Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001505.1 Hibiscus syriacus cultivar Beakdansim tig00002949_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: 235039
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2944 original size:23 final size:23
Alignment explanation
Indices: 2891--2945 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
2881 TCGAGGCACC
*
2891 GAATCCGAACGAGCTATGCAAGG
1 GAATCCGAGCGAGCTATGCAAGG
*
2914 GCAA-CCGAGCGAGCTATGCGAGG
1 G-AATCCGAGCGAGCTATGCAAGG
2937 GAATCCGAG
1 GAATCCGAG
2946 GTAGGTCGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 2 0.07
23 24 0.86
24 2 0.07
ACGTcount: A:0.31, C:0.24, G:0.35, T:0.11
Consensus pattern (23 bp):
GAATCCGAGCGAGCTATGCAAGG
Found at i:3003 original size:29 final size:29
Alignment explanation
Indices: 2961--3022 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
2951 TCGAGTGCTG
2961 CCTACAAGGTCGCCCGGAGGGCATGGCGA
1 CCTACAAGGTCGCCCGGAGGGCATGGCGA
2990 CCTACAAGGTCGCCCGGAGGGCATGGCGA
1 CCTACAAGGTCGCCCGGAGGGCATGGCGA
3019 CCTA
1 CCTA
3023 TGTTTTGGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.21, C:0.32, G:0.35, T:0.11
Consensus pattern (29 bp):
CCTACAAGGTCGCCCGGAGGGCATGGCGA
Found at i:7610 original size:52 final size:51
Alignment explanation
Indices: 7524--7672 Score: 239
Period size: 51 Copynumber: 2.9 Consensus size: 51
7514 TATAAGGTAT
7524 TATCTATTCAAAGATAAC-CTCAACCATTTGACATTGAACACTCACA-AGTAG
1 TATCT-TTCAAAGATAACTCTCAACCATTTGACATTGAACACTCACACA-TAG
7575 TATCTGTTCAAAGATAACTCTCAACCATTTGACATTGAACACTCACACATAG
1 TATCT-TTCAAAGATAACTCTCAACCATTTGACATTGAACACTCACACATAG
* *
7627 TATCTTTCAAAAATAACTCTCAACTATTTGACATTGAACACTCACA
1 TATCTTTCAAAGATAACTCTCAACCATTTGACATTGAACACTCACA
7673 TCCGTAGAAT
Statistics
Matches: 93, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
51 56 0.60
52 36 0.39
53 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.08, T:0.30
Consensus pattern (51 bp):
TATCTTTCAAAGATAACTCTCAACCATTTGACATTGAACACTCACACATAG
Found at i:8314 original size:35 final size:35
Alignment explanation
Indices: 8268--8343 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
8258 AAAACAGTCC
* * *
8268 TCAATTTCATTCTAAACCCCAATTTTCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
8303 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
8338 TCAATT
1 TCAATT
8344 AAATTCAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.39, C:0.22, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:8874 original size:128 final size:129
Alignment explanation
Indices: 8737--8982 Score: 395
Period size: 128 Copynumber: 1.9 Consensus size: 129
8727 TATTTATATA
* ** *
8737 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGAATCTGACATGTG
*
8802 TTAGCACATGATCATGACACGTGTCATTAGTG-ACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACGTGTCATTAGTGAACATGTCACCACCTAATTATTTATATATGCT
8865 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGAATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGAATCTGACATGTG
* * * *
8930 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACGTGTCATTAGTGA-ACATGTCACCACCTAATTA
8983 GAAGAAAATT
Statistics
Matches: 107, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
128 88 0.82
130 19 0.18
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.36
Consensus pattern (129 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGAATCTGACATGTG
TTAACACATGATCATGACACGTGTCATTAGTGAACATGTCACCACCTAATTATTTATATATGCT
Found at i:9465 original size:15 final size:17
Alignment explanation
Indices: 9440--9471 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
9430 ATTTCTTATT
9440 AAAAATAAAAT-ATTCA
1 AAAAATAAAATGATTCA
9456 AAAAAT-AAATGATTCA
1 AAAAATAAAATGATTCA
9472 TACATTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.66, C:0.06, G:0.03, T:0.25
Consensus pattern (17 bp):
AAAAATAAAATGATTCA
Found at i:9952 original size:140 final size:140
Alignment explanation
Indices: 9699--9952 Score: 295
Period size: 140 Copynumber: 1.8 Consensus size: 140
9689 AATAAAATTA
* * * *
9699 TTGGGGGACTGTTTTGCAAGTTTTAAAAGTTGGGGACCTAAATTCAAGTGCCTGAAAAGTTCAAT
1 TTGGGGGACTGTATTGCAAGTTTTAAAAGTTGGGGACCTAAATGCAACTGCCAGAAAAGTTCAAT
* * * *
9764 GACCGTTTATATAATTTACCCTAATTTTCTAACAGTGATTTAAGTTGGGGGACCATATTGCAAAC
66 GACCGATTATATAATTTACCCTAATTTTATAACACTGATTGAAGTTGGGGGACCATATTGCAAAC
9829 GGAATAAATG
131 GGAATAAATG
* *
9839 TTGGGGGACTGTATTGCAAGTTTTAAAAGTTGGGAGACCTAAATGCAAACT-TCAGAAATGTTCA
1 TTGGGGGACTGTATTGCAAGTTTTAAAAGTTGGG-GACCTAAATGC-AACTGCCAGAAAAGTTCA
* * *
9903 GTGATC-ATTACTATACTTTA-CCTATATATTATATAA-ACT-ATTGAA-TTGGG
64 ATGACCGATTA-TATAATTTACCCTA-AT-TT-TATAACACTGATTGAAGTTGGG
9953 TGATGGTCAT
Statistics
Matches: 95, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
140 45 0.47
141 39 0.41
142 7 0.07
143 4 0.04
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (140 bp):
TTGGGGGACTGTATTGCAAGTTTTAAAAGTTGGGGACCTAAATGCAACTGCCAGAAAAGTTCAAT
GACCGATTATATAATTTACCCTAATTTTATAACACTGATTGAAGTTGGGGGACCATATTGCAAAC
GGAATAAATG
Found at i:12419 original size:26 final size:25
Alignment explanation
Indices: 12373--12424 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
12363 GTTGGATCAT
12373 TATTGGACCTGGAATTGGATTTGGAC
1 TATTGGACCTGGAATTGGA-TTGGAC
*
12399 TATTGGACTTTGGAATT-GATTGGAC
1 TATTGGAC-CTGGAATTGGATTGGAC
12424 T
1 T
12425 TGACATGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 7 0.29
26 10 0.42
27 7 0.29
ACGTcount: A:0.23, C:0.10, G:0.29, T:0.38
Consensus pattern (25 bp):
TATTGGACCTGGAATTGGATTGGAC
Found at i:16340 original size:2 final size:2
Alignment explanation
Indices: 16333--16377 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
16323 AGAAATATTC
16333 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
16375 AT A
1 AT A
16378 GGTAAATCAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16692 original size:2 final size:2
Alignment explanation
Indices: 16685--16715 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
16675 AAATCATAAA
16685 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 A
16716 CTGAAATAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17388 original size:18 final size:19
Alignment explanation
Indices: 17367--17402 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
17357 AAATTAAATT
*
17367 TAAA-ATTATACCCAAACA
1 TAAACATTATACCAAAACA
17385 TAAACATTATACCAAAAC
1 TAAACATTATACCAAAAC
17403 CCTAATTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (19 bp):
TAAACATTATACCAAAACA
Found at i:33286 original size:2 final size:2
Alignment explanation
Indices: 33279--33303 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
33269 AATAAATTTC
33279 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
33304 TTTACTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34076 original size:10 final size:10
Alignment explanation
Indices: 34061--34087 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
34051 CCGACGTCCC
34061 AGCCACCTGA
1 AGCCACCTGA
34071 AGCCACCTGA
1 AGCCACCTGA
34081 AGCCACC
1 AGCCACC
34088 CTAATTGACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.44, G:0.19, T:0.07
Consensus pattern (10 bp):
AGCCACCTGA
Found at i:35519 original size:32 final size:32
Alignment explanation
Indices: 35483--35544 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
35473 TCTACATGTA
* *
35483 ATAAATTATTAATGTGACATATATCATGTCGC
1 ATAAAATAATAATGTGACATATATCATGTCGC
* * *
35515 ATAAAATAATGATGTGGCGTATATCATGTC
1 ATAAAATAATAATGTGACATATATCATGTC
35545 ATCCAAAATG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.35
Consensus pattern (32 bp):
ATAAAATAATAATGTGACATATATCATGTCGC
Found at i:39521 original size:12 final size:12
Alignment explanation
Indices: 39504--39555 Score: 77
Period size: 12 Copynumber: 4.3 Consensus size: 12
39494 AACCAACCAT
39504 TAATATTCAATC
1 TAATATTCAATC
**
39516 TAATATTTGATC
1 TAATATTCAATC
*
39528 TAATATTCAACC
1 TAATATTCAATC
39540 TAATATTCAATC
1 TAATATTCAATC
39552 TAAT
1 TAAT
39556 GTTGATAGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.40, C:0.15, G:0.02, T:0.42
Consensus pattern (12 bp):
TAATATTCAATC
Found at i:39605 original size:12 final size:12
Alignment explanation
Indices: 39588--39618 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
39578 ATTTTCTTTC
39588 AATTATAAAAAT
1 AATTATAAAAAT
39600 AATTATAAAAAT
1 AATTATAAAAAT
*
39612 AGTTATA
1 AATTATA
39619 TATTTCTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (12 bp):
AATTATAAAAAT
Found at i:40211 original size:18 final size:17
Alignment explanation
Indices: 40170--40211 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
40160 AAAATTTATA
40170 AAAAAATATTTAAAAAT
1 AAAAAATATTTAAAAAT
*
40187 ACTAAAATATTTAAAATAT
1 A-AAAAATATTTAAAA-AT
40206 AAAAAA
1 AAAAAA
40212 AATATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 1 0.05
18 17 0.81
19 3 0.14
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAAATATTTAAAAAT
Found at i:43950 original size:55 final size:55
Alignment explanation
Indices: 43866--43973 Score: 148
Period size: 55 Copynumber: 2.0 Consensus size: 55
43856 CGCTCCTATT
* *
43866 TTTCAGGATGCATGAAACTCGCACAATCTTCAACAAACGTCTCTGCTCTCTATGC
1 TTTCAGGATGCATGAAACTCGAACAATCTTCAACAAACGTCTCTGCTCCCTATGC
* *
43921 TTTCAGAGA-GCAT-AAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTAT
1 TTTCAG-GATGCATGAA-ACTCGAACAATCTTCAACAAACGTCTCTGCTCCCTAT
43974 TTCTTCAGGG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
54 2 0.04
55 43 0.91
56 2 0.04
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.29
Consensus pattern (55 bp):
TTTCAGGATGCATGAAACTCGAACAATCTTCAACAAACGTCTCTGCTCCCTATGC
Found at i:43981 original size:55 final size:55
Alignment explanation
Indices: 43860--43982 Score: 146
Period size: 55 Copynumber: 2.3 Consensus size: 55
43850 CGGGTTCGCT
*
43860 CCTATTT-TTCAGGATGCATGAAACTCGCACAATCTTCAACAAACGTCTCTGCTC
1 CCTATTTCTTCAGGATGCATGAAACTCGAACAATCTTCAACAAACGTCTCTGCTC
* * * *
43914 TCTA-TGCTTTCAGAGA-GCAT-AAGACTCGAACAATCTTCAACAATCGTGTCTGCTC
1 CCTATTTC-TTCAG-GATGCATGAA-ACTCGAACAATCTTCAACAAACGTCTCTGCTC
43969 CCTATTTCTTCAGG
1 CCTATTTCTTCAGG
43983 GAGTAGAACT
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
53 1 0.02
54 6 0.11
55 46 0.81
56 4 0.07
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.31
Consensus pattern (55 bp):
CCTATTTCTTCAGGATGCATGAAACTCGAACAATCTTCAACAAACGTCTCTGCTC
Found at i:44061 original size:54 final size:53
Alignment explanation
Indices: 43973--44587 Score: 997
Period size: 54 Copynumber: 11.5 Consensus size: 53
43963 CTGCTCCCTA
*
43973 TTTCTTCAGGGAGTAGAACTCCAACAATAATCTTCCTACGGGTCCGCTCTCTT
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
*
44026 TTTCTTCAGGGAGTAAGAACTCGAACAATATTCTTCCTACGGGTCCGCTCTCTT
1 TTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
* *
44080 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCAC-C-CTA
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
44131 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTT
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTC-TT
44185 TTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
1 TTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
* *
44239 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCATACGGG-CTCGCTCTCTA
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTC-CGCTCTCTT
*
44292 TTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTATGGGTCCGCTCTCTT
1 TTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
* *
44346 TTTCTTCAGAGAGTAGAACTCGAACAATAATCTTCCTACGGG-CTCGCTCTCTA
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTC-CGCTCTCTT
44399 TTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
1 TTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
* *
44453 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCATACGGG-CTCGCTCTCTA
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTC-CGCTCTCTT
*
44506 TTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTATGGGTCCGCTCTCTT
1 TTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
*
44560 TTTCTTCAGAGAGTAGAACTCGAACAAT
1 TTTCTTCAGGGAGTAGAACTCGAACAAT
44588 CTTCTGTTGC
Statistics
Matches: 525, Mismatches: 23, Indels: 28
0.91 0.04 0.05
Matches are distributed among these distances:
51 48 0.09
52 5 0.01
53 206 0.39
54 226 0.43
55 40 0.08
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (53 bp):
TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
Found at i:44090 original size:107 final size:107
Alignment explanation
Indices: 43965--44587 Score: 1051
Period size: 107 Copynumber: 5.8 Consensus size: 107
43955 AATCGTGTCT
* *
43965 GCTCCCTATTTCTTCAGGGAGT-AGAACTCCAACAATAATCTTCCTACGGGTCCGCTCTCTTTTT
1 GCTCTCTATTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTT
*
44029 CTTCAGGGAGTAAGAACTCGAACAATATTCTTCCTACGGG-TCC
66 CTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGCT-C
* * *
44072 GCTCTCTTTTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCAC-C-CTATTT
1 GCTCTCTATTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTT
44134 CTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGG-TCC
66 CTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGCT-C
*
44176 GCTCTCTTTTTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTT
1 GCTCTC-TATTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTT
*
44241 TCTTCAGGGAGTAGAACTCGAACAATAATCTTCATACGGGCTC
65 TCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGCTC
*
44284 GCTCTCTATTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTATGGGTCCGCTCTCTTTTT
1 GCTCTCTATTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTT
*
44349 CTTCAGAGAGTAGAACTCGAACAATAATCTTCCTACGGGCTC
66 CTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGCTC
44391 GCTCTCTATTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTT
1 GCTCTCTATTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTT
*
44456 CTTCAGGGAGTAGAACTCGAACAATAATCTTCATACGGGCTC
66 CTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGCTC
*
44498 GCTCTCTATTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTATGGGTCCGCTCTCTTTTT
1 GCTCTCTATTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTT
*
44563 CTTCAGAGAGTAGAACTCGAACAAT
66 CTTCAGGGAGTAGAACTCGAACAAT
44588 CTTCTGTTGC
Statistics
Matches: 493, Mismatches: 18, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
104 36 0.07
105 32 0.06
106 33 0.07
107 341 0.69
108 50 0.10
109 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (107 bp):
GCTCTCTATTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTT
CTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGCTC
Found at i:45945 original size:9 final size:9
Alignment explanation
Indices: 45929--46016 Score: 91
Period size: 8 Copynumber: 10.4 Consensus size: 9
45919 TTTGTTTTTG
45929 TTTT-ATTT
1 TTTTCATTT
45937 TTTTCATTT
1 TTTTCATTT
*
45946 TCTTCATTT
1 TTTTCATTT
*
45955 TCTTCA-TT
1 TTTTCATTT
45963 TTTTCATTT
1 TTTTCATTT
*
45972 TCTTCA-TT
1 TTTTCATTT
45980 TTTTCATTTT
1 TTTTCA-TTT
45990 TTTTCA--T
1 TTTTCATTT
45997 TTTTCA-TT
1 TTTTCATTT
46005 TTTTC-TTT
1 TTTTCATTT
46013 TTTT
1 TTTT
46017 TTCATCTTCA
Statistics
Matches: 70, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
7 7 0.10
8 30 0.43
9 25 0.36
10 8 0.11
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTCATTT
Found at i:45971 original size:26 final size:25
Alignment explanation
Indices: 45935--46016 Score: 114
Period size: 26 Copynumber: 3.2 Consensus size: 25
45925 TTTGTTTTAT
45935 TTTTTTCATTTTCTTCATTTTCTTCA
1 TTTTTTCATTTTCTTCATTTT-TTCA
45961 TTTTTTCATTTTCTTCATTTTTTCA
1 TTTTTTCATTTTCTTCATTTTTTCA
*
45986 TTTTTTTTCA-TTT-TTCATTTTTTCT
1 --TTTTTTCATTTTCTTCATTTTTTCA
46011 TTTTTT
1 TTTTTT
46017 TTCATCTTCA
Statistics
Matches: 53, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
23 6 0.11
25 15 0.28
26 24 0.45
27 8 0.15
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.76
Consensus pattern (25 bp):
TTTTTTCATTTTCTTCATTTTTTCA
Found at i:46017 original size:17 final size:17
Alignment explanation
Indices: 45929--46015 Score: 110
Period size: 17 Copynumber: 5.2 Consensus size: 17
45919 TTTGTTTTTG
*
45929 TTTT-ATTTTTTTCATT
1 TTTTCATTTTCTTCATT
45945 TTCTTCATTTTCTTCATT
1 TT-TTCATTTTCTTCATT
45963 TTTTCATTTTCTTCATT
1 TTTTCATTTTCTTCATT
*
45980 TTTTCATTTTTTTTCA-T
1 TTTTCA-TTTTCTTCATT
45997 TTTTCATTTT-TTC-TT
1 TTTTCATTTTCTTCATT
46012 TTTT
1 TTTT
46016 TTTCATCTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 9
0.86 0.03 0.12
Matches are distributed among these distances:
15 8 0.12
16 6 0.09
17 30 0.46
18 21 0.32
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTCATTTTCTTCATT
Found at i:46017 original size:25 final size:25
Alignment explanation
Indices: 45934--46021 Score: 99
Period size: 25 Copynumber: 3.4 Consensus size: 25
45924 TTTTGTTTTA
45934 TTTTTTTCA-TTTTC-TTCATTTTCTT
1 TTTTTTTCATTTTTCATT--TTTTCTT
* *
45959 CATTTTTTCATTTTCTTCATTTTTTCAT
1 -TTTTTTTCA-TTT-TTCATTTTTTCTT
45987 TTTTTTTCATTTTTCATTTTTTCTT
1 TTTTTTTCATTTTTCATTTTTTCTT
46012 TTTTTTTCAT
1 TTTTTTTCAT
46022 CTTCAAGCAA
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
25 22 0.41
26 11 0.20
27 8 0.15
28 8 0.15
29 3 0.06
30 2 0.04
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (25 bp):
TTTTTTTCATTTTTCATTTTTTCTT
Found at i:52428 original size:21 final size:21
Alignment explanation
Indices: 52361--52428 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
52351 GCGATGTGGA
* *
52361 CTTCTCGTCTTTACGAA-GGT
1 CTTCTCGTCTTTATGAATGCT
* *
52381 CTTCTCGTCTTGATGAATGGCA
1 CTTCTCGTCTTTATGAAT-GCT
52403 C-TCTCGTCTTTATGAATGCT
1 CTTCTCGTCTTTATGAATGCT
52423 CTTCTC
1 CTTCTC
52429 ATCCTTGGTA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
20 18 0.46
21 19 0.49
22 2 0.05
ACGTcount: A:0.15, C:0.26, G:0.18, T:0.41
Consensus pattern (21 bp):
CTTCTCGTCTTTATGAATGCT
Found at i:57188 original size:8 final size:8
Alignment explanation
Indices: 57175--57202 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
57165 TAATCTTCAA
57175 GAAAAGGT
1 GAAAAGGT
57183 GAAAAGGT
1 GAAAAGGT
57191 GAAAAGGT
1 GAAAAGGT
57199 GAAA
1 GAAA
57203 TACAAGGGAA
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:0.54, C:0.00, G:0.36, T:0.11
Consensus pattern (8 bp):
GAAAAGGT
Found at i:68158 original size:30 final size:30
Alignment explanation
Indices: 68124--68185 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
68114 ATAATAAGTT
68124 AACTAATCTATTATTTTTTAATAAATAATA
1 AACTAATCTATTATTTTTTAATAAATAATA
68154 AACTAATCTATTATTTTTTAATAAATAATA
1 AACTAATCTATTATTTTTTAATAAATAATA
68184 AA
1 AA
68186 ATATTATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (30 bp):
AACTAATCTATTATTTTTTAATAAATAATA
Found at i:68180 original size:27 final size:27
Alignment explanation
Indices: 68115--68181 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 27
68105 TAATAAAAAA
* *
68115 TAATAAGTTAACTAATCTATTATTTTT
1 TAATAAATAAACTAATCTATTATTTTT
68142 TAATAAATAATAAACTAATCTATTATTTTT
1 TAAT--A-AATAAACTAATCTATTATTTTT
68172 TAATAAATAA
1 TAATAAATAA
68182 TAAAATATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 9 0.26
28 1 0.03
29 1 0.03
30 24 0.69
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.46
Consensus pattern (27 bp):
TAATAAATAAACTAATCTATTATTTTT
Found at i:77056 original size:34 final size:34
Alignment explanation
Indices: 77006--77103 Score: 169
Period size: 34 Copynumber: 2.9 Consensus size: 34
76996 GGGAAATGAA
*
77006 TTCTGCGTTGTTGTTATTGTGGAAGTATTATTAG
1 TTCTGCGCTGTTGTTATTGTGGAAGTATTATTAG
*
77040 TTCTGCGCTGTAGTTATTGTGGAAGTATTATTAG
1 TTCTGCGCTGTTGTTATTGTGGAAGTATTATTAG
*
77074 TTCTGCTCTGTTGTTATTGTGGAAGTATTA
1 TTCTGCGCTGTTGTTATTGTGGAAGTATTA
77104 GTGTTTGTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 60 1.00
ACGTcount: A:0.18, C:0.08, G:0.26, T:0.48
Consensus pattern (34 bp):
TTCTGCGCTGTTGTTATTGTGGAAGTATTATTAG
Found at i:77216 original size:31 final size:31
Alignment explanation
Indices: 77181--77248 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
77171 TCAAAAAATA
* *
77181 TAAGATATAATCATTTTTATTTTTATTTAAT
1 TAAGATATAATCACTTTCATTTTTATTTAAT
** * *
77212 TAAGATATGGTCACTTTCGTTTTTATTTGAT
1 TAAGATATAATCACTTTCATTTTTATTTAAT
77243 TAAGAT
1 TAAGAT
77249 GTGATAACCC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.31, C:0.06, G:0.10, T:0.53
Consensus pattern (31 bp):
TAAGATATAATCACTTTCATTTTTATTTAAT
Found at i:79879 original size:31 final size:30
Alignment explanation
Indices: 79844--79903 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
79834 AAACTACACA
*
79844 TTTAGTACTTAAA-TTATCAGTTTTGTTTCAT
1 TTTAGTACCTAAACTT-TCA-TTTTGTTTCAT
*
79875 TTTAGTACCTAAACTTTTATTTTGTTTCA
1 TTTAGTACCTAAACTTTCATTTTGTTTCA
79904 AAATCATTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 10 0.38
31 14 0.54
32 2 0.08
ACGTcount: A:0.25, C:0.12, G:0.08, T:0.55
Consensus pattern (30 bp):
TTTAGTACCTAAACTTTCATTTTGTTTCAT
Found at i:96950 original size:2 final size:2
Alignment explanation
Indices: 96943--96969 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
96933 ATATTTTCAT
96943 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
96970 TATTACCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:97004 original size:11 final size:11
Alignment explanation
Indices: 96980--97017 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
96970 TATTACCATT
96980 TTAAAATT-AA
1 TTAAAATTAAA
96990 TTAAAATTAAA
1 TTAAAATTAAA
*
97001 TTAAAATATAGA
1 TTAAAAT-TAAA
97013 TTAAA
1 TTAAA
97018 TTGAATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 8 0.32
11 9 0.36
12 8 0.32
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
TTAAAATTAAA
Found at i:98637 original size:23 final size:23
Alignment explanation
Indices: 98602--98653 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
98592 TTAAGTGCTC
98602 TATTTTTGTAT-AATAAATTATAA
1 TATTTTTGTATAAAT-AATTATAA
*
98625 -ATTTTTTTAATAAATAATTATAA
1 TATTTTTGT-ATAAATAATTATAA
98648 TATTTT
1 TATTTT
98654 AACCGTAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 7 0.28
23 10 0.40
24 8 0.32
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
TATTTTTGTATAAATAATTATAA
Found at i:104561 original size:27 final size:27
Alignment explanation
Indices: 104513--104574 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
104503 TGATGGTAAT
104513 AATAAGAAAGATATAAACAATAAAAATA
1 AATAA-AAAGATATAAACAATAAAAATA
* * **
104541 AATAAAAAGATATATATAATAGTAATA
1 AATAAAAAGATATAAACAATAAAAATA
104568 AATAAAA
1 AATAAAA
104575 TAAAAAAAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 25 0.83
28 5 0.17
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.23
Consensus pattern (27 bp):
AATAAAAAGATATAAACAATAAAAATA
Found at i:104597 original size:16 final size:16
Alignment explanation
Indices: 104577--104610 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
104567 AAATAAAATA
104577 AAAAAAACTAAAAAACT
1 AAAAAAA-TAAAAAACT
*
104594 AAAAAAATAAATAACT
1 AAAAAAATAAAAAACT
104610 A
1 A
104611 TAATCAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (16 bp):
AAAAAAATAAAAAACT
Found at i:104867 original size:22 final size:21
Alignment explanation
Indices: 104833--104876 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
104823 GGGAGAGAGG
*
104833 GAAAAATATATAATAATAATA
1 GAAAAATAAATAATAATAATA
*
104854 GAAAAATTAAATAATAATTATA
1 GAAAAA-TAAATAATAATAATA
104876 G
1 G
104877 CATATAAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.30
Consensus pattern (21 bp):
GAAAAATAAATAATAATAATA
Found at i:104868 original size:19 final size:21
Alignment explanation
Indices: 104833--104871 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
104823 GGGAGAGAGG
104833 GAAAAATATATAATAATAATA
1 GAAAAATATATAATAATAATA
104854 GAAAAAT-TA-AATAATAAT
1 GAAAAATATATAATAATAAT
104872 TATAGCATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 2 0.11
21 7 0.39
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (21 bp):
GAAAAATATATAATAATAATA
Found at i:104949 original size:130 final size:132
Alignment explanation
Indices: 104764--105000 Score: 361
Period size: 130 Copynumber: 1.8 Consensus size: 132
104754 GCGTATAAGG
* * *
104764 TAAAATTAATGAAAAACATATAATAATATTAATTCCATATATATATAATAGCTAAATATGGGAGA
1 TAAAATTAATGAAAAACATATAATAATATTAATACCATATATATATAATAACTAAATATGAGAGA
** *
104829 GAGGGAAAAA-TATATAATAATAATAGAAAAATTAAATAATAATTATAGCATATAAAGTAAAATA
66 GAGAAAAAAACTATATAATAATAATAGAAAAACTAAATAATAATTATAGCATATAAAGTAAAATA
104893 AA
131 AA
* * *
104895 TAAAGTTAAT-AAAAATATATAATAATATTAATACCATATATATATAATAACTAAATATGAGAGG
1 TAAAATTAATGAAAAACATATAATAATATTAATACCATATATATATAATAACTAAATATGAGAGA
*
104959 GAGAAAAAAATCTATATAATAGTAATAGAAAAACTAAATAAT
66 GAGAAAAAAA-CTATATAATAATAATAGAAAAACTAAATAAT
105001 GAAGATAAAT
Statistics
Matches: 94, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
130 57 0.61
131 9 0.10
132 28 0.30
ACGTcount: A:0.57, C:0.04, G:0.09, T:0.29
Consensus pattern (132 bp):
TAAAATTAATGAAAAACATATAATAATATTAATACCATATATATATAATAACTAAATATGAGAGA
GAGAAAAAAACTATATAATAATAATAGAAAAACTAAATAATAATTATAGCATATAAAGTAAAATA
AA
Found at i:105367 original size:20 final size:20
Alignment explanation
Indices: 105342--105380 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
105332 AAGTAGAGAA
* *
105342 AAAATAATTATAATAATAAC
1 AAAATAATAAAAATAATAAC
105362 AAAATAATAAAAATAATAA
1 AAAATAATAAAAATAATAA
105381 GAATAACCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAATAATAAAAATAATAAC
Found at i:106314 original size:2 final size:2
Alignment explanation
Indices: 106301--106342 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
106291 TAATTAATAA
*
106301 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
106342 A
1 A
106343 ATTTACACTG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:106807 original size:105 final size:105
Alignment explanation
Indices: 106625--107092 Score: 812
Period size: 105 Copynumber: 4.5 Consensus size: 105
106615 AGCAAATTGT
* ** *
106625 GTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTG
1 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGCAGAAATTGGCTCTGAAATTGAGAAATGTTCG
106690 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* *
106730 GTTGTCTGGAGTCCAATATCCCTCGTTGTGAAGCAGAAATTAGCTCTGAAATTGAGAAATGTTCG
1 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGCAGAAATTGGCTCTGAAATTGAGAAATGTTCG
106795 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
106835 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGCAGAAATTGGCTCTGAAATTGAGAAATGTTCG
1 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGCAGAAATTGGCTCTGAAATTGAGAAATGTTCG
106900 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
*
106940 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTC-GAAATTGGCTCTGAAATTGAGAAATGTTT
1 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG-CAGAAATTGGCTCTGAAATTGAGAAATGTTC
* *
107004 GTTGAAAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTAC
65 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* **
107045 GTTGTCTGGAGTCCAATATCCTTCGTTATGAAGTTGAAATTGGCTCTG
1 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGCAGAAATTGGCTCTG
107093 GGTAAAACCT
Statistics
Matches: 348, Mismatches: 13, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
105 347 1.00
106 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (105 bp):
GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGCAGAAATTGGCTCTGAAATTGAGAAATGTTCG
TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
Found at i:107910 original size:48 final size:49
Alignment explanation
Indices: 107835--107928 Score: 118
Period size: 48 Copynumber: 1.9 Consensus size: 49
107825 TTTTTCCTCT
* * ** * *
107835 TTTTTCTTTTTTCAATTTAGGGTGCCCTTTCGGGTTTTCACCCTAAACG
1 TTTTTCTTTTTCCAACTTAGGACGCCCTCTCGGATTTTCACCCTAAACG
*
107884 TTTTT-TTTTTCCAACTTAGGACGCCCTCTCGGATTTTCATCCTAA
1 TTTTTCTTTTTCCAACTTAGGACGCCCTCTCGGATTTTCACCCTAA
107929 GCGAAGTATT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
48 33 0.87
49 5 0.13
ACGTcount: A:0.16, C:0.24, G:0.14, T:0.46
Consensus pattern (49 bp):
TTTTTCTTTTTCCAACTTAGGACGCCCTCTCGGATTTTCACCCTAAACG
Found at i:117348 original size:10 final size:10
Alignment explanation
Indices: 117323--117356 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
117313 AGCGTTAGTA
*
117323 AAATATAAAT
1 AAATAAAAAT
*
117333 AGATAAAAAT
1 AAATAAAAAT
117343 AAATAAAAAT
1 AAATAAAAAT
117353 AAAT
1 AAAT
117357 GGTAAATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:117371 original size:30 final size:31
Alignment explanation
Indices: 117328--117385 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 31
117318 TAGTAAAATA
* * *
117328 TAAATAGATAAAAATAAATAAAAATAAATGG
1 TAAATAGAAAAAAACAAAGAAAAATAAATGG
*
117359 TAAAT-GAAAAAAACATAGAAAAATAAA
1 TAAATAGAAAAAAACAAAGAAAAATAAA
117386 AAGGTTAGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 18 0.78
31 5 0.22
ACGTcount: A:0.71, C:0.02, G:0.09, T:0.19
Consensus pattern (31 bp):
TAAATAGAAAAAAACAAAGAAAAATAAATGG
Found at i:118429 original size:16 final size:15
Alignment explanation
Indices: 118400--118441 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
118390 TAATAGTAAT
118400 AAAT-AAAA-TAAAA
1 AAATAAAAACTAAAA
118413 AAACTAAAAACTAAAA
1 AAA-TAAAAACTAAAA
118429 AAATAAATAACTA
1 AAATAAA-AACTA
118442 TAATCAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 3 0.12
14 1 0.04
15 8 0.32
16 13 0.52
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (15 bp):
AAATAAAAACTAAAA
Found at i:118696 original size:16 final size:18
Alignment explanation
Indices: 118664--118697 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
118654 GGGAGAGAGG
118664 GAAAAATATATAATAATA
1 GAAAAATATATAATAATA
118682 GAAAAAT-TA-AATAATA
1 GAAAAATATATAATAATA
118698 ATTATAGCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 2 0.12
18 7 0.44
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (18 bp):
GAAAAATATATAATAATA
Found at i:118839 original size:127 final size:127
Alignment explanation
Indices: 118595--118847 Score: 298
Period size: 127 Copynumber: 2.0 Consensus size: 127
118585 GCGTATAAGG
* * *
118595 TAAAATTAATGAAAAACATATAATAATATTAATTCCATATATATATAATAGCTAAATATGGGAGA
1 TAAAATTAATGAAAAACATATAATAATATTAATACCATATATATATAATAACTAAATATGAGAGA
** * * * * *
118660 GAGGGAAAAATATATAATAATAGAAAAATTAAATAATAATTATAGCATATAAAGTAAAATAAA
66 GAGAAAAAAAAATATAATAATAGAAAAATGAAATAATAATAATAGAAGATAAA-TAAAATAAA
* *
118723 TAAAGTTAAT-AAAAACATATAATAATATTAATACCATATATATATAATAACTAAATATGAGAGG
1 TAAAATTAATGAAAAACATATAATAATATTAATACCATATATATATAATAACTAAATATGAGAGA
* * * *
118787 GAGAAAAAAAAATCTATATAATAGTAATA-GAAA-AACTAAATAAT-GAAGATAAATATAATAA
66 GAGAAAAAAAAATATA-ATAATAGAAAAATGAAATAA-T-AATAATAGAAGATAAATAAAATAA
118848 GAACAAAAAG
Statistics
Matches: 106, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
126 9 0.08
127 73 0.69
128 24 0.23
ACGTcount: A:0.58, C:0.04, G:0.09, T:0.28
Consensus pattern (127 bp):
TAAAATTAATGAAAAACATATAATAATATTAATACCATATATATATAATAACTAAATATGAGAGA
GAGAAAAAAAAATATAATAATAGAAAAATGAAATAATAATAATAGAAGATAAATAAAATAAA
Found at i:119192 original size:20 final size:20
Alignment explanation
Indices: 119167--119205 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
119157 AAGTAGAGAA
* *
119167 AAAATAATTATAATAATAAC
1 AAAATAATAAAAATAATAAC
119187 AAAATAATAAAAATAATAA
1 AAAATAATAAAAATAATAA
119206 GAATAACCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAATAATAAAAATAATAAC
Found at i:130047 original size:2 final size:2
Alignment explanation
Indices: 130035--130093 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
130025 TAAAACAAAT
*
130035 TA TA TA CA 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
130077 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
130094 TAAGTAAAAC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:135768 original size:21 final size:23
Alignment explanation
Indices: 135742--135784 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
135732 ATGTCAGATA
135742 TTTATA-AAT-TTATTTTTATAT
1 TTTATATAATATTATTTTTATAT
*
135763 TTTATATAATATTTTTTTTATA
1 TTTATATAATATTATTTTTATA
135785 GTGTTGGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 3 0.16
23 10 0.53
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTATATAATATTATTTTTATAT
Found at i:138153 original size:3 final size:3
Alignment explanation
Indices: 138145--138177 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
138135 CACCTTAATT
138145 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
138178 AAAGATAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:139724 original size:23 final size:23
Alignment explanation
Indices: 139693--139753 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
139683 TATTATTAAA
*
139693 ATTAAAATATAATAT-CTTTTATT
1 ATTATAATATAATATACTTTT-TT
*
139716 ATTATAATATAAT-TGAGTTTTTT
1 ATTATAATATAATAT-ACTTTTTT
*
139739 ATTATAATATTATAT
1 ATTATAATATAATAT
139754 TATTACTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
22 1 0.03
23 26 0.81
24 5 0.16
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (23 bp):
ATTATAATATAATATACTTTTTT
Found at i:139751 original size:8 final size:8
Alignment explanation
Indices: 139738--139812 Score: 52
Period size: 8 Copynumber: 9.5 Consensus size: 8
139728 TTGAGTTTTT
139738 TATTATAA
1 TATTATAA
*
139746 TATTATAT
1 TATTATAA
139754 TATTACTAA
1 TATTA-TAA
139763 TA-T-TAA
1 TATTATAA
139769 TA-TAT-A
1 TATTATAA
139775 TATATATATA
1 TAT-TATA-A
139785 TATTATAAA
1 TATTAT-AA
*
139794 TATTTTAA
1 TATTATAA
*
139802 TAAT-TAA
1 TATTATAA
139809 TATT
1 TATT
139813 TTGATTAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
6 9 0.16
7 7 0.13
8 21 0.38
9 13 0.24
10 5 0.09
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (8 bp):
TATTATAA
Found at i:143737 original size:12 final size:12
Alignment explanation
Indices: 143722--143786 Score: 78
Period size: 12 Copynumber: 5.4 Consensus size: 12
143712 ATGACATGAA
143722 TTCTGTTCTGAT
1 TTCTGTTCTGAT
*
143734 TTCTGATCTGGA-
1 TTCTGTTCT-GAT
143746 TTCTGTTCTGAT
1 TTCTGTTCTGAT
* *
143758 ATCTGTTCTGAA
1 TTCTGTTCTGAT
*
143770 TTCTGTTTTGAT
1 TTCTGTTCTGAT
143782 TTCTG
1 TTCTG
143787 ATATCTCCGT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 2 0.05
12 40 0.91
13 2 0.05
ACGTcount: A:0.12, C:0.15, G:0.18, T:0.54
Consensus pattern (12 bp):
TTCTGTTCTGAT
Found at i:143748 original size:24 final size:24
Alignment explanation
Indices: 143718--143788 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 24
143708 ATACATGACA
143718 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGATTTCTGATC
* * *
143742 TGGATTCTGTTCTGATATCTGTTC
1 TGAATTCTGTTCTGATTTCTGATC
*
143766 TGAATTCTGTTTTGATTTCTGAT
1 TGAATTCTGTTCTGATTTCTGAT
143789 ATCTCCGTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.15, C:0.14, G:0.18, T:0.52
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTGATC
Found at i:149825 original size:85 final size:85
Alignment explanation
Indices: 149722--149890 Score: 338
Period size: 85 Copynumber: 2.0 Consensus size: 85
149712 ATTGCACCAT
149722 TTGTTATGAATGTAAGAATATGGACATATCAAGTTTTATAATCCTCGATTAAAGAAGAAAGAGTC
1 TTGTTATGAATGTAAGAATATGGACATATCAAGTTTTATAATCCTCGATTAAAGAAGAAAGAGTC
149787 TTACCTTATAAGGTTCTTAA
66 TTACCTTATAAGGTTCTTAA
149807 TTGTTATGAATGTAAGAATATGGACATATCAAGTTTTATAATCCTCGATTAAAGAAGAAAGAGTC
1 TTGTTATGAATGTAAGAATATGGACATATCAAGTTTTATAATCCTCGATTAAAGAAGAAAGAGTC
149872 TTACCTTATAAGGTTCTTA
66 TTACCTTATAAGGTTCTTA
149891 TTATTTTCAC
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 84 1.00
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.36
Consensus pattern (85 bp):
TTGTTATGAATGTAAGAATATGGACATATCAAGTTTTATAATCCTCGATTAAAGAAGAAAGAGTC
TTACCTTATAAGGTTCTTAA
Found at i:149865 original size:41 final size:41
Alignment explanation
Indices: 149735--149865 Score: 97
Period size: 41 Copynumber: 3.1 Consensus size: 41
149725 TTATGAATGT
149735 AAGAATATGGACATATCAAGTTTTATAATCCTCGATTAAAG
1 AAGAATATGGACATATCAAGTTTTATAATCCTCGATTAAAG
* ** * * ** * * *
149776 AAGAAAGAGTCTTACCTTAT-AAGGTTCT-TAATTGT-TATGAATG
1 AAG-AATA-T-GGA-CATATCAA-GTTTTATAATCCTCGATTAAAG
149819 TAAGAATATGGACATATCAAGTTTTATAATCCTCGATTAAAG
1 -AAGAATATGGACATATCAAGTTTTATAATCCTCGATTAAAG
149861 AAGAA
1 AAGAA
149866 AGAGTCTTAC
Statistics
Matches: 61, Mismatches: 20, Indels: 18
0.62 0.20 0.18
Matches are distributed among these distances:
40 8 0.13
41 16 0.26
42 9 0.15
43 9 0.15
44 11 0.18
45 8 0.13
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (41 bp):
AAGAATATGGACATATCAAGTTTTATAATCCTCGATTAAAG
Found at i:158705 original size:10 final size:10
Alignment explanation
Indices: 158686--158745 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 10
158676 TGATCATATG
*
158686 ATTGACTTTT
1 ATTGAATTTT
158696 ATTGAATTTT
1 ATTGAATTTT
*** *
158706 CGAGACTTTT
1 ATTGAATTTT
158716 ATTGAATTTT
1 ATTGAATTTT
*
158726 -TTAGACTTTT
1 ATT-GAATTTT
158736 ATTGAATTTT
1 ATTGAATTTT
158746 TGACTTTATT
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
9 2 0.05
10 33 0.89
11 2 0.05
ACGTcount: A:0.25, C:0.07, G:0.12, T:0.57
Consensus pattern (10 bp):
ATTGAATTTT
Found at i:158746 original size:20 final size:20
Alignment explanation
Indices: 158689--158748 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
158679 TCATATGATT
*
158689 GACTTTTATTGAATTTTCGA
1 GACTTTTATTGAATTTTTGA
*
158709 GACTTTTATTGAATTTTTTA
1 GACTTTTATTGAATTTTTGA
158729 GACTTTTATTGAATTTTTGA
1 GACTTTTATTGAATTTTTGA
158749 CTTTATTCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.25, C:0.07, G:0.13, T:0.55
Consensus pattern (20 bp):
GACTTTTATTGAATTTTTGA
Found at i:161604 original size:162 final size:162
Alignment explanation
Indices: 161337--161660 Score: 639
Period size: 162 Copynumber: 2.0 Consensus size: 162
161327 TTTCACTTTA
*
161337 TGCCTATTTAGGCCTTTATTGCTTTTGCCTCCTCTAACAATCAGTTTTATTTGTTGCATTTGAAG
1 TGCCTATTTAGGCCTTTATTGCTTTTGCCTCCGCTAACAATCAGTTTTATTTGTTGCATTTGAAG
161402 GCAGCAAGTGAGGAGGCAACAAGAAGATTCGAGACGATAGTTCGACTGATGAATGAAGAGATTGT
66 GCAGCAAGTGAGGAGGCAACAAGAAGATTCGAGACGATAGTTCGACTGATGAATGAAGAGATTGT
161467 ACGTTTCCAGGAACCAAAAACACGAGACATGG
131 ACGTTTCCAGGAACCAAAAACACGAGACATGG
161499 TGCCTATTTAGGCCTTTATTGCTTTTGCCTCCGCTAACAATCAGTTTTATTTGTTGCATTTGAAG
1 TGCCTATTTAGGCCTTTATTGCTTTTGCCTCCGCTAACAATCAGTTTTATTTGTTGCATTTGAAG
161564 GCAGCAAGTGAGGAGGCAACAAGAAGATTCGAGACGATAGTTCGACTGATGAATGAAGAGATTGT
66 GCAGCAAGTGAGGAGGCAACAAGAAGATTCGAGACGATAGTTCGACTGATGAATGAAGAGATTGT
161629 ACGTTTCCAGGAACCAAAAACACGAGACATGG
131 ACGTTTCCAGGAACCAAAAACACGAGACATGG
161661 GGATTGCTTT
Statistics
Matches: 161, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
162 161 1.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (162 bp):
TGCCTATTTAGGCCTTTATTGCTTTTGCCTCCGCTAACAATCAGTTTTATTTGTTGCATTTGAAG
GCAGCAAGTGAGGAGGCAACAAGAAGATTCGAGACGATAGTTCGACTGATGAATGAAGAGATTGT
ACGTTTCCAGGAACCAAAAACACGAGACATGG
Found at i:171242 original size:15 final size:15
Alignment explanation
Indices: 171222--171303 Score: 112
Period size: 15 Copynumber: 5.5 Consensus size: 15
171212 TTTCGGAAAA
*
171222 TGAATTACTGGAGTT
1 TGAATTACTGGAATT
171237 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
171252 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
171267 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
171282 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
171296 TGAATTAC
1 TGAATTAC
171304 ATTTCTGGAA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
14 12 0.20
15 47 0.80
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.35
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:171267 original size:45 final size:44
Alignment explanation
Indices: 171216--171303 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 44
171206 TTGGTTTTTC
* **
171216 GGAAAATGAATTACTGGAGTTTGAATTACTGGAATTTGAATTACT
1 GGAAAATGAATTACTGGAATTTGAATT-CTGGAAAATGAATTACT
171261 GGAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
1 GGAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
171304 ATTTCTGGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 14 0.35
45 26 0.65
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.33
Consensus pattern (44 bp):
GGAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTACT
Found at i:171301 original size:29 final size:30
Alignment explanation
Indices: 171222--171303 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
171212 TTTCGGAAAA
***
171222 TGAATTACTGGAGTTTGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
171252 TGAATTACTGGAAAATGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
171282 TGAATT-CTGGAAAATGAATTAC
1 TGAATTACTGGAAAATGAATTAC
171304 ATTTCTGGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 16 0.33
30 33 0.67
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.35
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTGGAATT
Found at i:171309 original size:20 final size:20
Alignment explanation
Indices: 171286--171335 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
171276 GGAATTTGAA
171286 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
171306 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
171326 TTCTGGAAAA
1 TTCTGGAAAA
171336 CATCTGGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:171564 original size:28 final size:26
Alignment explanation
Indices: 171530--171692 Score: 91
Period size: 28 Copynumber: 5.9 Consensus size: 26
171520 TTTACTAAAA
171530 TATTATTGAAATATATAAATATATTAT
1 TATTATT-AAATATATAAATATATTAT
* *
171557 TCATTATTAAATATAAAAAATTTATTAT
1 T-ATTATTAAATAT-ATAAATATATTAT
* *
171585 ATATTATTAAA-ATA-AAATAAAATATCT
1 -TATTATTAAATATATAAAT-ATAT-TAT
* * *
171612 TATTTATTATAATATAATTGATTATTTTAT
1 TA-TTATTA-AATAT-A-TAAATATATTAT
* * *
171642 ATAGTATTAAAAATAT-AATATAATAT
1 -TATTATTAAATATATAAATATATTAT
171668 TATTA-TAAATATTAATAAATATATT
1 TATTATTAAATA-T-ATAAATATATT
171693 TTAAATATTT
Statistics
Matches: 103, Mismatches: 18, Indels: 30
0.68 0.12 0.20
Matches are distributed among these distances:
24 5 0.05
25 9 0.09
26 14 0.14
27 25 0.24
28 29 0.28
29 7 0.07
30 8 0.08
31 4 0.04
32 2 0.02
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (26 bp):
TATTATTAAATATATAAATATATTAT
Found at i:171581 original size:25 final size:26
Alignment explanation
Indices: 171530--171590 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 26
171520 TTTACTAAAA
*
171530 TATTATTGAAATATATAAATATATTAT
1 TATTATT-AAATATATAAAAATATTAT
171557 TCATTATTAAATATA-AAAAAT-TTAT
1 T-ATTATTAAATATATAAAAATATTAT
171582 TATATATTA
1 TAT-TATTA
171591 TTAAAATAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
24 2 0.06
25 10 0.32
26 5 0.16
27 8 0.26
28 6 0.19
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (26 bp):
TATTATTAAATATATAAAAATATTAT
Found at i:171589 original size:56 final size:54
Alignment explanation
Indices: 171529--171692 Score: 138
Period size: 56 Copynumber: 3.0 Consensus size: 54
171519 CTTTACTAAA
171529 ATATTATTGAAATATATAAATATATTATTCATTATTAAATATAAAAAATT-TATTAT
1 ATATTATT-AAATATATAAATATATTATT-ATTA-TAAATATAAAAAATTATATTAT
* * *** *
171585 ATATTATTAAAATAAAATAAAATATCTTATTTATTAT-AATATAATTGATTATTTTAT
1 ATATTATT-AAAT-ATAT-AAATATATTA-TTATTATAAATATAAAAAATTATATTAT
* * * *
171642 ATAGTATTAAAAATAT-AATATAATATTATTATAAATATTAATAAA-TATATT
1 ATATTATTAAATATATAAATATATTATTATTATAAATA-TAAAAAATTATATT
171693 TTAAATATTT
Statistics
Matches: 87, Mismatches: 15, Indels: 15
0.74 0.13 0.13
Matches are distributed among these distances:
52 7 0.08
53 16 0.18
54 5 0.06
55 3 0.03
56 25 0.29
57 16 0.18
58 13 0.15
59 2 0.02
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (54 bp):
ATATTATTAAATATATAAATATATTATTATTATAAATATAAAAAATTATATTAT
Found at i:171657 original size:31 final size:32
Alignment explanation
Indices: 171619--171690 Score: 83
Period size: 32 Copynumber: 2.1 Consensus size: 32
171609 TCTTATTTAT
*
171619 TATAATATAATTGATTATTTTATATAGTATTAA-AAA
1 TATAATATAA-T-ATTA--TTATA-AATATTAATAAA
171655 TATAATATAATATTATTATAAATATTAATAAA
1 TATAATATAATATTATTATAAATATTAATAAA
171687 TATA
1 TATA
171691 TTTTAAATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
31 7 0.21
32 12 0.35
34 4 0.12
35 1 0.03
36 10 0.29
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (32 bp):
TATAATATAATATTATTATAAATATTAATAAA
Found at i:171692 original size:21 final size:23
Alignment explanation
Indices: 171646--171701 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 23
171636 TTTTATATAG
*
171646 TATTAAAAATA-TAATATAATAT
1 TATTATAAATATTAATATAATAT
171668 TATTATAAATATTAATA-AATA-
1 TATTATAAATATTAATATAATAT
*
171689 TATTTTAAATATT
1 TATTATAAATATT
171702 TTAATAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 12 0.39
22 14 0.45
23 5 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TATTATAAATATTAATATAATAT
Found at i:171706 original size:23 final size:21
Alignment explanation
Indices: 171652--171701 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
171642 ATAGTATTAA
*
171652 AAATA-TAATATAATATTATTAT
1 AAATATTAATA-AATA-TATTTT
171674 AAATATTAATAAATATATTTT
1 AAATATTAATAAATATATTTT
171695 AAATATT
1 AAATATT
171702 TTAATAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 12 0.46
22 9 0.35
23 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AAATATTAATAAATATATTTT
Found at i:171952 original size:42 final size:42
Alignment explanation
Indices: 171893--172009 Score: 198
Period size: 42 Copynumber: 2.8 Consensus size: 42
171883 AATTACATTC
*
171893 CGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTTTTA
1 CGGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTTA
* *
171935 CGGAAAACGAATTACGTGAAACAAACACGGGGAAACATTTTC
1 CGGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTTA
*
171977 CGGAAAACGAATTACGTGAAACAAACACTGGAA
1 CGGAAAACGAATTACGTGAAACAAACACGGGAA
172010 TTCGGGGAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.15
Consensus pattern (42 bp):
CGGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTTA
Found at i:171956 original size:14 final size:15
Alignment explanation
Indices: 171895--171955 Score: 56
Period size: 14 Copynumber: 4.3 Consensus size: 15
171885 TTACATTCCG
171895 GAAAACGAATTACGT
1 GAAAACGAATTACGT
** *
171910 G-AAAC-AAACACGG
1 GAAAACGAATTACGT
**
171923 GAAAACGTTTTACG-
1 GAAAACGAATTACGT
171937 GAAAACGAATTACGT
1 GAAAACGAATTACGT
171952 GAAA
1 GAAA
171956 CAAACACGGG
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
13 6 0.18
14 20 0.59
15 8 0.24
ACGTcount: A:0.48, C:0.15, G:0.21, T:0.16
Consensus pattern (15 bp):
GAAAACGAATTACGT
Found at i:179252 original size:47 final size:47
Alignment explanation
Indices: 179192--179283 Score: 166
Period size: 47 Copynumber: 2.0 Consensus size: 47
179182 TCAATATTAC
179192 AATACTGCAATACTAACTGTTGCTATTTTACAGACTCACAAATATGT
1 AATACTGCAATACTAACTGTTGCTATTTTACAGACTCACAAATATGT
* *
179239 AATATTGCAATACTAACTGTTGTTATTTTACAGACTCACAAATAT
1 AATACTGCAATACTAACTGTTGCTATTTTACAGACTCACAAATAT
179284 AGCTTTGCTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (47 bp):
AATACTGCAATACTAACTGTTGCTATTTTACAGACTCACAAATATGT
Found at i:191088 original size:16 final size:17
Alignment explanation
Indices: 191069--191106 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
191059 AGTAAAATAT
191069 TTTTTA-AATAATTAC-A
1 TTTTTACAATAA-TACTA
191085 TTTTTACAATAATACTA
1 TTTTTACAATAATACTA
191102 TTTTT
1 TTTTT
191107 TCATCCCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTTACAATAATACTA
Found at i:191089 original size:17 final size:18
Alignment explanation
Indices: 191066--191107 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 18
191056 GGTAGTAAAA
191066 TATTTTTTA-AATAATTAC
1 TATTTTTTACAATAA-TAC
191084 -A-TTTTTACAATAATAC
1 TATTTTTTACAATAATAC
191100 TATTTTTT
1 TATTTTTT
191108 CATCCCATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
16 9 0.43
17 7 0.33
18 5 0.24
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTTTTTACAATAATAC
Found at i:191841 original size:75 final size:75
Alignment explanation
Indices: 191732--191872 Score: 210
Period size: 75 Copynumber: 1.9 Consensus size: 75
191722 GATAAAAATA
* * * *
191732 AATAAAATTTTAGAGTGGTCACCTTCAATGAAATGAGCAACTAATATAAATAAATTCGAATTTCA
1 AATAAAATTTTAGAGTGGACACCTTCAATAAAATGAACAACTAATATAAAGAAATTCGAATTTCA
191797 GGTTAGGCAT
66 GGTTAGGCAT
* * * *
191807 AATAAAATTTTAGGGTGGACACTTTTAATAAAATGAACAACTAGTATAAAGAAATTCGAATTTCA
1 AATAAAATTTTAGAGTGGACACCTTCAATAAAATGAACAACTAATATAAAGAAATTCGAATTTCA
191872 G
66 G
191873 TGTGGACACG
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 58 1.00
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (75 bp):
AATAAAATTTTAGAGTGGACACCTTCAATAAAATGAACAACTAATATAAAGAAATTCGAATTTCA
GGTTAGGCAT
Found at i:192312 original size:16 final size:17
Alignment explanation
Indices: 192291--192329 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
192281 TATTTTAAAG
*
192291 AAAATATT-TTGAGAGT
1 AAAATATTGATGAGAGT
192307 AAAATATTGATGAGAGT
1 AAAATATTGATGAGAGT
192324 ATAAAT
1 A-AAAT
192330 GAATCAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 8 0.40
18 4 0.20
ACGTcount: A:0.49, C:0.00, G:0.18, T:0.33
Consensus pattern (17 bp):
AAAATATTGATGAGAGT
Found at i:192828 original size:158 final size:159
Alignment explanation
Indices: 192498--192867 Score: 476
Period size: 157 Copynumber: 2.3 Consensus size: 159
192488 AGCATGTCAT
** *
192498 TTAAATTTAGTAAAAAAATGAACTTAAAATAAATAACAAATTGAATTAATAAGGAGATTATGAAA
1 TTAAATTTAGTAAAAAAATGAACTTAAAATAAATAACAAATTGAAGAAATAAGGACATTATGAAA
** * * *
192563 AATTGAAGGACTAAATTGAAAAATAAAAAGTTTGTTGTCAAAAAGAGGAATTGAAAGTACACATG
66 AATTGAAGGACTAAATTGAAAAATAAAAAAATTATTATCAAAAAGAGAAATTGAAAGTACACATG
*
192628 TATTCTACTATGGTTTAGGAGCATGTGGC
131 TATTCTACTATAGTTTAGGAGCATGTGGC
* * * * *
192657 TTAAATTTGGTAAAAATA-G-ATTTAAAATAAATGACGAATTGAAGAAATAAGGACATTATGAAA
1 TTAAATTTAGTAAAAAAATGAACTTAAAATAAATAACAAATTGAAGAAATAAGGACATTATGAAA
* **
192720 AATTGAAGGACTAAATTGAAAAATAAAAAAATTATTATCAAAAAAGAGAAATTGAAAGTATATGT
66 AATTGAAGGACTAAATTGAAAAATAAAAAAATTATTATC-AAAAAGAGAAATTGAAAGTACACAT
*
192785 GTATTCTACTATAGTTTAGGATCATGTGG-
130 GTATTCTACTATAGTTTAGGAGCATGTGGC
** * ** *
192814 TTCAAATTTAGTAAAAAAAACAGACTTAAAATGAAGGAGAAATTGAAGAAATAA
1 TT-AAATTTAGTAAAAAAATGA-ACTTAAAATAAATAACAAATTGAAGAAATAA
192868 TGAAATCAAT
Statistics
Matches: 180, Mismatches: 26, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
157 75 0.42
158 63 0.35
159 16 0.09
161 26 0.14
ACGTcount: A:0.49, C:0.05, G:0.17, T:0.28
Consensus pattern (159 bp):
TTAAATTTAGTAAAAAAATGAACTTAAAATAAATAACAAATTGAAGAAATAAGGACATTATGAAA
AATTGAAGGACTAAATTGAAAAATAAAAAAATTATTATCAAAAAGAGAAATTGAAAGTACACATG
TATTCTACTATAGTTTAGGAGCATGTGGC
Found at i:194520 original size:2 final size:2
Alignment explanation
Indices: 194513--194556 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
194503 GAAAGTGAAT
194513 TA TA TA 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
194555 TA
1 TA
194557 CTTTTTGATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:197109 original size:66 final size:66
Alignment explanation
Indices: 196991--197129 Score: 197
Period size: 66 Copynumber: 2.1 Consensus size: 66
196981 GAGTCAATGA
* ** * * * **
196991 TGCACGAGGTGGAGTGATTGTTGAATACTGTACATATCACTCAATGTGACTCATGTACCTTTGTG
1 TGCATGAGGTGGAGTGATAATTGAATACTGCACAAATCACTCAACGAAACTCATGTACCTTTGTG
197056 G
66 G
197057 TGCATGAGGTGGAGTGATAATTGAATACTGCACAAATCACTCAACGAAACTCATGTACCTTTGTG
1 TGCATGAGGTGGAGTGATAATTGAATACTGCACAAATCACTCAACGAAACTCATGTACCTTTGTG
197122 G
66 G
*
197123 TGTATGA
1 TGCATGA
197130 ATATTGTACA
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (66 bp):
TGCATGAGGTGGAGTGATAATTGAATACTGCACAAATCACTCAACGAAACTCATGTACCTTTGTG
G
Found at i:197214 original size:115 final size:115
Alignment explanation
Indices: 197012--197244 Score: 349
Period size: 115 Copynumber: 2.0 Consensus size: 115
197002 GAGTGATTGT
*
197012 TGAATACTGTACATATCACTCAATGTGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAA
1 TGAATACTGTACATATCACTCAATGAGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAA
* *
197077 TTGAATACTGCACAAATCACTCAACGAAACTCATGTACCTTTGTGGTGTA
66 TTGAATACTGCACAAATCACTCAACGAAACTCATGTACATTTATGGTGTA
* * *
197127 TGAATATTGTACATATTACTCAATGAGACTCATGTACCTTTGTGGTGCATGAGGTGTAGTGATAA
1 TGAATACTGTACATATCACTCAATGAGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAA
* * ** * **
197192 TTGAATATTGTACTGATCACTCAACGAGACTTGTGTACATTTATGGTGTA
66 TTGAATACTGCACAAATCACTCAACGAAACTCATGTACATTTATGGTGTA
197242 TGA
1 TGA
197245 GGTGTAGTGA
Statistics
Matches: 105, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
115 105 1.00
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.34
Consensus pattern (115 bp):
TGAATACTGTACATATCACTCAATGAGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAA
TTGAATACTGCACAAATCACTCAACGAAACTCATGTACATTTATGGTGTA
Found at i:197239 original size:66 final size:66
Alignment explanation
Indices: 197127--197254 Score: 177
Period size: 66 Copynumber: 1.9 Consensus size: 66
197117 TTGTGGTGTA
* * * *
197127 TGAATATTGTACATATTACTCAATGAGACTCATGTACCTTTGTGGTGCATGAGGTGTAGTGATAA
1 TGAATATTGTACATATCACTCAACGAGACTCATGTACATTTATGGTGCATGAGGTGTAGTGATAA
197192 T
66 T
** *
197193 TGAATATTGTAC-TGATCACTCAACGAGACTTGTGTACATTTATGGTGTATGAGGTGTAGTGA
1 TGAATATTGTACAT-ATCACTCAACGAGACTCATGTACATTTATGGTGCATGAGGTGTAGTGA
197255 CTATATGCTA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
65 1 0.02
66 53 0.98
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (66 bp):
TGAATATTGTACATATCACTCAACGAGACTCATGTACATTTATGGTGCATGAGGTGTAGTGATAA
T
Found at i:197749 original size:17 final size:17
Alignment explanation
Indices: 197723--197755 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
197713 CGAGAGTTAT
197723 ATTAAAATGTGAAATAA
1 ATTAAAATGTGAAATAA
*
197740 ATTAATATGTGAAATA
1 ATTAAAATGTGAAATA
197756 TCATAAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (17 bp):
ATTAAAATGTGAAATAA
Found at i:204187 original size:35 final size:37
Alignment explanation
Indices: 204118--204187 Score: 99
Period size: 35 Copynumber: 1.9 Consensus size: 37
204108 ATATAATTTG
* **
204118 AAATCATTTTGAAAATTATATAATATATGGTTTTTTT
1 AAATCATTTCGAAAATTATATAATATATAATTTTTTT
204155 AAAT-ATTTCGAAAA-TATATAATATATAATTTTT
1 AAATCATTTCGAAAATTATATAATATATAATTTTT
204188 GAAAACATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 17 0.57
36 9 0.30
37 4 0.13
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (37 bp):
AAATCATTTCGAAAATTATATAATATATAATTTTTTT
Found at i:204317 original size:73 final size:73
Alignment explanation
Indices: 204160--204370 Score: 186
Period size: 73 Copynumber: 2.9 Consensus size: 73
204150 TTTTTAAATA
* ** * **
204160 TTTCGAAA-ATATATAATATATAATTTTTGAAAACATTTTTGAAAATACATATTATATTGTTTTG
1 TTTCTAAATATATATAATATATAATTTTAAAAAACATTTTTGAAAAAACATATTATATAATTTTG
*
204224 AAAACTTT
66 AAAACTTG
* * * *
204232 TTTTTAAGTATATATAATATATAGCTTTTAAAAAAACA-TTTTGAAAAAACGTA-TATATAATTT
1 TTTCTAAATATATATAATATATA-ATTTT-AAAAAACATTTTTGAAAAAACATATTATATAATTT
204295 TGAAAA-TTAG
64 TGAAAACTT-G
* ** * *
204305 TTTCTAAATATATAT--TATATAATTTTGAAAATTAGTTTTT--AAAAATATATTATATAGTTTT
1 TTTCTAAATATATATAATATATAATTTTAAAAAACA-TTTTTGAAAAAACATATTATATAATTTT
204366 GAAAA
65 GAAAA
204371 TTATTTTTTT
Statistics
Matches: 112, Mismatches: 20, Indels: 16
0.76 0.14 0.11
Matches are distributed among these distances:
69 12 0.11
70 19 0.17
71 10 0.09
72 7 0.06
73 41 0.37
74 17 0.15
75 6 0.05
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (73 bp):
TTTCTAAATATATATAATATATAATTTTAAAAAACATTTTTGAAAAAACATATTATATAATTTTG
AAAACTTG
Found at i:204403 original size:39 final size:36
Alignment explanation
Indices: 204165--204418 Score: 175
Period size: 35 Copynumber: 7.1 Consensus size: 36
204155 AAATATTTCG
* * *
204165 AAAATATATAATATATAATTTTTGAAAA-CA-TTTTT
1 AAAATATATATTATAT-AGTTTTGAAAATTAGTTTTT
* * *
204200 GAAAATACATATTATATTGTTTTGAAAACTT-TTTTTT
1 -AAAATATATATTATATAGTTTTGAAAA-TTAGTTTTT
* * ** * *
204237 AAGTATATATAATATATAGCTTTT-AAAAAAACATTTTG
1 AA-AATATATATTATATAG-TTTTGAAAATTA-GTTTTT
* ** * *
204275 AAAAAACGTA-TATATAATTTTGAAAATTAGTTTCT
1 AAAATATATATTATATAGTTTTGAAAATTAGTTTTT
*
204310 -AAATATATATTATATAATTTTGAAAATTAGTTTTT
1 AAAATATATATTATATAGTTTTGAAAATTAGTTTTT
*
204345 AAAA-ATATATTATATAGTTTTGAAAATTATTTTTTTT
1 AAAATATATATTATATAGTTTTGAAAATTA--GTTTTT
* *
204382 AAAAGTATATATTGTATAGTTTT-AAAAAT-GTTTTT
1 AAAA-TATATATTATATAGTTTTGAAAATTAGTTTTT
204417 AA
1 AA
204419 TTAATTTATT
Statistics
Matches: 172, Mismatches: 32, Indels: 29
0.74 0.14 0.12
Matches are distributed among these distances:
34 6 0.03
35 71 0.41
36 30 0.17
37 34 0.20
38 15 0.09
39 16 0.09
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (36 bp):
AAAATATATATTATATAGTTTTGAAAATTAGTTTTT
Found at i:204447 original size:4 final size:4
Alignment explanation
Indices: 204422--204480 Score: 59
Period size: 4 Copynumber: 15.0 Consensus size: 4
204412 TTTTTAATTA
* ** *
204422 ATTT ATTA ATTT ATCC ATTT ATTT ATTT ATTT ATTT -TTT CATTT ACTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT -ATTT ATTT
204470 ATTT A-TT ATTT
1 ATTT ATTT ATTT
204481 GTTTCAGGTC
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
3 6 0.14
4 35 0.80
5 3 0.07
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (4 bp):
ATTT
Found at i:204485 original size:24 final size:24
Alignment explanation
Indices: 204422--204486 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
204412 TTTTTAATTA
* * * *
204422 ATTTATTAATTTATCCATTTATTT
1 ATTTATTTATTTTTTCATTTACTT
204446 ATTTATTTATTTTTTCATTTACTT
1 ATTTATTTATTTTTTCATTTACTT
204470 ATTTA-TTATTTGTTTCA
1 ATTTATTTATTT-TTTCA
204487 GGTCCAGGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 6 0.17
24 30 0.83
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.66
Consensus pattern (24 bp):
ATTTATTTATTTTTTCATTTACTT
Found at i:205039 original size:16 final size:16
Alignment explanation
Indices: 205018--205050 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
205008 GCAAATACAG
205018 AAACAAA-ACCCAAAAA
1 AAACAAATA-CCAAAAA
205034 AAACAAATACCAAAAA
1 AAACAAATACCAAAAA
205050 A
1 A
205051 TACCGAAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.94
17 1 0.06
ACGTcount: A:0.76, C:0.21, G:0.00, T:0.03
Consensus pattern (16 bp):
AAACAAATACCAAAAA
Found at i:205277 original size:12 final size:12
Alignment explanation
Indices: 205260--205289 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
205250 CCACCGCCGG
205260 CGGTGGCCGGCA
1 CGGTGGCCGGCA
*
205272 CGGTGGCCGGCG
1 CGGTGGCCGGCA
205284 CGGTGG
1 CGGTGG
205290 AGGGGCCACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.03, C:0.30, G:0.57, T:0.10
Consensus pattern (12 bp):
CGGTGGCCGGCA
Found at i:211358 original size:249 final size:249
Alignment explanation
Indices: 210925--211869 Score: 1598
Period size: 249 Copynumber: 3.8 Consensus size: 249
210915 TTTTAAACAA
* *
210925 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTTGAGTTCAACTA
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCCAAGACCTTTGAGTTCGACTA
*
210990 CGCTCA-----AAGGCATATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
66 CGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
* *
211050 CCTCGAGTTCGACTACGTTCAGCTTCGAATGCACATCATTTGCAGTATAACTTAAGTCAAGGAGG
131 CCTCGAGTTCGACTACGTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGG
211115 GTTATCTGCCAACTAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCAT
196 GTTATCTGCCAACTAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCAT
211169 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCCAAGACCTTTGAGTTCGACTA
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCCAAGACCTTTGAGTTCGACTA
211234 CGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
66 CGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
211299 CCTCGAGTTCGACTACGTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGG
131 CCTCGAGTTCGACTACGTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGG
211364 GTTATCTGCCAACTAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCAT
196 GTTATCTGCCAACTAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCAT
211418 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCCAAGACCTTTGAGTTCGACTA
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCCAAGACCTTTGAGTTCGACTA
*
211483 CGCTCAGCTCCAAGGCACATTATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
66 CGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
211548 CCTCGAGTTCGACTACGTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGG
131 CCTCGAGTTCGACTACGTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGG
211613 GTTATCTGCC-ACTAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCAT
196 GTTATCTGCCAACTAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCAT
* * * * * * *
211666 ATTATTTACAGCATAGCTCAAGGCCAGAAGGGCTGTCTG-CCCACCAAGACCTTCGAGTTCGACT
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAC-CCAAGACCTTTGAGTTCGACT
* * *
211730 ACACTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGA
65 ACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
* * * ** * * * *
211795 CCCCCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAG
130 CCCTCGAGTTCGACTACGTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAG
*
211860 GGCTATCTGC
195 GGTTATCTGC
211870 TAAAGACCTT
Statistics
Matches: 668, Mismatches: 27, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
244 69 0.10
247 2 0.00
248 223 0.33
249 374 0.56
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (249 bp):
ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCCAAGACCTTTGAGTTCGACTA
CGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
CCTCGAGTTCGACTACGTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGG
GTTATCTGCCAACTAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCAT
Found at i:211861 original size:497 final size:493
Alignment explanation
Indices: 210925--211869 Score: 1588
Period size: 497 Copynumber: 1.9 Consensus size: 493
210915 TTTTAAACAA
210925 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTTGAGTTCAACTA
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTTGAGTTCAACTA
*
210990 CGCTCAAAGGCATATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCG
66 CGCTCAAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCG
* *
211055 AGTTCGACTACGTTCAGCTTCGAATGCACATCATTTGCAGTATAACTTAAGTCAAGGAGGGTTAT
131 AGTTCGACTACGTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTAT
211120 CTGCCAACTAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAA
196 CTGCCAACTAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAA
* * * * *
211185 CTCAAGGCTAGAAGGGTTATCTGTCACCCAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
261 CTCAAGGCCAGAAGGGCTATCTGCCACCCAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGC
* * *
211250 ACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTAC
326 ACATCATTTGCAGAATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCCCAAGTTCGACTAC
** * *
211315 GTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACTAA
391 ACTCAGCTTCGAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGCTATCTGCCAACTAA
211380 AGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCAT
456 AGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCAT
* *
211418 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCCAAGACCTTTGAGTTCGACTA
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTTGAGTTCAACTA
*
211483 CGCTCAGCTCCAAGGCACATTATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
66 CGCTCA-----AAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
211548 CCTCGAGTTCGACTACGTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGG
126 CCTCGAGTTCGACTACGTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGG
*
211613 GTTATCTGCC-ACTAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATTATTTACAG
191 GTTATCTGCCAACTAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAG
* *
211677 CATAGCTCAAGGCCAGAAGGGCTGTCTGCC-CACCAAGACCTTCGAGTTCGACTACACTCAGCTC
256 CATAACTCAAGGCCAGAAGGGCTATCTGCCAC-CCAAGACCTTCGAGTTCGACTACACTCAGCTC
*
211741 CAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCCCAAGTTC
320 CAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCCCAAGTTC
* * * *
211806 GATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGC
385 GACTACACTCAGCTTCGAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGCTATCTGC
211870 TAAAGACCTT
Statistics
Matches: 420, Mismatches: 26, Indels: 8
0.93 0.06 0.02
Matches are distributed among these distances:
493 69 0.16
496 1 0.00
497 225 0.54
498 125 0.30
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (493 bp):
ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTTGAGTTCAACTA
CGCTCAAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCG
AGTTCGACTACGTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTAT
CTGCCAACTAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAA
CTCAAGGCCAGAAGGGCTATCTGCCACCCAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGC
ACATCATTTGCAGAATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCCCAAGTTCGACTAC
ACTCAGCTTCGAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGCTATCTGCCAACTAA
AGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCAT
Found at i:212616 original size:36 final size:36
Alignment explanation
Indices: 212517--212842 Score: 121
Period size: 36 Copynumber: 9.1 Consensus size: 36
212507 CCATTTTTTT
*
212517 ATATATAA--TTTGAAATCA-TTTTGAAAATTATATA
1 ATATATAATTTTTGAAAACATTTTTGAAAA-TATATA
** *** *
212551 ATATATGGTTTTTTTTAA-ATATTTCGAAAATATATA
1 ATATATAATTTTTGAAAACAT-TTTTGAAAATATATA
*
212587 ATATATAATTTTTGAAAACATTTTTGAAAATACAT-
1 ATATATAATTTTTGAAAACATTTTTGAAAATATATA
* * * *
212622 AT-TATATTGTTTTGAAAACTTTTTTTAAGTATATATA
1 ATATATAAT-TTTTGAAAACATTTTTGAA-AATATATA
** ** * **
212659 ATATA-GCTTTTAAAAAAACA-TTTTGAAAAAACGT-
1 ATATATAATTTT-TGAAAACATTTTTGAAAATATATA
**
212693 ATATATAA-TTTTG-AAA-ATTAGTTTCTAAATATATA
1 ATATATAATTTTTGAAAACATT--TTTGAAAATATATA
* *
212728 TTATATAA-TTTTGAAAATTAGTTTTT-AAAATATAT-
1 ATATATAATTTTTGAAAA-CA-TTTTTGAAAATATATA
* *
212763 ATATTATATAGTTTTGAAAATTAGTTTTT-AAAA-ATATA
1 ATA-TATA-ATTTTTGAAAA-CA-TTTTTGAAAATATATA
* * * * *
212801 TTATAT-AGTTTTGAAAATTAGTTTTTAAAAATATATT
1 ATATATAATTTTTGAAAA-CA-TTTTTGAAAATATATA
212838 ATATA
1 ATATA
212843 GTTTTGAAAA
Statistics
Matches: 223, Mismatches: 44, Indels: 47
0.71 0.14 0.15
Matches are distributed among these distances:
31 1 0.00
32 4 0.02
34 27 0.12
35 57 0.26
36 68 0.30
37 37 0.17
38 27 0.12
39 2 0.01
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.47
Consensus pattern (36 bp):
ATATATAATTTTTGAAAACATTTTTGAAAATATATA
Found at i:212646 original size:35 final size:34
Alignment explanation
Indices: 212535--212897 Score: 205
Period size: 35 Copynumber: 10.1 Consensus size: 34
212525 TTTGAAATCA
* * ** *
212535 TTTTGAAAATTATATAATATATGGTTTTTTTTAAATA
1 TTTTGAAAA-TATATATTATATAG--TTTTGAAAATT
* * * *
212572 TTTCGAAAATATATAATATATAATTTTTGAAAACAT
1 TTTTGAAAATATATATTATAT-AGTTTTGAAAA-TT
* *
212608 TTTTGAAAATACATATTATATTGTTTTGAAAACTT
1 TTTTGAAAATATATATTATATAGTTTTGAAAA-TT
* * * * **
212643 TTTT-TAAGTATATATAATATAGCTTTTAAAAAAACA
1 TTTTGAAAATATATATTATATAG-TTTT--GAAAATT
* ** *
212679 TTTTGAAAAAACGTA-TATATAATTTTGAAAATT
1 TTTTGAAAATATATATTATATAGTTTTGAAAATT
* ** *
212712 AGTTTCTAAATATATATTATATAATTTTGAAAATTAGT
1 -TTTTGAAAATATATATTATATAGTTTTGAAAA-T--T
*
212750 TTTTAAAATATATATATTATATAGTTTTGAAAATT
1 TTTTGAAA-ATATATATTATATAGTTTTGAAAATT
*
212785 AGTTTTTAAAA-ATATATTATATAGTTTTGAAAATT
1 --TTTTGAAAATATATATTATATAGTTTTGAAAATT
*
212820 AGTTTTTAAAA-ATATATTATATAGTTTTGAAAATTATTT
1 --TTTTGAAAATATATATTATATAGTTTTG-AAA--A-TT
* *
212859 TTTTTAAAAGTATATATTGTATAGTTTT-AAAATGT
1 TTTTGAAAA-TATATATTATATAGTTTTGAAAAT-T
212894 TTTT
1 TTTT
212898 AATTAATTTA
Statistics
Matches: 262, Mismatches: 43, Indels: 44
0.75 0.12 0.13
Matches are distributed among these distances:
33 4 0.02
34 23 0.09
35 106 0.40
36 44 0.17
37 42 0.16
38 25 0.10
39 18 0.07
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (34 bp):
TTTTGAAAATATATATTATATAGTTTTGAAAATT
Found at i:212778 original size:73 final size:70
Alignment explanation
Indices: 212694--212855 Score: 261
Period size: 73 Copynumber: 2.3 Consensus size: 70
212684 AAAAAACGTA
* *
212694 TATATAATTTTGAAAATTAGTTTCTAAATATATATTATATAATTTTGAAAATTAGTTTTTAAAAT
1 TATATAGTTTTGAAAATTAGTTTCTAAAAATATATTATATAATTTTGAAAATTAGTTTTT-AAA-
212759 ATATATAT
64 A-ATATAT
* *
212767 TATATAGTTTTGAAAATTAGTTTTTAAAAATATATTATATAGTTTTGAAAATTAGTTTTTAAAAA
1 TATATAGTTTTGAAAATTAGTTTCTAAAAATATATTATATAATTTTGAAAATTAGTTTTTAAAAA
212832 TATAT
66 TATAT
212837 TATATAGTTTTGAAAATTA
1 TATATAGTTTTGAAAATTA
212856 TTTTTTTTAA
Statistics
Matches: 85, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
70 25 0.29
71 1 0.01
72 3 0.04
73 56 0.66
ACGTcount: A:0.43, C:0.01, G:0.07, T:0.49
Consensus pattern (70 bp):
TATATAGTTTTGAAAATTAGTTTCTAAAAATATATTATATAATTTTGAAAATTAGTTTTTAAAAA
TATAT
Found at i:212835 original size:108 final size:105
Alignment explanation
Indices: 212694--212899 Score: 297
Period size: 108 Copynumber: 1.9 Consensus size: 105
212684 AAAAAACGTA
*
212694 TATATAATTTTGAAAATTAGTTTCTAAATATATATTATATAATTTTGAAAATTA-GTTTTTAAAA
1 TATATAATTTTGAAAATTAGTTTCTAAAAATATATTATATAATTTTGAAAATTATGTTTTTAAAA
212758 TATATATATTATATAGTTTTGAAAATTAGTTTTTAAAAATATAT
66 -ATATATATTATATAGTTTT-AAAA-T-GTTTTTAAAAATATAT
* * * *
212802 TATATAGTTTTGAAAATTAGTTTTTAAAAATATATTATATAGTTTTGAAAATTATTTTTTTTAAA
1 TATATAATTTTGAAAATTAGTTTCTAAAAATATATTATATAATTTTGAAAATTA-TGTTTTTAAA
* *
212867 AGTATATATTGTATAGTTTTAAAATGTTTTTAA
65 AATATATATTATATAGTTTTAAAATGTTTTTAA
212900 TTAATTTATT
Statistics
Matches: 89, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
106 8 0.09
107 1 0.01
108 54 0.61
109 17 0.19
110 9 0.10
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.50
Consensus pattern (105 bp):
TATATAATTTTGAAAATTAGTTTCTAAAAATATATTATATAATTTTGAAAATTATGTTTTTAAAA
ATATATATTATATAGTTTTAAAATGTTTTTAAAAATATAT
Found at i:212891 original size:73 final size:73
Alignment explanation
Indices: 212577--212899 Score: 282
Period size: 70 Copynumber: 4.5 Consensus size: 73
212567 AAATATTTCG
* * * * *
212577 AAAATATATAATATATAATTTTTGAAAA-CA-TTTTTGAAA-ATACATATTATATTGTTTTGAAA
1 AAAATATATATTATAT-AGTTTTGAAAATTAGTTTTT-AAATATATATATTATATAGTTTTGAAA
212639 ACTT--TTTTT
64 A-TTAGTTTTT
* * ** * * * ** *
212648 -AAGTATATATAATATAGCTTTT-AAAAAAACATTTTGAAA-AAACGTA-TATATAATTTTGAAA
1 AAAATATATATTATATAG-TTTTGAAAATTA-GTTTTTAAATATATATATTATATAGTTTTGAAA
*
212709 ATTAGTTTCT
64 ATTAGTTTTT
*
212719 -AAATATATATTATATAATTTTGAAAATTAGTTTTTAAAATATATATATTATATAGTTTTGAAAA
1 AAAATATATATTATATAGTTTTGAAAATTAGTTTTT-AAATATATATATTATATAGTTTTGAAAA
212783 TTAGTTTTT
65 TTAGTTTTT
212792 AAAA-ATATATTATATAGTTTTGAAAATTAGTTTTTAAA-A-ATATATTATATAGTTTTGAAAAT
1 AAAATATATATTATATAGTTTTGAAAATTAGTTTTTAAATATATATATTATATAGTTTTGAAAAT
*
212854 TATTTTTTTT
66 TA--GTTTTT
*
212864 AAAAGTATATATTGTATAGTTTT-AAAA-T-GTTTTTAA
1 AAAA-TATATATTATATAGTTTTGAAAATTAGTTTTTAA
212900 TTAATTTATT
Statistics
Matches: 211, Mismatches: 26, Indels: 30
0.79 0.10 0.11
Matches are distributed among these distances:
69 7 0.03
70 64 0.30
71 43 0.20
72 21 0.10
73 57 0.27
74 19 0.09
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.47
Consensus pattern (73 bp):
AAAATATATATTATATAGTTTTGAAAATTAGTTTTTAAATATATATATTATATAGTTTTGAAAAT
TAGTTTTT
Found at i:212928 original size:4 final size:4
Alignment explanation
Indices: 212903--212961 Score: 59
Period size: 4 Copynumber: 15.0 Consensus size: 4
212893 TTTTTAATTA
* ** *
212903 ATTT ATTA ATTT ATCC ATTT ATTT ATTT ATTT ATTT -TTT CATTT ACTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT -ATTT ATTT
212951 ATTT A-TT ATTT
1 ATTT ATTT ATTT
212962 GTTTCAGGTC
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
3 6 0.14
4 35 0.80
5 3 0.07
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (4 bp):
ATTT
Found at i:212966 original size:24 final size:24
Alignment explanation
Indices: 212903--212967 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
212893 TTTTTAATTA
* * * *
212903 ATTTATTAATTTATCCATTTATTT
1 ATTTATTTATTTTTTCATTTACTT
212927 ATTTATTTATTTTTTCATTTACTT
1 ATTTATTTATTTTTTCATTTACTT
212951 ATTTA-TTATTTGTTTCA
1 ATTTATTTATTT-TTTCA
212968 GGTCCAGGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 6 0.17
24 30 0.83
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.66
Consensus pattern (24 bp):
ATTTATTTATTTTTTCATTTACTT
Found at i:213520 original size:16 final size:16
Alignment explanation
Indices: 213499--213531 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
213489 GCAAATACAG
213499 AAACAAA-ACCCAAAAA
1 AAACAAATA-CCAAAAA
213515 AAACAAATACCAAAAA
1 AAACAAATACCAAAAA
213531 A
1 A
213532 TACCGAAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.94
17 1 0.06
ACGTcount: A:0.76, C:0.21, G:0.00, T:0.03
Consensus pattern (16 bp):
AAACAAATACCAAAAA
Found at i:213759 original size:12 final size:12
Alignment explanation
Indices: 213742--213771 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
213732 CCACCGCCGG
213742 CGGTGGCCGGCA
1 CGGTGGCCGGCA
*
213754 CGGTGGCCGGCG
1 CGGTGGCCGGCA
213766 CGGTGG
1 CGGTGG
213772 AGGGGCCACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.03, C:0.30, G:0.57, T:0.10
Consensus pattern (12 bp):
CGGTGGCCGGCA
Found at i:219399 original size:53 final size:53
Alignment explanation
Indices: 219319--219429 Score: 222
Period size: 53 Copynumber: 2.1 Consensus size: 53
219309 TATATATATC
219319 AGCTATTTTTCTACTCTTTAAAATAAAAAAGGTTATAGATGTTTCATAATTCT
1 AGCTATTTTTCTACTCTTTAAAATAAAAAAGGTTATAGATGTTTCATAATTCT
219372 AGCTATTTTTCTACTCTTTAAAATAAAAAAGGTTATAGATGTTTCATAATTCT
1 AGCTATTTTTCTACTCTTTAAAATAAAAAAGGTTATAGATGTTTCATAATTCT
219425 AGCTA
1 AGCTA
219430 AGAAATAACC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 58 1.00
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (53 bp):
AGCTATTTTTCTACTCTTTAAAATAAAAAAGGTTATAGATGTTTCATAATTCT
Found at i:219804 original size:2 final size:2
Alignment explanation
Indices: 219799--219831 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
219789 GTGTGTGAGT
219799 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
219832 TTTAGCGCAT
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:221037 original size:226 final size:223
Alignment explanation
Indices: 220639--221083 Score: 759
Period size: 226 Copynumber: 2.0 Consensus size: 223
220629 GTAAATTATC
* *
220639 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTA-CTTTAGT
**
220704 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
65 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATAATT
220769 TGTGTAAATTAAATTATTAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGA
130 TGTGTAAATTAAATTATTAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGA
220834 AACATAAATTACATAACTTTCAAAAAAGTA
195 AACATAAATTACATAACTTT-AAAAAAGTA
*
220864 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTAAATTA-TTTG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATT--ATTACTTTA
*
220928 GTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAAT-ATAA
63 GTTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATAA
*
220992 TTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAAT
128 TTTGTGTAAATTAAATTATT-AATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAT
221057 TGAAACATAAATTACATAACTTTAAAA
192 TGAAACATAAATTACATAACTTTAAAA
221084 GCAGTTTTAA
Statistics
Matches: 209, Mismatches: 7, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
225 62 0.30
226 143 0.68
228 4 0.02
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (223 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTACTTTAGTT
AATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATAATTT
GTGTAAATTAAATTATTAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAA
ACATAAATTACATAACTTTAAAAAAGTA
Found at i:221335 original size:19 final size:19
Alignment explanation
Indices: 221313--221358 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
221303 CGATATAACA
221313 GGTAAAATATGATAAAACC
1 GGTAAAATATGATAAAACC
*
221332 GGTAACAAAATGATAAAACC
1 GGTAA-AATATGATAAAACC
221352 -GTAAAAT
1 GGTAAAAT
221359 GATACCGGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 9 0.38
20 13 0.54
ACGTcount: A:0.54, C:0.11, G:0.15, T:0.20
Consensus pattern (19 bp):
GGTAAAATATGATAAAACC
Found at i:223609 original size:21 final size:21
Alignment explanation
Indices: 223563--223626 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
223553 AAGACAATCA
* *
223563 AGAGTCGAAGAG-AACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
223584 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
223604 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
223625 AG
1 AG
223627 GAATAAGGGG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 10 0.29
21 25 0.71
ACGTcount: A:0.39, C:0.16, G:0.30, T:0.16
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:226361 original size:197 final size:199
Alignment explanation
Indices: 225656--227200 Score: 2840
Period size: 197 Copynumber: 7.9 Consensus size: 199
225646 CAATATGGCC
* *
225656 AACAGGGTGCACCCATAAAGTGTCGATCC-TATATAAAAAGTGTCAATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
225720 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAA-TATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
225784 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
225849 GGAA
196 GGAA
225853 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAAC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAAC
225918 CCAAAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGG-TTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
*
225981 GAATATGTCTAAATAATGTGTCGACACT-A-ATAGTTTGTGTCGATACTTTTTTCCCAGAATGGA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAA
226044 TGGAA
195 TGGAA
226049 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
226113 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAA-TATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
226177 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
226242 GG-A
196 GGAA
226245 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
226309 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA-
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
226373 AATATGTCTAAATAATGTGTCGACACT-A-ATAG-TTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
226435 GGAA
196 GGAA
226439 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCC-AAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
226502 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
226567 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
226632 GGAA
196 GGAA
226636 AACAAGGTGCACCCATAAAGTGTCGATCC-TATATAAAAAGTGTCGAT-CCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
226699 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
226764 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
226829 GG-A
196 GGAA
226832 AACAAGGTGCACCCAT-AAGTG-CGATCCATATATAAAAAGTGTCGATCCC-AAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
226894 CAAAAGTATAATGTAATATGT-ATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
226958 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
227023 GG-A
196 GGAA
*
227026 AACAAGGTGTACCCATAAAGTGTCGATCCATATATAACAAAGTGTCGATCCCAAAATCATCGAAC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAA-AAAGTGTCGATCCCAAAATCATCGAAC
227091 CCAAAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
227155 GAATATGTCTAAATAATGT-TCGACACT-A-ATAGTTTGTGTCGATACT
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
227201 AATTTAATAT
Statistics
Matches: 1320, Mismatches: 5, Indels: 48
0.96 0.00 0.03
Matches are distributed among these distances:
193 124 0.09
194 259 0.20
195 140 0.11
196 240 0.18
197 340 0.26
198 156 0.12
199 61 0.05
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (199 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
GGAA
Found at i:226574 original size:390 final size:394
Alignment explanation
Indices: 225656--227200 Score: 2856
Period size: 390 Copynumber: 3.9 Consensus size: 394
225646 CAATATGGCC
* *
225656 AACAGGGTGCACCCATAAAGTGTCGATCC-TATATAAAAAGTGTCAATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
225720 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATATACCGGTTTTATGAGAGA
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATATACCGGTTTTATGAGAGA
225785 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATG
131 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATG
225850 GAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCG
196 GAAAACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCG
225915 AACCCAAAAGTATAATGTAATATGTAATTTTCAATCTAACCGGTACAATTATACCGG-TTTATGA
260 AACCCAAAAGTATAATGTAATATGTAATTTTCAATCTAACCGGTACAATTATACCGGTTTTATGA
*
225979 GAGAATATGTCTAAATAATGTGTCGACACTAATAGTTTGTGTCGATACTTTTTTCCCAGAATGGA
325 GAGAATATGTCTAAATAATGTGTCGACACTAATAGTTTGTGTCGATACTTTTTTCCCAGAATGAA
226044 TGGAA
390 TGGAA
226049 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
226113 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATATACCGGTTTTATGAGAGA
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATATACCGGTTTTATGAGAGA
226178 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATG
131 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATG
226243 G-AAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAATCATCGA
196 GAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGA
226306 ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGA
261 ACCCAAAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGA
226371 GA-AATATGTCTAAATAATGTGTCGACACTAATAG-TTGTGTCGATACTTTTTTCCCAGAATGAA
325 GAGAATATGTCTAAATAATGTGTCGACACTAATAGTTTGTGTCGATACTTTTTTCCCAGAATGAA
226434 TGGAA
390 TGGAA
226439 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCC-AAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
226502 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAA-TATACCGGTTTTATGAGAG
226567 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
130 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
226632 GGAAAACAAGGTGCACCCATAAAGTGTCGATCC-TATATAAAAAGTGTCGAT-CCAAAATCATCG
195 GGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
226695 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
260 AACCCAAAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
226760 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAAT
324 AGAGAATATGTCTAAATAATGTGTCGACACT-A-ATAGTTTGTGTCGATACTTTTTTCCCAGAAT
226825 GAATGG-A
387 GAATGGAA
226832 AACAAGGTGCACCCAT-AAGTG-CGATCCATATATAAAAAGTGTCGATCCC-AAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
226894 CAAAAGTATAATGTAATATGT-ATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAA-TATACCGGTTTTATGAGAG
226958 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
130 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
*
227023 GG-AAACAAGGTGTACCCATAAAGTGTCGATCCATATATAACAAAGTGTCGATCCCAAAATCATC
195 GGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAA-AAAGTGTCGATCCCAAAATCATC
227087 GAACCCAAAAGTATAATGTAATATGTAATTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
259 GAACCCAAAAGTATAATGTAATATGTAATTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
227152 AGAGAATATGTCTAAATAATGT-TCGACACTAATAGTTTGTGTCGATACT
324 AGAGAATATGTCTAAATAATGTGTCGACACTAATAGTTTGTGTCGATACT
227201 AATTTAATAT
Statistics
Matches: 1134, Mismatches: 4, Indels: 32
0.97 0.00 0.03
Matches are distributed among these distances:
389 78 0.07
390 330 0.29
391 272 0.24
392 170 0.15
393 247 0.22
394 37 0.03
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (394 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATATACCGGTTTTATGAGAGA
ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATG
GAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGA
ACCCAAAAGTATAATGTAATATGTAATTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
AGAATATGTCTAAATAATGTGTCGACACTAATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
GGAA
Found at i:228654 original size:3 final size:3
Alignment explanation
Indices: 228646--228716 Score: 72
Period size: 3 Copynumber: 24.0 Consensus size: 3
228636 TGAAGCTGAC
* * * ** *
228646 GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GA- GAT GAT GAC GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
228693 GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT
228717 CCAACAAGTA
Statistics
Matches: 54, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
2 2 0.04
3 52 0.96
ACGTcount: A:0.34, C:0.06, G:0.35, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:230190 original size:180 final size:181
Alignment explanation
Indices: 229888--230566 Score: 1089
Period size: 180 Copynumber: 3.8 Consensus size: 181
229878 CAAAGTTTTC
* * * *
229888 ACACTTTTTAATA-T-TGTCTGTACTTTATGTCCAGAATGAAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
* *
229951 AAAAAGTGTCG--ATTGAAAAAACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAAT
66 AAAAAGTGTCGACATT---TACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGT-AT
*
230014 ATAACCGGTATAAATATA-CGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
127 ATAACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
230068 ACACTTTCTAATA-TGTGTCGGTACTTT-TGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
230131 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTA-ATA
66 -AAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTATATA
*
230195 ACC-GTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCA
130 ACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
230246 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATT-GAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
*
230310 AAAAAGTGTCGACATTT--ACATCGGAACCCATATTTATAATGTAATAGATAATTTT-TATA-AA
66 AAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTATATAA
*
230371 CCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTTTATCG
131 CCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
* *
230422 ACACTTTCTAATATTGTGTCGGTACTTTATGTTCAGATTGGAAGAAAAATATGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
230487 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
66 -AAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGT-ATAT
230552 AACCGGTATAAAAAT
129 AACCGGTATAAAAAT
230567 GTGTCGTACC
Statistics
Matches: 469, Mismatches: 14, Indels: 29
0.92 0.03 0.06
Matches are distributed among these distances:
175 6 0.01
176 122 0.26
177 34 0.07
178 88 0.19
179 40 0.09
180 135 0.29
181 23 0.05
182 3 0.01
183 18 0.04
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (181 bp):
ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
AAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTATATAA
CCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:233713 original size:21 final size:23
Alignment explanation
Indices: 233663--233724 Score: 83
Period size: 21 Copynumber: 2.8 Consensus size: 23
233653 AATAGTAAAC
*
233663 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* *
233686 ATATAATGTAATAGGTA-TCGTT
1 ATATAATGTAATAGGTAGCCCTT
233708 -TATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
233725 TGGTTATATT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 16 0.46
22 3 0.09
23 16 0.46
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.37
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:233731 original size:21 final size:21
Alignment explanation
Indices: 233687--233738 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
233677 GTAGCCCTTA
*
233687 TATAATGTAATAGGTATCGTT
1 TATAATGTAATAGGTATCGGT
233708 TATAATGTAATAGGTAGT-GGT
1 TATAATGTAATAGGTA-TCGGT
*
233729 TATATTGTAA
1 TATAATGTAA
233739 AGTGTCTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.21, T:0.42
Consensus pattern (21 bp):
TATAATGTAATAGGTATCGGT
Found at i:234141 original size:22 final size:23
Alignment explanation
Indices: 234088--234153 Score: 91
Period size: 22 Copynumber: 3.0 Consensus size: 23
234078 GTAAACATTG
* *
234088 ATGTAATA-GTAGCCCTTATATA
1 ATGTAATAGGTAGTCGTTATATA
234110 ATGTAATAGGTA-TCGTTATATA
1 ATGTAATAGGTAGTCGTTATATA
*
234132 ATGTAATAGGTAGTGGTTATAT
1 ATGTAATAGGTAGTCGTTATAT
234154 TGTAAAGTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
22 28 0.72
23 11 0.28
ACGTcount: A:0.35, C:0.06, G:0.20, T:0.39
Consensus pattern (23 bp):
ATGTAATAGGTAGTCGTTATATA
Found at i:234725 original size:18 final size:18
Alignment explanation
Indices: 234704--234740 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
234694 GTAATTGGAG
234704 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
234722 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
234740 T
1 T
234741 ATATTTCGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Done.