Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167926.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_19, 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: 20060819
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 113000 characters in sequence are not A, C, G, or T
File 25 of 117
Found at i:3192254 original size:18 final size:19
Alignment explanation
Indices: 3192218--3192259 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
3192208 CAAATTAAAT
3192218 TATATATTTTTATTAATTTA
1 TATATATTTTTA-TAATTTA
*
3192238 TATATATTTTTA-AATTTT
1 TATATATTTTTATAATTTA
3192256 TATA
1 TATA
3192260 AAATAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
20 12 0.57
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TATATATTTTTATAATTTA
Found at i:3192316 original size:21 final size:21
Alignment explanation
Indices: 3192284--3192328 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3192274 ATTTTAATAT
* *
3192284 AAATCTATTTAAATATATTAA
1 AAATCTATTTAAAAATATAAA
3192305 AAAT-TATATTAAAAATATAAA
1 AAATCTAT-TTAAAAATATAAA
3192326 AAA
1 AAA
3192329 ATCAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATCTATTTAAAAATATAAA
Found at i:3192336 original size:134 final size:134
Alignment explanation
Indices: 3192189--3192463 Score: 473
Period size: 134 Copynumber: 2.0 Consensus size: 134
3192179 ATTTCAATGT
* *
3192189 AAAAAAT-AAAAAAATGAATCAAATTAAATTATATATTTTTATTAATTTATATATATTTTTAAAT
1 AAAAAATAAAAAAAATAAATCAAATCAAATTATATATTTTTATTAA-TT-TATATA-TTTTAAAT
3192253 TTTTATAAAATAAAAATAATTATTTTA-ATATAAATCTATTTAAATATATTAAAAATTATATTAA
63 TTTTATAAAATAAAAATAATTATTTTATATATAAATCTATTTAAATATATTAAAAATTATATTAA
3192317 AAATATA
128 AAATATA
*
3192324 AAAAAATCAAAAAAATAAATCAAATCAAATTATATATTTTTATTAATTTATATATTTTAAATTTT
1 AAAAAATAAAAAAAATAAATCAAATCAAATTATATATTTTTATTAATTTATATATTTTAAATTTT
3192389 TATAAAATAAAAATAATTATTTTATATATAAATCTATTTAAATATATTAAAAATTATATTAAAAA
66 TATAAAATAAAAATAATTATTTTATATATAAATCTATTTAAATATATTAAAAATTATATTAAAAA
3192454 TATA
131 TATA
*
3192458 TAAAAA
1 AAAAAA
3192464 CTTTAAATTT
Statistics
Matches: 135, Mismatches: 3, Indels: 5
0.94 0.02 0.03
Matches are distributed among these distances:
133 35 0.26
134 55 0.41
135 9 0.07
136 36 0.27
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (134 bp):
AAAAAATAAAAAAAATAAATCAAATCAAATTATATATTTTTATTAATTTATATATTTTAAATTTT
TATAAAATAAAAATAATTATTTTATATATAAATCTATTTAAATATATTAAAAATTATATTAAAAA
TATA
Found at i:3192450 original size:21 final size:22
Alignment explanation
Indices: 3192411--3192463 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
3192401 ATAATTATTT
* *
3192411 TATATATAAATCTATTTAAATA
1 TATATAAAAATCTATTTAAAAA
3192433 TAT-TAAAAAT-TATATTAAAAA
1 TATATAAAAATCTAT-TTAAAAA
3192454 TATATAAAAA
1 TATATAAAAA
3192464 CTTTAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 3 0.11
21 15 0.56
22 9 0.33
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
TATATAAAAATCTATTTAAAAA
Found at i:3192452 original size:11 final size:11
Alignment explanation
Indices: 3192428--3192463 Score: 56
Period size: 12 Copynumber: 3.3 Consensus size: 11
3192418 AAATCTATTT
3192428 AAATATATTAA
1 AAATATATTAA
3192439 AAATTATATTAA
1 AAA-TATATTAA
3192451 AAATATA-TAA
1 AAATATATTAA
3192461 AAA
1 AAA
3192464 CTTTAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 6 0.25
11 7 0.29
12 11 0.46
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATATATTAA
Found at i:3204854 original size:33 final size:33
Alignment explanation
Indices: 3204811--3204873 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
3204801 TGATCATACG
3204811 ACCCTAGCTAACGGGTAATAATAATTAGCATAA
1 ACCCTAGCTAACGGGTAATAATAATTAGCATAA
* * *
3204844 ACCCTGGCTAACGGGTTATAATAGTTAGCA
1 ACCCTAGCTAACGGGTAATAATAATTAGCA
3204874 ATGATCATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (33 bp):
ACCCTAGCTAACGGGTAATAATAATTAGCATAA
Found at i:3205714 original size:18 final size:18
Alignment explanation
Indices: 3205693--3205740 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
3205683 ATTTCTTCCT
3205693 TTTTTTATTTTTGT-TCAC
1 TTTTTTATTTTTGTGT-AC
** *
3205711 TTTTACATTTTTGTGTAT
1 TTTTTTATTTTTGTGTAC
3205729 TTTTTTATTTTT
1 TTTTTTATTTTT
3205741 TATTGTTTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 23 0.96
19 1 0.04
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.75
Consensus pattern (18 bp):
TTTTTTATTTTTGTGTAC
Found at i:3206104 original size:20 final size:20
Alignment explanation
Indices: 3206063--3206104 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
3206053 ATCATGGGCA
*
3206063 TTTTTTATATTTTCTTTATT
1 TTTTTTATATTTTCTTCATT
* *
3206083 TTTTTTAT-TTTTGTTCACT
1 TTTTTTATATTTTCTTCATT
3206102 TTT
1 TTT
3206105 ACTTTTTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.79
Consensus pattern (20 bp):
TTTTTTATATTTTCTTCATT
Found at i:3211998 original size:18 final size:18
Alignment explanation
Indices: 3211977--3212018 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
3211967 TTTATAAAAA
3211977 TTATT-TTAATTATAATAT
1 TTATTATTAATTATAAT-T
* *
3211995 TTATTATTATTTTTAATT
1 TTATTATTAATTATAATT
3212013 TTATTA
1 TTATTA
3212019 AAATCAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATTATTAATTATAATT
Found at i:3212508 original size:11 final size:10
Alignment explanation
Indices: 3212480--3212509 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
3212470 AAATAAAAAT
3212480 ATTTTTAATA
1 ATTTTTAATA
3212490 ATTTTTAATA
1 ATTTTTAATA
3212500 ATTTATTAAT
1 ATTT-TTAAT
3212510 TTTATAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.74
11 5 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:3214755 original size:7 final size:7
Alignment explanation
Indices: 3214743--3214775 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
3214733 CAAAAAGATG
3214743 CTATGCC
1 CTATGCC
3214750 CTATGCC
1 CTATGCC
3214757 CTATGCC
1 CTATGCC
3214764 CTATGCC
1 CTATGCC
3214771 CTATG
1 CTATG
3214776 AAAAAACGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.15, C:0.39, G:0.15, T:0.30
Consensus pattern (7 bp):
CTATGCC
Found at i:3217233 original size:20 final size:21
Alignment explanation
Indices: 3217173--3217237 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 21
3217163 TATCTTTTTC
* *
3217173 TTTTTA-ATTTGTTT-TATTA
1 TTTTTATATTTATTTATAATA
3217192 TTATTTATTATTTATTTA-AATA
1 TT-TTTA-TATTTATTTATAATA
3217214 TTTTTATATTT-TTTATAATA
1 TTTTTATATTTATTTATAATA
3217234 TTTT
1 TTTT
3217238 ATTTTGACAC
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
19 6 0.15
20 17 0.44
21 4 0.10
22 12 0.31
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTTTATATTTATTTATAATA
Found at i:3234296 original size:37 final size:35
Alignment explanation
Indices: 3234225--3234297 Score: 85
Period size: 37 Copynumber: 2.0 Consensus size: 35
3234215 TTTTTTTTTC
* *
3234225 ATATTTTAATTTAAAATTTAATCTGAACTTAATAA
1 ATATTTTAATTTAAAATTTAATATGAAATTAATAA
*
3234260 ATATATTTAATATTTAAATTTAATAT-AAATTAAATAA
1 ATAT-TTTAAT-TTAAAATTTAATATGAAATT-AATAA
3234297 A
1 A
3234298 AAATGATCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 4 0.12
36 10 0.31
37 18 0.56
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (35 bp):
ATATTTTAATTTAAAATTTAATATGAAATTAATAA
Found at i:3237945 original size:48 final size:48
Alignment explanation
Indices: 3237820--3237946 Score: 130
Period size: 48 Copynumber: 2.6 Consensus size: 48
3237810 GTTGAAGAAA
* * * * *
3237820 CCCAACCAGACGTCGACTGAAGTGGCTTTTCCTGAGTAGCTTTTTTAT
1 CCCAACCAGAAGTCGACTGAACTGGCTTTTCCTCAATAGCTTTGTTAT
* * *
3237868 CCCAACCACAAGTCGATTGAACTGCCTTTTCCTCAATCA-CTTTGTTAT
1 CCCAACCAGAAGTCGACTGAACTGGCTTTTCCTCAAT-AGCTTTGTTAT
* * * *
3237916 TCCAACCAGATGTTGACTGCACTGGCTTTTC
1 CCCAACCAGAAGTCGACTGAACTGGCTTTTC
3237947 TTGACCTGAT
Statistics
Matches: 63, Mismatches: 15, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
48 62 0.98
49 1 0.02
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (48 bp):
CCCAACCAGAAGTCGACTGAACTGGCTTTTCCTCAATAGCTTTGTTAT
Found at i:3238231 original size:162 final size:159
Alignment explanation
Indices: 3237964--3238288 Score: 515
Period size: 162 Copynumber: 2.0 Consensus size: 159
3237954 GATTTGTTAT
* *
3237964 CCCATTCACTTTTCTCTCTCCCTTGGTCCAGGTGGGTATCATTTCCACTGAAGCCAGATTCATGA
1 CCCATTCACTTTCCGCTCTCCCTTGGTCCAGGTGGGTATCATTTCCACTGAAGCCAGATTCATGA
* * *
3238029 ACTGCTACAATCTTCTGTCCCCAGGAAGTAGCATTATCCCAGCCACCCGATTTGGAAGATTCCTT
66 ACTGCTACAATCTTCTGTCCCCAAGAAGAAGCATTATCCCAGCCACCCAATTTGGAAGATTCCTT
*
3238094 GAAGGGTTTTTTAGGGATGGCATCTTGTGTGC
131 CAA-GG--TTTTAGGGATGGCATCTTGTGTGC
* *
3238126 CCCATTCACTTTCCGCTCTCCCTTGGTCCTGGTGGTTATCATTTCCACTGAAGCCAGATTCATGA
1 CCCATTCACTTTCCGCTCTCCCTTGGTCCAGGTGGGTATCATTTCCACTGAAGCCAGATTCATGA
* * *
3238191 ACTGCTACAATCTTCTTTCCCCAAGAAGAAGCATTATCCCAGCCACTCAATTTGGAAGATTCGTT
66 ACTGCTACAATCTTCTGTCCCCAAGAAGAAGCATTATCCCAGCCACCCAATTTGGAAGATTCCTT
*
3238256 CAAGGTTTTAGGGATGGCATCTTGTGTTC
131 CAAGGTTTTAGGGATGGCATCTTGTGTGC
3238285 CCCA
1 CCCA
3238289 CGCATCACTA
Statistics
Matches: 151, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
159 27 0.18
161 2 0.01
162 122 0.81
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.32
Consensus pattern (159 bp):
CCCATTCACTTTCCGCTCTCCCTTGGTCCAGGTGGGTATCATTTCCACTGAAGCCAGATTCATGA
ACTGCTACAATCTTCTGTCCCCAAGAAGAAGCATTATCCCAGCCACCCAATTTGGAAGATTCCTT
CAAGGTTTTAGGGATGGCATCTTGTGTGC
Found at i:3246324 original size:2 final size:2
Alignment explanation
Indices: 3246317--3246348 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3246307 TAATCTTGTA
*
3246317 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3246349 TTGTATCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:3249203 original size:22 final size:23
Alignment explanation
Indices: 3249177--3249220 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3249167 AATATACATT
3249177 CAGTTTTA-CTCTTAGTTTTTCA
1 CAGTTTTATCTCTTAGTTTTTCA
*
3249199 CAGTTTTATTTCTTAGTTTTTC
1 CAGTTTTATCTCTTAGTTTTTC
3249221 CACATGGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.16, C:0.16, G:0.09, T:0.59
Consensus pattern (23 bp):
CAGTTTTATCTCTTAGTTTTTCA
Found at i:3249323 original size:25 final size:24
Alignment explanation
Indices: 3249289--3249351 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 24
3249279 TGACTTCTAT
*
3249289 TTTAGGCCTTCATTACCGAACCCTA
1 TTTAAGCCTTCATTACCGAACCC-A
*
3249314 TTTAAGCCTTCATTATCGAACCCA
1 TTTAAGCCTTCATTACCGAACCCA
*
3249338 ATTAAGGCCTTCAT
1 TTTAA-GCCTTCAT
3249352 AGCCATTCTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 5 0.15
25 29 0.85
ACGTcount: A:0.27, C:0.29, G:0.11, T:0.33
Consensus pattern (24 bp):
TTTAAGCCTTCATTACCGAACCCA
Found at i:3253081 original size:22 final size:22
Alignment explanation
Indices: 3253056--3253099 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3253046 TGTATATTTA
*
3253056 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
3253078 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
3253100 GACAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:3262653 original size:19 final size:18
Alignment explanation
Indices: 3262624--3262663 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
3262614 CAATTTTCAA
*
3262624 TTTAAATATTTTTATTGT
1 TTTAAATATTTTTATTAT
3262642 TTTAATATATTTTTATTAT
1 TTTAA-ATATTTTTATTAT
3262661 TTT
1 TTT
3262664 TATCTTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (18 bp):
TTTAAATATTTTTATTAT
Found at i:3263186 original size:48 final size:46
Alignment explanation
Indices: 3263128--3263226 Score: 162
Period size: 48 Copynumber: 2.1 Consensus size: 46
3263118 AATCTTAAAG
3263128 TTAAAGGTATAACTTTTATTGTTTTAATCTCTTATTTATTGTTTCCTT
1 TTAAAGGTATAACTTTTATTGTTTTAATCTCTTATTTATTG-TT-CTT
* *
3263176 TTAAGGGTATAATTTTTATTGTTTTAATCTCTTATTTATTGTTCTT
1 TTAAAGGTATAACTTTTATTGTTTTAATCTCTTATTTATTGTTCTT
3263222 TTAAA
1 TTAAA
3263227 AAAAAAATCA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
46 7 0.15
47 2 0.04
48 39 0.81
ACGTcount: A:0.24, C:0.08, G:0.09, T:0.59
Consensus pattern (46 bp):
TTAAAGGTATAACTTTTATTGTTTTAATCTCTTATTTATTGTTCTT
Found at i:3263223 original size:23 final size:23
Alignment explanation
Indices: 3263149--3263225 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
3263139 ACTTTTATTG
3263149 TTTTAATCTCTTATTTATTGTTTCC
1 TTTTAATCTCTTATTTATTG-TT-C
** * * * *
3263174 TTTTAAGGGTATAATTT-TTATTG
1 TTTTAA-TCTCTTATTTATTGTTC
3263197 TTTTAATCTCTTATTTATTGTTC
1 TTTTAATCTCTTATTTATTGTTC
3263220 TTTTAA
1 TTTTAA
3263226 AAAAAAAATC
Statistics
Matches: 38, Mismatches: 12, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
22 6 0.16
23 16 0.42
24 2 0.05
25 8 0.21
26 6 0.16
ACGTcount: A:0.21, C:0.09, G:0.08, T:0.62
Consensus pattern (23 bp):
TTTTAATCTCTTATTTATTGTTC
Found at i:3266668 original size:20 final size:20
Alignment explanation
Indices: 3266643--3266684 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
3266633 GATTTTTGCT
3266643 AAAAAAAAAT-AAAAAAATG
1 AAAAAAAAATGAAAAAAATG
*
3266662 AAAAAAAACTGAAAAAAATG
1 AAAAAAAAATGAAAAAAATG
3266682 AAA
1 AAA
3266685 TAAGAGGTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.81, C:0.02, G:0.07, T:0.10
Consensus pattern (20 bp):
AAAAAAAAATGAAAAAAATG
Found at i:3266683 original size:9 final size:9
Alignment explanation
Indices: 3266645--3266684 Score: 55
Period size: 10 Copynumber: 4.3 Consensus size: 9
3266635 TTTTTGCTAA
3266645 AAAAAAAT-
1 AAAAAAATG
3266653 AAAAAAATG
1 AAAAAAATG
3266662 AAAAAAAACTG
1 -AAAAAAA-TG
3266673 AAAAAAATG
1 AAAAAAATG
3266682 AAA
1 AAA
3266685 TAAGAGGTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.28
9 5 0.17
10 14 0.48
11 2 0.07
ACGTcount: A:0.80, C:0.03, G:0.07, T:0.10
Consensus pattern (9 bp):
AAAAAAATG
Found at i:3267391 original size:12 final size:12
Alignment explanation
Indices: 3267374--3267419 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
3267364 TTTTTTGGTT
3267374 TTTTTGTATTTA
1 TTTTTGTATTTA
3267386 TTTTTGTATTTA
1 TTTTTGTATTTA
*
3267398 TATGTT-TATTT-
1 T-TTTTGTATTTA
*
3267409 TTTTAGTATTT
1 TTTTTGTATTT
3267420 TTGCATGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
10 2 0.07
11 6 0.21
12 18 0.62
13 3 0.10
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (12 bp):
TTTTTGTATTTA
Found at i:3269259 original size:26 final size:23
Alignment explanation
Indices: 3269223--3269271 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 23
3269213 TAGGGTATGT
3269223 TAGGTAAATAAGATTATGATATAA
1 TAGGTAAATAAGATTATGA-ATAA
*
3269247 TAGGATAAGATAATATTATGAATAA
1 TAGG-TAA-ATAAGATTATGAATAA
3269272 GATTAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 4 0.18
25 7 0.32
26 11 0.50
ACGTcount: A:0.51, C:0.00, G:0.16, T:0.33
Consensus pattern (23 bp):
TAGGTAAATAAGATTATGAATAA
Found at i:3270588 original size:23 final size:23
Alignment explanation
Indices: 3270562--3270610 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
3270552 TTTTTCAATA
3270562 TAATTGTTATTT-TATTTTATTTT
1 TAATT-TTATTTGTATTTTATTTT
* *
3270585 TAATTTTGTTTGTTTTTTATTTT
1 TAATTTTATTTGTATTTTATTTT
3270608 TAA
1 TAA
3270611 AAGACTAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.73
Consensus pattern (23 bp):
TAATTTTATTTGTATTTTATTTT
Found at i:3273102 original size:19 final size:20
Alignment explanation
Indices: 3273080--3273123 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
3273070 CATTTTCTCA
*
3273080 ATTTA-TTTATTTTTTAAAT
1 ATTTATTTTAGTTTTTAAAT
*
3273099 ATTTATTTTAGTTTTTAATT
1 ATTTATTTTAGTTTTTAAAT
3273119 ATTTA
1 ATTTA
3273124 ATTGAGTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (20 bp):
ATTTATTTTAGTTTTTAAAT
Found at i:3273139 original size:20 final size:20
Alignment explanation
Indices: 3273090--3273136 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
3273080 ATTTATTTAT
* * *
3273090 TTTTTAAATATTTATTTTAG
1 TTTTTAATTATTTAATTGAG
3273110 TTTTTAATTATTTAATTGAG
1 TTTTTAATTATTTAATTGAG
3273130 TTATTTA
1 TT-TTTA
3273137 TTAACAATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (20 bp):
TTTTTAATTATTTAATTGAG
Found at i:3278248 original size:13 final size:13
Alignment explanation
Indices: 3278230--3278259 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3278220 TTATTATTTT
*
3278230 ATAATAATAATTA
1 ATAATAATAAATA
3278243 ATAATAATAAATA
1 ATAATAATAAATA
3278256 ATAA
1 ATAA
3278260 AATTTATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
ATAATAATAAATA
Found at i:3278521 original size:22 final size:22
Alignment explanation
Indices: 3278477--3278521 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3278467 TTTCTTTTCC
* *
3278477 TTAATAAAATAATAAAAATTAA
1 TTAATAAAATAAGAAAAAGTAA
* *
3278499 TTAATAAATTAAGAATAAGTAA
1 TTAATAAAATAAGAAAAAGTAA
3278521 T
1 T
3278522 AAAAATGAGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (22 bp):
TTAATAAAATAAGAAAAAGTAA
Found at i:3289748 original size:12 final size:13
Alignment explanation
Indices: 3289728--3289761 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
3289718 ATATTTTGCT
3289728 TGAAAAAAA-AGAA
1 TGAAAAAAATA-AA
3289741 TGAAAAAAATAAA
1 TGAAAAAAATAAA
3289754 TGAAAAAA
1 TGAAAAAA
3289762 TGATGGCCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 19 0.95
14 1 0.05
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (13 bp):
TGAAAAAAATAAA
Found at i:3290754 original size:49 final size:48
Alignment explanation
Indices: 3290569--3290931 Score: 374
Period size: 49 Copynumber: 7.6 Consensus size: 48
3290559 GTTTTGAAAA
* *
3290569 AAGATGAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAAGAGCTTTTTC
1 AAGATGAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC
* *
3290617 AAGATTAA-TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCATTTT-
1 AAGATGAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC
* * *
3290663 AA-A--AATTTTTAAAGTTGTTGAGCTTCTGCTGAGAGAAACTTTTTC
1 AAGATGAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC
* * ** *
3290708 AAGATGAGATTTTTAAAGTCGTTAAGCCTCTATTTAGAGGAGCTTTTTTTTC
1 AAGATGA-ATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGC---TTTTTC
* * *
3290760 AAGATG-ATATTTTAAAGTTATTGAGCTTCTGCTTAGAGGAGC-TTTTC
1 AAGATGAAT-TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC
* * *
3290807 TAAGATAAGAA-TTTTAAAGTTGTTGAGCCTCTACTTAGAGGAGTTTTTTC
1 -AAGAT--GAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC
3290857 AAGAT-AATTTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-TATTTTC
1 AAGATGAA-TTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCT-TTTTC
*
3290905 -A-A-GAATTTTTAAAGTTATTGAGCCTCT
1 AAGATGAATTTTTAAAGTTGTTGAGCCTCT
3290932 TATTAGATGA
Statistics
Matches: 268, Mismatches: 28, Indels: 41
0.80 0.08 0.12
Matches are distributed among these distances:
43 2 0.01
44 34 0.13
45 24 0.09
46 8 0.03
47 43 0.16
48 48 0.18
49 61 0.23
50 8 0.03
51 28 0.10
52 12 0.04
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (48 bp):
AAGATGAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC
Found at i:3290805 original size:100 final size:97
Alignment explanation
Indices: 3290569--3290946 Score: 406
Period size: 100 Copynumber: 4.0 Consensus size: 97
3290559 GTTTTGAAAA
* *
3290569 AAGATGAA-ATTTTAAAGTTGTTGAGCCTCTGCTGAGAAGAGCTTTTTCAAGATTA-ATTTTAAA
1 AAGAT-AATATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATAAGATTTTAAA
* * *
3290632 GTTGTTGAGCCTCTGCTGAGAGGAGC-ATTTT-
65 GTTGTTGAGCCTCTACTTAGAGGAGCTTTTTTC
* * * *
3290663 AA-A-AAT-TTTTAAAGTTGTTGAGCTTCTGCTGAGAGAAACTTTTTCAAGATGAGATTTTTAAA
1 AAGATAATATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATAAGA-TTTTAAA
* * *
3290725 GTCGTTAAGCCTCTATTTAGAGGAGCTTTTTTTTC
65 GTTGTTGAGCCTCTACTTAGAGGAGC--TTTTTTC
* * * *
3290760 AAGATGATATTTTAAAGTTATTGAGCTTCTGCTTAGAGGAGC-TTTTCTAAGATAAGAATTTTAA
1 AAGATAATATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC-AAGATAAG-ATTTTAA
3290824 AGTTGTTGAGCCTCTACTTAGAGGAG-TTTTTTC
64 AGTTGTTGAGCCTCTACTTAGAGGAGCTTTTTTC
* *
3290857 AAGATAATTTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-TATTTTCAAG--AA-TTTTTAAA
1 AAGATAATATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCT-TTTTCAAGATAAGATTTTAAA
* *
3290918 GTTATTGAGCCTCTTA-TTAGATGAGCTTT
65 GTTGTTGAGCCTC-TACTTAGAGGAGCTTT
3290947 CTAAATTTAA
Statistics
Matches: 240, Mismatches: 28, Indels: 32
0.80 0.09 0.11
Matches are distributed among these distances:
91 43 0.18
92 1 0.00
93 56 0.23
94 7 0.03
95 2 0.01
96 4 0.02
97 48 0.20
98 6 0.03
99 7 0.03
100 65 0.27
101 1 0.00
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.40
Consensus pattern (97 bp):
AAGATAATATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATAAGATTTTAAAG
TTGTTGAGCCTCTACTTAGAGGAGCTTTTTTC
Found at i:3290916 original size:193 final size:191
Alignment explanation
Indices: 3290569--3290946 Score: 473
Period size: 193 Copynumber: 2.0 Consensus size: 191
3290559 GTTTTGAAAA
* *
3290569 AAGATGAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAAGAGCTTTTTCAAGATTAATTTTAAAGT
1 AAGATGAAATTTTAAAGTTATTGAGCCTCTGCTGAGAAGAGCTTTTTCAAGATGAATTTTAAAGT
* *
3290634 TGTTGAGCCTCTGCTGAGAGGAGCATTTTAAAAATTTTTAAAGTTGTTGAGCTTCTGCTGAGAGA
66 TGTTGAGCCTCTACTGAGAGGAGCATTTTAAAAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGA
*
3290699 AACTTTTTCAAGATGAGATTTTTAAAGTCGTTAAGCCTC-TATTTAGAGGAGCTTTTTTTTC
131 AACTTTTTCAAGATGAGATTTTTAAAGTCATTAAGCCTCTTA-TTAGAGGAGCTTTTTTTTC
* * * *
3290760 AAGATGATATTTTAAAGTTATTGAGCTTCTGCTTAGAGGAGC-TTTTCTAAGATAAGAATTTTAA
1 AAGATGAAATTTTAAAGTTATTGAGCCTCTGCTGAGAAGAGCTTTTTC-AAGAT--GAATTTTAA
* **
3290824 AGTTGTTGAGCCTCTACTTAGAGGAGTTTTTTCAAGATAATTTTTTAAAGTTGTTGAGCCTCTGC
63 AGTTGTTGAGCCTCTACTGAGAGGAGCATTTT-AA-A-AA-TTTTTAAAGTTGTTGAGCCTCTGC
* * * * *
3290889 TGAGAG-GAGTATTTTC-A-A-GA-ATTTTTAAAGTTATTGAGCCTCTTATTAGATGAGCTTT
124 TGAGAGAAACT-TTTTCAAGATGAGATTTTTAAAGTCATTAAGCCTCTTATTAGAGGAGCTTT
3290947 CTAAATTTAA
Statistics
Matches: 161, Mismatches: 17, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
190 5 0.03
191 42 0.26
193 67 0.42
194 6 0.04
195 2 0.01
196 5 0.03
197 34 0.21
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.40
Consensus pattern (191 bp):
AAGATGAAATTTTAAAGTTATTGAGCCTCTGCTGAGAAGAGCTTTTTCAAGATGAATTTTAAAGT
TGTTGAGCCTCTACTGAGAGGAGCATTTTAAAAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGA
AACTTTTTCAAGATGAGATTTTTAAAGTCATTAAGCCTCTTATTAGAGGAGCTTTTTTTTC
Found at i:3291269 original size:14 final size:14
Alignment explanation
Indices: 3291250--3291278 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3291240 GCGCCAGTCT
3291250 ATAAAAAAATAAAA
1 ATAAAAAAATAAAA
3291264 ATAAAAAAATAAAA
1 ATAAAAAAATAAAA
3291278 A
1 A
3291279 AATCACTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (14 bp):
ATAAAAAAATAAAA
Found at i:3291272 original size:9 final size:8
Alignment explanation
Indices: 3291250--3291281 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
3291240 GCGCCAGTCT
3291250 ATAAAAAA
1 ATAAAAAA
3291258 AT--AAAA
1 ATAAAAAA
3291264 ATAAAAAA
1 ATAAAAAA
3291272 ATAAAAAA
1 ATAAAAAA
3291280 AT
1 AT
3291282 CACTTTGACC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 6 0.27
8 16 0.73
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (8 bp):
ATAAAAAA
Found at i:3291900 original size:13 final size:13
Alignment explanation
Indices: 3291882--3291911 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3291872 TTATTGTTTT
*
3291882 ATAATAATAATTA
1 ATAATAATAAATA
3291895 ATAATAATAAATA
1 ATAATAATAAATA
3291908 ATAA
1 ATAA
3291912 AATTTATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
ATAATAATAAATA
Found at i:3291935 original size:15 final size:12
Alignment explanation
Indices: 3291879--3291928 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
3291869 TTTTTATTGT
3291879 TTTATAATAATAA
1 TTTATAATAA-AA
*
3291892 TTAATAATAATAA
1 TTTATAATAA-AA
3291905 ---ATAATAAAA
1 TTTATAATAAAA
3291914 TTTATAATAAAA
1 TTTATAATAAAA
3291926 TTT
1 TTT
3291929 TTGATAAGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
9 2 0.06
10 7 0.21
12 12 0.36
13 12 0.36
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TTTATAATAAAA
Found at i:3291983 original size:21 final size:21
Alignment explanation
Indices: 3291940--3291983 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3291930 TGATAAGTAT
* *
3291940 AATTAAATAAAAATAATACAA
1 AATTAAATAAAAATAAGAAAA
3291961 AATT-AATAAAAAATAAGAAAA
1 AATTAAAT-AAAAATAAGAAAA
3291982 AA
1 AA
3291984 AATTTTTATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.20
Consensus pattern (21 bp):
AATTAAATAAAAATAAGAAAA
Found at i:3293323 original size:34 final size:35
Alignment explanation
Indices: 3293266--3293342 Score: 88
Period size: 34 Copynumber: 2.2 Consensus size: 35
3293256 TATTTTGGTT
* * *
3293266 TTAATCGAATTAATCGATCAAATTGATTT-AATTCAA
1 TTAATC-AATTAATCCACCAAATTAATTTCAA-TCAA
3293302 TTAATCAATTAA-CCACCAAATTAATTTCAATCAA
1 TTAATCAATTAATCCACCAAATTAATTTCAATCAA
3293336 TT-ATCAA
1 TTAATCAA
3293343 ATATAATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
33 5 0.14
34 18 0.49
35 8 0.22
36 6 0.16
ACGTcount: A:0.44, C:0.16, G:0.04, T:0.36
Consensus pattern (35 bp):
TTAATCAATTAATCCACCAAATTAATTTCAATCAA
Found at i:3294096 original size:16 final size:17
Alignment explanation
Indices: 3294068--3294099 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3294058 AATATATGAA
3294068 TTAAAATTTTATTTTTC
1 TTAAAATTTTATTTTTC
3294085 TTAAAA-TTTATTTTT
1 TTAAAATTTTATTTTT
3294100 ATTACTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (17 bp):
TTAAAATTTTATTTTTC
Found at i:3294242 original size:20 final size:20
Alignment explanation
Indices: 3294196--3294243 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
3294186 TTTAAAATTT
* *
3294196 ATTTATAATATAATATTTTG
1 ATTTTTAATATAATAGTTTG
*
3294216 A-TTTTAATATATTAGTTTG
1 ATTTTTAATATAATAGTTTG
3294235 ATTTTTAAT
1 ATTTTTAAT
3294244 TCAAATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (20 bp):
ATTTTTAATATAATAGTTTG
Found at i:3294604 original size:17 final size:17
Alignment explanation
Indices: 3294555--3294612 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
3294545 TTAGATAAAA
* *
3294555 AATGATAAAATTACCTT
1 AATGATTAAATTACTTT
* *
3294572 AAT-AATAATATCACTTT
1 AATGATTAA-ATTACTTT
3294589 AATGATTAAATTACTTT
1 AATGATTAAATTACTTT
3294606 AATGATT
1 AATGATT
3294613 TTAAAAATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
16 3 0.09
17 26 0.79
18 4 0.12
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (17 bp):
AATGATTAAATTACTTT
Found at i:3300556 original size:460 final size:460
Alignment explanation
Indices: 3299696--3300618 Score: 1774
Period size: 460 Copynumber: 2.0 Consensus size: 460
3299686 TCACTCTTGT
3299696 ATTGCTTTCAGTTCAATGCACACGACTCTAAGCTGCAGTCGCCAGGCCTTTCAATCACAGTATCA
1 ATTGCTTTCAGTTCAATGCACACGACTCTAAGCTGCAGTCGCCAGGCCTTTCAATCACAGTATCA
3299761 GCAAAATCGAGTGCTTCAATTTCAAGAAAAAAACGTGTAAATTCTAGCCTACAATTGTCAACATG
66 GCAAAATCGAGTGCTTCAATTTCAAGAAAAAAACGTGTAAATTCTAGCCTACAATTGTCAACATG
3299826 ATATGACTAACAATTTAGCCAATAGCCTCTCCAAACGTAGCCTAATTTTTTAGCATGATTAGCAA
131 ATATGACTAACAATTTAGCCAATAGCCTCTCCAAACGTAGCCTAATTTTTTAGCATGATTAGCAA
3299891 GGCACCATGGTCTGAATCTAGTAGAAATGCACTGCTTAGAGTGACATGGTCTGACATATCACACG
196 GGCACCATGGTCTGAATCTAGTAGAAATGCACTGCTTAGAGTGACATGGTCTGACATATCACACG
*
3299956 AGGGAAATGCAGGGCATGATCAAATTCTAACTTGGTTTTGGACCCCCATAAAGTGGAGGGATGGA
261 AGGGAAATGCAGGGAATGATCAAATTCTAACTTGGTTTTGGACCCCCATAAAGTGGAGGGATGGA
3300021 CCCTTGTCAAGTCCTTTTCTCTGACCGATTCAGGAACTTGGAAATAATGGAGTAGAAACATATAC
326 CCCTTGTCAAGTCCTTTTCTCTGACCGATTCAGGAACTTGGAAATAATGGAGTAGAAACATATAC
3300086 ATATATTAGATTTGAAGCGATTCCTTTAGCAGTGTCTATCTGTTGATGACTTCGGTGGGAAAAAA
391 ATATATTAGATTTGAAGCGATTCCTTTAGCAGTGTCTATCTGTTGATGACTTCGGTGGGAAAAAA
3300151 ACAGC
456 ACAGC
3300156 ATTGCTTTCAGTTCAATGCACACGACTCTAAGCTGCAGTCGCCAGGCCTTTCAATCACAGTATCA
1 ATTGCTTTCAGTTCAATGCACACGACTCTAAGCTGCAGTCGCCAGGCCTTTCAATCACAGTATCA
* *
3300221 GCAAAATCGAGTGCTTCAATTTCAAGAATAAAAGGTGTAAATTCTAGCCTACAATTGTCAACATG
66 GCAAAATCGAGTGCTTCAATTTCAAGAAAAAAACGTGTAAATTCTAGCCTACAATTGTCAACATG
*
3300286 ATATGACTAACAATTTAGCCAATAGCCTCTCCAAACGTAGCCTAATTTTTTAGCATGATTAGCAT
131 ATATGACTAACAATTTAGCCAATAGCCTCTCCAAACGTAGCCTAATTTTTTAGCATGATTAGCAA
3300351 GGCACCATGGTCTGAATCTAGTAGAAATGCACTGCTTAGAGTGACATGGTCTGACATATCACACG
196 GGCACCATGGTCTGAATCTAGTAGAAATGCACTGCTTAGAGTGACATGGTCTGACATATCACACG
*
3300416 AGGGAAATGCAGGGAATGATCAAATTCTAACTTGGTTTTGGACCCTCATAAAGTGGAGGGATGGA
261 AGGGAAATGCAGGGAATGATCAAATTCTAACTTGGTTTTGGACCCCCATAAAGTGGAGGGATGGA
*
3300481 CCCTTTTCAAGTCCTTTTCTCTGACCGATTCAGGAACTTGGAAATAATGGAGTAGAAACATATAC
326 CCCTTGTCAAGTCCTTTTCTCTGACCGATTCAGGAACTTGGAAATAATGGAGTAGAAACATATAC
*
3300546 ATATATTAGATTTGAAGCGATTCCTTTAGCAGTGTCTATCTGTTGATGACTTTGGTGGGAAAAAA
391 ATATATTAGATTTGAAGCGATTCCTTTAGCAGTGTCTATCTGTTGATGACTTCGGTGGGAAAAAA
*
3300611 GCAGC
456 ACAGC
3300616 ATT
1 ATT
3300619 AACTTGCAGA
Statistics
Matches: 455, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
460 455 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (460 bp):
ATTGCTTTCAGTTCAATGCACACGACTCTAAGCTGCAGTCGCCAGGCCTTTCAATCACAGTATCA
GCAAAATCGAGTGCTTCAATTTCAAGAAAAAAACGTGTAAATTCTAGCCTACAATTGTCAACATG
ATATGACTAACAATTTAGCCAATAGCCTCTCCAAACGTAGCCTAATTTTTTAGCATGATTAGCAA
GGCACCATGGTCTGAATCTAGTAGAAATGCACTGCTTAGAGTGACATGGTCTGACATATCACACG
AGGGAAATGCAGGGAATGATCAAATTCTAACTTGGTTTTGGACCCCCATAAAGTGGAGGGATGGA
CCCTTGTCAAGTCCTTTTCTCTGACCGATTCAGGAACTTGGAAATAATGGAGTAGAAACATATAC
ATATATTAGATTTGAAGCGATTCCTTTAGCAGTGTCTATCTGTTGATGACTTCGGTGGGAAAAAA
ACAGC
Found at i:3310800 original size:17 final size:17
Alignment explanation
Indices: 3310775--3310810 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3310765 AATTTTAAAA
3310775 TTTTAAAATATAAATAT
1 TTTTAAAATATAAATAT
* *
3310792 TTTTTAAATTTAAATAT
1 TTTTAAAATATAAATAT
3310809 TT
1 TT
3310811 AATTATGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTAAAATATAAATAT
Found at i:3318770 original size:21 final size:19
Alignment explanation
Indices: 3318744--3318823 Score: 60
Period size: 21 Copynumber: 4.1 Consensus size: 19
3318734 TTTTTACGAA
3318744 TATTAAAATAGTCATATTTAT
1 TATTAAAATA-T-ATATTTAT
*
3318765 TATTAAAATA-AT-TATAT
1 TATTAAAATATATATTTAT
3318782 TATTAAAATAATTATATTT-T
1 TATTAAAAT-A-TATATTTAT
*
3318802 ATATTAAAAGTATCTA-TTAT
1 -TATTAAAA-TATATATTTAT
3318822 TA
1 TA
3318824 AATAATAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
17 13 0.27
18 3 0.06
19 4 0.08
20 7 0.14
21 21 0.43
22 1 0.02
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (19 bp):
TATTAAAATATATATTTAT
Found at i:3318799 original size:14 final size:17
Alignment explanation
Indices: 3318762--3318799 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
3318752 TAGTCATATT
3318762 TATTATTAAAATAATTA
1 TATTATTAAAATAATTA
3318779 TATTATTAAAATAATTA
1 TATTATTAAAATAATTA
3318796 TATT
1 TATT
3318800 TTATATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATTATTAAAATAATTA
Found at i:3319012 original size:36 final size:37
Alignment explanation
Indices: 3318954--3319031 Score: 88
Period size: 36 Copynumber: 2.1 Consensus size: 37
3318944 TCATATTTTA
* * *
3318954 AAAATAATATTATTAAATTATTTAACA-TTAATTATT
1 AAAATAATAATATTAAAATATTTAACATTTAAATATT
**
3318990 AAAATAATAATA-TAATAATATTTATTATTTAAATATT
1 AAAATAATAATATTAA-AATATTTAACATTTAAATATT
3319027 AAAAT
1 AAAAT
3319032 TATTTATGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
35 3 0.09
36 19 0.54
37 13 0.37
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (37 bp):
AAAATAATAATATTAAAATATTTAACATTTAAATATT
Found at i:3324614 original size:12 final size:12
Alignment explanation
Indices: 3324599--3324624 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3324589 TTTAAAATTA
3324599 AATTAATAAAAT
1 AATTAATAAAAT
3324611 AATTAATAAAAT
1 AATTAATAAAAT
3324623 AA
1 AA
3324625 AACTTTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AATTAATAAAAT
Found at i:3327342 original size:31 final size:31
Alignment explanation
Indices: 3327300--3327370 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
3327290 TTTTTAGATT
*
3327300 TTTTAAATTATTATATTT-ACTTCTTTCAATA
1 TTTTAATTTATTA-ATTTCACTTCTTTCAATA
* * * *
3327331 TTTTAATTTATTAATTTCATTTTTTTTAATT
1 TTTTAATTTATTAATTTCACTTCTTTCAATA
3327362 TTTTAATTT
1 TTTTAATTT
3327371 TGAATTTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 4 0.12
31 30 0.88
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (31 bp):
TTTTAATTTATTAATTTCACTTCTTTCAATA
Found at i:3327371 original size:15 final size:15
Alignment explanation
Indices: 3327331--3327388 Score: 57
Period size: 15 Copynumber: 3.8 Consensus size: 15
3327321 TCTTTCAATA
3327331 TTTTAATTTATTAATT
1 TTTTAATTT-TTAATT
3327347 TCATTT--TTTTTAATT
1 T--TTTAATTTTTAATT
*
3327362 TTTTAATTTTGAATT
1 TTTTAATTTTTAATT
*
3327377 TTTTAATATTTA
1 TTTTAATTTTTA
3327389 GAAATTTAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
13 3 0.09
15 25 0.71
16 4 0.11
18 3 0.09
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (15 bp):
TTTTAATTTTTAATT
Found at i:3328429 original size:29 final size:29
Alignment explanation
Indices: 3328370--3328456 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
3328360 AGTGAGTATT
* *
3328370 ATATTA-ATTAATAAA-TTTATAATTTAT
1 ATATTATATTAAAAAATTTTATAATTTAA
*
3328397 ATATTATATTAAAAAATTTTAAAATTTAA
1 ATATTATATTAAAAAATTTTATAATTTAA
* * *
3328426 ATATCATATTAAATAGTTATTATAATTTAA
1 ATATTATATTAAAAAATT-TTATAATTTAA
3328456 A
1 A
3328457 AATCATTTAT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
27 6 0.12
28 8 0.16
29 25 0.50
30 11 0.22
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (29 bp):
ATATTATATTAAAAAATTTTATAATTTAA
Found at i:3328455 original size:30 final size:29
Alignment explanation
Indices: 3328379--3328470 Score: 96
Period size: 29 Copynumber: 3.1 Consensus size: 29
3328369 TATATTAATT
* * *
3328379 AATAAATTTATAATTTATATATTATATTA
1 AATAATTTTATAATTTAAATATCATATTA
* *
3328408 AAAAATTTTAAAATTTAAATATCATATTA
1 AATAATTTTATAATTTAAATATCATATTA
* *
3328437 AATAGTTATTATAATTTAAAAATCAT-TTA
1 AATAATT-TTATAATTTAAATATCATATTA
3328466 TAATA
1 -AATA
3328471 TTAACTCATA
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
29 32 0.62
30 20 0.38
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (29 bp):
AATAATTTTATAATTTAAATATCATATTA
Found at i:3329808 original size:18 final size:18
Alignment explanation
Indices: 3329785--3329820 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3329775 ACACATTATG
*
3329785 AATATAAAATTAATATAA
1 AATATAAAAATAATATAA
3329803 AATATAAAAATAATATAA
1 AATATAAAAATAATATAA
3329821 TTTAAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AATATAAAAATAATATAA
Found at i:3329849 original size:23 final size:22
Alignment explanation
Indices: 3329788--3329857 Score: 72
Period size: 23 Copynumber: 3.2 Consensus size: 22
3329778 CATTATGAAT
*
3329788 ATAA-AATTAATATAAAATATA
1 ATAATAATTAATATAAAATTTA
* *
3329809 AAAATAATATAATTTAAAATTTA
1 ATAATAAT-TAATATAAAATTTA
*
3329832 ATAATAATTAGATGT-AAATTTA
1 ATAATAATTA-ATATAAAATTTA
3329854 ATAA
1 ATAA
3329858 AATAAAAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
21 3 0.07
22 16 0.39
23 22 0.54
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (22 bp):
ATAATAATTAATATAAAATTTA
Found at i:3332809 original size:16 final size:17
Alignment explanation
Indices: 3332778--3332815 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
3332768 TGAAATATAT
*
3332778 ATTTATAATATTATTAA
1 ATTTATAATATAATTAA
*
3332795 ATTTAT-ATATAATTAT
1 ATTTATAATATAATTAA
3332811 ATTTA
1 ATTTA
3332816 AAATTTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTATAATATAATTAA
Found at i:3333399 original size:2 final size:2
Alignment explanation
Indices: 3333394--3333423 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3333384 TGCATACTCA
*
3333394 AT AT AT AA 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
3333424 TTGCTCTTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3333955 original size:2 final size:2
Alignment explanation
Indices: 3333910--3333939 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3333900 GCACCATCAA
3333910 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3333940 AACACAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3338108 original size:30 final size:30
Alignment explanation
Indices: 3338038--3338145 Score: 108
Period size: 30 Copynumber: 3.6 Consensus size: 30
3338028 TTGATTTATA
* * *
3338038 TTAAAGGCTTATTTAGATACAAAATAAATG
1 TTAAAGGCTTATTTGGATACAAATTAAAGG
** *
3338068 TTAGGGGCTTATTTGGATATAAATTAAAGG
1 TTAAAGGCTTATTTGGATACAAATTAAAGG
* * **
3338098 TTAAAAGCTTATTTGGGTACAAATTAAAAC
1 TTAAAGGCTTATTTGGATACAAATTAAAGG
* *
3338128 TTAGAGGTTTATTTGGAT
1 TTAAAGGCTTATTTGGAT
3338146 GTAATAAAAG
Statistics
Matches: 61, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 61 1.00
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.37
Consensus pattern (30 bp):
TTAAAGGCTTATTTGGATACAAATTAAAGG
Found at i:3341583 original size:3 final size:3
Alignment explanation
Indices: 3341575--3341602 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3341565 AATAGATTTA
3341575 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3341603 GATTTAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3361708 original size:19 final size:20
Alignment explanation
Indices: 3361684--3361727 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
3361674 CATTATTAAT
3361684 TAATTAT-TTGATATTAAA-A
1 TAATTATATT-ATATTAAATA
3361703 TAATTATAATTATATTAAATA
1 TAATTAT-ATTATATTAAATA
3361724 TAAT
1 TAAT
3361728 AATAAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 7 0.32
20 8 0.36
21 7 0.32
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TAATTATATTATATTAAATA
Found at i:3361905 original size:21 final size:21
Alignment explanation
Indices: 3361873--3361941 Score: 56
Period size: 20 Copynumber: 3.4 Consensus size: 21
3361863 GTCTCGTTTG
3361873 ATTTTATTTTATATATATAAT
1 ATTTTATTTTATATATATAAT
* *
3361894 ATTTT-TTATTATTTAT-TTA-
1 ATTTTATT-TTATATATATAAT
* * *
3361913 ATTTTAATTTATATATTTTAT
1 ATTTTATTTTATATATATAAT
3361934 A-TTTATTT
1 ATTTTATTT
3361942 AATTTTATAA
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
19 12 0.31
20 14 0.36
21 13 0.33
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
ATTTTATTTTATATATATAAT
Found at i:3361924 original size:15 final size:16
Alignment explanation
Indices: 3361897--3361960 Score: 78
Period size: 15 Copynumber: 4.0 Consensus size: 16
3361887 ATATAATATT
3361897 TTTTATTATTTATTTAA
1 TTTTA-TATTTATTTAA
*
3361914 TTTTA-ATTTATAT-A
1 TTTTATATTTATTTAA
3361928 TTTTATATTTATTTAA
1 TTTTATATTTATTTAA
*
3361944 TTTTATAATTATATTAA
1 TTTTATATTTAT-TTAA
3361961 AATTTAATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
14 6 0.15
15 14 0.34
16 12 0.29
17 9 0.22
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTATATTTATTTAA
Found at i:3361937 original size:30 final size:32
Alignment explanation
Indices: 3361873--3361957 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 32
3361863 GTCTCGTTTG
* *
3361873 ATTTTATTTTATATATATAATATTTTTTATTATTT
1 ATTTAATTTTATA-AT-T-ATATATTTTATTATTT
*
3361908 ATTTAATTTTA-ATTTATATATTTTA-TATTT
1 ATTTAATTTTATAATTATATATTTTATTATTT
3361938 ATTTAATTTTATAATTATAT
1 ATTTAATTTTATAATTATAT
3361958 TAAAATTTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
30 16 0.36
31 16 0.36
32 1 0.02
33 1 0.02
34 1 0.02
35 10 0.22
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (32 bp):
ATTTAATTTTATAATTATATATTTTATTATTT
Found at i:3361941 original size:19 final size:18
Alignment explanation
Indices: 3361873--3361942 Score: 63
Period size: 19 Copynumber: 3.8 Consensus size: 18
3361863 GTCTCGTTTG
*
3361873 ATTTTATTTTATATATAT
1 ATTTTATTTTATTTATAT
* *
3361891 AATATT-TTTTA-TTATTT
1 -ATTTTATTTTATTTATAT
*
3361908 ATTTAATTTTAATTTATAT
1 ATTTTATTTT-ATTTATAT
3361927 ATTTTATATTTATTTA
1 ATTTTAT-TTTATTTA
3361943 ATTTTATAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
16 3 0.08
17 8 0.20
18 6 0.15
19 20 0.50
20 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTATTTTATTTATAT
Found at i:3362201 original size:12 final size:12
Alignment explanation
Indices: 3362184--3362208 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3362174 TTAGAAGGGC
3362184 TTAATATATATA
1 TTAATATATATA
3362196 TTAATATATATA
1 TTAATATATATA
3362208 T
1 T
3362209 ATGTATGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAATATATATA
Found at i:3362215 original size:4 final size:4
Alignment explanation
Indices: 3362208--3362238 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
3362198 AATATATATA
3362208 TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
3362239 AAACCTACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:3365486 original size:26 final size:27
Alignment explanation
Indices: 3365457--3365507 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
3365447 ACAAGATAAG
3365457 ATAATATTA-TTTTATTTAATTATATT
1 ATAATATTATTTTTATTTAATTATATT
*
3365483 ATAATATTATTTTTATTTTATTATA
1 ATAATATTATTTTTATTTAATTATA
3365508 ATTTTATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (27 bp):
ATAATATTATTTTTATTTAATTATATT
Found at i:3365493 original size:11 final size:11
Alignment explanation
Indices: 3365465--3365514 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
3365455 AGATAATATT
3365465 ATTTTATT-TA
1 ATTTTATTATA
*
3365475 ATTATATTATA
1 ATTTTATTATA
* * *
3365486 ATATTATTTTT
1 ATTTTATTATA
3365497 ATTTTATTATA
1 ATTTTATTATA
3365508 ATTTTAT
1 ATTTTAT
3365515 ATATTAAATA
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
10 7 0.23
11 24 0.77
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
ATTTTATTATA
Found at i:3369978 original size:15 final size:14
Alignment explanation
Indices: 3369957--3370007 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
3369947 TCCTGTTAAT
3369957 TTTAAATTAAATTA
1 TTTAAATTAAATTA
*
3369971 TTTAAAATTGAATTA
1 TTT-AAATTAAATTA
*
3369986 ATTAAATTAAATTA
1 TTTAAATTAAATTA
*
3370000 TTTTAATT
1 TTTAAATT
3370008 TTATTAATCA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 19 0.61
15 12 0.39
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (14 bp):
TTTAAATTAAATTA
Found at i:3372996 original size:16 final size:17
Alignment explanation
Indices: 3372975--3373011 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
3372965 ATTTTTTTTC
3372975 TTTTGTAAATA-TTTAA
1 TTTTGTAAATATTTTAA
*
3372991 TTTTGTTAATATTTTAA
1 TTTTGTAAATATTTTAA
3373008 TTTT
1 TTTT
3373012 TAGACTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (17 bp):
TTTTGTAAATATTTTAA
Found at i:3373230 original size:17 final size:17
Alignment explanation
Indices: 3373191--3373236 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
3373181 TTATTTCTTT
*
3373191 AATT-TTATATTTAT-A
1 AATTATTATATTAATAA
3373206 AA-TATTATATTAATAA
1 AATTATTATATTAATAA
3373222 AATTATTAT-TTAATA
1 AATTATTATATTAATA
3373237 CTTAATTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 1 0.04
15 11 0.41
16 9 0.33
17 6 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AATTATTATATTAATAA
Found at i:3373400 original size:15 final size:15
Alignment explanation
Indices: 3373380--3373417 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
3373370 TCTCTCATCC
3373380 TTTTTTTTTATTT--A
1 TTTTTTTTT-TTTGAA
3373394 TTTTTTTTTTTTGAA
1 TTTTTTTTTTTTGAA
3373409 TTTTTTTTT
1 TTTTTTTTT
3373418 CCTTTTCAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 3 0.14
14 9 0.41
15 10 0.45
ACGTcount: A:0.11, C:0.00, G:0.03, T:0.87
Consensus pattern (15 bp):
TTTTTTTTTTTTGAA
Found at i:3373872 original size:16 final size:17
Alignment explanation
Indices: 3373853--3373887 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
3373843 AATTTTATAT
3373853 ATTTTATA-TATATTTA
1 ATTTTATATTATATTTA
3373869 ATTTTATATTTATATTTA
1 ATTTTATA-TTATATTTA
3373887 A
1 A
3373888 AATAATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
18 9 0.53
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
ATTTTATATTATATTTA
Found at i:3374182 original size:20 final size:20
Alignment explanation
Indices: 3374157--3374202 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
3374147 TCTTGTTTTG
3374157 TTTTTAATATTTAAGAAATA
1 TTTTTAATATTTAAGAAATA
* * *
3374177 TTTTTAATATTTTATAAATT
1 TTTTTAATATTTAAGAAATA
3374197 TTTTTA
1 TTTTTA
3374203 TTGTCCCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
TTTTTAATATTTAAGAAATA
Found at i:3380517 original size:21 final size:21
Alignment explanation
Indices: 3380491--3380532 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3380481 AACAAAAACC
3380491 TTTTTTCTTTTCTCTTTGGGG
1 TTTTTTCTTTTCTCTTTGGGG
* * *
3380512 TTTTTTTTTTTTTTTTTGGGG
1 TTTTTTCTTTTCTCTTTGGGG
3380533 GGGGGGGGGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.00, C:0.07, G:0.19, T:0.74
Consensus pattern (21 bp):
TTTTTTCTTTTCTCTTTGGGG
Found at i:3380533 original size:1 final size:1
Alignment explanation
Indices: 3380529--3380556 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
3380519 TTTTTTTTTT
3380529 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
3380557 TGTGATTGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:3385106 original size:15 final size:15
Alignment explanation
Indices: 3385056--3385113 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
3385046 TTTATAAATA
3385056 ATATTATTATAT-TT
1 ATATTATTATATATT
*
3385070 A-ATTATAATATATT
1 ATATTATTATATATT
** *
3385084 ATCGTATTATATACT
1 ATATTATTATATATT
3385099 ATATTATTTATATAT
1 ATATTA-TTATATAT
3385114 CAATGATGCC
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
13 9 0.27
14 4 0.12
15 13 0.39
16 7 0.21
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (15 bp):
ATATTATTATATATT
Found at i:3385864 original size:162 final size:160
Alignment explanation
Indices: 3385595--3385957 Score: 534
Period size: 162 Copynumber: 2.2 Consensus size: 160
3385585 GCATTGTTCA
* * * * *
3385595 AGCCACTGATTTCATCTAAATCCAGTCCATCAAGCCAGTTAAATTCTGAGTCCTTCAAAGGGTCG
1 AGCCACTGATTTCATCTAAATCCAGTCCATCAAGCCGGTTAAACTCTAAGCCCTTCAAAGGGTCA
* * *
3385660 TCTTCAGTACCTGATTCTGGTATCATCAGCTTCTTGTTTACCCCAAATGTGGTATCATACTTGTC
66 TCTTCAGCACCTGATTCTGGTATAATCAGCTTCTTATTTACCCCAAATGTGGTATCATACTTGTC
3385725 AT-TGCATGCAGCTTCTAATCCACCATTATCCC
131 ATCT-C-TGCAGCTTCTAATCCACCATTAT-CC
3385757 AGCCACTGATTTCATCTAAATCCAGTCCATCAAGCCGGTTAAACTCTAAGCCCTT-AGAAGGGTC
1 AGCCACTGATTTCATCTAAATCCAGTCCATCAAGCCGGTTAAACTCTAAGCCCTTCA-AAGGGTC
3385821 ATCTTCAGCACCTGATTCTGGTATAATCAGCTTCTTATTTACCCCAAATGTGGTATCATACTTGT
65 ATCTTCAGCACCTGATTCTGGTATAATCAGCTTCTTATTTACCCCAAATGTGGTATCATACTTGT
* * *
3385886 CGTCCTCTGCAGGTTCTAATCCACCATTATTC
130 CAT-CTCTGCAGCTTCTAATCCACCATTATCC
*
3385918 AGGCCACTGATTTCATCTAAA-CTCAGCCCATCAAGCCGGT
1 A-GCCACTGATTTCATCTAAATC-CAGTCCATCAAGCCGGT
3385958 CATCTTCAAT
Statistics
Matches: 184, Mismatches: 12, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
161 4 0.02
162 178 0.97
163 1 0.01
164 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.32
Consensus pattern (160 bp):
AGCCACTGATTTCATCTAAATCCAGTCCATCAAGCCGGTTAAACTCTAAGCCCTTCAAAGGGTCA
TCTTCAGCACCTGATTCTGGTATAATCAGCTTCTTATTTACCCCAAATGTGGTATCATACTTGTC
ATCTCTGCAGCTTCTAATCCACCATTATCC
Found at i:3386966 original size:23 final size:23
Alignment explanation
Indices: 3386930--3386978 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
3386920 TTCTGAAGGA
*
3386930 AAAAACCCAACAAAATCTCGATG
1 AAAAACCCAACAAAAACTCGATG
* *
3386953 AAAAACGCAGCAAAAACTCGATG
1 AAAAACCCAACAAAAACTCGATG
3386976 AAA
1 AAA
3386979 GATGAGAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.55, C:0.22, G:0.12, T:0.10
Consensus pattern (23 bp):
AAAAACCCAACAAAAACTCGATG
Found at i:3388387 original size:11 final size:11
Alignment explanation
Indices: 3388337--3388402 Score: 51
Period size: 11 Copynumber: 5.6 Consensus size: 11
3388327 TATAATAAAA
3388337 AATTTAAATTT
1 AATTTAAATTT
*
3388348 AACTTGAAATTT
1 AA-TTTAAATTT
* *
3388360 AGTACTAAAAGTTT
1 A--ATTTAAA-TTT
3388374 AATTTAAATTT
1 AATTTAAATTT
**
3388385 AATCAAAATTT
1 AATTTAAATTT
3388396 AATTTAA
1 AATTTAA
3388403 GTTCGATAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
11 19 0.45
12 14 0.33
13 4 0.10
14 5 0.12
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.44
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:3388586 original size:8 final size:8
Alignment explanation
Indices: 3388564--3388606 Score: 59
Period size: 8 Copynumber: 5.1 Consensus size: 8
3388554 GAATTCACTT
3388564 ATTTTAAA
1 ATTTTAAA
3388572 GATTTTAAA
1 -ATTTTAAA
3388581 ATTTTAAA
1 ATTTTAAA
*
3388589 ATTGTTTAA
1 ATT-TTAAA
3388598 ATTTTAAA
1 ATTTTAAA
3388606 A
1 A
3388607 AAAAATTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
8 16 0.52
9 15 0.48
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (8 bp):
ATTTTAAA
Found at i:3388586 original size:17 final size:17
Alignment explanation
Indices: 3388564--3388606 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
3388554 GAATTCACTT
3388564 ATTTTAAAGATT-TTAAA
1 ATTTTAAA-ATTGTTAAA
*
3388581 ATTTTAAAATTGTTTAA
1 ATTTTAAAATTGTTAAA
3388598 ATTTTAAAA
1 ATTTTAAAA
3388607 AAAAATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (17 bp):
ATTTTAAAATTGTTAAA
Found at i:3392320 original size:2 final size:2
Alignment explanation
Indices: 3392313--3392339 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3392303 AGTTTATGTA
3392313 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
3392340 ACACACACAC
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3393831 original size:2 final size:2
Alignment explanation
Indices: 3393824--3393857 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3393814 TAAAGTGTGC
3393824 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
3393858 CTCAACCATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3397861 original size:32 final size:32
Alignment explanation
Indices: 3397809--3397870 Score: 74
Period size: 32 Copynumber: 1.9 Consensus size: 32
3397799 ATAATTAATT
* *
3397809 TTATATATAAATCAATTTAAATATATTAAAAA
1 TTATATATAAATCAATTTAAAAAAATTAAAAA
3397841 TTATAT-TAAGAT-AATATTAAAAAAATTAAA
1 TTATATATAA-ATCAAT-TTAAAAAAATTAAA
3397871 TTTAAAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
31 6 0.23
32 20 0.77
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (32 bp):
TTATATATAAATCAATTTAAAAAAATTAAAAA
Found at i:3400099 original size:25 final size:26
Alignment explanation
Indices: 3400066--3400114 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
3400056 ATATCCTTAA
* *
3400066 CTTTAGAAGTTATATTAGTGATTAGC
1 CTTTAGAAGTTAGATTAATGATTAGC
3400092 CTTT-GAAGTTAGATTAATGATTA
1 CTTTAGAAGTTAGATTAATGATTA
3400115 CTATATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.43
Consensus pattern (26 bp):
CTTTAGAAGTTAGATTAATGATTAGC
Found at i:3401960 original size:97 final size:97
Alignment explanation
Indices: 3401802--3401985 Score: 280
Period size: 97 Copynumber: 1.9 Consensus size: 97
3401792 ACATTAACGC
* * * * * ** *
3401802 AGTATTTGATTTGTACTTGTTTCGTATTGTCGTAGAAAATGATTTTTTATAACATACTCAATTAC
1 AGTATTTAATTTATAATTGTTTCGTATTGACATAGAAAACAATTTTTTATAACATACTCAATTAA
3401867 TGCATTAATTTAAATATTAACATAATTAATAG
66 TGCATTAATTTAAATATTAACATAATTAATAG
3401899 AGTATTTAATTTATAATTGTTTAC-TATTGACATAGAAAACAATTTTTTATAACATACTCAATTA
1 AGTATTTAATTTATAATTGTTT-CGTATTGACATAGAAAACAATTTTTTATAACATACTCAATTA
3401963 ATGCATTAATTTAAATATTAACA
65 ATGCATTAATTTAAATATTAACA
3401986 CAGTAATAGA
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
97 77 0.99
98 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (97 bp):
AGTATTTAATTTATAATTGTTTCGTATTGACATAGAAAACAATTTTTTATAACATACTCAATTAA
TGCATTAATTTAAATATTAACATAATTAATAG
Found at i:3402931 original size:12 final size:13
Alignment explanation
Indices: 3402905--3402931 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3402895 AAATCTCATA
3402905 TTTTTGAAAATTT
1 TTTTTGAAAATTT
3402918 TTTTTGAAAATTT
1 TTTTTGAAAATTT
3402931 T
1 T
3402932 ATCTTTGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (13 bp):
TTTTTGAAAATTT
Found at i:3406360 original size:3 final size:3
Alignment explanation
Indices: 3406352--3406380 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3406342 TTTATGTTGG
3406352 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3406381 CATTTTTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3406986 original size:19 final size:20
Alignment explanation
Indices: 3406941--3407002 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 20
3406931 TTATTCATTT
3406941 AAATAATAA-AA-AATAAATA
1 AAATAATAACAATAA-AAATA
*
3406960 GTAAATAATAACAA-AAAATTA
1 --AAATAATAACAATAAAAATA
*
3406981 AAATAATCACAATAAAAATA
1 AAATAATAACAATAAAAATA
3407001 AA
1 AA
3407003 TAAATTAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 11 0.31
20 8 0.22
21 13 0.36
22 4 0.11
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.21
Consensus pattern (20 bp):
AAATAATAACAATAAAAATA
Found at i:3407003 original size:19 final size:18
Alignment explanation
Indices: 3406940--3407005 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 18
3406930 ATTATTCATT
*
3406940 TAAATAATAAAAAATAAATA
1 TAAATAATAACAAA-AAA-A
*
3406960 GTAAATAATAACAAAAAAT
1 -TAAATAATAACAAAAAAA
*
3406979 TAAAATAATCACAATAAAAA
1 T-AAATAATAACAA-AAAAA
3406999 TAAATAA
1 TAAATAA
3407006 ATTAATTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
18 1 0.03
19 17 0.44
20 8 0.21
21 13 0.33
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.23
Consensus pattern (18 bp):
TAAATAATAACAAAAAAA
Found at i:3416751 original size:14 final size:14
Alignment explanation
Indices: 3416729--3416799 Score: 51
Period size: 13 Copynumber: 5.1 Consensus size: 14
3416719 TACCACTATC
*
3416729 AATACATATATTTA
1 AATAAATATATTTA
*
3416743 AATAAATATA-TAA
1 AATAAATATATTTA
*
3416756 AATAAA-AT-TAATA
1 AATAAATATAT-TTA
*
3416769 AATAAATTTATTT-
1 AATAAATATATTTA
3416782 AATATAATATAATTTA
1 AATA-AATAT-ATTTA
3416798 AA
1 AA
3416800 ATTATATAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
12 2 0.05
13 19 0.44
14 15 0.35
15 5 0.12
16 2 0.05
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (14 bp):
AATAAATATATTTA
Found at i:3416771 original size:13 final size:13
Alignment explanation
Indices: 3416755--3416827 Score: 53
Period size: 13 Copynumber: 5.6 Consensus size: 13
3416745 TAAATATATA
3416755 AAATAAAATTAAT
1 AAATAAAATTAAT
* *
3416768 AAATAAATTTATT
1 AAATAAAATTAAT
* *
3416781 TAATATAA-T-AT
1 AAATAAAATTAAT
*
3416792 AATTTAAAATT-AT
1 AA-ATAAAATTAAT
3416805 ATAATAAAATTAATT
1 A-AATAAAATTAA-T
3416820 AAATAAAA
1 AAATAAAA
3416828 AAATTTATAA
Statistics
Matches: 45, Mismatches: 10, Indels: 9
0.70 0.16 0.14
Matches are distributed among these distances:
11 2 0.04
12 5 0.11
13 27 0.60
14 9 0.20
15 2 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATAAAATTAAT
Found at i:3416775 original size:17 final size:17
Alignment explanation
Indices: 3416755--3416840 Score: 56
Period size: 17 Copynumber: 5.1 Consensus size: 17
3416745 TAAATATATA
3416755 AAATAAAATTAATAAAT
1 AAATAAAATTAATAAAT
** *
3416772 AAATTTATTTAATATAAT
1 AAATAAAATTAATA-AAT
3416790 ATAATTTAAAATT-AT--AT
1 A-AA--TAAAATTAATAAAT
3416807 -AATAAAATTAATTAAAT
1 AAATAAAATTAA-TAAAT
*
3416824 AAA-AAAATTTATAAAT
1 AAATAAAATTAATAAAT
3416840 A
1 A
3416841 TTTTTAACAA
Statistics
Matches: 53, Mismatches: 7, Indels: 19
0.67 0.09 0.24
Matches are distributed among these distances:
13 7 0.13
14 1 0.02
15 3 0.06
16 6 0.11
17 22 0.42
18 6 0.11
19 2 0.04
20 2 0.04
21 4 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATAAAATTAATAAAT
Found at i:3416801 original size:38 final size:37
Alignment explanation
Indices: 3416758--3416839 Score: 94
Period size: 38 Copynumber: 2.2 Consensus size: 37
3416748 ATATATAAAA
* * * *
3416758 TAAAATTA-ATAAATAAATTTATTTAATATAATATAATT
1 TAAAATTATAT-AATAAAATTAATTAA-ATAAAAAAATT
3416796 TAAAATTATATAATAAAATTAATTAAATAAAAAAATT
1 TAAAATTATATAATAAAATTAATTAAATAAAAAAATT
3416833 TATAAAT
1 TA-AAAT
3416840 ATTTTTAACA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
37 11 0.29
38 25 0.66
39 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (37 bp):
TAAAATTATATAATAAAATTAATTAAATAAAAAAATT
Found at i:3416809 original size:25 final size:24
Alignment explanation
Indices: 3416746--3416819 Score: 67
Period size: 25 Copynumber: 2.9 Consensus size: 24
3416736 ATATTTAAAT
* *
3416746 AAATATATAAAATAAAATTAATAAATA
1 AAAT-TATATAATAAAATTAAT--TTA
* * *
3416773 AATTTATTTAATATAATATAATTTA
1 AAATTATATAATAAAAT-TAATTTA
3416798 AAATTATATAATAAAATTAATT
1 AAATTATATAATAAAATTAATT
3416820 AAATAAAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
24 5 0.13
25 16 0.42
26 10 0.26
27 7 0.18
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
AAATTATATAATAAAATTAATTTA
Found at i:3422380 original size:4 final size:4
Alignment explanation
Indices: 3422362--3422418 Score: 51
Period size: 4 Copynumber: 13.0 Consensus size: 4
3422352 AATTTTACTT
* *
3422362 ATAA ATAA TATTAA ATAA ATAA ATAA ATAA ATTATA TTATA ATAT ATAA
1 ATAA ATAA -A-TAA ATAA ATAA ATAA ATAA A-TA-A ATA-A ATAA ATAA
3422411 ATAA ATAA
1 ATAA ATAA
3422419 TATTATAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 31 0.69
5 10 0.22
6 4 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (4 bp):
ATAA
Found at i:3422410 original size:23 final size:23
Alignment explanation
Indices: 3422362--3422454 Score: 125
Period size: 23 Copynumber: 3.9 Consensus size: 23
3422352 AATTTTACTT
*
3422362 ATAAATAATATTAAATAAATAAATAA
1 ATAAATAATATT--AT-AATATATAA
*
3422388 ATAAATTATATTATAATATATAA
1 ATAAATAATATTATAATATATAA
3422411 ATAAATAATATTATAATAT-TATA
1 ATAAATAATATTATAATATATA-A
3422434 ATAAATAATATTATAATATAT
1 ATAAATAATATTATAATATAT
3422455 TATTGATAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 6
0.87 0.04 0.08
Matches are distributed among these distances:
22 2 0.03
23 46 0.74
24 3 0.05
26 11 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
ATAAATAATATTATAATATATAA
Found at i:3422414 original size:31 final size:31
Alignment explanation
Indices: 3422365--3422441 Score: 101
Period size: 27 Copynumber: 2.6 Consensus size: 31
3422355 TTTACTTATA
3422365 AATAATATTA-AATAAATAAATAAATAA-AT
1 AATAATATTATAATAAATAAATAAATAATAT
*
3422394 --T-ATATTATAATATATAAATAAATAATAT
1 AATAATATTATAATAAATAAATAAATAATAT
*
3422422 TATAATATTATAATAAATAA
1 AATAATATTATAATAAATAA
3422442 TATTATAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
26 6 0.15
27 17 0.41
28 2 0.05
30 1 0.02
31 15 0.37
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (31 bp):
AATAATATTATAATAAATAAATAAATAATAT
Found at i:3422426 original size:8 final size:8
Alignment explanation
Indices: 3422395--3422452 Score: 68
Period size: 8 Copynumber: 7.5 Consensus size: 8
3422385 TAAATAAATT
3422395 ATATTATA
1 ATATTATA
3422403 ATA-TATA
1 ATATTATA
*
3422410 A-ATAAATA
1 ATAT-TATA
3422418 ATATTATA
1 ATATTATA
3422426 ATATTATA
1 ATATTATA
*
3422434 ATA-AATA
1 ATATTATA
3422441 ATATTATA
1 ATATTATA
3422449 ATAT
1 ATAT
3422453 ATTATTGATA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
6 1 0.02
7 11 0.26
8 28 0.67
9 2 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
ATATTATA
Found at i:3422450 original size:31 final size:30
Alignment explanation
Indices: 3422365--3422453 Score: 71
Period size: 28 Copynumber: 3.0 Consensus size: 30
3422355 TTTACTTATA
*
3422365 AATAATATTA-AATAAATAAATAAATAA-AT
1 AATAATATTATAATAAATAAAT-TATAATAT
* * *
3422394 TATATTATAATATATAAAT-AA--ATAATAT
1 AATAATATTATA-ATAAATAAATTATAATAT
*
3422422 TATAATATTATAATAAATAATATTATAATAT
1 AATAATATTATAATAAATAA-ATTATAATAT
3422453 A
1 A
3422454 TTATTGATAA
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
27 10 0.21
28 13 0.28
29 8 0.17
30 3 0.06
31 13 0.28
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (30 bp):
AATAATATTATAATAAATAAATTATAATAT
Found at i:3422450 original size:80 final size:80
Alignment explanation
Indices: 3422366--3422539 Score: 180
Period size: 80 Copynumber: 2.2 Consensus size: 80
3422356 TTACTTATAA
* **
3422366 ATAATAT-TAAATAAATAAATAAATAAATTA-TATTATAATATATAAATAAATAATATTATAATA
1 ATAATATAT-AATAAATAAAT-AATAAACTACTAAAATAATATATAAATAAATAATATTATAATA
3422429 T-TATAATAAATAATATT
64 TGT-TAATAAATAATATT
* ** * * * *
3422446 ATAATATATTATTGATAAATAATATACTACTAAAATAATATATTAATAGATAATATTATAGTATG
1 ATAATATATAATAAATAAATAATAAACTACTAAAATAATATATAAATAAATAATATTATAATATG
3422511 TTAATAAATAATA-T
66 TTAATAAATAATATT
*
3422525 A-AA-AAATAATAAATA
1 ATAATATATAATAAATA
3422540 GTTTTATTTT
Statistics
Matches: 77, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
77 8 0.10
78 2 0.03
79 9 0.12
80 56 0.73
81 2 0.03
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (80 bp):
ATAATATATAATAAATAAATAATAAACTACTAAAATAATATATAAATAAATAATATTATAATATG
TTAATAAATAATATT
Found at i:3422466 original size:23 final size:22
Alignment explanation
Indices: 3422395--3422471 Score: 66
Period size: 23 Copynumber: 3.4 Consensus size: 22
3422385 TAAATAAATT
* *
3422395 ATATTATAATATATAAATAAATA
1 ATATTATAATATATAATTATA-A
*
3422418 ATATTATAATATTATAA-TAAATA
1 ATATTATAATA-TATAATTATA-A
*
3422441 ATATTATAATATATTATTGATAA
1 ATATTATAATATATAATT-ATAA
*
3422464 ATAATATA
1 ATATTATA
3422472 CTACTAAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
22 4 0.08
23 37 0.77
24 7 0.15
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (22 bp):
ATATTATAATATATAATTATAA
Found at i:3422598 original size:19 final size:19
Alignment explanation
Indices: 3422551--3422622 Score: 69
Period size: 19 Copynumber: 3.8 Consensus size: 19
3422541 TTTTATTTTA
*
3422551 AATATTTTTATATTAACAT
1 AATATTTTAATATTAACAT
3422570 AATATTTTAATATTAA-AT
1 AATATTTTAATATTAACAT
* * *
3422588 ATTATTATTAAAATATAA-TT
1 AATATT-TTAATAT-TAACAT
3422608 AA-ATTTTAATATTAA
1 AATATTTTAATATTAA
3422623 TAATTTTAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
17 3 0.07
18 13 0.29
19 24 0.53
20 5 0.11
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (19 bp):
AATATTTTAATATTAACAT
Found at i:3422631 original size:9 final size:9
Alignment explanation
Indices: 3422614--3422685 Score: 55
Period size: 9 Copynumber: 8.6 Consensus size: 9
3422604 AATTAAATTT
*
3422614 TAATATTAA
1 TAATTTTAA
3422623 TAATTTTAA
1 TAATTTTAA
*
3422632 TAA--TAAA
1 TAATTTTAA
*
3422639 TAATTTCAA
1 TAATTTTAA
*
3422648 TAACTTTAA
1 TAATTTTAA
*
3422657 TAA--TAAA
1 TAATTTTAA
*
3422664 TAAATTTAA
1 TAATTTTAA
3422673 T-ATTTTAA
1 TAATTTTAA
3422681 TAATT
1 TAATT
3422686 ATTTTAATAT
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
7 12 0.24
8 7 0.14
9 31 0.62
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (9 bp):
TAATTTTAA
Found at i:3422642 original size:16 final size:16
Alignment explanation
Indices: 3422529--3422650 Score: 63
Period size: 15 Copynumber: 7.3 Consensus size: 16
3422519 TAATATAAAA
*
3422529 AATAATAAATAGTTTT
1 AATAATAAATAATTTT
**
3422545 -ATTTTAAAT-ATTTT
1 AATAATAAATAATTTT
* *
3422559 TATATTAACATAATATTTT
1 AATAATAA-AT-A-ATTTT
*
3422578 AATATTAAATATTATTATT
1 AATAATAAATA--ATT-TT
3422597 AA-AATATAATTAAATTTT
1 AATAATA-AA-T-AATTTT
*
3422615 AAT-ATTAATAATTTT
1 AATAATAAATAATTTT
*
3422630 AATAATAAATAATTTC
1 AATAATAAATAATTTT
3422646 AATAA
1 AATAA
3422651 CTTTAATAAT
Statistics
Matches: 85, Mismatches: 9, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
14 4 0.05
15 22 0.26
16 18 0.21
17 3 0.04
18 15 0.18
19 21 0.25
20 1 0.01
21 1 0.01
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (16 bp):
AATAATAAATAATTTT
Found at i:3422649 original size:25 final size:25
Alignment explanation
Indices: 3422619--3422684 Score: 100
Period size: 25 Copynumber: 2.7 Consensus size: 25
3422609 AATTTTAATA
3422619 TTAATAATTTTAATAATAAAT-AAT
1 TTAATAATTTTAATAATAAATAAAT
*
3422643 TTCAATAACTTTAATAATAAATAAAT
1 TT-AATAATTTTAATAATAAATAAAT
3422669 TTAAT-ATTTTAATAAT
1 TTAATAATTTTAATAAT
3422685 TATTTTAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
24 12 0.32
25 21 0.55
26 5 0.13
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (25 bp):
TTAATAATTTTAATAATAAATAAAT
Found at i:3422681 original size:21 final size:20
Alignment explanation
Indices: 3422657--3422696 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3422647 ATAACTTTAA
3422657 TAATAAATAAATTTAATATTT
1 TAAT-AATAAATTTAATATTT
* *
3422678 TAATAATTATTTTAATATT
1 TAATAATAAATTTAATATT
3422697 ATTTGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TAATAATAAATTTAATATTT
Found at i:3422685 original size:16 final size:15
Alignment explanation
Indices: 3422602--3422686 Score: 59
Period size: 16 Copynumber: 5.5 Consensus size: 15
3422592 TTATTAAAAT
3422602 ATAATTAA-ATTTTA
1 ATAATTAATATTTTA
3422616 AT-ATTAATAATTTTA
1 ATAATTAAT-ATTTTA
* *
3422631 ATAATAAATAATTTCA
1 ATAATTAAT-ATTTTA
* *
3422647 ATAACTTTAATA-ATAA
1 ATAA--TTAATATTTTA
3422663 ATAAATTTAATATTTTA
1 AT-AA-TTAATATTTTA
3422680 ATAATTA
1 ATAATTA
3422687 TTTTAATATT
Statistics
Matches: 57, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
13 5 0.09
14 2 0.04
15 11 0.19
16 28 0.49
17 7 0.12
18 4 0.07
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
ATAATTAATATTTTA
Found at i:3424904 original size:28 final size:28
Alignment explanation
Indices: 3424873--3424927 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
3424863 AGAACCGTAA
*
3424873 ATTTAAGTTTACATTGGATTTACAAATC
1 ATTTAAGTTTACATTAGATTTACAAATC
3424901 ATTTAAGTTTACATTAGATTTACAAAT
1 ATTTAAGTTTACATTAGATTTACAAAT
3424928 TACCCACCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (28 bp):
ATTTAAGTTTACATTAGATTTACAAATC
Found at i:3434230 original size:5 final size:5
Alignment explanation
Indices: 3434180--3434250 Score: 61
Period size: 5 Copynumber: 13.4 Consensus size: 5
3434170 ATTTTGAGAG
* ***
3434180 ATTTA ATTTTA ATTCGA ATTTA ATGTTA ATTTA AGTTTA CCATA ATTTA
1 ATTTA A-TTTA ATT-TA ATTTA AT-TTA ATTTA A-TTTA ATTTA ATTTA
*
3434229 ATTTA ATTTA ATCTA ATTTA AT
1 ATTTA ATTTA ATTTA ATTTA AT
3434251 GCTACATATA
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
5 34 0.65
6 18 0.35
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (5 bp):
ATTTA
Found at i:3434282 original size:10 final size:10
Alignment explanation
Indices: 3434222--3434282 Score: 50
Period size: 10 Copynumber: 5.6 Consensus size: 10
3434212 AAGTTTACCA
*
3434222 TAATTTAATT
1 TAATTTAATC
3434232 TAATTTAATC
1 TAATTTAATC
3434242 TAATTTAATGC
1 TAATTTAAT-C
* *
3434253 TACATATATTAGTT
1 T--A-AT-TTAATC
3434267 TAATTTAATC
1 TAATTTAATC
3434277 TAATTT
1 TAATTT
3434283 GAGATTTAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
10 28 0.68
11 4 0.10
12 1 0.02
13 1 0.02
14 3 0.07
15 4 0.10
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.52
Consensus pattern (10 bp):
TAATTTAATC
Found at i:3438261 original size:20 final size:20
Alignment explanation
Indices: 3438238--3438292 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 20
3438228 AAAATATATT
3438238 TAAAATTATTAAAATATTAA
1 TAAAATTATTAAAATATTAA
** * *
3438258 TAAAAAAATAAAAATTTTTAA
1 TAAAATTATTAAAA-TATTAA
3438279 T-AAATT-TTAAAATA
1 TAAAATTATTAAAATA
3438293 ATATTGATCT
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
18 1 0.04
19 5 0.19
20 14 0.54
21 6 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAAATTATTAAAATATTAA
Found at i:3438353 original size:17 final size:17
Alignment explanation
Indices: 3438331--3438364 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3438321 TCTGATAGGT
3438331 AAGCACCTCTATTTAAA
1 AAGCACCTCTATTTAAA
3438348 AAGCACCTCTATTTAAA
1 AAGCACCTCTATTTAAA
3438365 TCATTTTTAT
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:0.41, C:0.24, G:0.06, T:0.29
Consensus pattern (17 bp):
AAGCACCTCTATTTAAA
Found at i:3440288 original size:17 final size:17
Alignment explanation
Indices: 3440266--3440299 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3440256 ATATTTAAGT
*
3440266 AATTTTTCATTAACATA
1 AATTTTTCAATAACATA
*
3440283 AATTTTTTAATAACATA
1 AATTTTTCAATAACATA
3440300 TATTAATTCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTTTTCAATAACATA
Found at i:3440916 original size:29 final size:29
Alignment explanation
Indices: 3440859--3440917 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
3440849 AAGCTATTTC
*
3440859 ATAAATTAGGTATAACAGTTTTTTATAAT
1 ATAAATTAGGTATAACAGTTTTTGATAAT
* *
3440888 ATAAATTAGGTATAACGGTTTTTGCTAAT
1 ATAAATTAGGTATAACAGTTTTTGATAAT
3440917 A
1 A
3440918 ATTTAAAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.42
Consensus pattern (29 bp):
ATAAATTAGGTATAACAGTTTTTGATAAT
Found at i:3445043 original size:23 final size:24
Alignment explanation
Indices: 3444998--3445049 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
3444988 ATATCAATTA
3444998 AAAAATATTAAAATGTAAATAAAT
1 AAAAATATTAAAATGTAAATAAAT
* * **
3445022 TAAAAT-TTATAATGTATTTAAAT
1 AAAAATATTAAAATGTAAATAAAT
3445045 AAAAA
1 AAAAA
3445050 AAATTTTATT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (24 bp):
AAAAATATTAAAATGTAAATAAAT
Found at i:3445592 original size:2 final size:2
Alignment explanation
Indices: 3445585--3445617 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3445575 AAACCTCTTT
3445585 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3445618 GATTACATGT
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.