Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008639.1 Hibiscus syriacus cultivar Beakdansim tig00111614_pilon, whole genome shotgun sequence
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: 1076872
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:158786 original size:17 final size:17
Alignment explanation
Indices: 158764--158827 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 17
158754 AACATATATA
158764 ATTTATAAAAGTAAAAT
1 ATTTATAAAAGTAAAAT
*
158781 ATTTATTTAAAAATAATATATAT
1 ATTTA--TAAAAGT-A-A-A-AT
158804 AATTTATAAAAGTAAAAT
1 -ATTTATAAAAGTAAAAT
158822 ATTTAT
1 ATTTAT
158828 TTATAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
17 11 0.29
18 2 0.05
19 7 0.18
20 2 0.05
21 2 0.05
22 7 0.18
23 2 0.05
24 5 0.13
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
ATTTATAAAAGTAAAAT
Found at i:158788 original size:21 final size:21
Alignment explanation
Indices: 158764--158835 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
158754 AACATATATA
158764 ATTTATAAAAGTAAAATATTT
1 ATTTATAAAAGTAAAATATTT
* *
158785 ATTTA-AAAA-TAATATATATA
1 ATTTATAAAAGTAAAATAT-TT
158805 ATTTATAAAAGTAAAATATTT
1 ATTTATAAAAGTAAAATATTT
158826 ATTTATAAAA
1 ATTTATAAAA
158836 AAATATCAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
19 7 0.16
20 10 0.23
21 20 0.45
22 7 0.16
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (21 bp):
ATTTATAAAAGTAAAATATTT
Found at i:158802 original size:41 final size:41
Alignment explanation
Indices: 158748--158841 Score: 161
Period size: 41 Copynumber: 2.3 Consensus size: 41
158738 AAAACATTAA
*
158748 AAAAATAACATATATAATTTATAAAAGTAAAATATTTATTT
1 AAAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
158789 AAAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
1 AAAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
*
158830 ATAAAAAAATAT
1 A-AAAATAATAT
158842 CAGAAAATAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 41 0.82
42 9 0.18
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (41 bp):
AAAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
Found at i:159903 original size:20 final size:20
Alignment explanation
Indices: 159861--159920 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
159851 TTCGTCTCTG
*
159861 TTTTTGGATTGCTCTCT-TT
1 TTTTTGGATTGCTCTCTGTC
*
159880 TTTTTGGTTTGCTCTCTGTC
1 TTTTTGGATTGCTCTCTGTC
159900 TTTTTGGATTGCTCTCTGTC
1 TTTTTGGATTGCTCTCTGTC
159920 T
1 T
159921 CCTCTCGTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
19 16 0.43
20 21 0.57
ACGTcount: A:0.03, C:0.18, G:0.18, T:0.60
Consensus pattern (20 bp):
TTTTTGGATTGCTCTCTGTC
Found at i:160392 original size:3 final size:3
Alignment explanation
Indices: 160386--160485 Score: 146
Period size: 3 Copynumber: 32.7 Consensus size: 3
160376 ATTATTTATT
160386 TAA TAA TATA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TA-A TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** **
160433 TAA TAA TAA TAA TAA TAA TAA TTT TAA TTT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
160481 TAA TA
1 TAA TA
160486 GAATGAAAAA
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
3 81 0.92
4 7 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:163076 original size:10 final size:10
Alignment explanation
Indices: 163061--163101 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
163051 TTCATCACAC
163061 CAAATTCTCT
1 CAAATTCTCT
163071 CAAATTCTCT
1 CAAATTCTCT
* *
163081 CAATTTATCT
1 CAAATTCTCT
*
163091 CAAATACTCT
1 CAAATTCTCT
163101 C
1 C
163102 TCTGTTTAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:163183 original size:17 final size:18
Alignment explanation
Indices: 163142--163183 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
163132 AATATTATGT
*
163142 TTTTAATTTATTTAAGTA
1 TTTTACTTTATTTAAGTA
*
163160 GTTTACTTTATTTAA-TA
1 TTTTACTTTATTTAAGTA
163177 TTTTACT
1 TTTTACT
163184 AATATAATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.62
Consensus pattern (18 bp):
TTTTACTTTATTTAAGTA
Found at i:165522 original size:35 final size:33
Alignment explanation
Indices: 165483--165567 Score: 82
Period size: 35 Copynumber: 2.5 Consensus size: 33
165473 ATATTTCAGT
165483 TAATTTTGTT-TATTACCATTTAATATCAATTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
* *
165518 TAATTTGGTTATCATTTATCATTTAATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
165553 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
165568 TAAATACCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.57
36 1 0.02
37 3 0.07
38 11 0.26
ACGTcount: A:0.27, C:0.07, G:0.09, T:0.56
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:169607 original size:22 final size:23
Alignment explanation
Indices: 169577--169620 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
169567 AAAATATATT
169577 TATTAATATTTCTAATAATATAC
1 TATTAATATTTCTAATAATATAC
* *
169600 TATT-ATATTTTTAATATTATA
1 TATTAATATTTCTAATAATATA
169621 ATAAAATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAC
Found at i:169637 original size:32 final size:32
Alignment explanation
Indices: 169571--169649 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 32
169561 ATATTTAAAA
* * *
169571 TATATTTATTAATATTTCTAATAATATACTAT
1 TATATTTATTAATATTTATAATAAAATACAAT
169603 TATATTT-TTAATA-TTATAATAAAATGATCAAT
1 TATATTTATTAATATTTATAATAAAAT-A-CAAT
* *
169635 TATATATAATAATAT
1 TATATTTATTAATAT
169650 ATAAGATATT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
30 10 0.26
31 7 0.18
32 16 0.42
33 5 0.13
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAAAATACAAT
Found at i:169952 original size:32 final size:32
Alignment explanation
Indices: 169889--169952 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
169879 ATATAATTTA
*
169889 TAATATTTTATTTCAATAAAATATACCAATAT
1 TAATATTTTATTTCAATAAAATATACAAATAT
*
169921 TAATATTTT-TATT-AATAAAATTATATAAATAT
1 TAATATTTTAT-TTCAATAAAA-TATACAAATAT
169953 AATTTTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 8 0.29
32 20 0.71
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (32 bp):
TAATATTTTATTTCAATAAAATATACAAATAT
Found at i:170171 original size:14 final size:14
Alignment explanation
Indices: 170115--170165 Score: 84
Period size: 14 Copynumber: 3.5 Consensus size: 14
170105 CAAACATCAT
170115 AAAATGTTTTTCAG
1 AAAATGTTTTTCAG
170129 AAAATGTTTTTCAG
1 AAAATGTTTTTCAG
170143 AAAATGTTTTTTTCAG
1 AAAATG--TTTTTCAG
170159 AAAATGT
1 AAAATGT
170166 AATTCATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
14 21 0.60
16 14 0.40
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.43
Consensus pattern (14 bp):
AAAATGTTTTTCAG
Found at i:171767 original size:65 final size:64
Alignment explanation
Indices: 171654--171809 Score: 176
Period size: 65 Copynumber: 2.4 Consensus size: 64
171644 TACACTTGGG
* * * *
171654 GTGCATCGGTACACT-AATTACATTCGATGTTTCAAAAGAGTCAGGAGTGTATCGATGCAT-ATT
1 GTGCATCGGTACA-TAAAATGCATTCGATGTTTCAAAAGAGTCAGGAGTGCATCAATGCATGA--
171717 CT
63 CT
*
171719 GTGCATCGGTACATAAAATGCATTCGATGTTTCATTAAA-A-TCATGAGTGCATCAATGCATGAC
1 GTGCATCGGTACATAAAATGCATTCGATGTTTCA--AAAGAGTCAGGAGTGCATCAATGCATGAC
171782 T
64 T
* *
171783 GTGCATCGATACACAAAATGCATTCGA
1 GTGCATCGGTACATAAAATGCATTCGA
171810 ATTAGTGTGT
Statistics
Matches: 80, Mismatches: 7, Indels: 9
0.83 0.07 0.09
Matches are distributed among these distances:
64 28 0.35
65 47 0.59
66 2 0.03
67 3 0.04
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (64 bp):
GTGCATCGGTACATAAAATGCATTCGATGTTTCAAAAGAGTCAGGAGTGCATCAATGCATGACT
Found at i:175841 original size:19 final size:20
Alignment explanation
Indices: 175778--175865 Score: 58
Period size: 20 Copynumber: 4.3 Consensus size: 20
175768 TAAAAGTTTG
* *
175778 ATAATATAATAATTATTTT-
1 ATAATTTAATAAGTATTTTA
*
175797 ATAGTATTTAGATAAAT-TTATTA
1 ATA--ATTTA-ATAAGTATT-TTA
* *
175820 ATAATTTCATAA-TCTTTTA
1 ATAATTTAATAAGTATTTTA
175839 ATAAATTTAATAAGTATTTT-
1 AT-AATTTAATAAGTATTTTA
175859 ATAATTT
1 ATAATTT
175866 TTTAAACTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
19 14 0.25
20 17 0.30
21 15 0.27
22 7 0.12
23 3 0.05
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.51
Consensus pattern (20 bp):
ATAATTTAATAAGTATTTTA
Found at i:175846 original size:31 final size:31
Alignment explanation
Indices: 175803--175870 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
175793 TTTTATAGTA
*
175803 TTTAGATAAATTTATTAA-TAATTTCATAATCT
1 TTTA-ATAAATTTAATAAGT-ATTTCATAATCT
* *
175835 TTTAATAAATTTAATAAGTATTTTATAATTT
1 TTTAATAAATTTAATAAGTATTTCATAATCT
175866 TTTAA
1 TTTAA
175871 ACTTTATTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 27 0.84
32 5 0.16
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (31 bp):
TTTAATAAATTTAATAAGTATTTCATAATCT
Found at i:176634 original size:31 final size:31
Alignment explanation
Indices: 176591--176675 Score: 93
Period size: 31 Copynumber: 2.7 Consensus size: 31
176581 ATAAAGTTTA
176591 AAAAAATTATAAAATACTTATTAAATTTAT-T
1 AAAAAATTATAAAATA-TTATTAAATTTATCT
* *
176622 AAAAGATTATAAAATTATTAATAAATTTATCT
1 AAAAAATTATAAAA-TATTATTAAATTTATCT
* *
176654 -AAATACTATAAAATAATTATTA
1 AAAAAATTATAAAAT-ATTATTA
176676 TATTATCGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
30 1 0.02
31 42 0.91
32 3 0.07
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (31 bp):
AAAAAATTATAAAATATTATTAAATTTATCT
Found at i:177081 original size:18 final size:18
Alignment explanation
Indices: 177054--177107 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
177044 CTGGAATGTT
*
177054 TATGAGGGAATTAGAATC
1 TATGAAGGAATTAGAATC
177072 TATGAAGGAATTAGAATC
1 TATGAAGGAATTAGAATC
* *
177090 TGT-CAGGAATTAGAATC
1 TATGAAGGAATTAGAATC
177107 T
1 T
177108 GAATCTGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
17 14 0.42
18 19 0.58
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.30
Consensus pattern (18 bp):
TATGAAGGAATTAGAATC
Found at i:177099 original size:17 final size:18
Alignment explanation
Indices: 177060--177108 Score: 73
Period size: 17 Copynumber: 2.8 Consensus size: 18
177050 TGTTTATGAG
*
177060 GGAATTAGAATCTATGAA
1 GGAATTAGAATCTGTGAA
*
177078 GGAATTAGAATCTGT-CA
1 GGAATTAGAATCTGTGAA
177095 GGAATTAGAATCTG
1 GGAATTAGAATCTG
177109 AATCTGAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 15 0.52
18 14 0.48
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.29
Consensus pattern (18 bp):
GGAATTAGAATCTGTGAA
Found at i:177695 original size:15 final size:15
Alignment explanation
Indices: 177673--177765 Score: 62
Period size: 15 Copynumber: 5.8 Consensus size: 15
177663 AAAAAAAAGC
*
177673 AATAAAGATAAATAA
1 AATAAAGAAAAATAA
*
177688 ACTAAAGAAAAATAA
1 AATAAAGAAAAATAA
177703 AATAAATGAAAAA-AGGA
1 AATAAA-GAAAAATA--A
* * *
177720 AAAATAAGATAAAGAA
1 AATA-AAGAAAAATAA
*
177736 AATACATAAAAAAATAA
1 AATA-A-AGAAAAATAA
177753 AATAAAGATAAAA
1 AATAAAGA-AAAA
177766 AACTAAATAA
Statistics
Matches: 60, Mismatches: 11, Indels: 13
0.71 0.13 0.15
Matches are distributed among these distances:
15 21 0.35
16 16 0.27
17 20 0.33
18 3 0.05
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.15
Consensus pattern (15 bp):
AATAAAGAAAAATAA
Found at i:177709 original size:24 final size:23
Alignment explanation
Indices: 177673--177758 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 23
177663 AAAAAAAAGC
177673 AATAAAGATAAATAAACTAAAGAAA
1 AATAAA-ATAAATAAA-TAAAGAAA
177698 AATAAAATAAATGAAA-AAAGGAAA
1 AATAAAATAAAT-AAATAAA-GAAA
* * *
177722 AATAAGATAAAGAAAATACATAAAAA
1 AATAAAATAAA-TAAATA-A-AGAAA
177748 AATAAAATAAA
1 AATAAAATAAA
177759 GATAAAAAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
23 3 0.06
24 23 0.45
25 10 0.20
26 14 0.27
27 1 0.02
ACGTcount: A:0.74, C:0.02, G:0.08, T:0.15
Consensus pattern (23 bp):
AATAAAATAAATAAATAAAGAAA
Found at i:177765 original size:19 final size:17
Alignment explanation
Indices: 177741--178049 Score: 75
Period size: 18 Copynumber: 17.4 Consensus size: 17
177731 AAGAAAATAC
177741 ATAAAAAAATAAAATAAA
1 ATAAAAAAAT-AAATAAA
*
177759 GATAAAAAACTAAATAAA
1 -ATAAAAAAATAAATAAA
* *
177777 ATAAAGAACATTAAA-AAC
1 ATAAA-AA-AATAAATAAA
*
177795 A-AAAGAAATAGAA-AAA
1 ATAAAAAAATA-AATAAA
177811 ATGAAGAAAAATAAATAAA
1 AT-AA-AAAAATAAATAAA
* * *
177830 ATAATCAAAATAAAGATA
1 ATAA-AAAAATAAATAAA
* *
177848 ACAAGCAAAAT--A-AAA
1 ATAA-AAAAATAAATAAA
177863 ATAAAAATAA-AAATAAA
1 ATAAAAA-AATAAATAAA
*
177880 ATAAAGGAAAATACTAATAATTGT
1 ATAAA--AAAATA--AATAA---A
* *
177904 ATATACATAATAAAT-AA
1 ATA-AAAAAATAAATAAA
* * *
177921 ATAAATAAATAAACAAG
1 ATAAAAAAATAAATAAA
** * *
177938 AGGAAAATACAAATGAAA
1 ATAAAAAAATAAAT-AAA
* * *
177956 ATAAATATATAGATAAA
1 ATAAAAAAATAAATAAA
*
177973 ACTAATATAAA-AAATAAA
1 A-TAA-AAAAATAAATAAA
177991 ATAAGAATAAATAAATAAA
1 ATAA-AA-AAATAAATAAA
* *
178010 A-GAATAAATAAAT-AA
1 ATAAAAAAATAAATAAA
*
178025 CTAAATAAAATAAGA-AAA
1 ATAAA-AAAATAA-ATAAA
178043 ATAAAAA
1 ATAAAAA
178050 GTAAATATAT
Statistics
Matches: 213, Mismatches: 47, Indels: 62
0.66 0.15 0.19
Matches are distributed among these distances:
14 2 0.01
15 12 0.06
16 25 0.12
17 45 0.21
18 71 0.33
19 40 0.19
20 1 0.00
21 8 0.04
23 5 0.02
24 3 0.01
25 1 0.00
ACGTcount: A:0.71, C:0.04, G:0.06, T:0.19
Consensus pattern (17 bp):
ATAAAAAAATAAATAAA
Found at i:177767 original size:18 final size:17
Alignment explanation
Indices: 177741--177781 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
177731 AAGAAAATAC
*
177741 ATAAAAAAATAAAATAAA
1 ATAAAAAACT-AAATAAA
177759 GATAAAAAACTAAATAAA
1 -ATAAAAAACTAAATAAA
177777 ATAAA
1 ATAAA
177782 GAACATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 7 0.33
19 9 0.43
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.17
Consensus pattern (17 bp):
ATAAAAAACTAAATAAA
Found at i:177869 original size:12 final size:12
Alignment explanation
Indices: 177817--177884 Score: 59
Period size: 12 Copynumber: 5.8 Consensus size: 12
177807 AAAAATGAAG
177817 AAAAATAAATAA-
1 AAAAATAAA-AAT
* *
177829 AATAATCAAAAT
1 AAAAATAAAAAT
* * *
177841 AAAGATAACAAG
1 AAAAATAAAAAT
*
177853 CAAAATAAAAAT
1 AAAAATAAAAAT
177865 AAAAATAAAAAT
1 AAAAATAAAAAT
177877 -AAAATAAA
1 AAAAATAAA
177885 GGAAAATACT
Statistics
Matches: 43, Mismatches: 12, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
11 10 0.23
12 33 0.77
ACGTcount: A:0.76, C:0.04, G:0.03, T:0.16
Consensus pattern (12 bp):
AAAAATAAAAAT
Found at i:177921 original size:4 final size:4
Alignment explanation
Indices: 177912--178056 Score: 64
Period size: 4 Copynumber: 34.0 Consensus size: 4
177902 GTATATACAT
* * * *
177912 AATA AATA AATA AATA AATA AACA AGAGGA AA-A TACA AATGAA AATA
1 AATA AATA AATA AATA AATA AATA A-A-TA AATA AATA AAT--A AATA
* *
177959 AATA TATA GATAA AACTA ATATA AA-A AATAA AATAA GAATA AATA AATA
1 AATA AATA AAT-A AA-TA A-ATA AATA AAT-A AAT-A -AATA AATA AATA
* * *
178008 AA-A GAATA AATA AATA ACTA AATAA AATA AGAAA AATA AA-A AGTA AATA
1 AATA -AATA AATA AATA AATA AAT-A AATA A-ATA AATA AATA AATA AATA
178057 TATGAAAAAT
Statistics
Matches: 111, Mismatches: 14, Indels: 32
0.71 0.09 0.20
Matches are distributed among these distances:
3 8 0.07
4 68 0.61
5 24 0.22
6 11 0.10
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.20
Consensus pattern (4 bp):
AATA
Found at i:177991 original size:18 final size:19
Alignment explanation
Indices: 177979--178048 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 19
177969 TAAAACTAAT
177979 ATAAA-AAATAAAATAAGA
1 ATAAATAAATAAAATAAGA
* *
177997 ATAAATAAATAAAAGAATAA
1 ATAAATAAATAAAATAA-GA
*
178017 ATAAATAACT-AAATAA-A
1 ATAAATAAATAAAATAAGA
*
178034 ATAAGAAAAATAAAA
1 ATAA-ATAAATAAAA
178049 AGTAAATATA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
17 5 0.12
18 9 0.21
19 18 0.43
20 10 0.24
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.19
Consensus pattern (19 bp):
ATAAATAAATAAAATAAGA
Found at i:180659 original size:28 final size:28
Alignment explanation
Indices: 180619--180683 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
180609 CTCATTTATG
180619 TTTCTCTCTCTAAGAGAAAGAAACAAAA
1 TTTCTCTCTCTAAGAGAAAGAAACAAAA
* * *
180647 TTTCGCTCTCTAAGATAAAGAAACAAAG
1 TTTCTCTCTCTAAGAGAAAGAAACAAAA
180675 TTTCTCTCT
1 TTTCTCTCT
180684 AAAAATCTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (28 bp):
TTTCTCTCTCTAAGAGAAAGAAACAAAA
Found at i:181155 original size:22 final size:22
Alignment explanation
Indices: 181112--181156 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
181102 TGAACCCTTC
* *
181112 GGTGAGTCACCGGATCTACGAT
1 GGTGACTCACCGGAGCTACGAT
* *
181134 GGTGACTCACCGTAGCTTCGAT
1 GGTGACTCACCGGAGCTACGAT
181156 G
1 G
181157 AGTTGTGCGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.31, T:0.24
Consensus pattern (22 bp):
GGTGACTCACCGGAGCTACGAT
Found at i:181279 original size:22 final size:22
Alignment explanation
Indices: 181224--181282 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
181214 TGGGGAACAT
*
181224 AGCGGCGGAGCAGTTGGATGTA
1 AGCGGCGGAGCAGTTGGATATA
* **
181246 GGCGGCATAGCAGTTGGATATA
1 AGCGGCGGAGCAGTTGGATATA
*
181268 AGCGACGGAGCAGTT
1 AGCGGCGGAGCAGTT
181283 AGAGGCAACA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.25, C:0.15, G:0.41, T:0.19
Consensus pattern (22 bp):
AGCGGCGGAGCAGTTGGATATA
Found at i:181422 original size:19 final size:19
Alignment explanation
Indices: 181395--181433 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
181385 GGTTGTTGAA
181395 GAATCGGGTTCTTTGGGCC
1 GAATCGGGTTCTTTGGGCC
*
181414 GAATTGGGTTCTTTGGGCC
1 GAATCGGGTTCTTTGGGCC
181433 G
1 G
181434 GATCTGGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.10, C:0.18, G:0.38, T:0.33
Consensus pattern (19 bp):
GAATCGGGTTCTTTGGGCC
Found at i:181521 original size:17 final size:18
Alignment explanation
Indices: 181480--181522 Score: 72
Period size: 17 Copynumber: 2.5 Consensus size: 18
181470 TGCTGCGTTA
181480 TTTGGG-CTTGGATCATT
1 TTTGGGCCTTGGATCATT
181497 TTTGGGCCTT-GATCATT
1 TTTGGGCCTTGGATCATT
181514 TTTGGGCCT
1 TTTGGGCCT
181523 GACTCGGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 22 0.88
18 3 0.12
ACGTcount: A:0.09, C:0.16, G:0.28, T:0.47
Consensus pattern (18 bp):
TTTGGGCCTTGGATCATT
Found at i:181622 original size:20 final size:20
Alignment explanation
Indices: 181577--181640 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
181567 AAATATCTAC
* * *
181577 TATAATAAAATTTATTAT-T
1 TATAATAATATTTATAATAA
181596 TATTAATAATATTTATAATAA
1 TA-TAATAATATTTATAATAA
*
181617 TATAATAATAATATATAAATAA
1 TATAATAAT-ATTTAT-AATAA
181639 TA
1 TA
181641 GCGGGATGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 2 0.05
20 21 0.57
21 7 0.19
22 7 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TATAATAATATTTATAATAA
Found at i:182151 original size:137 final size:137
Alignment explanation
Indices: 181789--182165 Score: 515
Period size: 137 Copynumber: 2.8 Consensus size: 137
181779 AAACTAGTGT
* *
181789 ATGACATTGTTCATTCGTGATGAGGACATCT-AGCCATCTTTAAAGATATTTGAGATAAC-TCGG
1 ATGACATTGTTCCTTCGTGATGAGGACGTCTGA-CCATCTTTAAAGATATTTGAGATAACAT-GG
* ** * * *
181852 TTCCTTCGTGATGATGACATCTGACTATCTATGGATGATGATTCTCCTTTATGATGAGGAATTCT
64 TTCCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATGATGCTCCTTCATGATGAGGAATTCT
181917 GATAAATGG
129 GATAAATGG
* * *
181926 ATGACATTGTTCCTTCGTGATGAGGACGTTTGTCCATCTTTAAAGATATTTGAGATAACACGGTT
1 ATGACATTGTTCCTTCGTGATGAGGACGTCTGACCATCTTTAAAGATATTTGAGATAACATGGTT
* * *
181991 CCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATGATGCTTCTTCGTGATGAGGAGTTCTGA
66 CCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATGATGCTCCTTCATGATGAGGAATTCTGA
***
182056 TCGGTGG
131 TAAATGG
* * *
182063 ATGACATTGTTCCTTCGTGATGAGGACGTCTGACTATCTTTAAAGATATTTGAGATAGCATAGTT
1 ATGACATTGTTCCTTCGTGATGAGGACGTCTGACCATCTTTAAAGATATTTGAGATAACATGGTT
* * *
182128 CCTTCGTGATGAGGACGTTTGGTTATTTAAGGATGATG
66 CCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATG
182166 TTTCCTAAAA
Statistics
Matches: 212, Mismatches: 26, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
137 212 1.00
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (137 bp):
ATGACATTGTTCCTTCGTGATGAGGACGTCTGACCATCTTTAAAGATATTTGAGATAACATGGTT
CCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATGATGCTCCTTCATGATGAGGAATTCTGA
TAAATGG
Found at i:185349 original size:37 final size:36
Alignment explanation
Indices: 185291--185872 Score: 261
Period size: 40 Copynumber: 15.4 Consensus size: 36
185281 TGTCTCAAGG
* * * *
185291 GTTTTAAGAAAAACCATCTCAAGTGAGATAAATTTT
1 GTTTCAAGGAAAACTATCTCAAGCGAGATAAATTTT
* * * *
185327 GTTTCAAAGGAAAACTGTCTCAAGAGAGACAAAATTT
1 GTTTC-AAGGAAAACTATCTCAAGCGAGATAAATTTT
* * *
185364 GTTTCAAGGGAAAC-ATTTTCAA---AG-T---TTAT
1 GTTTCAAGGAAAACTA-TCTCAAGCGAGATAAATTTT
* * *
185393 GTTTCAA-GAGAAACTGTCTCAAGGGAGACAAAATTTT
1 GTTTCAAGGA-AAACTATCTCAAGCGAGA-TAAATTTT
* * * *
185430 GTTTCAA-GAGAAACTGTCTCAAGGGAGACAAAATTT
1 GTTTCAAGGA-AAACTATCTCAAGCGAGATAAATTTT
* * * * *
185466 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
1 GTTTCAAGGAAAACTATCTCAAGCGAGATAAATTTT
*
185502 GTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTTT
1 GTTTCAAGGAAAACTATCTCAAGCGAGAT-AAA--TTTT
* *
185541 GTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCT
1 GTTTCAAGGAAAACTATCTCAAGCGAGAT-AAAT-TT-T
* **
185580 GTTTCAAGGAAAAACAATCTTGAGCGAGATAAAATCTTCT
1 GTTTCAAGG-AAAACTATCTCAAGCGAGAT-AAAT-TT-T
* * *
185620 GTTTCAAGGAAAAACAATCTTAAGTGAGATAAAATATTCT
1 GTTTCAAGG-AAAACTATCTCAAGCGAGAT-AAAT-TT-T
* ** *
185660 GTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATATTTT
1 GTTTCAAGG-AAAACTATCTCAAGCGAGAT--AA-ATTTT
* * ** *
185700 GTTTCAAGGAAAAATAATATTGAGTGAGATAAAATCTTCT
1 GTTTCAAGGAAAACT-ATCTCAAGCGAGAT-AAAT-TT-T
* ** *
185740 GTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATGTTCT
1 GTTTCAAGG-AAAACTATCTCAAGCGAGAT-AAAT-TT-T
* * *
185780 GTTTCAAGGAAAAATAATCTTGAA-TGAGATAAAATCTTCT
1 GTTTCAAGGAAAACT-ATC-TCAAGCGAGAT-AAAT-TT-T
* *
185820 GTTTCAAGGAAAAACAATCTCGAA-TGAGATAAAATCTTCT
1 GTTTCAAGG-AAAACTATCTC-AAGCGAGAT-AAAT-TT-T
185860 GTTTCAAGGAAAA
1 GTTTCAAGGAAAA
185873 ACAATCTTGA
Statistics
Matches: 466, Mismatches: 51, Indels: 55
0.81 0.09 0.10
Matches are distributed among these distances:
28 1 0.00
29 18 0.04
32 2 0.00
33 2 0.00
36 81 0.17
37 66 0.14
38 4 0.01
39 62 0.13
40 213 0.46
41 15 0.03
42 2 0.00
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.29
Consensus pattern (36 bp):
GTTTCAAGGAAAACTATCTCAAGCGAGATAAATTTT
Found at i:185479 original size:36 final size:37
Alignment explanation
Indices: 185383--185588 Score: 254
Period size: 36 Copynumber: 5.5 Consensus size: 37
185373 GAAACATTTT
* * *
185383 CAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGA
1 CAAAATTT-TGTTTCAAGGGAAACTGTCTCAAGCGAGA
* *
185421 CAAAATTTTGTTTCAAGAGAAACTGTCTCAAGGGAGA
1 CAAAATTTTGTTTCAAGGGAAACTGTCTCAAGCGAGA
*
185458 CAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
1 CAAAATTTTGTTTCAAGGGAAACTGTCTCAAGCGAGA
*
185494 CAAAA-TTTGTTTCAAGGGAAACTATCTCAAGCGAGA
1 CAAAATTTTGTTTCAAGGGAAACTGTCTCAAGCGAGA
* * *
185530 TAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAGA
1 CAAAA--TTTTGTTTCAAGGGAAACTGTCTCAAGCGAGA
*
185569 TAAAATCTTCTGTTTCAAGG
1 CAAAAT-TT-TGTTTCAAGG
185589 AAAAACAATC
Statistics
Matches: 155, Mismatches: 8, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
36 67 0.43
37 35 0.23
38 9 0.06
39 44 0.28
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (37 bp):
CAAAATTTTGTTTCAAGGGAAACTGTCTCAAGCGAGA
Found at i:185599 original size:23 final size:23
Alignment explanation
Indices: 185572--185640 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 23
185562 AGCGAGATAA
185572 AATCTTCTGTTTCAAGGAAAAAC
1 AATCTTCTGTTTCAAGGAAAAAC
** * *
185595 AATC-T-TG-AGCGA-G-ATAA-
1 AATCTTCTGTTTCAAGGAAAAAC
185612 AATCTTCTGTTTCAAGGAAAAAC
1 AATCTTCTGTTTCAAGGAAAAAC
185635 AATCTT
1 AATCTT
185641 AAGTGAGATA
Statistics
Matches: 32, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
17 4 0.12
18 4 0.12
19 3 0.09
20 4 0.12
21 3 0.09
22 4 0.12
23 10 0.31
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.30
Consensus pattern (23 bp):
AATCTTCTGTTTCAAGGAAAAAC
Found at i:185704 original size:120 final size:120
Alignment explanation
Indices: 185501--186007 Score: 621
Period size: 120 Copynumber: 4.2 Consensus size: 120
185491 AGACAAAATT
* * * * * * * * **
185501 TGTTTCAAGG-GAAACTATCTCAAGCGAGATAAAATCTTTTGTTTCGAGG-GAAACTATCTCAAG
1 TGTTTCAAGGAAAAACAATCTTAAGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAG
* *
185564 CGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGCGAGATAAAATCTTC
66 TGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTC
*
185619 TGTTTCAAGGAAAAACAATCTTAAGTGAGATAAAATATTCTGTTTCAAGGAAAAACAATCTTGAG
1 TGTTTCAAGGAAAAACAATCTTAAGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAG
* * * *
185684 TGAGATAAAATATTTTGTTTCAAGGAAAAATAATATTGAGTGAGATAAAATCTTC
66 TGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTC
* * * *
185739 TGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATGTTCTGTTTCAAGGAAAAATAATCTTGAA
1 TGTTTCAAGGAAAAACAATCTTAAGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAG
* *
185804 TGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTCGAATGAGATAAAATCTTC
66 TGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTC
* *
185859 TGTTTCAAGGAAAAACAATCTTGAA-TGAAATAAAATCTTTTGTTTCAAGGAAAAACAATCTTGA
1 TGTTTCAAGGAAAAACAATCTT-AAGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGA
* * * * * * * *
185923 GTCAAATGAAAT-GTCTTGTTTCAAGGAAAAACAATCTTGAGTCAAATGAAAT-GTC
65 GTGAGATAAAATCTTC-TGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTC
* * *
185978 TTGTTTCAA-GTAAAACAGTCTCAAGTGAGA
1 -TGTTTCAAGGAAAAACAATCTTAAGTGAGA
186008 CAAACTCAGT
Statistics
Matches: 336, Mismatches: 47, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
118 12 0.04
119 50 0.15
120 273 0.81
121 1 0.00
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (120 bp):
TGTTTCAAGGAAAAACAATCTTAAGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAG
TGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTC
Found at i:185838 original size:23 final size:23
Alignment explanation
Indices: 185812--185920 Score: 66
Period size: 23 Copynumber: 5.3 Consensus size: 23
185802 AATGAGATAA
185812 AATCTTCTGTTTCAAGGAAAAAC
1 AATCTTCTGTTTCAAGGAAAAAC
* *
185835 AATC-TC-G----AATGAGATAA-
1 AATCTTCTGTTTCAAGGA-AAAAC
185852 AATCTTCTGTTTCAAGGAAAAAC
1 AATCTTCTGTTTCAAGGAAAAAC
*
185875 AATC-T-TG----AATGAAATAA-
1 AATCTTCTGTTTCAAGGAAA-AAC
*
185892 AATCTTTTGTTTCAAGGAAAAAC
1 AATCTTCTGTTTCAAGGAAAAAC
185915 AATCTT
1 AATCTT
185921 GAGTCAAATG
Statistics
Matches: 64, Mismatches: 6, Indels: 32
0.63 0.06 0.31
Matches are distributed among these distances:
17 18 0.28
18 8 0.12
19 3 0.05
21 3 0.05
22 8 0.12
23 24 0.38
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.31
Consensus pattern (23 bp):
AATCTTCTGTTTCAAGGAAAAAC
Found at i:185960 original size:21 final size:21
Alignment explanation
Indices: 185859--185961 Score: 60
Period size: 21 Copynumber: 5.1 Consensus size: 21
185849 TAAAATCTTC
185859 TGTTTCAAGGAAAAACAATCT
1 TGTTTCAAGGAAAAACAATCT
*
185880 TG----AATGAAATAA-AATCTTT
1 TGTTTCAAGGAAA-AACAATC--T
185899 TGTTTCAAGGAAAAACAATCT
1 TGTTTCAAGGAAAAACAATCT
** * **
185920 TGAGTCAA--ATGAAA-TGTCT
1 TGTTTCAAGGA-AAAACAATCT
185939 TGTTTCAAGGAAAAACAATCT
1 TGTTTCAAGGAAAAACAATCT
185960 TG
1 TG
185962 AGTCAAATGA
Statistics
Matches: 58, Mismatches: 12, Indels: 24
0.62 0.13 0.26
Matches are distributed among these distances:
17 10 0.17
18 2 0.03
19 13 0.22
20 6 0.10
21 15 0.26
22 2 0.03
23 10 0.17
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.31
Consensus pattern (21 bp):
TGTTTCAAGGAAAAACAATCT
Found at i:185987 original size:40 final size:40
Alignment explanation
Indices: 185526--185964 Score: 621
Period size: 40 Copynumber: 11.0 Consensus size: 40
185516 TATCTCAAGC
* * * * ** *
185526 GAGATAAAATCTTTTGTTTCGAGG-GAAACTATCTCAAGC
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
185565 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGC
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
185605 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTAAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
185645 GAGATAAAATATTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* * * *
185685 GAGATAAAATATTTTGTTTCAAGGAAAAATAATATTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
185725 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* * *
185765 GAGATAAAATGTTCTGTTTCAAGGAAAAATAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* *
185805 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTCGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
185845 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* *
185885 GAAATAAAATCTTTTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* * * *
185925 CAAATGAAAT-GTCTTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTC-TGTTTCAAGGAAAAACAATCTTGAGT
185965 CAAATGAAAT
Statistics
Matches: 367, Mismatches: 31, Indels: 3
0.92 0.08 0.01
Matches are distributed among these distances:
39 23 0.06
40 344 0.94
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.31
Consensus pattern (40 bp):
GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
Found at i:187460 original size:52 final size:52
Alignment explanation
Indices: 187372--187512 Score: 203
Period size: 52 Copynumber: 2.7 Consensus size: 52
187362 TATCCCAACC
* * * * *
187372 TTTTCATGCTAGTGTGAGCCTTCAAT-ATACCTCACATGGATCATTTCTGTCT
1 TTTTCATGCTAATGTGAACCTTC-ATGATGCCCCACATGGATCATTTCTATCT
*
187424 TTTTCATGATAATGTGAACCTTCATGATGCCCCACATGGATCATTTCTATCT
1 TTTTCATGCTAATGTGAACCTTCATGATGCCCCACATGGATCATTTCTATCT
*
187476 TTTTCATGCTGATGTGAACCTTCATGATGCCCCACAT
1 TTTTCATGCTAATGTGAACCTTCATGATGCCCCACAT
187513 AGATAATATG
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
51 2 0.03
52 78 0.98
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.38
Consensus pattern (52 bp):
TTTTCATGCTAATGTGAACCTTCATGATGCCCCACATGGATCATTTCTATCT
Found at i:190892 original size:17 final size:17
Alignment explanation
Indices: 190863--190895 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
190853 ATTTCTTCAA
190863 TCATCGAATGTTCTTCT
1 TCATCGAATGTTCTTCT
190880 TCAT-GAATCGTTCTTC
1 TCATCGAAT-GTTCTTC
190896 AACCAGTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.18, C:0.24, G:0.12, T:0.45
Consensus pattern (17 bp):
TCATCGAATGTTCTTCT
Found at i:190895 original size:55 final size:55
Alignment explanation
Indices: 190836--190943 Score: 130
Period size: 55 Copynumber: 2.0 Consensus size: 55
190826 CACATACATG
* * * *
190836 TCTTCAATCTGTTT-AAGATTTCTTCAATCATCGAATGTTC-TTCTTCATGAATCGT
1 TCTTCAACCAGTTTCAA-ATTTCTTCAATCATAGAATGTCCATT-TTCATGAATCGT
* *
190891 TCTTCAACCAGTTTCAAATTTCTTCATTCATAGGATGTCCATTTTCATGAATC
1 TCTTCAACCAGTTTCAAATTTCTTCAATCATAGAATGTCCATTTTCATGAATC
190944 ATTTGAATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
55 41 0.91
56 4 0.09
ACGTcount: A:0.25, C:0.21, G:0.10, T:0.44
Consensus pattern (55 bp):
TCTTCAACCAGTTTCAAATTTCTTCAATCATAGAATGTCCATTTTCATGAATCGT
Found at i:192146 original size:15 final size:16
Alignment explanation
Indices: 192128--192166 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
192118 ATGTCTTTTA
192128 AAAAAT-AATTTTAAG
1 AAAAATCAATTTTAAG
*
192143 AAAAATCATTTTTAAG
1 AAAAATCAATTTTAAG
192159 ACAAAATC
1 A-AAAATC
192167 GGTATGAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.29
16 9 0.43
17 6 0.29
ACGTcount: A:0.56, C:0.08, G:0.05, T:0.31
Consensus pattern (16 bp):
AAAAATCAATTTTAAG
Found at i:192495 original size:33 final size:33
Alignment explanation
Indices: 192458--192520 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
192448 TCCTATAAAG
192458 TAACTAATAATAAAAAATTAAATAAATATAATT
1 TAACTAATAATAAAAAATTAAATAAATATAATT
* * * *
192491 TAACTAATATTAATAAATTATATATATATA
1 TAACTAATAATAAAAAATTAAATAAATATA
192521 TATATATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (33 bp):
TAACTAATAATAAAAAATTAAATAAATATAATT
Found at i:192516 original size:2 final size:2
Alignment explanation
Indices: 192509--192553 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
192499 ATTAATAAAT
192509 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
192551 TA T
1 TA T
192554 GCGTATTACA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:203685 original size:120 final size:117
Alignment explanation
Indices: 203440--203734 Score: 389
Period size: 120 Copynumber: 2.5 Consensus size: 117
203430 GCATGAACTA
* * * ** * *
203440 CACGCAAATCACTATGG-AATATTTAAAAATAATTG-TTTTTTAAAGTTTCAACTAATAAAGCCT
1 CACGCAAATCTCCATGGAAAT-TTTAAAATTAATTGATTAGTCAAAGTTTCAACTAAT-CAGCCT
* * *
203503 TTTCTCAAACCCCATGCAATACCCATGAAAAATTTAAATTCATGCAAAGAATCC
64 TTTCTCAAACCCCATGAAATACCCATAAAAAATTAAAATTCATGCAAAGAATCC
*
203557 CACGCAAATCTCCATGGAAATTTTAAAATTAATTGATTAGTCAAAGTTTCAACTAATCAGGCTAA
1 CACGCAAATCTCCATGGAAATTTTAAAATTAATTGATTAGTCAAAGTTTCAACTAATCAGCCT--
* *
203622 TTTTTCAAACCCCATGAAATACCCATAAAAAAATTAAAATTTATGCAAAGAATCC
64 TTTCTCAAACCCCATGAAATACCCAT-AAAAAATTAAAATTCATGCAAAGAATCC
*
203677 C-CTTCAAATCTCCATGGAAATTTTAAAATTAATTGATTAGTCAAAGTTTCAACTAATC
1 CAC-GCAAATCTCCATGGAAATTTTAAAATTAATTGATTAGTCAAAGTTTCAACTAATC
203735 TCCACTTCTT
Statistics
Matches: 158, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
117 32 0.20
118 21 0.13
119 25 0.16
120 80 0.51
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (117 bp):
CACGCAAATCTCCATGGAAATTTTAAAATTAATTGATTAGTCAAAGTTTCAACTAATCAGCCTTT
TCTCAAACCCCATGAAATACCCATAAAAAATTAAAATTCATGCAAAGAATCC
Found at i:205502 original size:22 final size:22
Alignment explanation
Indices: 205475--205531 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
205465 AACATAGCGG
*
205475 CGGAGCAGTTGGATGTAGGCGA
1 CGGAGCAGTTGGATATAGGCGA
*
205497 CGGAGCAGTTGGATATAGGCGG
1 CGGAGCAGTTGGATATAGGCGA
* *
205519 CGAAGCAATTGGA
1 CGGAGCAGTTGGA
205532 GGCAGCACCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.26, C:0.14, G:0.42, T:0.18
Consensus pattern (22 bp):
CGGAGCAGTTGGATATAGGCGA
Found at i:205794 original size:15 final size:15
Alignment explanation
Indices: 205756--205796 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
205746 AAATATCTAC
205756 TATAATAA-AATTATT
1 TATAATAATAA-TATT
205771 TAT--TAATAATATT
1 TATAATAATAATATT
205784 TATAATAATAATA
1 TATAATAATAATA
205797 CAATAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 10 0.43
14 2 0.09
15 11 0.48
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TATAATAATAATATT
Found at i:205804 original size:14 final size:13
Alignment explanation
Indices: 205785--205831 Score: 69
Period size: 14 Copynumber: 3.5 Consensus size: 13
205775 AATAATATTT
205785 ATAATAATAATACA
1 ATAATAATAATA-A
205799 ATAATAATATATAA
1 ATAATAATA-ATAA
205813 ATAATAAT-ATAA
1 ATAATAATAATAA
205825 ATAATAA
1 ATAATAA
205832 CGGGACGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 11 0.34
14 18 0.56
15 3 0.09
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (13 bp):
ATAATAATAATAA
Found at i:205807 original size:26 final size:26
Alignment explanation
Indices: 205774--205831 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
205764 AATTATTTAT
* *
205774 TAATAATATTTATAATAATAATA-CAA
1 TAATAATATATA-AATAATAATATAAA
205800 TAATAATATATAAATAATAATATAAA
1 TAATAATATATAAATAATAATATAAA
205826 TAATAA
1 TAATAA
205832 CGGGACGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 10 0.34
26 19 0.66
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (26 bp):
TAATAATATATAAATAATAATATAAA
Found at i:206857 original size:165 final size:165
Alignment explanation
Indices: 206585--206914 Score: 660
Period size: 165 Copynumber: 2.0 Consensus size: 165
206575 AGTGAAGAAA
206585 GTGATGGATTATGAAGTGTTTTGGGGACTAGATTAACTGTTTTATTTTCTTGTTTCTGTGTAGTG
1 GTGATGGATTATGAAGTGTTTTGGGGACTAGATTAACTGTTTTATTTTCTTGTTTCTGTGTAGTG
206650 GAAGGATCGGAGGAAGAAATTCTGCATGCTCGTCGGGTGTATGTTGCAGCCGTTGACTTGTTGTG
66 GAAGGATCGGAGGAAGAAATTCTGCATGCTCGTCGGGTGTATGTTGCAGCCGTTGACTTGTTGTG
206715 TGAGATCTTCGGTTACTTTGCTAAATTTACTTTTG
131 TGAGATCTTCGGTTACTTTGCTAAATTTACTTTTG
206750 GTGATGGATTATGAAGTGTTTTGGGGACTAGATTAACTGTTTTATTTTCTTGTTTCTGTGTAGTG
1 GTGATGGATTATGAAGTGTTTTGGGGACTAGATTAACTGTTTTATTTTCTTGTTTCTGTGTAGTG
206815 GAAGGATCGGAGGAAGAAATTCTGCATGCTCGTCGGGTGTATGTTGCAGCCGTTGACTTGTTGTG
66 GAAGGATCGGAGGAAGAAATTCTGCATGCTCGTCGGGTGTATGTTGCAGCCGTTGACTTGTTGTG
206880 TGAGATCTTCGGTTACTTTGCTAAATTTACTTTTG
131 TGAGATCTTCGGTTACTTTGCTAAATTTACTTTTG
206915 ATATTATTAT
Statistics
Matches: 165, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
165 165 1.00
ACGTcount: A:0.19, C:0.12, G:0.28, T:0.41
Consensus pattern (165 bp):
GTGATGGATTATGAAGTGTTTTGGGGACTAGATTAACTGTTTTATTTTCTTGTTTCTGTGTAGTG
GAAGGATCGGAGGAAGAAATTCTGCATGCTCGTCGGGTGTATGTTGCAGCCGTTGACTTGTTGTG
TGAGATCTTCGGTTACTTTGCTAAATTTACTTTTG
Found at i:211385 original size:28 final size:27
Alignment explanation
Indices: 211345--211401 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
211335 ATATTTTTTG
211345 AATAGTTTAGGTA-TCTATTATGACACAA
1 AATAGTTTAGGTACT-TATTATGAC-CAA
* *
211373 AATATTTTAGGTACTTATTTTGACCAA
1 AATAGTTTAGGTACTTATTATGACCAA
211400 AA
1 AA
211402 AAATAACTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 5 0.19
28 20 0.77
29 1 0.04
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.39
Consensus pattern (27 bp):
AATAGTTTAGGTACTTATTATGACCAA
Found at i:211402 original size:28 final size:28
Alignment explanation
Indices: 211345--211449 Score: 88
Period size: 31 Copynumber: 3.6 Consensus size: 28
211335 ATATTTTTTG
* *
211345 AATAGTTTAGGTA-TCTATTATGA-CACAA
1 AATACTTTAGGTACT-TATTTTGACCA-AA
*
211373 AATATTTTAGGTACTTATTTTGACCAAAAA
1 AATACTTTAGGTACTTATTTTGACC--AAA
*
211403 AATAACTTTAAGTACTTATTTTGACCAAAA
1 AAT-ACTTTAGGTACTTATTTTGACC-AAA
* *
211433 AATACGTTAGATACTTA
1 AATACTTTAGGTACTTA
211450 AATGAAAAAG
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
28 19 0.29
29 13 0.20
30 12 0.18
31 21 0.32
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.37
Consensus pattern (28 bp):
AATACTTTAGGTACTTATTTTGACCAAA
Found at i:211447 original size:29 final size:31
Alignment explanation
Indices: 211379--211449 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
211369 ACAAAATATT
* *
211379 TTAGGTACTTATTTTGACCAAAAAAATAACT
1 TTAGATACTTATTTTGACCAAAAAAATAACG
211410 TTA-AGTACTTATTTTGACC-AAAAAAT-ACG
1 TTAGA-TACTTATTTTGACCAAAAAAATAACG
211439 TTAGATACTTA
1 TTAGATACTTA
211450 AATGAAAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
29 11 0.31
30 8 0.22
31 17 0.47
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.37
Consensus pattern (31 bp):
TTAGATACTTATTTTGACCAAAAAAATAACG
Found at i:212032 original size:211 final size:210
Alignment explanation
Indices: 211609--212037 Score: 765
Period size: 213 Copynumber: 2.0 Consensus size: 210
211599 GGGTTTAAAT
211609 TAAAATTTTCAAAAATTTTGAAGAGTTCAATTTAATTTTTTTTCAAAAAAAAAATTAGGGTCTAA
1 TAAAATTTTCAAAAATTTTGAAGAGTTCAATTTAATTTTTTTTCAAAAAAAAAATTAGGGTCTAA
*
211674 CTAAAATTTTTGAAAATTTGAGAGGCTTAATGAGAATTTTTAAAATTATAAGAGAGGTTTAATTA
66 CTAAAATTTTTGAAAATTTGAGAGGCTTAATGAGAACTTTTAAAATTATAAGAGAGGTTTAATTA
211739 AGACCATTAAAATTTTAAAAAACTTAATATGAATTTCTAAAAATTTTGTGGGGCCAAATTAATTT
131 AGACCATTAAAATTTT-AAAAACTTAATATGAATTTCTAAAAATTTTGTGGGGCCAAATTAATTT
211804 TTTTAATTTAATGATC
195 TTTTAATTTAATGATC
*
211820 TAAAATTTTCAAAAATTTTGAAGAGTTCAATTTATTTATTTTTTTCAAAAAAAAAAATTA-GGTC
1 TAAAATTTTCAAAAATTTTGAAGAGTTCAATTTA-AT-TTTTTTTC-AAAAAAAAAATTAGGGTC
*
211884 TAACTAAATTTTTTGAAAATTTGAGAGGCTTAATGAGAACTTTTAAAATTATAAGAGAGGTTTAA
63 TAACTAAAATTTTTGAAAATTTGAGAGGCTTAATGAGAACTTTTAAAATTATAAGAGAGGTTTAA
211949 TTAAGACCATTAAAAATTTT-AAAACTTAATATGAATTTCTAAAAATTTTGTGGGGCCAAATTAA
128 TTAAGACCATT-AAAATTTTAAAAACTTAATATGAATTTCTAAAAATTTTGTGGGGCCAAATTAA
212013 -TTTTTTAATTTAATGATC
192 TTTTTTTAATTTAATGATC
212031 TAAAATT
1 TAAAATT
212038 GATTTTTTTT
Statistics
Matches: 211, Mismatches: 3, Indels: 8
0.95 0.01 0.04
Matches are distributed among these distances:
211 59 0.28
212 45 0.21
213 86 0.41
214 21 0.10
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.40
Consensus pattern (210 bp):
TAAAATTTTCAAAAATTTTGAAGAGTTCAATTTAATTTTTTTTCAAAAAAAAAATTAGGGTCTAA
CTAAAATTTTTGAAAATTTGAGAGGCTTAATGAGAACTTTTAAAATTATAAGAGAGGTTTAATTA
AGACCATTAAAATTTTAAAAACTTAATATGAATTTCTAAAAATTTTGTGGGGCCAAATTAATTTT
TTTAATTTAATGATC
Found at i:213210 original size:6 final size:6
Alignment explanation
Indices: 213195--213224 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
213185 AGGAGACTAG
*
213195 TTTAAA TTTAAG TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
213225 AACAATTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:218238 original size:26 final size:26
Alignment explanation
Indices: 218204--218263 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
218194 TCTCCATCTG
*
218204 AAAAAAAA-TGTT-GAATGAAAGAAAGA
1 AAAAAAAATTGTTCGAAAG-AA-AAAGA
218230 AAAAAAAATTGTTCGAAAGAAAAAGA
1 AAAAAAAATTGTTCGAAAGAAAAAGA
218256 AAAAAAAA
1 AAAAAAAA
218264 GACATAAAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 21 0.68
27 6 0.19
28 4 0.13
ACGTcount: A:0.70, C:0.02, G:0.15, T:0.13
Consensus pattern (26 bp):
AAAAAAAATTGTTCGAAAGAAAAAGA
Found at i:220675 original size:19 final size:20
Alignment explanation
Indices: 220615--220662 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
220605 AGTTTCCAAT
* *
220615 TTCGCAATGCGATAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
220635 TTCGCAACGCGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
220655 TTCGCAAC
1 TTCGCAAC
220663 TGAATTTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (20 bp):
TTCGCAACGCGAAAGTCAAA
Found at i:220689 original size:20 final size:20
Alignment explanation
Indices: 220615--220699 Score: 70
Period size: 20 Copynumber: 4.3 Consensus size: 20
220605 AGTTTCCAAT
*
220615 TTCGCAATGCG-ATAGTCAAA
1 TTCGCAATGCGAAT-TTCAAA
* **
220635 TTCGCAACGCGAAAGTCAAA
1 TTCGCAATGCGAATTTCAAA
220655 TTCGCAA--CTGAATTTCAAA
1 TTCGCAATGC-GAATTTCAAA
* *
220674 TTTGCAATGCGAATTT-AAT
1 TTCGCAATGCGAATTTCAAA
220693 TTCGCAA
1 TTCGCAA
220700 CAGGTTTTAG
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
18 1 0.02
19 22 0.41
20 29 0.54
21 2 0.04
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.28
Consensus pattern (20 bp):
TTCGCAATGCGAATTTCAAA
Found at i:221466 original size:12 final size:12
Alignment explanation
Indices: 221445--221478 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
221435 ACCATATTTC
*
221445 CAATACCAAACA
1 CAATATCAAACA
221457 CAATATCAAACA
1 CAATATCAAACA
*
221469 CAATCTCAAA
1 CAATATCAAA
221479 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:221655 original size:24 final size:24
Alignment explanation
Indices: 221604--221657 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
221594 GTATTTGAAA
*
221604 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
221628 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
221652 TTTGAT
1 TTTGAT
221658 GATGTGATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:223929 original size:18 final size:18
Alignment explanation
Indices: 223906--223941 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
223896 AAGCAAAAGG
*
223906 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
223924 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
223942 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:225917 original size:42 final size:42
Alignment explanation
Indices: 225839--225938 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 42
225829 GGCGGGACCA
* * * ** * * *
225839 CTTGAACGATGACAGTGGCCTCTTGAACGGTGGGAGGGGCTT
1 CTTGAATGATGATAGGGGCCTCTTGAACAATAGGAGGCGCCT
225881 CTTCG-ATGATGATAGGGGCCTCTTGAACAATAGGAGGCGCCT
1 CTT-GAATGATGATAGGGGCCTCTTGAACAATAGGAGGCGCCT
225923 CTTGAATGATGATAGG
1 CTTGAATGATGATAGG
225939 TGCATCGGGC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
41 1 0.02
42 46 0.96
43 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.34, T:0.25
Consensus pattern (42 bp):
CTTGAATGATGATAGGGGCCTCTTGAACAATAGGAGGCGCCT
Found at i:226099 original size:4 final size:4
Alignment explanation
Indices: 226078--226115 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
226068 GGGCTGTTGA
* *
226078 AAAT AAAT TAAT ATAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
226116 TGCCGAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (4 bp):
AAAT
Found at i:230919 original size:18 final size:17
Alignment explanation
Indices: 230864--230920 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
230854 TCTTCATCAC
230864 AAAAAA-TGTT-GAAAA
1 AAAAAACTGTTCGAAAA
*
230879 AAAAATAGCAGTTCG-AAA
1 AAAAA-A-CTGTTCGAAAA
230897 AAAAAACTGTTCGAAAGA
1 AAAAAACTGTTCGAAA-A
230915 AAAAAA
1 AAAAAA
230921 AAAGATATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
15 5 0.15
16 7 0.21
17 3 0.09
18 18 0.53
19 1 0.03
ACGTcount: A:0.63, C:0.07, G:0.14, T:0.16
Consensus pattern (17 bp):
AAAAAACTGTTCGAAAA
Found at i:234703 original size:20 final size:20
Alignment explanation
Indices: 234687--234741 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
234677 TTTGAAACTT
234687 AAATTCGCAACGCGAAAATGA
1 AAATTCGCAACGCGAAAAT-A
234708 AAA-TCGCAACGCGAAAATGA
1 AAATTCGCAACGCGAAAAT-A
234728 AAATT-GCAACGCGA
1 AAATTCGCAACGCGA
234742 TTTTAGTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
20 29 0.88
21 4 0.12
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.13
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAATA
Found at i:235068 original size:22 final size:22
Alignment explanation
Indices: 235040--235090 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
235030 GATGGAGATA
235040 GACGGATTTCGTCGGAAATGGG
1 GACGGATTTCGTCGGAAATGGG
*
235062 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAAATGGG
235084 GACGGAT
1 GACGGAT
235091 GTCGCCGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.22, C:0.14, G:0.43, T:0.22
Consensus pattern (22 bp):
GACGGATTTCGTCGGAAATGGG
Found at i:235243 original size:20 final size:20
Alignment explanation
Indices: 235218--235302 Score: 107
Period size: 20 Copynumber: 4.2 Consensus size: 20
235208 ACGTAAAAAC
*
235218 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
235238 ATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
**
235258 ATTTGACTATCTTGTTGCGA
1 ATTTGACTATCGCGTTGCGA
* **
235278 ATTTAGAATATCGCAATGCGA
1 ATTT-GACTATCGCGTTGCGA
235299 ATTT
1 ATTT
235303 AGAAAATCGC
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
20 41 0.73
21 15 0.27
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (20 bp):
ATTTGACTATCGCGTTGCGA
Found at i:235297 original size:21 final size:21
Alignment explanation
Indices: 235273--235323 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
235263 ACTATCTTGT
*
235273 TGCGAATTTAGAATATCGCAA
1 TGCGAATTTAGAAAATCGCAA
235294 TGCGAATTTAGAAAATCGCAA
1 TGCGAATTTAGAAAATCGCAA
235315 TGCG-ATTTA
1 TGCGAATTTA
235324 CATATTCGCG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 5 0.17
21 24 0.83
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (21 bp):
TGCGAATTTAGAAAATCGCAA
Found at i:235376 original size:20 final size:20
Alignment explanation
Indices: 235327--235380 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
235317 CGATTTACAT
235327 ATTCGCGTTGCGAAATTGGA
1 ATTCGCGTTGCGAAATTGGA
* *
235347 A-ACTGGGTTGCGAAATTGGA
1 ATTC-GCGTTGCGAAATTGGA
235367 ATTCGCGTTGCGAA
1 ATTCGCGTTGCGAA
235381 TTTGTTGGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (20 bp):
ATTCGCGTTGCGAAATTGGA
Found at i:236498 original size:21 final size:21
Alignment explanation
Indices: 236456--236499 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
236446 GGAAATCATT
* * *
236456 GAAGAAGAGGTGGAGTATGAA
1 GAAGAAGAGGTAGAGGAAGAA
*
236477 GAAGTAGAGGTAGAGGAAGAA
1 GAAGAAGAGGTAGAGGAAGAA
236498 GA
1 GA
236500 GGTGGAAGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.43, T:0.11
Consensus pattern (21 bp):
GAAGAAGAGGTAGAGGAAGAA
Found at i:236510 original size:15 final size:15
Alignment explanation
Indices: 236474--236512 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
236464 GGTGGAGTAT
*
236474 GAAGAAGTAGAGGTA
1 GAAGAAGAAGAGGTA
* *
236489 GAGGAAGAAGAGGTG
1 GAAGAAGAAGAGGTA
236504 GAAGAAGAA
1 GAAGAAGAA
236513 ATTGAAGAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.44, T:0.08
Consensus pattern (15 bp):
GAAGAAGAAGAGGTA
Found at i:244614 original size:131 final size:134
Alignment explanation
Indices: 244425--244694 Score: 519
Period size: 131 Copynumber: 2.0 Consensus size: 134
244415 GAACCCGATT
244425 AACAATGGCCAGTCTGTAATGTGGTTAACATATATATATATATATATACGTGTATATGTATTTAT
1 AACAATGGCCAGTCTGTAATGTGGTTAACATATATATATATATATATACGTGTATATGTATTTAT
244490 CCTTGCATGTGTATCTCTAGGGGAGGGAAAAAACCAAAAAA-G-G-AGAATATAACCGGATTAAA
66 CCTTGCATGTGTATCTCTAGGGGAGGGAAAAAACCAAAAAAGGAGAAGAATATAACCGGATTAAA
244552 AAAA
131 AAAA
244556 AACAATGGCCAGTCTGTAATGTGGTTAACATATATATATATATATATACGTGTATATGTATTTAT
1 AACAATGGCCAGTCTGTAATGTGGTTAACATATATATATATATATATACGTGTATATGTATTTAT
244621 CCTTGCATGTGTATCTCTAGGGGAGGGAAAAAACCAAAAAAGGAGAAGAATATAACCGGATTAAA
66 CCTTGCATGTGTATCTCTAGGGGAGGGAAAAAACCAAAAAAGGAGAAGAATATAACCGGATTAAA
244686 AAAA
131 AAAA
244690 AACAA
1 AACAA
244695 AATTGTTGAA
Statistics
Matches: 136, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
131 106 0.78
132 1 0.01
133 1 0.01
134 28 0.21
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.28
Consensus pattern (134 bp):
AACAATGGCCAGTCTGTAATGTGGTTAACATATATATATATATATATACGTGTATATGTATTTAT
CCTTGCATGTGTATCTCTAGGGGAGGGAAAAAACCAAAAAAGGAGAAGAATATAACCGGATTAAA
AAAA
Found at i:253339 original size:122 final size:122
Alignment explanation
Indices: 253122--253367 Score: 492
Period size: 122 Copynumber: 2.0 Consensus size: 122
253112 AAAAAAGAAG
253122 ATCTATTGGTTTGTTATCATGTATTCGTGGGTATTTCTTTCTTTCTTTCTTTGCCTTCTTTGTTT
1 ATCTATTGGTTTGTTATCATGTATTCGTGGGTATTTCTTTCTTTCTTTCTTTGCCTTCTTTGTTT
253187 TACTTCGAGCTTTGCTTCTTCTTTACTTCTAAGCACTTCAAAACCCTAAATTTTCAC
66 TACTTCGAGCTTTGCTTCTTCTTTACTTCTAAGCACTTCAAAACCCTAAATTTTCAC
253244 ATCTATTGGTTTGTTATCATGTATTCGTGGGTATTTCTTTCTTTCTTTCTTTGCCTTCTTTGTTT
1 ATCTATTGGTTTGTTATCATGTATTCGTGGGTATTTCTTTCTTTCTTTCTTTGCCTTCTTTGTTT
253309 TACTTCGAGCTTTGCTTCTTCTTTACTTCTAAGCACTTCAAAACCCTAAATTTTCAC
66 TACTTCGAGCTTTGCTTCTTCTTTACTTCTAAGCACTTCAAAACCCTAAATTTTCAC
253366 AT
1 AT
253368 TTTCCCCATC
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
122 124 1.00
ACGTcount: A:0.17, C:0.21, G:0.11, T:0.51
Consensus pattern (122 bp):
ATCTATTGGTTTGTTATCATGTATTCGTGGGTATTTCTTTCTTTCTTTCTTTGCCTTCTTTGTTT
TACTTCGAGCTTTGCTTCTTCTTTACTTCTAAGCACTTCAAAACCCTAAATTTTCAC
Found at i:258602 original size:27 final size:27
Alignment explanation
Indices: 258569--258644 Score: 136
Period size: 27 Copynumber: 2.9 Consensus size: 27
258559 GTACCACTCT
258569 AAGTTAAAACCTTTTGGTCCTATCTAC
1 AAGTTAAAACCTTTTGGTCCTATCTAC
*
258596 AAGTTAAAACCTTTTGGTTCTATCTAC
1 AAGTTAAAACCTTTTGGTCCTATCTAC
258623 AAGTTAAAACCTTTTGG-CCTAT
1 AAGTTAAAACCTTTTGGTCCTAT
258645 TTACGAAGAT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
26 4 0.09
27 43 0.91
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (27 bp):
AAGTTAAAACCTTTTGGTCCTATCTAC
Found at i:259983 original size:12 final size:12
Alignment explanation
Indices: 259966--260022 Score: 64
Period size: 12 Copynumber: 4.9 Consensus size: 12
259956 TATAAAATTA
259966 TTTTTCTTTTAC
1 TTTTTCTTTTAC
*
259978 TTTTTCTTTCAC
1 TTTTTCTTTTAC
259990 TTTTTC-TTTA-
1 TTTTTCTTTTAC
* *
260000 TTTTTCTTTAAA
1 TTTTTCTTTTAC
*
260012 GTTTTCTTTTA
1 TTTTTCTTTTA
260023 AATTCTAAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
10 6 0.16
11 6 0.16
12 26 0.68
ACGTcount: A:0.12, C:0.14, G:0.02, T:0.72
Consensus pattern (12 bp):
TTTTTCTTTTAC
Found at i:260016 original size:22 final size:23
Alignment explanation
Indices: 259967--260020 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
259957 ATAAAATTAT
* **
259967 TTTTCTTTTACTTTTTCTTTCACT
1 TTTTC-TTTACTTTTTCTTTAAAG
259991 TTTTCTTTA-TTTTTCTTTAAAG
1 TTTTCTTTACTTTTTCTTTAAAG
260013 TTTTCTTT
1 TTTTCTTT
260021 TAAATTCTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 18 0.67
23 4 0.15
24 5 0.19
ACGTcount: A:0.11, C:0.15, G:0.02, T:0.72
Consensus pattern (23 bp):
TTTTCTTTACTTTTTCTTTAAAG
Found at i:260633 original size:19 final size:19
Alignment explanation
Indices: 260597--260632 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
260587 CTTTTTAATC
*
260597 TTTTATTTTCTTACTTTTA
1 TTTTATTTTATTACTTTTA
260616 TTTTATTTTATT-CTTTT
1 TTTTATTTTATTACTTTT
260633 TCATCCATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTATTTTATTACTTTTA
Found at i:263055 original size:23 final size:23
Alignment explanation
Indices: 263029--263084 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
263019 AGTCCCAAGG
*
263029 GACCACATAGGTTTGTCCTGAAA
1 GACCACATAGGTTTGTCCCGAAA
** *
263052 GACCACATAATTTTGTCCCGAAG
1 GACCACATAGGTTTGTCCCGAAA
263075 GACCACATAG
1 GACCACATAG
263085 AACCTTCGAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (23 bp):
GACCACATAGGTTTGTCCCGAAA
Found at i:269646 original size:23 final size:22
Alignment explanation
Indices: 269618--269697 Score: 88
Period size: 23 Copynumber: 3.5 Consensus size: 22
269608 ATTGTCACGA
269618 AAGACCACATAAATTTGTCCTG
1 AAGACCACATAAATTTGTCCTG
***
269640 AATGACCACATTGGTTTGTCCTG
1 AA-GACCACATAAATTTGTCCTG
* *
269663 AAGAACCACATAATTTTGTCTTG
1 AAG-ACCACATAAATTTGTCCTG
269686 AAGGACCACATA
1 AA-GACCACATA
269698 GAACCCTCAA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
22 3 0.06
23 44 0.92
24 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (22 bp):
AAGACCACATAAATTTGTCCTG
Found at i:276067 original size:20 final size:20
Alignment explanation
Indices: 276042--276105 Score: 101
Period size: 20 Copynumber: 3.1 Consensus size: 20
276032 GCTTGGAGCG
*
276042 TGGGGGGAATCGGTACCCCC
1 TGGGGGGAATCTGTACCCCC
*
276062 TGGGGGGAATCTGTTCCCCC
1 TGGGGGGAATCTGTACCCCC
276082 TGGGGGGGAATCTGTACCCCC
1 T-GGGGGGAATCTGTACCCCC
276103 TGG
1 TGG
276106 ACAATCTGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 21 0.52
21 19 0.47
ACGTcount: A:0.12, C:0.28, G:0.39, T:0.20
Consensus pattern (20 bp):
TGGGGGGAATCTGTACCCCC
Found at i:278886 original size:21 final size:20
Alignment explanation
Indices: 278849--278950 Score: 125
Period size: 20 Copynumber: 5.0 Consensus size: 20
278839 CCGTTAGACA
*
278849 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCTGTACCCCCTG
*
278869 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCTGTACCCCCT-G
* *
278890 GGGGGAATCTGT-TCCCCTA
1 GGGGGAATCTGTACCCCCTG
* *
278909 GGGGAAATCTATACCCCCTG
1 GGGGGAATCTGTACCCCCTG
278929 GGGGTGAATCTGTACCCCCTG
1 GGGG-GAATCTGTACCCCCTG
278950 G
1 G
278951 ACAATCTGAT
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
19 10 0.14
20 33 0.47
21 27 0.39
ACGTcount: A:0.17, C:0.28, G:0.35, T:0.20
Consensus pattern (20 bp):
GGGGGAATCTGTACCCCCTG
Found at i:279358 original size:3 final size:3
Alignment explanation
Indices: 279352--279436 Score: 118
Period size: 3 Copynumber: 28.0 Consensus size: 3
279342 TTTGTTTTTT
* * *
279352 TTA TTA TTA TTA TTG TTA TTA TCA TTA TTA -TA TTA GTTA GTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
279397 TTA TTAA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
279437 ATTTATTACA
Statistics
Matches: 73, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
2 2 0.03
3 65 0.89
4 6 0.08
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:280649 original size:23 final size:21
Alignment explanation
Indices: 280597--280649 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 21
280587 TATTCACTGA
280597 TTTTAA-TTTTTTACCATAAG
1 TTTTAATTTTTTTACCATAAG
** *
280617 TTTTCTTTTTTTTACTCCTATAG
1 TTTTAATTTTTTTAC-CATA-AG
280640 TTTTAATTTT
1 TTTTAATTTT
280650 CTCTATTTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 4 0.16
21 8 0.32
22 3 0.12
23 10 0.40
ACGTcount: A:0.21, C:0.11, G:0.04, T:0.64
Consensus pattern (21 bp):
TTTTAATTTTTTTACCATAAG
Found at i:280817 original size:14 final size:14
Alignment explanation
Indices: 280798--280835 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
280788 TTTTATTCAA
280798 ATTATTATTTTTTT
1 ATTATTATTTTTTT
280812 ATTATTATTATTTTT
1 ATTATTATT-TTTTT
280827 -TTATT-TTTT
1 ATTATTATTTT
280836 AATATCAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 2 0.09
13 2 0.09
14 14 0.61
15 5 0.22
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
ATTATTATTTTTTT
Found at i:280818 original size:17 final size:17
Alignment explanation
Indices: 280798--280831 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
280788 TTTTATTCAA
280798 ATTATTATTTTTTTATT
1 ATTATTATTTTTTTATT
280815 ATTATTATTTTTTTATT
1 ATTATTATTTTTTTATT
280832 TTTTAATATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
ATTATTATTTTTTTATT
Found at i:283142 original size:26 final size:26
Alignment explanation
Indices: 283104--283158 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
283094 GCTTTATCAT
*
283104 TTTACATCCACATTTTTACATTTGCA
1 TTTACATCCACATCTTTACATTTGCA
** * *
283130 TTTACATTGACATCTTTGCATTTTCA
1 TTTACATCCACATCTTTACATTTGCA
283156 TTT
1 TTT
283159 TGCATTTGTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.24, C:0.20, G:0.05, T:0.51
Consensus pattern (26 bp):
TTTACATCCACATCTTTACATTTGCA
Found at i:283252 original size:20 final size:20
Alignment explanation
Indices: 283211--283257 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
283201 CATTCACATC
*
283211 TTTACATTTTTACGTTTTTA
1 TTTACATTTTCACGTTTTTA
*
283231 TTTACATTTTCA-TTTTTGTA
1 TTTACATTTTCACGTTTT-TA
283251 TTTACAT
1 TTTACAT
283258 CTTTGCACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.21, C:0.11, G:0.04, T:0.64
Consensus pattern (20 bp):
TTTACATTTTCACGTTTTTA
Found at i:285683 original size:19 final size:19
Alignment explanation
Indices: 285650--285693 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
285640 CTCATTCATT
285650 AGAAAAAAAGAAAAAAGAA
1 AGAAAAAAAGAAAAAAGAA
285669 AGAAATAAAAG-AAAAAGAA
1 AGAAA-AAAAGAAAAAAGAA
285688 A-AAAAA
1 AGAAAAA
285694 TTGAATCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 2 0.08
18 3 0.12
19 14 0.58
20 5 0.21
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (19 bp):
AGAAAAAAAGAAAAAAGAA
Found at i:288924 original size:47 final size:48
Alignment explanation
Indices: 288833--289022 Score: 195
Period size: 54 Copynumber: 3.7 Consensus size: 48
288823 GAAGCCACAA
* * * *
288833 GAAAGGATGAATGTGTTGTCAAATGTTTTACGAAAATTTGGGCAG-AG
1 GAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTAGGCAGCAG
*
288880 GAAATGATGAATATGTTGTCAAATGTTTTACGAACATCTAGGCAGAAGCCACAG
1 GAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTAGGC---AG---CAG
288934 GAAA-GAATGAATGTGTTGTCAAATGTTTTACGAACATCTAGGCAGAAACCACAG
1 GAAATG-ATGAATGTGTTGTCAAATGTTTTACGAACATCTAGGCAG------CAG
*
288988 GAAATGATGAATGTGTTGTCAAATGTTTTATGAAC
1 GAAATGATGAATGTGTTGTCAAATGTTTTACGAAC
289023 CAATGATTAT
Statistics
Matches: 124, Mismatches: 7, Indels: 17
0.84 0.05 0.11
Matches are distributed among these distances:
47 38 0.31
50 2 0.02
51 2 0.02
53 1 0.01
54 80 0.65
55 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.28
Consensus pattern (48 bp):
GAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTAGGCAGCAG
Found at i:288944 original size:54 final size:54
Alignment explanation
Indices: 288878--289022 Score: 247
Period size: 54 Copynumber: 2.7 Consensus size: 54
288868 ATTTGGGCAG
* *
288878 AGGAAATGATGAATATGTTGTCAAATGTTTTACGAACATCTAGGCAGAAGCCAC
1 AGGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTAGGCAGAAACCAC
288932 AGGAAA-GAATGAATGTGTTGTCAAATGTTTTACGAACATCTAGGCAGAAACCAC
1 AGGAAATG-ATGAATGTGTTGTCAAATGTTTTACGAACATCTAGGCAGAAACCAC
*
288986 AGGAAATGATGAATGTGTTGTCAAATGTTTTATGAAC
1 AGGAAATGATGAATGTGTTGTCAAATGTTTTACGAAC
289023 CAATGATTAT
Statistics
Matches: 86, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
53 1 0.01
54 84 0.98
55 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (54 bp):
AGGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTAGGCAGAAACCAC
Found at i:289413 original size:22 final size:23
Alignment explanation
Indices: 289388--289554 Score: 170
Period size: 22 Copynumber: 7.6 Consensus size: 23
289378 ACATCTACAT
289388 TCTTCAAAGATGATAAATTCAT-
1 TCTTCAAAGATGATAAATTCATC
*
289410 TCTTCAAAGATGATAGATTCAT-
1 TCTTCAAAGATGATAAATTCATC
* * *
289432 TCTTCAAAGATTATATA-TCCTC
1 TCTTCAAAGATGATAAATTCATC
* *
289454 TCTTTAAAGATGATAGA-TCATC
1 TCTTCAAAGATGATAAATTCATC
*
289476 TCTTCAAAGATGATAGATTC-TC
1 TCTTCAAAGATGATAAATTCATC
*
289498 TCTTCAAATATGATAAATTC-TC
1 TCTTCAAAGATGATAAATTCATC
* *
289520 TTTTCAAAGATGACAGAA-TC-TC
1 TCTTCAAAGATGATA-AATTCATC
*
289542 TTTTCAAAGATGA
1 TCTTCAAAGATGA
289555 CAGCTTTACT
Statistics
Matches: 128, Mismatches: 14, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
21 3 0.02
22 121 0.95
23 4 0.03
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (23 bp):
TCTTCAAAGATGATAAATTCATC
Found at i:289502 original size:66 final size:66
Alignment explanation
Indices: 289388--289554 Score: 198
Period size: 66 Copynumber: 2.5 Consensus size: 66
289378 ACATCTACAT
* * * *
289388 TCTTCAAAGATGATAAATTCAT-TCTTCAAAGATGATAGATTCATTCTTCAAAGATTATATATCC
1 TCTTTAAAGATGATAGA-TCATCTCTTCAAAGATGATAGATTCATTCTTCAAAGATGATAAATCC
289452 TC
65 TC
* *
289454 TCTTTAAAGATGATAGATCATCTCTTCAAAGATGATAGATTC-TCTCTTCAAATATGATAAATTC
1 TCTTTAAAGATGATAGATCATCTCTTCAAAGATGATAGATTCAT-TCTTCAAAGATGATAAATCC
289518 TC
65 TC
* *
289520 T-TTTCAAAGATGACAGAATC-TCTTTTCAAAGATGA
1 TCTTT-AAAGATGATAG-ATCATCTCTTCAAAGATGA
289555 CAGCTTTACT
Statistics
Matches: 89, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
65 8 0.09
66 78 0.88
67 3 0.03
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (66 bp):
TCTTTAAAGATGATAGATCATCTCTTCAAAGATGATAGATTCATTCTTCAAAGATGATAAATCCT
C
Found at i:290458 original size:135 final size:135
Alignment explanation
Indices: 290214--290590 Score: 531
Period size: 135 Copynumber: 2.8 Consensus size: 135
290204 CTATTTCCCA
* * * ** *
290214 CATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAACCTTCGGGTCATCCATAAT-ACCTACAGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGTCATCTGT-ATGACCTTCAGT
* * * ** * *
290278 GCAAGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTTCAGTGCAGTATATTTTCAAAGCCT
65 GCATGATGTTTTCAAAACCTTCAGGTCATCCATAAGACCTACAGTGCAGGATATTTTCAAAGCCT
290343 TCGGGT
130 TCGGGT
* *
290349 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAGTCTTCGGGTCATTTGTATGACCTTCAGTG
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGTCATCTGTATGACCTTCAGTG
* *
290414 CATGATGTTTTCAAAACCTTCAGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAATCCTT
66 CATGATGTTTTCAAAACCTTCAGGTCATCCATAAGACCTACAGTGCAGGATATTTTCAAAGCCTT
290479 CGGGT
131 CGGGT
* * *
290484 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAGCCTTTGGATCATCTGTAAGACCTTCAGTG
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGTCATCTGTATGACCTTCAGTG
* **
290549 CATAATGTTTTCAAAAATTTCAGGTCATCCATAAGACCTACA
66 CATGATGTTTTCAAAACCTTCAGGTCATCCATAAGACCTACA
290591 TTTCCAGAAG
Statistics
Matches: 216, Mismatches: 25, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
134 2 0.01
135 214 0.99
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (135 bp):
CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGTCATCTGTATGACCTTCAGTG
CATGATGTTTTCAAAACCTTCAGGTCATCCATAAGACCTACAGTGCAGGATATTTTCAAAGCCTT
CGGGT
Found at i:290577 original size:45 final size:45
Alignment explanation
Indices: 290214--290587 Score: 471
Period size: 45 Copynumber: 8.3 Consensus size: 45
290204 CTATTTCCCA
* *
290214 CATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
** * * * *
290259 CATCCATAATACCTACAGTGCAAGATGTTTTCAAAGCCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
290304 CATCTGTAAGACCTTCAGTGCA-GTATATTTTCAAAGCCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCATG-ATGTTTTCAAAACCTTCGGGT
**
290349 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAGTCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
290394 CATTTGTATGACCTTCAGTGCATGATGTTTTCAAAACCTTCAGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
** * * *
290439 CATCCATAAGACCTACAGTGCAGGATGTTTTCAAATCCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
290484 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAGCCTTTGGAT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* ** *
290529 CATCTGTAAGACCTTCAGTGCATAATGTTTTCAAAAATTTCAGGT
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
**
290574 CATCCATAAGACCT
1 CATCTGTAAGACCT
290588 ACATTTCCAG
Statistics
Matches: 286, Mismatches: 41, Indels: 4
0.86 0.12 0.01
Matches are distributed among these distances:
44 1 0.00
45 284 0.99
46 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (45 bp):
CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:290807 original size:123 final size:123
Alignment explanation
Indices: 290588--290917 Score: 597
Period size: 123 Copynumber: 2.7 Consensus size: 123
290578 CATAAGACCT
* * *
290588 ACATTTCCAGAAGGAGTTCATAATGAGAAGAATTCATCTGAAGAGGAAGAAAAAGTTCATAATAA
1 ACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGA
*
290653 GAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAACATCA
66 GAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAACATCA
*
290711 ACATTTCCAGAAGGAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGA
1 ACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGA
*
290776 GAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGCATCA
66 GAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAACATCA
290834 ACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGA
1 ACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGA
*
290899 GAAGAACTTGTTCGACCTT
66 GAAGAACTTGTTCAACCTT
290918 AGCTTGATTC
Statistics
Matches: 199, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
123 199 1.00
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (123 bp):
ACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGA
GAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAACATCA
Found at i:291160 original size:137 final size:138
Alignment explanation
Indices: 290830--291190 Score: 548
Period size: 139 Copynumber: 2.6 Consensus size: 138
290820 ATAGATCAGC
290830 ATCAACATTTCCAGAAGG-AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT
1 ATCAACATTTCCAG-AGGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT
* * * *
290894 AATGAGAAGAACTTGTTCGACCTTAGCTTGATTCATCACCTATGGAGTTGAATGAAATAAGAACC
65 AATGAGAAGAACTTGTTCAACCTTAGCTTAATTCATCACATATGAAGTTGAAT-AAATAAGAACC
290959 TCACTTGAGG
129 TCACTTGAGG
* * * *
290969 ATCAACATTTTCAGAGGAAGTTCATAATGAGAATAACTCATCTGAAGAGAAAGAAGAAGTTCATG
1 ATCAACATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* *
291034 ATGAGAAGAACTTGTTCAACCTTAGCTTAATTCATCACATATGAAGTTGAAT-CA-ACGATACCT
66 ATGAGAAGAACTTGTTCAACCTTAGCTTAATTCATCACATATGAAGTTGAATAAATAAGA-ACCT
**
291097 CTTTTGAGG
130 CACTTGAGG
*
291106 ATCAACATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATA
1 ATCAACATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
*
291171 ATGAGAAGAACTTATTCAAC
66 ATGAGAAGAACTTGTTCAAC
291191 ATTTTGCTAG
Statistics
Matches: 202, Mismatches: 18, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
136 3 0.01
137 91 0.45
138 3 0.01
139 105 0.52
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (138 bp):
ATCAACATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTAGCTTAATTCATCACATATGAAGTTGAATAAATAAGAACCTC
ACTTGAGG
Found at i:291417 original size:3 final size:3
Alignment explanation
Indices: 291404--291486 Score: 80
Period size: 3 Copynumber: 28.3 Consensus size: 3
291394 GGTCTATTTG
* * * *
291404 TTA TCA TTA TTA TTA TTA TTG TTA TTG TTA TTA TCA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
291451 TTA TTA ATA TTA ATA TTA ATA TTA TTA AT- TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
291487 AGGCCCTAAA
Statistics
Matches: 62, Mismatches: 16, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
2 3 0.05
3 59 0.95
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:296251 original size:13 final size:14
Alignment explanation
Indices: 296233--296265 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
296223 TATATCTTAC
*
296233 TCCTAACTTA-AAA
1 TCCTAAATTATAAA
296246 TCCTAAATTATAAA
1 TCCTAAATTATAAA
296260 TCCTAA
1 TCCTAA
296266 GATAAGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.33
Consensus pattern (14 bp):
TCCTAAATTATAAA
Found at i:296290 original size:14 final size:14
Alignment explanation
Indices: 296271--296340 Score: 52
Period size: 14 Copynumber: 4.9 Consensus size: 14
296261 CCTAAGATAA
296271 GATTTAGGGTTTAT
1 GATTTAGGGTTTAT
296285 GATTTAGAGG-TTAT
1 GATTTAG-GGTTTAT
* * *
296299 AGAGTTATGATTTAT
1 -GATTTAGGGTTTAT
* * *
296314 GGTTTAAGATTTAT
1 GATTTAGGGTTTAT
*
296328 AATTTAGGGTTTA
1 GATTTAGGGTTTA
296341 AGTTAGAGGT
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
14 32 0.74
15 11 0.26
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (14 bp):
GATTTAGGGTTTAT
Found at i:296327 original size:21 final size:20
Alignment explanation
Indices: 296280--296342 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
296270 AGATTTAGGG
*
296280 TTTATGATTTAGAGGTTATAGA
1 TTTATGATTTAG-GTTTA-AGA
*
296302 GTTATGATTTATGGTTTAAGA
1 TTTATGATTTA-GGTTTAAGA
*
296323 TTTATAATTTAGGGTTTAAG
1 TTTATGATTTA-GGTTTAAG
296343 TTAGAGGTAG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 20 0.57
22 14 0.40
23 1 0.03
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (20 bp):
TTTATGATTTAGGTTTAAGA
Found at i:297645 original size:29 final size:29
Alignment explanation
Indices: 297603--297675 Score: 137
Period size: 29 Copynumber: 2.5 Consensus size: 29
297593 ATGTTTTTTT
*
297603 AGTTTAGTGCCTAATATTTATTTCGTTCC
1 AGTTTGGTGCCTAATATTTATTTCGTTCC
297632 AGTTTGGTGCCTAATATTTATTTCGTTCC
1 AGTTTGGTGCCTAATATTTATTTCGTTCC
297661 AGTTTGGTGCCTAAT
1 AGTTTGGTGCCTAAT
297676 GTTCCATTCC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.19, C:0.16, G:0.18, T:0.47
Consensus pattern (29 bp):
AGTTTGGTGCCTAATATTTATTTCGTTCC
Found at i:305996 original size:30 final size:31
Alignment explanation
Indices: 305918--305996 Score: 76
Period size: 31 Copynumber: 2.6 Consensus size: 31
305908 AGTGACCAAA
*
305918 ATGTAAGTTTTG-AAAGTTTGATGGCTAAAGT
1 ATGTAA-TTTTGAAAAGTTTGAGGGCTAAAGT
* *
305949 AT-AAATTTTATAAAAGTTT-AGGGACTAAA-T
1 ATGTAATTTT-GAAAAGTTTGAGGG-CTAAAGT
305979 ATGTAATTTTGAAAAGTT
1 ATGTAATTTTGAAAAGTT
305997 CAATATTTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
29 4 0.10
30 15 0.38
31 20 0.51
ACGTcount: A:0.39, C:0.03, G:0.19, T:0.39
Consensus pattern (31 bp):
ATGTAATTTTGAAAAGTTTGAGGGCTAAAGT
Found at i:308766 original size:14 final size:14
Alignment explanation
Indices: 308747--308784 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
308737 CAAGAGTAAA
308747 TCAGTTTGAATAGC
1 TCAGTTTGAATAGC
308761 TCAGTTTGAATAGC
1 TCAGTTTGAATAGC
*
308775 TCGGTTTGAA
1 TCAGTTTGAA
308785 AGTTTTAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (14 bp):
TCAGTTTGAATAGC
Found at i:309537 original size:152 final size:153
Alignment explanation
Indices: 309261--309565 Score: 603
Period size: 152 Copynumber: 2.0 Consensus size: 153
309251 ATTTTACGAA
309261 TATGCATGCTAAATGAAACATAAAAATTGTTAAAGGAATGTTTTGAAATGAAACAAAGTTTTAAA
1 TATGCATGCTAAATGAAACATAAAAATTGTTAAAGGAATGTTTTGAAATGAAACAAAGTTTTAAA
309326 CATTTATTTTCAGTAAATGTTTGAAAAGTTGATGTGATATATTTAATTCGTATTTCGAAACGTAT
66 CATTTATTTTCAGTAAATGTTTGAAAAGTTGATGTGATATATTTAATTCGTATTTCGAAACGTAT
309391 ACGAGATATAGGTGTTA-ATCAC
131 ACGAGATATAGGTGTTACATCAC
309413 TATGCATGCTAAATGAAACATAAAAATTGTTAAAGGAATGTTTTGAAATGAAACAAAGTTTTAAA
1 TATGCATGCTAAATGAAACATAAAAATTGTTAAAGGAATGTTTTGAAATGAAACAAAGTTTTAAA
309478 CATTTATTTTCAGTAAATGTTTGAAAAGTTGATGTGATATATTTAATTCGTATTTCGAAACGTAT
66 CATTTATTTTCAGTAAATGTTTGAAAAGTTGATGTGATATATTTAATTCGTATTTCGAAACGTAT
309543 ACGAGATATAGGTGTTACATCAC
131 ACGAGATATAGGTGTTACATCAC
309566 ACGTAAAAGC
Statistics
Matches: 152, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
152 147 0.97
153 5 0.03
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.36
Consensus pattern (153 bp):
TATGCATGCTAAATGAAACATAAAAATTGTTAAAGGAATGTTTTGAAATGAAACAAAGTTTTAAA
CATTTATTTTCAGTAAATGTTTGAAAAGTTGATGTGATATATTTAATTCGTATTTCGAAACGTAT
ACGAGATATAGGTGTTACATCAC
Found at i:309663 original size:74 final size:74
Alignment explanation
Indices: 309542--309689 Score: 296
Period size: 74 Copynumber: 2.0 Consensus size: 74
309532 TCGAAACGTA
309542 TACGAGATATAGGTGTTACATCACACGTAAAAGCACTTTGTCCTCCGATTCTGCATGTCCCAGTG
1 TACGAGATATAGGTGTTACATCACACGTAAAAGCACTTTGTCCTCCGATTCTGCATGTCCCAGTG
309607 GCGTTTGAG
66 GCGTTTGAG
309616 TACGAGATATAGGTGTTACATCACACGTAAAAGCACTTTGTCCTCCGATTCTGCATGTCCCAGTG
1 TACGAGATATAGGTGTTACATCACACGTAAAAGCACTTTGTCCTCCGATTCTGCATGTCCCAGTG
309681 GCGTTTGAG
66 GCGTTTGAG
309690 AGATGAAACT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (74 bp):
TACGAGATATAGGTGTTACATCACACGTAAAAGCACTTTGTCCTCCGATTCTGCATGTCCCAGTG
GCGTTTGAG
Found at i:313088 original size:22 final size:23
Alignment explanation
Indices: 313063--313112 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
313053 GGATGACGTC
313063 TGACCCGACCCG-ACCCGACCGT
1 TGACCCGACCCGAACCCGACCGT
*
313085 TGACCCGACTCGAACCCGACCGT
1 TGACCCGACCCGAACCCGACCGT
313108 TGACC
1 TGACC
313113 GTTGACTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.20, C:0.46, G:0.22, T:0.12
Consensus pattern (23 bp):
TGACCCGACCCGAACCCGACCGT
Found at i:320333 original size:22 final size:23
Alignment explanation
Indices: 320305--320353 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
320295 GGTCTGACCC
320305 GACCCGACCCG-ACCCAACCGTT
1 GACCCGACCCGAACCCAACCGTT
* *
320327 GACCCGACCCGAACTCGACCGTT
1 GACCCGACCCGAACCCAACCGTT
320350 GACC
1 GACC
320354 GTTGACTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.22, C:0.47, G:0.20, T:0.10
Consensus pattern (23 bp):
GACCCGACCCGAACCCAACCGTT
Found at i:320388 original size:22 final size:21
Alignment explanation
Indices: 320363--320404 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
320353 CGTTGACTTT
320363 CTTTGACCAGAACCTTAAATGG
1 CTTTGA-CAGAACCTTAAATGG
* *
320385 CTTTGACTGACCCTTAAATG
1 CTTTGACAGAACCTTAAATG
320405 ACCGTAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.31
Consensus pattern (21 bp):
CTTTGACAGAACCTTAAATGG
Found at i:322313 original size:29 final size:29
Alignment explanation
Indices: 322280--322337 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
322270 AAATATTTTT
*
322280 GTTCCAATTTGGTACCTAACGTTTATTTC
1 GTTCCAATTTGGTACCTAACATTTATTTC
* * *
322309 GTTCCAGTTTGGTGCCTAACATTTCTTTC
1 GTTCCAATTTGGTACCTAACATTTATTTC
322338 CCTCTCCTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.17, C:0.22, G:0.16, T:0.45
Consensus pattern (29 bp):
GTTCCAATTTGGTACCTAACATTTATTTC
Found at i:323360 original size:21 final size:21
Alignment explanation
Indices: 323336--323385 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
323326 TTGTGTGCAT
323336 CGATGCACATTCATTGTGTAC
1 CGATGCACATTCATTGTGTAC
323357 CGATGCACATTCATTGTGTAC
1 CGATGCACATTCATTGTGTAC
323378 CGATGCAC
1 CGATGCAC
323386 TCTCTATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (21 bp):
CGATGCACATTCATTGTGTAC
Found at i:325560 original size:29 final size:29
Alignment explanation
Indices: 325518--325582 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
325508 AGAAGAGATG
* * * *
325518 GAAAGAAACGTTAGGCATCAAACTGAAAT
1 GAAATAAACGTTAGACACCAAACTGAAAC
* *
325547 GAAATAAATGTTAGACACCAAACTGGAAC
1 GAAATAAACGTTAGACACCAAACTGAAAC
325576 GAAATAA
1 GAAATAA
325583 TTTATTCTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.51, C:0.14, G:0.18, T:0.17
Consensus pattern (29 bp):
GAAATAAACGTTAGACACCAAACTGAAAC
Found at i:326224 original size:16 final size:16
Alignment explanation
Indices: 326205--326241 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
326195 CATACATTTT
326205 ATTATACATTATCTTA
1 ATTATACATTATCTTA
*
326221 ATTATACATTATTTTA
1 ATTATACATTATCTTA
326237 ATTAT
1 ATTAT
326242 TTTATGTGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTATACATTATCTTA
Found at i:331058 original size:22 final size:24
Alignment explanation
Indices: 331023--331070 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
331013 TTATATAATG
331023 ATTAGAATATAACTTT-AAATTTT
1 ATTAGAATATAACTTTCAAATTTT
*
331046 ATTAGTAT-TAACTTTCAAATTTT
1 ATTAGAATATAACTTTCAAATTTT
331069 AT
1 AT
331071 CTTAGATAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (24 bp):
ATTAGAATATAACTTTCAAATTTT
Found at i:332690 original size:22 final size:22
Alignment explanation
Indices: 332662--332716 Score: 85
Period size: 21 Copynumber: 2.5 Consensus size: 22
332652 GAAATTTTTT
* *
332662 TTATCTTTTTTTTTATATTATG
1 TTATCTTTTTTTTTATAATAAG
332684 TTATC-TTTTTTTTATAATAAG
1 TTATCTTTTTTTTTATAATAAG
332705 TTATCTTTTTTT
1 TTATCTTTTTTT
332717 AGTATACTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 19 0.63
22 11 0.37
ACGTcount: A:0.20, C:0.05, G:0.04, T:0.71
Consensus pattern (22 bp):
TTATCTTTTTTTTTATAATAAG
Found at i:335230 original size:2 final size:2
Alignment explanation
Indices: 335223--335262 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
335213 TAAAACTCTA
335223 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
335263 TAATGCGATT
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:342933 original size:13 final size:13
Alignment explanation
Indices: 342915--342939 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
342905 TAAAGAAAGA
342915 AAAGGGGAAAAAT
1 AAAGGGGAAAAAT
342928 AAAGGGGAAAAA
1 AAAGGGGAAAAA
342940 AAGAAATATA
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:0.64, C:0.00, G:0.32, T:0.04
Consensus pattern (13 bp):
AAAGGGGAAAAAT
Found at i:343905 original size:26 final size:24
Alignment explanation
Indices: 343876--343921 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 24
343866 TATCAAGTTC
343876 AACTAGAACTTGAAATATAATATT
1 AACTAGAACTTGAAATATAATATT
343900 -A--A-AACTTGAAATATAATATT
1 AACTAGAACTTGAAATATAATATT
343920 AA
1 AA
343922 AACTTGAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
20 18 0.86
21 2 0.10
23 1 0.05
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.33
Consensus pattern (24 bp):
AACTAGAACTTGAAATATAATATT
Found at i:343907 original size:20 final size:20
Alignment explanation
Indices: 343882--343929 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
343872 GTTCAACTAG
343882 AACTTGAAATATAATATTAA
1 AACTTGAAATATAATATTAA
343902 AACTTGAAATATAATATTAA
1 AACTTGAAATATAATATTAA
343922 AACTTGAA
1 AACTTGAA
343930 CTCAAAAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.33
Consensus pattern (20 bp):
AACTTGAAATATAATATTAA
Found at i:344516 original size:18 final size:18
Alignment explanation
Indices: 344493--344527 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
344483 CCGATTCTTC
344493 CGACCGGTCT-AACCGGTT
1 CGACCGGT-TGAACCGGTT
344511 CGACCGGTTGAACCGGT
1 CGACCGGTTGAACCGGT
344528 AGCACGGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 1 0.06
18 15 0.94
ACGTcount: A:0.17, C:0.31, G:0.31, T:0.20
Consensus pattern (18 bp):
CGACCGGTTGAACCGGTT
Done.