Multiple sequence alignment - TraesCS7A01G384800

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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 TraesCS7A01G384800 chr7A 100.000 2834 0 0 1 2834 561304521 561301688 0.000000e+00 5234
1 TraesCS7A01G384800 chr7A 100.000 2640 0 0 3101 5740 561301421 561298782 0.000000e+00 4876
2 TraesCS7A01G384800 chr7A 92.574 606 38 5 1 601 448103259 448103862 0.000000e+00 863
3 TraesCS7A01G384800 chr7A 92.092 607 40 6 1 601 657638234 657638838 0.000000e+00 848
4 TraesCS7A01G384800 chr7A 92.699 589 38 5 1 587 720918355 720918940 0.000000e+00 845
5 TraesCS7A01G384800 chr7A 91.276 619 44 8 1 613 516137592 516136978 0.000000e+00 835
6 TraesCS7A01G384800 chr7A 96.947 131 3 1 607 737 540886199 540886070 9.680000e-53 219
7 TraesCS7A01G384800 chr7A 95.385 130 6 0 610 739 140763950 140764079 2.100000e-49 207
8 TraesCS7A01G384800 chr7A 95.385 130 6 0 610 739 141052841 141052970 2.100000e-49 207
9 TraesCS7A01G384800 chr7A 95.385 130 6 0 610 739 141307628 141307757 2.100000e-49 207
10 TraesCS7A01G384800 chr7A 95.385 130 6 0 610 739 141647619 141647748 2.100000e-49 207
11 TraesCS7A01G384800 chr7A 95.385 130 6 0 610 739 141898800 141898929 2.100000e-49 207
12 TraesCS7A01G384800 chr7A 94.074 135 8 0 605 739 626604964 626605098 7.540000e-49 206
13 TraesCS7A01G384800 chr7B 94.845 2095 78 21 755 2832 523803418 523801337 0.000000e+00 3243
14 TraesCS7A01G384800 chr7B 95.958 1435 51 4 3934 5366 523800329 523798900 0.000000e+00 2322
15 TraesCS7A01G384800 chr7B 97.593 831 17 2 3101 3931 523801250 523800423 0.000000e+00 1421
16 TraesCS7A01G384800 chr7D 95.512 1805 53 4 3935 5739 495424252 495422476 0.000000e+00 2859
17 TraesCS7A01G384800 chr7D 95.918 1617 46 11 1235 2832 495426927 495425312 0.000000e+00 2603
18 TraesCS7A01G384800 chr7D 97.160 845 21 2 3103 3946 495425169 495424327 0.000000e+00 1424
19 TraesCS7A01G384800 chr7D 92.434 608 34 7 1 601 530666739 530666137 0.000000e+00 857
20 TraesCS7A01G384800 chr7D 91.403 442 20 11 755 1191 495427700 495427272 1.780000e-164 590
21 TraesCS7A01G384800 chr7D 90.080 373 32 3 5372 5739 452869439 452869811 4.020000e-131 479
22 TraesCS7A01G384800 chr7D 90.000 370 34 2 5373 5739 209561218 209561587 5.200000e-130 475
23 TraesCS7A01G384800 chr7D 89.276 373 35 4 5372 5739 75223457 75223829 4.050000e-126 462
24 TraesCS7A01G384800 chr7D 89.488 371 31 6 5372 5739 436090764 436091129 4.050000e-126 462
25 TraesCS7A01G384800 chr3D 92.131 610 40 8 1 605 332415927 332415321 0.000000e+00 854
26 TraesCS7A01G384800 chr1A 92.257 607 39 6 1 601 64854213 64854817 0.000000e+00 854
27 TraesCS7A01G384800 chr1A 92.079 606 42 4 1 601 536655369 536654765 0.000000e+00 848
28 TraesCS7A01G384800 chr3A 92.118 609 39 7 1 604 658885419 658884815 0.000000e+00 850
29 TraesCS7A01G384800 chr5B 90.000 370 35 1 5372 5739 63603851 63604220 1.450000e-130 477
30 TraesCS7A01G384800 chr4A 90.027 371 34 2 5372 5739 521642388 521642018 1.450000e-130 477
31 TraesCS7A01G384800 chr5A 89.516 372 34 3 5372 5739 377495501 377495131 3.130000e-127 466
32 TraesCS7A01G384800 chr4B 89.674 368 35 2 5375 5739 445779820 445780187 3.130000e-127 466
33 TraesCS7A01G384800 chr6D 95.312 128 6 0 610 737 379557153 379557280 2.710000e-48 204
34 TraesCS7A01G384800 chr2A 91.096 146 11 2 611 756 135482660 135482517 4.540000e-46 196
35 TraesCS7A01G384800 chr4D 89.286 112 11 1 3136 3246 216637439 216637328 7.760000e-29 139


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 TraesCS7A01G384800 chr7A 561298782 561304521 5739 True 5055.000000 5234 100.00000 1 5740 2 chr7A.!!$R3 5739
1 TraesCS7A01G384800 chr7A 448103259 448103862 603 False 863.000000 863 92.57400 1 601 1 chr7A.!!$F6 600
2 TraesCS7A01G384800 chr7A 657638234 657638838 604 False 848.000000 848 92.09200 1 601 1 chr7A.!!$F8 600
3 TraesCS7A01G384800 chr7A 720918355 720918940 585 False 845.000000 845 92.69900 1 587 1 chr7A.!!$F9 586
4 TraesCS7A01G384800 chr7A 516136978 516137592 614 True 835.000000 835 91.27600 1 613 1 chr7A.!!$R1 612
5 TraesCS7A01G384800 chr7B 523798900 523803418 4518 True 2328.666667 3243 96.13200 755 5366 3 chr7B.!!$R1 4611
6 TraesCS7A01G384800 chr7D 495422476 495427700 5224 True 1869.000000 2859 94.99825 755 5739 4 chr7D.!!$R2 4984
7 TraesCS7A01G384800 chr7D 530666137 530666739 602 True 857.000000 857 92.43400 1 601 1 chr7D.!!$R1 600
8 TraesCS7A01G384800 chr3D 332415321 332415927 606 True 854.000000 854 92.13100 1 605 1 chr3D.!!$R1 604
9 TraesCS7A01G384800 chr1A 64854213 64854817 604 False 854.000000 854 92.25700 1 601 1 chr1A.!!$F1 600
10 TraesCS7A01G384800 chr1A 536654765 536655369 604 True 848.000000 848 92.07900 1 601 1 chr1A.!!$R1 600
11 TraesCS7A01G384800 chr3A 658884815 658885419 604 True 850.000000 850 92.11800 1 604 1 chr3A.!!$R1 603

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
628 640 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13 F
733 745 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20 F
735 747 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85 F
736 748 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59 F
763 775 0.238289 AAAGACATCCAAACGCAGCG 59.762 50.000 14.82 14.82 0.00 5.18 F
1191 1208 1.004918 CGAGAGCGGGGTTTTCTGT 60.005 57.895 0.00 0.00 0.00 3.41 F
1192 1209 1.014564 CGAGAGCGGGGTTTTCTGTC 61.015 60.000 0.00 0.00 0.00 3.51 F
1200 1217 1.076332 GGGTTTTCTGTCACGATCCG 58.924 55.000 0.00 0.00 0.00 4.18 F
1470 1790 1.541379 CCGAATTCCCGGTTCCTTTT 58.459 50.000 0.00 0.00 44.23 2.27 F
2808 3147 1.665679 GTCACATGTCAGGTATTGCGG 59.334 52.381 0.00 0.00 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1934 2269 0.623723 GGTGCCTTGGGGAGAATGTA 59.376 55.000 0.00 0.00 33.58 2.29 R
2104 2439 1.000993 ACGAGAGTCCAGATGGCCT 59.999 57.895 3.32 0.00 44.19 5.19 R
2228 2567 3.831323 TCCAGATGCCTTCACAGAAAAA 58.169 40.909 0.00 0.00 0.00 1.94 R
2613 2952 4.320788 GGAAATGACAAAAGGCAGAGACAG 60.321 45.833 0.00 0.00 0.00 3.51 R
3280 3672 5.643348 CCGCATAGTGGCAGAATGAATAATA 59.357 40.000 12.01 0.00 39.69 0.98 R
3605 3999 7.755822 ACGCCTTATTTATTTATTTTTGACGCA 59.244 29.630 0.00 0.00 0.00 5.24 R
3939 4333 6.494893 TGGCTTAATTACAGCAAGTAACAG 57.505 37.500 16.35 3.34 44.95 3.16 R
4002 4488 5.050644 TGCAATGTAAGCACTCAGAAATG 57.949 39.130 0.00 0.00 37.02 2.32 R
4038 4524 5.659079 AGAGTTCCAGTTCAGTATTAGGGAG 59.341 44.000 0.00 0.00 0.00 4.30 R
5371 5859 0.555769 ACCACACCACTTGGGATTGT 59.444 50.000 0.00 0.00 41.15 2.71 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
173 174 5.710099 TCTTGTAGAATTGATTTTTCGGCCT 59.290 36.000 0.00 0.00 0.00 5.19
303 305 6.517529 CGAACCATCCCTTGTTTTTCCATTTA 60.518 38.462 0.00 0.00 0.00 1.40
412 420 4.778213 AAAAGCCTGCAGATCTACCATA 57.222 40.909 17.39 0.00 0.00 2.74
505 514 5.346181 TGGAATGTGACCGTATATGAACA 57.654 39.130 0.00 0.00 0.00 3.18
513 522 6.128418 TGTGACCGTATATGAACATTTGTGTG 60.128 38.462 0.00 0.00 0.00 3.82
552 561 8.238631 AGAAACACGTATTTTACAAGTTTGTGT 58.761 29.630 7.73 0.00 42.31 3.72
583 592 1.130938 TCGTCGCGTGCAAGTTCTATA 59.869 47.619 5.77 0.00 0.00 1.31
620 632 3.409570 TCGTAAGATGATACTCCCTCCG 58.590 50.000 0.00 0.00 45.01 4.63
621 633 3.147629 CGTAAGATGATACTCCCTCCGT 58.852 50.000 0.00 0.00 43.02 4.69
622 634 3.188873 CGTAAGATGATACTCCCTCCGTC 59.811 52.174 0.00 0.00 43.02 4.79
623 635 2.296073 AGATGATACTCCCTCCGTCC 57.704 55.000 0.00 0.00 0.00 4.79
624 636 0.882474 GATGATACTCCCTCCGTCCG 59.118 60.000 0.00 0.00 0.00 4.79
625 637 0.539901 ATGATACTCCCTCCGTCCGG 60.540 60.000 0.00 0.00 0.00 5.14
626 638 1.150081 GATACTCCCTCCGTCCGGA 59.850 63.158 0.00 0.00 42.90 5.14
627 639 0.466922 GATACTCCCTCCGTCCGGAA 60.467 60.000 5.23 0.00 44.66 4.30
628 640 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
629 641 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
630 642 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
631 643 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
632 644 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
633 645 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
634 646 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
635 647 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
636 648 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
637 649 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
638 650 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
639 651 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
640 652 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
641 653 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
642 654 6.918800 CCGTCCGGAAATACTTGTCATCAAG 61.919 48.000 5.23 6.44 45.65 3.02
643 655 8.994207 CCGTCCGGAAATACTTGTCATCAAGA 62.994 46.154 5.23 0.31 44.37 3.02
660 672 8.812513 TCATCAAGATGAATAAAAGTGGATGT 57.187 30.769 10.16 0.00 44.14 3.06
661 673 9.904198 TCATCAAGATGAATAAAAGTGGATGTA 57.096 29.630 10.16 0.00 44.14 2.29
712 724 9.696917 ACACCTCTTTTTATTCATTTTCATGAC 57.303 29.630 0.00 0.00 39.28 3.06
713 725 9.695526 CACCTCTTTTTATTCATTTTCATGACA 57.304 29.630 0.00 0.00 39.28 3.58
723 735 8.915871 ATTCATTTTCATGACAAGTATTTCCG 57.084 30.769 0.00 0.00 39.28 4.30
724 736 6.851609 TCATTTTCATGACAAGTATTTCCGG 58.148 36.000 0.00 0.00 34.22 5.14
725 737 6.657117 TCATTTTCATGACAAGTATTTCCGGA 59.343 34.615 0.00 0.00 34.22 5.14
726 738 5.873179 TTTCATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 0.00 4.79
727 739 3.517602 TCATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
728 740 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
729 741 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
730 742 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
731 743 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
732 744 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
733 745 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
734 746 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
735 747 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
736 748 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
737 749 0.967380 TTTCCGGACGGAGGGAGTAC 60.967 60.000 13.64 0.00 46.06 2.73
738 750 2.044650 CCGGACGGAGGGAGTACA 60.045 66.667 4.40 0.00 37.50 2.90
739 751 2.413142 CCGGACGGAGGGAGTACAC 61.413 68.421 4.40 0.00 37.50 2.90
740 752 1.378250 CGGACGGAGGGAGTACACT 60.378 63.158 0.00 0.00 0.00 3.55
741 753 0.964358 CGGACGGAGGGAGTACACTT 60.964 60.000 0.00 0.00 0.00 3.16
742 754 0.531200 GGACGGAGGGAGTACACTTG 59.469 60.000 0.00 0.00 0.00 3.16
743 755 1.254954 GACGGAGGGAGTACACTTGT 58.745 55.000 0.00 0.00 0.00 3.16
744 756 2.440409 GACGGAGGGAGTACACTTGTA 58.560 52.381 0.00 0.00 0.00 2.41
745 757 2.821969 GACGGAGGGAGTACACTTGTAA 59.178 50.000 0.00 0.00 31.52 2.41
746 758 3.233507 ACGGAGGGAGTACACTTGTAAA 58.766 45.455 0.00 0.00 31.52 2.01
761 773 4.481930 TTGTAAAGACATCCAAACGCAG 57.518 40.909 0.00 0.00 34.86 5.18
762 774 2.225491 TGTAAAGACATCCAAACGCAGC 59.775 45.455 0.00 0.00 0.00 5.25
763 775 0.238289 AAAGACATCCAAACGCAGCG 59.762 50.000 14.82 14.82 0.00 5.18
795 807 2.488153 GGTTGCCTGAAATCCACTGTAC 59.512 50.000 0.00 0.00 0.00 2.90
796 808 3.146066 GTTGCCTGAAATCCACTGTACA 58.854 45.455 0.00 0.00 0.00 2.90
862 876 2.505557 CGCGTCCGGTAGAACCAC 60.506 66.667 0.00 0.00 38.47 4.16
880 894 3.127376 ACCACGACGCCCAATTATAAAAC 59.873 43.478 0.00 0.00 0.00 2.43
966 982 1.079127 AGAAACGCCTCACATCCCG 60.079 57.895 0.00 0.00 0.00 5.14
1127 1144 3.995506 CTCAACACCCATCCCGCCC 62.996 68.421 0.00 0.00 0.00 6.13
1152 1169 1.467678 CCCCTCAATCGATCCGCTCT 61.468 60.000 0.00 0.00 0.00 4.09
1191 1208 1.004918 CGAGAGCGGGGTTTTCTGT 60.005 57.895 0.00 0.00 0.00 3.41
1192 1209 1.014564 CGAGAGCGGGGTTTTCTGTC 61.015 60.000 0.00 0.00 0.00 3.51
1200 1217 1.076332 GGGTTTTCTGTCACGATCCG 58.924 55.000 0.00 0.00 0.00 4.18
1205 1222 1.945354 TTCTGTCACGATCCGCTCCC 61.945 60.000 0.00 0.00 0.00 4.30
1216 1233 4.065281 CGCTCCCTTTCCCGTCGT 62.065 66.667 0.00 0.00 0.00 4.34
1225 1242 2.472414 TTTCCCGTCGTGGAATGGGG 62.472 60.000 13.69 0.00 43.72 4.96
1260 1578 1.790387 GCAACTGGATGCGACTGAC 59.210 57.895 0.00 0.00 36.45 3.51
1389 1707 2.295070 GCACTTCGGTTATTTGGGTTGT 59.705 45.455 0.00 0.00 0.00 3.32
1469 1789 3.259592 CCGAATTCCCGGTTCCTTT 57.740 52.632 0.00 0.00 44.23 3.11
1470 1790 1.541379 CCGAATTCCCGGTTCCTTTT 58.459 50.000 0.00 0.00 44.23 2.27
1472 1792 2.094906 CCGAATTCCCGGTTCCTTTTTC 60.095 50.000 0.00 0.00 44.23 2.29
1473 1793 2.817844 CGAATTCCCGGTTCCTTTTTCT 59.182 45.455 0.00 0.00 0.00 2.52
1520 1853 3.765511 TGGATGCTCTCCTTTCATTTTGG 59.234 43.478 7.31 0.00 45.21 3.28
1528 1861 6.294731 GCTCTCCTTTCATTTTGGTACACAAT 60.295 38.462 0.00 0.00 39.55 2.71
1532 1865 8.655651 TCCTTTCATTTTGGTACACAATTTTC 57.344 30.769 0.00 0.00 36.49 2.29
1582 1915 3.426695 GCTTGATTCACTGATTCAACGGG 60.427 47.826 10.88 5.24 31.54 5.28
1672 2006 5.694006 TGCGTGATTTTCCCACATTTTTAAG 59.306 36.000 0.00 0.00 34.36 1.85
1682 2016 4.402474 CCCACATTTTTAAGGGATCAGGAC 59.598 45.833 0.00 0.00 44.30 3.85
1731 2065 5.374071 ACCGGTTCTTGAAGTCTAAACAAT 58.626 37.500 0.00 0.00 0.00 2.71
1748 2082 2.747446 ACAATTTGCAGACATACCCGTC 59.253 45.455 0.00 0.00 36.08 4.79
1788 2122 7.797038 TTAAGAGGACCTGTACTTTGTTTTC 57.203 36.000 0.00 0.00 0.00 2.29
1934 2269 7.707624 TGATACATCCTTCTGAAAGCAATTT 57.292 32.000 0.00 0.00 0.00 1.82
1971 2306 2.361483 ATGTGCGGCAGCCAATCA 60.361 55.556 13.30 7.07 44.33 2.57
2111 2446 7.750903 GCGAAATAGTTTTATCATTAGGCCATC 59.249 37.037 5.01 0.00 0.00 3.51
2169 2504 7.973388 TCTGTTTTGTTAACTGAAATGAAGTGG 59.027 33.333 7.22 0.00 0.00 4.00
2187 2522 7.987750 GAAGTGGTCTTCTTCCTTAGAAAAT 57.012 36.000 1.37 0.00 44.58 1.82
2315 2654 3.118956 GCACAGTGGAGTCTGTAGCTTAT 60.119 47.826 1.84 0.00 45.37 1.73
2405 2744 4.082125 CAGGCAAGTAATTGTTTCCCTCT 58.918 43.478 4.65 0.00 0.00 3.69
2804 3143 4.528206 TCTCTGTGTCACATGTCAGGTATT 59.472 41.667 6.03 0.00 0.00 1.89
2808 3147 1.665679 GTCACATGTCAGGTATTGCGG 59.334 52.381 0.00 0.00 0.00 5.69
3249 3641 4.769488 TCCAGATAGCAGACAGGTGATATC 59.231 45.833 0.00 0.00 43.30 1.63
3477 3871 5.046014 AGACAAGGTGAGTTGATGCTTCTAT 60.046 40.000 0.88 0.00 0.00 1.98
3478 3872 6.155221 AGACAAGGTGAGTTGATGCTTCTATA 59.845 38.462 0.88 0.00 0.00 1.31
3538 3932 5.125417 AGCAAGAAACTGTGAACTGCTAAAA 59.875 36.000 6.07 0.00 0.00 1.52
3933 4327 4.156008 GTCGAATAACAGTCCAAGGCAATT 59.844 41.667 0.00 0.00 0.00 2.32
3934 4328 4.764823 TCGAATAACAGTCCAAGGCAATTT 59.235 37.500 0.00 0.00 0.00 1.82
3939 4333 9.087424 GAATAACAGTCCAAGGCAATTTTATTC 57.913 33.333 0.00 0.00 0.00 1.75
3952 4438 6.868339 GGCAATTTTATTCTGTTACTTGCTGT 59.132 34.615 0.00 0.00 38.19 4.40
3953 4439 8.026607 GGCAATTTTATTCTGTTACTTGCTGTA 58.973 33.333 0.00 0.00 38.19 2.74
4002 4488 6.741358 GTGATTATACTTGCACCTTTTTCGTC 59.259 38.462 0.00 0.00 0.00 4.20
4023 4509 5.091431 GTCATTTCTGAGTGCTTACATTGC 58.909 41.667 0.00 0.00 30.18 3.56
4038 4524 7.492020 TGCTTACATTGCAATTATTGGACAATC 59.508 33.333 9.83 0.00 37.51 2.67
4323 4809 2.862512 ACAAAACTTGTCGTGTTGCTG 58.137 42.857 0.00 0.00 43.36 4.41
4452 4938 0.844661 TAGTGGCCCAAGTGGATGGT 60.845 55.000 0.00 0.00 38.91 3.55
4580 5066 3.474798 TCTCCTTACCACTCATCCTGT 57.525 47.619 0.00 0.00 0.00 4.00
4745 5231 6.014242 TCACAGATGTTAAGGATTGAGAGTGT 60.014 38.462 0.00 0.00 0.00 3.55
4980 5466 1.859703 GCACTGCTCTCATCAAGATCG 59.140 52.381 0.00 0.00 32.19 3.69
4981 5467 2.738000 GCACTGCTCTCATCAAGATCGT 60.738 50.000 0.00 0.00 32.19 3.73
5033 5519 6.862209 TGTAGTTGCTCACTTTGTTTCAAAT 58.138 32.000 0.00 0.00 36.88 2.32
5044 5530 7.286546 TCACTTTGTTTCAAATATCCTTGGTCA 59.713 33.333 0.00 0.00 0.00 4.02
5063 5549 4.274459 GGTCATCTAGGACATTGACATTGC 59.726 45.833 4.52 0.00 40.14 3.56
5108 5594 9.357652 CCACCAATTTCTTTGACAATATGTTAG 57.642 33.333 0.00 0.00 37.53 2.34
5239 5727 4.169461 ACATCCATTTCAGATTGGGGAGAT 59.831 41.667 1.07 0.00 33.62 2.75
5252 5740 2.844348 TGGGGAGATTACCTTGGAAGAC 59.156 50.000 0.00 0.00 0.00 3.01
5308 5796 8.894592 AGTCCATACCCTCAATATTATGATGTT 58.105 33.333 0.00 0.00 0.00 2.71
5309 5797 8.950210 GTCCATACCCTCAATATTATGATGTTG 58.050 37.037 1.09 1.09 36.16 3.33
5371 5859 6.262193 ACTTTTCTTTGTTTGAAACGGAGA 57.738 33.333 3.37 6.36 33.77 3.71
5389 5877 1.202927 AGACAATCCCAAGTGGTGTGG 60.203 52.381 0.00 0.00 35.77 4.17
5404 5892 3.074412 GGTGTGGTGGTGTCTCTATTTG 58.926 50.000 0.00 0.00 0.00 2.32
5408 5896 3.568007 GTGGTGGTGTCTCTATTTGCAAA 59.432 43.478 15.44 15.44 0.00 3.68
5452 5940 8.029522 TGTCTTCTATTTCATCGGATGCTATAC 58.970 37.037 13.15 4.70 0.00 1.47
5465 5953 8.492673 TCGGATGCTATACCATTCATAATTTC 57.507 34.615 0.00 0.00 0.00 2.17
5502 5990 4.054671 GGAATAGCACTCACACTAGCATC 58.945 47.826 0.00 0.00 0.00 3.91
5529 6017 6.179756 AGTCACATAAACCATGATAGCAACA 58.820 36.000 0.00 0.00 38.10 3.33
5535 6023 7.776969 ACATAAACCATGATAGCAACAATCTCT 59.223 33.333 0.00 0.00 38.10 3.10
5619 6107 2.305009 GGCAATTCTAGCAGCCTCATT 58.695 47.619 0.00 0.00 43.70 2.57
5688 6176 7.826918 TTTTAACCATAGCAACACTAGGTTT 57.173 32.000 0.00 0.00 40.20 3.27
5703 6191 9.581099 AACACTAGGTTTCACTTTAATTTGTTG 57.419 29.630 0.00 0.00 35.82 3.33
5739 6227 7.753580 GGTGCTTTAATATTACTTTTGCGAACT 59.246 33.333 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
156 157 5.922739 AAACAAGGCCGAAAAATCAATTC 57.077 34.783 0.00 0.00 0.00 2.17
199 201 9.384764 CAATGATCATTCATGTCTAGATAGCAT 57.615 33.333 18.16 0.00 41.83 3.79
385 393 5.047731 GGTAGATCTGCAGGCTTTTTCTTTT 60.048 40.000 15.13 0.00 0.00 2.27
412 420 3.677648 ACTGTAAGCCCGCGACGT 61.678 61.111 8.23 0.00 37.60 4.34
463 472 3.057806 CCATGTACGCAGACATATCCGTA 60.058 47.826 0.41 0.00 37.99 4.02
471 480 2.028567 TCACATTCCATGTACGCAGACA 60.029 45.455 0.00 0.00 42.70 3.41
505 514 5.132502 TCTGGTCATCAAACTCACACAAAT 58.867 37.500 0.00 0.00 0.00 2.32
513 522 3.560068 ACGTGTTTCTGGTCATCAAACTC 59.440 43.478 0.00 0.00 32.28 3.01
552 561 2.182014 CACGCGACGATCAGTTTGATA 58.818 47.619 15.93 0.00 37.20 2.15
583 592 8.692710 TCATCTTACGAGGTAAATACATCAGTT 58.307 33.333 6.12 0.00 36.86 3.16
601 613 3.506844 GGACGGAGGGAGTATCATCTTAC 59.493 52.174 0.00 0.00 36.25 2.34
604 616 1.545875 CGGACGGAGGGAGTATCATCT 60.546 57.143 0.00 0.00 36.25 2.90
605 617 0.882474 CGGACGGAGGGAGTATCATC 59.118 60.000 0.00 0.00 36.25 2.92
606 618 0.539901 CCGGACGGAGGGAGTATCAT 60.540 60.000 4.40 0.00 34.77 2.45
607 619 1.152819 CCGGACGGAGGGAGTATCA 60.153 63.158 4.40 0.00 34.77 2.15
608 620 0.466922 TTCCGGACGGAGGGAGTATC 60.467 60.000 13.64 0.00 46.06 2.24
609 621 0.032813 TTTCCGGACGGAGGGAGTAT 60.033 55.000 13.64 0.00 46.06 2.12
610 622 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
611 623 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
612 624 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
613 625 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
614 626 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
615 627 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
616 628 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
617 629 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
618 630 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
619 631 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
620 632 5.470845 CTTGATGACAAGTATTTCCGGAC 57.529 43.478 1.83 0.00 45.73 4.79
632 644 8.634335 TCCACTTTTATTCATCTTGATGACAA 57.366 30.769 12.28 7.53 34.65 3.18
633 645 8.680001 CATCCACTTTTATTCATCTTGATGACA 58.320 33.333 12.28 5.64 0.00 3.58
634 646 8.680903 ACATCCACTTTTATTCATCTTGATGAC 58.319 33.333 12.28 0.00 32.39 3.06
635 647 8.812513 ACATCCACTTTTATTCATCTTGATGA 57.187 30.769 9.02 9.02 32.39 2.92
686 698 9.696917 GTCATGAAAATGAATAAAAAGAGGTGT 57.303 29.630 0.00 0.00 31.60 4.16
687 699 9.695526 TGTCATGAAAATGAATAAAAAGAGGTG 57.304 29.630 0.00 0.00 31.60 4.00
698 710 7.975616 CCGGAAATACTTGTCATGAAAATGAAT 59.024 33.333 0.00 0.00 31.60 2.57
699 711 7.175816 TCCGGAAATACTTGTCATGAAAATGAA 59.824 33.333 0.00 0.00 31.60 2.57
700 712 6.657117 TCCGGAAATACTTGTCATGAAAATGA 59.343 34.615 0.00 0.00 0.00 2.57
701 713 6.747280 GTCCGGAAATACTTGTCATGAAAATG 59.253 38.462 5.23 0.00 0.00 2.32
702 714 6.403200 CGTCCGGAAATACTTGTCATGAAAAT 60.403 38.462 5.23 0.00 0.00 1.82
703 715 5.106869 CGTCCGGAAATACTTGTCATGAAAA 60.107 40.000 5.23 0.00 0.00 2.29
704 716 4.390603 CGTCCGGAAATACTTGTCATGAAA 59.609 41.667 5.23 0.00 0.00 2.69
705 717 3.930229 CGTCCGGAAATACTTGTCATGAA 59.070 43.478 5.23 0.00 0.00 2.57
706 718 3.517602 CGTCCGGAAATACTTGTCATGA 58.482 45.455 5.23 0.00 0.00 3.07
707 719 2.607635 CCGTCCGGAAATACTTGTCATG 59.392 50.000 5.23 0.00 37.50 3.07
708 720 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
709 721 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
710 722 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
711 723 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
712 724 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
713 725 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
714 726 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
715 727 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
716 728 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
717 729 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
718 730 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
719 731 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
720 732 2.273449 GTACTCCCTCCGTCCGGA 59.727 66.667 0.00 0.00 42.90 5.14
721 733 2.044650 TGTACTCCCTCCGTCCGG 60.045 66.667 0.00 0.00 0.00 5.14
722 734 0.964358 AAGTGTACTCCCTCCGTCCG 60.964 60.000 0.00 0.00 0.00 4.79
723 735 0.531200 CAAGTGTACTCCCTCCGTCC 59.469 60.000 0.00 0.00 0.00 4.79
724 736 1.254954 ACAAGTGTACTCCCTCCGTC 58.745 55.000 0.00 0.00 0.00 4.79
725 737 2.592102 TACAAGTGTACTCCCTCCGT 57.408 50.000 0.00 0.00 0.00 4.69
726 738 3.508793 TCTTTACAAGTGTACTCCCTCCG 59.491 47.826 0.00 0.00 0.00 4.63
727 739 4.282703 TGTCTTTACAAGTGTACTCCCTCC 59.717 45.833 0.00 0.00 30.91 4.30
728 740 5.464030 TGTCTTTACAAGTGTACTCCCTC 57.536 43.478 0.00 0.00 30.91 4.30
729 741 5.046520 GGATGTCTTTACAAGTGTACTCCCT 60.047 44.000 0.00 0.00 39.58 4.20
730 742 5.176592 GGATGTCTTTACAAGTGTACTCCC 58.823 45.833 0.00 0.00 39.58 4.30
731 743 5.790593 TGGATGTCTTTACAAGTGTACTCC 58.209 41.667 0.00 0.00 39.58 3.85
732 744 7.568861 CGTTTGGATGTCTTTACAAGTGTACTC 60.569 40.741 0.00 0.00 39.58 2.59
733 745 6.202188 CGTTTGGATGTCTTTACAAGTGTACT 59.798 38.462 0.00 0.00 39.58 2.73
734 746 6.360329 CGTTTGGATGTCTTTACAAGTGTAC 58.640 40.000 0.00 0.00 39.58 2.90
735 747 5.049954 GCGTTTGGATGTCTTTACAAGTGTA 60.050 40.000 0.00 0.00 39.58 2.90
736 748 4.261031 GCGTTTGGATGTCTTTACAAGTGT 60.261 41.667 0.00 0.00 39.58 3.55
737 749 4.219033 GCGTTTGGATGTCTTTACAAGTG 58.781 43.478 0.00 0.00 39.58 3.16
738 750 3.880490 TGCGTTTGGATGTCTTTACAAGT 59.120 39.130 0.00 0.00 39.58 3.16
739 751 4.466828 CTGCGTTTGGATGTCTTTACAAG 58.533 43.478 0.00 0.00 39.58 3.16
740 752 3.304391 GCTGCGTTTGGATGTCTTTACAA 60.304 43.478 0.00 0.00 39.58 2.41
741 753 2.225491 GCTGCGTTTGGATGTCTTTACA 59.775 45.455 0.00 0.00 40.69 2.41
742 754 2.724839 CGCTGCGTTTGGATGTCTTTAC 60.725 50.000 14.93 0.00 0.00 2.01
743 755 1.463056 CGCTGCGTTTGGATGTCTTTA 59.537 47.619 14.93 0.00 0.00 1.85
744 756 0.238289 CGCTGCGTTTGGATGTCTTT 59.762 50.000 14.93 0.00 0.00 2.52
745 757 0.884704 ACGCTGCGTTTGGATGTCTT 60.885 50.000 23.57 0.00 36.35 3.01
746 758 1.301716 ACGCTGCGTTTGGATGTCT 60.302 52.632 23.57 0.00 36.35 3.41
747 759 3.253955 ACGCTGCGTTTGGATGTC 58.746 55.556 23.57 0.00 36.35 3.06
756 768 0.796312 CCATAACTTCAACGCTGCGT 59.204 50.000 23.57 23.57 43.97 5.24
757 769 0.796312 ACCATAACTTCAACGCTGCG 59.204 50.000 21.91 21.91 0.00 5.18
758 770 2.584791 CAACCATAACTTCAACGCTGC 58.415 47.619 0.00 0.00 0.00 5.25
759 771 2.584791 GCAACCATAACTTCAACGCTG 58.415 47.619 0.00 0.00 0.00 5.18
760 772 1.539827 GGCAACCATAACTTCAACGCT 59.460 47.619 0.00 0.00 0.00 5.07
761 773 1.539827 AGGCAACCATAACTTCAACGC 59.460 47.619 0.00 0.00 37.17 4.84
762 774 2.811431 TCAGGCAACCATAACTTCAACG 59.189 45.455 0.00 0.00 37.17 4.10
763 775 4.846779 TTCAGGCAACCATAACTTCAAC 57.153 40.909 0.00 0.00 37.17 3.18
770 782 3.763360 CAGTGGATTTCAGGCAACCATAA 59.237 43.478 0.00 0.00 33.19 1.90
795 807 1.780931 GGCGAGCGGCAAATTTTTG 59.219 52.632 11.71 0.00 46.16 2.44
796 808 1.732683 CGGCGAGCGGCAAATTTTT 60.733 52.632 16.52 0.00 46.16 1.94
829 843 2.904131 CGGCCTCCCTTCCTTCTC 59.096 66.667 0.00 0.00 0.00 2.87
830 844 3.403558 GCGGCCTCCCTTCCTTCT 61.404 66.667 0.00 0.00 0.00 2.85
831 845 4.840005 CGCGGCCTCCCTTCCTTC 62.840 72.222 0.00 0.00 0.00 3.46
850 864 2.505557 GCGTCGTGGTTCTACCGG 60.506 66.667 0.00 0.00 42.58 5.28
851 865 2.505557 GGCGTCGTGGTTCTACCG 60.506 66.667 0.00 0.00 42.58 4.02
858 872 2.695127 TTATAATTGGGCGTCGTGGT 57.305 45.000 0.00 0.00 0.00 4.16
862 876 4.796312 CCAAAGTTTTATAATTGGGCGTCG 59.204 41.667 7.44 0.00 38.89 5.12
966 982 2.942376 TCGAAGAGACAGAGAGATGCTC 59.058 50.000 0.00 0.00 44.29 4.26
1127 1144 1.462238 ATCGATTGAGGGGGAGGGG 60.462 63.158 0.00 0.00 0.00 4.79
1178 1195 0.953960 ATCGTGACAGAAAACCCCGC 60.954 55.000 0.00 0.00 0.00 6.13
1191 1208 1.515954 GAAAGGGAGCGGATCGTGA 59.484 57.895 0.00 0.00 0.00 4.35
1192 1209 1.521681 GGAAAGGGAGCGGATCGTG 60.522 63.158 0.00 0.00 0.00 4.35
1200 1217 2.434359 CACGACGGGAAAGGGAGC 60.434 66.667 0.00 0.00 0.00 4.70
1260 1578 0.614697 AATGGGGAAAAAGGAGCGGG 60.615 55.000 0.00 0.00 0.00 6.13
1268 1586 4.651962 ACCGAAGAGAAAAATGGGGAAAAA 59.348 37.500 0.00 0.00 0.00 1.94
1463 1783 4.141574 TGAAGTTCCCGAGAGAAAAAGGAA 60.142 41.667 0.00 0.00 34.27 3.36
1465 1785 3.498777 GTGAAGTTCCCGAGAGAAAAAGG 59.501 47.826 0.00 0.00 0.00 3.11
1467 1787 4.145365 TGTGAAGTTCCCGAGAGAAAAA 57.855 40.909 0.00 0.00 0.00 1.94
1468 1788 3.830744 TGTGAAGTTCCCGAGAGAAAA 57.169 42.857 0.00 0.00 0.00 2.29
1469 1789 3.664107 CATGTGAAGTTCCCGAGAGAAA 58.336 45.455 0.00 0.00 0.00 2.52
1470 1790 2.612972 GCATGTGAAGTTCCCGAGAGAA 60.613 50.000 0.00 0.00 0.00 2.87
1472 1792 1.338105 TGCATGTGAAGTTCCCGAGAG 60.338 52.381 0.00 0.00 0.00 3.20
1473 1793 0.684535 TGCATGTGAAGTTCCCGAGA 59.315 50.000 0.00 0.00 0.00 4.04
1520 1853 2.417239 TGCGGATCGGAAAATTGTGTAC 59.583 45.455 4.16 0.00 0.00 2.90
1528 1861 1.234821 GCCATATGCGGATCGGAAAA 58.765 50.000 9.19 0.00 0.00 2.29
1582 1915 5.715434 TTAAGGGTGCTAACAAATCAACC 57.285 39.130 0.00 0.00 37.84 3.77
1672 2006 2.820197 GTCCAACTTTTGTCCTGATCCC 59.180 50.000 0.00 0.00 0.00 3.85
1682 2016 6.372659 AGTGCAGATATACAGTCCAACTTTTG 59.627 38.462 0.00 0.00 0.00 2.44
1748 2082 7.439655 GGTCCTCTTAATTGCATACAACTAGAG 59.560 40.741 0.00 0.00 38.99 2.43
1788 2122 3.025978 TGCCAGGAATCATAAAGCTTGG 58.974 45.455 0.00 0.00 0.00 3.61
1934 2269 0.623723 GGTGCCTTGGGGAGAATGTA 59.376 55.000 0.00 0.00 33.58 2.29
1971 2306 1.547372 GATTTCACAACTGCCATGGCT 59.453 47.619 35.53 15.87 42.51 4.75
2104 2439 1.000993 ACGAGAGTCCAGATGGCCT 59.999 57.895 3.32 0.00 44.19 5.19
2169 2504 8.672815 CATTCAGGATTTTCTAAGGAAGAAGAC 58.327 37.037 0.00 0.00 44.95 3.01
2187 2522 7.602644 GTCTAGTTGTGACATTAACATTCAGGA 59.397 37.037 7.88 0.00 34.80 3.86
2225 2564 6.009589 TCCAGATGCCTTCACAGAAAAATTA 58.990 36.000 0.00 0.00 0.00 1.40
2228 2567 3.831323 TCCAGATGCCTTCACAGAAAAA 58.169 40.909 0.00 0.00 0.00 1.94
2315 2654 5.139727 TGCAAAAGATCTTTCCTTGGAGAA 58.860 37.500 20.71 0.00 31.45 2.87
2428 2767 7.312154 TCTTTTGTATACGAAGCAATGCAAAT 58.688 30.769 8.35 0.00 38.08 2.32
2613 2952 4.320788 GGAAATGACAAAAGGCAGAGACAG 60.321 45.833 0.00 0.00 0.00 3.51
3280 3672 5.643348 CCGCATAGTGGCAGAATGAATAATA 59.357 40.000 12.01 0.00 39.69 0.98
3605 3999 7.755822 ACGCCTTATTTATTTATTTTTGACGCA 59.244 29.630 0.00 0.00 0.00 5.24
3939 4333 6.494893 TGGCTTAATTACAGCAAGTAACAG 57.505 37.500 16.35 3.34 44.95 3.16
4002 4488 5.050644 TGCAATGTAAGCACTCAGAAATG 57.949 39.130 0.00 0.00 37.02 2.32
4038 4524 5.659079 AGAGTTCCAGTTCAGTATTAGGGAG 59.341 44.000 0.00 0.00 0.00 4.30
4580 5066 5.556915 ACCAGATGTTAAACAAGATCCGAA 58.443 37.500 0.00 0.00 0.00 4.30
4745 5231 2.673775 TCCCCATGACAAGCAAAGAA 57.326 45.000 0.00 0.00 0.00 2.52
4768 5254 3.793801 GCAGGCTAAGTCTGATACACGAG 60.794 52.174 4.32 0.00 37.47 4.18
4778 5264 1.528129 GCAAACAGCAGGCTAAGTCT 58.472 50.000 0.00 0.00 44.79 3.24
4895 5381 6.116126 GGAGATTAGCTGTACAACATTTCCT 58.884 40.000 0.00 0.00 0.00 3.36
4945 5431 4.023980 AGCAGTGCATACTAAGACCACTA 58.976 43.478 19.20 0.00 35.20 2.74
4952 5438 4.941657 TGATGAGAGCAGTGCATACTAAG 58.058 43.478 19.20 0.00 34.74 2.18
4980 5466 4.516698 CCATCACTCAGCCATAACCATAAC 59.483 45.833 0.00 0.00 0.00 1.89
4981 5467 4.446167 CCCATCACTCAGCCATAACCATAA 60.446 45.833 0.00 0.00 0.00 1.90
5033 5519 6.042093 GTCAATGTCCTAGATGACCAAGGATA 59.958 42.308 0.00 0.00 41.34 2.59
5044 5530 4.445448 GGAGGCAATGTCAATGTCCTAGAT 60.445 45.833 4.47 0.00 0.00 1.98
5063 5549 4.263068 GGTGGTCCAATATCACATAGGAGG 60.263 50.000 0.00 0.00 33.45 4.30
5108 5594 6.582437 ACACCACGATTTTTGTTTTTCATC 57.418 33.333 0.00 0.00 0.00 2.92
5239 5727 9.184523 CCAAAATATGTATGTCTTCCAAGGTAA 57.815 33.333 0.00 0.00 0.00 2.85
5252 5740 5.132502 TCCCACTCAGCCAAAATATGTATG 58.867 41.667 0.00 0.00 0.00 2.39
5308 5796 2.619697 TCCAAGGGATTTGAATGGCA 57.380 45.000 0.00 0.00 39.21 4.92
5309 5797 2.103601 CCATCCAAGGGATTTGAATGGC 59.896 50.000 0.00 0.00 43.56 4.40
5371 5859 0.555769 ACCACACCACTTGGGATTGT 59.444 50.000 0.00 0.00 41.15 2.71
5389 5877 8.986477 ATTAAATTTGCAAATAGAGACACCAC 57.014 30.769 24.35 0.00 0.00 4.16
5423 5911 7.445121 AGCATCCGATGAAATAGAAGACATTA 58.555 34.615 12.79 0.00 0.00 1.90
5440 5928 8.321353 AGAAATTATGAATGGTATAGCATCCGA 58.679 33.333 17.34 5.57 0.00 4.55
5465 5953 6.884836 AGTGCTATTCCTTTTACCTTACCAAG 59.115 38.462 0.00 0.00 0.00 3.61
5481 5969 4.942852 AGATGCTAGTGTGAGTGCTATTC 58.057 43.478 0.00 0.00 0.00 1.75
5482 5970 6.097554 ACTTAGATGCTAGTGTGAGTGCTATT 59.902 38.462 0.00 0.00 0.00 1.73
5483 5971 5.596361 ACTTAGATGCTAGTGTGAGTGCTAT 59.404 40.000 0.00 0.00 0.00 2.97
5484 5972 4.950475 ACTTAGATGCTAGTGTGAGTGCTA 59.050 41.667 0.00 0.00 0.00 3.49
5485 5973 3.766591 ACTTAGATGCTAGTGTGAGTGCT 59.233 43.478 0.00 0.00 0.00 4.40
5486 5974 4.109050 GACTTAGATGCTAGTGTGAGTGC 58.891 47.826 0.00 0.00 0.00 4.40
5502 5990 8.338259 GTTGCTATCATGGTTTATGTGACTTAG 58.662 37.037 0.00 0.00 38.01 2.18
5535 6023 7.541783 GCATGCATGTTGTCTCAGTTAAAATAA 59.458 33.333 26.79 0.00 0.00 1.40
5546 6034 1.542915 AGTTGGCATGCATGTTGTCTC 59.457 47.619 26.79 9.66 0.00 3.36
5547 6035 1.624336 AGTTGGCATGCATGTTGTCT 58.376 45.000 26.79 16.96 0.00 3.41
5584 6072 7.276438 GCTAGAATTGCCAAACCTGATAAAAAG 59.724 37.037 0.00 0.00 0.00 2.27
5589 6077 4.854173 TGCTAGAATTGCCAAACCTGATA 58.146 39.130 0.00 0.00 0.00 2.15
5593 6081 1.821136 GCTGCTAGAATTGCCAAACCT 59.179 47.619 0.00 0.00 0.00 3.50
5664 6152 7.502895 TGAAACCTAGTGTTGCTATGGTTAAAA 59.497 33.333 0.00 0.00 38.76 1.52
5688 6176 6.800072 AAACCCCTCAACAAATTAAAGTGA 57.200 33.333 0.00 0.00 0.00 3.41
5703 6191 7.997223 AGTAATATTAAAGCACCTAAACCCCTC 59.003 37.037 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.