Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008373.1 Hibiscus syriacus cultivar Beakdansim tig00111129_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: 1027749
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:526369 original size:50 final size:50
Alignment explanation
Indices: 526264--526369 Score: 113
Period size: 50 Copynumber: 2.1 Consensus size: 50
526254 GATCAGGGGG
* * * * * * * *
526264 CGCGCTATACTCACGTGGCGCCAGATCACCGTATATCGTGGGACAGGAGG
1 CGCGCTATACCCACGTAGCACCAAATCAACGTATAACGTGAGACAGGAGA
**
526314 CGCGCTATACCCACGTAGCACCAAATCAACGTATAACGTGATTCAGGAGA
1 CGCGCTATACCCACGTAGCACCAAATCAACGTATAACGTGAGACAGGAGA
*
526364 TGCGCT
1 CGCGCT
526370 TTACTGCTAC
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.19
Consensus pattern (50 bp):
CGCGCTATACCCACGTAGCACCAAATCAACGTATAACGTGAGACAGGAGA
Found at i:531326 original size:13 final size:13
Alignment explanation
Indices: 531299--531333 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
531289 CAATGGTGAC
*
531299 GAAATTTTA-AGT
1 GAAATTTGAGAGT
531311 GAAATTTGAGAGT
1 GAAATTTGAGAGT
531324 GAAATTTGAG
1 GAAATTTGAG
531334 GATTGATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 8 0.38
13 13 0.62
ACGTcount: A:0.40, C:0.00, G:0.26, T:0.34
Consensus pattern (13 bp):
GAAATTTGAGAGT
Found at i:532600 original size:70 final size:69
Alignment explanation
Indices: 532488--532626 Score: 260
Period size: 70 Copynumber: 2.0 Consensus size: 69
532478 TCCACTTACC
*
532488 CAACTTTTAGAATCATTTTTCATAGACGTAAAACCCAGTAGATGGGCCATTATTTGCATGAAAAC
1 CAACTTTTAGAATCATTTTTCATAGACATAAAACCCAGTAGATGGGCCATTATTTGCATGAAAAC
532553 TTGA
66 TTGA
532557 CAACTTTTAGAATCATTTTTTCATAGACATAAAACCCAGTAGATGGGCCATTATTTGCATGAAAA
1 CAACTTTTAGAATCA-TTTTTCATAGACATAAAACCCAGTAGATGGGCCATTATTTGCATGAAAA
532622 CTTGA
65 CTTGA
532627 AGAAAAAAAA
Statistics
Matches: 68, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
69 15 0.22
70 53 0.78
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Consensus pattern (69 bp):
CAACTTTTAGAATCATTTTTCATAGACATAAAACCCAGTAGATGGGCCATTATTTGCATGAAAAC
TTGA
Found at i:533711 original size:2 final size:2
Alignment explanation
Indices: 533704--533729 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
533694 ATTTATAATT
533704 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
533730 AAAAATTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:536995 original size:21 final size:21
Alignment explanation
Indices: 536949--537179 Score: 235
Period size: 20 Copynumber: 11.3 Consensus size: 21
536939 GATTCTGACT
**
536949 ATCGCATTGCGATTT-CCCAA
1 ATCGCATTGCGATTTACGTAA
* * *
536969 ATTCGCGTTGCGATTTTCCTAA
1 A-TCGCATTGCGATTTACGTAA
* * * *
536991 ATCGCAATGCGAATTAGGAAA
1 ATCGCATTGCGATTTACGTAA
*
537012 ATCGCAATGCGA-TTACGTAA
1 ATCGCATTGCGATTTACGTAA
*
537032 ATCGCAATGCGAATTTACGT-A
1 ATCGCATTGCG-ATTTACGTAA
537053 ATCGCATTGCGATTTACGT-A
1 ATCGCATTGCGATTTACGTAA
*
537073 TTCGCATTGCGATTTACGT-A
1 ATCGCATTGCGATTTACGTAA
* * *
537093 TTCGCATTGCGATTTTCCTAA
1 ATCGCATTGCGATTTACGTAA
*
537114 TTCGCATTGCGATTTACGT-A
1 ATCGCATTGCGATTTACGTAA
537134 ATCGCATTGCGATTTACGT-A
1 ATCGCATTGCGATTTACGTAA
*
537154 TTCGCATTGCGATTTA-GTAA
1 ATCGCATTGCGATTTACGTAA
537174 ATCGCA
1 ATCGCA
537180 ACGAGATTCT
Statistics
Matches: 185, Mismatches: 20, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
19 2 0.01
20 104 0.56
21 68 0.37
22 11 0.06
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (21 bp):
ATCGCATTGCGATTTACGTAA
Found at i:537040 original size:41 final size:42
Alignment explanation
Indices: 536977--537180 Score: 172
Period size: 41 Copynumber: 5.0 Consensus size: 42
536967 AAATTCGCGT
* * *
536977 TGCGATTTTCCTAAATCGCAATGCGAA-TTAGGAAAATCGCAA
1 TGCGATTTACGTAAATCGCAATGCGAATTTACG-AAATCGCAA
* *
537019 TGCGA-TTACGTAAATCGCAATGCGAATTTACGTAATCGCAT
1 TGCGATTTACGTAAATCGCAATGCGAATTTACGAAATCGCAA
* * * * *
537060 TGCGATTTACGT-ATTCGCATTGCG-ATTTACGTATTCGCAT
1 TGCGATTTACGTAAATCGCAATGCGAATTTACGAAATCGCAA
* * * * * *
537100 TGCGATTTTCCTAATTCGCATTGCG-ATTTACGTAATCGCAT
1 TGCGATTTACGTAAATCGCAATGCGAATTTACGAAATCGCAA
* *
537141 TGCGATTTACGT-ATTCGCATTGCG-ATTTA-GTAAATCGCAA
1 TGCGATTTACGTAAATCGCAATGCGAATTTACG-AAATCGCAA
537181 CGAGATTCTG
Statistics
Matches: 143, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
39 1 0.01
40 49 0.34
41 78 0.55
42 15 0.10
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (42 bp):
TGCGATTTACGTAAATCGCAATGCGAATTTACGAAATCGCAA
Found at i:537119 original size:61 final size:60
Alignment explanation
Indices: 536949--537168 Score: 253
Period size: 61 Copynumber: 3.6 Consensus size: 60
536939 GATTCTGACT
* ** * * * * *
536949 ATCGCATTGCGATTTCCCAAATTCGCGTTGCGATTTTCCTAAATCGCAATGCGAATTAGGAAA
1 ATCGCATTGCGATTT-ACGTATTCGCATTGCGATTTTCCT-AATCGCATTGCGATTTACG-TA
* * * * *
537012 ATCGCAATGCGA-TTACGTAAATCGCAATGCGAATTTACGTAATCGCATTGCGATTTACGTA
1 ATCGCATTGCGATTTACGT-ATTCGCATTGCG-ATTTTCCTAATCGCATTGCGATTTACGTA
*
537073 TTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTA
1 ATCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTAA-TCGCATTGCGATTTACGTA
537134 ATCGCATTGCGATTTACGTATTCGCATTGCGATTT
1 ATCGCATTGCGATTTACGTATTCGCATTGCGATTT
537169 AGTAAATCGC
Statistics
Matches: 133, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
60 8 0.06
61 75 0.56
62 33 0.25
63 17 0.13
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (60 bp):
ATCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTAATCGCATTGCGATTTACGTA
Found at i:537220 original size:81 final size:81
Alignment explanation
Indices: 537033--537203 Score: 195
Period size: 81 Copynumber: 2.1 Consensus size: 81
537023 ATTACGTAAA
* * *
537033 TCGCAATGCGAATTTACGTAATCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGC
1 TCGCAATACG-ATTTACGAAATCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGC
** * **
537098 ATTGCGATTTTCCTAAT
65 AACGAGATTTGACTAAT
* * *
537115 TCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCATTGCGATTTA-GTAAATCGC
1 TCGCAATACGATTTACGAAATCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT-AATCGC
537179 AACGAGATTCTGACT-A-
65 AACGAGATT-TGACTAAT
537195 TCGCAATAC
1 TCGCAATAC
537204 TGAATTTCAA
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
80 9 0.12
81 57 0.73
82 12 0.15
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (81 bp):
TCGCAATACGATTTACGAAATCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCA
ACGAGATTTGACTAAT
Found at i:540644 original size:14 final size:14
Alignment explanation
Indices: 540625--540679 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
540615 GCGAAATGAA
540625 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
540639 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
540658 AATCGCAACGAGAG
1 AATCGCAACGAGAG
540672 AATCGCAA
1 AATCGCAA
540680 TGCAAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:540649 original size:33 final size:33
Alignment explanation
Indices: 540607--540733 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
540597 GGAAATGACT
540607 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
540640 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
540673 ATCGCAATGCAAAATGAAAATCGCAATGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
540706 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
540734 CGAATTTAGT
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 88 1.00
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:540663 original size:19 final size:19
Alignment explanation
Indices: 540587--540737 Score: 98
Period size: 19 Copynumber: 8.7 Consensus size: 19
540577 CTTAATATCT
* **
540587 ATCGCAACGCGGAAATGACT
1 ATCGCAATGC-GAAATGAAA
540607 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
540626 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
540640 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
540659 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
540673 ATCGCAATGCAAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
540692 ATCGCAAT--G--A-GGGA
1 ATCGCAATGCGAAATGAAA
*
540706 ATCGCAAAGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
540725 ATCGCAACGCGAA
1 ATCGCAATGCGAA
540738 TTTAGTTTCG
Statistics
Matches: 101, Mismatches: 15, Indels: 31
0.69 0.10 0.21
Matches are distributed among these distances:
14 29 0.29
15 3 0.03
16 4 0.04
17 4 0.04
18 3 0.03
19 49 0.49
20 9 0.09
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:540901 original size:14 final size:14
Alignment explanation
Indices: 540882--540918 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
540872 CATCAATTAA
540882 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
540896 ACAAATCATCTTTT
1 ACAAATCAACTTTT
540910 ACAAATCAA
1 ACAAATCAA
540919 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:542335 original size:21 final size:21
Alignment explanation
Indices: 542269--542335 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
542259 ATGAATCGGG
*
542269 CTCTTGAAAGGTGGGA-GGGA
1 CTCTTGAATGGTGGGAGGGGA
* * ** * *
542289 CCTCTTCAATGATGACAGTGGC
1 -CTCTTGAATGGTGGGAGGGGA
542311 CTCTTGAATGGTGGGAGGGGA
1 CTCTTGAATGGTGGGAGGGGA
542332 CTCT
1 CTCT
542336 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.21, C:0.18, G:0.36, T:0.25
Consensus pattern (21 bp):
CTCTTGAATGGTGGGAGGGGA
Found at i:542354 original size:42 final size:41
Alignment explanation
Indices: 542269--542391 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
542259 ATGAATCGGG
* * * *
542269 CTCTTGAAAGGTGGGA-GGGACCTCTTCAATGATGACAGTGGC
1 CTCTTGAATGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
542311 CTCTTGAATGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAATGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
542353 CTCTTCAATGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAATGGTGGGAGGGGACTCTCGA-GGATGACAGG
542392 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.24, C:0.16, G:0.37, T:0.24
Consensus pattern (41 bp):
CTCTTGAATGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:542828 original size:19 final size:19
Alignment explanation
Indices: 542788--542914 Score: 120
Period size: 19 Copynumber: 6.8 Consensus size: 19
542778 TCTGGAACTT
*
542788 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG--AAATG
**
542809 ACTATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
542828 AAAATCGCAACGAGAGAATG
1 AAAATCGCAACGCGA-AATG
*
542848 AAAATCGCAACGCGAAACG
1 AAAATCGCAACGCGAAATG
542867 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
* * *
542881 AGAATCACAATGCGAAATG
1 AAAATCGCAACGCGAAATG
542900 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
542915 TTATAGTTTC
Statistics
Matches: 87, Mismatches: 13, Indels: 14
0.76 0.11 0.12
Matches are distributed among these distances:
14 9 0.10
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 43 0.49
20 18 0.21
21 11 0.13
ACGTcount: A:0.47, C:0.20, G:0.21, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:542857 original size:39 final size:39
Alignment explanation
Indices: 542788--542885 Score: 142
Period size: 39 Copynumber: 2.5 Consensus size: 39
542778 TCTGGAACTT
* * ** *
542788 AAAATCGCAACGTGAAAAATGACTATCGCAACGCGAAATG
1 AAAATCGCAACGAG-AGAATGAAAATCGCAACGCGAAACG
542828 AAAATCGCAACGAGAGAATGAAAATCGCAACGCGAAACG
1 AAAATCGCAACGAGAGAATGAAAATCGCAACGCGAAACG
542867 AAAATCGCAACGAGAGAAT
1 AAAATCGCAACGAGAGAAT
542886 CACAATGCGA
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
39 40 0.75
40 13 0.25
ACGTcount: A:0.48, C:0.19, G:0.21, T:0.11
Consensus pattern (39 bp):
AAAATCGCAACGAGAGAATGAAAATCGCAACGCGAAACG
Found at i:542903 original size:33 final size:36
Alignment explanation
Indices: 542816--542911 Score: 117
Period size: 33 Copynumber: 2.7 Consensus size: 36
542806 ATGACTATCG
*
542816 CAACGCGAAATGAAAATCGCAACGAGAGAATGAAAATCG
1 CAACGCGAAATGAAAATCGCAAC--GAGAATG-AAATCA
*
542855 CAACGCGAAACGAAAATCGCAACGAG-A-G-AATCA
1 CAACGCGAAATGAAAATCGCAACGAGAATGAAATCA
*
542888 CAATGCGAAATGAAAATCGCAACG
1 CAACGCGAAATGAAAATCGCAACG
542912 CGATTATAGT
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
33 26 0.49
35 1 0.02
36 1 0.02
37 3 0.06
39 22 0.42
ACGTcount: A:0.48, C:0.21, G:0.22, T:0.09
Consensus pattern (36 bp):
CAACGCGAAATGAAAATCGCAACGAGAATGAAATCA
Found at i:542933 original size:19 final size:19
Alignment explanation
Indices: 542911--543048 Score: 137
Period size: 19 Copynumber: 7.4 Consensus size: 19
542901 AAATCGCAAC
*
542911 GCGATTATAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
*
542930 GCGATTTTTGGTTTCGCGTT
1 GCGA-TTTTAGTTTCGCGTT
542950 GCGATTTT-G--T--CGTT
1 GCGATTTTAGTTTCGCGTT
*
542964 GCGATTTTCA-TTTTGCGTT
1 GCGATTTT-AGTTTCGCGTT
*
542983 GCGATTTTCGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
*
543002 GCGATTTTCGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
*
543021 GCGATTTTCA-TTCTCTCGTT
1 GCGATTTT-AGTT-TCGCGTT
543041 GCGATTTT
1 GCGATTTT
543049 CATTTCAACC
Statistics
Matches: 103, Mismatches: 6, Indels: 19
0.80 0.05 0.15
Matches are distributed among these distances:
14 12 0.12
16 1 0.01
17 1 0.01
18 1 0.01
19 57 0.55
20 31 0.30
ACGTcount: A:0.09, C:0.18, G:0.25, T:0.49
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:543261 original size:94 final size:93
Alignment explanation
Indices: 543145--543446 Score: 532
Period size: 94 Copynumber: 3.2 Consensus size: 93
543135 ATGGATTGCA
* *
543145 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGTT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
*
543210 TAGCAGAATTGGCAGCAAACGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
* *
543238 TTACTTTCAACCAAAAGAAAAAACAAAGACAAATACTAACTTCATAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
543303 TTAGCAGAATTGGCAGCAACCGAACAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
543332 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
543397 TTAGCAGAATTGGCAGCAACCGAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
543426 TTACTTCAACCAAAAGACAAA
1 TTACTTCAACCAAAAGACAAA
543447 TACTAACTTC
Statistics
Matches: 201, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
93 21 0.10
94 180 0.90
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (93 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:543504 original size:78 final size:79
Alignment explanation
Indices: 543356--543508 Score: 229
Period size: 78 Copynumber: 1.9 Consensus size: 79
543346 AAGACAAAAC
*
543356 AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
1 AAAGACAAATACTAACTTCACAGTGTTAAAGAAT--A-AGTTTAGCAGAATTAGCAGCAACCGAA
543421 TAAATTTACTTCAACCA
63 TAAATTTACTTCAACCA
* *
543438 AAAGACAAATACTAACTTCACGGTGTTAATA-AAT-AGTTTAGCAGTATTAGCAGCAACCGAATA
1 AAAGACAAATACTAACTTCACAGTGTTAA-AGAATAAGTTTAGCAGAATTAGCAGCAACCGAATA
543501 AATTTACT
65 AATTTACT
543509 AAGCAATCTA
Statistics
Matches: 67, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
78 35 0.52
82 31 0.46
83 1 0.01
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (79 bp):
AAAGACAAATACTAACTTCACAGTGTTAAAGAATAAGTTTAGCAGAATTAGCAGCAACCGAATAA
ATTTACTTCAACCA
Found at i:545259 original size:19 final size:19
Alignment explanation
Indices: 545195--545326 Score: 148
Period size: 19 Copynumber: 7.1 Consensus size: 19
545185 TCTTTTGGTT
**
545195 GAAATGAAAATCGCAACAA
1 GAAATGAAAATCGCAACGC
545214 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
545234 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
*
545254 GAAATGAAAATAGCAA--C
1 GAAATGAAAATCGCAACGC
*
545271 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
545287 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
545306 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
545325 GA
1 GA
545327 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
14 9 0.09
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 48 0.51
20 30 0.32
21 2 0.02
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:545376 original size:19 final size:18
Alignment explanation
Indices: 545333--545379 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 18
545323 GCGATTTTGG
545333 TTTCGCGTTGCGATTCTC
1 TTTCGCGTTGCGATTCTC
545351 --T--CGTTGCGATTCTC
1 TTTCGCGTTGCGATTCTC
545365 ATTTCGCGTTGCGAT
1 -TTTCGCGTTGCGAT
545380 AGTCATTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 9
0.73 0.00 0.27
Matches are distributed among these distances:
14 13 0.54
16 1 0.04
17 1 0.04
19 9 0.38
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.43
Consensus pattern (18 bp):
TTTCGCGTTGCGATTCTC
Found at i:545385 original size:19 final size:20
Alignment explanation
Indices: 545352--545397 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
545342 GCGATTCTCT
*
545352 CGTTGCGATTCTCA-TTTCG
1 CGTTGCGATACTCATTTTCG
*
545371 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATACTCATTTTCG
*
545391 TGTTGCG
1 CGTTGCG
545398 GTTTTCCTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.11, C:0.22, G:0.26, T:0.41
Consensus pattern (20 bp):
CGTTGCGATACTCATTTTCG
Found at i:545988 original size:21 final size:21
Alignment explanation
Indices: 545958--546198 Score: 287
Period size: 20 Copynumber: 11.8 Consensus size: 21
545948 GCTATGTAAA
*
545958 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACCTAAT
* *
545979 TCGTATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACCTAAT
*
546000 TCGCATTGCGATTTACGTAA-
1 TCGCATTGCGATTTACCTAAT
*
546020 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACCTAAT
*
546041 TCGCATTGCGATTTACGTAA-
1 TCGCATTGCGATTTACCTAAT
*
546061 TCGCATTGCGATTTACAT-AT
1 TCGCATTGCGATTTACCTAAT
*
546081 TCGCATTGCGATTTACGT-AT
1 TCGCATTGCGATTTACCTAAT
**
546101 TCGCATTGCGATTTTTCTAAT
1 TCGCATTGCGATTTACCTAAT
*
546122 TCGCATTGCGATTTACGTAA-
1 TCGCATTGCGATTTACCTAAT
* * *
546142 TCGCGTTGTGATTTTCCTAAT
1 TCGCATTGCGATTTACCTAAT
* *
546163 TTGCATTGCGATTTACGTAA-
1 TCGCATTGCGATTTACCTAAT
*
546183 TCGCGTTGCGATTTAC
1 TCGCATTGCGATTTAC
546199 GTATTTGCAT
Statistics
Matches: 189, Mismatches: 27, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
19 1 0.01
20 99 0.52
21 89 0.47
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTACCTAAT
Found at i:546037 original size:41 final size:41
Alignment explanation
Indices: 545958--546196 Score: 363
Period size: 41 Copynumber: 5.8 Consensus size: 41
545948 GCTATGTAAA
* * *
545958 TCGCATTGCGATTTTCCTAATTCGTATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGTAA-TCGCATTGCGATTTTCCTAAT
546000 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
* *
546041 TCGCATTGCGATTTACGTAATCGCATTGCGATTTACAT-AT
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
* *
546081 TCGCATTGCGATTTACGTATTCGCATTGCGATTTTTCTAAT
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
* *
546122 TCGCATTGCGATTTACGTAATCGCGTTGTGATTTTCCTAAT
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
* *
546163 TTGCATTGCGATTTACGTAATCGCGTTGCGATTT
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTT
546197 ACGTATTTGC
Statistics
Matches: 181, Mismatches: 15, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
40 36 0.20
41 127 0.70
42 18 0.10
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
Found at i:546176 original size:122 final size:123
Alignment explanation
Indices: 545958--546209 Score: 407
Period size: 122 Copynumber: 2.1 Consensus size: 123
545948 GCTATGTAAA
* *
545958 TCGCATTGCGATTTTCCTAATTCGTATTGCGATTTTCCTAATTCGCATTGCGATTTACGTAATCG
1 TCGCATTGCGATTTACCTAATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTAATCG
546023 CATTGCGATTTTCCTAATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACATAT
66 CATTGCGATTTTCCTAATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACATAT
* *
546081 TCGCATTGCGATTTACGT-ATTCGCATTGCGATTTTTCTAATTCGCATTGCGATTTACGTAATCG
1 TCGCATTGCGATTTACCTAATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTAATCG
* * * * *
546145 CGTTGTGATTTTCCTAATTTGCATTGCGATTTACGTAATCGCGTTGCGATTTACGTAT
66 CATTGCGATTTTCCTAATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACATAT
*
546203 TTGCATT
1 TCGCATT
546210 ACGAATTAGG
Statistics
Matches: 119, Mismatches: 10, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
122 103 0.87
123 16 0.13
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.42
Consensus pattern (123 bp):
TCGCATTGCGATTTACCTAATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTAATCG
CATTGCGATTTTCCTAATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACATAT
Found at i:546226 original size:41 final size:41
Alignment explanation
Indices: 545984--546227 Score: 177
Period size: 41 Copynumber: 6.0 Consensus size: 41
545974 CTAATTCGTA
* * * * * *
545984 TTGCGATTTTCCTAATTCGCATTGCGATTTACGTAATCGCA
1 TTGCGATTTACCTAATTTGCATTACGAATTACGAAATCGCG
* * * * * *
546025 TTGCGATTTTCCTAATTCGCATTGCGATTTACGTAATCGCA
1 TTGCGATTTACCTAATTTGCATTACGAATTACGAAATCGCG
* * * * * * *
546066 TTGCGATTTACAT-ATTCGCATTGCGATTTACGTATTCGCA
1 TTGCGATTTACCTAATTTGCATTACGAATTACGAAATCGCG
** * * * *
546106 TTGCGATTTTTCTAATTCGCATTGCGATTTACGTAATCGCG
1 TTGCGATTTACCTAATTTGCATTACGAATTACGAAATCGCG
* * * * *
546147 TTGTGATTTTCCTAATTTGCATTGCGATTTACGTAATCGCG
1 TTGCGATTTACCTAATTTGCATTACGAATTACGAAATCGCG
* *
546188 TTGCGATTTACGT-ATTTGCATTACGAATTAGGAAAATCGC
1 TTGCGATTTACCTAATTTGCATTACGAATTACG-AAATCGC
546228 AACGCGAATT
Statistics
Matches: 183, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
40 52 0.28
41 131 0.72
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (41 bp):
TTGCGATTTACCTAATTTGCATTACGAATTACGAAATCGCG
Found at i:546237 original size:21 final size:21
Alignment explanation
Indices: 546211--546255 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
546201 ATTTGCATTA
546211 CGAATTAGGAAAATCGCAACG
1 CGAATTAGGAAAATCGCAACG
* * *
546232 CGAATTTGGGAAATCGCAATG
1 CGAATTAGGAAAATCGCAACG
546253 CGA
1 CGA
546256 TAGTCAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.18, G:0.27, T:0.18
Consensus pattern (21 bp):
CGAATTAGGAAAATCGCAACG
Found at i:547483 original size:21 final size:20
Alignment explanation
Indices: 547397--547554 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
547387 AAATGACCAA
**
547397 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
547416 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
547436 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
547456 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
547477 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
547498 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
547518 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
547539 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
547555 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:547583 original size:20 final size:20
Alignment explanation
Indices: 547521--547714 Score: 203
Period size: 20 Copynumber: 9.7 Consensus size: 20
547511 CGATTTTCCA
* ** *
547521 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
547541 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
547561 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
547581 AAATCGCAACATGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
547601 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
547621 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
547641 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * * *
547661 AAATTGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
547681 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
547702 AAATCGCAACGCG
1 AAATCGCAACGCG
547715 ATATTTAAAG
Statistics
Matches: 142, Mismatches: 27, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
19 2 0.01
20 123 0.87
21 16 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:547605 original size:60 final size:60
Alignment explanation
Indices: 547541--547711 Score: 225
Period size: 60 Copynumber: 2.8 Consensus size: 60
547531 GCGAATATGA
* *
547541 AAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTAAATCGCAACATGTATCCGT
1 AAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAAATCGCAACACGTATCCGT
* *** * * *
547601 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAAATCGCAACACGTATCCGT
* **
547661 AAATTGCAACGATAATACATAAAATCGCAACGCGTATCCGTAAATCGCAAC
1 AAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTAAATCGCAAC
547712 GCGATATTTA
Statistics
Matches: 92, Mismatches: 18, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 64 0.70
61 28 0.30
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAAATCGCAACACGTATCCGT
Found at i:548129 original size:33 final size:33
Alignment explanation
Indices: 548090--548160 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
548080 TTCACTTAGA
* *
548090 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
548123 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
548156 TTTCA
1 TTTCA
548161 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:548265 original size:20 final size:19
Alignment explanation
Indices: 548240--548344 Score: 87
Period size: 20 Copynumber: 5.6 Consensus size: 19
548230 TACAGAAGAG
548240 TCGCAACGAGATAAATGAAA
1 TCGCAACGAGA-AAATGAAA
* **
548260 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGA-AA
548280 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATG-AAA
548301 TCGCAACGAG---A-G-AA
1 TCGCAACGAGAAAATGAAA
*
548315 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATG-AAA
548334 TCGCAACGAGA
1 TCGCAACGAGA
548345 GAATCGCACG
Statistics
Matches: 68, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 16 0.24
20 22 0.32
21 14 0.21
22 1 0.01
ACGTcount: A:0.45, C:0.19, G:0.25, T:0.11
Consensus pattern (19 bp):
TCGCAACGAGAAAATGAAA
Found at i:548296 original size:40 final size:41
Alignment explanation
Indices: 548239--548348 Score: 139
Period size: 33 Copynumber: 2.9 Consensus size: 41
548229 TTACAGAAGA
*
548239 GTCGCAACGAGATAAATG-AAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
548279 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAG-A--A--
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
*
548315 -TCGCAAC--GCGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
548349 CGCACGCGAA
Statistics
Matches: 65, Mismatches: 2, Indels: 11
0.83 0.03 0.14
Matches are distributed among these distances:
33 23 0.35
34 1 0.02
35 7 0.11
38 1 0.02
40 18 0.28
41 15 0.23
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:548318 original size:14 final size:14
Alignment explanation
Indices: 548299--548352 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
548289 GAGAAATGAA
548299 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
548313 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
548332 AATCGCAACGAGAG
1 AATCGCAACGAGAG
548346 AATCGCA
1 AATCGCA
548353 CGCGAAACCA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:548331 original size:33 final size:32
Alignment explanation
Indices: 548291--548370 Score: 133
Period size: 33 Copynumber: 2.5 Consensus size: 32
548281 CGCAACGAGA
548291 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGC-ACGC
548324 GAAATGAAAATCGCAACGAGAGAATCGCACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCACGC
**
548356 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
548371 TTGCGATTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 17 0.38
33 28 0.62
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (32 bp):
GAAATGAAAATCGCAACGAGAGAATCGCACGC
Found at i:548418 original size:33 final size:33
Alignment explanation
Indices: 548371--548484 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
548361 CAAAATCGCA
548371 TTGCGA-TTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
548403 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
548436 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
548469 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
548485 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
32 6 0.08
33 71 0.92
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:548425 original size:19 final size:17
Alignment explanation
Indices: 548366--548482 Score: 81
Period size: 14 Copynumber: 7.1 Consensus size: 17
548356 GAAACCAAAA
*
548366 TCGCATTGCGATTTCATT
1 TCGCGTTGCGATTTCA-T
548384 TCGCGTTGCGA-TTC--
1 TCGCGTTGCGATTTCAT
*
548398 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCA-T
548417 TCGCGTTGCGA-TTC--
1 TCGCGTTGCGATTTCAT
*
548431 TCTCGTTGCGATTGTCAT
1 TCGCGTTGCGATT-TCAT
548449 CTCGCGTTGCGA-TTC--
1 -TCGCGTTGCGATTTCAT
*
548464 TCTCGTTGCGATTTTCAT
1 TCGCGTTGCGA-TTTCAT
548482 T
1 T
548483 TCAACCAAAA
Statistics
Matches: 79, Mismatches: 6, Indels: 28
0.70 0.05 0.25
Matches are distributed among these distances:
14 30 0.38
15 1 0.01
16 8 0.10
17 8 0.10
18 12 0.15
19 20 0.25
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.44
Consensus pattern (17 bp):
TCGCGTTGCGATTTCAT
Found at i:550329 original size:93 final size:93
Alignment explanation
Indices: 550170--550642 Score: 912
Period size: 93 Copynumber: 5.1 Consensus size: 93
550160 TAGATTGCTT
* *
550170 AGTAAATTTATTCGGTTGCTGCCAATTATGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
550235 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
550263 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
550328 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
550356 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
550421 TTTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
550448 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
550513 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
550541 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
550606 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
550634 AGTAAATTT
1 AGTAAATTT
550643 ATCCATTCAA
Statistics
Matches: 375, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
92 91 0.24
93 284 0.76
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:550521 original size:185 final size:186
Alignment explanation
Indices: 550170--550642 Score: 912
Period size: 185 Copynumber: 2.5 Consensus size: 186
550160 TAGATTGCTT
* *
550170 AGTAAATTTATTCGGTTGCTGCCAATTATGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
550235 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
*
550300 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTATAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
550356 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
550421 TTTGTCTTTGTTTTGTC-TTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
550485 GTGTATTCTATAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTATAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
550541 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
550606 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
550643 ATCCATTCAA
Statistics
Matches: 283, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
185 184 0.65
186 99 0.35
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTATAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:550726 original size:19 final size:19
Alignment explanation
Indices: 550702--550814 Score: 120
Period size: 19 Copynumber: 6.5 Consensus size: 19
550692 CACGAAACTT
550702 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
**
550721 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAACC
550740 AAAATCGCAA--CG--A-C
1 AAAATCGCAACGCGAAACC
*
550754 AGAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
550773 AAAATCGCAA--CG--A-C
1 AAAATCGCAACGCGAAACC
*
550787 AAGATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
550806 AAAATCGCA
1 AAAATCGCA
550815 TTGCGATTTT
Statistics
Matches: 77, Mismatches: 7, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
14 19 0.25
15 2 0.03
16 4 0.05
17 4 0.05
18 2 0.03
19 46 0.60
ACGTcount: A:0.47, C:0.28, G:0.18, T:0.07
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACC
Found at i:550765 original size:33 final size:32
Alignment explanation
Indices: 550722--550814 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
550712 CGCGAAACCA
**
550722 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
550754 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
550787 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
550815 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:550812 original size:52 final size:51
Alignment explanation
Indices: 550702--550814 Score: 131
Period size: 52 Copynumber: 2.2 Consensus size: 51
550692 CACGAAACTT
* *
550702 AAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAAGCGAAAC-AC
* * *
550754 AGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGATCGCAACGCGAAAC-C
1 AAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-AT-GAAAAGCGAAACAC
550806 AAAATCGCA
1 AAAATCGCA
550815 TTGCGATTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
52 41 0.79
53 3 0.06
54 8 0.15
ACGTcount: A:0.47, C:0.28, G:0.18, T:0.07
Consensus pattern (51 bp):
AAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAAGCGAAACAC
Found at i:550832 original size:19 final size:19
Alignment explanation
Indices: 550810--550944 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
550800 GAAACCAAAA
*
550810 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
550829 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
550845 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
550862 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
550878 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
550895 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
550914 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
550934 TCGTGTTGCGA
1 TCGCGTTGCGA
550945 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:550851 original size:14 final size:14
Alignment explanation
Indices: 550832--550888 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
550822 TTTCATTTCG
550832 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
550846 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
550863 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
550879 CGTTGCGATT
1 CGTTGCGATT
550889 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:550857 original size:33 final size:33
Alignment explanation
Indices: 550815--550907 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
550805 CAAAATCGCA
*
550815 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
550848 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
550881 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
550908 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:552890 original size:14 final size:14
Alignment explanation
Indices: 552871--552906 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
552861 ATTGTTTAAT
552871 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
552885 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
552899 TGATTTGT
1 TGATTTGT
552907 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:553037 original size:19 final size:19
Alignment explanation
Indices: 553013--553112 Score: 138
Period size: 19 Copynumber: 5.5 Consensus size: 19
553003 AAAATTGACT
553013 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
553032 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
553051 TTCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
553065 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
553084 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
553104 ATCGCAATG
1 ATCGCAATG
553113 GGAGAATCGC
Statistics
Matches: 71, Mismatches: 4, Indels: 11
0.83 0.05 0.13
Matches are distributed among these distances:
14 9 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 38 0.54
20 18 0.25
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:553142 original size:53 final size:53
Alignment explanation
Indices: 553013--553129 Score: 200
Period size: 53 Copynumber: 2.2 Consensus size: 53
553003 AAAATTGACT
*
553013 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAATTCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
* *
553065 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAATGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
553118 ATCGCAATGCGA
1 ATCGCAATGCGA
553130 TTTTAATTTC
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
52 29 0.48
53 32 0.52
ACGTcount: A:0.43, C:0.17, G:0.25, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:553147 original size:19 final size:19
Alignment explanation
Indices: 553119--553285 Score: 168
Period size: 19 Copynumber: 9.6 Consensus size: 19
553109 AATGGGAGAA
* *
553119 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
553138 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
553154 TCG--TTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
553170 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
553189 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
553205 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
553222 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
553241 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
553257 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
553274 TCCGCATTGCGA
1 T-CGCATTGCGA
553286 AATGTAATGG
Statistics
Matches: 124, Mismatches: 8, Indels: 31
0.76 0.05 0.19
Matches are distributed among these distances:
14 18 0.15
15 3 0.02
16 22 0.18
17 14 0.11
18 8 0.06
19 53 0.43
20 6 0.05
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:553162 original size:33 final size:33
Alignment explanation
Indices: 553125--553285 Score: 150
Period size: 33 Copynumber: 4.7 Consensus size: 33
553115 AGAATCGCAA
*
553125 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
553158 TGCGA-TTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
* * * * *
553195 TGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCAT
1 TGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGT
553228 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
553261 TGCGATTTTCATTTCCGCATTGCGA
1 TGCGATTTTCATTT-CGCATTGCGA
553286 AATGTAATGG
Statistics
Matches: 102, Mismatches: 13, Indels: 25
0.73 0.09 0.18
Matches are distributed among these distances:
31 9 0.09
32 22 0.22
33 31 0.30
34 13 0.13
35 6 0.06
37 8 0.08
38 1 0.01
39 3 0.03
40 9 0.09
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:553241 original size:52 final size:52
Alignment explanation
Indices: 553119--553285 Score: 300
Period size: 52 Copynumber: 3.2 Consensus size: 52
553109 AATGGGAGAA
* *
553119 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
553170 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
553222 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
553274 TCCGCATTGCGA
1 T-CGCATTGCGA
553286 AATGTAATGG
Statistics
Matches: 112, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
51 42 0.38
52 60 0.54
53 10 0.09
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:553368 original size:19 final size:19
Alignment explanation
Indices: 553344--553440 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
553334 AAAATTGACT
553344 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
553363 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
553382 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
553396 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
553415 ATCGCAATGCGGAAATG-AA
1 ATCGCAATGC-GAAATGAAA
553434 ATCGCAA
1 ATCGCAA
553441 CGAGAGAATC
Statistics
Matches: 70, Mismatches: 2, Indels: 12
0.83 0.02 0.14
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 48 0.69
20 6 0.09
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:553472 original size:52 final size:53
Alignment explanation
Indices: 553344--553459 Score: 218
Period size: 52 Copynumber: 2.2 Consensus size: 53
553334 AAAATTGACT
553344 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
553396 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATG-AAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
553448 ATCGCAATGCGA
1 ATCGCAATGCGA
553460 TTTTCATTTC
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
52 57 0.90
53 6 0.10
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:556004 original size:24 final size:24
Alignment explanation
Indices: 555970--556016 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
555960 CTGAAACATC
555970 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
555994 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
556017 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:556727 original size:20 final size:20
Alignment explanation
Indices: 556699--556948 Score: 268
Period size: 20 Copynumber: 12.5 Consensus size: 20
556689 AAATTTCAGT
* *
556699 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
556719 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
556739 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
556759 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
556779 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
556799 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
556819 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
556839 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
556859 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
556879 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCTC
* *
556899 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCTC
* ** *
556919 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCTC
556939 GTTGCGATTT
1 GTTGCGATTT
556949 TGGAAAATCG
Statistics
Matches: 200, Mismatches: 28, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 199 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:562039 original size:19 final size:19
Alignment explanation
Indices: 562003--562042 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
561993 TAAGTTACAA
*
562003 TTGATGTAGGTGTAAGATT
1 TTGATGTAGGTATAAGATT
* *
562022 TTGATGTAGTTATGAGATT
1 TTGATGTAGGTATAAGATT
562041 TT
1 TT
562043 TGAATTTATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (19 bp):
TTGATGTAGGTATAAGATT
Found at i:562183 original size:13 final size:13
Alignment explanation
Indices: 562139--562183 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
562129 TACTTTTTAT
562139 ATTAATTATAATC
1 ATTAATTATAATC
*
562152 CTTATATTATAAATC
1 ATTA-ATTAT-AATC
562167 -TTAATTATAATC
1 ATTAATTATAATC
562179 ATTAA
1 ATTAA
562184 ATTAATTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 4 0.14
13 12 0.43
14 8 0.29
15 4 0.14
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTAATTATAATC
Found at i:562368 original size:7 final size:7
Alignment explanation
Indices: 562345--562378 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
562335 AGATTAATTT
*
562345 ATTTAAG
1 ATTTAAA
*
562352 ATTAAAA
1 ATTTAAA
562359 ATTTAAA
1 ATTTAAA
562366 ATTTAAA
1 ATTTAAA
562373 ATTTAA
1 ATTTAA
562379 GTATCAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (7 bp):
ATTTAAA
Found at i:573524 original size:22 final size:23
Alignment explanation
Indices: 573490--573532 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
573480 ATCTAAAAAT
573490 AAGTAAAATATATATAATTTATAA
1 AAGTAAAATATAT-TAATTTATAA
573514 AAGTAAAATAT-TT-ATTTAT
1 AAGTAAAATATATTAATTTAT
573533 TTAAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 1 0.05
23 1 0.05
24 11 0.58
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (23 bp):
AAGTAAAATATATTAATTTATAA
Found at i:573776 original size:25 final size:22
Alignment explanation
Indices: 573729--573780 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 22
573719 ACATAATAAT
573729 AACAATAATAATTAAATATATA
1 AACAATAATAATTAAATATATA
573751 AACATATAA-AATATAAATATAAATA
1 AACA-ATAATAAT-TAAATAT--ATA
573776 AACAA
1 AACAA
573781 CAACAACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
22 7 0.27
23 11 0.42
24 1 0.04
25 7 0.27
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (22 bp):
AACAATAATAATTAAATATATA
Found at i:573944 original size:8 final size:8
Alignment explanation
Indices: 573931--573958 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
573921 GCATGTATAA
573931 ATAAATAC
1 ATAAATAC
573939 ATAAATAC
1 ATAAATAC
573947 ATAAATAC
1 ATAAATAC
573955 ATAA
1 ATAA
573959 TTGAACAGTA
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:0.64, C:0.11, G:0.00, T:0.25
Consensus pattern (8 bp):
ATAAATAC
Found at i:579869 original size:13 final size:13
Alignment explanation
Indices: 579851--579875 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
579841 TTGATGTCTC
579851 TGTTCTTCTTCTA
1 TGTTCTTCTTCTA
579864 TGTTCTTCTTCT
1 TGTTCTTCTTCT
579876 CCTTTTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.24, G:0.08, T:0.64
Consensus pattern (13 bp):
TGTTCTTCTTCTA
Found at i:580291 original size:6 final size:6
Alignment explanation
Indices: 580282--580335 Score: 63
Period size: 6 Copynumber: 9.0 Consensus size: 6
580272 ATATATATAT
* * * * *
580282 ATAATA ATAATA ATAATA AAAATA AAAATA AAAATA AAAATA ATAAAA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
580330 ATAATA
1 ATAATA
580336 TGAAAAAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (6 bp):
ATAATA
Found at i:580296 original size:9 final size:9
Alignment explanation
Indices: 580284--580335 Score: 70
Period size: 9 Copynumber: 5.8 Consensus size: 9
580274 ATATATATAT
*
580284 AATAATAAT
1 AATAATAAA
580293 AATAATAAA
1 AATAATAAA
580302 AATAA-AAA
1 AATAATAAA
*
580310 TAAAAATAAA
1 -AATAATAAA
580320 AATAATAAA
1 AATAATAAA
580329 AATAATA
1 AATAATA
580336 TGAAAAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
8 3 0.08
9 32 0.84
10 3 0.08
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
AATAATAAA
Found at i:580342 original size:27 final size:27
Alignment explanation
Indices: 580282--580333 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
580272 ATATATATAT
* *
580282 ATAATAATAATAATAATAAAAATAAAA
1 ATAAAAATAAAAATAATAAAAATAAAA
580309 ATAAAAATAAAAATAATAAAAATAA
1 ATAAAAATAAAAATAATAAAAATAA
580334 TATGAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (27 bp):
ATAAAAATAAAAATAATAAAAATAAAA
Found at i:580549 original size:45 final size:45
Alignment explanation
Indices: 580483--580571 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 45
580473 GAAGTCCTAT
* * *
580483 CATCTTGCACTGTAGGTCTTACAGATGATCCGAAGGTTTTGAAAG
1 CATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAG
580528 CATCATGCACTGAAGAG-CTTACAGATGACCCGAAGGTTTTGAAA
1 CATCATGCACTGAAG-GTCTTACAGATGACCCGAAGGTTTTGAAA
580572 ATATCAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
45 39 0.98
46 1 0.03
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (45 bp):
CATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAG
Found at i:580646 original size:77 final size:76
Alignment explanation
Indices: 580512--580724 Score: 306
Period size: 76 Copynumber: 2.8 Consensus size: 76
580502 TACAGATGAT
* * **
580512 CCGAAGG--TTTTGAAAGCATCATGCACTGAAGAG-CTTACAGATGACCCGAAGGTTTTGAAAAT
1 CCGAAGGCCTTTTGAAAACATCCTGCACTGAAG-GTCTTATGGATGACCCGAAGGTTTTGAAAAT
580574 ATCAAAAAAGCTC
65 ATC-AAAAAGCTC
* * *
580587 CCGAGGGCTTTTTGAAAACATCCTGCACTGCAGGTCTTATGGATGACCCGAAGGTTTTGAAAATA
1 CCGAAGGCCTTTTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGTTTTGAAAATA
580652 TCAAAAAGCTC
66 TCAAAAAGCTC
* *
580663 CCGAAGGCCTTTTGAAAACATCCTACACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAA
1 CCGAAGGCCTTTTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGTTTTGAAA
580725 GCATCATGCA
Statistics
Matches: 125, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
75 6 0.05
76 68 0.54
77 51 0.41
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.25
Consensus pattern (76 bp):
CCGAAGGCCTTTTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGTTTTGAAAATA
TCAAAAAGCTC
Found at i:580737 original size:45 final size:45
Alignment explanation
Indices: 580662--580775 Score: 131
Period size: 45 Copynumber: 2.5 Consensus size: 45
580652 TCAAAAAGCT
* * **
580662 CCCGAAGGCCTTTTGAAAACATCCTACACTG-TAGGTCTTATGGATGA
1 CCCGAAGG--TTTTGAAAACATCATACACTGAAAGG-CTTACAGATGA
* *
580709 CCCGAAGGTTTTGAAAGCATCATGCACTGAAAGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATACACTGAAAGGCTTACAGATGA
*
580754 CCCGAAGGTTTTGAAAATATCA
1 CCCGAAGGTTTTGAAAACATCA
580776 AAAAACTATG
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
45 47 0.81
46 3 0.05
47 8 0.14
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCATACACTGAAAGGCTTACAGATGA
Found at i:581753 original size:23 final size:23
Alignment explanation
Indices: 581716--581779 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
581706 TAGCTCGTAT
*
581716 AATTGCATCGAAGTGCCACATAG
1 AATTGCACCGAAGTGCCACATAG
* * *
581739 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACATAG
*
581762 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
581780 TATAATAATG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.28, C:0.25, G:0.27, T:0.20
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACATAG
Found at i:581966 original size:103 final size:101
Alignment explanation
Indices: 581795--582010 Score: 387
Period size: 103 Copynumber: 2.1 Consensus size: 101
581785 TAATGTCCAT
* *
581795 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
581860 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAAT--ATATATGTCCCG
*
581898 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
581963 GACTTCACACATGTTCCAAAGAATATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATATATATGTCCCG
581999 AAGGACCACATA
1 AAGGACCACATA
582011 GACCCTCGAC
Statistics
Matches: 110, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
101 24 0.22
103 86 0.78
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.26
Consensus pattern (101 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATATATATGTCCCG
Found at i:582151 original size:24 final size:24
Alignment explanation
Indices: 582123--582175 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
582113 TGTAGTTCTT
*
582123 TCACATAGCTCATCAT-CATATAAA
1 TCACATAGCCCAT-ATACATATAAA
*
582147 TCACATATCCCATATACATATAAA
1 TCACATAGCCCATATACATATAAA
582171 -CACAT
1 TCACAT
582176 GGTTCACTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 7 0.27
24 19 0.73
ACGTcount: A:0.43, C:0.26, G:0.02, T:0.28
Consensus pattern (24 bp):
TCACATAGCCCATATACATATAAA
Found at i:590258 original size:19 final size:21
Alignment explanation
Indices: 590221--590263 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
590211 TAACTTTTTC
590221 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
590241 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
590261 TTT
1 TTT
590264 ACTTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:590271 original size:20 final size:20
Alignment explanation
Indices: 590221--590271 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
590211 TAACTTTTTC
590221 TTTTA-TCTTTCATTATTAA
1 TTTTACTCTTTCATTATTAA
*
590240 TTTTTCTCTTTCATT-TTAA
1 TTTTACTCTTTCATTATTAA
*
590259 CTTTTACTTTTTC
1 -TTTTACTCTTTC
590272 TCTTTCTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 8 0.30
20 19 0.70
ACGTcount: A:0.18, C:0.16, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTACTCTTTCATTATTAA
Found at i:603371 original size:44 final size:45
Alignment explanation
Indices: 603292--603376 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 45
603282 TGCATCAAAC
* *
603292 AAAACTTTTACATGTAGGGGACAACTTTCAATCCTAGCTTCAACA
1 AAAACTTTTACATATAGGGGACAACTTTCAATCCTAACTTCAACA
* **
603337 AAAAC-TTTACATATAGGGGATAACTTTCCCTCCTAACTTC
1 AAAACTTTTACATATAGGGGACAACTTTCAATCCTAACTTC
603377 TCTAAAGCGC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
44 30 0.86
45 5 0.14
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.31
Consensus pattern (45 bp):
AAAACTTTTACATATAGGGGACAACTTTCAATCCTAACTTCAACA
Found at i:605302 original size:28 final size:28
Alignment explanation
Indices: 605240--605302 Score: 65
Period size: 28 Copynumber: 2.2 Consensus size: 28
605230 AATACTTGAA
* * *
605240 AATTATATATAAATATTATGAAAATAAT
1 AATTATATATAAAAATTATGAAAAAAAG
* *
605268 AAGTATATA-AAAAATTTTGAAAAGAAAG
1 AATTATATATAAAAATTATGAAAA-AAAG
605296 AATTATA
1 AATTATA
605303 AATTAAATAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
27 12 0.43
28 16 0.57
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (28 bp):
AATTATATATAAAAATTATGAAAAAAAG
Found at i:606239 original size:16 final size:16
Alignment explanation
Indices: 606190--606263 Score: 51
Period size: 19 Copynumber: 4.1 Consensus size: 16
606180 ATATAATCAT
606190 ATAAAATTAAAATATAA
1 ATAAAATTAAAA-ATAA
*
606207 ATAAACAATGACTAAAATAA
1 AT-AA-AATTA--AAAATAA
606227 ATAAAATTAAAAAGT-A
1 ATAAAATTAAAAA-TAA
606243 ATAAAACTTGTAAAAATAA
1 ATAAAA--T-TAAAAATAA
606262 AT
1 AT
606264 GAAAGTAGTG
Statistics
Matches: 46, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
16 11 0.24
17 3 0.07
18 8 0.17
19 15 0.33
20 6 0.13
21 3 0.07
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.26
Consensus pattern (16 bp):
ATAAAATTAAAAATAA
Found at i:607540 original size:3 final size:3
Alignment explanation
Indices: 607532--607606 Score: 60
Period size: 3 Copynumber: 23.7 Consensus size: 3
607522 ATTTTTTATT
* **
607532 TAA TAA TAA TATA TATA TATA TATA TAA TAA TAC TAA TTT TAA TAA TAA
1 TAA TAA TAA TA-A TA-A TA-A TA-A TAA TAA TAA TAA TAA TAA TAA TAA
* * *
607581 TAA TAA AAA TAA AAA TAA AAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
607607 TGAAAAAATT
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
3 44 0.75
4 15 0.25
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:607684 original size:3 final size:3
Alignment explanation
Indices: 607676--607742 Score: 71
Period size: 3 Copynumber: 21.7 Consensus size: 3
607666 ATTTTTTATT
* **
607676 TAA TAA TAA TAA TATA TATA TAA TAC TAA TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
607723 TAA TAA AAA TAA AAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
607743 TGAAAAAATT
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
3 46 0.87
4 7 0.13
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:607825 original size:3 final size:3
Alignment explanation
Indices: 607812--607876 Score: 67
Period size: 3 Copynumber: 21.0 Consensus size: 3
607802 ATTTTTTATT
* * **
607812 TAA TTA TAA TAA TATA TATA TAA TAA TAA TAC TAA TTT TAA TAA TAA
1 TAA TAA TAA TAA TA-A TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
607859 TAA TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA
607877 AAATGATATG
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
3 44 0.86
4 7 0.14
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:607856 original size:142 final size:141
Alignment explanation
Indices: 607502--607925 Score: 741
Period size: 136 Copynumber: 3.0 Consensus size: 141
607492 CTGTAATCAG
607502 GCCCCGATTTTGGGCCTTGTATTTTTTATTTAATAATAATATATATATATATATATAATAATACT
1 GCCCCGATTTTGGGCCTTGTATTTTTTATTTAAT-ATAATA-ATATATATATA-ATAATAATACT
*
607567 AATTTTAATAATAATAATAAAAATAAAAATAAAAATAATATGAAAAAATTAGTGTTTACAGAAGG
63 AATTTTAATAATAATAATAATAATAAAAATAAAAATAATATGAAAAAATTAGTGTTTACAGAAGG
607632 CAATAAAAAATGCT
128 CAATAAAAAATGCT
607646 GCCCCGATTTTGGGCCTTGTATTTTTTATTT-A-ATAATAATA-ATATAT-AT-ATAATACTAAT
1 GCCCCGATTTTGGGCCTTGTATTTTTTATTTAATATAATAATATATATATAATAATAATACTAAT
607706 TTTAATAATAATAATAATAATAAAAATAAAAATAATATGAAAAAATTAGTGTTTACAGAAGGCAA
66 TTTAATAATAATAATAATAATAAAAATAAAAATAATATGAAAAAATTAGTGTTTACAGAAGGCAA
*
607771 TAAAAAATGTT
131 TAAAAAATGCT
*
607782 GCCGCGATTTTGGGCCTTGTATTTTTTATTTAATTATAATAATATATATATAATAATAATACTAA
1 GCCCCGATTTTGGGCCTTGTATTTTTTATTTAA-TATAATAATATATATATAATAATAATACTAA
*
607847 TTTTAATAATAATAATAATAATAAAAATAAAAATGATATGAAAAAATTAGTGTTTACAGAAGGCA
65 TTTTAATAATAATAATAATAATAAAAATAAAAATAATATGAAAAAATTAGTGTTTACAGAAGGCA
607912 ATAAAAAATGCT
130 ATAAAAAATGCT
607924 GC
1 GC
607926 TGGTTGAGAA
Statistics
Matches: 269, Mismatches: 5, Indels: 14
0.93 0.02 0.05
Matches are distributed among these distances:
136 115 0.43
137 3 0.01
139 15 0.06
140 9 0.03
141 8 0.03
142 87 0.32
143 1 0.00
144 31 0.12
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.36
Consensus pattern (141 bp):
GCCCCGATTTTGGGCCTTGTATTTTTTATTTAATATAATAATATATATATAATAATAATACTAAT
TTTAATAATAATAATAATAATAAAAATAAAAATAATATGAAAAAATTAGTGTTTACAGAAGGCAA
TAAAAAATGCT
Found at i:625866 original size:14 final size:15
Alignment explanation
Indices: 625837--625875 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
625827 GATATAATTG
*
625837 AAAATATTTTATATA
1 AAAATATATTATATA
625852 AAAATATATTA-ATA
1 AAAATATATTATATA
*
625866 AAAAAATATT
1 AAAATATATT
625876 CAGTGGGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAATATATTATATA
Found at i:625872 original size:16 final size:15
Alignment explanation
Indices: 625837--625875 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
625827 GATATAATTG
* *
625837 AAAATATTTTATATA
1 AAAATATTTAATAAA
625852 AAAATATATTAATAAA
1 AAAATAT-TTAATAAA
625868 AAAATATT
1 AAAATATT
625876 CAGTGGGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAATATTTAATAAA
Found at i:626845 original size:28 final size:28
Alignment explanation
Indices: 626791--626846 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
626781 CTTTTATTTG
*
626791 AAGTTAATATAATAAATATATATTTTTT
1 AAGTTAATATAATAAATAAATATTTTTT
*
626819 AAGTTAATA-AA-AAATAAAGTATATTTT
1 AAGTTAATATAATAAATAAA-TATTTTTT
626846 A
1 A
626847 TATCTTAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 6 0.24
27 10 0.40
28 9 0.36
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (28 bp):
AAGTTAATATAATAAATAAATATTTTTT
Found at i:626901 original size:29 final size:30
Alignment explanation
Indices: 626840--626909 Score: 90
Period size: 29 Copynumber: 2.3 Consensus size: 30
626830 AAATAAAGTA
626840 TATTTTATATCTTAACTTTTAAAAATATATTT
1 TATTTT-TATCTTAACTTTT-AAAATATATTT
626872 TATTTTTAT-TTAACTTATT-AAATATATTT
1 TATTTTTATCTTAACTT-TTAAAATATATTT
*
626901 TACTTTTAT
1 TATTTTTAT
626910 ACTCTATTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
29 18 0.50
30 7 0.19
31 5 0.14
32 6 0.17
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (30 bp):
TATTTTTATCTTAACTTTTAAAATATATTT
Found at i:638382 original size:24 final size:20
Alignment explanation
Indices: 638355--638412 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
638345 GCATGGGTAG
638355 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
638379 TGCATCGATACACTGTAGAA
1 TGCATCGATGCACTGTAGAA
*
638399 TGTATCGATGCACT
1 TGCATCGATGCACT
638413 TCAAGGGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 16 0.52
22 1 0.03
23 2 0.06
24 12 0.39
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:639350 original size:32 final size:31
Alignment explanation
Indices: 639308--639416 Score: 125
Period size: 31 Copynumber: 3.5 Consensus size: 31
639298 AGAGTCAAGG
639308 GTTTACCTATGTTCTACGGAACATATGGAA-A
1 GTTTACCTATGTTCTACGGAACATAT-GAACA
*
639339 GTTTTACCTATG-TCTTTC-GAGACATATGAACA
1 G-TTTACCTATGTTC-TACGGA-ACATATGAACA
* *
639371 GTATACCTATGTTCTAAGGAACATATGAACA
1 GTTTACCTATGTTCTACGGAACATATGAACA
*
639402 GTTTACCTAGGTTCT
1 GTTTACCTATGTTCT
639417 TCGGGACCTA
Statistics
Matches: 66, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
31 42 0.64
32 24 0.36
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGAACA
Found at i:644636 original size:2 final size:2
Alignment explanation
Indices: 644629--644681 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
644619 CATGAGTTAG
644629 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
644671 AT AT AT AT AT A
1 AT AT AT AT AT A
644682 GGAATTTGTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:645413 original size:22 final size:22
Alignment explanation
Indices: 645387--645504 Score: 182
Period size: 22 Copynumber: 5.4 Consensus size: 22
645377 GGGTATATTA
*
645387 GTCCTTCGAGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
645409 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
645431 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
* * *
645453 GTCTTTTGGGACGTATCCAATG
1 GTCCTTCGGGACGTATCCAGTG
* *
645475 GTCATTCGGGACGTATCTAGTG
1 GTCCTTCGGGACGTATCCAGTG
645497 GTCCTTCG
1 GTCCTTCG
645505 AGACATAATA
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 87 1.00
ACGTcount: A:0.15, C:0.25, G:0.30, T:0.31
Consensus pattern (22 bp):
GTCCTTCGGGACGTATCCAGTG
Found at i:647293 original size:32 final size:32
Alignment explanation
Indices: 647252--647359 Score: 98
Period size: 31 Copynumber: 3.4 Consensus size: 32
647242 GAGTCGAGGG
*
647252 TTTACCTATGTTCTACGGAACATATGGAAAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
647284 TTTACCTATG-TCTTTC-GAGACATATGGACA-T
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* * * * *
647315 TATATCTATGTTATAAGGAACATATAGACAG-
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
647346 TTTACCTAGGTTCT
1 TTTACCTATGTTCT
647360 TTGAGACCTA
Statistics
Matches: 59, Mismatches: 12, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
31 34 0.58
32 25 0.42
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.37
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:647339 original size:63 final size:62
Alignment explanation
Indices: 647257--647375 Score: 159
Period size: 63 Copynumber: 1.9 Consensus size: 62
647247 GAGGGTTTAC
* * * *
647257 CTATGTTCTACGGAACATATGGAAAGTTTTACCTATG-TCTTTCGAGACATATGGACATTATAT
1 CTATGTTATAAGGAACATATAGAAAG-TTTACCTAGGTTCTTT-GAGACATATGGACATTATAT
* *
647320 CTATGTTATAAGGAACATATAGACAGTTTACCTAGGTTCTTTGAGACCTATGGACA
1 CTATGTTATAAGGAACATATAGAAAGTTTACCTAGGTTCTTTGAGACATATGGACA
647376 GTTGTCGAGG
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
62 22 0.45
63 27 0.55
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Consensus pattern (62 bp):
CTATGTTATAAGGAACATATAGAAAGTTTACCTAGGTTCTTTGAGACATATGGACATTATAT
Found at i:649428 original size:16 final size:16
Alignment explanation
Indices: 649409--649439 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
649399 TTCTTTTTCT
649409 AAAAAAT-AAATAAAC
1 AAAAAATGAAATAAAC
649424 AAAAAATGAAATAAAC
1 AAAAAATGAAATAAAC
649440 GTAGTAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.77, C:0.06, G:0.03, T:0.13
Consensus pattern (16 bp):
AAAAAATGAAATAAAC
Found at i:650732 original size:13 final size:13
Alignment explanation
Indices: 650716--650770 Score: 62
Period size: 12 Copynumber: 4.4 Consensus size: 13
650706 CATAATGAAA
*
650716 ATAAATAAATAGT
1 ATAAATAAATAAT
650729 ATAAATAAAATAAT
1 ATAAAT-AAATAAT
650743 A-AAATAAA-AAT
1 ATAAATAAATAAT
*
650754 ATATATAAA-AAT
1 ATAAATAAATAAT
650766 ATAAA
1 ATAAA
650771 AATGTATGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
11 4 0.11
12 16 0.43
13 10 0.27
14 7 0.19
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (13 bp):
ATAAATAAATAAT
Found at i:650751 original size:47 final size:47
Alignment explanation
Indices: 650700--650795 Score: 115
Period size: 47 Copynumber: 2.0 Consensus size: 47
650690 GAAAAGAAAC
*
650700 TAAAAACATA-ATGAAAATA-AATAAATAGTATAAATAAAATAATAAAA
1 TAAAAACATATATAAAAATATAA-AAAT-GTATAAATAAAATAATAAAA
* ** *
650747 TAAAAATATATATAAAAATATAAAAATGTATGTATAATATAATAAAA
1 TAAAAACATATATAAAAATATAAAAATGTATAAATAAAATAATAAAA
650794 TA
1 TA
650796 CTAAATAGTA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
47 28 0.67
48 12 0.29
49 2 0.05
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (47 bp):
TAAAAACATATATAAAAATATAAAAATGTATAAATAAAATAATAAAA
Found at i:650756 original size:25 final size:26
Alignment explanation
Indices: 650718--650771 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
650708 TAATGAAAAT
*
650718 AAATAAATAGTATAAAT-AAAATAATA
1 AAATAAATAATATAAATAAAAAT-ATA
*
650744 AAATAAA-AATATATATAAAAATATA
1 AAATAAATAATATAAATAAAAATATA
650769 AAA
1 AAA
650772 ATGTATGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (26 bp):
AAATAAATAATATAAATAAAAATATA
Found at i:650811 original size:21 final size:19
Alignment explanation
Indices: 650787--650839 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 19
650777 TGTATAATAT
650787 AATAAAATACTAAATAGTAAA
1 AATAAAATACTAAAT-G-AAA
*
650808 AATAATAATAAATAAATGAAA
1 AATAA-AAT-ACTAAATGAAA
650829 AATAAATATAC
1 AATAAA-ATAC
650840 ATATATTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
20 2 0.07
21 15 0.56
22 4 0.15
23 6 0.22
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (19 bp):
AATAAAATACTAAATGAAA
Found at i:650931 original size:13 final size:13
Alignment explanation
Indices: 650913--650938 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
650903 TAACGTTAGG
650913 AAAATATAGTAAA
1 AAAATATAGTAAA
650926 AAAATATAGTAAA
1 AAAATATAGTAAA
650939 TAAGTAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (13 bp):
AAAATATAGTAAA
Found at i:650972 original size:5 final size:5
Alignment explanation
Indices: 650962--651016 Score: 51
Period size: 5 Copynumber: 10.8 Consensus size: 5
650952 ATAAAAAATA
* *
650962 ATAAT ATAAT AT-AT ATAA- ATATAT AATAAT AGGAAA ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATA-AT -ATAAT A-TAAT ATAAT ATAAT
651008 ATAAT ATAA
1 ATAAT ATAA
651017 CGTAAAGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
4 7 0.17
5 26 0.63
6 5 0.12
7 3 0.07
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (5 bp):
ATAAT
Found at i:650982 original size:10 final size:9
Alignment explanation
Indices: 650959--651016 Score: 50
Period size: 8 Copynumber: 6.4 Consensus size: 9
650949 TAGATAAAAA
650959 ATAATA-AT
1 ATAATATAT
650967 ATAATATAT
1 ATAATATAT
650976 ATAA-ATAT
1 ATAATATAT
650984 ATAATA-AT
1 ATAATATAT
* *
650992 AGGAAAATAAT
1 A-TAATAT-AT
651003 ATAATATAAT
1 ATAATAT-AT
651013 ATAA
1 ATAA
651017 CGTAAAGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
8 17 0.41
9 10 0.24
10 11 0.27
11 3 0.07
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (9 bp):
ATAATATAT
Found at i:651534 original size:37 final size:37
Alignment explanation
Indices: 651493--651577 Score: 116
Period size: 37 Copynumber: 2.3 Consensus size: 37
651483 GGATCCTATC
* *
651493 TTTAGGAGTTTAAATAATAGTAGAACTCTATCATATT
1 TTTAGGAGTTTAAATAATAGCAAAACTCTATCATATT
* ** *
651530 TTTAGGAGTTTGAATCCTAGCAAAATTCTATCATATT
1 TTTAGGAGTTTAAATAATAGCAAAACTCTATCATATT
651567 TTTAGGAGTTT
1 TTTAGGAGTTT
651578 GAATCCTAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.42
Consensus pattern (37 bp):
TTTAGGAGTTTAAATAATAGCAAAACTCTATCATATT
Found at i:652523 original size:106 final size:106
Alignment explanation
Indices: 652339--653507 Score: 1782
Period size: 106 Copynumber: 11.0 Consensus size: 106
652329 GCATTGTTCC
* * * * * * *
652339 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAATCGAGAAATTGTTTGGTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
652404 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
652445 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
652510 CCAGCGGTTCCTTCTTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
652551 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
652616 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * * *
652657 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCACCGAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
652722 CCAACAGTCCCTTCATCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
652763 GAGTCCAATATCATTCGTTATGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
652828 CCAGCGGTCCCCTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * * *
652869 GAGTCCAATATTTTTCGCTGTGAAATTGAAATTCGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
652934 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTATCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
652975 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
653040 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCTTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
653081 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
653146 CCAGCGGTCCCTTCGTCATGAAGTTGAATTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
653187 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
653252 CAAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
653293 GAGTCCAATATCCTTCGTTGTGAAGTT-AAATTGGCTATGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
653357 CTAGCAGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
653398 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATTTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
** * * *
653463 CCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
653504 GAGT
1 GAGT
653508 GACACGATAT
Statistics
Matches: 973, Mismatches: 89, Indels: 2
0.91 0.08 0.00
Matches are distributed among these distances:
105 96 0.10
106 877 0.90
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:654490 original size:22 final size:22
Alignment explanation
Indices: 654464--654519 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
654454 TTGTGTTTAG
*
654464 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
654486 TCAAAGGTTTGACATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
654508 TCAAAGGTTTGA
1 TCAAAGGTTTGA
654520 TGGGGTAGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGACATTTGATGC
Found at i:655148 original size:23 final size:21
Alignment explanation
Indices: 655112--655184 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 21
655102 TGCATGTACT
* *
655112 TTTTTGTCCCTTTTCCTTTTTG
1 TTTTTGT-TCTTTTCTTTTTTG
* *
655134 ATTTTTGTTCTTTTTTTTTTTCT
1 -TTTTTGTTCTTTTCTTTTTT-G
655157 TTTTTGCTTCTTTTCTTTTTTG
1 TTTTTG-TTCTTTTCTTTTTTG
655179 TTTTTG
1 TTTTTG
655185 CCCTTTTTGT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
22 22 0.52
23 20 0.48
ACGTcount: A:0.01, C:0.14, G:0.08, T:0.77
Consensus pattern (21 bp):
TTTTTGTTCTTTTCTTTTTTG
Found at i:655153 original size:28 final size:29
Alignment explanation
Indices: 655122--655182 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
655112 TTTTTGTCCC
*
655122 TTTTCCTTTTTGATTTTTGTTCTTTTTTT-
1 TTTTCCTTTTTGATTCTT-TTCTTTTTTTG
* *
655151 TTTTCTTTTTTGCTTCTTTTC-TTTTTTG
1 TTTTCCTTTTTGATTCTTTTCTTTTTTTG
655179 TTTT
1 TTTT
655183 TGCCCTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 6 0.21
28 7 0.25
29 15 0.54
ACGTcount: A:0.02, C:0.11, G:0.07, T:0.80
Consensus pattern (29 bp):
TTTTCCTTTTTGATTCTTTTCTTTTTTTG
Found at i:655185 original size:22 final size:22
Alignment explanation
Indices: 655121--655185 Score: 78
Period size: 22 Copynumber: 2.9 Consensus size: 22
655111 TTTTTTGTCC
*
655121 CTTTTCCTTTTTGATTTTTG-TT
1 CTTTTCTTTTTTG-TTTTTGCTT
* *
655143 CTTTTTTTTTTTCTTTTTTGCTT
1 CTTTTCTTTTTT-GTTTTTGCTT
655166 CTTTTCTTTTTTGTTTTTGC
1 CTTTTCTTTTTTGTTTTTGC
655186 CCTTTTTGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 23 0.64
23 13 0.36
ACGTcount: A:0.02, C:0.14, G:0.08, T:0.77
Consensus pattern (22 bp):
CTTTTCTTTTTTGTTTTTGCTT
Found at i:659958 original size:13 final size:13
Alignment explanation
Indices: 659942--660015 Score: 51
Period size: 14 Copynumber: 5.4 Consensus size: 13
659932 CATAATGAAA
*
659942 ATAAATAAATAGT
1 ATAAATAAATAAT
659955 ATAAATAAAATAAT
1 ATAAAT-AAATAAT
659969 A-AAATAAAATATAT
1 ATAAAT-AAATA-AT
* *
659983 ATATATATATATAT
1 ATAAATAAATA-AT
* *
659997 ATATATATATATAT
1 ATAAATAAATA-AT
660011 ATAAA
1 ATAAA
660016 AATGTATGTA
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
13 16 0.30
14 35 0.65
15 3 0.06
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (13 bp):
ATAAATAAATAAT
Found at i:659984 original size:2 final size:2
Alignment explanation
Indices: 659977--660013 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
659967 ATAAAATAAA
659977 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 A
660014 AAAATGTATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:660178 original size:13 final size:13
Alignment explanation
Indices: 660160--660185 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
660150 TAACGTTAGG
660160 AAAATATAGTAAA
1 AAAATATAGTAAA
660173 AAAATATAGTAAA
1 AAAATATAGTAAA
660186 TAAGTAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (13 bp):
AAAATATAGTAAA
Found at i:660305 original size:2 final size:2
Alignment explanation
Indices: 660295--660326 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
660285 AAAAAAATAA
660295 AT AT A- 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 A
660327 GAGTTAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:660765 original size:37 final size:37
Alignment explanation
Indices: 660724--660808 Score: 116
Period size: 37 Copynumber: 2.3 Consensus size: 37
660714 GGATCCTATC
* *
660724 TTTAGGAGTTTAAATAATAGTAGAACTCTATCATATT
1 TTTAGGAGTTTAAATAATAGCAAAACTCTATCATATT
* ** *
660761 TTTAGGAGTTTGAATCCTAGCAAAATTCTATCATATT
1 TTTAGGAGTTTAAATAATAGCAAAACTCTATCATATT
660798 TTTAGGAGTTT
1 TTTAGGAGTTT
660809 GAATTCTAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.42
Consensus pattern (37 bp):
TTTAGGAGTTTAAATAATAGCAAAACTCTATCATATT
Found at i:667541 original size:123 final size:123
Alignment explanation
Indices: 667305--667533 Score: 302
Period size: 123 Copynumber: 1.9 Consensus size: 123
667295 GTAAAAATAG
* * *
667305 AAATTGAAATTACATAATATTCTATTGTGGTATATGAGCACGTGATTCCAATTTGGTAAAAAAAA
1 AAATTGAAATTACATAATATTCTATAGTGGTATATGAGCACGTGATTCAAATTTGATAAAAAAAA
*
667370 TACATAAAATAAAGGATAAATTGAAGAAATTAAAAAAATTATGAAAATTTGAGAGACT
66 TACATAAAATAAAAGATAAATTGAAGAAATTAAAAAAATTATGAAAATTTGAGAGACT
* * * * * *
667428 AAATTGAAGTTACATAGGTATTCTATAGTTGTATATGAGCATGT-AGTTTAAATTTGATAAAAAC
1 AAATTGAAATTACATA-ATATTCTATAGTGGTATATGAGCACGTGA-TTCAAATTTGATAAAAAA
* * *
667492 AA-ACTTAAAATAAAAGATGAATTGAAGAAA-TAAGAAAATTAT
64 AATACATAAAATAAAAGATAAATTGAAGAAATTAAAAAAATTAT
667534 ACTAAATTGA
Statistics
Matches: 91, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
122 11 0.12
123 41 0.45
124 39 0.43
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.31
Consensus pattern (123 bp):
AAATTGAAATTACATAATATTCTATAGTGGTATATGAGCACGTGATTCAAATTTGATAAAAAAAA
TACATAAAATAAAAGATAAATTGAAGAAATTAAAAAAATTATGAAAATTTGAGAGACT
Found at i:667625 original size:144 final size:147
Alignment explanation
Indices: 667428--667729 Score: 373
Period size: 144 Copynumber: 2.1 Consensus size: 147
667418 TTGAGAGACT
* * *
667428 AAATTGAAGTTACATAGGTATTCTATAGTTGTATATGAGCATGTAGTTTAAATTTGATAAAAACA
1 AAATTGAAGTTACATAGGTATTCTATAGTTGTATATGAGCATGTAGATCAAATTTAATAAAAACA
**
667493 AACTTAAAATAAAAGATGAATTGAAGAAATA-AGAAAATTATACTAAATT-GA-AAAATAAAAAA
66 AACTTAAAATAAAAGATGAATTGAAGAAATAGAG-AAATTATAAAAAATTAGACAAAATAAAAAA
667555 AA-TATTATCAAAAAGAG
130 AATTATTATCAAAAAGAG
* ** * *
667572 GAATTGAAGTTACATATTTATTCTATTG-TGTTATATTAGCATG-AGGATCAAATTTAATAAAAA
1 AAATTGAAGTTACATAGGTATTCTATAGTTG-TATATGAGCATGTA-GATCAAATTTAATAAAAA
* * * *
667635 CGAACTTAAAATAAATGATGAATTGAATAAATAGAGAAATTATAAAAAATTAAAGACTAAATAAA
64 CAAACTTAAAATAAAAGATGAATTGAAGAAATAGAGAAATTATAAAAAATT--AGACAAAATAAA
*
667700 AAAAATTTATTATCAAAAAGAT
127 AAAAA-TTATTATCAAAAAGAG
667722 AAATTGAA
1 AAATTGAA
667730 AGTACATTTG
Statistics
Matches: 133, Mismatches: 16, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
143 3 0.02
144 93 0.70
145 2 0.02
147 2 0.02
148 12 0.09
150 21 0.16
ACGTcount: A:0.52, C:0.05, G:0.12, T:0.30
Consensus pattern (147 bp):
AAATTGAAGTTACATAGGTATTCTATAGTTGTATATGAGCATGTAGATCAAATTTAATAAAAACA
AACTTAAAATAAAAGATGAATTGAAGAAATAGAGAAATTATAAAAAATTAGACAAAATAAAAAAA
ATTATTATCAAAAAGAG
Found at i:667783 original size:150 final size:144
Alignment explanation
Indices: 667477--667784 Score: 315
Period size: 144 Copynumber: 2.1 Consensus size: 144
667467 CATGTAGTTT
**
667477 AAATTT-GATAAAAACAAACTTAAAATAAAAGATGAATTGAAGAAATAAGAAAATTATACTAAAT
1 AAATTTAG-TAAAAACAAACTTAAAATAAAAGATGAATTGAAGAAATAAGAAAATTATAAAAAAT
* **
667541 TGAAAAATAAAAAAAATATTATCAAAAAGAGGAATTGAAGTTACATATTTATTCTATTGTGTTAT
65 TGAAAAATAAAAAAAATATTATCAAAAAGAGAAATTGAAGTTACATATTTATAATATTGTGTTAT
* * *
667606 ATTAGCATGAGGATC
130 ATGAACATGAGGATA
* * * *
667621 AAATTTAATAAAAACGAACTTAAAATAAATGATGAATTGAATAAAT-AGAGAAATTATAAAAAAT
1 AAATTTAGTAAAAACAAACTTAAAATAAAAGATGAATTGAAGAAATAAGA-AAATTATAAAAAAT
* *
667685 TAAAGACTAAATAAAAAAAATTTATTATCAAAAAGATAAATTGAAAG-TACAT-TTGTATAATA-
65 T---GA-AAAATAAAAAAAA--TATTATCAAAAAGAGAAATTG-AAGTTACATATT-TATAATAT
*
667747 TGATGATT-TATGAACATG-TGACTA
122 TG-TG-TTATATGAACATGAGGA-TA
667771 AAATTTAGTAAAAA
1 AAATTTAGTAAAAA
667785 ATTGATTTAA
Statistics
Matches: 135, Mismatches: 16, Indels: 20
0.79 0.09 0.12
Matches are distributed among these distances:
143 3 0.02
144 54 0.40
147 2 0.01
148 12 0.09
149 6 0.04
150 53 0.39
151 5 0.04
ACGTcount: A:0.54, C:0.05, G:0.11, T:0.30
Consensus pattern (144 bp):
AAATTTAGTAAAAACAAACTTAAAATAAAAGATGAATTGAAGAAATAAGAAAATTATAAAAAATT
GAAAAATAAAAAAAATATTATCAAAAAGAGAAATTGAAGTTACATATTTATAATATTGTGTTATA
TGAACATGAGGATA
Found at i:679668 original size:17 final size:17
Alignment explanation
Indices: 679636--679689 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
679626 AGTCAACGAG
*
679636 CAGTCAACGGTCGGTCAA
1 CAGTCAAC-ATCGGTCAA
*
679654 CGGTCAACATCGGTCAA
1 CAGTCAACATCGGTCAA
* *
679671 CAGTCAACGTCAGTCAA
1 CAGTCAACATCGGTCAA
679688 CA
1 CA
679690 ATTAACGGCT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
17 24 0.77
18 7 0.23
ACGTcount: A:0.31, C:0.30, G:0.22, T:0.17
Consensus pattern (17 bp):
CAGTCAACATCGGTCAA
Found at i:681774 original size:20 final size:20
Alignment explanation
Indices: 681749--681789 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
681739 CGTTTTCTTC
681749 CGGTATGTCGTTGAAGGAGG
1 CGGTATGTCGTTGAAGGAGG
681769 CGGTATGTCGTTGAAGGAGG
1 CGGTATGTCGTTGAAGGAGG
681789 C
1 C
681790 AAGCTCCGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.12, G:0.44, T:0.24
Consensus pattern (20 bp):
CGGTATGTCGTTGAAGGAGG
Found at i:683537 original size:23 final size:23
Alignment explanation
Indices: 683510--683558 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
683500 TGGTTGTTGG
683510 TTTAATGG-ATATTTAGACTTTAT
1 TTTAATGGTATATTTA-ACTTTAT
*
683533 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
683556 TTT
1 TTT
683559 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:690610 original size:20 final size:20
Alignment explanation
Indices: 690587--690631 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
690577 TTAACTTTTT
*
690587 CTTTTCTCTTTCATCCTTAA
1 CTTTTCTATTTCATCCTTAA
**
690607 CTTTTCTATTTCATTTTTAA
1 CTTTTCTATTTCATCCTTAA
690627 CTTTT
1 CTTTT
690632 ACTTTTTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.62
Consensus pattern (20 bp):
CTTTTCTATTTCATCCTTAA
Found at i:693912 original size:23 final size:23
Alignment explanation
Indices: 693885--693933 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
693875 TGGTCGTTGG
693885 TTTAATGG-ATATTTAGACTTTAT
1 TTTAATGGTATATTTA-ACTTTAT
*
693908 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
693931 TTT
1 TTT
693934 GGTTCTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:695588 original size:75 final size:74
Alignment explanation
Indices: 695465--695655 Score: 319
Period size: 75 Copynumber: 2.5 Consensus size: 74
695455 AGTTTGTCCA
*
695465 GAGGGAACCGATTCCCCCCAAGGAGGTACCGATTCCCCCTGAATGGTTTGGCTCCGAGAAATAAC
1 GAGGGAACCGATTCCCCCCAAGG-GGTACCGATTCCCCCTGAATGGTTTGGCTCCAAGAAATAAC
695530 AGAATGCTCG
65 AGAATGCTCG
*
695540 GAGGGAACCGATTCCCCTCCAAGGGGTACTGATTCCCCCTGAATGGTTTGGCTCCAAGAAATAAC
1 GAGGGAACCGATTCCCC-CCAAGGGGTACCGATTCCCCCTGAATGGTTTGGCTCCAAGAAATAAC
*
695605 TGAATGCTCG
65 AGAATGCTCG
*
695615 GAGGGAACTGATTCCCCCCAAGGGGGTACCGATTCCCCCTG
1 GAGGGAACCGATTCCCCCCAA-GGGGTACCGATTCCCCCTG
695656 TTCAATGGTC
Statistics
Matches: 109, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
74 4 0.04
75 99 0.91
76 6 0.06
ACGTcount: A:0.25, C:0.29, G:0.27, T:0.20
Consensus pattern (74 bp):
GAGGGAACCGATTCCCCCCAAGGGGTACCGATTCCCCCTGAATGGTTTGGCTCCAAGAAATAACA
GAATGCTCG
Found at i:705784 original size:2 final size:2
Alignment explanation
Indices: 705777--705803 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
705767 GTATGAGATA
705777 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
705804 AAGGAAAATA
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
Done.