Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006559.1 Hibiscus syriacus cultivar Beakdansim tig00016031_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: 89155
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:4087 original size:24 final size:24
Alignment explanation
Indices: 4056--4135 Score: 83
Period size: 24 Copynumber: 3.4 Consensus size: 24
4046 GAAACTTCCG
4056 CGTAGAATTTGCACCGAAGTACCA
1 CGTAGAATTTGCACCGAAGTACCA
* *
4080 CGTAGAATATGCACCGAAGTGCCA
1 CGTAGAATTTGCACCGAAGTACCA
* * * *
4104 CATAG-ATTTGTC-TCGAAGGACCG
1 CGTAGAATTTG-CACCGAAGTACCA
4127 CGTAGAATT
1 CGTAGAATT
4136 GTCCTGAAGG
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
23 15 0.33
24 30 0.67
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.23
Consensus pattern (24 bp):
CGTAGAATTTGCACCGAAGTACCA
Found at i:4131 original size:47 final size:46
Alignment explanation
Indices: 4069--4179 Score: 127
Period size: 46 Copynumber: 2.4 Consensus size: 46
4059 AGAATTTGCA
* * *
4069 CCGAAGTACCACGTAGAATATG-CACCGAAGTG-CCACATAGATTTGTC
1 CCGAAGGACCGCGTAGAAT-TGTC-CCGAAG-GACCACATAGAATTGTC
* *
4116 TCGAAGGACCGCGTAGAATTGTCCTGAAGGACCACATAGAATTGTC
1 CCGAAGGACCGCGTAGAATTGTCCCGAAGGACCACATAGAATTGTC
*
4162 CCGAAAGACCGCGTAGAA
1 CCGAAGGACCGCGTAGAA
4180 CCCTCGACTC
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
45 1 0.02
46 37 0.67
47 17 0.31
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.19
Consensus pattern (46 bp):
CCGAAGGACCGCGTAGAATTGTCCCGAAGGACCACATAGAATTGTC
Found at i:4132 original size:23 final size:22
Alignment explanation
Indices: 4053--4179 Score: 85
Period size: 23 Copynumber: 5.5 Consensus size: 22
4043 GTCGAAACTT
* *
4053 CCGCGTAGAATTTGCACCGAAGTA
1 CCGCGTAGAA-TTG-TCCGAAGGA
* *
4077 CCACGTAGAATATGCACCGAAGTG-
1 CCGCGTAGAAT-TG-TCCGAAG-GA
* * *
4101 CCACATAGATTTGTCTCGAAGGA
1 CCGCGTAGAATTGTC-CGAAGGA
4124 CCGCGTAGAATTGTCCTGAAGGA
1 CCGCGTAGAATTGTCC-GAAGGA
* * *
4147 CCACATAGAATTGTCCCGAAAGA
1 CCGCGTAGAATTGT-CCGAAGGA
4170 CCGCGTAGAA
1 CCGCGTAGAA
4180 CCCTCGACTC
Statistics
Matches: 84, Mismatches: 13, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
22 3 0.04
23 51 0.61
24 30 0.36
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.20
Consensus pattern (22 bp):
CCGCGTAGAATTGTCCGAAGGA
Found at i:10384 original size:2 final size:2
Alignment explanation
Indices: 10377--10422 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
10367 CTATCGATCC
10377 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10419 AT AT
1 AT AT
10423 GAATAATATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12655 original size:38 final size:38
Alignment explanation
Indices: 12613--12710 Score: 178
Period size: 38 Copynumber: 2.6 Consensus size: 38
12603 GTCAGCAAAA
* *
12613 CGGCCACAAACTCTATGAAAAAGATAAGTACAGATTGT
1 CGGCCATAAACTCTATGAAAAAGATAAGAACAGATTGT
12651 CGGCCATAAACTCTATGAAAAAGATAAGAACAGATTGT
1 CGGCCATAAACTCTATGAAAAAGATAAGAACAGATTGT
12689 CGGCCATAAACTCTATGAAAAA
1 CGGCCATAAACTCTATGAAAAA
12711 AGATTGAAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 58 1.00
ACGTcount: A:0.44, C:0.18, G:0.17, T:0.20
Consensus pattern (38 bp):
CGGCCATAAACTCTATGAAAAAGATAAGAACAGATTGT
Found at i:15949 original size:2 final size:2
Alignment explanation
Indices: 15942--16047 Score: 82
Period size: 2 Copynumber: 53.5 Consensus size: 2
15932 AACAATTTTA
* *
15942 AT AT AT AT -T AT AGT AT AT AT AT A- AT AT AA AT AT CCT -T AT A-
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
*
15982 AGT AT AT AGT AT A- AGT AT AC AT -T AT ACT -T AT AT AT AT AT AT
1 A-T AT AT A-T AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT
16023 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
16048 ATACTTTTTT
Statistics
Matches: 86, Mismatches: 5, Indels: 26
0.74 0.04 0.22
Matches are distributed among these distances:
1 7 0.08
2 71 0.83
3 8 0.09
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:16802 original size:2 final size:2
Alignment explanation
Indices: 16797--17099 Score: 110
Period size: 2 Copynumber: 160.5 Consensus size: 2
16787 TTAAATAACC
*
16797 AT AT AT -T AT AT TT AT A- AGT AT AT A- AT AT A- AGT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT
* *
16836 AT ACT -T AT A- AT AT AT AC AT -T AT ACT -T TT AT AT AT AT AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* * *
16876 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AA AGT AC AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* *
16918 A- AGT AT A- AT AT AC AT AT AT AT -T AT A- AT -T AT A- AT AT AA
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
16955 AT AT -T AT ACT -T AT AA AT AT AT A- AGT AT AT AT AT A- AT GT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* * * * * * *
16995 AC AT TT AT A- AT GT AT ACT -T AT TT AT A- AT GT AC AC AT -T AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
*
17034 AT TT A- AT A- AGT AT AT AT AT AT AT ACT -T AT AT -T AT AT ACT
1 AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T
17073 AT AT AT A- AT AT A- AGT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A
17100 CAACTTAAGT
Statistics
Matches: 227, Mismatches: 30, Indels: 88
0.66 0.09 0.26
Matches are distributed among these distances:
1 31 0.14
2 182 0.80
3 14 0.06
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:16827 original size:13 final size:13
Alignment explanation
Indices: 16809--16838 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
16799 ATATTATATT
16809 TATAAGTATATAA
1 TATAAGTATATAA
*
16822 TATAAGTATATAT
1 TATAAGTATATAA
16835 TATA
1 TATA
16839 CTTATAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (13 bp):
TATAAGTATATAA
Found at i:17017 original size:17 final size:15
Alignment explanation
Indices: 16985--17031 Score: 67
Period size: 15 Copynumber: 3.0 Consensus size: 15
16975 TAAGTATATA
16985 TATAATGTATACATT
1 TATAATGTATACATT
17000 TATAATGTATACTTATT
1 TATAATGTATAC--ATT
*
17017 TATAATGTACACATT
1 TATAATGTATACATT
17032 ATATTTAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 15 0.52
17 14 0.48
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (15 bp):
TATAATGTATACATT
Found at i:17108 original size:22 final size:20
Alignment explanation
Indices: 17040--17109 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 20
17030 TTATATTTAA
*
17040 TAAGTATATATATATATACT
1 TAAGTATATATATATAAACT
*
17060 TATATTATATACTATATATAA-T
1 TA-AGTATATA-TATATA-AACT
17082 ATAAGTATATATATTATACAACT
1 -TAAGTATATATA-TATA-AACT
17105 TAAGT
1 TAAGT
17110 TTGAACCAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
20 2 0.05
21 9 0.22
22 25 0.62
23 4 0.10
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (20 bp):
TAAGTATATATATATAAACT
Found at i:17623 original size:43 final size:43
Alignment explanation
Indices: 17556--17646 Score: 155
Period size: 43 Copynumber: 2.1 Consensus size: 43
17546 ACCAGGTAAC
17556 TCATTTAGGTGAGATTTGAAAAGTTGCATAAGCTTGAAGCATG
1 TCATTTAGGTGAGATTTGAAAAGTTGCATAAGCTTGAAGCATG
* **
17599 TCATTTATGTGAGATTTGGTAAGTTGCATAAGCTTGAAGCATG
1 TCATTTAGGTGAGATTTGAAAAGTTGCATAAGCTTGAAGCATG
17642 TCATT
1 TCATT
17647 ATAAATTGCA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.30, C:0.10, G:0.24, T:0.36
Consensus pattern (43 bp):
TCATTTAGGTGAGATTTGAAAAGTTGCATAAGCTTGAAGCATG
Found at i:18078 original size:20 final size:20
Alignment explanation
Indices: 18053--18104 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
18043 CTAGTACCAT
18053 AGTATCGATACTCGACCAGG
1 AGTATCGATACTCGACCAGG
18073 AGTATCGATACTCGACCAGG
1 AGTATCGATACTCGACCAGG
18093 AGTATCGATACT
1 AGTATCGATACT
18105 ACCTTACCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (20 bp):
AGTATCGATACTCGACCAGG
Found at i:18162 original size:20 final size:20
Alignment explanation
Indices: 18133--18175 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
18123 ATAATAGTTA
*
18133 GTGGGTATCAATACCGATAG
1 GTGGGCATCAATACCGATAG
*
18153 GTGGGCATCAGTACCGATAG
1 GTGGGCATCAATACCGATAG
18173 GTG
1 GTG
18176 TGTATCGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.16, G:0.35, T:0.23
Consensus pattern (20 bp):
GTGGGCATCAATACCGATAG
Found at i:18221 original size:20 final size:20
Alignment explanation
Indices: 18177--18221 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
18167 CGATAGGTGT
*
18177 GTATCGATACTAGAGGTGCA
1 GTATCGATACTAAAGGTGCA
*
18197 ATATCGATACTAAAAGGT-CA
1 GTATCGATACT-AAAGGTGCA
18217 GTATC
1 GTATC
18222 AGTACTGACG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.27
Consensus pattern (20 bp):
GTATCGATACTAAAGGTGCA
Found at i:19579 original size:21 final size:19
Alignment explanation
Indices: 19546--19785 Score: 94
Period size: 19 Copynumber: 12.8 Consensus size: 19
19536 GTTAGTAATC
19546 ATAATAATATAATATAAAT
1 ATAATAATATAATATAAAT
19565 ATAATATACTATAATAT-AAT
1 ATAATA-A-TATAATATAAAT
* * * *
19585 AAAACAATTTTA-AT-AAT
1 ATAATAATATAATATAAAT
* **
19602 AT-GTACCATAATATAAAT
1 ATAATAATATAATATAAAT
* * *
19620 ATTAT-ATGTAATGT-AAT
1 ATAATAATATAATATAAAT
* *
19637 ACTATATAGTAT-ATATAATAC
1 A-TA-ATAATATAATATAA-AT
19658 ATAA-AATATAAATATAAAT
1 ATAATAATAT-AATATAAAT
* * *
19677 ATTATATTATAATATATAT
1 ATAATAATATAATATAAAT
* * *
19696 ATAACTATAAATACTATACTAT
1 ATAA-TA-ATATAATATA-AAT
*
19718 ATAAT-ATATATATATATAT
1 ATAATAATATA-ATATAAAT
*
19737 ATAA-ACTAT-A-ATAAAT
1 ATAATAATATAATATAAAT
*
19753 AT-ATAATAATGATATAAAT
1 ATAATAAT-ATAATATAAAT
19772 ATAAT-ATATAATAT
1 ATAATAATATAATAT
19786 TGGGATCATT
Statistics
Matches: 162, Mismatches: 36, Indels: 47
0.66 0.15 0.19
Matches are distributed among these distances:
15 1 0.01
16 12 0.07
17 15 0.09
18 25 0.15
19 53 0.33
20 31 0.19
21 18 0.11
22 7 0.04
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (19 bp):
ATAATAATATAATATAAAT
Found at i:19585 original size:31 final size:31
Alignment explanation
Indices: 19549--19755 Score: 93
Period size: 31 Copynumber: 6.3 Consensus size: 31
19539 AGTAATCATA
19549 ATAATATAATATAAATATAATATACTATAAT
1 ATAATATAATATAAATATAATATACTATAAT
* * *
19580 ATAATA-AA-ACAATTTTAATAATATGTACCATAAT
1 ATAATATAATATAA--AT-ATAATA--TACTATAAT
* * *
19614 ATAAATATTATATGTAATGTAATACTATATAGTATATAT
1 AT-AATA-TA-ATATAA-AT-ATA--ATATACTATA-AT
* * *
19653 AATACATAAAATATAAATATAA-ATATTATATT
1 -ATA-ATATAATATAAATATAATATACTATAAT
*
19685 ATAATATATATATAACTATAA-ATACTATACTAT
1 ATAATATA-ATATAAATATAATATACTATA--AT
* *
19718 ATAATAT-ATATATATATATATAAACTATAAT
1 ATAATATAATATAAATATA-ATATACTATAAT
19749 A-AATATA
1 ATAATATA
19756 TAATAATGAT
Statistics
Matches: 135, Mismatches: 20, Indels: 42
0.69 0.10 0.21
Matches are distributed among these distances:
29 3 0.02
30 11 0.08
31 40 0.30
32 8 0.06
33 22 0.16
34 11 0.08
35 4 0.03
36 3 0.02
37 2 0.01
38 17 0.13
39 6 0.04
40 8 0.06
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (31 bp):
ATAATATAATATAAATATAATATACTATAAT
Found at i:19651 original size:2 final size:2
Alignment explanation
Indices: 19639--19785 Score: 84
Period size: 2 Copynumber: 76.5 Consensus size: 2
19629 AATGTAATAC
* * * *
19639 TA TA TA GTA TA TA TA -A TA CA TA -A AA TA TA AA TA TA AA TA T-
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
19679 TA TA T- TA TA -A TA TA TA TA TA -A CTA TA AA TA CTA TA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA -TA TA
* *
19719 TA -A TA TA TA TA TA TA TA TA TA AA CTA TA -A TA AA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
*
19759 TA -A TGA TA TA AA TA TA -A TA TA TA -A TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA T
19786 TGGGATCATT
Statistics
Matches: 112, Mismatches: 15, Indels: 36
0.69 0.09 0.22
Matches are distributed among these distances:
1 12 0.11
2 90 0.80
3 10 0.09
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.40
Consensus pattern (2 bp):
TA
Found at i:19726 original size:33 final size:31
Alignment explanation
Indices: 19646--19785 Score: 125
Period size: 33 Copynumber: 4.5 Consensus size: 31
19636 TACTATATAG
*
19646 TATATATAATACATA-AAATATAA-ATATAAA-
1 TATATAT-ATA-ATATATATATAATATATAAAC
19676 TATTATATTATAATATATATATAACTATA-AATAC
1 TA-TATA-TATAATATATATATAA-TATATAA-AC
19710 TATACTATATAATATATATATATATATATAAAC
1 TATA-TATATAATATATATATA-ATATATAAAC
19743 TATA-ATA-AATATATA-ATAATGATATAAA-
1 TATATATATAATATATATATAAT-ATATAAAC
19771 TATAATATATAATAT
1 TAT-ATATATAATAT
19786 TGGGATCATT
Statistics
Matches: 95, Mismatches: 1, Indels: 27
0.77 0.01 0.22
Matches are distributed among these distances:
28 5 0.05
29 11 0.12
30 16 0.17
31 22 0.23
32 3 0.03
33 31 0.33
34 7 0.07
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.40
Consensus pattern (31 bp):
TATATATATAATATATATATAATATATAAAC
Found at i:19751 original size:76 final size:75
Alignment explanation
Indices: 19609--19784 Score: 182
Period size: 76 Copynumber: 2.3 Consensus size: 75
19599 AATATGTACC
* * * *
19609 ATAATATAAATATTATATGTAAT-GTAATACTATATAGTATATATAATACATAAAATATAAATAT
1 ATAATATAAATATAATATATAATACT-ATACTATATAATATATATAATACATAAAATAT-AATAT
*
19673 AAATAT-TATATT
64 AAATATATA-ATA
* *
19685 ATAATATATATATAACTATA-AATACTATACTATATAATATATATATATATATATAAACTAT-A-
1 ATAATATAAATATAA-TATATAATACTATACTATATAATATATATA-ATACATA-AAA-TATAAT
19747 ATAAATATATAATA
62 ATAAATATATAATA
*
19761 ATGATATAAATATAATATATAATA
1 ATAATATAAATATAATATATAATA
19785 TTGGGATCAT
Statistics
Matches: 84, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
75 4 0.05
76 61 0.73
77 13 0.15
78 3 0.04
79 3 0.04
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (75 bp):
ATAATATAAATATAATATATAATACTATACTATATAATATATATAATACATAAAATATAATATAA
ATATATAATA
Found at i:19785 original size:5 final size:5
Alignment explanation
Indices: 19549--19779 Score: 90
Period size: 5 Copynumber: 45.6 Consensus size: 5
19539 AGTAATCATA
* * *
19549 ATAAT ATAAT ATAAAT ATAAT ATACT ATAAT ATAAT A-AA- ACAATT TTAAT
1 ATAAT ATAAT AT-AAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAA-T ATAAT
* ** * * * *
19599 A-ATAT GTACC ATAAT ATAA- ATATT AT-AT GTAAT GTAAT ACT-AT ATAGT
1 ATA-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A-TAAT ATAAT
* * * *
19647 AT-AT ATAAT A-CAT AAAAT ATAAAT ATAA- ATATT ATATT ATAAT ATATAT
1 ATAAT ATAAT ATAAT ATAAT AT-AAT ATAAT ATAAT ATAAT ATAAT ATA-AT
*
19696 ATAACT ATAA- ATACT ATACTAT ATAAT AT-AT AT-AT ATATAT ATAAACT
1 ATAA-T ATAAT ATAAT ATA--AT ATAAT ATAAT ATAAT ATA-AT AT-AA-T
* *
19744 ATAAT AAATAT ATAAT AATGAT ATAAAT ATAAT ATA
1 ATAAT ATA-AT ATAAT -ATAAT AT-AAT ATAAT ATA
19780 TAATATTGGG
Statistics
Matches: 172, Mismatches: 28, Indels: 52
0.68 0.11 0.21
Matches are distributed among these distances:
3 1 0.01
4 31 0.18
5 89 0.52
6 43 0.25
7 8 0.05
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:19785 original size:31 final size:32
Alignment explanation
Indices: 19663--19785 Score: 127
Period size: 33 Copynumber: 3.9 Consensus size: 32
19653 AATACATAAA
*
19663 ATATAA-ATATAAA-TATTATATTATAATATAT
1 ATATAATATATAAACTATAATA-TATAATATAT
*
19694 ATATAACTATA-AATACTATACTATATAATATAT
1 ATATAA-TATATAA-ACTATAATATATAATATAT
19727 ATATATATATATAAACTAT-A-ATA-AATATAT
1 ATATA-ATATATAAACTATAATATATAATATAT
19757 A-ATAATGATATAAA-TATAATATATAATAT
1 ATATAAT-ATATAAACTATAATATATAATAT
19786 TGGGATCATT
Statistics
Matches: 79, Mismatches: 3, Indels: 20
0.77 0.03 0.20
Matches are distributed among these distances:
28 5 0.06
29 11 0.14
30 11 0.14
31 14 0.18
32 2 0.03
33 28 0.35
34 8 0.10
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (32 bp):
ATATAATATATAAACTATAATATATAATATAT
Found at i:21096 original size:2 final size:2
Alignment explanation
Indices: 21089--21113 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21079 CACATTTAAA
21089 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
21114 CACTCTATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22804 original size:8 final size:8
Alignment explanation
Indices: 22793--22826 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
22783 ATATTTTATA
22793 TATTTAAT
1 TATTTAAT
22801 TATTTAAT
1 TATTTAAT
*
22809 TATTTAAC
1 TATTTAAT
22817 TATTTAAT
1 TATTTAAT
22825 TA
1 TA
22827 CTTATCCGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (8 bp):
TATTTAAT
Found at i:22842 original size:2 final size:2
Alignment explanation
Indices: 22835--22875 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
22825 TACTTATCCG
22835 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22876 TAATAACTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:23265 original size:54 final size:54
Alignment explanation
Indices: 23130--23394 Score: 286
Period size: 54 Copynumber: 4.9 Consensus size: 54
23120 TTTTCAACAT
* **
23130 CGGGTTCGCTCCCTATCGCTTCAGGGA-ACATAGAACTCGAATAATCTTCTGCTAA
1 CGGGTTCGCTCCCTCTTTCTTCAGGGAGA-ATAGAACTCGAA-AATCTTCTGCTAA
* *
23185 CGGGTTCGCTCCCTATTGT-TTCAGGGAGTATAGAACTC-AAGAATCTTCTGCTAA
1 CGGGTTCGCTCCCTCTT-TCTTCAGGGAGAATAGAACTCGAA-AATCTTCTGCTAA
* * * * * *
23239 CCGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTTCTTCAAA
1 CGGGTTCGCTCCCTCTTTCTTCAGGGAGAATAGAACTCGAAAATCTTCTGCTAA
* * * * *
23293 TGAGTTCGCTCCCTCTTTCTTCAGGGAGAATAGAACTCGAATATCTTCTTCAAA
1 CGGGTTCGCTCCCTCTTTCTTCAGGGAGAATAGAACTCGAAAATCTTCTGCTAA
* * *
23347 CGGGTTTGCTCCCTCTCTC-TCTAGGGAGAATAGAACTCGAATATCTTC
1 CGGGTTCGCTCCCTCTTTCTTC-AGGGAGAATAGAACTCGAAAATCTTC
23395 AACAATCGTG
Statistics
Matches: 185, Mismatches: 20, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
53 3 0.02
54 147 0.79
55 35 0.19
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (54 bp):
CGGGTTCGCTCCCTCTTTCTTCAGGGAGAATAGAACTCGAAAATCTTCTGCTAA
Found at i:23411 original size:54 final size:52
Alignment explanation
Indices: 23159--23421 Score: 212
Period size: 54 Copynumber: 4.9 Consensus size: 52
23149 TTCAGGGAAC
* * * *
23159 ATAGAACTCGAATAATCTTCTGCTAA-CGGGTTCGCTCCCTATTGT-TTCAGGGAGT
1 ATAGAACTCGAAT-ATCTTCTTC-AATCGAGTT-GCTCCCTCTT-TCTT-AGGGAGA
* * * *
23214 ATAGAACTC-AAGAATCTTCTGCTAACCG-GTTCGCTCCCTCTTTCTTTAGGGAGT
1 ATAGAACTCGAA-TATCTTCTTC-AATCGAGTT-GCTCCCTCTTTC-TTAGGGAGA
*
23268 ATAGAACTCGAACATCTTCTTCAAAT-GAGTTCGCTCCCTCTTTCTTCAGGGAGA
1 ATAGAACTCGAATATCTTCTTC-AATCGAGTT-GCTCCCTCTTTCTT-AGGGAGA
* * *
23322 ATAGAACTCGAATATCTTCTTCAAACGGGTTTGCTCCCTCTCTCTCTAGGGAGA
1 ATAGAACTCGAATATCTTCTTCAATCGAG-TTGCTCCCTCTTTCT-TAGGGAGA
** * *
23376 ATAGAACTCGAATATCTTCAACAATCGTGTCTGCTCCCTATTTCTT
1 ATAGAACTCGAATATCTTCTTCAATCGAGT-TGCTCCCTCTTTCTT
23422 CAGAGAGTAT
Statistics
Matches: 180, Mismatches: 17, Indels: 24
0.81 0.08 0.11
Matches are distributed among these distances:
53 8 0.04
54 154 0.86
55 18 0.10
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.33
Consensus pattern (52 bp):
ATAGAACTCGAATATCTTCTTCAATCGAGTTGCTCCCTCTTTCTTAGGGAGA
Found at i:23412 original size:108 final size:108
Alignment explanation
Indices: 23188--23424 Score: 284
Period size: 108 Copynumber: 2.2 Consensus size: 108
23178 CTGCTAACGG
* *
23188 GTTCGCTCCCTATTGT-TTCAGGGAGTATAGAACTCAAGAATCTTCTGCTAACCGGTTCGCTCCC
1 GTTCGCTCCCTATT-TCTTCAGGGAGAATAGAACTCAAGAATCTTCTGCAAACCGGTTCGCTCCC
* * * **
23252 TCTTTCTTTAGGGAGTATAGAACTCGAACATCTTCTTCAAATGA
65 TCTCTCTCTAGGGAGAATAGAACTCGAACATCTTCAACAAATGA
* * * * *
23296 GTTCGCTCCCTCTTTCTTCAGGGAGAATAGAACTCGAA-TATCTTCTTCAAACGGGTTTGCTCCC
1 GTTCGCTCCCTATTTCTTCAGGGAGAATAGAACTC-AAGAATCTTCTGCAAACCGGTTCGCTCCC
* *
23360 TCTCTCTCTAGGGAGAATAGAACTCGAATATCTTCAAC-AAT-C
65 TCTCTCTCTAGGGAGAATAGAACTCGAACATCTTCAACAAATGA
23402 GTGTCTGCTCCCTATTTCTTCAG
1 GT-TC-GCTCCCTATTTCTTCAG
23425 AGAGTATAAG
Statistics
Matches: 110, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
106 2 0.02
107 6 0.05
108 100 0.91
109 2 0.02
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33
Consensus pattern (108 bp):
GTTCGCTCCCTATTTCTTCAGGGAGAATAGAACTCAAGAATCTTCTGCAAACCGGTTCGCTCCCT
CTCTCTCTAGGGAGAATAGAACTCGAACATCTTCAACAAATGA
Found at i:23414 original size:162 final size:163
Alignment explanation
Indices: 23133--23432 Score: 360
Period size: 162 Copynumber: 1.8 Consensus size: 163
23123 TCAACATCGG
*
23133 GTTCGCTCCCTATCGCTTCAGGGAACATAGAACTCGAATAATCTTCTGCTAACGGGTTCGCTCCC
1 GTTCGCTCCCTATCGCTTCAGGGAACATAGAACTCGAATAATCTTCTGCAAACGGGTTCGCTCCC
* * * ** * *
23198 TATTGTTTCAGGGAGTATAGAACTCAAGAATCTTCTGCTAACCGGTTCGCTCCCTCTTTCTTTAG
66 TATTCTCTCAGGGAGAATAGAACTCAAGAATCTTCAACTAACCGGTTCGCTCCCTATTTCTTCAG
*
23263 GGAGTATAGAACTCGAACATCTTCTTCAAATGA
131 AGAGTATAGAACTCGAACATCTTCTTCAAATGA
* ** * *
23296 GTTCGCTCCCTCTTTCTTCAGGGAGA-ATAGAACTCGAAT-ATCTTCTTCAAACGGGTTTGCTCC
1 GTTCGCTCCCTATCGCTTCAGGGA-ACATAGAACTCGAATAATCTTCTGCAAACGGGTTCGCTCC
* * *
23359 CT-CTCTCTCTAGGGAGAATAGAACTCGAA-TATCTTCAAC-AATC-GTGTCTGCTCCCTATTTC
65 CTATTCTCTC-AGGGAGAATAGAACTC-AAGAATCTTCAACTAACCGGT-TC-GCTCCCTATTTC
23420 TTCAGAGAGTATA
126 TTCAGAGAGTATA
23433 AGACCCAAAC
Statistics
Matches: 115, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
160 2 0.02
161 9 0.08
162 67 0.58
163 36 0.31
164 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.32
Consensus pattern (163 bp):
GTTCGCTCCCTATCGCTTCAGGGAACATAGAACTCGAATAATCTTCTGCAAACGGGTTCGCTCCC
TATTCTCTCAGGGAGAATAGAACTCAAGAATCTTCAACTAACCGGTTCGCTCCCTATTTCTTCAG
AGAGTATAGAACTCGAACATCTTCTTCAAATGA
Found at i:23452 original size:55 final size:55
Alignment explanation
Indices: 23381--23679 Score: 438
Period size: 55 Copynumber: 5.4 Consensus size: 55
23371 GGAGAATAGA
* * *
23381 ACTCGAA-TATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACGATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * * * *
23435 ACCCAAACAATCTTCAACAAATCTTGTCTGCTCCCTATTCCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAAC-GATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
*
23491 ACTCGAACAATCTTCAATGATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACGATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * *
23546 ACCCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGGGAGTATAAG
1 ACTCGAACAATCTTCAACGATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
** *
23601 ACTCGAACAATCTTCAACGATCGCCTCTTCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACGATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
23656 ACTCGAACAATCTTCAACGATCGT
1 ACTCGAACAATCTTCAACGATCGT
23680 TGGGAAACCT
Statistics
Matches: 222, Mismatches: 21, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
54 5 0.02
55 167 0.75
56 50 0.23
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.29
Consensus pattern (55 bp):
ACTCGAACAATCTTCAACGATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
Found at i:24702 original size:7 final size:7
Alignment explanation
Indices: 24666--24717 Score: 52
Period size: 7 Copynumber: 7.0 Consensus size: 7
24656 TTGAACCCTC
24666 ATTTTTT
1 ATTTTTT
24673 CATTTTTT
1 -ATTTTTT
24681 -TTTTCATT
1 ATTTT--TT
24689 CATTTTTT
1 -ATTTTTT
24697 ATTTTTT
1 ATTTTTT
*
24704 ATTTTTC
1 ATTTTTT
24711 ATTTTTT
1 ATTTTTT
24718 TCATTTTCAC
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
6 4 0.11
7 19 0.50
8 11 0.29
10 4 0.11
ACGTcount: A:0.13, C:0.08, G:0.00, T:0.79
Consensus pattern (7 bp):
ATTTTTT
Found at i:24703 original size:21 final size:21
Alignment explanation
Indices: 24664--24717 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 21
24654 TCTTGAACCC
*
24664 TCATTTTTTCATTTTTTTTTTCAT
1 TCATTTTTT-A-TTTTTTATT-AT
*
24688 TCATTTTTTATTTTTTATTTT
1 TCATTTTTTATTTTTTATTAT
24709 TCATTTTTT
1 TCATTTTTT
24718 TCATTTTCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 10 0.36
22 8 0.29
23 1 0.04
24 9 0.32
ACGTcount: A:0.13, C:0.09, G:0.00, T:0.78
Consensus pattern (21 bp):
TCATTTTTTATTTTTTATTAT
Found at i:28252 original size:8 final size:8
Alignment explanation
Indices: 28239--28266 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
28229 AAAAGAAGAT
28239 ATATATAC
1 ATATATAC
28247 ATATATAC
1 ATATATAC
28255 ATATATAC
1 ATATATAC
28263 ATAT
1 ATAT
28267 GGGAGAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATATAC
Found at i:36420 original size:2 final size:2
Alignment explanation
Indices: 36413--36437 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
36403 CACATTTAAA
36413 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
36438 CACTCTATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38130 original size:8 final size:8
Alignment explanation
Indices: 38119--38152 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
38109 ATATTTTATA
38119 TATTTAAT
1 TATTTAAT
38127 TATTTAAT
1 TATTTAAT
*
38135 TATTTAAC
1 TATTTAAT
38143 TATTTAAT
1 TATTTAAT
38151 TA
1 TA
38153 CTTATCCGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (8 bp):
TATTTAAT
Found at i:38168 original size:2 final size:2
Alignment explanation
Indices: 38161--38221 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
38151 TACTTATCCG
38161 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
38203 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
38222 TAATAACTAC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39786 original size:18 final size:18
Alignment explanation
Indices: 39752--39786 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39742 AATATAAAAT
* *
39752 TAAAATATGATTCATTTA
1 TAAAATATAATTAATTTA
39770 TAAAATATAATTAATTT
1 TAAAATATAATTAATTT
39787 GCTTTGAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (18 bp):
TAAAATATAATTAATTTA
Found at i:40325 original size:2 final size:2
Alignment explanation
Indices: 40318--40388 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
40308 ATGGTACTAA
40318 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40360 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40389 AGACTAAAGA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42537 original size:117 final size:109
Alignment explanation
Indices: 42331--42622 Score: 349
Period size: 117 Copynumber: 2.6 Consensus size: 109
42321 AAGCGTTGGA
42331 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTTGTTGGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAA-TTCTTCTC-C-T-TTGGATGAGTTCTTCTCATTATGAAC
* *
42396 TCTTCATTGAAAAAGTTGATCCATCTCCTTT-TGTGATGGAATCGAATCAAGG
62 TCTCCACTGAAAAAGTTGATCCATCT-CTTTCTGTGATGGAATCG-A--AA-G
42448 TTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAA-TTCTTC-TCCT--TTGGATGAGTTCTTCTCATTATGAAC
* * *
42513 TCTCCACTGAAAATGTTGATCCATCTCTTTCTGTGATGGACTTGAAAG
62 TCTCCACTGAAAAAGTTGATCCATCTCTTTCTGTGATGGAATCGAAAG
* * * *
42561 --GAACAAGTTCTTATCATTATGAACT-TTCTCCTTTGGGACGATTTCTTCTCATTATGAACTCT
1 TTGAACAAGTTCTTCTCATTATGAATTCTTCTCCTTT-GGATGAGTTCTTCTCATTATGAACTCT
42623 TAATTGGAAA
Statistics
Matches: 160, Mismatches: 11, Indels: 18
0.85 0.06 0.10
Matches are distributed among these distances:
106 2 0.01
107 25 0.16
108 4 0.03
109 3 0.02
110 1 0.01
111 22 0.14
113 1 0.01
114 2 0.01
116 6 0.04
117 92 0.57
118 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (109 bp):
TTGAACAAGTTCTTCTCATTATGAATTCTTCTCCTTTGGATGAGTTCTTCTCATTATGAACTCTC
CACTGAAAAAGTTGATCCATCTCTTTCTGTGATGGAATCGAAAG
Found at i:43047 original size:136 final size:136
Alignment explanation
Indices: 42561--43043 Score: 717
Period size: 136 Copynumber: 3.6 Consensus size: 136
42551 GACTTGAAAG
* * * * *
42561 GAACAAGTTCTTATCATTATGAAC-T-TTCT-CCT-T-TGGGACGATTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
* * * *
42621 CTTAATTGGAAATGTCAATCCATCAAGTGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGA
66 CTCAATTGGAAATGTCGATCCCTCAAGTGAGGTGTCACTGATTCGAAATGCCATGAATCGAGTGA
42686 TAGGTC
131 TAGGTC
*
42692 AAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
*
42757 CTCAATTGGAAATGTCGATCCCTCAAGTGAGGTGTCACTGATTCGAAATGCTATGAATCGAGTGA
66 CTCAATTGGAAATGTCGATCCCTCAAGTGAGGTGTCACTGATTCGAAATGCCATGAATCGAGTGA
42822 TAGGTC
131 TAGGTC
* *
42828 GAACAAGCTCTTCTCATTATGAACTTTTTCTCCCTCTGTCGGATGAGTTATTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
* * * * *
42893 CTTC-ACTGGAAATATTGATCCCTCAAGCGAGGTGTCACTGATTCGAAACGCCATGAATCGAGTG
66 C-TCAATTGGAAATGTCGATCCCTCAAGTGAGGTGTCACTGATTCGAAATGCCATGAATCGAGTG
42957 ATAGGTC
130 ATAGGTC
* * *
42964 GAATAGGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
*
43029 CTCCATTGGAAATGT
66 CTCAATTGGAAATGT
43044 TGATACATCT
Statistics
Matches: 318, Mismatches: 27, Indels: 9
0.90 0.08 0.03
Matches are distributed among these distances:
131 21 0.07
132 1 0.00
133 4 0.01
134 3 0.01
135 3 0.01
136 284 0.89
137 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (136 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
CTCAATTGGAAATGTCGATCCCTCAAGTGAGGTGTCACTGATTCGAAATGCCATGAATCGAGTGA
TAGGTC
Found at i:43986 original size:40 final size:39
Alignment explanation
Indices: 43914--43996 Score: 107
Period size: 39 Copynumber: 2.1 Consensus size: 39
43904 CAAACCCTCC
43914 TTTTTCTCTTTTCATTTTTTCATTTCTTTTTGTTCATTT
1 TTTTTCTCTTTTCATTTTTTCATTTCTTTTTGTTCATTT
* *
43953 TTTTTCT-TTTTCATGTTTTT-ATCTTTTTATTTGTTCCTTT
1 TTTTTCTCTTTTCAT-TTTTTCAT-TTCTT-TTTGTTCATTT
43993 TTTT
1 TTTT
43997 CTTCAAGCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
38 9 0.23
39 16 0.41
40 14 0.36
ACGTcount: A:0.07, C:0.13, G:0.04, T:0.76
Consensus pattern (39 bp):
TTTTTCTCTTTTCATTTTTTCATTTCTTTTTGTTCATTT
Found at i:54685 original size:52 final size:52
Alignment explanation
Indices: 54628--54731 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
54618 TTGGACAAAT
54628 CTGAGAACAAAGAT-AAAAATGTTAGTAAGACAATAATAAAATGAAGCAATTA
1 CTGAGAACAAAGATAAAAAAT-TTAGTAAGACAATAATAAAATGAAGCAATTA
54680 CTGAGAACAAAGATAAAAAATTTAGTAAGACAATAATAAAATGAAGCAATTA
1 CTGAGAACAAAGATAAAAAATTTAGTAAGACAATAATAAAATGAAGCAATTA
54732 AAAACTTCAA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
52 45 0.88
53 6 0.12
ACGTcount: A:0.57, C:0.08, G:0.14, T:0.21
Consensus pattern (52 bp):
CTGAGAACAAAGATAAAAAATTTAGTAAGACAATAATAAAATGAAGCAATTA
Found at i:55495 original size:2 final size:2
Alignment explanation
Indices: 55488--55513 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
55478 TAATAAAATA
55488 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
55514 TAATGAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55796 original size:2 final size:2
Alignment explanation
Indices: 55789--55827 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
55779 ATGGTACTAA
55789 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
55828 AGACTAAAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:57088 original size:20 final size:20
Alignment explanation
Indices: 57065--57102 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
57055 AAAATGCATT
57065 AAAAATGATGAAAATAATAG
1 AAAAATGATGAAAATAATAG
57085 AAAAATGATGAAAATAAT
1 AAAAATGATGAAAATAAT
57103 TGATACCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.13, T:0.21
Consensus pattern (20 bp):
AAAAATGATGAAAATAATAG
Found at i:58297 original size:30 final size:30
Alignment explanation
Indices: 58263--58335 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
58253 CCCGAAGGAC
58263 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
58293 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
58323 CTGTCCATAGGTC
1 CTATCCAGAGGTC
58336 CCGAAGAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:58359 original size:31 final size:31
Alignment explanation
Indices: 58321--58385 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
58311 GATCCTCGGT
*
58321 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACATAGGTA
* * **
58352 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATAGGTCCCGAAGAACATAGGTA
58383 AAC
1 AAC
58386 CCTCGACTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAGAACATAGGTA
Found at i:58549 original size:17 final size:19
Alignment explanation
Indices: 58517--58552 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
58507 CATATATCTC
58517 ATATCATATCACATGTATT
1 ATATCATATCACATGTATT
58536 ATAT-ATAT-ACATGTATT
1 ATATCATATCACATGTATT
58553 CATGTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (19 bp):
ATATCATATCACATGTATT
Found at i:59147 original size:64 final size:65
Alignment explanation
Indices: 59036--59186 Score: 191
Period size: 64 Copynumber: 2.3 Consensus size: 65
59026 TCTTTCAATG
* * * * * *
59036 AAGGTATGCATCGATGCACTA-CTTGTGCATCGGTGCATAAAATGCATTCGATGTTTTTATTTTA
1 AAGGAATGCATCGATGCATTATCTTATGCATCGATGCATAAAAGGCATTCGATGTTCTTATTTT-
59100 A
65 A
* *
59101 AAGG-ATGCATCGATGCATTATC-TATGCATCGATGCATCAAAGGCATTCGATGTTCTTCTTTTA
1 AAGGAATGCATCGATGCATTATCTTATGCATCGATGCATAAAAGGCATTCGATGTTCTTATTTTA
59164 AAGGAATGCATCGATGCACTTAT
1 AAGGAATGCATCGATGCA-TTAT
59187 GAATGTGCAT
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
63 5 0.07
64 62 0.82
65 9 0.12
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.34
Consensus pattern (65 bp):
AAGGAATGCATCGATGCATTATCTTATGCATCGATGCATAAAAGGCATTCGATGTTCTTATTTTA
Found at i:62196 original size:21 final size:21
Alignment explanation
Indices: 62166--62210 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
62156 CAAGCTTAAC
62166 TTTCAAATCA-AAATTTTCTT
1 TTTCAAATCATAAATTTTCTT
* *
62186 TTTCTAAATCATTAATTTTGTT
1 TTTC-AAATCATAAATTTTCTT
62208 TTT
1 TTT
62211 AAAAGCTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 6 0.29
22 11 0.52
ACGTcount: A:0.29, C:0.11, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTCAAATCATAAATTTTCTT
Found at i:69407 original size:180 final size:179
Alignment explanation
Indices: 69049--69606 Score: 591
Period size: 197 Copynumber: 3.0 Consensus size: 179
69039 AAAAGTAAGA
* * * * *
69049 AAATGATTTCAAAAGTTTCTTACTTAGTAAGTCCTTTGGGCTATCAGTAAGTATTTCAAGCATGA
1 AAATGATTTCCAAAGTTTCTTACTTAGTAAGTCCTTTGGGCCATCAATAAGTCTTTCGAGCATGA
* ** * * * *
69114 TGCCTAAATCCTTCAGCCATCCATAATACC-TTCGAGCAGAATGTTTTCACATGATTATCGAAAA
66 TGCCTAAATCTTTGGGCCATCCATAAGACCTTTAG-GCAGGATGTTTTCACATGATTTTCGAAAA
* *
69178 ATGAGAAAGCT-ATTTCCAAAGCTTGTCATTTAAATCTTTTGTGAAAATTG
130 ATGAGAAA-CTGATTTCCAAAGCTTCTCATTTAAATCTTTTCTGAAAATTG
69228 AAATGATTTCCAAAGTTTCTTACTTAGTAAGTCCTTTGGGCCATCAATAAGTCTTTCGAGCATGA
1 AAATGATTTCCAAAGTTTCTTACTTAGTAAGTCCTTTGGGCCATCAATAAGTCTTTCGAGCATGA
* * * *
69293 TGCCTAAAACATTTGGGCCATCTATAAGACCTTTAGGCAGGATATATTCACATGATTTTCGAAAA
66 TGCCTAAATC-TTTGGGCCATCCATAAGACCTTTAGGCAGGATGTTTTCACATGATTTTCGAAAA
* * *
69358 TTGAGAAATTGATTTCCAAAGCTTCTCATTTAAATCTTTTCTTAAAATTG
130 ATGAGAAACTGATTTCCAAAGCTTCTCATTTAAATCTTTTCTGAAAATTG
69408 ATTTTTTAAAAGTGAGAAAACGATTTCCAAAGTTTCTTACTTAGTAAGTCCTTTGGGCCATCAAT
1 --------AAA-T--------GATTTCCAAAGTTTCTTACTTAGTAAGTCCTTTGGGCCATCAAT
* * * * ** *
69473 AAGTCTTTCGAGCGTGAGGCTTAAATCCTTCGGGCCATCCATAAGACCTTCGGGCAAGATGTTTT
49 AAGTCTTTCGAGCATGATGCCTAAAT-CTTTGGGCCATCCATAAGACCTTTAGGCAGGATGTTTT
* ** **
69538 CGA-ATTATTTTTTAAAAAATGAGAAAGAGATTTCCAAAGCTTCTCATTTAAATCTTTTCTGAAA
113 C-ACATGA-TTTTCGAAAAATGAGAAACTGATTTCCAAAGCTTCTCATTTAAATCTTTTCTGAAA
69602 ATTG
176 ATTG
69606 A
1 A
69607 TTTTTTAAAA
Statistics
Matches: 317, Mismatches: 39, Indels: 35
0.81 0.10 0.09
Matches are distributed among these distances:
179 70 0.22
180 83 0.26
181 3 0.01
188 3 0.01
189 1 0.00
190 1 0.00
197 100 0.32
198 56 0.18
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (179 bp):
AAATGATTTCCAAAGTTTCTTACTTAGTAAGTCCTTTGGGCCATCAATAAGTCTTTCGAGCATGA
TGCCTAAATCTTTGGGCCATCCATAAGACCTTTAGGCAGGATGTTTTCACATGATTTTCGAAAAA
TGAGAAACTGATTTCCAAAGCTTCTCATTTAAATCTTTTCTGAAAATTG
Found at i:69639 original size:198 final size:197
Alignment explanation
Indices: 69232--69731 Score: 682
Period size: 198 Copynumber: 2.5 Consensus size: 197
69222 AAATTGAAAT
69232 GATTTCCAAAGTTTCTTACTTAGTAAGTCCTTTGGGCCATCAATAAGTCTTTCGAGCATGATGCC
1 GATTTCCAAAGTTTCTTACTTAGTAAGTCCTTTGGGCCATCAATAAGTCTTTCGAGCATGATGCC
* * ** * * * *
69297 TAAAACATTTGGGCCATCTATAAGACCTTTAGGCAGGATATATTCACATGATTTTCGAAAATTGA
66 TAAATCCTTTGGGCCATCTATAAGACCTTCGGGCAAGATGTATTCACATGATTTTCAAAAAATGA
** * *
69362 GAAATTGATTTCCAAAGCTTCTCATTTAAATCTTTTCTTAAAATTGATTTTTTAAAAGTGAGAAA
131 GAAAGAGATTTCCAAAGCTTCTCATTTAAATCTTTTCTGAAAATTGATTTTTTAAAAGTAAGAAA
69427 AC
196 AC
* * *
69429 GATTTCCAAAGTTTCTTACTTAGTAAGTCCTTTGGGCCATCAATAAGTCTTTCGAGCGTGAGGCT
1 GATTTCCAAAGTTTCTTACTTAGTAAGTCCTTTGGGCCATCAATAAGTCTTTCGAGCATGATGCC
* * * * *
69494 TAAATCCTTCGGGCCATCCATAAGACCTTCGGGCAAGATGTTTTCGA-ATTATTTTTTAAAAAAT
66 TAAATCCTTTGGGCCATCTATAAGACCTTCGGGCAAGATGTATTC-ACATGA-TTTTCAAAAAAT
69558 GAGAAAGAGATTTCCAAAGCTTCTCATTTAAATCTTTTCTGAAAATTGATTTTTTAAAAGTAAGA
129 GAGAAAGAGATTTCCAAAGCTTCTCATTTAAATCTTTTCTGAAAATTGATTTTTTAAAAGTAAGA
69623 AAAC
194 AAAC
* * * * * * *
69627 GATTTACAAAGTTTCTTACTTAGTAAGT-CTTTCAGGTCATTAGTAAGCCTTTTGAGCATGATGC
1 GATTTCCAAAGTTTCTTACTTAGTAAGTCCTTT-GGGCCATCAATAAGTCTTTCGAGCATGATGC
* *
69691 CTAAATCCTTTGGGTCATCTATAAG-CCTTTCGAGCAAGATG
65 CTAAATCCTTTGGGCCATCTATAAGACC-TTCGGGCAAGATG
69732 ATAAGTCCTT
Statistics
Matches: 265, Mismatches: 34, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
197 107 0.40
198 158 0.60
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (197 bp):
GATTTCCAAAGTTTCTTACTTAGTAAGTCCTTTGGGCCATCAATAAGTCTTTCGAGCATGATGCC
TAAATCCTTTGGGCCATCTATAAGACCTTCGGGCAAGATGTATTCACATGATTTTCAAAAAATGA
GAAAGAGATTTCCAAAGCTTCTCATTTAAATCTTTTCTGAAAATTGATTTTTTAAAAGTAAGAAA
AC
Found at i:69758 original size:20 final size:20
Alignment explanation
Indices: 69733--69802 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
69723 AGCAAGATGA
69733 TAAGTCCTTCGGGCCATCTG
1 TAAGTCCTTCGGGCCATCTG
69753 TAAGTCCTTCGGGCCATCTG
1 TAAGTCCTTCGGGCCATCTG
69773 TAAGTCCTTCGGGCCATCTG
1 TAAGTCCTTCGGGCCATCTG
*
69793 TAAGACCTTC
1 TAAGTCCTTC
69803 AGGCAGGATG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.17, C:0.30, G:0.23, T:0.30
Consensus pattern (20 bp):
TAAGTCCTTCGGGCCATCTG
Found at i:69862 original size:9 final size:9
Alignment explanation
Indices: 69841--69880 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
69831 AAACAAAAAT
69841 AAAAAA-GA
1 AAAAAATGA
*
69849 GAAAAATGAA
1 AAAAAATG-A
69859 AAAAAATGA
1 AAAAAATGA
69868 AAAAAATGA
1 AAAAAATGA
69877 AAAA
1 AAAA
69881 TGCTAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 5 0.18
9 15 0.54
10 8 0.29
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.07
Consensus pattern (9 bp):
AAAAAATGA
Found at i:69863 original size:10 final size:10
Alignment explanation
Indices: 69850--69880 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
69840 TAAAAAAGAG
69850 AAAAATGAAA
1 AAAAATGAAA
69860 AAAAATG-AA
1 AAAAATGAAA
69869 AAAAATGAAA
1 AAAAATGAAA
69879 AA
1 AA
69881 TGCTAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.10
Consensus pattern (10 bp):
AAAAATGAAA
Found at i:69871 original size:26 final size:26
Alignment explanation
Indices: 69835--69892 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
69825 GTTCAAAAAC
69835 AAAAAT-AAAAAAGA-GAAAAATGAAA
1 AAAAATGAAAAAA-ATGAAAAATGAAA
**
69860 AAAAATGAAAAAAATGAAAAATGCTA
1 AAAAATGAAAAAAATGAAAAATGAAA
69886 AAAAATG
1 AAAAATG
69893 TAAGAAGTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 7 0.24
26 22 0.76
ACGTcount: A:0.74, C:0.02, G:0.12, T:0.12
Consensus pattern (26 bp):
AAAAATGAAAAAAATGAAAAATGAAA
Found at i:69872 original size:19 final size:18
Alignment explanation
Indices: 69841--69880 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
69831 AAACAAAAAT
*
69841 AAAAAAGAGAAAAATGAA
1 AAAAAAGAAAAAAATGAA
69859 AAAAAATGAAAAAAATGAA
1 AAAAAA-GAAAAAAATGAA
69878 AAA
1 AAA
69881 TGCTAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.07
Consensus pattern (18 bp):
AAAAAAGAAAAAAATGAA
Found at i:73755 original size:457 final size:457
Alignment explanation
Indices: 72901--73814 Score: 1819
Period size: 457 Copynumber: 2.0 Consensus size: 457
72891 CTAGGCTTAC
72901 CCTGAGGAGATATTTATAGCCTTCAAATTCCTAAATACAAGCTAAAGATAATTTCTAAAATAATA
1 CCTGAGGAGATATTTATAGCCTTCAAATTCCTAAATACAAGCTAAAGATAATTTCTAAAATAATA
72966 TCTTAAATCCTAAATAAAACATTTAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAAATA
66 TCTTAAATCCTAAATAAAACATTTAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAAATA
73031 AAATAATATTTCAAATAATATCCTAAATCATAATTGAAATACTAAAACCTATTTAAACTAAAATA
131 AAATAATATTTCAAATAATATCCTAAATCATAATTGAAATACTAAAACCTATTTAAACTAAAATA
73096 CTTAAAACAAAGATAAAATATAATTTTTAAAATATTATCCTAAAACTTGAGTTTAATCCAAATCC
196 CTTAAAACAAAGATAAAATATAATTTTTAAAATATTATCCTAAAACTTGAGTTTAATCCAAATCC
73161 GAATTCCAGAAACGTGCGACCAATCCATTCATGCTTCTAGAAACGCTGATTGGATCTTCTAGAAG
261 GAATTCCAGAAACGTGCGACCAATCCATTCATGCTTCTAGAAACGCTGATTGGATCTTCTAGAAG
73226 GTGCTGACGTCAAACCGTGTCATGCCTAGAATCGTTCTCATGTCTCCATCCGTGACCAATTAATA
326 GTGCTGACGTCAAACCGTGTCATGCCTAGAATCGTTCTCATGTCTCCATCCGTGACCAATTAATA
73291 AAAAATTGTAGAATGCACCCGTTTTAATACTAATTCTGGAGAGTAAGACACTGCACGAAAATAAG
391 AAAAATTGTAGAATGCACCCGTTTTAATACTAATTCTGGAGAGTAAGACACTGCACGAAAATAAG
73356 CA
456 CA
73358 CCTGAGGAGATATTTATAGCCTTCAAATTCCTAAATACAAGCTAAAGATAATTTCTAAAATAATA
1 CCTGAGGAGATATTTATAGCCTTCAAATTCCTAAATACAAGCTAAAGATAATTTCTAAAATAATA
*
73423 TCTTAAATCCTATATAAAACATTTAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAAATA
66 TCTTAAATCCTAAATAAAACATTTAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAAATA
73488 AAATAATATTTCAAATAATATCCTAAATCATAATTGAAATACTAAAACCTATTTAAACTAAAATA
131 AAATAATATTTCAAATAATATCCTAAATCATAATTGAAATACTAAAACCTATTTAAACTAAAATA
73553 CTTAAAACAAAGATAAAATATAATTTTTAAAATATTATCCTAAAACTTGAGTTTAATCCAAATCC
196 CTTAAAACAAAGATAAAATATAATTTTTAAAATATTATCCTAAAACTTGAGTTTAATCCAAATCC
73618 GAATTCCAGAAACGTGCGACCAATCCATTCATGCTTCTAGAAACGCTGATTGGATCTTCTAGAAG
261 GAATTCCAGAAACGTGCGACCAATCCATTCATGCTTCTAGAAACGCTGATTGGATCTTCTAGAAG
73683 GTGCTGACGTCAAACCGTGTCATGCCTAGAATCGTTCTCATGTCTCCATCCGTGACCAATTAATA
326 GTGCTGACGTCAAACCGTGTCATGCCTAGAATCGTTCTCATGTCTCCATCCGTGACCAATTAATA
73748 AAAAATTGTAGAATGCACCCGTTTTAATACTAATTCTGGAGAGTAAGACACTGCACGAAAATAAG
391 AAAAATTGTAGAATGCACCCGTTTTAATACTAATTCTGGAGAGTAAGACACTGCACGAAAATAAG
73813 CA
456 CA
73815 TAACATAACA
Statistics
Matches: 456, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
457 456 1.00
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.29
Consensus pattern (457 bp):
CCTGAGGAGATATTTATAGCCTTCAAATTCCTAAATACAAGCTAAAGATAATTTCTAAAATAATA
TCTTAAATCCTAAATAAAACATTTAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAAATA
AAATAATATTTCAAATAATATCCTAAATCATAATTGAAATACTAAAACCTATTTAAACTAAAATA
CTTAAAACAAAGATAAAATATAATTTTTAAAATATTATCCTAAAACTTGAGTTTAATCCAAATCC
GAATTCCAGAAACGTGCGACCAATCCATTCATGCTTCTAGAAACGCTGATTGGATCTTCTAGAAG
GTGCTGACGTCAAACCGTGTCATGCCTAGAATCGTTCTCATGTCTCCATCCGTGACCAATTAATA
AAAAATTGTAGAATGCACCCGTTTTAATACTAATTCTGGAGAGTAAGACACTGCACGAAAATAAG
CA
Found at i:78405 original size:14 final size:14
Alignment explanation
Indices: 78383--78424 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
78373 ATGATAAATT
* *
78383 AACACAAACGAATA
1 AACATAAACGAACA
78397 AACATAAACGAACA
1 AACATAAACGAACA
*
78411 CA-ATAAACGAACA
1 AACATAAACGAACA
78424 A
1 A
78425 CACAAACACA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.64, C:0.21, G:0.07, T:0.07
Consensus pattern (14 bp):
AACATAAACGAACA
Found at i:84056 original size:13 final size:13
Alignment explanation
Indices: 84038--84068 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
84028 AGAGAGGTTG
84038 TTAGCTTAACAGA
1 TTAGCTTAACAGA
84051 TTAGCTTAACAGA
1 TTAGCTTAACAGA
*
84064 GTAGC
1 TTAGC
84069 ATTGTTTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (13 bp):
TTAGCTTAACAGA
Found at i:87725 original size:24 final size:24
Alignment explanation
Indices: 87693--87748 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
87683 TTGGAGTGAT
87693 GGTCGCACGTGATAATGCTTCTAG
1 GGTCGCACGTGATAATGCTTCTAG
87717 GGTCGCACGTGATAATGCTTCTAG
1 GGTCGCACGTGATAATGCTTCTAG
87741 GGTCGCAC
1 GGTCGCAC
87749 CACTTGACTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.20, C:0.23, G:0.30, T:0.27
Consensus pattern (24 bp):
GGTCGCACGTGATAATGCTTCTAG
Done.