Multiple sequence alignment - TraesCS4A01G097000

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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 TraesCS4A01G097000 chr4A 100.000 4628 0 0 1 4628 106584338 106579711 0.000000e+00 8547.0
1 TraesCS4A01G097000 chr4B 91.625 3821 161 65 681 4445 442585840 442589557 0.000000e+00 5136.0
2 TraesCS4A01G097000 chr4B 86.398 669 77 7 1 666 442559506 442560163 0.000000e+00 719.0
3 TraesCS4A01G097000 chr4B 89.362 188 11 1 4441 4628 442590581 442590759 1.300000e-55 228.0
4 TraesCS4A01G097000 chr4D 92.085 3487 138 53 1188 4628 358715395 358718789 0.000000e+00 4783.0
5 TraesCS4A01G097000 chr4D 95.285 509 12 5 681 1188 358714868 358715365 0.000000e+00 797.0
6 TraesCS4A01G097000 chr7D 85.294 68 8 2 605 670 88074442 88074375 8.310000e-08 69.4
7 TraesCS4A01G097000 chr3A 97.143 35 1 0 598 632 338687930 338687896 5.000000e-05 60.2


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 TraesCS4A01G097000 chr4A 106579711 106584338 4627 True 8547 8547 100.0000 1 4628 1 chr4A.!!$R1 4627
1 TraesCS4A01G097000 chr4B 442585840 442590759 4919 False 2682 5136 90.4935 681 4628 2 chr4B.!!$F2 3947
2 TraesCS4A01G097000 chr4B 442559506 442560163 657 False 719 719 86.3980 1 666 1 chr4B.!!$F1 665
3 TraesCS4A01G097000 chr4D 358714868 358718789 3921 False 2790 4783 93.6850 681 4628 2 chr4D.!!$F1 3947

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
359 362 0.034059 CGCCAGCTATTAGGGTCCTG 59.966 60.0 0.00 0.0 0.0 3.86 F
927 931 0.452585 GCTCGTACTCCCACACTCTC 59.547 60.0 0.00 0.0 0.0 3.20 F
1508 1542 0.317479 GTGAGACTTACGGCCACAGT 59.683 55.0 2.24 0.0 0.0 3.55 F
1981 2017 0.321671 TCAAAGACCGCCCTTCTCAG 59.678 55.0 0.00 0.0 0.0 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1497 1531 0.180642 TCACCAAAACTGTGGCCGTA 59.819 50.0 0.0 0.0 43.00 4.02 R
2885 2938 0.608640 GTCCCTCGGATCAACACACT 59.391 55.0 0.0 0.0 32.73 3.55 R
3088 3144 0.174845 GTGCATGTGGAGGCGTACTA 59.825 55.0 0.0 0.0 0.00 1.82 R
3928 4022 0.622738 AGGGAGAGCACATGGATGGT 60.623 55.0 0.0 0.0 0.00 3.55 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
21 22 4.524318 CGAGCCCCGCCGTGTAAT 62.524 66.667 0.00 0.00 0.00 1.89
22 23 2.124860 GAGCCCCGCCGTGTAATT 60.125 61.111 0.00 0.00 0.00 1.40
23 24 1.144496 GAGCCCCGCCGTGTAATTA 59.856 57.895 0.00 0.00 0.00 1.40
24 25 0.250166 GAGCCCCGCCGTGTAATTAT 60.250 55.000 0.00 0.00 0.00 1.28
28 29 1.223187 CCCGCCGTGTAATTATGGAC 58.777 55.000 5.76 0.00 0.00 4.02
59 60 6.458784 TCCCTTCCCTATTGAACTACCTATT 58.541 40.000 0.00 0.00 0.00 1.73
61 62 6.329197 CCCTTCCCTATTGAACTACCTATTCA 59.671 42.308 0.00 0.00 34.27 2.57
115 116 3.915437 AAAACCAACGCCATACTTGAG 57.085 42.857 0.00 0.00 0.00 3.02
129 130 6.180472 CCATACTTGAGTTGGTGGTAAAGAT 58.820 40.000 0.00 0.00 0.00 2.40
157 158 4.921991 AGATTGGGGAAATGATATCTGGGA 59.078 41.667 3.98 0.00 0.00 4.37
160 161 4.803452 TGGGGAAATGATATCTGGGAAAC 58.197 43.478 3.98 0.00 0.00 2.78
164 165 5.359860 GGGAAATGATATCTGGGAAACGTTT 59.640 40.000 14.57 14.57 0.00 3.60
186 188 1.985622 TGGATGAAGGTCCAGGGAAT 58.014 50.000 0.00 0.00 43.20 3.01
188 190 1.846439 GGATGAAGGTCCAGGGAATGA 59.154 52.381 0.00 0.00 38.20 2.57
189 191 2.444766 GGATGAAGGTCCAGGGAATGAT 59.555 50.000 0.00 0.00 38.20 2.45
190 192 3.117360 GGATGAAGGTCCAGGGAATGATT 60.117 47.826 0.00 0.00 38.20 2.57
195 197 2.649312 AGGTCCAGGGAATGATTTCACA 59.351 45.455 0.00 0.00 37.76 3.58
197 199 4.026052 GGTCCAGGGAATGATTTCACATT 58.974 43.478 0.00 0.00 42.19 2.71
199 201 5.413499 GTCCAGGGAATGATTTCACATTTG 58.587 41.667 0.00 0.00 40.03 2.32
201 203 5.185635 TCCAGGGAATGATTTCACATTTGTC 59.814 40.000 0.00 0.00 40.03 3.18
205 207 4.560035 GGAATGATTTCACATTTGTCTGCG 59.440 41.667 0.00 0.00 40.03 5.18
212 214 3.737172 ATTTGTCTGCGCGGTGGC 61.737 61.111 17.37 8.57 0.00 5.01
243 245 4.245660 GACAGAAAATGCCTTTTAAGCCC 58.754 43.478 0.00 0.00 34.73 5.19
244 246 3.645687 ACAGAAAATGCCTTTTAAGCCCA 59.354 39.130 0.00 0.00 34.73 5.36
245 247 4.102367 ACAGAAAATGCCTTTTAAGCCCAA 59.898 37.500 0.00 0.00 34.73 4.12
265 267 5.645497 CCCAAAAACTGTCATCCTCTTCTAG 59.355 44.000 0.00 0.00 0.00 2.43
267 269 6.936900 CCAAAAACTGTCATCCTCTTCTAGAA 59.063 38.462 4.81 4.81 0.00 2.10
271 273 9.579932 AAAACTGTCATCCTCTTCTAGAAAAAT 57.420 29.630 6.63 0.00 0.00 1.82
272 274 8.558973 AACTGTCATCCTCTTCTAGAAAAATG 57.441 34.615 6.63 7.88 0.00 2.32
273 275 6.597280 ACTGTCATCCTCTTCTAGAAAAATGC 59.403 38.462 6.63 5.51 0.00 3.56
324 327 6.406961 GGGAAAACATTCATAAAGGTCATCCC 60.407 42.308 1.84 1.84 42.10 3.85
340 343 5.124617 GGTCATCCCTTCATGAGAAAAGTTC 59.875 44.000 0.00 0.00 33.29 3.01
345 348 3.120060 CCTTCATGAGAAAAGTTCGCCAG 60.120 47.826 0.00 0.00 32.35 4.85
349 352 3.334583 TGAGAAAAGTTCGCCAGCTAT 57.665 42.857 0.00 0.00 34.02 2.97
351 354 4.827692 TGAGAAAAGTTCGCCAGCTATTA 58.172 39.130 0.00 0.00 34.02 0.98
356 359 1.413077 AGTTCGCCAGCTATTAGGGTC 59.587 52.381 0.00 0.00 0.00 4.46
359 362 0.034059 CGCCAGCTATTAGGGTCCTG 59.966 60.000 0.00 0.00 0.00 3.86
372 375 2.519691 AGGGTCCTGAAATTATGGCCAT 59.480 45.455 24.45 24.45 0.00 4.40
376 379 3.003689 GTCCTGAAATTATGGCCATGACG 59.996 47.826 29.04 8.94 0.00 4.35
377 380 2.951642 CCTGAAATTATGGCCATGACGT 59.048 45.455 29.04 11.47 0.00 4.34
380 383 5.067153 CCTGAAATTATGGCCATGACGTTTA 59.933 40.000 29.04 13.12 0.00 2.01
393 396 7.591426 GGCCATGACGTTTAAGAATATGAATTC 59.409 37.037 0.00 0.00 41.65 2.17
399 402 6.828785 ACGTTTAAGAATATGAATTCAGGCCT 59.171 34.615 14.54 0.00 43.44 5.19
403 406 3.887716 AGAATATGAATTCAGGCCTGCAC 59.112 43.478 28.91 17.65 43.44 4.57
405 408 4.712051 ATATGAATTCAGGCCTGCACTA 57.288 40.909 28.91 13.10 0.00 2.74
416 420 5.011738 TCAGGCCTGCACTATATTTACCTAC 59.988 44.000 28.91 0.00 0.00 3.18
440 444 8.594881 ACTATATGTAGAACATTAGTGCTTGC 57.405 34.615 3.17 0.00 39.88 4.01
441 445 6.867662 ATATGTAGAACATTAGTGCTTGCC 57.132 37.500 0.00 0.00 39.88 4.52
445 449 0.796312 AACATTAGTGCTTGCCGTCG 59.204 50.000 0.00 0.00 0.00 5.12
450 454 1.100510 TAGTGCTTGCCGTCGTCTAT 58.899 50.000 0.00 0.00 0.00 1.98
452 456 1.065701 AGTGCTTGCCGTCGTCTATAG 59.934 52.381 0.00 0.00 0.00 1.31
461 465 5.243207 TGCCGTCGTCTATAGATAGAATCA 58.757 41.667 5.57 5.33 40.77 2.57
552 556 2.474410 ACAGTTGGAAGGAATCGACC 57.526 50.000 0.00 0.00 0.00 4.79
553 557 1.003233 ACAGTTGGAAGGAATCGACCC 59.997 52.381 0.00 0.00 0.00 4.46
569 573 2.483714 CGACCCCGACAAATCATCTCAT 60.484 50.000 0.00 0.00 38.22 2.90
596 600 9.559732 AAGAAAAATGTTTAGGAAATCTTTGGG 57.440 29.630 0.00 0.00 0.00 4.12
600 604 7.797121 AATGTTTAGGAAATCTTTGGGTCAT 57.203 32.000 0.00 0.00 0.00 3.06
603 607 6.889722 TGTTTAGGAAATCTTTGGGTCATAGG 59.110 38.462 0.00 0.00 0.00 2.57
609 613 7.350921 AGGAAATCTTTGGGTCATAGGAATAGA 59.649 37.037 0.00 0.00 0.00 1.98
611 615 9.408648 GAAATCTTTGGGTCATAGGAATAGAAA 57.591 33.333 0.00 0.00 0.00 2.52
614 618 9.942526 ATCTTTGGGTCATAGGAATAGAAAAAT 57.057 29.630 0.00 0.00 0.00 1.82
615 619 9.408648 TCTTTGGGTCATAGGAATAGAAAAATC 57.591 33.333 0.00 0.00 0.00 2.17
616 620 9.189156 CTTTGGGTCATAGGAATAGAAAAATCA 57.811 33.333 0.00 0.00 0.00 2.57
617 621 9.713684 TTTGGGTCATAGGAATAGAAAAATCAT 57.286 29.630 0.00 0.00 0.00 2.45
724 728 2.208872 ACAAGGCCTTATCTGGGTGAT 58.791 47.619 20.00 0.00 39.11 3.06
790 794 3.002791 TGCGAAAGGAGCAGTTTATCAG 58.997 45.455 0.00 0.00 40.01 2.90
791 795 3.262420 GCGAAAGGAGCAGTTTATCAGA 58.738 45.455 0.00 0.00 34.19 3.27
792 796 3.684788 GCGAAAGGAGCAGTTTATCAGAA 59.315 43.478 0.00 0.00 34.19 3.02
793 797 4.154195 GCGAAAGGAGCAGTTTATCAGAAA 59.846 41.667 0.00 0.00 34.19 2.52
794 798 5.334879 GCGAAAGGAGCAGTTTATCAGAAAA 60.335 40.000 0.00 0.00 34.19 2.29
795 799 6.668323 CGAAAGGAGCAGTTTATCAGAAAAA 58.332 36.000 0.00 0.00 0.00 1.94
918 922 3.450115 AGCCCACGCTCGTACTCC 61.450 66.667 0.00 0.00 43.95 3.85
920 924 3.066190 CCCACGCTCGTACTCCCA 61.066 66.667 0.00 0.00 0.00 4.37
922 926 2.632544 CCACGCTCGTACTCCCACA 61.633 63.158 0.00 0.00 0.00 4.17
924 928 1.602888 ACGCTCGTACTCCCACACT 60.603 57.895 0.00 0.00 0.00 3.55
925 929 1.136984 CGCTCGTACTCCCACACTC 59.863 63.158 0.00 0.00 0.00 3.51
926 930 1.306642 CGCTCGTACTCCCACACTCT 61.307 60.000 0.00 0.00 0.00 3.24
927 931 0.452585 GCTCGTACTCCCACACTCTC 59.547 60.000 0.00 0.00 0.00 3.20
928 932 1.096416 CTCGTACTCCCACACTCTCC 58.904 60.000 0.00 0.00 0.00 3.71
1194 1228 1.196766 ACCTCCAAGTACGGTTCCCC 61.197 60.000 0.00 0.00 0.00 4.81
1197 1231 2.181975 CTCCAAGTACGGTTCCCCTTA 58.818 52.381 0.00 0.00 0.00 2.69
1228 1262 2.726351 CCTCCCCGTCCAGCTTCTC 61.726 68.421 0.00 0.00 0.00 2.87
1280 1314 3.219281 TCCTTTGTTTGCTTAGGTGGTC 58.781 45.455 0.00 0.00 0.00 4.02
1362 1396 1.190643 CGCTTCCCCTCTTCTCTTCT 58.809 55.000 0.00 0.00 0.00 2.85
1364 1398 1.484653 GCTTCCCCTCTTCTCTTCTCC 59.515 57.143 0.00 0.00 0.00 3.71
1365 1399 2.826488 CTTCCCCTCTTCTCTTCTCCA 58.174 52.381 0.00 0.00 0.00 3.86
1369 1403 1.068434 CCCTCTTCTCTTCTCCATCGC 59.932 57.143 0.00 0.00 0.00 4.58
1497 1531 2.034879 CGGCGCCAATGTGAGACTT 61.035 57.895 28.98 0.00 0.00 3.01
1498 1532 0.739462 CGGCGCCAATGTGAGACTTA 60.739 55.000 28.98 0.00 0.00 2.24
1502 1536 0.727398 GCCAATGTGAGACTTACGGC 59.273 55.000 0.20 0.20 0.00 5.68
1505 1539 1.732259 CAATGTGAGACTTACGGCCAC 59.268 52.381 2.24 0.00 0.00 5.01
1508 1542 0.317479 GTGAGACTTACGGCCACAGT 59.683 55.000 2.24 0.00 0.00 3.55
1514 1548 1.314730 CTTACGGCCACAGTTTTGGT 58.685 50.000 2.24 0.00 39.09 3.67
1522 1556 2.315176 CCACAGTTTTGGTGATTGGGA 58.685 47.619 0.00 0.00 38.54 4.37
1567 1603 2.073816 CTAATGGCGTTTTCCGTCTGT 58.926 47.619 0.00 0.00 43.10 3.41
1727 1763 1.712977 CTTCTCAGAGCCGCCATTGC 61.713 60.000 0.00 0.00 0.00 3.56
1784 1820 3.314635 CCTTTGCTAATGAGTCATCAGCC 59.685 47.826 22.97 8.01 39.29 4.85
1785 1821 2.229675 TGCTAATGAGTCATCAGCCG 57.770 50.000 22.97 4.67 39.29 5.52
1833 1869 1.495951 GTTCGTGAATGTGCGGGAC 59.504 57.895 0.00 0.00 0.00 4.46
1981 2017 0.321671 TCAAAGACCGCCCTTCTCAG 59.678 55.000 0.00 0.00 0.00 3.35
1983 2019 1.275291 CAAAGACCGCCCTTCTCAGTA 59.725 52.381 0.00 0.00 0.00 2.74
1984 2020 0.896226 AAGACCGCCCTTCTCAGTAC 59.104 55.000 0.00 0.00 0.00 2.73
1986 2022 1.957765 GACCGCCCTTCTCAGTACCC 61.958 65.000 0.00 0.00 0.00 3.69
1987 2023 1.987855 CCGCCCTTCTCAGTACCCA 60.988 63.158 0.00 0.00 0.00 4.51
1988 2024 1.218316 CGCCCTTCTCAGTACCCAC 59.782 63.158 0.00 0.00 0.00 4.61
1989 2025 1.602771 GCCCTTCTCAGTACCCACC 59.397 63.158 0.00 0.00 0.00 4.61
1999 2038 2.091541 CAGTACCCACCAAAATCGCAT 58.908 47.619 0.00 0.00 0.00 4.73
2020 2059 4.600692 TCTTTTTAGGAAGGCAAAAGCC 57.399 40.909 0.00 0.00 37.41 4.35
2111 2150 4.070552 GGGAGCCTCGACTGCGTT 62.071 66.667 0.00 0.00 38.98 4.84
2159 2198 4.838486 CTCCAGCGCGACTCCGTC 62.838 72.222 12.10 0.00 38.24 4.79
2212 2253 4.648762 TCACTGAATTCCAACACCACAATT 59.351 37.500 2.27 0.00 0.00 2.32
2213 2254 5.830457 TCACTGAATTCCAACACCACAATTA 59.170 36.000 2.27 0.00 0.00 1.40
2216 2257 6.267471 ACTGAATTCCAACACCACAATTACAT 59.733 34.615 2.27 0.00 0.00 2.29
2217 2258 7.450014 ACTGAATTCCAACACCACAATTACATA 59.550 33.333 2.27 0.00 0.00 2.29
2219 2260 8.249638 TGAATTCCAACACCACAATTACATATG 58.750 33.333 2.27 0.00 0.00 1.78
2222 2263 6.918626 TCCAACACCACAATTACATATGTTG 58.081 36.000 14.77 9.04 43.11 3.33
2223 2264 6.491745 TCCAACACCACAATTACATATGTTGT 59.508 34.615 14.77 9.73 42.34 3.32
2224 2265 6.806249 CCAACACCACAATTACATATGTTGTC 59.194 38.462 14.77 0.00 42.34 3.18
2225 2266 7.309133 CCAACACCACAATTACATATGTTGTCT 60.309 37.037 14.77 0.00 42.34 3.41
2226 2267 7.377766 ACACCACAATTACATATGTTGTCTC 57.622 36.000 14.77 0.00 39.87 3.36
2272 2313 5.715279 TGTGCTGGTTAGTCTAATCTACTGT 59.285 40.000 4.52 0.00 0.00 3.55
2590 2639 4.635765 TGCCTTGCAAATTACTACTGCTAG 59.364 41.667 0.00 4.23 38.25 3.42
2591 2640 4.636206 GCCTTGCAAATTACTACTGCTAGT 59.364 41.667 0.00 0.00 37.27 2.57
2592 2641 5.815740 GCCTTGCAAATTACTACTGCTAGTA 59.184 40.000 0.00 0.00 37.27 1.82
2593 2642 6.238130 GCCTTGCAAATTACTACTGCTAGTAC 60.238 42.308 0.00 0.00 37.27 2.73
2624 2673 2.063266 GACCTCACACGCACGAAATAA 58.937 47.619 0.00 0.00 0.00 1.40
2666 2715 2.279517 CCGTACCGAGCTGCCATC 60.280 66.667 0.00 0.00 0.00 3.51
2676 2725 2.079925 GAGCTGCCATCGTTTCTTTCT 58.920 47.619 0.00 0.00 0.00 2.52
2677 2726 2.485814 GAGCTGCCATCGTTTCTTTCTT 59.514 45.455 0.00 0.00 0.00 2.52
2678 2727 2.887152 AGCTGCCATCGTTTCTTTCTTT 59.113 40.909 0.00 0.00 0.00 2.52
2679 2728 3.057946 AGCTGCCATCGTTTCTTTCTTTC 60.058 43.478 0.00 0.00 0.00 2.62
2680 2729 3.304659 GCTGCCATCGTTTCTTTCTTTCA 60.305 43.478 0.00 0.00 0.00 2.69
2753 2806 5.687770 TGTTTTGATCGCTCTCAATCAAA 57.312 34.783 6.45 6.45 45.41 2.69
2884 2937 7.732025 TGTACCACACCAGGAGTATAATATTG 58.268 38.462 0.00 0.00 0.00 1.90
2885 2938 7.565768 TGTACCACACCAGGAGTATAATATTGA 59.434 37.037 0.00 0.00 0.00 2.57
2886 2939 7.067496 ACCACACCAGGAGTATAATATTGAG 57.933 40.000 0.00 0.00 0.00 3.02
2941 2997 2.736995 TGCAGGCGTACGCACTTC 60.737 61.111 37.99 26.16 44.11 3.01
2943 2999 2.730672 GCAGGCGTACGCACTTCTG 61.731 63.158 37.99 32.70 44.11 3.02
3003 3059 3.714487 AAACCGTGGCAGTGGCAGT 62.714 57.895 21.25 12.74 43.71 4.40
3027 3083 4.017877 GTGTGCACGCACCTGCTC 62.018 66.667 25.05 1.99 45.63 4.26
3179 3235 0.389948 GTGCGGATCTTGTTCGGACT 60.390 55.000 0.00 0.00 40.96 3.85
3184 3240 3.553096 GCGGATCTTGTTCGGACTGATAT 60.553 47.826 0.00 0.00 0.00 1.63
3187 3243 6.390721 CGGATCTTGTTCGGACTGATATTAT 58.609 40.000 0.00 0.00 0.00 1.28
3188 3244 6.309009 CGGATCTTGTTCGGACTGATATTATG 59.691 42.308 0.00 0.00 0.00 1.90
3189 3245 7.378966 GGATCTTGTTCGGACTGATATTATGA 58.621 38.462 0.00 0.00 0.00 2.15
3190 3246 8.037758 GGATCTTGTTCGGACTGATATTATGAT 58.962 37.037 0.00 0.00 0.00 2.45
3192 3248 9.862371 ATCTTGTTCGGACTGATATTATGATAC 57.138 33.333 0.00 0.00 0.00 2.24
3193 3249 9.078990 TCTTGTTCGGACTGATATTATGATACT 57.921 33.333 0.00 0.00 0.00 2.12
3199 3255 9.961264 TCGGACTGATATTATGATACTAACTCT 57.039 33.333 0.00 0.00 0.00 3.24
3215 3271 4.514577 CTAGGTCGTGCAGGGCGG 62.515 72.222 6.56 0.00 0.00 6.13
3438 3494 2.385875 CGACGACGACGAGGAGGAA 61.386 63.158 15.32 0.00 42.66 3.36
3440 3496 1.979831 GACGACGACGAGGAGGAAGG 61.980 65.000 15.32 0.00 42.66 3.46
3443 3502 1.995646 GACGACGAGGAGGAAGGAGC 61.996 65.000 0.00 0.00 0.00 4.70
3659 3729 1.391577 TGCCCATTCATTCATCACCG 58.608 50.000 0.00 0.00 0.00 4.94
3660 3730 1.340893 TGCCCATTCATTCATCACCGT 60.341 47.619 0.00 0.00 0.00 4.83
3762 3851 3.428045 GGCAATTGTTCCATCTGTGTAGC 60.428 47.826 7.40 0.00 0.00 3.58
3780 3869 2.024176 GCTTCGATCCCAAGCTGTAA 57.976 50.000 14.25 0.00 42.63 2.41
3806 3895 4.775236 AGATCCAGTCAGTCCAAATAAGC 58.225 43.478 0.00 0.00 0.00 3.09
3871 3961 5.699458 CCGTAGAGTTGTTGAAAGGTTGTAT 59.301 40.000 0.00 0.00 0.00 2.29
3891 3981 1.700042 ATGTCCGGATTCAGAGGGGC 61.700 60.000 7.81 0.00 0.00 5.80
3928 4022 8.106462 TGATGATAATGAGAACCCAGTACAAAA 58.894 33.333 0.00 0.00 0.00 2.44
3964 4058 2.091885 TCCCTCCATGTAATTTGGCCTC 60.092 50.000 3.32 0.00 34.06 4.70
4036 4138 2.352323 GCAAGTGTTATTTTGGGGTCCG 60.352 50.000 0.00 0.00 0.00 4.79
4059 4162 4.456911 GGTTGTGCTTTCTGAATCTGATGA 59.543 41.667 0.00 0.00 0.00 2.92
4060 4163 5.125097 GGTTGTGCTTTCTGAATCTGATGAT 59.875 40.000 0.00 0.00 33.70 2.45
4061 4164 5.813080 TGTGCTTTCTGAATCTGATGATG 57.187 39.130 0.00 0.00 32.44 3.07
4062 4165 4.638865 TGTGCTTTCTGAATCTGATGATGG 59.361 41.667 0.00 0.00 32.44 3.51
4063 4166 3.630769 TGCTTTCTGAATCTGATGATGGC 59.369 43.478 0.00 0.00 32.44 4.40
4064 4167 3.303857 GCTTTCTGAATCTGATGATGGCG 60.304 47.826 0.00 0.00 32.44 5.69
4065 4168 3.825143 TTCTGAATCTGATGATGGCGA 57.175 42.857 0.00 0.00 32.44 5.54
4070 4173 0.465705 ATCTGATGATGGCGAACCGT 59.534 50.000 0.00 0.00 39.70 4.83
4080 4183 0.743345 GGCGAACCGTGCTTAGGATT 60.743 55.000 0.00 0.00 0.00 3.01
4084 4187 2.677037 CGAACCGTGCTTAGGATTCCTT 60.677 50.000 11.25 0.00 34.61 3.36
4144 4247 2.437359 CCCTTTGGCTCAGCTCGG 60.437 66.667 0.00 0.00 0.00 4.63
4241 4346 3.334891 TCAACGGGGATGGGTGGG 61.335 66.667 0.00 0.00 0.00 4.61
4275 4380 1.269723 AGCAAAAGGCCTAGCGAAAAC 59.730 47.619 5.16 0.00 46.50 2.43
4333 4438 1.752198 TGGAGTGTGTACCACAGGC 59.248 57.895 14.39 5.75 45.43 4.85
4334 4439 1.051556 TGGAGTGTGTACCACAGGCA 61.052 55.000 14.39 0.00 45.43 4.75
4355 4460 2.599578 ACAAGCAGCTTGGCAGGG 60.600 61.111 33.54 12.53 44.81 4.45
4357 4462 3.907130 AAGCAGCTTGGCAGGGGT 61.907 61.111 6.93 0.00 35.83 4.95
4372 4477 3.009612 GGGTTAAACCGCAGTGTGA 57.990 52.632 4.93 0.00 39.83 3.58
4384 4489 2.543861 CGCAGTGTGAAGTGTAGAGTGT 60.544 50.000 0.00 0.00 0.00 3.55
4425 4531 1.614903 CTGGGCAAAGCATGTTTCAGA 59.385 47.619 0.00 0.00 0.00 3.27
4429 4535 3.243839 GGGCAAAGCATGTTTCAGAAGAA 60.244 43.478 0.00 0.00 0.00 2.52
4436 4542 0.944386 TGTTTCAGAAGAACAGCGGC 59.056 50.000 0.00 0.00 32.39 6.53
4473 5607 4.442192 GGGTCACTGGATCTTGCTTACTAG 60.442 50.000 0.00 0.00 0.00 2.57
4474 5608 4.160626 GGTCACTGGATCTTGCTTACTAGT 59.839 45.833 0.00 0.00 0.00 2.57
4475 5609 5.360144 GGTCACTGGATCTTGCTTACTAGTA 59.640 44.000 0.00 0.00 0.00 1.82
4476 5610 6.460399 GGTCACTGGATCTTGCTTACTAGTAG 60.460 46.154 2.23 0.00 0.00 2.57
4477 5611 6.095720 GTCACTGGATCTTGCTTACTAGTAGT 59.904 42.308 8.14 8.14 0.00 2.73
4478 5612 7.282675 GTCACTGGATCTTGCTTACTAGTAGTA 59.717 40.741 5.90 5.90 0.00 1.82
4479 5613 7.282675 TCACTGGATCTTGCTTACTAGTAGTAC 59.717 40.741 9.62 0.63 28.93 2.73
4480 5614 7.283580 CACTGGATCTTGCTTACTAGTAGTACT 59.716 40.741 9.62 8.14 28.93 2.73
4481 5615 8.492782 ACTGGATCTTGCTTACTAGTAGTACTA 58.507 37.037 9.62 9.66 28.93 1.82
4561 5695 0.323816 ATCACGTCCTCAGGCTCAGA 60.324 55.000 0.00 0.00 0.00 3.27
4563 5697 2.347322 ACGTCCTCAGGCTCAGAGC 61.347 63.158 14.69 14.69 41.46 4.09
4584 5718 3.351416 GGGCGCCGAAACGTCTTT 61.351 61.111 22.54 0.00 37.90 2.52
4612 5746 3.068165 AGAAATGCGAGGATGTATGTCGA 59.932 43.478 0.00 0.00 35.70 4.20
4614 5748 0.030773 TGCGAGGATGTATGTCGAGC 59.969 55.000 0.00 0.00 35.70 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.250166 ATAATTACACGGCGGGGCTC 60.250 55.000 16.11 0.00 0.00 4.70
10 11 0.856641 CGTCCATAATTACACGGCGG 59.143 55.000 13.24 2.35 0.00 6.13
14 15 4.684703 GGATCCTTCGTCCATAATTACACG 59.315 45.833 3.84 6.98 35.76 4.49
50 51 4.277921 GCTACGCTAAGGTGAATAGGTAGT 59.722 45.833 0.00 0.00 32.55 2.73
59 60 1.610554 GGTGGGCTACGCTAAGGTGA 61.611 60.000 0.00 0.00 0.00 4.02
61 62 2.718073 CGGTGGGCTACGCTAAGGT 61.718 63.158 0.00 0.00 0.00 3.50
98 99 2.151202 CAACTCAAGTATGGCGTTGGT 58.849 47.619 0.00 0.00 0.00 3.67
115 116 7.201821 CCCAATCTTATGATCTTTACCACCAAC 60.202 40.741 0.00 0.00 31.51 3.77
129 130 8.111545 CCAGATATCATTTCCCCAATCTTATGA 58.888 37.037 5.32 0.00 0.00 2.15
157 158 3.506067 GGACCTTCATCCATGAAACGTTT 59.494 43.478 14.57 14.57 45.26 3.60
160 161 2.710377 TGGACCTTCATCCATGAAACG 58.290 47.619 3.64 0.22 44.14 3.60
186 188 2.665245 CGCGCAGACAAATGTGAAATCA 60.665 45.455 8.75 0.00 32.27 2.57
188 190 1.401409 CCGCGCAGACAAATGTGAAAT 60.401 47.619 8.75 0.00 32.27 2.17
189 191 0.040514 CCGCGCAGACAAATGTGAAA 60.041 50.000 8.75 0.00 32.27 2.69
190 192 1.163420 ACCGCGCAGACAAATGTGAA 61.163 50.000 8.75 0.00 32.27 3.18
195 197 3.737172 GCCACCGCGCAGACAAAT 61.737 61.111 8.75 0.00 0.00 2.32
199 201 2.747507 AAAATTGCCACCGCGCAGAC 62.748 55.000 8.75 0.00 40.53 3.51
201 203 1.664333 AAAAATTGCCACCGCGCAG 60.664 52.632 8.75 0.00 40.53 5.18
232 234 5.017294 TGACAGTTTTTGGGCTTAAAAGG 57.983 39.130 0.00 0.00 31.80 3.11
233 235 5.696270 GGATGACAGTTTTTGGGCTTAAAAG 59.304 40.000 0.00 0.00 31.80 2.27
236 238 4.479158 AGGATGACAGTTTTTGGGCTTAA 58.521 39.130 0.00 0.00 0.00 1.85
243 245 7.969536 TTCTAGAAGAGGATGACAGTTTTTG 57.030 36.000 0.00 0.00 0.00 2.44
244 246 8.980481 TTTTCTAGAAGAGGATGACAGTTTTT 57.020 30.769 5.12 0.00 0.00 1.94
245 247 8.980481 TTTTTCTAGAAGAGGATGACAGTTTT 57.020 30.769 5.12 0.00 0.00 2.43
271 273 9.627123 AGCAGTTTTAGTTATATAGAAATGGCA 57.373 29.630 0.00 0.00 0.00 4.92
324 327 3.669023 GCTGGCGAACTTTTCTCATGAAG 60.669 47.826 0.00 0.00 33.28 3.02
340 343 0.034059 CAGGACCCTAATAGCTGGCG 59.966 60.000 0.00 0.00 0.00 5.69
345 348 5.416013 GCCATAATTTCAGGACCCTAATAGC 59.584 44.000 0.00 0.00 0.00 2.97
349 352 3.529734 TGGCCATAATTTCAGGACCCTAA 59.470 43.478 0.00 0.00 0.00 2.69
351 354 1.929494 TGGCCATAATTTCAGGACCCT 59.071 47.619 0.00 0.00 0.00 4.34
356 359 2.951642 ACGTCATGGCCATAATTTCAGG 59.048 45.455 20.30 3.17 0.00 3.86
359 362 6.791303 TCTTAAACGTCATGGCCATAATTTC 58.209 36.000 20.30 6.34 0.00 2.17
372 375 7.201696 GGCCTGAATTCATATTCTTAAACGTCA 60.202 37.037 8.96 0.00 40.68 4.35
376 379 6.920210 GCAGGCCTGAATTCATATTCTTAAAC 59.080 38.462 37.21 7.77 40.68 2.01
377 380 6.606796 TGCAGGCCTGAATTCATATTCTTAAA 59.393 34.615 37.21 0.00 40.68 1.52
380 383 4.340381 GTGCAGGCCTGAATTCATATTCTT 59.660 41.667 37.21 0.00 40.68 2.52
393 396 4.357918 AGGTAAATATAGTGCAGGCCTG 57.642 45.455 29.34 29.34 0.00 4.85
416 420 7.148738 CGGCAAGCACTAATGTTCTACATATAG 60.149 40.741 0.00 0.00 37.97 1.31
425 429 1.201921 CGACGGCAAGCACTAATGTTC 60.202 52.381 0.00 0.00 0.00 3.18
452 456 9.855021 GCTAGGACTCTCTTATTTGATTCTATC 57.145 37.037 0.00 0.00 0.00 2.08
461 465 9.095700 CTTTATAGGGCTAGGACTCTCTTATTT 57.904 37.037 0.00 0.00 0.00 1.40
497 501 8.686334 ACATACATGTGATCGCATACATATAGA 58.314 33.333 20.90 2.07 40.03 1.98
498 502 8.862550 ACATACATGTGATCGCATACATATAG 57.137 34.615 20.90 9.76 40.03 1.31
548 552 1.134818 TGAGATGATTTGTCGGGGTCG 60.135 52.381 0.00 0.00 37.82 4.79
552 556 6.925610 TTTCTTATGAGATGATTTGTCGGG 57.074 37.500 0.00 0.00 0.00 5.14
553 557 9.229784 CATTTTTCTTATGAGATGATTTGTCGG 57.770 33.333 0.00 0.00 0.00 4.79
588 592 9.942526 ATTTTTCTATTCCTATGACCCAAAGAT 57.057 29.630 0.00 0.00 0.00 2.40
691 695 5.975988 AAGGCCTTGTTTGATCTATAGGA 57.024 39.130 19.73 0.00 0.00 2.94
724 728 4.072839 TGTTTACAAACACACTGTCACCA 58.927 39.130 3.44 0.00 43.45 4.17
1315 1349 4.025401 GCTTGTGGCGGTTCACGG 62.025 66.667 0.00 0.00 44.51 4.94
1497 1531 0.180642 TCACCAAAACTGTGGCCGTA 59.819 50.000 0.00 0.00 43.00 4.02
1498 1532 0.467290 ATCACCAAAACTGTGGCCGT 60.467 50.000 0.00 0.00 43.00 5.68
1502 1536 2.035832 GTCCCAATCACCAAAACTGTGG 59.964 50.000 0.00 0.00 44.92 4.17
1505 1539 2.958355 ACAGTCCCAATCACCAAAACTG 59.042 45.455 0.00 0.00 38.80 3.16
1508 1542 3.909732 AGAACAGTCCCAATCACCAAAA 58.090 40.909 0.00 0.00 0.00 2.44
1514 1548 2.553028 GCTCCAAGAACAGTCCCAATCA 60.553 50.000 0.00 0.00 0.00 2.57
1567 1603 3.761752 TCGAACATCAGGATCTGTACACA 59.238 43.478 0.00 0.00 32.61 3.72
1784 1820 1.654220 CTGCACCTCCAAAACCACG 59.346 57.895 0.00 0.00 0.00 4.94
1785 1821 1.463553 CCCTGCACCTCCAAAACCAC 61.464 60.000 0.00 0.00 0.00 4.16
1981 2017 2.365582 AGATGCGATTTTGGTGGGTAC 58.634 47.619 0.00 0.00 0.00 3.34
1983 2019 1.923356 AAGATGCGATTTTGGTGGGT 58.077 45.000 0.00 0.00 0.00 4.51
1984 2020 3.317603 AAAAGATGCGATTTTGGTGGG 57.682 42.857 0.00 0.00 0.00 4.61
1986 2022 5.708948 TCCTAAAAAGATGCGATTTTGGTG 58.291 37.500 0.00 0.00 30.52 4.17
1987 2023 5.975693 TCCTAAAAAGATGCGATTTTGGT 57.024 34.783 0.00 0.00 30.52 3.67
1988 2024 5.807011 CCTTCCTAAAAAGATGCGATTTTGG 59.193 40.000 0.00 0.00 30.52 3.28
1989 2025 5.289434 GCCTTCCTAAAAAGATGCGATTTTG 59.711 40.000 0.00 0.00 30.52 2.44
2173 2214 8.441312 AATTCAGTGATGTTTTTGCAAGAAAT 57.559 26.923 3.66 1.19 0.00 2.17
2189 2230 3.289407 TGTGGTGTTGGAATTCAGTGA 57.711 42.857 7.93 0.00 0.00 3.41
2212 2253 6.413892 TCATTTGCTGGAGACAACATATGTA 58.586 36.000 9.21 0.00 42.66 2.29
2213 2254 5.255687 TCATTTGCTGGAGACAACATATGT 58.744 37.500 1.41 1.41 42.66 2.29
2216 2257 5.587443 CAGATCATTTGCTGGAGACAACATA 59.413 40.000 0.00 0.00 42.06 2.29
2217 2258 4.398358 CAGATCATTTGCTGGAGACAACAT 59.602 41.667 0.00 0.00 42.06 2.71
2219 2260 4.005650 TCAGATCATTTGCTGGAGACAAC 58.994 43.478 0.00 0.00 42.06 3.32
2222 2263 3.065095 GCTTCAGATCATTTGCTGGAGAC 59.935 47.826 0.00 0.00 39.62 3.36
2223 2264 3.276857 GCTTCAGATCATTTGCTGGAGA 58.723 45.455 0.00 0.00 39.62 3.71
2224 2265 2.358267 GGCTTCAGATCATTTGCTGGAG 59.642 50.000 0.00 0.00 40.11 3.86
2225 2266 2.291089 TGGCTTCAGATCATTTGCTGGA 60.291 45.455 0.00 0.00 33.05 3.86
2226 2267 2.097036 TGGCTTCAGATCATTTGCTGG 58.903 47.619 0.00 0.00 33.05 4.85
2272 2313 2.642311 TCCTGTAGAAGCCAATCCACAA 59.358 45.455 0.00 0.00 0.00 3.33
2516 2557 1.298859 GGTGGCACCGTCATCTGAAC 61.299 60.000 22.83 0.00 0.00 3.18
2590 2639 3.003480 GTGAGGTCAGCAATGGAAGTAC 58.997 50.000 0.00 0.00 0.00 2.73
2591 2640 2.637382 TGTGAGGTCAGCAATGGAAGTA 59.363 45.455 0.00 0.00 0.00 2.24
2592 2641 1.421268 TGTGAGGTCAGCAATGGAAGT 59.579 47.619 0.00 0.00 0.00 3.01
2593 2642 1.808945 GTGTGAGGTCAGCAATGGAAG 59.191 52.381 0.00 0.00 0.00 3.46
2624 2673 2.644798 AGCTCCCACTGTTAGGTTGAAT 59.355 45.455 0.00 0.00 0.00 2.57
2666 2715 3.421888 CGTGCCAATGAAAGAAAGAAACG 59.578 43.478 0.00 0.00 0.00 3.60
2676 2725 2.556189 ACTATTGTGCGTGCCAATGAAA 59.444 40.909 14.67 0.57 34.51 2.69
2677 2726 2.158559 ACTATTGTGCGTGCCAATGAA 58.841 42.857 14.67 1.08 34.51 2.57
2678 2727 1.819928 ACTATTGTGCGTGCCAATGA 58.180 45.000 14.67 3.71 34.51 2.57
2679 2728 3.755965 TTACTATTGTGCGTGCCAATG 57.244 42.857 14.67 9.47 34.51 2.82
2680 2729 4.981806 AATTACTATTGTGCGTGCCAAT 57.018 36.364 11.45 11.45 36.53 3.16
2753 2806 3.766545 TGCTAGCCTTGAAAACCAATCT 58.233 40.909 13.29 0.00 33.68 2.40
2884 2937 0.895530 TCCCTCGGATCAACACACTC 59.104 55.000 0.00 0.00 0.00 3.51
2885 2938 0.608640 GTCCCTCGGATCAACACACT 59.391 55.000 0.00 0.00 32.73 3.55
2886 2939 0.736325 CGTCCCTCGGATCAACACAC 60.736 60.000 0.00 0.00 32.73 3.82
2936 2992 7.389053 ACAAGAAGGATTAAACTAGCAGAAGTG 59.611 37.037 0.00 0.00 0.00 3.16
2939 2995 7.174946 CCAACAAGAAGGATTAAACTAGCAGAA 59.825 37.037 0.00 0.00 0.00 3.02
2940 2996 6.655003 CCAACAAGAAGGATTAAACTAGCAGA 59.345 38.462 0.00 0.00 0.00 4.26
2941 2997 6.431234 ACCAACAAGAAGGATTAAACTAGCAG 59.569 38.462 0.00 0.00 0.00 4.24
2943 2999 6.819397 ACCAACAAGAAGGATTAAACTAGC 57.181 37.500 0.00 0.00 0.00 3.42
3088 3144 0.174845 GTGCATGTGGAGGCGTACTA 59.825 55.000 0.00 0.00 0.00 1.82
3122 3178 4.237445 TCCGAGGGAGATGTCGAC 57.763 61.111 9.11 9.11 38.50 4.20
3155 3211 1.683790 GAACAAGATCCGCACCGTCG 61.684 60.000 0.00 0.00 0.00 5.12
3156 3212 1.683790 CGAACAAGATCCGCACCGTC 61.684 60.000 0.00 0.00 0.00 4.79
3184 3240 6.769341 TGCACGACCTAGAGTTAGTATCATAA 59.231 38.462 0.00 0.00 0.00 1.90
3187 3243 4.520179 TGCACGACCTAGAGTTAGTATCA 58.480 43.478 0.00 0.00 0.00 2.15
3188 3244 4.023878 CCTGCACGACCTAGAGTTAGTATC 60.024 50.000 0.00 0.00 0.00 2.24
3189 3245 3.884091 CCTGCACGACCTAGAGTTAGTAT 59.116 47.826 0.00 0.00 0.00 2.12
3190 3246 3.276857 CCTGCACGACCTAGAGTTAGTA 58.723 50.000 0.00 0.00 0.00 1.82
3191 3247 2.093106 CCTGCACGACCTAGAGTTAGT 58.907 52.381 0.00 0.00 0.00 2.24
3192 3248 1.405821 CCCTGCACGACCTAGAGTTAG 59.594 57.143 0.00 0.00 0.00 2.34
3193 3249 1.471119 CCCTGCACGACCTAGAGTTA 58.529 55.000 0.00 0.00 0.00 2.24
3194 3250 1.889530 GCCCTGCACGACCTAGAGTT 61.890 60.000 0.00 0.00 0.00 3.01
3195 3251 2.352032 GCCCTGCACGACCTAGAGT 61.352 63.158 0.00 0.00 0.00 3.24
3196 3252 2.496817 GCCCTGCACGACCTAGAG 59.503 66.667 0.00 0.00 0.00 2.43
3197 3253 3.449227 CGCCCTGCACGACCTAGA 61.449 66.667 0.00 0.00 0.00 2.43
3198 3254 4.514577 CCGCCCTGCACGACCTAG 62.515 72.222 0.00 0.00 0.00 3.02
3215 3271 2.435586 AGATGCTGCACACCTCGC 60.436 61.111 3.57 0.00 0.00 5.03
3438 3494 2.610233 AGCCTGCCTTCTGCTCCT 60.610 61.111 0.00 0.00 42.00 3.69
3440 3496 2.438075 CCAGCCTGCCTTCTGCTC 60.438 66.667 0.00 0.00 42.00 4.26
3443 3502 1.078567 GACTCCAGCCTGCCTTCTG 60.079 63.158 0.00 0.00 0.00 3.02
3610 3669 0.872021 GGCTATGGCTTGTCGTCGAG 60.872 60.000 0.00 0.00 38.73 4.04
3655 3725 2.271821 TGACGTATCATGACACGGTG 57.728 50.000 28.35 6.58 42.35 4.94
3656 3726 2.540973 CGATGACGTATCATGACACGGT 60.541 50.000 28.35 15.09 46.01 4.83
3657 3727 2.044135 CGATGACGTATCATGACACGG 58.956 52.381 28.35 12.12 46.01 4.94
3678 3766 0.750546 GCAGCCAGCTCCATCATTGA 60.751 55.000 0.00 0.00 41.15 2.57
3762 3851 1.936547 GCTTACAGCTTGGGATCGAAG 59.063 52.381 0.00 0.00 38.45 3.79
3780 3869 2.836636 TGGACTGACTGGATCTAGCT 57.163 50.000 5.91 0.00 0.00 3.32
3806 3895 2.551270 GCAACGACCGCACTCTTG 59.449 61.111 0.00 0.00 0.00 3.02
3851 3941 7.390718 GGACATATACAACCTTTCAACAACTCT 59.609 37.037 0.00 0.00 0.00 3.24
3871 3961 1.717032 CCCCTCTGAATCCGGACATA 58.283 55.000 6.12 0.00 0.00 2.29
3891 3981 5.027293 TCATTATCATCATATCGGGCCAG 57.973 43.478 4.39 0.00 0.00 4.85
3928 4022 0.622738 AGGGAGAGCACATGGATGGT 60.623 55.000 0.00 0.00 0.00 3.55
3964 4058 4.554363 CGACGTAGCCCGAGCCAG 62.554 72.222 0.00 0.00 41.25 4.85
3970 4064 4.554363 CCTGAGCGACGTAGCCCG 62.554 72.222 17.44 3.26 44.03 6.13
4010 4104 4.202212 ACCCCAAAATAACACTTGCAGAAC 60.202 41.667 0.00 0.00 0.00 3.01
4036 4138 4.456911 TCATCAGATTCAGAAAGCACAACC 59.543 41.667 0.00 0.00 0.00 3.77
4059 4162 1.449601 CCTAAGCACGGTTCGCCAT 60.450 57.895 0.00 0.00 37.00 4.40
4060 4163 1.895020 ATCCTAAGCACGGTTCGCCA 61.895 55.000 0.00 0.00 37.00 5.69
4061 4164 0.743345 AATCCTAAGCACGGTTCGCC 60.743 55.000 0.00 0.00 0.00 5.54
4062 4165 0.651031 GAATCCTAAGCACGGTTCGC 59.349 55.000 0.00 0.00 0.00 4.70
4063 4166 1.134788 AGGAATCCTAAGCACGGTTCG 60.135 52.381 0.00 0.00 28.47 3.95
4064 4167 2.678336 CAAGGAATCCTAAGCACGGTTC 59.322 50.000 0.46 0.00 31.13 3.62
4065 4168 2.304761 TCAAGGAATCCTAAGCACGGTT 59.695 45.455 0.46 0.00 31.13 4.44
4070 4173 1.134401 CCGCTCAAGGAATCCTAAGCA 60.134 52.381 26.25 4.02 31.13 3.91
4080 4183 0.898326 TCTGTACTGCCGCTCAAGGA 60.898 55.000 0.00 0.00 0.00 3.36
4084 4187 1.586541 CAGTCTGTACTGCCGCTCA 59.413 57.895 0.00 0.00 46.28 4.26
4117 4220 0.398381 AGCCAAAGGGAAACTTGCCA 60.398 50.000 2.63 0.00 41.75 4.92
4144 4247 4.687215 TCGCCACCTCAGCACAGC 62.687 66.667 0.00 0.00 0.00 4.40
4241 4346 2.741486 TTTGCTGCTCCCGGTACACC 62.741 60.000 0.00 0.00 0.00 4.16
4275 4380 2.842485 GTCAATTTCGCTGCTCATTTCG 59.158 45.455 0.00 0.00 0.00 3.46
4331 4436 3.300765 AAGCTGCTTGTGCCTGCC 61.301 61.111 15.16 0.00 38.02 4.85
4332 4437 2.049433 CAAGCTGCTTGTGCCTGC 60.049 61.111 29.38 0.00 36.79 4.85
4333 4438 2.649034 CCAAGCTGCTTGTGCCTG 59.351 61.111 33.16 18.37 39.58 4.85
4334 4439 3.300765 GCCAAGCTGCTTGTGCCT 61.301 61.111 33.16 2.45 39.58 4.75
4355 4460 1.944709 ACTTCACACTGCGGTTTAACC 59.055 47.619 3.64 3.64 34.05 2.85
4357 4462 2.634600 ACACTTCACACTGCGGTTTAA 58.365 42.857 0.00 0.00 0.00 1.52
4372 4477 4.160626 GCCATCCTTCTACACTCTACACTT 59.839 45.833 0.00 0.00 0.00 3.16
4384 4489 2.427453 GTCGAACTGAGCCATCCTTCTA 59.573 50.000 0.00 0.00 0.00 2.10
4425 4531 0.882042 CACTGTCTGCCGCTGTTCTT 60.882 55.000 0.00 0.00 0.00 2.52
4429 4535 2.029666 GTCACTGTCTGCCGCTGT 59.970 61.111 0.00 0.00 0.00 4.40
4436 4542 3.595691 GACCCAGTGTCACTGTCTG 57.404 57.895 27.20 18.55 44.50 3.51
4473 5607 3.999663 AGTGTCAGGTCACGTAGTACTAC 59.000 47.826 21.06 21.06 41.61 2.73
4474 5608 4.277515 AGTGTCAGGTCACGTAGTACTA 57.722 45.455 0.00 0.00 41.61 1.82
4475 5609 3.137446 AGTGTCAGGTCACGTAGTACT 57.863 47.619 0.00 0.00 41.61 2.73
4476 5610 3.562505 CAAGTGTCAGGTCACGTAGTAC 58.437 50.000 0.00 0.00 41.61 2.73
4477 5611 2.555325 CCAAGTGTCAGGTCACGTAGTA 59.445 50.000 0.00 0.00 41.61 1.82
4479 5613 1.611977 TCCAAGTGTCAGGTCACGTAG 59.388 52.381 0.00 0.00 42.40 3.51
4480 5614 1.338973 GTCCAAGTGTCAGGTCACGTA 59.661 52.381 0.00 0.00 42.40 3.57
4481 5615 0.104304 GTCCAAGTGTCAGGTCACGT 59.896 55.000 0.00 0.00 42.40 4.49
4524 5658 4.031089 CGTGATGTCAAGTCGATTCTCTTG 59.969 45.833 7.07 7.07 41.36 3.02
4570 5704 1.266124 GGCAAAAAGACGTTTCGGCG 61.266 55.000 0.00 0.00 41.28 6.46
4574 5708 4.318050 GCATTTCTGGCAAAAAGACGTTTC 60.318 41.667 0.00 0.00 0.00 2.78
4584 5718 1.473677 CATCCTCGCATTTCTGGCAAA 59.526 47.619 0.00 0.00 0.00 3.68


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

AutoCloner maintained by Alex Coulton.