Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397259.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_147.0, 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: 10737078
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 75620 characters in sequence are not A, C, G, or T
File 1 of 22
Found at i:5477 original size:14 final size:14
Alignment explanation
Indices: 5458--5491 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5448 GCAATATATT
*
5458 TCTCTTGCTTTCTC
1 TCTCTTGCGTTCTC
*
5472 TCTCTTTCGTTCTC
1 TCTCTTGCGTTCTC
5486 TCTCTT
1 TCTCTT
5492 TTTACCCAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.00, C:0.35, G:0.06, T:0.59
Consensus pattern (14 bp):
TCTCTTGCGTTCTC
Found at i:6624 original size:167 final size:167
Alignment explanation
Indices: 6342--6678 Score: 523
Period size: 167 Copynumber: 2.0 Consensus size: 167
6332 ACTCCTGAAT
* *
6342 AAGAAATTGAATTAATACTGCCCAAAAGGGTCTCCCATAATTTCATTTTCTTCCTTTGTATACTT
1 AAGAAATTGAATTAATACTACCCAAAAGGGTCTCCCATAATTTCATTTTCTTCCTTTATATACTT
* *
6407 TTACAGTCGTTATCTTATGGAAGAAGTTCTGGTTATTTGTTGTTTAGGATATATGTATCTTCTTT
66 TTACACTCATTATCTTATGGAAGAAGTTCTGGTTATTTGTTGTTTAGGATATATGTATCTTCTTT
6472 GACCTTGTATGTTTGTCTATACTTGTTATCCTCGCAG
131 GACCTTGTATGTTTGTCTATACTTGTTATCCTCGCAG
* * * * * *
6509 AAGAAGTTGAATTTATGCTACCC-AAATGGTCTCCCATAATTTCATTTTCTTCCTTTATTTGCTT
1 AAGAAATTGAATTAATACTACCCAAAAGGGTCTCCCATAATTTCATTTTCTTCCTTTATATACTT
* *
6573 TTGCACTCATTATCCTTATGGAAGAAGTTGTGGTTATTTGTTGTTTAGGATATATGTATCTTCTT
66 TTACACTCATTAT-CTTATGGAAGAAGTTCTGGTTATTTGTTGTTTAGGATATATGTATCTTCTT
* * *
6638 TGATCTTGTATGTTTGTCTATACTTGTTATCTTTGCAG
130 TGACCTTGTATGTTTGTCTATACTTGTTATCCTCGCAG
6676 AAG
1 AAG
6679 TTGTGGCTAA
Statistics
Matches: 154, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
166 47 0.31
167 107 0.69
ACGTcount: A:0.23, C:0.15, G:0.16, T:0.45
Consensus pattern (167 bp):
AAGAAATTGAATTAATACTACCCAAAAGGGTCTCCCATAATTTCATTTTCTTCCTTTATATACTT
TTACACTCATTATCTTATGGAAGAAGTTCTGGTTATTTGTTGTTTAGGATATATGTATCTTCTTT
GACCTTGTATGTTTGTCTATACTTGTTATCCTCGCAG
Found at i:14110 original size:80 final size:80
Alignment explanation
Indices: 13976--14129 Score: 227
Period size: 80 Copynumber: 1.9 Consensus size: 80
13966 TTTTCTAAAT
* * * * *
13976 CTTCTGTTCCAGCATAAATCTAGTCCTTGATATAAAGTCCATAGTTGTACTGATAGTGAAAAAGA
1 CTTCTGTTCCAACATAAATCTAATCCTTGATATAAAGTCCACAATTCTACTGATAGTGAAAAAGA
14041 GAGCCTTATCTCAAC
66 GAGCCTTATCTCAAC
* * *
14056 CTTCTGTTCTAACATAATTCTAATCCTTGATATAAAGTCCACAATTCTATTGATAGTGAAAAAGA
1 CTTCTGTTCCAACATAAATCTAATCCTTGATATAAAGTCCACAATTCTACTGATAGTGAAAAAGA
*
14121 GATCCTTAT
66 GAGCCTTAT
14130 ATTATCTGCA
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
80 65 1.00
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.34
Consensus pattern (80 bp):
CTTCTGTTCCAACATAAATCTAATCCTTGATATAAAGTCCACAATTCTACTGATAGTGAAAAAGA
GAGCCTTATCTCAAC
Found at i:24871 original size:22 final size:22
Alignment explanation
Indices: 24857--24899 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
24847 TGAACAATAA
24857 AAATAGTAAAAATGAAAAAAAAC
1 AAATA-TAAAAATGAAAAAAAAC
*
24880 AAATAT-AAAATAAAAAAAAA
1 AAATATAAAAATGAAAAAAAA
24900 GAAAAATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 13 0.68
22 1 0.05
23 5 0.26
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (22 bp):
AAATATAAAAATGAAAAAAAAC
Found at i:29873 original size:102 final size:102
Alignment explanation
Indices: 29762--29951 Score: 242
Period size: 102 Copynumber: 1.9 Consensus size: 102
29752 CTATTGGTTG
* * *
29762 CAAGTTTTATCACTCATTCTTTAACCATAGCTT-ATCATTCATATTTCAGCCACG-AGCTTTACC
1 CAAGCTTTATCACTCATTCTTTAACCATA-ATTCATCACTCATATTTCA-CC-CGTAGCTTTACC
29825 ACTCAT-ATTTGGCTACAATGATATATTTTCTATAGGTCA
63 ACTCATAATTTGGCTACAATGATATATTTTCTATAGGTCA
* ** *
29864 CAAGCTTTATCGCTCATTCTTTAACGGTAATTCATCACTCATATTTCACCCGTTAGCTTTATCAC
1 CAAGCTTTATCACTCATTCTTTAACCATAATTCATCACTCATATTTCACCCG-TAGCTTTACCAC
* *
29929 TCATAATTTGTCTATAATGATAT
65 TCATAATTTGGCTACAATGATAT
29952 TATGCTATTG
Statistics
Matches: 75, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
100 2 0.03
101 4 0.05
102 53 0.71
103 16 0.21
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (102 bp):
CAAGCTTTATCACTCATTCTTTAACCATAATTCATCACTCATATTTCACCCGTAGCTTTACCACT
CATAATTTGGCTACAATGATATATTTTCTATAGGTCA
Found at i:29973 original size:102 final size:100
Alignment explanation
Indices: 29737--29983 Score: 239
Period size: 102 Copynumber: 2.4 Consensus size: 100
29727 ATACTTAGAT
* * * * * *
29737 TACAATGACATTATGCTATTGGTTGCAAGTTTTATCACTCATTCTTTAACCATAGCTTATCATTC
1 TACAATGATATTATGCTATT-GCTGCAAGCTTTATCGCTCATTCTTTAACCATAGATTATCACTC
29802 ATATTTCAGCCACGAGCTTTACCACTCATATTTGGC
65 ATATTTCAGCCACGAGCTTTACCACTCATATTTGGC
* * * * * **
29838 TACAATGATATATTTTCTATAGGTCACAAGCTTTATCGCTCATTCTTTAACGGTA-ATTCATCAC
1 TACAATGATAT-TATGCTATTGCT-GCAAGCTTTATCGCTCATTCTTTAACCATAGATT-ATCAC
* *
29902 TCATATTTCA-CC-CGTTAGCTTTATCACTCATAATTTGTC
63 TCATATTTCAGCCACG--AGCTTTACCACTCAT-ATTTGGC
* * *
29941 TATAATGATATTATGCTATTGACTGCATGCTTTATAGCTCATT
1 TACAATGATATTATGCTATTG-CTGCAAGCTTTATCGCTCATT
29984 TCTTGGCCCT
Statistics
Matches: 117, Mismatches: 22, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
100 2 0.02
101 16 0.14
102 82 0.70
103 17 0.15
ACGTcount: A:0.27, C:0.21, G:0.11, T:0.40
Consensus pattern (100 bp):
TACAATGATATTATGCTATTGCTGCAAGCTTTATCGCTCATTCTTTAACCATAGATTATCACTCA
TATTTCAGCCACGAGCTTTACCACTCATATTTGGC
Found at i:32037 original size:15 final size:15
Alignment explanation
Indices: 32017--32143 Score: 67
Period size: 15 Copynumber: 8.4 Consensus size: 15
32007 AGAGAGTAAA
*
32017 ATGTTACTGCCTAAG
1 ATGTTACTACCTAAG
* *
32032 ATGTTATTACTTAAG
1 ATGTTACTACCTAAG
* *
32047 GTGTTACTATCTAAG
1 ATGTTACTACCTAAG
* *
32062 ATATTACTATCTAA-
1 ATGTTACTACCTAAG
* *
32076 AGTGTTATTACTTAAAG
1 A-TGTTACTACCT-AAG
* *
32093 ACGTTACTATCTAAG
1 ATGTTACTACCTAAG
* * * ** *
32108 GTATTATTGTCTAAA
1 ATGTTACTACCTAAG
32123 ATGTTACTACCTAAG
1 ATGTTACTACCTAAG
*
32138 GTGTTA
1 ATGTTA
32144 TAGCACAAAG
Statistics
Matches: 79, Mismatches: 30, Indels: 6
0.69 0.26 0.05
Matches are distributed among these distances:
14 1 0.01
15 68 0.86
16 9 0.11
17 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (15 bp):
ATGTTACTACCTAAG
Found at i:32113 original size:46 final size:45
Alignment explanation
Indices: 32027--32137 Score: 132
Period size: 46 Copynumber: 2.4 Consensus size: 45
32017 ATGTTACTGC
* **
32027 CTAAGATGTTATTACTTAAGGTGTTACTATCTAAGATATTACTAT
1 CTAAAATGTTATTACTTAAGACGTTACTATCTAAGATATTACTAT
* * * *
32072 CTAAAGTGTTATTACTTAAAGACGTTACTATCTAAGGTATTATTGT
1 CTAAAATGTTATTACTT-AAGACGTTACTATCTAAGATATTACTAT
* *
32118 CTAAAATGTTACTACCTAAG
1 CTAAAATGTTATTACTTAAG
32138 GTGTTATAGC
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
45 18 0.33
46 37 0.67
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.40
Consensus pattern (45 bp):
CTAAAATGTTATTACTTAAGACGTTACTATCTAAGATATTACTAT
Found at i:32369 original size:18 final size:18
Alignment explanation
Indices: 32348--32404 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
32338 GAAAACACTC
32348 AAAACAATTAGAACAAGT
1 AAAACAATTAGAACAAGT
** *
32366 AAAAC-ATT-GTTTCATGT
1 AAAACAATTAG-AACAAGT
32383 AAAACAATTAGAACAAGT
1 AAAACAATTAGAACAAGT
32401 AAAA
1 AAAA
32405 TACTAGTTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
16 1 0.03
17 12 0.40
18 16 0.53
19 1 0.03
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.23
Consensus pattern (18 bp):
AAAACAATTAGAACAAGT
Found at i:36304 original size:3 final size:3
Alignment explanation
Indices: 36296--36326 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
36286 TTGCTTAAGC
*
36296 ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
36327 AATTTCCCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:39307 original size:21 final size:21
Alignment explanation
Indices: 39281--39326 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
39271 GTGGTTTGGG
*
39281 TGAGTGTTCTTGGGACGTTAT
1 TGAGTGTTCTTGGGAAGTTAT
39302 TGAGTGTTCTTGGGAAGTTAT
1 TGAGTGTTCTTGGGAAGTTAT
39323 TGAG
1 TGAG
39327 AAAGAGTGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.17, C:0.07, G:0.35, T:0.41
Consensus pattern (21 bp):
TGAGTGTTCTTGGGAAGTTAT
Found at i:40784 original size:29 final size:29
Alignment explanation
Indices: 40742--40804 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
40732 TTGGTCCATA
40742 AGAGCAATTTGTCACTCTAAAGATCCTCT
1 AGAGCAATTTGTCACTCTAAAGATCCTCT
40771 AGAGCAATTTGTCACTCTAAAGATCCTCT
1 AGAGCAATTTGTCACTCTAAAGATCCTCT
40800 AGAGC
1 AGAGC
40805 TTCCAGCTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.29
Consensus pattern (29 bp):
AGAGCAATTTGTCACTCTAAAGATCCTCT
Found at i:43991 original size:17 final size:17
Alignment explanation
Indices: 43969--44004 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
43959 TTTTTTTTAA
*
43969 AAAAAATAAAATAAAAT
1 AAAAAATAAAAAAAAAT
43986 AAAAAATAAAAAAAAAT
1 AAAAAATAAAAAAAAAT
44003 AA
1 AA
44005 TTAAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (17 bp):
AAAAAATAAAAAAAAAT
Found at i:43998 original size:14 final size:14
Alignment explanation
Indices: 43967--44014 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
43957 CATTTTTTTT
43967 AAAAAAAATAAA-A
1 AAAAAAAATAAATA
*
43980 TAAAATAAA-AAATA
1 -AAAAAAAATAAATA
*
43994 AAAAAAAATAATTA
1 AAAAAAAATAAATA
44008 AAAAAAA
1 AAAAAAA
44015 CTGAATAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 10 0.34
14 19 0.66
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (14 bp):
AAAAAAAATAAATA
Found at i:49106 original size:21 final size:22
Alignment explanation
Indices: 49039--49106 Score: 81
Period size: 21 Copynumber: 3.1 Consensus size: 22
49029 TATTTCATTT
49039 TATTTATTATTA-TAATATTTTA
1 TATTTA-TATTATTAATATTTTA
49061 TAATTTAT-TT-TTAATATCTTTA
1 T-ATTTATATTATTAATAT-TTTA
49083 TATTTATATTATTAAT-TTTTA
1 TATTTATATTATTAATATTTTA
49104 TAT
1 TAT
49107 AATATCATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
21 21 0.51
22 10 0.24
23 10 0.24
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (22 bp):
TATTTATATTATTAATATTTTA
Found at i:50436 original size:20 final size:20
Alignment explanation
Indices: 50398--50437 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
50388 NNNNNNNNCT
* *
50398 CATCATACATTTAATCATCC
1 CATCATACATTCAAACATCC
*
50418 CATCATCCATTCAAACATCC
1 CATCATACATTCAAACATCC
50438 TTCAAATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.30
Consensus pattern (20 bp):
CATCATACATTCAAACATCC
Found at i:53946 original size:16 final size:17
Alignment explanation
Indices: 53921--53958 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
53911 ATCAATCAAT
*
53921 AAAAATAAAAAATAAAG
1 AAAAATAAAAAAGAAAG
*
53938 AAAAA-AAAAGAGAAAG
1 AAAAATAAAAAAGAAAG
53954 AAAAA
1 AAAAA
53959 GTGAGTGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (17 bp):
AAAAATAAAAAAGAAAG
Found at i:55255 original size:22 final size:22
Alignment explanation
Indices: 55205--55260 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
55195 GAGCAACCTT
* **
55205 TTCTTTAAAACCTCTGGGTACA
1 TTCTTCAAAACCTCCAGGTACA
*
55227 -TCTTCAAAACCTCCAGGTATA
1 TTCTTCAAAACCTCCAGGTACA
55248 TTCTTCAAAACCT
1 TTCTTCAAAACCT
55261 TGAGGTAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 17 0.59
22 12 0.41
ACGTcount: A:0.30, C:0.27, G:0.09, T:0.34
Consensus pattern (22 bp):
TTCTTCAAAACCTCCAGGTACA
Found at i:55266 original size:22 final size:22
Alignment explanation
Indices: 55205--55267 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
55195 GAGCAACCTT
*
55205 TTCTTTAAAACCTCTG-GGTACA
1 TTCTTCAAAACCT-TGAGGTACA
** *
55227 -TCTTCAAAACCTCCAGGTATA
1 TTCTTCAAAACCTTGAGGTACA
55248 TTCTTCAAAACCTTGAGGTA
1 TTCTTCAAAACCTTGAGGTA
55268 ATTAGTTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
21 16 0.48
22 17 0.52
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (22 bp):
TTCTTCAAAACCTTGAGGTACA
Found at i:55358 original size:21 final size:21
Alignment explanation
Indices: 55329--55368 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
55319 AGCAACCTTT
*
55329 TCTTTAAAACCTCCAGGTACA
1 TCTTCAAAACCTCCAGGTACA
*
55350 TCTTCAAAACCTCCGGGTA
1 TCTTCAAAACCTCCAGGTA
55369 ATTAGTTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.30, G:0.12, T:0.28
Consensus pattern (21 bp):
TCTTCAAAACCTCCAGGTACA
Found at i:55408 original size:101 final size:101
Alignment explanation
Indices: 55227--55469 Score: 335
Period size: 101 Copynumber: 2.4 Consensus size: 101
55217 TCTGGGTACA
* * *
55227 TCTTCAAAACCTCCAGGTATATTCTTCAAAACCT-TGAGGTAATTAGTTTTTAGATTTCATTAAA
1 TCTTTAAAACCTCCAGGTACA-TCTTCAAAACCTCTG-GGTAATTAGTTTTCAGATTTCATTAAA
* * * *
55291 AGTTATGTAGCCTCATTTGCAGATGATGAGCAACCTTT
64 AGTTATGTAGCCTCATTGGCAGATAAGGAGCAACATTT
* *
55329 TCTTTAAAACCTCCAGGTACATCTTCAAAACCTCCGGGTAATTAGTTTTCAGATTTTATTAAAAG
1 TCTTTAAAACCTCCAGGTACATCTTCAAAACCTCTGGGTAATTAGTTTTCAGATTTCATTAAAAG
*
55394 TTATGTAGCCTCATTGGGAGATAAGGAGCAACATTT
66 TTATGTAGCCTCATTGGCAGATAAGGAGCAACATTT
* ***
55430 TCTTTAAAATCTTTGGGTACATCTTCAAAACCTCTGGGTA
1 TCTTTAAAACCTCCAGGTACATCTTCAAAACCTCTGGGTA
55470 TATCCTTCAA
Statistics
Matches: 125, Mismatches: 15, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
101 105 0.84
102 20 0.16
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (101 bp):
TCTTTAAAACCTCCAGGTACATCTTCAAAACCTCTGGGTAATTAGTTTTCAGATTTCATTAAAAG
TTATGTAGCCTCATTGGCAGATAAGGAGCAACATTT
Found at i:55480 original size:22 final size:21
Alignment explanation
Indices: 55443--55485 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
55433 TTAAAATCTT
55443 TGGGTACATCTTCAAAACCTC
1 TGGGTACATCTTCAAAACCTC
*
55464 TGGGTATATCCTTCAAAACCTC
1 TGGGTACAT-CTTCAAAACCTC
55486 CAAGTAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (21 bp):
TGGGTACATCTTCAAAACCTC
Found at i:55485 original size:123 final size:122
Alignment explanation
Indices: 55329--55561 Score: 349
Period size: 123 Copynumber: 1.9 Consensus size: 122
55319 AGCAACCTTT
* ** * *
55329 TCTTTAAAACCTCCAGGTACATCTTCAAAACCTCCGGGTAATTAGTTTTCAGATTTTATTAAAAG
1 TCTTCAAAACCTCCAGGTACATCTTCAAAACCTCCAAGTAATTAGTTTCCAGATTTCATTAAAAG
* *
55394 TTATGTAGCCTCATTGGGAGATAAGGAGCAACATTTTCTTTAAAATCTTTGGGTACA
66 TTACGTAGCCTCATTGGGAGATAAGGAGCAACATTTTATTTAAAATCTTTGGGTACA
** *
55451 TCTTCAAAACCTCTGGGTATATCCTTCAAAACCTCCAAGTAATTAGTTTCCAGATTTCATTAAAA
1 TCTTCAAAACCTCCAGGTACAT-CTTCAAAACCTCCAAGTAATTAGTTTCCAGATTTCATTAAAA
* *
55516 GTTACGTAGCCTCATTTGGAGATGAGGAGCAACATTTTATTTAAAA
65 GTTACGTAGCCTCATTGGGAGATAAGGAGCAACATTTTATTTAAAA
55562 ACCTCCGAGT
Statistics
Matches: 98, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
122 18 0.18
123 80 0.82
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Consensus pattern (122 bp):
TCTTCAAAACCTCCAGGTACATCTTCAAAACCTCCAAGTAATTAGTTTCCAGATTTCATTAAAAG
TTACGTAGCCTCATTGGGAGATAAGGAGCAACATTTTATTTAAAATCTTTGGGTACA
Found at i:55831 original size:20 final size:19
Alignment explanation
Indices: 55786--55843 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
55776 TCTTTTTTTT
55786 AAAAATAATAA-TAATAAATA
1 AAAAAT-ATAATTAA-AAATA
*
55806 ATAAATATAATTAAAAATTA
1 AAAAATATAATTAAAAA-TA
55826 AAAAATATAATTTAAAAA
1 AAAAATATAA-TTAAAAA
55844 AAAGTTGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
19 7 0.21
20 19 0.58
21 7 0.21
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAATATAATTAAAAATA
Found at i:58070 original size:189 final size:189
Alignment explanation
Indices: 57698--58088 Score: 534
Period size: 189 Copynumber: 2.1 Consensus size: 189
57688 CGAGCATAGG
* *
57698 CCCGATGATGGGACTTTCTGAGGAAGCTTGCGAAGGCGAGTTTCTTCGGTAAACTCCCTAAGTGA
1 CCCGATGATGGGACTTTCCGAGCAAGCTTGCGAAGGCGAGTTTCTTCGGTAAACTCCCTAAGTGA
* * * *
57763 AAAAGTTACTTTCGAATCCCACTAGTACGATGAGAGGGTTCAAAAAATATCTTTAATAAAAAAAC
66 AAAAGATACTTCCGAATCCCACCAGTACGATGAGAAGGTTCAAAAAATATCTTTAATAAAAAAAC
* * * *
57828 TTTTGCTTGTATTAGGATTTACATTCATGAAAACATCGTTTTTACTTGCAAACGATTA-
131 TTTTGCTCGTATTAGGATTTACATTCATGAAAACATCATTTTTACTCGCAAACGACTAT
* * * *
57886 CCACGATGATGGGGCTTTCCGAGCAAGCTTGCGAAGGTGAGTTTCTTCGGTAAACTCCGTAGGTG
1 CC-CGATGATGGGACTTTCCGAGCAAGCTTGCGAAGGCGAGTTTCTTCGGTAAACTCCCTAAGTG
* * *
57951 AAAAAGATACTTCCGGATCCCACCAGTACGATGGGAAGGTTCAGATAAATATCTTTAAT-AAAAA
65 AAAAAGATACTTCCGAATCCCACCAGTACGATGAGAAGGTTCA-AAAAATATCTTTAATAAAAAA
* * * ** * *
58015 GCTTTTGCTCGTATTAGGATTTGCATTCGTGAAAATGTTATTTTTTCTCGCAAACGACTAT
129 ACTTTTGCTCGTATTAGGATTTACATTCATGAAAACATCATTTTTACTCGCAAACGACTAT
58076 CCCGATGATGGGA
1 CCCGATGATGGGA
58089 TCTACTCGTT
Statistics
Matches: 175, Mismatches: 25, Indels: 5
0.85 0.12 0.02
Matches are distributed among these distances:
188 2 0.01
189 157 0.90
190 16 0.09
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (189 bp):
CCCGATGATGGGACTTTCCGAGCAAGCTTGCGAAGGCGAGTTTCTTCGGTAAACTCCCTAAGTGA
AAAAGATACTTCCGAATCCCACCAGTACGATGAGAAGGTTCAAAAAATATCTTTAATAAAAAAAC
TTTTGCTCGTATTAGGATTTACATTCATGAAAACATCATTTTTACTCGCAAACGACTAT
Found at i:58140 original size:189 final size:189
Alignment explanation
Indices: 57700--58163 Score: 438
Period size: 189 Copynumber: 2.5 Consensus size: 189
57690 AGCATAGGCC
* * * * * * * * * * *
57700 CGATGATGGGACTTTCTGAGGAAGCTTGCGAAGGCGAGTTTCTTCGGTAAACTCCCTAAGTGAAA
1 CGATGATGGGGCTCTCCGAGCAAACTTACGAAGGTGAATTTCATCGGCAAACTCCCTAGGTGAAA
* * * * *
57765 AAGTTACTTTCGAATCCCACTAGTACGATGAGAGGGTTCAAAAAATATCTTTAATAAAAAAACTT
66 AAGATACTTCCGGATCCCACCAGTACGATGAGAAGGTTCAAAAAATATCTTTAATAAAAAAACTT
* * * *
57830 TTGCTTGTATTAGGATTTACATTCATGAAAACATCGTTTTTACTTGCAAACGATTACCA
131 TTGCTCGTATTAGGATTTACATTCATGAAAACATCATTTTTACTCGCAAACGACTACCA
* * * * * * *
57889 CGATGATGGGGCTTTCCGAGCAAGCTTGCGAAGGTGAGTTTCTTCGGTAAACTCCGTAGGTGAAA
1 CGATGATGGGGCTCTCCGAGCAAACTTACGAAGGTGAATTTCATCGGCAAACTCCCTAGGTGAAA
* * *
57954 AAGATACTTCCGGATCCCACCAGTACGATGGGAAGGTTCAGATAAATATCTTTAAT-AAAAAGCT
66 AAGATACTTCCGGATCCCACCAGTACGATGAGAAGGTTCA-AAAAATATCTTTAATAAAAAAACT
* * ** * *
58018 TTTGCTCGTATTAGGATTTGCATTCGTGAAAATGTTATTTTTTCTCGCAAACGACTATCC-
130 TTTGCTCGTATTAGGATTTACATTCATGAAAACATCATTTTTACTCGCAAACGACTA-CCA
* ** **
58078 CGATGAT-GGGATCTACTCG-TTAAACTTACGAAGGTGAATTT-ATCGGGCATTCTCCCTAGGTG
1 CGATGATGGGGCTCT-C-CGAGCAAACTTACGAAGGTGAATTTCATC-GGCAAACTCCCTAGGTG
* *
58140 -AGAGGATAC-TCTCGGATCCCACCA
63 AAAAAGATACTTC-CGGATCCCACCA
58164 ACATGATGGG
Statistics
Matches: 231, Mismatches: 38, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
187 2 0.01
188 26 0.11
189 185 0.80
190 18 0.08
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (189 bp):
CGATGATGGGGCTCTCCGAGCAAACTTACGAAGGTGAATTTCATCGGCAAACTCCCTAGGTGAAA
AAGATACTTCCGGATCCCACCAGTACGATGAGAAGGTTCAAAAAATATCTTTAATAAAAAAACTT
TTGCTCGTATTAGGATTTACATTCATGAAAACATCATTTTTACTCGCAAACGACTACCA
Found at i:78553 original size:231 final size:226
Alignment explanation
Indices: 78268--78688 Score: 587
Period size: 227 Copynumber: 1.8 Consensus size: 226
78258 GAAATAATTA
*
78268 AATTTTAAATCTTAACGTAAATGTATGAGAGTTAACGTAAAAAGTAATTTAAATAAAAAAATCAA
1 AATTTTAAATCTTAACATAAATGTATGAGAGTTAACGTAAAAAGTAATTTAAATAAAAAAATCAA
*
78333 ATTTTAGTAAAAAACAAACATTTAAATTTATATTCT-TGGACTT-AAAGTATTTAATGATATACA
66 ATTTTA--AAAAAA-AAA-ATTTAAATTTATATTCTCTGG--TTAAAAGTATTTAACGATATACA
*
78396 AATACTAATTTTTAAAGAAAGAAAAATAAGAATAAAAATAATTATAGTTCAAAATTGACATAAGA
125 AATACTAACTTTTAAAGAAAGAAAAATAAGAATAAAAATAATTATAGTTCAAAATTGACAT-AGA
78461 AAGCTTTGCCATAAAAACTTATAAAGGAGGAATAAACC
189 AAGCTTTGCCATAAAAACTTATAAAGGAGGAATAAACC
* * * * *
78499 AATTTTAAATCTTAACATAAATGTCTGAGGGTTAACGTTACAAGTTAA-TTAAATAAAAAAATCT
1 AATTTTAAATCTTAACATAAATGTATGAGAGTTAACGTAAAAAG-TAATTTAAATAAAAAAATCA
** * * **
78563 AATTTTAATGAAAAAAATTTAAGTTTATATTTTCTGGTTAAAAGTATTTAACGATATACAAATTT
65 AATTTTAAAAAAAAAAATTTAAATTTATATTCTCTGGTTAAAAGTATTTAACGATATACAAATAC
* * * *
78628 TAACTTTTAAATAAAGAATAATAAGGATAAAAATAATTATAGTTCAAAATTGATATAGAAA
130 TAACTTTTAAAGAAAGAAAAATAAGAATAAAAATAATTATAGTTCAAAATTGACATAGAAA
78689 AGTTTAGATA
Statistics
Matches: 169, Mismatches: 18, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
226 7 0.04
227 88 0.52
228 6 0.04
229 4 0.02
231 61 0.36
232 3 0.02
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (226 bp):
AATTTTAAATCTTAACATAAATGTATGAGAGTTAACGTAAAAAGTAATTTAAATAAAAAAATCAA
ATTTTAAAAAAAAAAATTTAAATTTATATTCTCTGGTTAAAAGTATTTAACGATATACAAATACT
AACTTTTAAAGAAAGAAAAATAAGAATAAAAATAATTATAGTTCAAAATTGACATAGAAAGCTTT
GCCATAAAAACTTATAAAGGAGGAATAAACC
Found at i:79167 original size:250 final size:245
Alignment explanation
Indices: 78472--79215 Score: 850
Period size: 241 Copynumber: 3.0 Consensus size: 245
78462 AGCTTTGCCA
* * ** *
78472 TAAAAACTTATAAAGG-AGGAATAAACCAATTTTAAATCTTAACATAAATGTCTGAGGGTTAACG
1 TAAAAACTTATAAAGGTA-GAATAAACCAATATTAAATCTTAAC-TAAATAT-TGAGAATTAACA
* * * *
78536 TTACAAGTTAATTAAATAAAAAAATCTAATTTTAATG-AAAAAAAT-TTAAGTTTATATTTTCTG
63 TTACAAGTCAATTAAAT-AAAAAATCTAATTTTAATGAAAAAAAATATTAAATTTATATTCTCGG
* * *
78599 GTTAAAAGTATTTAACGATATACAAATTTTAACTTTTAAATAAAGAATAATAAGGATAAAAATAA
127 GTT-AAAGTGTTTAACGATATAAAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAATAA
* * *
78664 TTATAGTTCAAAATTGATATAGAAAAGT-TTAGATATAAAACTATAAGAAATGACG
191 TTATAGTTCAAAATTGACATAGAAAAGTCTT-GACATAAAACTATAAGAATTGACG
* * ** *
78719 TAAAAACTTAGAAAGGT-GAAAAAATTAA-ATTCTAAATCTTAAC---ATA---A-CA-TAACAT
1 TAAAAACTTATAAAGGTAGAATAAACCAATA-T-TAAATCTTAACTAAATATTGAGAATTAACAT
* * ** ** *
78774 AACAAATCAATTAAGGGAAAAAAAGTAATTTCAATGAAAAATAAATATTTAAATTTATATTCTCG
64 TACAAGTCAATTAA-ATAAAAAATCTAATTTTAATGAAAAA-AAATA-TTAAATTTATATTCTCG
* * * * *
78839 GGCTAAAAATGTATAACGATACAAAAATTTTAATTTTTAAATAAAGAATAATAAGGACAAAAATA
126 GG-TTAAAGTGTTTAACGATATAAAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAATA
*
78904 ATTATAGTTCAAAATTGACATAGAAAAGTCTTGACGTAAAACTATAAGAATTGACG
190 ATTATAGTTCAAAATTGACATAGAAAAGTCTTGACATAAAACTATAAGAATTGACG
* *
78960 TAAAAACTTATAAAGGTAGAATAAACGAATATTAAATATTAACGTAAATATGTGAGAATTAACAT
1 TAAAAACTTATAAAGGTAGAATAAACCAATATTAAATCTTAAC-TAAATAT-TGAGAATTAACAT
79025 TACAAGTCAATTAAATAAACGAAATCTAATTTTAATGAAAAAAAATATTCAAATTTATATTCTCG
64 TACAAGTCAATTAAATAAA--AAATCTAATTTTAATGAAAAAAAATATT-AAATTTATATTCTCG
*
79090 GGTTAAAGTGTTTAACGATATATAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAATAA
126 GGTTAAAGTGTTTAACGATATAAAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAATAA
* * * * * **
79155 TTATAATTCAAAATTGACGTAGAAAAATCTTGACATAAAATTGTAAGAATAAACG
191 TTATAGTTCAAAATTGACATAGAAAAGTCTTGACATAAAACTATAAGAATTGACG
79210 TAAAAA
1 TAAAAA
79216 TTTAAAAAAG
Statistics
Matches: 413, Mismatches: 59, Indels: 47
0.80 0.11 0.09
Matches are distributed among these distances:
237 32 0.08
238 4 0.01
239 5 0.01
241 144 0.35
242 12 0.03
243 3 0.01
245 3 0.01
246 9 0.02
247 26 0.06
249 1 0.00
250 116 0.28
251 40 0.10
252 18 0.04
ACGTcount: A:0.51, C:0.07, G:0.11, T:0.31
Consensus pattern (245 bp):
TAAAAACTTATAAAGGTAGAATAAACCAATATTAAATCTTAACTAAATATTGAGAATTAACATTA
CAAGTCAATTAAATAAAAAATCTAATTTTAATGAAAAAAAATATTAAATTTATATTCTCGGGTTA
AAGTGTTTAACGATATAAAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAATAATTATA
GTTCAAAATTGACATAGAAAAGTCTTGACATAAAACTATAAGAATTGACG
Found at i:79254 original size:250 final size:247
Alignment explanation
Indices: 78472--79263 Score: 844
Period size: 250 Copynumber: 3.2 Consensus size: 247
78462 AGCTTTGCCA
* ** * * * * ** *
78472 TAAAAACTTATAAAGGAGGAATAAAC-CAATTTTAAATCTTAACATAAATGTCTGAGGGTTAACG
1 TAAAAACTTAAAAAGGAAAAAT-AACTAAATTTTAAATCTTAACGTAAATATGTGAGAATTAACA
* * * *
78536 TTACAAGTTAATTAAATAAAAAAATCTAATTTTAATG-AAAAAAAT-TTAAGTTTATATTTTCTG
65 TTACAAGTCAATTAAAT-AAAAAATCTAATTTTAATGAAAAAAAATATTAAATTTATATTCTCGG
* * *
78599 GTTAAAAGTATTTAACGATATACAAATTTTAACTTTTAAATAAAGAATAATAAGGATAAAAATAA
129 GTT-AAAGTGTTTAACGATATAAAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAATAA
* *
78664 TTATAGTTCAAAATTGATATAGAAAAGT-TTAGATATAAAACTATAAGAA-ATGACG
193 TTATAGTTCAAAATTGACATAGAAAAGTCTT-GACATAAAACTATAAGAATA-GACG
* * * * *
78719 TAAAAACTTAGAAAGGTGAAAA-AATTAAATTCTAAATCTTAAC----ATA----A-CA-TAACA
1 TAAAAACTTAAAAAGG-AAAAATAACTAAATTTTAAATCTTAACGTAAATATGTGAGAATTAACA
* * ** ** *
78773 TAACAAATCAATTAAGGGAAAAAAAGTAATTTCAATGAAAAATAAATATTTAAATTTATATTCTC
65 TTACAAGTCAATTAA-ATAAAAAATCTAATTTTAATGAAAAA-AAATA-TTAAATTTATATTCTC
* * * * *
78838 GGGCTAAAAATGTATAACGATACAAAAATTTTAATTTTTAAATAAAGAATAATAAGGACAAAAAT
127 GGG-TTAAAGTGTTTAACGATATAAAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAAT
* *
78903 AATTATAGTTCAAAATTGACATAGAAAAGTCTTGACGTAAAACTATAAGAATTGACG
191 AATTATAGTTCAAAATTGACATAGAAAAGTCTTGACATAAAACTATAAGAATAGACG
* * * * * *
78960 TAAAAACTTATAAAGGTAGAATAAAC-GAATATTAAATATTAACGTAAATATGTGAGAATTAACA
1 TAAAAACTTAAAAAGGAAAAAT-AACTAAATTTTAAATCTTAACGTAAATATGTGAGAATTAACA
79024 TTACAAGTCAATTAAATAAACGAAATCTAATTTTAATGAAAAAAAATATTCAAATTTATATTCTC
65 TTACAAGTCAATTAAATAAA--AAATCTAATTTTAATGAAAAAAAATATT-AAATTTATATTCTC
*
79089 GGGTTAAAGTGTTTAACGATATATAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAATA
127 GGGTTAAAGTGTTTAACGATATAAAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAATA
* * * * * *
79154 ATTATAATTCAAAATTGACGTAGAAAAATCTTGACATAAAATTGTAAGAATAAACG
192 ATTATAGTTCAAAATTGACATAGAAAAGTCTTGACATAAAACTATAAGAATAGACG
* * * *
79210 TAAAAATTTAAAAAAGAAAAATAACTAAATTTTAAATTTTAACGTAAATGTGTG
1 TAAAAACTTAAAAAGGAAAAATAACTAAATTTTAAATCTTAACGTAAATATGTG
79264 TTCAAATTTG
Statistics
Matches: 446, Mismatches: 73, Indels: 49
0.79 0.13 0.09
Matches are distributed among these distances:
237 32 0.07
238 4 0.01
239 5 0.01
240 3 0.01
241 145 0.33
242 5 0.01
243 2 0.00
245 3 0.01
246 2 0.00
247 30 0.07
248 2 0.00
249 4 0.01
250 151 0.34
251 40 0.09
252 18 0.04
ACGTcount: A:0.51, C:0.07, G:0.11, T:0.31
Consensus pattern (247 bp):
TAAAAACTTAAAAAGGAAAAATAACTAAATTTTAAATCTTAACGTAAATATGTGAGAATTAACAT
TACAAGTCAATTAAATAAAAAATCTAATTTTAATGAAAAAAAATATTAAATTTATATTCTCGGGT
TAAAGTGTTTAACGATATAAAAATTTTAATTTTTAAATAAAGAATAATAAGGATAAAAATAATTA
TAGTTCAAAATTGACATAGAAAAGTCTTGACATAAAACTATAAGAATAGACG
Found at i:79997 original size:35 final size:35
Alignment explanation
Indices: 79951--80018 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
79941 TTATCAGTGG
79951 TGATAGCCATGTGTAGTGTGAGAGAGCACATGACA
1 TGATAGCCATGTGTAGTGTGAGAGAGCACATGACA
* *
79986 TGATAGCCATGTGTGGTGTGGGAGAGCACATGA
1 TGATAGCCATGTGTAGTGTGAGAGAGCACATGA
80019 ATTTGGTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.28, C:0.13, G:0.35, T:0.24
Consensus pattern (35 bp):
TGATAGCCATGTGTAGTGTGAGAGAGCACATGACA
Found at i:80519 original size:21 final size:21
Alignment explanation
Indices: 80495--80535 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
80485 TTTTATAATG
*
80495 TAAGTATTGATACTTATAGTA
1 TAAGTATTGATACCTATAGTA
*
80516 TAAGTATTGATGCCTATAGT
1 TAAGTATTGATACCTATAGT
80536 CTATTTTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.41
Consensus pattern (21 bp):
TAAGTATTGATACCTATAGTA
Found at i:92042 original size:15 final size:14
Alignment explanation
Indices: 91998--92049 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
91988 TTATTTTAAA
91998 TTTATTTTATTTTT
1 TTTATTTTATTTTT
92012 TCTT-TTTT-TCTTTT
1 T-TTATTTTAT-TTTT
92026 TTTATTTTAATTTTT
1 TTTATTTT-ATTTTT
*
92041 TTTAATTTA
1 TTTATTTTA
92050 GTGAGAGAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
13 3 0.09
14 15 0.47
15 13 0.41
16 1 0.03
ACGTcount: A:0.15, C:0.04, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTATTTTATTTTT
Found at i:118781 original size:2 final size:2
Alignment explanation
Indices: 118774--118803 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
118764 TAGCACAGTT
118774 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
118804 AACTGAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:119378 original size:10 final size:11
Alignment explanation
Indices: 119359--119383 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
119349 GGATTTGGGA
119359 TTTTCTTTTTT
1 TTTTCTTTTTT
119370 TTTTCTTTTTT
1 TTTTCTTTTTT
119381 TTT
1 TTT
119384 AAAAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:121801 original size:3 final size:3
Alignment explanation
Indices: 121793--121818 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
121783 AGAGCCACAT
121793 CAA CAA CAA CAA CAA CAA CAA CAA CA
1 CAA CAA CAA CAA CAA CAA CAA CAA CA
121819 GAAGAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.35, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:124167 original size:18 final size:18
Alignment explanation
Indices: 124132--124167 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
124122 TATAAAAAAA
* *
124132 TTAAAATATTTTTTTTAT
1 TTAAAATATTATTATTAT
124150 TTAAAATATTATTATTAT
1 TTAAAATATTATTATTAT
124168 ATTTTGTAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTAAAATATTATTATTAT
Found at i:129020 original size:17 final size:18
Alignment explanation
Indices: 128992--129026 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
128982 CCTTACCTTG
128992 GCAAGCAAAATCCCAAAT
1 GCAAGCAAAATCCCAAAT
129010 GCAAG-AAAATCCCAAAT
1 GCAAGCAAAATCCCAAAT
129027 TCATCTTGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.51, C:0.26, G:0.11, T:0.11
Consensus pattern (18 bp):
GCAAGCAAAATCCCAAAT
Found at i:130639 original size:25 final size:24
Alignment explanation
Indices: 130588--130635 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
130578 TTTTTAATCA
130588 AATCTTGTGGTTATATGATCAAAT
1 AATCTTGTGGTTATATGATCAAAT
*
130612 AATCTTGTGTGTTATTTG-TCAAAT
1 AATCTTGTG-GTTATATGATCAAAT
130636 TAATATTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.46
Consensus pattern (24 bp):
AATCTTGTGGTTATATGATCAAAT
Found at i:138656 original size:93 final size:94
Alignment explanation
Indices: 138497--138683 Score: 358
Period size: 93 Copynumber: 2.0 Consensus size: 94
138487 GAAGACCAGC
138497 ATAGTTAACTTTCTTCACTAGTGGATGGGAAGAAAGGAACTCAGCAATCTTTTGTGCATTTTCCT
1 ATAGTTAACTTTCTTCACTAGTGGATGGGAAGAAAGGAACTCAGCAATCTTTTGTGCATTTTCCT
*
138562 GTT-AGAGATTCAGAAATGTTAGTTTCAA
66 GTTAAGAGATTCAGAAACGTTAGTTTCAA
138590 ATAGTTAACTTTCTTCACTAGTGGATGGGAAGAAAGGAACTCAGCAATCTTTTGTGCATTTTCCT
1 ATAGTTAACTTTCTTCACTAGTGGATGGGAAGAAAGGAACTCAGCAATCTTTTGTGCATTTTCCT
138655 GTTAAGAGATTCAGAAACGTTAGTTTCAA
66 GTTAAGAGATTCAGAAACGTTAGTTTCAA
138684 GTTTGAACTT
Statistics
Matches: 92, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
93 68 0.74
94 24 0.26
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.35
Consensus pattern (94 bp):
ATAGTTAACTTTCTTCACTAGTGGATGGGAAGAAAGGAACTCAGCAATCTTTTGTGCATTTTCCT
GTTAAGAGATTCAGAAACGTTAGTTTCAA
Found at i:141100 original size:2 final size:2
Alignment explanation
Indices: 141093--141121 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
141083 ACAATAGCTA
141093 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 A
141122 AATTGCAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:159453 original size:26 final size:26
Alignment explanation
Indices: 159416--159466 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
159406 GCAAGCACGC
*
159416 TTTCATTGCTTGAAATATTTGCATTT
1 TTTCATTCCTTGAAATATTTGCATTT
*
159442 TTTCATTCCTTGCAATATTTGCATT
1 TTTCATTCCTTGAAATATTTGCATT
159467 ACTTAATGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.22, C:0.16, G:0.10, T:0.53
Consensus pattern (26 bp):
TTTCATTCCTTGAAATATTTGCATTT
Found at i:163283 original size:35 final size:35
Alignment explanation
Indices: 163226--163321 Score: 111
Period size: 35 Copynumber: 2.7 Consensus size: 35
163216 GTCATTGGAA
* * *
163226 TTAATTGATTAAAATTTTTTAATTAAATTGTTGGGC
1 TTAATTGATT-AAATTATTTAATTAAATTATTAGGC
* *
163262 TTAATTAATTAAATTATTTAATTAAGTTATTAGGC
1 TTAATTGATTAAATTATTTAATTAAATTATTAGGC
* **
163297 CTAATTGATTAAATTAAATAATTAA
1 TTAATTGATTAAATTATTTAATTAA
163322 CTTAACTAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
35 42 0.82
36 9 0.18
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (35 bp):
TTAATTGATTAAATTATTTAATTAAATTATTAGGC
Found at i:163304 original size:71 final size:68
Alignment explanation
Indices: 163162--163309 Score: 172
Period size: 71 Copynumber: 2.1 Consensus size: 68
163152 TCTTAAGCAC
* * * * *
163162 TTGATTAAAATTGTTTAATTAAGTTGTGCCTAATTAATTAAATTGTTTATTTAGGTCATTGGAAT
1 TTGATTAAAATTGTTTAATTAAGTTGGGCCTAATTAATTAAATTATTTAATTAAGTCATTGGAAC
163227 TAA
66 TAA
* * *
163230 TTGATTAAAATTTTTTAATTAAATTGTTGGGCTTAATTAATTAAATTATTTAATTAAGTTATTAG
1 TTGATTAAAATTGTTTAATT-AA--GTTGGGCCTAATTAATTAAATTATTTAATTAAGTCATT-G
*
163295 G-CCTAA
62 GAACTAA
163301 TTGATTAAA
1 TTGATTAAA
163310 TTAAATAATT
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
68 19 0.28
69 2 0.03
71 44 0.66
72 2 0.03
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (68 bp):
TTGATTAAAATTGTTTAATTAAGTTGGGCCTAATTAATTAAATTATTTAATTAAGTCATTGGAAC
TAA
Found at i:168631 original size:15 final size:16
Alignment explanation
Indices: 168611--168651 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
168601 TGAGAAAATG
168611 ATGATTGTAGAGAA-T
1 ATGATTGTAGAGAATT
168626 ATGATTGCTGAGAGAATT
1 ATGATTG-T-AGAGAATT
168644 AT-ATTGTA
1 ATGATTGTA
168652 ATGTTTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 8 0.35
16 2 0.09
17 10 0.43
18 3 0.13
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (16 bp):
ATGATTGTAGAGAATT
Found at i:170480 original size:2 final size:2
Alignment explanation
Indices: 170473--170497 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
170463 GGCTGCAATA
170473 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
170498 TGGTTTTGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:173310 original size:15 final size:15
Alignment explanation
Indices: 173286--173315 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
173276 TGAAGAGGTA
*
173286 TATATGTATTTGAGT
1 TATATATATTTGAGT
173301 TATATATATTTGAGT
1 TATATATATTTGAGT
173316 GTGTTACTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (15 bp):
TATATATATTTGAGT
Found at i:199704 original size:45 final size:47
Alignment explanation
Indices: 199629--199751 Score: 121
Period size: 45 Copynumber: 2.6 Consensus size: 47
199619 GTAATAATAA
* *
199629 AAATTATAGA-CAAGGGTAATTTTGTCTTTTTGTA-A-AAATA-TGAGT
1 AAATTATA-ATCAAAGGTAATTTTATCTTTTTG-AGATAAATAGTGAGT
* * *
199674 AAATTATAATCAAAGGTATTTTTATTTTTTTGAGATAAATATGTGATT
1 AAATTATAATCAAAGGTAATTTTATCTTTTTGAGATAAATA-GTGAGT
*
199722 AAATTATAATC-AAGGTTAATTTTAACTTTT
1 AAATTATAATCAAAGG-TAATTTTATCTTTT
199752 GGTAGAAATT
Statistics
Matches: 64, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
44 2 0.03
45 27 0.42
46 5 0.08
47 4 0.06
48 26 0.41
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.45
Consensus pattern (47 bp):
AAATTATAATCAAAGGTAATTTTATCTTTTTGAGATAAATAGTGAGT
Found at i:204318 original size:47 final size:48
Alignment explanation
Indices: 204247--204450 Score: 276
Period size: 47 Copynumber: 4.2 Consensus size: 48
204237 CCAGCCCGGC
*
204247 GGGCCGCA-GGGGGAATCGGGACTCGTGGGAGCCGGAGGGGGCGGGCA
1 GGGCCGCAGGGGGGAACCGGGACTCGTGGGAGCCGGAGGGGGCGGGCA
* *
204294 GCGCCGCAGGGGGGAA-CGGGACTCGTGGGAGCCGGAGGGGGGCGGGTA
1 GGGCCGCAGGGGGGAACCGGGACTCGTGGGAGCCGGA-GGGGGCGGGCA
204342 -GGCCGCA-GGGGGAACCGGGACTCGT-GGAGCCGGAGGAGGG-GCGGCA
1 GGGCCGCAGGGGGGAACCGGGACTCGTGGGAGCCGGAGG-GGGCG-GGCA
204388 GGGCCGCAGGGGGGAACCGGGACTCGGCCGTGGGAGCCGGAGGGGGCGGGCA
1 GGGCCGCAGGGGGGAACCGGGACT----CGTGGGAGCCGGAGGGGGCGGGCA
204440 GGGCCGCAGGG
1 GGGCCGCAGGG
204451 CGAAAGGCGC
Statistics
Matches: 140, Mismatches: 4, Indels: 21
0.85 0.02 0.13
Matches are distributed among these distances:
45 3 0.02
46 22 0.16
47 50 0.36
48 32 0.23
52 21 0.15
53 12 0.09
ACGTcount: A:0.15, C:0.23, G:0.57, T:0.05
Consensus pattern (48 bp):
GGGCCGCAGGGGGGAACCGGGACTCGTGGGAGCCGGAGGGGGCGGGCA
Found at i:206901 original size:92 final size:91
Alignment explanation
Indices: 206735--206905 Score: 213
Period size: 92 Copynumber: 1.9 Consensus size: 91
206725 GCTAGATGAT
* * * *
206735 GAAACTGCAACTTTTTGAGACTTGTAGTTGGGACCTTATTGTTGTGGGGTTGAATGGCTGGTCTG
1 GAAACTGCAACTTTTTGAGACTTGTAGTTGGGACCTTATTGCTATGGGGTTGAATGACTGATCTG
*
206800 GAATGTTTTGAGAAGGTTTGTTAATG
66 AAATGTTTTGAGAAGGTTTGTTAATG
* *
206826 GAAATTGCAACTTTTTGAGACCTTGTAGTTGGGA-CTTTTTAGCTATGGGGTTGAATGACAT-AT
1 GAAACTGCAACTTTTTGAGA-CTTGTAGTTGGGACCTTATT-GCTATGGGGTTGAATGAC-TGAT
*
206889 TTGAAACT-TTTTGAGAA
63 CTGAAA-TGTTTTGAGAA
206906 AGCCAAATGA
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
91 24 0.35
92 42 0.62
93 2 0.03
ACGTcount: A:0.24, C:0.09, G:0.28, T:0.39
Consensus pattern (91 bp):
GAAACTGCAACTTTTTGAGACTTGTAGTTGGGACCTTATTGCTATGGGGTTGAATGACTGATCTG
AAATGTTTTGAGAAGGTTTGTTAATG
Found at i:216304 original size:19 final size:19
Alignment explanation
Indices: 216282--216321 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
216272 AGATTTAGAA
*
216282 AAATGAGGGGAAAGAGAGG
1 AAATGAGGAGAAAGAGAGG
*
216301 AAATGAGGAGAGAGAGAGG
1 AAATGAGGAGAAAGAGAGG
216320 AA
1 AA
216322 GAAGGGAGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.45, T:0.05
Consensus pattern (19 bp):
AAATGAGGAGAAAGAGAGG
Found at i:226389 original size:2 final size:2
Alignment explanation
Indices: 226382--226413 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
226372 TAGCAACACA
226382 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
226414 GCGCGCAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:231986 original size:26 final size:26
Alignment explanation
Indices: 231943--232010 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
231933 TTGTTTCTTC
* * *
231943 AAAAAGAAAAGGACAAATCGATTT-TG
1 AAAAAGAAAA-AAGAAATCGATTTCTA
*
231969 AAAAAGAGAAAAAGAAATTGATTTCTA
1 AAAAAGA-AAAAAGAAATCGATTTCTA
231996 AAAAAGAAAAAAGAA
1 AAAAAGAAAAAAGAA
232011 TCTATCCAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 25 0.69
27 11 0.31
ACGTcount: A:0.63, C:0.04, G:0.16, T:0.16
Consensus pattern (26 bp):
AAAAAGAAAAAAGAAATCGATTTCTA
Found at i:233903 original size:42 final size:42
Alignment explanation
Indices: 233844--234048 Score: 189
Period size: 42 Copynumber: 4.9 Consensus size: 42
233834 GCTTCTCAGG
*
233844 CGTAATTAAATATCCAAAGAATTTCAAAGTCCATTTTCCAAA
1 CGTAATCAAATATCCAAAGAATTTCAAAGTCCATTTTCCAAA
* * * *
233886 CGTAATCAAATAACCAAAGAATTCCAAAGTCTATTTCCCAAA
1 CGTAATCAAATATCCAAAGAATTTCAAAGTCCATTTTCCAAA
* * * *
233928 CATAATCAAATGTCCAAATAATTTCAAAGTCCATTTTCCAAG
1 CGTAATCAAATATCCAAAGAATTTCAAAGTCCATTTTCCAAA
* * * * * *** * *
233970 CGGAACCATATATCTAAACAATTTTGGAGTCCA-CTTCCTAAG
1 CGTAATCAAATATCCAAAGAATTTCAAAGTCCATTTTCC-AAA
* *
234012 CGTAATCAAATATTC-AAGAAGTTTCAAAGTTCATTTT
1 CGTAATCAAATATCCAAAGAA-TTTCAAAGTCCATTTT
234049 TTTTCCAAAT
Statistics
Matches: 125, Mismatches: 35, Indels: 5
0.76 0.21 0.03
Matches are distributed among these distances:
41 8 0.06
42 115 0.92
43 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.30
Consensus pattern (42 bp):
CGTAATCAAATATCCAAAGAATTTCAAAGTCCATTTTCCAAA
Found at i:235078 original size:52 final size:53
Alignment explanation
Indices: 234975--235108 Score: 164
Period size: 52 Copynumber: 2.5 Consensus size: 53
234965 TTTTAGATTA
** *
234975 AAAGAATCGATTCCTAGAAATTGAGAAGTTGGTTTTTGCAAGTCTAGAATTCC
1 AAAGAATCGATTCCTAGAAATCAAGAAGTTGGTTCTTGCAAGTCTAGAATTCC
** * * *
235028 -ATTAATCAATTCCAAGAAATCAAGAAGTTGGTTCTTGCAAGT-TTGAAATTCC
1 AAAGAATCGATTCCTAGAAATCAAGAAGTTGGTTCTTGCAAGTCTAG-AATTCC
*
235080 AAAGAATCGATTCTTAGAAATCAAGAAGT
1 AAAGAATCGATTCCTAGAAATCAAGAAGT
235109 CGACTCTTAG
Statistics
Matches: 66, Mismatches: 13, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
51 2 0.03
52 41 0.62
53 23 0.35
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (53 bp):
AAAGAATCGATTCCTAGAAATCAAGAAGTTGGTTCTTGCAAGTCTAGAATTCC
Found at i:236365 original size:64 final size:64
Alignment explanation
Indices: 236251--236405 Score: 168
Period size: 64 Copynumber: 2.4 Consensus size: 64
236241 CTTAGAGCTT
* ** * ** *
236251 TCACATGGTGTGAGGTAACATTTAACACATGATAAATTGTCTCTGGTATGATGATGATAGTG-C
1 TCACACGGTGTGAGGTAACATTCCACACATGATAAATTGACTCTAATATGATGATAATAGTGTC
* * * *
236314 TCTACACGGTGTGAGGTAACATTCCACACATGATGAATTGAGTTTAATATGATGATAATAGTGTT
1 TC-ACACGGTGTGAGGTAACATTCCACACATGATAAATTGACTCTAATATGATGATAATAGTGTC
* * *
236379 TCAGACGTTGTGAGATAACATTCCACA
1 TCACACGGTGTGAGGTAACATTCCACA
236406 TGTGGTGTCA
Statistics
Matches: 76, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
63 2 0.03
64 72 0.95
65 2 0.03
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (64 bp):
TCACACGGTGTGAGGTAACATTCCACACATGATAAATTGACTCTAATATGATGATAATAGTGTC
Found at i:258234 original size:22 final size:22
Alignment explanation
Indices: 258204--258253 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
258194 ACATGCACAC
* *
258204 ATATGTGTGTATATGTATGTAT
1 ATATATGTGTATATATATGTAT
* *
258226 ATATATGTGTTTGTATATGTAT
1 ATATATGTGTATATATATGTAT
258248 ATATAT
1 ATATAT
258254 CTACACATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.52
Consensus pattern (22 bp):
ATATATGTGTATATATATGTAT
Found at i:258714 original size:30 final size:30
Alignment explanation
Indices: 258653--258714 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
258643 TCAAACCCTA
* *
258653 ATACTTTTATTTTGAGACAAATAACTCCTT
1 ATACTTTAATTTTGAGACAAATAAATCCTT
* *
258683 ATACTTTAATTTTGA-ATTAAATAAATTCTT
1 ATACTTTAATTTTGAGA-CAAATAAATCCTT
258713 AT
1 AT
258715 GACTAATGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (30 bp):
ATACTTTAATTTTGAGACAAATAAATCCTT
Found at i:279848 original size:10 final size:10
Alignment explanation
Indices: 279829--279858 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
279819 AGTTTAAGTA
279829 TTAATTATTT
1 TTAATTATTT
*
279839 TTAGTTATTT
1 TTAATTATTT
279849 TTAATTATTT
1 TTAATTATTT
279859 ATTTTATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (10 bp):
TTAATTATTT
Found at i:287791 original size:18 final size:19
Alignment explanation
Indices: 287768--287803 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
287758 ATATTAAACA
*
287768 AAATAAAATA-TAAAAAAT
1 AAATAAAAAATTAAAAAAT
287786 AAATAAAAAATTAAAAAA
1 AAATAAAAAATTAAAAAA
287804 GTGGAGCTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (19 bp):
AAATAAAAAATTAAAAAAT
Found at i:295740 original size:27 final size:27
Alignment explanation
Indices: 295683--295744 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
295673 TTAAAAGAAT
*
295683 TTAAATAAATTTTATTTTTTATTATGA
1 TTAAATAAATTTTATTTTTTATTAAGA
*
295710 TTAATTAAATTTTATCTTTATT-TTAAG-
1 TTAAATAAATTTTAT-TTT-TTATTAAGA
295737 TTAAATAA
1 TTAAATAA
295745 GTCATTATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 21 0.70
28 7 0.23
29 2 0.07
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (27 bp):
TTAAATAAATTTTATTTTTTATTAAGA
Found at i:295985 original size:29 final size:29
Alignment explanation
Indices: 295910--295985 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 29
295900 AATTATTAAT
* **
295910 TATAAAATTTTATTTAATTAAAATAAAAA
1 TATAAAAATTTATTTAAACAAAATAAAAA
* ** *
295939 TATATAAATTTAACTAAACATAAT-AAAA
1 TATAAAAATTTATTTAAACAAAATAAAAA
295967 TAATAAAAATTTATTTAAA
1 T-ATAAAAATTTATTTAAA
295986 ATTTTTAAAC
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
28 5 0.14
29 31 0.86
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (29 bp):
TATAAAAATTTATTTAAACAAAATAAAAA
Found at i:300601 original size:16 final size:16
Alignment explanation
Indices: 300580--300613 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
300570 ATTTTCCCCA
*
300580 TTCAATGTAGATATAC
1 TTCAATGCAGATATAC
300596 TTCAATGCAGATATAC
1 TTCAATGCAGATATAC
300612 TT
1 TT
300614 TCTTACGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (16 bp):
TTCAATGCAGATATAC
Found at i:306564 original size:16 final size:17
Alignment explanation
Indices: 306543--306574 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
306533 GTATTAGAAT
306543 TTAAAATTTTA-TTTGA
1 TTAAAATTTTAGTTTGA
306559 TTAAAATTTTAGTTTG
1 TTAAAATTTTAGTTTG
306575 TGCATAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.56
Consensus pattern (17 bp):
TTAAAATTTTAGTTTGA
Found at i:309484 original size:76 final size:76
Alignment explanation
Indices: 309334--309493 Score: 203
Period size: 76 Copynumber: 2.1 Consensus size: 76
309324 ACACGTCATG
* * * * * *
309334 ATGTTACATGCTATGGTTAAGTTGTTACATGTCATGTTAAAAAAAAATACTGTTATTACACGCCA
1 ATGTTACATGCCATGATTAAGTTGTTACACGTCATATTAAAAAAAAATACTATTATTACACGCAA
***
309399 TGGGTAAAAAC
66 TGCACAAAAAC
* * *
309410 ATGTTACATGCCATGATTAGGTTGTTACACGTCATATTGAAAAAAAATACTATTATTATACGCAA
1 ATGTTACATGCCATGATTAAGTTGTTACACGTCATATTAAAAAAAAATACTATTATTACACGCAA
309475 TGCACAAAAAC
66 TGCACAAAAAC
*
309486 AAGTTACA
1 ATGTTACA
309494 CACTATAATT
Statistics
Matches: 71, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
76 71 1.00
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.31
Consensus pattern (76 bp):
ATGTTACATGCCATGATTAAGTTGTTACACGTCATATTAAAAAAAAATACTATTATTACACGCAA
TGCACAAAAAC
Found at i:326272 original size:33 final size:31
Alignment explanation
Indices: 326234--326313 Score: 101
Period size: 33 Copynumber: 2.5 Consensus size: 31
326224 TTTTGTAATG
326234 TTATAATTAAATTAAAAAAAATTAAAATAGAA
1 TTATAATTAAATTAAAAAAAATTAAAATA-AA
**
326266 TATATAA-TATAATTATCAAAAATTAAAATAAA
1 T-TATAATTA-AATTAAAAAAAATTAAAATAAA
326298 TTA-AATTAAATTAAAA
1 TTATAATTAAATTAAAA
326314 TTTATATAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
30 8 0.20
31 4 0.10
32 6 0.15
33 23 0.56
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (31 bp):
TTATAATTAAATTAAAAAAAATTAAAATAAA
Found at i:326379 original size:41 final size:40
Alignment explanation
Indices: 326331--326411 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 40
326321 AATATAGGTA
* *
326331 AAAGAAATTAAAATAAAATATATAATATAAAAAATTATATT
1 AAAGAAATGAAAATAAAATATATAACATAAAAAA-TATATT
* *
326372 AAAGAAATGAAAATAAAATATATGACATTAAAAATATATT
1 AAAGAAATGAAAATAAAATATATAACATAAAAAATATATT
326412 TAATAGATGA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 6 0.17
41 30 0.83
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.30
Consensus pattern (40 bp):
AAAGAAATGAAAATAAAATATATAACATAAAAAATATATT
Found at i:326630 original size:15 final size:15
Alignment explanation
Indices: 326607--326649 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
326597 ATGTTATTTC
*
326607 CTTACAATCACATTA
1 CTTATAATCACATTA
326622 CTTATAATCACATTA
1 CTTATAATCACATTA
326637 CTTATAATCACAT
1 CTTATAATCACAT
326650 GGTATTGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (15 bp):
CTTATAATCACATTA
Found at i:328694 original size:54 final size:54
Alignment explanation
Indices: 328635--328739 Score: 124
Period size: 54 Copynumber: 1.9 Consensus size: 54
328625 AGTCGTTATA
* * *
328635 AGGGTTATCG-CTTGATTCCATTTAAAAGCAATAATCCCTT-TAGTGGATTATATG
1 AGGGTTATCGTCTTG-TCCCATTAAAAAGCAAGAAT-CCTTATAGTGGATTATATG
* *
328689 AGGGTTATTGTTTTGTCCCATTAAAAAGCAAGAATCCTTGATAGTGGATTA
1 AGGGTTATCGTCTTGTCCCATTAAAAAGCAAGAATCCTT-ATAGTGGATTA
328740 AAATTCTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
53 4 0.09
54 26 0.60
55 13 0.30
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.36
Consensus pattern (54 bp):
AGGGTTATCGTCTTGTCCCATTAAAAAGCAAGAATCCTTATAGTGGATTATATG
Found at i:338828 original size:28 final size:28
Alignment explanation
Indices: 338767--338828 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 28
338757 AGGGTAAAGT
338767 TATTTTTTAAAATATAACGTGTAACAAA
1 TATTTTTTAAAATATAACGTGTAACAAA
* * *
338795 TCTTTTTT--AATATTACGTGTGACAACA
1 TATTTTTTAAAATATAACGTGTAACAA-A
338822 TATTTTT
1 TATTTTT
338829 AATATGGTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 15 0.52
27 7 0.24
28 7 0.24
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.47
Consensus pattern (28 bp):
TATTTTTTAAAATATAACGTGTAACAAA
Found at i:342194 original size:41 final size:41
Alignment explanation
Indices: 342149--342238 Score: 99
Period size: 41 Copynumber: 2.2 Consensus size: 41
342139 TATATGTCTT
* * *
342149 TTACATGTTGTTACATGCTATTTCATTTTACTCATACAGTG
1 TTACATGTTCTAACATGCCATTTCATTTTACTCATACAGTG
* ** **
342190 TTACATCTTCTAATGTGCCATTTTGTTTTACTCATACAGTG
1 TTACATGTTCTAACATGCCATTTCATTTTACTCATACAGTG
*
342231 TTAAATGT
1 TTACATGT
342239 CACGGCTTGT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.24, C:0.17, G:0.12, T:0.47
Consensus pattern (41 bp):
TTACATGTTCTAACATGCCATTTCATTTTACTCATACAGTG
Found at i:342435 original size:70 final size:70
Alignment explanation
Indices: 342353--342583 Score: 207
Period size: 71 Copynumber: 3.3 Consensus size: 70
342343 CACCATTTCA
* * ** *
342353 TTATATTGTTACATGACGCA-CTTGTTAGTTATTGTTTACCTTTTCTTGTCACACGCCATCTCAA
1 TTATATTGTTACACG-C-CATCTTGTTAGATATCATTTACATTTTCTTGTCACACGCCATCTCAA
*
342417 A-AATTC
64 AGAAGTC
* * * * *
342423 TTATATTGTTACACGCCATTCTTGTTTGATGTCATTTACATTTTCTTGTCACATGCTATTTCAAA
1 TTATATTGTTACACGCCA-TCTTGTTAGATATCATTTACATTTTCTTGTCACACGCCATCTCAAA
342488 GAAGTC
65 GAAGTC
* * * * ** *
342494 TTATATTGTTACACGTCATTCTTATTAGATGTCATTTACATCTTCTTGTCACATACCATTTCAAA
1 TTATATTGTTACACGCCA-TCTTGTTAGATATCATTTACATTTTCTTGTCACACGCCATCTCAAA
* *
342559 -AACATA
65 GAA-GTC
*
342565 TTATATTATTACACGCCAT
1 TTATATTGTTACACGCCAT
342584 AAATTGGCAG
Statistics
Matches: 136, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
68 2 0.01
69 1 0.01
70 53 0.39
71 80 0.59
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.43
Consensus pattern (70 bp):
TTATATTGTTACACGCCATCTTGTTAGATATCATTTACATTTTCTTGTCACACGCCATCTCAAAG
AAGTC
Found at i:342525 original size:71 final size:70
Alignment explanation
Indices: 342387--342583 Score: 259
Period size: 71 Copynumber: 2.8 Consensus size: 70
342377 TTAGTTATTG
* * * * * *
342387 TTTACCTTTTCTTGTCACACGCCATCTCAAAAATTCTTATATTGTTACACGCCATTCTTGTTTGA
1 TTTACATTTTCTTGTCACATGCCATTTCAAAAAGTCTTATATTGTTACACGCCATTCTTATTAGA
342452 TGTCA
66 TGTCA
* *
342457 TTTACATTTTCTTGTCACATGCTATTTCAAAGAAGTCTTATATTGTTACACGTCATTCTTATTAG
1 TTTACATTTTCTTGTCACATGCCATTTCAAA-AAGTCTTATATTGTTACACGCCATTCTTATTAG
342522 ATGTCA
65 ATGTCA
* * * * *
342528 TTTACATCTTCTTGTCACATACCATTTCAAAAACATATTATATTATTACACGCCAT
1 TTTACATTTTCTTGTCACATGCCATTTCAAAAA-GTCTTATATTGTTACACGCCAT
342584 AAATTGGCAG
Statistics
Matches: 110, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
70 29 0.26
71 81 0.74
ACGTcount: A:0.27, C:0.21, G:0.09, T:0.43
Consensus pattern (70 bp):
TTTACATTTTCTTGTCACATGCCATTTCAAAAAGTCTTATATTGTTACACGCCATTCTTATTAGA
TGTCA
Found at i:346356 original size:241 final size:240
Alignment explanation
Indices: 345783--346412 Score: 755
Period size: 241 Copynumber: 2.6 Consensus size: 240
345773 CATGCACAAG
* * * * * * *
345783 TAAGCTAGACCCAAAAACAATTAGCCCATAATGTGTAACACTCTAGATATATGAAATTCATTGTT
1 TAAGCTAGACCC-AAAACAATTAACCCATAATGTGCAACACACCAGATAAAAGAAATTTATTGTT
* * * ** *
345848 GTTACACATTATGCAGACTAAGTAAAATATTGTTACACTCCATGTATATATGTTTTTACATGA-C
65 GTTACACATTATGCAGACTAAGTACAATGTTGTTACACGCCATGCCTATATGTTTTTACA-CACC
* * *
345912 AAGTATAATTACTTATTTGTTACATGTCATGAATGAATCCTAAATGAAACATTGTTACACGATAT
129 ATGTATAATTACTTATTTGTTACA-GCCATGAATGAATCCTAAATCAAACATTGTTACACGATAT
* * * * *
345977 GCCATGTCGAGTATGTGGTTTTAACACTAAACGCCATACATGTAATGC
193 GCCATGCCGAGCATGCGGTTTTAACACTAAACACCATACATATAATGC
* * * *
346025 TAAGCTAGACCCAAAAGAAGTTAACCCATAATGTGCAACACACCAAATAAAAGAAACTTATTATT
1 TAAGCTAGACCCAAAACAA-TTAACCCATAATGTGCAACACACCAGATAAAAGAAATTTATTGTT
* ** * * * *
346090 GTTGCATGTTATGCAGACCAAGTACAATGTTGTTACACGCTACGCCTATATGTTCTTACACACCA
65 GTTACACATTATGCAGACTAAGTACAATGTTGTTACACGCCATGCCTATATGTTTTTACACACCA
** *
346155 TGTATAATTACTTATTTGTCATACA-CCATGAATGAATCCTAAA-CCCACATTGTTACATGATAT
130 TGTATAATTACTTATTTGT--TACAGCCATGAATGAATCCTAAATCAAACATTGTTACACGATAT
*
346218 GCCATGCCGAGCATGCGG-TTTACACACTACACACCATACATATAATGC
193 GCCATGCCGAGCATGCGGTTTTA-ACACTAAACACCATACATATAATGC
* * * * *
346266 TAAGATAGACCCAATAATAATTAACCCATAATGTACAACACGCCAGATAGAAGAAATTTATTGTT
1 TAAGCTAGACCCAA-AACAATTAACCCATAATGTGCAACACACCAGATAAAAGAAATTTATTGTT
* * * *
346331 GTTAAACACTATGCAAACTAAGTACAATGTTGTTACATGCCATGCCTATATGTTTTTACACACCA
65 GTTACACATTATGCAGACTAAGTACAATGTTGTTACACGCCATGCCTATATGTTTTTACACACCA
346396 TGTATAATTACTTATTT
130 TGTATAATTACTTATTT
346413 TGGGTTGAAA
Statistics
Matches: 327, Mismatches: 55, Indels: 13
0.83 0.14 0.03
Matches are distributed among these distances:
240 4 0.01
241 183 0.56
242 136 0.42
244 4 0.01
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.31
Consensus pattern (240 bp):
TAAGCTAGACCCAAAACAATTAACCCATAATGTGCAACACACCAGATAAAAGAAATTTATTGTTG
TTACACATTATGCAGACTAAGTACAATGTTGTTACACGCCATGCCTATATGTTTTTACACACCAT
GTATAATTACTTATTTGTTACAGCCATGAATGAATCCTAAATCAAACATTGTTACACGATATGCC
ATGCCGAGCATGCGGTTTTAACACTAAACACCATACATATAATGC
Found at i:346441 original size:15 final size:15
Alignment explanation
Indices: 346421--346459 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
346411 TTTGGGTTGA
346421 AAGTATTTAGAAATG
1 AAGTATTTAGAAATG
346436 AAGTATTTAGAAATG
1 AAGTATTTAGAAATG
346451 AAGTATTTA
1 AAGTATTTA
346460 AAAACTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.18, T:0.36
Consensus pattern (15 bp):
AAGTATTTAGAAATG
Found at i:349512 original size:13 final size:13
Alignment explanation
Indices: 349494--349524 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
349484 AAAGCCATGC
*
349494 ATCATTAGATAAT
1 ATCATTAAATAAT
349507 ATCATTAAATAAT
1 ATCATTAAATAAT
349520 ATCAT
1 ATCAT
349525 GAATAGGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.48, C:0.10, G:0.03, T:0.39
Consensus pattern (13 bp):
ATCATTAAATAAT
Found at i:360058 original size:16 final size:17
Alignment explanation
Indices: 360037--360068 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
360027 TGACTTCCAA
360037 AATAATT-TTTTTATTT
1 AATAATTATTTTTATTT
360053 AATAATTATTTTTATT
1 AATAATTATTTTTATT
360069 CTTCAAACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
AATAATTATTTTTATTT
Found at i:360253 original size:36 final size:40
Alignment explanation
Indices: 360213--360303 Score: 100
Period size: 41 Copynumber: 2.4 Consensus size: 40
360203 CCAAACTCCC
*
360213 TATATTTTAATA-T-GAA-TC-TAACTTATCATAATATAT
1 TATATTTTAATAGTCGAACTCATAACTTATCATAACATAT
* * * *
360249 TATATCTTAACAGTCTAACTCAATAGCTTATCATAACATAT
1 TATATTTTAATAGTCGAACTC-ATAACTTATCATAACATAT
360290 TATATTTTAATAGT
1 TATATTTTAATAGT
360304 TCAACCCAAG
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
36 10 0.23
37 1 0.02
38 2 0.05
39 2 0.05
41 28 0.65
ACGTcount: A:0.40, C:0.12, G:0.04, T:0.44
Consensus pattern (40 bp):
TATATTTTAATAGTCGAACTCATAACTTATCATAACATAT
Found at i:362602 original size:66 final size:66
Alignment explanation
Indices: 362496--362635 Score: 226
Period size: 66 Copynumber: 2.1 Consensus size: 66
362486 TCTCTATTTT
* * *
362496 TTTTGTTTCGTAGGAGACTTGGATAAAGAAATTGATTATTCAGCTGAGGTTAAGTTCTCCATTAG
1 TTTTGTTTCGCAGGAGACTTGGATAAAGAAATTAATTATTCAGCCGAGGTTAAGTTCTCCATTAG
362561 G
66 G
* * *
362562 TTTTGTTTTGCAGGAGACTTGGATAAAGAAATTAATTATTCCGCCGAGGTTAAGTTTTCCATTAG
1 TTTTGTTTCGCAGGAGACTTGGATAAAGAAATTAATTATTCAGCCGAGGTTAAGTTCTCCATTAG
362627 G
66 G
362628 TTTTGTTT
1 TTTTGTTT
362636 ATGATTATTT
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.41
Consensus pattern (66 bp):
TTTTGTTTCGCAGGAGACTTGGATAAAGAAATTAATTATTCAGCCGAGGTTAAGTTCTCCATTAG
G
Found at i:379190 original size:2 final size:2
Alignment explanation
Indices: 379183--379219 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
379173 GCTGTGTATG
*
379183 TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
379220 TGAGATTCTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:379324 original size:26 final size:26
Alignment explanation
Indices: 379290--379342 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
379280 GTATTAATTT
379290 TTTTATTATATAAAT-GAAAATTTAAA
1 TTTTATTATATAAATAGAAAA-TTAAA
* *
379316 TTTTATTATTTGAATAGAAAATTAAA
1 TTTTATTATATAAATAGAAAATTAAA
379342 T
1 T
379343 ACATATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (26 bp):
TTTTATTATATAAATAGAAAATTAAA
Found at i:388119 original size:5 final size:6
Alignment explanation
Indices: 388096--388137 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
388086 AAAAAACCAA
*
388096 AAAAAG AAAAAGG AAAAA- AGAAAAG CAAAAG AAAAAG AAAAA
1 AAAAAG AAAAA-G AAAAAG A-AAAAG AAAAAG AAAAAG AAAAA
388138 CACCCCGCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
5 1 0.03
6 24 0.77
7 6 0.19
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:389805 original size:3 final size:3
Alignment explanation
Indices: 389792--389822 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
389782 AAAAGTAGTC
*
389792 AAG ATG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
389823 GCCCGTGGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:390917 original size:15 final size:16
Alignment explanation
Indices: 390899--390928 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
390889 AAGAGCTTGC
390899 AGAAGAGAAG-GAGAA
1 AGAAGAGAAGAGAGAA
390914 AGAAGAGAAGAGAGA
1 AGAAGAGAAGAGAGA
390929 GGGGGAGGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (16 bp):
AGAAGAGAAGAGAGAA
Found at i:391040 original size:5 final size:5
Alignment explanation
Indices: 391036--391066 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
391026 TCTCGATGGG
*
391036 GTGGG GTGGT GTGGT GTGGT GTGGT GTGGT G
1 GTGGT GTGGT GTGGT GTGGT GTGGT GTGGT G
391067 CGTTGTCGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.65, T:0.35
Consensus pattern (5 bp):
GTGGT
Found at i:393047 original size:26 final size:29
Alignment explanation
Indices: 393009--393062 Score: 69
Period size: 26 Copynumber: 2.0 Consensus size: 29
392999 TTTATTTAAT
*
393009 TTAAATTATAAAA-TA-TAT-TTAATATG
1 TTAAATTAAAAAATTAGTATCTTAATATG
*
393035 TTAATTTAAAAAATTAGTATCTTAATAT
1 TTAAATTAAAAAATTAGTATCTTAATAT
393063 TCAAATACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 11 0.48
27 2 0.09
28 3 0.13
29 7 0.30
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (29 bp):
TTAAATTAAAAAATTAGTATCTTAATATG
Found at i:396354 original size:3 final size:3
Alignment explanation
Indices: 396346--396379 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
396336 CATTTACAAA
396346 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
396380 CATCATTGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:398502 original size:2 final size:2
Alignment explanation
Indices: 398495--398531 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
398485 GCTTATTTAT
* *
398495 AC AC AC AC AC AC AC AC AC AC AC AC AC AT AC AT AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
398532 TATTTTGATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.43, G:0.00, T:0.05
Consensus pattern (2 bp):
AC
Found at i:403551 original size:20 final size:20
Alignment explanation
Indices: 403526--403571 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
403516 TCATCATTAT
*
403526 CATTTTGGAATGTATCGATA
1 CATTTTGGAATGTATCCATA
403546 CATTTTGGAATGTATCCATA
1 CATTTTGGAATGTATCCATA
*
403566 TATTTT
1 CATTTT
403572 AATAAGAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.46
Consensus pattern (20 bp):
CATTTTGGAATGTATCCATA
Found at i:403849 original size:21 final size:22
Alignment explanation
Indices: 403824--403910 Score: 83
Period size: 21 Copynumber: 4.1 Consensus size: 22
403814 AAACTTTTTT
403824 AAACAAGTTTAAAAACT-ATTC
1 AAACAAGTTTAAAAACTCATTC
*
403845 AAACAAGTTCAAAAACTCATTC
1 AAACAAGTTTAAAAACTCATTC
* **
403867 -CAGTAGCTTTAAAAA-TCATTC
1 AAACAAG-TTTAAAAACTCATTC
* *
403888 AAACAAGTTCAAAGA-TCATTC
1 AAACAAGTTTAAAAACTCATTC
403909 AA
1 AA
403911 GCAATTTTGA
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
21 39 0.74
22 14 0.26
ACGTcount: A:0.48, C:0.18, G:0.07, T:0.26
Consensus pattern (22 bp):
AAACAAGTTTAAAAACTCATTC
Found at i:404027 original size:21 final size:21
Alignment explanation
Indices: 403997--404052 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
403987 AATTAAGTTT
403997 AAAAACTCATTCAAACAACTTC
1 AAAAA-TCATTCAAACAACTTC
* * * *
404019 AAAAATCATTGAAATAATTTT
1 AAAAATCATTCAAACAACTTC
*
404040 AAAGATCATTCAA
1 AAAAATCATTCAA
404053 GCAATTTTCA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 23 0.82
22 5 0.18
ACGTcount: A:0.52, C:0.16, G:0.04, T:0.29
Consensus pattern (21 bp):
AAAAATCATTCAAACAACTTC
Found at i:419147 original size:2 final size:2
Alignment explanation
Indices: 419140--419164 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
419130 CATATCTCAA
419140 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
419165 ATATCTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:422157 original size:2 final size:2
Alignment explanation
Indices: 422150--422179 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
422140 AATATCTTCA
422150 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
422180 TGTACTTGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:424157 original size:21 final size:20
Alignment explanation
Indices: 424116--424157 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
424106 GAGAATTCTG
*
424116 AATTTAGTATTTCTTTTCAA
1 AATTTAGTATTTCTTTGCAA
424136 AATTTA-TGATTTACTTTGCAA
1 AATTTAGT-ATTT-CTTTGCAA
424157 A
1 A
424158 TTTCTATTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 1 0.05
20 10 0.53
21 8 0.42
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (20 bp):
AATTTAGTATTTCTTTGCAA
Found at i:425261 original size:17 final size:17
Alignment explanation
Indices: 425239--425272 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
425229 ACCAAAAAGT
425239 ATAAACTAAATCGAAGC
1 ATAAACTAAATCGAAGC
425256 ATAAACTAAATCGAAGC
1 ATAAACTAAATCGAAGC
425273 CTCATATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.18, G:0.12, T:0.18
Consensus pattern (17 bp):
ATAAACTAAATCGAAGC
Found at i:426494 original size:26 final size:24
Alignment explanation
Indices: 426465--426514 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
426455 AAGTAAAAAC
426465 AAAAAAAACAAAAAAGAAGAGAAAGA
1 AAAAAAAACAAAAAAG--GAGAAAGA
*
426491 AAAAAAAAGAAAAAAGGAGAAAGA
1 AAAAAAAACAAAAAAGGAGAAAGA
426515 GGTGTGAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.35
26 15 0.65
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (24 bp):
AAAAAAAACAAAAAAGGAGAAAGA
Found at i:426503 original size:24 final size:25
Alignment explanation
Indices: 426466--426514 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
426456 AGTAAAAACA
426466 AAAAAAACAAAAAAGAA-GAGAAAGA
1 AAAAAAACAAAAAA-AAGGAGAAAGA
*
426491 AAAAAAA-AGAAAAAAGGAGAAAGA
1 AAAAAAACAAAAAAAAGGAGAAAGA
426515 GGTGTGAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 2 0.09
24 13 0.59
25 7 0.32
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (25 bp):
AAAAAAACAAAAAAAAGGAGAAAGA
Found at i:440292 original size:24 final size:24
Alignment explanation
Indices: 440264--440309 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
440254 ATCCACTATT
440264 AAGAAGAAAAGAGAAA-GAAGAAGA
1 AAGAAGAAAAG-GAAAGGAAGAAGA
*
440288 AAGAAGGAAAGGAAAGGAAGAA
1 AAGAAGAAAAGGAAAGGAAGAA
440310 AGGAAGGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (24 bp):
AAGAAGAAAAGGAAAGGAAGAAGA
Found at i:440307 original size:21 final size:21
Alignment explanation
Indices: 440264--440334 Score: 72
Period size: 21 Copynumber: 3.2 Consensus size: 21
440254 ATCCACTATT
*
440264 AAGAAGAAAAGAGAAAGAAGAAGA
1 AAGAAGGAAAG-GAAAG--GAAGA
440288 AAGAAGGAAAGGAAAGGAAGA
1 AAGAAGGAAAGGAAAGGAAGA
* *
440309 AAGGAAGGAGA-GAAAGGTAGA
1 AA-GAAGGAAAGGAAAGGAAGA
440330 AAGAA
1 AAGAA
440335 AGAATAAGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
20 3 0.07
21 18 0.42
22 7 0.16
23 5 0.12
24 10 0.23
ACGTcount: A:0.63, C:0.00, G:0.35, T:0.01
Consensus pattern (21 bp):
AAGAAGGAAAGGAAAGGAAGA
Found at i:445972 original size:19 final size:20
Alignment explanation
Indices: 445944--445982 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
445934 ATGCTCTATC
445944 TTTTTTATTA-A-TTTAAAA
1 TTTTTTATTACATTTTAAAA
445962 TTTTATTATTACATTTTAAAA
1 TTTT-TTATTACATTTTAAAA
445983 AAATAGGGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 6 0.33
20 1 0.06
21 7 0.39
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTTTATTACATTTTAAAA
Found at i:450137 original size:3 final size:3
Alignment explanation
Indices: 450129--450155 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
450119 TGAAATATTA
450129 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
450156 CTAGCACATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:454709 original size:34 final size:34
Alignment explanation
Indices: 454671--454745 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
454661 GGGCTCAAGT
* *
454671 ATAACCCTTAT-AACGCCTTTTGACAAGAACAAAC
1 ATAACCCTT-TCAACGCCTTTTCACAACAACAAAC
* *
454705 ATAACCCTTTCAGCGCCTTTTCACAACAACAAGC
1 ATAACCCTTTCAACGCCTTTTCACAACAACAAAC
*
454739 ATGACCC
1 ATAACCC
454746 ACACAATGCT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 1 0.03
34 34 0.97
ACGTcount: A:0.36, C:0.32, G:0.09, T:0.23
Consensus pattern (34 bp):
ATAACCCTTTCAACGCCTTTTCACAACAACAAAC
Found at i:454864 original size:29 final size:29
Alignment explanation
Indices: 454768--454869 Score: 125
Period size: 29 Copynumber: 3.5 Consensus size: 29
454758 TTCATGGGAA
*
454768 CAAGCATAACTTCTTACCTTTTCAAGGAT
1 CAAGCATAACCTCTTACCTTTTCAAGGAT
* *
454797 CAAGTATAACCTTTTACCTTTTCAAGGAT
1 CAAGCATAACCTCTTACCTTTTCAAGGAT
** *
454826 CAAGTGTAACCTCTTGCCTTTTCAAGGAT
1 CAAGCATAACCTCTTACCTTTTCAAGGAT
*
454855 -TAGACATAACCTCTT
1 CAAG-CATAACCTCTT
454870 TACAACAGTG
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
28 2 0.03
29 61 0.97
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (29 bp):
CAAGCATAACCTCTTACCTTTTCAAGGAT
Found at i:457789 original size:41 final size:41
Alignment explanation
Indices: 457735--457821 Score: 174
Period size: 41 Copynumber: 2.1 Consensus size: 41
457725 GAGTTATTCA
457735 AACATTAAATTGTAACAAGAACATGTCATGATAGTATTTTC
1 AACATTAAATTGTAACAAGAACATGTCATGATAGTATTTTC
457776 AACATTAAATTGTAACAAGAACATGTCATGATAGTATTTTC
1 AACATTAAATTGTAACAAGAACATGTCATGATAGTATTTTC
457817 AACAT
1 AACAT
457822 AAGGCATATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (41 bp):
AACATTAAATTGTAACAAGAACATGTCATGATAGTATTTTC
Found at i:462926 original size:32 final size:32
Alignment explanation
Indices: 462885--462948 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
462875 GTTATGTATG
462885 ACAATTGACATATGTCTACCTTAATCGCAAAT
1 ACAATTGACATATGTCTACCTTAATCGCAAAT
462917 ACAATTGACATATGTCTACCTTAATCGCAAAT
1 ACAATTGACATATGTCTACCTTAATCGCAAAT
462949 CAGATCATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (32 bp):
ACAATTGACATATGTCTACCTTAATCGCAAAT
Found at i:490791 original size:26 final size:24
Alignment explanation
Indices: 490730--490791 Score: 58
Period size: 26 Copynumber: 2.6 Consensus size: 24
490720 TTTCAGTTAT
490730 TATTATA-ATTTT-ATATATTTTA
1 TATTATATATTTTAATATATTTTA
* *
490752 T-TTTTATTTCTTTAATATATGTTTTA
1 TATTATATAT-TTTAATATA--TTTTA
490778 TATTATATATTTTA
1 TATTATATATTTTA
490792 TTTTAATTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
21 4 0.13
22 2 0.07
23 3 0.10
24 5 0.17
26 10 0.33
27 6 0.20
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (24 bp):
TATTATATATTTTAATATATTTTA
Found at i:490896 original size:38 final size:35
Alignment explanation
Indices: 490834--490908 Score: 87
Period size: 38 Copynumber: 2.1 Consensus size: 35
490824 TTAATTTTTT
* *
490834 TATATTTTATTTTATTCTAATTTTTGATTCTTATATTA
1 TATATTTTATTTTAATATAATTTTT-ATT-TTA-ATTA
**
490872 TATATTTTATTTTAATATTTTTTTTATTTTAATTA
1 TATATTTTATTTTAATATAATTTTTATTTTAATTA
490907 TA
1 TA
490909 ACAGTATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
35 6 0.18
36 3 0.09
37 3 0.09
38 21 0.64
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (35 bp):
TATATTTTATTTTAATATAATTTTTATTTTAATTA
Found at i:494217 original size:39 final size:39
Alignment explanation
Indices: 494173--494251 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
494163 TTACATCATT
*
494173 AGGTGGTAAAATCGATCATACAATCAATAATAGAGTGGA
1 AGGTGGTAAAATCGATCATACAATCAACAATAGAGTGGA
494212 AGGTGGTAAAATCGATCATACAATCAACAATAGAGTGGA
1 AGGTGGTAAAATCGATCATACAATCAACAATAGAGTGGA
494251 A
1 A
494252 CCTTACATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.22
Consensus pattern (39 bp):
AGGTGGTAAAATCGATCATACAATCAACAATAGAGTGGA
Found at i:498883 original size:17 final size:18
Alignment explanation
Indices: 498861--498894 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
498851 GAATCAATTG
498861 ACCCTTCTCA-CCTTGAC
1 ACCCTTCTCAGCCTTGAC
498878 ACCCTTCTCAGCCTTGA
1 ACCCTTCTCAGCCTTGA
498895 TTTCTTGGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.18, C:0.44, G:0.09, T:0.29
Consensus pattern (18 bp):
ACCCTTCTCAGCCTTGAC
Found at i:511695 original size:124 final size:124
Alignment explanation
Indices: 511475--511719 Score: 323
Period size: 124 Copynumber: 2.0 Consensus size: 124
511465 ACTGTAAATG
* * * * *
511475 TTTTCCATTGTGATTTTCAGTGTTAGTGGCCATTAAATAAGTTAACTTTGTTTCCGCGGTGCTTT
1 TTTTCCATTGTGATTTCCAATGTCAGTGGCCATTAAATAAGTAAACTTTGTTTCCGCGATGCTTT
* * * *
511540 CCCTTATCTTTAATTCTATACTGAAAACCAAATACAACTCTCCCTCTCTTTATTCTCCC
66 CCCTTATCTTCAATTCCATACTCAAAACCAAATACAACTCTCCCTCTCTTGATTCTCCC
* * *
511599 TTTTCTATTGTGATTTCCAATGTCAGTGGCCATTAAATAAGTAAACTTTGTTTCCATC-ATGTTT
1 TTTTCCATTGTGATTTCCAATGTCAGTGGCCATTAAATAAGTAAACTTTGTTTCC-GCGATGCTT
* * *
511663 TTCC-TATCCTTCAATTCCATATTCAAAACCAAATACAACTCTCCTTCTCTTGATTCT
65 TCCCTTAT-CTTCAATTCCATACTCAAAACCAAATACAACTCTCCCTCTCTTGATTCT
511720 TTCGTTTTGG
Statistics
Matches: 104, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
123 3 0.03
124 100 0.96
125 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.42
Consensus pattern (124 bp):
TTTTCCATTGTGATTTCCAATGTCAGTGGCCATTAAATAAGTAAACTTTGTTTCCGCGATGCTTT
CCCTTATCTTCAATTCCATACTCAAAACCAAATACAACTCTCCCTCTCTTGATTCTCCC
Found at i:511796 original size:14 final size:14
Alignment explanation
Indices: 511777--511811 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
511767 ATTCAATTTA
511777 TTGTTAAGATGTTT
1 TTGTTAAGATGTTT
* *
511791 TTGTTAATATTTTT
1 TTGTTAAGATGTTT
511805 TTGTTAA
1 TTGTTAA
511812 ACTTAACATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.14, T:0.63
Consensus pattern (14 bp):
TTGTTAAGATGTTT
Found at i:523523 original size:22 final size:20
Alignment explanation
Indices: 523495--523541 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
523485 TCGAGTAAAA
523495 TTTCTTTACTCCATCTAAATAT
1 TTTCTTTACT-C-TCTAAATAT
* *
523517 TTTCTTTTCTCTTTAAATAT
1 TTTCTTTACTCTCTAAATAT
523537 TTTCT
1 TTTCT
523542 CTTATAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 13 0.57
21 1 0.04
22 9 0.39
ACGTcount: A:0.21, C:0.19, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTCTTTACTCTCTAAATAT
Found at i:530456 original size:12 final size:12
Alignment explanation
Indices: 530435--530485 Score: 54
Period size: 11 Copynumber: 4.5 Consensus size: 12
530425 TTTAAAATTT
530435 AAAA-AAAATAA
1 AAAATAAAATAA
530446 AAAATAAAATAA
1 AAAATAAAATAA
*
530458 AAAACAAAAT-A
1 AAAATAAAATAA
* *
530469 GAAAGAAAA-AA
1 AAAATAAAATAA
530480 AAAATA
1 AAAATA
530486 CTTGAATGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
11 17 0.52
12 16 0.48
ACGTcount: A:0.84, C:0.02, G:0.04, T:0.10
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:530459 original size:17 final size:15
Alignment explanation
Indices: 530434--530485 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 15
530424 TTTTAAAATT
530434 TAAAAAAAATAAAAAA
1 TAAAAAAAA-AAAAAA
530450 TAAAATAAAAAACAAAA
1 TAAAA-AAAAAA-AAAA
530467 TAGAAAGAAAAAAAAAA
1 TA-AAA-AAAAAAAAAA
530484 TA
1 TA
530486 CTTGAATGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
16 7 0.22
17 16 0.50
18 9 0.28
ACGTcount: A:0.83, C:0.02, G:0.04, T:0.12
Consensus pattern (15 bp):
TAAAAAAAAAAAAAA
Found at i:530724 original size:17 final size:16
Alignment explanation
Indices: 530697--530738 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 16
530687 TAATTTGAGT
530697 TTTTTTAAAAAAAATTTA
1 TTTTTT-AAAAAAA-TTA
530715 TTTTTTAAAAAAATTA
1 TTTTTTAAAAAAATTA
530731 TTTTTTAA
1 TTTTTTAA
530739 TAGCTTTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 11 0.46
17 7 0.29
18 6 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTTTTAAAAAAATTA
Found at i:532455 original size:2 final size:2
Alignment explanation
Indices: 532448--532477 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
532438 CTAGCTTCAA
532448 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
532478 TAATTTGTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:533346 original size:19 final size:19
Alignment explanation
Indices: 533308--533352 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
533298 ACATGACACA
* *
533308 ATTAATCTATTTAGACATG
1 ATTAATATATTTAAACATG
*
533327 ATTAATATATTTAAATATG
1 ATTAATATATTTAAACATG
*
533346 AATAATA
1 ATTAATA
533353 AGTTTTTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (19 bp):
ATTAATATATTTAAACATG
Found at i:544425 original size:16 final size:15
Alignment explanation
Indices: 544404--544443 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
544394 GGTCGGCAGG
*
544404 GAAGAAAAAGAAAGGA
1 GAAGAAAAAG-AAGAA
544420 GAAGAAAGAAGAAGAA
1 GAAGAAA-AAGAAGAA
544436 GAAGAAAA
1 GAAGAAAA
544444 GGGAACAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 18 0.82
17 3 0.14
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (15 bp):
GAAGAAAAAGAAGAA
Found at i:551922 original size:37 final size:38
Alignment explanation
Indices: 551881--551952 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 38
551871 TTATACATAT
551881 AAAGTACATTCGGCTAA-AATTGTCATATGG-GAAAAAA
1 AAAGTACATTCGGCTAAGAATT-TCATATGGAGAAAAAA
* *
551918 AAAGTATATTTGGCTAAGAATTTCATATGGAGAAA
1 AAAGTACATTCGGCTAAGAATTTCATATGGAGAAA
551953 CAGCTGGTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
37 23 0.74
38 8 0.26
ACGTcount: A:0.44, C:0.08, G:0.19, T:0.28
Consensus pattern (38 bp):
AAAGTACATTCGGCTAAGAATTTCATATGGAGAAAAAA
Found at i:564876 original size:62 final size:61
Alignment explanation
Indices: 564755--566452 Score: 703
Period size: 62 Copynumber: 27.7 Consensus size: 61
564745 ATTATAATTG
* * * * ** * * **
564755 GACTTAAATATCTTGGATGCTAGTTT-GATCAGGCTTAAACTATTTCATGCCAATGTAACTA
1 GACTTATACATCTTGGATGCTAATTTAAATTGGGCTTAAACTATTT-GTACCAACATAACTA
* * * *
564816 GACTTATACATTTTGAATGCTAATTTAAATTGGGCTTAAGCTTATTTGTACTAACATAACTA
1 GACTTATACATCTTGGATGCTAATTTAAATTGGGCTTAAAC-TATTTGTACCAACATAACTA
* * * * * *
564878 TACTTATACATCTTGGATACTAGTTTAAATTGGGCTTAAACTCTTTGTGCCAACATAGCTA
1 GACTTATACATCTTGGATGCTAATTTAAATTGGGCTTAAACTATTTGTACCAACATAACTA
* * ** * * *
564939 GACTTAAACATCTTGGATGCTAA-CTAAATTGGGCTTAAACATATTTGTGTCAATATAATTG
1 GACTTATACATCTTGGATGCTAATTTAAATTGGGCTTAAAC-TATTTGTACCAACATAACTA
* * ** * * * * *
565000 GACTTAAACATCTTGGATG-TTAGCTAAATTTGGGTTTAAATCTCTTTGTGCCAATATAGCTA
1 GACTTATACATCTTGGATGCTAATTTAAA-TTGGGCTTAAA-CTATTTGTACCAACATAACTA
* ** * * * * * * *
565062 GACTTAAACATCTTGGATGCT-AGCTAGATTAGGCTTAAACATCTTTGTGCTAATATAACTG
1 GACTTATACATCTTGGATGCTAATTTAAATTGGGCTTAAAC-TATTTGTACCAACATAACTA
* ** * * *
565123 GACTTGA-ACATTTTGGATGCT-AGCTAAATTTGGGCTTAAATCTCTTTGTGCCAACATAGCTA
1 GACTT-ATACATCTTGGATGCTAATTTAAA-TTGGGCTTAAA-CTATTTGTACCAACATAACTA
* * * ** * * * ** *
565185 GACTTAAACATCTTGAATACT-AGCTAAATTGGGCTTAAACCCACTTTGTGCTAATGTAACTG
1 GACTTATACATCTTGGATGCTAATTTAAATTGGGCTTAAA-CTA-TTTGTACCAACATAACTA
* * * * * * **
565247 GACTTAAACATCTTGGATGCCAGTTT-GATTAGGC-TAAACTTATTTGTGCCAGTATAACTA
1 GACTTATACATCTTGGATGCTAATTTAAATTGGGCTTAAAC-TATTTGTACCAACATAACTA
* * * * * * * *
565307 GACTTGTACATCTTGGATACTAGTTTTAATTTGGCTTAAACTTTTTGTGCCAACATATCTA
1 GACTTATACATCTTGGATGCTAATTTAAATTGGGCTTAAACTATTTGTACCAACATAACTA
** * * * * *
565368 GACTTA-AGCATCTTGGATGCT-AGCTAAATTGGGCCTAAACATCTTTGTGCTAATATAACTA
1 GACTTATA-CATCTTGGATGCTAATTTAAATTGGGCTTAAAC-TATTTGTACCAACATAACTA
* * * * * *
565429 GACTTAAACATCTTGGATGC-CAGTTAAATTTGGGCTTAAATCTCTTGGTACCAACATAGCTTA
1 GACTTATACATCTTGGATGCTAATTTAAA-TTGGGCTTAAA-CTATTTGTACCAACATAAC-TA
* ** * * * * * *
565492 -ACTTAAACATCTTGGATGCTAGCTT-AATTGGGCCTTAAATGTCTTTATCCCAATATAACTG
1 GACTTATACATCTTGGATGCTAATTTAAATTGGG-CTTAAA-CTATTTGTACCAACATAACTA
* * * * * * * *
565553 GACTTAAATC-TCTTGGATGC-CAGTTAAATTTGGGCTTAAATCTCTTTGTGCTAGCATAGCTA
1 GACTTATA-CATCTTGGATGCTAATTTAAA-TTGGGCTTAAA-CTATTTGTACCAACATAACTA
* * ** * * * *
565615 GACTTAAATATCTTGGATGCT-AGCTAAATTGGGCTCAAACGTCTTTGTGCCAATATAAC-A
1 GACTTATACATCTTGGATGCTAATTTAAATTGGGCTTAAAC-TATTTGTACCAACATAACTA
* * * ** * * * *
565675 GGGCTTAAACATCTTGGATG-TCAGCTAAATTTGGGCTTAAATCTCTTTATGCCAACCTAACTA
1 -GACTTATACATCTTGGATGCTAATTTAAA-TTGGGCTTAAA-CTATTTGTACCAACATAACTA
* * ** * * * *
565738 GACTTAAACATCTTGGATACT-AGCTAAATTAGGCTTAAACATCTTTGTGCCAATC-TAACTG
1 GACTTATACATCTTGGATGCTAATTTAAATTGGGCTTAAAC-TATTTGTACCAA-CATAACTA
* ** ** * * * **
565799 GACTTAAACATCTTGGATGCT-AGCTAAATTTTAGCTTAAATCTCTTTGTGCTAACATAGTTA
1 GACTTATACATCTTGGATGCTAATTTAAA-TTGGGCTTAAA-CTATTTGTACCAACATAACTA
* * * * *
565861 GACTTAAACATCTTAGATGCT-AGTTAAATTGGGCTTAAA-TATCTTTGTGCCAATATAACTA
1 GACTTATACATCTTGGATGCTAATTTAAATTGGGCTTAAACTA--TTTGTACCAACATAACTA
* ** * * * * **
565922 GACTTAAACATCTTGGATGCT-AGCTAAATTTGGGTTTAAATCTCTTTATGCCAACATTGCTA
1 GACTTATACATCTTGGATGCTAATTTAAA-TTGGGCTTAAA-CTATTTGTACCAACATAACTA
* * ** * * * * *** * **
565984 GACTTAAACATCTTAGATGCT-AGCTAAATTAGGCTTAAATGTCTTTATGTTAATATATTTA
1 GACTTATACATCTTGGATGCTAATTTAAATTGGGCTTAAA-CTATTTGTACCAACATAACTA
* * **** * * * * *
566045 GTCTTAAACATCTTGGATGC-CGGCTAAATTTGTGCTTAAATCTCTTTATGCCAACATAGCTA
1 GACTTATACATCTTGGATGCTAATTTAAA-TTGGGCTTAAA-CTATTTGTACCAACATAACTA
* * ** * * *
566107 GACTTAAACATCTTGGATGC-CAGCTAAATTGGGCTTAAA-TATCTTTGTGCCCATATAACTA
1 GACTTATACATCTTGGATGCTAATTTAAATTGGGCTTAAACTA--TTTGTACCAACATAACTA
* * * * * * * *
566168 GACTTAAACATCTTAGATCCTAA-CTAAATTTGGGCTTAAATCTCTTTGTGCCAATATAGCTA
1 GACTTATACATCTTGGATGCTAATTTAAA-TTGGGCTTAAA-CTATTTGTACCAACATAACTA
* ** * * * *
566230 GACTTAAACATCTTGGATGCT-AGCTAAATTGGGTTTAAACATTTTTGTGCCAATATAACTA
1 GACTTATACATCTTGGATGCTAATTTAAATTGGGCTTAAAC-TATTTGTACCAACATAACTA
* * * * ** * * * *
566291 GACTTAAATATCTTGGGTGC-CAGCTAAGTTTAGGCTTAAATCTCTTTGTACCAACATAGCTA
1 GACTTATACATCTTGGATGCTAATTTAA-ATTGGGCTTAAA-CTATTTGTACCAACATAACTA
* * ** * * * *
566353 GACTTAAACATCTTGGATACT-AGCTAAATTGGGCTTAAA-TATCTTTGTGCCAATATAATTG
1 GACTTATACATCTTGGATGCTAATTTAAATTGGGCTTAAACTA--TTTGTACCAACATAACTA
* * *
566414 GGCTTAAACATCTTGGATGCCAA-TTAAATTGGGCTTAAA
1 GACTTATACATCTTGGATGCTAATTTAAATTGGGCTTAAA
566453 TCCTCTAGTT
Statistics
Matches: 1336, Mismatches: 235, Indels: 132
0.78 0.14 0.08
Matches are distributed among these distances:
59 3 0.00
60 75 0.06
61 604 0.45
62 627 0.47
63 25 0.02
64 2 0.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (61 bp):
GACTTATACATCTTGGATGCTAATTTAAATTGGGCTTAAACTATTTGTACCAACATAACTA
Found at i:564929 original size:123 final size:124
Alignment explanation
Indices: 564755--566454 Score: 1758
Period size: 123 Copynumber: 13.8 Consensus size: 124
564745 ATTATAATTG
* * ** ** * * *
564755 GACTTAAATATCTTGGATGCTAGTTTGATCAGGCTTAAA-CTATTTCATGCCAATGTAACTAGAC
1 GACTTAAACATCTTGGATGCTAGCTAAATTGGGCTTAAATCTCTTT-GTGCCAATATAACTAGAC
* * * ** * * * * *
564819 TTATACATTTTGAATGCTAATTTAAA-TTGGGCTT-AAGCTTATTTGTACTAACATAACTA
65 TTAAACATCTTGGATGCTAAGCTAAATTTGGGCTTAAATC-TCTTTGTGCCAACATAGCTA
* * * * * *
564878 TACTTATACATCTTGGATACTAGTTTAAATTGGGCTTAAA-CTCTTTGTGCCAACATAGCTAGAC
1 GACTTAAACATCTTGGATGCTAG-CTAAATTGGGCTTAAATCTCTTTGTGCCAATATAACTAGAC
* * * ** *
564942 TTAAACATCTTGGATGCTAA-CTAAA-TTGGGCTTAAA-CATATTTGTGTCAATATAATTG
65 TTAAACATCTTGGATGCTAAGCTAAATTTGGGCTTAAATC-TCTTTGTGCCAACATAGCTA
* * *
565000 GACTTAAACATCTTGGATGTTAGCTAAATTTGGGTTTAAATCTCTTTGTGCCAATATAGCTAGAC
1 GACTTAAACATCTTGGATGCTAGCTAAA-TTGGGCTTAAATCTCTTTGTGCCAATATAACTAGAC
* * * * * *
565065 TTAAACATCTTGGATGCT-AGCTAGA-TTAGGCTTAAA-CATCTTTGTGCTAATATAACTG
65 TTAAACATCTTGGATGCTAAGCTAAATTTGGGCTTAAATC-TCTTTGTGCCAACATAGCTA
* * * *
565123 GACTTGAACATTTTGGATGCTAGCTAAATTTGGGCTTAAATCTCTTTGTGCCAACATAGCTAGAC
1 GACTTAAACATCTTGGATGCTAGCTAAA-TTGGGCTTAAATCTCTTTGTGCCAATATAACTAGAC
* * * * * ** * *
565188 TTAAACATCTTGAATACT-AGCTAAA-TTGGGCTTAAACCCACTTTGTGCTAATGTAACTG
65 TTAAACATCTTGGATGCTAAGCTAAATTTGGGCTTAAA-TCTCTTTGTGCCAACATAGCTA
* * ** * * *
565247 GACTTAAACATCTTGGATGCCAGTTTGATTAGGC-TAAA-CTTATTTGTGCCAGTATAACTAGAC
1 GACTTAAACATCTTGGATGCTAGCTAAATTGGGCTTAAATC-TCTTTGTGCCAATATAACTAGAC
** * * * * *
565310 TTGTACATCTTGGATACT-AGTTTTAATTT-GGCTTAAA-CTTTTTGTGCCAACATATCTA
65 TTAAACATCTTGGATGCTAAG-CTAAATTTGGGCTTAAATCTCTTTGTGCCAACATAGCTA
* * *
565368 GACTTAAGCATCTTGGATGCTAGCTAAATTGGGCCTAAA-CATCTTTGTGCTAATATAACTAGAC
1 GACTTAAACATCTTGGATGCTAGCTAAATTGGGCTTAAATC-TCTTTGTGCCAATATAACTAGAC
* * * *
565432 TTAAACATCTTGGATGC-CAGTTAAATTTGGGCTTAAATCTCTTGGTACCAACATAGCTTA
65 TTAAACATCTTGGATGCTAAGCTAAATTTGGGCTTAAATCTCTTTGTGCCAACATAGC-TA
* * * * *
565492 -ACTTAAACATCTTGGATGCTAGCTTAATTGGGCCTTAAATGTCTTTATCCCAATATAACTGGAC
1 GACTTAAACATCTTGGATGCTAGCTAAATTGGG-CTTAAATCTCTTTGTGCCAATATAACTAGAC
* * * *
565556 TTAAATC-TCTTGGATGC-CAGTTAAATTTGGGCTTAAATCTCTTTGTGCTAGCATAGCTA
65 TTAAA-CATCTTGGATGCTAAGCTAAATTTGGGCTTAAATCTCTTTGTGCCAACATAGCTA
* * *
565615 GACTTAAATATCTTGGATGCTAGCTAAATTGGGCTCAAA-CGTCTTTGTGCCAATATAAC-AGGG
1 GACTTAAACATCTTGGATGCTAGCTAAATTGGGCTTAAATC-TCTTTGTGCCAATATAACTA-GA
* * * *
565678 CTTAAACATCTTGGATG-TCAGCTAAATTTGGGCTTAAATCTCTTTATGCCAACCTAACTA
64 CTTAAACATCTTGGATGCTAAGCTAAATTTGGGCTTAAATCTCTTTGTGCCAACATAGCTA
* * * *
565738 GACTTAAACATCTTGGATACTAGCTAAATTAGGCTTAAA-CATCTTTGTGCCAATCTAACTGGAC
1 GACTTAAACATCTTGGATGCTAGCTAAATTGGGCTTAAATC-TCTTTGTGCCAATATAACTAGAC
** * *
565802 TTAAACATCTTGGATGCT-AGCTAAATTTTAGCTTAAATCTCTTTGTGCTAACATAGTTA
65 TTAAACATCTTGGATGCTAAGCTAAATTTGGGCTTAAATCTCTTTGTGCCAACATAGCTA
* * *
565861 GACTTAAACATCTTAGATGCTAGTTAAATTGGGCTTAAATATCTTTGTGCCAATATAACTAGACT
1 GACTTAAACATCTTGGATGCTAGCTAAATTGGGCTTAAATCTCTTTGTGCCAATATAACTAGACT
* * *
565926 TAAACATCTTGGATGCT-AGCTAAATTTGGGTTTAAATCTCTTTATGCCAACATTGCTA
66 TAAACATCTTGGATGCTAAGCTAAATTTGGGCTTAAATCTCTTTGTGCCAACATAGCTA
* * * * ** ** *
565984 GACTTAAACATCTTAGATGCTAGCTAAATTAGGCTTAAATGTCTTTATGTTAATATATTTAGTCT
1 GACTTAAACATCTTGGATGCTAGCTAAATTGGGCTTAAATCTCTTTGTGCCAATATAACTAGACT
** * *
566049 TAAACATCTTGGATGC-CGGCTAAATTTGTGCTTAAATCTCTTTATGCCAACATAGCTA
66 TAAACATCTTGGATGCTAAGCTAAATTTGGGCTTAAATCTCTTTGTGCCAACATAGCTA
* * *
566107 GACTTAAACATCTTGGATGCCAGCTAAATTGGGCTTAAATATCTTTGTGCCCATATAACTAGACT
1 GACTTAAACATCTTGGATGCTAGCTAAATTGGGCTTAAATCTCTTTGTGCCAATATAACTAGACT
* * *
566172 TAAACATCTTAGATCCTAA-CTAAATTTGGGCTTAAATCTCTTTGTGCCAATATAGCTA
66 TAAACATCTTGGATGCTAAGCTAAATTTGGGCTTAAATCTCTTTGTGCCAACATAGCTA
* *
566230 GACTTAAACATCTTGGATGCTAGCTAAATTGGGTTTAAA-CATTTTTGTGCCAATATAACTAGAC
1 GACTTAAACATCTTGGATGCTAGCTAAATTGGGCTTAAATC-TCTTTGTGCCAATATAACTAGAC
* * * * * *
566294 TTAAATATCTTGGGTGC-CAGCTAAGTTTAGGCTTAAATCTCTTTGTACCAACATAGCTA
65 TTAAACATCTTGGATGCTAAGCTAAATTTGGGCTTAAATCTCTTTGTGCCAACATAGCTA
* * * * *
566353 GACTTAAACATCTTGGATACTAGCTAAATTGGGCTTAAATATCTTTGTGCCAATATAATTGGGCT
1 GACTTAAACATCTTGGATGCTAGCTAAATTGGGCTTAAATCTCTTTGTGCCAATATAACTAGACT
* *
566418 TAAACATCTTGGATGCCAA-TTAAA-TTGGGCTTAAATC
66 TAAACATCTTGGATGCTAAGCTAAATTTGGGCTTAAATC
566455 CTCTAGTTTT
Statistics
Matches: 1343, Mismatches: 202, Indels: 65
0.83 0.13 0.04
Matches are distributed among these distances:
121 54 0.04
122 160 0.12
123 959 0.71
124 168 0.13
125 2 0.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (124 bp):
GACTTAAACATCTTGGATGCTAGCTAAATTGGGCTTAAATCTCTTTGTGCCAATATAACTAGACT
TAAACATCTTGGATGCTAAGCTAAATTTGGGCTTAAATCTCTTTGTGCCAACATAGCTA
Done.