Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 105 of 171
Found at i:33835371 original size:23 final size:22
Alignment explanation
Indices: 33835327--33835376 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
33835317 AAATTCCTGC
* *
33835327 TAAAATAAAATACAGTGGTAAAA
1 TAAAATAAAATAAAGTGCT-AAA
33835350 TAAAATAAAAGTAAAGT-CTAAA
1 TAAAATAAAA-TAAAGTGCTAAA
33835372 TAAAA
1 TAAAA
33835377 CTAGACTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 8 0.33
23 11 0.46
24 5 0.21
ACGTcount: A:0.64, C:0.04, G:0.10, T:0.22
Consensus pattern (22 bp):
TAAAATAAAATAAAGTGCTAAA
Found at i:33839247 original size:2 final size:2
Alignment explanation
Indices: 33839240--33839270 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
33839230 CTAATCTCCC
33839240 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
33839271 GAGTATACCA
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:33839367 original size:3 final size:3
Alignment explanation
Indices: 33839359--33839391 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
33839349 TGTTCTTTTA
33839359 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
33839392 TTACAACAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:33842128 original size:17 final size:17
Alignment explanation
Indices: 33842106--33842189 Score: 78
Period size: 17 Copynumber: 4.9 Consensus size: 17
33842096 ACCCATTTTT
* * *
33842106 AATTTATTTTAAGTTTG
1 AATTTATTATAAATTTA
*
33842123 AATTTAGTATAAATTTA
1 AATTTATTATAAATTTA
* *
33842140 AATTTATTGTGAATTTA
1 AATTTATTATAAATTTA
* *
33842157 AGTTTATTGTAAATTTA
1 AATTTATTATAAATTTA
*
33842174 AATTTAATTAAAAATT
1 AATTT-ATTATAAATT
33842190 AAAAAATTCC
Statistics
Matches: 54, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
17 46 0.85
18 8 0.15
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.51
Consensus pattern (17 bp):
AATTTATTATAAATTTA
Found at i:33842212 original size:24 final size:24
Alignment explanation
Indices: 33842184--33842238 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
33842174 AATTTAATTA
33842184 AAAATTAAAAAATTCCAAATGTCC
1 AAAATTAAAAAATTCCAAATGTCC
33842208 AAAATTAAAAAATTCCAAATGTCC
1 AAAATTAAAAAATTCCAAATGTCC
33842232 AAAATTA
1 AAAATTA
33842239 CAAAGTCTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.56, C:0.15, G:0.04, T:0.25
Consensus pattern (24 bp):
AAAATTAAAAAATTCCAAATGTCC
Found at i:33842912 original size:3 final size:3
Alignment explanation
Indices: 33842904--33842955 Score: 79
Period size: 3 Copynumber: 17.3 Consensus size: 3
33842894 TAAATAACAT
*
33842904 TAA TAA TAA TGA TAA TAA TAA -ATA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
33842949 TAA TAA T
1 TAA TAA T
33842956 TAAATAAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 1 0.02
3 43 0.96
4 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:33844128 original size:30 final size:28
Alignment explanation
Indices: 33844034--33844418 Score: 141
Period size: 29 Copynumber: 13.2 Consensus size: 28
33844024 CAGAAATCAT
*
33844034 ATTTTGACCCTCGAACATTCCAAAAATTAC
1 ATTTTGACCC-CAAAC-TTCCAAAAATTAC
* *
33844064 ATTTCGACCCCCAAACTTCCTAAAAATCAC
1 ATTTTGA-CCCCAAACTTCC-AAAAATTAC
*
33844094 ATTTTTGACCCCAAACTTCTCAAAAATTAT
1 A-TTTTGACCCCAAACTTC-CAAAAATTAC
**
33844124 ATTTTTGACCTTAAACTTTCC-AAAATTACC
1 A-TTTTGACCCCAAAC-TTCCAAAAATTA-C
** * **
33844154 ATTTT-ACTCCCGGA-TGTCTAAAAATTGT
1 ATTTTGAC-CCCAAACT-TCCAAAAATTAC
* **
33844182 ATTTTTAACCCCGAATTTTCCAAAAATTATC
1 A-TTTTGACCCC-AAACTTCCAAAAATTA-C
* *
33844213 ATTTT-ACCCCCGAACATCC-AAAATTACC
1 ATTTTGA-CCCCAAACTTCCAAAAATTA-C
33844241 ATTTT-ACCCCCAAACATT-CAAAAATTACC
1 ATTTTGA-CCCCAAAC-TTCCAAAAATTA-C
*
33844270 ATTTT-ACCCTCGAACATT-CAAAAATTACC
1 ATTTTGACCC-CAAAC-TTCCAAAAATTA-C
* *
33844299 ATTTT-ACCCTC-GAGTGTCCAAAAATTATC
1 ATTTTGACCC-CAAACT-TCCAAAAATTA-C
* * *
33844328 ATTTTGCCCCCGAAGTGTCC-AAAATTACC
1 ATTTTGACCCCAAACT-TCCAAAAATTA-C
* *
33844357 ATTTTG-CCCTCGAAGTGTCC-AAAATTACC
1 ATTTTGACCC-CAAACT-TCCAAAAATTA-C
* * * *
33844386 ATTTTGCCCCCGAGCATCCAAAAATTAC
1 ATTTTGACCCCAAACTTCCAAAAATTAC
*
33844414 GTTTT
1 ATTTT
33844419 TGACACCGTT
Statistics
Matches: 290, Mismatches: 40, Indels: 52
0.76 0.10 0.14
Matches are distributed among these distances:
27 2 0.01
28 44 0.15
29 145 0.50
30 85 0.29
31 14 0.05
ACGTcount: A:0.34, C:0.27, G:0.07, T:0.32
Consensus pattern (28 bp):
ATTTTGACCCCAAACTTCCAAAAATTAC
Found at i:33844149 original size:29 final size:30
Alignment explanation
Indices: 33844027--33844151 Score: 98
Period size: 30 Copynumber: 4.2 Consensus size: 30
33844017 AACTATCCAG
* *
33844027 AAATCATA-TTTTGACCCTCGAACATTC-CAA
1 AAATTATATTTTTGACCC-CAAAC-TTCTCAA
* *
33844057 AAATTACA-TTTCGACCCCCAAACTTC-CTAA
1 AAATTATATTTTTGA-CCCCAAACTTCTC-AA
* *
33844087 AAATCACATTTTTGACCCCAAACTTCTCAA
1 AAATTATATTTTTGACCCCAAACTTCTCAA
** *
33844117 AAATTATATTTTTGACCTTAAACTT-TCCA
1 AAATTATATTTTTGACCCCAAACTTCTCAA
33844146 AAATTA
1 AAATTA
33844152 CCATTTTACT
Statistics
Matches: 80, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
29 13 0.16
30 58 0.73
31 9 0.11
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.33
Consensus pattern (30 bp):
AAATTATATTTTTGACCCCAAACTTCTCAA
Found at i:33844221 original size:29 final size:29
Alignment explanation
Indices: 33844145--33844413 Score: 189
Period size: 29 Copynumber: 9.3 Consensus size: 29
33844135 TAAACTTTCC
* *
33844145 AAAATTACCATTTTACTCCCGGA-TGTCTA
1 AAAATTACCATTTTAC-CCCGAAGTGTCCA
** * *
33844174 AAAATT-GTATTTTTAACCCCGAATTTTCCA
1 AAAATTACCA-TTTT-ACCCCGAAGTGTCCA
* **
33844204 AAAATTATCATTTTACCCCCGAA-CATCC-
1 AAAATTACCATTTTA-CCCCGAAGTGTCCA
* *** *
33844232 AAAATTACCATTTTACCCCCAAACATTCA
1 AAAATTACCATTTTACCCCGAAGTGTCCA
*
33844261 AAAATTACCATTTTACCCTCGAACAT-T-CA
1 AAAATTACCATTTTACCC-CGAA-GTGTCCA
33844290 AAAATTACCATTTTACCCTCG-AGTGTCCA
1 AAAATTACCATTTTACCC-CGAAGTGTCCA
* *
33844319 AAAATTATCATTTTGCCCCCGAAGTGTCC-
1 AAAATTACCATTTT-ACCCCGAAGTGTCCA
*
33844348 AAAATTACCATTTTGCCCTCGAAGTGTCC-
1 AAAATTACCATTTTACCC-CGAAGTGTCCA
* **
33844377 AAAATTACCATTTTGCCCCCG-AGCATCCA
1 AAAATTACCATTTT-ACCCCGAAGTGTCCA
33844406 AAAATTAC
1 AAAATTAC
33844414 GTTTTTGACA
Statistics
Matches: 202, Mismatches: 22, Indels: 32
0.79 0.09 0.12
Matches are distributed among these distances:
27 7 0.03
28 29 0.14
29 124 0.61
30 40 0.20
31 2 0.01
ACGTcount: A:0.34, C:0.28, G:0.08, T:0.31
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCGAAGTGTCCA
Found at i:33844275 original size:87 final size:88
Alignment explanation
Indices: 33844145--33844413 Score: 264
Period size: 87 Copynumber: 3.1 Consensus size: 88
33844135 TAAACTTTCC
* ** ** *
33844145 AAAATTACCATTTTACTCCC-GGATGTCTAAAAATT-GTATTTTTAACCC-CGAATTTTCCAAAA
1 AAAATTACCATTTTACCCCCAAAATGTC-AAAAATTACCA-TTTT-ACCCTCGAACTTTCCAAAA
* *
33844207 ATTATCATTTTACCCCCGAACATCC-
63 ATTACCATTTTACCCCCGAGCATCCA
*
33844232 AAAATTACCATTTTACCCCCAAACAT-TCAAAAATTACCATTTTACCCTCGAACATT-CAAAAAT
1 AAAATTACCATTTTACCCCCAAA-ATGTCAAAAATTACCATTTTACCCTCGAACTTTCCAAAAAT
* **
33844295 TACCATTTTACCCTCGAGTGTCCA
65 TACCATTTTACCCCCGAGCATCCA
* * * * * * * *
33844319 AAAATTATCATTTTGCCCCCGAAGTGTCCAAAATTACCATTTTGCCCTCGAAGTGTCC-AAAATT
1 AAAATTACCATTTTACCCCCAAAATGTCAAAAATTACCATTTTACCCTCGAACTTTCCAAAAATT
*
33844383 ACCATTTTGCCCCCGAGCATCCA
66 ACCATTTTACCCCCGAGCATCCA
33844406 AAAATTAC
1 AAAATTAC
33844414 GTTTTTGACA
Statistics
Matches: 149, Mismatches: 26, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
86 30 0.20
87 113 0.76
88 4 0.03
89 2 0.01
ACGTcount: A:0.34, C:0.28, G:0.08, T:0.31
Consensus pattern (88 bp):
AAAATTACCATTTTACCCCCAAAATGTCAAAAATTACCATTTTACCCTCGAACTTTCCAAAAATT
ACCATTTTACCCCCGAGCATCCA
Found at i:33844420 original size:29 final size:29
Alignment explanation
Indices: 33844200--33844413 Score: 209
Period size: 29 Copynumber: 7.4 Consensus size: 29
33844190 CCCCGAATTT
* *
33844200 TCCAAAAATTATCATTTTACCCCCGAACA
1 TCCAAAAATTACCATTTTACCCCCGAGCA
* *
33844229 TCC-AAAATTACCATTTTACCCCCAAACA
1 TCCAAAAATTACCATTTTACCCCCGAGCA
* * *
33844257 TTCAAAAATTACCATTTTACCCTCGAACA
1 TCCAAAAATTACCATTTTACCCCCGAGCA
* * **
33844286 TTCAAAAATTACCATTTTACCCTCGAGTG
1 TCCAAAAATTACCATTTTACCCCCGAGCA
* * **
33844315 TCCAAAAATTATCATTTTGCCCCCGAAGTG
1 TCCAAAAATTACCATTTTACCCCCG-AGCA
* * **
33844345 TCC-AAAATTACCATTTTGCCCTCGAAGTG
1 TCCAAAAATTACCATTTTACCCCCG-AGCA
*
33844374 TCC-AAAATTACCATTTTGCCCCCGAGCA
1 TCCAAAAATTACCATTTTACCCCCGAGCA
33844402 TCCAAAAATTAC
1 TCCAAAAATTAC
33844414 GTTTTTGACA
Statistics
Matches: 165, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
28 30 0.18
29 128 0.78
30 7 0.04
ACGTcount: A:0.34, C:0.29, G:0.07, T:0.29
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTACCCCCGAGCA
Found at i:33844420 original size:58 final size:57
Alignment explanation
Indices: 33844204--33844413 Score: 235
Period size: 58 Copynumber: 3.6 Consensus size: 57
33844194 GAATTTTCCA
* * * * *
33844204 AAAATTATCATTTTACCCCCGAACATCCAAAATTACCATTTTACCCCCAAACAT-TCA
1 AAAATTACCATTTTACCCCCGAACATCCAAAATTACCATTTTACCCTCGAA-GTGTCC
* *
33844261 AAAATTACCATTTTACCCTCGAACATTCAAAAATTACCATTTTACCCTCG-AGTGTCC
1 AAAATTACCATTTTACCCCCGAACA-TCCAAAATTACCATTTTACCCTCGAAGTGTCC
* * ** *
33844318 AAAAATTATCATTTTGCCCCCGAAGTGTCCAAAATTACCATTTTGCCCTCGAAGTGTCC
1 -AAAATTACCATTTTACCCCCGAA-CATCCAAAATTACCATTTTACCCTCGAAGTGTCC
* *
33844377 AAAATTACCATTTTGCCCCCGAGCATCCAAAAATTAC
1 AAAATTACCATTTTACCCCCGAACATCC-AAAATTAC
33844414 GTTTTTGACA
Statistics
Matches: 129, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
56 1 0.01
57 29 0.22
58 92 0.71
59 7 0.05
ACGTcount: A:0.34, C:0.29, G:0.08, T:0.29
Consensus pattern (57 bp):
AAAATTACCATTTTACCCCCGAACATCCAAAATTACCATTTTACCCTCGAAGTGTCC
Found at i:33848568 original size:12 final size:12
Alignment explanation
Indices: 33848543--33848601 Score: 59
Period size: 13 Copynumber: 4.8 Consensus size: 12
33848533 ATAGCAAACA
33848543 TTTT-TTTTCTTC
1 TTTTCTTTTC-TC
33848555 TTTTCTTTTCTC
1 TTTTCTTTTCTC
*
33848567 TTTTCTTTTTTTC
1 TTTTC-TTTTCTC
33848580 TTTAT-TTTTCTC
1 TTT-TCTTTTCTC
33848592 ATTTTCTTTT
1 -TTTTCTTTT
33848602 TTCAAGTGAC
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
12 18 0.45
13 21 0.52
14 1 0.03
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTCTTTTCTC
Found at i:33848580 original size:25 final size:26
Alignment explanation
Indices: 33848541--33848603 Score: 87
Period size: 25 Copynumber: 2.5 Consensus size: 26
33848531 TTATAGCAAA
*
33848541 CATTTT-TTTTCTTCTTT-TCTTTTCT
1 CATTTTCTTTTTTTCTTTAT-TTTTCT
33848566 C-TTTTCTTTTTTTCTTTATTTTTCT
1 CATTTTCTTTTTTTCTTTATTTTTCT
33848591 CATTTTCTTTTTT
1 CATTTTCTTTTTT
33848604 CAAGTGACTG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
24 4 0.12
25 18 0.53
26 12 0.35
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (26 bp):
CATTTTCTTTTTTTCTTTATTTTTCT
Found at i:33858597 original size:21 final size:20
Alignment explanation
Indices: 33858557--33858601 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 20
33858547 CTAGATTTAT
33858557 CGATACAAGTATGATTTCTAC
1 CGATACAAGTATGA-TTCTAC
33858578 CGATACAAGTCATGCA-TCTAC
1 CGATACAAGT-ATG-ATTCTAC
33858599 CGA
1 CGA
33858602 CACCAAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 18 0.82
22 3 0.14
23 1 0.05
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (20 bp):
CGATACAAGTATGATTCTAC
Found at i:33866223 original size:21 final size:21
Alignment explanation
Indices: 33866199--33866261 Score: 56
Period size: 21 Copynumber: 2.9 Consensus size: 21
33866189 CGATATAAGC
*
33866199 ATACAAACTACCGATACATCA
1 ATACAAACTACCGATACAGCA
33866220 ATACTATTAACTACCGATACTAGCA
1 ATAC-A--AACTACCGATAC-AGCA
* *
33866245 ATTC-AACTATCGATACA
1 ATACAAACTACCGATACA
33866262 ACTCAAGTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
20 1 0.03
21 15 0.43
22 1 0.03
24 12 0.34
25 6 0.17
ACGTcount: A:0.43, C:0.25, G:0.06, T:0.25
Consensus pattern (21 bp):
ATACAAACTACCGATACAGCA
Found at i:33872712 original size:30 final size:30
Alignment explanation
Indices: 33872664--33872721 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
33872654 TTTGTGGTCC
* ** *
33872664 AAGTGTAAATATTTAAAATGTGAGGGGTTA
1 AAGTATAAATATAAAAAATGTGAAGGGTTA
*
33872694 AAGTATAAATATAAAAAATTTGAAGGGT
1 AAGTATAAATATAAAAAATGTGAAGGGT
33872722 CAATAGTGCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.22, T:0.31
Consensus pattern (30 bp):
AAGTATAAATATAAAAAATGTGAAGGGTTA
Found at i:33874559 original size:6 final size:6
Alignment explanation
Indices: 33874534--33874572 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
33874524 ACAATTCATA
* * *
33874534 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
33874573 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:33882629 original size:25 final size:24
Alignment explanation
Indices: 33882601--33882653 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
33882591 ATTTTATGGG
*
33882601 TTTT-AATTTCTGGGTTAATGGAATT
1 TTTTAAATTTCT-CGTTAAT-GAATT
33882626 TTTTAAATTTCTCGTTAATGAATT
1 TTTTAAATTTCTCGTTAATGAATT
33882650 TTTT
1 TTTT
33882654 GGGTAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 9 0.35
25 10 0.38
26 7 0.27
ACGTcount: A:0.25, C:0.06, G:0.13, T:0.57
Consensus pattern (24 bp):
TTTTAAATTTCTCGTTAATGAATT
Found at i:33890749 original size:29 final size:31
Alignment explanation
Indices: 33890687--33890762 Score: 102
Period size: 29 Copynumber: 2.5 Consensus size: 31
33890677 TTAAATTATT
* *
33890687 AATAGTAAAATTATATTTTAATTTTTTTAAA
1 AATAATAAAATTATAATTTAATTTTTTTAAA
33890718 AATAATAAAATT-TAATTTAA-TTTTTTAAA
1 AATAATAAAATTATAATTTAATTTTTTTAAA
* *
33890747 AATTATAAAAATATAA
1 AATAATAAAATTATAA
33890763 ACTATTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 19 0.47
30 10 0.25
31 11 0.28
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (31 bp):
AATAATAAAATTATAATTTAATTTTTTTAAA
Found at i:33901536 original size:17 final size:16
Alignment explanation
Indices: 33901514--33901546 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
33901504 AAAAAATCAG
33901514 AAAAAAATGCAAAAGAA
1 AAAAAAATG-AAAAGAA
33901531 AAAAAAATGAAAAGAA
1 AAAAAAATGAAAAGAA
33901547 TGTGTTTCGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.79, C:0.03, G:0.12, T:0.06
Consensus pattern (16 bp):
AAAAAAATGAAAAGAA
Found at i:33903689 original size:25 final size:25
Alignment explanation
Indices: 33903661--33903709 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
33903651 TTCTATGAAA
33903661 TTCGTTTTAATACAGGGTTTATTTG
1 TTCGTTTTAATACAGGGTTTATTTG
33903686 TTCGTTTTAATACAGGGTTTATTT
1 TTCGTTTTAATACAGGGTTTATTT
33903710 ATTTATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.20, C:0.08, G:0.18, T:0.53
Consensus pattern (25 bp):
TTCGTTTTAATACAGGGTTTATTTG
Found at i:33903807 original size:5 final size:5
Alignment explanation
Indices: 33903796--33903827 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
33903786 TGTGATGGAC
*
33903796 TTCCT TTTCT TTCCT TTCCT TTCCT TTCCT TT
1 TTCCT TTCCT TTCCT TTCCT TTCCT TTCCT TT
33903828 TTTTTTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (5 bp):
TTCCT
Found at i:33904158 original size:19 final size:18
Alignment explanation
Indices: 33904136--33904188 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
33904126 CATGCTAAAT
*
33904136 TTTTAATTTTTTTATGAA
1 TTTTAATATTTTTATGAA
*
33904154 CTTTTTATAATTTTT-TGAA
1 -TTTTAAT-ATTTTTATGAA
33904173 TTTTAAATATTTTTAT
1 TTTT-AATATTTTTAT
33904189 TTTTATATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 10 0.36
19 13 0.46
20 5 0.18
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (18 bp):
TTTTAATATTTTTATGAA
Found at i:33905499 original size:22 final size:22
Alignment explanation
Indices: 33905447--33905500 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
33905437 TTTCGAATCG
33905447 AATTAATTATTAATCGAACTTT
1 AATTAATTATTAATCGAACTTT
** *
33905469 AAAAAAATTATTAATC-AATTTT
1 -AATTAATTATTAATCGAACTTT
33905491 AATTGAATTA
1 AATT-AATTA
33905501 ATTCAATTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 2 0.08
22 10 0.40
23 13 0.52
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.43
Consensus pattern (22 bp):
AATTAATTATTAATCGAACTTT
Found at i:33905522 original size:40 final size:39
Alignment explanation
Indices: 33905473--33905549 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 39
33905463 AACTTTAAAA
* *
33905473 AAATTATTAATCAATTTTAATTGAATTAATTC-AATTAACT
1 AAATAATTAATCAAATTTAATTG-ATTAA-TCAAATTAACT
* *
33905513 AAATAATTAATTAAATTTGATTGATTAATCAAATTAA
1 AAATAATTAATCAAATTTAATTGATTAATCAAATTAA
33905550 TTTAATTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
38 2 0.06
39 11 0.34
40 19 0.59
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (39 bp):
AAATAATTAATCAAATTTAATTGATTAATCAAATTAACT
Found at i:33911384 original size:19 final size:18
Alignment explanation
Indices: 33911346--33911402 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
33911336 GATGTTTAAT
*
33911346 TAATTTCTAATAATTATTA
1 TAATTT-TAATAATTTTTA
*
33911365 TAAATTTTAATATTTTTTA
1 T-AATTTTAATAATTTTTA
*
33911384 TAATTTTCATAATTTTTA
1 TAATTTTAATAATTTTTA
33911402 T
1 T
33911403 GTTTAAATCT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 16 0.48
19 12 0.36
20 5 0.15
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (18 bp):
TAATTTTAATAATTTTTA
Found at i:33912644 original size:12 final size:12
Alignment explanation
Indices: 33912624--33912667 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
33912614 TCACGAACAA
*
33912624 GCTCATTTATTG
1 GCTCGTTTATTG
**
33912636 GCTCGTTTATAA
1 GCTCGTTTATTG
33912648 GCTCGTTTATTG
1 GCTCGTTTATTG
*
33912660 ACTCGTTT
1 GCTCGTTT
33912668 GTAGCTTGTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.16, C:0.18, G:0.18, T:0.48
Consensus pattern (12 bp):
GCTCGTTTATTG
Found at i:33912678 original size:23 final size:24
Alignment explanation
Indices: 33912622--33912681 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
33912612 ATTCACGAAC
* *
33912622 AAGCTCATTTATTGGCTCGTTTAT
1 AAGCTCGTTTATTGACTCGTTTAT
*
33912646 AAGCTCGTTTATTGACTCGTTTGT
1 AAGCTCGTTTATTGACTCGTTTAT
*
33912670 -AGCTTGTTTATT
1 AAGCTCGTTTATT
33912682 TATTAATGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 11 0.34
24 21 0.66
ACGTcount: A:0.18, C:0.15, G:0.18, T:0.48
Consensus pattern (24 bp):
AAGCTCGTTTATTGACTCGTTTAT
Found at i:33928709 original size:26 final size:26
Alignment explanation
Indices: 33928657--33928710 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
33928647 ACTTATGAGT
** ***
33928657 AAAATAAATTGTTTTTTTTTCTTTAA
1 AAAATAAATTGTTTTTTAATAAGTAA
33928683 AAAATAAATTGTTTTTTAATAAGTAA
1 AAAATAAATTGTTTTTTAATAAGTAA
33928709 AA
1 AA
33928711 TGAATAGTTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (26 bp):
AAAATAAATTGTTTTTTAATAAGTAA
Found at i:33928895 original size:17 final size:17
Alignment explanation
Indices: 33928873--33928926 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
33928863 TAAGTTTCTA
33928873 AAATTTATTTGAATTTG
1 AAATTTATTTGAATTTG
* * *
33928890 AAA-TT-TTAGAA-CTA
1 AAATTTATTTGAATTTG
*
33928904 AAATTTATTTGAATTCG
1 AAATTTATTTGAATTTG
33928921 AAATTT
1 AAATTT
33928927 TGTTCTAAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 6
0.68 0.17 0.15
Matches are distributed among these distances:
14 4 0.15
15 7 0.26
16 7 0.26
17 9 0.33
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (17 bp):
AAATTTATTTGAATTTG
Found at i:33928937 original size:30 final size:31
Alignment explanation
Indices: 33928868--33928939 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 31
33928858 TTCAGTAAGT
*
33928868 TTCTAAAATTTATTTGAATTTGAAATTTTAG
1 TTCTAAAATTTATTTGAATTCGAAATTTTAG
**
33928899 AACTAAAATTTATTTGAATTCGAAATTTT-G
1 TTCTAAAATTTATTTGAATTCGAAATTTTAG
33928929 TTCTAAAATTT
1 TTCTAAAATTT
33928940 CAAATTGAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 10 0.28
31 26 0.72
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.49
Consensus pattern (31 bp):
TTCTAAAATTTATTTGAATTCGAAATTTTAG
Found at i:33929113 original size:30 final size:31
Alignment explanation
Indices: 33929043--33929114 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
33929033 TTTGATTTAG
* * *
33929043 TACTTAAACTTGATATTTTTTCTTAATTTGG
1 TACTTAAACTTGACACTTTTTCTTAATTTGA
*
33929074 TATTTAAACTTGACACTTTTT-TT-ATGTTGA
1 TACTTAAACTTGACACTTTTTCTTAAT-TTGA
33929104 TACTTAAACTT
1 TACTTAAACTT
33929115 TTTGGGGTCC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 2 0.06
30 15 0.43
31 18 0.51
ACGTcount: A:0.28, C:0.11, G:0.08, T:0.53
Consensus pattern (31 bp):
TACTTAAACTTGACACTTTTTCTTAATTTGA
Found at i:33936790 original size:17 final size:17
Alignment explanation
Indices: 33936765--33936817 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
33936755 TACAACGACA
*
33936765 AATGGAAATGCAATGAC
1 AATGTAAATGCAATGAC
*
33936782 AATGTAAATGCAGTGAC
1 AATGTAAATGCAATGAC
33936799 AAT-TAAAATGCAATGAC
1 AATGT-AAATGCAATGAC
33936816 AA
1 AA
33936818 AGGGAATGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
16 1 0.03
17 31 0.97
ACGTcount: A:0.49, C:0.11, G:0.19, T:0.21
Consensus pattern (17 bp):
AATGTAAATGCAATGAC
Found at i:33936832 original size:34 final size:34
Alignment explanation
Indices: 33936770--33936839 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 34
33936760 CGACAAATGG
* *
33936770 AAATGCAATGACAATGTAAATGCAGTGACAATTA
1 AAATGCAATGACAAAGGAAATGCAGTGACAATTA
* **
33936804 AAATGCAATGACAAAGGGAATGTGGTGACAATTA
1 AAATGCAATGACAAAGGAAATGCAGTGACAATTA
33936838 AA
1 AA
33936840 TTACAGCTAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.47, C:0.10, G:0.21, T:0.21
Consensus pattern (34 bp):
AAATGCAATGACAAAGGAAATGCAGTGACAATTA
Found at i:33943398 original size:21 final size:21
Alignment explanation
Indices: 33943372--33943411 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
33943362 GTACACGATT
**
33943372 TTGATGTGGTTGCATTTGATC
1 TTGATGTGAATGCATTTGATC
33943393 TTGATGTGAATGCATTTGA
1 TTGATGTGAATGCATTTGA
33943412 GTATTGTGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.07, G:0.28, T:0.45
Consensus pattern (21 bp):
TTGATGTGAATGCATTTGATC
Found at i:33956822 original size:21 final size:22
Alignment explanation
Indices: 33956796--33956869 Score: 109
Period size: 21 Copynumber: 3.5 Consensus size: 22
33956786 GGAGTTTTTG
*
33956796 GTATCGGTAGATG-CATGACTT
1 GTATCGGTAGAAGTCATGACTT
*
33956817 GTATCGGTAAAAGTCATG-CTT
1 GTATCGGTAGAAGTCATGACTT
33956838 GTATCGGTAGAAGTCAT-ACTT
1 GTATCGGTAGAAGTCATGACTT
33956859 GTATCGGTAGA
1 GTATCGGTAGA
33956870 GCTAGCACAA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
21 44 0.92
22 4 0.08
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (22 bp):
GTATCGGTAGAAGTCATGACTT
Found at i:33957329 original size:77 final size:77
Alignment explanation
Indices: 33957202--33957368 Score: 212
Period size: 77 Copynumber: 2.2 Consensus size: 77
33957192 TATTCGTTGG
* * *
33957202 TTATCCGACTAGCACTAGGTGCAAAACATTTGTTGGTATATCTAACTAGAGCTGGGCTCACTATT
1 TTATCCGACTAGCACTAGGTGCAAAACATTTGTTGGCATATCCAACTAGAGCTAGGCTCACTATT
* *
33957267 TACATTGTCGAT
66 GACATTATCGAT
* * *
33957279 TTATCCGACTAGCA-TTGG-GCATAAAACATTTTTTGGCATATCCAACTAGAGCTAGGCTCATTA
1 TTATCCGACTAGCACTAGGTGC--AAAACATTTGTTGGCATATCCAACTAGAGCTAGGCTCACTA
* *
33957342 TTGATATTATCGGT
64 TTGACATTATCGAT
33957356 TTATCCGACTAGC
1 TTATCCGACTAGC
33957369 GCTGAGCACA
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
75 2 0.03
76 3 0.04
77 73 0.94
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.34
Consensus pattern (77 bp):
TTATCCGACTAGCACTAGGTGCAAAACATTTGTTGGCATATCCAACTAGAGCTAGGCTCACTATT
GACATTATCGAT
Found at i:33957507 original size:17 final size:17
Alignment explanation
Indices: 33957485--33957528 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
33957475 CAAGGTTGTT
33957485 ATGGAAATTGTTATAAG
1 ATGGAAATTGTTATAAG
33957502 ATGGAAATTGTTATAAG
1 ATGGAAATTGTTATAAG
*
33957519 ATGCAAATTG
1 ATGGAAATTG
33957529 GAAGTGATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.41, C:0.02, G:0.23, T:0.34
Consensus pattern (17 bp):
ATGGAAATTGTTATAAG
Found at i:33961493 original size:34 final size:33
Alignment explanation
Indices: 33961450--33961563 Score: 129
Period size: 34 Copynumber: 3.4 Consensus size: 33
33961440 AGTGTTTTTT
* *
33961450 TGTGTTGGATGGATTAGCTCTTACGAGCATTTAG
1 TGTGTTGGATGGACTAGCTCTTACAAGCATTT-G
*
33961484 TGTGTTGGATGGACTAGCTCATACAAGCATTTG
1 TGTGTTGGATGGACTAGCTCTTACAAGCATTTG
* * * *
33961517 CTGTGTTGGTTGGACTAACTCTTATATGCATTTGG
1 -TGTGTTGGATGGACTAGCTCTTACAAGCATTT-G
*
33961552 TGTGTTAGATGG
1 TGTGTTGGATGG
33961564 TTAACTGTGT
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
33 1 0.01
34 66 0.97
35 1 0.01
ACGTcount: A:0.20, C:0.12, G:0.29, T:0.39
Consensus pattern (33 bp):
TGTGTTGGATGGACTAGCTCTTACAAGCATTTG
Found at i:33962519 original size:21 final size:21
Alignment explanation
Indices: 33962457--33962511 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
33962447 GTGGATAGAC
33962457 GGGTAGCCACATGGGCGTGTT
1 GGGTAGCCACATGGGCGTGTT
*
33962478 GGGTAGCCACACGGGCGTGTT
1 GGGTAGCCACATGGGCGTGTT
33962499 GGGTAGCCACATG
1 GGGTAGCCACATG
33962512 ACCATGTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.16, C:0.22, G:0.42, T:0.20
Consensus pattern (21 bp):
GGGTAGCCACATGGGCGTGTT
Found at i:33962616 original size:20 final size:21
Alignment explanation
Indices: 33962588--33962630 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
33962578 GTAGTGAAAA
* *
33962588 TTTTCATTT-TTCCTTAAATG
1 TTTTCATTTGGTCCCTAAATG
*
33962608 TTTTGATTTGGTCCCTAAATG
1 TTTTCATTTGGTCCCTAAATG
33962629 TT
1 TT
33962631 CCTAACATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.19, C:0.14, G:0.12, T:0.56
Consensus pattern (21 bp):
TTTTCATTTGGTCCCTAAATG
Found at i:33967449 original size:34 final size:34
Alignment explanation
Indices: 33967406--33967558 Score: 209
Period size: 34 Copynumber: 4.5 Consensus size: 34
33967396 GTTATAGTGT
*
33967406 TTTGGTGTGTTGAATGGACTAGCTCTTACGAGCA
1 TTTGGTGTGTTGGATGGACTAGCTCTTACGAGCA
** *
33967440 TTTGGTGTGTCAGATGGACTAGCTTTTACGAGCA
1 TTTGGTGTGTTGGATGGACTAGCTCTTACGAGCA
*
33967474 TTTAGTGTGTTGGATGGACTAGCTCTTACGAGCA
1 TTTGGTGTGTTGGATGGACTAGCTCTTACGAGCA
* * * *
33967508 TTTGGTGTGTTGGTTGGACTGGATCTTA-TATGCA
1 TTTGGTGTGTTGGATGGACTAGCTCTTACGA-GCA
33967542 TTTGGTGTGTTGGATGG
1 TTTGGTGTGTTGGATGG
33967559 TTAACCGTGT
Statistics
Matches: 104, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
33 1 0.01
34 103 0.99
ACGTcount: A:0.18, C:0.12, G:0.32, T:0.39
Consensus pattern (34 bp):
TTTGGTGTGTTGGATGGACTAGCTCTTACGAGCA
Found at i:33973542 original size:34 final size:34
Alignment explanation
Indices: 33973504--33973656 Score: 243
Period size: 34 Copynumber: 4.5 Consensus size: 34
33973494 GTTACAATTT
*
33973504 TTTGGTGTGTTGGATGGATTAGCTCTTACGAGCA
1 TTTGGTGTGTTGGATGGACTAGCTCTTACGAGCA
*
33973538 TTTGGTGTGTTGGATGGACTAGCTTTTACGAGCA
1 TTTGGTGTGTTGGATGGACTAGCTCTTACGAGCA
* *
33973572 TTTGGTGTGTTGGTTGAACTAGCTCTTACGAGCA
1 TTTGGTGTGTTGGATGGACTAGCTCTTACGAGCA
* * *
33973606 TTTAGTGGGTTGGTTGGACTAGCTCTTACGAGCA
1 TTTGGTGTGTTGGATGGACTAGCTCTTACGAGCA
33973640 TTTGGTGTGTTGGATGG
1 TTTGGTGTGTTGGATGG
33973657 TTAACCATGT
Statistics
Matches: 108, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 108 1.00
ACGTcount: A:0.16, C:0.12, G:0.33, T:0.39
Consensus pattern (34 bp):
TTTGGTGTGTTGGATGGACTAGCTCTTACGAGCA
Found at i:33974660 original size:21 final size:21
Alignment explanation
Indices: 33974628--33974673 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
33974618 GCTCATGAGT
* *
33974628 ATGTGAGGTAGCCACATAGGC
1 ATGTGAGGTAGCCACACAGCC
33974649 ATGTG-GGATAGCCACACAGCC
1 ATGTGAGG-TAGCCACACAGCC
33974670 ATGT
1 ATGT
33974674 TTAGAGCCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.28, C:0.22, G:0.30, T:0.20
Consensus pattern (21 bp):
ATGTGAGGTAGCCACACAGCC
Found at i:33977951 original size:106 final size:107
Alignment explanation
Indices: 33977812--33978032 Score: 390
Period size: 107 Copynumber: 2.1 Consensus size: 107
33977802 TTTACTAAAT
* *
33977812 ATAATTTAACGTAATTATAATTATTAATTATAATGATTTCGTTAAATATT-AAAACATGGAAATT
1 ATAATTTAACGTAATTATAATTATTAATTATAATGATTTCGTTAAATATTAAAAAAATAGAAATT
* *
33977876 AATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCC
66 AATATCATTTTGGAAAGAATATAATGTTTTAATAAACCTTCC
33977918 ATAATTTAACGTAATTATAATTATTAATTATAATGATTTCGTTAAATATTAAAAAAATAGAAATT
1 ATAATTTAACGTAATTATAATTATTAATTATAATGATTTCGTTAAATATTAAAAAAATAGAAATT
33977983 AATATCATTTTGGAAAGAATATAATGTTTTAATAAACCTTCC
66 AATATCATTTTGGAAAGAATATAATGTTTTAATAAACCTTCC
33978025 ATATATTT
1 ATA-ATTT
33978033 CTTTAAAGGA
Statistics
Matches: 109, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
106 50 0.46
107 55 0.50
108 4 0.04
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.41
Consensus pattern (107 bp):
ATAATTTAACGTAATTATAATTATTAATTATAATGATTTCGTTAAATATTAAAAAAATAGAAATT
AATATCATTTTGGAAAGAATATAATGTTTTAATAAACCTTCC
Found at i:33978409 original size:123 final size:123
Alignment explanation
Indices: 33977962--33978399 Score: 675
Period size: 123 Copynumber: 3.6 Consensus size: 123
33977952 GATTTCGTTA
* * *
33977962 AATATTAAAAAAATAGAAATTAATATCATTTTGG-AAAGAATATAATGTTTTAATAAACCTTCCA
1 AATATTAAAAACATGGAAGTTAATATCATTTTGGAAAAG-ATATAATGTTTTAATAAACCTTCCA
33978026 TATAT-TTCTTTAAAGGAATATTTCCATTTTAATATTAGATATTATATAAAAAGAAATTG
65 TATATATT-TTTAAAGGAATATTTCCATTTTAATATTAGATATTATATAAAAAGAAATTG
* * * *
33978085 AATATTAAAAACATGGAAGTTAATATCGTTTTGGAAAAGATATAACGTTTTAATAAATCTTTCAT
1 AATATTAAAAACATGGAAGTTAATATCATTTTGGAAAAGATATAATGTTTTAATAAACCTTCCAT
*
33978150 ATATATTTTTAAAGGAATATTTCTATTTTAATATTAGATATTATATAAAAAGAAATTG
66 ATATATTTTTAAAGGAATATTTCCATTTTAATATTAGATATTATATAAAAAGAAATTG
* * *
33978208 AATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAAGATATAATGTTTTAATAAATCTTTCAT
1 AATATTAAAAACATGGAAGTTAATATCATTTTGGAAAAGATATAATGTTTTAATAAACCTTCCAT
* * *
33978273 ATATATTTTTAAAGGAATATTTCCATTTTAATATGAAATATTATATAAAAGGAAATTG
66 ATATATTTTTAAAGGAATATTTCCATTTTAATATTAGATATTATATAAAAAGAAATTG
* * *
33978331 AATATTAAAAACATGCAAGTTAATATC-TTTCTAGAAATGATATAATGTTTTAATAAACCTTCCA
1 AATATTAAAAACATGGAAGTTAATATCATTT-TGGAAAAGATATAATGTTTTAATAAACCTTCCA
33978395 TATAT
65 TATAT
33978400 TTCTCTAAAG
Statistics
Matches: 293, Mismatches: 19, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
122 3 0.01
123 284 0.97
124 6 0.02
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (123 bp):
AATATTAAAAACATGGAAGTTAATATCATTTTGGAAAAGATATAATGTTTTAATAAACCTTCCAT
ATATATTTTTAAAGGAATATTTCCATTTTAATATTAGATATTATATAAAAAGAAATTG
Found at i:33981972 original size:24 final size:25
Alignment explanation
Indices: 33981898--33982065 Score: 162
Period size: 24 Copynumber: 6.6 Consensus size: 25
33981888 ATAAATTTTA
* * *
33981898 CGAAAGAGCGACATTCTGTTTGGCT
1 CGAAAGAGCGATATTCTATCTGGCT
*
33981923 CGTAAGAGCGATATTCTAAATTCTGGCT
1 CGAAAGAGCGATATTCT--A-TCTGGCT
*
33981951 CAAAAGAGCGAT-TTCTATCTGGCT
1 CGAAAGAGCGATATTCTATCTGGCT
33981975 CGAAAGAGCGAT-TTCTATCTGGCT
1 CGAAAGAGCGATATTCTATCTGGCT
*
33981999 CGTAAGAGCGATATTCTGAATTCTGGCT
1 CGAAAGAGCGATATTCT--A-TCTGGCT
* * * *
33982027 TGAAAGAGCAATATTCTGTATGGCT
1 CGAAAGAGCGATATTCTATCTGGCT
*
33982052 CGTAAGAGC-ATATT
1 CGAAAGAGCGATATT
33982066 TCTGTCTAGA
Statistics
Matches: 121, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
24 46 0.38
25 33 0.27
27 5 0.04
28 37 0.31
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (25 bp):
CGAAAGAGCGATATTCTATCTGGCT
Found at i:33982025 original size:76 final size:78
Alignment explanation
Indices: 33981898--33982060 Score: 222
Period size: 76 Copynumber: 2.1 Consensus size: 78
33981888 ATAAATTTTA
* * *
33981898 CGAAAGAGCGACATTCTGTTTGGCTCGTAAGAGCGATATTCTAAATTCTGGCTCAAAAGAGCGAT
1 CGAAAGAGCGACATTCTATCTGGCTCGTAAGAGCGATATTCTAAATTCTGGCTCAAAAGAGCAAT
*
33981963 -TTCTATCTGGCT
66 ATTCTATATGGCT
* * **
33981975 CGAAAGAGCGA-TTTCTATCTGGCTCGTAAGAGCGATATTCTGAATTCTGGCTTGAAAGAGCAAT
1 CGAAAGAGCGACATTCTATCTGGCTCGTAAGAGCGATATTCTAAATTCTGGCTCAAAAGAGCAAT
*
33982039 ATTCTGTATGGCT
66 ATTCTATATGGCT
*
33982052 CGTAAGAGC
1 CGAAAGAGC
33982061 ATATTTCTGT
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
76 46 0.61
77 29 0.39
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (78 bp):
CGAAAGAGCGACATTCTATCTGGCTCGTAAGAGCGATATTCTAAATTCTGGCTCAAAAGAGCAAT
ATTCTATATGGCT
Found at i:33983460 original size:23 final size:22
Alignment explanation
Indices: 33983428--33983574 Score: 159
Period size: 23 Copynumber: 6.5 Consensus size: 22
33983418 GTTGGGGAAA
*
33983428 CAGTAAGCACACACAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
33983450 CCAGTAGGCACACACAGTGCAAT
1 -CAGTAGGCACACACAGTGCAAT
33983473 CCAGTAGGCACACACAGTGCAAT
1 -CAGTAGGCACACACAGTGCAAT
* ** * ***
33983496 CAATAGGTGCACATAACACAAAT
1 CAGTAGGCACACACAGTGC-AAT
33983519 CAGTAGGCACACACAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
** *
33983541 CAGTAGGTGCACATAGTGCAAAT
1 CAGTAGGCACACACAGTGC-AAT
33983564 CAGTAGGCACA
1 CAGTAGGCACA
33983575 TACCTCTTTA
Statistics
Matches: 102, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
22 31 0.30
23 71 0.70
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.15
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Found at i:33983535 original size:45 final size:45
Alignment explanation
Indices: 33983474--33983574 Score: 166
Period size: 45 Copynumber: 2.2 Consensus size: 45
33983464 CAGTGCAATC
33983474 CAGTAGGCACACACAGTGCAATCAATAGGTGCACATAACACAAAT
1 CAGTAGGCACACACAGTGCAATCAATAGGTGCACATAACACAAAT
* ***
33983519 CAGTAGGCACACACAGTGCAATCAGTAGGTGCACATAGTGCAAAT
1 CAGTAGGCACACACAGTGCAATCAATAGGTGCACATAACACAAAT
33983564 CAGTAGGCACA
1 CAGTAGGCACA
33983575 TACCTCTTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.16
Consensus pattern (45 bp):
CAGTAGGCACACACAGTGCAATCAATAGGTGCACATAACACAAAT
Found at i:34002025 original size:19 final size:18
Alignment explanation
Indices: 34001997--34002033 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
34001987 ATTAGATCAC
34001997 TCTTTATCGATGCAATTTT
1 TCTTTATCGATGC-ATTTT
*
34002016 TCTTTGTCGATGCATTTT
1 TCTTTATCGATGCATTTT
34002034 CAGACGAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.16, C:0.16, G:0.14, T:0.54
Consensus pattern (18 bp):
TCTTTATCGATGCATTTT
Found at i:34011795 original size:20 final size:19
Alignment explanation
Indices: 34011761--34011799 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
34011751 GCAAGAAGTG
*
34011761 ATTTAAATTTCATGATTTA
1 ATTTAAATTTAATGATTTA
34011780 ATTTAGAATTTAATGATTTA
1 ATTTA-AATTTAATGATTTA
34011800 TTGATTTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (19 bp):
ATTTAAATTTAATGATTTA
Found at i:34012028 original size:25 final size:25
Alignment explanation
Indices: 34012000--34012130 Score: 120
Period size: 25 Copynumber: 5.1 Consensus size: 25
34011990 CTCTAAATTT
*
34012000 TGGCTCAAAAGAGCGATATTCTATC
1 TGGCTCGAAAGAGCGATATTCTATC
* *
34012025 TGGCTCGAAAGAGTGATATTCTGTC
1 TGGCTCGAAAGAGCGATATTCTATC
* * *
34012050 TGGCTTGTAAGAGTGATATTCTAAATCC
1 TGGCTCGAAAGAGCGATATTCT--AT-C
* * * *
34012078 TAGCTCGAAAGATCAATATTCTGTC
1 TGGCTCGAAAGAGCGATATTCTATC
*
34012103 TGGCTCGTAAGAGC-ATATTTCTATC
1 TGGCTCGAAAGAGCGATA-TTCTATC
34012128 TGG
1 TGG
34012131 ACTCATAAGA
Statistics
Matches: 85, Mismatches: 17, Indels: 8
0.77 0.15 0.07
Matches are distributed among these distances:
24 3 0.04
25 63 0.74
26 1 0.01
27 1 0.01
28 17 0.20
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (25 bp):
TGGCTCGAAAGAGCGATATTCTATC
Found at i:34014749 original size:96 final size:96
Alignment explanation
Indices: 34014585--34014772 Score: 306
Period size: 96 Copynumber: 2.0 Consensus size: 96
34014575 GACCTTAGTT
* *
34014585 GACCCACCTAAAGGGGTTAAACCCATAGGGTGCAAGTAGGTTTTCAAGAAGAAAATTGACATGGA
1 GACCCACCTAAAGGGGTTAAACCCATAAGGTGCAAGTAGGTTTTCAAGAAGAAAATCGACATGGA
34014650 TGGTAATGTACAAACATACAAAGGGTGGTTG
66 TGGTAATGTACAAACATACAAAGGGTGGTTG
* *
34014681 GACCCACCTGAAGGGGTTAAACCCATAAGGTGCAAGTGGGTTTTCAAGAAGAAAATCGACACT-G
1 GACCCACCTAAAGGGGTTAAACCCATAAGGTGCAAGTAGGTTTTCAAGAAGAAAATCGACA-TGG
* *
34014745 ATGGTAGTGTATAAACATACAAAGGGTG
65 ATGGTAATGTACAAACATACAAAGGGTG
34014773 ATTAGTTGCT
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
96 84 0.99
97 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.27, T:0.21
Consensus pattern (96 bp):
GACCCACCTAAAGGGGTTAAACCCATAAGGTGCAAGTAGGTTTTCAAGAAGAAAATCGACATGGA
TGGTAATGTACAAACATACAAAGGGTGGTTG
Found at i:34017300 original size:14 final size:13
Alignment explanation
Indices: 34017271--34017308 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
34017261 ATTTTAACGC
*
34017271 AATTATAATTTTT
1 AATTATAATATTT
34017284 AATTATAATGATTT
1 AATTATAAT-ATTT
34017298 AATTA-AATATT
1 AATTATAATATT
34017309 AAAACATGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 3 0.13
13 12 0.52
14 8 0.35
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (13 bp):
AATTATAATATTT
Found at i:34017438 original size:123 final size:123
Alignment explanation
Indices: 34017298--34017536 Score: 381
Period size: 123 Copynumber: 1.9 Consensus size: 123
34017288 ATAATGATTT
34017298 AATTAAATATTAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTT
1 AATTAAATATTAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTT
* *
34017363 CCATATATTTCTTTAAAG-GGATATTTCCATTTTAATATGAGATATTATATAAAAGAA
66 CCATATATTTCTCTAAAGAAGATATTTCCATTTTAATATGAGATATTATATAAAAGAA
*
34017420 AATTTAATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCT
1 AATTAAATATT-AAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCT
* * *
34017485 TTCATATATTTCTCTAAAGATATATATATTTCTATTTTAATATGAGATATTA
65 TCCATATATTTCTCTAAAG--A-AGATATTTCCATTTTAATATGAGATATTA
34017537 AAATTAAACG
Statistics
Matches: 106, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
122 10 0.09
123 70 0.66
127 26 0.25
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (123 bp):
AATTAAATATTAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTT
CCATATATTTCTCTAAAGAAGATATTTCCATTTTAATATGAGATATTATATAAAAGAA
Found at i:34028209 original size:23 final size:24
Alignment explanation
Indices: 34028161--34028210 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
34028151 ATGACCTATA
* * *
34028161 GTTCCTAACCTCTTCTATATCTAT
1 GTTCCTAACATCTTCAATATCAAT
34028185 GTTCCTAACAT-TTCAATATCAAT
1 GTTCCTAACATCTTCAATATCAAT
34028208 GTT
1 GTT
34028211 ATTTATATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (24 bp):
GTTCCTAACATCTTCAATATCAAT
Found at i:34030829 original size:325 final size:325
Alignment explanation
Indices: 34030239--34030891 Score: 1279
Period size: 325 Copynumber: 2.0 Consensus size: 325
34030229 TCCATGGCAC
*
34030239 AAAGTTATCGTGGGATTACTGATGGTTGTGATTGATCTAAAAATGAATAATTGTTAGTATTGTTA
1 AAAGTTATCGTGGAATTACTGATGGTTGTGATTGATCTAAAAATGAATAATTGTTAGTATTGTTA
34030304 AATGATAATCATAACTATATCCTAAAAATTTCGTAATAATTCATCTTAACAATGCAAAAACTAAA
66 AATGATAATCATAACTATATCCTAAAAATTTCGTAATAATTCATCTTAACAATGCAAAAACTAAA
34030369 ATCACTAAAGACATTGCCTCCCTGACAATAACGCCAACAACTTGACTGCCTCCGAACGTACTGCC
131 ATCACTAAAGACATTGCCTCCCTGACAATAACGCCAACAACTTGACTGCCTCCGAACGTACTGCC
34030434 GTTCAACAAGTATTTTGGGCTTCCGCAAGTATACAGGTCTAGTTGTAATATAGTTACAACGAAGT
196 GTTCAACAAGTATTTTGGGCTTCCGCAAGTATACAGGTCTAGTTGTAATATAGTTACAACGAAGT
34030499 AAAGAGTACTTTCAGGATCCTACCCAAAGGAGGCAAAGTACTAGTAACTTTAATTTCCTACACAG
261 AAAGAGTACTTTCAGGATCCTACCCAAAGGAGGCAAAGTACTAGTAACTTTAATTTCCTACACAG
34030564 AAAGTTATCGTGGAATTACTGATGGTTGTGATTGATCTAAAAATGAATAATTGTTAGTATTGTTA
1 AAAGTTATCGTGGAATTACTGATGGTTGTGATTGATCTAAAAATGAATAATTGTTAGTATTGTTA
34030629 AATGATAATCATAACTATATCCTAAAAATTTCGTAATAATTCATCTTAACAATGCAAAAACTAAA
66 AATGATAATCATAACTATATCCTAAAAATTTCGTAATAATTCATCTTAACAATGCAAAAACTAAA
34030694 ATCACTAAAGACATTGCCTCCCTGACAATAACGCCAACAACTTGACTGCCTCCGAACGTACTGCC
131 ATCACTAAAGACATTGCCTCCCTGACAATAACGCCAACAACTTGACTGCCTCCGAACGTACTGCC
34030759 GTTCAACAAGTATTTTGGGCTTCCGCAAGTATACAGGTCTAGTTGTAATATAGTTACAACGAAGT
196 GTTCAACAAGTATTTTGGGCTTCCGCAAGTATACAGGTCTAGTTGTAATATAGTTACAACGAAGT
* *
34030824 AAAGAGTAGTTTCAGGATCCTATCCAAAGGAGGCAAAGTACTAGTAACTTTAATTTCCTACACAG
261 AAAGAGTACTTTCAGGATCCTACCCAAAGGAGGCAAAGTACTAGTAACTTTAATTTCCTACACAG
34030889 AAA
1 AAA
34030892 AGATCTAATT
Statistics
Matches: 325, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
325 325 1.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (325 bp):
AAAGTTATCGTGGAATTACTGATGGTTGTGATTGATCTAAAAATGAATAATTGTTAGTATTGTTA
AATGATAATCATAACTATATCCTAAAAATTTCGTAATAATTCATCTTAACAATGCAAAAACTAAA
ATCACTAAAGACATTGCCTCCCTGACAATAACGCCAACAACTTGACTGCCTCCGAACGTACTGCC
GTTCAACAAGTATTTTGGGCTTCCGCAAGTATACAGGTCTAGTTGTAATATAGTTACAACGAAGT
AAAGAGTACTTTCAGGATCCTACCCAAAGGAGGCAAAGTACTAGTAACTTTAATTTCCTACACAG
Found at i:34032436 original size:41 final size:41
Alignment explanation
Indices: 34032303--34032447 Score: 146
Period size: 41 Copynumber: 3.4 Consensus size: 41
34032293 AACTTGATGT
* * *
34032303 ATAAATGGAAGACTCGTGTCTCGGGTTGAGCATGAGAGTTTATAC
1 ATAAA-GGAAGACTCATGTCTCGGGATGAGCATGAGA--TTAT-G
* * * * * *
34032348 AAAAAGGAAGACTCGTGACTCAGAATTGAGCATGAGAATATG
1 ATAAAGGAAGACTCATGTCTCGGGA-TGAGCATGAGATTATG
* *
34032390 TTAAAGGAAGACTCATGTCTCGGGATGAGAATGAGATTATG
1 ATAAAGGAAGACTCATGTCTCGGGATGAGCATGAGATTATG
34032431 ATAAAGGAAGACTCATG
1 ATAAAGGAAGACTCATG
34032448 CCTTGGGAAT
Statistics
Matches: 83, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
41 30 0.36
42 19 0.23
43 3 0.04
44 16 0.19
45 15 0.18
ACGTcount: A:0.37, C:0.12, G:0.28, T:0.24
Consensus pattern (41 bp):
ATAAAGGAAGACTCATGTCTCGGGATGAGCATGAGATTATG
Found at i:34032488 original size:45 final size:41
Alignment explanation
Indices: 34032309--34032498 Score: 119
Period size: 41 Copynumber: 4.4 Consensus size: 41
34032299 ATGTATAAAT
* * * * *
34032309 GGAAGACTCGTGTCTCGGGTTGAGCATGAGAGTTTATACAAAAA
1 GGAAGACTCATGCCTCGGGATGAGAATGAGA--TTAT-GAAAAA
* * * * * * **
34032353 GGAAGACTCGTGACTCAGAATTGAGCATGAGAATATGTTAAA
1 GGAAGACTCATGCCTCGGGA-TGAGAATGAGATTATGAAAAA
* *
34032395 GGAAGACTCATGTCTCGGGATGAGAATGAGATTATGATAAA
1 GGAAGACTCATGCCTCGGGATGAGAATGAGATTATGAAAAA
* ** *
34032436 GGAAGACTCATGCCTTGGGAATGAGTGTGAGGTTATGTTTAAAAA
1 GGAAGACTCATGCCTCGGG-ATGAGAATGAGATTATG---AAAAA
* *
34032481 GGAAGACTTATGACTCGG
1 GGAAGACTCATGCCTCGG
34032499 TAGAGCATAA
Statistics
Matches: 117, Mismatches: 24, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
41 35 0.30
42 33 0.28
43 3 0.03
44 16 0.14
45 30 0.26
ACGTcount: A:0.34, C:0.12, G:0.29, T:0.25
Consensus pattern (41 bp):
GGAAGACTCATGCCTCGGGATGAGAATGAGATTATGAAAAA
Found at i:34033205 original size:21 final size:21
Alignment explanation
Indices: 34033181--34033240 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
34033171 TAGGACCATG
*
34033181 ACTTGTTTCGGTAGAAGTTAC
1 ACTTGTATCGGTAGAAGTTAC
* * *
34033202 ACTTGTATCGATAGAACTTTC
1 ACTTGTATCGGTAGAAGTTAC
**
34033223 ACAAGTATCGGTAGAAGT
1 ACTTGTATCGGTAGAAGT
34033241 CTGCACTGTT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (21 bp):
ACTTGTATCGGTAGAAGTTAC
Found at i:34034379 original size:15 final size:16
Alignment explanation
Indices: 34034354--34034383 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
34034344 AGAGAAGGAG
34034354 GAGATGACGATGAGAA
1 GAGATGACGATGAGAA
34034370 GAGA-GACGATGAGA
1 GAGATGACGATGAGA
34034384 TGGATTTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.07, G:0.40, T:0.10
Consensus pattern (16 bp):
GAGATGACGATGAGAA
Found at i:34057651 original size:17 final size:16
Alignment explanation
Indices: 34057631--34057673 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
34057621 ATTGAGAGAT
34057631 AAAAATAAATAAATAA
1 AAAAATAAATAAATAA
34057647 CAAAACA-AAATAAATAA
1 -AAAA-ATAAATAAATAA
34057664 AGAAAATAAA
1 A-AAAATAAA
34057674 CAAACGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 2 0.09
17 20 0.87
18 1 0.04
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.14
Consensus pattern (16 bp):
AAAAATAAATAAATAA
Found at i:34062667 original size:2 final size:2
Alignment explanation
Indices: 34062660--34062699 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
34062650 CGGTTAATAA
34062660 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
34062700 CAATTAAAGA
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:34071588 original size:20 final size:21
Alignment explanation
Indices: 34071563--34071601 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
34071553 TAATTTTTCG
34071563 ATAAAAATAT-ATAAAATTTT
1 ATAAAAATATAATAAAATTTT
34071583 ATAAAAATATAATAAAATT
1 ATAAAAATATAATAAAATT
34071602 ATAAATAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
ATAAAAATATAATAAAATTTT
Found at i:34072126 original size:20 final size:20
Alignment explanation
Indices: 34072101--34072139 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
34072091 TTAAAGTTTT
34072101 ATTTATA-AGATTATTATTTC
1 ATTTATAGA-ATTATTATTTC
34072121 ATTTATAGAATTATTATTT
1 ATTTATAGAATTATTATTT
34072140 TAATAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (20 bp):
ATTTATAGAATTATTATTTC
Found at i:34072868 original size:14 final size:15
Alignment explanation
Indices: 34072849--34072882 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
34072839 AATTAAGAAT
34072849 ATATTTT-TATATTA
1 ATATTTTATATATTA
34072863 ATATTTTATATATTA
1 ATATTTTATATATTA
34072878 A-ATTT
1 ATATTT
34072883 AAATTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATATTTTATATATTA
Found at i:34076846 original size:46 final size:46
Alignment explanation
Indices: 34076779--34076899 Score: 161
Period size: 46 Copynumber: 2.6 Consensus size: 46
34076769 GATTAAAGAG
*
34076779 AAACAAATCCCTGAAATTGTGGAAGACAAATGCCAACAATTTAACC
1 AAACAAATCCCTGAAATTGTGGAAGACAAATGCCAACAATCTAACC
* * * * * **
34076825 AAACAAATCCCTGAAATTGTGGAATATAGATGCCTACACTCTAGTC
1 AAACAAATCCCTGAAATTGTGGAAGACAAATGCCAACAATCTAACC
*
34076871 AAACAAATCCTTGAAATTGTGGAAGACAA
1 AAACAAATCCCTGAAATTGTGGAAGACAA
34076900 CTTGATTTGA
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 63 1.00
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (46 bp):
AAACAAATCCCTGAAATTGTGGAAGACAAATGCCAACAATCTAACC
Found at i:34081551 original size:60 final size:59
Alignment explanation
Indices: 34081447--34081618 Score: 172
Period size: 60 Copynumber: 2.9 Consensus size: 59
34081437 TTAATATAAC
* *
34081447 ATTTGATACCTGAACTCTCCACTTTTTCTTAATTT-AGTACCTAAACTCTTTTTTGACCTA
1 ATTTGATACCTGAACT-TACACTTTTTCTTAATTTGA-TAACTAAACTCTTTTTTGACCTA
* *
34081507 TTTTGGTACCTGAACTTGACACTTTTTCTTAATTTGATAACTAAACT-TTTTTT-ATCC-A
1 ATTTGATACCTGAACTT-ACACTTTTTCTTAATTTGATAACTAAACTCTTTTTTGA-CCTA
* * * * * *
34081565 ATTTGATACTTGAACTTAACATTTTTTCCTAATTTGGTATCTAAGCTTCTTTTT
1 ATTTGATACCTGAACTT-ACACTTTTTCTTAATTTGATAACTAAAC-TCTTTTT
34081619 AGATTTAGTT
Statistics
Matches: 94, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
58 39 0.41
59 10 0.11
60 44 0.47
61 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.08, T:0.48
Consensus pattern (59 bp):
ATTTGATACCTGAACTTACACTTTTTCTTAATTTGATAACTAAACTCTTTTTTGACCTA
Found at i:34081591 original size:58 final size:57
Alignment explanation
Indices: 34081447--34081619 Score: 170
Period size: 58 Copynumber: 2.9 Consensus size: 57
34081437 TTAATATAAC
* *
34081447 ATTTGATACCTGAACTCTCCACTTTTTCTTAATTT-AGTACCTAAACTCTTTTTTGACCTA
1 ATTTGATACCTGAACT-TACACTTTTTCTTAATTTGA-TAACTAAACT-TTTTTT-ACCTA
* *
34081507 TTTTGGTACCTGAACTTGACACTTTTTCTTAATTTGATAACTAAACTTTTTTTATCC-A
1 ATTTGATACCTGAACTT-ACACTTTTTCTTAATTTGATAACTAAACTTTTTTTA-CCTA
* * * * * *
34081565 ATTTGATACTTGAACTTAACATTTTTTCCTAATTTGGTATCTAAGCTTCTTTTTA
1 ATTTGATACCTGAACTT-ACACTTTTTCTTAATTTGATAACTAAACTT-TTTTTA
34081620 GATTTAGTTT
Statistics
Matches: 96, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
58 41 0.43
59 15 0.16
60 39 0.41
61 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.08, T:0.48
Consensus pattern (57 bp):
ATTTGATACCTGAACTTACACTTTTTCTTAATTTGATAACTAAACTTTTTTTACCTA
Found at i:34081860 original size:58 final size:60
Alignment explanation
Indices: 34081785--34081927 Score: 159
Period size: 59 Copynumber: 2.4 Consensus size: 60
34081775 AAAAAATTAG
* * **
34081785 GTACCAAATTAGGAAAAA-TAGTCAAATTCAG-GTACCAAATTGGACC-CCAAAAAGTTTAA
1 GTACCAAATTAAGAAAAAGT-GTCAAATT-AGAGTACCAAATTAGACCAAAAAAAAGTTTAA
* * * *
34081844 GTACCAACTTAA-AAAAAGTGTCAAGTTTGAGTGCCAAATTAGACCAAAAAAAAGTTTAA
1 GTACCAAATTAAGAAAAAGTGTCAAATTAGAGTACCAAATTAGACCAAAAAAAAGTTTAA
*
34081903 GTACCAAATTAAGAAAAAATGTCAA
1 GTACCAAATTAAGAAAAAGTGTCAA
34081928 GTTCTAATAT
Statistics
Matches: 70, Mismatches: 10, Indels: 7
0.80 0.11 0.08
Matches are distributed among these distances:
57 1 0.01
58 25 0.36
59 33 0.47
60 11 0.16
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (60 bp):
GTACCAAATTAAGAAAAAGTGTCAAATTAGAGTACCAAATTAGACCAAAAAAAAGTTTAA
Found at i:34082494 original size:22 final size:22
Alignment explanation
Indices: 34082444--34082494 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
34082434 ACTATTGTTA
*
34082444 TGTTATTGTTTTGCTACCATTT
1 TGTTATTGTATTGCTACCATTT
* * *
34082466 CGCTATTGTATTGCTACTATTT
1 TGTTATTGTATTGCTACCATTT
34082488 TGTTATT
1 TGTTATT
34082495 ATTTAGATAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.16, C:0.14, G:0.14, T:0.57
Consensus pattern (22 bp):
TGTTATTGTATTGCTACCATTT
Found at i:34093257 original size:2 final size:2
Alignment explanation
Indices: 34093250--34093282 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
34093240 ATCATACTCA
34093250 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34093283 AGTATGTCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34095832 original size:5 final size:5
Alignment explanation
Indices: 34095822--34095852 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
34095812 ACATATATCT
34095822 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC T
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC T
34095853 CTTTTATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:34100394 original size:20 final size:20
Alignment explanation
Indices: 34100366--34100411 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
34100356 TTGTAATAGA
*
34100366 TAGCATGAAATATTTTTTCC
1 TAGCGTGAAATATTTTTTCC
34100386 TAGCGTGAAATATTTTTTCC
1 TAGCGTGAAATATTTTTTCC
*
34100406 TTGCGT
1 TAGCGT
34100412 TAACCTAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46
Consensus pattern (20 bp):
TAGCGTGAAATATTTTTTCC
Found at i:34103087 original size:21 final size:21
Alignment explanation
Indices: 34103061--34103111 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
34103051 AGTATTCTGG
*
34103061 TTGTAATTTTGTTGCTACTAA
1 TTGTAATTTTATTGCTACTAA
* * *
34103082 TTGTAATTGTATTGCTGCTGA
1 TTGTAATTTTATTGCTACTAA
34103103 TTGTAATTT
1 TTGTAATTT
34103112 CTTTGTCTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.22, C:0.08, G:0.18, T:0.53
Consensus pattern (21 bp):
TTGTAATTTTATTGCTACTAA
Found at i:34106889 original size:21 final size:21
Alignment explanation
Indices: 34106841--34106889 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
34106831 TTCAAATCTT
*
34106841 ATTTCTTTTTAAAATCTAAAA
1 ATTTATTTTTAAAATCTAAAA
* * * *
34106862 ATATATTTTTAAATTTTATAA
1 ATTTATTTTTAAAATCTAAAA
34106883 ATTTATT
1 ATTTATT
34106890 AAATATTATT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTTATTTTTAAAATCTAAAA
Found at i:34110128 original size:30 final size:31
Alignment explanation
Indices: 34110108--34110168 Score: 108
Period size: 30 Copynumber: 2.0 Consensus size: 31
34110098 TGTCTTCGTG
34110108 AATTCCTTCTTCTAGATCCA-TCATCCCTGT
1 AATTCCTTCTTCTAGATCCATTCATCCCTGT
34110138 AATTCCTTCTTCTAGATCCA-TCATCCCTGT
1 AATTCCTTCTTCTAGATCCATTCATCCCTGT
34110168 A
1 A
34110169 CGAGTTAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.21, C:0.33, G:0.07, T:0.39
Consensus pattern (31 bp):
AATTCCTTCTTCTAGATCCATTCATCCCTGT
Found at i:34122578 original size:13 final size:14
Alignment explanation
Indices: 34122559--34122591 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
34122549 GACTTTGTCA
34122559 CTTTTTACACTTTT
1 CTTTTTACACTTTT
*
34122573 -TTTTTACTCTTTT
1 CTTTTTACACTTTT
34122586 CTTTTT
1 CTTTTT
34122592 GTATTTTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (14 bp):
CTTTTTACACTTTT
Found at i:34122620 original size:22 final size:22
Alignment explanation
Indices: 34122573--34122614 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
34122563 TTACACTTTT
*
34122573 TTTTTACTCTTTTCTTTTTGTA
1 TTTTTACTCATTTCTTTTTGTA
34122595 TTTTTACTCATTT-TTTTTGT
1 TTTTTACTCATTTCTTTTTGT
34122615 TCTTTTCACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.10, C:0.12, G:0.05, T:0.74
Consensus pattern (22 bp):
TTTTTACTCATTTCTTTTTGTA
Found at i:34127874 original size:11 final size:11
Alignment explanation
Indices: 34127858--34127887 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
34127848 ACCTATTTGA
34127858 AAACCTAAAGC
1 AAACCTAAAGC
34127869 AAACCTAAAGC
1 AAACCTAAAGC
*
34127880 CAACCTAA
1 AAACCTAA
34127888 CCACGTGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.53, C:0.30, G:0.07, T:0.10
Consensus pattern (11 bp):
AAACCTAAAGC
Found at i:34133038 original size:18 final size:19
Alignment explanation
Indices: 34132995--34133038 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
34132985 CTTGAGAAAT
34132995 CAAAAAAGTAAAAACTAAA
1 CAAAAAAGTAAAAACTAAA
*
34133014 -AATAAAGT-AAAACTAAA
1 CAAAAAAGTAAAAACTAAA
34133031 CAAAAAAG
1 CAAAAAAG
34133039 AGTGAGCTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.73, C:0.09, G:0.07, T:0.11
Consensus pattern (19 bp):
CAAAAAAGTAAAAACTAAA
Found at i:34136950 original size:14 final size:14
Alignment explanation
Indices: 34136931--34136958 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
34136921 GTAAGCCAAA
34136931 ACTTATCTATTTTG
1 ACTTATCTATTTTG
34136945 ACTTATCTATTTTG
1 ACTTATCTATTTTG
34136959 GCTTGTATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.57
Consensus pattern (14 bp):
ACTTATCTATTTTG
Found at i:34144942 original size:24 final size:24
Alignment explanation
Indices: 34144915--34145048 Score: 88
Period size: 24 Copynumber: 5.4 Consensus size: 24
34144905 TATAAGTTGA
34144915 CGAGCGTAAACGTGTGCAAGCTGG
1 CGAGCGTAAACGTGTGCAAGCTGG
* * * ** *
34144939 CGAGTGTAAATGAATATAAAAGCTGA
1 CGAGCGTAAACG--TGTGCAAGCTGG
*
34144965 CGAGCGTAAAAGTGTGCAAGCTGG
1 CGAGCGTAAACGTGTGCAAGCTGG
* *** ** *
34144989 CGAGTGTAAACACACATATAAGCTGA
1 CGAGCGT-AA-ACGTGTGCAAGCTGG
* *
34145015 CGAGCGTAAATGTGTGCAAGCTAG
1 CGAGCGTAAACGTGTGCAAGCTGG
34145039 CGAGCGTAAA
1 CGAGCGTAAA
34145049 ACGCAATGAA
Statistics
Matches: 77, Mismatches: 29, Indels: 8
0.68 0.25 0.07
Matches are distributed among these distances:
24 41 0.53
25 4 0.05
26 32 0.42
ACGTcount: A:0.35, C:0.16, G:0.30, T:0.19
Consensus pattern (24 bp):
CGAGCGTAAACGTGTGCAAGCTGG
Found at i:34144980 original size:50 final size:50
Alignment explanation
Indices: 34144901--34145048 Score: 208
Period size: 50 Copynumber: 3.0 Consensus size: 50
34144891 TAAAGTAACG
* * *
34144901 CATATATAAGTTGACGAGCGTAAACGTGTGCAAGCTGGCGAGTGTAAATGA
1 CATATATAAGCTGACGAGCGTAAAAGTGTGCAAGCTGGCGAGTGTAAA-CA
*
34144952 -ATATAAAAGCTGACGAGCGTAAAAGTGTGCAAGCTGGCGAGTGTAAACA
1 CATATATAAGCTGACGAGCGTAAAAGTGTGCAAGCTGGCGAGTGTAAACA
* * * *
34145001 CACATATAAGCTGACGAGCGTAAATGTGTGCAAGCTAGCGAGCGTAAA
1 CATATATAAGCTGACGAGCGTAAAAGTGTGCAAGCTGGCGAGTGTAAA
34145049 ACGCAATGAA
Statistics
Matches: 87, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
49 1 0.01
50 86 0.99
ACGTcount: A:0.36, C:0.16, G:0.28, T:0.20
Consensus pattern (50 bp):
CATATATAAGCTGACGAGCGTAAAAGTGTGCAAGCTGGCGAGTGTAAACA
Found at i:34152745 original size:18 final size:18
Alignment explanation
Indices: 34152696--34152738 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
34152686 AAAATACCCA
* *
34152696 AACCCATGAGCTCGACTC
1 AACCCGTGAGCCCGACTC
34152714 AACCCGTGAGCCCGACTC
1 AACCCGTGAGCCCGACTC
*
34152732 TACCCGT
1 AACCCGT
34152739 TGACCCGTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.23, C:0.42, G:0.19, T:0.16
Consensus pattern (18 bp):
AACCCGTGAGCCCGACTC
Found at i:34154323 original size:2 final size:2
Alignment explanation
Indices: 34154316--34154340 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34154306 AATGGGTAAA
34154316 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
34154341 GACATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:34154688 original size:199 final size:199
Alignment explanation
Indices: 34154348--34154739 Score: 631
Period size: 199 Copynumber: 2.0 Consensus size: 199
34154338 ACAGACATAT
* * *
34154348 ATATAAGCCTTTATATTATGCTTTGCGTAGGTGACTGTAAGTATACTTAAATGGTATATGTTATC
1 ATATAAGCCTTTATATTATGCTTTGCGTAGGTAACTGTAACTATACTCAAATGGTATATGTTATC
* * *
34154413 ATATTTTAGGATGCTTTTAGGTGTGTTTTAAGTTTTGGTAGATAGTGTTACGAATTGGGTTAGAC
66 ATATTTTAGGATGCTTCTAGGTATGTTTTAAGTTTTGGTAGATAGTGTTACGAATTAGGTTAGAC
34154478 ATTTAAATCAAATGAGTGATAGTTAAATACGTTTTTAAGTATTTATGGGCACACACAGGCTGTAT
131 ATTTAAATCAAATGAGTGATAGTTAAATACGTTTTTAAGTATTTATGGGCACACACAGGCTGTAT
34154543 ATAC
196 ATAC
* * *
34154547 ATATAAGCCTTTATATTATGCTTTGTGTAGGTAATTGTAACTGTACTCAAATGGTATATGTTATC
1 ATATAAGCCTTTATATTATGCTTTGCGTAGGTAACTGTAACTATACTCAAATGGTATATGTTATC
* * * *
34154612 ATATTTTAGGATGCTTCTATGTATGTTTTAAGTTTTGGTAGATAGTGTTATGAATTAGGTTTGGC
66 ATATTTTAGGATGCTTCTAGGTATGTTTTAAGTTTTGGTAGATAGTGTTACGAATTAGGTTAGAC
* * * *
34154677 ATTTAAATCAAATGAGTGATATTTGAATACGTTTTTAAGTATTTTTGGGCACACATAGGCTGT
131 ATTTAAATCAAATGAGTGATAGTTAAATACGTTTTTAAGTATTTATGGGCACACACAGGCTGT
34154740 TCACGGGCGT
Statistics
Matches: 176, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
199 176 1.00
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.42
Consensus pattern (199 bp):
ATATAAGCCTTTATATTATGCTTTGCGTAGGTAACTGTAACTATACTCAAATGGTATATGTTATC
ATATTTTAGGATGCTTCTAGGTATGTTTTAAGTTTTGGTAGATAGTGTTACGAATTAGGTTAGAC
ATTTAAATCAAATGAGTGATAGTTAAATACGTTTTTAAGTATTTATGGGCACACACAGGCTGTAT
ATAC
Found at i:34160884 original size:50 final size:50
Alignment explanation
Indices: 34160829--34161176 Score: 402
Period size: 50 Copynumber: 7.0 Consensus size: 50
34160819 TAAAGTAACA
* * * *
34160829 CATATATAAGCTGACGAGCGTAAATGTGTGCAAACTGGTGAGCGTAAACG
1 CATATATAAGTTGACGAGCGTAAACGTGTGCAAGCTGGCGAGCGTAAACG
* * * *
34160879 CATATAAAAGTTGACGAGAGTAAACGTGTGCAAGCTGGTGAGCGTAAACA
1 CATATATAAGTTGACGAGCGTAAACGTGTGCAAGCTGGCGAGCGTAAACG
* * * *
34160929 CATATATAAGCTGACGAGTGTAAACGTGTGCAAGCTGACGAGCGTAAACA
1 CATATATAAGTTGACGAGCGTAAACGTGTGCAAGCTGGCGAGCGTAAACG
* * * *
34160979 CATATA-AA-TTGACGAGCGTAAACATGTGCAAGCTGACGAGCATAAACA
1 CATATATAAGTTGACGAGCGTAAACGTGTGCAAGCTGGCGAGCGTAAACG
* * *
34161027 CAT-TAATAAGTTGACGAGTGTAAACATGTGCAAGCTGGCGAGCGTAAATG
1 CATAT-ATAAGTTGACGAGCGTAAACGTGTGCAAGCTGGCGAGCGTAAACG
* *
34161077 CATATAT-AGTTGACGAGCGTAAACGTGTGCAAGCTGACGAGTGTAAACG
1 CATATATAAGTTGACGAGCGTAAACGTGTGCAAGCTGGCGAGCGTAAACG
* ** * *
34161126 --TGTGCAAGCTGACGAGTGTAAACGTGTGCAAGCTGGCGAGCGTAAAACG
1 CATATATAAGTTGACGAGCGTAAACGTGTGCAAGCTGGCGAGCGT-AAACG
34161175 CA
1 CA
34161177 ACGAATAGGT
Statistics
Matches: 258, Mismatches: 32, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
47 3 0.01
48 73 0.28
49 46 0.18
50 135 0.52
51 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.28, T:0.21
Consensus pattern (50 bp):
CATATATAAGTTGACGAGCGTAAACGTGTGCAAGCTGGCGAGCGTAAACG
Found at i:34160967 original size:24 final size:24
Alignment explanation
Indices: 34160836--34161171 Score: 224
Period size: 24 Copynumber: 13.7 Consensus size: 24
34160826 ACACATATAT
*
34160836 AAGCTGACGAGCGTAAATGTGTGC
1 AAGCTGACGAGCGTAAACGTGTGC
* ** * **
34160860 AAACTGGTGAGCGTAAACGCATATAA
1 AAGCTGACGAGCGTAAACG--TGTGC
* *
34160886 AAGTTGACGAGAGTAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTGTGC
** * * **
34160910 AAGCTGGTGAGCGTAAACACATATAT
1 AAGCTGACGAGCGT-AA-ACGTGTGC
*
34160936 AAGCTGACGAGTGTAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTGTGC
*** **
34160960 AAGCTGACGAGCGTAAACACATAT
1 AAGCTGACGAGCGTAAACGTGTGC
** *
34160984 AAATTGACGAGCGTAAACATGTGC
1 AAGCTGACGAGCGTAAACGTGTGC
* * **
34161008 AAGCTGACGAGCATAAACACAT-TAAT
1 AAGCTGACGAGCGT-AA-ACGTGT-GC
* * *
34161034 AAGTTGACGAGTGTAAACATGTGC
1 AAGCTGACGAGCGTAAACGTGTGC
* * ** **
34161058 AAGCTGGCGAGCGTAAATGCATAT
1 AAGCTGACGAGCGTAAACGTGTGC
*
34161082 ATAGTTGACGAGCGTAAACGTGTGC
1 A-AGCTGACGAGCGTAAACGTGTGC
*
34161107 AAGCTGACGAGTGTAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTGTGC
*
34161131 AAGCTGACGAGTGTAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTGTGC
*
34161155 AAGCTGGCGAGCGTAAA
1 AAGCTGACGAGCGTAAA
34161172 ACGCAACGAA
Statistics
Matches: 231, Mismatches: 72, Indels: 18
0.72 0.22 0.06
Matches are distributed among these distances:
24 158 0.68
25 27 0.12
26 46 0.20
ACGTcount: A:0.35, C:0.16, G:0.28, T:0.21
Consensus pattern (24 bp):
AAGCTGACGAGCGTAAACGTGTGC
Found at i:34161028 original size:98 final size:98
Alignment explanation
Indices: 34160825--34161176 Score: 458
Period size: 98 Copynumber: 3.6 Consensus size: 98
34160815 AAAGTAAAGT
* * * *
34160825 AACACATATATAAGCTGACGAGCGTAAATGTGTGCAAACTGGTGAGCGTAAACGCATATAAAAGT
1 AACACATATATAAGCTGACGAGTGTAAACGTGTGCAAGCTGGCGAGCGTAAACGCATAT-AAA-T
* **
34160890 TGACGAGAGTAAACGTGTGCAAGCTGGTGAGCGTA
64 TGACGAGCGTAAACGTGTGCAAGCTGACGAGCGTA
* *
34160925 AACACATATATAAGCTGACGAGTGTAAACGTGTGCAAGCTGACGAGCGTAAACACATATAAATTG
1 AACACATATATAAGCTGACGAGTGTAAACGTGTGCAAGCTGGCGAGCGTAAACGCATATAAATTG
* *
34160990 ACGAGCGTAAACATGTGCAAGCTGACGAGCATA
66 ACGAGCGTAAACGTGTGCAAGCTGACGAGCGTA
* * * *
34161023 AACACAT-TAATAAGTTGACGAGTGTAAACATGTGCAAGCTGGCGAGCGTAAATGCATATATAGT
1 AACACATAT-ATAAGCTGACGAGTGTAAACGTGTGCAAGCTGGCGAGCGTAAACGCATATA-AAT
*
34161087 TGACGAGCGTAAACGTGTGCAAGCTGACGAGTGT-
64 TGACGAGCGTAAACGTGTGCAAGCTGACGAGCGTA
* * **
34161121 AA-ACGTGTGCAAGCTGACGAGTGTAAACGTGTGCAAGCTGGCGAGCGTAAAACGCA
1 AACACATATATAAGCTGACGAGTGTAAACGTGTGCAAGCTGGCGAGCGT-AAACGCA
34161177 ACGAATAGGT
Statistics
Matches: 222, Mismatches: 26, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
97 40 0.18
98 93 0.42
99 36 0.16
100 53 0.24
ACGTcount: A:0.36, C:0.17, G:0.27, T:0.20
Consensus pattern (98 bp):
AACACATATATAAGCTGACGAGTGTAAACGTGTGCAAGCTGGCGAGCGTAAACGCATATAAATTG
ACGAGCGTAAACGTGTGCAAGCTGACGAGCGTA
Found at i:34172922 original size:18 final size:18
Alignment explanation
Indices: 34172899--34172934 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
34172889 TTGAACCCTT
34172899 ATAGTTGAATTAACACAC
1 ATAGTTGAATTAACACAC
34172917 ATAGTTGAATTAACACAC
1 ATAGTTGAATTAACACAC
34172935 GGTGTGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (18 bp):
ATAGTTGAATTAACACAC
Found at i:34174329 original size:19 final size:19
Alignment explanation
Indices: 34174307--34174351 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
34174297 TTATATTAGG
34174307 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
34174326 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
34174345 ATTTAAT
1 ATTTAAT
34174352 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:34177133 original size:21 final size:20
Alignment explanation
Indices: 34177095--34177133 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
34177085 ATGATTCTTG
*
34177095 TTTGCTAAGTTAATTTTGAT
1 TTTGCTAAGTTAAATTTGAT
*
34177115 TTTGCTATGATTAAATTTG
1 TTTGCTAAG-TTAAATTTG
34177134 TCTCCACTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.26, C:0.05, G:0.15, T:0.54
Consensus pattern (20 bp):
TTTGCTAAGTTAAATTTGAT
Found at i:34177714 original size:107 final size:103
Alignment explanation
Indices: 34177544--34177740 Score: 232
Period size: 107 Copynumber: 1.9 Consensus size: 103
34177534 TGTGTTAGAT
* * * * *
34177544 TGAGTAACCGGGGTGGAGTGCTTAGTTGTCATTTCACTTCGTGTCAAAAGGGCTAACACATTCTA
1 TGAGTAACCGGGATGGAGTGCTTAGGTGGCATTTCACTTCGCGTCAAAAGGGCCAACACATTCT-
34177609 CAAAAAAAAAGAGAGAATAAAAAAATTGAGAGCATGTTGGGC
65 CAAAAAAAAA-A-A-AATAAAAAAATTGAGAGCATGTTGGGC
* ** * *** *
34177651 TGAGTAACCGGGATGGAGTGCTTCGGTGGCATTTCTTTTCGCGTCAAAAGGTCCAATGTATTCTT
1 TGAGTAACCGGGATGGAGTGCTTAGGTGGCATTTCACTTCGCGTCAAAAGGGCCAACACATTCTC
*
34177716 AAAGAAAAAAAAATAAAAAAATTGA
66 AAAAAAAAAAAAATAAAAAAATTGA
34177741 TAAAATAAAA
Statistics
Matches: 76, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
103 14 0.18
104 1 0.01
105 1 0.01
106 8 0.11
107 52 0.68
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.26
Consensus pattern (103 bp):
TGAGTAACCGGGATGGAGTGCTTAGGTGGCATTTCACTTCGCGTCAAAAGGGCCAACACATTCTC
AAAAAAAAAAAAATAAAAAAATTGAGAGCATGTTGGGC
Found at i:34178295 original size:19 final size:19
Alignment explanation
Indices: 34178273--34178317 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
34178263 TTATATTAGG
34178273 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
34178292 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
34178311 ATTTAAT
1 ATTTAAT
34178318 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:34179140 original size:15 final size:16
Alignment explanation
Indices: 34179120--34179149 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34179110 CTTTCTTATT
34179120 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
34179135 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
34179150 TTTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAA
Found at i:34179165 original size:21 final size:21
Alignment explanation
Indices: 34179116--34179173 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 21
34179106 TCGACTTTCT
*
34179116 TATTTTCTATTTCTTTTAATTC
1 TATTTTCT-TTTTTTTTAATTC
34179138 TATTTTCTTTTATTTTTAATTC
1 TATTTTCTTTT-TTTTTAATTC
34179160 TA-TTTCTTTTTTTT
1 TATTTTCTTTTTTTT
34179174 CCTCAAATTG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
20 4 0.12
21 11 0.32
22 19 0.56
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.74
Consensus pattern (21 bp):
TATTTTCTTTTTTTTTAATTC
Found at i:34179529 original size:15 final size:15
Alignment explanation
Indices: 34179509--34179547 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
34179499 TAGATGACTT
34179509 CCTAGGGTTGTCAGG
1 CCTAGGGTTGTCAGG
34179524 CCTAGGGTTGTCAGG
1 CCTAGGGTTGTCAGG
*
34179539 CTTAGGGTT
1 CCTAGGGTT
34179548 TAAGTTCTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.13, C:0.18, G:0.38, T:0.31
Consensus pattern (15 bp):
CCTAGGGTTGTCAGG
Found at i:34194290 original size:2 final size:2
Alignment explanation
Indices: 34194283--34194322 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
34194273 TTAGTGAATA
34194283 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
34194323 GATTTTAAGT
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:34197613 original size:29 final size:29
Alignment explanation
Indices: 34197554--34197614 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
34197544 TGAAAATGTG
34197554 ATTTAATGACTAAATCGTAAATTTTGAAAA
1 ATTTAATGACTAAA-CGTAAATTTTGAAAA
*
34197584 ATTTGATGACTAAA-GTACAA-TTTGATAAA
1 ATTTAATGACTAAACGTA-AATTTTGA-AAA
34197613 AT
1 AT
34197615 AGAAAAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 8 0.29
29 7 0.25
30 13 0.46
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.36
Consensus pattern (29 bp):
ATTTAATGACTAAACGTAAATTTTGAAAA
Found at i:34202675 original size:25 final size:24
Alignment explanation
Indices: 34202642--34202689 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
34202632 AGTAAATAAG
* *
34202642 TTCTTTTGTTAAAATTTGCATCCAT
1 TTCTATTGTTAAAAATTG-ATCCAT
34202667 TTCTATTGTTAAAAATTGATCCA
1 TTCTATTGTTAAAAATTGATCCA
34202690 CGTATGTCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.48
Consensus pattern (24 bp):
TTCTATTGTTAAAAATTGATCCAT
Found at i:34206943 original size:57 final size:56
Alignment explanation
Indices: 34206864--34206990 Score: 161
Period size: 57 Copynumber: 2.2 Consensus size: 56
34206854 CATATGTACC
*
34206864 AAATTAAGAAAAAATACTAAGTTCAGT-TATCAAATTGGATAAAAAAAATTTAAATGCCT
1 AAATTAA-AAAAAATACTAAGTTCA-TATATCAAATTGGATAAAAAAAA-TTAAAT-ACT
* *
34206923 -AATTAAAAAAAAT-GTCAAGTTTATATATCAAATTGGATAAAAAAAATTAAATACT
1 AAATTAAAAAAAATACT-AAGTTCATATATCAAATTGGATAAAAAAAATTAAATACT
34206978 AAATTAAAAAAAA
1 AAATTAAAAAAAA
34206991 ATTAAATACC
Statistics
Matches: 62, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
55 2 0.03
56 20 0.32
57 34 0.55
58 6 0.10
ACGTcount: A:0.57, C:0.06, G:0.08, T:0.28
Consensus pattern (56 bp):
AAATTAAAAAAAATACTAAGTTCATATATCAAATTGGATAAAAAAAATTAAATACT
Found at i:34206991 original size:23 final size:23
Alignment explanation
Indices: 34206961--34207004 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
34206951 CAAATTGGAT
*
34206961 AAAAAAAATTAAATACTAAATTA
1 AAAAAAAATTAAATACCAAATTA
34206984 AAAAAAAATTAAATACCAAAT
1 AAAAAAAATTAAATACCAAAT
34207005 ATTATATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (23 bp):
AAAAAAAATTAAATACCAAATTA
Found at i:34208495 original size:11 final size:12
Alignment explanation
Indices: 34208479--34208507 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
34208469 AATAATAATT
34208479 TTATTTAGAT-A
1 TTATTTAGATAA
34208490 TTATTTAGATAA
1 TTATTTAGATAA
34208502 TTATTT
1 TTATTT
34208508 TTTAGTGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (12 bp):
TTATTTAGATAA
Found at i:34211726 original size:14 final size:14
Alignment explanation
Indices: 34211707--34211736 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
34211697 GTACTCGTCC
*
34211707 AATTACCTTGTCAT
1 AATTACCTTGACAT
34211721 AATTACCTTGACAT
1 AATTACCTTGACAT
34211735 AA
1 AA
34211737 GTGTCTTACA
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:0.37, C:0.20, G:0.07, T:0.37
Consensus pattern (14 bp):
AATTACCTTGACAT
Found at i:34219935 original size:15 final size:16
Alignment explanation
Indices: 34219919--34219968 Score: 61
Period size: 14 Copynumber: 3.2 Consensus size: 16
34219909 GTTTGGACTT
34219919 GGTTCAATTGGGTTT-
1 GGTTCAATTGGGTTTA
*
34219934 GGTTCACTTTGGGTTTA
1 GGTTCA-ATTGGGTTTA
34219951 GGTT--ATTGGGTTTA
1 GGTTCAATTGGGTTTA
34219965 GGTT
1 GGTT
34219969 TGGGCTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 13 0.42
15 6 0.19
16 8 0.26
17 4 0.13
ACGTcount: A:0.12, C:0.06, G:0.34, T:0.48
Consensus pattern (16 bp):
GGTTCAATTGGGTTTA
Found at i:34226907 original size:17 final size:16
Alignment explanation
Indices: 34226880--34226911 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
34226870 GTCGGTCAAC
34226880 GGTTTGACTTGGTTTG
1 GGTTTGACTTGGTTTG
34226896 GGTTTGGACTTGGTTT
1 GGTTT-GACTTGGTTT
34226912 AATTGGGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.06, C:0.06, G:0.38, T:0.50
Consensus pattern (16 bp):
GGTTTGACTTGGTTTG
Found at i:34226923 original size:15 final size:15
Alignment explanation
Indices: 34226905--34226957 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
34226895 GGGTTTGGAC
34226905 TTGGTTTAATTGGGT
1 TTGGTTTAATTGGGT
* *
34226920 TTGGTTCACTTTGGGT
1 TTGGTTTA-ATTGGGT
*
34226936 TTGGGTT-ATTGGGT
1 TTGGTTTAATTGGGT
34226950 TTAGGTTT
1 TT-GGTTT
34226958 GGGCTTAAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
14 8 0.27
15 11 0.37
16 11 0.37
ACGTcount: A:0.09, C:0.04, G:0.34, T:0.53
Consensus pattern (15 bp):
TTGGTTTAATTGGGT
Found at i:34229428 original size:23 final size:23
Alignment explanation
Indices: 34229402--34229451 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
34229392 AACATGCATG
34229402 AATACTATTTGAAACGGATTTAA
1 AATACTATTTGAAACGGATTTAA
34229425 AATACTATTTGAAACGGATTTAA
1 AATACTATTTGAAACGGATTTAA
34229448 AATA
1 AATA
34229452 AGTTAGAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.34
Consensus pattern (23 bp):
AATACTATTTGAAACGGATTTAA
Found at i:34230623 original size:7 final size:6
Alignment explanation
Indices: 34230594--34230626 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
34230584 TGTACATATA
34230594 TCCTTT TCCTTT TCCTTT TCCTTAT TCCTTT TC
1 TCCTTT TCCTTT TCCTTT TCCTT-T TCCTTT TC
34230627 ATTTATGCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.64
Consensus pattern (6 bp):
TCCTTT
Found at i:34237375 original size:19 final size:21
Alignment explanation
Indices: 34237327--34237373 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
34237317 GTCTATTAAA
34237327 ATAAAAATGTATAAAACACAT
1 ATAAAAATGTATAAAACACAT
34237348 ATAAAAATGTATAAAACACAT
1 ATAAAAATGTATAAAACACAT
34237369 -TAAAA
1 ATAAAA
34237374 TGAAGTCTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.64, C:0.09, G:0.04, T:0.23
Consensus pattern (21 bp):
ATAAAAATGTATAAAACACAT
Found at i:34238034 original size:20 final size:20
Alignment explanation
Indices: 34237993--34238042 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
34237983 ACCAAAATTT
* **
34237993 TATTTTAA-TACAATATTTA
1 TATTTTAATTATAATATGCA
34238012 TATTTTAATTATAATATGCA
1 TATTTTAATTATAATATGCA
34238032 TATTTT-ATTAT
1 TATTTTAATTAT
34238043 CTCAATCACG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (20 bp):
TATTTTAATTATAATATGCA
Found at i:34239708 original size:17 final size:17
Alignment explanation
Indices: 34239657--34239708 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
34239647 GGCCCGGCCA
*
34239657 TTTTTA-ATTTTATAAT
1 TTTTTATATTATATAAT
** * *
34239673 AATTTATATTATGTTAT
1 TTTTTATATTATATAAT
34239690 TTTTTATATTATATAAT
1 TTTTTATATTATATAAT
34239707 TT
1 TT
34239709 AGAACATGTT
Statistics
Matches: 26, Mismatches: 9, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
16 4 0.15
17 22 0.85
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
TTTTTATATTATATAAT
Found at i:34239718 original size:31 final size:32
Alignment explanation
Indices: 34239656--34239719 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 32
34239646 CGGCCCGGCC
* * **
34239656 ATTTTTAATTTTATAATAATTTATATTATGTT
1 ATTTTTAATATTATAATAATTTAGAACATGTT
*
34239688 ATTTTTTATATTAT-ATAATTTAGAACATGTT
1 ATTTTTAATATTATAATAATTTAGAACATGTT
34239719 A
1 A
34239720 AAAAATAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 15 0.56
32 12 0.44
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.58
Consensus pattern (32 bp):
ATTTTTAATATTATAATAATTTAGAACATGTT
Found at i:34240410 original size:20 final size:19
Alignment explanation
Indices: 34240357--34240419 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 19
34240347 TAAACGTAAG
34240357 AAAAATATTCTTTTATATAA
1 AAAAATATT-TTTTATATAA
34240377 AAATTAAT-TTTTTTA-ATAA
1 AAA--AATATTTTTTATATAA
34240396 ATAAAATATTATTTTATATAA
1 A-AAAATATT-TTTTATATAA
34240417 AAA
1 AAA
34240420 TTAACTTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
18 3 0.08
19 7 0.19
20 17 0.46
21 7 0.19
22 3 0.08
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
AAAAATATTTTTTATATAA
Found at i:34240420 original size:23 final size:23
Alignment explanation
Indices: 34240373--34240420 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
34240363 ATTCTTTTAT
*
34240373 ATAAAAATTAATTTTTTTAATAA
1 ATAAAAATTAATTTTTATAATAA
34240396 ATAAAATATT-ATTTTATATAA-AA
1 ATAAAA-ATTAATTTT-TATAATAA
34240419 AT
1 AT
34240421 TAACTTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
ATAAAAATTAATTTTTATAATAA
Found at i:34241605 original size:26 final size:26
Alignment explanation
Indices: 34241576--34241665 Score: 105
Period size: 26 Copynumber: 3.5 Consensus size: 26
34241566 ACAATACAAC
34241576 AAAATTATAATAAAAAAACATAAATA
1 AAAATTATAATAAAAAAACATAAATA
*
34241602 AAAATCCA-AATAAACAACAACA-AAAT-
1 AAAAT-TATAATAAA-AA-AACATAAATA
*
34241628 AAAATTATAATAAAAAAACATAAACA
1 AAAATTATAATAAAAAAACATAAATA
*
34241654 AAAATTAAAATA
1 AAAATTATAATA
34241666 CAGCAGAAAC
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
24 4 0.07
25 6 0.11
26 33 0.61
27 7 0.13
28 4 0.07
ACGTcount: A:0.72, C:0.09, G:0.00, T:0.19
Consensus pattern (26 bp):
AAAATTATAATAAAAAAACATAAATA
Found at i:34241665 original size:52 final size:52
Alignment explanation
Indices: 34241562--34241665 Score: 154
Period size: 52 Copynumber: 2.0 Consensus size: 52
34241552 CAACAACAAC
* * * *
34241562 AACAACAATACAACAAAATTATAATAAAAAAACATAAATAAAAATCCAAATA
1 AACAACAACAAAACAAAATTATAATAAAAAAACATAAACAAAAATCAAAATA
* *
34241614 AACAACAACAAAATAAAATTATAATAAAAAAACATAAACAAAAATTAAAATA
1 AACAACAACAAAACAAAATTATAATAAAAAAACATAAACAAAAATCAAAATA
34241666 CAGCAGAAAC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.71, C:0.12, G:0.00, T:0.17
Consensus pattern (52 bp):
AACAACAACAAAACAAAATTATAATAAAAAAACATAAACAAAAATCAAAATA
Done.