Multiple sequence alignment - TraesCS5D01G353500

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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 TraesCS5D01G353500 chr5D 100.000 6044 0 0 1 6044 435775363 435781406 0.000000e+00 11162.0
1 TraesCS5D01G353500 chr5B 94.885 2600 82 20 720 3306 529488466 529491027 0.000000e+00 4017.0
2 TraesCS5D01G353500 chr5B 90.954 2244 127 24 3297 5515 529491083 529493275 0.000000e+00 2950.0
3 TraesCS5D01G353500 chr5B 85.714 455 12 24 3 434 529487551 529487975 1.200000e-116 431.0
4 TraesCS5D01G353500 chr5B 91.975 162 13 0 5883 6044 529493599 529493760 1.690000e-55 228.0
5 TraesCS5D01G353500 chr5B 91.667 108 5 3 5728 5832 529493500 529493606 4.880000e-31 147.0
6 TraesCS5D01G353500 chr5B 100.000 30 0 0 688 717 529488448 529488477 8.460000e-04 56.5
7 TraesCS5D01G353500 chr5A 91.643 2872 132 42 560 3401 549573700 549576493 0.000000e+00 3875.0
8 TraesCS5D01G353500 chr5A 93.619 2241 123 12 3405 5643 549576618 549578840 0.000000e+00 3328.0
9 TraesCS5D01G353500 chr5A 84.929 564 30 30 24 548 549572922 549573469 2.500000e-143 520.0
10 TraesCS5D01G353500 chr5A 86.081 273 12 10 5744 6016 549578940 549579186 2.780000e-68 270.0


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 TraesCS5D01G353500 chr5D 435775363 435781406 6043 False 11162.000000 11162 100.0000 1 6044 1 chr5D.!!$F1 6043
1 TraesCS5D01G353500 chr5B 529487551 529493760 6209 False 1304.916667 4017 92.5325 3 6044 6 chr5B.!!$F1 6041
2 TraesCS5D01G353500 chr5A 549572922 549579186 6264 False 1998.250000 3875 89.0680 24 6016 4 chr5A.!!$F1 5992

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
859 1407 0.106469 TCTAGTCCAGATCTGCCGCT 60.106 55.0 17.76 15.29 0.0 5.52 F
861 1409 0.106469 TAGTCCAGATCTGCCGCTCT 60.106 55.0 17.76 11.61 0.0 4.09 F
2585 3138 0.036388 GGAGAACAGGTGCGGAATGA 60.036 55.0 0.00 0.00 0.0 2.57 F
3733 4478 0.398696 TGCCGCTCTCCCTTAAAACA 59.601 50.0 0.00 0.00 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2586 3139 0.308684 CAGCAACATGTTGACGTGCT 59.691 50.000 36.65 25.83 42.93 4.40 R
2587 3140 0.661187 CCAGCAACATGTTGACGTGC 60.661 55.000 36.65 24.10 42.93 5.34 R
4275 5023 1.002033 CGCATCAGCCTGGATAAAAGC 60.002 52.381 0.00 0.00 37.52 3.51 R
5305 6067 0.040646 TCCTTGCTCCTTCTCCGGTA 59.959 55.000 0.00 0.00 0.00 4.02 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
56 62 1.195448 CTCAACTGCGCCAGTACAAAG 59.805 52.381 4.18 0.00 44.62 2.77
132 139 4.832608 CCAAGGGTCCGCCGCTAC 62.833 72.222 0.00 0.00 34.81 3.58
205 221 6.923508 GCAAACAAACTTTGGAGCTAATTACT 59.076 34.615 6.47 0.00 34.12 2.24
206 222 7.096065 GCAAACAAACTTTGGAGCTAATTACTG 60.096 37.037 6.47 0.00 34.12 2.74
207 223 7.582667 AACAAACTTTGGAGCTAATTACTGT 57.417 32.000 6.47 0.00 34.12 3.55
208 224 8.685838 AACAAACTTTGGAGCTAATTACTGTA 57.314 30.769 6.47 0.00 34.12 2.74
209 225 8.095937 ACAAACTTTGGAGCTAATTACTGTAC 57.904 34.615 6.47 0.00 34.12 2.90
210 226 7.937394 ACAAACTTTGGAGCTAATTACTGTACT 59.063 33.333 6.47 0.00 34.12 2.73
230 250 1.529226 TACCTGGCAAACAATGGACG 58.471 50.000 0.00 0.00 0.00 4.79
369 401 3.498071 CCACCACCACCACCACCT 61.498 66.667 0.00 0.00 0.00 4.00
372 404 3.174987 CCACCACCACCACCTCCA 61.175 66.667 0.00 0.00 0.00 3.86
373 405 2.538141 CCACCACCACCACCTCCAT 61.538 63.158 0.00 0.00 0.00 3.41
401 458 2.113433 CCTCCTCACCGTCGTCGAT 61.113 63.158 2.98 0.00 39.71 3.59
414 471 5.231568 ACCGTCGTCGATATTTCATCTTTTC 59.768 40.000 2.98 0.00 39.71 2.29
416 473 6.345093 CCGTCGTCGATATTTCATCTTTTCTC 60.345 42.308 2.98 0.00 39.71 2.87
551 849 1.694169 CCTCCCACCACCATAGCCT 60.694 63.158 0.00 0.00 0.00 4.58
553 851 0.692419 CTCCCACCACCATAGCCTCT 60.692 60.000 0.00 0.00 0.00 3.69
591 1109 1.305381 CCCTTCCGTCCTCCACTCT 60.305 63.158 0.00 0.00 0.00 3.24
666 1192 4.166888 GCGGCTGCTCCATCAGGA 62.167 66.667 11.21 0.00 43.21 3.86
717 1243 2.125350 GAGGTTCAGGCTCAGGCG 60.125 66.667 0.00 0.00 39.81 5.52
718 1244 4.400961 AGGTTCAGGCTCAGGCGC 62.401 66.667 0.00 0.00 39.81 6.53
719 1245 4.400961 GGTTCAGGCTCAGGCGCT 62.401 66.667 7.64 0.00 39.81 5.92
720 1246 2.817396 GTTCAGGCTCAGGCGCTC 60.817 66.667 7.64 0.00 39.81 5.03
721 1247 3.313524 TTCAGGCTCAGGCGCTCA 61.314 61.111 7.64 0.00 39.81 4.26
722 1248 3.306595 TTCAGGCTCAGGCGCTCAG 62.307 63.158 7.64 1.45 39.81 3.35
723 1249 4.834453 CAGGCTCAGGCGCTCAGG 62.834 72.222 7.64 0.00 39.81 3.86
824 1350 2.750350 CAGTCCCCTCCACACCAC 59.250 66.667 0.00 0.00 0.00 4.16
833 1361 3.330720 CCACACCACCCTCCTCCC 61.331 72.222 0.00 0.00 0.00 4.30
834 1362 2.203998 CACACCACCCTCCTCCCT 60.204 66.667 0.00 0.00 0.00 4.20
845 1393 1.941820 TCCTCCCTGCCCCTCTAGT 60.942 63.158 0.00 0.00 0.00 2.57
855 1403 1.337118 CCCCTCTAGTCCAGATCTGC 58.663 60.000 17.76 4.68 31.13 4.26
856 1404 1.337118 CCCTCTAGTCCAGATCTGCC 58.663 60.000 17.76 9.65 31.13 4.85
857 1405 0.958091 CCTCTAGTCCAGATCTGCCG 59.042 60.000 17.76 4.89 31.13 5.69
858 1406 0.313672 CTCTAGTCCAGATCTGCCGC 59.686 60.000 17.76 8.98 31.13 6.53
859 1407 0.106469 TCTAGTCCAGATCTGCCGCT 60.106 55.000 17.76 15.29 0.00 5.52
860 1408 0.313672 CTAGTCCAGATCTGCCGCTC 59.686 60.000 17.76 5.18 0.00 5.03
861 1409 0.106469 TAGTCCAGATCTGCCGCTCT 60.106 55.000 17.76 11.61 0.00 4.09
862 1410 1.067250 GTCCAGATCTGCCGCTCTC 59.933 63.158 17.76 0.00 0.00 3.20
863 1411 1.076412 TCCAGATCTGCCGCTCTCT 60.076 57.895 17.76 0.00 0.00 3.10
864 1412 1.106351 TCCAGATCTGCCGCTCTCTC 61.106 60.000 17.76 0.00 0.00 3.20
865 1413 1.008652 CAGATCTGCCGCTCTCTCG 60.009 63.158 10.38 0.00 0.00 4.04
953 1506 1.564348 GCCTCTGACCAAAGGGGAATA 59.436 52.381 0.00 0.00 40.70 1.75
962 1515 5.773176 TGACCAAAGGGGAATAAAAAGACTC 59.227 40.000 0.00 0.00 41.15 3.36
972 1525 1.963172 AAAAAGACTCCCGCTTTCGT 58.037 45.000 0.00 0.00 34.68 3.85
975 1528 0.608640 AAGACTCCCGCTTTCGTGAT 59.391 50.000 0.00 0.00 0.00 3.06
982 1535 1.676014 CCCGCTTTCGTGATTCCTCTT 60.676 52.381 0.00 0.00 0.00 2.85
984 1537 1.321743 CGCTTTCGTGATTCCTCTTCG 59.678 52.381 0.00 0.00 0.00 3.79
986 1539 1.321743 CTTTCGTGATTCCTCTTCGCG 59.678 52.381 0.00 0.00 45.76 5.87
987 1540 1.076533 TTCGTGATTCCTCTTCGCGC 61.077 55.000 0.00 0.00 44.46 6.86
990 1543 2.962253 GATTCCTCTTCGCGCCGG 60.962 66.667 0.00 0.00 0.00 6.13
1043 1596 1.229209 AGGAGGAGAAGGCGGTGAA 60.229 57.895 0.00 0.00 0.00 3.18
1344 1897 2.189521 GTCCGCATCAACCCCGAT 59.810 61.111 0.00 0.00 0.00 4.18
1348 1901 2.180204 CGCATCAACCCCGATGACC 61.180 63.158 5.13 0.00 44.67 4.02
1709 2262 2.923035 ACCGCCACCTAGCAGTGT 60.923 61.111 0.00 0.00 35.93 3.55
1716 2269 2.906354 CCACCTAGCAGTGTTGGATAC 58.094 52.381 5.45 0.00 35.93 2.24
1932 2485 4.864334 CCGGAGGCCAGTGATGCC 62.864 72.222 5.01 2.36 46.14 4.40
2010 2563 3.925238 GCATACGAGCAACGCCCG 61.925 66.667 0.00 0.00 46.94 6.13
2400 2953 4.213564 AGTCAAGGAAGCTTATGGTGAG 57.786 45.455 0.00 0.00 0.00 3.51
2442 2995 1.304464 CACTGGGAAAGGGAAGGCC 60.304 63.158 0.00 0.00 0.00 5.19
2576 3129 1.068741 GAGTGTTGTCGGAGAACAGGT 59.931 52.381 19.59 10.99 39.69 4.00
2577 3130 1.202533 AGTGTTGTCGGAGAACAGGTG 60.203 52.381 19.59 0.00 39.69 4.00
2578 3131 0.531974 TGTTGTCGGAGAACAGGTGC 60.532 55.000 15.81 0.00 39.69 5.01
2579 3132 1.300620 TTGTCGGAGAACAGGTGCG 60.301 57.895 0.00 0.00 39.69 5.34
2580 3133 2.432628 GTCGGAGAACAGGTGCGG 60.433 66.667 0.00 0.00 39.69 5.69
2581 3134 2.599281 TCGGAGAACAGGTGCGGA 60.599 61.111 0.00 0.00 0.00 5.54
2582 3135 2.204461 TCGGAGAACAGGTGCGGAA 61.204 57.895 0.00 0.00 0.00 4.30
2583 3136 1.079127 CGGAGAACAGGTGCGGAAT 60.079 57.895 0.00 0.00 0.00 3.01
2584 3137 1.361668 CGGAGAACAGGTGCGGAATG 61.362 60.000 0.00 0.00 0.00 2.67
2585 3138 0.036388 GGAGAACAGGTGCGGAATGA 60.036 55.000 0.00 0.00 0.00 2.57
2586 3139 1.610624 GGAGAACAGGTGCGGAATGAA 60.611 52.381 0.00 0.00 0.00 2.57
2587 3140 1.734465 GAGAACAGGTGCGGAATGAAG 59.266 52.381 0.00 0.00 0.00 3.02
2807 3360 0.588252 CTGCTGTCAAACGGTTCTGG 59.412 55.000 0.00 0.00 0.00 3.86
2963 3516 0.534203 GTGGCAACCTTTCCTCGACA 60.534 55.000 0.00 0.00 0.00 4.35
3064 3617 1.728971 CTGAGGAACATTGTGAGTCGC 59.271 52.381 0.00 0.00 0.00 5.19
3069 3622 2.263077 GAACATTGTGAGTCGCGAGAT 58.737 47.619 10.24 0.00 45.19 2.75
3103 3656 3.698040 GGCAATGTGATTCCTCATGTTCT 59.302 43.478 0.00 0.00 32.98 3.01
3105 3658 4.397103 GCAATGTGATTCCTCATGTTCTCA 59.603 41.667 0.00 0.00 32.98 3.27
3116 3669 4.439700 CCTCATGTTCTCATTTCACATGCC 60.440 45.833 6.63 0.00 45.02 4.40
3118 3671 4.397103 TCATGTTCTCATTTCACATGCCTC 59.603 41.667 6.63 0.00 45.02 4.70
3136 3689 3.251972 GCCTCTGCATCCTAATTTAGTGC 59.748 47.826 10.55 10.55 37.47 4.40
3249 3802 5.945144 TTAAGGGGTAGCACTTACTTAGG 57.055 43.478 16.07 0.00 32.61 2.69
3280 3833 9.013490 GTTGTTGCAGCTAAAATTATGTATCAG 57.987 33.333 1.17 0.00 0.00 2.90
3408 4031 3.524095 TGAAATGATGTGGAAGTGGGT 57.476 42.857 0.00 0.00 0.00 4.51
3475 4220 4.336889 TCATTGGACTCAGTTTCTTCGT 57.663 40.909 0.00 0.00 0.00 3.85
3478 4223 4.659111 TTGGACTCAGTTTCTTCGTGTA 57.341 40.909 0.00 0.00 0.00 2.90
3574 4319 3.499918 AGGTGCAGAAACTGAAAAGATCG 59.500 43.478 2.81 0.00 32.44 3.69
3579 4324 4.722346 GCAGAAACTGAAAAGATCGTAGCG 60.722 45.833 2.81 0.00 32.44 4.26
3580 4325 3.927142 AGAAACTGAAAAGATCGTAGCGG 59.073 43.478 0.00 0.00 0.00 5.52
3606 4351 7.910683 GCTGAAAAGGAAATAAGGAAGTTATCG 59.089 37.037 0.00 0.00 30.39 2.92
3612 4357 7.848128 AGGAAATAAGGAAGTTATCGACAAGA 58.152 34.615 0.00 0.00 30.39 3.02
3717 4462 2.225467 GAGCTCATTCAAGGGTATGCC 58.775 52.381 9.40 0.00 0.00 4.40
3733 4478 0.398696 TGCCGCTCTCCCTTAAAACA 59.601 50.000 0.00 0.00 0.00 2.83
3734 4479 1.202830 TGCCGCTCTCCCTTAAAACAA 60.203 47.619 0.00 0.00 0.00 2.83
3735 4480 1.199327 GCCGCTCTCCCTTAAAACAAC 59.801 52.381 0.00 0.00 0.00 3.32
3850 4598 7.962918 ACTTGAGTATTTTCACATACGCAAATC 59.037 33.333 10.08 0.00 44.08 2.17
3900 4648 7.257722 GCACTACCTTGCAATATTGTTAATGT 58.742 34.615 16.61 15.37 42.49 2.71
3937 4685 4.397420 TGAGGCACACAATTAACAGTGAT 58.603 39.130 14.14 0.00 39.03 3.06
4066 4814 6.583806 CAGTCTTTTCCATTGCATGTTCTTAC 59.416 38.462 0.00 0.00 0.00 2.34
4081 4829 9.116067 GCATGTTCTTACCAGGTTATATGTTTA 57.884 33.333 0.00 0.00 0.00 2.01
4305 5053 1.228063 GCTGATGCGGATGTGGGAT 60.228 57.895 0.00 0.00 0.00 3.85
4611 5359 7.121168 CCGCCCATCTTTGTGATATGTAATAAT 59.879 37.037 0.00 0.00 33.36 1.28
4734 5482 0.106015 AAAGGCAGGGTATGATGGCC 60.106 55.000 0.00 0.00 42.61 5.36
4872 5620 0.531090 TGTCCGCACAGGTGTTACAC 60.531 55.000 6.99 6.99 41.99 2.90
4902 5650 1.372128 CCAAGCCGAAAACAGCAGC 60.372 57.895 0.00 0.00 0.00 5.25
4915 5663 4.756458 GCAGCCTGCAGTCGAGCT 62.756 66.667 12.82 11.22 44.26 4.09
5018 5766 2.178521 GAAAGCTCGAGTCGCCGA 59.821 61.111 15.13 0.00 37.03 5.54
5118 5866 3.425162 AGAAAACTGACCCTGGTGATC 57.575 47.619 0.00 0.00 0.00 2.92
5161 5910 2.892425 CCGTGGCTCGATTCTGGC 60.892 66.667 10.96 0.00 42.86 4.85
5186 5935 0.450983 GCTTTCAGCTGATGCACTCC 59.549 55.000 26.96 7.87 42.74 3.85
5241 6003 4.202295 GGCTCAGACATGATGATACCTCAA 60.202 45.833 0.00 0.00 34.37 3.02
5251 6013 6.065976 TGATGATACCTCAACCTTGTTGAT 57.934 37.500 9.85 0.04 34.37 2.57
5286 6048 0.623194 TTTGAGGATTGGATGGCCGA 59.377 50.000 0.00 0.00 36.79 5.54
5298 6060 1.003839 TGGCCGACCATCTGTTCAC 60.004 57.895 0.00 0.00 42.67 3.18
5299 6061 1.003839 GGCCGACCATCTGTTCACA 60.004 57.895 0.00 0.00 35.26 3.58
5300 6062 1.021390 GGCCGACCATCTGTTCACAG 61.021 60.000 0.02 0.02 39.63 3.66
5312 6074 1.548719 TGTTCACAGACCATACCGGAG 59.451 52.381 9.46 0.00 38.63 4.63
5313 6075 1.822990 GTTCACAGACCATACCGGAGA 59.177 52.381 9.46 0.00 38.63 3.71
5345 6115 4.023707 GGAAACTGTGGTGTGAATCAAGAG 60.024 45.833 0.00 0.00 0.00 2.85
5352 6122 2.354259 GTGTGAATCAAGAGGAGGCAG 58.646 52.381 0.00 0.00 0.00 4.85
5354 6124 2.027745 TGTGAATCAAGAGGAGGCAGTC 60.028 50.000 0.00 0.00 0.00 3.51
5355 6125 1.205655 TGAATCAAGAGGAGGCAGTCG 59.794 52.381 0.00 0.00 0.00 4.18
5389 6159 2.668550 TCAGCAGCACAGCAGCAG 60.669 61.111 9.01 0.96 43.44 4.24
5416 6186 2.019984 CCAATCCCTGAGCTAAGCAAC 58.980 52.381 0.00 0.00 0.00 4.17
5462 6232 2.110352 GGGGTTTCCATACACCGCG 61.110 63.158 0.00 0.00 36.39 6.46
5463 6233 2.757056 GGGTTTCCATACACCGCGC 61.757 63.158 0.00 0.00 33.34 6.86
5499 6269 2.715046 ACAAATCGATGGTCATGCTGT 58.285 42.857 0.00 0.00 0.00 4.40
5508 6278 1.364626 GGTCATGCTGTCAGGCTTCG 61.365 60.000 1.14 0.00 0.00 3.79
5513 6283 1.004440 GCTGTCAGGCTTCGGAACT 60.004 57.895 1.14 0.00 0.00 3.01
5514 6284 1.294659 GCTGTCAGGCTTCGGAACTG 61.295 60.000 1.14 2.78 0.00 3.16
5515 6285 0.671781 CTGTCAGGCTTCGGAACTGG 60.672 60.000 8.08 0.00 33.19 4.00
5518 6288 1.672356 CAGGCTTCGGAACTGGTGG 60.672 63.158 1.49 0.00 0.00 4.61
5546 6316 1.064611 AGAGCTGCATCCTGCTGAATT 60.065 47.619 2.49 0.00 44.92 2.17
5548 6318 0.527817 GCTGCATCCTGCTGAATTGC 60.528 55.000 9.77 0.00 45.31 3.56
5554 6324 2.180017 CTGCTGAATTGCCGGTGC 59.820 61.111 1.90 0.00 38.26 5.01
5565 6335 2.734723 CCGGTGCACAGACGAGTG 60.735 66.667 20.43 0.00 42.37 3.51
5566 6336 2.027605 CGGTGCACAGACGAGTGT 59.972 61.111 20.43 0.00 41.52 3.55
5580 6350 3.118454 GTGTCGGACATGGCGGTG 61.118 66.667 14.78 0.00 0.00 4.94
5598 6368 2.815647 CCTGAAGCGCCGAGGAAC 60.816 66.667 2.29 0.00 0.00 3.62
5667 6506 4.729856 GGCGCCGGTACTTGACGT 62.730 66.667 12.58 0.00 0.00 4.34
5719 6558 7.725818 CGTAGGATATATAGATGGCTAACGA 57.274 40.000 0.00 0.00 0.00 3.85
5720 6559 8.151141 CGTAGGATATATAGATGGCTAACGAA 57.849 38.462 0.00 0.00 0.00 3.85
5721 6560 8.784994 CGTAGGATATATAGATGGCTAACGAAT 58.215 37.037 0.00 0.00 0.00 3.34
5723 6562 7.877003 AGGATATATAGATGGCTAACGAATCG 58.123 38.462 0.00 0.00 0.00 3.34
5726 6565 0.249911 AGATGGCTAACGAATCGCCC 60.250 55.000 1.15 0.00 43.12 6.13
5727 6566 0.249911 GATGGCTAACGAATCGCCCT 60.250 55.000 1.15 0.00 43.12 5.19
5728 6567 0.532862 ATGGCTAACGAATCGCCCTG 60.533 55.000 1.15 0.00 43.12 4.45
5729 6568 1.887707 GGCTAACGAATCGCCCTGG 60.888 63.158 1.15 0.00 37.86 4.45
5730 6569 2.534903 GCTAACGAATCGCCCTGGC 61.535 63.158 1.15 0.00 37.85 4.85
5731 6570 1.144057 CTAACGAATCGCCCTGGCT 59.856 57.895 1.15 0.00 39.32 4.75
5732 6571 1.153449 TAACGAATCGCCCTGGCTG 60.153 57.895 1.15 0.24 39.32 4.85
5733 6572 1.895020 TAACGAATCGCCCTGGCTGT 61.895 55.000 1.15 0.00 39.32 4.40
5734 6573 2.436646 CGAATCGCCCTGGCTGTT 60.437 61.111 6.60 0.66 39.32 3.16
5735 6574 2.753966 CGAATCGCCCTGGCTGTTG 61.754 63.158 6.60 0.00 39.32 3.33
5736 6575 1.675641 GAATCGCCCTGGCTGTTGT 60.676 57.895 6.60 0.00 39.32 3.32
5737 6576 1.228552 AATCGCCCTGGCTGTTGTT 60.229 52.632 6.60 0.00 39.32 2.83
5738 6577 1.244019 AATCGCCCTGGCTGTTGTTC 61.244 55.000 6.60 0.00 39.32 3.18
5739 6578 2.410322 ATCGCCCTGGCTGTTGTTCA 62.410 55.000 6.60 0.00 39.32 3.18
5740 6579 2.908073 CGCCCTGGCTGTTGTTCAC 61.908 63.158 6.60 0.00 39.32 3.18
5741 6580 2.564721 GCCCTGGCTGTTGTTCACC 61.565 63.158 0.00 0.00 38.26 4.02
5814 6653 5.449107 AGATATGATTCAATTGGTGCAGC 57.551 39.130 9.47 9.47 0.00 5.25
5821 6660 0.390124 CAATTGGTGCAGCTGGTTGT 59.610 50.000 17.12 0.00 0.00 3.32
5822 6661 1.122227 AATTGGTGCAGCTGGTTGTT 58.878 45.000 17.12 0.36 0.00 2.83
5823 6662 1.122227 ATTGGTGCAGCTGGTTGTTT 58.878 45.000 17.12 0.00 0.00 2.83
5824 6663 0.175302 TTGGTGCAGCTGGTTGTTTG 59.825 50.000 17.12 0.00 0.00 2.93
5825 6664 0.969917 TGGTGCAGCTGGTTGTTTGT 60.970 50.000 17.12 0.00 0.00 2.83
5826 6665 0.175531 GGTGCAGCTGGTTGTTTGTT 59.824 50.000 17.12 0.00 0.00 2.83
5827 6666 1.405391 GGTGCAGCTGGTTGTTTGTTT 60.405 47.619 17.12 0.00 0.00 2.83
5828 6667 1.660104 GTGCAGCTGGTTGTTTGTTTG 59.340 47.619 17.12 0.00 0.00 2.93
5829 6668 1.274728 TGCAGCTGGTTGTTTGTTTGT 59.725 42.857 17.12 0.00 0.00 2.83
5856 6695 0.667993 TTTTGTGTACAGCTGCTGGC 59.332 50.000 31.00 22.93 42.19 4.85
5869 6708 3.074412 GCTGCTGGCTAACTGAACTTAA 58.926 45.455 0.00 0.00 38.06 1.85
5871 6710 4.319177 CTGCTGGCTAACTGAACTTAACT 58.681 43.478 0.00 0.00 0.00 2.24
5872 6711 4.065088 TGCTGGCTAACTGAACTTAACTG 58.935 43.478 0.00 0.00 0.00 3.16
5873 6712 4.202315 TGCTGGCTAACTGAACTTAACTGA 60.202 41.667 0.00 0.00 0.00 3.41
5874 6713 4.755123 GCTGGCTAACTGAACTTAACTGAA 59.245 41.667 0.00 0.00 0.00 3.02
5875 6714 5.238650 GCTGGCTAACTGAACTTAACTGAAA 59.761 40.000 0.00 0.00 0.00 2.69
5876 6715 6.613755 TGGCTAACTGAACTTAACTGAAAC 57.386 37.500 0.00 0.00 0.00 2.78
5877 6716 5.529800 TGGCTAACTGAACTTAACTGAAACC 59.470 40.000 0.00 0.00 0.00 3.27
5878 6717 5.529800 GGCTAACTGAACTTAACTGAAACCA 59.470 40.000 0.00 0.00 0.00 3.67
5879 6718 6.038936 GGCTAACTGAACTTAACTGAAACCAA 59.961 38.462 0.00 0.00 0.00 3.67
5880 6719 6.910972 GCTAACTGAACTTAACTGAAACCAAC 59.089 38.462 0.00 0.00 0.00 3.77
5881 6720 5.830000 ACTGAACTTAACTGAAACCAACC 57.170 39.130 0.00 0.00 0.00 3.77
5897 6736 3.947834 ACCAACCTGTTGTTTTCTCTCTG 59.052 43.478 9.03 0.00 38.85 3.35
5899 6738 4.201950 CCAACCTGTTGTTTTCTCTCTGTG 60.202 45.833 9.03 0.00 38.85 3.66
5902 6741 3.242870 CCTGTTGTTTTCTCTCTGTGTGC 60.243 47.826 0.00 0.00 0.00 4.57
5914 6753 2.600420 CTCTGTGTGCGTGTGTCATATC 59.400 50.000 0.00 0.00 0.00 1.63
5987 6826 0.309302 CCGATCAGTGAGCCTCTACG 59.691 60.000 2.13 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 62 3.626924 ACGGGTGTGAGGTGGAGC 61.627 66.667 0.00 0.00 0.00 4.70
125 132 4.452733 AGCCTGGTTCGTAGCGGC 62.453 66.667 15.32 15.32 39.82 6.53
126 133 2.202756 GAGCCTGGTTCGTAGCGG 60.203 66.667 0.00 0.00 0.00 5.52
127 134 2.579787 CGAGCCTGGTTCGTAGCG 60.580 66.667 22.67 0.00 31.98 4.26
128 135 2.886124 GCGAGCCTGGTTCGTAGC 60.886 66.667 29.17 12.92 38.46 3.58
129 136 0.669318 TTTGCGAGCCTGGTTCGTAG 60.669 55.000 29.17 7.12 38.46 3.51
130 137 0.947180 GTTTGCGAGCCTGGTTCGTA 60.947 55.000 29.17 24.25 38.46 3.43
131 138 2.110213 TTTGCGAGCCTGGTTCGT 59.890 55.556 29.17 0.00 38.46 3.85
132 139 1.901650 GAGTTTGCGAGCCTGGTTCG 61.902 60.000 25.90 25.90 39.17 3.95
133 140 1.869690 GAGTTTGCGAGCCTGGTTC 59.130 57.895 0.00 0.00 0.00 3.62
134 141 1.961277 CGAGTTTGCGAGCCTGGTT 60.961 57.895 0.00 0.00 0.00 3.67
135 142 2.357517 CGAGTTTGCGAGCCTGGT 60.358 61.111 0.00 0.00 0.00 4.00
136 143 3.793144 GCGAGTTTGCGAGCCTGG 61.793 66.667 0.00 0.00 0.00 4.45
205 221 3.823873 CCATTGTTTGCCAGGTAAGTACA 59.176 43.478 0.00 0.00 0.00 2.90
206 222 4.076394 TCCATTGTTTGCCAGGTAAGTAC 58.924 43.478 0.00 0.00 0.00 2.73
207 223 4.076394 GTCCATTGTTTGCCAGGTAAGTA 58.924 43.478 0.00 0.00 0.00 2.24
208 224 2.890945 GTCCATTGTTTGCCAGGTAAGT 59.109 45.455 0.00 0.00 0.00 2.24
209 225 2.095263 CGTCCATTGTTTGCCAGGTAAG 60.095 50.000 0.00 0.00 0.00 2.34
210 226 1.883275 CGTCCATTGTTTGCCAGGTAA 59.117 47.619 0.00 0.00 0.00 2.85
230 250 4.841246 TCCCCTGCTCTTTATAATCTCTCC 59.159 45.833 0.00 0.00 0.00 3.71
369 401 1.219213 GAGGAGGGAGGAGAGAATGGA 59.781 57.143 0.00 0.00 0.00 3.41
372 404 1.062505 GGTGAGGAGGGAGGAGAGAAT 60.063 57.143 0.00 0.00 0.00 2.40
373 405 0.336737 GGTGAGGAGGGAGGAGAGAA 59.663 60.000 0.00 0.00 0.00 2.87
401 458 5.492524 AGACAGGGGGAGAAAAGATGAAATA 59.507 40.000 0.00 0.00 0.00 1.40
414 471 2.747855 GCGCAAAGACAGGGGGAG 60.748 66.667 0.30 0.00 0.00 4.30
450 507 1.826921 TGCGGCGGTTTTACCCAAA 60.827 52.632 9.78 0.00 33.75 3.28
534 598 0.692419 AGAGGCTATGGTGGTGGGAG 60.692 60.000 0.00 0.00 0.00 4.30
551 849 2.024369 TGGGGCTACTGTATCACTGAGA 60.024 50.000 0.00 0.00 0.00 3.27
553 851 2.108168 GTGGGGCTACTGTATCACTGA 58.892 52.381 0.00 0.00 0.00 3.41
649 1175 4.166888 TCCTGATGGAGCAGCCGC 62.167 66.667 0.00 0.00 40.66 6.53
657 1183 2.824546 GCGGATGCTCCTGATGGA 59.175 61.111 1.51 0.00 40.69 3.41
667 1193 0.316841 TGAAAAACCCAAGCGGATGC 59.683 50.000 0.00 0.00 43.24 3.91
833 1361 1.133199 AGATCTGGACTAGAGGGGCAG 60.133 57.143 0.00 0.00 39.20 4.85
834 1362 0.937441 AGATCTGGACTAGAGGGGCA 59.063 55.000 0.00 0.00 39.20 5.36
845 1393 1.076412 AGAGAGCGGCAGATCTGGA 60.076 57.895 23.89 0.00 44.10 3.86
953 1506 1.602377 CACGAAAGCGGGAGTCTTTTT 59.398 47.619 0.00 0.00 45.89 1.94
962 1515 0.108138 AGAGGAATCACGAAAGCGGG 60.108 55.000 0.00 0.00 43.89 6.13
972 1525 2.202743 CGGCGCGAAGAGGAATCA 60.203 61.111 12.10 0.00 0.00 2.57
1344 1897 0.036732 GGAAGTGGATGTGCTGGTCA 59.963 55.000 0.00 0.00 0.00 4.02
1348 1901 1.446907 GAGTGGAAGTGGATGTGCTG 58.553 55.000 0.00 0.00 0.00 4.41
1709 2262 1.906105 GCCAGGTGGGTCGTATCCAA 61.906 60.000 0.00 0.00 39.65 3.53
1716 2269 4.143333 CCGTAGCCAGGTGGGTCG 62.143 72.222 3.43 8.27 46.04 4.79
1797 2350 1.227438 CTGGTGTGAAACGGACGGT 60.227 57.895 0.00 0.00 42.39 4.83
1842 2395 3.648067 TGATGTTGAAGAAGGTCTGGACT 59.352 43.478 0.67 0.00 0.00 3.85
1914 2467 4.864334 GCATCACTGGCCTCCGGG 62.864 72.222 3.32 0.00 33.40 5.73
1945 2498 2.221981 GCGCATAGCTGGTATTGAAGAC 59.778 50.000 0.30 0.00 44.04 3.01
1989 2542 1.809619 GCGTTGCTCGTATGCTCCA 60.810 57.895 4.16 0.00 42.13 3.86
1991 2544 2.526120 GGGCGTTGCTCGTATGCTC 61.526 63.158 4.16 0.00 42.13 4.26
2019 2572 2.898729 AATAGTGGACTCTGGCATCG 57.101 50.000 0.00 0.00 0.00 3.84
2400 2953 1.270550 CCATTCAACAGGTGCTTGTCC 59.729 52.381 0.00 0.00 0.00 4.02
2411 2964 0.827089 CCCAGTGTGCCCATTCAACA 60.827 55.000 0.00 0.00 0.00 3.33
2442 2995 1.741770 CCGACCTTCCTCCTTTGCG 60.742 63.158 0.00 0.00 0.00 4.85
2576 3129 0.882484 TTGACGTGCTTCATTCCGCA 60.882 50.000 0.00 0.00 0.00 5.69
2577 3130 0.452784 GTTGACGTGCTTCATTCCGC 60.453 55.000 0.00 0.00 0.00 5.54
2578 3131 0.865111 TGTTGACGTGCTTCATTCCG 59.135 50.000 0.00 0.00 0.00 4.30
2579 3132 2.226437 ACATGTTGACGTGCTTCATTCC 59.774 45.455 0.00 0.00 36.36 3.01
2580 3133 3.542712 ACATGTTGACGTGCTTCATTC 57.457 42.857 0.00 0.00 36.36 2.67
2581 3134 3.631144 CAACATGTTGACGTGCTTCATT 58.369 40.909 30.69 0.00 42.93 2.57
2582 3135 2.605338 GCAACATGTTGACGTGCTTCAT 60.605 45.455 36.65 0.00 42.93 2.57
2583 3136 1.268488 GCAACATGTTGACGTGCTTCA 60.268 47.619 36.65 0.00 42.93 3.02
2584 3137 1.002468 AGCAACATGTTGACGTGCTTC 60.002 47.619 36.65 18.84 42.93 3.86
2585 3138 1.024271 AGCAACATGTTGACGTGCTT 58.976 45.000 36.65 12.70 42.93 3.91
2586 3139 0.308684 CAGCAACATGTTGACGTGCT 59.691 50.000 36.65 25.83 42.93 4.40
2587 3140 0.661187 CCAGCAACATGTTGACGTGC 60.661 55.000 36.65 24.10 42.93 5.34
2614 3167 1.470632 CGTCTTCTCTGATCCTGTGCC 60.471 57.143 0.00 0.00 0.00 5.01
2615 3168 1.203523 ACGTCTTCTCTGATCCTGTGC 59.796 52.381 0.00 0.00 0.00 4.57
2622 3175 6.127619 TGTCATCAACATACGTCTTCTCTGAT 60.128 38.462 0.00 0.00 31.20 2.90
2807 3360 6.310224 TGTTTAGAAACTGCAAAAGAACAAGC 59.690 34.615 6.69 0.00 39.59 4.01
2963 3516 7.490657 TTCCCACATGTATAGTTTCTGTAGT 57.509 36.000 0.00 0.00 0.00 2.73
3064 3617 7.967854 TCACATTGCCAAAATAAAGTAATCTCG 59.032 33.333 0.00 0.00 0.00 4.04
3069 3622 8.592809 AGGAATCACATTGCCAAAATAAAGTAA 58.407 29.630 0.00 0.00 0.00 2.24
3116 3669 4.877823 TGTGCACTAAATTAGGATGCAGAG 59.122 41.667 19.41 0.00 46.29 3.35
3118 3671 4.877823 TCTGTGCACTAAATTAGGATGCAG 59.122 41.667 19.41 12.10 46.29 4.41
3126 3679 7.929245 TGTACTTTGACTCTGTGCACTAAATTA 59.071 33.333 19.41 5.99 0.00 1.40
3136 3689 6.447162 TCACATACTGTACTTTGACTCTGTG 58.553 40.000 6.22 6.22 33.39 3.66
3188 3741 9.654663 AAACTCCTAATTGTAATCAGTCAGTAC 57.345 33.333 0.00 0.00 0.00 2.73
3194 3747 8.552296 AGATGGAAACTCCTAATTGTAATCAGT 58.448 33.333 0.00 0.00 37.46 3.41
3241 3794 6.001460 AGCTGCAACAACAATACCTAAGTAA 58.999 36.000 1.02 0.00 30.59 2.24
3244 3797 6.494893 TTAGCTGCAACAACAATACCTAAG 57.505 37.500 1.02 0.00 0.00 2.18
3249 3802 9.139174 ACATAATTTTAGCTGCAACAACAATAC 57.861 29.630 1.02 0.00 0.00 1.89
3308 3926 9.899226 GTGGACCTATTCAAAGCATATTTATTC 57.101 33.333 0.00 0.00 0.00 1.75
3408 4031 5.706833 TGCAGAGTGATAAGAAAAGCATTGA 59.293 36.000 0.00 0.00 0.00 2.57
3475 4220 4.093743 TCCTCTTCAGCCTGTAATGTACA 58.906 43.478 0.00 0.00 37.13 2.90
3478 4223 2.503356 CCTCCTCTTCAGCCTGTAATGT 59.497 50.000 0.00 0.00 0.00 2.71
3574 4319 4.201920 CCTTATTTCCTTTTCAGCCGCTAC 60.202 45.833 0.00 0.00 0.00 3.58
3579 4324 5.984695 ACTTCCTTATTTCCTTTTCAGCC 57.015 39.130 0.00 0.00 0.00 4.85
3580 4325 7.910683 CGATAACTTCCTTATTTCCTTTTCAGC 59.089 37.037 0.00 0.00 0.00 4.26
3606 4351 7.659390 ACCTGAATAGCTATGCTTATTCTTGTC 59.341 37.037 13.09 0.53 40.44 3.18
3612 4357 7.282585 TCACAACCTGAATAGCTATGCTTATT 58.717 34.615 13.09 1.77 40.44 1.40
3717 4462 3.139077 ACTGTTGTTTTAAGGGAGAGCG 58.861 45.455 0.00 0.00 0.00 5.03
3733 4478 2.290705 GGGGTATGTGCAGGTTACTGTT 60.291 50.000 0.00 0.00 46.62 3.16
3734 4479 1.280998 GGGGTATGTGCAGGTTACTGT 59.719 52.381 0.00 0.00 46.62 3.55
3824 4572 6.795098 TTGCGTATGTGAAAATACTCAAGT 57.205 33.333 0.00 0.00 34.46 3.16
3830 4578 6.468956 CCACTGATTTGCGTATGTGAAAATAC 59.531 38.462 0.00 0.00 0.00 1.89
3900 4648 2.103373 GCCTCACTATCACCTCACTCA 58.897 52.381 0.00 0.00 0.00 3.41
3937 4685 8.621532 ACATACTTTTTCTAACTGCTCATTGA 57.378 30.769 0.00 0.00 0.00 2.57
4028 4776 4.513318 GGAAAAGACTGTCCTGTTTGAGAG 59.487 45.833 3.76 0.00 0.00 3.20
4086 4834 9.542462 CTGAATCCTGATGCATGAAAATAAAAT 57.458 29.630 2.46 0.00 0.00 1.82
4091 4839 5.068723 GGACTGAATCCTGATGCATGAAAAT 59.931 40.000 2.46 0.00 45.22 1.82
4133 4881 3.825585 TCTTGCAATGCACTACATGGAAA 59.174 39.130 7.72 0.00 39.60 3.13
4134 4882 3.419943 TCTTGCAATGCACTACATGGAA 58.580 40.909 7.72 0.00 39.60 3.53
4220 4968 6.419413 ACCAACATGTGCGTAAATAAAAACAG 59.581 34.615 0.00 0.00 0.00 3.16
4221 4969 6.273825 ACCAACATGTGCGTAAATAAAAACA 58.726 32.000 0.00 0.00 0.00 2.83
4234 4982 4.439153 CCAATATCACAGACCAACATGTGC 60.439 45.833 0.00 0.00 45.12 4.57
4275 5023 1.002033 CGCATCAGCCTGGATAAAAGC 60.002 52.381 0.00 0.00 37.52 3.51
4305 5053 6.712095 GGATCTGATGGCATTCTAACATAACA 59.288 38.462 0.00 0.00 0.00 2.41
4551 5299 1.407437 CCAGGAGAAAATGGAGGGACG 60.407 57.143 0.00 0.00 39.02 4.79
4734 5482 3.954258 GGTCCCTGTCCATTCCTTTATTG 59.046 47.826 0.00 0.00 0.00 1.90
4860 5608 2.663852 GCGCCGTGTAACACCTGT 60.664 61.111 0.00 0.00 35.74 4.00
4902 5650 1.447489 CCTCAAGCTCGACTGCAGG 60.447 63.158 19.93 0.36 34.99 4.85
4915 5663 6.376864 TCCATCGCTTCAAAAATATTCCTCAA 59.623 34.615 0.00 0.00 0.00 3.02
5018 5766 2.300437 GGAACACTACTGCCACTCTCTT 59.700 50.000 0.00 0.00 0.00 2.85
5118 5866 2.744202 GCACACTACAGTTCCAATCTGG 59.256 50.000 0.00 0.00 39.43 3.86
5241 6003 7.836183 AGCCTATTATTCTCAAATCAACAAGGT 59.164 33.333 0.00 0.00 0.00 3.50
5251 6013 8.906867 CAATCCTCAAAGCCTATTATTCTCAAA 58.093 33.333 0.00 0.00 0.00 2.69
5298 6060 1.683917 CTCCTTCTCCGGTATGGTCTG 59.316 57.143 0.00 0.00 39.52 3.51
5299 6061 2.030045 GCTCCTTCTCCGGTATGGTCT 61.030 57.143 0.00 0.00 39.52 3.85
5300 6062 0.389757 GCTCCTTCTCCGGTATGGTC 59.610 60.000 0.00 0.00 39.52 4.02
5301 6063 0.325296 TGCTCCTTCTCCGGTATGGT 60.325 55.000 0.00 0.00 39.52 3.55
5302 6064 0.830648 TTGCTCCTTCTCCGGTATGG 59.169 55.000 0.00 3.21 40.09 2.74
5303 6065 1.202580 CCTTGCTCCTTCTCCGGTATG 60.203 57.143 0.00 0.00 0.00 2.39
5305 6067 0.040646 TCCTTGCTCCTTCTCCGGTA 59.959 55.000 0.00 0.00 0.00 4.02
5306 6068 0.836400 TTCCTTGCTCCTTCTCCGGT 60.836 55.000 0.00 0.00 0.00 5.28
5307 6069 0.324943 TTTCCTTGCTCCTTCTCCGG 59.675 55.000 0.00 0.00 0.00 5.14
5308 6070 1.002544 AGTTTCCTTGCTCCTTCTCCG 59.997 52.381 0.00 0.00 0.00 4.63
5309 6071 2.224646 ACAGTTTCCTTGCTCCTTCTCC 60.225 50.000 0.00 0.00 0.00 3.71
5312 6074 1.882623 CCACAGTTTCCTTGCTCCTTC 59.117 52.381 0.00 0.00 0.00 3.46
5313 6075 1.215423 ACCACAGTTTCCTTGCTCCTT 59.785 47.619 0.00 0.00 0.00 3.36
5345 6115 4.874977 GTAGCCGCGACTGCCTCC 62.875 72.222 8.23 0.00 38.08 4.30
5352 6122 4.735132 TGCACAGGTAGCCGCGAC 62.735 66.667 8.23 0.00 0.00 5.19
5354 6124 3.264897 GATGCACAGGTAGCCGCG 61.265 66.667 0.00 0.00 0.00 6.46
5355 6125 1.884926 GAGATGCACAGGTAGCCGC 60.885 63.158 0.00 0.00 0.00 6.53
5389 6159 4.424711 TCAGGGATTGGCCGCCAC 62.425 66.667 13.00 0.73 37.63 5.01
5440 6210 1.406887 CGGTGTATGGAAACCCCTCAG 60.407 57.143 0.00 0.00 35.38 3.35
5477 6247 4.260985 ACAGCATGACCATCGATTTGTTA 58.739 39.130 0.00 0.00 39.69 2.41
5499 6269 1.371183 CACCAGTTCCGAAGCCTGA 59.629 57.895 1.26 0.00 0.00 3.86
5508 6278 1.975680 TCTTCTACCACCACCAGTTCC 59.024 52.381 0.00 0.00 0.00 3.62
5513 6283 0.976641 CAGCTCTTCTACCACCACCA 59.023 55.000 0.00 0.00 0.00 4.17
5514 6284 0.391793 GCAGCTCTTCTACCACCACC 60.392 60.000 0.00 0.00 0.00 4.61
5515 6285 0.321671 TGCAGCTCTTCTACCACCAC 59.678 55.000 0.00 0.00 0.00 4.16
5518 6288 1.484240 AGGATGCAGCTCTTCTACCAC 59.516 52.381 0.22 0.00 0.00 4.16
5548 6318 2.734723 CACTCGTCTGTGCACCGG 60.735 66.667 15.69 0.00 0.00 5.28
5554 6324 0.241213 ATGTCCGACACTCGTCTGTG 59.759 55.000 2.57 0.00 40.23 3.66
5562 6332 3.311110 ACCGCCATGTCCGACACT 61.311 61.111 2.57 0.00 0.00 3.55
5580 6350 4.760047 TTCCTCGGCGCTTCAGGC 62.760 66.667 7.64 0.00 37.64 4.85
5586 6356 2.034879 CATTGTGTTCCTCGGCGCT 61.035 57.895 7.64 0.00 0.00 5.92
5596 6366 0.178938 TCACCATGCCCCATTGTGTT 60.179 50.000 8.63 0.00 38.25 3.32
5598 6368 0.899253 TGTCACCATGCCCCATTGTG 60.899 55.000 3.74 3.74 38.38 3.33
5614 6414 0.941463 CGTCCGGCTCTGCATATGTC 60.941 60.000 4.29 0.00 0.00 3.06
5650 6450 3.340953 TACGTCAAGTACCGGCGCC 62.341 63.158 19.07 19.07 0.00 6.53
5651 6451 1.870901 CTACGTCAAGTACCGGCGC 60.871 63.158 0.00 0.00 0.00 6.53
5652 6452 0.247974 CTCTACGTCAAGTACCGGCG 60.248 60.000 0.00 0.00 0.00 6.46
5653 6453 0.100146 CCTCTACGTCAAGTACCGGC 59.900 60.000 0.00 0.00 0.00 6.13
5654 6454 0.100146 GCCTCTACGTCAAGTACCGG 59.900 60.000 0.00 0.00 0.00 5.28
5655 6455 0.100146 GGCCTCTACGTCAAGTACCG 59.900 60.000 0.00 0.00 0.00 4.02
5687 6526 6.091034 CCATCTATATATCCTACGGTCGATCG 59.909 46.154 18.18 18.18 0.00 3.69
5723 6562 2.564721 GGTGAACAACAGCCAGGGC 61.565 63.158 0.97 0.97 40.63 5.19
5726 6565 0.817634 TTCCGGTGAACAACAGCCAG 60.818 55.000 0.00 0.00 43.16 4.85
5727 6566 0.817634 CTTCCGGTGAACAACAGCCA 60.818 55.000 0.00 0.00 43.16 4.75
5728 6567 0.818040 ACTTCCGGTGAACAACAGCC 60.818 55.000 0.00 0.00 43.16 4.85
5729 6568 1.021968 AACTTCCGGTGAACAACAGC 58.978 50.000 0.00 0.00 42.73 4.40
5730 6569 3.775661 AAAACTTCCGGTGAACAACAG 57.224 42.857 0.00 0.00 0.00 3.16
5814 6653 6.054035 ACAAACAAACAAACAAACAACCAG 57.946 33.333 0.00 0.00 0.00 4.00
5821 6660 8.447833 TGTACACAAAACAAACAAACAAACAAA 58.552 25.926 0.00 0.00 0.00 2.83
5822 6661 7.970384 TGTACACAAAACAAACAAACAAACAA 58.030 26.923 0.00 0.00 0.00 2.83
5823 6662 7.534085 TGTACACAAAACAAACAAACAAACA 57.466 28.000 0.00 0.00 0.00 2.83
5824 6663 6.571887 GCTGTACACAAAACAAACAAACAAAC 59.428 34.615 0.00 0.00 0.00 2.93
5825 6664 6.480320 AGCTGTACACAAAACAAACAAACAAA 59.520 30.769 0.00 0.00 0.00 2.83
5826 6665 5.986135 AGCTGTACACAAAACAAACAAACAA 59.014 32.000 0.00 0.00 0.00 2.83
5827 6666 5.403766 CAGCTGTACACAAAACAAACAAACA 59.596 36.000 5.25 0.00 0.00 2.83
5828 6667 5.667644 GCAGCTGTACACAAAACAAACAAAC 60.668 40.000 16.64 0.00 0.00 2.93
5829 6668 4.387256 GCAGCTGTACACAAAACAAACAAA 59.613 37.500 16.64 0.00 0.00 2.83
5856 6695 7.282450 AGGTTGGTTTCAGTTAAGTTCAGTTAG 59.718 37.037 0.00 0.00 0.00 2.34
5875 6714 3.947834 CAGAGAGAAAACAACAGGTTGGT 59.052 43.478 15.84 7.00 43.33 3.67
5876 6715 3.947834 ACAGAGAGAAAACAACAGGTTGG 59.052 43.478 15.84 0.00 44.45 3.77
5877 6716 4.396166 ACACAGAGAGAAAACAACAGGTTG 59.604 41.667 10.45 10.45 45.58 3.77
5878 6717 4.396166 CACACAGAGAGAAAACAACAGGTT 59.604 41.667 0.00 0.00 42.98 3.50
5879 6718 3.941483 CACACAGAGAGAAAACAACAGGT 59.059 43.478 0.00 0.00 0.00 4.00
5880 6719 3.242870 GCACACAGAGAGAAAACAACAGG 60.243 47.826 0.00 0.00 0.00 4.00
5881 6720 3.544834 CGCACACAGAGAGAAAACAACAG 60.545 47.826 0.00 0.00 0.00 3.16
5897 6736 2.028045 CGAAGATATGACACACGCACAC 59.972 50.000 0.00 0.00 0.00 3.82
5899 6738 1.005975 GCGAAGATATGACACACGCAC 60.006 52.381 0.00 0.00 43.18 5.34
5902 6741 0.846401 CGGCGAAGATATGACACACG 59.154 55.000 0.00 0.00 0.00 4.49
5930 6769 2.110213 GAAGACACGGCACACCCA 59.890 61.111 0.00 0.00 0.00 4.51
5987 6826 6.316890 GGACGGATAGACAGATAGATTAGTCC 59.683 46.154 0.00 0.00 35.75 3.85


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

AutoCloner maintained by Alex Coulton.