Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 168 of 259
Found at i:54527448 original size:45 final size:45
Alignment explanation
Indices: 54527201--54527461 Score: 117
Period size: 45 Copynumber: 5.8 Consensus size: 45
54527191 TTCAATTTGT
* * * * *
54527201 TCCACTGCAACTTCAGGAAAATAAGATTCGCTATCTTC-AGTCTGC
1 TCCACTACAACTTCAGGGAAATAAGATTCACAATCTTCGA-TCTAC
* * * * * ** *
54527246 TCCACTGCAACTTCAGGGAGATAAGACTCGCTAT-TTTTAGTCTGC
1 TCCACTACAACTTCAGGGAAATAAGATTCACAATCTTCGA-TCTAC
* * * ** * *
54527291 TCCACTGCAACTTCAAGGAGATAAGACTT-GTAA-CTTC-AACTTGC
1 TCCACTACAACTTCAGGGAAATAAGA-TTCACAATCTTCGATC-TAC
** * *
54527335 TCCACTGTAATTTCAGGGAGATAAGATT---AATGGCTTCGATCTAC
1 TCCACTACAACTTCAGGGAAATAAGATTCACAAT--CTTCGATCTAC
* * * *
54527379 TCCACTGCAACTTCAGGGAGATAAGATTCACCATCTTCGATCTAT
1 TCCACTACAACTTCAGGGAAATAAGATTCACAATCTTCGATCTAC
* * *
54527424 TCCACTACTA-TCTCGGGGAAATAAGATTTACAATCTTC
1 TCCACTACAACT-TCAGGGAAATAAGATTCACAATCTTC
54527462 AGTCTGTTTC
Statistics
Matches: 179, Mismatches: 25, Indels: 24
0.79 0.11 0.11
Matches are distributed among these distances:
41 2 0.01
43 3 0.02
44 62 0.35
45 109 0.61
46 1 0.01
47 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (45 bp):
TCCACTACAACTTCAGGGAAATAAGATTCACAATCTTCGATCTAC
Found at i:54527677 original size:177 final size:177
Alignment explanation
Indices: 54527414--54527983 Score: 560
Period size: 177 Copynumber: 3.2 Consensus size: 177
54527404 ATTCACCATC
* * ** * * *
54527414 TTCGATCTATTCCACTACTATCTCGGGGAAATAAGATTTACAATCTTCAGTCTGTTTCCTTGCTA
1 TTCGATCTACTCCACTACT-GCTTAGGGAGATAAGATCTACAATCTTCAGTCTGCTTCCTTGCTA
* * * *
54527479 CATCAGGAAGATAAGACTACAATCTTC-GACCTACTCCTTTACTACCTCAGGGAGATAAAGCTGG
65 CATCAAGAAGATAAGACTACAATCTTCAG-CCTGCTCCTTTACTACCTCAGGGAGATAAGGCTAG
* *
54527543 TGGCTAAAATCTACTCCCCTGCTACCTCGGGAAGATAAGCTTTGCCGTT
129 TGGCTAAAATCTGCTCCCCTGCTACCTCGGGAAGATAAGATTTGCCGTT
*
54527592 TTCGATCTACTCCACTACTGCTTAGGGAGAGAAGATCTACAATCTTCAGTCTGCTTCCTTGCTAC
1 TTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAGTCTGCTTCCTTGCTAC
* * * *
54527657 ATCAAGAAGATAATACTACAATTTTCAGCTTGCT-CTCTTACTACCTCAAGGAGATAAGGCTAGT
66 ATCAAGAAGATAAGACTACAATCTTCAGCCTGCTCCT-TTACTACCTCAGGGAGATAAGGCTAGT
** * * * * * *
54527721 GGCTAAAATCTGCTCGTCTGCTACTTCAGGAAGATAGGAGTCGCCATT
130 GGCTAAAATCTGCTCCCCTGCTACCTCGGGAAGATAAGATTTGCCGTT
* * * * * * * * * * *
54527769 TTCGATTTGCCCCACTGCT-ATCTCGAGGATACAAGATCTACAATCTTCAGTCTACTCCCTCGCT
1 TTCGATCTACTCCACTACTGCT-TAG-GGAGATAAGATCTACAATCTTCAGTCTGCTTCCTTGCT
* * * * **
54527833 ACCTC-AGAAAGATAAGACTACAATCTTCAGCCTGCTGCC-TTGCT-GCTTAGGGAGGCAAGGCT
64 ACATCAAG-AAGATAAGACTACAATCTTCAGCCTGCT-CCTTTACTACCTCAGGGAGATAAGGCT
* * ** *
54527895 AGTGGCTGAAATCTGCTCCCTTATTACCTCAGGG-AGATAAGATTTGCCGTC
127 AGTGGCTAAAATCTGCTCCCCTGCTACCTC-GGGAAGATAAGATTTGCCGTT
** *
54527946 TTCGATCTGTTCCACTACTGCCTAGGGAGATAAGATCT
1 TTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCT
54527984 GTAATCTTTA
Statistics
Matches: 314, Mismatches: 69, Indels: 20
0.78 0.17 0.05
Matches are distributed among these distances:
176 14 0.04
177 212 0.68
178 87 0.28
180 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.29
Consensus pattern (177 bp):
TTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAGTCTGCTTCCTTGCTAC
ATCAAGAAGATAAGACTACAATCTTCAGCCTGCTCCTTTACTACCTCAGGGAGATAAGGCTAGTG
GCTAAAATCTGCTCCCCTGCTACCTCGGGAAGATAAGATTTGCCGTT
Found at i:54527706 original size:44 final size:44
Alignment explanation
Indices: 54527628--54527713 Score: 104
Period size: 44 Copynumber: 2.0 Consensus size: 44
54527618 GAGAGAAGAT
*
54527628 CTACAATCTTCAGTCTGCTTCCTTGCTACATCAAGAAGATAATA
1 CTACAATCTTCAGTCTGCTTCCTTACTACATCAAGAAGATAATA
* * *
54527672 CTACAATTTTCAG-CTTGC-TCTCTTACTACCTCAAGGAGATAA
1 CTACAATCTTCAGTC-TGCTTC-CTTACTACATCAAGAAGATAA
54527714 GGCTAGTGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
43 3 0.08
44 33 0.92
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.33
Consensus pattern (44 bp):
CTACAATCTTCAGTCTGCTTCCTTACTACATCAAGAAGATAATA
Found at i:54527973 original size:44 final size:44
Alignment explanation
Indices: 54527925--54528350 Score: 260
Period size: 44 Copynumber: 9.8 Consensus size: 44
54527915 TTATTACCTC
* * *
54527925 AGGGAGATAAGATTTGCCGTCTTCGATCTGTTCCACTACTGCCT
1 AGGGAGATAAGATTTGCAGTCTTCGATCTGCTCCACTACTGCTT
* * * * * *
54527969 AGGGAGATAAGATCTGTAATCTT-TAGCTTACTCCACTACTGCTT
1 AGGGAGATAAGATTTGCAGTCTTCGATC-TGCTCCACTACTGCTT
* * ** * ** *
54528013 AGAGAGAT-AGA-ATGGTGGCTTAAATATGCTCCACTACTGCTT
1 AGGGAGATAAGATTTGCAGTCTTCGATCTGCTCCACTACTGCTT
* * * *
54528055 AGGGAGACAAGATTCGCTGTCTTCGATCTGCTTCACTACTGCTT
1 AGGGAGATAAGATTTGCAGTCTTCGATCTGCTCCACTACTGCTT
* * * * * *
54528099 AGGGAGAAAAGATCTGTAATCTTC-AGCCTACTCCACTACTGCTT
1 AGGGAGATAAGATTTGCAGTCTTCGA-TCTGCTCCACTACTGCTT
* ** *
54528143 AGGGAGATAAGATGGTG--G-CTTAAATCTGCTCCACTAATGCTT
1 AGGGAGATAAGAT-TTGCAGTCTTCGATCTGCTCCACTACTGCTT
* * ** *
54528185 AGGGAGACAAGCTTCACCGTCTTCGATCTGCTCCACTACTGCTT
1 AGGGAGATAAGATTTGCAGTCTTCGATCTGCTCCACTACTGCTT
* * * * *
54528229 AGGGAGATAAGATCTGTAATCTTC-AGCCTGCTCCACTACTGCTC
1 AGGGAGATAAGATTTGCAGTCTTCGA-TCTGCTCCACTACTGCTT
* ** ** * ** *
54528273 AGGGAGACAAG-GCTGGTGGCTTAAATCTGCTCCACTACTACTT
1 AGGGAGATAAGATTTGCAGTCTTCGATCTGCTCCACTACTGCTT
* * *
54528316 AGGGAGACAAGATTAGCCA-TCTTCTATCTGCTCCA
1 AGGGAGATAAGATTTG-CAGTCTTCGATCTGCTCCA
54528351 TTGCTACCTC
Statistics
Matches: 287, Mismatches: 81, Indels: 28
0.72 0.20 0.07
Matches are distributed among these distances:
42 55 0.19
43 45 0.16
44 185 0.64
45 2 0.01
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.29
Consensus pattern (44 bp):
AGGGAGATAAGATTTGCAGTCTTCGATCTGCTCCACTACTGCTT
Found at i:54528079 original size:130 final size:130
Alignment explanation
Indices: 54527925--54528350 Score: 604
Period size: 130 Copynumber: 3.3 Consensus size: 130
54527915 TTATTACCTC
* * *
54527925 AGGGAGATAAGATTTGCCGTCTTCGATCTGTTCCACTACTGCCTAGGGAGATAAGATCTGTAATC
1 AGGGAGACAAGATTCGCCGTCTTCGATCTGTTCCACTACTGCTTAGGGAGATAAGATCTGTAATC
* * * *
54527990 TTTAGCTTACTCCACTACTGCTTAGAGAGATAGAATGGTGGCTTAAATATGCTCCACTACTGCTT
66 TTCAGCCTACTCCACTACTGCTTAGGGAGATAGAATGGTGGCTTAAATCTGCTCCACTACTGCTT
* *
54528055 AGGGAGACAAGATTCGCTGTCTTCGATCTGCTT-CACTACTGCTTAGGGAGAAAAGATCTGTAAT
1 AGGGAGACAAGATTCGCCGTCTTCGATCTG-TTCCACTACTGCTTAGGGAGATAAGATCTGTAAT
*
54528119 CTTCAGCCTACTCCACTACTGCTTAGGGAGATA-AGATGGTGGCTTAAATCTGCTCCACTAATGC
65 CTTCAGCCTACTCCACTACTGCTTAGGGAGATAGA-ATGGTGGCTTAAATCTGCTCCACTACTGC
54528183 TT
129 TT
* * *
54528185 AGGGAGACAAGCTTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATC
1 AGGGAGACAAGATTCGCCGTCTTCGATCTGTTCCACTACTGCTTAGGGAGATAAGATCTGTAATC
* * * ** *
54528250 TTCAGCCTGCTCCACTACTGCTCAGGGAGACAAGGCTGGTGGCTTAAATCTGCTCCACTACTACT
66 TTCAGCCTACTCCACTACTGCTTAGGGAGA-TAGAATGGTGGCTTAAATCTGCTCCACTACTGCT
54528315 T
130 T
* * * *
54528316 AGGGAGACAAGATTAGCCATCTTCTATCTGCTCCA
1 AGGGAGACAAGATTCGCCGTCTTCGATCTGTTCCA
54528351 TTGCTACCTC
Statistics
Matches: 264, Mismatches: 27, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
129 2 0.01
130 201 0.76
131 61 0.23
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.29
Consensus pattern (130 bp):
AGGGAGACAAGATTCGCCGTCTTCGATCTGTTCCACTACTGCTTAGGGAGATAAGATCTGTAATC
TTCAGCCTACTCCACTACTGCTTAGGGAGATAGAATGGTGGCTTAAATCTGCTCCACTACTGCTT
Found at i:54528184 original size:86 final size:86
Alignment explanation
Indices: 54528041--54528242 Score: 223
Period size: 86 Copynumber: 2.3 Consensus size: 86
54528031 CTTAAATATG
* * ** * *
54528041 CTCCACTACTGCTTAGGGAGACAAGATTCGCTGTCTTCGATCTGCTTCACTACTGCTTAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAAGA-TCGCTGGCTTAAATCTGCTCCACTAATGCTTAGGGAGA
54528106 AAAGATCTGT-A-ATCTTC-AGCCTA
65 AAAG--CT-TCACATCTTCGA-CCTA
* *
54528129 CTCCACTACTGCTTAGGGAGATAAGAT-GGTGGCTTAAATCTGCTCCACTAATGCTTAGGGAGAC
1 CTCCACTACTGCTTAGGGAGATAAGATCGCTGGCTTAAATCTGCTCCACTAATGCTTAGGGAGAA
* * *
54528193 AAGCTTCACCGTCTTCGATCTG
66 AAGCTTCA-CATCTTCGACCTA
54528215 CTCCACTACTGCTTAGGGAGATAAGATC
1 CTCCACTACTGCTTAGGGAGATAAGATC
54528243 TGTAATCTTC
Statistics
Matches: 98, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
83 1 0.01
84 3 0.03
86 67 0.68
87 2 0.02
88 25 0.26
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (86 bp):
CTCCACTACTGCTTAGGGAGATAAGATCGCTGGCTTAAATCTGCTCCACTAATGCTTAGGGAGAA
AAGCTTCACATCTTCGACCTA
Found at i:54530123 original size:19 final size:20
Alignment explanation
Indices: 54530090--54530127 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
54530080 CCACGATTCT
54530090 TTTTTTTATTATTTTTGCTC
1 TTTTTTTATTATTTTTGCTC
*
54530110 TTTTTTTCTT-TTTTTGCT
1 TTTTTTTATTATTTTTGCT
54530128 GCCTTTGCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.05, C:0.11, G:0.05, T:0.79
Consensus pattern (20 bp):
TTTTTTTATTATTTTTGCTC
Found at i:54536685 original size:55 final size:53
Alignment explanation
Indices: 54536564--54536714 Score: 134
Period size: 55 Copynumber: 2.8 Consensus size: 53
54536554 AAACTATATG
* * * * *
54536564 ATAAATAATATATAAAAATAATAAAATA-ATAGA-ATA-AGTGAAATAT-AATAA
1 ATAAATAATATATATATATAATAAAA-ACATA-ACATATAATAAAATGTGAATAA
* *
54536615 ATAAATAATATATATATAGTAA-AAATATATAACATATAATAAAATGTGAATATA
1 ATAAATAATATATATATA-TAATAAAAACATAACATATAATAAAATGTGAATA-A
*
54536669 ATAGAATAA-ATAATATATATAATAAAAACATAACATATAGTAAAAT
1 ATA-AATAATAT-ATATATATAATAAAAACATAACATATAATAAAAT
54536715 TTATAAAATG
Statistics
Matches: 82, Mismatches: 9, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
50 2 0.02
51 25 0.30
52 10 0.12
53 4 0.05
54 9 0.11
55 32 0.39
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (53 bp):
ATAAATAATATATATATATAATAAAAACATAACATATAATAAAATGTGAATAA
Found at i:54538204 original size:23 final size:22
Alignment explanation
Indices: 54538178--54538246 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
54538168 TATATAATGT
54538178 AATAACAATGAAGACAAAAATAA
1 AATAACAATGAA-ACAAAAATAA
** *
54538201 AATAAGGATGAAACAATAAT--
1 AATAACAATGAAACAAAAATAA
* *
54538221 AATAA-AATAAAATAAAAATAA
1 AATAACAATGAAACAAAAATAA
54538242 CAATA
1 -AATA
54538247 CATTAATAAG
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
19 10 0.28
20 5 0.14
22 11 0.31
23 10 0.28
ACGTcount: A:0.70, C:0.06, G:0.07, T:0.17
Consensus pattern (22 bp):
AATAACAATGAAACAAAAATAA
Found at i:54538223 original size:3 final size:3
Alignment explanation
Indices: 54538215--54538318 Score: 58
Period size: 3 Copynumber: 35.0 Consensus size: 3
54538205 AGGATGAAAC
* * * *
54538215 AAT AAT AAT AA- AAT AA- AAT AAA AAT AAC AAT ACATT AAT AAG AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-A-T AAT AAT AAT
** *
54538260 AAT AAT -AT GTT AAT -AT AA- ATAT AAT AAT AAT AAT AAT GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
54538303 ACA- AATT AAT AAT AAT
1 A-AT AA-T AAT AAT AAT
54538319 GATGATGTAA
Statistics
Matches: 77, Mismatches: 13, Indels: 22
0.69 0.12 0.20
Matches are distributed among these distances:
2 10 0.13
3 59 0.77
4 6 0.08
5 2 0.03
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:54538240 original size:22 final size:25
Alignment explanation
Indices: 54538196--54538246 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
54538186 TGAAGACAAA
* *
54538196 AATAAAATAAGGATGAAACAATAAT
1 AATAAAATAAGAATGAAACAATAAC
54538221 AATAAAATAA-AAT-AAA-AATAAC
1 AATAAAATAAGAATGAAACAATAAC
54538243 AATA
1 AATA
54538247 CATTAATAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 9 0.38
23 3 0.12
24 2 0.08
25 10 0.42
ACGTcount: A:0.71, C:0.04, G:0.06, T:0.20
Consensus pattern (25 bp):
AATAAAATAAGAATGAAACAATAAC
Found at i:54538254 original size:30 final size:29
Alignment explanation
Indices: 54538194--54538255 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
54538184 AATGAAGACA
**
54538194 AAAATAAAATAAGGATGAAACAATAATAAT
1 AAAATAAAATAAAAAT-AAACAATAATAAT
54538224 AAAATAAAATAAAAAT-AACAATACATTAAT
1 AAAATAAAATAAAAATAAACAATA-A-TAAT
54538254 AA
1 AA
54538256 GAGTAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 7 0.25
29 1 0.04
30 20 0.71
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (29 bp):
AAAATAAAATAAAAATAAACAATAATAAT
Found at i:54538312 original size:28 final size:28
Alignment explanation
Indices: 54538259--54538340 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
54538249 TTAATAAGAG
* *
54538259 TAATAATATGTTAATATAAATATAATAA
1 TAATAATATGATAATACAAATATAATAA
54538287 TAATAATAATGATAATACAAAT-TAATAA
1 TAATAAT-ATGATAATACAAATATAATAA
* *
54538315 TAATGATGATG-TAAGTAAAAATATAA
1 TAATAAT-ATGATAA-TACAAATATAA
54538341 GTAAATGCAA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
27 3 0.07
28 28 0.61
29 15 0.33
ACGTcount: A:0.57, C:0.01, G:0.07, T:0.34
Consensus pattern (28 bp):
TAATAATATGATAATACAAATATAATAA
Found at i:54538565 original size:3 final size:3
Alignment explanation
Indices: 54538559--54538619 Score: 72
Period size: 3 Copynumber: 20.3 Consensus size: 3
54538549 AATAATACGT
*
54538559 TAA TAA TAA TAA TAA TAG TAA -ATA TAA TAA TAA TAA TAA TAA -ATA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TA-A
*
54538604 TAA TAA TAA AAA TAA T
1 TAA TAA TAA TAA TAA T
54538620 TAATTTGAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
2 2 0.04
3 46 0.92
4 2 0.04
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:54538587 original size:21 final size:21
Alignment explanation
Indices: 54538561--54538619 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
54538551 TAATACGTTA
*
54538561 ATAATAATAATAATAGTAAAT
1 ATAATAATAATAATAATAAAT
54538582 ATAATAATAATAATAATAAAT
1 ATAATAATAATAATAATAAAT
*
54538603 ATAATAATAAAAATAAT
1 ATAATAATAATAATAAT
54538620 TAATTTGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
ATAATAATAATAATAATAAAT
Found at i:54563100 original size:24 final size:22
Alignment explanation
Indices: 54563068--54563121 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
54563058 GTAGTTCCTG
*
54563068 ACTCATTTAAATGGGTGTGGGATT
1 ACTCATTTAAA-CGGTGT-GGATT
*
54563092 ACTCGTTTAAACGGTGTGGATT
1 ACTCATTTAAACGGTGTGGATT
54563114 ACTCATTT
1 ACTCATTT
54563122 TTGAAACTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 12 0.44
23 5 0.19
24 10 0.37
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.39
Consensus pattern (22 bp):
ACTCATTTAAACGGTGTGGATT
Found at i:54564557 original size:23 final size:22
Alignment explanation
Indices: 54564531--54564575 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
54564521 TATATAATGC
54564531 AATAACAATGAAGACAAAAATAA
1 AATAACAATGAA-ACAAAAATAA
** *
54564554 AATAAGGATGAAACAATAATAA
1 AATAACAATGAAACAAAAATAA
54564576 TAAATAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.67, C:0.07, G:0.11, T:0.16
Consensus pattern (22 bp):
AATAACAATGAAACAAAAATAA
Found at i:54564576 original size:3 final size:3
Alignment explanation
Indices: 54564568--54564642 Score: 64
Period size: 3 Copynumber: 24.0 Consensus size: 3
54564558 AGGATGAAAC
* *
54564568 AAT AAT AAT AAAT AAAT AAA AAT AAC AAT ACATT AAT AAT -AT AAT AAT
1 AAT AAT AAT -AAT -AAT AAT AAT AAT AAT A-A-T AAT AAT AAT AAT AAT
*
54564616 AAT AAT GAT AAT AA- AATT AAT AAT AAT
1 AAT AAT AAT AAT AAT AA-T AAT AAT AAT
54564643 GATGATGTAA
Statistics
Matches: 60, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
2 4 0.07
3 43 0.72
4 11 0.18
5 2 0.03
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:54564890 original size:12 final size:12
Alignment explanation
Indices: 54564872--54564901 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
54564862 TAGTAGTAAT
54564872 AATAATAATAAA
1 AATAATAATAAA
*
54564884 GATAATAATAAA
1 AATAATAATAAA
54564896 AATAAT
1 AATAAT
54564902 TAATTTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (12 bp):
AATAATAATAAA
Found at i:54565844 original size:23 final size:24
Alignment explanation
Indices: 54565792--54565851 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
54565782 TTTAAACCTT
*
54565792 GCAGGTGGCAGAGCAAGCGGAGGA
1 GCAGGTGGCAGAGCAAACGGAGGA
* * *
54565816 GTAGGTGGCTGA-CAAACGGTGGA
1 GCAGGTGGCAGAGCAAACGGAGGA
54565839 GCAGGTGGTCAGA
1 GCAGGTGG-CAGA
54565852 AGATTAGCAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
23 16 0.55
24 13 0.45
ACGTcount: A:0.27, C:0.15, G:0.47, T:0.12
Consensus pattern (24 bp):
GCAGGTGGCAGAGCAAACGGAGGA
Found at i:54566460 original size:44 final size:43
Alignment explanation
Indices: 54566277--54566931 Score: 200
Period size: 44 Copynumber: 14.7 Consensus size: 43
54566267 TGCTCCATTG
**
54566277 CTCCACTGCAACTTCAAGGAGATAAGATTTGTAACTTCAATCTA
1 CTCCACTGCAACTTC-AGGAGATAAGATTTGTGGCTTCAATCTA
** * *
54566321 CTCCACTTTATCTTCAGGGAGATAAGATTTGTGG--T-AAT-TCG
1 CTCCACTGCAACTTCA-GGAGATAAGATTTGTGGCTTCAATCT-A
* * * * * *
54566362 CTCCTCTACAACTTCA-GAGGTATGAGATTTGCTGTCTTCAGTCTG
1 CTCCACTGCAACTTCAGGA-G-ATAAGATTTG-TGGCTTCAATCTA
* * *
54566407 CTCCGCTGCAACTTCAGGAAGATAGGACTTGTGGCTTCAATCTA
1 CTCCACTGCAACTTCAGG-AGATAAGATTTGTGGCTTCAATCTA
* * * ** *
54566451 CTCCACTGCAACTTCAAGTAGATAAGATTTTCCATGGTAGATTTGATCCGA
1 CTCCACTGCAACTTC-AGGAGATAAGA--TT---T-GTGGCTTCAAT-CTA
* * * * * * **
54566502 C-CTACTGCAACTTCA-GAGGTATAAGACTCGTCGTTTAAATCCG
1 CTCCACTGCAACTTCAGGA-G-ATAAGATTTGTGGCTTCAATCTA
* * * * *
54566545 CTCCACTACAACTTCAGGGAGATAGGATTAGTTGTCTTCAGTCTA
1 CTCCACTGCAACTTCA-GGAGATAAGATTTG-TGGCTTCAATCTA
* * * *** * * *
54566590 CCCCGCTGCAACTTCAGGGAGATAAGACTTGTAATTTTAACCTG
1 CTCCACTGCAACTTCA-GGAGATAAGATTTGTGGCTTCAATCTA
* * * *
54566634 CTCCACTGCAATTTCAAGGAGATAAG-GTT-T-GCTAT-GATCTG
1 CTCCACTGCAACTTC-AGGAGATAAGATTTGTGGCT-TCAATCTA
* * * * * *
54566675 CTCTATTGCAACTTCAGCGAGATAAGATCTATAATTTATAGCTTCAATTTG
1 CTCCACTGCAACTTCAG-GAGATAAG-------ATTTGTGGCTTCAATCTA
* * * ** * *
54566726 TTCCACTGCAACTTCAGGAAATAAGATTCGCTATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGAGATAAGATTTG-TGGCTTCAATCTA
* * *** * * *
54566770 CTCCACTGCAACTTCAGGGAGATAAGACTCGCTATTTTTAGTCTG
1 CTCCACTGCAACTTCA-GGAGATAAGATTTG-TGGCTTCAATCTA
* ** *
54566815 CTCCACTGCAACTTCAAGGAGATAAGACTTGTAACTTCAA-CTTG
1 CTCCACTGCAACTTC-AGGAGATAAGATTTGTGGCTTCAATC-TA
* * ** *
54566859 CTCCACTGTAATTTCAGGGAGATAAGATTAATGGCTTCGATCTA
1 CTCCACTGCAACTTCA-GGAGATAAGATTTGTGGCTTCAATCTA
54566903 CTCCACTGCAACTTCAGGGAGATAAGATT
1 CTCCACTGCAACTTCA-GGAGATAAGATT
54566932 CACCATCTTC
Statistics
Matches: 457, Mismatches: 109, Indels: 90
0.70 0.17 0.14
Matches are distributed among these distances:
39 2 0.00
40 4 0.01
41 49 0.11
42 5 0.01
43 10 0.02
44 202 0.44
45 112 0.25
46 7 0.02
47 1 0.00
48 2 0.00
49 5 0.01
50 34 0.07
51 24 0.05
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (43 bp):
CTCCACTGCAACTTCAGGAGATAAGATTTGTGGCTTCAATCTA
Found at i:54566813 original size:45 final size:45
Alignment explanation
Indices: 54566505--54566843 Score: 192
Period size: 45 Copynumber: 7.6 Consensus size: 45
54566495 GATCCGACCT
* ** * * *
54566505 ACTGCAACTTCAGAGG-TATAAGACTCG-TCGTTTAAATCCGCTCC
1 ACTGCAACTTCAG-GGAGATAAGACTCGCTATTTTTAGTCTGCTCC
* * * * * * * * * *
54566549 ACTACAACTTCAGGGAGATAGGATTAGTTGTCTTCAGTCTACCCC
1 ACTGCAACTTCAGGGAGATAAGACTCGCTATTTTTAGTCTGCTCC
* * * **
54566594 GCTGCAACTTCAGGGAGATAAGACTTG-TAATTTTAACCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGACTCGCTATTTTTAGTCTGCTCC
* * ** * * *
54566638 ACTGCAATTTCAAGGAGATAAGGTTTGCTA---TGA-TCTGCTCT
1 ACTGCAACTTCAGGGAGATAAGACTCGCTATTTTTAGTCTGCTCC
* * ** * *
54566679 ATTGCAACTTCAGCGAGATAAGA-TCTATAATTTATAGCTTCAATTTGTTCC
1 ACTGCAACTTCAGGGAGATAAGACTCGCT-ATTTTTAG--TC----TGCTCC
* * * *
54566730 ACTGCAACTTCA-GGAAATAAGATTCGCTATCTTCAGTCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGACTCGCTATTTTTAGTCTGCTCC
54566774 ACTGCAACTTCAGGGAGATAAGACTCGCTATTTTTAGTCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGACTCGCTATTTTTAGTCTGCTCC
*
54566819 ACTGCAACTTCAAGGAGATAAGACT
1 ACTGCAACTTCAGGGAGATAAGACT
54566844 TGTAACTTCA
Statistics
Matches: 219, Mismatches: 60, Indels: 31
0.71 0.19 0.10
Matches are distributed among these distances:
40 2 0.01
41 25 0.11
42 2 0.01
43 2 0.01
44 68 0.31
45 85 0.39
47 2 0.01
48 2 0.01
50 13 0.06
51 18 0.08
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (45 bp):
ACTGCAACTTCAGGGAGATAAGACTCGCTATTTTTAGTCTGCTCC
Found at i:54566973 original size:45 final size:45
Alignment explanation
Indices: 54566727--54566986 Score: 117
Period size: 45 Copynumber: 5.8 Consensus size: 45
54566717 TTCAATTTGT
* * * *
54566727 TCCACTGCAACTTCA-GGAAATAAGATTCGCTATCTTC-AGTCTGC
1 TCCACTACAACTTCAGGGAAATAAGATTCACAATCTTCGA-TCTAC
* * * * * ** *
54566771 TCCACTGCAACTTCAGGGAGATAAGACTCGCTAT-TTTTAGTCTGC
1 TCCACTACAACTTCAGGGAAATAAGATTCACAATCTTCGA-TCTAC
* * * ** * *
54566816 TCCACTGCAACTTCAAGGAGATAAGACTT-GTAA-CTTC-AACTTGC
1 TCCACTACAACTTCAGGGAAATAAGA-TTCACAATCTTCGATC-TAC
** * *
54566860 TCCACTGTAATTTCAGGGAGATAAGATT---AATGGCTTCGATCTAC
1 TCCACTACAACTTCAGGGAAATAAGATTCACAAT--CTTCGATCTAC
* * * *
54566904 TCCACTGCAACTTCAGGGAGATAAGATTCACCATCTTCGATCTAT
1 TCCACTACAACTTCAGGGAAATAAGATTCACAATCTTCGATCTAC
* * *
54566949 TCCACTACTA-TCTCGGGGAAATAAGATTTACAATCTTC
1 TCCACTACAACT-TCAGGGAAATAAGATTCACAATCTTC
54566987 AGTCTGTTTC
Statistics
Matches: 179, Mismatches: 24, Indels: 25
0.79 0.11 0.11
Matches are distributed among these distances:
41 2 0.01
43 3 0.02
44 77 0.43
45 94 0.53
46 1 0.01
47 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (45 bp):
TCCACTACAACTTCAGGGAAATAAGATTCACAATCTTCGATCTAC
Found at i:54567055 original size:177 final size:178
Alignment explanation
Indices: 54566872--54567488 Score: 541
Period size: 177 Copynumber: 3.5 Consensus size: 178
54566862 CACTGTAATT
* * *** * *
54566872 TCAGGGAGATAAGATTAATGGCTTCGATCTACTCCACTGCAACTTCAGGGAGATAAGATTCACCA
1 TCAGGGAGATAAGACTAGTGGCTAAAATCTACTCCACTGCTACTTCAGGGAGATAAGATTCGCCA
* * * * *
54566937 TCTTCGATCTATTCCACTACTATCTCGGGGAAATAAGATTTACAATCTTCAGTCTGTTTCCTTGC
66 TTTTCGATCTACTCCACTACTATCTCGGGGAAACAAGATCTACAATCTTCAGTCTGCTTCCTTGC
54567002 TACATCAGGAAGATAAGACTACAATCTTC-GACCTACTC-CTTTACTA-C
131 TACATCAGGAAGATAAGACTACAATCTTCAG-CCTACTCTC-TTACTACC
* * * * *
54567049 TCAGGGAGATAA-AGCTGGTGGCTAAAATCTACTCCCCTGCTACCTC-GGGAAGATAAGCTTTGC
1 TCAGGGAGATAAGA-CTAGTGGCTAAAATCTACTCCACTGCTACTTCAGGG-AGATAAGATTCGC
* * ** * *
54567112 CGTTTTCGATCTACTCCACTACT-GCTTAGGGAGAGAAGATCTACAATCTTCAGTCTGCTTCCTT
64 CATTTTCGATCTACTCCACTACTATCTCGGGGAAACAAGATCTACAATCTTCAGTCTGCTTCCTT
* * * * *
54567176 GCTACATCAAGAAGATAATACTACAATTTTCAGCTTGCTCTCTTACTACC
129 GCTACATCAGGAAGATAAGACTACAATCTTCAGCCTACTCTCTTACTACC
* * * ** * * *
54567226 TCAAGGAGATAAGGCTAGTGGCTAAAATCTGCTCGTCTGCTACTTCAGGAAGATAGGAGTCGCCA
1 TCAGGGAGATAAGACTAGTGGCTAAAATCTACTCCACTGCTACTTCAGGGAGATAAGATTCGCCA
* * * * * * * * *
54567291 TTTTCGATTTGCCCCACTGCTATCTCGAGGATACAAGATCTACAATCTTCAGTCTACTCCCTCGC
66 TTTTCGATCTACTCCACTACTATCTCGGGGAAACAAGATCTACAATCTTCAGTCTGCTTCCTTGC
* * * * *
54567356 TACCTCAGAAAGATAAGACTACAATCTTCAGCCTGCTGC-CTTGCT-GC
131 TACATCAGGAAGATAAGACTACAATCTTCAGCCTACT-CTCTTACTACC
* ** * * * ** * *
54567403 TTAGGGAGGCAAGGCTAGTGGCTGAAATCTGCTCC-CTTATTACCTCAGGGAGATAAGATTTGCC
1 TCAGGGAGATAAGACTAGTGGCTAAAATCTACTCCAC-TGCTACTTCAGGGAGATAAGATTCGCC
* * **
54567467 GTCTTCGATCTGTTCCACTACT
65 ATTTTCGATCTACTCCACTACT
54567489 GCCTAGGGAG
Statistics
Matches: 350, Mismatches: 80, Indels: 20
0.78 0.18 0.04
Matches are distributed among these distances:
176 78 0.22
177 199 0.57
178 72 0.21
179 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (178 bp):
TCAGGGAGATAAGACTAGTGGCTAAAATCTACTCCACTGCTACTTCAGGGAGATAAGATTCGCCA
TTTTCGATCTACTCCACTACTATCTCGGGGAAACAAGATCTACAATCTTCAGTCTGCTTCCTTGC
TACATCAGGAAGATAAGACTACAATCTTCAGCCTACTCTCTTACTACC
Found at i:54567230 original size:44 final size:44
Alignment explanation
Indices: 54567152--54567237 Score: 104
Period size: 44 Copynumber: 2.0 Consensus size: 44
54567142 GAGAGAAGAT
*
54567152 CTACAATCTTCAGTCTGCTTCCTTGCTACATCAAGAAGATAATA
1 CTACAATCTTCAGTCTGCTTCCTTACTACATCAAGAAGATAATA
* * *
54567196 CTACAATTTTCAG-CTTGC-TCTCTTACTACCTCAAGGAGATAA
1 CTACAATCTTCAGTC-TGCTTC-CTTACTACATCAAGAAGATAA
54567238 GGCTAGTGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
43 3 0.08
44 33 0.92
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.33
Consensus pattern (44 bp):
CTACAATCTTCAGTCTGCTTCCTTACTACATCAAGAAGATAATA
Found at i:54567497 original size:44 final size:44
Alignment explanation
Indices: 54567449--54567874 Score: 260
Period size: 44 Copynumber: 9.8 Consensus size: 44
54567439 TTATTACCTC
* * *
54567449 AGGGAGATAAGATTTGCCGTCTTCGATCTGTTCCACTACTGCCT
1 AGGGAGATAAGATTTGCAGTCTTCGATCTGCTCCACTACTGCTT
* * * * * *
54567493 AGGGAGATAAGATCTGTAATCTT-TAGCTTACTCCACTACTGCTT
1 AGGGAGATAAGATTTGCAGTCTTCGATC-TGCTCCACTACTGCTT
* * ** * ** *
54567537 AGAGAGAT-AGA-ATGGTGGCTTAAATATGCTCCACTACTGCTT
1 AGGGAGATAAGATTTGCAGTCTTCGATCTGCTCCACTACTGCTT
* * * *
54567579 AGGGAGACAAGATTCGCTGTCTTCGATCTGCTTCACTACTGCTT
1 AGGGAGATAAGATTTGCAGTCTTCGATCTGCTCCACTACTGCTT
* * * * * *
54567623 AGGGAGAAAAGATCTGTAATCTTC-AGCCTACTCCACTACTGCTT
1 AGGGAGATAAGATTTGCAGTCTTCGA-TCTGCTCCACTACTGCTT
* ** *
54567667 AGGGAGATAAGATGGTG--G-CTTAAATCTGCTCCACTAATGCTT
1 AGGGAGATAAGAT-TTGCAGTCTTCGATCTGCTCCACTACTGCTT
* * ** *
54567709 AGGGAGACAAGCTTCACCGTCTTCGATCTGCTCCACTACTGCTT
1 AGGGAGATAAGATTTGCAGTCTTCGATCTGCTCCACTACTGCTT
* * * * *
54567753 AGGGAGATAAGATCTGTAATCTTC-AGCCTGCTCCACTACTGCTC
1 AGGGAGATAAGATTTGCAGTCTTCGA-TCTGCTCCACTACTGCTT
* ** ** * ** *
54567797 AGGGAGACAAG-GCTGGTGGCTTAAATCTGCTCCACTACTACTT
1 AGGGAGATAAGATTTGCAGTCTTCGATCTGCTCCACTACTGCTT
* * *
54567840 AGGGAGACAAGATTAGCCA-TCTTCTATCTGCTCCA
1 AGGGAGATAAGATTTG-CAGTCTTCGATCTGCTCCA
54567875 TTGCTACCTC
Statistics
Matches: 287, Mismatches: 81, Indels: 28
0.72 0.20 0.07
Matches are distributed among these distances:
42 55 0.19
43 45 0.16
44 185 0.64
45 2 0.01
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.29
Consensus pattern (44 bp):
AGGGAGATAAGATTTGCAGTCTTCGATCTGCTCCACTACTGCTT
Found at i:54567603 original size:130 final size:130
Alignment explanation
Indices: 54567449--54567874 Score: 604
Period size: 130 Copynumber: 3.3 Consensus size: 130
54567439 TTATTACCTC
* * *
54567449 AGGGAGATAAGATTTGCCGTCTTCGATCTGTTCCACTACTGCCTAGGGAGATAAGATCTGTAATC
1 AGGGAGACAAGATTCGCCGTCTTCGATCTGTTCCACTACTGCTTAGGGAGATAAGATCTGTAATC
* * * *
54567514 TTTAGCTTACTCCACTACTGCTTAGAGAGATAGAATGGTGGCTTAAATATGCTCCACTACTGCTT
66 TTCAGCCTACTCCACTACTGCTTAGGGAGATAGAATGGTGGCTTAAATCTGCTCCACTACTGCTT
* *
54567579 AGGGAGACAAGATTCGCTGTCTTCGATCTGCTT-CACTACTGCTTAGGGAGAAAAGATCTGTAAT
1 AGGGAGACAAGATTCGCCGTCTTCGATCTG-TTCCACTACTGCTTAGGGAGATAAGATCTGTAAT
*
54567643 CTTCAGCCTACTCCACTACTGCTTAGGGAGATA-AGATGGTGGCTTAAATCTGCTCCACTAATGC
65 CTTCAGCCTACTCCACTACTGCTTAGGGAGATAGA-ATGGTGGCTTAAATCTGCTCCACTACTGC
54567707 TT
129 TT
* * *
54567709 AGGGAGACAAGCTTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATC
1 AGGGAGACAAGATTCGCCGTCTTCGATCTGTTCCACTACTGCTTAGGGAGATAAGATCTGTAATC
* * * ** *
54567774 TTCAGCCTGCTCCACTACTGCTCAGGGAGACAAGGCTGGTGGCTTAAATCTGCTCCACTACTACT
66 TTCAGCCTACTCCACTACTGCTTAGGGAGA-TAGAATGGTGGCTTAAATCTGCTCCACTACTGCT
54567839 T
130 T
* * * *
54567840 AGGGAGACAAGATTAGCCATCTTCTATCTGCTCCA
1 AGGGAGACAAGATTCGCCGTCTTCGATCTGTTCCA
54567875 TTGCTACCTC
Statistics
Matches: 264, Mismatches: 27, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
129 2 0.01
130 201 0.76
131 61 0.23
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.29
Consensus pattern (130 bp):
AGGGAGACAAGATTCGCCGTCTTCGATCTGTTCCACTACTGCTTAGGGAGATAAGATCTGTAATC
TTCAGCCTACTCCACTACTGCTTAGGGAGATAGAATGGTGGCTTAAATCTGCTCCACTACTGCTT
Found at i:54567708 original size:86 final size:86
Alignment explanation
Indices: 54567565--54567766 Score: 223
Period size: 86 Copynumber: 2.3 Consensus size: 86
54567555 CTTAAATATG
* * ** * *
54567565 CTCCACTACTGCTTAGGGAGACAAGATTCGCTGTCTTCGATCTGCTTCACTACTGCTTAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAAGA-TCGCTGGCTTAAATCTGCTCCACTAATGCTTAGGGAGA
54567630 AAAGATCTGT-A-ATCTTC-AGCCTA
65 AAAG--CT-TCACATCTTCGA-CCTA
* *
54567653 CTCCACTACTGCTTAGGGAGATAAGAT-GGTGGCTTAAATCTGCTCCACTAATGCTTAGGGAGAC
1 CTCCACTACTGCTTAGGGAGATAAGATCGCTGGCTTAAATCTGCTCCACTAATGCTTAGGGAGAA
* * *
54567717 AAGCTTCACCGTCTTCGATCTG
66 AAGCTTCA-CATCTTCGACCTA
54567739 CTCCACTACTGCTTAGGGAGATAAGATC
1 CTCCACTACTGCTTAGGGAGATAAGATC
54567767 TGTAATCTTC
Statistics
Matches: 98, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
83 1 0.01
84 3 0.03
86 67 0.68
87 2 0.02
88 25 0.26
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (86 bp):
CTCCACTACTGCTTAGGGAGATAAGATCGCTGGCTTAAATCTGCTCCACTAATGCTTAGGGAGAA
AAGCTTCACATCTTCGACCTA
Found at i:54569638 original size:20 final size:20
Alignment explanation
Indices: 54569613--54569651 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
54569603 CCACGATTCT
54569613 TTTTTTTATTATTTTTGCTC
1 TTTTTTTATTATTTTTGCTC
* *
54569633 TTTTTTTCTTTTTTTTGCT
1 TTTTTTTATTATTTTTGCT
54569652 GCCTTTGCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.05, C:0.10, G:0.05, T:0.79
Consensus pattern (20 bp):
TTTTTTTATTATTTTTGCTC
Found at i:54576090 original size:21 final size:19
Alignment explanation
Indices: 54576024--54576110 Score: 50
Period size: 21 Copynumber: 4.2 Consensus size: 19
54576014 TATATAGTCA
54576024 AATATATAACATATAATAAAT
1 AATATA-AACATAT-ATAAAT
* *
54576045 -TTATAAACAAAATATATAAT
1 AATATAAAC-ATATATA-AAT
*
54576065 GATATAAACTATATGATAAAT
1 AATATAAAC-ATAT-ATAAAT
* *
54576086 AATATATAAAATAATAAAAAT
1 AATATA-AACAT-ATATAAAT
54576107 AATA
1 AATA
54576111 GAATAAGTGA
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
19 6 0.12
20 10 0.19
21 29 0.56
22 7 0.13
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.32
Consensus pattern (19 bp):
AATATAAACATATATAAAT
Found at i:54576219 original size:55 final size:59
Alignment explanation
Indices: 54576121--54576231 Score: 167
Period size: 59 Copynumber: 1.9 Consensus size: 59
54576111 GAATAAGTGA
*
54576121 AATATAATAAAATAAATAATATATATATAGTAAAAATATATAACATATAATAAAATGTG
1 AATATAATAAAATAAATAATATATATATAGTAAAAATACATAACATATAATAAAATGTG
* *
54576180 AATATAATAGAATAAATAATATATATA-A-T-AAAA-ACATAACATATAGTAAAAT
1 AATATAATAAAATAAATAATATATATATAGTAAAAATACATAACATATAATAAAAT
54576232 TTATAAAAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
55 17 0.35
56 4 0.08
57 1 0.02
58 1 0.02
59 26 0.53
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (59 bp):
AATATAATAAAATAAATAATATATATATAGTAAAAATACATAACATATAATAAAATGTG
Found at i:54577722 original size:23 final size:22
Alignment explanation
Indices: 54577696--54577764 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
54577686 TATATAATGT
54577696 AATAACAATGAAGACAAAAATAA
1 AATAACAATGAA-ACAAAAATAA
** *
54577719 AATAAGGATGAAACAATAAT--
1 AATAACAATGAAACAAAAATAA
* *
54577739 AATAA-AATAAAATAAAAATAA
1 AATAACAATGAAACAAAAATAA
54577760 CAATA
1 -AATA
54577765 CATTAATAAG
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
19 10 0.28
20 5 0.14
22 11 0.31
23 10 0.28
ACGTcount: A:0.70, C:0.06, G:0.07, T:0.17
Consensus pattern (22 bp):
AATAACAATGAAACAAAAATAA
Found at i:54577741 original size:3 final size:3
Alignment explanation
Indices: 54577733--54577837 Score: 67
Period size: 3 Copynumber: 35.0 Consensus size: 3
54577723 AGGATGAAAC
* * * *
54577733 AAT AAT AAT AA- AAT AA- AAT AAA AAT AAC AAT ACATT AAT AAG AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-A-T AAT AAT AAT
** *
54577778 AAT AAT -AT GTT AAT -AT AAAT AAT AAT AAT AAT AAT AAT GAT AAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
54577822 ACA- AATT AAT AAT AAT
1 A-AT AA-T AAT AAT AAT
54577838 GATGATGTAA
Statistics
Matches: 79, Mismatches: 13, Indels: 20
0.71 0.12 0.18
Matches are distributed among these distances:
2 9 0.11
3 61 0.77
4 7 0.09
5 2 0.03
ACGTcount: A:0.63, C:0.03, G:0.04, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:54577758 original size:22 final size:25
Alignment explanation
Indices: 54577714--54577764 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
54577704 TGAAGACAAA
* *
54577714 AATAAAATAAGGATGAAACAATAAT
1 AATAAAATAAGAATGAAACAATAAC
54577739 AATAAAATAA-AAT-AAA-AATAAC
1 AATAAAATAAGAATGAAACAATAAC
54577761 AATA
1 AATA
54577765 CATTAATAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 9 0.38
23 3 0.12
24 2 0.08
25 10 0.42
ACGTcount: A:0.71, C:0.04, G:0.06, T:0.20
Consensus pattern (25 bp):
AATAAAATAAGAATGAAACAATAAC
Found at i:54577772 original size:30 final size:29
Alignment explanation
Indices: 54577712--54577773 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
54577702 AATGAAGACA
**
54577712 AAAATAAAATAAGGATGAAACAATAATAAT
1 AAAATAAAATAAAAAT-AAACAATAATAAT
54577742 AAAATAAAATAAAAAT-AACAATACATTAAT
1 AAAATAAAATAAAAATAAACAATA-A-TAAT
54577772 AA
1 AA
54577774 GAGTAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 7 0.25
29 1 0.04
30 20 0.71
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (29 bp):
AAAATAAAATAAAAATAAACAATAATAAT
Found at i:54577855 original size:28 final size:28
Alignment explanation
Indices: 54577777--54577855 Score: 72
Period size: 28 Copynumber: 2.8 Consensus size: 28
54577767 TTAATAAGAG
* *
54577777 TAATAAT-ATGTTAATATAAATAATAATAA
1 TAATAATAATGATAATA-AAA-ATTAATAA
*
54577806 TAATAATAATGATAATACAAATTAATAA
1 TAATAATAATGATAATAAAAATTAATAA
* *
54577834 TAATGATGATG-TAAGTAAAAAT
1 TAATAATAATGATAA-TAAAAAT
54577856 ATAAGTAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
27 3 0.07
28 22 0.52
29 9 0.21
30 8 0.19
ACGTcount: A:0.57, C:0.01, G:0.08, T:0.34
Consensus pattern (28 bp):
TAATAATAATGATAATAAAAATTAATAA
Found at i:54578085 original size:3 final size:3
Alignment explanation
Indices: 54578079--54578139 Score: 72
Period size: 3 Copynumber: 20.3 Consensus size: 3
54578069 AATAATACGT
*
54578079 TAA TAA TAA TAA TAA TAG TAA -ATA TAA TAA TAA TAA TAA TAA -ATA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TA-A
*
54578124 TAA TAA TAA AAA TAA T
1 TAA TAA TAA TAA TAA T
54578140 TAATTTGAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
2 2 0.04
3 46 0.92
4 2 0.04
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:54578107 original size:21 final size:21
Alignment explanation
Indices: 54578081--54578139 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
54578071 TAATACGTTA
*
54578081 ATAATAATAATAATAGTAAAT
1 ATAATAATAATAATAATAAAT
54578102 ATAATAATAATAATAATAAAT
1 ATAATAATAATAATAATAAAT
*
54578123 ATAATAATAAAAATAAT
1 ATAATAATAATAATAAT
54578140 TAATTTGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
ATAATAATAATAATAATAAAT
Found at i:54591396 original size:20 final size:20
Alignment explanation
Indices: 54591363--54591401 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
54591353 TTATTATTAA
*
54591363 TTTTATATGTAAAATATATT
1 TTTTATATGTAAAAAATATT
54591383 TTTTATATAG-AAAAAATAT
1 TTTTATAT-GTAAAAAATAT
54591402 CCATTCTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
TTTTATATGTAAAAAATATT
Found at i:54594187 original size:56 final size:56
Alignment explanation
Indices: 54594055--54594200 Score: 147
Period size: 56 Copynumber: 2.6 Consensus size: 56
54594045 ATTATGCTTT
* * *
54594055 TTTTTTAAAAAAAATTAATTAAGCTCTCCTAATTTTTTTGAAAATTTTCATGAATACACA
1 TTTTTT-AAAAAAATTAATT-AGATC-CCCAAATTTTTT-AAAATTTTCATGAATACACA
* * * *
54594115 TTTTCT-AAAAATTTAATTAGATCCCCAAATTTTTT-AAATTTTCATTAA-ACTTCTA
1 TTTTTTAAAAAAATTAATTAGATCCCCAAATTTTTTAAAATTTTCATGAATAC-AC-A
54594170 TTTTTTAAAAAAATTAATTAGA-CCCCAAATT
1 TTTTTTAAAAAAATTAATTAGATCCCCAAATT
54594201 CTTAGTCGTA
Statistics
Matches: 74, Mismatches: 9, Indels: 11
0.79 0.10 0.12
Matches are distributed among these distances:
53 2 0.03
54 13 0.18
55 15 0.20
56 24 0.32
57 4 0.05
58 11 0.15
60 5 0.07
ACGTcount: A:0.40, C:0.13, G:0.03, T:0.44
Consensus pattern (56 bp):
TTTTTTAAAAAAATTAATTAGATCCCCAAATTTTTTAAAATTTTCATGAATACACA
Found at i:54594869 original size:14 final size:15
Alignment explanation
Indices: 54594850--54594878 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
54594840 TTTAATAGTT
54594850 TTAAATATT-TTTTA
1 TTAAATATTCTTTTA
54594864 TTAAATATTCTTTTA
1 TTAAATATTCTTTTA
54594879 ACATATTTAC
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:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
TTAAATATTCTTTTA
Found at i:54594904 original size:17 final size:17
Alignment explanation
Indices: 54594882--54594920 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
54594872 TCTTTTAACA
54594882 TATTTA-CATTATAGTAT
1 TATTTATCATTATAG-AT
*
54594899 TATTTATTATTATAGAT
1 TATTTATCATTATAGAT
54594916 TATTT
1 TATTT
54594921 TTTATACCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (17 bp):
TATTTATCATTATAGAT
Found at i:54599515 original size:19 final size:19
Alignment explanation
Indices: 54599473--54599515 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
54599463 TTAGATATCC
*
54599473 TTAAATTATGTTTCACATT
1 TTAAATTATGTTTCAAATT
*
54599492 CTAAATTTAT-TTTCAAATT
1 TTAAA-TTATGTTTCAAATT
54599511 TTAAA
1 TTAAA
54599516 ATGTACTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.51
Consensus pattern (19 bp):
TTAAATTATGTTTCAAATT
Found at i:54604207 original size:37 final size:37
Alignment explanation
Indices: 54604157--54604228 Score: 144
Period size: 37 Copynumber: 1.9 Consensus size: 37
54604147 TAGGGGAATG
54604157 TTTTCGTCCTAGTAGAGGTCTTCGACAAGGTGACCTA
1 TTTTCGTCCTAGTAGAGGTCTTCGACAAGGTGACCTA
54604194 TTTTCGTCCTAGTAGAGGTCTTCGACAAGGTGACC
1 TTTTCGTCCTAGTAGAGGTCTTCGACAAGGTGACC
54604229 CTTTGAGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.21, C:0.22, G:0.25, T:0.32
Consensus pattern (37 bp):
TTTTCGTCCTAGTAGAGGTCTTCGACAAGGTGACCTA
Found at i:54606936 original size:20 final size:20
Alignment explanation
Indices: 54606882--54606942 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
54606872 ATAGGCTTTT
*
54606882 GCTTTCCCAATAAAATATAG
1 GCTTTCCCAGTAAAATATAG
*
54606902 GCTTT---AG-ATAATATAG
1 GCTTTCCCAGTAAAATATAG
54606918 GCTTTCCCAGTAAAATATAG
1 GCTTTCCCAGTAAAATATAG
54606938 GCTTT
1 GCTTT
54606943 ATTGATATTC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
16 13 0.38
17 1 0.03
19 2 0.06
20 18 0.53
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (20 bp):
GCTTTCCCAGTAAAATATAG
Found at i:54607340 original size:51 final size:52
Alignment explanation
Indices: 54607284--54607394 Score: 145
Period size: 51 Copynumber: 2.2 Consensus size: 52
54607274 AATTTGTATA
* * * * *
54607284 TAAAAAATTTAACCCTCAACTTTTACATATTA-TATCAATTTAGTCATAATT-
1 TAAAAAAATTAACCCTCAAATATTACA-AATAGTATCAATTTAATCATAATTC
*
54607335 TAAAAAAATTAACCCTCAAATATTACAAATAGTTTCAATTTAATCATAATTC
1 TAAAAAAATTAACCCTCAAATATTACAAATAGTATCAATTTAATCATAATTC
54607387 TAAAAAAA
1 TAAAAAAA
54607395 GTTTTATGGA
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
50 3 0.06
51 41 0.79
52 8 0.15
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (52 bp):
TAAAAAAATTAACCCTCAAATATTACAAATAGTATCAATTTAATCATAATTC
Found at i:54607695 original size:39 final size:39
Alignment explanation
Indices: 54607611--54607699 Score: 101
Period size: 39 Copynumber: 2.3 Consensus size: 39
54607601 AGCTTAATAC
*
54607611 TATTATATTAATAATAATTTTTAAAAAAAATATTTAAAA
1 TATTATATTTATAATAATTTTTAAAAAAAATATTTAAAA
* * * *
54607650 TATTATATTTTTAAT-ATTTTTAAACATACATATTT-AAT
1 TATTATATTTATAATAATTTTTAAA-AAAAATATTTAAAA
54607688 TATTTATATTTA
1 TA-TTATATTTA
54607700 GTCATATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
38 13 0.31
39 29 0.69
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (39 bp):
TATTATATTTATAATAATTTTTAAAAAAAATATTTAAAA
Found at i:54607809 original size:15 final size:15
Alignment explanation
Indices: 54607770--54607811 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
54607760 TTTCAATTTT
*
54607770 ATTTT-AATAATA-A
1 ATTTTAAATAAAATA
54607783 ATTTTAAA-AAAATA
1 ATTTTAAATAAAATA
54607797 ATTTTAAATAAAATA
1 ATTTTAAATAAAATA
54607812 TTATTCACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 8 0.32
14 11 0.44
15 6 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTTTAAATAAAATA
Found at i:54607863 original size:15 final size:15
Alignment explanation
Indices: 54607838--54607899 Score: 61
Period size: 15 Copynumber: 3.8 Consensus size: 15
54607828 GAAAATATTC
54607838 AATATAATATTTTAAT
1 AATA-AATATTTTAAT
54607854 AATAAATATTTATTATAGT
1 AATAAATA-TT-TTA-A-T
* *
54607873 TATAAATATATTAAT
1 AATAAATATTTTAAT
54607888 AATAAATATTTT
1 AATAAATATTTT
54607900 GTAGTATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
15 15 0.39
16 7 0.18
17 6 0.16
18 2 0.05
19 8 0.21
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (15 bp):
AATAAATATTTTAAT
Found at i:54608377 original size:14 final size:14
Alignment explanation
Indices: 54608358--54608396 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
54608348 CCAGAAAAGT
54608358 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
54608372 AAATCATTTTCTAG
1 AAATCATTTTCCAG
*
54608386 AAGTCATTTTC
1 AAATCATTTTC
54608397 AGTAAAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:54613132 original size:29 final size:30
Alignment explanation
Indices: 54613068--54613133 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
54613058 ATTTGGCCTT
* * * *
54613068 ATTTGATTCTTTTTAATAGTACAGGTATTA
1 ATTTGATTCTATTTAATAATACAGGGACTA
* *
54613098 AATTGATT-TATTTAATAATAGAGGGACTA
1 ATTTGATTCTATTTAATAATACAGGGACTA
54613127 ATTTGAT
1 ATTTGAT
54613134 ACAGTAATAC
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (30 bp):
ATTTGATTCTATTTAATAATACAGGGACTA
Found at i:54614909 original size:16 final size:16
Alignment explanation
Indices: 54614888--54614918 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
54614878 CAATACTATC
54614888 CTTGTACTTACTTGCT
1 CTTGTACTTACTTGCT
54614904 CTTGTACTTACTTGC
1 CTTGTACTTACTTGC
54614919 AGCTCACCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.26, G:0.13, T:0.48
Consensus pattern (16 bp):
CTTGTACTTACTTGCT
Found at i:54615791 original size:8 final size:8
Alignment explanation
Indices: 54615767--54615803 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
54615757 TCAAAGTACA
54615767 ATTTTATT
1 ATTTTATT
*
54615775 A-TATATT
1 ATTTTATT
54615782 ATTTTATT
1 ATTTTATT
54615790 ATTTTATT
1 ATTTTATT
54615798 ATTTTA
1 ATTTTA
54615804 GAGAGAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
7 6 0.23
8 20 0.77
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (8 bp):
ATTTTATT
Found at i:54617509 original size:18 final size:19
Alignment explanation
Indices: 54617486--54617528 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
54617476 ATTTAATTTT
* *
54617486 TATATAAAAATTACAT-AA
1 TATATAAAAATAAAATAAA
54617504 TATATAAAAATAAAATAAA
1 TATATAAAAATAAAATAAA
54617523 TATATA
1 TATATA
54617529 TATCATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
TATATAAAAATAAAATAAA
Found at i:54621785 original size:2 final size:2
Alignment explanation
Indices: 54621778--54621829 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
54621768 GTTTATAAAG
54621778 CT CT CT 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 CT CT CT
54621820 CT CT CT CT CT
1 CT CT CT CT CT
54621830 TGGCTTATGC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:54628685 original size:13 final size:13
Alignment explanation
Indices: 54628667--54628691 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54628657 TTTTTTATAG
54628667 AAATATAATAATA
1 AAATATAATAATA
54628680 AAATATAATAAT
1 AAATATAATAAT
54628692 TATTTATCAT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATATAATAATA
Found at i:54629162 original size:12 final size:12
Alignment explanation
Indices: 54629145--54629169 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54629135 TTGGTGGCAC
54629145 AAAAAAATAAAA
1 AAAAAAATAAAA
54629157 AAAAAAATAAAA
1 AAAAAAATAAAA
54629169 A
1 A
54629170 TCACTTGGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (12 bp):
AAAAAAATAAAA
Found at i:54629607 original size:23 final size:23
Alignment explanation
Indices: 54629546--54629600 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
54629536 AAATCCGCTC
**
54629546 ATATTATTTTTAA-AAAATATTT
1 ATATTATTTTTAATTTAATATTT
54629568 ATATTATTTTTAATTTAATATTT
1 ATATTATTTTTAATTTAATATTT
*
54629591 -TATTTTTTTT
1 ATATTATTTTT
54629601 CTATTTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 22 0.76
23 7 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
ATATTATTTTTAATTTAATATTT
Found at i:54630247 original size:15 final size:14
Alignment explanation
Indices: 54630220--54630269 Score: 68
Period size: 13 Copynumber: 3.6 Consensus size: 14
54630210 CAAAATTCAA
54630220 AAAATATAAAAATT
1 AAAATATAAAAATT
54630234 AAAAT-TAATCAAATT
1 AAAATATAA--AAATT
54630249 AAAATATAAAAATT
1 AAAATATAAAAATT
54630263 -AAATATA
1 AAAATATA
54630270 CACCTTATAC
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
13 10 0.30
14 10 0.30
15 10 0.30
16 3 0.09
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAATATAAAAATT
Found at i:54630247 original size:23 final size:23
Alignment explanation
Indices: 54630221--54630264 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
54630211 AAAATTCAAA
*
54630221 AAATATAAAA-ATTAAAATTAATC
1 AAAT-TAAAATATAAAAATTAATC
54630244 AAATTAAAATATAAAAATTAA
1 AAATTAAAATATAAAAATTAA
54630265 ATATACACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (23 bp):
AAATTAAAATATAAAAATTAATC
Found at i:54636295 original size:13 final size:11
Alignment explanation
Indices: 54636267--54636309 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
54636257 AGTTAAATAT
54636267 TATTTTATTAA
1 TATTTTATTAA
54636278 TATTTTACTTAGA
1 TATTTTA-TTA-A
*
54636291 TA-TTTATTAT
1 TATTTTATTAA
54636301 TATTTTATT
1 TATTTTATT
54636310 TAGAAAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 2 0.07
11 16 0.57
12 7 0.25
13 3 0.11
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:54636296 original size:23 final size:23
Alignment explanation
Indices: 54636270--54636313 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
54636260 TAAATATTAT
54636270 TTTATTAATATTTTACTTAGATA
1 TTTATTAATATTTTACTTAGATA
* *
54636293 TTTATTATTATTTTATTTAGA
1 TTTATTAATATTTTACTTAGA
54636314 AAATGGTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (23 bp):
TTTATTAATATTTTACTTAGATA
Found at i:54645229 original size:30 final size:30
Alignment explanation
Indices: 54645194--54645250 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
54645184 TAGGCATTTC
*
54645194 CACACGAGTAAACCACACGCCCGTGTGAGG
1 CACACGAGCAAACCACACGCCCGTGTGAGG
* **
54645224 CACACGGGCAGTCCACACGCCCGTGTG
1 CACACGAGCAAACCACACGCCCGTGTG
54645251 TCATGGCCGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.25, C:0.37, G:0.28, T:0.11
Consensus pattern (30 bp):
CACACGAGCAAACCACACGCCCGTGTGAGG
Found at i:54649318 original size:23 final size:23
Alignment explanation
Indices: 54649273--54649315 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
54649263 CTATCATTTT
54649273 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
54649296 TCTAAGTAAAA-ATTAATAAA
1 TCTAAATAAAATAATAATAAA
54649316 ATAATATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:54651444 original size:44 final size:44
Alignment explanation
Indices: 54651396--54651486 Score: 128
Period size: 44 Copynumber: 2.1 Consensus size: 44
54651386 TTTGAAATAA
* * *
54651396 AATAGAAATTGTGATAATTTCACATTTTAAAATAATTATAATTT
1 AATAGAAATTGTGATAATTACACATTTAAAAATAAATATAATTT
* **
54651440 AATAGAAGTTGTGATAATTACTTATTTAAAAATAAATATAATTT
1 AATAGAAATTGTGATAATTACACATTTAAAAATAAATATAATTT
54651484 AAT
1 AAT
54651487 TTAAAATTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (44 bp):
AATAGAAATTGTGATAATTACACATTTAAAAATAAATATAATTT
Found at i:54651960 original size:32 final size:31
Alignment explanation
Indices: 54651923--54652004 Score: 76
Period size: 33 Copynumber: 2.5 Consensus size: 31
54651913 TATTTTATGT
* * *
54651923 TAATTACTACAATTAAAAATATAATATTTAAAA
1 TAATTA-TA-AATTAAAAACATAAAAATTAAAA
54651956 -AATTATTAAATATTAAAAACATAAAAATTAAAA
1 TAATTA-T-AA-ATTAAAAACATAAAAATTAAAA
54651989 TTAATTATAAATTAAA
1 -TAATTATAAATTAAA
54652005 TAAAAATGAC
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
32 13 0.32
33 22 0.54
34 1 0.02
35 5 0.12
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (31 bp):
TAATTATAAATTAAAAACATAAAAATTAAAA
Found at i:54652112 original size:4 final size:4
Alignment explanation
Indices: 54652103--54652129 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
54652093 TTTATTTTTC
54652103 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
54652130 TTGCTTAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:54659096 original size:6 final size:6
Alignment explanation
Indices: 54659085--54659122 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
54659075 ATTATGCAAT
54659085 CCATCA CCATCA CCATCA CCATCA CCATCA CCATCA CC
1 CCATCA CCATCA CCATCA CCATCA CCATCA CCATCA CC
54659123 TACCCAATGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.32, C:0.53, G:0.00, T:0.16
Consensus pattern (6 bp):
CCATCA
Found at i:54664643 original size:20 final size:20
Alignment explanation
Indices: 54664618--54664659 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
54664608 ATGACTCACC
54664618 ATTGTTAATTTAGTCGAAAA
1 ATTGTTAATTTAGTCGAAAA
54664638 ATTGTTAATTTAGTCGAAAA
1 ATTGTTAATTTAGTCGAAAA
54664658 AT
1 AT
54664660 AATTTAGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.40
Consensus pattern (20 bp):
ATTGTTAATTTAGTCGAAAA
Found at i:54664664 original size:16 final size:17
Alignment explanation
Indices: 54664622--54664667 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 17
54664612 CTCACCATTG
54664622 TTAATTTAGTCGAAAAA
1 TTAATTTAGTCGAAAAA
54664639 TTGTTAATTTAGTCGAAAAA
1 ---TTAATTTAGTCGAAAAA
54664659 -TAATTTAGT
1 TTAATTTAGT
54664668 AACCTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 9 0.35
20 17 0.65
ACGTcount: A:0.41, C:0.04, G:0.13, T:0.41
Consensus pattern (17 bp):
TTAATTTAGTCGAAAAA
Found at i:54684123 original size:21 final size:21
Alignment explanation
Indices: 54684083--54684123 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
54684073 TTTAGGATGG
*
54684083 ATGTTTTGAGCTTGTTTAATC
1 ATGTTTTGAGCTTGTATAATC
54684104 ATGTTTTGAG-TTGGTATAAT
1 ATGTTTTGAGCTT-GTATAAT
54684124 TGATGGCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.22, C:0.05, G:0.22, T:0.51
Consensus pattern (21 bp):
ATGTTTTGAGCTTGTATAATC
Found at i:54690182 original size:13 final size:13
Alignment explanation
Indices: 54690166--54690191 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54690156 GAGTTTATAA
54690166 ATAATTAATAGAG
1 ATAATTAATAGAG
54690179 ATAATTAATAGAG
1 ATAATTAATAGAG
54690192 CAAAATCATA
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:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (13 bp):
ATAATTAATAGAG
Found at i:54692033 original size:30 final size:30
Alignment explanation
Indices: 54691997--54692059 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
54691987 ACTTATTTTA
54691997 TTGTTAATTTTCTTAATATTTTAAAGGCAT
1 TTGTTAATTTTCTTAATATTTTAAAGGCAT
* * *
54692027 TTGTTAATTTTTTTATTATTTTAGAGGCAT
1 TTGTTAATTTTCTTAATATTTTAAAGGCAT
54692057 TTG
1 TTG
54692060 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.25, C:0.05, G:0.13, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTCTTAATATTTTAAAGGCAT
Found at i:54692214 original size:13 final size:11
Alignment explanation
Indices: 54692180--54692207 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
54692170 TATATATATT
54692180 TAAAAATAATA
1 TAAAAATAATA
54692191 TAAAAATAATA
1 TAAAAATAATA
54692202 TAAAAA
1 TAAAAA
54692208 ATTAATACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:54693849 original size:14 final size:14
Alignment explanation
Indices: 54693830--54693857 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
54693820 GCTACTGATT
54693830 ACAATGTTGTGTTG
1 ACAATGTTGTGTTG
54693844 ACAATGTTGTGTTG
1 ACAATGTTGTGTTG
54693858 TTAATCTAAG
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:0.07, G:0.29, T:0.43
Consensus pattern (14 bp):
ACAATGTTGTGTTG
Found at i:54694099 original size:19 final size:20
Alignment explanation
Indices: 54694064--54694113 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
54694054 AAAAGAATTG
54694064 TACTATTTTTTACTGTTTTGC-
1 TACTATTTTTTA-TGTTTT-CT
54694085 TACTATTTTTT-TGTTTTCT
1 TACTATTTTTTATGTTTTCT
54694104 TACTATTTTT
1 TACTATTTTT
54694114 CTATCATTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 1 0.04
19 16 0.57
21 11 0.39
ACGTcount: A:0.14, C:0.12, G:0.06, T:0.68
Consensus pattern (20 bp):
TACTATTTTTTATGTTTTCT
Found at i:54696064 original size:11 final size:11
Alignment explanation
Indices: 54696048--54696072 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
54696038 CCTTCCAACC
54696048 ATTATCCTAAT
1 ATTATCCTAAT
54696059 ATTATCCTAAT
1 ATTATCCTAAT
54696070 ATT
1 ATT
54696073 TTTTTGTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (11 bp):
ATTATCCTAAT
Found at i:54696218 original size:18 final size:19
Alignment explanation
Indices: 54696178--54696221 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
54696168 CGTATTGATT
*
54696178 TATTTTTATTTATTTCAAT
1 TATTTTTATTTATTTCAAA
54696197 TATTTTTATTT-TTAT-AAA
1 TATTTTTATTTATT-TCAAA
54696215 TATTTTT
1 TATTTTT
54696222 CAATGTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (19 bp):
TATTTTTATTTATTTCAAA
Found at i:54714371 original size:30 final size:30
Alignment explanation
Indices: 54714330--54714392 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
54714320 TTTTTTTTGA
*
54714330 AAGATCCGAAACATGATCTTCAACGGTAGC
1 AAGATCCGAAACATGATCTTCAACGGTAAC
*
54714360 AAGATCGGAAACATGATCTTCAACGGTAAC
1 AAGATCCGAAACATGATCTTCAACGGTAAC
54714390 AAG
1 AAG
54714393 CTTGGCGGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.19
Consensus pattern (30 bp):
AAGATCCGAAACATGATCTTCAACGGTAAC
Found at i:54714458 original size:30 final size:30
Alignment explanation
Indices: 54714417--54714473 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
54714407 TTGAAATATA
*
54714417 CGAAGCATGATCTTCAACGGTAACAAGATC
1 CGAAACATGATCTTCAACGGTAACAAGATC
*
54714447 CGAAACATGATCTTCAGCGGTAACAAG
1 CGAAACATGATCTTCAACGGTAACAAG
54714474 CTTGGCGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (30 bp):
CGAAACATGATCTTCAACGGTAACAAGATC
Found at i:54714460 original size:81 final size:81
Alignment explanation
Indices: 54714325--54714524 Score: 346
Period size: 81 Copynumber: 2.5 Consensus size: 81
54714315 TTAATTTTTT
* * * *
54714325 TTTGAAAGATCCGAAACATGATCTTCAACGGTAGCAAGATCGGAAACATGATCTTCAACGGTAAC
1 TTTGAAATATCCGAAGCATGATCTTCAACGGTAACAAGATCCGAAACATGATCTTCAACGGTAAC
54714390 AAGCTTGGCGGTGAAG
66 AAGCTTGGCGGTGAAG
* *
54714406 TTTGAAATATACGAAGCATGATCTTCAACGGTAACAAGATCCGAAACATGATCTTCAGCGGTAAC
1 TTTGAAATATCCGAAGCATGATCTTCAACGGTAACAAGATCCGAAACATGATCTTCAACGGTAAC
54714471 AAGCTTGGCGGTGAAG
66 AAGCTTGGCGGTGAAG
54714487 TTTGAAATATCCGAAGCATGATCTTCAACGGTAACAAG
1 TTTGAAATATCCGAAGCATGATCTTCAACGGTAACAAG
54714525 CTTGGCGGTG
Statistics
Matches: 112, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 112 1.00
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.23
Consensus pattern (81 bp):
TTTGAAATATCCGAAGCATGATCTTCAACGGTAACAAGATCCGAAACATGATCTTCAACGGTAAC
AAGCTTGGCGGTGAAG
Found at i:54715582 original size:39 final size:39
Alignment explanation
Indices: 54715518--54715598 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 39
54715508 ATAAAAGTGG
*
54715518 AATTTGACATGTGAAAAATAGTCTTA-TACTTTATATTTT
1 AATTTGACATGTGAAAAATAGTCTTATTAATTT-TATTTT
* *
54715557 AATTT-ACATGTTAAAAATTATTCTTATTAATTTTATTTT
1 AATTTGACATGTGAAAAA-TAGTCTTATTAATTTTATTTT
54715596 AAT
1 AAT
54715599 ATACTAAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 11 0.30
39 21 0.57
40 5 0.14
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (39 bp):
AATTTGACATGTGAAAAATAGTCTTATTAATTTTATTTT
Found at i:54721602 original size:21 final size:22
Alignment explanation
Indices: 54721572--54721618 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
54721562 TTTTATGGCC
**
54721572 TTTTTAG-AAATTTGGTTTTTT
1 TTTTTAGAAAATTTGGGATTTT
*
54721593 TTTTTTGAAAATTTGGGATTTT
1 TTTTTAGAAAATTTGGGATTTT
54721615 TTTT
1 TTTT
54721619 GTAATTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.19, C:0.00, G:0.15, T:0.66
Consensus pattern (22 bp):
TTTTTAGAAAATTTGGGATTTT
Found at i:54735778 original size:151 final size:151
Alignment explanation
Indices: 54735499--54735810 Score: 615
Period size: 151 Copynumber: 2.1 Consensus size: 151
54735489 TGAAATGTTA
54735499 AAGGTAATTTCAGTCAAATTATACTCGACTAAGGATTTAGTCCTATACTTTGATTTGACATATTT
1 AAGG-AATTTCAGTCAAATTATACTCGACTAAGGATTTAGTCCTATACTTTGATTTGACATATTT
54735564 TGGTACTCTTATTATTATTAGGTTAAAATATGCTATAGGTCCCTGTACTCTTTGTAAATTTGAAA
65 TGGTACTCTTATTATTATTAGGTTAAAATATGCTATAGGTCCCTGTACTCTTTGTAAATTTGAAA
54735629 TTAGTCCTCTTACTTCTATTTC
130 TTAGTCCTCTTACTTCTATTTC
54735651 AAGGAATTTCAGTCAAATTATACTCGACTAAGGATTTAGTCCTATACTTTGATTTGACATATTTT
1 AAGGAATTTCAGTCAAATTATACTCGACTAAGGATTTAGTCCTATACTTTGATTTGACATATTTT
54735716 GGTACTCTTATTATTATTAGGTTAAAATATGCTATAGGTCCCTGTACTCTTTGTAAATTTGAAAT
66 GGTACTCTTATTATTATTAGGTTAAAATATGCTATAGGTCCCTGTACTCTTTGTAAATTTGAAAT
54735781 TAGTCCTCTTACTTCTATTTC
131 TAGTCCTCTTACTTCTATTTC
54735802 AAGGAATTT
1 AAGGAATTT
54735811 AGTTCTACTT
Statistics
Matches: 160, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
151 156 0.98
152 4 0.03
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (151 bp):
AAGGAATTTCAGTCAAATTATACTCGACTAAGGATTTAGTCCTATACTTTGATTTGACATATTTT
GGTACTCTTATTATTATTAGGTTAAAATATGCTATAGGTCCCTGTACTCTTTGTAAATTTGAAAT
TAGTCCTCTTACTTCTATTTC
Found at i:54737281 original size:8 final size:8
Alignment explanation
Indices: 54737251--54737289 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
54737241 ATTGGTTTGG
54737251 TTTTTAAAA
1 TTTTT-AAA
*
54737260 TATTTAATA
1 TTTTTAA-A
54737269 TTTTTAAA
1 TTTTTAAA
54737277 TTTTTAAA
1 TTTTTAAA
54737285 TTTTT
1 TTTTT
54737290 TAAAAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
8 16 0.59
9 11 0.41
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TTTTTAAA
Found at i:54737290 original size:17 final size:16
Alignment explanation
Indices: 54737251--54737305 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
54737241 ATTGGTTTGG
*
54737251 TTTTTAAAATATTTAA
1 TTTTTTAAATATTTAA
*
54737267 TATTTTTAAATTTTTAAA
1 T-TTTTTAAATATTT-AA
*
54737285 TTTTTTAAAAATTTTAA
1 TTTTTTAAATA-TTTAA
54737302 TTTT
1 TTTT
54737306 GAATTAAGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
16 1 0.03
17 25 0.78
18 6 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTTTAAATATTTAA
Found at i:54737299 original size:18 final size:16
Alignment explanation
Indices: 54737251--54737305 Score: 65
Period size: 18 Copynumber: 3.2 Consensus size: 16
54737241 ATTGGTTTGG
54737251 TTTTTAAAATATTTAAT
1 TTTTTAAAAT-TTTAAT
*
54737268 ATTTTTAAATTTTTAAAT
1 -TTTTTAAAATTTT-AAT
54737286 TTTTTAAAAATTTTAAT
1 TTTTT-AAAATTTTAAT
54737303 TTT
1 TTT
54737306 GAATTAAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
17 14 0.42
18 19 0.58
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTTAAAATTTTAAT
Found at i:54740948 original size:28 final size:30
Alignment explanation
Indices: 54740917--54740976 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 30
54740907 GTTATTGTAG
54740917 TATTTATATATT-TAG-AATTTAG-TCTTTA
1 TATTTATAT-TTCTAGAAATTTAGATCTTTA
*
54740945 TATTTTTATTTCTAGAAATTTAGATTCTTTA
1 TATTTATATTTCTAGAAATTTAGA-TCTTTA
54740976 T
1 T
54740977 TTTTCAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 2 0.07
28 11 0.41
29 7 0.26
31 7 0.26
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.58
Consensus pattern (30 bp):
TATTTATATTTCTAGAAATTTAGATCTTTA
Found at i:54741402 original size:21 final size:21
Alignment explanation
Indices: 54741378--54741417 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
54741368 TTGTATTTGT
54741378 ATTTTTATT-TTTTAAAAAATA
1 ATTTTT-TTATTTTAAAAAATA
54741399 ATTTTTTTATTTTAAAAAA
1 ATTTTTTTATTTTAAAAAA
54741418 GTAAGGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTTTTTATTTTAAAAAATA
Found at i:54741697 original size:27 final size:25
Alignment explanation
Indices: 54741636--54741698 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
54741626 ATTTGATGAG
*
54741636 AATAATTTATTAAATAAAAATAAAAT
1 AATAATTT-TTAAATAAAAACAAAAT
* *
54741662 AATATTTTTTAAAATTAAAACAAAAT
1 AATAATTTTT-AAATAAAAACAAAAT
54741688 AATAAATTTTT
1 AAT-AATTTTT
54741699 TTGACAATGC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
25 2 0.06
26 23 0.74
27 6 0.19
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (25 bp):
AATAATTTTTAAATAAAAACAAAAT
Found at i:54742082 original size:29 final size:29
Alignment explanation
Indices: 54742040--54742109 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 29
54742030 ATAAGTAAGT
* *
54742040 CCTTAAAGTATTTTTGT-ATCTAAAGAAGC
1 CCTTAAACTATTTTT-TAACCTAAAGAAGC
* *
54742069 CCTTAAACTTTTTTTTACACCTAAATAAGC
1 CCTTAAACTATTTTTTA-ACCTAAAGAAGC
54742099 CCTTAAACTAT
1 CCTTAAACTAT
54742110 AATGACTTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 1 0.03
29 13 0.38
30 20 0.59
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (29 bp):
CCTTAAACTATTTTTTAACCTAAAGAAGC
Found at i:54759248 original size:36 final size:36
Alignment explanation
Indices: 54759194--54759265 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
54759184 AATTATATTT
* *
54759194 TTTTATAAAAAACGTAAAAAATAAAAAAATGTAAAA
1 TTTTATAAAAAACATAAAAAATAAAAAAATGCAAAA
* *
54759230 TTTTATAAAAATA-ATAAAAAATTATAAAATGCAAAA
1 TTTTATAAAAA-ACATAAAAAATAAAAAAATGCAAAA
54759266 AAAAAATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 30 0.97
37 1 0.03
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.28
Consensus pattern (36 bp):
TTTTATAAAAAACATAAAAAATAAAAAAATGCAAAA
Found at i:54759563 original size:182 final size:180
Alignment explanation
Indices: 54759277--54759640 Score: 446
Period size: 182 Copynumber: 2.0 Consensus size: 180
54759267 AAAAATATTT
* *
54759277 TTAACAATTAACTTTAACTATTGATTGTTAAAGTTAACGACCCCTAGTTTTTTTCAATTAAAGTC
1 TTAACAATTAACTTTAACTATTGATCGTTAAAGTTAACGACCCCTA-TTTTTTTAAATTAAAGTC
* ** * * * *
54759342 ATCGCGTGTTGCAACATAGTGTGATATGTGGCAAAAAATGAT-AATAA-AAAAATCAATAAAAGT
65 ATCACGTGTCACAACATAGCGTGACATGTAGCAAAAAATGATAAAAAATAAAAATCAATAAAAGT
* **
54759405 TATAGAAAAATTATGAAATGGTTCTTTTGGTATGATAATTTTTATAAATTTTTTC
130 TATAGAAAAATTAT-AAA--ATT-TTTTGGTACAATAATTTTTATAAATTTTTTC
* * * * *
54759460 TTAACAATTAGCTTTAATTGTTGATCGTTAAAGTTAATGACCTCT-TTTTTTTAAAATTAAAGTC
1 TTAACAATTAACTTTAACTATTGATCGTTAAAGTTAACGACCCCTATTTTTTT-AAATTAAAGTC
**
54759524 ATCACGTGTCACAACATAGCGTGACATGTAGTGAAAAATGATAAAAAAAATAAAAATCAATAAAA
65 ATCACGTGTCACAACATAGCGTGACATGTAGCAAAAAATGAT--AAAAAATAAAAATCAATAAAA
* *
54759589 GTTATAGAAAAATTGTAAAATTTTTTGGTACAATAATTTTTATAATTTTTTT
128 GTTATAGAAAAATTATAAAATTTTTTGGTACAATAATTTTTATAAATTTTTT
54759641 ACGAAATTTA
Statistics
Matches: 155, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
181 7 0.05
182 71 0.46
183 41 0.26
185 7 0.05
186 29 0.19
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (180 bp):
TTAACAATTAACTTTAACTATTGATCGTTAAAGTTAACGACCCCTATTTTTTTAAATTAAAGTCA
TCACGTGTCACAACATAGCGTGACATGTAGCAAAAAATGATAAAAAATAAAAATCAATAAAAGTT
ATAGAAAAATTATAAAATTTTTTGGTACAATAATTTTTATAAATTTTTTC
Found at i:54759742 original size:28 final size:28
Alignment explanation
Indices: 54759693--54759747 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
54759683 ACTTTATAAA
* *
54759693 ATTTTATAATTTTTTTATATTTCTATAT
1 ATTTTATAATTCTTTTAGATTTCTATAT
*
54759721 ATTTTATAA-TCTTTTACGATTTTTATA
1 ATTTTATAATTCTTTTA-GATTTCTATA
54759748 AAAATTTACC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (28 bp):
ATTTTATAATTCTTTTAGATTTCTATAT
Found at i:54759820 original size:37 final size:37
Alignment explanation
Indices: 54759779--54759851 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 37
54759769 TTTTCTAATT
*
54759779 TTTAAGAAAATTT-TA-ATATTTGAATTTTTTTTTAAAA
1 TTTAAGAAAATTTATAGAT-TTT-AATTTTTTTATAAAA
* *
54759816 TTTAATAATATTTATAGATTTTAATTTTTTTATAAA
1 TTTAAGAAAATTTATAGATTTTAATTTTTTTATAAA
54759852 TTTTTTCTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
37 24 0.77
38 5 0.16
39 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (37 bp):
TTTAAGAAAATTTATAGATTTTAATTTTTTTATAAAA
Found at i:54759958 original size:85 final size:85
Alignment explanation
Indices: 54759883--54760049 Score: 223
Period size: 85 Copynumber: 2.0 Consensus size: 85
54759873 ATCAGGGTCT
* * *
54759883 TAATTACTT-TTTTTGAAAAA-GTTTGAGGGTCTTTTTTGATACATTTTGAAAGTTCAAGTATCC
1 TAATTACTTCTTTTTGAAAAATGTTTGAGGGT-ATTTTCGATACATTTTGAAAGTTCAAGTACCC
54759946 AATTGAGTTAAAAAAAAGTAG
65 AATTGAGTTAAAAAAAAGTAG
* * *
54759967 TAATTACTTCTTTTTTAAAAATGTTTGAGGGTATTTTCGATGCATTTTGAAATTTCAAGTACCCA
1 TAATTACTTCTTTTTGAAAAATGTTTGAGGGTATTTTCGATACATTTTGAAAGTTCAAGTACCC-
*
54760032 AATT-AGTGCAAAAAAAAG
65 AATTGAGT-TAAAAAAAAG
54760050 GGACTTAATT
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
84 9 0.12
85 40 0.56
86 23 0.32
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.40
Consensus pattern (85 bp):
TAATTACTTCTTTTTGAAAAATGTTTGAGGGTATTTTCGATACATTTTGAAAGTTCAAGTACCCA
ATTGAGTTAAAAAAAAGTAG
Found at i:54760083 original size:86 final size:84
Alignment explanation
Indices: 54759876--54760083 Score: 208
Period size: 85 Copynumber: 2.4 Consensus size: 84
54759866 TAATAAAATC
* * *
54759876 AGGGTCTTAATTACTTTTTTTGAAAAAGTTTGAGGGTCTTTTTTGATACATTTTGAAAGTTCAAG
1 AGGGACTTAATT-C-TTTTTTGAAAAAGTTTGAGGGTCATTTTCGATACATTTTGAAAGTTCAAG
* *
54759941 TATCCAATTGAGTTAAAAAAA
64 TACCCAATTGAGTCAAAAAAA
* * * * *
54759962 AGTAGTAATTACTTCTTTTTT-AAAAATGTTTGAGGGT-ATTTTCGATGCATTTTGAAATTTCAA
1 AG--GGACTTAATTCTTTTTTGAAAAA-GTTTGAGGGTCATTTTCGATACATTTTGAAAGTTCAA
54760025 GTACCCAAATT-AGTGCAAAAAAA
63 GTACCC-AATTGAGT-CAAAAAAA
54760048 AGGGACTTAATTGCTTTTTTCGAAACAA-TTTGAGGG
1 AGGGACTTAATT-CTTTTTT-GAAA-AAGTTTGAGGG
54760084 GTTTTTTTCA
Statistics
Matches: 100, Mismatches: 13, Indels: 18
0.76 0.10 0.14
Matches are distributed among these distances:
84 7 0.07
85 42 0.42
86 39 0.39
87 4 0.04
88 8 0.08
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.39
Consensus pattern (84 bp):
AGGGACTTAATTCTTTTTTGAAAAAGTTTGAGGGTCATTTTCGATACATTTTGAAAGTTCAAGTA
CCCAATTGAGTCAAAAAAA
Found at i:54762650 original size:15 final size:15
Alignment explanation
Indices: 54762632--54762676 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
54762622 ATTTTCTAGG
*
54762632 TTTGTTTAATTTTTT
1 TTTGTTTAATTATTT
*
54762647 TTTGTCTAGATTATTT
1 TTTGTTTA-ATTATTT
*
54762663 TTTCTTTAATTATT
1 TTTGTTTAATTATT
54762677 ATTAAAGAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.18, C:0.04, G:0.07, T:0.71
Consensus pattern (15 bp):
TTTGTTTAATTATTT
Found at i:54765771 original size:16 final size:16
Alignment explanation
Indices: 54765747--54765777 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54765737 TTAATTATTA
54765747 ATTACAACTCTATTTC
1 ATTACAACTCTATTTC
*
54765763 ATTATAACTCTATTT
1 ATTACAACTCTATTT
54765778 TATTCCAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.19, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTACAACTCTATTTC
Found at i:54773515 original size:2 final size:2
Alignment explanation
Indices: 54773480--54773504 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54773470 CAATCAAAAA
54773480 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 T
54773505 GTTTGTCTCT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:54776038 original size:3 final size:3
Alignment explanation
Indices: 54776030--54776055 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
54776020 TAATAAAGCG
54776030 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
54776056 TGATCCATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:54776411 original size:29 final size:29
Alignment explanation
Indices: 54776358--54776423 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
54776348 AAAATTTATA
*
54776358 TTTAAAAAAATATAAAAAACATT-AATTT
1 TTTAAAAAAATATAAAAAACATTAAAATT
* *
54776386 TTTAAAGAACATATAAAGAAA-GTTAAAATT
1 TTTAAA-AAAATATAAA-AAACATTAAAATT
54776416 TTTAAAAA
1 TTTAAAAA
54776424 TTTCTAAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
28 6 0.19
29 13 0.41
30 13 0.41
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (29 bp):
TTTAAAAAAATATAAAAAACATTAAAATT
Found at i:54776640 original size:21 final size:21
Alignment explanation
Indices: 54776611--54776652 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
54776601 GAATAATTTC
* *
54776611 ATTTGATTTGACTCAACTTGA
1 ATTTCATTTCACTCAACTTGA
*
54776632 ATTTCATTTCACTCCACTTGA
1 ATTTCATTTCACTCAACTTGA
54776653 TTCAAAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (21 bp):
ATTTCATTTCACTCAACTTGA
Found at i:54776888 original size:13 final size:13
Alignment explanation
Indices: 54776870--54776894 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54776860 TAGGATTGAT
54776870 TTAATATTTATTA
1 TTAATATTTATTA
54776883 TTAATATTTATT
1 TTAATATTTATT
54776895 TTCAAAATAA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTAATATTTATTA
Found at i:54785658 original size:31 final size:31
Alignment explanation
Indices: 54785632--54785696 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
54785622 AATTTTTTGT
54785632 TCAATTTTT-TCTGTTTATATCGATTTTCAAG
1 TCAATTTTTCT-TGTTTATATCGATTTTCAAG
54785663 TCAATTTTTCTTGTTTATATCGATTTTCAAG
1 TCAATTTTTCTTGTTTATATCGATTTTCAAG
54785694 TCA
1 TCA
54785697 GTTGATTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 32 0.97
32 1 0.03
ACGTcount: A:0.23, C:0.14, G:0.09, T:0.54
Consensus pattern (31 bp):
TCAATTTTTCTTGTTTATATCGATTTTCAAG
Found at i:54793067 original size:22 final size:21
Alignment explanation
Indices: 54793032--54793107 Score: 68
Period size: 22 Copynumber: 3.7 Consensus size: 21
54793022 AAAAGGTATC
* *
54793032 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
54793053 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
54793076 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
54793095 TGC-AATCATATCT
1 TACAAATCATATCT
54793108 AAGATTGTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
18 6 0.13
19 11 0.24
20 1 0.02
21 3 0.07
22 15 0.33
23 10 0.22
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:54793124 original size:35 final size:37
Alignment explanation
Indices: 54793061--54793158 Score: 150
Period size: 35 Copynumber: 2.7 Consensus size: 37
54793051 ATTACAAAAT
54793061 CATATC-T-TCTAAGATTGCATATCATATCTAAGATTG
1 CATATCATATCTAAGATTG-ATATCATATCTAAGATTG
54793097 CA-ATCATATCTAAGATTG-TATCATATCTAAGATTG
1 CATATCATATCTAAGATTGATATCATATCTAAGATTG
54793132 CATATCATATCTAAGATTGCATATCAT
1 CATATCATATCTAAGATTG-ATATCAT
54793159 TGAAGATTAT
Statistics
Matches: 57, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
35 22 0.39
36 19 0.33
37 10 0.18
38 6 0.11
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (37 bp):
CATATCATATCTAAGATTGATATCATATCTAAGATTG
Found at i:54793166 original size:17 final size:19
Alignment explanation
Indices: 54793068--54793158 Score: 161
Period size: 19 Copynumber: 4.9 Consensus size: 19
54793058 AATCATATCT
54793068 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
54793087 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
54793105 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
54793122 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
54793141 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
54793159 TGAAGATTAT
Statistics
Matches: 69, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
17 16 0.23
18 16 0.23
19 37 0.54
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:54793314 original size:21 final size:20
Alignment explanation
Indices: 54793277--54793315 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
54793267 TTGGACTTCG
**
54793277 TTTTTTTTTGGGTTTATTAT
1 TTTTTTTTTGGACTTATTAT
54793297 TTTTGTTTTTGGACTTATT
1 TTTT-TTTTTGGACTTATT
54793316 TCTGGGCCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.10, C:0.03, G:0.15, T:0.72
Consensus pattern (20 bp):
TTTTTTTTTGGACTTATTAT
Found at i:54793629 original size:45 final size:45
Alignment explanation
Indices: 54793508--54793643 Score: 184
Period size: 45 Copynumber: 3.0 Consensus size: 45
54793498 AGAAGGCGAT
*
54793508 ATCTGCTATCTTTGATTTGCTCCCCGTCTAATACAGAGATGCCAA
1 ATCTGCTATCTTCGATTTGCTCCCCGTCTAATACAGAGATGCCAA
* * * * *
54793553 ATCTGCT-TCTTCAATCTGCTCCCCATATAATATAGAGATGCCAA
1 ATCTGCTATCTTCGATTTGCTCCCCGTCTAATACAGAGATGCCAA
* * *
54793597 ATCTGTTATCTTCGATTTGCTCTCCGTCTAATACAGAGAGGCCAA
1 ATCTGCTATCTTCGATTTGCTCCCCGTCTAATACAGAGATGCCAA
54793642 AT
1 AT
54793644 TTTTCATCTT
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
44 37 0.49
45 39 0.51
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (45 bp):
ATCTGCTATCTTCGATTTGCTCCCCGTCTAATACAGAGATGCCAA
Found at i:54793816 original size:78 final size:78
Alignment explanation
Indices: 54793680--54793892 Score: 336
Period size: 78 Copynumber: 2.7 Consensus size: 78
54793670 AAACACATGG
* *
54793680 AGGTTAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTTGA
1 AGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTAGA
54793745 TCTGCTTCAATGA
66 TCTGCTTCAATGA
* *
54793758 AGGTCATATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTAGA
1 AGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTAGA
*
54793823 TCTGCTTTAATGA
66 TCTGCTTCAATGA
* * * **
54793836 AGGTCAGATCTGCTATGTTTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATC
1 AGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
54793893 TGTTTCTTTG
Statistics
Matches: 123, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
78 123 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (78 bp):
AGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTAGA
TCTGCTTCAATGA
Found at i:54794184 original size:78 final size:78
Alignment explanation
Indices: 54794055--54794424 Score: 580
Period size: 78 Copynumber: 4.7 Consensus size: 78
54794045 AAAACATCCA
* *
54794055 AAGGTTAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATTATCTTGG
1 AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
54794120 ATCTGCTTCAATG
66 ATCTGCTTCAATG
* *
54794133 AAGGTCCA-ATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCACCTTG
1 AAGGT-CAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTG
54794197 GATCTGCTTCAATG
65 GATCTGCTTCAATG
* *
54794211 AAGGTCAGATCTGCTGTGTCTTCGATCTGTTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
1 AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
*
54794276 ATTTGCTTCAATG
66 ATCTGCTTCAATG
* * *
54794289 AATGTCAGATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATCCCAAATCATCTTGG
1 AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
* *
54794354 ATCTGCTTCGATA
66 ATCTGCTTCAATG
* * **
54794367 AAGGTCAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATC
1 AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
54794425 TGTTTCTTCG
Statistics
Matches: 268, Mismatches: 22, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
77 2 0.01
78 265 0.99
79 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (78 bp):
AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
ATCTGCTTCAATG
Found at i:54794553 original size:87 final size:89
Alignment explanation
Indices: 54794457--54794618 Score: 222
Period size: 89 Copynumber: 1.8 Consensus size: 89
54794447 ATAGTACAGA
* *
54794457 GATGCCAAATCATCTTAGATCTGCTTC-A-GCGTAAACA-CGTGAAAGCCAAATCTGCTATGTCT
1 GATGCCAAATCATCTTAGATCTACTTCGATGCGAAAACATC-TGAAAGCCAAATCTGCTATGTCT
54794519 TCGATCTGCTCCTTGTCAACACAAG
65 TCGATCTGCTCCTTGTCAACACAAG
* * * ** *
54794544 GATGCCAAATCATCTTGGATCTACTTCGATGTGAAAACATCTGAAGGTTAGATCTGCTATGTCTT
1 GATGCCAAATCATCTTAGATCTACTTCGATGCGAAAACATCTGAAAGCCAAATCTGCTATGTCTT
54794609 CGATCTGCTC
66 CGATCTGCTC
54794619 TCCGTCGAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
87 25 0.39
88 1 0.02
89 37 0.58
90 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (89 bp):
GATGCCAAATCATCTTAGATCTACTTCGATGCGAAAACATCTGAAAGCCAAATCTGCTATGTCTT
CGATCTGCTCCTTGTCAACACAAG
Found at i:54794591 original size:454 final size:451
Alignment explanation
Indices: 54793680--54794570 Score: 1059
Period size: 454 Copynumber: 2.0 Consensus size: 451
54793670 AAACACATGG
* * *
54793680 AGGTTAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTTGA
1 AGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCACCTTGGA
*
54793745 TCTGCTTCAATGAAGGTCATATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCC
66 TCTGCTTCAATGAAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCC
* * *
54793810 AAATCATCTTAGATCTGCTTTAATGAAGGTCAGATCTGCTATGTTTTCGATCTGCTCTCCGTCGA
131 AAATCATCTTAGATCTGCTTCAATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCGA
** * * * * ** *
54793875 ATATGGAGATGCCAAATCTGTTTCTTTGATTTGTTCTCTGACAGTACAGAGATGCCAAATCATCT
196 ATACAGAGATCCCAAATC--TATCTTGGATCTGTTCGATGAAAGTACAGAGATGCCAAATCATCT
* **
54793940 TAGATCTGCTTCAGCGTAAACAGGTGAAAGCCAAATCTGCTATGTCTTCGATCTGCTCCTTTTCA
259 TAGATCTGCTTCAGCGTAAACAGGAGAAAGCCAAATCTGCTATGTCTTCGATCTGCTCCTGAT-A
* * ** *
54794005 ACGTAAGGATGCCAAATCATCTTGGATCTACTTCGATGTGAAAACATCCAAAGGTTAGATCTGCT
323 ACGTAAGGATGCCAAATCATCTTAGATCTACTTCGACGTGAAAACATCCAAAGGCCAAATCTGCT
* * *
54794070 ATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATTATCTTGGATCTGCTTCAATGA
388 ATGTCTTCGATCTGCTCCCCGTCTAACACAGAGATGCCAAATCATCTTGGATCTACTTCAATGA
*
54794134 AGGTCCA-ATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCACCTTGG
1 AGGT-CAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCACCTTGG
*
54794198 ATCTGCTTCAATGAAGGTCAGATCTGCTGTGTCTTCGATCTGTTCCCCGTCTAATACAGAGATGC
65 ATCTGCTTCAATGAAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGC
* * * * *
54794263 CAAATCATCTTGGATTTGCTTCAATGAATGTCAGATCTGCTGTGTCTTCGATCTGCTCCCCGTCT
130 CAAATCATCTTAGATCTGCTTCAATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCG
** * *
54794328 AATACAGAGATCCCAAATC-ATCTTGGATCTGCTTCGAT-AAAGGT-CAGATCTG-C-TAT-GTC
195 AATACAGAGATCCCAAATCTATCTTGGATCTG-TTCGATGAAA-GTACAGAGATGCCAAATCATC
* * * * * *
54794387 TTCGATCTGCTCTCCGTCG-AATA-TGGAG-ATGCCAAATCTG-T-T-TCTTCGATTTGTTCTCT
258 TTAGATCTGCT-TCAG-CGTAA-ACAGGAGAAAGCCAAATCTGCTATGTCTTCGATCTGCTC-CT
* * *
54794446 GAT-A-GTACAGAGATGCCAAATCATCTTAGATCTGCTTC-AGCGT-AAACACGT-GAAA-GCCA
319 GATAACGTA-AG-GATGCCAAATCATCTTAGATCTACTTCGA-CGTGAAA-ACATCCAAAGGCCA
**
54794505 AATCTGCTATGTCTTCGATCTGCTCCTTGTC-AACACA-AGGATGCCAAATCATCTTGGATCTAC
380 AATCTGCTATGTCTTCGATCTGCTCCCCGTCTAACACAGA-GATGCCAAATCATCTTGGATCTAC
54794568 TTC
444 TTC
54794571 GATGTGAAAA
Statistics
Matches: 376, Mismatches: 49, Indels: 36
0.82 0.11 0.08
Matches are distributed among these distances:
441 1 0.00
442 30 0.08
443 33 0.09
444 10 0.03
445 42 0.11
446 4 0.01
447 1 0.00
448 23 0.06
449 10 0.03
450 4 0.01
451 17 0.05
452 6 0.02
454 194 0.52
455 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (451 bp):
AGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCACCTTGGA
TCTGCTTCAATGAAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCC
AAATCATCTTAGATCTGCTTCAATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCGA
ATACAGAGATCCCAAATCTATCTTGGATCTGTTCGATGAAAGTACAGAGATGCCAAATCATCTTA
GATCTGCTTCAGCGTAAACAGGAGAAAGCCAAATCTGCTATGTCTTCGATCTGCTCCTGATAACG
TAAGGATGCCAAATCATCTTAGATCTACTTCGACGTGAAAACATCCAAAGGCCAAATCTGCTATG
TCTTCGATCTGCTCCCCGTCTAACACAGAGATGCCAAATCATCTTGGATCTACTTCAATGA
Found at i:54803227 original size:22 final size:22
Alignment explanation
Indices: 54803192--54803249 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
54803182 AAAAGGTATC
* *
54803192 TACAAATTAAATCTT-TAAGAT
1 TACAAATCATATCTTCTAAGAT
54803213 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
54803236 TGCATATCATATCT
1 TACAAATCATATCT
54803250 AAGATTGCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 20 0.65
23 8 0.26
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:54803252 original size:19 final size:19
Alignment explanation
Indices: 54803228--54803318 Score: 161
Period size: 19 Copynumber: 4.9 Consensus size: 19
54803218 AATCATATCT
54803228 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
54803247 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
54803265 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
54803282 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
54803301 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
54803319 TGAAAATTAT
Statistics
Matches: 69, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
17 16 0.23
18 16 0.23
19 37 0.54
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:54803284 original size:35 final size:37
Alignment explanation
Indices: 54803221--54803318 Score: 150
Period size: 35 Copynumber: 2.7 Consensus size: 37
54803211 ATTACAAAAT
54803221 CATATC-T-TCTAAGATTGCATATCATATCTAAGATTG
1 CATATCATATCTAAGATTG-ATATCATATCTAAGATTG
54803257 CA-ATCATATCTAAGATTG-TATCATATCTAAGATTG
1 CATATCATATCTAAGATTGATATCATATCTAAGATTG
54803292 CATATCATATCTAAGATTGCATATCAT
1 CATATCATATCTAAGATTG-ATATCAT
54803319 TGAAAATTAT
Statistics
Matches: 57, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
35 22 0.39
36 19 0.33
37 10 0.18
38 6 0.11
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (37 bp):
CATATCATATCTAAGATTGATATCATATCTAAGATTG
Found at i:54803474 original size:21 final size:20
Alignment explanation
Indices: 54803437--54803475 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
54803427 TTGGACTTCG
**
54803437 TTTTTTTTTGGGTTTATTAT
1 TTTTTTTTTGGACTTATTAT
54803457 TTTTGTTTTTGGACTTATT
1 TTTT-TTTTTGGACTTATT
54803476 TCTGGGCCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.10, C:0.03, G:0.15, T:0.72
Consensus pattern (20 bp):
TTTTTTTTTGGACTTATTAT
Found at i:54809253 original size:22 final size:22
Alignment explanation
Indices: 54809228--54809292 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
54809218 TAACTTATAT
* * *
54809228 ATTATGATTAACTTATTAATTA
1 ATTATAATTAAATCATTAATTA
*
54809250 ATTATAATTAAATCATTAATTC
1 ATTATAATTAAATCATTAATTA
54809272 ATTA-ACATT-AATC-TTAATTA
1 ATTATA-ATTAAATCATTAATTA
54809292 A
1 A
54809293 CACTTTTGGC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 7 0.19
21 5 0.14
22 25 0.68
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.46
Consensus pattern (22 bp):
ATTATAATTAAATCATTAATTA
Found at i:54814168 original size:47 final size:47
Alignment explanation
Indices: 54814069--54814196 Score: 148
Period size: 47 Copynumber: 2.7 Consensus size: 47
54814059 AATCGATAAG
* * ** *
54814069 TACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTTATCTCGGAG
1 TACCTATATCATGGCCCGTAGCCAAATCAAGGTAACTCATCTCAAAA
* * * * *
54814116 CACCTATATCACGGCCCGTAGCCGAATCAAGGTAACTCCTTTCAAAA
1 TACCTATATCATGGCCCGTAGCCAAATCAAGGTAACTCATCTCAAAA
**
54814163 TACCTATATCATGGCCCGTAGAAAAATCAAGGTA
1 TACCTATATCATGGCCCGTAGCCAAATCAAGGTA
54814197 TTATTCATAC
Statistics
Matches: 66, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
47 66 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (47 bp):
TACCTATATCATGGCCCGTAGCCAAATCAAGGTAACTCATCTCAAAA
Done.