Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold6
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: 1308201
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
File 2 of 11
Found at i:94885 original size:12 final size:12
Alignment explanation
Indices: 94868--94892 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
94858 AGTTACAAGC
94868 TGGTAATATAAG
1 TGGTAATATAAG
94880 TGGTAATATAAG
1 TGGTAATATAAG
94892 T
1 T
94893 AGTTGTGGTT
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:0.40, C:0.00, G:0.24, T:0.36
Consensus pattern (12 bp):
TGGTAATATAAG
Found at i:96217 original size:2 final size:2
Alignment explanation
Indices: 96210--96239 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
96200 TGTAAATTTA
96210 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
96240 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:99333 original size:1 final size:1
Alignment explanation
Indices: 99327--99357 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
99317 AATGCTATTC
99327 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
99358 TTCATGAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:105610 original size:2 final size:2
Alignment explanation
Indices: 105603--105631 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
105593 CAAGACCCCA
105603 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
105632 TAGCAGATCA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:105837 original size:2 final size:2
Alignment explanation
Indices: 105830--105866 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
105820 TTTTTGGTGG
*
105830 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GG GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
105867 TTTTATATTG
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:0.54, T:0.00
Consensus pattern (2 bp):
GA
Found at i:106277 original size:21 final size:19
Alignment explanation
Indices: 106251--106316 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 19
106241 TAAAAATAAT
106251 ATATTAATTATAAGTTTTATA
1 ATATTAATT-TAA-TTTTATA
106272 ATATTAATTTAATTTTAT-
1 ATATTAATTTAATTTTATA
* * **
106290 AT-TTTATTTAAATGCATA
1 ATATTAATTTAATTTTATA
106308 ATATTAATT
1 ATATTAATT
106317 AGAATTTATC
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
17 11 0.29
18 4 0.11
19 11 0.29
20 3 0.08
21 9 0.24
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.55
Consensus pattern (19 bp):
ATATTAATTTAATTTTATA
Found at i:107119 original size:3 final size:3
Alignment explanation
Indices: 107111--107144 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
107101 TATCATAATT
107111 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
107145 CAATTAAATA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:107455 original size:22 final size:23
Alignment explanation
Indices: 107430--107485 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 23
107420 TTTTTGAAAA
*
107430 TATTAAATTATTTATATA-ATTT
1 TATTAAATTATTTAAATAGATTT
107452 TATTAAA-TA-TTAAATAGATTT
1 TATTAAATTATTTAAATAGATTT
107473 TA-TAAATTTATTT
1 TATTAAA-TTATTT
107486 TTTACTATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 10 0.34
21 8 0.28
22 9 0.31
23 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
TATTAAATTATTTAAATAGATTT
Found at i:107476 original size:29 final size:29
Alignment explanation
Indices: 107427--107484 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
107417 TTTTTTTTGA
* *
107427 AAATATTAAATTATTTATATAATTTTATT
1 AAATATTAAATGATTTATATAAATTTATT
107456 AAATATTAAATAGATTT-TATAAATTTATT
1 AAATATTAAAT-GATTTATATAAATTTATT
107485 TTTTACTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (29 bp):
AAATATTAAATGATTTATATAAATTTATT
Found at i:107812 original size:223 final size:223
Alignment explanation
Indices: 107417--107818 Score: 569
Period size: 222 Copynumber: 1.8 Consensus size: 223
107407 TGCTCAATTT
* ***
107417 TTTTTTTTGAAAATATTAAATTATTTATATAATTTTATTAAATATTAAATAGATTTTATAAATTT
1 TTTTTTTTGAAAATATTAAATTATTTATAGAACCCTATTAAATATTAAATAGATTTTATAAATTT
* * * * * * *
107482 ATTTTTTACTATTTTTAATTGAATTAATATTATTTTATTCGATAATATTAAATTCAATCAAAAAT
66 ATTTTTTACTATTTTTAATTAAATTAATATCATTTAATTAGATAACACTAAACTCAATCAAAAAT
*
107547 TTATATATAAAGATTATTAATATTAAATTACGTGATTAAATTTATATTATAAGTTAATCATATAT
131 TTATATATAAAGATTACTAATATTAAATTACGTGATTAAATTTATATTATAAGTTAATCATATAT
107612 CAATTCAATTAATGAAAAAGTATACAAG
196 CAATTCAATTAATGAAAAAGTATACAAG
*
107640 TTTTTTTT-AAAA-ATTAAATTATTTATAGAACCCTATTAATGTATTAAATAGATTTTATAAATT
1 TTTTTTTTGAAAATATTAAATTATTTATAGAACCCTATTAA-ATATTAAATAGATTTTATAAATT
** * *
107703 TA-TTTTTA-TCATTTTTTAATTAAATTGGTATCATTTAATTAGGTGACACTAAACTCAATCAGA
65 TATTTTTTACT-A-TTTTTAATTAAATTAATATCATTTAATTAGATAACACTAAACTCAATCA-A
* *
107766 AAATTTATATATAAAGATTACTGATATTAAATTATGTGATTAAATTTATATTA
127 AAATTTATATATAAAGATTACTAATATTAAATTACGTGATTAAATTTATATTA
107819 CGAATTAATC
Statistics
Matches: 156, Mismatches: 19, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
220 1 0.01
221 30 0.19
222 66 0.42
223 59 0.38
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (223 bp):
TTTTTTTTGAAAATATTAAATTATTTATAGAACCCTATTAAATATTAAATAGATTTTATAAATTT
ATTTTTTACTATTTTTAATTAAATTAATATCATTTAATTAGATAACACTAAACTCAATCAAAAAT
TTATATATAAAGATTACTAATATTAAATTACGTGATTAAATTTATATTATAAGTTAATCATATAT
CAATTCAATTAATGAAAAAGTATACAAG
Found at i:107847 original size:223 final size:223
Alignment explanation
Indices: 107417--107847 Score: 559
Period size: 223 Copynumber: 1.9 Consensus size: 223
107407 TGCTCAATTT
* ***
107417 TTTTTTTTGAAAATATTAAATTATTTATATAATTTTATTAAATATTAAATAGATTTTATAAATTT
1 TTTTTTTTGAAAATATTAAATTATTTATAGAACCCTATTAAATATTAAATAGATTTTATAAATTT
* * * * * * *
107482 ATTTTTTACTATTTTTAATTGAATTAATATTATTTTATTCGATAATATTAAATTCAATCAAAAAT
66 ATTTTTTACTATTTTTAATTAAATTAATATCATTTAATTAGATAACACTAAACTCAATCAAAAAT
* * * * *
107547 TTATATATAAAGATTATTAATATTAAATTACGTGATTAAATTTATATTATAAGTTAATCATATAT
131 TTATATATAAAGATTACTAATATTAAATTACGTGATTAAATTTATATTAGAAGTTAATCAGACAC
107612 CAATTCAATTAATGAAAAAGTATACAAG
196 CAATTCAATTAATGAAAAAGTATACAAG
*
107640 TTTTTTTT-AAAA-ATTAAATTATTTATAGAACCCTATTAATGTATTAAATAGATTTTATAAATT
1 TTTTTTTTGAAAATATTAAATTATTTATAGAACCCTATTAA-ATATTAAATAGATTTTATAAATT
** * *
107703 TA-TTTTTA-TCATTTTTTAATTAAATTGGTATCATTTAATTAGGTGACACTAAACTCAATCAGA
65 TATTTTTTACT-A-TTTTTAATTAAATTAATATCATTTAATTAGATAACACTAAACTCAATCA-A
* *
107766 AAATTTATATATAAAGATTACTGATATTAAATTATGTGATTAAATTTATATTACGAA-TTAATCA
127 AAATTTATATATAAAGATTACTAATATTAAATTACGTGATTAAATTTATATTA-GAAGTTAATCA
107830 GACACCAACTT-AATTAAT
191 GACACCAA-TTCAATTAAT
107848 AAATTTTACT
Statistics
Matches: 179, Mismatches: 23, Indels: 12
0.84 0.11 0.06
Matches are distributed among these distances:
220 1 0.01
221 30 0.17
222 66 0.37
223 78 0.44
224 4 0.02
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (223 bp):
TTTTTTTTGAAAATATTAAATTATTTATAGAACCCTATTAAATATTAAATAGATTTTATAAATTT
ATTTTTTACTATTTTTAATTAAATTAATATCATTTAATTAGATAACACTAAACTCAATCAAAAAT
TTATATATAAAGATTACTAATATTAAATTACGTGATTAAATTTATATTAGAAGTTAATCAGACAC
CAATTCAATTAATGAAAAAGTATACAAG
Found at i:110447 original size:33 final size:35
Alignment explanation
Indices: 110410--110476 Score: 102
Period size: 33 Copynumber: 2.0 Consensus size: 35
110400 ATGTGTGCAT
110410 ATATATTAAATTTATTATATTA-A-TTATATTTAA
1 ATATATTAAATTTATTATATTATATTTATATTTAA
* *
110443 ATATATTATATTTATTATGTTATATTTATATTTA
1 ATATATTAAATTTATTATATTATATTTATATTTA
110477 TAAAAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 20 0.67
34 1 0.03
35 9 0.30
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (35 bp):
ATATATTAAATTTATTATATTATATTTATATTTAA
Found at i:110449 original size:24 final size:25
Alignment explanation
Indices: 110409--110460 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
110399 TATGTGTGCA
*
110409 TATATATTAAATTTATTATATTAAT
1 TATATATTAAATATATTATATTAAT
*
110434 TATAT-TTAAATATATTATATTTAT
1 TATATATTAAATATATTATATTAAT
110458 TAT
1 TAT
110461 GTTATATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TATATATTAAATATATTATATTAAT
Found at i:110467 original size:14 final size:14
Alignment explanation
Indices: 110408--110471 Score: 60
Period size: 14 Copynumber: 4.6 Consensus size: 14
110398 ATATGTGTGC
* *
110408 ATATATATTAAATT
1 ATATTTATTATATT
110422 -TATTATATTA-ATT
1 ATATT-TATTATATT
*
110435 ATATTTAAATATATT
1 ATATTT-ATTATATT
*
110450 ATATTTATTATGTT
1 ATATTTATTATATT
110464 ATATTTAT
1 ATATTTAT
110472 ATTTATAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
13 7 0.17
14 26 0.62
15 9 0.21
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (14 bp):
ATATTTATTATATT
Found at i:110801 original size:25 final size:24
Alignment explanation
Indices: 110722--110803 Score: 68
Period size: 25 Copynumber: 3.5 Consensus size: 24
110712 GAAGAAAGTT
*
110722 TTATATATTTGAT-AA-TTTACATA
1 TTATATATTT-ATAAATTTTATATA
*
110745 TTA-AT-TATA-AAATTTTATATA
1 TTATATATTTATAAATTTTATATA
*
110766 TTATATTTTTATAAATTTTAATATA
1 TTATATATTTATAAATTTT-ATATA
110791 TTA-ATAATTTATA
1 TTATAT-ATTTATA
110804 TTATATAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
20 3 0.06
21 12 0.25
22 4 0.08
23 6 0.12
24 9 0.19
25 14 0.29
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (24 bp):
TTATATATTTATAAATTTTATATA
Found at i:110966 original size:20 final size:21
Alignment explanation
Indices: 110933--110977 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
110923 TAAATTATAA
110933 TTAAAATATTAATAAA-AATAT
1 TTAAAATATTAATAAATAAT-T
110954 TTAAAAT-TTAATAAATAATT
1 TTAAAATATTAATAAATAATT
110974 TTAA
1 TTAA
110978 TTAATATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAAAATATTAATAAATAATT
Found at i:111039 original size:59 final size:59
Alignment explanation
Indices: 110927--111056 Score: 133
Period size: 59 Copynumber: 2.2 Consensus size: 59
110917 AATATTTAAA
* **
110927 TTATAATTAAAATATTAATAAAAATATTTAAAATTTAATAAATAATTTTAATTAATATT-T
1 TTATAATT-AAATATTAATAAAAATATTTAAAATTAAATAAATAATTAAAATTAA-ATTAT
***
110987 TTATAATTAAAT-TTACATAAAAATATTTTTTTATTAAAT-AATAATTAAAATTAAATTAAT
1 TTATAATTAAATATTA-ATAAAAATA-TTTAAAATTAAATAAATAATTAAAATTAAATT-AT
111047 TTA-AATTAAA
1 TTATAATTAAA
111057 AAAATTATAA
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
58 6 0.10
59 33 0.55
60 21 0.35
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (59 bp):
TTATAATTAAATATTAATAAAAATATTTAAAATTAAATAAATAATTAAAATTAAATTAT
Found at i:111052 original size:15 final size:15
Alignment explanation
Indices: 111028--111092 Score: 51
Period size: 15 Copynumber: 4.2 Consensus size: 15
111018 TATTAAATAA
*
111028 TAATTAAAATTAAAT
1 TAATTTAAATTAAAT
111043 TAATTTAAATTAAA-
1 TAATTTAAATTAAAT
* * *
111057 AAAATTATAATCAAAATT
1 TAATTTA-AAT-TAAA-T
*
111075 TAATTTAAAATAAAT
1 TAATTTAAATTAAAT
111090 TAA
1 TAA
111093 ATCAATCATA
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
14 5 0.13
15 20 0.53
16 6 0.16
17 2 0.05
18 5 0.13
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (15 bp):
TAATTTAAATTAAAT
Found at i:111055 original size:32 final size:33
Alignment explanation
Indices: 111019--111094 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 33
111009 ATATTTTTTT
*
111019 ATTAAATAATAATTAAAAT-TAAA-TTAATTTAA
1 ATTAAATAA-AATTAAAATCAAAATTTAATTTAA
*
111051 ATTAAA-AAAATTATAATCAAAATTTAATTTAA
1 ATTAAATAAAATTAAAATCAAAATTTAATTTAA
* *
111083 AATAAATTAAAT
1 ATTAAATAAAAT
111095 CAATCATATT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 8 0.22
31 5 0.14
32 20 0.54
33 4 0.11
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (33 bp):
ATTAAATAAAATTAAAATCAAAATTTAATTTAA
Found at i:111074 original size:27 final size:27
Alignment explanation
Indices: 111044--111097 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
111034 AAATTAAATT
111044 AATTTAAATTAAAA-AAATTATAATCAA
1 AATTTAAATTAAAATAAATTA-AATCAA
*
111071 AATTTAATTTAAAATAAATTAAATCAA
1 AATTTAAATTAAAATAAATTAAATCAA
111098 TCATATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (27 bp):
AATTTAAATTAAAATAAATTAAATCAA
Found at i:111107 original size:14 final size:14
Alignment explanation
Indices: 111082--111133 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
111072 ATTTAATTTA
111082 AAATAA-ATTAAAT
1 AAATAATATTAAAT
* *
111095 CAATCATATTAAAT
1 AAATAATATTAAAT
111109 AAATAATATTAATTAT
1 AAATAATATTAA--AT
111125 AAAT-ATATT
1 AAATAATATT
111134 CACGTCATAC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 4 0.12
14 17 0.53
15 5 0.16
16 6 0.19
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATAATATTAAAT
Found at i:111910 original size:16 final size:15
Alignment explanation
Indices: 111883--111917 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 15
111873 AATATGTAAA
111883 TAAATATATATTTTAT
1 TAAATATATATTTT-T
111899 TAAATATATATTTTT
1 TAAATATATATTTTT
111914 TAAA
1 TAAA
111918 AAATAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TAAATATATATTTTT
Found at i:111921 original size:18 final size:19
Alignment explanation
Indices: 111879--111922 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 19
111869 TTTAAATATG
111879 TAAATAAATATATATTTTAT
1 TAAA-AAATATATATTTTAT
111899 T---AAATATATATTTT-T
1 TAAAAAATATATATTTTAT
111914 TAAAAAATA
1 TAAAAAATA
111923 ATAATACAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 8
0.72 0.00 0.28
Matches are distributed among these distances:
15 2 0.10
16 13 0.62
18 5 0.24
20 1 0.05
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TAAAAAATATATATTTTAT
Found at i:112334 original size:29 final size:31
Alignment explanation
Indices: 112288--112346 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 31
112278 TAATTAAAAA
112288 ATAATATATTATTAAAAAATTATAAATATAAT
1 ATAATATATTATTAAAAAATTATAAA-ATAAT
*
112320 ATAA-ATATT-TT-AAAATTTATAAAATAA
1 ATAATATATTATTAAAAAATTATAAAATAA
112347 AAATTATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 4 0.15
29 11 0.42
30 2 0.08
31 5 0.19
32 4 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (31 bp):
ATAATATATTATTAAAAAATTATAAAATAAT
Found at i:112381 original size:40 final size:43
Alignment explanation
Indices: 112302--112386 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 43
112292 TATATTATTA
*
112302 AAAAATTATAAATATAATATAAATATTTTAAAATTTATAAAAT
1 AAAAATTATAAATATAATATAAATATTTTAAAATGTATAAAAT
* * *
112345 AAAAATTATTAATAT-AT-TAAA-ATTTTTATATGTATAAAAT
1 AAAAATTATAAATATAATATAAATATTTTAAAATGTATAAAAT
112385 AA
1 AA
112387 TATTTTTATA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
40 18 0.47
41 4 0.11
42 2 0.05
43 14 0.37
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (43 bp):
AAAAATTATAAATATAATATAAATATTTTAAAATGTATAAAAT
Found at i:112404 original size:22 final size:22
Alignment explanation
Indices: 112366--112430 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
112356 ATATATTAAA
*
112366 ATTTTTATATGTATAAAATAAT
1 ATTTTTATATATATAAAATAAT
112388 ATTTTTATA-ATATTAAAAT-AT
1 ATTTTTATATATA-TAAAATAAT
* * *
112409 AAATATTATAAATATAAAATAA
1 -ATTTTTATATATATAAAATAA
112431 ATATGTAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
21 4 0.11
22 28 0.78
23 4 0.11
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
ATTTTTATATATATAAAATAAT
Found at i:112413 original size:14 final size:15
Alignment explanation
Indices: 112396--112426 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
112386 ATATTTTTAT
112396 AATATTA-AAATATA
1 AATATTATAAATATA
112410 AATATTATAAATATA
1 AATATTATAAATATA
112425 AA
1 AA
112427 ATAAATATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AATATTATAAATATA
Found at i:114389 original size:13 final size:14
Alignment explanation
Indices: 114371--114418 Score: 53
Period size: 13 Copynumber: 3.3 Consensus size: 14
114361 AAAATAATAC
114371 ATATATAATA-AAA
1 ATATATAATATAAA
114384 ATATATAATATAAAA
1 ATATATAATAT-AAA
*
114399 ATTTATGTAATATAAA
1 A--TATATAATATAAA
114415 ATAT
1 ATAT
114419 TAACATGTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 10 0.33
14 3 0.10
15 4 0.13
16 4 0.13
17 9 0.30
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (14 bp):
ATATATAATATAAA
Found at i:114394 original size:20 final size:20
Alignment explanation
Indices: 114320--114395 Score: 62
Period size: 22 Copynumber: 3.5 Consensus size: 20
114310 CATATATTTT
* *
114320 TATATAAAAAATAATTAAAATA
1 TATATAATATATAA-TAAAA-A
* *
114342 TAATATAAGATATTATAAAAA
1 T-ATATAATATATAATAAAAA
*
114363 AATAATACATATATAATAAAAA
1 TAT-ATA-ATATATAATAAAAA
114385 TATATAATATA
1 TATATAATATA
114396 AAAATTTATG
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
20 7 0.16
21 7 0.16
22 20 0.45
23 10 0.23
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (20 bp):
TATATAATATATAATAAAAA
Found at i:114396 original size:15 final size:15
Alignment explanation
Indices: 114339--114415 Score: 50
Period size: 17 Copynumber: 4.9 Consensus size: 15
114329 AATAATTAAA
*
114339 ATATAATAT-AAGAT
1 ATATAATATAAAAAT
*
114353 ATTATAA-AAAAATAAT
1 A-TATAATATAAA-AAT
*
114369 ACATATATAATAAAAAT
1 ATATA-AT-ATAAAAAT
114386 ATATAATATAAAAATTT
1 ATATAATATAAAAA--T
*
114403 ATGTAATATAAAA
1 ATATAATATAAAA
114416 TATTAACATG
Statistics
Matches: 49, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
14 2 0.04
15 17 0.35
16 6 0.12
17 20 0.41
18 4 0.08
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (15 bp):
ATATAATATAAAAAT
Found at i:114494 original size:11 final size:11
Alignment explanation
Indices: 114464--114497 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
114454 TAAATAAGAT
114464 TATAATATAAA
1 TATAATATAAA
*
114475 AAT-ATATAAA
1 TATAATATAAA
114485 TATAATATAAA
1 TATAATATAAA
114496 TA
1 TA
114498 CATAAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TATAATATAAA
Found at i:114496 original size:19 final size:20
Alignment explanation
Indices: 114464--114504 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
114454 TAAATAAGAT
*
114464 TATAATATAAAAATATATAAA
1 TATAATAT-AAAATACATAAA
114485 TATAATAT-AAATACATAAA
1 TATAATATAAAATACATAAA
114504 T
1 T
114505 TATTGAACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
21 8 0.42
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
TATAATATAAAATACATAAA
Found at i:114631 original size:19 final size:19
Alignment explanation
Indices: 114607--114649 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
114597 TTGGCTCATA
114607 ATTTTTTTAT-ATCATATT
1 ATTTTTTTATAATCATATT
114625 -TATTTTTTATAATCATATT
1 AT-TTTTTTATAATCATATT
114644 ATTTTT
1 ATTTTT
114650 AAAATTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 1 0.05
18 8 0.36
19 12 0.55
20 1 0.05
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTTTTTTATAATCATATT
Found at i:114650 original size:17 final size:18
Alignment explanation
Indices: 114609--114649 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
114599 GGCTCATAAT
114609 TTTTTTATATCATATTTA
1 TTTTTTATATCATATTTA
114627 TTTTTTATAATCATA-TTA
1 TTTTTTAT-ATCATATTTA
114645 TTTTT
1 TTTTT
114650 AAAATTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTTTATATCATATTTA
Found at i:114759 original size:2 final size:2
Alignment explanation
Indices: 114752--114854 Score: 53
Period size: 2 Copynumber: 55.0 Consensus size: 2
114742 TTAATAATTC
* *
114752 AT AT AT AT AT AT AT AT CAT AT CGT AT AT -T AT -T TT AT -T A- AT
1 AT AT AT AT AT AT AT AT -AT AT -AT AT AT AT AT AT AT AT AT AT AT
* * * * *
114792 -T AT AT AA AT AT A- AT AT AT -T AA AT -T TT AA AT AT AA AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
114829 AT AT GT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
114855 TAATACTCTT
Statistics
Matches: 76, Mismatches: 14, Indels: 22
0.68 0.12 0.20
Matches are distributed among these distances:
1 9 0.12
2 64 0.84
3 3 0.04
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:115171 original size:18 final size:19
Alignment explanation
Indices: 115113--115172 Score: 58
Period size: 17 Copynumber: 3.4 Consensus size: 19
115103 TTAATATGTG
115113 TATTTTAT-TTAT-ATTAA
1 TATTTTATATTATAATTAA
* *
115130 AATTTTA-A-TATATTTAA
1 TATTTTATATTATAATTAA
*
115147 TAATTTATATTATAATT-A
1 TATTTTATATTATAATTAA
115165 TATTTTAT
1 TATTTTAT
115173 TTTAAAATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
16 3 0.09
17 15 0.45
18 9 0.27
19 6 0.18
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTTTATATTATAATTAA
Found at i:115174 original size:30 final size:30
Alignment explanation
Indices: 115119--115182 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
115109 TGTGTATTTT
*
115119 ATTTATATTAAAATTTTAATATA-TTTAATA
1 ATTTATATTAAAATTATAATATATTTTAA-A
* * *
115149 ATTTATATTATAATTATATTTTATTTTAAA
1 ATTTATATTAAAATTATAATATATTTTAAA
115179 ATTT
1 ATTT
115183 TAATTGAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 24 0.83
31 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (30 bp):
ATTTATATTAAAATTATAATATATTTTAAA
Found at i:115540 original size:14 final size:13
Alignment explanation
Indices: 115520--115553 Score: 59
Period size: 14 Copynumber: 2.5 Consensus size: 13
115510 TAATTTTAAA
115520 ATTTTATTTTTAT
1 ATTTTATTTTTAT
115533 ATTATTATTTTTAT
1 ATT-TTATTTTTAT
115547 ATTTTAT
1 ATTTTAT
115554 AATTAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
ATTTTATTTTTAT
Found at i:115996 original size:13 final size:13
Alignment explanation
Indices: 115974--116018 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
115964 ATTAGGCACC
115974 ATAATT-TATATT
1 ATAATTATATATT
115986 ATAATTATATATT
1 ATAATTATATATT
*
115999 -T--TAATATATT
1 ATAATTATATATT
116009 ATAATTATAT
1 ATAATTATAT
116019 TTAAAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
10 8 0.30
11 1 0.04
12 7 0.26
13 11 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATAATTATATATT
Found at i:116027 original size:20 final size:23
Alignment explanation
Indices: 115981--116062 Score: 80
Period size: 23 Copynumber: 3.5 Consensus size: 23
115971 ACCATAATTT
*
115981 ATATTATAATTATATATTTTAAT
1 ATATTATAATTATATATTTTAAA
116004 ATATTATAA-T-TATA-TTTAAA
1 ATATTATAATTATATATTTTAAA
*
116024 ATATTTTATATTTATATAAATTTTAAA
1 ATA--TTATAATTATAT--ATTTTAAA
116051 ATATTAATAATT
1 ATATT-ATAATT
116063 TTTATGATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
20 8 0.17
21 4 0.08
22 6 0.12
23 10 0.21
24 3 0.06
25 2 0.04
26 6 0.12
27 9 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
ATATTATAATTATATATTTTAAA
Found at i:116592 original size:2 final size:2
Alignment explanation
Indices: 116585--116614 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
116575 CTACTATCCA
116585 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
116615 TTAAAACAAA
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:119582 original size:13 final size:14
Alignment explanation
Indices: 119557--119586 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
119547 GAAAGTTTAA
119557 TCTTTTCTCCTTTT
1 TCTTTTCTCCTTTT
119571 TCTTTT-TCCTTTT
1 TCTTTTCTCCTTTT
119584 TCT
1 TCT
119587 AAGGAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (14 bp):
TCTTTTCTCCTTTT
Found at i:122810 original size:119 final size:118
Alignment explanation
Indices: 122600--122836 Score: 447
Period size: 119 Copynumber: 2.0 Consensus size: 118
122590 TTAATAAAAA
*
122600 AAAACAGAATTACATAGGTAACAAATACTTTTTACTATATATCAATCTTTTTGTCAAAGAAATCC
1 AAAACAGAATTACATAGGTAACAAATACTTTTTACTATATATCAATCTTTTTGCCAAAGAAATCC
122665 GTAAGTAATGTAGACCCCCTAAATTCAAAAGCTGGCTTCATCCATAAATTTTC
66 GTAAGTAATGTAGACCCCCTAAATTCAAAAGCTGGCTTCATCCATAAATTTTC
122718 AAAACAGAATTACATAGGTAACAAATACTTTTTACTATGATATCAATCTTTTTGCCAAAGAAATC
1 AAAACAGAATTACATAGGTAACAAATACTTTTTACTAT-ATATCAATCTTTTTGCCAAAGAAATC
*
122783 CTTAAGTAATGTAGACCCCCTAAATTCAAAAGCTGGCTTCATCCATAAATTTTC
65 CGTAAGTAATGTAGACCCCCTAAATTCAAAAGCTGGCTTCATCCATAAATTTTC
122837 TCACTTAGCA
Statistics
Matches: 116, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
118 38 0.33
119 78 0.67
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (118 bp):
AAAACAGAATTACATAGGTAACAAATACTTTTTACTATATATCAATCTTTTTGCCAAAGAAATCC
GTAAGTAATGTAGACCCCCTAAATTCAAAAGCTGGCTTCATCCATAAATTTTC
Found at i:124362 original size:16 final size:17
Alignment explanation
Indices: 124330--124380 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 17
124320 ATTCAATTAA
* *
124330 AAATAACAATTAATATT
1 AAATAAAAATAAATATT
*
124347 AAAT-ATAATAAATATT
1 AAATAAAAATAAATATT
*
124363 CAATAAAAATAAAT-TT
1 AAATAAAAATAAATATT
124379 AA
1 AA
124381 GTTTATTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 16 0.57
17 12 0.43
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATAAAAATAAATATT
Found at i:126092 original size:19 final size:19
Alignment explanation
Indices: 126070--126108 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
126060 GATTAAAAAA
* *
126070 ATATTTTATATTTATATTT
1 ATATTTTATAATTAAATTT
126089 ATATTTTATAATTAAATTT
1 ATATTTTATAATTAAATTT
126108 A
1 A
126109 AATTAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATATTTTATAATTAAATTT
Found at i:126154 original size:5 final size:5
Alignment explanation
Indices: 126139--126229 Score: 73
Period size: 5 Copynumber: 18.0 Consensus size: 5
126129 ATTTAATAAT
*
126139 AATTAA AATTA AATTA AATTA ATTTA AATTATA AATT- -ATTA AATTTA
1 AATT-A AATTA AATTA AATTA AATTA AA-T-TA AATTA AATTA AA-TTA
* * *
126186 AATTT AATTCA AATAA AATTA AATT- TATTA AATTA AA-TA AATTA
1 AATTA AATT-A AATTA AATTA AATTA AATTA AATTA AATTA AATTA
126230 CTTAATTTTT
Statistics
Matches: 69, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
3 3 0.04
4 7 0.10
5 41 0.59
6 14 0.20
7 4 0.06
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (5 bp):
AATTA
Found at i:126180 original size:36 final size:35
Alignment explanation
Indices: 126131--126229 Score: 103
Period size: 36 Copynumber: 2.8 Consensus size: 35
126121 ATTTTATTAT
* * *
126131 TTAATAATAATTAAAATTAAATTAAATTAATTTAAA
1 TTAA-AATTATTAAAATTAAATTAAATTAAATAAAA
* *
126167 TTATAAATTATTAAATTTAAATTTAATTCAAATAAAA
1 TTA-AAATTATTAAAATTAAATTAAATT-AAATAAAA
*
126204 TTAAATTTATT-AAATTAAA-TAAATTA
1 TTAAAATTATTAAAATTAAATTAAATTA
126230 CTTAATTTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
33 1 0.02
34 5 0.09
35 7 0.13
36 30 0.57
37 10 0.19
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (35 bp):
TTAAAATTATTAAAATTAAATTAAATTAAATAAAA
Found at i:126186 original size:52 final size:53
Alignment explanation
Indices: 126129--126248 Score: 131
Period size: 52 Copynumber: 2.3 Consensus size: 53
126119 TTATTTTATT
*
126129 ATTT-AATAATAATTAAAATTAAATTAAATTAATTTAAATT-ATAAATTA-TTAA
1 ATTTAAAT-ATAATTAAAATAAAATTAAATTAA-TTAAATTAATAAATTACTTAA
* * *
126181 ATTTAAATTTAATTCAAATAAAATTAAATTTATTAAATTAAATAAATTACTTAA
1 ATTTAAATATAATTAAAATAAAATTAAATTAATTAAATT-AATAAATTACTTAA
*
126235 TTTTTAAATA-AATT
1 -ATTTAAATATAATT
126249 TAACGTAATC
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
51 7 0.12
52 24 0.42
53 11 0.19
54 8 0.14
55 7 0.12
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (53 bp):
ATTTAAATATAATTAAAATAAAATTAAATTAATTAAATTAATAAATTACTTAA
Found at i:126202 original size:21 final size:20
Alignment explanation
Indices: 126139--126223 Score: 75
Period size: 21 Copynumber: 4.2 Consensus size: 20
126129 ATTTAATAAT
* * *
126139 AATTAAAATTAAATTAAATT
1 AATTTAAATTTAATTAAATA
*
126159 AATTTAAATTATAAATT-ATTA
1 AATTTAAATT-T-AATTAAATA
126180 AATTTAAATTTAATTCAAATA
1 AATTTAAATTTAATT-AAATA
*
126201 AAATTAAATTT-ATTAAATTA
1 AATTTAAATTTAATTAAA-TA
126221 AAT
1 AAT
126224 AAATTACTTA
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
19 7 0.13
20 17 0.32
21 25 0.47
22 4 0.08
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (20 bp):
AATTTAAATTTAATTAAATA
Found at i:126635 original size:21 final size:21
Alignment explanation
Indices: 126610--126654 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
126600 AAATCGACGC
*
126610 TAATAATGAG-TTTAATTATTA
1 TAATAATAAGATTTAA-TATTA
*
126631 TAATATTAAGATTTAATATTA
1 TAATAATAAGATTTAATATTA
126652 TAA
1 TAA
126655 ATTTATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (21 bp):
TAATAATAAGATTTAATATTA
Found at i:126752 original size:27 final size:27
Alignment explanation
Indices: 126722--126776 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
126712 AGTGGGAATA
*
126722 AAAAATATTTGTTAAAAAT-ATTATTTT
1 AAAAATATAT-TTAAAAATAATTATTTT
*
126749 AAAAATATATTTATAAATAATTATTTT
1 AAAAATATATTTAAAAATAATTATTTT
126776 A
1 A
126777 TTTTAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (27 bp):
AAAAATATATTTAAAAATAATTATTTT
Found at i:126759 original size:13 final size:13
Alignment explanation
Indices: 126722--126776 Score: 60
Period size: 14 Copynumber: 4.1 Consensus size: 13
126712 AGTGGGAATA
126722 AAAAATAT-TTGTT
1 AAAAATATATT-TT
126735 AAAAATATTATTTT
1 AAAAATA-TATTTT
126749 AAAAATATATTTAT
1 AAAAATATATTT-T
126763 AAATAAT-TATTTT
1 AAA-AATATATTTT
126776 A
1 A
126777 TTTTAAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
13 14 0.37
14 19 0.50
15 5 0.13
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (13 bp):
AAAAATATATTTT
Found at i:126792 original size:22 final size:22
Alignment explanation
Indices: 126764--126813 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
126754 TATATTTATA
** *
126764 AATAATTATTTTATTTTAAAAT
1 AATAATTATCATATTTAAAAAT
126786 AATAATTATCATATTTAAAAAT
1 AATAATTATCATATTTAAAAAT
126808 AATAAT
1 AATAAT
126814 AAATTTAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
AATAATTATCATATTTAAAAAT
Found at i:126810 original size:19 final size:19
Alignment explanation
Indices: 126755--126810 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 19
126745 TTTTAAAAAT
* *
126755 ATATTTATAAATAATTATT
1 ATATTTAAAAATAATTATC
*
126774 TTATTTTAAAATAATAATTATC
1 ATA-TTT-AAA-AATAATTATC
126796 ATATTTAAAAATAAT
1 ATATTTAAAAATAAT
126811 AATAAATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
19 8 0.27
20 6 0.20
21 5 0.17
22 11 0.37
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
ATATTTAAAAATAATTATC
Found at i:126896 original size:25 final size:26
Alignment explanation
Indices: 126826--126910 Score: 70
Period size: 25 Copynumber: 3.3 Consensus size: 26
126816 ATTTAAATAT
126826 TTTAAATTAATAA-TAAATAATGATTA
1 TTTAAATTAATAATTAAATAAT-ATTA
* *
126852 -TTAAA-TATTCACTTAAATAAT-TTA
1 TTTAAATTAAT-AATTAAATAATATTA
* *
126876 TTTAAATTAATAATTATATAAATATTT
1 TTTAAATTAATAATTAAAT-AATATTA
126903 TATTAAAT
1 T-TTAAAT
126911 AGTTATAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
24 6 0.13
25 17 0.37
26 14 0.30
27 3 0.07
28 6 0.13
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.47
Consensus pattern (26 bp):
TTTAAATTAATAATTAAATAATATTA
Found at i:127243 original size:13 final size:13
Alignment explanation
Indices: 127220--127252 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
127210 TTTTAAATAT
127220 TTTAAATATT-AA
1 TTTAAATATTAAA
127232 TTTAAATCATTAAA
1 TTTAAAT-ATTAAA
127246 TTTAAAT
1 TTTAAAT
127253 TAAATTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 3 0.16
14 9 0.47
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTAAATATTAAA
Found at i:127703 original size:22 final size:22
Alignment explanation
Indices: 127675--127716 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
127665 AATGAAGAAG
127675 CATAATTCGTACAATTATTAAC
1 CATAATTCGTACAATTATTAAC
127697 CATAATTCGTACAATTATTA
1 CATAATTCGTACAATTATTA
127717 TAATATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (22 bp):
CATAATTCGTACAATTATTAAC
Found at i:127848 original size:10 final size:10
Alignment explanation
Indices: 127833--127887 Score: 67
Period size: 10 Copynumber: 5.4 Consensus size: 10
127823 TAAGTTAAAA
127833 ATTTTAATTT
1 ATTTTAATTT
127843 ATTTT-ATTT
1 ATTTTAATTT
127852 ATATTTAAGTTT
1 AT-TTTAA-TTT
*
127864 AATTTAATTT
1 ATTTTAATTT
*
127874 ATTTTAAATT
1 ATTTTAATTT
127884 ATTT
1 ATTT
127888 ATATTTAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
9 6 0.15
10 23 0.59
11 6 0.15
12 4 0.10
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (10 bp):
ATTTTAATTT
Found at i:127889 original size:4 final size:5
Alignment explanation
Indices: 127835--127896 Score: 56
Period size: 5 Copynumber: 12.2 Consensus size: 5
127825 AGTTAAAAAT
* * *
127835 TTTAA TTT-A TTTTA TTTATA TTTAA GTTTAA TTTAA TTTAT TTTAA ATT-A
1 TTTAA TTTAA TTTAA TTTA-A TTTAA -TTTAA TTTAA TTTAA TTTAA TTTAA
127885 TTTATA TTTAA T
1 TTTA-A TTTAA T
127897 ATTTATAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
4 7 0.15
5 25 0.53
6 15 0.32
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (5 bp):
TTTAA
Found at i:128150 original size:42 final size:42
Alignment explanation
Indices: 128096--128186 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
128086 ATTTCCCATG
* *
128096 ATGGTAAGCAAAATCGAC-GCGATTCAATTGATCGTCCCTAAA
1 ATGGTAACCAAAATCGACAG-GATTCAATTGATCGTCCCCAAA
* *
128138 ATGGTAACCAAAATGGACAGTATTCAATTGATCGTCCCCAAA
1 ATGGTAACCAAAATCGACAGGATTCAATTGATCGTCCCCAAA
128180 ATGGTAA
1 ATGGTAA
128187 GCTAAATCAG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 43 0.98
43 1 0.02
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (42 bp):
ATGGTAACCAAAATCGACAGGATTCAATTGATCGTCCCCAAA
Found at i:134800 original size:16 final size:15
Alignment explanation
Indices: 134781--134815 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
134771 TGGTTGATGC
134781 TTTTACTGTTTTTTTT
1 TTTTACT-TTTTTTTT
*
134797 TTTTGCTTTTTTTTT
1 TTTTACTTTTTTTTT
134812 TTTT
1 TTTT
134816 TTTCAAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.03, C:0.06, G:0.06, T:0.86
Consensus pattern (15 bp):
TTTTACTTTTTTTTT
Found at i:140326 original size:290 final size:289
Alignment explanation
Indices: 139785--140340 Score: 841
Period size: 290 Copynumber: 1.9 Consensus size: 289
139775 CTTCATGTTG
* * *
139785 ATTTTGAAGCACAGAATACCTATCTTGATGTCAGTGGAGCTTTAGCAAGTGAACCAAATATATTG
1 ATTTTGAAGCACAGAATACCTATCTTGATGTCAGTAGAGCTTTACCAAGTGAAACAAATATATTG
** *
139850 CTCAATTCAAATAAATTTCTTTCTAGATATAATCAAATGGCTTAACTTTCTTCCCTAGGTGGTTT
66 AGCAATCCAAATAAATTTCTTTCTAGATATAATCAAATGGCTTAACTTTCTTCCCTAGGTGGTTT
*
139915 TCTGTTTCTCAAAAAAGGGGGAAAGAAGTTCATGAAAGCAGCAGAACTTGGCAATTCATTGCTAT
131 TCTGTTTCTCAAAAAA-GGGGAAAAAAGTTCATGAAAGCAGCAGAACTTGGCAATTCATTGCTAT
* * * *
139980 CAATTGGAATTGACTTTCATTACTGTGGGATATTGCAATCCTCTGGTTGCTTTTTTTTTTTTAAG
195 CAATTGGAATTGACTTTCATCACTGTGGGATATTGCAACCCTCTAGTTGCTTTTTTTTTCTTAAG
140045 TTCATCACATTCATGTCTTCATAAATTGGT
260 TTCATCACATTCATGTCTTCATAAATTGGT
* * *
140075 ATTTTGAAGTACAGAATATCTATCTTGATGTCGGTAGAGCTTTACCAAGTGAAACAAATATATTG
1 ATTTTGAAGCACAGAATACCTATCTTGATGTCAGTAGAGCTTTACCAAGTGAAACAAATATATTG
* * *
140140 AGCAATCCAAATAAATTTCTTTCTAGATCTAA-CTAAATGGTTTGAA-TTTCTTCCCTTGGTGGT
66 AGCAATCCAAATAAATTTCTTTCTAGATATAATC-AAATGGCTT-AACTTTCTTCCCTAGGTGGT
*
140203 TTTCTGTTTCTCAAAAGAA-GGGAAAAAAGTTCATGAAAGCAGCATAACTTGGCAAATT-ATTGC
129 TTTCTGTTTCTCAAAA-AAGGGGAAAAAAGTTCATGAAAGCAGCAGAACTTGGC-AATTCATTGC
* * * *
140266 TATTAATTGTAATTGATTTTTATCACTGTGGGATATTGCAACCCTCTAGTTGCTTTTTTTTTCTT
192 TATCAATTGGAATTGACTTTCATCACTGTGGGATATTGCAACCCTCTAGTTGCTTTTTTTTTCTT
140331 AAGTTCATCA
257 AAGTTCATCA
140341 ATGTCTTCAT
Statistics
Matches: 240, Mismatches: 22, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
289 105 0.44
290 131 0.55
291 4 0.02
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (289 bp):
ATTTTGAAGCACAGAATACCTATCTTGATGTCAGTAGAGCTTTACCAAGTGAAACAAATATATTG
AGCAATCCAAATAAATTTCTTTCTAGATATAATCAAATGGCTTAACTTTCTTCCCTAGGTGGTTT
TCTGTTTCTCAAAAAAGGGGAAAAAAGTTCATGAAAGCAGCAGAACTTGGCAATTCATTGCTATC
AATTGGAATTGACTTTCATCACTGTGGGATATTGCAACCCTCTAGTTGCTTTTTTTTTCTTAAGT
TCATCACATTCATGTCTTCATAAATTGGT
Found at i:147173 original size:36 final size:36
Alignment explanation
Indices: 147126--147197 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
147116 TTGTTGACAA
*
147126 AGCCTTGAAGGCCGT-ATGCCTAAAGAGTCGAATACT
1 AGCCTAGAAGGCCGTGA-GCCTAAAGAGTCGAATACT
*
147162 AGCCTAGAAGGCTGTGAGCCTAAAGAGTCGAATACT
1 AGCCTAGAAGGCCGTGAGCCTAAAGAGTCGAATACT
147198 TTAGATGTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 32 0.97
37 1 0.03
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (36 bp):
AGCCTAGAAGGCCGTGAGCCTAAAGAGTCGAATACT
Found at i:147583 original size:2 final size:2
Alignment explanation
Indices: 147576--147612 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
147566 GTTTTCGTTT
147576 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
147613 TTTAGCAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:149658 original size:2 final size:2
Alignment explanation
Indices: 149651--149687 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
149641 TATACATACT
149651 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
149688 CTGCTAGCTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:150249 original size:20 final size:20
Alignment explanation
Indices: 150211--150249 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
150201 TTTTATTATT
*
150211 TTTTTATTAAGATTTCTTAA
1 TTTTTATTAAGATTACTTAA
150231 TTTTTA-TAAGATTGACTTA
1 TTTTTATTAAGATT-ACTTA
150250 TACGTATCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.31, C:0.05, G:0.08, T:0.56
Consensus pattern (20 bp):
TTTTTATTAAGATTACTTAA
Found at i:150391 original size:2 final size:2
Alignment explanation
Indices: 150386--150414 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
150376 CGTGTGTGTG
150386 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 T
150415 GCACACACAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:152324 original size:30 final size:30
Alignment explanation
Indices: 152251--152354 Score: 117
Period size: 30 Copynumber: 3.4 Consensus size: 30
152241 CATTAAAGGA
152251 TAAGGGCTTATTTG-G-GTAAAAGCTAAAAGTGT
1 TAAGGGCTTATTTGAGTGTAAAA--TAAAA--GT
*
152283 TAAGGGTTTATTTGAGTGTAAAATAAAAGT
1 TAAGGGCTTATTTGAGTGTAAAATAAAAGT
*
152313 TAAGAGCTTATTTGAGTGT--AATAAAAGT
1 TAAGGGCTTATTTGAGTGTAAAATAAAAGT
152341 ATAAGGGCTTATTT
1 -TAAGGGCTTATTT
152355 AGATAAACTT
Statistics
Matches: 65, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
28 9 0.14
29 12 0.18
30 19 0.29
32 18 0.28
33 1 0.02
34 6 0.09
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.36
Consensus pattern (30 bp):
TAAGGGCTTATTTGAGTGTAAAATAAAAGT
Found at i:154605 original size:2 final size:2
Alignment explanation
Indices: 154600--154635 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
154590 ATATATATAT
154600 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
154636 TATTTAGACA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:154797 original size:21 final size:21
Alignment explanation
Indices: 154773--154816 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
154763 TTGAATTATA
154773 TAATAAATATATT-AATATTTT
1 TAATAAATAT-TTAAATATTTT
**
154794 TAATATGTATTTAAATATTTT
1 TAATAAATATTTAAATATTTT
154815 TA
1 TA
154817 TTTATTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TAATAAATATTTAAATATTTT
Found at i:154824 original size:18 final size:18
Alignment explanation
Indices: 154786--154840 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
154776 TAAATATATT
154786 AATATTTTTAATATGTATTTA
1 AATATTTTT-AT-T-TATTTA
154807 AATATTTTTATTTATTTA
1 AATATTTTTATTTATTTA
*
154825 AA-ATTTATTATATATT
1 AATATTT-TTATTTATT
154841 ATATATAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
17 4 0.12
18 16 0.50
19 1 0.03
20 2 0.06
21 9 0.28
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
AATATTTTTATTTATTTA
Found at i:154878 original size:13 final size:15
Alignment explanation
Indices: 154851--154897 Score: 55
Period size: 13 Copynumber: 3.3 Consensus size: 15
154841 ATATATAAAA
154851 AAATTAAA-TATAAT
1 AAATTAAATTATAAT
154865 -AATTAAATTA-AAT
1 AAATTAAATTATAAT
*
154878 AAATATAAATTATATT
1 AAAT-TAAATTATAAT
154894 AAAT
1 AAAT
154898 ATTATAAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
13 10 0.36
14 5 0.18
15 7 0.25
16 6 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATTAAATTATAAT
Found at i:154894 original size:20 final size:22
Alignment explanation
Indices: 154855--154898 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
154845 ATAAAAAAAT
154855 TAAATATAATAATTAAATTAAA
1 TAAATATAATAATTAAATTAAA
*
154877 TAAATAT-A-AATTATATTAAA
1 TAAATATAATAATTAAATTAAA
154897 TA
1 TA
154899 TTATAAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 1 0.05
22 7 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAATATAATAATTAAATTAAA
Found at i:155815 original size:44 final size:43
Alignment explanation
Indices: 155725--155815 Score: 96
Period size: 44 Copynumber: 2.1 Consensus size: 43
155715 AAATATATTA
* * *
155725 AAATATTAAAAAAAAATTATATTAATATCTATATTTTATAATT
1 AAATATTAAAAAAAAATTATATTAATATCTAAATTTCATAACT
* *
155768 AAAT-TTAAATAAAAATATTATTTTAATATTTAAATATTCA-AACT
1 AAATATTAAA-AAAAA-ATTATATTAATATCTAAAT-TTCATAACT
155812 AAAT
1 AAAT
155816 CAATGCAGAG
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
42 5 0.12
43 9 0.22
44 23 0.57
45 3 0.08
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (43 bp):
AAATATTAAAAAAAAATTATATTAATATCTAAATTTCATAACT
Found at i:156440 original size:25 final size:25
Alignment explanation
Indices: 156398--156455 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 25
156388 TCAACCTATT
*
156398 TTTTTAATTATGTAATATATAT-TAA
1 TTTTTATTTATGTAATAT-TATGTAA
156423 TTTTATATTTATGT-ATATTATGTAA
1 TTTT-TATTTATGTAATATTATGTAA
156448 TTTTTATT
1 TTTTTATT
156456 ATATAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 7 0.23
25 15 0.50
26 8 0.27
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (25 bp):
TTTTTATTTATGTAATATTATGTAA
Found at i:156555 original size:15 final size:15
Alignment explanation
Indices: 156535--156588 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
156525 AAATAAATTT
156535 ATTAAATTATTAAAA
1 ATTAAATTATTAAAA
*
156550 ATTAAAATTTTTTAAAA
1 ATT-AAA-TTATTAAAA
* *
156567 ACTAAATTATAAAAA
1 ATTAAATTATTAAAA
*
156582 AATAAAT
1 ATTAAAT
156589 CTAAACAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
15 16 0.50
16 6 0.19
17 10 0.31
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (15 bp):
ATTAAATTATTAAAA
Found at i:157696 original size:20 final size:21
Alignment explanation
Indices: 157654--157698 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
157644 ATATATTTGT
* *
157654 TTAA-TTTTTAATTATTTTTA
1 TTAATTTTTTAATCATTTTAA
157674 TTAATTTTTTAATCA-TTTAA
1 TTAATTTTTTAATCATTTTAA
157694 TTAAT
1 TTAAT
157699 AAAAAAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
TTAATTTTTTAATCATTTTAA
Found at i:163452 original size:59 final size:58
Alignment explanation
Indices: 163343--163457 Score: 151
Period size: 59 Copynumber: 2.0 Consensus size: 58
163333 ATTTAAATAC
* **
163343 CTTAGATTAAGGACTAGTGTATTACAAATAATTTAAATCCCTTGATTTAAGAGATTCT
1 CTTAGATTAAGGACTAGTGCACCACAAATAATTTAAATCCCTTGATTTAAGAGATTCT
** *
163401 CTTAGATTAAGGACTAGTGCACCACTATCTAATTTAAATCCCTTAGA-TTAAGGGATT
1 CTTAGATTAAGGACTAGTGCACCAC-AAATAATTTAAATCCCTT-GATTTAAGAGATT
163458 TTGACCTAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
58 22 0.45
59 25 0.51
60 2 0.04
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (58 bp):
CTTAGATTAAGGACTAGTGCACCACAAATAATTTAAATCCCTTGATTTAAGAGATTCT
Found at i:164118 original size:17 final size:17
Alignment explanation
Indices: 164096--164133 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
164086 TCATGCATGA
164096 ACTGGCTTATCACACTT
1 ACTGGCTTATCACACTT
164113 ACTGGCTTATCACACTT
1 ACTGGCTTATCACACTT
164130 ACTG
1 ACTG
164134 AGTATGCTAT
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:0.24, C:0.29, G:0.13, T:0.34
Consensus pattern (17 bp):
ACTGGCTTATCACACTT
Found at i:164351 original size:25 final size:26
Alignment explanation
Indices: 164294--164351 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 26
164284 TTTTCCTGTC
164294 TCTGCTAACAAATCAGTCGCATACCT
1 TCTGCTAACAAATCAGTCGCATACCT
*
164320 T-TACTAACAAATCAGTCAG-ATA-CT
1 TCTGCTAACAAATCAGTC-GCATACCT
164344 TCTGCTAA
1 TCTGCTAA
164352 GATATGTAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 3 0.11
25 23 0.82
26 2 0.07
ACGTcount: A:0.34, C:0.26, G:0.10, T:0.29
Consensus pattern (26 bp):
TCTGCTAACAAATCAGTCGCATACCT
Found at i:168329 original size:53 final size:53
Alignment explanation
Indices: 168249--168351 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
168239 CTAATGCCCT
* * ** *
168249 ACTATCTAATTTAAATCCCTTAGATTAAGGATTAGTGTATCACTATCTAACCC
1 ACTATCTAATTTAAATACCTTAGATTAAGGACTAGTACACCACTATCTAACCC
*
168302 ACTATCTAATTTAAATACTTTAGATTAAGGACTAGTACACCACTATCTAA
1 ACTATCTAATTTAAATACCTTAGATTAAGGACTAGTACACCACTATCTAA
168352 TTTAAATTCC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (53 bp):
ACTATCTAATTTAAATACCTTAGATTAAGGACTAGTACACCACTATCTAACCC
Found at i:168488 original size:2 final size:2
Alignment explanation
Indices: 168477--168505 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
168467 ACACTTCAAC
168477 AT AT -T 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
168506 TACTTATAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:170122 original size:19 final size:19
Alignment explanation
Indices: 170098--170136 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
170088 TTCTTATTGA
170098 TAGAACAGAATTTGTAAGT
1 TAGAACAGAATTTGTAAGT
170117 TAGAACAGAATTTGTAAGT
1 TAGAACAGAATTTGTAAGT
170136 T
1 T
170137 TTTTTCTGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.33
Consensus pattern (19 bp):
TAGAACAGAATTTGTAAGT
Found at i:173239 original size:5 final size:5
Alignment explanation
Indices: 173231--173304 Score: 54
Period size: 5 Copynumber: 16.0 Consensus size: 5
173221 ATAAAAATTA
* * *
173231 AATAT AATAT AATA- AATAT AATAA AAT-T TATTT AAATAT AAT-T AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT -AATAT AATAT AATAT
*
173279 -A-AT AATTT AATAT -ATAT -ATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT
173305 TTATATTTAA
Statistics
Matches: 55, Mismatches: 7, Indels: 14
0.72 0.09 0.18
Matches are distributed among these distances:
3 2 0.04
4 20 0.36
5 30 0.55
6 3 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
AATAT
Found at i:173268 original size:24 final size:23
Alignment explanation
Indices: 173240--173308 Score: 61
Period size: 24 Copynumber: 3.0 Consensus size: 23
173230 AAATATAATA
173240 TAATAAATATAATAAAATTTATT
1 TAATAAATATAATAAAATTTATT
* *
173263 TAAATATAAT-TAATATAA-TAATT
1 T-AATA-AATATAATAAAATTTATT
* *
173286 TAATATATATATATAATATTTAT
1 TAATAAATATA-ATAAAATTTAT
173309 ATTTAAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 9
0.70 0.12 0.18
Matches are distributed among these distances:
21 2 0.06
22 6 0.17
23 10 0.29
24 14 0.40
25 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TAATAAATATAATAAAATTTATT
Found at i:173289 original size:8 final size:8
Alignment explanation
Indices: 173273--173358 Score: 57
Period size: 8 Copynumber: 10.0 Consensus size: 8
173263 TAAATATAAT
*
173273 TAATATAA
1 TAATTTAA
173281 TAATTTAA
1 TAATTTAA
*
173289 TATATATATA
1 TA-ATTTA-A
*
173299 TAATATTTA
1 TAAT-TTAA
173308 T-ATTTAA
1 TAATTTAA
*
173315 AAATTTAA
1 TAATTTAA
*
173323 TATTTTAA
1 TAATTTAA
173331 TAATTTATA
1 TAATTTA-A
173340 TATTATTTATA
1 TA--ATTTA-A
173351 TAATTTAA
1 TAATTTAA
173359 ATAAAAATAT
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
7 3 0.05
8 30 0.48
9 16 0.26
10 4 0.06
11 9 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TAATTTAA
Found at i:173312 original size:26 final size:22
Alignment explanation
Indices: 173226--173315 Score: 67
Period size: 26 Copynumber: 3.9 Consensus size: 22
173216 CATTAATAAA
*
173226 AATTAAATATAATATAATAAATAT
1 AATT-AATATAATAT-TTAAATAT
* *
173250 AA-TAAAAT-TTATTTAAATAT
1 AATTAATATAATATTTAAATAT
173270 AATTAATATAATAATTTAATATAT
1 AATTAATATAAT-ATTTAA-ATAT
*
173294 ATATATAATATTTATATTTAAA
1 A-AT-TAATA-TAATATTTAAA
173316 AATTTAATAT
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
20 9 0.17
21 8 0.15
22 5 0.09
23 7 0.13
24 7 0.13
25 3 0.06
26 11 0.21
27 3 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AATTAATATAATATTTAAATAT
Found at i:173350 original size:9 final size:9
Alignment explanation
Indices: 173266--173362 Score: 53
Period size: 8 Copynumber: 10.7 Consensus size: 9
173256 ATTTATTTAA
173266 ATATAATTAAT
1 ATATAATT--T
173277 ATAATAATTT
1 AT-ATAATTT
*
173287 A-ATATATAT
1 ATATA-ATTT
173296 ATATAATATT
1 ATATAAT-TT
173306 -TAT-ATTT
1 ATATAATTT
*
173313 A-AAAATTT
1 ATATAATTT
*
173321 A-ATATTTT
1 ATATAATTT
173329 A-ATAATTT
1 ATATAATTT
173337 ATATATTATTT
1 ATATA--ATTT
173348 ATATAATTT
1 ATATAATTT
*
173357 AAATAA
1 ATATAA
173363 AAATATAACA
Statistics
Matches: 70, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
7 3 0.04
8 23 0.33
9 21 0.30
10 6 0.09
11 11 0.16
12 6 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
ATATAATTT
Found at i:173705 original size:23 final size:23
Alignment explanation
Indices: 173677--173720 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
173667 TTGATTGAAT
*
173677 TTATTTTT-TAATTATATAATATA
1 TTATTTTTAAAATTA-ATAATATA
173700 TTATTTTTAAAATTAATAATA
1 TTATTTTTAAAATTAATAATA
173721 AAAATATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTATTTTTAAAATTAATAATATA
Found at i:174032 original size:29 final size:26
Alignment explanation
Indices: 173983--174037 Score: 83
Period size: 29 Copynumber: 2.0 Consensus size: 26
173973 AATAAAACAA
173983 TTTTTTTTTGTCTTTTACTTTAACTT
1 TTTTTTTTTGTCTTTTACTTTAACTT
174009 TTTTTTTCATTGTCTTTTAACTTTAACTT
1 TTTTTTT--TTGTCTTTT-ACTTTAACTT
174038 ATTGACACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 7 0.27
28 9 0.35
29 10 0.38
ACGTcount: A:0.15, C:0.13, G:0.04, T:0.69
Consensus pattern (26 bp):
TTTTTTTTTGTCTTTTACTTTAACTT
Found at i:174048 original size:29 final size:28
Alignment explanation
Indices: 173990--174048 Score: 64
Period size: 29 Copynumber: 2.1 Consensus size: 28
173980 CAATTTTTTT
* ****
173990 TTGTCTTTTACTTTAACTTTTTTTTTCA
1 TTGTCTTTTACTTTAACTTATTGACACA
174018 TTGTCTTTTAACTTTAACTTATTGACACA
1 TTGTCTTTT-ACTTTAACTTATTGACACA
174047 TT
1 TT
174049 TCTCAACCAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.20, C:0.15, G:0.05, T:0.59
Consensus pattern (28 bp):
TTGTCTTTTACTTTAACTTATTGACACA
Found at i:174862 original size:18 final size:19
Alignment explanation
Indices: 174841--174881 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
174831 CAACATTTTT
174841 TTAATTTAAA-A-AAAATAA
1 TTAATTTAAATATAAAA-AA
174859 TTAA-TTAAATATAAAAAA
1 TTAATTTAAATATAAAAAA
174877 TTAAT
1 TTAAT
174882 AAAAAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TTAATTTAAATATAAAAAA
Found at i:175726 original size:108 final size:108
Alignment explanation
Indices: 175528--175754 Score: 350
Period size: 108 Copynumber: 2.1 Consensus size: 108
175518 TTATCTTTTA
* *
175528 AATATTGAAAAAAGGTTTTGATTAGATGGTCCAATCAATTTAATTGATTGGATAAAAAATCAAAA
1 AATATTGAAAAAAAGTTTTGATTAGATGGTCCAATCAATTCAATTGATTGGATAAAAAATCAAAA
**
175593 TCTTATAATTTGGTCCCTACTTTCGATTTATTAACCTTAACTT
66 TCTTATAATTTGAACCCTACTTTCGATTTATTAACCTTAACTT
* *
175636 AATATTGAAAAAAAGTTTTGATTAGATGGTCCAATCAATTCAATTGATTGGATAAAAAAATCGAG
1 AATATTGAAAAAAAGTTTTGATTAGATGGTCCAATCAATTCAATTGATTGGAT-AAAAAATCAAA
175701 ATCTTATAATTT-AACCTCTAC-TTCGATTTATTAACCTTAACTT
65 ATCTTATAATTTGAACC-CTACTTTCGATTTATTAACCTTAACTT
* *
175744 AAGATGGAAAA
1 AATATTGAAAA
175755 GAATTTTTTT
Statistics
Matches: 109, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
108 84 0.77
109 25 0.23
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (108 bp):
AATATTGAAAAAAAGTTTTGATTAGATGGTCCAATCAATTCAATTGATTGGATAAAAAATCAAAA
TCTTATAATTTGAACCCTACTTTCGATTTATTAACCTTAACTT
Found at i:176087 original size:10 final size:10
Alignment explanation
Indices: 176067--176096 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
176057 TTTAAATTAT
176067 TATTT-AAAA
1 TATTTAAAAA
176076 TATTTAAAAA
1 TATTTAAAAA
176086 TATTTAAAAA
1 TATTTAAAAA
176096 T
1 T
176097 TAATTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.25
10 15 0.75
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
TATTTAAAAA
Found at i:176132 original size:21 final size:20
Alignment explanation
Indices: 176094--176143 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
176084 AATATTTAAA
176094 AATTA-ATTT-TATTTTTAT
1 AATTATATTTATATTTTTAT
176112 -ATTAATATTTATATATTTTAT
1 AATT-ATATTTATAT-TTTTAT
176133 AATTATATTTA
1 AATTATATTTA
176144 AATAAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
17 3 0.11
18 1 0.04
19 4 0.15
20 3 0.11
21 13 0.48
22 3 0.11
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
AATTATATTTATATTTTTAT
Found at i:176181 original size:19 final size:20
Alignment explanation
Indices: 176131--176181 Score: 50
Period size: 22 Copynumber: 2.4 Consensus size: 20
176121 TATATATTTT
176131 ATAATTATATTTAAATAAAAA
1 ATAATT-TATTTAAATAAAAA
*
176152 ATATTATTTTATTT-AATAAATA
1 ATA--A-TTTATTTAAATAAAAA
176174 ATAATTTA
1 ATAATTTA
176182 CTCGAGAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
19 4 0.15
20 1 0.04
21 3 0.12
22 10 0.38
23 6 0.23
24 2 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATAATTTATTTAAATAAAAA
Found at i:176391 original size:2 final size:2
Alignment explanation
Indices: 176384--176409 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
176374 AACAAATGTA
176384 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
176410 CATAAGAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:177725 original size:15 final size:15
Alignment explanation
Indices: 177701--177751 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
177691 AAAAATTTAA
*
177701 AAAATA-TAAATATT
1 AAAATATTAAATACT
177715 AAAATATTAAAT-CT
1 AAAATATTAAATACT
177729 AATAATATTAAA-ACT
1 AA-AATATTAAATACT
177744 AAAATATT
1 AAAATATT
177752 TTTTTATTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 15 0.45
15 18 0.55
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (15 bp):
AAAATATTAAATACT
Found at i:177885 original size:33 final size:34
Alignment explanation
Indices: 177838--177921 Score: 89
Period size: 34 Copynumber: 2.5 Consensus size: 34
177828 ACTTCACTTT
* *
177838 AGACTGAATTATAGTGGTGATC-TTTAAAAGGGC
1 AGACTCAATAATAGTGGTGATCTTTTAAAAGGGC
* * * **
177871 AGACTTAATAATAGTAGTTATCTTTTTTAAGGGC
1 AGACTCAATAATAGTGGTGATCTTTTAAAAGGGC
*
177905 AGACTCAATAATGGTGG
1 AGACTCAATAATAGTGG
177922 GAATTACTTT
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
33 18 0.44
34 23 0.56
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.33
Consensus pattern (34 bp):
AGACTCAATAATAGTGGTGATCTTTTAAAAGGGC
Found at i:178067 original size:28 final size:28
Alignment explanation
Indices: 178034--178125 Score: 89
Period size: 28 Copynumber: 3.2 Consensus size: 28
178024 TCAATTTAAA
*
178034 ATTTAAATTAATAATAAAAAATATTTTT
1 ATTTAAATTAATTATAAAAAATATTTTT
*
178062 ATTTAAATTTAATTAT-AATAATATTTTAAT
1 ATTTAAA-TTAATTATAAAAAATATTTT--T
* *
178092 ATTTTAATAAATTATAAAATAAT-TTTTT
1 ATTTAAATTAATTATAAAA-AATATTTTT
178120 AATTTA
1 -ATTTA
178126 TTCAGTTCAA
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
28 18 0.35
29 18 0.35
30 13 0.25
31 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
ATTTAAATTAATTATAAAAAATATTTTT
Found at i:178593 original size:2 final size:2
Alignment explanation
Indices: 178586--178612 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
178576 CATAATATTA
178586 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 A
178613 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:178617 original size:2 final size:2
Alignment explanation
Indices: 178612--178643 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
178602 ATATATATAT
178612 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
178644 TCTTATAATA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:178790 original size:5 final size:5
Alignment explanation
Indices: 178780--178805 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
178770 TTAAATAATT
178780 TTATA TTATA TTATA TTATA TTATA T
1 TTATA TTATA TTATA TTATA TTATA T
178806 ATTAATTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:179755 original size:17 final size:17
Alignment explanation
Indices: 179712--179755 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
179702 TATGTTGATT
* *
179712 TATAATTATTATATATA
1 TATAATTATGATATAAA
179729 TAT-ATATATGATATAAA
1 TATAAT-TATGATATAAA
179746 TATAATTATG
1 TATAATTATG
179756 TGTAAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 2 0.09
17 19 0.83
18 2 0.09
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (17 bp):
TATAATTATGATATAAA
Found at i:179917 original size:18 final size:17
Alignment explanation
Indices: 179894--179931 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
179884 TTAAAACTTA
179894 TTATATTAGTATATT-TTT
1 TTATATTA-TA-ATTATTT
179912 TTATATTATAATTATTT
1 TTATATTATAATTATTT
179929 TTA
1 TTA
179932 AAATATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.16
17 8 0.42
18 8 0.42
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (17 bp):
TTATATTATAATTATTT
Found at i:179945 original size:18 final size:18
Alignment explanation
Indices: 179896--179952 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
179886 AAAACTTATT
**
179896 ATATTAGTATATTTTT-TT
1 ATATTA-TATATTTTTAAA
179914 ATATTATAATTATTTTTAAA
1 ATATTAT-A-TATTTTTAAA
*
179934 ATATTATATATTTATAAA
1 ATATTATATATTTTTAAA
179952 A
1 A
179953 ATTTTGATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 1 0.03
18 17 0.52
19 8 0.24
20 7 0.21
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
ATATTATATATTTTTAAA
Found at i:180032 original size:17 final size:17
Alignment explanation
Indices: 180010--180048 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
180000 TGTAATGTAT
180010 ATATTAT-TTTTCATATC
1 ATATTATATTTT-ATATC
*
180027 ATATTATATTTTATATT
1 ATATTATATTTTATATC
180044 ATATT
1 ATATT
180049 TTAATTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (17 bp):
ATATTATATTTTATATC
Found at i:180059 original size:23 final size:20
Alignment explanation
Indices: 180028--180079 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 20
180018 TTTCATATCA
180028 TATTATATTTTATATTATATTT
1 TATTATATTTTATATT-T-TTT
180050 TAATTATATTTTATATTTTTT
1 T-ATTATATTTTATATTTTTT
180071 TATTATATT
1 TATTATATT
180080 ATGTTAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.28
21 4 0.14
22 2 0.07
23 15 0.52
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TATTATATTTTATATTTTTT
Found at i:180081 original size:18 final size:19
Alignment explanation
Indices: 180037--180081 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
180027 ATATTATATT
180037 TTATATTATATTTTAATTA
1 TTATATTATATTTTAATTA
* *
180056 -TATTTTATATTTT-TTTA
1 TTATATTATATTTTAATTA
180073 TTATATTAT
1 TTATATTAT
180082 GTTAAATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTATATTATATTTTAATTA
Found at i:180340 original size:20 final size:20
Alignment explanation
Indices: 180311--180378 Score: 59
Period size: 19 Copynumber: 3.4 Consensus size: 20
180301 GATAATAATT
180311 TATA-TTATATAAATTTTAA
1 TATATTTATATAAATTTTAA
* *
180330 TATATTTATATATA-TTTAT
1 TATATTTATATAAATTTTAA
* * *
180349 TATATTTTTATTATTTTTATA
1 TATATTTATATAAATTTTA-A
180370 TTATATTTA
1 -TATATTTA
180379 AAATTATCAG
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
19 18 0.49
20 12 0.32
22 7 0.19
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TATATTTATATAAATTTTAA
Found at i:180378 original size:11 final size:11
Alignment explanation
Indices: 180310--180378 Score: 60
Period size: 11 Copynumber: 6.8 Consensus size: 11
180300 TGATAATAAT
180310 TTATA-TTATA
1 TTATATTTATA
*
180320 -TAAATTT-TA
1 TTATATTTATA
*
180329 ATATATTTATA
1 TTATATTTATA
180340 -TATA-TT-TA
1 TTATATTTATA
*
180348 TTATATTTTTA
1 TTATATTTATA
*
180359 TTATTTTTATA
1 TTATATTTATA
180370 TTATATTTA
1 TTATATTTA
180379 AAATTATCAG
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
8 2 0.04
9 11 0.23
10 14 0.29
11 21 0.44
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TTATATTTATA
Found at i:182979 original size:2 final size:2
Alignment explanation
Indices: 182972--182997 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
182962 TCACATCCCC
182972 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
182998 GTCTAGATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:187269 original size:12 final size:12
Alignment explanation
Indices: 187238--187359 Score: 96
Period size: 11 Copynumber: 10.6 Consensus size: 12
187228 ATTTGACGTA
187238 AATATAAAA-AT
1 AATATAAAATAT
187249 AAT-TAAAATAT
1 AATATAAAATAT
*
187260 TATATAAAATAT
1 AATATAAAATAT
187272 AATATAAAA-AT
1 AATATAAAATAT
**
187283 AATATATATTTAAT
1 AATATA-AAAT-AT
** *
187297 AATATTTAATTT
1 AATATAAAATAT
*
187309 ATTAT-AAATAT
1 AATATAAAATAT
*
187320 AATATAAAAAAT
1 AATATAAAATAT
*
187332 AATAT-AAATAA
1 AATATAAAATAT
187343 AATAT-AAATAT
1 AATATAAAATAT
187354 -ATATAA
1 AATATAA
187360 TATGAATTAT
Statistics
Matches: 87, Mismatches: 17, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
10 9 0.10
11 38 0.44
12 32 0.37
13 1 0.01
14 7 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AATATAAAATAT
Found at i:187275 original size:5 final size:5
Alignment explanation
Indices: 187267--187445 Score: 66
Period size: 5 Copynumber: 34.8 Consensus size: 5
187257 TATTATATAA
* * * * *
187267 AATAT AATAT AAAAAT AATAT ATATTT AATA- ATATTT AATTT ATTAT
1 AATAT AATAT -AATAT AATAT A-ATAT AATAT A-ATAT AATAT AATAT
*
187314 AAATAT AATAT AA-A- AA-AT AATAT AAATAA AATAT AA-AT ATATAT
1 -AATAT AATAT AATAT AATAT AATAT -AATAT AATAT AATAT A-ATAT
* * * * * *
187358 AATAT GAATTAT AAATAT ATTA- AATTT TATTT AAATAT AAAAT AATTT
1 AATAT -AA-TAT -AATAT AATAT AATAT AATAT -AATAT AATAT AATAT
* * *
187406 AAATAT AATTAT CATAT AATAA AATAT -ATAA AATAT AATA
1 -AATAT AA-TAT AATAT AATAT AATAT AATAT AATAT AATA
187446 CTTACATACG
Statistics
Matches: 130, Mismatches: 27, Indels: 34
0.68 0.14 0.18
Matches are distributed among these distances:
3 3 0.02
4 12 0.09
5 74 0.57
6 36 0.28
7 5 0.04
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:187287 original size:23 final size:23
Alignment explanation
Indices: 187238--187359 Score: 83
Period size: 23 Copynumber: 5.3 Consensus size: 23
187228 ATTTGACGTA
187238 AATATAAAA-ATAAT-TAAAATAT
1 AATATAAAATATAATATAAAA-AT
*
187260 TATATAAAATATAATATAAAAAT
1 AATATAAAATATAATATAAAAAT
** ** *
187283 AATATATATTTAATAATATTTAATT
1 AATATA-AAAT-ATAATATAAAAAT
*
187308 TAT-TATAAATATAATATAAAAAAT
1 AATATA-AAATATAATAT-AAAAAT
* *
187332 AATAT-AAATAAAATATAAATAT
1 AATATAAAATATAATATAAAAAT
187354 -ATATAA
1 AATATAA
187360 TATGAATTAT
Statistics
Matches: 77, Mismatches: 16, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
21 4 0.05
22 14 0.18
23 29 0.38
24 17 0.22
25 13 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AATATAAAATATAATATAAAAAT
Found at i:187325 original size:60 final size:60
Alignment explanation
Indices: 187250--187362 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
187240 TATAAAAATA
* * * *
187250 ATTAAAATATTATATAAAATATAATATAAA-AATAATATATATTTA-ATAATATTTAATTT
1 ATTAAAATATAATATAAAAAATAATATAAATAA-AATATAAATATATATAATATTTAATTT
187309 ATTATAAATATAATATAAAAAATAATATAAATAAAATATAAATATATATAATAT
1 ATTA-AAATATAATATAAAAAATAATATAAATAAAATATAAATATATATAATAT
187363 GAATTATAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
59 4 0.09
60 34 0.72
61 9 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (60 bp):
ATTAAAATATAATATAAAAAATAATATAAATAAAATATAAATATATATAATATTTAATTT
Found at i:187337 original size:17 final size:17
Alignment explanation
Indices: 187315--187359 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
187305 ATTTATTATA
187315 AATATAATATAAAAAAT
1 AATATAATATAAAAAAT
*
187332 AATATAA-ATAAAATAT
1 AATATAATATAAAAAAT
187348 AA-ATATATATAA
1 AATATA-ATATAA
187360 TATGAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 3 0.12
16 11 0.44
17 11 0.44
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AATATAATATAAAAAAT
Found at i:187351 original size:6 final size:6
Alignment explanation
Indices: 187311--187376 Score: 54
Period size: 6 Copynumber: 11.7 Consensus size: 6
187301 TTTAATTTAT
*
187311 TATAAA TAT-AA TATAAA -AAATAA TATAAA TA-AAA TATAAA TAT--A
1 TATAAA TATAAA TATAAA TATA-AA TATAAA TATAAA TATAAA TATAAA
*
187355 TAT-AA TATGAAT TATAAA TATA
1 TATAAA TAT-AAA TATAAA TATA
187377 TTAAATTTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
4 4 0.08
5 16 0.33
6 23 0.47
7 6 0.12
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (6 bp):
TATAAA
Found at i:187372 original size:22 final size:21
Alignment explanation
Indices: 187261--187442 Score: 81
Period size: 22 Copynumber: 8.6 Consensus size: 21
187251 TTAAAATATT
*
187261 ATATAAA-ATATA-ATATAAA
1 ATATAAATATATATAAATAAA
* *
187280 A-AT-AATATATATTTAATAAT
1 ATATAAATATATA-TAAATAAA
* * *
187300 AT-TTAATTTATTATAAATATA
1 ATATAAATATA-TATAAATAAA
*
187321 ATATAAAAAATAATATAAATAAA
1 ATAT-AAATAT-ATATAAATAAA
*
187344 ATATAAATATATATAATATGAA
1 ATATAAATATATATAA-ATAAA
* ***
187366 TTATAAATATAT-TAAATTTT
1 ATATAAATATATATAAATAAA
* * * *
187386 ATTTAAATATAAAATAATTTAA
1 ATATAAATAT-ATATAAATAAA
*
187408 ATATAATTATCATAT-AATAAA
1 ATATAAATAT-ATATAAATAAA
*
187429 ATATATAAAATATA
1 ATATA-AATATATA
187443 ATACTTACAT
Statistics
Matches: 119, Mismatches: 31, Indels: 24
0.68 0.18 0.14
Matches are distributed among these distances:
17 2 0.02
18 7 0.06
19 1 0.01
20 16 0.13
21 34 0.29
22 42 0.35
23 16 0.13
24 1 0.01
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.40
Consensus pattern (21 bp):
ATATAAATATATATAAATAAA
Found at i:187617 original size:24 final size:24
Alignment explanation
Indices: 187571--187617 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
187561 CATATATTTA
*
187571 AAATTTATATAATATTAATATATC
1 AAATTTATATAATATTAAAATATC
*
187595 AAATTTATTTAA-ATATAAAATAT
1 AAATTTATATAATAT-TAAAATAT
187618 TTAAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
AAATTTATATAATATTAAAATATC
Done.