGGATTTTGCTCTTCCAC
1 --CTGACTACTACCGTGAAGTAGAAGAATTTGTAGTGCCAACGGAGGCGGATTTTGCTCTTCCAC
105795 CAGA
64 CAGA
* * *
105799 CTGACTACTACCGTGAAGTAGAAGAATTTGTAGTGCC-ACTAGAGGCGGATTTCGCACTTCCACC
1 CTGACTACTACCGTGAAGTAGAAGAATTTGTAGTGCCAAC-GGAGGCGGATTTTGCTCTTCCACC
*
105863 GGA
65 AGA
105866 CT
1 CT
105868 CTGATTACAA
Statistics
Matches: 126, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
66 2 0.02
67 62 0.49
69 62 0.49
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.24
Consensus pattern (67 bp):
CTGACTACTACCGTGAAGTAGAAGAATTTGTAGTGCCAACGGAGGCGGATTTTGCTCTTCCACCA
GA
Found at i:105961 original size:63 final size:63
Alignment explanation
Indices: 105853--105973 Score: 174
Period size: 63 Copynumber: 1.9 Consensus size: 63
105843 GCGGATTTCG
* * *
105853 CACTTCCACCGGACTCTGATTACAACTTAGGCTCTGACTATTACCATGAAGGAGATGAGTTTT
1 CACTTCCACCAGACTCTGACTACAACTTAGGCCCTGACTATTACCATGAAGGAGATGAGTTTT
*
105916 CACTTCCACCAGACTCTGACTACGACTTAGGCCCT-ACCT-TCTACCATGAAGGAGATGA
1 CACTTCCACCAGACTCTGACTACAACTTAGGCCCTGA-CTAT-TACCATGAAGGAGATGA
105974 ATTTGCAGTG
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.26
Consensus pattern (63 bp):
CACTTCCACCAGACTCTGACTACAACTTAGGCCCTGACTATTACCATGAAGGAGATGAGTTTT
Found at i:105988 original size:63 final size:63
Alignment explanation
Indices: 105847--105989 Score: 164
Period size: 63 Copynumber: 2.3 Consensus size: 63
105837 CTAGAGGCGG
* * * *
105847 ATTTCGCACTTCCACCGGACTCTGATTACAACTTAGGCTCTGACTATTACCATGAAGGAGATGA
1 ATTT-GCACTGCCACCAGACTCTGACTACAACTTAGGCCCTGACTATTACCATGAAGGAGATGA
* * * *
105911 GTTTTCACTTCCACCAGACTCTGACTACGACTTAGGCCCT-ACCT-TCTACCATGAAGGAGATGA
1 ATTTGCACTGCCACCAGACTCTGACTACAACTTAGGCCCTGA-CTAT-TACCATGAAGGAGATGA
*
105974 ATTTGCAGTGCCACCA
1 ATTTGCACTGCCACCA
105990 ATGGAGGATA
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
62 2 0.03
63 62 0.93
64 3 0.04
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (63 bp):
ATTTGCACTGCCACCAGACTCTGACTACAACTTAGGCCCTGACTATTACCATGAAGGAGATGA
Found at i:106597 original size:63 final size:63
Alignment explanation
Indices: 106513--106631 Score: 170
Period size: 63 Copynumber: 1.9 Consensus size: 63
106503 ATTTGTTACC
* *
106513 TATTTAACTTTGAATATTAAAGAT-AATTATATCCTTTTAAATATTTTAAATTAAAATCATATA
1 TATTTAACTTTGAATAGTAAAGATGAATT-TATCCTTTTAAATATTTCAAATTAAAATCATATA
* *
106576 TATTTAAGTTT-AAGTAGTAAAGATGACTTTATCCTTTTAAATATTTCAAATTAAAA
1 TATTTAACTTTGAA-TAGTAAAGATGAATTTATCCTTTTAAATATTTCAAATTAAAA
106632 GATATTATTA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
62 2 0.04
63 45 0.90
64 3 0.06
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.45
Consensus pattern (63 bp):
TATTTAACTTTGAATAGTAAAGATGAATTTATCCTTTTAAATATTTCAAATTAAAATCATATA
Found at i:112688 original size:8 final size:8
Alignment explanation
Indices: 112675--112702 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
112665 TGTATATGCT
112675 CTTTTATG
1 CTTTTATG
112683 CTTTTATG
1 CTTTTATG
112691 CTTTTATG
1 CTTTTATG
112699 CTTT
1 CTTT
112703 GCCTCTCCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.11, C:0.14, G:0.11, T:0.64
Consensus pattern (8 bp):
CTTTTATG
Found at i:115793 original size:2 final size:2
Alignment explanation
Indices: 115786--115840 Score: 85
Period size: 2 Copynumber: 27.5 Consensus size: 2
115776 AAAATTTAAA
115786 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
115828 CA- AT AA AT AT AT A
1 -AT AT AT AT AT AT A
115841 AAGTAAACAA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
1 1 0.02
2 47 0.96
3 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:116359 original size:2 final size:2
Alignment explanation
Indices: 116352--116379 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
116342 GGGAATCAAA
116352 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
116380 GGTGTCGGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:117482 original size:60 final size:61
Alignment explanation
Indices: 117377--117494 Score: 154
Period size: 60 Copynumber: 2.0 Consensus size: 61
117367 CACTAGGAGG
117377 TCCTCAAACTATGACATCTATAATAAATTAGTTCTTAAATATTAAAACATTCT-TTATCAA
1 TCCTCAAACTATGACATCTATAATAAATTAGTTCTTAAATATTAAAACATTCTATTATCAA
** *
117437 TCCTCAAACTATGATCATC-ATTCTAAATTAGTGTC-TAAGCT-TTAAAACATTCTATTAT
1 TCCTCAAACTATGA-CATCTATAATAAATTAGT-TCTTAA-ATATTAAAACATTCTATTAT
117495 AAATTATCAT
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
60 40 0.78
61 11 0.22
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.39
Consensus pattern (61 bp):
TCCTCAAACTATGACATCTATAATAAATTAGTTCTTAAATATTAAAACATTCTATTATCAA
Found at i:118530 original size:4 final size:4
Alignment explanation
Indices: 118521--118614 Score: 65
Period size: 4 Copynumber: 25.0 Consensus size: 4
118511 ATAATTATTT
* * * * *
118521 TATA TATA TATA -ATA T-TA -ATA AATT TA-A TTTA AATA TAAA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * *
118565 TATA TATA TATA TATA -ATA TTTA TATA TTTA -ATT TAAA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
118611 TATA
1 TATA
118615 CCCGGCCCGA
Statistics
Matches: 67, Mismatches: 17, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
3 12 0.18
4 55 0.82
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (4 bp):
TATA
Found at i:118532 original size:6 final size:6
Alignment explanation
Indices: 118521--118614 Score: 65
Period size: 6 Copynumber: 16.7 Consensus size: 6
118511 ATAATTATTT
* * * * *
118521 TATATA TATATA -ATAT- TA-ATA AATTTA -ATTTA AATATA AATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * *
118565 TATATA TATATA TATA-A TATTTA TATATT TA-ATT TAAATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
118611 TATA
1 TATA
118615 CCCGGCCCGA
Statistics
Matches: 73, Mismatches: 9, Indels: 12
0.78 0.10 0.13
Matches are distributed among these distances:
4 2 0.03
5 20 0.27
6 51 0.70
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (6 bp):
TATATA
Found at i:118583 original size:48 final size:48
Alignment explanation
Indices: 118521--118614 Score: 161
Period size: 48 Copynumber: 2.0 Consensus size: 48
118511 ATAATTATTT
118521 TATATATATATAATATTAATAAATTTAATTTAAATATAAATATATATA
1 TATATATATATAATATTAATAAATTTAATTTAAATATAAATATATATA
* * *
118569 TATATATATATAATATTTATATATTTAATTTAAATATATATATATA
1 TATATATATATAATATTAATAAATTTAATTTAAATATAAATATATA
118615 CCCGGCCCGA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (48 bp):
TATATATATATAATATTAATAAATTTAATTTAAATATAAATATATATA
Found at i:123873 original size:13 final size:15
Alignment explanation
Indices: 123837--123873 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
123827 TTAAAATATT
123837 AAATATATTATATAA
1 AAATATATTATATAA
123852 AAATAATATT-TA-AA
1 AAAT-ATATTATATAA
123866 AAATATAT
1 AAATATAT
123874 CAGATGAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 4 0.19
14 6 0.29
15 6 0.29
16 5 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATATATTATATAA
Found at i:126183 original size:2 final size:2
Alignment explanation
Indices: 126176--126218 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
126166 TATCTTTCAA
126176 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
126218 A
1 A
126219 CATACTTGGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:127295 original size:25 final size:25
Alignment explanation
Indices: 127243--127295 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
127233 TAGATAAGTG
* *
127243 AATTTATAAAATTTTAAGAATTATA
1 AATTTATAAAATTTTAAGAATAAAA
* *
127268 AATTTATAAAATTTTAGGGATAAAA
1 AATTTATAAAATTTTAAGAATAAAA
127293 AAT
1 AAT
127296 AAATTATCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.40
Consensus pattern (25 bp):
AATTTATAAAATTTTAAGAATAAAA
Found at i:129791 original size:21 final size:21
Alignment explanation
Indices: 129765--129807 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
129755 TTTTCGGGCT
* *
129765 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
129786 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
129807 A
1 A
129808 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:129867 original size:66 final size:68
Alignment explanation
Indices: 129787--129938 Score: 227
Period size: 67 Copynumber: 2.2 Consensus size: 68
129777 ACCCATTCAA
* *
129787 GGGGAACCGATACCCCTTCAACGAATATG-ATTTCCAGAATGCTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
129851 -GG
66 GGG
* * *
129853 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGAATGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
129918 GGGG
66 -GGG
*
129922 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
129939 ATGAGAAAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
66 26 0.34
67 33 0.43
69 18 0.23
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.18
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
GGG
Found at i:130277 original size:29 final size:29
Alignment explanation
Indices: 130243--130314 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
130233 CATATTATGA
* *
130243 TACATGACATGAATTTATATTAAATGTAT
1 TACATGACATGAATTCATATGAAATGTAT
*
130272 TACATGACATGAATTCATATGATATGTAT
1 TACATGACATGAATTCATATGAAATGTAT
*
130301 TGCATGACATGAAT
1 TACATGACATGAAT
130315 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.38
Consensus pattern (29 bp):
TACATGACATGAATTCATATGAAATGTAT
Found at i:130370 original size:30 final size:30
Alignment explanation
Indices: 130328--130404 Score: 118
Period size: 30 Copynumber: 2.5 Consensus size: 30
130318 CAGAAAAGTT
* *
130328 ATATGAGCTATGTGATAAAGGTATGTAAATG
1 ATATGA-CTATGTGATAAAGGTATGGAAATA
130359 ATATGACTATGTGATAAAGGTATGGAAATA
1 ATATGACTATGTGATAAAGGTATGGAAATA
*
130389 ATATGACTACGTGATA
1 ATATGACTATGTGATA
130405 TGAACTACGG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
30 37 0.86
31 6 0.14
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.31
Consensus pattern (30 bp):
ATATGACTATGTGATAAAGGTATGGAAATA
Found at i:130681 original size:23 final size:23
Alignment explanation
Indices: 130615--130673 Score: 102
Period size: 22 Copynumber: 2.6 Consensus size: 23
130605 ATCATTATAT
*
130615 GGCACTACGGTGCAATTCTAC-G
1 GGCACTTCGGTGCAATTCTACGG
130637 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
130660 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
130674 TTTATACGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 20 0.57
23 15 0.43
ACGTcount: A:0.19, C:0.27, G:0.31, T:0.24
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:131935 original size:42 final size:42
Alignment explanation
Indices: 131852--131936 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
131842 GGGAAACGAA
**
131852 CAGAGCTATGGAAATCAAGCTAGTTAAGAGTGCATTTCACAC
1 CAGAGCTATGGAAATCAAGCTAGTTAAGAGTGCATCCCACAC
* * *
131894 CAGAGCTTTGGAAATCGAGCTAGTTAAGGGTGCATCCCACAC
1 CAGAGCTATGGAAATCAAGCTAGTTAAGAGTGCATCCCACAC
131936 C
1 C
131937 GGTGAGATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (42 bp):
CAGAGCTATGGAAATCAAGCTAGTTAAGAGTGCATCCCACAC
Found at i:133367 original size:26 final size:25
Alignment explanation
Indices: 133315--133366 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
133305 AAGAAAATAG
133315 TAAAGAAATTTAAACATGAACCATTT
1 TAAAGAAATTT-AACATGAACCATTT
*
133341 TAAAGAAATTT-ACATGACACCTTTT
1 TAAAGAAATTTAACATGA-ACCATTT
133366 T
1 T
133367 TCTCAAAGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 6 0.25
25 7 0.29
26 11 0.46
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.35
Consensus pattern (25 bp):
TAAAGAAATTTAACATGAACCATTT
Found at i:134670 original size:56 final size:56
Alignment explanation
Indices: 134605--134719 Score: 221
Period size: 56 Copynumber: 2.1 Consensus size: 56
134595 AATCTTTCTT
134605 TAACCTTATATTAAAGTTGTCGTACAGGAGAAATACTAAAAAAATAAATATCAAAA
1 TAACCTTATATTAAAGTTGTCGTACAGGAGAAATACTAAAAAAATAAATATCAAAA
*
134661 TAACCTTATATTAAAGTTGTTGTACAGGAGAAATACTAAAAAAATAAATATCAAAA
1 TAACCTTATATTAAAGTTGTCGTACAGGAGAAATACTAAAAAAATAAATATCAAAA
134717 TAA
1 TAA
134720 ATGTTTTAAT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.28
Consensus pattern (56 bp):
TAACCTTATATTAAAGTTGTCGTACAGGAGAAATACTAAAAAAATAAATATCAAAA
Found at i:136093 original size:2 final size:2
Alignment explanation
Indices: 136086--136129 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
136076 ACTACATAAC
136086 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
136127 TA T
1 TA T
136130 TATTACTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:139938 original size:17 final size:17
Alignment explanation
Indices: 139916--139950 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
139906 GAATTGTTTA
139916 AGTTTC-AGTTTAAATAT
1 AGTTTCAAG-TTAAATAT
139933 AGTTTCAAGTTAAATAT
1 AGTTTCAAGTTAAATAT
139950 A
1 A
139951 ATTATAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.88
18 2 0.12
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (17 bp):
AGTTTCAAGTTAAATAT
Found at i:140340 original size:22 final size:22
Alignment explanation
Indices: 140308--140361 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
140298 TCGCTTTAAT
*
140308 TATTGGTGAGAGAGAAAAAGAA
1 TATTGGCGAGAGAGAAAAAGAA
140330 TATTGGCGAGAGAGAAAAAGAA
1 TATTGGCGAGAGAGAAAAAGAA
140352 TATTGGCGAG
1 TATTGGCGAG
140362 GGAAAGGTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.44, C:0.04, G:0.33, T:0.19
Consensus pattern (22 bp):
TATTGGCGAGAGAGAAAAAGAA
Found at i:142082 original size:24 final size:24
Alignment explanation
Indices: 142048--142154 Score: 88
Period size: 24 Copynumber: 4.5 Consensus size: 24
142038 AAACGGAGAT
* *
142048 ATCAGAAATCAAAATATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
142072 ATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
142096 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** * *
142120 ATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
142144 ATCAGAAATCA
1 ATCAGAAATCA
142155 GATAAAATAT
Statistics
Matches: 60, Mismatches: 23, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.48, C:0.16, G:0.13, T:0.23
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:142154 original size:48 final size:48
Alignment explanation
Indices: 142048--142156 Score: 110
Period size: 48 Copynumber: 2.3 Consensus size: 48
142038 AAACGGAGAT
* * * * *
142048 ATCAGAAATCAAAATATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * * *
142096 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
142144 ATCAGAAATCAGA
1 ATCAGAAATCAGA
142157 TAAAATATTC
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.23
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:143303 original size:18 final size:18
Alignment explanation
Indices: 143282--143317 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
143272 CTTTCATCCG
*
143282 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
143300 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
143318 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:144641 original size:7 final size:7
Alignment explanation
Indices: 144629--144660 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
144619 TGGTCAACTC
144629 CGGTCAA
1 CGGTCAA
144636 CGGTCAA
1 CGGTCAA
144643 CGGGTCAA
1 C-GGTCAA
144651 CGGTCAA
1 CGGTCAA
144658 CGG
1 CGG
144661 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:144650 original size:15 final size:15
Alignment explanation
Indices: 144630--144676 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
144620 GGTCAACTCC
144630 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
144645 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
144660 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
144673 GGTC
1 GGTC
144677 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:144681 original size:18 final size:18
Alignment explanation
Indices: 144658--144734 Score: 110
Period size: 18 Copynumber: 4.6 Consensus size: 18
144648 CAACGGTCAA
144658 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
144676 CGGGTCGGGTCAA-----
1 CGGGTCGGGTCAACGGGT
*
144689 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTCAACGGGT
144707 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
144725 CGGGTCGGGT
1 CGGGTCGGGT
144735 TGTGACTGGT
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
13 12 0.23
18 40 0.77
ACGTcount: A:0.12, C:0.21, G:0.51, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:144690 original size:31 final size:31
Alignment explanation
Indices: 144652--144730 Score: 149
Period size: 31 Copynumber: 2.5 Consensus size: 31
144642 ACGGGTCAAC
144652 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
*
144683 GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
144714 GGTCAACGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
144731 GGGTTGTGAC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.14, C:0.22, G:0.48, T:0.16
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
Found at i:144694 original size:8 final size:8
Alignment explanation
Indices: 144630--144676 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
144620 GGTCAACTCC
144630 GGTCAAC-
1 GGTCAACG
144637 GGTCAACG
1 GGTCAACG
144645 GGTCAAC-
1 GGTCAACG
144652 GGTCAACG
1 GGTCAACG
144660 GGT---CG
1 GGTCAACG
144665 GGTCAACG
1 GGTCAACG
144673 GGTC
1 GGTC
144677 GGGTCGGGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.14
7 14 0.40
8 16 0.46
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:144730 original size:13 final size:13
Alignment explanation
Indices: 144637--144712 Score: 71
Period size: 13 Copynumber: 5.3 Consensus size: 13
144627 TCCGGTCAAC
*
144637 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
144652 GGTCAACGGGTCG
1 GGTCAACGGGTCG
144665 GGTCAACGGGTCGGGTCG
1 GGTCAA-----CGGGTCG
144683 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
144696 GGTAAACGGGTCG
1 GGTCAACGGGTCG
144709 GGTC
1 GGTC
144713 GGGTCAACGG
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
13 28 0.53
15 12 0.23
18 13 0.25
ACGTcount: A:0.17, C:0.22, G:0.45, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:146862 original size:24 final size:24
Alignment explanation
Indices: 146828--146934 Score: 88
Period size: 24 Copynumber: 4.5 Consensus size: 24
146818 AAACGGAGAT
* *
146828 ATCAGAAATCAAAATATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
146852 ATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
146876 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** * *
146900 ATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
146924 ATCAGAAATCA
1 ATCAGAAATCA
146935 GATAAAATAT
Statistics
Matches: 60, Mismatches: 23, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.48, C:0.16, G:0.13, T:0.23
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:146934 original size:48 final size:48
Alignment explanation
Indices: 146828--146936 Score: 110
Period size: 48 Copynumber: 2.3 Consensus size: 48
146818 AAACGGAGAT
* * * * *
146828 ATCAGAAATCAAAATATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * * *
146876 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
146924 ATCAGAAATCAGA
1 ATCAGAAATCAGA
146937 TAAAATATTC
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.23
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:148082 original size:18 final size:18
Alignment explanation
Indices: 148061--148096 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
148051 CTTTCATCCG
*
148061 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
148079 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
148097 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:149420 original size:7 final size:7
Alignment explanation
Indices: 149408--149438 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
149398 TGGTCAACTC
149408 CGGTCAA
1 CGGTCAA
149415 CGGTCAA
1 CGGTCAA
149422 CGGTCAA
1 CGGTCAA
149429 CGGTCAA
1 CGGTCAA
149436 CGG
1 CGG
149439 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:149459 original size:18 final size:18
Alignment explanation
Indices: 149436--149512 Score: 110
Period size: 18 Copynumber: 4.6 Consensus size: 18
149426 CAACGGTCAA
149436 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
149454 CGGGTCGGGTCAA-----
1 CGGGTCGGGTCAACGGGT
*
149467 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTCAACGGGT
149485 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
149503 CGGGTCGGGT
1 CGGGTCGGGT
149513 TGTGACTGGT
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
13 12 0.23
18 40 0.77
ACGTcount: A:0.12, C:0.21, G:0.51, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:149465 original size:31 final size:31
Alignment explanation
Indices: 149430--149508 Score: 149
Period size: 31 Copynumber: 2.5 Consensus size: 31
149420 AACGGTCAAC
149430 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
*
149461 GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
149492 GGTCAACGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
149509 GGGTTGTGAC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.14, C:0.22, G:0.48, T:0.16
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
Found at i:149508 original size:13 final size:13
Alignment explanation
Indices: 149430--149490 Score: 68
Period size: 13 Copynumber: 4.3 Consensus size: 13
149420 AACGGTCAAC
149430 GGTCAACGGGTCG
1 GGTCAACGGGTCG
149443 GGTCAACGGGTCGGGTCG
1 GGTCAA-----CGGGTCG
149461 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
149474 GGTAAACGGGTCG
1 GGTCAACGGGTCG
149487 GGTC
1 GGTC
149491 GGGTCAACGG
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
13 28 0.68
18 13 0.32
ACGTcount: A:0.15, C:0.21, G:0.48, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:151637 original size:24 final size:24
Alignment explanation
Indices: 151603--151709 Score: 88
Period size: 24 Copynumber: 4.5 Consensus size: 24
151593 AAACGGAGAT
* *
151603 ATCAGAAATCAAAATATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
151627 ATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
151651 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** * *
151675 ATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
151699 ATCAGAAATCA
1 ATCAGAAATCA
151710 GATAAAATAT
Statistics
Matches: 60, Mismatches: 23, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.48, C:0.16, G:0.13, T:0.23
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:151709 original size:48 final size:48
Alignment explanation
Indices: 151603--151711 Score: 110
Period size: 48 Copynumber: 2.3 Consensus size: 48
151593 AAACGGAGAT
* * * * *
151603 ATCAGAAATCAAAATATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * * *
151651 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
151699 ATCAGAAATCAGA
1 ATCAGAAATCAGA
151712 TAAAATATTC
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.23
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:152857 original size:18 final size:18
Alignment explanation
Indices: 152836--152871 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
152826 CTTTCATCCG
*
152836 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
152854 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
152872 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:154190 original size:7 final size:7
Alignment explanation
Indices: 154178--154209 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
154168 TGGTCAACTC
154178 CGGTCAA
1 CGGTCAA
154185 CGGTCAA
1 CGGTCAA
154192 CGGGTCAA
1 C-GGTCAA
154200 CGGTCAA
1 CGGTCAA
154207 CGG
1 CGG
154210 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:154199 original size:15 final size:15
Alignment explanation
Indices: 154179--154225 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
154169 GGTCAACTCC
154179 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
154194 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
154209 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
154222 GGTC
1 GGTC
154226 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:154230 original size:18 final size:18
Alignment explanation
Indices: 154207--154282 Score: 101
Period size: 18 Copynumber: 4.6 Consensus size: 18
154197 CAACGGTCAA
154207 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
154225 CGGGTCGGGTCAA-----
1 CGGGTCGGGTCAACGGGT
*
154238 CGGGTC-GGTAAACGGGT
1 CGGGTCGGGTCAACGGGT
154255 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
154273 CGGGTCGGGT
1 CGGGTCGGGT
154283 TGTGACTGGT
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
12 5 0.10
13 6 0.12
17 6 0.12
18 33 0.66
ACGTcount: A:0.12, C:0.21, G:0.50, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:154243 original size:8 final size:8
Alignment explanation
Indices: 154179--154225 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
154169 GGTCAACTCC
154179 GGTCAAC-
1 GGTCAACG
154186 GGTCAACG
1 GGTCAACG
154194 GGTCAAC-
1 GGTCAACG
154201 GGTCAACG
1 GGTCAACG
154209 GGT---CG
1 GGTCAACG
154214 GGTCAACG
1 GGTCAACG
154222 GGTC
1 GGTC
154226 GGGTCGGGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.14
7 14 0.40
8 16 0.46
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:154254 original size:30 final size:30
Alignment explanation
Indices: 154201--154275 Score: 132
Period size: 30 Copynumber: 2.5 Consensus size: 30
154191 ACGGGTCAAC
*
154201 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTC-GGTAAACGGGTCGGGTCG
154232 GGTCAACGGGTCGGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGTAAACGGGTCGGGTCG
154262 GGTCAACGGGTCGG
1 GGTCAACGGGTCGG
154276 GTCGGGTTGT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
30 31 0.72
31 12 0.28
ACGTcount: A:0.15, C:0.21, G:0.48, T:0.16
Consensus pattern (30 bp):
GGTCAACGGGTCGGTAAACGGGTCGGGTCG
Found at i:154278 original size:13 final size:13
Alignment explanation
Indices: 154186--154230 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
154176 TCCGGTCAAC
*
154186 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
154201 GGTCAACGGGTCG
1 GGTCAACGGGTCG
154214 GGTCAACGGGTCG
1 GGTCAACGGGTCG
154227 GGTC
1 GGTC
154231 GGGTCAACGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 17 0.59
15 12 0.41
ACGTcount: A:0.18, C:0.24, G:0.42, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:158198 original size:6 final size:6
Alignment explanation
Indices: 158187--158213 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
158177 GTCAAGCAAA
158187 CGGATT CGGATT CGGATT CGGATT CGG
1 CGGATT CGGATT CGGATT CGGATT CGG
158214 TTTCTGTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.19, G:0.37, T:0.30
Consensus pattern (6 bp):
CGGATT
Found at i:159742 original size:14 final size:14
Alignment explanation
Indices: 159723--159752 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
159713 GATTTATGAG
159723 ATAGAAAGACGATC
1 ATAGAAAGACGATC
*
159737 ATAGAAAGAGGATC
1 ATAGAAAGACGATC
159751 AT
1 AT
159753 TTCTTGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.10, G:0.23, T:0.17
Consensus pattern (14 bp):
ATAGAAAGACGATC
Found at i:160367 original size:57 final size:57
Alignment explanation
Indices: 160303--160416 Score: 185
Period size: 57 Copynumber: 2.0 Consensus size: 57
160293 GACTATAATT
* *
160303 TTTATTTTCTAACAAGAAGATG-ATCTTGCGCTTTGGAACTATTCGTATTATAAAACC
1 TTTATTTTATAACAAGAAGATGAAT-TTGCACTTTGGAACTATTCGTATTATAAAACC
*
160360 TTTATTTTATAACAAGAAGATGAATTTGCACTTTGGAATTATTCGTATTATAAAACC
1 TTTATTTTATAACAAGAAGATGAATTTGCACTTTGGAACTATTCGTATTATAAAACC
160417 ATTAAAGATG
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
57 51 0.96
58 2 0.04
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.39
Consensus pattern (57 bp):
TTTATTTTATAACAAGAAGATGAATTTGCACTTTGGAACTATTCGTATTATAAAACC
Found at i:160814 original size:23 final size:23
Alignment explanation
Indices: 160754--160816 Score: 58
Period size: 23 Copynumber: 2.7 Consensus size: 23
160744 TAGCGTTTGC
** *
160754 GAACATATTTATTTAACGTTCGT
1 GAACATATTCCTTTAACGTTCAT
*
160777 G-A-ATATGTCCGTTTAGCGTTCAT
1 GAACATAT-TCC-TTTAACGTTCAT
160800 GAACATATTCCTTTAAC
1 GAACATATTCCTTTAAC
160817 ATTCGTTTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
21 4 0.13
22 2 0.06
23 17 0.55
24 4 0.13
25 4 0.13
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (23 bp):
GAACATATTCCTTTAACGTTCAT
Found at i:170725 original size:25 final size:26
Alignment explanation
Indices: 170686--170735 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
170676 GGAACCTTTC
* *
170686 CTTTTTCTTTTGATAAATAATTTATT
1 CTTTTTCTTTGGATAAATAAATTATT
*
170712 CTTTTT-TTTGGATAAGTAAATTAT
1 CTTTTTCTTTGGATAAATAAATTAT
170736 ATGCCATCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.28, C:0.06, G:0.08, T:0.58
Consensus pattern (26 bp):
CTTTTTCTTTGGATAAATAAATTATT
Found at i:179908 original size:15 final size:14
Alignment explanation
Indices: 179874--179908 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
179864 TGAACCTCTA
179874 AAATAATAATTTTT
1 AAATAATAATTTTT
179888 AGAATAATAATTTTAT
1 A-AATAATAATTTT-T
179904 AAATA
1 AAATA
179909 TTCGATCACC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 1 0.05
15 16 0.84
16 2 0.11
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (14 bp):
AAATAATAATTTTT
Found at i:196175 original size:28 final size:28
Alignment explanation
Indices: 196134--196188 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
196124 AGTTCACATT
196134 ATCATAAAATAATAATAATTTTGTTTTC
1 ATCATAAAATAATAATAATTTTGTTTTC
*
196162 ATCATCAAAA-AATAATATTTTTGTTTT
1 ATCAT-AAAATAATAATAATTTTGTTTT
196189 ATAATTTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (28 bp):
ATCATAAAATAATAATAATTTTGTTTTC
Found at i:196534 original size:60 final size:60
Alignment explanation
Indices: 196401--196537 Score: 152
Period size: 60 Copynumber: 2.3 Consensus size: 60
196391 ACATCCCCCT
* * * * *
196401 AAATCATTCAAAAGTTTAGGGATCAATATAGAATGAGGGTCGTAGTTTAGAGATGAATTTA
1 AAAT-ATTCAAAAGTTTAGAGATCAATATAGAATAAGAGTCCTAATTTAGAGATGAATTTA
* *
196462 AAATGTTCAAAAGTTTAGAGATCAATTTAGAATAAGAGTCCTAATTTA-AGAATG-ATATTA
1 AAATATTCAAAAGTTTAGAGATCAATATAGAATAAGAGTCCTAATTTAGAG-ATGAAT-TTA
* *
196522 GAATATTTAAAAGTTT
1 AAATATTCAAAAGTTT
196538 GATGACTAAT
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
59 4 0.06
60 56 0.88
61 4 0.06
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.34
Consensus pattern (60 bp):
AAATATTCAAAAGTTTAGAGATCAATATAGAATAAGAGTCCTAATTTAGAGATGAATTTA
Found at i:203502 original size:42 final size:42
Alignment explanation
Indices: 203450--203703 Score: 239
Period size: 42 Copynumber: 6.1 Consensus size: 42
203440 AAATTCAACC
* * * *
203450 CAATTATTGTCGAGTTGAGTTTTCGAACGATCTACTCTCGTT
1 CAATCATTGTCGAGTCGAGCTTTCGAACGACCTACTCTCGTT
* * * *
203492 CAATCATTGTCGAGTCGAACTTTCCAACAACCTACTCCCGTT
1 CAATCATTGTCGAGTCGAGCTTTCGAACGACCTACTCTCGTT
* * * * * * *
203534 CAATCATTGTCGGGTTGAGTTTTTTCAAATGACATACTCTTGTT
1 CAATCATTGTCGAGTCGAG--CTTTCGAACGACCTACTCTCGTT
* * *
203578 CAATCATTGTCGAGT----TTTTC-AGACAACCTACTCTTGTT
1 CAATCATTGTCGAGTCGAGCTTTCGA-ACGACCTACTCTCGTT
* *
203616 CAATCATTGTCGAGTCGAACTTTCGAACGACCTACTCTAGTT
1 CAATCATTGTCGAGTCGAGCTTTCGAACGACCTACTCTCGTT
* *
203658 CAATCATTGTCGAGTCGAGCTTTGGAACTACCTACTCTCAGTT
1 CAATCATTGTCGAGTCGAGCTTTCGAACGACCTACTCTC-GTT
203701 CAA
1 CAA
203704 GTATGATGGT
Statistics
Matches: 174, Mismatches: 29, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
37 1 0.01
38 33 0.19
42 103 0.59
43 7 0.04
44 30 0.17
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.35
Consensus pattern (42 bp):
CAATCATTGTCGAGTCGAGCTTTCGAACGACCTACTCTCGTT
Found at i:205325 original size:24 final size:24
Alignment explanation
Indices: 205293--205366 Score: 130
Period size: 24 Copynumber: 3.1 Consensus size: 24
205283 CATGCACGCC
205293 CAGCGACCTAGGTAGGTCGCCATG
1 CAGCGACCTAGGTAGGTCGCCATG
* *
205317 CAGTGACCTAGGTAGGTCGCAATG
1 CAGCGACCTAGGTAGGTCGCCATG
205341 CAGCGACCTAGGTAGGTCGCCATG
1 CAGCGACCTAGGTAGGTCGCCATG
205365 CA
1 CA
205367 ATCCCAAAGG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.23, C:0.27, G:0.32, T:0.18
Consensus pattern (24 bp):
CAGCGACCTAGGTAGGTCGCCATG
Found at i:218083 original size:31 final size:31
Alignment explanation
Indices: 218002--218085 Score: 107
Period size: 30 Copynumber: 2.7 Consensus size: 31
217992 GTTCAAGTTT
*
218002 TTTCGAGATCGAGTCGAGCTTCAATTTTTTA
1 TTTCGAAATCGAGTCGAGCTTCAATTTTTTA
* * * *
218033 TTTCG-AGTCAAGTCTAGCTTCATTTTTTTA
1 TTTCGAAATCGAGTCGAGCTTCAATTTTTTA
*
218063 TTTCGAAATTGAGTCGAGCTTCA
1 TTTCGAAATCGAGTCGAGCTTCA
218086 CAATATTAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
30 25 0.58
31 18 0.42
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.43
Consensus pattern (31 bp):
TTTCGAAATCGAGTCGAGCTTCAATTTTTTA
Found at i:221743 original size:30 final size:29
Alignment explanation
Indices: 221693--221766 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 29
221683 ACCTTGATTG
* * * * *
221693 AATTTAAGGGTCAAATTGACATTTTATCTA
1 AATTTAA-GGTTAAAATGACACTTCATCAA
221723 AATTTATAGGTTAAAATGACACTTCATCAA
1 AATTTA-AGGTTAAAATGACACTTCATCAA
221753 AATTTAAGGTTAAA
1 AATTTAAGGTTAAA
221767 TTAGTATTCT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
29 8 0.21
30 29 0.76
31 1 0.03
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (29 bp):
AATTTAAGGTTAAAATGACACTTCATCAA
Found at i:226503 original size:20 final size:21
Alignment explanation
Indices: 226478--226517 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
226468 TGAATAGTGC
226478 AATATTAAATTATG-TTTTAA
1 AATATTAAATTATGATTTTAA
226498 AATATTAAATTATGATTTTA
1 AATATTAAATTATGATTTTA
226518 TGTGATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (21 bp):
AATATTAAATTATGATTTTAA
Found at i:228877 original size:29 final size:31
Alignment explanation
Indices: 228844--228903 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
228834 AATCATTACA
228844 ACCTTAACTG-T-TGTAAGGAGTGACTTAAT
1 ACCTTAACTGTTCTGTAAGGAGTGACTTAAT
* *
228873 ACCTTAACTGTTCTTTAAGGTGTGACTTAAT
1 ACCTTAACTGTTCTGTAAGGAGTGACTTAAT
228904 TAAATTTCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 10 0.37
30 1 0.04
31 16 0.59
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.38
Consensus pattern (31 bp):
ACCTTAACTGTTCTGTAAGGAGTGACTTAAT
Found at i:234935 original size:103 final size:102
Alignment explanation
Indices: 234745--234949 Score: 304
Period size: 103 Copynumber: 2.0 Consensus size: 102
234735 ATTAAATATT
* *
234745 CTCAATCATTTGGCAATGAACATTCGTATTCGTAATATATTTAGTGATGAACCCGAAATTTTAAA
1 CTCAATCATTTGGCAATGAACATTAGTATTCGCAATATATTTAGTGATGAACCCGAAATTTTAAA
* *
234810 GAATAACAACAAATTTCTTAACCATTAA-AGTCGATTC
66 AAATAACAACAAATTTCTTAACCACTAAGA-TCGATTC
* * * *
234847 CTCAATCTTTTGGCAATGAACGTTAGTATTCGCGATATATTTAGTGTTTGAACCCGAAATTTTAA
1 CTCAATCATTTGGCAATGAACATTAGTATTCGCAATATATTTAGTG-ATGAACCCGAAATTTTAA
*
234912 AAAATAACAACAAATTTTTTAACCACTAAGATCGATTC
65 AAAATAACAACAAATTTCTTAACCACTAAGATCGATTC
234950 GTTGATGCTT
Statistics
Matches: 92, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
102 41 0.45
103 50 0.54
104 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (102 bp):
CTCAATCATTTGGCAATGAACATTAGTATTCGCAATATATTTAGTGATGAACCCGAAATTTTAAA
AAATAACAACAAATTTCTTAACCACTAAGATCGATTC
Found at i:238197 original size:2 final size:2
Alignment explanation
Indices: 238186--238232 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
238176 ATAATTAAAA
*
238186 AT AT -T AT AT AT AT AT TT AT A- 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
238226 AT AT AT A
1 AT AT AT A
238233 AAGACACATA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:240170 original size:20 final size:20
Alignment explanation
Indices: 240145--240184 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
240135 TTTGGTTCAC
240145 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
240165 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
240185 AATAAGATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.30, T:0.25
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:240192 original size:16 final size:18
Alignment explanation
Indices: 240145--240195 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 18
240135 TTTGGTTCAC
240145 GGAATGTAAGATTACCAGT
1 GGAA-GTAAGATTACCAGT
240164 GGGAATGTAAGATTACCAGT
1 -GGAA-GTAAGATTACCAGT
240184 -GAA-TAAGATTAC
1 GGAAGTAAGATTAC
240196 TGAGAATGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.29
18 3 0.10
20 19 0.61
ACGTcount: A:0.39, C:0.10, G:0.25, T:0.25
Consensus pattern (18 bp):
GGAAGTAAGATTACCAGT
Found at i:247729 original size:25 final size:26
Alignment explanation
Indices: 247669--247729 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 26
247659 TTTTAAAGAA
247669 ATTTTATTTCTATATTAGTATTTCAAC
1 ATTTTATTT-TATATTAGTATTTCAAC
* * *
247696 -TTTGATTTTAT-TTATTATTTTAAC
1 ATTTTATTTTATATTAGTATTTCAAC
247720 ATTTTATTTT
1 ATTTTATTTT
247730 TATCAAATGA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 11 0.38
25 11 0.38
26 7 0.24
ACGTcount: A:0.26, C:0.07, G:0.03, T:0.64
Consensus pattern (26 bp):
ATTTTATTTTATATTAGTATTTCAAC
Found at i:248208 original size:27 final size:27
Alignment explanation
Indices: 248169--248221 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
248159 ACATAAAAAC
248169 AATCATAACCCACACATCTAAATCAAT
1 AATCATAACCCACACATCTAAATCAAT
* *
248196 AATCATAAGCCACACGTCTAAATCAA
1 AATCATAACCCACACATCTAAATCAA
248222 CGCATGCTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.47, C:0.28, G:0.04, T:0.21
Consensus pattern (27 bp):
AATCATAACCCACACATCTAAATCAAT
Found at i:249579 original size:2 final size:2
Alignment explanation
Indices: 249572--249598 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
249562 GTATTTATTC
249572 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
249599 AACCTGATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:253864 original size:6 final size:6
Alignment explanation
Indices: 253845--253874 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
253835 TCTCATGGTA
253845 AAAAAT ATAAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT A-AAAAT AAAAAT AAAAAT AAAAA
253875 GAATTTCAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:261582 original size:11 final size:11
Alignment explanation
Indices: 261566--261607 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
261556 TCGTCTCGTC
261566 TCGGGTCGTGG
1 TCGGGTCGTGG
261577 TCGGGTCGTGG
1 TCGGGTCGTGG
*
261588 CCGGGGTCGTGG
1 TC-GGGTCGTGG
261600 TCGGGTCG
1 TCGGGTCG
261608 ATCTCCACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.00, C:0.21, G:0.55, T:0.24
Consensus pattern (11 bp):
TCGGGTCGTGG
Found at i:261596 original size:12 final size:12
Alignment explanation
Indices: 261568--261604 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
261558 GTCTCGTCTC
261568 GGGTCGTGGTC-
1 GGGTCGTGGTCG
*
261579 GGGTCGTGGCCG
1 GGGTCGTGGTCG
261591 GGGTCGTGGTCG
1 GGGTCGTGGTCG
261603 GG
1 GG
261605 TCGATCTCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.00, C:0.19, G:0.59, T:0.22
Consensus pattern (12 bp):
GGGTCGTGGTCG
Found at i:262275 original size:16 final size:15
Alignment explanation
Indices: 262254--262287 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
262244 CTTCGAAGAT
262254 ATAATAAATAATAATA
1 ATAATAAATAATAA-A
*
262270 ATAATAAATTATAAA
1 ATAATAAATAATAAA
262285 ATA
1 ATA
262288 CCCTAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
ATAATAAATAATAAA
Found at i:265188 original size:105 final size:105
Alignment explanation
Indices: 265006--265323 Score: 458
Period size: 105 Copynumber: 3.0 Consensus size: 105
264996 TGAAGTTTTA
* * *
265006 CTTCTTTGTAGAACTATTGATCATTACAGTCTGCACATTCATATCTTAGGCAGTTGTAGCTGGAT
1 CTTCTTTGTAGAACTATTGATCAGTATAGTCAGCACATTCATATCTTAGGCAGTTGTAGCTGGAT
265071 AGGCTTAAGTCCCTTTATTTCCTCGTCTTCCTTGACAATG
66 AGGCTTAAGTCCCTTTATTTCCTCGTCTTCCTTGACAATG
* * *
265111 CTTCTTTGTAGAACTATTGATCGGTATAATCAGCACATTCATATCTTAGGCAGGTGTAGCTGGAT
1 CTTCTTTGTAGAACTATTGATCAGTATAGTCAGCACATTCATATCTTAGGCAGTTGTAGCTGGAT
* * * *
265176 TGGCTTAAGTCCCTTTATTTCATCGTCTTACTTGACAATT
66 AGGCTTAAGTCCCTTTATTTCCTCGTCTTCCTTGACAATG
* * * * *
265216 CTTCTTTGTAGAACTATTTATTAGTATGGTCAGTACATTCATATCTTAGGCAGTTGCAGCTGGAT
1 CTTCTTTGTAGAACTATTGATCAGTATAGTCAGCACATTCATATCTTAGGCAGTTGTAGCTGGAT
* * *
265281 AGGCTTAAATTCCTTTATTTCGC-CGTCTTCCTTGACAAGG
66 AGGCTTAAGTCCCTTTATTTC-CTCGTCTTCCTTGACAATG
265321 CTT
1 CTT
265324 ATGGTAATTT
Statistics
Matches: 187, Mismatches: 25, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
105 187 1.00
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (105 bp):
CTTCTTTGTAGAACTATTGATCAGTATAGTCAGCACATTCATATCTTAGGCAGTTGTAGCTGGAT
AGGCTTAAGTCCCTTTATTTCCTCGTCTTCCTTGACAATG
Found at i:269644 original size:2 final size:2
Alignment explanation
Indices: 269637--269661 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
269627 CATACCGGAG
269637 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
269662 CATAATTTTT
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:272877 original size:16 final size:15
Alignment explanation
Indices: 272856--272899 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
272846 AAAGTTGATA
272856 ATATTATAATTATCTT
1 ATATTATAATT-TCTT
*
272872 ATATTATCAATTTTTT
1 ATATTAT-AATTTCTT
*
272888 ATGTTATAATTT
1 ATATTATAATTT
272900 TTTGTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.20
16 16 0.64
17 4 0.16
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (15 bp):
ATATTATAATTTCTT
Found at i:274741 original size:28 final size:28
Alignment explanation
Indices: 274709--274766 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
274699 TTCTTCGTTT
*
274709 ACATTATTTCGTCAAGCCAATGTTTGAA
1 ACATTATGTCGTCAAGCCAATGTTTGAA
* *
274737 ACATTGTGTCGTCGAGCCAATGTTTGAA
1 ACATTATGTCGTCAAGCCAATGTTTGAA
274765 AC
1 AC
274767 CAATGTTGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (28 bp):
ACATTATGTCGTCAAGCCAATGTTTGAA
Found at i:277189 original size:17 final size:17
Alignment explanation
Indices: 277155--277189 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
277145 ATTATAGATT
*
277155 ATTTAATAAAAAATAAA
1 ATTTAATAAAAAACAAA
*
277172 ATTTAATAATAAACAAA
1 ATTTAATAAAAAACAAA
277189 A
1 A
277190 AATAAATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
ATTTAATAAAAAACAAA
Done.