Multiple sequence alignment - TraesCS6D01G306700

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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 TraesCS6D01G306700 chr6D 100.000 5614 0 0 1 5614 417759461 417753848 0.000000e+00 10368.0
1 TraesCS6D01G306700 chr6B 94.377 2561 115 11 2771 5307 626452192 626454747 0.000000e+00 3904.0
2 TraesCS6D01G306700 chr6B 88.210 2358 160 57 342 2625 626449823 626452136 0.000000e+00 2706.0
3 TraesCS6D01G306700 chr6B 88.509 322 28 6 986 1304 529894809 529895124 1.140000e-101 381.0
4 TraesCS6D01G306700 chr6B 92.593 108 8 0 5441 5548 626454836 626454943 7.530000e-34 156.0
5 TraesCS6D01G306700 chr6A 95.852 2290 75 8 2772 5052 560208609 560206331 0.000000e+00 3685.0
6 TraesCS6D01G306700 chr6A 92.546 1999 85 33 680 2625 560210812 560208825 0.000000e+00 2808.0
7 TraesCS6D01G306700 chr6A 84.517 704 84 8 6 687 560211548 560210848 0.000000e+00 673.0
8 TraesCS6D01G306700 chr6A 89.892 277 22 5 5114 5386 560206330 560206056 8.950000e-93 351.0
9 TraesCS6D01G306700 chr6A 96.552 174 6 0 5441 5614 560205415 560205242 7.120000e-74 289.0
10 TraesCS6D01G306700 chr6A 92.568 148 10 1 2628 2774 560208789 560208642 1.580000e-50 211.0
11 TraesCS6D01G306700 chr3D 87.313 402 39 7 986 1382 479953639 479954033 3.080000e-122 449.0
12 TraesCS6D01G306700 chr7B 84.653 404 45 9 989 1382 263733013 263733409 2.450000e-103 387.0
13 TraesCS6D01G306700 chr2B 88.820 322 27 6 986 1304 795472777 795473092 2.450000e-103 387.0
14 TraesCS6D01G306700 chr4A 84.289 401 46 9 992 1382 712001596 712001989 5.310000e-100 375.0
15 TraesCS6D01G306700 chr1A 87.692 325 31 6 986 1307 563782489 563782171 2.470000e-98 370.0
16 TraesCS6D01G306700 chr3B 87.812 320 29 7 986 1302 732832867 732833179 3.200000e-97 366.0
17 TraesCS6D01G306700 chr7D 81.197 234 20 10 3620 3842 2234966 2234746 3.480000e-37 167.0
18 TraesCS6D01G306700 chr7D 81.364 220 18 14 3620 3829 2235506 2235300 2.090000e-34 158.0
19 TraesCS6D01G306700 chr7A 78.481 237 26 13 3620 3842 1841888 1841663 1.270000e-26 132.0
20 TraesCS6D01G306700 chr4B 82.418 91 8 3 99 185 498875493 498875579 7.800000e-09 73.1


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 TraesCS6D01G306700 chr6D 417753848 417759461 5613 True 10368.000000 10368 100.000000 1 5614 1 chr6D.!!$R1 5613
1 TraesCS6D01G306700 chr6B 626449823 626454943 5120 False 2255.333333 3904 91.726667 342 5548 3 chr6B.!!$F2 5206
2 TraesCS6D01G306700 chr6A 560205242 560211548 6306 True 1336.166667 3685 91.987833 6 5614 6 chr6A.!!$R1 5608

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
269 270 0.400213 TTTGAGTTGCGGGTGGAGAT 59.600 50.0 0.00 0.0 0.00 2.75 F
316 317 0.600255 CCGAACCACTGTCCACAGAC 60.600 60.0 13.75 0.0 46.59 3.51 F
954 1053 0.693049 GAGAAAACAGGGGAGGCAGA 59.307 55.0 0.00 0.0 0.00 4.26 F
1348 1460 0.099968 CTCGTCCGGTTCTGCGATTA 59.900 55.0 0.00 0.0 32.79 1.75 F
2259 2412 0.244721 CATCTGGTGCAGTCTGTCGA 59.755 55.0 0.93 0.0 32.61 4.20 F
2502 2656 0.387239 GCTTAGTTTGCGGTTGCTGG 60.387 55.0 0.00 0.0 43.34 4.85 F
3093 3327 0.449388 GCGGTTCTGGAAGCAGATTG 59.551 55.0 12.05 0.0 38.62 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1263 1373 0.239347 CAGCAGAAGCCAAAGAACCG 59.761 55.000 0.00 0.0 43.56 4.44 R
1334 1445 0.307760 GGCAATAATCGCAGAACCGG 59.692 55.000 0.00 0.0 43.58 5.28 R
2246 2399 0.861837 CCAAGTTCGACAGACTGCAC 59.138 55.000 1.25 0.0 0.00 4.57 R
2458 2612 1.064758 ACCACTGAAAGCACCAAGTCA 60.065 47.619 0.00 0.0 37.60 3.41 R
4223 4462 0.888736 TGTTGGGTCCAGTCATTGCG 60.889 55.000 0.00 0.0 0.00 4.85 R
4460 4699 0.108233 TGTACCGGCGAACCCAATAC 60.108 55.000 9.30 0.0 0.00 1.89 R
5074 5392 0.039180 TGGCGAGAGAACTGTCCCTA 59.961 55.000 0.00 0.0 0.00 3.53 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
45 46 1.015109 GACCACTCTAGCGATGACGA 58.985 55.000 0.00 0.00 42.66 4.20
48 49 0.651031 CACTCTAGCGATGACGACGA 59.349 55.000 0.00 0.00 42.66 4.20
51 52 0.803380 TCTAGCGATGACGACGACGA 60.803 55.000 15.32 0.00 42.66 4.20
52 53 0.651042 CTAGCGATGACGACGACGAC 60.651 60.000 15.32 8.68 42.66 4.34
57 58 0.914551 GATGACGACGACGACAATGG 59.085 55.000 15.32 0.00 45.19 3.16
64 65 2.100631 CGACGACAATGGCAGGGAC 61.101 63.158 0.00 0.00 0.00 4.46
118 119 2.034879 GTACGAGGTCACCGTCCGA 61.035 63.158 12.24 0.00 40.95 4.55
130 131 3.507233 TCACCGTCCGATACAAGTTAGTT 59.493 43.478 0.00 0.00 0.00 2.24
133 134 5.287035 CACCGTCCGATACAAGTTAGTTTAC 59.713 44.000 0.00 0.00 0.00 2.01
137 138 6.740905 CGTCCGATACAAGTTAGTTTACGTTA 59.259 38.462 0.00 0.00 0.00 3.18
138 139 7.270365 CGTCCGATACAAGTTAGTTTACGTTAA 59.730 37.037 0.00 0.00 0.00 2.01
157 158 8.364129 ACGTTAATTAGGTTTTAGTTGAACGA 57.636 30.769 0.00 0.00 39.25 3.85
159 160 9.095529 CGTTAATTAGGTTTTAGTTGAACGAAC 57.904 33.333 0.00 0.00 38.48 3.95
162 163 6.900568 TTAGGTTTTAGTTGAACGAACGAA 57.099 33.333 0.14 0.00 39.80 3.85
168 169 8.011106 GGTTTTAGTTGAACGAACGAAATATCA 58.989 33.333 0.14 0.00 38.48 2.15
176 177 7.757526 TGAACGAACGAAATATCATCCAATTT 58.242 30.769 0.14 0.00 0.00 1.82
203 204 3.627395 ATTCTGGCCGAAGTTATGTCA 57.373 42.857 13.92 0.00 34.56 3.58
205 206 1.899814 TCTGGCCGAAGTTATGTCAGT 59.100 47.619 0.00 0.00 0.00 3.41
211 212 4.156008 GGCCGAAGTTATGTCAGTTTGAAT 59.844 41.667 0.00 0.00 0.00 2.57
219 220 8.408043 AGTTATGTCAGTTTGAATGAATTCCA 57.592 30.769 2.27 0.00 35.97 3.53
227 228 8.030692 TCAGTTTGAATGAATTCCATCATGTTC 58.969 33.333 2.27 0.00 39.90 3.18
228 229 7.815549 CAGTTTGAATGAATTCCATCATGTTCA 59.184 33.333 2.27 0.00 39.90 3.18
230 231 6.211587 TGAATGAATTCCATCATGTTCACC 57.788 37.500 2.27 0.00 39.90 4.02
231 232 5.953548 TGAATGAATTCCATCATGTTCACCT 59.046 36.000 2.27 0.00 39.90 4.00
260 261 1.798223 TCCGAATGAGTTTGAGTTGCG 59.202 47.619 0.00 0.00 0.00 4.85
263 264 1.880027 GAATGAGTTTGAGTTGCGGGT 59.120 47.619 0.00 0.00 0.00 5.28
269 270 0.400213 TTTGAGTTGCGGGTGGAGAT 59.600 50.000 0.00 0.00 0.00 2.75
274 275 2.331893 TTGCGGGTGGAGATTTGCG 61.332 57.895 0.00 0.00 0.00 4.85
280 281 1.244019 GGTGGAGATTTGCGGCAAGT 61.244 55.000 15.78 13.28 0.00 3.16
290 291 2.568090 CGGCAAGTGTTGGATGGC 59.432 61.111 0.00 0.00 36.39 4.40
296 297 2.676471 GTGTTGGATGGCCGGCTT 60.676 61.111 28.56 14.87 36.79 4.35
297 298 2.361104 TGTTGGATGGCCGGCTTC 60.361 61.111 28.56 22.43 36.79 3.86
316 317 0.600255 CCGAACCACTGTCCACAGAC 60.600 60.000 13.75 0.00 46.59 3.51
357 379 6.998074 CCATGTTGAAGATGCCCTTATACTTA 59.002 38.462 0.00 0.00 34.68 2.24
365 387 8.548880 AAGATGCCCTTATACTTACACTTAGA 57.451 34.615 0.00 0.00 32.24 2.10
393 415 6.339587 TGTCTTAATTTTCAACATGGTCCC 57.660 37.500 0.00 0.00 0.00 4.46
398 420 7.726291 TCTTAATTTTCAACATGGTCCCAGTAA 59.274 33.333 0.00 0.00 0.00 2.24
406 428 5.313280 ACATGGTCCCAGTAAACACTTTA 57.687 39.130 0.00 0.00 0.00 1.85
433 455 8.404889 TGATGTGTTTTCAAAGTGTAAATGTG 57.595 30.769 0.00 0.00 0.00 3.21
437 459 8.300286 TGTGTTTTCAAAGTGTAAATGTGAAGA 58.700 29.630 0.00 0.00 30.43 2.87
444 466 9.478768 TCAAAGTGTAAATGTGAAGAATACGTA 57.521 29.630 0.00 0.00 0.00 3.57
487 509 1.346068 AGGTCACCTCAGTTCTCAAGC 59.654 52.381 0.00 0.00 0.00 4.01
490 512 2.999355 GTCACCTCAGTTCTCAAGCATC 59.001 50.000 0.00 0.00 0.00 3.91
494 517 3.518705 ACCTCAGTTCTCAAGCATCATCT 59.481 43.478 0.00 0.00 0.00 2.90
600 623 7.549134 TCCAGTGATATAAACCGCATGATATTC 59.451 37.037 0.00 0.00 0.00 1.75
675 700 2.606108 GGGTACCGTACTTGTAAACCG 58.394 52.381 5.65 0.00 40.86 4.44
687 712 5.667466 ACTTGTAAACCGGGAGTATGTATG 58.333 41.667 6.32 0.00 0.00 2.39
688 713 5.188359 ACTTGTAAACCGGGAGTATGTATGT 59.812 40.000 6.32 0.00 0.00 2.29
754 822 6.431278 GGAAGAAAAGAAGGAGAAACGAAAG 58.569 40.000 0.00 0.00 0.00 2.62
789 858 1.202568 CGAAGCAGAACACGCACAG 59.797 57.895 0.00 0.00 0.00 3.66
797 866 0.730265 GAACACGCACAGGTTGTTCA 59.270 50.000 8.46 0.00 38.80 3.18
954 1053 0.693049 GAGAAAACAGGGGAGGCAGA 59.307 55.000 0.00 0.00 0.00 4.26
1164 1274 4.761058 AGAGGAGAGGGCGGCGAA 62.761 66.667 12.98 0.00 0.00 4.70
1268 1379 1.006571 TGAGCGTTCACTCCGGTTC 60.007 57.895 0.00 0.00 35.99 3.62
1348 1460 0.099968 CTCGTCCGGTTCTGCGATTA 59.900 55.000 0.00 0.00 32.79 1.75
1359 1471 2.899976 TCTGCGATTATTGCCTTCGAA 58.100 42.857 1.53 0.00 34.92 3.71
1372 1491 0.324943 CTTCGAACATGGTCCCTGGT 59.675 55.000 4.85 0.00 0.00 4.00
1383 1502 2.896685 TGGTCCCTGGTTTGCTAATTTG 59.103 45.455 0.00 0.00 0.00 2.32
1388 1507 3.578688 CCTGGTTTGCTAATTTGCTGTC 58.421 45.455 12.99 3.50 0.00 3.51
1394 1513 5.050837 GGTTTGCTAATTTGCTGTCTTGTTG 60.051 40.000 12.99 0.00 0.00 3.33
1576 1695 8.985805 ACTACTCTAATTCTTTTGGTAAACGTG 58.014 33.333 0.00 0.00 0.00 4.49
1626 1770 7.562454 TCTAGTTCTTTTCGTGTTCCAATTT 57.438 32.000 0.00 0.00 0.00 1.82
1808 1952 5.959618 ATGTGGTTTTCTAGTGCCTTAAC 57.040 39.130 0.00 0.00 0.00 2.01
2011 2162 4.302559 AGATAGAACACCAAAACCCCTC 57.697 45.455 0.00 0.00 0.00 4.30
2165 2316 6.278363 ACTAAGCACGAAAAGTTTCTCAGTA 58.722 36.000 0.00 0.00 35.07 2.74
2246 2399 6.485830 TTATTTCCCTAGTCAGACATCTGG 57.514 41.667 8.99 0.00 43.91 3.86
2259 2412 0.244721 CATCTGGTGCAGTCTGTCGA 59.755 55.000 0.93 0.00 32.61 4.20
2502 2656 0.387239 GCTTAGTTTGCGGTTGCTGG 60.387 55.000 0.00 0.00 43.34 4.85
2520 2674 1.070134 TGGACTGTACTGCACTGAACC 59.930 52.381 0.00 0.00 0.00 3.62
2523 2677 3.006537 GGACTGTACTGCACTGAACCTAA 59.993 47.826 0.00 0.00 0.00 2.69
2625 2785 7.969536 ACAAAACTATCATAATCTAGCGCAT 57.030 32.000 11.47 0.00 0.00 4.73
2626 2786 8.023050 ACAAAACTATCATAATCTAGCGCATC 57.977 34.615 11.47 0.00 0.00 3.91
2682 2875 3.999663 GCATCCTACTTGGTGCTGATATC 59.000 47.826 0.00 0.00 38.73 1.63
2684 2877 4.944619 TCCTACTTGGTGCTGATATCTG 57.055 45.455 3.98 4.68 37.07 2.90
2734 2928 6.639632 TTCTTTTTGCTAGTTGATTGAGCT 57.360 33.333 0.00 0.00 37.12 4.09
2736 2930 5.182001 TCTTTTTGCTAGTTGATTGAGCTCC 59.818 40.000 12.15 0.00 37.12 4.70
2932 3166 3.006940 GTGTGGTGTGTGTTCTCAGAAA 58.993 45.455 0.00 0.00 0.00 2.52
2959 3193 6.480763 TGGACTAGGCTTTCATTTGTAATCA 58.519 36.000 0.00 0.00 0.00 2.57
2993 3227 9.110502 CAGTAATTAACTCTTATTGGGGAAGAC 57.889 37.037 0.00 0.00 35.76 3.01
3052 3286 7.451255 TGAATAACAAGGACACATCTTTTCCAT 59.549 33.333 0.00 0.00 0.00 3.41
3093 3327 0.449388 GCGGTTCTGGAAGCAGATTG 59.551 55.000 12.05 0.00 38.62 2.67
3141 3375 6.017933 GTGCACTTCATATCTCGTCTTTTTG 58.982 40.000 10.32 0.00 0.00 2.44
3155 3389 4.105486 GTCTTTTTGCTCTTTTCGCAAGT 58.895 39.130 0.00 0.00 46.69 3.16
3190 3424 7.013655 CAGATAGAAATTAACCATGGGTCCTTG 59.986 40.741 18.09 0.00 33.12 3.61
3203 3437 2.558359 GGGTCCTTGACACTGAATTTGG 59.442 50.000 0.00 0.00 32.50 3.28
3281 3515 5.706833 TCAACTTATTCAATGCTCTGCTTCA 59.293 36.000 0.00 0.00 0.00 3.02
3285 3519 6.881065 ACTTATTCAATGCTCTGCTTCAACTA 59.119 34.615 0.00 0.00 0.00 2.24
3459 3696 1.209504 CGGTGATGGTAATCCTGTGGT 59.790 52.381 0.00 0.00 34.23 4.16
3518 3755 2.706339 ACCTGATGTCCAGCAGAATC 57.294 50.000 13.77 0.00 46.99 2.52
3561 3798 4.471904 AGCAGATTATTCTTCACACGGA 57.528 40.909 0.00 0.00 0.00 4.69
3989 4226 1.814394 CAGCTGCTTCAAAGGTATGCA 59.186 47.619 0.00 0.00 0.00 3.96
4051 4290 5.643379 ATCGAAGATAAGCTCATCTCCTC 57.357 43.478 0.00 0.00 45.12 3.71
4175 4414 4.906065 TGCAGCAACAAGGATATCATTC 57.094 40.909 4.83 0.00 0.00 2.67
4191 4430 2.953648 TCATTCGGCATGCTGATGATTT 59.046 40.909 29.15 9.85 32.13 2.17
4199 4438 5.924254 CGGCATGCTGATGATTTTATTGATT 59.076 36.000 22.55 0.00 0.00 2.57
4223 4462 2.639065 TGGTTGATATTCCAGCGTTCC 58.361 47.619 0.00 0.00 0.00 3.62
4304 4543 3.194755 GTGGTTTTGTTGGAAGGTTCTGT 59.805 43.478 0.00 0.00 0.00 3.41
4418 4657 4.595762 TCTATACCGTGGTCTTTATGGC 57.404 45.455 0.00 0.00 0.00 4.40
4438 4677 2.422597 CCCTATTTCTGTGACGCACAA 58.577 47.619 12.53 1.00 44.08 3.33
4487 4726 3.056322 GGGTTCGCCGGTACATATTCTAT 60.056 47.826 1.90 0.00 38.45 1.98
4499 4738 4.384056 ACATATTCTATGCTGTGCTGTCC 58.616 43.478 0.00 0.00 0.00 4.02
4535 4774 1.142965 GGCTGGTTTGTTGCCGTTT 59.857 52.632 0.00 0.00 37.11 3.60
4652 4895 1.542492 AGCATGGGAGCAGAAACTTG 58.458 50.000 0.00 0.00 36.85 3.16
4655 4898 2.089980 CATGGGAGCAGAAACTTGAGG 58.910 52.381 0.00 0.00 0.00 3.86
4680 4923 2.143122 TCGTCAGGCAGAACAACAATC 58.857 47.619 0.00 0.00 0.00 2.67
4681 4924 1.136252 CGTCAGGCAGAACAACAATCG 60.136 52.381 0.00 0.00 0.00 3.34
4727 4970 5.008019 TGTTTTCTGAAGATGAAGTCAGTGC 59.992 40.000 0.97 0.00 41.69 4.40
4776 5030 6.903534 TGAATCTCCCTTCCTACTTAGTCATT 59.096 38.462 0.00 0.00 0.00 2.57
4777 5031 6.739331 ATCTCCCTTCCTACTTAGTCATTG 57.261 41.667 0.00 0.00 0.00 2.82
4891 5146 8.986847 CAATACATCATCATGAGGACTCTTTAC 58.013 37.037 13.05 0.00 31.79 2.01
4917 5174 6.220930 TGTCTATATGTTTTATGGCTCCGAC 58.779 40.000 0.00 0.00 0.00 4.79
4951 5208 0.394352 GCCCTCGGTGAATCCATTGT 60.394 55.000 0.00 0.00 35.57 2.71
4952 5209 1.382522 CCCTCGGTGAATCCATTGTG 58.617 55.000 0.00 0.00 35.57 3.33
5055 5373 4.697592 TTTTTCGGCCCGATTCGA 57.302 50.000 6.69 0.00 35.23 3.71
5056 5374 2.462503 TTTTTCGGCCCGATTCGAG 58.537 52.632 6.69 0.00 35.23 4.04
5057 5375 0.037139 TTTTTCGGCCCGATTCGAGA 60.037 50.000 6.69 0.00 35.23 4.04
5058 5376 0.177141 TTTTCGGCCCGATTCGAGAT 59.823 50.000 6.69 0.00 35.23 2.75
5059 5377 0.177141 TTTCGGCCCGATTCGAGATT 59.823 50.000 6.69 0.00 35.23 2.40
5060 5378 0.529773 TTCGGCCCGATTCGAGATTG 60.530 55.000 6.69 0.00 35.23 2.67
5061 5379 1.956170 CGGCCCGATTCGAGATTGG 60.956 63.158 7.83 0.58 0.00 3.16
5062 5380 1.598130 GGCCCGATTCGAGATTGGG 60.598 63.158 20.42 20.42 44.16 4.12
5063 5381 1.445942 GCCCGATTCGAGATTGGGA 59.554 57.895 25.42 0.00 44.09 4.37
5064 5382 0.601311 GCCCGATTCGAGATTGGGAG 60.601 60.000 25.42 9.70 44.09 4.30
5065 5383 0.601311 CCCGATTCGAGATTGGGAGC 60.601 60.000 20.22 0.00 44.09 4.70
5066 5384 0.390860 CCGATTCGAGATTGGGAGCT 59.609 55.000 7.83 0.00 0.00 4.09
5067 5385 1.495878 CGATTCGAGATTGGGAGCTG 58.504 55.000 0.00 0.00 0.00 4.24
5068 5386 1.202463 CGATTCGAGATTGGGAGCTGT 60.202 52.381 0.00 0.00 0.00 4.40
5069 5387 2.739932 CGATTCGAGATTGGGAGCTGTT 60.740 50.000 0.00 0.00 0.00 3.16
5070 5388 2.859165 TTCGAGATTGGGAGCTGTTT 57.141 45.000 0.00 0.00 0.00 2.83
5071 5389 2.099141 TCGAGATTGGGAGCTGTTTG 57.901 50.000 0.00 0.00 0.00 2.93
5072 5390 1.089920 CGAGATTGGGAGCTGTTTGG 58.910 55.000 0.00 0.00 0.00 3.28
5073 5391 1.611673 CGAGATTGGGAGCTGTTTGGT 60.612 52.381 0.00 0.00 0.00 3.67
5074 5392 2.519013 GAGATTGGGAGCTGTTTGGTT 58.481 47.619 0.00 0.00 0.00 3.67
5075 5393 3.686016 GAGATTGGGAGCTGTTTGGTTA 58.314 45.455 0.00 0.00 0.00 2.85
5076 5394 3.690460 AGATTGGGAGCTGTTTGGTTAG 58.310 45.455 0.00 0.00 0.00 2.34
5077 5395 2.286365 TTGGGAGCTGTTTGGTTAGG 57.714 50.000 0.00 0.00 0.00 2.69
5078 5396 0.404040 TGGGAGCTGTTTGGTTAGGG 59.596 55.000 0.00 0.00 0.00 3.53
5079 5397 0.696501 GGGAGCTGTTTGGTTAGGGA 59.303 55.000 0.00 0.00 0.00 4.20
5080 5398 1.613520 GGGAGCTGTTTGGTTAGGGAC 60.614 57.143 0.00 0.00 0.00 4.46
5081 5399 1.073284 GGAGCTGTTTGGTTAGGGACA 59.927 52.381 0.00 0.00 0.00 4.02
5082 5400 2.427506 GAGCTGTTTGGTTAGGGACAG 58.572 52.381 0.00 0.00 41.76 3.51
5083 5401 1.774856 AGCTGTTTGGTTAGGGACAGT 59.225 47.619 4.52 0.00 41.11 3.55
5084 5402 2.174854 AGCTGTTTGGTTAGGGACAGTT 59.825 45.455 4.52 0.00 41.11 3.16
5085 5403 2.552743 GCTGTTTGGTTAGGGACAGTTC 59.447 50.000 4.52 0.00 41.11 3.01
5086 5404 3.747708 GCTGTTTGGTTAGGGACAGTTCT 60.748 47.826 4.52 0.00 41.11 3.01
5087 5405 4.065789 CTGTTTGGTTAGGGACAGTTCTC 58.934 47.826 0.00 0.00 35.84 2.87
5088 5406 3.714798 TGTTTGGTTAGGGACAGTTCTCT 59.285 43.478 0.00 0.00 36.18 3.10
5089 5407 4.202326 TGTTTGGTTAGGGACAGTTCTCTC 60.202 45.833 0.00 0.00 33.19 3.20
5090 5408 2.168496 TGGTTAGGGACAGTTCTCTCG 58.832 52.381 0.00 0.00 33.19 4.04
5091 5409 1.135053 GGTTAGGGACAGTTCTCTCGC 60.135 57.143 0.00 0.00 33.19 5.03
5092 5410 1.135053 GTTAGGGACAGTTCTCTCGCC 60.135 57.143 0.00 0.00 33.19 5.54
5093 5411 0.039180 TAGGGACAGTTCTCTCGCCA 59.961 55.000 0.00 0.00 33.19 5.69
5094 5412 1.079750 GGGACAGTTCTCTCGCCAC 60.080 63.158 0.00 0.00 0.00 5.01
5095 5413 1.666011 GGACAGTTCTCTCGCCACA 59.334 57.895 0.00 0.00 0.00 4.17
5096 5414 0.389166 GGACAGTTCTCTCGCCACAG 60.389 60.000 0.00 0.00 0.00 3.66
5097 5415 1.005630 ACAGTTCTCTCGCCACAGC 60.006 57.895 0.00 0.00 0.00 4.40
5098 5416 1.005748 CAGTTCTCTCGCCACAGCA 60.006 57.895 0.00 0.00 39.83 4.41
5099 5417 1.013005 CAGTTCTCTCGCCACAGCAG 61.013 60.000 0.00 0.00 39.83 4.24
5100 5418 1.005630 GTTCTCTCGCCACAGCAGT 60.006 57.895 0.00 0.00 39.83 4.40
5101 5419 1.005748 TTCTCTCGCCACAGCAGTG 60.006 57.895 1.56 1.56 45.47 3.66
5102 5420 1.748329 TTCTCTCGCCACAGCAGTGT 61.748 55.000 8.55 0.00 44.39 3.55
5103 5421 1.301244 CTCTCGCCACAGCAGTGTT 60.301 57.895 8.55 0.00 44.39 3.32
5104 5422 0.038251 CTCTCGCCACAGCAGTGTTA 60.038 55.000 8.55 0.00 44.39 2.41
5105 5423 0.391228 TCTCGCCACAGCAGTGTTAA 59.609 50.000 8.55 0.00 44.39 2.01
5106 5424 1.202592 TCTCGCCACAGCAGTGTTAAA 60.203 47.619 8.55 0.00 44.39 1.52
5107 5425 1.601903 CTCGCCACAGCAGTGTTAAAA 59.398 47.619 8.55 0.00 44.39 1.52
5108 5426 1.332375 TCGCCACAGCAGTGTTAAAAC 59.668 47.619 8.55 0.00 44.39 2.43
5109 5427 1.333619 CGCCACAGCAGTGTTAAAACT 59.666 47.619 8.55 0.00 44.39 2.66
5188 5506 8.755696 TGTAAACTGTAATGATTTCATTTGCC 57.244 30.769 10.81 1.90 43.48 4.52
5196 5517 7.655328 TGTAATGATTTCATTTGCCGTTCTTTT 59.345 29.630 10.81 0.00 43.48 2.27
5201 5522 4.647424 TCATTTGCCGTTCTTTTTCACT 57.353 36.364 0.00 0.00 0.00 3.41
5292 5613 4.038271 TCCAGTTCTTGCCATCTCATTT 57.962 40.909 0.00 0.00 0.00 2.32
5323 5644 9.698617 GATGTTTGTGTTAATTTCTATACGGTC 57.301 33.333 0.00 0.00 0.00 4.79
5333 5654 7.464830 AATTTCTATACGGTCTGATGTTTCG 57.535 36.000 0.00 0.00 0.00 3.46
5344 5666 2.749076 CTGATGTTTCGGAATCTGGCAA 59.251 45.455 0.00 0.00 0.00 4.52
5353 5675 1.690352 GGAATCTGGCAATTCCCATGG 59.310 52.381 21.17 4.14 46.08 3.66
5371 5693 1.621317 TGGCAGTGGTCTACAAATCGA 59.379 47.619 0.00 0.00 0.00 3.59
5390 6288 5.023533 TCGACATCTTGAAAAGGATAGGG 57.976 43.478 0.00 0.00 46.24 3.53
5393 6291 5.880332 CGACATCTTGAAAAGGATAGGGAAA 59.120 40.000 0.00 0.00 46.24 3.13
5417 6315 4.818534 TCAGCAGCTAAAACTTGTGAAG 57.181 40.909 0.00 0.00 0.00 3.02
5420 6318 3.316308 AGCAGCTAAAACTTGTGAAGTGG 59.684 43.478 0.00 0.00 41.91 4.00
5483 6395 1.690633 TGGCCATGTCTCCCTCTCC 60.691 63.158 0.00 0.00 0.00 3.71
5560 6472 2.835431 ACGAGGCGATCAGAGGGG 60.835 66.667 0.00 0.00 0.00 4.79
5562 6474 2.123251 GAGGCGATCAGAGGGGGA 60.123 66.667 0.00 0.00 0.00 4.81
5571 6483 0.041833 TCAGAGGGGGAGTCTCCTTG 59.958 60.000 18.58 5.75 36.57 3.61
5608 6520 1.529438 TCCTTCACGAAATCGCAACAC 59.471 47.619 2.15 0.00 44.43 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 0.617820 GCTAGAGTGGTCCCCTCCAA 60.618 60.000 0.00 0.00 39.34 3.53
20 21 2.128507 CGCTAGAGTGGTCCCCTCC 61.129 68.421 0.00 0.00 0.00 4.30
33 34 0.651042 GTCGTCGTCGTCATCGCTAG 60.651 60.000 1.33 0.00 38.33 3.42
35 36 2.097918 GTCGTCGTCGTCATCGCT 59.902 61.111 1.33 0.00 38.33 4.93
36 37 1.132199 ATTGTCGTCGTCGTCATCGC 61.132 55.000 2.91 0.00 35.45 4.58
40 41 1.731613 GCCATTGTCGTCGTCGTCA 60.732 57.895 1.33 0.00 38.33 4.35
45 46 2.047274 CCCTGCCATTGTCGTCGT 60.047 61.111 0.00 0.00 0.00 4.34
48 49 2.047274 CGTCCCTGCCATTGTCGT 60.047 61.111 0.00 0.00 0.00 4.34
87 88 4.527157 CGTACGCTCGGTCGGTCC 62.527 72.222 0.52 0.00 0.00 4.46
100 101 1.372087 ATCGGACGGTGACCTCGTAC 61.372 60.000 0.00 0.00 41.22 3.67
133 134 9.095529 GTTCGTTCAACTAAAACCTAATTAACG 57.904 33.333 0.00 0.00 37.80 3.18
137 138 7.481275 TCGTTCGTTCAACTAAAACCTAATT 57.519 32.000 0.00 0.00 32.09 1.40
138 139 7.481275 TTCGTTCGTTCAACTAAAACCTAAT 57.519 32.000 0.00 0.00 32.09 1.73
168 169 8.877864 TCGGCCAGAATTTATATAAATTGGAT 57.122 30.769 29.48 16.59 43.67 3.41
176 177 9.431887 GACATAACTTCGGCCAGAATTTATATA 57.568 33.333 21.08 7.37 40.48 0.86
191 192 8.955061 AATTCATTCAAACTGACATAACTTCG 57.045 30.769 0.00 0.00 0.00 3.79
203 204 7.816031 GTGAACATGATGGAATTCATTCAAACT 59.184 33.333 7.93 0.00 38.53 2.66
205 206 7.038870 AGGTGAACATGATGGAATTCATTCAAA 60.039 33.333 7.93 0.00 38.53 2.69
211 212 4.920999 TCAGGTGAACATGATGGAATTCA 58.079 39.130 7.93 0.00 31.11 2.57
219 220 4.460382 GGACACAATTCAGGTGAACATGAT 59.540 41.667 0.00 0.00 36.49 2.45
227 228 3.073678 TCATTCGGACACAATTCAGGTG 58.926 45.455 0.00 0.00 41.95 4.00
228 229 3.244561 ACTCATTCGGACACAATTCAGGT 60.245 43.478 0.00 0.00 0.00 4.00
230 231 5.049474 TCAAACTCATTCGGACACAATTCAG 60.049 40.000 0.00 0.00 0.00 3.02
231 232 4.819088 TCAAACTCATTCGGACACAATTCA 59.181 37.500 0.00 0.00 0.00 2.57
260 261 1.937546 CTTGCCGCAAATCTCCACCC 61.938 60.000 7.33 0.00 0.00 4.61
263 264 0.537143 ACACTTGCCGCAAATCTCCA 60.537 50.000 7.33 0.00 0.00 3.86
269 270 0.031857 CATCCAACACTTGCCGCAAA 59.968 50.000 7.33 0.00 0.00 3.68
274 275 2.973082 GGCCATCCAACACTTGCC 59.027 61.111 0.00 0.00 0.00 4.52
280 281 2.361104 GAAGCCGGCCATCCAACA 60.361 61.111 26.15 0.00 0.00 3.33
296 297 0.757561 TCTGTGGACAGTGGTTCGGA 60.758 55.000 6.68 0.00 44.12 4.55
297 298 0.600255 GTCTGTGGACAGTGGTTCGG 60.600 60.000 6.68 0.00 44.12 4.30
324 325 3.825308 CATCTTCAACATGGTTTGTCCG 58.175 45.455 0.00 0.00 37.68 4.79
325 326 3.578688 GCATCTTCAACATGGTTTGTCC 58.421 45.455 0.00 0.00 37.68 4.02
328 329 2.564062 AGGGCATCTTCAACATGGTTTG 59.436 45.455 0.00 0.00 0.00 2.93
329 330 2.893424 AGGGCATCTTCAACATGGTTT 58.107 42.857 0.00 0.00 0.00 3.27
332 333 5.380043 AGTATAAGGGCATCTTCAACATGG 58.620 41.667 0.00 0.00 36.93 3.66
333 334 6.949352 AAGTATAAGGGCATCTTCAACATG 57.051 37.500 0.00 0.00 36.93 3.21
334 335 7.499232 GTGTAAGTATAAGGGCATCTTCAACAT 59.501 37.037 0.00 0.00 36.93 2.71
368 390 7.016072 TGGGACCATGTTGAAAATTAAGACAAT 59.984 33.333 0.00 0.00 0.00 2.71
375 397 7.287927 TGTTTACTGGGACCATGTTGAAAATTA 59.712 33.333 0.00 0.00 0.00 1.40
406 428 9.598517 ACATTTACACTTTGAAAACACATCATT 57.401 25.926 0.00 0.00 0.00 2.57
437 459 7.275341 TCGGTCGTGATGTTATTTTTACGTATT 59.725 33.333 0.00 0.00 33.68 1.89
444 466 5.138800 CGATCGGTCGTGATGTTATTTTT 57.861 39.130 10.62 0.00 42.78 1.94
445 467 4.772046 CGATCGGTCGTGATGTTATTTT 57.228 40.909 10.62 0.00 42.78 1.82
570 593 7.220740 TCATGCGGTTTATATCACTGGATTTA 58.779 34.615 0.00 0.00 34.89 1.40
589 612 7.376866 AGCGAAATTTAAGTTGAATATCATGCG 59.623 33.333 0.00 0.00 0.00 4.73
647 672 5.077134 ACAAGTACGGTACCCTTGTATTC 57.923 43.478 24.98 5.85 45.06 1.75
675 700 7.924947 GGAAAGTTGTACTACATACATACTCCC 59.075 40.741 10.09 0.00 43.46 4.30
687 712 6.619232 GCACGTTTATGGGAAAGTTGTACTAC 60.619 42.308 0.00 0.00 0.00 2.73
688 713 5.409214 GCACGTTTATGGGAAAGTTGTACTA 59.591 40.000 0.00 0.00 0.00 1.82
726 794 5.241728 CGTTTCTCCTTCTTTTCTTCCCAAT 59.758 40.000 0.00 0.00 0.00 3.16
754 822 1.977009 CGGGCCTGTTTCTTTCCCC 60.977 63.158 2.29 0.00 33.43 4.81
789 858 1.087501 GGAAGCTCCGATGAACAACC 58.912 55.000 0.00 0.00 0.00 3.77
812 881 1.077089 GAGTTAGCCGTTGGAGCGAC 61.077 60.000 0.00 0.00 34.64 5.19
875 944 0.723459 GCGCGTCACTTTTTAACCGG 60.723 55.000 8.43 0.00 0.00 5.28
877 946 0.386352 GGGCGCGTCACTTTTTAACC 60.386 55.000 14.93 0.00 0.00 2.85
878 947 0.308376 TGGGCGCGTCACTTTTTAAC 59.692 50.000 14.93 0.00 0.00 2.01
881 950 2.719354 GTGGGCGCGTCACTTTTT 59.281 55.556 14.93 0.00 32.78 1.94
937 1036 0.955919 CGTCTGCCTCCCCTGTTTTC 60.956 60.000 0.00 0.00 0.00 2.29
954 1053 1.620798 GGGGGAGTAGGGTTAAGTCGT 60.621 57.143 0.00 0.00 0.00 4.34
1142 1252 2.440430 CGCCCTCTCCTCTCCGAA 60.440 66.667 0.00 0.00 0.00 4.30
1257 1367 0.472471 AAGCCAAAGAACCGGAGTGA 59.528 50.000 9.46 0.00 0.00 3.41
1258 1368 0.875059 GAAGCCAAAGAACCGGAGTG 59.125 55.000 9.46 0.00 0.00 3.51
1259 1369 0.765510 AGAAGCCAAAGAACCGGAGT 59.234 50.000 9.46 0.00 0.00 3.85
1263 1373 0.239347 CAGCAGAAGCCAAAGAACCG 59.761 55.000 0.00 0.00 43.56 4.44
1268 1379 2.544486 GGAACAACAGCAGAAGCCAAAG 60.544 50.000 0.00 0.00 43.56 2.77
1334 1445 0.307760 GGCAATAATCGCAGAACCGG 59.692 55.000 0.00 0.00 43.58 5.28
1348 1460 1.463674 GGACCATGTTCGAAGGCAAT 58.536 50.000 0.00 0.00 0.00 3.56
1359 1471 1.072266 TAGCAAACCAGGGACCATGT 58.928 50.000 5.25 0.00 0.00 3.21
1372 1491 5.049167 CCAACAAGACAGCAAATTAGCAAA 58.951 37.500 0.00 0.00 36.85 3.68
1383 1502 1.989706 TTAACCCCCAACAAGACAGC 58.010 50.000 0.00 0.00 0.00 4.40
1388 1507 3.306019 GCACAGAATTAACCCCCAACAAG 60.306 47.826 0.00 0.00 0.00 3.16
1394 1513 1.763968 GGAGCACAGAATTAACCCCC 58.236 55.000 0.00 0.00 0.00 5.40
1498 1617 3.695060 CCTGAGGACTTCGTTAAGAGCTA 59.305 47.826 0.00 0.00 36.50 3.32
1576 1695 3.006940 TCCACCGTATCAAATGTTCTGC 58.993 45.455 0.00 0.00 0.00 4.26
1626 1770 5.159925 CACAACACGGCAATCATTTGAATA 58.840 37.500 0.00 0.00 34.60 1.75
1934 2082 1.211703 CTGCTTGGTTTGGGGGTTTTT 59.788 47.619 0.00 0.00 0.00 1.94
2165 2316 8.954950 TGAACCACATTAACAAAAATCAATGT 57.045 26.923 0.00 0.00 41.14 2.71
2246 2399 0.861837 CCAAGTTCGACAGACTGCAC 59.138 55.000 1.25 0.00 0.00 4.57
2259 2412 2.764010 GTGAACCTCAAAACCCCAAGTT 59.236 45.455 0.00 0.00 41.81 2.66
2458 2612 1.064758 ACCACTGAAAGCACCAAGTCA 60.065 47.619 0.00 0.00 37.60 3.41
2502 2656 2.821991 AGGTTCAGTGCAGTACAGTC 57.178 50.000 0.00 0.00 0.00 3.51
2520 2674 8.527810 TGGCTATTTTTCCACAATAGGTTTTAG 58.472 33.333 0.00 0.00 35.53 1.85
2523 2677 6.926630 TGGCTATTTTTCCACAATAGGTTT 57.073 33.333 0.00 0.00 35.53 3.27
2607 2767 9.526713 AAGTTATGATGCGCTAGATTATGATAG 57.473 33.333 9.73 0.00 0.00 2.08
2719 2913 2.169352 TCAGGGAGCTCAATCAACTAGC 59.831 50.000 17.19 0.00 36.48 3.42
2932 3166 4.666512 ACAAATGAAAGCCTAGTCCATGT 58.333 39.130 0.00 0.00 0.00 3.21
2993 3227 9.886132 AGGACCAAGTATTGTAACTAGTAAATG 57.114 33.333 0.00 0.00 46.99 2.32
3014 3248 5.189145 TCCTTGTTATTCAGGAGTTAGGACC 59.811 44.000 0.00 0.00 0.00 4.46
3052 3286 5.235616 CGCCGCTTTTATTCAGAACCTATAA 59.764 40.000 0.00 0.00 0.00 0.98
3093 3327 5.234972 CACCTTTGAAAGAAAATCAGGTTGC 59.765 40.000 6.49 0.00 0.00 4.17
3155 3389 8.806429 TGGTTAATTTCTATCTGAAGCAATCA 57.194 30.769 0.00 0.00 35.89 2.57
3190 3424 4.157289 ACATCTGCATCCAAATTCAGTGTC 59.843 41.667 0.00 0.00 29.42 3.67
3203 3437 2.208431 GCTGAGGTACACATCTGCATC 58.792 52.381 17.37 0.00 46.16 3.91
3459 3696 1.879380 CGCCACTCAATTTGGTCTCAA 59.121 47.619 0.00 0.00 36.40 3.02
3518 3755 6.038356 GCTTATTCATGGAATTCAAGTGTGG 58.962 40.000 7.93 0.00 33.95 4.17
3748 3985 7.670364 TCTTGATCTTCTCTAACATGTGTGAA 58.330 34.615 0.00 0.00 0.00 3.18
3858 4095 6.071108 TGTCAGAAGCATATCTATAAGCCTCC 60.071 42.308 0.00 0.00 0.00 4.30
4026 4263 7.450014 AGAGGAGATGAGCTTATCTTCGATAAA 59.550 37.037 20.85 0.00 37.69 1.40
4051 4290 7.327761 CCTGCAAAACAAGTCATGATAAAAGAG 59.672 37.037 0.00 0.00 0.00 2.85
4175 4414 4.862350 TCAATAAAATCATCAGCATGCCG 58.138 39.130 15.66 3.71 34.76 5.69
4191 4430 8.601047 TGGAATATCAACCAACCAATCAATAA 57.399 30.769 0.00 0.00 32.93 1.40
4199 4438 2.290641 ACGCTGGAATATCAACCAACCA 60.291 45.455 0.00 0.00 35.67 3.67
4223 4462 0.888736 TGTTGGGTCCAGTCATTGCG 60.889 55.000 0.00 0.00 0.00 4.85
4304 4543 1.225983 CCCACCCAGTGTGTCAACA 59.774 57.895 0.00 0.00 43.85 3.33
4418 4657 2.093306 TGTGCGTCACAGAAATAGGG 57.907 50.000 8.32 0.00 39.62 3.53
4438 4677 0.537371 CAAACCGAGAGCCTTGGGTT 60.537 55.000 11.80 9.05 45.14 4.11
4460 4699 0.108233 TGTACCGGCGAACCCAATAC 60.108 55.000 9.30 0.00 0.00 1.89
4487 4726 0.321919 GGATCAAGGACAGCACAGCA 60.322 55.000 0.00 0.00 0.00 4.41
4535 4774 2.627221 GCTCCAGTCTGATAGAGATGCA 59.373 50.000 0.00 0.00 31.63 3.96
4652 4895 2.386661 TCTGCCTGACGAATTTCCTC 57.613 50.000 0.00 0.00 0.00 3.71
4655 4898 3.003275 TGTTGTTCTGCCTGACGAATTTC 59.997 43.478 0.00 0.00 0.00 2.17
4727 4970 3.430098 GCCAGAAGATGACACTCCTACTG 60.430 52.174 0.00 0.00 0.00 2.74
4776 5030 2.091610 TCATCAAAACCTGGTTCACCCA 60.092 45.455 13.36 0.00 42.51 4.51
4777 5031 2.593026 TCATCAAAACCTGGTTCACCC 58.407 47.619 13.36 0.00 34.29 4.61
4792 5046 3.890756 ACAAAAGAGCACAACCATCATCA 59.109 39.130 0.00 0.00 0.00 3.07
4793 5047 4.022935 TGACAAAAGAGCACAACCATCATC 60.023 41.667 0.00 0.00 0.00 2.92
4794 5048 3.890756 TGACAAAAGAGCACAACCATCAT 59.109 39.130 0.00 0.00 0.00 2.45
4891 5146 6.929049 TCGGAGCCATAAAACATATAGACAAG 59.071 38.462 0.00 0.00 0.00 3.16
4917 5174 1.172180 AGGGCAATGTCCACACAACG 61.172 55.000 6.67 0.00 35.64 4.10
4951 5208 5.812652 GTTGGTGACGACAAAAGAATAACA 58.187 37.500 0.00 0.00 44.70 2.41
5052 5370 1.339055 CCAAACAGCTCCCAATCTCGA 60.339 52.381 0.00 0.00 0.00 4.04
5053 5371 1.089920 CCAAACAGCTCCCAATCTCG 58.910 55.000 0.00 0.00 0.00 4.04
5054 5372 2.206576 ACCAAACAGCTCCCAATCTC 57.793 50.000 0.00 0.00 0.00 2.75
5055 5373 2.683211 AACCAAACAGCTCCCAATCT 57.317 45.000 0.00 0.00 0.00 2.40
5056 5374 2.755103 CCTAACCAAACAGCTCCCAATC 59.245 50.000 0.00 0.00 0.00 2.67
5057 5375 2.557452 CCCTAACCAAACAGCTCCCAAT 60.557 50.000 0.00 0.00 0.00 3.16
5058 5376 1.203001 CCCTAACCAAACAGCTCCCAA 60.203 52.381 0.00 0.00 0.00 4.12
5059 5377 0.404040 CCCTAACCAAACAGCTCCCA 59.596 55.000 0.00 0.00 0.00 4.37
5060 5378 0.696501 TCCCTAACCAAACAGCTCCC 59.303 55.000 0.00 0.00 0.00 4.30
5061 5379 1.073284 TGTCCCTAACCAAACAGCTCC 59.927 52.381 0.00 0.00 0.00 4.70
5062 5380 2.224548 ACTGTCCCTAACCAAACAGCTC 60.225 50.000 1.49 0.00 42.23 4.09
5063 5381 1.774856 ACTGTCCCTAACCAAACAGCT 59.225 47.619 1.49 0.00 42.23 4.24
5064 5382 2.271944 ACTGTCCCTAACCAAACAGC 57.728 50.000 1.49 0.00 42.23 4.40
5065 5383 4.065789 GAGAACTGTCCCTAACCAAACAG 58.934 47.826 0.00 0.00 43.69 3.16
5066 5384 3.714798 AGAGAACTGTCCCTAACCAAACA 59.285 43.478 0.00 0.00 0.00 2.83
5067 5385 4.316645 GAGAGAACTGTCCCTAACCAAAC 58.683 47.826 0.00 0.00 0.00 2.93
5068 5386 3.006537 CGAGAGAACTGTCCCTAACCAAA 59.993 47.826 0.00 0.00 0.00 3.28
5069 5387 2.561419 CGAGAGAACTGTCCCTAACCAA 59.439 50.000 0.00 0.00 0.00 3.67
5070 5388 2.168496 CGAGAGAACTGTCCCTAACCA 58.832 52.381 0.00 0.00 0.00 3.67
5071 5389 1.135053 GCGAGAGAACTGTCCCTAACC 60.135 57.143 0.00 0.00 0.00 2.85
5072 5390 1.135053 GGCGAGAGAACTGTCCCTAAC 60.135 57.143 0.00 0.00 0.00 2.34
5073 5391 1.183549 GGCGAGAGAACTGTCCCTAA 58.816 55.000 0.00 0.00 0.00 2.69
5074 5392 0.039180 TGGCGAGAGAACTGTCCCTA 59.961 55.000 0.00 0.00 0.00 3.53
5075 5393 1.228894 TGGCGAGAGAACTGTCCCT 60.229 57.895 0.00 0.00 0.00 4.20
5076 5394 1.079750 GTGGCGAGAGAACTGTCCC 60.080 63.158 0.00 0.00 0.00 4.46
5077 5395 0.389166 CTGTGGCGAGAGAACTGTCC 60.389 60.000 0.00 0.00 0.00 4.02
5078 5396 1.011451 GCTGTGGCGAGAGAACTGTC 61.011 60.000 0.00 0.00 0.00 3.51
5079 5397 1.005630 GCTGTGGCGAGAGAACTGT 60.006 57.895 0.00 0.00 0.00 3.55
5080 5398 1.005748 TGCTGTGGCGAGAGAACTG 60.006 57.895 0.00 0.00 42.25 3.16
5081 5399 1.291588 CTGCTGTGGCGAGAGAACT 59.708 57.895 0.00 0.00 42.25 3.01
5082 5400 1.005630 ACTGCTGTGGCGAGAGAAC 60.006 57.895 0.00 0.00 42.25 3.01
5083 5401 1.005748 CACTGCTGTGGCGAGAGAA 60.006 57.895 15.43 0.00 42.25 2.87
5084 5402 2.653115 CACTGCTGTGGCGAGAGA 59.347 61.111 15.43 0.00 42.25 3.10
5092 5410 6.881805 ACTGGTCAGTTTTAACACTGCTGTG 61.882 44.000 20.83 20.83 43.51 3.66
5093 5411 3.616219 TGGTCAGTTTTAACACTGCTGT 58.384 40.909 15.52 0.00 43.51 4.40
5094 5412 3.627577 ACTGGTCAGTTTTAACACTGCTG 59.372 43.478 15.52 9.72 43.51 4.41
5095 5413 3.886123 ACTGGTCAGTTTTAACACTGCT 58.114 40.909 15.52 0.00 43.51 4.24
5107 5425 5.763204 CACCTACAATTTACAACTGGTCAGT 59.237 40.000 0.00 0.00 44.94 3.41
5108 5426 5.763204 ACACCTACAATTTACAACTGGTCAG 59.237 40.000 0.00 0.00 0.00 3.51
5109 5427 5.686753 ACACCTACAATTTACAACTGGTCA 58.313 37.500 0.00 0.00 0.00 4.02
5110 5428 7.569957 CGTTACACCTACAATTTACAACTGGTC 60.570 40.741 0.00 0.00 0.00 4.02
5111 5429 6.203338 CGTTACACCTACAATTTACAACTGGT 59.797 38.462 0.00 0.00 0.00 4.00
5112 5430 6.203338 ACGTTACACCTACAATTTACAACTGG 59.797 38.462 0.00 0.00 0.00 4.00
5128 5446 6.034470 CCAAATGCAAATCAATACGTTACACC 59.966 38.462 0.00 0.00 0.00 4.16
5175 5493 6.019156 GTGAAAAAGAACGGCAAATGAAATCA 60.019 34.615 0.00 0.00 0.00 2.57
5277 5598 4.305539 TCTCCAAAATGAGATGGCAAGA 57.694 40.909 0.00 0.00 36.48 3.02
5318 5639 2.233922 AGATTCCGAAACATCAGACCGT 59.766 45.455 0.00 0.00 0.00 4.83
5323 5644 2.358957 TGCCAGATTCCGAAACATCAG 58.641 47.619 0.00 0.00 0.00 2.90
5344 5666 1.212935 GTAGACCACTGCCATGGGAAT 59.787 52.381 15.13 0.00 44.81 3.01
5349 5671 2.352651 CGATTTGTAGACCACTGCCATG 59.647 50.000 0.00 0.00 0.00 3.66
5353 5675 2.683968 TGTCGATTTGTAGACCACTGC 58.316 47.619 0.00 0.00 36.61 4.40
5371 5693 8.670521 AATTTTCCCTATCCTTTTCAAGATGT 57.329 30.769 0.00 0.00 0.00 3.06
5390 6288 6.697019 TCACAAGTTTTAGCTGCTGAATTTTC 59.303 34.615 13.43 2.34 0.00 2.29
5393 6291 5.772825 TCACAAGTTTTAGCTGCTGAATT 57.227 34.783 13.43 0.00 0.00 2.17
5417 6315 2.360475 GCCTGCCCAACTCTCCAC 60.360 66.667 0.00 0.00 0.00 4.02
5420 6318 2.045536 CTGGCCTGCCCAACTCTC 60.046 66.667 3.32 0.00 44.81 3.20
5483 6395 1.611851 AGAGGTGAGGTGAGGCTGG 60.612 63.158 0.00 0.00 0.00 4.85
5560 6472 1.065854 CACCATGGTCAAGGAGACTCC 60.066 57.143 16.53 14.15 46.72 3.85
5562 6474 0.326264 GCACCATGGTCAAGGAGACT 59.674 55.000 16.53 0.00 46.72 3.24
5571 6483 1.211457 AGGAGATGAAGCACCATGGTC 59.789 52.381 16.53 10.30 0.00 4.02


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

AutoCloner maintained by Alex Coulton.