Multiple sequence alignment - TraesCS2B01G356300

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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 TraesCS2B01G356300 chr2B 100.000 3251 0 0 1 3251 508252106 508248856 0.000000e+00 6004.0
1 TraesCS2B01G356300 chr2B 100.000 1597 0 0 3608 5204 508248499 508246903 0.000000e+00 2950.0
2 TraesCS2B01G356300 chr2D 91.139 1896 95 32 670 2549 430465099 430463261 0.000000e+00 2503.0
3 TraesCS2B01G356300 chr2D 93.314 1017 37 18 3629 4641 430462468 430461479 0.000000e+00 1472.0
4 TraesCS2B01G356300 chr2D 97.143 700 18 2 2548 3245 430463223 430462524 0.000000e+00 1181.0
5 TraesCS2B01G356300 chr2D 94.495 218 12 0 4707 4924 430461458 430461241 2.320000e-88 337.0
6 TraesCS2B01G356300 chr2D 89.524 210 14 6 4996 5204 430460734 430460532 5.170000e-65 259.0
7 TraesCS2B01G356300 chr2D 77.607 326 34 20 266 587 380933909 380934199 1.500000e-35 161.0
8 TraesCS2B01G356300 chr2A 88.702 1788 112 34 670 2455 555820987 555822686 0.000000e+00 2100.0
9 TraesCS2B01G356300 chr2A 95.798 952 31 9 3696 4641 555823579 555824527 0.000000e+00 1528.0
10 TraesCS2B01G356300 chr2A 95.448 703 27 2 2548 3245 555822789 555823491 0.000000e+00 1116.0
11 TraesCS2B01G356300 chr2A 92.237 219 13 4 4707 4924 555824548 555824763 1.820000e-79 307.0
12 TraesCS2B01G356300 chr2A 85.441 261 20 7 4958 5204 555825305 555825561 6.690000e-64 255.0
13 TraesCS2B01G356300 chr2A 94.366 71 3 1 2480 2549 555822681 555822751 1.980000e-19 108.0
14 TraesCS2B01G356300 chr2A 89.610 77 7 1 4633 4709 520610044 520610119 4.290000e-16 97.1
15 TraesCS2B01G356300 chr6D 86.304 533 65 6 1031 1559 266959526 266958998 1.630000e-159 573.0
16 TraesCS2B01G356300 chr6D 84.642 293 43 2 3781 4073 266955821 266955531 1.830000e-74 291.0
17 TraesCS2B01G356300 chr6A 86.304 533 65 6 1031 1559 379662665 379662137 1.630000e-159 573.0
18 TraesCS2B01G356300 chr6A 84.880 291 42 2 3783 4073 379658381 379658093 5.100000e-75 292.0
19 TraesCS2B01G356300 chr6A 79.630 378 47 13 66 419 594371860 594371489 1.450000e-60 244.0
20 TraesCS2B01G356300 chr6A 86.525 141 14 4 266 405 594371488 594371352 3.250000e-32 150.0
21 TraesCS2B01G356300 chr6B 86.090 532 68 5 1031 1559 415040798 415040270 7.560000e-158 568.0
22 TraesCS2B01G356300 chr6B 84.536 291 43 2 3783 4073 415036962 415036674 2.370000e-73 287.0
23 TraesCS2B01G356300 chr6B 91.549 71 5 1 4639 4709 119017147 119017216 4.290000e-16 97.1
24 TraesCS2B01G356300 chr7A 83.212 548 53 17 69 587 555476967 555477504 2.840000e-127 466.0
25 TraesCS2B01G356300 chr7B 80.000 620 75 23 1 589 697282926 697283527 3.750000e-111 412.0
26 TraesCS2B01G356300 chr7B 91.549 71 5 1 4639 4709 672837032 672837101 4.290000e-16 97.1
27 TraesCS2B01G356300 chr1B 85.795 352 45 3 1071 1421 634782719 634783066 8.230000e-98 368.0
28 TraesCS2B01G356300 chr1B 86.695 233 31 0 1189 1421 634998319 634998551 5.170000e-65 259.0
29 TraesCS2B01G356300 chr1B 93.333 75 3 2 4635 4709 153689844 153689772 5.510000e-20 110.0
30 TraesCS2B01G356300 chr1A 83.686 331 45 5 1029 1359 553061372 553061693 2.350000e-78 303.0
31 TraesCS2B01G356300 chr1A 91.304 69 6 0 1350 1418 553066383 553066451 1.540000e-15 95.3
32 TraesCS2B01G356300 chr5D 81.867 375 42 9 67 419 82196938 82196568 5.100000e-75 292.0
33 TraesCS2B01G356300 chr5D 79.525 337 28 22 266 597 82196567 82196267 8.840000e-48 202.0
34 TraesCS2B01G356300 chr5D 93.243 74 4 1 4636 4709 538166860 538166788 1.980000e-19 108.0
35 TraesCS2B01G356300 chr1D 88.106 227 26 1 1195 1421 461785071 461785296 8.590000e-68 268.0
36 TraesCS2B01G356300 chr3B 92.958 71 4 1 4639 4709 667306624 667306693 9.220000e-18 102.0
37 TraesCS2B01G356300 chr5B 91.549 71 5 1 4639 4709 672748259 672748190 4.290000e-16 97.1
38 TraesCS2B01G356300 chr3D 90.541 74 6 1 4636 4709 121536148 121536220 4.290000e-16 97.1
39 TraesCS2B01G356300 chr3A 90.541 74 6 1 4636 4709 158695194 158695266 4.290000e-16 97.1


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 TraesCS2B01G356300 chr2B 508246903 508252106 5203 True 4477.000000 6004 100.000000 1 5204 2 chr2B.!!$R1 5203
1 TraesCS2B01G356300 chr2D 430460532 430465099 4567 True 1150.400000 2503 93.123000 670 5204 5 chr2D.!!$R1 4534
2 TraesCS2B01G356300 chr2A 555820987 555825561 4574 False 902.333333 2100 91.998667 670 5204 6 chr2A.!!$F2 4534
3 TraesCS2B01G356300 chr6D 266955531 266959526 3995 True 432.000000 573 85.473000 1031 4073 2 chr6D.!!$R1 3042
4 TraesCS2B01G356300 chr6A 379658093 379662665 4572 True 432.500000 573 85.592000 1031 4073 2 chr6A.!!$R1 3042
5 TraesCS2B01G356300 chr6B 415036674 415040798 4124 True 427.500000 568 85.313000 1031 4073 2 chr6B.!!$R1 3042
6 TraesCS2B01G356300 chr7A 555476967 555477504 537 False 466.000000 466 83.212000 69 587 1 chr7A.!!$F1 518
7 TraesCS2B01G356300 chr7B 697282926 697283527 601 False 412.000000 412 80.000000 1 589 1 chr7B.!!$F2 588
8 TraesCS2B01G356300 chr5D 82196267 82196938 671 True 247.000000 292 80.696000 67 597 2 chr5D.!!$R2 530

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
423 600 0.106894 CGAAGATTGGGAGGTAGGCC 59.893 60.0 0.0 0.0 0.0 5.19 F
424 601 0.106894 GAAGATTGGGAGGTAGGCCG 59.893 60.0 0.0 0.0 40.5 6.13 F
426 603 0.263765 AGATTGGGAGGTAGGCCGTA 59.736 55.0 0.0 0.0 40.5 4.02 F
780 964 0.389948 CCCACTTACCAGAGACGTGC 60.390 60.0 0.0 0.0 0.0 5.34 F
1921 2130 1.027357 ATTGCGGTCATTCATGCCTC 58.973 50.0 0.0 0.0 0.0 4.70 F
2356 2914 0.250684 AACCATGATGTGACGTGCCA 60.251 50.0 0.0 0.0 0.0 4.92 F
3991 7180 0.035152 TGAAGCGGGTCATTGCAGAT 60.035 50.0 0.0 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1957 2194 0.109532 TCGCCCTCCACATTTGACAA 59.890 50.0 0.00 0.0 0.00 3.18 R
1958 2195 0.109532 TTCGCCCTCCACATTTGACA 59.890 50.0 0.00 0.0 0.00 3.58 R
1963 2200 0.181350 GAGGATTCGCCCTCCACATT 59.819 55.0 0.00 0.0 45.44 2.71 R
1970 2207 0.324738 TCAGACTGAGGATTCGCCCT 60.325 55.0 0.00 0.0 39.77 5.19 R
3164 5958 1.800805 ATGAGCTGACCACAGAAACG 58.199 50.0 0.00 0.0 46.03 3.60 R
4073 7262 0.391130 TTCAGGCGTGCATCAGGTAC 60.391 55.0 0.35 0.0 0.00 3.34 R
4925 8132 0.392998 ACATCCCTGACCGTGCATTC 60.393 55.0 0.00 0.0 0.00 2.67 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
39 40 5.710984 CATAATTACTCCGTCTATCCGCTT 58.289 41.667 0.00 0.00 0.00 4.68
44 45 0.892755 TCCGTCTATCCGCTTGTTGT 59.107 50.000 0.00 0.00 0.00 3.32
45 46 1.274167 TCCGTCTATCCGCTTGTTGTT 59.726 47.619 0.00 0.00 0.00 2.83
61 62 5.083533 TGTTGTTGATTCCAGCAAAACTT 57.916 34.783 0.00 0.00 43.42 2.66
89 90 1.615392 GTTCCAGCTTTTCCACTGCAT 59.385 47.619 0.00 0.00 32.37 3.96
182 183 2.580601 AACGGTCCAGCTAGGCGTT 61.581 57.895 11.71 11.71 40.00 4.84
185 186 1.522569 GGTCCAGCTAGGCGTTGAT 59.477 57.895 0.00 0.00 37.29 2.57
398 575 3.264845 GGGGGAAGTGGGGAGCAA 61.265 66.667 0.00 0.00 0.00 3.91
422 599 0.831307 ACGAAGATTGGGAGGTAGGC 59.169 55.000 0.00 0.00 0.00 3.93
423 600 0.106894 CGAAGATTGGGAGGTAGGCC 59.893 60.000 0.00 0.00 0.00 5.19
424 601 0.106894 GAAGATTGGGAGGTAGGCCG 59.893 60.000 0.00 0.00 40.50 6.13
426 603 0.263765 AGATTGGGAGGTAGGCCGTA 59.736 55.000 0.00 0.00 40.50 4.02
427 604 0.680061 GATTGGGAGGTAGGCCGTAG 59.320 60.000 0.00 0.00 40.50 3.51
458 638 4.408276 CGGTGGAGAAGATAAGGGATAGA 58.592 47.826 0.00 0.00 0.00 1.98
460 640 5.399113 GGTGGAGAAGATAAGGGATAGAGT 58.601 45.833 0.00 0.00 0.00 3.24
521 703 0.813821 GAAGTCTGATTTGCTGGGCC 59.186 55.000 0.00 0.00 0.00 5.80
590 773 2.542824 CGCACCCAAACACTTACCTTTG 60.543 50.000 0.00 0.00 0.00 2.77
592 775 3.118920 GCACCCAAACACTTACCTTTGTT 60.119 43.478 0.00 0.00 37.55 2.83
593 776 4.621983 GCACCCAAACACTTACCTTTGTTT 60.622 41.667 0.00 0.00 44.84 2.83
599 782 4.483476 ACACTTACCTTTGTTTGATCGC 57.517 40.909 0.00 0.00 0.00 4.58
600 783 4.134563 ACACTTACCTTTGTTTGATCGCT 58.865 39.130 0.00 0.00 0.00 4.93
601 784 4.213482 ACACTTACCTTTGTTTGATCGCTC 59.787 41.667 0.00 0.00 0.00 5.03
602 785 3.432252 ACTTACCTTTGTTTGATCGCTCG 59.568 43.478 0.00 0.00 0.00 5.03
603 786 0.517316 ACCTTTGTTTGATCGCTCGC 59.483 50.000 0.00 0.00 0.00 5.03
604 787 0.798776 CCTTTGTTTGATCGCTCGCT 59.201 50.000 0.00 0.00 0.00 4.93
605 788 1.201965 CCTTTGTTTGATCGCTCGCTC 60.202 52.381 0.00 0.00 0.00 5.03
606 789 0.438445 TTTGTTTGATCGCTCGCTCG 59.562 50.000 0.00 0.00 0.00 5.03
607 790 1.955529 TTGTTTGATCGCTCGCTCGC 61.956 55.000 0.00 0.00 0.00 5.03
608 791 2.126110 TTTGATCGCTCGCTCGCA 60.126 55.556 0.00 0.00 0.00 5.10
609 792 1.519234 TTTGATCGCTCGCTCGCAT 60.519 52.632 0.00 0.00 0.00 4.73
610 793 1.083806 TTTGATCGCTCGCTCGCATT 61.084 50.000 0.00 0.00 0.00 3.56
611 794 1.755405 TTGATCGCTCGCTCGCATTG 61.755 55.000 0.00 0.00 0.00 2.82
612 795 3.555264 GATCGCTCGCTCGCATTGC 62.555 63.158 0.00 0.00 0.00 3.56
614 797 3.933498 CGCTCGCTCGCATTGCAT 61.933 61.111 9.69 0.00 0.00 3.96
615 798 2.406401 GCTCGCTCGCATTGCATT 59.594 55.556 9.69 0.00 0.00 3.56
616 799 1.937846 GCTCGCTCGCATTGCATTG 60.938 57.895 9.69 4.20 0.00 2.82
617 800 1.937846 CTCGCTCGCATTGCATTGC 60.938 57.895 20.91 20.91 39.29 3.56
618 801 2.202505 CGCTCGCATTGCATTGCA 60.203 55.556 27.63 7.38 42.91 4.08
619 802 1.587876 CGCTCGCATTGCATTGCAT 60.588 52.632 27.63 0.00 42.91 3.96
620 803 1.807242 CGCTCGCATTGCATTGCATG 61.807 55.000 27.63 20.67 42.91 4.06
621 804 0.526739 GCTCGCATTGCATTGCATGA 60.527 50.000 27.63 18.38 42.91 3.07
622 805 1.477105 CTCGCATTGCATTGCATGAG 58.523 50.000 27.63 22.41 42.91 2.90
623 806 1.064952 CTCGCATTGCATTGCATGAGA 59.935 47.619 27.63 16.66 42.91 3.27
624 807 1.679153 TCGCATTGCATTGCATGAGAT 59.321 42.857 27.63 0.00 42.91 2.75
625 808 2.051423 CGCATTGCATTGCATGAGATC 58.949 47.619 27.63 2.31 42.91 2.75
626 809 2.051423 GCATTGCATTGCATGAGATCG 58.949 47.619 24.71 0.22 42.31 3.69
627 810 2.051423 CATTGCATTGCATGAGATCGC 58.949 47.619 12.95 0.00 38.76 4.58
628 811 1.385528 TTGCATTGCATGAGATCGCT 58.614 45.000 12.95 0.00 38.76 4.93
629 812 0.661020 TGCATTGCATGAGATCGCTG 59.339 50.000 7.38 0.00 31.71 5.18
630 813 0.660595 GCATTGCATGAGATCGCTGC 60.661 55.000 3.15 11.82 36.45 5.25
631 814 0.945099 CATTGCATGAGATCGCTGCT 59.055 50.000 16.93 1.61 36.84 4.24
632 815 1.333931 CATTGCATGAGATCGCTGCTT 59.666 47.619 16.93 6.71 36.84 3.91
633 816 1.456296 TTGCATGAGATCGCTGCTTT 58.544 45.000 16.93 0.00 36.84 3.51
634 817 1.456296 TGCATGAGATCGCTGCTTTT 58.544 45.000 16.93 0.00 36.84 2.27
635 818 1.399440 TGCATGAGATCGCTGCTTTTC 59.601 47.619 16.93 0.00 36.84 2.29
636 819 1.399440 GCATGAGATCGCTGCTTTTCA 59.601 47.619 0.00 0.00 33.15 2.69
637 820 2.539142 GCATGAGATCGCTGCTTTTCAG 60.539 50.000 0.00 0.00 45.62 3.02
638 821 2.749280 TGAGATCGCTGCTTTTCAGA 57.251 45.000 0.00 0.00 45.72 3.27
639 822 3.257469 TGAGATCGCTGCTTTTCAGAT 57.743 42.857 0.00 0.00 45.72 2.90
640 823 3.603532 TGAGATCGCTGCTTTTCAGATT 58.396 40.909 0.00 0.00 45.72 2.40
641 824 3.620374 TGAGATCGCTGCTTTTCAGATTC 59.380 43.478 0.00 0.00 45.72 2.52
642 825 2.941720 AGATCGCTGCTTTTCAGATTCC 59.058 45.455 0.00 0.00 45.72 3.01
643 826 2.183478 TCGCTGCTTTTCAGATTCCA 57.817 45.000 0.00 0.00 45.72 3.53
644 827 1.806542 TCGCTGCTTTTCAGATTCCAC 59.193 47.619 0.00 0.00 45.72 4.02
645 828 1.135575 CGCTGCTTTTCAGATTCCACC 60.136 52.381 0.00 0.00 45.72 4.61
646 829 1.203287 GCTGCTTTTCAGATTCCACCC 59.797 52.381 0.00 0.00 45.72 4.61
647 830 1.470098 CTGCTTTTCAGATTCCACCCG 59.530 52.381 0.00 0.00 45.72 5.28
648 831 1.202879 TGCTTTTCAGATTCCACCCGT 60.203 47.619 0.00 0.00 0.00 5.28
649 832 1.468914 GCTTTTCAGATTCCACCCGTC 59.531 52.381 0.00 0.00 0.00 4.79
650 833 2.876079 GCTTTTCAGATTCCACCCGTCT 60.876 50.000 0.00 0.00 0.00 4.18
651 834 2.762535 TTTCAGATTCCACCCGTCTC 57.237 50.000 0.00 0.00 0.00 3.36
652 835 1.639722 TTCAGATTCCACCCGTCTCA 58.360 50.000 0.00 0.00 0.00 3.27
653 836 1.639722 TCAGATTCCACCCGTCTCAA 58.360 50.000 0.00 0.00 0.00 3.02
654 837 1.275291 TCAGATTCCACCCGTCTCAAC 59.725 52.381 0.00 0.00 0.00 3.18
692 876 5.120053 CACGATTGTACTATTTCTGTGCACA 59.880 40.000 20.37 20.37 30.31 4.57
711 895 2.627699 ACAGACATTGCCGACCATTTTT 59.372 40.909 0.00 0.00 0.00 1.94
736 920 5.699458 TCTTCAACAGAAAAAGATACCCGTC 59.301 40.000 0.00 0.00 0.00 4.79
738 922 2.968675 ACAGAAAAAGATACCCGTCCG 58.031 47.619 0.00 0.00 0.00 4.79
740 924 2.671396 CAGAAAAAGATACCCGTCCGTG 59.329 50.000 0.00 0.00 0.00 4.94
741 925 2.301009 AGAAAAAGATACCCGTCCGTGT 59.699 45.455 0.00 0.00 0.00 4.49
742 926 2.845363 AAAAGATACCCGTCCGTGTT 57.155 45.000 0.00 0.00 0.00 3.32
743 927 2.845363 AAAGATACCCGTCCGTGTTT 57.155 45.000 0.00 0.00 0.00 2.83
744 928 2.375173 AAGATACCCGTCCGTGTTTC 57.625 50.000 0.00 0.00 0.00 2.78
745 929 0.533951 AGATACCCGTCCGTGTTTCC 59.466 55.000 0.00 0.00 0.00 3.13
746 930 0.533951 GATACCCGTCCGTGTTTCCT 59.466 55.000 0.00 0.00 0.00 3.36
750 934 1.512156 CCCGTCCGTGTTTCCTTTGG 61.512 60.000 0.00 0.00 0.00 3.28
768 952 2.527123 TGGTGACGGGCCCACTTA 60.527 61.111 24.92 0.98 35.05 2.24
780 964 0.389948 CCCACTTACCAGAGACGTGC 60.390 60.000 0.00 0.00 0.00 5.34
812 996 2.012554 GCGGAGGAGGCTTTAAAGGTC 61.013 57.143 16.78 1.02 0.00 3.85
813 997 1.278127 CGGAGGAGGCTTTAAAGGTCA 59.722 52.381 16.78 0.00 0.00 4.02
819 1003 3.305403 GGAGGCTTTAAAGGTCAGCAAAC 60.305 47.826 16.78 0.00 35.05 2.93
830 1015 2.545742 GGTCAGCAAACACCCAACAATC 60.546 50.000 0.00 0.00 0.00 2.67
839 1024 1.158007 ACCCAACAATCCCAAGGACT 58.842 50.000 0.00 0.00 32.98 3.85
840 1025 2.041081 CACCCAACAATCCCAAGGACTA 59.959 50.000 0.00 0.00 32.98 2.59
843 1028 3.763897 CCCAACAATCCCAAGGACTAAAG 59.236 47.826 0.00 0.00 32.98 1.85
844 1029 4.407365 CCAACAATCCCAAGGACTAAAGT 58.593 43.478 0.00 0.00 32.98 2.66
852 1037 3.383185 CCCAAGGACTAAAGTGCAAAACA 59.617 43.478 4.39 0.00 38.96 2.83
944 1129 1.629464 GGAATCCTTCCTCCCTCCCTT 60.629 57.143 0.00 0.00 46.57 3.95
947 1132 1.694525 CCTTCCTCCCTCCCTTCCC 60.695 68.421 0.00 0.00 0.00 3.97
952 1141 3.281787 TCCCTCCCTTCCCTCCGT 61.282 66.667 0.00 0.00 0.00 4.69
1229 1418 2.191641 GAGCAGGTCATGGAGGCC 59.808 66.667 0.00 0.00 44.66 5.19
1585 1774 1.193874 CGTTCGCTCCCTGTTGTTTAC 59.806 52.381 0.00 0.00 0.00 2.01
1848 2042 8.756486 TCTGAATTTGTGACCATGATGATATT 57.244 30.769 0.00 0.00 0.00 1.28
1921 2130 1.027357 ATTGCGGTCATTCATGCCTC 58.973 50.000 0.00 0.00 0.00 4.70
1922 2131 1.368345 TTGCGGTCATTCATGCCTCG 61.368 55.000 0.00 0.00 0.00 4.63
1937 2153 5.182950 TCATGCCTCGTAATGTTGAAATTGT 59.817 36.000 0.00 0.00 0.00 2.71
1953 2190 6.726379 TGAAATTGTGGGTAGATCCATGTAA 58.274 36.000 0.00 0.00 39.26 2.41
1954 2191 7.178573 TGAAATTGTGGGTAGATCCATGTAAA 58.821 34.615 0.00 0.00 39.26 2.01
1955 2192 7.671819 TGAAATTGTGGGTAGATCCATGTAAAA 59.328 33.333 0.00 0.00 39.26 1.52
1956 2193 8.608185 AAATTGTGGGTAGATCCATGTAAAAT 57.392 30.769 0.00 0.00 39.26 1.82
1957 2194 8.608185 AATTGTGGGTAGATCCATGTAAAATT 57.392 30.769 0.00 0.00 39.26 1.82
1958 2195 8.608185 ATTGTGGGTAGATCCATGTAAAATTT 57.392 30.769 0.00 0.00 39.26 1.82
1959 2196 7.403312 TGTGGGTAGATCCATGTAAAATTTG 57.597 36.000 0.00 0.00 39.26 2.32
1960 2197 6.951198 TGTGGGTAGATCCATGTAAAATTTGT 59.049 34.615 0.00 0.00 39.26 2.83
1961 2198 7.122055 TGTGGGTAGATCCATGTAAAATTTGTC 59.878 37.037 0.00 0.00 39.26 3.18
1962 2199 7.122055 GTGGGTAGATCCATGTAAAATTTGTCA 59.878 37.037 0.00 0.00 39.26 3.58
1963 2200 7.671819 TGGGTAGATCCATGTAAAATTTGTCAA 59.328 33.333 0.00 0.00 38.11 3.18
1964 2201 8.527810 GGGTAGATCCATGTAAAATTTGTCAAA 58.472 33.333 0.00 0.00 38.11 2.69
1968 2205 9.426837 AGATCCATGTAAAATTTGTCAAATGTG 57.573 29.630 11.54 4.87 0.00 3.21
1969 2206 7.959689 TCCATGTAAAATTTGTCAAATGTGG 57.040 32.000 11.54 12.03 0.00 4.17
1970 2207 7.730084 TCCATGTAAAATTTGTCAAATGTGGA 58.270 30.769 11.54 13.69 0.00 4.02
1971 2208 7.871973 TCCATGTAAAATTTGTCAAATGTGGAG 59.128 33.333 11.54 0.36 0.00 3.86
1972 2209 7.118101 CCATGTAAAATTTGTCAAATGTGGAGG 59.882 37.037 11.54 5.17 0.00 4.30
1973 2210 6.520272 TGTAAAATTTGTCAAATGTGGAGGG 58.480 36.000 11.54 0.00 0.00 4.30
1974 2211 3.683365 AATTTGTCAAATGTGGAGGGC 57.317 42.857 11.54 0.00 0.00 5.19
1975 2212 0.958091 TTTGTCAAATGTGGAGGGCG 59.042 50.000 0.00 0.00 0.00 6.13
2063 2326 3.955650 TGTGGTGTAGCTTAGAAGGTC 57.044 47.619 0.00 0.00 37.92 3.85
2075 2633 7.731882 AGCTTAGAAGGTCTTTTTAGTGAAC 57.268 36.000 0.00 0.00 29.15 3.18
2175 2733 9.687210 GTAATTTCCTTGTTTTCCTCGTTTATT 57.313 29.630 0.00 0.00 0.00 1.40
2176 2734 8.812147 AATTTCCTTGTTTTCCTCGTTTATTC 57.188 30.769 0.00 0.00 0.00 1.75
2177 2735 7.576861 TTTCCTTGTTTTCCTCGTTTATTCT 57.423 32.000 0.00 0.00 0.00 2.40
2178 2736 7.576861 TTCCTTGTTTTCCTCGTTTATTCTT 57.423 32.000 0.00 0.00 0.00 2.52
2179 2737 7.576861 TCCTTGTTTTCCTCGTTTATTCTTT 57.423 32.000 0.00 0.00 0.00 2.52
2180 2738 8.680039 TCCTTGTTTTCCTCGTTTATTCTTTA 57.320 30.769 0.00 0.00 0.00 1.85
2263 2821 9.846248 AACTCATTGCTGAATTTACAAATAGTC 57.154 29.630 0.00 0.00 0.00 2.59
2291 2849 6.575162 AAGTACAAAAATCTGTAGGCCTTG 57.425 37.500 12.58 1.21 32.49 3.61
2293 2851 5.940470 AGTACAAAAATCTGTAGGCCTTGAG 59.060 40.000 12.58 7.58 32.49 3.02
2295 2853 4.082125 CAAAAATCTGTAGGCCTTGAGGT 58.918 43.478 12.58 0.00 37.57 3.85
2299 2857 1.351017 TCTGTAGGCCTTGAGGTTTGG 59.649 52.381 12.58 0.00 37.57 3.28
2300 2858 1.073923 CTGTAGGCCTTGAGGTTTGGT 59.926 52.381 12.58 0.00 37.57 3.67
2301 2859 1.073284 TGTAGGCCTTGAGGTTTGGTC 59.927 52.381 12.58 0.00 37.57 4.02
2302 2860 1.073284 GTAGGCCTTGAGGTTTGGTCA 59.927 52.381 12.58 0.00 37.57 4.02
2303 2861 0.555769 AGGCCTTGAGGTTTGGTCAA 59.444 50.000 0.00 0.00 37.57 3.18
2304 2862 1.063266 AGGCCTTGAGGTTTGGTCAAA 60.063 47.619 0.00 0.00 33.56 2.69
2356 2914 0.250684 AACCATGATGTGACGTGCCA 60.251 50.000 0.00 0.00 0.00 4.92
2390 2948 9.739276 GGTATCATGGATTCTGGATGTATTTAA 57.261 33.333 0.00 0.00 0.00 1.52
2436 2994 1.472480 CTGCCGTCCCAAATAAACAGG 59.528 52.381 0.00 0.00 0.00 4.00
2451 3009 0.916086 ACAGGTGGGTGAACTTGACA 59.084 50.000 0.00 0.00 31.92 3.58
2455 3013 2.154462 GGTGGGTGAACTTGACATCTG 58.846 52.381 0.00 0.00 0.00 2.90
2466 3024 7.276658 GTGAACTTGACATCTGTTGACCTATAG 59.723 40.741 0.00 0.00 0.00 1.31
2480 3038 7.979537 TGTTGACCTATAGATTCATGTGTGTAC 59.020 37.037 0.00 0.00 0.00 2.90
2526 3292 2.178912 TGAGGTTAGCTTGGTTTCCG 57.821 50.000 0.00 0.00 0.00 4.30
2742 5275 2.095718 GGTGATCACGAAGTTTTGCTCC 60.096 50.000 19.33 0.00 41.61 4.70
2871 5404 0.322975 AGTCTTGCCGTGAGATTGCT 59.677 50.000 0.00 0.00 0.00 3.91
3164 5958 6.481644 CAGGAGGTAAGATTTCAGCATACTTC 59.518 42.308 0.00 0.00 0.00 3.01
3179 5973 1.583054 ACTTCGTTTCTGTGGTCAGC 58.417 50.000 0.00 0.00 41.10 4.26
3187 5981 3.599730 TTCTGTGGTCAGCTCATACTG 57.400 47.619 0.00 0.00 41.10 2.74
3208 6002 5.885912 ACTGCGAGTGGTTAATTGGATTAAT 59.114 36.000 0.00 0.00 37.11 1.40
3245 6039 4.520492 AGAAATGCTGGTTAACACTTCCTG 59.480 41.667 8.10 0.00 0.00 3.86
3246 6040 2.270352 TGCTGGTTAACACTTCCTGG 57.730 50.000 8.10 0.00 0.00 4.45
3247 6041 1.493022 TGCTGGTTAACACTTCCTGGT 59.507 47.619 8.10 0.00 0.00 4.00
3248 6042 2.706723 TGCTGGTTAACACTTCCTGGTA 59.293 45.455 8.10 0.00 0.00 3.25
3249 6043 3.329520 TGCTGGTTAACACTTCCTGGTAT 59.670 43.478 8.10 0.00 0.00 2.73
3250 6044 4.202524 TGCTGGTTAACACTTCCTGGTATT 60.203 41.667 8.10 0.00 0.00 1.89
3627 6421 3.876274 GACATGCCTAGTGAGTTCTGA 57.124 47.619 0.00 0.00 0.00 3.27
3652 6454 4.314961 TGTAGTCGCACATGATTTTGACT 58.685 39.130 0.00 7.77 39.73 3.41
3673 6475 3.273434 TCTCATCCGCTCTTTTGGAATG 58.727 45.455 0.00 0.00 37.90 2.67
3805 6994 4.433186 GCATTGTGTTGCAGGTAATGTA 57.567 40.909 13.12 0.00 42.31 2.29
3913 7102 3.386237 GCCCTGCTCCTGTCGTCT 61.386 66.667 0.00 0.00 0.00 4.18
3991 7180 0.035152 TGAAGCGGGTCATTGCAGAT 60.035 50.000 0.00 0.00 0.00 2.90
4073 7262 5.167121 CAGTGATCGCTAATCTGGATTAGG 58.833 45.833 23.44 16.42 46.37 2.69
4121 7310 5.472137 CGATTCTTTTGGAGGACTGGTTTAA 59.528 40.000 0.00 0.00 0.00 1.52
4133 7322 3.819337 GACTGGTTTAAAGGTCCCAACTC 59.181 47.826 0.00 0.00 0.00 3.01
4134 7323 3.154710 CTGGTTTAAAGGTCCCAACTCC 58.845 50.000 0.00 0.00 0.00 3.85
4176 7365 5.618056 ACAGCATTAGATCGGCAATTATG 57.382 39.130 4.91 0.00 0.00 1.90
4180 7371 6.361481 CAGCATTAGATCGGCAATTATGTTTG 59.639 38.462 4.91 0.00 0.00 2.93
4220 7411 3.134804 CCACGAGGATTATTCTTCCCACT 59.865 47.826 0.00 0.00 36.89 4.00
4293 7484 6.327154 GCTACCTTAAATTTAAACGGCATGT 58.673 36.000 11.62 4.11 0.00 3.21
4340 7531 1.484653 TCGTGGTTATCACTCCCATGG 59.515 52.381 4.14 4.14 43.94 3.66
4345 7536 2.561569 GTTATCACTCCCATGGAACCG 58.438 52.381 15.22 0.00 0.00 4.44
4347 7538 0.620410 ATCACTCCCATGGAACCGGA 60.620 55.000 15.22 4.39 0.00 5.14
4352 7543 1.212935 CTCCCATGGAACCGGAAATCT 59.787 52.381 15.22 0.00 0.00 2.40
4364 7555 3.421844 CCGGAAATCTGGTCCTCTTTTT 58.578 45.455 0.00 0.00 37.62 1.94
4365 7556 3.440522 CCGGAAATCTGGTCCTCTTTTTC 59.559 47.826 0.00 0.00 37.62 2.29
4366 7557 4.072131 CGGAAATCTGGTCCTCTTTTTCA 58.928 43.478 0.00 0.00 32.53 2.69
4388 7580 4.471386 CAGGAAAGGGAATCTGGTCTTCTA 59.529 45.833 0.00 0.00 0.00 2.10
4395 7587 4.949856 GGGAATCTGGTCTTCTAAATTGCA 59.050 41.667 0.00 0.00 0.00 4.08
4464 7657 3.721087 AATCCTGTCCCCTGTTACTTG 57.279 47.619 0.00 0.00 0.00 3.16
4467 7660 2.838202 TCCTGTCCCCTGTTACTTGATC 59.162 50.000 0.00 0.00 0.00 2.92
4471 7664 5.045869 CCTGTCCCCTGTTACTTGATCTTTA 60.046 44.000 0.00 0.00 0.00 1.85
4613 7820 8.575589 ACAAAATACATGTGAAATAGTTCAGCA 58.424 29.630 9.11 8.06 44.44 4.41
4620 7827 6.882610 TGTGAAATAGTTCAGCAGTTTGAT 57.117 33.333 5.73 0.00 44.44 2.57
4623 7830 6.798959 GTGAAATAGTTCAGCAGTTTGATGAC 59.201 38.462 5.73 0.00 43.03 3.06
4642 7849 9.950680 TTGATGACATTTCAAAGAAAACTACTC 57.049 29.630 0.00 0.00 34.61 2.59
4643 7850 8.567948 TGATGACATTTCAAAGAAAACTACTCC 58.432 33.333 0.00 0.00 34.61 3.85
4644 7851 7.272037 TGACATTTCAAAGAAAACTACTCCC 57.728 36.000 0.00 0.00 0.00 4.30
4646 7853 7.228706 TGACATTTCAAAGAAAACTACTCCCTC 59.771 37.037 0.00 0.00 0.00 4.30
4647 7854 7.290813 ACATTTCAAAGAAAACTACTCCCTCT 58.709 34.615 0.00 0.00 0.00 3.69
4648 7855 7.229506 ACATTTCAAAGAAAACTACTCCCTCTG 59.770 37.037 0.00 0.00 0.00 3.35
4649 7856 5.888982 TCAAAGAAAACTACTCCCTCTGT 57.111 39.130 0.00 0.00 0.00 3.41
4650 7857 5.855045 TCAAAGAAAACTACTCCCTCTGTC 58.145 41.667 0.00 0.00 0.00 3.51
4651 7858 4.893829 AAGAAAACTACTCCCTCTGTCC 57.106 45.455 0.00 0.00 0.00 4.02
4652 7859 3.174779 AGAAAACTACTCCCTCTGTCCC 58.825 50.000 0.00 0.00 0.00 4.46
4653 7860 1.558233 AAACTACTCCCTCTGTCCCG 58.442 55.000 0.00 0.00 0.00 5.14
4654 7861 0.408700 AACTACTCCCTCTGTCCCGT 59.591 55.000 0.00 0.00 0.00 5.28
4655 7862 1.293062 ACTACTCCCTCTGTCCCGTA 58.707 55.000 0.00 0.00 0.00 4.02
4656 7863 1.637553 ACTACTCCCTCTGTCCCGTAA 59.362 52.381 0.00 0.00 0.00 3.18
4659 7866 1.273098 ACTCCCTCTGTCCCGTAATGT 60.273 52.381 0.00 0.00 0.00 2.71
4661 7868 3.028850 CTCCCTCTGTCCCGTAATGTAA 58.971 50.000 0.00 0.00 0.00 2.41
4662 7869 3.028850 TCCCTCTGTCCCGTAATGTAAG 58.971 50.000 0.00 0.00 0.00 2.34
4663 7870 3.028850 CCCTCTGTCCCGTAATGTAAGA 58.971 50.000 0.00 0.00 0.00 2.10
4664 7871 3.181478 CCCTCTGTCCCGTAATGTAAGAC 60.181 52.174 0.00 0.00 0.00 3.01
4665 7872 3.446161 CCTCTGTCCCGTAATGTAAGACA 59.554 47.826 0.00 0.00 36.16 3.41
4666 7873 4.099573 CCTCTGTCCCGTAATGTAAGACAT 59.900 45.833 0.00 0.00 41.31 3.06
4668 7875 6.045072 TCTGTCCCGTAATGTAAGACATTT 57.955 37.500 9.92 0.00 45.80 2.32
4669 7876 6.469410 TCTGTCCCGTAATGTAAGACATTTT 58.531 36.000 9.92 0.00 45.80 1.82
4670 7877 6.938030 TCTGTCCCGTAATGTAAGACATTTTT 59.062 34.615 9.92 0.00 45.80 1.94
4699 7906 6.787085 ACTACACTAGTGTCAAAAAGCATC 57.213 37.500 31.11 0.00 43.74 3.91
4700 7907 6.525629 ACTACACTAGTGTCAAAAAGCATCT 58.474 36.000 31.11 5.44 43.74 2.90
4701 7908 6.992715 ACTACACTAGTGTCAAAAAGCATCTT 59.007 34.615 31.11 4.99 43.74 2.40
4702 7909 8.148351 ACTACACTAGTGTCAAAAAGCATCTTA 58.852 33.333 31.11 8.36 43.74 2.10
4703 7910 7.986085 ACACTAGTGTCAAAAAGCATCTTAT 57.014 32.000 22.95 0.00 40.24 1.73
4705 7912 9.672673 ACACTAGTGTCAAAAAGCATCTTATAT 57.327 29.630 22.95 0.00 40.24 0.86
4753 7960 3.286751 GCACGCTTGGCAGGAACA 61.287 61.111 0.00 0.00 0.00 3.18
4764 7971 2.093288 TGGCAGGAACAGAGCTAGAATG 60.093 50.000 0.00 0.00 0.00 2.67
4765 7972 2.559440 GCAGGAACAGAGCTAGAATGG 58.441 52.381 0.00 0.00 0.00 3.16
4771 7978 5.045286 AGGAACAGAGCTAGAATGGTGATTT 60.045 40.000 0.00 0.00 0.00 2.17
4776 7983 7.168219 ACAGAGCTAGAATGGTGATTTAACAA 58.832 34.615 0.00 0.00 0.00 2.83
4924 8131 2.571212 TGCCCTTTAGTTGTGTCACAG 58.429 47.619 5.67 0.00 0.00 3.66
4925 8132 1.880027 GCCCTTTAGTTGTGTCACAGG 59.120 52.381 5.67 3.42 0.00 4.00
4927 8134 3.815809 CCCTTTAGTTGTGTCACAGGAA 58.184 45.455 5.67 0.00 0.00 3.36
4929 8136 4.216257 CCCTTTAGTTGTGTCACAGGAATG 59.784 45.833 5.67 4.63 0.00 2.67
4930 8137 4.320494 CCTTTAGTTGTGTCACAGGAATGC 60.320 45.833 5.67 0.00 0.00 3.56
4932 8139 1.949525 AGTTGTGTCACAGGAATGCAC 59.050 47.619 5.67 0.00 0.00 4.57
4933 8140 0.943673 TTGTGTCACAGGAATGCACG 59.056 50.000 5.67 0.00 32.60 5.34
4934 8141 0.884259 TGTGTCACAGGAATGCACGG 60.884 55.000 0.18 0.00 32.60 4.94
4951 8549 4.134563 GCACGGTCAGGGATGTTATAATT 58.865 43.478 0.00 0.00 0.00 1.40
4952 8550 4.578928 GCACGGTCAGGGATGTTATAATTT 59.421 41.667 0.00 0.00 0.00 1.82
4953 8551 5.067283 GCACGGTCAGGGATGTTATAATTTT 59.933 40.000 0.00 0.00 0.00 1.82
4954 8552 6.494842 CACGGTCAGGGATGTTATAATTTTG 58.505 40.000 0.00 0.00 0.00 2.44
4975 8722 3.060602 GCTACTCGTTTCAGCTTTCTGT 58.939 45.455 0.00 0.00 41.10 3.41
4978 8725 1.599071 CTCGTTTCAGCTTTCTGTGCA 59.401 47.619 0.00 0.00 41.10 4.57
4990 8737 0.315251 TCTGTGCACGACTGAAGAGG 59.685 55.000 13.13 0.00 30.10 3.69
4991 8738 0.032678 CTGTGCACGACTGAAGAGGT 59.967 55.000 13.13 0.00 0.00 3.85
4993 8740 0.861837 GTGCACGACTGAAGAGGTTG 59.138 55.000 0.00 0.00 0.00 3.77
5020 8776 0.610232 GCCAAGCCAATCAGTCCAGT 60.610 55.000 0.00 0.00 0.00 4.00
5038 8794 7.173907 CAGTCCAGTCAACTTTGATTTACATCT 59.826 37.037 0.00 0.00 39.73 2.90
5061 8817 1.991965 CACATAACATGCAAAACCGGC 59.008 47.619 0.00 0.00 0.00 6.13
5062 8818 1.615883 ACATAACATGCAAAACCGGCA 59.384 42.857 0.00 0.00 46.66 5.69
5063 8819 2.036475 ACATAACATGCAAAACCGGCAA 59.964 40.909 0.00 0.00 45.60 4.52
5064 8820 3.260740 CATAACATGCAAAACCGGCAAT 58.739 40.909 0.00 0.00 45.60 3.56
5158 8919 0.999406 CAAGTCACCGAAGTATGGCG 59.001 55.000 0.00 0.00 0.00 5.69
5178 8939 3.683281 GCGTTCATGTAGGTAAATCCCCA 60.683 47.826 0.00 0.00 36.75 4.96
5186 8947 5.954757 TGTAGGTAAATCCCCACAAAAGAA 58.045 37.500 0.00 0.00 36.75 2.52
5190 8951 7.387265 AGGTAAATCCCCACAAAAGAAAAAT 57.613 32.000 0.00 0.00 36.75 1.82
5192 8953 8.939932 AGGTAAATCCCCACAAAAGAAAAATTA 58.060 29.630 0.00 0.00 36.75 1.40
5193 8954 9.562408 GGTAAATCCCCACAAAAGAAAAATTAA 57.438 29.630 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.857588 CGGAGTAATTATGCTACCATCGTC 59.142 45.833 0.00 0.00 32.85 4.20
39 40 4.734398 AGTTTTGCTGGAATCAACAACA 57.266 36.364 0.46 0.00 29.77 3.33
44 45 4.309099 GCATGAAGTTTTGCTGGAATCAA 58.691 39.130 0.00 0.00 35.95 2.57
45 46 3.306225 GGCATGAAGTTTTGCTGGAATCA 60.306 43.478 0.00 0.00 38.88 2.57
89 90 1.112315 ACGGGATTTTGCTGCAACCA 61.112 50.000 15.72 5.18 0.00 3.67
145 146 2.886859 GATGTCGGTGCTACATCCG 58.113 57.895 5.14 0.00 44.87 4.18
165 166 2.995574 AACGCCTAGCTGGACCGT 60.996 61.111 9.29 9.29 36.37 4.83
182 183 2.511373 CGCCGTTGCTAGCCATCA 60.511 61.111 13.29 0.00 34.43 3.07
185 186 3.691342 AGACGCCGTTGCTAGCCA 61.691 61.111 13.29 0.00 34.43 4.75
206 207 2.332654 GGCAAGCGGTGGAAACGAT 61.333 57.895 0.00 0.00 0.00 3.73
386 563 1.133915 TCGTTCTTTTGCTCCCCACTT 60.134 47.619 0.00 0.00 0.00 3.16
396 573 3.821033 ACCTCCCAATCTTCGTTCTTTTG 59.179 43.478 0.00 0.00 0.00 2.44
398 575 3.790089 ACCTCCCAATCTTCGTTCTTT 57.210 42.857 0.00 0.00 0.00 2.52
423 600 2.494918 CACCGCTTCTCCCCTACG 59.505 66.667 0.00 0.00 0.00 3.51
424 601 1.677637 CTCCACCGCTTCTCCCCTAC 61.678 65.000 0.00 0.00 0.00 3.18
426 603 2.685380 CTCCACCGCTTCTCCCCT 60.685 66.667 0.00 0.00 0.00 4.79
427 604 2.245438 CTTCTCCACCGCTTCTCCCC 62.245 65.000 0.00 0.00 0.00 4.81
428 605 1.219393 CTTCTCCACCGCTTCTCCC 59.781 63.158 0.00 0.00 0.00 4.30
429 606 0.827368 ATCTTCTCCACCGCTTCTCC 59.173 55.000 0.00 0.00 0.00 3.71
430 607 3.491792 CCTTATCTTCTCCACCGCTTCTC 60.492 52.174 0.00 0.00 0.00 2.87
431 608 2.432510 CCTTATCTTCTCCACCGCTTCT 59.567 50.000 0.00 0.00 0.00 2.85
474 654 1.422950 CGCGTGTATTTACGGTGGGG 61.423 60.000 0.00 0.00 43.87 4.96
478 658 1.199789 TGAGACGCGTGTATTTACGGT 59.800 47.619 20.70 0.00 43.87 4.83
479 659 1.580704 GTGAGACGCGTGTATTTACGG 59.419 52.381 20.70 0.00 43.87 4.02
481 661 2.946133 CGTGAGACGCGTGTATTTAC 57.054 50.000 20.70 9.44 33.65 2.01
503 683 0.613012 GGGCCCAGCAAATCAGACTT 60.613 55.000 19.95 0.00 0.00 3.01
504 684 1.000396 GGGCCCAGCAAATCAGACT 60.000 57.895 19.95 0.00 0.00 3.24
590 773 1.756375 ATGCGAGCGAGCGATCAAAC 61.756 55.000 8.89 0.00 40.67 2.93
592 775 1.519234 AATGCGAGCGAGCGATCAA 60.519 52.632 8.89 0.00 40.67 2.57
593 776 2.104928 AATGCGAGCGAGCGATCA 59.895 55.556 8.89 0.00 40.67 2.92
594 777 2.543383 CAATGCGAGCGAGCGATC 59.457 61.111 0.00 0.00 40.67 3.69
595 778 3.634072 GCAATGCGAGCGAGCGAT 61.634 61.111 0.00 0.00 40.67 4.58
597 780 3.444717 AATGCAATGCGAGCGAGCG 62.445 57.895 0.00 0.00 40.67 5.03
598 781 1.937846 CAATGCAATGCGAGCGAGC 60.938 57.895 0.00 0.00 37.71 5.03
599 782 1.937846 GCAATGCAATGCGAGCGAG 60.938 57.895 11.65 0.00 36.45 5.03
600 783 2.100797 GCAATGCAATGCGAGCGA 59.899 55.556 11.65 0.00 36.45 4.93
606 789 2.051423 CGATCTCATGCAATGCAATGC 58.949 47.619 19.99 19.99 46.21 3.56
607 790 2.051423 GCGATCTCATGCAATGCAATG 58.949 47.619 13.45 11.33 46.21 2.82
608 791 1.954382 AGCGATCTCATGCAATGCAAT 59.046 42.857 13.45 0.00 46.21 3.56
609 792 1.064952 CAGCGATCTCATGCAATGCAA 59.935 47.619 13.45 0.00 46.21 4.08
610 793 0.661020 CAGCGATCTCATGCAATGCA 59.339 50.000 11.44 11.44 46.21 3.96
611 794 0.660595 GCAGCGATCTCATGCAATGC 60.661 55.000 0.00 0.00 46.21 3.56
613 796 1.676746 AAGCAGCGATCTCATGCAAT 58.323 45.000 13.84 2.66 42.45 3.56
614 797 1.456296 AAAGCAGCGATCTCATGCAA 58.544 45.000 13.84 0.00 42.45 4.08
615 798 1.399440 GAAAAGCAGCGATCTCATGCA 59.601 47.619 13.84 0.00 42.45 3.96
616 799 1.399440 TGAAAAGCAGCGATCTCATGC 59.601 47.619 5.74 5.74 40.29 4.06
617 800 2.934553 TCTGAAAAGCAGCGATCTCATG 59.065 45.455 0.00 0.00 44.52 3.07
618 801 3.257469 TCTGAAAAGCAGCGATCTCAT 57.743 42.857 0.00 0.00 44.52 2.90
619 802 2.749280 TCTGAAAAGCAGCGATCTCA 57.251 45.000 0.00 0.00 44.52 3.27
620 803 3.002144 GGAATCTGAAAAGCAGCGATCTC 59.998 47.826 0.00 0.00 44.52 2.75
621 804 2.941720 GGAATCTGAAAAGCAGCGATCT 59.058 45.455 0.00 0.00 44.52 2.75
622 805 2.679837 TGGAATCTGAAAAGCAGCGATC 59.320 45.455 0.00 0.00 44.52 3.69
623 806 2.421424 GTGGAATCTGAAAAGCAGCGAT 59.579 45.455 0.00 0.00 44.52 4.58
624 807 1.806542 GTGGAATCTGAAAAGCAGCGA 59.193 47.619 0.00 0.00 44.52 4.93
625 808 1.135575 GGTGGAATCTGAAAAGCAGCG 60.136 52.381 0.00 0.00 44.52 5.18
626 809 1.203287 GGGTGGAATCTGAAAAGCAGC 59.797 52.381 0.00 0.00 44.52 5.25
627 810 1.470098 CGGGTGGAATCTGAAAAGCAG 59.530 52.381 0.00 0.00 46.31 4.24
628 811 1.202879 ACGGGTGGAATCTGAAAAGCA 60.203 47.619 0.00 0.00 0.00 3.91
629 812 1.468914 GACGGGTGGAATCTGAAAAGC 59.531 52.381 0.00 0.00 0.00 3.51
630 813 3.003480 GAGACGGGTGGAATCTGAAAAG 58.997 50.000 0.00 0.00 0.00 2.27
631 814 2.370519 TGAGACGGGTGGAATCTGAAAA 59.629 45.455 0.00 0.00 0.00 2.29
632 815 1.974957 TGAGACGGGTGGAATCTGAAA 59.025 47.619 0.00 0.00 0.00 2.69
633 816 1.639722 TGAGACGGGTGGAATCTGAA 58.360 50.000 0.00 0.00 0.00 3.02
634 817 1.275291 GTTGAGACGGGTGGAATCTGA 59.725 52.381 0.00 0.00 0.00 3.27
635 818 1.726853 GTTGAGACGGGTGGAATCTG 58.273 55.000 0.00 0.00 0.00 2.90
636 819 0.246635 CGTTGAGACGGGTGGAATCT 59.753 55.000 0.00 0.00 45.32 2.40
637 820 2.750815 CGTTGAGACGGGTGGAATC 58.249 57.895 0.00 0.00 45.32 2.52
655 838 2.671396 ACAATCGTGCTGATACGGAAAC 59.329 45.455 0.00 0.00 43.85 2.78
656 839 2.967362 ACAATCGTGCTGATACGGAAA 58.033 42.857 0.00 0.00 43.85 3.13
657 840 2.665649 ACAATCGTGCTGATACGGAA 57.334 45.000 0.00 0.00 43.85 4.30
658 841 2.686405 AGTACAATCGTGCTGATACGGA 59.314 45.455 0.00 0.00 43.85 4.69
659 842 3.079960 AGTACAATCGTGCTGATACGG 57.920 47.619 0.00 0.00 43.85 4.02
660 843 6.637254 AGAAATAGTACAATCGTGCTGATACG 59.363 38.462 0.00 0.00 44.98 3.06
661 844 7.435488 ACAGAAATAGTACAATCGTGCTGATAC 59.565 37.037 0.00 0.00 38.66 2.24
662 845 7.435192 CACAGAAATAGTACAATCGTGCTGATA 59.565 37.037 0.00 0.00 38.66 2.15
663 846 6.256539 CACAGAAATAGTACAATCGTGCTGAT 59.743 38.462 0.00 0.00 38.66 2.90
664 847 5.576774 CACAGAAATAGTACAATCGTGCTGA 59.423 40.000 0.00 0.00 38.66 4.26
665 848 5.725042 GCACAGAAATAGTACAATCGTGCTG 60.725 44.000 18.06 0.00 42.88 4.41
666 849 4.330074 GCACAGAAATAGTACAATCGTGCT 59.670 41.667 18.06 0.00 42.88 4.40
667 850 4.092821 TGCACAGAAATAGTACAATCGTGC 59.907 41.667 18.26 18.26 45.58 5.34
668 851 5.120053 TGTGCACAGAAATAGTACAATCGTG 59.880 40.000 17.42 0.00 0.00 4.35
711 895 6.059484 ACGGGTATCTTTTTCTGTTGAAGAA 58.941 36.000 0.00 0.00 43.37 2.52
714 898 4.758165 GGACGGGTATCTTTTTCTGTTGAA 59.242 41.667 0.00 0.00 0.00 2.69
715 899 4.320870 GGACGGGTATCTTTTTCTGTTGA 58.679 43.478 0.00 0.00 0.00 3.18
716 900 3.124636 CGGACGGGTATCTTTTTCTGTTG 59.875 47.826 0.00 0.00 0.00 3.33
720 904 2.301009 ACACGGACGGGTATCTTTTTCT 59.699 45.455 0.00 0.00 0.00 2.52
726 910 0.533951 GGAAACACGGACGGGTATCT 59.466 55.000 0.00 0.00 0.00 1.98
727 911 0.533951 AGGAAACACGGACGGGTATC 59.466 55.000 0.00 0.00 0.00 2.24
731 915 1.512156 CCAAAGGAAACACGGACGGG 61.512 60.000 0.00 0.00 0.00 5.28
736 920 0.383949 CACCACCAAAGGAAACACGG 59.616 55.000 0.00 0.00 0.00 4.94
738 922 1.064952 CGTCACCACCAAAGGAAACAC 59.935 52.381 0.00 0.00 0.00 3.32
740 924 0.666374 CCGTCACCACCAAAGGAAAC 59.334 55.000 0.00 0.00 0.00 2.78
741 925 0.466555 CCCGTCACCACCAAAGGAAA 60.467 55.000 0.00 0.00 0.00 3.13
742 926 1.149627 CCCGTCACCACCAAAGGAA 59.850 57.895 0.00 0.00 0.00 3.36
743 927 2.833227 CCCGTCACCACCAAAGGA 59.167 61.111 0.00 0.00 0.00 3.36
744 928 2.983592 GCCCGTCACCACCAAAGG 60.984 66.667 0.00 0.00 0.00 3.11
745 929 2.983592 GGCCCGTCACCACCAAAG 60.984 66.667 0.00 0.00 0.00 2.77
746 930 4.589675 GGGCCCGTCACCACCAAA 62.590 66.667 5.69 0.00 0.00 3.28
764 948 0.889306 GAGGCACGTCTCTGGTAAGT 59.111 55.000 0.00 0.00 0.00 2.24
768 952 0.613292 ATGAGAGGCACGTCTCTGGT 60.613 55.000 18.20 5.25 43.51 4.00
780 964 0.826715 TCCTCCGCAAGAATGAGAGG 59.173 55.000 8.32 8.32 43.02 3.69
812 996 1.270252 GGGATTGTTGGGTGTTTGCTG 60.270 52.381 0.00 0.00 0.00 4.41
813 997 1.047801 GGGATTGTTGGGTGTTTGCT 58.952 50.000 0.00 0.00 0.00 3.91
819 1003 1.203050 AGTCCTTGGGATTGTTGGGTG 60.203 52.381 0.00 0.00 32.73 4.61
830 1015 3.383185 TGTTTTGCACTTTAGTCCTTGGG 59.617 43.478 0.00 0.00 0.00 4.12
839 1024 4.981806 ACTTGAGCTGTTTTGCACTTTA 57.018 36.364 0.00 0.00 34.99 1.85
840 1025 3.874392 ACTTGAGCTGTTTTGCACTTT 57.126 38.095 0.00 0.00 34.99 2.66
843 1028 3.971032 ACTACTTGAGCTGTTTTGCAC 57.029 42.857 0.00 0.00 34.99 4.57
844 1029 3.813166 GGTACTACTTGAGCTGTTTTGCA 59.187 43.478 0.00 0.00 34.99 4.08
852 1037 3.301274 GGAGATGGGTACTACTTGAGCT 58.699 50.000 0.00 0.00 0.00 4.09
1289 1478 3.338676 GATTCGATGACGGCGGGC 61.339 66.667 13.24 3.01 40.21 6.13
1304 1493 2.045438 TTGTTGCGGCGGATGGAT 60.045 55.556 9.78 0.00 0.00 3.41
1585 1774 5.738909 AGGTCTGAAGGTGAATCATGTAAG 58.261 41.667 0.00 0.00 0.00 2.34
1696 1885 7.648039 AACTCTCCTCTTAACCATGTACTAG 57.352 40.000 0.00 0.00 0.00 2.57
1921 2130 6.489127 TCTACCCACAATTTCAACATTACG 57.511 37.500 0.00 0.00 0.00 3.18
1922 2131 7.122055 TGGATCTACCCACAATTTCAACATTAC 59.878 37.037 0.00 0.00 38.00 1.89
1937 2153 7.178573 TGACAAATTTTACATGGATCTACCCA 58.821 34.615 0.00 0.00 41.05 4.51
1953 2190 3.554752 CGCCCTCCACATTTGACAAATTT 60.555 43.478 10.77 2.09 0.00 1.82
1954 2191 2.029110 CGCCCTCCACATTTGACAAATT 60.029 45.455 10.77 0.94 0.00 1.82
1955 2192 1.545582 CGCCCTCCACATTTGACAAAT 59.454 47.619 7.62 7.62 0.00 2.32
1956 2193 0.958091 CGCCCTCCACATTTGACAAA 59.042 50.000 2.48 2.48 0.00 2.83
1957 2194 0.109532 TCGCCCTCCACATTTGACAA 59.890 50.000 0.00 0.00 0.00 3.18
1958 2195 0.109532 TTCGCCCTCCACATTTGACA 59.890 50.000 0.00 0.00 0.00 3.58
1959 2196 1.401905 GATTCGCCCTCCACATTTGAC 59.598 52.381 0.00 0.00 0.00 3.18
1960 2197 1.681780 GGATTCGCCCTCCACATTTGA 60.682 52.381 0.00 0.00 32.72 2.69
1961 2198 0.740737 GGATTCGCCCTCCACATTTG 59.259 55.000 0.00 0.00 32.72 2.32
1962 2199 0.625849 AGGATTCGCCCTCCACATTT 59.374 50.000 0.00 0.00 37.37 2.32
1963 2200 0.181350 GAGGATTCGCCCTCCACATT 59.819 55.000 0.00 0.00 45.44 2.71
1964 2201 1.832912 GAGGATTCGCCCTCCACAT 59.167 57.895 0.00 0.00 45.44 3.21
1965 2202 3.309582 GAGGATTCGCCCTCCACA 58.690 61.111 0.00 0.00 45.44 4.17
1970 2207 0.324738 TCAGACTGAGGATTCGCCCT 60.325 55.000 0.00 0.00 39.77 5.19
1971 2208 0.755686 ATCAGACTGAGGATTCGCCC 59.244 55.000 11.52 0.00 37.37 6.13
1972 2209 2.478831 GAATCAGACTGAGGATTCGCC 58.521 52.381 11.52 0.00 39.78 5.54
1975 2212 3.118482 TGCCAGAATCAGACTGAGGATTC 60.118 47.826 11.52 9.85 46.15 2.52
2075 2633 9.410556 CCAATAGTTCAGTTAAATTGGTTTCTG 57.589 33.333 4.57 0.00 41.00 3.02
2208 2766 3.441163 CAAGTCAAGCGCAAATGCATAT 58.559 40.909 11.47 0.00 42.21 1.78
2263 2821 9.614792 AGGCCTACAGATTTTTGTACTTATTAG 57.385 33.333 1.29 0.00 32.56 1.73
2293 2851 7.593644 GTGTATTCTACATTGTTTGACCAAACC 59.406 37.037 19.28 5.88 43.73 3.27
2295 2853 8.349245 CAGTGTATTCTACATTGTTTGACCAAA 58.651 33.333 0.00 0.00 40.31 3.28
2356 2914 5.457197 CCAGAATCCATGATACCAACCTCAT 60.457 44.000 0.00 0.00 32.37 2.90
2390 2948 5.375655 ACCTATTGGCTATTATTTCCTGGGT 59.624 40.000 0.00 0.00 36.63 4.51
2436 2994 2.851195 ACAGATGTCAAGTTCACCCAC 58.149 47.619 0.00 0.00 0.00 4.61
2451 3009 7.930325 CACACATGAATCTATAGGTCAACAGAT 59.070 37.037 0.00 0.00 0.00 2.90
2455 3013 7.167635 CGTACACACATGAATCTATAGGTCAAC 59.832 40.741 0.00 3.48 0.00 3.18
2466 3024 7.169140 TGTTGATATAGCGTACACACATGAATC 59.831 37.037 0.00 0.00 0.00 2.52
2480 3038 9.143631 TGATATTCATGTTCTGTTGATATAGCG 57.856 33.333 0.00 0.00 0.00 4.26
2641 4468 5.459762 CACAAGTCGAGCAATTGTTTTCATT 59.540 36.000 7.40 0.00 35.04 2.57
2742 5275 3.549299 GCATATTTGGCAATCCTCTCG 57.451 47.619 0.00 0.00 0.00 4.04
3164 5958 1.800805 ATGAGCTGACCACAGAAACG 58.199 50.000 0.00 0.00 46.03 3.60
3179 5973 4.271049 CCAATTAACCACTCGCAGTATGAG 59.729 45.833 0.00 0.00 39.69 2.90
3187 5981 7.860872 CCTAAATTAATCCAATTAACCACTCGC 59.139 37.037 0.00 0.00 37.53 5.03
3208 6002 2.223249 GCATTTCTCGCAATCGCCTAAA 60.223 45.455 0.00 0.00 35.26 1.85
3620 6414 2.361119 TGTGCGACTACAACTCAGAACT 59.639 45.455 0.00 0.00 0.00 3.01
3621 6415 2.739292 TGTGCGACTACAACTCAGAAC 58.261 47.619 0.00 0.00 0.00 3.01
3622 6416 3.005367 TCATGTGCGACTACAACTCAGAA 59.995 43.478 0.00 0.00 33.69 3.02
3623 6417 2.556622 TCATGTGCGACTACAACTCAGA 59.443 45.455 0.00 0.00 33.69 3.27
3624 6418 2.946564 TCATGTGCGACTACAACTCAG 58.053 47.619 0.00 0.00 33.69 3.35
3625 6419 3.592898 ATCATGTGCGACTACAACTCA 57.407 42.857 0.00 0.00 33.69 3.41
3626 6420 4.928661 AAATCATGTGCGACTACAACTC 57.071 40.909 0.00 0.00 33.69 3.01
3627 6421 4.754618 TCAAAATCATGTGCGACTACAACT 59.245 37.500 0.00 0.00 33.69 3.16
3652 6454 3.055167 TCATTCCAAAAGAGCGGATGAGA 60.055 43.478 0.00 0.00 0.00 3.27
3805 6994 1.817087 AGATGGCATGATCCTGACCT 58.183 50.000 3.81 0.00 0.00 3.85
3913 7102 3.181484 GCAAATGCCTCAACATCATAGCA 60.181 43.478 0.00 0.00 34.31 3.49
3991 7180 1.771854 TCCTTTGTCCTGTACTTGCCA 59.228 47.619 0.00 0.00 0.00 4.92
4073 7262 0.391130 TTCAGGCGTGCATCAGGTAC 60.391 55.000 0.35 0.00 0.00 3.34
4121 7310 1.059913 CACTCAGGAGTTGGGACCTT 58.940 55.000 0.00 0.00 40.20 3.50
4159 7348 8.450578 TTCTCAAACATAATTGCCGATCTAAT 57.549 30.769 0.00 0.00 0.00 1.73
4176 7365 7.090808 GTGGGTTCCTCAATTATTTCTCAAAC 58.909 38.462 0.00 0.00 0.00 2.93
4180 7371 5.183228 TCGTGGGTTCCTCAATTATTTCTC 58.817 41.667 0.00 0.00 0.00 2.87
4194 7385 4.127907 GGAAGAATAATCCTCGTGGGTTC 58.872 47.826 5.05 4.84 37.86 3.62
4220 7411 6.294286 GGTGTTTTGCCTTGCTACAAAGTATA 60.294 38.462 0.00 0.00 37.11 1.47
4340 7531 1.555533 AGAGGACCAGATTTCCGGTTC 59.444 52.381 0.00 0.00 38.29 3.62
4345 7536 4.460731 CCTGAAAAAGAGGACCAGATTTCC 59.539 45.833 0.00 0.00 31.48 3.13
4347 7538 5.324832 TCCTGAAAAAGAGGACCAGATTT 57.675 39.130 0.00 0.00 34.49 2.17
4352 7543 3.436470 CCCTTTCCTGAAAAAGAGGACCA 60.436 47.826 0.00 0.00 39.44 4.02
4364 7555 2.921221 AGACCAGATTCCCTTTCCTGA 58.079 47.619 0.00 0.00 0.00 3.86
4365 7556 3.265479 AGAAGACCAGATTCCCTTTCCTG 59.735 47.826 0.00 0.00 0.00 3.86
4366 7557 3.536287 AGAAGACCAGATTCCCTTTCCT 58.464 45.455 0.00 0.00 0.00 3.36
4388 7580 3.991773 GACAGTGACATGCATTGCAATTT 59.008 39.130 16.46 2.43 43.62 1.82
4395 7587 5.010314 ACAAAATCTGACAGTGACATGCATT 59.990 36.000 0.00 0.00 0.00 3.56
4556 7763 9.829507 TGACTACCATGTTTTTGATTTTGAATT 57.170 25.926 0.00 0.00 0.00 2.17
4558 7765 9.474920 GATGACTACCATGTTTTTGATTTTGAA 57.525 29.630 0.00 0.00 35.17 2.69
4559 7766 8.637099 TGATGACTACCATGTTTTTGATTTTGA 58.363 29.630 0.00 0.00 35.17 2.69
4560 7767 8.815141 TGATGACTACCATGTTTTTGATTTTG 57.185 30.769 0.00 0.00 35.17 2.44
4561 7768 9.829507 TTTGATGACTACCATGTTTTTGATTTT 57.170 25.926 0.00 0.00 35.17 1.82
4571 7778 8.402798 TGTATTTTGTTTGATGACTACCATGT 57.597 30.769 0.00 0.00 35.17 3.21
4620 7827 7.060421 AGGGAGTAGTTTTCTTTGAAATGTCA 58.940 34.615 0.00 0.00 0.00 3.58
4623 7830 7.229506 ACAGAGGGAGTAGTTTTCTTTGAAATG 59.770 37.037 0.00 0.00 0.00 2.32
4641 7848 2.832643 TACATTACGGGACAGAGGGA 57.167 50.000 0.00 0.00 0.00 4.20
4642 7849 3.028850 TCTTACATTACGGGACAGAGGG 58.971 50.000 0.00 0.00 0.00 4.30
4643 7850 3.446161 TGTCTTACATTACGGGACAGAGG 59.554 47.826 0.00 0.00 33.74 3.69
4644 7851 4.713824 TGTCTTACATTACGGGACAGAG 57.286 45.455 0.00 0.00 33.74 3.35
4676 7883 6.525629 AGATGCTTTTTGACACTAGTGTAGT 58.474 36.000 27.98 6.32 45.05 2.73
4677 7884 7.426929 AAGATGCTTTTTGACACTAGTGTAG 57.573 36.000 27.98 20.94 45.05 2.74
4753 7960 8.814038 AATTGTTAAATCACCATTCTAGCTCT 57.186 30.769 0.00 0.00 0.00 4.09
4924 8131 1.097547 CATCCCTGACCGTGCATTCC 61.098 60.000 0.00 0.00 0.00 3.01
4925 8132 0.392998 ACATCCCTGACCGTGCATTC 60.393 55.000 0.00 0.00 0.00 2.67
4927 8134 0.908910 TAACATCCCTGACCGTGCAT 59.091 50.000 0.00 0.00 0.00 3.96
4929 8136 2.902705 TATAACATCCCTGACCGTGC 57.097 50.000 0.00 0.00 0.00 5.34
4930 8137 6.494842 CAAAATTATAACATCCCTGACCGTG 58.505 40.000 0.00 0.00 0.00 4.94
4932 8139 5.299279 AGCAAAATTATAACATCCCTGACCG 59.701 40.000 0.00 0.00 0.00 4.79
4933 8140 6.715347 AGCAAAATTATAACATCCCTGACC 57.285 37.500 0.00 0.00 0.00 4.02
4934 8141 8.451908 AGTAGCAAAATTATAACATCCCTGAC 57.548 34.615 0.00 0.00 0.00 3.51
4951 8549 4.024893 CAGAAAGCTGAAACGAGTAGCAAA 60.025 41.667 0.00 0.00 45.17 3.68
4952 8550 3.494626 CAGAAAGCTGAAACGAGTAGCAA 59.505 43.478 0.00 0.00 45.17 3.91
4953 8551 3.059884 CAGAAAGCTGAAACGAGTAGCA 58.940 45.455 0.00 0.00 45.17 3.49
4954 8552 3.060602 ACAGAAAGCTGAAACGAGTAGC 58.939 45.455 0.00 0.00 45.17 3.58
4975 8722 0.750249 TCAACCTCTTCAGTCGTGCA 59.250 50.000 0.00 0.00 0.00 4.57
4978 8725 1.000283 CAGCTCAACCTCTTCAGTCGT 60.000 52.381 0.00 0.00 0.00 4.34
4990 8737 2.338785 GGCTTGGCCTCAGCTCAAC 61.339 63.158 22.31 6.60 46.69 3.18
4991 8738 2.034687 GGCTTGGCCTCAGCTCAA 59.965 61.111 22.31 0.00 46.69 3.02
5011 8767 6.353323 TGTAAATCAAAGTTGACTGGACTGA 58.647 36.000 0.00 0.00 40.49 3.41
5020 8776 7.036996 TGTGCAAGATGTAAATCAAAGTTGA 57.963 32.000 0.00 0.00 42.14 3.18
5091 8848 8.181573 TGGAACTTGAAATGAATAGCGTTTATC 58.818 33.333 0.00 0.00 35.89 1.75
5093 8850 7.441890 TGGAACTTGAAATGAATAGCGTTTA 57.558 32.000 0.00 0.00 35.89 2.01
5103 8860 3.505680 CCGGTCATTGGAACTTGAAATGA 59.494 43.478 0.00 0.00 37.84 2.57
5158 8919 4.850680 TGTGGGGATTTACCTACATGAAC 58.149 43.478 0.00 0.00 45.57 3.18


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

AutoCloner maintained by Alex Coulton.