Multiple sequence alignment - TraesCS2A01G472900

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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 TraesCS2A01G472900 chr2A 100.000 4141 0 0 1 4141 714230099 714225959 0.000000e+00 7648.0
1 TraesCS2A01G472900 chr2A 88.889 63 5 2 3490 3550 10409002 10408940 4.440000e-10 76.8
2 TraesCS2A01G472900 chr2D 91.293 2676 150 35 1316 3965 576206327 576203709 0.000000e+00 3574.0
3 TraesCS2A01G472900 chr2D 89.446 578 48 6 798 1374 576206768 576206203 0.000000e+00 717.0
4 TraesCS2A01G472900 chr2D 92.739 303 21 1 6 307 576214994 576214692 1.770000e-118 436.0
5 TraesCS2A01G472900 chr2D 89.241 316 27 5 295 606 576207288 576206976 5.020000e-104 388.0
6 TraesCS2A01G472900 chr2D 91.064 235 18 2 618 849 576206992 576206758 8.640000e-82 315.0
7 TraesCS2A01G472900 chr2D 94.709 189 8 2 3954 4141 576202358 576202171 4.050000e-75 292.0
8 TraesCS2A01G472900 chr2B 90.998 2044 135 22 1316 3344 692176036 692174027 0.000000e+00 2710.0
9 TraesCS2A01G472900 chr2B 89.815 756 57 10 619 1372 692176651 692175914 0.000000e+00 952.0
10 TraesCS2A01G472900 chr2B 86.634 606 68 9 6 606 692177233 692176636 0.000000e+00 658.0
11 TraesCS2A01G472900 chr2B 89.899 99 10 0 4043 4141 692173042 692172944 1.210000e-25 128.0
12 TraesCS2A01G472900 chr1B 79.535 215 39 5 192 403 666303188 666302976 9.270000e-32 148.0
13 TraesCS2A01G472900 chr5D 77.391 230 44 7 128 354 115028447 115028671 3.360000e-26 130.0
14 TraesCS2A01G472900 chr4A 91.667 72 4 2 3495 3565 632143668 632143598 9.470000e-17 99.0
15 TraesCS2A01G472900 chr4D 79.259 135 26 2 197 330 386483128 386482995 4.410000e-15 93.5
16 TraesCS2A01G472900 chr5B 79.070 129 23 3 204 330 338655039 338654913 7.380000e-13 86.1
17 TraesCS2A01G472900 chr4B 94.643 56 2 1 3494 3549 646867507 646867453 7.380000e-13 86.1
18 TraesCS2A01G472900 chr4B 91.667 60 4 1 3491 3549 459067615 459067674 9.540000e-12 82.4
19 TraesCS2A01G472900 chr7D 94.444 54 3 0 3496 3549 180223903 180223956 2.650000e-12 84.2
20 TraesCS2A01G472900 chr6D 92.857 56 3 1 3494 3549 17267755 17267809 3.430000e-11 80.5
21 TraesCS2A01G472900 chr6A 89.231 65 6 1 3486 3549 378192602 378192666 3.430000e-11 80.5
22 TraesCS2A01G472900 chr3B 87.692 65 7 1 3486 3549 605450242 605450306 1.600000e-09 75.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G472900 chr2A 714225959 714230099 4140 True 7648.0 7648 100.0000 1 4141 1 chr2A.!!$R2 4140
1 TraesCS2A01G472900 chr2D 576202171 576207288 5117 True 1057.2 3574 91.1506 295 4141 5 chr2D.!!$R2 3846
2 TraesCS2A01G472900 chr2B 692172944 692177233 4289 True 1112.0 2710 89.3365 6 4141 4 chr2B.!!$R1 4135

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
918 967 0.033504 CTGCACTTACCCACGACACT 59.966 55.0 0.00 0.0 0.0 3.55 F
1342 1391 0.036164 TTCCATGGTACGCTTGCAGT 59.964 50.0 12.58 0.0 0.0 4.40 F
1349 1398 0.245539 GTACGCTTGCAGTACCCTCA 59.754 55.0 12.90 0.0 38.7 3.86 F
2008 2064 0.396139 AGCATGCATCGAAACCCCAT 60.396 50.0 21.98 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2172 2231 0.545071 CCAGAATTTGGGCCTTGGGT 60.545 55.000 4.53 0.0 43.75 4.51 R
2665 2738 1.002087 TCCTTTTCCTCTTGCTCGGTC 59.998 52.381 0.00 0.0 0.00 4.79 R
2896 2969 1.970640 TGAGTTCTCTTAGCTGCACCA 59.029 47.619 1.02 0.0 0.00 4.17 R
3624 3957 0.537653 AAGAACCTCTTAGCTCGGCC 59.462 55.000 0.00 0.0 34.42 6.13 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
29 30 2.185350 CAGCTCGGGTAGTGGCTG 59.815 66.667 0.00 0.00 44.45 4.85
99 100 4.171103 GGTACGGCGGGCATCCTT 62.171 66.667 13.24 0.00 0.00 3.36
100 101 2.895372 GTACGGCGGGCATCCTTG 60.895 66.667 13.24 0.00 0.00 3.61
112 113 2.422803 GGCATCCTTGTGGCCTATTGTA 60.423 50.000 3.32 0.00 44.32 2.41
117 118 2.878406 CCTTGTGGCCTATTGTATTCCG 59.122 50.000 3.32 0.00 0.00 4.30
118 119 1.961793 TGTGGCCTATTGTATTCCGC 58.038 50.000 3.32 0.00 0.00 5.54
121 122 0.953960 GGCCTATTGTATTCCGCCCG 60.954 60.000 0.00 0.00 0.00 6.13
141 142 1.377856 GAGGTGAAGAGGGCTTGCC 60.378 63.158 2.49 2.49 33.61 4.52
142 143 2.361737 GGTGAAGAGGGCTTGCCC 60.362 66.667 22.29 22.29 33.61 5.36
163 164 2.168496 GGGTGAAAACCCTCTTTAGCC 58.832 52.381 6.68 0.00 46.39 3.93
168 169 0.039764 AAACCCTCTTTAGCCCTGCC 59.960 55.000 0.00 0.00 0.00 4.85
213 214 1.341606 GCGTCGTCTCCTTCTTGAAG 58.658 55.000 3.55 3.55 0.00 3.02
215 216 1.715993 GTCGTCTCCTTCTTGAAGGC 58.284 55.000 21.16 9.27 39.80 4.35
216 217 1.000955 GTCGTCTCCTTCTTGAAGGCA 59.999 52.381 21.16 9.83 39.80 4.75
218 219 2.093973 TCGTCTCCTTCTTGAAGGCATC 60.094 50.000 21.16 13.16 39.80 3.91
244 245 1.066787 GGTTCCTCTTCGTCCTCCTTG 60.067 57.143 0.00 0.00 0.00 3.61
251 252 1.001406 CTTCGTCCTCCTTGTTGCTCT 59.999 52.381 0.00 0.00 0.00 4.09
275 277 2.483889 GGAAACCTTGATCCCTAGAGCG 60.484 54.545 0.00 0.00 0.00 5.03
362 364 1.468520 TGCATGGCTTCTTAACTTCGC 59.531 47.619 0.00 0.00 0.00 4.70
374 376 0.249489 AACTTCGCTGTGACTCGCTT 60.249 50.000 0.00 0.00 0.00 4.68
385 387 1.303888 ACTCGCTTACGGTGGAGGA 60.304 57.895 0.00 0.00 40.63 3.71
456 458 1.075601 TTGGGGGTCATGAAGCTTCT 58.924 50.000 26.09 9.99 0.00 2.85
457 459 1.075601 TGGGGGTCATGAAGCTTCTT 58.924 50.000 26.09 17.82 0.00 2.52
458 460 1.004745 TGGGGGTCATGAAGCTTCTTC 59.995 52.381 26.09 13.38 0.00 2.87
459 461 1.373570 GGGGTCATGAAGCTTCTTCG 58.626 55.000 26.09 14.57 0.00 3.79
462 464 2.354203 GGGTCATGAAGCTTCTTCGTCT 60.354 50.000 26.09 2.72 0.00 4.18
496 499 0.822944 TTGGGTGCATGTGTGGTCTG 60.823 55.000 0.00 0.00 0.00 3.51
498 501 0.823356 GGGTGCATGTGTGGTCTGTT 60.823 55.000 0.00 0.00 0.00 3.16
502 505 0.239347 GCATGTGTGGTCTGTTGAGC 59.761 55.000 0.00 0.00 40.79 4.26
513 516 1.064758 TCTGTTGAGCTGTTGGGTGTT 60.065 47.619 0.00 0.00 0.00 3.32
545 548 5.163513 GTTGGTTCGATGATGATTGCTTTT 58.836 37.500 0.00 0.00 0.00 2.27
582 587 5.975693 AACCCTTTTTCGAAATAGATGCA 57.024 34.783 24.41 1.32 0.00 3.96
589 594 4.857871 TTCGAAATAGATGCAACCGAAG 57.142 40.909 0.00 0.00 32.04 3.79
590 595 4.118093 TCGAAATAGATGCAACCGAAGA 57.882 40.909 0.00 0.00 0.00 2.87
591 596 4.693283 TCGAAATAGATGCAACCGAAGAT 58.307 39.130 0.00 0.00 0.00 2.40
592 597 5.838529 TCGAAATAGATGCAACCGAAGATA 58.161 37.500 0.00 0.00 0.00 1.98
593 598 6.277605 TCGAAATAGATGCAACCGAAGATAA 58.722 36.000 0.00 0.00 0.00 1.75
594 599 6.759356 TCGAAATAGATGCAACCGAAGATAAA 59.241 34.615 0.00 0.00 0.00 1.40
595 600 7.279090 TCGAAATAGATGCAACCGAAGATAAAA 59.721 33.333 0.00 0.00 0.00 1.52
596 601 7.373441 CGAAATAGATGCAACCGAAGATAAAAC 59.627 37.037 0.00 0.00 0.00 2.43
597 602 7.624360 AATAGATGCAACCGAAGATAAAACA 57.376 32.000 0.00 0.00 0.00 2.83
598 603 5.957842 AGATGCAACCGAAGATAAAACAA 57.042 34.783 0.00 0.00 0.00 2.83
599 604 5.942872 AGATGCAACCGAAGATAAAACAAG 58.057 37.500 0.00 0.00 0.00 3.16
600 605 4.497473 TGCAACCGAAGATAAAACAAGG 57.503 40.909 0.00 0.00 0.00 3.61
601 606 3.254657 TGCAACCGAAGATAAAACAAGGG 59.745 43.478 0.00 0.00 0.00 3.95
602 607 3.504520 GCAACCGAAGATAAAACAAGGGA 59.495 43.478 0.00 0.00 0.00 4.20
603 608 4.379499 GCAACCGAAGATAAAACAAGGGAG 60.379 45.833 0.00 0.00 0.00 4.30
604 609 4.635699 ACCGAAGATAAAACAAGGGAGT 57.364 40.909 0.00 0.00 0.00 3.85
605 610 4.981812 ACCGAAGATAAAACAAGGGAGTT 58.018 39.130 0.00 0.00 0.00 3.01
606 611 5.382616 ACCGAAGATAAAACAAGGGAGTTT 58.617 37.500 0.00 0.00 43.13 2.66
608 613 6.322969 ACCGAAGATAAAACAAGGGAGTTTTT 59.677 34.615 9.69 0.00 46.39 1.94
631 636 3.905493 TGGGGTGATAAAACAAGGGAA 57.095 42.857 0.00 0.00 0.00 3.97
654 659 0.248012 TCCGCATAATCACCACGTGT 59.752 50.000 15.65 0.00 34.79 4.49
709 714 0.108520 TACGGGCCTCTAAAACTGCG 60.109 55.000 0.84 0.00 0.00 5.18
718 723 3.433615 CCTCTAAAACTGCGGTTTCTCTG 59.566 47.826 23.44 13.77 43.90 3.35
727 733 1.269723 GCGGTTTCTCTGGGGAAAAAG 59.730 52.381 0.00 0.00 37.02 2.27
760 768 2.592993 CCCTCTCTTCCAACCGCCA 61.593 63.158 0.00 0.00 0.00 5.69
832 881 1.302192 CCAACCGTCACGTCCCAAT 60.302 57.895 0.00 0.00 0.00 3.16
842 891 2.235402 TCACGTCCCAATTCCTAGAACC 59.765 50.000 0.00 0.00 0.00 3.62
843 892 1.206371 ACGTCCCAATTCCTAGAACCG 59.794 52.381 0.00 0.00 0.00 4.44
844 893 1.664873 GTCCCAATTCCTAGAACCGC 58.335 55.000 0.00 0.00 0.00 5.68
845 894 0.544697 TCCCAATTCCTAGAACCGCC 59.455 55.000 0.00 0.00 0.00 6.13
846 895 0.814010 CCCAATTCCTAGAACCGCCG 60.814 60.000 0.00 0.00 0.00 6.46
847 896 1.436983 CCAATTCCTAGAACCGCCGC 61.437 60.000 0.00 0.00 0.00 6.53
848 897 1.520787 AATTCCTAGAACCGCCGCG 60.521 57.895 5.59 5.59 0.00 6.46
918 967 0.033504 CTGCACTTACCCACGACACT 59.966 55.000 0.00 0.00 0.00 3.55
922 971 0.883833 ACTTACCCACGACACTACCG 59.116 55.000 0.00 0.00 0.00 4.02
989 1038 4.436998 CTCCACCACTCCGGCGAC 62.437 72.222 9.30 0.00 39.03 5.19
1005 1054 1.002624 GACCCGAGTTGCCATGGAA 60.003 57.895 18.40 0.00 0.00 3.53
1118 1167 1.152902 AGCAGCAGCAACAGGTTCA 60.153 52.632 3.17 0.00 45.49 3.18
1120 1169 1.450531 GCAGCAGCAACAGGTTCAGT 61.451 55.000 0.00 0.00 41.58 3.41
1160 1209 2.515901 GGCCTATCCGGTTGCCAT 59.484 61.111 17.30 0.20 43.46 4.40
1199 1248 0.859374 CACGTCGTCTCTGATCAGCG 60.859 60.000 18.36 15.41 0.00 5.18
1200 1249 1.297967 CGTCGTCTCTGATCAGCGG 60.298 63.158 18.36 12.71 0.00 5.52
1211 1260 3.089217 TCAGCGGATGATGGCCCA 61.089 61.111 0.00 0.00 31.12 5.36
1216 1265 1.077501 CGGATGATGGCCCACTTGT 60.078 57.895 0.00 0.00 0.00 3.16
1244 1293 1.011904 CGGCAATGCAACTCGATCG 60.012 57.895 9.36 9.36 0.00 3.69
1322 1371 1.685224 TGGGACATCAACAGGAGCC 59.315 57.895 0.00 0.00 0.00 4.70
1323 1372 0.842030 TGGGACATCAACAGGAGCCT 60.842 55.000 0.00 0.00 0.00 4.58
1324 1373 0.329596 GGGACATCAACAGGAGCCTT 59.670 55.000 0.00 0.00 0.00 4.35
1325 1374 1.680249 GGGACATCAACAGGAGCCTTC 60.680 57.143 0.00 0.00 0.00 3.46
1326 1375 1.680249 GGACATCAACAGGAGCCTTCC 60.680 57.143 0.00 0.00 44.39 3.46
1327 1376 1.003580 GACATCAACAGGAGCCTTCCA 59.996 52.381 0.00 0.00 46.64 3.53
1328 1377 1.637553 ACATCAACAGGAGCCTTCCAT 59.362 47.619 0.00 0.00 46.64 3.41
1329 1378 2.022195 CATCAACAGGAGCCTTCCATG 58.978 52.381 0.00 0.00 46.64 3.66
1330 1379 0.329261 TCAACAGGAGCCTTCCATGG 59.671 55.000 4.97 4.97 46.64 3.66
1331 1380 0.038744 CAACAGGAGCCTTCCATGGT 59.961 55.000 12.58 0.00 46.64 3.55
1332 1381 1.281867 CAACAGGAGCCTTCCATGGTA 59.718 52.381 12.58 0.02 46.64 3.25
1333 1382 0.912486 ACAGGAGCCTTCCATGGTAC 59.088 55.000 12.58 0.00 46.64 3.34
1334 1383 0.179073 CAGGAGCCTTCCATGGTACG 60.179 60.000 12.58 0.84 46.64 3.67
1335 1384 1.523938 GGAGCCTTCCATGGTACGC 60.524 63.158 12.58 11.31 43.45 4.42
1336 1385 1.522569 GAGCCTTCCATGGTACGCT 59.477 57.895 18.04 18.04 0.00 5.07
1337 1386 0.107654 GAGCCTTCCATGGTACGCTT 60.108 55.000 18.72 7.24 0.00 4.68
1338 1387 0.392998 AGCCTTCCATGGTACGCTTG 60.393 55.000 12.58 0.00 0.00 4.01
1339 1388 1.993369 GCCTTCCATGGTACGCTTGC 61.993 60.000 12.58 2.73 0.00 4.01
1340 1389 0.676466 CCTTCCATGGTACGCTTGCA 60.676 55.000 12.58 0.00 0.00 4.08
1341 1390 0.729116 CTTCCATGGTACGCTTGCAG 59.271 55.000 12.58 0.00 0.00 4.41
1342 1391 0.036164 TTCCATGGTACGCTTGCAGT 59.964 50.000 12.58 0.00 0.00 4.40
1343 1392 0.899019 TCCATGGTACGCTTGCAGTA 59.101 50.000 12.58 0.00 0.00 2.74
1344 1393 1.006832 CCATGGTACGCTTGCAGTAC 58.993 55.000 2.57 14.48 42.58 2.73
1348 1397 3.046280 GTACGCTTGCAGTACCCTC 57.954 57.895 12.90 0.00 38.70 4.30
1349 1398 0.245539 GTACGCTTGCAGTACCCTCA 59.754 55.000 12.90 0.00 38.70 3.86
1350 1399 0.970640 TACGCTTGCAGTACCCTCAA 59.029 50.000 0.00 0.00 0.00 3.02
1351 1400 0.602905 ACGCTTGCAGTACCCTCAAC 60.603 55.000 0.00 0.00 0.00 3.18
1352 1401 1.298859 CGCTTGCAGTACCCTCAACC 61.299 60.000 0.00 0.00 0.00 3.77
1353 1402 1.298859 GCTTGCAGTACCCTCAACCG 61.299 60.000 0.00 0.00 0.00 4.44
1354 1403 0.673644 CTTGCAGTACCCTCAACCGG 60.674 60.000 0.00 0.00 0.00 5.28
1355 1404 2.436115 GCAGTACCCTCAACCGGC 60.436 66.667 0.00 0.00 0.00 6.13
1356 1405 2.125673 CAGTACCCTCAACCGGCG 60.126 66.667 0.00 0.00 0.00 6.46
1357 1406 4.078516 AGTACCCTCAACCGGCGC 62.079 66.667 0.00 0.00 0.00 6.53
1383 1432 1.976474 GGCATTCGAACCCCAGCAA 60.976 57.895 0.00 0.00 0.00 3.91
1399 1448 1.103398 GCAAGCGCCTTCCATGGTAT 61.103 55.000 12.58 0.00 0.00 2.73
1406 1455 2.351835 CGCCTTCCATGGTATACTCTCG 60.352 54.545 12.58 2.51 0.00 4.04
1407 1456 2.028930 GCCTTCCATGGTATACTCTCGG 60.029 54.545 12.58 0.00 0.00 4.63
1489 1544 2.345760 CCACTCCATGTTGGCCAGC 61.346 63.158 13.50 13.50 37.47 4.85
1680 1735 2.904011 GTCTCACTGACCTCTACGTG 57.096 55.000 0.00 0.00 39.69 4.49
1708 1763 3.927481 GAAGTGCACCTCCCTGGCC 62.927 68.421 14.63 0.00 40.22 5.36
1811 1866 2.285743 GGAAGGTGGAGAGGGCCT 60.286 66.667 5.25 5.25 0.00 5.19
2006 2062 0.947244 CTAGCATGCATCGAAACCCC 59.053 55.000 21.98 0.00 0.00 4.95
2008 2064 0.396139 AGCATGCATCGAAACCCCAT 60.396 50.000 21.98 0.00 0.00 4.00
2009 2065 0.461135 GCATGCATCGAAACCCCATT 59.539 50.000 14.21 0.00 0.00 3.16
2010 2066 1.134729 GCATGCATCGAAACCCCATTT 60.135 47.619 14.21 0.00 0.00 2.32
2013 2069 4.753233 CATGCATCGAAACCCCATTTAAA 58.247 39.130 0.00 0.00 0.00 1.52
2014 2070 4.873746 TGCATCGAAACCCCATTTAAAA 57.126 36.364 0.00 0.00 0.00 1.52
2017 2073 5.477291 TGCATCGAAACCCCATTTAAAACTA 59.523 36.000 0.00 0.00 0.00 2.24
2018 2074 5.803461 GCATCGAAACCCCATTTAAAACTAC 59.197 40.000 0.00 0.00 0.00 2.73
2019 2075 6.349860 GCATCGAAACCCCATTTAAAACTACT 60.350 38.462 0.00 0.00 0.00 2.57
2020 2076 6.806388 TCGAAACCCCATTTAAAACTACTC 57.194 37.500 0.00 0.00 0.00 2.59
2096 2155 1.985684 GATTTTTGTGCAGCGTTAGGC 59.014 47.619 0.00 0.00 44.05 3.93
2189 2248 0.545071 CCACCCAAGGCCCAAATTCT 60.545 55.000 0.00 0.00 0.00 2.40
2225 2287 2.097110 ACAGGTGGTAAGTGACTGGA 57.903 50.000 0.00 0.00 33.63 3.86
2262 2327 2.933260 TGCGATACATAATGTTGCGTGT 59.067 40.909 0.00 0.00 31.47 4.49
2271 2336 2.418368 ATGTTGCGTGTGTCCCATAT 57.582 45.000 0.00 0.00 0.00 1.78
2272 2337 3.552132 ATGTTGCGTGTGTCCCATATA 57.448 42.857 0.00 0.00 0.00 0.86
2273 2338 2.899976 TGTTGCGTGTGTCCCATATAG 58.100 47.619 0.00 0.00 0.00 1.31
2279 2344 5.294356 TGCGTGTGTCCCATATAGTAATTC 58.706 41.667 0.00 0.00 0.00 2.17
2318 2385 6.480981 TGTTTAAATATCTACTGCCCGCTAAC 59.519 38.462 0.00 0.00 0.00 2.34
2371 2438 1.364626 GATTCAGCCTGCGTGACCTG 61.365 60.000 0.00 0.00 0.00 4.00
2412 2479 1.683917 GTATGTCGAGTCCTGCATCCT 59.316 52.381 0.00 0.00 0.00 3.24
2453 2520 2.710902 CCGCTGGAGGACGTCATCA 61.711 63.158 29.07 16.44 0.00 3.07
2459 2526 3.356639 GAGGACGTCATCAGCGGCA 62.357 63.158 24.24 0.00 39.49 5.69
2555 2628 1.357690 CGGCGGCGTACATTCTCTA 59.642 57.895 24.74 0.00 0.00 2.43
2606 2679 8.317891 TCATTCATCTTTGTACGTACAATTGT 57.682 30.769 34.66 22.35 44.72 2.71
2644 2717 4.648626 TTTCCTGCAGCTGCGCCT 62.649 61.111 32.11 0.00 45.83 5.52
2896 2969 7.720515 ACATTTTCATGTGTCATTTGGGATTTT 59.279 29.630 0.00 0.00 42.46 1.82
3031 3104 6.154445 TGGAGAAAAGACAACTGTACGATAC 58.846 40.000 0.00 0.00 0.00 2.24
3251 3327 2.540516 TGTCGTTGTTGTGGACGTAATG 59.459 45.455 0.00 0.00 40.03 1.90
3262 3338 9.168451 TGTTGTGGACGTAATGATAAACATATT 57.832 29.630 0.00 0.00 38.38 1.28
3263 3339 9.997482 GTTGTGGACGTAATGATAAACATATTT 57.003 29.630 0.00 0.00 38.38 1.40
3401 3727 7.202016 ACATATGTTGTGGTTGTAGTCTTTG 57.798 36.000 1.41 0.00 37.11 2.77
3487 3818 5.705902 TGAAGATGTTCGATTCAACTCGTA 58.294 37.500 0.00 0.00 39.62 3.43
3549 3882 5.241728 GCTCCCCACCTGAATATATTTCAAC 59.758 44.000 0.00 0.00 0.00 3.18
3550 3883 5.373222 TCCCCACCTGAATATATTTCAACG 58.627 41.667 0.00 0.00 0.00 4.10
3565 3898 2.474612 AACGGGGTGTTGCAACGTC 61.475 57.895 23.79 18.26 40.00 4.34
3612 3945 0.108186 AGAGATGATCACGCCGCAAA 60.108 50.000 0.00 0.00 0.00 3.68
3615 3948 1.369091 GATGATCACGCCGCAAACCT 61.369 55.000 0.00 0.00 0.00 3.50
3618 3951 2.240612 GATCACGCCGCAAACCTGAC 62.241 60.000 0.00 0.00 0.00 3.51
3624 3957 1.497278 CCGCAAACCTGACGTGATG 59.503 57.895 0.00 0.00 0.00 3.07
3627 3960 1.875963 CAAACCTGACGTGATGGCC 59.124 57.895 0.00 0.00 0.00 5.36
3629 3962 2.107041 AAACCTGACGTGATGGCCGA 62.107 55.000 0.00 0.00 0.00 5.54
3641 3974 0.466124 ATGGCCGAGCTAAGAGGTTC 59.534 55.000 0.00 0.00 0.00 3.62
3662 3995 7.400339 AGGTTCTTAATCTATGTGACAAGGAGA 59.600 37.037 0.00 0.00 0.00 3.71
3713 4046 4.773674 TCAAAGTTAGTCGATTCTACCCCA 59.226 41.667 0.00 0.00 0.00 4.96
3714 4047 4.732672 AAGTTAGTCGATTCTACCCCAC 57.267 45.455 0.00 0.00 0.00 4.61
3790 4123 1.089920 ACATTGATTGTGAGAGGCGC 58.910 50.000 0.00 0.00 37.11 6.53
3807 4140 2.551912 GCGTGGGAGGTGTTGTTGG 61.552 63.158 0.00 0.00 0.00 3.77
3829 4164 0.250295 ACCACATGTCGTTGGTCAGG 60.250 55.000 0.00 0.00 0.00 3.86
3832 4167 1.531149 CACATGTCGTTGGTCAGGTTC 59.469 52.381 0.00 0.00 0.00 3.62
3849 4184 3.671716 GGTTCAACCTTGGTACGATTCT 58.328 45.455 0.00 0.00 34.73 2.40
3861 4197 7.435488 CCTTGGTACGATTCTAATACTTGTCAG 59.565 40.741 0.00 0.00 0.00 3.51
3867 4203 6.477033 ACGATTCTAATACTTGTCAGACATGC 59.523 38.462 14.87 0.00 0.00 4.06
3869 4205 4.682787 TCTAATACTTGTCAGACATGCCG 58.317 43.478 14.87 2.98 0.00 5.69
3877 4213 1.208358 CAGACATGCCGTGCAACAG 59.792 57.895 2.68 0.09 43.62 3.16
3891 4227 2.295909 TGCAACAGGGCATGTAAAGAAC 59.704 45.455 4.75 0.00 43.00 3.01
3892 4228 2.668279 GCAACAGGGCATGTAAAGAACG 60.668 50.000 4.75 0.00 43.00 3.95
3899 4235 2.351350 GGCATGTAAAGAACGGGTGTTG 60.351 50.000 0.00 0.00 38.78 3.33
3903 4239 2.204237 GTAAAGAACGGGTGTTGACGT 58.796 47.619 0.00 0.00 46.48 4.34
3938 4274 5.104982 GGTGGAAGCATCATGGGAAAATTTA 60.105 40.000 0.00 0.00 0.00 1.40
4027 5726 1.788229 AAGACCTTGGGTTTGTTGGG 58.212 50.000 0.00 0.00 35.25 4.12
4059 6221 1.980232 CAGATTGCAAGCAGCCCCA 60.980 57.895 18.24 0.00 44.83 4.96
4084 6246 3.054287 TCAGGTATGTCGGAAGAGAGAGT 60.054 47.826 0.00 0.00 43.49 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 3.077556 CCAGCCACTACCCGAGCT 61.078 66.667 0.00 0.00 35.52 4.09
90 91 0.106015 AATAGGCCACAAGGATGCCC 60.106 55.000 5.01 0.00 46.55 5.36
92 93 1.767759 ACAATAGGCCACAAGGATGC 58.232 50.000 5.01 0.00 36.89 3.91
94 95 4.729868 GGAATACAATAGGCCACAAGGAT 58.270 43.478 5.01 0.00 36.89 3.24
99 100 1.476110 GGCGGAATACAATAGGCCACA 60.476 52.381 5.01 0.00 40.24 4.17
100 101 1.235724 GGCGGAATACAATAGGCCAC 58.764 55.000 5.01 0.00 40.24 5.01
117 118 3.787001 CCTCTTCACCTCCCGGGC 61.787 72.222 18.49 0.00 39.10 6.13
118 119 3.083997 CCCTCTTCACCTCCCGGG 61.084 72.222 16.85 16.85 41.89 5.73
121 122 1.301293 CAAGCCCTCTTCACCTCCC 59.699 63.158 0.00 0.00 0.00 4.30
215 216 0.721718 GAAGAGGAACCGCAACGATG 59.278 55.000 0.00 0.00 0.00 3.84
216 217 0.736325 CGAAGAGGAACCGCAACGAT 60.736 55.000 0.00 0.00 0.00 3.73
218 219 1.615107 GACGAAGAGGAACCGCAACG 61.615 60.000 0.00 10.16 0.00 4.10
223 224 0.966370 AGGAGGACGAAGAGGAACCG 60.966 60.000 0.00 0.00 0.00 4.44
244 245 0.961753 CAAGGTTTCCCCAGAGCAAC 59.038 55.000 0.00 0.00 34.66 4.17
318 320 0.889186 GAACCGCAAGCTCCAAGGAA 60.889 55.000 4.75 0.00 0.00 3.36
362 364 0.732880 CCACCGTAAGCGAGTCACAG 60.733 60.000 0.00 0.00 41.33 3.66
385 387 2.963371 GCTTGACGTCTCCGGAGT 59.037 61.111 30.17 13.30 38.78 3.85
409 411 3.751518 ACTCCAAGCAAACTAACGGAAT 58.248 40.909 0.00 0.00 0.00 3.01
439 441 1.756430 GAAGAAGCTTCATGACCCCC 58.244 55.000 27.57 0.00 0.00 5.40
443 445 4.241681 AGAAGACGAAGAAGCTTCATGAC 58.758 43.478 27.57 15.87 40.26 3.06
444 446 4.527509 AGAAGACGAAGAAGCTTCATGA 57.472 40.909 27.57 0.00 40.26 3.07
445 447 4.450419 ACAAGAAGACGAAGAAGCTTCATG 59.550 41.667 27.57 18.04 40.91 3.07
446 448 4.636249 ACAAGAAGACGAAGAAGCTTCAT 58.364 39.130 27.57 17.00 40.26 2.57
447 449 4.060038 ACAAGAAGACGAAGAAGCTTCA 57.940 40.909 27.57 0.00 40.26 3.02
448 450 6.096695 AGATACAAGAAGACGAAGAAGCTTC 58.903 40.000 19.11 19.11 38.58 3.86
450 452 5.652994 AGATACAAGAAGACGAAGAAGCT 57.347 39.130 0.00 0.00 0.00 3.74
451 453 5.635700 ACAAGATACAAGAAGACGAAGAAGC 59.364 40.000 0.00 0.00 0.00 3.86
452 454 7.087639 AGACAAGATACAAGAAGACGAAGAAG 58.912 38.462 0.00 0.00 0.00 2.85
456 458 5.926542 CCAAGACAAGATACAAGAAGACGAA 59.073 40.000 0.00 0.00 0.00 3.85
457 459 5.470368 CCAAGACAAGATACAAGAAGACGA 58.530 41.667 0.00 0.00 0.00 4.20
458 460 4.627467 CCCAAGACAAGATACAAGAAGACG 59.373 45.833 0.00 0.00 0.00 4.18
459 461 5.409826 CACCCAAGACAAGATACAAGAAGAC 59.590 44.000 0.00 0.00 0.00 3.01
462 464 4.072131 GCACCCAAGACAAGATACAAGAA 58.928 43.478 0.00 0.00 0.00 2.52
496 499 2.094234 ACAAAACACCCAACAGCTCAAC 60.094 45.455 0.00 0.00 0.00 3.18
498 501 1.846007 ACAAAACACCCAACAGCTCA 58.154 45.000 0.00 0.00 0.00 4.26
502 505 2.882137 ACCGATACAAAACACCCAACAG 59.118 45.455 0.00 0.00 0.00 3.16
513 516 3.927854 TCATCGAACCAACCGATACAAA 58.072 40.909 0.00 0.00 43.93 2.83
571 576 8.181573 TGTTTTATCTTCGGTTGCATCTATTTC 58.818 33.333 0.00 0.00 0.00 2.17
572 577 8.050778 TGTTTTATCTTCGGTTGCATCTATTT 57.949 30.769 0.00 0.00 0.00 1.40
582 587 4.981812 ACTCCCTTGTTTTATCTTCGGTT 58.018 39.130 0.00 0.00 0.00 4.44
607 612 4.969359 TCCCTTGTTTTATCACCCCAAAAA 59.031 37.500 0.00 0.00 0.00 1.94
608 613 4.557705 TCCCTTGTTTTATCACCCCAAAA 58.442 39.130 0.00 0.00 0.00 2.44
609 614 4.200447 TCCCTTGTTTTATCACCCCAAA 57.800 40.909 0.00 0.00 0.00 3.28
610 615 3.905493 TCCCTTGTTTTATCACCCCAA 57.095 42.857 0.00 0.00 0.00 4.12
611 616 3.905493 TTCCCTTGTTTTATCACCCCA 57.095 42.857 0.00 0.00 0.00 4.96
612 617 4.530553 ACAATTCCCTTGTTTTATCACCCC 59.469 41.667 0.00 0.00 45.98 4.95
613 618 5.738619 ACAATTCCCTTGTTTTATCACCC 57.261 39.130 0.00 0.00 45.98 4.61
631 636 1.939934 CGTGGTGATTATGCGGACAAT 59.060 47.619 0.00 0.00 0.00 2.71
709 714 3.056536 GCATCTTTTTCCCCAGAGAAACC 60.057 47.826 0.00 0.00 35.53 3.27
718 723 1.545841 AAGACGGCATCTTTTTCCCC 58.454 50.000 0.00 0.00 46.05 4.81
760 768 3.645975 CGTTTTGCCCGACGTGCT 61.646 61.111 3.51 0.00 34.75 4.40
812 861 2.356673 GGGACGTGACGGTTGGAC 60.357 66.667 10.66 0.00 0.00 4.02
832 881 4.807039 GCGCGGCGGTTCTAGGAA 62.807 66.667 25.03 0.00 0.00 3.36
922 971 2.741211 GGAAGTTGCCGACGGGAC 60.741 66.667 17.22 7.91 34.06 4.46
963 1012 0.038159 GAGTGGTGGAGGAAGACGTG 60.038 60.000 0.00 0.00 0.00 4.49
964 1013 1.186267 GGAGTGGTGGAGGAAGACGT 61.186 60.000 0.00 0.00 0.00 4.34
965 1014 1.592223 GGAGTGGTGGAGGAAGACG 59.408 63.158 0.00 0.00 0.00 4.18
966 1015 1.592223 CGGAGTGGTGGAGGAAGAC 59.408 63.158 0.00 0.00 0.00 3.01
989 1038 1.750399 CCTTCCATGGCAACTCGGG 60.750 63.158 6.96 0.00 37.61 5.14
1181 1230 1.425825 CGCTGATCAGAGACGACGT 59.574 57.895 27.04 0.00 0.00 4.34
1199 1248 0.034186 TGACAAGTGGGCCATCATCC 60.034 55.000 10.70 0.00 0.00 3.51
1200 1249 1.952296 GATGACAAGTGGGCCATCATC 59.048 52.381 24.47 24.47 39.04 2.92
1210 1259 2.444624 CCGACGCCGATGACAAGTG 61.445 63.158 0.00 0.00 38.22 3.16
1211 1260 2.126071 CCGACGCCGATGACAAGT 60.126 61.111 0.00 0.00 38.22 3.16
1216 1265 2.889988 CATTGCCGACGCCGATGA 60.890 61.111 0.00 0.00 38.22 2.92
1261 1310 3.046087 CTGCTGCACGTGGACCAG 61.046 66.667 18.88 17.56 0.00 4.00
1300 1349 0.541392 TCCTGTTGATGTCCCATCGG 59.459 55.000 0.25 0.00 0.00 4.18
1301 1350 1.945387 CTCCTGTTGATGTCCCATCG 58.055 55.000 0.25 0.00 0.00 3.84
1302 1351 1.673168 GCTCCTGTTGATGTCCCATC 58.327 55.000 0.00 0.00 0.00 3.51
1303 1352 0.257039 GGCTCCTGTTGATGTCCCAT 59.743 55.000 0.00 0.00 0.00 4.00
1304 1353 0.842030 AGGCTCCTGTTGATGTCCCA 60.842 55.000 0.00 0.00 0.00 4.37
1305 1354 0.329596 AAGGCTCCTGTTGATGTCCC 59.670 55.000 0.00 0.00 0.00 4.46
1306 1355 1.680249 GGAAGGCTCCTGTTGATGTCC 60.680 57.143 0.00 0.00 38.88 4.02
1307 1356 1.003580 TGGAAGGCTCCTGTTGATGTC 59.996 52.381 0.00 0.00 42.94 3.06
1308 1357 1.067295 TGGAAGGCTCCTGTTGATGT 58.933 50.000 0.00 0.00 42.94 3.06
1309 1358 2.022195 CATGGAAGGCTCCTGTTGATG 58.978 52.381 0.00 0.00 42.94 3.07
1310 1359 1.064166 CCATGGAAGGCTCCTGTTGAT 60.064 52.381 5.56 0.00 42.94 2.57
1311 1360 0.329261 CCATGGAAGGCTCCTGTTGA 59.671 55.000 5.56 0.00 42.94 3.18
1312 1361 0.038744 ACCATGGAAGGCTCCTGTTG 59.961 55.000 21.47 0.00 42.94 3.33
1313 1362 1.282157 GTACCATGGAAGGCTCCTGTT 59.718 52.381 21.47 0.00 42.94 3.16
1314 1363 0.912486 GTACCATGGAAGGCTCCTGT 59.088 55.000 21.47 0.00 42.94 4.00
1315 1364 0.179073 CGTACCATGGAAGGCTCCTG 60.179 60.000 21.47 0.00 42.94 3.86
1316 1365 1.972660 GCGTACCATGGAAGGCTCCT 61.973 60.000 21.47 0.00 42.94 3.69
1317 1366 1.523938 GCGTACCATGGAAGGCTCC 60.524 63.158 21.47 0.00 42.81 4.70
1318 1367 0.107654 AAGCGTACCATGGAAGGCTC 60.108 55.000 21.47 2.06 0.00 4.70
1319 1368 0.392998 CAAGCGTACCATGGAAGGCT 60.393 55.000 21.47 19.34 0.00 4.58
1320 1369 1.993369 GCAAGCGTACCATGGAAGGC 61.993 60.000 21.47 17.35 0.00 4.35
1321 1370 0.676466 TGCAAGCGTACCATGGAAGG 60.676 55.000 21.47 7.55 0.00 3.46
1322 1371 0.729116 CTGCAAGCGTACCATGGAAG 59.271 55.000 21.47 10.09 0.00 3.46
1323 1372 0.036164 ACTGCAAGCGTACCATGGAA 59.964 50.000 21.47 0.00 37.60 3.53
1324 1373 0.899019 TACTGCAAGCGTACCATGGA 59.101 50.000 21.47 0.00 37.60 3.41
1325 1374 1.006832 GTACTGCAAGCGTACCATGG 58.993 55.000 11.19 11.19 37.60 3.66
1330 1379 0.245539 TGAGGGTACTGCAAGCGTAC 59.754 55.000 14.39 14.39 37.60 3.67
1331 1380 0.970640 TTGAGGGTACTGCAAGCGTA 59.029 50.000 0.00 0.00 37.60 4.42
1332 1381 0.602905 GTTGAGGGTACTGCAAGCGT 60.603 55.000 0.00 0.00 37.60 5.07
1333 1382 1.298859 GGTTGAGGGTACTGCAAGCG 61.299 60.000 8.48 0.00 37.60 4.68
1334 1383 1.298859 CGGTTGAGGGTACTGCAAGC 61.299 60.000 12.02 12.02 37.60 4.01
1335 1384 0.673644 CCGGTTGAGGGTACTGCAAG 60.674 60.000 0.00 0.00 42.29 4.01
1336 1385 1.373435 CCGGTTGAGGGTACTGCAA 59.627 57.895 0.00 0.00 0.00 4.08
1337 1386 3.065306 CCGGTTGAGGGTACTGCA 58.935 61.111 0.00 0.00 0.00 4.41
1338 1387 2.436115 GCCGGTTGAGGGTACTGC 60.436 66.667 1.90 0.00 0.00 4.40
1339 1388 2.125673 CGCCGGTTGAGGGTACTG 60.126 66.667 1.90 0.00 0.00 2.74
1340 1389 4.078516 GCGCCGGTTGAGGGTACT 62.079 66.667 1.90 0.00 0.00 2.73
1357 1406 2.894879 TTCGAATGCCATCGCCGG 60.895 61.111 0.00 0.00 42.44 6.13
1358 1407 2.324477 GTTCGAATGCCATCGCCG 59.676 61.111 0.00 0.00 42.44 6.46
1359 1408 2.715624 GGTTCGAATGCCATCGCC 59.284 61.111 0.00 0.00 42.44 5.54
1360 1409 2.715624 GGGTTCGAATGCCATCGC 59.284 61.111 0.00 0.00 42.44 4.58
1361 1410 1.439353 CTGGGGTTCGAATGCCATCG 61.439 60.000 0.00 2.10 44.04 3.84
1362 1411 1.728490 GCTGGGGTTCGAATGCCATC 61.728 60.000 0.00 0.00 0.00 3.51
1363 1412 1.754234 GCTGGGGTTCGAATGCCAT 60.754 57.895 0.00 0.00 0.00 4.40
1364 1413 2.361104 GCTGGGGTTCGAATGCCA 60.361 61.111 0.00 0.00 0.00 4.92
1365 1414 1.937546 CTTGCTGGGGTTCGAATGCC 61.938 60.000 0.00 0.00 0.00 4.40
1383 1432 1.344763 GAGTATACCATGGAAGGCGCT 59.655 52.381 21.47 8.31 0.00 5.92
1407 1456 2.436115 GGCGCTGGTTGAGGGTAC 60.436 66.667 7.64 0.00 36.97 3.34
1465 1520 2.672996 AACATGGAGTGGCACCGC 60.673 61.111 15.27 6.79 0.00 5.68
1474 1529 2.345760 GGTGCTGGCCAACATGGAG 61.346 63.158 12.91 0.00 40.96 3.86
1489 1544 2.767445 CGCCCATCATGTGCTGGTG 61.767 63.158 2.58 2.91 35.59 4.17
1573 1628 0.038599 TGCATCTGCTGGTGTTGGAT 59.961 50.000 5.69 0.00 42.66 3.41
1609 1664 3.771160 GGACATCACCTCCGGCGT 61.771 66.667 6.01 0.00 0.00 5.68
1680 1735 1.149148 GGTGCACTTCTTCGTCTTCC 58.851 55.000 17.98 0.00 0.00 3.46
1695 1750 4.828296 CCATGGCCAGGGAGGTGC 62.828 72.222 33.03 0.00 40.61 5.01
1732 1787 4.087892 CACCAGAGGCTCCGGGTG 62.088 72.222 30.03 30.03 44.17 4.61
1994 2050 4.816392 AGTTTTAAATGGGGTTTCGATGC 58.184 39.130 0.00 0.00 0.00 3.91
2010 2066 9.856488 GATCGATTGCATATAGGAGTAGTTTTA 57.144 33.333 0.00 0.00 0.00 1.52
2013 2069 6.556212 CGATCGATTGCATATAGGAGTAGTT 58.444 40.000 10.26 0.00 0.00 2.24
2014 2070 5.449314 GCGATCGATTGCATATAGGAGTAGT 60.449 44.000 28.97 0.00 37.15 2.73
2017 2073 3.429547 GGCGATCGATTGCATATAGGAGT 60.430 47.826 33.04 0.00 38.98 3.85
2018 2074 3.119291 GGCGATCGATTGCATATAGGAG 58.881 50.000 33.04 1.91 38.98 3.69
2019 2075 2.495669 TGGCGATCGATTGCATATAGGA 59.504 45.455 33.04 9.60 38.98 2.94
2020 2076 2.892374 TGGCGATCGATTGCATATAGG 58.108 47.619 33.04 2.78 38.98 2.57
2120 2179 1.153978 GTATGTTCCGTCCGTCGCA 60.154 57.895 0.00 0.00 38.35 5.10
2172 2231 0.545071 CCAGAATTTGGGCCTTGGGT 60.545 55.000 4.53 0.00 43.75 4.51
2189 2248 1.883275 CTGTAAATTCGTTGGGTGCCA 59.117 47.619 0.00 0.00 0.00 4.92
2243 2305 4.505300 GACACACGCAACATTATGTATCG 58.495 43.478 14.37 14.37 33.51 2.92
2248 2310 1.809547 TGGGACACACGCAACATTATG 59.190 47.619 0.00 0.00 38.47 1.90
2298 2363 4.957684 AGTTAGCGGGCAGTAGATATTT 57.042 40.909 0.00 0.00 0.00 1.40
2312 2379 5.912528 ACGAAAATGTAGTGAAAGTTAGCG 58.087 37.500 0.00 0.00 0.00 4.26
2318 2385 8.122952 AGAAACAGAACGAAAATGTAGTGAAAG 58.877 33.333 0.00 0.00 0.00 2.62
2412 2479 3.146066 CCGGTTTTGTTCCTCATCTTGA 58.854 45.455 0.00 0.00 0.00 3.02
2555 2628 1.276421 CTGAAGATTCACGGAGGTGGT 59.724 52.381 0.00 0.00 44.50 4.16
2606 2679 3.216800 ACGTAGAGTAGTGTCACCAACA 58.783 45.455 0.00 0.00 34.78 3.33
2665 2738 1.002087 TCCTTTTCCTCTTGCTCGGTC 59.998 52.381 0.00 0.00 0.00 4.79
2896 2969 1.970640 TGAGTTCTCTTAGCTGCACCA 59.029 47.619 1.02 0.00 0.00 4.17
3031 3104 3.493002 CCTCTGCATCAGCTCCTTAAGAG 60.493 52.174 3.36 0.92 46.29 2.85
3264 3340 9.256477 CCGTGAATACACATATGTTTAGTACAT 57.744 33.333 5.37 0.00 46.32 2.29
3265 3341 8.252417 ACCGTGAATACACATATGTTTAGTACA 58.748 33.333 5.37 3.98 46.20 2.90
3266 3342 8.537223 CACCGTGAATACACATATGTTTAGTAC 58.463 37.037 5.37 4.69 46.20 2.73
3267 3343 8.252417 ACACCGTGAATACACATATGTTTAGTA 58.748 33.333 5.37 6.31 46.20 1.82
3268 3344 7.064134 CACACCGTGAATACACATATGTTTAGT 59.936 37.037 5.37 3.36 46.20 2.24
3269 3345 7.064134 ACACACCGTGAATACACATATGTTTAG 59.936 37.037 5.37 0.00 46.20 1.85
3270 3346 6.874664 ACACACCGTGAATACACATATGTTTA 59.125 34.615 5.37 4.74 46.20 2.01
3271 3347 5.703592 ACACACCGTGAATACACATATGTTT 59.296 36.000 5.37 2.11 46.20 2.83
3272 3348 5.242434 ACACACCGTGAATACACATATGTT 58.758 37.500 5.37 0.84 46.20 2.71
3273 3349 4.827692 ACACACCGTGAATACACATATGT 58.172 39.130 5.28 1.41 46.20 2.29
3274 3350 5.580691 AGAACACACCGTGAATACACATATG 59.419 40.000 5.28 0.00 46.20 1.78
3275 3351 5.730550 AGAACACACCGTGAATACACATAT 58.269 37.500 5.28 0.00 46.20 1.78
3276 3352 5.142061 AGAACACACCGTGAATACACATA 57.858 39.130 5.28 0.00 46.20 2.29
3277 3353 4.002906 AGAACACACCGTGAATACACAT 57.997 40.909 5.28 0.00 46.20 3.21
3278 3354 3.462483 AGAACACACCGTGAATACACA 57.538 42.857 5.28 0.00 46.20 3.72
3549 3882 3.656045 GGACGTTGCAACACCCCG 61.656 66.667 28.01 16.60 0.00 5.73
3550 3883 0.606944 TATGGACGTTGCAACACCCC 60.607 55.000 28.01 23.04 0.00 4.95
3563 3896 5.584253 AGGCTATGACGATGTATATGGAC 57.416 43.478 0.00 0.00 0.00 4.02
3565 3898 5.965922 TCAAGGCTATGACGATGTATATGG 58.034 41.667 0.00 0.00 0.00 2.74
3612 3945 2.994995 TCGGCCATCACGTCAGGT 60.995 61.111 2.24 0.00 0.00 4.00
3615 3948 1.600511 TTAGCTCGGCCATCACGTCA 61.601 55.000 2.24 0.00 0.00 4.35
3618 3951 0.596083 CTCTTAGCTCGGCCATCACG 60.596 60.000 2.24 0.00 0.00 4.35
3624 3957 0.537653 AAGAACCTCTTAGCTCGGCC 59.462 55.000 0.00 0.00 34.42 6.13
3627 3960 7.593273 CACATAGATTAAGAACCTCTTAGCTCG 59.407 40.741 0.00 0.00 39.80 5.03
3629 3962 8.417884 GTCACATAGATTAAGAACCTCTTAGCT 58.582 37.037 0.00 0.00 39.80 3.32
3641 3974 7.384660 GCTCATCTCCTTGTCACATAGATTAAG 59.615 40.741 0.00 0.00 0.00 1.85
3685 4018 6.308282 GGTAGAATCGACTAACTTTGACACTG 59.692 42.308 0.00 0.00 0.00 3.66
3713 4046 5.288804 GCACACAATTAAATGGTGTTCAGT 58.711 37.500 2.84 0.00 42.72 3.41
3714 4047 4.685628 GGCACACAATTAAATGGTGTTCAG 59.314 41.667 2.84 0.00 42.72 3.02
3789 4122 2.551912 CCAACAACACCTCCCACGC 61.552 63.158 0.00 0.00 0.00 5.34
3790 4123 1.153046 ACCAACAACACCTCCCACG 60.153 57.895 0.00 0.00 0.00 4.94
3800 4133 2.774439 GACATGTGGTCACCAACAAC 57.226 50.000 1.15 0.00 46.19 3.32
3807 4140 1.808512 TGACCAACGACATGTGGTCAC 60.809 52.381 24.61 12.99 45.52 3.67
3829 4164 6.980051 ATTAGAATCGTACCAAGGTTGAAC 57.020 37.500 0.00 0.00 0.00 3.18
3832 4167 7.548075 ACAAGTATTAGAATCGTACCAAGGTTG 59.452 37.037 0.00 0.00 0.00 3.77
3849 4184 4.180817 CACGGCATGTCTGACAAGTATTA 58.819 43.478 15.31 0.00 0.00 0.98
3861 4197 2.562912 CCTGTTGCACGGCATGTC 59.437 61.111 0.00 0.00 38.76 3.06
3867 4203 1.240641 TTACATGCCCTGTTGCACGG 61.241 55.000 0.00 0.00 45.48 4.94
3869 4205 1.885887 TCTTTACATGCCCTGTTGCAC 59.114 47.619 0.00 0.00 45.48 4.57
3877 4213 0.808755 CACCCGTTCTTTACATGCCC 59.191 55.000 0.00 0.00 0.00 5.36
3891 4227 2.729882 CTCTAAAGAACGTCAACACCCG 59.270 50.000 0.00 0.00 0.00 5.28
3892 4228 3.064931 CCTCTAAAGAACGTCAACACCC 58.935 50.000 0.00 0.00 0.00 4.61
3899 4235 1.897802 TCCACCCCTCTAAAGAACGTC 59.102 52.381 0.00 0.00 0.00 4.34
3903 4239 2.344592 TGCTTCCACCCCTCTAAAGAA 58.655 47.619 0.00 0.00 0.00 2.52
3938 4274 6.127140 ACACCACAAGACTAGTAAACAAGACT 60.127 38.462 0.00 0.00 0.00 3.24
3949 4285 3.326747 GCAACCTACACCACAAGACTAG 58.673 50.000 0.00 0.00 0.00 2.57
4027 5726 0.257039 AATCTGGGAGTCATGGGTGC 59.743 55.000 0.00 0.00 0.00 5.01
4033 6195 1.005097 TGCTTGCAATCTGGGAGTCAT 59.995 47.619 0.00 0.00 0.00 3.06
4059 6221 1.743958 CTCTTCCGACATACCTGACGT 59.256 52.381 0.00 0.00 38.59 4.34
4084 6246 1.948834 CAACAAGATGGGCATATGCGA 59.051 47.619 21.04 10.83 43.26 5.10


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

AutoCloner maintained by Alex Coulton.