Multiple sequence alignment - TraesCS5D01G383000

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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 TraesCS5D01G383000 chr5D 100.000 4452 0 0 1 4452 452559690 452564141 0.000000e+00 8222.0
1 TraesCS5D01G383000 chr5D 96.809 94 3 0 2184 2277 403752198 403752291 1.660000e-34 158.0
2 TraesCS5D01G383000 chr5D 94.681 94 5 0 2184 2277 78435075 78435168 3.590000e-31 147.0
3 TraesCS5D01G383000 chr5D 84.375 64 5 5 1138 1197 36761831 36761893 1.730000e-04 58.4
4 TraesCS5D01G383000 chr5A 91.214 3130 167 38 1366 4449 571465522 571468589 0.000000e+00 4157.0
5 TraesCS5D01G383000 chr5A 86.838 1322 74 50 6 1284 571464116 571465380 0.000000e+00 1386.0
6 TraesCS5D01G383000 chr5A 75.641 156 20 16 1138 1276 25888061 25888215 1.340000e-05 62.1
7 TraesCS5D01G383000 chr5B 90.385 1664 82 26 1366 3016 552922003 552923601 0.000000e+00 2115.0
8 TraesCS5D01G383000 chr5B 93.909 1215 47 14 3052 4258 552923592 552924787 0.000000e+00 1808.0
9 TraesCS5D01G383000 chr5B 89.903 723 36 15 575 1284 552921170 552921868 0.000000e+00 896.0
10 TraesCS5D01G383000 chr5B 80.455 527 28 36 6 495 552920601 552921089 2.570000e-87 333.0
11 TraesCS5D01G383000 chr5B 96.644 149 5 0 4253 4401 552925479 552925627 9.560000e-62 248.0
12 TraesCS5D01G383000 chr5B 93.103 116 4 3 1 113 552918445 552918559 2.750000e-37 167.0
13 TraesCS5D01G383000 chr5B 84.375 64 5 5 1138 1197 27506690 27506752 1.730000e-04 58.4
14 TraesCS5D01G383000 chrUn 97.872 94 2 0 2184 2277 114922848 114922941 3.560000e-36 163.0
15 TraesCS5D01G383000 chr7D 97.872 94 2 0 2184 2277 567810407 567810314 3.560000e-36 163.0
16 TraesCS5D01G383000 chr4A 96.809 94 2 1 2184 2277 53816152 53816060 5.960000e-34 156.0
17 TraesCS5D01G383000 chr7B 94.737 38 1 1 1937 1974 32095853 32095889 1.730000e-04 58.4
18 TraesCS5D01G383000 chr6D 84.375 64 5 5 1138 1197 196357154 196357216 1.730000e-04 58.4
19 TraesCS5D01G383000 chr3A 88.000 50 4 2 1149 1197 50434779 50434827 1.730000e-04 58.4
20 TraesCS5D01G383000 chr2D 100.000 29 0 0 4119 4147 484088845 484088817 2.000000e-03 54.7


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 TraesCS5D01G383000 chr5D 452559690 452564141 4451 False 8222.000000 8222 100.000000 1 4452 1 chr5D.!!$F4 4451
1 TraesCS5D01G383000 chr5A 571464116 571468589 4473 False 2771.500000 4157 89.026000 6 4449 2 chr5A.!!$F2 4443
2 TraesCS5D01G383000 chr5B 552918445 552925627 7182 False 927.833333 2115 90.733167 1 4401 6 chr5B.!!$F2 4400

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
590 2844 0.036858 GCTCTCTGCTCCGGTTTCTT 60.037 55.0 0.0 0.0 38.95 2.52 F
2359 4709 0.111253 AGTCTGGAGGCAACAAAGGG 59.889 55.0 0.0 0.0 41.41 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2410 4760 0.109873 CGAAGCGACCGTTGTACTCT 60.110 55.0 0.0 0.0 0.00 3.24 R
4103 6535 0.905357 AGGAAGACCGAATCACTGGG 59.095 55.0 0.0 0.0 41.83 4.45 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
164 2342 0.179034 GTCCTGCATCCACATCTCCC 60.179 60.000 0.00 0.00 0.00 4.30
165 2343 0.326904 TCCTGCATCCACATCTCCCT 60.327 55.000 0.00 0.00 0.00 4.20
167 2345 1.129917 CTGCATCCACATCTCCCTCT 58.870 55.000 0.00 0.00 0.00 3.69
168 2346 1.070445 CTGCATCCACATCTCCCTCTC 59.930 57.143 0.00 0.00 0.00 3.20
183 2378 0.478507 CTCTCCCTCCCCTCTCTCTC 59.521 65.000 0.00 0.00 0.00 3.20
191 2386 3.535962 CCTCTCTCTCCTGCCGCC 61.536 72.222 0.00 0.00 0.00 6.13
212 2407 4.498682 GCCTGTTGCTTGCCATTATTAGAG 60.499 45.833 0.00 0.00 36.87 2.43
213 2408 4.883585 CCTGTTGCTTGCCATTATTAGAGA 59.116 41.667 0.00 0.00 0.00 3.10
214 2409 5.008415 CCTGTTGCTTGCCATTATTAGAGAG 59.992 44.000 0.00 0.00 0.00 3.20
215 2410 5.744171 TGTTGCTTGCCATTATTAGAGAGA 58.256 37.500 0.00 0.00 0.00 3.10
216 2411 6.179756 TGTTGCTTGCCATTATTAGAGAGAA 58.820 36.000 0.00 0.00 0.00 2.87
217 2412 6.317140 TGTTGCTTGCCATTATTAGAGAGAAG 59.683 38.462 0.00 0.00 0.00 2.85
218 2413 6.239217 TGCTTGCCATTATTAGAGAGAAGA 57.761 37.500 0.00 0.00 0.00 2.87
229 2424 1.062505 AGAGAGAAGATGGTCTCCCCC 60.063 57.143 0.00 0.00 44.43 5.40
230 2425 0.719015 AGAGAAGATGGTCTCCCCCA 59.281 55.000 0.00 0.00 44.43 4.96
231 2426 1.127343 GAGAAGATGGTCTCCCCCAG 58.873 60.000 0.00 0.00 38.51 4.45
282 2483 1.281925 TGGCTTGATTCCCCTCTCCC 61.282 60.000 0.00 0.00 0.00 4.30
334 2536 1.153997 GTCGCTCTGGTTCGTCCTC 60.154 63.158 1.80 0.00 37.07 3.71
336 2538 1.444553 CGCTCTGGTTCGTCCTCAC 60.445 63.158 1.80 0.00 37.07 3.51
341 2544 1.152419 TGGTTCGTCCTCACTCCCA 60.152 57.895 1.80 0.00 37.07 4.37
343 2546 1.292541 GTTCGTCCTCACTCCCACC 59.707 63.158 0.00 0.00 0.00 4.61
344 2547 1.155390 TTCGTCCTCACTCCCACCT 59.845 57.895 0.00 0.00 0.00 4.00
345 2548 0.898789 TTCGTCCTCACTCCCACCTC 60.899 60.000 0.00 0.00 0.00 3.85
346 2549 2.701780 CGTCCTCACTCCCACCTCG 61.702 68.421 0.00 0.00 0.00 4.63
347 2550 2.680352 TCCTCACTCCCACCTCGC 60.680 66.667 0.00 0.00 0.00 5.03
348 2551 3.775654 CCTCACTCCCACCTCGCC 61.776 72.222 0.00 0.00 0.00 5.54
349 2552 2.681778 CTCACTCCCACCTCGCCT 60.682 66.667 0.00 0.00 0.00 5.52
350 2553 2.680352 TCACTCCCACCTCGCCTC 60.680 66.667 0.00 0.00 0.00 4.70
399 2612 2.995258 CTGCTCAAAGTTCTCTCTGCTC 59.005 50.000 0.00 0.00 0.00 4.26
402 2615 2.995258 CTCAAAGTTCTCTCTGCTCTGC 59.005 50.000 0.00 0.00 0.00 4.26
403 2616 2.632028 TCAAAGTTCTCTCTGCTCTGCT 59.368 45.455 0.00 0.00 0.00 4.24
404 2617 3.829026 TCAAAGTTCTCTCTGCTCTGCTA 59.171 43.478 0.00 0.00 0.00 3.49
405 2618 4.082300 TCAAAGTTCTCTCTGCTCTGCTAG 60.082 45.833 0.00 0.00 0.00 3.42
414 2627 2.475666 GCTCTGCTAGCCCTTGTTG 58.524 57.895 13.29 0.00 46.25 3.33
415 2628 1.028868 GCTCTGCTAGCCCTTGTTGG 61.029 60.000 13.29 0.00 46.25 3.77
450 2663 0.322906 CCTTCTGAAAGTCAGGGGGC 60.323 60.000 5.46 0.00 44.39 5.80
512 2725 1.081094 GCACAGCCATGGAAAATTGC 58.919 50.000 18.40 11.94 0.00 3.56
535 2783 6.378280 TGCTTCAGTTTTCCTCTTCTTCTTTT 59.622 34.615 0.00 0.00 0.00 2.27
555 2803 5.757850 TTTTTGCCAACACAAACAAAACT 57.242 30.435 0.00 0.00 40.58 2.66
556 2804 4.739046 TTTGCCAACACAAACAAAACTG 57.261 36.364 0.00 0.00 34.68 3.16
561 2809 4.310769 CCAACACAAACAAAACTGGTTCA 58.689 39.130 0.00 0.00 0.00 3.18
562 2810 4.934602 CCAACACAAACAAAACTGGTTCAT 59.065 37.500 0.00 0.00 0.00 2.57
566 2814 5.043248 CACAAACAAAACTGGTTCATCTCC 58.957 41.667 0.00 0.00 0.00 3.71
580 2834 2.254773 ATCTCCCCTGGCTCTCTGCT 62.255 60.000 0.00 0.00 42.39 4.24
590 2844 0.036858 GCTCTCTGCTCCGGTTTCTT 60.037 55.000 0.00 0.00 38.95 2.52
617 2871 1.832719 TTCGGGTTTCATCTCGGCCA 61.833 55.000 2.24 0.00 0.00 5.36
620 2874 0.181350 GGGTTTCATCTCGGCCATCT 59.819 55.000 2.24 0.00 0.00 2.90
622 2876 1.303309 GTTTCATCTCGGCCATCTGG 58.697 55.000 2.24 0.00 38.53 3.86
663 2920 3.737172 GCGCGTTTCCTGTGGCAT 61.737 61.111 8.43 0.00 0.00 4.40
664 2921 2.395360 GCGCGTTTCCTGTGGCATA 61.395 57.895 8.43 0.00 0.00 3.14
665 2922 1.423845 CGCGTTTCCTGTGGCATAC 59.576 57.895 0.00 0.00 0.00 2.39
779 3036 6.074356 CCCACTTGCTTCGTTTCTTTAATTTG 60.074 38.462 0.00 0.00 0.00 2.32
830 3087 5.503662 TCGTTTTTGTTTTTACCTCCTCC 57.496 39.130 0.00 0.00 0.00 4.30
842 3099 1.388065 CCTCCTCCGCTCCTACACTG 61.388 65.000 0.00 0.00 0.00 3.66
881 3138 7.398618 TCCTCTTTAATTATTGGTTTGGCATGA 59.601 33.333 0.00 0.00 0.00 3.07
897 3154 2.954318 GCATGAGTGGTTGGATGCTTAT 59.046 45.455 0.00 0.00 38.53 1.73
898 3155 4.136796 GCATGAGTGGTTGGATGCTTATA 58.863 43.478 0.00 0.00 38.53 0.98
951 3208 1.227380 CTGGCCCGAAGAGAATCCG 60.227 63.158 0.00 0.00 33.66 4.18
990 3247 5.278758 CGTTTAATTCCTTCCTTGGCAAAGA 60.279 40.000 1.11 0.00 35.19 2.52
1059 3316 1.152567 CAATGGTGGTGGTGGTGGT 60.153 57.895 0.00 0.00 0.00 4.16
1060 3317 1.152567 AATGGTGGTGGTGGTGGTG 60.153 57.895 0.00 0.00 0.00 4.17
1061 3318 2.655077 AATGGTGGTGGTGGTGGTGG 62.655 60.000 0.00 0.00 0.00 4.61
1285 3574 1.690893 CTGCTCTGCCTCCTTGCTATA 59.309 52.381 0.00 0.00 0.00 1.31
1306 3595 4.150897 AGCAAGAATTCGGTATGGCTTA 57.849 40.909 0.00 0.00 0.00 3.09
1308 3597 5.133221 AGCAAGAATTCGGTATGGCTTATT 58.867 37.500 0.00 0.00 0.00 1.40
1309 3598 6.296026 AGCAAGAATTCGGTATGGCTTATTA 58.704 36.000 0.00 0.00 0.00 0.98
1327 3616 2.785540 TAGTTGGATCTGTGCATGCA 57.214 45.000 18.46 18.46 0.00 3.96
1329 3618 1.816835 AGTTGGATCTGTGCATGCAAG 59.183 47.619 24.58 20.60 35.05 4.01
1330 3619 1.814394 GTTGGATCTGTGCATGCAAGA 59.186 47.619 24.58 24.74 35.05 3.02
1331 3620 2.426024 GTTGGATCTGTGCATGCAAGAT 59.574 45.455 29.39 29.39 35.05 2.40
1350 3639 0.322098 TATGCCGGTGAACACAAGGG 60.322 55.000 1.90 10.80 33.27 3.95
1351 3640 2.063015 ATGCCGGTGAACACAAGGGA 62.063 55.000 1.90 14.44 36.06 4.20
1352 3641 1.527380 GCCGGTGAACACAAGGGAA 60.527 57.895 1.90 0.00 33.27 3.97
1353 3642 0.893727 GCCGGTGAACACAAGGGAAT 60.894 55.000 1.90 0.00 33.27 3.01
1354 3643 0.881118 CCGGTGAACACAAGGGAATG 59.119 55.000 7.25 0.00 0.00 2.67
1355 3644 1.544537 CCGGTGAACACAAGGGAATGA 60.545 52.381 7.25 0.00 0.00 2.57
1358 3647 4.199310 CGGTGAACACAAGGGAATGATAT 58.801 43.478 7.25 0.00 0.00 1.63
1359 3648 4.035558 CGGTGAACACAAGGGAATGATATG 59.964 45.833 7.25 0.00 0.00 1.78
1360 3649 5.192927 GGTGAACACAAGGGAATGATATGA 58.807 41.667 7.25 0.00 0.00 2.15
1361 3650 5.066505 GGTGAACACAAGGGAATGATATGAC 59.933 44.000 7.25 0.00 0.00 3.06
1362 3651 5.647658 GTGAACACAAGGGAATGATATGACA 59.352 40.000 0.00 0.00 0.00 3.58
1364 3653 5.441718 ACACAAGGGAATGATATGACACT 57.558 39.130 0.00 0.00 0.00 3.55
1368 3695 7.336931 ACACAAGGGAATGATATGACACTTAAC 59.663 37.037 0.00 0.00 0.00 2.01
1463 3792 6.485830 TCTCCTCCTCATATGACGAAAAAT 57.514 37.500 0.00 0.00 0.00 1.82
1522 3862 7.611467 ACTTGGTATGAACTAGATGAATTTGCA 59.389 33.333 0.00 0.00 0.00 4.08
1531 3871 8.929260 AACTAGATGAATTTGCATATGATGGA 57.071 30.769 6.97 0.00 0.00 3.41
1605 3949 7.710475 GCAGGCTTGCTTTATATTATCCAAAAA 59.290 33.333 14.45 0.00 46.95 1.94
1719 4064 7.288672 GTCTCCAAGTCTGTTATTTTTGTACG 58.711 38.462 0.00 0.00 0.00 3.67
1751 4096 8.800332 AGATAAGCTTTTCTTTGATGAACATGT 58.200 29.630 13.03 0.00 36.25 3.21
1752 4097 8.976986 ATAAGCTTTTCTTTGATGAACATGTC 57.023 30.769 3.20 0.00 36.25 3.06
1798 4143 1.153329 TGCTCCCGTGTTTGTTCGT 60.153 52.632 0.00 0.00 0.00 3.85
1799 4144 1.278637 GCTCCCGTGTTTGTTCGTG 59.721 57.895 0.00 0.00 0.00 4.35
1861 4210 7.093992 GCCCTATCTCTATGTGATAAGAACAC 58.906 42.308 0.00 0.00 38.55 3.32
1879 4228 2.730672 CGCGGCTGTGCTCAGTTAC 61.731 63.158 16.59 7.27 43.05 2.50
1928 4277 3.678072 TGCTTATTATTACCGCGATGCTC 59.322 43.478 8.23 0.00 0.00 4.26
1929 4278 3.678072 GCTTATTATTACCGCGATGCTCA 59.322 43.478 8.23 0.00 0.00 4.26
1930 4279 4.330074 GCTTATTATTACCGCGATGCTCAT 59.670 41.667 8.23 0.00 0.00 2.90
1931 4280 5.163854 GCTTATTATTACCGCGATGCTCATT 60.164 40.000 8.23 0.00 0.00 2.57
1932 4281 6.035650 GCTTATTATTACCGCGATGCTCATTA 59.964 38.462 8.23 0.00 0.00 1.90
1933 4282 7.254455 GCTTATTATTACCGCGATGCTCATTAT 60.254 37.037 8.23 0.00 0.00 1.28
1934 4283 5.778161 TTATTACCGCGATGCTCATTATG 57.222 39.130 8.23 0.00 0.00 1.90
1935 4284 3.378911 TTACCGCGATGCTCATTATGA 57.621 42.857 8.23 0.00 0.00 2.15
1936 4285 2.462456 ACCGCGATGCTCATTATGAT 57.538 45.000 8.23 0.00 0.00 2.45
2063 4413 6.542574 TGACATTTTGAACATGAAATTGGC 57.457 33.333 0.00 0.00 0.00 4.52
2091 4441 6.071560 TGGCCTCGTCTAACCATATACTAATG 60.072 42.308 3.32 0.00 0.00 1.90
2344 4694 1.988107 TGCTCAGGGAATTTGGAGTCT 59.012 47.619 0.00 0.00 0.00 3.24
2359 4709 0.111253 AGTCTGGAGGCAACAAAGGG 59.889 55.000 0.00 0.00 41.41 3.95
2373 4723 1.074296 AAAGGGGAGAAGGCCTTGGT 61.074 55.000 26.25 10.13 0.00 3.67
2389 4739 2.672996 GTGCACTCCGCCACCATT 60.673 61.111 10.32 0.00 41.33 3.16
2413 4763 4.504916 CAGTCGCCGCTCCCAGAG 62.505 72.222 0.00 0.00 0.00 3.35
2420 4770 1.153823 CCGCTCCCAGAGTACAACG 60.154 63.158 0.00 0.00 31.39 4.10
2431 4781 0.109873 AGTACAACGGTCGCTTCGAG 60.110 55.000 0.00 0.00 36.23 4.04
2522 4874 3.960102 TGTCCCAACTTTTCAGCTGAAAT 59.040 39.130 35.66 22.86 42.83 2.17
2523 4875 4.405358 TGTCCCAACTTTTCAGCTGAAATT 59.595 37.500 35.66 26.56 42.83 1.82
2543 4895 5.712152 ATTTTGTTTCTGGATGTCTCCAC 57.288 39.130 0.00 0.00 46.95 4.02
2551 4903 2.746362 CTGGATGTCTCCACTTTTCAGC 59.254 50.000 0.00 0.00 46.95 4.26
2561 4913 4.968259 TCCACTTTTCAGCTGCTAACTTA 58.032 39.130 9.47 0.00 0.00 2.24
2618 4970 1.123077 CTGACCAGTGCTATGGCCTA 58.877 55.000 3.32 0.00 44.80 3.93
2633 4985 1.205417 GGCCTACTTACCACTTACGCA 59.795 52.381 0.00 0.00 0.00 5.24
2688 5040 2.488153 GTGCTCTATTTTGGACGCCTTT 59.512 45.455 0.00 0.00 0.00 3.11
2746 5102 2.730382 TCTGTTCATCGTAGCCTGGTA 58.270 47.619 0.00 0.00 0.00 3.25
2751 5107 2.201022 ATCGTAGCCTGGTAGCCGG 61.201 63.158 0.00 0.00 0.00 6.13
2817 5173 3.444742 TGAATGCAAAGCAGTATGAAGGG 59.555 43.478 0.00 0.00 43.65 3.95
2891 5247 4.142038 GTGAAAGGAAGAAAGGTAAGCCA 58.858 43.478 0.00 0.00 37.19 4.75
2911 5270 1.168714 GCACTTCCACCAAGTCCATC 58.831 55.000 0.00 0.00 44.14 3.51
2925 5284 5.814705 CCAAGTCCATCTCATTTACAGAGAC 59.185 44.000 0.00 0.00 44.23 3.36
2930 5289 4.406972 CCATCTCATTTACAGAGACTGGGA 59.593 45.833 0.00 0.00 44.23 4.37
2953 5312 5.357742 AAAACAAACCTCTTCCATTTGCT 57.642 34.783 0.00 0.00 36.91 3.91
3014 5418 3.473923 TCTCATTGCCGCTTATGATCA 57.526 42.857 0.00 0.00 30.91 2.92
3015 5419 4.011966 TCTCATTGCCGCTTATGATCAT 57.988 40.909 13.81 13.81 30.91 2.45
3016 5420 3.999001 TCTCATTGCCGCTTATGATCATC 59.001 43.478 12.53 0.00 30.91 2.92
3017 5421 4.001652 CTCATTGCCGCTTATGATCATCT 58.998 43.478 12.53 0.00 30.91 2.90
3018 5422 4.392047 TCATTGCCGCTTATGATCATCTT 58.608 39.130 12.53 0.00 0.00 2.40
3019 5423 4.823442 TCATTGCCGCTTATGATCATCTTT 59.177 37.500 12.53 0.00 0.00 2.52
3020 5424 5.300034 TCATTGCCGCTTATGATCATCTTTT 59.700 36.000 12.53 0.00 0.00 2.27
3021 5425 4.556942 TGCCGCTTATGATCATCTTTTG 57.443 40.909 12.53 0.89 0.00 2.44
3022 5426 4.198530 TGCCGCTTATGATCATCTTTTGA 58.801 39.130 12.53 0.00 39.12 2.69
3023 5427 4.639755 TGCCGCTTATGATCATCTTTTGAA 59.360 37.500 12.53 0.00 38.03 2.69
3024 5428 5.125257 TGCCGCTTATGATCATCTTTTGAAA 59.875 36.000 12.53 0.00 38.03 2.69
3025 5429 5.456822 GCCGCTTATGATCATCTTTTGAAAC 59.543 40.000 12.53 0.00 38.03 2.78
3026 5430 5.678483 CCGCTTATGATCATCTTTTGAAACG 59.322 40.000 12.53 6.94 38.03 3.60
3027 5431 5.678483 CGCTTATGATCATCTTTTGAAACGG 59.322 40.000 12.53 0.00 38.03 4.44
3028 5432 6.456853 CGCTTATGATCATCTTTTGAAACGGA 60.457 38.462 12.53 0.00 38.03 4.69
3029 5433 6.909357 GCTTATGATCATCTTTTGAAACGGAG 59.091 38.462 12.53 0.00 38.03 4.63
3030 5434 5.824904 ATGATCATCTTTTGAAACGGAGG 57.175 39.130 1.18 0.00 38.03 4.30
3031 5435 3.440173 TGATCATCTTTTGAAACGGAGGC 59.560 43.478 0.00 0.00 38.03 4.70
3032 5436 2.857483 TCATCTTTTGAAACGGAGGCA 58.143 42.857 0.00 0.00 0.00 4.75
3033 5437 3.218453 TCATCTTTTGAAACGGAGGCAA 58.782 40.909 0.00 0.00 0.00 4.52
3034 5438 3.634448 TCATCTTTTGAAACGGAGGCAAA 59.366 39.130 0.00 0.00 0.00 3.68
3035 5439 4.098654 TCATCTTTTGAAACGGAGGCAAAA 59.901 37.500 0.00 0.00 38.68 2.44
3038 5442 4.664150 TTTTGAAACGGAGGCAAAAGAT 57.336 36.364 0.00 0.00 36.80 2.40
3039 5443 4.664150 TTTGAAACGGAGGCAAAAGATT 57.336 36.364 0.00 0.00 0.00 2.40
3040 5444 3.641437 TGAAACGGAGGCAAAAGATTG 57.359 42.857 0.00 0.00 39.65 2.67
3041 5445 3.218453 TGAAACGGAGGCAAAAGATTGA 58.782 40.909 0.00 0.00 38.94 2.57
3042 5446 3.004315 TGAAACGGAGGCAAAAGATTGAC 59.996 43.478 0.00 0.00 45.54 3.18
3043 5447 1.534729 ACGGAGGCAAAAGATTGACC 58.465 50.000 0.00 0.00 46.44 4.02
3044 5448 1.073923 ACGGAGGCAAAAGATTGACCT 59.926 47.619 4.84 4.84 46.44 3.85
3045 5449 2.162681 CGGAGGCAAAAGATTGACCTT 58.837 47.619 6.17 0.00 46.44 3.50
3046 5450 3.244770 ACGGAGGCAAAAGATTGACCTTA 60.245 43.478 6.17 0.00 46.44 2.69
3047 5451 3.947834 CGGAGGCAAAAGATTGACCTTAT 59.052 43.478 6.17 0.00 46.44 1.73
3048 5452 4.035675 CGGAGGCAAAAGATTGACCTTATC 59.964 45.833 6.17 0.00 46.44 1.75
3049 5453 4.035675 GGAGGCAAAAGATTGACCTTATCG 59.964 45.833 6.17 0.00 46.44 2.92
3050 5454 4.843728 AGGCAAAAGATTGACCTTATCGA 58.156 39.130 0.00 0.00 46.44 3.59
3051 5455 5.440610 AGGCAAAAGATTGACCTTATCGAT 58.559 37.500 2.16 2.16 46.44 3.59
3052 5456 5.888161 AGGCAAAAGATTGACCTTATCGATT 59.112 36.000 1.71 0.00 46.44 3.34
3053 5457 7.054124 AGGCAAAAGATTGACCTTATCGATTA 58.946 34.615 1.71 0.00 46.44 1.75
3054 5458 7.721399 AGGCAAAAGATTGACCTTATCGATTAT 59.279 33.333 1.71 0.00 46.44 1.28
3055 5459 7.805071 GGCAAAAGATTGACCTTATCGATTATG 59.195 37.037 1.71 0.00 38.75 1.90
3056 5460 8.559536 GCAAAAGATTGACCTTATCGATTATGA 58.440 33.333 1.71 0.00 38.94 2.15
3146 5553 0.944311 GCGCTTCCTCAACACGAAGA 60.944 55.000 0.00 0.00 38.18 2.87
3147 5554 1.497991 CGCTTCCTCAACACGAAGAA 58.502 50.000 1.12 0.00 38.18 2.52
3148 5555 1.864711 CGCTTCCTCAACACGAAGAAA 59.135 47.619 1.12 0.00 38.18 2.52
3376 5792 0.672711 CGCTGCCGATCATCATGGAT 60.673 55.000 0.00 0.00 36.29 3.41
3609 6026 1.001706 GAAAACTCCGGTGCTGGTTTC 60.002 52.381 0.00 7.71 32.43 2.78
3694 6111 5.819379 CAGTGTACTACGGGTATGAACTCTA 59.181 44.000 0.00 0.00 32.56 2.43
3706 6126 6.295349 GGGTATGAACTCTATGGTATCAGGTG 60.295 46.154 0.00 0.00 0.00 4.00
3707 6127 5.815233 ATGAACTCTATGGTATCAGGTGG 57.185 43.478 0.00 0.00 0.00 4.61
3708 6128 4.620723 TGAACTCTATGGTATCAGGTGGT 58.379 43.478 0.00 0.00 0.00 4.16
3709 6129 5.773091 TGAACTCTATGGTATCAGGTGGTA 58.227 41.667 0.00 0.00 0.00 3.25
3710 6130 6.382087 TGAACTCTATGGTATCAGGTGGTAT 58.618 40.000 0.00 0.00 0.00 2.73
3711 6131 6.493802 TGAACTCTATGGTATCAGGTGGTATC 59.506 42.308 0.00 0.00 0.00 2.24
3712 6132 6.220881 ACTCTATGGTATCAGGTGGTATCT 57.779 41.667 0.00 0.00 0.00 1.98
3713 6133 6.013379 ACTCTATGGTATCAGGTGGTATCTG 58.987 44.000 0.00 0.00 0.00 2.90
3714 6134 5.965486 TCTATGGTATCAGGTGGTATCTGT 58.035 41.667 0.00 0.00 34.15 3.41
3715 6135 4.963318 ATGGTATCAGGTGGTATCTGTG 57.037 45.455 0.00 0.00 34.15 3.66
3819 6249 6.538189 AGTTGGAGTTTGTTTGTTTGTTTG 57.462 33.333 0.00 0.00 0.00 2.93
3821 6251 6.540551 AGTTGGAGTTTGTTTGTTTGTTTGTT 59.459 30.769 0.00 0.00 0.00 2.83
3822 6252 6.927294 TGGAGTTTGTTTGTTTGTTTGTTT 57.073 29.167 0.00 0.00 0.00 2.83
3823 6253 7.321745 TGGAGTTTGTTTGTTTGTTTGTTTT 57.678 28.000 0.00 0.00 0.00 2.43
3824 6254 8.433421 TGGAGTTTGTTTGTTTGTTTGTTTTA 57.567 26.923 0.00 0.00 0.00 1.52
3860 6290 8.942338 AAGACATAAAATCTATTGTACTCGCA 57.058 30.769 0.00 0.00 0.00 5.10
4036 6468 3.147826 CCTTGCAGGGGGAAAAACT 57.852 52.632 7.05 0.00 0.00 2.66
4060 6492 1.640069 CACGGCTGCGATCTTCATG 59.360 57.895 0.00 0.00 0.00 3.07
4103 6535 6.710744 TGAATTCAAACTCCAACCTAGACTTC 59.289 38.462 5.45 0.00 0.00 3.01
4104 6536 4.618920 TCAAACTCCAACCTAGACTTCC 57.381 45.455 0.00 0.00 0.00 3.46
4106 6538 2.715763 ACTCCAACCTAGACTTCCCA 57.284 50.000 0.00 0.00 0.00 4.37
4107 6539 2.541466 ACTCCAACCTAGACTTCCCAG 58.459 52.381 0.00 0.00 0.00 4.45
4108 6540 2.158143 ACTCCAACCTAGACTTCCCAGT 60.158 50.000 0.00 0.00 35.17 4.00
4109 6541 2.234908 CTCCAACCTAGACTTCCCAGTG 59.765 54.545 0.00 0.00 31.22 3.66
4110 6542 2.158219 TCCAACCTAGACTTCCCAGTGA 60.158 50.000 0.00 0.00 31.22 3.41
4111 6543 2.840651 CCAACCTAGACTTCCCAGTGAT 59.159 50.000 0.00 0.00 31.22 3.06
4112 6544 3.264450 CCAACCTAGACTTCCCAGTGATT 59.736 47.826 0.00 0.00 31.22 2.57
4113 6545 4.508662 CAACCTAGACTTCCCAGTGATTC 58.491 47.826 0.00 0.00 31.22 2.52
4114 6546 2.761208 ACCTAGACTTCCCAGTGATTCG 59.239 50.000 0.00 0.00 31.22 3.34
4115 6547 2.101582 CCTAGACTTCCCAGTGATTCGG 59.898 54.545 0.00 0.00 31.22 4.30
4116 6548 1.645710 AGACTTCCCAGTGATTCGGT 58.354 50.000 0.00 0.00 31.22 4.69
4117 6549 1.550976 AGACTTCCCAGTGATTCGGTC 59.449 52.381 0.00 0.00 31.22 4.79
4118 6550 1.550976 GACTTCCCAGTGATTCGGTCT 59.449 52.381 0.00 0.00 31.22 3.85
4119 6551 1.978580 ACTTCCCAGTGATTCGGTCTT 59.021 47.619 0.00 0.00 0.00 3.01
4120 6552 2.028020 ACTTCCCAGTGATTCGGTCTTC 60.028 50.000 0.00 0.00 0.00 2.87
4121 6553 0.902531 TCCCAGTGATTCGGTCTTCC 59.097 55.000 0.00 0.00 0.00 3.46
4122 6554 0.905357 CCCAGTGATTCGGTCTTCCT 59.095 55.000 0.00 0.00 0.00 3.36
4251 6700 9.877137 GTTGAAAATAAATTTCCACAAATCCAC 57.123 29.630 0.00 0.00 45.67 4.02
4392 7538 6.068853 AGGATTGAAGATTTCACCCCAATCTA 60.069 38.462 0.00 0.00 39.61 1.98
4401 7547 7.620888 AGATTTCACCCCAATCTATCAACAAAT 59.379 33.333 0.00 0.00 38.89 2.32
4416 7562 4.648762 TCAACAAATTGAAAGAAGGCTGGA 59.351 37.500 0.00 0.00 41.99 3.86
4441 7587 4.280174 GGATGCTCAACCATGCTTTCATAT 59.720 41.667 0.00 0.00 31.69 1.78
4442 7588 5.474532 GGATGCTCAACCATGCTTTCATATA 59.525 40.000 0.00 0.00 31.69 0.86
4449 7595 8.303780 TCAACCATGCTTTCATATAATGGAAA 57.696 30.769 6.98 2.07 40.23 3.13
4450 7596 8.756927 TCAACCATGCTTTCATATAATGGAAAA 58.243 29.630 6.98 0.00 40.23 2.29
4451 7597 9.550406 CAACCATGCTTTCATATAATGGAAAAT 57.450 29.630 6.98 0.00 40.23 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.594303 TTCGGTGCAGTGGGCTTG 60.594 61.111 0.00 0.00 45.15 4.01
164 2342 0.478507 GAGAGAGAGGGGAGGGAGAG 59.521 65.000 0.00 0.00 0.00 3.20
165 2343 0.996762 GGAGAGAGAGGGGAGGGAGA 60.997 65.000 0.00 0.00 0.00 3.71
167 2345 1.087725 AGGAGAGAGAGGGGAGGGA 59.912 63.158 0.00 0.00 0.00 4.20
168 2346 1.232792 CAGGAGAGAGAGGGGAGGG 59.767 68.421 0.00 0.00 0.00 4.30
191 2386 5.819379 TCTCTCTAATAATGGCAAGCAACAG 59.181 40.000 0.00 0.00 0.00 3.16
229 2424 0.812014 CATCTCAGGCTCAGCTGCTG 60.812 60.000 23.31 23.31 0.00 4.41
230 2425 1.523046 CATCTCAGGCTCAGCTGCT 59.477 57.895 9.47 0.00 0.00 4.24
231 2426 2.181521 GCATCTCAGGCTCAGCTGC 61.182 63.158 9.47 0.00 0.00 5.25
264 2465 1.534203 GGGAGAGGGGAATCAAGCC 59.466 63.158 0.00 0.00 0.00 4.35
266 2467 1.700042 CGGGGGAGAGGGGAATCAAG 61.700 65.000 0.00 0.00 0.00 3.02
334 2536 3.775654 GGAGGCGAGGTGGGAGTG 61.776 72.222 0.00 0.00 0.00 3.51
348 2551 1.338389 ACACGTATGGAAAACCGGGAG 60.338 52.381 6.32 0.00 0.00 4.30
349 2552 0.686224 ACACGTATGGAAAACCGGGA 59.314 50.000 6.32 0.00 0.00 5.14
350 2553 2.001872 GTACACGTATGGAAAACCGGG 58.998 52.381 6.32 0.00 0.00 5.73
407 2620 3.256631 CAGAGATTTTCCACCCAACAAGG 59.743 47.826 0.00 0.00 37.03 3.61
408 2621 3.256631 CCAGAGATTTTCCACCCAACAAG 59.743 47.826 0.00 0.00 0.00 3.16
409 2622 3.230134 CCAGAGATTTTCCACCCAACAA 58.770 45.455 0.00 0.00 0.00 2.83
410 2623 2.875296 CCAGAGATTTTCCACCCAACA 58.125 47.619 0.00 0.00 0.00 3.33
411 2624 1.546029 GCCAGAGATTTTCCACCCAAC 59.454 52.381 0.00 0.00 0.00 3.77
412 2625 1.549950 GGCCAGAGATTTTCCACCCAA 60.550 52.381 0.00 0.00 0.00 4.12
413 2626 0.039618 GGCCAGAGATTTTCCACCCA 59.960 55.000 0.00 0.00 0.00 4.51
414 2627 0.332972 AGGCCAGAGATTTTCCACCC 59.667 55.000 5.01 0.00 0.00 4.61
415 2628 2.095461 GAAGGCCAGAGATTTTCCACC 58.905 52.381 5.01 0.00 0.00 4.61
416 2629 2.751806 CAGAAGGCCAGAGATTTTCCAC 59.248 50.000 5.01 0.00 0.00 4.02
417 2630 2.644299 TCAGAAGGCCAGAGATTTTCCA 59.356 45.455 5.01 0.00 0.00 3.53
450 2663 1.067283 TGGAAAGAAGAGAGCAGAGCG 60.067 52.381 0.00 0.00 0.00 5.03
509 2722 5.440610 AGAAGAAGAGGAAAACTGAAGCAA 58.559 37.500 0.00 0.00 0.00 3.91
511 2724 6.384258 AAAGAAGAAGAGGAAAACTGAAGC 57.616 37.500 0.00 0.00 0.00 3.86
535 2783 3.499918 CCAGTTTTGTTTGTGTTGGCAAA 59.500 39.130 0.00 0.00 36.17 3.68
537 2785 2.037772 ACCAGTTTTGTTTGTGTTGGCA 59.962 40.909 0.00 0.00 0.00 4.92
549 2797 2.821969 CAGGGGAGATGAACCAGTTTTG 59.178 50.000 0.00 0.00 0.00 2.44
550 2798 2.225117 CCAGGGGAGATGAACCAGTTTT 60.225 50.000 0.00 0.00 0.00 2.43
551 2799 1.355720 CCAGGGGAGATGAACCAGTTT 59.644 52.381 0.00 0.00 0.00 2.66
552 2800 0.995024 CCAGGGGAGATGAACCAGTT 59.005 55.000 0.00 0.00 0.00 3.16
555 2803 1.229951 AGCCAGGGGAGATGAACCA 60.230 57.895 0.00 0.00 0.00 3.67
556 2804 0.985490 AGAGCCAGGGGAGATGAACC 60.985 60.000 0.00 0.00 0.00 3.62
561 2809 1.765657 GCAGAGAGCCAGGGGAGAT 60.766 63.158 0.00 0.00 37.23 2.75
562 2810 2.364842 GCAGAGAGCCAGGGGAGA 60.365 66.667 0.00 0.00 37.23 3.71
580 2834 1.002087 GAAGAGCCAGAAGAAACCGGA 59.998 52.381 9.46 0.00 0.00 5.14
590 2844 0.984230 ATGAAACCCGAAGAGCCAGA 59.016 50.000 0.00 0.00 0.00 3.86
633 2890 0.307760 AACGCGCAAGAAACCAAGAG 59.692 50.000 5.73 0.00 43.02 2.85
663 2920 3.844640 TGCCATGAGCTAGTGGATAGTA 58.155 45.455 18.49 0.00 44.23 1.82
664 2921 2.682594 TGCCATGAGCTAGTGGATAGT 58.317 47.619 18.49 0.00 44.23 2.12
665 2922 3.597255 CATGCCATGAGCTAGTGGATAG 58.403 50.000 18.49 5.17 44.23 2.08
748 3005 2.356667 GAAGCAAGTGGGGAGGGG 59.643 66.667 0.00 0.00 0.00 4.79
779 3036 7.605410 TCGCGGGGAATAGAATAAAATTATC 57.395 36.000 6.13 0.00 0.00 1.75
830 3087 2.290367 CAGAGAGATCAGTGTAGGAGCG 59.710 54.545 0.00 0.00 0.00 5.03
881 3138 5.615289 CTTAGCTATAAGCATCCAACCACT 58.385 41.667 0.00 0.00 45.56 4.00
897 3154 2.430694 TGCAGGATCTTTCGCTTAGCTA 59.569 45.455 1.76 0.00 0.00 3.32
898 3155 1.208052 TGCAGGATCTTTCGCTTAGCT 59.792 47.619 1.76 0.00 0.00 3.32
951 3208 2.113243 AAACGGGAGTGTCAGAGGCC 62.113 60.000 0.00 0.00 46.69 5.19
990 3247 0.975135 AGCTCATCATCGCTGCCTAT 59.025 50.000 0.00 0.00 34.69 2.57
1219 3482 3.403558 GACCTCAGGAGCCCCACC 61.404 72.222 0.00 0.00 33.88 4.61
1221 3484 3.615811 AGGACCTCAGGAGCCCCA 61.616 66.667 0.00 0.00 33.88 4.96
1285 3574 2.717639 AGCCATACCGAATTCTTGCT 57.282 45.000 3.52 0.00 0.00 3.91
1295 3584 5.639506 CAGATCCAACTAATAAGCCATACCG 59.360 44.000 0.00 0.00 0.00 4.02
1298 3587 5.997746 GCACAGATCCAACTAATAAGCCATA 59.002 40.000 0.00 0.00 0.00 2.74
1306 3595 3.623703 TGCATGCACAGATCCAACTAAT 58.376 40.909 18.46 0.00 0.00 1.73
1308 3597 2.785540 TGCATGCACAGATCCAACTA 57.214 45.000 18.46 0.00 0.00 2.24
1309 3598 1.816835 CTTGCATGCACAGATCCAACT 59.183 47.619 22.58 0.00 0.00 3.16
1327 3616 2.779755 TGTGTTCACCGGCATATCTT 57.220 45.000 0.00 0.00 0.00 2.40
1329 3618 1.670811 CCTTGTGTTCACCGGCATATC 59.329 52.381 0.00 0.00 0.00 1.63
1330 3619 1.681780 CCCTTGTGTTCACCGGCATAT 60.682 52.381 0.00 0.00 0.00 1.78
1331 3620 0.322098 CCCTTGTGTTCACCGGCATA 60.322 55.000 0.00 0.00 0.00 3.14
1358 3647 6.995686 TGCCAAGATTTAAGAGTTAAGTGTCA 59.004 34.615 0.00 0.00 0.00 3.58
1359 3648 7.387948 TCTGCCAAGATTTAAGAGTTAAGTGTC 59.612 37.037 0.00 0.00 0.00 3.67
1360 3649 7.173390 GTCTGCCAAGATTTAAGAGTTAAGTGT 59.827 37.037 0.00 0.00 34.13 3.55
1361 3650 7.361286 GGTCTGCCAAGATTTAAGAGTTAAGTG 60.361 40.741 0.00 0.00 34.13 3.16
1362 3651 6.655425 GGTCTGCCAAGATTTAAGAGTTAAGT 59.345 38.462 0.00 0.00 34.13 2.24
1364 3653 5.944007 GGGTCTGCCAAGATTTAAGAGTTAA 59.056 40.000 0.00 0.00 34.13 2.01
1368 3695 4.227864 AGGGTCTGCCAAGATTTAAGAG 57.772 45.455 0.00 0.00 34.13 2.85
1425 3754 6.099845 TGAGGAGGAGAAAAGAGTTAAGTGTT 59.900 38.462 0.00 0.00 0.00 3.32
1432 3761 6.406400 CGTCATATGAGGAGGAGAAAAGAGTT 60.406 42.308 18.51 0.00 32.08 3.01
1463 3792 7.176490 TCAAACCTATTTTCTTCCGGGAATTA 58.824 34.615 10.44 0.00 0.00 1.40
1522 3862 6.430308 GTCTTGTTCATCAGCATCCATCATAT 59.570 38.462 0.00 0.00 0.00 1.78
1531 3871 4.392047 TGACAAGTCTTGTTCATCAGCAT 58.608 39.130 19.09 0.00 45.52 3.79
1605 3949 3.591977 AGGTAACCAGTGCCCTTCTAATT 59.408 43.478 0.00 0.00 37.17 1.40
1609 3953 2.337359 TAGGTAACCAGTGCCCTTCT 57.663 50.000 0.00 0.00 37.17 2.85
1619 3963 4.165372 CCTAATCTTGGGCTTAGGTAACCA 59.835 45.833 2.21 0.00 39.34 3.67
1621 3965 5.625568 TCCTAATCTTGGGCTTAGGTAAC 57.374 43.478 8.76 0.00 42.99 2.50
1751 4096 3.969287 AGCTCAGCTGTGAACTAATGA 57.031 42.857 19.61 0.00 37.57 2.57
1798 4143 8.248904 ACATAAAAATAGGGCTAATGATTGCA 57.751 30.769 0.00 0.00 0.00 4.08
1799 4144 9.626045 GTACATAAAAATAGGGCTAATGATTGC 57.374 33.333 0.00 0.00 0.00 3.56
1861 4210 2.432456 TAACTGAGCACAGCCGCG 60.432 61.111 11.37 0.00 46.95 6.46
1932 4281 8.416329 GGGCACTTTTATTGACTCATAAATCAT 58.584 33.333 0.00 0.00 0.00 2.45
1933 4282 7.615365 AGGGCACTTTTATTGACTCATAAATCA 59.385 33.333 0.00 0.00 0.00 2.57
1934 4283 8.000780 AGGGCACTTTTATTGACTCATAAATC 57.999 34.615 0.00 0.00 0.00 2.17
1935 4284 7.836183 AGAGGGCACTTTTATTGACTCATAAAT 59.164 33.333 0.00 0.00 0.00 1.40
1936 4285 7.175104 AGAGGGCACTTTTATTGACTCATAAA 58.825 34.615 0.00 0.00 0.00 1.40
1992 4342 8.296713 GCCTTATCACATCACTGTAAAAGAAAA 58.703 33.333 0.00 0.00 33.14 2.29
1993 4343 7.446931 TGCCTTATCACATCACTGTAAAAGAAA 59.553 33.333 0.00 0.00 33.14 2.52
2063 4413 2.403252 ATGGTTAGACGAGGCCAAAG 57.597 50.000 5.01 0.00 34.39 2.77
2091 4441 0.179108 CAAGAGCTACCGTGTAGCCC 60.179 60.000 23.78 16.72 41.25 5.19
2092 4442 0.815734 TCAAGAGCTACCGTGTAGCC 59.184 55.000 23.78 17.65 41.25 3.93
2148 4498 3.192001 TGGACAGACGTGTATGTTACTCC 59.808 47.826 1.40 0.00 36.88 3.85
2289 4639 6.226787 TCAAAATCACAACCACAAAAGTGTT 58.773 32.000 0.00 0.00 35.07 3.32
2305 4655 5.532032 TGAGCATCACAGTTTCTCAAAATCA 59.468 36.000 0.00 0.00 42.56 2.57
2307 4657 5.048224 CCTGAGCATCACAGTTTCTCAAAAT 60.048 40.000 0.00 0.00 42.56 1.82
2344 4694 1.065410 TCTCCCCTTTGTTGCCTCCA 61.065 55.000 0.00 0.00 0.00 3.86
2359 4709 1.973812 GTGCACCAAGGCCTTCTCC 60.974 63.158 17.29 5.00 0.00 3.71
2410 4760 0.109873 CGAAGCGACCGTTGTACTCT 60.110 55.000 0.00 0.00 0.00 3.24
2413 4763 0.386478 ACTCGAAGCGACCGTTGTAC 60.386 55.000 0.00 0.00 0.00 2.90
2420 4770 2.677979 GGCCAAACTCGAAGCGACC 61.678 63.158 0.00 0.00 0.00 4.79
2431 4781 2.675423 GAAGGACCCGGGCCAAAC 60.675 66.667 28.68 17.89 0.00 2.93
2499 4851 2.297701 TCAGCTGAAAAGTTGGGACAC 58.702 47.619 15.67 0.00 39.29 3.67
2504 4856 6.667007 ACAAAATTTCAGCTGAAAAGTTGG 57.333 33.333 38.53 33.13 45.81 3.77
2512 4864 5.850557 TCCAGAAACAAAATTTCAGCTGA 57.149 34.783 13.74 13.74 0.00 4.26
2543 4895 4.515191 TGTGGTAAGTTAGCAGCTGAAAAG 59.485 41.667 20.43 0.00 36.78 2.27
2551 4903 5.238432 TGAAACACATGTGGTAAGTTAGCAG 59.762 40.000 28.64 6.65 36.78 4.24
2561 4913 4.090761 AGACATCTGAAACACATGTGGT 57.909 40.909 28.64 21.46 34.19 4.16
2618 4970 5.163893 CGATTTCATTGCGTAAGTGGTAAGT 60.164 40.000 0.00 0.00 41.68 2.24
2633 4985 4.142687 CCAAAGCTTACCGTCGATTTCATT 60.143 41.667 0.00 0.00 0.00 2.57
2697 5049 6.722129 AGGAAGGCGTTAGAGAATAGTATCAT 59.278 38.462 0.00 0.00 0.00 2.45
2703 5055 6.819146 AGAAAAAGGAAGGCGTTAGAGAATAG 59.181 38.462 0.00 0.00 0.00 1.73
2751 5107 1.668047 GCATTCAGTGGCAAGAGCAAC 60.668 52.381 0.00 0.00 45.47 4.17
2911 5270 6.486657 TGTTTTTCCCAGTCTCTGTAAATGAG 59.513 38.462 0.00 0.00 0.00 2.90
2925 5284 3.704061 TGGAAGAGGTTTGTTTTTCCCAG 59.296 43.478 0.00 0.00 37.17 4.45
2930 5289 5.744171 AGCAAATGGAAGAGGTTTGTTTTT 58.256 33.333 0.00 0.00 35.75 1.94
2966 5325 5.094429 TGAATGAAATGTTGAGTGACGTG 57.906 39.130 0.00 0.00 0.00 4.49
3014 5418 4.664150 TTTTGCCTCCGTTTCAAAAGAT 57.336 36.364 0.00 0.00 35.53 2.40
3017 5421 4.664150 ATCTTTTGCCTCCGTTTCAAAA 57.336 36.364 0.00 0.00 37.36 2.44
3018 5422 4.098654 TCAATCTTTTGCCTCCGTTTCAAA 59.901 37.500 0.00 0.00 32.61 2.69
3019 5423 3.634448 TCAATCTTTTGCCTCCGTTTCAA 59.366 39.130 0.00 0.00 32.61 2.69
3020 5424 3.004315 GTCAATCTTTTGCCTCCGTTTCA 59.996 43.478 0.00 0.00 32.61 2.69
3021 5425 3.565516 GTCAATCTTTTGCCTCCGTTTC 58.434 45.455 0.00 0.00 32.61 2.78
3022 5426 2.296190 GGTCAATCTTTTGCCTCCGTTT 59.704 45.455 0.00 0.00 32.61 3.60
3023 5427 1.886542 GGTCAATCTTTTGCCTCCGTT 59.113 47.619 0.00 0.00 32.61 4.44
3024 5428 1.073923 AGGTCAATCTTTTGCCTCCGT 59.926 47.619 0.00 0.00 35.68 4.69
3025 5429 1.826385 AGGTCAATCTTTTGCCTCCG 58.174 50.000 0.00 0.00 35.68 4.63
3026 5430 4.035675 CGATAAGGTCAATCTTTTGCCTCC 59.964 45.833 0.00 0.00 37.97 4.30
3027 5431 4.876107 TCGATAAGGTCAATCTTTTGCCTC 59.124 41.667 0.00 0.00 37.97 4.70
3028 5432 4.843728 TCGATAAGGTCAATCTTTTGCCT 58.156 39.130 0.00 0.00 39.51 4.75
3029 5433 5.757850 ATCGATAAGGTCAATCTTTTGCC 57.242 39.130 0.00 0.00 32.61 4.52
3030 5434 8.559536 TCATAATCGATAAGGTCAATCTTTTGC 58.440 33.333 0.00 0.00 32.61 3.68
3035 5439 9.597170 CATGATCATAATCGATAAGGTCAATCT 57.403 33.333 8.15 0.00 34.39 2.40
3036 5440 8.824781 CCATGATCATAATCGATAAGGTCAATC 58.175 37.037 8.15 4.28 34.39 2.67
3037 5441 7.281774 GCCATGATCATAATCGATAAGGTCAAT 59.718 37.037 8.15 0.53 34.39 2.57
3038 5442 6.595326 GCCATGATCATAATCGATAAGGTCAA 59.405 38.462 8.15 0.00 34.39 3.18
3039 5443 6.108687 GCCATGATCATAATCGATAAGGTCA 58.891 40.000 8.15 4.19 34.39 4.02
3040 5444 5.233050 CGCCATGATCATAATCGATAAGGTC 59.767 44.000 8.15 0.00 34.39 3.85
3041 5445 5.111989 CGCCATGATCATAATCGATAAGGT 58.888 41.667 8.15 0.00 34.39 3.50
3042 5446 4.025396 GCGCCATGATCATAATCGATAAGG 60.025 45.833 20.49 11.40 34.39 2.69
3043 5447 4.567959 TGCGCCATGATCATAATCGATAAG 59.432 41.667 20.49 3.14 34.39 1.73
3044 5448 4.502962 TGCGCCATGATCATAATCGATAA 58.497 39.130 20.49 7.96 34.39 1.75
3045 5449 4.114794 CTGCGCCATGATCATAATCGATA 58.885 43.478 20.49 11.29 34.39 2.92
3046 5450 2.934553 CTGCGCCATGATCATAATCGAT 59.065 45.455 20.49 0.00 34.39 3.59
3047 5451 2.340337 CTGCGCCATGATCATAATCGA 58.660 47.619 20.49 0.00 34.39 3.59
3048 5452 1.201998 GCTGCGCCATGATCATAATCG 60.202 52.381 8.15 12.55 34.39 3.34
3049 5453 2.539346 GCTGCGCCATGATCATAATC 57.461 50.000 8.15 0.00 0.00 1.75
3146 5553 0.850883 TCCTTGCCATCCCCCTCTTT 60.851 55.000 0.00 0.00 0.00 2.52
3147 5554 1.230281 TCCTTGCCATCCCCCTCTT 60.230 57.895 0.00 0.00 0.00 2.85
3148 5555 2.003548 GTCCTTGCCATCCCCCTCT 61.004 63.158 0.00 0.00 0.00 3.69
3391 5807 2.045926 CACTTGAAGGGGGCGGAG 60.046 66.667 0.00 0.00 0.00 4.63
3609 6026 2.488528 CCCATCATCACAAGATCCCTGG 60.489 54.545 0.00 0.00 30.20 4.45
3694 6111 4.298626 ACACAGATACCACCTGATACCAT 58.701 43.478 0.00 0.00 35.69 3.55
3706 6126 9.817809 TTTGATACTTATTCTGACACAGATACC 57.182 33.333 2.30 0.00 40.39 2.73
3709 6129 9.950496 AAGTTTGATACTTATTCTGACACAGAT 57.050 29.630 2.30 0.00 45.22 2.90
3710 6130 9.424319 GAAGTTTGATACTTATTCTGACACAGA 57.576 33.333 0.00 0.00 47.00 3.41
3711 6131 9.208022 TGAAGTTTGATACTTATTCTGACACAG 57.792 33.333 0.00 0.00 47.00 3.66
3712 6132 9.208022 CTGAAGTTTGATACTTATTCTGACACA 57.792 33.333 0.00 0.00 47.00 3.72
3713 6133 8.660373 CCTGAAGTTTGATACTTATTCTGACAC 58.340 37.037 0.00 0.00 47.00 3.67
3714 6134 7.824289 CCCTGAAGTTTGATACTTATTCTGACA 59.176 37.037 0.00 0.00 47.00 3.58
3715 6135 7.824779 ACCCTGAAGTTTGATACTTATTCTGAC 59.175 37.037 0.00 0.00 47.00 3.51
3860 6290 9.956720 GCAGACAAGCTTACAAATCATATATTT 57.043 29.630 0.00 0.00 0.00 1.40
3916 6346 9.933723 AGCTGTAAAAAGATTGCAAGAATATTT 57.066 25.926 4.94 5.40 0.00 1.40
4103 6535 0.905357 AGGAAGACCGAATCACTGGG 59.095 55.000 0.00 0.00 41.83 4.45
4104 6536 2.761208 ACTAGGAAGACCGAATCACTGG 59.239 50.000 0.00 0.00 41.83 4.00
4106 6538 3.698289 TCACTAGGAAGACCGAATCACT 58.302 45.455 0.00 0.00 41.83 3.41
4107 6539 4.657436 ATCACTAGGAAGACCGAATCAC 57.343 45.455 0.00 0.00 41.83 3.06
4108 6540 4.709886 TGAATCACTAGGAAGACCGAATCA 59.290 41.667 0.00 0.00 41.83 2.57
4109 6541 5.163499 ACTGAATCACTAGGAAGACCGAATC 60.163 44.000 0.00 0.00 41.83 2.52
4110 6542 4.712337 ACTGAATCACTAGGAAGACCGAAT 59.288 41.667 0.00 0.00 41.83 3.34
4111 6543 4.087182 ACTGAATCACTAGGAAGACCGAA 58.913 43.478 0.00 0.00 41.83 4.30
4112 6544 3.698289 ACTGAATCACTAGGAAGACCGA 58.302 45.455 0.00 0.00 41.83 4.69
4113 6545 5.524284 CATACTGAATCACTAGGAAGACCG 58.476 45.833 0.00 0.00 41.83 4.79
4114 6546 5.163405 TGCATACTGAATCACTAGGAAGACC 60.163 44.000 0.00 0.00 0.00 3.85
4115 6547 5.907207 TGCATACTGAATCACTAGGAAGAC 58.093 41.667 0.00 0.00 0.00 3.01
4116 6548 5.893824 TCTGCATACTGAATCACTAGGAAGA 59.106 40.000 0.00 0.00 0.00 2.87
4117 6549 6.154203 TCTGCATACTGAATCACTAGGAAG 57.846 41.667 0.00 0.00 0.00 3.46
4118 6550 6.324770 TCATCTGCATACTGAATCACTAGGAA 59.675 38.462 0.00 0.00 0.00 3.36
4119 6551 5.835280 TCATCTGCATACTGAATCACTAGGA 59.165 40.000 0.00 0.00 0.00 2.94
4120 6552 6.094193 TCATCTGCATACTGAATCACTAGG 57.906 41.667 0.00 0.00 0.00 3.02
4121 6553 8.302438 TGTATCATCTGCATACTGAATCACTAG 58.698 37.037 0.00 0.00 0.00 2.57
4122 6554 8.181904 TGTATCATCTGCATACTGAATCACTA 57.818 34.615 0.00 0.00 0.00 2.74
4220 6669 5.994668 TGTGGAAATTTATTTTCAACCCTGC 59.005 36.000 0.00 0.00 44.56 4.85
4392 7538 5.305128 TCCAGCCTTCTTTCAATTTGTTGAT 59.695 36.000 0.00 0.00 0.00 2.57
4401 7547 3.424703 CATCCTTCCAGCCTTCTTTCAA 58.575 45.455 0.00 0.00 0.00 2.69
4412 7558 2.022195 CATGGTTGAGCATCCTTCCAG 58.978 52.381 0.00 0.00 33.26 3.86
4416 7562 2.226962 AAGCATGGTTGAGCATCCTT 57.773 45.000 9.83 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.