Multiple sequence alignment - TraesCS5A01G173600

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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 TraesCS5A01G173600 chr5A 100.000 3356 0 0 1 3356 367076436 367079791 0.000000e+00 6198.0
1 TraesCS5A01G173600 chr5D 93.732 1037 40 10 914 1937 277683203 277684227 0.000000e+00 1531.0
2 TraesCS5A01G173600 chr5D 91.842 760 30 13 2091 2842 277690047 277690782 0.000000e+00 1031.0
3 TraesCS5A01G173600 chr5D 83.382 686 53 33 1 644 277682221 277682887 2.240000e-161 579.0
4 TraesCS5A01G173600 chr5D 95.876 97 2 1 2001 2095 277684242 277684338 4.480000e-34 156.0
5 TraesCS5A01G173600 chr5B 95.341 880 31 7 2002 2877 315893822 315894695 0.000000e+00 1389.0
6 TraesCS5A01G173600 chr5B 93.333 525 27 3 840 1359 315892350 315892871 0.000000e+00 769.0
7 TraesCS5A01G173600 chr5B 93.983 482 25 3 2001 2482 642584220 642584697 0.000000e+00 726.0
8 TraesCS5A01G173600 chr5B 89.217 575 33 12 82 651 315891574 315892124 0.000000e+00 691.0
9 TraesCS5A01G173600 chr5B 93.333 390 12 7 1548 1937 315893436 315893811 6.290000e-157 564.0
10 TraesCS5A01G173600 chr5B 95.082 183 8 1 1756 1937 642584025 642584207 1.520000e-73 287.0
11 TraesCS5A01G173600 chr5B 95.376 173 7 1 1348 1520 315892894 315893065 1.190000e-69 274.0
12 TraesCS5A01G173600 chr5B 94.000 150 9 0 693 842 315892120 315892269 9.370000e-56 228.0
13 TraesCS5A01G173600 chr5B 92.254 142 10 1 3216 3356 315895210 315895351 2.040000e-47 200.0
14 TraesCS5A01G173600 chr3B 93.971 481 25 2 2002 2482 56532331 56532807 0.000000e+00 725.0
15 TraesCS5A01G173600 chr3B 95.628 183 8 0 1755 1937 56532136 56532318 9.110000e-76 294.0
16 TraesCS5A01G173600 chr3B 96.154 78 3 0 1755 1832 34657173 34657096 9.770000e-26 128.0
17 TraesCS5A01G173600 chr3B 92.941 85 5 1 1755 1839 689934222 689934305 4.550000e-24 122.0
18 TraesCS5A01G173600 chr2B 91.333 150 8 2 2896 3040 158305617 158305766 2.040000e-47 200.0
19 TraesCS5A01G173600 chr2B 100.000 28 0 0 793 820 257899265 257899238 6.000000e-03 52.8
20 TraesCS5A01G173600 chr6B 86.000 150 16 2 2896 3040 326967154 326967005 4.480000e-34 156.0
21 TraesCS5A01G173600 chr2D 91.176 102 9 0 2929 3030 561317212 561317111 4.520000e-29 139.0
22 TraesCS5A01G173600 chrUn 96.154 78 3 0 1755 1832 343780745 343780668 9.770000e-26 128.0
23 TraesCS5A01G173600 chr4A 96.154 78 3 0 1755 1832 648464746 648464823 9.770000e-26 128.0
24 TraesCS5A01G173600 chr4A 96.154 78 3 0 1755 1832 710919764 710919841 9.770000e-26 128.0
25 TraesCS5A01G173600 chr3D 100.000 31 0 0 3042 3072 603306671 603306701 1.300000e-04 58.4
26 TraesCS5A01G173600 chr3A 100.000 28 0 0 793 820 22225868 22225895 6.000000e-03 52.8


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 TraesCS5A01G173600 chr5A 367076436 367079791 3355 False 6198.000000 6198 100.000000 1 3356 1 chr5A.!!$F1 3355
1 TraesCS5A01G173600 chr5D 277690047 277690782 735 False 1031.000000 1031 91.842000 2091 2842 1 chr5D.!!$F1 751
2 TraesCS5A01G173600 chr5D 277682221 277684338 2117 False 755.333333 1531 90.996667 1 2095 3 chr5D.!!$F2 2094
3 TraesCS5A01G173600 chr5B 315891574 315895351 3777 False 587.857143 1389 93.264857 82 3356 7 chr5B.!!$F1 3274
4 TraesCS5A01G173600 chr5B 642584025 642584697 672 False 506.500000 726 94.532500 1756 2482 2 chr5B.!!$F2 726
5 TraesCS5A01G173600 chr3B 56532136 56532807 671 False 509.500000 725 94.799500 1755 2482 2 chr3B.!!$F2 727

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
656 719 0.109781 CGTGCTTTGCTTATTGCGGT 60.110 50.0 0.00 0.00 46.63 5.68 F
671 734 0.311477 GCGGTCTTCTCGTAGGATCC 59.689 60.0 2.48 2.48 0.00 3.36 F
2075 2747 0.323360 TGCCCCTTCCAATGCAGTAC 60.323 55.0 0.00 0.00 0.00 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1677 2348 0.182775 AGCCAAAGGACTTGAACCGT 59.817 50.0 0.00 0.0 37.17 4.83 R
2128 2802 0.388649 GCATAGTAGGGCCATCGTCG 60.389 60.0 6.18 0.0 0.00 5.12 R
2903 3640 0.172578 CAGGAAGCATCGTCCGTGTA 59.827 55.0 0.00 0.0 40.36 2.90 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
49 52 5.217393 GTTTTGTCAAAACCGATTACTCCC 58.783 41.667 24.70 1.51 43.78 4.30
59 73 3.187700 CCGATTACTCCCGACTCAAAAG 58.812 50.000 0.00 0.00 0.00 2.27
61 75 4.491676 CGATTACTCCCGACTCAAAAGAA 58.508 43.478 0.00 0.00 0.00 2.52
70 84 6.481643 TCCCGACTCAAAAGAAAAGGATTAT 58.518 36.000 0.00 0.00 0.00 1.28
71 85 6.374333 TCCCGACTCAAAAGAAAAGGATTATG 59.626 38.462 0.00 0.00 0.00 1.90
72 86 6.151144 CCCGACTCAAAAGAAAAGGATTATGT 59.849 38.462 0.00 0.00 0.00 2.29
73 87 7.335924 CCCGACTCAAAAGAAAAGGATTATGTA 59.664 37.037 0.00 0.00 0.00 2.29
74 88 8.726988 CCGACTCAAAAGAAAAGGATTATGTAA 58.273 33.333 0.00 0.00 0.00 2.41
161 177 6.927294 AATAAAGGGACGCTAATCTTCTTG 57.073 37.500 0.00 0.00 0.00 3.02
188 204 2.756283 CGGTCTCCCTCGCTTCCT 60.756 66.667 0.00 0.00 0.00 3.36
226 242 7.659652 AAAAGGAAAATAGTTGTCTCTCTCG 57.340 36.000 0.00 0.00 0.00 4.04
267 286 1.990160 AACCTCCGCAACACCAGGAA 61.990 55.000 0.00 0.00 33.10 3.36
268 287 1.672356 CCTCCGCAACACCAGGAAG 60.672 63.158 0.00 0.00 33.10 3.46
269 288 1.371183 CTCCGCAACACCAGGAAGA 59.629 57.895 0.00 0.00 33.10 2.87
309 328 4.315588 GGACGAACCGAGGAGAGA 57.684 61.111 0.00 0.00 0.00 3.10
341 361 1.972795 TGGTTTGTCGCTACCCTAACT 59.027 47.619 0.00 0.00 33.34 2.24
354 374 2.970640 ACCCTAACTTGTTCCGAGACTT 59.029 45.455 0.00 0.00 0.00 3.01
446 466 1.668628 CGTTTTCCCGCCTCCAATTTG 60.669 52.381 0.00 0.00 0.00 2.32
447 467 0.972883 TTTTCCCGCCTCCAATTTGG 59.027 50.000 9.28 9.28 39.43 3.28
448 468 0.178947 TTTCCCGCCTCCAATTTGGT 60.179 50.000 14.98 0.00 39.03 3.67
449 469 0.897863 TTCCCGCCTCCAATTTGGTG 60.898 55.000 14.98 12.36 39.03 4.17
450 470 1.304052 CCCGCCTCCAATTTGGTGA 60.304 57.895 17.09 0.00 39.03 4.02
451 471 1.595093 CCCGCCTCCAATTTGGTGAC 61.595 60.000 17.09 6.42 39.03 3.67
452 472 1.501741 CGCCTCCAATTTGGTGACG 59.498 57.895 17.09 14.00 39.03 4.35
453 473 1.883021 GCCTCCAATTTGGTGACGG 59.117 57.895 17.09 12.95 39.03 4.79
454 474 1.883021 CCTCCAATTTGGTGACGGC 59.117 57.895 17.09 0.00 39.03 5.68
455 475 1.595093 CCTCCAATTTGGTGACGGCC 61.595 60.000 17.09 0.00 39.03 6.13
456 476 1.922135 CTCCAATTTGGTGACGGCCG 61.922 60.000 26.86 26.86 39.03 6.13
459 479 1.529713 AATTTGGTGACGGCCGGTT 60.530 52.632 31.76 9.62 0.00 4.44
490 549 1.139654 CCGGCCATGAAGATCTTCTCA 59.860 52.381 30.45 16.84 40.14 3.27
492 551 2.158986 CGGCCATGAAGATCTTCTCACT 60.159 50.000 30.45 13.73 40.14 3.41
521 580 1.083489 GATCGATTTGAACGTGCCCA 58.917 50.000 0.00 0.00 0.00 5.36
531 590 2.953821 CGTGCCCATGCTCGTTTT 59.046 55.556 1.29 0.00 46.34 2.43
532 591 2.167161 CGTGCCCATGCTCGTTTTA 58.833 52.632 1.29 0.00 46.34 1.52
562 621 3.136443 TCTTGGTTCCTGGCTACATATGG 59.864 47.826 7.80 0.00 0.00 2.74
601 664 3.061831 CAGTAGTGCGATCAAGAGCTTTG 59.938 47.826 0.00 0.00 0.00 2.77
649 712 2.499197 TGTGAATCCGTGCTTTGCTTA 58.501 42.857 0.00 0.00 0.00 3.09
650 713 3.081061 TGTGAATCCGTGCTTTGCTTAT 58.919 40.909 0.00 0.00 0.00 1.73
651 714 3.505680 TGTGAATCCGTGCTTTGCTTATT 59.494 39.130 0.00 0.00 0.00 1.40
652 715 3.853671 GTGAATCCGTGCTTTGCTTATTG 59.146 43.478 0.00 0.00 0.00 1.90
653 716 2.566952 ATCCGTGCTTTGCTTATTGC 57.433 45.000 0.00 0.00 43.25 3.56
654 717 0.167908 TCCGTGCTTTGCTTATTGCG 59.832 50.000 0.00 0.00 46.63 4.85
655 718 0.798009 CCGTGCTTTGCTTATTGCGG 60.798 55.000 0.00 0.00 46.63 5.69
656 719 0.109781 CGTGCTTTGCTTATTGCGGT 60.110 50.000 0.00 0.00 46.63 5.68
657 720 1.617740 GTGCTTTGCTTATTGCGGTC 58.382 50.000 0.00 0.00 46.63 4.79
658 721 1.200020 GTGCTTTGCTTATTGCGGTCT 59.800 47.619 0.00 0.00 46.63 3.85
659 722 1.885887 TGCTTTGCTTATTGCGGTCTT 59.114 42.857 0.00 0.00 46.63 3.01
660 723 2.095263 TGCTTTGCTTATTGCGGTCTTC 60.095 45.455 0.00 0.00 46.63 2.87
661 724 2.162408 GCTTTGCTTATTGCGGTCTTCT 59.838 45.455 0.00 0.00 46.63 2.85
662 725 3.729163 GCTTTGCTTATTGCGGTCTTCTC 60.729 47.826 0.00 0.00 46.63 2.87
663 726 1.640428 TGCTTATTGCGGTCTTCTCG 58.360 50.000 0.00 0.00 46.63 4.04
664 727 1.067142 TGCTTATTGCGGTCTTCTCGT 60.067 47.619 0.00 0.00 46.63 4.18
665 728 2.164827 TGCTTATTGCGGTCTTCTCGTA 59.835 45.455 0.00 0.00 46.63 3.43
666 729 2.789893 GCTTATTGCGGTCTTCTCGTAG 59.210 50.000 0.00 0.00 0.00 3.51
667 730 3.372954 CTTATTGCGGTCTTCTCGTAGG 58.627 50.000 0.00 0.00 0.00 3.18
668 731 1.471119 ATTGCGGTCTTCTCGTAGGA 58.529 50.000 0.00 0.00 0.00 2.94
669 732 1.471119 TTGCGGTCTTCTCGTAGGAT 58.529 50.000 0.00 0.00 0.00 3.24
670 733 1.022735 TGCGGTCTTCTCGTAGGATC 58.977 55.000 0.00 0.00 0.00 3.36
671 734 0.311477 GCGGTCTTCTCGTAGGATCC 59.689 60.000 2.48 2.48 0.00 3.36
672 735 0.587285 CGGTCTTCTCGTAGGATCCG 59.413 60.000 5.98 0.00 0.00 4.18
673 736 1.677942 GGTCTTCTCGTAGGATCCGT 58.322 55.000 5.98 0.00 0.00 4.69
674 737 2.022934 GGTCTTCTCGTAGGATCCGTT 58.977 52.381 5.98 0.00 0.00 4.44
675 738 3.209410 GGTCTTCTCGTAGGATCCGTTA 58.791 50.000 5.98 0.00 0.00 3.18
676 739 3.003171 GGTCTTCTCGTAGGATCCGTTAC 59.997 52.174 5.98 3.52 0.00 2.50
677 740 2.868583 TCTTCTCGTAGGATCCGTTACG 59.131 50.000 21.64 21.64 42.86 3.18
678 741 0.940126 TCTCGTAGGATCCGTTACGC 59.060 55.000 22.46 4.91 41.65 4.42
679 742 0.942962 CTCGTAGGATCCGTTACGCT 59.057 55.000 22.46 1.17 41.65 5.07
680 743 0.940126 TCGTAGGATCCGTTACGCTC 59.060 55.000 22.46 0.00 41.65 5.03
681 744 0.942962 CGTAGGATCCGTTACGCTCT 59.057 55.000 17.56 0.00 36.61 4.09
682 745 2.138320 CGTAGGATCCGTTACGCTCTA 58.862 52.381 17.56 0.00 36.61 2.43
683 746 2.157279 CGTAGGATCCGTTACGCTCTAG 59.843 54.545 17.56 0.00 36.61 2.43
684 747 2.345124 AGGATCCGTTACGCTCTAGT 57.655 50.000 5.98 0.00 0.00 2.57
685 748 3.482156 AGGATCCGTTACGCTCTAGTA 57.518 47.619 5.98 0.00 0.00 1.82
686 749 3.813443 AGGATCCGTTACGCTCTAGTAA 58.187 45.455 5.98 0.00 34.56 2.24
735 798 2.148916 AGCAACGATGAGTTTGACGA 57.851 45.000 0.00 0.00 42.02 4.20
737 800 1.525197 GCAACGATGAGTTTGACGACA 59.475 47.619 0.00 0.00 42.02 4.35
776 839 7.413000 CGGTATTGTAGTTCTGAACTTGGATTG 60.413 40.741 26.33 8.25 42.81 2.67
801 864 5.602978 TCCATCCTGTTTTATCTACTCCCTC 59.397 44.000 0.00 0.00 0.00 4.30
803 866 4.955335 TCCTGTTTTATCTACTCCCTCCA 58.045 43.478 0.00 0.00 0.00 3.86
830 999 6.073222 TCCTTTTTACTCTGCTCGATTTGTTC 60.073 38.462 0.00 0.00 0.00 3.18
880 1136 3.637432 TCGTGTTGATGGCATTGTTTTC 58.363 40.909 0.00 0.00 0.00 2.29
888 1144 4.022068 TGATGGCATTGTTTTCTTGACCTC 60.022 41.667 0.00 0.00 0.00 3.85
916 1172 9.444600 TTCTTTATTATCTTGACTTGGTACACC 57.555 33.333 0.00 0.00 39.29 4.16
940 1196 6.594937 CCTATTGTTGCTTGTAAATTGCCATT 59.405 34.615 0.00 0.00 0.00 3.16
942 1198 5.212532 TGTTGCTTGTAAATTGCCATTCT 57.787 34.783 0.00 0.00 0.00 2.40
944 1200 4.095410 TGCTTGTAAATTGCCATTCTCG 57.905 40.909 0.00 0.00 0.00 4.04
946 1202 4.022416 TGCTTGTAAATTGCCATTCTCGTT 60.022 37.500 0.00 0.00 0.00 3.85
949 1230 6.751888 GCTTGTAAATTGCCATTCTCGTTATT 59.248 34.615 0.00 0.00 0.00 1.40
956 1237 7.807977 ATTGCCATTCTCGTTATTCATTACT 57.192 32.000 0.00 0.00 0.00 2.24
1022 1304 1.611936 GGAGGGTTCCAGTTTGAGAGC 60.612 57.143 0.00 0.00 43.45 4.09
1120 1402 1.167851 GCTGGTTTCTATGCTGCACA 58.832 50.000 3.57 0.00 0.00 4.57
1194 1476 0.662374 AGGTGTGTCGAAGTTACGCG 60.662 55.000 3.53 3.53 0.00 6.01
1399 1727 3.536956 TGACCGTCCTTGTGGATTATC 57.463 47.619 0.00 0.00 45.29 1.75
1413 1741 5.123820 TGTGGATTATCTGCTTCCTTTTTCG 59.876 40.000 0.00 0.00 0.00 3.46
1459 1787 2.419297 GGCATACCTTGAGTCCACTCTG 60.419 54.545 8.19 1.70 43.25 3.35
1482 1810 5.523188 TGCAAACTTTGATTGGATGTTTCAC 59.477 36.000 5.65 0.00 0.00 3.18
1511 1839 8.359875 TGTATCATAATGTGGAACCAACATTT 57.640 30.769 18.66 9.53 35.87 2.32
1665 2336 2.039084 CAGAGTTAGCCTCAGTTGGGTT 59.961 50.000 0.00 0.00 43.12 4.11
1675 2346 1.152546 AGTTGGGTTGGGCAGGTTC 60.153 57.895 0.00 0.00 0.00 3.62
1676 2347 1.456705 GTTGGGTTGGGCAGGTTCA 60.457 57.895 0.00 0.00 0.00 3.18
1677 2348 1.045911 GTTGGGTTGGGCAGGTTCAA 61.046 55.000 0.00 0.00 0.00 2.69
1678 2349 1.045911 TTGGGTTGGGCAGGTTCAAC 61.046 55.000 0.00 0.00 41.61 3.18
1679 2350 2.561037 GGGTTGGGCAGGTTCAACG 61.561 63.158 0.00 0.00 42.81 4.10
1680 2351 2.561037 GGTTGGGCAGGTTCAACGG 61.561 63.158 0.00 0.00 42.81 4.44
1681 2352 1.826487 GTTGGGCAGGTTCAACGGT 60.826 57.895 0.00 0.00 34.75 4.83
1682 2353 1.076632 TTGGGCAGGTTCAACGGTT 60.077 52.632 0.00 0.00 0.00 4.44
1789 2460 9.883142 TTTTGATAGTCCAAGTCAAAACAAAAT 57.117 25.926 8.04 0.00 43.17 1.82
1957 2629 9.613428 TTTTGACATAGTTAGGGATTCAGTATG 57.387 33.333 0.00 0.00 37.54 2.39
1958 2630 6.759272 TGACATAGTTAGGGATTCAGTATGC 58.241 40.000 0.00 0.00 34.76 3.14
1959 2631 6.326323 TGACATAGTTAGGGATTCAGTATGCA 59.674 38.462 0.00 0.00 34.76 3.96
1960 2632 6.763355 ACATAGTTAGGGATTCAGTATGCAG 58.237 40.000 0.00 0.00 34.76 4.41
1961 2633 6.327626 ACATAGTTAGGGATTCAGTATGCAGT 59.672 38.462 0.00 0.00 34.76 4.40
1962 2634 5.700402 AGTTAGGGATTCAGTATGCAGTT 57.300 39.130 0.00 0.00 34.76 3.16
1963 2635 6.808321 AGTTAGGGATTCAGTATGCAGTTA 57.192 37.500 0.00 0.00 34.76 2.24
1964 2636 6.821388 AGTTAGGGATTCAGTATGCAGTTAG 58.179 40.000 0.00 0.00 34.76 2.34
1965 2637 4.696479 AGGGATTCAGTATGCAGTTAGG 57.304 45.455 0.00 0.00 34.76 2.69
1966 2638 3.392616 AGGGATTCAGTATGCAGTTAGGG 59.607 47.826 0.00 0.00 34.76 3.53
1967 2639 3.391296 GGGATTCAGTATGCAGTTAGGGA 59.609 47.826 0.00 0.00 34.76 4.20
1968 2640 4.042187 GGGATTCAGTATGCAGTTAGGGAT 59.958 45.833 0.00 0.00 34.76 3.85
1969 2641 5.456763 GGGATTCAGTATGCAGTTAGGGATT 60.457 44.000 0.00 0.00 34.76 3.01
1970 2642 5.703130 GGATTCAGTATGCAGTTAGGGATTC 59.297 44.000 0.00 0.00 34.76 2.52
1971 2643 5.692115 TTCAGTATGCAGTTAGGGATTCA 57.308 39.130 0.00 0.00 34.76 2.57
1972 2644 5.282055 TCAGTATGCAGTTAGGGATTCAG 57.718 43.478 0.00 0.00 34.76 3.02
1973 2645 4.716784 TCAGTATGCAGTTAGGGATTCAGT 59.283 41.667 0.00 0.00 34.76 3.41
1974 2646 5.897250 TCAGTATGCAGTTAGGGATTCAGTA 59.103 40.000 0.00 0.00 34.76 2.74
1975 2647 6.554982 TCAGTATGCAGTTAGGGATTCAGTAT 59.445 38.462 0.00 0.00 34.76 2.12
1976 2648 7.071196 TCAGTATGCAGTTAGGGATTCAGTATT 59.929 37.037 0.00 0.00 34.76 1.89
1977 2649 7.386299 CAGTATGCAGTTAGGGATTCAGTATTC 59.614 40.741 0.00 0.00 0.00 1.75
1978 2650 5.692115 TGCAGTTAGGGATTCAGTATTCA 57.308 39.130 0.00 0.00 0.00 2.57
1979 2651 5.674525 TGCAGTTAGGGATTCAGTATTCAG 58.325 41.667 0.00 0.00 0.00 3.02
1980 2652 5.189736 TGCAGTTAGGGATTCAGTATTCAGT 59.810 40.000 0.00 0.00 0.00 3.41
1981 2653 5.525378 GCAGTTAGGGATTCAGTATTCAGTG 59.475 44.000 0.00 0.00 0.00 3.66
1982 2654 5.525378 CAGTTAGGGATTCAGTATTCAGTGC 59.475 44.000 0.00 0.00 0.00 4.40
1983 2655 5.189736 AGTTAGGGATTCAGTATTCAGTGCA 59.810 40.000 0.00 0.00 0.00 4.57
1984 2656 4.785346 AGGGATTCAGTATTCAGTGCAT 57.215 40.909 0.00 0.00 0.00 3.96
1985 2657 5.894298 AGGGATTCAGTATTCAGTGCATA 57.106 39.130 0.00 0.00 0.00 3.14
1986 2658 6.445451 AGGGATTCAGTATTCAGTGCATAT 57.555 37.500 0.00 0.00 0.00 1.78
1987 2659 6.236409 AGGGATTCAGTATTCAGTGCATATG 58.764 40.000 0.00 0.00 0.00 1.78
1988 2660 5.106396 GGGATTCAGTATTCAGTGCATATGC 60.106 44.000 21.09 21.09 42.50 3.14
2075 2747 0.323360 TGCCCCTTCCAATGCAGTAC 60.323 55.000 0.00 0.00 0.00 2.73
2085 2759 5.628797 TCCAATGCAGTACATATCTTGGA 57.371 39.130 8.23 8.23 38.88 3.53
2128 2802 9.930693 CCTATGTTTCCTATTATCTTCCACTAC 57.069 37.037 0.00 0.00 0.00 2.73
2260 2938 2.053277 GGGAGACTCCGGACACTCC 61.053 68.421 29.66 29.66 45.50 3.85
2342 3020 4.900684 ACTACTGAGGAGGAAGAAAAAGC 58.099 43.478 0.00 0.00 0.00 3.51
2344 3022 3.749226 ACTGAGGAGGAAGAAAAAGCTG 58.251 45.455 0.00 0.00 0.00 4.24
2345 3023 3.392616 ACTGAGGAGGAAGAAAAAGCTGA 59.607 43.478 0.00 0.00 0.00 4.26
2346 3024 4.002316 CTGAGGAGGAAGAAAAAGCTGAG 58.998 47.826 0.00 0.00 0.00 3.35
2347 3025 3.648067 TGAGGAGGAAGAAAAAGCTGAGA 59.352 43.478 0.00 0.00 0.00 3.27
2526 3206 5.415701 GGTTGCTCCTGATCTGTAAATTCAA 59.584 40.000 0.00 0.00 0.00 2.69
2554 3236 7.517614 TGAAGTACTTTTGGCATTTCATACA 57.482 32.000 10.02 0.00 0.00 2.29
2563 3245 3.181501 TGGCATTTCATACACGCTTTAGC 60.182 43.478 0.00 0.00 37.78 3.09
2650 3332 7.647715 CGGGATGTTTGAATATAACATTGTTCC 59.352 37.037 5.07 2.56 44.05 3.62
2680 3362 6.610075 ATTTGGTGGATGCTTATTTTCACT 57.390 33.333 0.00 0.00 0.00 3.41
2681 3363 5.389859 TTGGTGGATGCTTATTTTCACTG 57.610 39.130 0.00 0.00 0.00 3.66
2682 3364 4.661222 TGGTGGATGCTTATTTTCACTGA 58.339 39.130 0.00 0.00 0.00 3.41
2683 3365 4.701651 TGGTGGATGCTTATTTTCACTGAG 59.298 41.667 0.00 0.00 0.00 3.35
2684 3366 4.702131 GGTGGATGCTTATTTTCACTGAGT 59.298 41.667 0.00 0.00 0.00 3.41
2685 3367 5.392380 GGTGGATGCTTATTTTCACTGAGTG 60.392 44.000 6.18 6.18 34.45 3.51
2687 3369 5.769662 TGGATGCTTATTTTCACTGAGTGTT 59.230 36.000 12.93 0.00 34.79 3.32
2688 3370 6.939730 TGGATGCTTATTTTCACTGAGTGTTA 59.060 34.615 12.93 0.00 34.79 2.41
2689 3371 7.611467 TGGATGCTTATTTTCACTGAGTGTTAT 59.389 33.333 12.93 7.19 34.79 1.89
2690 3372 7.912250 GGATGCTTATTTTCACTGAGTGTTATG 59.088 37.037 12.93 4.82 34.79 1.90
2761 3443 2.413837 ACGAGTTGTGGTGTTATCTGC 58.586 47.619 0.00 0.00 0.00 4.26
2783 3465 9.824216 TCTGCTGTAGTAGGGAGTAATTTATAT 57.176 33.333 0.00 0.00 0.00 0.86
2799 3481 9.632638 GTAATTTATATCATCCCCATAGTGCAT 57.367 33.333 0.00 0.00 0.00 3.96
2821 3503 8.028354 TGCATAGTGTCTTAAATGGTTTCATTG 58.972 33.333 0.00 0.00 42.29 2.82
2886 3623 5.115480 CAGTAAACAAATTTGCCTTGGTGT 58.885 37.500 18.12 0.00 31.23 4.16
2887 3624 5.584251 CAGTAAACAAATTTGCCTTGGTGTT 59.416 36.000 18.12 0.02 31.23 3.32
2888 3625 6.758886 CAGTAAACAAATTTGCCTTGGTGTTA 59.241 34.615 18.12 2.13 31.23 2.41
2890 3627 6.616774 AAACAAATTTGCCTTGGTGTTATG 57.383 33.333 18.12 0.00 0.00 1.90
2892 3629 5.679601 ACAAATTTGCCTTGGTGTTATGTT 58.320 33.333 18.12 0.00 0.00 2.71
2893 3630 6.821388 ACAAATTTGCCTTGGTGTTATGTTA 58.179 32.000 18.12 0.00 0.00 2.41
2894 3631 7.275920 ACAAATTTGCCTTGGTGTTATGTTAA 58.724 30.769 18.12 0.00 0.00 2.01
2896 3633 7.961325 AATTTGCCTTGGTGTTATGTTAAAG 57.039 32.000 0.00 0.00 0.00 1.85
2897 3634 4.513198 TGCCTTGGTGTTATGTTAAAGC 57.487 40.909 0.00 0.00 0.00 3.51
2899 3636 4.022416 TGCCTTGGTGTTATGTTAAAGCAG 60.022 41.667 0.00 0.00 0.00 4.24
2901 3638 5.460646 CCTTGGTGTTATGTTAAAGCAGTG 58.539 41.667 0.00 0.00 0.00 3.66
2903 3640 4.141287 TGGTGTTATGTTAAAGCAGTGCT 58.859 39.130 13.14 13.14 42.56 4.40
2904 3641 5.309638 TGGTGTTATGTTAAAGCAGTGCTA 58.690 37.500 20.09 1.77 38.25 3.49
2906 3643 5.180492 GGTGTTATGTTAAAGCAGTGCTACA 59.820 40.000 20.09 19.37 38.25 2.74
2907 3644 6.077838 GTGTTATGTTAAAGCAGTGCTACAC 58.922 40.000 20.09 20.86 38.25 2.90
2908 3645 5.107259 TGTTATGTTAAAGCAGTGCTACACG 60.107 40.000 20.09 0.00 38.25 4.49
2909 3646 2.139917 TGTTAAAGCAGTGCTACACGG 58.860 47.619 20.09 0.00 38.25 4.94
2913 3650 1.802337 AAGCAGTGCTACACGGACGA 61.802 55.000 20.09 0.00 38.25 4.20
2915 3652 1.413767 GCAGTGCTACACGGACGATG 61.414 60.000 8.18 0.00 39.64 3.84
2916 3653 1.153823 AGTGCTACACGGACGATGC 60.154 57.895 0.00 0.00 39.64 3.91
2917 3654 1.153823 GTGCTACACGGACGATGCT 60.154 57.895 0.00 0.00 0.00 3.79
2918 3655 0.736325 GTGCTACACGGACGATGCTT 60.736 55.000 0.00 0.00 0.00 3.91
2919 3656 0.457853 TGCTACACGGACGATGCTTC 60.458 55.000 0.00 0.00 0.00 3.86
2920 3657 1.146358 GCTACACGGACGATGCTTCC 61.146 60.000 0.00 0.00 0.00 3.46
2921 3658 0.456221 CTACACGGACGATGCTTCCT 59.544 55.000 0.00 0.00 0.00 3.36
2940 3677 2.100031 GCACGATGCACGATGGACA 61.100 57.895 14.18 0.00 44.26 4.02
2941 3678 1.634757 GCACGATGCACGATGGACAA 61.635 55.000 14.18 0.00 44.26 3.18
2942 3679 0.795698 CACGATGCACGATGGACAAA 59.204 50.000 14.18 0.00 45.77 2.83
2943 3680 1.196581 CACGATGCACGATGGACAAAA 59.803 47.619 14.18 0.00 45.77 2.44
2944 3681 1.464608 ACGATGCACGATGGACAAAAG 59.535 47.619 14.18 0.00 45.77 2.27
2946 3683 1.199789 GATGCACGATGGACAAAAGCA 59.800 47.619 0.00 0.00 34.78 3.91
2948 3685 1.199789 TGCACGATGGACAAAAGCATC 59.800 47.619 0.00 0.00 0.00 3.91
2949 3686 1.468054 GCACGATGGACAAAAGCATCC 60.468 52.381 0.00 0.00 35.37 3.51
2955 3692 2.886913 TGGACAAAAGCATCCATTGGA 58.113 42.857 8.08 8.08 40.17 3.53
2956 3693 3.443052 TGGACAAAAGCATCCATTGGAT 58.557 40.909 12.62 12.62 44.21 3.41
2958 3695 4.186159 GGACAAAAGCATCCATTGGATTG 58.814 43.478 15.75 13.79 39.79 2.67
2964 3701 6.549433 AAAGCATCCATTGGATTGTATTGT 57.451 33.333 15.75 0.00 39.79 2.71
2967 3704 5.895534 AGCATCCATTGGATTGTATTGTCTT 59.104 36.000 15.75 0.00 39.79 3.01
2968 3705 5.981315 GCATCCATTGGATTGTATTGTCTTG 59.019 40.000 15.75 3.04 39.79 3.02
2969 3706 5.581126 TCCATTGGATTGTATTGTCTTGC 57.419 39.130 0.00 0.00 0.00 4.01
2971 3708 5.479724 TCCATTGGATTGTATTGTCTTGCAA 59.520 36.000 0.00 0.00 41.89 4.08
2974 3711 7.010738 CCATTGGATTGTATTGTCTTGCAAATC 59.989 37.037 0.00 0.00 40.91 2.17
2975 3712 6.839124 TGGATTGTATTGTCTTGCAAATCT 57.161 33.333 0.00 0.00 40.91 2.40
2992 3729 6.403333 CAAATCTGCATTGTTCAAGGAATG 57.597 37.500 1.37 0.00 33.46 2.67
2998 3735 4.100707 CATTGTTCAAGGAATGCATCGT 57.899 40.909 0.00 0.00 0.00 3.73
3000 3737 2.083774 TGTTCAAGGAATGCATCGTCC 58.916 47.619 9.11 9.11 0.00 4.79
3001 3738 2.083774 GTTCAAGGAATGCATCGTCCA 58.916 47.619 17.74 0.00 36.28 4.02
3003 3740 2.789213 TCAAGGAATGCATCGTCCAAA 58.211 42.857 17.74 2.20 36.28 3.28
3004 3741 3.153130 TCAAGGAATGCATCGTCCAAAA 58.847 40.909 17.74 1.89 36.28 2.44
3005 3742 3.571828 TCAAGGAATGCATCGTCCAAAAA 59.428 39.130 17.74 0.35 36.28 1.94
3006 3743 4.220382 TCAAGGAATGCATCGTCCAAAAAT 59.780 37.500 17.74 0.00 36.28 1.82
3007 3744 4.376340 AGGAATGCATCGTCCAAAAATC 57.624 40.909 17.74 0.22 36.28 2.17
3008 3745 3.108144 GGAATGCATCGTCCAAAAATCG 58.892 45.455 11.83 0.00 33.79 3.34
3010 3747 2.610219 TGCATCGTCCAAAAATCGTG 57.390 45.000 0.00 0.00 0.00 4.35
3011 3748 1.259316 GCATCGTCCAAAAATCGTGC 58.741 50.000 0.00 0.00 0.00 5.34
3012 3749 1.400888 GCATCGTCCAAAAATCGTGCA 60.401 47.619 0.00 0.00 34.54 4.57
3013 3750 2.731968 GCATCGTCCAAAAATCGTGCAT 60.732 45.455 0.00 0.00 34.54 3.96
3014 3751 2.610219 TCGTCCAAAAATCGTGCATG 57.390 45.000 0.00 0.00 0.00 4.06
3015 3752 0.984109 CGTCCAAAAATCGTGCATGC 59.016 50.000 11.82 11.82 0.00 4.06
3017 3754 1.720852 GTCCAAAAATCGTGCATGCAC 59.279 47.619 35.76 35.76 43.01 4.57
3018 3755 1.339291 TCCAAAAATCGTGCATGCACA 59.661 42.857 40.95 30.30 46.47 4.57
3021 3758 3.181528 CCAAAAATCGTGCATGCACAATC 60.182 43.478 40.95 21.42 46.47 2.67
3022 3759 1.898938 AAATCGTGCATGCACAATCG 58.101 45.000 40.95 30.34 46.47 3.34
3023 3760 0.804364 AATCGTGCATGCACAATCGT 59.196 45.000 40.95 23.03 46.47 3.73
3024 3761 0.097499 ATCGTGCATGCACAATCGTG 59.903 50.000 40.95 27.28 46.47 4.35
3025 3762 1.207339 CGTGCATGCACAATCGTGT 59.793 52.632 40.95 0.00 46.47 4.49
3039 3776 5.152097 ACAATCGTGTGTAGAGTAGTTTCG 58.848 41.667 0.00 0.00 36.31 3.46
3040 3777 3.818961 TCGTGTGTAGAGTAGTTTCGG 57.181 47.619 0.00 0.00 0.00 4.30
3041 3778 3.141398 TCGTGTGTAGAGTAGTTTCGGT 58.859 45.455 0.00 0.00 0.00 4.69
3044 3781 5.412594 TCGTGTGTAGAGTAGTTTCGGTTAT 59.587 40.000 0.00 0.00 0.00 1.89
3045 3782 5.510674 CGTGTGTAGAGTAGTTTCGGTTATG 59.489 44.000 0.00 0.00 0.00 1.90
3046 3783 6.385033 GTGTGTAGAGTAGTTTCGGTTATGT 58.615 40.000 0.00 0.00 0.00 2.29
3047 3784 6.865205 GTGTGTAGAGTAGTTTCGGTTATGTT 59.135 38.462 0.00 0.00 0.00 2.71
3048 3785 8.023128 GTGTGTAGAGTAGTTTCGGTTATGTTA 58.977 37.037 0.00 0.00 0.00 2.41
3049 3786 8.023128 TGTGTAGAGTAGTTTCGGTTATGTTAC 58.977 37.037 0.00 0.00 0.00 2.50
3057 3874 9.741647 GTAGTTTCGGTTATGTTACTAGCTAAT 57.258 33.333 0.00 0.00 0.00 1.73
3064 3881 9.962783 CGGTTATGTTACTAGCTAATTTACTCT 57.037 33.333 0.00 0.00 0.00 3.24
3091 3908 0.036952 ACCAGCCTCATGACTTCGTG 60.037 55.000 0.00 0.00 0.00 4.35
3108 3925 7.095397 TGACTTCGTGACATTAAAAGTACATGG 60.095 37.037 0.00 0.00 30.68 3.66
3109 3926 6.932400 ACTTCGTGACATTAAAAGTACATGGA 59.068 34.615 0.00 0.00 0.00 3.41
3158 3976 7.042187 TGCATTTCATTGTGACATTTTTACACC 60.042 33.333 0.00 0.00 34.18 4.16
3163 3981 5.759506 TTGTGACATTTTTACACCGATGT 57.240 34.783 0.00 0.00 43.30 3.06
3172 3990 3.377253 TTACACCGATGTACTCCCTCT 57.623 47.619 0.00 0.00 41.12 3.69
3173 3991 1.475403 ACACCGATGTACTCCCTCTG 58.525 55.000 0.00 0.00 37.26 3.35
3209 4034 5.783111 AGTCAGCAACATTTATTTTGGGAC 58.217 37.500 0.00 0.00 0.00 4.46
3217 4042 2.423446 TTATTTTGGGACGGGGTAGC 57.577 50.000 0.00 0.00 0.00 3.58
3304 4164 6.923928 TTTTTGAAAATTTCAGGCTCCAAG 57.076 33.333 8.51 0.00 41.38 3.61
3347 4208 9.520515 AAATCCTCACTTGTTTGTATGATACTT 57.479 29.630 4.03 0.00 0.00 2.24
3352 4213 7.103641 TCACTTGTTTGTATGATACTTCCTCC 58.896 38.462 4.03 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 0.531090 GTTTTGACAAAACCCCCGGC 60.531 55.000 26.54 6.08 43.78 6.13
45 48 3.740115 TCCTTTTCTTTTGAGTCGGGAG 58.260 45.455 0.00 0.00 0.00 4.30
125 141 6.071165 GCGTCCCTTTATTTAGGCCTACTATA 60.071 42.308 13.46 10.62 33.73 1.31
126 142 5.279859 GCGTCCCTTTATTTAGGCCTACTAT 60.280 44.000 13.46 11.66 33.73 2.12
127 143 4.039609 GCGTCCCTTTATTTAGGCCTACTA 59.960 45.833 13.46 3.84 33.73 1.82
267 286 4.130118 TCGCTTTTGCTTCTTCTTCTTCT 58.870 39.130 0.00 0.00 44.80 2.85
268 287 4.462307 CTCGCTTTTGCTTCTTCTTCTTC 58.538 43.478 0.00 0.00 44.80 2.87
269 288 3.304324 GCTCGCTTTTGCTTCTTCTTCTT 60.304 43.478 0.00 0.00 44.80 2.52
309 328 3.243401 GCGACAAACCAACCTCTTGATTT 60.243 43.478 0.00 0.00 0.00 2.17
341 361 0.032952 CGTGGGAAGTCTCGGAACAA 59.967 55.000 0.00 0.00 0.00 2.83
354 374 0.105224 TCAGAAAAGCGTTCGTGGGA 59.895 50.000 0.00 0.00 0.00 4.37
446 466 4.974989 ACGAAACCGGCCGTCACC 62.975 66.667 26.12 9.55 33.23 4.02
471 491 2.158986 AGTGAGAAGATCTTCATGGCCG 60.159 50.000 31.79 0.00 41.84 6.13
521 580 5.163854 CCAAGAACGAGAATAAAACGAGCAT 60.164 40.000 0.00 0.00 0.00 3.79
527 586 6.371389 CAGGAACCAAGAACGAGAATAAAAC 58.629 40.000 0.00 0.00 0.00 2.43
531 590 3.618997 GCCAGGAACCAAGAACGAGAATA 60.619 47.826 0.00 0.00 0.00 1.75
532 591 2.876079 GCCAGGAACCAAGAACGAGAAT 60.876 50.000 0.00 0.00 0.00 2.40
569 632 2.074124 GCACTACTGCTGCGAGAAC 58.926 57.895 6.18 0.00 40.63 3.01
601 664 1.519455 AGATCGCAGCACGCTAACC 60.519 57.895 0.00 0.00 43.23 2.85
649 712 1.471119 TCCTACGAGAAGACCGCAAT 58.529 50.000 0.00 0.00 0.00 3.56
650 713 1.404391 GATCCTACGAGAAGACCGCAA 59.596 52.381 0.00 0.00 0.00 4.85
651 714 1.022735 GATCCTACGAGAAGACCGCA 58.977 55.000 0.00 0.00 0.00 5.69
652 715 0.311477 GGATCCTACGAGAAGACCGC 59.689 60.000 3.84 0.00 0.00 5.68
653 716 0.587285 CGGATCCTACGAGAAGACCG 59.413 60.000 10.75 0.00 0.00 4.79
654 717 1.677942 ACGGATCCTACGAGAAGACC 58.322 55.000 10.75 0.00 34.93 3.85
655 718 3.303001 CGTAACGGATCCTACGAGAAGAC 60.303 52.174 22.70 3.24 42.73 3.01
656 719 2.868583 CGTAACGGATCCTACGAGAAGA 59.131 50.000 22.70 0.00 42.73 2.87
657 720 2.601741 GCGTAACGGATCCTACGAGAAG 60.602 54.545 28.38 7.47 42.73 2.85
658 721 1.331756 GCGTAACGGATCCTACGAGAA 59.668 52.381 28.38 0.00 42.73 2.87
659 722 0.940126 GCGTAACGGATCCTACGAGA 59.060 55.000 28.38 0.55 42.73 4.04
660 723 0.942962 AGCGTAACGGATCCTACGAG 59.057 55.000 28.38 9.46 42.73 4.18
661 724 0.940126 GAGCGTAACGGATCCTACGA 59.060 55.000 28.38 3.50 42.73 3.43
662 725 0.942962 AGAGCGTAACGGATCCTACG 59.057 55.000 22.77 22.77 42.92 3.51
663 726 3.137533 ACTAGAGCGTAACGGATCCTAC 58.862 50.000 10.75 5.64 0.00 3.18
664 727 3.482156 ACTAGAGCGTAACGGATCCTA 57.518 47.619 10.75 0.00 0.00 2.94
665 728 2.345124 ACTAGAGCGTAACGGATCCT 57.655 50.000 10.75 0.00 0.00 3.24
666 729 4.558538 TTTACTAGAGCGTAACGGATCC 57.441 45.455 0.00 0.00 0.00 3.36
667 730 5.628606 GGAATTTACTAGAGCGTAACGGATC 59.371 44.000 0.00 0.00 0.00 3.36
668 731 5.508657 GGGAATTTACTAGAGCGTAACGGAT 60.509 44.000 0.00 0.00 0.00 4.18
669 732 4.202050 GGGAATTTACTAGAGCGTAACGGA 60.202 45.833 0.00 0.00 0.00 4.69
670 733 4.047142 GGGAATTTACTAGAGCGTAACGG 58.953 47.826 0.00 0.00 0.00 4.44
671 734 4.929781 AGGGAATTTACTAGAGCGTAACG 58.070 43.478 0.00 0.00 0.00 3.18
685 748 7.993183 CCGGAGCATACATATATAAGGGAATTT 59.007 37.037 0.00 0.00 0.00 1.82
686 749 7.347222 TCCGGAGCATACATATATAAGGGAATT 59.653 37.037 0.00 0.00 0.00 2.17
735 798 2.157305 TACCGTCATCCGCCGTTTGT 62.157 55.000 0.00 0.00 34.38 2.83
737 800 0.108041 AATACCGTCATCCGCCGTTT 60.108 50.000 0.00 0.00 34.38 3.60
751 814 7.390718 ACAATCCAAGTTCAGAACTACAATACC 59.609 37.037 16.46 0.00 41.91 2.73
776 839 5.367060 AGGGAGTAGATAAAACAGGATGGAC 59.633 44.000 0.00 0.00 43.62 4.02
801 864 2.996621 CGAGCAGAGTAAAAAGGACTGG 59.003 50.000 0.00 0.00 0.00 4.00
803 866 4.810191 ATCGAGCAGAGTAAAAAGGACT 57.190 40.909 0.00 0.00 0.00 3.85
830 999 9.321590 CAATGTTATATGTGCTACATGATTTCG 57.678 33.333 0.00 0.00 39.53 3.46
909 1165 6.563222 TTTACAAGCAACAATAGGTGTACC 57.437 37.500 0.00 0.00 40.60 3.34
912 1168 5.925969 GCAATTTACAAGCAACAATAGGTGT 59.074 36.000 0.00 0.00 44.64 4.16
916 1172 7.546667 AGAATGGCAATTTACAAGCAACAATAG 59.453 33.333 0.00 0.00 0.00 1.73
919 1175 5.609423 AGAATGGCAATTTACAAGCAACAA 58.391 33.333 0.00 0.00 0.00 2.83
940 1196 8.129840 GCAGAGTTAGAGTAATGAATAACGAGA 58.870 37.037 0.00 0.00 34.17 4.04
942 1198 7.915923 CAGCAGAGTTAGAGTAATGAATAACGA 59.084 37.037 0.00 0.00 34.17 3.85
944 1200 8.198109 TCCAGCAGAGTTAGAGTAATGAATAAC 58.802 37.037 0.00 0.00 0.00 1.89
946 1202 7.898014 TCCAGCAGAGTTAGAGTAATGAATA 57.102 36.000 0.00 0.00 0.00 1.75
949 1230 6.798427 AATCCAGCAGAGTTAGAGTAATGA 57.202 37.500 0.00 0.00 0.00 2.57
976 1258 5.308497 TGTTCCTGGTACAAGGAAACTGATA 59.692 40.000 29.77 6.89 43.40 2.15
986 1268 2.356125 CCCTCCATGTTCCTGGTACAAG 60.356 54.545 10.29 6.00 38.70 3.16
1022 1304 5.013547 AGATAAGTCCATCATCTACCGGAG 58.986 45.833 9.46 0.60 0.00 4.63
1065 1347 0.174162 CAGCAGCTAAACCAATGCCC 59.826 55.000 0.00 0.00 39.51 5.36
1098 1380 1.814394 TGCAGCATAGAAACCAGCAAG 59.186 47.619 0.00 0.00 0.00 4.01
1120 1402 1.710809 ACTGCCAACCTTAGGTCCATT 59.289 47.619 3.62 0.00 33.12 3.16
1194 1476 2.749280 CAAGAATTGCCAAGGTTCCC 57.251 50.000 0.00 0.00 40.39 3.97
1353 1644 4.983671 ACCGAATTAGAAATTTCAGGCC 57.016 40.909 19.99 0.00 0.00 5.19
1448 1776 3.206150 TCAAAGTTTGCAGAGTGGACTC 58.794 45.455 10.90 0.00 43.17 3.36
1459 1787 5.754890 AGTGAAACATCCAATCAAAGTTTGC 59.245 36.000 10.90 0.00 41.43 3.68
1482 1810 7.336679 TGTTGGTTCCACATTATGATACAAGAG 59.663 37.037 0.00 0.00 0.00 2.85
1628 2299 5.450376 AACTCTGCGTACATATTTTGACG 57.550 39.130 0.00 0.00 38.32 4.35
1665 2336 1.527380 GAACCGTTGAACCTGCCCA 60.527 57.895 0.00 0.00 0.00 5.36
1675 2346 1.269051 GCCAAAGGACTTGAACCGTTG 60.269 52.381 0.00 0.00 43.03 4.10
1676 2347 1.029681 GCCAAAGGACTTGAACCGTT 58.970 50.000 0.00 0.00 37.17 4.44
1677 2348 0.182775 AGCCAAAGGACTTGAACCGT 59.817 50.000 0.00 0.00 37.17 4.83
1678 2349 1.001378 CAAGCCAAAGGACTTGAACCG 60.001 52.381 12.02 0.00 44.89 4.44
1679 2350 2.031870 ACAAGCCAAAGGACTTGAACC 58.968 47.619 19.66 0.00 44.89 3.62
1680 2351 5.453567 AATACAAGCCAAAGGACTTGAAC 57.546 39.130 19.66 0.00 44.89 3.18
1681 2352 5.221422 CCAAATACAAGCCAAAGGACTTGAA 60.221 40.000 19.66 0.00 44.89 2.69
1682 2353 4.280677 CCAAATACAAGCCAAAGGACTTGA 59.719 41.667 19.66 9.29 44.89 3.02
1937 2609 6.763355 ACTGCATACTGAATCCCTAACTATG 58.237 40.000 0.00 0.00 0.00 2.23
1939 2611 6.808321 AACTGCATACTGAATCCCTAACTA 57.192 37.500 0.00 0.00 0.00 2.24
1941 2613 5.992217 CCTAACTGCATACTGAATCCCTAAC 59.008 44.000 0.00 0.00 0.00 2.34
1942 2614 5.071788 CCCTAACTGCATACTGAATCCCTAA 59.928 44.000 0.00 0.00 0.00 2.69
1943 2615 4.593206 CCCTAACTGCATACTGAATCCCTA 59.407 45.833 0.00 0.00 0.00 3.53
1945 2617 3.391296 TCCCTAACTGCATACTGAATCCC 59.609 47.826 0.00 0.00 0.00 3.85
1946 2618 4.689612 TCCCTAACTGCATACTGAATCC 57.310 45.455 0.00 0.00 0.00 3.01
1948 2620 6.126652 ACTGAATCCCTAACTGCATACTGAAT 60.127 38.462 0.00 0.00 0.00 2.57
1951 2623 5.028549 ACTGAATCCCTAACTGCATACTG 57.971 43.478 0.00 0.00 0.00 2.74
1952 2624 7.071196 TGAATACTGAATCCCTAACTGCATACT 59.929 37.037 0.00 0.00 0.00 2.12
1953 2625 7.217200 TGAATACTGAATCCCTAACTGCATAC 58.783 38.462 0.00 0.00 0.00 2.39
1954 2626 7.071196 ACTGAATACTGAATCCCTAACTGCATA 59.929 37.037 0.00 0.00 0.00 3.14
1955 2627 6.126652 ACTGAATACTGAATCCCTAACTGCAT 60.127 38.462 0.00 0.00 0.00 3.96
1956 2628 5.189736 ACTGAATACTGAATCCCTAACTGCA 59.810 40.000 0.00 0.00 0.00 4.41
1957 2629 5.525378 CACTGAATACTGAATCCCTAACTGC 59.475 44.000 0.00 0.00 0.00 4.40
1958 2630 5.525378 GCACTGAATACTGAATCCCTAACTG 59.475 44.000 0.00 0.00 0.00 3.16
1959 2631 5.189736 TGCACTGAATACTGAATCCCTAACT 59.810 40.000 0.00 0.00 0.00 2.24
1960 2632 5.428253 TGCACTGAATACTGAATCCCTAAC 58.572 41.667 0.00 0.00 0.00 2.34
1961 2633 5.692115 TGCACTGAATACTGAATCCCTAA 57.308 39.130 0.00 0.00 0.00 2.69
1962 2634 5.894298 ATGCACTGAATACTGAATCCCTA 57.106 39.130 0.00 0.00 0.00 3.53
1963 2635 4.785346 ATGCACTGAATACTGAATCCCT 57.215 40.909 0.00 0.00 0.00 4.20
1964 2636 5.106396 GCATATGCACTGAATACTGAATCCC 60.106 44.000 22.84 0.00 41.59 3.85
1965 2637 5.936054 GCATATGCACTGAATACTGAATCC 58.064 41.667 22.84 0.00 41.59 3.01
1981 2653 4.392940 ACTGAATCCCTAACTGCATATGC 58.607 43.478 21.09 21.09 42.50 3.14
1982 2654 7.389232 TCATACTGAATCCCTAACTGCATATG 58.611 38.462 0.00 0.00 0.00 1.78
1983 2655 7.559335 TCATACTGAATCCCTAACTGCATAT 57.441 36.000 0.00 0.00 0.00 1.78
1984 2656 6.994421 TCATACTGAATCCCTAACTGCATA 57.006 37.500 0.00 0.00 0.00 3.14
1985 2657 5.894298 TCATACTGAATCCCTAACTGCAT 57.106 39.130 0.00 0.00 0.00 3.96
1986 2658 5.692115 TTCATACTGAATCCCTAACTGCA 57.308 39.130 0.00 0.00 30.26 4.41
1987 2659 5.880332 TGTTTCATACTGAATCCCTAACTGC 59.120 40.000 0.00 0.00 36.11 4.40
1988 2660 8.511604 AATGTTTCATACTGAATCCCTAACTG 57.488 34.615 0.00 0.00 36.11 3.16
1989 2661 9.838339 CTAATGTTTCATACTGAATCCCTAACT 57.162 33.333 0.00 0.00 36.11 2.24
1990 2662 9.057089 CCTAATGTTTCATACTGAATCCCTAAC 57.943 37.037 0.00 0.00 36.11 2.34
1991 2663 8.217799 CCCTAATGTTTCATACTGAATCCCTAA 58.782 37.037 0.00 0.00 36.11 2.69
1992 2664 7.202186 CCCCTAATGTTTCATACTGAATCCCTA 60.202 40.741 0.00 0.00 36.11 3.53
1993 2665 6.410853 CCCCTAATGTTTCATACTGAATCCCT 60.411 42.308 0.00 0.00 36.11 4.20
1994 2666 5.770162 CCCCTAATGTTTCATACTGAATCCC 59.230 44.000 0.00 0.00 36.11 3.85
1995 2667 6.601332 TCCCCTAATGTTTCATACTGAATCC 58.399 40.000 0.00 0.00 36.11 3.01
1996 2668 7.939039 TCATCCCCTAATGTTTCATACTGAATC 59.061 37.037 0.00 0.00 36.11 2.52
1997 2669 7.815383 TCATCCCCTAATGTTTCATACTGAAT 58.185 34.615 0.00 0.00 36.11 2.57
1998 2670 7.206789 TCATCCCCTAATGTTTCATACTGAA 57.793 36.000 0.00 0.00 34.03 3.02
1999 2671 6.823286 TCATCCCCTAATGTTTCATACTGA 57.177 37.500 0.00 0.00 0.00 3.41
2128 2802 0.388649 GCATAGTAGGGCCATCGTCG 60.389 60.000 6.18 0.00 0.00 5.12
2260 2938 2.126307 CGCAGACCCTGACACGAG 60.126 66.667 0.00 0.00 32.44 4.18
2342 3020 7.323420 TGATACATTGACTTAGTGGTTCTCAG 58.677 38.462 0.00 0.00 0.00 3.35
2344 3022 7.439655 GGATGATACATTGACTTAGTGGTTCTC 59.560 40.741 0.00 0.00 0.00 2.87
2345 3023 7.126421 AGGATGATACATTGACTTAGTGGTTCT 59.874 37.037 0.00 0.00 0.00 3.01
2346 3024 7.225538 CAGGATGATACATTGACTTAGTGGTTC 59.774 40.741 0.00 0.00 39.69 3.62
2347 3025 7.050377 CAGGATGATACATTGACTTAGTGGTT 58.950 38.462 0.00 0.00 39.69 3.67
2526 3206 6.872920 TGAAATGCCAAAAGTACTTCAAACT 58.127 32.000 8.95 0.00 0.00 2.66
2563 3245 2.222886 CGACCATGAACTTCAGCGATTG 60.223 50.000 0.00 0.00 0.00 2.67
2680 3362 2.829120 TCATCGGGTCACATAACACTCA 59.171 45.455 0.00 0.00 0.00 3.41
2681 3363 3.119101 AGTCATCGGGTCACATAACACTC 60.119 47.826 0.00 0.00 0.00 3.51
2682 3364 2.832129 AGTCATCGGGTCACATAACACT 59.168 45.455 0.00 0.00 0.00 3.55
2683 3365 2.930040 CAGTCATCGGGTCACATAACAC 59.070 50.000 0.00 0.00 0.00 3.32
2684 3366 2.829120 TCAGTCATCGGGTCACATAACA 59.171 45.455 0.00 0.00 0.00 2.41
2685 3367 3.448686 CTCAGTCATCGGGTCACATAAC 58.551 50.000 0.00 0.00 0.00 1.89
2687 3369 2.031870 CCTCAGTCATCGGGTCACATA 58.968 52.381 0.00 0.00 0.00 2.29
2688 3370 0.826715 CCTCAGTCATCGGGTCACAT 59.173 55.000 0.00 0.00 0.00 3.21
2689 3371 1.888436 GCCTCAGTCATCGGGTCACA 61.888 60.000 0.00 0.00 0.00 3.58
2690 3372 1.153549 GCCTCAGTCATCGGGTCAC 60.154 63.158 0.00 0.00 0.00 3.67
2742 3424 2.413112 CAGCAGATAACACCACAACTCG 59.587 50.000 0.00 0.00 0.00 4.18
2783 3465 3.317406 ACACTATGCACTATGGGGATGA 58.683 45.455 0.00 0.00 0.00 2.92
2844 3527 9.662545 GTTTACTGTAACATAGCGGTTTTTAAA 57.337 29.630 0.00 0.00 32.29 1.52
2847 3530 7.261829 TGTTTACTGTAACATAGCGGTTTTT 57.738 32.000 0.00 0.00 33.31 1.94
2849 3532 6.864360 TTGTTTACTGTAACATAGCGGTTT 57.136 33.333 0.00 0.00 37.81 3.27
2855 3538 9.691362 AAGGCAAATTTGTTTACTGTAACATAG 57.309 29.630 19.03 0.00 37.81 2.23
2863 3546 5.115480 ACACCAAGGCAAATTTGTTTACTG 58.885 37.500 19.03 13.05 0.00 2.74
2864 3547 5.351948 ACACCAAGGCAAATTTGTTTACT 57.648 34.783 19.03 9.83 0.00 2.24
2886 3623 4.390603 CCGTGTAGCACTGCTTTAACATAA 59.609 41.667 9.30 0.00 40.44 1.90
2887 3624 3.930229 CCGTGTAGCACTGCTTTAACATA 59.070 43.478 9.30 0.00 40.44 2.29
2888 3625 2.742053 CCGTGTAGCACTGCTTTAACAT 59.258 45.455 9.30 0.00 40.44 2.71
2890 3627 2.157085 GTCCGTGTAGCACTGCTTTAAC 59.843 50.000 9.30 2.01 40.44 2.01
2892 3629 1.667756 CGTCCGTGTAGCACTGCTTTA 60.668 52.381 9.30 0.00 40.44 1.85
2893 3630 0.944311 CGTCCGTGTAGCACTGCTTT 60.944 55.000 9.30 0.00 40.44 3.51
2894 3631 1.372997 CGTCCGTGTAGCACTGCTT 60.373 57.895 9.30 0.00 40.44 3.91
2896 3633 1.153823 ATCGTCCGTGTAGCACTGC 60.154 57.895 0.00 0.00 31.34 4.40
2897 3634 1.413767 GCATCGTCCGTGTAGCACTG 61.414 60.000 0.00 0.00 31.34 3.66
2899 3636 0.736325 AAGCATCGTCCGTGTAGCAC 60.736 55.000 0.00 0.00 0.00 4.40
2901 3638 1.146358 GGAAGCATCGTCCGTGTAGC 61.146 60.000 0.00 0.00 0.00 3.58
2903 3640 0.172578 CAGGAAGCATCGTCCGTGTA 59.827 55.000 0.00 0.00 40.36 2.90
2904 3641 1.079819 CAGGAAGCATCGTCCGTGT 60.080 57.895 0.00 0.00 40.36 4.49
2906 3643 2.125512 GCAGGAAGCATCGTCCGT 60.126 61.111 0.00 0.00 44.79 4.69
2924 3661 1.464608 CTTTTGTCCATCGTGCATCGT 59.535 47.619 8.22 0.00 40.80 3.73
2926 3663 1.199789 TGCTTTTGTCCATCGTGCATC 59.800 47.619 0.00 0.00 0.00 3.91
2927 3664 1.246649 TGCTTTTGTCCATCGTGCAT 58.753 45.000 0.00 0.00 0.00 3.96
2929 3666 1.468054 GGATGCTTTTGTCCATCGTGC 60.468 52.381 0.00 0.00 38.93 5.34
2930 3667 1.811965 TGGATGCTTTTGTCCATCGTG 59.188 47.619 0.00 0.00 39.51 4.35
2931 3668 2.198827 TGGATGCTTTTGTCCATCGT 57.801 45.000 0.00 0.00 39.51 3.73
2936 3673 4.186159 CAATCCAATGGATGCTTTTGTCC 58.814 43.478 16.52 0.00 42.27 4.02
2937 3674 4.824289 ACAATCCAATGGATGCTTTTGTC 58.176 39.130 16.52 0.00 42.27 3.18
2938 3675 4.895668 ACAATCCAATGGATGCTTTTGT 57.104 36.364 16.52 13.48 42.27 2.83
2940 3677 6.949715 ACAATACAATCCAATGGATGCTTTT 58.050 32.000 16.52 5.37 42.27 2.27
2941 3678 6.381994 AGACAATACAATCCAATGGATGCTTT 59.618 34.615 16.52 5.01 42.27 3.51
2942 3679 5.895534 AGACAATACAATCCAATGGATGCTT 59.104 36.000 16.52 5.70 42.27 3.91
2943 3680 5.452255 AGACAATACAATCCAATGGATGCT 58.548 37.500 16.52 6.37 42.27 3.79
2944 3681 5.779529 AGACAATACAATCCAATGGATGC 57.220 39.130 16.52 0.73 42.27 3.91
2946 3683 5.657745 TGCAAGACAATACAATCCAATGGAT 59.342 36.000 9.36 9.36 45.46 3.41
2948 3685 5.327616 TGCAAGACAATACAATCCAATGG 57.672 39.130 0.00 0.00 0.00 3.16
2949 3686 7.762615 AGATTTGCAAGACAATACAATCCAATG 59.237 33.333 0.00 0.00 38.31 2.82
2950 3687 7.762615 CAGATTTGCAAGACAATACAATCCAAT 59.237 33.333 0.00 0.00 38.31 3.16
2952 3689 6.623486 CAGATTTGCAAGACAATACAATCCA 58.377 36.000 0.00 0.00 38.31 3.41
2969 3706 6.403333 CATTCCTTGAACAATGCAGATTTG 57.597 37.500 0.00 0.00 0.00 2.32
2977 3714 4.100529 GACGATGCATTCCTTGAACAATG 58.899 43.478 0.00 0.00 33.77 2.82
2978 3715 3.129287 GGACGATGCATTCCTTGAACAAT 59.871 43.478 9.78 0.00 0.00 2.71
2979 3716 2.487762 GGACGATGCATTCCTTGAACAA 59.512 45.455 9.78 0.00 0.00 2.83
2980 3717 2.083774 GGACGATGCATTCCTTGAACA 58.916 47.619 9.78 0.00 0.00 3.18
2981 3718 2.083774 TGGACGATGCATTCCTTGAAC 58.916 47.619 16.58 0.00 32.55 3.18
2982 3719 2.488204 TGGACGATGCATTCCTTGAA 57.512 45.000 16.58 0.00 32.55 2.69
2983 3720 2.488204 TTGGACGATGCATTCCTTGA 57.512 45.000 16.58 2.80 32.55 3.02
2984 3721 3.574284 TTTTGGACGATGCATTCCTTG 57.426 42.857 16.58 1.55 32.55 3.61
2985 3722 4.675146 CGATTTTTGGACGATGCATTCCTT 60.675 41.667 16.58 0.00 32.55 3.36
2988 3725 3.543494 CACGATTTTTGGACGATGCATTC 59.457 43.478 0.00 0.00 0.00 2.67
2990 3727 2.731968 GCACGATTTTTGGACGATGCAT 60.732 45.455 0.00 0.00 35.74 3.96
2992 3729 1.259316 GCACGATTTTTGGACGATGC 58.741 50.000 0.00 0.00 0.00 3.91
2993 3730 2.610219 TGCACGATTTTTGGACGATG 57.390 45.000 0.00 0.00 0.00 3.84
2994 3731 2.731968 GCATGCACGATTTTTGGACGAT 60.732 45.455 14.21 0.00 0.00 3.73
2995 3732 1.400888 GCATGCACGATTTTTGGACGA 60.401 47.619 14.21 0.00 0.00 4.20
2997 3734 1.720852 GTGCATGCACGATTTTTGGAC 59.279 47.619 33.20 7.91 37.19 4.02
2998 3735 2.063156 GTGCATGCACGATTTTTGGA 57.937 45.000 33.20 0.00 37.19 3.53
3017 3754 4.557690 CCGAAACTACTCTACACACGATTG 59.442 45.833 0.00 0.00 0.00 2.67
3018 3755 4.217118 ACCGAAACTACTCTACACACGATT 59.783 41.667 0.00 0.00 0.00 3.34
3021 3758 3.549299 ACCGAAACTACTCTACACACG 57.451 47.619 0.00 0.00 0.00 4.49
3022 3759 6.385033 ACATAACCGAAACTACTCTACACAC 58.615 40.000 0.00 0.00 0.00 3.82
3023 3760 6.579666 ACATAACCGAAACTACTCTACACA 57.420 37.500 0.00 0.00 0.00 3.72
3024 3761 8.239998 AGTAACATAACCGAAACTACTCTACAC 58.760 37.037 0.00 0.00 0.00 2.90
3025 3762 8.340618 AGTAACATAACCGAAACTACTCTACA 57.659 34.615 0.00 0.00 0.00 2.74
3026 3763 9.928236 CTAGTAACATAACCGAAACTACTCTAC 57.072 37.037 0.00 0.00 0.00 2.59
3027 3764 8.616076 GCTAGTAACATAACCGAAACTACTCTA 58.384 37.037 0.00 0.00 0.00 2.43
3028 3765 7.338957 AGCTAGTAACATAACCGAAACTACTCT 59.661 37.037 0.00 0.00 0.00 3.24
3029 3766 7.479150 AGCTAGTAACATAACCGAAACTACTC 58.521 38.462 0.00 0.00 0.00 2.59
3030 3767 7.401955 AGCTAGTAACATAACCGAAACTACT 57.598 36.000 0.00 0.00 0.00 2.57
3031 3768 9.741647 ATTAGCTAGTAACATAACCGAAACTAC 57.258 33.333 0.00 0.00 0.00 2.73
3033 3770 9.662947 AAATTAGCTAGTAACATAACCGAAACT 57.337 29.630 0.00 0.00 0.00 2.66
3037 3774 9.956720 GAGTAAATTAGCTAGTAACATAACCGA 57.043 33.333 0.00 0.00 0.00 4.69
3048 3785 8.852135 GGTCATAGTGAGAGTAAATTAGCTAGT 58.148 37.037 0.00 0.00 0.00 2.57
3049 3786 8.851145 TGGTCATAGTGAGAGTAAATTAGCTAG 58.149 37.037 0.00 0.00 0.00 3.42
3057 3874 4.353777 AGGCTGGTCATAGTGAGAGTAAA 58.646 43.478 0.00 0.00 0.00 2.01
3064 3881 2.432146 GTCATGAGGCTGGTCATAGTGA 59.568 50.000 0.00 0.00 35.30 3.41
3073 3890 0.247460 TCACGAAGTCATGAGGCTGG 59.753 55.000 0.00 0.00 41.61 4.85
3127 3944 8.789881 AAAATGTCACAATGAAATGCATTTTG 57.210 26.923 24.81 20.44 44.68 2.44
3147 3965 5.183228 AGGGAGTACATCGGTGTAAAAATG 58.817 41.667 10.76 0.00 42.18 2.32
3149 3967 4.529377 AGAGGGAGTACATCGGTGTAAAAA 59.471 41.667 10.76 0.00 42.18 1.94
3163 3981 6.552350 ACTTACAACTTTGTACAGAGGGAGTA 59.448 38.462 17.01 12.60 42.84 2.59
3172 3990 5.644206 TGTTGCTGACTTACAACTTTGTACA 59.356 36.000 1.18 0.00 45.07 2.90
3173 3991 6.114221 TGTTGCTGACTTACAACTTTGTAC 57.886 37.500 1.18 0.00 45.07 2.90
3209 4034 3.258372 ACATAGTGATGTATGCTACCCCG 59.742 47.826 0.00 0.00 44.77 5.73
3304 4164 1.901464 TTTTTGGCCACCGAGCTCC 60.901 57.895 3.88 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.