Multiple sequence alignment - TraesCS3D01G037500

Loading Multiple Alignment...

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 TraesCS3D01G037500 chr3D 100.000 5062 0 0 1 5062 13586303 13581242 0.000000e+00 9348
1 TraesCS3D01G037500 chr3A 88.325 4531 248 113 499 4840 23392243 23396681 0.000000e+00 5177
2 TraesCS3D01G037500 chr3A 92.857 224 11 4 4837 5060 23397997 23398215 2.270000e-83 320
3 TraesCS3D01G037500 chr3A 93.258 89 5 1 1 88 23391733 23391821 4.110000e-26 130
4 TraesCS3D01G037500 chr3B 87.810 4397 253 123 613 4856 19873293 19869027 0.000000e+00 4889
5 TraesCS3D01G037500 chr3B 86.035 401 22 13 229 605 19873724 19873334 2.840000e-107 399
6 TraesCS3D01G037500 chr3B 94.203 138 7 1 4848 4984 19868878 19868741 5.140000e-50 209
7 TraesCS3D01G037500 chr3B 85.185 108 8 5 1 100 19873897 19873790 2.490000e-18 104


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 TraesCS3D01G037500 chr3D 13581242 13586303 5061 True 9348.000000 9348 100.00000 1 5062 1 chr3D.!!$R1 5061
1 TraesCS3D01G037500 chr3A 23391733 23398215 6482 False 1875.666667 5177 91.48000 1 5060 3 chr3A.!!$F1 5059
2 TraesCS3D01G037500 chr3B 19868741 19873897 5156 True 1400.250000 4889 88.30825 1 4984 4 chr3B.!!$R1 4983

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
869 1159 0.174617 CTCTCGCCACTTTCCTCTCC 59.825 60.0 0.00 0.0 0.00 3.71 F
966 1282 0.391793 AAAGCTAGCTTCTCCACCGC 60.392 55.0 29.42 0.0 34.84 5.68 F
996 1312 0.445436 CTAGAGCAAGCAACCAAGCG 59.555 55.0 0.00 0.0 40.15 4.68 F
2112 2549 0.466555 GAGCTAGAGGAGAAGGCCGA 60.467 60.0 0.00 0.0 0.00 5.54 F
3577 4070 0.038618 CCGTGAGTGACCGTCATCAA 60.039 55.0 4.13 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2028 2438 0.681733 TCTTCCTCTGCTTCGTTGCT 59.318 50.0 4.36 0.00 0.00 3.91 R
2632 3075 0.827507 ACATGCCCCTGAAAAGCGTT 60.828 50.0 0.00 0.00 0.00 4.84 R
2852 3295 0.867746 GAACGACTCTGCATGCACAA 59.132 50.0 18.46 7.09 0.00 3.33 R
3638 4147 0.176680 GCCGGCTCTTCTTCTGATCA 59.823 55.0 22.15 0.00 0.00 2.92 R
4491 5033 0.395173 TCTCGTGACCGATCCATCCA 60.395 55.0 0.00 0.00 43.27 3.41 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
60 68 2.689034 GGGAGCTACAGCCCCAGT 60.689 66.667 17.86 0.00 45.24 4.00
63 71 1.219393 GAGCTACAGCCCCAGTCAC 59.781 63.158 0.00 0.00 43.38 3.67
100 224 0.953003 GGTAGAGCCAGCTACTACCG 59.047 60.000 21.70 0.00 43.92 4.02
105 229 0.679002 AGCCAGCTACTACCGAACGA 60.679 55.000 0.00 0.00 0.00 3.85
120 244 4.787999 CGACTACCGTGAGAAGGC 57.212 61.111 0.00 0.00 0.00 4.35
126 250 4.760047 CCGTGAGAAGGCGGTGGG 62.760 72.222 0.00 0.00 42.73 4.61
156 280 3.007614 GGAAGTAGACACCTAAGCAACCA 59.992 47.826 0.00 0.00 0.00 3.67
160 284 1.705186 AGACACCTAAGCAACCACCAT 59.295 47.619 0.00 0.00 0.00 3.55
210 334 3.624777 CACCATTGGATCCTTACAAGCT 58.375 45.455 14.23 0.00 0.00 3.74
214 338 1.289160 TGGATCCTTACAAGCTGGCT 58.711 50.000 14.23 0.00 0.00 4.75
218 342 2.185004 TCCTTACAAGCTGGCTGAAC 57.815 50.000 0.00 0.00 0.00 3.18
219 343 1.419762 TCCTTACAAGCTGGCTGAACA 59.580 47.619 0.00 0.00 0.00 3.18
221 345 1.537202 CTTACAAGCTGGCTGAACACC 59.463 52.381 0.00 0.00 0.00 4.16
222 346 0.602638 TACAAGCTGGCTGAACACCG 60.603 55.000 0.00 0.00 0.00 4.94
223 347 2.980233 AAGCTGGCTGAACACCGC 60.980 61.111 0.00 0.00 0.00 5.68
224 348 3.772853 AAGCTGGCTGAACACCGCA 62.773 57.895 0.00 0.00 31.79 5.69
225 349 4.030452 GCTGGCTGAACACCGCAC 62.030 66.667 0.00 0.00 0.00 5.34
250 441 1.313812 AAGGAGATCGAGTCGGCGTT 61.314 55.000 13.54 5.39 0.00 4.84
252 443 1.136984 GAGATCGAGTCGGCGTTGT 59.863 57.895 13.54 0.00 0.00 3.32
255 446 2.279937 GATCGAGTCGGCGTTGTTGC 62.280 60.000 13.54 0.00 0.00 4.17
264 455 2.193536 GCGTTGTTGCCAGGAAGGT 61.194 57.895 0.00 0.00 40.61 3.50
315 511 7.065443 GGTTTTCCAACGTATGAATAGCTTAGT 59.935 37.037 0.00 0.00 40.31 2.24
318 514 5.597182 TCCAACGTATGAATAGCTTAGTCCT 59.403 40.000 0.00 0.00 0.00 3.85
322 518 5.597182 ACGTATGAATAGCTTAGTCCTTGGA 59.403 40.000 0.00 0.00 0.00 3.53
348 548 4.465632 AACGTGCATGTTGTATCTCCTA 57.534 40.909 23.20 0.00 0.00 2.94
365 565 4.528596 TCTCCTACTGAACTTTCTCCTTGG 59.471 45.833 0.00 0.00 0.00 3.61
366 566 3.008049 TCCTACTGAACTTTCTCCTTGGC 59.992 47.826 0.00 0.00 0.00 4.52
367 567 3.244561 CCTACTGAACTTTCTCCTTGGCA 60.245 47.826 0.00 0.00 0.00 4.92
368 568 2.576615 ACTGAACTTTCTCCTTGGCAC 58.423 47.619 0.00 0.00 0.00 5.01
369 569 1.532868 CTGAACTTTCTCCTTGGCACG 59.467 52.381 0.00 0.00 0.00 5.34
370 570 0.238553 GAACTTTCTCCTTGGCACGC 59.761 55.000 0.00 0.00 0.00 5.34
371 571 1.507141 AACTTTCTCCTTGGCACGCG 61.507 55.000 3.53 3.53 0.00 6.01
372 572 1.961277 CTTTCTCCTTGGCACGCGT 60.961 57.895 5.58 5.58 0.00 6.01
373 573 2.175184 CTTTCTCCTTGGCACGCGTG 62.175 60.000 34.01 34.01 0.00 5.34
376 576 2.031919 TCCTTGGCACGCGTGATT 59.968 55.556 41.19 1.06 0.00 2.57
377 577 0.739462 CTCCTTGGCACGCGTGATTA 60.739 55.000 41.19 23.07 0.00 1.75
420 627 1.532868 GTGCAGGTGATCACAACTCAC 59.467 52.381 26.47 21.21 42.75 3.51
466 673 1.092921 ACCACAACAAAGCGAGCGAA 61.093 50.000 0.00 0.00 0.00 4.70
471 678 1.557443 AACAAAGCGAGCGAACGAGG 61.557 55.000 5.91 0.00 35.09 4.63
472 679 2.432628 AAAGCGAGCGAACGAGGG 60.433 61.111 5.91 0.00 35.09 4.30
473 680 2.927580 AAAGCGAGCGAACGAGGGA 61.928 57.895 5.91 0.00 35.09 4.20
474 681 2.430382 AAAGCGAGCGAACGAGGGAA 62.430 55.000 5.91 0.00 35.09 3.97
475 682 2.820767 AAGCGAGCGAACGAGGGAAG 62.821 60.000 5.91 0.00 35.09 3.46
497 704 3.808466 TTGATGTGAGGTGCTAGCTAG 57.192 47.619 16.84 16.84 0.00 3.42
498 705 3.018423 TGATGTGAGGTGCTAGCTAGA 57.982 47.619 25.15 6.86 0.00 2.43
501 708 2.649190 TGTGAGGTGCTAGCTAGAGAG 58.351 52.381 25.15 0.02 0.00 3.20
502 709 2.239907 TGTGAGGTGCTAGCTAGAGAGA 59.760 50.000 25.15 1.58 0.00 3.10
525 739 1.723273 GTTATACCAAACCCGCGGC 59.277 57.895 22.85 0.00 0.00 6.53
649 917 4.865776 ACTGCTCAGCTCTCGTAATAATC 58.134 43.478 0.00 0.00 0.00 1.75
780 1053 5.551233 TGAAAATCTCTCTACACCACCTTG 58.449 41.667 0.00 0.00 0.00 3.61
781 1054 3.618690 AATCTCTCTACACCACCTTGC 57.381 47.619 0.00 0.00 0.00 4.01
783 1056 2.609747 TCTCTCTACACCACCTTGCTT 58.390 47.619 0.00 0.00 0.00 3.91
784 1057 2.972713 TCTCTCTACACCACCTTGCTTT 59.027 45.455 0.00 0.00 0.00 3.51
787 1068 4.832248 TCTCTACACCACCTTGCTTTATG 58.168 43.478 0.00 0.00 0.00 1.90
789 1070 2.969821 ACACCACCTTGCTTTATGGA 57.030 45.000 4.89 0.00 36.04 3.41
809 1090 3.608760 GGGAGCCGAGCTATAAACC 57.391 57.895 0.00 0.00 39.88 3.27
847 1128 2.969628 TCTTCGCTTTGATCTCTCCC 57.030 50.000 0.00 0.00 0.00 4.30
849 1130 1.208052 CTTCGCTTTGATCTCTCCCCA 59.792 52.381 0.00 0.00 0.00 4.96
850 1131 0.537188 TCGCTTTGATCTCTCCCCAC 59.463 55.000 0.00 0.00 0.00 4.61
851 1132 0.539051 CGCTTTGATCTCTCCCCACT 59.461 55.000 0.00 0.00 0.00 4.00
852 1133 1.472376 CGCTTTGATCTCTCCCCACTC 60.472 57.143 0.00 0.00 0.00 3.51
853 1134 1.836802 GCTTTGATCTCTCCCCACTCT 59.163 52.381 0.00 0.00 0.00 3.24
869 1159 0.174617 CTCTCGCCACTTTCCTCTCC 59.825 60.000 0.00 0.00 0.00 3.71
924 1223 1.080569 CATTGCGGTTGGTTGGCTC 60.081 57.895 0.00 0.00 0.00 4.70
966 1282 0.391793 AAAGCTAGCTTCTCCACCGC 60.392 55.000 29.42 0.00 34.84 5.68
996 1312 0.445436 CTAGAGCAAGCAACCAAGCG 59.555 55.000 0.00 0.00 40.15 4.68
1016 1332 2.159296 CGTACACATCATCGGAGGTTGA 60.159 50.000 7.63 0.00 35.53 3.18
1034 1360 1.683790 GATTTGCCACTCGTCGTCGG 61.684 60.000 1.55 0.00 37.69 4.79
1071 1397 0.815213 GATGCGTAATGGGAGCAGCA 60.815 55.000 0.00 0.00 45.36 4.41
1088 1414 0.948141 GCAGCTCGTGTTGCTCTTCT 60.948 55.000 17.47 0.00 45.15 2.85
1102 1431 2.887337 CTCTTCTTCTTCTTCTCCGGC 58.113 52.381 0.00 0.00 0.00 6.13
1148 1501 0.682209 ATGGCCAGCAGCTTGTTAGG 60.682 55.000 13.05 0.00 43.05 2.69
1284 1637 1.529713 CTCCTCCTCGCCTACCTCC 60.530 68.421 0.00 0.00 0.00 4.30
1285 1638 2.002018 CTCCTCCTCGCCTACCTCCT 62.002 65.000 0.00 0.00 0.00 3.69
1455 1833 4.796231 GAGCGTCGTGGCCGTGAT 62.796 66.667 0.00 0.00 35.01 3.06
1458 1836 2.095847 GCGTCGTGGCCGTGATAAA 61.096 57.895 0.00 0.00 35.01 1.40
1460 1838 0.734942 CGTCGTGGCCGTGATAAACT 60.735 55.000 0.00 0.00 35.01 2.66
1462 1840 2.609350 GTCGTGGCCGTGATAAACTTA 58.391 47.619 0.00 0.00 35.01 2.24
1464 1842 2.029200 TCGTGGCCGTGATAAACTTACA 60.029 45.455 0.00 0.00 35.01 2.41
1481 1859 2.131776 ACAGAGAGTAACTCCGGGAG 57.868 55.000 22.40 22.40 45.96 4.30
1578 1962 2.338984 GCCGTGTTCGAGGACACT 59.661 61.111 16.19 0.00 45.96 3.55
1673 2060 3.068881 CTTGGAGGTGGCGGAGAA 58.931 61.111 0.00 0.00 0.00 2.87
1807 2209 3.721868 CCGAAGAGGCCAGGGTTA 58.278 61.111 5.01 0.00 0.00 2.85
1900 2302 2.097160 CGTCGTCGTCACTACCGG 59.903 66.667 0.00 0.00 0.00 5.28
1934 2336 5.048507 CGTTAAAGGCAATCTCCTAGGTAC 58.951 45.833 9.08 0.00 34.82 3.34
1945 2347 5.321934 TCTCCTAGGTACCTAGATTCCAC 57.678 47.826 39.54 0.44 46.56 4.02
1947 2349 5.435707 TCTCCTAGGTACCTAGATTCCACTT 59.564 44.000 39.54 8.66 46.56 3.16
1953 2355 4.401837 GGTACCTAGATTCCACTTCGTTCT 59.598 45.833 4.06 0.00 0.00 3.01
2007 2409 5.244851 ACTTCTCAGCTTGATCTTACACTGA 59.755 40.000 0.00 0.00 33.42 3.41
2028 2438 3.394674 TTGTCATACGGTTGCAGAGAA 57.605 42.857 0.00 0.00 0.00 2.87
2045 2455 1.070758 AGAAGCAACGAAGCAGAGGAA 59.929 47.619 6.62 0.00 36.85 3.36
2049 2459 1.337260 GCAACGAAGCAGAGGAAGAGA 60.337 52.381 0.00 0.00 0.00 3.10
2050 2460 2.676463 GCAACGAAGCAGAGGAAGAGAT 60.676 50.000 0.00 0.00 0.00 2.75
2051 2461 3.429547 GCAACGAAGCAGAGGAAGAGATA 60.430 47.826 0.00 0.00 0.00 1.98
2053 2463 5.355596 CAACGAAGCAGAGGAAGAGATAAT 58.644 41.667 0.00 0.00 0.00 1.28
2064 2483 4.022762 AGGAAGAGATAATGACGGTGATCG 60.023 45.833 0.00 0.00 45.88 3.69
2086 2505 2.432628 GAAGACGGGCGTGGAGTG 60.433 66.667 0.00 0.00 0.00 3.51
2097 2516 0.605589 CGTGGAGTGGAAGAAGAGCT 59.394 55.000 0.00 0.00 0.00 4.09
2112 2549 0.466555 GAGCTAGAGGAGAAGGCCGA 60.467 60.000 0.00 0.00 0.00 5.54
2137 2574 3.110178 CCGGACGTGAAGCGGTTC 61.110 66.667 20.13 20.13 46.52 3.62
2149 2586 3.244105 CGGTTCGTGAACAGCCAG 58.756 61.111 14.16 0.00 42.85 4.85
2344 2781 0.677414 ACTCGGACCTCTTCTCGTCC 60.677 60.000 0.00 0.00 44.36 4.79
2457 2894 0.889306 AAGCTCACCGAGACAGGTAC 59.111 55.000 0.00 0.00 43.89 3.34
2458 2895 0.966370 AGCTCACCGAGACAGGTACC 60.966 60.000 2.73 2.73 43.89 3.34
2461 2898 2.933573 CTCACCGAGACAGGTACCTAT 58.066 52.381 15.80 1.84 43.89 2.57
2462 2899 3.746751 GCTCACCGAGACAGGTACCTATA 60.747 52.174 15.80 0.00 43.89 1.31
2463 2900 3.813443 TCACCGAGACAGGTACCTATAC 58.187 50.000 15.80 8.98 43.89 1.47
2466 2903 3.201708 ACCGAGACAGGTACCTATACACT 59.798 47.826 15.80 9.41 43.89 3.55
2467 2904 4.410228 ACCGAGACAGGTACCTATACACTA 59.590 45.833 15.80 0.00 43.89 2.74
2468 2905 5.104360 ACCGAGACAGGTACCTATACACTAA 60.104 44.000 15.80 0.00 43.89 2.24
2482 2925 7.279313 ACCTATACACTAAATTGTTTACTGCCG 59.721 37.037 0.00 0.00 0.00 5.69
2512 2955 9.383519 TGATTGTATCTAGGAAAACTGATGAAC 57.616 33.333 0.00 0.00 0.00 3.18
2517 2960 5.869579 TCTAGGAAAACTGATGAACTTGCT 58.130 37.500 0.00 0.00 0.00 3.91
2518 2961 5.934625 TCTAGGAAAACTGATGAACTTGCTC 59.065 40.000 0.00 0.00 0.00 4.26
2519 2962 4.464008 AGGAAAACTGATGAACTTGCTCA 58.536 39.130 0.00 0.00 0.00 4.26
2540 2983 5.175859 TCATCATCATCATCATCATCACCG 58.824 41.667 0.00 0.00 0.00 4.94
2560 3003 5.470098 CACCGAATATTCCCCAAGTTATCAG 59.530 44.000 9.87 0.00 0.00 2.90
2632 3075 2.817258 CCCGTATTTCCAGTTCTTTGCA 59.183 45.455 0.00 0.00 0.00 4.08
2796 3239 9.662545 CAATGTTCCATTTTAAATTTGTGTTCC 57.337 29.630 0.00 0.00 0.00 3.62
2827 3270 4.212214 GGCTGAAGAATTATGGACGATGAC 59.788 45.833 0.00 0.00 0.00 3.06
2847 3290 0.790207 GACGTCGATGCATGTGTGTT 59.210 50.000 2.46 0.00 0.00 3.32
2848 3291 0.512518 ACGTCGATGCATGTGTGTTG 59.487 50.000 2.46 0.00 0.00 3.33
2849 3292 0.512518 CGTCGATGCATGTGTGTTGT 59.487 50.000 2.46 0.00 0.00 3.32
2850 3293 1.722435 CGTCGATGCATGTGTGTTGTG 60.722 52.381 2.46 0.00 0.00 3.33
2851 3294 0.238025 TCGATGCATGTGTGTTGTGC 59.762 50.000 2.46 0.00 39.26 4.57
2852 3295 0.239082 CGATGCATGTGTGTTGTGCT 59.761 50.000 2.46 0.00 39.52 4.40
3078 3521 0.683412 GGAACTACACCACCTTCCGT 59.317 55.000 0.00 0.00 0.00 4.69
3156 3602 2.281484 GTGGCGCAGGAGTTCCAA 60.281 61.111 10.83 0.00 38.89 3.53
3201 3647 0.984230 TCATGGAGAACGAGCCCTTT 59.016 50.000 0.00 0.00 0.00 3.11
3207 3653 0.326264 AGAACGAGCCCTTTGAGCAT 59.674 50.000 0.00 0.00 0.00 3.79
3285 3731 1.473278 GTCCCAGAGTTCAGAGGTACG 59.527 57.143 0.00 0.00 0.00 3.67
3286 3732 1.075050 TCCCAGAGTTCAGAGGTACGT 59.925 52.381 0.00 0.00 0.00 3.57
3288 3734 1.473278 CCAGAGTTCAGAGGTACGTCC 59.527 57.143 11.83 0.00 0.00 4.79
3289 3735 1.473278 CAGAGTTCAGAGGTACGTCCC 59.527 57.143 11.83 0.00 36.75 4.46
3290 3736 0.816373 GAGTTCAGAGGTACGTCCCC 59.184 60.000 11.83 0.00 36.75 4.81
3291 3737 0.113776 AGTTCAGAGGTACGTCCCCA 59.886 55.000 11.83 0.00 36.75 4.96
3292 3738 0.531200 GTTCAGAGGTACGTCCCCAG 59.469 60.000 11.83 1.02 36.75 4.45
3293 3739 1.255667 TTCAGAGGTACGTCCCCAGC 61.256 60.000 11.83 0.00 36.75 4.85
3295 3741 2.682494 GAGGTACGTCCCCAGCCA 60.682 66.667 4.15 0.00 36.75 4.75
3296 3742 2.040606 AGGTACGTCCCCAGCCAT 59.959 61.111 0.00 0.00 36.75 4.40
3297 3743 2.189521 GGTACGTCCCCAGCCATG 59.810 66.667 0.00 0.00 0.00 3.66
3313 3759 2.862530 GCCATGCATTGATCTGTCATGC 60.863 50.000 1.13 10.85 38.36 4.06
3315 3761 3.818773 CCATGCATTGATCTGTCATGCTA 59.181 43.478 15.87 7.36 38.53 3.49
3318 3764 6.403309 CCATGCATTGATCTGTCATGCTATAC 60.403 42.308 15.87 0.00 38.53 1.47
3352 3845 7.925993 TGTACTGAATTTTTACTGACTGGTTG 58.074 34.615 0.00 0.00 0.00 3.77
3568 4061 1.507141 CCAACAAGGCCGTGAGTGAC 61.507 60.000 26.25 0.00 0.00 3.67
3570 4063 2.738521 CAAGGCCGTGAGTGACCG 60.739 66.667 14.14 0.00 0.00 4.79
3571 4064 3.231736 AAGGCCGTGAGTGACCGT 61.232 61.111 0.00 0.00 0.00 4.83
3572 4065 3.222354 AAGGCCGTGAGTGACCGTC 62.222 63.158 0.00 0.00 0.00 4.79
3573 4066 3.986006 GGCCGTGAGTGACCGTCA 61.986 66.667 0.00 0.00 0.00 4.35
3574 4067 2.261671 GCCGTGAGTGACCGTCAT 59.738 61.111 4.13 0.00 0.00 3.06
3575 4068 1.805945 GCCGTGAGTGACCGTCATC 60.806 63.158 4.13 4.54 0.00 2.92
3577 4070 0.038618 CCGTGAGTGACCGTCATCAA 60.039 55.000 4.13 0.00 0.00 2.57
3579 4072 1.920574 CGTGAGTGACCGTCATCAATC 59.079 52.381 4.13 2.33 42.63 2.67
3594 4103 5.515270 GTCATCAATCAAGTGTTCATGCATG 59.485 40.000 21.07 21.07 0.00 4.06
3596 4105 3.256136 TCAATCAAGTGTTCATGCATGCA 59.744 39.130 25.04 25.04 0.00 3.96
3597 4106 4.081917 TCAATCAAGTGTTCATGCATGCAT 60.082 37.500 27.46 27.46 37.08 3.96
3610 4119 2.417339 CATGCATGCATTCCTACTGC 57.583 50.000 30.32 0.00 40.10 4.40
3702 4213 3.819188 GCCTGAAGCGGATCAAGG 58.181 61.111 0.00 0.00 0.00 3.61
3711 4222 2.190578 GGATCAAGGTGCGGGAGG 59.809 66.667 0.00 0.00 0.00 4.30
3897 4408 3.876589 TTCTTCCCCGCGCACTGAC 62.877 63.158 8.75 0.00 0.00 3.51
3898 4409 4.379243 CTTCCCCGCGCACTGACT 62.379 66.667 8.75 0.00 0.00 3.41
3899 4410 4.680237 TTCCCCGCGCACTGACTG 62.680 66.667 8.75 0.00 0.00 3.51
3922 4441 1.475403 TCTCATCAGAACCTCCGTCC 58.525 55.000 0.00 0.00 0.00 4.79
3976 4495 5.596772 TGCAACCTAGCTACTTTTCCTTTTT 59.403 36.000 0.00 0.00 34.99 1.94
4007 4526 8.857694 TTATTTCGTTCACCTTATCTTCCTTT 57.142 30.769 0.00 0.00 0.00 3.11
4050 4569 5.147162 AGCGACAAAAGAAAAGATAAAGCG 58.853 37.500 0.00 0.00 0.00 4.68
4212 4735 2.726681 CGGTGTTGTAAAGGCGTAATGC 60.727 50.000 0.00 0.00 45.38 3.56
4261 4785 3.733960 GGCCCGTTTCCGTCTTGC 61.734 66.667 0.00 0.00 0.00 4.01
4269 4797 0.106918 TTTCCGTCTTGCAGTTGGGT 60.107 50.000 0.00 0.00 0.00 4.51
4298 4826 1.271271 TGTGGTGCATGCTGACATACA 60.271 47.619 20.33 14.61 33.67 2.29
4323 4862 7.488792 CACACACAGAGATAAAAGAGAGAGATG 59.511 40.741 0.00 0.00 0.00 2.90
4356 4895 1.295101 CGGCAGTACCATGTCACCA 59.705 57.895 0.00 0.00 39.03 4.17
4365 4904 0.241749 CCATGTCACCATGTGTGTGC 59.758 55.000 12.26 8.50 45.83 4.57
4437 4976 2.093783 CGGACGGCTTTGATAGTTTGAC 59.906 50.000 0.00 0.00 0.00 3.18
4445 4984 4.855388 GCTTTGATAGTTTGACATGTGCAG 59.145 41.667 1.15 0.00 0.00 4.41
4446 4985 5.563475 GCTTTGATAGTTTGACATGTGCAGT 60.563 40.000 1.15 0.00 0.00 4.40
4461 5003 0.600057 GCAGTGCTTTAGGCTTTGCT 59.400 50.000 8.18 0.00 42.84 3.91
4469 5011 3.826466 CTTTAGGCTTTGCTTTTCCTCG 58.174 45.455 0.00 0.00 0.00 4.63
4476 5018 2.842208 TTGCTTTTCCTCGTGTGTTG 57.158 45.000 0.00 0.00 0.00 3.33
4478 5020 0.317854 GCTTTTCCTCGTGTGTTGCC 60.318 55.000 0.00 0.00 0.00 4.52
4573 5115 1.893808 ACGCACTTGGACTTGCCTG 60.894 57.895 0.00 0.00 35.14 4.85
4587 5129 3.694072 ACTTGCCTGCGCATTTAAGATAA 59.306 39.130 24.96 8.47 46.67 1.75
4595 5137 3.839954 GCGCATTTAAGATAACCACGTCG 60.840 47.826 0.30 0.00 0.00 5.12
4621 5164 3.824443 CGCCCTCCTTTTCCTTTTTCTTA 59.176 43.478 0.00 0.00 0.00 2.10
4722 5271 4.509970 TGCGAAAAAGCTATGTATATGCGT 59.490 37.500 0.00 0.00 38.13 5.24
4760 5309 2.286872 CCAGTTGGAAGATAGCAGCAG 58.713 52.381 0.00 0.00 37.39 4.24
4844 6717 1.577328 GGGTGTCGATGTTGGTGCTG 61.577 60.000 0.00 0.00 0.00 4.41
4922 6796 0.882927 TAGCACGGTCACAAAGTGGC 60.883 55.000 0.00 0.00 37.44 5.01
4956 6830 1.665137 GGGTCAAAAGGAGTAGGGGA 58.335 55.000 0.00 0.00 0.00 4.81
4977 6851 2.093235 AGAGAACTCAGGCTGGCAATAC 60.093 50.000 15.73 3.31 0.00 1.89
5010 6884 4.228210 AGCGGGGTATTGATTCATATCCAT 59.772 41.667 7.35 0.00 0.00 3.41
5012 6886 4.883585 CGGGGTATTGATTCATATCCATGG 59.116 45.833 4.97 4.97 32.61 3.66
5015 6889 5.513233 GGTATTGATTCATATCCATGGCCT 58.487 41.667 6.96 0.00 32.61 5.19
5016 6890 5.591877 GGTATTGATTCATATCCATGGCCTC 59.408 44.000 6.96 0.00 32.61 4.70
5017 6891 3.339253 TGATTCATATCCATGGCCTCG 57.661 47.619 6.96 0.00 32.61 4.63
5018 6892 2.012673 GATTCATATCCATGGCCTCGC 58.987 52.381 6.96 0.00 32.61 5.03
5019 6893 0.320683 TTCATATCCATGGCCTCGCG 60.321 55.000 6.96 0.00 32.61 5.87
5020 6894 1.184970 TCATATCCATGGCCTCGCGA 61.185 55.000 9.26 9.26 32.61 5.87
5060 6934 0.322098 CGTGCATGTCCCTACCCAAA 60.322 55.000 0.00 0.00 0.00 3.28
5061 6935 1.681780 CGTGCATGTCCCTACCCAAAT 60.682 52.381 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 229 3.285371 CCGCCTTCTCACGGTAGT 58.715 61.111 0.00 0.00 44.46 2.73
122 246 2.240162 CTACTTCCCCTGTCGCCCAC 62.240 65.000 0.00 0.00 0.00 4.61
123 247 1.987855 CTACTTCCCCTGTCGCCCA 60.988 63.158 0.00 0.00 0.00 5.36
124 248 1.684734 TCTACTTCCCCTGTCGCCC 60.685 63.158 0.00 0.00 0.00 6.13
125 249 1.255667 TGTCTACTTCCCCTGTCGCC 61.256 60.000 0.00 0.00 0.00 5.54
126 250 0.108756 GTGTCTACTTCCCCTGTCGC 60.109 60.000 0.00 0.00 0.00 5.19
127 251 0.531200 GGTGTCTACTTCCCCTGTCG 59.469 60.000 0.00 0.00 0.00 4.35
128 252 1.939980 AGGTGTCTACTTCCCCTGTC 58.060 55.000 0.00 0.00 0.00 3.51
129 253 3.442076 CTTAGGTGTCTACTTCCCCTGT 58.558 50.000 0.00 0.00 0.00 4.00
130 254 2.168728 GCTTAGGTGTCTACTTCCCCTG 59.831 54.545 0.00 0.00 0.00 4.45
131 255 2.225547 TGCTTAGGTGTCTACTTCCCCT 60.226 50.000 0.00 0.00 0.00 4.79
132 256 2.185387 TGCTTAGGTGTCTACTTCCCC 58.815 52.381 0.00 0.00 0.00 4.81
133 257 3.597255 GTTGCTTAGGTGTCTACTTCCC 58.403 50.000 0.00 0.00 0.00 3.97
175 299 3.256960 GGTGGCCTCCCAAGACCA 61.257 66.667 13.20 0.00 44.33 4.02
200 324 1.537202 GTGTTCAGCCAGCTTGTAAGG 59.463 52.381 0.00 0.00 0.00 2.69
214 338 2.709125 CTTCCTCGGTGCGGTGTTCA 62.709 60.000 0.00 0.00 0.00 3.18
218 342 3.649277 CTCCTTCCTCGGTGCGGTG 62.649 68.421 0.00 0.00 0.00 4.94
219 343 3.382832 CTCCTTCCTCGGTGCGGT 61.383 66.667 0.00 0.00 0.00 5.68
221 345 1.066587 GATCTCCTTCCTCGGTGCG 59.933 63.158 0.00 0.00 0.00 5.34
222 346 1.066587 CGATCTCCTTCCTCGGTGC 59.933 63.158 0.00 0.00 0.00 5.01
223 347 0.665835 CTCGATCTCCTTCCTCGGTG 59.334 60.000 0.00 0.00 33.38 4.94
224 348 0.256464 ACTCGATCTCCTTCCTCGGT 59.744 55.000 0.00 0.00 33.38 4.69
225 349 0.948678 GACTCGATCTCCTTCCTCGG 59.051 60.000 0.00 0.00 33.38 4.63
255 446 0.401738 TCTTGAAGCCACCTTCCTGG 59.598 55.000 1.43 0.00 45.53 4.45
261 452 2.319844 CCCTTTTTCTTGAAGCCACCT 58.680 47.619 0.00 0.00 0.00 4.00
264 455 2.765689 TCCCCTTTTTCTTGAAGCCA 57.234 45.000 0.00 0.00 0.00 4.75
348 548 2.576615 GTGCCAAGGAGAAAGTTCAGT 58.423 47.619 0.00 0.00 0.00 3.41
365 565 1.076332 AAGAGGTTAATCACGCGTGC 58.924 50.000 33.63 19.02 0.00 5.34
366 566 1.201921 GCAAGAGGTTAATCACGCGTG 60.202 52.381 32.76 32.76 0.00 5.34
367 567 1.076332 GCAAGAGGTTAATCACGCGT 58.924 50.000 5.58 5.58 0.00 6.01
368 568 1.359848 AGCAAGAGGTTAATCACGCG 58.640 50.000 3.53 3.53 0.00 6.01
369 569 3.188460 TCAAAGCAAGAGGTTAATCACGC 59.812 43.478 0.00 0.00 34.49 5.34
370 570 4.670221 GCTCAAAGCAAGAGGTTAATCACG 60.670 45.833 0.00 0.00 41.89 4.35
371 571 4.727475 GCTCAAAGCAAGAGGTTAATCAC 58.273 43.478 0.00 0.00 41.89 3.06
420 627 6.539649 TGTAGCACTTGTTTTTAGTAGCTG 57.460 37.500 0.00 0.00 34.34 4.24
466 673 2.169352 CCTCACATCAATCTTCCCTCGT 59.831 50.000 0.00 0.00 0.00 4.18
471 678 2.996631 AGCACCTCACATCAATCTTCC 58.003 47.619 0.00 0.00 0.00 3.46
472 679 3.559242 GCTAGCACCTCACATCAATCTTC 59.441 47.826 10.63 0.00 0.00 2.87
473 680 3.199508 AGCTAGCACCTCACATCAATCTT 59.800 43.478 18.83 0.00 0.00 2.40
474 681 2.770802 AGCTAGCACCTCACATCAATCT 59.229 45.455 18.83 0.00 0.00 2.40
475 682 3.191078 AGCTAGCACCTCACATCAATC 57.809 47.619 18.83 0.00 0.00 2.67
497 704 2.486951 TTGGTATAACGCGCTCTCTC 57.513 50.000 5.73 0.00 0.00 3.20
498 705 2.537401 GTTTGGTATAACGCGCTCTCT 58.463 47.619 5.73 0.00 0.00 3.10
501 708 0.654160 GGGTTTGGTATAACGCGCTC 59.346 55.000 5.73 0.00 32.42 5.03
502 709 2.771435 GGGTTTGGTATAACGCGCT 58.229 52.632 5.73 0.00 32.42 5.92
649 917 2.349886 GCAAGCAAGTAATCTCCGAGTG 59.650 50.000 0.00 0.00 0.00 3.51
769 1042 3.681593 GTCCATAAAGCAAGGTGGTGTA 58.318 45.455 0.00 0.00 33.47 2.90
771 1044 1.468520 CGTCCATAAAGCAAGGTGGTG 59.531 52.381 0.00 0.00 33.47 4.17
780 1053 1.887707 CGGCTCCCGTCCATAAAGC 60.888 63.158 0.00 0.00 42.73 3.51
781 1054 4.438346 CGGCTCCCGTCCATAAAG 57.562 61.111 0.00 0.00 42.73 1.85
847 1128 0.390472 GAGGAAAGTGGCGAGAGTGG 60.390 60.000 0.00 0.00 0.00 4.00
849 1130 0.892063 GAGAGGAAAGTGGCGAGAGT 59.108 55.000 0.00 0.00 0.00 3.24
850 1131 0.174617 GGAGAGGAAAGTGGCGAGAG 59.825 60.000 0.00 0.00 0.00 3.20
851 1132 1.258445 GGGAGAGGAAAGTGGCGAGA 61.258 60.000 0.00 0.00 0.00 4.04
852 1133 1.219393 GGGAGAGGAAAGTGGCGAG 59.781 63.158 0.00 0.00 0.00 5.03
853 1134 1.229209 AGGGAGAGGAAAGTGGCGA 60.229 57.895 0.00 0.00 0.00 5.54
869 1159 1.585006 CTTGCTGCTTTGCTCCAGG 59.415 57.895 0.00 0.00 0.00 4.45
924 1223 0.605083 GCTTTGGCCAAGGAAGGAAG 59.395 55.000 30.20 18.06 32.37 3.46
966 1282 2.052060 GCTCTAGAGGCGTACGCG 60.052 66.667 31.78 18.76 43.06 6.01
970 1286 1.135083 GTTGCTTGCTCTAGAGGCGTA 60.135 52.381 21.23 6.05 0.00 4.42
996 1312 3.520290 TCAACCTCCGATGATGTGTAC 57.480 47.619 0.00 0.00 0.00 2.90
1016 1332 1.736645 CCGACGACGAGTGGCAAAT 60.737 57.895 9.28 0.00 42.66 2.32
1034 1360 4.266070 TATCTGCTCCGACGCCGC 62.266 66.667 0.00 0.00 0.00 6.53
1044 1370 2.899900 TCCCATTACGCATCTATCTGCT 59.100 45.455 0.00 0.00 40.06 4.24
1071 1397 1.342819 AGAAGAAGAGCAACACGAGCT 59.657 47.619 0.00 0.00 46.82 4.09
1078 1404 3.677596 CGGAGAAGAAGAAGAAGAGCAAC 59.322 47.826 0.00 0.00 0.00 4.17
1088 1414 1.292223 CACCGCCGGAGAAGAAGAA 59.708 57.895 11.71 0.00 0.00 2.52
1102 1431 3.726517 CCTGCGAGCCAAACACCG 61.727 66.667 0.00 0.00 0.00 4.94
1148 1501 3.160748 GGGCAGGAGGAGGAGCTC 61.161 72.222 4.71 4.71 0.00 4.09
1284 1637 1.892819 TTGGCGAGGAGGAAGAGCAG 61.893 60.000 0.00 0.00 0.00 4.24
1285 1638 1.892819 CTTGGCGAGGAGGAAGAGCA 61.893 60.000 0.00 0.00 0.00 4.26
1359 1736 6.070653 TGCCTGAATTGAAGGAGCAATAATTT 60.071 34.615 7.79 0.00 37.50 1.82
1443 1821 2.029200 TGTAAGTTTATCACGGCCACGA 60.029 45.455 2.24 0.00 44.60 4.35
1455 1833 5.416952 CCCGGAGTTACTCTCTGTAAGTTTA 59.583 44.000 12.41 0.00 45.40 2.01
1458 1836 3.009916 TCCCGGAGTTACTCTCTGTAAGT 59.990 47.826 12.41 0.00 45.40 2.24
1460 1838 3.618351 CTCCCGGAGTTACTCTCTGTAA 58.382 50.000 12.41 0.00 45.40 2.41
1462 1840 1.341187 CCTCCCGGAGTTACTCTCTGT 60.341 57.143 13.62 0.00 45.40 3.41
1464 1842 0.259356 CCCTCCCGGAGTTACTCTCT 59.741 60.000 13.62 0.00 42.40 3.10
1499 1877 2.573869 CTCCAGCGACGATGTGGT 59.426 61.111 12.66 0.00 32.73 4.16
1501 1879 2.202797 CCCTCCAGCGACGATGTG 60.203 66.667 12.66 3.87 0.00 3.21
1504 1882 2.835431 CTCCCCTCCAGCGACGAT 60.835 66.667 0.00 0.00 0.00 3.73
1543 1927 0.599204 GCCTCGTCGAACCAGAACAA 60.599 55.000 0.00 0.00 0.00 2.83
1673 2060 4.927782 TGTGAAAGGCGCGGCTGT 62.928 61.111 36.94 32.28 0.00 4.40
1843 2245 1.300697 GATACCCATCCGTCGCCAC 60.301 63.158 0.00 0.00 0.00 5.01
1849 2251 1.046472 TTCTGCCGATACCCATCCGT 61.046 55.000 0.00 0.00 0.00 4.69
1900 2302 5.560966 TTGCCTTTAACGGAATCATTCTC 57.439 39.130 1.37 0.00 0.00 2.87
1915 2317 3.737263 AGGTACCTAGGAGATTGCCTTT 58.263 45.455 17.98 0.00 39.50 3.11
1934 2336 7.493367 AGAATAAGAACGAAGTGGAATCTAGG 58.507 38.462 0.00 0.00 45.00 3.02
1945 2347 4.416620 AGTGAGCGAGAATAAGAACGAAG 58.583 43.478 0.00 0.00 0.00 3.79
1947 2349 4.156190 AGAAGTGAGCGAGAATAAGAACGA 59.844 41.667 0.00 0.00 0.00 3.85
1953 2355 7.411912 CGATGAAAAAGAAGTGAGCGAGAATAA 60.412 37.037 0.00 0.00 0.00 1.40
2007 2409 3.610040 TCTCTGCAACCGTATGACAAT 57.390 42.857 0.00 0.00 0.00 2.71
2028 2438 0.681733 TCTTCCTCTGCTTCGTTGCT 59.318 50.000 4.36 0.00 0.00 3.91
2064 2483 2.432628 CACGCCCGTCTTCAGGAC 60.433 66.667 0.00 0.00 41.28 3.85
2067 2486 2.125912 CTCCACGCCCGTCTTCAG 60.126 66.667 0.00 0.00 0.00 3.02
2079 2498 3.093057 TCTAGCTCTTCTTCCACTCCAC 58.907 50.000 0.00 0.00 0.00 4.02
2086 2505 3.636764 CCTTCTCCTCTAGCTCTTCTTCC 59.363 52.174 0.00 0.00 0.00 3.46
2097 2516 1.453379 CCGTCGGCCTTCTCCTCTA 60.453 63.158 0.00 0.00 0.00 2.43
2457 2894 7.493320 TCGGCAGTAAACAATTTAGTGTATAGG 59.507 37.037 14.53 4.20 44.56 2.57
2458 2895 8.415192 TCGGCAGTAAACAATTTAGTGTATAG 57.585 34.615 14.53 6.85 44.56 1.31
2461 2898 7.675962 ATTCGGCAGTAAACAATTTAGTGTA 57.324 32.000 14.53 2.71 44.56 2.90
2462 2899 6.569179 ATTCGGCAGTAAACAATTTAGTGT 57.431 33.333 14.53 0.00 44.56 3.55
2463 2900 7.081349 TCAATTCGGCAGTAAACAATTTAGTG 58.919 34.615 10.50 10.50 45.19 2.74
2466 2903 8.085296 ACAATCAATTCGGCAGTAAACAATTTA 58.915 29.630 0.00 0.00 0.00 1.40
2467 2904 6.928492 ACAATCAATTCGGCAGTAAACAATTT 59.072 30.769 0.00 0.00 0.00 1.82
2468 2905 6.454795 ACAATCAATTCGGCAGTAAACAATT 58.545 32.000 0.00 0.00 0.00 2.32
2512 2955 6.372659 TGATGATGATGATGATGATGAGCAAG 59.627 38.462 0.00 0.00 0.00 4.01
2517 2960 5.046878 TCGGTGATGATGATGATGATGATGA 60.047 40.000 0.00 0.00 0.00 2.92
2518 2961 5.175859 TCGGTGATGATGATGATGATGATG 58.824 41.667 0.00 0.00 0.00 3.07
2519 2962 5.416271 TCGGTGATGATGATGATGATGAT 57.584 39.130 0.00 0.00 0.00 2.45
2540 2983 7.939039 TGATGACTGATAACTTGGGGAATATTC 59.061 37.037 6.93 6.93 0.00 1.75
2560 3003 7.230510 AGTTGATCTAGTAGAGGTGATGATGAC 59.769 40.741 5.98 0.00 0.00 3.06
2632 3075 0.827507 ACATGCCCCTGAAAAGCGTT 60.828 50.000 0.00 0.00 0.00 4.84
2784 3227 1.269726 CGGCAGCAGGAACACAAATTT 60.270 47.619 0.00 0.00 0.00 1.82
2827 3270 1.341467 CACACATGCATCGACGTCG 59.659 57.895 31.30 31.30 41.45 5.12
2850 3293 1.134075 CGACTCTGCATGCACAAGC 59.866 57.895 18.46 11.79 42.57 4.01
2851 3294 0.870393 AACGACTCTGCATGCACAAG 59.130 50.000 18.46 18.90 0.00 3.16
2852 3295 0.867746 GAACGACTCTGCATGCACAA 59.132 50.000 18.46 7.09 0.00 3.33
3156 3602 1.072159 GAGCAGCACCTGGAACTGT 59.928 57.895 17.60 8.27 33.87 3.55
3225 3671 0.460311 AGTTCTTCATCCGGGCGTAG 59.540 55.000 0.00 0.00 0.00 3.51
3285 3731 0.757935 ATCAATGCATGGCTGGGGAC 60.758 55.000 0.00 0.00 0.00 4.46
3286 3732 0.468585 GATCAATGCATGGCTGGGGA 60.469 55.000 0.00 0.00 0.00 4.81
3288 3734 0.673985 CAGATCAATGCATGGCTGGG 59.326 55.000 0.00 0.00 32.00 4.45
3289 3735 1.337071 GACAGATCAATGCATGGCTGG 59.663 52.381 17.27 3.99 36.66 4.85
3290 3736 2.021457 TGACAGATCAATGCATGGCTG 58.979 47.619 0.00 8.28 37.65 4.85
3291 3737 2.430248 TGACAGATCAATGCATGGCT 57.570 45.000 0.00 0.00 0.00 4.75
3292 3738 2.862530 GCATGACAGATCAATGCATGGC 60.863 50.000 0.00 0.00 38.69 4.40
3293 3739 2.623416 AGCATGACAGATCAATGCATGG 59.377 45.455 18.75 0.00 39.68 3.66
3295 3741 6.235664 TGTATAGCATGACAGATCAATGCAT 58.764 36.000 18.75 0.00 39.68 3.96
3296 3742 5.613329 TGTATAGCATGACAGATCAATGCA 58.387 37.500 18.75 0.00 39.68 3.96
3297 3743 6.738832 ATGTATAGCATGACAGATCAATGC 57.261 37.500 12.25 12.25 38.69 3.56
3326 3772 8.402472 CAACCAGTCAGTAAAAATTCAGTACAA 58.598 33.333 0.00 0.00 0.00 2.41
3328 3774 8.149973 TCAACCAGTCAGTAAAAATTCAGTAC 57.850 34.615 0.00 0.00 0.00 2.73
3329 3775 8.783093 CATCAACCAGTCAGTAAAAATTCAGTA 58.217 33.333 0.00 0.00 0.00 2.74
3330 3776 7.285401 ACATCAACCAGTCAGTAAAAATTCAGT 59.715 33.333 0.00 0.00 0.00 3.41
3331 3777 7.592533 CACATCAACCAGTCAGTAAAAATTCAG 59.407 37.037 0.00 0.00 0.00 3.02
3333 3779 6.363357 GCACATCAACCAGTCAGTAAAAATTC 59.637 38.462 0.00 0.00 0.00 2.17
3334 3780 6.183360 TGCACATCAACCAGTCAGTAAAAATT 60.183 34.615 0.00 0.00 0.00 1.82
3335 3781 5.301551 TGCACATCAACCAGTCAGTAAAAAT 59.698 36.000 0.00 0.00 0.00 1.82
3336 3782 4.642437 TGCACATCAACCAGTCAGTAAAAA 59.358 37.500 0.00 0.00 0.00 1.94
3337 3783 4.036262 GTGCACATCAACCAGTCAGTAAAA 59.964 41.667 13.17 0.00 0.00 1.52
3338 3784 3.563808 GTGCACATCAACCAGTCAGTAAA 59.436 43.478 13.17 0.00 0.00 2.01
3340 3833 2.103941 TGTGCACATCAACCAGTCAGTA 59.896 45.455 17.42 0.00 0.00 2.74
3342 3835 1.534163 CTGTGCACATCAACCAGTCAG 59.466 52.381 22.00 0.00 0.00 3.51
3346 3839 1.162698 CCTCTGTGCACATCAACCAG 58.837 55.000 22.00 6.84 0.00 4.00
3352 3845 0.177604 CCTCCTCCTCTGTGCACATC 59.822 60.000 22.00 0.00 0.00 3.06
3424 3917 1.475751 GCCATGAACGTCCTGATGGAT 60.476 52.381 9.59 0.00 45.29 3.41
3568 4061 4.655027 CATGAACACTTGATTGATGACGG 58.345 43.478 0.00 0.00 0.00 4.79
3570 4063 5.050644 TGCATGAACACTTGATTGATGAC 57.949 39.130 0.00 0.00 0.00 3.06
3571 4064 5.646606 CATGCATGAACACTTGATTGATGA 58.353 37.500 22.59 0.00 0.00 2.92
3572 4065 4.267690 GCATGCATGAACACTTGATTGATG 59.732 41.667 30.64 0.00 0.00 3.07
3573 4066 4.081917 TGCATGCATGAACACTTGATTGAT 60.082 37.500 30.64 0.00 0.00 2.57
3574 4067 3.256136 TGCATGCATGAACACTTGATTGA 59.744 39.130 30.64 0.00 0.00 2.57
3575 4068 3.580731 TGCATGCATGAACACTTGATTG 58.419 40.909 30.64 0.23 0.00 2.67
3614 4123 9.787532 TCAACACAAAAACAAAACATTCAAAAA 57.212 22.222 0.00 0.00 0.00 1.94
3615 4124 9.956720 ATCAACACAAAAACAAAACATTCAAAA 57.043 22.222 0.00 0.00 0.00 2.44
3616 4125 9.604626 GATCAACACAAAAACAAAACATTCAAA 57.395 25.926 0.00 0.00 0.00 2.69
3617 4126 8.777413 TGATCAACACAAAAACAAAACATTCAA 58.223 25.926 0.00 0.00 0.00 2.69
3618 4127 8.315391 TGATCAACACAAAAACAAAACATTCA 57.685 26.923 0.00 0.00 0.00 2.57
3619 4128 8.655092 TCTGATCAACACAAAAACAAAACATTC 58.345 29.630 0.00 0.00 0.00 2.67
3620 4129 8.545229 TCTGATCAACACAAAAACAAAACATT 57.455 26.923 0.00 0.00 0.00 2.71
3621 4130 8.545229 TTCTGATCAACACAAAAACAAAACAT 57.455 26.923 0.00 0.00 0.00 2.71
3622 4131 7.869937 TCTTCTGATCAACACAAAAACAAAACA 59.130 29.630 0.00 0.00 0.00 2.83
3623 4132 8.238481 TCTTCTGATCAACACAAAAACAAAAC 57.762 30.769 0.00 0.00 0.00 2.43
3624 4133 8.824159 TTCTTCTGATCAACACAAAAACAAAA 57.176 26.923 0.00 0.00 0.00 2.44
3625 4134 8.303156 TCTTCTTCTGATCAACACAAAAACAAA 58.697 29.630 0.00 0.00 0.00 2.83
3626 4135 7.825681 TCTTCTTCTGATCAACACAAAAACAA 58.174 30.769 0.00 0.00 0.00 2.83
3627 4136 7.389803 TCTTCTTCTGATCAACACAAAAACA 57.610 32.000 0.00 0.00 0.00 2.83
3638 4147 0.176680 GCCGGCTCTTCTTCTGATCA 59.823 55.000 22.15 0.00 0.00 2.92
3702 4213 3.151022 CTCCTCCTCCTCCCGCAC 61.151 72.222 0.00 0.00 0.00 5.34
3711 4222 3.775654 CACCGCCACCTCCTCCTC 61.776 72.222 0.00 0.00 0.00 3.71
3897 4408 3.004629 CGGAGGTTCTGATGAGATCTCAG 59.995 52.174 28.26 16.32 43.61 3.35
3898 4409 2.954989 CGGAGGTTCTGATGAGATCTCA 59.045 50.000 27.03 27.03 44.59 3.27
3899 4410 2.955660 ACGGAGGTTCTGATGAGATCTC 59.044 50.000 16.21 16.21 32.36 2.75
3900 4411 2.955660 GACGGAGGTTCTGATGAGATCT 59.044 50.000 0.00 0.00 0.00 2.75
4006 4525 8.662141 GTCGCTACACCAATATAAAGAGAAAAA 58.338 33.333 0.00 0.00 0.00 1.94
4007 4526 7.820386 TGTCGCTACACCAATATAAAGAGAAAA 59.180 33.333 0.00 0.00 0.00 2.29
4050 4569 3.220447 TGCCTACGCAAACACTACC 57.780 52.632 0.00 0.00 43.74 3.18
4261 4785 1.068125 CACATCACATGCACCCAACTG 60.068 52.381 0.00 0.00 0.00 3.16
4269 4797 4.496429 TGCACCACATCACATGCA 57.504 50.000 0.00 0.00 45.45 3.96
4298 4826 7.178274 ACATCTCTCTCTTTTATCTCTGTGTGT 59.822 37.037 0.00 0.00 0.00 3.72
4365 4904 0.102120 TTTTGCTTTGGGCTGTGTCG 59.898 50.000 0.00 0.00 42.39 4.35
4372 4911 4.777384 CCCACTTTTGCTTTGGGC 57.223 55.556 0.00 0.00 43.69 5.36
4419 4958 4.072131 ACATGTCAAACTATCAAAGCCGT 58.928 39.130 0.00 0.00 0.00 5.68
4437 4976 3.708195 GCCTAAAGCACTGCACATG 57.292 52.632 3.30 0.00 42.97 3.21
4461 5003 1.440938 CGGGCAACACACGAGGAAAA 61.441 55.000 0.00 0.00 39.74 2.29
4469 5011 1.284715 GTAAAGCCGGGCAACACAC 59.715 57.895 23.09 7.59 39.74 3.82
4491 5033 0.395173 TCTCGTGACCGATCCATCCA 60.395 55.000 0.00 0.00 43.27 3.41
4537 5079 1.336148 CGTGACATGCATTTGCTGGTT 60.336 47.619 0.00 0.00 42.66 3.67
4573 5115 3.604392 GACGTGGTTATCTTAAATGCGC 58.396 45.455 0.00 0.00 0.00 6.09
4641 5184 4.487019 AGCGAGACTGCTTTTTCTACTAC 58.513 43.478 0.00 0.00 44.46 2.73
4642 5185 4.785511 AGCGAGACTGCTTTTTCTACTA 57.214 40.909 0.00 0.00 44.46 1.82
4643 5186 3.669251 AGCGAGACTGCTTTTTCTACT 57.331 42.857 0.00 0.00 44.46 2.57
4722 5271 1.748879 GCCATAGCGCTTCCAACCA 60.749 57.895 18.68 0.00 0.00 3.67
4760 5309 1.888512 TCAACAGATGCCTCCTTTTGC 59.111 47.619 0.00 0.00 0.00 3.68
4956 6830 0.990374 ATTGCCAGCCTGAGTTCTCT 59.010 50.000 0.00 0.00 0.00 3.10
5031 6905 1.718757 GACATGCACGGGAATGAGCC 61.719 60.000 14.15 0.00 33.88 4.70
5038 6912 2.363975 GGTAGGGACATGCACGGGA 61.364 63.158 0.00 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.