Multiple sequence alignment - TraesCS4A01G434800

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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 TraesCS4A01G434800 chr4A 100.000 5583 0 0 1 5583 705503781 705509363 0.000000e+00 10310.0
1 TraesCS4A01G434800 chr7D 93.056 4637 197 57 1 4596 22580177 22584729 0.000000e+00 6663.0
2 TraesCS4A01G434800 chr7D 80.317 630 53 26 4981 5577 22585174 22585765 1.450000e-110 411.0
3 TraesCS4A01G434800 chr7A 93.627 2338 71 29 17 2313 22931387 22933687 0.000000e+00 3421.0
4 TraesCS4A01G434800 chr7A 91.154 1933 136 21 2685 4610 22934162 22936066 0.000000e+00 2590.0
5 TraesCS4A01G434800 chr7A 99.048 210 2 0 2478 2687 22933853 22934062 1.470000e-100 377.0
6 TraesCS4A01G434800 chr7A 91.620 179 6 5 2333 2505 22933678 22933853 7.230000e-59 239.0
7 TraesCS4A01G434800 chr7A 100.000 36 0 0 5161 5196 22936645 22936680 3.610000e-07 67.6


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 TraesCS4A01G434800 chr4A 705503781 705509363 5582 False 10310.00 10310 100.0000 1 5583 1 chr4A.!!$F1 5582
1 TraesCS4A01G434800 chr7D 22580177 22585765 5588 False 3537.00 6663 86.6865 1 5577 2 chr7D.!!$F1 5576
2 TraesCS4A01G434800 chr7A 22931387 22936680 5293 False 1338.92 3421 95.0898 17 5196 5 chr7A.!!$F1 5179

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
699 702 0.806102 CTGATGGCGTAACGTGAGGG 60.806 60.0 0.00 0.0 0.00 4.30 F
830 833 1.408969 TTTCAGGGCAAAGGTGTTCC 58.591 50.0 0.00 0.0 0.00 3.62 F
1823 1864 2.464157 AGCCTTTTTCGGAGACTGAG 57.536 50.0 0.00 0.0 34.32 3.35 F
3257 3438 0.904865 TGTCCCTCAGTGAAGCGGAT 60.905 55.0 6.55 0.0 0.00 4.18 F
4273 4461 0.250252 TGCGCTTTCCTGATGTGTGA 60.250 50.0 9.73 0.0 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1823 1864 1.087501 GAAAGCACCAGTTCCGGATC 58.912 55.000 4.15 4.19 0.0 3.36 R
2105 2152 1.833630 TCTGACAAGGAGCATAGGTGG 59.166 52.381 0.00 0.00 0.0 4.61 R
3493 3676 0.026285 CCGAAATAAGGTTCAGCGCG 59.974 55.000 0.00 0.00 0.0 6.86 R
4282 4470 0.035056 GGTAGTTCCCTGCAGCACAT 60.035 55.000 8.66 0.00 0.0 3.21 R
5121 5464 0.036765 GTCTGACCATAACGCCCACA 60.037 55.000 0.00 0.00 0.0 4.17 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
59 60 4.201881 GGTCTGTTGCTTACGAACAACTTT 60.202 41.667 7.32 0.00 45.07 2.66
515 518 5.410355 AGCACAATAATTTTCATGGCACT 57.590 34.783 0.00 0.00 0.00 4.40
516 519 5.797051 AGCACAATAATTTTCATGGCACTT 58.203 33.333 0.00 0.00 0.00 3.16
544 547 7.498900 TCTGTTTTTATTGTCACTGTCTCATGT 59.501 33.333 0.00 0.00 0.00 3.21
549 552 8.932945 TTTATTGTCACTGTCTCATGTATCTC 57.067 34.615 0.00 0.00 0.00 2.75
600 603 2.897271 TCTGTCAGCTCTCTTCTCCT 57.103 50.000 0.00 0.00 0.00 3.69
626 629 4.185394 TCACTGCGAGTTTTCAGTTTGTA 58.815 39.130 0.00 0.00 41.19 2.41
699 702 0.806102 CTGATGGCGTAACGTGAGGG 60.806 60.000 0.00 0.00 0.00 4.30
715 718 4.023193 CGTGAGGGTATGCTTGAAAGTTTT 60.023 41.667 0.00 0.00 0.00 2.43
791 794 5.471797 TGAACATTAGCATTTCTTCCAACGA 59.528 36.000 0.00 0.00 0.00 3.85
802 805 4.402056 TCTTCCAACGATCTAATCCACC 57.598 45.455 0.00 0.00 0.00 4.61
803 806 3.134081 TCTTCCAACGATCTAATCCACCC 59.866 47.826 0.00 0.00 0.00 4.61
830 833 1.408969 TTTCAGGGCAAAGGTGTTCC 58.591 50.000 0.00 0.00 0.00 3.62
1012 1015 7.957002 TCTAGCTAATAAAATGGAGAGGTGAG 58.043 38.462 0.00 0.00 0.00 3.51
1033 1036 3.885901 AGTTGACTCTTTCCCTCTTTTGC 59.114 43.478 0.00 0.00 0.00 3.68
1034 1037 2.863809 TGACTCTTTCCCTCTTTTGCC 58.136 47.619 0.00 0.00 0.00 4.52
1041 1044 2.496899 TCCCTCTTTTGCCAGATGAC 57.503 50.000 0.00 0.00 0.00 3.06
1066 1069 4.566004 TGAGCTTCCAACACTGTACATAC 58.434 43.478 0.00 0.00 0.00 2.39
1070 1073 4.378459 GCTTCCAACACTGTACATACTTGC 60.378 45.833 0.00 0.00 0.00 4.01
1075 1079 5.932303 CCAACACTGTACATACTTGCTAACT 59.068 40.000 0.00 0.00 0.00 2.24
1076 1080 6.426937 CCAACACTGTACATACTTGCTAACTT 59.573 38.462 0.00 0.00 0.00 2.66
1077 1081 7.041372 CCAACACTGTACATACTTGCTAACTTT 60.041 37.037 0.00 0.00 0.00 2.66
1172 1176 4.858692 CGTGCAATCAATAAAGAAAGTGGG 59.141 41.667 0.00 0.00 0.00 4.61
1189 1193 2.835764 GTGGGGAAGTGGTATGTCACTA 59.164 50.000 3.69 0.00 46.17 2.74
1237 1263 5.277442 GCATTACTTTTTGCATTGTTGTGCT 60.277 36.000 0.00 0.00 45.27 4.40
1252 1278 3.911137 GCTGGAGGTTAGCAAGCC 58.089 61.111 0.00 0.00 40.81 4.35
1309 1340 5.062183 GTGAAACACTTCCTTTTCAGTTTGC 59.938 40.000 0.00 0.00 41.29 3.68
1343 1374 6.937465 ACTCTGATATATCTTCACGACTAGCA 59.063 38.462 13.79 0.00 0.00 3.49
1405 1436 7.557358 TCTTTCACCTTGTTGACATATATGCAT 59.443 33.333 12.79 3.79 0.00 3.96
1419 1450 7.170277 ACATATATGCATATGCCTGTTCTTCA 58.830 34.615 26.21 3.07 45.44 3.02
1496 1527 3.868757 TCTCCGTGAAGTGAAGGTATG 57.131 47.619 0.00 0.00 0.00 2.39
1498 1529 3.056821 TCTCCGTGAAGTGAAGGTATGTG 60.057 47.826 0.00 0.00 0.00 3.21
1509 1550 9.378551 GAAGTGAAGGTATGTGATGTTACATAA 57.621 33.333 0.00 0.00 43.11 1.90
1823 1864 2.464157 AGCCTTTTTCGGAGACTGAG 57.536 50.000 0.00 0.00 34.32 3.35
2017 2060 5.583495 CCTAGACCGATACTTGAAGAAGTG 58.417 45.833 0.00 0.00 42.66 3.16
2021 2064 7.876936 AGACCGATACTTGAAGAAGTGTATA 57.123 36.000 0.00 0.00 42.66 1.47
2112 2159 8.923270 TCTTTTGTTTTTCATCTTTCCACCTAT 58.077 29.630 0.00 0.00 0.00 2.57
2124 2171 1.833630 TCCACCTATGCTCCTTGTCAG 59.166 52.381 0.00 0.00 0.00 3.51
2234 2282 1.067142 CCGACAAGGCTAACACTGCTA 60.067 52.381 0.00 0.00 0.00 3.49
2263 2312 6.099341 ACATTTTGAGCGGTTTTATTGATCC 58.901 36.000 0.00 0.00 0.00 3.36
2265 2314 5.975693 TTTGAGCGGTTTTATTGATCCTT 57.024 34.783 0.00 0.00 0.00 3.36
2314 2363 2.288666 TCTTGACAGAAAGTGTGCACC 58.711 47.619 15.69 5.76 40.56 5.01
2315 2364 2.016318 CTTGACAGAAAGTGTGCACCA 58.984 47.619 15.69 0.00 40.56 4.17
2419 2468 6.533819 TGACTAACATGTGTCGGTAAAAAG 57.466 37.500 0.00 0.00 36.10 2.27
2462 2514 5.235850 TCCTTAAATGCTACTGTGTTCCA 57.764 39.130 0.00 0.00 0.00 3.53
2697 2878 8.575565 ACAGCTTAAATCATAGTACATACACG 57.424 34.615 0.00 0.00 0.00 4.49
2806 2987 5.189736 AGCAGTTGGTGAGTGGAGAATATTA 59.810 40.000 0.00 0.00 0.00 0.98
2807 2988 6.058183 GCAGTTGGTGAGTGGAGAATATTAT 58.942 40.000 0.00 0.00 0.00 1.28
2887 3068 2.050144 CTAGACATGTGGGCTATGGGT 58.950 52.381 1.15 0.00 0.00 4.51
2929 3110 1.072505 GCACCGACCTCTTTTCCCA 59.927 57.895 0.00 0.00 0.00 4.37
2963 3144 4.458295 ACACATGATCCTTTTTCTGCTGAG 59.542 41.667 0.00 0.00 0.00 3.35
3059 3240 6.064717 AGTTTGCTGGGAGCTAAATATTAGG 58.935 40.000 0.00 0.00 42.97 2.69
3103 3284 2.948979 TGAAATAACCATCATCGGCCAC 59.051 45.455 2.24 0.00 0.00 5.01
3109 3290 3.297134 ACCATCATCGGCCACTTTAAT 57.703 42.857 2.24 0.00 0.00 1.40
3201 3382 7.444183 TCTTTTGTGGTATGTTCTTCCAAGTAG 59.556 37.037 0.00 0.00 32.82 2.57
3216 3397 2.464157 AGTAGTTGCTCAAGTGAGGC 57.536 50.000 10.25 3.62 42.29 4.70
3257 3438 0.904865 TGTCCCTCAGTGAAGCGGAT 60.905 55.000 6.55 0.00 0.00 4.18
3380 3563 5.369993 GGTAGAATCTTTTGATACCCCTCCT 59.630 44.000 0.00 0.00 38.40 3.69
3381 3564 5.638530 AGAATCTTTTGATACCCCTCCTC 57.361 43.478 0.00 0.00 38.40 3.71
3382 3565 4.101741 AGAATCTTTTGATACCCCTCCTCG 59.898 45.833 0.00 0.00 38.40 4.63
3383 3566 1.485066 TCTTTTGATACCCCTCCTCGC 59.515 52.381 0.00 0.00 0.00 5.03
3384 3567 1.486726 CTTTTGATACCCCTCCTCGCT 59.513 52.381 0.00 0.00 0.00 4.93
3385 3568 1.120530 TTTGATACCCCTCCTCGCTC 58.879 55.000 0.00 0.00 0.00 5.03
3392 3575 2.124693 CCCTCCTCGCTCTCCAGTC 61.125 68.421 0.00 0.00 0.00 3.51
3405 3588 5.563867 CGCTCTCCAGTCCTGAGATTATTAC 60.564 48.000 0.00 0.00 0.00 1.89
3418 3601 8.246871 CCTGAGATTATTACGAGCTATTGATGA 58.753 37.037 0.00 0.00 0.00 2.92
3431 3614 7.256756 AGCTATTGATGACTAAATGCTGTTC 57.743 36.000 0.00 0.00 0.00 3.18
3527 3710 9.924650 ACCTTATTTCGGTAAGTATCATATCAC 57.075 33.333 0.00 0.00 31.69 3.06
3546 3729 2.874701 CACCAGTTTCTGTCTGTCCTTG 59.125 50.000 0.00 0.00 0.00 3.61
3587 3770 7.308408 CGATCATGTTCAGATTAATGATTGGCT 60.308 37.037 4.71 0.00 39.31 4.75
3694 3877 9.359653 CCTTCTTTCAGGTCATAATATTTCCAT 57.640 33.333 0.00 0.00 0.00 3.41
3712 3895 2.936498 CCATCGTCTTTCCATACCACAC 59.064 50.000 0.00 0.00 0.00 3.82
3739 3922 0.801872 TGCATTGATTCGGTTCGTGG 59.198 50.000 0.00 0.00 0.00 4.94
3747 3930 1.393487 TTCGGTTCGTGGACCTGACA 61.393 55.000 0.00 0.00 37.56 3.58
3749 3932 0.531090 CGGTTCGTGGACCTGACAAA 60.531 55.000 0.00 0.00 37.56 2.83
3873 4058 8.978539 TCACGCTTATATGACTTGTATCATTTC 58.021 33.333 0.00 0.00 39.97 2.17
3875 4060 7.116376 ACGCTTATATGACTTGTATCATTTCCG 59.884 37.037 0.00 0.00 39.97 4.30
3912 4097 8.772705 GTTGTTGAAGCAATTCAAATAATGGAA 58.227 29.630 5.07 0.00 41.95 3.53
4020 4205 3.119245 TCAATAACTCGTACCTGAGCACC 60.119 47.826 0.00 0.00 39.68 5.01
4025 4213 2.380410 CGTACCTGAGCACCAACGC 61.380 63.158 0.00 0.00 0.00 4.84
4116 4304 2.095252 GCTGACGAAGGAGAACGCC 61.095 63.158 0.00 0.00 0.00 5.68
4175 4363 2.271800 GAGGAGCAACGGTGAGTATTG 58.728 52.381 3.55 0.00 0.00 1.90
4189 4377 6.569780 GGTGAGTATTGTTGTTTTGTTCCTT 58.430 36.000 0.00 0.00 0.00 3.36
4190 4378 6.695713 GGTGAGTATTGTTGTTTTGTTCCTTC 59.304 38.462 0.00 0.00 0.00 3.46
4192 4380 7.757624 GTGAGTATTGTTGTTTTGTTCCTTCAA 59.242 33.333 0.00 0.00 0.00 2.69
4193 4381 8.307483 TGAGTATTGTTGTTTTGTTCCTTCAAA 58.693 29.630 0.00 0.00 35.83 2.69
4194 4382 9.145865 GAGTATTGTTGTTTTGTTCCTTCAAAA 57.854 29.630 0.00 0.00 42.50 2.44
4208 4396 7.040755 TGTTCCTTCAAAACATGTATGTAGTGG 60.041 37.037 0.00 4.22 40.80 4.00
4209 4397 6.539173 TCCTTCAAAACATGTATGTAGTGGT 58.461 36.000 0.00 0.00 40.80 4.16
4222 4410 3.670625 TGTAGTGGTGTACTTGGAATGC 58.329 45.455 0.00 0.00 40.89 3.56
4223 4411 3.326588 TGTAGTGGTGTACTTGGAATGCT 59.673 43.478 0.00 0.00 40.89 3.79
4228 4416 2.558359 GGTGTACTTGGAATGCTGCTTT 59.442 45.455 0.00 0.00 0.00 3.51
4229 4417 3.756434 GGTGTACTTGGAATGCTGCTTTA 59.244 43.478 0.00 0.00 0.00 1.85
4230 4418 4.399303 GGTGTACTTGGAATGCTGCTTTAT 59.601 41.667 0.00 0.00 0.00 1.40
4235 4423 5.473039 ACTTGGAATGCTGCTTTATGTTTC 58.527 37.500 0.00 0.00 0.00 2.78
4246 4434 6.371809 TGCTTTATGTTTCGTTCAAAGTCT 57.628 33.333 0.00 0.00 0.00 3.24
4247 4435 7.485418 TGCTTTATGTTTCGTTCAAAGTCTA 57.515 32.000 0.00 0.00 0.00 2.59
4248 4436 8.094798 TGCTTTATGTTTCGTTCAAAGTCTAT 57.905 30.769 0.00 0.00 0.00 1.98
4261 4449 4.937620 TCAAAGTCTATGATCTTGCGCTTT 59.062 37.500 9.73 0.00 0.00 3.51
4262 4450 5.063944 TCAAAGTCTATGATCTTGCGCTTTC 59.936 40.000 9.73 0.46 0.00 2.62
4265 4453 3.247173 GTCTATGATCTTGCGCTTTCCTG 59.753 47.826 9.73 0.00 0.00 3.86
4269 4457 2.012673 GATCTTGCGCTTTCCTGATGT 58.987 47.619 9.73 0.00 0.00 3.06
4270 4458 1.159285 TCTTGCGCTTTCCTGATGTG 58.841 50.000 9.73 0.00 0.00 3.21
4271 4459 0.877071 CTTGCGCTTTCCTGATGTGT 59.123 50.000 9.73 0.00 0.00 3.72
4272 4460 0.592637 TTGCGCTTTCCTGATGTGTG 59.407 50.000 9.73 0.00 0.00 3.82
4273 4461 0.250252 TGCGCTTTCCTGATGTGTGA 60.250 50.000 9.73 0.00 0.00 3.58
4274 4462 1.089920 GCGCTTTCCTGATGTGTGAT 58.910 50.000 0.00 0.00 0.00 3.06
4275 4463 1.470098 GCGCTTTCCTGATGTGTGATT 59.530 47.619 0.00 0.00 0.00 2.57
4277 4465 3.495193 CGCTTTCCTGATGTGTGATTTG 58.505 45.455 0.00 0.00 0.00 2.32
4278 4466 3.671433 CGCTTTCCTGATGTGTGATTTGG 60.671 47.826 0.00 0.00 0.00 3.28
4279 4467 3.256631 GCTTTCCTGATGTGTGATTTGGT 59.743 43.478 0.00 0.00 0.00 3.67
4280 4468 4.262164 GCTTTCCTGATGTGTGATTTGGTT 60.262 41.667 0.00 0.00 0.00 3.67
4281 4469 5.452078 TTTCCTGATGTGTGATTTGGTTC 57.548 39.130 0.00 0.00 0.00 3.62
4282 4470 4.097551 TCCTGATGTGTGATTTGGTTCA 57.902 40.909 0.00 0.00 0.00 3.18
4285 4473 4.219070 CCTGATGTGTGATTTGGTTCATGT 59.781 41.667 0.00 0.00 0.00 3.21
4286 4474 5.123805 TGATGTGTGATTTGGTTCATGTG 57.876 39.130 0.00 0.00 0.00 3.21
4287 4475 3.367992 TGTGTGATTTGGTTCATGTGC 57.632 42.857 0.00 0.00 0.00 4.57
4306 4497 2.187163 GCAGGGAACTACCTCGCC 59.813 66.667 0.00 0.00 39.34 5.54
4307 4498 2.901042 CAGGGAACTACCTCGCCC 59.099 66.667 0.00 0.00 39.34 6.13
4309 4500 3.846430 GGGAACTACCTCGCCCCG 61.846 72.222 0.00 0.00 38.98 5.73
4596 4787 2.903357 CTGAGGACCATCCCACCG 59.097 66.667 0.00 0.00 37.19 4.94
4599 4790 1.686110 GAGGACCATCCCACCGACT 60.686 63.158 0.00 0.00 37.19 4.18
4658 4910 4.683721 TCGCCGCCGCCAAGTTTA 62.684 61.111 0.00 0.00 0.00 2.01
4669 4923 3.751175 CCGCCAAGTTTATGTCTCTTTCA 59.249 43.478 0.00 0.00 0.00 2.69
4671 4925 5.447818 CCGCCAAGTTTATGTCTCTTTCATC 60.448 44.000 0.00 0.00 0.00 2.92
4685 4939 4.055360 TCTTTCATCGTTCGTGTTGTGAT 58.945 39.130 0.00 0.00 0.00 3.06
4704 4961 6.454795 TGTGATTGAAAATAAAAGCCAGTCC 58.545 36.000 0.00 0.00 0.00 3.85
4707 4964 2.823154 TGAAAATAAAAGCCAGTCCCCG 59.177 45.455 0.00 0.00 0.00 5.73
4708 4965 1.847328 AAATAAAAGCCAGTCCCCGG 58.153 50.000 0.00 0.00 0.00 5.73
4728 4985 4.544689 CTCGCGTCTGCTCGGAGG 62.545 72.222 5.77 0.00 39.65 4.30
4742 5008 3.462678 GAGGCGGTGGGGAGACTC 61.463 72.222 0.00 0.00 0.00 3.36
4754 5020 1.478916 GGGAGACTCAAGAGTACTGCC 59.521 57.143 17.35 17.35 42.66 4.85
4756 5022 1.813786 GAGACTCAAGAGTACTGCCGT 59.186 52.381 0.00 0.00 42.66 5.68
4778 5044 2.358322 TTCCTTTGGGCTTTCGAGTT 57.642 45.000 0.00 0.00 0.00 3.01
4780 5046 1.953686 TCCTTTGGGCTTTCGAGTTTG 59.046 47.619 0.00 0.00 0.00 2.93
4799 5065 5.707298 AGTTTGAGAAACGTGGATGATGATT 59.293 36.000 0.00 0.00 45.88 2.57
4800 5066 6.878923 AGTTTGAGAAACGTGGATGATGATTA 59.121 34.615 0.00 0.00 45.88 1.75
4801 5067 7.554118 AGTTTGAGAAACGTGGATGATGATTAT 59.446 33.333 0.00 0.00 45.88 1.28
4802 5068 8.826710 GTTTGAGAAACGTGGATGATGATTATA 58.173 33.333 0.00 0.00 0.00 0.98
4803 5069 9.559732 TTTGAGAAACGTGGATGATGATTATAT 57.440 29.630 0.00 0.00 0.00 0.86
4804 5070 8.538409 TGAGAAACGTGGATGATGATTATATG 57.462 34.615 0.00 0.00 0.00 1.78
4805 5071 7.118245 TGAGAAACGTGGATGATGATTATATGC 59.882 37.037 0.00 0.00 0.00 3.14
4806 5072 7.164122 AGAAACGTGGATGATGATTATATGCT 58.836 34.615 0.00 0.00 0.00 3.79
4844 5115 2.276244 CAACGATCGCTTGCGCAG 60.276 61.111 16.60 6.32 35.30 5.18
4845 5116 2.432456 AACGATCGCTTGCGCAGA 60.432 55.556 16.60 5.00 35.30 4.26
4855 5126 1.667724 GCTTGCGCAGATTATGTGACT 59.332 47.619 11.31 0.00 42.31 3.41
4865 5136 5.692814 CAGATTATGTGACTTTGTGTGTGG 58.307 41.667 0.00 0.00 0.00 4.17
4870 5141 0.254462 TGACTTTGTGTGTGGAGCCA 59.746 50.000 0.00 0.00 0.00 4.75
4878 5149 0.035317 TGTGTGGAGCCACTGATGTC 59.965 55.000 19.47 5.31 46.30 3.06
4885 5156 1.188219 AGCCACTGATGTCTCGTGGT 61.188 55.000 17.20 7.23 42.74 4.16
4888 5159 2.418746 GCCACTGATGTCTCGTGGTTAT 60.419 50.000 17.20 0.00 42.74 1.89
4900 5171 6.367695 TGTCTCGTGGTTATACTTGTTGATTG 59.632 38.462 0.00 0.00 0.00 2.67
4903 5176 5.350365 TCGTGGTTATACTTGTTGATTGCTC 59.650 40.000 0.00 0.00 0.00 4.26
4920 5193 1.667724 GCTCTGGTCGTTGATCCATTG 59.332 52.381 0.00 0.00 33.01 2.82
4922 5195 1.905894 TCTGGTCGTTGATCCATTGGA 59.094 47.619 8.08 8.08 35.55 3.53
4939 5212 1.171308 GGAGATGCTTTGCTTGCTCA 58.829 50.000 0.00 0.00 0.00 4.26
4950 5230 1.242076 GCTTGCTCACATGGTTCAGT 58.758 50.000 0.00 0.00 0.00 3.41
4983 5263 0.604073 TGCATGGCTGGTGATGTTTG 59.396 50.000 0.00 0.00 0.00 2.93
4992 5312 3.057526 GCTGGTGATGTTTGTTTACTCCC 60.058 47.826 0.00 0.00 0.00 4.30
5009 5329 4.150359 ACTCCCGTGGGTATTACTCTATG 58.850 47.826 4.53 0.00 36.47 2.23
5011 5331 5.163055 ACTCCCGTGGGTATTACTCTATGTA 60.163 44.000 4.53 0.00 36.47 2.29
5012 5332 5.319453 TCCCGTGGGTATTACTCTATGTAG 58.681 45.833 4.53 0.00 36.47 2.74
5013 5333 5.075493 CCCGTGGGTATTACTCTATGTAGT 58.925 45.833 0.00 0.00 32.08 2.73
5014 5334 6.044287 TCCCGTGGGTATTACTCTATGTAGTA 59.956 42.308 4.53 0.00 36.47 1.82
5015 5335 6.373774 CCCGTGGGTATTACTCTATGTAGTAG 59.626 46.154 0.00 0.00 33.62 2.57
5047 5372 1.300465 CGGGAGCTGTCATGGATCG 60.300 63.158 0.00 0.00 0.00 3.69
5055 5380 1.141881 GTCATGGATCGCGTGAGGT 59.858 57.895 5.77 0.00 0.00 3.85
5065 5390 1.065358 CGCGTGAGGTGACGTATTTT 58.935 50.000 0.00 0.00 41.54 1.82
5110 5453 0.952497 CGCGAGGGATGATGGATTGG 60.952 60.000 0.00 0.00 0.00 3.16
5118 5461 4.026052 GGGATGATGGATTGGTTTCTGTT 58.974 43.478 0.00 0.00 0.00 3.16
5119 5462 4.467438 GGGATGATGGATTGGTTTCTGTTT 59.533 41.667 0.00 0.00 0.00 2.83
5120 5463 5.394553 GGGATGATGGATTGGTTTCTGTTTC 60.395 44.000 0.00 0.00 0.00 2.78
5121 5464 5.420104 GGATGATGGATTGGTTTCTGTTTCT 59.580 40.000 0.00 0.00 0.00 2.52
5122 5465 5.710513 TGATGGATTGGTTTCTGTTTCTG 57.289 39.130 0.00 0.00 0.00 3.02
5123 5466 5.139727 TGATGGATTGGTTTCTGTTTCTGT 58.860 37.500 0.00 0.00 0.00 3.41
5137 5480 0.687920 TTCTGTGGGCGTTATGGTCA 59.312 50.000 0.00 0.00 0.00 4.02
5155 5498 3.272334 GACCGCGTGGGCATCATC 61.272 66.667 18.24 0.00 45.78 2.92
5156 5499 4.094646 ACCGCGTGGGCATCATCA 62.095 61.111 21.14 0.00 40.62 3.07
5157 5500 2.592574 CCGCGTGGGCATCATCAT 60.593 61.111 7.26 0.00 39.92 2.45
5158 5501 2.610694 CCGCGTGGGCATCATCATC 61.611 63.158 7.26 0.00 39.92 2.92
5159 5502 1.888638 CGCGTGGGCATCATCATCA 60.889 57.895 0.00 0.00 39.92 3.07
5196 5539 0.171455 GACTACGTAGCAGCAGCAGT 59.829 55.000 22.40 1.60 45.49 4.40
5219 5562 7.691463 CAGTGCAGTAAAACTAGTACTAGTACG 59.309 40.741 30.89 21.23 44.96 3.67
5220 5563 7.389053 AGTGCAGTAAAACTAGTACTAGTACGT 59.611 37.037 30.89 21.54 44.96 3.57
5221 5564 8.656849 GTGCAGTAAAACTAGTACTAGTACGTA 58.343 37.037 30.89 20.69 44.96 3.57
5222 5565 8.656849 TGCAGTAAAACTAGTACTAGTACGTAC 58.343 37.037 30.89 27.66 44.96 3.67
5239 5582 2.262211 GTACGTACGTAGGCCTTTTGG 58.738 52.381 27.48 0.00 44.18 3.28
5244 5587 1.743995 CGTAGGCCTTTTGGGACCG 60.744 63.158 12.58 0.00 46.87 4.79
5245 5588 1.681076 GTAGGCCTTTTGGGACCGA 59.319 57.895 12.58 0.00 46.87 4.69
5246 5589 0.392595 GTAGGCCTTTTGGGACCGAG 60.393 60.000 12.58 0.00 46.87 4.63
5276 5619 4.056125 GCCGCTGCCAAAACCCTC 62.056 66.667 0.00 0.00 0.00 4.30
5278 5621 2.597217 CGCTGCCAAAACCCTCCA 60.597 61.111 0.00 0.00 0.00 3.86
5290 5639 0.773700 ACCCTCCATCCATCCATCCC 60.774 60.000 0.00 0.00 0.00 3.85
5293 5642 1.075050 CCTCCATCCATCCATCCCTTG 59.925 57.143 0.00 0.00 0.00 3.61
5300 5649 3.125376 ATCCATCCCTTGGCCGCTC 62.125 63.158 0.00 0.00 46.01 5.03
5312 5661 3.869272 CCGCTCGCCTGCATTCAC 61.869 66.667 0.00 0.00 0.00 3.18
5313 5662 3.869272 CGCTCGCCTGCATTCACC 61.869 66.667 0.00 0.00 0.00 4.02
5314 5663 2.747460 GCTCGCCTGCATTCACCA 60.747 61.111 0.00 0.00 0.00 4.17
5315 5664 2.758089 GCTCGCCTGCATTCACCAG 61.758 63.158 0.00 0.00 0.00 4.00
5316 5665 1.078918 CTCGCCTGCATTCACCAGA 60.079 57.895 0.00 0.00 32.03 3.86
5317 5666 0.463295 CTCGCCTGCATTCACCAGAT 60.463 55.000 0.00 0.00 32.03 2.90
5322 5671 2.286872 CCTGCATTCACCAGATCAGAC 58.713 52.381 0.00 0.00 32.03 3.51
5325 5674 1.293924 CATTCACCAGATCAGACGGC 58.706 55.000 0.00 0.00 0.00 5.68
5381 5744 1.820906 CCCCCTCATCACGTGCATG 60.821 63.158 11.67 15.05 0.00 4.06
5399 5763 3.341823 CATGTCTTCTTCTTGACCAGGG 58.658 50.000 0.00 0.00 32.67 4.45
5406 5770 2.716424 TCTTCTTGACCAGGGGAAACAT 59.284 45.455 0.00 0.00 0.00 2.71
5412 5776 1.295423 CCAGGGGAAACATCGTCGT 59.705 57.895 0.00 0.00 0.00 4.34
5413 5777 1.019278 CCAGGGGAAACATCGTCGTG 61.019 60.000 0.00 0.00 0.00 4.35
5414 5778 1.375523 AGGGGAAACATCGTCGTGC 60.376 57.895 0.00 0.00 0.00 5.34
5415 5779 2.396157 GGGGAAACATCGTCGTGCC 61.396 63.158 0.00 0.00 0.00 5.01
5432 5796 1.805428 GCCTCCCGTGTGCATTGTTT 61.805 55.000 0.00 0.00 0.00 2.83
5452 5816 2.923035 ACTACCCTGCGTGCTGGT 60.923 61.111 15.41 12.89 36.15 4.00
5453 5817 2.434884 CTACCCTGCGTGCTGGTG 60.435 66.667 15.41 9.91 33.55 4.17
5454 5818 4.697756 TACCCTGCGTGCTGGTGC 62.698 66.667 15.41 0.00 40.20 5.01
5465 5829 0.469705 TGCTGGTGCTGGGTCATTTT 60.470 50.000 0.00 0.00 40.48 1.82
5500 5864 6.547141 CCAGCTTTGAATCCATGGTAAGATTA 59.453 38.462 12.58 0.00 32.91 1.75
5525 5892 5.267776 GCATGCCAAATAATTTGCATCAAC 58.732 37.500 6.36 0.00 39.31 3.18
5530 5897 5.357596 GCCAAATAATTTGCATCAACCCAAT 59.642 36.000 0.00 0.00 39.31 3.16
5539 5906 1.747355 CATCAACCCAATCAGCCTCAC 59.253 52.381 0.00 0.00 0.00 3.51
5542 5909 1.779061 AACCCAATCAGCCTCACGGT 61.779 55.000 0.00 0.00 0.00 4.83
5547 5914 2.102420 CCAATCAGCCTCACGGTACATA 59.898 50.000 0.00 0.00 0.00 2.29
5553 5920 3.749088 CAGCCTCACGGTACATACAAAAA 59.251 43.478 0.00 0.00 0.00 1.94
5560 5927 8.388103 CCTCACGGTACATACAAAAATCTTTAG 58.612 37.037 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 4.764172 AGCAACAGACCTATAGCTGAAAG 58.236 43.478 12.67 4.98 36.07 2.62
59 60 4.160439 TGGTGTTGAAACCTGCAAATACAA 59.840 37.500 0.00 0.00 41.16 2.41
515 518 8.735315 TGAGACAGTGACAATAAAAACAGAAAA 58.265 29.630 0.00 0.00 0.00 2.29
516 519 8.275015 TGAGACAGTGACAATAAAAACAGAAA 57.725 30.769 0.00 0.00 0.00 2.52
544 547 1.133945 ACCTGCTGAGAGCGAGAGATA 60.134 52.381 0.00 0.00 46.26 1.98
549 552 0.458197 CAGAACCTGCTGAGAGCGAG 60.458 60.000 0.00 0.00 46.26 5.03
600 603 4.521130 ACTGAAAACTCGCAGTGATAGA 57.479 40.909 0.00 0.00 43.26 1.98
626 629 1.238439 CACACCAAAGATCAAGCCGT 58.762 50.000 0.00 0.00 0.00 5.68
699 702 9.797473 GCTTAAATTCAAAACTTTCAAGCATAC 57.203 29.630 0.00 0.00 36.69 2.39
715 718 5.185442 TCATGCATTGTCCTGCTTAAATTCA 59.815 36.000 0.00 0.00 42.75 2.57
791 794 7.561356 CCTGAAATTAAACAGGGTGGATTAGAT 59.439 37.037 14.57 0.00 46.76 1.98
803 806 4.990426 CACCTTTGCCCTGAAATTAAACAG 59.010 41.667 0.00 0.00 0.00 3.16
830 833 8.141268 ACCCATACTTTGTGACAAATAAACTTG 58.859 33.333 11.58 0.59 0.00 3.16
1012 1015 3.004839 GGCAAAAGAGGGAAAGAGTCAAC 59.995 47.826 0.00 0.00 0.00 3.18
1033 1036 2.995283 TGGAAGCTCATTGTCATCTGG 58.005 47.619 0.00 0.00 0.00 3.86
1034 1037 3.754850 TGTTGGAAGCTCATTGTCATCTG 59.245 43.478 0.00 0.00 0.00 2.90
1041 1044 3.814842 TGTACAGTGTTGGAAGCTCATTG 59.185 43.478 0.00 0.00 0.00 2.82
1127 1131 3.204526 CCAAACACTACCAAACGTACCA 58.795 45.455 0.00 0.00 0.00 3.25
1172 1176 3.933332 GCAAGTAGTGACATACCACTTCC 59.067 47.826 1.71 0.00 44.32 3.46
1189 1193 4.556592 AACATGCAAATATTGGGCAAGT 57.443 36.364 16.25 15.10 40.70 3.16
1237 1263 1.685224 CCAGGCTTGCTAACCTCCA 59.315 57.895 0.00 0.00 32.56 3.86
1366 1397 6.782494 ACAAGGTGAAAGAAAATCCAGGTATT 59.218 34.615 0.00 0.00 0.00 1.89
1419 1450 3.820467 TCATTTTCTTGATTGCGACCTGT 59.180 39.130 0.00 0.00 0.00 4.00
1509 1550 4.461431 CCATGATGCAATATGGCTACATGT 59.539 41.667 25.33 2.69 41.46 3.21
1559 1600 7.458397 AGGGACTGTTGAAGTTGAAACATATA 58.542 34.615 2.12 0.00 40.07 0.86
1560 1601 6.306987 AGGGACTGTTGAAGTTGAAACATAT 58.693 36.000 2.12 0.00 40.07 1.78
1823 1864 1.087501 GAAAGCACCAGTTCCGGATC 58.912 55.000 4.15 4.19 0.00 3.36
2017 2060 7.205297 TGGATACTGGTAACGCTCTTTTATAC 58.795 38.462 0.00 0.00 42.51 1.47
2021 2064 4.546829 TGGATACTGGTAACGCTCTTTT 57.453 40.909 0.00 0.00 42.51 2.27
2105 2152 1.833630 TCTGACAAGGAGCATAGGTGG 59.166 52.381 0.00 0.00 0.00 4.61
2124 2171 2.798976 TTGCATGAAACCACAGCTTC 57.201 45.000 0.00 0.00 0.00 3.86
2272 2321 3.701040 AGCAAGGGAACGCATAATCAATT 59.299 39.130 0.00 0.00 0.00 2.32
2284 2333 2.550830 TCTGTCAAGAGCAAGGGAAC 57.449 50.000 0.00 0.00 0.00 3.62
2314 2363 9.547753 GCTACCTTTACATATATATCCCACATG 57.452 37.037 0.00 0.00 0.00 3.21
2315 2364 9.279233 TGCTACCTTTACATATATATCCCACAT 57.721 33.333 0.00 0.00 0.00 3.21
2357 2406 6.763715 TCAAGTGTCCCTATTATGCCTAAT 57.236 37.500 0.00 0.00 0.00 1.73
2440 2489 5.235850 TGGAACACAGTAGCATTTAAGGA 57.764 39.130 0.00 0.00 0.00 3.36
2462 2514 5.511386 AGGTCAATCTGAACTCTCCAAAT 57.489 39.130 0.00 0.00 41.32 2.32
2697 2878 5.823045 ACATTAGTATCCTTGCTTTAGTGCC 59.177 40.000 0.00 0.00 0.00 5.01
2807 2988 7.245419 GCAATTTGCTTTCTTGTAAAGGAAA 57.755 32.000 14.11 16.08 41.86 3.13
2887 3068 4.540359 AAAAAGCTCTGCAATAATGGCA 57.460 36.364 0.00 0.00 39.32 4.92
2911 3092 0.955919 CTGGGAAAAGAGGTCGGTGC 60.956 60.000 0.00 0.00 0.00 5.01
2929 3110 2.171448 GGATCATGTGTACCTTGAGCCT 59.829 50.000 18.71 1.82 45.56 4.58
3022 3203 4.567747 CCCAGCAAACTATTAGGACCAACT 60.568 45.833 0.00 0.00 0.00 3.16
3023 3204 3.694566 CCCAGCAAACTATTAGGACCAAC 59.305 47.826 0.00 0.00 0.00 3.77
3037 3218 4.827284 GCCTAATATTTAGCTCCCAGCAAA 59.173 41.667 0.00 0.00 45.56 3.68
3127 3308 5.810080 ATGGGGTGCTTTCTAGACTATAC 57.190 43.478 0.00 0.00 0.00 1.47
3128 3309 7.512746 ACATTATGGGGTGCTTTCTAGACTATA 59.487 37.037 0.00 0.00 0.00 1.31
3129 3310 6.330250 ACATTATGGGGTGCTTTCTAGACTAT 59.670 38.462 0.00 0.00 0.00 2.12
3162 3343 4.648762 ACCACAAAAGAATCACCACATCAA 59.351 37.500 0.00 0.00 0.00 2.57
3201 3382 1.251251 AATGGCCTCACTTGAGCAAC 58.749 50.000 3.32 0.00 40.75 4.17
3380 3563 0.257328 ATCTCAGGACTGGAGAGCGA 59.743 55.000 0.00 0.00 44.04 4.93
3381 3564 1.110442 AATCTCAGGACTGGAGAGCG 58.890 55.000 0.00 0.00 44.04 5.03
3382 3565 4.953940 AATAATCTCAGGACTGGAGAGC 57.046 45.455 0.00 0.00 44.04 4.09
3383 3566 5.765677 TCGTAATAATCTCAGGACTGGAGAG 59.234 44.000 0.00 0.00 44.04 3.20
3384 3567 5.691896 TCGTAATAATCTCAGGACTGGAGA 58.308 41.667 0.00 0.00 44.83 3.71
3385 3568 5.563867 GCTCGTAATAATCTCAGGACTGGAG 60.564 48.000 0.00 0.00 0.00 3.86
3392 3575 8.246871 TCATCAATAGCTCGTAATAATCTCAGG 58.753 37.037 0.00 0.00 0.00 3.86
3405 3588 5.464722 ACAGCATTTAGTCATCAATAGCTCG 59.535 40.000 0.00 0.00 0.00 5.03
3431 3614 4.574013 GCTTCCAGACTGTTGAGAATATGG 59.426 45.833 0.93 0.00 0.00 2.74
3493 3676 0.026285 CCGAAATAAGGTTCAGCGCG 59.974 55.000 0.00 0.00 0.00 6.86
3527 3710 3.475566 TCAAGGACAGACAGAAACTGG 57.524 47.619 0.00 0.00 39.38 4.00
3546 3729 1.201343 GATCGCTTCGCCACTACTTC 58.799 55.000 0.00 0.00 0.00 3.01
3561 3744 6.800408 GCCAATCATTAATCTGAACATGATCG 59.200 38.462 0.00 0.00 35.70 3.69
3587 3770 3.603532 TGTGGCAAATGCAAAAGTTGAA 58.396 36.364 7.80 0.00 44.36 2.69
3694 3877 4.338012 TCTAGTGTGGTATGGAAAGACGA 58.662 43.478 0.00 0.00 0.00 4.20
3695 3878 4.713824 TCTAGTGTGGTATGGAAAGACG 57.286 45.455 0.00 0.00 0.00 4.18
3712 3895 5.389202 CGAACCGAATCAATGCATCATCTAG 60.389 44.000 0.00 0.00 0.00 2.43
3739 3922 7.096065 GCTGACATAAACAATTTTTGTCAGGTC 60.096 37.037 32.43 22.65 45.98 3.85
3747 3930 6.232692 AGCATGGCTGACATAAACAATTTTT 58.767 32.000 0.00 0.00 37.84 1.94
3749 3932 5.410355 AGCATGGCTGACATAAACAATTT 57.590 34.783 0.00 0.00 37.84 1.82
3797 3982 2.888414 TGTTGCATATCCGGTCGATCTA 59.112 45.455 0.00 0.00 31.92 1.98
3875 4060 3.682858 TGCTTCAACAACGGTATTCTAGC 59.317 43.478 0.00 0.00 0.00 3.42
3912 4097 1.341383 CCTTTAGCCCCAACTGCAGAT 60.341 52.381 23.35 5.41 0.00 2.90
4020 4205 3.741476 GCTCTTGCTGGGGCGTTG 61.741 66.667 0.00 0.00 42.25 4.10
4089 4277 2.428890 CTCCTTCGTCAGCTTATGGTCT 59.571 50.000 0.00 0.00 0.00 3.85
4090 4278 2.427453 TCTCCTTCGTCAGCTTATGGTC 59.573 50.000 0.00 0.00 0.00 4.02
4189 4377 7.446769 AGTACACCACTACATACATGTTTTGA 58.553 34.615 2.30 0.00 41.97 2.69
4190 4378 7.667043 AGTACACCACTACATACATGTTTTG 57.333 36.000 2.30 5.24 41.97 2.44
4192 4380 6.653320 CCAAGTACACCACTACATACATGTTT 59.347 38.462 2.30 0.00 41.97 2.83
4193 4381 6.014070 TCCAAGTACACCACTACATACATGTT 60.014 38.462 2.30 0.00 41.97 2.71
4194 4382 5.482526 TCCAAGTACACCACTACATACATGT 59.517 40.000 2.69 2.69 44.48 3.21
4195 4383 5.972935 TCCAAGTACACCACTACATACATG 58.027 41.667 0.00 0.00 36.04 3.21
4196 4384 6.614694 TTCCAAGTACACCACTACATACAT 57.385 37.500 0.00 0.00 36.04 2.29
4197 4385 6.403049 CATTCCAAGTACACCACTACATACA 58.597 40.000 0.00 0.00 36.04 2.29
4198 4386 5.293569 GCATTCCAAGTACACCACTACATAC 59.706 44.000 0.00 0.00 36.04 2.39
4199 4387 5.188948 AGCATTCCAAGTACACCACTACATA 59.811 40.000 0.00 0.00 36.04 2.29
4208 4396 3.923017 AAAGCAGCATTCCAAGTACAC 57.077 42.857 0.00 0.00 0.00 2.90
4209 4397 5.009631 ACATAAAGCAGCATTCCAAGTACA 58.990 37.500 0.00 0.00 0.00 2.90
4222 4410 6.430451 AGACTTTGAACGAAACATAAAGCAG 58.570 36.000 0.00 0.00 32.97 4.24
4223 4411 6.371809 AGACTTTGAACGAAACATAAAGCA 57.628 33.333 0.00 0.00 32.97 3.91
4228 4416 9.653287 AAGATCATAGACTTTGAACGAAACATA 57.347 29.630 0.00 0.00 0.00 2.29
4229 4417 8.446273 CAAGATCATAGACTTTGAACGAAACAT 58.554 33.333 0.00 0.00 0.00 2.71
4230 4418 7.571244 GCAAGATCATAGACTTTGAACGAAACA 60.571 37.037 0.00 0.00 0.00 2.83
4235 4423 4.780324 GCGCAAGATCATAGACTTTGAACG 60.780 45.833 0.30 1.81 43.02 3.95
4246 4434 3.541996 TCAGGAAAGCGCAAGATCATA 57.458 42.857 11.47 0.00 43.02 2.15
4247 4435 2.408271 TCAGGAAAGCGCAAGATCAT 57.592 45.000 11.47 0.00 43.02 2.45
4248 4436 2.011947 CATCAGGAAAGCGCAAGATCA 58.988 47.619 11.47 0.00 43.02 2.92
4252 4440 0.877071 ACACATCAGGAAAGCGCAAG 59.123 50.000 11.47 0.00 43.44 4.01
4261 4449 4.097551 TGAACCAAATCACACATCAGGA 57.902 40.909 0.00 0.00 0.00 3.86
4262 4450 4.219070 ACATGAACCAAATCACACATCAGG 59.781 41.667 0.00 0.00 30.82 3.86
4265 4453 3.922240 GCACATGAACCAAATCACACATC 59.078 43.478 0.00 0.00 30.82 3.06
4269 4457 2.288334 GCAGCACATGAACCAAATCACA 60.288 45.455 0.00 0.00 30.82 3.58
4270 4458 2.288334 TGCAGCACATGAACCAAATCAC 60.288 45.455 0.00 0.00 30.82 3.06
4271 4459 1.962100 TGCAGCACATGAACCAAATCA 59.038 42.857 0.00 0.00 0.00 2.57
4272 4460 2.602878 CTGCAGCACATGAACCAAATC 58.397 47.619 0.00 0.00 0.00 2.17
4273 4461 1.274167 CCTGCAGCACATGAACCAAAT 59.726 47.619 8.66 0.00 0.00 2.32
4274 4462 0.675083 CCTGCAGCACATGAACCAAA 59.325 50.000 8.66 0.00 0.00 3.28
4275 4463 1.180456 CCCTGCAGCACATGAACCAA 61.180 55.000 8.66 0.00 0.00 3.67
4277 4465 0.895100 TTCCCTGCAGCACATGAACC 60.895 55.000 8.66 0.00 0.00 3.62
4278 4466 0.242017 GTTCCCTGCAGCACATGAAC 59.758 55.000 8.66 11.11 34.64 3.18
4279 4467 0.111061 AGTTCCCTGCAGCACATGAA 59.889 50.000 8.66 2.64 0.00 2.57
4280 4468 0.983467 TAGTTCCCTGCAGCACATGA 59.017 50.000 8.66 0.00 0.00 3.07
4281 4469 1.089920 GTAGTTCCCTGCAGCACATG 58.910 55.000 8.66 0.00 0.00 3.21
4282 4470 0.035056 GGTAGTTCCCTGCAGCACAT 60.035 55.000 8.66 0.00 0.00 3.21
4285 4473 1.888436 CGAGGTAGTTCCCTGCAGCA 61.888 60.000 8.66 0.00 34.03 4.41
4286 4474 1.153549 CGAGGTAGTTCCCTGCAGC 60.154 63.158 8.66 0.00 34.03 5.25
4287 4475 1.153549 GCGAGGTAGTTCCCTGCAG 60.154 63.158 6.78 6.78 34.03 4.41
4306 4497 2.190578 GGGATGTGCTCCTTCGGG 59.809 66.667 0.00 0.00 44.28 5.14
4307 4498 1.144936 GAGGGATGTGCTCCTTCGG 59.855 63.158 0.00 0.00 44.28 4.30
4309 4500 1.522580 GCGAGGGATGTGCTCCTTC 60.523 63.158 0.00 0.00 44.74 3.46
4440 4631 2.240162 CTCCGGTTGGTGGGCTCTAC 62.240 65.000 0.00 0.00 36.30 2.59
4599 4790 2.951475 GATTATTGTGGCGGGCGGGA 62.951 60.000 0.00 0.00 0.00 5.14
4606 4797 1.648720 CCGCTGGATTATTGTGGCG 59.351 57.895 0.00 0.00 41.84 5.69
4641 4893 3.961838 ATAAACTTGGCGGCGGCGA 62.962 57.895 36.87 25.58 41.24 5.54
4645 4897 0.373716 GAGACATAAACTTGGCGGCG 59.626 55.000 0.51 0.51 0.00 6.46
4658 4910 3.914312 ACACGAACGATGAAAGAGACAT 58.086 40.909 0.14 0.00 0.00 3.06
4669 4923 4.804608 TTTCAATCACAACACGAACGAT 57.195 36.364 0.14 0.00 0.00 3.73
4671 4925 6.961358 TTATTTTCAATCACAACACGAACG 57.039 33.333 0.00 0.00 0.00 3.95
4685 4939 3.257127 CGGGGACTGGCTTTTATTTTCAA 59.743 43.478 0.00 0.00 0.00 2.69
4710 4967 4.544689 CTCCGAGCAGACGCGAGG 62.545 72.222 15.93 1.96 45.49 4.63
4711 4968 4.544689 CCTCCGAGCAGACGCGAG 62.545 72.222 15.93 2.87 45.49 5.03
4716 4973 4.803426 CACCGCCTCCGAGCAGAC 62.803 72.222 0.00 0.00 36.29 3.51
4726 4983 3.846405 TTGAGTCTCCCCACCGCCT 62.846 63.158 0.00 0.00 0.00 5.52
4728 4985 2.232298 CTCTTGAGTCTCCCCACCGC 62.232 65.000 0.00 0.00 0.00 5.68
4732 4998 2.808919 CAGTACTCTTGAGTCTCCCCA 58.191 52.381 6.55 0.00 0.00 4.96
4740 5006 2.440539 AACACGGCAGTACTCTTGAG 57.559 50.000 0.00 0.00 0.00 3.02
4742 5008 1.798813 GGAAACACGGCAGTACTCTTG 59.201 52.381 0.00 0.00 0.00 3.02
4750 5016 1.659794 CCCAAAGGAAACACGGCAG 59.340 57.895 0.00 0.00 33.47 4.85
4754 5020 1.599419 CGAAAGCCCAAAGGAAACACG 60.599 52.381 0.00 0.00 33.47 4.49
4756 5022 1.953686 CTCGAAAGCCCAAAGGAAACA 59.046 47.619 0.00 0.00 33.47 2.83
4778 5044 8.992073 CATATAATCATCATCCACGTTTCTCAA 58.008 33.333 0.00 0.00 0.00 3.02
4780 5046 7.332926 AGCATATAATCATCATCCACGTTTCTC 59.667 37.037 0.00 0.00 0.00 2.87
4799 5065 5.799435 CGCACACAAATCACAAAAGCATATA 59.201 36.000 0.00 0.00 0.00 0.86
4800 5066 4.622313 CGCACACAAATCACAAAAGCATAT 59.378 37.500 0.00 0.00 0.00 1.78
4801 5067 3.980134 CGCACACAAATCACAAAAGCATA 59.020 39.130 0.00 0.00 0.00 3.14
4802 5068 2.796031 CGCACACAAATCACAAAAGCAT 59.204 40.909 0.00 0.00 0.00 3.79
4803 5069 2.159324 TCGCACACAAATCACAAAAGCA 60.159 40.909 0.00 0.00 0.00 3.91
4804 5070 2.458951 TCGCACACAAATCACAAAAGC 58.541 42.857 0.00 0.00 0.00 3.51
4805 5071 3.242712 GGTTCGCACACAAATCACAAAAG 59.757 43.478 0.00 0.00 0.00 2.27
4806 5072 3.182967 GGTTCGCACACAAATCACAAAA 58.817 40.909 0.00 0.00 0.00 2.44
4844 5115 5.617751 GCTCCACACACAAAGTCACATAATC 60.618 44.000 0.00 0.00 0.00 1.75
4845 5116 4.216257 GCTCCACACACAAAGTCACATAAT 59.784 41.667 0.00 0.00 0.00 1.28
4870 5141 5.185249 ACAAGTATAACCACGAGACATCAGT 59.815 40.000 0.00 0.00 0.00 3.41
4878 5149 5.351465 AGCAATCAACAAGTATAACCACGAG 59.649 40.000 0.00 0.00 0.00 4.18
4885 5156 5.580691 CGACCAGAGCAATCAACAAGTATAA 59.419 40.000 0.00 0.00 0.00 0.98
4888 5159 3.244078 ACGACCAGAGCAATCAACAAGTA 60.244 43.478 0.00 0.00 0.00 2.24
4900 5171 1.667724 CAATGGATCAACGACCAGAGC 59.332 52.381 0.00 0.00 39.62 4.09
4903 5176 2.093500 TCTCCAATGGATCAACGACCAG 60.093 50.000 0.87 0.00 39.62 4.00
4920 5193 1.135460 GTGAGCAAGCAAAGCATCTCC 60.135 52.381 0.00 0.00 0.00 3.71
4922 5195 1.612676 TGTGAGCAAGCAAAGCATCT 58.387 45.000 0.00 0.00 0.00 2.90
4970 5250 3.057526 GGGAGTAAACAAACATCACCAGC 60.058 47.826 0.00 0.00 0.00 4.85
4983 5263 4.403752 AGAGTAATACCCACGGGAGTAAAC 59.596 45.833 9.72 0.51 44.67 2.01
4992 5312 6.429078 TGCTACTACATAGAGTAATACCCACG 59.571 42.308 0.00 0.00 31.57 4.94
5031 5356 1.953138 CGCGATCCATGACAGCTCC 60.953 63.158 0.00 0.00 0.00 4.70
5065 5390 3.680937 CCGGTACTCGCAACTGAAATAAA 59.319 43.478 0.00 0.00 37.59 1.40
5068 5393 1.722011 CCGGTACTCGCAACTGAAAT 58.278 50.000 0.00 0.00 37.59 2.17
5099 5442 5.776716 ACAGAAACAGAAACCAATCCATCAT 59.223 36.000 0.00 0.00 0.00 2.45
5110 5453 1.021968 ACGCCCACAGAAACAGAAAC 58.978 50.000 0.00 0.00 0.00 2.78
5118 5461 0.687920 TGACCATAACGCCCACAGAA 59.312 50.000 0.00 0.00 0.00 3.02
5119 5462 0.249120 CTGACCATAACGCCCACAGA 59.751 55.000 0.00 0.00 0.00 3.41
5120 5463 0.249120 TCTGACCATAACGCCCACAG 59.751 55.000 0.00 0.00 0.00 3.66
5121 5464 0.036765 GTCTGACCATAACGCCCACA 60.037 55.000 0.00 0.00 0.00 4.17
5122 5465 0.743345 GGTCTGACCATAACGCCCAC 60.743 60.000 21.70 0.00 38.42 4.61
5123 5466 1.600107 GGTCTGACCATAACGCCCA 59.400 57.895 21.70 0.00 38.42 5.36
5137 5480 3.740128 GATGATGCCCACGCGGTCT 62.740 63.158 12.47 0.00 38.08 3.85
5151 5494 7.868906 AACATTACACACATGATGATGATGA 57.131 32.000 0.00 0.00 33.36 2.92
5152 5495 8.185505 TCAAACATTACACACATGATGATGATG 58.814 33.333 0.00 0.00 33.36 3.07
5153 5496 8.186163 GTCAAACATTACACACATGATGATGAT 58.814 33.333 0.00 0.00 33.36 2.45
5154 5497 7.391275 AGTCAAACATTACACACATGATGATGA 59.609 33.333 0.00 0.05 33.36 2.92
5155 5498 7.532571 AGTCAAACATTACACACATGATGATG 58.467 34.615 0.00 0.00 35.49 3.07
5156 5499 7.692460 AGTCAAACATTACACACATGATGAT 57.308 32.000 0.00 0.00 0.00 2.45
5157 5500 7.148656 CGTAGTCAAACATTACACACATGATGA 60.149 37.037 0.00 0.00 0.00 2.92
5158 5501 6.955407 CGTAGTCAAACATTACACACATGATG 59.045 38.462 0.00 0.00 0.00 3.07
5159 5502 6.649141 ACGTAGTCAAACATTACACACATGAT 59.351 34.615 0.00 0.00 29.74 2.45
5196 5539 7.672983 ACGTACTAGTACTAGTTTTACTGCA 57.327 36.000 34.30 15.58 43.35 4.41
5201 5544 9.003112 CGTACGTACGTACTAGTACTAGTTTTA 57.997 37.037 40.05 21.47 46.22 1.52
5203 5546 7.433873 CGTACGTACGTACTAGTACTAGTTT 57.566 40.000 40.05 22.62 46.22 2.66
5219 5562 2.262211 CCAAAAGGCCTACGTACGTAC 58.738 52.381 23.60 15.90 0.00 3.67
5220 5563 1.204467 CCCAAAAGGCCTACGTACGTA 59.796 52.381 25.41 25.41 0.00 3.57
5221 5564 0.037046 CCCAAAAGGCCTACGTACGT 60.037 55.000 25.98 25.98 0.00 3.57
5222 5565 0.247185 TCCCAAAAGGCCTACGTACG 59.753 55.000 15.01 15.01 34.51 3.67
5268 5611 2.091111 GGATGGATGGATGGAGGGTTTT 60.091 50.000 0.00 0.00 0.00 2.43
5273 5616 1.075050 CAAGGGATGGATGGATGGAGG 59.925 57.143 0.00 0.00 0.00 4.30
5274 5617 2.581216 CAAGGGATGGATGGATGGAG 57.419 55.000 0.00 0.00 0.00 3.86
5300 5649 0.745486 TGATCTGGTGAATGCAGGCG 60.745 55.000 0.00 0.00 0.00 5.52
5302 5651 2.286872 GTCTGATCTGGTGAATGCAGG 58.713 52.381 0.00 0.00 0.00 4.85
5303 5652 1.931841 CGTCTGATCTGGTGAATGCAG 59.068 52.381 0.00 0.00 0.00 4.41
5304 5653 1.405933 CCGTCTGATCTGGTGAATGCA 60.406 52.381 0.00 0.00 0.00 3.96
5306 5655 1.293924 GCCGTCTGATCTGGTGAATG 58.706 55.000 0.00 0.00 0.00 2.67
5308 5657 0.904865 AGGCCGTCTGATCTGGTGAA 60.905 55.000 0.00 0.00 0.00 3.18
5309 5658 1.305297 AGGCCGTCTGATCTGGTGA 60.305 57.895 0.00 0.00 0.00 4.02
5312 5661 1.440893 CTGAGGCCGTCTGATCTGG 59.559 63.158 0.00 0.00 0.00 3.86
5313 5662 1.227205 GCTGAGGCCGTCTGATCTG 60.227 63.158 0.00 0.00 0.00 2.90
5314 5663 3.215245 GCTGAGGCCGTCTGATCT 58.785 61.111 0.00 0.00 0.00 2.75
5332 5681 2.730094 AGCAACGCAGCTTTTGGG 59.270 55.556 5.91 0.00 43.70 4.12
5381 5744 1.978580 TCCCCTGGTCAAGAAGAAGAC 59.021 52.381 0.00 0.00 0.00 3.01
5399 5763 1.359459 GGAGGCACGACGATGTTTCC 61.359 60.000 0.00 4.59 0.00 3.13
5412 5776 2.672651 CAATGCACACGGGAGGCA 60.673 61.111 10.88 10.88 42.43 4.75
5413 5777 1.805428 AAACAATGCACACGGGAGGC 61.805 55.000 0.00 0.00 0.00 4.70
5414 5778 1.199097 GTAAACAATGCACACGGGAGG 59.801 52.381 0.00 0.00 0.00 4.30
5415 5779 1.876799 TGTAAACAATGCACACGGGAG 59.123 47.619 0.00 0.00 0.00 4.30
5426 5790 3.071479 CACGCAGGGTAGTGTAAACAAT 58.929 45.455 0.00 0.00 33.97 2.71
5432 5796 1.589630 CAGCACGCAGGGTAGTGTA 59.410 57.895 0.00 0.00 40.26 2.90
5452 5816 6.042552 TGGAAAAGAATAAAAATGACCCAGCA 59.957 34.615 0.00 0.00 0.00 4.41
5453 5817 6.463360 TGGAAAAGAATAAAAATGACCCAGC 58.537 36.000 0.00 0.00 0.00 4.85
5454 5818 6.591448 GCTGGAAAAGAATAAAAATGACCCAG 59.409 38.462 0.00 0.00 39.26 4.45
5455 5819 6.269769 AGCTGGAAAAGAATAAAAATGACCCA 59.730 34.615 0.00 0.00 0.00 4.51
5456 5820 6.701340 AGCTGGAAAAGAATAAAAATGACCC 58.299 36.000 0.00 0.00 0.00 4.46
5457 5821 8.498358 CAAAGCTGGAAAAGAATAAAAATGACC 58.502 33.333 0.00 0.00 0.00 4.02
5465 5829 7.537596 TGGATTCAAAGCTGGAAAAGAATAA 57.462 32.000 5.30 0.00 0.00 1.40
5500 5864 3.630892 TGCAAATTATTTGGCATGCCT 57.369 38.095 35.53 19.66 40.94 4.75
5539 5906 8.259049 TGGTCTAAAGATTTTTGTATGTACCG 57.741 34.615 0.00 0.00 0.00 4.02
5560 5927 1.235281 GGCAAGACCCGTCTTTGGTC 61.235 60.000 7.37 1.17 46.95 4.02


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

AutoCloner maintained by Alex Coulton.