Multiple sequence alignment - TraesCS2D01G433100

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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 TraesCS2D01G433100 chr2D 100.000 9406 0 0 1 9406 544872594 544881999 0.000000e+00 17370.0
1 TraesCS2D01G433100 chr2D 97.645 552 11 2 8811 9360 612544565 612544014 0.000000e+00 946.0
2 TraesCS2D01G433100 chr2D 97.297 37 1 0 4131 4167 544876688 544876724 7.890000e-06 63.9
3 TraesCS2D01G433100 chr2D 97.297 37 1 0 4095 4131 544876724 544876760 7.890000e-06 63.9
4 TraesCS2D01G433100 chr2A 93.555 2979 115 25 5775 8725 688625792 688622863 0.000000e+00 4366.0
5 TraesCS2D01G433100 chr2A 95.808 1646 54 11 4134 5772 688627483 688625846 0.000000e+00 2643.0
6 TraesCS2D01G433100 chr2A 84.365 2584 180 90 315 2759 688631424 688628926 0.000000e+00 2327.0
7 TraesCS2D01G433100 chr2A 95.734 1383 50 4 2758 4131 688628832 688627450 0.000000e+00 2218.0
8 TraesCS2D01G433100 chr2B 95.172 2527 88 14 6298 8813 651357104 651359607 0.000000e+00 3960.0
9 TraesCS2D01G433100 chr2B 96.864 2296 59 7 2098 4382 651351703 651353996 0.000000e+00 3829.0
10 TraesCS2D01G433100 chr2B 88.010 2085 109 65 1 2012 651349668 651351684 0.000000e+00 2335.0
11 TraesCS2D01G433100 chr2B 96.707 1397 33 7 4381 5772 651354158 651355546 0.000000e+00 2313.0
12 TraesCS2D01G433100 chr2B 95.628 366 9 1 5771 6129 651355585 651355950 1.760000e-161 580.0
13 TraesCS2D01G433100 chr2B 97.661 171 2 1 6131 6299 651356880 651357050 9.240000e-75 292.0
14 TraesCS2D01G433100 chr1D 99.273 550 4 0 8812 9361 364840152 364839603 0.000000e+00 994.0
15 TraesCS2D01G433100 chr1D 97.459 551 12 2 8812 9360 410455289 410455839 0.000000e+00 939.0
16 TraesCS2D01G433100 chr1D 81.911 293 44 7 33 317 365430227 365430518 1.220000e-58 239.0
17 TraesCS2D01G433100 chr1D 80.952 294 44 9 33 315 23973676 23973968 1.230000e-53 222.0
18 TraesCS2D01G433100 chr7D 99.271 549 3 1 8812 9360 457113343 457113890 0.000000e+00 990.0
19 TraesCS2D01G433100 chr7D 98.370 552 7 2 8811 9360 608122522 608121971 0.000000e+00 968.0
20 TraesCS2D01G433100 chr7D 98.007 552 9 2 8812 9361 525913638 525914189 0.000000e+00 957.0
21 TraesCS2D01G433100 chr3D 98.373 553 7 2 8812 9362 91802953 91803505 0.000000e+00 970.0
22 TraesCS2D01G433100 chr5D 97.658 555 9 3 8810 9362 275196275 275196827 0.000000e+00 950.0
23 TraesCS2D01G433100 chr5D 97.459 551 12 2 8812 9360 58020294 58020844 0.000000e+00 939.0
24 TraesCS2D01G433100 chr7A 92.289 402 31 0 5144 5545 47399581 47399982 1.060000e-158 571.0
25 TraesCS2D01G433100 chr6B 82.510 263 44 2 30 292 632892402 632892662 7.350000e-56 230.0
26 TraesCS2D01G433100 chr6A 80.277 289 50 7 31 315 562950194 562950479 2.660000e-50 211.0
27 TraesCS2D01G433100 chrUn 81.298 262 45 2 44 304 344010318 344010060 9.570000e-50 209.0
28 TraesCS2D01G433100 chrUn 81.298 262 45 2 44 304 420086916 420086658 9.570000e-50 209.0
29 TraesCS2D01G433100 chr4D 80.843 261 42 7 33 285 13309434 13309694 2.070000e-46 198.0
30 TraesCS2D01G433100 chr6D 79.225 284 49 9 38 313 291218453 291218172 1.250000e-43 189.0


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 TraesCS2D01G433100 chr2D 544872594 544881999 9405 False 17370.000000 17370 100.0000 1 9406 1 chr2D.!!$F1 9405
1 TraesCS2D01G433100 chr2D 612544014 612544565 551 True 946.000000 946 97.6450 8811 9360 1 chr2D.!!$R1 549
2 TraesCS2D01G433100 chr2A 688622863 688631424 8561 True 2888.500000 4366 92.3655 315 8725 4 chr2A.!!$R1 8410
3 TraesCS2D01G433100 chr2B 651349668 651359607 9939 False 2218.166667 3960 95.0070 1 8813 6 chr2B.!!$F1 8812
4 TraesCS2D01G433100 chr1D 364839603 364840152 549 True 994.000000 994 99.2730 8812 9361 1 chr1D.!!$R1 549
5 TraesCS2D01G433100 chr1D 410455289 410455839 550 False 939.000000 939 97.4590 8812 9360 1 chr1D.!!$F3 548
6 TraesCS2D01G433100 chr7D 457113343 457113890 547 False 990.000000 990 99.2710 8812 9360 1 chr7D.!!$F1 548
7 TraesCS2D01G433100 chr7D 608121971 608122522 551 True 968.000000 968 98.3700 8811 9360 1 chr7D.!!$R1 549
8 TraesCS2D01G433100 chr7D 525913638 525914189 551 False 957.000000 957 98.0070 8812 9361 1 chr7D.!!$F2 549
9 TraesCS2D01G433100 chr3D 91802953 91803505 552 False 970.000000 970 98.3730 8812 9362 1 chr3D.!!$F1 550
10 TraesCS2D01G433100 chr5D 275196275 275196827 552 False 950.000000 950 97.6580 8810 9362 1 chr5D.!!$F2 552
11 TraesCS2D01G433100 chr5D 58020294 58020844 550 False 939.000000 939 97.4590 8812 9360 1 chr5D.!!$F1 548

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
646 667 0.036306 ATCCACCCCTTCGTTGTCAC 59.964 55.000 0.00 0.00 0.00 3.67 F
1808 1955 0.625316 AATAGCTGTCACCATGGGCA 59.375 50.000 18.09 10.96 0.00 5.36 F
1898 2045 0.527565 GCCCATTACCACTGTTGCTG 59.472 55.000 0.00 0.00 0.00 4.41 F
2026 2174 1.121967 GTCAAGTTTGTAGCGTCGTCG 59.878 52.381 0.00 0.00 40.37 5.12 F
2213 2363 1.243902 TTTTTAGCGGGGTTCAGCTG 58.756 50.000 7.63 7.63 44.32 4.24 F
2551 2729 1.339055 CGCTTTCTCACCCATCCTTCA 60.339 52.381 0.00 0.00 0.00 3.02 F
3192 3494 2.229792 TCATGGAGGTTTCACTGTTGC 58.770 47.619 0.00 0.00 0.00 4.17 F
3718 4021 3.220110 CGTGAGTAGCCCCTATCAGTAA 58.780 50.000 0.00 0.00 0.00 2.24 F
5331 5807 1.655484 GCAATGCATTTTGCCCCTAC 58.345 50.000 9.83 0.00 44.94 3.18 F
7042 8574 1.210478 ACCAGTAGGCCAATACAGCAG 59.790 52.381 5.01 0.00 39.06 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1880 2027 0.527565 GCAGCAACAGTGGTAATGGG 59.472 55.000 0.00 0.0 33.05 4.00 R
3192 3494 2.526304 ATGGACCATCATACCGTTCG 57.474 50.000 0.00 0.0 0.00 3.95 R
3758 4061 4.651778 ACAACCTCAAGCAATAGTTAGCA 58.348 39.130 0.00 0.0 0.00 3.49 R
4067 4372 6.600882 AAGAGCATTCCAGAAAATGTTGAT 57.399 33.333 0.00 0.0 38.60 2.57 R
4350 4655 9.529823 TGTAGATACAGAACTAGGAGAGAAAAA 57.470 33.333 0.00 0.0 0.00 1.94 R
4613 5082 1.497286 TGCCCCAATACCCAGATAACC 59.503 52.381 0.00 0.0 0.00 2.85 R
5266 5740 1.486310 GAGGACACCAGCATGTATGGA 59.514 52.381 21.57 0.0 40.51 3.41 R
5348 5824 0.320374 AGCACAGCAACGCCTAACTA 59.680 50.000 0.00 0.0 0.00 2.24 R
7212 8744 1.145119 GGAAAACCCACTCCTGGAAGT 59.855 52.381 0.00 0.0 40.55 3.01 R
8543 10081 0.322456 GTGTATGCCAGCACCAAGGA 60.322 55.000 0.00 0.0 0.00 3.36 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
22 23 1.153756 CCCACCCAAAGGTCAAGCT 59.846 57.895 0.00 0.00 46.45 3.74
36 39 6.305272 AGGTCAAGCTGAGATTTGAAGATA 57.695 37.500 0.00 0.00 35.29 1.98
45 48 6.018098 GCTGAGATTTGAAGATATGGTGTCAG 60.018 42.308 0.00 0.00 0.00 3.51
61 64 5.063880 GGTGTCAGGTGTTTCAGTTCTATT 58.936 41.667 0.00 0.00 0.00 1.73
62 65 5.179555 GGTGTCAGGTGTTTCAGTTCTATTC 59.820 44.000 0.00 0.00 0.00 1.75
63 66 5.758296 GTGTCAGGTGTTTCAGTTCTATTCA 59.242 40.000 0.00 0.00 0.00 2.57
66 69 4.697352 CAGGTGTTTCAGTTCTATTCAGGG 59.303 45.833 0.00 0.00 0.00 4.45
67 70 4.010349 GGTGTTTCAGTTCTATTCAGGGG 58.990 47.826 0.00 0.00 0.00 4.79
68 71 4.506802 GGTGTTTCAGTTCTATTCAGGGGT 60.507 45.833 0.00 0.00 0.00 4.95
69 72 5.070685 GTGTTTCAGTTCTATTCAGGGGTT 58.929 41.667 0.00 0.00 0.00 4.11
70 73 5.181433 GTGTTTCAGTTCTATTCAGGGGTTC 59.819 44.000 0.00 0.00 0.00 3.62
71 74 5.163141 TGTTTCAGTTCTATTCAGGGGTTCA 60.163 40.000 0.00 0.00 0.00 3.18
72 75 5.576563 TTCAGTTCTATTCAGGGGTTCAA 57.423 39.130 0.00 0.00 0.00 2.69
77 80 4.993705 TCTATTCAGGGGTTCAACAACT 57.006 40.909 0.00 0.00 32.50 3.16
85 88 2.484241 GGGGTTCAACAACTACGACTGT 60.484 50.000 0.00 0.00 32.50 3.55
87 90 2.542595 GGTTCAACAACTACGACTGTGG 59.457 50.000 0.00 0.00 32.50 4.17
91 94 0.317479 ACAACTACGACTGTGGCTCC 59.683 55.000 0.00 0.00 0.00 4.70
95 98 2.564553 CTACGACTGTGGCTCCAGGC 62.565 65.000 9.09 5.33 37.11 4.85
108 111 1.128809 TCCAGGCCGTTGGTCCTTAA 61.129 55.000 10.68 0.00 39.35 1.85
112 115 1.377612 GCCGTTGGTCCTTAAGGGT 59.622 57.895 21.53 0.00 35.92 4.34
120 123 1.673923 GGTCCTTAAGGGTACGTGCAC 60.674 57.143 21.53 6.82 36.25 4.57
131 134 0.038892 TACGTGCACGAAGACTTCCC 60.039 55.000 42.94 0.00 43.02 3.97
137 140 2.815647 CGAAGACTTCCCGGCTGC 60.816 66.667 9.63 0.00 0.00 5.25
144 147 3.466791 CTTCCCGGCTGCCATCGAT 62.467 63.158 20.29 0.00 0.00 3.59
153 156 2.288666 GCTGCCATCGATAAGGTCAAA 58.711 47.619 0.00 0.00 0.00 2.69
180 183 0.318441 CGATATGGGAGTGGCGACAT 59.682 55.000 0.00 0.00 46.14 3.06
183 186 1.744320 TATGGGAGTGGCGACATCGG 61.744 60.000 0.00 0.00 46.14 4.18
195 198 1.006571 ACATCGGCGTGTCGTTCTT 60.007 52.632 6.85 0.00 0.00 2.52
210 213 5.477984 TGTCGTTCTTATGGTGGTAGTAGTT 59.522 40.000 0.00 0.00 0.00 2.24
223 226 4.164604 TGGTAGTAGTTGTTTGGTGGTCTT 59.835 41.667 0.00 0.00 0.00 3.01
229 232 7.287810 AGTAGTTGTTTGGTGGTCTTAGAATT 58.712 34.615 0.00 0.00 0.00 2.17
231 234 7.418337 AGTTGTTTGGTGGTCTTAGAATTTT 57.582 32.000 0.00 0.00 0.00 1.82
239 242 8.877864 TGGTGGTCTTAGAATTTTGATGTAAT 57.122 30.769 0.00 0.00 0.00 1.89
274 277 4.385825 TGAGGTGCTTTGTACTTTCGATT 58.614 39.130 0.00 0.00 0.00 3.34
294 300 7.591165 TCGATTAACTTTGATAGTAGATCCGG 58.409 38.462 0.00 0.00 35.54 5.14
305 311 6.433093 TGATAGTAGATCCGGATCATTTTCGA 59.567 38.462 38.83 21.97 40.22 3.71
309 315 5.485662 AGATCCGGATCATTTTCGAAAAC 57.514 39.130 38.83 14.06 40.22 2.43
311 317 5.414454 AGATCCGGATCATTTTCGAAAACAA 59.586 36.000 38.83 15.89 40.22 2.83
312 318 5.440234 TCCGGATCATTTTCGAAAACAAA 57.560 34.783 24.68 13.52 0.00 2.83
313 319 5.833082 TCCGGATCATTTTCGAAAACAAAA 58.167 33.333 24.68 11.19 0.00 2.44
314 320 6.273825 TCCGGATCATTTTCGAAAACAAAAA 58.726 32.000 24.68 9.55 0.00 1.94
360 366 1.093159 AGACGAGTGGACGTATGGAC 58.907 55.000 0.00 0.00 46.52 4.02
403 410 1.883084 CCTGCGCCCTCGTGTAATC 60.883 63.158 4.18 0.00 38.14 1.75
521 539 1.810030 GCAGAATCCACGACGGGAC 60.810 63.158 0.00 0.00 40.44 4.46
522 540 1.589630 CAGAATCCACGACGGGACA 59.410 57.895 0.00 0.00 40.44 4.02
523 541 0.458543 CAGAATCCACGACGGGACAG 60.459 60.000 0.00 0.00 40.44 3.51
524 542 1.153628 GAATCCACGACGGGACAGG 60.154 63.158 0.00 0.00 40.44 4.00
646 667 0.036306 ATCCACCCCTTCGTTGTCAC 59.964 55.000 0.00 0.00 0.00 3.67
703 742 4.109675 GGCACGTATGGCCCACCT 62.110 66.667 0.00 0.00 45.87 4.00
773 818 6.389091 CAGTCAGCTAGGATAGAATAAGCAG 58.611 44.000 0.00 0.00 42.77 4.24
774 819 5.047377 AGTCAGCTAGGATAGAATAAGCAGC 60.047 44.000 0.00 0.00 42.77 5.25
775 820 4.835056 TCAGCTAGGATAGAATAAGCAGCA 59.165 41.667 0.00 0.00 42.77 4.41
777 822 5.638657 CAGCTAGGATAGAATAAGCAGCAAG 59.361 44.000 0.00 0.00 42.77 4.01
779 824 5.868801 GCTAGGATAGAATAAGCAGCAAGAG 59.131 44.000 0.00 0.00 42.77 2.85
781 826 6.100404 AGGATAGAATAAGCAGCAAGAGAG 57.900 41.667 0.00 0.00 0.00 3.20
782 827 5.011943 AGGATAGAATAAGCAGCAAGAGAGG 59.988 44.000 0.00 0.00 0.00 3.69
783 828 5.011533 GGATAGAATAAGCAGCAAGAGAGGA 59.988 44.000 0.00 0.00 0.00 3.71
784 829 4.405116 AGAATAAGCAGCAAGAGAGGAG 57.595 45.455 0.00 0.00 0.00 3.69
786 831 4.099881 AGAATAAGCAGCAAGAGAGGAGAG 59.900 45.833 0.00 0.00 0.00 3.20
790 837 1.959508 GCAGCAAGAGAGGAGAGGAGA 60.960 57.143 0.00 0.00 0.00 3.71
796 843 3.080660 AGAGAGGAGAGGAGAGGAGAT 57.919 52.381 0.00 0.00 0.00 2.75
812 859 4.376225 GGAGATGCCTAGTAGTACTCCT 57.624 50.000 5.96 0.00 39.20 3.69
813 860 5.502089 GGAGATGCCTAGTAGTACTCCTA 57.498 47.826 5.96 0.00 39.20 2.94
814 861 5.493809 GGAGATGCCTAGTAGTACTCCTAG 58.506 50.000 14.07 14.07 39.20 3.02
815 862 5.013391 GGAGATGCCTAGTAGTACTCCTAGT 59.987 48.000 18.20 3.39 39.20 2.57
816 863 6.213195 GGAGATGCCTAGTAGTACTCCTAGTA 59.787 46.154 18.20 9.50 39.20 1.82
817 864 7.248743 AGATGCCTAGTAGTACTCCTAGTAG 57.751 44.000 18.20 9.55 44.40 2.57
849 900 1.116308 AAAAACGGGAAGGTTGGTGG 58.884 50.000 0.00 0.00 0.00 4.61
868 919 6.895782 TGGTGGTTATCTTCCCATTAACTAG 58.104 40.000 0.00 0.00 32.32 2.57
869 920 6.445786 TGGTGGTTATCTTCCCATTAACTAGT 59.554 38.462 0.00 0.00 32.32 2.57
870 921 7.624478 TGGTGGTTATCTTCCCATTAACTAGTA 59.376 37.037 0.00 0.00 32.32 1.82
871 922 8.148999 GGTGGTTATCTTCCCATTAACTAGTAG 58.851 40.741 0.00 0.00 32.32 2.57
877 928 8.709272 ATCTTCCCATTAACTAGTAGGAGTAC 57.291 38.462 0.00 0.00 0.00 2.73
973 1025 1.413118 AAACAAAACAGGGGGCAGAG 58.587 50.000 0.00 0.00 0.00 3.35
989 1041 5.292765 GGGCAGAGGAAAAGAAAAGAAAAG 58.707 41.667 0.00 0.00 0.00 2.27
1013 1065 2.044123 AGCCAAGGAAAATAGCCGAG 57.956 50.000 0.00 0.00 0.00 4.63
1198 1266 1.229529 GTCCACCCTCTTCCTCCCA 60.230 63.158 0.00 0.00 0.00 4.37
1202 1270 2.124996 CCCTCTTCCTCCCACCCA 59.875 66.667 0.00 0.00 0.00 4.51
1204 1272 1.229658 CCTCTTCCTCCCACCCACT 60.230 63.158 0.00 0.00 0.00 4.00
1205 1273 1.557269 CCTCTTCCTCCCACCCACTG 61.557 65.000 0.00 0.00 0.00 3.66
1229 1325 1.757118 TCTCTCTTCATCCCGCGATTT 59.243 47.619 8.23 0.00 0.00 2.17
1230 1326 2.131183 CTCTCTTCATCCCGCGATTTC 58.869 52.381 8.23 0.00 0.00 2.17
1232 1328 1.863454 CTCTTCATCCCGCGATTTCTG 59.137 52.381 8.23 0.00 0.00 3.02
1233 1329 1.207089 TCTTCATCCCGCGATTTCTGT 59.793 47.619 8.23 0.00 0.00 3.41
1235 1331 2.107950 TCATCCCGCGATTTCTGTTT 57.892 45.000 8.23 0.00 0.00 2.83
1236 1332 2.006888 TCATCCCGCGATTTCTGTTTC 58.993 47.619 8.23 0.00 0.00 2.78
1237 1333 1.006832 ATCCCGCGATTTCTGTTTCG 58.993 50.000 8.23 0.00 38.37 3.46
1312 1411 4.489771 CCGAGCCCAATCCGCCTT 62.490 66.667 0.00 0.00 0.00 4.35
1313 1412 2.897350 CGAGCCCAATCCGCCTTC 60.897 66.667 0.00 0.00 0.00 3.46
1315 1414 4.129148 AGCCCAATCCGCCTTCCC 62.129 66.667 0.00 0.00 0.00 3.97
1473 1594 2.951745 CTGTGATCGTCGCCGCTC 60.952 66.667 0.00 0.00 0.00 5.03
1474 1595 3.683587 CTGTGATCGTCGCCGCTCA 62.684 63.158 0.00 0.00 36.92 4.26
1475 1596 2.951745 GTGATCGTCGCCGCTCAG 60.952 66.667 0.00 0.00 39.62 3.35
1768 1912 3.181446 GCCTCATTCTCCTCCTATTTGCT 60.181 47.826 0.00 0.00 0.00 3.91
1770 1914 5.546526 CCTCATTCTCCTCCTATTTGCTAC 58.453 45.833 0.00 0.00 0.00 3.58
1779 1926 4.141914 CCTCCTATTTGCTACGTTCCTTCT 60.142 45.833 0.00 0.00 0.00 2.85
1785 1932 3.953712 TGCTACGTTCCTTCTGAATCA 57.046 42.857 0.00 0.00 34.90 2.57
1792 1939 5.902681 ACGTTCCTTCTGAATCATCGAATA 58.097 37.500 0.00 0.00 34.90 1.75
1799 1946 5.520376 TCTGAATCATCGAATAGCTGTCA 57.480 39.130 0.00 0.00 0.00 3.58
1804 1951 3.721035 TCATCGAATAGCTGTCACCATG 58.279 45.455 0.00 0.00 0.00 3.66
1807 1954 1.312815 GAATAGCTGTCACCATGGGC 58.687 55.000 18.09 9.38 0.00 5.36
1808 1955 0.625316 AATAGCTGTCACCATGGGCA 59.375 50.000 18.09 10.96 0.00 5.36
1822 1969 3.306989 CCATGGGCATTAGCTCTTCGATA 60.307 47.826 2.85 0.00 43.51 2.92
1871 2018 0.801251 AGCTTTTGACTGCTCATCGC 59.199 50.000 0.00 0.00 33.90 4.58
1880 2027 1.439228 TGCTCATCGCAGGACTAGC 59.561 57.895 0.00 0.00 45.47 3.42
1898 2045 0.527565 GCCCATTACCACTGTTGCTG 59.472 55.000 0.00 0.00 0.00 4.41
1900 2047 1.538047 CCATTACCACTGTTGCTGCT 58.462 50.000 0.00 0.00 0.00 4.24
1933 2080 4.436584 GCTAGCATGTTTAGTCAACTGCTG 60.437 45.833 10.63 11.54 43.67 4.41
1958 2106 4.413087 AGTTTCGTCTGTATGAACTAGCG 58.587 43.478 0.00 0.00 30.24 4.26
1959 2107 4.155462 AGTTTCGTCTGTATGAACTAGCGA 59.845 41.667 0.00 0.00 30.24 4.93
2026 2174 1.121967 GTCAAGTTTGTAGCGTCGTCG 59.878 52.381 0.00 0.00 40.37 5.12
2082 2231 5.835819 TCACAAATGGGGAGAAAAATGTACA 59.164 36.000 0.00 0.00 0.00 2.90
2132 2281 5.899120 TGTTCTGAGGTACACTACTCATC 57.101 43.478 0.00 0.00 42.33 2.92
2161 2311 2.093447 ACTTCAGCATTCCCCTAAGTCG 60.093 50.000 0.00 0.00 0.00 4.18
2165 2315 3.118884 TCAGCATTCCCCTAAGTCGTAAC 60.119 47.826 0.00 0.00 0.00 2.50
2213 2363 1.243902 TTTTTAGCGGGGTTCAGCTG 58.756 50.000 7.63 7.63 44.32 4.24
2238 2388 6.296026 AGCAATGTTGTAGGTAAACTTCTCA 58.704 36.000 0.00 0.00 0.00 3.27
2263 2437 2.772568 TGACGTGCATTTGAACAAGG 57.227 45.000 0.00 0.00 0.00 3.61
2296 2470 7.331440 CCATGCACTTTTAAGCAACATTTATGA 59.669 33.333 0.00 0.00 44.88 2.15
2339 2515 6.036191 TGTTTGTATGCGCTATAAACGATTCA 59.964 34.615 21.70 10.54 41.69 2.57
2497 2675 1.970640 ACTTTTGAAAGATGCCACCCC 59.029 47.619 10.26 0.00 39.31 4.95
2551 2729 1.339055 CGCTTTCTCACCCATCCTTCA 60.339 52.381 0.00 0.00 0.00 3.02
2738 2945 7.621428 TGTAGACTATTATAGCGGATGGTAC 57.379 40.000 0.00 0.00 0.00 3.34
2792 3094 5.698545 GGCTTTATGTATCCTGATCAGTGAC 59.301 44.000 21.11 15.08 0.00 3.67
3000 3302 3.561213 CTGCGGCTGAGCATGACG 61.561 66.667 6.82 0.97 46.97 4.35
3022 3324 4.025979 CGAGCATATCGTTGAACTTTACCC 60.026 45.833 0.00 0.00 46.62 3.69
3192 3494 2.229792 TCATGGAGGTTTCACTGTTGC 58.770 47.619 0.00 0.00 0.00 4.17
3396 3699 8.161699 TGGTCAAAATCTGTAAGTTTACTTCC 57.838 34.615 0.00 0.00 37.40 3.46
3718 4021 3.220110 CGTGAGTAGCCCCTATCAGTAA 58.780 50.000 0.00 0.00 0.00 2.24
3758 4061 6.950860 ATGTTTTGGATGGTATTTTCCCTT 57.049 33.333 0.00 0.00 0.00 3.95
4067 4372 7.609146 GCATATCATTCACCATAAGGATCTTGA 59.391 37.037 0.00 0.00 38.69 3.02
4130 4435 5.879223 AGAGCAATGATTTCTTCGATGAAGT 59.121 36.000 12.82 10.70 40.24 3.01
4239 4544 4.883585 ACTGCGATTGATATGTGGTCATTT 59.116 37.500 0.00 0.00 35.70 2.32
4442 4908 8.389779 TGCTGAGTTTAATGTTGTTAATCTCA 57.610 30.769 15.18 15.18 37.89 3.27
4455 4922 9.629878 TGTTGTTAATCTCACCCTTTTTAGTTA 57.370 29.630 0.00 0.00 0.00 2.24
4681 5150 5.346281 CAGAATGTTAAGTGAAGACGAGGTC 59.654 44.000 0.00 0.00 0.00 3.85
4729 5198 9.829507 TTCCACAAAATAACATTGATTTCTGTT 57.170 25.926 0.00 0.00 38.95 3.16
5200 5674 8.948631 TTTTAGACTGCTAGTATCTGAAATGG 57.051 34.615 0.00 0.00 0.00 3.16
5301 5776 6.126409 TGGTGTCCTCTTGAGTTGTAATTTT 58.874 36.000 0.00 0.00 0.00 1.82
5331 5807 1.655484 GCAATGCATTTTGCCCCTAC 58.345 50.000 9.83 0.00 44.94 3.18
5345 5821 3.332485 TGCCCCTACAAAGGTTATCTTGT 59.668 43.478 0.00 0.00 41.89 3.16
5346 5822 4.202631 TGCCCCTACAAAGGTTATCTTGTT 60.203 41.667 0.00 0.00 41.89 2.83
5347 5823 5.014333 TGCCCCTACAAAGGTTATCTTGTTA 59.986 40.000 0.00 0.00 41.89 2.41
5348 5824 6.127101 GCCCCTACAAAGGTTATCTTGTTAT 58.873 40.000 0.00 0.00 41.89 1.89
5349 5825 7.092354 TGCCCCTACAAAGGTTATCTTGTTATA 60.092 37.037 0.00 0.00 41.89 0.98
5350 5826 7.444487 GCCCCTACAAAGGTTATCTTGTTATAG 59.556 40.741 0.00 0.00 41.89 1.31
5462 5941 3.827302 ACGGAGTATAGGCATTGTAGGAG 59.173 47.826 0.00 0.00 41.94 3.69
5470 5949 3.555966 AGGCATTGTAGGAGTATTTGCC 58.444 45.455 2.89 2.89 46.59 4.52
6051 6588 8.138074 GCTTGGGGTTTGAAATTATCTATCTTC 58.862 37.037 0.00 0.00 0.00 2.87
6115 6652 7.611467 AGGCTGTGACAAATAAACTTATCATCA 59.389 33.333 0.00 0.00 0.00 3.07
6327 7849 9.602568 AGATAGCTTTCTACCTTAACTAAAAGC 57.397 33.333 4.72 9.06 45.46 3.51
6328 7850 8.734218 ATAGCTTTCTACCTTAACTAAAAGCC 57.266 34.615 12.51 0.00 45.97 4.35
6329 7851 6.780901 AGCTTTCTACCTTAACTAAAAGCCT 58.219 36.000 12.51 0.67 45.97 4.58
6330 7852 7.914859 AGCTTTCTACCTTAACTAAAAGCCTA 58.085 34.615 12.51 0.00 45.97 3.93
6331 7853 8.380867 AGCTTTCTACCTTAACTAAAAGCCTAA 58.619 33.333 12.51 0.00 45.97 2.69
6332 7854 9.006839 GCTTTCTACCTTAACTAAAAGCCTAAA 57.993 33.333 6.41 0.00 41.53 1.85
6355 7877 8.460831 AAAACACAGTTTAGTTTTAGCTTGTG 57.539 30.769 0.00 0.00 43.77 3.33
6500 8022 3.459969 GGTCTTTCCCCTCAGGTGATAAT 59.540 47.826 0.00 0.00 36.75 1.28
6585 8107 8.698973 TTGTCCATTAAAACTGAAATGTCCTA 57.301 30.769 0.00 0.00 32.34 2.94
6586 8108 8.698973 TGTCCATTAAAACTGAAATGTCCTAA 57.301 30.769 0.00 0.00 32.34 2.69
6587 8109 9.137459 TGTCCATTAAAACTGAAATGTCCTAAA 57.863 29.630 0.00 0.00 32.34 1.85
6628 8160 3.380637 GCGAACAGATGTCTACCTCCTAA 59.619 47.826 0.00 0.00 0.00 2.69
6629 8161 4.038162 GCGAACAGATGTCTACCTCCTAAT 59.962 45.833 0.00 0.00 0.00 1.73
6630 8162 5.241064 GCGAACAGATGTCTACCTCCTAATA 59.759 44.000 0.00 0.00 0.00 0.98
6757 8289 7.040478 TGGAAGCTATGGTGATGTTAATAATGC 60.040 37.037 0.00 0.00 0.00 3.56
7042 8574 1.210478 ACCAGTAGGCCAATACAGCAG 59.790 52.381 5.01 0.00 39.06 4.24
7077 8609 3.673902 CCGATGCCACCACATGAATATA 58.326 45.455 0.00 0.00 0.00 0.86
7212 8744 7.606456 GTCATTCTAGTTGGAGACCACAAATAA 59.394 37.037 0.00 0.00 30.78 1.40
7226 8758 3.758554 CACAAATAACTTCCAGGAGTGGG 59.241 47.826 0.00 0.00 45.11 4.61
7233 8765 1.144913 CTTCCAGGAGTGGGTTTTCCA 59.855 52.381 0.00 0.00 45.11 3.53
7309 8841 0.109132 CCTTTGCCCTCATTTGACGC 60.109 55.000 0.00 0.00 0.00 5.19
7397 8929 4.084223 GGAATTGTGTGCTCAAATTGCTTG 60.084 41.667 14.43 0.00 36.25 4.01
7739 9274 6.313905 AGAATCAAGACATAACAATCCACGTC 59.686 38.462 0.00 0.00 0.00 4.34
7740 9275 4.888917 TCAAGACATAACAATCCACGTCA 58.111 39.130 0.00 0.00 0.00 4.35
7741 9276 5.487433 TCAAGACATAACAATCCACGTCAT 58.513 37.500 0.00 0.00 0.00 3.06
7742 9277 6.635755 TCAAGACATAACAATCCACGTCATA 58.364 36.000 0.00 0.00 0.00 2.15
7788 9323 8.647226 CAAGTTATGCCAACTAATTACTTTTGC 58.353 33.333 1.58 0.00 0.00 3.68
7865 9400 0.037605 CACCCGTCCTACTGTTCCAC 60.038 60.000 0.00 0.00 0.00 4.02
8026 9561 2.512896 CCTGCATGGCCTCCCTAC 59.487 66.667 3.32 0.00 0.00 3.18
8222 9758 5.086104 AGCATATTTTAGTGTGGACTCGT 57.914 39.130 0.00 0.00 33.21 4.18
8291 9827 0.957395 AGTTGCGATGGTTCTGGCTG 60.957 55.000 0.00 0.00 0.00 4.85
8473 10009 0.390340 CAGACTCAGCGCTGCCTTAA 60.390 55.000 32.44 14.12 0.00 1.85
8474 10010 0.108424 AGACTCAGCGCTGCCTTAAG 60.108 55.000 32.44 24.68 0.00 1.85
8475 10011 0.108615 GACTCAGCGCTGCCTTAAGA 60.109 55.000 32.44 12.56 0.00 2.10
8476 10012 0.108424 ACTCAGCGCTGCCTTAAGAG 60.108 55.000 32.44 23.26 0.00 2.85
8478 10014 0.321671 TCAGCGCTGCCTTAAGAGTT 59.678 50.000 32.44 0.00 0.00 3.01
8479 10015 1.548719 TCAGCGCTGCCTTAAGAGTTA 59.451 47.619 32.44 7.78 0.00 2.24
8480 10016 1.661112 CAGCGCTGCCTTAAGAGTTAC 59.339 52.381 26.68 0.00 0.00 2.50
8482 10018 2.073816 GCGCTGCCTTAAGAGTTACAA 58.926 47.619 3.36 0.00 0.00 2.41
8483 10019 2.094417 GCGCTGCCTTAAGAGTTACAAG 59.906 50.000 3.36 0.00 0.00 3.16
8484 10020 3.585862 CGCTGCCTTAAGAGTTACAAGA 58.414 45.455 3.36 0.00 0.00 3.02
8485 10021 4.184629 CGCTGCCTTAAGAGTTACAAGAT 58.815 43.478 3.36 0.00 0.00 2.40
8495 10031 9.757227 CTTAAGAGTTACAAGATTATCCCAGAG 57.243 37.037 0.00 0.00 0.00 3.35
8497 10033 7.741554 AGAGTTACAAGATTATCCCAGAGTT 57.258 36.000 0.00 0.00 0.00 3.01
8524 10061 6.974622 ACATTGTTTTTAACTGTTCTCTGCTG 59.025 34.615 0.00 0.00 0.00 4.41
8529 10066 2.246719 AACTGTTCTCTGCTGTCACC 57.753 50.000 0.00 0.00 0.00 4.02
8540 10077 1.440850 CTGTCACCGTTGCAATGCG 60.441 57.895 13.42 7.80 0.00 4.73
8543 10081 0.593773 GTCACCGTTGCAATGCGTTT 60.594 50.000 13.42 0.00 0.00 3.60
8554 10092 0.314935 AATGCGTTTCCTTGGTGCTG 59.685 50.000 0.00 0.00 0.00 4.41
8561 10099 0.403655 TTCCTTGGTGCTGGCATACA 59.596 50.000 0.00 0.00 0.00 2.29
8565 10103 1.470098 CTTGGTGCTGGCATACACTTC 59.530 52.381 17.17 5.72 36.99 3.01
8566 10104 0.692476 TGGTGCTGGCATACACTTCT 59.308 50.000 17.17 0.00 36.99 2.85
8569 10108 2.154462 GTGCTGGCATACACTTCTGTT 58.846 47.619 12.17 0.00 33.92 3.16
8576 10115 3.689649 GGCATACACTTCTGTTCGGAAAT 59.310 43.478 0.00 0.00 0.00 2.17
8581 10120 4.451900 ACACTTCTGTTCGGAAATCTTGT 58.548 39.130 0.00 0.00 0.00 3.16
8582 10121 5.607477 ACACTTCTGTTCGGAAATCTTGTA 58.393 37.500 0.00 0.00 0.00 2.41
8583 10122 5.696724 ACACTTCTGTTCGGAAATCTTGTAG 59.303 40.000 0.00 0.00 0.00 2.74
8584 10123 5.696724 CACTTCTGTTCGGAAATCTTGTAGT 59.303 40.000 0.00 0.00 0.00 2.73
8589 10128 7.636326 TCTGTTCGGAAATCTTGTAGTTTTTC 58.364 34.615 0.00 0.00 0.00 2.29
8669 10213 2.633488 CGAAATTCCCCTTCTGAGACC 58.367 52.381 0.00 0.00 0.00 3.85
8672 10216 4.265893 GAAATTCCCCTTCTGAGACCTTC 58.734 47.826 0.00 0.00 0.00 3.46
8673 10217 2.415983 TTCCCCTTCTGAGACCTTCA 57.584 50.000 0.00 0.00 0.00 3.02
8763 10307 4.326278 TCTCGTGATACATTTGCGAACTTC 59.674 41.667 0.00 0.00 0.00 3.01
8764 10308 4.242475 TCGTGATACATTTGCGAACTTCT 58.758 39.130 0.00 0.00 0.00 2.85
8766 10310 4.091365 CGTGATACATTTGCGAACTTCTGA 59.909 41.667 0.00 0.00 0.00 3.27
8767 10311 5.554636 GTGATACATTTGCGAACTTCTGAG 58.445 41.667 0.00 0.00 0.00 3.35
8768 10312 4.631377 TGATACATTTGCGAACTTCTGAGG 59.369 41.667 0.00 0.00 0.00 3.86
8769 10313 2.851195 ACATTTGCGAACTTCTGAGGT 58.149 42.857 0.00 0.00 0.00 3.85
8770 10314 3.214328 ACATTTGCGAACTTCTGAGGTT 58.786 40.909 4.71 4.71 0.00 3.50
8771 10315 4.385825 ACATTTGCGAACTTCTGAGGTTA 58.614 39.130 5.06 0.00 0.00 2.85
8785 10329 8.328758 ACTTCTGAGGTTATGTATGAAATTCCA 58.671 33.333 0.00 0.00 0.00 3.53
8790 10334 9.308000 TGAGGTTATGTATGAAATTCCAGTTTT 57.692 29.630 0.00 0.00 0.00 2.43
9364 10910 2.498077 CTGGATCTCAGTCCGAGCA 58.502 57.895 0.00 0.00 41.98 4.26
9365 10911 0.820226 CTGGATCTCAGTCCGAGCAA 59.180 55.000 0.00 0.00 41.98 3.91
9366 10912 1.205655 CTGGATCTCAGTCCGAGCAAA 59.794 52.381 0.00 0.00 41.98 3.68
9367 10913 1.623311 TGGATCTCAGTCCGAGCAAAA 59.377 47.619 0.00 0.00 41.98 2.44
9368 10914 2.003301 GGATCTCAGTCCGAGCAAAAC 58.997 52.381 0.00 0.00 41.98 2.43
9369 10915 1.656095 GATCTCAGTCCGAGCAAAACG 59.344 52.381 0.00 0.00 41.98 3.60
9375 10921 2.725008 CCGAGCAAAACGGCCAAA 59.275 55.556 2.24 0.00 43.74 3.28
9376 10922 1.066587 CCGAGCAAAACGGCCAAAA 59.933 52.632 2.24 0.00 43.74 2.44
9377 10923 1.212455 CCGAGCAAAACGGCCAAAAC 61.212 55.000 2.24 0.00 43.74 2.43
9378 10924 0.248866 CGAGCAAAACGGCCAAAACT 60.249 50.000 2.24 0.00 0.00 2.66
9379 10925 1.208259 GAGCAAAACGGCCAAAACTG 58.792 50.000 2.24 0.00 0.00 3.16
9380 10926 0.179086 AGCAAAACGGCCAAAACTGG 60.179 50.000 2.24 0.00 0.00 4.00
9381 10927 1.157257 GCAAAACGGCCAAAACTGGG 61.157 55.000 2.24 0.00 0.00 4.45
9387 10933 3.274067 GCCAAAACTGGGCCGTAG 58.726 61.111 0.00 0.00 45.87 3.51
9388 10934 2.989881 GCCAAAACTGGGCCGTAGC 61.990 63.158 0.00 0.00 45.87 3.58
9389 10935 2.686816 CCAAAACTGGGCCGTAGCG 61.687 63.158 0.00 0.00 41.24 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 6.070021 ACCTGACACCATATCTTCAAATCTCA 60.070 38.462 0.00 0.00 0.00 3.27
36 39 3.117888 AGAACTGAAACACCTGACACCAT 60.118 43.478 0.00 0.00 0.00 3.55
45 48 4.010349 CCCCTGAATAGAACTGAAACACC 58.990 47.826 0.00 0.00 0.00 4.16
61 64 2.040939 TCGTAGTTGTTGAACCCCTGA 58.959 47.619 0.00 0.00 31.81 3.86
62 65 2.140717 GTCGTAGTTGTTGAACCCCTG 58.859 52.381 0.00 0.00 31.81 4.45
63 66 2.044758 AGTCGTAGTTGTTGAACCCCT 58.955 47.619 0.00 0.00 31.81 4.79
66 69 2.542595 CCACAGTCGTAGTTGTTGAACC 59.457 50.000 0.00 0.00 31.81 3.62
67 70 2.033151 GCCACAGTCGTAGTTGTTGAAC 60.033 50.000 0.00 0.00 0.00 3.18
68 71 2.159014 AGCCACAGTCGTAGTTGTTGAA 60.159 45.455 0.00 0.00 0.00 2.69
69 72 1.411246 AGCCACAGTCGTAGTTGTTGA 59.589 47.619 0.00 0.00 0.00 3.18
70 73 1.792949 GAGCCACAGTCGTAGTTGTTG 59.207 52.381 0.00 0.00 0.00 3.33
71 74 1.270147 GGAGCCACAGTCGTAGTTGTT 60.270 52.381 0.00 0.00 0.00 2.83
72 75 0.317479 GGAGCCACAGTCGTAGTTGT 59.683 55.000 0.00 0.00 0.00 3.32
77 80 2.646175 GCCTGGAGCCACAGTCGTA 61.646 63.158 0.00 0.00 36.75 3.43
91 94 0.676782 CCTTAAGGACCAACGGCCTG 60.677 60.000 17.21 0.00 37.39 4.85
95 98 1.404583 CGTACCCTTAAGGACCAACGG 60.405 57.143 23.74 6.61 39.89 4.44
108 111 1.177256 AGTCTTCGTGCACGTACCCT 61.177 55.000 35.74 24.09 40.80 4.34
112 115 0.038892 GGGAAGTCTTCGTGCACGTA 60.039 55.000 35.74 27.02 40.80 3.57
120 123 2.815647 GCAGCCGGGAAGTCTTCG 60.816 66.667 2.18 0.00 0.00 3.79
131 134 0.946221 GACCTTATCGATGGCAGCCG 60.946 60.000 8.54 0.93 0.00 5.52
137 140 2.210116 CCGGTTTGACCTTATCGATGG 58.790 52.381 8.54 3.97 35.66 3.51
144 147 1.186917 TCGGAGCCGGTTTGACCTTA 61.187 55.000 9.29 0.00 40.25 2.69
153 156 1.908793 CTCCCATATCGGAGCCGGT 60.909 63.158 9.29 4.20 43.01 5.28
180 183 0.457166 CCATAAGAACGACACGCCGA 60.457 55.000 0.00 0.00 0.00 5.54
183 186 0.719465 CCACCATAAGAACGACACGC 59.281 55.000 0.00 0.00 0.00 5.34
190 193 7.094933 CCAAACAACTACTACCACCATAAGAAC 60.095 40.741 0.00 0.00 0.00 3.01
195 198 5.513441 CCACCAAACAACTACTACCACCATA 60.513 44.000 0.00 0.00 0.00 2.74
210 213 7.069331 ACATCAAAATTCTAAGACCACCAAACA 59.931 33.333 0.00 0.00 0.00 2.83
274 277 8.651589 ATGATCCGGATCTACTATCAAAGTTA 57.348 34.615 37.39 17.71 38.60 2.24
288 291 5.229921 TGTTTTCGAAAATGATCCGGATC 57.770 39.130 33.41 33.41 38.29 3.36
292 298 6.200097 ACCTTTTTGTTTTCGAAAATGATCCG 59.800 34.615 24.93 12.91 40.88 4.18
294 300 9.209297 CAAACCTTTTTGTTTTCGAAAATGATC 57.791 29.630 24.93 13.27 40.88 2.92
305 311 8.614469 TTGAATCAGTCAAACCTTTTTGTTTT 57.386 26.923 0.00 0.00 43.43 2.43
343 349 0.524862 GTGTCCATACGTCCACTCGT 59.475 55.000 0.00 0.00 45.97 4.18
385 392 1.883084 GATTACACGAGGGCGCAGG 60.883 63.158 10.83 0.00 42.48 4.85
396 403 3.732048 TTCCTCCCCCTTTGATTACAC 57.268 47.619 0.00 0.00 0.00 2.90
403 410 1.146982 TGTCCTTTTCCTCCCCCTTTG 59.853 52.381 0.00 0.00 0.00 2.77
524 542 4.537433 CGAGGTAGGCCTGCCTGC 62.537 72.222 43.14 30.57 45.93 4.85
606 627 3.649889 TTGCCTGCCTGCCTGCTA 61.650 61.111 2.40 0.00 0.00 3.49
687 726 2.824041 CAGGTGGGCCATACGTGC 60.824 66.667 10.70 0.00 37.19 5.34
703 742 0.182299 TCATTGTGGGTGTGTCTGCA 59.818 50.000 0.00 0.00 0.00 4.41
773 818 1.064017 TCCTCTCCTCTCCTCTCTTGC 60.064 57.143 0.00 0.00 0.00 4.01
774 819 2.509548 TCTCCTCTCCTCTCCTCTCTTG 59.490 54.545 0.00 0.00 0.00 3.02
775 820 2.858644 TCTCCTCTCCTCTCCTCTCTT 58.141 52.381 0.00 0.00 0.00 2.85
777 822 2.815589 GCATCTCCTCTCCTCTCCTCTC 60.816 59.091 0.00 0.00 0.00 3.20
779 824 1.620822 GCATCTCCTCTCCTCTCCTC 58.379 60.000 0.00 0.00 0.00 3.71
781 826 0.188342 AGGCATCTCCTCTCCTCTCC 59.812 60.000 0.00 0.00 43.20 3.71
782 827 2.108250 ACTAGGCATCTCCTCTCCTCTC 59.892 54.545 0.00 0.00 43.20 3.20
783 828 2.143602 ACTAGGCATCTCCTCTCCTCT 58.856 52.381 0.00 0.00 43.20 3.69
784 829 2.675658 ACTAGGCATCTCCTCTCCTC 57.324 55.000 0.00 0.00 43.20 3.71
786 831 3.518992 ACTACTAGGCATCTCCTCTCC 57.481 52.381 0.00 0.00 43.20 3.71
790 837 7.158355 ACTAGGAGTACTACTAGGCATCTCCT 61.158 46.154 35.22 18.48 46.16 3.69
796 843 5.471424 TCCTACTAGGAGTACTACTAGGCA 58.529 45.833 35.22 24.75 46.16 4.75
849 900 9.145442 ACTCCTACTAGTTAATGGGAAGATAAC 57.855 37.037 0.00 0.00 0.00 1.89
868 919 6.536731 TTGATTATCGACGAGTACTCCTAC 57.463 41.667 17.23 7.74 0.00 3.18
869 920 6.539826 TGTTTGATTATCGACGAGTACTCCTA 59.460 38.462 17.23 0.72 0.00 2.94
870 921 5.356190 TGTTTGATTATCGACGAGTACTCCT 59.644 40.000 17.23 5.65 0.00 3.69
871 922 5.454877 GTGTTTGATTATCGACGAGTACTCC 59.545 44.000 17.23 3.24 0.00 3.85
877 928 6.695713 TGATTAGGTGTTTGATTATCGACGAG 59.304 38.462 3.01 0.00 0.00 4.18
973 1025 6.597672 TGGCTTTTCCTTTTCTTTTCTTTTCC 59.402 34.615 0.00 0.00 35.26 3.13
989 1041 3.676049 CGGCTATTTTCCTTGGCTTTTCC 60.676 47.826 0.00 0.00 0.00 3.13
1016 1068 3.358076 CTCGTGTTCCTCCGCCTCC 62.358 68.421 0.00 0.00 0.00 4.30
1115 1182 2.664835 ATTCCGCTCGGAGGGAGGAT 62.665 60.000 22.15 10.30 46.06 3.24
1173 1241 2.232298 GAAGAGGGTGGACTGGCTCG 62.232 65.000 0.00 0.00 0.00 5.03
1198 1266 1.203112 TGAAGAGAGAGAGCAGTGGGT 60.203 52.381 0.00 0.00 0.00 4.51
1202 1270 2.387757 GGGATGAAGAGAGAGAGCAGT 58.612 52.381 0.00 0.00 0.00 4.40
1204 1272 1.397672 CGGGATGAAGAGAGAGAGCA 58.602 55.000 0.00 0.00 0.00 4.26
1205 1273 0.031994 GCGGGATGAAGAGAGAGAGC 59.968 60.000 0.00 0.00 0.00 4.09
1229 1325 1.533731 GGCGGATGAAAACGAAACAGA 59.466 47.619 0.00 0.00 0.00 3.41
1230 1326 1.724654 CGGCGGATGAAAACGAAACAG 60.725 52.381 0.00 0.00 0.00 3.16
1232 1328 0.236449 ACGGCGGATGAAAACGAAAC 59.764 50.000 13.24 0.00 0.00 2.78
1233 1329 0.945813 AACGGCGGATGAAAACGAAA 59.054 45.000 13.24 0.00 0.00 3.46
1235 1331 0.881159 ACAACGGCGGATGAAAACGA 60.881 50.000 19.51 0.00 0.00 3.85
1236 1332 0.040781 AACAACGGCGGATGAAAACG 60.041 50.000 19.51 0.00 0.00 3.60
1237 1333 1.404477 CAACAACGGCGGATGAAAAC 58.596 50.000 19.51 0.00 0.00 2.43
1309 1408 1.151450 CGGATTGGGATGGGGAAGG 59.849 63.158 0.00 0.00 0.00 3.46
1311 1410 0.771127 GATCGGATTGGGATGGGGAA 59.229 55.000 0.00 0.00 0.00 3.97
1312 1411 1.133809 GGATCGGATTGGGATGGGGA 61.134 60.000 0.00 0.00 0.00 4.81
1313 1412 1.380302 GGATCGGATTGGGATGGGG 59.620 63.158 0.00 0.00 0.00 4.96
1315 1414 0.478072 TTGGGATCGGATTGGGATGG 59.522 55.000 0.00 0.00 0.00 3.51
1768 1912 4.976224 TCGATGATTCAGAAGGAACGTA 57.024 40.909 0.00 0.00 38.60 3.57
1770 1914 5.107683 GCTATTCGATGATTCAGAAGGAACG 60.108 44.000 0.00 0.00 38.60 3.95
1779 1926 4.141959 TGGTGACAGCTATTCGATGATTCA 60.142 41.667 6.17 0.00 35.01 2.57
1799 1946 1.475751 CGAAGAGCTAATGCCCATGGT 60.476 52.381 11.73 0.00 40.80 3.55
1804 1951 3.126000 GCAATATCGAAGAGCTAATGCCC 59.874 47.826 0.00 0.00 43.63 5.36
1807 1954 6.775939 TTCAGCAATATCGAAGAGCTAATG 57.224 37.500 4.98 0.00 43.63 1.90
1808 1955 7.658982 TGAATTCAGCAATATCGAAGAGCTAAT 59.341 33.333 3.38 4.20 43.63 1.73
1837 1984 6.372659 AGTCAAAAGCTACATCAACATGGTAG 59.627 38.462 0.00 0.00 33.82 3.18
1871 2018 2.119495 AGTGGTAATGGGCTAGTCCTG 58.881 52.381 15.92 0.00 34.39 3.86
1874 2021 3.270877 CAACAGTGGTAATGGGCTAGTC 58.729 50.000 0.00 0.00 0.00 2.59
1880 2027 0.527565 GCAGCAACAGTGGTAATGGG 59.472 55.000 0.00 0.00 33.05 4.00
1898 2045 2.559785 TGCTAGCAAGGAGCAAAGC 58.440 52.632 16.84 7.29 46.71 3.51
1933 2080 6.021626 CGCTAGTTCATACAGACGAAACTAAC 60.022 42.308 0.00 0.00 0.00 2.34
1958 2106 4.632153 TGAAACTCCAGCACTCTAAACTC 58.368 43.478 0.00 0.00 0.00 3.01
1959 2107 4.689612 TGAAACTCCAGCACTCTAAACT 57.310 40.909 0.00 0.00 0.00 2.66
2026 2174 5.414454 TCAGTTGCACTTAATGGGTACAATC 59.586 40.000 0.00 0.00 0.00 2.67
2094 2243 8.594550 ACCTCAGAACATTCTTACTAGCTAAAA 58.405 33.333 0.00 0.00 34.74 1.52
2132 2281 2.012673 GGAATGCTGAAGTGGCTACAG 58.987 52.381 2.02 0.00 35.14 2.74
2199 2349 4.400961 GCTCAGCTGAACCCCGCT 62.401 66.667 18.85 0.00 36.83 5.52
2213 2363 6.426937 TGAGAAGTTTACCTACAACATTGCTC 59.573 38.462 0.00 0.00 0.00 4.26
2238 2388 4.489810 TGTTCAAATGCACGTCAAACTTT 58.510 34.783 0.00 0.00 0.00 2.66
2339 2515 8.209584 GCATCTCCATGTCTCATATGGTAATAT 58.790 37.037 2.13 0.00 44.35 1.28
2551 2729 0.615544 CATCATTGTGGGCTGGGGTT 60.616 55.000 0.00 0.00 0.00 4.11
2777 3079 7.194112 TGTTTATTGGTCACTGATCAGGATA 57.806 36.000 26.08 8.61 0.00 2.59
2827 3129 6.481644 TCAATTACTTGTCAACAAAAATGCCC 59.518 34.615 0.00 0.00 35.15 5.36
3000 3302 4.272748 GGGGTAAAGTTCAACGATATGCTC 59.727 45.833 0.00 0.00 0.00 4.26
3022 3324 5.316987 ACCTGAGTACCAAAATGAGAAAGG 58.683 41.667 0.00 0.00 0.00 3.11
3192 3494 2.526304 ATGGACCATCATACCGTTCG 57.474 50.000 0.00 0.00 0.00 3.95
3718 4021 9.941325 TCCAAAACATAATAGTGCAAAATTCAT 57.059 25.926 0.00 0.00 0.00 2.57
3758 4061 4.651778 ACAACCTCAAGCAATAGTTAGCA 58.348 39.130 0.00 0.00 0.00 3.49
4067 4372 6.600882 AAGAGCATTCCAGAAAATGTTGAT 57.399 33.333 0.00 0.00 38.60 2.57
4350 4655 9.529823 TGTAGATACAGAACTAGGAGAGAAAAA 57.470 33.333 0.00 0.00 0.00 1.94
4442 4908 7.907841 ACTGACCAAAATAACTAAAAAGGGT 57.092 32.000 0.00 0.00 0.00 4.34
4473 4940 2.809696 GGTAAAGCTCGCCTGTGTAAAA 59.190 45.455 0.00 0.00 0.00 1.52
4525 4994 6.642707 TGCCCCCTATAAATGTTTTATTCG 57.357 37.500 0.00 0.00 0.00 3.34
4613 5082 1.497286 TGCCCCAATACCCAGATAACC 59.503 52.381 0.00 0.00 0.00 2.85
4681 5150 2.423577 CACAAGAAACTTACCCCCTCG 58.576 52.381 0.00 0.00 0.00 4.63
5200 5674 2.755103 CCTCTAGTTCCCCAAAACATGC 59.245 50.000 0.00 0.00 0.00 4.06
5266 5740 1.486310 GAGGACACCAGCATGTATGGA 59.514 52.381 21.57 0.00 40.51 3.41
5301 5776 6.050454 CAAAATGCATTGCTTTCAAAGACA 57.950 33.333 13.82 0.00 35.56 3.41
5331 5807 8.548721 CGCCTAACTATAACAAGATAACCTTTG 58.451 37.037 0.00 0.00 31.42 2.77
5345 5821 2.933906 GCACAGCAACGCCTAACTATAA 59.066 45.455 0.00 0.00 0.00 0.98
5346 5822 2.167693 AGCACAGCAACGCCTAACTATA 59.832 45.455 0.00 0.00 0.00 1.31
5347 5823 1.066143 AGCACAGCAACGCCTAACTAT 60.066 47.619 0.00 0.00 0.00 2.12
5348 5824 0.320374 AGCACAGCAACGCCTAACTA 59.680 50.000 0.00 0.00 0.00 2.24
5349 5825 1.071471 AGCACAGCAACGCCTAACT 59.929 52.632 0.00 0.00 0.00 2.24
5350 5826 1.207593 CAGCACAGCAACGCCTAAC 59.792 57.895 0.00 0.00 0.00 2.34
5470 5949 5.888161 ACTCTAATACCAAGCCCAAATTGAG 59.112 40.000 0.00 0.00 0.00 3.02
5818 6348 7.227314 TGCACATGGATCTGAATTATGTAAGAC 59.773 37.037 0.00 0.00 31.34 3.01
5911 6441 2.435805 GAGACAGGCTCATATGGACCAA 59.564 50.000 14.86 0.00 43.38 3.67
6000 6530 9.178427 GCACATCATCTAGCTTAATTTCAATTC 57.822 33.333 0.00 0.00 0.00 2.17
6051 6588 7.490962 TGCAAATATACTTGTTATTCCTCCG 57.509 36.000 0.00 0.00 0.00 4.63
6329 7851 9.562583 CACAAGCTAAAACTAAACTGTGTTTTA 57.437 29.630 11.69 11.69 43.40 1.52
6330 7852 8.301002 TCACAAGCTAAAACTAAACTGTGTTTT 58.699 29.630 10.87 10.87 44.96 2.43
6331 7853 7.822658 TCACAAGCTAAAACTAAACTGTGTTT 58.177 30.769 7.50 1.33 37.92 2.83
6332 7854 7.385778 TCACAAGCTAAAACTAAACTGTGTT 57.614 32.000 7.50 0.00 0.00 3.32
6333 7855 6.995511 TCACAAGCTAAAACTAAACTGTGT 57.004 33.333 7.50 0.00 0.00 3.72
6355 7877 9.688592 AGAAAGAAAGATTGAATGAATGTGTTC 57.311 29.630 0.00 0.00 34.85 3.18
6450 7972 1.992277 CCAGTGACCTCCTCCTGGG 60.992 68.421 0.00 0.00 40.65 4.45
6500 8022 5.717178 ACTCAGGAGCAACATAAGAGAGTAA 59.283 40.000 0.00 0.00 32.58 2.24
6628 8160 5.147767 GCATTTTTGGAGGATAGGGGTTAT 58.852 41.667 0.00 0.00 0.00 1.89
6629 8161 4.542697 GCATTTTTGGAGGATAGGGGTTA 58.457 43.478 0.00 0.00 0.00 2.85
6630 8162 3.374764 GCATTTTTGGAGGATAGGGGTT 58.625 45.455 0.00 0.00 0.00 4.11
6713 8245 1.495878 CATAGCTGCTAGCAAGACCG 58.504 55.000 19.86 7.74 45.56 4.79
6757 8289 7.054124 ACCTAATGGTGAGTAATACATGTTGG 58.946 38.462 2.30 0.00 46.51 3.77
6845 8377 3.555795 GGCTCAATCGAATGCCTCTATCA 60.556 47.826 12.13 0.00 41.92 2.15
7042 8574 1.303309 CATCGGCATGTTCTTCCTCC 58.697 55.000 0.00 0.00 0.00 4.30
7077 8609 1.911357 TCCTTGTCCATGCTGAGATGT 59.089 47.619 0.00 0.00 0.00 3.06
7212 8744 1.145119 GGAAAACCCACTCCTGGAAGT 59.855 52.381 0.00 0.00 40.55 3.01
7226 8758 3.425659 AGAAGAAGCCTCCATGGAAAAC 58.574 45.455 17.00 8.03 38.35 2.43
7233 8765 3.390639 CCATGACTAGAAGAAGCCTCCAT 59.609 47.826 0.00 0.00 0.00 3.41
7273 8805 4.737054 CAAAGGTGGAGCATTATGTGAAC 58.263 43.478 0.00 0.00 0.00 3.18
7309 8841 3.006859 TGGAGCTGATGTATCCGGTAATG 59.993 47.826 0.00 0.00 35.78 1.90
7397 8929 4.992381 ACATTCAGACGAACTTTACAGC 57.008 40.909 0.00 0.00 32.81 4.40
7739 9274 9.327628 CTTGGAAAGGAGCAGATCATATATATG 57.672 37.037 15.47 15.47 41.27 1.78
7844 9379 1.542187 GGAACAGTAGGACGGGTGCT 61.542 60.000 0.00 0.00 34.87 4.40
7865 9400 3.872560 GTTGAAACCACCGTAACTGAG 57.127 47.619 0.00 0.00 0.00 3.35
8291 9827 5.641636 TGCAGGAAAGAAAAAGAAAACCAAC 59.358 36.000 0.00 0.00 0.00 3.77
8438 9974 1.045350 TCTGGATTCCTGAGGCTCGG 61.045 60.000 16.65 16.65 0.00 4.63
8446 9982 0.809241 GCGCTGAGTCTGGATTCCTG 60.809 60.000 0.00 3.59 0.00 3.86
8473 10009 7.741554 AACTCTGGGATAATCTTGTAACTCT 57.258 36.000 0.00 0.00 0.00 3.24
8474 10010 9.315525 GTAAACTCTGGGATAATCTTGTAACTC 57.684 37.037 0.00 0.00 0.00 3.01
8475 10011 8.822805 TGTAAACTCTGGGATAATCTTGTAACT 58.177 33.333 0.00 0.00 0.00 2.24
8476 10012 9.614792 ATGTAAACTCTGGGATAATCTTGTAAC 57.385 33.333 0.00 0.00 0.00 2.50
8478 10014 9.613428 CAATGTAAACTCTGGGATAATCTTGTA 57.387 33.333 0.00 0.00 0.00 2.41
8479 10015 8.109634 ACAATGTAAACTCTGGGATAATCTTGT 58.890 33.333 0.00 0.00 0.00 3.16
8480 10016 8.511604 ACAATGTAAACTCTGGGATAATCTTG 57.488 34.615 0.00 0.00 0.00 3.02
8482 10018 9.533831 AAAACAATGTAAACTCTGGGATAATCT 57.466 29.630 0.00 0.00 0.00 2.40
8497 10033 8.682710 AGCAGAGAACAGTTAAAAACAATGTAA 58.317 29.630 0.00 0.00 0.00 2.41
8518 10055 0.534877 ATTGCAACGGTGACAGCAGA 60.535 50.000 3.55 0.00 38.35 4.26
8519 10056 0.386352 CATTGCAACGGTGACAGCAG 60.386 55.000 3.55 0.48 38.35 4.24
8524 10061 0.593773 AAACGCATTGCAACGGTGAC 60.594 50.000 17.49 0.00 0.00 3.67
8529 10066 0.777631 CAAGGAAACGCATTGCAACG 59.222 50.000 0.00 4.29 30.93 4.10
8540 10077 1.202348 GTATGCCAGCACCAAGGAAAC 59.798 52.381 0.00 0.00 0.00 2.78
8543 10081 0.322456 GTGTATGCCAGCACCAAGGA 60.322 55.000 0.00 0.00 0.00 3.36
8554 10092 2.380084 TCCGAACAGAAGTGTATGCC 57.620 50.000 0.00 0.00 35.08 4.40
8561 10099 5.855045 ACTACAAGATTTCCGAACAGAAGT 58.145 37.500 0.00 0.00 0.00 3.01
8565 10103 6.856426 GGAAAAACTACAAGATTTCCGAACAG 59.144 38.462 10.78 0.00 40.82 3.16
8566 10104 6.731164 GGAAAAACTACAAGATTTCCGAACA 58.269 36.000 10.78 0.00 40.82 3.18
8576 10115 6.940298 CAGGTATCAAGGGAAAAACTACAAGA 59.060 38.462 0.00 0.00 0.00 3.02
8581 10120 5.013704 TCTGCAGGTATCAAGGGAAAAACTA 59.986 40.000 15.13 0.00 0.00 2.24
8582 10121 4.082125 CTGCAGGTATCAAGGGAAAAACT 58.918 43.478 5.57 0.00 0.00 2.66
8583 10122 4.079253 TCTGCAGGTATCAAGGGAAAAAC 58.921 43.478 15.13 0.00 0.00 2.43
8584 10123 4.380843 TCTGCAGGTATCAAGGGAAAAA 57.619 40.909 15.13 0.00 0.00 1.94
8589 10128 3.012518 CAGTTTCTGCAGGTATCAAGGG 58.987 50.000 15.13 0.00 0.00 3.95
8669 10213 3.644884 ACCACAGAACTACGACTGAAG 57.355 47.619 0.00 0.00 37.54 3.02
8672 10216 2.794910 CACAACCACAGAACTACGACTG 59.205 50.000 0.00 0.00 39.65 3.51
8673 10217 2.429610 ACACAACCACAGAACTACGACT 59.570 45.455 0.00 0.00 0.00 4.18
8678 10222 4.223556 TCCAAACACAACCACAGAACTA 57.776 40.909 0.00 0.00 0.00 2.24
8684 10228 2.167281 CCACATTCCAAACACAACCACA 59.833 45.455 0.00 0.00 0.00 4.17
8749 10293 2.851195 ACCTCAGAAGTTCGCAAATGT 58.149 42.857 0.00 0.00 0.00 2.71
8751 10295 5.003804 ACATAACCTCAGAAGTTCGCAAAT 58.996 37.500 0.00 0.00 0.00 2.32
8763 10307 8.511604 AACTGGAATTTCATACATAACCTCAG 57.488 34.615 0.00 0.00 0.00 3.35
8764 10308 8.877864 AAACTGGAATTTCATACATAACCTCA 57.122 30.769 0.00 0.00 0.00 3.86
8766 10310 9.927668 CAAAAACTGGAATTTCATACATAACCT 57.072 29.630 0.00 0.00 0.00 3.50
8767 10311 9.705290 ACAAAAACTGGAATTTCATACATAACC 57.295 29.630 0.00 0.00 0.00 2.85
8785 10329 3.626930 TGCTCAGGGTGTTACAAAAACT 58.373 40.909 0.00 0.00 0.00 2.66
8790 10334 2.356382 CGTTTTGCTCAGGGTGTTACAA 59.644 45.455 0.00 0.00 0.00 2.41
8823 10367 4.072131 TGACTTCACTTGATAAAGGCACC 58.928 43.478 0.00 0.00 33.16 5.01
9362 10908 1.157257 CCCAGTTTTGGCCGTTTTGC 61.157 55.000 0.00 0.00 43.58 3.68
9363 10909 1.157257 GCCCAGTTTTGGCCGTTTTG 61.157 55.000 0.00 0.00 43.58 2.44
9364 10910 1.145156 GCCCAGTTTTGGCCGTTTT 59.855 52.632 0.00 0.00 43.58 2.43
9365 10911 2.818841 GCCCAGTTTTGGCCGTTT 59.181 55.556 0.00 0.00 43.58 3.60
9371 10917 2.686816 CGCTACGGCCCAGTTTTGG 61.687 63.158 0.00 0.00 44.60 3.28
9372 10918 2.867472 CGCTACGGCCCAGTTTTG 59.133 61.111 0.00 0.00 34.44 2.44
9373 10919 3.053896 GCGCTACGGCCCAGTTTT 61.054 61.111 0.00 0.00 34.44 2.43


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

AutoCloner maintained by Alex Coulton.