Multiple sequence alignment - TraesCS6B01G271800

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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 TraesCS6B01G271800 chr6B 100.000 5733 0 0 1 5733 490263064 490257332 0.000000e+00 10587.0
1 TraesCS6B01G271800 chr6A 90.760 3474 213 46 2297 5725 469427200 469430610 0.000000e+00 4538.0
2 TraesCS6B01G271800 chr6A 93.869 1680 67 17 637 2295 469425588 469427252 0.000000e+00 2499.0
3 TraesCS6B01G271800 chr6A 90.659 546 16 14 1 533 469425069 469425592 0.000000e+00 693.0
4 TraesCS6B01G271800 chr6D 92.170 2516 118 39 2297 4780 330108944 330111412 0.000000e+00 3482.0
5 TraesCS6B01G271800 chr6D 91.637 1674 86 22 632 2288 330107355 330108991 0.000000e+00 2266.0
6 TraesCS6B01G271800 chr6D 89.827 521 18 8 1 508 330106789 330107287 2.250000e-178 636.0
7 TraesCS6B01G271800 chr6D 92.343 431 14 6 4786 5213 330111500 330111914 3.820000e-166 595.0
8 TraesCS6B01G271800 chr6D 88.889 252 26 2 5335 5584 330112046 330112297 5.580000e-80 309.0
9 TraesCS6B01G271800 chr6D 88.068 176 13 5 5557 5725 330112297 330112471 9.740000e-48 202.0
10 TraesCS6B01G271800 chr7A 95.833 48 1 1 3674 3721 575281069 575281023 6.160000e-10 76.8
11 TraesCS6B01G271800 chr3D 95.745 47 2 0 3675 3721 424659572 424659618 6.160000e-10 76.8
12 TraesCS6B01G271800 chr3A 95.745 47 2 0 3675 3721 564342560 564342514 6.160000e-10 76.8
13 TraesCS6B01G271800 chr7D 97.674 43 1 0 3679 3721 176171804 176171762 2.220000e-09 75.0
14 TraesCS6B01G271800 chr5D 95.652 46 2 0 3675 3720 527572664 527572709 2.220000e-09 75.0
15 TraesCS6B01G271800 chr5D 95.652 46 2 0 3675 3720 527602227 527602272 2.220000e-09 75.0
16 TraesCS6B01G271800 chr5D 93.750 48 3 0 3674 3721 476275184 476275231 7.970000e-09 73.1
17 TraesCS6B01G271800 chr1B 93.878 49 3 0 3673 3721 70315147 70315099 2.220000e-09 75.0
18 TraesCS6B01G271800 chr1B 90.566 53 4 1 3680 3731 328153806 328153858 1.030000e-07 69.4
19 TraesCS6B01G271800 chr5B 87.500 56 5 2 5213 5268 402744322 402744269 4.800000e-06 63.9


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G271800 chr6B 490257332 490263064 5732 True 10587.000000 10587 100.000000 1 5733 1 chr6B.!!$R1 5732
1 TraesCS6B01G271800 chr6A 469425069 469430610 5541 False 2576.666667 4538 91.762667 1 5725 3 chr6A.!!$F1 5724
2 TraesCS6B01G271800 chr6D 330106789 330112471 5682 False 1248.333333 3482 90.489000 1 5725 6 chr6D.!!$F1 5724


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
900 933 0.107268 TGTCATCATCATGGCGGGAG 59.893 55.0 0.00 0.0 37.45 4.30 F
1426 1475 0.249155 GCATTACGGCTACGGCTACA 60.249 55.0 0.00 0.0 46.48 2.74 F
2449 2504 0.257039 ATTCAGGGCATGGAGGTGAC 59.743 55.0 0.00 0.0 0.00 3.67 F
3290 3386 0.609662 ACCGCACCCGTGTTAACTAT 59.390 50.0 7.22 0.0 0.00 2.12 F
4114 4225 0.523966 GGATCAGTCGGGATCTAGCG 59.476 60.0 10.84 0.0 42.63 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2016 2065 0.458543 CCGATGACTTCCGGTGAGTG 60.459 60.0 16.09 4.09 40.78 3.51 R
3271 3367 0.609662 ATAGTTAACACGGGTGCGGT 59.390 50.0 8.61 0.00 0.00 5.68 R
3802 3901 0.179070 GCAGGGCTGTAGAGTTAGGC 60.179 60.0 0.00 0.00 38.62 3.93 R
4409 4520 0.250038 AGCTCGCTTTGCTCAACAGA 60.250 50.0 0.00 0.00 35.67 3.41 R
4922 5115 0.331616 ATGGACCAAGGGTTGCCTAC 59.668 55.0 0.00 0.00 35.25 3.18 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 1.216977 CATTCGGGCAGTGGTACGA 59.783 57.895 0.00 0.00 0.00 3.43
96 97 4.827692 TGCACACCCTACTAACAGTAATG 58.172 43.478 0.00 0.00 29.00 1.90
242 248 1.589993 CACCGCAGCGTATCCTCTG 60.590 63.158 15.05 0.00 0.00 3.35
262 268 2.436292 CAGAGCAGAGCAGGGCAC 60.436 66.667 0.00 0.00 0.00 5.01
263 269 2.607134 AGAGCAGAGCAGGGCACT 60.607 61.111 0.00 0.00 0.00 4.40
264 270 2.125188 GAGCAGAGCAGGGCACTC 60.125 66.667 0.00 0.00 0.00 3.51
287 298 1.802880 CGTTGATCCGGTGATGGAGAC 60.803 57.143 0.00 0.00 42.45 3.36
445 464 4.443266 GCAGTCCTCGCCTCGCTT 62.443 66.667 0.00 0.00 0.00 4.68
446 465 2.202676 CAGTCCTCGCCTCGCTTC 60.203 66.667 0.00 0.00 0.00 3.86
447 466 3.453679 AGTCCTCGCCTCGCTTCC 61.454 66.667 0.00 0.00 0.00 3.46
448 467 3.760035 GTCCTCGCCTCGCTTCCA 61.760 66.667 0.00 0.00 0.00 3.53
558 577 3.315949 CCCCTCCGTTTCCCGTCA 61.316 66.667 0.00 0.00 33.66 4.35
559 578 2.047560 CCCTCCGTTTCCCGTCAC 60.048 66.667 0.00 0.00 33.66 3.67
561 580 2.337532 CTCCGTTTCCCGTCACGT 59.662 61.111 0.00 0.00 34.47 4.49
562 581 1.300388 CTCCGTTTCCCGTCACGTT 60.300 57.895 0.00 0.00 34.47 3.99
564 583 2.312436 CCGTTTCCCGTCACGTTCC 61.312 63.158 0.00 0.00 34.47 3.62
565 584 2.312436 CGTTTCCCGTCACGTTCCC 61.312 63.158 0.00 0.00 0.00 3.97
566 585 1.962822 GTTTCCCGTCACGTTCCCC 60.963 63.158 0.00 0.00 0.00 4.81
567 586 2.441675 TTTCCCGTCACGTTCCCCA 61.442 57.895 0.00 0.00 0.00 4.96
568 587 2.663423 TTTCCCGTCACGTTCCCCAC 62.663 60.000 0.00 0.00 0.00 4.61
569 588 3.931247 CCCGTCACGTTCCCCACA 61.931 66.667 0.00 0.00 0.00 4.17
570 589 2.663852 CCGTCACGTTCCCCACAC 60.664 66.667 0.00 0.00 0.00 3.82
571 590 2.420043 CGTCACGTTCCCCACACT 59.580 61.111 0.00 0.00 0.00 3.55
572 591 1.663702 CGTCACGTTCCCCACACTC 60.664 63.158 0.00 0.00 0.00 3.51
573 592 1.663702 GTCACGTTCCCCACACTCG 60.664 63.158 0.00 0.00 0.00 4.18
574 593 2.357034 CACGTTCCCCACACTCGG 60.357 66.667 0.00 0.00 0.00 4.63
575 594 2.522436 ACGTTCCCCACACTCGGA 60.522 61.111 0.00 0.00 0.00 4.55
576 595 2.261671 CGTTCCCCACACTCGGAG 59.738 66.667 2.83 2.83 0.00 4.63
577 596 2.663196 GTTCCCCACACTCGGAGG 59.337 66.667 10.23 1.07 0.00 4.30
578 597 3.319198 TTCCCCACACTCGGAGGC 61.319 66.667 10.23 0.00 0.00 4.70
581 600 3.066190 CCCACACTCGGAGGCGTA 61.066 66.667 10.23 0.00 0.00 4.42
582 601 2.490217 CCACACTCGGAGGCGTAG 59.510 66.667 10.23 0.00 0.00 3.51
610 629 7.064134 CGCAGATACTATTAGAAGAGATCGTCT 59.936 40.741 3.80 3.80 38.26 4.18
611 630 9.373603 GCAGATACTATTAGAAGAGATCGTCTA 57.626 37.037 0.00 1.94 36.21 2.59
616 635 8.836268 ACTATTAGAAGAGATCGTCTATCGTT 57.164 34.615 6.37 0.00 39.79 3.85
617 636 8.714179 ACTATTAGAAGAGATCGTCTATCGTTG 58.286 37.037 6.37 1.90 39.79 4.10
618 637 6.922247 TTAGAAGAGATCGTCTATCGTTGT 57.078 37.500 6.37 0.00 39.79 3.32
619 638 8.604640 ATTAGAAGAGATCGTCTATCGTTGTA 57.395 34.615 6.37 0.00 39.79 2.41
620 639 8.604640 TTAGAAGAGATCGTCTATCGTTGTAT 57.395 34.615 6.37 0.00 39.79 2.29
621 640 6.893759 AGAAGAGATCGTCTATCGTTGTATG 58.106 40.000 0.00 0.00 39.79 2.39
622 641 5.614923 AGAGATCGTCTATCGTTGTATGG 57.385 43.478 0.00 0.00 39.79 2.74
623 642 4.456222 AGAGATCGTCTATCGTTGTATGGG 59.544 45.833 0.00 0.00 39.79 4.00
624 643 4.142790 AGATCGTCTATCGTTGTATGGGT 58.857 43.478 0.00 0.00 39.79 4.51
625 644 3.703286 TCGTCTATCGTTGTATGGGTG 57.297 47.619 0.00 0.00 40.80 4.61
626 645 2.359848 TCGTCTATCGTTGTATGGGTGG 59.640 50.000 0.00 0.00 40.80 4.61
627 646 2.545113 CGTCTATCGTTGTATGGGTGGG 60.545 54.545 0.00 0.00 34.52 4.61
628 647 2.433239 GTCTATCGTTGTATGGGTGGGT 59.567 50.000 0.00 0.00 0.00 4.51
629 648 2.432874 TCTATCGTTGTATGGGTGGGTG 59.567 50.000 0.00 0.00 0.00 4.61
630 649 0.393808 ATCGTTGTATGGGTGGGTGC 60.394 55.000 0.00 0.00 0.00 5.01
670 689 1.006220 CAAGAAAACAAGGGGCGCC 60.006 57.895 21.18 21.18 0.00 6.53
671 690 2.207229 AAGAAAACAAGGGGCGCCC 61.207 57.895 38.57 38.57 45.90 6.13
716 737 1.546998 GCCCGGAAAAAGAAGGAAGGA 60.547 52.381 0.73 0.00 0.00 3.36
723 744 2.753055 AAAGAAGGAAGGAGCGAGTC 57.247 50.000 0.00 0.00 0.00 3.36
745 766 2.384382 AGCGAGTGCAAACAAATTTCG 58.616 42.857 0.00 0.00 46.23 3.46
891 924 0.172578 GTCCGTCGGTGTCATCATCA 59.827 55.000 11.88 0.00 0.00 3.07
900 933 0.107268 TGTCATCATCATGGCGGGAG 59.893 55.000 0.00 0.00 37.45 4.30
941 974 4.789123 CCCGGGGCCGATCGTTTT 62.789 66.667 14.71 0.00 42.83 2.43
942 975 2.187424 CCGGGGCCGATCGTTTTA 59.813 61.111 15.09 0.00 42.83 1.52
943 976 1.885850 CCGGGGCCGATCGTTTTAG 60.886 63.158 15.09 0.00 42.83 1.85
944 977 1.885850 CGGGGCCGATCGTTTTAGG 60.886 63.158 15.09 0.00 42.83 2.69
945 978 1.523524 GGGGCCGATCGTTTTAGGA 59.476 57.895 15.09 0.00 0.00 2.94
1376 1419 4.308458 CCGCCACGACCAACTCCA 62.308 66.667 0.00 0.00 0.00 3.86
1377 1420 3.041940 CGCCACGACCAACTCCAC 61.042 66.667 0.00 0.00 0.00 4.02
1426 1475 0.249155 GCATTACGGCTACGGCTACA 60.249 55.000 0.00 0.00 46.48 2.74
1428 1477 1.066605 CATTACGGCTACGGCTACAGT 59.933 52.381 0.00 0.00 46.48 3.55
1552 1601 4.883300 CGTCGGAGCGCGTCTACC 62.883 72.222 8.43 5.46 0.00 3.18
1698 1747 2.631418 ATGTGTTCGACGACTACCAG 57.369 50.000 0.00 0.00 0.00 4.00
2085 2134 2.251642 ACAGTTTGTTCGAGCGGCC 61.252 57.895 0.00 0.00 0.00 6.13
2220 2269 5.235305 AGTTTCATTGATGTTATGGCGAC 57.765 39.130 0.00 0.00 0.00 5.19
2265 2314 9.071276 ACTGGCATATTTTCTGATATACTTTGG 57.929 33.333 0.00 0.00 0.00 3.28
2449 2504 0.257039 ATTCAGGGCATGGAGGTGAC 59.743 55.000 0.00 0.00 0.00 3.67
2734 2796 6.371548 TGGTGACAAATATTTACTGAGAGCAC 59.628 38.462 0.00 3.44 37.44 4.40
2736 2798 7.094805 GGTGACAAATATTTACTGAGAGCACAA 60.095 37.037 0.00 0.00 0.00 3.33
2740 2802 8.454106 ACAAATATTTACTGAGAGCACAATGTC 58.546 33.333 0.00 0.00 0.00 3.06
2741 2803 8.453320 CAAATATTTACTGAGAGCACAATGTCA 58.547 33.333 0.00 0.00 0.00 3.58
2742 2804 8.743085 AATATTTACTGAGAGCACAATGTCAT 57.257 30.769 0.00 0.00 0.00 3.06
2743 2805 6.674694 ATTTACTGAGAGCACAATGTCATC 57.325 37.500 0.00 0.00 0.00 2.92
2744 2806 3.977134 ACTGAGAGCACAATGTCATCT 57.023 42.857 0.00 0.00 0.00 2.90
2745 2807 4.283363 ACTGAGAGCACAATGTCATCTT 57.717 40.909 0.00 0.00 0.00 2.40
2746 2808 4.649692 ACTGAGAGCACAATGTCATCTTT 58.350 39.130 0.00 0.00 0.00 2.52
2747 2809 5.068636 ACTGAGAGCACAATGTCATCTTTT 58.931 37.500 0.00 0.00 0.00 2.27
2748 2810 5.533903 ACTGAGAGCACAATGTCATCTTTTT 59.466 36.000 0.00 0.00 0.00 1.94
2806 2868 1.999048 CCATGTTTGCGCAATGACAT 58.001 45.000 26.90 26.90 33.27 3.06
2807 2869 2.339418 CCATGTTTGCGCAATGACATT 58.661 42.857 28.97 16.52 30.78 2.71
2808 2870 2.737783 CCATGTTTGCGCAATGACATTT 59.262 40.909 28.97 14.32 30.78 2.32
2809 2871 3.181528 CCATGTTTGCGCAATGACATTTC 60.182 43.478 28.97 12.47 30.78 2.17
2810 2872 3.089573 TGTTTGCGCAATGACATTTCA 57.910 38.095 25.64 1.84 35.73 2.69
2811 2873 3.651206 TGTTTGCGCAATGACATTTCAT 58.349 36.364 25.64 0.00 44.98 2.57
2812 2874 3.674281 TGTTTGCGCAATGACATTTCATC 59.326 39.130 25.64 0.00 42.00 2.92
2814 2876 3.409851 TGCGCAATGACATTTCATCTC 57.590 42.857 8.16 0.00 42.00 2.75
2948 3034 5.036916 TGGAGACCAAATACCCAGATTAGT 58.963 41.667 0.00 0.00 0.00 2.24
2979 3065 8.988064 TTAAATTTGCGTGCCATATTTAAAGA 57.012 26.923 0.00 0.00 40.80 2.52
3068 3154 9.860898 GTTTAGTTTCATTTGAAAGGATGCTAT 57.139 29.630 5.99 0.00 43.82 2.97
3174 3270 4.312443 TCTTGTTGGCTCCTTAGTAAACG 58.688 43.478 0.00 0.00 0.00 3.60
3214 3310 6.668541 TGAAAATCTCTTATGCAGCACTAC 57.331 37.500 0.00 0.00 0.00 2.73
3235 3331 3.190535 ACTTTCAATAATGTGGGACGTGC 59.809 43.478 0.00 0.00 0.00 5.34
3274 3370 9.265901 ACTGAGATTATTTTTCTCATATGACCG 57.734 33.333 0.00 0.00 46.26 4.79
3290 3386 0.609662 ACCGCACCCGTGTTAACTAT 59.390 50.000 7.22 0.00 0.00 2.12
3601 3697 9.265901 CCTTGACATCTTAGGTACATATTTCAG 57.734 37.037 0.00 0.00 0.00 3.02
3629 3725 2.165167 CCTGTCGGTACACTACTTCCA 58.835 52.381 0.00 0.00 0.00 3.53
3693 3792 6.011122 TCTATTAAGAAGTACTCCCTCCGT 57.989 41.667 0.00 0.00 0.00 4.69
3694 3793 7.141758 TCTATTAAGAAGTACTCCCTCCGTA 57.858 40.000 0.00 0.00 0.00 4.02
3695 3794 7.577303 TCTATTAAGAAGTACTCCCTCCGTAA 58.423 38.462 0.00 0.00 0.00 3.18
3696 3795 8.055181 TCTATTAAGAAGTACTCCCTCCGTAAA 58.945 37.037 0.00 0.00 0.00 2.01
3697 3796 6.521151 TTAAGAAGTACTCCCTCCGTAAAG 57.479 41.667 0.00 0.00 0.00 1.85
3698 3797 4.313020 AGAAGTACTCCCTCCGTAAAGA 57.687 45.455 0.00 0.00 0.00 2.52
3700 3799 5.082425 AGAAGTACTCCCTCCGTAAAGAAA 58.918 41.667 0.00 0.00 0.00 2.52
3702 3801 6.894103 AGAAGTACTCCCTCCGTAAAGAAATA 59.106 38.462 0.00 0.00 0.00 1.40
3704 3803 8.773033 AAGTACTCCCTCCGTAAAGAAATATA 57.227 34.615 0.00 0.00 0.00 0.86
3705 3804 8.773033 AGTACTCCCTCCGTAAAGAAATATAA 57.227 34.615 0.00 0.00 0.00 0.98
3707 3806 6.522946 ACTCCCTCCGTAAAGAAATATAAGC 58.477 40.000 0.00 0.00 0.00 3.09
3708 3807 5.535333 TCCCTCCGTAAAGAAATATAAGCG 58.465 41.667 0.00 0.00 0.00 4.68
3709 3808 4.151867 CCCTCCGTAAAGAAATATAAGCGC 59.848 45.833 0.00 0.00 0.00 5.92
3710 3809 4.748102 CCTCCGTAAAGAAATATAAGCGCA 59.252 41.667 11.47 0.00 0.00 6.09
3711 3810 5.408604 CCTCCGTAAAGAAATATAAGCGCAT 59.591 40.000 11.47 0.00 0.00 4.73
3712 3811 6.073222 CCTCCGTAAAGAAATATAAGCGCATT 60.073 38.462 11.47 3.50 0.00 3.56
3713 3812 7.254227 TCCGTAAAGAAATATAAGCGCATTT 57.746 32.000 11.47 6.66 0.00 2.32
3714 3813 8.367943 TCCGTAAAGAAATATAAGCGCATTTA 57.632 30.769 11.47 0.00 0.00 1.40
3715 3814 8.492748 TCCGTAAAGAAATATAAGCGCATTTAG 58.507 33.333 11.47 0.00 0.00 1.85
3716 3815 8.492748 CCGTAAAGAAATATAAGCGCATTTAGA 58.507 33.333 11.47 0.00 0.00 2.10
3720 3819 9.884465 AAAGAAATATAAGCGCATTTAGATCAC 57.116 29.630 11.47 1.90 0.00 3.06
3743 3842 5.106237 ACGAGTAACATTCTCAGTCCAGTAC 60.106 44.000 0.00 0.00 32.79 2.73
3760 3859 7.811713 AGTCCAGTACGTTATTAAGTTTCAGTC 59.188 37.037 0.00 0.00 0.00 3.51
3801 3900 9.953565 TTTTTACATATTGTGTAGAGGCTAACT 57.046 29.630 0.00 0.00 43.79 2.24
3802 3901 8.942338 TTTACATATTGTGTAGAGGCTAACTG 57.058 34.615 0.00 0.00 43.79 3.16
3803 3902 5.360591 ACATATTGTGTAGAGGCTAACTGC 58.639 41.667 0.00 0.00 39.91 4.40
3816 3915 3.449632 GCTAACTGCCTAACTCTACAGC 58.550 50.000 0.00 0.00 33.35 4.40
3887 3997 6.351371 CCGAGTAATCAATATCCCTACATGCT 60.351 42.308 0.00 0.00 0.00 3.79
3917 4027 3.545703 AGGTGAACTTTCCTGAACACTG 58.454 45.455 0.00 0.00 32.29 3.66
4114 4225 0.523966 GGATCAGTCGGGATCTAGCG 59.476 60.000 10.84 0.00 42.63 4.26
4219 4330 2.034687 GGATGGCTGGCACTGTGT 59.965 61.111 5.88 0.00 0.00 3.72
4372 4483 2.779742 TTACCGCCATGCAAGCCCTT 62.780 55.000 6.51 0.00 0.00 3.95
4375 4486 2.575461 GCCATGCAAGCCCTTGTC 59.425 61.111 9.53 3.42 42.31 3.18
4384 4495 1.192146 AAGCCCTTGTCTCCAGCGTA 61.192 55.000 0.00 0.00 0.00 4.42
4438 4549 2.530177 CAAAGCGAGCTGATCTTCGTA 58.470 47.619 13.54 0.00 0.00 3.43
4453 4564 1.631405 TCGTAACCCGGGAAAGAGAA 58.369 50.000 32.02 2.73 37.11 2.87
4531 4642 0.185901 TGAACAAGAAGCTGGCCCTT 59.814 50.000 0.00 0.00 0.00 3.95
4690 4801 1.524482 GGAGACCCTGAGACATGCC 59.476 63.158 0.00 0.00 0.00 4.40
4725 4836 3.501349 TGTCCAGAGAGAGTGCTAAAGT 58.499 45.455 0.00 0.00 0.00 2.66
4735 4846 4.518249 AGAGTGCTAAAGTTTCATAGCCC 58.482 43.478 6.43 0.00 43.05 5.19
4751 4862 0.810648 GCCCGATTTTGCATCTGACA 59.189 50.000 0.00 0.00 0.00 3.58
4752 4863 1.202222 GCCCGATTTTGCATCTGACAG 60.202 52.381 0.00 0.00 0.00 3.51
4753 4864 2.358957 CCCGATTTTGCATCTGACAGA 58.641 47.619 7.80 7.80 0.00 3.41
4754 4865 2.096496 CCCGATTTTGCATCTGACAGAC 59.904 50.000 7.47 0.00 0.00 3.51
4847 5040 0.674581 CTGGGCGAATGCTTCTGACA 60.675 55.000 0.00 0.00 42.25 3.58
4898 5091 9.482627 CTGACTTCTGAGTTTTAGTAAATGACT 57.517 33.333 0.00 0.00 38.03 3.41
4908 5101 8.515414 AGTTTTAGTAAATGACTGAGATTTGCC 58.485 33.333 0.00 0.00 39.39 4.52
4909 5102 8.515414 GTTTTAGTAAATGACTGAGATTTGCCT 58.485 33.333 0.00 0.00 39.39 4.75
4910 5103 8.635765 TTTAGTAAATGACTGAGATTTGCCTT 57.364 30.769 0.00 0.00 39.39 4.35
4911 5104 6.506500 AGTAAATGACTGAGATTTGCCTTG 57.493 37.500 0.00 0.00 36.87 3.61
4912 5105 3.863142 AATGACTGAGATTTGCCTTGC 57.137 42.857 0.00 0.00 0.00 4.01
4913 5106 1.159285 TGACTGAGATTTGCCTTGCG 58.841 50.000 0.00 0.00 0.00 4.85
4914 5107 0.179179 GACTGAGATTTGCCTTGCGC 60.179 55.000 0.00 0.00 38.31 6.09
4964 5157 5.858381 TCAGAATAGAACAGCTGTTGAAGT 58.142 37.500 35.67 21.58 38.56 3.01
4965 5158 6.993079 TCAGAATAGAACAGCTGTTGAAGTA 58.007 36.000 35.67 20.24 38.56 2.24
4966 5159 7.093354 TCAGAATAGAACAGCTGTTGAAGTAG 58.907 38.462 35.67 18.68 38.56 2.57
5046 5242 1.838112 TCAGCGCATTGAATCCCTTT 58.162 45.000 11.47 0.00 0.00 3.11
5156 5355 5.165676 GGTCGTATTGTTCTGTACATGTCA 58.834 41.667 0.00 0.00 36.44 3.58
5162 5361 4.521130 TGTTCTGTACATGTCAGAGTCC 57.479 45.455 20.08 15.05 41.87 3.85
5166 5365 3.010420 CTGTACATGTCAGAGTCCGAGA 58.990 50.000 15.93 0.00 35.20 4.04
5241 5440 2.218953 CATCATGTGATGCAAAGGCC 57.781 50.000 9.81 0.00 44.44 5.19
5250 5449 0.755327 ATGCAAAGGCCGGGGTAATC 60.755 55.000 2.18 0.00 40.13 1.75
5253 5452 3.709348 AAAGGCCGGGGTAATCGCC 62.709 63.158 2.18 0.00 42.32 5.54
5259 5458 1.433837 CCGGGGTAATCGCCTTTTCG 61.434 60.000 0.00 0.00 43.37 3.46
5352 5561 6.128553 GCAGTCGAACAAACTCTCATAAATGA 60.129 38.462 0.00 0.00 35.16 2.57
5355 5564 5.924254 TCGAACAAACTCTCATAAATGACGT 59.076 36.000 0.00 0.00 32.50 4.34
5456 5717 7.859891 GAAAATGTCAACAAAAACATGTTCG 57.140 32.000 12.39 6.32 41.44 3.95
5516 5777 9.669887 AAATGGCATATGTTGTGATGTAAAAAT 57.330 25.926 0.00 0.00 0.00 1.82
5578 5871 8.902806 ACATATGTTGTTTTGTCAGAGAGAAAA 58.097 29.630 1.41 0.00 33.74 2.29
5579 5872 9.734620 CATATGTTGTTTTGTCAGAGAGAAAAA 57.265 29.630 4.00 0.00 36.75 1.94
5676 5970 1.741528 CACATAGGAGCATGTGCACA 58.258 50.000 24.08 24.08 46.66 4.57
5678 5972 3.469739 CACATAGGAGCATGTGCACATA 58.530 45.455 30.92 15.70 46.66 2.29
5680 5974 2.916702 TAGGAGCATGTGCACATAGG 57.083 50.000 30.92 20.69 45.16 2.57
5681 5975 1.206878 AGGAGCATGTGCACATAGGA 58.793 50.000 30.92 3.82 45.16 2.94
5682 5976 1.140452 AGGAGCATGTGCACATAGGAG 59.860 52.381 30.92 19.63 45.16 3.69
5683 5977 0.942962 GAGCATGTGCACATAGGAGC 59.057 55.000 30.92 27.41 45.16 4.70
5728 6027 8.883954 TCAATTATTGAAAACTGTTGCATTGA 57.116 26.923 5.03 1.02 36.59 2.57
5729 6028 9.491675 TCAATTATTGAAAACTGTTGCATTGAT 57.508 25.926 5.03 0.00 36.59 2.57
5730 6029 9.749490 CAATTATTGAAAACTGTTGCATTGATC 57.251 29.630 0.00 0.00 0.00 2.92
5731 6030 7.887996 TTATTGAAAACTGTTGCATTGATCC 57.112 32.000 0.00 0.00 0.00 3.36
5732 6031 4.933505 TGAAAACTGTTGCATTGATCCA 57.066 36.364 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 3.260884 TCTCAGCCGAGTAAAAGACCAAT 59.739 43.478 0.00 0.00 40.44 3.16
96 97 1.147153 GCTACTGGAGTGCCCATCC 59.853 63.158 0.00 0.00 45.57 3.51
242 248 4.486503 CCCTGCTCTGCTCTGGCC 62.487 72.222 0.00 0.00 37.74 5.36
424 443 3.768922 GAGGCGAGGACTGCTGCT 61.769 66.667 0.00 0.00 0.00 4.24
460 479 6.045955 TCTCCATTTAACCAGTTTTGTTTGC 58.954 36.000 0.00 0.00 0.00 3.68
558 577 2.522436 TCCGAGTGTGGGGAACGT 60.522 61.111 0.00 0.00 0.00 3.99
559 578 2.261671 CTCCGAGTGTGGGGAACG 59.738 66.667 0.00 0.00 0.00 3.95
561 580 3.319198 GCCTCCGAGTGTGGGGAA 61.319 66.667 0.00 0.00 0.00 3.97
564 583 3.064987 CTACGCCTCCGAGTGTGGG 62.065 68.421 0.00 0.00 38.29 4.61
565 584 2.490217 CTACGCCTCCGAGTGTGG 59.510 66.667 0.00 0.00 38.29 4.17
566 585 2.202623 GCTACGCCTCCGAGTGTG 60.203 66.667 0.00 0.00 38.29 3.82
567 586 3.450115 GGCTACGCCTCCGAGTGT 61.450 66.667 0.00 0.00 46.69 3.55
578 597 4.941325 TCTAATAGTATCTGCGGCTACG 57.059 45.455 0.00 0.00 44.63 3.51
579 598 6.372103 TCTCTTCTAATAGTATCTGCGGCTAC 59.628 42.308 0.00 0.00 0.00 3.58
580 599 6.473758 TCTCTTCTAATAGTATCTGCGGCTA 58.526 40.000 0.00 0.00 0.00 3.93
581 600 5.317808 TCTCTTCTAATAGTATCTGCGGCT 58.682 41.667 0.00 0.00 0.00 5.52
582 601 5.630661 TCTCTTCTAATAGTATCTGCGGC 57.369 43.478 0.00 0.00 0.00 6.53
583 602 6.092944 ACGATCTCTTCTAATAGTATCTGCGG 59.907 42.308 0.00 0.00 0.00 5.69
584 603 7.064134 AGACGATCTCTTCTAATAGTATCTGCG 59.936 40.741 0.00 0.00 0.00 5.18
585 604 8.263940 AGACGATCTCTTCTAATAGTATCTGC 57.736 38.462 0.00 0.00 0.00 4.26
590 609 9.926158 AACGATAGACGATCTCTTCTAATAGTA 57.074 33.333 0.00 0.00 45.77 1.82
591 610 8.714179 CAACGATAGACGATCTCTTCTAATAGT 58.286 37.037 0.00 0.00 45.77 2.12
592 611 8.714179 ACAACGATAGACGATCTCTTCTAATAG 58.286 37.037 0.00 0.00 45.77 1.73
593 612 8.604640 ACAACGATAGACGATCTCTTCTAATA 57.395 34.615 0.00 0.00 45.77 0.98
594 613 7.499321 ACAACGATAGACGATCTCTTCTAAT 57.501 36.000 0.00 0.00 45.77 1.73
595 614 6.922247 ACAACGATAGACGATCTCTTCTAA 57.078 37.500 0.00 0.00 45.77 2.10
610 629 1.134340 GCACCCACCCATACAACGATA 60.134 52.381 0.00 0.00 0.00 2.92
611 630 0.393808 GCACCCACCCATACAACGAT 60.394 55.000 0.00 0.00 0.00 3.73
612 631 1.003112 GCACCCACCCATACAACGA 60.003 57.895 0.00 0.00 0.00 3.85
613 632 2.395360 CGCACCCACCCATACAACG 61.395 63.158 0.00 0.00 0.00 4.10
614 633 1.302993 ACGCACCCACCCATACAAC 60.303 57.895 0.00 0.00 0.00 3.32
615 634 1.302913 CACGCACCCACCCATACAA 60.303 57.895 0.00 0.00 0.00 2.41
616 635 2.349376 CACGCACCCACCCATACA 59.651 61.111 0.00 0.00 0.00 2.29
617 636 2.038269 CACACGCACCCACCCATAC 61.038 63.158 0.00 0.00 0.00 2.39
618 637 2.349376 CACACGCACCCACCCATA 59.651 61.111 0.00 0.00 0.00 2.74
619 638 4.659172 CCACACGCACCCACCCAT 62.659 66.667 0.00 0.00 0.00 4.00
626 645 3.670377 GAAAGGCCCACACGCACC 61.670 66.667 0.00 0.00 0.00 5.01
627 646 3.670377 GGAAAGGCCCACACGCAC 61.670 66.667 0.00 0.00 0.00 5.34
716 737 4.468615 GCACTCGCTCGACTCGCT 62.469 66.667 0.00 0.00 34.30 4.93
723 744 2.036556 AATTTGTTTGCACTCGCTCG 57.963 45.000 0.00 0.00 39.64 5.03
845 878 3.834231 GGGGTTGATGGGGAAATGATATG 59.166 47.826 0.00 0.00 0.00 1.78
871 904 0.456221 GATGATGACACCGACGGACT 59.544 55.000 23.38 4.05 0.00 3.85
900 933 1.496403 GCTTATAAGCGGCCGTGTCC 61.496 60.000 28.70 10.05 42.88 4.02
933 966 3.921677 TCACCACAGTCCTAAAACGATC 58.078 45.455 0.00 0.00 0.00 3.69
934 967 4.553330 ATCACCACAGTCCTAAAACGAT 57.447 40.909 0.00 0.00 0.00 3.73
935 968 4.062293 CAATCACCACAGTCCTAAAACGA 58.938 43.478 0.00 0.00 0.00 3.85
936 969 3.188460 CCAATCACCACAGTCCTAAAACG 59.812 47.826 0.00 0.00 0.00 3.60
937 970 3.057526 GCCAATCACCACAGTCCTAAAAC 60.058 47.826 0.00 0.00 0.00 2.43
938 971 3.153919 GCCAATCACCACAGTCCTAAAA 58.846 45.455 0.00 0.00 0.00 1.52
939 972 2.107378 TGCCAATCACCACAGTCCTAAA 59.893 45.455 0.00 0.00 0.00 1.85
941 974 1.278985 CTGCCAATCACCACAGTCCTA 59.721 52.381 0.00 0.00 0.00 2.94
942 975 0.037303 CTGCCAATCACCACAGTCCT 59.963 55.000 0.00 0.00 0.00 3.85
943 976 0.250901 ACTGCCAATCACCACAGTCC 60.251 55.000 0.00 0.00 39.04 3.85
944 977 1.267806 CAACTGCCAATCACCACAGTC 59.732 52.381 0.00 0.00 42.34 3.51
945 978 1.321474 CAACTGCCAATCACCACAGT 58.679 50.000 0.00 0.00 44.96 3.55
1005 1045 1.531365 CAGCTTGGACCCCTTGCAA 60.531 57.895 0.00 0.00 33.86 4.08
1359 1402 4.308458 TGGAGTTGGTCGTGGCGG 62.308 66.667 0.00 0.00 0.00 6.13
1361 1404 2.668550 GGTGGAGTTGGTCGTGGC 60.669 66.667 0.00 0.00 0.00 5.01
1366 1409 2.032071 CGGGTGGTGGAGTTGGTC 59.968 66.667 0.00 0.00 0.00 4.02
1370 1413 4.265056 GGTGCGGGTGGTGGAGTT 62.265 66.667 0.00 0.00 0.00 3.01
1390 1433 2.126228 CGGGAACTGAAGCGCGTA 60.126 61.111 8.43 0.00 36.31 4.42
1422 1465 1.202313 GGCTCAGGCTCGTAACTGTAG 60.202 57.143 0.00 0.00 38.73 2.74
1426 1475 1.592223 GTGGCTCAGGCTCGTAACT 59.408 57.895 0.00 0.00 38.73 2.24
1428 1477 2.978824 GGTGGCTCAGGCTCGTAA 59.021 61.111 0.00 0.00 38.73 3.18
1698 1747 1.578583 AACAGTAGTTGTCGTGCACC 58.421 50.000 12.15 0.00 39.73 5.01
2004 2053 4.373116 TGAGTGCGAACGGAGGCC 62.373 66.667 0.00 0.00 0.00 5.19
2013 2062 1.532604 ATGACTTCCGGTGAGTGCGA 61.533 55.000 16.09 3.09 0.00 5.10
2016 2065 0.458543 CCGATGACTTCCGGTGAGTG 60.459 60.000 16.09 4.09 40.78 3.51
2085 2134 4.457496 ACCGCCCAGACTGCATCG 62.457 66.667 0.00 0.00 0.00 3.84
2105 2154 1.453379 TCGACCTCCAGGATCGGTC 60.453 63.158 15.40 15.40 42.90 4.79
2220 2269 5.163713 GCCAGTTCTAGAAGCAACAAATAGG 60.164 44.000 5.12 0.00 0.00 2.57
2449 2504 1.806542 CAACCTCCAACATCCAACTCG 59.193 52.381 0.00 0.00 0.00 4.18
2503 2558 1.428869 AGAGTTTCTGCAGGGTGACT 58.571 50.000 15.13 12.29 0.00 3.41
2685 2747 8.746530 CCAGTAGTATTTAGTAGGAGTCAAACA 58.253 37.037 0.00 0.00 0.00 2.83
2686 2748 8.747471 ACCAGTAGTATTTAGTAGGAGTCAAAC 58.253 37.037 0.00 0.00 0.00 2.93
2688 2750 8.111545 TCACCAGTAGTATTTAGTAGGAGTCAA 58.888 37.037 0.00 0.00 0.00 3.18
2689 2751 7.555554 GTCACCAGTAGTATTTAGTAGGAGTCA 59.444 40.741 0.00 0.00 0.00 3.41
2764 2826 5.944049 CACTATGAAAAGATGCATTGTGC 57.056 39.130 0.00 0.00 45.29 4.57
2765 2827 4.802039 GGCACTATGAAAAGATGCATTGTG 59.198 41.667 0.00 0.00 44.95 3.33
2766 2828 4.463539 TGGCACTATGAAAAGATGCATTGT 59.536 37.500 0.00 0.00 38.05 2.71
2767 2829 5.001237 TGGCACTATGAAAAGATGCATTG 57.999 39.130 0.00 0.00 38.05 2.82
2768 2830 5.128171 ACATGGCACTATGAAAAGATGCATT 59.872 36.000 0.00 0.00 38.05 3.56
2769 2831 4.647853 ACATGGCACTATGAAAAGATGCAT 59.352 37.500 0.00 0.00 38.05 3.96
2770 2832 4.018490 ACATGGCACTATGAAAAGATGCA 58.982 39.130 0.00 0.00 38.05 3.96
2771 2833 4.644103 ACATGGCACTATGAAAAGATGC 57.356 40.909 0.00 0.00 35.51 3.91
2776 2838 3.573598 CGCAAACATGGCACTATGAAAA 58.426 40.909 0.00 0.00 0.00 2.29
2810 2872 7.284944 GGATCAACATTTCATCTTTCTGGAGAT 59.715 37.037 0.00 0.00 36.84 2.75
2811 2873 6.600822 GGATCAACATTTCATCTTTCTGGAGA 59.399 38.462 0.00 0.00 0.00 3.71
2812 2874 6.602406 AGGATCAACATTTCATCTTTCTGGAG 59.398 38.462 0.00 0.00 0.00 3.86
2814 2876 6.770746 AGGATCAACATTTCATCTTTCTGG 57.229 37.500 0.00 0.00 0.00 3.86
2897 2983 9.530633 AAAGGAGCTTTTACACGATATTACTAG 57.469 33.333 0.00 0.00 28.27 2.57
2962 3048 8.325282 GGTTAAATTTCTTTAAATATGGCACGC 58.675 33.333 0.00 0.00 38.28 5.34
3137 3233 9.346725 GAGCCAACAAGATAGTTTAAATGAAAG 57.653 33.333 0.00 0.00 0.00 2.62
3153 3249 3.435671 CCGTTTACTAAGGAGCCAACAAG 59.564 47.826 0.00 0.00 0.00 3.16
3214 3310 3.440173 AGCACGTCCCACATTATTGAAAG 59.560 43.478 0.00 0.00 0.00 2.62
3271 3367 0.609662 ATAGTTAACACGGGTGCGGT 59.390 50.000 8.61 0.00 0.00 5.68
3272 3368 1.395608 CAATAGTTAACACGGGTGCGG 59.604 52.381 8.61 0.00 0.00 5.69
3273 3369 2.070783 ACAATAGTTAACACGGGTGCG 58.929 47.619 8.61 0.00 0.00 5.34
3274 3370 2.413634 GCACAATAGTTAACACGGGTGC 60.414 50.000 21.29 21.29 42.73 5.01
3290 3386 9.624697 GAACAAAAATAATCAGATGTAGCACAA 57.375 29.630 0.00 0.00 0.00 3.33
3318 3414 4.682563 TCTTCAGACTGGAAGAGGAGAAT 58.317 43.478 1.81 0.00 46.16 2.40
3601 3697 2.560105 AGTGTACCGACAGGGAACTAAC 59.440 50.000 0.00 0.00 43.47 2.34
3629 3725 2.172717 AGCAGACAACCAGTGTAAAGGT 59.827 45.455 0.00 0.00 41.96 3.50
3677 3776 4.313020 TCTTTACGGAGGGAGTACTTCT 57.687 45.455 0.01 0.06 0.00 2.85
3694 3793 9.884465 GTGATCTAAATGCGCTTATATTTCTTT 57.116 29.630 9.73 0.00 0.00 2.52
3695 3794 8.223769 CGTGATCTAAATGCGCTTATATTTCTT 58.776 33.333 9.73 0.00 0.00 2.52
3696 3795 7.598869 TCGTGATCTAAATGCGCTTATATTTCT 59.401 33.333 9.73 0.00 0.00 2.52
3697 3796 7.729836 TCGTGATCTAAATGCGCTTATATTTC 58.270 34.615 9.73 0.00 0.00 2.17
3698 3797 7.385205 ACTCGTGATCTAAATGCGCTTATATTT 59.615 33.333 9.73 8.84 0.00 1.40
3700 3799 6.390721 ACTCGTGATCTAAATGCGCTTATAT 58.609 36.000 9.73 0.00 0.00 0.86
3702 3801 4.621991 ACTCGTGATCTAAATGCGCTTAT 58.378 39.130 9.73 0.00 0.00 1.73
3704 3803 2.893637 ACTCGTGATCTAAATGCGCTT 58.106 42.857 9.73 0.00 0.00 4.68
3705 3804 2.586258 ACTCGTGATCTAAATGCGCT 57.414 45.000 9.73 0.00 0.00 5.92
3707 3806 5.890110 ATGTTACTCGTGATCTAAATGCG 57.110 39.130 0.00 0.00 0.00 4.73
3708 3807 7.222805 TGAGAATGTTACTCGTGATCTAAATGC 59.777 37.037 0.00 0.00 37.22 3.56
3709 3808 8.634475 TGAGAATGTTACTCGTGATCTAAATG 57.366 34.615 0.00 0.00 37.22 2.32
3710 3809 8.470805 ACTGAGAATGTTACTCGTGATCTAAAT 58.529 33.333 0.00 0.00 37.22 1.40
3711 3810 7.827701 ACTGAGAATGTTACTCGTGATCTAAA 58.172 34.615 0.00 0.00 37.22 1.85
3712 3811 7.392494 ACTGAGAATGTTACTCGTGATCTAA 57.608 36.000 0.00 0.00 37.22 2.10
3713 3812 6.038382 GGACTGAGAATGTTACTCGTGATCTA 59.962 42.308 0.00 0.00 37.22 1.98
3714 3813 5.163602 GGACTGAGAATGTTACTCGTGATCT 60.164 44.000 0.00 0.00 37.22 2.75
3715 3814 5.038033 GGACTGAGAATGTTACTCGTGATC 58.962 45.833 0.00 0.00 37.22 2.92
3716 3815 4.462834 TGGACTGAGAATGTTACTCGTGAT 59.537 41.667 0.00 0.00 37.22 3.06
3717 3816 3.824443 TGGACTGAGAATGTTACTCGTGA 59.176 43.478 0.00 0.00 37.22 4.35
3718 3817 4.169508 CTGGACTGAGAATGTTACTCGTG 58.830 47.826 0.00 0.00 37.22 4.35
3719 3818 3.827302 ACTGGACTGAGAATGTTACTCGT 59.173 43.478 0.00 0.00 37.22 4.18
3720 3819 4.442375 ACTGGACTGAGAATGTTACTCG 57.558 45.455 0.00 0.00 37.22 4.18
3760 3859 2.845363 AAAAATTTCCAGGCAGCTGG 57.155 45.000 17.12 2.74 45.53 4.85
3801 3900 1.195115 CAGGGCTGTAGAGTTAGGCA 58.805 55.000 0.00 0.00 40.87 4.75
3802 3901 0.179070 GCAGGGCTGTAGAGTTAGGC 60.179 60.000 0.00 0.00 38.62 3.93
3803 3902 1.195115 TGCAGGGCTGTAGAGTTAGG 58.805 55.000 0.00 0.00 0.00 2.69
3804 3903 3.550437 AATGCAGGGCTGTAGAGTTAG 57.450 47.619 0.00 0.00 0.00 2.34
3805 3904 4.224147 TGTAAATGCAGGGCTGTAGAGTTA 59.776 41.667 0.00 0.00 0.00 2.24
3806 3905 2.887151 AAATGCAGGGCTGTAGAGTT 57.113 45.000 0.00 0.00 0.00 3.01
3807 3906 2.571653 TGTAAATGCAGGGCTGTAGAGT 59.428 45.455 0.00 0.00 0.00 3.24
3808 3907 3.201290 CTGTAAATGCAGGGCTGTAGAG 58.799 50.000 0.00 0.00 33.11 2.43
3862 3972 5.812642 GCATGTAGGGATATTGATTACTCGG 59.187 44.000 0.00 0.00 0.00 4.63
3887 3997 5.370289 TCAGGAAAGTTCACCTAGGGTAAAA 59.630 40.000 14.81 0.00 32.11 1.52
3917 4027 4.860072 AGATTGCAAAGAAAGAAACCGAC 58.140 39.130 1.71 0.00 0.00 4.79
4114 4225 2.746362 CAAGTCCACTTCAAGCTCCATC 59.254 50.000 0.00 0.00 33.11 3.51
4219 4330 3.053320 TCTCCTCCTGCTGATAGTTGAGA 60.053 47.826 0.00 0.00 0.00 3.27
4372 4483 1.372499 GTTGCGTACGCTGGAGACA 60.372 57.895 36.99 15.67 42.51 3.41
4375 4486 2.048597 TGGTTGCGTACGCTGGAG 60.049 61.111 36.99 0.00 42.51 3.86
4409 4520 0.250038 AGCTCGCTTTGCTCAACAGA 60.250 50.000 0.00 0.00 35.67 3.41
4411 4522 0.532640 TCAGCTCGCTTTGCTCAACA 60.533 50.000 0.00 0.00 38.92 3.33
4419 4530 2.924290 GTTACGAAGATCAGCTCGCTTT 59.076 45.455 10.65 0.00 0.00 3.51
4438 4549 2.583143 CACTTTTCTCTTTCCCGGGTT 58.417 47.619 22.86 0.00 0.00 4.11
4453 4564 3.652869 TCTCCAGAATCCTGTTCCACTTT 59.347 43.478 0.00 0.00 38.74 2.66
4518 4629 2.282745 GCACAAGGGCCAGCTTCT 60.283 61.111 6.18 0.00 0.00 2.85
4678 4789 1.205655 TCTTCTTCGGCATGTCTCAGG 59.794 52.381 0.00 0.00 0.00 3.86
4690 4801 3.329386 TCTGGACAGCATTTCTTCTTCG 58.671 45.455 0.00 0.00 0.00 3.79
4725 4836 3.953612 AGATGCAAAATCGGGCTATGAAA 59.046 39.130 0.00 0.00 0.00 2.69
4735 4846 3.434641 AGTGTCTGTCAGATGCAAAATCG 59.565 43.478 5.68 0.00 0.00 3.34
4751 4862 3.838244 TGTTTGTTGGCTCTAGTGTCT 57.162 42.857 0.00 0.00 0.00 3.41
4752 4863 4.789802 GCTTTGTTTGTTGGCTCTAGTGTC 60.790 45.833 0.00 0.00 0.00 3.67
4753 4864 3.066760 GCTTTGTTTGTTGGCTCTAGTGT 59.933 43.478 0.00 0.00 0.00 3.55
4754 4865 3.316308 AGCTTTGTTTGTTGGCTCTAGTG 59.684 43.478 0.00 0.00 0.00 2.74
4847 5040 9.147732 AGAATTTCTCCACCAAAACTAAAATCT 57.852 29.630 0.00 0.00 0.00 2.40
4892 5085 2.163010 CGCAAGGCAAATCTCAGTCATT 59.837 45.455 0.00 0.00 0.00 2.57
4893 5086 1.741706 CGCAAGGCAAATCTCAGTCAT 59.258 47.619 0.00 0.00 0.00 3.06
4894 5087 1.159285 CGCAAGGCAAATCTCAGTCA 58.841 50.000 0.00 0.00 0.00 3.41
4908 5101 2.716828 CCTACACGACGTGCGCAAG 61.717 63.158 27.11 21.97 46.04 4.01
4909 5102 2.731721 CCTACACGACGTGCGCAA 60.732 61.111 27.11 9.93 46.04 4.85
4913 5106 2.664436 GGTTGCCTACACGACGTGC 61.664 63.158 27.11 14.13 36.98 5.34
4914 5107 2.025418 GGGTTGCCTACACGACGTG 61.025 63.158 25.72 25.72 39.75 4.49
4915 5108 1.751349 AAGGGTTGCCTACACGACGT 61.751 55.000 0.00 0.00 34.43 4.34
4916 5109 1.005394 AAGGGTTGCCTACACGACG 60.005 57.895 0.00 0.00 34.43 5.12
4917 5110 0.953960 CCAAGGGTTGCCTACACGAC 60.954 60.000 0.00 0.00 34.43 4.34
4919 5112 0.953960 GACCAAGGGTTGCCTACACG 60.954 60.000 0.00 0.00 35.25 4.49
4920 5113 0.608308 GGACCAAGGGTTGCCTACAC 60.608 60.000 0.00 0.00 35.25 2.90
4921 5114 1.063070 TGGACCAAGGGTTGCCTACA 61.063 55.000 0.00 0.00 35.25 2.74
4922 5115 0.331616 ATGGACCAAGGGTTGCCTAC 59.668 55.000 0.00 0.00 35.25 3.18
4923 5116 0.623723 GATGGACCAAGGGTTGCCTA 59.376 55.000 0.00 0.00 35.25 3.93
4964 5157 4.286032 CCTGCCCATATTTACCTGCTACTA 59.714 45.833 0.00 0.00 0.00 1.82
4965 5158 3.073062 CCTGCCCATATTTACCTGCTACT 59.927 47.826 0.00 0.00 0.00 2.57
4966 5159 3.181443 ACCTGCCCATATTTACCTGCTAC 60.181 47.826 0.00 0.00 0.00 3.58
5008 5204 4.036027 GCTGAATATTGCACAGTACATGCT 59.964 41.667 19.31 6.45 43.77 3.79
5156 5355 5.419155 TCAACATAATTCACTCTCGGACTCT 59.581 40.000 0.00 0.00 0.00 3.24
5162 5361 8.229811 TGACAATTTCAACATAATTCACTCTCG 58.770 33.333 0.00 0.00 0.00 4.04
5236 5435 4.185286 GGCGATTACCCCGGCCTT 62.185 66.667 0.00 0.00 45.18 4.35
5240 5439 1.433837 CGAAAAGGCGATTACCCCGG 61.434 60.000 0.00 0.00 0.00 5.73
5241 5440 0.741927 ACGAAAAGGCGATTACCCCG 60.742 55.000 0.00 0.00 34.83 5.73
5315 5523 1.990799 TCGACTGCAACATCTAACCG 58.009 50.000 0.00 0.00 0.00 4.44
5352 5561 3.096852 TGAATACCTGATCTGGTGACGT 58.903 45.455 29.04 14.13 41.05 4.34
5355 5564 5.875224 TGTTTTGAATACCTGATCTGGTGA 58.125 37.500 29.04 15.94 41.05 4.02
5431 5690 7.330700 ACGAACATGTTTTTGTTGACATTTTCT 59.669 29.630 13.36 0.00 39.24 2.52
5432 5691 7.422179 CACGAACATGTTTTTGTTGACATTTTC 59.578 33.333 13.36 5.67 39.85 2.29
5456 5717 6.491394 ACATAACACACATGTACAAACACAC 58.509 36.000 0.00 0.00 38.45 3.82
5579 5872 9.353999 GTTTGTGTCTTCTAAATGTGAGTTTTT 57.646 29.630 0.00 0.00 0.00 1.94
5580 5873 8.519526 TGTTTGTGTCTTCTAAATGTGAGTTTT 58.480 29.630 0.00 0.00 0.00 2.43
5676 5970 3.893326 GGGCAATGTTTTTGCTCCTAT 57.107 42.857 9.86 0.00 44.36 2.57
5680 5974 3.231734 GGGGGCAATGTTTTTGCTC 57.768 52.632 9.86 5.99 44.82 4.26
5707 6006 7.440198 TGGATCAATGCAACAGTTTTCAATAA 58.560 30.769 0.00 0.00 0.00 1.40



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

AutoCloner maintained by Alex Coulton.