Multiple sequence alignment - TraesCS3D01G208600

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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 TraesCS3D01G208600 chr3D 100.000 2271 0 0 1 2271 275777033 275774763 0.000000e+00 4194.0
1 TraesCS3D01G208600 chr7D 98.846 693 7 1 744 1435 620473769 620474461 0.000000e+00 1234.0
2 TraesCS3D01G208600 chr7D 98.505 535 8 0 209 743 620473075 620473609 0.000000e+00 944.0
3 TraesCS3D01G208600 chr7D 91.954 87 6 1 76 161 397581138 397581052 1.100000e-23 121.0
4 TraesCS3D01G208600 chr1D 95.298 638 27 3 1636 2271 238493021 238493657 0.000000e+00 1009.0
5 TraesCS3D01G208600 chr1D 94.872 39 1 1 1637 1674 206075844 206075806 2.440000e-05 60.2
6 TraesCS3D01G208600 chr6A 95.506 623 22 4 1637 2258 184437675 184438292 0.000000e+00 990.0
7 TraesCS3D01G208600 chr7A 94.357 638 24 6 1636 2271 34325725 34326352 0.000000e+00 968.0
8 TraesCS3D01G208600 chr7A 92.063 693 37 10 209 888 59603737 59603050 0.000000e+00 959.0
9 TraesCS3D01G208600 chr7A 93.320 494 29 3 941 1433 622333614 622334104 0.000000e+00 726.0
10 TraesCS3D01G208600 chr7A 93.402 485 29 3 953 1436 59602807 59602325 0.000000e+00 715.0
11 TraesCS3D01G208600 chr7A 90.659 546 40 5 209 743 622333059 622333604 0.000000e+00 715.0
12 TraesCS3D01G208600 chr7A 90.000 90 9 0 69 158 32527933 32528022 1.430000e-22 117.0
13 TraesCS3D01G208600 chr1A 93.887 638 32 5 1637 2271 468705465 468704832 0.000000e+00 955.0
14 TraesCS3D01G208600 chr1A 89.603 529 49 5 1637 2161 222383237 222383763 0.000000e+00 667.0
15 TraesCS3D01G208600 chr1A 84.058 69 11 0 1858 1926 514200548 514200480 1.460000e-07 67.6
16 TraesCS3D01G208600 chr1A 100.000 35 0 0 1634 1668 93963164 93963198 5.240000e-07 65.8
17 TraesCS3D01G208600 chr6B 92.790 638 43 3 1637 2271 422471672 422472309 0.000000e+00 920.0
18 TraesCS3D01G208600 chr6B 83.333 750 95 16 269 1001 687877294 687878030 0.000000e+00 665.0
19 TraesCS3D01G208600 chr6B 84.990 493 56 12 962 1442 687878034 687878520 3.390000e-133 484.0
20 TraesCS3D01G208600 chr6B 90.909 88 7 1 77 163 679732992 679732905 1.430000e-22 117.0
21 TraesCS3D01G208600 chr7B 91.786 560 40 6 883 1437 668983060 668982502 0.000000e+00 774.0
22 TraesCS3D01G208600 chr7B 88.276 580 42 13 244 813 668983632 668983069 0.000000e+00 671.0
23 TraesCS3D01G208600 chr5A 93.964 497 26 4 941 1436 595401755 595401262 0.000000e+00 749.0
24 TraesCS3D01G208600 chr5A 90.842 546 39 5 209 743 595402310 595401765 0.000000e+00 721.0
25 TraesCS3D01G208600 chr4A 93.964 497 26 4 941 1436 596980802 596980309 0.000000e+00 749.0
26 TraesCS3D01G208600 chr4A 91.209 546 37 3 209 743 596981357 596980812 0.000000e+00 732.0
27 TraesCS3D01G208600 chr4A 89.927 546 44 5 209 743 423444628 423444083 0.000000e+00 693.0
28 TraesCS3D01G208600 chr4A 90.578 467 42 2 245 711 691555258 691554794 3.200000e-173 617.0
29 TraesCS3D01G208600 chr4A 89.157 498 24 10 941 1437 423444073 423443605 5.400000e-166 593.0
30 TraesCS3D01G208600 chr4A 88.889 90 10 0 69 158 296623749 296623838 6.630000e-21 111.0
31 TraesCS3D01G208600 chr4B 83.600 750 94 14 269 1001 582558003 582558740 0.000000e+00 676.0
32 TraesCS3D01G208600 chr4B 88.298 94 10 1 70 162 378766248 378766155 6.630000e-21 111.0
33 TraesCS3D01G208600 chr1B 82.690 751 99 19 269 1001 48483759 48484496 2.460000e-179 638.0
34 TraesCS3D01G208600 chr3A 76.656 604 112 23 840 1436 681292468 681291887 7.880000e-80 307.0
35 TraesCS3D01G208600 chr3A 91.710 193 7 1 1434 1617 365179582 365179774 2.240000e-65 259.0
36 TraesCS3D01G208600 chr3A 92.683 82 6 0 77 158 425605799 425605880 3.960000e-23 119.0
37 TraesCS3D01G208600 chr3B 90.052 191 6 4 1437 1617 362275292 362275105 3.770000e-58 235.0
38 TraesCS3D01G208600 chr3B 90.805 87 6 2 73 158 460106293 460106378 5.130000e-22 115.0
39 TraesCS3D01G208600 chr2A 90.426 94 9 0 74 167 79496860 79496767 8.520000e-25 124.0
40 TraesCS3D01G208600 chr5B 90.000 90 7 2 77 164 691453445 691453534 5.130000e-22 115.0
41 TraesCS3D01G208600 chr2B 97.059 34 1 0 1635 1668 314766120 314766087 8.760000e-05 58.4


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 TraesCS3D01G208600 chr3D 275774763 275777033 2270 True 4194.0 4194 100.0000 1 2271 1 chr3D.!!$R1 2270
1 TraesCS3D01G208600 chr7D 620473075 620474461 1386 False 1089.0 1234 98.6755 209 1435 2 chr7D.!!$F1 1226
2 TraesCS3D01G208600 chr1D 238493021 238493657 636 False 1009.0 1009 95.2980 1636 2271 1 chr1D.!!$F1 635
3 TraesCS3D01G208600 chr6A 184437675 184438292 617 False 990.0 990 95.5060 1637 2258 1 chr6A.!!$F1 621
4 TraesCS3D01G208600 chr7A 34325725 34326352 627 False 968.0 968 94.3570 1636 2271 1 chr7A.!!$F2 635
5 TraesCS3D01G208600 chr7A 59602325 59603737 1412 True 837.0 959 92.7325 209 1436 2 chr7A.!!$R1 1227
6 TraesCS3D01G208600 chr7A 622333059 622334104 1045 False 720.5 726 91.9895 209 1433 2 chr7A.!!$F3 1224
7 TraesCS3D01G208600 chr1A 468704832 468705465 633 True 955.0 955 93.8870 1637 2271 1 chr1A.!!$R1 634
8 TraesCS3D01G208600 chr1A 222383237 222383763 526 False 667.0 667 89.6030 1637 2161 1 chr1A.!!$F2 524
9 TraesCS3D01G208600 chr6B 422471672 422472309 637 False 920.0 920 92.7900 1637 2271 1 chr6B.!!$F1 634
10 TraesCS3D01G208600 chr6B 687877294 687878520 1226 False 574.5 665 84.1615 269 1442 2 chr6B.!!$F2 1173
11 TraesCS3D01G208600 chr7B 668982502 668983632 1130 True 722.5 774 90.0310 244 1437 2 chr7B.!!$R1 1193
12 TraesCS3D01G208600 chr5A 595401262 595402310 1048 True 735.0 749 92.4030 209 1436 2 chr5A.!!$R1 1227
13 TraesCS3D01G208600 chr4A 596980309 596981357 1048 True 740.5 749 92.5865 209 1436 2 chr4A.!!$R3 1227
14 TraesCS3D01G208600 chr4A 423443605 423444628 1023 True 643.0 693 89.5420 209 1437 2 chr4A.!!$R2 1228
15 TraesCS3D01G208600 chr4B 582558003 582558740 737 False 676.0 676 83.6000 269 1001 1 chr4B.!!$F1 732
16 TraesCS3D01G208600 chr1B 48483759 48484496 737 False 638.0 638 82.6900 269 1001 1 chr1B.!!$F1 732
17 TraesCS3D01G208600 chr3A 681291887 681292468 581 True 307.0 307 76.6560 840 1436 1 chr3A.!!$R1 596

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
179 180 0.392998 AATGGCTTAGACACGCCCAG 60.393 55.0 0.0 0.0 45.71 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1501 1962 0.033796 CCATCATGGTCAGGTTGGCT 60.034 55.0 0.0 0.0 31.35 4.75 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
17 18 3.981308 AGTGGCCGGAAAATGACG 58.019 55.556 5.05 0.00 0.00 4.35
22 23 4.174129 CCGGAAAATGACGGCGCC 62.174 66.667 19.07 19.07 43.96 6.53
23 24 4.174129 CGGAAAATGACGGCGCCC 62.174 66.667 23.46 8.57 0.00 6.13
24 25 3.822192 GGAAAATGACGGCGCCCC 61.822 66.667 23.46 14.05 0.00 5.80
38 39 4.501714 CCCCGTTCGCCGATTCGA 62.502 66.667 7.83 0.00 39.56 3.71
39 40 2.507547 CCCGTTCGCCGATTCGAA 60.508 61.111 7.83 0.00 44.96 3.71
50 51 2.769376 CCGATTCGAAACGGTTTCATG 58.231 47.619 31.70 15.63 43.53 3.07
51 52 2.158841 CCGATTCGAAACGGTTTCATGT 59.841 45.455 31.70 15.19 43.53 3.21
52 53 3.404564 CGATTCGAAACGGTTTCATGTC 58.595 45.455 27.57 20.19 39.63 3.06
53 54 2.934107 TTCGAAACGGTTTCATGTCG 57.066 45.000 27.57 17.20 39.63 4.35
54 55 0.509499 TCGAAACGGTTTCATGTCGC 59.491 50.000 27.57 5.49 39.63 5.19
55 56 0.511221 CGAAACGGTTTCATGTCGCT 59.489 50.000 27.57 0.00 39.63 4.93
56 57 1.070175 CGAAACGGTTTCATGTCGCTT 60.070 47.619 27.57 0.00 39.63 4.68
57 58 2.156117 CGAAACGGTTTCATGTCGCTTA 59.844 45.455 27.57 0.00 39.63 3.09
58 59 3.181524 CGAAACGGTTTCATGTCGCTTAT 60.182 43.478 27.57 0.00 39.63 1.73
59 60 3.740044 AACGGTTTCATGTCGCTTATG 57.260 42.857 0.00 0.00 0.00 1.90
60 61 2.967362 ACGGTTTCATGTCGCTTATGA 58.033 42.857 0.00 0.00 33.00 2.15
61 62 2.930040 ACGGTTTCATGTCGCTTATGAG 59.070 45.455 0.00 0.00 36.07 2.90
62 63 3.186909 CGGTTTCATGTCGCTTATGAGA 58.813 45.455 0.00 0.00 36.07 3.27
63 64 3.000322 CGGTTTCATGTCGCTTATGAGAC 60.000 47.826 5.67 5.67 42.19 3.36
64 65 4.184629 GGTTTCATGTCGCTTATGAGACT 58.815 43.478 12.51 0.00 42.31 3.24
65 66 4.268884 GGTTTCATGTCGCTTATGAGACTC 59.731 45.833 12.51 0.00 42.31 3.36
66 67 4.718940 TTCATGTCGCTTATGAGACTCA 57.281 40.909 7.80 7.80 42.31 3.41
67 68 4.718940 TCATGTCGCTTATGAGACTCAA 57.281 40.909 9.70 0.00 42.31 3.02
68 69 4.424626 TCATGTCGCTTATGAGACTCAAC 58.575 43.478 9.70 2.48 42.31 3.18
69 70 4.158579 TCATGTCGCTTATGAGACTCAACT 59.841 41.667 9.70 0.00 42.31 3.16
70 71 5.357032 TCATGTCGCTTATGAGACTCAACTA 59.643 40.000 9.70 0.00 42.31 2.24
71 72 5.638596 TGTCGCTTATGAGACTCAACTAA 57.361 39.130 9.70 3.92 42.31 2.24
72 73 6.208988 TGTCGCTTATGAGACTCAACTAAT 57.791 37.500 9.70 0.00 42.31 1.73
73 74 6.631016 TGTCGCTTATGAGACTCAACTAATT 58.369 36.000 9.70 0.00 42.31 1.40
74 75 7.768240 TGTCGCTTATGAGACTCAACTAATTA 58.232 34.615 9.70 0.00 42.31 1.40
75 76 7.915923 TGTCGCTTATGAGACTCAACTAATTAG 59.084 37.037 9.70 11.05 42.31 1.73
76 77 7.916450 GTCGCTTATGAGACTCAACTAATTAGT 59.084 37.037 12.50 12.50 39.42 2.24
77 78 9.117183 TCGCTTATGAGACTCAACTAATTAGTA 57.883 33.333 18.31 3.34 34.99 1.82
78 79 9.171701 CGCTTATGAGACTCAACTAATTAGTAC 57.828 37.037 18.31 8.15 34.99 2.73
83 84 8.880991 TGAGACTCAACTAATTAGTACTTCCT 57.119 34.615 18.31 12.54 34.99 3.36
84 85 8.958506 TGAGACTCAACTAATTAGTACTTCCTC 58.041 37.037 18.31 19.11 34.99 3.71
85 86 8.296211 AGACTCAACTAATTAGTACTTCCTCC 57.704 38.462 18.31 4.33 34.99 4.30
86 87 7.067251 AGACTCAACTAATTAGTACTTCCTCCG 59.933 40.741 18.31 3.40 34.99 4.63
87 88 6.662663 ACTCAACTAATTAGTACTTCCTCCGT 59.337 38.462 18.31 3.93 34.99 4.69
88 89 7.178097 ACTCAACTAATTAGTACTTCCTCCGTT 59.822 37.037 18.31 0.00 34.99 4.44
89 90 7.899973 TCAACTAATTAGTACTTCCTCCGTTT 58.100 34.615 18.31 0.00 34.99 3.60
90 91 8.031277 TCAACTAATTAGTACTTCCTCCGTTTC 58.969 37.037 18.31 0.00 34.99 2.78
91 92 7.472334 ACTAATTAGTACTTCCTCCGTTTCA 57.528 36.000 16.60 0.00 34.13 2.69
92 93 7.899973 ACTAATTAGTACTTCCTCCGTTTCAA 58.100 34.615 16.60 0.00 34.13 2.69
93 94 8.370182 ACTAATTAGTACTTCCTCCGTTTCAAA 58.630 33.333 16.60 0.00 34.13 2.69
94 95 9.211485 CTAATTAGTACTTCCTCCGTTTCAAAA 57.789 33.333 0.00 0.00 0.00 2.44
95 96 8.631480 AATTAGTACTTCCTCCGTTTCAAAAT 57.369 30.769 0.00 0.00 0.00 1.82
96 97 9.729281 AATTAGTACTTCCTCCGTTTCAAAATA 57.271 29.630 0.00 0.00 0.00 1.40
97 98 9.729281 ATTAGTACTTCCTCCGTTTCAAAATAA 57.271 29.630 0.00 0.00 0.00 1.40
98 99 9.558396 TTAGTACTTCCTCCGTTTCAAAATAAA 57.442 29.630 0.00 0.00 0.00 1.40
99 100 8.631480 AGTACTTCCTCCGTTTCAAAATAAAT 57.369 30.769 0.00 0.00 0.00 1.40
100 101 8.512138 AGTACTTCCTCCGTTTCAAAATAAATG 58.488 33.333 0.00 0.00 0.00 2.32
101 102 7.519032 ACTTCCTCCGTTTCAAAATAAATGA 57.481 32.000 0.00 0.00 0.00 2.57
102 103 7.368059 ACTTCCTCCGTTTCAAAATAAATGAC 58.632 34.615 0.00 0.00 0.00 3.06
103 104 6.262193 TCCTCCGTTTCAAAATAAATGACC 57.738 37.500 0.00 0.00 0.00 4.02
104 105 5.184287 TCCTCCGTTTCAAAATAAATGACCC 59.816 40.000 0.00 0.00 0.00 4.46
105 106 5.047660 CCTCCGTTTCAAAATAAATGACCCA 60.048 40.000 0.00 0.00 0.00 4.51
106 107 6.406692 TCCGTTTCAAAATAAATGACCCAA 57.593 33.333 0.00 0.00 0.00 4.12
107 108 6.217294 TCCGTTTCAAAATAAATGACCCAAC 58.783 36.000 0.00 0.00 0.00 3.77
108 109 6.041069 TCCGTTTCAAAATAAATGACCCAACT 59.959 34.615 0.00 0.00 0.00 3.16
109 110 6.704050 CCGTTTCAAAATAAATGACCCAACTT 59.296 34.615 0.00 0.00 0.00 2.66
110 111 7.225734 CCGTTTCAAAATAAATGACCCAACTTT 59.774 33.333 0.00 0.00 0.00 2.66
111 112 9.250624 CGTTTCAAAATAAATGACCCAACTTTA 57.749 29.630 0.00 0.00 0.00 1.85
154 155 9.831737 AATTGAGTCATCTATTTTGAAACGAAG 57.168 29.630 0.00 0.00 28.12 3.79
155 156 7.364522 TGAGTCATCTATTTTGAAACGAAGG 57.635 36.000 0.00 0.00 0.00 3.46
156 157 6.371548 TGAGTCATCTATTTTGAAACGAAGGG 59.628 38.462 0.00 0.00 0.00 3.95
157 158 6.472887 AGTCATCTATTTTGAAACGAAGGGA 58.527 36.000 0.00 0.00 0.00 4.20
158 159 6.940298 AGTCATCTATTTTGAAACGAAGGGAA 59.060 34.615 0.00 0.00 0.00 3.97
159 160 7.611855 AGTCATCTATTTTGAAACGAAGGGAAT 59.388 33.333 0.00 0.00 0.00 3.01
160 161 8.889717 GTCATCTATTTTGAAACGAAGGGAATA 58.110 33.333 0.00 0.00 0.00 1.75
161 162 9.456147 TCATCTATTTTGAAACGAAGGGAATAA 57.544 29.630 0.00 0.00 0.00 1.40
164 165 8.682710 TCTATTTTGAAACGAAGGGAATAATGG 58.317 33.333 0.00 0.00 0.00 3.16
165 166 4.712122 TTGAAACGAAGGGAATAATGGC 57.288 40.909 0.00 0.00 0.00 4.40
166 167 3.963129 TGAAACGAAGGGAATAATGGCT 58.037 40.909 0.00 0.00 0.00 4.75
167 168 4.340617 TGAAACGAAGGGAATAATGGCTT 58.659 39.130 0.00 0.00 0.00 4.35
168 169 5.502079 TGAAACGAAGGGAATAATGGCTTA 58.498 37.500 0.00 0.00 0.00 3.09
169 170 5.588648 TGAAACGAAGGGAATAATGGCTTAG 59.411 40.000 0.00 0.00 0.00 2.18
170 171 5.367945 AACGAAGGGAATAATGGCTTAGA 57.632 39.130 0.00 0.00 0.00 2.10
171 172 4.704965 ACGAAGGGAATAATGGCTTAGAC 58.295 43.478 0.00 0.00 0.00 2.59
172 173 4.163458 ACGAAGGGAATAATGGCTTAGACA 59.837 41.667 0.00 0.00 0.00 3.41
173 174 4.511826 CGAAGGGAATAATGGCTTAGACAC 59.488 45.833 0.00 0.00 0.00 3.67
174 175 4.073293 AGGGAATAATGGCTTAGACACG 57.927 45.455 0.00 0.00 0.00 4.49
175 176 2.548480 GGGAATAATGGCTTAGACACGC 59.452 50.000 0.00 0.00 0.00 5.34
176 177 2.548480 GGAATAATGGCTTAGACACGCC 59.452 50.000 0.00 0.00 46.46 5.68
177 178 2.256117 ATAATGGCTTAGACACGCCC 57.744 50.000 0.00 0.00 45.71 6.13
178 179 0.906066 TAATGGCTTAGACACGCCCA 59.094 50.000 0.00 0.00 45.71 5.36
179 180 0.392998 AATGGCTTAGACACGCCCAG 60.393 55.000 0.00 0.00 45.71 4.45
180 181 2.125106 GGCTTAGACACGCCCAGG 60.125 66.667 0.00 0.00 40.43 4.45
181 182 2.820037 GCTTAGACACGCCCAGGC 60.820 66.667 0.00 0.00 37.85 4.85
182 183 2.125106 CTTAGACACGCCCAGGCC 60.125 66.667 2.37 0.00 37.98 5.19
183 184 3.682292 CTTAGACACGCCCAGGCCC 62.682 68.421 0.00 0.00 37.98 5.80
325 329 2.434702 TCGAGGCCTTCCTATTCCTTTC 59.565 50.000 6.77 0.00 44.46 2.62
454 482 2.742053 CGCGAAAAATCAAGGAGGAGAA 59.258 45.455 0.00 0.00 0.00 2.87
599 628 1.226435 CGCTCGAGTGTCTAGCCAC 60.226 63.158 17.90 0.00 32.22 5.01
833 1044 4.764896 TGCATAGCTCGCATCCTG 57.235 55.556 6.64 0.00 33.55 3.86
1108 1565 4.745125 GTGTCATCAGTTGAAAGACGAAGA 59.255 41.667 11.13 0.00 36.54 2.87
1451 1912 3.791640 TGGACACGCCAGATGACT 58.208 55.556 0.00 0.00 43.33 3.41
1452 1913 2.057830 TGGACACGCCAGATGACTT 58.942 52.632 0.00 0.00 43.33 3.01
1453 1914 0.320683 TGGACACGCCAGATGACTTG 60.321 55.000 0.00 0.00 43.33 3.16
1454 1915 0.320771 GGACACGCCAGATGACTTGT 60.321 55.000 0.00 0.00 36.34 3.16
1455 1916 1.071605 GACACGCCAGATGACTTGTC 58.928 55.000 0.00 0.00 0.00 3.18
1456 1917 0.392706 ACACGCCAGATGACTTGTCA 59.607 50.000 5.89 5.89 0.00 3.58
1457 1918 1.073964 CACGCCAGATGACTTGTCAG 58.926 55.000 9.39 0.00 0.00 3.51
1458 1919 0.681733 ACGCCAGATGACTTGTCAGT 59.318 50.000 9.39 0.00 35.17 3.41
1459 1920 1.070758 ACGCCAGATGACTTGTCAGTT 59.929 47.619 9.39 0.00 31.22 3.16
1460 1921 1.462283 CGCCAGATGACTTGTCAGTTG 59.538 52.381 9.39 9.22 31.22 3.16
1461 1922 2.498167 GCCAGATGACTTGTCAGTTGT 58.502 47.619 9.39 0.00 31.22 3.32
1462 1923 2.481952 GCCAGATGACTTGTCAGTTGTC 59.518 50.000 9.39 2.41 31.22 3.18
1463 1924 3.732212 CCAGATGACTTGTCAGTTGTCA 58.268 45.455 9.39 0.00 43.53 3.58
1464 1925 3.496130 CCAGATGACTTGTCAGTTGTCAC 59.504 47.826 9.39 3.88 42.43 3.67
1465 1926 4.375272 CAGATGACTTGTCAGTTGTCACT 58.625 43.478 9.39 5.44 42.43 3.41
1475 1936 3.121559 CAGTTGTCACTGTGTGTGTTG 57.878 47.619 7.79 0.00 44.96 3.33
1476 1937 1.468520 AGTTGTCACTGTGTGTGTTGC 59.531 47.619 7.79 0.00 46.27 4.17
1477 1938 1.468520 GTTGTCACTGTGTGTGTTGCT 59.531 47.619 7.79 0.00 46.27 3.91
1478 1939 1.819928 TGTCACTGTGTGTGTTGCTT 58.180 45.000 7.79 0.00 46.27 3.91
1479 1940 2.979240 TGTCACTGTGTGTGTTGCTTA 58.021 42.857 7.79 0.00 46.27 3.09
1480 1941 2.935849 TGTCACTGTGTGTGTTGCTTAG 59.064 45.455 7.79 0.00 46.27 2.18
1481 1942 2.936498 GTCACTGTGTGTGTTGCTTAGT 59.064 45.455 7.79 0.00 46.27 2.24
1482 1943 3.374058 GTCACTGTGTGTGTTGCTTAGTT 59.626 43.478 7.79 0.00 46.27 2.24
1483 1944 4.569162 GTCACTGTGTGTGTTGCTTAGTTA 59.431 41.667 7.79 0.00 46.27 2.24
1484 1945 5.236478 GTCACTGTGTGTGTTGCTTAGTTAT 59.764 40.000 7.79 0.00 46.27 1.89
1485 1946 5.820423 TCACTGTGTGTGTTGCTTAGTTATT 59.180 36.000 7.79 0.00 46.27 1.40
1486 1947 5.909054 CACTGTGTGTGTTGCTTAGTTATTG 59.091 40.000 0.00 0.00 41.53 1.90
1487 1948 5.588648 ACTGTGTGTGTTGCTTAGTTATTGT 59.411 36.000 0.00 0.00 0.00 2.71
1488 1949 6.094881 ACTGTGTGTGTTGCTTAGTTATTGTT 59.905 34.615 0.00 0.00 0.00 2.83
1489 1950 7.281324 ACTGTGTGTGTTGCTTAGTTATTGTTA 59.719 33.333 0.00 0.00 0.00 2.41
1490 1951 7.635423 TGTGTGTGTTGCTTAGTTATTGTTAG 58.365 34.615 0.00 0.00 0.00 2.34
1491 1952 7.281324 TGTGTGTGTTGCTTAGTTATTGTTAGT 59.719 33.333 0.00 0.00 0.00 2.24
1492 1953 8.767085 GTGTGTGTTGCTTAGTTATTGTTAGTA 58.233 33.333 0.00 0.00 0.00 1.82
1493 1954 8.767085 TGTGTGTTGCTTAGTTATTGTTAGTAC 58.233 33.333 0.00 0.00 0.00 2.73
1494 1955 8.985805 GTGTGTTGCTTAGTTATTGTTAGTACT 58.014 33.333 0.00 0.00 0.00 2.73
1495 1956 9.199982 TGTGTTGCTTAGTTATTGTTAGTACTC 57.800 33.333 0.00 0.00 0.00 2.59
1496 1957 8.371053 GTGTTGCTTAGTTATTGTTAGTACTCG 58.629 37.037 0.00 0.00 0.00 4.18
1497 1958 8.298854 TGTTGCTTAGTTATTGTTAGTACTCGA 58.701 33.333 0.00 0.00 0.00 4.04
1498 1959 9.298774 GTTGCTTAGTTATTGTTAGTACTCGAT 57.701 33.333 0.00 0.00 0.00 3.59
1499 1960 9.512435 TTGCTTAGTTATTGTTAGTACTCGATC 57.488 33.333 0.00 0.00 0.00 3.69
1500 1961 7.854422 TGCTTAGTTATTGTTAGTACTCGATCG 59.146 37.037 9.36 9.36 0.00 3.69
1501 1962 8.066595 GCTTAGTTATTGTTAGTACTCGATCGA 58.933 37.037 18.32 18.32 0.00 3.59
1502 1963 9.583530 CTTAGTTATTGTTAGTACTCGATCGAG 57.416 37.037 36.95 36.95 46.91 4.04
1503 1964 6.428799 AGTTATTGTTAGTACTCGATCGAGC 58.571 40.000 38.12 25.47 45.54 5.03
1504 1965 3.687572 TTGTTAGTACTCGATCGAGCC 57.312 47.619 38.12 29.29 45.54 4.70
1505 1966 2.635714 TGTTAGTACTCGATCGAGCCA 58.364 47.619 38.12 26.13 45.54 4.75
1506 1967 3.011818 TGTTAGTACTCGATCGAGCCAA 58.988 45.455 38.12 24.89 45.54 4.52
1507 1968 3.181503 TGTTAGTACTCGATCGAGCCAAC 60.182 47.826 38.12 31.71 45.54 3.77
1508 1969 0.739561 AGTACTCGATCGAGCCAACC 59.260 55.000 38.12 23.07 45.54 3.77
1509 1970 0.739561 GTACTCGATCGAGCCAACCT 59.260 55.000 38.12 23.25 45.54 3.50
1510 1971 0.738975 TACTCGATCGAGCCAACCTG 59.261 55.000 38.12 18.31 45.54 4.00
1511 1972 0.965866 ACTCGATCGAGCCAACCTGA 60.966 55.000 38.12 5.36 45.54 3.86
1512 1973 0.526524 CTCGATCGAGCCAACCTGAC 60.527 60.000 30.41 0.00 35.31 3.51
1513 1974 1.519455 CGATCGAGCCAACCTGACC 60.519 63.158 10.26 0.00 0.00 4.02
1514 1975 1.596934 GATCGAGCCAACCTGACCA 59.403 57.895 0.00 0.00 0.00 4.02
1515 1976 0.179000 GATCGAGCCAACCTGACCAT 59.821 55.000 0.00 0.00 0.00 3.55
1516 1977 0.107508 ATCGAGCCAACCTGACCATG 60.108 55.000 0.00 0.00 0.00 3.66
1517 1978 1.191489 TCGAGCCAACCTGACCATGA 61.191 55.000 0.00 0.00 0.00 3.07
1518 1979 0.107508 CGAGCCAACCTGACCATGAT 60.108 55.000 0.00 0.00 0.00 2.45
1519 1980 1.386533 GAGCCAACCTGACCATGATG 58.613 55.000 0.00 0.00 0.00 3.07
1520 1981 0.033796 AGCCAACCTGACCATGATGG 60.034 55.000 10.53 10.53 45.02 3.51
1534 1995 5.673337 CCATGATGGTATTCTGTAAACGG 57.327 43.478 2.54 0.00 31.35 4.44
1535 1996 5.123227 CCATGATGGTATTCTGTAAACGGT 58.877 41.667 2.54 0.00 31.35 4.83
1536 1997 6.285224 CCATGATGGTATTCTGTAAACGGTA 58.715 40.000 2.54 0.00 31.35 4.02
1537 1998 6.934645 CCATGATGGTATTCTGTAAACGGTAT 59.065 38.462 2.54 0.00 31.35 2.73
1538 1999 7.095229 CCATGATGGTATTCTGTAAACGGTATG 60.095 40.741 2.54 0.00 31.35 2.39
1539 2000 6.880484 TGATGGTATTCTGTAAACGGTATGT 58.120 36.000 0.00 0.00 0.00 2.29
1540 2001 8.009622 TGATGGTATTCTGTAAACGGTATGTA 57.990 34.615 0.00 0.00 0.00 2.29
1541 2002 8.644216 TGATGGTATTCTGTAAACGGTATGTAT 58.356 33.333 0.00 0.00 0.00 2.29
1543 2004 9.918630 ATGGTATTCTGTAAACGGTATGTATAC 57.081 33.333 0.00 0.00 0.00 1.47
1544 2005 9.135189 TGGTATTCTGTAAACGGTATGTATACT 57.865 33.333 4.17 0.00 33.81 2.12
1548 2009 8.752005 TTCTGTAAACGGTATGTATACTAGGT 57.248 34.615 4.17 0.00 33.81 3.08
1549 2010 8.158169 TCTGTAAACGGTATGTATACTAGGTG 57.842 38.462 4.17 0.00 33.81 4.00
1550 2011 7.229306 TCTGTAAACGGTATGTATACTAGGTGG 59.771 40.741 4.17 0.00 33.81 4.61
1551 2012 7.059788 TGTAAACGGTATGTATACTAGGTGGA 58.940 38.462 4.17 0.00 33.81 4.02
1552 2013 6.645790 AAACGGTATGTATACTAGGTGGAG 57.354 41.667 4.17 0.00 33.81 3.86
1553 2014 4.660168 ACGGTATGTATACTAGGTGGAGG 58.340 47.826 4.17 0.00 33.81 4.30
1554 2015 4.352001 ACGGTATGTATACTAGGTGGAGGA 59.648 45.833 4.17 0.00 33.81 3.71
1555 2016 5.163055 ACGGTATGTATACTAGGTGGAGGAA 60.163 44.000 4.17 0.00 33.81 3.36
1556 2017 5.415077 CGGTATGTATACTAGGTGGAGGAAG 59.585 48.000 4.17 0.00 33.81 3.46
1557 2018 6.550163 GGTATGTATACTAGGTGGAGGAAGA 58.450 44.000 4.17 0.00 33.81 2.87
1558 2019 6.433716 GGTATGTATACTAGGTGGAGGAAGAC 59.566 46.154 4.17 0.00 33.81 3.01
1559 2020 4.801164 TGTATACTAGGTGGAGGAAGACC 58.199 47.826 4.17 0.00 0.00 3.85
1560 2021 2.431954 TACTAGGTGGAGGAAGACCG 57.568 55.000 0.00 0.00 41.83 4.79
1561 2022 0.408700 ACTAGGTGGAGGAAGACCGT 59.591 55.000 0.00 0.00 41.83 4.83
1562 2023 1.637553 ACTAGGTGGAGGAAGACCGTA 59.362 52.381 0.00 0.00 41.83 4.02
1563 2024 2.022934 CTAGGTGGAGGAAGACCGTAC 58.977 57.143 0.00 0.00 41.83 3.67
1564 2025 0.408700 AGGTGGAGGAAGACCGTACT 59.591 55.000 0.00 0.00 41.83 2.73
1565 2026 1.203149 AGGTGGAGGAAGACCGTACTT 60.203 52.381 0.00 0.00 41.83 2.24
1566 2027 1.067071 GGTGGAGGAAGACCGTACTTG 60.067 57.143 0.00 0.00 41.83 3.16
1567 2028 1.617357 GTGGAGGAAGACCGTACTTGT 59.383 52.381 0.00 0.00 41.83 3.16
1568 2029 1.616865 TGGAGGAAGACCGTACTTGTG 59.383 52.381 0.00 0.00 41.83 3.33
1569 2030 1.672145 GGAGGAAGACCGTACTTGTGC 60.672 57.143 0.00 0.00 41.83 4.57
1570 2031 1.000506 GAGGAAGACCGTACTTGTGCA 59.999 52.381 0.00 0.00 41.83 4.57
1571 2032 1.145803 GGAAGACCGTACTTGTGCAC 58.854 55.000 10.75 10.75 0.00 4.57
1572 2033 1.539496 GGAAGACCGTACTTGTGCACA 60.539 52.381 17.42 17.42 0.00 4.57
1573 2034 2.413837 GAAGACCGTACTTGTGCACAT 58.586 47.619 22.39 9.53 0.00 3.21
1574 2035 2.543777 AGACCGTACTTGTGCACATT 57.456 45.000 22.39 13.44 0.00 2.71
1575 2036 2.413837 AGACCGTACTTGTGCACATTC 58.586 47.619 22.39 10.28 0.00 2.67
1576 2037 2.139917 GACCGTACTTGTGCACATTCA 58.860 47.619 22.39 4.74 0.00 2.57
1577 2038 2.546368 GACCGTACTTGTGCACATTCAA 59.454 45.455 22.39 4.31 0.00 2.69
1578 2039 3.146066 ACCGTACTTGTGCACATTCAAT 58.854 40.909 22.39 7.18 0.00 2.57
1579 2040 4.320023 ACCGTACTTGTGCACATTCAATA 58.680 39.130 22.39 3.03 0.00 1.90
1580 2041 4.391830 ACCGTACTTGTGCACATTCAATAG 59.608 41.667 22.39 16.11 0.00 1.73
1581 2042 4.334443 CGTACTTGTGCACATTCAATAGC 58.666 43.478 22.39 5.18 0.00 2.97
1582 2043 4.093408 CGTACTTGTGCACATTCAATAGCT 59.907 41.667 22.39 7.23 0.00 3.32
1583 2044 4.430137 ACTTGTGCACATTCAATAGCTG 57.570 40.909 22.39 3.80 0.00 4.24
1584 2045 2.925578 TGTGCACATTCAATAGCTGC 57.074 45.000 17.42 0.00 0.00 5.25
1585 2046 2.161030 TGTGCACATTCAATAGCTGCA 58.839 42.857 17.42 0.00 35.52 4.41
1586 2047 2.756207 TGTGCACATTCAATAGCTGCAT 59.244 40.909 17.42 0.00 39.88 3.96
1587 2048 3.113322 GTGCACATTCAATAGCTGCATG 58.887 45.455 13.17 0.00 39.88 4.06
1588 2049 2.100087 TGCACATTCAATAGCTGCATGG 59.900 45.455 1.02 0.00 33.40 3.66
1589 2050 2.739292 CACATTCAATAGCTGCATGGC 58.261 47.619 1.02 0.00 33.40 4.40
1590 2051 2.361119 CACATTCAATAGCTGCATGGCT 59.639 45.455 5.70 5.70 45.29 4.75
1591 2052 2.621998 ACATTCAATAGCTGCATGGCTC 59.378 45.455 3.37 0.00 42.97 4.70
1592 2053 2.423446 TTCAATAGCTGCATGGCTCA 57.577 45.000 3.37 0.00 42.97 4.26
1593 2054 1.671979 TCAATAGCTGCATGGCTCAC 58.328 50.000 3.37 0.00 42.97 3.51
1594 2055 1.065272 TCAATAGCTGCATGGCTCACA 60.065 47.619 3.37 0.00 42.97 3.58
1595 2056 1.954382 CAATAGCTGCATGGCTCACAT 59.046 47.619 3.37 0.00 42.97 3.21
1608 2069 5.121221 TGGCTCACATGTATAGTACATCG 57.879 43.478 0.00 0.52 45.83 3.84
1609 2070 4.825085 TGGCTCACATGTATAGTACATCGA 59.175 41.667 0.00 0.00 45.83 3.59
1610 2071 5.476945 TGGCTCACATGTATAGTACATCGAT 59.523 40.000 0.00 0.00 45.83 3.59
1611 2072 6.015434 TGGCTCACATGTATAGTACATCGATT 60.015 38.462 0.00 0.00 45.83 3.34
1612 2073 6.868864 GGCTCACATGTATAGTACATCGATTT 59.131 38.462 0.00 0.00 45.83 2.17
1613 2074 7.385205 GGCTCACATGTATAGTACATCGATTTT 59.615 37.037 0.00 0.00 45.83 1.82
1614 2075 8.765219 GCTCACATGTATAGTACATCGATTTTT 58.235 33.333 0.00 0.00 45.83 1.94
1839 2300 8.349983 AGATTACATTATATTGGGCACGAAAAC 58.650 33.333 0.00 0.00 0.00 2.43
2128 2594 5.779529 ACAGTCAGACAAATGAGCAAATT 57.220 34.783 2.66 0.00 0.00 1.82
2242 2712 8.931385 ATACTCGCTCCGTAAACTTTTATAAA 57.069 30.769 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.674322 CCGTCATTTTCCGGCCACT 60.674 57.895 2.24 0.00 37.43 4.00
1 2 2.874751 CCGTCATTTTCCGGCCAC 59.125 61.111 2.24 0.00 37.43 5.01
5 6 4.174129 GGCGCCGTCATTTTCCGG 62.174 66.667 12.58 0.00 46.90 5.14
6 7 4.174129 GGGCGCCGTCATTTTCCG 62.174 66.667 22.54 0.00 0.00 4.30
7 8 3.822192 GGGGCGCCGTCATTTTCC 61.822 66.667 22.54 9.60 0.00 3.13
8 9 4.174129 CGGGGCGCCGTCATTTTC 62.174 66.667 32.15 2.98 0.00 2.29
21 22 3.993376 TTCGAATCGGCGAACGGGG 62.993 63.158 28.51 13.09 44.43 5.73
22 23 2.507547 TTCGAATCGGCGAACGGG 60.508 61.111 28.51 14.57 44.43 5.28
31 32 3.404564 GACATGAAACCGTTTCGAATCG 58.595 45.455 19.20 19.20 42.55 3.34
32 33 3.404564 CGACATGAAACCGTTTCGAATC 58.595 45.455 17.16 12.90 42.55 2.52
33 34 2.412325 GCGACATGAAACCGTTTCGAAT 60.412 45.455 17.16 5.48 42.55 3.34
34 35 1.070443 GCGACATGAAACCGTTTCGAA 60.070 47.619 17.16 0.00 42.55 3.71
35 36 0.509499 GCGACATGAAACCGTTTCGA 59.491 50.000 17.16 8.53 42.55 3.71
36 37 0.511221 AGCGACATGAAACCGTTTCG 59.489 50.000 17.16 8.39 42.55 3.46
37 38 2.681152 AAGCGACATGAAACCGTTTC 57.319 45.000 15.81 15.81 40.08 2.78
38 39 3.749088 TCATAAGCGACATGAAACCGTTT 59.251 39.130 0.00 0.00 29.55 3.60
39 40 3.331150 TCATAAGCGACATGAAACCGTT 58.669 40.909 0.00 0.00 29.55 4.44
40 41 2.930040 CTCATAAGCGACATGAAACCGT 59.070 45.455 0.00 0.00 32.20 4.83
41 42 3.000322 GTCTCATAAGCGACATGAAACCG 60.000 47.826 0.00 0.00 32.20 4.44
42 43 4.184629 AGTCTCATAAGCGACATGAAACC 58.815 43.478 0.00 0.00 31.94 3.27
43 44 4.864806 TGAGTCTCATAAGCGACATGAAAC 59.135 41.667 0.00 0.00 31.94 2.78
44 45 5.072040 TGAGTCTCATAAGCGACATGAAA 57.928 39.130 0.00 0.00 31.94 2.69
45 46 4.718940 TGAGTCTCATAAGCGACATGAA 57.281 40.909 0.00 0.00 31.94 2.57
46 47 4.158579 AGTTGAGTCTCATAAGCGACATGA 59.841 41.667 2.68 0.00 31.94 3.07
47 48 4.428209 AGTTGAGTCTCATAAGCGACATG 58.572 43.478 2.68 0.00 31.94 3.21
48 49 4.727507 AGTTGAGTCTCATAAGCGACAT 57.272 40.909 2.68 0.00 31.94 3.06
49 50 5.638596 TTAGTTGAGTCTCATAAGCGACA 57.361 39.130 2.68 0.00 31.94 4.35
50 51 7.916450 ACTAATTAGTTGAGTCTCATAAGCGAC 59.084 37.037 12.50 0.00 31.13 5.19
51 52 7.997482 ACTAATTAGTTGAGTCTCATAAGCGA 58.003 34.615 12.50 0.00 31.13 4.93
52 53 9.171701 GTACTAATTAGTTGAGTCTCATAAGCG 57.828 37.037 22.66 0.00 37.73 4.68
57 58 9.482175 AGGAAGTACTAATTAGTTGAGTCTCAT 57.518 33.333 22.66 7.16 37.73 2.90
58 59 8.880991 AGGAAGTACTAATTAGTTGAGTCTCA 57.119 34.615 22.66 0.00 37.73 3.27
59 60 8.407832 GGAGGAAGTACTAATTAGTTGAGTCTC 58.592 40.741 22.66 20.31 37.73 3.36
60 61 7.067251 CGGAGGAAGTACTAATTAGTTGAGTCT 59.933 40.741 22.66 14.57 37.73 3.24
61 62 7.148103 ACGGAGGAAGTACTAATTAGTTGAGTC 60.148 40.741 22.66 14.25 37.73 3.36
62 63 6.662663 ACGGAGGAAGTACTAATTAGTTGAGT 59.337 38.462 22.66 6.67 37.73 3.41
63 64 7.098074 ACGGAGGAAGTACTAATTAGTTGAG 57.902 40.000 22.66 7.64 37.73 3.02
64 65 7.472334 AACGGAGGAAGTACTAATTAGTTGA 57.528 36.000 22.66 3.69 37.73 3.18
65 66 7.816031 TGAAACGGAGGAAGTACTAATTAGTTG 59.184 37.037 22.66 5.52 37.73 3.16
66 67 7.899973 TGAAACGGAGGAAGTACTAATTAGTT 58.100 34.615 22.66 5.72 37.73 2.24
67 68 7.472334 TGAAACGGAGGAAGTACTAATTAGT 57.528 36.000 21.35 21.35 40.24 2.24
68 69 8.767478 TTTGAAACGGAGGAAGTACTAATTAG 57.233 34.615 11.05 11.05 0.00 1.73
69 70 9.729281 ATTTTGAAACGGAGGAAGTACTAATTA 57.271 29.630 0.00 0.00 0.00 1.40
70 71 8.631480 ATTTTGAAACGGAGGAAGTACTAATT 57.369 30.769 0.00 0.00 0.00 1.40
71 72 9.729281 TTATTTTGAAACGGAGGAAGTACTAAT 57.271 29.630 0.00 0.00 0.00 1.73
72 73 9.558396 TTTATTTTGAAACGGAGGAAGTACTAA 57.442 29.630 0.00 0.00 0.00 2.24
73 74 9.729281 ATTTATTTTGAAACGGAGGAAGTACTA 57.271 29.630 0.00 0.00 0.00 1.82
74 75 8.512138 CATTTATTTTGAAACGGAGGAAGTACT 58.488 33.333 0.00 0.00 0.00 2.73
75 76 8.508875 TCATTTATTTTGAAACGGAGGAAGTAC 58.491 33.333 0.00 0.00 0.00 2.73
76 77 8.508875 GTCATTTATTTTGAAACGGAGGAAGTA 58.491 33.333 0.00 0.00 0.00 2.24
77 78 7.368059 GTCATTTATTTTGAAACGGAGGAAGT 58.632 34.615 0.00 0.00 0.00 3.01
78 79 6.806739 GGTCATTTATTTTGAAACGGAGGAAG 59.193 38.462 0.00 0.00 0.00 3.46
79 80 6.294843 GGGTCATTTATTTTGAAACGGAGGAA 60.295 38.462 0.00 0.00 0.00 3.36
80 81 5.184287 GGGTCATTTATTTTGAAACGGAGGA 59.816 40.000 0.00 0.00 0.00 3.71
81 82 5.047660 TGGGTCATTTATTTTGAAACGGAGG 60.048 40.000 0.00 0.00 0.00 4.30
82 83 6.019779 TGGGTCATTTATTTTGAAACGGAG 57.980 37.500 0.00 0.00 0.00 4.63
83 84 6.041069 AGTTGGGTCATTTATTTTGAAACGGA 59.959 34.615 0.00 0.00 0.00 4.69
84 85 6.220201 AGTTGGGTCATTTATTTTGAAACGG 58.780 36.000 0.00 0.00 0.00 4.44
85 86 7.707774 AAGTTGGGTCATTTATTTTGAAACG 57.292 32.000 0.00 0.00 0.00 3.60
128 129 9.831737 CTTCGTTTCAAAATAGATGACTCAATT 57.168 29.630 0.00 0.00 0.00 2.32
129 130 8.454106 CCTTCGTTTCAAAATAGATGACTCAAT 58.546 33.333 0.00 0.00 0.00 2.57
130 131 7.094805 CCCTTCGTTTCAAAATAGATGACTCAA 60.095 37.037 0.00 0.00 0.00 3.02
131 132 6.371548 CCCTTCGTTTCAAAATAGATGACTCA 59.628 38.462 0.00 0.00 0.00 3.41
132 133 6.594159 TCCCTTCGTTTCAAAATAGATGACTC 59.406 38.462 0.00 0.00 0.00 3.36
133 134 6.472887 TCCCTTCGTTTCAAAATAGATGACT 58.527 36.000 0.00 0.00 0.00 3.41
134 135 6.737254 TCCCTTCGTTTCAAAATAGATGAC 57.263 37.500 0.00 0.00 0.00 3.06
135 136 7.938140 ATTCCCTTCGTTTCAAAATAGATGA 57.062 32.000 0.00 0.00 0.00 2.92
138 139 8.682710 CCATTATTCCCTTCGTTTCAAAATAGA 58.317 33.333 0.00 0.00 0.00 1.98
139 140 7.435192 GCCATTATTCCCTTCGTTTCAAAATAG 59.565 37.037 0.00 0.00 0.00 1.73
140 141 7.123547 AGCCATTATTCCCTTCGTTTCAAAATA 59.876 33.333 0.00 0.00 0.00 1.40
141 142 6.070824 AGCCATTATTCCCTTCGTTTCAAAAT 60.071 34.615 0.00 0.00 0.00 1.82
142 143 5.245075 AGCCATTATTCCCTTCGTTTCAAAA 59.755 36.000 0.00 0.00 0.00 2.44
143 144 4.770010 AGCCATTATTCCCTTCGTTTCAAA 59.230 37.500 0.00 0.00 0.00 2.69
144 145 4.340617 AGCCATTATTCCCTTCGTTTCAA 58.659 39.130 0.00 0.00 0.00 2.69
145 146 3.963129 AGCCATTATTCCCTTCGTTTCA 58.037 40.909 0.00 0.00 0.00 2.69
146 147 4.983671 AAGCCATTATTCCCTTCGTTTC 57.016 40.909 0.00 0.00 0.00 2.78
147 148 5.589050 GTCTAAGCCATTATTCCCTTCGTTT 59.411 40.000 0.00 0.00 0.00 3.60
148 149 5.123936 GTCTAAGCCATTATTCCCTTCGTT 58.876 41.667 0.00 0.00 0.00 3.85
149 150 4.163458 TGTCTAAGCCATTATTCCCTTCGT 59.837 41.667 0.00 0.00 0.00 3.85
150 151 4.511826 GTGTCTAAGCCATTATTCCCTTCG 59.488 45.833 0.00 0.00 0.00 3.79
151 152 4.511826 CGTGTCTAAGCCATTATTCCCTTC 59.488 45.833 0.00 0.00 0.00 3.46
152 153 4.451900 CGTGTCTAAGCCATTATTCCCTT 58.548 43.478 0.00 0.00 0.00 3.95
153 154 3.744530 GCGTGTCTAAGCCATTATTCCCT 60.745 47.826 0.00 0.00 0.00 4.20
154 155 2.548480 GCGTGTCTAAGCCATTATTCCC 59.452 50.000 0.00 0.00 0.00 3.97
155 156 3.879932 GCGTGTCTAAGCCATTATTCC 57.120 47.619 0.00 0.00 0.00 3.01
164 165 2.820037 GCCTGGGCGTGTCTAAGC 60.820 66.667 0.00 0.00 0.00 3.09
165 166 2.125106 GGCCTGGGCGTGTCTAAG 60.125 66.667 3.84 0.00 43.06 2.18
166 167 3.712907 GGGCCTGGGCGTGTCTAA 61.713 66.667 14.63 0.00 43.06 2.10
214 215 4.570874 GGAGCCCCTGGATTCGGC 62.571 72.222 3.74 3.74 43.35 5.54
454 482 2.190578 GGGCTGCTACTCCGCATT 59.809 61.111 0.00 0.00 39.52 3.56
471 499 3.152261 AGTTCTTATCGCGAACAGGAG 57.848 47.619 15.24 7.06 42.37 3.69
599 628 3.681897 AGAGCAAAGCACGTTCTGAATAG 59.318 43.478 0.00 0.00 0.00 1.73
1442 1903 3.496130 GTGACAACTGACAAGTCATCTGG 59.504 47.826 3.01 0.00 43.35 3.86
1443 1904 4.375272 AGTGACAACTGACAAGTCATCTG 58.625 43.478 3.01 6.72 43.35 2.90
1444 1905 4.679373 AGTGACAACTGACAAGTCATCT 57.321 40.909 3.01 5.53 43.35 2.90
1463 1924 5.588648 ACAATAACTAAGCAACACACACAGT 59.411 36.000 0.00 0.00 0.00 3.55
1464 1925 6.060028 ACAATAACTAAGCAACACACACAG 57.940 37.500 0.00 0.00 0.00 3.66
1465 1926 6.443934 AACAATAACTAAGCAACACACACA 57.556 33.333 0.00 0.00 0.00 3.72
1466 1927 7.636326 ACTAACAATAACTAAGCAACACACAC 58.364 34.615 0.00 0.00 0.00 3.82
1467 1928 7.795482 ACTAACAATAACTAAGCAACACACA 57.205 32.000 0.00 0.00 0.00 3.72
1468 1929 8.985805 AGTACTAACAATAACTAAGCAACACAC 58.014 33.333 0.00 0.00 0.00 3.82
1469 1930 9.199982 GAGTACTAACAATAACTAAGCAACACA 57.800 33.333 0.00 0.00 0.00 3.72
1470 1931 8.371053 CGAGTACTAACAATAACTAAGCAACAC 58.629 37.037 0.00 0.00 0.00 3.32
1471 1932 8.298854 TCGAGTACTAACAATAACTAAGCAACA 58.701 33.333 0.00 0.00 0.00 3.33
1472 1933 8.679288 TCGAGTACTAACAATAACTAAGCAAC 57.321 34.615 0.00 0.00 0.00 4.17
1473 1934 9.512435 GATCGAGTACTAACAATAACTAAGCAA 57.488 33.333 0.00 0.00 0.00 3.91
1474 1935 7.854422 CGATCGAGTACTAACAATAACTAAGCA 59.146 37.037 10.26 0.00 0.00 3.91
1475 1936 8.066595 TCGATCGAGTACTAACAATAACTAAGC 58.933 37.037 15.15 0.00 0.00 3.09
1476 1937 9.583530 CTCGATCGAGTACTAACAATAACTAAG 57.416 37.037 32.23 5.21 37.47 2.18
1477 1938 8.066595 GCTCGATCGAGTACTAACAATAACTAA 58.933 37.037 37.59 3.51 43.70 2.24
1478 1939 7.307632 GGCTCGATCGAGTACTAACAATAACTA 60.308 40.741 37.59 3.83 43.70 2.24
1479 1940 6.428799 GCTCGATCGAGTACTAACAATAACT 58.571 40.000 37.59 0.00 43.70 2.24
1480 1941 5.624491 GGCTCGATCGAGTACTAACAATAAC 59.376 44.000 37.59 20.37 43.70 1.89
1481 1942 5.297527 TGGCTCGATCGAGTACTAACAATAA 59.702 40.000 37.59 15.49 43.70 1.40
1482 1943 4.818005 TGGCTCGATCGAGTACTAACAATA 59.182 41.667 37.59 16.08 43.70 1.90
1483 1944 3.630769 TGGCTCGATCGAGTACTAACAAT 59.369 43.478 37.59 0.00 43.70 2.71
1484 1945 3.011818 TGGCTCGATCGAGTACTAACAA 58.988 45.455 37.59 17.07 43.70 2.83
1485 1946 2.635714 TGGCTCGATCGAGTACTAACA 58.364 47.619 37.59 25.24 43.70 2.41
1486 1947 3.361414 GTTGGCTCGATCGAGTACTAAC 58.639 50.000 37.59 30.43 43.70 2.34
1487 1948 2.357009 GGTTGGCTCGATCGAGTACTAA 59.643 50.000 37.59 25.68 43.70 2.24
1488 1949 1.945394 GGTTGGCTCGATCGAGTACTA 59.055 52.381 37.59 26.49 43.70 1.82
1489 1950 0.739561 GGTTGGCTCGATCGAGTACT 59.260 55.000 37.59 0.00 43.70 2.73
1490 1951 0.739561 AGGTTGGCTCGATCGAGTAC 59.260 55.000 37.59 30.76 43.70 2.73
1491 1952 0.738975 CAGGTTGGCTCGATCGAGTA 59.261 55.000 37.59 26.98 43.70 2.59
1492 1953 0.965866 TCAGGTTGGCTCGATCGAGT 60.966 55.000 37.59 20.00 43.70 4.18
1493 1954 0.526524 GTCAGGTTGGCTCGATCGAG 60.527 60.000 35.25 35.25 44.56 4.04
1494 1955 1.511305 GTCAGGTTGGCTCGATCGA 59.489 57.895 18.32 18.32 0.00 3.59
1495 1956 1.519455 GGTCAGGTTGGCTCGATCG 60.519 63.158 9.36 9.36 0.00 3.69
1496 1957 0.179000 ATGGTCAGGTTGGCTCGATC 59.821 55.000 0.00 0.00 0.00 3.69
1497 1958 0.107508 CATGGTCAGGTTGGCTCGAT 60.108 55.000 0.00 0.00 0.00 3.59
1498 1959 1.191489 TCATGGTCAGGTTGGCTCGA 61.191 55.000 0.00 0.00 0.00 4.04
1499 1960 0.107508 ATCATGGTCAGGTTGGCTCG 60.108 55.000 0.00 0.00 0.00 5.03
1500 1961 1.386533 CATCATGGTCAGGTTGGCTC 58.613 55.000 0.00 0.00 0.00 4.70
1501 1962 0.033796 CCATCATGGTCAGGTTGGCT 60.034 55.000 0.00 0.00 31.35 4.75
1502 1963 2.496942 CCATCATGGTCAGGTTGGC 58.503 57.895 0.00 0.00 31.35 4.52
1512 1973 5.123227 ACCGTTTACAGAATACCATCATGG 58.877 41.667 0.54 0.54 45.02 3.66
1513 1974 7.441157 ACATACCGTTTACAGAATACCATCATG 59.559 37.037 0.00 0.00 0.00 3.07
1514 1975 7.506114 ACATACCGTTTACAGAATACCATCAT 58.494 34.615 0.00 0.00 0.00 2.45
1515 1976 6.880484 ACATACCGTTTACAGAATACCATCA 58.120 36.000 0.00 0.00 0.00 3.07
1517 1978 9.918630 GTATACATACCGTTTACAGAATACCAT 57.081 33.333 0.00 0.00 33.59 3.55
1518 1979 9.135189 AGTATACATACCGTTTACAGAATACCA 57.865 33.333 5.50 0.00 35.25 3.25
1522 1983 9.359653 ACCTAGTATACATACCGTTTACAGAAT 57.640 33.333 5.50 0.00 35.25 2.40
1523 1984 8.623903 CACCTAGTATACATACCGTTTACAGAA 58.376 37.037 5.50 0.00 35.25 3.02
1524 1985 7.229306 CCACCTAGTATACATACCGTTTACAGA 59.771 40.741 5.50 0.00 35.25 3.41
1525 1986 7.229306 TCCACCTAGTATACATACCGTTTACAG 59.771 40.741 5.50 0.00 35.25 2.74
1526 1987 7.059788 TCCACCTAGTATACATACCGTTTACA 58.940 38.462 5.50 0.00 35.25 2.41
1527 1988 7.308830 CCTCCACCTAGTATACATACCGTTTAC 60.309 44.444 5.50 0.00 33.57 2.01
1528 1989 6.716628 CCTCCACCTAGTATACATACCGTTTA 59.283 42.308 5.50 0.00 33.79 2.01
1529 1990 5.537674 CCTCCACCTAGTATACATACCGTTT 59.462 44.000 5.50 0.00 33.79 3.60
1530 1991 5.075493 CCTCCACCTAGTATACATACCGTT 58.925 45.833 5.50 0.00 33.79 4.44
1531 1992 4.352001 TCCTCCACCTAGTATACATACCGT 59.648 45.833 5.50 0.00 33.79 4.83
1532 1993 4.914983 TCCTCCACCTAGTATACATACCG 58.085 47.826 5.50 0.00 33.79 4.02
1533 1994 6.433716 GTCTTCCTCCACCTAGTATACATACC 59.566 46.154 5.50 0.00 33.79 2.73
1534 1995 6.433716 GGTCTTCCTCCACCTAGTATACATAC 59.566 46.154 5.50 0.00 0.00 2.39
1535 1996 6.550163 GGTCTTCCTCCACCTAGTATACATA 58.450 44.000 5.50 0.00 0.00 2.29
1536 1997 5.395611 GGTCTTCCTCCACCTAGTATACAT 58.604 45.833 5.50 0.00 0.00 2.29
1537 1998 4.688045 CGGTCTTCCTCCACCTAGTATACA 60.688 50.000 5.50 0.00 0.00 2.29
1538 1999 3.819902 CGGTCTTCCTCCACCTAGTATAC 59.180 52.174 0.00 0.00 0.00 1.47
1539 2000 3.461085 ACGGTCTTCCTCCACCTAGTATA 59.539 47.826 0.00 0.00 0.00 1.47
1540 2001 2.244252 ACGGTCTTCCTCCACCTAGTAT 59.756 50.000 0.00 0.00 0.00 2.12
1541 2002 1.637553 ACGGTCTTCCTCCACCTAGTA 59.362 52.381 0.00 0.00 0.00 1.82
1542 2003 0.408700 ACGGTCTTCCTCCACCTAGT 59.591 55.000 0.00 0.00 0.00 2.57
1543 2004 2.022934 GTACGGTCTTCCTCCACCTAG 58.977 57.143 0.00 0.00 0.00 3.02
1544 2005 1.637553 AGTACGGTCTTCCTCCACCTA 59.362 52.381 0.00 0.00 0.00 3.08
1545 2006 0.408700 AGTACGGTCTTCCTCCACCT 59.591 55.000 0.00 0.00 0.00 4.00
1546 2007 1.067071 CAAGTACGGTCTTCCTCCACC 60.067 57.143 0.00 0.00 0.00 4.61
1547 2008 1.617357 ACAAGTACGGTCTTCCTCCAC 59.383 52.381 0.00 0.00 0.00 4.02
1548 2009 1.616865 CACAAGTACGGTCTTCCTCCA 59.383 52.381 0.00 0.00 0.00 3.86
1549 2010 1.672145 GCACAAGTACGGTCTTCCTCC 60.672 57.143 0.00 0.00 0.00 4.30
1550 2011 1.000506 TGCACAAGTACGGTCTTCCTC 59.999 52.381 0.00 0.00 0.00 3.71
1551 2012 1.045407 TGCACAAGTACGGTCTTCCT 58.955 50.000 0.00 0.00 0.00 3.36
1552 2013 1.145803 GTGCACAAGTACGGTCTTCC 58.854 55.000 13.17 0.00 0.00 3.46
1553 2014 1.860676 TGTGCACAAGTACGGTCTTC 58.139 50.000 19.28 0.00 32.48 2.87
1554 2015 2.543777 ATGTGCACAAGTACGGTCTT 57.456 45.000 25.72 0.00 32.48 3.01
1555 2016 2.224185 TGAATGTGCACAAGTACGGTCT 60.224 45.455 25.72 0.00 32.48 3.85
1556 2017 2.139917 TGAATGTGCACAAGTACGGTC 58.860 47.619 25.72 12.38 32.48 4.79
1557 2018 2.248280 TGAATGTGCACAAGTACGGT 57.752 45.000 25.72 1.57 32.48 4.83
1558 2019 3.829886 ATTGAATGTGCACAAGTACGG 57.170 42.857 25.72 0.00 32.48 4.02
1559 2020 4.093408 AGCTATTGAATGTGCACAAGTACG 59.907 41.667 25.72 10.22 32.48 3.67
1560 2021 5.327091 CAGCTATTGAATGTGCACAAGTAC 58.673 41.667 25.72 15.11 0.00 2.73
1561 2022 4.142622 GCAGCTATTGAATGTGCACAAGTA 60.143 41.667 25.72 9.92 34.18 2.24
1562 2023 3.366679 GCAGCTATTGAATGTGCACAAGT 60.367 43.478 25.72 15.19 34.18 3.16
1563 2024 3.176708 GCAGCTATTGAATGTGCACAAG 58.823 45.455 25.72 16.36 34.18 3.16
1564 2025 2.557490 TGCAGCTATTGAATGTGCACAA 59.443 40.909 25.72 7.65 39.17 3.33
1565 2026 2.161030 TGCAGCTATTGAATGTGCACA 58.839 42.857 24.08 24.08 39.17 4.57
1566 2027 2.925578 TGCAGCTATTGAATGTGCAC 57.074 45.000 10.75 10.75 39.17 4.57
1568 2029 2.739292 CCATGCAGCTATTGAATGTGC 58.261 47.619 0.00 3.03 40.74 4.57
1569 2030 2.361119 AGCCATGCAGCTATTGAATGTG 59.639 45.455 0.00 0.00 40.74 3.21
1570 2031 2.621998 GAGCCATGCAGCTATTGAATGT 59.378 45.455 0.00 0.00 45.15 2.71
1571 2032 2.621526 TGAGCCATGCAGCTATTGAATG 59.378 45.455 0.00 0.00 45.15 2.67
1572 2033 2.621998 GTGAGCCATGCAGCTATTGAAT 59.378 45.455 0.00 0.00 45.15 2.57
1573 2034 2.019249 GTGAGCCATGCAGCTATTGAA 58.981 47.619 0.00 0.00 45.15 2.69
1574 2035 1.065272 TGTGAGCCATGCAGCTATTGA 60.065 47.619 0.00 0.00 45.15 2.57
1575 2036 1.385528 TGTGAGCCATGCAGCTATTG 58.614 50.000 0.00 0.00 45.15 1.90
1576 2037 1.954382 CATGTGAGCCATGCAGCTATT 59.046 47.619 0.00 0.00 45.15 1.73
1577 2038 1.605753 CATGTGAGCCATGCAGCTAT 58.394 50.000 0.00 0.00 45.15 2.97
1578 2039 3.089788 CATGTGAGCCATGCAGCTA 57.910 52.632 0.00 0.00 45.15 3.32
1622 2083 9.476928 GGTATCATCTAGTACCCAACATATACT 57.523 37.037 0.00 0.00 35.40 2.12
1623 2084 9.476928 AGGTATCATCTAGTACCCAACATATAC 57.523 37.037 4.13 0.00 41.01 1.47
1624 2085 9.696572 GAGGTATCATCTAGTACCCAACATATA 57.303 37.037 4.13 0.00 41.01 0.86
1625 2086 7.339721 CGAGGTATCATCTAGTACCCAACATAT 59.660 40.741 4.13 0.00 41.01 1.78
1626 2087 6.657966 CGAGGTATCATCTAGTACCCAACATA 59.342 42.308 4.13 0.00 41.01 2.29
1627 2088 5.477291 CGAGGTATCATCTAGTACCCAACAT 59.523 44.000 4.13 0.00 41.01 2.71
1628 2089 4.825634 CGAGGTATCATCTAGTACCCAACA 59.174 45.833 4.13 0.00 41.01 3.33
1629 2090 4.321082 GCGAGGTATCATCTAGTACCCAAC 60.321 50.000 4.13 0.00 41.01 3.77
1630 2091 3.825014 GCGAGGTATCATCTAGTACCCAA 59.175 47.826 4.13 0.00 41.01 4.12
1631 2092 3.418995 GCGAGGTATCATCTAGTACCCA 58.581 50.000 4.13 0.00 41.01 4.51
1632 2093 2.419324 CGCGAGGTATCATCTAGTACCC 59.581 54.545 0.00 0.00 41.01 3.69
1633 2094 2.159544 GCGCGAGGTATCATCTAGTACC 60.160 54.545 12.10 0.02 40.52 3.34
1634 2095 2.474196 CGCGCGAGGTATCATCTAGTAC 60.474 54.545 28.94 0.00 0.00 2.73
1792 2253 8.862325 AATCTCACATTAAGGATGTTGTAACA 57.138 30.769 0.00 0.00 46.80 2.41
2242 2712 8.161699 TCGCTAGAAAAGTTATCCAAAAGTTT 57.838 30.769 0.00 0.00 34.27 2.66


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

AutoCloner maintained by Alex Coulton.