Multiple sequence alignment - TraesCS5D01G200500

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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 TraesCS5D01G200500 chr5D 100.000 4920 0 0 1 4920 302966809 302971728 0.000000e+00 9086
1 TraesCS5D01G200500 chr5B 94.842 2346 92 14 772 3112 347983400 347985721 0.000000e+00 3635
2 TraesCS5D01G200500 chr5B 95.780 1730 63 6 3198 4920 347985718 347987444 0.000000e+00 2782
3 TraesCS5D01G200500 chr5B 82.295 305 30 10 423 723 347974234 347974518 4.920000e-60 243
4 TraesCS5D01G200500 chr5B 89.423 104 4 3 3111 3208 474772887 474772785 1.860000e-24 124
5 TraesCS5D01G200500 chr5A 94.811 1561 69 10 1559 3112 394758761 394757206 0.000000e+00 2423
6 TraesCS5D01G200500 chr5A 91.667 1332 84 14 3198 4523 394757209 394755899 0.000000e+00 1820
7 TraesCS5D01G200500 chr5A 96.651 866 26 1 743 1605 394759615 394758750 0.000000e+00 1435
8 TraesCS5D01G200500 chr5A 86.615 650 71 9 4 642 394761018 394760374 0.000000e+00 704
9 TraesCS5D01G200500 chr5A 95.628 366 8 3 4563 4920 394755900 394755535 9.180000e-162 580
10 TraesCS5D01G200500 chr5A 75.888 394 60 20 39 417 402908964 402908591 8.470000e-38 169
11 TraesCS5D01G200500 chr4A 75.351 499 101 15 1 482 648770732 648771225 2.310000e-53 220
12 TraesCS5D01G200500 chr3B 75.309 486 94 15 3 471 730820309 730820785 4.990000e-50 209
13 TraesCS5D01G200500 chr7B 74.369 515 111 17 1 498 362021505 362022015 3.000000e-47 200
14 TraesCS5D01G200500 chr7B 90.196 102 3 3 3106 3201 473406786 473406686 5.170000e-25 126
15 TraesCS5D01G200500 chr7B 88.679 106 5 3 3102 3201 589348423 589348319 6.690000e-24 122
16 TraesCS5D01G200500 chr2B 74.600 500 103 14 1 482 40938232 40937739 1.080000e-46 198
17 TraesCS5D01G200500 chr6B 73.796 519 115 12 1 501 678533612 678533097 8.410000e-43 185
18 TraesCS5D01G200500 chr4B 92.079 101 3 2 3107 3202 28147648 28147548 2.390000e-28 137
19 TraesCS5D01G200500 chr1A 90.654 107 4 2 3104 3204 351606755 351606861 2.390000e-28 137
20 TraesCS5D01G200500 chr1B 91.753 97 2 2 3111 3201 56752392 56752488 4.000000e-26 130
21 TraesCS5D01G200500 chr1D 84.615 130 19 1 10 138 467644869 467644740 1.440000e-25 128
22 TraesCS5D01G200500 chr6D 90.816 98 3 3 3111 3202 464266185 464266282 5.170000e-25 126
23 TraesCS5D01G200500 chr6D 89.320 103 4 3 3105 3201 200398815 200398714 6.690000e-24 122
24 TraesCS5D01G200500 chr7A 89.423 104 4 4 3109 3206 511927413 511927311 1.860000e-24 124


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 TraesCS5D01G200500 chr5D 302966809 302971728 4919 False 9086.0 9086 100.0000 1 4920 1 chr5D.!!$F1 4919
1 TraesCS5D01G200500 chr5B 347983400 347987444 4044 False 3208.5 3635 95.3110 772 4920 2 chr5B.!!$F2 4148
2 TraesCS5D01G200500 chr5A 394755535 394761018 5483 True 1392.4 2423 93.0744 4 4920 5 chr5A.!!$R2 4916

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
373 383 0.040692 TCAACGAAGGAGTCACGTCG 60.041 55.0 12.68 12.68 39.31 5.12 F
378 388 0.179184 GAAGGAGTCACGTCGAGCTC 60.179 60.0 2.73 2.73 0.00 4.09 F
2072 2780 0.254178 TTCCTGGCCTGCTCAATCTC 59.746 55.0 3.32 0.00 0.00 2.75 F
2188 2896 1.017177 TTATTGGACACGCGGACTGC 61.017 55.0 12.47 0.00 41.47 4.40 F
3119 3832 3.019564 TGCGTTACTTAGTACTCCCTCC 58.980 50.0 0.00 0.00 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1938 2646 0.744874 CCGGCAGAATAACCTCGAGA 59.255 55.0 15.71 0.00 0.00 4.04 R
2167 2875 0.892755 AGTCCGCGTGTCCAATAAGA 59.107 50.0 4.92 0.00 0.00 2.10 R
3183 3896 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.0 0.00 0.00 0.00 3.28 R
3184 3897 1.002069 TAGTACTCCCTCCGTCCCAA 58.998 55.0 0.00 0.00 0.00 4.12 R
4791 5519 0.806868 ACATCTGGTTTCAGCGCATG 59.193 50.0 11.47 5.22 40.69 4.06 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
34 36 2.096248 GTTTGTTCAACCAGGGTGTCA 58.904 47.619 3.79 2.66 0.00 3.58
73 75 1.557371 TGTGGTGGACTTGTGTCTTCA 59.443 47.619 0.00 0.00 42.54 3.02
99 101 1.792057 CCGTTGCGATGACGTTTGC 60.792 57.895 0.00 0.00 41.98 3.68
101 103 0.785708 CGTTGCGATGACGTTTGCTC 60.786 55.000 1.36 0.00 41.98 4.26
104 106 1.291184 TGCGATGACGTTTGCTCCAG 61.291 55.000 1.36 0.00 41.98 3.86
111 113 3.127533 GTTTGCTCCAGCGCCGAT 61.128 61.111 2.29 0.00 45.83 4.18
131 133 0.537653 GTGGAGCTTGGGAGGTAGTC 59.462 60.000 0.00 0.00 32.79 2.59
149 159 3.561143 AGTCCAGGAGTATAGTCTGCAG 58.439 50.000 7.63 7.63 0.00 4.41
162 172 1.733912 GTCTGCAGCGATGACATTTGA 59.266 47.619 9.47 0.00 0.00 2.69
168 178 3.735240 GCAGCGATGACATTTGAAAAACA 59.265 39.130 4.02 0.00 0.00 2.83
189 199 0.184692 TGGATTGTGTGCTGGGTTCA 59.815 50.000 0.00 0.00 0.00 3.18
191 201 1.895131 GGATTGTGTGCTGGGTTCATT 59.105 47.619 0.00 0.00 0.00 2.57
192 202 3.088532 GGATTGTGTGCTGGGTTCATTA 58.911 45.455 0.00 0.00 0.00 1.90
200 210 1.802508 GCTGGGTTCATTATTTGCGGC 60.803 52.381 0.00 0.00 0.00 6.53
219 229 4.323417 CGGCTGGCATATATGGTTTCTTA 58.677 43.478 14.51 0.00 0.00 2.10
227 237 7.011950 TGGCATATATGGTTTCTTACTTTGACG 59.988 37.037 14.51 0.00 0.00 4.35
239 249 5.400485 TCTTACTTTGACGTTTTAGTCGAGC 59.600 40.000 0.00 0.00 43.70 5.03
240 250 2.798847 ACTTTGACGTTTTAGTCGAGCC 59.201 45.455 0.00 0.00 43.70 4.70
246 256 2.816087 ACGTTTTAGTCGAGCCAGAGTA 59.184 45.455 0.00 0.00 0.00 2.59
248 258 3.509740 GTTTTAGTCGAGCCAGAGTACC 58.490 50.000 0.00 0.00 0.00 3.34
255 265 3.570550 GTCGAGCCAGAGTACCAGATATT 59.429 47.826 0.00 0.00 0.00 1.28
261 271 7.056844 AGCCAGAGTACCAGATATTAAGTTC 57.943 40.000 0.00 0.00 0.00 3.01
274 284 3.529634 TTAAGTTCGATGGCGTGTTTG 57.470 42.857 0.00 0.00 38.98 2.93
277 287 1.228003 TTCGATGGCGTGTTTGGGT 60.228 52.632 0.00 0.00 38.98 4.51
282 292 0.538516 ATGGCGTGTTTGGGTTGCTA 60.539 50.000 0.00 0.00 0.00 3.49
302 312 1.916181 ACCCCGACCAGATTCTTTCAT 59.084 47.619 0.00 0.00 0.00 2.57
304 314 3.716872 ACCCCGACCAGATTCTTTCATAT 59.283 43.478 0.00 0.00 0.00 1.78
306 316 3.499918 CCCGACCAGATTCTTTCATATGC 59.500 47.826 0.00 0.00 0.00 3.14
307 317 4.129380 CCGACCAGATTCTTTCATATGCA 58.871 43.478 0.00 0.00 0.00 3.96
309 319 5.277683 CCGACCAGATTCTTTCATATGCAAG 60.278 44.000 8.62 8.62 0.00 4.01
330 340 4.595986 AGTTATTCGCCTTTGGTAACCAT 58.404 39.130 0.00 0.00 31.53 3.55
357 367 6.003326 TGAGGTCTGAAAAGTTGCATATCAA 58.997 36.000 0.00 0.00 0.00 2.57
373 383 0.040692 TCAACGAAGGAGTCACGTCG 60.041 55.000 12.68 12.68 39.31 5.12
378 388 0.179184 GAAGGAGTCACGTCGAGCTC 60.179 60.000 2.73 2.73 0.00 4.09
381 391 3.384014 GAGTCACGTCGAGCTCGGG 62.384 68.421 33.98 26.92 40.29 5.14
382 392 4.477975 GTCACGTCGAGCTCGGGG 62.478 72.222 33.98 26.59 40.29 5.73
391 401 1.985116 GAGCTCGGGGTGAAGAGGT 60.985 63.158 0.00 0.00 46.37 3.85
416 426 4.013728 TCCGTCATATTTTTCCTTGGTGG 58.986 43.478 0.00 0.00 37.10 4.61
419 429 4.638421 CGTCATATTTTTCCTTGGTGGCTA 59.362 41.667 0.00 0.00 35.26 3.93
425 436 2.337359 TTCCTTGGTGGCTACTAGGT 57.663 50.000 17.00 0.00 33.30 3.08
428 439 1.276622 CTTGGTGGCTACTAGGTGGT 58.723 55.000 0.00 0.00 0.00 4.16
429 440 0.981183 TTGGTGGCTACTAGGTGGTG 59.019 55.000 0.00 0.00 0.00 4.17
431 442 1.265454 GGTGGCTACTAGGTGGTGCT 61.265 60.000 0.00 0.00 0.00 4.40
438 449 0.838122 ACTAGGTGGTGCTTGAGGCT 60.838 55.000 0.00 0.00 42.39 4.58
447 458 0.978907 TGCTTGAGGCTGATGACAGA 59.021 50.000 0.00 0.00 46.03 3.41
453 464 2.460330 GGCTGATGACAGACGTTGG 58.540 57.895 0.00 0.00 46.03 3.77
468 479 1.093159 GTTGGCATCAAGCTCAGGAG 58.907 55.000 0.00 0.00 44.79 3.69
470 481 1.210538 TGGCATCAAGCTCAGGAGAT 58.789 50.000 0.00 0.00 44.79 2.75
477 488 5.453057 GCATCAAGCTCAGGAGATTCTTCTA 60.453 44.000 0.00 0.00 41.15 2.10
481 492 6.610830 TCAAGCTCAGGAGATTCTTCTATCTT 59.389 38.462 0.00 0.00 34.42 2.40
556 567 4.646945 TGGCTGATGGTCTTTTGTGTAAAA 59.353 37.500 0.00 0.00 34.75 1.52
661 732 3.364920 CGACACATACTAGCACACACAAG 59.635 47.826 0.00 0.00 0.00 3.16
687 758 9.794685 GTAGAAAAATGAGGAGGATTTGAATTC 57.205 33.333 0.00 0.00 0.00 2.17
711 782 6.071221 TCCATGGAATCTCAAAATTTGACCTG 60.071 38.462 13.46 5.35 35.46 4.00
731 802 7.607607 TGACCTGAACTACTAGTAATAACACGA 59.392 37.037 3.76 0.00 0.00 4.35
732 803 8.340618 ACCTGAACTACTAGTAATAACACGAA 57.659 34.615 3.76 0.00 0.00 3.85
733 804 8.239998 ACCTGAACTACTAGTAATAACACGAAC 58.760 37.037 3.76 0.00 0.00 3.95
735 806 9.784680 CTGAACTACTAGTAATAACACGAACAT 57.215 33.333 3.76 0.00 0.00 2.71
736 807 9.563898 TGAACTACTAGTAATAACACGAACATG 57.436 33.333 3.76 0.00 0.00 3.21
739 810 9.784680 ACTACTAGTAATAACACGAACATGAAG 57.215 33.333 3.76 0.00 0.00 3.02
740 811 9.999009 CTACTAGTAATAACACGAACATGAAGA 57.001 33.333 3.76 0.00 0.00 2.87
753 1420 9.322776 CACGAACATGAAGAGAAGAAAATAAAG 57.677 33.333 0.00 0.00 0.00 1.85
756 1423 9.833182 GAACATGAAGAGAAGAAAATAAAGGAC 57.167 33.333 0.00 0.00 0.00 3.85
1096 1764 4.468689 GGCAGACCAGGTACGGCC 62.469 72.222 14.28 14.28 39.70 6.13
1126 1794 1.499049 GCGTCTCGGTCACTTTTTCT 58.501 50.000 0.00 0.00 0.00 2.52
1213 1881 1.602327 GCCTCCTTAGTTCGTCCGGT 61.602 60.000 0.00 0.00 0.00 5.28
1329 2001 1.982073 GCCTGCCAATCGCTGTGTAC 61.982 60.000 0.00 0.00 38.78 2.90
1468 2140 5.682234 TCTTCATTCAGATTCAGGTGCTA 57.318 39.130 0.00 0.00 0.00 3.49
1475 2147 6.500684 TTCAGATTCAGGTGCTACATTTTC 57.499 37.500 0.00 0.00 0.00 2.29
1493 2165 7.530010 ACATTTTCTGTGTGTATGTGATTAGC 58.470 34.615 0.00 0.00 36.48 3.09
1529 2201 4.694339 AGCTTTTGATATGTAGGTCGGTC 58.306 43.478 0.00 0.00 0.00 4.79
1652 2359 7.040271 TGCCTACATCATGGTATGAATGAATTG 60.040 37.037 1.62 0.00 43.50 2.32
1814 2521 1.207089 TGAATGCTTCCTACCTGTCGG 59.793 52.381 0.00 0.00 0.00 4.79
1831 2538 1.009829 CGGTATTCTCACAAGCCTGC 58.990 55.000 0.00 0.00 0.00 4.85
1863 2570 6.909550 ATGTTGTTCAACCTAGGCATTTTA 57.090 33.333 9.30 0.00 0.00 1.52
1880 2587 8.421002 AGGCATTTTATGTTTGTTTAACTCTGT 58.579 29.630 0.00 0.00 37.64 3.41
1937 2645 4.958897 CCGGTGCGGGGTTTCCAA 62.959 66.667 0.00 0.00 44.15 3.53
1938 2646 2.675075 CGGTGCGGGGTTTCCAAT 60.675 61.111 0.00 0.00 34.36 3.16
1953 2661 5.294552 GGTTTCCAATCTCGAGGTTATTCTG 59.705 44.000 11.34 0.00 0.00 3.02
2072 2780 0.254178 TTCCTGGCCTGCTCAATCTC 59.746 55.000 3.32 0.00 0.00 2.75
2150 2858 9.791801 TTGCTAACTATTATCATGGCTTATTGA 57.208 29.630 0.00 0.00 0.00 2.57
2167 2875 8.398665 GGCTTATTGATGAACTTCGATAGTTTT 58.601 33.333 12.25 5.87 47.00 2.43
2179 2887 8.252964 ACTTCGATAGTTTTCTTATTGGACAC 57.747 34.615 0.00 0.00 31.29 3.67
2181 2889 5.290158 TCGATAGTTTTCTTATTGGACACGC 59.710 40.000 0.00 0.00 37.40 5.34
2188 2896 1.017177 TTATTGGACACGCGGACTGC 61.017 55.000 12.47 0.00 41.47 4.40
2403 3112 8.635765 ATTAATCTTTTCAGCCAGTTCAACTA 57.364 30.769 0.00 0.00 0.00 2.24
2422 3131 5.995565 ACTATGGTAGTCAGTGTTGCTTA 57.004 39.130 0.00 0.00 32.47 3.09
2473 3182 7.363355 CCAGAGTTTCTTAGCTTCTGTGAGATA 60.363 40.741 8.18 0.00 0.00 1.98
2501 3210 9.683069 AGTTTTCATTATTACTTTTCAGCTGTG 57.317 29.630 14.67 5.50 0.00 3.66
2853 3565 4.526970 ACCACATCCTGAATACACCATTC 58.473 43.478 0.00 0.00 43.01 2.67
2879 3591 3.445096 GCACCTCATCTTTTGGCATTACT 59.555 43.478 0.00 0.00 0.00 2.24
2881 3593 5.404946 CACCTCATCTTTTGGCATTACTTG 58.595 41.667 0.00 0.00 0.00 3.16
3038 3751 5.700373 GCATGTTTGTTCATTACATTTGGGT 59.300 36.000 0.00 0.00 36.44 4.51
3039 3752 6.347563 GCATGTTTGTTCATTACATTTGGGTG 60.348 38.462 0.00 0.00 36.44 4.61
3068 3781 6.650390 AGCATCCAATTTCGCTAAAACATTTT 59.350 30.769 0.00 0.00 31.60 1.82
3114 3827 8.908172 ATAGTTCTTTGCGTTACTTAGTACTC 57.092 34.615 0.00 0.00 0.00 2.59
3115 3828 6.155136 AGTTCTTTGCGTTACTTAGTACTCC 58.845 40.000 0.00 0.00 0.00 3.85
3116 3829 5.064441 TCTTTGCGTTACTTAGTACTCCC 57.936 43.478 0.00 0.00 0.00 4.30
3117 3830 4.768968 TCTTTGCGTTACTTAGTACTCCCT 59.231 41.667 0.00 0.00 0.00 4.20
3118 3831 4.708726 TTGCGTTACTTAGTACTCCCTC 57.291 45.455 0.00 0.00 0.00 4.30
3119 3832 3.019564 TGCGTTACTTAGTACTCCCTCC 58.980 50.000 0.00 0.00 0.00 4.30
3120 3833 3.019564 GCGTTACTTAGTACTCCCTCCA 58.980 50.000 0.00 0.00 0.00 3.86
3121 3834 3.635836 GCGTTACTTAGTACTCCCTCCAT 59.364 47.826 0.00 0.00 0.00 3.41
3122 3835 4.261530 GCGTTACTTAGTACTCCCTCCATC 60.262 50.000 0.00 0.00 0.00 3.51
3123 3836 4.277921 CGTTACTTAGTACTCCCTCCATCC 59.722 50.000 0.00 0.00 0.00 3.51
3124 3837 5.206587 GTTACTTAGTACTCCCTCCATCCA 58.793 45.833 0.00 0.00 0.00 3.41
3125 3838 4.348020 ACTTAGTACTCCCTCCATCCAA 57.652 45.455 0.00 0.00 0.00 3.53
3126 3839 4.695606 ACTTAGTACTCCCTCCATCCAAA 58.304 43.478 0.00 0.00 0.00 3.28
3127 3840 5.098663 ACTTAGTACTCCCTCCATCCAAAA 58.901 41.667 0.00 0.00 0.00 2.44
3128 3841 5.550403 ACTTAGTACTCCCTCCATCCAAAAA 59.450 40.000 0.00 0.00 0.00 1.94
3129 3842 6.217693 ACTTAGTACTCCCTCCATCCAAAAAT 59.782 38.462 0.00 0.00 0.00 1.82
3130 3843 7.404980 ACTTAGTACTCCCTCCATCCAAAAATA 59.595 37.037 0.00 0.00 0.00 1.40
3131 3844 6.652205 AGTACTCCCTCCATCCAAAAATAA 57.348 37.500 0.00 0.00 0.00 1.40
3132 3845 6.663734 AGTACTCCCTCCATCCAAAAATAAG 58.336 40.000 0.00 0.00 0.00 1.73
3133 3846 5.536497 ACTCCCTCCATCCAAAAATAAGT 57.464 39.130 0.00 0.00 0.00 2.24
3134 3847 5.264395 ACTCCCTCCATCCAAAAATAAGTG 58.736 41.667 0.00 0.00 0.00 3.16
3135 3848 5.222337 ACTCCCTCCATCCAAAAATAAGTGT 60.222 40.000 0.00 0.00 0.00 3.55
3136 3849 5.261216 TCCCTCCATCCAAAAATAAGTGTC 58.739 41.667 0.00 0.00 0.00 3.67
3137 3850 5.015178 TCCCTCCATCCAAAAATAAGTGTCT 59.985 40.000 0.00 0.00 0.00 3.41
3138 3851 5.358160 CCCTCCATCCAAAAATAAGTGTCTC 59.642 44.000 0.00 0.00 0.00 3.36
3139 3852 5.945784 CCTCCATCCAAAAATAAGTGTCTCA 59.054 40.000 0.00 0.00 0.00 3.27
3140 3853 6.434028 CCTCCATCCAAAAATAAGTGTCTCAA 59.566 38.462 0.00 0.00 0.00 3.02
3141 3854 7.362401 CCTCCATCCAAAAATAAGTGTCTCAAG 60.362 40.741 0.00 0.00 0.00 3.02
3142 3855 6.071952 TCCATCCAAAAATAAGTGTCTCAAGC 60.072 38.462 0.00 0.00 0.00 4.01
3143 3856 6.071728 CCATCCAAAAATAAGTGTCTCAAGCT 60.072 38.462 0.00 0.00 0.00 3.74
3144 3857 6.959639 TCCAAAAATAAGTGTCTCAAGCTT 57.040 33.333 0.00 0.00 0.00 3.74
3145 3858 8.514594 CATCCAAAAATAAGTGTCTCAAGCTTA 58.485 33.333 0.00 0.00 0.00 3.09
3146 3859 8.099364 TCCAAAAATAAGTGTCTCAAGCTTAG 57.901 34.615 0.00 0.00 0.00 2.18
3147 3860 7.719633 TCCAAAAATAAGTGTCTCAAGCTTAGT 59.280 33.333 0.00 0.00 0.00 2.24
3148 3861 8.999431 CCAAAAATAAGTGTCTCAAGCTTAGTA 58.001 33.333 0.00 0.00 0.00 1.82
3149 3862 9.813080 CAAAAATAAGTGTCTCAAGCTTAGTAC 57.187 33.333 0.00 0.00 0.00 2.73
3150 3863 9.555727 AAAAATAAGTGTCTCAAGCTTAGTACA 57.444 29.630 0.00 0.36 0.00 2.90
3151 3864 9.555727 AAAATAAGTGTCTCAAGCTTAGTACAA 57.444 29.630 0.00 0.00 0.00 2.41
3152 3865 8.535690 AATAAGTGTCTCAAGCTTAGTACAAC 57.464 34.615 0.00 0.00 0.00 3.32
3153 3866 5.793030 AGTGTCTCAAGCTTAGTACAACT 57.207 39.130 0.00 0.00 0.00 3.16
3154 3867 6.163135 AGTGTCTCAAGCTTAGTACAACTT 57.837 37.500 0.00 0.00 0.00 2.66
3155 3868 6.583562 AGTGTCTCAAGCTTAGTACAACTTT 58.416 36.000 0.00 0.00 0.00 2.66
3156 3869 6.480320 AGTGTCTCAAGCTTAGTACAACTTTG 59.520 38.462 0.00 0.00 0.00 2.77
3157 3870 5.236478 TGTCTCAAGCTTAGTACAACTTTGC 59.764 40.000 0.00 0.00 0.00 3.68
3158 3871 5.236478 GTCTCAAGCTTAGTACAACTTTGCA 59.764 40.000 0.00 0.00 31.06 4.08
3159 3872 5.236478 TCTCAAGCTTAGTACAACTTTGCAC 59.764 40.000 0.00 0.00 31.06 4.57
3160 3873 5.123227 TCAAGCTTAGTACAACTTTGCACT 58.877 37.500 0.00 0.65 38.32 4.40
3161 3874 6.285224 TCAAGCTTAGTACAACTTTGCACTA 58.715 36.000 0.00 0.00 36.29 2.74
3162 3875 6.764085 TCAAGCTTAGTACAACTTTGCACTAA 59.236 34.615 12.27 12.27 42.00 2.24
3163 3876 7.281324 TCAAGCTTAGTACAACTTTGCACTAAA 59.719 33.333 13.37 0.10 42.98 1.85
3178 3891 6.295039 TGCACTAAAGTTAGTACAAAGTGC 57.705 37.500 15.57 15.57 46.07 4.40
3179 3892 6.053005 TGCACTAAAGTTAGTACAAAGTGCT 58.947 36.000 21.01 0.00 46.06 4.40
3180 3893 6.540914 TGCACTAAAGTTAGTACAAAGTGCTT 59.459 34.615 21.01 6.68 46.06 3.91
3181 3894 7.711772 TGCACTAAAGTTAGTACAAAGTGCTTA 59.288 33.333 21.01 3.88 46.06 3.09
3182 3895 8.718734 GCACTAAAGTTAGTACAAAGTGCTTAT 58.281 33.333 15.25 0.00 44.46 1.73
3187 3900 9.744468 AAAGTTAGTACAAAGTGCTTATTTTGG 57.256 29.630 0.00 0.00 38.33 3.28
3188 3901 7.882179 AGTTAGTACAAAGTGCTTATTTTGGG 58.118 34.615 0.00 0.00 38.33 4.12
3189 3902 7.722285 AGTTAGTACAAAGTGCTTATTTTGGGA 59.278 33.333 0.00 0.00 38.33 4.37
3190 3903 6.327279 AGTACAAAGTGCTTATTTTGGGAC 57.673 37.500 0.00 0.00 38.33 4.46
3191 3904 4.237349 ACAAAGTGCTTATTTTGGGACG 57.763 40.909 0.00 0.00 38.33 4.79
3192 3905 3.005367 ACAAAGTGCTTATTTTGGGACGG 59.995 43.478 0.00 0.00 38.33 4.79
3193 3906 2.871096 AGTGCTTATTTTGGGACGGA 57.129 45.000 0.00 0.00 0.00 4.69
3194 3907 2.711542 AGTGCTTATTTTGGGACGGAG 58.288 47.619 0.00 0.00 0.00 4.63
3195 3908 1.743394 GTGCTTATTTTGGGACGGAGG 59.257 52.381 0.00 0.00 0.00 4.30
3196 3909 1.340600 TGCTTATTTTGGGACGGAGGG 60.341 52.381 0.00 0.00 0.00 4.30
3201 3914 0.978907 TTTTGGGACGGAGGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73
3294 4007 4.331168 CAGCCTGAACTACTAATTGTCTGC 59.669 45.833 0.00 0.00 0.00 4.26
3311 4024 4.202141 TGTCTGCTGTGCTTAAAATTGCTT 60.202 37.500 0.00 0.00 0.00 3.91
3365 4078 5.239306 TGTGTGCTATATTCTGCTTATTGGC 59.761 40.000 0.00 0.00 0.00 4.52
3477 4190 2.301583 TGATCCTCAACGTGATTCACCA 59.698 45.455 11.12 0.00 0.00 4.17
3552 4265 1.600413 GGAACCTTCAGTTTTGCGCTG 60.600 52.381 9.73 0.00 39.40 5.18
3811 4524 6.872020 TGTTGAGTTACAGGTATTTGCTAGAC 59.128 38.462 0.00 0.00 0.00 2.59
3984 4698 9.269453 TGCTTCAACTAATTATGATCTGAGATG 57.731 33.333 0.00 0.00 0.00 2.90
4044 4759 3.963383 TTTCTTTCTGGAAGTCGCAAC 57.037 42.857 0.00 0.00 36.70 4.17
4367 5087 4.636206 AGGGCAGATTTTTCGTACAATCTC 59.364 41.667 0.94 0.00 37.60 2.75
4376 5096 9.695884 GATTTTTCGTACAATCTCTCTGATTTC 57.304 33.333 0.00 0.00 43.00 2.17
4416 5136 6.149129 TGTTCTGTAGATAGATCACGCATT 57.851 37.500 0.00 0.00 0.00 3.56
4454 5174 1.334556 TGTGTGTGTGCATGAAAGAGC 59.665 47.619 0.00 0.00 0.00 4.09
4459 5179 2.291465 TGTGTGCATGAAAGAGCTTGAC 59.709 45.455 0.00 0.00 0.00 3.18
4461 5181 0.518636 TGCATGAAAGAGCTTGACGC 59.481 50.000 0.00 0.00 39.57 5.19
4469 5189 4.152402 TGAAAGAGCTTGACGCATAAGTTC 59.848 41.667 0.00 0.00 42.61 3.01
4478 5198 5.216566 TGACGCATAAGTTCAAGTAATGC 57.783 39.130 0.00 0.00 39.59 3.56
4526 5246 2.897271 TTGCAGGGCCTAATTCTTCA 57.103 45.000 5.28 0.00 0.00 3.02
4767 5495 2.097825 GCCTGCCTGAGTGATTTTCAT 58.902 47.619 0.00 0.00 0.00 2.57
4784 5512 5.862678 TTTCATACCATCGTGTCCTCATA 57.137 39.130 0.00 0.00 0.00 2.15
4791 5519 4.281182 ACCATCGTGTCCTCATATAACTCC 59.719 45.833 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.213677 GTTGAACAAACTAGTTCCCAAATCC 58.786 40.000 8.95 0.00 45.62 3.01
1 2 6.183360 TGGTTGAACAAACTAGTTCCCAAATC 60.183 38.462 8.95 2.01 45.62 2.17
2 3 5.659079 TGGTTGAACAAACTAGTTCCCAAAT 59.341 36.000 8.95 0.00 45.62 2.32
16 17 2.305928 CATGACACCCTGGTTGAACAA 58.694 47.619 0.00 0.00 0.00 2.83
34 36 0.108804 AAAGATGTCGTCGTCGCCAT 60.109 50.000 0.00 0.00 38.35 4.40
39 41 1.455786 CACCACAAAGATGTCGTCGTC 59.544 52.381 0.00 0.00 37.82 4.20
89 91 2.680913 GCGCTGGAGCAAACGTCAT 61.681 57.895 0.00 0.00 42.21 3.06
90 92 3.345808 GCGCTGGAGCAAACGTCA 61.346 61.111 0.00 0.00 42.21 4.35
99 101 4.147449 TCCACATCGGCGCTGGAG 62.147 66.667 17.88 11.78 30.27 3.86
104 106 3.869272 CAAGCTCCACATCGGCGC 61.869 66.667 0.00 0.00 46.59 6.53
111 113 0.178903 ACTACCTCCCAAGCTCCACA 60.179 55.000 0.00 0.00 0.00 4.17
114 116 0.617820 TGGACTACCTCCCAAGCTCC 60.618 60.000 0.00 0.00 38.49 4.70
121 123 3.398629 ACTATACTCCTGGACTACCTCCC 59.601 52.174 0.00 0.00 38.49 4.30
131 133 1.000827 CGCTGCAGACTATACTCCTGG 60.001 57.143 20.43 0.00 0.00 4.45
139 141 3.465742 AATGTCATCGCTGCAGACTAT 57.534 42.857 20.43 3.80 33.56 2.12
140 142 2.931969 CAAATGTCATCGCTGCAGACTA 59.068 45.455 20.43 1.05 33.56 2.59
149 159 5.404968 TCCATTGTTTTTCAAATGTCATCGC 59.595 36.000 0.00 0.00 39.62 4.58
168 178 1.895131 GAACCCAGCACACAATCCATT 59.105 47.619 0.00 0.00 0.00 3.16
200 210 8.345565 GTCAAAGTAAGAAACCATATATGCCAG 58.654 37.037 7.24 0.00 0.00 4.85
219 229 2.798847 GGCTCGACTAAAACGTCAAAGT 59.201 45.455 0.00 0.00 33.54 2.66
227 237 3.057033 TGGTACTCTGGCTCGACTAAAAC 60.057 47.826 0.00 0.00 0.00 2.43
239 249 7.273320 TCGAACTTAATATCTGGTACTCTGG 57.727 40.000 0.00 0.00 0.00 3.86
240 250 7.810282 CCATCGAACTTAATATCTGGTACTCTG 59.190 40.741 0.00 0.00 0.00 3.35
246 256 4.202223 ACGCCATCGAACTTAATATCTGGT 60.202 41.667 0.00 0.00 39.41 4.00
248 258 4.745125 ACACGCCATCGAACTTAATATCTG 59.255 41.667 0.00 0.00 39.41 2.90
255 265 1.801771 CCAAACACGCCATCGAACTTA 59.198 47.619 0.00 0.00 39.41 2.24
261 271 1.081509 CAACCCAAACACGCCATCG 60.082 57.895 0.00 0.00 42.43 3.84
277 287 0.539986 GAATCTGGTCGGGGTAGCAA 59.460 55.000 0.00 0.00 0.00 3.91
282 292 1.358152 TGAAAGAATCTGGTCGGGGT 58.642 50.000 0.00 0.00 0.00 4.95
286 296 5.295292 ACTTGCATATGAAAGAATCTGGTCG 59.705 40.000 27.27 0.89 34.26 4.79
302 312 4.013728 ACCAAAGGCGAATAACTTGCATA 58.986 39.130 0.00 0.00 0.00 3.14
304 314 2.235016 ACCAAAGGCGAATAACTTGCA 58.765 42.857 0.00 0.00 0.00 4.08
306 316 4.216687 TGGTTACCAAAGGCGAATAACTTG 59.783 41.667 0.00 0.00 0.00 3.16
307 317 4.400120 TGGTTACCAAAGGCGAATAACTT 58.600 39.130 0.00 0.00 0.00 2.66
309 319 4.976224 ATGGTTACCAAAGGCGAATAAC 57.024 40.909 8.63 0.00 36.95 1.89
330 340 5.596836 ATGCAACTTTTCAGACCTCAAAA 57.403 34.783 0.00 0.00 0.00 2.44
357 367 1.867615 CTCGACGTGACTCCTTCGT 59.132 57.895 0.00 0.00 40.49 3.85
361 371 2.392181 CGAGCTCGACGTGACTCCT 61.392 63.158 32.06 0.00 43.02 3.69
373 383 1.985116 ACCTCTTCACCCCGAGCTC 60.985 63.158 2.73 2.73 0.00 4.09
378 388 1.522569 GGATCACCTCTTCACCCCG 59.477 63.158 0.00 0.00 0.00 5.73
381 391 0.895530 TGACGGATCACCTCTTCACC 59.104 55.000 0.00 0.00 0.00 4.02
382 392 2.969628 ATGACGGATCACCTCTTCAC 57.030 50.000 0.00 0.00 37.79 3.18
391 401 5.356751 CACCAAGGAAAAATATGACGGATCA 59.643 40.000 0.00 0.00 39.83 2.92
416 426 1.134670 CCTCAAGCACCACCTAGTAGC 60.135 57.143 0.00 0.00 0.00 3.58
419 429 1.679898 GCCTCAAGCACCACCTAGT 59.320 57.895 0.00 0.00 42.97 2.57
429 440 1.367659 GTCTGTCATCAGCCTCAAGC 58.632 55.000 0.00 0.00 41.10 4.01
431 442 0.969149 ACGTCTGTCATCAGCCTCAA 59.031 50.000 0.00 0.00 41.10 3.02
438 449 1.001860 TGATGCCAACGTCTGTCATCA 59.998 47.619 15.49 15.49 40.56 3.07
447 458 0.957395 CCTGAGCTTGATGCCAACGT 60.957 55.000 0.00 0.00 44.23 3.99
453 464 3.196939 AGAATCTCCTGAGCTTGATGC 57.803 47.619 0.00 0.00 43.29 3.91
455 466 6.783977 AGATAGAAGAATCTCCTGAGCTTGAT 59.216 38.462 0.00 0.00 37.10 2.57
531 542 2.624838 ACACAAAAGACCATCAGCCAAG 59.375 45.455 0.00 0.00 0.00 3.61
594 664 5.841237 AGTCCAGTTCCTAGCATGTATACAT 59.159 40.000 12.75 12.75 36.96 2.29
639 710 2.941428 TGTGTGTGCTAGTATGTGTCG 58.059 47.619 0.00 0.00 0.00 4.35
661 732 9.794685 GAATTCAAATCCTCCTCATTTTTCTAC 57.205 33.333 0.00 0.00 0.00 2.59
687 758 6.071221 TCAGGTCAAATTTTGAGATTCCATGG 60.071 38.462 12.02 4.97 41.01 3.66
711 782 9.778993 TCATGTTCGTGTTATTACTAGTAGTTC 57.221 33.333 8.40 0.00 0.00 3.01
731 802 9.579932 AGTCCTTTATTTTCTTCTCTTCATGTT 57.420 29.630 0.00 0.00 0.00 2.71
732 803 9.579932 AAGTCCTTTATTTTCTTCTCTTCATGT 57.420 29.630 0.00 0.00 0.00 3.21
764 1431 8.519799 TCACAGTCCTTTATTTTCTGTTTCTT 57.480 30.769 0.00 0.00 37.27 2.52
1096 1764 2.278013 GAGACGCGAGGTAAGCCG 60.278 66.667 15.93 0.00 40.50 5.52
1108 1776 1.192534 GCAGAAAAAGTGACCGAGACG 59.807 52.381 0.00 0.00 0.00 4.18
1126 1794 2.265739 GGACAGGAGCATCACGCA 59.734 61.111 0.00 0.00 46.13 5.24
1213 1881 2.202395 AACCGAAACGAGGACCGGA 61.202 57.895 9.46 0.00 44.29 5.14
1468 2140 7.530010 GCTAATCACATACACACAGAAAATGT 58.470 34.615 0.00 0.00 45.43 2.71
1475 2147 5.731278 CAATCGCTAATCACATACACACAG 58.269 41.667 0.00 0.00 0.00 3.66
1521 2193 1.414181 GGACATGATCATGACCGACCT 59.586 52.381 36.37 16.34 42.01 3.85
1529 2201 3.275999 TGAACAGCAGGACATGATCATG 58.724 45.455 29.95 29.95 42.22 3.07
1652 2359 2.833794 TCGCCATGGTATAGCTTCAAC 58.166 47.619 14.67 0.00 0.00 3.18
1814 2521 3.754188 CAAGCAGGCTTGTGAGAATAC 57.246 47.619 22.52 0.00 45.91 1.89
1831 2538 5.125100 AGGTTGAACAACATACATGCAAG 57.875 39.130 17.43 0.00 42.85 4.01
1863 2570 9.614792 AGAAGAACTACAGAGTTAAACAAACAT 57.385 29.630 0.00 0.00 46.23 2.71
1933 2641 3.181465 GGCAGAATAACCTCGAGATTGGA 60.181 47.826 15.71 0.00 0.00 3.53
1937 2645 1.341531 CCGGCAGAATAACCTCGAGAT 59.658 52.381 15.71 4.86 0.00 2.75
1938 2646 0.744874 CCGGCAGAATAACCTCGAGA 59.255 55.000 15.71 0.00 0.00 4.04
2020 2728 7.900782 ACGACAATGTAATATATTAGTGGCC 57.099 36.000 5.39 0.00 0.00 5.36
2072 2780 8.059461 AGTTAAGGGGAAACTGATAAAATAGGG 58.941 37.037 0.00 0.00 35.87 3.53
2167 2875 0.892755 AGTCCGCGTGTCCAATAAGA 59.107 50.000 4.92 0.00 0.00 2.10
2181 2889 3.508840 GGGCCAAATCGCAGTCCG 61.509 66.667 4.39 0.00 38.61 4.79
2188 2896 4.279169 AGAATATGATGTTGGGCCAAATCG 59.721 41.667 22.82 0.00 0.00 3.34
2403 3112 6.952773 TTTTTAAGCAACACTGACTACCAT 57.047 33.333 0.00 0.00 0.00 3.55
2438 3147 9.654663 GAAGCTAAGAAACTCTGGTATTCTAAA 57.345 33.333 0.00 0.00 33.26 1.85
2473 3182 9.683069 CAGCTGAAAAGTAATAATGAAAACTGT 57.317 29.630 8.42 0.00 0.00 3.55
2501 3210 3.370978 TCGTTCAAGCTAAGCTACAATGC 59.629 43.478 0.00 0.00 38.25 3.56
2853 3565 1.089920 CCAAAAGATGAGGTGCCTCG 58.910 55.000 12.97 0.00 45.48 4.63
2983 3695 8.072567 GTGCACTCATAGACCAAAATAATCATC 58.927 37.037 10.32 0.00 0.00 2.92
3038 3751 3.940209 AGCGAAATTGGATGCTTTTCA 57.060 38.095 11.56 0.00 32.89 2.69
3039 3752 6.145371 TGTTTTAGCGAAATTGGATGCTTTTC 59.855 34.615 0.00 4.06 38.82 2.29
3108 3821 6.217693 ACTTATTTTTGGATGGAGGGAGTACT 59.782 38.462 0.00 0.00 0.00 2.73
3109 3822 6.318900 CACTTATTTTTGGATGGAGGGAGTAC 59.681 42.308 0.00 0.00 0.00 2.73
3110 3823 6.011981 ACACTTATTTTTGGATGGAGGGAGTA 60.012 38.462 0.00 0.00 0.00 2.59
3111 3824 5.222337 ACACTTATTTTTGGATGGAGGGAGT 60.222 40.000 0.00 0.00 0.00 3.85
3112 3825 5.264395 ACACTTATTTTTGGATGGAGGGAG 58.736 41.667 0.00 0.00 0.00 4.30
3113 3826 5.015178 AGACACTTATTTTTGGATGGAGGGA 59.985 40.000 0.00 0.00 0.00 4.20
3114 3827 5.264395 AGACACTTATTTTTGGATGGAGGG 58.736 41.667 0.00 0.00 0.00 4.30
3115 3828 5.945784 TGAGACACTTATTTTTGGATGGAGG 59.054 40.000 0.00 0.00 0.00 4.30
3116 3829 7.452880 TTGAGACACTTATTTTTGGATGGAG 57.547 36.000 0.00 0.00 0.00 3.86
3117 3830 6.071952 GCTTGAGACACTTATTTTTGGATGGA 60.072 38.462 0.00 0.00 0.00 3.41
3118 3831 6.071728 AGCTTGAGACACTTATTTTTGGATGG 60.072 38.462 0.00 0.00 0.00 3.51
3119 3832 6.917533 AGCTTGAGACACTTATTTTTGGATG 58.082 36.000 0.00 0.00 0.00 3.51
3120 3833 7.530426 AAGCTTGAGACACTTATTTTTGGAT 57.470 32.000 0.00 0.00 0.00 3.41
3121 3834 6.959639 AAGCTTGAGACACTTATTTTTGGA 57.040 33.333 0.00 0.00 0.00 3.53
3122 3835 7.875971 ACTAAGCTTGAGACACTTATTTTTGG 58.124 34.615 9.86 0.00 0.00 3.28
3123 3836 9.813080 GTACTAAGCTTGAGACACTTATTTTTG 57.187 33.333 9.86 0.00 0.00 2.44
3124 3837 9.555727 TGTACTAAGCTTGAGACACTTATTTTT 57.444 29.630 9.86 0.00 0.00 1.94
3125 3838 9.555727 TTGTACTAAGCTTGAGACACTTATTTT 57.444 29.630 9.86 0.00 0.00 1.82
3126 3839 8.989980 GTTGTACTAAGCTTGAGACACTTATTT 58.010 33.333 9.86 0.00 0.00 1.40
3127 3840 8.368668 AGTTGTACTAAGCTTGAGACACTTATT 58.631 33.333 9.86 0.00 0.00 1.40
3128 3841 7.897864 AGTTGTACTAAGCTTGAGACACTTAT 58.102 34.615 9.86 0.00 0.00 1.73
3129 3842 7.286215 AGTTGTACTAAGCTTGAGACACTTA 57.714 36.000 9.86 0.00 0.00 2.24
3130 3843 6.163135 AGTTGTACTAAGCTTGAGACACTT 57.837 37.500 9.86 0.00 0.00 3.16
3131 3844 5.793030 AGTTGTACTAAGCTTGAGACACT 57.207 39.130 9.86 7.29 0.00 3.55
3132 3845 6.650372 CAAAGTTGTACTAAGCTTGAGACAC 58.350 40.000 9.86 7.18 0.00 3.67
3133 3846 5.236478 GCAAAGTTGTACTAAGCTTGAGACA 59.764 40.000 9.86 7.12 0.00 3.41
3134 3847 5.236478 TGCAAAGTTGTACTAAGCTTGAGAC 59.764 40.000 9.86 4.39 31.81 3.36
3135 3848 5.236478 GTGCAAAGTTGTACTAAGCTTGAGA 59.764 40.000 9.86 0.00 40.10 3.27
3136 3849 5.444122 GTGCAAAGTTGTACTAAGCTTGAG 58.556 41.667 9.86 5.36 40.10 3.02
3137 3850 5.418310 GTGCAAAGTTGTACTAAGCTTGA 57.582 39.130 9.86 0.00 40.10 3.02
3156 3869 6.541111 AGCACTTTGTACTAACTTTAGTGC 57.459 37.500 17.73 17.73 45.17 4.40
3161 3874 9.744468 CCAAAATAAGCACTTTGTACTAACTTT 57.256 29.630 0.00 0.00 31.84 2.66
3162 3875 8.357402 CCCAAAATAAGCACTTTGTACTAACTT 58.643 33.333 0.00 0.00 31.84 2.66
3163 3876 7.722285 TCCCAAAATAAGCACTTTGTACTAACT 59.278 33.333 0.00 0.00 31.84 2.24
3164 3877 7.806487 GTCCCAAAATAAGCACTTTGTACTAAC 59.194 37.037 0.00 0.00 31.84 2.34
3165 3878 7.308109 CGTCCCAAAATAAGCACTTTGTACTAA 60.308 37.037 0.00 0.00 31.84 2.24
3166 3879 6.148150 CGTCCCAAAATAAGCACTTTGTACTA 59.852 38.462 0.00 0.00 31.84 1.82
3167 3880 5.048991 CGTCCCAAAATAAGCACTTTGTACT 60.049 40.000 0.00 0.00 31.84 2.73
3168 3881 5.151389 CGTCCCAAAATAAGCACTTTGTAC 58.849 41.667 0.00 0.00 31.84 2.90
3169 3882 4.216687 CCGTCCCAAAATAAGCACTTTGTA 59.783 41.667 0.00 0.00 31.84 2.41
3170 3883 3.005367 CCGTCCCAAAATAAGCACTTTGT 59.995 43.478 0.00 0.00 31.84 2.83
3171 3884 3.254657 TCCGTCCCAAAATAAGCACTTTG 59.745 43.478 0.00 0.00 33.25 2.77
3172 3885 3.492337 TCCGTCCCAAAATAAGCACTTT 58.508 40.909 0.00 0.00 0.00 2.66
3173 3886 3.081804 CTCCGTCCCAAAATAAGCACTT 58.918 45.455 0.00 0.00 0.00 3.16
3174 3887 2.618045 CCTCCGTCCCAAAATAAGCACT 60.618 50.000 0.00 0.00 0.00 4.40
3175 3888 1.743394 CCTCCGTCCCAAAATAAGCAC 59.257 52.381 0.00 0.00 0.00 4.40
3176 3889 1.340600 CCCTCCGTCCCAAAATAAGCA 60.341 52.381 0.00 0.00 0.00 3.91
3177 3890 1.064979 TCCCTCCGTCCCAAAATAAGC 60.065 52.381 0.00 0.00 0.00 3.09
3178 3891 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
3179 3892 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
3180 3893 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3181 3894 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
3182 3895 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
3183 3896 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
3184 3897 1.002069 TAGTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
3185 3898 1.002069 TTAGTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
3186 3899 1.064091 ACTTAGTACTCCCTCCGTCCC 60.064 57.143 0.00 0.00 0.00 4.46
3187 3900 2.433662 ACTTAGTACTCCCTCCGTCC 57.566 55.000 0.00 0.00 0.00 4.79
3188 3901 3.619419 AGAACTTAGTACTCCCTCCGTC 58.381 50.000 0.00 0.00 0.00 4.79
3189 3902 3.735720 AGAACTTAGTACTCCCTCCGT 57.264 47.619 0.00 0.00 0.00 4.69
3190 3903 4.220163 ACAAAGAACTTAGTACTCCCTCCG 59.780 45.833 0.00 0.00 0.00 4.63
3191 3904 5.245526 TGACAAAGAACTTAGTACTCCCTCC 59.754 44.000 0.00 0.00 0.00 4.30
3192 3905 6.157904 GTGACAAAGAACTTAGTACTCCCTC 58.842 44.000 0.00 0.00 0.00 4.30
3193 3906 5.601313 TGTGACAAAGAACTTAGTACTCCCT 59.399 40.000 0.00 0.00 0.00 4.20
3194 3907 5.850614 TGTGACAAAGAACTTAGTACTCCC 58.149 41.667 0.00 0.00 0.00 4.30
3195 3908 7.964604 ATTGTGACAAAGAACTTAGTACTCC 57.035 36.000 0.62 0.00 0.00 3.85
3201 3914 9.950680 ACAACATAATTGTGACAAAGAACTTAG 57.049 29.630 9.40 0.00 35.83 2.18
3294 4007 6.867816 TGGATTGTAAGCAATTTTAAGCACAG 59.132 34.615 0.00 0.00 44.61 3.66
3477 4190 4.703379 AAGATATGCCTTAAGCTGAGCT 57.297 40.909 0.00 0.00 44.23 4.09
3787 4500 6.313164 GGTCTAGCAAATACCTGTAACTCAAC 59.687 42.308 0.00 0.00 0.00 3.18
4333 5053 3.667282 CTGCCCTGTGTGCTGTGC 61.667 66.667 0.00 0.00 0.00 4.57
4367 5087 9.844257 AGTAGGAATTTTAGATGGAAATCAGAG 57.156 33.333 0.00 0.00 0.00 3.35
4376 5096 9.319143 CTACAGAACAGTAGGAATTTTAGATGG 57.681 37.037 0.00 0.00 38.22 3.51
4388 5108 6.566942 GCGTGATCTATCTACAGAACAGTAGG 60.567 46.154 0.00 0.00 41.39 3.18
4454 5174 5.734498 GCATTACTTGAACTTATGCGTCAAG 59.266 40.000 15.59 15.59 42.26 3.02
4459 5179 4.031028 GCAGCATTACTTGAACTTATGCG 58.969 43.478 0.00 0.00 44.65 4.73
4461 5181 7.693951 GTGTTAGCAGCATTACTTGAACTTATG 59.306 37.037 0.00 0.00 0.00 1.90
4469 5189 5.362556 AACTGTGTTAGCAGCATTACTTG 57.637 39.130 0.00 0.00 39.96 3.16
4478 5198 4.811555 TGTAGCAAAACTGTGTTAGCAG 57.188 40.909 7.53 0.00 41.92 4.24
4526 5246 5.661458 CAGACATTGGAAACTACCGATACT 58.339 41.667 0.00 0.00 33.19 2.12
4767 5495 5.475909 GGAGTTATATGAGGACACGATGGTA 59.524 44.000 0.00 0.00 0.00 3.25
4784 5512 2.017049 GGTTTCAGCGCATGGAGTTAT 58.983 47.619 11.47 0.00 0.00 1.89
4791 5519 0.806868 ACATCTGGTTTCAGCGCATG 59.193 50.000 11.47 5.22 40.69 4.06
4835 5563 4.466015 TCCAAAAGGCATTAATGAGTTCCC 59.534 41.667 19.73 9.97 0.00 3.97
4886 5617 7.549134 TGAAGGTATTATCACATGACAGAACAC 59.451 37.037 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.