Multiple sequence alignment - TraesCS5B01G404000

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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 TraesCS5B01G404000 chr5B 100.000 3337 0 0 896 4232 580366866 580363530 0.000000e+00 6163.0
1 TraesCS5B01G404000 chr5B 100.000 673 0 0 1 673 580367761 580367089 0.000000e+00 1243.0
2 TraesCS5B01G404000 chr5D 91.827 2912 119 58 919 3794 473003560 473000732 0.000000e+00 3949.0
3 TraesCS5B01G404000 chr5D 81.143 700 100 16 2350 3034 551984531 551985213 2.240000e-147 532.0
4 TraesCS5B01G404000 chr5D 90.087 343 23 6 3797 4131 473000678 473000339 6.500000e-118 435.0
5 TraesCS5B01G404000 chr5D 84.935 385 12 10 1 370 473004779 473004426 8.710000e-92 348.0
6 TraesCS5B01G404000 chr5D 85.424 295 27 9 373 662 473003962 473003679 4.140000e-75 292.0
7 TraesCS5B01G404000 chr5D 75.743 606 83 34 1776 2343 551983997 551984576 3.270000e-61 246.0
8 TraesCS5B01G404000 chr5A 90.759 2370 123 57 901 3210 592639032 592636699 0.000000e+00 3075.0
9 TraesCS5B01G404000 chr5A 92.612 582 22 9 3221 3797 592636635 592636070 0.000000e+00 817.0
10 TraesCS5B01G404000 chr5A 88.034 351 33 3 3797 4140 592636019 592635671 1.420000e-109 407.0
11 TraesCS5B01G404000 chr5A 84.314 306 26 9 373 669 592639420 592639128 3.220000e-71 279.0
12 TraesCS5B01G404000 chr1A 82.388 670 92 11 2377 3034 564320579 564319924 1.030000e-155 560.0
13 TraesCS5B01G404000 chr7A 81.073 671 99 13 2376 3034 367840874 367841528 1.050000e-140 510.0
14 TraesCS5B01G404000 chrUn 79.473 531 79 23 1776 2292 63569549 63569035 2.420000e-92 350.0
15 TraesCS5B01G404000 chr4A 79.559 499 87 9 2546 3034 616429362 616428869 4.050000e-90 342.0
16 TraesCS5B01G404000 chr4A 83.041 171 25 3 1089 1257 40860255 40860423 7.330000e-33 152.0
17 TraesCS5B01G404000 chr4B 84.211 171 23 3 1089 1257 519824585 519824417 3.390000e-36 163.0
18 TraesCS5B01G404000 chr4D 85.315 143 21 0 1089 1231 423429821 423429679 9.480000e-32 148.0
19 TraesCS5B01G404000 chr2A 80.645 155 22 7 1078 1228 705068479 705068629 3.460000e-21 113.0
20 TraesCS5B01G404000 chr2D 80.000 140 24 4 1091 1228 564384018 564384155 2.690000e-17 100.0
21 TraesCS5B01G404000 chr2B 78.431 153 29 4 1078 1228 675514541 675514691 3.480000e-16 97.1
22 TraesCS5B01G404000 chr3B 81.319 91 13 3 1174 1262 823029116 823029204 2.110000e-08 71.3


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 TraesCS5B01G404000 chr5B 580363530 580367761 4231 True 3703.0 6163 100.00000 1 4232 2 chr5B.!!$R1 4231
1 TraesCS5B01G404000 chr5D 473000339 473004779 4440 True 1256.0 3949 88.06825 1 4131 4 chr5D.!!$R1 4130
2 TraesCS5B01G404000 chr5D 551983997 551985213 1216 False 389.0 532 78.44300 1776 3034 2 chr5D.!!$F1 1258
3 TraesCS5B01G404000 chr5A 592635671 592639420 3749 True 1144.5 3075 88.92975 373 4140 4 chr5A.!!$R1 3767
4 TraesCS5B01G404000 chr1A 564319924 564320579 655 True 560.0 560 82.38800 2377 3034 1 chr1A.!!$R1 657
5 TraesCS5B01G404000 chr7A 367840874 367841528 654 False 510.0 510 81.07300 2376 3034 1 chr7A.!!$F1 658
6 TraesCS5B01G404000 chrUn 63569035 63569549 514 True 350.0 350 79.47300 1776 2292 1 chrUn.!!$R1 516

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
588 1069 0.033504 CCGTCCATCCAATCCTACGG 59.966 60.0 0.00 0.0 43.20 4.02 F
976 1474 0.179004 AGAGCTCGGATCTCGTGGAT 60.179 55.0 8.37 0.0 40.32 3.41 F
1302 1812 0.179081 CCTTCCCCTTCCGTCGATTC 60.179 60.0 0.00 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1861 2381 0.185901 AGGCAAACTGGCAGAGGAAA 59.814 50.0 23.66 0.0 46.46 3.13 R
2346 2924 0.689745 TCCCAGGAACCCAGGATACG 60.690 60.0 0.00 0.0 46.39 3.06 R
3289 3972 0.106619 TGCAACCCTACCACCGTTTT 60.107 50.0 0.00 0.0 0.00 2.43 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
110 111 1.788481 GCTCGCCCGTTTTTCTCTC 59.212 57.895 0.00 0.00 0.00 3.20
154 170 1.592669 CTGCCTCGGCCTCGTAATG 60.593 63.158 0.00 0.00 41.09 1.90
155 171 2.280186 GCCTCGGCCTCGTAATGG 60.280 66.667 0.00 0.00 37.69 3.16
182 198 7.136822 TGAATAAATATCTGCCACCACTACT 57.863 36.000 0.00 0.00 0.00 2.57
224 240 4.051922 CACTTATCGAAGGCCACTATCAC 58.948 47.826 5.01 0.00 36.95 3.06
249 265 2.274645 CCCGCAATCAAAGGCCACA 61.275 57.895 5.01 0.00 0.00 4.17
250 266 1.606885 CCCGCAATCAAAGGCCACAT 61.607 55.000 5.01 0.00 0.00 3.21
251 267 1.102154 CCGCAATCAAAGGCCACATA 58.898 50.000 5.01 0.00 0.00 2.29
252 268 1.682854 CCGCAATCAAAGGCCACATAT 59.317 47.619 5.01 0.00 0.00 1.78
253 269 2.884012 CCGCAATCAAAGGCCACATATA 59.116 45.455 5.01 0.00 0.00 0.86
254 270 3.058016 CCGCAATCAAAGGCCACATATAG 60.058 47.826 5.01 0.00 0.00 1.31
255 271 3.058016 CGCAATCAAAGGCCACATATAGG 60.058 47.826 5.01 0.00 0.00 2.57
256 272 4.144297 GCAATCAAAGGCCACATATAGGA 58.856 43.478 5.01 0.00 0.00 2.94
257 273 4.217118 GCAATCAAAGGCCACATATAGGAG 59.783 45.833 5.01 0.00 0.00 3.69
258 274 3.492102 TCAAAGGCCACATATAGGAGC 57.508 47.619 5.01 0.00 0.00 4.70
259 275 2.777114 TCAAAGGCCACATATAGGAGCA 59.223 45.455 5.01 0.00 0.00 4.26
260 276 2.880890 CAAAGGCCACATATAGGAGCAC 59.119 50.000 5.01 0.00 0.00 4.40
261 277 2.109229 AGGCCACATATAGGAGCACT 57.891 50.000 5.01 0.00 0.00 4.40
262 278 1.974236 AGGCCACATATAGGAGCACTC 59.026 52.381 5.01 0.00 0.00 3.51
301 317 7.457024 AATGGTTTGTTTATTAGCCGTAACT 57.543 32.000 0.00 0.00 0.00 2.24
306 322 7.648908 GGTTTGTTTATTAGCCGTAACTTTTGT 59.351 33.333 0.00 0.00 0.00 2.83
370 386 1.645710 AGCTGCAAGTAGGGTGTACT 58.354 50.000 1.02 0.00 35.30 2.73
371 387 1.550976 AGCTGCAAGTAGGGTGTACTC 59.449 52.381 1.02 0.00 35.30 2.59
420 897 6.239008 CCGTTATAATTGGGCTCAAATGTGAT 60.239 38.462 1.42 0.00 36.36 3.06
421 898 7.040755 CCGTTATAATTGGGCTCAAATGTGATA 60.041 37.037 1.42 0.00 36.36 2.15
422 899 8.349245 CGTTATAATTGGGCTCAAATGTGATAA 58.651 33.333 1.42 0.66 36.36 1.75
423 900 9.683069 GTTATAATTGGGCTCAAATGTGATAAG 57.317 33.333 1.42 0.00 36.36 1.73
470 947 4.319622 CCACCGATAGTCAGTCGATTAGTC 60.320 50.000 0.00 0.00 41.40 2.59
476 953 4.039151 AGTCAGTCGATTAGTCATGCAG 57.961 45.455 0.00 0.00 0.00 4.41
482 959 1.602311 GATTAGTCATGCAGGCAGGG 58.398 55.000 6.06 0.00 0.00 4.45
483 960 0.466922 ATTAGTCATGCAGGCAGGGC 60.467 55.000 1.80 1.80 32.01 5.19
497 974 3.256960 GGGCCCCACCTGTCAGAA 61.257 66.667 12.23 0.00 39.10 3.02
508 985 4.173256 CACCTGTCAGAAAACCAACAAAC 58.827 43.478 0.00 0.00 0.00 2.93
539 1016 0.111639 CACCGGGGAAAGGAAAGGAA 59.888 55.000 6.32 0.00 0.00 3.36
542 1019 0.965866 CGGGGAAAGGAAAGGAAGGC 60.966 60.000 0.00 0.00 0.00 4.35
543 1020 0.114364 GGGGAAAGGAAAGGAAGGCA 59.886 55.000 0.00 0.00 0.00 4.75
545 1022 1.550327 GGAAAGGAAAGGAAGGCAGG 58.450 55.000 0.00 0.00 0.00 4.85
546 1023 1.075536 GGAAAGGAAAGGAAGGCAGGA 59.924 52.381 0.00 0.00 0.00 3.86
547 1024 2.441410 GAAAGGAAAGGAAGGCAGGAG 58.559 52.381 0.00 0.00 0.00 3.69
548 1025 0.701147 AAGGAAAGGAAGGCAGGAGG 59.299 55.000 0.00 0.00 0.00 4.30
551 1029 1.280457 GAAAGGAAGGCAGGAGGAGA 58.720 55.000 0.00 0.00 0.00 3.71
555 1033 0.251634 GGAAGGCAGGAGGAGACAAG 59.748 60.000 0.00 0.00 0.00 3.16
556 1034 0.980423 GAAGGCAGGAGGAGACAAGT 59.020 55.000 0.00 0.00 0.00 3.16
558 1039 0.178921 AGGCAGGAGGAGACAAGTCA 60.179 55.000 2.72 0.00 0.00 3.41
560 1041 1.072331 GGCAGGAGGAGACAAGTCAAA 59.928 52.381 2.72 0.00 0.00 2.69
567 1048 2.076863 GGAGACAAGTCAAACCATCCG 58.923 52.381 2.72 0.00 0.00 4.18
571 1052 0.796312 CAAGTCAAACCATCCGTCCG 59.204 55.000 0.00 0.00 0.00 4.79
588 1069 0.033504 CCGTCCATCCAATCCTACGG 59.966 60.000 0.00 0.00 43.20 4.02
621 1102 1.066605 CAGGATAACCACCGTAGACCG 59.933 57.143 0.00 0.00 38.94 4.79
622 1103 1.064463 AGGATAACCACCGTAGACCGA 60.064 52.381 0.00 0.00 37.42 4.69
624 1105 1.066152 GATAACCACCGTAGACCGACC 59.934 57.143 0.00 0.00 39.56 4.79
625 1106 1.305219 TAACCACCGTAGACCGACCG 61.305 60.000 0.00 0.00 39.56 4.79
632 1117 3.129502 TAGACCGACCGCCACTCG 61.130 66.667 0.00 0.00 38.08 4.18
919 1404 1.996898 TCATTCATTCGTTCGTTCCCG 59.003 47.619 0.00 0.00 0.00 5.14
931 1416 2.035155 TTCCCGGAGAGACGAGCA 59.965 61.111 0.73 0.00 35.47 4.26
971 1469 2.265182 GGGGAGAGCTCGGATCTCG 61.265 68.421 8.37 0.00 43.45 4.04
972 1470 1.527380 GGGAGAGCTCGGATCTCGT 60.527 63.158 8.37 0.00 43.45 4.18
973 1471 1.652012 GGAGAGCTCGGATCTCGTG 59.348 63.158 8.37 0.00 43.45 4.35
974 1472 1.652012 GAGAGCTCGGATCTCGTGG 59.348 63.158 8.37 0.00 40.32 4.94
975 1473 0.816018 GAGAGCTCGGATCTCGTGGA 60.816 60.000 8.37 0.00 40.32 4.02
976 1474 0.179004 AGAGCTCGGATCTCGTGGAT 60.179 55.000 8.37 0.00 40.32 3.41
977 1475 1.072489 AGAGCTCGGATCTCGTGGATA 59.928 52.381 8.37 0.00 40.32 2.59
978 1476 2.088423 GAGCTCGGATCTCGTGGATAT 58.912 52.381 0.00 0.00 40.32 1.63
979 1477 2.490115 GAGCTCGGATCTCGTGGATATT 59.510 50.000 0.00 0.00 40.32 1.28
980 1478 2.894126 AGCTCGGATCTCGTGGATATTT 59.106 45.455 0.00 0.00 40.32 1.40
989 1496 6.766467 GGATCTCGTGGATATTTTAGTTGGTT 59.234 38.462 0.00 0.00 34.33 3.67
992 1499 6.592607 TCTCGTGGATATTTTAGTTGGTTGTC 59.407 38.462 0.00 0.00 0.00 3.18
1276 1786 0.525882 GCGTACGCTCTTCTCCTTCC 60.526 60.000 31.95 0.00 38.26 3.46
1277 1787 0.809385 CGTACGCTCTTCTCCTTCCA 59.191 55.000 0.52 0.00 0.00 3.53
1302 1812 0.179081 CCTTCCCCTTCCGTCGATTC 60.179 60.000 0.00 0.00 0.00 2.52
1316 1826 1.146358 CGATTCGAGTTTCTCCCGGC 61.146 60.000 0.00 0.00 0.00 6.13
1323 1833 0.898789 AGTTTCTCCCGGCTTCTCGA 60.899 55.000 0.00 0.00 0.00 4.04
1330 1840 0.319900 CCCGGCTTCTCGATATGGTG 60.320 60.000 0.00 0.00 0.00 4.17
1331 1841 0.673985 CCGGCTTCTCGATATGGTGA 59.326 55.000 0.00 0.00 0.00 4.02
1332 1842 1.273606 CCGGCTTCTCGATATGGTGAT 59.726 52.381 0.00 0.00 0.00 3.06
1333 1843 2.492088 CCGGCTTCTCGATATGGTGATA 59.508 50.000 0.00 0.00 0.00 2.15
1340 1850 7.268586 GCTTCTCGATATGGTGATATATGGTT 58.731 38.462 0.00 0.00 0.00 3.67
1342 1852 7.954666 TCTCGATATGGTGATATATGGTTGA 57.045 36.000 0.00 0.00 0.00 3.18
1365 1875 1.286880 GCGGTGCTGATTTTGCTGT 59.713 52.632 0.00 0.00 0.00 4.40
1759 2274 2.548920 GGGGATAATTCAGGTGAGAGCG 60.549 54.545 0.00 0.00 0.00 5.03
1762 2277 0.530744 TAATTCAGGTGAGAGCGCGT 59.469 50.000 8.43 0.00 0.00 6.01
1831 2351 2.438763 CAGAGATTGGAGGCAAGGATCT 59.561 50.000 0.00 0.00 0.00 2.75
1848 2368 7.678218 GCAAGGATCTCTGATTGTTGATAACAC 60.678 40.741 0.00 0.00 41.97 3.32
1861 2381 1.539827 GATAACACCTGCGGCTTTTGT 59.460 47.619 0.00 0.00 0.00 2.83
1889 2409 3.698040 CTGCCAGTTTGCCTGATTTAGAT 59.302 43.478 0.00 0.00 44.49 1.98
1922 2442 5.464168 ACTTTGCTTGCACACTGAAATATC 58.536 37.500 0.00 0.00 0.00 1.63
1923 2443 5.009911 ACTTTGCTTGCACACTGAAATATCA 59.990 36.000 0.00 0.00 0.00 2.15
1924 2444 5.450592 TTGCTTGCACACTGAAATATCAA 57.549 34.783 0.00 0.00 34.49 2.57
1930 2450 7.219535 GCTTGCACACTGAAATATCAAATAGTG 59.780 37.037 0.00 0.00 35.35 2.74
1932 2452 7.977904 TGCACACTGAAATATCAAATAGTGAG 58.022 34.615 8.94 2.76 40.43 3.51
1934 2454 8.834465 GCACACTGAAATATCAAATAGTGAGAT 58.166 33.333 8.94 0.00 39.95 2.75
1986 2515 6.668283 TCAGAGCTCCCTAATTTGTACTAGTT 59.332 38.462 10.93 0.00 0.00 2.24
2000 2529 7.476540 TTGTACTAGTTCAGAGCCATTAGAA 57.523 36.000 0.00 0.00 0.00 2.10
2003 2533 3.636153 AGTTCAGAGCCATTAGAACCC 57.364 47.619 0.00 0.00 40.82 4.11
2089 2620 3.703001 TGACCCCTTCTGTTCAATCTC 57.297 47.619 0.00 0.00 0.00 2.75
2131 2703 3.130734 TGGGGTTAGATGAAGTAGGCT 57.869 47.619 0.00 0.00 0.00 4.58
2187 2759 7.823745 AGAAGATATTCACTGTGTTTTTGGT 57.176 32.000 7.79 0.00 0.00 3.67
2250 2824 2.294233 AGCGAACACTGAAATTGCACAT 59.706 40.909 0.00 0.00 0.00 3.21
2372 2976 2.513738 CCTGGGTTCCTGGGATCATAAA 59.486 50.000 0.00 0.00 38.71 1.40
2373 2977 3.140895 CCTGGGTTCCTGGGATCATAAAT 59.859 47.826 0.00 0.00 38.71 1.40
2406 3018 9.213777 GGATTCCTGGTATCATAGTCCATATAA 57.786 37.037 14.25 0.00 0.00 0.98
2456 3068 7.932120 AAGATACTCCATTTATCGTTCGAAG 57.068 36.000 0.00 0.00 32.12 3.79
2535 3149 6.146837 CACTCATCAGTTAGTTTGTCCTCTTG 59.853 42.308 0.00 0.00 0.00 3.02
2542 3156 3.214696 AGTTTGTCCTCTTGGGAGTTG 57.785 47.619 0.00 0.00 46.10 3.16
2618 3232 7.380602 GGATAACATGAGCTAACAATTGATTGC 59.619 37.037 13.59 13.18 41.38 3.56
2668 3282 6.774673 TGGTGATGTATACTTGAAGAAACCA 58.225 36.000 0.00 4.48 0.00 3.67
2892 3509 7.012989 GGTAGGTTCCAATGTAACAATACCATC 59.987 40.741 13.54 0.00 38.87 3.51
2900 3517 8.632679 CCAATGTAACAATACCATCTGCTATTT 58.367 33.333 0.00 0.00 0.00 1.40
2902 3519 9.632638 AATGTAACAATACCATCTGCTATTTCT 57.367 29.630 0.00 0.00 0.00 2.52
2903 3520 8.662781 TGTAACAATACCATCTGCTATTTCTC 57.337 34.615 0.00 0.00 0.00 2.87
2940 3560 3.123050 TCCGCGTATGAATCATCTGTTG 58.877 45.455 4.92 0.00 0.00 3.33
2960 3580 2.162608 TGGACCAAATGAAATAACGCCG 59.837 45.455 0.00 0.00 0.00 6.46
2967 3597 6.127842 ACCAAATGAAATAACGCCGAAGTTAT 60.128 34.615 8.88 8.88 45.96 1.89
2979 3609 2.595386 CGAAGTTATTTTGTGCAGGGC 58.405 47.619 0.00 0.00 0.00 5.19
2994 3624 0.392998 AGGGCATAGCAAACCGACTG 60.393 55.000 0.00 0.00 0.00 3.51
3276 3959 6.871844 GCAGAAGCTCAGACCATATATATGA 58.128 40.000 21.97 3.84 35.22 2.15
3277 3960 7.499292 GCAGAAGCTCAGACCATATATATGAT 58.501 38.462 21.97 6.81 35.22 2.45
3278 3961 7.652909 GCAGAAGCTCAGACCATATATATGATC 59.347 40.741 21.97 15.71 35.22 2.92
3279 3962 8.693625 CAGAAGCTCAGACCATATATATGATCA 58.306 37.037 21.97 0.00 35.75 2.92
3280 3963 8.916062 AGAAGCTCAGACCATATATATGATCAG 58.084 37.037 21.97 12.83 35.75 2.90
3281 3964 7.600231 AGCTCAGACCATATATATGATCAGG 57.400 40.000 21.97 12.05 35.75 3.86
3282 3965 6.554228 AGCTCAGACCATATATATGATCAGGG 59.446 42.308 21.97 13.60 35.75 4.45
3287 3970 7.565029 CAGACCATATATATGATCAGGGTGGTA 59.435 40.741 21.97 0.00 37.55 3.25
3289 3972 7.662083 ACCATATATATGATCAGGGTGGTAGA 58.338 38.462 21.97 0.00 35.81 2.59
3524 4211 8.944029 TGAACTAGAACGGTAGCAGTATATATC 58.056 37.037 0.00 0.00 0.00 1.63
3561 4248 3.508840 GCACCCCGGATTTCAGCG 61.509 66.667 0.73 0.00 0.00 5.18
3563 4250 2.106683 CACCCCGGATTTCAGCGTC 61.107 63.158 0.73 0.00 0.00 5.19
3794 4496 1.191535 CGGGGAAAAGGGGAAATTCC 58.808 55.000 2.79 2.79 41.53 3.01
3856 4609 2.681344 CCTAATTCCGGCACCAAGTTAC 59.319 50.000 0.00 0.00 0.00 2.50
3867 4627 1.070601 ACCAAGTTACCCGTGTACACC 59.929 52.381 20.11 5.05 0.00 4.16
3869 4629 2.137523 CAAGTTACCCGTGTACACCAC 58.862 52.381 20.11 9.15 40.89 4.16
3876 4636 0.103390 CCGTGTACACCACTGACACA 59.897 55.000 20.11 0.00 42.93 3.72
3888 4648 1.481240 CTGACACAGTGACAGTGACG 58.519 55.000 20.94 9.62 40.16 4.35
3897 4657 2.046892 ACAGTGACGCCATCAGCC 60.047 61.111 0.00 0.00 38.28 4.85
3948 4708 4.870363 TGCAAAAGCTACCAAATGTCTTC 58.130 39.130 0.00 0.00 0.00 2.87
3949 4709 4.237724 GCAAAAGCTACCAAATGTCTTCC 58.762 43.478 0.00 0.00 0.00 3.46
3991 4751 1.080705 GCGTACCAAGCGACAGACT 60.081 57.895 0.00 0.00 0.00 3.24
4015 4775 1.812922 GCGGATCAGTGAGGTGCAG 60.813 63.158 0.00 0.00 0.00 4.41
4040 4800 0.105453 TCCAGCCCAGGAGGATAGTC 60.105 60.000 0.00 0.00 38.24 2.59
4054 4814 4.030913 AGGATAGTCGGAAGTGGAATTCA 58.969 43.478 7.93 0.00 0.00 2.57
4068 4828 6.568869 AGTGGAATTCAGAATCTTCTACTCG 58.431 40.000 7.93 0.00 36.38 4.18
4114 4875 0.889186 GCAAGGCCTCGTTTCAAGGA 60.889 55.000 5.23 0.00 35.83 3.36
4127 4888 1.864669 TCAAGGAATCCCCCATTTGC 58.135 50.000 0.00 0.00 34.66 3.68
4132 4893 1.063266 GGAATCCCCCATTTGCACCTA 60.063 52.381 0.00 0.00 0.00 3.08
4134 4895 1.308877 ATCCCCCATTTGCACCTAGT 58.691 50.000 0.00 0.00 0.00 2.57
4140 4901 1.737793 CCATTTGCACCTAGTCGAACC 59.262 52.381 0.00 0.00 0.00 3.62
4141 4902 1.737793 CATTTGCACCTAGTCGAACCC 59.262 52.381 0.00 0.00 0.00 4.11
4142 4903 1.053424 TTTGCACCTAGTCGAACCCT 58.947 50.000 0.00 0.00 0.00 4.34
4143 4904 0.606604 TTGCACCTAGTCGAACCCTC 59.393 55.000 0.00 0.00 0.00 4.30
4144 4905 1.139095 GCACCTAGTCGAACCCTCG 59.861 63.158 0.00 0.00 46.87 4.63
4182 4943 3.825908 AAATTAAGGAGTTCAGCCCCA 57.174 42.857 0.00 0.00 0.00 4.96
4183 4944 3.825908 AATTAAGGAGTTCAGCCCCAA 57.174 42.857 0.00 0.00 0.00 4.12
4184 4945 2.879103 TTAAGGAGTTCAGCCCCAAG 57.121 50.000 0.00 0.00 0.00 3.61
4185 4946 0.328258 TAAGGAGTTCAGCCCCAAGC 59.672 55.000 0.00 0.00 44.25 4.01
4186 4947 2.361737 GGAGTTCAGCCCCAAGCC 60.362 66.667 0.00 0.00 45.47 4.35
4187 4948 2.747855 GAGTTCAGCCCCAAGCCG 60.748 66.667 0.00 0.00 45.47 5.52
4188 4949 3.249189 AGTTCAGCCCCAAGCCGA 61.249 61.111 0.00 0.00 45.47 5.54
4189 4950 2.747855 GTTCAGCCCCAAGCCGAG 60.748 66.667 0.00 0.00 45.47 4.63
4190 4951 4.722700 TTCAGCCCCAAGCCGAGC 62.723 66.667 0.00 0.00 45.47 5.03
4194 4955 4.722700 GCCCCAAGCCGAGCTCAA 62.723 66.667 15.40 0.00 38.25 3.02
4195 4956 2.747855 CCCCAAGCCGAGCTCAAC 60.748 66.667 15.40 4.56 38.25 3.18
4196 4957 2.348998 CCCAAGCCGAGCTCAACT 59.651 61.111 15.40 7.13 38.25 3.16
4197 4958 1.743252 CCCAAGCCGAGCTCAACTC 60.743 63.158 15.40 0.00 38.25 3.01
4198 4959 1.294780 CCAAGCCGAGCTCAACTCT 59.705 57.895 15.40 1.35 43.85 3.24
4199 4960 0.739112 CCAAGCCGAGCTCAACTCTC 60.739 60.000 15.40 0.00 43.85 3.20
4200 4961 0.246086 CAAGCCGAGCTCAACTCTCT 59.754 55.000 15.40 0.00 43.85 3.10
4201 4962 0.972883 AAGCCGAGCTCAACTCTCTT 59.027 50.000 15.40 4.17 43.85 2.85
4202 4963 1.840737 AGCCGAGCTCAACTCTCTTA 58.159 50.000 15.40 0.00 43.85 2.10
4203 4964 2.383855 AGCCGAGCTCAACTCTCTTAT 58.616 47.619 15.40 0.00 43.85 1.73
4204 4965 2.763448 AGCCGAGCTCAACTCTCTTATT 59.237 45.455 15.40 0.00 43.85 1.40
4205 4966 3.196685 AGCCGAGCTCAACTCTCTTATTT 59.803 43.478 15.40 0.00 43.85 1.40
4206 4967 3.935828 GCCGAGCTCAACTCTCTTATTTT 59.064 43.478 15.40 0.00 43.85 1.82
4207 4968 4.393371 GCCGAGCTCAACTCTCTTATTTTT 59.607 41.667 15.40 0.00 43.85 1.94
4208 4969 5.672321 GCCGAGCTCAACTCTCTTATTTTTG 60.672 44.000 15.40 0.00 43.85 2.44
4209 4970 5.319931 CGAGCTCAACTCTCTTATTTTTGC 58.680 41.667 15.40 0.00 43.85 3.68
4210 4971 5.121454 CGAGCTCAACTCTCTTATTTTTGCT 59.879 40.000 15.40 0.00 43.85 3.91
4211 4972 6.493449 AGCTCAACTCTCTTATTTTTGCTC 57.507 37.500 0.00 0.00 0.00 4.26
4212 4973 5.121454 AGCTCAACTCTCTTATTTTTGCTCG 59.879 40.000 0.00 0.00 0.00 5.03
4213 4974 5.120830 GCTCAACTCTCTTATTTTTGCTCGA 59.879 40.000 0.00 0.00 0.00 4.04
4214 4975 6.467723 TCAACTCTCTTATTTTTGCTCGAC 57.532 37.500 0.00 0.00 0.00 4.20
4215 4976 5.989168 TCAACTCTCTTATTTTTGCTCGACA 59.011 36.000 0.00 0.00 0.00 4.35
4216 4977 5.847670 ACTCTCTTATTTTTGCTCGACAC 57.152 39.130 0.00 0.00 0.00 3.67
4217 4978 4.386049 ACTCTCTTATTTTTGCTCGACACG 59.614 41.667 0.00 0.00 0.00 4.49
4218 4979 3.678072 TCTCTTATTTTTGCTCGACACGG 59.322 43.478 0.00 0.00 0.00 4.94
4219 4980 2.739913 TCTTATTTTTGCTCGACACGGG 59.260 45.455 0.00 0.00 0.00 5.28
4226 4987 2.432628 CTCGACACGGGCCACTTC 60.433 66.667 4.39 0.00 0.00 3.01
4227 4988 2.915659 TCGACACGGGCCACTTCT 60.916 61.111 4.39 0.00 0.00 2.85
4228 4989 2.030562 CGACACGGGCCACTTCTT 59.969 61.111 4.39 0.00 0.00 2.52
4229 4990 2.317609 CGACACGGGCCACTTCTTG 61.318 63.158 4.39 0.00 0.00 3.02
4230 4991 1.070786 GACACGGGCCACTTCTTGA 59.929 57.895 4.39 0.00 0.00 3.02
4231 4992 0.534203 GACACGGGCCACTTCTTGAA 60.534 55.000 4.39 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 91 3.646735 GAGAAAAACGGGCGAGCGC 62.647 63.158 6.27 6.27 41.06 5.92
91 92 1.956620 GAGAGAAAAACGGGCGAGCG 61.957 60.000 0.00 0.00 0.00 5.03
92 93 1.636570 GGAGAGAAAAACGGGCGAGC 61.637 60.000 0.00 0.00 0.00 5.03
93 94 1.352156 CGGAGAGAAAAACGGGCGAG 61.352 60.000 0.00 0.00 0.00 5.03
94 95 1.373748 CGGAGAGAAAAACGGGCGA 60.374 57.895 0.00 0.00 0.00 5.54
95 96 2.388232 CCGGAGAGAAAAACGGGCG 61.388 63.158 0.00 0.00 42.48 6.13
96 97 0.604511 TTCCGGAGAGAAAAACGGGC 60.605 55.000 3.34 0.00 45.97 6.13
97 98 1.439679 CTTCCGGAGAGAAAAACGGG 58.560 55.000 3.34 0.00 45.97 5.28
99 100 2.067013 GTCCTTCCGGAGAGAAAAACG 58.933 52.381 3.34 0.00 40.84 3.60
100 101 2.424557 GGTCCTTCCGGAGAGAAAAAC 58.575 52.381 3.34 0.00 40.84 2.43
101 102 2.853235 GGTCCTTCCGGAGAGAAAAA 57.147 50.000 3.34 0.00 40.84 1.94
147 163 6.371548 GCAGATATTTATTCAGGCCATTACGA 59.628 38.462 5.01 0.00 0.00 3.43
154 170 3.507622 GGTGGCAGATATTTATTCAGGCC 59.492 47.826 0.00 0.00 40.51 5.19
155 171 4.022849 GTGGTGGCAGATATTTATTCAGGC 60.023 45.833 0.00 0.00 0.00 4.85
157 173 7.220030 AGTAGTGGTGGCAGATATTTATTCAG 58.780 38.462 0.00 0.00 0.00 3.02
182 198 2.290008 TGGACTTTTTGCTGATAGGCGA 60.290 45.455 0.00 0.00 34.52 5.54
224 240 0.169672 CTTTGATTGCGGGACAGCTG 59.830 55.000 13.48 13.48 38.13 4.24
255 271 1.735920 CGCAGTGAGTGGAGTGCTC 60.736 63.158 0.00 0.00 39.72 4.26
256 272 1.539560 ATCGCAGTGAGTGGAGTGCT 61.540 55.000 0.00 0.00 39.72 4.40
257 273 0.671781 AATCGCAGTGAGTGGAGTGC 60.672 55.000 0.00 0.00 38.69 4.40
258 274 2.654749 TAATCGCAGTGAGTGGAGTG 57.345 50.000 0.00 0.00 0.00 3.51
259 275 3.525537 CATTAATCGCAGTGAGTGGAGT 58.474 45.455 0.00 0.00 0.00 3.85
260 276 2.868583 CCATTAATCGCAGTGAGTGGAG 59.131 50.000 0.00 0.00 0.00 3.86
261 277 2.236146 ACCATTAATCGCAGTGAGTGGA 59.764 45.455 7.33 0.00 0.00 4.02
262 278 2.632377 ACCATTAATCGCAGTGAGTGG 58.368 47.619 0.00 0.00 0.00 4.00
263 279 4.083324 ACAAACCATTAATCGCAGTGAGTG 60.083 41.667 0.00 0.00 0.00 3.51
264 280 4.072131 ACAAACCATTAATCGCAGTGAGT 58.928 39.130 0.00 0.00 0.00 3.41
265 281 4.685169 ACAAACCATTAATCGCAGTGAG 57.315 40.909 0.00 0.00 0.00 3.51
321 337 4.373116 AACGGCCGTGATCGCTGT 62.373 61.111 34.95 10.92 35.49 4.40
323 339 2.852495 AATCAACGGCCGTGATCGCT 62.852 55.000 34.95 17.57 35.54 4.93
370 386 4.458989 GTGTCATAAACAATCCTTGCTGGA 59.541 41.667 1.70 1.70 40.31 3.86
371 387 4.460382 AGTGTCATAAACAATCCTTGCTGG 59.540 41.667 0.00 0.00 40.31 4.85
406 883 6.370166 GCTATCTACTTATCACATTTGAGCCC 59.630 42.308 0.00 0.00 34.35 5.19
420 897 2.033801 GGTCGTTGCCGCTATCTACTTA 59.966 50.000 0.00 0.00 0.00 2.24
421 898 1.202382 GGTCGTTGCCGCTATCTACTT 60.202 52.381 0.00 0.00 0.00 2.24
422 899 0.384669 GGTCGTTGCCGCTATCTACT 59.615 55.000 0.00 0.00 0.00 2.57
423 900 0.384669 AGGTCGTTGCCGCTATCTAC 59.615 55.000 0.00 0.00 0.00 2.59
482 959 1.179174 GGTTTTCTGACAGGTGGGGC 61.179 60.000 1.81 0.00 0.00 5.80
483 960 0.184933 TGGTTTTCTGACAGGTGGGG 59.815 55.000 1.81 0.00 0.00 4.96
497 974 3.377172 CGTCTTCTGGAGTTTGTTGGTTT 59.623 43.478 0.00 0.00 0.00 3.27
508 985 2.125912 CCGGTGCGTCTTCTGGAG 60.126 66.667 0.00 0.00 32.26 3.86
539 1016 0.178921 TGACTTGTCTCCTCCTGCCT 60.179 55.000 2.35 0.00 0.00 4.75
542 1019 2.104792 TGGTTTGACTTGTCTCCTCCTG 59.895 50.000 2.35 0.00 0.00 3.86
543 1020 2.408565 TGGTTTGACTTGTCTCCTCCT 58.591 47.619 2.35 0.00 0.00 3.69
545 1022 3.339141 GGATGGTTTGACTTGTCTCCTC 58.661 50.000 2.35 3.31 0.00 3.71
546 1023 2.289694 CGGATGGTTTGACTTGTCTCCT 60.290 50.000 2.35 0.00 0.00 3.69
547 1024 2.076863 CGGATGGTTTGACTTGTCTCC 58.923 52.381 2.35 3.56 0.00 3.71
548 1025 2.737252 GACGGATGGTTTGACTTGTCTC 59.263 50.000 2.35 0.00 0.00 3.36
551 1029 1.876416 CGGACGGATGGTTTGACTTGT 60.876 52.381 0.00 0.00 0.00 3.16
555 1033 1.017701 GGACGGACGGATGGTTTGAC 61.018 60.000 0.00 0.00 0.00 3.18
556 1034 1.294138 GGACGGACGGATGGTTTGA 59.706 57.895 0.00 0.00 0.00 2.69
558 1039 0.107848 GATGGACGGACGGATGGTTT 60.108 55.000 0.00 0.00 0.00 3.27
560 1041 2.432300 GGATGGACGGACGGATGGT 61.432 63.158 0.00 0.00 0.00 3.55
567 1048 1.269621 CGTAGGATTGGATGGACGGAC 60.270 57.143 0.00 0.00 0.00 4.79
621 1102 4.451150 TGATGGCGAGTGGCGGTC 62.451 66.667 0.00 0.00 44.92 4.79
622 1103 4.760047 GTGATGGCGAGTGGCGGT 62.760 66.667 0.00 0.00 44.92 5.68
625 1106 4.408821 TGGGTGATGGCGAGTGGC 62.409 66.667 0.00 0.00 42.51 5.01
895 1380 4.342772 GGAACGAACGAATGAATGAATGG 58.657 43.478 0.14 0.00 0.00 3.16
896 1381 4.342772 GGGAACGAACGAATGAATGAATG 58.657 43.478 0.14 0.00 0.00 2.67
897 1382 4.616181 GGGAACGAACGAATGAATGAAT 57.384 40.909 0.14 0.00 0.00 2.57
919 1404 2.101380 GTCGCTGCTCGTCTCTCC 59.899 66.667 0.00 0.00 39.67 3.71
931 1416 1.820481 GCTCCTCCTAGTCGTCGCT 60.820 63.158 0.00 0.00 0.00 4.93
971 1469 7.175990 TCCTTGACAACCAACTAAAATATCCAC 59.824 37.037 0.00 0.00 0.00 4.02
972 1470 7.235079 TCCTTGACAACCAACTAAAATATCCA 58.765 34.615 0.00 0.00 0.00 3.41
973 1471 7.148069 CCTCCTTGACAACCAACTAAAATATCC 60.148 40.741 0.00 0.00 0.00 2.59
974 1472 7.610305 TCCTCCTTGACAACCAACTAAAATATC 59.390 37.037 0.00 0.00 0.00 1.63
975 1473 7.466804 TCCTCCTTGACAACCAACTAAAATAT 58.533 34.615 0.00 0.00 0.00 1.28
976 1474 6.843752 TCCTCCTTGACAACCAACTAAAATA 58.156 36.000 0.00 0.00 0.00 1.40
977 1475 5.701224 TCCTCCTTGACAACCAACTAAAAT 58.299 37.500 0.00 0.00 0.00 1.82
978 1476 5.118729 TCCTCCTTGACAACCAACTAAAA 57.881 39.130 0.00 0.00 0.00 1.52
979 1477 4.781775 TCCTCCTTGACAACCAACTAAA 57.218 40.909 0.00 0.00 0.00 1.85
980 1478 4.104102 ACATCCTCCTTGACAACCAACTAA 59.896 41.667 0.00 0.00 0.00 2.24
989 1496 1.630369 CCCTCAACATCCTCCTTGACA 59.370 52.381 0.00 0.00 0.00 3.58
992 1499 0.622665 AGCCCTCAACATCCTCCTTG 59.377 55.000 0.00 0.00 0.00 3.61
1265 1772 1.152271 AGGGGAAGTGGAAGGAGAAGA 59.848 52.381 0.00 0.00 0.00 2.87
1267 1774 1.985895 GAAGGGGAAGTGGAAGGAGAA 59.014 52.381 0.00 0.00 0.00 2.87
1268 1775 1.657804 GAAGGGGAAGTGGAAGGAGA 58.342 55.000 0.00 0.00 0.00 3.71
1269 1776 0.621082 GGAAGGGGAAGTGGAAGGAG 59.379 60.000 0.00 0.00 0.00 3.69
1270 1777 0.845102 GGGAAGGGGAAGTGGAAGGA 60.845 60.000 0.00 0.00 0.00 3.36
1271 1778 1.691823 GGGAAGGGGAAGTGGAAGG 59.308 63.158 0.00 0.00 0.00 3.46
1276 1786 1.691823 GGAAGGGGAAGGGGAAGTG 59.308 63.158 0.00 0.00 0.00 3.16
1277 1787 1.923909 CGGAAGGGGAAGGGGAAGT 60.924 63.158 0.00 0.00 0.00 3.01
1302 1812 0.458716 GAGAAGCCGGGAGAAACTCG 60.459 60.000 2.18 0.00 42.84 4.18
1316 1826 8.470002 TCAACCATATATCACCATATCGAGAAG 58.530 37.037 0.00 0.00 0.00 2.85
1323 1833 5.118990 GCGCTCAACCATATATCACCATAT 58.881 41.667 0.00 0.00 0.00 1.78
1330 1840 0.366871 CGCGCGCTCAACCATATATC 59.633 55.000 30.48 0.00 0.00 1.63
1331 1841 1.014044 CCGCGCGCTCAACCATATAT 61.014 55.000 30.48 0.00 0.00 0.86
1332 1842 1.663388 CCGCGCGCTCAACCATATA 60.663 57.895 30.48 0.00 0.00 0.86
1333 1843 2.967076 CCGCGCGCTCAACCATAT 60.967 61.111 30.48 0.00 0.00 1.78
1365 1875 1.880894 CCTGCCGAGACAAGACGTA 59.119 57.895 0.00 0.00 0.00 3.57
1723 2238 1.695597 CCCCTTGATCCTCCAGGCT 60.696 63.158 0.00 0.00 34.44 4.58
1759 2274 1.221414 GGTAGCATCCTCATCAACGC 58.779 55.000 0.00 0.00 0.00 4.84
1762 2277 3.777106 GGATGGTAGCATCCTCATCAA 57.223 47.619 36.04 0.00 45.78 2.57
1831 2351 3.684305 CGCAGGTGTTATCAACAATCAGA 59.316 43.478 0.00 0.00 44.16 3.27
1861 2381 0.185901 AGGCAAACTGGCAGAGGAAA 59.814 50.000 23.66 0.00 46.46 3.13
1930 2450 7.636359 GTGATGCAATTTCGTTACAGTTATCTC 59.364 37.037 0.00 0.00 0.00 2.75
1932 2452 7.240674 TGTGATGCAATTTCGTTACAGTTATC 58.759 34.615 0.00 0.00 0.00 1.75
1934 2454 6.425417 TCTGTGATGCAATTTCGTTACAGTTA 59.575 34.615 17.42 2.21 39.31 2.24
1935 2455 5.238432 TCTGTGATGCAATTTCGTTACAGTT 59.762 36.000 17.42 0.00 39.31 3.16
1936 2456 4.754618 TCTGTGATGCAATTTCGTTACAGT 59.245 37.500 17.42 0.00 39.31 3.55
1986 2515 3.904339 GGATAGGGTTCTAATGGCTCTGA 59.096 47.826 0.00 0.00 0.00 3.27
2000 2529 6.677076 ACATTAGTTAAGTTCCAGGATAGGGT 59.323 38.462 0.00 0.00 0.00 4.34
2003 2533 9.838339 AATGACATTAGTTAAGTTCCAGGATAG 57.162 33.333 0.00 0.00 0.00 2.08
2111 2683 3.130734 AGCCTACTTCATCTAACCCCA 57.869 47.619 0.00 0.00 0.00 4.96
2131 2703 7.291416 TGGGCTAGTTACCATTTCTGACATATA 59.709 37.037 0.00 0.00 0.00 0.86
2187 2759 5.738619 TCTTCAGTATGGTCAGCAAGTTA 57.261 39.130 0.00 0.00 36.16 2.24
2250 2824 3.018856 CACCAGGATTGCTGCAATAGAA 58.981 45.455 26.32 0.00 33.90 2.10
2285 2859 6.325028 CAGGAATCCAGGACTGAGAATACTAA 59.675 42.308 0.61 0.00 32.86 2.24
2292 2866 1.623557 CCCAGGAATCCAGGACTGAGA 60.624 57.143 12.76 0.00 31.24 3.27
2329 2907 5.003804 GGATACGTTATGATCCCAGCAATT 58.996 41.667 4.01 0.00 36.39 2.32
2346 2924 0.689745 TCCCAGGAACCCAGGATACG 60.690 60.000 0.00 0.00 46.39 3.06
2372 2976 7.908917 ACTATGATACCAGGAATCCAGGATAAT 59.091 37.037 18.16 7.58 34.08 1.28
2373 2977 7.256399 ACTATGATACCAGGAATCCAGGATAA 58.744 38.462 18.16 2.90 34.08 1.75
2480 3092 7.123247 ACAAAAAGGCAAGCATAGACTAATCAT 59.877 33.333 0.00 0.00 0.00 2.45
2488 3100 4.766373 TGATGACAAAAAGGCAAGCATAGA 59.234 37.500 0.00 0.00 39.98 1.98
2535 3149 2.478292 TCATAGGTTCTCCCAACTCCC 58.522 52.381 0.00 0.00 34.66 4.30
2542 3156 7.067496 TGAACTTCATATCATAGGTTCTCCC 57.933 40.000 0.00 0.00 35.52 4.30
2668 3282 3.352611 AATGGGTCCAGGCTATACTCT 57.647 47.619 0.00 0.00 0.00 3.24
2892 3509 1.656652 CCCCACACGAGAAATAGCAG 58.343 55.000 0.00 0.00 0.00 4.24
2900 3517 1.527380 GCAAAACCCCCACACGAGA 60.527 57.895 0.00 0.00 0.00 4.04
2902 3519 1.527380 GAGCAAAACCCCCACACGA 60.527 57.895 0.00 0.00 0.00 4.35
2903 3520 2.561037 GGAGCAAAACCCCCACACG 61.561 63.158 0.00 0.00 0.00 4.49
2940 3560 2.420722 TCGGCGTTATTTCATTTGGTCC 59.579 45.455 6.85 0.00 0.00 4.46
2960 3580 3.658757 TGCCCTGCACAAAATAACTTC 57.341 42.857 0.00 0.00 31.71 3.01
2967 3597 1.336131 TTGCTATGCCCTGCACAAAA 58.664 45.000 0.00 0.00 43.04 2.44
2979 3609 0.447801 GCACCAGTCGGTTTGCTATG 59.552 55.000 0.00 0.00 46.31 2.23
3271 3954 5.454755 CCGTTTTCTACCACCCTGATCATAT 60.455 44.000 0.00 0.00 0.00 1.78
3272 3955 4.141801 CCGTTTTCTACCACCCTGATCATA 60.142 45.833 0.00 0.00 0.00 2.15
3273 3956 3.370527 CCGTTTTCTACCACCCTGATCAT 60.371 47.826 0.00 0.00 0.00 2.45
3274 3957 2.027561 CCGTTTTCTACCACCCTGATCA 60.028 50.000 0.00 0.00 0.00 2.92
3275 3958 2.027469 ACCGTTTTCTACCACCCTGATC 60.027 50.000 0.00 0.00 0.00 2.92
3276 3959 1.982958 ACCGTTTTCTACCACCCTGAT 59.017 47.619 0.00 0.00 0.00 2.90
3277 3960 1.071071 CACCGTTTTCTACCACCCTGA 59.929 52.381 0.00 0.00 0.00 3.86
3278 3961 1.519408 CACCGTTTTCTACCACCCTG 58.481 55.000 0.00 0.00 0.00 4.45
3279 3962 0.399075 CCACCGTTTTCTACCACCCT 59.601 55.000 0.00 0.00 0.00 4.34
3280 3963 0.109153 ACCACCGTTTTCTACCACCC 59.891 55.000 0.00 0.00 0.00 4.61
3281 3964 2.613725 CCTACCACCGTTTTCTACCACC 60.614 54.545 0.00 0.00 0.00 4.61
3282 3965 2.613725 CCCTACCACCGTTTTCTACCAC 60.614 54.545 0.00 0.00 0.00 4.16
3287 3970 1.816572 GCAACCCTACCACCGTTTTCT 60.817 52.381 0.00 0.00 0.00 2.52
3289 3972 0.106619 TGCAACCCTACCACCGTTTT 60.107 50.000 0.00 0.00 0.00 2.43
3524 4211 6.405842 GGGTGCCCTTTCTAAATTTCAGTATG 60.406 42.308 0.00 0.00 37.54 2.39
3561 4248 1.667724 CCAGCACGGATGAATTCAGAC 59.332 52.381 14.54 10.13 36.56 3.51
3563 4250 1.399440 CACCAGCACGGATGAATTCAG 59.601 52.381 14.54 2.96 38.63 3.02
3728 4428 1.066143 CGGATAAAGAGCCACACCACT 60.066 52.381 0.00 0.00 0.00 4.00
3794 4496 8.006590 CAGACTTCTCAATAAAGAAACAACTCG 58.993 37.037 0.00 0.00 34.95 4.18
3869 4629 1.481240 CGTCACTGTCACTGTGTCAG 58.519 55.000 26.07 26.07 39.01 3.51
3876 4636 0.037882 CTGATGGCGTCACTGTCACT 60.038 55.000 5.03 0.00 32.22 3.41
3886 4646 1.304381 ATTTGGTGGCTGATGGCGT 60.304 52.632 0.00 0.00 42.94 5.68
3888 4648 0.174162 GACATTTGGTGGCTGATGGC 59.826 55.000 0.00 0.00 40.90 4.40
3991 4751 1.202758 ACCTCACTGATCCGCACAAAA 60.203 47.619 0.00 0.00 0.00 2.44
4015 4775 3.672295 CTCCTGGGCTGGAACGAGC 62.672 68.421 0.00 0.35 35.43 5.03
4040 4800 5.181748 AGAAGATTCTGAATTCCACTTCCG 58.818 41.667 18.44 0.00 35.89 4.30
4054 4814 7.201839 GGGAATCAACTACGAGTAGAAGATTCT 60.202 40.741 30.97 17.59 44.41 2.40
4068 4828 4.275936 CCGATTTGGATGGGAATCAACTAC 59.724 45.833 0.00 0.00 42.00 2.73
4114 4875 1.645919 ACTAGGTGCAAATGGGGGATT 59.354 47.619 0.00 0.00 0.00 3.01
4160 4921 4.488770 TGGGGCTGAACTCCTTAATTTTT 58.511 39.130 0.00 0.00 0.00 1.94
4161 4922 4.126520 TGGGGCTGAACTCCTTAATTTT 57.873 40.909 0.00 0.00 0.00 1.82
4162 4923 3.825908 TGGGGCTGAACTCCTTAATTT 57.174 42.857 0.00 0.00 0.00 1.82
4163 4924 3.701664 CTTGGGGCTGAACTCCTTAATT 58.298 45.455 0.00 0.00 0.00 1.40
4164 4925 2.621668 GCTTGGGGCTGAACTCCTTAAT 60.622 50.000 0.00 0.00 38.06 1.40
4165 4926 1.271926 GCTTGGGGCTGAACTCCTTAA 60.272 52.381 0.00 0.00 38.06 1.85
4166 4927 0.328258 GCTTGGGGCTGAACTCCTTA 59.672 55.000 0.00 0.00 38.06 2.69
4167 4928 1.075659 GCTTGGGGCTGAACTCCTT 59.924 57.895 0.00 0.00 38.06 3.36
4168 4929 2.759795 GCTTGGGGCTGAACTCCT 59.240 61.111 0.00 0.00 38.06 3.69
4169 4930 2.361737 GGCTTGGGGCTGAACTCC 60.362 66.667 0.00 0.00 41.46 3.85
4177 4938 4.722700 TTGAGCTCGGCTTGGGGC 62.723 66.667 9.64 0.00 39.88 5.80
4178 4939 2.747855 GTTGAGCTCGGCTTGGGG 60.748 66.667 9.64 0.00 39.88 4.96
4179 4940 1.743252 GAGTTGAGCTCGGCTTGGG 60.743 63.158 9.64 0.00 39.88 4.12
4180 4941 3.882025 GAGTTGAGCTCGGCTTGG 58.118 61.111 9.64 0.00 39.88 3.61
4187 4948 6.493449 AGCAAAAATAAGAGAGTTGAGCTC 57.507 37.500 6.82 6.82 44.45 4.09
4188 4949 5.121454 CGAGCAAAAATAAGAGAGTTGAGCT 59.879 40.000 0.00 0.00 31.27 4.09
4189 4950 5.120830 TCGAGCAAAAATAAGAGAGTTGAGC 59.879 40.000 0.00 0.00 0.00 4.26
4190 4951 6.146184 TGTCGAGCAAAAATAAGAGAGTTGAG 59.854 38.462 0.00 0.00 0.00 3.02
4191 4952 5.989168 TGTCGAGCAAAAATAAGAGAGTTGA 59.011 36.000 0.00 0.00 0.00 3.18
4192 4953 6.074005 GTGTCGAGCAAAAATAAGAGAGTTG 58.926 40.000 0.00 0.00 0.00 3.16
4193 4954 5.107453 CGTGTCGAGCAAAAATAAGAGAGTT 60.107 40.000 0.00 0.00 0.00 3.01
4194 4955 4.386049 CGTGTCGAGCAAAAATAAGAGAGT 59.614 41.667 0.00 0.00 0.00 3.24
4195 4956 4.201628 CCGTGTCGAGCAAAAATAAGAGAG 60.202 45.833 0.00 0.00 0.00 3.20
4196 4957 3.678072 CCGTGTCGAGCAAAAATAAGAGA 59.322 43.478 0.00 0.00 0.00 3.10
4197 4958 3.181520 CCCGTGTCGAGCAAAAATAAGAG 60.182 47.826 0.00 0.00 0.00 2.85
4198 4959 2.739913 CCCGTGTCGAGCAAAAATAAGA 59.260 45.455 0.00 0.00 0.00 2.10
4199 4960 2.727916 GCCCGTGTCGAGCAAAAATAAG 60.728 50.000 0.00 0.00 0.00 1.73
4200 4961 1.198178 GCCCGTGTCGAGCAAAAATAA 59.802 47.619 0.00 0.00 0.00 1.40
4201 4962 0.800012 GCCCGTGTCGAGCAAAAATA 59.200 50.000 0.00 0.00 0.00 1.40
4202 4963 1.579429 GCCCGTGTCGAGCAAAAAT 59.421 52.632 0.00 0.00 0.00 1.82
4203 4964 2.548295 GGCCCGTGTCGAGCAAAAA 61.548 57.895 0.00 0.00 0.00 1.94
4204 4965 2.975799 GGCCCGTGTCGAGCAAAA 60.976 61.111 0.00 0.00 0.00 2.44
4205 4966 4.243008 TGGCCCGTGTCGAGCAAA 62.243 61.111 0.00 0.00 0.00 3.68
4206 4967 4.980805 GTGGCCCGTGTCGAGCAA 62.981 66.667 0.00 0.00 0.00 3.91
4208 4969 4.681978 AAGTGGCCCGTGTCGAGC 62.682 66.667 0.00 0.00 0.00 5.03
4209 4970 2.432628 GAAGTGGCCCGTGTCGAG 60.433 66.667 0.00 0.00 0.00 4.04
4210 4971 2.504274 AAGAAGTGGCCCGTGTCGA 61.504 57.895 0.00 0.00 0.00 4.20
4211 4972 2.030562 AAGAAGTGGCCCGTGTCG 59.969 61.111 0.00 0.00 0.00 4.35
4212 4973 0.534203 TTCAAGAAGTGGCCCGTGTC 60.534 55.000 0.00 0.00 0.00 3.67
4213 4974 1.529796 TTCAAGAAGTGGCCCGTGT 59.470 52.632 0.00 0.00 0.00 4.49
4214 4975 4.473643 TTCAAGAAGTGGCCCGTG 57.526 55.556 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.