Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 87 of 163
Found at i:28235355 original size:2 final size:2
Alignment explanation
Indices: 28235350--28235384 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
28235340 ATTTTATATA
28235350 TG TG TG TG 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 TG TG TG TG T
28235385 CATATTTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:28244111 original size:12 final size:12
Alignment explanation
Indices: 28244094--28244118 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28244084 AAAATGCATT
28244094 ATTAATAAAATA
1 ATTAATAAAATA
28244106 ATTAATAAAATA
1 ATTAATAAAATA
28244118 A
1 A
28244119 CACATGAACT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATTAATAAAATA
Found at i:28247659 original size:20 final size:20
Alignment explanation
Indices: 28247634--28247712 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
28247624 TAAAATTTTC
28247634 CACAAAGGCTAACATAATAG
1 CACAAAGGCTAACATAATAG
* * *
28247654 CACAAAGGCAATATATAAAGTACAC
1 CACAAAGGCTA-ACAT-AA-T--AG
28247679 CACAAAGGCTAACATAATAG
1 CACAAAGGCTAACATAATAG
*
28247699 CATAAAGGCTAACA
1 CACAAAGGCTAACA
28247713 GAATGCCATA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
20 24 0.51
21 3 0.06
22 3 0.06
23 3 0.06
24 3 0.06
25 11 0.23
ACGTcount: A:0.51, C:0.20, G:0.14, T:0.15
Consensus pattern (20 bp):
CACAAAGGCTAACATAATAG
Found at i:28247722 original size:20 final size:21
Alignment explanation
Indices: 28247682--28247764 Score: 73
Period size: 20 Copynumber: 4.0 Consensus size: 21
28247672 AGTACACCAC
*
28247682 AAAGGCTAACATAATAG-CAT
1 AAAGGCTAACAGAATAGCCAT
28247702 AAAGGCTAACAGAAT-GCCAT
1 AAAGGCTAACAGAATAGCCAT
* * *
28247722 AAAGGCCCATTCAGAATACGCCAC
1 AAAGG-CTA-ACAGAATA-GCCAT
*
28247746 ATAGGCTAACAGAAT-GCCA
1 AAAGGCTAACAGAATAGCCA
28247765 CCTATGTGAT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
19 1 0.02
20 26 0.51
21 2 0.04
22 12 0.24
23 2 0.04
24 8 0.16
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.16
Consensus pattern (21 bp):
AAAGGCTAACAGAATAGCCAT
Found at i:28253720 original size:36 final size:37
Alignment explanation
Indices: 28253680--28253776 Score: 90
Period size: 37 Copynumber: 2.6 Consensus size: 37
28253670 GTCTCCAATT
* * *
28253680 TCACATTTCAGTTCAATTTCACTTTTTCACTTTCAA-
1 TCACATTTCAATTCAATTTCACATTTCCACTTTCAAG
* * *
28253716 TCACAATTCAATTCAAAATTCACATTTCCATTTTCAAG
1 TCACATTTCAATTC-AATTTCACATTTCCACTTTCAAG
* *
28253754 TCA-ATATTCATTTCAATTCCACA
1 TCACAT-TTCAATTCAATTTCACA
28253777 CTTATATTCT
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
36 12 0.25
37 26 0.54
38 10 0.21
ACGTcount: A:0.32, C:0.25, G:0.02, T:0.41
Consensus pattern (37 bp):
TCACATTTCAATTCAATTTCACATTTCCACTTTCAAG
Found at i:28260136 original size:13 final size:13
Alignment explanation
Indices: 28260118--28260142 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28260108 CACAAACGAT
28260118 AAAATTTTCACAC
1 AAAATTTTCACAC
28260131 AAAATTTTCACA
1 AAAATTTTCACA
28260143 AATATAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAATTTTCACAC
Found at i:28273014 original size:87 final size:89
Alignment explanation
Indices: 28272889--28273057 Score: 193
Period size: 87 Copynumber: 1.9 Consensus size: 89
28272879 TAATTAAGTC
* *
28272889 CTTTTTTTTACACTCAATTAAGTATTTAAACTTTTAAAATACATCAAAAAAGCCCT-AAA-ATTT
1 CTTTTTTTTACACTCAATTAAGTACTTAAACTTCTAAAATACATCAAAAAAGCCCTCAAACATTT
28272952 AAAAAAAAAACAATTAAGCCCCTA
66 AAAAAAAAAACAATTAAGCCCCTA
* * ** * * *
28272976 CTTTTTTTTGCACTCAATTGAA-TACTTGAA-TTGCTAAAATGTATCAAAAAGGTCCTCAAACTT
1 CTTTTTTTTACACTCAATT-AAGTACTTAAACTT-CTAAAATACATCAAAAAAGCCCTCAAACAT
* *
28273039 TTTAAAAAAACACAATTAA
64 TTAAAAAAAAAACAATTAA
28273058 ACAATTGTTT
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
86 2 0.03
87 42 0.63
88 5 0.07
89 18 0.27
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.34
Consensus pattern (89 bp):
CTTTTTTTTACACTCAATTAAGTACTTAAACTTCTAAAATACATCAAAAAAGCCCTCAAACATTT
AAAAAAAAAACAATTAAGCCCCTA
Found at i:28273231 original size:20 final size:20
Alignment explanation
Indices: 28273186--28273232 Score: 78
Period size: 19 Copynumber: 2.4 Consensus size: 20
28273176 AATTATAATA
*
28273186 AATAAATATTATTAAATTTT
1 AATAAAAATTATTAAATTTT
28273206 -ATAAAAATTATTAAATTTT
1 AATAAAAATTATTAAATTTT
28273225 AATAAAAA
1 AATAAAAA
28273233 ATATAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AATAAAAATTATTAAATTTT
Found at i:28273278 original size:38 final size:36
Alignment explanation
Indices: 28273229--28273318 Score: 99
Period size: 38 Copynumber: 2.4 Consensus size: 36
28273219 AATTTTAATA
28273229 AAAAATATAAAAATTGGAAATAAAATTAGAAAAATCAT
1 AAAAATATAAAAATT-GAAA-AAAATTAGAAAAATCAT
* * ** *
28273267 AAAAATATAAAAAGTGTAAAATTTTATAAAAATCAT
1 AAAAATATAAAAATTGAAAAAAATTAGAAAAATCAT
28273303 AAAATATTATAAAAAT
1 AAAA-A-TATAAAAAT
28273319 CCCTAATTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
36 18 0.41
37 4 0.09
38 22 0.50
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (36 bp):
AAAAATATAAAAATTGAAAAAAATTAGAAAAATCAT
Found at i:28273296 original size:19 final size:19
Alignment explanation
Indices: 28273253--28273319 Score: 77
Period size: 19 Copynumber: 3.6 Consensus size: 19
28273243 TGGAAATAAA
*
28273253 ATTAGAAAAATCATAAAA-
1 ATTATAAAAATCATAAAAT
*
28273271 A-TATAAAAAGT-GTAAAAT
1 ATTATAAAAA-TCATAAAAT
*
28273289 TTTATAAAAATCATAAAAT
1 ATTATAAAAATCATAAAAT
28273308 ATTATAAAAATC
1 ATTATAAAAATC
28273320 CCTAATTTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
17 12 0.30
18 3 0.08
19 25 0.62
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.30
Consensus pattern (19 bp):
ATTATAAAAATCATAAAAT
Found at i:28273314 original size:10 final size:9
Alignment explanation
Indices: 28273173--28273318 Score: 73
Period size: 9 Copynumber: 15.7 Consensus size: 9
28273163 ACACATGACA
28273173 AAAAATTAT
1 AAAAATTAT
*
28273182 AATAA--AT
1 AAAAATTAT
*
28273189 AAATATTATT
1 AAAAATTA-T
**
28273199 AAATTTTAT
1 AAAAATTAT
28273208 AAAAATTATT
1 AAAAATTA-T
**
28273218 AAATTTTAAT
1 AAAAATT-AT
*
28273228 AAAAAATAT
1 AAAAATTAT
*
28273237 AAAAATTGGAA
1 AAAAATT--AT
*
28273248 ATAAAATTAG
1 A-AAAATTAT
*
28273258 AAAAATCAT
1 AAAAATTAT
28273267 AAAAA-TAT
1 AAAAATTAT
* *
28273275 AAAAAGTGT
1 AAAAATTAT
*
28273284 AAAATTTTAT
1 AAAA-ATTAT
*
28273294 AAAAATCAT
1 AAAAATTAT
28273303 AAAATATTAT
1 AAAA-ATTAT
28273313 AAAAAT
1 AAAAAT
28273319 CCCTAATTTA
Statistics
Matches: 102, Mismatches: 24, Indels: 22
0.69 0.16 0.15
Matches are distributed among these distances:
7 5 0.05
8 7 0.07
9 46 0.45
10 35 0.34
11 3 0.03
12 6 0.06
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (9 bp):
AAAAATTAT
Found at i:28273517 original size:19 final size:18
Alignment explanation
Indices: 28273493--28273575 Score: 69
Period size: 19 Copynumber: 4.3 Consensus size: 18
28273483 CTAAATAGTC
28273493 TTTTTTATGCATTTTATAT
1 TTTTTTATG-ATTTTATAT
28273512 TTTTTTATGATTTTTATAAAAT
1 TTTTTTATGA-TTTTAT---AT
***
28273534 TTTACAAT-ATTTTATAT
1 TTTTTTATGATTTTATAT
*
28273551 TTTTTTACGATTTTATTAT
1 TTTTTTATGATTTTA-TAT
28273570 TTTTTT
1 TTTTTT
28273576 TCTATTTTAT
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
17 6 0.12
18 7 0.14
19 24 0.47
20 6 0.12
21 1 0.02
22 7 0.14
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (18 bp):
TTTTTTATGATTTTATAT
Found at i:28273582 original size:19 final size:19
Alignment explanation
Indices: 28273541--28273592 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
28273531 AATTTTACAA
28273541 TATTTTA-TATTTTTTTAC
1 TATTTTATTATTTTTTTAC
* *
28273559 GATTTTATTATTTTTTTTC
1 TATTTTATTATTTTTTTAC
28273578 TATTTTATTATTTTT
1 TATTTTATTATTTTT
28273593 ATTAAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 6 0.20
19 24 0.80
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (19 bp):
TATTTTATTATTTTTTTAC
Found at i:28275174 original size:15 final size:16
Alignment explanation
Indices: 28275142--28275176 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
28275132 CATTAACATG
28275142 TATTTTTTAATATATT
1 TATTTTTTAATATATT
28275158 TATTTTTTAATAT-TT
1 TATTTTTTAATATATT
28275173 TATT
1 TATT
28275177 ATATCTCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTTTTTAATATATT
Found at i:28277512 original size:2 final size:2
Alignment explanation
Indices: 28277505--28277531 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28277495 CTTGAGGTAC
28277505 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
28277532 ATCCTTATTA
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:28280208 original size:17 final size:17
Alignment explanation
Indices: 28280173--28280528 Score: 163
Period size: 17 Copynumber: 20.2 Consensus size: 17
28280163 GACACAATTT
* *
28280173 TTTTTAAAAAACGAAAA
1 TTTTTGAAACACGAAAA
* *
28280190 TTTATGAAACACGAGAATT
1 TTTTTGAAACACGA-AA-A
28280209 TTTTTGAAACACGAAAA
1 TTTTTGAAACACGAAAA
**
28280226 TTTTCAAAACATCG-AAA
1 TTTTTGAAACA-CGAAAA
**
28280243 TTTTTGAAAACACGAGGA
1 TTTTTG-AAACACGAAAA
* *
28280261 TTTTTTAAATACGAAAA
1 TTTTTGAAACACGAAAA
* *
28280278 -ATTTGAAAACAAGAAAA
1 TTTTTG-AAACACGAAAA
* *
28280295 TTTTTAAAATACGAAAA
1 TTTTTGAAACACGAAAA
*
28280312 TTTTAGAAACACGAAAA
1 TTTTTGAAACACGAAAA
*
28280329 TTTTTGAAACAC-AGAAG
1 TTTTTGAAACACGA-AAA
*
28280346 TTTTTAGAAAAAACGAAAA
1 TTTTT-G-AAACACGAAAA
* * **
28280365 ATTTTGAAA-ATTGGAATT
1 TTTTTGAAACA--CGAAAA
28280383 TTTTTGAAAACAC-AAGAA
1 TTTTTG-AAACACGAA-AA
*
28280401 TTTTTGAAAAACATGAAAA
1 TTTTTG--AAACACGAAAA
*
28280420 TTTTTG--CCACGAAAA
1 TTTTTGAAACACGAAAA
* * **
28280435 -ATTTGAAA-ATTGGAATT
1 TTTTTGAAACA--CGAAAA
*
28280452 TTTTTGAAAACACGAGAA
1 TTTTTG-AAACACGAAAA
*
28280470 TTTTTGAAAAACATGAAAA
1 TTTTTG--AAACACGAAAA
* **
28280489 TTTTTGCAACACGGGAA
1 TTTTTGAAACACGAAAA
*
28280506 TTTTTGAAAACCCGGAAAA
1 TTTTTG-AAACAC-GAAAA
28280525 TTTT
1 TTTT
28280529 CCGATTTTTT
Statistics
Matches: 249, Mismatches: 62, Indels: 54
0.68 0.17 0.15
Matches are distributed among these distances:
14 4 0.02
15 8 0.03
16 5 0.02
17 108 0.43
18 52 0.21
19 67 0.27
20 5 0.02
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.31
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:28280211 original size:36 final size:35
Alignment explanation
Indices: 28280126--28280247 Score: 117
Period size: 36 Copynumber: 3.5 Consensus size: 35
28280116 GATCCGATTA
*
28280126 AAACACGAGAATTTTTTTAAAAAACACGAGAATTTTG
1 AAACACGAGAATTTTTTT-AAAAA-ACGAAAATTTTG
* *
28280163 -GACAC-A-ATTTTTTTTAAAAAACGAAAATTTATG
1 AAACACGAGAATTTTTTTAAAAAACGAAAATTT-TG
* * *
28280196 AAACACGAGAATTTTTTTGAAACACGAAAATTTTCA
1 AAACACGAGAATTTTTTTAAAAAACGAAAATTTT-G
28280232 AAACATCGA-AATTTTT
1 AAACA-CGAGAATTTTT
28280248 GAAAACACGA
Statistics
Matches: 71, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
32 9 0.13
33 7 0.10
34 12 0.17
35 3 0.04
36 37 0.52
37 3 0.04
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (35 bp):
AAACACGAGAATTTTTTTAAAAAACGAAAATTTTG
Found at i:28280335 original size:52 final size:52
Alignment explanation
Indices: 28280187--28280528 Score: 191
Period size: 51 Copynumber: 6.5 Consensus size: 52
28280177 TAAAAAACGA
* * * *
28280187 AAATTTATG-AAACACGAGAATTTTTTTGAAACACGAAAATTTTCAAAACATCG
1 AAATTTTTGAAAACACGA-AA-ATTTTTGAAACACGAAAATTTTGAAAACATAG
** * * *
28280240 AAATTTTTGAAAACACGAGGATTTTTTAAATACGAAAAATTTGAAAACA-AG
1 AAATTTTTGAAAACACGAAAATTTTTGAAACACGAAAATTTTGAAAACATAG
* * *
28280291 AAAATTTTT-AAAATACGAAAATTTTAGAAACACGAAAATTTTTG-AAACACAG
1 -AAATTTTTGAAAACACGAAAATTTTTGAAACACGAAAA-TTTTGAAAACATAG
* * * * ** *
28280343 AAGTTTTTAGAAAAAACGAAAAATTTTGAAA-ATTGGAATTTTTTTGAAAACACA-
1 AAATTTTT-GAAAACACGAAAATTTTTGAAACA--CGAA-AATTTTGAAAACATAG
* * * * *
28280397 AGAATTTTTGAAAAACATGAAAATTTTTG--CCACGAAAAATTTGAAAA-TTGG
1 A-AATTTTTG-AAAACACGAAAATTTTTGAAACACGAAAATTTTGAAAACATAG
* * * * **
28280448 AATTTTTTTGAAAACACGAGAATTTTTGAAAAACATGAAAATTTTTG-CAACACGG
1 AA-ATTTTTGAAAACACGAAAATTTTTG--AAACACGAAAA-TTTTGAAAACATAG
* *
28280503 GAATTTTTGAAAACCCGGAAAATTTT
1 AAATTTTTGAAAACAC-GAAAATTTT
28280529 CCGATTTTTT
Statistics
Matches: 219, Mismatches: 48, Indels: 42
0.71 0.16 0.14
Matches are distributed among these distances:
50 17 0.08
51 51 0.23
52 42 0.19
53 26 0.12
54 40 0.18
55 43 0.20
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.31
Consensus pattern (52 bp):
AAATTTTTGAAAACACGAAAATTTTTGAAACACGAAAATTTTGAAAACATAG
Found at i:28280446 original size:69 final size:70
Alignment explanation
Indices: 28280358--28280495 Score: 260
Period size: 69 Copynumber: 2.0 Consensus size: 70
28280348 TTTAGAAAAA
28280358 ACGAAAAATTTTGAAAATTGGAATTTTTTTGAAAACACAAGAATTTTTGAAAAACATGAAAATTT
1 ACGAAAAATTTTGAAAATTGGAATTTTTTTGAAAACACAAGAATTTTTGAAAAACATGAAAATTT
28280423 TTGCC
66 TTGCC
*
28280428 ACGAAAAA-TTTGAAAATTGGAATTTTTTTGAAAACACGAGAATTTTTGAAAAACATGAAAATTT
1 ACGAAAAATTTTGAAAATTGGAATTTTTTTGAAAACACAAGAATTTTTGAAAAACATGAAAATTT
28280492 TTGC
66 TTGC
28280496 AACACGGGAA
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
69 59 0.88
70 8 0.12
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (70 bp):
ACGAAAAATTTTGAAAATTGGAATTTTTTTGAAAACACAAGAATTTTTGAAAAACATGAAAATTT
TTGCC
Found at i:28280524 original size:36 final size:36
Alignment explanation
Indices: 28280391--28280528 Score: 122
Period size: 36 Copynumber: 3.9 Consensus size: 36
28280381 TTTTTTTGAA
* *
28280391 AACACAAGAATTTTTGAAAAACATGAAAATTTTTGC
1 AACACGAGAATTTTTGAAAAACAGGAAAATTTTTGC
** ** ** *
28280427 --CACGA-AAAATTTG-AAAATTGGAATTTTTTTGAA
1 AACACGAGAATTTTTGAAAAACAGGAAAATTTTTG-C
*
28280460 AACACGAGAATTTTTGAAAAACATGAAAATTTTTGC
1 AACACGAGAATTTTTGAAAAACAGGAAAATTTTTGC
* * *
28280496 AACACGGGAATTTTTGAAAACCCGGAAAATTTT
1 AACACGAGAATTTTTGAAAAACAGGAAAATTTT
28280529 CCGATTTTTT
Statistics
Matches: 76, Mismatches: 21, Indels: 10
0.71 0.20 0.09
Matches are distributed among these distances:
32 13 0.17
33 6 0.08
34 4 0.05
35 5 0.07
36 35 0.46
37 13 0.17
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.31
Consensus pattern (36 bp):
AACACGAGAATTTTTGAAAAACAGGAAAATTTTTGC
Found at i:28280660 original size:21 final size:20
Alignment explanation
Indices: 28280634--28280675 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
28280624 TGTTACCTTA
28280634 TTTTTGAAAACACGAGAAATT
1 TTTTTGAAAACACGA-AAATT
*
28280655 TTTTTGAAGACACGAAAATT
1 TTTTTGAAAACACGAAAATT
28280675 T
1 T
28280676 CGAAACCCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (20 bp):
TTTTTGAAAACACGAAAATT
Found at i:28281298 original size:6 final size:6
Alignment explanation
Indices: 28281287--28281343 Score: 105
Period size: 6 Copynumber: 9.3 Consensus size: 6
28281277 NNNNNNNTTT
28281287 TTTTTG TTTTTG CTTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
1 TTTTTG TTTTTG -TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
28281336 TTTTTG TT
1 TTTTTG TT
28281344 GTTTTTTTCT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
6 44 0.88
7 6 0.12
ACGTcount: A:0.00, C:0.02, G:0.16, T:0.82
Consensus pattern (6 bp):
TTTTTG
Found at i:28281571 original size:16 final size:16
Alignment explanation
Indices: 28281552--28281582 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28281542 TTCTCCTTCC
28281552 TCTTTTCTTTCTCTCT
1 TCTTTTCTTTCTCTCT
*
28281568 TCTTTTCTTTTTCTC
1 TCTTTTCTTTCTCTC
28281583 GAAGCTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (16 bp):
TCTTTTCTTTCTCTCT
Found at i:28281894 original size:29 final size:29
Alignment explanation
Indices: 28281823--28281936 Score: 165
Period size: 29 Copynumber: 3.9 Consensus size: 29
28281813 TAATTTTGAG
* * *
28281823 AAAGTTTAGAGGTCAAAATGTAATTTTTAG
1 AAAGTTTAGGGGTCAAAATGTAA-TTTCAA
*
28281853 AAAGTTTAGGGGTTAAAATGTAATTTCAA
1 AAAGTTTAGGGGTCAAAATGTAATTTCAA
*
28281882 AAAGTTTATGGGTCAAAATGTAATTTCAA
1 AAAGTTTAGGGGTCAAAATGTAATTTCAA
*
28281911 AAAGTTTAGGGGTCAAAATGCAATTT
1 AAAGTTTAGGGGTCAAAATGTAATTT
28281937 TTTATTTTTT
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
29 55 0.72
30 21 0.28
ACGTcount: A:0.40, C:0.05, G:0.20, T:0.34
Consensus pattern (29 bp):
AAAGTTTAGGGGTCAAAATGTAATTTCAA
Found at i:28282491 original size:80 final size:78
Alignment explanation
Indices: 28282135--28283113 Score: 1121
Period size: 80 Copynumber: 12.3 Consensus size: 78
28282125 GCTTCGGCGT
* * *
28282135 GTGACCCGAGGCTCAACTCACCTCTCACAATATGAGTTGA-TTTTTGAAATACAGAAA-TT-GAA
1 GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTTAAAA
*
28282197 -AAATACCTCGAC
66 GAAATACCTCGGC
* * * *
28282209 GTGACTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACA-AAAATT-GAA
1 GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTTAAAA
*
28282271 -AAATACCTCGAC
66 GAAATACCTCGGC
* * *
28282283 GTGACTCAAGGCTCAACTCACCTCTCGCAATAAGAGTTGATTTTTTTTTTGAAAATACA-AAATT
1 GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTTTGAAAA-ACAGAAATT
*
28282347 TAAAAGAAATACCTCAGC
61 TAAAAGAAATACCTCGGC
* *
28282365 ATGTGACCCGAGGCTCAACTCACCTCTTGCATTATGAGTTGATTTTTTGAAAAACAGAAATTTAA
1 --GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTTAA
* *
28282430 ACGAAATACTTCGGC
64 AAGAAATACCTCGGC
* *
28282445 GTGACTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAATAC-GAAATTTA
1 GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTGAAAA-ACAGAAATTTA
28282509 AAAGAAATACCTCGGC
63 AAAGAAATACCTCGGC
* *
28282525 ATGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTG-AAAGCAGAAATTTAA
1 --GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTTAA
28282589 AAGAAATACCTCGGC
64 AAGAAATACCTCGGC
*
28282604 ATGTG-TCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTGATTTTTTTTTTG-AAAACAG
1 --GTGACCCGAGGCTCAACTCACCTCTCGCAATATGA---G-TTGA----TTTTTTGAAAAACAG
28282667 AAATTTAAAAGAAATACCTCGGC
56 AAATTTAAAAGAAATACCTCGGC
* ** ** *
28282690 ATGGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTAAAATAGAAATTTAAA
1 GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAAACAGAAATTTAAA
28282755 AGAAATACCTCGGC
65 AGAAATACCTCGGC
* ** *
28282769 ATGGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTAAACAACAGAAATTTA
1 GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTGAAA-AACAGAAATTTA
*
28282834 AAAGAAATACCTCAGC
63 AAAGAAATACCTCGGC
* *
28282850 GTGCAACCCGAGGCTCAACTCACCTCTCGCAATATGAGGTGA-TTTTCGAAAAAAGCAGAAATTT
1 GTG--ACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG-AAAAA-CAGAAATTT
*
28282914 AAAA-AAATACCTCAGC
62 AAAAGAAATACCTCGGC
*
28282930 GTGCGACCCGAGGCTTAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAAAGCAGAAATTT
1 GT--GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG-AAAAA-CAGAAATTT
*
28282994 AAAA-AAATACCTCAGC
62 AAAAGAAATACCTCGGC
* *
28283010 GTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTTGAAAAAGCAGAAATTTAA
1 GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAAA-CAGAAATTTAA
* * *
28283074 AAAAAATACATCAGC
64 AAGAAATACCTCGGC
28283089 GTGACCCGAGGCTCAACTCACCTCT
1 GTGACCCGAGGCTCAACTCACCTCT
28283114 GNNNNNNNNN
Statistics
Matches: 817, Mismatches: 49, Indels: 73
0.87 0.05 0.08
Matches are distributed among these distances:
73 3 0.00
74 105 0.13
77 12 0.01
78 114 0.14
79 156 0.19
80 183 0.22
81 53 0.06
82 53 0.06
83 34 0.04
84 37 0.05
85 31 0.04
86 36 0.04
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (78 bp):
GTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTTAAAA
GAAATACCTCGGC
Found at i:28283114 original size:79 final size:78
Alignment explanation
Indices: 28282653--28283113 Score: 583
Period size: 79 Copynumber: 5.8 Consensus size: 78
28282643 GATTGATTTT
* * **
28282653 TTTTTTG-AAAACAGAAATTTAAAAGAAATACCTCGGCATGGTCCGAGGCTCAACTCACCTCTCG
1 TTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCG
28282717 CAATATGAGTTGA
66 CAATATGAGTTGA
** * * * **
28282730 TTTTTTTTTAAAATAGAAATTTAAAAGAAATACCTCGGCATGGTCCGAGGCTCAACTCACCTCTC
1 -TTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTC
28282795 GCAATATGAGTTGA
65 GCAATATGAGTTGA
*
28282809 TTTTTTTTTAAACAACAGAAATTTAAAAGAAATACCTCAGCGTGCAACCCGAGGCTCAACTCACC
1 --TTTTTTGAAA-AACAGAAATTTAAAAGAAATACCTCAGCGTG--ACCCGAGGCTCAACTCACC
*
28282874 TCTCGCAATATGAGGTGA
61 TCTCGCAATATGAGTTGA
* *
28282892 -TTTTCGAAAAAAGCAGAAATTTAAAA-AAATACCTCAGCGTGCGACCCGAGGCTTAACTCACCT
1 TTTTTTG-AAAAA-CAGAAATTTAAAAGAAATACCTCAGCGT--GACCCGAGGCTCAACTCACCT
28282955 CTCGCAATATGAGTTGA
62 CTCGCAATATGAGTTGA
28282972 -TTTTTGAAAAAAGCAGAAATTTAAAA-AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT
1 TTTTTTG-AAAAA-CAGAAATTTAAAAGAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT
* *
28283035 -GTATTATGAGTTGA
64 CGCAATATGAGTTGA
* *
28283049 TTTTTTTGAAAAAGCAGAAATTTAAAAAAAATACATCAGCGTGACCCGAGGCTCAACTCACCTCT
1 -TTTTTTGAAAAA-CAGAAATTTAAAAGAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT
28283114 GNNNNNNNNN
Statistics
Matches: 353, Mismatches: 18, Indels: 23
0.90 0.05 0.06
Matches are distributed among these distances:
77 12 0.03
78 47 0.13
79 111 0.31
80 104 0.29
81 44 0.12
82 1 0.00
83 34 0.10
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.27
Consensus pattern (78 bp):
TTTTTTGAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCG
CAATATGAGTTGA
Found at i:28285018 original size:11 final size:10
Alignment explanation
Indices: 28285002--28285081 Score: 65
Period size: 11 Copynumber: 7.5 Consensus size: 10
28284992 TTCATCTTGA
28285002 TTTTTCTTTCT
1 TTTTTCTTT-T
28285013 TTTTTCTTTT
1 TTTTTCTTTT
*
28285023 TTTTCCTTTT
1 TTTTTCTTTT
28285033 TTCTTGT-TTTT
1 TT-TT-TCTTTT
*
28285044 TTTGTTGTTTT
1 TTT-TTCTTTT
28285055 TTTTT-TGTTT
1 TTTTTCT-TTT
28285065 TTTTGTCTATTT
1 TTTT-TCT-TTT
28285077 TTTTT
1 TTTTT
28285082 TTCAGGCATA
Statistics
Matches: 59, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
9 1 0.02
10 23 0.39
11 27 0.46
12 8 0.14
ACGTcount: A:0.01, C:0.09, G:0.06, T:0.84
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:28285022 original size:17 final size:17
Alignment explanation
Indices: 28285002--28285044 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
28284992 TTCATCTTGA
28285002 TTTTTCTTT-CTTTTTTC
1 TTTTT-TTTCCTTTTTTC
28285019 TTTTTTTTCCTTTTTTC
1 TTTTTTTTCCTTTTTTC
28285036 TTGTTTTTT
1 TT-TTTTTT
28285045 TTGTTGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.12
17 15 0.62
18 6 0.25
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (17 bp):
TTTTTTTTCCTTTTTTC
Found at i:28285031 original size:10 final size:9
Alignment explanation
Indices: 28285002--28285080 Score: 56
Period size: 8 Copynumber: 8.6 Consensus size: 9
28284992 TTCATCTTGA
28285002 TTTTTCTTTCT
1 TTTTTC-TT-T
28285013 TTTTTCTTT
1 TTTTTCTTT
*
28285022 TTTTTC-CT
1 TTTTTCTTT
28285030 TTTTTCTTGT
1 TTTTTCTT-T
*
28285040 TTTTT-TTG
1 TTTTTCTTT
*
28285048 TTGTT-TTT
1 TTTTTCTTT
*
28285056 TTTTTGTTT
1 TTTTTCTTT
28285065 TTTTGTCTATT
1 TTTT-TCT-TT
28285076 TTTTT
1 TTTTT
28285081 TTTCAGGCAT
Statistics
Matches: 56, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
8 17 0.30
9 16 0.29
10 11 0.20
11 12 0.21
ACGTcount: A:0.01, C:0.09, G:0.06, T:0.84
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:28285044 original size:12 final size:12
Alignment explanation
Indices: 28285029--28285084 Score: 69
Period size: 12 Copynumber: 4.6 Consensus size: 12
28285019 TTTTTTTTCC
28285029 TTTTTTCTTGTT
1 TTTTTTCTTGTT
*
28285041 TTTTTTGTTGTT
1 TTTTTTCTTGTT
28285053 TTTTTT-TTGTT
1 TTTTTTCTTGTT
*
28285064 TTTTTGTCTATTTT
1 TTTTT-TCT-TGTT
28285078 TTTTTTC
1 TTTTTTC
28285085 AGGCATAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
11 10 0.26
12 18 0.46
13 3 0.08
14 8 0.21
ACGTcount: A:0.02, C:0.05, G:0.09, T:0.84
Consensus pattern (12 bp):
TTTTTTCTTGTT
Found at i:28285056 original size:14 final size:13
Alignment explanation
Indices: 28285012--28285068 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 13
28285002 TTTTTCTTTC
*
28285012 TTTTTTCTTTTTT
1 TTTTTTGTTTTTT
28285025 TTCCTTTT-TTCTTGTT
1 TT--TTTTGTT-TT-TT
28285041 TTTTTTGTTGTTTT
1 TTTTTTGTT-TTTT
28285055 TTTTTTGTTTTTT
1 TTTTTTGTTTTTT
28285068 T
1 T
28285069 GTCTATTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
13 7 0.18
14 17 0.45
15 10 0.26
16 4 0.11
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (13 bp):
TTTTTTGTTTTTT
Found at i:28285060 original size:28 final size:27
Alignment explanation
Indices: 28285002--28285080 Score: 67
Period size: 28 Copynumber: 2.9 Consensus size: 27
28284992 TTCATCTTGA
28285002 TTTTTCTTTCTTTTTTCTTTTTTTTCCT
1 TTTTTCTTTCTTTTTTCTTTTTTTT-CT
*
28285030 TTTTTCTTGT-TTTTTT-TGTTGTTTT-T
1 TTTTTCTT-TCTTTTTTCT-TTTTTTTCT
* *
28285056 TTTTTGTTT-TTTTGTCTATTTTTTT
1 TTTTTCTTTCTTTTTTCT-TTTTTTT
28285081 TTTCAGGCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
25 6 0.14
26 15 0.35
27 1 0.02
28 20 0.47
29 1 0.02
ACGTcount: A:0.01, C:0.09, G:0.06, T:0.84
Consensus pattern (27 bp):
TTTTTCTTTCTTTTTTCTTTTTTTTCT
Found at i:28285069 original size:22 final size:24
Alignment explanation
Indices: 28285029--28285083 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 24
28285019 TTTTTTTTCC
* *
28285029 TTTTTTCTTGTTTTTTTTGT-TGT
1 TTTTTTTTTGTTTTTTTTGTCTAT
28285052 TTTTTTTTTG-TTTTTTTGTCTAT
1 TTTTTTTTTGTTTTTTTTGTCTAT
28285075 TTTTTTTTT
1 TTTTTTTTT
28285084 CAGGCATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 9 0.31
23 20 0.69
ACGTcount: A:0.02, C:0.04, G:0.09, T:0.85
Consensus pattern (24 bp):
TTTTTTTTTGTTTTTTTTGTCTAT
Found at i:28294866 original size:16 final size:16
Alignment explanation
Indices: 28294845--28294878 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
28294835 GAATTGAACC
28294845 TCTTTTTTCTCTTTTT
1 TCTTTTTTCTCTTTTT
*
28294861 TCTTTTTTCTTTTTTT
1 TCTTTTTTCTCTTTTT
28294877 TC
1 TC
28294879 CTTCTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (16 bp):
TCTTTTTTCTCTTTTT
Found at i:28294877 original size:11 final size:11
Alignment explanation
Indices: 28294845--28294927 Score: 69
Period size: 11 Copynumber: 7.3 Consensus size: 11
28294835 GAATTGAACC
28294845 TCTTTTTTCTCTT
1 TCTTTTTT-T-TT
*
28294858 T-TTTCTTTTT
1 TCTTTTTTTTT
28294868 TCTTTTTTTTCCT
1 TCTTTTTTTT--T
**
28294881 TCTTTTTTCCT
1 TCTTTTTTTTT
* *
28294892 TCTCTTTTTCT
1 TCTTTTTTTTT
*
28294903 TCTTTTTCTTT
1 TCTTTTTTTTT
28294914 TCTTTTTTTTT
1 TCTTTTTTTTT
28294925 TCT
1 TCT
28294928 CTGCTGGGCC
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
10 3 0.05
11 39 0.68
12 5 0.09
13 10 0.18
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TCTTTTTTTTT
Found at i:28294885 original size:20 final size:19
Alignment explanation
Indices: 28294856--28294919 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 19
28294846 CTTTTTTCTC
28294856 TTTT-TTCTTTTTTCTTTT
1 TTTTCTTCTTTTTTCTTTT
28294874 TTTTCCTTCTTTTTTCCTTCTCT
1 TTTT-CTTCTTTTTT-CTT-T-T
28294897 TTTTCTTC-TTTTTCTTTT
1 TTTTCTTCTTTTTTCTTTT
28294915 CTTTT
1 -TTTT
28294920 TTTTTTCTCT
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
18 5 0.12
19 5 0.12
20 12 0.30
21 8 0.20
22 5 0.12
23 5 0.12
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTCTTCTTTTTTCTTTT
Found at i:28294917 original size:33 final size:31
Alignment explanation
Indices: 28294860--28294921 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 31
28294850 TTTCTCTTTT
*
28294860 TTCTTTTTTCTTTTTTTTCCTTCTTTTTTCC
1 TTCTTTTTTCTTCTTTTTCCTTCTTTTTTCC
*
28294891 TTCTCTTTTTCTTCTTTTTCTTTTCTTTTTT
1 TTCT-TTTTTCTTCTTTTTC-CTTCTTTTTT
28294922 TTTTCTCTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 4 0.15
32 14 0.52
33 9 0.33
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (31 bp):
TTCTTTTTTCTTCTTTTTCCTTCTTTTTTCC
Found at i:28295099 original size:6 final size:6
Alignment explanation
Indices: 28295078--28295144 Score: 107
Period size: 6 Copynumber: 10.8 Consensus size: 6
28295068 TTTTTTGGGC
*
28295078 TTGTTT CTTTTTT TTGTTT TTGCTTT TTGTTT TTGTTT TTGTTT TTGTTT
1 TTGTTT -TTGTTT TTGTTT TTG-TTT TTGTTT TTGTTT TTGTTT TTGTTT
28295128 TTGTTT TTGTTT TTGTT
1 TTGTTT TTGTTT TTGTT
28295145 GTTTTTTTCT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
6 46 0.81
7 11 0.19
ACGTcount: A:0.00, C:0.03, G:0.15, T:0.82
Consensus pattern (6 bp):
TTGTTT
Found at i:28295372 original size:16 final size:16
Alignment explanation
Indices: 28295353--28295383 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28295343 TTCTCCTTCC
28295353 TCTTTTCTTTCTCTCT
1 TCTTTTCTTTCTCTCT
*
28295369 TCTTTTCTTTTTCTC
1 TCTTTTCTTTCTCTC
28295384 GAAGCTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (16 bp):
TCTTTTCTTTCTCTCT
Found at i:28295695 original size:29 final size:29
Alignment explanation
Indices: 28295624--28295737 Score: 165
Period size: 29 Copynumber: 3.9 Consensus size: 29
28295614 TAATTTTGAG
* * *
28295624 AAAGTTTAGAGGTCAAAATGTAATTTTTAG
1 AAAGTTTAGGGGTCAAAATGTAA-TTTCAA
*
28295654 AAAGTTTAGGGGTTAAAATGTAATTTCAA
1 AAAGTTTAGGGGTCAAAATGTAATTTCAA
*
28295683 AAAGTTTATGGGTCAAAATGTAATTTCAA
1 AAAGTTTAGGGGTCAAAATGTAATTTCAA
*
28295712 AAAGTTTAGGGGTCAAAATGCAATTT
1 AAAGTTTAGGGGTCAAAATGTAATTT
28295738 TTTATTTTTT
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
29 55 0.72
30 21 0.28
ACGTcount: A:0.40, C:0.05, G:0.20, T:0.34
Consensus pattern (29 bp):
AAAGTTTAGGGGTCAAAATGTAATTTCAA
Found at i:28298137 original size:37 final size:35
Alignment explanation
Indices: 28298086--28298195 Score: 109
Period size: 37 Copynumber: 3.0 Consensus size: 35
28298076 TTCCAAAAAG
*
28298086 TAATATTATTTTAATAGTTTAATATTAAATTTAATA
1 TAATATTATCTTAATAGTTTAATATT-AATTTAATA
*
28298122 TAATACTTATCTTAATAGTATT-TTATTAATTTAATA
1 TAATA-TTATCTTAATAGT-TTAATATTAATTTAATA
*
28298158 TTAAAGTGATTATCTTAATA-TTAAAT-TTAATTTAATA
1 -T-AA-T-ATTATCTTAATAGTTTAATATTAATTTAATA
28298195 T
1 T
28298196 TTATCTACAA
Statistics
Matches: 63, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
36 15 0.24
37 29 0.46
38 6 0.10
39 12 0.19
40 1 0.02
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.52
Consensus pattern (35 bp):
TAATATTATCTTAATAGTTTAATATTAATTTAATA
Found at i:28299972 original size:82 final size:82
Alignment explanation
Indices: 28299835--28299999 Score: 242
Period size: 82 Copynumber: 2.0 Consensus size: 82
28299825 ATAGGCCCCA
* * * *
28299835 ATTATGGGTTTGAGCAAAAAAGCGAGGCCCGTTTAGAAAACGGTTCGGGCCTCGGGCGCCACTTT
1 ATTATGGGTTTGAGAAAAAAAGCAAGGCCCGTTTAGAAAACGGTCCGGGCCTCGGGCACCACTTT
28299900 TTTGGCTAGAGCCCGGC
66 TTTGGCTAGAGCCCGGC
* * *
28299917 ATTATGGGTTTGGGAAAAAAAGTAAGGCCCGTTTAGAAAACTGG-CCGGGCCTCGGGCACTACTT
1 ATTATGGGTTTGAGAAAAAAAGCAAGGCCCGTTTAGAAAAC-GGTCCGGGCCTCGGGCACCACTT
*
28299981 TTTTGGCTCGAGCCCGGC
65 TTTTGGCTAGAGCCCGGC
28299999 A
1 A
28300000 CGGCCCGACC
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
82 72 0.97
83 2 0.03
ACGTcount: A:0.23, C:0.22, G:0.31, T:0.24
Consensus pattern (82 bp):
ATTATGGGTTTGAGAAAAAAAGCAAGGCCCGTTTAGAAAACGGTCCGGGCCTCGGGCACCACTTT
TTTGGCTAGAGCCCGGC
Found at i:28300076 original size:37 final size:37
Alignment explanation
Indices: 28300025--28300098 Score: 114
Period size: 39 Copynumber: 2.0 Consensus size: 37
28300015 TATAATAAAT
28300025 AAATATTTTTTATTC-TTTAATTTTAAAATATTTTTA
1 AAATATTTTTTATTCTTTTAATTTTAAAATATTTTTA
*
28300061 AAATACTTTTTTATTCTTTTTATTTTTAAAATATTTTT
1 AAATA-TTTTTTATTC-TTTTAATTTTAAAATATTTTT
28300099 TTTGGTGTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
36 5 0.15
37 10 0.29
39 19 0.56
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (37 bp):
AAATATTTTTTATTCTTTTAATTTTAAAATATTTTTA
Found at i:28303600 original size:3 final size:3
Alignment explanation
Indices: 28303594--28303625 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
28303584 TCATGATGAT
*
28303594 GAG GAG GAG GAG GAG GAG GAG GAG GAA GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
28303626 TAAGCAGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:28306718 original size:2 final size:2
Alignment explanation
Indices: 28306707--28306744 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
28306697 ATTCAAAGCA
*
28306707 AT AT AT -T AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28306745 ATTATAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:28311313 original size:334 final size:334
Alignment explanation
Indices: 28310877--28311544 Score: 1300
Period size: 334 Copynumber: 2.0 Consensus size: 334
28310867 GCACTCTAGT
28310877 TGTACCAATCATCTTCAAAGAAGGAAGAGCCTGTATAGAACAATATGTTTTATGAAAAATAAAGG
1 TGTACCAATCATCTTCAAAGAAGGAAGAGCCTGTATAGAACAATATGTTTTATGAAAAATAAAGG
28310942 AACAAGGTAATGTAGTAGTGAGTTTAGTGACAGATAAAAGATTAAAAGTGAATTGAGGAACATAA
66 AACAAGGTAATGTAGTAGTGAGTTTAGTGACAGATAAAAGATTAAAAGTGAATTGAGGAACATAA
*
28311007 AGAACATTAGTAATGTAAAGGCTATTATTGAAAATGACTGTACTAGAAATTCGAGCACAAAATTT
131 AGAACATTAGTAATGTAAAGGCTATTATTGAAAATGACTGTACCAGAAATTCGAGCACAAAATTT
*
28311072 AGTGCCATTTGGAAGGTTGATGTATATAGGTTTAATGGAATGAAAAGAAGCAAAAAAGGATAAAG
196 AGTGCCATTTGAAAGGTTGATGTATATAGGTTTAATGGAATGAAAAGAAGCAAAAAAGGATAAAG
28311137 AATGAGTAATATGATCAGTGGCACCTGTGTCAATGATCCAATGATGGGATTGAAGAGAAAAAAGG
261 AATGAGTAATATGATCAGTGGCACCTGTGTCAATGATCCAATGATGGGATTGAAGAGAAAAAAGG
28311202 TTACCTGAG
326 TTACCTGAG
28311211 TGTACCAATCATCTTCAAAGAAGGAAGAGCCTGTATAGAACAATATGTTTTATGAAAAATAAAGG
1 TGTACCAATCATCTTCAAAGAAGGAAGAGCCTGTATAGAACAATATGTTTTATGAAAAATAAAGG
28311276 AACAAGGTAATGTAGTAGTGAGTTTAGTGACAGATAAAAGATTAAAAGTGAATTGAGGAACATAA
66 AACAAGGTAATGTAGTAGTGAGTTTAGTGACAGATAAAAGATTAAAAGTGAATTGAGGAACATAA
*
28311341 AGAACATTAGTAATGTAAAGGCTATTATTGAAAATGACTGTACCAGAAATTCGAGCACAAACTTT
131 AGAACATTAGTAATGTAAAGGCTATTATTGAAAATGACTGTACCAGAAATTCGAGCACAAAATTT
*
28311406 AGTGCCATTTGAAAGGTTGATGTATATAGGTTTAATGGAATGAAAAGAAGCAAAAAGGGATAAAG
196 AGTGCCATTTGAAAGGTTGATGTATATAGGTTTAATGGAATGAAAAGAAGCAAAAAAGGATAAAG
28311471 AATGAGTAATATGATCAGTGGCACCTGTGTCAATGATCCAATGATGGGATTGAAGAGAAAAAAGG
261 AATGAGTAATATGATCAGTGGCACCTGTGTCAATGATCCAATGATGGGATTGAAGAGAAAAAAGG
28311536 TTACCTGAG
326 TTACCTGAG
28311545 GATGGGGAAG
Statistics
Matches: 330, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
334 330 1.00
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.26
Consensus pattern (334 bp):
TGTACCAATCATCTTCAAAGAAGGAAGAGCCTGTATAGAACAATATGTTTTATGAAAAATAAAGG
AACAAGGTAATGTAGTAGTGAGTTTAGTGACAGATAAAAGATTAAAAGTGAATTGAGGAACATAA
AGAACATTAGTAATGTAAAGGCTATTATTGAAAATGACTGTACCAGAAATTCGAGCACAAAATTT
AGTGCCATTTGAAAGGTTGATGTATATAGGTTTAATGGAATGAAAAGAAGCAAAAAAGGATAAAG
AATGAGTAATATGATCAGTGGCACCTGTGTCAATGATCCAATGATGGGATTGAAGAGAAAAAAGG
TTACCTGAG
Found at i:28312235 original size:20 final size:23
Alignment explanation
Indices: 28312200--28312240 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
28312190 GTGACGGAGC
28312200 GATCATCTTGCTTGAA-AGCATT
1 GATCATCTTGCTTGAAGAGCATT
28312222 GATC-TCTT-CTTGAAGAGCA
1 GATCATCTTGCTTGAAGAGCA
28312241 GAAATGCGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 8 0.44
22 4 0.22
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (23 bp):
GATCATCTTGCTTGAAGAGCATT
Found at i:28313294 original size:31 final size:30
Alignment explanation
Indices: 28313244--28313326 Score: 125
Period size: 30 Copynumber: 2.8 Consensus size: 30
28313234 TCCATCTCTC
28313244 ACATTTTGGATAATTTTAATTTT-AATATAT
1 ACATTTTGGATAATTTTAATTTTAAATA-AT
*
28313274 ACATTTTGTATATATTTTAATTTTAAATAAT
1 ACATTTTGGATA-ATTTTAATTTTAAATAAT
28313305 A-ATTTTGGATAATTTTAATTTT
1 ACATTTTGGATAATTTTAATTTT
28313327 GTTCAGTTCT
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
29 11 0.22
30 20 0.41
31 14 0.29
32 4 0.08
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.55
Consensus pattern (30 bp):
ACATTTTGGATAATTTTAATTTTAAATAAT
Found at i:28317651 original size:30 final size:30
Alignment explanation
Indices: 28317605--28317693 Score: 116
Period size: 25 Copynumber: 3.1 Consensus size: 30
28317595 ATTTCTTATG
*
28317605 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
28317636 CCAATATTTGATACCCATATCTTTGAC-TT
1 CCAATATTTGATACCCATATCTTTGACTTT
*
28317665 ----TATTTGATACCCATATATTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
28317691 CCA
1 CCA
28317694 TAAATATGGA
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
25 22 0.42
26 2 0.04
29 2 0.04
30 19 0.37
31 7 0.13
ACGTcount: A:0.27, C:0.25, G:0.07, T:0.42
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:28317660 original size:15 final size:15
Alignment explanation
Indices: 28317615--28317661 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
28317605 CCAATATCTC
28317615 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
28317630 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
28317645 GATACCCATATCTTT
1 GATACCCATATCTTT
28317660 GA
1 GA
28317662 CTTTATTTGA
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
14 4 0.17
15 16 0.67
16 4 0.17
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:28322313 original size:30 final size:29
Alignment explanation
Indices: 28322279--28322359 Score: 125
Period size: 25 Copynumber: 2.9 Consensus size: 29
28322269 CCAGTATCTC
28322279 GATACCCATATCTTTGACTTTCCAATATTT
1 GATACCCATATCTTTGACTTTCC-ATATTT
28322309 GATACCCATATCTTTGAC-TT---TATTT
1 GATACCCATATCTTTGACTTTCCATATTT
28322334 GATACCCATATCTTTGACTTTCCATA
1 GATACCCATATCTTTGACTTTCCATA
28322360 AATATGGATG
Statistics
Matches: 47, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
25 23 0.49
26 2 0.04
29 4 0.09
30 18 0.38
ACGTcount: A:0.26, C:0.23, G:0.07, T:0.43
Consensus pattern (29 bp):
GATACCCATATCTTTGACTTTCCATATTT
Found at i:28322324 original size:15 final size:15
Alignment explanation
Indices: 28322279--28322325 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
28322269 CCAGTATCTC
28322279 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
28322294 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
28322309 GATACCCATATCTTT
1 GATACCCATATCTTT
28322324 GA
1 GA
28322326 CTTTATTTGA
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
14 4 0.17
15 16 0.67
16 4 0.17
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:28322568 original size:22 final size:22
Alignment explanation
Indices: 28322535--28322576 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
28322525 AAAATGTTCT
28322535 AAAAATTCT-AAAATAAAAATG
1 AAAAATTCTAAAAATAAAAATG
*
28322556 AAAAACTTTTAAAAATAAAAA
1 AAAAA-TTCTAAAAATAAAAA
28322577 AAAAACCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 3 0.17
23 10 0.56
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (22 bp):
AAAAATTCTAAAAATAAAAATG
Found at i:28330291 original size:23 final size:23
Alignment explanation
Indices: 28330265--28330310 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
28330255 TATAAGAAAA
28330265 CTCTACTTTAACATCATTTTCAT
1 CTCTACTTTAACATCATTTTCAT
28330288 CTCTACTTTAACATCATTTTCAT
1 CTCTACTTTAACATCATTTTCAT
28330311 GTTTTTTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (23 bp):
CTCTACTTTAACATCATTTTCAT
Found at i:28332732 original size:13 final size:13
Alignment explanation
Indices: 28332714--28332747 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
28332704 ATTCATTTAG
28332714 CATTTCACATTTT
1 CATTTCACATTTT
*
28332727 CATTTCAAGATTTT
1 CATTTC-ACATTTT
28332741 CATTTCA
1 CATTTCA
28332748 AATGTCCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.26, C:0.21, G:0.03, T:0.50
Consensus pattern (13 bp):
CATTTCACATTTT
Found at i:28332739 original size:14 final size:14
Alignment explanation
Indices: 28332722--28332748 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28332712 AGCATTTCAC
28332722 ATTTTCATTTCAAG
1 ATTTTCATTTCAAG
28332736 ATTTTCATTTCAA
1 ATTTTCATTTCAA
28332749 ATGTCCCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.15, G:0.04, T:0.52
Consensus pattern (14 bp):
ATTTTCATTTCAAG
Found at i:28333091 original size:43 final size:43
Alignment explanation
Indices: 28333030--28333114 Score: 161
Period size: 43 Copynumber: 2.0 Consensus size: 43
28333020 TGCTCACATG
*
28333030 AGCTGTGGGTCGGGATGTTAGGCTACACGATGCTGTTTACACA
1 AGCTGTGGGTCAGGATGTTAGGCTACACGATGCTGTTTACACA
28333073 AGCTGTGGGTCAGGATGTTAGGCTACACGATGCTGTTTACAC
1 AGCTGTGGGTCAGGATGTTAGGCTACACGATGCTGTTTACAC
28333115 TAATAGCGAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.28
Consensus pattern (43 bp):
AGCTGTGGGTCAGGATGTTAGGCTACACGATGCTGTTTACACA
Found at i:28344167 original size:90 final size:91
Alignment explanation
Indices: 28344014--28344194 Score: 355
Period size: 90 Copynumber: 2.0 Consensus size: 91
28344004 TTTTTCATGT
28344014 ACAATATAACCAGTTTAGAACAAAATCCTTTTGAACAAACAAAAAATGTACTTTGTTTTTCAACA
1 ACAATATAACCAGTTTAGAACAAAATCCTTTTGAACAAACAAAAAATGTACTTTGTTTTTCAACA
28344079 TATTATTAAATTAAC-TAAAAAATAA
66 TATTATTAAATTAACTTAAAAAATAA
28344104 ACAATATAACCAGTTTAGAACAAAATCCTTTTGAACAAACAAAAAATGTACTTTGTTTTTCAACA
1 ACAATATAACCAGTTTAGAACAAAATCCTTTTGAACAAACAAAAAATGTACTTTGTTTTTCAACA
28344169 TATTATTAAATTAACTTAAAAAATAA
66 TATTATTAAATTAACTTAAAAAATAA
28344195 TTATAATTTA
Statistics
Matches: 90, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
90 80 0.89
91 10 0.11
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.33
Consensus pattern (91 bp):
ACAATATAACCAGTTTAGAACAAAATCCTTTTGAACAAACAAAAAATGTACTTTGTTTTTCAACA
TATTATTAAATTAACTTAAAAAATAA
Found at i:28352408 original size:26 final size:25
Alignment explanation
Indices: 28352353--28352409 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
28352343 TTACAAACCC
* *
28352353 ACAAAATATGACAAATAATCATATT
1 ACAAAATATAACAAATAATAATATT
28352378 ACAAAATA-AACAAATAAATAATAATT
1 ACAAAATATAACAAAT-AATAAT-ATT
28352404 ACAAAA
1 ACAAAA
28352410 AAATGTATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 6 0.21
25 13 0.46
26 9 0.32
ACGTcount: A:0.65, C:0.11, G:0.02, T:0.23
Consensus pattern (25 bp):
ACAAAATATAACAAATAATAATATT
Found at i:28369741 original size:43 final size:43
Alignment explanation
Indices: 28369688--28369958 Score: 308
Period size: 43 Copynumber: 6.3 Consensus size: 43
28369678 TTTTAGAAAT
* * * **
28369688 AAACGCCGCTATAGAACAAGACCTTTAGCGGCGCTTTTAACAC
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCAC
* * * *
28369731 AAACGCCGCTATAGAACAAGACCTTTAGCGGCGCTTTTCACAC
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCAC
* *
28369774 AAACGCCGCTAAAGATCATGACTTTTAGTGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCAC
* * * * * * *
28369817 AACCGTCACTAAAGATCATGACTTTTAGCAGCACTTTTCCTAC
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCAC
* *
28369860 AAAAGCCGCTATAGGTCATGACTTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCAC
* * * * *
28369903 AAACGCCGCTATAGATCATCACTTTTAACGACACTTTTCTCAC
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCAC
*
28369946 AAACGCTGCTATA
1 AAACGCCGCTATA
28369959 AAACATTTAG
Statistics
Matches: 197, Mismatches: 31, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 197 1.00
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCAC
Found at i:28370094 original size:43 final size:43
Alignment explanation
Indices: 28370028--28370114 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
28370018 ACATATGCAA
* * *
28370028 GGTAATAAAACATACAATGCATTTTCTTAATCAAGTAAATCTT
1 GGTAATAAAACATACAATACATTTACTTAATCAAGGAAATCTT
* *
28370071 GGTAATAAAAGATATAATACATTTACTTAATCAAGGAAATCTT
1 GGTAATAAAACATACAATACATTTACTTAATCAAGGAAATCTT
28370114 G
1 G
28370115 TACATCATTG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (43 bp):
GGTAATAAAACATACAATACATTTACTTAATCAAGGAAATCTT
Found at i:28374005 original size:15 final size:13
Alignment explanation
Indices: 28373966--28374037 Score: 56
Period size: 15 Copynumber: 5.1 Consensus size: 13
28373956 ACTAGTTTAT
28373966 CTAAACACTAAACC
1 CTAAAC-CTAAACC
*
28373980 ATAAACCTAAACC
1 CTAAACCTAAACC
28373993 CTAAAATCCTAAACC
1 CT-AAA-CCTAAACC
*
28374008 CTTAACAC-ATAACC
1 CTAAAC-CTA-AACC
28374022 TCTAAACCTTAAACC
1 -CTAAACC-TAAACC
28374037 C
1 C
28374038 CAGCCTTTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
13 10 0.21
14 17 0.36
15 19 0.40
16 1 0.02
ACGTcount: A:0.46, C:0.35, G:0.00, T:0.19
Consensus pattern (13 bp):
CTAAACCTAAACC
Found at i:28374055 original size:7 final size:7
Alignment explanation
Indices: 28374045--28374098 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
28374035 CCCCAGCCTT
28374045 TAAACCA
1 TAAACCA
28374052 TAAACCA
1 TAAACCA
*
28374059 TAAATCA
1 TAAACCA
* *
28374066 TAACCCC
1 TAAACCA
28374073 TAAACTCA
1 TAAAC-CA
*
28374081 TAATCCA
1 TAAACCA
*
28374088 TAAACCT
1 TAAACCA
28374095 TAAA
1 TAAA
28374099 ATAGTAACTC
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
7 32 0.86
8 5 0.14
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (7 bp):
TAAACCA
Found at i:28374554 original size:41 final size:40
Alignment explanation
Indices: 28374467--28374696 Score: 257
Period size: 41 Copynumber: 5.7 Consensus size: 40
28374457 AAAAAAATTT
* * ** *
28374467 GCGGCGCTTTTTCAAAAACGCC-ATAAAA-TAGAGGATTA
1 GCGGCGCTTTTTAAAAAACGCCGCTAAAACCCGAGCATTA
* * *
28374505 GCGGCGCTTTTTTAAAAACGCTGCTAAAGCCCTGAGCATTA
1 GCGGCGCTTTTTAAAAAACGCCGCTAAAACCC-GAGCATTA
** *
28374546 GCGGCGCTTTTCCAAAAACGCCGCTAAAAACACGAGCATTA
1 GCGGCGCTTTTTAAAAAACGCCGCT-AAAACCCGAGCATTA
*
28374587 GCGGCGCTTTTTAAAAAATGCCGCTAAAACCCTGAGCATTA
1 GCGGCGCTTTTTAAAAAACGCCGCTAAAACCC-GAGCATTA
* *
28374628 GCGGCGCTTTTTCAAAAGCGCCGCTAAAAACCCGAGCATTA
1 GCGGCGCTTTTTAAAAAACGCCGCT-AAAACCCGAGCATTA
* * *
28374669 GCGGCACTTTTTAAAAAATGCCACTAAA
1 GCGGCGCTTTTTAAAAAACGCCGCTAAA
28374697 GCCCCGAAAA
Statistics
Matches: 162, Mismatches: 24, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
38 20 0.12
39 4 0.02
40 9 0.06
41 117 0.72
42 12 0.07
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.23
Consensus pattern (40 bp):
GCGGCGCTTTTTAAAAAACGCCGCTAAAACCCGAGCATTA
Found at i:28374598 original size:82 final size:82
Alignment explanation
Indices: 28374467--28374700 Score: 339
Period size: 82 Copynumber: 2.9 Consensus size: 82
28374457 AAAAAAATTT
* * * * * *
28374467 GCGGCGCTTTTTCAAAAACGCC-AT-AAAATA-GAGGATTAGCGGCGCTTTTTTAAAAACGCTGC
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAAACACGAGCATTAGCGGCGCTTTTTAAAAAATGCCGC
28374529 TAAAGCCCTGAGCATTA
66 TAAAGCCCTGAGCATTA
*
28374546 GCGGCGCTTTTCCAAAAACGCCGCTAAAAACACGAGCATTAGCGGCGCTTTTTAAAAAATGCCGC
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAAACACGAGCATTAGCGGCGCTTTTTAAAAAATGCCGC
*
28374611 TAAAACCCTGAGCATTA
66 TAAAGCCCTGAGCATTA
* * * *
28374628 GCGGCGCTTTTTCAAAAGCGCCGCTAAAAACCCGAGCATTAGCGGCACTTTTTAAAAAATGCCAC
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAAACACGAGCATTAGCGGCGCTTTTTAAAAAATGCCGC
28374693 TAAAGCCC
66 TAAAGCCC
28374701 CGAAAACTCA
Statistics
Matches: 138, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
79 21 0.15
80 1 0.01
81 5 0.04
82 111 0.80
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (82 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAAACACGAGCATTAGCGGCGCTTTTTAAAAAATGCCGC
TAAAGCCCTGAGCATTA
Found at i:28374826 original size:40 final size:39
Alignment explanation
Indices: 28374751--28374869 Score: 125
Period size: 39 Copynumber: 3.1 Consensus size: 39
28374741 GCGGTGCTTA
* * *
28374751 TTGGAAAACGCCTCTAATGCTC-ATTTTTAGTGGCGTTT
1 TTGGAAAACGCCGCTAATACTCGATTTTTAGCGGCGTTT
* *
28374789 TTCGGAAAGCGCCGCTAATACTCGATCTTTAGCGGCGTTT
1 TT-GGAAAACGCCGCTAATACTCGATTTTTAGCGGCGTTT
** * *
28374829 TTTTAAAACGCCGCTAATGA-TTGATTTTTAGCGGAGTTT
1 TTGGAAAACGCCGCTAAT-ACTCGATTTTTAGCGGCGTTT
28374868 TT
1 TT
28374870 TTATCCAAAC
Statistics
Matches: 67, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
38 2 0.03
39 48 0.72
40 17 0.25
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (39 bp):
TTGGAAAACGCCGCTAATACTCGATTTTTAGCGGCGTTT
Found at i:28378892 original size:18 final size:18
Alignment explanation
Indices: 28378869--28378923 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
28378859 TATCTTTGGG
28378869 TCTTTACTTTCTTTTTAT
1 TCTTTACTTTCTTTTTAT
* * *
28378887 TCTTTATTTTATTCTTAT
1 TCTTTACTTTCTTTTTAT
*
28378905 T-TTTAC--TCTTTCTAT
1 TCTTTACTTTCTTTTTAT
28378920 TCTT
1 TCTT
28378924 ATATTTCATA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
15 7 0.24
16 2 0.07
17 4 0.14
18 16 0.55
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (18 bp):
TCTTTACTTTCTTTTTAT
Found at i:28383529 original size:18 final size:19
Alignment explanation
Indices: 28383492--28383528 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
28383482 TTTTAAAAAA
*
28383492 TATAAAT-TTTAGAATTTT
1 TATAAATATTTTGAATTTT
28383510 TATAAATATTTTGAATTTT
1 TATAAATATTTTGAATTTT
28383529 AAAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:28383534 original size:18 final size:21
Alignment explanation
Indices: 28383497--28383540 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
28383487 AAAAATATAA
*
28383497 ATTTTAGAATTTTTATAAA-T
1 ATTTTAGAATTTTTAAAAATT
28383517 ATTTT-GAA-TTTTAAAAATT
1 ATTTTAGAATTTTTAAAAATT
28383536 ATTTT
1 ATTTT
28383541 TATTTTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 8 0.36
19 9 0.41
20 5 0.23
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (21 bp):
ATTTTAGAATTTTTAAAAATT
Found at i:28383547 original size:19 final size:18
Alignment explanation
Indices: 28383505--28383547 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
28383495 AAATTTTAGA
*
28383505 ATTTTTATAAATATTTTG
1 ATTTTTAAAAATATTTTG
* *
28383523 AATTTTAAAAATTATTTTT
1 ATTTTTAAAAA-TATTTTG
28383542 ATTTTT
1 ATTTTT
28383548 TTGTAATTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
ATTTTTAAAAATATTTTG
Found at i:28384000 original size:51 final size:52
Alignment explanation
Indices: 28383940--28384040 Score: 159
Period size: 51 Copynumber: 2.0 Consensus size: 52
28383930 TTCATTTTCA
28383940 TTTTAGAGAAAACCAAAATCATTTCCAAATGATT-CCATTTCTCCATTTTTG
1 TTTTAGAGAAAACCAAAATCATTTCCAAATGATTCCCATTTCTCCATTTTTG
* * * *
28383991 TTTTGGAGAAAACCATAATCATTTCCAAATGTTTCCCGTTTCTCCATTTT
1 TTTTAGAGAAAACCAAAATCATTTCCAAATGATTCCCATTTCTCCATTTT
28384041 CACCATTTCT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
51 31 0.69
52 14 0.31
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.41
Consensus pattern (52 bp):
TTTTAGAGAAAACCAAAATCATTTCCAAATGATTCCCATTTCTCCATTTTTG
Found at i:28391117 original size:50 final size:50
Alignment explanation
Indices: 28391041--28391141 Score: 157
Period size: 50 Copynumber: 2.0 Consensus size: 50
28391031 ACCTTATTGT
* **
28391041 AATCAATGTCAAATAGAAGAAAAGTAGTTCTCTATTGATTCTACTTGTGC
1 AATCAATGTCAAATAGAAGAAAAGTAGTTCTATAAGGATTCTACTTGTGC
* *
28391091 AATCAATGTCAAATAGAAGAATAGTAGTTCTATAAGGATTTTACTTGTGC
1 AATCAATGTCAAATAGAAGAAAAGTAGTTCTATAAGGATTCTACTTGTGC
28391141 A
1 A
28391142 GCCTGGTCCG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.34
Consensus pattern (50 bp):
AATCAATGTCAAATAGAAGAAAAGTAGTTCTATAAGGATTCTACTTGTGC
Found at i:28399726 original size:40 final size:40
Alignment explanation
Indices: 28399671--28399806 Score: 195
Period size: 40 Copynumber: 3.4 Consensus size: 40
28399661 GCTTGTATAG
*
28399671 GTTTGCACTTTGGTGCTTCAGATTGCACAATTGTGCCTTT
1 GTTTGCACTTTGGTGCTTCTGATTGCACAATTGTGCCTTT
* *
28399711 GTTTGCACTTTGGTGCCTCTGATTGCACAATCGTG-CTTCT
1 GTTTGCACTTTGGTGCTTCTGATTGCACAATTGTGCCTT-T
* *
28399751 GTTTGCACTTCGGTG-TCTCTGGTTGCACAATTGTGCCTTT
1 GTTTGCACTTTGGTGCT-TCTGATTGCACAATTGTGCCTTT
28399791 GTTTGCACTTTGGTGC
1 GTTTGCACTTTGGTGC
28399807 CCCTATCAGC
Statistics
Matches: 84, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
39 3 0.04
40 78 0.93
41 3 0.04
ACGTcount: A:0.12, C:0.22, G:0.24, T:0.42
Consensus pattern (40 bp):
GTTTGCACTTTGGTGCTTCTGATTGCACAATTGTGCCTTT
Found at i:28399807 original size:20 final size:20
Alignment explanation
Indices: 28399671--28399807 Score: 93
Period size: 20 Copynumber: 6.8 Consensus size: 20
28399661 GCTTGTATAG
*
28399671 GTTTGCACTTTGGTG-CTTCA
1 GTTTGCACTTTGGTGCCTT-T
* *
28399691 GATTGCACAATT-GTGCCTTT
1 GTTTGCAC-TTTGGTGCCTTT
*
28399711 GTTTGCACTTTGGTGCCTCT
1 GTTTGCACTTTGGTGCCTTT
* ** *
28399731 GATTGCACAATCGTG-CTTCT
1 GTTTGCACTTTGGTGCCTT-T
* * *
28399751 GTTTGCACTTCGGTGTCTCT
1 GTTTGCACTTTGGTGCCTTT
* *
28399771 GGTTGCACAATT-GTGCCTTT
1 GTTTGCAC-TTTGGTGCCTTT
28399791 GTTTGCACTTTGGTGCC
1 GTTTGCACTTTGGTGCC
28399808 CCTATCAGCA
Statistics
Matches: 86, Mismatches: 24, Indels: 14
0.69 0.19 0.11
Matches are distributed among these distances:
19 6 0.07
20 72 0.84
21 8 0.09
ACGTcount: A:0.12, C:0.23, G:0.24, T:0.42
Consensus pattern (20 bp):
GTTTGCACTTTGGTGCCTTT
Found at i:28403063 original size:28 final size:28
Alignment explanation
Indices: 28402999--28403071 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
28402989 ATGACTTTAC
28402999 CATATATGTGGAAGTCCACAAGGACAAT
1 CATATATGTGGAAGTCCACAAGGACAAT
* *
28403027 CTTACATGTGGAAGTCCACAAGGA-AATT
1 CATATATGTGGAAGTCCACAAGGACAA-T
* *
28403055 CATGTATGTGAAAGTCC
1 CATATATGTGGAAGTCC
28403072 GCAGGACTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 2 0.05
28 36 0.95
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.25
Consensus pattern (28 bp):
CATATATGTGGAAGTCCACAAGGACAAT
Found at i:28409183 original size:1 final size:1
Alignment explanation
Indices: 28409149--28409174 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
28409139 ATTGTTATTC
28409149 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
28409175 GGTTTTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:28409291 original size:1 final size:1
Alignment explanation
Indices: 28409247--28409283 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
28409237 GAGATTTTCA
28409247 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
28409284 GGTTTTTTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:28414450 original size:35 final size:34
Alignment explanation
Indices: 28414327--28414510 Score: 98
Period size: 33 Copynumber: 5.5 Consensus size: 34
28414317 ATGTTTATAT
* * * * *
28414327 GTAAGACCATAGTTGGGCTATGACATTTTAATGAA
1 GTAAGACCATAGCTGGGATATGGCATATTGAT-AA
* * * *
28414362 --AAGACCATAACTGGGTTATGACACT-TTGA-AC
1 GTAAGACCATAGCTGGGATATGGCA-TATTGATAA
* * *
28414393 GTAAGACCAT-GGTTGGACTATGGCAGTATTTATAA
1 GTAAGACCATAGCTGGGA-TATGGCA-TATTGATAA
*
28414428 GTAAGACCATAGCTGGGATATGGCAT-TCTGATGA
1 GTAAGACCATAGCTGGGATATGGCATAT-TGATAA
* * *
28414462 -TAAGACCATAACTGGGTTATGGCACTA-CGA-AA
1 GTAAGACCATAGCTGGGATATGGCA-TATTGATAA
*
28414494 GTAAGACCATGGCTGGG
1 GTAAGACCATAGCTGGG
28414511 CCATGGAAAT
Statistics
Matches: 115, Mismatches: 23, Indels: 24
0.71 0.14 0.15
Matches are distributed among these distances:
31 1 0.01
32 4 0.03
33 77 0.67
34 10 0.09
35 18 0.16
36 5 0.04
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.27
Consensus pattern (34 bp):
GTAAGACCATAGCTGGGATATGGCATATTGATAA
Found at i:28414472 original size:101 final size:101
Alignment explanation
Indices: 28414292--28414516 Score: 297
Period size: 101 Copynumber: 2.2 Consensus size: 101
28414282 GAGTTGACAG
* * * * * *
28414292 GTAATACCATGGTTGGACCATGGCAATGTTTATATGTAAGACCATAGTTGGGCTATGACATTTTA
1 GTAAGACCATGGTTGGACCATGGCAATATTTATAAGTAAGACCATAGCTGGGATATGACATTCTA
** *
28414357 ATGAAAAGACCATAACTGGGTTATGACACTTTGAAC
66 ATGAAAAGACCATAACTGGGTTATGACACTACGAAA
* * * *
28414393 GTAAGACCATGGTTGGACTATGGCAGTATTTATAAGTAAGACCATAGCTGGGATATGGCATTCTG
1 GTAAGACCATGGTTGGACCATGGCAATATTTATAAGTAAGACCATAGCTGGGATATGACATTCTA
* *
28414458 ATGATAAGACCATAACTGGGTTATGGCACTACGAAA
66 ATGAAAAGACCATAACTGGGTTATGACACTACGAAA
* *
28414494 GTAAGACCATGGCTGGGCCATGG
1 GTAAGACCATGGTTGGACCATGG
28414517 AAATGCATGT
Statistics
Matches: 106, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
101 106 1.00
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.28
Consensus pattern (101 bp):
GTAAGACCATGGTTGGACCATGGCAATATTTATAAGTAAGACCATAGCTGGGATATGACATTCTA
ATGAAAAGACCATAACTGGGTTATGACACTACGAAA
Found at i:28416810 original size:9 final size:10
Alignment explanation
Indices: 28416795--28416840 Score: 51
Period size: 9 Copynumber: 4.7 Consensus size: 10
28416785 GGAAGAGAGA
28416795 AAGAAAGGAG
1 AAGAAAGGAG
28416805 -AGAAAGGAG
1 AAGAAAGGAG
*
28416814 AAGAAAAGAAG
1 AAG-AAAGGAG
*
28416825 AAG-AAGAAG
1 AAGAAAGGAG
28416834 AAGAAAG
1 AAGAAAG
28416841 AAAGAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
9 18 0.56
10 5 0.16
11 9 0.28
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (10 bp):
AAGAAAGGAG
Found at i:28416845 original size:20 final size:21
Alignment explanation
Indices: 28416786--28416851 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 21
28416776 GCACCCACCG
28416786 GAAGAGAGAAAGAAAGGAGAGAAA
1 GAAGA-AGAAAGAAA-GA-AGAAA
*
28416810 GGAGAAGAAA-AGAAGAAG-AA
1 GAAGAAGAAAGA-AAGAAGAAA
*
28416830 GAAGAAGAAAGAAAGAAAAAA
1 GAAGAAGAAAGAAAGAAGAAA
28416851 G
1 G
28416852 GTAATGTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
20 16 0.44
21 6 0.17
22 3 0.08
23 7 0.19
24 4 0.11
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (21 bp):
GAAGAAGAAAGAAAGAAGAAA
Found at i:28416845 original size:23 final size:21
Alignment explanation
Indices: 28416786--28416846 Score: 54
Period size: 23 Copynumber: 2.8 Consensus size: 21
28416776 GCACCCACCG
*
28416786 GAAGAGAGAAAGAAAGGAGAGA
1 GAAGA-AGAAAGAAAGAAGAGA
*
28416808 -AAGGAG-AAGAAAAGAAGAAGAA
1 GAAGAAGAAAG-AAAGAAG-AG-A
28416830 GAAGAAGAAAGAAAGAA
1 GAAGAAGAAAGAAAGAA
28416847 AAAAGGTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
19 3 0.10
20 8 0.26
21 5 0.16
22 1 0.03
23 11 0.35
24 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (21 bp):
GAAGAAGAAAGAAAGAAGAGA
Found at i:28416892 original size:47 final size:47
Alignment explanation
Indices: 28416841--28416934 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
28416831 AAGAAGAAAG
28416841 AAAGAAAAAAGGTAATGTATAATTTTAGTAAATAATTTTGTTTATAA
1 AAAGAAAAAAGGTAATGTATAATTTTAGTAAATAATTTTGTTTATAA
*
28416888 AAAGAAAAAAGGTAATGTATTATTTTAGTAAATAATTTTGTTTATAA
1 AAAGAAAAAAGGTAATGTATAATTTTAGTAAATAATTTTGTTTATAA
28416935 TTTAAAGAGT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (47 bp):
AAAGAAAAAAGGTAATGTATAATTTTAGTAAATAATTTTGTTTATAA
Found at i:28417105 original size:33 final size:33
Alignment explanation
Indices: 28417068--28417169 Score: 96
Period size: 33 Copynumber: 3.3 Consensus size: 33
28417058 ATTTTAAAAT
28417068 TAAATTGTTAGTTAGTAATTTAGGATTATGTTA
1 TAAATTGTTAGTTAGTAATTTAGGATTATGTTA
*
28417101 TAAATTGTT-G-T-GT--TTGTA--ATTATTTTA
1 TAAATTGTTAGTTAGTAATT-TAGGATTATGTTA
*
28417128 -AAATTAATTTA-TTAGTAATTTAGGATTATGTTA
1 TAAATT--GTTAGTTAGTAATTTAGGATTATGTTA
28417161 TAAATTGTT
1 TAAATTGTT
28417170 GTGTTTAGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 23
0.67 0.05 0.28
Matches are distributed among these distances:
26 5 0.09
27 8 0.15
28 4 0.07
29 3 0.06
30 4 0.07
31 3 0.06
32 5 0.09
33 17 0.31
34 5 0.09
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (33 bp):
TAAATTGTTAGTTAGTAATTTAGGATTATGTTA
Found at i:28417161 original size:60 final size:64
Alignment explanation
Indices: 28417053--28417175 Score: 218
Period size: 60 Copynumber: 2.0 Consensus size: 64
28417043 AATTTTTTTA
28417053 TAATTATTTTAAAATTAAATTGTTAGTTAGTAATTTAGGATTATGTTATAAATTGTTGTGTTTG
1 TAATTATTTTAAAATTAAATTGTTAGTTAGTAATTTAGGATTATGTTATAAATTGTTGTGTTTG
28417117 TAATTATTTTAAAATT-AA-T-TTA-TTAGTAATTTAGGATTATGTTATAAATTGTTGTGTTT
1 TAATTATTTTAAAATTAAATTGTTAGTTAGTAATTTAGGATTATGTTATAAATTGTTGTGTTT
28417176 AGTTTAGTAT
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
60 37 0.63
61 3 0.05
62 1 0.02
63 2 0.03
64 16 0.27
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (64 bp):
TAATTATTTTAAAATTAAATTGTTAGTTAGTAATTTAGGATTATGTTATAAATTGTTGTGTTTG
Found at i:28417770 original size:15 final size:15
Alignment explanation
Indices: 28417750--28417789 Score: 71
Period size: 16 Copynumber: 2.6 Consensus size: 15
28417740 TTAACTCATT
28417750 TAATTTTATATAATG
1 TAATTTTATATAATG
28417765 TAATTTTTATATAATG
1 TAA-TTTTATATAATG
28417781 TAATTTTAT
1 TAATTTTAT
28417790 TTGATTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 9 0.38
16 15 0.62
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (15 bp):
TAATTTTATATAATG
Found at i:28419986 original size:76 final size:75
Alignment explanation
Indices: 28419829--28420129 Score: 442
Period size: 75 Copynumber: 4.0 Consensus size: 75
28419819 AATAACTTCA
* * * *
28419829 TATTTATGTAATGAATTTTT-TCCATTTTATTTATCAATTTTATGGTTTTTTTGCAATTTAAATA
1 TATTTATGTAATGACTTTTTCGCCATTTCAGTTATCAATTTTATGGTTTTTTTGCAATTTAAATA
*
28419893 GTTAACTTTG
66 GTAAACTTTG
* * *
28419903 TATTTATGTAATGACTTTTTTGCCATTTTATTTATCAATTTTATGGTTTTTTTTGCAATTTAAAT
1 TATTTATGTAATGACTTTTTCGCCATTTCAGTTATCAATTTTATGG-TTTTTTTGCAATTTAAAT
28419968 AGTAAACTTTG
65 AGTAAACTTTG
*
28419979 TATTTATGTAATGACTTTTTCGCTATTTCAGTTATCAATTTTATGGTTTTTTTGCAATTTAAATA
1 TATTTATGTAATGACTTTTTCGCCATTTCAGTTATCAATTTTATGGTTTTTTTGCAATTTAAATA
28420044 GTAAACTTTG
66 GTAAACTTTG
* * * *
28420054 TATTTATGTAATGACTTTTTCACTATTTCAGTTATCAATTTTATGTTTTTTTTTGTAATTTAAAT
1 TATTTATGTAATGACTTTTTCGCCATTTCAGTTATCAATTTTATG-GTTTTTTTGCAATTTAAAT
*
28420119 AAATAAACTTT
65 -AGTAAACTTT
28420130 AGACTAACTT
Statistics
Matches: 212, Mismatches: 11, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
74 19 0.09
75 97 0.46
76 87 0.41
77 9 0.04
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.55
Consensus pattern (75 bp):
TATTTATGTAATGACTTTTTCGCCATTTCAGTTATCAATTTTATGGTTTTTTTGCAATTTAAATA
GTAAACTTTG
Found at i:28420095 original size:151 final size:151
Alignment explanation
Indices: 28419816--28420129 Score: 463
Period size: 151 Copynumber: 2.1 Consensus size: 151
28419806 GTTTTGTAAT
** * * *
28419816 ATAAAT-AACTTCATATTTATGTAATGAATTTTTTCCATTTTATTTATCAATTTTATGGTTTTTT
1 ATAAATAAACTTTGTATTTATGTAATGAACTTTTTCCATTTCAGTTATCAATTTTATGGTTTTTT
* ** * *
28419880 TGCAATTTAAATAGTTAACTTTGTATTTATGTAATGACTTTTTTGCCATTTTATTTATCAATTTT
66 TGCAATTTAAATAGTAAACTTTGTATTTATGTAATGACTTTTTCACCATTTCAGTTATCAATTTT
28419945 ATGGTTTTTTTTGCAATTTAA
131 ATGGTTTTTTTTGCAATTTAA
*
28419966 AT-AGTAAACTTTGTATTTATGTAATG-ACTTTTTCGCTATTTCAGTTATCAATTTTATGGTTTT
1 ATAAATAAACTTTGTATTTATGTAATGAACTTTTTC-C-ATTTCAGTTATCAATTTTATGGTTTT
*
28420029 TTTGCAATTTAAATAGTAAACTTTGTATTTATGTAATGACTTTTTCACTATTTCAGTTATCAATT
64 TTTGCAATTTAAATAGTAAACTTTGTATTTATGTAATGACTTTTTCACCATTTCAGTTATCAATT
* *
28420094 TTATGTTTTTTTTTGTAATTTAA
129 TTATGGTTTTTTTTGCAATTTAA
28420117 ATAAATAAACTTT
1 ATAAATAAACTTT
28420130 AGACTAACTT
Statistics
Matches: 145, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
149 9 0.06
150 21 0.14
151 106 0.73
152 9 0.06
ACGTcount: A:0.29, C:0.08, G:0.09, T:0.54
Consensus pattern (151 bp):
ATAAATAAACTTTGTATTTATGTAATGAACTTTTTCCATTTCAGTTATCAATTTTATGGTTTTTT
TGCAATTTAAATAGTAAACTTTGTATTTATGTAATGACTTTTTCACCATTTCAGTTATCAATTTT
ATGGTTTTTTTTGCAATTTAA
Found at i:28423033 original size:21 final size:20
Alignment explanation
Indices: 28423004--28423049 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
28422994 CGAAATGCAA
28423004 TCAACCTAACA-TGAATTAAAT
1 TCAACCTAA-ATTG-ATTAAAT
*
28423025 TCAAGCTAAATTGATTAAAT
1 TCAACCTAAATTGATTAAAT
28423045 T-AACC
1 TCAACC
28423050 ATTCCAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.30
Consensus pattern (20 bp):
TCAACCTAAATTGATTAAAT
Found at i:28424997 original size:18 final size:17
Alignment explanation
Indices: 28424962--28425007 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
28424952 AAATATATTA
*
28424962 TCCT-TCTT-TTTGTTT
1 TCCTATCTTCTTTCTTT
*
28424977 TCCTTTCTTTCTTTCTTT
1 TCCTATC-TTCTTTCTTT
28424995 TCCTATCTTCTTT
1 TCCTATCTTCTTT
28425008 TAAAAAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 4 0.15
16 2 0.08
17 8 0.31
18 12 0.46
ACGTcount: A:0.02, C:0.26, G:0.02, T:0.70
Consensus pattern (17 bp):
TCCTATCTTCTTTCTTT
Found at i:28425052 original size:73 final size:74
Alignment explanation
Indices: 28424923--28425080 Score: 273
Period size: 73 Copynumber: 2.1 Consensus size: 74
28424913 TAACAAAACT
*
28424923 CTATATTCTATTTAAAAAGAAATAAACTAAAATATATTATCCTTCTTTTTGTTTTCCTTTCTTTC
1 CTATCTTCT-TTTAAAAAGAAATAAACTAAAATATATTATCCTTCTTTTTGTTTTCCTTTCTTTC
*
28424988 TTTCTT-TTC
65 TTTCTTCTCC
*
28424997 CTATCTTCTTTTAAAAAGAAATAAACTAAAATATATTATCCTTTTTTTTGTTTTCCTTTCTTTCT
1 CTATCTTCTTTTAAAAAGAAATAAACTAAAATATATTATCCTTCTTTTTGTTTTCCTTTCTTTCT
28425062 TTCTTCTCC
66 TTCTTCTCC
28425071 CTATCTTCTT
1 CTATCTTCTT
28425081 ACTTCTATTT
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
73 60 0.75
74 20 0.25
ACGTcount: A:0.26, C:0.18, G:0.03, T:0.53
Consensus pattern (74 bp):
CTATCTTCTTTTAAAAAGAAATAAACTAAAATATATTATCCTTCTTTTTGTTTTCCTTTCTTTCT
TTCTTCTCC
Found at i:28425309 original size:19 final size:20
Alignment explanation
Indices: 28425280--28425317 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
28425270 TGCCACCCAT
*
28425280 AAAATAATAATTTAAAAAAC
1 AAAATAATAATATAAAAAAC
28425300 AAAA-AATAATATAAAAAA
1 AAAATAATAATATAAAAAA
28425318 GTAGTTGCGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAATAATAATATAAAAAAC
Found at i:28427743 original size:43 final size:44
Alignment explanation
Indices: 28427675--28427764 Score: 119
Period size: 43 Copynumber: 2.1 Consensus size: 44
28427665 TGTTGTGGCT
* * * * *
28427675 TTTGTAGCTAGAATCGCCTCAAAAGATCATGTTCTTTAGCGGCG
1 TTTGTAGCTAAAAGCGCCTCAAAAGATCATATTCTATAGCGCCG
*
28427719 TTTGTAG-TAAAAGCGCCTCTAAAGATCATATTCTATAGCGCCG
1 TTTGTAGCTAAAAGCGCCTCAAAAGATCATATTCTATAGCGCCG
28427762 TTT
1 TTT
28427765 TCTCACATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
43 33 0.82
44 7 0.17
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (44 bp):
TTTGTAGCTAAAAGCGCCTCAAAAGATCATATTCTATAGCGCCG
Found at i:28428386 original size:23 final size:23
Alignment explanation
Indices: 28428351--28428401 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
28428341 GGGAAATAAA
* *
28428351 AAAAATAAGTTAGGGAATTGGGG
1 AAAATTAAATTAGGGAATTGGGG
*
28428374 AAAATTAAATTAGGGATTTGGGG
1 AAAATTAAATTAGGGAATTGGGG
28428397 AAAAT
1 AAAAT
28428402 GATTTGGGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.45, C:0.00, G:0.29, T:0.25
Consensus pattern (23 bp):
AAAATTAAATTAGGGAATTGGGG
Found at i:28428535 original size:41 final size:40
Alignment explanation
Indices: 28428479--28428614 Score: 139
Period size: 40 Copynumber: 3.3 Consensus size: 40
28428469 ATTCGCGGTG
* * * *
28428479 TTTATGGGCAAAATGCCGTTATTGCTTTACCTTTAGCGGCG
1 TTTATGAG-AAAATGCCGCTATTGCTTTACCTTTTGCGGCA
*
28428520 TTTATGAGAAGAATGCCGCTATTGTTTTTAACCTTTTGCGGCA
1 TTTATGAGAA-AATGCCGCTATTG-CTTT-ACCTTTTGCGGCA
* * *
28428563 TTTATGCA-AAAACGCCACTATTGCTTTACCTTTTGCTGCA
1 TTTATG-AGAAAATGCCGCTATTGCTTTACCTTTTGCGGCA
*
28428603 TTTATGGGAAAA
1 TTTATGAGAAAA
28428615 ATGACGTTAA
Statistics
Matches: 80, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
40 24 0.30
41 22 0.28
42 14 0.17
43 19 0.24
44 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (40 bp):
TTTATGAGAAAATGCCGCTATTGCTTTACCTTTTGCGGCA
Found at i:28428604 original size:40 final size:41
Alignment explanation
Indices: 28428498--28428608 Score: 127
Period size: 43 Copynumber: 2.7 Consensus size: 41
28428488 AAAATGCCGT
* * * *
28428498 TATTGCTTTACCTTTAGCGGCGTTTATGAGAAGAATGCCGC
1 TATTGCTTTACCTTTTGCGGCATTTATGAGAAGAACGCCAC
*
28428539 TATTGTTTTTAACCTTTTGCGGCATTTATGCA-AA-AACGCCAC
1 TATTG-CTTT-ACCTTTTGCGGCATTTATG-AGAAGAACGCCAC
*
28428581 TATTGCTTTACCTTTTGCTGCATTTATG
1 TATTGCTTTACCTTTTGCGGCATTTATG
28428609 GGAAAAATGA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
40 18 0.30
41 8 0.13
42 14 0.23
43 19 0.32
44 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.41
Consensus pattern (41 bp):
TATTGCTTTACCTTTTGCGGCATTTATGAGAAGAACGCCAC
Found at i:28429053 original size:16 final size:17
Alignment explanation
Indices: 28429015--28429057 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
28429005 CTCAAGTGCA
*
28429015 TTTTCTTTTGAGTGTTT
1 TTTTCTTTTGAGTCTTT
* *
28429032 TGTTCTTTTG-TTCTTT
1 TTTTCTTTTGAGTCTTT
28429048 TTTTCTTTTG
1 TTTTCTTTTG
28429058 CATTTTTGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.02, C:0.09, G:0.14, T:0.74
Consensus pattern (17 bp):
TTTTCTTTTGAGTCTTT
Found at i:28434016 original size:20 final size:20
Alignment explanation
Indices: 28433977--28434018 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
28433967 ATCTCAAATC
**
28433977 TTTTATTAGTTTGATTTTTT
1 TTTTATTAGTTTGAAATTTT
*
28433997 TTTTCTTAGTTTGAAATTTT
1 TTTTATTAGTTTGAAATTTT
28434017 TT
1 TT
28434019 AAGCCCTTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.02, G:0.10, T:0.71
Consensus pattern (20 bp):
TTTTATTAGTTTGAAATTTT
Found at i:28453603 original size:36 final size:36
Alignment explanation
Indices: 28453556--28453627 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
28453546 CATACACATA
28453556 GTGTAAATCCATTAAATTCATTCTGAGATCATATAG
1 GTGTAAATCCATTAAATTCATTCTGAGATCATATAG
28453592 GTGTAAATCCATTAAATTCATTCTGAGATCATATAG
1 GTGTAAATCCATTAAATTCATTCTGAGATCATATAG
28453628 TTCATTTTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (36 bp):
GTGTAAATCCATTAAATTCATTCTGAGATCATATAG
Found at i:28460332 original size:27 final size:27
Alignment explanation
Indices: 28460286--28460378 Score: 127
Period size: 27 Copynumber: 3.4 Consensus size: 27
28460276 TCCAAAATAC
28460286 GCCACAAAGGC-AGTTCATACAGAGTAT
1 GCCACAAAGGCTA-TTCATACAGAGTAT
*
28460313 GCTACAAAGGCTATAT-ATACAGAGTAT
1 GCCACAAAGGCTAT-TCATACAGAGTAT
* *
28460340 GCCACAAGGGCTATTCATTCAGAGTAT
1 GCCACAAAGGCTATTCATACAGAGTAT
28460367 GCCACAAAGGCT
1 GCCACAAAGGCT
28460379 GATAGGATGC
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
26 1 0.02
27 55 0.95
28 2 0.03
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (27 bp):
GCCACAAAGGCTATTCATACAGAGTAT
Found at i:28464946 original size:30 final size:30
Alignment explanation
Indices: 28464910--28464968 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
28464900 TACGAGCTTT
28464910 GGGGAAAAAGTGTAAATATGCAAAAGTTTA
1 GGGGAAAAAGTGTAAATATGCAAAAGTTTA
* * * *
28464940 GGGGAAAAATTGTAATTTTGCCAAAGTTT
1 GGGGAAAAAGTGTAAATATGCAAAAGTTT
28464969 GAGTCAAGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.05, G:0.25, T:0.29
Consensus pattern (30 bp):
GGGGAAAAAGTGTAAATATGCAAAAGTTTA
Found at i:28465549 original size:51 final size:50
Alignment explanation
Indices: 28465494--28465631 Score: 204
Period size: 50 Copynumber: 2.7 Consensus size: 50
28465484 AATGGCCACA
* * *
28465494 TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAAGGCCTTGGTCACG
1 TGTGTAGTACTATGTGTAGGCTACTATGTGTACCGGAAAG-CTTGATCACG
* *
28465545 TGTGTAGTACTATGTGTAGGCTACTATGTGAACCAGAAAGCTTGATCACG
1 TGTGTAGTACTATGTGTAGGCTACTATGTGTACCGGAAAGCTTGATCACG
* *
28465595 TGTGTAGTACTATGTGTAGGCTACTACGTGTATCGGA
1 TGTGTAGTACTATGTGTAGGCTACTATGTGTACCGGA
28465632 TGACAATGGT
Statistics
Matches: 78, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 42 0.54
51 36 0.46
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (50 bp):
TGTGTAGTACTATGTGTAGGCTACTATGTGTACCGGAAAGCTTGATCACG
Found at i:28465611 original size:50 final size:51
Alignment explanation
Indices: 28465494--28465620 Score: 202
Period size: 51 Copynumber: 2.5 Consensus size: 51
28465484 AATGGCCACA
* * * * *
28465494 TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAAGGCCTTGGTCACG
1 TGTGTAGTACTATGTGTAGGCTACTATGTGAACCAGAAAGCCTTGATCACG
28465545 TGTGTAGTACTATGTGTAGGCTACTATGTGAACCAGAAAG-CTTGATCACG
1 TGTGTAGTACTATGTGTAGGCTACTATGTGAACCAGAAAGCCTTGATCACG
28465595 TGTGTAGTACTATGTGTAGGCTACTA
1 TGTGTAGTACTATGTGTAGGCTACTA
28465621 CGTGTATCGG
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
50 35 0.49
51 36 0.51
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (51 bp):
TGTGTAGTACTATGTGTAGGCTACTATGTGAACCAGAAAGCCTTGATCACG
Found at i:28466889 original size:606 final size:607
Alignment explanation
Indices: 28465737--28466949 Score: 2410
Period size: 606 Copynumber: 2.0 Consensus size: 607
28465727 ATGAATATGT
28465737 TATTGAAATGTGATAAATTGCAAACAGTAACTGAAGTAATGAAGTCTCGTACTGTGCCAACAAAT
1 TATTGAAATGTGATAAATTGCAAACAGTAACTGAAGTAATGAAGTCTCGTACTGTGCCAACAAAT
28465802 TAAATTGTTATTGAATATTGAATAAATTGTTATAGTGTTACATGAGTGAGTGAATTTGAAACAGA
66 TAAATTGTTATTGAATATTGAATAAATTGTTATAGTGTTACATGAGTGAGTGAATTTGAAACAGA
28465867 ATAGATTTGGGCATTGACAGTGACGTTAGTTTGAAAAATCACCAAAAGTTATAGGAATTGAGTTA
131 ATAGATTTGGGCATTGACAGTGACGTTAGTTTGAAAAATCACCAAAAGTTATAGGAATTGAGTTA
28465932 CTGGTTGAATGAGATATGAAATTAAATCTTAATTAGTCTATTTTCATATAAAAGAGAAAGAATAG
196 CTGGTTGAATGAGATATGAAATTAAATCTTAATTAGTCTATTTTCATATAAAAGAGAAAGAATAG
28465997 ACAAAAGAGTTATATATTCTAAGGTATTGGAATTTTAGTGAGACAGGGTCAGAATAATTTCAAAA
261 ACAAAAGAGTTATATATTCTAAGGTATTGGAATTTTAGTGAGACAGGGTCAGAATAATTTCAAAA
28466062 TTCCCTATTCTGACTTTGAAAAATCACTAAAAATTGTACAAAAATAATTATGTTTTGTAATTTAC
326 TTCCCTATTCTGACTTTGAAAAATCACTAAAAATTGTACAAAAATAATTATGTTTTGTAATTTAC
28466127 ATGTCTAAATTTCTCAATGAGTTTATTTTCAAGAGAAACAAACGGAAATATCATTTGAATTCTGT
391 ATGTCTAAATTTCTCAATGAGTTTATTTTCAAGAGAAACAAACGGAAATATCATTTGAATTCTGT
28466192 ACAAAGAGATAATTAATTTTTAGTGAAGAGGACTTAGAGCTGTCGAGCAGTGAAATAGGGAAAAT
456 ACAAAGAGATAATTAATTTTTAGTGAAGAGGACTTAGAGCTGTCGAGCAGTGAAATAGGGAAAAT
28466257 TTTAAAGAATAAAATGTACTAATTGGATAAACCAAAAATTCTAAAAATTTTATGGTAAGAAGATA
521 TTTAAAGAATAAAATGTACTAATTGGATAAACCAAAAATTCTAAAAATTTTATGGTAAGAAGATA
28466322 TATGAGTCTAG-TTCAGGGAAA
586 TATGAGTCTAGTTTCAGGGAAA
28466343 TATTGAAATGTGATAAATTGCAAACAGTAACTGAAGTAATGAAGTCTCGTACTGTGCCAACAAAT
1 TATTGAAATGTGATAAATTGCAAACAGTAACTGAAGTAATGAAGTCTCGTACTGTGCCAACAAAT
28466408 TAAATTGTTATTGAATATTGAATAAATTGTTATAGTGTTACATGAGTGAGTGAATTTGAAACAGA
66 TAAATTGTTATTGAATATTGAATAAATTGTTATAGTGTTACATGAGTGAGTGAATTTGAAACAGA
28466473 ATAGATTTGGGCATTGACAGTGACGTTAGTTTGAAAAATCACCAAAAGTTATAGGAATTGAGTTA
131 ATAGATTTGGGCATTGACAGTGACGTTAGTTTGAAAAATCACCAAAAGTTATAGGAATTGAGTTA
28466538 CTGGTTGAATGAGATATGAAATTAAATCTTAATTAGTCTATTTTCATATAAAAGAGAAAGAATAG
196 CTGGTTGAATGAGATATGAAATTAAATCTTAATTAGTCTATTTTCATATAAAAGAGAAAGAATAG
28466603 ACAAAAGAGTTATATATTCTAAGGTATTGGAATTTTAGTGAGACAGGGTCAGAATAATTTCAAAA
261 ACAAAAGAGTTATATATTCTAAGGTATTGGAATTTTAGTGAGACAGGGTCAGAATAATTTCAAAA
28466668 TTCCCTATTCTGACTTTGAAAAATCACTAAAAATTGTACAAAAATAATTATGTTTTGTAATTTAC
326 TTCCCTATTCTGACTTTGAAAAATCACTAAAAATTGTACAAAAATAATTATGTTTTGTAATTTAC
28466733 ATGTCTAAATTTCTCAATGAGTTTATTTTCAAGAGAAACAAACGGAAATATCATTTGAATTCTGT
391 ATGTCTAAATTTCTCAATGAGTTTATTTTCAAGAGAAACAAACGGAAATATCATTTGAATTCTGT
*
28466798 ACAAAGAGATAATTAATTTTTAGTGAAGAGGACTTAGAGCTGTCGAGCAGTGAAATAGGGGAAAT
456 ACAAAGAGATAATTAATTTTTAGTGAAGAGGACTTAGAGCTGTCGAGCAGTGAAATAGGGAAAAT
28466863 TTTAAAGAATAAAATGTACTAATTGGATAAACCAAAAATTCTAAAAATTTTATGGTAAGAAGATA
521 TTTAAAGAATAAAATGTACTAATTGGATAAACCAAAAATTCTAAAAATTTTATGGTAAGAAGATA
28466928 TATGAGTCTAGTTTCAGGGAAA
586 TATGAGTCTAGTTTCAGGGAAA
28466950 ATTTACAGAT
Statistics
Matches: 605, Mismatches: 1, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
606 595 0.98
607 10 0.02
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.33
Consensus pattern (607 bp):
TATTGAAATGTGATAAATTGCAAACAGTAACTGAAGTAATGAAGTCTCGTACTGTGCCAACAAAT
TAAATTGTTATTGAATATTGAATAAATTGTTATAGTGTTACATGAGTGAGTGAATTTGAAACAGA
ATAGATTTGGGCATTGACAGTGACGTTAGTTTGAAAAATCACCAAAAGTTATAGGAATTGAGTTA
CTGGTTGAATGAGATATGAAATTAAATCTTAATTAGTCTATTTTCATATAAAAGAGAAAGAATAG
ACAAAAGAGTTATATATTCTAAGGTATTGGAATTTTAGTGAGACAGGGTCAGAATAATTTCAAAA
TTCCCTATTCTGACTTTGAAAAATCACTAAAAATTGTACAAAAATAATTATGTTTTGTAATTTAC
ATGTCTAAATTTCTCAATGAGTTTATTTTCAAGAGAAACAAACGGAAATATCATTTGAATTCTGT
ACAAAGAGATAATTAATTTTTAGTGAAGAGGACTTAGAGCTGTCGAGCAGTGAAATAGGGAAAAT
TTTAAAGAATAAAATGTACTAATTGGATAAACCAAAAATTCTAAAAATTTTATGGTAAGAAGATA
TATGAGTCTAGTTTCAGGGAAA
Found at i:28468822 original size:18 final size:18
Alignment explanation
Indices: 28468801--28468846 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
28468791 CCCAAGCATT
28468801 CAACCCAACCTAATTACC
1 CAACCCAACCTAATTACC
*
28468819 CAACCCAACTTAATTACC
1 CAACCCAACCTAATTACC
28468837 CAACCCAACC
1 CAACCCAACC
28468847 CAATCATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.39, C:0.46, G:0.00, T:0.15
Consensus pattern (18 bp):
CAACCCAACCTAATTACC
Found at i:28468967 original size:9 final size:9
Alignment explanation
Indices: 28468953--28468992 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
28468943 GTAGTGATTC
28468953 AATTCGGTT
1 AATTCGGTT
*
28468962 AATTCGGGT
1 AATTCGGTT
*
28468971 AATTCGTTT
1 AATTCGGTT
28468980 AATTCGGTT
1 AATTCGGTT
28468989 AATT
1 AATT
28468993 TTTAACCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.45
Consensus pattern (9 bp):
AATTCGGTT
Found at i:28476888 original size:21 final size:21
Alignment explanation
Indices: 28476851--28476919 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
28476841 CGCCCAAGTC
*
28476851 GTGTGGCTT-CACACATGGCT
1 GTGTGGCTTCCTCACATGGCT
* *
28476871 GTGTGGCTTCCTCACATGCCC
1 GTGTGGCTTCCTCACATGGCT
*
28476892 GTGAGGCTTCCTCACAT-GCTT
1 GTGTGGCTTCCTCACATGGC-T
28476913 GTGTGGC
1 GTGTGGC
28476920 CAGACCGTGC
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
20 10 0.25
21 30 0.75
ACGTcount: A:0.12, C:0.29, G:0.29, T:0.30
Consensus pattern (21 bp):
GTGTGGCTTCCTCACATGGCT
Found at i:28481977 original size:10 final size:10
Alignment explanation
Indices: 28481962--28481986 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
28481952 GCCTAAGATG
28481962 TGAATTGCAT
1 TGAATTGCAT
28481972 TGAATTGCAT
1 TGAATTGCAT
28481982 TGAAT
1 TGAAT
28481987 ATGAATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (10 bp):
TGAATTGCAT
Found at i:28482649 original size:24 final size:24
Alignment explanation
Indices: 28482575--28482655 Score: 78
Period size: 24 Copynumber: 3.3 Consensus size: 24
28482565 TGGCTATCCG
28482575 GAGCTTCCCGATTAATTGCTCTTCA-
1 GAGCTTCCCGATT-ATTGCTCTT-AT
* **
28482600 GAGCTACCCG-TTATTGGCTCGCAT
1 GAGCTTCCCGATTATT-GCTCTTAT
28482624 GAGCTTCCCGATTA-TGACTCTTAT
1 GAGCTTCCCGATTATTG-CTCTTAT
28482648 GAGCTTCC
1 GAGCTTCC
28482656 TATTATACAG
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
23 5 0.11
24 29 0.63
25 12 0.26
ACGTcount: A:0.19, C:0.28, G:0.20, T:0.33
Consensus pattern (24 bp):
GAGCTTCCCGATTATTGCTCTTAT
Found at i:28482693 original size:25 final size:25
Alignment explanation
Indices: 28482665--28482718 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
28482655 CTATTATACA
* *
28482665 GCTCAGATAAGCTTCCCGTTACATG
1 GCTCACATAAGCTTCCCATTACATG
* *
28482690 GCTCACATGAGCTTCCCATTATATG
1 GCTCACATAAGCTTCCCATTACATG
28482715 GCTC
1 GCTC
28482719 GAGAGAGAGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.22, C:0.30, G:0.19, T:0.30
Consensus pattern (25 bp):
GCTCACATAAGCTTCCCATTACATG
Found at i:28487281 original size:6 final size:6
Alignment explanation
Indices: 28487267--28487314 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
28487257 TTATTATTCG
* * *
28487267 TCTCTC TCTCAC TCTCAC TCT--C TCACTC TCTCAC TCTCAC TCTCAC
1 TCTCAC TCTCAC TCTCAC TCTCAC TCTCAC TCTCAC TCTCAC TCTCAC
28487313 TC
1 TC
28487315 ACTCACACGC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
4 3 0.08
6 33 0.92
ACGTcount: A:0.12, C:0.50, G:0.00, T:0.38
Consensus pattern (6 bp):
TCTCAC
Found at i:28487289 original size:14 final size:14
Alignment explanation
Indices: 28487270--28487320 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
28487260 TTATTCGTCT
28487270 CTCTCTCACTCTCA
1 CTCTCTCACTCTCA
*
28487284 CTCTCTCACTCTCT
1 CTCTCTCACTCTCA
*
28487298 CACTCTCACTCTCA
1 CTCTCTCACTCTCA
*
28487312 CTCACTCAC
1 CTCTCTCAC
28487321 ACGCACATTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.16, C:0.51, G:0.00, T:0.33
Consensus pattern (14 bp):
CTCTCTCACTCTCA
Found at i:28487320 original size:8 final size:8
Alignment explanation
Indices: 28487268--28487318 Score: 57
Period size: 8 Copynumber: 6.4 Consensus size: 8
28487258 TATTATTCGT
*
28487268 CTCTCTCT
1 CTCTCTCA
*
28487276 CACTCTCA
1 CTCTCTCA
28487284 CTCTCTCA
1 CTCTCTCA
28487292 CTCTCTCA
1 CTCTCTCA
* *
28487300 CTCTCACT
1 CTCTCTCA
*
28487308 CTCACTCA
1 CTCTCTCA
28487316 CTC
1 CTC
28487319 ACACGCACAT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
8 35 1.00
ACGTcount: A:0.14, C:0.51, G:0.00, T:0.35
Consensus pattern (8 bp):
CTCTCTCA
Found at i:28489037 original size:19 final size:19
Alignment explanation
Indices: 28489015--28489058 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
28489005 GTCTGGTATA
*
28489015 GATACTGTTTTAGTATATC
1 GATACTGTTTTAGGATATC
*
28489034 GATACCTTTTTTAGGATATC
1 GATA-CTGTTTTAGGATATC
28489054 GATAC
1 GATAC
28489059 CTTAGTGCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (19 bp):
GATACTGTTTTAGGATATC
Found at i:28489047 original size:20 final size:20
Alignment explanation
Indices: 28489022--28489061 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
28489012 ATAGATACTG
*
28489022 TTTTAGTATATCGATACCTT
1 TTTTAGGATATCGATACCTT
28489042 TTTTAGGATATCGATACCTT
1 TTTTAGGATATCGATACCTT
28489062 AGTGCTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTTAGGATATCGATACCTT
Found at i:28492244 original size:27 final size:27
Alignment explanation
Indices: 28492206--28492269 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 27
28492196 TAACTAACTG
*
28492206 TAATACCCCTATAGGGTAAAATGACCA
1 TAATGCCCCTATAGGGTAAAATGACCA
* *
28492233 TAATGCCCCTATAGGGTAAACTGACCG
1 TAATGCCCCTATAGGGTAAAATGACCA
*
28492260 TAAAGCCCCT
1 TAATGCCCCT
28492270 GAAAGTAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (27 bp):
TAATGCCCCTATAGGGTAAAATGACCA
Found at i:28492379 original size:27 final size:27
Alignment explanation
Indices: 28492339--28492594 Score: 309
Period size: 27 Copynumber: 9.5 Consensus size: 27
28492329 GATTGATTTT
* * *
28492339 TAGGGTAAAATGACCATAATGCCCCTT
1 TAGGGTAAACTGACCGTAATGCCCCTG
* * *
28492366 TAAGGTAAACTGACTGTAATACCCCTG
1 TAGGGTAAACTGACCGTAATGCCCCTG
* * *
28492393 TAGGGTAAAATGACTGTAATACCCCTG
1 TAGGGTAAACTGACCGTAATGCCCCTG
*
28492420 TAGGGTAAACTGACCGTAATGCCTCTG
1 TAGGGTAAACTGACCGTAATGCCCCTG
* *
28492447 TAGGGTAAACTGACCATAATGCCCCCG
1 TAGGGTAAACTGACCGTAATGCCCCTG
*
28492474 TAGGGTAAACTGACCGTAATACCCCTG
1 TAGGGTAAACTGACCGTAATGCCCCTG
* *
28492501 TAGGGTAAAATGACTGTAATGCCCCTG
1 TAGGGTAAACTGACCGTAATGCCCCTG
*
28492528 T-GAGGTAAACTGACCGTAATCCCCCTG
1 TAG-GGTAAACTGACCGTAATGCCCCTG
* * *
28492555 TAGGGTAAAATGACTGTAATACCCCTG
1 TAGGGTAAACTGACCGTAATGCCCCTG
*
28492582 GAGGGTAAA-TGAC
1 TAGGGTAAACTGAC
28492595 TATTTTGCAC
Statistics
Matches: 199, Mismatches: 28, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
26 5 0.03
27 193 0.97
28 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (27 bp):
TAGGGTAAACTGACCGTAATGCCCCTG
Found at i:28492427 original size:54 final size:54
Alignment explanation
Indices: 28492339--28492594 Score: 354
Period size: 54 Copynumber: 4.8 Consensus size: 54
28492329 GATTGATTTT
** * * *
28492339 TAGGGTAAAATGACCATAATGCCCCTTTAAGGTAAACTGACTGTAATACCCCTG
1 TAGGGTAAAATGACTGTAATGCCCCTGTAGGGTAAACTGACCGTAATACCCCTG
* * *
28492393 TAGGGTAAAATGACTGTAATACCCCTGTAGGGTAAACTGACCGTAATGCCTCTG
1 TAGGGTAAAATGACTGTAATGCCCCTGTAGGGTAAACTGACCGTAATACCCCTG
* ** *
28492447 TAGGGTAAACTGACCATAATGCCCCCGTAGGGTAAACTGACCGTAATACCCCTG
1 TAGGGTAAAATGACTGTAATGCCCCTGTAGGGTAAACTGACCGTAATACCCCTG
*
28492501 TAGGGTAAAATGACTGTAATGCCCCTGT-GAGGTAAACTGACCGTAATCCCCCTG
1 TAGGGTAAAATGACTGTAATGCCCCTGTAG-GGTAAACTGACCGTAATACCCCTG
* *
28492555 TAGGGTAAAATGACTGTAATACCCCTGGAGGGTAAA-TGAC
1 TAGGGTAAAATGACTGTAATGCCCCTGTAGGGTAAACTGAC
28492595 TATTTTGCAC
Statistics
Matches: 178, Mismatches: 22, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
53 5 0.03
54 172 0.97
55 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (54 bp):
TAGGGTAAAATGACTGTAATGCCCCTGTAGGGTAAACTGACCGTAATACCCCTG
Found at i:28492477 original size:81 final size:80
Alignment explanation
Indices: 28492339--28492594 Score: 354
Period size: 81 Copynumber: 3.2 Consensus size: 80
28492329 GATTGATTTT
* * * * *
28492339 TAGGGTAAAATGACCATAATGCCCCTTTAAGGTAAACTGACTGTAATACCCCTGTAGGGTAAAAT
1 TAGGGTAAAATGACCGTAATGCCCCTGTAGGGTAAACTGACCGTAAT-CCCCCGTAGGGTAAAAT
28492404 GACTGTAATACCCCTG
65 GACTGTAATACCCCTG
* * * *
28492420 TAGGGTAAACTGACCGTAATGCCTCTGTAGGGTAAACTGACCATAATGCCCCCGTAGGGTAAACT
1 TAGGGTAAAATGACCGTAATGCCCCTGTAGGGTAAACTGACCGTAAT-CCCCCGTAGGGTAAAAT
*
28492485 GACCGTAATACCCCTG
65 GACTGTAATACCCCTG
*
28492501 TAGGGTAAAATGACTGTAATGCCCCTGT-GAGGTAAACTGACCGTAATCCCCCTGTAGGGTAAAA
1 TAGGGTAAAATGACCGTAATGCCCCTGTAG-GGTAAACTGACCGTAATCCCCC-GTAGGGTAAAA
28492565 TGACTGTAATACCCCTG
64 TGACTGTAATACCCCTG
*
28492582 GAGGGT-AAATGAC
1 TAGGGTAAAATGAC
28492595 TATTTTGCAC
Statistics
Matches: 155, Mismatches: 18, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
80 13 0.08
81 142 0.92
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (80 bp):
TAGGGTAAAATGACCGTAATGCCCCTGTAGGGTAAACTGACCGTAATCCCCCGTAGGGTAAAATG
ACTGTAATACCCCTG
Found at i:28492654 original size:23 final size:24
Alignment explanation
Indices: 28492628--28492680 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
28492618 GATTGAATTA
28492628 TCTGTGGTT-AAATGACTAATTTG
1 TCTGTGGTTGAAATGACTAATTTG
* ** *
28492651 TCTGTGTTTGGTATGACTGATTTG
1 TCTGTGGTTGAAATGACTAATTTG
28492675 TCTGTG
1 TCTGTG
28492681 ATTTGAATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.17, C:0.09, G:0.26, T:0.47
Consensus pattern (24 bp):
TCTGTGGTTGAAATGACTAATTTG
Done.