Multiple sequence alignment - TraesCS1A01G438200

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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 TraesCS1A01G438200 chr1A 100.000 3156 0 0 1 3156 587951349 587954504 0.000000e+00 5829.0
1 TraesCS1A01G438200 chr1A 89.418 378 40 0 162 539 513647040 513647417 7.920000e-131 477.0
2 TraesCS1A01G438200 chr1A 90.184 163 15 1 2 163 513646850 513647012 8.870000e-51 211.0
3 TraesCS1A01G438200 chr1A 77.366 243 55 0 251 493 555070578 555070820 9.120000e-31 145.0
4 TraesCS1A01G438200 chr1A 93.333 45 3 0 1059 1103 468410950 468410906 2.030000e-07 67.6
5 TraesCS1A01G438200 chr1A 93.333 45 3 0 1059 1103 468462121 468462077 2.030000e-07 67.6
6 TraesCS1A01G438200 chr1A 91.667 48 4 0 1056 1103 588664673 588664720 2.030000e-07 67.6
7 TraesCS1A01G438200 chr1A 95.122 41 1 1 1053 1092 587911053 587911093 2.630000e-06 63.9
8 TraesCS1A01G438200 chr1D 92.303 1546 94 14 1627 3156 488674628 488676164 0.000000e+00 2172.0
9 TraesCS1A01G438200 chr1D 94.331 635 31 3 1000 1629 488646185 488646819 0.000000e+00 968.0
10 TraesCS1A01G438200 chr1D 86.753 385 13 12 641 1006 488644092 488644457 8.200000e-106 394.0
11 TraesCS1A01G438200 chr1D 77.101 345 52 17 1487 1804 488630337 488630681 1.160000e-39 174.0
12 TraesCS1A01G438200 chr1D 93.333 45 3 0 1059 1103 368675525 368675481 2.030000e-07 67.6
13 TraesCS1A01G438200 chr1D 91.667 48 4 0 1056 1103 488589632 488589679 2.030000e-07 67.6
14 TraesCS1A01G438200 chr1D 91.304 46 4 0 1056 1101 488642910 488642955 2.630000e-06 63.9
15 TraesCS1A01G438200 chr6B 90.107 374 37 0 162 535 52163304 52163677 1.320000e-133 486.0
16 TraesCS1A01G438200 chrUn 88.837 215 24 0 836 1050 8822353 8822567 6.710000e-67 265.0
17 TraesCS1A01G438200 chr2B 84.038 213 26 6 2212 2422 747817801 747817595 6.900000e-47 198.0
18 TraesCS1A01G438200 chr2B 78.829 222 42 4 2212 2432 800193727 800193510 9.120000e-31 145.0
19 TraesCS1A01G438200 chr5D 84.409 186 25 1 2212 2397 483516514 483516695 2.500000e-41 180.0
20 TraesCS1A01G438200 chr5D 82.530 166 25 1 2213 2378 443905916 443905755 3.280000e-30 143.0
21 TraesCS1A01G438200 chr4B 82.723 191 27 3 2212 2401 259475982 259476167 7.000000e-37 165.0
22 TraesCS1A01G438200 chr3B 79.426 209 37 3 2213 2421 733273073 733272871 3.280000e-30 143.0
23 TraesCS1A01G438200 chr3B 83.117 154 25 1 2212 2365 59943686 59943534 4.240000e-29 139.0
24 TraesCS1A01G438200 chr7D 83.117 154 22 1 2212 2365 619113542 619113691 1.530000e-28 137.0
25 TraesCS1A01G438200 chr1B 90.164 61 4 1 913 973 680999065 680999007 9.390000e-11 78.7
26 TraesCS1A01G438200 chr1B 93.023 43 3 0 1059 1101 681036648 681036606 2.630000e-06 63.9


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 TraesCS1A01G438200 chr1A 587951349 587954504 3155 False 5829.0 5829 100.000 1 3156 1 chr1A.!!$F3 3155
1 TraesCS1A01G438200 chr1A 513646850 513647417 567 False 344.0 477 89.801 2 539 2 chr1A.!!$F5 537
2 TraesCS1A01G438200 chr1D 488674628 488676164 1536 False 2172.0 2172 92.303 1627 3156 1 chr1D.!!$F3 1529
3 TraesCS1A01G438200 chr1D 488642910 488646819 3909 False 475.3 968 90.796 641 1629 3 chr1D.!!$F4 988

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
549 580 0.182061 TGAGCCATCCTTGCATCTCC 59.818 55.0 0.0 0.0 0.0 3.71 F
552 583 0.473326 GCCATCCTTGCATCTCCTCT 59.527 55.0 0.0 0.0 0.0 3.69 F
1966 4267 0.466124 CCTACCCCTCTACTTGCAGC 59.534 60.0 0.0 0.0 0.0 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1966 4267 1.005037 TGAGTACACCTGCAAGCGG 60.005 57.895 0.0 0.0 0.0 5.52 R
2071 4374 1.202651 CCTAACCCTAACATCCTGCCG 60.203 57.143 0.0 0.0 0.0 5.69 R
2868 5184 0.674895 CTCCACCCTGCCTTCTTTCG 60.675 60.000 0.0 0.0 0.0 3.46 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
56 58 3.368116 CGTAGTGAAGGTAGGTGGGAAAG 60.368 52.174 0.00 0.00 0.00 2.62
59 61 2.370849 GTGAAGGTAGGTGGGAAAGTGA 59.629 50.000 0.00 0.00 0.00 3.41
68 70 2.041115 GGGAAAGTGAAGCGGCTCC 61.041 63.158 1.45 0.00 0.00 4.70
71 73 2.470938 GAAAGTGAAGCGGCTCCCCT 62.471 60.000 1.45 0.00 0.00 4.79
147 149 3.008517 TCAGGCGGCCATGGAGAA 61.009 61.111 23.09 0.00 0.00 2.87
295 326 1.043116 ATCACTCCCGAATCCTCGCA 61.043 55.000 0.00 0.00 44.04 5.10
317 348 3.285215 GGCATGGCAGCGAGATGG 61.285 66.667 15.47 0.00 34.64 3.51
349 380 1.855295 TTATGTACTCCCCTGCACGA 58.145 50.000 0.00 0.00 0.00 4.35
370 401 2.631696 GAAATCGCGCATCCACCGTG 62.632 60.000 8.75 0.00 37.53 4.94
377 408 1.741770 GCATCCACCGTGACTCCAC 60.742 63.158 0.00 0.00 39.86 4.02
378 409 1.671166 CATCCACCGTGACTCCACA 59.329 57.895 0.00 0.00 43.34 4.17
379 410 0.390340 CATCCACCGTGACTCCACAG 60.390 60.000 0.00 0.00 43.34 3.66
545 576 4.230603 CGTGAGCCATCCTTGCAT 57.769 55.556 0.00 0.00 0.00 3.96
546 577 2.020131 CGTGAGCCATCCTTGCATC 58.980 57.895 0.00 0.00 0.00 3.91
547 578 0.463295 CGTGAGCCATCCTTGCATCT 60.463 55.000 0.00 0.00 0.00 2.90
548 579 1.307097 GTGAGCCATCCTTGCATCTC 58.693 55.000 0.00 0.00 0.00 2.75
549 580 0.182061 TGAGCCATCCTTGCATCTCC 59.818 55.000 0.00 0.00 0.00 3.71
552 583 0.473326 GCCATCCTTGCATCTCCTCT 59.527 55.000 0.00 0.00 0.00 3.69
553 584 1.133853 GCCATCCTTGCATCTCCTCTT 60.134 52.381 0.00 0.00 0.00 2.85
554 585 2.686118 GCCATCCTTGCATCTCCTCTTT 60.686 50.000 0.00 0.00 0.00 2.52
555 586 3.629087 CCATCCTTGCATCTCCTCTTTT 58.371 45.455 0.00 0.00 0.00 2.27
556 587 3.631227 CCATCCTTGCATCTCCTCTTTTC 59.369 47.826 0.00 0.00 0.00 2.29
557 588 4.267536 CATCCTTGCATCTCCTCTTTTCA 58.732 43.478 0.00 0.00 0.00 2.69
558 589 3.679389 TCCTTGCATCTCCTCTTTTCAC 58.321 45.455 0.00 0.00 0.00 3.18
560 591 3.415212 CTTGCATCTCCTCTTTTCACCA 58.585 45.455 0.00 0.00 0.00 4.17
561 592 2.783135 TGCATCTCCTCTTTTCACCAC 58.217 47.619 0.00 0.00 0.00 4.16
562 593 2.087646 GCATCTCCTCTTTTCACCACC 58.912 52.381 0.00 0.00 0.00 4.61
566 597 2.158667 TCTCCTCTTTTCACCACCCAAC 60.159 50.000 0.00 0.00 0.00 3.77
567 598 1.566703 TCCTCTTTTCACCACCCAACA 59.433 47.619 0.00 0.00 0.00 3.33
568 599 1.956477 CCTCTTTTCACCACCCAACAG 59.044 52.381 0.00 0.00 0.00 3.16
569 600 1.956477 CTCTTTTCACCACCCAACAGG 59.044 52.381 0.00 0.00 43.78 4.00
580 611 1.056660 CCCAACAGGTCACTAGGTGT 58.943 55.000 0.00 0.00 34.79 4.16
581 612 1.002087 CCCAACAGGTCACTAGGTGTC 59.998 57.143 0.00 0.00 34.79 3.67
582 613 1.691976 CCAACAGGTCACTAGGTGTCA 59.308 52.381 0.00 0.00 34.79 3.58
584 615 3.589988 CAACAGGTCACTAGGTGTCATC 58.410 50.000 0.00 0.00 34.79 2.92
585 616 3.176924 ACAGGTCACTAGGTGTCATCT 57.823 47.619 0.00 0.00 34.79 2.90
586 617 3.511477 ACAGGTCACTAGGTGTCATCTT 58.489 45.455 0.00 0.00 34.79 2.40
587 618 4.673968 ACAGGTCACTAGGTGTCATCTTA 58.326 43.478 0.00 0.00 34.79 2.10
588 619 4.707448 ACAGGTCACTAGGTGTCATCTTAG 59.293 45.833 0.00 0.00 34.79 2.18
589 620 4.098654 CAGGTCACTAGGTGTCATCTTAGG 59.901 50.000 0.00 0.00 34.79 2.69
590 621 4.024670 GGTCACTAGGTGTCATCTTAGGT 58.975 47.826 0.00 0.00 34.79 3.08
592 623 4.023980 TCACTAGGTGTCATCTTAGGTGG 58.976 47.826 11.18 0.00 34.79 4.61
593 624 3.769844 CACTAGGTGTCATCTTAGGTGGT 59.230 47.826 0.00 0.00 0.00 4.16
595 626 5.067936 CACTAGGTGTCATCTTAGGTGGTAG 59.932 48.000 0.00 0.00 0.00 3.18
596 627 4.062490 AGGTGTCATCTTAGGTGGTAGT 57.938 45.455 0.00 0.00 0.00 2.73
597 628 4.426704 AGGTGTCATCTTAGGTGGTAGTT 58.573 43.478 0.00 0.00 0.00 2.24
598 629 4.223032 AGGTGTCATCTTAGGTGGTAGTTG 59.777 45.833 0.00 0.00 0.00 3.16
599 630 4.020485 GGTGTCATCTTAGGTGGTAGTTGT 60.020 45.833 0.00 0.00 0.00 3.32
601 632 6.098017 GTGTCATCTTAGGTGGTAGTTGTAC 58.902 44.000 0.00 0.00 0.00 2.90
602 633 5.776208 TGTCATCTTAGGTGGTAGTTGTACA 59.224 40.000 0.00 0.00 0.00 2.90
603 634 6.098017 GTCATCTTAGGTGGTAGTTGTACAC 58.902 44.000 0.00 0.00 0.00 2.90
604 635 4.771590 TCTTAGGTGGTAGTTGTACACG 57.228 45.455 0.00 0.00 0.00 4.49
606 637 1.708341 AGGTGGTAGTTGTACACGGT 58.292 50.000 0.00 0.00 0.00 4.83
607 638 2.041701 AGGTGGTAGTTGTACACGGTT 58.958 47.619 0.00 0.00 0.00 4.44
608 639 2.435437 AGGTGGTAGTTGTACACGGTTT 59.565 45.455 0.00 0.00 0.00 3.27
609 640 2.545106 GGTGGTAGTTGTACACGGTTTG 59.455 50.000 0.00 0.00 0.00 2.93
610 641 2.545106 GTGGTAGTTGTACACGGTTTGG 59.455 50.000 0.00 0.00 0.00 3.28
611 642 2.433604 TGGTAGTTGTACACGGTTTGGA 59.566 45.455 0.00 0.00 0.00 3.53
612 643 3.118482 TGGTAGTTGTACACGGTTTGGAA 60.118 43.478 0.00 0.00 0.00 3.53
614 645 4.516321 GGTAGTTGTACACGGTTTGGAAAT 59.484 41.667 0.00 0.00 0.00 2.17
615 646 5.700373 GGTAGTTGTACACGGTTTGGAAATA 59.300 40.000 0.00 0.00 0.00 1.40
616 647 6.204495 GGTAGTTGTACACGGTTTGGAAATAA 59.796 38.462 0.00 0.00 0.00 1.40
617 648 6.887626 AGTTGTACACGGTTTGGAAATAAT 57.112 33.333 0.00 0.00 0.00 1.28
618 649 6.905578 AGTTGTACACGGTTTGGAAATAATC 58.094 36.000 0.00 0.00 0.00 1.75
619 650 6.713450 AGTTGTACACGGTTTGGAAATAATCT 59.287 34.615 0.00 0.00 0.00 2.40
620 651 7.879160 AGTTGTACACGGTTTGGAAATAATCTA 59.121 33.333 0.00 0.00 0.00 1.98
621 652 7.599630 TGTACACGGTTTGGAAATAATCTAC 57.400 36.000 0.00 0.00 0.00 2.59
622 653 7.160049 TGTACACGGTTTGGAAATAATCTACA 58.840 34.615 0.00 0.00 0.00 2.74
625 656 6.713450 ACACGGTTTGGAAATAATCTACAAGT 59.287 34.615 0.00 0.00 0.00 3.16
626 657 7.094933 ACACGGTTTGGAAATAATCTACAAGTC 60.095 37.037 0.00 0.00 0.00 3.01
627 658 6.938030 ACGGTTTGGAAATAATCTACAAGTCA 59.062 34.615 0.00 0.00 0.00 3.41
628 659 7.446013 ACGGTTTGGAAATAATCTACAAGTCAA 59.554 33.333 0.00 0.00 0.00 3.18
629 660 8.458843 CGGTTTGGAAATAATCTACAAGTCAAT 58.541 33.333 0.00 0.00 0.00 2.57
641 672 6.849502 TCTACAAGTCAATAGAACTGGTACG 58.150 40.000 0.00 0.00 0.00 3.67
642 673 5.464030 ACAAGTCAATAGAACTGGTACGT 57.536 39.130 0.00 0.00 0.00 3.57
644 675 4.715527 AGTCAATAGAACTGGTACGTCC 57.284 45.455 0.00 0.00 0.00 4.79
719 1272 9.762933 ACGTCTTAGTAGTAAGAGTAGGATTAG 57.237 37.037 18.46 6.33 44.38 1.73
739 1292 2.820787 AGGTTGTTTTGTCGGTTGTTCA 59.179 40.909 0.00 0.00 0.00 3.18
747 1300 7.301789 TGTTTTGTCGGTTGTTCATGTATATG 58.698 34.615 0.00 0.00 35.57 1.78
750 1303 7.528481 TTGTCGGTTGTTCATGTATATGTAC 57.472 36.000 2.81 2.81 35.76 2.90
771 1324 2.831685 TACACAACCTTGCGTGAGAT 57.168 45.000 0.00 0.00 36.91 2.75
773 1326 3.120321 ACACAACCTTGCGTGAGATTA 57.880 42.857 0.00 0.00 36.91 1.75
823 1385 1.698165 ATCTAGTGCGTGTGTTCGTG 58.302 50.000 0.00 0.00 0.00 4.35
828 1390 1.153529 TGCGTGTGTTCGTGGTTCT 60.154 52.632 0.00 0.00 0.00 3.01
832 1394 1.661617 CGTGTGTTCGTGGTTCTTTGA 59.338 47.619 0.00 0.00 0.00 2.69
833 1395 2.536130 CGTGTGTTCGTGGTTCTTTGAC 60.536 50.000 0.00 0.00 0.00 3.18
834 1396 1.661617 TGTGTTCGTGGTTCTTTGACG 59.338 47.619 0.00 0.00 34.38 4.35
835 1397 1.662122 GTGTTCGTGGTTCTTTGACGT 59.338 47.619 0.00 0.00 34.69 4.34
836 1398 1.661617 TGTTCGTGGTTCTTTGACGTG 59.338 47.619 0.00 0.00 34.69 4.49
837 1399 1.928503 GTTCGTGGTTCTTTGACGTGA 59.071 47.619 0.00 0.00 34.69 4.35
838 1400 2.519377 TCGTGGTTCTTTGACGTGAT 57.481 45.000 0.00 0.00 34.69 3.06
839 1401 2.828877 TCGTGGTTCTTTGACGTGATT 58.171 42.857 0.00 0.00 34.69 2.57
840 1402 2.542178 TCGTGGTTCTTTGACGTGATTG 59.458 45.455 0.00 0.00 34.69 2.67
841 1403 2.542178 CGTGGTTCTTTGACGTGATTGA 59.458 45.455 0.00 0.00 0.00 2.57
842 1404 3.186409 CGTGGTTCTTTGACGTGATTGAT 59.814 43.478 0.00 0.00 0.00 2.57
843 1405 4.666655 CGTGGTTCTTTGACGTGATTGATC 60.667 45.833 0.00 0.00 0.00 2.92
844 1406 4.452455 GTGGTTCTTTGACGTGATTGATCT 59.548 41.667 0.00 0.00 0.00 2.75
845 1407 5.049405 GTGGTTCTTTGACGTGATTGATCTT 60.049 40.000 0.00 0.00 0.00 2.40
846 1408 5.049474 TGGTTCTTTGACGTGATTGATCTTG 60.049 40.000 0.00 0.00 0.00 3.02
847 1409 5.049405 GGTTCTTTGACGTGATTGATCTTGT 60.049 40.000 0.00 0.00 0.00 3.16
848 1410 6.147164 GGTTCTTTGACGTGATTGATCTTGTA 59.853 38.462 0.00 0.00 0.00 2.41
849 1411 6.951256 TCTTTGACGTGATTGATCTTGTAG 57.049 37.500 0.00 0.00 0.00 2.74
850 1412 5.869344 TCTTTGACGTGATTGATCTTGTAGG 59.131 40.000 0.00 0.00 0.00 3.18
851 1413 3.521560 TGACGTGATTGATCTTGTAGGC 58.478 45.455 0.00 0.00 0.00 3.93
852 1414 2.535984 GACGTGATTGATCTTGTAGGCG 59.464 50.000 0.00 0.00 0.00 5.52
853 1415 2.165641 ACGTGATTGATCTTGTAGGCGA 59.834 45.455 0.00 0.00 0.00 5.54
854 1416 3.186909 CGTGATTGATCTTGTAGGCGAA 58.813 45.455 0.00 0.00 0.00 4.70
872 1434 2.418628 CGAATCCCAACACACATACACC 59.581 50.000 0.00 0.00 0.00 4.16
895 1457 4.205996 CGTTCTCGTGAATCAATCTAGCTG 59.794 45.833 2.88 0.00 34.40 4.24
1009 3305 2.202987 CTGCGGTCATGGAGGAGC 60.203 66.667 0.00 0.00 0.00 4.70
1031 3327 1.901085 GATGGCTCGGTGGTTCTCT 59.099 57.895 0.00 0.00 0.00 3.10
1038 3334 1.079543 CGGTGGTTCTCTGCTCCAG 60.080 63.158 0.00 0.00 31.54 3.86
1169 3465 5.966742 ATTAGCCAGAAACAAGAGGAAAC 57.033 39.130 0.00 0.00 0.00 2.78
1212 3508 7.331193 GTCGTACTTGTTTAATCTGACCTGAAT 59.669 37.037 0.00 0.00 0.00 2.57
1219 3515 7.676004 TGTTTAATCTGACCTGAATCTGTACA 58.324 34.615 0.00 0.00 0.00 2.90
1227 3523 7.178451 TCTGACCTGAATCTGTACATCTTTACA 59.822 37.037 0.00 0.00 0.00 2.41
1242 3538 8.615878 ACATCTTTACATACTGCTGTTTGTAA 57.384 30.769 25.04 25.04 43.54 2.41
1254 3550 3.853307 GCTGTTTGTAACACATGACTGCC 60.853 47.826 0.00 0.00 35.51 4.85
1306 3602 2.159476 CCTGGTTGATTTGAGCATGTCG 60.159 50.000 0.00 0.00 0.00 4.35
1339 3635 7.338196 TCATCCCTTTAGCAAATCATTAAACGA 59.662 33.333 0.00 0.00 0.00 3.85
1466 3762 8.453238 ACACTGTTAGTCGATCAATCTACTAT 57.547 34.615 5.52 0.00 35.74 2.12
1529 3825 4.825085 CACTGAACAAGGCCCTTACTTAAA 59.175 41.667 0.00 0.00 0.00 1.52
1625 3926 6.861065 TTGAACCTCACTTTATTGACAGAC 57.139 37.500 0.00 0.00 0.00 3.51
1629 3930 4.593206 ACCTCACTTTATTGACAGACAGGA 59.407 41.667 0.00 0.00 0.00 3.86
1636 3937 6.820656 ACTTTATTGACAGACAGGACATGATC 59.179 38.462 0.00 0.00 0.00 2.92
1782 4083 1.153667 CAGAAGGAGGACGAGCTGC 60.154 63.158 0.00 0.00 0.00 5.25
1885 4186 7.772757 GGATACAAAATCACTTGATCTCCTTCT 59.227 37.037 0.00 0.00 32.75 2.85
1922 4223 9.301153 GTTTGTTTGTTTGACAGAAGTTGATAT 57.699 29.630 0.00 0.00 0.00 1.63
1960 4261 4.016479 TCTCATTTGACCTACCCCTCTACT 60.016 45.833 0.00 0.00 0.00 2.57
1962 4263 4.469945 TCATTTGACCTACCCCTCTACTTG 59.530 45.833 0.00 0.00 0.00 3.16
1966 4267 0.466124 CCTACCCCTCTACTTGCAGC 59.534 60.000 0.00 0.00 0.00 5.25
2040 4343 5.685841 CAAGGTGACACTTTACGTTTATGG 58.314 41.667 5.39 0.00 0.00 2.74
2058 4361 0.823356 GGTGGTGCTTTCCTGCTTGA 60.823 55.000 0.00 0.00 0.00 3.02
2064 4367 3.065925 GGTGCTTTCCTGCTTGATATCAC 59.934 47.826 4.48 0.00 0.00 3.06
2071 4374 0.815213 TGCTTGATATCACTGGCGCC 60.815 55.000 22.73 22.73 0.00 6.53
2111 4414 3.091545 GGGCCAGAAATCAATGAAGACA 58.908 45.455 4.39 0.00 0.00 3.41
2130 4433 6.610741 AGACAACATTCAAAGACTGAGAAC 57.389 37.500 0.00 0.00 34.81 3.01
2184 4487 2.637872 AGAGTTTGGTTAGCTAGCACCA 59.362 45.455 20.10 20.10 41.55 4.17
2238 4542 8.017373 AGTGAATTACAGAAAACATCGACATTG 58.983 33.333 0.00 0.00 0.00 2.82
2246 4550 6.797033 CAGAAAACATCGACATTGAAGGTTAC 59.203 38.462 0.00 0.00 0.00 2.50
2254 4558 2.552315 ACATTGAAGGTTACGGTTGCAG 59.448 45.455 0.00 0.00 0.00 4.41
2271 4575 6.743575 GTTGCAGAAACCACACTTCTATAT 57.256 37.500 0.00 0.00 31.84 0.86
2315 4619 7.765695 AATTCTGAGGCTAATGTTTTGAAGA 57.234 32.000 0.00 0.00 0.00 2.87
2316 4620 7.765695 ATTCTGAGGCTAATGTTTTGAAGAA 57.234 32.000 0.00 0.00 0.00 2.52
2340 4644 3.715628 AAACACTAGTTGGCAGCTTTG 57.284 42.857 9.73 9.89 38.17 2.77
2342 4646 1.142870 ACACTAGTTGGCAGCTTTGGA 59.857 47.619 9.73 0.00 0.00 3.53
2344 4648 0.798776 CTAGTTGGCAGCTTTGGACG 59.201 55.000 9.73 0.00 0.00 4.79
2348 4652 0.820871 TTGGCAGCTTTGGACGTTTT 59.179 45.000 0.00 0.00 0.00 2.43
2350 4654 2.025155 TGGCAGCTTTGGACGTTTTAA 58.975 42.857 0.00 0.00 0.00 1.52
2352 4656 2.607038 GGCAGCTTTGGACGTTTTAAGG 60.607 50.000 0.00 0.00 0.00 2.69
2353 4657 2.292292 GCAGCTTTGGACGTTTTAAGGA 59.708 45.455 0.00 0.00 0.00 3.36
2354 4658 3.057526 GCAGCTTTGGACGTTTTAAGGAT 60.058 43.478 0.00 0.00 0.00 3.24
2355 4659 4.155280 GCAGCTTTGGACGTTTTAAGGATA 59.845 41.667 0.00 0.00 0.00 2.59
2375 4679 3.668141 AATTATGACATGTGGAGCCCA 57.332 42.857 1.15 0.00 0.00 5.36
2394 4698 2.737783 CCACTTTTATTGACGTGGCGTA 59.262 45.455 0.00 0.00 41.37 4.42
2412 4716 3.184541 CGTAACGGTTTGGACTAGATGG 58.815 50.000 0.00 0.00 0.00 3.51
2423 4727 2.874701 GGACTAGATGGCGTTAGACGTA 59.125 50.000 0.00 0.00 44.73 3.57
2429 4733 5.713822 AGATGGCGTTAGACGTATTTTTC 57.286 39.130 2.27 0.00 44.73 2.29
2430 4734 5.416947 AGATGGCGTTAGACGTATTTTTCT 58.583 37.500 2.27 0.00 44.73 2.52
2432 4736 5.272167 TGGCGTTAGACGTATTTTTCTTG 57.728 39.130 2.27 0.00 44.73 3.02
2433 4737 4.086574 GGCGTTAGACGTATTTTTCTTGC 58.913 43.478 2.27 0.00 44.73 4.01
2473 4778 1.360393 AAACAGCCAACTCCCCTGGA 61.360 55.000 0.00 0.00 35.85 3.86
2509 4814 0.035915 GCACAAACTCTCCTCCCCTC 60.036 60.000 0.00 0.00 0.00 4.30
2510 4815 1.352083 CACAAACTCTCCTCCCCTCA 58.648 55.000 0.00 0.00 0.00 3.86
2516 4821 4.247380 CTCCTCCCCTCATGCCGC 62.247 72.222 0.00 0.00 0.00 6.53
2619 4924 2.520536 GCCGCCACTCCCCTATCAT 61.521 63.158 0.00 0.00 0.00 2.45
2621 4926 0.833834 CCGCCACTCCCCTATCATCT 60.834 60.000 0.00 0.00 0.00 2.90
2630 4935 1.363807 CCTATCATCTGTGCGCCGA 59.636 57.895 4.18 0.00 0.00 5.54
2651 4956 2.885644 CGTTCCCTCGCCACATCG 60.886 66.667 0.00 0.00 0.00 3.84
2721 5037 2.264480 CCGACATTGGCGAGGACA 59.736 61.111 14.86 0.00 0.00 4.02
2761 5077 0.108424 AAGGCGCAGTTCTAGCTCTG 60.108 55.000 10.83 8.85 35.12 3.35
2762 5078 1.520342 GGCGCAGTTCTAGCTCTGG 60.520 63.158 10.83 6.94 32.94 3.86
2763 5079 2.170434 GCGCAGTTCTAGCTCTGGC 61.170 63.158 0.30 11.21 39.06 4.85
2764 5080 1.520342 CGCAGTTCTAGCTCTGGCC 60.520 63.158 0.00 0.00 39.73 5.36
2776 5092 1.938596 TCTGGCCTCCTCTCCCTCT 60.939 63.158 3.32 0.00 0.00 3.69
2785 5101 1.034838 CCTCTCCCTCTCACTCACCG 61.035 65.000 0.00 0.00 0.00 4.94
2819 5135 2.668550 GCCGGGAAAACGAGCTGT 60.669 61.111 2.18 0.00 35.47 4.40
2823 5139 1.896660 GGGAAAACGAGCTGTGGCA 60.897 57.895 0.00 0.00 41.70 4.92
2826 5142 0.317854 GAAAACGAGCTGTGGCAACC 60.318 55.000 0.00 0.00 41.70 3.77
2918 5234 1.522569 GGGAAGATGGAGGTGGTCG 59.477 63.158 0.00 0.00 0.00 4.79
2920 5236 0.175989 GGAAGATGGAGGTGGTCGAC 59.824 60.000 7.13 7.13 0.00 4.20
2940 5256 2.747855 CTCGGGCTGCTTTCCACC 60.748 66.667 0.00 0.00 0.00 4.61
2954 5270 3.052082 CACCTGCACCAAGCTCCG 61.052 66.667 0.00 0.00 45.94 4.63
2991 5307 3.749064 GAGCACTGTCTCCGCCGA 61.749 66.667 0.00 0.00 0.00 5.54
3013 5329 0.107459 GATCAGGCGAGCTCCCTTTT 60.107 55.000 18.10 10.41 0.00 2.27
3029 5345 1.643868 TTTTCGGCTGGCGCATACTG 61.644 55.000 19.55 2.00 38.10 2.74
3031 5347 3.264897 CGGCTGGCGCATACTGTC 61.265 66.667 11.55 0.00 38.10 3.51
3034 5350 1.884926 GCTGGCGCATACTGTCTCC 60.885 63.158 10.83 0.00 35.78 3.71
3042 5358 0.179100 CATACTGTCTCCGCCACCAG 60.179 60.000 0.00 0.00 0.00 4.00
3059 5375 3.130516 CACCAGCCATCTTTCTCGTACTA 59.869 47.826 0.00 0.00 0.00 1.82
3065 5381 5.240623 AGCCATCTTTCTCGTACTATCTCTG 59.759 44.000 0.00 0.00 0.00 3.35
3069 5385 4.335874 TCTTTCTCGTACTATCTCTGCCAC 59.664 45.833 0.00 0.00 0.00 5.01
3093 5409 3.512516 GCCGCAAGATGAGTGCCC 61.513 66.667 0.00 0.00 38.86 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.135915 TCGCTCCTCTCTTCAAGCATC 59.864 52.381 0.00 0.00 34.39 3.91
37 38 2.372172 CACTTTCCCACCTACCTTCACT 59.628 50.000 0.00 0.00 0.00 3.41
41 42 2.224793 GCTTCACTTTCCCACCTACCTT 60.225 50.000 0.00 0.00 0.00 3.50
56 58 4.821589 CGAGGGGAGCCGCTTCAC 62.822 72.222 7.57 0.00 39.38 3.18
71 73 4.896829 CTAGAGCGGGGGAGGCGA 62.897 72.222 0.00 0.00 35.00 5.54
128 130 4.864334 CTCCATGGCCGCCTGACC 62.864 72.222 11.61 0.00 0.00 4.02
215 246 4.357947 GTCTCGAGGTGCGGTGCA 62.358 66.667 13.56 0.00 41.33 4.57
295 326 0.966875 TCTCGCTGCCATGCCATTTT 60.967 50.000 0.00 0.00 0.00 1.82
317 348 4.201783 GGAGTACATAAACATTGGCGACAC 60.202 45.833 0.00 0.00 42.67 3.67
319 350 3.311596 GGGAGTACATAAACATTGGCGAC 59.688 47.826 0.00 0.00 0.00 5.19
329 360 2.181125 TCGTGCAGGGGAGTACATAAA 58.819 47.619 6.56 0.00 0.00 1.40
349 380 1.705337 CGGTGGATGCGCGATTTCTT 61.705 55.000 12.10 0.00 0.00 2.52
370 401 8.306859 TCATCCTGATTGATGACTGTGGAGTC 62.307 46.154 0.00 0.00 44.65 3.36
377 408 4.049869 CGTCTCATCCTGATTGATGACTG 58.950 47.826 0.00 0.00 44.65 3.51
378 409 3.069300 CCGTCTCATCCTGATTGATGACT 59.931 47.826 0.00 0.00 44.65 3.41
379 410 3.068732 TCCGTCTCATCCTGATTGATGAC 59.931 47.826 0.00 0.00 44.65 3.06
385 416 1.686052 GCTCTCCGTCTCATCCTGATT 59.314 52.381 0.00 0.00 0.00 2.57
396 427 2.026879 GGCGAGATGCTCTCCGTC 59.973 66.667 7.36 0.00 45.43 4.79
409 440 2.808315 GAGCTGATTCTCCGGCGA 59.192 61.111 9.30 0.00 42.98 5.54
528 559 0.463295 AGATGCAAGGATGGCTCACG 60.463 55.000 0.00 0.00 34.64 4.35
533 564 0.473326 AGAGGAGATGCAAGGATGGC 59.527 55.000 0.00 0.00 33.57 4.40
534 565 3.294038 AAAGAGGAGATGCAAGGATGG 57.706 47.619 0.00 0.00 0.00 3.51
535 566 4.096081 GTGAAAAGAGGAGATGCAAGGATG 59.904 45.833 0.00 0.00 0.00 3.51
536 567 4.268359 GTGAAAAGAGGAGATGCAAGGAT 58.732 43.478 0.00 0.00 0.00 3.24
537 568 3.560025 GGTGAAAAGAGGAGATGCAAGGA 60.560 47.826 0.00 0.00 0.00 3.36
538 569 2.751806 GGTGAAAAGAGGAGATGCAAGG 59.248 50.000 0.00 0.00 0.00 3.61
539 570 3.190118 GTGGTGAAAAGAGGAGATGCAAG 59.810 47.826 0.00 0.00 0.00 4.01
541 572 2.553028 GGTGGTGAAAAGAGGAGATGCA 60.553 50.000 0.00 0.00 0.00 3.96
542 573 2.087646 GGTGGTGAAAAGAGGAGATGC 58.912 52.381 0.00 0.00 0.00 3.91
543 574 2.040278 TGGGTGGTGAAAAGAGGAGATG 59.960 50.000 0.00 0.00 0.00 2.90
544 575 2.348472 TGGGTGGTGAAAAGAGGAGAT 58.652 47.619 0.00 0.00 0.00 2.75
545 576 1.814429 TGGGTGGTGAAAAGAGGAGA 58.186 50.000 0.00 0.00 0.00 3.71
546 577 2.230660 GTTGGGTGGTGAAAAGAGGAG 58.769 52.381 0.00 0.00 0.00 3.69
547 578 1.566703 TGTTGGGTGGTGAAAAGAGGA 59.433 47.619 0.00 0.00 0.00 3.71
548 579 1.956477 CTGTTGGGTGGTGAAAAGAGG 59.044 52.381 0.00 0.00 0.00 3.69
549 580 1.956477 CCTGTTGGGTGGTGAAAAGAG 59.044 52.381 0.00 0.00 0.00 2.85
561 592 1.002087 GACACCTAGTGACCTGTTGGG 59.998 57.143 0.96 0.00 36.96 4.12
562 593 1.691976 TGACACCTAGTGACCTGTTGG 59.308 52.381 0.96 0.00 36.96 3.77
566 597 4.098654 CCTAAGATGACACCTAGTGACCTG 59.901 50.000 0.96 0.00 36.96 4.00
567 598 4.264442 ACCTAAGATGACACCTAGTGACCT 60.264 45.833 0.96 0.00 36.96 3.85
568 599 4.024670 ACCTAAGATGACACCTAGTGACC 58.975 47.826 0.96 0.00 36.96 4.02
569 600 4.142138 CCACCTAAGATGACACCTAGTGAC 60.142 50.000 0.96 0.00 36.96 3.67
570 601 4.023980 CCACCTAAGATGACACCTAGTGA 58.976 47.826 0.96 0.00 36.96 3.41
572 603 4.062490 ACCACCTAAGATGACACCTAGT 57.938 45.455 0.00 0.00 0.00 2.57
573 604 5.202004 ACTACCACCTAAGATGACACCTAG 58.798 45.833 0.00 0.00 0.00 3.02
574 605 5.202746 ACTACCACCTAAGATGACACCTA 57.797 43.478 0.00 0.00 0.00 3.08
575 606 4.062490 ACTACCACCTAAGATGACACCT 57.938 45.455 0.00 0.00 0.00 4.00
576 607 4.020485 ACAACTACCACCTAAGATGACACC 60.020 45.833 0.00 0.00 0.00 4.16
577 608 5.148651 ACAACTACCACCTAAGATGACAC 57.851 43.478 0.00 0.00 0.00 3.67
578 609 5.776208 TGTACAACTACCACCTAAGATGACA 59.224 40.000 0.00 0.00 0.00 3.58
580 611 5.106038 CGTGTACAACTACCACCTAAGATGA 60.106 44.000 0.00 0.00 0.00 2.92
581 612 5.100259 CGTGTACAACTACCACCTAAGATG 58.900 45.833 0.00 0.00 0.00 2.90
582 613 4.159135 CCGTGTACAACTACCACCTAAGAT 59.841 45.833 0.00 0.00 0.00 2.40
584 615 3.256631 ACCGTGTACAACTACCACCTAAG 59.743 47.826 0.00 0.00 0.00 2.18
585 616 3.230134 ACCGTGTACAACTACCACCTAA 58.770 45.455 0.00 0.00 0.00 2.69
586 617 2.875296 ACCGTGTACAACTACCACCTA 58.125 47.619 0.00 0.00 0.00 3.08
587 618 1.708341 ACCGTGTACAACTACCACCT 58.292 50.000 0.00 0.00 0.00 4.00
588 619 2.531522 AACCGTGTACAACTACCACC 57.468 50.000 0.00 0.00 0.00 4.61
589 620 2.545106 CCAAACCGTGTACAACTACCAC 59.455 50.000 0.00 0.00 0.00 4.16
590 621 2.433604 TCCAAACCGTGTACAACTACCA 59.566 45.455 0.00 0.00 0.00 3.25
592 623 5.678132 ATTTCCAAACCGTGTACAACTAC 57.322 39.130 0.00 0.00 0.00 2.73
593 624 7.879160 AGATTATTTCCAAACCGTGTACAACTA 59.121 33.333 0.00 0.00 0.00 2.24
595 626 6.905578 AGATTATTTCCAAACCGTGTACAAC 58.094 36.000 0.00 0.00 0.00 3.32
596 627 7.660617 TGTAGATTATTTCCAAACCGTGTACAA 59.339 33.333 0.00 0.00 0.00 2.41
597 628 7.160049 TGTAGATTATTTCCAAACCGTGTACA 58.840 34.615 0.00 0.00 0.00 2.90
598 629 7.599630 TGTAGATTATTTCCAAACCGTGTAC 57.400 36.000 0.00 0.00 0.00 2.90
599 630 7.879160 ACTTGTAGATTATTTCCAAACCGTGTA 59.121 33.333 0.00 0.00 0.00 2.90
601 632 7.094975 TGACTTGTAGATTATTTCCAAACCGTG 60.095 37.037 0.00 0.00 0.00 4.94
602 633 6.938030 TGACTTGTAGATTATTTCCAAACCGT 59.062 34.615 0.00 0.00 0.00 4.83
603 634 7.372451 TGACTTGTAGATTATTTCCAAACCG 57.628 36.000 0.00 0.00 0.00 4.44
615 646 7.974501 CGTACCAGTTCTATTGACTTGTAGATT 59.025 37.037 0.00 0.00 0.00 2.40
616 647 7.122353 ACGTACCAGTTCTATTGACTTGTAGAT 59.878 37.037 0.00 0.00 0.00 1.98
617 648 6.432162 ACGTACCAGTTCTATTGACTTGTAGA 59.568 38.462 0.00 0.00 0.00 2.59
618 649 6.618811 ACGTACCAGTTCTATTGACTTGTAG 58.381 40.000 0.00 0.00 0.00 2.74
619 650 6.349611 GGACGTACCAGTTCTATTGACTTGTA 60.350 42.308 0.00 0.00 38.79 2.41
620 651 5.464030 ACGTACCAGTTCTATTGACTTGT 57.536 39.130 0.00 0.00 0.00 3.16
621 652 4.863131 GGACGTACCAGTTCTATTGACTTG 59.137 45.833 0.00 0.00 38.79 3.16
622 653 4.771054 AGGACGTACCAGTTCTATTGACTT 59.229 41.667 0.00 0.00 42.04 3.01
625 656 5.163581 GCTAAGGACGTACCAGTTCTATTGA 60.164 44.000 0.00 0.00 42.04 2.57
626 657 5.041940 GCTAAGGACGTACCAGTTCTATTG 58.958 45.833 0.00 0.00 42.04 1.90
627 658 4.954826 AGCTAAGGACGTACCAGTTCTATT 59.045 41.667 0.00 0.00 42.04 1.73
628 659 4.534797 AGCTAAGGACGTACCAGTTCTAT 58.465 43.478 0.00 0.00 42.04 1.98
629 660 3.960571 AGCTAAGGACGTACCAGTTCTA 58.039 45.455 0.00 0.00 42.04 2.10
630 661 2.805194 AGCTAAGGACGTACCAGTTCT 58.195 47.619 0.00 0.00 42.04 3.01
631 662 3.488890 GCTAGCTAAGGACGTACCAGTTC 60.489 52.174 7.70 0.00 42.04 3.01
634 665 2.299521 AGCTAGCTAAGGACGTACCAG 58.700 52.381 17.69 0.00 42.04 4.00
635 666 2.431954 AGCTAGCTAAGGACGTACCA 57.568 50.000 17.69 0.00 42.04 3.25
636 667 3.252944 CCTAAGCTAGCTAAGGACGTACC 59.747 52.174 19.70 0.00 39.35 3.34
637 668 3.882288 ACCTAAGCTAGCTAAGGACGTAC 59.118 47.826 19.70 0.00 33.16 3.67
638 669 3.881688 CACCTAAGCTAGCTAAGGACGTA 59.118 47.826 19.70 3.66 33.16 3.57
641 672 3.032459 ACCACCTAAGCTAGCTAAGGAC 58.968 50.000 19.70 0.00 33.16 3.85
642 673 3.399952 ACCACCTAAGCTAGCTAAGGA 57.600 47.619 19.70 2.99 33.16 3.36
644 675 5.477291 TGCTATACCACCTAAGCTAGCTAAG 59.523 44.000 19.70 12.16 35.95 2.18
719 1272 3.219052 TGAACAACCGACAAAACAACC 57.781 42.857 0.00 0.00 0.00 3.77
823 1385 5.049405 ACAAGATCAATCACGTCAAAGAACC 60.049 40.000 0.00 0.00 0.00 3.62
828 1390 4.391830 GCCTACAAGATCAATCACGTCAAA 59.608 41.667 0.00 0.00 0.00 2.69
832 1394 2.165641 TCGCCTACAAGATCAATCACGT 59.834 45.455 0.00 0.00 0.00 4.49
833 1395 2.809446 TCGCCTACAAGATCAATCACG 58.191 47.619 0.00 0.00 0.00 4.35
834 1396 4.212214 GGATTCGCCTACAAGATCAATCAC 59.788 45.833 0.00 0.00 0.00 3.06
835 1397 4.380531 GGATTCGCCTACAAGATCAATCA 58.619 43.478 0.00 0.00 0.00 2.57
836 1398 3.748568 GGGATTCGCCTACAAGATCAATC 59.251 47.826 0.00 0.00 36.66 2.67
837 1399 3.136443 TGGGATTCGCCTACAAGATCAAT 59.864 43.478 0.00 0.00 36.66 2.57
838 1400 2.503765 TGGGATTCGCCTACAAGATCAA 59.496 45.455 0.00 0.00 36.66 2.57
839 1401 2.115427 TGGGATTCGCCTACAAGATCA 58.885 47.619 0.00 0.00 36.66 2.92
840 1402 2.872858 GTTGGGATTCGCCTACAAGATC 59.127 50.000 0.00 0.00 36.66 2.75
841 1403 2.238646 TGTTGGGATTCGCCTACAAGAT 59.761 45.455 0.00 0.00 36.66 2.40
842 1404 1.626321 TGTTGGGATTCGCCTACAAGA 59.374 47.619 0.00 0.00 36.66 3.02
843 1405 1.737793 GTGTTGGGATTCGCCTACAAG 59.262 52.381 8.97 0.00 34.53 3.16
844 1406 1.072489 TGTGTTGGGATTCGCCTACAA 59.928 47.619 8.97 0.00 34.53 2.41
845 1407 0.687920 TGTGTTGGGATTCGCCTACA 59.312 50.000 0.00 2.05 36.66 2.74
846 1408 1.084289 GTGTGTTGGGATTCGCCTAC 58.916 55.000 0.00 0.00 36.66 3.18
847 1409 0.687920 TGTGTGTTGGGATTCGCCTA 59.312 50.000 0.00 0.00 36.66 3.93
848 1410 0.038166 ATGTGTGTTGGGATTCGCCT 59.962 50.000 0.00 0.00 36.66 5.52
849 1411 1.400494 GTATGTGTGTTGGGATTCGCC 59.600 52.381 0.00 0.00 0.00 5.54
850 1412 2.080693 TGTATGTGTGTTGGGATTCGC 58.919 47.619 0.00 0.00 0.00 4.70
851 1413 2.418628 GGTGTATGTGTGTTGGGATTCG 59.581 50.000 0.00 0.00 0.00 3.34
852 1414 2.418628 CGGTGTATGTGTGTTGGGATTC 59.581 50.000 0.00 0.00 0.00 2.52
853 1415 2.224670 ACGGTGTATGTGTGTTGGGATT 60.225 45.455 0.00 0.00 0.00 3.01
854 1416 1.349688 ACGGTGTATGTGTGTTGGGAT 59.650 47.619 0.00 0.00 0.00 3.85
872 1434 4.205996 CAGCTAGATTGATTCACGAGAACG 59.794 45.833 0.00 0.00 45.75 3.95
895 1457 1.670967 GCCTTGCTTGATTTCACCAGC 60.671 52.381 0.00 0.00 32.02 4.85
990 1552 4.147449 TCCTCCATGACCGCAGCG 62.147 66.667 8.18 8.18 0.00 5.18
1014 3310 1.599047 CAGAGAACCACCGAGCCAT 59.401 57.895 0.00 0.00 0.00 4.40
1015 3311 3.059982 CAGAGAACCACCGAGCCA 58.940 61.111 0.00 0.00 0.00 4.75
1026 3322 1.080501 CGTTCGCTGGAGCAGAGAA 60.081 57.895 0.00 0.00 45.12 2.87
1087 3383 5.627367 CAGAATTTAATACCTCGCTCGAGAG 59.373 44.000 18.75 14.32 44.53 3.20
1092 3388 4.570772 TGCACAGAATTTAATACCTCGCTC 59.429 41.667 0.00 0.00 0.00 5.03
1103 3399 5.160641 GCTTTTCCGATTGCACAGAATTTA 58.839 37.500 0.00 0.00 0.00 1.40
1104 3400 3.989817 GCTTTTCCGATTGCACAGAATTT 59.010 39.130 0.00 0.00 0.00 1.82
1136 3432 4.778213 TTCTGGCTAATACAAGAGGCAT 57.222 40.909 0.00 0.00 45.99 4.40
1169 3465 9.234384 CAAGTACGACCATGATAAGTAAGTAAG 57.766 37.037 0.00 0.00 0.00 2.34
1212 3508 7.170393 ACAGCAGTATGTAAAGATGTACAGA 57.830 36.000 0.33 0.00 37.41 3.41
1219 3515 8.504005 GTGTTACAAACAGCAGTATGTAAAGAT 58.496 33.333 6.71 0.00 43.10 2.40
1227 3523 5.997746 AGTCATGTGTTACAAACAGCAGTAT 59.002 36.000 0.00 0.00 43.10 2.12
1242 3538 1.542915 GATTTGCAGGCAGTCATGTGT 59.457 47.619 0.00 0.00 0.00 3.72
1295 3591 4.391830 GGATGAGTAAAACGACATGCTCAA 59.608 41.667 9.74 0.00 40.77 3.02
1306 3602 7.826690 TGATTTGCTAAAGGGATGAGTAAAAC 58.173 34.615 0.00 0.00 30.29 2.43
1339 3635 7.944729 AAACCACAGCAACATCTATCTTATT 57.055 32.000 0.00 0.00 0.00 1.40
1348 3644 6.199937 AGATATCAAAACCACAGCAACATC 57.800 37.500 5.32 0.00 0.00 3.06
1435 3731 1.596603 TCGACTAACAGTGTCCGTGA 58.403 50.000 0.00 0.00 0.00 4.35
1572 3872 4.758674 CAGAATGCATCCCCATAGTTACTG 59.241 45.833 0.00 0.00 0.00 2.74
1582 3883 6.899393 TCAAAATATACAGAATGCATCCCC 57.101 37.500 0.00 0.00 42.53 4.81
1615 3916 5.282055 GGATCATGTCCTGTCTGTCAATA 57.718 43.478 0.00 0.00 44.16 1.90
1707 4008 5.405571 GCTGGATTGGTACACATAGATAACG 59.594 44.000 0.00 0.00 39.29 3.18
1775 4076 1.297378 CAACGCATCATGCAGCTCG 60.297 57.895 11.00 0.00 45.36 5.03
1782 4083 2.283298 AGCCTTAGACAACGCATCATG 58.717 47.619 0.00 0.00 0.00 3.07
1848 4149 9.975218 AAGTGATTTTGTATCCTACATAAGGTT 57.025 29.630 0.00 0.00 46.62 3.50
1885 4186 7.872993 TGTCAAACAAACAAACAGGACATTAAA 59.127 29.630 0.00 0.00 0.00 1.52
1966 4267 1.005037 TGAGTACACCTGCAAGCGG 60.005 57.895 0.00 0.00 0.00 5.52
2040 4343 1.251251 ATCAAGCAGGAAAGCACCAC 58.749 50.000 0.00 0.00 36.85 4.16
2058 4361 3.814615 CTGCCGGCGCCAGTGATAT 62.815 63.158 28.98 0.00 0.00 1.63
2071 4374 1.202651 CCTAACCCTAACATCCTGCCG 60.203 57.143 0.00 0.00 0.00 5.69
2111 4414 6.603201 TCTTTGGTTCTCAGTCTTTGAATGTT 59.397 34.615 0.00 0.00 34.81 2.71
2130 4433 4.796038 AATTCAACTGAGCCATCTTTGG 57.204 40.909 0.00 0.00 46.66 3.28
2184 4487 4.997395 ACACAAAGTCATCAAAGATAGCGT 59.003 37.500 0.00 0.00 0.00 5.07
2196 4499 6.949352 AATTCACTCTTCACACAAAGTCAT 57.051 33.333 0.00 0.00 0.00 3.06
2238 4542 2.031420 GGTTTCTGCAACCGTAACCTTC 60.031 50.000 5.92 0.00 45.98 3.46
2271 4575 9.921637 CAGAATTAGTGGTTTTTGGCTTAAATA 57.078 29.630 0.00 0.00 0.00 1.40
2276 4580 5.011023 CCTCAGAATTAGTGGTTTTTGGCTT 59.989 40.000 0.00 0.00 0.00 4.35
2277 4581 4.524328 CCTCAGAATTAGTGGTTTTTGGCT 59.476 41.667 0.00 0.00 0.00 4.75
2288 4592 8.635765 TTCAAAACATTAGCCTCAGAATTAGT 57.364 30.769 0.00 0.00 0.00 2.24
2340 4644 9.878599 CATGTCATAATTATCCTTAAAACGTCC 57.121 33.333 0.00 0.00 0.00 4.79
2348 4652 7.168219 GGCTCCACATGTCATAATTATCCTTA 58.832 38.462 0.00 0.00 0.00 2.69
2350 4654 5.515534 GGGCTCCACATGTCATAATTATCCT 60.516 44.000 0.00 0.00 0.00 3.24
2352 4656 5.316167 TGGGCTCCACATGTCATAATTATC 58.684 41.667 0.00 0.00 0.00 1.75
2353 4657 5.323382 TGGGCTCCACATGTCATAATTAT 57.677 39.130 0.00 0.00 0.00 1.28
2354 4658 4.787135 TGGGCTCCACATGTCATAATTA 57.213 40.909 0.00 0.00 0.00 1.40
2355 4659 3.668141 TGGGCTCCACATGTCATAATT 57.332 42.857 0.00 0.00 0.00 1.40
2375 4679 3.120923 CGTTACGCCACGTCAATAAAAGT 60.121 43.478 0.00 0.00 41.54 2.66
2394 4698 1.674817 CGCCATCTAGTCCAAACCGTT 60.675 52.381 0.00 0.00 0.00 4.44
2412 4716 3.772010 CGCAAGAAAAATACGTCTAACGC 59.228 43.478 0.00 0.00 43.63 4.84
2429 4733 5.432885 TTCCTAAAGGAGTTTTTCGCAAG 57.567 39.130 0.00 0.00 46.36 4.01
2430 4734 5.125739 TGTTTCCTAAAGGAGTTTTTCGCAA 59.874 36.000 0.00 0.00 46.36 4.85
2432 4736 5.177725 TGTTTCCTAAAGGAGTTTTTCGC 57.822 39.130 0.00 0.00 46.36 4.70
2433 4737 7.030768 TGTTTGTTTCCTAAAGGAGTTTTTCG 58.969 34.615 0.00 0.00 46.36 3.46
2557 4862 4.530857 ATGCGCAGGCCTACCGAC 62.531 66.667 24.37 16.66 42.76 4.79
2558 4863 4.529219 CATGCGCAGGCCTACCGA 62.529 66.667 24.37 12.37 42.76 4.69
2607 4912 1.043816 CGCACAGATGATAGGGGAGT 58.956 55.000 0.00 0.00 0.00 3.85
2630 4935 4.353437 GTGGCGAGGGAACGACGT 62.353 66.667 0.00 0.00 45.00 4.34
2643 4948 3.740128 ATCTGGCGGTCGATGTGGC 62.740 63.158 0.00 0.00 0.00 5.01
2696 5012 3.781307 CCAATGTCGGGCGGGAGA 61.781 66.667 0.00 0.00 0.00 3.71
2738 5054 1.975363 GCTAGAACTGCGCCTTGCTG 61.975 60.000 4.18 0.00 46.63 4.41
2761 5077 1.760480 GTGAGAGGGAGAGGAGGCC 60.760 68.421 0.00 0.00 0.00 5.19
2762 5078 0.755327 GAGTGAGAGGGAGAGGAGGC 60.755 65.000 0.00 0.00 0.00 4.70
2763 5079 0.628522 TGAGTGAGAGGGAGAGGAGG 59.371 60.000 0.00 0.00 0.00 4.30
2764 5080 1.684869 GGTGAGTGAGAGGGAGAGGAG 60.685 61.905 0.00 0.00 0.00 3.69
2793 5109 1.545841 GTTTTCCCGGCTGGATTCTT 58.454 50.000 15.09 0.00 44.66 2.52
2801 5117 2.358737 CAGCTCGTTTTCCCGGCT 60.359 61.111 0.00 0.00 35.65 5.52
2823 5139 3.210012 ATGGCCAGAGCAACGGGTT 62.210 57.895 13.05 0.00 42.56 4.11
2826 5142 3.197790 CGATGGCCAGAGCAACGG 61.198 66.667 13.05 0.00 42.56 4.44
2866 5182 2.034221 ACCCTGCCTTCTTTCGCC 59.966 61.111 0.00 0.00 0.00 5.54
2868 5184 0.674895 CTCCACCCTGCCTTCTTTCG 60.675 60.000 0.00 0.00 0.00 3.46
2869 5185 0.962855 GCTCCACCCTGCCTTCTTTC 60.963 60.000 0.00 0.00 0.00 2.62
2870 5186 1.075659 GCTCCACCCTGCCTTCTTT 59.924 57.895 0.00 0.00 0.00 2.52
2898 5214 0.914417 GACCACCTCCATCTTCCCCA 60.914 60.000 0.00 0.00 0.00 4.96
2935 5251 2.431683 GAGCTTGGTGCAGGTGGA 59.568 61.111 0.00 0.00 45.94 4.02
2936 5252 2.674380 GGAGCTTGGTGCAGGTGG 60.674 66.667 0.00 0.00 45.94 4.61
2991 5307 2.515071 GGGAGCTCGCCTGATCCAT 61.515 63.158 19.61 0.00 43.72 3.41
3013 5329 3.716539 GACAGTATGCGCCAGCCGA 62.717 63.158 4.18 0.00 42.53 5.54
3029 5345 4.101448 ATGGCTGGTGGCGGAGAC 62.101 66.667 0.00 0.00 42.94 3.36
3031 5347 2.826777 AAAGATGGCTGGTGGCGGAG 62.827 60.000 0.00 0.00 42.94 4.63
3034 5350 1.372087 GAGAAAGATGGCTGGTGGCG 61.372 60.000 0.00 0.00 42.94 5.69
3042 5358 5.457140 CAGAGATAGTACGAGAAAGATGGC 58.543 45.833 0.00 0.00 0.00 4.40
3059 5375 2.191375 CATGGCCGTGGCAGAGAT 59.809 61.111 17.90 0.00 42.43 2.75


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

AutoCloner maintained by Alex Coulton.