Multiple sequence alignment - TraesCS6A01G071500

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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 TraesCS6A01G071500 chr6A 100.000 5238 0 0 1 5238 39144293 39149530 0.000000e+00 9673.0
1 TraesCS6A01G071500 chr6B 94.064 1853 83 13 1030 2867 72182967 72184807 0.000000e+00 2787.0
2 TraesCS6A01G071500 chr6B 98.259 517 6 1 4722 5238 478890390 478890903 0.000000e+00 902.0
3 TraesCS6A01G071500 chr6B 83.420 959 92 32 3253 4170 72185391 72186323 0.000000e+00 828.0
4 TraesCS6A01G071500 chr6B 85.413 569 64 10 6 561 72180151 72180713 1.640000e-159 573.0
5 TraesCS6A01G071500 chr6B 91.878 394 17 3 2866 3253 72184965 72185349 2.150000e-148 536.0
6 TraesCS6A01G071500 chr6B 85.915 426 48 9 4159 4574 72186341 72186764 1.340000e-120 444.0
7 TraesCS6A01G071500 chr6B 91.813 171 12 1 787 955 72181031 72181201 2.440000e-58 237.0
8 TraesCS6A01G071500 chr6D 92.642 1427 64 19 1847 3253 34975975 34977380 0.000000e+00 2015.0
9 TraesCS6A01G071500 chr6D 85.535 954 91 20 3251 4169 34977420 34978361 0.000000e+00 953.0
10 TraesCS6A01G071500 chr6D 88.786 651 62 7 6 651 34973933 34974577 0.000000e+00 787.0
11 TraesCS6A01G071500 chr6D 87.568 555 62 6 4162 4715 34978388 34978936 2.060000e-178 636.0
12 TraesCS6A01G071500 chr6D 90.065 463 37 8 1030 1487 34975049 34975507 4.520000e-165 592.0
13 TraesCS6A01G071500 chr6D 90.536 317 20 6 655 966 34974644 34974955 1.360000e-110 411.0
14 TraesCS6A01G071500 chr2B 99.614 518 1 1 4721 5238 8560854 8560338 0.000000e+00 944.0
15 TraesCS6A01G071500 chr7B 99.420 517 3 0 4722 5238 64175540 64176056 0.000000e+00 939.0
16 TraesCS6A01G071500 chr7B 97.897 523 11 0 4716 5238 706855395 706855917 0.000000e+00 905.0
17 TraesCS6A01G071500 chr7B 80.818 1173 140 48 3454 4580 608474723 608475856 0.000000e+00 841.0
18 TraesCS6A01G071500 chr5B 98.833 514 6 0 4725 5238 637140046 637139533 0.000000e+00 917.0
19 TraesCS6A01G071500 chr3B 98.453 517 8 0 4722 5238 687652961 687653477 0.000000e+00 911.0
20 TraesCS6A01G071500 chr3B 98.259 517 7 1 4722 5238 687623166 687623680 0.000000e+00 904.0
21 TraesCS6A01G071500 chr3B 98.259 517 8 1 4722 5238 768735867 768735352 0.000000e+00 904.0
22 TraesCS6A01G071500 chr3B 100.000 29 0 0 623 651 507274520 507274548 3.000000e-03 54.7
23 TraesCS6A01G071500 chr5A 97.683 518 11 1 4721 5238 322888525 322889041 0.000000e+00 889.0
24 TraesCS6A01G071500 chr7D 83.721 688 81 23 3906 4580 560674540 560675209 5.760000e-174 621.0
25 TraesCS6A01G071500 chr7D 83.285 688 78 28 3906 4580 560684350 560685013 2.700000e-167 599.0
26 TraesCS6A01G071500 chr7A 81.306 781 95 28 3458 4204 644854560 644855323 2.100000e-163 586.0
27 TraesCS6A01G071500 chr7A 80.260 461 57 17 4243 4679 644855334 644855784 3.040000e-82 316.0


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 TraesCS6A01G071500 chr6A 39144293 39149530 5237 False 9673.000000 9673 100.000000 1 5238 1 chr6A.!!$F1 5237
1 TraesCS6A01G071500 chr6B 478890390 478890903 513 False 902.000000 902 98.259000 4722 5238 1 chr6B.!!$F1 516
2 TraesCS6A01G071500 chr6B 72180151 72186764 6613 False 900.833333 2787 88.750500 6 4574 6 chr6B.!!$F2 4568
3 TraesCS6A01G071500 chr6D 34973933 34978936 5003 False 899.000000 2015 89.188667 6 4715 6 chr6D.!!$F1 4709
4 TraesCS6A01G071500 chr2B 8560338 8560854 516 True 944.000000 944 99.614000 4721 5238 1 chr2B.!!$R1 517
5 TraesCS6A01G071500 chr7B 64175540 64176056 516 False 939.000000 939 99.420000 4722 5238 1 chr7B.!!$F1 516
6 TraesCS6A01G071500 chr7B 706855395 706855917 522 False 905.000000 905 97.897000 4716 5238 1 chr7B.!!$F3 522
7 TraesCS6A01G071500 chr7B 608474723 608475856 1133 False 841.000000 841 80.818000 3454 4580 1 chr7B.!!$F2 1126
8 TraesCS6A01G071500 chr5B 637139533 637140046 513 True 917.000000 917 98.833000 4725 5238 1 chr5B.!!$R1 513
9 TraesCS6A01G071500 chr3B 687652961 687653477 516 False 911.000000 911 98.453000 4722 5238 1 chr3B.!!$F3 516
10 TraesCS6A01G071500 chr3B 687623166 687623680 514 False 904.000000 904 98.259000 4722 5238 1 chr3B.!!$F2 516
11 TraesCS6A01G071500 chr3B 768735352 768735867 515 True 904.000000 904 98.259000 4722 5238 1 chr3B.!!$R1 516
12 TraesCS6A01G071500 chr5A 322888525 322889041 516 False 889.000000 889 97.683000 4721 5238 1 chr5A.!!$F1 517
13 TraesCS6A01G071500 chr7D 560674540 560675209 669 False 621.000000 621 83.721000 3906 4580 1 chr7D.!!$F1 674
14 TraesCS6A01G071500 chr7D 560684350 560685013 663 False 599.000000 599 83.285000 3906 4580 1 chr7D.!!$F2 674
15 TraesCS6A01G071500 chr7A 644854560 644855784 1224 False 451.000000 586 80.783000 3458 4679 2 chr7A.!!$F1 1221

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
967 1203 0.172127 TCAGCTCAGCTCTGCTTACG 59.828 55.000 0.00 0.0 36.4 3.18 F
968 1204 0.805322 CAGCTCAGCTCTGCTTACGG 60.805 60.000 0.00 0.0 36.4 4.02 F
1022 1258 0.955919 CAAACCGGGCCTCTCTCAAC 60.956 60.000 6.32 0.0 0.0 3.18 F
3035 5267 1.197721 CCGAAACATGAGTGCAACCTC 59.802 52.381 0.00 0.0 37.8 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2666 4739 1.821216 CCCTTTCACGCAACACCTAT 58.179 50.000 0.0 0.0 0.0 2.57 R
3035 5267 6.697455 TGAAATTCGACAAGATATTCCTCTCG 59.303 38.462 0.0 0.0 0.0 4.04 R
3178 5417 2.172505 TCTCTTCACAGGCAAGGTTTCA 59.827 45.455 0.0 0.0 0.0 2.69 R
4661 7059 0.542702 AACAAGGACCTGGCAATGGG 60.543 55.000 0.0 0.0 0.0 4.00 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
54 55 4.572985 TTCTGCATTTGAACCTTGTCTG 57.427 40.909 0.00 0.00 0.00 3.51
99 100 3.423154 CAAAGGTGGCTCGACGGC 61.423 66.667 0.00 0.00 38.97 5.68
138 139 0.729116 CCATGAAAGAAGTCGCGCAT 59.271 50.000 8.75 0.00 0.00 4.73
181 182 4.475028 TGCGTTGTTGCAGAAGAATTATG 58.525 39.130 0.00 0.00 41.00 1.90
258 259 1.738350 CGACGAGGCTTAGAGAACAGA 59.262 52.381 0.00 0.00 0.00 3.41
259 260 2.161808 CGACGAGGCTTAGAGAACAGAA 59.838 50.000 0.00 0.00 0.00 3.02
263 264 6.282199 ACGAGGCTTAGAGAACAGAATTTA 57.718 37.500 0.00 0.00 0.00 1.40
264 265 6.334202 ACGAGGCTTAGAGAACAGAATTTAG 58.666 40.000 0.00 0.00 0.00 1.85
265 266 5.233263 CGAGGCTTAGAGAACAGAATTTAGC 59.767 44.000 0.00 0.00 0.00 3.09
266 267 5.432645 AGGCTTAGAGAACAGAATTTAGCC 58.567 41.667 0.00 0.00 44.54 3.93
267 268 4.271291 GGCTTAGAGAACAGAATTTAGCCG 59.729 45.833 0.00 0.00 36.64 5.52
268 269 5.109903 GCTTAGAGAACAGAATTTAGCCGA 58.890 41.667 0.00 0.00 0.00 5.54
270 271 3.512680 AGAGAACAGAATTTAGCCGACG 58.487 45.455 0.00 0.00 0.00 5.12
277 291 3.863424 CAGAATTTAGCCGACGTGTGTAT 59.137 43.478 0.00 0.00 0.00 2.29
281 295 3.300852 TTAGCCGACGTGTGTATGAAA 57.699 42.857 0.00 0.00 0.00 2.69
289 303 6.410845 CCGACGTGTGTATGAAATTTATCTG 58.589 40.000 0.00 0.00 0.00 2.90
300 314 6.426980 TGAAATTTATCTGTGCAGCAGTAG 57.573 37.500 13.59 0.00 45.23 2.57
307 321 2.762887 TCTGTGCAGCAGTAGAAGCTAT 59.237 45.455 13.59 0.00 45.23 2.97
308 322 3.196469 TCTGTGCAGCAGTAGAAGCTATT 59.804 43.478 13.59 0.00 45.23 1.73
309 323 3.525537 TGTGCAGCAGTAGAAGCTATTC 58.474 45.455 0.00 0.00 41.14 1.75
310 324 2.869192 GTGCAGCAGTAGAAGCTATTCC 59.131 50.000 0.00 0.00 41.14 3.01
311 325 2.501316 TGCAGCAGTAGAAGCTATTCCA 59.499 45.455 0.00 0.00 41.14 3.53
329 343 2.624364 TCCAGTTAACTAGTCGTGCACA 59.376 45.455 18.64 0.81 0.00 4.57
470 484 2.362369 CCTCTGCCCAGACGGTGAT 61.362 63.158 0.00 0.00 33.22 3.06
473 487 4.758251 TGCCCAGACGGTGATGCG 62.758 66.667 0.00 0.00 0.00 4.73
478 492 3.695606 AGACGGTGATGCGCAGGT 61.696 61.111 18.32 8.42 0.00 4.00
479 493 3.490759 GACGGTGATGCGCAGGTG 61.491 66.667 18.32 6.29 0.00 4.00
571 585 0.185901 ACAAAGGAGGAGCTGGCAAA 59.814 50.000 0.00 0.00 0.00 3.68
584 598 4.338879 AGCTGGCAAACTTATCAAGTCAT 58.661 39.130 0.00 0.00 41.91 3.06
627 641 7.207383 TCATATATTCAAATATACGCCCTCCG 58.793 38.462 4.92 0.00 36.85 4.63
640 654 0.828677 CCCTCCGTCCCGAATTAGTT 59.171 55.000 0.00 0.00 0.00 2.24
647 661 4.220382 TCCGTCCCGAATTAGTTGTCTTAA 59.780 41.667 0.00 0.00 0.00 1.85
651 665 6.959311 CGTCCCGAATTAGTTGTCTTAAATTG 59.041 38.462 0.00 0.00 0.00 2.32
652 666 7.148540 CGTCCCGAATTAGTTGTCTTAAATTGA 60.149 37.037 0.00 0.00 0.00 2.57
653 667 7.961283 GTCCCGAATTAGTTGTCTTAAATTGAC 59.039 37.037 0.00 0.00 35.21 3.18
678 756 5.044993 ACAACTAATTTGGGACGGGGTAATA 60.045 40.000 0.00 0.00 39.84 0.98
681 759 3.851458 ATTTGGGACGGGGTAATAGAC 57.149 47.619 0.00 0.00 0.00 2.59
726 804 0.979665 CTGTCACCACAGGAGTCCAT 59.020 55.000 12.86 0.00 45.75 3.41
763 841 3.026694 TCGAGTCATCACAGGATCACAT 58.973 45.455 0.00 0.00 24.85 3.21
812 1044 2.031258 TGTGTGTGTGGTGTAAGTGG 57.969 50.000 0.00 0.00 0.00 4.00
857 1089 6.483385 TGATGCATGCAAAATAAAAGGTTG 57.517 33.333 26.68 0.00 0.00 3.77
889 1121 3.558829 CCGATGATCTCATTGTCAGTTGG 59.441 47.826 6.66 0.00 36.57 3.77
932 1164 0.256752 TCCATTGCTGGAGGTGGATG 59.743 55.000 2.11 0.00 46.95 3.51
963 1199 2.580276 GCTCAGCTCAGCTCTGCT 59.420 61.111 0.67 4.30 36.40 4.24
964 1200 1.078988 GCTCAGCTCAGCTCTGCTT 60.079 57.895 0.67 0.00 36.40 3.91
965 1201 0.175302 GCTCAGCTCAGCTCTGCTTA 59.825 55.000 0.67 0.01 36.40 3.09
967 1203 0.172127 TCAGCTCAGCTCTGCTTACG 59.828 55.000 0.00 0.00 36.40 3.18
968 1204 0.805322 CAGCTCAGCTCTGCTTACGG 60.805 60.000 0.00 0.00 36.40 4.02
969 1205 1.216710 GCTCAGCTCTGCTTACGGT 59.783 57.895 0.00 0.00 36.40 4.83
973 1209 2.187163 GCTCTGCTTACGGTCCCC 59.813 66.667 0.00 0.00 0.00 4.81
1007 1243 3.365265 CCAGCGCCAGGGACAAAC 61.365 66.667 2.29 0.00 0.00 2.93
1015 1251 3.647771 AGGGACAAACCGGGCCTC 61.648 66.667 6.32 0.00 40.11 4.70
1016 1252 3.647771 GGGACAAACCGGGCCTCT 61.648 66.667 6.32 0.00 40.11 3.69
1018 1254 2.593956 GGACAAACCGGGCCTCTCT 61.594 63.158 6.32 0.00 0.00 3.10
1019 1255 1.079057 GACAAACCGGGCCTCTCTC 60.079 63.158 6.32 0.00 0.00 3.20
1021 1257 1.374947 CAAACCGGGCCTCTCTCAA 59.625 57.895 6.32 0.00 0.00 3.02
1022 1258 0.955919 CAAACCGGGCCTCTCTCAAC 60.956 60.000 6.32 0.00 0.00 3.18
1023 1259 2.450479 AAACCGGGCCTCTCTCAACG 62.450 60.000 6.32 0.00 0.00 4.10
1024 1260 4.821589 CCGGGCCTCTCTCAACGC 62.822 72.222 0.84 0.00 0.00 4.84
1026 1262 3.760035 GGGCCTCTCTCAACGCGA 61.760 66.667 15.93 0.00 0.00 5.87
1027 1263 2.507324 GGCCTCTCTCAACGCGAC 60.507 66.667 15.93 0.00 0.00 5.19
1028 1264 2.507324 GCCTCTCTCAACGCGACC 60.507 66.667 15.93 0.00 0.00 4.79
1081 3020 3.749064 GAGTCGCTGGCACGGAGA 61.749 66.667 9.05 0.00 42.33 3.71
1114 3053 2.436646 CCAAGCCCACCACGCTAG 60.437 66.667 0.00 0.00 34.84 3.42
1127 3066 2.351244 CGCTAGTCCCACTCCAGCA 61.351 63.158 0.00 0.00 31.06 4.41
1139 3078 2.249413 CTCCAGCATCTTCCCACGCT 62.249 60.000 0.00 0.00 34.29 5.07
1424 3364 3.188667 GCCGGTAAAAAGAAAGACTCCAG 59.811 47.826 1.90 0.00 0.00 3.86
1451 3393 4.191544 GCTGCTCCTGTAAATGATGTACA 58.808 43.478 0.00 0.00 0.00 2.90
1461 3403 8.562892 CCTGTAAATGATGTACATGGAAGATTC 58.437 37.037 14.43 0.00 39.39 2.52
1487 3461 3.807071 GCTTAGAGCTCTGTTCTATTGGC 59.193 47.826 26.78 11.90 38.45 4.52
1762 3785 8.842280 AGAAAATTGGAACGTATTTTGTGTCTA 58.158 29.630 10.63 0.00 36.05 2.59
2053 4122 5.261216 ACAATAAATGGTCTTCCGGTGAAT 58.739 37.500 0.00 0.00 36.30 2.57
2102 4171 2.945668 GCTGGGTTATTTCTAGGCAGTG 59.054 50.000 0.00 0.00 0.00 3.66
2130 4199 4.430137 AAGTTGCTCAATGTATGCACAG 57.570 40.909 0.00 0.00 38.30 3.66
2159 4228 6.690194 ATCAATGTAGTGATCTTTGCCTTC 57.310 37.500 0.00 0.00 32.65 3.46
2170 4239 1.298157 TTTGCCTTCGGACAGATGCG 61.298 55.000 0.00 0.00 41.78 4.73
2195 4264 9.109533 CGTTGTTTAATGTCGCTTACTTATTTT 57.890 29.630 0.00 0.00 0.00 1.82
2226 4295 4.041740 TCTAGTCGACACATGCCAATAC 57.958 45.455 19.50 0.00 0.00 1.89
2455 4528 5.432885 AAAGGGTAATTTGAGTTGACGTG 57.567 39.130 0.00 0.00 0.00 4.49
2598 4671 1.218316 GTGAGGTTGGTCCGCTAGG 59.782 63.158 0.00 0.00 41.99 3.02
2633 4706 5.984233 TTATGCCTGACGTCATTGTATTC 57.016 39.130 20.40 4.06 0.00 1.75
2666 4739 3.810941 GTGTTGTCTACGTCCAATTTCCA 59.189 43.478 0.00 0.00 0.00 3.53
2942 5174 3.062639 GCCTTTATGATCCATGCGTATCG 59.937 47.826 0.00 0.00 0.00 2.92
2966 5198 8.770828 TCGGAGAGATGTTTAAGTTAGTTTTTG 58.229 33.333 0.00 0.00 0.00 2.44
2983 5215 9.615295 TTAGTTTTTGTTTGTAAACTCACTGTC 57.385 29.630 8.74 0.00 42.06 3.51
3009 5241 4.080807 TGTTGTTCCCAAGTGAGTACTGAA 60.081 41.667 0.00 0.00 37.19 3.02
3035 5267 1.197721 CCGAAACATGAGTGCAACCTC 59.802 52.381 0.00 0.00 37.80 3.85
3121 5356 7.695480 TGGATAAGCTTGCACTTTTGTAATA 57.305 32.000 9.86 0.00 0.00 0.98
3174 5413 2.622942 TCATGTTTTGTCCAGAAGTGCC 59.377 45.455 0.00 0.00 0.00 5.01
3178 5417 2.887152 GTTTTGTCCAGAAGTGCCTGAT 59.113 45.455 0.00 0.00 36.29 2.90
3201 5440 1.131638 ACCTTGCCTGTGAAGAGACA 58.868 50.000 0.00 0.00 0.00 3.41
3202 5441 1.490490 ACCTTGCCTGTGAAGAGACAA 59.510 47.619 0.00 0.00 0.00 3.18
3203 5442 2.149578 CCTTGCCTGTGAAGAGACAAG 58.850 52.381 0.00 0.00 35.43 3.16
3204 5443 2.224378 CCTTGCCTGTGAAGAGACAAGA 60.224 50.000 5.29 0.00 37.32 3.02
3205 5444 2.827800 TGCCTGTGAAGAGACAAGAG 57.172 50.000 0.00 0.00 0.00 2.85
3206 5445 2.319844 TGCCTGTGAAGAGACAAGAGA 58.680 47.619 0.00 0.00 0.00 3.10
3207 5446 2.298446 TGCCTGTGAAGAGACAAGAGAG 59.702 50.000 0.00 0.00 0.00 3.20
3208 5447 2.298729 GCCTGTGAAGAGACAAGAGAGT 59.701 50.000 0.00 0.00 0.00 3.24
3209 5448 3.613910 GCCTGTGAAGAGACAAGAGAGTC 60.614 52.174 0.00 0.00 38.81 3.36
3257 5538 5.354767 TGTGCACATTTGTTTGCTTGAATA 58.645 33.333 17.42 0.00 39.62 1.75
3307 5588 2.488153 AGAACGTAAGATGCAAAAGGCC 59.512 45.455 0.00 0.00 41.61 5.19
3316 5597 0.328258 TGCAAAAGGCCTACTCTCCC 59.672 55.000 5.16 0.00 43.89 4.30
3317 5598 0.744771 GCAAAAGGCCTACTCTCCCG 60.745 60.000 5.16 0.00 36.11 5.14
3346 5627 1.047801 AACCCAAATGCTTCACCCAC 58.952 50.000 0.00 0.00 0.00 4.61
3347 5628 0.831711 ACCCAAATGCTTCACCCACC 60.832 55.000 0.00 0.00 0.00 4.61
3352 5633 1.560505 AATGCTTCACCCACCCAATC 58.439 50.000 0.00 0.00 0.00 2.67
3357 5638 0.774096 TTCACCCACCCAATCCCTCA 60.774 55.000 0.00 0.00 0.00 3.86
3363 5644 2.501316 CCCACCCAATCCCTCAAATTTC 59.499 50.000 0.00 0.00 0.00 2.17
3365 5646 3.172339 CACCCAATCCCTCAAATTTCCA 58.828 45.455 0.00 0.00 0.00 3.53
3367 5648 3.181407 ACCCAATCCCTCAAATTTCCACT 60.181 43.478 0.00 0.00 0.00 4.00
3368 5649 3.448660 CCCAATCCCTCAAATTTCCACTC 59.551 47.826 0.00 0.00 0.00 3.51
3369 5650 3.448660 CCAATCCCTCAAATTTCCACTCC 59.551 47.826 0.00 0.00 0.00 3.85
3370 5651 4.347607 CAATCCCTCAAATTTCCACTCCT 58.652 43.478 0.00 0.00 0.00 3.69
3388 5669 1.270305 CCTTCCTTGACTTCTGCGACA 60.270 52.381 0.00 0.00 0.00 4.35
3391 5672 2.688507 TCCTTGACTTCTGCGACAATC 58.311 47.619 0.00 0.00 0.00 2.67
3392 5673 1.391485 CCTTGACTTCTGCGACAATCG 59.609 52.381 0.00 0.00 43.89 3.34
3409 5690 5.984725 ACAATCGTTACCATATTCTGACCA 58.015 37.500 0.00 0.00 0.00 4.02
3413 5694 6.140303 TCGTTACCATATTCTGACCAGTAC 57.860 41.667 0.00 0.00 0.00 2.73
3497 5778 0.873054 CAGCTGACTGGCTCAAAGTG 59.127 55.000 8.42 0.00 41.00 3.16
3524 5805 8.744568 AGGATAAATTTCTTAGCTTTGAGGAG 57.255 34.615 0.00 0.00 0.00 3.69
3576 5857 7.231467 ACACCAAAAGGTAGTCAGTGATAATT 58.769 34.615 0.00 0.00 0.00 1.40
3632 5913 1.662446 GACGAGCGTGTTTCCGGAA 60.662 57.895 14.35 14.35 0.00 4.30
3638 5919 1.535462 AGCGTGTTTCCGGAATTTGAG 59.465 47.619 19.62 10.00 0.00 3.02
3682 5963 7.887996 TTCATTGAAATGCTCATAACAAACC 57.112 32.000 0.00 0.00 36.36 3.27
3685 5966 7.395772 TCATTGAAATGCTCATAACAAACCCTA 59.604 33.333 0.00 0.00 36.36 3.53
3693 5974 7.601856 TGCTCATAACAAACCCTATTTTCTTG 58.398 34.615 0.00 0.00 0.00 3.02
3731 6014 1.593793 CGTGCATGCACATCTGATTCG 60.594 52.381 40.95 24.98 46.47 3.34
3778 6063 3.130869 TCATGCTGGCCAATTGTGTATTC 59.869 43.478 7.01 0.00 0.00 1.75
3781 6066 3.130869 TGCTGGCCAATTGTGTATTCATC 59.869 43.478 7.01 0.00 0.00 2.92
3782 6067 3.793129 GCTGGCCAATTGTGTATTCATCG 60.793 47.826 7.01 0.00 0.00 3.84
3830 6125 2.512515 GGCCTGATCCTCGCACAC 60.513 66.667 0.00 0.00 0.00 3.82
3831 6126 2.265739 GCCTGATCCTCGCACACA 59.734 61.111 0.00 0.00 0.00 3.72
3841 6136 0.376152 CTCGCACACAGATGCCATTC 59.624 55.000 0.00 0.00 42.99 2.67
3868 6166 1.299773 GAATCGGAGAGCCAGCTCG 60.300 63.158 13.70 3.57 46.90 5.03
3888 6186 5.592054 CTCGAGATAACTGCATCTTTACCA 58.408 41.667 6.58 0.00 35.37 3.25
3904 6202 6.359804 TCTTTACCAGCATGATATTGAAGCT 58.640 36.000 0.00 0.00 39.69 3.74
3934 6255 6.272318 TGTTGGCTTTTCTGACAATTTAGTG 58.728 36.000 0.00 0.00 37.29 2.74
3937 6258 5.009610 TGGCTTTTCTGACAATTTAGTGGAC 59.990 40.000 0.00 0.00 0.00 4.02
3952 6273 7.946655 TTTAGTGGACGCATTATTCTGATAG 57.053 36.000 0.00 0.00 0.00 2.08
3984 6305 6.152323 ACTTAATAGTCTACCGAACTGCAGAA 59.848 38.462 23.35 0.00 0.00 3.02
3998 6319 3.385755 ACTGCAGAACAAGCTTTGGAATT 59.614 39.130 23.35 0.00 34.12 2.17
4035 6356 6.047870 AGTTCATAGAGAGCTTATGTGCTTG 58.952 40.000 4.27 0.00 44.17 4.01
4041 6363 1.929836 GAGCTTATGTGCTTGACTCCG 59.070 52.381 0.00 0.00 44.17 4.63
4043 6365 1.394917 GCTTATGTGCTTGACTCCGTG 59.605 52.381 0.00 0.00 0.00 4.94
4052 6374 3.128764 TGCTTGACTCCGTGACTGTATAG 59.871 47.826 0.00 0.00 0.00 1.31
4059 6381 4.202060 ACTCCGTGACTGTATAGCTTGATG 60.202 45.833 0.00 0.00 0.00 3.07
4082 6407 1.005867 CCCCACACACAATGCTTGC 60.006 57.895 0.00 0.00 0.00 4.01
4089 6414 1.125384 CACACAATGCTTGCGAAATGC 59.875 47.619 0.00 0.00 46.70 3.56
4110 6435 8.519492 AATGCATGTGTTAGTTTGATACAAAC 57.481 30.769 16.36 16.36 0.00 2.93
4112 6437 7.656412 TGCATGTGTTAGTTTGATACAAACAT 58.344 30.769 22.99 13.64 32.81 2.71
4146 6473 3.307242 CGCTTAATTTCTTCTGTCGGGAG 59.693 47.826 0.00 0.00 0.00 4.30
4149 6476 5.163844 GCTTAATTTCTTCTGTCGGGAGTTC 60.164 44.000 0.00 0.00 0.00 3.01
4156 6483 3.379445 GTCGGGAGTTCGGAGGCA 61.379 66.667 0.00 0.00 0.00 4.75
4171 6498 3.350833 GGAGGCAGAACAGTTCATTCAT 58.649 45.455 15.85 1.57 0.00 2.57
4174 6535 5.130292 AGGCAGAACAGTTCATTCATTTG 57.870 39.130 15.85 4.29 0.00 2.32
4192 6553 7.696992 TCATTTGTAATTCTACCTGGTTTCC 57.303 36.000 3.84 0.00 0.00 3.13
4213 6576 2.093921 CGACTTCCTTTCTTCTCCCCTC 60.094 54.545 0.00 0.00 0.00 4.30
4214 6577 2.237643 GACTTCCTTTCTTCTCCCCTCC 59.762 54.545 0.00 0.00 0.00 4.30
4216 6579 1.958288 TCCTTTCTTCTCCCCTCCTG 58.042 55.000 0.00 0.00 0.00 3.86
4220 6583 0.415429 TTCTTCTCCCCTCCTGCTCT 59.585 55.000 0.00 0.00 0.00 4.09
4221 6584 0.032615 TCTTCTCCCCTCCTGCTCTC 60.033 60.000 0.00 0.00 0.00 3.20
4222 6585 1.002274 TTCTCCCCTCCTGCTCTCC 59.998 63.158 0.00 0.00 0.00 3.71
4223 6586 1.522917 TTCTCCCCTCCTGCTCTCCT 61.523 60.000 0.00 0.00 0.00 3.69
4233 6596 4.397417 CCTCCTGCTCTCCTTAATTGTTTG 59.603 45.833 0.00 0.00 0.00 2.93
4241 6604 7.665559 TGCTCTCCTTAATTGTTTGTTCTACAT 59.334 33.333 0.00 0.00 0.00 2.29
4271 6635 9.775854 CTATGAAATCACAATACTTCCAGAGAT 57.224 33.333 0.00 0.00 0.00 2.75
4280 6644 8.258007 CACAATACTTCCAGAGATAACTACCAA 58.742 37.037 0.00 0.00 0.00 3.67
4300 6664 9.314321 CTACCAACACATTTTCTATCGTCTATT 57.686 33.333 0.00 0.00 0.00 1.73
4333 6697 4.754114 GCTCCTCCAGATTTAAGCATACAG 59.246 45.833 0.00 0.00 0.00 2.74
4375 6739 6.698380 TGTACTATTCAAGAGGAACAACTCC 58.302 40.000 0.00 0.00 45.81 3.85
4448 6816 5.068329 TCAACCAATGAATGTACAAGCAACA 59.932 36.000 0.00 0.00 34.30 3.33
4454 6822 5.512753 TGAATGTACAAGCAACACACATT 57.487 34.783 0.00 0.00 41.28 2.71
4474 6850 7.104043 ACATTTGTGATTATGATCAGTTGGG 57.896 36.000 0.09 0.00 42.73 4.12
4481 6857 4.422073 TTATGATCAGTTGGGCCTACAG 57.578 45.455 20.07 12.34 0.00 2.74
4617 7015 5.258841 TGTGGATGATTTCATGAGCTTCTT 58.741 37.500 0.00 0.00 36.57 2.52
4640 7038 8.251026 TCTTGAGTTACCTAATGTACAGTCATG 58.749 37.037 0.00 0.00 0.00 3.07
4651 7049 1.888215 ACAGTCATGTGCAGTGAAGG 58.112 50.000 3.45 2.48 38.57 3.46
4660 7058 0.685785 TGCAGTGAAGGCCCAAACAA 60.686 50.000 0.00 0.00 0.00 2.83
4661 7059 0.249447 GCAGTGAAGGCCCAAACAAC 60.249 55.000 0.00 0.00 0.00 3.32
4668 7066 1.302431 GGCCCAAACAACCCATTGC 60.302 57.895 0.00 0.00 39.66 3.56
4671 7069 0.035176 CCCAAACAACCCATTGCCAG 59.965 55.000 0.00 0.00 39.66 4.85
4680 7078 0.542702 CCCATTGCCAGGTCCTTGTT 60.543 55.000 0.00 0.00 0.00 2.83
4682 7080 1.331214 CATTGCCAGGTCCTTGTTGT 58.669 50.000 0.00 0.00 0.00 3.32
4686 7084 0.668535 GCCAGGTCCTTGTTGTTGTC 59.331 55.000 0.00 0.00 0.00 3.18
4687 7085 1.750682 GCCAGGTCCTTGTTGTTGTCT 60.751 52.381 0.00 0.00 0.00 3.41
4688 7086 1.949525 CCAGGTCCTTGTTGTTGTCTG 59.050 52.381 0.00 0.00 0.00 3.51
4689 7087 2.643551 CAGGTCCTTGTTGTTGTCTGT 58.356 47.619 0.00 0.00 0.00 3.41
4690 7088 2.355756 CAGGTCCTTGTTGTTGTCTGTG 59.644 50.000 0.00 0.00 0.00 3.66
4691 7089 1.065551 GGTCCTTGTTGTTGTCTGTGC 59.934 52.381 0.00 0.00 0.00 4.57
4692 7090 2.017049 GTCCTTGTTGTTGTCTGTGCT 58.983 47.619 0.00 0.00 0.00 4.40
4693 7091 2.016318 TCCTTGTTGTTGTCTGTGCTG 58.984 47.619 0.00 0.00 0.00 4.41
4694 7092 1.745087 CCTTGTTGTTGTCTGTGCTGT 59.255 47.619 0.00 0.00 0.00 4.40
4695 7093 2.223340 CCTTGTTGTTGTCTGTGCTGTC 60.223 50.000 0.00 0.00 0.00 3.51
4696 7094 2.106477 TGTTGTTGTCTGTGCTGTCA 57.894 45.000 0.00 0.00 0.00 3.58
4697 7095 2.642427 TGTTGTTGTCTGTGCTGTCAT 58.358 42.857 0.00 0.00 0.00 3.06
4698 7096 3.802866 TGTTGTTGTCTGTGCTGTCATA 58.197 40.909 0.00 0.00 0.00 2.15
4699 7097 4.195416 TGTTGTTGTCTGTGCTGTCATAA 58.805 39.130 0.00 0.00 0.00 1.90
4700 7098 4.637977 TGTTGTTGTCTGTGCTGTCATAAA 59.362 37.500 0.00 0.00 0.00 1.40
4701 7099 5.124617 TGTTGTTGTCTGTGCTGTCATAAAA 59.875 36.000 0.00 0.00 0.00 1.52
4702 7100 5.168526 TGTTGTCTGTGCTGTCATAAAAC 57.831 39.130 0.00 0.00 0.00 2.43
4703 7101 4.881273 TGTTGTCTGTGCTGTCATAAAACT 59.119 37.500 0.00 0.00 0.00 2.66
4704 7102 5.007626 TGTTGTCTGTGCTGTCATAAAACTC 59.992 40.000 0.00 0.00 0.00 3.01
4705 7103 4.065088 TGTCTGTGCTGTCATAAAACTCC 58.935 43.478 0.00 0.00 0.00 3.85
4706 7104 4.202357 TGTCTGTGCTGTCATAAAACTCCT 60.202 41.667 0.00 0.00 0.00 3.69
4707 7105 4.153117 GTCTGTGCTGTCATAAAACTCCTG 59.847 45.833 0.00 0.00 0.00 3.86
4708 7106 4.067896 CTGTGCTGTCATAAAACTCCTGT 58.932 43.478 0.00 0.00 0.00 4.00
4709 7107 5.011635 TCTGTGCTGTCATAAAACTCCTGTA 59.988 40.000 0.00 0.00 0.00 2.74
4710 7108 5.616270 TGTGCTGTCATAAAACTCCTGTAA 58.384 37.500 0.00 0.00 0.00 2.41
4711 7109 5.700832 TGTGCTGTCATAAAACTCCTGTAAG 59.299 40.000 0.00 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.158394 AGCAAGACTGTTCAAGCAAGAAAA 59.842 37.500 0.00 0.00 0.00 2.29
7 8 3.696051 AGCAAGACTGTTCAAGCAAGAAA 59.304 39.130 0.00 0.00 0.00 2.52
8 9 3.065786 CAGCAAGACTGTTCAAGCAAGAA 59.934 43.478 0.00 0.00 41.86 2.52
9 10 2.615447 CAGCAAGACTGTTCAAGCAAGA 59.385 45.455 0.00 0.00 41.86 3.02
10 11 2.996155 CAGCAAGACTGTTCAAGCAAG 58.004 47.619 0.00 0.00 41.86 4.01
22 23 4.801891 TCAAATGCAGAAATCAGCAAGAC 58.198 39.130 4.56 0.00 41.62 3.01
27 28 4.184079 AGGTTCAAATGCAGAAATCAGC 57.816 40.909 0.00 0.00 0.00 4.26
33 34 4.036734 GTCAGACAAGGTTCAAATGCAGAA 59.963 41.667 0.00 0.00 0.00 3.02
36 37 3.316029 CAGTCAGACAAGGTTCAAATGCA 59.684 43.478 2.66 0.00 0.00 3.96
37 38 3.565482 TCAGTCAGACAAGGTTCAAATGC 59.435 43.478 2.66 0.00 0.00 3.56
54 55 2.898705 CTGCTGTGGACCTAATCAGTC 58.101 52.381 0.00 0.00 0.00 3.51
99 100 8.252997 TTCATGGATGATATTACGAACTCGTCG 61.253 40.741 8.24 0.00 45.25 5.12
109 110 7.513968 GCGACTTCTTTCATGGATGATATTAC 58.486 38.462 0.00 0.00 36.56 1.89
138 139 1.067416 GTGGCCATCATACGCGAGA 59.933 57.895 15.93 8.27 0.00 4.04
183 184 2.013483 CATAAGCCTCGCGAGCTCG 61.013 63.158 31.37 31.37 40.49 5.03
249 250 3.056749 ACGTCGGCTAAATTCTGTTCTCT 60.057 43.478 0.00 0.00 0.00 3.10
252 253 2.735134 ACACGTCGGCTAAATTCTGTTC 59.265 45.455 0.00 0.00 0.00 3.18
258 259 3.852286 TCATACACACGTCGGCTAAATT 58.148 40.909 0.00 0.00 0.00 1.82
259 260 3.513680 TCATACACACGTCGGCTAAAT 57.486 42.857 0.00 0.00 0.00 1.40
263 264 2.380084 ATTTCATACACACGTCGGCT 57.620 45.000 0.00 0.00 0.00 5.52
264 265 3.465122 AAATTTCATACACACGTCGGC 57.535 42.857 0.00 0.00 0.00 5.54
265 266 6.035650 ACAGATAAATTTCATACACACGTCGG 59.964 38.462 0.00 0.00 0.00 4.79
266 267 6.894517 CACAGATAAATTTCATACACACGTCG 59.105 38.462 0.00 0.00 0.00 5.12
267 268 6.682863 GCACAGATAAATTTCATACACACGTC 59.317 38.462 0.00 0.00 0.00 4.34
268 269 6.148645 TGCACAGATAAATTTCATACACACGT 59.851 34.615 0.00 0.00 0.00 4.49
270 271 6.470235 GCTGCACAGATAAATTTCATACACAC 59.530 38.462 0.81 0.00 0.00 3.82
289 303 2.869192 GGAATAGCTTCTACTGCTGCAC 59.131 50.000 0.00 0.00 41.32 4.57
300 314 6.472808 CACGACTAGTTAACTGGAATAGCTTC 59.527 42.308 24.08 9.21 0.00 3.86
307 321 3.068448 TGTGCACGACTAGTTAACTGGAA 59.932 43.478 24.08 1.12 0.00 3.53
308 322 2.624364 TGTGCACGACTAGTTAACTGGA 59.376 45.455 24.08 3.28 0.00 3.86
309 323 3.021269 TGTGCACGACTAGTTAACTGG 57.979 47.619 18.56 17.57 0.00 4.00
310 324 5.374080 CAATTGTGCACGACTAGTTAACTG 58.626 41.667 18.56 10.41 0.00 3.16
311 325 4.451096 CCAATTGTGCACGACTAGTTAACT 59.549 41.667 9.51 13.68 0.00 2.24
329 343 4.057432 CAAACATTTTCCTGCGACCAATT 58.943 39.130 0.00 0.00 0.00 2.32
368 382 6.430925 CCTCAACCATCTTTATGTTCAACTCA 59.569 38.462 0.00 0.00 0.00 3.41
452 466 2.362369 ATCACCGTCTGGGCAGAGG 61.362 63.158 0.00 0.00 41.55 3.69
455 469 2.821366 GCATCACCGTCTGGGCAG 60.821 66.667 0.00 0.00 40.62 4.85
478 492 2.650116 GCCGTCTTCAGGAGCTCCA 61.650 63.158 33.90 12.52 38.89 3.86
479 493 2.185608 GCCGTCTTCAGGAGCTCC 59.814 66.667 26.22 26.22 0.00 4.70
509 523 1.227823 CTGCTCCACCACGAAACCA 60.228 57.895 0.00 0.00 0.00 3.67
548 562 0.689623 CCAGCTCCTCCTTTGTCAGT 59.310 55.000 0.00 0.00 0.00 3.41
571 585 5.939764 TGGCTACTGATGACTTGATAAGT 57.060 39.130 0.00 0.00 46.38 2.24
584 598 6.753913 ATATGAGATCCTTTTGGCTACTGA 57.246 37.500 0.00 0.00 40.12 3.41
627 641 7.961283 GTCAATTTAAGACAACTAATTCGGGAC 59.039 37.037 0.00 0.00 36.06 4.46
640 654 9.743057 CCAAATTAGTTGTGTCAATTTAAGACA 57.257 29.630 0.00 0.00 37.74 3.41
647 661 5.278758 CCGTCCCAAATTAGTTGTGTCAATT 60.279 40.000 0.00 0.00 35.23 2.32
651 665 2.486592 CCCGTCCCAAATTAGTTGTGTC 59.513 50.000 0.00 0.00 35.23 3.67
652 666 2.510613 CCCGTCCCAAATTAGTTGTGT 58.489 47.619 0.00 0.00 35.23 3.72
653 667 1.816224 CCCCGTCCCAAATTAGTTGTG 59.184 52.381 0.00 0.00 35.23 3.33
659 736 4.720773 TGTCTATTACCCCGTCCCAAATTA 59.279 41.667 0.00 0.00 0.00 1.40
660 737 3.524380 TGTCTATTACCCCGTCCCAAATT 59.476 43.478 0.00 0.00 0.00 1.82
678 756 2.775911 TGCTTGCTATGCTCTTGTCT 57.224 45.000 0.00 0.00 0.00 3.41
681 759 2.121116 GCATGCTTGCTATGCTCTTG 57.879 50.000 16.80 1.56 45.64 3.02
732 810 5.869344 CCTGTGATGACTCGAACAAATAAGA 59.131 40.000 0.00 0.00 0.00 2.10
739 817 2.825532 TGATCCTGTGATGACTCGAACA 59.174 45.455 0.00 0.00 0.00 3.18
763 841 9.462174 GTATGATGAAACAACATGAAAAACTCA 57.538 29.630 0.00 0.00 38.81 3.41
785 863 4.630894 ACACCACACACACAAAAGTATG 57.369 40.909 0.00 0.00 0.00 2.39
786 864 5.883673 ACTTACACCACACACACAAAAGTAT 59.116 36.000 0.00 0.00 0.00 2.12
788 866 4.076394 ACTTACACCACACACACAAAAGT 58.924 39.130 0.00 0.00 0.00 2.66
792 1024 2.027100 TCCACTTACACCACACACACAA 60.027 45.455 0.00 0.00 0.00 3.33
812 1044 5.756833 TCAGCATGATGATACATCAGTGTTC 59.243 40.000 10.16 6.86 42.56 3.18
857 1089 6.037610 ACAATGAGATCATCGGTAAGAAAAGC 59.962 38.462 0.00 0.00 35.10 3.51
889 1121 5.474876 AGGAACAAGATTGATTGGTTCTGAC 59.525 40.000 0.00 0.00 34.28 3.51
955 1191 2.359967 GGGGACCGTAAGCAGAGCT 61.360 63.158 0.00 0.00 40.86 4.09
1000 1236 2.046217 GAGAGGCCCGGTTTGTCC 60.046 66.667 0.00 0.00 0.00 4.02
1002 1238 1.415672 TTGAGAGAGGCCCGGTTTGT 61.416 55.000 0.00 0.00 0.00 2.83
1006 1242 3.382832 CGTTGAGAGAGGCCCGGT 61.383 66.667 0.00 0.00 0.00 5.28
1007 1243 4.821589 GCGTTGAGAGAGGCCCGG 62.822 72.222 0.00 0.00 0.00 5.73
1010 1246 2.507324 GTCGCGTTGAGAGAGGCC 60.507 66.667 5.77 0.00 0.00 5.19
1012 1248 1.878656 AAGGGTCGCGTTGAGAGAGG 61.879 60.000 5.77 0.00 0.00 3.69
1015 1251 1.289066 TCAAGGGTCGCGTTGAGAG 59.711 57.895 5.77 0.00 0.00 3.20
1016 1252 3.450507 TCAAGGGTCGCGTTGAGA 58.549 55.556 5.77 0.00 0.00 3.27
1018 1254 2.342279 CCTCAAGGGTCGCGTTGA 59.658 61.111 5.77 7.91 0.00 3.18
1019 1255 3.423154 GCCTCAAGGGTCGCGTTG 61.423 66.667 5.77 2.99 37.43 4.10
1072 3011 4.410400 CTTGGGGGTCTCCGTGCC 62.410 72.222 0.00 0.00 36.01 5.01
1078 3017 1.179174 GGTTTGTGCTTGGGGGTCTC 61.179 60.000 0.00 0.00 0.00 3.36
1080 3019 2.207229 GGGTTTGTGCTTGGGGGTC 61.207 63.158 0.00 0.00 0.00 4.46
1081 3020 2.123033 GGGTTTGTGCTTGGGGGT 60.123 61.111 0.00 0.00 0.00 4.95
1085 3024 1.069596 GGCTTGGGTTTGTGCTTGG 59.930 57.895 0.00 0.00 0.00 3.61
1086 3025 1.069596 GGGCTTGGGTTTGTGCTTG 59.930 57.895 0.00 0.00 0.00 4.01
1087 3026 1.382420 TGGGCTTGGGTTTGTGCTT 60.382 52.632 0.00 0.00 0.00 3.91
1088 3027 2.133641 GTGGGCTTGGGTTTGTGCT 61.134 57.895 0.00 0.00 0.00 4.40
1114 3053 0.107459 GGAAGATGCTGGAGTGGGAC 60.107 60.000 0.00 0.00 0.00 4.46
1127 3066 2.125512 GTGCGAGCGTGGGAAGAT 60.126 61.111 0.00 0.00 0.00 2.40
1226 3166 1.852157 TTCTCCCGCCATCCAAGCTT 61.852 55.000 0.00 0.00 0.00 3.74
1227 3167 2.262774 CTTCTCCCGCCATCCAAGCT 62.263 60.000 0.00 0.00 0.00 3.74
1231 3171 2.721167 CGTCTTCTCCCGCCATCCA 61.721 63.158 0.00 0.00 0.00 3.41
1424 3364 2.489329 TCATTTACAGGAGCAGCAAAGC 59.511 45.455 0.00 0.00 0.00 3.51
1434 3374 7.194112 TCTTCCATGTACATCATTTACAGGA 57.806 36.000 5.07 4.29 33.95 3.86
1438 3378 9.330063 TCAGAATCTTCCATGTACATCATTTAC 57.670 33.333 5.07 0.00 34.09 2.01
1451 3393 4.959723 GCTCTAAGCTCAGAATCTTCCAT 58.040 43.478 0.00 0.00 38.45 3.41
1487 3461 2.095567 CCACTCCAGAAATCAAACGCTG 60.096 50.000 0.00 0.00 0.00 5.18
1679 3679 4.453480 TCAGGTGGGGATGGATAAATTC 57.547 45.455 0.00 0.00 0.00 2.17
1685 3685 3.501019 GCATTATTCAGGTGGGGATGGAT 60.501 47.826 0.00 0.00 0.00 3.41
1743 3766 5.992829 ACACATAGACACAAAATACGTTCCA 59.007 36.000 0.00 0.00 0.00 3.53
1799 3822 5.879777 AGGCCATTGCAATAATTTGTTAACC 59.120 36.000 12.53 2.06 40.13 2.85
2110 4179 3.678289 TCTGTGCATACATTGAGCAACT 58.322 40.909 0.00 0.00 40.35 3.16
2159 4228 3.120338 ACATTAAACAACGCATCTGTCCG 60.120 43.478 0.00 0.00 0.00 4.79
2195 4264 5.128992 TGTGTCGACTAGAGTTGCATTAA 57.871 39.130 17.92 0.00 0.00 1.40
2236 4305 2.419673 CCAATGTCATGTCGCTAAGCAA 59.580 45.455 0.00 0.00 0.00 3.91
2248 4317 5.715439 TCCTTCCTAATCACCAATGTCAT 57.285 39.130 0.00 0.00 0.00 3.06
2365 4435 7.912250 CCAACATTGAAGTCAATAGCAGTTATC 59.088 37.037 6.22 0.00 44.10 1.75
2374 4444 6.303054 TGTCTTCCCAACATTGAAGTCAATA 58.697 36.000 6.22 0.00 44.10 1.90
2598 4671 3.561310 TCAGGCATAATCAATTGCGAGAC 59.439 43.478 0.00 0.00 39.78 3.36
2657 4730 2.491693 ACGCAACACCTATGGAAATTGG 59.508 45.455 0.00 0.00 0.00 3.16
2666 4739 1.821216 CCCTTTCACGCAACACCTAT 58.179 50.000 0.00 0.00 0.00 2.57
3035 5267 6.697455 TGAAATTCGACAAGATATTCCTCTCG 59.303 38.462 0.00 0.00 0.00 4.04
3174 5413 2.507484 TCACAGGCAAGGTTTCATCAG 58.493 47.619 0.00 0.00 0.00 2.90
3178 5417 2.172505 TCTCTTCACAGGCAAGGTTTCA 59.827 45.455 0.00 0.00 0.00 2.69
3201 5440 5.296151 TGTTTGAATCCACAGACTCTCTT 57.704 39.130 0.00 0.00 0.00 2.85
3202 5441 4.963318 TGTTTGAATCCACAGACTCTCT 57.037 40.909 0.00 0.00 0.00 3.10
3203 5442 4.816385 TGTTGTTTGAATCCACAGACTCTC 59.184 41.667 0.00 0.00 0.00 3.20
3204 5443 4.780815 TGTTGTTTGAATCCACAGACTCT 58.219 39.130 0.00 0.00 0.00 3.24
3205 5444 5.695851 ATGTTGTTTGAATCCACAGACTC 57.304 39.130 0.00 0.00 0.00 3.36
3206 5445 6.469782 AAATGTTGTTTGAATCCACAGACT 57.530 33.333 0.00 0.00 0.00 3.24
3207 5446 6.756074 TCAAAATGTTGTTTGAATCCACAGAC 59.244 34.615 0.00 0.00 42.94 3.51
3208 5447 6.871844 TCAAAATGTTGTTTGAATCCACAGA 58.128 32.000 0.00 0.00 42.94 3.41
3307 5588 4.511826 GGTTAAATCATTGCGGGAGAGTAG 59.488 45.833 0.00 0.00 0.00 2.57
3316 5597 4.183101 AGCATTTGGGTTAAATCATTGCG 58.817 39.130 0.00 0.00 36.87 4.85
3317 5598 5.642919 TGAAGCATTTGGGTTAAATCATTGC 59.357 36.000 0.00 0.00 36.87 3.56
3346 5627 3.444029 AGTGGAAATTTGAGGGATTGGG 58.556 45.455 0.00 0.00 0.00 4.12
3347 5628 3.448660 GGAGTGGAAATTTGAGGGATTGG 59.551 47.826 0.00 0.00 0.00 3.16
3352 5633 3.092301 GGAAGGAGTGGAAATTTGAGGG 58.908 50.000 0.00 0.00 0.00 4.30
3357 5638 5.066913 AGTCAAGGAAGGAGTGGAAATTT 57.933 39.130 0.00 0.00 0.00 1.82
3363 5644 2.873649 GCAGAAGTCAAGGAAGGAGTGG 60.874 54.545 0.00 0.00 0.00 4.00
3365 5646 1.001406 CGCAGAAGTCAAGGAAGGAGT 59.999 52.381 0.00 0.00 0.00 3.85
3367 5648 1.000955 GTCGCAGAAGTCAAGGAAGGA 59.999 52.381 0.00 0.00 39.69 3.36
3368 5649 1.270305 TGTCGCAGAAGTCAAGGAAGG 60.270 52.381 0.00 0.00 39.69 3.46
3369 5650 2.154854 TGTCGCAGAAGTCAAGGAAG 57.845 50.000 0.00 0.00 39.69 3.46
3370 5651 2.613026 TTGTCGCAGAAGTCAAGGAA 57.387 45.000 0.00 0.00 39.69 3.36
3388 5669 6.235231 ACTGGTCAGAATATGGTAACGATT 57.765 37.500 4.84 0.00 42.51 3.34
3391 5672 5.898174 TGTACTGGTCAGAATATGGTAACG 58.102 41.667 4.84 0.00 42.51 3.18
3392 5673 6.706270 CCATGTACTGGTCAGAATATGGTAAC 59.294 42.308 4.84 0.00 40.49 2.50
3409 5690 8.264347 ACAAATGAAAAGGAAAAACCATGTACT 58.736 29.630 0.00 0.00 42.04 2.73
3413 5694 7.307930 GCCTACAAATGAAAAGGAAAAACCATG 60.308 37.037 0.00 0.00 42.04 3.66
3497 5778 9.178758 TCCTCAAAGCTAAGAAATTTATCCTTC 57.821 33.333 0.00 0.00 0.00 3.46
3524 5805 5.350091 GCAGATTCCTCTCAAGTTCTTGTAC 59.650 44.000 11.52 0.00 0.00 2.90
3576 5857 4.712337 TCTTGGAAAGCAAAAGGGTGTAAA 59.288 37.500 0.00 0.00 45.70 2.01
3632 5913 6.459670 TGATAAGCATGCATCAACTCAAAT 57.540 33.333 21.98 0.00 0.00 2.32
3638 5919 7.709269 ATGAAATTGATAAGCATGCATCAAC 57.291 32.000 26.72 18.14 42.33 3.18
3713 5996 1.741528 ACGAATCAGATGTGCATGCA 58.258 45.000 18.46 18.46 0.00 3.96
3739 6022 3.884091 GCATGAATTCCTTCTGCAGAGAT 59.116 43.478 17.43 7.27 36.44 2.75
3742 6025 3.014623 CAGCATGAATTCCTTCTGCAGA 58.985 45.455 13.74 13.74 39.69 4.26
3743 6026 2.099263 CCAGCATGAATTCCTTCTGCAG 59.901 50.000 7.63 7.63 39.69 4.41
3745 6028 1.202382 GCCAGCATGAATTCCTTCTGC 60.202 52.381 2.27 7.08 39.69 4.26
3746 6029 1.407979 GGCCAGCATGAATTCCTTCTG 59.592 52.381 0.00 3.24 39.69 3.02
3747 6030 1.006281 TGGCCAGCATGAATTCCTTCT 59.994 47.619 0.00 0.00 39.69 2.85
3749 6032 1.941377 TTGGCCAGCATGAATTCCTT 58.059 45.000 5.11 0.00 39.69 3.36
3778 6063 1.328680 CCGGCTCTGAATTGAACGATG 59.671 52.381 0.00 0.00 0.00 3.84
3781 6066 1.002366 CTCCGGCTCTGAATTGAACG 58.998 55.000 0.00 0.00 0.00 3.95
3782 6067 0.729690 GCTCCGGCTCTGAATTGAAC 59.270 55.000 0.00 0.00 35.22 3.18
3854 6152 0.886938 TATCTCGAGCTGGCTCTCCG 60.887 60.000 18.57 8.16 40.69 4.63
3855 6153 1.000717 GTTATCTCGAGCTGGCTCTCC 60.001 57.143 18.57 0.00 40.69 3.71
3864 6162 4.446051 GGTAAAGATGCAGTTATCTCGAGC 59.554 45.833 7.81 0.00 36.42 5.03
3868 6166 5.118990 TGCTGGTAAAGATGCAGTTATCTC 58.881 41.667 0.00 0.00 36.42 2.75
3888 6186 3.147629 GGCTCAGCTTCAATATCATGCT 58.852 45.455 0.00 0.00 0.00 3.79
3934 6255 6.844696 TGAAACTATCAGAATAATGCGTCC 57.155 37.500 0.00 0.00 33.04 4.79
3952 6273 9.201127 AGTTCGGTAGACTATTAAGTTTGAAAC 57.799 33.333 0.00 0.00 35.56 2.78
3984 6305 7.716123 TCAAATGATTTCAATTCCAAAGCTTGT 59.284 29.630 0.00 0.00 0.00 3.16
3998 6319 8.671921 GCTCTCTATGAACTTCAAATGATTTCA 58.328 33.333 9.25 9.25 33.62 2.69
4035 6356 3.377485 TCAAGCTATACAGTCACGGAGTC 59.623 47.826 0.00 0.00 41.61 3.36
4041 6363 5.269505 AGACCATCAAGCTATACAGTCAC 57.730 43.478 8.33 0.00 0.00 3.67
4043 6365 4.877282 GGAGACCATCAAGCTATACAGTC 58.123 47.826 0.00 0.00 0.00 3.51
4082 6407 7.020602 TGTATCAAACTAACACATGCATTTCG 58.979 34.615 0.00 0.00 0.00 3.46
4110 6435 7.697691 AGAAATTAAGCGAACCTCATACAATG 58.302 34.615 0.00 0.00 0.00 2.82
4112 6437 7.606456 AGAAGAAATTAAGCGAACCTCATACAA 59.394 33.333 0.00 0.00 0.00 2.41
4115 6440 7.103641 ACAGAAGAAATTAAGCGAACCTCATA 58.896 34.615 0.00 0.00 0.00 2.15
4146 6473 1.149148 GAACTGTTCTGCCTCCGAAC 58.851 55.000 13.13 0.00 40.79 3.95
4149 6476 1.734465 GAATGAACTGTTCTGCCTCCG 59.266 52.381 20.18 0.00 0.00 4.63
4171 6498 5.702209 GTCGGAAACCAGGTAGAATTACAAA 59.298 40.000 0.00 0.00 0.00 2.83
4174 6535 5.082251 AGTCGGAAACCAGGTAGAATTAC 57.918 43.478 0.00 0.00 0.00 1.89
4192 6553 1.903183 AGGGGAGAAGAAAGGAAGTCG 59.097 52.381 0.00 0.00 0.00 4.18
4213 6576 5.474876 AGAACAAACAATTAAGGAGAGCAGG 59.525 40.000 0.00 0.00 0.00 4.85
4214 6577 6.566197 AGAACAAACAATTAAGGAGAGCAG 57.434 37.500 0.00 0.00 0.00 4.24
4216 6579 7.435068 TGTAGAACAAACAATTAAGGAGAGC 57.565 36.000 0.00 0.00 0.00 4.09
4220 6583 9.461312 AGCATATGTAGAACAAACAATTAAGGA 57.539 29.630 4.29 0.00 0.00 3.36
4241 6604 9.276590 CTGGAAGTATTGTGATTTCATAGCATA 57.723 33.333 0.00 0.00 0.00 3.14
4271 6635 8.308931 AGACGATAGAAAATGTGTTGGTAGTTA 58.691 33.333 0.00 0.00 41.38 2.24
4280 6644 9.214957 TGTTTCAATAGACGATAGAAAATGTGT 57.785 29.630 0.00 0.00 41.38 3.72
4300 6664 3.576078 TCTGGAGGAGCTTTTGTTTCA 57.424 42.857 0.00 0.00 0.00 2.69
4373 6737 3.573538 CACCTTCATCCATGTGTTTTGGA 59.426 43.478 0.00 0.00 46.86 3.53
4375 6739 3.573538 TCCACCTTCATCCATGTGTTTTG 59.426 43.478 0.00 0.00 0.00 2.44
4376 6741 3.843422 TCCACCTTCATCCATGTGTTTT 58.157 40.909 0.00 0.00 0.00 2.43
4448 6816 7.363181 CCCAACTGATCATAATCACAAATGTGT 60.363 37.037 12.87 0.00 45.76 3.72
4454 6822 3.953612 GGCCCAACTGATCATAATCACAA 59.046 43.478 0.00 0.00 36.98 3.33
4474 6850 5.175673 GCAAAAACACAATCTTTCTGTAGGC 59.824 40.000 0.00 0.00 0.00 3.93
4481 6857 4.332268 TGGCAAGCAAAAACACAATCTTTC 59.668 37.500 0.00 0.00 0.00 2.62
4546 6924 9.685828 TTGTTTATTTTTAGGGAAACATTCTCG 57.314 29.630 0.00 0.00 40.44 4.04
4591 6989 3.952323 AGCTCATGAAATCATCCACAAGG 59.048 43.478 0.00 0.00 33.61 3.61
4617 7015 7.320399 CACATGACTGTACATTAGGTAACTCA 58.680 38.462 0.00 0.00 40.58 3.41
4640 7038 1.363807 GTTTGGGCCTTCACTGCAC 59.636 57.895 4.53 0.00 0.00 4.57
4651 7049 1.302431 GGCAATGGGTTGTTTGGGC 60.302 57.895 0.00 0.00 37.65 5.36
4660 7058 1.077265 CAAGGACCTGGCAATGGGT 59.923 57.895 0.00 0.00 38.70 4.51
4661 7059 0.542702 AACAAGGACCTGGCAATGGG 60.543 55.000 0.00 0.00 0.00 4.00
4668 7066 1.949525 CAGACAACAACAAGGACCTGG 59.050 52.381 0.00 0.00 0.00 4.45
4671 7069 1.065551 GCACAGACAACAACAAGGACC 59.934 52.381 0.00 0.00 0.00 4.46
4680 7078 4.881273 AGTTTTATGACAGCACAGACAACA 59.119 37.500 0.00 0.00 0.00 3.33
4682 7080 4.515191 GGAGTTTTATGACAGCACAGACAA 59.485 41.667 0.00 0.00 0.00 3.18
4686 7084 4.067896 ACAGGAGTTTTATGACAGCACAG 58.932 43.478 0.00 0.00 0.00 3.66
4687 7085 4.085357 ACAGGAGTTTTATGACAGCACA 57.915 40.909 0.00 0.00 0.00 4.57
4688 7086 5.122396 CCTTACAGGAGTTTTATGACAGCAC 59.878 44.000 0.00 0.00 37.67 4.40
4689 7087 5.245531 CCTTACAGGAGTTTTATGACAGCA 58.754 41.667 0.00 0.00 37.67 4.41
4690 7088 4.095036 GCCTTACAGGAGTTTTATGACAGC 59.905 45.833 0.00 0.00 37.67 4.40
4691 7089 5.491982 AGCCTTACAGGAGTTTTATGACAG 58.508 41.667 0.00 0.00 37.67 3.51
4692 7090 5.248477 AGAGCCTTACAGGAGTTTTATGACA 59.752 40.000 0.00 0.00 37.67 3.58
4693 7091 5.735766 AGAGCCTTACAGGAGTTTTATGAC 58.264 41.667 0.00 0.00 37.67 3.06
4694 7092 6.374417 AAGAGCCTTACAGGAGTTTTATGA 57.626 37.500 0.00 0.00 37.67 2.15
4695 7093 7.454260 AAAAGAGCCTTACAGGAGTTTTATG 57.546 36.000 0.00 0.00 37.67 1.90


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

AutoCloner maintained by Alex Coulton.