Multiple sequence alignment - TraesCS4B01G166400

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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 TraesCS4B01G166400 chr4B 100.000 6011 0 0 1 6011 359720098 359726108 0.000000e+00 11101.0
1 TraesCS4B01G166400 chr4B 87.302 126 15 1 424 549 472208996 472209120 6.280000e-30 143.0
2 TraesCS4B01G166400 chr4D 94.597 3868 101 36 541 4332 263952132 263948297 0.000000e+00 5886.0
3 TraesCS4B01G166400 chr4D 88.438 986 80 14 5037 6011 263942059 263941097 0.000000e+00 1158.0
4 TraesCS4B01G166400 chr4D 93.296 716 17 10 4330 5030 263942999 263942300 0.000000e+00 1027.0
5 TraesCS4B01G166400 chr4D 91.008 367 29 2 63 426 263952496 263952131 5.410000e-135 492.0
6 TraesCS4B01G166400 chr4D 88.983 118 13 0 425 542 337412403 337412286 4.850000e-31 147.0
7 TraesCS4B01G166400 chr4D 88.983 118 13 0 425 542 367720542 367720659 4.850000e-31 147.0
8 TraesCS4B01G166400 chr4A 91.712 3475 131 55 842 4228 217650796 217654201 0.000000e+00 4676.0
9 TraesCS4B01G166400 chr4A 87.331 963 39 23 4235 5174 217654300 217655202 0.000000e+00 1026.0
10 TraesCS4B01G166400 chr4A 86.968 376 47 1 5638 6011 218197051 218197426 7.200000e-114 422.0
11 TraesCS4B01G166400 chr4A 80.513 390 44 13 44 416 217628188 217628562 2.760000e-68 270.0
12 TraesCS4B01G166400 chr4A 80.256 390 45 13 44 416 217566942 217567316 1.280000e-66 265.0
13 TraesCS4B01G166400 chr4A 79.795 391 45 19 44 416 217593917 217594291 2.780000e-63 254.0
14 TraesCS4B01G166400 chr4A 81.232 357 21 25 539 856 217628720 217629069 4.650000e-61 246.0
15 TraesCS4B01G166400 chr4A 91.736 121 10 0 425 545 669083961 669084081 1.040000e-37 169.0
16 TraesCS4B01G166400 chr4A 82.791 215 9 10 539 730 217594449 217594658 3.730000e-37 167.0
17 TraesCS4B01G166400 chr4A 82.407 216 9 10 539 730 217567474 217567684 1.730000e-35 161.0
18 TraesCS4B01G166400 chr4A 90.756 119 11 0 425 543 589013492 589013610 6.240000e-35 159.0
19 TraesCS4B01G166400 chr4A 98.182 55 1 0 4235 4289 217654269 217654215 4.960000e-16 97.1
20 TraesCS4B01G166400 chr4A 100.000 32 0 0 4276 4307 217654266 217654297 6.510000e-05 60.2
21 TraesCS4B01G166400 chr2D 78.853 279 59 0 3909 4187 71761159 71760881 7.950000e-44 189.0
22 TraesCS4B01G166400 chr2B 78.495 279 60 0 3909 4187 108232919 108232641 3.700000e-42 183.0
23 TraesCS4B01G166400 chr1B 89.916 119 12 0 424 542 642765725 642765843 2.900000e-33 154.0
24 TraesCS4B01G166400 chr5B 88.525 122 14 0 421 542 628698613 628698492 1.350000e-31 148.0
25 TraesCS4B01G166400 chr5B 87.705 122 15 0 421 542 625119064 625118943 6.280000e-30 143.0
26 TraesCS4B01G166400 chr7D 86.614 127 17 0 423 549 417915549 417915423 2.260000e-29 141.0
27 TraesCS4B01G166400 chr7B 86.667 75 7 3 5173 5244 552785977 552786051 4.990000e-11 80.5
28 TraesCS4B01G166400 chr3B 94.872 39 2 0 5200 5238 671408903 671408865 1.810000e-05 62.1


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 TraesCS4B01G166400 chr4B 359720098 359726108 6010 False 11101.000000 11101 100.000000 1 6011 1 chr4B.!!$F1 6010
1 TraesCS4B01G166400 chr4D 263948297 263952496 4199 True 3189.000000 5886 92.802500 63 4332 2 chr4D.!!$R3 4269
2 TraesCS4B01G166400 chr4D 263941097 263942999 1902 True 1092.500000 1158 90.867000 4330 6011 2 chr4D.!!$R2 1681
3 TraesCS4B01G166400 chr4A 217650796 217655202 4406 False 1920.733333 4676 93.014333 842 5174 3 chr4A.!!$F7 4332
4 TraesCS4B01G166400 chr4A 217628188 217629069 881 False 258.000000 270 80.872500 44 856 2 chr4A.!!$F6 812
5 TraesCS4B01G166400 chr4A 217566942 217567684 742 False 213.000000 265 81.331500 44 730 2 chr4A.!!$F4 686
6 TraesCS4B01G166400 chr4A 217593917 217594658 741 False 210.500000 254 81.293000 44 730 2 chr4A.!!$F5 686

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
440 463 0.463295 AGATACTCGCTCCGTCCGAA 60.463 55.000 0.00 0.00 33.92 4.30 F
651 728 0.706433 ATCCCAGTGGCCTTTGTCAT 59.294 50.000 3.32 0.00 0.00 3.06 F
1012 1135 1.074395 TCACCACCACCACCACCTA 60.074 57.895 0.00 0.00 0.00 3.08 F
2284 2457 1.153249 CAGGCCTTTTATCCGCGGA 60.153 57.895 33.12 33.12 0.00 5.54 F
3885 4104 0.457851 GCTCGGATAGACAGTGCACT 59.542 55.000 15.25 15.25 34.44 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1384 1508 1.079681 ATTAACCGAACGGAGCGCA 60.080 52.632 20.14 0.0 38.96 6.09 R
2268 2441 1.153229 ACTCCGCGGATAAAAGGCC 60.153 57.895 31.19 0.0 0.00 5.19 R
2515 2689 4.039609 GCAAAATGGGGATGATTAAGGAGG 59.960 45.833 0.00 0.0 0.00 4.30 R
3887 4106 0.251386 TCTTCGTCCTGAGCCTGAGT 60.251 55.000 0.00 0.0 0.00 3.41 R
5182 5769 0.106967 GGCTGGGTTCATCCTCCTTC 60.107 60.000 0.00 0.0 36.25 3.46 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
197 201 5.560953 GCCGCTGAAATGGATTTATCTACAC 60.561 44.000 0.00 0.00 0.00 2.90
199 203 5.444122 GCTGAAATGGATTTATCTACACGC 58.556 41.667 0.00 0.00 0.00 5.34
215 219 2.674852 ACACGCATTTCAGTGCTAGATG 59.325 45.455 0.00 0.00 42.88 2.90
216 220 2.674852 CACGCATTTCAGTGCTAGATGT 59.325 45.455 0.00 0.00 42.88 3.06
230 234 1.571919 AGATGTATCCGTTTGAGCGC 58.428 50.000 0.00 0.00 0.00 5.92
233 237 0.739462 TGTATCCGTTTGAGCGCTGG 60.739 55.000 18.48 10.09 0.00 4.85
250 254 3.050619 GCTGGTCGGTTAATATGAGACG 58.949 50.000 0.00 0.00 33.04 4.18
253 257 3.067180 TGGTCGGTTAATATGAGACGGAC 59.933 47.826 12.03 12.03 40.66 4.79
255 259 2.945008 TCGGTTAATATGAGACGGACGT 59.055 45.455 0.00 0.00 0.00 4.34
389 412 3.340814 TTTCCTCACCTTCATCTCAGC 57.659 47.619 0.00 0.00 0.00 4.26
394 417 2.943690 CTCACCTTCATCTCAGCATTGG 59.056 50.000 0.00 0.00 0.00 3.16
406 429 0.464373 AGCATTGGTCCTACATGGCG 60.464 55.000 0.00 0.00 35.26 5.69
418 441 4.633126 TCCTACATGGCGTATATACTCGTC 59.367 45.833 11.05 1.12 35.26 4.20
424 447 6.598457 ACATGGCGTATATACTCGTCTAAGAT 59.402 38.462 11.05 0.00 32.71 2.40
425 448 7.767659 ACATGGCGTATATACTCGTCTAAGATA 59.232 37.037 11.05 0.00 32.71 1.98
427 450 7.326454 TGGCGTATATACTCGTCTAAGATACT 58.674 38.462 11.05 0.00 32.71 2.12
428 451 7.490725 TGGCGTATATACTCGTCTAAGATACTC 59.509 40.741 11.05 0.00 32.71 2.59
430 453 7.546277 CGTATATACTCGTCTAAGATACTCGC 58.454 42.308 11.05 0.00 0.00 5.03
431 454 7.431960 CGTATATACTCGTCTAAGATACTCGCT 59.568 40.741 11.05 0.00 0.00 4.93
433 456 3.132925 ACTCGTCTAAGATACTCGCTCC 58.867 50.000 0.00 0.00 0.00 4.70
436 459 2.096811 CGTCTAAGATACTCGCTCCGTC 60.097 54.545 0.00 0.00 0.00 4.79
437 460 2.223845 GTCTAAGATACTCGCTCCGTCC 59.776 54.545 0.00 0.00 0.00 4.79
440 463 0.463295 AGATACTCGCTCCGTCCGAA 60.463 55.000 0.00 0.00 33.92 4.30
471 497 6.291377 TGTCCCTCAAATGAATGTATCTAGC 58.709 40.000 0.00 0.00 0.00 3.42
472 498 6.126796 TGTCCCTCAAATGAATGTATCTAGCA 60.127 38.462 0.00 0.00 0.00 3.49
473 499 6.203723 GTCCCTCAAATGAATGTATCTAGCAC 59.796 42.308 0.00 0.00 0.00 4.40
474 500 5.471456 CCCTCAAATGAATGTATCTAGCACC 59.529 44.000 0.00 0.00 0.00 5.01
475 501 6.057533 CCTCAAATGAATGTATCTAGCACCA 58.942 40.000 0.00 0.00 0.00 4.17
476 502 6.543465 CCTCAAATGAATGTATCTAGCACCAA 59.457 38.462 0.00 0.00 0.00 3.67
478 504 7.112122 TCAAATGAATGTATCTAGCACCAAGT 58.888 34.615 0.00 0.00 0.00 3.16
479 505 7.611467 TCAAATGAATGTATCTAGCACCAAGTT 59.389 33.333 0.00 0.00 0.00 2.66
480 506 8.892723 CAAATGAATGTATCTAGCACCAAGTTA 58.107 33.333 0.00 0.00 0.00 2.24
481 507 8.668510 AATGAATGTATCTAGCACCAAGTTAG 57.331 34.615 0.00 0.00 32.79 2.34
482 508 7.182817 TGAATGTATCTAGCACCAAGTTAGT 57.817 36.000 0.00 0.00 33.25 2.24
483 509 8.301252 TGAATGTATCTAGCACCAAGTTAGTA 57.699 34.615 0.00 0.00 33.25 1.82
484 510 8.924303 TGAATGTATCTAGCACCAAGTTAGTAT 58.076 33.333 0.00 0.00 33.25 2.12
485 511 9.765795 GAATGTATCTAGCACCAAGTTAGTATT 57.234 33.333 0.00 0.00 33.25 1.89
492 518 9.636789 TCTAGCACCAAGTTAGTATTAGATACA 57.363 33.333 1.42 0.00 38.21 2.29
495 521 8.368668 AGCACCAAGTTAGTATTAGATACATCC 58.631 37.037 1.42 0.00 38.21 3.51
515 541 8.620116 ACATCCATTTAAAAGACAAATTTGGG 57.380 30.769 21.74 9.33 0.00 4.12
516 542 8.435982 ACATCCATTTAAAAGACAAATTTGGGA 58.564 29.630 21.74 13.92 0.00 4.37
517 543 8.720562 CATCCATTTAAAAGACAAATTTGGGAC 58.279 33.333 21.74 12.39 0.00 4.46
518 544 7.796054 TCCATTTAAAAGACAAATTTGGGACA 58.204 30.769 21.74 0.00 0.00 4.02
532 558 2.294074 TGGGACAACCTTTTTCAGACG 58.706 47.619 0.00 0.00 41.11 4.18
533 559 2.092861 TGGGACAACCTTTTTCAGACGA 60.093 45.455 0.00 0.00 41.11 4.20
535 561 3.003378 GGGACAACCTTTTTCAGACGAAG 59.997 47.826 0.00 0.00 35.85 3.79
536 562 3.003378 GGACAACCTTTTTCAGACGAAGG 59.997 47.826 8.78 8.78 44.34 3.46
537 563 2.949644 ACAACCTTTTTCAGACGAAGGG 59.050 45.455 13.27 4.70 43.33 3.95
571 631 1.545582 CCATGAGCACCAACGGATTTT 59.454 47.619 0.00 0.00 0.00 1.82
581 641 5.007332 GCACCAACGGATTTTCGAATATACT 59.993 40.000 8.86 0.00 0.00 2.12
625 685 7.037297 TGGAGAAAGAAAATTCTATGTCTCCCT 60.037 37.037 27.29 9.00 46.56 4.20
651 728 0.706433 ATCCCAGTGGCCTTTGTCAT 59.294 50.000 3.32 0.00 0.00 3.06
885 998 1.134280 GGGATGAGTGAGTGGATGGTG 60.134 57.143 0.00 0.00 0.00 4.17
887 1000 1.556911 GATGAGTGAGTGGATGGTGGT 59.443 52.381 0.00 0.00 0.00 4.16
894 1007 1.347707 GAGTGGATGGTGGTTGAGTGA 59.652 52.381 0.00 0.00 0.00 3.41
1011 1134 2.367648 TCACCACCACCACCACCT 60.368 61.111 0.00 0.00 0.00 4.00
1012 1135 1.074395 TCACCACCACCACCACCTA 60.074 57.895 0.00 0.00 0.00 3.08
1141 1265 5.788450 TCGAATCTTGCTTCTTCTTCTTCT 58.212 37.500 0.00 0.00 0.00 2.85
1142 1266 6.226787 TCGAATCTTGCTTCTTCTTCTTCTT 58.773 36.000 0.00 0.00 0.00 2.52
1143 1267 6.146837 TCGAATCTTGCTTCTTCTTCTTCTTG 59.853 38.462 0.00 0.00 0.00 3.02
1144 1268 6.073331 CGAATCTTGCTTCTTCTTCTTCTTGT 60.073 38.462 0.00 0.00 0.00 3.16
1145 1269 7.519649 CGAATCTTGCTTCTTCTTCTTCTTGTT 60.520 37.037 0.00 0.00 0.00 2.83
1146 1270 6.610741 TCTTGCTTCTTCTTCTTCTTGTTC 57.389 37.500 0.00 0.00 0.00 3.18
1147 1271 6.352516 TCTTGCTTCTTCTTCTTCTTGTTCT 58.647 36.000 0.00 0.00 0.00 3.01
1148 1272 6.825721 TCTTGCTTCTTCTTCTTCTTGTTCTT 59.174 34.615 0.00 0.00 0.00 2.52
1149 1273 7.337942 TCTTGCTTCTTCTTCTTCTTGTTCTTT 59.662 33.333 0.00 0.00 0.00 2.52
1150 1274 7.396540 TGCTTCTTCTTCTTCTTGTTCTTTT 57.603 32.000 0.00 0.00 0.00 2.27
1151 1275 7.830739 TGCTTCTTCTTCTTCTTGTTCTTTTT 58.169 30.769 0.00 0.00 0.00 1.94
1152 1276 7.970614 TGCTTCTTCTTCTTCTTGTTCTTTTTC 59.029 33.333 0.00 0.00 0.00 2.29
1153 1277 8.187480 GCTTCTTCTTCTTCTTGTTCTTTTTCT 58.813 33.333 0.00 0.00 0.00 2.52
1156 1280 9.454859 TCTTCTTCTTCTTGTTCTTTTTCTTCT 57.545 29.630 0.00 0.00 0.00 2.85
1159 1283 9.454859 TCTTCTTCTTGTTCTTTTTCTTCTTCT 57.545 29.630 0.00 0.00 0.00 2.85
1174 1298 2.752030 TCTTCTTCCCGTCATCTCCAT 58.248 47.619 0.00 0.00 0.00 3.41
1384 1508 1.954258 GCTTCTTTGCCTGCTCCTCAT 60.954 52.381 0.00 0.00 0.00 2.90
1424 1548 4.335416 TCCAAAGATTCGCCATTTCTCTT 58.665 39.130 0.00 0.00 0.00 2.85
1503 1630 1.461091 TTCTTGAGCGGTGTCGGAGT 61.461 55.000 0.00 0.00 36.79 3.85
1897 2025 2.168106 CCTCTTCATCACCCTCACTCAG 59.832 54.545 0.00 0.00 0.00 3.35
1921 2049 5.397534 GTCATGCTACCAATTACGTACGTAG 59.602 44.000 25.56 17.37 31.71 3.51
1926 2054 6.708502 TGCTACCAATTACGTACGTAGGTATA 59.291 38.462 29.96 22.98 32.33 1.47
1927 2055 7.015877 GCTACCAATTACGTACGTAGGTATAC 58.984 42.308 29.96 24.08 32.33 1.47
1976 2134 6.147821 GCCGTCGTGGTATTTAGACTAGTATA 59.852 42.308 0.00 0.00 41.21 1.47
2021 2188 6.438763 GGGATGGTGATTGAATAAAATCGTC 58.561 40.000 0.00 0.00 39.06 4.20
2030 2197 9.309516 TGATTGAATAAAATCGTCCTACTACAC 57.690 33.333 0.00 0.00 39.06 2.90
2062 2229 4.218417 TCAAGTCTTTGGGATTAAAGCAGC 59.782 41.667 0.00 0.00 37.53 5.25
2135 2304 7.062255 GCCTTCTTGTATTGAAACTTGTAATGC 59.938 37.037 0.00 0.00 0.00 3.56
2243 2416 6.981762 AATCTGACAAGTAAGATGAGCAAG 57.018 37.500 0.83 0.00 31.20 4.01
2268 2441 4.556104 GCCAACTTGATGTATGCTATGCAG 60.556 45.833 0.00 0.00 43.65 4.41
2284 2457 1.153249 CAGGCCTTTTATCCGCGGA 60.153 57.895 33.12 33.12 0.00 5.54
2312 2485 6.148480 CCGATTAGCTTAGCTTTAGATTGCAT 59.852 38.462 13.44 0.00 40.44 3.96
2515 2689 7.952671 TGTATATTGGACTCACAGAAGGTATC 58.047 38.462 0.00 0.00 0.00 2.24
2664 2838 3.981071 TGCAGAAAGCCTACATACACT 57.019 42.857 0.00 0.00 44.83 3.55
2760 2934 8.423349 TGATGTTTTGAGATTTGAACTCCATTT 58.577 29.630 0.00 0.00 33.95 2.32
3024 3203 0.956633 ATCGATTGATGCACATGGCC 59.043 50.000 0.00 0.00 43.89 5.36
3137 3316 7.096551 TGGAAAGTTATTCTTGGCTTTATTGC 58.903 34.615 0.00 0.00 36.40 3.56
3197 3376 6.423604 GGAATAACAACACAAAAATGACCTGG 59.576 38.462 0.00 0.00 0.00 4.45
3885 4104 0.457851 GCTCGGATAGACAGTGCACT 59.542 55.000 15.25 15.25 34.44 4.40
3887 4106 1.745653 CTCGGATAGACAGTGCACTCA 59.254 52.381 18.64 2.68 0.00 3.41
4045 4264 0.917533 ATGAGAATGGAGCAGCTGGT 59.082 50.000 20.31 20.31 0.00 4.00
4196 4415 4.318332 TGCTTGTGAATGAGACAAGGTAG 58.682 43.478 13.08 0.00 46.98 3.18
4228 4447 7.503230 TCTTTCCCTTTTTCCGTGTTAATAGTT 59.497 33.333 0.00 0.00 0.00 2.24
4414 4735 2.739913 CAGCATTTTGATTGGCTGTTGG 59.260 45.455 0.00 0.00 46.47 3.77
4415 4736 1.465777 GCATTTTGATTGGCTGTTGGC 59.534 47.619 0.00 0.00 40.90 4.52
4416 4737 2.872842 GCATTTTGATTGGCTGTTGGCT 60.873 45.455 0.00 0.00 41.46 4.75
4417 4738 2.529780 TTTTGATTGGCTGTTGGCTG 57.470 45.000 0.00 0.00 41.46 4.85
4418 4739 1.412079 TTTGATTGGCTGTTGGCTGT 58.588 45.000 0.00 0.00 41.46 4.40
4667 4993 2.379972 TGGTTAACCCAAGTGTGGTTG 58.620 47.619 21.97 0.00 45.50 3.77
5030 5369 5.206587 GAGGGAGGGATAGCCGTATTATTA 58.793 45.833 0.00 0.00 33.83 0.98
5032 5371 6.210522 AGGGAGGGATAGCCGTATTATTATT 58.789 40.000 0.00 0.00 33.83 1.40
5033 5372 6.677076 AGGGAGGGATAGCCGTATTATTATTT 59.323 38.462 0.00 0.00 33.83 1.40
5035 5374 8.488668 GGGAGGGATAGCCGTATTATTATTTTA 58.511 37.037 0.00 0.00 33.83 1.52
5127 5704 3.782443 GGGGAGCCGTCCGACAAT 61.782 66.667 0.00 0.00 45.05 2.71
5128 5705 2.267961 GGGAGCCGTCCGACAATT 59.732 61.111 0.00 0.00 45.05 2.32
5129 5706 1.376812 GGGAGCCGTCCGACAATTT 60.377 57.895 0.00 0.00 45.05 1.82
5130 5707 0.958876 GGGAGCCGTCCGACAATTTT 60.959 55.000 0.00 0.00 45.05 1.82
5131 5708 0.879090 GGAGCCGTCCGACAATTTTT 59.121 50.000 0.00 0.00 31.37 1.94
5170 5754 0.185416 TTTCAACCGGTTAGCCCCAA 59.815 50.000 21.79 3.82 0.00 4.12
5197 5784 3.721087 TTTGAGAAGGAGGATGAACCC 57.279 47.619 0.00 0.00 40.05 4.11
5211 5798 0.747283 GAACCCAGCCTCTGCATCAG 60.747 60.000 0.00 0.00 41.13 2.90
5215 5802 0.252479 CCAGCCTCTGCATCAGAACT 59.748 55.000 0.00 0.00 40.18 3.01
5334 5922 3.212685 CCATTGGATCTTGCTCCTTCTC 58.787 50.000 0.00 0.00 36.20 2.87
5363 5953 3.186409 CGTCGCCATTAACCATAATCCTG 59.814 47.826 0.00 0.00 29.08 3.86
5366 5956 2.562738 GCCATTAACCATAATCCTGCCC 59.437 50.000 0.00 0.00 29.08 5.36
5369 5959 0.109723 TAACCATAATCCTGCCCGCC 59.890 55.000 0.00 0.00 0.00 6.13
5411 6001 1.619827 CATGTTTGACCACCATGGCTT 59.380 47.619 13.04 0.00 42.67 4.35
5418 6008 1.181098 ACCACCATGGCTTGCTTCAC 61.181 55.000 13.04 0.00 42.67 3.18
5456 6046 3.270960 AGCCCATTAACCCTTCAATACCA 59.729 43.478 0.00 0.00 0.00 3.25
5457 6047 3.383505 GCCCATTAACCCTTCAATACCAC 59.616 47.826 0.00 0.00 0.00 4.16
5464 6054 1.474330 CCTTCAATACCACCCAAGCC 58.526 55.000 0.00 0.00 0.00 4.35
5473 6063 1.042559 CCACCCAAGCCGCCATAAAT 61.043 55.000 0.00 0.00 0.00 1.40
5476 6066 0.754957 CCCAAGCCGCCATAAATCCA 60.755 55.000 0.00 0.00 0.00 3.41
5487 6077 3.364366 GCCATAAATCCATCTTCGCTTCG 60.364 47.826 0.00 0.00 0.00 3.79
5494 6084 2.060980 ATCTTCGCTTCGAGGGCCT 61.061 57.895 5.25 5.25 37.14 5.19
5524 6115 9.755804 GATTTTCTTCCAACTTCTTCAATTTCT 57.244 29.630 0.00 0.00 0.00 2.52
5529 6120 8.299570 TCTTCCAACTTCTTCAATTTCTTATGC 58.700 33.333 0.00 0.00 0.00 3.14
5535 6126 3.621268 TCTTCAATTTCTTATGCGGACGG 59.379 43.478 0.00 0.00 0.00 4.79
5548 6139 2.562912 GACGGCACATGCACCAAG 59.437 61.111 6.15 0.00 44.36 3.61
5587 6178 3.119245 TGCCCAGTCGATTAACTAGACAC 60.119 47.826 0.00 0.00 37.36 3.67
5651 6242 3.968837 ATCGTCCCCTACACCGCCA 62.969 63.158 0.00 0.00 0.00 5.69
5669 6260 1.103398 CAATCCCCCTCGTTCATGCC 61.103 60.000 0.00 0.00 0.00 4.40
5719 6310 4.180946 CGTGCGTCTCCTCCTCGG 62.181 72.222 0.00 0.00 0.00 4.63
5777 6372 0.392595 GCGGAGTTAGGGTTTGGGAG 60.393 60.000 0.00 0.00 0.00 4.30
5796 6391 1.071385 AGATTGGATCGAGGACATGGC 59.929 52.381 0.00 0.00 0.00 4.40
5802 6397 0.669077 ATCGAGGACATGGCGACTAC 59.331 55.000 0.00 0.00 36.83 2.73
5817 6412 0.107654 ACTACCAATCAGGGCGCTTC 60.108 55.000 7.64 0.00 43.89 3.86
5824 6419 4.161295 CAGGGCGCTTCCGGATCA 62.161 66.667 4.15 0.00 34.94 2.92
5827 6422 2.472909 GGGCGCTTCCGGATCAAAG 61.473 63.158 4.15 0.00 34.94 2.77
5834 6429 3.134458 GCTTCCGGATCAAAGGATAGTG 58.866 50.000 4.15 0.00 36.28 2.74
5840 6435 4.811557 CCGGATCAAAGGATAGTGAAGAAC 59.188 45.833 0.00 0.00 32.67 3.01
5845 6440 6.531503 TCAAAGGATAGTGAAGAACGATCT 57.468 37.500 0.00 0.00 39.94 2.75
5846 6441 7.640597 TCAAAGGATAGTGAAGAACGATCTA 57.359 36.000 0.00 0.00 39.94 1.98
5865 6460 0.178970 AGAGGCCATGATGGAATGCC 60.179 55.000 17.22 9.06 40.96 4.40
5872 6467 0.186873 ATGATGGAATGCCTGGGACC 59.813 55.000 0.00 0.00 34.31 4.46
5895 6490 6.032094 CCGGAAGAAACTGATTTTGATGATG 58.968 40.000 0.00 0.00 0.00 3.07
5903 6498 6.808008 ACTGATTTTGATGATGTCGTCTTT 57.192 33.333 4.08 0.00 33.19 2.52
5910 6505 4.245660 TGATGATGTCGTCTTTGAGGAAC 58.754 43.478 4.08 0.00 33.19 3.62
5915 6510 4.336889 TGTCGTCTTTGAGGAACAAGAT 57.663 40.909 0.00 0.00 39.77 2.40
5921 6516 3.072915 TCTTTGAGGAACAAGATCAGCCA 59.927 43.478 0.00 0.00 39.77 4.75
5922 6517 2.479566 TGAGGAACAAGATCAGCCAC 57.520 50.000 0.00 0.00 0.00 5.01
5936 6531 3.834799 CCACCGTCGGAGGCTACC 61.835 72.222 20.51 0.00 33.69 3.18
5946 6541 2.365105 AGGCTACCCGCTGGCTTA 60.365 61.111 0.00 0.00 39.13 3.09
5967 6562 8.139989 GGCTTACTCTGATCAAATTGCATATTT 58.860 33.333 0.00 0.00 0.00 1.40
5996 6591 9.890915 AAAGAATATGGAGAGTTCTAGGTCTAT 57.109 33.333 0.00 0.00 32.26 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 8.053026 TCTATAGATTAAGCTAGCGGGTTTAG 57.947 38.462 9.55 1.98 36.91 1.85
171 175 3.953612 AGATAAATCCATTTCAGCGGCAA 59.046 39.130 1.45 0.00 0.00 4.52
199 203 5.292765 ACGGATACATCTAGCACTGAAATG 58.707 41.667 0.00 0.00 0.00 2.32
215 219 0.739813 ACCAGCGCTCAAACGGATAC 60.740 55.000 16.89 0.00 0.00 2.24
216 220 0.459585 GACCAGCGCTCAAACGGATA 60.460 55.000 16.89 0.00 0.00 2.59
230 234 3.317149 TCCGTCTCATATTAACCGACCAG 59.683 47.826 0.00 0.00 0.00 4.00
233 237 3.242870 ACGTCCGTCTCATATTAACCGAC 60.243 47.826 0.00 0.00 0.00 4.79
265 269 9.988815 AAGACACATCTCACCATATATTTAGTC 57.011 33.333 0.00 0.00 32.34 2.59
305 309 9.760660 GGTTGATCGAATTTAGTTATATGCATC 57.239 33.333 0.19 0.00 0.00 3.91
357 380 7.632861 TGAAGGTGAGGAAAATATCATGAGAA 58.367 34.615 0.09 0.00 0.00 2.87
358 381 7.199167 TGAAGGTGAGGAAAATATCATGAGA 57.801 36.000 0.09 0.00 0.00 3.27
359 382 7.937942 AGATGAAGGTGAGGAAAATATCATGAG 59.062 37.037 0.09 0.00 0.00 2.90
360 383 7.809238 AGATGAAGGTGAGGAAAATATCATGA 58.191 34.615 0.00 0.00 0.00 3.07
361 384 7.718314 TGAGATGAAGGTGAGGAAAATATCATG 59.282 37.037 0.00 0.00 0.00 3.07
389 412 2.613026 TACGCCATGTAGGACCAATG 57.387 50.000 0.00 0.00 41.22 2.82
394 417 4.394300 ACGAGTATATACGCCATGTAGGAC 59.606 45.833 10.56 0.00 41.22 3.85
406 429 8.633075 AGCGAGTATCTTAGACGAGTATATAC 57.367 38.462 4.60 4.60 0.00 1.47
418 441 1.194997 CGGACGGAGCGAGTATCTTAG 59.805 57.143 0.00 0.00 0.00 2.18
424 447 0.597568 TTTTTCGGACGGAGCGAGTA 59.402 50.000 0.00 0.00 0.00 2.59
425 448 1.364901 TTTTTCGGACGGAGCGAGT 59.635 52.632 0.00 0.00 0.00 4.18
449 475 6.291377 GTGCTAGATACATTCATTTGAGGGA 58.709 40.000 0.00 0.00 0.00 4.20
452 478 7.281774 ACTTGGTGCTAGATACATTCATTTGAG 59.718 37.037 0.00 0.00 0.00 3.02
454 480 7.325660 ACTTGGTGCTAGATACATTCATTTG 57.674 36.000 0.00 0.00 0.00 2.32
457 483 7.796054 ACTAACTTGGTGCTAGATACATTCAT 58.204 34.615 0.00 0.00 0.00 2.57
459 485 9.765795 AATACTAACTTGGTGCTAGATACATTC 57.234 33.333 0.00 0.00 0.00 2.67
462 488 9.636789 TCTAATACTAACTTGGTGCTAGATACA 57.363 33.333 0.00 0.00 0.00 2.29
469 495 8.368668 GGATGTATCTAATACTAACTTGGTGCT 58.631 37.037 0.00 0.00 36.70 4.40
489 515 9.717942 CCCAAATTTGTCTTTTAAATGGATGTA 57.282 29.630 16.73 0.00 0.00 2.29
491 517 8.720562 GTCCCAAATTTGTCTTTTAAATGGATG 58.279 33.333 16.73 0.00 0.00 3.51
492 518 8.435982 TGTCCCAAATTTGTCTTTTAAATGGAT 58.564 29.630 16.73 0.00 0.00 3.41
494 520 8.341903 GTTGTCCCAAATTTGTCTTTTAAATGG 58.658 33.333 16.73 6.90 0.00 3.16
495 521 8.341903 GGTTGTCCCAAATTTGTCTTTTAAATG 58.658 33.333 16.73 0.00 0.00 2.32
501 527 5.692115 AAGGTTGTCCCAAATTTGTCTTT 57.308 34.783 16.73 1.29 34.66 2.52
502 528 5.692115 AAAGGTTGTCCCAAATTTGTCTT 57.308 34.783 16.73 6.12 34.66 3.01
504 530 5.877564 TGAAAAAGGTTGTCCCAAATTTGTC 59.122 36.000 16.73 7.66 34.66 3.18
505 531 5.810095 TGAAAAAGGTTGTCCCAAATTTGT 58.190 33.333 16.73 0.00 34.66 2.83
506 532 6.037062 GTCTGAAAAAGGTTGTCCCAAATTTG 59.963 38.462 11.40 11.40 34.66 2.32
509 535 4.202111 CGTCTGAAAAAGGTTGTCCCAAAT 60.202 41.667 0.00 0.00 34.66 2.32
512 538 2.092861 TCGTCTGAAAAAGGTTGTCCCA 60.093 45.455 0.00 0.00 34.66 4.37
513 539 2.567985 TCGTCTGAAAAAGGTTGTCCC 58.432 47.619 0.00 0.00 0.00 4.46
514 540 3.003378 CCTTCGTCTGAAAAAGGTTGTCC 59.997 47.826 9.93 0.00 35.79 4.02
515 541 3.003378 CCCTTCGTCTGAAAAAGGTTGTC 59.997 47.826 14.71 0.00 38.30 3.18
516 542 2.949644 CCCTTCGTCTGAAAAAGGTTGT 59.050 45.455 14.71 0.00 38.30 3.32
517 543 3.211045 TCCCTTCGTCTGAAAAAGGTTG 58.789 45.455 14.71 4.76 38.30 3.77
518 544 3.118000 ACTCCCTTCGTCTGAAAAAGGTT 60.118 43.478 14.71 1.35 38.30 3.50
520 546 3.127425 ACTCCCTTCGTCTGAAAAAGG 57.873 47.619 10.81 10.81 39.44 3.11
521 547 5.050295 GTGTTACTCCCTTCGTCTGAAAAAG 60.050 44.000 0.00 0.00 32.66 2.27
522 548 4.812626 GTGTTACTCCCTTCGTCTGAAAAA 59.187 41.667 0.00 0.00 32.66 1.94
523 549 4.141892 TGTGTTACTCCCTTCGTCTGAAAA 60.142 41.667 0.00 0.00 32.66 2.29
524 550 3.385433 TGTGTTACTCCCTTCGTCTGAAA 59.615 43.478 0.00 0.00 32.66 2.69
525 551 2.960384 TGTGTTACTCCCTTCGTCTGAA 59.040 45.455 0.00 0.00 0.00 3.02
526 552 2.589720 TGTGTTACTCCCTTCGTCTGA 58.410 47.619 0.00 0.00 0.00 3.27
527 553 3.594603 ATGTGTTACTCCCTTCGTCTG 57.405 47.619 0.00 0.00 0.00 3.51
529 555 5.068198 TGGTATATGTGTTACTCCCTTCGTC 59.932 44.000 0.00 0.00 0.00 4.20
532 558 7.062749 TCATGGTATATGTGTTACTCCCTTC 57.937 40.000 0.00 0.00 0.00 3.46
533 559 6.464465 GCTCATGGTATATGTGTTACTCCCTT 60.464 42.308 0.00 0.00 0.00 3.95
535 561 5.221641 TGCTCATGGTATATGTGTTACTCCC 60.222 44.000 0.00 0.00 0.00 4.30
536 562 5.696724 GTGCTCATGGTATATGTGTTACTCC 59.303 44.000 0.00 0.00 0.00 3.85
537 563 5.696724 GGTGCTCATGGTATATGTGTTACTC 59.303 44.000 0.00 0.00 0.00 2.59
581 641 9.559732 CTTTCTCCATATCAACAATGGTATGTA 57.440 33.333 7.97 0.00 45.40 2.29
617 677 1.146774 TGGGATTTGCAAAGGGAGACA 59.853 47.619 18.19 7.69 0.00 3.41
625 685 0.471591 AGGCCACTGGGATTTGCAAA 60.472 50.000 15.44 15.44 35.59 3.68
651 728 0.401395 ACTCCCCCTTGACCTTCACA 60.401 55.000 0.00 0.00 0.00 3.58
885 998 1.305930 GGGCGTCCATTCACTCAACC 61.306 60.000 0.00 0.00 0.00 3.77
887 1000 0.605319 GTGGGCGTCCATTCACTCAA 60.605 55.000 14.23 0.00 46.09 3.02
894 1007 1.079127 CTTCGAGTGGGCGTCCATT 60.079 57.895 14.23 8.42 46.09 3.16
1011 1134 5.183331 GGGCGAATGGCGATAGATAGATATA 59.817 44.000 0.00 0.00 44.92 0.86
1012 1135 4.021894 GGGCGAATGGCGATAGATAGATAT 60.022 45.833 0.00 0.00 44.92 1.63
1064 1188 1.423161 GGGATGAGGATTGAGGAAGGG 59.577 57.143 0.00 0.00 0.00 3.95
1141 1265 5.650703 ACGGGAAGAAGAAGAAAAAGAACAA 59.349 36.000 0.00 0.00 0.00 2.83
1142 1266 5.190677 ACGGGAAGAAGAAGAAAAAGAACA 58.809 37.500 0.00 0.00 0.00 3.18
1143 1267 5.296035 TGACGGGAAGAAGAAGAAAAAGAAC 59.704 40.000 0.00 0.00 0.00 3.01
1144 1268 5.433526 TGACGGGAAGAAGAAGAAAAAGAA 58.566 37.500 0.00 0.00 0.00 2.52
1145 1269 5.031066 TGACGGGAAGAAGAAGAAAAAGA 57.969 39.130 0.00 0.00 0.00 2.52
1146 1270 5.703130 AGATGACGGGAAGAAGAAGAAAAAG 59.297 40.000 0.00 0.00 0.00 2.27
1147 1271 5.621193 AGATGACGGGAAGAAGAAGAAAAA 58.379 37.500 0.00 0.00 0.00 1.94
1148 1272 5.228945 AGATGACGGGAAGAAGAAGAAAA 57.771 39.130 0.00 0.00 0.00 2.29
1149 1273 4.322801 GGAGATGACGGGAAGAAGAAGAAA 60.323 45.833 0.00 0.00 0.00 2.52
1150 1274 3.195825 GGAGATGACGGGAAGAAGAAGAA 59.804 47.826 0.00 0.00 0.00 2.52
1151 1275 2.761208 GGAGATGACGGGAAGAAGAAGA 59.239 50.000 0.00 0.00 0.00 2.87
1152 1276 2.497675 TGGAGATGACGGGAAGAAGAAG 59.502 50.000 0.00 0.00 0.00 2.85
1153 1277 2.536066 TGGAGATGACGGGAAGAAGAA 58.464 47.619 0.00 0.00 0.00 2.52
1154 1278 2.231716 TGGAGATGACGGGAAGAAGA 57.768 50.000 0.00 0.00 0.00 2.87
1155 1279 4.672587 TTATGGAGATGACGGGAAGAAG 57.327 45.455 0.00 0.00 0.00 2.85
1156 1280 5.183228 GTTTTATGGAGATGACGGGAAGAA 58.817 41.667 0.00 0.00 0.00 2.52
1157 1281 4.383770 GGTTTTATGGAGATGACGGGAAGA 60.384 45.833 0.00 0.00 0.00 2.87
1158 1282 3.877508 GGTTTTATGGAGATGACGGGAAG 59.122 47.826 0.00 0.00 0.00 3.46
1159 1283 3.264706 TGGTTTTATGGAGATGACGGGAA 59.735 43.478 0.00 0.00 0.00 3.97
1160 1284 2.841266 TGGTTTTATGGAGATGACGGGA 59.159 45.455 0.00 0.00 0.00 5.14
1161 1285 3.275617 TGGTTTTATGGAGATGACGGG 57.724 47.619 0.00 0.00 0.00 5.28
1174 1298 6.485313 TCGCAGAGATTCTTTTCTTGGTTTTA 59.515 34.615 0.00 0.00 0.00 1.52
1384 1508 1.079681 ATTAACCGAACGGAGCGCA 60.080 52.632 20.14 0.00 38.96 6.09
1424 1548 3.776969 AGGAATCTCACATGTAGGAGCAA 59.223 43.478 0.00 0.00 0.00 3.91
1491 1618 2.183555 CCCTTACTCCGACACCGC 59.816 66.667 0.00 0.00 0.00 5.68
1558 1685 2.827190 AGACCGTGGCGCGAGATA 60.827 61.111 23.75 0.00 44.77 1.98
1646 1773 4.617520 TTCCAGCGCGTCTGCCAA 62.618 61.111 20.45 13.83 41.50 4.52
1897 2025 4.107622 ACGTACGTAATTGGTAGCATGAC 58.892 43.478 21.41 0.00 0.00 3.06
1926 2054 7.703621 GCAATGAAGCTATGACACAATTAATGT 59.296 33.333 0.00 0.00 45.34 2.71
1927 2055 7.168637 GGCAATGAAGCTATGACACAATTAATG 59.831 37.037 0.00 0.00 34.17 1.90
1934 2070 2.009051 CGGCAATGAAGCTATGACACA 58.991 47.619 0.00 0.00 34.17 3.72
1976 2134 5.129815 TCCCGCTATACAAAGGTAATTCACT 59.870 40.000 0.00 0.00 32.19 3.41
1989 2147 2.969262 TCAATCACCATCCCGCTATACA 59.031 45.455 0.00 0.00 0.00 2.29
1993 2151 4.698201 TTATTCAATCACCATCCCGCTA 57.302 40.909 0.00 0.00 0.00 4.26
1994 2152 3.576078 TTATTCAATCACCATCCCGCT 57.424 42.857 0.00 0.00 0.00 5.52
1995 2153 4.647424 TTTTATTCAATCACCATCCCGC 57.353 40.909 0.00 0.00 0.00 6.13
1996 2154 5.008613 ACGATTTTATTCAATCACCATCCCG 59.991 40.000 0.00 0.00 33.35 5.14
2021 2188 5.967088 ACTTGAGCAACATAGTGTAGTAGG 58.033 41.667 0.00 0.00 0.00 3.18
2030 2197 4.326826 TCCCAAAGACTTGAGCAACATAG 58.673 43.478 0.00 0.00 34.14 2.23
2062 2229 3.744942 CCATCCATGACAAAGATAGCTCG 59.255 47.826 0.00 0.00 0.00 5.03
2071 2238 1.617850 GTTGGCACCATCCATGACAAA 59.382 47.619 0.00 0.00 46.50 2.83
2223 2396 4.142945 GCACTTGCTCATCTTACTTGTCAG 60.143 45.833 0.00 0.00 38.21 3.51
2243 2416 4.790766 GCATAGCATACATCAAGTTGGCAC 60.791 45.833 2.34 0.00 32.43 5.01
2268 2441 1.153229 ACTCCGCGGATAAAAGGCC 60.153 57.895 31.19 0.00 0.00 5.19
2284 2457 6.658188 ATCTAAAGCTAAGCTAATCGGACT 57.342 37.500 0.00 0.00 38.25 3.85
2292 2465 9.559732 TTGATAATGCAATCTAAAGCTAAGCTA 57.440 29.630 0.00 0.00 38.25 3.32
2330 2504 6.467723 AAATTCTTACTAGAAGCACACACG 57.532 37.500 0.00 0.00 43.33 4.49
2515 2689 4.039609 GCAAAATGGGGATGATTAAGGAGG 59.960 45.833 0.00 0.00 0.00 4.30
2551 2725 6.782988 ACCCACTATAGTCTGCATAACTACAT 59.217 38.462 1.26 1.90 32.30 2.29
2557 2731 6.524734 CATGAACCCACTATAGTCTGCATAA 58.475 40.000 1.26 0.00 0.00 1.90
2760 2934 6.830324 AGGAAATAGCACAAATCATAGCTTCA 59.170 34.615 0.00 0.00 38.47 3.02
2926 3101 4.204573 GCTCAGTATTAGCTTAACACGACG 59.795 45.833 0.00 0.00 37.01 5.12
3024 3203 4.940046 AGACCAGTTGATGCTCATTGTTAG 59.060 41.667 0.00 0.00 0.00 2.34
3095 3274 1.764723 TCCATCGAATGCTCCTGACAT 59.235 47.619 0.00 0.00 0.00 3.06
3137 3316 8.981724 ATCAATCATGAAAACAATTCAGACAG 57.018 30.769 0.00 0.00 39.49 3.51
3885 4104 0.539669 TTCGTCCTGAGCCTGAGTGA 60.540 55.000 0.00 0.00 0.00 3.41
3887 4106 0.251386 TCTTCGTCCTGAGCCTGAGT 60.251 55.000 0.00 0.00 0.00 3.41
4000 4219 2.504367 GCCACCAGCTGAAAGTTCTTA 58.496 47.619 17.39 0.00 38.99 2.10
4045 4264 1.351076 TCACCTTGTCATGCTCCTGA 58.649 50.000 0.00 0.00 0.00 3.86
4196 4415 6.509656 ACACGGAAAAAGGGAAAGAAATAAC 58.490 36.000 0.00 0.00 0.00 1.89
4414 4735 3.670377 GACCCCAACGCCAACAGC 61.670 66.667 0.00 0.00 38.52 4.40
4415 4736 1.966451 GAGACCCCAACGCCAACAG 60.966 63.158 0.00 0.00 0.00 3.16
4416 4737 1.122632 TAGAGACCCCAACGCCAACA 61.123 55.000 0.00 0.00 0.00 3.33
4417 4738 0.035739 TTAGAGACCCCAACGCCAAC 59.964 55.000 0.00 0.00 0.00 3.77
4418 4739 0.035739 GTTAGAGACCCCAACGCCAA 59.964 55.000 0.00 0.00 0.00 4.52
5002 5341 1.909287 GCTATCCCTCCCTCCGGAC 60.909 68.421 0.00 0.00 33.32 4.79
5035 5374 8.617290 ACTGAAGAAGAACCGTTATGTTTTAT 57.383 30.769 0.00 0.00 0.00 1.40
5179 5766 2.191400 CTGGGTTCATCCTCCTTCTCA 58.809 52.381 0.00 0.00 36.25 3.27
5180 5767 1.134250 GCTGGGTTCATCCTCCTTCTC 60.134 57.143 0.00 0.00 36.25 2.87
5182 5769 0.106967 GGCTGGGTTCATCCTCCTTC 60.107 60.000 0.00 0.00 36.25 3.46
5194 5781 1.203441 TTCTGATGCAGAGGCTGGGT 61.203 55.000 0.00 0.00 41.75 4.51
5197 5784 2.975732 TAGTTCTGATGCAGAGGCTG 57.024 50.000 0.00 0.00 41.75 4.85
5211 5798 4.778534 AATATGGCTGCATGCATAGTTC 57.221 40.909 22.97 9.58 45.15 3.01
5215 5802 6.377712 TGCTTAATAATATGGCTGCATGCATA 59.622 34.615 22.97 11.22 45.15 3.14
5275 5862 5.221224 CCTTTTTGTTATGCTCTGTTGGTGA 60.221 40.000 0.00 0.00 0.00 4.02
5334 5922 1.140161 TTAATGGCGACGAGACGGG 59.860 57.895 0.00 0.00 0.00 5.28
5363 5953 3.640000 CGATCGATGTTGGCGGGC 61.640 66.667 10.26 0.00 0.00 6.13
5366 5956 1.005347 GTTAACCGATCGATGTTGGCG 60.005 52.381 18.66 0.00 0.00 5.69
5369 5959 4.399978 GGTTTGTTAACCGATCGATGTTG 58.600 43.478 18.66 1.10 44.12 3.33
5411 6001 2.972713 AGGTGAGGTAGAAAGTGAAGCA 59.027 45.455 0.00 0.00 0.00 3.91
5418 6008 2.838202 TGGGCTTAGGTGAGGTAGAAAG 59.162 50.000 0.00 0.00 0.00 2.62
5456 6046 0.755327 GGATTTATGGCGGCTTGGGT 60.755 55.000 11.43 0.00 0.00 4.51
5457 6047 0.754957 TGGATTTATGGCGGCTTGGG 60.755 55.000 11.43 0.00 0.00 4.12
5464 6054 2.146342 AGCGAAGATGGATTTATGGCG 58.854 47.619 0.00 0.00 0.00 5.69
5473 6063 1.816537 CCCTCGAAGCGAAGATGGA 59.183 57.895 0.00 0.00 34.74 3.41
5476 6066 0.755698 TAGGCCCTCGAAGCGAAGAT 60.756 55.000 0.00 0.00 34.74 2.40
5487 6077 3.117512 TGGAAGAAAATCCATAGGCCCTC 60.118 47.826 0.00 0.00 44.52 4.30
5515 6106 2.096819 GCCGTCCGCATAAGAAATTGAA 59.903 45.455 0.00 0.00 37.47 2.69
5516 6107 1.668751 GCCGTCCGCATAAGAAATTGA 59.331 47.619 0.00 0.00 37.47 2.57
5517 6108 1.400142 TGCCGTCCGCATAAGAAATTG 59.600 47.619 0.00 0.00 44.64 2.32
5518 6109 1.745232 TGCCGTCCGCATAAGAAATT 58.255 45.000 0.00 0.00 44.64 1.82
5535 6126 1.198637 GAGACTTCTTGGTGCATGTGC 59.801 52.381 0.00 0.00 42.50 4.57
5548 6139 0.109039 GCAGAGGGACGTGAGACTTC 60.109 60.000 0.00 0.00 0.00 3.01
5587 6178 2.751806 AGGTAACCCTAACGAGAAGTCG 59.248 50.000 0.00 0.00 45.71 4.18
5625 6216 4.014406 GGTGTAGGGGACGATTTTTCAAT 58.986 43.478 0.00 0.00 0.00 2.57
5630 6221 0.392060 GCGGTGTAGGGGACGATTTT 60.392 55.000 0.00 0.00 0.00 1.82
5651 6242 1.227383 GGCATGAACGAGGGGGATT 59.773 57.895 0.00 0.00 0.00 3.01
5683 6274 3.008517 TCGCCCCTTGATCAGCCA 61.009 61.111 0.00 0.00 0.00 4.75
5706 6297 2.756283 AAGGCCGAGGAGGAGACG 60.756 66.667 0.00 0.00 45.00 4.18
5709 6300 2.685380 ACCAAGGCCGAGGAGGAG 60.685 66.667 21.49 0.00 45.00 3.69
5710 6301 3.003173 CACCAAGGCCGAGGAGGA 61.003 66.667 21.49 0.00 45.00 3.71
5719 6310 4.643387 AGCGACACCCACCAAGGC 62.643 66.667 0.00 0.00 35.39 4.35
5759 6350 1.272807 TCTCCCAAACCCTAACTCCG 58.727 55.000 0.00 0.00 0.00 4.63
5777 6372 1.517242 GCCATGTCCTCGATCCAATC 58.483 55.000 0.00 0.00 0.00 2.67
5796 6391 1.883084 GCGCCCTGATTGGTAGTCG 60.883 63.158 0.00 0.00 0.00 4.18
5802 6397 3.204827 CGGAAGCGCCCTGATTGG 61.205 66.667 2.29 0.00 0.00 3.16
5817 6412 4.672587 TCTTCACTATCCTTTGATCCGG 57.327 45.455 0.00 0.00 32.18 5.14
5824 6419 7.013846 CCTCTAGATCGTTCTTCACTATCCTTT 59.986 40.741 0.48 0.00 33.17 3.11
5827 6422 5.335348 GCCTCTAGATCGTTCTTCACTATCC 60.335 48.000 0.48 0.00 33.17 2.59
5834 6429 3.319405 TCATGGCCTCTAGATCGTTCTTC 59.681 47.826 3.32 0.00 33.17 2.87
5840 6435 2.174360 TCCATCATGGCCTCTAGATCG 58.826 52.381 3.32 0.00 37.47 3.69
5845 6440 1.074405 GGCATTCCATCATGGCCTCTA 59.926 52.381 3.32 0.00 42.57 2.43
5846 6441 0.178970 GGCATTCCATCATGGCCTCT 60.179 55.000 3.32 0.00 42.57 3.69
5865 6460 0.685097 TCAGTTTCTTCCGGTCCCAG 59.315 55.000 0.00 0.00 0.00 4.45
5872 6467 6.615088 ACATCATCAAAATCAGTTTCTTCCG 58.385 36.000 0.00 0.00 0.00 4.30
5895 6490 4.307432 TGATCTTGTTCCTCAAAGACGAC 58.693 43.478 0.00 0.00 35.48 4.34
5903 6498 1.003580 GGTGGCTGATCTTGTTCCTCA 59.996 52.381 0.00 0.00 0.00 3.86
5910 6505 1.811266 CCGACGGTGGCTGATCTTG 60.811 63.158 5.48 0.00 0.00 3.02
5936 6531 0.461548 TGATCAGAGTAAGCCAGCGG 59.538 55.000 0.00 0.00 0.00 5.52
5939 6534 4.397103 TGCAATTTGATCAGAGTAAGCCAG 59.603 41.667 0.00 0.00 0.00 4.85
5967 6562 9.357161 GACCTAGAACTCTCCATATTCTTTCTA 57.643 37.037 0.00 0.00 34.55 2.10


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

AutoCloner maintained by Alex Coulton.