Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold220
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: 3999181
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 12171 characters in sequence are not A, C, G, or T
File 16 of 19
Found at i:3359444 original size:14 final size:17
Alignment explanation
Indices: 3359387--3359446 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
3359377 TAATTAATAA
*
3359387 TATTATATTAATTAATTA-
1 TATTAT-TTTATT-ATTAT
3359405 TATTATTTTATTATTAT
1 TATTATTTTATTATTAT
*
3359422 TATTTTTTTATT-TT-T
1 TATTATTTTATTATTAT
3359437 TA-TATTTTAT
1 TATTATTTTAT
3359447 AAAAAAATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
14 7 0.18
15 3 0.08
16 6 0.16
17 16 0.42
18 6 0.16
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TATTATTTTATTATTAT
Found at i:3359522 original size:19 final size:18
Alignment explanation
Indices: 3359498--3359536 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3359488 ATTATGTTTG
*
3359498 TAAATAATTAAAATTATTT
1 TAAATAAGT-AAATTATTT
*
3359517 TAAATAGGTAAATTATTT
1 TAAATAAGTAAATTATTT
3359535 TA
1 TA
3359537 TTAAATTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (18 bp):
TAAATAAGTAAATTATTT
Found at i:3360236 original size:16 final size:15
Alignment explanation
Indices: 3360182--3360238 Score: 62
Period size: 16 Copynumber: 3.7 Consensus size: 15
3360172 AGAGAGAGTA
3360182 TGATTTGATGGAACAT
1 TGATTTGAT-GAACAT
*
3360198 TGCTTTGCATGAAC-T
1 TGATTTG-ATGAACAT
*
3360213 TAATTTGATAGAACAT
1 TGATTTGAT-GAACAT
3360229 TGATTTGATG
1 TGATTTGATG
3360239 GGGCATTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
14 2 0.06
15 11 0.32
16 19 0.56
17 2 0.06
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (15 bp):
TGATTTGATGAACAT
Found at i:3361825 original size:20 final size:19
Alignment explanation
Indices: 3361786--3361826 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
3361776 TAAAATTTTT
*
3361786 AAAAATTAAATATTTTATA
1 AAAAATTAAATATTTCATA
3361805 AAAAATTAAATATGTTCATA
1 AAAAATTAAATAT-TTCATA
3361825 AA
1 AA
3361827 TATAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (19 bp):
AAAAATTAAATATTTCATA
Found at i:3361890 original size:20 final size:20
Alignment explanation
Indices: 3361865--3361906 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
3361855 ATTTATAAAA
3361865 ATAAATAATAAATATTAATT
1 ATAAATAATAAATATTAATT
* * *
3361885 ATAAATATTTAATATTATTT
1 ATAAATAATAAATATTAATT
3361905 AT
1 AT
3361907 TTTTTAAATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATAAATAATAAATATTAATT
Found at i:3361995 original size:22 final size:23
Alignment explanation
Indices: 3361969--3362016 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
3361959 ACCTTAAATT
* *
3361969 AATTATTAAATATTTTATT-TAA
1 AATTAATAAATATTTAATTATAA
*
3361991 AATTAATAATTATTTAATTATAA
1 AATTAATAAATATTTAATTATAA
3362014 AAT
1 AAT
3362017 ATCCGAGCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
AATTAATAAATATTTAATTATAA
Found at i:3365229 original size:1 final size:1
Alignment explanation
Indices: 3365223--3365250 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
3365213 GTTTCTCAAT
3365223 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
3365251 GCAACAGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:3384548 original size:17 final size:16
Alignment explanation
Indices: 3384497--3384548 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
3384487 AAAAAATGAT
*
3384497 AATATAAAAATATTTAA
1 AATA-AAAAATATTTTA
* * *
3384514 AATATAAAATAATATA
1 AATAAAAAATATTTTA
3384530 AATAAATAAATATTTTA
1 AATAAA-AAATATTTTA
3384547 AA
1 AA
3384549 ATTTATATAA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
16 13 0.48
17 14 0.52
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AATAAAAAATATTTTA
Found at i:3384592 original size:18 final size:17
Alignment explanation
Indices: 3384545--3384638 Score: 74
Period size: 18 Copynumber: 5.5 Consensus size: 17
3384535 ATAAATATTT
3384545 TAAAATTTATAT-AATA
1 TAAAATTTATATAAATA
3384561 T--AATTTAT-TAAAATA
1 TAAAATTTATAT-AAATA
3384576 TCAAAATTTATATAAATA
1 T-AAAATTTATATAAATA
*
3384594 TAAATATTTTAATATAATTA
1 TAAA-A-TTT-ATATAAATA
*
3384614 TAAAA-TTA-AAAAATA
1 TAAAATTTATATAAATA
3384629 TAATAATTTA
1 TAA-AATTTA
3384639 ACACGATTTT
Statistics
Matches: 64, Mismatches: 3, Indels: 21
0.73 0.03 0.24
Matches are distributed among these distances:
13 1 0.02
14 7 0.11
15 13 0.20
16 4 0.06
17 8 0.12
18 14 0.22
19 5 0.08
20 12 0.19
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:3386124 original size:17 final size:17
Alignment explanation
Indices: 3386069--3386140 Score: 58
Period size: 18 Copynumber: 4.1 Consensus size: 17
3386059 TTAGAATATC
*
3386069 ATATAATTAAATAAATTT
1 ATATAATTAAAT-TATTT
* *
3386087 -TGATAATATCAATAATTT
1 AT-ATAAT-TAAATTATTT
*
3386105 ATATTATATAAATT-TTT
1 ATATAAT-TAAATTATTT
3386122 ATATAATTAAATTATTT
1 ATATAATTAAATTATTT
3386139 AT
1 AT
3386141 TTTTATTTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
16 6 0.13
17 15 0.33
18 19 0.42
19 5 0.11
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (17 bp):
ATATAATTAAATTATTT
Found at i:3386134 original size:16 final size:18
Alignment explanation
Indices: 3386089--3386140 Score: 63
Period size: 17 Copynumber: 3.0 Consensus size: 18
3386079 ATAAATTTTG
* *
3386089 ATAATATCAATAATTTAT
1 ATAATATAAATTATTTAT
*
3386107 ATTATATAAATT-TTTAT
1 ATAATATAAATTATTTAT
3386124 ATAAT-TAAATTATTTAT
1 ATAATATAAATTATTTAT
3386141 TTTTATTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 6 0.21
17 14 0.48
18 9 0.31
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
ATAATATAAATTATTTAT
Found at i:3388213 original size:2 final size:2
Alignment explanation
Indices: 3388206--3388247 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3388196 ACTACGAATG
3388206 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3388248 TTAAGTAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3393965 original size:13 final size:13
Alignment explanation
Indices: 3393947--3393972 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3393937 CAGTAGTAAG
3393947 CTACTCTTTCTTA
1 CTACTCTTTCTTA
3393960 CTACTCTTTCTTA
1 CTACTCTTTCTTA
3393973 GTGTAGTGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.00, T:0.54
Consensus pattern (13 bp):
CTACTCTTTCTTA
Found at i:3395985 original size:25 final size:25
Alignment explanation
Indices: 3395957--3396005 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
3395947 TAAAGAATAA
*
3395957 TTAATATAATTATAA-AAAATTAAAT
1 TTAA-ATAATAATAATAAAATTAAAT
*
3395982 TTAAATTATAATAATAAAATTAAA
1 TTAAATAATAATAATAAAATTAAA
3396006 AGTATTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
TTAAATAATAATAATAAAATTAAAT
Found at i:3396346 original size:18 final size:19
Alignment explanation
Indices: 3396313--3396348 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3396303 AAATAAAAAT
3396313 AATTTAATTAGTATTTTAA
1 AATTTAATTAGTATTTTAA
3396332 AATTTAATT-GTATTTTA
1 AATTTAATTAGTATTTTA
3396349 TGTATTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (19 bp):
AATTTAATTAGTATTTTAA
Found at i:3396964 original size:16 final size:15
Alignment explanation
Indices: 3396945--3396976 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
3396935 TACTTCATTT
3396945 AAAAATTTTAAAATAA
1 AAAAATTTT-AAATAA
3396961 AAAAATTTTAAATAA
1 AAAAATTTTAAATAA
3396976 A
1 A
3396977 TCGAATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAAAATTTTAAATAA
Found at i:3398030 original size:19 final size:20
Alignment explanation
Indices: 3397986--3398035 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
3397976 TTTTTTAAAA
*
3397986 AATAAAATAAAAACTTATAT
1 AATAAAATAAAAACTAATAT
3398006 AA-AAAATTAAAAA-TAAT-T
1 AATAAAA-TAAAAACTAATAT
3398024 AATAAAATAAAA
1 AATAAAATAAAA
3398036 TTATTTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 8 0.30
19 11 0.41
20 8 0.30
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (20 bp):
AATAAAATAAAAACTAATAT
Found at i:3399160 original size:21 final size:20
Alignment explanation
Indices: 3399136--3399183 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 20
3399126 AAATTTTAAT
3399136 ATATATTTATATATTAAAA-TA
1 ATATATTTA-ATA-TAAAATTA
*
3399157 ATATTTTTAATATAAAATTA
1 ATATATTTAATATAAAATTA
3399177 A-ATATTT
1 ATATATTT
3399184 TAATTTACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 10 0.42
20 6 0.25
21 8 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATATTTAATATAAAATTA
Found at i:3399172 original size:19 final size:23
Alignment explanation
Indices: 3399131--3399184 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 23
3399121 TTTAAAAATT
*
3399131 TTAATATATATTTATATATTAAAA
1 TTAA-ATATTTTTATATATTAAAA
3399155 -T-AATATTTTTA-ATA-TAAAA
1 TTAAATATTTTTATATATTAAAA
3399174 TTAAATATTTT
1 TTAAATATTTT
3399185 AATTTACATA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
19 5 0.19
20 4 0.15
21 16 0.59
22 1 0.04
23 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTAAATATTTTTATATATTAAAA
Found at i:3399185 original size:20 final size:20
Alignment explanation
Indices: 3399114--3399187 Score: 57
Period size: 20 Copynumber: 3.6 Consensus size: 20
3399104 ATTATTTATA
**
3399114 TAAATATTTTAA-A-AATTT
1 TAAATATTTTAATATAAAAT
3399132 TAATATATATTTATATATTAAAA-
1 TAA-ATAT-TTTA-ATA-TAAAAT
3399155 T-AATATTTTTAATATAAAAT
1 TAAATA-TTTTAATATAAAAT
3399175 TAAATATTTTAAT
1 TAAATATTTTAAT
3399188 TTACATATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 16
0.71 0.03 0.25
Matches are distributed among these distances:
18 3 0.07
19 9 0.20
20 15 0.33
21 12 0.27
22 3 0.07
23 1 0.02
24 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TAAATATTTTAATATAAAAT
Found at i:3399614 original size:18 final size:18
Alignment explanation
Indices: 3399573--3399620 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
3399563 AATGATAATA
*
3399573 AATAATTTGT-ATTTATT
1 AATAATTTATAATTTATT
*
3399590 AATTAATTTATAATTTTTT
1 AA-TAATTTATAATTTATT
3399609 AATAATATTATA
1 AATAAT-TTATA
3399621 TGAATCAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 2 0.08
18 11 0.42
19 13 0.50
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
AATAATTTATAATTTATT
Found at i:3401374 original size:35 final size:34
Alignment explanation
Indices: 3401283--3401380 Score: 160
Period size: 34 Copynumber: 2.9 Consensus size: 34
3401273 GAGTTAGCTT
3401283 TAGATAGCAAAATTGCTCGTCCATGGTCTAGGTC
1 TAGATAGCAAAATTGCTCGTCCATGGTCTAGGTC
3401317 TAGATAGCAAAATTGCTCGTCCATGGTCTAGGTC
1 TAGATAGCAAAATTGCTCGTCCATGGTCTAGGTC
* * *
3401351 TAGGTAGCAAAAATTGCTTGTCCATTGTCT
1 TAGATAGC-AAAATTGCTCGTCCATGGTCT
3401381 GGCATGACGT
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
34 41 0.68
35 19 0.32
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (34 bp):
TAGATAGCAAAATTGCTCGTCCATGGTCTAGGTC
Found at i:3409759 original size:2 final size:2
Alignment explanation
Indices: 3409752--3409777 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3409742 AACTGCTGAA
3409752 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
3409778 TTTTTTCTTA
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:3410403 original size:2 final size:2
Alignment explanation
Indices: 3410398--3410433 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3410388 TATCTATCCC
3410398 CT CT CT 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 CT CT CT
3410434 TTCTTGAAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3414695 original size:28 final size:28
Alignment explanation
Indices: 3414663--3414723 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
3414653 CCTTCTTCTT
*
3414663 CTTGAACCCAAATAACGTTGGCTTTGAC
1 CTTGAACCCAAATAACGTTGGATTTGAC
*
3414691 CTTGAACCGAAATAACGTTGGATTTGAC
1 CTTGAACCCAAATAACGTTGGATTTGAC
3414719 CTTGA
1 CTTGA
3414724 TGTACGAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.30
Consensus pattern (28 bp):
CTTGAACCCAAATAACGTTGGATTTGAC
Found at i:3424693 original size:1 final size:1
Alignment explanation
Indices: 3424687--3424711 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
3424677 ACCAATAGAG
3424687 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
3424712 CCCTTACTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3428587 original size:18 final size:18
Alignment explanation
Indices: 3428540--3428585 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
3428530 TTTTGTTAAA
*
3428540 AAATTTTAAATATTAAGT
1 AAATATTAAATATTAAGT
3428558 AAATATTAAATATATAA-T
1 AAATATTAAATAT-TAAGT
3428576 AAATACTTAA
1 AAATA-TTAA
3428586 TAAAATGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (18 bp):
AAATATTAAATATTAAGT
Found at i:3428876 original size:71 final size:72
Alignment explanation
Indices: 3428793--3428936 Score: 236
Period size: 71 Copynumber: 2.0 Consensus size: 72
3428783 ACACCAGACA
* * *
3428793 AAACACCGATTTGACCAATTGGTCTTGCCTAATTTTTTCAACATTGCATTGTATCCTCTC-TTTG
1 AAACACCAATTTGACCAATCGGTCTAGCCTAATTTTTTCAACATTGCATTGTATCCTCTCTTTTG
*
3428857 TGTAGTT
66 TGCAGTT
*
3428864 AAACACCAATTTGACCAATCGGTCTAGCCTGATTTTTTCAACATTGCATTGTATCCTCTCTTTTG
1 AAACACCAATTTGACCAATCGGTCTAGCCTAATTTTTTCAACATTGCATTGTATCCTCTCTTTTG
3428929 TGCAGTT
66 TGCAGTT
3428936 A
1 A
3428937 GATCTTATAA
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
71 56 0.84
72 11 0.16
ACGTcount: A:0.24, C:0.22, G:0.14, T:0.40
Consensus pattern (72 bp):
AAACACCAATTTGACCAATCGGTCTAGCCTAATTTTTTCAACATTGCATTGTATCCTCTCTTTTG
TGCAGTT
Found at i:3429076 original size:31 final size:34
Alignment explanation
Indices: 3429013--3429112 Score: 97
Period size: 33 Copynumber: 3.1 Consensus size: 34
3429003 AGTAATATAA
* *
3429013 ATATAAA-AT-TAATATATAAATATGTCAAATTTT
1 ATATAAATATATAATATTTTAATATGT-AAATTTT
3429046 ATAT-AATA-A-AA-ATTATTAATATGTAAATTTT
1 ATATAAATATATAATATT-TTAATATGTAAATTTT
* *
3429077 TTATAAATATATAATATTTTAAT-TATAAATTTT
1 ATATAAATATATAATATTTTAATATGTAAATTTT
3429110 ATA
1 ATA
3429113 CAAAAATAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
31 12 0.22
32 16 0.29
33 17 0.31
34 7 0.13
35 3 0.05
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (34 bp):
ATATAAATATATAATATTTTAATATGTAAATTTT
Found at i:3429085 original size:19 final size:21
Alignment explanation
Indices: 3429057--3429106 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
3429047 TATAATAAAA
* *
3429057 ATTATTAATATGTAA-ATTTT
1 ATTATAAATATATAATATTTT
3429077 -TTATAAATATATAATATTTT
1 ATTATAAATATATAATATTTT
3429097 AATTATAAAT
1 -ATTATAAAT
3429107 TTTATACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 12 0.48
20 5 0.20
22 8 0.32
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
ATTATAAATATATAATATTTT
Found at i:3429144 original size:2 final size:2
Alignment explanation
Indices: 3429128--3429171 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
3429118 ATAAAAAATA
*
3429128 AT AT AA AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3429169 AT A
1 AT A
3429172 AAATAAGGTC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3432336 original size:2 final size:2
Alignment explanation
Indices: 3432329--3432362 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
3432319 CAAATTCTAT
* *
3432329 TA TA TA TA TA TA TA TA TA CA TC TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3432363 ATAATAATAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3432693 original size:15 final size:14
Alignment explanation
Indices: 3432686--3432723 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
3432676 TTATTTATAT
3432686 TTAAATT-AATTAAA
1 TTAAATTAAATT-AA
3432700 TTAAATTAAATTAA
1 TTAAATTAAATTAA
3432714 TTAAA-TAAAT
1 TTAAATTAAAT
3432724 AATAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.22
14 14 0.61
15 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TTAAATTAAATTAA
Found at i:3432701 original size:5 final size:5
Alignment explanation
Indices: 3432686--3432723 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
3432676 TTATTTATAT
3432686 TTAAA TT-AA TTAAA TTAAA TTAAA TT-AA TTAAA -TAAA T
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA T
3432724 AATAAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
4 12 0.40
5 18 0.60
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TTAAA
Found at i:3432708 original size:19 final size:18
Alignment explanation
Indices: 3432686--3432723 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
3432676 TTATTTATAT
3432686 TTAAATTAATTAAATTAAA
1 TTAAATTAATTAAA-TAAA
3432705 TTAAATTAATTAAATAAA
1 TTAAATTAATTAAATAAA
3432723 T
1 T
3432724 AATAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TTAAATTAATTAAATAAA
Found at i:3433454 original size:21 final size:21
Alignment explanation
Indices: 3433406--3433454 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
3433396 CCATCGCCCT
3433406 CACCGCCGCCACCGCCACCAC
1 CACCGCCGCCACCGCCACCAC
** *
3433427 CGTCGCCGCCTCCGCCACCAC
1 CACCGCCGCCACCGCCACCAC
3433448 CACCGCC
1 CACCGCC
3433455 TTCTCTAACA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.65, G:0.16, T:0.04
Consensus pattern (21 bp):
CACCGCCGCCACCGCCACCAC
Found at i:3437529 original size:131 final size:123
Alignment explanation
Indices: 3437298--3437536 Score: 284
Period size: 124 Copynumber: 1.9 Consensus size: 123
3437288 CTTAACAGAA
* * * *
3437298 AAAAAATAATATTTTATTAAGTTTAAAAAATTATACTGATAAATTAAAATTTAATTATTATGTTT
1 AAAAAATAATATTTAATTAAGTTTAAAAAATTACACTAATAAATTAAAATATAATTATTATGTTT
* *
3437363 TTATAAAAATAAAAACTTTTAAAATAAAAAAAGTTTTTTATTATCATTTTTAATAAAAT
66 TTATAAAAATAAAAAATGTTAAAATAAAAAAAG-TTTTTATTATCATTTTTAATAAAAT
*
3437422 AAAAAATAATATTTAATTAAGTTTAAAAAATTACATTAAATACAACATTAATAA-ATAATTATTA
1 AAAAAATAATATTTAATTAAGTTTAAAAAATTACACT-AAT--AA-ATTAA-AATATAATTATT-
* * *
3437486 AT-TATTATATTTAAAAATAAAAAATGTTAAATTAAAAATAGTTTTTATTAT
60 ATGT-TT-T-TATAAAAATAAAAAATGTTAAAATAAAAAAAGTTTTTATTAT
3437537 AATAATATTT
Statistics
Matches: 96, Mismatches: 10, Indels: 12
0.81 0.08 0.10
Matches are distributed among these distances:
124 34 0.35
125 2 0.02
127 2 0.02
128 14 0.15
129 6 0.06
130 11 0.11
131 27 0.28
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (123 bp):
AAAAAATAATATTTAATTAAGTTTAAAAAATTACACTAATAAATTAAAATATAATTATTATGTTT
TTATAAAAATAAAAAATGTTAAAATAAAAAAAGTTTTTATTATCATTTTTAATAAAAT
Found at i:3437824 original size:22 final size:21
Alignment explanation
Indices: 3437787--3437869 Score: 71
Period size: 22 Copynumber: 3.8 Consensus size: 21
3437777 TAATGATAAT
3437787 TTTTTTAATTCTTTAAATATTA
1 TTTTTTAATT-TTTAAATATTA
* *
3437809 TTTTTTAATTTGTT-AATGTAAA
1 TTTTTTAATTT-TTAAATAT-TA
3437831 TTTTTTAAATTTAATTAAATATTA
1 TTTTTT-AATTT--TTAAATATTA
*
3437855 -TTTTTATTTTTTAAA
1 TTTTTTAATTTTTAAA
3437870 AAATAAATAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
20 5 0.10
21 5 0.10
22 23 0.46
23 10 0.20
24 3 0.06
25 4 0.08
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTTTTAATTTTTAAATATTA
Found at i:3437946 original size:23 final size:23
Alignment explanation
Indices: 3437906--3437952 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
3437896 TTATAAAAAT
* *
3437906 ATATAATTATTTTTAATTTATTA
1 ATATAATTATTTTAAATTAATTA
3437929 ATATAATT-TTTTAAAATTAATTA
1 ATATAATTATTTT-AAATTAATTA
3437952 A
1 A
3437953 AATATTGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
ATATAATTATTTTAAATTAATTA
Found at i:3440892 original size:17 final size:15
Alignment explanation
Indices: 3440866--3440907 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
3440856 AAAATAATTT
3440866 AATA-TTTTTAAAACA
1 AATATTTTTTAAAA-A
*
3440881 TAATTTTTTTTAAAAA
1 -AATATTTTTTAAAAA
3440897 AATATTTTTTA
1 AATATTTTTTA
3440908 TTCTGGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 10 0.43
16 4 0.17
17 9 0.39
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
AATATTTTTTAAAAA
Found at i:3447282 original size:16 final size:16
Alignment explanation
Indices: 3447253--3447285 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3447243 TATTAATATT
3447253 ATTTATATTTATTTAA
1 ATTTATATTTATTTAA
3447269 ATTTA-ATTTAATTTAA
1 ATTTATATTT-ATTTAA
3447285 A
1 A
3447286 ATATAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTATATTTATTTAA
Found at i:3447637 original size:17 final size:17
Alignment explanation
Indices: 3447591--3447650 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
3447581 GTTTAACTTA
3447591 TTTTTAAATA-AATTTT
1 TTTTTAAATATAATTTT
* *
3447607 ATTTTT-CATTTAATTTT
1 -TTTTTAAATATAATTTT
3447624 TTTTTAAATATAATATTT
1 TTTTTAAATATAAT-TTT
3447642 TTATTTAAA
1 TT-TTTAAA
3447651 ATTTTTAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 7 0.20
17 17 0.49
18 5 0.14
19 6 0.17
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTTAAATATAATTTT
Found at i:3448594 original size:2 final size:2
Alignment explanation
Indices: 3448589--3448615 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3448579 GTTTTTTTAA
3448589 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
3448616 TACTAAGCCT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3451317 original size:24 final size:24
Alignment explanation
Indices: 3451286--3451334 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
3451276 AAGCTACATG
3451286 TGTGTATGTACATATATATATATA
1 TGTGTATGTACATATATATATATA
*
3451310 TGTGTATGTTCATATATATATATA
1 TGTGTATGTACATATATATATATA
3451334 T
1 T
3451335 ATATTCTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.49
Consensus pattern (24 bp):
TGTGTATGTACATATATATATATA
Found at i:3451903 original size:27 final size:28
Alignment explanation
Indices: 3451873--3451953 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 28
3451863 TATTAATTTT
3451873 TAATTAATTTTATTAAATATTAAATAA-
1 TAATTAATTTTATTAAATATTAAATAAG
* * *
3451900 TAATT-ATTTAATTTTAATAATAAATAAG
1 TAATTAATTTTA-TTAAATATTAAATAAG
* * * *
3451928 T-ATTAAATATAATAAATATTTAATAA
1 TAATTAATTTTATTAAATATTAAATAA
3451954 AATATATATG
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
26 5 0.12
27 32 0.78
28 4 0.10
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (28 bp):
TAATTAATTTTATTAAATATTAAATAAG
Found at i:3451918 original size:20 final size:20
Alignment explanation
Indices: 3451860--3451922 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
3451850 TTTAATTTTA
3451860 AATTA-TTAATTTTTAATTAAT
1 AATTATTTAA-TTTTAA-TAAT
* * *
3451881 -TTTATTAAATATTAAATAAT
1 AATTATTTAAT-TTTAATAAT
3451901 AATTATTTAATTTTAATAAT
1 AATTATTTAATTTTAATAAT
3451921 AA
1 AA
3451923 ATAAGTATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
20 18 0.55
21 15 0.45
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
AATTATTTAATTTTAATAAT
Found at i:3451954 original size:20 final size:21
Alignment explanation
Indices: 3451916--3451959 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
3451906 TTTAATTTTA
*
3451916 ATAATAAATAAGT-ATTAAAT
1 ATAATAAATAAGTAATAAAAT
**
3451936 ATAATAAATATTTAATAAAAT
1 ATAATAAATAAGTAATAAAAT
3451957 ATA
1 ATA
3451960 TATGTAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
ATAATAAATAAGTAATAAAAT
Found at i:3451957 original size:16 final size:16
Alignment explanation
Indices: 3451917--3451972 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 16
3451907 TTAATTTTAA
*
3451917 TAAT-AAATAAGTATT
1 TAATAAAATAAATATT
* *
3451932 AAATATAATAAATATT
1 TAATAAAATAAATATT
* *
3451948 TAATAAAATATATATG
1 TAATAAAATAAATATT
*
3451964 TAATTAAAT
1 TAATAAAAT
3451973 TTTATAATTT
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
15 3 0.09
16 29 0.91
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (16 bp):
TAATAAAATAAATATT
Found at i:3452082 original size:10 final size:10
Alignment explanation
Indices: 3452039--3452082 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
3452029 AAAAATAGTT
*
3452039 TTTTTTTTAA
1 TTTTTTATAA
3452049 TTTTTTATCAA
1 TTTTTTAT-AA
*
3452060 TTTTTAATAA
1 TTTTTTATAA
*
3452070 TTTTTTATTA
1 TTTTTTATAA
3452080 TTT
1 TTT
3452083 AAATTTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 20 0.69
11 9 0.31
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:3458762 original size:2 final size:2
Alignment explanation
Indices: 3458755--3458786 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3458745 AACTTTTTGC
3458755 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3458787 TAGATGCAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3459908 original size:16 final size:16
Alignment explanation
Indices: 3459878--3459917 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
3459868 TATGTAAATA
3459878 TAAAATTTAAATATTAT
1 TAAAATTTAAATATT-T
*
3459895 TAATATTT-AATATTT
1 TAAAATTTAAATATTT
3459910 TAAAATTT
1 TAAAATTT
3459918 TAAACATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 6 0.29
17 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAAAATTTAAATATTT
Found at i:3459919 original size:16 final size:17
Alignment explanation
Indices: 3459878--3459920 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
3459868 TATGTAAATA
*
3459878 TAAAATTTAAATATTAT
1 TAAAATTTTAATATTAT
*
3459895 TAATA-TTTAATATT-T
1 TAAAATTTTAATATTAT
3459910 TAAAATTTTAA
1 TAAAATTTTAA
3459921 ACATCAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 5 0.23
16 13 0.59
17 4 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TAAAATTTTAATATTAT
Found at i:3460171 original size:20 final size:21
Alignment explanation
Indices: 3460146--3460184 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3460136 TTAAAATGAT
*
3460146 ATTTAAAAT-TAATTATATTA
1 ATTTAAAATAAAATTATATTA
3460166 ATTTAAAATAAAATTATAT
1 ATTTAAAATAAAATTATAT
3460185 ATATTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
ATTTAAAATAAAATTATATTA
Found at i:3461031 original size:26 final size:29
Alignment explanation
Indices: 3460994--3461059 Score: 84
Period size: 27 Copynumber: 2.3 Consensus size: 29
3460984 ATATTTTATT
*
3460994 TTAAATATAATA-AAAATAATTAAA-ATA
1 TTAAATTTAATATAAAATAATTAAATATA
*
3461021 -TAAATTTAATATAAAATATTTAAATATA
1 TTAAATTTAATATAAAATAATTAAATATA
3461049 TTAAAATTTAA
1 TT-AAATTTAA
3461060 AATATAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
26 10 0.30
27 11 0.33
28 3 0.09
29 1 0.03
30 8 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (29 bp):
TTAAATTTAATATAAAATAATTAAATATA
Found at i:3461049 original size:17 final size:15
Alignment explanation
Indices: 3460993--3461066 Score: 57
Period size: 17 Copynumber: 4.8 Consensus size: 15
3460983 TATATTTTAT
3460993 TTTAAATATAATAAAAA
1 TTTAAA-AT-ATAAAAA
3461010 TAATTAAAATAT--AAA
1 T--TTAAAATATAAAAA
3461025 TTT--AATATAAAATA
1 TTTAAAATATAAAA-A
*
3461039 TTTAAATATATTAAAA
1 TTTAAA-ATATAAAAA
3461055 TTTAAAATATAA
1 TTTAAAATATAA
3461067 TTATAACACA
Statistics
Matches: 47, Mismatches: 2, Indels: 18
0.70 0.03 0.27
Matches are distributed among these distances:
11 5 0.11
13 4 0.09
14 4 0.09
15 9 0.19
16 8 0.17
17 10 0.21
18 2 0.04
19 5 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TTTAAAATATAAAAA
Found at i:3461069 original size:18 final size:18
Alignment explanation
Indices: 3461004--3461069 Score: 66
Period size: 18 Copynumber: 3.7 Consensus size: 18
3460994 TTAAATATAA
*
3461004 TAAAA-ATAATTAAAATA
1 TAAAATATAATTAAAATT
*
3461021 T-AAATTTAATATAAAATAT
1 TAAAATATAAT-TAAAAT-T
*
3461040 TTAAATAT-ATTAAAATT
1 TAAAATATAATTAAAATT
3461057 TAAAATATAATTA
1 TAAAATATAATTA
3461070 TAACACATCT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
16 3 0.08
17 13 0.32
18 16 0.40
19 3 0.08
20 5 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATATAATTAAAATT
Found at i:3461474 original size:17 final size:17
Alignment explanation
Indices: 3461454--3461486 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3461444 AAATAATATA
3461454 TATTAATTGATTTTTAT
1 TATTAATTGATTTTTAT
*
3461471 TATTAATTTATTTTTA
1 TATTAATTGATTTTTA
3461487 AAAAATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
TATTAATTGATTTTTAT
Found at i:3462136 original size:21 final size:21
Alignment explanation
Indices: 3462112--3462151 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3462102 GGGTATTGTT
* * *
3462112 ATTATTATTTTTTTTTGTTTA
1 ATTAGTATTTGTTTCTGTTTA
3462133 ATTAGTATTTGTTTCTGTT
1 ATTAGTATTTGTTTCTGTT
3462152 AAACTGGTCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.10, T:0.70
Consensus pattern (21 bp):
ATTAGTATTTGTTTCTGTTTA
Found at i:3467823 original size:23 final size:22
Alignment explanation
Indices: 3467797--3467847 Score: 84
Period size: 23 Copynumber: 2.3 Consensus size: 22
3467787 AGTAATCATG
3467797 AATTGTGAACGTAACGGATATC
1 AATTGTGAACGTAACGGATATC
*
3467819 AAATTGTGAACGTAATGGATATC
1 -AATTGTGAACGTAACGGATATC
3467842 AATTGT
1 AATTGT
3467848 ATTTGTTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 6 0.22
23 21 0.78
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (22 bp):
AATTGTGAACGTAACGGATATC
Found at i:3470646 original size:14 final size:14
Alignment explanation
Indices: 3470619--3470666 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
3470609 AAATTTAAAC
3470619 ATAAAT-TA-TAAT
1 ATAAATATATTAAT
3470631 ATAAATATATTAAT
1 ATAAATATATTAAT
*
3470645 ATATCATA-ATTAAT
1 ATA-AATATATTAAT
3470659 AT-AATATA
1 ATAAATATA
3470667 AATTATTCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
12 9 0.30
13 3 0.10
14 15 0.50
15 3 0.10
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (14 bp):
ATAAATATATTAAT
Found at i:3470662 original size:33 final size:32
Alignment explanation
Indices: 3470625--3470736 Score: 99
Period size: 33 Copynumber: 3.5 Consensus size: 32
3470615 AAACATAAAT
3470625 TATAATATAAATATATTAATATATCATAATTAA
1 TATAATATAAATATATTAATATAT-ATAATTAA
* *
3470658 TATAATATAAAT-TATTCATATAT-TAAATTTTA
1 TATAATATAAATATATTAATATATAT-AA-TTAA
*
3470690 TATAAATATATAATATTTTAGATATA-ATAA-TAA
1 TAT-AATATA-AATATATTA-ATATATATAATTAA
*
3470723 TAT-ATAAAAATATA
1 TATAATATAAATATA
3470737 CAAATTATTA
Statistics
Matches: 65, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
30 6 0.09
31 6 0.09
32 16 0.25
33 23 0.35
34 3 0.05
35 5 0.08
36 6 0.09
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.44
Consensus pattern (32 bp):
TATAATATAAATATATTAATATATATAATTAA
Found at i:3470705 original size:27 final size:26
Alignment explanation
Indices: 3470636--3470728 Score: 73
Period size: 27 Copynumber: 3.5 Consensus size: 26
3470626 ATAATATAAA
*
3470636 TATATTAATATATCATA-ATTAATAT
1 TATATAAATATATCATATATTAATAT
* *
3470661 AATATAAAT-TATTCATATATTAAATTT
1 TATATAAATATA-TCATATATT-AATAT
* *
3470688 TATATAAATATATAATATTTTAGATAT
1 TATATAAATATATCATATATTA-ATAT
*
3470715 AATAATAATATATA
1 TAT-ATAA-ATATA
3470729 AAAATATACA
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
24 2 0.04
25 12 0.23
26 4 0.08
27 24 0.45
28 6 0.11
29 5 0.09
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (26 bp):
TATATAAATATATCATATATTAATAT
Found at i:3470722 original size:20 final size:20
Alignment explanation
Indices: 3470675--3470725 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
3470665 TAAATTATTC
*
3470675 ATATATTAA-ATTTTATATAA
1 ATATA-TAATATTTTAGATAA
3470695 ATATATAATATTTTAGATATA
1 ATATATAATATTTTAGATA-A
3470716 ATA-ATAATAT
1 ATATATAATAT
3470726 ATAAAAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 3 0.11
20 21 0.75
21 4 0.14
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
ATATATAATATTTTAGATAA
Found at i:3471599 original size:32 final size:31
Alignment explanation
Indices: 3471528--3471649 Score: 129
Period size: 32 Copynumber: 3.9 Consensus size: 31
3471518 TTTTATTGAT
* *
3471528 ATTAATTATAAATTTAATAA-ATTAGACATA
1 ATTACTTATAAATTTAATAATATTAAACATA
* * *
3471558 ATTATTTATAAATTTAATGAATATTAAATAAA
1 ATTACTTATAAATTTAAT-AATATTAAACATA
* * *
3471590 ATTACTTATAGATTTTATAAATATTATACATA
1 ATTACTTATAAATTTAAT-AATATTAAACATA
*
3471622 ATTACTCATAAATTTAATAATTATTAAA
1 ATTACTTATAAATTTAATAA-TATTAAA
3471650 AAATTTTAAC
Statistics
Matches: 74, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
30 17 0.23
31 4 0.05
32 53 0.72
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (31 bp):
ATTACTTATAAATTTAATAATATTAAACATA
Found at i:3471702 original size:15 final size:14
Alignment explanation
Indices: 3471676--3471719 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
3471666 ATTAAAATAA
* *
3471676 ATATTGACCTTCGT
1 ATATTGATCTTCCT
3471690 ATATTTGATCTTCCT
1 ATA-TTGATCTTCCT
*
3471705 TTATTGATCTTCCT
1 ATATTGATCTTCCT
3471719 A
1 A
3471720 ACTCGTATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.20, C:0.20, G:0.09, T:0.50
Consensus pattern (14 bp):
ATATTGATCTTCCT
Found at i:3473856 original size:18 final size:17
Alignment explanation
Indices: 3473833--3473867 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3473823 TGTCAACATT
*
3473833 TATTTAACGAAATATATA
1 TATTTAACAAAAT-TATA
3473851 TATTTAACAAAATTATA
1 TATTTAACAAAATTATA
3473868 AAATAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (17 bp):
TATTTAACAAAATTATA
Found at i:3479309 original size:18 final size:21
Alignment explanation
Indices: 3479286--3479332 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
3479276 TATTTCGAAT
3479286 TAAATAT-TAA-T-AAATAAA
1 TAAATATATAATTAAAATAAA
3479304 TAAATAATATAATTAAAATAAA
1 TAAAT-ATATAATTAAAATAAA
3479326 -AAATATA
1 TAAATATA
3479333 ATTGCATCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 5 0.20
19 2 0.08
20 6 0.24
21 5 0.20
22 7 0.28
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
TAAATATATAATTAAAATAAA
Found at i:3479333 original size:18 final size:18
Alignment explanation
Indices: 3479301--3479335 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3479291 ATTAATAAAT
*
3479301 AAATAAATAATATAATTA
1 AAATAAAAAATATAATTA
3479319 AAATAAAAAATATAATT
1 AAATAAAAAATATAATT
3479336 GCATCTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATAAAAAATATAATTA
Found at i:3484811 original size:26 final size:26
Alignment explanation
Indices: 3484782--3484840 Score: 118
Period size: 26 Copynumber: 2.3 Consensus size: 26
3484772 AGTCATCGCC
3484782 GTTGTCAGGACAACTGAAGTTACCAA
1 GTTGTCAGGACAACTGAAGTTACCAA
3484808 GTTGTCAGGACAACTGAAGTTACCAA
1 GTTGTCAGGACAACTGAAGTTACCAA
3484834 GTTGTCA
1 GTTGTCA
3484841 CTAACTCTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (26 bp):
GTTGTCAGGACAACTGAAGTTACCAA
Found at i:3485196 original size:2 final size:2
Alignment explanation
Indices: 3485189--3485227 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
3485179 CAAGTCTGCC
3485189 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3485228 TTCTCAAGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3486687 original size:6 final size:6
Alignment explanation
Indices: 3486676--3486702 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3486666 TTAGTATGCA
3486676 TTTTCT TTTTCT TTTTCT TTTTCT TTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTT
3486703 ACCATTTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTCT
Found at i:3490883 original size:17 final size:19
Alignment explanation
Indices: 3490858--3490895 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
3490848 TATTGATATG
*
3490858 TTTATTAATGTTTA-TTGT
1 TTTATTAATATTTATTTGT
3490876 TTTA-TAATATTTATTTGT
1 TTTATTAATATTTATTTGT
3490894 TT
1 TT
3490896 ATTTTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (19 bp):
TTTATTAATATTTATTTGT
Found at i:3490909 original size:22 final size:25
Alignment explanation
Indices: 3490866--3490913 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 25
3490856 TGTTTATTAA
3490866 TGTTTATTGTTTTATAATATTTATT
1 TGTTTATTGTTTTATAATATTTATT
3490891 TGTTTATT-TTTTA-AA-ATTTATT
1 TGTTTATTGTTTTATAATATTTATT
3490913 T
1 T
3490914 ATTAGTCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.35
23 2 0.09
24 5 0.22
25 8 0.35
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (25 bp):
TGTTTATTGTTTTATAATATTTATT
Found at i:3491653 original size:2 final size:2
Alignment explanation
Indices: 3491646--3491685 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3491636 AGTTATACTA
3491646 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3491686 GTTAGAGAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3493304 original size:16 final size:17
Alignment explanation
Indices: 3493283--3493324 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
3493273 CACATTAATA
*
3493283 ATAATTAAATTTTT-TT
1 ATAATTAAATTTTTGTG
3493299 ATAATTTAAATTTTTGTG
1 ATAA-TTAAATTTTTGTG
3493317 ATAATTAA
1 ATAATTAA
3493325 TTACTCAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 4 0.17
17 14 0.61
18 5 0.22
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (17 bp):
ATAATTAAATTTTTGTG
Found at i:3493642 original size:2 final size:2
Alignment explanation
Indices: 3493635--3493659 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3493625 TCAAGTACCA
3493635 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 A
3493660 AACAGTGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3494327 original size:2 final size:2
Alignment explanation
Indices: 3494320--3494345 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3494310 TTGCTTAAAA
3494320 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
3494346 GCAATGCAAA
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:3495239 original size:4 final size:4
Alignment explanation
Indices: 3495232--3495277 Score: 83
Period size: 4 Copynumber: 11.5 Consensus size: 4
3495222 TATATATATA
*
3495232 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATA TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
3495278 GTTAGAGTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:3500448 original size:2 final size:2
Alignment explanation
Indices: 3500441--3500466 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3500431 TAGCATTCAG
3500441 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
3500467 TTTACCTTTA
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:3503310 original size:40 final size:40
Alignment explanation
Indices: 3503266--3503390 Score: 120
Period size: 40 Copynumber: 3.3 Consensus size: 40
3503256 ACATCGAATC
*
3503266 TAAATAAAAAATTTATAATTTATATTAATTTAATTTAATT
1 TAAATAAAAAATTTATAATTTAAATTAATTTAATTTAATT
* ** ** *
3503306 TAAAT-AAAAA---A-AATCTGCATT-A-TTACATCGAATC
1 TAAATAAAAAATTTATAATTTAAATTAATTTA-ATTTAATT
*
3503340 TAAATAAAAAATTTATAATTTAAATCAATTTAATTTAATT
1 TAAATAAAAAATTTATAATTTAAATTAATTTAATTTAATT
3503380 TAAATAAAAAA
1 TAAATAAAAAA
3503391 AATTTAAAAT
Statistics
Matches: 64, Mismatches: 13, Indels: 16
0.69 0.14 0.17
Matches are distributed among these distances:
33 3 0.05
34 11 0.17
35 12 0.19
36 1 0.02
38 1 0.02
39 11 0.17
40 22 0.34
41 3 0.05
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.40
Consensus pattern (40 bp):
TAAATAAAAAATTTATAATTTAAATTAATTTAATTTAATT
Found at i:3503370 original size:74 final size:74
Alignment explanation
Indices: 3503246--3503393 Score: 278
Period size: 74 Copynumber: 2.0 Consensus size: 74
3503236 ATCAACCCAA
* *
3503246 CTGCATTATTACATCGAATCTAAATAAAAAATTTATAATTTATATTAATTTAATTTAATTTAAAT
1 CTGCATTATTACATCGAATCTAAATAAAAAATTTATAATTTAAATCAATTTAATTTAATTTAAAT
3503311 AAAAAAAAT
66 AAAAAAAAT
3503320 CTGCATTATTACATCGAATCTAAATAAAAAATTTATAATTTAAATCAATTTAATTTAATTTAAAT
1 CTGCATTATTACATCGAATCTAAATAAAAAATTTATAATTTAAATCAATTTAATTTAATTTAAAT
3503385 AAAAAAAAT
66 AAAAAAAAT
3503394 TTAAAATATA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 72 1.00
ACGTcount: A:0.51, C:0.07, G:0.03, T:0.39
Consensus pattern (74 bp):
CTGCATTATTACATCGAATCTAAATAAAAAATTTATAATTTAAATCAATTTAATTTAATTTAAAT
AAAAAAAAT
Found at i:3503394 original size:20 final size:19
Alignment explanation
Indices: 3503340--3503397 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 19
3503330 ACATCGAATC
*
3503340 TAAATAAAAAATTTATAATT
1 TAAATAAAAAAATT-TAATT
***
3503360 TAAATCAATTTAATTTAATT
1 TAAAT-AAAAAAATTTAATT
3503380 TAAATAAAAAAAATTTAA
1 TAAAT-AAAAAAATTTAA
3503398 AATATAACTT
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
20 24 0.83
21 5 0.17
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATAAAAAAATTTAATT
Found at i:3508619 original size:3 final size:3
Alignment explanation
Indices: 3508613--3508642 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3508603 TGTTGCCTCC
3508613 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
3508643 TGGATTGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
GTT
Found at i:3509175 original size:24 final size:23
Alignment explanation
Indices: 3509139--3509201 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
3509129 CGGACAAATC
* *
3509139 CATAAATAGAAAATTATT-TATTT
1 CATAAA-ATAAAATTATTAAATTT
3509162 CATTAATAATAAAATTATTAAATTT
1 CA-TAA-AATAAAATTATTAAATTT
*
3509187 TATAAAATAAAATTA
1 CATAAAATAAAATTA
3509202 AAAAATTATC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
23 12 0.35
24 16 0.47
25 6 0.18
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (23 bp):
CATAAAATAAAATTATTAAATTT
Found at i:3509210 original size:31 final size:32
Alignment explanation
Indices: 3509172--3509232 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 32
3509162 CATTAATAAT
*
3509172 AAAATTATTAAAT-TTTATAAAA-TAAAATTAA
1 AAAATTATCAAATATTT-TAAAATTAAAATTAA
3509203 AAAATTATCAAATATTTTAAAATTAAAATT
1 AAAATTATCAAATATTTTAAAATTAAAATT
3509233 TTTATTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 17 0.63
32 10 0.37
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (32 bp):
AAAATTATCAAATATTTTAAAATTAAAATTAA
Found at i:3509537 original size:20 final size:20
Alignment explanation
Indices: 3509481--3509541 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
3509471 TAATATTATA
*
3509481 AATAAAAA-TTATAATTATAT
1 AATAAAAATTTATAAATAT-T
* *
3509501 AATTAAAATTCATAAATATT
1 AATAAAAATTTATAAATATT
*
3509521 AATAAAAATTTAAAAAT-TT
1 AATAAAAATTTATAAATATT
3509540 AA
1 AA
3509542 GTTTGTTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
19 4 0.12
20 22 0.65
21 8 0.24
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAAAAATTTATAAATATT
Found at i:3510900 original size:29 final size:30
Alignment explanation
Indices: 3510865--3510922 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
3510855 TTTAATTTTG
**
3510865 TAAATAATTTTTTATATTTTAATT-ATATC
1 TAAATAAAATTTTATATTTTAATTCATATC
*
3510894 TAAATAAAATTTTATCTTTTAATTCATAT
1 TAAATAAAATTTTATATTTTAATTCATAT
3510923 AAAATTTCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (30 bp):
TAAATAAAATTTTATATTTTAATTCATATC
Found at i:3515840 original size:2 final size:2
Alignment explanation
Indices: 3515835--3515871 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3515825 TTTTGTGTTT
*
3515835 TG TG TG TG TG TG TG TG TG TG TG TG CG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
3515872 AATGGACCTT
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:0.00, C:0.03, G:0.49, T:0.49
Consensus pattern (2 bp):
TG
Found at i:3524445 original size:14 final size:14
Alignment explanation
Indices: 3524426--3524452 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3524416 TTTCATTTAA
3524426 TAAAATTATTATTT
1 TAAAATTATTATTT
3524440 TAAAATTATTATT
1 TAAAATTATTATT
3524453 CTTTTAAAGT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TAAAATTATTATTT
Found at i:3525294 original size:2 final size:2
Alignment explanation
Indices: 3525287--3525339 Score: 56
Period size: 2 Copynumber: 27.0 Consensus size: 2
3525277 ACTCAAGTTT
*
3525287 TA TA TA TA TA TA TA TG TA TA -A GT- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* *
3525328 TG TA TG TA TA TA
1 TA TA TA TA TA TA
3525340 ATCTCAAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3526101 original size:22 final size:22
Alignment explanation
Indices: 3526073--3526131 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
3526063 ACTAATATTA
*
3526073 ATTTATATTTATATATT-TTAT
1 ATTTATATTTATATATTATAAT
3526094 ATATTATATTTATAT-TTATAAT
1 AT-TTATATTTATATATTATAAT
3526116 ATTATATATTTATATA
1 ATT-TATATTTATATA
3526132 AAGTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 5 0.15
22 28 0.85
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTTATATTTATATATTATAAT
Found at i:3526106 original size:28 final size:27
Alignment explanation
Indices: 3526067--3526130 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 27
3526057 TAAATTACTA
*
3526067 ATATTA-ATTTATATTTATATATTTTAT
1 ATATTATATTTATATTTATA-ATATTAT
3526094 ATATTATATTTATATTTATAATATTAT
1 ATATTATATTTATATTTATAATATTAT
3526121 ATATTTATAT
1 ATA-TTATAT
3526131 AAAGTTTAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
27 15 0.44
28 19 0.56
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (27 bp):
ATATTATATTTATATTTATAATATTAT
Found at i:3528318 original size:2 final size:2
Alignment explanation
Indices: 3528311--3528338 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3528301 GTTTATTCAC
3528311 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
3528339 TTGCGTGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3528689 original size:17 final size:18
Alignment explanation
Indices: 3528669--3528702 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3528659 AAATTAAAAA
3528669 AATTA-AAATTTTATTTG
1 AATTATAAATTTTATTTG
*
3528686 AATTATAATTTTTATTT
1 AATTATAAATTTTATTT
3528703 AGTTTTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
AATTATAAATTTTATTTG
Found at i:3528786 original size:21 final size:23
Alignment explanation
Indices: 3528760--3528803 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3528750 TATTTAATAT
*
3528760 AATTTAT-ATT-TTTAAGTTAAA
1 AATTTATAATTATTTAAATTAAA
3528781 AATTTATAATTATTTAAATTAAA
1 AATTTATAATTATTTAAATTAAA
3528804 TTAAATGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 3 0.15
23 10 0.50
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
AATTTATAATTATTTAAATTAAA
Found at i:3530055 original size:16 final size:17
Alignment explanation
Indices: 3530034--3530069 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
3530024 GAACATATTT
3530034 AAATATATAA-TTTTTA
1 AAATATATAATTTTTTA
3530050 AAATATATAATTTTTTA
1 AAATATATAATTTTTTA
3530067 AAA
1 AAA
3530070 AAAACAGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATATATAATTTTTTA
Found at i:3531687 original size:17 final size:18
Alignment explanation
Indices: 3531654--3531704 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
3531644 ATATATTACG
3531654 TAAATATAAACATAAAATTA
1 TAAATAT-AA-ATAAAATTA
* *
3531674 TAAA-ATATATAAAATTT
1 TAAATATAAATAAAATTA
3531691 TAAATATAAATAAA
1 TAAATATAAATAAA
3531705 TACATAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 12 0.44
18 9 0.33
19 2 0.07
20 4 0.15
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAATATAAATAAAATTA
Found at i:3531754 original size:28 final size:28
Alignment explanation
Indices: 3531695--3531749 Score: 78
Period size: 26 Copynumber: 2.0 Consensus size: 28
3531685 AAATTTTAAA
3531695 TATAAATAAATACATAAATTAAATTTAT
1 TATAAATAAATACATAAATTAAATTTAT
* *
3531723 TATAAATAAA-A-ATATATTATATTTAT
1 TATAAATAAATACATAAATTAAATTTAT
3531749 T
1 T
3531750 GTATATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 14 0.56
27 1 0.04
28 10 0.40
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (28 bp):
TATAAATAAATACATAAATTAAATTTAT
Found at i:3533376 original size:19 final size:20
Alignment explanation
Indices: 3533327--3533376 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
3533317 TAACAGACCT
*
3533327 ATTAAATTTAATTTAAATTT
1 ATTAAATTTAATTTAAATTA
* * *
3533347 ATAAAAATTAA-TTCAATTA
1 ATTAAATTTAATTTAAATTA
3533366 ATTAAATTTAA
1 ATTAAATTTAA
3533377 ATTTCACTCA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
ATTAAATTTAATTTAAATTA
Found at i:3534021 original size:13 final size:14
Alignment explanation
Indices: 3534000--3534029 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
3533990 AAATTTTGAT
3534000 ATTGAATTAATTTA
1 ATTGAATTAATTTA
3534014 ATTG-ATTAATTTA
1 ATTGAATTAATTTA
3534027 ATT
1 ATT
3534030 AAAAAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (14 bp):
ATTGAATTAATTTA
Found at i:3534250 original size:16 final size:16
Alignment explanation
Indices: 3534231--3534265 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3534221 TAATAAATTT
3534231 TAATATATTAAAATAA
1 TAATATATTAAAATAA
* *
3534247 TAATGTATTAATATAA
1 TAATATATTAAAATAA
3534263 TAA
1 TAA
3534266 CTTTGTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (16 bp):
TAATATATTAAAATAA
Found at i:3540428 original size:2 final size:2
Alignment explanation
Indices: 3540421--3540449 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3540411 ATGACCCTAG
3540421 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
3540450 ATATATATAT
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:3541012 original size:11 final size:11
Alignment explanation
Indices: 3540957--3541044 Score: 53
Period size: 11 Copynumber: 8.5 Consensus size: 11
3540947 CACTAAAATT
3540957 TTTAAATTTAA
1 TTTAAATTTAA
*
3540968 TTTGAATTTAA
1 TTTAAATTTAA
* *
3540979 -TTAGTATTTAT
1 TTTA-AATTTAA
*
3540990 TTTTAA---AA
1 TTTAAATTTAA
3540998 TTTAAATTTAA
1 TTTAAATTTAA
* *
3541009 TTTAAAATAAA
1 TTTAAATTTAA
**
3541020 AATAAATTT-A
1 TTTAAATTTAA
3541030 TTTAAATTT-A
1 TTTAAATTTAA
3541040 TTTAA
1 TTTAA
3541045 TAAAAATAAA
Statistics
Matches: 56, Mismatches: 16, Indels: 11
0.67 0.19 0.13
Matches are distributed among these distances:
8 6 0.11
10 16 0.29
11 32 0.57
12 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:3541047 original size:29 final size:31
Alignment explanation
Indices: 3540997--3541057 Score: 99
Period size: 29 Copynumber: 2.0 Consensus size: 31
3540987 TATTTTTAAA
3540997 ATTTAAATTTAATTTAAAATAAAAATAAATTT
1 ATTTAAATTTAATTT-AAATAAAAATAAATTT
3541029 ATTTAAATTT-ATTT-AATAAAAATAAATTT
1 ATTTAAATTTAATTTAAATAAAAATAAATTT
3541058 TAATTTTACA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 15 0.52
31 4 0.14
32 10 0.34
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (31 bp):
ATTTAAATTTAATTTAAATAAAAATAAATTT
Found at i:3541320 original size:16 final size:17
Alignment explanation
Indices: 3541299--3541333 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3541289 TTGGTTTAGT
3541299 AAAA-TTAAATATTATA
1 AAAATTTAAATATTATA
*
3541315 AAAATTTAAATATTTTA
1 AAAATTTAAATATTATA
3541332 AA
1 AA
3541334 GTAATTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAATTTAAATATTATA
Found at i:3541728 original size:13 final size:13
Alignment explanation
Indices: 3541691--3541739 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
3541681 ATTATTAAAT
3541691 ATATATAAATATTA
1 ATATATAAA-ATTA
*
3541705 ATATAAAAAATTA
1 ATATATAAAATTA
* *
3541718 ATATTTAAAATAA
1 ATATATAAAATTA
*
3541731 ATAAATAAA
1 ATATATAAA
3541740 TTTTTGAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
13 21 0.72
14 8 0.28
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
ATATATAAAATTA
Found at i:3541730 original size:20 final size:20
Alignment explanation
Indices: 3541698--3541736 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3541688 AATATATATA
*
3541698 AATATTAATATAAA-AAATT
1 AATATTAAAATAAATAAATT
3541717 AATATTTAAAATAAATAAAT
1 AATA-TTAAAATAAATAAAT
3541737 AAATTTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 9 0.53
21 4 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AATATTAAAATAAATAAATT
Found at i:3542140 original size:13 final size:13
Alignment explanation
Indices: 3542124--3542148 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3542114 TTCAATTTCT
3542124 TTTTTTATTTTTA
1 TTTTTTATTTTTA
3542137 TTTTTTATTTTT
1 TTTTTTATTTTT
3542149 TGAATTTGTT
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:3547644 original size:14 final size:14
Alignment explanation
Indices: 3547612--3547653 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
3547602 AATAAAAATA
3547612 TTAAATTAATAAAGA-
1 TTAAATT-ATAAA-AC
*
3547627 TTAAATTTTAAAAC
1 TTAAATTATAAAAC
3547641 TTAAATTATAAAA
1 TTAAATTATAAAA
3547654 AATTTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 1 0.04
14 16 0.67
15 7 0.29
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (14 bp):
TTAAATTATAAAAC
Found at i:3548410 original size:20 final size:19
Alignment explanation
Indices: 3548341--3548411 Score: 60
Period size: 20 Copynumber: 3.8 Consensus size: 19
3548331 TTTTTTAAAT
*
3548341 ATAAAAAATATAATATATAC
1 ATAAAAAATATAA-ATATAA
3548361 ATAAAAAA-ATTAAA-A-AA
1 ATAAAAAATA-TAAATATAA
**
3548378 AT-AAGTATATAAATATAA
1 ATAAAAAATATAAATATAA
3548396 ATAAAAAATTATAAAT
1 ATAAAAAA-TATAAAT
3548412 TTATAAAAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
16 7 0.17
17 5 0.12
18 5 0.12
19 5 0.12
20 18 0.45
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.28
Consensus pattern (19 bp):
ATAAAAAATATAAATATAA
Found at i:3549002 original size:14 final size:14
Alignment explanation
Indices: 3548980--3549009 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3548970 AATCAAACTA
*
3548980 ATGTTTGTGTGTAT
1 ATGTGTGTGTGTAT
3548994 ATGTGTGTGTGTAT
1 ATGTGTGTGTGTAT
3549008 AT
1 AT
3549010 ATCGTTCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.30, T:0.53
Consensus pattern (14 bp):
ATGTGTGTGTGTAT
Found at i:3551496 original size:2 final size:2
Alignment explanation
Indices: 3551489--3551515 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3551479 TCAAATTTTG
3551489 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
3551516 AAATCTTTCT
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:3552465 original size:2 final size:2
Alignment explanation
Indices: 3552458--3552488 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3552448 TTATTACGTT
3552458 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 T
3552489 TTTACAGTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3555699 original size:14 final size:13
Alignment explanation
Indices: 3555680--3555718 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
3555670 TTTATTCAAT
*
3555680 TATTTATTTATTTC
1 TATTTATTT-TATC
3555694 TATTTATATTTATC
1 TATTTAT-TTTATC
3555708 TATTTATTTTA
1 TATTTATTTTA
3555719 GATATAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 4 0.17
14 17 0.74
15 2 0.09
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (13 bp):
TATTTATTTTATC
Found at i:3556956 original size:48 final size:48
Alignment explanation
Indices: 3556899--3556992 Score: 188
Period size: 48 Copynumber: 2.0 Consensus size: 48
3556889 GTGAAGTAGT
3556899 AAGTACCCAGAAACAAGAAAAGATCGTTTTTATAGTGAAAAAAAATCA
1 AAGTACCCAGAAACAAGAAAAGATCGTTTTTATAGTGAAAAAAAATCA
3556947 AAGTACCCAGAAACAAGAAAAGATCGTTTTTATAGTGAAAAAAAAT
1 AAGTACCCAGAAACAAGAAAAGATCGTTTTTATAGTGAAAAAAAAT
3556993 ATCAAACCTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.52, C:0.12, G:0.15, T:0.21
Consensus pattern (48 bp):
AAGTACCCAGAAACAAGAAAAGATCGTTTTTATAGTGAAAAAAAATCA
Found at i:3557992 original size:29 final size:29
Alignment explanation
Indices: 3557938--3558027 Score: 76
Period size: 30 Copynumber: 3.1 Consensus size: 29
3557928 TAAGCATGCA
*
3557938 AAATGTAC-AAAATTT-TTTTATAATATAAT
1 AAATATACAAAAATTTATTTT-T-ATATAAT
3557967 AAATATACAAAAATTTATTTTTATATAAT
1 AAATATACAAAAATTTATTTTTATATAAT
*** * * *
3557996 TTTTATATAAATAGTTTATTATTATATAAT
1 AAATATACAAA-AATTTATTTTTATATAAT
3558026 AA
1 AA
3558028 TATCAATTAA
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
29 21 0.43
30 24 0.49
31 4 0.08
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (29 bp):
AAATATACAAAAATTTATTTTTATATAAT
Found at i:3558044 original size:18 final size:18
Alignment explanation
Indices: 3558016--3558065 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
3558006 ATAGTTTATT
3558016 ATTATAT-AATAATATCA
1 ATTATATAAATAATATCA
*
3558033 ATTA-ATTAAAT-ATAATTA
1 ATTATA-TAAATAAT-ATCA
3558051 ATTATATAAATAATA
1 ATTATATAAATAATA
3558066 AAAATAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 9
0.73 0.03 0.24
Matches are distributed among these distances:
16 1 0.04
17 7 0.26
18 16 0.59
19 3 0.11
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTATATAAATAATATCA
Found at i:3558051 original size:14 final size:15
Alignment explanation
Indices: 3558026--3558054 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3558016 ATTATATAAT
3558026 AATATCAATTAATTA
1 AATATCAATTAATTA
3558041 AATAT-AATTAATTA
1 AATATCAATTAATTA
3558055 TATAAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
AATATCAATTAATTA
Found at i:3558851 original size:5 final size:5
Alignment explanation
Indices: 3558841--3558881 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
3558831 AGAAAACATA
*
3558841 AATAT AATAT AA-AT AAT-T AATTAA AATAT AATAT AATAT AA
1 AATAT AATAT AATAT AATAT AA-TAT AATAT AATAT AATAT AA
3558882 ACATATTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
4 7 0.23
5 22 0.71
6 2 0.06
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:3558867 original size:24 final size:26
Alignment explanation
Indices: 3558840--3558932 Score: 86
Period size: 27 Copynumber: 3.7 Consensus size: 26
3558830 TAGAAAACAT
**
3558840 AAATATAATATAA-ATAATTA-ATTA
1 AAATATAATATAATATAAACATATTA
3558864 AAATATAATATAATATAAACATATTA
1 AAATATAATATAATATAAACATATTA
* * *
3558890 AAATAT-ATACAATATATAATATTTTTA
1 AAATATAATATAATATA-AACA-TATTA
*
3558917 AAATA-ATTATAATATA
1 AAATATAATATAATATA
3558933 TAAAAATATA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
24 13 0.23
25 14 0.25
26 13 0.23
27 17 0.30
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (26 bp):
AAATATAATATAATATAAACATATTA
Done.