Multiple sequence alignment - TraesCS6B01G420300

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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 TraesCS6B01G420300 chr6B 100.000 2777 0 0 1 2777 691786884 691789660 0.000000e+00 5129.0
1 TraesCS6B01G420300 chr6B 85.948 612 71 12 1272 1872 691632597 691631990 9.510000e-180 640.0
2 TraesCS6B01G420300 chr6B 100.000 189 0 0 2957 3145 691789840 691790028 1.790000e-92 350.0
3 TraesCS6B01G420300 chr6B 85.816 141 13 4 706 841 691633886 691633748 3.270000e-30 143.0
4 TraesCS6B01G420300 chr6A 82.949 1560 173 45 1272 2777 601147684 601149204 0.000000e+00 1321.0
5 TraesCS6B01G420300 chr6A 79.241 790 86 38 531 1270 601146138 601146899 2.190000e-131 479.0
6 TraesCS6B01G420300 chr6A 86.389 360 31 11 680 1022 600964822 600964464 8.230000e-101 377.0
7 TraesCS6B01G420300 chr6A 90.146 274 27 0 1272 1545 601032270 601031997 1.070000e-94 357.0
8 TraesCS6B01G420300 chr6A 83.934 305 31 6 222 523 601143830 601144119 3.090000e-70 276.0
9 TraesCS6B01G420300 chr6A 75.662 604 83 38 706 1270 600913925 600913347 3.130000e-60 243.0
10 TraesCS6B01G420300 chr6A 88.953 172 16 2 2974 3145 601149249 601149417 3.180000e-50 209.0
11 TraesCS6B01G420300 chr6A 84.404 218 20 11 679 895 601033452 601033248 5.320000e-48 202.0
12 TraesCS6B01G420300 chr6A 86.598 194 10 9 1 193 601143654 601143832 1.910000e-47 200.0
13 TraesCS6B01G420300 chr6A 94.531 128 7 0 1143 1270 600963837 600963710 6.880000e-47 198.0
14 TraesCS6B01G420300 chr6A 82.353 170 22 6 1695 1859 600958137 600957971 1.180000e-29 141.0
15 TraesCS6B01G420300 chr6A 87.719 114 14 0 1272 1385 600960613 600960500 1.970000e-27 134.0
16 TraesCS6B01G420300 chr6A 89.216 102 3 3 1004 1104 600964006 600963912 1.530000e-23 121.0
17 TraesCS6B01G420300 chr6A 89.062 64 5 2 662 724 601146033 601146095 9.350000e-11 78.7
18 TraesCS6B01G420300 chr6D 83.803 994 117 23 1272 2234 454826728 454827708 0.000000e+00 904.0
19 TraesCS6B01G420300 chr6D 83.146 979 114 22 1272 2223 454748679 454747725 0.000000e+00 846.0
20 TraesCS6B01G420300 chr6D 84.740 616 70 13 1272 1870 454658136 454657528 2.090000e-166 595.0
21 TraesCS6B01G420300 chr6D 83.521 443 23 16 22 446 454661079 454660669 4.960000e-98 368.0
22 TraesCS6B01G420300 chr6D 83.130 409 57 9 2378 2777 454747640 454747235 2.310000e-96 363.0
23 TraesCS6B01G420300 chr6D 76.098 774 112 46 531 1270 454659642 454658908 1.400000e-88 337.0
24 TraesCS6B01G420300 chr6D 96.571 175 6 0 2958 3132 454747210 454747036 1.100000e-74 291.0
25 TraesCS6B01G420300 chr6D 76.583 521 72 31 779 1270 454825424 454825923 1.130000e-59 241.0
26 TraesCS6B01G420300 chr6D 93.750 96 4 2 32 126 454822398 454822492 3.270000e-30 143.0
27 TraesCS6B01G420300 chr6D 90.291 103 10 0 531 633 420003303 420003405 5.470000e-28 135.0
28 TraesCS6B01G420300 chr6D 85.455 110 8 2 224 326 454822522 454822630 1.190000e-19 108.0
29 TraesCS6B01G420300 chr6D 90.625 64 4 2 662 724 454824016 454824078 2.010000e-12 84.2
30 TraesCS6B01G420300 chr7A 91.262 103 9 0 530 632 724947963 724948065 1.180000e-29 141.0
31 TraesCS6B01G420300 chr7A 94.872 39 2 0 2537 2575 585069665 585069627 9.420000e-06 62.1
32 TraesCS6B01G420300 chr5D 90.566 106 10 0 531 636 455740402 455740297 1.180000e-29 141.0
33 TraesCS6B01G420300 chr3D 91.262 103 9 0 531 633 577584203 577584101 1.180000e-29 141.0
34 TraesCS6B01G420300 chr1B 91.176 102 9 0 531 632 423711097 423710996 4.230000e-29 139.0
35 TraesCS6B01G420300 chr4D 89.091 110 11 1 531 639 46502567 46502676 5.470000e-28 135.0
36 TraesCS6B01G420300 chr3B 90.291 103 10 0 531 633 371013920 371014022 5.470000e-28 135.0
37 TraesCS6B01G420300 chr1D 89.091 110 10 2 531 638 11354717 11354608 5.470000e-28 135.0
38 TraesCS6B01G420300 chr1A 89.091 110 11 1 531 639 266520538 266520647 5.470000e-28 135.0


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 TraesCS6B01G420300 chr6B 691786884 691790028 3144 False 2739.500000 5129 100.000000 1 3145 2 chr6B.!!$F1 3144
1 TraesCS6B01G420300 chr6B 691631990 691633886 1896 True 391.500000 640 85.882000 706 1872 2 chr6B.!!$R1 1166
2 TraesCS6B01G420300 chr6A 601143654 601149417 5763 False 427.283333 1321 85.122833 1 3145 6 chr6A.!!$F1 3144
3 TraesCS6B01G420300 chr6A 601031997 601033452 1455 True 279.500000 357 87.275000 679 1545 2 chr6A.!!$R3 866
4 TraesCS6B01G420300 chr6A 600913347 600913925 578 True 243.000000 243 75.662000 706 1270 1 chr6A.!!$R1 564
5 TraesCS6B01G420300 chr6D 454747036 454748679 1643 True 500.000000 846 87.615667 1272 3132 3 chr6D.!!$R2 1860
6 TraesCS6B01G420300 chr6D 454657528 454661079 3551 True 433.333333 595 81.453000 22 1870 3 chr6D.!!$R1 1848
7 TraesCS6B01G420300 chr6D 454822398 454827708 5310 False 296.040000 904 86.043200 32 2234 5 chr6D.!!$F2 2202

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
130 131 0.106708 GCATATGCTCGGGAACCTGA 59.893 55.0 20.64 2.25 42.52 3.86 F
154 155 0.178068 AAGCGGCTGGTATCGTGAAT 59.822 50.0 1.81 0.00 0.00 2.57 F
155 156 0.178068 AGCGGCTGGTATCGTGAATT 59.822 50.0 0.00 0.00 0.00 2.17 F
1225 4579 0.036388 ATGCCGTCGATTGACAAGGT 60.036 50.0 13.58 0.00 45.80 3.50 F
1751 5943 0.236711 CGGTGACTTGCTTGCAGAAG 59.763 55.0 0.00 0.00 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1077 4385 0.178068 AGTGGTCGAGCTTGTGTGTT 59.822 50.000 16.64 0.0 0.00 3.32 R
1078 4386 0.530650 CAGTGGTCGAGCTTGTGTGT 60.531 55.000 16.64 0.0 0.00 3.72 R
1713 5905 1.000060 CGTCTCGTACAAACTTCCCCA 60.000 52.381 0.00 0.0 0.00 4.96 R
2040 6266 1.103398 CAATTCCGTGATGAGCCCCC 61.103 60.000 0.00 0.0 0.00 5.40 R
2553 6806 2.092968 GGTTCATGTCTATGGCAGTGGA 60.093 50.000 0.00 0.0 34.97 4.02 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
125 126 2.425592 CCGGCATATGCTCGGGAA 59.574 61.111 32.77 0.00 44.99 3.97
126 127 1.961277 CCGGCATATGCTCGGGAAC 60.961 63.158 32.77 15.56 44.99 3.62
127 128 1.961277 CGGCATATGCTCGGGAACC 60.961 63.158 26.12 6.93 43.67 3.62
128 129 1.451936 GGCATATGCTCGGGAACCT 59.548 57.895 26.12 0.00 44.55 3.50
129 130 0.886490 GGCATATGCTCGGGAACCTG 60.886 60.000 26.12 0.00 44.55 4.00
130 131 0.106708 GCATATGCTCGGGAACCTGA 59.893 55.000 20.64 2.25 42.52 3.86
153 154 0.459585 GAAGCGGCTGGTATCGTGAA 60.460 55.000 1.81 0.00 0.00 3.18
154 155 0.178068 AAGCGGCTGGTATCGTGAAT 59.822 50.000 1.81 0.00 0.00 2.57
155 156 0.178068 AGCGGCTGGTATCGTGAATT 59.822 50.000 0.00 0.00 0.00 2.17
156 157 0.582005 GCGGCTGGTATCGTGAATTC 59.418 55.000 0.00 0.00 0.00 2.17
157 158 0.852777 CGGCTGGTATCGTGAATTCG 59.147 55.000 0.04 0.00 0.00 3.34
158 159 1.801395 CGGCTGGTATCGTGAATTCGT 60.801 52.381 0.04 0.00 0.00 3.85
159 160 1.593006 GGCTGGTATCGTGAATTCGTG 59.407 52.381 0.04 0.00 0.00 4.35
160 161 2.536365 GCTGGTATCGTGAATTCGTGA 58.464 47.619 0.04 1.35 0.00 4.35
161 162 3.123804 GCTGGTATCGTGAATTCGTGAT 58.876 45.455 14.40 14.40 0.00 3.06
193 194 4.935205 CCATGTTTGAGATTCCAGAACGTA 59.065 41.667 0.00 0.00 0.00 3.57
196 197 4.988540 TGTTTGAGATTCCAGAACGTACTG 59.011 41.667 0.00 0.00 37.61 2.74
206 207 2.924290 CAGAACGTACTGGAAAGCTAGC 59.076 50.000 6.62 6.62 34.64 3.42
207 208 2.826725 AGAACGTACTGGAAAGCTAGCT 59.173 45.455 12.68 12.68 0.00 3.32
208 209 4.015084 AGAACGTACTGGAAAGCTAGCTA 58.985 43.478 19.70 0.34 0.00 3.32
209 210 3.779271 ACGTACTGGAAAGCTAGCTAC 57.221 47.619 19.70 14.93 0.00 3.58
210 211 2.426381 ACGTACTGGAAAGCTAGCTACC 59.574 50.000 24.99 24.99 0.00 3.18
211 212 2.688958 CGTACTGGAAAGCTAGCTACCT 59.311 50.000 28.81 18.50 0.00 3.08
212 213 3.243134 CGTACTGGAAAGCTAGCTACCTC 60.243 52.174 28.81 20.84 0.00 3.85
213 214 3.108847 ACTGGAAAGCTAGCTACCTCT 57.891 47.619 28.81 17.40 0.00 3.69
214 215 3.028130 ACTGGAAAGCTAGCTACCTCTC 58.972 50.000 28.81 17.08 0.00 3.20
215 216 3.295973 CTGGAAAGCTAGCTACCTCTCT 58.704 50.000 28.81 9.21 0.00 3.10
216 217 3.704061 CTGGAAAGCTAGCTACCTCTCTT 59.296 47.826 28.81 16.02 0.00 2.85
217 218 3.702045 TGGAAAGCTAGCTACCTCTCTTC 59.298 47.826 28.81 21.52 0.00 2.87
218 219 3.958147 GGAAAGCTAGCTACCTCTCTTCT 59.042 47.826 19.70 0.00 0.00 2.85
219 220 4.202111 GGAAAGCTAGCTACCTCTCTTCTG 60.202 50.000 19.70 0.00 0.00 3.02
220 221 2.944129 AGCTAGCTACCTCTCTTCTGG 58.056 52.381 17.69 0.00 0.00 3.86
221 222 1.339929 GCTAGCTACCTCTCTTCTGGC 59.660 57.143 7.70 0.00 0.00 4.85
222 223 1.606668 CTAGCTACCTCTCTTCTGGCG 59.393 57.143 0.00 0.00 0.00 5.69
223 224 0.323908 AGCTACCTCTCTTCTGGCGT 60.324 55.000 0.00 0.00 0.00 5.68
224 225 0.179124 GCTACCTCTCTTCTGGCGTG 60.179 60.000 0.00 0.00 0.00 5.34
225 226 0.179124 CTACCTCTCTTCTGGCGTGC 60.179 60.000 0.00 0.00 0.00 5.34
237 261 2.255252 GCGTGCTTTGACGGCATT 59.745 55.556 0.00 0.00 41.86 3.56
287 314 2.997315 CTCGTGCTGGTCCTCCCA 60.997 66.667 0.00 0.00 42.51 4.37
290 317 3.311110 GTGCTGGTCCTCCCACGA 61.311 66.667 0.00 0.00 38.72 4.35
337 371 2.262915 GGCCCGTGTCTCTCTGTG 59.737 66.667 0.00 0.00 0.00 3.66
340 377 1.908793 CCCGTGTCTCTCTGTGGGT 60.909 63.158 0.00 0.00 31.82 4.51
343 380 1.535833 CGTGTCTCTCTGTGGGTAGT 58.464 55.000 0.00 0.00 0.00 2.73
368 405 3.243359 TCCTGCCAATCTTTTTCCTGT 57.757 42.857 0.00 0.00 0.00 4.00
370 407 2.629617 CCTGCCAATCTTTTTCCTGTGT 59.370 45.455 0.00 0.00 0.00 3.72
373 410 2.224018 GCCAATCTTTTTCCTGTGTGCA 60.224 45.455 0.00 0.00 0.00 4.57
386 423 2.029666 GTGCACAGCTCACGTCCT 59.970 61.111 13.17 0.00 0.00 3.85
448 493 3.675775 GCAGCCGATTTAAAATCAGGCAA 60.676 43.478 20.58 0.00 46.34 4.52
466 511 7.638134 TCAGGCAATTTTTCAATGCTAAAAAC 58.362 30.769 0.00 0.00 38.30 2.43
469 514 7.914871 AGGCAATTTTTCAATGCTAAAAACAAC 59.085 29.630 0.00 0.00 38.30 3.32
490 596 5.138125 ACAATTTAGGAACCATTGTGCTG 57.862 39.130 7.06 0.00 39.22 4.41
508 631 6.723282 TGTGCTGCAAAATTTTAAATCCAAC 58.277 32.000 2.77 0.00 0.00 3.77
525 648 5.633655 TCCAACTTTGAAAGGGTACTACA 57.366 39.130 10.02 0.00 0.00 2.74
526 649 5.370679 TCCAACTTTGAAAGGGTACTACAC 58.629 41.667 10.02 0.00 0.00 2.90
528 651 5.469084 CCAACTTTGAAAGGGTACTACACTC 59.531 44.000 10.02 0.00 24.25 3.51
529 652 6.289064 CAACTTTGAAAGGGTACTACACTCT 58.711 40.000 10.02 0.00 40.91 3.24
541 2745 9.490083 AGGGTACTACACTCTAAAATAAGTGAT 57.510 33.333 9.32 0.00 44.54 3.06
560 2764 7.602517 AGTGATTCTACACTCTAAAACATGC 57.397 36.000 0.00 0.00 46.36 4.06
571 2775 9.712305 ACACTCTAAAACATGCCTATATACATC 57.288 33.333 0.00 0.00 0.00 3.06
579 2783 6.573434 ACATGCCTATATACATCCGTATGTG 58.427 40.000 3.56 0.00 45.99 3.21
580 2784 6.379988 ACATGCCTATATACATCCGTATGTGA 59.620 38.462 3.56 0.00 45.99 3.58
582 2786 8.576442 CATGCCTATATACATCCGTATGTGATA 58.424 37.037 3.56 1.40 45.99 2.15
583 2787 8.166422 TGCCTATATACATCCGTATGTGATAG 57.834 38.462 3.56 9.99 45.99 2.08
584 2788 7.085116 GCCTATATACATCCGTATGTGATAGC 58.915 42.308 3.56 4.50 45.99 2.97
585 2789 7.594714 CCTATATACATCCGTATGTGATAGCC 58.405 42.308 3.56 0.00 45.99 3.93
586 2790 4.737855 ATACATCCGTATGTGATAGCCC 57.262 45.455 3.56 0.00 45.99 5.19
587 2791 1.272490 ACATCCGTATGTGATAGCCCG 59.728 52.381 0.00 0.00 44.79 6.13
588 2792 1.272490 CATCCGTATGTGATAGCCCGT 59.728 52.381 0.00 0.00 0.00 5.28
594 2798 3.245284 CGTATGTGATAGCCCGTTTGAAG 59.755 47.826 0.00 0.00 0.00 3.02
600 2804 4.933400 GTGATAGCCCGTTTGAAGTCTTTA 59.067 41.667 0.00 0.00 0.00 1.85
627 2831 8.857694 AAAGACAAATATTTAGGAACGAAGGA 57.142 30.769 0.00 0.00 0.00 3.36
632 2836 9.901172 ACAAATATTTAGGAACGAAGGAAGTAT 57.099 29.630 0.00 0.00 0.00 2.12
639 2843 9.649167 TTTAGGAACGAAGGAAGTATCTTTAAG 57.351 33.333 0.00 0.00 0.00 1.85
641 2845 6.439692 AGGAACGAAGGAAGTATCTTTAAGGA 59.560 38.462 0.00 0.00 0.00 3.36
642 2846 7.125963 AGGAACGAAGGAAGTATCTTTAAGGAT 59.874 37.037 5.33 5.33 0.00 3.24
644 2848 9.813446 GAACGAAGGAAGTATCTTTAAGGATTA 57.187 33.333 5.30 0.00 0.00 1.75
645 2849 9.819267 AACGAAGGAAGTATCTTTAAGGATTAG 57.181 33.333 5.30 0.00 0.00 1.73
646 2850 8.979534 ACGAAGGAAGTATCTTTAAGGATTAGT 58.020 33.333 5.30 0.00 0.00 2.24
647 2851 9.465985 CGAAGGAAGTATCTTTAAGGATTAGTC 57.534 37.037 5.30 1.38 0.00 2.59
658 2862 1.777941 GGATTAGTCCTGGACGGTCT 58.222 55.000 20.49 6.38 41.60 3.85
659 2863 1.682323 GGATTAGTCCTGGACGGTCTC 59.318 57.143 20.49 14.95 41.60 3.36
660 2864 2.376109 GATTAGTCCTGGACGGTCTCA 58.624 52.381 20.49 3.83 37.67 3.27
666 2870 3.775316 AGTCCTGGACGGTCTCAATATTT 59.225 43.478 20.49 0.00 37.67 1.40
668 2872 4.941873 GTCCTGGACGGTCTCAATATTTTT 59.058 41.667 11.71 0.00 0.00 1.94
669 2873 5.064834 GTCCTGGACGGTCTCAATATTTTTC 59.935 44.000 11.71 0.00 0.00 2.29
670 2874 5.045869 TCCTGGACGGTCTCAATATTTTTCT 60.046 40.000 8.23 0.00 0.00 2.52
671 2875 5.065218 CCTGGACGGTCTCAATATTTTTCTG 59.935 44.000 8.23 0.00 0.00 3.02
673 2877 6.001460 TGGACGGTCTCAATATTTTTCTGTT 58.999 36.000 8.23 0.00 0.00 3.16
726 2935 8.472413 AGTCAAATCCAGGACATTTCAATAATG 58.528 33.333 0.00 0.00 36.50 1.90
735 2944 3.243168 ACATTTCAATAATGCTGCGCGAT 60.243 39.130 12.10 0.00 0.00 4.58
765 3740 2.925563 GCATAGCTTTTGTCATGCAACC 59.074 45.455 11.19 0.00 42.61 3.77
801 4072 1.966451 GGACCTTTCCGTGGCAGTG 60.966 63.158 0.00 0.00 29.98 3.66
856 4132 3.538614 GCCCTATGTCGGCTCAGA 58.461 61.111 0.00 0.00 43.48 3.27
961 4254 2.043852 GAGACGAGCCTCCCCTCA 60.044 66.667 0.00 0.00 0.00 3.86
962 4255 2.363147 AGACGAGCCTCCCCTCAC 60.363 66.667 0.00 0.00 0.00 3.51
966 4259 2.294078 CGAGCCTCCCCTCACCTTT 61.294 63.158 0.00 0.00 0.00 3.11
983 4276 3.858868 TTCCGCTCACGCACTCCAC 62.859 63.158 0.00 0.00 38.22 4.02
984 4277 4.363990 CCGCTCACGCACTCCACT 62.364 66.667 0.00 0.00 38.22 4.00
989 4282 2.740055 CACGCACTCCACTCCAGC 60.740 66.667 0.00 0.00 0.00 4.85
1009 4307 1.783711 CGAGTATTGCATCGCAGTCTC 59.216 52.381 0.00 0.00 40.61 3.36
1016 4314 1.284982 GCATCGCAGTCTCGTTGTGT 61.285 55.000 0.00 0.00 33.22 3.72
1021 4319 1.062002 CGCAGTCTCGTTGTGTTGTTT 59.938 47.619 0.00 0.00 0.00 2.83
1022 4320 2.705154 GCAGTCTCGTTGTGTTGTTTC 58.295 47.619 0.00 0.00 0.00 2.78
1025 4323 0.299300 TCTCGTTGTGTTGTTTCGCG 59.701 50.000 0.00 0.00 0.00 5.87
1026 4324 1.253044 CTCGTTGTGTTGTTTCGCGC 61.253 55.000 0.00 0.00 0.00 6.86
1027 4325 1.297304 CGTTGTGTTGTTTCGCGCT 60.297 52.632 5.56 0.00 0.00 5.92
1036 4344 2.074920 GTTTCGCGCTTGCTTTCCG 61.075 57.895 5.56 0.00 36.08 4.30
1070 4378 0.788391 GCACGTTAACCGGACAGAAG 59.212 55.000 9.46 0.00 42.24 2.85
1071 4379 1.870993 GCACGTTAACCGGACAGAAGT 60.871 52.381 9.46 0.00 42.24 3.01
1072 4380 2.056577 CACGTTAACCGGACAGAAGTC 58.943 52.381 9.46 0.00 44.21 3.01
1073 4381 1.682854 ACGTTAACCGGACAGAAGTCA 59.317 47.619 9.46 0.00 46.80 3.41
1074 4382 2.056577 CGTTAACCGGACAGAAGTCAC 58.943 52.381 9.46 0.00 46.80 3.67
1075 4383 2.544277 CGTTAACCGGACAGAAGTCACA 60.544 50.000 9.46 0.00 46.80 3.58
1076 4384 3.660865 GTTAACCGGACAGAAGTCACAT 58.339 45.455 9.46 0.00 46.80 3.21
1077 4385 4.616604 CGTTAACCGGACAGAAGTCACATA 60.617 45.833 9.46 0.00 46.80 2.29
1078 4386 5.232463 GTTAACCGGACAGAAGTCACATAA 58.768 41.667 9.46 0.00 46.80 1.90
1090 4398 3.059884 AGTCACATAACACACAAGCTCG 58.940 45.455 0.00 0.00 0.00 5.03
1091 4399 3.057019 GTCACATAACACACAAGCTCGA 58.943 45.455 0.00 0.00 0.00 4.04
1137 4456 3.181510 CGAAGGCAATTTGGTACTACTGC 60.182 47.826 0.00 0.00 0.00 4.40
1138 4457 3.721087 AGGCAATTTGGTACTACTGCT 57.279 42.857 0.00 0.00 0.00 4.24
1139 4458 4.837093 AGGCAATTTGGTACTACTGCTA 57.163 40.909 0.00 0.00 0.00 3.49
1140 4459 4.770795 AGGCAATTTGGTACTACTGCTAG 58.229 43.478 0.00 0.00 0.00 3.42
1141 4460 4.225267 AGGCAATTTGGTACTACTGCTAGT 59.775 41.667 0.00 0.00 37.04 2.57
1225 4579 0.036388 ATGCCGTCGATTGACAAGGT 60.036 50.000 13.58 0.00 45.80 3.50
1259 4613 4.728110 ATGAAGCAGCGGCAGCCA 62.728 61.111 13.30 6.27 46.67 4.75
1369 5550 2.355115 CAAGCCCACCTACCCCAC 59.645 66.667 0.00 0.00 0.00 4.61
1427 5608 1.515954 CGCCCACGTCCTTGTCTAT 59.484 57.895 0.00 0.00 33.53 1.98
1500 5681 2.581354 CCCACTTCCTCCAGCTCG 59.419 66.667 0.00 0.00 0.00 5.03
1520 5701 2.579738 GGCGACCTCTTCCCTCAC 59.420 66.667 0.00 0.00 0.00 3.51
1544 5725 3.252400 CAACATAACCGCCAAGTACGTA 58.748 45.455 0.00 0.00 0.00 3.57
1550 5737 1.336240 ACCGCCAAGTACGTAGACAAC 60.336 52.381 0.00 0.00 0.00 3.32
1574 5765 6.863126 ACAATTTCAACCTGTTTGATTCGATC 59.137 34.615 0.00 0.00 43.99 3.69
1581 5772 0.746563 GTTTGATTCGATCCGGGGCA 60.747 55.000 0.00 0.00 0.00 5.36
1606 5797 0.955428 TGCTTGCTCACCGTGGATTC 60.955 55.000 0.00 0.00 0.00 2.52
1619 5810 1.971167 GGATTCTGTTGGCGTGGCA 60.971 57.895 0.00 0.00 0.00 4.92
1634 5826 2.758089 GGCATGCAGGTGCGAAGAG 61.758 63.158 21.36 0.00 45.97 2.85
1643 5835 1.959226 GTGCGAAGAGGACGGCAAA 60.959 57.895 0.00 0.00 0.00 3.68
1691 5883 2.279073 CGGAGGCTGAGGGACCTA 59.721 66.667 0.00 0.00 36.05 3.08
1717 5909 2.990066 GAGTTCACTCCACTATGGGG 57.010 55.000 0.00 0.00 45.84 4.96
1739 5931 1.952296 AGTTTGTACGAGACGGTGACT 59.048 47.619 0.00 0.00 0.00 3.41
1751 5943 0.236711 CGGTGACTTGCTTGCAGAAG 59.763 55.000 0.00 0.00 0.00 2.85
1788 5980 1.551908 GCCCATTGTTCCCATGGCAA 61.552 55.000 6.09 5.94 34.24 4.52
1816 6018 3.735591 GTGCCTACTTGTAACAGGACAA 58.264 45.455 0.00 0.00 36.98 3.18
1850 6052 2.807967 TCCGATGAAACAAACAGAGCAG 59.192 45.455 0.00 0.00 0.00 4.24
1869 6071 3.946558 GCAGAGCAGGAATGAAAGAAGAT 59.053 43.478 0.00 0.00 0.00 2.40
1872 6074 5.646793 CAGAGCAGGAATGAAAGAAGATGAA 59.353 40.000 0.00 0.00 0.00 2.57
1927 6132 7.015289 CACGGAATTGTGTATTTCTACAAGTG 58.985 38.462 0.00 0.00 39.51 3.16
2002 6225 2.229675 AAACAAAGCAAAGCAGGAGC 57.770 45.000 0.00 0.00 42.56 4.70
2005 6228 0.956633 CAAAGCAAAGCAGGAGCAGA 59.043 50.000 0.00 0.00 45.49 4.26
2015 6241 2.028203 AGCAGGAGCAGAAGAAGACTTC 60.028 50.000 7.14 7.14 44.29 3.01
2044 6270 4.356436 AGAAGAAATCAGGATTTTGGGGG 58.644 43.478 8.53 0.00 40.77 5.40
2045 6271 2.470990 AGAAATCAGGATTTTGGGGGC 58.529 47.619 8.53 0.00 40.77 5.80
2052 6278 1.114627 GGATTTTGGGGGCTCATCAC 58.885 55.000 0.00 0.00 0.00 3.06
2058 6285 1.227383 GGGGGCTCATCACGGAATT 59.773 57.895 0.00 0.00 0.00 2.17
2070 6297 4.066646 TCACGGAATTGTGTCTTTCTGA 57.933 40.909 0.00 0.00 40.74 3.27
2103 6330 7.390440 AGAATGCAGCATGTAGTAAAAGTTGTA 59.610 33.333 9.18 0.00 39.31 2.41
2155 6386 1.486310 TGGGTCGATGGAGAAGAATGG 59.514 52.381 0.00 0.00 0.00 3.16
2175 6406 8.360390 AGAATGGGTCTTACAAGTTTGATTTTC 58.640 33.333 0.00 0.00 29.66 2.29
2223 6457 6.599244 TCACAGGGAGAGTAAATTGCAAATAG 59.401 38.462 1.71 0.00 0.00 1.73
2225 6459 4.889995 AGGGAGAGTAAATTGCAAATAGCC 59.110 41.667 1.71 0.00 44.83 3.93
2226 6460 4.644685 GGGAGAGTAAATTGCAAATAGCCA 59.355 41.667 1.71 0.00 44.83 4.75
2227 6461 5.450550 GGGAGAGTAAATTGCAAATAGCCAC 60.451 44.000 1.71 0.00 44.83 5.01
2228 6462 5.125417 GGAGAGTAAATTGCAAATAGCCACA 59.875 40.000 1.71 0.00 44.83 4.17
2229 6463 6.350110 GGAGAGTAAATTGCAAATAGCCACAA 60.350 38.462 1.71 0.00 44.83 3.33
2230 6464 7.174107 AGAGTAAATTGCAAATAGCCACAAT 57.826 32.000 1.71 0.00 44.83 2.71
2231 6465 8.292444 AGAGTAAATTGCAAATAGCCACAATA 57.708 30.769 1.71 0.00 44.83 1.90
2232 6466 8.408601 AGAGTAAATTGCAAATAGCCACAATAG 58.591 33.333 1.71 0.00 44.83 1.73
2233 6467 8.066612 AGTAAATTGCAAATAGCCACAATAGT 57.933 30.769 1.71 0.00 44.83 2.12
2234 6468 9.184523 AGTAAATTGCAAATAGCCACAATAGTA 57.815 29.630 1.71 0.00 44.83 1.82
2235 6469 9.233232 GTAAATTGCAAATAGCCACAATAGTAC 57.767 33.333 1.71 0.00 44.83 2.73
2236 6470 5.828299 TTGCAAATAGCCACAATAGTACC 57.172 39.130 0.00 0.00 44.83 3.34
2237 6471 4.204012 TGCAAATAGCCACAATAGTACCC 58.796 43.478 0.00 0.00 44.83 3.69
2238 6472 3.568430 GCAAATAGCCACAATAGTACCCC 59.432 47.826 0.00 0.00 37.23 4.95
2239 6473 4.688874 GCAAATAGCCACAATAGTACCCCT 60.689 45.833 0.00 0.00 37.23 4.79
2240 6474 5.455612 GCAAATAGCCACAATAGTACCCCTA 60.456 44.000 0.00 0.00 37.23 3.53
2241 6475 6.597562 CAAATAGCCACAATAGTACCCCTAA 58.402 40.000 0.00 0.00 0.00 2.69
2242 6476 6.835029 AATAGCCACAATAGTACCCCTAAA 57.165 37.500 0.00 0.00 0.00 1.85
2243 6477 6.835029 ATAGCCACAATAGTACCCCTAAAA 57.165 37.500 0.00 0.00 0.00 1.52
2244 6478 5.523883 AGCCACAATAGTACCCCTAAAAA 57.476 39.130 0.00 0.00 0.00 1.94
2274 6508 4.322725 CCACAACAGTTGGCAGAGATACTA 60.323 45.833 17.76 0.00 34.12 1.82
2282 6516 6.595326 CAGTTGGCAGAGATACTATTGTTTCA 59.405 38.462 1.28 0.00 0.00 2.69
2320 6555 6.552445 TTTGGTTTTCTCATTGAAGGGAAA 57.448 33.333 0.00 0.00 35.89 3.13
2322 6557 7.847711 TTGGTTTTCTCATTGAAGGGAAATA 57.152 32.000 0.00 0.00 35.89 1.40
2346 6581 9.905171 ATAATATCGACATATCAAGATGATCCG 57.095 33.333 0.00 0.00 38.26 4.18
2353 6588 3.692257 ATCAAGATGATCCGATCCCAC 57.308 47.619 5.91 0.00 29.59 4.61
2355 6590 2.366590 TCAAGATGATCCGATCCCACAG 59.633 50.000 5.91 0.00 0.00 3.66
2360 6595 3.475566 TGATCCGATCCCACAGAATTC 57.524 47.619 5.91 0.00 0.00 2.17
2507 6760 2.159114 GCCATCCATGCGTGGTAAATTT 60.159 45.455 24.24 0.00 46.16 1.82
2572 6825 2.840038 ACTCCACTGCCATAGACATGAA 59.160 45.455 0.00 0.00 33.67 2.57
2661 6918 0.907486 CTTCATGGACTCTGGCTGGA 59.093 55.000 0.00 0.00 0.00 3.86
2668 6925 2.087646 GGACTCTGGCTGGATGAAAAC 58.912 52.381 0.00 0.00 0.00 2.43
2672 6929 1.144708 TCTGGCTGGATGAAAACACCA 59.855 47.619 0.00 0.00 0.00 4.17
2686 6943 7.282332 TGAAAACACCATGTCATGTATGAAA 57.718 32.000 17.11 0.00 38.75 2.69
2710 6967 6.925610 ATCATACAAGCATACAACGTTGAT 57.074 33.333 33.66 19.07 0.00 2.57
2719 6976 4.750098 GCATACAACGTTGATAGCCTATGT 59.250 41.667 33.66 11.22 0.00 2.29
2728 6985 5.121298 CGTTGATAGCCTATGTCAATCATGG 59.879 44.000 0.00 0.00 40.61 3.66
2747 7004 7.377766 TCATGGTAGAAATAACAGAGCAAAC 57.622 36.000 0.00 0.00 0.00 2.93
3004 7261 1.578206 GACCCGCTCCTGTTTTGCTC 61.578 60.000 0.00 0.00 0.00 4.26
3059 7316 6.025539 TGATAGCATCCTTATCCATGTACCT 58.974 40.000 0.00 0.00 0.00 3.08
3105 7362 0.673333 TGCCATAGAACACACCAGCG 60.673 55.000 0.00 0.00 0.00 5.18
3107 7364 0.036388 CCATAGAACACACCAGCGGT 60.036 55.000 0.00 0.00 35.62 5.68
3132 7389 5.338300 GCATCCTTCCTCTTCTTCTTCTTCT 60.338 44.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 1.352352 ACTGGTTTGATCACAGGAGGG 59.648 52.381 14.35 0.00 36.57 4.30
38 39 1.808945 GCCTGACTGGTTTGATCACAG 59.191 52.381 9.61 9.61 38.35 3.66
39 40 1.545428 GGCCTGACTGGTTTGATCACA 60.545 52.381 0.00 0.00 38.35 3.58
40 41 1.168714 GGCCTGACTGGTTTGATCAC 58.831 55.000 0.00 0.00 38.35 3.06
117 118 4.452733 CCCGTCAGGTTCCCGAGC 62.453 72.222 0.00 0.00 35.12 5.03
118 119 2.227089 CTTCCCGTCAGGTTCCCGAG 62.227 65.000 0.00 0.00 36.75 4.63
119 120 2.203669 TTCCCGTCAGGTTCCCGA 60.204 61.111 0.00 0.00 36.75 5.14
120 121 2.264794 CTTCCCGTCAGGTTCCCG 59.735 66.667 0.00 0.00 36.75 5.14
122 123 2.434359 CGCTTCCCGTCAGGTTCC 60.434 66.667 0.00 0.00 36.75 3.62
123 124 2.434359 CCGCTTCCCGTCAGGTTC 60.434 66.667 0.00 0.00 36.75 3.62
124 125 4.699522 GCCGCTTCCCGTCAGGTT 62.700 66.667 0.00 0.00 36.75 3.50
129 130 2.973180 GATACCAGCCGCTTCCCGTC 62.973 65.000 0.00 0.00 34.38 4.79
130 131 3.081409 ATACCAGCCGCTTCCCGT 61.081 61.111 0.00 0.00 34.38 5.28
153 154 0.908910 TGGGGCAGTACATCACGAAT 59.091 50.000 0.00 0.00 0.00 3.34
154 155 0.908910 ATGGGGCAGTACATCACGAA 59.091 50.000 0.00 0.00 0.00 3.85
155 156 0.177836 CATGGGGCAGTACATCACGA 59.822 55.000 0.00 0.00 0.00 4.35
156 157 0.107703 ACATGGGGCAGTACATCACG 60.108 55.000 0.00 0.00 0.00 4.35
157 158 2.128771 AACATGGGGCAGTACATCAC 57.871 50.000 0.00 0.00 0.00 3.06
158 159 2.040947 TCAAACATGGGGCAGTACATCA 59.959 45.455 0.00 0.00 0.00 3.07
159 160 2.684881 CTCAAACATGGGGCAGTACATC 59.315 50.000 0.00 0.00 0.00 3.06
160 161 2.308570 TCTCAAACATGGGGCAGTACAT 59.691 45.455 0.00 0.00 0.00 2.29
161 162 1.702401 TCTCAAACATGGGGCAGTACA 59.298 47.619 0.00 0.00 0.00 2.90
193 194 3.028130 GAGAGGTAGCTAGCTTTCCAGT 58.972 50.000 25.49 19.51 33.58 4.00
196 197 3.958147 AGAAGAGAGGTAGCTAGCTTTCC 59.042 47.826 29.69 23.66 36.07 3.13
197 198 4.202111 CCAGAAGAGAGGTAGCTAGCTTTC 60.202 50.000 27.48 27.48 35.79 2.62
198 199 3.704061 CCAGAAGAGAGGTAGCTAGCTTT 59.296 47.826 24.88 20.36 33.58 3.51
199 200 3.295973 CCAGAAGAGAGGTAGCTAGCTT 58.704 50.000 24.88 15.38 33.58 3.74
200 201 2.944129 CCAGAAGAGAGGTAGCTAGCT 58.056 52.381 24.94 24.94 36.62 3.32
201 202 1.339929 GCCAGAAGAGAGGTAGCTAGC 59.660 57.143 15.19 15.19 0.00 3.42
202 203 1.606668 CGCCAGAAGAGAGGTAGCTAG 59.393 57.143 0.00 0.00 0.00 3.42
203 204 1.064611 ACGCCAGAAGAGAGGTAGCTA 60.065 52.381 0.00 0.00 0.00 3.32
204 205 0.323908 ACGCCAGAAGAGAGGTAGCT 60.324 55.000 0.00 0.00 0.00 3.32
205 206 0.179124 CACGCCAGAAGAGAGGTAGC 60.179 60.000 0.00 0.00 0.00 3.58
206 207 0.179124 GCACGCCAGAAGAGAGGTAG 60.179 60.000 0.00 0.00 0.00 3.18
207 208 0.612174 AGCACGCCAGAAGAGAGGTA 60.612 55.000 0.00 0.00 0.00 3.08
208 209 1.476007 AAGCACGCCAGAAGAGAGGT 61.476 55.000 0.00 0.00 0.00 3.85
209 210 0.321122 AAAGCACGCCAGAAGAGAGG 60.321 55.000 0.00 0.00 0.00 3.69
210 211 0.795085 CAAAGCACGCCAGAAGAGAG 59.205 55.000 0.00 0.00 0.00 3.20
211 212 0.392706 TCAAAGCACGCCAGAAGAGA 59.607 50.000 0.00 0.00 0.00 3.10
212 213 0.514691 GTCAAAGCACGCCAGAAGAG 59.485 55.000 0.00 0.00 0.00 2.85
213 214 1.221466 CGTCAAAGCACGCCAGAAGA 61.221 55.000 0.00 0.00 31.96 2.87
214 215 1.205064 CGTCAAAGCACGCCAGAAG 59.795 57.895 0.00 0.00 31.96 2.85
215 216 2.250939 CCGTCAAAGCACGCCAGAA 61.251 57.895 0.00 0.00 38.52 3.02
216 217 2.664851 CCGTCAAAGCACGCCAGA 60.665 61.111 0.00 0.00 38.52 3.86
217 218 4.389576 GCCGTCAAAGCACGCCAG 62.390 66.667 0.00 0.00 38.52 4.85
219 220 2.747507 AAATGCCGTCAAAGCACGCC 62.748 55.000 0.00 0.00 44.40 5.68
220 221 0.939106 AAAATGCCGTCAAAGCACGC 60.939 50.000 0.00 0.00 44.40 5.34
221 222 0.777631 CAAAATGCCGTCAAAGCACG 59.222 50.000 0.00 0.00 44.40 5.34
222 223 0.508213 GCAAAATGCCGTCAAAGCAC 59.492 50.000 0.00 0.00 44.40 4.40
223 224 0.388659 AGCAAAATGCCGTCAAAGCA 59.611 45.000 0.00 0.00 46.52 3.91
224 225 1.192980 CAAGCAAAATGCCGTCAAAGC 59.807 47.619 0.00 0.00 46.52 3.51
225 226 1.192980 GCAAGCAAAATGCCGTCAAAG 59.807 47.619 0.00 0.00 46.52 2.77
237 261 1.157257 TCTTCGCTGACGCAAGCAAA 61.157 50.000 10.22 0.00 43.73 3.68
253 280 2.945668 ACGAGTTGCTTCTTTGCTTCTT 59.054 40.909 0.00 0.00 0.00 2.52
287 314 2.517402 CGGAGCTAGAGCCCTCGT 60.517 66.667 0.00 0.00 43.38 4.18
290 317 2.443016 CACCGGAGCTAGAGCCCT 60.443 66.667 9.46 0.00 43.38 5.19
337 371 0.035739 TTGGCAGGAACGAACTACCC 59.964 55.000 0.00 0.00 0.00 3.69
340 377 3.695830 AAGATTGGCAGGAACGAACTA 57.304 42.857 0.00 0.00 0.00 2.24
343 380 3.005367 GGAAAAAGATTGGCAGGAACGAA 59.995 43.478 0.00 0.00 0.00 3.85
368 405 2.280119 GGACGTGAGCTGTGCACA 60.280 61.111 20.37 20.37 36.06 4.57
370 407 2.340078 GAGGACGTGAGCTGTGCA 59.660 61.111 0.00 0.00 0.00 4.57
373 410 2.920645 CGTGGAGGACGTGAGCTGT 61.921 63.158 0.00 0.00 43.50 4.40
386 423 4.367023 GGTGCACCTACGCGTGGA 62.367 66.667 29.12 4.04 34.16 4.02
404 441 2.043752 TACCGTCCGATGCTCCCA 60.044 61.111 0.00 0.00 0.00 4.37
466 511 5.406175 CAGCACAATGGTTCCTAAATTGTTG 59.594 40.000 0.00 0.00 41.39 3.33
469 514 3.928375 GCAGCACAATGGTTCCTAAATTG 59.072 43.478 0.00 0.00 37.33 2.32
477 583 4.816786 AAATTTTGCAGCACAATGGTTC 57.183 36.364 7.56 0.00 38.31 3.62
508 631 8.897872 TTTTAGAGTGTAGTACCCTTTCAAAG 57.102 34.615 0.00 0.00 0.00 2.77
535 2739 7.119846 GGCATGTTTTAGAGTGTAGAATCACTT 59.880 37.037 0.00 0.00 46.81 3.16
556 2760 6.805713 TCACATACGGATGTATATAGGCATG 58.194 40.000 14.23 0.00 44.82 4.06
560 2764 7.309255 GGGCTATCACATACGGATGTATATAGG 60.309 44.444 27.55 13.23 44.82 2.57
571 2775 1.864711 CAAACGGGCTATCACATACGG 59.135 52.381 0.00 0.00 0.00 4.02
579 2783 6.490566 TTTAAAGACTTCAAACGGGCTATC 57.509 37.500 0.00 0.00 0.00 2.08
580 2784 6.887626 TTTTAAAGACTTCAAACGGGCTAT 57.112 33.333 0.00 0.00 0.00 2.97
582 2786 5.358725 TCTTTTTAAAGACTTCAAACGGGCT 59.641 36.000 0.89 0.00 39.95 5.19
583 2787 5.584442 TCTTTTTAAAGACTTCAAACGGGC 58.416 37.500 0.89 0.00 39.95 6.13
600 2804 9.908152 CCTTCGTTCCTAAATATTTGTCTTTTT 57.092 29.630 11.05 0.00 0.00 1.94
618 2822 8.719560 AATCCTTAAAGATACTTCCTTCGTTC 57.280 34.615 0.00 0.00 0.00 3.95
621 2825 9.465985 GACTAATCCTTAAAGATACTTCCTTCG 57.534 37.037 0.00 0.00 0.00 3.79
639 2843 1.682323 GAGACCGTCCAGGACTAATCC 59.318 57.143 17.95 2.59 44.84 3.01
641 2845 2.526888 TGAGACCGTCCAGGACTAAT 57.473 50.000 17.95 2.39 44.84 1.73
642 2846 2.297698 TTGAGACCGTCCAGGACTAA 57.702 50.000 17.95 0.88 44.84 2.24
645 2849 3.821421 AATATTGAGACCGTCCAGGAC 57.179 47.619 9.92 9.92 45.00 3.85
646 2850 4.837093 AAAATATTGAGACCGTCCAGGA 57.163 40.909 0.00 0.00 45.00 3.86
649 2853 5.556915 ACAGAAAAATATTGAGACCGTCCA 58.443 37.500 0.00 0.00 0.00 4.02
650 2854 6.496338 AACAGAAAAATATTGAGACCGTCC 57.504 37.500 0.00 0.00 0.00 4.79
651 2855 9.887406 TTTTAACAGAAAAATATTGAGACCGTC 57.113 29.630 0.00 0.00 0.00 4.79
691 2895 2.225369 CCTGGATTTGACTTTCCCCCTT 60.225 50.000 0.00 0.00 0.00 3.95
694 2898 2.225017 TGTCCTGGATTTGACTTTCCCC 60.225 50.000 0.00 0.00 32.67 4.81
735 2944 4.340666 TGACAAAAGCTATGCTGGTTTTCA 59.659 37.500 10.26 0.00 43.09 2.69
853 4129 1.767759 GATGGGTGGGTTTGGATCTG 58.232 55.000 0.00 0.00 0.00 2.90
856 4132 1.306296 CCGATGGGTGGGTTTGGAT 59.694 57.895 0.00 0.00 0.00 3.41
904 4185 0.676466 TTATGGAAGTGGTGCAGCCG 60.676 55.000 14.36 0.00 41.21 5.52
950 4243 1.925972 GGAAAGGTGAGGGGAGGCT 60.926 63.158 0.00 0.00 0.00 4.58
983 4276 1.135046 CGATGCAATACTCGCTGGAG 58.865 55.000 0.00 0.00 46.13 3.86
984 4277 3.272766 CGATGCAATACTCGCTGGA 57.727 52.632 0.00 0.00 0.00 3.86
989 4282 1.783711 GAGACTGCGATGCAATACTCG 59.216 52.381 3.09 3.09 38.41 4.18
990 4283 1.783711 CGAGACTGCGATGCAATACTC 59.216 52.381 0.00 1.99 38.41 2.59
1007 4305 1.253044 GCGCGAAACAACACAACGAG 61.253 55.000 12.10 0.00 0.00 4.18
1009 4307 0.859788 AAGCGCGAAACAACACAACG 60.860 50.000 12.10 0.00 0.00 4.10
1016 4314 0.593773 GGAAAGCAAGCGCGAAACAA 60.594 50.000 12.10 0.00 45.49 2.83
1021 4319 2.845752 ATACCGGAAAGCAAGCGCGA 62.846 55.000 12.10 0.00 45.49 5.87
1022 4320 1.149361 TATACCGGAAAGCAAGCGCG 61.149 55.000 9.46 0.00 45.49 6.86
1025 4323 5.277828 CCACTATTTATACCGGAAAGCAAGC 60.278 44.000 9.46 0.00 0.00 4.01
1026 4324 6.053005 TCCACTATTTATACCGGAAAGCAAG 58.947 40.000 9.46 0.00 0.00 4.01
1027 4325 5.991861 TCCACTATTTATACCGGAAAGCAA 58.008 37.500 9.46 0.00 0.00 3.91
1036 4344 6.201615 GGTTAACGTGCTCCACTATTTATACC 59.798 42.308 0.00 0.00 31.34 2.73
1070 4378 3.057019 TCGAGCTTGTGTGTTATGTGAC 58.943 45.455 0.00 0.00 0.00 3.67
1071 4379 3.057019 GTCGAGCTTGTGTGTTATGTGA 58.943 45.455 0.00 0.00 0.00 3.58
1072 4380 2.157668 GGTCGAGCTTGTGTGTTATGTG 59.842 50.000 7.51 0.00 0.00 3.21
1073 4381 2.224185 TGGTCGAGCTTGTGTGTTATGT 60.224 45.455 16.64 0.00 0.00 2.29
1074 4382 2.157668 GTGGTCGAGCTTGTGTGTTATG 59.842 50.000 16.64 0.00 0.00 1.90
1075 4383 2.037251 AGTGGTCGAGCTTGTGTGTTAT 59.963 45.455 16.64 0.00 0.00 1.89
1076 4384 1.411246 AGTGGTCGAGCTTGTGTGTTA 59.589 47.619 16.64 0.00 0.00 2.41
1077 4385 0.178068 AGTGGTCGAGCTTGTGTGTT 59.822 50.000 16.64 0.00 0.00 3.32
1078 4386 0.530650 CAGTGGTCGAGCTTGTGTGT 60.531 55.000 16.64 0.00 0.00 3.72
1090 4398 2.408271 TGCTTGGATGATCAGTGGTC 57.592 50.000 0.09 0.00 0.00 4.02
1091 4399 2.240414 TGATGCTTGGATGATCAGTGGT 59.760 45.455 0.09 0.00 0.00 4.16
1116 4435 4.010349 AGCAGTAGTACCAAATTGCCTTC 58.990 43.478 7.61 0.00 32.21 3.46
1137 4456 8.821894 GGATGTTGAAGTAAGATTGCTAACTAG 58.178 37.037 0.00 0.00 0.00 2.57
1138 4457 8.318412 TGGATGTTGAAGTAAGATTGCTAACTA 58.682 33.333 0.00 0.00 0.00 2.24
1139 4458 7.119846 GTGGATGTTGAAGTAAGATTGCTAACT 59.880 37.037 0.00 0.00 0.00 2.24
1140 4459 7.094805 TGTGGATGTTGAAGTAAGATTGCTAAC 60.095 37.037 0.00 0.00 0.00 2.34
1141 4460 6.939730 TGTGGATGTTGAAGTAAGATTGCTAA 59.060 34.615 0.00 0.00 0.00 3.09
1152 4502 6.258727 GTCGATCAATATGTGGATGTTGAAGT 59.741 38.462 0.00 0.00 41.43 3.01
1238 4592 1.153409 CTGCCGCTGCTTCATCTCT 60.153 57.895 0.70 0.00 38.71 3.10
1266 4620 2.821366 GGTCATGGACGGCTGCTG 60.821 66.667 6.98 6.98 32.65 4.41
1305 5486 1.909141 CTGCTGCTGAAGTTGAGCGG 61.909 60.000 17.82 17.82 44.42 5.52
1382 5563 1.323136 CGTCACGAACGTCGGTGTAC 61.323 60.000 15.79 12.19 45.59 2.90
1500 5681 3.066233 GAGGGAAGAGGTCGCCGAC 62.066 68.421 9.15 9.15 40.05 4.79
1520 5701 3.305094 CGTACTTGGCGGTTATGTTGTAG 59.695 47.826 0.00 0.00 0.00 2.74
1544 5725 6.279513 TCAAACAGGTTGAAATTGTTGTCT 57.720 33.333 0.00 0.00 43.43 3.41
1581 5772 1.174712 ACGGTGAGCAAGCAAGCAAT 61.175 50.000 3.19 0.00 36.85 3.56
1606 5797 3.620300 CTGCATGCCACGCCAACAG 62.620 63.158 16.68 0.00 0.00 3.16
1619 5810 1.078848 GTCCTCTTCGCACCTGCAT 60.079 57.895 0.00 0.00 42.21 3.96
1634 5826 3.758931 GCCATGGGTTTGCCGTCC 61.759 66.667 15.13 0.00 34.97 4.79
1709 5901 4.081807 GTCTCGTACAAACTTCCCCATAGT 60.082 45.833 0.00 0.00 0.00 2.12
1712 5904 2.353406 CGTCTCGTACAAACTTCCCCAT 60.353 50.000 0.00 0.00 0.00 4.00
1713 5905 1.000060 CGTCTCGTACAAACTTCCCCA 60.000 52.381 0.00 0.00 0.00 4.96
1717 5909 2.723143 GTCACCGTCTCGTACAAACTTC 59.277 50.000 0.00 0.00 0.00 3.01
1739 5931 1.181098 GGCCCTTCTTCTGCAAGCAA 61.181 55.000 0.00 0.00 0.00 3.91
1788 5980 2.536761 TACAAGTAGGCACGCTTTGT 57.463 45.000 0.00 0.00 0.00 2.83
1831 6033 3.666374 GCTCTGCTCTGTTTGTTTCATCG 60.666 47.826 0.00 0.00 0.00 3.84
1850 6052 5.879223 TCTTCATCTTCTTTCATTCCTGCTC 59.121 40.000 0.00 0.00 0.00 4.26
1899 6104 5.470437 TGTAGAAATACACAATTCCGTGCAA 59.530 36.000 0.00 0.00 40.73 4.08
1904 6109 7.129109 ACACTTGTAGAAATACACAATTCCG 57.871 36.000 0.00 0.00 34.34 4.30
1959 6180 9.473007 TTTATCATTCTGAACCCAAATGACATA 57.527 29.630 0.00 0.00 40.95 2.29
1976 6197 6.158598 TCCTGCTTTGCTTTGTTTATCATTC 58.841 36.000 0.00 0.00 0.00 2.67
1988 6211 1.202855 TCTTCTGCTCCTGCTTTGCTT 60.203 47.619 0.00 0.00 40.48 3.91
2019 6245 6.440328 CCCCCAAAATCCTGATTTCTTCTTAA 59.560 38.462 5.64 0.00 39.88 1.85
2040 6266 1.103398 CAATTCCGTGATGAGCCCCC 61.103 60.000 0.00 0.00 0.00 5.40
2044 6270 2.350522 AGACACAATTCCGTGATGAGC 58.649 47.619 3.12 0.00 39.34 4.26
2045 6271 4.692625 AGAAAGACACAATTCCGTGATGAG 59.307 41.667 3.12 0.00 39.34 2.90
2052 6278 5.207768 CACTTTCAGAAAGACACAATTCCG 58.792 41.667 26.72 0.00 41.02 4.30
2058 6285 3.872696 TCTGCACTTTCAGAAAGACACA 58.127 40.909 26.72 18.84 39.89 3.72
2112 6342 7.706179 CCCAAATGACGTTAGCATTTATTCATT 59.294 33.333 11.91 0.24 42.33 2.57
2114 6344 6.151985 ACCCAAATGACGTTAGCATTTATTCA 59.848 34.615 11.91 0.00 42.33 2.57
2115 6345 6.560711 ACCCAAATGACGTTAGCATTTATTC 58.439 36.000 11.91 0.00 42.33 1.75
2124 6354 2.607635 CCATCGACCCAAATGACGTTAG 59.392 50.000 0.00 0.00 0.00 2.34
2243 6477 3.727726 GCCAACTGTTGTGGCTATTTTT 58.272 40.909 18.38 0.00 44.72 1.94
2244 6478 3.385193 GCCAACTGTTGTGGCTATTTT 57.615 42.857 18.38 0.00 44.72 1.82
2255 6489 6.054860 ACAATAGTATCTCTGCCAACTGTT 57.945 37.500 0.00 0.00 0.00 3.16
2257 6491 6.595326 TGAAACAATAGTATCTCTGCCAACTG 59.405 38.462 0.00 0.00 0.00 3.16
2295 6530 6.745794 TCCCTTCAATGAGAAAACCAAAAT 57.254 33.333 0.00 0.00 35.40 1.82
2320 6555 9.905171 CGGATCATCTTGATATGTCGATATTAT 57.095 33.333 0.00 0.00 37.20 1.28
2322 6557 8.000780 TCGGATCATCTTGATATGTCGATATT 57.999 34.615 0.00 0.00 37.20 1.28
2369 6610 4.285863 AGTTTGAAATTGTGTCCCCTCAA 58.714 39.130 0.00 0.00 0.00 3.02
2425 6676 6.892485 AGAATGTCATGGACTGTCAATATGA 58.108 36.000 10.38 12.53 33.15 2.15
2481 6734 1.430632 CACGCATGGATGGCAGTTC 59.569 57.895 0.00 0.00 0.00 3.01
2532 6785 9.440761 AGTGGAGTCATCTTCTATAAATAGGTT 57.559 33.333 0.00 0.00 0.00 3.50
2553 6806 2.092968 GGTTCATGTCTATGGCAGTGGA 60.093 50.000 0.00 0.00 34.97 4.02
2638 6895 3.618351 CAGCCAGAGTCCATGAAGAAAT 58.382 45.455 0.00 0.00 0.00 2.17
2661 6918 7.465353 TTCATACATGACATGGTGTTTTCAT 57.535 32.000 19.39 0.00 36.36 2.57
2686 6943 6.735678 TCAACGTTGTATGCTTGTATGATT 57.264 33.333 26.47 0.00 0.00 2.57
2710 6967 6.994421 TTCTACCATGATTGACATAGGCTA 57.006 37.500 0.00 0.00 37.46 3.93
2719 6976 7.337938 TGCTCTGTTATTTCTACCATGATTGA 58.662 34.615 0.00 0.00 0.00 2.57
2728 6985 6.374333 TCCATGGTTTGCTCTGTTATTTCTAC 59.626 38.462 12.58 0.00 0.00 2.59
2747 7004 6.379133 TCCTGATTTCTTCTTTCATTCCATGG 59.621 38.462 4.97 4.97 0.00 3.66
2956 7213 7.148623 GGAAAAGATGGACTAAAGACTGTAACG 60.149 40.741 0.00 0.00 0.00 3.18
2968 7225 3.118408 CGGGTCATGGAAAAGATGGACTA 60.118 47.826 0.00 0.00 0.00 2.59
3059 7316 4.504864 CCTTTATCACCAGTCAGTTCACCA 60.505 45.833 0.00 0.00 0.00 4.17
3105 7362 2.238395 AGAAGAAGAGGAAGGATGCACC 59.762 50.000 0.00 0.00 39.35 5.01
3107 7364 3.843027 AGAAGAAGAAGAGGAAGGATGCA 59.157 43.478 0.00 0.00 0.00 3.96
3110 7367 6.350949 CGAAGAAGAAGAAGAAGAGGAAGGAT 60.351 42.308 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.