Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007849.1 Hibiscus syriacus cultivar Beakdansim tig00110206_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: 3141433
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 12
Found at i:629824 original size:16 final size:17
Alignment explanation
Indices: 629805--629836 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
629795 ATTTTAGAAA
629805 AATAAAAA-ATATTATC
1 AATAAAAATATATTATC
629821 AATAAAAATATATTAT
1 AATAAAAATATATTAT
629837 AATTTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
AATAAAAATATATTATC
Found at i:638133 original size:13 final size:13
Alignment explanation
Indices: 638115--638141 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
638105 CAATTGGAAG
638115 CCAAACTTCAACA
1 CCAAACTTCAACA
638128 CCAAACTTCAACA
1 CCAAACTTCAACA
638141 C
1 C
638142 TTGGCTCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.41, G:0.00, T:0.15
Consensus pattern (13 bp):
CCAAACTTCAACA
Found at i:646082 original size:18 final size:19
Alignment explanation
Indices: 646055--646093 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
646045 TGATCTTAGT
646055 AATATAATA-TAATTTATA
1 AATATAATATTAATTTATA
*
646073 AATATTATATTAATTTATA
1 AATATAATATTAATTTATA
646092 AA
1 AA
646094 CAACTTGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AATATAATATTAATTTATA
Found at i:651442 original size:60 final size:60
Alignment explanation
Indices: 651341--651453 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
651331 ATAGTTGGGT
* * * *
651341 GACCATTTTGTAACTTTTAATAGTTGAATGACTCAAAAAAGTAATATCCTATAGTCAATG
1 GACCATTTTATAACTTTTAATAGTCGAATAACTCAAAAAAGTAACATCCTATAGTCAATG
* * *
651401 GACCATTTTATAATTTTTAATAGTCCG-ATAACTCGATAAAGTAACATCCTATA
1 GACCATTTTATAACTTTTAATAGT-CGAATAACTCAAAAAAGTAACATCCTATA
651454 ATTAGAGATC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
60 44 0.98
61 1 0.02
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (60 bp):
GACCATTTTATAACTTTTAATAGTCGAATAACTCAAAAAAGTAACATCCTATAGTCAATG
Found at i:652203 original size:13 final size:13
Alignment explanation
Indices: 652187--652211 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
652177 ATACTAATAA
652187 ATTTATTTTTTAT
1 ATTTATTTTTTAT
652200 ATTTATTTTTTA
1 ATTTATTTTTTA
652212 AAATCATATT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTATTTTTTAT
Found at i:654093 original size:18 final size:19
Alignment explanation
Indices: 654054--654097 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
654044 CTTTTATTGT
*
654054 TTATTAAAAAAGTAATAGA
1 TTATTAAAAAAGCAATAGA
654073 TTATTAAAATAA-CAATA-A
1 TTATTAAAA-AAGCAATAGA
654091 TTATTAA
1 TTATTAA
654098 TCAGTAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
19 13 0.57
20 2 0.09
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (19 bp):
TTATTAAAAAAGCAATAGA
Found at i:654453 original size:20 final size:20
Alignment explanation
Indices: 654359--654727 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
654349 GATTTTCTAT
* ** *
654359 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
654379 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
654399 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
654419 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
654439 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
654459 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
654479 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
654499 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
654519 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
654539 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
654559 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
654579 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
654599 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
654619 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
654639 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
654659 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
654679 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
654699 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
654719 AATCACAAC
1 AATCGCAAC
654728 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:655449 original size:24 final size:23
Alignment explanation
Indices: 655410--655455 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
655400 AAATTTGGTC
655410 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGA-TTTGATA
655434 TTGGTCAATA-CACGGATTTGAT
1 TTGGTCAATATC-CGGATTTGAT
655456 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (23 bp):
TTGGTCAATATCCGGATTTGATA
Found at i:655647 original size:12 final size:12
Alignment explanation
Indices: 655630--655654 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
655620 ATATAATCCT
655630 GAAGAAGAAAAA
1 GAAGAAGAAAAA
655642 GAAGAAGAAAAA
1 GAAGAAGAAAAA
655654 G
1 G
655655 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:657950 original size:19 final size:19
Alignment explanation
Indices: 657928--658215 Score: 329
Period size: 19 Copynumber: 16.4 Consensus size: 19
657918 CGGAAAATAC
*
657928 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
657947 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
657961 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
657981 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
657995 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
658014 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
658033 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
658047 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
658066 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
658085 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
658099 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
658118 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
658137 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
658156 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
658170 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
658189 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
658208 AATCGCAA
1 AATCGCAA
658216 CGAGATAATC
Statistics
Matches: 232, Mismatches: 11, Indels: 52
0.79 0.04 0.18
Matches are distributed among these distances:
14 48 0.21
15 2 0.01
16 16 0.07
17 14 0.06
18 3 0.01
19 136 0.59
20 13 0.06
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:658015 original size:33 final size:33
Alignment explanation
Indices: 657928--658196 Score: 255
Period size: 33 Copynumber: 7.8 Consensus size: 33
657918 CGGAAAATAC
* *
657928 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAA
*
657961 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAA
*
657995 AATCGCAACGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
658033 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
* *
658066 AATCGCAATGCGAAATGAAAATCGCAACGACAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
*
658099 AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
658137 AATCGCAATGCGAAATGAAAATCGCAACGA-AA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
658169 GAATCGCAATGCGAAATGAAAATCGCAA
1 -AATCGCAATGCGAAATGAAAATCGCAA
658197 TGCGAAATGA
Statistics
Matches: 205, Mismatches: 13, Indels: 36
0.81 0.05 0.14
Matches are distributed among these distances:
32 2 0.01
33 109 0.53
34 31 0.15
35 7 0.03
36 6 0.03
37 3 0.01
38 47 0.23
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:658043 original size:52 final size:52
Alignment explanation
Indices: 657956--658196 Score: 357
Period size: 52 Copynumber: 4.6 Consensus size: 52
657946 AAATCCCAAC
*
657956 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
658009 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
658061 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
658113 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
658168 A-G--AATCGCAATGCGAAATGAAAATCGCAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA
658197 TGCGAAATGA
Statistics
Matches: 177, Mismatches: 6, Indels: 11
0.91 0.03 0.06
Matches are distributed among these distances:
52 144 0.81
53 16 0.09
54 2 0.01
55 5 0.03
56 1 0.01
57 9 0.05
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:658084 original size:71 final size:69
Alignment explanation
Indices: 657928--658215 Score: 317
Period size: 71 Copynumber: 4.1 Consensus size: 69
657918 CGGAAAATAC
* *
657928 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA-AATCGCAATGCGGAAATGAAAATCGCAA--
1 AATCGCAATGCGAAATGAAAATCGCAACGA--AAGAATCGCAA-GC-G-AATGAAAATCGCAATG
*
657989 CG--A-GAG
61 CGAAATGAA
* *
657995 AATCGCAACGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CG-A-GAGAATCGCAATG
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G--AATCGCAAGCGAATGAAAATCGCAATG
658057 CGAAATGAA
61 CGAAATGAA
* *
658066 AATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATTAAAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAA-GCG-AATGAAAATCGCAATGCGA
658131 AATGAA
64 AATGAA
658137 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAA-GCG-AATGAAAATCGCAATGCGA
658202 AATGAA
64 AATGAA
658208 AATCGCAA
1 AATCGCAA
658216 CGAGATAATC
Statistics
Matches: 195, Mismatches: 9, Indels: 30
0.83 0.04 0.13
Matches are distributed among these distances:
66 18 0.09
67 27 0.14
68 7 0.04
69 6 0.03
70 4 0.02
71 125 0.64
72 8 0.04
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.14
Consensus pattern (69 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAAGCGAATGAAAATCGCAATGCGAAA
TGAA
Found at i:658140 original size:123 final size:124
Alignment explanation
Indices: 657995--658253 Score: 459
Period size: 123 Copynumber: 2.1 Consensus size: 124
657985 GCAACGAGAG
* *
657995 AATCGCAACGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
658060 AATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATTA-A
66 AATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATTATA
658118 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
* *
658183 AATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATTATA
66 AATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATTATA
*
658242 AA-CGCATTGCGA
1 AATCGCAATGCGA
658254 TTTTCATTTC
Statistics
Matches: 130, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
123 127 0.98
124 3 0.02
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (124 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
AATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATTATA
Found at i:658197 original size:52 final size:50
Alignment explanation
Indices: 657961--658237 Score: 273
Period size: 52 Copynumber: 5.3 Consensus size: 50
657951 CCAACATGAA
*
657961 AATCGCAATGCGGAAATGAAAATCGCAACG--AGAGAATCGCAACGCGAAATG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAAAGAAAATCGCAA-GCGAAA-G
*
658012 AAAATCGCAATGCGAAATGAAAATCGCAACG--AGAGAATCGCAATGCGAAATG
1 --AATCGCAATGCGAAATGAAAATCGCAACGAAAGAAAATCGCAA-GCGAAA-G
* *
658064 AAAATCGCAATGCGAAATGAAAATCGCAACGACAG--AATCGCAATGCGAAATTAA
1 --AATCGCAATGCGAAATGAAAATCGCAACGAAAGAAAATCGCAA-GCG-AA--AG
658118 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAAAG
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAA-GAAAATCGCAAGCGAAAG
* *
658170 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAT
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAA-GAAAATCGCAAGCGAAAG
658222 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
658238 TATAAACGCA
Statistics
Matches: 208, Mismatches: 6, Indels: 21
0.89 0.03 0.09
Matches are distributed among these distances:
52 175 0.84
53 13 0.06
54 8 0.04
55 4 0.02
57 8 0.04
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (50 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAAGAAAATCGCAAGCGAAAG
Found at i:658253 original size:52 final size:52
Alignment explanation
Indices: 657928--658237 Score: 267
Period size: 52 Copynumber: 5.9 Consensus size: 52
657918 CGGAAAATAC
* *
657928 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA-AATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA--AAGAATCGCAATGC-GAAATGAA
*
657981 AATCGCAA--CG--A-GAGAATCGCAACGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
*
658033 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
* *
658085 AATCGCAA--CGACA-G--AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG-AA--AGAATCGCAATGCGAAATGAA
658137 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
* *
658189 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAAT
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAAT
658238 TATAAACGCA
Statistics
Matches: 232, Mismatches: 8, Indels: 35
0.84 0.03 0.13
Matches are distributed among these distances:
48 9 0.04
49 3 0.01
50 1 0.00
51 3 0.01
52 175 0.75
53 21 0.09
54 8 0.03
55 4 0.02
57 8 0.03
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.14
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
Found at i:658334 original size:19 final size:19
Alignment explanation
Indices: 658244--658326 Score: 113
Period size: 20 Copynumber: 4.6 Consensus size: 19
658234 AAATTATAAA
658244 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
658263 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
658283 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
658299 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
658316 CGCATTGCGAT
1 CGCATTGCGAT
658327 AGTCATTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.11
16 7 0.12
17 7 0.12
19 17 0.30
20 19 0.34
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:658452 original size:14 final size:14
Alignment explanation
Indices: 658433--658469 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
658423 CATCAATTAC
658433 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
658447 ACAAATCATCTTTT
1 ACAAATCAACTTTT
658461 ACAAATCAA
1 ACAAATCAA
658470 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:658747 original size:14 final size:14
Alignment explanation
Indices: 658728--658784 Score: 69
Period size: 14 Copynumber: 3.7 Consensus size: 14
658718 TTGAAATGAA
658728 AATCGCAACGAGAG
1 AATCGCAACGAGAG
658742 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
658759 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
658775 AATCGCAACG
1 AATCGCAACG
658785 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 18 0.47
16 6 0.16
17 6 0.16
19 8 0.21
ACGTcount: A:0.40, C:0.25, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:658765 original size:33 final size:33
Alignment explanation
Indices: 658720--658803 Score: 150
Period size: 33 Copynumber: 2.5 Consensus size: 33
658710 TCTTTTGGTT
658720 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
658753 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
658786 GAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
658804 CGAAATGAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:658766 original size:19 final size:19
Alignment explanation
Indices: 658742--658825 Score: 97
Period size: 19 Copynumber: 4.7 Consensus size: 19
658732 GCAACGAGAG
* *
658742 AATCGCAACGCGAGATGAC
1 AATCGCAACGCGAAATGAA
*
658761 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
658775 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
658794 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
658813 AATCGCAATGCGA
1 AATCGCAACGCGA
658826 TTTTGGTTTC
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 41 0.72
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:658856 original size:14 final size:14
Alignment explanation
Indices: 658837--658891 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
658827 TTTGGTTTCG
658837 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
658851 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
658870 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
658884 CGTTGCGA
1 CGTTGCGA
658892 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:658869 original size:33 final size:33
Alignment explanation
Indices: 658821--658891 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
658811 AAAATCGCAA
**
658821 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
658854 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
658887 TGCGA
1 TGCGA
658892 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:658899 original size:33 final size:33
Alignment explanation
Indices: 658832--658913 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
658822 GCGATTTTGG
***
658832 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
658865 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
658898 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
658914 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:658918 original size:20 final size:20
Alignment explanation
Indices: 658844--658932 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
658834 TCGCGTTGCG
658844 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
658864 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
658877 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
658897 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
658917 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
658933 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:659054 original size:33 final size:33
Alignment explanation
Indices: 659012--659082 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
659002 AATACTAACT
*
659012 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
659045 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
659078 TGAAA
1 TGAAA
659083 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:659316 original size:22 final size:22
Alignment explanation
Indices: 659264--659318 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
659254 TGGTTGTGAG
**
659264 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
659286 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
659308 GGATTTCTTCG
1 GGATTTCTTCG
659319 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:659488 original size:20 final size:20
Alignment explanation
Indices: 659463--659655 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
659453 CTTTAAATAT
659463 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
659483 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
659505 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
659524 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
659544 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
659564 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
659584 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
659604 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
659624 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
659644 CGCGTTGCGATT
1 CGCGTTGCGATT
659656 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:659650 original size:60 final size:60
Alignment explanation
Indices: 659463--659655 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
659453 CTTTAAATAT
**
659463 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
659524 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
659584 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
659644 CGCGTTGCGATT
1 CGCGTTGCGATT
659656 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:659736 original size:20 final size:20
Alignment explanation
Indices: 659711--659762 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
659701 AAGAATCGCG
*
659711 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
659731 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
659751 TTGCGATTCTGG
1 TTGCGATTCTGG
659763 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:665395 original size:29 final size:29
Alignment explanation
Indices: 665357--665439 Score: 127
Period size: 26 Copynumber: 3.0 Consensus size: 29
665347 ATTTTTTTCT
*
665357 TTACTGTCAGAGCGACAAGTGTTTTATTG
1 TTACTCTCAGAGCGACAAGTGTTTTATTG
*
665386 TTACTCTCAGAGCGACAAGTG--AT-TTG
1 TTACTCTCAGAGCGACAAGTGTTTTATTG
665412 TTACTCTCAGAGCGACAAGTGTTTTATT
1 TTACTCTCAGAGCGACAAGTGTTTTATT
665440 TTGTGTTTCT
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
26 24 0.50
27 1 0.02
28 1 0.02
29 22 0.46
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (29 bp):
TTACTCTCAGAGCGACAAGTGTTTTATTG
Found at i:670441 original size:108 final size:108
Alignment explanation
Indices: 670264--670480 Score: 434
Period size: 108 Copynumber: 2.0 Consensus size: 108
670254 ATATAATATC
670264 ATTAAATTTTAATAGGAATATCTTTTCAAGAAATTATATCTAAATTCTCCATTTAATAGGCACAC
1 ATTAAATTTTAATAGGAATATCTTTTCAAGAAATTATATCTAAATTCTCCATTTAATAGGCACAC
670329 GTGTTTAGAGTTTGATCCATTTATTTTAGGTAAATACCACATT
66 GTGTTTAGAGTTTGATCCATTTATTTTAGGTAAATACCACATT
670372 ATTAAATTTTAATAGGAATATCTTTTCAAGAAATTATATCTAAATTCTCCATTTAATAGGCACAC
1 ATTAAATTTTAATAGGAATATCTTTTCAAGAAATTATATCTAAATTCTCCATTTAATAGGCACAC
670437 GTGTTTAGAGTTTGATCCATTTATTTTAGGTAAATACCACATT
66 GTGTTTAGAGTTTGATCCATTTATTTTAGGTAAATACCACATT
670480 A
1 A
670481 GGTCTAAGTT
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
108 109 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (108 bp):
ATTAAATTTTAATAGGAATATCTTTTCAAGAAATTATATCTAAATTCTCCATTTAATAGGCACAC
GTGTTTAGAGTTTGATCCATTTATTTTAGGTAAATACCACATT
Found at i:672230 original size:29 final size:30
Alignment explanation
Indices: 672176--672246 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
672166 CTCTTTTAGG
* *
672176 TATTCTTATATTCTATCAACTAAATA-T-T
1 TATTCTTATATTTTATCAACCAAATACTAT
*
672204 TATATCTTATATTTTATCAACCGAATACTAT
1 TAT-TCTTATATTTTATCAACCAAATACTAT
672235 TATT-TTATATTT
1 TATTCTTATATTT
672247 CAATTAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 3 0.08
29 28 0.76
30 2 0.05
31 4 0.11
ACGTcount: A:0.34, C:0.13, G:0.01, T:0.52
Consensus pattern (30 bp):
TATTCTTATATTTTATCAACCAAATACTAT
Found at i:673522 original size:19 final size:19
Alignment explanation
Indices: 673488--673536 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
673478 AAAACGTTTT
* *
673488 TATGAACAATAATATACGG
1 TATGAACAGTAATATAAGG
* * *
673507 TTTGAACAGTATTATAATG
1 TATGAACAGTAATATAAGG
673526 TATGAACAGTA
1 TATGAACAGTA
673537 CTGTGAATAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.33
Consensus pattern (19 bp):
TATGAACAGTAATATAAGG
Found at i:673555 original size:24 final size:23
Alignment explanation
Indices: 673520--673567 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
673510 GAACAGTATT
* *
673520 ATAATGTATGAACAGTACTGTGA
1 ATAATGTATGAACAATACCGTGA
673543 ATAATGATATGAACAATACCGTGA
1 ATAATG-TATGAACAATACCGTGA
673567 A
1 A
673568 CAATACCGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.44, C:0.10, G:0.19, T:0.27
Consensus pattern (23 bp):
ATAATGTATGAACAATACCGTGA
Found at i:674181 original size:23 final size:23
Alignment explanation
Indices: 674155--674199 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
674145 CACCACAGCT
*
674155 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
674178 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
674200 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:674861 original size:19 final size:20
Alignment explanation
Indices: 674824--674861 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
674814 TTTTTATATA
*
674824 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
674844 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
674862 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:674912 original size:21 final size:21
Alignment explanation
Indices: 674888--674929 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
674878 TTCATATTCG
* *
674888 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
674909 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
674930 CAGCCCAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.26, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:680564 original size:21 final size:21
Alignment explanation
Indices: 680540--680581 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
680530 TTCATATTCG
* *
680540 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
680561 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
680582 CAGCCCAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.26, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:682187 original size:32 final size:32
Alignment explanation
Indices: 682130--682263 Score: 168
Period size: 32 Copynumber: 4.3 Consensus size: 32
682120 GTTCCTACGA
682130 ACATAGGTAA--CTGTCCATATGTCCCGAAAG
1 ACATAGGTAATTCTGTCCATATGTCCCGAAAG
* * *
682160 ACATAGGTAATTCTGTCTATATATCCCGAAAT
1 ACATAGGTAATTCTGTCCATATGTCCCGAAAG
*
682192 ACATAGGTAATACTGTCCATATGTCCCGAAAG
1 ACATAGGTAATTCTGTCCATATGTCCCGAAAG
* * *
682224 ACGTAAGT-ATAT-TGCCCATATGTCCCGAAAG
1 ACATAGGTAAT-TCTGTCCATATGTCCCGAAAG
682255 ACATAGGTA
1 ACATAGGTA
682264 CTCCCTCGAC
Statistics
Matches: 87, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
30 10 0.11
31 26 0.30
32 51 0.59
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (32 bp):
ACATAGGTAATTCTGTCCATATGTCCCGAAAG
Found at i:683040 original size:30 final size:30
Alignment explanation
Indices: 682971--683037 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
682961 TACTCTAATT
* * *
682971 TTTCCTTTCTTGAACTAAAGAAAGTGTTAC
1 TTTCATTTCTTGAACTAAAGAAAGTCTTAA
* *
683001 TTTCATTTCTTGGACTAACGAAAG-CTTAA
1 TTTCATTTCTTGAACTAAAGAAAGTCTTAA
683030 TTTCATTT
1 TTTCATTT
683038 TCTCTTATGG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 11 0.34
30 21 0.66
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.43
Consensus pattern (30 bp):
TTTCATTTCTTGAACTAAAGAAAGTCTTAA
Found at i:687867 original size:22 final size:22
Alignment explanation
Indices: 687837--687902 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
687827 TGTGAGGTTG
687837 TGCA-CGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
687858 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
687880 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
687902 T
1 T
687903 ATGTCCATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
21 4 0.09
22 40 0.91
ACGTcount: A:0.27, C:0.26, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:688155 original size:30 final size:31
Alignment explanation
Indices: 688114--688173 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
688104 GTAGCCTAGT
*
688114 ATTTTCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
688144 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
688174 ACGTTTTCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:688220 original size:29 final size:29
Alignment explanation
Indices: 688187--688257 Score: 99
Period size: 29 Copynumber: 2.5 Consensus size: 29
688177 TTTTCTGCAT
**
688187 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
* *
688216 ATTCATGTCATGTAATACCTTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
688245 ATTCAT-TCATGTA
1 ATTCATGTCATGTA
688258 TCATAATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
28 7 0.18
29 31 0.82
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:688675 original size:67 final size:65
Alignment explanation
Indices: 688559--688704 Score: 179
Period size: 67 Copynumber: 2.2 Consensus size: 65
688549 TTTTTCTCAT
* * *
688559 GGGGAATCGGTT-CCCCCCCTAGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGA
1 GGGGTATCGGTTCCCCCCCCTAGGGGTACCGATTCCCCTCAAGCAATCTGGAA-ATCAT-T-CGA
688623 TGA
63 TGA
* * * *
688626 GGGGTATCGGTTCCCCCCCCTGGGGGTACCGATT-CCCTCTAGCATTCTGGAAATCATTCGTTGA
1 GGGGTATCGGTTCCCCCCCCTAGGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATTCGATGA
*
688690 AGGGTATCGGTTCCC
1 GGGGTATCGGTTCCC
688705 TTGAATGGGT
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
64 19 0.27
65 1 0.01
66 4 0.06
67 27 0.39
68 19 0.27
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.27
Consensus pattern (65 bp):
GGGGTATCGGTTCCCCCCCCTAGGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATTCGATGA
Found at i:688723 original size:20 final size:19
Alignment explanation
Indices: 688686--688724 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
688676 AAATCATTCG
* *
688686 TTGAAGGGTATCGGTTCCC
1 TTGAAGGGTACCGATTCCC
688705 TTGAATGGGTACCGATTCCC
1 TTGAA-GGGTACCGATTCCC
688725 CTAACCCAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.18, C:0.23, G:0.28, T:0.31
Consensus pattern (19 bp):
TTGAAGGGTACCGATTCCC
Found at i:689207 original size:17 final size:19
Alignment explanation
Indices: 689185--689219 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
689175 ACGTTGAGAG
689185 AAGGAAG-A-GAAGAAAAT
1 AAGGAAGAAGGAAGAAAAT
689202 AAGGAAGAAGGAAGAAAA
1 AAGGAAGAAGGAAGAAAA
689220 GAAATGGGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 1 0.06
19 8 0.50
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.03
Consensus pattern (19 bp):
AAGGAAGAAGGAAGAAAAT
Found at i:694782 original size:22 final size:22
Alignment explanation
Indices: 694765--694831 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
694755 CTCGTATAAA
694765 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
694787 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
694809 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
694831 T
1 T
694832 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:695092 original size:30 final size:31
Alignment explanation
Indices: 695051--695110 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
695041 TAGCCATAGT
*
695051 ATTTTCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
695081 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
695111 AACGTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:695167 original size:29 final size:29
Alignment explanation
Indices: 695125--695196 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
695115 TTTTCTGCAT
**
695125 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
* *
695154 ATTCATGTCATGTAATACCTTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
695183 ATTCATGTCATGTA
1 ATTCATGTCATGTA
695197 TCATAATATG
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:0.38, C:0.14, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:695627 original size:68 final size:69
Alignment explanation
Indices: 695500--695652 Score: 211
Period size: 68 Copynumber: 2.2 Consensus size: 69
695490 TTTTTCTCAT
* * *
695500 GGGGGAATCGGTT-CCCCCCCTAGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACG
1 GGGGGTATCGGTTCCCCCCCCTAGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACG
695564 ATGA
66 ATGA
* * * *
695568 GGGGGTATCGGTTCCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAA-ATCATATTCG
1 GGGGGTATCGGTTCCCCCCCCTAGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACG
*
695632 TTGA
66 ATGA
*
695636 AGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
695653 TTGAATGGGG
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
68 39 0.52
69 36 0.48
ACGTcount: A:0.19, C:0.28, G:0.27, T:0.26
Consensus pattern (69 bp):
GGGGGTATCGGTTCCCCCCCCTAGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACG
ATGA
Found at i:695663 original size:22 final size:21
Alignment explanation
Indices: 695632--695675 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
695622 ATCATATTCG
* *
695632 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
695653 TTGAATGGGGTACCGATTCCCC
1 TTGAA-GGGGTACCGATTCCCC
695675 T
1 T
695676 AACCCAGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.16, C:0.25, G:0.30, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:695664 original size:68 final size:69
Alignment explanation
Indices: 695501--695675 Score: 194
Period size: 68 Copynumber: 2.6 Consensus size: 69
695491 TTTTCTCATG
* * * * *
695501 GGGGAATCGGTTCCCCCC-CTAGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGA
1 GGGGTATCGGTTCCCCCCAATGGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGA
*
695565 TGAG
66 TGAA
** * * * *
695569 GGGGTATCGGTTCCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAA-ATCATATTCGT
1 GGGGTATCGGTTCCCCCCAATGGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGA
695633 TGAA
66 TGAA
**
695637 GGGGTATCGGTTCCCCTTGAAT-GGGGTACCGATTCCCCT
1 GGGGTATCGGTTCCCC-CCAATGGGGGTACCGATTCCCCT
695676 AACCCAGAAT
Statistics
Matches: 92, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
68 61 0.66
69 31 0.34
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.27
Consensus pattern (69 bp):
GGGGTATCGGTTCCCCCCAATGGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGA
TGAA
Found at i:696158 original size:17 final size:19
Alignment explanation
Indices: 696136--696170 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
696126 ACGTTGAGAG
696136 AAGGAAG-A-GAAGAAAAT
1 AAGGAAGAAGGAAGAAAAT
696153 AAGGAAGAAGGAAGAAAA
1 AAGGAAGAAGGAAGAAAA
696171 GAAATAGGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 1 0.06
19 8 0.50
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.03
Consensus pattern (19 bp):
AAGGAAGAAGGAAGAAAAT
Found at i:700957 original size:21 final size:21
Alignment explanation
Indices: 700931--700975 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
700921 GATTTCTGGG
* *
700931 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
700952 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
700973 CAA
1 CAA
700976 ACGAACAACA
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:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:701577 original size:18 final size:18
Alignment explanation
Indices: 701554--701588 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
701544 TTAGGAGATT
701554 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
701572 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
701589 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:702660 original size:149 final size:149
Alignment explanation
Indices: 702480--702943 Score: 869
Period size: 149 Copynumber: 3.1 Consensus size: 149
702470 GAGTCGAGGG
702480 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
702545 ATATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ATATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
702610 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
702629 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
702694 ATATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ATATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
702759 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
702778 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
* *
702843 ACT-TGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTAGTCCTTATGGACATCATT
66 A-TATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
*
702907 ATATGGCACTACGGTGTAAT
130 ATATGGCACTACGGTGCAAT
702927 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
702944 TGCAATTATA
Statistics
Matches: 310, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
148 1 0.00
149 308 0.99
150 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ATATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:702944 original size:23 final size:23
Alignment explanation
Indices: 702911--702955 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
702901 ATCATTATAT
* *
702911 GGCACTACGGTGTAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
702934 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
702956 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:717751 original size:18 final size:19
Alignment explanation
Indices: 717730--717783 Score: 53
Period size: 17 Copynumber: 3.1 Consensus size: 19
717720 TAAAATATTT
*
717730 TAAATGCTTT-TTATATAA
1 TAAATGCTTTATTATAAAA
*
717748 TAAA-GTTTTATTATAAAA
1 TAAATGCTTTATTATAAAA
*
717766 TAAAT--TTTATTACAAAA
1 TAAATGCTTTATTATAAAA
717783 T
1 T
717784 GAATATTGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 16 0.52
18 15 0.48
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (19 bp):
TAAATGCTTTATTATAAAA
Found at i:717775 original size:17 final size:18
Alignment explanation
Indices: 717740--717783 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
717730 TAAATGCTTT
*
717740 TTATATAATAAAGTTTTA
1 TTATAAAATAAAGTTTTA
717758 TTATAAAATAAA-TTTTA
1 TTATAAAATAAAGTTTTA
*
717775 TTACAAAAT
1 TTATAAAAT
717784 GAATATTGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
TTATAAAATAAAGTTTTA
Found at i:719397 original size:22 final size:21
Alignment explanation
Indices: 719349--719421 Score: 75
Period size: 22 Copynumber: 3.7 Consensus size: 21
719339 TTTGGTTTAC
*
719349 GGAATATAAGATTA--TTATG
1 GGAATAAAAGATTACCTTATG
*
719368 AGAATAAAAGATTACCTTACTG
1 GGAATAAAAGATTACCTTA-TG
719390 GGAATAAAAGATTACC--A-G
1 GGAATAAAAGATTACCTTATG
*
719408 AGAATAAAAGATTA
1 GGAATAAAAGATTA
719422 TCAGAAAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
18 14 0.30
19 12 0.26
20 1 0.02
21 3 0.06
22 17 0.36
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (21 bp):
GGAATAAAAGATTACCTTATG
Found at i:719414 original size:18 final size:18
Alignment explanation
Indices: 719367--719432 Score: 69
Period size: 18 Copynumber: 3.4 Consensus size: 18
719357 AGATTATTAT
719367 GAGAATAAAAGATTACCTTA
1 GAGAATAAAAGATTACC--A
*
719387 CTGGGAATAAAAGATTACCA
1 --GAGAATAAAAGATTACCA
*
719407 GAGAATAAAAGATTATCA
1 GAGAATAAAAGATTACCA
*
719425 GAAAATAA
1 GAGAATAA
719433 GATTACTGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
18 23 0.57
20 1 0.03
22 16 0.40
ACGTcount: A:0.53, C:0.09, G:0.17, T:0.21
Consensus pattern (18 bp):
GAGAATAAAAGATTACCA
Found at i:719678 original size:37 final size:37
Alignment explanation
Indices: 719608--719679 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 37
719598 AAGTTATTTA
*
719608 TATATATATTTTTTTAAAAAATTAAACTCATAAAATT
1 TATATATATTTTTTTAAAAAATTAAAATCATAAAATT
719645 TATATA-ATTTTTTTAAAAAAATTGAAAAT-ATAAAA
1 TATATATATTTTTTT-AAAAAATT-AAAATCATAAAA
719680 AGGTTTAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 8 0.25
37 20 0.62
38 4 0.12
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (37 bp):
TATATATATTTTTTTAAAAAATTAAAATCATAAAATT
Found at i:722281 original size:36 final size:36
Alignment explanation
Indices: 722234--722347 Score: 147
Period size: 36 Copynumber: 3.1 Consensus size: 36
722224 TATTCATCAG
*
722234 CATGCCCGGATTCATACCCATGTTCATCTCCACTCC
1 CATGCCCGGATTCATACCCATGTTCATCCCCACTCC
* * *
722270 CATGCCTGGATTCATACCCATGTTCATCCCCATTTC
1 CATGCCCGGATTCATACCCATGTTCATCCCCACTCC
* *
722306 CATGCCCGGATTCATACTCATGTGGTTCATCCCCATTCC
1 CATGCCCGGATTCATACCCA--T-GTTCATCCCCACTCC
722345 CAT
1 CAT
722348 AGGCTGTTGA
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
36 50 0.74
38 1 0.01
39 17 0.25
ACGTcount: A:0.19, C:0.38, G:0.12, T:0.31
Consensus pattern (36 bp):
CATGCCCGGATTCATACCCATGTTCATCCCCACTCC
Found at i:723576 original size:33 final size:33
Alignment explanation
Indices: 723161--723865 Score: 488
Period size: 33 Copynumber: 21.4 Consensus size: 33
723151 CTTGCTTGGA
* * *
723161 CAGGTTGGCAATGTGGGTTAGCATTTGGCTGTG
1 CAGGTTGGCCATTTGGATTAGCATTTGGCTGTG
* * * *
723194 -TGAGTTGGCCGTTTGGGTTAGTATTTGGCTGTG
1 CAG-GTTGGCCATTTGGATTAGCATTTGGCTGTG
* * *
723227 CAGGTTGACCATTGGGATTAGCATTTGGCAGTG
1 CAGGTTGGCCATTTGGATTAGCATTTGGCTGTG
* ** *
723260 CTGGTTCTCCATATT-GATTAGCATTTGGATGTG
1 CAGGTTGGCCAT-TTGGATTAGCATTTGGCTGTG
* ** **
723293 -TGAGTTGGCCATTCAGATTAGTGTTTGGCTGTG
1 CAG-GTTGGCCATTTGGATTAGCATTTGGCTGTG
* * *
723326 CAGGTAGGTCATATGGATTAGCATTTGGCTGTG
1 CAGGTTGGCCATTTGGATTAGCATTTGGCTGTG
* * *
723359 CAGGTTGGCCATATGGATTAGCACTTGGTTGTG
1 CAGGTTGGCCATTTGGATTAGCATTTGGCTGTG
* ** *
723392 CAGGTTGGACATAGGGATTAGCATTTTGCTGTG
1 CAGGTTGGCCATTTGGATTAGCATTTGGCTGTG
* * *
723425 CAGGCTGGCCATTTGGATTAGCATTTAGCTGCG
1 CAGGTTGGCCATTTGGATTAGCATTTGGCTGTG
** *
723458 TGGGTCT-GCCATTTGGATTAGCATTTGGCTGGG
1 CAGGT-TGGCCATTTGGATTAGCATTTGGCTGTG
* *
723491 CAGGTTGGCCATTTGGATTAGCAGTTGACTGTG
1 CAGGTTGGCCATTTGGATTAGCATTTGGCTGTG
* * **
723524 CTGGTTGACCATAGGGATTAGCATTTGGCTGTG
1 CAGGTTGGCCATTTGGATTAGCATTTGGCTGTG
* * ** *
723557 TC-GGATGGCCATTTAGATTAGTGTTTGGTTGTG
1 -CAGGTTGGCCATTTGGATTAGCATTTGGCTGTG
* ** * * **
723590 CAGGTTGGACATAGGGACTAGCATTTGACTGCA
1 CAGGTTGGCCATTTGGATTAGCATTTGGCTGTG
* * * *
723623 CGGGTTGACCGTTTGGATTAGCATTTGACTGTG
1 CAGGTTGGCCATTTGGATTAGCATTTGGCTGTG
* * ** *
723656 CCGGTTGACCATAGGGATTAGCATTTTGCTGAATG
1 CAGGTTGGCCATTTGGATTAGCATTTGGCTG--TG
*
723691 --GGTTGGCCATTTGGATTAGCATTTGCCTGTG
1 CAGGTTGGCCATTTGGATTAGCATTTGGCTGTG
** ** **
723722 CAGGTTGGCCATAGGGATTTTCATTTGGAAGTG
1 CAGGTTGGCCATTTGGATTAGCATTTGGCTGTG
** * * *
723755 TGGGTTGGCCATATGGATCAGCATTTGGCTGCG
1 CAGGTTGGCCATTTGGATTAGCATTTGGCTGTG
* * ** * ** * *
723788 TAGGTTGGCTATAAGGATTAACGCTTGACAGTG
1 CAGGTTGGCCATTTGGATTAGCATTTGGCTGTG
* * * * * **
723821 CAGATTGGCCATATGCATTAGGACTTGGCTGCC
1 CAGGTTGGCCATTTGGATTAGCATTTGGCTGTG
723854 CAGGTTGGCCAT
1 CAGGTTGGCCAT
723866 ACATATTAGC
Statistics
Matches: 516, Mismatches: 142, Indels: 28
0.75 0.21 0.04
Matches are distributed among these distances:
31 2 0.00
32 6 0.01
33 501 0.97
34 5 0.01
35 2 0.00
ACGTcount: A:0.18, C:0.15, G:0.33, T:0.34
Consensus pattern (33 bp):
CAGGTTGGCCATTTGGATTAGCATTTGGCTGTG
Found at i:728533 original size:89 final size:93
Alignment explanation
Indices: 728430--728614 Score: 254
Period size: 91 Copynumber: 2.0 Consensus size: 93
728420 AATTTTATTT
* * *
728430 TTTATTACGAACTACCGCTTGTCAATTTATAAGAAAAAAGGGAAAATGAAAA-CA-CA-TATATA
1 TTTATCACGAACTACCACTTGTCAATTTATAAG-AAAAAGGGAAAATGAAAAGCATAAGTATATA
728492 TCAACTTGGAGAGTGAAAACAATGAAA-G
65 TCAACTTGGAGAGTGAAAACAATGAAATG
* * *
728520 TTTATCAC-AACTACCACTTGTCAGTTTATAAGAAAAAGGGAAAATGAAAAGCATAAGTGTATGT
1 TTTATCACGAACTACCACTTGTCAATTTATAAGAAAAAGGGAAAATGAAAAGCATAAGTATATAT
**
728584 CAACTTGGAGAGTGAAGGCAATGAAATG
66 CAACTTGGAGAGTGAAAACAATGAAATG
728612 TTT
1 TTT
728615 TGCTCAAAAT
Statistics
Matches: 83, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
88 18 0.22
89 24 0.29
90 8 0.10
91 29 0.35
92 4 0.05
ACGTcount: A:0.43, C:0.12, G:0.19, T:0.26
Consensus pattern (93 bp):
TTTATCACGAACTACCACTTGTCAATTTATAAGAAAAAGGGAAAATGAAAAGCATAAGTATATAT
CAACTTGGAGAGTGAAAACAATGAAATG
Found at i:739714 original size:12 final size:13
Alignment explanation
Indices: 739689--739717 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
739679 TTAAAATCTC
739689 TAAATTCTTAAAA
1 TAAATTCTTAAAA
739702 TAAATTC-TAAAA
1 TAAATTCTTAAAA
739714 TAAA
1 TAAA
739718 CAATGGTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (13 bp):
TAAATTCTTAAAA
Found at i:739926 original size:27 final size:26
Alignment explanation
Indices: 739878--739929 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
739868 TAGATATTTG
* *
739878 AAATTTAAATATTTAAGTATTTTTTT
1 AAATTTAAAAATTTAAGAATTTTTTT
739904 AAATTTAAAAAATTTAAGAATTTTTT
1 AAATTT-AAAAATTTAAGAATTTTTT
739930 GAAAACTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (26 bp):
AAATTTAAAAATTTAAGAATTTTTTT
Found at i:739939 original size:27 final size:27
Alignment explanation
Indices: 739888--739946 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
739878 AAATTTAAAT
* * **
739888 ATTTAAGTATTTTTTTAAATTTAAAAA
1 ATTTAAGAATTTTTTGAAAACTAAAAA
*
739915 ATTTAAGAATTTTTTGAAAACTAAAAT
1 ATTTAAGAATTTTTTGAAAACTAAAAA
739942 ATTTA
1 ATTTA
739947 CAGATATTAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (27 bp):
ATTTAAGAATTTTTTGAAAACTAAAAA
Found at i:741673 original size:2 final size:2
Alignment explanation
Indices: 741666--741690 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
741656 TATCTATAGT
741666 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
741691 ATGTTCTATA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:746312 original size:16 final size:16
Alignment explanation
Indices: 746291--746323 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
746281 TAATAAATAA
*
746291 ACGAACATAAACGAAC
1 ACGAACATAAACAAAC
746307 ACGAACATAAACAAAC
1 ACGAACATAAACAAAC
746323 A
1 A
746324 AATTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.61, C:0.24, G:0.09, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACAAAC
Found at i:746417 original size:16 final size:16
Alignment explanation
Indices: 746392--746472 Score: 126
Period size: 16 Copynumber: 5.1 Consensus size: 16
746382 TAATAAATAA
*
746392 ACGAATATAAACGAAC
1 ACGAACATAAACGAAC
746408 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
746424 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
*
746440 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
*
746456 ACGAATATAAACGAAC
1 ACGAACATAAACGAAC
746472 A
1 A
746473 TAAGCGTTGG
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 61 1.00
ACGTcount: A:0.57, C:0.20, G:0.12, T:0.11
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:747582 original size:10 final size:10
Alignment explanation
Indices: 747567--747638 Score: 54
Period size: 10 Copynumber: 6.4 Consensus size: 10
747557 ATAAATGAAT
747567 GAACATAAAC
1 GAACATAAAC
747577 GAACATAACCGAAC
1 GAACAT-A---AAC
747591 GAACATAAAC
1 GAACATAAAC
747601 GAACATAATCGAAC
1 GAACAT-A---AAC
747615 GAACATAAAC
1 GAACATAAAC
* *
747625 AAACATAATC
1 GAACATAAAC
747635 GAAC
1 GAAC
747639 GAACATAACC
Statistics
Matches: 51, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
10 29 0.57
11 2 0.04
13 2 0.04
14 18 0.35
ACGTcount: A:0.56, C:0.22, G:0.11, T:0.11
Consensus pattern (10 bp):
GAACATAAAC
Found at i:747591 original size:14 final size:13
Alignment explanation
Indices: 747574--747653 Score: 73
Period size: 14 Copynumber: 6.3 Consensus size: 13
747564 AATGAACATA
747574 AACGAACATAACCG
1 AACGAACATAA-CG
747588 AACGAACAT-A--
1 AACGAACATAACG
747598 AACGAACATAATCG
1 AACGAACATAA-CG
747612 AACGAACAT-A--
1 AACGAACATAACG
*
747622 AACAAACATAATCG
1 AACGAACATAA-CG
747636 AACGAACATAACCG
1 AACGAACATAA-CG
747650 AACG
1 AACG
747654 TTCACGAACG
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
10 17 0.31
11 2 0.04
13 2 0.04
14 34 0.62
ACGTcount: A:0.54, C:0.24, G:0.12, T:0.10
Consensus pattern (13 bp):
AACGAACATAACG
Found at i:747663 original size:24 final size:24
Alignment explanation
Indices: 747554--747652 Score: 146
Period size: 24 Copynumber: 4.1 Consensus size: 24
747544 GGTTAGGCTA
*
747554 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
*
747578 AACATAACCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
*
747602 AACATAATCGAACGAACATAAACA
1 AACATAATCGAACGAACATAAACG
*
747626 AACATAATCGAACGAACATAACCG
1 AACATAATCGAACGAACATAAACG
747650 AAC
1 AAC
747653 GTTCACGAAC
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
23 2 0.03
24 66 0.97
ACGTcount: A:0.56, C:0.21, G:0.11, T:0.12
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:749126 original size:11 final size:11
Alignment explanation
Indices: 749110--749148 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
749100 AACCCATTTA
*
749110 AAAAATTAAAT
1 AAAAATTAATT
749121 AAAAATTAATT
1 AAAAATTAATT
* *
749132 CAAATTTAATT
1 AAAAATTAATT
749143 AAAAAT
1 AAAAAT
749149 CAAAGAAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (11 bp):
AAAAATTAATT
Found at i:751620 original size:113 final size:114
Alignment explanation
Indices: 751405--751622 Score: 314
Period size: 113 Copynumber: 1.9 Consensus size: 114
751395 TTTGGGGCAC
** * *
751405 AATAGTGGCATTTTTTGAAAAAAAAGCGTCGCAATAGGTCCATATATAGTGGTATTTATTGGAAA
1 AATAGTGGCATTTTTTGAAAAAAAAGCGTCGCAATAAATCCATATATAGTGGCATTTATTAGAAA
* *
751470 AACGCCACTATATATATACTTTTTTGGGCATTTTTTTGGGTTGCACGAT
66 AACACCACTATATATATACTTTTTTGGGCACTTTTTTGGGTTGCACGAT
* *** *
751519 AATAGTGGCGTTTTTTTTGAAAAAA-CGTCGCAATAAATCCATATATAGTGGCGTTTATTAGAAA
1 AATAGTGGCATTTTTTGAAAAAAAAGCGTCGCAATAAATCCATATATAGTGGCATTTATTAGAAA
751583 AACACCACTATATATATACCTTTTTTGGGC-CTTTTTTGGG
66 AACACCACTATATATATA-CTTTTTTGGGCACTTTTTTGGG
751623 GGCCTTGCGC
Statistics
Matches: 92, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
113 60 0.65
114 32 0.35
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (114 bp):
AATAGTGGCATTTTTTGAAAAAAAAGCGTCGCAATAAATCCATATATAGTGGCATTTATTAGAAA
AACACCACTATATATATACTTTTTTGGGCACTTTTTTGGGTTGCACGAT
Found at i:752635 original size:13 final size:13
Alignment explanation
Indices: 752617--752641 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
752607 GTTATATTTT
752617 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
752630 AAAAAAGAAAAA
1 AAAAAAGAAAAA
752642 TATTATCCGA
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:754846 original size:190 final size:190
Alignment explanation
Indices: 754523--754903 Score: 762
Period size: 190 Copynumber: 2.0 Consensus size: 190
754513 TTAAGTAGTC
754523 TGTTTCTTTAGTCTGTAGAATATGCTGGTGTTCAAATGTCCTCACTAAATGCTGGTTTCATATAG
1 TGTTTCTTTAGTCTGTAGAATATGCTGGTGTTCAAATGTCCTCACTAAATGCTGGTTTCATATAG
754588 GTACCGTAAAGCACAGTTGGCTCTTCAGAAAGGAGAAGAAGATCTTGCGCGTGAAGCCCTCAAGA
66 GTACCGTAAAGCACAGTTGGCTCTTCAGAAAGGAGAAGAAGATCTTGCGCGTGAAGCCCTCAAGA
754653 GGCGTAAATCTTTTGCTGTAAGATGTCATCTTGCTAGAAAATTGACTTCTGAGCATTCTT
131 GGCGTAAATCTTTTGCTGTAAGATGTCATCTTGCTAGAAAATTGACTTCTGAGCATTCTT
754713 TGTTTCTTTAGTCTGTAGAATATGCTGGTGTTCAAATGTCCTCACTAAATGCTGGTTTCATATAG
1 TGTTTCTTTAGTCTGTAGAATATGCTGGTGTTCAAATGTCCTCACTAAATGCTGGTTTCATATAG
754778 GTACCGTAAAGCACAGTTGGCTCTTCAGAAAGGAGAAGAAGATCTTGCGCGTGAAGCCCTCAAGA
66 GTACCGTAAAGCACAGTTGGCTCTTCAGAAAGGAGAAGAAGATCTTGCGCGTGAAGCCCTCAAGA
754843 GGCGTAAATCTTTTGCTGTAAGATGTCATCTTGCTAGAAAATTGACTTCTGAGCATTCTT
131 GGCGTAAATCTTTTGCTGTAAGATGTCATCTTGCTAGAAAATTGACTTCTGAGCATTCTT
754903 T
1 T
754904 ATAAAATCAT
Statistics
Matches: 191, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
190 191 1.00
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.33
Consensus pattern (190 bp):
TGTTTCTTTAGTCTGTAGAATATGCTGGTGTTCAAATGTCCTCACTAAATGCTGGTTTCATATAG
GTACCGTAAAGCACAGTTGGCTCTTCAGAAAGGAGAAGAAGATCTTGCGCGTGAAGCCCTCAAGA
GGCGTAAATCTTTTGCTGTAAGATGTCATCTTGCTAGAAAATTGACTTCTGAGCATTCTT
Found at i:763303 original size:30 final size:30
Alignment explanation
Indices: 763267--763326 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
763257 TATCTACCAC
763267 CCTTCCCCATCTCCCTGCTATACTTTCCAG
1 CCTTCCCCATCTCCCTGCTATACTTTCCAG
763297 CCTTCCCCATCTCCCTGCTATACTTTCCAG
1 CCTTCCCCATCTCCCTGCTATACTTTCCAG
763327 AAAAGAATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.13, C:0.47, G:0.07, T:0.33
Consensus pattern (30 bp):
CCTTCCCCATCTCCCTGCTATACTTTCCAG
Found at i:774478 original size:36 final size:36
Alignment explanation
Indices: 774426--774500 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
774416 CATTGAAATC
774426 ATATTTTGTATGTTAATGTAAATACATTTGATTCGT
1 ATATTTTGTATGTTAATGTAAATACATTTGATTCGT
*
774462 ATATTTTGTATTTTAATGTAAATACATTTGATTCGT
1 ATATTTTGTATGTTAATGTAAATACATTTGATTCGT
774498 ATA
1 ATA
774501 CTTTAACATG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (36 bp):
ATATTTTGTATGTTAATGTAAATACATTTGATTCGT
Found at i:774861 original size:21 final size:21
Alignment explanation
Indices: 774728--774853 Score: 161
Period size: 21 Copynumber: 6.1 Consensus size: 21
774718 GTTTCTAGAT
* *
774728 TCGCAACGCGAACTTTGACTA
1 TCGCAATGCGAACTTGGACTA
* *
774749 TCGCATTGTGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
774770 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
774791 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
*
774812 TCGCAATGCTAA-TAT-G--TA
1 TCGCAATGCGAACT-TGGACTA
*
774830 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
774851 TCG
1 TCG
774854 TATTGCGATT
Statistics
Matches: 92, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
18 14 0.15
19 2 0.02
20 2 0.02
21 74 0.80
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:774896 original size:21 final size:21
Alignment explanation
Indices: 774870--774970 Score: 141
Period size: 21 Copynumber: 4.8 Consensus size: 21
774860 GATTTACATA
774870 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
774891 TTCGCATTGCGATAGTCGAAA
1 TTCGCATTGCGATAGTCCAAG
* * *
774912 TTCGTATTGCGATAGT-CGAC
1 TTCGCATTGCGATAGTCCAAG
774932 TATCGCATTGCGATAGTCCAAG
1 T-TCGCATTGCGATAGTCCAAG
774954 TTCGCATTGCGATAGTC
1 TTCGCATTGCGATAGTC
774971 GTGGTCGTAG
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
20 2 0.03
21 64 0.93
22 3 0.04
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.31
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:774922 original size:42 final size:43
Alignment explanation
Indices: 774847--774970 Score: 146
Period size: 42 Copynumber: 3.0 Consensus size: 43
774837 GCGAACTTCG
* * * *
774847 ACTATCGTATTGCGAT-TTACATATTCGCATTGCGATAGTCCA
1 ACTATCGCATTGCGATAGTCCAAATTCGCATTGCGATAGTCCA
* * * *
774889 AGT-TCGCATTGCGATAGTCGAAATTCGTATTGCGATAGT-CG
1 ACTATCGCATTGCGATAGTCCAAATTCGCATTGCGATAGTCCA
*
774930 ACTATCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTC
1 ACTATCGCATTGCGATAGTCCAAATTCGCATTGCGATAGTC
774971 GTGGTCGTAG
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
41 14 0.21
42 53 0.79
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (43 bp):
ACTATCGCATTGCGATAGTCCAAATTCGCATTGCGATAGTCCA
Found at i:774983 original size:12 final size:12
Alignment explanation
Indices: 774966--774999 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
774956 CGCATTGCGA
774966 TAGTCGTGGTCG
1 TAGTCGTGGTCG
*
774978 TAGTCGTGATCG
1 TAGTCGTGGTCG
*
774990 TGGTCGTGGT
1 TAGTCGTGGT
775000 AATACGTGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.09, C:0.15, G:0.41, T:0.35
Consensus pattern (12 bp):
TAGTCGTGGTCG
Found at i:775103 original size:21 final size:21
Alignment explanation
Indices: 775078--775193 Score: 171
Period size: 21 Copynumber: 5.5 Consensus size: 21
775068 ATACCACCAG
775078 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
775099 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
775120 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
* * *
775141 TCACAATGCGAATTTCGACTA
1 TCGCAATGCGAACTTGGACTA
775162 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
775183 TCGCAATGCGA
1 TCGCAATGCGA
775194 TAGTCGAAGT
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
20 1 0.01
21 84 0.98
22 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:775149 original size:63 final size:63
Alignment explanation
Indices: 775081--775200 Score: 222
Period size: 63 Copynumber: 1.9 Consensus size: 63
775071 CCACCAGTCG
*
775081 CAATGCGAACTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGATAGTCGACTATCA
1 CAATGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGATAGTCGACTATCA
*
775144 CAATGCGAATTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGATAGTCGA
1 CAATGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGATAGTCGA
775201 AGTTCGCATT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (63 bp):
CAATGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGATAGTCGACTATCA
Found at i:775207 original size:21 final size:21
Alignment explanation
Indices: 775183--775318 Score: 170
Period size: 21 Copynumber: 6.5 Consensus size: 21
775173 ACTTGGACTA
* *
775183 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
775204 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* * *
775225 TTGCATTGCGATAGT-CGACT
1 TCGCATTGCGATAGTCCAAGT
* *
775245 ATCGCATTGCGAT-TTACATA-T
1 -TCGCATTGCGATAGTCCA-AGT
775266 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
775287 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
775308 TCGCATTGCGA
1 TCGCATTGCGA
775319 ATTTGGAAAC
Statistics
Matches: 100, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
20 17 0.17
21 82 0.82
22 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:775235 original size:63 final size:62
Alignment explanation
Indices: 775099--775297 Score: 190
Period size: 63 Copynumber: 3.2 Consensus size: 62
775089 ACTTGGACTA
* * * * * * * *
775099 TCGCAATGCGAACTTGGACTATCGCAATGCGATAGTCGACTATCACAATGCGA-ATTTCGACT
1 TCGCATTGCGAACTTGGACTATCGCAATGCGATAGTCGAAT-TCGCATTGCGATAGTCCAAGT
*
775161 ATCGCAATGCGAACTTGGACTATCGCAATGCGATAGTCGAAGTTCGCATTGCGATAGTCCAAGT
1 -TCGCATTGCGAACTTGGACTATCGCAATGCGATAGTCGAA-TTCGCATTGCGATAGTCCAAGT
* * * * *
775225 TTGCATTGCGATA-GTCGACTATCGCATTGCGAT-TTAC-ATATTCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGA-ACTTGGACTATCGCAATGCGATAGT-CGA-ATTCGCATTGCGATAGTCCAAGT
775287 TCGCATTGCGA
1 TCGCATTGCGA
775298 TAGTCCAAGT
Statistics
Matches: 117, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
62 34 0.29
63 76 0.65
64 7 0.06
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.28
Consensus pattern (62 bp):
TCGCATTGCGAACTTGGACTATCGCAATGCGATAGTCGAATTCGCATTGCGATAGTCCAAGT
Found at i:779822 original size:14 final size:14
Alignment explanation
Indices: 779803--779840 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
779793 TCGGTAATAT
779803 GTTCGTTTACT-TTC
1 GTTCGTTTA-TGTTC
779817 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
*
779831 GTTCATTTAT
1 GTTCGTTTAT
779841 ATTTAGGTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 1 0.05
14 21 0.95
ACGTcount: A:0.11, C:0.16, G:0.16, T:0.58
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:780483 original size:13 final size:13
Alignment explanation
Indices: 780467--780491 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
780457 TATTTTAATT
780467 TTGCATTTCCTTC
1 TTGCATTTCCTTC
780480 TTGCATTTCCTT
1 TTGCATTTCCTT
780492 TGTATTTACT
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:0.08, C:0.28, G:0.08, T:0.56
Consensus pattern (13 bp):
TTGCATTTCCTTC
Found at i:792424 original size:2 final size:2
Alignment explanation
Indices: 792412--792458 Score: 85
Period size: 2 Copynumber: 23.0 Consensus size: 2
792402 AATTATTTAT
792412 TA TA GTA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
792455 TA TA
1 TA TA
792459 GAGCATTAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:794433 original size:25 final size:25
Alignment explanation
Indices: 794402--794453 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
794392 TAAAGAATTA
* *
794402 TCGCACGTGAAGCTGGTGCAGCAAT
1 TCGCACGTAAAGCTGGTCCAGCAAT
794427 TCGCACGTAAAGCTGGTCCAGCAAT
1 TCGCACGTAAAGCTGGTCCAGCAAT
794452 TC
1 TC
794454 AGGCCCCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.21
Consensus pattern (25 bp):
TCGCACGTAAAGCTGGTCCAGCAAT
Found at i:802999 original size:2 final size:2
Alignment explanation
Indices: 802994--803034 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
802984 AAATACACCA
*
802994 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
803035 AACTTTACTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:804713 original size:2 final size:2
Alignment explanation
Indices: 804666--804700 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
804656 ATTCTATAGT
804666 TA TA TA TA 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 TA TA TA TA T
804701 TAAAAGTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:804727 original size:21 final size:20
Alignment explanation
Indices: 804703--804741 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
804693 ATATATATTA
*
804703 AAAGTATATATTACAAAAAAT
1 AAAGGATATATTA-AAAAAAT
*
804724 AAAGGATTTATTAAAAAA
1 AAAGGATATATTAAAAAA
804742 GGATATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.62, C:0.03, G:0.08, T:0.28
Consensus pattern (20 bp):
AAAGGATATATTAAAAAAAT
Found at i:805196 original size:2 final size:2
Alignment explanation
Indices: 805189--805221 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
805179 GAGTAAGGAA
805189 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 A
805222 ATCATGTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:811735 original size:130 final size:130
Alignment explanation
Indices: 811582--811829 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
811572 TATTTATATA
*
811582 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * *
811647 TTAGCACATGATCATGACACGTGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
*
811712 ATCAGTTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * * *
811777 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCTCCTAATTA
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTA
811830 GAAGAAAATT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.37
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:811860 original size:130 final size:129
Alignment explanation
Indices: 811596--811860 Score: 300
Period size: 130 Copynumber: 2.0 Consensus size: 129
811586 ATTTGGTCCT
* *
811596 AAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * *** * * ***** *
811661 TGACACGTGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATGCTATCAGTTTGGTCCT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
811726 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * * * *
811791 TGATATGTGTTATTGGTGACACATGTCACCTCCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
811855 -A
128 CA
811856 AAATT
1 AAATT
811861 TGGGTCTTTG
Statistics
Matches: 112, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
130 100 0.89
132 7 0.06
133 5 0.04
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:812188 original size:28 final size:27
Alignment explanation
Indices: 812157--812219 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
812147 AGTTGATACA
*
812157 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
812185 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
812213 ATATTTT
1 ATATTTT
812220 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:812318 original size:16 final size:18
Alignment explanation
Indices: 812297--812330 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
812287 ATTTCTTATT
812297 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
812313 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
812331 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:812478 original size:21 final size:21
Alignment explanation
Indices: 812454--812496 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
812444 TATTACCTTA
812454 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
812475 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
812496 A
1 A
812497 GGGTTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:812514 original size:35 final size:35
Alignment explanation
Indices: 812465--812550 Score: 109
Period size: 35 Copynumber: 2.5 Consensus size: 35
812455 ATTGAAGTAT
** * *
812465 TTTAGAATTTAATTGAAGTATTTTAGAATTTAGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
* *
812500 TTTAGAATAAAATTGAATTACTTTAGAAATTGGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
*
812535 TTTAGAATGAAATTGA
1 TTTAGAATAAAATTGA
812551 TGACTGTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.38, C:0.01, G:0.20, T:0.41
Consensus pattern (35 bp):
TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
Found at i:812735 original size:29 final size:29
Alignment explanation
Indices: 812681--812738 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
812671 ACAAACGGAA
* *
812681 TAAATGTTGGGGGACTGTATTACAAGTTT
1 TAAATGTTGGGGGACTGAAATACAAGTTT
*
812710 TAAATGTTGGGGGACCT-AAATGCAAGTTT
1 TAAATGTTGGGGGA-CTGAAATACAAGTTT
812739 CAGAAATGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 23 0.92
30 2 0.08
ACGTcount: A:0.29, C:0.09, G:0.28, T:0.34
Consensus pattern (29 bp):
TAAATGTTGGGGGACTGAAATACAAGTTT
Found at i:817185 original size:11 final size:11
Alignment explanation
Indices: 817169--817196 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
817159 TGATCATGTT
817169 TGTTTGTTTAA
1 TGTTTGTTTAA
817180 TGTTTGTTTAA
1 TGTTTGTTTAA
817191 TGTTTG
1 TGTTTG
817197 GTAATCGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.21, T:0.64
Consensus pattern (11 bp):
TGTTTGTTTAA
Found at i:817434 original size:24 final size:24
Alignment explanation
Indices: 817391--817436 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
817381 GTAAATAAGT
*
817391 TTATAAATGAGCCAATAAACAAGC
1 TTATAAATGAGCCAACAAACAAGC
* *
817415 TTATAAATGAGTCGACAAACAA
1 TTATAAATGAGCCAACAAACAA
817437 ACTTGTTTGT
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:0.50, C:0.15, G:0.13, T:0.22
Consensus pattern (24 bp):
TTATAAATGAGCCAACAAACAAGC
Found at i:827734 original size:6 final size:6
Alignment explanation
Indices: 827725--827774 Score: 100
Period size: 6 Copynumber: 8.3 Consensus size: 6
827715 ATTTGAAGGT
827725 GAAGAC GAAGAC GAAGAC GAAGAC GAAGAC GAAGAC GAAGAC GAAGAC
1 GAAGAC GAAGAC GAAGAC GAAGAC GAAGAC GAAGAC GAAGAC GAAGAC
827773 GA
1 GA
827775 GATCTATAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.50, C:0.16, G:0.34, T:0.00
Consensus pattern (6 bp):
GAAGAC
Found at i:828447 original size:17 final size:15
Alignment explanation
Indices: 828423--828465 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
828413 TTGATATGTT
828423 AAATAATTAATAACTA
1 AAATAATTAAT-ACTA
* *
828439 AACATAATTCATACTT
1 AA-ATAATTAATACTA
828455 AAATAATTAAT
1 AAATAATTAAT
828466 GATGAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 8 0.35
16 7 0.30
17 8 0.35
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (15 bp):
AAATAATTAATACTA
Found at i:829545 original size:18 final size:19
Alignment explanation
Indices: 829522--829560 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
829512 TTTTAAATTT
*
829522 AAAAAAATTTAAAAAACCA
1 AAAAAAATTGAAAAAACCA
829541 AAAAAAATTGAAAAAACCA
1 AAAAAAATTGAAAAAACCA
829560 A
1 A
829561 CTCCTATACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.74, C:0.10, G:0.03, T:0.13
Consensus pattern (19 bp):
AAAAAAATTGAAAAAACCA
Found at i:841484 original size:2 final size:2
Alignment explanation
Indices: 841471--841508 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
841461 CAAAACTGGG
*
841471 TA TA TG TA TA TA 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 TA TA TA TA TA TA
841509 AAACTTCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:845583 original size:2 final size:2
Alignment explanation
Indices: 845576--845628 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
845566 GTTTAACGGG
845576 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
845618 AT AT AT AT AT A
1 AT AT AT AT AT A
845629 AGGAATTCAA
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:854274 original size:21 final size:21
Alignment explanation
Indices: 854248--854295 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
854238 TAATTTTCAA
*
854248 ACATTGTTGCACCTAATTTTG
1 ACATTGTTACACCTAATTTTG
854269 ACATTGTTACACCTAATTTTG
1 ACATTGTTACACCTAATTTTG
854290 ACATTG
1 ACATTG
854296 CAATATTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
ACATTGTTACACCTAATTTTG
Found at i:857998 original size:19 final size:20
Alignment explanation
Indices: 857974--858024 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
857964 AATGACCAAT
857974 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
857993 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
858013 AAAATCGCAACG
1 AAAATCGCAACG
858025 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:858034 original size:20 final size:20
Alignment explanation
Indices: 858011--858064 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
858001 AACGCGATTT
*
858011 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
858031 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
858051 AGAAAATCGCAACG
1 AGAAAATCGCAACG
858065 CGAGCTTCCA
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:0.52, C:0.19, G:0.19, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:858124 original size:20 final size:20
Alignment explanation
Indices: 858099--858392 Score: 320
Period size: 20 Copynumber: 14.4 Consensus size: 20
858089 TTTAGAAGAA
**
858099 AATCGCAATGCGATTGATTG
1 AATCGCAATGCGATTGAGAG
* * *
858119 AATCGCAACGCGATTTATAG
1 AATCGCAATGCGATTGAGAG
858139 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGAGAG
* * *
858159 AGTCGCAACGCGATTTAGAAGAA
1 AATCGCAATGCGA-TT-G-AGAG
*
858182 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
*
858202 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
**
858222 AATCGCAATGCGATTGATTG
1 AATCGCAATGCGATTGAGAG
* *
858242 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAG
858262 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGAGAG
* * *
858282 AGTCGCAACGCGATTTAGAAGAA
1 AATCGCAATGCGA-TT-G-AGAG
*
858305 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
*
858325 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
*
858345 AATCGCAATGCGA-TGTATAG
1 AATCGCAATGCGATTG-AGAG
**
858365 AATCGCAATGCGACCGAGAG
1 AATCGCAATGCGATTGAGAG
858385 AATCGCAA
1 AATCGCAA
858393 CGTTAAAAAG
Statistics
Matches: 236, Mismatches: 30, Indels: 16
0.84 0.11 0.06
Matches are distributed among these distances:
19 2 0.01
20 195 0.83
21 7 0.03
22 4 0.02
23 28 0.12
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (20 bp):
AATCGCAATGCGATTGAGAG
Found at i:858190 original size:83 final size:83
Alignment explanation
Indices: 858078--858377 Score: 335
Period size: 83 Copynumber: 3.7 Consensus size: 83
858068 GCTTCCAAGT
** *
858078 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATTGAATCGCAACGCGATTTATAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAACGCGATTTAAAGAATC
*
858143 GCAATGCGATTGAGAGAG
66 GCAATGCGATTGAGAGAA
* * * * *
858161 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAACGCGATTTAAAGAATC
**
858226 GCAATGCGATTGATTGAA
66 GCAATGCGATTGAGAGAA
* * *
858244 TCGCAATGCGATTTA-TAG--AATCGCAATGCGATTGAGAGAGTCGCAACGCGATTTAGAAGAAA
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAACGCGATTTA-AAG--A
*
858306 ATCGCAATGCGACTGAGAGAA
63 ATCGCAATGCGATTGAGAGAA
* * * * *
858327 TCGCAATGCGA-CT-G-AGAGAATCGCAATGCGA-TGTATAGAATCGCAATGCGA
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTG-AGAGAATCGCAACGCGA
858378 CCGAGAGAAT
Statistics
Matches: 185, Mismatches: 25, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
80 32 0.17
81 4 0.02
82 5 0.03
83 144 0.78
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.21
Consensus pattern (83 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAACGCGATTTAAAGAATC
GCAATGCGATTGAGAGAA
Found at i:858235 original size:103 final size:103
Alignment explanation
Indices: 858078--858394 Score: 363
Period size: 103 Copynumber: 3.1 Consensus size: 103
858068 GCTTCCAAGT
* * ** * *
858078 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATTGAATCGCAACGCGATTTATAGAATC
1 TCGCAACGCGATCTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGATAGAATC
*
858143 GCAATGCGATTGAGAGAGTCGCAACGCGATTTAGAAGAAAA
66 GCAATGCGATTGAGAGAATCGCAACGCGA-TT-G-AGAAAA
* * *
858184 TCGCAATGCGA-CT-G-AGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGATTGAATC
1 TCGCAACGCGATCTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGATAGAATC
* * * * *
858246 GCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAG
66 GCAATGCGATTGAGAGAATCGCAACGCGATTGAGAAAA
* * *
858284 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
1 TCGCAACGCGATCTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGATAGAATC
* * ** *
858349 GCAATGCGA-TGTATAGAATCGCAATGCGACCGAGAGAA
66 GCAATGCGATTG-AGAGAATCGCAACGCGATTGAGAAAA
858387 TCGCAACG
1 TCGCAACG
858395 TTAAAAAGAA
Statistics
Matches: 182, Mismatches: 25, Indels: 11
0.83 0.11 0.05
Matches are distributed among these distances:
100 14 0.08
101 2 0.01
102 4 0.02
103 150 0.82
104 1 0.01
105 1 0.01
106 10 0.05
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.20
Consensus pattern (103 bp):
TCGCAACGCGATCTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGATAGAATC
GCAATGCGATTGAGAGAATCGCAACGCGATTGAGAAAA
Found at i:858392 original size:123 final size:123
Alignment explanation
Indices: 858099--858377 Score: 524
Period size: 123 Copynumber: 2.3 Consensus size: 123
858089 TTTAGAAGAA
*
858099 AATCGCAATGCGATTGATTGAATCGCAACGCGATTTATAGAATCGCAATGCGATTGAGAGAGTCG
1 AATCGCAATGCGATTGATTGAATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAGTCG
858164 CAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
66 CAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
858222 AATCGCAATGCGATTGATTGAATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAGTCG
1 AATCGCAATGCGATTGATTGAATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAGTCG
858287 CAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
66 CAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
*
858345 AATCGCAATGCGA-TGTATAGAATCGCAATGCGA
1 AATCGCAATGCGATTG-ATTGAATCGCAATGCGA
858378 CCGAGAGAAT
Statistics
Matches: 153, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
122 2 0.01
123 151 0.99
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.21
Consensus pattern (123 bp):
AATCGCAATGCGATTGATTGAATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAGTCG
CAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
Found at i:858408 original size:20 final size:20
Alignment explanation
Indices: 858385--858424 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
858375 CGACCGAGAG
*
858385 AATCGCAACGTTAAAAAGAA
1 AATCGCAACGGTAAAAAGAA
*
858405 AATCGCAACGGTCAAAAGAA
1 AATCGCAACGGTAAAAAGAA
858425 TAGTTAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.17, G:0.17, T:0.12
Consensus pattern (20 bp):
AATCGCAACGGTAAAAAGAA
Found at i:858411 original size:123 final size:123
Alignment explanation
Indices: 858099--858414 Score: 391
Period size: 123 Copynumber: 2.6 Consensus size: 123
858089 TTTAGAAGAA
* * *** * * *** * *
858099 AATCGCAATGCGATTGATTGAATCGCAACGCGATTTATAGAATCGCAATGCGATTGAGAGAGTCG
1 AATCGCAATGCGATTGATAGAATCGCAATGCGACCGAGAGAATCGCAACGCGAAAAAGAAAATCG
858164 CAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
66 CAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
* *** * * *** * *
858222 AATCGCAATGCGATTGATTGAATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAGTCG
1 AATCGCAATGCGATTGATAGAATCGCAATGCGACCGAGAGAATCGCAACGCGAAAAAGAAAATCG
858287 CAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
66 CAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
**
858345 AATCGCAATGCGA-TGTATAGAATCGCAATGCGACCGAGAGAATCGCAACGTTAAAAAGAAAATC
1 AATCGCAATGCGATTG-ATAGAATCGCAATGCGACCGAGAGAATCGCAACGCGAAAAAGAAAATC
858409 GCAACG
65 GCAACG
858415 GTCAAAAGAA
Statistics
Matches: 178, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
122 2 0.01
123 176 0.99
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.20
Consensus pattern (123 bp):
AATCGCAATGCGATTGATAGAATCGCAATGCGACCGAGAGAATCGCAACGCGAAAAAGAAAATCG
CAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
Done.