Multiple sequence alignment - TraesCS1D01G225100

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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 TraesCS1D01G225100 chr1D 100.000 3158 0 0 1 3158 313661662 313664819 0.000000e+00 5832
1 TraesCS1D01G225100 chr1B 95.052 970 45 2 1473 2439 423922542 423923511 0.000000e+00 1522
2 TraesCS1D01G225100 chr1B 91.326 807 56 9 656 1457 423921760 423922557 0.000000e+00 1090
3 TraesCS1D01G225100 chr1B 90.610 426 37 2 45 470 423920920 423921342 2.130000e-156 562
4 TraesCS1D01G225100 chr1A 94.356 815 41 2 645 1456 393998793 393999605 0.000000e+00 1245
5 TraesCS1D01G225100 chr1A 88.843 977 85 14 1471 2439 393999589 394000549 0.000000e+00 1179
6 TraesCS1D01G225100 chr1A 93.684 570 24 7 1 564 393998233 393998796 0.000000e+00 843
7 TraesCS1D01G225100 chr1A 89.720 107 7 4 313 417 12716817 12716921 1.980000e-27 134
8 TraesCS1D01G225100 chr2D 95.186 644 30 1 2516 3158 647842370 647843013 0.000000e+00 1016
9 TraesCS1D01G225100 chr2D 92.593 648 37 3 2521 3158 118538838 118538192 0.000000e+00 920
10 TraesCS1D01G225100 chr2D 91.770 644 46 5 2521 3158 15827890 15827248 0.000000e+00 889
11 TraesCS1D01G225100 chr2D 90.867 646 52 6 2519 3158 643680146 643680790 0.000000e+00 859
12 TraesCS1D01G225100 chr5D 94.523 639 34 1 2521 3158 426794143 426793505 0.000000e+00 985
13 TraesCS1D01G225100 chr6D 91.385 650 47 5 2518 3158 383214583 383215232 0.000000e+00 881
14 TraesCS1D01G225100 chr6D 91.264 641 52 3 2521 3158 82563845 82564484 0.000000e+00 870
15 TraesCS1D01G225100 chr7D 91.022 646 52 5 2517 3158 115039102 115038459 0.000000e+00 867
16 TraesCS1D01G225100 chr3D 90.867 646 52 6 2517 3158 463076867 463077509 0.000000e+00 859
17 TraesCS1D01G225100 chr2B 83.531 589 97 0 1560 2148 34475983 34476571 4.600000e-153 551
18 TraesCS1D01G225100 chr2B 82.683 589 102 0 1560 2148 34454484 34455072 1.000000e-144 523
19 TraesCS1D01G225100 chrUn 82.712 590 102 0 1559 2148 252346305 252346894 2.790000e-145 525
20 TraesCS1D01G225100 chrUn 82.712 590 102 0 1559 2148 335750031 335750620 2.790000e-145 525
21 TraesCS1D01G225100 chrUn 82.462 593 104 0 1559 2151 146898070 146897478 1.300000e-143 520
22 TraesCS1D01G225100 chrUn 82.462 593 104 0 1559 2151 154083246 154082654 1.300000e-143 520
23 TraesCS1D01G225100 chrUn 89.720 107 7 4 313 417 311465707 311465811 1.980000e-27 134
24 TraesCS1D01G225100 chr2A 82.631 593 103 0 1559 2151 22938694 22938102 2.790000e-145 525
25 TraesCS1D01G225100 chr4B 74.718 443 100 7 1000 1436 28157822 28158258 1.500000e-43 187
26 TraesCS1D01G225100 chr4B 74.550 444 99 9 1000 1436 28150494 28150930 6.960000e-42 182
27 TraesCS1D01G225100 chr4B 73.165 436 103 10 1008 1436 28153464 28153892 9.130000e-31 145
28 TraesCS1D01G225100 chr4A 74.229 454 107 6 1000 1448 584112759 584112311 6.960000e-42 182
29 TraesCS1D01G225100 chr4A 74.229 454 107 6 1000 1448 584115923 584115475 6.960000e-42 182
30 TraesCS1D01G225100 chr4A 73.789 454 109 6 1000 1448 584109600 584109152 1.510000e-38 171
31 TraesCS1D01G225100 chr4A 76.471 306 66 3 1000 1302 584106440 584106138 9.060000e-36 161
32 TraesCS1D01G225100 chr4A 74.277 346 85 3 1105 1448 584118976 584118633 3.280000e-30 143
33 TraesCS1D01G225100 chr4D 73.756 442 106 6 1000 1436 16252284 16252720 7.010000e-37 165


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 TraesCS1D01G225100 chr1D 313661662 313664819 3157 False 5832 5832 100.000000 1 3158 1 chr1D.!!$F1 3157
1 TraesCS1D01G225100 chr1B 423920920 423923511 2591 False 1058 1522 92.329333 45 2439 3 chr1B.!!$F1 2394
2 TraesCS1D01G225100 chr1A 393998233 394000549 2316 False 1089 1245 92.294333 1 2439 3 chr1A.!!$F2 2438
3 TraesCS1D01G225100 chr2D 647842370 647843013 643 False 1016 1016 95.186000 2516 3158 1 chr2D.!!$F2 642
4 TraesCS1D01G225100 chr2D 118538192 118538838 646 True 920 920 92.593000 2521 3158 1 chr2D.!!$R2 637
5 TraesCS1D01G225100 chr2D 15827248 15827890 642 True 889 889 91.770000 2521 3158 1 chr2D.!!$R1 637
6 TraesCS1D01G225100 chr2D 643680146 643680790 644 False 859 859 90.867000 2519 3158 1 chr2D.!!$F1 639
7 TraesCS1D01G225100 chr5D 426793505 426794143 638 True 985 985 94.523000 2521 3158 1 chr5D.!!$R1 637
8 TraesCS1D01G225100 chr6D 383214583 383215232 649 False 881 881 91.385000 2518 3158 1 chr6D.!!$F2 640
9 TraesCS1D01G225100 chr6D 82563845 82564484 639 False 870 870 91.264000 2521 3158 1 chr6D.!!$F1 637
10 TraesCS1D01G225100 chr7D 115038459 115039102 643 True 867 867 91.022000 2517 3158 1 chr7D.!!$R1 641
11 TraesCS1D01G225100 chr3D 463076867 463077509 642 False 859 859 90.867000 2517 3158 1 chr3D.!!$F1 641
12 TraesCS1D01G225100 chr2B 34475983 34476571 588 False 551 551 83.531000 1560 2148 1 chr2B.!!$F2 588
13 TraesCS1D01G225100 chr2B 34454484 34455072 588 False 523 523 82.683000 1560 2148 1 chr2B.!!$F1 588
14 TraesCS1D01G225100 chrUn 252346305 252346894 589 False 525 525 82.712000 1559 2148 1 chrUn.!!$F1 589
15 TraesCS1D01G225100 chrUn 335750031 335750620 589 False 525 525 82.712000 1559 2148 1 chrUn.!!$F3 589
16 TraesCS1D01G225100 chrUn 146897478 146898070 592 True 520 520 82.462000 1559 2151 1 chrUn.!!$R1 592
17 TraesCS1D01G225100 chrUn 154082654 154083246 592 True 520 520 82.462000 1559 2151 1 chrUn.!!$R2 592
18 TraesCS1D01G225100 chr2A 22938102 22938694 592 True 525 525 82.631000 1559 2151 1 chr2A.!!$R1 592

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
67 68 0.316689 AGAAAAACAAAGGCGCGACG 60.317 50.0 12.10 0.0 0.00 5.12 F
833 1152 0.506932 CAGTACAACTTCGTGCACGG 59.493 55.0 36.41 24.5 40.29 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1103 1425 0.256752 CATCCAACCCTCATGCCTCA 59.743 55.0 0.0 0.0 0.00 3.86 R
2429 2757 0.037975 CCAGCATTTGAGGCAACCAC 60.038 55.0 0.0 0.0 37.17 4.16 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
38 39 0.742281 CAGGCTCGCAGCACAGTATT 60.742 55.000 9.78 0.00 44.75 1.89
39 40 0.824109 AGGCTCGCAGCACAGTATTA 59.176 50.000 9.78 0.00 44.75 0.98
40 41 1.414181 AGGCTCGCAGCACAGTATTAT 59.586 47.619 9.78 0.00 44.75 1.28
67 68 0.316689 AGAAAAACAAAGGCGCGACG 60.317 50.000 12.10 0.00 0.00 5.12
245 246 1.000396 GGCCTTCATCCCTGCAAGT 60.000 57.895 0.00 0.00 0.00 3.16
308 309 9.454859 CTTCCTCTAAATTTCACTTAGGTCATT 57.545 33.333 0.00 0.00 0.00 2.57
388 389 7.044183 GCAAAAGCCATTGTTGTTTACATTTTG 60.044 33.333 0.00 0.00 40.88 2.44
446 447 5.607939 TTTCCAATTCGGTAGCATAGAGA 57.392 39.130 0.00 0.00 35.57 3.10
447 448 5.808366 TTCCAATTCGGTAGCATAGAGAT 57.192 39.130 0.00 0.00 35.57 2.75
539 579 1.388065 CCTCCTAGTCACAGCCGAGG 61.388 65.000 0.00 0.00 0.00 4.63
564 604 5.354234 CCTGCTTAATACCTCATGTTCGTTT 59.646 40.000 0.00 0.00 0.00 3.60
565 605 6.537301 CCTGCTTAATACCTCATGTTCGTTTA 59.463 38.462 0.00 0.00 0.00 2.01
566 606 7.226720 CCTGCTTAATACCTCATGTTCGTTTAT 59.773 37.037 0.00 0.00 0.00 1.40
567 607 8.500753 TGCTTAATACCTCATGTTCGTTTATT 57.499 30.769 0.00 0.00 0.00 1.40
568 608 8.952278 TGCTTAATACCTCATGTTCGTTTATTT 58.048 29.630 0.00 0.00 0.00 1.40
586 626 9.955208 CGTTTATTTAAACTTAAACTGAAGGGT 57.045 29.630 16.63 0.00 42.46 4.34
591 631 8.584063 TTTAAACTTAAACTGAAGGGTGAACT 57.416 30.769 0.00 0.00 0.00 3.01
592 632 8.584063 TTAAACTTAAACTGAAGGGTGAACTT 57.416 30.769 0.00 0.00 0.00 2.66
593 633 7.476540 AAACTTAAACTGAAGGGTGAACTTT 57.523 32.000 0.00 0.00 0.00 2.66
594 634 7.476540 AACTTAAACTGAAGGGTGAACTTTT 57.523 32.000 0.00 0.00 0.00 2.27
595 635 7.476540 ACTTAAACTGAAGGGTGAACTTTTT 57.523 32.000 0.00 0.00 0.00 1.94
596 636 7.320399 ACTTAAACTGAAGGGTGAACTTTTTG 58.680 34.615 0.00 0.00 0.00 2.44
597 637 4.736126 AACTGAAGGGTGAACTTTTTGG 57.264 40.909 0.00 0.00 0.00 3.28
598 638 2.430694 ACTGAAGGGTGAACTTTTTGGC 59.569 45.455 0.00 0.00 0.00 4.52
599 639 1.407258 TGAAGGGTGAACTTTTTGGCG 59.593 47.619 0.00 0.00 0.00 5.69
600 640 1.679153 GAAGGGTGAACTTTTTGGCGA 59.321 47.619 0.00 0.00 0.00 5.54
601 641 1.770294 AGGGTGAACTTTTTGGCGAA 58.230 45.000 0.00 0.00 0.00 4.70
602 642 2.104170 AGGGTGAACTTTTTGGCGAAA 58.896 42.857 0.00 0.00 0.00 3.46
603 643 2.498078 AGGGTGAACTTTTTGGCGAAAA 59.502 40.909 11.95 11.95 35.94 2.29
604 644 3.133901 AGGGTGAACTTTTTGGCGAAAAT 59.866 39.130 12.85 0.00 36.68 1.82
605 645 3.493129 GGGTGAACTTTTTGGCGAAAATC 59.507 43.478 12.85 9.35 36.68 2.17
606 646 4.116238 GGTGAACTTTTTGGCGAAAATCA 58.884 39.130 12.85 11.65 36.68 2.57
607 647 4.568760 GGTGAACTTTTTGGCGAAAATCAA 59.431 37.500 12.85 0.00 36.68 2.57
608 648 5.489335 GTGAACTTTTTGGCGAAAATCAAC 58.511 37.500 12.85 6.34 36.68 3.18
609 649 5.290885 GTGAACTTTTTGGCGAAAATCAACT 59.709 36.000 12.85 0.00 36.68 3.16
610 650 5.518487 TGAACTTTTTGGCGAAAATCAACTC 59.482 36.000 12.85 6.54 36.68 3.01
611 651 4.368315 ACTTTTTGGCGAAAATCAACTCC 58.632 39.130 12.85 0.00 36.68 3.85
612 652 2.697431 TTTGGCGAAAATCAACTCCG 57.303 45.000 0.00 0.00 0.00 4.63
613 653 1.885560 TTGGCGAAAATCAACTCCGA 58.114 45.000 0.00 0.00 0.00 4.55
614 654 1.885560 TGGCGAAAATCAACTCCGAA 58.114 45.000 0.00 0.00 0.00 4.30
615 655 1.533731 TGGCGAAAATCAACTCCGAAC 59.466 47.619 0.00 0.00 0.00 3.95
616 656 1.533731 GGCGAAAATCAACTCCGAACA 59.466 47.619 0.00 0.00 0.00 3.18
617 657 2.031508 GGCGAAAATCAACTCCGAACAA 60.032 45.455 0.00 0.00 0.00 2.83
618 658 3.226347 GCGAAAATCAACTCCGAACAAG 58.774 45.455 0.00 0.00 0.00 3.16
619 659 3.303791 GCGAAAATCAACTCCGAACAAGT 60.304 43.478 0.00 0.00 0.00 3.16
620 660 4.788521 GCGAAAATCAACTCCGAACAAGTT 60.789 41.667 0.00 0.00 37.44 2.66
624 664 2.389713 CAACTCCGAACAAGTTGCTG 57.610 50.000 1.81 0.00 44.94 4.41
625 665 1.670811 CAACTCCGAACAAGTTGCTGT 59.329 47.619 1.81 0.00 44.94 4.40
626 666 1.299541 ACTCCGAACAAGTTGCTGTG 58.700 50.000 1.81 0.00 0.00 3.66
627 667 1.299541 CTCCGAACAAGTTGCTGTGT 58.700 50.000 1.81 0.00 0.00 3.72
628 668 1.670811 CTCCGAACAAGTTGCTGTGTT 59.329 47.619 1.81 0.00 40.61 3.32
629 669 2.088423 TCCGAACAAGTTGCTGTGTTT 58.912 42.857 1.81 0.00 38.07 2.83
630 670 2.096819 TCCGAACAAGTTGCTGTGTTTC 59.903 45.455 1.81 0.00 38.07 2.78
631 671 2.450160 CGAACAAGTTGCTGTGTTTCC 58.550 47.619 1.81 0.00 38.07 3.13
632 672 2.097466 CGAACAAGTTGCTGTGTTTCCT 59.903 45.455 1.81 0.00 38.07 3.36
633 673 3.427503 CGAACAAGTTGCTGTGTTTCCTT 60.428 43.478 1.81 0.00 38.07 3.36
634 674 4.494484 GAACAAGTTGCTGTGTTTCCTTT 58.506 39.130 1.81 0.00 38.07 3.11
635 675 3.848726 ACAAGTTGCTGTGTTTCCTTTG 58.151 40.909 1.81 0.00 0.00 2.77
636 676 3.189285 CAAGTTGCTGTGTTTCCTTTGG 58.811 45.455 0.00 0.00 0.00 3.28
637 677 2.733956 AGTTGCTGTGTTTCCTTTGGA 58.266 42.857 0.00 0.00 0.00 3.53
638 678 3.096092 AGTTGCTGTGTTTCCTTTGGAA 58.904 40.909 0.00 0.00 40.27 3.53
646 686 1.770294 TTTCCTTTGGAAACCTGCGT 58.230 45.000 7.60 0.00 45.42 5.24
647 687 1.770294 TTCCTTTGGAAACCTGCGTT 58.230 45.000 0.00 0.00 38.93 4.84
725 1044 4.275936 GGTTGTTCTCACAGTTACAGCAAT 59.724 41.667 0.00 0.00 33.22 3.56
833 1152 0.506932 CAGTACAACTTCGTGCACGG 59.493 55.000 36.41 24.50 40.29 4.94
892 1214 5.646577 ATACAAGTACCTGTGACTCTGAC 57.353 43.478 7.40 0.00 0.00 3.51
988 1310 3.573967 GGAAGCAATTTGGAAGAGGACAA 59.426 43.478 0.00 0.00 0.00 3.18
1103 1425 3.507162 TGATGACTTGTCAATGGTGGT 57.493 42.857 7.57 0.00 0.00 4.16
1104 1426 3.148412 TGATGACTTGTCAATGGTGGTG 58.852 45.455 7.57 0.00 0.00 4.17
1124 1446 1.217057 AGGCATGAGGGTTGGATGGT 61.217 55.000 0.00 0.00 0.00 3.55
1131 1453 2.127708 GAGGGTTGGATGGTGGAGTAT 58.872 52.381 0.00 0.00 0.00 2.12
1226 1548 2.535788 CGTTCAACGCCGGAAACCA 61.536 57.895 5.05 0.00 33.65 3.67
1279 1601 4.117685 TGATCTCAGCAATGATGAGTTCG 58.882 43.478 25.14 3.89 45.03 3.95
1287 1609 0.327924 ATGATGAGTTCGGGGCAACA 59.672 50.000 0.00 0.00 39.74 3.33
1292 1614 0.875059 GAGTTCGGGGCAACAAAGAG 59.125 55.000 0.00 0.00 39.74 2.85
1401 1723 1.352622 ACTGGAGGACAAAGGGTGCA 61.353 55.000 0.00 0.00 40.89 4.57
1404 1726 0.890996 GGAGGACAAAGGGTGCAGTG 60.891 60.000 0.00 0.00 40.89 3.66
1436 1758 1.407437 GGATCAAGGCCAGTGTGGTAG 60.407 57.143 5.01 0.00 40.46 3.18
1456 1778 7.497909 GTGGTAGGTACATTTATGCTACATGTT 59.502 37.037 2.30 0.00 33.19 2.71
1457 1779 7.713507 TGGTAGGTACATTTATGCTACATGTTC 59.286 37.037 2.30 0.00 33.19 3.18
1458 1780 7.931948 GGTAGGTACATTTATGCTACATGTTCT 59.068 37.037 2.30 0.00 33.19 3.01
1459 1781 9.326413 GTAGGTACATTTATGCTACATGTTCTT 57.674 33.333 2.30 0.00 33.19 2.52
1461 1783 9.243105 AGGTACATTTATGCTACATGTTCTTTT 57.757 29.630 2.30 0.00 33.19 2.27
1462 1784 9.855021 GGTACATTTATGCTACATGTTCTTTTT 57.145 29.630 2.30 0.00 33.19 1.94
1483 1805 7.700322 TTTTTGCGAAAACATTTATGCTACA 57.300 28.000 7.81 0.00 30.07 2.74
1484 1806 7.881643 TTTTGCGAAAACATTTATGCTACAT 57.118 28.000 0.00 0.00 0.00 2.29
1485 1807 6.867799 TTGCGAAAACATTTATGCTACATG 57.132 33.333 0.00 0.00 0.00 3.21
1486 1808 5.948588 TGCGAAAACATTTATGCTACATGT 58.051 33.333 2.69 2.69 32.31 3.21
1498 1820 9.611284 ATTTATGCTACATGTTAATTGCATACG 57.389 29.630 19.65 0.00 41.23 3.06
1542 1864 4.005650 ACATGTCAGAATGGTGTGTGATC 58.994 43.478 0.00 0.00 36.16 2.92
1550 1872 6.923508 TCAGAATGGTGTGTGATCGAATATAC 59.076 38.462 0.00 0.00 36.16 1.47
1590 1912 2.158827 AGGTTGTTGTTGGGCATTTTCC 60.159 45.455 0.00 0.00 0.00 3.13
2091 2413 7.174946 GGCGAGAATGGATATTTAAGAATGGAA 59.825 37.037 0.00 0.00 0.00 3.53
2115 2437 1.002087 GACATCACCGACAAGAAGGGT 59.998 52.381 0.00 0.00 33.37 4.34
2148 2470 0.250467 CCATGGAGCCTTCATACCCG 60.250 60.000 5.56 0.00 0.00 5.28
2171 2493 3.692593 ACGGCATAGTTAAACCATCCAAC 59.307 43.478 0.00 0.00 0.00 3.77
2228 2550 7.545362 AATACATGCATGTCTCTTGTTCTAC 57.455 36.000 34.54 0.00 41.97 2.59
2233 2555 5.470368 TGCATGTCTCTTGTTCTACTGTAC 58.530 41.667 0.00 0.00 0.00 2.90
2248 2570 8.344098 GTTCTACTGTACTATCTCCATACACAC 58.656 40.741 0.00 0.00 0.00 3.82
2359 2687 8.015185 AGTATAAAATGCAATGCAAGAAGGAT 57.985 30.769 13.45 4.12 43.62 3.24
2376 2704 9.565213 CAAGAAGGATGATATGAAAAGTTCAAC 57.435 33.333 0.00 0.00 43.95 3.18
2378 2706 9.300681 AGAAGGATGATATGAAAAGTTCAACAA 57.699 29.630 0.00 0.00 43.95 2.83
2388 2716 6.910995 TGAAAAGTTCAACAAAAGGACGTTA 58.089 32.000 0.00 0.00 36.59 3.18
2405 2733 7.328737 AGGACGTTATAGACTTGTATTGCTTT 58.671 34.615 0.00 0.00 0.00 3.51
2414 2742 5.594317 AGACTTGTATTGCTTTCACCAAACT 59.406 36.000 0.00 0.00 0.00 2.66
2429 2757 0.035458 AAACTGCAAGGTCCTCCGAG 59.965 55.000 0.00 0.00 39.30 4.63
2433 2761 2.584391 GCAAGGTCCTCCGAGTGGT 61.584 63.158 0.00 0.00 39.05 4.16
2435 2763 0.320771 CAAGGTCCTCCGAGTGGTTG 60.321 60.000 0.00 0.00 39.05 3.77
2436 2764 2.047179 GGTCCTCCGAGTGGTTGC 60.047 66.667 0.00 0.00 36.30 4.17
2438 2766 2.203788 TCCTCCGAGTGGTTGCCT 60.204 61.111 0.00 0.00 36.30 4.75
2439 2767 2.266055 CCTCCGAGTGGTTGCCTC 59.734 66.667 0.00 0.00 36.30 4.70
2440 2768 2.583441 CCTCCGAGTGGTTGCCTCA 61.583 63.158 0.00 0.00 36.30 3.86
2441 2769 1.371183 CTCCGAGTGGTTGCCTCAA 59.629 57.895 0.00 0.00 36.30 3.02
2442 2770 0.250295 CTCCGAGTGGTTGCCTCAAA 60.250 55.000 0.00 0.00 36.30 2.69
2443 2771 0.400213 TCCGAGTGGTTGCCTCAAAT 59.600 50.000 0.00 0.00 36.30 2.32
2444 2772 0.523072 CCGAGTGGTTGCCTCAAATG 59.477 55.000 0.00 0.00 0.00 2.32
2445 2773 0.109597 CGAGTGGTTGCCTCAAATGC 60.110 55.000 0.00 0.00 0.00 3.56
2446 2774 1.251251 GAGTGGTTGCCTCAAATGCT 58.749 50.000 0.00 0.00 0.00 3.79
2447 2775 0.963962 AGTGGTTGCCTCAAATGCTG 59.036 50.000 0.00 0.00 0.00 4.41
2448 2776 0.037975 GTGGTTGCCTCAAATGCTGG 60.038 55.000 0.00 0.00 0.00 4.85
2449 2777 1.079612 GGTTGCCTCAAATGCTGGC 60.080 57.895 9.34 9.34 46.26 4.85
2452 2780 2.575461 GCCTCAAATGCTGGCACC 59.425 61.111 10.80 0.00 45.46 5.01
2453 2781 2.277591 GCCTCAAATGCTGGCACCA 61.278 57.895 10.80 0.00 45.46 4.17
2454 2782 1.610554 GCCTCAAATGCTGGCACCAT 61.611 55.000 10.80 0.00 45.46 3.55
2455 2783 0.458669 CCTCAAATGCTGGCACCATC 59.541 55.000 0.00 0.00 0.00 3.51
2456 2784 0.099968 CTCAAATGCTGGCACCATCG 59.900 55.000 0.00 0.00 0.00 3.84
2457 2785 1.140161 CAAATGCTGGCACCATCGG 59.860 57.895 0.00 0.00 0.00 4.18
2458 2786 1.304381 AAATGCTGGCACCATCGGT 60.304 52.632 0.00 0.00 35.62 4.69
2459 2787 1.315257 AAATGCTGGCACCATCGGTC 61.315 55.000 0.00 0.00 31.02 4.79
2460 2788 2.202236 AATGCTGGCACCATCGGTCT 62.202 55.000 0.00 0.00 31.02 3.85
2461 2789 2.821366 GCTGGCACCATCGGTCTG 60.821 66.667 0.00 0.00 31.02 3.51
2462 2790 2.981302 CTGGCACCATCGGTCTGA 59.019 61.111 0.00 0.00 31.02 3.27
2463 2791 1.524002 CTGGCACCATCGGTCTGAT 59.476 57.895 0.00 0.00 38.01 2.90
2471 2799 3.615597 ATCGGTCTGATGGTCTCCA 57.384 52.632 0.00 0.00 35.45 3.86
2472 2800 1.866015 ATCGGTCTGATGGTCTCCAA 58.134 50.000 0.00 0.00 36.95 3.53
2473 2801 1.186200 TCGGTCTGATGGTCTCCAAG 58.814 55.000 0.00 0.00 36.95 3.61
2474 2802 1.186200 CGGTCTGATGGTCTCCAAGA 58.814 55.000 0.00 0.00 36.95 3.02
2475 2803 1.759445 CGGTCTGATGGTCTCCAAGAT 59.241 52.381 0.00 0.00 36.95 2.40
2476 2804 2.223923 CGGTCTGATGGTCTCCAAGATC 60.224 54.545 0.00 0.00 36.95 2.75
2477 2805 3.037549 GGTCTGATGGTCTCCAAGATCT 58.962 50.000 0.00 0.00 36.95 2.75
2478 2806 3.181467 GGTCTGATGGTCTCCAAGATCTG 60.181 52.174 0.00 0.00 36.95 2.90
2479 2807 3.703556 GTCTGATGGTCTCCAAGATCTGA 59.296 47.826 0.00 0.00 36.95 3.27
2480 2808 3.959449 TCTGATGGTCTCCAAGATCTGAG 59.041 47.826 0.00 0.00 36.95 3.35
2481 2809 3.959449 CTGATGGTCTCCAAGATCTGAGA 59.041 47.826 8.35 8.35 36.95 3.27
2482 2810 4.554683 TGATGGTCTCCAAGATCTGAGAT 58.445 43.478 14.08 0.00 39.63 2.75
2483 2811 5.709594 TGATGGTCTCCAAGATCTGAGATA 58.290 41.667 14.08 8.51 39.63 1.98
2484 2812 5.774184 TGATGGTCTCCAAGATCTGAGATAG 59.226 44.000 14.08 4.48 39.63 2.08
2485 2813 4.478203 TGGTCTCCAAGATCTGAGATAGG 58.522 47.826 14.08 0.00 39.63 2.57
2486 2814 3.831911 GGTCTCCAAGATCTGAGATAGGG 59.168 52.174 14.08 0.00 39.63 3.53
2487 2815 4.448493 GGTCTCCAAGATCTGAGATAGGGA 60.448 50.000 14.08 2.11 39.63 4.20
2488 2816 4.766891 GTCTCCAAGATCTGAGATAGGGAG 59.233 50.000 21.40 21.40 39.63 4.30
2489 2817 4.667382 TCTCCAAGATCTGAGATAGGGAGA 59.333 45.833 24.03 24.03 45.35 3.71
2490 2818 5.315645 TCTCCAAGATCTGAGATAGGGAGAT 59.684 44.000 24.03 0.00 43.37 2.75
2491 2819 5.579047 TCCAAGATCTGAGATAGGGAGATC 58.421 45.833 0.00 0.00 41.64 2.75
2497 2825 7.965718 AGATCTGAGATAGGGAGATCTTTTTG 58.034 38.462 0.00 0.00 46.77 2.44
2498 2826 6.491714 TCTGAGATAGGGAGATCTTTTTGG 57.508 41.667 0.00 0.00 36.27 3.28
2499 2827 5.041191 TGAGATAGGGAGATCTTTTTGGC 57.959 43.478 0.00 0.00 36.27 4.52
2500 2828 4.061596 GAGATAGGGAGATCTTTTTGGCG 58.938 47.826 0.00 0.00 36.27 5.69
2501 2829 2.038387 TAGGGAGATCTTTTTGGCGC 57.962 50.000 0.00 0.00 0.00 6.53
2502 2830 0.681243 AGGGAGATCTTTTTGGCGCC 60.681 55.000 22.73 22.73 0.00 6.53
2503 2831 1.667154 GGGAGATCTTTTTGGCGCCC 61.667 60.000 26.77 5.30 0.00 6.13
2504 2832 0.681243 GGAGATCTTTTTGGCGCCCT 60.681 55.000 26.77 11.09 0.00 5.19
2505 2833 0.735471 GAGATCTTTTTGGCGCCCTC 59.265 55.000 26.77 16.48 0.00 4.30
2506 2834 0.329596 AGATCTTTTTGGCGCCCTCT 59.670 50.000 26.77 11.16 0.00 3.69
2507 2835 0.735471 GATCTTTTTGGCGCCCTCTC 59.265 55.000 26.77 7.22 0.00 3.20
2508 2836 0.329596 ATCTTTTTGGCGCCCTCTCT 59.670 50.000 26.77 0.00 0.00 3.10
2509 2837 0.110486 TCTTTTTGGCGCCCTCTCTT 59.890 50.000 26.77 0.00 0.00 2.85
2510 2838 0.242017 CTTTTTGGCGCCCTCTCTTG 59.758 55.000 26.77 4.17 0.00 3.02
2511 2839 0.467290 TTTTTGGCGCCCTCTCTTGT 60.467 50.000 26.77 0.00 0.00 3.16
2512 2840 0.889186 TTTTGGCGCCCTCTCTTGTC 60.889 55.000 26.77 0.00 0.00 3.18
2513 2841 2.748058 TTTGGCGCCCTCTCTTGTCC 62.748 60.000 26.77 0.00 0.00 4.02
2514 2842 3.394836 GGCGCCCTCTCTTGTCCT 61.395 66.667 18.11 0.00 0.00 3.85
2540 2868 2.510238 GCATCTTCAGCCGCGTCT 60.510 61.111 4.92 0.00 0.00 4.18
2550 2878 2.664851 CCGCGTCTTCAACAGGCA 60.665 61.111 4.92 0.00 0.00 4.75
2551 2879 2.034879 CCGCGTCTTCAACAGGCAT 61.035 57.895 4.92 0.00 0.00 4.40
2554 2882 1.334960 CGCGTCTTCAACAGGCATTTT 60.335 47.619 0.00 0.00 0.00 1.82
2602 2931 2.538512 AAAAACGGCCTAGTCGTCTT 57.461 45.000 0.00 0.00 45.33 3.01
2645 2978 4.966787 GGGCCGAAACTGGTGCCA 62.967 66.667 0.00 0.00 45.83 4.92
2918 3253 1.294780 CAGCCGAAGCAGAGGAAGT 59.705 57.895 0.00 0.00 43.56 3.01
2991 3326 2.156051 GAAGTTCAGCGACGGGAGGT 62.156 60.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 6.037172 GCGCCTTTGTTTTTCTCTCTATGATA 59.963 38.462 0.00 0.00 0.00 2.15
39 40 5.163713 GCGCCTTTGTTTTTCTCTCTATGAT 60.164 40.000 0.00 0.00 0.00 2.45
40 41 4.154195 GCGCCTTTGTTTTTCTCTCTATGA 59.846 41.667 0.00 0.00 0.00 2.15
212 213 2.812619 GGCCGATCCAGAGAAGGGG 61.813 68.421 0.00 0.00 34.01 4.79
388 389 0.249447 GGCCTTTGTTGTGAACCTGC 60.249 55.000 0.00 0.00 0.00 4.85
505 545 1.090052 GGAGGTCAATACGCAGTGGC 61.090 60.000 0.00 0.00 45.73 5.01
539 579 3.248602 CGAACATGAGGTATTAAGCAGGC 59.751 47.826 0.00 0.00 0.00 4.85
565 605 9.197306 AGTTCACCCTTCAGTTTAAGTTTAAAT 57.803 29.630 0.86 0.00 35.35 1.40
566 606 8.584063 AGTTCACCCTTCAGTTTAAGTTTAAA 57.416 30.769 0.00 0.00 0.00 1.52
567 607 8.584063 AAGTTCACCCTTCAGTTTAAGTTTAA 57.416 30.769 0.00 0.00 0.00 1.52
568 608 8.584063 AAAGTTCACCCTTCAGTTTAAGTTTA 57.416 30.769 0.00 0.00 0.00 2.01
569 609 7.476540 AAAGTTCACCCTTCAGTTTAAGTTT 57.523 32.000 0.00 0.00 0.00 2.66
570 610 7.476540 AAAAGTTCACCCTTCAGTTTAAGTT 57.523 32.000 0.00 0.00 0.00 2.66
571 611 7.320399 CAAAAAGTTCACCCTTCAGTTTAAGT 58.680 34.615 0.00 0.00 0.00 2.24
572 612 6.756542 CCAAAAAGTTCACCCTTCAGTTTAAG 59.243 38.462 0.00 0.00 0.00 1.85
573 613 6.635755 CCAAAAAGTTCACCCTTCAGTTTAA 58.364 36.000 0.00 0.00 0.00 1.52
574 614 5.394773 GCCAAAAAGTTCACCCTTCAGTTTA 60.395 40.000 0.00 0.00 0.00 2.01
575 615 4.622933 GCCAAAAAGTTCACCCTTCAGTTT 60.623 41.667 0.00 0.00 0.00 2.66
576 616 3.118775 GCCAAAAAGTTCACCCTTCAGTT 60.119 43.478 0.00 0.00 0.00 3.16
577 617 2.430694 GCCAAAAAGTTCACCCTTCAGT 59.569 45.455 0.00 0.00 0.00 3.41
578 618 2.543653 CGCCAAAAAGTTCACCCTTCAG 60.544 50.000 0.00 0.00 0.00 3.02
579 619 1.407258 CGCCAAAAAGTTCACCCTTCA 59.593 47.619 0.00 0.00 0.00 3.02
580 620 1.679153 TCGCCAAAAAGTTCACCCTTC 59.321 47.619 0.00 0.00 0.00 3.46
581 621 1.770294 TCGCCAAAAAGTTCACCCTT 58.230 45.000 0.00 0.00 0.00 3.95
582 622 1.770294 TTCGCCAAAAAGTTCACCCT 58.230 45.000 0.00 0.00 0.00 4.34
583 623 2.588027 TTTCGCCAAAAAGTTCACCC 57.412 45.000 0.00 0.00 0.00 4.61
584 624 4.116238 TGATTTTCGCCAAAAAGTTCACC 58.884 39.130 0.00 0.00 40.09 4.02
585 625 5.290885 AGTTGATTTTCGCCAAAAAGTTCAC 59.709 36.000 0.00 0.00 40.09 3.18
586 626 5.415221 AGTTGATTTTCGCCAAAAAGTTCA 58.585 33.333 0.00 0.00 40.09 3.18
587 627 5.051039 GGAGTTGATTTTCGCCAAAAAGTTC 60.051 40.000 0.00 0.00 40.09 3.01
588 628 4.808895 GGAGTTGATTTTCGCCAAAAAGTT 59.191 37.500 0.00 0.00 40.09 2.66
589 629 4.368315 GGAGTTGATTTTCGCCAAAAAGT 58.632 39.130 0.00 0.00 40.09 2.66
590 630 3.425193 CGGAGTTGATTTTCGCCAAAAAG 59.575 43.478 0.00 0.00 40.09 2.27
591 631 3.066900 TCGGAGTTGATTTTCGCCAAAAA 59.933 39.130 0.00 0.00 40.98 1.94
592 632 2.619177 TCGGAGTTGATTTTCGCCAAAA 59.381 40.909 0.00 0.00 35.92 2.44
593 633 2.222886 TCGGAGTTGATTTTCGCCAAA 58.777 42.857 0.00 0.00 0.00 3.28
594 634 1.885560 TCGGAGTTGATTTTCGCCAA 58.114 45.000 0.00 0.00 0.00 4.52
595 635 1.533731 GTTCGGAGTTGATTTTCGCCA 59.466 47.619 0.00 0.00 0.00 5.69
596 636 1.533731 TGTTCGGAGTTGATTTTCGCC 59.466 47.619 0.00 0.00 0.00 5.54
597 637 2.961522 TGTTCGGAGTTGATTTTCGC 57.038 45.000 0.00 0.00 0.00 4.70
598 638 4.468095 ACTTGTTCGGAGTTGATTTTCG 57.532 40.909 0.00 0.00 0.00 3.46
606 646 1.670811 CACAGCAACTTGTTCGGAGTT 59.329 47.619 0.00 0.00 37.82 3.01
607 647 1.299541 CACAGCAACTTGTTCGGAGT 58.700 50.000 0.00 0.00 0.00 3.85
608 648 1.299541 ACACAGCAACTTGTTCGGAG 58.700 50.000 0.00 0.00 0.00 4.63
609 649 1.745232 AACACAGCAACTTGTTCGGA 58.255 45.000 0.00 0.00 29.75 4.55
610 650 2.450160 GAAACACAGCAACTTGTTCGG 58.550 47.619 0.00 0.00 34.82 4.30
611 651 2.097466 AGGAAACACAGCAACTTGTTCG 59.903 45.455 0.00 0.00 34.82 3.95
612 652 3.782889 AGGAAACACAGCAACTTGTTC 57.217 42.857 0.00 0.00 34.82 3.18
613 653 4.244862 CAAAGGAAACACAGCAACTTGTT 58.755 39.130 0.00 0.00 37.55 2.83
614 654 3.368323 CCAAAGGAAACACAGCAACTTGT 60.368 43.478 0.00 0.00 0.00 3.16
615 655 3.119173 TCCAAAGGAAACACAGCAACTTG 60.119 43.478 0.00 0.00 0.00 3.16
616 656 3.096092 TCCAAAGGAAACACAGCAACTT 58.904 40.909 0.00 0.00 0.00 2.66
617 657 2.733956 TCCAAAGGAAACACAGCAACT 58.266 42.857 0.00 0.00 0.00 3.16
618 658 3.518634 TTCCAAAGGAAACACAGCAAC 57.481 42.857 0.00 0.00 38.93 4.17
628 668 1.770294 AACGCAGGTTTCCAAAGGAA 58.230 45.000 0.00 0.00 40.27 3.36
629 669 2.642154 TAACGCAGGTTTCCAAAGGA 57.358 45.000 0.00 0.00 37.58 3.36
630 670 2.817258 TCATAACGCAGGTTTCCAAAGG 59.183 45.455 0.00 0.00 37.58 3.11
631 671 3.365969 GGTCATAACGCAGGTTTCCAAAG 60.366 47.826 0.00 0.00 37.58 2.77
632 672 2.554893 GGTCATAACGCAGGTTTCCAAA 59.445 45.455 0.00 0.00 37.58 3.28
633 673 2.156098 GGTCATAACGCAGGTTTCCAA 58.844 47.619 0.00 0.00 37.58 3.53
634 674 1.612199 GGGTCATAACGCAGGTTTCCA 60.612 52.381 0.00 0.00 38.19 3.53
635 675 1.092348 GGGTCATAACGCAGGTTTCC 58.908 55.000 0.00 0.00 38.19 3.13
636 676 2.109425 AGGGTCATAACGCAGGTTTC 57.891 50.000 0.00 0.00 40.65 2.78
637 677 3.199071 TGATAGGGTCATAACGCAGGTTT 59.801 43.478 0.00 0.00 40.65 3.27
638 678 2.769663 TGATAGGGTCATAACGCAGGTT 59.230 45.455 0.00 0.00 40.65 3.50
639 679 2.394632 TGATAGGGTCATAACGCAGGT 58.605 47.619 0.00 0.00 40.65 4.00
640 680 3.685139 ATGATAGGGTCATAACGCAGG 57.315 47.619 0.00 0.00 45.67 4.85
677 996 0.457166 TTATGCCGGAGTTCACGTCG 60.457 55.000 5.05 0.00 0.00 5.12
725 1044 2.975410 ATTGTGAACGAGACGTACGA 57.025 45.000 24.41 0.00 39.99 3.43
833 1152 4.201970 GGAGATAGCTACATAGATGCGGTC 60.202 50.000 0.00 0.00 0.00 4.79
871 1193 4.726583 AGTCAGAGTCACAGGTACTTGTA 58.273 43.478 10.65 0.00 34.60 2.41
872 1194 3.567397 AGTCAGAGTCACAGGTACTTGT 58.433 45.455 4.53 4.53 34.60 3.16
892 1214 9.716556 ATGGAACTAGGTGGGAATATATAGTAG 57.283 37.037 0.00 0.00 0.00 2.57
988 1310 2.291735 TGATGGCCATGTTTGATCAGGT 60.292 45.455 26.56 0.00 0.00 4.00
1083 1405 3.148412 CACCACCATTGACAAGTCATCA 58.852 45.455 3.43 0.00 39.64 3.07
1103 1425 0.256752 CATCCAACCCTCATGCCTCA 59.743 55.000 0.00 0.00 0.00 3.86
1104 1426 0.466922 CCATCCAACCCTCATGCCTC 60.467 60.000 0.00 0.00 0.00 4.70
1124 1446 0.452987 GTACACGCGACCATACTCCA 59.547 55.000 15.93 0.00 0.00 3.86
1131 1453 1.007038 GTCCTTGTACACGCGACCA 60.007 57.895 15.93 0.00 0.00 4.02
1165 1487 5.679601 AGCCTTGAATATCTCAAACCTCTC 58.320 41.667 3.16 0.00 43.54 3.20
1196 1518 2.316792 CGTTGAACGACTCGATGAACT 58.683 47.619 13.13 0.00 46.05 3.01
1226 1548 1.072806 TGATGCTGAGCCAGAACTTGT 59.927 47.619 0.23 0.00 32.44 3.16
1279 1601 2.224042 CCTTGTTTCTCTTTGTTGCCCC 60.224 50.000 0.00 0.00 0.00 5.80
1287 1609 4.588951 GGAATGAACCCCTTGTTTCTCTTT 59.411 41.667 0.00 0.00 37.29 2.52
1378 1700 0.995024 CCCTTTGTCCTCCAGTCCAT 59.005 55.000 0.00 0.00 0.00 3.41
1401 1723 2.837947 TGATCCTTGATGGGAGTCACT 58.162 47.619 0.00 0.00 38.92 3.41
1404 1726 2.747799 GCCTTGATCCTTGATGGGAGTC 60.748 54.545 0.00 0.00 38.92 3.36
1459 1781 7.700322 TGTAGCATAAATGTTTTCGCAAAAA 57.300 28.000 0.00 0.00 31.13 1.94
1461 1783 7.275697 CATGTAGCATAAATGTTTTCGCAAA 57.724 32.000 0.00 0.00 31.47 3.68
1462 1784 6.867799 CATGTAGCATAAATGTTTTCGCAA 57.132 33.333 0.00 0.00 31.47 4.85
1472 1794 9.611284 CGTATGCAATTAACATGTAGCATAAAT 57.389 29.630 21.07 7.59 43.82 1.40
1473 1795 8.616942 ACGTATGCAATTAACATGTAGCATAAA 58.383 29.630 21.07 8.72 43.82 1.40
1474 1796 8.148807 ACGTATGCAATTAACATGTAGCATAA 57.851 30.769 21.07 9.67 43.82 1.90
1475 1797 7.722795 ACGTATGCAATTAACATGTAGCATA 57.277 32.000 18.01 18.01 42.16 3.14
1476 1798 6.618287 ACGTATGCAATTAACATGTAGCAT 57.382 33.333 19.40 19.40 44.09 3.79
1477 1799 7.439655 TCATACGTATGCAATTAACATGTAGCA 59.560 33.333 27.23 5.56 36.34 3.49
1478 1800 7.792925 TCATACGTATGCAATTAACATGTAGC 58.207 34.615 27.23 0.00 33.76 3.58
2008 2330 0.598158 TTTGTACCGTCACTGGTCGC 60.598 55.000 0.00 0.00 42.62 5.19
2091 2413 3.815401 CCTTCTTGTCGGTGATGTCTTTT 59.185 43.478 0.00 0.00 0.00 2.27
2148 2470 3.537580 TGGATGGTTTAACTATGCCGTC 58.462 45.455 10.03 0.00 36.56 4.79
2171 2493 6.036408 CCATGTCTATATGTGAATATGTGGCG 59.964 42.308 0.00 0.00 0.00 5.69
2228 2550 5.066117 ACACGTGTGTATGGAGATAGTACAG 59.934 44.000 22.71 0.00 42.90 2.74
2248 2570 5.170625 GTGTAACACAATTTACAAGCACACG 59.829 40.000 0.00 0.00 42.27 4.49
2347 2675 7.893124 ACTTTTCATATCATCCTTCTTGCAT 57.107 32.000 0.00 0.00 0.00 3.96
2359 2687 7.860373 CGTCCTTTTGTTGAACTTTTCATATCA 59.140 33.333 0.00 0.00 39.84 2.15
2376 2704 7.903431 GCAATACAAGTCTATAACGTCCTTTTG 59.097 37.037 0.00 0.00 0.00 2.44
2378 2706 7.328737 AGCAATACAAGTCTATAACGTCCTTT 58.671 34.615 0.00 0.00 0.00 3.11
2405 2733 0.550914 AGGACCTTGCAGTTTGGTGA 59.449 50.000 7.35 0.00 33.74 4.02
2414 2742 2.583441 CCACTCGGAGGACCTTGCA 61.583 63.158 10.23 0.00 0.00 4.08
2429 2757 0.037975 CCAGCATTTGAGGCAACCAC 60.038 55.000 0.00 0.00 37.17 4.16
2436 2764 0.458669 GATGGTGCCAGCATTTGAGG 59.541 55.000 11.18 0.00 36.31 3.86
2438 2766 1.314534 CCGATGGTGCCAGCATTTGA 61.315 55.000 11.18 0.00 36.31 2.69
2439 2767 1.140161 CCGATGGTGCCAGCATTTG 59.860 57.895 11.18 6.93 36.31 2.32
2440 2768 1.304381 ACCGATGGTGCCAGCATTT 60.304 52.632 11.18 0.00 36.31 2.32
2441 2769 1.750399 GACCGATGGTGCCAGCATT 60.750 57.895 11.18 0.00 36.31 3.56
2442 2770 2.124570 GACCGATGGTGCCAGCAT 60.125 61.111 9.51 9.51 39.30 3.79
2443 2771 3.321648 AGACCGATGGTGCCAGCA 61.322 61.111 0.00 0.00 35.25 4.41
2444 2772 2.599645 ATCAGACCGATGGTGCCAGC 62.600 60.000 0.00 0.00 35.25 4.85
2445 2773 0.812811 CATCAGACCGATGGTGCCAG 60.813 60.000 0.00 0.00 46.73 4.85
2446 2774 1.221566 CATCAGACCGATGGTGCCA 59.778 57.895 0.00 0.00 46.73 4.92
2447 2775 4.131376 CATCAGACCGATGGTGCC 57.869 61.111 0.00 0.00 46.73 5.01
2453 2781 1.759445 CTTGGAGACCATCAGACCGAT 59.241 52.381 0.00 0.00 31.53 4.18
2454 2782 1.186200 CTTGGAGACCATCAGACCGA 58.814 55.000 0.00 0.00 31.53 4.69
2455 2783 1.186200 TCTTGGAGACCATCAGACCG 58.814 55.000 0.00 0.00 31.53 4.79
2456 2784 3.037549 AGATCTTGGAGACCATCAGACC 58.962 50.000 0.00 0.00 31.53 3.85
2457 2785 3.703556 TCAGATCTTGGAGACCATCAGAC 59.296 47.826 0.00 0.00 31.53 3.51
2458 2786 3.959449 CTCAGATCTTGGAGACCATCAGA 59.041 47.826 4.41 0.00 31.53 3.27
2459 2787 3.959449 TCTCAGATCTTGGAGACCATCAG 59.041 47.826 8.35 0.00 35.34 2.90
2460 2788 3.986435 TCTCAGATCTTGGAGACCATCA 58.014 45.455 8.35 0.00 35.34 3.07
2461 2789 5.185635 CCTATCTCAGATCTTGGAGACCATC 59.814 48.000 13.45 0.00 42.49 3.51
2462 2790 5.085920 CCTATCTCAGATCTTGGAGACCAT 58.914 45.833 13.45 3.30 42.49 3.55
2463 2791 4.478203 CCTATCTCAGATCTTGGAGACCA 58.522 47.826 13.45 5.77 42.49 4.02
2464 2792 3.831911 CCCTATCTCAGATCTTGGAGACC 59.168 52.174 13.45 0.00 42.49 3.85
2465 2793 4.735369 TCCCTATCTCAGATCTTGGAGAC 58.265 47.826 13.45 0.00 42.49 3.36
2466 2794 4.667382 TCTCCCTATCTCAGATCTTGGAGA 59.333 45.833 19.07 19.07 43.53 3.71
2467 2795 4.996793 TCTCCCTATCTCAGATCTTGGAG 58.003 47.826 16.10 16.10 39.57 3.86
2468 2796 5.579047 GATCTCCCTATCTCAGATCTTGGA 58.421 45.833 0.00 0.00 39.61 3.53
2469 2797 5.920193 GATCTCCCTATCTCAGATCTTGG 57.080 47.826 0.00 0.00 39.61 3.61
2473 2801 7.160726 CCAAAAAGATCTCCCTATCTCAGATC 58.839 42.308 0.00 0.00 42.00 2.75
2474 2802 6.465607 GCCAAAAAGATCTCCCTATCTCAGAT 60.466 42.308 0.00 0.00 35.10 2.90
2475 2803 5.163258 GCCAAAAAGATCTCCCTATCTCAGA 60.163 44.000 0.00 0.00 35.10 3.27
2476 2804 5.062528 GCCAAAAAGATCTCCCTATCTCAG 58.937 45.833 0.00 0.00 35.10 3.35
2477 2805 4.443457 CGCCAAAAAGATCTCCCTATCTCA 60.443 45.833 0.00 0.00 35.10 3.27
2478 2806 4.061596 CGCCAAAAAGATCTCCCTATCTC 58.938 47.826 0.00 0.00 35.10 2.75
2479 2807 3.745797 GCGCCAAAAAGATCTCCCTATCT 60.746 47.826 0.00 0.00 37.84 1.98
2480 2808 2.550180 GCGCCAAAAAGATCTCCCTATC 59.450 50.000 0.00 0.00 0.00 2.08
2481 2809 2.576615 GCGCCAAAAAGATCTCCCTAT 58.423 47.619 0.00 0.00 0.00 2.57
2482 2810 1.408266 GGCGCCAAAAAGATCTCCCTA 60.408 52.381 24.80 0.00 0.00 3.53
2483 2811 0.681243 GGCGCCAAAAAGATCTCCCT 60.681 55.000 24.80 0.00 0.00 4.20
2484 2812 1.667154 GGGCGCCAAAAAGATCTCCC 61.667 60.000 30.85 0.98 0.00 4.30
2485 2813 0.681243 AGGGCGCCAAAAAGATCTCC 60.681 55.000 30.85 5.70 0.00 3.71
2486 2814 0.735471 GAGGGCGCCAAAAAGATCTC 59.265 55.000 30.85 18.53 0.00 2.75
2487 2815 0.329596 AGAGGGCGCCAAAAAGATCT 59.670 50.000 30.85 13.56 0.00 2.75
2488 2816 0.735471 GAGAGGGCGCCAAAAAGATC 59.265 55.000 30.85 13.29 0.00 2.75
2489 2817 0.329596 AGAGAGGGCGCCAAAAAGAT 59.670 50.000 30.85 5.95 0.00 2.40
2490 2818 0.110486 AAGAGAGGGCGCCAAAAAGA 59.890 50.000 30.85 0.00 0.00 2.52
2491 2819 0.242017 CAAGAGAGGGCGCCAAAAAG 59.758 55.000 30.85 7.49 0.00 2.27
2492 2820 0.467290 ACAAGAGAGGGCGCCAAAAA 60.467 50.000 30.85 0.00 0.00 1.94
2493 2821 0.889186 GACAAGAGAGGGCGCCAAAA 60.889 55.000 30.85 0.00 0.00 2.44
2494 2822 1.302511 GACAAGAGAGGGCGCCAAA 60.303 57.895 30.85 0.00 0.00 3.28
2495 2823 2.347490 GACAAGAGAGGGCGCCAA 59.653 61.111 30.85 0.00 0.00 4.52
2496 2824 2.798445 TAGGACAAGAGAGGGCGCCA 62.798 60.000 30.85 0.00 0.00 5.69
2497 2825 1.614241 TTAGGACAAGAGAGGGCGCC 61.614 60.000 21.18 21.18 0.00 6.53
2498 2826 0.460459 GTTAGGACAAGAGAGGGCGC 60.460 60.000 0.00 0.00 0.00 6.53
2499 2827 1.187087 AGTTAGGACAAGAGAGGGCG 58.813 55.000 0.00 0.00 0.00 6.13
2500 2828 4.024670 TCTTAGTTAGGACAAGAGAGGGC 58.975 47.826 0.00 0.00 0.00 5.19
2501 2829 4.098807 GCTCTTAGTTAGGACAAGAGAGGG 59.901 50.000 13.31 0.00 40.06 4.30
2502 2830 4.707448 TGCTCTTAGTTAGGACAAGAGAGG 59.293 45.833 13.31 0.00 40.06 3.69
2503 2831 5.906113 TGCTCTTAGTTAGGACAAGAGAG 57.094 43.478 13.31 2.34 40.06 3.20
2504 2832 6.191315 AGATGCTCTTAGTTAGGACAAGAGA 58.809 40.000 13.31 1.47 40.06 3.10
2505 2833 6.463995 AGATGCTCTTAGTTAGGACAAGAG 57.536 41.667 6.27 6.27 40.31 2.85
2506 2834 6.437477 TGAAGATGCTCTTAGTTAGGACAAGA 59.563 38.462 0.00 0.00 36.73 3.02
2507 2835 6.634805 TGAAGATGCTCTTAGTTAGGACAAG 58.365 40.000 0.00 0.00 36.73 3.16
2508 2836 6.605471 TGAAGATGCTCTTAGTTAGGACAA 57.395 37.500 0.00 0.00 36.73 3.18
2509 2837 5.394663 GCTGAAGATGCTCTTAGTTAGGACA 60.395 44.000 0.00 0.00 36.73 4.02
2510 2838 5.047188 GCTGAAGATGCTCTTAGTTAGGAC 58.953 45.833 0.00 0.00 36.73 3.85
2511 2839 4.100189 GGCTGAAGATGCTCTTAGTTAGGA 59.900 45.833 0.00 0.00 36.73 2.94
2512 2840 4.376146 GGCTGAAGATGCTCTTAGTTAGG 58.624 47.826 0.00 0.00 36.73 2.69
2513 2841 4.047822 CGGCTGAAGATGCTCTTAGTTAG 58.952 47.826 0.00 0.00 36.73 2.34
2514 2842 3.738281 GCGGCTGAAGATGCTCTTAGTTA 60.738 47.826 0.00 0.00 36.73 2.24
2529 2857 1.664649 CTGTTGAAGACGCGGCTGA 60.665 57.895 19.28 1.14 0.00 4.26
2540 2868 1.344114 GCCTGGAAAATGCCTGTTGAA 59.656 47.619 0.00 0.00 0.00 2.69
2601 2930 0.948678 CGAAAAACGGGCTTCTGGAA 59.051 50.000 0.00 0.00 38.46 3.53
2602 2931 1.512156 GCGAAAAACGGGCTTCTGGA 61.512 55.000 0.00 0.00 42.83 3.86
2645 2978 4.021925 GTTCTGCCTGGGTCCGCT 62.022 66.667 0.00 0.00 0.00 5.52
2746 3080 2.746277 CGGGAAGAAACAGCGGGG 60.746 66.667 0.00 0.00 0.00 5.73


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

AutoCloner maintained by Alex Coulton.