Multiple sequence alignment - TraesCS2B01G598100

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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 TraesCS2B01G598100 chr2B 100.000 3459 0 0 1 3459 781086447 781082989 0.000000e+00 6388.0
1 TraesCS2B01G598100 chr2B 91.308 2508 141 45 969 3445 781150279 781152740 0.000000e+00 3352.0
2 TraesCS2B01G598100 chr2B 84.859 2021 205 46 969 2910 780874602 780872604 0.000000e+00 1943.0
3 TraesCS2B01G598100 chr2B 88.130 1449 117 26 1438 2863 780829667 780828251 0.000000e+00 1672.0
4 TraesCS2B01G598100 chr2B 95.724 421 17 1 554 973 781245904 781245484 0.000000e+00 676.0
5 TraesCS2B01G598100 chr2B 84.687 431 50 10 2987 3401 780872586 780872156 1.920000e-112 416.0
6 TraesCS2B01G598100 chr2A 90.397 1614 125 13 969 2572 776170225 776168632 0.000000e+00 2095.0
7 TraesCS2B01G598100 chr2A 86.268 1624 161 28 969 2566 776213495 776215082 0.000000e+00 1707.0
8 TraesCS2B01G598100 chr2A 91.968 249 19 1 2987 3234 776168251 776168003 7.110000e-92 348.0
9 TraesCS2B01G598100 chr2A 88.202 178 14 7 2576 2751 776168660 776168488 4.530000e-49 206.0
10 TraesCS2B01G598100 chr2A 95.868 121 5 0 2576 2696 776215060 776215180 2.720000e-46 196.0
11 TraesCS2B01G598100 chr2A 84.158 202 21 8 2797 2989 776168479 776168280 5.900000e-43 185.0
12 TraesCS2B01G598100 chr2A 90.000 120 11 1 595 714 776211152 776211270 1.660000e-33 154.0
13 TraesCS2B01G598100 chr2A 98.148 54 1 0 554 607 776205851 776205904 1.020000e-15 95.3
14 TraesCS2B01G598100 chr6D 86.719 1649 171 25 969 2581 69108147 69106511 0.000000e+00 1788.0
15 TraesCS2B01G598100 chr6D 81.644 1618 219 42 969 2567 458990240 458988682 0.000000e+00 1271.0
16 TraesCS2B01G598100 chr6D 81.123 1621 234 36 969 2567 459063865 459062295 0.000000e+00 1232.0
17 TraesCS2B01G598100 chr6D 94.643 56 3 0 2574 2629 69106493 69106438 1.710000e-13 87.9
18 TraesCS2B01G598100 chr2D 86.322 1645 177 24 969 2578 117631812 117633443 0.000000e+00 1748.0
19 TraesCS2B01G598100 chr2D 86.109 1663 159 24 1260 2865 651422738 651421091 0.000000e+00 1725.0
20 TraesCS2B01G598100 chr2D 87.139 1384 148 18 969 2334 651432309 651433680 0.000000e+00 1543.0
21 TraesCS2B01G598100 chr2D 83.307 1258 141 31 969 2192 651575345 651576567 0.000000e+00 1096.0
22 TraesCS2B01G598100 chr2D 86.454 251 31 2 2987 3234 651527957 651528207 4.400000e-69 272.0
23 TraesCS2B01G598100 chr2D 89.313 131 13 1 2987 3116 651490458 651490588 2.760000e-36 163.0
24 TraesCS2B01G598100 chr2D 94.643 56 3 0 2574 2629 117633464 117633519 1.710000e-13 87.9
25 TraesCS2B01G598100 chr2D 94.545 55 3 0 3180 3234 651598142 651598196 6.150000e-13 86.1
26 TraesCS2B01G598100 chr4A 80.848 1556 222 37 969 2478 632616301 632617826 0.000000e+00 1153.0
27 TraesCS2B01G598100 chr4A 86.000 150 21 0 3012 3161 616703693 616703842 9.930000e-36 161.0
28 TraesCS2B01G598100 chr5B 79.234 1541 251 44 969 2478 703858883 703857381 0.000000e+00 1009.0
29 TraesCS2B01G598100 chr5B 86.777 121 16 0 3027 3147 699609346 699609226 6.020000e-28 135.0
30 TraesCS2B01G598100 chr5B 89.474 57 4 2 3123 3178 699635879 699635824 1.720000e-08 71.3
31 TraesCS2B01G598100 chr6B 99.096 553 4 1 1 553 716377660 716378211 0.000000e+00 992.0
32 TraesCS2B01G598100 chrUn 98.915 553 5 1 1 553 220114040 220114591 0.000000e+00 987.0
33 TraesCS2B01G598100 chr1B 98.915 553 5 1 1 553 665164408 665164959 0.000000e+00 987.0
34 TraesCS2B01G598100 chr1B 98.736 554 5 2 1 553 665183101 665183653 0.000000e+00 983.0
35 TraesCS2B01G598100 chr1B 98.205 557 8 2 1 556 665210021 665210576 0.000000e+00 972.0
36 TraesCS2B01G598100 chr1B 97.148 561 7 5 1 553 665148285 665148844 0.000000e+00 939.0
37 TraesCS2B01G598100 chr1B 93.972 564 18 3 1 555 4532076 4532632 0.000000e+00 839.0
38 TraesCS2B01G598100 chr1B 90.710 183 17 0 791 973 559587367 559587549 9.590000e-61 244.0
39 TraesCS2B01G598100 chr5A 98.556 554 6 2 1 553 629316706 629317258 0.000000e+00 977.0
40 TraesCS2B01G598100 chr5A 98.553 553 7 1 1 553 629335614 629336165 0.000000e+00 976.0
41 TraesCS2B01G598100 chr5D 85.075 134 20 0 3014 3147 551407149 551407016 1.670000e-28 137.0


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 TraesCS2B01G598100 chr2B 781082989 781086447 3458 True 6388.000000 6388 100.00000 1 3459 1 chr2B.!!$R2 3458
1 TraesCS2B01G598100 chr2B 781150279 781152740 2461 False 3352.000000 3352 91.30800 969 3445 1 chr2B.!!$F1 2476
2 TraesCS2B01G598100 chr2B 780828251 780829667 1416 True 1672.000000 1672 88.13000 1438 2863 1 chr2B.!!$R1 1425
3 TraesCS2B01G598100 chr2B 780872156 780874602 2446 True 1179.500000 1943 84.77300 969 3401 2 chr2B.!!$R4 2432
4 TraesCS2B01G598100 chr2A 776168003 776170225 2222 True 708.500000 2095 88.68125 969 3234 4 chr2A.!!$R1 2265
5 TraesCS2B01G598100 chr2A 776211152 776215180 4028 False 685.666667 1707 90.71200 595 2696 3 chr2A.!!$F2 2101
6 TraesCS2B01G598100 chr6D 458988682 458990240 1558 True 1271.000000 1271 81.64400 969 2567 1 chr6D.!!$R1 1598
7 TraesCS2B01G598100 chr6D 459062295 459063865 1570 True 1232.000000 1232 81.12300 969 2567 1 chr6D.!!$R2 1598
8 TraesCS2B01G598100 chr6D 69106438 69108147 1709 True 937.950000 1788 90.68100 969 2629 2 chr6D.!!$R3 1660
9 TraesCS2B01G598100 chr2D 651421091 651422738 1647 True 1725.000000 1725 86.10900 1260 2865 1 chr2D.!!$R1 1605
10 TraesCS2B01G598100 chr2D 651432309 651433680 1371 False 1543.000000 1543 87.13900 969 2334 1 chr2D.!!$F1 1365
11 TraesCS2B01G598100 chr2D 651575345 651576567 1222 False 1096.000000 1096 83.30700 969 2192 1 chr2D.!!$F4 1223
12 TraesCS2B01G598100 chr2D 117631812 117633519 1707 False 917.950000 1748 90.48250 969 2629 2 chr2D.!!$F6 1660
13 TraesCS2B01G598100 chr4A 632616301 632617826 1525 False 1153.000000 1153 80.84800 969 2478 1 chr4A.!!$F2 1509
14 TraesCS2B01G598100 chr5B 703857381 703858883 1502 True 1009.000000 1009 79.23400 969 2478 1 chr5B.!!$R3 1509
15 TraesCS2B01G598100 chr6B 716377660 716378211 551 False 992.000000 992 99.09600 1 553 1 chr6B.!!$F1 552
16 TraesCS2B01G598100 chrUn 220114040 220114591 551 False 987.000000 987 98.91500 1 553 1 chrUn.!!$F1 552
17 TraesCS2B01G598100 chr1B 665164408 665164959 551 False 987.000000 987 98.91500 1 553 1 chr1B.!!$F4 552
18 TraesCS2B01G598100 chr1B 665183101 665183653 552 False 983.000000 983 98.73600 1 553 1 chr1B.!!$F5 552
19 TraesCS2B01G598100 chr1B 665210021 665210576 555 False 972.000000 972 98.20500 1 556 1 chr1B.!!$F6 555
20 TraesCS2B01G598100 chr1B 665148285 665148844 559 False 939.000000 939 97.14800 1 553 1 chr1B.!!$F3 552
21 TraesCS2B01G598100 chr1B 4532076 4532632 556 False 839.000000 839 93.97200 1 555 1 chr1B.!!$F1 554
22 TraesCS2B01G598100 chr5A 629316706 629317258 552 False 977.000000 977 98.55600 1 553 1 chr5A.!!$F1 552
23 TraesCS2B01G598100 chr5A 629335614 629336165 551 False 976.000000 976 98.55300 1 553 1 chr5A.!!$F2 552

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
849 1288 0.031010 ACTCCCACCATCCCTCTACC 60.031 60.0 0.0 0.0 0.0 3.18 F
928 1367 0.105778 CTCATTCCTTCCTCGCCTCC 59.894 60.0 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2233 4357 1.141665 CTCGCACCCGATGATCACA 59.858 57.895 0.0 0.0 43.47 3.58 R
2857 5034 1.745489 GCCTCCGAACGCCTCAATT 60.745 57.895 0.0 0.0 0.00 2.32 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
252 269 8.103305 TCTAGTCAAGTCCAATTGATTTAGCTT 58.897 33.333 7.12 0.00 41.05 3.74
561 579 8.661352 AAAAATGGAATCAAACAGTAACCAAG 57.339 30.769 0.00 0.00 0.00 3.61
562 580 5.982890 ATGGAATCAAACAGTAACCAAGG 57.017 39.130 0.00 0.00 0.00 3.61
563 581 4.798882 TGGAATCAAACAGTAACCAAGGT 58.201 39.130 0.00 0.00 0.00 3.50
564 582 5.942961 TGGAATCAAACAGTAACCAAGGTA 58.057 37.500 0.00 0.00 0.00 3.08
565 583 6.366340 TGGAATCAAACAGTAACCAAGGTAA 58.634 36.000 0.00 0.00 0.00 2.85
566 584 6.263617 TGGAATCAAACAGTAACCAAGGTAAC 59.736 38.462 0.00 0.00 0.00 2.50
567 585 6.263617 GGAATCAAACAGTAACCAAGGTAACA 59.736 38.462 0.00 0.00 41.41 2.41
568 586 7.201839 GGAATCAAACAGTAACCAAGGTAACAA 60.202 37.037 0.00 0.00 41.41 2.83
569 587 7.833285 ATCAAACAGTAACCAAGGTAACAAT 57.167 32.000 0.00 0.00 41.41 2.71
570 588 7.266922 TCAAACAGTAACCAAGGTAACAATC 57.733 36.000 0.00 0.00 41.41 2.67
571 589 5.934935 AACAGTAACCAAGGTAACAATCG 57.065 39.130 0.00 0.00 41.41 3.34
572 590 5.217978 ACAGTAACCAAGGTAACAATCGA 57.782 39.130 0.00 0.00 41.41 3.59
573 591 5.235516 ACAGTAACCAAGGTAACAATCGAG 58.764 41.667 0.00 0.00 41.41 4.04
574 592 5.221581 ACAGTAACCAAGGTAACAATCGAGT 60.222 40.000 0.00 0.00 41.41 4.18
575 593 5.120208 CAGTAACCAAGGTAACAATCGAGTG 59.880 44.000 11.98 11.98 41.41 3.51
576 594 4.345859 AACCAAGGTAACAATCGAGTGA 57.654 40.909 21.18 0.00 41.41 3.41
577 595 3.926616 ACCAAGGTAACAATCGAGTGAG 58.073 45.455 21.18 0.00 41.41 3.51
578 596 3.323979 ACCAAGGTAACAATCGAGTGAGT 59.676 43.478 21.18 9.35 41.41 3.41
579 597 4.202326 ACCAAGGTAACAATCGAGTGAGTT 60.202 41.667 21.18 6.92 41.41 3.01
580 598 5.011329 ACCAAGGTAACAATCGAGTGAGTTA 59.989 40.000 21.18 5.85 41.41 2.24
581 599 5.577164 CCAAGGTAACAATCGAGTGAGTTAG 59.423 44.000 21.18 3.04 41.41 2.34
582 600 6.387465 CAAGGTAACAATCGAGTGAGTTAGA 58.613 40.000 21.18 0.00 41.41 2.10
583 601 6.197364 AGGTAACAATCGAGTGAGTTAGAG 57.803 41.667 21.18 0.00 41.41 2.43
584 602 5.944599 AGGTAACAATCGAGTGAGTTAGAGA 59.055 40.000 21.18 0.00 41.41 3.10
585 603 6.028987 GGTAACAATCGAGTGAGTTAGAGAC 58.971 44.000 21.18 5.04 0.00 3.36
586 604 4.343811 ACAATCGAGTGAGTTAGAGACG 57.656 45.455 21.18 0.00 0.00 4.18
587 605 4.001652 ACAATCGAGTGAGTTAGAGACGA 58.998 43.478 21.18 0.00 0.00 4.20
588 606 4.093703 ACAATCGAGTGAGTTAGAGACGAG 59.906 45.833 21.18 0.00 0.00 4.18
589 607 3.589495 TCGAGTGAGTTAGAGACGAGA 57.411 47.619 0.00 0.00 0.00 4.04
590 608 3.513662 TCGAGTGAGTTAGAGACGAGAG 58.486 50.000 0.00 0.00 0.00 3.20
591 609 2.029970 CGAGTGAGTTAGAGACGAGAGC 59.970 54.545 0.00 0.00 0.00 4.09
592 610 3.267483 GAGTGAGTTAGAGACGAGAGCT 58.733 50.000 0.00 0.00 0.00 4.09
593 611 3.006940 AGTGAGTTAGAGACGAGAGCTG 58.993 50.000 0.00 0.00 0.00 4.24
607 625 6.486993 AGACGAGAGCTGAATGTGTATACATA 59.513 38.462 9.18 6.83 46.54 2.29
610 628 6.799441 CGAGAGCTGAATGTGTATACATAGAC 59.201 42.308 9.18 5.51 46.54 2.59
627 645 6.037098 ACATAGACGAAGAACAGTCTTATGC 58.963 40.000 3.37 0.00 44.42 3.14
633 651 4.201628 CGAAGAACAGTCTTATGCCGAAAG 60.202 45.833 0.00 0.00 44.42 2.62
662 680 3.118408 TGGTTCTGTTGCTGTACTGAACT 60.118 43.478 22.61 0.00 46.98 3.01
673 691 5.122239 TGCTGTACTGAACTTGCAATCATAC 59.878 40.000 0.00 7.44 36.09 2.39
679 697 9.410556 GTACTGAACTTGCAATCATACAAAAAT 57.589 29.630 0.00 0.00 0.00 1.82
701 719 9.438163 AAAATAATGGGACCACTGATTTATCAT 57.562 29.630 0.00 0.00 36.02 2.45
732 750 4.519540 AAAATCATTTCCAGTCAACCCG 57.480 40.909 0.00 0.00 0.00 5.28
733 751 1.463674 ATCATTTCCAGTCAACCCGC 58.536 50.000 0.00 0.00 0.00 6.13
734 752 0.400213 TCATTTCCAGTCAACCCGCT 59.600 50.000 0.00 0.00 0.00 5.52
735 753 0.804989 CATTTCCAGTCAACCCGCTC 59.195 55.000 0.00 0.00 0.00 5.03
737 755 0.034896 TTTCCAGTCAACCCGCTCTC 59.965 55.000 0.00 0.00 0.00 3.20
738 756 1.827399 TTCCAGTCAACCCGCTCTCC 61.827 60.000 0.00 0.00 0.00 3.71
739 757 2.583441 CCAGTCAACCCGCTCTCCA 61.583 63.158 0.00 0.00 0.00 3.86
740 758 1.374758 CAGTCAACCCGCTCTCCAC 60.375 63.158 0.00 0.00 0.00 4.02
741 759 1.837051 AGTCAACCCGCTCTCCACA 60.837 57.895 0.00 0.00 0.00 4.17
744 762 1.966451 CAACCCGCTCTCCACAACC 60.966 63.158 0.00 0.00 0.00 3.77
745 763 3.530910 AACCCGCTCTCCACAACCG 62.531 63.158 0.00 0.00 0.00 4.44
746 764 4.760047 CCCGCTCTCCACAACCGG 62.760 72.222 0.00 0.00 38.71 5.28
750 768 2.656069 GCTCTCCACAACCGGCCTA 61.656 63.158 0.00 0.00 0.00 3.93
752 770 2.240162 CTCTCCACAACCGGCCTACC 62.240 65.000 0.00 0.00 0.00 3.18
753 771 3.324108 TCCACAACCGGCCTACCC 61.324 66.667 0.00 0.00 0.00 3.69
754 772 4.419921 CCACAACCGGCCTACCCC 62.420 72.222 0.00 0.00 0.00 4.95
757 775 4.462280 CAACCGGCCTACCCCGTC 62.462 72.222 0.00 0.00 46.71 4.79
761 779 3.846430 CGGCCTACCCCGTCCTTC 61.846 72.222 0.00 0.00 43.24 3.46
762 780 3.846430 GGCCTACCCCGTCCTTCG 61.846 72.222 0.00 0.00 39.52 3.79
765 783 3.072468 CTACCCCGTCCTTCGCCA 61.072 66.667 0.00 0.00 38.35 5.69
766 784 2.604079 TACCCCGTCCTTCGCCAA 60.604 61.111 0.00 0.00 38.35 4.52
767 785 2.847435 CTACCCCGTCCTTCGCCAAC 62.847 65.000 0.00 0.00 38.35 3.77
770 788 4.675029 CCGTCCTTCGCCAACCGT 62.675 66.667 0.00 0.00 38.35 4.83
771 789 2.663852 CGTCCTTCGCCAACCGTT 60.664 61.111 0.00 0.00 38.35 4.44
773 791 2.975799 TCCTTCGCCAACCGTTGC 60.976 61.111 5.68 1.19 38.35 4.17
774 792 4.038080 CCTTCGCCAACCGTTGCC 62.038 66.667 5.68 0.00 38.35 4.52
775 793 3.283684 CTTCGCCAACCGTTGCCA 61.284 61.111 5.68 0.00 38.35 4.92
776 794 2.829003 TTCGCCAACCGTTGCCAA 60.829 55.556 5.68 0.00 38.35 4.52
779 797 2.733945 GCCAACCGTTGCCAACAT 59.266 55.556 8.51 0.00 0.00 2.71
780 798 1.372872 GCCAACCGTTGCCAACATC 60.373 57.895 8.51 0.00 0.00 3.06
783 801 0.318614 CAACCGTTGCCAACATCACC 60.319 55.000 8.51 0.00 0.00 4.02
784 802 0.467290 AACCGTTGCCAACATCACCT 60.467 50.000 8.51 0.00 0.00 4.00
786 804 1.086696 CCGTTGCCAACATCACCTAG 58.913 55.000 8.51 0.00 0.00 3.02
788 806 1.826385 GTTGCCAACATCACCTAGCT 58.174 50.000 1.91 0.00 0.00 3.32
789 807 1.470098 GTTGCCAACATCACCTAGCTG 59.530 52.381 1.91 0.00 0.00 4.24
790 808 0.677731 TGCCAACATCACCTAGCTGC 60.678 55.000 0.00 0.00 0.00 5.25
791 809 1.379642 GCCAACATCACCTAGCTGCC 61.380 60.000 0.00 0.00 0.00 4.85
792 810 0.749454 CCAACATCACCTAGCTGCCC 60.749 60.000 0.00 0.00 0.00 5.36
795 813 0.990282 ACATCACCTAGCTGCCCCAT 60.990 55.000 0.00 0.00 0.00 4.00
796 814 0.536687 CATCACCTAGCTGCCCCATG 60.537 60.000 0.00 0.00 0.00 3.66
798 816 2.286425 ACCTAGCTGCCCCATGGT 60.286 61.111 11.73 0.00 0.00 3.55
799 817 2.194056 CCTAGCTGCCCCATGGTG 59.806 66.667 11.73 0.00 0.00 4.17
800 818 2.517875 CTAGCTGCCCCATGGTGC 60.518 66.667 12.90 12.90 34.77 5.01
801 819 4.127744 TAGCTGCCCCATGGTGCC 62.128 66.667 17.16 1.83 35.00 5.01
804 822 2.604079 CTGCCCCATGGTGCCAAA 60.604 61.111 17.16 0.00 0.00 3.28
805 823 1.991167 CTGCCCCATGGTGCCAAAT 60.991 57.895 17.16 0.00 0.00 2.32
806 824 1.963464 CTGCCCCATGGTGCCAAATC 61.963 60.000 17.16 0.00 0.00 2.17
808 826 1.266867 GCCCCATGGTGCCAAATCTT 61.267 55.000 8.18 0.00 0.00 2.40
809 827 0.826062 CCCCATGGTGCCAAATCTTC 59.174 55.000 11.73 0.00 0.00 2.87
817 1256 2.359900 GTGCCAAATCTTCATCTCCGT 58.640 47.619 0.00 0.00 0.00 4.69
819 1258 1.594862 GCCAAATCTTCATCTCCGTCG 59.405 52.381 0.00 0.00 0.00 5.12
821 1260 3.119291 CCAAATCTTCATCTCCGTCGAG 58.881 50.000 0.00 0.00 37.48 4.04
825 1264 1.994507 CTTCATCTCCGTCGAGCCGT 61.995 60.000 0.00 0.00 35.94 5.68
828 1267 2.762234 ATCTCCGTCGAGCCGTCAC 61.762 63.158 0.00 0.00 35.94 3.67
835 1274 4.436998 CGAGCCGTCACCACTCCC 62.437 72.222 0.00 0.00 0.00 4.30
836 1275 3.311110 GAGCCGTCACCACTCCCA 61.311 66.667 0.00 0.00 0.00 4.37
837 1276 3.591254 GAGCCGTCACCACTCCCAC 62.591 68.421 0.00 0.00 0.00 4.61
840 1279 2.592993 CCGTCACCACTCCCACCAT 61.593 63.158 0.00 0.00 0.00 3.55
843 1282 1.923395 TCACCACTCCCACCATCCC 60.923 63.158 0.00 0.00 0.00 3.85
846 1285 1.307343 CCACTCCCACCATCCCTCT 60.307 63.158 0.00 0.00 0.00 3.69
849 1288 0.031010 ACTCCCACCATCCCTCTACC 60.031 60.000 0.00 0.00 0.00 3.18
850 1289 0.266152 CTCCCACCATCCCTCTACCT 59.734 60.000 0.00 0.00 0.00 3.08
853 1292 1.123928 CCACCATCCCTCTACCTCAC 58.876 60.000 0.00 0.00 0.00 3.51
854 1293 1.343478 CCACCATCCCTCTACCTCACT 60.343 57.143 0.00 0.00 0.00 3.41
857 1296 2.043227 CCATCCCTCTACCTCACTTCC 58.957 57.143 0.00 0.00 0.00 3.46
858 1297 2.043227 CATCCCTCTACCTCACTTCCC 58.957 57.143 0.00 0.00 0.00 3.97
860 1299 2.581365 TCCCTCTACCTCACTTCCCTA 58.419 52.381 0.00 0.00 0.00 3.53
861 1300 2.244252 TCCCTCTACCTCACTTCCCTAC 59.756 54.545 0.00 0.00 0.00 3.18
862 1301 2.024273 CCCTCTACCTCACTTCCCTACA 60.024 54.545 0.00 0.00 0.00 2.74
863 1302 3.374318 CCCTCTACCTCACTTCCCTACAT 60.374 52.174 0.00 0.00 0.00 2.29
864 1303 3.892588 CCTCTACCTCACTTCCCTACATC 59.107 52.174 0.00 0.00 0.00 3.06
865 1304 4.386986 CCTCTACCTCACTTCCCTACATCT 60.387 50.000 0.00 0.00 0.00 2.90
866 1305 5.163077 CCTCTACCTCACTTCCCTACATCTA 60.163 48.000 0.00 0.00 0.00 1.98
867 1306 5.692928 TCTACCTCACTTCCCTACATCTAC 58.307 45.833 0.00 0.00 0.00 2.59
868 1307 4.332683 ACCTCACTTCCCTACATCTACA 57.667 45.455 0.00 0.00 0.00 2.74
869 1308 4.024670 ACCTCACTTCCCTACATCTACAC 58.975 47.826 0.00 0.00 0.00 2.90
870 1309 3.066900 CCTCACTTCCCTACATCTACACG 59.933 52.174 0.00 0.00 0.00 4.49
871 1310 2.426024 TCACTTCCCTACATCTACACGC 59.574 50.000 0.00 0.00 0.00 5.34
872 1311 2.165641 CACTTCCCTACATCTACACGCA 59.834 50.000 0.00 0.00 0.00 5.24
873 1312 3.031736 ACTTCCCTACATCTACACGCAT 58.968 45.455 0.00 0.00 0.00 4.73
875 1314 4.037684 ACTTCCCTACATCTACACGCATAC 59.962 45.833 0.00 0.00 0.00 2.39
876 1315 2.889045 TCCCTACATCTACACGCATACC 59.111 50.000 0.00 0.00 0.00 2.73
877 1316 2.029290 CCCTACATCTACACGCATACCC 60.029 54.545 0.00 0.00 0.00 3.69
878 1317 2.626266 CCTACATCTACACGCATACCCA 59.374 50.000 0.00 0.00 0.00 4.51
880 1319 1.828595 ACATCTACACGCATACCCACA 59.171 47.619 0.00 0.00 0.00 4.17
881 1320 2.235155 ACATCTACACGCATACCCACAA 59.765 45.455 0.00 0.00 0.00 3.33
882 1321 2.373540 TCTACACGCATACCCACAAC 57.626 50.000 0.00 0.00 0.00 3.32
883 1322 1.619332 TCTACACGCATACCCACAACA 59.381 47.619 0.00 0.00 0.00 3.33
884 1323 2.235155 TCTACACGCATACCCACAACAT 59.765 45.455 0.00 0.00 0.00 2.71
885 1324 1.448985 ACACGCATACCCACAACATC 58.551 50.000 0.00 0.00 0.00 3.06
886 1325 1.271108 ACACGCATACCCACAACATCA 60.271 47.619 0.00 0.00 0.00 3.07
887 1326 1.809547 CACGCATACCCACAACATCAA 59.190 47.619 0.00 0.00 0.00 2.57
888 1327 1.810151 ACGCATACCCACAACATCAAC 59.190 47.619 0.00 0.00 0.00 3.18
889 1328 1.132262 CGCATACCCACAACATCAACC 59.868 52.381 0.00 0.00 0.00 3.77
890 1329 1.132262 GCATACCCACAACATCAACCG 59.868 52.381 0.00 0.00 0.00 4.44
894 1333 1.313772 CCCACAACATCAACCGTTGA 58.686 50.000 16.15 16.15 45.30 3.18
895 1334 1.678627 CCCACAACATCAACCGTTGAA 59.321 47.619 17.64 2.33 45.30 2.69
896 1335 2.542824 CCCACAACATCAACCGTTGAAC 60.543 50.000 17.64 0.00 45.30 3.18
897 1336 2.357637 CCACAACATCAACCGTTGAACT 59.642 45.455 17.64 3.42 45.30 3.01
898 1337 3.548014 CCACAACATCAACCGTTGAACTC 60.548 47.826 17.64 0.00 45.30 3.01
899 1338 2.286833 ACAACATCAACCGTTGAACTCG 59.713 45.455 17.64 9.62 45.30 4.18
900 1339 2.234300 ACATCAACCGTTGAACTCGT 57.766 45.000 17.64 9.87 43.95 4.18
901 1340 2.132762 ACATCAACCGTTGAACTCGTC 58.867 47.619 17.64 0.00 43.95 4.20
904 1343 2.466846 TCAACCGTTGAACTCGTCTTC 58.533 47.619 11.63 0.00 36.59 2.87
905 1344 2.100252 TCAACCGTTGAACTCGTCTTCT 59.900 45.455 11.63 0.00 36.59 2.85
906 1345 2.864343 CAACCGTTGAACTCGTCTTCTT 59.136 45.455 5.23 0.00 0.00 2.52
907 1346 2.470821 ACCGTTGAACTCGTCTTCTTG 58.529 47.619 0.00 0.00 0.00 3.02
908 1347 1.792949 CCGTTGAACTCGTCTTCTTGG 59.207 52.381 0.00 0.00 0.00 3.61
909 1348 1.192534 CGTTGAACTCGTCTTCTTGGC 59.807 52.381 0.00 0.00 0.00 4.52
911 1350 2.440539 TGAACTCGTCTTCTTGGCTC 57.559 50.000 0.00 0.00 0.00 4.70
912 1351 1.686587 TGAACTCGTCTTCTTGGCTCA 59.313 47.619 0.00 0.00 0.00 4.26
914 1353 3.244215 TGAACTCGTCTTCTTGGCTCATT 60.244 43.478 0.00 0.00 0.00 2.57
916 1355 2.275318 CTCGTCTTCTTGGCTCATTCC 58.725 52.381 0.00 0.00 0.00 3.01
918 1357 2.303022 TCGTCTTCTTGGCTCATTCCTT 59.697 45.455 0.00 0.00 0.00 3.36
920 1359 3.013219 GTCTTCTTGGCTCATTCCTTCC 58.987 50.000 0.00 0.00 0.00 3.46
922 1361 3.054802 TCTTCTTGGCTCATTCCTTCCTC 60.055 47.826 0.00 0.00 0.00 3.71
923 1362 1.208052 TCTTGGCTCATTCCTTCCTCG 59.792 52.381 0.00 0.00 0.00 4.63
924 1363 0.392998 TTGGCTCATTCCTTCCTCGC 60.393 55.000 0.00 0.00 0.00 5.03
925 1364 1.524849 GGCTCATTCCTTCCTCGCC 60.525 63.158 0.00 0.00 0.00 5.54
926 1365 1.524482 GCTCATTCCTTCCTCGCCT 59.476 57.895 0.00 0.00 0.00 5.52
927 1366 0.531753 GCTCATTCCTTCCTCGCCTC 60.532 60.000 0.00 0.00 0.00 4.70
928 1367 0.105778 CTCATTCCTTCCTCGCCTCC 59.894 60.000 0.00 0.00 0.00 4.30
929 1368 0.617535 TCATTCCTTCCTCGCCTCCA 60.618 55.000 0.00 0.00 0.00 3.86
930 1369 0.471617 CATTCCTTCCTCGCCTCCAT 59.528 55.000 0.00 0.00 0.00 3.41
933 1372 1.045350 TCCTTCCTCGCCTCCATGAG 61.045 60.000 0.00 0.00 0.00 2.90
934 1373 1.333636 CCTTCCTCGCCTCCATGAGT 61.334 60.000 0.00 0.00 0.00 3.41
935 1374 0.179089 CTTCCTCGCCTCCATGAGTG 60.179 60.000 0.00 0.00 0.00 3.51
936 1375 0.614697 TTCCTCGCCTCCATGAGTGA 60.615 55.000 0.00 0.00 0.00 3.41
937 1376 0.397675 TCCTCGCCTCCATGAGTGAT 60.398 55.000 0.00 0.00 0.00 3.06
938 1377 0.249784 CCTCGCCTCCATGAGTGATG 60.250 60.000 0.00 0.00 0.00 3.07
939 1378 0.463204 CTCGCCTCCATGAGTGATGT 59.537 55.000 0.00 0.00 0.00 3.06
940 1379 0.461548 TCGCCTCCATGAGTGATGTC 59.538 55.000 0.00 0.00 0.00 3.06
941 1380 0.873312 CGCCTCCATGAGTGATGTCG 60.873 60.000 0.00 0.00 0.00 4.35
942 1381 0.461548 GCCTCCATGAGTGATGTCGA 59.538 55.000 0.00 0.00 0.00 4.20
943 1382 1.537776 GCCTCCATGAGTGATGTCGAG 60.538 57.143 0.00 0.00 0.00 4.04
946 1631 0.531532 CCATGAGTGATGTCGAGGGC 60.532 60.000 0.00 0.00 0.00 5.19
948 1633 2.021068 ATGAGTGATGTCGAGGGCGG 62.021 60.000 0.00 0.00 38.28 6.13
959 1644 2.524394 AGGGCGGCCATATCGTCT 60.524 61.111 31.59 3.02 32.30 4.18
960 1645 2.357517 GGGCGGCCATATCGTCTG 60.358 66.667 25.33 0.00 32.30 3.51
961 1646 2.421739 GGCGGCCATATCGTCTGT 59.578 61.111 15.62 0.00 0.00 3.41
964 1649 0.810031 GCGGCCATATCGTCTGTGTT 60.810 55.000 2.24 0.00 0.00 3.32
965 1650 1.651987 CGGCCATATCGTCTGTGTTT 58.348 50.000 2.24 0.00 0.00 2.83
967 1652 2.738643 CGGCCATATCGTCTGTGTTTCT 60.739 50.000 2.24 0.00 0.00 2.52
1057 3045 0.969917 GTGCTCTGAGCTCCAGGAGA 60.970 60.000 28.04 14.40 42.97 3.71
1239 3227 2.510238 GAGCCATTCGCGCTGAGT 60.510 61.111 5.56 0.00 44.76 3.41
1386 3395 6.868622 TCATCTTCTCTACCAACTTAAGCTC 58.131 40.000 1.29 0.00 0.00 4.09
1594 3606 7.203255 ACCTTCTTTCTAATTTAGTGCACAC 57.797 36.000 21.04 0.00 0.00 3.82
2233 4357 2.555757 GCACCTGAACTTGAAGATGCTT 59.444 45.455 0.00 0.00 0.00 3.91
2713 4879 8.818622 ATTCCGTACCTACTATATGCTGATTA 57.181 34.615 0.00 0.00 0.00 1.75
2810 4986 4.838423 TGGAACAGAGGTTGAATGTAGAGA 59.162 41.667 0.00 0.00 37.36 3.10
2837 5014 4.708726 ATCTGTGCACCTTTTTGCTATC 57.291 40.909 15.69 0.00 43.41 2.08
2857 5034 7.344612 TGCTATCTGTTGAGAAATTCCCTACTA 59.655 37.037 0.00 0.00 0.00 1.82
2867 5044 4.772886 AATTCCCTACTAATTGAGGCGT 57.227 40.909 0.00 0.00 0.00 5.68
2870 5047 2.100252 TCCCTACTAATTGAGGCGTTCG 59.900 50.000 0.00 0.00 0.00 3.95
2871 5048 2.470821 CCTACTAATTGAGGCGTTCGG 58.529 52.381 0.00 0.00 0.00 4.30
2875 5052 0.461339 TAATTGAGGCGTTCGGAGGC 60.461 55.000 0.00 0.00 35.97 4.70
2916 5101 2.003301 GAGGCGTTCTCTGTTTGGATC 58.997 52.381 1.54 0.00 39.38 3.36
2918 5103 2.832129 AGGCGTTCTCTGTTTGGATCTA 59.168 45.455 0.00 0.00 0.00 1.98
2926 5111 6.611613 TCTCTGTTTGGATCTAACTGACAT 57.388 37.500 12.97 0.00 32.40 3.06
2989 5174 4.163441 TCACTTTGGTCACCAGAAATGA 57.837 40.909 0.00 0.00 33.81 2.57
2995 5211 4.271696 TGGTCACCAGAAATGACAGTAG 57.728 45.455 0.00 0.00 46.89 2.57
3056 5272 6.046593 TGGTCTACCAATGTCGATGATAAAC 58.953 40.000 0.00 0.00 44.35 2.01
3104 5321 5.394224 ACAGCAGAGGTACTTTAGTCTTC 57.606 43.478 0.00 0.00 41.55 2.87
3146 5363 3.421844 AGTGTTCAAAGGTAGCATTCCC 58.578 45.455 0.00 0.00 0.00 3.97
3153 5370 5.876357 TCAAAGGTAGCATTCCCCATATAC 58.124 41.667 0.00 0.00 0.00 1.47
3157 5374 5.415961 AGGTAGCATTCCCCATATACTTCT 58.584 41.667 0.00 0.00 0.00 2.85
3163 5380 1.691976 TCCCCATATACTTCTGCACCG 59.308 52.381 0.00 0.00 0.00 4.94
3165 5382 1.691976 CCCATATACTTCTGCACCGGA 59.308 52.381 9.46 0.00 0.00 5.14
3184 5401 2.202892 GTTGCCGATCGACCTCCC 60.203 66.667 18.66 0.00 0.00 4.30
3200 5417 6.781014 TCGACCTCCCTTATTATGTTGTATCT 59.219 38.462 0.00 0.00 0.00 1.98
3241 5490 1.600916 AAGGAGCCAACTTCCGCAC 60.601 57.895 0.00 0.00 0.00 5.34
3242 5491 2.281484 GGAGCCAACTTCCGCACA 60.281 61.111 0.00 0.00 0.00 4.57
3245 5494 0.317854 GAGCCAACTTCCGCACAAAC 60.318 55.000 0.00 0.00 0.00 2.93
3266 5515 0.035820 GGTATCCCGCACAAGGTTGA 60.036 55.000 0.00 0.00 0.00 3.18
3318 5567 3.622163 CAGATGTGAATGTCTCCTTCAGC 59.378 47.826 0.00 0.00 33.49 4.26
3324 5573 1.273759 ATGTCTCCTTCAGCAGCAGA 58.726 50.000 0.00 0.00 0.00 4.26
3325 5574 1.051008 TGTCTCCTTCAGCAGCAGAA 58.949 50.000 0.00 0.00 0.00 3.02
3393 5642 3.487544 GCACACGGATTCAAAATAGCCTC 60.488 47.826 0.00 0.00 0.00 4.70
3408 5657 1.630878 AGCCTCCCTGGTTTGAACTAG 59.369 52.381 0.73 0.73 37.27 2.57
3412 5661 3.583086 CCTCCCTGGTTTGAACTAGAAGA 59.417 47.826 8.59 4.83 39.59 2.87
3424 5673 4.021456 TGAACTAGAAGAATCACGCTCCAA 60.021 41.667 0.00 0.00 0.00 3.53
3445 5694 8.479313 TCCAATTACGCATCATTCTACATATC 57.521 34.615 0.00 0.00 0.00 1.63
3446 5695 8.314021 TCCAATTACGCATCATTCTACATATCT 58.686 33.333 0.00 0.00 0.00 1.98
3447 5696 8.385858 CCAATTACGCATCATTCTACATATCTG 58.614 37.037 0.00 0.00 0.00 2.90
3448 5697 8.929746 CAATTACGCATCATTCTACATATCTGT 58.070 33.333 0.00 0.00 39.49 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
545 563 7.308348 CGATTGTTACCTTGGTTACTGTTTGAT 60.308 37.037 9.82 0.00 0.00 2.57
555 573 4.202326 ACTCACTCGATTGTTACCTTGGTT 60.202 41.667 2.44 0.00 0.00 3.67
557 575 3.926616 ACTCACTCGATTGTTACCTTGG 58.073 45.455 2.44 0.00 0.00 3.61
558 576 6.387465 TCTAACTCACTCGATTGTTACCTTG 58.613 40.000 2.44 0.00 0.00 3.61
559 577 6.433404 TCTCTAACTCACTCGATTGTTACCTT 59.567 38.462 2.44 0.00 0.00 3.50
560 578 5.944599 TCTCTAACTCACTCGATTGTTACCT 59.055 40.000 2.44 0.00 0.00 3.08
561 579 6.028987 GTCTCTAACTCACTCGATTGTTACC 58.971 44.000 2.44 0.00 0.00 2.85
562 580 5.733572 CGTCTCTAACTCACTCGATTGTTAC 59.266 44.000 2.44 0.00 0.00 2.50
563 581 5.640783 TCGTCTCTAACTCACTCGATTGTTA 59.359 40.000 2.44 2.01 0.00 2.41
564 582 4.454847 TCGTCTCTAACTCACTCGATTGTT 59.545 41.667 2.44 0.96 0.00 2.83
565 583 4.001652 TCGTCTCTAACTCACTCGATTGT 58.998 43.478 2.44 0.00 0.00 2.71
566 584 4.330347 TCTCGTCTCTAACTCACTCGATTG 59.670 45.833 0.00 0.00 0.00 2.67
567 585 4.505808 TCTCGTCTCTAACTCACTCGATT 58.494 43.478 0.00 0.00 0.00 3.34
568 586 4.116961 CTCTCGTCTCTAACTCACTCGAT 58.883 47.826 0.00 0.00 0.00 3.59
569 587 3.513662 CTCTCGTCTCTAACTCACTCGA 58.486 50.000 0.00 0.00 0.00 4.04
570 588 2.029970 GCTCTCGTCTCTAACTCACTCG 59.970 54.545 0.00 0.00 0.00 4.18
571 589 3.063452 CAGCTCTCGTCTCTAACTCACTC 59.937 52.174 0.00 0.00 0.00 3.51
572 590 3.006940 CAGCTCTCGTCTCTAACTCACT 58.993 50.000 0.00 0.00 0.00 3.41
573 591 3.004171 TCAGCTCTCGTCTCTAACTCAC 58.996 50.000 0.00 0.00 0.00 3.51
574 592 3.336138 TCAGCTCTCGTCTCTAACTCA 57.664 47.619 0.00 0.00 0.00 3.41
575 593 4.095782 ACATTCAGCTCTCGTCTCTAACTC 59.904 45.833 0.00 0.00 0.00 3.01
576 594 4.013728 ACATTCAGCTCTCGTCTCTAACT 58.986 43.478 0.00 0.00 0.00 2.24
577 595 4.101942 CACATTCAGCTCTCGTCTCTAAC 58.898 47.826 0.00 0.00 0.00 2.34
578 596 3.759086 ACACATTCAGCTCTCGTCTCTAA 59.241 43.478 0.00 0.00 0.00 2.10
579 597 3.348119 ACACATTCAGCTCTCGTCTCTA 58.652 45.455 0.00 0.00 0.00 2.43
580 598 2.166829 ACACATTCAGCTCTCGTCTCT 58.833 47.619 0.00 0.00 0.00 3.10
581 599 2.645730 ACACATTCAGCTCTCGTCTC 57.354 50.000 0.00 0.00 0.00 3.36
582 600 4.640647 TGTATACACATTCAGCTCTCGTCT 59.359 41.667 0.08 0.00 0.00 4.18
583 601 4.921547 TGTATACACATTCAGCTCTCGTC 58.078 43.478 0.08 0.00 0.00 4.20
584 602 4.983671 TGTATACACATTCAGCTCTCGT 57.016 40.909 0.08 0.00 0.00 4.18
585 603 6.799441 GTCTATGTATACACATTCAGCTCTCG 59.201 42.308 7.96 0.00 42.98 4.04
586 604 6.799441 CGTCTATGTATACACATTCAGCTCTC 59.201 42.308 7.96 0.00 42.98 3.20
587 605 6.486993 TCGTCTATGTATACACATTCAGCTCT 59.513 38.462 7.96 0.00 42.98 4.09
588 606 6.669278 TCGTCTATGTATACACATTCAGCTC 58.331 40.000 7.96 0.00 42.98 4.09
589 607 6.635030 TCGTCTATGTATACACATTCAGCT 57.365 37.500 7.96 0.00 42.98 4.24
590 608 7.139392 TCTTCGTCTATGTATACACATTCAGC 58.861 38.462 7.96 0.00 42.98 4.26
591 609 8.959058 GTTCTTCGTCTATGTATACACATTCAG 58.041 37.037 7.96 1.30 42.98 3.02
592 610 8.463607 TGTTCTTCGTCTATGTATACACATTCA 58.536 33.333 7.96 0.00 42.98 2.57
593 611 8.851960 TGTTCTTCGTCTATGTATACACATTC 57.148 34.615 7.96 0.00 42.98 2.67
607 625 3.673594 CGGCATAAGACTGTTCTTCGTCT 60.674 47.826 0.00 0.00 41.48 4.18
610 628 2.876091 TCGGCATAAGACTGTTCTTCG 58.124 47.619 0.00 0.00 41.48 3.79
622 640 2.500098 ACCACTAGCTCTTTCGGCATAA 59.500 45.455 0.00 0.00 0.00 1.90
623 641 2.108168 ACCACTAGCTCTTTCGGCATA 58.892 47.619 0.00 0.00 0.00 3.14
625 643 0.685097 AACCACTAGCTCTTTCGGCA 59.315 50.000 0.00 0.00 0.00 5.69
627 645 2.028930 ACAGAACCACTAGCTCTTTCGG 60.029 50.000 0.00 0.00 0.00 4.30
633 651 2.072298 CAGCAACAGAACCACTAGCTC 58.928 52.381 0.00 0.00 31.43 4.09
662 680 7.768120 GGTCCCATTATTTTTGTATGATTGCAA 59.232 33.333 0.00 0.00 0.00 4.08
673 691 9.533253 GATAAATCAGTGGTCCCATTATTTTTG 57.467 33.333 8.06 0.00 0.00 2.44
679 697 8.108999 CCATATGATAAATCAGTGGTCCCATTA 58.891 37.037 3.65 0.00 40.64 1.90
714 732 1.004745 AGCGGGTTGACTGGAAATGAT 59.995 47.619 0.00 0.00 0.00 2.45
715 733 0.400213 AGCGGGTTGACTGGAAATGA 59.600 50.000 0.00 0.00 0.00 2.57
716 734 0.804989 GAGCGGGTTGACTGGAAATG 59.195 55.000 0.00 0.00 0.00 2.32
718 736 0.034896 GAGAGCGGGTTGACTGGAAA 59.965 55.000 0.00 0.00 0.00 3.13
719 737 1.671742 GAGAGCGGGTTGACTGGAA 59.328 57.895 0.00 0.00 0.00 3.53
720 738 2.283529 GGAGAGCGGGTTGACTGGA 61.284 63.158 0.00 0.00 0.00 3.86
723 741 1.407656 TTGTGGAGAGCGGGTTGACT 61.408 55.000 0.00 0.00 0.00 3.41
724 742 1.070786 TTGTGGAGAGCGGGTTGAC 59.929 57.895 0.00 0.00 0.00 3.18
726 744 1.966451 GGTTGTGGAGAGCGGGTTG 60.966 63.158 0.00 0.00 0.00 3.77
727 745 2.430367 GGTTGTGGAGAGCGGGTT 59.570 61.111 0.00 0.00 0.00 4.11
728 746 4.003788 CGGTTGTGGAGAGCGGGT 62.004 66.667 0.00 0.00 34.64 5.28
732 750 2.656069 TAGGCCGGTTGTGGAGAGC 61.656 63.158 1.90 0.00 0.00 4.09
733 751 1.218316 GTAGGCCGGTTGTGGAGAG 59.782 63.158 1.90 0.00 0.00 3.20
734 752 2.288025 GGTAGGCCGGTTGTGGAGA 61.288 63.158 1.90 0.00 0.00 3.71
735 753 2.267961 GGTAGGCCGGTTGTGGAG 59.732 66.667 1.90 0.00 0.00 3.86
737 755 4.419921 GGGGTAGGCCGGTTGTGG 62.420 72.222 1.90 0.00 34.97 4.17
738 756 4.770874 CGGGGTAGGCCGGTTGTG 62.771 72.222 1.90 0.00 34.97 3.33
740 758 4.462280 GACGGGGTAGGCCGGTTG 62.462 72.222 1.90 0.00 34.97 3.77
744 762 3.846430 GAAGGACGGGGTAGGCCG 61.846 72.222 0.00 0.00 46.30 6.13
745 763 3.846430 CGAAGGACGGGGTAGGCC 61.846 72.222 0.00 0.00 40.48 5.19
746 764 4.525949 GCGAAGGACGGGGTAGGC 62.526 72.222 0.00 0.00 42.83 3.93
747 765 3.846430 GGCGAAGGACGGGGTAGG 61.846 72.222 0.00 0.00 42.83 3.18
748 766 2.652095 TTGGCGAAGGACGGGGTAG 61.652 63.158 0.00 0.00 42.83 3.18
750 768 4.324991 GTTGGCGAAGGACGGGGT 62.325 66.667 0.00 0.00 42.83 4.95
753 771 4.675029 ACGGTTGGCGAAGGACGG 62.675 66.667 0.00 0.00 42.83 4.79
754 772 2.663852 AACGGTTGGCGAAGGACG 60.664 61.111 0.00 0.00 45.66 4.79
755 773 2.943653 CAACGGTTGGCGAAGGAC 59.056 61.111 13.03 0.00 0.00 3.85
757 775 4.038080 GGCAACGGTTGGCGAAGG 62.038 66.667 28.02 0.00 46.51 3.46
765 783 0.467290 AGGTGATGTTGGCAACGGTT 60.467 50.000 24.03 12.32 42.51 4.44
766 784 0.398696 TAGGTGATGTTGGCAACGGT 59.601 50.000 24.03 15.82 42.51 4.83
767 785 1.086696 CTAGGTGATGTTGGCAACGG 58.913 55.000 24.03 4.43 42.51 4.44
768 786 0.447801 GCTAGGTGATGTTGGCAACG 59.552 55.000 24.03 9.26 42.51 4.10
769 787 1.470098 CAGCTAGGTGATGTTGGCAAC 59.530 52.381 23.12 23.12 0.00 4.17
770 788 1.825090 CAGCTAGGTGATGTTGGCAA 58.175 50.000 17.08 0.00 0.00 4.52
771 789 0.677731 GCAGCTAGGTGATGTTGGCA 60.678 55.000 25.66 0.00 34.02 4.92
773 791 0.749454 GGGCAGCTAGGTGATGTTGG 60.749 60.000 25.66 0.00 34.02 3.77
774 792 0.749454 GGGGCAGCTAGGTGATGTTG 60.749 60.000 25.66 0.00 34.02 3.33
775 793 1.207488 TGGGGCAGCTAGGTGATGTT 61.207 55.000 25.66 0.00 34.02 2.71
776 794 0.990282 ATGGGGCAGCTAGGTGATGT 60.990 55.000 25.66 3.29 34.02 3.06
779 797 2.377810 CCATGGGGCAGCTAGGTGA 61.378 63.158 25.66 4.75 0.00 4.02
780 798 2.194056 CCATGGGGCAGCTAGGTG 59.806 66.667 17.67 17.67 0.00 4.00
783 801 2.517875 GCACCATGGGGCAGCTAG 60.518 66.667 34.41 4.84 37.90 3.42
784 802 4.127744 GGCACCATGGGGCAGCTA 62.128 66.667 38.70 0.00 38.28 3.32
788 806 1.988956 GATTTGGCACCATGGGGCA 60.989 57.895 38.70 28.73 37.90 5.36
789 807 1.266867 AAGATTTGGCACCATGGGGC 61.267 55.000 31.91 31.91 37.90 5.80
790 808 0.826062 GAAGATTTGGCACCATGGGG 59.174 55.000 18.09 14.63 41.29 4.96
791 809 1.559368 TGAAGATTTGGCACCATGGG 58.441 50.000 18.09 6.26 0.00 4.00
792 810 3.028850 AGATGAAGATTTGGCACCATGG 58.971 45.455 11.19 11.19 0.00 3.66
795 813 2.726821 GGAGATGAAGATTTGGCACCA 58.273 47.619 0.00 0.00 0.00 4.17
796 814 1.672881 CGGAGATGAAGATTTGGCACC 59.327 52.381 0.00 0.00 0.00 5.01
798 816 2.632377 GACGGAGATGAAGATTTGGCA 58.368 47.619 0.00 0.00 0.00 4.92
799 817 1.594862 CGACGGAGATGAAGATTTGGC 59.405 52.381 0.00 0.00 0.00 4.52
800 818 3.119291 CTCGACGGAGATGAAGATTTGG 58.881 50.000 0.00 0.00 43.27 3.28
801 819 2.537625 GCTCGACGGAGATGAAGATTTG 59.462 50.000 0.00 0.00 43.27 2.32
803 821 1.067821 GGCTCGACGGAGATGAAGATT 59.932 52.381 0.00 0.00 43.27 2.40
804 822 0.671251 GGCTCGACGGAGATGAAGAT 59.329 55.000 0.00 0.00 43.27 2.40
805 823 1.715862 CGGCTCGACGGAGATGAAGA 61.716 60.000 0.00 0.00 43.27 2.87
806 824 1.298713 CGGCTCGACGGAGATGAAG 60.299 63.158 0.00 0.00 43.27 3.02
808 826 2.437895 ACGGCTCGACGGAGATGA 60.438 61.111 0.00 0.00 43.27 2.92
809 827 2.024871 GACGGCTCGACGGAGATG 59.975 66.667 0.00 0.00 43.27 2.90
817 1256 3.371063 GGAGTGGTGACGGCTCGA 61.371 66.667 0.00 0.00 36.29 4.04
819 1258 3.311110 TGGGAGTGGTGACGGCTC 61.311 66.667 0.00 0.00 35.18 4.70
821 1260 4.699522 GGTGGGAGTGGTGACGGC 62.700 72.222 0.00 0.00 0.00 5.68
825 1264 1.923395 GGGATGGTGGGAGTGGTGA 60.923 63.158 0.00 0.00 0.00 4.02
828 1267 0.031111 TAGAGGGATGGTGGGAGTGG 60.031 60.000 0.00 0.00 0.00 4.00
831 1270 0.266152 AGGTAGAGGGATGGTGGGAG 59.734 60.000 0.00 0.00 0.00 4.30
835 1274 2.166907 AGTGAGGTAGAGGGATGGTG 57.833 55.000 0.00 0.00 0.00 4.17
836 1275 2.627217 GGAAGTGAGGTAGAGGGATGGT 60.627 54.545 0.00 0.00 0.00 3.55
837 1276 2.043227 GGAAGTGAGGTAGAGGGATGG 58.957 57.143 0.00 0.00 0.00 3.51
840 1279 1.394532 AGGGAAGTGAGGTAGAGGGA 58.605 55.000 0.00 0.00 0.00 4.20
843 1282 4.798882 AGATGTAGGGAAGTGAGGTAGAG 58.201 47.826 0.00 0.00 0.00 2.43
846 1285 5.198965 GTGTAGATGTAGGGAAGTGAGGTA 58.801 45.833 0.00 0.00 0.00 3.08
849 1288 3.489398 GCGTGTAGATGTAGGGAAGTGAG 60.489 52.174 0.00 0.00 0.00 3.51
850 1289 2.426024 GCGTGTAGATGTAGGGAAGTGA 59.574 50.000 0.00 0.00 0.00 3.41
853 1292 3.735237 ATGCGTGTAGATGTAGGGAAG 57.265 47.619 0.00 0.00 0.00 3.46
854 1293 3.319972 GGTATGCGTGTAGATGTAGGGAA 59.680 47.826 0.00 0.00 0.00 3.97
857 1296 2.626266 TGGGTATGCGTGTAGATGTAGG 59.374 50.000 0.00 0.00 0.00 3.18
858 1297 3.067601 TGTGGGTATGCGTGTAGATGTAG 59.932 47.826 0.00 0.00 0.00 2.74
860 1299 1.828595 TGTGGGTATGCGTGTAGATGT 59.171 47.619 0.00 0.00 0.00 3.06
861 1300 2.595124 TGTGGGTATGCGTGTAGATG 57.405 50.000 0.00 0.00 0.00 2.90
862 1301 2.235155 TGTTGTGGGTATGCGTGTAGAT 59.765 45.455 0.00 0.00 0.00 1.98
863 1302 1.619332 TGTTGTGGGTATGCGTGTAGA 59.381 47.619 0.00 0.00 0.00 2.59
864 1303 2.087501 TGTTGTGGGTATGCGTGTAG 57.912 50.000 0.00 0.00 0.00 2.74
865 1304 2.028020 TGATGTTGTGGGTATGCGTGTA 60.028 45.455 0.00 0.00 0.00 2.90
866 1305 1.271108 TGATGTTGTGGGTATGCGTGT 60.271 47.619 0.00 0.00 0.00 4.49
867 1306 1.447945 TGATGTTGTGGGTATGCGTG 58.552 50.000 0.00 0.00 0.00 5.34
868 1307 1.810151 GTTGATGTTGTGGGTATGCGT 59.190 47.619 0.00 0.00 0.00 5.24
869 1308 1.132262 GGTTGATGTTGTGGGTATGCG 59.868 52.381 0.00 0.00 0.00 4.73
870 1309 1.132262 CGGTTGATGTTGTGGGTATGC 59.868 52.381 0.00 0.00 0.00 3.14
871 1310 2.432444 ACGGTTGATGTTGTGGGTATG 58.568 47.619 0.00 0.00 0.00 2.39
872 1311 2.817258 CAACGGTTGATGTTGTGGGTAT 59.183 45.455 15.66 0.00 41.32 2.73
873 1312 2.158798 TCAACGGTTGATGTTGTGGGTA 60.159 45.455 19.07 0.00 45.33 3.69
875 1314 1.313772 TCAACGGTTGATGTTGTGGG 58.686 50.000 19.07 0.00 45.33 4.61
876 1315 2.357637 AGTTCAACGGTTGATGTTGTGG 59.642 45.455 22.97 0.00 45.33 4.17
877 1316 3.617669 GAGTTCAACGGTTGATGTTGTG 58.382 45.455 22.97 0.00 45.33 3.33
878 1317 2.286833 CGAGTTCAACGGTTGATGTTGT 59.713 45.455 22.97 7.39 45.33 3.32
880 1319 2.542595 GACGAGTTCAACGGTTGATGTT 59.457 45.455 22.97 12.13 39.84 2.71
881 1320 2.132762 GACGAGTTCAACGGTTGATGT 58.867 47.619 22.97 17.94 39.84 3.06
882 1321 2.404215 AGACGAGTTCAACGGTTGATG 58.596 47.619 22.97 15.31 39.84 3.07
883 1322 2.814280 AGACGAGTTCAACGGTTGAT 57.186 45.000 22.97 10.35 39.84 2.57
884 1323 2.100252 AGAAGACGAGTTCAACGGTTGA 59.900 45.455 19.07 19.07 38.04 3.18
885 1324 2.470821 AGAAGACGAGTTCAACGGTTG 58.529 47.619 14.62 14.62 34.93 3.77
886 1325 2.864343 CAAGAAGACGAGTTCAACGGTT 59.136 45.455 0.00 0.00 34.93 4.44
887 1326 2.470821 CAAGAAGACGAGTTCAACGGT 58.529 47.619 0.00 0.00 34.93 4.83
888 1327 1.792949 CCAAGAAGACGAGTTCAACGG 59.207 52.381 0.00 0.00 34.93 4.44
889 1328 1.192534 GCCAAGAAGACGAGTTCAACG 59.807 52.381 0.00 0.00 0.00 4.10
890 1329 2.476997 GAGCCAAGAAGACGAGTTCAAC 59.523 50.000 0.00 0.00 0.00 3.18
894 1333 3.330267 GAATGAGCCAAGAAGACGAGTT 58.670 45.455 0.00 0.00 0.00 3.01
895 1334 2.354203 GGAATGAGCCAAGAAGACGAGT 60.354 50.000 0.00 0.00 0.00 4.18
896 1335 2.093764 AGGAATGAGCCAAGAAGACGAG 60.094 50.000 0.00 0.00 0.00 4.18
897 1336 1.902508 AGGAATGAGCCAAGAAGACGA 59.097 47.619 0.00 0.00 0.00 4.20
898 1337 2.393271 AGGAATGAGCCAAGAAGACG 57.607 50.000 0.00 0.00 0.00 4.18
899 1338 3.013219 GGAAGGAATGAGCCAAGAAGAC 58.987 50.000 0.00 0.00 0.00 3.01
900 1339 2.915604 AGGAAGGAATGAGCCAAGAAGA 59.084 45.455 0.00 0.00 0.00 2.87
901 1340 3.277715 GAGGAAGGAATGAGCCAAGAAG 58.722 50.000 0.00 0.00 0.00 2.85
904 1343 1.661341 CGAGGAAGGAATGAGCCAAG 58.339 55.000 0.00 0.00 0.00 3.61
905 1344 0.392998 GCGAGGAAGGAATGAGCCAA 60.393 55.000 0.00 0.00 0.00 4.52
906 1345 1.221840 GCGAGGAAGGAATGAGCCA 59.778 57.895 0.00 0.00 0.00 4.75
907 1346 1.524849 GGCGAGGAAGGAATGAGCC 60.525 63.158 0.00 0.00 36.08 4.70
908 1347 0.531753 GAGGCGAGGAAGGAATGAGC 60.532 60.000 0.00 0.00 0.00 4.26
909 1348 0.105778 GGAGGCGAGGAAGGAATGAG 59.894 60.000 0.00 0.00 0.00 2.90
911 1350 0.471617 ATGGAGGCGAGGAAGGAATG 59.528 55.000 0.00 0.00 0.00 2.67
912 1351 0.471617 CATGGAGGCGAGGAAGGAAT 59.528 55.000 0.00 0.00 0.00 3.01
914 1353 1.001631 TCATGGAGGCGAGGAAGGA 59.998 57.895 0.00 0.00 0.00 3.36
916 1355 0.179089 CACTCATGGAGGCGAGGAAG 60.179 60.000 0.00 0.00 33.35 3.46
918 1357 0.397675 ATCACTCATGGAGGCGAGGA 60.398 55.000 0.00 0.00 33.35 3.71
920 1359 0.463204 ACATCACTCATGGAGGCGAG 59.537 55.000 0.00 0.00 36.72 5.03
922 1361 0.873312 CGACATCACTCATGGAGGCG 60.873 60.000 0.00 0.00 36.72 5.52
923 1362 0.461548 TCGACATCACTCATGGAGGC 59.538 55.000 0.00 0.00 36.72 4.70
924 1363 1.068281 CCTCGACATCACTCATGGAGG 59.932 57.143 0.00 0.00 35.68 4.30
925 1364 1.068281 CCCTCGACATCACTCATGGAG 59.932 57.143 0.00 0.00 36.72 3.86
926 1365 1.114627 CCCTCGACATCACTCATGGA 58.885 55.000 0.00 0.00 36.72 3.41
927 1366 0.531532 GCCCTCGACATCACTCATGG 60.532 60.000 0.00 0.00 36.72 3.66
928 1367 0.873312 CGCCCTCGACATCACTCATG 60.873 60.000 0.00 0.00 38.10 3.07
929 1368 1.439228 CGCCCTCGACATCACTCAT 59.561 57.895 0.00 0.00 38.10 2.90
930 1369 2.710902 CCGCCCTCGACATCACTCA 61.711 63.158 0.00 0.00 38.10 3.41
935 1374 2.172483 ATATGGCCGCCCTCGACATC 62.172 60.000 7.03 0.00 38.10 3.06
936 1375 2.172483 GATATGGCCGCCCTCGACAT 62.172 60.000 7.03 0.00 38.10 3.06
937 1376 2.842462 ATATGGCCGCCCTCGACA 60.842 61.111 7.03 0.00 38.10 4.35
938 1377 2.048127 GATATGGCCGCCCTCGAC 60.048 66.667 7.03 0.00 38.10 4.20
939 1378 3.680786 CGATATGGCCGCCCTCGA 61.681 66.667 16.88 0.00 38.10 4.04
940 1379 3.916392 GACGATATGGCCGCCCTCG 62.916 68.421 19.06 19.06 35.56 4.63
941 1380 2.048127 GACGATATGGCCGCCCTC 60.048 66.667 7.03 0.21 0.00 4.30
942 1381 2.524394 AGACGATATGGCCGCCCT 60.524 61.111 7.03 0.00 0.00 5.19
943 1382 2.357517 CAGACGATATGGCCGCCC 60.358 66.667 7.03 0.00 0.00 6.13
946 1631 1.593006 GAAACACAGACGATATGGCCG 59.407 52.381 0.00 0.00 0.00 6.13
948 1633 2.609459 CCAGAAACACAGACGATATGGC 59.391 50.000 0.00 0.00 0.00 4.40
959 1644 0.819259 GTGCCTGAGCCAGAAACACA 60.819 55.000 4.00 0.00 38.69 3.72
960 1645 1.518903 GGTGCCTGAGCCAGAAACAC 61.519 60.000 4.00 8.37 38.69 3.32
961 1646 1.228245 GGTGCCTGAGCCAGAAACA 60.228 57.895 4.00 0.00 38.69 2.83
964 1649 1.834856 CTGAGGTGCCTGAGCCAGAA 61.835 60.000 0.00 0.00 38.69 3.02
965 1650 2.203832 TGAGGTGCCTGAGCCAGA 60.204 61.111 0.00 0.00 38.69 3.86
967 1652 4.025858 GCTGAGGTGCCTGAGCCA 62.026 66.667 17.09 0.00 45.35 4.75
1386 3395 3.840468 TGCAGCAAGAACATAAATGCAG 58.160 40.909 0.00 0.00 41.18 4.41
1594 3606 4.135306 AGAATGAGTCATGCATGCTAAGG 58.865 43.478 22.25 0.58 29.75 2.69
1787 3819 7.033791 TGGAGAACTTTAACATGAGATACGAC 58.966 38.462 0.00 0.00 0.00 4.34
2042 4160 5.050159 GGACAAGGTGACAAAAATTGCAATC 60.050 40.000 13.38 0.00 0.00 2.67
2233 4357 1.141665 CTCGCACCCGATGATCACA 59.858 57.895 0.00 0.00 43.47 3.58
2713 4879 3.390967 CCCCAAAACAAGACAGGGAAAAT 59.609 43.478 0.00 0.00 42.25 1.82
2802 4978 7.341805 AGGTGCACAGATATTTTTCTCTACAT 58.658 34.615 20.43 0.00 0.00 2.29
2810 4986 6.544038 GCAAAAAGGTGCACAGATATTTTT 57.456 33.333 20.43 17.73 44.29 1.94
2837 5014 8.792830 TCAATTAGTAGGGAATTTCTCAACAG 57.207 34.615 0.00 0.00 0.00 3.16
2857 5034 1.745489 GCCTCCGAACGCCTCAATT 60.745 57.895 0.00 0.00 0.00 2.32
2860 5037 4.373116 GTGCCTCCGAACGCCTCA 62.373 66.667 0.00 0.00 0.00 3.86
2867 5044 1.770294 AACAAAAAGGTGCCTCCGAA 58.230 45.000 0.00 0.00 41.99 4.30
2870 5047 1.760029 TCCAAACAAAAAGGTGCCTCC 59.240 47.619 0.00 0.00 0.00 4.30
2871 5048 3.751479 ATCCAAACAAAAAGGTGCCTC 57.249 42.857 0.00 0.00 0.00 4.70
2875 5052 5.754890 CCTCAAGAATCCAAACAAAAAGGTG 59.245 40.000 0.00 0.00 0.00 4.00
2878 5055 4.445385 CGCCTCAAGAATCCAAACAAAAAG 59.555 41.667 0.00 0.00 0.00 2.27
2916 5101 6.428159 AGTTTGCAACCTTCTATGTCAGTTAG 59.572 38.462 0.00 0.00 0.00 2.34
2918 5103 5.133221 AGTTTGCAACCTTCTATGTCAGTT 58.867 37.500 0.00 0.00 0.00 3.16
3056 5272 2.768527 TGAGCTGGGTTATCCTCTGAAG 59.231 50.000 0.00 0.00 36.20 3.02
3104 5321 1.890979 CTGAGGGCGGCTAATGCAG 60.891 63.158 9.56 5.87 41.91 4.41
3146 5363 3.393800 CTTCCGGTGCAGAAGTATATGG 58.606 50.000 0.00 0.00 36.74 2.74
3153 5370 1.576421 GCAACTTCCGGTGCAGAAG 59.424 57.895 9.73 11.52 45.12 2.85
3163 5380 0.806492 GAGGTCGATCGGCAACTTCC 60.806 60.000 22.85 2.36 0.00 3.46
3165 5382 1.218316 GGAGGTCGATCGGCAACTT 59.782 57.895 22.85 5.87 0.00 2.66
3200 5417 4.222810 TGAGGCAACAAGCTCTTCAGTATA 59.777 41.667 0.00 0.00 44.79 1.47
3255 5504 1.134946 AGTGCAAGTTCAACCTTGTGC 59.865 47.619 0.00 0.00 43.03 4.57
3318 5567 5.892160 TGGAAGAAGATTGAATTCTGCTG 57.108 39.130 7.05 0.00 37.10 4.41
3393 5642 5.412904 GTGATTCTTCTAGTTCAAACCAGGG 59.587 44.000 0.00 0.00 0.00 4.45
3408 5657 3.544244 GCGTAATTGGAGCGTGATTCTTC 60.544 47.826 0.00 0.00 0.00 2.87
3412 5661 1.732941 TGCGTAATTGGAGCGTGATT 58.267 45.000 0.00 0.00 0.00 2.57
3424 5673 9.794685 CTACAGATATGTAGAATGATGCGTAAT 57.205 33.333 20.52 0.00 43.16 1.89


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

AutoCloner maintained by Alex Coulton.