Multiple sequence alignment - TraesCS5B01G017000

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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 TraesCS5B01G017000 chr5B 100.000 2585 0 0 1888 4472 15560091 15557507 0.000000e+00 4774.0
1 TraesCS5B01G017000 chr5B 100.000 1718 0 0 1 1718 15561978 15560261 0.000000e+00 3173.0
2 TraesCS5B01G017000 chr5B 88.392 1318 121 13 1888 3184 16003492 16002186 0.000000e+00 1557.0
3 TraesCS5B01G017000 chr5B 81.765 861 84 34 814 1635 16004392 16003566 0.000000e+00 652.0
4 TraesCS5B01G017000 chr5B 87.838 370 33 6 3183 3545 16002122 16001758 1.490000e-114 424.0
5 TraesCS5B01G017000 chr5B 95.000 140 5 2 644 783 202239365 202239228 7.530000e-53 219.0
6 TraesCS5B01G017000 chr5B 80.205 293 44 8 3543 3828 16001692 16001407 1.630000e-49 207.0
7 TraesCS5B01G017000 chr5B 87.805 164 14 3 1 163 16004659 16004501 2.120000e-43 187.0
8 TraesCS5B01G017000 chr5B 92.453 53 4 0 573 625 16004443 16004391 4.800000e-10 76.8
9 TraesCS5B01G017000 chr5A 93.654 1954 96 17 1888 3824 15866758 15864816 0.000000e+00 2896.0
10 TraesCS5B01G017000 chr5A 94.080 946 33 10 777 1718 15867715 15866789 0.000000e+00 1415.0
11 TraesCS5B01G017000 chr5A 91.629 657 37 10 1 656 15868350 15867711 0.000000e+00 893.0
12 TraesCS5B01G017000 chr5A 88.467 659 49 16 3829 4472 15864763 15864117 0.000000e+00 771.0
13 TraesCS5B01G017000 chr5D 93.422 1961 94 17 1888 3824 22401347 22399398 0.000000e+00 2874.0
14 TraesCS5B01G017000 chr5D 88.619 1318 117 13 1888 3184 22435081 22433776 0.000000e+00 1572.0
15 TraesCS5B01G017000 chr5D 95.026 945 27 5 777 1718 22402305 22401378 0.000000e+00 1467.0
16 TraesCS5B01G017000 chr5D 92.109 659 37 8 1 656 22402947 22402301 0.000000e+00 915.0
17 TraesCS5B01G017000 chr5D 86.433 656 55 20 3829 4472 22399346 22398713 0.000000e+00 688.0
18 TraesCS5B01G017000 chr5D 80.732 820 73 29 888 1669 22435901 22435129 1.090000e-155 560.0
19 TraesCS5B01G017000 chr5D 89.337 347 30 3 3183 3524 22433712 22433368 3.200000e-116 429.0
20 TraesCS5B01G017000 chr5D 97.710 131 2 1 653 783 241844204 241844075 1.620000e-54 224.0
21 TraesCS5B01G017000 chr5D 96.269 134 4 1 653 786 115924522 115924654 7.530000e-53 219.0
22 TraesCS5B01G017000 chr5D 93.706 143 7 2 638 779 286408529 286408670 3.500000e-51 213.0
23 TraesCS5B01G017000 chr5D 82.716 243 33 6 3553 3793 22433308 22433073 1.630000e-49 207.0
24 TraesCS5B01G017000 chr5D 85.802 162 15 5 1 162 22436270 22436117 9.950000e-37 165.0
25 TraesCS5B01G017000 chr5D 83.019 159 19 6 4060 4215 213477868 213478021 2.170000e-28 137.0
26 TraesCS5B01G017000 chr5D 81.988 161 24 4 4060 4218 283009685 283009842 1.010000e-26 132.0
27 TraesCS5B01G017000 chr2B 87.736 212 24 1 1888 2099 178773376 178773167 3.450000e-61 246.0
28 TraesCS5B01G017000 chr2B 98.425 127 2 0 653 779 199013852 199013726 1.620000e-54 224.0
29 TraesCS5B01G017000 chr4B 97.692 130 3 0 655 784 340640768 340640639 1.620000e-54 224.0
30 TraesCS5B01G017000 chr2A 97.692 130 3 0 652 781 333746030 333746159 1.620000e-54 224.0
31 TraesCS5B01G017000 chr2A 84.516 155 20 3 4061 4214 549290426 549290275 2.790000e-32 150.0
32 TraesCS5B01G017000 chr7A 96.992 133 3 1 647 779 593450697 593450828 5.820000e-54 222.0
33 TraesCS5B01G017000 chr6A 94.444 144 6 1 653 796 545123726 545123585 2.090000e-53 220.0
34 TraesCS5B01G017000 chr6A 90.476 42 2 2 1678 1717 63593745 63593704 2.000000e-03 54.7
35 TraesCS5B01G017000 chr7D 84.615 156 20 3 4061 4215 623793585 623793433 7.750000e-33 152.0
36 TraesCS5B01G017000 chr3A 83.125 160 20 4 4060 4215 310691932 310692088 6.030000e-29 139.0
37 TraesCS5B01G017000 chr3B 84.138 145 20 2 4075 4219 528176327 528176186 2.170000e-28 137.0
38 TraesCS5B01G017000 chr2D 82.581 155 25 1 4061 4215 406958412 406958564 7.800000e-28 135.0
39 TraesCS5B01G017000 chr2D 94.444 36 1 1 1680 1714 580114125 580114090 2.000000e-03 54.7
40 TraesCS5B01G017000 chr7B 100.000 32 0 0 1687 1718 499929051 499929020 4.830000e-05 60.2
41 TraesCS5B01G017000 chr6B 100.000 32 0 0 1687 1718 2471683 2471652 4.830000e-05 60.2
42 TraesCS5B01G017000 chr3D 100.000 32 0 0 1687 1718 59293768 59293799 4.830000e-05 60.2
43 TraesCS5B01G017000 chr3D 97.143 35 0 1 1685 1718 37758300 37758334 1.740000e-04 58.4
44 TraesCS5B01G017000 chr1B 100.000 32 0 0 1687 1718 17695223 17695254 4.830000e-05 60.2


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 TraesCS5B01G017000 chr5B 15557507 15561978 4471 True 3973.50 4774 100.000000 1 4472 2 chr5B.!!$R2 4471
1 TraesCS5B01G017000 chr5B 16001407 16004659 3252 True 517.30 1557 86.409667 1 3828 6 chr5B.!!$R3 3827
2 TraesCS5B01G017000 chr5A 15864117 15868350 4233 True 1493.75 2896 91.957500 1 4472 4 chr5A.!!$R1 4471
3 TraesCS5B01G017000 chr5D 22398713 22402947 4234 True 1486.00 2874 91.747500 1 4472 4 chr5D.!!$R2 4471
4 TraesCS5B01G017000 chr5D 22433073 22436270 3197 True 586.60 1572 85.441200 1 3793 5 chr5D.!!$R3 3792

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
780 799 0.115745 TTTGGGACGGAGGGAGTACT 59.884 55.0 0.0 0.0 0.00 2.73 F
2632 2725 0.398318 GTCAGGACTGGCCTCTTGTT 59.602 55.0 0.0 0.0 46.97 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2656 2749 1.068741 GAGGTGAACACAAGGAGACGT 59.931 52.381 7.25 0.0 0.00 4.34 R
3972 4298 0.034670 GGCTCCTGTTTCTCTGCCAT 60.035 55.000 0.00 0.0 40.04 4.40 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
65 66 4.400251 CGTGTGTTAAGGATGGTAGGTAGA 59.600 45.833 0.00 0.00 0.00 2.59
95 98 8.641541 CATTTCAGGCCACCAAAAAGTATATAT 58.358 33.333 5.01 0.00 0.00 0.86
96 99 9.875708 ATTTCAGGCCACCAAAAAGTATATATA 57.124 29.630 5.01 0.00 0.00 0.86
139 146 7.812191 TCCAAATTTGACATGTTAGTATGTTGC 59.188 33.333 19.86 0.00 41.15 4.17
140 147 7.814107 CCAAATTTGACATGTTAGTATGTTGCT 59.186 33.333 19.86 0.00 41.15 3.91
141 148 9.838975 CAAATTTGACATGTTAGTATGTTGCTA 57.161 29.630 13.08 0.00 41.15 3.49
170 181 7.148255 TGCTACACAATTCATTAATGTCTGTCC 60.148 37.037 14.97 6.43 0.00 4.02
268 279 3.084786 ACAGCCTGAGGAATAACAAAGC 58.915 45.455 0.65 0.00 0.00 3.51
314 325 1.519408 CACCTTGGAAGTAACACCCG 58.481 55.000 0.00 0.00 0.00 5.28
396 408 0.531311 ACAACACGGTCGGTTTCCTC 60.531 55.000 0.00 0.00 0.00 3.71
399 411 4.368543 ACGGTCGGTTTCCTCGGC 62.369 66.667 0.00 0.00 0.00 5.54
400 412 4.367023 CGGTCGGTTTCCTCGGCA 62.367 66.667 0.00 0.00 33.45 5.69
401 413 2.741211 GGTCGGTTTCCTCGGCAC 60.741 66.667 0.00 0.00 33.45 5.01
419 431 1.665916 CGACACACCAGGTCAGCAG 60.666 63.158 0.00 0.00 34.97 4.24
421 433 3.046087 CACACCAGGTCAGCAGCG 61.046 66.667 0.00 0.00 0.00 5.18
479 493 9.838339 GGTCCTCTCTATCATTTAAAATTCTCA 57.162 33.333 0.00 0.00 0.00 3.27
488 502 7.845617 TCATTTAAAATTCTCAACGAAACGG 57.154 32.000 0.00 0.00 34.79 4.44
515 529 4.355543 AACATACTGCTAAACAATGGCG 57.644 40.909 0.00 0.00 0.00 5.69
571 587 5.163612 GGGTGAGAATAATCAGTTGCTTTCC 60.164 44.000 0.00 0.00 0.00 3.13
603 622 7.592938 TGCCATTGTTTAGAAGTAGTTCAATG 58.407 34.615 12.77 12.21 39.76 2.82
657 676 1.731750 GCACGGTCTTCTTCGTACTCC 60.732 57.143 0.00 0.00 37.88 3.85
658 677 1.135460 CACGGTCTTCTTCGTACTCCC 60.135 57.143 0.00 0.00 37.88 4.30
659 678 1.271817 ACGGTCTTCTTCGTACTCCCT 60.272 52.381 0.00 0.00 37.88 4.20
660 679 1.401199 CGGTCTTCTTCGTACTCCCTC 59.599 57.143 0.00 0.00 0.00 4.30
661 680 1.750206 GGTCTTCTTCGTACTCCCTCC 59.250 57.143 0.00 0.00 0.00 4.30
662 681 1.401199 GTCTTCTTCGTACTCCCTCCG 59.599 57.143 0.00 0.00 0.00 4.63
664 683 1.401199 CTTCTTCGTACTCCCTCCGTC 59.599 57.143 0.00 0.00 0.00 4.79
665 684 0.393537 TCTTCGTACTCCCTCCGTCC 60.394 60.000 0.00 0.00 0.00 4.79
666 685 1.379044 TTCGTACTCCCTCCGTCCC 60.379 63.158 0.00 0.00 0.00 4.46
667 686 2.044650 CGTACTCCCTCCGTCCCA 60.045 66.667 0.00 0.00 0.00 4.37
668 687 1.679977 CGTACTCCCTCCGTCCCAA 60.680 63.158 0.00 0.00 0.00 4.12
669 688 1.252904 CGTACTCCCTCCGTCCCAAA 61.253 60.000 0.00 0.00 0.00 3.28
670 689 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
671 690 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
672 691 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
673 692 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
674 693 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
675 694 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
676 695 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
677 696 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
678 697 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
679 698 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
680 699 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
681 700 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
682 701 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
683 702 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
684 703 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
685 704 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
686 705 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
687 706 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
688 707 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
689 708 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
690 709 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
698 717 8.622157 TCTTGTCTTAGATTTGTCTAGATACGG 58.378 37.037 0.00 0.00 0.00 4.02
699 718 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
700 719 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
701 720 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
702 721 7.539366 GTCTTAGATTTGTCTAGATACGGATGC 59.461 40.741 0.00 0.00 0.00 3.91
703 722 5.791336 AGATTTGTCTAGATACGGATGCA 57.209 39.130 0.00 0.00 0.00 3.96
704 723 6.352016 AGATTTGTCTAGATACGGATGCAT 57.648 37.500 0.00 0.00 0.00 3.96
705 724 6.393990 AGATTTGTCTAGATACGGATGCATC 58.606 40.000 18.81 18.81 0.00 3.91
706 725 5.791336 TTTGTCTAGATACGGATGCATCT 57.209 39.130 25.28 10.06 35.67 2.90
707 726 6.894339 TTTGTCTAGATACGGATGCATCTA 57.106 37.500 25.28 12.00 33.58 1.98
708 727 6.894339 TTGTCTAGATACGGATGCATCTAA 57.106 37.500 25.28 11.93 34.25 2.10
709 728 6.255596 TGTCTAGATACGGATGCATCTAAC 57.744 41.667 25.28 10.33 34.25 2.34
710 729 5.768164 TGTCTAGATACGGATGCATCTAACA 59.232 40.000 25.28 12.86 34.25 2.41
711 730 6.087522 GTCTAGATACGGATGCATCTAACAC 58.912 44.000 25.28 14.23 34.25 3.32
712 731 6.004574 TCTAGATACGGATGCATCTAACACT 58.995 40.000 25.28 19.49 34.25 3.55
713 732 7.119407 GTCTAGATACGGATGCATCTAACACTA 59.881 40.741 25.28 19.55 34.25 2.74
714 733 6.650427 AGATACGGATGCATCTAACACTAA 57.350 37.500 25.28 4.42 29.66 2.24
715 734 7.050970 AGATACGGATGCATCTAACACTAAA 57.949 36.000 25.28 2.95 29.66 1.85
716 735 7.497595 AGATACGGATGCATCTAACACTAAAA 58.502 34.615 25.28 1.60 29.66 1.52
717 736 5.796350 ACGGATGCATCTAACACTAAAAC 57.204 39.130 25.28 4.07 0.00 2.43
718 737 4.328983 ACGGATGCATCTAACACTAAAACG 59.671 41.667 25.28 17.07 0.00 3.60
719 738 4.588278 GGATGCATCTAACACTAAAACGC 58.412 43.478 25.28 0.54 0.00 4.84
720 739 4.094294 GGATGCATCTAACACTAAAACGCA 59.906 41.667 25.28 0.00 0.00 5.24
721 740 5.391523 GGATGCATCTAACACTAAAACGCAA 60.392 40.000 25.28 0.00 0.00 4.85
722 741 4.778904 TGCATCTAACACTAAAACGCAAC 58.221 39.130 0.00 0.00 0.00 4.17
723 742 4.513692 TGCATCTAACACTAAAACGCAACT 59.486 37.500 0.00 0.00 0.00 3.16
724 743 5.697178 TGCATCTAACACTAAAACGCAACTA 59.303 36.000 0.00 0.00 0.00 2.24
725 744 6.128661 TGCATCTAACACTAAAACGCAACTAG 60.129 38.462 0.00 0.00 0.00 2.57
726 745 6.090358 GCATCTAACACTAAAACGCAACTAGA 59.910 38.462 0.00 0.00 0.00 2.43
727 746 7.201530 GCATCTAACACTAAAACGCAACTAGAT 60.202 37.037 0.00 0.00 0.00 1.98
728 747 9.297586 CATCTAACACTAAAACGCAACTAGATA 57.702 33.333 0.00 0.00 0.00 1.98
729 748 8.679288 TCTAACACTAAAACGCAACTAGATAC 57.321 34.615 0.00 0.00 0.00 2.24
730 749 8.298854 TCTAACACTAAAACGCAACTAGATACA 58.701 33.333 0.00 0.00 0.00 2.29
731 750 7.900782 AACACTAAAACGCAACTAGATACAT 57.099 32.000 0.00 0.00 0.00 2.29
732 751 7.521509 ACACTAAAACGCAACTAGATACATC 57.478 36.000 0.00 0.00 0.00 3.06
733 752 6.534079 ACACTAAAACGCAACTAGATACATCC 59.466 38.462 0.00 0.00 0.00 3.51
734 753 5.747197 ACTAAAACGCAACTAGATACATCCG 59.253 40.000 0.00 0.00 0.00 4.18
735 754 3.795623 AACGCAACTAGATACATCCGT 57.204 42.857 0.00 0.00 0.00 4.69
736 755 4.906065 AACGCAACTAGATACATCCGTA 57.094 40.909 0.00 0.00 0.00 4.02
737 756 5.449107 AACGCAACTAGATACATCCGTAT 57.551 39.130 0.00 0.00 41.16 3.06
738 757 5.449107 ACGCAACTAGATACATCCGTATT 57.551 39.130 0.00 0.00 38.48 1.89
739 758 5.839621 ACGCAACTAGATACATCCGTATTT 58.160 37.500 0.00 0.00 38.48 1.40
740 759 6.973843 ACGCAACTAGATACATCCGTATTTA 58.026 36.000 0.00 0.00 38.48 1.40
741 760 7.082602 ACGCAACTAGATACATCCGTATTTAG 58.917 38.462 0.00 8.04 43.54 1.85
742 761 7.040892 ACGCAACTAGATACATCCGTATTTAGA 60.041 37.037 13.92 0.00 41.85 2.10
743 762 7.270793 CGCAACTAGATACATCCGTATTTAGAC 59.729 40.741 13.92 5.51 41.85 2.59
744 763 8.080417 GCAACTAGATACATCCGTATTTAGACA 58.920 37.037 13.92 0.00 41.85 3.41
745 764 9.961265 CAACTAGATACATCCGTATTTAGACAA 57.039 33.333 13.92 0.00 41.85 3.18
754 773 9.530633 ACATCCGTATTTAGACAAATCTAAGAC 57.469 33.333 0.00 0.83 45.93 3.01
755 774 9.529325 CATCCGTATTTAGACAAATCTAAGACA 57.471 33.333 9.81 0.00 45.93 3.41
757 776 9.582431 TCCGTATTTAGACAAATCTAAGACAAG 57.418 33.333 9.81 3.88 45.93 3.16
758 777 9.582431 CCGTATTTAGACAAATCTAAGACAAGA 57.418 33.333 9.81 0.00 45.93 3.02
766 785 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
767 786 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
768 787 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
769 788 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
770 789 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
771 790 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
772 791 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
773 792 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
774 793 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
775 794 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
776 795 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
777 796 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
778 797 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
779 798 0.978907 TTTTGGGACGGAGGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73
780 799 0.115745 TTTGGGACGGAGGGAGTACT 59.884 55.000 0.00 0.00 0.00 2.73
821 840 2.544685 CTGCGAGGAATAGACAAGGTG 58.455 52.381 0.00 0.00 0.00 4.00
867 892 9.884636 ATGTAGTATGACAATGCTAACAAGTAA 57.115 29.630 0.00 0.00 33.42 2.24
868 893 9.146984 TGTAGTATGACAATGCTAACAAGTAAC 57.853 33.333 0.00 0.00 33.42 2.50
969 1007 4.825085 TGGTTGGTGTTATCCTTTTCTGTC 59.175 41.667 0.00 0.00 0.00 3.51
1023 1063 3.278157 GGCACCTTTACAGCAGCC 58.722 61.111 0.00 0.00 33.04 4.85
1026 1066 2.742372 ACCTTTACAGCAGCCGCG 60.742 61.111 0.00 0.00 45.49 6.46
1027 1067 3.499737 CCTTTACAGCAGCCGCGG 61.500 66.667 24.05 24.05 45.49 6.46
1028 1068 4.166011 CTTTACAGCAGCCGCGGC 62.166 66.667 42.34 42.34 45.49 6.53
1063 1103 0.543749 GGTTCTAGTCATGGCTGGCT 59.456 55.000 10.89 0.00 41.24 4.75
1079 1119 1.181098 GGCTTCTTGGGAGCTGCAAA 61.181 55.000 7.79 0.00 0.00 3.68
1169 1209 5.316167 TCTCTGCTAAAATTGAGCTTTGGA 58.684 37.500 3.71 0.00 40.76 3.53
1188 1228 5.664294 TGGATTGGATTTGAATTCAGGTG 57.336 39.130 8.41 0.00 0.00 4.00
1440 1518 3.140325 TGGTTGACAAGATCTGGTTCC 57.860 47.619 3.70 8.39 0.00 3.62
1632 1710 7.604549 ACATGCATAGAGATCTCAGTAAGATG 58.395 38.462 24.39 18.29 45.06 2.90
1925 2016 7.942990 AGGATTATAGGACTTGTTTAGACTCG 58.057 38.462 0.00 0.00 0.00 4.18
1955 2048 7.982919 CCCAAGAAAATCATGATGAAAATAGCA 59.017 33.333 9.46 0.00 0.00 3.49
2006 2099 4.810491 TGAATTTGCTTTGCTTCTGGTTTC 59.190 37.500 0.00 0.00 0.00 2.78
2140 2233 2.834549 CAACCAGGAGGATACAGTCACT 59.165 50.000 0.00 0.00 38.69 3.41
2230 2323 6.170675 ACGAGCATTAATTCTCTTCACAAC 57.829 37.500 12.38 0.00 0.00 3.32
2361 2454 7.386851 ACTGCATTTGTGAGTACATACTACTT 58.613 34.615 0.00 0.00 36.50 2.24
2397 2490 6.070881 CCTCCCTCATCTCCATATAGAGTTTG 60.071 46.154 0.00 0.00 35.28 2.93
2632 2725 0.398318 GTCAGGACTGGCCTCTTGTT 59.602 55.000 0.00 0.00 46.97 2.83
2654 2747 1.267532 GCGATATGGTCACAAGCAACG 60.268 52.381 0.00 0.00 36.29 4.10
2656 2749 2.670905 CGATATGGTCACAAGCAACGAA 59.329 45.455 0.00 0.00 36.29 3.85
2749 2842 4.780815 TGGTTGAGAACAATTGTGAGACT 58.219 39.130 12.82 9.40 38.32 3.24
2814 2907 5.169295 GTCTTAAGTACCGTTGCTCTGAAT 58.831 41.667 1.63 0.00 0.00 2.57
2817 2910 6.367969 TCTTAAGTACCGTTGCTCTGAATTTC 59.632 38.462 1.63 0.00 0.00 2.17
2849 2942 0.438830 GTGTTGAAGATGGCGACGAC 59.561 55.000 0.00 0.00 0.00 4.34
3050 3143 2.288666 TGGGCTAATTTCATCGCAGTC 58.711 47.619 0.00 0.00 0.00 3.51
3070 3163 7.411696 CGCAGTCGACTACTACAAGGTATATAG 60.412 44.444 19.57 0.26 35.76 1.31
3073 3185 9.487790 AGTCGACTACTACAAGGTATATAGTTC 57.512 37.037 18.46 0.00 36.36 3.01
3130 3242 3.067106 GTGTGTTCCACGAGATGACAAT 58.933 45.455 0.00 0.00 37.14 2.71
3236 3421 6.136071 GCGCATATTTCGTGAAATGAACTAT 58.864 36.000 16.12 0.95 42.51 2.12
3333 3518 2.115910 TCAAGGCTTGCCAGGTGG 59.884 61.111 22.31 0.00 38.53 4.61
3368 3553 1.681538 TTGCTTCCGCCTTTGTTGTA 58.318 45.000 0.00 0.00 34.43 2.41
3375 3560 5.503520 GCTTCCGCCTTTGTTGTACATATAC 60.504 44.000 0.00 0.00 0.00 1.47
3401 3586 7.307042 CGCCTCTTGATATCTTTGTTATGTGAG 60.307 40.741 3.98 0.00 0.00 3.51
3418 3615 2.421424 GTGAGTCATGACATGGCCTTTC 59.579 50.000 27.02 13.54 34.84 2.62
3430 3628 1.754226 TGGCCTTTCTTTTGTGGTGTC 59.246 47.619 3.32 0.00 0.00 3.67
3465 3663 4.393680 CGAGGATCTAGTGTAGTATGCTCC 59.606 50.000 0.00 0.00 34.42 4.70
3479 3677 4.241555 CTCCGCCTGAATCCGGGG 62.242 72.222 0.00 0.82 44.45 5.73
3483 3681 1.377987 CGCCTGAATCCGGGGAAAA 60.378 57.895 0.00 0.00 39.31 2.29
3505 3703 0.443869 GGACATGTAGCAACTGCACG 59.556 55.000 0.00 0.00 45.16 5.34
3561 3827 1.766496 ACTTCTCAGGTGGTTTTCGGA 59.234 47.619 0.00 0.00 0.00 4.55
3567 3833 1.812571 CAGGTGGTTTTCGGATCCTTG 59.187 52.381 10.75 0.00 0.00 3.61
3570 3836 2.683362 GGTGGTTTTCGGATCCTTGATC 59.317 50.000 10.75 0.00 38.25 2.92
3574 3840 4.700213 TGGTTTTCGGATCCTTGATCTTTC 59.300 41.667 10.75 0.00 38.91 2.62
3584 3850 1.396301 CTTGATCTTTCTGGCTGACGC 59.604 52.381 0.00 0.00 0.00 5.19
3592 3858 0.246635 TCTGGCTGACGCTAACCTTC 59.753 55.000 0.00 0.00 36.09 3.46
3600 3866 4.494855 GCTGACGCTAACCTTCATGAAATC 60.495 45.833 9.88 0.00 0.00 2.17
3633 3899 1.028330 AACTGGAGATGCATGGCGTG 61.028 55.000 2.46 1.31 0.00 5.34
3634 3900 1.153309 CTGGAGATGCATGGCGTGA 60.153 57.895 11.71 0.00 0.00 4.35
3635 3901 0.534427 CTGGAGATGCATGGCGTGAT 60.534 55.000 11.71 1.02 0.00 3.06
3636 3902 0.107066 TGGAGATGCATGGCGTGATT 60.107 50.000 11.71 0.00 0.00 2.57
3674 3940 7.542890 TCAAGATGAGACAAGACATACTCTTC 58.457 38.462 0.00 0.00 37.08 2.87
3680 3946 8.594881 TGAGACAAGACATACTCTTCTTTTTC 57.405 34.615 0.00 0.00 37.08 2.29
3683 3949 9.620259 AGACAAGACATACTCTTCTTTTTCTTT 57.380 29.630 0.00 0.00 37.08 2.52
3729 3995 1.917872 TCCAGATTTCCCAAAACCGG 58.082 50.000 0.00 0.00 0.00 5.28
3742 4009 3.807071 CCAAAACCGGAAGTTGAAAATGG 59.193 43.478 9.46 0.00 39.19 3.16
3749 4016 2.609491 GGAAGTTGAAAATGGCGGGTTC 60.609 50.000 0.00 0.00 0.00 3.62
3751 4018 0.037697 GTTGAAAATGGCGGGTTCCC 60.038 55.000 0.00 0.00 0.00 3.97
3805 4077 7.686438 AGTGCATTACAACAGTTGATTCATA 57.314 32.000 20.56 0.00 0.00 2.15
3839 4159 2.489722 TCTCGGAGACACACATCAAGAG 59.510 50.000 2.97 0.00 0.00 2.85
3840 4160 2.230025 CTCGGAGACACACATCAAGAGT 59.770 50.000 0.00 0.00 0.00 3.24
3972 4298 2.354729 CATGGGAGGGACGGCAAA 59.645 61.111 0.00 0.00 0.00 3.68
3974 4300 1.076777 ATGGGAGGGACGGCAAATG 60.077 57.895 0.00 0.00 0.00 2.32
3975 4301 2.440247 GGGAGGGACGGCAAATGG 60.440 66.667 0.00 0.00 0.00 3.16
3976 4302 3.140814 GGAGGGACGGCAAATGGC 61.141 66.667 0.00 0.00 43.74 4.40
3987 4313 2.358939 GCAAATGGCAGAGAAACAGG 57.641 50.000 0.00 0.00 43.97 4.00
3988 4314 1.888512 GCAAATGGCAGAGAAACAGGA 59.111 47.619 0.00 0.00 43.97 3.86
3989 4315 2.094854 GCAAATGGCAGAGAAACAGGAG 60.095 50.000 0.00 0.00 43.97 3.69
3990 4316 1.831580 AATGGCAGAGAAACAGGAGC 58.168 50.000 0.00 0.00 0.00 4.70
3991 4317 0.034670 ATGGCAGAGAAACAGGAGCC 60.035 55.000 0.00 0.00 42.32 4.70
3992 4318 1.377856 GGCAGAGAAACAGGAGCCC 60.378 63.158 0.00 0.00 36.17 5.19
3993 4319 1.743252 GCAGAGAAACAGGAGCCCG 60.743 63.158 0.00 0.00 0.00 6.13
4030 4357 7.095355 CGGTAGCAAGTCAGTTGTAAAAGTAAT 60.095 37.037 0.00 0.00 38.55 1.89
4041 4368 9.760660 CAGTTGTAAAAGTAATCATAGAAGTGC 57.239 33.333 0.00 0.00 0.00 4.40
4044 4371 7.324935 TGTAAAAGTAATCATAGAAGTGCGGA 58.675 34.615 0.00 0.00 0.00 5.54
4048 4375 6.650427 AGTAATCATAGAAGTGCGGACATA 57.350 37.500 10.52 0.00 0.00 2.29
4056 4383 2.094762 AGTGCGGACATAGGTCAAAC 57.905 50.000 10.52 4.31 46.17 2.93
4065 4392 5.913514 CGGACATAGGTCAAACTAATACTCG 59.086 44.000 10.08 0.00 46.17 4.18
4070 4397 3.114065 GGTCAAACTAATACTCGCTCCG 58.886 50.000 0.00 0.00 0.00 4.63
4086 4413 4.098960 TCGCTCCGTTCCAAACTATAAGAT 59.901 41.667 0.00 0.00 0.00 2.40
4087 4414 4.209288 CGCTCCGTTCCAAACTATAAGATG 59.791 45.833 0.00 0.00 0.00 2.90
4132 4461 4.925061 GCATATGCAGACTAAGATGAGC 57.075 45.455 22.84 0.00 41.59 4.26
4157 4486 9.030301 GCAAACAAACATACTAAAACATGTCTT 57.970 29.630 0.00 0.00 34.32 3.01
4206 4535 9.229784 GTTACGACATCTTATATTTCAGAACGA 57.770 33.333 0.00 0.00 0.00 3.85
4215 4544 9.144298 TCTTATATTTCAGAACGAAGGGAGTAT 57.856 33.333 0.00 0.00 34.32 2.12
4285 4614 8.654230 TCTTCAGATATTAATTCTGTGCAGTC 57.346 34.615 18.74 0.00 41.13 3.51
4291 4620 2.949714 AATTCTGTGCAGTCGAAACG 57.050 45.000 0.00 0.00 0.00 3.60
4306 4635 2.159761 CGAAACGTATGTCGGTGCATTT 60.160 45.455 8.00 0.00 44.69 2.32
4319 4648 3.262420 GGTGCATTTGACTATGTCGTCT 58.738 45.455 0.00 0.00 34.95 4.18
4331 4660 4.700692 ACTATGTCGTCTCTTAACTGCAGA 59.299 41.667 23.35 0.00 0.00 4.26
4347 4687 4.764172 CTGCAGATCTAAAAGGCAGTAGT 58.236 43.478 19.03 0.00 45.11 2.73
4401 4741 4.488126 TGCTCACTCACAGCAAAAATAC 57.512 40.909 0.00 0.00 44.02 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 4.224370 ACCTACCATCCTTAACACACGATT 59.776 41.667 0.00 0.00 0.00 3.34
65 66 1.786937 TTGGTGGCCTGAAATGTGTT 58.213 45.000 3.32 0.00 0.00 3.32
140 147 9.836864 AGACATTAATGAATTGTGTAGCAGATA 57.163 29.630 22.16 0.00 0.00 1.98
141 148 8.618677 CAGACATTAATGAATTGTGTAGCAGAT 58.381 33.333 22.16 0.00 0.00 2.90
142 149 7.607607 ACAGACATTAATGAATTGTGTAGCAGA 59.392 33.333 22.16 0.00 0.00 4.26
170 181 1.990799 TTAACAGGTCGACGCTCATG 58.009 50.000 9.92 5.72 0.00 3.07
268 279 0.758685 TGTTTCTTGGGTGGCCAAGG 60.759 55.000 7.24 0.00 44.99 3.61
396 408 4.602259 ACCTGGTGTGTCGTGCCG 62.602 66.667 0.00 0.00 0.00 5.69
399 411 1.956170 GCTGACCTGGTGTGTCGTG 60.956 63.158 2.82 0.00 35.46 4.35
400 412 2.369257 CTGCTGACCTGGTGTGTCGT 62.369 60.000 2.82 0.00 35.46 4.34
401 413 1.665916 CTGCTGACCTGGTGTGTCG 60.666 63.158 2.82 0.00 35.46 4.35
402 414 1.963338 GCTGCTGACCTGGTGTGTC 60.963 63.158 2.82 0.00 0.00 3.67
403 415 2.111878 GCTGCTGACCTGGTGTGT 59.888 61.111 2.82 0.00 0.00 3.72
419 431 1.786579 GGAAAAGAAATGTGTGTGCGC 59.213 47.619 0.00 0.00 0.00 6.09
421 433 2.223711 ACCGGAAAAGAAATGTGTGTGC 60.224 45.455 9.46 0.00 0.00 4.57
450 464 6.801718 TTTTAAATGATAGAGAGGACCCGA 57.198 37.500 0.00 0.00 0.00 5.14
479 493 5.391203 GCAGTATGTTATTTCCCGTTTCGTT 60.391 40.000 0.00 0.00 39.31 3.85
480 494 4.093850 GCAGTATGTTATTTCCCGTTTCGT 59.906 41.667 0.00 0.00 39.31 3.85
482 496 5.813080 AGCAGTATGTTATTTCCCGTTTC 57.187 39.130 0.00 0.00 39.31 2.78
488 502 7.435192 GCCATTGTTTAGCAGTATGTTATTTCC 59.565 37.037 0.00 0.00 39.31 3.13
515 529 2.094417 GCAAGTGATTAAGAGACGGCAC 59.906 50.000 0.00 0.00 0.00 5.01
657 676 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
658 677 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
659 678 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
660 679 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
661 680 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
662 681 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
664 683 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
672 691 8.622157 CCGTATCTAGACAAATCTAAGACAAGA 58.378 37.037 0.00 0.00 36.98 3.02
673 692 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
674 693 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
675 694 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
676 695 7.539366 GCATCCGTATCTAGACAAATCTAAGAC 59.461 40.741 0.00 0.00 36.98 3.01
677 696 7.230712 TGCATCCGTATCTAGACAAATCTAAGA 59.769 37.037 0.00 0.00 36.98 2.10
678 697 7.371159 TGCATCCGTATCTAGACAAATCTAAG 58.629 38.462 0.00 0.00 36.98 2.18
679 698 7.284919 TGCATCCGTATCTAGACAAATCTAA 57.715 36.000 0.00 0.00 36.98 2.10
680 699 6.894339 TGCATCCGTATCTAGACAAATCTA 57.106 37.500 0.00 0.00 36.29 1.98
681 700 5.791336 TGCATCCGTATCTAGACAAATCT 57.209 39.130 0.00 0.00 39.15 2.40
682 701 6.393990 AGATGCATCCGTATCTAGACAAATC 58.606 40.000 23.06 0.00 42.15 2.17
683 702 6.352016 AGATGCATCCGTATCTAGACAAAT 57.648 37.500 23.06 0.00 42.15 2.32
684 703 5.791336 AGATGCATCCGTATCTAGACAAA 57.209 39.130 23.06 0.00 42.15 2.83
685 704 6.264518 TGTTAGATGCATCCGTATCTAGACAA 59.735 38.462 23.06 0.00 44.49 3.18
686 705 5.768164 TGTTAGATGCATCCGTATCTAGACA 59.232 40.000 23.06 11.68 44.49 3.41
687 706 6.072397 AGTGTTAGATGCATCCGTATCTAGAC 60.072 42.308 23.06 8.90 44.49 2.59
688 707 6.004574 AGTGTTAGATGCATCCGTATCTAGA 58.995 40.000 23.06 0.00 44.49 2.43
689 708 6.260870 AGTGTTAGATGCATCCGTATCTAG 57.739 41.667 23.06 0.00 44.49 2.43
690 709 7.754851 TTAGTGTTAGATGCATCCGTATCTA 57.245 36.000 23.06 16.18 42.15 1.98
691 710 6.650427 TTAGTGTTAGATGCATCCGTATCT 57.350 37.500 23.06 17.09 45.39 1.98
692 711 7.564988 GTTTTAGTGTTAGATGCATCCGTATC 58.435 38.462 23.06 11.17 34.68 2.24
693 712 6.200286 CGTTTTAGTGTTAGATGCATCCGTAT 59.800 38.462 23.06 7.24 0.00 3.06
694 713 5.517411 CGTTTTAGTGTTAGATGCATCCGTA 59.483 40.000 23.06 7.32 0.00 4.02
695 714 4.328983 CGTTTTAGTGTTAGATGCATCCGT 59.671 41.667 23.06 8.39 0.00 4.69
696 715 4.782195 GCGTTTTAGTGTTAGATGCATCCG 60.782 45.833 23.06 14.77 0.00 4.18
697 716 4.094294 TGCGTTTTAGTGTTAGATGCATCC 59.906 41.667 23.06 8.72 0.00 3.51
698 717 5.216566 TGCGTTTTAGTGTTAGATGCATC 57.783 39.130 19.37 19.37 0.00 3.91
699 718 5.181245 AGTTGCGTTTTAGTGTTAGATGCAT 59.819 36.000 0.00 0.00 0.00 3.96
700 719 4.513692 AGTTGCGTTTTAGTGTTAGATGCA 59.486 37.500 0.00 0.00 0.00 3.96
701 720 5.030874 AGTTGCGTTTTAGTGTTAGATGC 57.969 39.130 0.00 0.00 0.00 3.91
702 721 7.576750 TCTAGTTGCGTTTTAGTGTTAGATG 57.423 36.000 0.00 0.00 0.00 2.90
703 722 9.298774 GTATCTAGTTGCGTTTTAGTGTTAGAT 57.701 33.333 0.00 0.00 32.11 1.98
704 723 8.298854 TGTATCTAGTTGCGTTTTAGTGTTAGA 58.701 33.333 0.00 0.00 0.00 2.10
705 724 8.456904 TGTATCTAGTTGCGTTTTAGTGTTAG 57.543 34.615 0.00 0.00 0.00 2.34
706 725 8.991243 ATGTATCTAGTTGCGTTTTAGTGTTA 57.009 30.769 0.00 0.00 0.00 2.41
707 726 7.064253 GGATGTATCTAGTTGCGTTTTAGTGTT 59.936 37.037 0.00 0.00 0.00 3.32
708 727 6.534079 GGATGTATCTAGTTGCGTTTTAGTGT 59.466 38.462 0.00 0.00 0.00 3.55
709 728 6.291637 CGGATGTATCTAGTTGCGTTTTAGTG 60.292 42.308 0.00 0.00 0.00 2.74
710 729 5.747197 CGGATGTATCTAGTTGCGTTTTAGT 59.253 40.000 0.00 0.00 0.00 2.24
711 730 5.747197 ACGGATGTATCTAGTTGCGTTTTAG 59.253 40.000 0.00 0.00 0.00 1.85
712 731 5.653507 ACGGATGTATCTAGTTGCGTTTTA 58.346 37.500 0.00 0.00 0.00 1.52
713 732 4.501071 ACGGATGTATCTAGTTGCGTTTT 58.499 39.130 0.00 0.00 0.00 2.43
714 733 4.119442 ACGGATGTATCTAGTTGCGTTT 57.881 40.909 0.00 0.00 0.00 3.60
715 734 3.795623 ACGGATGTATCTAGTTGCGTT 57.204 42.857 0.00 0.00 0.00 4.84
716 735 5.449107 AATACGGATGTATCTAGTTGCGT 57.551 39.130 0.00 0.00 40.42 5.24
717 736 7.270793 GTCTAAATACGGATGTATCTAGTTGCG 59.729 40.741 0.00 0.00 40.42 4.85
718 737 8.080417 TGTCTAAATACGGATGTATCTAGTTGC 58.920 37.037 0.00 0.00 40.42 4.17
719 738 9.961265 TTGTCTAAATACGGATGTATCTAGTTG 57.039 33.333 0.00 0.00 40.42 3.16
728 747 9.530633 GTCTTAGATTTGTCTAAATACGGATGT 57.469 33.333 0.26 0.00 36.66 3.06
729 748 9.529325 TGTCTTAGATTTGTCTAAATACGGATG 57.471 33.333 0.26 0.00 36.66 3.51
731 750 9.582431 CTTGTCTTAGATTTGTCTAAATACGGA 57.418 33.333 0.26 0.00 36.66 4.69
732 751 9.582431 TCTTGTCTTAGATTTGTCTAAATACGG 57.418 33.333 0.26 0.99 36.66 4.02
740 759 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
741 760 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
742 761 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
743 762 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
744 763 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
745 764 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
746 765 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
747 766 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
748 767 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
749 768 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
750 769 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
751 770 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
752 771 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
753 772 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
754 773 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
755 774 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
756 775 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
757 776 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
758 777 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
759 778 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
760 779 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
761 780 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
762 781 1.002069 TAGTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
763 782 1.002069 TTAGTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
764 783 2.149973 TTTAGTACTCCCTCCGTCCC 57.850 55.000 0.00 0.00 0.00 4.46
765 784 4.210331 TGTATTTAGTACTCCCTCCGTCC 58.790 47.826 0.00 0.00 34.27 4.79
766 785 4.277921 CCTGTATTTAGTACTCCCTCCGTC 59.722 50.000 0.00 0.00 34.27 4.79
767 786 4.079558 TCCTGTATTTAGTACTCCCTCCGT 60.080 45.833 0.00 0.00 34.27 4.69
768 787 4.467769 TCCTGTATTTAGTACTCCCTCCG 58.532 47.826 0.00 0.00 34.27 4.63
769 788 9.939424 ATATATCCTGTATTTAGTACTCCCTCC 57.061 37.037 0.00 0.00 34.27 4.30
772 791 9.819267 GCAATATATCCTGTATTTAGTACTCCC 57.181 37.037 0.00 0.00 34.27 4.30
775 794 9.877178 GCAGCAATATATCCTGTATTTAGTACT 57.123 33.333 0.00 0.00 34.27 2.73
776 795 9.877178 AGCAGCAATATATCCTGTATTTAGTAC 57.123 33.333 12.37 0.00 0.00 2.73
777 796 9.875691 CAGCAGCAATATATCCTGTATTTAGTA 57.124 33.333 12.37 0.00 0.00 1.82
778 797 7.335422 GCAGCAGCAATATATCCTGTATTTAGT 59.665 37.037 12.37 0.00 41.58 2.24
779 798 7.465111 CGCAGCAGCAATATATCCTGTATTTAG 60.465 40.741 0.82 0.00 42.27 1.85
780 799 6.313658 CGCAGCAGCAATATATCCTGTATTTA 59.686 38.462 0.82 0.00 42.27 1.40
862 887 1.144298 GGTGAGGGGTGGTTGTTACTT 59.856 52.381 0.00 0.00 0.00 2.24
864 889 0.769247 AGGTGAGGGGTGGTTGTTAC 59.231 55.000 0.00 0.00 0.00 2.50
865 890 1.061546 GAGGTGAGGGGTGGTTGTTA 58.938 55.000 0.00 0.00 0.00 2.41
866 891 0.697854 AGAGGTGAGGGGTGGTTGTT 60.698 55.000 0.00 0.00 0.00 2.83
867 892 0.697854 AAGAGGTGAGGGGTGGTTGT 60.698 55.000 0.00 0.00 0.00 3.32
868 893 0.036875 GAAGAGGTGAGGGGTGGTTG 59.963 60.000 0.00 0.00 0.00 3.77
969 1007 5.476945 GCTATAGAGAAAGAGGAGAAGAGGG 59.523 48.000 3.21 0.00 0.00 4.30
1063 1103 0.604578 GCATTTGCAGCTCCCAAGAA 59.395 50.000 0.00 0.00 41.59 2.52
1079 1119 3.634504 TGCTGGAATCTTACATTGGCAT 58.365 40.909 0.00 0.00 0.00 4.40
1169 1209 3.198417 GCCCACCTGAATTCAAATCCAAT 59.802 43.478 9.88 0.00 0.00 3.16
1188 1228 3.112709 GTCGAGCACTTGTCGCCC 61.113 66.667 0.00 0.00 37.35 6.13
1367 1426 7.041721 ACTCAAAATTTGTTCTTGTTCCTTCC 58.958 34.615 5.56 0.00 0.00 3.46
1436 1514 2.719046 CGCATTCTGTTTGTTTCGGAAC 59.281 45.455 0.00 0.00 33.80 3.62
1440 1518 2.399396 ACCGCATTCTGTTTGTTTCG 57.601 45.000 0.00 0.00 0.00 3.46
1891 1982 6.099845 ACAAGTCCTATAATCCTAACTGGGTG 59.900 42.308 0.00 0.00 36.20 4.61
1981 2074 3.385755 ACCAGAAGCAAAGCAAATTCAGT 59.614 39.130 0.00 0.00 0.00 3.41
2006 2099 4.690748 TGGCAACGAGTTATTCTGAAGAAG 59.309 41.667 0.00 0.00 37.03 2.85
2104 2197 1.132640 GTTGTCGAAGGTGATGCGC 59.867 57.895 0.00 0.00 0.00 6.09
2140 2233 4.633126 GCAGAAGCTACATTCAACTGATCA 59.367 41.667 0.00 0.00 37.91 2.92
2230 2323 4.456911 ACACCATTCTGTAGAACATTGCAG 59.543 41.667 0.00 0.00 36.80 4.41
2361 2454 4.767908 AGATGAGGGAGGAAGGCATATTA 58.232 43.478 0.00 0.00 0.00 0.98
2430 2523 2.795329 CCAGTGCTGGTTCCTACAATT 58.205 47.619 9.96 0.00 45.53 2.32
2632 2725 3.194861 GTTGCTTGTGACCATATCGCTA 58.805 45.455 0.00 0.00 38.75 4.26
2654 2747 1.865340 GGTGAACACAAGGAGACGTTC 59.135 52.381 7.25 0.00 38.55 3.95
2656 2749 1.068741 GAGGTGAACACAAGGAGACGT 59.931 52.381 7.25 0.00 0.00 4.34
2749 2842 4.659111 TGTTTCGTGTGAAGGAAGTAGA 57.341 40.909 0.00 0.00 35.06 2.59
2791 2884 4.170292 TCAGAGCAACGGTACTTAAGAC 57.830 45.455 10.09 3.11 0.00 3.01
2801 2894 4.424061 TCAATGAAATTCAGAGCAACGG 57.576 40.909 1.10 0.00 31.22 4.44
2814 2907 7.770201 TCTTCAACACAGTGAAATCAATGAAA 58.230 30.769 16.77 3.58 43.86 2.69
2817 2910 6.584942 CCATCTTCAACACAGTGAAATCAATG 59.415 38.462 7.81 9.13 46.23 2.82
2849 2942 1.168407 ATTCGCCAGCATCCATTCCG 61.168 55.000 0.00 0.00 0.00 4.30
3151 3263 8.794335 AGGTTTTAGAAGTCTTCATGTTATCC 57.206 34.615 14.97 7.89 0.00 2.59
3236 3421 2.311463 CCTCCCTCGCTTCTCTGAATA 58.689 52.381 0.00 0.00 0.00 1.75
3368 3553 7.671302 ACAAAGATATCAAGAGGCGTATATGT 58.329 34.615 5.32 0.00 0.00 2.29
3375 3560 6.479990 TCACATAACAAAGATATCAAGAGGCG 59.520 38.462 5.32 0.00 0.00 5.52
3401 3586 4.240096 CAAAAGAAAGGCCATGTCATGAC 58.760 43.478 19.27 19.27 0.00 3.06
3418 3615 2.192624 CAAAAGGCGACACCACAAAAG 58.807 47.619 0.00 0.00 43.14 2.27
3465 3663 0.751643 ATTTTCCCCGGATTCAGGCG 60.752 55.000 0.73 0.00 0.00 5.52
3479 3677 5.123820 TGCAGTTGCTACATGTCCTATTTTC 59.876 40.000 0.00 0.00 42.66 2.29
3483 3681 3.535561 GTGCAGTTGCTACATGTCCTAT 58.464 45.455 0.00 0.00 42.66 2.57
3505 3703 5.689068 GCCGTACATACCTTGTTCTATGTAC 59.311 44.000 14.12 14.12 45.42 2.90
3526 3724 1.482593 AGAAGTTCTATCCTGGTGCCG 59.517 52.381 2.75 0.00 0.00 5.69
3561 3827 3.681034 CGTCAGCCAGAAAGATCAAGGAT 60.681 47.826 0.00 0.00 0.00 3.24
3567 3833 2.586258 TAGCGTCAGCCAGAAAGATC 57.414 50.000 0.00 0.00 46.67 2.75
3570 3836 1.079503 GGTTAGCGTCAGCCAGAAAG 58.920 55.000 0.00 0.00 46.67 2.62
3574 3840 0.037326 TGAAGGTTAGCGTCAGCCAG 60.037 55.000 0.00 0.00 46.67 4.85
3584 3850 3.374988 TGCAGCGATTTCATGAAGGTTAG 59.625 43.478 8.41 1.75 0.00 2.34
3613 3879 0.745845 ACGCCATGCATCTCCAGTTC 60.746 55.000 0.00 0.00 0.00 3.01
3674 3940 8.190784 TGTCTTTCTTCTAGCCAAAAGAAAAAG 58.809 33.333 14.52 13.00 45.72 2.27
3680 3946 7.913674 AGTATGTCTTTCTTCTAGCCAAAAG 57.086 36.000 4.92 4.92 0.00 2.27
3683 3949 7.399191 TCCTAAGTATGTCTTTCTTCTAGCCAA 59.601 37.037 0.00 0.00 37.56 4.52
3729 3995 2.609491 GGAACCCGCCATTTTCAACTTC 60.609 50.000 0.00 0.00 0.00 3.01
3766 4033 6.883756 TGTAATGCACTATCCAACATCTTCAA 59.116 34.615 0.00 0.00 0.00 2.69
3805 4077 5.703592 GTGTCTCCGAGAGTACATCATATCT 59.296 44.000 0.00 0.00 0.00 1.98
3812 4084 2.791655 TGTGTGTCTCCGAGAGTACAT 58.208 47.619 15.04 0.00 33.48 2.29
3863 4183 9.868277 TCAAAAATAGCCATAACAATAAACCAG 57.132 29.630 0.00 0.00 0.00 4.00
3972 4298 0.034670 GGCTCCTGTTTCTCTGCCAT 60.035 55.000 0.00 0.00 40.04 4.40
3974 4300 1.377856 GGGCTCCTGTTTCTCTGCC 60.378 63.158 0.00 0.00 39.61 4.85
3975 4301 1.743252 CGGGCTCCTGTTTCTCTGC 60.743 63.158 0.00 0.00 0.00 4.26
3976 4302 1.078848 CCGGGCTCCTGTTTCTCTG 60.079 63.158 0.00 0.00 0.00 3.35
3977 4303 1.128188 AACCGGGCTCCTGTTTCTCT 61.128 55.000 6.32 0.00 26.53 3.10
3978 4304 0.250770 AAACCGGGCTCCTGTTTCTC 60.251 55.000 6.32 0.00 36.48 2.87
3979 4305 0.537371 CAAACCGGGCTCCTGTTTCT 60.537 55.000 6.32 0.00 38.53 2.52
3980 4306 1.956802 CAAACCGGGCTCCTGTTTC 59.043 57.895 6.32 0.00 38.53 2.78
3981 4307 2.200337 GCAAACCGGGCTCCTGTTT 61.200 57.895 6.32 7.59 40.58 2.83
3982 4308 2.597510 GCAAACCGGGCTCCTGTT 60.598 61.111 6.32 0.00 32.49 3.16
3983 4309 3.570212 AGCAAACCGGGCTCCTGT 61.570 61.111 6.32 0.00 36.81 4.00
3990 4316 3.242897 TACCGTGGAGCAAACCGGG 62.243 63.158 6.32 0.00 44.57 5.73
3991 4317 1.740296 CTACCGTGGAGCAAACCGG 60.740 63.158 0.00 0.00 45.72 5.28
3992 4318 2.388232 GCTACCGTGGAGCAAACCG 61.388 63.158 3.51 0.00 39.84 4.44
3993 4319 1.302192 TGCTACCGTGGAGCAAACC 60.302 57.895 8.19 0.00 46.71 3.27
4030 4357 3.296854 ACCTATGTCCGCACTTCTATGA 58.703 45.455 0.00 0.00 0.00 2.15
4036 4363 2.038557 AGTTTGACCTATGTCCGCACTT 59.961 45.455 0.00 0.00 41.01 3.16
4038 4365 2.094762 AGTTTGACCTATGTCCGCAC 57.905 50.000 0.00 0.00 41.01 5.34
4041 4368 5.913514 CGAGTATTAGTTTGACCTATGTCCG 59.086 44.000 0.00 0.00 41.01 4.79
4044 4371 6.461231 GGAGCGAGTATTAGTTTGACCTATGT 60.461 42.308 0.00 0.00 0.00 2.29
4048 4375 3.181489 CGGAGCGAGTATTAGTTTGACCT 60.181 47.826 0.00 0.00 0.00 3.85
4056 4383 3.431922 TTGGAACGGAGCGAGTATTAG 57.568 47.619 0.00 0.00 0.00 1.73
4065 4392 5.116882 ACATCTTATAGTTTGGAACGGAGC 58.883 41.667 0.00 0.00 36.23 4.70
4116 4443 4.006780 TGTTTGCTCATCTTAGTCTGCA 57.993 40.909 0.00 0.00 0.00 4.41
4117 4444 5.149977 GTTTGTTTGCTCATCTTAGTCTGC 58.850 41.667 0.00 0.00 0.00 4.26
4126 4455 8.795786 TGTTTTAGTATGTTTGTTTGCTCATC 57.204 30.769 0.00 0.00 0.00 2.92
4161 4490 9.851043 GTCGTAACTTTTCTATGAATTAGATGC 57.149 33.333 0.00 0.00 36.81 3.91
4184 4513 7.096023 CCCTTCGTTCTGAAATATAAGATGTCG 60.096 40.741 0.00 0.00 35.79 4.35
4185 4514 7.926555 TCCCTTCGTTCTGAAATATAAGATGTC 59.073 37.037 0.00 0.00 35.79 3.06
4206 4535 4.696479 ATTGCTTCGATGATACTCCCTT 57.304 40.909 1.89 0.00 0.00 3.95
4215 4544 7.870826 TCTTTTCTTACAAATTGCTTCGATGA 58.129 30.769 1.89 0.00 0.00 2.92
4285 4614 0.996462 ATGCACCGACATACGTTTCG 59.004 50.000 0.00 0.00 40.78 3.46
4291 4620 4.570772 ACATAGTCAAATGCACCGACATAC 59.429 41.667 12.87 0.00 31.92 2.39
4306 4635 4.457949 TGCAGTTAAGAGACGACATAGTCA 59.542 41.667 0.00 0.00 43.24 3.41
4319 4648 5.804639 TGCCTTTTAGATCTGCAGTTAAGA 58.195 37.500 14.67 6.12 0.00 2.10
4359 4699 8.239314 TGAGCATCAAGACTTAATTTGATCAAC 58.761 33.333 7.89 0.00 45.97 3.18
4360 4700 8.339344 TGAGCATCAAGACTTAATTTGATCAA 57.661 30.769 3.38 3.38 45.97 2.57
4361 4701 7.926674 TGAGCATCAAGACTTAATTTGATCA 57.073 32.000 0.00 0.00 45.97 2.92
4438 4778 9.822727 TCTAATCAAGATACCTACATGTATCCA 57.177 33.333 5.91 0.00 45.36 3.41


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

AutoCloner maintained by Alex Coulton.