Multiple sequence alignment - TraesCS1B01G132900

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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 TraesCS1B01G132900 chr1B 100.000 4016 0 0 768 4783 167931012 167935027 0.000000e+00 7417.0
1 TraesCS1B01G132900 chr1B 100.000 297 0 0 1 297 167930245 167930541 2.520000e-152 549.0
2 TraesCS1B01G132900 chr1B 99.000 100 0 1 4685 4783 55408793 55408694 1.370000e-40 178.0
3 TraesCS1B01G132900 chr1B 99.000 100 0 1 4685 4783 55423422 55423323 1.370000e-40 178.0
4 TraesCS1B01G132900 chr1B 98.958 96 1 0 4688 4783 435159432 435159337 6.360000e-39 172.0
5 TraesCS1B01G132900 chr1D 98.338 1985 25 2 875 2851 110496891 110498875 0.000000e+00 3476.0
6 TraesCS1B01G132900 chr1D 94.582 1329 42 6 2881 4201 110498871 110500177 0.000000e+00 2028.0
7 TraesCS1B01G132900 chr1D 95.531 179 7 1 120 297 110496142 110496320 7.830000e-73 285.0
8 TraesCS1B01G132900 chr1D 85.784 204 22 3 4444 4644 110502402 110502601 4.850000e-50 209.0
9 TraesCS1B01G132900 chr1D 93.443 122 7 1 1 121 110496052 110496173 3.800000e-41 180.0
10 TraesCS1B01G132900 chr1A 96.335 1719 54 6 2485 4197 115361629 115363344 0.000000e+00 2817.0
11 TraesCS1B01G132900 chr1A 96.838 1423 36 7 777 2198 115358537 115359951 0.000000e+00 2370.0
12 TraesCS1B01G132900 chr1A 99.340 303 2 0 2191 2493 115360126 115360428 2.520000e-152 549.0
13 TraesCS1B01G132900 chr1A 90.268 298 13 6 1 297 115357692 115357974 4.520000e-100 375.0
14 TraesCS1B01G132900 chr1A 100.000 95 0 0 4689 4783 575249827 575249921 4.920000e-40 176.0
15 TraesCS1B01G132900 chr1A 100.000 95 0 0 4689 4783 575253132 575253226 4.920000e-40 176.0
16 TraesCS1B01G132900 chr2A 88.482 191 21 1 1501 1690 621588583 621588393 3.720000e-56 230.0
17 TraesCS1B01G132900 chr6D 80.682 264 41 3 1429 1690 284884854 284884599 3.780000e-46 196.0
18 TraesCS1B01G132900 chr3B 100.000 95 0 0 4689 4783 746268428 746268334 4.920000e-40 176.0
19 TraesCS1B01G132900 chr2B 95.495 111 3 2 4673 4783 45519352 45519460 4.920000e-40 176.0
20 TraesCS1B01G132900 chr2B 100.000 95 0 0 4689 4783 637937308 637937402 4.920000e-40 176.0
21 TraesCS1B01G132900 chr2B 92.920 113 5 2 4671 4783 106974116 106974007 1.380000e-35 161.0
22 TraesCS1B01G132900 chr5B 92.857 42 3 0 3340 3381 36740961 36740920 1.440000e-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 TraesCS1B01G132900 chr1B 167930245 167935027 4782 False 3983.00 7417 100.00000 1 4783 2 chr1B.!!$F1 4782
1 TraesCS1B01G132900 chr1D 110496052 110502601 6549 False 1235.60 3476 93.53560 1 4644 5 chr1D.!!$F1 4643
2 TraesCS1B01G132900 chr1A 115357692 115363344 5652 False 1527.75 2817 95.69525 1 4197 4 chr1A.!!$F1 4196

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
107 109 3.041946 ACCCTCTCTCTCTCTCTCTCTC 58.958 54.545 0.00 0.00 0.00 3.20 F
844 931 3.304659 GCAGTGTCATACAACCCACAAAG 60.305 47.826 0.00 0.00 0.00 2.77 F
1353 1441 2.839486 TCCGAGCTGTCAAATTGTCT 57.161 45.000 0.00 0.00 0.00 3.41 F
2088 2176 1.216678 TGGTTCTGTTGGGTCCAATGT 59.783 47.619 5.66 0.00 38.28 2.71 F
2818 4309 1.399714 CAACATGATCTGGCAGGCAT 58.600 50.000 15.73 15.32 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1047 1135 0.532573 GCTCAACATCCTCGTCCTCA 59.467 55.000 0.00 0.00 0.00 3.86 R
1992 2080 1.342819 CATCTTTCCCTCTAGGCCTCG 59.657 57.143 9.68 1.83 34.51 4.63 R
2526 4005 2.029290 GGTGAGCTAAGAACAGAACGGA 60.029 50.000 0.00 0.00 0.00 4.69 R
3539 5053 0.535335 ATCGTGACCACTTATGCCGT 59.465 50.000 0.00 0.00 0.00 5.68 R
4388 6167 0.179059 TGCTTCGTGAGTGCCAGAAA 60.179 50.000 0.00 0.00 0.00 2.52 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
81 83 4.680537 ACGGTGGTCGGAGCCTCT 62.681 66.667 4.54 0.00 44.45 3.69
102 104 3.145559 AGGTACCCTCTCTCTCTCTCT 57.854 52.381 8.74 0.00 0.00 3.10
103 105 3.046374 AGGTACCCTCTCTCTCTCTCTC 58.954 54.545 8.74 0.00 0.00 3.20
104 106 3.046374 GGTACCCTCTCTCTCTCTCTCT 58.954 54.545 0.00 0.00 0.00 3.10
105 107 3.071167 GGTACCCTCTCTCTCTCTCTCTC 59.929 56.522 0.00 0.00 0.00 3.20
106 108 3.136641 ACCCTCTCTCTCTCTCTCTCT 57.863 52.381 0.00 0.00 0.00 3.10
107 109 3.041946 ACCCTCTCTCTCTCTCTCTCTC 58.958 54.545 0.00 0.00 0.00 3.20
108 110 3.310954 ACCCTCTCTCTCTCTCTCTCTCT 60.311 52.174 0.00 0.00 0.00 3.10
109 111 3.323403 CCCTCTCTCTCTCTCTCTCTCTC 59.677 56.522 0.00 0.00 0.00 3.20
110 112 4.222336 CCTCTCTCTCTCTCTCTCTCTCT 58.778 52.174 0.00 0.00 0.00 3.10
111 113 4.280677 CCTCTCTCTCTCTCTCTCTCTCTC 59.719 54.167 0.00 0.00 0.00 3.20
112 114 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
113 115 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
114 116 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
115 117 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
116 118 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
117 119 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
122 124 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
126 128 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
130 132 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
134 136 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
138 140 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
142 144 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
829 916 5.634896 CCTTTGAATGACTATTGCAGTGTC 58.365 41.667 8.31 8.31 37.72 3.67
835 922 6.878389 TGAATGACTATTGCAGTGTCATACAA 59.122 34.615 22.49 13.32 46.67 2.41
844 931 3.304659 GCAGTGTCATACAACCCACAAAG 60.305 47.826 0.00 0.00 0.00 2.77
927 1015 4.712476 CCATCTATTTTGAGGTCCTGAGG 58.288 47.826 0.00 0.00 0.00 3.86
1047 1135 4.235762 ACAGGTGGCAGCGACGTT 62.236 61.111 11.51 0.00 0.00 3.99
1353 1441 2.839486 TCCGAGCTGTCAAATTGTCT 57.161 45.000 0.00 0.00 0.00 3.41
1440 1528 5.744007 GCTCATCCATCTGATTGATACCACA 60.744 44.000 4.13 0.00 33.36 4.17
1697 1785 3.385384 TCTGCAGGAGGTGAGGCG 61.385 66.667 15.13 0.00 0.00 5.52
1992 2080 6.810182 ACAATGCATATTTTCAGTTTGAGAGC 59.190 34.615 0.00 0.00 0.00 4.09
2088 2176 1.216678 TGGTTCTGTTGGGTCCAATGT 59.783 47.619 5.66 0.00 38.28 2.71
2526 4005 7.575720 GCACAGTACTTCCTGCAATTTTCTATT 60.576 37.037 10.70 0.00 35.83 1.73
2641 4120 8.834749 TTGTAATATGTTGTGTTAGCTGTGTA 57.165 30.769 0.00 0.00 0.00 2.90
2818 4309 1.399714 CAACATGATCTGGCAGGCAT 58.600 50.000 15.73 15.32 0.00 4.40
2967 4458 8.145767 TGTGAAAGAGAAAATCAGCATTGAAAT 58.854 29.630 0.00 0.00 36.78 2.17
3001 4492 4.550669 TGCTCTCTCCCATCTTATCTTGA 58.449 43.478 0.00 0.00 0.00 3.02
3002 4493 4.588106 TGCTCTCTCCCATCTTATCTTGAG 59.412 45.833 0.00 0.00 0.00 3.02
3003 4494 4.588528 GCTCTCTCCCATCTTATCTTGAGT 59.411 45.833 0.00 0.00 0.00 3.41
3004 4495 5.772672 GCTCTCTCCCATCTTATCTTGAGTA 59.227 44.000 0.00 0.00 0.00 2.59
3005 4496 6.437162 GCTCTCTCCCATCTTATCTTGAGTAT 59.563 42.308 0.00 0.00 0.00 2.12
3006 4497 7.613801 GCTCTCTCCCATCTTATCTTGAGTATA 59.386 40.741 0.00 0.00 0.00 1.47
3007 4498 9.699410 CTCTCTCCCATCTTATCTTGAGTATAT 57.301 37.037 0.00 0.00 0.00 0.86
3010 4501 9.828691 TCTCCCATCTTATCTTGAGTATATTCA 57.171 33.333 0.00 0.00 0.00 2.57
3061 4570 6.238759 GGATTCTCCCCAAATATTTCAGTTCG 60.239 42.308 0.00 0.00 0.00 3.95
3218 4727 7.352739 AGTACAAGAAAACTAGCATTTTCACG 58.647 34.615 16.56 11.03 46.57 4.35
3381 4892 9.638239 TGTTTTCTTCTAATACAAAATGATGCC 57.362 29.630 0.00 0.00 0.00 4.40
3440 4951 3.671008 TGACATAGCACCGTGTAGTTT 57.329 42.857 0.00 0.00 0.00 2.66
3539 5053 4.087182 TGGTGGGTAAATAATTTCCGCAA 58.913 39.130 0.00 0.00 0.00 4.85
3553 5067 1.423845 CGCAACGGCATAAGTGGTC 59.576 57.895 0.00 0.00 41.24 4.02
3554 5068 1.295357 CGCAACGGCATAAGTGGTCA 61.295 55.000 0.00 0.00 41.24 4.02
3688 5205 6.094881 GGCATGTTTAGTTTCTATAGGTGCAA 59.905 38.462 0.00 0.00 0.00 4.08
3773 5290 2.678934 TCCCGTTCCAGGACTCCG 60.679 66.667 0.00 0.00 0.00 4.63
3808 5325 2.008268 GAGTTTCATGGCCATGGCGG 62.008 60.000 38.81 21.12 43.06 6.13
3825 5342 3.126831 GGCGGTCATGTCATTCTCTAAG 58.873 50.000 0.00 0.00 0.00 2.18
3898 5415 5.045797 GGTTAAGGAGAAGTGGGTATTCAGT 60.046 44.000 0.00 0.00 0.00 3.41
3921 5438 5.010617 GTGCCATCTTTTTCCTTCAAGGTTA 59.989 40.000 2.50 0.00 36.53 2.85
3961 5478 0.237235 GACAAATCTTTGGCGTCGCA 59.763 50.000 20.50 2.14 42.34 5.10
4036 5553 1.887344 TACACATCAGCCGAGCAGCA 61.887 55.000 0.00 0.00 34.23 4.41
4053 5570 1.405105 AGCATTGCAACTTTGTCACGT 59.595 42.857 11.91 0.00 0.00 4.49
4107 5624 4.156008 GCCTCAGATTTGTTGTAATCGGTT 59.844 41.667 0.00 0.00 39.09 4.44
4167 5684 7.568349 TGATATCCAAAGCATCAGTTCTAGTT 58.432 34.615 0.00 0.00 0.00 2.24
4210 5743 7.388437 TGAGATTTTAATGCAAAAGCCTGATT 58.612 30.769 0.00 0.00 42.30 2.57
4216 5749 8.900983 TTTAATGCAAAAGCCTGATTTTTAGT 57.099 26.923 0.00 0.00 30.01 2.24
4222 5755 6.424812 GCAAAAGCCTGATTTTTAGTTGACAT 59.575 34.615 0.00 0.00 30.01 3.06
4245 5778 7.118390 ACATGAAATATAAGCATAGAAGCGACC 59.882 37.037 0.00 0.00 40.15 4.79
4247 5780 7.161404 TGAAATATAAGCATAGAAGCGACCAT 58.839 34.615 0.00 0.00 40.15 3.55
4248 5781 7.331934 TGAAATATAAGCATAGAAGCGACCATC 59.668 37.037 0.00 0.00 40.15 3.51
4251 5784 3.550437 AGCATAGAAGCGACCATCTTT 57.450 42.857 0.00 0.00 40.15 2.52
4254 5787 5.428253 AGCATAGAAGCGACCATCTTTTTA 58.572 37.500 0.00 0.00 40.15 1.52
4257 5790 7.171678 AGCATAGAAGCGACCATCTTTTTATAC 59.828 37.037 0.00 0.00 40.15 1.47
4258 5791 7.571428 GCATAGAAGCGACCATCTTTTTATACC 60.571 40.741 0.00 0.00 0.00 2.73
4259 5792 5.123936 AGAAGCGACCATCTTTTTATACCC 58.876 41.667 0.00 0.00 0.00 3.69
4260 5793 4.772886 AGCGACCATCTTTTTATACCCT 57.227 40.909 0.00 0.00 0.00 4.34
4261 5794 4.704965 AGCGACCATCTTTTTATACCCTC 58.295 43.478 0.00 0.00 0.00 4.30
4262 5795 4.163458 AGCGACCATCTTTTTATACCCTCA 59.837 41.667 0.00 0.00 0.00 3.86
4264 5797 5.007724 GCGACCATCTTTTTATACCCTCAAG 59.992 44.000 0.00 0.00 0.00 3.02
4265 5798 5.527582 CGACCATCTTTTTATACCCTCAAGG 59.472 44.000 0.00 0.00 43.78 3.61
4329 6031 2.124278 GGCGGACCCTCAAATCCC 60.124 66.667 0.00 0.00 0.00 3.85
4330 6032 2.124278 GCGGACCCTCAAATCCCC 60.124 66.667 0.00 0.00 0.00 4.81
4332 6034 1.224592 CGGACCCTCAAATCCCCAG 59.775 63.158 0.00 0.00 0.00 4.45
4333 6035 1.271840 CGGACCCTCAAATCCCCAGA 61.272 60.000 0.00 0.00 0.00 3.86
4334 6036 1.226311 GGACCCTCAAATCCCCAGAT 58.774 55.000 0.00 0.00 0.00 2.90
4336 6038 1.846439 GACCCTCAAATCCCCAGATCA 59.154 52.381 0.00 0.00 0.00 2.92
4337 6039 2.444766 GACCCTCAAATCCCCAGATCAT 59.555 50.000 0.00 0.00 0.00 2.45
4338 6040 2.861317 ACCCTCAAATCCCCAGATCATT 59.139 45.455 0.00 0.00 0.00 2.57
4341 6043 4.352001 CCCTCAAATCCCCAGATCATTCTA 59.648 45.833 0.00 0.00 0.00 2.10
4342 6044 5.514484 CCCTCAAATCCCCAGATCATTCTAG 60.514 48.000 0.00 0.00 0.00 2.43
4347 6126 7.895429 TCAAATCCCCAGATCATTCTAGTTTTT 59.105 33.333 0.00 0.00 0.00 1.94
4377 6156 4.400884 TCTGGAAAGCAGATCAGACTAGTC 59.599 45.833 15.41 15.41 32.10 2.59
4380 6159 4.867608 GGAAAGCAGATCAGACTAGTCAAC 59.132 45.833 24.44 11.96 0.00 3.18
4388 6167 5.421693 AGATCAGACTAGTCAACAAGAGCAT 59.578 40.000 24.44 0.00 0.00 3.79
4394 6173 4.999950 ACTAGTCAACAAGAGCATTTCTGG 59.000 41.667 0.00 0.00 35.91 3.86
4401 6180 1.818642 AGAGCATTTCTGGCACTCAC 58.181 50.000 3.76 0.00 33.93 3.51
4414 6193 1.466167 GCACTCACGAAGCATGATGTT 59.534 47.619 0.00 0.00 0.00 2.71
4416 6195 2.481568 CACTCACGAAGCATGATGTTGT 59.518 45.455 0.00 0.00 0.00 3.32
4417 6196 2.481568 ACTCACGAAGCATGATGTTGTG 59.518 45.455 0.00 0.02 0.00 3.33
4419 6198 2.738314 TCACGAAGCATGATGTTGTGAG 59.262 45.455 8.55 0.00 31.81 3.51
4420 6199 1.466167 ACGAAGCATGATGTTGTGAGC 59.534 47.619 0.00 0.00 0.00 4.26
4421 6200 1.202110 CGAAGCATGATGTTGTGAGCC 60.202 52.381 0.00 0.00 0.00 4.70
4422 6201 1.814394 GAAGCATGATGTTGTGAGCCA 59.186 47.619 0.00 0.00 0.00 4.75
4423 6202 1.460504 AGCATGATGTTGTGAGCCAG 58.539 50.000 0.00 0.00 0.00 4.85
4424 6203 1.003928 AGCATGATGTTGTGAGCCAGA 59.996 47.619 0.00 0.00 0.00 3.86
4425 6204 1.814394 GCATGATGTTGTGAGCCAGAA 59.186 47.619 0.00 0.00 0.00 3.02
4427 6206 3.829948 CATGATGTTGTGAGCCAGAAAC 58.170 45.455 0.00 0.00 0.00 2.78
4428 6207 1.872952 TGATGTTGTGAGCCAGAAACG 59.127 47.619 0.00 0.00 0.00 3.60
4430 6209 1.745232 TGTTGTGAGCCAGAAACGTT 58.255 45.000 0.00 0.00 0.00 3.99
4431 6210 2.088423 TGTTGTGAGCCAGAAACGTTT 58.912 42.857 14.57 14.57 0.00 3.60
4432 6211 2.159448 TGTTGTGAGCCAGAAACGTTTG 60.159 45.455 20.10 5.54 0.00 2.93
4433 6212 1.745232 TGTGAGCCAGAAACGTTTGT 58.255 45.000 20.10 12.30 0.00 2.83
4434 6213 2.088423 TGTGAGCCAGAAACGTTTGTT 58.912 42.857 20.10 1.67 40.98 2.83
4446 7945 4.712122 AACGTTTGTTTCATGGTGAAGT 57.288 36.364 0.00 0.00 37.70 3.01
4448 7947 3.181491 ACGTTTGTTTCATGGTGAAGTGG 60.181 43.478 0.00 0.00 37.70 4.00
4454 7953 3.755112 TTCATGGTGAAGTGGTTACGA 57.245 42.857 0.00 0.00 31.83 3.43
4463 7962 5.631096 GGTGAAGTGGTTACGAAACTAGTAC 59.369 44.000 0.00 0.00 35.81 2.73
4466 7965 5.635417 AGTGGTTACGAAACTAGTACTCC 57.365 43.478 0.00 0.00 35.81 3.85
4469 7968 6.266330 AGTGGTTACGAAACTAGTACTCCTTT 59.734 38.462 0.00 0.00 35.81 3.11
4470 7969 6.584184 GTGGTTACGAAACTAGTACTCCTTTC 59.416 42.308 0.00 6.87 35.81 2.62
4472 7971 7.147976 GGTTACGAAACTAGTACTCCTTTCAA 58.852 38.462 18.48 8.69 35.81 2.69
4473 7972 7.816513 GGTTACGAAACTAGTACTCCTTTCAAT 59.183 37.037 18.48 11.72 35.81 2.57
4474 7973 9.201127 GTTACGAAACTAGTACTCCTTTCAATT 57.799 33.333 18.48 9.31 32.54 2.32
4475 7974 7.886405 ACGAAACTAGTACTCCTTTCAATTC 57.114 36.000 18.48 6.86 0.00 2.17
4480 7979 2.993899 AGTACTCCTTTCAATTCACGCG 59.006 45.455 3.53 3.53 0.00 6.01
4488 7987 0.459585 TCAATTCACGCGGCCTCTAC 60.460 55.000 12.47 0.00 0.00 2.59
4494 7993 1.141881 ACGCGGCCTCTACAGAATG 59.858 57.895 12.47 0.00 46.00 2.67
4524 8023 8.972458 TTTTACATTGTATAATAGAGGCTGCA 57.028 30.769 0.50 0.00 0.00 4.41
4525 8024 7.962964 TTACATTGTATAATAGAGGCTGCAC 57.037 36.000 0.50 0.00 0.00 4.57
4584 8086 9.651913 TTTTTAGGAATTCATGTAAATCAAGCC 57.348 29.630 7.93 0.00 0.00 4.35
4589 8091 9.205513 AGGAATTCATGTAAATCAAGCCTTATT 57.794 29.630 7.93 0.00 0.00 1.40
4629 8131 9.722056 GTAGCAAATAACTTGTAATCTTCATGG 57.278 33.333 0.00 0.00 37.36 3.66
4631 8133 8.806146 AGCAAATAACTTGTAATCTTCATGGTT 58.194 29.630 0.00 0.00 37.36 3.67
4670 8172 3.624326 CGAAGGATGCTGTTTGTTTCA 57.376 42.857 0.00 0.00 0.00 2.69
4671 8173 3.963665 CGAAGGATGCTGTTTGTTTCAA 58.036 40.909 0.00 0.00 0.00 2.69
4672 8174 4.549458 CGAAGGATGCTGTTTGTTTCAAT 58.451 39.130 0.00 0.00 0.00 2.57
4673 8175 4.984161 CGAAGGATGCTGTTTGTTTCAATT 59.016 37.500 0.00 0.00 0.00 2.32
4674 8176 5.463061 CGAAGGATGCTGTTTGTTTCAATTT 59.537 36.000 0.00 0.00 0.00 1.82
4675 8177 6.018832 CGAAGGATGCTGTTTGTTTCAATTTT 60.019 34.615 0.00 0.00 0.00 1.82
4676 8178 6.607735 AGGATGCTGTTTGTTTCAATTTTG 57.392 33.333 0.00 0.00 0.00 2.44
4677 8179 5.528320 AGGATGCTGTTTGTTTCAATTTTGG 59.472 36.000 0.00 0.00 0.00 3.28
4678 8180 5.296531 GGATGCTGTTTGTTTCAATTTTGGT 59.703 36.000 0.00 0.00 0.00 3.67
4679 8181 6.183360 GGATGCTGTTTGTTTCAATTTTGGTT 60.183 34.615 0.00 0.00 0.00 3.67
4680 8182 6.566197 TGCTGTTTGTTTCAATTTTGGTTT 57.434 29.167 0.00 0.00 0.00 3.27
4681 8183 6.376978 TGCTGTTTGTTTCAATTTTGGTTTG 58.623 32.000 0.00 0.00 0.00 2.93
4682 8184 6.205464 TGCTGTTTGTTTCAATTTTGGTTTGA 59.795 30.769 0.00 0.00 0.00 2.69
4683 8185 7.094463 TGCTGTTTGTTTCAATTTTGGTTTGAT 60.094 29.630 0.00 0.00 33.37 2.57
4684 8186 7.754475 GCTGTTTGTTTCAATTTTGGTTTGATT 59.246 29.630 0.00 0.00 33.37 2.57
4685 8187 8.961294 TGTTTGTTTCAATTTTGGTTTGATTG 57.039 26.923 0.00 0.00 33.37 2.67
4686 8188 8.571336 TGTTTGTTTCAATTTTGGTTTGATTGT 58.429 25.926 0.00 0.00 33.37 2.71
4687 8189 9.404348 GTTTGTTTCAATTTTGGTTTGATTGTT 57.596 25.926 0.00 0.00 33.37 2.83
4688 8190 9.617975 TTTGTTTCAATTTTGGTTTGATTGTTC 57.382 25.926 0.00 0.00 33.37 3.18
4689 8191 8.558973 TGTTTCAATTTTGGTTTGATTGTTCT 57.441 26.923 0.00 0.00 33.37 3.01
4690 8192 8.449397 TGTTTCAATTTTGGTTTGATTGTTCTG 58.551 29.630 0.00 0.00 33.37 3.02
4691 8193 8.450180 GTTTCAATTTTGGTTTGATTGTTCTGT 58.550 29.630 0.00 0.00 33.37 3.41
4692 8194 8.558973 TTCAATTTTGGTTTGATTGTTCTGTT 57.441 26.923 0.00 0.00 33.37 3.16
4693 8195 7.972527 TCAATTTTGGTTTGATTGTTCTGTTG 58.027 30.769 0.00 0.00 33.60 3.33
4694 8196 6.923928 ATTTTGGTTTGATTGTTCTGTTGG 57.076 33.333 0.00 0.00 0.00 3.77
4695 8197 5.667539 TTTGGTTTGATTGTTCTGTTGGA 57.332 34.783 0.00 0.00 0.00 3.53
4696 8198 5.667539 TTGGTTTGATTGTTCTGTTGGAA 57.332 34.783 0.00 0.00 0.00 3.53
4697 8199 5.667539 TGGTTTGATTGTTCTGTTGGAAA 57.332 34.783 0.00 0.00 35.51 3.13
4698 8200 6.232581 TGGTTTGATTGTTCTGTTGGAAAT 57.767 33.333 0.00 0.00 35.51 2.17
4699 8201 7.353414 TGGTTTGATTGTTCTGTTGGAAATA 57.647 32.000 0.00 0.00 35.51 1.40
4700 8202 7.961351 TGGTTTGATTGTTCTGTTGGAAATAT 58.039 30.769 0.00 0.00 35.51 1.28
4701 8203 7.871973 TGGTTTGATTGTTCTGTTGGAAATATG 59.128 33.333 0.00 0.00 35.51 1.78
4702 8204 8.087750 GGTTTGATTGTTCTGTTGGAAATATGA 58.912 33.333 0.00 0.00 35.51 2.15
4703 8205 9.132521 GTTTGATTGTTCTGTTGGAAATATGAG 57.867 33.333 0.00 0.00 35.51 2.90
4704 8206 6.855836 TGATTGTTCTGTTGGAAATATGAGC 58.144 36.000 0.00 0.00 35.51 4.26
4705 8207 6.433716 TGATTGTTCTGTTGGAAATATGAGCA 59.566 34.615 0.00 0.00 35.51 4.26
4706 8208 6.647334 TTGTTCTGTTGGAAATATGAGCAA 57.353 33.333 0.00 0.00 35.51 3.91
4707 8209 6.839124 TGTTCTGTTGGAAATATGAGCAAT 57.161 33.333 0.00 0.00 35.51 3.56
4708 8210 7.230849 TGTTCTGTTGGAAATATGAGCAATT 57.769 32.000 0.00 0.00 35.51 2.32
4709 8211 7.669427 TGTTCTGTTGGAAATATGAGCAATTT 58.331 30.769 0.00 0.00 35.51 1.82
4710 8212 8.801299 TGTTCTGTTGGAAATATGAGCAATTTA 58.199 29.630 0.00 0.00 35.51 1.40
4711 8213 9.076596 GTTCTGTTGGAAATATGAGCAATTTAC 57.923 33.333 0.00 0.00 35.51 2.01
4712 8214 7.771183 TCTGTTGGAAATATGAGCAATTTACC 58.229 34.615 0.00 0.00 0.00 2.85
4713 8215 6.559810 TGTTGGAAATATGAGCAATTTACCG 58.440 36.000 0.00 0.00 0.00 4.02
4714 8216 6.375736 TGTTGGAAATATGAGCAATTTACCGA 59.624 34.615 0.00 0.00 0.00 4.69
4715 8217 7.094162 TGTTGGAAATATGAGCAATTTACCGAA 60.094 33.333 0.00 0.00 0.00 4.30
4716 8218 7.581213 TGGAAATATGAGCAATTTACCGAAT 57.419 32.000 0.00 0.00 0.00 3.34
4717 8219 7.424803 TGGAAATATGAGCAATTTACCGAATG 58.575 34.615 0.00 0.00 0.00 2.67
4718 8220 7.284261 TGGAAATATGAGCAATTTACCGAATGA 59.716 33.333 0.00 0.00 0.00 2.57
4719 8221 8.299570 GGAAATATGAGCAATTTACCGAATGAT 58.700 33.333 0.00 0.00 0.00 2.45
4720 8222 9.683069 GAAATATGAGCAATTTACCGAATGATT 57.317 29.630 0.00 0.00 0.00 2.57
4761 8263 9.521841 ACTAGATAAAGCATGACTAGTATAGCA 57.478 33.333 13.36 0.74 44.39 3.49
4763 8265 8.415950 AGATAAAGCATGACTAGTATAGCAGT 57.584 34.615 13.36 5.20 44.39 4.40
4764 8266 8.303156 AGATAAAGCATGACTAGTATAGCAGTG 58.697 37.037 13.36 0.00 44.39 3.66
4765 8267 6.471233 AAAGCATGACTAGTATAGCAGTGA 57.529 37.500 13.36 0.00 44.39 3.41
4766 8268 6.662865 AAGCATGACTAGTATAGCAGTGAT 57.337 37.500 13.36 0.00 44.39 3.06
4767 8269 7.767250 AAGCATGACTAGTATAGCAGTGATA 57.233 36.000 13.36 0.00 44.39 2.15
4768 8270 7.767250 AGCATGACTAGTATAGCAGTGATAA 57.233 36.000 13.36 0.00 44.39 1.75
4769 8271 8.183104 AGCATGACTAGTATAGCAGTGATAAA 57.817 34.615 13.36 0.00 44.39 1.40
4770 8272 8.642432 AGCATGACTAGTATAGCAGTGATAAAA 58.358 33.333 13.36 0.00 44.39 1.52
4771 8273 8.704234 GCATGACTAGTATAGCAGTGATAAAAC 58.296 37.037 0.00 0.00 44.39 2.43
4772 8274 9.750125 CATGACTAGTATAGCAGTGATAAAACA 57.250 33.333 0.00 0.00 44.39 2.83
4774 8276 9.803315 TGACTAGTATAGCAGTGATAAAACAAG 57.197 33.333 0.00 0.00 44.39 3.16
4775 8277 8.649973 ACTAGTATAGCAGTGATAAAACAAGC 57.350 34.615 0.00 0.00 44.39 4.01
4776 8278 6.927294 AGTATAGCAGTGATAAAACAAGCC 57.073 37.500 0.00 0.00 0.00 4.35
4777 8279 6.414732 AGTATAGCAGTGATAAAACAAGCCA 58.585 36.000 0.00 0.00 0.00 4.75
4778 8280 7.056635 AGTATAGCAGTGATAAAACAAGCCAT 58.943 34.615 0.00 0.00 0.00 4.40
4779 8281 4.445452 AGCAGTGATAAAACAAGCCATG 57.555 40.909 0.00 0.00 0.00 3.66
4780 8282 2.925563 GCAGTGATAAAACAAGCCATGC 59.074 45.455 0.00 0.00 0.00 4.06
4781 8283 3.173599 CAGTGATAAAACAAGCCATGCG 58.826 45.455 0.00 0.00 0.00 4.73
4782 8284 3.081061 AGTGATAAAACAAGCCATGCGA 58.919 40.909 0.00 0.00 0.00 5.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 104 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
103 105 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
104 106 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
105 107 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
106 108 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
107 109 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
108 110 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
109 111 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
110 112 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
111 113 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
112 114 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
113 115 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
114 116 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
115 117 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
116 118 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
117 119 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
122 124 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
126 128 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
130 132 3.386078 GCAGAGAGAGAGAGAGAGAGAGA 59.614 52.174 0.00 0.00 0.00 3.10
134 136 1.490490 GGGCAGAGAGAGAGAGAGAGA 59.510 57.143 0.00 0.00 0.00 3.10
138 140 0.329931 AACGGGCAGAGAGAGAGAGA 59.670 55.000 0.00 0.00 0.00 3.10
142 144 1.967535 CACAACGGGCAGAGAGAGA 59.032 57.895 0.00 0.00 0.00 3.10
767 770 7.692291 CGATTGCGATTTGTAGTTAATGAAACT 59.308 33.333 0.00 0.00 45.07 2.66
768 771 7.511506 GCGATTGCGATTTGTAGTTAATGAAAC 60.512 37.037 0.00 0.00 40.82 2.78
769 772 6.467682 GCGATTGCGATTTGTAGTTAATGAAA 59.532 34.615 0.00 0.00 40.82 2.69
770 773 5.963004 GCGATTGCGATTTGTAGTTAATGAA 59.037 36.000 0.00 0.00 40.82 2.57
771 774 5.498159 GCGATTGCGATTTGTAGTTAATGA 58.502 37.500 0.00 0.00 40.82 2.57
772 775 5.773637 GCGATTGCGATTTGTAGTTAATG 57.226 39.130 0.00 0.00 40.82 1.90
829 916 7.557719 AGGAATATTCTCTTTGTGGGTTGTATG 59.442 37.037 14.95 0.00 0.00 2.39
835 922 5.191722 TGCTAGGAATATTCTCTTTGTGGGT 59.808 40.000 14.95 0.00 0.00 4.51
844 931 6.287525 AGAAAGCACTGCTAGGAATATTCTC 58.712 40.000 14.95 5.73 38.25 2.87
927 1015 1.270550 CTGCATCAGGTGTTTGGTTCC 59.729 52.381 0.00 0.00 0.00 3.62
942 1030 0.402504 TCCCGGTTTAACACCTGCAT 59.597 50.000 0.00 0.00 44.69 3.96
1030 1118 4.235762 AACGTCGCTGCCACCTGT 62.236 61.111 0.00 0.00 0.00 4.00
1047 1135 0.532573 GCTCAACATCCTCGTCCTCA 59.467 55.000 0.00 0.00 0.00 3.86
1239 1327 3.965539 CTGCTTGTCGGCTCCCTGG 62.966 68.421 0.00 0.00 0.00 4.45
1353 1441 5.876357 AGAGCAACCACAAAATAGTCCTTA 58.124 37.500 0.00 0.00 0.00 2.69
1992 2080 1.342819 CATCTTTCCCTCTAGGCCTCG 59.657 57.143 9.68 1.83 34.51 4.63
2088 2176 8.741603 TTTCATGAAAGATAATGATGAGCTCA 57.258 30.769 20.79 20.79 38.53 4.26
2526 4005 2.029290 GGTGAGCTAAGAACAGAACGGA 60.029 50.000 0.00 0.00 0.00 4.69
2641 4120 3.586429 ACCAGTCCAAACAAATGGGAAT 58.414 40.909 0.00 0.00 41.05 3.01
2967 4458 6.065976 TGGGAGAGAGCAAAATATTCTCAA 57.934 37.500 4.59 0.00 39.79 3.02
3007 4498 8.772705 GGAAAAATTCAATGTGCATAAGTTGAA 58.227 29.630 12.70 12.70 42.61 2.69
3008 4499 7.930325 TGGAAAAATTCAATGTGCATAAGTTGA 59.070 29.630 0.00 0.00 0.00 3.18
3009 4500 8.085720 TGGAAAAATTCAATGTGCATAAGTTG 57.914 30.769 0.00 0.00 0.00 3.16
3010 4501 7.388500 CCTGGAAAAATTCAATGTGCATAAGTT 59.612 33.333 0.00 0.00 0.00 2.66
3011 4502 6.875195 CCTGGAAAAATTCAATGTGCATAAGT 59.125 34.615 0.00 0.00 0.00 2.24
3012 4503 6.314400 CCCTGGAAAAATTCAATGTGCATAAG 59.686 38.462 0.00 0.00 0.00 1.73
3013 4504 6.013898 TCCCTGGAAAAATTCAATGTGCATAA 60.014 34.615 0.00 0.00 0.00 1.90
3014 4505 5.483231 TCCCTGGAAAAATTCAATGTGCATA 59.517 36.000 0.00 0.00 0.00 3.14
3015 4506 4.286549 TCCCTGGAAAAATTCAATGTGCAT 59.713 37.500 0.00 0.00 0.00 3.96
3016 4507 3.645212 TCCCTGGAAAAATTCAATGTGCA 59.355 39.130 0.00 0.00 0.00 4.57
3017 4508 4.270245 TCCCTGGAAAAATTCAATGTGC 57.730 40.909 0.00 0.00 0.00 4.57
3018 4509 6.704310 AGAATCCCTGGAAAAATTCAATGTG 58.296 36.000 0.00 0.00 31.90 3.21
3061 4570 3.119352 GGAACTGAGCAAATGACCATTCC 60.119 47.826 0.00 0.00 0.00 3.01
3187 4696 6.281848 TGCTAGTTTTCTTGTACTTCGTTG 57.718 37.500 0.00 0.00 0.00 4.10
3218 4727 6.575162 AATCTCATTTGGTTACCAGTGTTC 57.425 37.500 3.65 0.00 33.81 3.18
3328 4839 4.220602 AGGTGGCATCAAATTGGTAGAAAC 59.779 41.667 0.00 0.00 0.00 2.78
3344 4855 3.565307 AGAAGAAAACATCAAGGTGGCA 58.435 40.909 0.00 0.00 0.00 4.92
3381 4892 2.030540 TCCAAGTAGAACGACTTCACGG 60.031 50.000 0.00 0.00 37.57 4.94
3491 5005 3.012518 ACCTAAATGAGATGCAGTGTGC 58.987 45.455 0.00 0.00 45.29 4.57
3492 5006 5.220739 GCTAACCTAAATGAGATGCAGTGTG 60.221 44.000 0.00 0.00 0.00 3.82
3493 5007 4.878397 GCTAACCTAAATGAGATGCAGTGT 59.122 41.667 0.00 0.00 0.00 3.55
3494 5008 5.007430 CAGCTAACCTAAATGAGATGCAGTG 59.993 44.000 0.00 0.00 0.00 3.66
3499 5013 4.818546 CCACCAGCTAACCTAAATGAGATG 59.181 45.833 0.00 0.00 0.00 2.90
3539 5053 0.535335 ATCGTGACCACTTATGCCGT 59.465 50.000 0.00 0.00 0.00 5.68
3553 5067 2.037641 TCATCAAGGCCCATCTATCGTG 59.962 50.000 0.00 0.00 0.00 4.35
3554 5068 2.037772 GTCATCAAGGCCCATCTATCGT 59.962 50.000 0.00 0.00 0.00 3.73
3688 5205 2.159382 CGCCATTTACAGGGTCAAAGT 58.841 47.619 0.00 0.00 0.00 2.66
3808 5325 9.239002 GTACATGTACTTAGAGAATGACATGAC 57.761 37.037 25.56 8.82 44.37 3.06
3898 5415 3.575805 ACCTTGAAGGAAAAAGATGGCA 58.424 40.909 19.83 0.00 37.67 4.92
3921 5438 3.766591 TCAACAAAAACACACATGGGACT 59.233 39.130 0.00 0.00 0.00 3.85
3961 5478 4.404640 AGGATTTGATCATCATCGGCAAT 58.595 39.130 0.00 0.00 0.00 3.56
4036 5553 4.142491 TGAAGAACGTGACAAAGTTGCAAT 60.142 37.500 0.59 0.00 0.00 3.56
4053 5570 5.012458 ACAGTCTGACCATCATCTTGAAGAA 59.988 40.000 6.91 0.00 0.00 2.52
4167 5684 3.625313 TCTCAGCAAATGTCGTGAAAACA 59.375 39.130 0.00 0.00 0.00 2.83
4216 5749 8.498358 CGCTTCTATGCTTATATTTCATGTCAA 58.502 33.333 0.00 0.00 0.00 3.18
4222 5755 6.521162 TGGTCGCTTCTATGCTTATATTTCA 58.479 36.000 0.00 0.00 0.00 2.69
4240 5773 4.448210 TGAGGGTATAAAAAGATGGTCGC 58.552 43.478 0.00 0.00 0.00 5.19
4245 5778 6.037172 CACGTCCTTGAGGGTATAAAAAGATG 59.963 42.308 0.00 0.00 36.25 2.90
4247 5780 5.012354 ACACGTCCTTGAGGGTATAAAAAGA 59.988 40.000 0.00 0.00 36.25 2.52
4248 5781 5.243207 ACACGTCCTTGAGGGTATAAAAAG 58.757 41.667 0.00 0.00 36.25 2.27
4251 5784 3.833650 TGACACGTCCTTGAGGGTATAAA 59.166 43.478 0.00 0.00 36.25 1.40
4254 5787 1.933021 TGACACGTCCTTGAGGGTAT 58.067 50.000 0.00 0.00 36.25 2.73
4257 5790 1.276421 AGATTGACACGTCCTTGAGGG 59.724 52.381 0.00 0.00 35.41 4.30
4258 5791 2.341257 CAGATTGACACGTCCTTGAGG 58.659 52.381 0.00 0.00 0.00 3.86
4259 5792 1.728971 GCAGATTGACACGTCCTTGAG 59.271 52.381 0.00 0.00 0.00 3.02
4260 5793 1.069978 TGCAGATTGACACGTCCTTGA 59.930 47.619 0.00 0.00 0.00 3.02
4261 5794 1.511850 TGCAGATTGACACGTCCTTG 58.488 50.000 0.00 0.00 0.00 3.61
4262 5795 1.873591 GTTGCAGATTGACACGTCCTT 59.126 47.619 0.00 0.00 0.00 3.36
4264 5797 1.225855 TGTTGCAGATTGACACGTCC 58.774 50.000 0.00 0.00 0.00 4.79
4265 5798 4.864916 ATATGTTGCAGATTGACACGTC 57.135 40.909 0.00 0.00 0.00 4.34
4295 5997 2.561569 CGCCTTTGGGATGTACTTAGG 58.438 52.381 0.00 0.00 33.58 2.69
4301 6003 1.605453 GGTCCGCCTTTGGGATGTA 59.395 57.895 0.00 0.00 35.67 2.29
4311 6013 2.680370 GGGATTTGAGGGTCCGCCT 61.680 63.158 0.00 0.00 35.28 5.52
4312 6014 2.124278 GGGATTTGAGGGTCCGCC 60.124 66.667 0.00 0.00 35.28 6.13
4313 6015 2.124278 GGGGATTTGAGGGTCCGC 60.124 66.667 0.00 0.00 39.76 5.54
4357 6136 4.727507 TGACTAGTCTGATCTGCTTTCC 57.272 45.455 23.01 0.00 0.00 3.13
4358 6137 5.473931 TGTTGACTAGTCTGATCTGCTTTC 58.526 41.667 23.01 0.00 0.00 2.62
4362 6141 5.065704 TCTTGTTGACTAGTCTGATCTGC 57.934 43.478 23.01 6.66 0.00 4.26
4367 6146 5.474578 AATGCTCTTGTTGACTAGTCTGA 57.525 39.130 23.01 9.63 0.00 3.27
4377 6156 2.295349 AGTGCCAGAAATGCTCTTGTTG 59.705 45.455 0.00 0.00 29.07 3.33
4380 6159 2.095364 GTGAGTGCCAGAAATGCTCTTG 60.095 50.000 0.00 0.00 33.10 3.02
4388 6167 0.179059 TGCTTCGTGAGTGCCAGAAA 60.179 50.000 0.00 0.00 0.00 2.52
4394 6173 1.081892 ACATCATGCTTCGTGAGTGC 58.918 50.000 0.00 0.00 32.64 4.40
4401 6180 1.202110 GGCTCACAACATCATGCTTCG 60.202 52.381 0.00 0.00 0.00 3.79
4414 6193 1.745232 ACAAACGTTTCTGGCTCACA 58.255 45.000 11.37 0.00 0.00 3.58
4416 6195 3.414549 GAAACAAACGTTTCTGGCTCA 57.585 42.857 11.37 0.00 45.80 4.26
4424 6203 4.862018 CACTTCACCATGAAACAAACGTTT 59.138 37.500 7.96 7.96 35.73 3.60
4425 6204 4.420168 CACTTCACCATGAAACAAACGTT 58.580 39.130 0.00 0.00 35.73 3.99
4427 6206 3.181491 ACCACTTCACCATGAAACAAACG 60.181 43.478 0.00 0.00 35.73 3.60
4428 6207 4.385358 ACCACTTCACCATGAAACAAAC 57.615 40.909 0.00 0.00 35.73 2.93
4430 6209 4.035792 CGTAACCACTTCACCATGAAACAA 59.964 41.667 0.00 0.00 35.73 2.83
4431 6210 3.562141 CGTAACCACTTCACCATGAAACA 59.438 43.478 0.00 0.00 35.73 2.83
4432 6211 3.810941 TCGTAACCACTTCACCATGAAAC 59.189 43.478 0.00 0.00 35.73 2.78
4433 6212 4.074627 TCGTAACCACTTCACCATGAAA 57.925 40.909 0.00 0.00 35.73 2.69
4434 6213 3.755112 TCGTAACCACTTCACCATGAA 57.245 42.857 0.00 0.00 34.79 2.57
4435 6214 3.755112 TTCGTAACCACTTCACCATGA 57.245 42.857 0.00 0.00 0.00 3.07
4436 6215 3.813166 AGTTTCGTAACCACTTCACCATG 59.187 43.478 0.85 0.00 34.71 3.66
4437 6216 4.081322 AGTTTCGTAACCACTTCACCAT 57.919 40.909 0.85 0.00 34.71 3.55
4438 6217 3.547054 AGTTTCGTAACCACTTCACCA 57.453 42.857 0.85 0.00 34.71 4.17
4439 6218 4.625028 ACTAGTTTCGTAACCACTTCACC 58.375 43.478 0.85 0.00 34.71 4.02
4440 6219 6.442112 AGTACTAGTTTCGTAACCACTTCAC 58.558 40.000 0.00 0.00 34.71 3.18
4441 6220 6.294176 GGAGTACTAGTTTCGTAACCACTTCA 60.294 42.308 0.00 0.00 34.71 3.02
4442 6221 6.072230 AGGAGTACTAGTTTCGTAACCACTTC 60.072 42.308 0.00 0.00 34.71 3.01
4446 7945 6.265196 TGAAAGGAGTACTAGTTTCGTAACCA 59.735 38.462 18.08 4.55 34.71 3.67
4448 7947 8.754230 ATTGAAAGGAGTACTAGTTTCGTAAC 57.246 34.615 18.08 0.00 32.58 2.50
4454 7953 6.147328 GCGTGAATTGAAAGGAGTACTAGTTT 59.853 38.462 0.00 0.00 0.00 2.66
4463 7962 0.179189 GCCGCGTGAATTGAAAGGAG 60.179 55.000 4.92 0.00 0.00 3.69
4466 7965 0.179189 GAGGCCGCGTGAATTGAAAG 60.179 55.000 4.92 0.00 0.00 2.62
4469 7968 0.459585 GTAGAGGCCGCGTGAATTGA 60.460 55.000 4.92 0.00 0.00 2.57
4470 7969 0.739462 TGTAGAGGCCGCGTGAATTG 60.739 55.000 4.92 0.00 0.00 2.32
4472 7971 1.141881 CTGTAGAGGCCGCGTGAAT 59.858 57.895 4.92 0.00 0.00 2.57
4473 7972 1.529152 TTCTGTAGAGGCCGCGTGAA 61.529 55.000 4.92 1.83 0.00 3.18
4474 7973 1.320344 ATTCTGTAGAGGCCGCGTGA 61.320 55.000 4.92 0.00 0.00 4.35
4475 7974 1.141881 ATTCTGTAGAGGCCGCGTG 59.858 57.895 4.92 0.00 0.00 5.34
4480 7979 3.567478 AATGGACATTCTGTAGAGGCC 57.433 47.619 0.00 0.00 0.00 5.19
4512 8011 6.380846 TCAAATTAATTGGTGCAGCCTCTATT 59.619 34.615 14.36 10.06 39.62 1.73
4513 8012 5.893255 TCAAATTAATTGGTGCAGCCTCTAT 59.107 36.000 14.36 0.00 39.62 1.98
4514 8013 5.260424 TCAAATTAATTGGTGCAGCCTCTA 58.740 37.500 14.36 0.00 39.62 2.43
4562 8061 9.866655 ATAAGGCTTGATTTACATGAATTCCTA 57.133 29.630 10.69 0.00 0.00 2.94
4563 8062 8.773033 ATAAGGCTTGATTTACATGAATTCCT 57.227 30.769 10.69 0.00 0.00 3.36
4644 8146 3.573967 ACAAACAGCATCCTTCGGATTTT 59.426 39.130 0.00 0.00 39.79 1.82
4645 8147 3.157087 ACAAACAGCATCCTTCGGATTT 58.843 40.909 0.00 0.00 39.79 2.17
4646 8148 2.795329 ACAAACAGCATCCTTCGGATT 58.205 42.857 0.00 0.00 39.79 3.01
4647 8149 2.496899 ACAAACAGCATCCTTCGGAT 57.503 45.000 0.00 0.00 44.21 4.18
4648 8150 2.270352 AACAAACAGCATCCTTCGGA 57.730 45.000 0.00 0.00 35.55 4.55
4649 8151 2.293122 TGAAACAAACAGCATCCTTCGG 59.707 45.455 0.00 0.00 0.00 4.30
4650 8152 3.624326 TGAAACAAACAGCATCCTTCG 57.376 42.857 0.00 0.00 0.00 3.79
4651 8153 6.849588 AAATTGAAACAAACAGCATCCTTC 57.150 33.333 0.00 0.00 0.00 3.46
4652 8154 6.038492 CCAAAATTGAAACAAACAGCATCCTT 59.962 34.615 0.00 0.00 0.00 3.36
4653 8155 5.528320 CCAAAATTGAAACAAACAGCATCCT 59.472 36.000 0.00 0.00 0.00 3.24
4654 8156 5.296531 ACCAAAATTGAAACAAACAGCATCC 59.703 36.000 0.00 0.00 0.00 3.51
4655 8157 6.362210 ACCAAAATTGAAACAAACAGCATC 57.638 33.333 0.00 0.00 0.00 3.91
4656 8158 6.756299 AACCAAAATTGAAACAAACAGCAT 57.244 29.167 0.00 0.00 0.00 3.79
4657 8159 6.205464 TCAAACCAAAATTGAAACAAACAGCA 59.795 30.769 0.00 0.00 34.04 4.41
4658 8160 6.606768 TCAAACCAAAATTGAAACAAACAGC 58.393 32.000 0.00 0.00 34.04 4.40
4659 8161 9.063739 CAATCAAACCAAAATTGAAACAAACAG 57.936 29.630 0.00 0.00 39.98 3.16
4660 8162 8.571336 ACAATCAAACCAAAATTGAAACAAACA 58.429 25.926 1.65 0.00 39.98 2.83
4661 8163 8.962857 ACAATCAAACCAAAATTGAAACAAAC 57.037 26.923 1.65 0.00 39.98 2.93
4662 8164 9.617975 GAACAATCAAACCAAAATTGAAACAAA 57.382 25.926 1.65 0.00 39.98 2.83
4663 8165 9.007901 AGAACAATCAAACCAAAATTGAAACAA 57.992 25.926 1.65 0.00 39.98 2.83
4664 8166 8.449397 CAGAACAATCAAACCAAAATTGAAACA 58.551 29.630 1.65 0.00 39.98 2.83
4665 8167 8.450180 ACAGAACAATCAAACCAAAATTGAAAC 58.550 29.630 1.65 0.00 39.98 2.78
4666 8168 8.558973 ACAGAACAATCAAACCAAAATTGAAA 57.441 26.923 1.65 0.00 39.98 2.69
4667 8169 8.449397 CAACAGAACAATCAAACCAAAATTGAA 58.551 29.630 1.65 0.00 39.98 2.69
4668 8170 7.065563 CCAACAGAACAATCAAACCAAAATTGA 59.934 33.333 1.65 0.00 40.76 2.57
4669 8171 7.065563 TCCAACAGAACAATCAAACCAAAATTG 59.934 33.333 0.00 0.00 36.64 2.32
4670 8172 7.108847 TCCAACAGAACAATCAAACCAAAATT 58.891 30.769 0.00 0.00 0.00 1.82
4671 8173 6.648192 TCCAACAGAACAATCAAACCAAAAT 58.352 32.000 0.00 0.00 0.00 1.82
4672 8174 6.042638 TCCAACAGAACAATCAAACCAAAA 57.957 33.333 0.00 0.00 0.00 2.44
4673 8175 5.667539 TCCAACAGAACAATCAAACCAAA 57.332 34.783 0.00 0.00 0.00 3.28
4674 8176 5.667539 TTCCAACAGAACAATCAAACCAA 57.332 34.783 0.00 0.00 0.00 3.67
4675 8177 5.667539 TTTCCAACAGAACAATCAAACCA 57.332 34.783 0.00 0.00 32.95 3.67
4676 8178 8.087750 TCATATTTCCAACAGAACAATCAAACC 58.912 33.333 0.00 0.00 32.95 3.27
4677 8179 9.132521 CTCATATTTCCAACAGAACAATCAAAC 57.867 33.333 0.00 0.00 32.95 2.93
4678 8180 7.814107 GCTCATATTTCCAACAGAACAATCAAA 59.186 33.333 0.00 0.00 32.95 2.69
4679 8181 7.039853 TGCTCATATTTCCAACAGAACAATCAA 60.040 33.333 0.00 0.00 32.95 2.57
4680 8182 6.433716 TGCTCATATTTCCAACAGAACAATCA 59.566 34.615 0.00 0.00 32.95 2.57
4681 8183 6.855836 TGCTCATATTTCCAACAGAACAATC 58.144 36.000 0.00 0.00 32.95 2.67
4682 8184 6.839124 TGCTCATATTTCCAACAGAACAAT 57.161 33.333 0.00 0.00 32.95 2.71
4683 8185 6.647334 TTGCTCATATTTCCAACAGAACAA 57.353 33.333 0.00 0.00 32.95 2.83
4684 8186 6.839124 ATTGCTCATATTTCCAACAGAACA 57.161 33.333 0.00 0.00 32.95 3.18
4685 8187 9.076596 GTAAATTGCTCATATTTCCAACAGAAC 57.923 33.333 0.00 0.00 32.95 3.01
4686 8188 8.250332 GGTAAATTGCTCATATTTCCAACAGAA 58.750 33.333 0.00 0.00 0.00 3.02
4687 8189 7.415095 CGGTAAATTGCTCATATTTCCAACAGA 60.415 37.037 0.00 0.00 0.00 3.41
4688 8190 6.692681 CGGTAAATTGCTCATATTTCCAACAG 59.307 38.462 0.00 0.00 0.00 3.16
4689 8191 6.375736 TCGGTAAATTGCTCATATTTCCAACA 59.624 34.615 0.00 0.00 0.00 3.33
4690 8192 6.791303 TCGGTAAATTGCTCATATTTCCAAC 58.209 36.000 0.00 0.00 0.00 3.77
4691 8193 7.397892 TTCGGTAAATTGCTCATATTTCCAA 57.602 32.000 0.00 0.00 0.00 3.53
4692 8194 7.284261 TCATTCGGTAAATTGCTCATATTTCCA 59.716 33.333 0.00 0.00 0.00 3.53
4693 8195 7.648142 TCATTCGGTAAATTGCTCATATTTCC 58.352 34.615 0.00 0.00 0.00 3.13
4694 8196 9.683069 AATCATTCGGTAAATTGCTCATATTTC 57.317 29.630 0.00 0.00 0.00 2.17
4735 8237 9.521841 TGCTATACTAGTCATGCTTTATCTAGT 57.478 33.333 0.00 0.00 42.25 2.57
4737 8239 9.521841 ACTGCTATACTAGTCATGCTTTATCTA 57.478 33.333 0.00 0.00 0.00 1.98
4738 8240 8.303156 CACTGCTATACTAGTCATGCTTTATCT 58.697 37.037 0.00 0.00 0.00 1.98
4739 8241 8.300286 TCACTGCTATACTAGTCATGCTTTATC 58.700 37.037 0.00 0.00 0.00 1.75
4740 8242 8.183104 TCACTGCTATACTAGTCATGCTTTAT 57.817 34.615 0.00 0.00 0.00 1.40
4741 8243 7.582667 TCACTGCTATACTAGTCATGCTTTA 57.417 36.000 0.00 0.00 0.00 1.85
4742 8244 6.471233 TCACTGCTATACTAGTCATGCTTT 57.529 37.500 0.00 0.00 0.00 3.51
4743 8245 6.662865 ATCACTGCTATACTAGTCATGCTT 57.337 37.500 0.00 0.00 0.00 3.91
4744 8246 7.767250 TTATCACTGCTATACTAGTCATGCT 57.233 36.000 0.00 0.00 0.00 3.79
4745 8247 8.704234 GTTTTATCACTGCTATACTAGTCATGC 58.296 37.037 0.00 2.68 0.00 4.06
4746 8248 9.750125 TGTTTTATCACTGCTATACTAGTCATG 57.250 33.333 0.00 0.00 0.00 3.07
4748 8250 9.803315 CTTGTTTTATCACTGCTATACTAGTCA 57.197 33.333 0.00 0.00 0.00 3.41
4749 8251 8.756864 GCTTGTTTTATCACTGCTATACTAGTC 58.243 37.037 0.00 0.00 0.00 2.59
4750 8252 7.711339 GGCTTGTTTTATCACTGCTATACTAGT 59.289 37.037 0.00 0.00 0.00 2.57
4751 8253 7.710907 TGGCTTGTTTTATCACTGCTATACTAG 59.289 37.037 0.00 0.00 0.00 2.57
4752 8254 7.561251 TGGCTTGTTTTATCACTGCTATACTA 58.439 34.615 0.00 0.00 0.00 1.82
4753 8255 6.414732 TGGCTTGTTTTATCACTGCTATACT 58.585 36.000 0.00 0.00 0.00 2.12
4754 8256 6.677781 TGGCTTGTTTTATCACTGCTATAC 57.322 37.500 0.00 0.00 0.00 1.47
4755 8257 6.238731 GCATGGCTTGTTTTATCACTGCTATA 60.239 38.462 2.12 0.00 0.00 1.31
4756 8258 5.450965 GCATGGCTTGTTTTATCACTGCTAT 60.451 40.000 2.12 0.00 0.00 2.97
4757 8259 4.142403 GCATGGCTTGTTTTATCACTGCTA 60.142 41.667 2.12 0.00 0.00 3.49
4758 8260 3.367703 GCATGGCTTGTTTTATCACTGCT 60.368 43.478 2.12 0.00 0.00 4.24
4759 8261 2.925563 GCATGGCTTGTTTTATCACTGC 59.074 45.455 2.12 0.00 0.00 4.40
4760 8262 3.119884 TCGCATGGCTTGTTTTATCACTG 60.120 43.478 2.12 0.00 0.00 3.66
4761 8263 3.081061 TCGCATGGCTTGTTTTATCACT 58.919 40.909 2.12 0.00 0.00 3.41
4762 8264 3.485947 TCGCATGGCTTGTTTTATCAC 57.514 42.857 2.12 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.