Multiple sequence alignment - TraesCS5A01G406200

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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 TraesCS5A01G406200 chr5A 100.000 3674 0 0 1 3674 597740551 597744224 0.000000e+00 6785.0
1 TraesCS5A01G406200 chr5A 97.436 39 1 0 590 628 37983866 37983828 2.370000e-07 67.6
2 TraesCS5A01G406200 chr5A 97.222 36 0 1 813 848 650556799 650556765 3.960000e-05 60.2
3 TraesCS5A01G406200 chr5B 90.196 2805 153 49 934 3673 586621724 586618977 0.000000e+00 3544.0
4 TraesCS5A01G406200 chr5B 88.931 262 21 4 312 573 586622190 586621937 2.130000e-82 316.0
5 TraesCS5A01G406200 chr5B 84.566 311 16 9 1 281 586622575 586622267 2.790000e-71 279.0
6 TraesCS5A01G406200 chr5B 89.231 195 14 2 627 814 586621922 586621728 1.710000e-58 237.0
7 TraesCS5A01G406200 chr5B 95.349 43 2 0 586 628 370274991 370274949 6.580000e-08 69.4
8 TraesCS5A01G406200 chr5B 97.436 39 1 0 590 628 33986208 33986170 2.370000e-07 67.6
9 TraesCS5A01G406200 chr5B 92.857 42 3 0 817 858 6560089 6560130 1.100000e-05 62.1
10 TraesCS5A01G406200 chr5B 97.059 34 1 0 592 625 262827275 262827308 1.430000e-04 58.4
11 TraesCS5A01G406200 chr5D 90.139 2799 167 41 942 3673 478610485 478607729 0.000000e+00 3539.0
12 TraesCS5A01G406200 chr5D 96.296 81 2 1 1 81 478611481 478611402 8.280000e-27 132.0
13 TraesCS5A01G406200 chr7B 83.524 1663 183 40 1022 2680 672484799 672486374 0.000000e+00 1469.0
14 TraesCS5A01G406200 chr7B 97.222 36 0 1 817 851 641257996 641258031 3.960000e-05 60.2
15 TraesCS5A01G406200 chr7A 83.333 1518 177 30 1022 2533 681794753 681796200 0.000000e+00 1332.0
16 TraesCS5A01G406200 chr7D 84.941 1016 117 21 1441 2448 591292855 591293842 0.000000e+00 996.0
17 TraesCS5A01G406200 chr7D 87.532 385 36 5 1022 1406 591290239 591290611 5.630000e-118 435.0
18 TraesCS5A01G406200 chr7D 100.000 29 0 0 861 889 611837622 611837594 2.000000e-03 54.7
19 TraesCS5A01G406200 chr3D 82.101 933 139 20 999 1923 592592297 592593209 0.000000e+00 773.0
20 TraesCS5A01G406200 chr3D 82.382 613 105 3 2074 2684 592593870 592594481 6.990000e-147 531.0
21 TraesCS5A01G406200 chr3B 79.615 986 172 22 1004 1980 794585174 794584209 0.000000e+00 680.0
22 TraesCS5A01G406200 chr3B 81.609 609 109 3 2074 2680 794583607 794583000 5.480000e-138 501.0
23 TraesCS5A01G406200 chr3B 79.811 634 124 4 2057 2687 794793857 794793225 3.340000e-125 459.0
24 TraesCS5A01G406200 chr3B 79.811 634 124 4 2057 2687 794819571 794818939 3.340000e-125 459.0
25 TraesCS5A01G406200 chr3B 80.032 621 119 4 2057 2676 794580328 794579712 4.330000e-124 455.0
26 TraesCS5A01G406200 chr3B 79.872 626 120 5 2057 2680 794573166 794572545 1.560000e-123 453.0
27 TraesCS5A01G406200 chr3B 97.500 40 1 0 817 856 752295105 752295144 6.580000e-08 69.4
28 TraesCS5A01G406200 chr3B 100.000 33 0 0 817 849 783006608 783006576 1.100000e-05 62.1
29 TraesCS5A01G406200 chr3A 81.549 607 110 2 2075 2680 723673042 723672437 1.970000e-137 499.0
30 TraesCS5A01G406200 chr1A 87.719 57 5 2 859 914 240320440 240320385 8.520000e-07 65.8
31 TraesCS5A01G406200 chr1A 97.143 35 1 0 587 621 131523057 131523091 3.960000e-05 60.2
32 TraesCS5A01G406200 chr6A 95.000 40 2 0 817 856 490481850 490481889 3.060000e-06 63.9
33 TraesCS5A01G406200 chr2D 95.000 40 0 2 811 849 608770149 608770111 1.100000e-05 62.1
34 TraesCS5A01G406200 chr2A 100.000 33 0 0 817 849 749102974 749103006 1.100000e-05 62.1
35 TraesCS5A01G406200 chr2A 92.683 41 0 2 592 629 668460841 668460801 5.130000e-04 56.5
36 TraesCS5A01G406200 chrUn 100.000 32 0 0 590 621 85399290 85399321 3.960000e-05 60.2
37 TraesCS5A01G406200 chr4A 85.965 57 6 2 859 914 578275736 578275791 3.960000e-05 60.2
38 TraesCS5A01G406200 chr2B 100.000 32 0 0 590 621 226474816 226474785 3.960000e-05 60.2
39 TraesCS5A01G406200 chr2B 92.500 40 3 0 590 629 754638819 754638858 1.430000e-04 58.4
40 TraesCS5A01G406200 chr4B 97.059 34 0 1 817 849 167362920 167362953 5.130000e-04 56.5


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 TraesCS5A01G406200 chr5A 597740551 597744224 3673 False 6785.000000 6785 100.000000 1 3674 1 chr5A.!!$F1 3673
1 TraesCS5A01G406200 chr5B 586618977 586622575 3598 True 1094.000000 3544 88.231000 1 3673 4 chr5B.!!$R3 3672
2 TraesCS5A01G406200 chr5D 478607729 478611481 3752 True 1835.500000 3539 93.217500 1 3673 2 chr5D.!!$R1 3672
3 TraesCS5A01G406200 chr7B 672484799 672486374 1575 False 1469.000000 1469 83.524000 1022 2680 1 chr7B.!!$F2 1658
4 TraesCS5A01G406200 chr7A 681794753 681796200 1447 False 1332.000000 1332 83.333000 1022 2533 1 chr7A.!!$F1 1511
5 TraesCS5A01G406200 chr7D 591290239 591293842 3603 False 715.500000 996 86.236500 1022 2448 2 chr7D.!!$F1 1426
6 TraesCS5A01G406200 chr3D 592592297 592594481 2184 False 652.000000 773 82.241500 999 2684 2 chr3D.!!$F1 1685
7 TraesCS5A01G406200 chr3B 794579712 794585174 5462 True 545.333333 680 80.418667 1004 2680 3 chr3B.!!$R5 1676
8 TraesCS5A01G406200 chr3B 794793225 794793857 632 True 459.000000 459 79.811000 2057 2687 1 chr3B.!!$R3 630
9 TraesCS5A01G406200 chr3B 794818939 794819571 632 True 459.000000 459 79.811000 2057 2687 1 chr3B.!!$R4 630
10 TraesCS5A01G406200 chr3B 794572545 794573166 621 True 453.000000 453 79.872000 2057 2680 1 chr3B.!!$R2 623
11 TraesCS5A01G406200 chr3A 723672437 723673042 605 True 499.000000 499 81.549000 2075 2680 1 chr3A.!!$R1 605

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
207 264 0.105039 CATCGGCCCTACACTTCCTC 59.895 60.0 0.00 0.00 0.00 3.71 F
476 581 0.251787 ACCTGGGCCAATGAAAGGAC 60.252 55.0 8.04 0.00 0.00 3.85 F
603 708 0.252742 AGGTCCTCCCTCCGTTTCAT 60.253 55.0 0.00 0.00 40.71 2.57 F
924 1511 0.872388 AAAAACGCTAACGCTGGGAG 59.128 50.0 0.00 0.00 45.53 4.30 F
1013 1601 0.877743 CGATCGATGGAGCTAGCTCA 59.122 55.0 38.32 26.81 44.40 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1980 4842 0.041535 AAAGGGGATGCATGGCAGAA 59.958 50.000 2.46 0.0 43.65 3.02 R
2011 5419 0.104855 TCATACTCCGCAGATGTGGC 59.895 55.000 7.57 0.0 45.04 5.01 R
2372 5782 0.968393 GGTCCAGCTCTTCTCGTCCT 60.968 60.000 0.00 0.0 0.00 3.85 R
2484 5894 1.595311 TCATACCAGGGCACATCCTT 58.405 50.000 0.00 0.0 34.31 3.36 R
2892 9594 2.165641 TCGAAAGAGTCCATGCGTACAT 59.834 45.455 0.00 0.0 33.88 2.29 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
77 78 3.131046 ACAGCAAGGCCAAGCAATATAAC 59.869 43.478 19.83 0.00 0.00 1.89
132 186 1.058695 GATTTCCGTCGCTTGTGTACG 59.941 52.381 0.00 0.00 36.42 3.67
135 189 1.154169 CCGTCGCTTGTGTACGCTA 60.154 57.895 8.10 0.00 35.36 4.26
142 196 2.550978 GCTTGTGTACGCTACATGGAT 58.449 47.619 8.10 0.00 41.34 3.41
158 212 6.436843 ACATGGATTCTCGATTTGTTTACC 57.563 37.500 0.00 0.00 0.00 2.85
199 253 0.882042 CTGTCATGCATCGGCCCTAC 60.882 60.000 0.00 0.00 40.13 3.18
207 264 0.105039 CATCGGCCCTACACTTCCTC 59.895 60.000 0.00 0.00 0.00 3.71
215 272 2.766828 CCCTACACTTCCTCGGAAATCT 59.233 50.000 0.00 0.00 33.34 2.40
262 323 5.410439 ACATGCATTTGGATTTTGCTCTTTC 59.590 36.000 0.00 0.00 37.28 2.62
300 386 1.966451 CGCCCCTTTCACCTGACAC 60.966 63.158 0.00 0.00 0.00 3.67
301 387 1.150536 GCCCCTTTCACCTGACACA 59.849 57.895 0.00 0.00 0.00 3.72
310 396 5.765182 CCTTTCACCTGACACAGTTTCTTAT 59.235 40.000 0.00 0.00 0.00 1.73
334 439 0.322906 CTTGCCTCCCCTGTTTCTCC 60.323 60.000 0.00 0.00 0.00 3.71
379 484 5.159925 TGTTGATTTTGTTGCGATGTATGG 58.840 37.500 0.00 0.00 0.00 2.74
392 497 4.261741 GCGATGTATGGATTCTTTGCCAAT 60.262 41.667 0.00 0.00 37.78 3.16
401 506 7.041635 TGGATTCTTTGCCAATATACATGTG 57.958 36.000 9.11 0.00 0.00 3.21
414 519 8.623903 CCAATATACATGTGTAGCTGTGATTTT 58.376 33.333 9.11 0.00 33.52 1.82
450 555 1.279271 AGGGGTAGATGCTCACAACAC 59.721 52.381 0.00 0.00 0.00 3.32
455 560 3.551890 GGTAGATGCTCACAACACGTATG 59.448 47.826 0.00 0.00 0.00 2.39
458 563 0.865111 TGCTCACAACACGTATGCAC 59.135 50.000 0.00 0.00 32.35 4.57
468 573 1.453745 CGTATGCACCTGGGCCAAT 60.454 57.895 8.04 0.00 0.00 3.16
469 574 1.727511 CGTATGCACCTGGGCCAATG 61.728 60.000 8.04 10.55 0.00 2.82
476 581 0.251787 ACCTGGGCCAATGAAAGGAC 60.252 55.000 8.04 0.00 0.00 3.85
480 585 1.146774 TGGGCCAATGAAAGGACTTGA 59.853 47.619 2.13 0.00 33.44 3.02
487 592 1.133363 TGAAAGGACTTGAACCCGGA 58.867 50.000 0.73 0.00 0.00 5.14
489 594 2.907696 TGAAAGGACTTGAACCCGGATA 59.092 45.455 0.73 0.00 0.00 2.59
526 631 8.576442 ACCACTGAAATCTAACCATTTAAGTTG 58.424 33.333 0.00 0.00 35.87 3.16
532 637 8.816640 AAATCTAACCATTTAAGTTGCACTTG 57.183 30.769 10.59 0.00 39.11 3.16
538 643 4.744631 CCATTTAAGTTGCACTTGGTTCAC 59.255 41.667 10.59 0.00 39.11 3.18
573 678 6.156519 GTGATTTGGGAGGACATTTTTGTAC 58.843 40.000 0.00 0.00 0.00 2.90
574 679 5.835819 TGATTTGGGAGGACATTTTTGTACA 59.164 36.000 0.00 0.00 0.00 2.90
575 680 6.325028 TGATTTGGGAGGACATTTTTGTACAA 59.675 34.615 3.59 3.59 0.00 2.41
576 681 6.546428 TTTGGGAGGACATTTTTGTACAAA 57.454 33.333 17.01 17.01 0.00 2.83
578 683 4.956700 TGGGAGGACATTTTTGTACAAACA 59.043 37.500 20.43 14.83 0.00 2.83
590 695 5.986501 TTGTACAAACACAAAAAGGTCCT 57.013 34.783 5.64 0.00 35.53 3.85
591 696 5.570234 TGTACAAACACAAAAAGGTCCTC 57.430 39.130 0.00 0.00 0.00 3.71
592 697 4.399934 TGTACAAACACAAAAAGGTCCTCC 59.600 41.667 0.00 0.00 0.00 4.30
593 698 2.764010 ACAAACACAAAAAGGTCCTCCC 59.236 45.455 0.00 0.00 0.00 4.30
595 700 2.658807 ACACAAAAAGGTCCTCCCTC 57.341 50.000 0.00 0.00 45.47 4.30
596 701 1.145119 ACACAAAAAGGTCCTCCCTCC 59.855 52.381 0.00 0.00 45.47 4.30
597 702 0.400594 ACAAAAAGGTCCTCCCTCCG 59.599 55.000 0.00 0.00 45.47 4.63
598 703 0.400594 CAAAAAGGTCCTCCCTCCGT 59.599 55.000 0.00 0.00 45.47 4.69
599 704 1.146452 AAAAAGGTCCTCCCTCCGTT 58.854 50.000 0.00 0.00 45.47 4.44
600 705 1.146452 AAAAGGTCCTCCCTCCGTTT 58.854 50.000 0.00 0.00 45.47 3.60
601 706 0.691332 AAAGGTCCTCCCTCCGTTTC 59.309 55.000 0.00 0.00 45.47 2.78
602 707 0.473117 AAGGTCCTCCCTCCGTTTCA 60.473 55.000 0.00 0.00 45.47 2.69
603 708 0.252742 AGGTCCTCCCTCCGTTTCAT 60.253 55.000 0.00 0.00 40.71 2.57
604 709 1.007963 AGGTCCTCCCTCCGTTTCATA 59.992 52.381 0.00 0.00 40.71 2.15
605 710 1.835531 GGTCCTCCCTCCGTTTCATAA 59.164 52.381 0.00 0.00 0.00 1.90
606 711 2.438392 GGTCCTCCCTCCGTTTCATAAT 59.562 50.000 0.00 0.00 0.00 1.28
607 712 3.467803 GTCCTCCCTCCGTTTCATAATG 58.532 50.000 0.00 0.00 0.00 1.90
608 713 3.112263 TCCTCCCTCCGTTTCATAATGT 58.888 45.455 0.00 0.00 0.00 2.71
609 714 4.100498 GTCCTCCCTCCGTTTCATAATGTA 59.900 45.833 0.00 0.00 0.00 2.29
610 715 4.717778 TCCTCCCTCCGTTTCATAATGTAA 59.282 41.667 0.00 0.00 0.00 2.41
611 716 5.057149 CCTCCCTCCGTTTCATAATGTAAG 58.943 45.833 0.00 0.00 0.00 2.34
612 717 5.163343 CCTCCCTCCGTTTCATAATGTAAGA 60.163 44.000 0.00 0.00 0.00 2.10
613 718 6.464465 CCTCCCTCCGTTTCATAATGTAAGAT 60.464 42.308 0.00 0.00 0.00 2.40
614 719 6.288294 TCCCTCCGTTTCATAATGTAAGATG 58.712 40.000 0.00 0.00 0.00 2.90
615 720 6.055588 CCCTCCGTTTCATAATGTAAGATGT 58.944 40.000 0.00 0.00 0.00 3.06
616 721 6.542370 CCCTCCGTTTCATAATGTAAGATGTT 59.458 38.462 0.00 0.00 0.00 2.71
617 722 7.067008 CCCTCCGTTTCATAATGTAAGATGTTT 59.933 37.037 0.00 0.00 0.00 2.83
618 723 8.458843 CCTCCGTTTCATAATGTAAGATGTTTT 58.541 33.333 0.00 0.00 0.00 2.43
619 724 9.840427 CTCCGTTTCATAATGTAAGATGTTTTT 57.160 29.630 0.00 0.00 0.00 1.94
645 750 5.942872 ACATTAGAAATTGGCAAGTCTTCG 58.057 37.500 18.14 11.16 0.00 3.79
658 763 6.210584 TGGCAAGTCTTCGGATATGATATGTA 59.789 38.462 0.00 0.00 0.00 2.29
659 764 7.093333 TGGCAAGTCTTCGGATATGATATGTAT 60.093 37.037 0.00 0.00 0.00 2.29
660 765 7.436673 GGCAAGTCTTCGGATATGATATGTATC 59.563 40.741 0.00 0.00 0.00 2.24
667 772 5.763698 TCGGATATGATATGTATCTCCGACC 59.236 44.000 19.54 9.17 44.75 4.79
720 825 2.544267 GCACAGGAACACACTAAGACAC 59.456 50.000 0.00 0.00 0.00 3.67
726 831 3.554337 GGAACACACTAAGACACGGTGAT 60.554 47.826 16.29 3.23 35.28 3.06
727 832 3.026630 ACACACTAAGACACGGTGATG 57.973 47.619 16.29 5.59 35.28 3.07
729 834 0.992072 CACTAAGACACGGTGATGCG 59.008 55.000 16.29 1.78 33.32 4.73
791 1378 1.675483 TCATTTGTGTCGCTTGCACTT 59.325 42.857 0.00 0.00 37.70 3.16
802 1389 2.675032 CGCTTGCACTTCATGGACTCTA 60.675 50.000 0.00 0.00 0.00 2.43
814 1401 8.598041 ACTTCATGGACTCTAGATTTGTTTACT 58.402 33.333 0.00 0.00 0.00 2.24
817 1404 9.871238 TCATGGACTCTAGATTTGTTTACTAAC 57.129 33.333 0.00 0.00 34.75 2.34
818 1405 9.877178 CATGGACTCTAGATTTGTTTACTAACT 57.123 33.333 0.00 0.00 35.24 2.24
820 1407 8.529476 TGGACTCTAGATTTGTTTACTAACTCC 58.471 37.037 0.00 0.00 35.24 3.85
821 1408 7.980662 GGACTCTAGATTTGTTTACTAACTCCC 59.019 40.741 0.00 0.00 35.24 4.30
822 1409 8.667592 ACTCTAGATTTGTTTACTAACTCCCT 57.332 34.615 0.00 0.00 35.24 4.20
823 1410 9.102453 ACTCTAGATTTGTTTACTAACTCCCTT 57.898 33.333 0.00 0.00 35.24 3.95
824 1411 9.589111 CTCTAGATTTGTTTACTAACTCCCTTC 57.411 37.037 0.00 0.00 35.24 3.46
825 1412 8.248945 TCTAGATTTGTTTACTAACTCCCTTCG 58.751 37.037 0.00 0.00 35.24 3.79
826 1413 6.766429 AGATTTGTTTACTAACTCCCTTCGT 58.234 36.000 0.00 0.00 35.24 3.85
827 1414 7.222161 AGATTTGTTTACTAACTCCCTTCGTT 58.778 34.615 0.00 0.00 35.24 3.85
828 1415 7.718314 AGATTTGTTTACTAACTCCCTTCGTTT 59.282 33.333 0.00 0.00 35.24 3.60
829 1416 6.849588 TTGTTTACTAACTCCCTTCGTTTC 57.150 37.500 0.00 0.00 35.24 2.78
830 1417 5.916318 TGTTTACTAACTCCCTTCGTTTCA 58.084 37.500 0.00 0.00 35.24 2.69
831 1418 6.527423 TGTTTACTAACTCCCTTCGTTTCAT 58.473 36.000 0.00 0.00 35.24 2.57
832 1419 7.669427 TGTTTACTAACTCCCTTCGTTTCATA 58.331 34.615 0.00 0.00 35.24 2.15
833 1420 8.149647 TGTTTACTAACTCCCTTCGTTTCATAA 58.850 33.333 0.00 0.00 35.24 1.90
834 1421 9.159364 GTTTACTAACTCCCTTCGTTTCATAAT 57.841 33.333 0.00 0.00 0.00 1.28
841 1428 9.765795 AACTCCCTTCGTTTCATAATATAAGAG 57.234 33.333 0.00 0.00 0.00 2.85
842 1429 7.873505 ACTCCCTTCGTTTCATAATATAAGAGC 59.126 37.037 0.00 0.00 0.00 4.09
843 1430 6.866770 TCCCTTCGTTTCATAATATAAGAGCG 59.133 38.462 0.00 0.00 0.00 5.03
844 1431 6.645415 CCCTTCGTTTCATAATATAAGAGCGT 59.355 38.462 0.00 0.00 0.00 5.07
845 1432 7.170998 CCCTTCGTTTCATAATATAAGAGCGTT 59.829 37.037 0.00 0.00 0.00 4.84
846 1433 8.548721 CCTTCGTTTCATAATATAAGAGCGTTT 58.451 33.333 0.00 0.00 0.00 3.60
847 1434 9.916397 CTTCGTTTCATAATATAAGAGCGTTTT 57.084 29.630 0.00 0.00 0.00 2.43
849 1436 9.697250 TCGTTTCATAATATAAGAGCGTTTTTG 57.303 29.630 0.00 0.00 0.00 2.44
850 1437 9.697250 CGTTTCATAATATAAGAGCGTTTTTGA 57.303 29.630 0.00 0.00 0.00 2.69
863 1450 8.819643 AGAGCGTTTTTGATATTATACTCTCC 57.180 34.615 0.00 0.00 0.00 3.71
864 1451 7.595502 AGAGCGTTTTTGATATTATACTCTCCG 59.404 37.037 0.00 0.00 0.00 4.63
865 1452 7.208080 AGCGTTTTTGATATTATACTCTCCGT 58.792 34.615 0.00 0.00 0.00 4.69
866 1453 7.381678 AGCGTTTTTGATATTATACTCTCCGTC 59.618 37.037 0.00 0.00 0.00 4.79
867 1454 7.381678 GCGTTTTTGATATTATACTCTCCGTCT 59.618 37.037 0.00 0.00 0.00 4.18
868 1455 8.903723 CGTTTTTGATATTATACTCTCCGTCTC 58.096 37.037 0.00 0.00 0.00 3.36
869 1456 9.745880 GTTTTTGATATTATACTCTCCGTCTCA 57.254 33.333 0.00 0.00 0.00 3.27
882 1469 8.330466 ACTCTCCGTCTCATAATATAAGAGTG 57.670 38.462 0.00 0.00 39.43 3.51
883 1470 7.940137 ACTCTCCGTCTCATAATATAAGAGTGT 59.060 37.037 0.00 0.00 39.43 3.55
884 1471 8.693120 TCTCCGTCTCATAATATAAGAGTGTT 57.307 34.615 0.00 0.00 0.00 3.32
885 1472 9.132923 TCTCCGTCTCATAATATAAGAGTGTTT 57.867 33.333 0.00 0.00 0.00 2.83
886 1473 9.186323 CTCCGTCTCATAATATAAGAGTGTTTG 57.814 37.037 0.00 0.00 0.00 2.93
887 1474 8.692710 TCCGTCTCATAATATAAGAGTGTTTGT 58.307 33.333 0.00 0.00 0.00 2.83
888 1475 8.755941 CCGTCTCATAATATAAGAGTGTTTGTG 58.244 37.037 0.00 0.00 0.00 3.33
889 1476 9.516314 CGTCTCATAATATAAGAGTGTTTGTGA 57.484 33.333 0.00 0.00 0.00 3.58
912 1499 5.480281 CACTGCATAAAGTGTAAAAACGC 57.520 39.130 0.00 0.00 42.21 4.84
913 1500 5.212194 CACTGCATAAAGTGTAAAAACGCT 58.788 37.500 0.00 0.00 42.21 5.07
914 1501 6.367421 CACTGCATAAAGTGTAAAAACGCTA 58.633 36.000 0.00 0.00 42.21 4.26
915 1502 6.853872 CACTGCATAAAGTGTAAAAACGCTAA 59.146 34.615 0.00 0.00 42.21 3.09
916 1503 6.854381 ACTGCATAAAGTGTAAAAACGCTAAC 59.146 34.615 0.00 0.00 0.00 2.34
918 1505 5.219713 GCATAAAGTGTAAAAACGCTAACGC 60.220 40.000 0.00 0.00 45.53 4.84
919 1506 4.541085 AAAGTGTAAAAACGCTAACGCT 57.459 36.364 0.00 0.00 45.53 5.07
920 1507 3.515071 AGTGTAAAAACGCTAACGCTG 57.485 42.857 0.00 0.00 45.53 5.18
921 1508 2.222445 AGTGTAAAAACGCTAACGCTGG 59.778 45.455 0.00 0.00 45.53 4.85
922 1509 1.532007 TGTAAAAACGCTAACGCTGGG 59.468 47.619 0.00 0.00 45.53 4.45
923 1510 1.799994 GTAAAAACGCTAACGCTGGGA 59.200 47.619 0.00 0.00 45.53 4.37
924 1511 0.872388 AAAAACGCTAACGCTGGGAG 59.128 50.000 0.00 0.00 45.53 4.30
925 1512 0.953960 AAAACGCTAACGCTGGGAGG 60.954 55.000 0.00 0.00 45.53 4.30
926 1513 2.798148 AAACGCTAACGCTGGGAGGG 62.798 60.000 0.00 0.00 45.53 4.30
927 1514 3.458163 CGCTAACGCTGGGAGGGA 61.458 66.667 0.00 0.00 31.91 4.20
928 1515 2.501610 GCTAACGCTGGGAGGGAG 59.498 66.667 0.00 0.00 31.91 4.30
929 1516 3.095347 GCTAACGCTGGGAGGGAGG 62.095 68.421 0.00 0.00 31.91 4.30
932 1519 2.873557 TAACGCTGGGAGGGAGGGAG 62.874 65.000 0.00 0.00 31.91 4.30
936 1523 2.020137 CTGGGAGGGAGGGAGTAGT 58.980 63.158 0.00 0.00 0.00 2.73
950 1537 6.445451 AGGGAGTAGTATATACCTCGTTCA 57.555 41.667 9.32 0.00 0.00 3.18
965 1552 5.010820 ACCTCGTTCAAAGTCCTATATAGCC 59.989 44.000 4.04 0.00 0.00 3.93
1013 1601 0.877743 CGATCGATGGAGCTAGCTCA 59.122 55.000 38.32 26.81 44.40 4.26
1033 1621 1.178534 AATGGCAGAAACCACACCCG 61.179 55.000 0.00 0.00 44.17 5.28
1052 1640 1.623359 GTTCAGCTCGTCTGCTACAG 58.377 55.000 0.00 0.00 41.98 2.74
1285 1886 3.073735 CGCTGGTGCTCTCCTCCT 61.074 66.667 0.00 0.00 36.97 3.69
1374 1975 1.377725 GGACGTCCTCACCTACGGA 60.378 63.158 27.64 0.00 43.25 4.69
1530 4369 4.175489 CGGTCCGTCGTCGCTGAT 62.175 66.667 2.08 0.00 35.54 2.90
1831 4674 1.680522 GATGGAGAGCGAGGAAGCCA 61.681 60.000 0.00 0.00 38.01 4.75
1892 4750 2.743928 CCTGCTGCGGTTCCAGAC 60.744 66.667 7.82 0.00 34.77 3.51
1942 4804 1.144969 GAACGAGAATGTCAACGGCA 58.855 50.000 0.00 0.00 0.00 5.69
1963 4825 4.090642 GCATCTTGTTCGTAAGTCACTCAG 59.909 45.833 0.00 0.00 39.48 3.35
1966 4828 2.739292 TGTTCGTAAGTCACTCAGCAC 58.261 47.619 0.00 0.00 39.48 4.40
1968 4830 2.981140 GTTCGTAAGTCACTCAGCACTC 59.019 50.000 0.00 0.00 39.48 3.51
1971 4833 2.030717 CGTAAGTCACTCAGCACTCACT 60.031 50.000 0.00 0.00 0.00 3.41
1980 4842 1.977854 TCAGCACTCACTACCACCATT 59.022 47.619 0.00 0.00 0.00 3.16
1984 5388 2.744202 GCACTCACTACCACCATTTCTG 59.256 50.000 0.00 0.00 0.00 3.02
2002 5406 1.075748 GCCATGCATCCCCTTTCCT 60.076 57.895 0.00 0.00 0.00 3.36
2007 5415 2.830370 CATCCCCTTTCCTGCGCC 60.830 66.667 4.18 0.00 0.00 6.53
2008 5416 3.338250 ATCCCCTTTCCTGCGCCA 61.338 61.111 4.18 0.00 0.00 5.69
2009 5417 3.350031 ATCCCCTTTCCTGCGCCAG 62.350 63.158 4.18 1.92 0.00 4.85
2036 5444 2.941453 TCTGCGGAGTATGAAGTGTC 57.059 50.000 3.10 0.00 0.00 3.67
2041 5449 2.924290 GCGGAGTATGAAGTGTCTCAAC 59.076 50.000 0.00 0.00 0.00 3.18
2042 5450 3.367498 GCGGAGTATGAAGTGTCTCAACT 60.367 47.826 0.00 0.00 0.00 3.16
2043 5451 4.169508 CGGAGTATGAAGTGTCTCAACTG 58.830 47.826 0.00 0.00 0.00 3.16
2044 5452 4.321304 CGGAGTATGAAGTGTCTCAACTGT 60.321 45.833 0.00 0.00 0.00 3.55
2045 5453 5.542779 GGAGTATGAAGTGTCTCAACTGTT 58.457 41.667 0.00 0.00 0.00 3.16
2047 5455 6.146347 GGAGTATGAAGTGTCTCAACTGTTTC 59.854 42.308 0.00 0.00 0.00 2.78
2051 5459 6.817765 TGAAGTGTCTCAACTGTTTCTTTT 57.182 33.333 0.00 0.00 0.00 2.27
2052 5460 7.915293 TGAAGTGTCTCAACTGTTTCTTTTA 57.085 32.000 0.00 0.00 0.00 1.52
2238 5647 2.690026 GCTCCACTACCTCCAGATGGTA 60.690 54.545 0.00 0.00 38.88 3.25
2719 9421 1.334243 GCATCTTTGGCTGCAGAGATC 59.666 52.381 20.43 7.25 38.28 2.75
2860 9562 7.733402 TTTTATCCACAAGTACAACTACCAC 57.267 36.000 0.00 0.00 0.00 4.16
2863 9565 3.054878 CCACAAGTACAACTACCACGTC 58.945 50.000 0.00 0.00 0.00 4.34
2897 9599 6.020678 GCAAATCGCATCCAAAGTTTATGTAC 60.021 38.462 0.00 0.00 41.79 2.90
2899 9601 3.062909 TCGCATCCAAAGTTTATGTACGC 59.937 43.478 0.00 0.00 0.00 4.42
2908 9612 4.737855 AGTTTATGTACGCATGGACTCT 57.262 40.909 0.00 0.00 36.58 3.24
2911 9615 5.581085 AGTTTATGTACGCATGGACTCTTTC 59.419 40.000 0.00 0.00 36.58 2.62
2943 9647 7.491048 ACAATATGAAATGAAATAAACGCACCC 59.509 33.333 0.00 0.00 0.00 4.61
2948 9652 6.153680 TGAAATGAAATAAACGCACCCCTTAT 59.846 34.615 0.00 0.00 0.00 1.73
2966 9670 7.149973 CCCCTTATAATTTGTCATGCATTCTG 58.850 38.462 0.00 0.00 0.00 3.02
2990 9694 0.107654 AGTTTATGCTGAGCCCGGTC 60.108 55.000 0.23 0.00 0.00 4.79
2996 9700 3.790437 CTGAGCCCGGTCAGCCAT 61.790 66.667 10.69 0.00 37.74 4.40
3000 9704 1.937546 GAGCCCGGTCAGCCATTTTG 61.938 60.000 0.00 0.00 34.09 2.44
3011 9715 4.873827 GTCAGCCATTTTGCATGATTTGAT 59.126 37.500 0.00 0.00 0.00 2.57
3064 9768 5.925506 TTGATCTCAACCATTGCATCAAT 57.074 34.783 9.77 0.00 36.03 2.57
3069 9773 5.656480 TCTCAACCATTGCATCAATCAATG 58.344 37.500 8.32 8.32 46.20 2.82
3089 9815 2.492088 TGGTCACGTCCTATGACTCAAG 59.508 50.000 5.22 0.00 44.88 3.02
3101 9827 8.660373 GTCCTATGACTCAAGTATTCAAAACTG 58.340 37.037 0.00 0.00 38.53 3.16
3122 9849 5.134339 ACTGAAATATGGGGCCTCTTTGATA 59.866 40.000 3.07 0.00 0.00 2.15
3125 9852 5.865977 AATATGGGGCCTCTTTGATATGA 57.134 39.130 3.07 0.00 0.00 2.15
3156 9883 8.842942 GCTAAAAGCATAAGGACAGAAAATAC 57.157 34.615 0.00 0.00 41.89 1.89
3167 9894 8.970859 AAGGACAGAAAATACATAGGATTCAG 57.029 34.615 0.00 0.00 0.00 3.02
3238 9980 2.957680 TGTGCACCACATGAGATTTGTT 59.042 40.909 15.69 0.00 39.62 2.83
3242 9984 3.667960 GCACCACATGAGATTTGTTCGAC 60.668 47.826 0.00 0.00 0.00 4.20
3271 10014 3.475566 TCCTTACATGCAGCATAGACC 57.524 47.619 7.82 0.00 0.00 3.85
3273 10016 3.392285 TCCTTACATGCAGCATAGACCAT 59.608 43.478 7.82 0.00 0.00 3.55
3275 10018 5.071653 TCCTTACATGCAGCATAGACCATAA 59.928 40.000 7.82 0.30 0.00 1.90
3277 10020 3.144506 ACATGCAGCATAGACCATAAGC 58.855 45.455 7.82 0.00 0.00 3.09
3293 10036 8.329502 AGACCATAAGCCAAGTTTCTATAGTTT 58.670 33.333 0.00 0.00 0.00 2.66
3340 10086 5.511386 AAGTTCACAGAATCTCCTGGAAT 57.489 39.130 0.00 0.00 38.44 3.01
3342 10088 6.627087 AGTTCACAGAATCTCCTGGAATTA 57.373 37.500 0.00 0.00 38.44 1.40
3346 10092 7.113658 TCACAGAATCTCCTGGAATTACTAC 57.886 40.000 0.00 0.00 38.44 2.73
3348 10094 6.983307 CACAGAATCTCCTGGAATTACTACAG 59.017 42.308 0.00 0.00 38.44 2.74
3352 10098 8.997734 AGAATCTCCTGGAATTACTACAGAATT 58.002 33.333 0.00 0.00 34.21 2.17
3353 10099 9.620259 GAATCTCCTGGAATTACTACAGAATTT 57.380 33.333 0.00 0.00 34.21 1.82
3372 10118 9.196552 CAGAATTTATTTGAACAGAAGAAACCC 57.803 33.333 0.00 0.00 0.00 4.11
3373 10119 8.923270 AGAATTTATTTGAACAGAAGAAACCCA 58.077 29.630 0.00 0.00 0.00 4.51
3378 10124 9.753674 TTATTTGAACAGAAGAAACCCAGATAT 57.246 29.630 0.00 0.00 0.00 1.63
3428 10175 4.500375 GGCAGGCCTGATAATCAAATTGTC 60.500 45.833 37.21 12.65 0.00 3.18
3442 10189 4.083537 TCAAATTGTCGCTACATGGTCAAC 60.084 41.667 0.00 0.00 34.97 3.18
3470 10217 6.493458 GGTGGCTAATACATTTGGTTGGATAT 59.507 38.462 0.00 0.00 0.00 1.63
3488 10235 7.046292 TGGATATGAATCAAAGCCATTCTTG 57.954 36.000 0.00 0.00 34.67 3.02
3495 10242 6.095860 TGAATCAAAGCCATTCTTGACCATAG 59.904 38.462 0.00 0.00 34.67 2.23
3528 10275 6.763355 TCTCAGTGCTAGAAGAAAACAGATT 58.237 36.000 0.00 0.00 0.00 2.40
3530 10277 6.524734 TCAGTGCTAGAAGAAAACAGATTGA 58.475 36.000 0.00 0.00 0.00 2.57
3563 10325 1.378382 CGATTGGGATGGGCACACA 60.378 57.895 0.00 0.00 0.00 3.72
3565 10327 0.532115 GATTGGGATGGGCACACAAC 59.468 55.000 0.00 0.00 33.42 3.32
3571 10333 1.382522 GATGGGCACACAACGATGAT 58.617 50.000 0.00 0.00 0.00 2.45
3572 10334 2.560504 GATGGGCACACAACGATGATA 58.439 47.619 0.00 0.00 0.00 2.15
3573 10335 2.022764 TGGGCACACAACGATGATAG 57.977 50.000 0.00 0.00 0.00 2.08
3574 10336 1.552792 TGGGCACACAACGATGATAGA 59.447 47.619 0.00 0.00 0.00 1.98
3632 10395 8.411683 GGAGATTAAAGCAATGATTGACTTCAT 58.588 33.333 9.76 7.70 37.96 2.57
3634 10397 9.186837 AGATTAAAGCAATGATTGACTTCATCT 57.813 29.630 9.76 15.84 35.29 2.90
3637 10400 7.934855 AAAGCAATGATTGACTTCATCTAGT 57.065 32.000 9.76 0.00 35.29 2.57
3639 10402 8.659925 AAGCAATGATTGACTTCATCTAGTAG 57.340 34.615 9.76 0.00 35.29 2.57
3673 10436 7.039504 AAAGAATTTGCAAGTACATCTGGATGT 60.040 33.333 18.35 18.35 45.35 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 4.647291 AAGAGACGCACGAATTAACTTG 57.353 40.909 0.00 0.00 0.00 3.16
132 186 5.741388 AACAAATCGAGAATCCATGTAGC 57.259 39.130 0.00 0.00 0.00 3.58
135 189 5.943416 TGGTAAACAAATCGAGAATCCATGT 59.057 36.000 0.00 0.00 0.00 3.21
142 196 8.208718 CCAAGATATGGTAAACAAATCGAGAA 57.791 34.615 0.00 0.00 44.85 2.87
178 232 1.890979 GGGCCGATGCATGACAGAG 60.891 63.158 2.46 0.00 40.13 3.35
199 253 2.005451 CTGCAGATTTCCGAGGAAGTG 58.995 52.381 8.42 5.78 35.38 3.16
262 323 6.033966 GGGCGGAACAAGATAAATTTACAAG 58.966 40.000 0.00 0.00 0.00 3.16
300 386 3.350833 AGGCAAGGCAGATAAGAAACTG 58.649 45.455 0.00 0.00 37.22 3.16
301 387 3.615155 GAGGCAAGGCAGATAAGAAACT 58.385 45.455 0.00 0.00 0.00 2.66
310 396 3.333219 CAGGGGAGGCAAGGCAGA 61.333 66.667 0.00 0.00 0.00 4.26
334 439 1.812571 AGCCAGTGTGGAATAAAAGCG 59.187 47.619 0.00 0.00 40.96 4.68
379 484 7.805071 GCTACACATGTATATTGGCAAAGAATC 59.195 37.037 3.01 0.00 0.00 2.52
423 528 0.032416 AGCATCTACCCCTGTACGGT 60.032 55.000 0.00 0.00 37.40 4.83
425 530 1.067212 GTGAGCATCTACCCCTGTACG 59.933 57.143 0.00 0.00 34.92 3.67
429 534 1.278985 TGTTGTGAGCATCTACCCCTG 59.721 52.381 0.00 0.00 34.92 4.45
430 535 1.279271 GTGTTGTGAGCATCTACCCCT 59.721 52.381 0.00 0.00 34.92 4.79
431 536 1.739067 GTGTTGTGAGCATCTACCCC 58.261 55.000 0.00 0.00 34.92 4.95
432 537 1.337823 ACGTGTTGTGAGCATCTACCC 60.338 52.381 0.00 0.00 34.92 3.69
433 538 2.080286 ACGTGTTGTGAGCATCTACC 57.920 50.000 0.00 0.00 34.92 3.18
434 539 3.000322 GCATACGTGTTGTGAGCATCTAC 60.000 47.826 0.00 0.00 34.92 2.59
450 555 1.453745 ATTGGCCCAGGTGCATACG 60.454 57.895 0.00 0.00 0.00 3.06
455 560 1.593265 CTTTCATTGGCCCAGGTGC 59.407 57.895 0.00 0.00 0.00 5.01
458 563 0.040204 AGTCCTTTCATTGGCCCAGG 59.960 55.000 0.00 0.00 0.00 4.45
468 573 1.133363 TCCGGGTTCAAGTCCTTTCA 58.867 50.000 0.00 0.00 0.00 2.69
469 574 2.491675 ATCCGGGTTCAAGTCCTTTC 57.508 50.000 0.00 0.00 0.00 2.62
476 581 4.335594 GGAACAAATCTATCCGGGTTCAAG 59.664 45.833 14.97 0.00 37.08 3.02
480 585 3.617284 GTGGAACAAATCTATCCGGGTT 58.383 45.455 0.00 0.00 44.16 4.11
487 592 7.177878 AGATTTCAGTGGTGGAACAAATCTAT 58.822 34.615 10.41 0.00 44.16 1.98
489 594 5.388654 AGATTTCAGTGGTGGAACAAATCT 58.611 37.500 7.53 7.53 44.16 2.40
526 631 2.859806 GCAAGACATGTGAACCAAGTGC 60.860 50.000 1.15 0.00 0.00 4.40
538 643 2.821378 TCCCAAATCACAGCAAGACATG 59.179 45.455 0.00 0.00 0.00 3.21
573 678 3.452755 GGGAGGACCTTTTTGTGTTTG 57.547 47.619 0.00 0.00 35.85 2.93
585 690 1.492764 TATGAAACGGAGGGAGGACC 58.507 55.000 0.00 0.00 40.67 4.46
587 692 3.112263 ACATTATGAAACGGAGGGAGGA 58.888 45.455 0.00 0.00 0.00 3.71
588 693 3.560636 ACATTATGAAACGGAGGGAGG 57.439 47.619 0.00 0.00 0.00 4.30
589 694 5.914033 TCTTACATTATGAAACGGAGGGAG 58.086 41.667 0.00 0.00 0.00 4.30
590 695 5.943349 TCTTACATTATGAAACGGAGGGA 57.057 39.130 0.00 0.00 0.00 4.20
591 696 6.055588 ACATCTTACATTATGAAACGGAGGG 58.944 40.000 0.00 0.00 0.00 4.30
592 697 7.553881 AACATCTTACATTATGAAACGGAGG 57.446 36.000 0.00 0.00 0.00 4.30
593 698 9.840427 AAAAACATCTTACATTATGAAACGGAG 57.160 29.630 0.00 0.00 0.00 4.63
616 721 8.203485 AGACTTGCCAATTTCTAATGTCAAAAA 58.797 29.630 0.00 0.00 0.00 1.94
617 722 7.725251 AGACTTGCCAATTTCTAATGTCAAAA 58.275 30.769 0.00 0.00 0.00 2.44
618 723 7.288810 AGACTTGCCAATTTCTAATGTCAAA 57.711 32.000 0.00 0.00 0.00 2.69
619 724 6.899393 AGACTTGCCAATTTCTAATGTCAA 57.101 33.333 0.00 0.00 0.00 3.18
620 725 6.348458 CGAAGACTTGCCAATTTCTAATGTCA 60.348 38.462 0.00 0.00 0.00 3.58
621 726 6.024049 CGAAGACTTGCCAATTTCTAATGTC 58.976 40.000 0.00 0.00 0.00 3.06
622 727 5.106157 CCGAAGACTTGCCAATTTCTAATGT 60.106 40.000 0.00 0.00 0.00 2.71
623 728 5.123820 TCCGAAGACTTGCCAATTTCTAATG 59.876 40.000 0.00 0.00 0.00 1.90
624 729 5.253330 TCCGAAGACTTGCCAATTTCTAAT 58.747 37.500 0.00 0.00 0.00 1.73
625 730 4.647611 TCCGAAGACTTGCCAATTTCTAA 58.352 39.130 0.00 0.00 0.00 2.10
633 738 5.012046 ACATATCATATCCGAAGACTTGCCA 59.988 40.000 0.00 0.00 0.00 4.92
645 750 8.871629 ATAGGTCGGAGATACATATCATATCC 57.128 38.462 1.88 0.00 40.67 2.59
658 763 8.265055 TCATTTTGACTTAAATAGGTCGGAGAT 58.735 33.333 0.00 0.00 40.67 2.75
659 764 7.617225 TCATTTTGACTTAAATAGGTCGGAGA 58.383 34.615 0.00 0.00 35.32 3.71
660 765 7.843490 TCATTTTGACTTAAATAGGTCGGAG 57.157 36.000 0.00 0.00 35.32 4.63
675 780 8.336806 TGCTCATCAAATTTGTTTCATTTTGAC 58.663 29.630 17.47 5.86 39.94 3.18
690 795 3.254166 GTGTGTTCCTGTGCTCATCAAAT 59.746 43.478 0.00 0.00 0.00 2.32
720 825 1.006086 TGTTTCATAGCGCATCACCG 58.994 50.000 11.47 0.00 0.00 4.94
726 831 5.296531 ACATATCATTGTGTTTCATAGCGCA 59.703 36.000 11.47 0.00 0.00 6.09
727 832 5.622448 CACATATCATTGTGTTTCATAGCGC 59.378 40.000 0.00 0.00 41.65 5.92
729 834 5.916883 GGCACATATCATTGTGTTTCATAGC 59.083 40.000 6.46 0.00 46.93 2.97
791 1378 9.871238 GTTAGTAAACAAATCTAGAGTCCATGA 57.129 33.333 0.00 0.00 35.56 3.07
802 1389 6.766429 ACGAAGGGAGTTAGTAAACAAATCT 58.234 36.000 0.00 0.00 38.12 2.40
815 1402 9.765795 CTCTTATATTATGAAACGAAGGGAGTT 57.234 33.333 0.00 0.00 0.00 3.01
816 1403 7.873505 GCTCTTATATTATGAAACGAAGGGAGT 59.126 37.037 0.00 0.00 0.00 3.85
817 1404 7.062371 CGCTCTTATATTATGAAACGAAGGGAG 59.938 40.741 0.00 0.00 0.00 4.30
818 1405 6.866770 CGCTCTTATATTATGAAACGAAGGGA 59.133 38.462 0.00 0.00 0.00 4.20
819 1406 6.645415 ACGCTCTTATATTATGAAACGAAGGG 59.355 38.462 0.00 0.00 0.00 3.95
820 1407 7.639162 ACGCTCTTATATTATGAAACGAAGG 57.361 36.000 0.00 0.00 0.00 3.46
821 1408 9.916397 AAAACGCTCTTATATTATGAAACGAAG 57.084 29.630 0.00 0.00 0.00 3.79
823 1410 9.697250 CAAAAACGCTCTTATATTATGAAACGA 57.303 29.630 0.00 0.00 0.00 3.85
824 1411 9.697250 TCAAAAACGCTCTTATATTATGAAACG 57.303 29.630 0.00 0.00 0.00 3.60
837 1424 9.262358 GGAGAGTATAATATCAAAAACGCTCTT 57.738 33.333 0.00 0.00 35.15 2.85
838 1425 7.595502 CGGAGAGTATAATATCAAAAACGCTCT 59.404 37.037 0.00 0.00 35.15 4.09
839 1426 7.381678 ACGGAGAGTATAATATCAAAAACGCTC 59.618 37.037 0.00 0.00 34.36 5.03
840 1427 7.208080 ACGGAGAGTATAATATCAAAAACGCT 58.792 34.615 0.00 0.00 0.00 5.07
841 1428 7.381678 AGACGGAGAGTATAATATCAAAAACGC 59.618 37.037 0.00 0.00 0.00 4.84
842 1429 8.798748 AGACGGAGAGTATAATATCAAAAACG 57.201 34.615 0.00 0.00 0.00 3.60
843 1430 9.745880 TGAGACGGAGAGTATAATATCAAAAAC 57.254 33.333 0.00 0.00 0.00 2.43
856 1443 9.438228 CACTCTTATATTATGAGACGGAGAGTA 57.562 37.037 0.00 0.00 39.25 2.59
857 1444 7.940137 ACACTCTTATATTATGAGACGGAGAGT 59.060 37.037 0.00 0.00 41.23 3.24
858 1445 8.330466 ACACTCTTATATTATGAGACGGAGAG 57.670 38.462 0.00 0.00 34.90 3.20
859 1446 8.693120 AACACTCTTATATTATGAGACGGAGA 57.307 34.615 0.00 0.00 34.90 3.71
860 1447 9.186323 CAAACACTCTTATATTATGAGACGGAG 57.814 37.037 0.00 0.00 34.90 4.63
861 1448 8.692710 ACAAACACTCTTATATTATGAGACGGA 58.307 33.333 0.00 0.00 34.90 4.69
862 1449 8.755941 CACAAACACTCTTATATTATGAGACGG 58.244 37.037 0.00 0.00 34.90 4.79
863 1450 9.516314 TCACAAACACTCTTATATTATGAGACG 57.484 33.333 0.00 0.00 34.90 4.18
881 1468 4.919206 CACTTTATGCAGTGTCACAAACA 58.081 39.130 5.62 0.38 39.59 2.83
891 1478 5.432885 AGCGTTTTTACACTTTATGCAGT 57.567 34.783 0.00 0.00 0.00 4.40
892 1479 6.031003 CGTTAGCGTTTTTACACTTTATGCAG 59.969 38.462 0.00 0.00 0.00 4.41
893 1480 5.846994 CGTTAGCGTTTTTACACTTTATGCA 59.153 36.000 0.00 0.00 0.00 3.96
894 1481 5.219713 GCGTTAGCGTTTTTACACTTTATGC 60.220 40.000 0.00 0.00 40.81 3.14
895 1482 6.282795 GCGTTAGCGTTTTTACACTTTATG 57.717 37.500 0.00 0.00 40.81 1.90
911 1498 2.501610 CTCCCTCCCAGCGTTAGC 59.498 66.667 0.00 0.00 45.58 3.09
912 1499 2.435693 CCCTCCCTCCCAGCGTTAG 61.436 68.421 0.00 0.00 0.00 2.34
913 1500 2.365105 CCCTCCCTCCCAGCGTTA 60.365 66.667 0.00 0.00 0.00 3.18
914 1501 4.332543 TCCCTCCCTCCCAGCGTT 62.333 66.667 0.00 0.00 0.00 4.84
915 1502 4.787280 CTCCCTCCCTCCCAGCGT 62.787 72.222 0.00 0.00 0.00 5.07
916 1503 3.375443 TACTCCCTCCCTCCCAGCG 62.375 68.421 0.00 0.00 0.00 5.18
917 1504 1.458588 CTACTCCCTCCCTCCCAGC 60.459 68.421 0.00 0.00 0.00 4.85
918 1505 1.232909 TACTACTCCCTCCCTCCCAG 58.767 60.000 0.00 0.00 0.00 4.45
919 1506 1.937098 ATACTACTCCCTCCCTCCCA 58.063 55.000 0.00 0.00 0.00 4.37
920 1507 4.079269 GGTATATACTACTCCCTCCCTCCC 60.079 54.167 12.54 0.00 0.00 4.30
921 1508 4.795165 AGGTATATACTACTCCCTCCCTCC 59.205 50.000 12.54 0.00 0.00 4.30
922 1509 5.396660 CGAGGTATATACTACTCCCTCCCTC 60.397 52.000 12.54 5.88 36.04 4.30
923 1510 4.474287 CGAGGTATATACTACTCCCTCCCT 59.526 50.000 12.54 0.00 36.04 4.20
924 1511 4.227073 ACGAGGTATATACTACTCCCTCCC 59.773 50.000 12.54 0.00 36.04 4.30
925 1512 5.434182 ACGAGGTATATACTACTCCCTCC 57.566 47.826 12.54 0.00 36.04 4.30
926 1513 6.471146 TGAACGAGGTATATACTACTCCCTC 58.529 44.000 12.54 8.45 36.07 4.30
927 1514 6.445451 TGAACGAGGTATATACTACTCCCT 57.555 41.667 12.54 0.07 0.00 4.20
928 1515 7.230309 ACTTTGAACGAGGTATATACTACTCCC 59.770 40.741 12.54 0.00 0.00 4.30
929 1516 8.164058 ACTTTGAACGAGGTATATACTACTCC 57.836 38.462 12.54 0.00 0.00 3.85
932 1519 8.164058 AGGACTTTGAACGAGGTATATACTAC 57.836 38.462 12.54 6.36 0.00 2.73
950 1537 4.907875 TCCAGCTTGGCTATATAGGACTTT 59.092 41.667 11.72 0.00 36.40 2.66
993 1581 1.160989 GAGCTAGCTCCATCGATCGA 58.839 55.000 30.89 21.86 37.11 3.59
1013 1601 1.047801 GGGTGTGGTTTCTGCCATTT 58.952 50.000 0.00 0.00 41.08 2.32
1052 1640 1.005630 ACAAGGACGCAGAGCAGAC 60.006 57.895 0.00 0.00 0.00 3.51
1374 1975 0.539051 CGAAGGAGATGTTCTGCCCT 59.461 55.000 0.00 0.00 35.21 5.19
1664 4503 1.595929 TTGAACCCGGACAAGACGC 60.596 57.895 0.73 0.00 0.00 5.19
1942 4804 4.238514 GCTGAGTGACTTACGAACAAGAT 58.761 43.478 0.00 0.00 0.00 2.40
1963 4825 2.744202 CAGAAATGGTGGTAGTGAGTGC 59.256 50.000 0.00 0.00 0.00 4.40
1966 4828 2.290260 TGGCAGAAATGGTGGTAGTGAG 60.290 50.000 0.00 0.00 0.00 3.51
1968 4830 2.198827 TGGCAGAAATGGTGGTAGTG 57.801 50.000 0.00 0.00 0.00 2.74
1971 4833 1.272369 TGCATGGCAGAAATGGTGGTA 60.272 47.619 0.00 0.00 33.32 3.25
1980 4842 0.041535 AAAGGGGATGCATGGCAGAA 59.958 50.000 2.46 0.00 43.65 3.02
1984 5388 1.075748 AGGAAAGGGGATGCATGGC 60.076 57.895 2.46 0.00 0.00 4.40
2011 5419 0.104855 TCATACTCCGCAGATGTGGC 59.895 55.000 7.57 0.00 45.04 5.01
2013 5421 2.862536 CACTTCATACTCCGCAGATGTG 59.137 50.000 0.00 0.00 32.38 3.21
2014 5422 2.497675 ACACTTCATACTCCGCAGATGT 59.502 45.455 0.00 0.00 0.00 3.06
2015 5423 3.119291 GACACTTCATACTCCGCAGATG 58.881 50.000 0.00 0.00 0.00 2.90
2016 5424 3.027412 AGACACTTCATACTCCGCAGAT 58.973 45.455 0.00 0.00 0.00 2.90
2017 5425 2.423892 GAGACACTTCATACTCCGCAGA 59.576 50.000 0.00 0.00 0.00 4.26
2018 5426 2.164422 TGAGACACTTCATACTCCGCAG 59.836 50.000 0.00 0.00 0.00 5.18
2036 5444 7.012327 TGTCCTGATGTAAAAGAAACAGTTGAG 59.988 37.037 0.00 0.00 0.00 3.02
2041 5449 9.185192 GAAAATGTCCTGATGTAAAAGAAACAG 57.815 33.333 0.00 0.00 0.00 3.16
2042 5450 8.912988 AGAAAATGTCCTGATGTAAAAGAAACA 58.087 29.630 0.00 0.00 0.00 2.83
2043 5451 9.399403 GAGAAAATGTCCTGATGTAAAAGAAAC 57.601 33.333 0.00 0.00 0.00 2.78
2044 5452 8.576442 GGAGAAAATGTCCTGATGTAAAAGAAA 58.424 33.333 0.00 0.00 0.00 2.52
2045 5453 7.094805 CGGAGAAAATGTCCTGATGTAAAAGAA 60.095 37.037 0.00 0.00 31.14 2.52
2047 5455 6.546395 CGGAGAAAATGTCCTGATGTAAAAG 58.454 40.000 0.00 0.00 31.14 2.27
2051 5459 3.531538 GCGGAGAAAATGTCCTGATGTA 58.468 45.455 0.00 0.00 31.14 2.29
2052 5460 2.359900 GCGGAGAAAATGTCCTGATGT 58.640 47.619 0.00 0.00 31.14 3.06
2372 5782 0.968393 GGTCCAGCTCTTCTCGTCCT 60.968 60.000 0.00 0.00 0.00 3.85
2484 5894 1.595311 TCATACCAGGGCACATCCTT 58.405 50.000 0.00 0.00 34.31 3.36
2719 9421 5.770417 ACAGTAAAAAGGTACACTCTCTCG 58.230 41.667 0.00 0.00 0.00 4.04
2737 9439 9.443323 ACAAAGTACAATGCAACATATACAGTA 57.557 29.630 0.00 0.00 0.00 2.74
2750 9452 9.716507 ATAACATATTTCGACAAAGTACAATGC 57.283 29.630 0.00 0.00 0.00 3.56
2863 9565 4.996113 GCGATTTGCACGTATGGG 57.004 55.556 0.00 0.00 45.45 4.00
2877 9579 3.062909 GCGTACATAAACTTTGGATGCGA 59.937 43.478 0.00 0.00 30.68 5.10
2884 9586 5.351465 AGAGTCCATGCGTACATAAACTTTG 59.649 40.000 0.00 0.00 32.95 2.77
2892 9594 2.165641 TCGAAAGAGTCCATGCGTACAT 59.834 45.455 0.00 0.00 33.88 2.29
2929 9633 7.977293 ACAAATTATAAGGGGTGCGTTTATTTC 59.023 33.333 0.00 0.00 0.00 2.17
2938 9642 4.099266 TGCATGACAAATTATAAGGGGTGC 59.901 41.667 0.00 0.00 0.00 5.01
2940 9644 6.840705 AGAATGCATGACAAATTATAAGGGGT 59.159 34.615 0.00 0.00 0.00 4.95
2966 9670 3.746492 CCGGGCTCAGCATAAACTAATAC 59.254 47.826 0.00 0.00 0.00 1.89
2990 9694 5.811399 AATCAAATCATGCAAAATGGCTG 57.189 34.783 0.00 0.00 34.04 4.85
3000 9704 9.065871 GTCCGCTTTATTATAATCAAATCATGC 57.934 33.333 0.00 0.00 0.00 4.06
3011 9715 9.841295 ATTAACCAGAAGTCCGCTTTATTATAA 57.159 29.630 0.00 0.00 34.61 0.98
3022 9726 3.629142 AAGGGATTAACCAGAAGTCCG 57.371 47.619 0.00 0.00 41.20 4.79
3030 9734 5.222233 TGGTTGAGATCAAAGGGATTAACCA 60.222 40.000 0.00 0.00 44.03 3.67
3064 9768 3.520290 GTCATAGGACGTGACCATTGA 57.480 47.619 0.00 0.00 39.99 2.57
3089 9815 6.098266 AGGCCCCATATTTCAGTTTTGAATAC 59.902 38.462 0.00 0.00 42.60 1.89
3101 9827 6.248433 TCATATCAAAGAGGCCCCATATTTC 58.752 40.000 0.00 0.00 0.00 2.17
3142 9869 8.772250 TCTGAATCCTATGTATTTTCTGTCCTT 58.228 33.333 0.00 0.00 0.00 3.36
3156 9883 4.648651 TGGCATGTGATCTGAATCCTATG 58.351 43.478 0.00 0.00 32.01 2.23
3167 9894 4.365723 GGAATTCAACATGGCATGTGATC 58.634 43.478 31.99 22.62 44.07 2.92
3218 9947 3.568538 GAACAAATCTCATGTGGTGCAC 58.431 45.455 8.80 8.80 34.56 4.57
3275 10018 9.740710 AAGATTGTAAACTATAGAAACTTGGCT 57.259 29.630 6.78 0.00 0.00 4.75
3312 10058 6.656693 CCAGGAGATTCTGTGAACTTTAATGT 59.343 38.462 0.00 0.00 33.14 2.71
3320 10066 6.410540 AGTAATTCCAGGAGATTCTGTGAAC 58.589 40.000 0.00 0.00 31.70 3.18
3346 10092 9.196552 GGGTTTCTTCTGTTCAAATAAATTCTG 57.803 33.333 0.00 0.00 0.00 3.02
3348 10094 9.196552 CTGGGTTTCTTCTGTTCAAATAAATTC 57.803 33.333 0.00 0.00 0.00 2.17
3352 10098 9.753674 ATATCTGGGTTTCTTCTGTTCAAATAA 57.246 29.630 0.00 0.00 0.00 1.40
3354 10100 9.927081 ATATATCTGGGTTTCTTCTGTTCAAAT 57.073 29.630 0.00 0.00 0.00 2.32
3408 10155 3.316308 GCGACAATTTGATTATCAGGCCT 59.684 43.478 0.00 0.00 0.00 5.19
3428 10175 0.036388 ACCCTGTTGACCATGTAGCG 60.036 55.000 0.00 0.00 0.00 4.26
3442 10189 3.631250 ACCAAATGTATTAGCCACCCTG 58.369 45.455 0.00 0.00 0.00 4.45
3470 10217 4.151121 TGGTCAAGAATGGCTTTGATTCA 58.849 39.130 0.00 0.00 33.60 2.57
3476 10223 4.019174 CCACTATGGTCAAGAATGGCTTT 58.981 43.478 0.00 0.00 30.71 3.51
3477 10224 3.624777 CCACTATGGTCAAGAATGGCTT 58.375 45.455 0.00 0.00 32.43 4.35
3495 10242 3.728845 TCTAGCACTGAGAAAACACCAC 58.271 45.455 0.00 0.00 0.00 4.16
3528 10275 4.129380 CAATCGCCAAGATACCAATCTCA 58.871 43.478 0.00 0.00 41.81 3.27
3530 10277 3.480470 CCAATCGCCAAGATACCAATCT 58.520 45.455 0.00 0.00 44.67 2.40
3587 10349 4.078571 TCTCCACCTATAGTCCTTGGATGT 60.079 45.833 9.06 0.00 35.79 3.06
3592 10354 6.931840 GCTTTAATCTCCACCTATAGTCCTTG 59.068 42.308 0.00 0.00 0.00 3.61
3603 10365 6.096001 AGTCAATCATTGCTTTAATCTCCACC 59.904 38.462 0.00 0.00 0.00 4.61
3638 10401 9.991906 TGTACTTGCAAATTCTTTACTACTACT 57.008 29.630 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.