Multiple sequence alignment - TraesCS1B01G420100

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1B01G420100 chr1B 100.000 2007 0 0 520 2526 643245621 643247627 0.000000e+00 3707
1 TraesCS1B01G420100 chr1B 100.000 163 0 0 1 163 643245102 643245264 4.080000e-78 302
2 TraesCS1B01G420100 chr1D 89.702 1107 50 28 617 1700 466479732 466480797 0.000000e+00 1354
3 TraesCS1B01G420100 chr1D 91.753 582 26 8 1953 2526 466481214 466481781 0.000000e+00 789
4 TraesCS1B01G420100 chr1D 88.462 208 18 3 1745 1951 466480915 466481117 1.940000e-61 246
5 TraesCS1B01G420100 chr1A 88.989 1108 66 26 617 1691 558590693 558591777 0.000000e+00 1319
6 TraesCS1B01G420100 chr1A 86.479 355 27 8 1812 2165 558592181 558592515 1.100000e-98 370
7 TraesCS1B01G420100 chr1A 97.561 123 3 0 2404 2526 558592894 558593016 7.080000e-51 211


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G420100 chr1B 643245102 643247627 2525 False 2004.500000 3707 100.000000 1 2526 2 chr1B.!!$F1 2525
1 TraesCS1B01G420100 chr1D 466479732 466481781 2049 False 796.333333 1354 89.972333 617 2526 3 chr1D.!!$F1 1909
2 TraesCS1B01G420100 chr1A 558590693 558593016 2323 False 633.333333 1319 91.009667 617 2526 3 chr1A.!!$F1 1909

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
593 594 0.036483 TGCATGCATGGTCTGTACGT 60.036 50.0 27.34 0.0 0.0 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1970 2397 0.041312 ATAAATCGCCGACGCAATGC 60.041 50.0 0.0 0.0 39.84 3.56 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 9.162764 GCTAGGATGAAATACTTTACTTTGTGA 57.837 33.333 0.00 0.00 27.86 3.58
28 29 8.045176 AGGATGAAATACTTTACTTTGTGAGC 57.955 34.615 0.00 0.00 27.86 4.26
29 30 6.961554 GGATGAAATACTTTACTTTGTGAGCG 59.038 38.462 0.00 0.00 0.00 5.03
30 31 7.148474 GGATGAAATACTTTACTTTGTGAGCGA 60.148 37.037 0.00 0.00 0.00 4.93
31 32 7.117241 TGAAATACTTTACTTTGTGAGCGAG 57.883 36.000 0.00 0.00 0.00 5.03
32 33 6.704493 TGAAATACTTTACTTTGTGAGCGAGT 59.296 34.615 0.00 0.00 0.00 4.18
33 34 7.868922 TGAAATACTTTACTTTGTGAGCGAGTA 59.131 33.333 0.00 0.00 0.00 2.59
34 35 7.578169 AATACTTTACTTTGTGAGCGAGTAC 57.422 36.000 0.00 0.00 0.00 2.73
35 36 3.979495 ACTTTACTTTGTGAGCGAGTACG 59.021 43.478 0.00 0.00 42.93 3.67
45 46 4.832767 CGAGTACGCGTGAGTTCA 57.167 55.556 24.59 0.00 0.00 3.18
46 47 2.626648 CGAGTACGCGTGAGTTCAG 58.373 57.895 24.59 2.66 0.00 3.02
47 48 1.396543 CGAGTACGCGTGAGTTCAGC 61.397 60.000 24.59 1.41 0.00 4.26
48 49 0.109689 GAGTACGCGTGAGTTCAGCT 60.110 55.000 24.59 6.57 0.00 4.24
49 50 1.129998 GAGTACGCGTGAGTTCAGCTA 59.870 52.381 24.59 0.00 0.00 3.32
50 51 1.130749 AGTACGCGTGAGTTCAGCTAG 59.869 52.381 24.59 0.00 0.00 3.42
51 52 0.179171 TACGCGTGAGTTCAGCTAGC 60.179 55.000 24.59 6.62 0.00 3.42
52 53 1.153939 CGCGTGAGTTCAGCTAGCT 60.154 57.895 12.68 12.68 0.00 3.32
53 54 0.098905 CGCGTGAGTTCAGCTAGCTA 59.901 55.000 18.86 0.00 0.00 3.32
54 55 1.551145 GCGTGAGTTCAGCTAGCTAC 58.449 55.000 18.86 13.43 0.00 3.58
55 56 1.816370 CGTGAGTTCAGCTAGCTACG 58.184 55.000 18.86 18.37 0.00 3.51
56 57 1.397343 CGTGAGTTCAGCTAGCTACGA 59.603 52.381 24.33 14.00 32.58 3.43
57 58 2.032302 CGTGAGTTCAGCTAGCTACGAT 59.968 50.000 24.33 9.94 32.58 3.73
58 59 3.623863 GTGAGTTCAGCTAGCTACGATC 58.376 50.000 18.86 13.73 0.00 3.69
59 60 3.314080 GTGAGTTCAGCTAGCTACGATCT 59.686 47.826 18.86 15.20 0.00 2.75
60 61 3.562141 TGAGTTCAGCTAGCTACGATCTC 59.438 47.826 23.69 23.69 0.00 2.75
61 62 3.546724 AGTTCAGCTAGCTACGATCTCA 58.453 45.455 18.86 0.00 0.00 3.27
62 63 3.563808 AGTTCAGCTAGCTACGATCTCAG 59.436 47.826 18.86 1.34 0.00 3.35
63 64 3.477210 TCAGCTAGCTACGATCTCAGA 57.523 47.619 18.86 4.07 0.00 3.27
64 65 4.014569 TCAGCTAGCTACGATCTCAGAT 57.985 45.455 18.86 0.00 0.00 2.90
65 66 4.000325 TCAGCTAGCTACGATCTCAGATC 59.000 47.826 18.86 4.35 0.00 2.75
66 67 4.002982 CAGCTAGCTACGATCTCAGATCT 58.997 47.826 18.86 2.87 0.00 2.75
67 68 4.002982 AGCTAGCTACGATCTCAGATCTG 58.997 47.826 17.69 17.07 0.00 2.90
68 69 3.126858 GCTAGCTACGATCTCAGATCTGG 59.873 52.174 22.42 13.07 0.00 3.86
69 70 3.500448 AGCTACGATCTCAGATCTGGA 57.500 47.619 22.42 17.66 0.00 3.86
70 71 4.032960 AGCTACGATCTCAGATCTGGAT 57.967 45.455 22.42 21.14 0.00 3.41
71 72 4.009675 AGCTACGATCTCAGATCTGGATC 58.990 47.826 27.54 27.54 35.67 3.36
73 74 4.458989 GCTACGATCTCAGATCTGGATCTT 59.541 45.833 30.58 27.21 45.31 2.40
74 75 4.852134 ACGATCTCAGATCTGGATCTTG 57.148 45.455 30.58 24.04 45.31 3.02
75 76 3.005684 ACGATCTCAGATCTGGATCTTGC 59.994 47.826 30.58 17.85 45.31 4.01
76 77 3.614630 CGATCTCAGATCTGGATCTTGCC 60.615 52.174 30.58 17.63 45.31 4.52
77 78 2.045524 TCTCAGATCTGGATCTTGCCC 58.954 52.381 22.42 0.00 45.31 5.36
78 79 0.755079 TCAGATCTGGATCTTGCCCG 59.245 55.000 22.42 0.53 45.31 6.13
79 80 0.250209 CAGATCTGGATCTTGCCCGG 60.250 60.000 15.38 0.00 45.31 5.73
80 81 1.599240 GATCTGGATCTTGCCCGGC 60.599 63.158 1.04 1.04 35.04 6.13
81 82 2.049627 GATCTGGATCTTGCCCGGCT 62.050 60.000 11.61 0.00 35.04 5.52
82 83 2.335092 ATCTGGATCTTGCCCGGCTG 62.335 60.000 11.61 3.78 0.00 4.85
83 84 3.329889 TGGATCTTGCCCGGCTGT 61.330 61.111 11.61 0.00 0.00 4.40
84 85 1.971505 CTGGATCTTGCCCGGCTGTA 61.972 60.000 11.61 0.00 0.00 2.74
85 86 1.344953 TGGATCTTGCCCGGCTGTAT 61.345 55.000 11.61 0.68 0.00 2.29
86 87 0.886490 GGATCTTGCCCGGCTGTATG 60.886 60.000 11.61 0.00 0.00 2.39
87 88 0.886490 GATCTTGCCCGGCTGTATGG 60.886 60.000 11.61 0.00 0.00 2.74
93 94 1.292223 CCCGGCTGTATGGGTATCG 59.708 63.158 0.00 0.00 40.76 2.92
94 95 1.374252 CCGGCTGTATGGGTATCGC 60.374 63.158 0.00 0.00 0.00 4.58
95 96 1.733041 CGGCTGTATGGGTATCGCG 60.733 63.158 0.00 0.00 0.00 5.87
96 97 1.366366 GGCTGTATGGGTATCGCGT 59.634 57.895 5.77 0.00 0.00 6.01
97 98 0.249741 GGCTGTATGGGTATCGCGTT 60.250 55.000 5.77 0.00 0.00 4.84
98 99 0.859232 GCTGTATGGGTATCGCGTTG 59.141 55.000 5.77 0.00 0.00 4.10
99 100 1.805120 GCTGTATGGGTATCGCGTTGT 60.805 52.381 5.77 0.00 0.00 3.32
100 101 1.858458 CTGTATGGGTATCGCGTTGTG 59.142 52.381 5.77 0.00 0.00 3.33
101 102 1.205179 TGTATGGGTATCGCGTTGTGT 59.795 47.619 5.77 0.00 0.00 3.72
102 103 2.273557 GTATGGGTATCGCGTTGTGTT 58.726 47.619 5.77 0.00 0.00 3.32
103 104 1.083489 ATGGGTATCGCGTTGTGTTG 58.917 50.000 5.77 0.00 0.00 3.33
104 105 0.951525 TGGGTATCGCGTTGTGTTGG 60.952 55.000 5.77 0.00 0.00 3.77
105 106 0.952010 GGGTATCGCGTTGTGTTGGT 60.952 55.000 5.77 0.00 0.00 3.67
106 107 1.672441 GGGTATCGCGTTGTGTTGGTA 60.672 52.381 5.77 0.00 0.00 3.25
107 108 2.273557 GGTATCGCGTTGTGTTGGTAT 58.726 47.619 5.77 0.00 0.00 2.73
108 109 3.446799 GGTATCGCGTTGTGTTGGTATA 58.553 45.455 5.77 0.00 0.00 1.47
109 110 3.243643 GGTATCGCGTTGTGTTGGTATAC 59.756 47.826 5.77 2.27 0.00 1.47
110 111 2.435533 TCGCGTTGTGTTGGTATACA 57.564 45.000 5.77 0.00 0.00 2.29
111 112 2.962125 TCGCGTTGTGTTGGTATACAT 58.038 42.857 5.77 0.00 0.00 2.29
112 113 4.107363 TCGCGTTGTGTTGGTATACATA 57.893 40.909 5.77 0.00 0.00 2.29
113 114 3.858812 TCGCGTTGTGTTGGTATACATAC 59.141 43.478 5.77 2.63 0.00 2.39
128 129 6.815142 GGTATACATACCCTAGCCATTTAACG 59.185 42.308 5.01 0.00 45.62 3.18
129 130 6.675413 ATACATACCCTAGCCATTTAACGA 57.325 37.500 0.00 0.00 0.00 3.85
130 131 5.362105 ACATACCCTAGCCATTTAACGAA 57.638 39.130 0.00 0.00 0.00 3.85
131 132 5.121105 ACATACCCTAGCCATTTAACGAAC 58.879 41.667 0.00 0.00 0.00 3.95
132 133 2.624636 ACCCTAGCCATTTAACGAACG 58.375 47.619 0.00 0.00 0.00 3.95
133 134 2.234414 ACCCTAGCCATTTAACGAACGA 59.766 45.455 0.14 0.00 0.00 3.85
134 135 3.264104 CCCTAGCCATTTAACGAACGAA 58.736 45.455 0.14 0.00 0.00 3.85
135 136 3.685756 CCCTAGCCATTTAACGAACGAAA 59.314 43.478 0.14 0.00 0.00 3.46
136 137 4.334481 CCCTAGCCATTTAACGAACGAAAT 59.666 41.667 0.14 0.00 0.00 2.17
137 138 5.499047 CCTAGCCATTTAACGAACGAAATC 58.501 41.667 0.14 0.00 0.00 2.17
138 139 5.064198 CCTAGCCATTTAACGAACGAAATCA 59.936 40.000 0.14 0.00 0.00 2.57
139 140 5.365403 AGCCATTTAACGAACGAAATCAA 57.635 34.783 0.14 0.00 0.00 2.57
140 141 5.949735 AGCCATTTAACGAACGAAATCAAT 58.050 33.333 0.14 0.00 0.00 2.57
141 142 5.799936 AGCCATTTAACGAACGAAATCAATG 59.200 36.000 0.14 2.79 0.00 2.82
142 143 5.004345 GCCATTTAACGAACGAAATCAATGG 59.996 40.000 0.14 11.05 41.57 3.16
143 144 5.514914 CCATTTAACGAACGAAATCAATGGG 59.485 40.000 0.14 0.00 37.04 4.00
144 145 5.692613 TTTAACGAACGAAATCAATGGGT 57.307 34.783 0.14 0.00 0.00 4.51
145 146 3.824414 AACGAACGAAATCAATGGGTC 57.176 42.857 0.14 0.00 0.00 4.46
146 147 2.773487 ACGAACGAAATCAATGGGTCA 58.227 42.857 0.14 0.00 0.00 4.02
147 148 3.343617 ACGAACGAAATCAATGGGTCAT 58.656 40.909 0.14 0.00 0.00 3.06
148 149 3.756434 ACGAACGAAATCAATGGGTCATT 59.244 39.130 0.14 0.00 34.04 2.57
149 150 4.938832 ACGAACGAAATCAATGGGTCATTA 59.061 37.500 0.14 0.00 32.35 1.90
150 151 5.064707 ACGAACGAAATCAATGGGTCATTAG 59.935 40.000 0.14 0.00 32.35 1.73
151 152 4.900635 ACGAAATCAATGGGTCATTAGC 57.099 40.909 0.00 0.00 32.35 3.09
152 153 3.312421 ACGAAATCAATGGGTCATTAGCG 59.688 43.478 0.00 0.00 32.35 4.26
153 154 3.312421 CGAAATCAATGGGTCATTAGCGT 59.688 43.478 0.00 0.00 32.35 5.07
154 155 4.552767 CGAAATCAATGGGTCATTAGCGTC 60.553 45.833 0.00 0.00 32.35 5.19
155 156 3.558931 ATCAATGGGTCATTAGCGTCA 57.441 42.857 0.00 0.00 32.35 4.35
156 157 2.627945 TCAATGGGTCATTAGCGTCAC 58.372 47.619 0.00 0.00 32.35 3.67
157 158 2.027653 TCAATGGGTCATTAGCGTCACA 60.028 45.455 0.00 0.00 32.35 3.58
158 159 2.024176 ATGGGTCATTAGCGTCACAC 57.976 50.000 0.00 0.00 0.00 3.82
159 160 0.036765 TGGGTCATTAGCGTCACACC 60.037 55.000 0.00 0.00 0.00 4.16
160 161 0.036765 GGGTCATTAGCGTCACACCA 60.037 55.000 0.00 0.00 0.00 4.17
161 162 1.406887 GGGTCATTAGCGTCACACCAT 60.407 52.381 0.00 0.00 0.00 3.55
162 163 1.933853 GGTCATTAGCGTCACACCATC 59.066 52.381 0.00 0.00 0.00 3.51
541 542 5.733620 ATAGTCCTCTCCTCGAGTACTAG 57.266 47.826 12.31 0.00 38.11 2.57
542 543 3.377573 AGTCCTCTCCTCGAGTACTAGT 58.622 50.000 12.31 0.00 38.11 2.57
543 544 4.545678 AGTCCTCTCCTCGAGTACTAGTA 58.454 47.826 12.31 0.00 38.11 1.82
544 545 4.342092 AGTCCTCTCCTCGAGTACTAGTAC 59.658 50.000 23.03 23.03 38.11 2.73
546 547 5.534654 GTCCTCTCCTCGAGTACTAGTACTA 59.465 48.000 30.80 17.99 45.63 1.82
547 548 5.534654 TCCTCTCCTCGAGTACTAGTACTAC 59.465 48.000 30.80 22.51 45.63 2.73
548 549 5.431420 TCTCCTCGAGTACTAGTACTACG 57.569 47.826 30.80 29.91 45.63 3.51
549 550 4.884744 TCTCCTCGAGTACTAGTACTACGT 59.115 45.833 30.80 13.17 45.63 3.57
550 551 5.008217 TCTCCTCGAGTACTAGTACTACGTC 59.992 48.000 30.80 19.23 45.63 4.34
551 552 3.971871 CCTCGAGTACTAGTACTACGTCG 59.028 52.174 30.80 27.59 45.63 5.12
552 553 3.364062 TCGAGTACTAGTACTACGTCGC 58.636 50.000 30.80 18.13 45.63 5.19
553 554 2.150238 CGAGTACTAGTACTACGTCGCG 59.850 54.545 30.80 24.27 45.63 5.87
554 555 3.109619 GAGTACTAGTACTACGTCGCGT 58.890 50.000 30.80 10.03 45.63 6.01
555 556 2.854777 AGTACTAGTACTACGTCGCGTG 59.145 50.000 29.96 2.22 43.98 5.34
556 557 0.371645 ACTAGTACTACGTCGCGTGC 59.628 55.000 5.77 0.00 41.39 5.34
557 558 0.315706 CTAGTACTACGTCGCGTGCC 60.316 60.000 5.77 0.00 41.39 5.01
558 559 1.018752 TAGTACTACGTCGCGTGCCA 61.019 55.000 5.77 0.00 41.39 4.92
559 560 2.148365 GTACTACGTCGCGTGCCAC 61.148 63.158 5.77 0.00 41.39 5.01
560 561 3.649896 TACTACGTCGCGTGCCACG 62.650 63.158 13.95 13.95 45.88 4.94
588 589 2.795973 CCGTGCATGCATGGTCTG 59.204 61.111 39.68 21.56 45.48 3.51
589 590 2.042259 CCGTGCATGCATGGTCTGT 61.042 57.895 39.68 0.00 45.48 3.41
590 591 0.744057 CCGTGCATGCATGGTCTGTA 60.744 55.000 39.68 7.62 45.48 2.74
591 592 0.374758 CGTGCATGCATGGTCTGTAC 59.625 55.000 28.79 11.73 0.00 2.90
592 593 0.374758 GTGCATGCATGGTCTGTACG 59.625 55.000 25.64 0.00 0.00 3.67
593 594 0.036483 TGCATGCATGGTCTGTACGT 60.036 50.000 27.34 0.00 0.00 3.57
594 595 0.374758 GCATGCATGGTCTGTACGTG 59.625 55.000 27.34 0.00 0.00 4.49
595 596 0.374758 CATGCATGGTCTGTACGTGC 59.625 55.000 19.40 0.00 38.00 5.34
596 597 0.036483 ATGCATGGTCTGTACGTGCA 60.036 50.000 18.13 18.13 45.72 4.57
597 598 0.036483 TGCATGGTCTGTACGTGCAT 60.036 50.000 6.84 0.00 40.67 3.96
598 599 0.374758 GCATGGTCTGTACGTGCATG 59.625 55.000 6.84 3.82 37.66 4.06
599 600 0.374758 CATGGTCTGTACGTGCATGC 59.625 55.000 11.82 11.82 0.00 4.06
600 601 0.036483 ATGGTCTGTACGTGCATGCA 60.036 50.000 18.46 18.46 0.00 3.96
601 602 0.250081 TGGTCTGTACGTGCATGCAA 60.250 50.000 24.58 3.69 0.00 4.08
602 603 0.165944 GGTCTGTACGTGCATGCAAC 59.834 55.000 24.58 17.92 0.00 4.17
603 604 0.865111 GTCTGTACGTGCATGCAACA 59.135 50.000 24.58 21.63 0.00 3.33
604 605 1.464608 GTCTGTACGTGCATGCAACAT 59.535 47.619 24.58 13.29 0.00 2.71
605 606 1.731709 TCTGTACGTGCATGCAACATC 59.268 47.619 24.58 13.88 0.00 3.06
606 607 0.441921 TGTACGTGCATGCAACATCG 59.558 50.000 24.58 23.22 0.00 3.84
607 608 0.857311 GTACGTGCATGCAACATCGC 60.857 55.000 24.58 7.89 0.00 4.58
608 609 1.976478 TACGTGCATGCAACATCGCC 61.976 55.000 24.58 7.08 0.00 5.54
609 610 2.567569 GTGCATGCAACATCGCCA 59.432 55.556 24.58 0.00 0.00 5.69
610 611 1.802715 GTGCATGCAACATCGCCAC 60.803 57.895 24.58 2.21 0.00 5.01
611 612 2.202650 GCATGCAACATCGCCACC 60.203 61.111 14.21 0.00 0.00 4.61
612 613 2.703798 GCATGCAACATCGCCACCT 61.704 57.895 14.21 0.00 0.00 4.00
613 614 1.430632 CATGCAACATCGCCACCTC 59.569 57.895 0.00 0.00 0.00 3.85
614 615 1.750399 ATGCAACATCGCCACCTCC 60.750 57.895 0.00 0.00 0.00 4.30
615 616 3.499737 GCAACATCGCCACCTCCG 61.500 66.667 0.00 0.00 0.00 4.63
619 620 0.179084 AACATCGCCACCTCCGTATG 60.179 55.000 0.00 0.00 0.00 2.39
636 637 7.934120 CCTCCGTATGGATCTCTCTTTAATTTT 59.066 37.037 3.55 0.00 45.33 1.82
638 639 7.652105 TCCGTATGGATCTCTCTTTAATTTTCG 59.348 37.037 0.00 0.00 40.17 3.46
640 641 8.480853 CGTATGGATCTCTCTTTAATTTTCGTC 58.519 37.037 0.00 0.00 0.00 4.20
710 711 1.153369 CGTGGGCCCACAGTATCTG 60.153 63.158 45.40 28.22 46.47 2.90
722 723 3.248841 CACAGTATCTGTACGAGCGATCT 59.751 47.826 0.00 0.00 43.43 2.75
724 725 5.050295 CACAGTATCTGTACGAGCGATCTTA 60.050 44.000 0.00 0.00 43.43 2.10
727 728 5.932883 AGTATCTGTACGAGCGATCTTATCA 59.067 40.000 0.00 0.00 35.92 2.15
733 734 1.340657 GAGCGATCTTATCAGCGGCG 61.341 60.000 0.51 0.51 35.20 6.46
735 736 1.372251 CGATCTTATCAGCGGCGCT 60.372 57.895 31.35 31.35 40.77 5.92
737 738 1.005630 ATCTTATCAGCGGCGCTCC 60.006 57.895 34.22 2.36 36.40 4.70
788 806 4.082523 ATGTCACCTCGCCACCGG 62.083 66.667 0.00 0.00 34.56 5.28
807 825 1.349357 GGGTCAGGGAATCAGGATAGC 59.651 57.143 0.00 0.00 0.00 2.97
850 868 2.530406 CCCTCCCTATGGGCCTCC 60.530 72.222 4.53 0.00 43.94 4.30
928 947 2.231215 ACAGCATCCACGATCTAAGC 57.769 50.000 0.00 0.00 0.00 3.09
981 1000 1.141019 ACGCCCACTGTATACGCAG 59.859 57.895 0.00 0.00 41.92 5.18
983 1002 0.870307 CGCCCACTGTATACGCAGTC 60.870 60.000 0.00 0.00 46.81 3.51
984 1003 0.870307 GCCCACTGTATACGCAGTCG 60.870 60.000 0.00 0.00 46.81 4.18
985 1004 0.870307 CCCACTGTATACGCAGTCGC 60.870 60.000 0.00 0.00 46.81 5.19
1143 1162 8.413229 AGGTACTTTACTTTACACACGACTTAA 58.587 33.333 0.00 0.00 27.25 1.85
1156 1175 8.766000 ACACACGACTTAATAAACATATGACA 57.234 30.769 10.38 0.00 0.00 3.58
1159 1178 8.653338 ACACGACTTAATAAACATATGACACAC 58.347 33.333 10.38 0.00 0.00 3.82
1160 1179 8.114290 CACGACTTAATAAACATATGACACACC 58.886 37.037 10.38 0.00 0.00 4.16
1161 1180 7.820386 ACGACTTAATAAACATATGACACACCA 59.180 33.333 10.38 0.00 0.00 4.17
1162 1181 8.826710 CGACTTAATAAACATATGACACACCAT 58.173 33.333 10.38 0.00 0.00 3.55
1163 1182 9.935682 GACTTAATAAACATATGACACACCATG 57.064 33.333 10.38 0.00 0.00 3.66
1164 1183 8.405531 ACTTAATAAACATATGACACACCATGC 58.594 33.333 10.38 0.00 0.00 4.06
1165 1184 6.772360 AATAAACATATGACACACCATGCA 57.228 33.333 10.38 0.00 0.00 3.96
1166 1185 4.439305 AAACATATGACACACCATGCAC 57.561 40.909 10.38 0.00 0.00 4.57
1167 1186 2.009051 ACATATGACACACCATGCACG 58.991 47.619 10.38 0.00 0.00 5.34
1168 1187 1.016627 ATATGACACACCATGCACGC 58.983 50.000 0.00 0.00 0.00 5.34
1169 1188 0.321122 TATGACACACCATGCACGCA 60.321 50.000 0.00 0.00 0.00 5.24
1170 1189 1.855213 ATGACACACCATGCACGCAC 61.855 55.000 0.00 0.00 0.00 5.34
1206 1227 4.415150 ACCAGCTCCGGCACATGG 62.415 66.667 11.77 11.77 41.70 3.66
1527 1548 0.652592 CCACGCGGCAAGATCTAAAG 59.347 55.000 12.47 0.00 0.00 1.85
1550 1573 1.475682 CTGCAATCAAGGCCTTCTTCC 59.524 52.381 17.29 2.96 32.41 3.46
1554 1577 1.978361 ATCAAGGCCTTCTTCCTCCT 58.022 50.000 17.29 0.00 32.41 3.69
1555 1578 1.280457 TCAAGGCCTTCTTCCTCCTC 58.720 55.000 17.29 0.00 32.41 3.71
1558 1581 2.736826 GGCCTTCTTCCTCCTCCCG 61.737 68.421 0.00 0.00 0.00 5.14
1559 1582 2.904131 CCTTCTTCCTCCTCCCGC 59.096 66.667 0.00 0.00 0.00 6.13
1590 1613 2.205074 GCTTGTGTACCATGGATCTCG 58.795 52.381 21.47 1.35 0.00 4.04
1645 1686 9.778741 TCTGTTGATACTTGATCTTTGTACTTT 57.221 29.630 0.00 0.00 35.37 2.66
1723 1799 6.640518 TGGTTTTTGTACCATGTTTTTGCTA 58.359 32.000 0.00 0.00 43.14 3.49
1831 2163 1.065102 CACGTACATACTCCCTCCGTG 59.935 57.143 0.00 0.00 38.29 4.94
1832 2164 0.030369 CGTACATACTCCCTCCGTGC 59.970 60.000 0.00 0.00 0.00 5.34
1833 2165 0.030369 GTACATACTCCCTCCGTGCG 59.970 60.000 0.00 0.00 0.00 5.34
1834 2166 0.394762 TACATACTCCCTCCGTGCGT 60.395 55.000 0.00 0.00 0.00 5.24
1837 2169 2.881539 ATACTCCCTCCGTGCGTCGA 62.882 60.000 0.00 0.00 42.86 4.20
1845 2177 0.386352 TCCGTGCGTCGAAACTACTG 60.386 55.000 0.00 0.00 42.86 2.74
1853 2185 3.185797 GCGTCGAAACTACTGTCCATTTT 59.814 43.478 0.00 0.00 0.00 1.82
1871 2203 6.589523 TCCATTTTTGCGACAAATAATTCAGG 59.410 34.615 5.97 7.01 0.00 3.86
1874 2206 4.695217 TTGCGACAAATAATTCAGGACC 57.305 40.909 0.00 0.00 0.00 4.46
1879 2211 3.877508 GACAAATAATTCAGGACCGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
1881 2213 4.130118 CAAATAATTCAGGACCGAGGGAG 58.870 47.826 0.00 0.00 0.00 4.30
1884 2216 1.777941 ATTCAGGACCGAGGGAGTAC 58.222 55.000 0.00 0.00 0.00 2.73
1898 2230 5.402997 AGGGAGTACTTACTAACAGTTGC 57.597 43.478 0.00 0.00 36.50 4.17
1928 2260 3.735591 CCGGCGGGAAATTAGATCTTAA 58.264 45.455 20.56 0.00 34.06 1.85
1930 2262 4.124238 CGGCGGGAAATTAGATCTTAACA 58.876 43.478 0.00 0.00 0.00 2.41
1981 2408 0.377905 TCAATCATGCATTGCGTCGG 59.622 50.000 0.00 0.00 41.72 4.79
2022 2450 7.782049 TCCAACTGACATTATAACACTCCTAG 58.218 38.462 0.00 0.00 0.00 3.02
2038 2466 4.090090 CTCCTAGAAGACACTGGAAAGGA 58.910 47.826 0.00 0.00 0.00 3.36
2051 2479 4.935808 ACTGGAAAGGATACGCTTAACAAG 59.064 41.667 0.00 0.00 46.39 3.16
2130 2562 6.404734 GGGCTAGAAAACTACATGTCCATTTG 60.405 42.308 0.00 0.00 0.00 2.32
2140 2572 2.655090 TGTCCATTTGTCAGGCTCAA 57.345 45.000 0.00 0.00 0.00 3.02
2190 2622 0.192566 TGTAGAACAGGGGGTCCACT 59.807 55.000 0.00 0.00 34.83 4.00
2218 2650 1.442526 GCACATCATCTTGGCCTCCG 61.443 60.000 3.32 0.00 0.00 4.63
2219 2651 1.153086 ACATCATCTTGGCCTCCGC 60.153 57.895 3.32 0.00 0.00 5.54
2245 2677 0.606944 TTTCCATTGGGGGTCGAACG 60.607 55.000 2.09 0.00 37.22 3.95
2265 2697 2.216898 GCAATGGAGATACAGACAGGC 58.783 52.381 0.00 0.00 0.00 4.85
2270 2702 0.029567 GAGATACAGACAGGCGTCCG 59.970 60.000 5.98 0.00 43.73 4.79
2338 2770 8.400947 ACAATGCTCTGAACACATATTTACATC 58.599 33.333 0.00 0.00 0.00 3.06
2344 2776 9.941664 CTCTGAACACATATTTACATCCATTTC 57.058 33.333 0.00 0.00 0.00 2.17
2345 2777 9.460019 TCTGAACACATATTTACATCCATTTCA 57.540 29.630 0.00 0.00 0.00 2.69
2346 2778 9.507280 CTGAACACATATTTACATCCATTTCAC 57.493 33.333 0.00 0.00 0.00 3.18
2510 3082 0.911769 TTGGTGCCGATCTTGGAGAT 59.088 50.000 0.00 0.00 37.73 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.162764 TCACAAAGTAAAGTATTTCATCCTAGC 57.837 33.333 0.00 0.00 40.09 3.42
2 3 9.162764 GCTCACAAAGTAAAGTATTTCATCCTA 57.837 33.333 0.00 0.00 40.09 2.94
3 4 7.148407 CGCTCACAAAGTAAAGTATTTCATCCT 60.148 37.037 0.00 0.00 40.09 3.24
4 5 6.961554 CGCTCACAAAGTAAAGTATTTCATCC 59.038 38.462 0.00 0.00 40.09 3.51
5 6 7.739295 TCGCTCACAAAGTAAAGTATTTCATC 58.261 34.615 0.00 0.00 40.09 2.92
6 7 7.387948 ACTCGCTCACAAAGTAAAGTATTTCAT 59.612 33.333 0.00 0.00 40.09 2.57
7 8 6.704493 ACTCGCTCACAAAGTAAAGTATTTCA 59.296 34.615 0.00 0.00 40.09 2.69
8 9 7.118422 ACTCGCTCACAAAGTAAAGTATTTC 57.882 36.000 0.00 0.00 40.09 2.17
9 10 7.148853 CGTACTCGCTCACAAAGTAAAGTATTT 60.149 37.037 0.00 0.00 43.42 1.40
10 11 6.307318 CGTACTCGCTCACAAAGTAAAGTATT 59.693 38.462 0.00 0.00 0.00 1.89
11 12 5.798934 CGTACTCGCTCACAAAGTAAAGTAT 59.201 40.000 0.00 0.00 0.00 2.12
12 13 5.149273 CGTACTCGCTCACAAAGTAAAGTA 58.851 41.667 0.00 0.00 0.00 2.24
13 14 3.979495 CGTACTCGCTCACAAAGTAAAGT 59.021 43.478 0.00 0.00 0.00 2.66
14 15 4.547956 CGTACTCGCTCACAAAGTAAAG 57.452 45.455 0.00 0.00 0.00 1.85
28 29 1.396543 GCTGAACTCACGCGTACTCG 61.397 60.000 13.44 3.23 40.37 4.18
29 30 0.109689 AGCTGAACTCACGCGTACTC 60.110 55.000 13.44 6.77 0.00 2.59
30 31 1.130749 CTAGCTGAACTCACGCGTACT 59.869 52.381 13.44 2.00 0.00 2.73
31 32 1.536149 CTAGCTGAACTCACGCGTAC 58.464 55.000 13.44 1.88 0.00 3.67
32 33 0.179171 GCTAGCTGAACTCACGCGTA 60.179 55.000 13.44 0.00 0.00 4.42
33 34 1.444553 GCTAGCTGAACTCACGCGT 60.445 57.895 5.58 5.58 0.00 6.01
34 35 0.098905 TAGCTAGCTGAACTCACGCG 59.901 55.000 27.68 3.53 0.00 6.01
35 36 1.551145 GTAGCTAGCTGAACTCACGC 58.449 55.000 27.68 2.48 0.00 5.34
36 37 1.397343 TCGTAGCTAGCTGAACTCACG 59.603 52.381 27.68 25.08 0.00 4.35
37 38 3.314080 AGATCGTAGCTAGCTGAACTCAC 59.686 47.826 27.68 14.75 0.00 3.51
38 39 3.546724 AGATCGTAGCTAGCTGAACTCA 58.453 45.455 27.68 7.92 0.00 3.41
39 40 3.562141 TGAGATCGTAGCTAGCTGAACTC 59.438 47.826 27.68 25.50 0.00 3.01
40 41 3.546724 TGAGATCGTAGCTAGCTGAACT 58.453 45.455 27.68 19.29 0.00 3.01
41 42 3.562141 TCTGAGATCGTAGCTAGCTGAAC 59.438 47.826 27.68 16.99 0.00 3.18
42 43 3.809905 TCTGAGATCGTAGCTAGCTGAA 58.190 45.455 27.68 12.40 0.00 3.02
43 44 3.477210 TCTGAGATCGTAGCTAGCTGA 57.523 47.619 27.68 17.01 0.00 4.26
44 45 4.002982 AGATCTGAGATCGTAGCTAGCTG 58.997 47.826 27.68 11.72 0.00 4.24
45 46 4.002982 CAGATCTGAGATCGTAGCTAGCT 58.997 47.826 23.12 23.12 0.00 3.32
46 47 3.126858 CCAGATCTGAGATCGTAGCTAGC 59.873 52.174 24.62 6.62 0.00 3.42
47 48 4.574892 TCCAGATCTGAGATCGTAGCTAG 58.425 47.826 24.62 2.45 0.00 3.42
48 49 4.625607 TCCAGATCTGAGATCGTAGCTA 57.374 45.455 24.62 0.00 0.00 3.32
49 50 3.500448 TCCAGATCTGAGATCGTAGCT 57.500 47.619 24.62 0.00 0.00 3.32
50 51 4.009675 AGATCCAGATCTGAGATCGTAGC 58.990 47.826 29.10 17.24 45.77 3.58
51 52 5.619757 GCAAGATCCAGATCTGAGATCGTAG 60.620 48.000 29.10 25.15 46.75 3.51
52 53 4.217334 GCAAGATCCAGATCTGAGATCGTA 59.783 45.833 29.10 6.82 46.75 3.43
53 54 3.005684 GCAAGATCCAGATCTGAGATCGT 59.994 47.826 29.10 26.46 46.75 3.73
54 55 3.577667 GCAAGATCCAGATCTGAGATCG 58.422 50.000 29.10 22.58 46.75 3.69
55 56 3.306919 GGGCAAGATCCAGATCTGAGATC 60.307 52.174 28.83 28.83 46.75 2.75
56 57 2.638855 GGGCAAGATCCAGATCTGAGAT 59.361 50.000 24.62 22.00 46.75 2.75
57 58 2.045524 GGGCAAGATCCAGATCTGAGA 58.954 52.381 24.62 18.50 46.75 3.27
58 59 1.270199 CGGGCAAGATCCAGATCTGAG 60.270 57.143 24.62 13.85 46.75 3.35
59 60 0.755079 CGGGCAAGATCCAGATCTGA 59.245 55.000 24.62 10.55 46.75 3.27
60 61 0.250209 CCGGGCAAGATCCAGATCTG 60.250 60.000 16.24 16.24 46.75 2.90
62 63 1.599240 GCCGGGCAAGATCCAGATC 60.599 63.158 15.62 0.00 38.09 2.75
63 64 2.074948 AGCCGGGCAAGATCCAGAT 61.075 57.895 23.09 0.00 0.00 2.90
64 65 2.688666 AGCCGGGCAAGATCCAGA 60.689 61.111 23.09 0.00 0.00 3.86
65 66 1.971505 TACAGCCGGGCAAGATCCAG 61.972 60.000 23.09 2.76 0.00 3.86
66 67 1.344953 ATACAGCCGGGCAAGATCCA 61.345 55.000 23.09 0.00 0.00 3.41
67 68 0.886490 CATACAGCCGGGCAAGATCC 60.886 60.000 23.09 0.00 0.00 3.36
68 69 0.886490 CCATACAGCCGGGCAAGATC 60.886 60.000 23.09 0.00 0.00 2.75
69 70 1.149174 CCATACAGCCGGGCAAGAT 59.851 57.895 23.09 7.77 0.00 2.40
70 71 2.589540 CCATACAGCCGGGCAAGA 59.410 61.111 23.09 5.43 0.00 3.02
71 72 2.516930 CCCATACAGCCGGGCAAG 60.517 66.667 23.09 15.66 35.09 4.01
76 77 1.374252 GCGATACCCATACAGCCGG 60.374 63.158 0.00 0.00 0.00 6.13
77 78 1.733041 CGCGATACCCATACAGCCG 60.733 63.158 0.00 0.00 0.00 5.52
78 79 0.249741 AACGCGATACCCATACAGCC 60.250 55.000 15.93 0.00 0.00 4.85
79 80 0.859232 CAACGCGATACCCATACAGC 59.141 55.000 15.93 0.00 0.00 4.40
80 81 1.858458 CACAACGCGATACCCATACAG 59.142 52.381 15.93 0.00 0.00 2.74
81 82 1.205179 ACACAACGCGATACCCATACA 59.795 47.619 15.93 0.00 0.00 2.29
82 83 1.930567 ACACAACGCGATACCCATAC 58.069 50.000 15.93 0.00 0.00 2.39
83 84 2.272678 CAACACAACGCGATACCCATA 58.727 47.619 15.93 0.00 0.00 2.74
84 85 1.083489 CAACACAACGCGATACCCAT 58.917 50.000 15.93 0.00 0.00 4.00
85 86 0.951525 CCAACACAACGCGATACCCA 60.952 55.000 15.93 0.00 0.00 4.51
86 87 0.952010 ACCAACACAACGCGATACCC 60.952 55.000 15.93 0.00 0.00 3.69
87 88 1.712401 TACCAACACAACGCGATACC 58.288 50.000 15.93 0.00 0.00 2.73
88 89 3.858812 TGTATACCAACACAACGCGATAC 59.141 43.478 15.93 6.72 0.00 2.24
89 90 4.107363 TGTATACCAACACAACGCGATA 57.893 40.909 15.93 0.00 0.00 2.92
90 91 2.962125 TGTATACCAACACAACGCGAT 58.038 42.857 15.93 0.00 0.00 4.58
91 92 2.435533 TGTATACCAACACAACGCGA 57.564 45.000 15.93 0.00 0.00 5.87
92 93 4.172796 GTATGTATACCAACACAACGCG 57.827 45.455 3.53 3.53 30.75 6.01
104 105 7.605449 TCGTTAAATGGCTAGGGTATGTATAC 58.395 38.462 0.00 0.00 0.00 1.47
105 106 7.779754 TCGTTAAATGGCTAGGGTATGTATA 57.220 36.000 0.00 0.00 0.00 1.47
106 107 6.675413 TCGTTAAATGGCTAGGGTATGTAT 57.325 37.500 0.00 0.00 0.00 2.29
107 108 6.282930 GTTCGTTAAATGGCTAGGGTATGTA 58.717 40.000 0.00 0.00 0.00 2.29
108 109 5.121105 GTTCGTTAAATGGCTAGGGTATGT 58.879 41.667 0.00 0.00 0.00 2.29
109 110 4.210537 CGTTCGTTAAATGGCTAGGGTATG 59.789 45.833 0.00 0.00 0.00 2.39
110 111 4.099881 TCGTTCGTTAAATGGCTAGGGTAT 59.900 41.667 0.00 0.00 0.00 2.73
111 112 3.446873 TCGTTCGTTAAATGGCTAGGGTA 59.553 43.478 0.00 0.00 0.00 3.69
112 113 2.234414 TCGTTCGTTAAATGGCTAGGGT 59.766 45.455 0.00 0.00 0.00 4.34
113 114 2.896168 TCGTTCGTTAAATGGCTAGGG 58.104 47.619 0.00 0.00 0.00 3.53
114 115 4.932268 TTTCGTTCGTTAAATGGCTAGG 57.068 40.909 0.00 0.00 0.00 3.02
115 116 6.102006 TGATTTCGTTCGTTAAATGGCTAG 57.898 37.500 0.00 0.00 0.00 3.42
116 117 6.483385 TTGATTTCGTTCGTTAAATGGCTA 57.517 33.333 0.00 0.00 0.00 3.93
117 118 5.365403 TTGATTTCGTTCGTTAAATGGCT 57.635 34.783 0.00 0.00 0.00 4.75
118 119 5.004345 CCATTGATTTCGTTCGTTAAATGGC 59.996 40.000 0.00 0.00 37.19 4.40
119 120 5.514914 CCCATTGATTTCGTTCGTTAAATGG 59.485 40.000 0.00 0.00 41.51 3.16
120 121 6.090129 ACCCATTGATTTCGTTCGTTAAATG 58.910 36.000 0.00 0.00 0.00 2.32
121 122 6.072397 TGACCCATTGATTTCGTTCGTTAAAT 60.072 34.615 0.00 0.00 0.00 1.40
122 123 5.238868 TGACCCATTGATTTCGTTCGTTAAA 59.761 36.000 0.00 0.00 0.00 1.52
123 124 4.755629 TGACCCATTGATTTCGTTCGTTAA 59.244 37.500 0.00 0.00 0.00 2.01
124 125 4.316645 TGACCCATTGATTTCGTTCGTTA 58.683 39.130 0.00 0.00 0.00 3.18
125 126 3.142951 TGACCCATTGATTTCGTTCGTT 58.857 40.909 0.00 0.00 0.00 3.85
126 127 2.773487 TGACCCATTGATTTCGTTCGT 58.227 42.857 0.00 0.00 0.00 3.85
127 128 4.355543 AATGACCCATTGATTTCGTTCG 57.644 40.909 0.00 0.00 32.39 3.95
128 129 5.273944 GCTAATGACCCATTGATTTCGTTC 58.726 41.667 2.71 0.00 35.54 3.95
129 130 4.201910 CGCTAATGACCCATTGATTTCGTT 60.202 41.667 2.71 0.00 35.54 3.85
130 131 3.312421 CGCTAATGACCCATTGATTTCGT 59.688 43.478 2.71 0.00 35.54 3.85
131 132 3.312421 ACGCTAATGACCCATTGATTTCG 59.688 43.478 2.71 2.42 35.54 3.46
132 133 4.335315 TGACGCTAATGACCCATTGATTTC 59.665 41.667 2.71 0.00 35.54 2.17
133 134 4.096382 GTGACGCTAATGACCCATTGATTT 59.904 41.667 2.71 0.00 35.54 2.17
134 135 3.627577 GTGACGCTAATGACCCATTGATT 59.372 43.478 2.71 0.00 35.54 2.57
135 136 3.206150 GTGACGCTAATGACCCATTGAT 58.794 45.455 2.71 0.00 35.54 2.57
136 137 2.027653 TGTGACGCTAATGACCCATTGA 60.028 45.455 2.71 0.00 35.54 2.57
137 138 2.095853 GTGTGACGCTAATGACCCATTG 59.904 50.000 2.71 0.00 35.54 2.82
138 139 2.356135 GTGTGACGCTAATGACCCATT 58.644 47.619 0.00 0.00 37.80 3.16
139 140 1.406887 GGTGTGACGCTAATGACCCAT 60.407 52.381 0.00 0.00 0.00 4.00
140 141 0.036765 GGTGTGACGCTAATGACCCA 60.037 55.000 0.00 0.00 0.00 4.51
141 142 0.036765 TGGTGTGACGCTAATGACCC 60.037 55.000 0.00 0.00 0.00 4.46
142 143 1.933853 GATGGTGTGACGCTAATGACC 59.066 52.381 0.00 0.00 0.00 4.02
523 524 9.956885 ACGTAGTACTAGTACTCGAGGAGAGGA 62.957 48.148 35.23 19.35 46.72 3.71
524 525 7.902431 ACGTAGTACTAGTACTCGAGGAGAGG 61.902 50.000 35.23 25.65 46.72 3.69
526 527 4.884744 ACGTAGTACTAGTACTCGAGGAGA 59.115 45.833 35.23 20.91 44.58 3.71
527 528 5.181690 ACGTAGTACTAGTACTCGAGGAG 57.818 47.826 35.23 24.84 44.58 3.69
568 569 1.099295 AGACCATGCATGCACGGATG 61.099 55.000 37.40 23.90 32.98 3.51
569 570 1.099295 CAGACCATGCATGCACGGAT 61.099 55.000 37.40 22.55 32.98 4.18
570 571 1.746239 CAGACCATGCATGCACGGA 60.746 57.895 37.40 9.11 32.98 4.69
571 572 0.744057 TACAGACCATGCATGCACGG 60.744 55.000 30.19 30.19 35.12 4.94
572 573 0.374758 GTACAGACCATGCATGCACG 59.625 55.000 25.37 16.18 0.00 5.34
573 574 0.374758 CGTACAGACCATGCATGCAC 59.625 55.000 25.37 15.85 0.00 4.57
574 575 0.036483 ACGTACAGACCATGCATGCA 60.036 50.000 25.04 25.04 0.00 3.96
575 576 0.374758 CACGTACAGACCATGCATGC 59.625 55.000 21.69 11.82 0.00 4.06
576 577 0.374758 GCACGTACAGACCATGCATG 59.625 55.000 20.19 20.19 35.29 4.06
577 578 0.036483 TGCACGTACAGACCATGCAT 60.036 50.000 0.00 0.00 38.58 3.96
578 579 0.036483 ATGCACGTACAGACCATGCA 60.036 50.000 0.00 0.00 44.19 3.96
579 580 0.374758 CATGCACGTACAGACCATGC 59.625 55.000 0.00 0.00 35.61 4.06
580 581 0.374758 GCATGCACGTACAGACCATG 59.625 55.000 14.21 1.42 36.08 3.66
581 582 0.036483 TGCATGCACGTACAGACCAT 60.036 50.000 18.46 0.00 0.00 3.55
582 583 0.250081 TTGCATGCACGTACAGACCA 60.250 50.000 22.58 0.00 0.00 4.02
583 584 0.165944 GTTGCATGCACGTACAGACC 59.834 55.000 22.58 0.00 0.00 3.85
584 585 0.865111 TGTTGCATGCACGTACAGAC 59.135 50.000 22.58 14.65 0.00 3.51
585 586 1.731709 GATGTTGCATGCACGTACAGA 59.268 47.619 22.58 3.91 0.00 3.41
586 587 1.527591 CGATGTTGCATGCACGTACAG 60.528 52.381 22.58 7.81 0.00 2.74
587 588 0.441921 CGATGTTGCATGCACGTACA 59.558 50.000 22.58 22.40 0.00 2.90
588 589 0.857311 GCGATGTTGCATGCACGTAC 60.857 55.000 22.58 17.01 34.15 3.67
589 590 1.423450 GCGATGTTGCATGCACGTA 59.577 52.632 22.58 10.14 34.15 3.57
590 591 2.176546 GCGATGTTGCATGCACGT 59.823 55.556 22.58 16.59 34.15 4.49
591 592 2.577644 GGCGATGTTGCATGCACG 60.578 61.111 22.58 21.27 36.28 5.34
592 593 1.802715 GTGGCGATGTTGCATGCAC 60.803 57.895 22.58 16.00 36.28 4.57
593 594 2.567569 GTGGCGATGTTGCATGCA 59.432 55.556 18.46 18.46 36.28 3.96
594 595 2.202650 GGTGGCGATGTTGCATGC 60.203 61.111 11.82 11.82 36.28 4.06
595 596 1.430632 GAGGTGGCGATGTTGCATG 59.569 57.895 0.00 0.00 36.28 4.06
596 597 1.750399 GGAGGTGGCGATGTTGCAT 60.750 57.895 0.00 0.00 36.28 3.96
597 598 2.359850 GGAGGTGGCGATGTTGCA 60.360 61.111 0.00 0.00 36.28 4.08
598 599 2.845752 TACGGAGGTGGCGATGTTGC 62.846 60.000 0.00 0.00 0.00 4.17
599 600 0.179084 ATACGGAGGTGGCGATGTTG 60.179 55.000 0.00 0.00 0.00 3.33
600 601 0.179084 CATACGGAGGTGGCGATGTT 60.179 55.000 0.00 0.00 0.00 2.71
601 602 1.441729 CATACGGAGGTGGCGATGT 59.558 57.895 0.00 0.00 0.00 3.06
602 603 1.300931 CCATACGGAGGTGGCGATG 60.301 63.158 0.00 0.00 31.21 3.84
603 604 1.456892 TCCATACGGAGGTGGCGAT 60.457 57.895 0.00 0.00 35.91 4.58
604 605 2.043752 TCCATACGGAGGTGGCGA 60.044 61.111 0.00 0.00 35.91 5.54
613 614 7.438459 ACGAAAATTAAAGAGAGATCCATACGG 59.562 37.037 0.00 0.00 0.00 4.02
614 615 8.354011 ACGAAAATTAAAGAGAGATCCATACG 57.646 34.615 0.00 0.00 0.00 3.06
615 616 9.314321 TGACGAAAATTAAAGAGAGATCCATAC 57.686 33.333 0.00 0.00 0.00 2.39
619 620 6.313905 TGCTGACGAAAATTAAAGAGAGATCC 59.686 38.462 0.00 0.00 0.00 3.36
636 637 1.204704 ACGGATCATCTTTGCTGACGA 59.795 47.619 0.00 0.00 0.00 4.20
638 639 1.063174 GCACGGATCATCTTTGCTGAC 59.937 52.381 0.00 0.00 0.00 3.51
640 641 0.379669 GGCACGGATCATCTTTGCTG 59.620 55.000 9.92 0.00 33.55 4.41
710 711 2.235020 CGCTGATAAGATCGCTCGTAC 58.765 52.381 0.00 0.00 0.00 3.67
722 723 4.585526 CGGGAGCGCCGCTGATAA 62.586 66.667 20.07 0.00 39.88 1.75
788 806 1.349357 GGCTATCCTGATTCCCTGACC 59.651 57.143 0.00 0.00 0.00 4.02
941 960 4.704833 TGGTTCTGGAGCTGCGGC 62.705 66.667 10.33 10.33 39.06 6.53
981 1000 3.611792 GCGATCGAGCTGTGCGAC 61.612 66.667 21.57 0.00 40.94 5.19
982 1001 2.889154 ATTGCGATCGAGCTGTGCGA 62.889 55.000 21.57 0.00 42.48 5.10
983 1002 2.520039 ATTGCGATCGAGCTGTGCG 61.520 57.895 21.57 0.00 38.13 5.34
984 1003 1.011463 CATTGCGATCGAGCTGTGC 60.011 57.895 21.57 0.00 38.13 4.57
985 1004 1.640069 CCATTGCGATCGAGCTGTG 59.360 57.895 21.57 9.14 38.13 3.66
1130 1149 9.857957 TGTCATATGTTTATTAAGTCGTGTGTA 57.142 29.630 1.90 0.00 0.00 2.90
1143 1162 5.220835 CGTGCATGGTGTGTCATATGTTTAT 60.221 40.000 1.90 0.00 0.00 1.40
1147 1166 2.009051 CGTGCATGGTGTGTCATATGT 58.991 47.619 1.90 0.00 0.00 2.29
1150 1169 0.321122 TGCGTGCATGGTGTGTCATA 60.321 50.000 8.27 0.00 0.00 2.15
1152 1171 2.203126 TGCGTGCATGGTGTGTCA 60.203 55.556 8.27 0.00 0.00 3.58
1155 1174 4.388080 CGGTGCGTGCATGGTGTG 62.388 66.667 8.27 0.00 0.00 3.82
1156 1175 4.617520 TCGGTGCGTGCATGGTGT 62.618 61.111 8.27 0.00 0.00 4.16
1159 1178 3.190849 CTCTCGGTGCGTGCATGG 61.191 66.667 8.27 0.00 0.00 3.66
1160 1179 3.857854 GCTCTCGGTGCGTGCATG 61.858 66.667 0.09 0.09 0.00 4.06
1161 1180 3.881952 TTGCTCTCGGTGCGTGCAT 62.882 57.895 0.00 0.00 32.28 3.96
1162 1181 4.600576 TTGCTCTCGGTGCGTGCA 62.601 61.111 0.00 0.00 0.00 4.57
1163 1182 4.077188 GTTGCTCTCGGTGCGTGC 62.077 66.667 0.00 0.00 0.00 5.34
1164 1183 2.661537 TGTTGCTCTCGGTGCGTG 60.662 61.111 0.00 0.00 0.00 5.34
1165 1184 2.356313 CTGTTGCTCTCGGTGCGT 60.356 61.111 0.00 0.00 0.00 5.24
1166 1185 2.049156 TCTGTTGCTCTCGGTGCG 60.049 61.111 0.00 0.00 0.00 5.34
1167 1186 2.386660 GCTCTGTTGCTCTCGGTGC 61.387 63.158 0.00 0.00 0.00 5.01
1168 1187 2.091112 CGCTCTGTTGCTCTCGGTG 61.091 63.158 0.00 0.00 0.00 4.94
1169 1188 2.259818 CGCTCTGTTGCTCTCGGT 59.740 61.111 0.00 0.00 0.00 4.69
1170 1189 2.091112 CACGCTCTGTTGCTCTCGG 61.091 63.158 0.00 0.00 0.00 4.63
1527 1548 0.455005 GAAGGCCTTGATTGCAGAGC 59.545 55.000 26.25 0.00 0.00 4.09
1603 1641 5.733676 TCAACAGAGCAAGCACATAGATAA 58.266 37.500 0.00 0.00 0.00 1.75
1614 1652 6.981762 AAGATCAAGTATCAACAGAGCAAG 57.018 37.500 0.00 0.00 37.03 4.01
1615 1653 6.712095 ACAAAGATCAAGTATCAACAGAGCAA 59.288 34.615 0.00 0.00 37.03 3.91
1616 1654 6.233434 ACAAAGATCAAGTATCAACAGAGCA 58.767 36.000 0.00 0.00 37.03 4.26
1617 1655 6.734104 ACAAAGATCAAGTATCAACAGAGC 57.266 37.500 0.00 0.00 37.03 4.09
1645 1686 6.038603 GCAGCATCTTTCCAATTACTGATACA 59.961 38.462 0.00 0.00 0.00 2.29
1723 1799 6.655848 TGACAAGTAATTTAAACCGCCAGTAT 59.344 34.615 0.00 0.00 0.00 2.12
1781 1997 2.777969 ACGTAGAGCCGTGAGTAGG 58.222 57.895 0.00 0.00 40.08 3.18
1789 2005 3.181967 GCTGTGCACGTAGAGCCG 61.182 66.667 13.13 0.00 45.43 5.52
1831 2163 1.992170 ATGGACAGTAGTTTCGACGC 58.008 50.000 0.00 0.00 0.00 5.19
1832 2164 4.985044 AAAATGGACAGTAGTTTCGACG 57.015 40.909 0.00 0.00 0.00 5.12
1833 2165 4.909880 GCAAAAATGGACAGTAGTTTCGAC 59.090 41.667 0.00 0.00 0.00 4.20
1834 2166 4.319190 CGCAAAAATGGACAGTAGTTTCGA 60.319 41.667 0.00 0.00 0.00 3.71
1837 2169 4.336993 TGTCGCAAAAATGGACAGTAGTTT 59.663 37.500 0.00 0.00 35.89 2.66
1845 2177 7.344910 TGAATTATTTGTCGCAAAAATGGAC 57.655 32.000 8.65 0.00 0.00 4.02
1853 2185 3.126171 CGGTCCTGAATTATTTGTCGCAA 59.874 43.478 0.00 0.00 0.00 4.85
1871 2203 4.265073 TGTTAGTAAGTACTCCCTCGGTC 58.735 47.826 0.00 0.00 37.73 4.79
1874 2206 5.638783 CAACTGTTAGTAAGTACTCCCTCG 58.361 45.833 0.00 0.00 37.73 4.63
1879 2211 5.346281 CAGCAGCAACTGTTAGTAAGTACTC 59.654 44.000 0.00 0.00 34.42 2.59
1881 2213 4.143094 GCAGCAGCAACTGTTAGTAAGTAC 60.143 45.833 7.70 0.00 39.96 2.73
1884 2216 3.070018 AGCAGCAGCAACTGTTAGTAAG 58.930 45.455 3.17 0.00 45.49 2.34
1928 2260 5.583061 TCAGACATTAACGAAACAAGTGTGT 59.417 36.000 0.00 0.00 40.75 3.72
1930 2262 6.861065 ATCAGACATTAACGAAACAAGTGT 57.139 33.333 0.00 0.00 0.00 3.55
1970 2397 0.041312 ATAAATCGCCGACGCAATGC 60.041 50.000 0.00 0.00 39.84 3.56
1981 2408 5.576384 TCAGTTGGATTTTTGCATAAATCGC 59.424 36.000 26.15 21.07 42.68 4.58
2022 2450 2.930682 GCGTATCCTTTCCAGTGTCTTC 59.069 50.000 0.00 0.00 0.00 2.87
2051 2479 1.002315 ACCCTGTTTTCCATGCAATGC 59.998 47.619 0.00 0.00 44.97 3.56
2084 2513 6.550481 AGCCCACTTCTATACTAGTTAACCTC 59.450 42.308 0.00 0.00 0.00 3.85
2130 2562 4.276926 AGATTTTTCACACTTGAGCCTGAC 59.723 41.667 0.00 0.00 31.71 3.51
2166 2598 0.912486 ACCCCCTGTTCTACATGAGC 59.088 55.000 0.00 0.00 0.00 4.26
2167 2599 1.486726 GGACCCCCTGTTCTACATGAG 59.513 57.143 0.00 0.00 0.00 2.90
2190 2622 3.007635 CAAGATGATGTGCTGCTGAAGA 58.992 45.455 0.00 0.00 0.00 2.87
2218 2650 1.339920 CCCCCAATGGAAATTTGGTGC 60.340 52.381 0.00 0.00 41.74 5.01
2219 2651 1.984424 ACCCCCAATGGAAATTTGGTG 59.016 47.619 0.00 0.00 41.74 4.17
2245 2677 2.216898 GCCTGTCTGTATCTCCATTGC 58.783 52.381 0.00 0.00 0.00 3.56
2265 2697 3.930848 AGGTTTATGTAAGCTTTCGGACG 59.069 43.478 3.20 0.00 41.68 4.79
2270 2702 7.041372 TGACTTGTGAGGTTTATGTAAGCTTTC 60.041 37.037 3.20 0.00 44.30 2.62
2338 2770 3.562973 CCAGATCATTCGGAGTGAAATGG 59.437 47.826 17.12 17.12 40.71 3.16
2344 2776 1.293924 GTGCCAGATCATTCGGAGTG 58.706 55.000 0.00 0.00 0.00 3.51
2345 2777 0.904649 TGTGCCAGATCATTCGGAGT 59.095 50.000 0.00 0.00 0.00 3.85
2346 2778 2.251409 ATGTGCCAGATCATTCGGAG 57.749 50.000 0.00 0.00 0.00 4.63
2419 2991 4.152647 CCCATATCTAGACACTAGTGGCA 58.847 47.826 30.11 15.03 42.32 4.92


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.