Multiple sequence alignment - TraesCS2B01G532100

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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 TraesCS2B01G532100 chr2B 100.000 2771 0 0 1 2771 727682437 727679667 0.000000e+00 5118.0
1 TraesCS2B01G532100 chr2B 88.563 1399 124 18 1138 2502 727654361 727652965 0.000000e+00 1664.0
2 TraesCS2B01G532100 chr2B 100.000 511 0 0 3062 3572 727679376 727678866 0.000000e+00 944.0
3 TraesCS2B01G532100 chr2B 78.769 650 111 12 1138 1761 763805186 763805834 9.230000e-111 411.0
4 TraesCS2B01G532100 chr2B 73.646 554 118 20 1745 2287 641075301 641074765 4.710000e-44 189.0
5 TraesCS2B01G532100 chr2B 75.000 328 49 19 761 1056 727654732 727654406 1.740000e-23 121.0
6 TraesCS2B01G532100 chr2A 93.037 1666 96 8 933 2590 733041266 733039613 0.000000e+00 2416.0
7 TraesCS2B01G532100 chr2A 88.020 1394 126 21 1138 2502 733029688 733028307 0.000000e+00 1611.0
8 TraesCS2B01G532100 chr2A 83.852 514 71 8 3062 3572 733038214 733037710 2.490000e-131 479.0
9 TraesCS2B01G532100 chr2A 80.310 645 67 28 62 666 733042224 733041600 1.970000e-117 433.0
10 TraesCS2B01G532100 chr2A 74.150 588 122 26 1741 2316 680501729 680501160 2.160000e-52 217.0
11 TraesCS2B01G532100 chr2A 87.407 135 12 4 757 888 733041594 733041462 2.220000e-32 150.0
12 TraesCS2B01G532100 chr2D 93.274 1576 97 3 933 2504 598803469 598801899 0.000000e+00 2314.0
13 TraesCS2B01G532100 chr2D 88.481 1415 128 18 1110 2502 598746963 598745562 0.000000e+00 1677.0
14 TraesCS2B01G532100 chr2D 87.987 616 49 15 58 666 598804351 598803754 0.000000e+00 704.0
15 TraesCS2B01G532100 chr2D 88.347 369 42 1 3204 3572 598800179 598799812 3.270000e-120 442.0
16 TraesCS2B01G532100 chr2D 87.903 124 12 3 757 878 598803748 598803626 3.720000e-30 143.0
17 TraesCS2B01G532100 chr2D 88.660 97 11 0 3062 3158 598800283 598800187 6.260000e-23 119.0
18 TraesCS2B01G532100 chr2D 85.981 107 13 2 772 877 598747304 598747199 2.910000e-21 113.0
19 TraesCS2B01G532100 chr2D 100.000 30 0 0 669 698 409263134 409263163 4.980000e-04 56.5
20 TraesCS2B01G532100 chr6A 73.983 688 135 31 1375 2049 565108758 565109414 4.610000e-59 239.0
21 TraesCS2B01G532100 chr6A 73.837 688 136 31 1375 2049 565057707 565058363 2.140000e-57 233.0
22 TraesCS2B01G532100 chr6A 100.000 30 0 0 669 698 121650364 121650335 4.980000e-04 56.5
23 TraesCS2B01G532100 chr4D 77.917 240 47 6 3117 3353 403294993 403294757 1.030000e-30 145.0
24 TraesCS2B01G532100 chr4D 94.444 36 2 0 669 704 99185823 99185788 4.980000e-04 56.5
25 TraesCS2B01G532100 chr3D 75.781 256 55 7 3071 3323 92378509 92378760 4.840000e-24 122.0
26 TraesCS2B01G532100 chr3A 84.043 94 4 5 669 762 564342470 564342552 2.960000e-11 80.5
27 TraesCS2B01G532100 chr5D 91.304 46 2 2 1987 2031 323866808 323866852 1.070000e-05 62.1
28 TraesCS2B01G532100 chrUn 89.362 47 4 1 2005 2051 122077656 122077701 1.390000e-04 58.4
29 TraesCS2B01G532100 chr6D 94.737 38 0 2 668 705 29874346 29874311 1.390000e-04 58.4
30 TraesCS2B01G532100 chr6D 94.737 38 0 2 669 706 400060114 400060149 1.390000e-04 58.4
31 TraesCS2B01G532100 chr3B 94.737 38 0 2 669 706 787272600 787272635 1.390000e-04 58.4
32 TraesCS2B01G532100 chr7D 100.000 30 0 0 669 698 254156792 254156763 4.980000e-04 56.5
33 TraesCS2B01G532100 chr1A 94.595 37 1 1 669 705 104438591 104438556 4.980000e-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 TraesCS2B01G532100 chr2B 727678866 727682437 3571 True 3031.0 5118 100.0000 1 3572 2 chr2B.!!$R3 3571
1 TraesCS2B01G532100 chr2B 727652965 727654732 1767 True 892.5 1664 81.7815 761 2502 2 chr2B.!!$R2 1741
2 TraesCS2B01G532100 chr2B 763805186 763805834 648 False 411.0 411 78.7690 1138 1761 1 chr2B.!!$F1 623
3 TraesCS2B01G532100 chr2A 733028307 733029688 1381 True 1611.0 1611 88.0200 1138 2502 1 chr2A.!!$R2 1364
4 TraesCS2B01G532100 chr2A 733037710 733042224 4514 True 869.5 2416 86.1515 62 3572 4 chr2A.!!$R3 3510
5 TraesCS2B01G532100 chr2A 680501160 680501729 569 True 217.0 217 74.1500 1741 2316 1 chr2A.!!$R1 575
6 TraesCS2B01G532100 chr2D 598745562 598747304 1742 True 895.0 1677 87.2310 772 2502 2 chr2D.!!$R1 1730
7 TraesCS2B01G532100 chr2D 598799812 598804351 4539 True 744.4 2314 89.2342 58 3572 5 chr2D.!!$R2 3514
8 TraesCS2B01G532100 chr6A 565108758 565109414 656 False 239.0 239 73.9830 1375 2049 1 chr6A.!!$F2 674
9 TraesCS2B01G532100 chr6A 565057707 565058363 656 False 233.0 233 73.8370 1375 2049 1 chr6A.!!$F1 674

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
889 1029 0.539051 ACCTGTCAGTAGCCAGCATC 59.461 55.0 0.0 0.0 0.00 3.91 F
1243 1482 0.739813 CCGCCGTTCGAGGAAGAAAT 60.740 55.0 0.0 0.0 41.67 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2508 2804 0.442310 CACGCGTGACTACAAATGGG 59.558 55.0 34.93 0.93 0.00 4.00 R
3236 5277 0.320697 ACGCCAAAGGGTCTGACTAC 59.679 55.0 7.85 1.52 32.94 2.73 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
29 30 3.419828 CGACAAGCACAGGCACAA 58.580 55.556 0.00 0.00 44.61 3.33
30 31 1.009675 CGACAAGCACAGGCACAAC 60.010 57.895 0.00 0.00 44.61 3.32
31 32 1.360192 GACAAGCACAGGCACAACC 59.640 57.895 0.00 0.00 44.61 3.77
32 33 1.379710 ACAAGCACAGGCACAACCA 60.380 52.632 0.00 0.00 44.61 3.67
33 34 1.066257 CAAGCACAGGCACAACCAC 59.934 57.895 0.00 0.00 44.61 4.16
34 35 2.480610 AAGCACAGGCACAACCACG 61.481 57.895 0.00 0.00 44.61 4.94
35 36 4.629115 GCACAGGCACAACCACGC 62.629 66.667 0.00 0.00 43.14 5.34
36 37 3.208383 CACAGGCACAACCACGCA 61.208 61.111 0.00 0.00 43.14 5.24
37 38 2.901840 ACAGGCACAACCACGCAG 60.902 61.111 0.00 0.00 43.14 5.18
39 40 1.596752 CAGGCACAACCACGCAGTA 60.597 57.895 0.00 0.00 41.61 2.74
40 41 1.301716 AGGCACAACCACGCAGTAG 60.302 57.895 0.00 0.00 41.61 2.57
41 42 2.556287 GCACAACCACGCAGTAGC 59.444 61.111 0.00 0.00 41.61 3.58
42 43 2.250939 GCACAACCACGCAGTAGCA 61.251 57.895 0.00 0.00 41.61 3.49
43 44 1.862123 CACAACCACGCAGTAGCAG 59.138 57.895 0.00 0.00 41.61 4.24
44 45 1.961277 ACAACCACGCAGTAGCAGC 60.961 57.895 0.00 0.00 41.61 5.25
45 46 1.960763 CAACCACGCAGTAGCAGCA 60.961 57.895 0.00 0.00 41.61 4.41
46 47 1.669115 AACCACGCAGTAGCAGCAG 60.669 57.895 0.00 0.00 41.61 4.24
47 48 3.494336 CCACGCAGTAGCAGCAGC 61.494 66.667 0.00 0.00 41.61 5.25
48 49 2.739671 CACGCAGTAGCAGCAGCA 60.740 61.111 3.17 0.00 41.61 4.41
49 50 2.433838 ACGCAGTAGCAGCAGCAG 60.434 61.111 3.17 0.00 41.94 4.24
50 51 3.862402 CGCAGTAGCAGCAGCAGC 61.862 66.667 3.17 0.46 45.49 5.25
51 52 2.745100 GCAGTAGCAGCAGCAGCA 60.745 61.111 12.92 0.00 45.49 4.41
52 53 2.751913 GCAGTAGCAGCAGCAGCAG 61.752 63.158 12.92 0.00 45.49 4.24
81 82 2.440430 CTCCTTCCTCCTCCGCGA 60.440 66.667 8.23 0.00 0.00 5.87
167 191 0.926155 CAGACATTCAGACCGATGCG 59.074 55.000 0.00 0.00 0.00 4.73
230 254 5.083533 AGAAGATCAGGCAGAAAGTAGTG 57.916 43.478 0.00 0.00 0.00 2.74
299 323 1.586154 ATCTTGCAGTTTTCCCGCCG 61.586 55.000 0.00 0.00 0.00 6.46
325 352 2.292267 ACTGCTTGTGTTCCTGTTCTG 58.708 47.619 0.00 0.00 0.00 3.02
353 394 0.890542 TGAATTTGCAGCCGCTCAGT 60.891 50.000 0.00 0.00 39.64 3.41
388 429 0.580104 CGTCCGCTTCAGTCGTTTTT 59.420 50.000 0.00 0.00 0.00 1.94
434 476 3.070018 CTCTGAGTTTGAAACTGCGGAT 58.930 45.455 16.25 0.00 43.03 4.18
444 486 3.303189 CTGCGGATCAGGGTCACT 58.697 61.111 0.00 0.00 39.15 3.41
467 511 1.817357 TCGCGTCTGAGAGTCCTTTA 58.183 50.000 5.77 0.00 0.00 1.85
477 521 4.017126 TGAGAGTCCTTTAGAATCGAGCA 58.983 43.478 0.00 0.00 44.40 4.26
478 522 4.462834 TGAGAGTCCTTTAGAATCGAGCAA 59.537 41.667 0.00 0.00 44.40 3.91
479 523 5.127845 TGAGAGTCCTTTAGAATCGAGCAAT 59.872 40.000 0.00 0.00 44.40 3.56
481 525 5.814705 AGAGTCCTTTAGAATCGAGCAATTG 59.185 40.000 0.00 0.00 44.40 2.32
482 526 5.734720 AGTCCTTTAGAATCGAGCAATTGA 58.265 37.500 10.34 0.00 0.00 2.57
483 527 6.352516 AGTCCTTTAGAATCGAGCAATTGAT 58.647 36.000 10.34 1.34 0.00 2.57
484 528 6.259608 AGTCCTTTAGAATCGAGCAATTGATG 59.740 38.462 10.34 0.00 0.00 3.07
485 529 5.528690 TCCTTTAGAATCGAGCAATTGATGG 59.471 40.000 10.34 4.13 0.00 3.51
486 530 5.528690 CCTTTAGAATCGAGCAATTGATGGA 59.471 40.000 10.88 10.88 0.00 3.41
495 539 1.892329 GCAATTGATGGAGTGGGTGGT 60.892 52.381 10.34 0.00 0.00 4.16
519 563 7.416326 GGTGGTTTGATCAATTCAGGGTATTAC 60.416 40.741 9.40 0.00 35.27 1.89
525 569 7.106890 TGATCAATTCAGGGTATTACGTGAAA 58.893 34.615 0.00 0.00 45.01 2.69
526 570 6.978343 TCAATTCAGGGTATTACGTGAAAG 57.022 37.500 0.00 9.12 45.01 2.62
532 576 3.390311 AGGGTATTACGTGAAAGGGGATC 59.610 47.826 0.00 0.00 0.00 3.36
533 577 3.387397 GGTATTACGTGAAAGGGGATCG 58.613 50.000 0.00 0.00 0.00 3.69
537 581 0.909623 ACGTGAAAGGGGATCGGATT 59.090 50.000 0.00 0.00 0.00 3.01
608 669 1.065401 CGAGTCTGAGGCTGAGCTAAG 59.935 57.143 3.72 0.00 0.00 2.18
638 699 2.223711 GCCAAAATGTCAAACCGAGTGT 60.224 45.455 0.00 0.00 0.00 3.55
671 732 3.383620 CAATGGTTGGTTGCAGCTAAA 57.616 42.857 0.00 0.00 0.00 1.85
672 733 3.319755 CAATGGTTGGTTGCAGCTAAAG 58.680 45.455 0.00 0.00 0.00 1.85
673 734 2.356665 TGGTTGGTTGCAGCTAAAGA 57.643 45.000 0.00 0.00 0.00 2.52
674 735 2.660572 TGGTTGGTTGCAGCTAAAGAA 58.339 42.857 0.00 0.00 0.00 2.52
675 736 3.027412 TGGTTGGTTGCAGCTAAAGAAA 58.973 40.909 0.00 0.00 0.00 2.52
676 737 3.640967 TGGTTGGTTGCAGCTAAAGAAAT 59.359 39.130 0.00 0.00 0.00 2.17
677 738 4.830046 TGGTTGGTTGCAGCTAAAGAAATA 59.170 37.500 0.00 0.00 0.00 1.40
678 739 5.480073 TGGTTGGTTGCAGCTAAAGAAATAT 59.520 36.000 0.00 0.00 0.00 1.28
679 740 6.661377 TGGTTGGTTGCAGCTAAAGAAATATA 59.339 34.615 0.00 0.00 0.00 0.86
680 741 7.177568 TGGTTGGTTGCAGCTAAAGAAATATAA 59.822 33.333 0.00 0.00 0.00 0.98
681 742 7.702348 GGTTGGTTGCAGCTAAAGAAATATAAG 59.298 37.037 0.00 0.00 0.00 1.73
682 743 8.458843 GTTGGTTGCAGCTAAAGAAATATAAGA 58.541 33.333 0.00 0.00 0.00 2.10
683 744 8.213518 TGGTTGCAGCTAAAGAAATATAAGAG 57.786 34.615 0.00 0.00 0.00 2.85
684 745 7.135467 GGTTGCAGCTAAAGAAATATAAGAGC 58.865 38.462 0.00 0.00 0.00 4.09
685 746 6.530913 TGCAGCTAAAGAAATATAAGAGCG 57.469 37.500 0.00 0.00 33.69 5.03
686 747 6.049149 TGCAGCTAAAGAAATATAAGAGCGT 58.951 36.000 0.00 0.00 33.69 5.07
687 748 6.201044 TGCAGCTAAAGAAATATAAGAGCGTC 59.799 38.462 0.00 0.00 33.69 5.19
688 749 6.422400 GCAGCTAAAGAAATATAAGAGCGTCT 59.578 38.462 0.00 0.00 33.69 4.18
689 750 7.595502 GCAGCTAAAGAAATATAAGAGCGTCTA 59.404 37.037 0.00 0.00 33.69 2.59
690 751 9.123709 CAGCTAAAGAAATATAAGAGCGTCTAG 57.876 37.037 0.00 0.00 33.69 2.43
691 752 9.069082 AGCTAAAGAAATATAAGAGCGTCTAGA 57.931 33.333 0.00 0.00 33.69 2.43
692 753 9.849166 GCTAAAGAAATATAAGAGCGTCTAGAT 57.151 33.333 0.00 0.00 0.00 1.98
695 756 9.685828 AAAGAAATATAAGAGCGTCTAGATCAC 57.314 33.333 0.00 0.00 37.82 3.06
696 757 8.630054 AGAAATATAAGAGCGTCTAGATCACT 57.370 34.615 0.00 0.00 37.82 3.41
697 758 9.727859 AGAAATATAAGAGCGTCTAGATCACTA 57.272 33.333 0.00 0.00 37.82 2.74
698 759 9.982291 GAAATATAAGAGCGTCTAGATCACTAG 57.018 37.037 0.00 0.00 45.21 2.57
699 760 5.873179 ATAAGAGCGTCTAGATCACTAGC 57.127 43.478 0.00 0.00 43.97 3.42
700 761 3.201353 AGAGCGTCTAGATCACTAGCA 57.799 47.619 0.00 0.00 43.97 3.49
701 762 3.750371 AGAGCGTCTAGATCACTAGCAT 58.250 45.455 0.00 0.00 43.97 3.79
702 763 4.141287 AGAGCGTCTAGATCACTAGCATT 58.859 43.478 0.00 0.00 43.97 3.56
703 764 4.582656 AGAGCGTCTAGATCACTAGCATTT 59.417 41.667 0.00 0.00 43.97 2.32
704 765 5.765677 AGAGCGTCTAGATCACTAGCATTTA 59.234 40.000 0.00 0.00 43.97 1.40
705 766 6.007936 AGCGTCTAGATCACTAGCATTTAG 57.992 41.667 0.00 0.00 43.97 1.85
706 767 5.765677 AGCGTCTAGATCACTAGCATTTAGA 59.234 40.000 0.00 0.00 43.97 2.10
707 768 6.432783 AGCGTCTAGATCACTAGCATTTAGAT 59.567 38.462 0.00 0.00 43.97 1.98
708 769 7.040062 AGCGTCTAGATCACTAGCATTTAGATT 60.040 37.037 0.00 0.00 43.97 2.40
709 770 8.237949 GCGTCTAGATCACTAGCATTTAGATTA 58.762 37.037 0.00 0.00 43.97 1.75
710 771 9.549509 CGTCTAGATCACTAGCATTTAGATTAC 57.450 37.037 0.00 0.00 43.97 1.89
715 776 9.979578 AGATCACTAGCATTTAGATTACTGAAG 57.020 33.333 0.00 0.00 0.00 3.02
716 777 9.757227 GATCACTAGCATTTAGATTACTGAAGT 57.243 33.333 0.00 0.00 0.00 3.01
723 784 9.539825 AGCATTTAGATTACTGAAGTAGTGATG 57.460 33.333 0.00 0.00 40.65 3.07
724 785 9.319143 GCATTTAGATTACTGAAGTAGTGATGT 57.681 33.333 0.00 0.00 40.65 3.06
729 790 8.912787 AGATTACTGAAGTAGTGATGTAAACG 57.087 34.615 0.00 0.00 40.65 3.60
730 791 6.939551 TTACTGAAGTAGTGATGTAAACGC 57.060 37.500 0.00 0.00 40.65 4.84
731 792 5.135508 ACTGAAGTAGTGATGTAAACGCT 57.864 39.130 0.00 0.00 38.49 5.07
732 793 5.162075 ACTGAAGTAGTGATGTAAACGCTC 58.838 41.667 0.00 0.00 38.49 5.03
733 794 5.047943 ACTGAAGTAGTGATGTAAACGCTCT 60.048 40.000 0.00 0.00 38.49 4.09
734 795 5.779922 TGAAGTAGTGATGTAAACGCTCTT 58.220 37.500 0.00 0.00 29.98 2.85
735 796 6.916440 TGAAGTAGTGATGTAAACGCTCTTA 58.084 36.000 0.00 0.00 29.98 2.10
736 797 6.805271 TGAAGTAGTGATGTAAACGCTCTTAC 59.195 38.462 0.00 0.00 29.98 2.34
737 798 6.263516 AGTAGTGATGTAAACGCTCTTACA 57.736 37.500 9.20 9.20 43.89 2.41
738 799 6.091437 AGTAGTGATGTAAACGCTCTTACAC 58.909 40.000 9.02 0.00 42.88 2.90
739 800 5.135508 AGTGATGTAAACGCTCTTACACT 57.864 39.130 9.02 0.00 42.88 3.55
740 801 5.162075 AGTGATGTAAACGCTCTTACACTC 58.838 41.667 9.02 8.74 42.88 3.51
741 802 4.326548 GTGATGTAAACGCTCTTACACTCC 59.673 45.833 9.02 4.27 42.88 3.85
742 803 4.021807 TGATGTAAACGCTCTTACACTCCA 60.022 41.667 9.02 6.17 42.88 3.86
743 804 4.530710 TGTAAACGCTCTTACACTCCAT 57.469 40.909 3.99 0.00 36.97 3.41
744 805 4.890088 TGTAAACGCTCTTACACTCCATT 58.110 39.130 3.99 0.00 36.97 3.16
745 806 5.302360 TGTAAACGCTCTTACACTCCATTT 58.698 37.500 3.99 0.00 36.97 2.32
746 807 5.407387 TGTAAACGCTCTTACACTCCATTTC 59.593 40.000 3.99 0.00 36.97 2.17
747 808 3.963428 ACGCTCTTACACTCCATTTCT 57.037 42.857 0.00 0.00 0.00 2.52
748 809 4.273148 ACGCTCTTACACTCCATTTCTT 57.727 40.909 0.00 0.00 0.00 2.52
749 810 4.642429 ACGCTCTTACACTCCATTTCTTT 58.358 39.130 0.00 0.00 0.00 2.52
750 811 5.790593 ACGCTCTTACACTCCATTTCTTTA 58.209 37.500 0.00 0.00 0.00 1.85
751 812 5.638234 ACGCTCTTACACTCCATTTCTTTAC 59.362 40.000 0.00 0.00 0.00 2.01
752 813 5.220228 CGCTCTTACACTCCATTTCTTTACG 60.220 44.000 0.00 0.00 0.00 3.18
753 814 5.063564 GCTCTTACACTCCATTTCTTTACGG 59.936 44.000 0.00 0.00 0.00 4.02
754 815 6.349243 TCTTACACTCCATTTCTTTACGGA 57.651 37.500 0.00 0.00 0.00 4.69
770 831 2.320781 ACGGAGGGAGTATCAATCAGG 58.679 52.381 0.00 0.00 36.25 3.86
778 839 0.886490 GTATCAATCAGGGCCCTGCG 60.886 60.000 42.34 31.64 43.31 5.18
842 903 2.158534 ACCATTTACAGGTCCAAGCACA 60.159 45.455 0.00 0.00 32.90 4.57
844 905 1.975660 TTTACAGGTCCAAGCACACC 58.024 50.000 0.00 0.00 0.00 4.16
857 918 1.073763 AGCACACCCTACAGCAATCAA 59.926 47.619 0.00 0.00 0.00 2.57
889 1029 0.539051 ACCTGTCAGTAGCCAGCATC 59.461 55.000 0.00 0.00 0.00 3.91
894 1034 1.114627 TCAGTAGCCAGCATCATCGT 58.885 50.000 0.00 0.00 0.00 3.73
915 1055 2.540265 AACTCTCCACTGAGCTTGTG 57.460 50.000 12.18 12.18 38.58 3.33
924 1064 4.997395 TCCACTGAGCTTGTGAATTAGTTC 59.003 41.667 18.48 0.00 37.60 3.01
927 1067 5.121454 CACTGAGCTTGTGAATTAGTTCTCC 59.879 44.000 13.45 0.00 37.60 3.71
928 1068 4.579869 TGAGCTTGTGAATTAGTTCTCCC 58.420 43.478 0.00 0.00 35.33 4.30
929 1069 4.041567 TGAGCTTGTGAATTAGTTCTCCCA 59.958 41.667 0.00 0.00 35.33 4.37
930 1070 5.184892 AGCTTGTGAATTAGTTCTCCCAT 57.815 39.130 0.00 0.00 35.33 4.00
945 1171 1.171308 CCCATTGCTTGTCTGACCAG 58.829 55.000 5.17 4.87 0.00 4.00
1016 1250 2.512286 CATGTCGGCGGCTGTCAT 60.512 61.111 14.51 14.46 0.00 3.06
1017 1251 1.227234 CATGTCGGCGGCTGTCATA 60.227 57.895 18.68 0.00 0.00 2.15
1046 1280 4.142227 CGGTAAGTAAGATACACCTGCACT 60.142 45.833 0.00 0.00 0.00 4.40
1049 1287 4.207891 AGTAAGATACACCTGCACTTGG 57.792 45.455 0.00 0.00 0.00 3.61
1070 1308 4.883585 TGGCAGAATAATTAAGCTGGTCTG 59.116 41.667 15.55 10.50 35.28 3.51
1076 1314 8.125448 CAGAATAATTAAGCTGGTCTGTTTAGC 58.875 37.037 9.09 0.00 37.71 3.09
1089 1327 6.538742 TGGTCTGTTTAGCTGATAATAAGCAC 59.461 38.462 0.00 0.00 43.37 4.40
1135 1373 6.378280 CCTTGATTAGTTTTCCACCAGCTAAT 59.622 38.462 0.00 0.00 35.74 1.73
1136 1374 7.556275 CCTTGATTAGTTTTCCACCAGCTAATA 59.444 37.037 0.00 0.00 33.93 0.98
1137 1375 9.125026 CTTGATTAGTTTTCCACCAGCTAATAT 57.875 33.333 0.00 0.00 33.93 1.28
1142 1380 9.609346 TTAGTTTTCCACCAGCTAATATAACTC 57.391 33.333 0.00 0.00 0.00 3.01
1232 1471 3.554692 CAGACGATGCCGCCGTTC 61.555 66.667 0.00 0.00 40.67 3.95
1243 1482 0.739813 CCGCCGTTCGAGGAAGAAAT 60.740 55.000 0.00 0.00 41.67 2.17
1275 1519 1.203237 TCATGGCCAAGATCTCCGAA 58.797 50.000 10.96 0.00 0.00 4.30
1294 1538 4.560128 CGAAGAGATCAACAGAAGGAACA 58.440 43.478 0.00 0.00 0.00 3.18
1297 1541 5.146010 AGAGATCAACAGAAGGAACAGAC 57.854 43.478 0.00 0.00 0.00 3.51
1557 1823 1.304381 GCAGGAAGGGTTCATGGCA 60.304 57.895 3.74 0.00 41.45 4.92
1739 2020 3.071206 GGAGAGGCTCGAGTGGCA 61.071 66.667 15.13 0.00 34.73 4.92
1848 2129 2.124570 CCGGCCAACATCCTCCTG 60.125 66.667 2.24 0.00 0.00 3.86
1854 2135 1.599047 CAACATCCTCCTGACCGCT 59.401 57.895 0.00 0.00 0.00 5.52
2121 2402 1.742308 AGTGGGTGTGGGACAAGTAT 58.258 50.000 0.00 0.00 44.16 2.12
2465 2761 1.167851 CCGACAGTTGCAATGGTGAT 58.832 50.000 0.59 0.00 0.00 3.06
2508 2804 1.098712 TGACGACACAGGGGTTTTGC 61.099 55.000 0.00 0.00 0.00 3.68
2574 2870 7.016153 TCTGTTTCCAGTTTACATGTAGGAT 57.984 36.000 11.27 0.00 39.82 3.24
2575 2871 7.458397 TCTGTTTCCAGTTTACATGTAGGATT 58.542 34.615 11.27 0.00 39.82 3.01
2577 2873 8.472007 TGTTTCCAGTTTACATGTAGGATTTT 57.528 30.769 11.27 0.00 0.00 1.82
2605 3064 7.919313 TTATAAATAGCACCGTAGACTTTCG 57.081 36.000 0.00 0.00 0.00 3.46
2610 3069 2.993899 AGCACCGTAGACTTTCGATTTG 59.006 45.455 0.00 0.00 0.00 2.32
2611 3070 2.735134 GCACCGTAGACTTTCGATTTGT 59.265 45.455 0.00 0.00 0.00 2.83
2612 3071 3.423123 GCACCGTAGACTTTCGATTTGTG 60.423 47.826 0.00 0.00 0.00 3.33
2647 3109 8.677300 ACAACGATTTAGCTCATATGACAATTT 58.323 29.630 0.00 0.00 0.00 1.82
2649 3111 8.668510 ACGATTTAGCTCATATGACAATTTCT 57.331 30.769 0.00 0.00 0.00 2.52
2683 3228 8.799367 ACTAGTAAAAGAGTGTTTGTTGGTTTT 58.201 29.630 0.00 0.00 0.00 2.43
2703 4706 7.665145 TGGTTTTCATCACTCTCATTGATAACA 59.335 33.333 0.00 0.00 34.07 2.41
2704 4707 8.514594 GGTTTTCATCACTCTCATTGATAACAA 58.485 33.333 0.00 0.00 40.42 2.83
2737 4740 2.364579 ACGGTAAGGCCCATCGGA 60.365 61.111 11.91 0.00 0.00 4.55
2766 4769 3.181462 ACTCACTGTTGATGCAAGTCTCA 60.181 43.478 0.00 0.00 0.00 3.27
2770 4773 3.136763 CTGTTGATGCAAGTCTCACACT 58.863 45.455 0.00 0.00 36.64 3.55
3100 5141 4.832823 TCCGGAGCTATGTTGATTATCTCA 59.167 41.667 0.00 0.00 0.00 3.27
3121 5162 6.541278 TCTCAATGAGATCTTAGGCACAAATG 59.459 38.462 9.18 0.00 33.35 2.32
3200 5241 5.027460 ACCCAAAAAGGTTGTTAAAGGTCT 58.973 37.500 0.00 0.00 36.44 3.85
3201 5242 5.128171 ACCCAAAAAGGTTGTTAAAGGTCTC 59.872 40.000 0.00 0.00 36.44 3.36
3202 5243 5.128008 CCCAAAAAGGTTGTTAAAGGTCTCA 59.872 40.000 0.00 0.00 34.66 3.27
3216 5257 9.196552 GTTAAAGGTCTCATTGAAAAATTGGAG 57.803 33.333 0.00 0.00 0.00 3.86
3252 5293 4.636206 GCAATAAGTAGTCAGACCCTTTGG 59.364 45.833 8.07 1.87 37.80 3.28
3293 5334 2.114825 GGGTTCGATAACTAAGCGTCG 58.885 52.381 0.00 0.00 35.81 5.12
3318 5359 0.536460 TGGGAAAAGGCACGAGAACC 60.536 55.000 0.00 0.00 0.00 3.62
3325 5366 2.035442 GGCACGAGAACCTTCTGCC 61.035 63.158 0.00 2.10 37.73 4.85
3333 5374 1.642762 AGAACCTTCTGCCATCCCAAT 59.357 47.619 0.00 0.00 35.89 3.16
3348 5389 1.312815 CCAATCGGATCTCAAAGGGC 58.687 55.000 0.00 0.00 0.00 5.19
3349 5390 1.133976 CCAATCGGATCTCAAAGGGCT 60.134 52.381 0.00 0.00 0.00 5.19
3355 5396 3.070159 TCGGATCTCAAAGGGCTTCATAG 59.930 47.826 0.00 0.00 0.00 2.23
3376 5417 1.630878 ACCCAGAGATCAAAGTGGACC 59.369 52.381 0.00 0.00 31.04 4.46
3377 5418 1.065126 CCCAGAGATCAAAGTGGACCC 60.065 57.143 0.00 0.00 31.04 4.46
3378 5419 1.912043 CCAGAGATCAAAGTGGACCCT 59.088 52.381 0.00 0.00 31.04 4.34
3379 5420 2.307098 CCAGAGATCAAAGTGGACCCTT 59.693 50.000 0.00 0.00 31.04 3.95
3384 5425 5.003096 AGATCAAAGTGGACCCTTGATTT 57.997 39.130 12.41 6.63 0.00 2.17
3396 5437 7.882791 GTGGACCCTTGATTTTTAATTTGGAAT 59.117 33.333 0.00 0.00 0.00 3.01
3430 5473 7.885009 AAACCTTGTTAGCTAAGTGGTTTTA 57.115 32.000 27.39 0.00 41.65 1.52
3462 5505 4.789012 ATTGTATGTGGACTTTGGCAAG 57.211 40.909 0.00 0.00 35.92 4.01
3521 5564 7.769044 GTGTATCTCTAGAGCAAAACCCAAATA 59.231 37.037 15.35 1.03 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.216122 GCTTGTCGCATCTCTCATCC 58.784 55.000 0.00 0.00 38.92 3.51
1 2 1.931906 TGCTTGTCGCATCTCTCATC 58.068 50.000 0.00 0.00 45.47 2.92
11 12 2.833533 TTGTGCCTGTGCTTGTCGC 61.834 57.895 0.00 0.00 38.71 5.19
12 13 1.009675 GTTGTGCCTGTGCTTGTCG 60.010 57.895 0.00 0.00 38.71 4.35
13 14 1.360192 GGTTGTGCCTGTGCTTGTC 59.640 57.895 0.00 0.00 38.71 3.18
14 15 1.379710 TGGTTGTGCCTGTGCTTGT 60.380 52.632 0.00 0.00 38.71 3.16
15 16 1.066257 GTGGTTGTGCCTGTGCTTG 59.934 57.895 0.00 0.00 38.71 4.01
16 17 2.480610 CGTGGTTGTGCCTGTGCTT 61.481 57.895 0.00 0.00 38.71 3.91
17 18 2.901840 CGTGGTTGTGCCTGTGCT 60.902 61.111 0.00 0.00 38.71 4.40
18 19 4.629115 GCGTGGTTGTGCCTGTGC 62.629 66.667 0.00 0.00 38.35 4.57
19 20 3.185082 CTGCGTGGTTGTGCCTGTG 62.185 63.158 0.00 0.00 38.35 3.66
20 21 2.318519 TACTGCGTGGTTGTGCCTGT 62.319 55.000 0.00 0.00 38.35 4.00
21 22 1.568612 CTACTGCGTGGTTGTGCCTG 61.569 60.000 0.00 0.00 38.35 4.85
22 23 1.301716 CTACTGCGTGGTTGTGCCT 60.302 57.895 0.00 0.00 38.35 4.75
23 24 2.966309 GCTACTGCGTGGTTGTGCC 61.966 63.158 0.00 0.00 37.90 5.01
24 25 2.175184 CTGCTACTGCGTGGTTGTGC 62.175 60.000 0.00 0.00 43.34 4.57
25 26 1.862123 CTGCTACTGCGTGGTTGTG 59.138 57.895 0.00 0.00 43.34 3.33
26 27 1.961277 GCTGCTACTGCGTGGTTGT 60.961 57.895 0.00 0.00 43.34 3.32
27 28 1.904852 CTGCTGCTACTGCGTGGTTG 61.905 60.000 0.00 0.00 43.34 3.77
28 29 1.669115 CTGCTGCTACTGCGTGGTT 60.669 57.895 0.00 0.00 43.34 3.67
29 30 2.047844 CTGCTGCTACTGCGTGGT 60.048 61.111 0.00 0.00 43.34 4.16
30 31 3.494336 GCTGCTGCTACTGCGTGG 61.494 66.667 8.53 0.00 43.34 4.94
31 32 2.737688 CTGCTGCTGCTACTGCGTG 61.738 63.158 17.00 0.00 43.34 5.34
32 33 2.433838 CTGCTGCTGCTACTGCGT 60.434 61.111 17.00 0.00 43.34 5.24
33 34 3.862402 GCTGCTGCTGCTACTGCG 61.862 66.667 22.10 0.16 43.34 5.18
34 35 2.745100 TGCTGCTGCTGCTACTGC 60.745 61.111 27.67 14.65 40.48 4.40
35 36 3.487417 CTGCTGCTGCTGCTACTG 58.513 61.111 27.67 13.98 40.48 2.74
41 42 0.809385 AGTATTTGCTGCTGCTGCTG 59.191 50.000 27.67 16.73 40.48 4.41
42 43 1.093159 GAGTATTTGCTGCTGCTGCT 58.907 50.000 27.67 13.59 40.48 4.24
43 44 0.247974 CGAGTATTTGCTGCTGCTGC 60.248 55.000 22.51 22.51 40.48 5.25
44 45 0.247974 GCGAGTATTTGCTGCTGCTG 60.248 55.000 17.00 0.77 40.48 4.41
45 46 1.372087 GGCGAGTATTTGCTGCTGCT 61.372 55.000 17.00 0.00 40.48 4.24
46 47 1.063166 GGCGAGTATTTGCTGCTGC 59.937 57.895 8.89 8.89 40.20 5.25
47 48 0.654683 GAGGCGAGTATTTGCTGCTG 59.345 55.000 0.00 0.00 33.93 4.41
48 49 0.462759 GGAGGCGAGTATTTGCTGCT 60.463 55.000 0.00 0.00 33.93 4.24
49 50 0.462759 AGGAGGCGAGTATTTGCTGC 60.463 55.000 0.00 0.00 33.93 5.25
50 51 1.936547 GAAGGAGGCGAGTATTTGCTG 59.063 52.381 0.00 0.00 33.93 4.41
51 52 1.134371 GGAAGGAGGCGAGTATTTGCT 60.134 52.381 0.00 0.00 33.93 3.91
52 53 1.134371 AGGAAGGAGGCGAGTATTTGC 60.134 52.381 0.00 0.00 0.00 3.68
53 54 2.483889 GGAGGAAGGAGGCGAGTATTTG 60.484 54.545 0.00 0.00 0.00 2.32
54 55 1.763545 GGAGGAAGGAGGCGAGTATTT 59.236 52.381 0.00 0.00 0.00 1.40
55 56 1.062810 AGGAGGAAGGAGGCGAGTATT 60.063 52.381 0.00 0.00 0.00 1.89
56 57 0.558712 AGGAGGAAGGAGGCGAGTAT 59.441 55.000 0.00 0.00 0.00 2.12
81 82 2.986413 AGGTGCGAGAGTGCGACT 60.986 61.111 0.00 0.00 37.81 4.18
139 163 7.208225 TCGGTCTGAATGTCTGATATAGAAG 57.792 40.000 0.00 0.00 37.12 2.85
140 164 7.597386 CATCGGTCTGAATGTCTGATATAGAA 58.403 38.462 0.00 0.00 37.12 2.10
167 191 0.737715 CTGACCTCGGCACAGCTAAC 60.738 60.000 0.00 0.00 0.00 2.34
230 254 5.408356 TGCGTCAGTATCTTCTTTCTTACC 58.592 41.667 0.00 0.00 0.00 2.85
309 336 2.614057 GACCACAGAACAGGAACACAAG 59.386 50.000 0.00 0.00 0.00 3.16
325 352 2.416431 GGCTGCAAATTCAGATGACCAC 60.416 50.000 0.50 0.00 36.19 4.16
353 394 3.132925 CGGACGGTTAAGGTTCAGAAAA 58.867 45.455 0.00 0.00 0.00 2.29
398 439 7.663081 TCAAACTCAGAGATCATAGCAGTTTTT 59.337 33.333 3.79 0.00 31.76 1.94
419 461 1.200020 CCCTGATCCGCAGTTTCAAAC 59.800 52.381 0.00 0.00 43.33 2.93
446 488 0.523966 AAGGACTCTCAGACGCGAAG 59.476 55.000 15.93 4.55 0.00 3.79
448 490 1.738350 CTAAAGGACTCTCAGACGCGA 59.262 52.381 15.93 0.00 0.00 5.87
449 491 1.738350 TCTAAAGGACTCTCAGACGCG 59.262 52.381 3.53 3.53 0.00 6.01
451 493 4.333095 TCGATTCTAAAGGACTCTCAGACG 59.667 45.833 0.00 0.00 0.00 4.18
467 511 3.875727 CACTCCATCAATTGCTCGATTCT 59.124 43.478 0.00 0.00 0.00 2.40
477 521 1.272648 CCACCACCCACTCCATCAATT 60.273 52.381 0.00 0.00 0.00 2.32
478 522 0.332632 CCACCACCCACTCCATCAAT 59.667 55.000 0.00 0.00 0.00 2.57
479 523 1.065410 ACCACCACCCACTCCATCAA 61.065 55.000 0.00 0.00 0.00 2.57
481 525 0.112412 AAACCACCACCCACTCCATC 59.888 55.000 0.00 0.00 0.00 3.51
482 526 0.178964 CAAACCACCACCCACTCCAT 60.179 55.000 0.00 0.00 0.00 3.41
483 527 1.228793 CAAACCACCACCCACTCCA 59.771 57.895 0.00 0.00 0.00 3.86
484 528 0.112412 ATCAAACCACCACCCACTCC 59.888 55.000 0.00 0.00 0.00 3.85
485 529 1.202879 TGATCAAACCACCACCCACTC 60.203 52.381 0.00 0.00 0.00 3.51
486 530 0.850100 TGATCAAACCACCACCCACT 59.150 50.000 0.00 0.00 0.00 4.00
495 539 6.317642 CGTAATACCCTGAATTGATCAAACCA 59.682 38.462 13.09 11.92 37.67 3.67
519 563 1.940613 GAAATCCGATCCCCTTTCACG 59.059 52.381 0.00 0.00 0.00 4.35
525 569 2.252714 GAGCTAGAAATCCGATCCCCT 58.747 52.381 0.00 0.00 0.00 4.79
526 570 1.067495 CGAGCTAGAAATCCGATCCCC 60.067 57.143 0.00 0.00 0.00 4.81
532 576 1.871080 ATTGGCGAGCTAGAAATCCG 58.129 50.000 0.00 0.00 0.00 4.18
533 577 4.142381 ACAAAATTGGCGAGCTAGAAATCC 60.142 41.667 0.00 0.00 0.00 3.01
537 581 4.072131 AGAACAAAATTGGCGAGCTAGAA 58.928 39.130 0.00 0.00 0.00 2.10
595 656 1.754226 ACACTAGCTTAGCTCAGCCTC 59.246 52.381 16.24 0.00 41.12 4.70
596 657 1.859302 ACACTAGCTTAGCTCAGCCT 58.141 50.000 16.24 6.68 41.12 4.58
597 658 3.363341 CTACACTAGCTTAGCTCAGCC 57.637 52.381 16.24 0.00 41.12 4.85
638 699 0.613260 ACCATTGCTCTCCGCTTGTA 59.387 50.000 0.00 0.00 40.11 2.41
666 727 9.849166 ATCTAGACGCTCTTATATTTCTTTAGC 57.151 33.333 0.00 0.00 0.00 3.09
669 730 9.685828 GTGATCTAGACGCTCTTATATTTCTTT 57.314 33.333 0.00 0.00 0.00 2.52
671 732 8.630054 AGTGATCTAGACGCTCTTATATTTCT 57.370 34.615 0.00 0.00 0.00 2.52
672 733 9.982291 CTAGTGATCTAGACGCTCTTATATTTC 57.018 37.037 10.41 0.00 44.52 2.17
673 734 8.455682 GCTAGTGATCTAGACGCTCTTATATTT 58.544 37.037 10.41 0.00 44.52 1.40
674 735 7.608376 TGCTAGTGATCTAGACGCTCTTATATT 59.392 37.037 10.41 0.00 44.52 1.28
675 736 7.106890 TGCTAGTGATCTAGACGCTCTTATAT 58.893 38.462 10.41 0.00 44.52 0.86
676 737 6.465084 TGCTAGTGATCTAGACGCTCTTATA 58.535 40.000 10.41 0.00 44.52 0.98
677 738 5.309638 TGCTAGTGATCTAGACGCTCTTAT 58.690 41.667 10.41 0.00 44.52 1.73
678 739 4.704965 TGCTAGTGATCTAGACGCTCTTA 58.295 43.478 10.41 0.00 44.52 2.10
679 740 3.546724 TGCTAGTGATCTAGACGCTCTT 58.453 45.455 10.41 0.00 44.52 2.85
680 741 3.201353 TGCTAGTGATCTAGACGCTCT 57.799 47.619 10.41 7.61 44.52 4.09
681 742 4.497473 AATGCTAGTGATCTAGACGCTC 57.503 45.455 10.41 0.00 44.52 5.03
682 743 4.927978 AAATGCTAGTGATCTAGACGCT 57.072 40.909 0.00 4.20 44.52 5.07
683 744 6.003234 TCTAAATGCTAGTGATCTAGACGC 57.997 41.667 0.00 0.00 44.52 5.19
684 745 9.549509 GTAATCTAAATGCTAGTGATCTAGACG 57.450 37.037 0.00 0.00 44.52 4.18
689 750 9.979578 CTTCAGTAATCTAAATGCTAGTGATCT 57.020 33.333 0.00 0.00 0.00 2.75
690 751 9.757227 ACTTCAGTAATCTAAATGCTAGTGATC 57.243 33.333 0.00 0.00 0.00 2.92
697 758 9.539825 CATCACTACTTCAGTAATCTAAATGCT 57.460 33.333 0.00 0.00 34.98 3.79
698 759 9.319143 ACATCACTACTTCAGTAATCTAAATGC 57.681 33.333 0.00 0.00 34.98 3.56
703 764 9.999009 CGTTTACATCACTACTTCAGTAATCTA 57.001 33.333 0.00 0.00 34.98 1.98
704 765 7.488471 GCGTTTACATCACTACTTCAGTAATCT 59.512 37.037 0.00 0.00 34.98 2.40
705 766 7.488471 AGCGTTTACATCACTACTTCAGTAATC 59.512 37.037 0.00 0.00 34.98 1.75
706 767 7.321153 AGCGTTTACATCACTACTTCAGTAAT 58.679 34.615 0.00 0.00 34.98 1.89
707 768 6.684686 AGCGTTTACATCACTACTTCAGTAA 58.315 36.000 0.00 0.00 34.98 2.24
708 769 6.150641 AGAGCGTTTACATCACTACTTCAGTA 59.849 38.462 0.00 0.00 34.98 2.74
709 770 5.047943 AGAGCGTTTACATCACTACTTCAGT 60.048 40.000 0.00 0.00 38.32 3.41
710 771 5.403246 AGAGCGTTTACATCACTACTTCAG 58.597 41.667 0.00 0.00 0.00 3.02
711 772 5.386958 AGAGCGTTTACATCACTACTTCA 57.613 39.130 0.00 0.00 0.00 3.02
712 773 6.805271 TGTAAGAGCGTTTACATCACTACTTC 59.195 38.462 10.73 0.00 38.31 3.01
713 774 6.585322 GTGTAAGAGCGTTTACATCACTACTT 59.415 38.462 15.81 0.00 43.27 2.24
714 775 6.072064 AGTGTAAGAGCGTTTACATCACTACT 60.072 38.462 15.81 7.39 43.27 2.57
715 776 6.091437 AGTGTAAGAGCGTTTACATCACTAC 58.909 40.000 15.81 5.73 43.27 2.73
716 777 6.263516 AGTGTAAGAGCGTTTACATCACTA 57.736 37.500 15.81 0.00 43.27 2.74
717 778 5.135508 AGTGTAAGAGCGTTTACATCACT 57.864 39.130 15.81 8.44 43.27 3.41
718 779 4.326548 GGAGTGTAAGAGCGTTTACATCAC 59.673 45.833 15.81 11.25 43.27 3.06
719 780 4.021807 TGGAGTGTAAGAGCGTTTACATCA 60.022 41.667 15.81 12.53 43.27 3.07
720 781 4.491676 TGGAGTGTAAGAGCGTTTACATC 58.508 43.478 15.81 13.65 43.27 3.06
721 782 4.530710 TGGAGTGTAAGAGCGTTTACAT 57.469 40.909 15.81 8.01 43.27 2.29
722 783 4.530710 ATGGAGTGTAAGAGCGTTTACA 57.469 40.909 10.73 10.73 40.28 2.41
723 784 5.638234 AGAAATGGAGTGTAAGAGCGTTTAC 59.362 40.000 6.48 6.48 34.78 2.01
724 785 5.790593 AGAAATGGAGTGTAAGAGCGTTTA 58.209 37.500 0.00 0.00 0.00 2.01
725 786 4.642429 AGAAATGGAGTGTAAGAGCGTTT 58.358 39.130 0.00 0.00 0.00 3.60
726 787 4.273148 AGAAATGGAGTGTAAGAGCGTT 57.727 40.909 0.00 0.00 0.00 4.84
727 788 3.963428 AGAAATGGAGTGTAAGAGCGT 57.037 42.857 0.00 0.00 0.00 5.07
728 789 5.220228 CGTAAAGAAATGGAGTGTAAGAGCG 60.220 44.000 0.00 0.00 0.00 5.03
729 790 5.063564 CCGTAAAGAAATGGAGTGTAAGAGC 59.936 44.000 0.00 0.00 0.00 4.09
730 791 6.395629 TCCGTAAAGAAATGGAGTGTAAGAG 58.604 40.000 0.00 0.00 30.80 2.85
731 792 6.349243 TCCGTAAAGAAATGGAGTGTAAGA 57.651 37.500 0.00 0.00 30.80 2.10
732 793 6.648725 CTCCGTAAAGAAATGGAGTGTAAG 57.351 41.667 4.28 0.00 44.50 2.34
739 800 3.178865 ACTCCCTCCGTAAAGAAATGGA 58.821 45.455 0.00 0.00 33.43 3.41
740 801 3.629142 ACTCCCTCCGTAAAGAAATGG 57.371 47.619 0.00 0.00 0.00 3.16
741 802 5.914033 TGATACTCCCTCCGTAAAGAAATG 58.086 41.667 0.00 0.00 0.00 2.32
742 803 6.555463 TTGATACTCCCTCCGTAAAGAAAT 57.445 37.500 0.00 0.00 0.00 2.17
743 804 6.155565 TGATTGATACTCCCTCCGTAAAGAAA 59.844 38.462 0.00 0.00 0.00 2.52
744 805 5.659525 TGATTGATACTCCCTCCGTAAAGAA 59.340 40.000 0.00 0.00 0.00 2.52
745 806 5.205821 TGATTGATACTCCCTCCGTAAAGA 58.794 41.667 0.00 0.00 0.00 2.52
746 807 5.509840 CCTGATTGATACTCCCTCCGTAAAG 60.510 48.000 0.00 0.00 0.00 1.85
747 808 4.344102 CCTGATTGATACTCCCTCCGTAAA 59.656 45.833 0.00 0.00 0.00 2.01
748 809 3.895656 CCTGATTGATACTCCCTCCGTAA 59.104 47.826 0.00 0.00 0.00 3.18
749 810 3.497332 CCTGATTGATACTCCCTCCGTA 58.503 50.000 0.00 0.00 0.00 4.02
750 811 2.320781 CCTGATTGATACTCCCTCCGT 58.679 52.381 0.00 0.00 0.00 4.69
751 812 1.620819 CCCTGATTGATACTCCCTCCG 59.379 57.143 0.00 0.00 0.00 4.63
752 813 1.349357 GCCCTGATTGATACTCCCTCC 59.651 57.143 0.00 0.00 0.00 4.30
753 814 1.349357 GGCCCTGATTGATACTCCCTC 59.651 57.143 0.00 0.00 0.00 4.30
754 815 1.439543 GGCCCTGATTGATACTCCCT 58.560 55.000 0.00 0.00 0.00 4.20
755 816 0.402121 GGGCCCTGATTGATACTCCC 59.598 60.000 17.04 0.00 0.00 4.30
778 839 2.930682 AGACGATTAAGAAAGAAGGCGC 59.069 45.455 0.00 0.00 0.00 6.53
824 885 2.514803 GGTGTGCTTGGACCTGTAAAT 58.485 47.619 0.00 0.00 0.00 1.40
831 892 0.321653 CTGTAGGGTGTGCTTGGACC 60.322 60.000 0.00 0.00 0.00 4.46
842 903 4.862641 AGGTAATTGATTGCTGTAGGGT 57.137 40.909 0.00 0.00 0.00 4.34
844 905 7.865706 AGTTTAGGTAATTGATTGCTGTAGG 57.134 36.000 0.00 0.00 0.00 3.18
857 918 7.364497 GGCTACTGACAGGTAAGTTTAGGTAAT 60.364 40.741 7.51 0.00 0.00 1.89
889 1029 3.119316 AGCTCAGTGGAGAGTTAACGATG 60.119 47.826 0.00 0.00 44.26 3.84
894 1034 3.641436 TCACAAGCTCAGTGGAGAGTTAA 59.359 43.478 16.47 0.00 44.26 2.01
915 1055 5.649831 AGACAAGCAATGGGAGAACTAATTC 59.350 40.000 0.00 0.00 34.78 2.17
924 1064 1.271543 TGGTCAGACAAGCAATGGGAG 60.272 52.381 2.17 0.00 0.00 4.30
927 1067 1.538512 CACTGGTCAGACAAGCAATGG 59.461 52.381 4.66 0.00 0.00 3.16
928 1068 2.224606 ACACTGGTCAGACAAGCAATG 58.775 47.619 4.66 0.00 30.76 2.82
929 1069 2.498167 GACACTGGTCAGACAAGCAAT 58.502 47.619 4.66 0.00 43.73 3.56
930 1070 1.953559 GACACTGGTCAGACAAGCAA 58.046 50.000 4.66 0.00 43.73 3.91
1016 1250 5.163519 GGTGTATCTTACTTACCGGTTGCTA 60.164 44.000 15.04 0.00 0.00 3.49
1017 1251 4.382362 GGTGTATCTTACTTACCGGTTGCT 60.382 45.833 15.04 0.00 0.00 3.91
1023 1257 4.110482 GTGCAGGTGTATCTTACTTACCG 58.890 47.826 0.00 0.00 36.55 4.02
1046 1280 5.357878 CAGACCAGCTTAATTATTCTGCCAA 59.642 40.000 8.28 0.00 0.00 4.52
1049 1287 6.442513 AACAGACCAGCTTAATTATTCTGC 57.557 37.500 8.28 2.12 33.73 4.26
1089 1327 5.550290 AGGAACAAACCCAGCAATTTAATG 58.450 37.500 0.00 0.00 0.00 1.90
1139 1377 9.700024 CTGGATAAATCGAGACAAGAACGGAGT 62.700 44.444 0.00 0.00 37.26 3.85
1140 1378 4.740695 GGATAAATCGAGACAAGAACGGAG 59.259 45.833 0.00 0.00 0.00 4.63
1141 1379 4.158949 TGGATAAATCGAGACAAGAACGGA 59.841 41.667 0.00 0.00 0.00 4.69
1142 1380 4.430007 TGGATAAATCGAGACAAGAACGG 58.570 43.478 0.00 0.00 0.00 4.44
1232 1471 8.721478 TGATCTTCTTGTAAAATTTCTTCCTCG 58.279 33.333 0.00 0.00 0.00 4.63
1243 1482 6.009589 TCTTGGCCATGATCTTCTTGTAAAA 58.990 36.000 17.00 0.00 0.00 1.52
1275 1519 4.590647 TGTCTGTTCCTTCTGTTGATCTCT 59.409 41.667 0.00 0.00 0.00 3.10
1294 1538 1.744368 CGCATGCTTCCAGCTGTCT 60.744 57.895 17.13 0.00 42.97 3.41
1297 1541 1.355563 CATCGCATGCTTCCAGCTG 59.644 57.895 17.13 6.78 42.97 4.24
1313 1569 1.003839 ACCACGTCGTTGATGGCAT 60.004 52.632 0.00 0.00 36.96 4.40
1320 1576 0.109919 TCTCGATCACCACGTCGTTG 60.110 55.000 0.00 0.00 38.85 4.10
1368 1624 0.173481 TCGGCTTCTCGTTGAGGATG 59.827 55.000 0.00 0.00 0.00 3.51
1424 1680 1.465794 GAGCTCGGTGGAGTAGTTCT 58.534 55.000 0.00 0.00 42.53 3.01
1557 1823 3.133014 CCGATGGTGCCGATCTCT 58.867 61.111 0.00 0.00 0.00 3.10
1708 1977 1.304217 TCTCCTTTCTCTCGCCGGT 60.304 57.895 1.90 0.00 0.00 5.28
1709 1978 1.435515 CTCTCCTTTCTCTCGCCGG 59.564 63.158 0.00 0.00 0.00 6.13
1848 2129 3.112709 GGCGTGAAGTCAGCGGTC 61.113 66.667 0.00 0.00 0.00 4.79
1854 2135 1.227823 CACCTTGGGCGTGAAGTCA 60.228 57.895 0.00 0.00 32.77 3.41
2132 2413 0.811616 GGACACGATGGACTCCATGC 60.812 60.000 15.78 6.40 45.26 4.06
2465 2761 2.832129 GGATCAGTGGACTTGACACCTA 59.168 50.000 0.00 0.00 39.63 3.08
2508 2804 0.442310 CACGCGTGACTACAAATGGG 59.558 55.000 34.93 0.93 0.00 4.00
2536 2832 2.359107 CAGAGCAAAGCCTCCGCA 60.359 61.111 0.00 0.00 37.52 5.69
2537 2833 1.518903 AAACAGAGCAAAGCCTCCGC 61.519 55.000 0.00 0.00 32.17 5.54
2582 2878 7.263100 TCGAAAGTCTACGGTGCTATTTATA 57.737 36.000 0.00 0.00 0.00 0.98
2583 2879 6.140303 TCGAAAGTCTACGGTGCTATTTAT 57.860 37.500 0.00 0.00 0.00 1.40
2594 2890 5.003590 GCTAGACACAAATCGAAAGTCTACG 59.996 44.000 0.00 0.00 39.92 3.51
2611 3070 3.678072 GCTAAATCGTTGTGTGCTAGACA 59.322 43.478 0.00 0.00 0.00 3.41
2612 3071 3.927142 AGCTAAATCGTTGTGTGCTAGAC 59.073 43.478 0.00 0.00 0.00 2.59
2623 3082 9.113838 AGAAATTGTCATATGAGCTAAATCGTT 57.886 29.630 5.42 0.00 0.00 3.85
2653 3115 9.490379 CCAACAAACACTCTTTTACTAGTAGAT 57.510 33.333 3.59 0.00 0.00 1.98
2661 3123 7.876896 TGAAAACCAACAAACACTCTTTTAC 57.123 32.000 0.00 0.00 0.00 2.01
2683 3228 7.335171 CACCTTTGTTATCAATGAGAGTGATGA 59.665 37.037 0.00 0.00 36.41 2.92
2703 4706 2.920912 TCGAGCGGGGTCACCTTT 60.921 61.111 0.00 0.00 36.97 3.11
2704 4707 3.692406 GTCGAGCGGGGTCACCTT 61.692 66.667 0.00 0.00 36.97 3.50
2737 4740 3.890756 TGCATCAACAGTGAGTTTTCCAT 59.109 39.130 0.00 0.00 38.74 3.41
2742 4745 4.202441 AGACTTGCATCAACAGTGAGTTT 58.798 39.130 0.00 0.00 38.74 2.66
2747 4750 2.874086 TGTGAGACTTGCATCAACAGTG 59.126 45.455 0.00 0.00 0.00 3.66
3100 5141 8.049117 TCTTACATTTGTGCCTAAGATCTCATT 58.951 33.333 0.00 0.00 0.00 2.57
3121 5162 7.159322 TGAGGTCTTACTCTCACAATCTTAC 57.841 40.000 0.00 0.00 38.32 2.34
3225 5266 6.223351 AGGGTCTGACTACTTATTGCTAAC 57.777 41.667 7.85 0.00 0.00 2.34
3236 5277 0.320697 ACGCCAAAGGGTCTGACTAC 59.679 55.000 7.85 1.52 32.94 2.73
3252 5293 4.045104 CCATGAGAAGATGTGTACTACGC 58.955 47.826 0.00 0.00 0.00 4.42
3293 5334 1.893062 GTGCCTTTTCCCATGGAGC 59.107 57.895 15.22 6.60 31.21 4.70
3318 5359 0.181114 TCCGATTGGGATGGCAGAAG 59.819 55.000 0.00 0.00 40.94 2.85
3333 5374 1.275666 TGAAGCCCTTTGAGATCCGA 58.724 50.000 0.00 0.00 0.00 4.55
3348 5389 6.047870 CACTTTGATCTCTGGGTCTATGAAG 58.952 44.000 0.00 0.00 0.00 3.02
3349 5390 5.104776 CCACTTTGATCTCTGGGTCTATGAA 60.105 44.000 0.00 0.00 0.00 2.57
3355 5396 2.355209 GGTCCACTTTGATCTCTGGGTC 60.355 54.545 0.00 0.00 0.00 4.46
3430 5473 9.625747 AAAGTCCACATACAATTTCCAATTTTT 57.374 25.926 0.00 0.00 0.00 1.94
3448 5491 2.488153 GGACATACTTGCCAAAGTCCAC 59.512 50.000 11.08 0.00 43.34 4.02
3462 5505 8.507249 GGAACATATTTATTCAGCAGGACATAC 58.493 37.037 0.00 0.00 0.00 2.39
3521 5564 4.162651 AGCCCAAAATTGTGAATCTTCCT 58.837 39.130 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.