Multiple sequence alignment - TraesCS6A01G111200

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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 TraesCS6A01G111200 chr6A 100.000 6939 0 0 1 6939 80685075 80692013 0.000000e+00 12815.0
1 TraesCS6A01G111200 chr6D 92.976 3730 208 29 834 4540 62885396 62889094 0.000000e+00 5387.0
2 TraesCS6A01G111200 chr6D 94.574 2396 97 14 4570 6937 62889093 62891483 0.000000e+00 3674.0
3 TraesCS6A01G111200 chr6D 92.144 751 53 3 9 758 62884657 62885402 0.000000e+00 1055.0
4 TraesCS6A01G111200 chr6D 87.059 340 24 9 5889 6212 62893798 62894133 3.950000e-97 366.0
5 TraesCS6A01G111200 chr6D 83.448 435 29 11 6518 6924 123124755 123124336 1.420000e-96 364.0
6 TraesCS6A01G111200 chr6B 89.718 2305 179 31 744 3034 136499193 136501453 0.000000e+00 2891.0
7 TraesCS6A01G111200 chr6B 95.991 1347 37 7 5164 6510 136505292 136506621 0.000000e+00 2172.0
8 TraesCS6A01G111200 chr6B 87.555 1133 63 29 4047 5134 136504192 136505291 0.000000e+00 1240.0
9 TraesCS6A01G111200 chr6B 87.846 938 68 14 3121 4044 136503129 136504034 0.000000e+00 1059.0
10 TraesCS6A01G111200 chr6B 83.450 429 40 17 6520 6923 576267535 576267113 3.060000e-98 370.0
11 TraesCS6A01G111200 chr6B 85.135 74 10 1 1 73 626461608 626461535 2.680000e-09 75.0
12 TraesCS6A01G111200 chr1D 86.574 432 26 15 6519 6922 460919528 460919101 1.370000e-121 448.0
13 TraesCS6A01G111200 chr1D 83.636 440 31 16 6517 6921 444732909 444732476 6.570000e-100 375.0
14 TraesCS6A01G111200 chr7D 84.529 446 35 17 6517 6933 422616991 422617431 1.800000e-110 411.0
15 TraesCS6A01G111200 chr7D 80.998 421 44 9 6521 6918 184573349 184572942 1.130000e-77 302.0
16 TraesCS6A01G111200 chr7D 87.324 71 7 2 1 71 139108771 139108839 5.770000e-11 80.5
17 TraesCS6A01G111200 chr1B 84.112 428 34 11 6522 6921 262523403 262522982 3.930000e-102 383.0
18 TraesCS6A01G111200 chr1B 82.588 425 43 9 6522 6921 662607179 662606761 5.150000e-91 346.0
19 TraesCS6A01G111200 chr4D 83.803 426 41 8 6522 6923 430817656 430818077 5.080000e-101 379.0
20 TraesCS6A01G111200 chr4D 83.258 442 41 9 6508 6921 505256166 505256602 6.570000e-100 375.0
21 TraesCS6A01G111200 chr4D 94.000 50 3 0 3030 3079 16197732 16197781 7.460000e-10 76.8
22 TraesCS6A01G111200 chr3A 83.524 437 38 6 6522 6928 114046744 114046312 1.830000e-100 377.0
23 TraesCS6A01G111200 chr2A 85.014 367 30 6 6522 6865 757931587 757931951 3.980000e-92 350.0
24 TraesCS6A01G111200 chr2B 84.000 325 29 5 6522 6824 28172385 28172708 2.450000e-74 291.0
25 TraesCS6A01G111200 chr1A 86.636 217 24 4 6704 6918 549662140 549662353 1.160000e-57 235.0
26 TraesCS6A01G111200 chr7A 80.208 288 34 11 6519 6784 520590028 520589742 1.970000e-45 195.0
27 TraesCS6A01G111200 chr4B 93.939 66 2 2 3 68 666328898 666328961 1.590000e-16 99.0
28 TraesCS6A01G111200 chr4B 93.750 64 2 2 3 66 666385450 666385511 2.060000e-15 95.3
29 TraesCS6A01G111200 chr4B 93.750 64 2 2 3 66 666408705 666408766 2.060000e-15 95.3
30 TraesCS6A01G111200 chr4B 92.063 63 2 3 3 65 666289456 666289515 1.240000e-12 86.1
31 TraesCS6A01G111200 chrUn 90.909 66 3 3 1 65 195612858 195612795 1.240000e-12 86.1
32 TraesCS6A01G111200 chr3D 95.833 48 2 0 3031 3078 158075623 158075670 2.080000e-10 78.7
33 TraesCS6A01G111200 chr4A 87.879 66 6 2 3 67 584075432 584075368 7.460000e-10 76.8
34 TraesCS6A01G111200 chr5B 92.308 52 4 0 3023 3074 254577879 254577930 2.680000e-09 75.0


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 TraesCS6A01G111200 chr6A 80685075 80692013 6938 False 12815.0 12815 100.00000 1 6939 1 chr6A.!!$F1 6938
1 TraesCS6A01G111200 chr6D 62884657 62894133 9476 False 2620.5 5387 91.68825 9 6937 4 chr6D.!!$F1 6928
2 TraesCS6A01G111200 chr6B 136499193 136506621 7428 False 1840.5 2891 90.27750 744 6510 4 chr6B.!!$F1 5766

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
665 667 0.172578 TCGCCGAAGTCGTCAATGAT 59.827 50.000 0.00 0.00 37.74 2.45 F
943 947 0.458889 CAAAATAGTCGTCCGCCCGA 60.459 55.000 0.00 0.00 33.79 5.14 F
2101 2105 0.391661 GATGCCGAGCTTGGTCAAGA 60.392 55.000 21.55 1.41 40.79 3.02 F
2106 2110 0.449388 CGAGCTTGGTCAAGATTGGC 59.551 55.000 14.20 0.00 40.79 4.52 F
2840 2853 0.622136 TGGACCTCTACCGCTCTACA 59.378 55.000 0.00 0.00 0.00 2.74 F
4491 6330 0.320697 GGCTAAGTGTCCAGTCGGTT 59.679 55.000 0.00 0.00 0.00 4.44 F
4492 6331 1.270678 GGCTAAGTGTCCAGTCGGTTT 60.271 52.381 0.00 0.00 0.00 3.27 F
5659 7504 1.596477 GGATGCTCATGTCGAGGCC 60.596 63.158 0.00 0.00 42.55 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2004 2008 0.764890 AGAGCTGCCAACACCTACAA 59.235 50.000 0.00 0.00 0.00 2.41 R
2680 2690 0.543749 AATCTCCTGCTGCCTACCAC 59.456 55.000 0.00 0.00 0.00 4.16 R
3072 3086 0.529773 ACTGTTGCTCAAACGCTCGA 60.530 50.000 0.00 0.00 42.10 4.04 R
3073 3087 1.136690 TACTGTTGCTCAAACGCTCG 58.863 50.000 0.00 0.00 42.10 5.03 R
4626 6465 2.031682 GCTCCAGTTTATATGCTTGCCG 60.032 50.000 0.00 0.00 0.00 5.69 R
5581 7426 0.172578 TGCGGGACATCTCTAACACG 59.827 55.000 0.00 0.00 0.00 4.49 R
5935 7780 1.263752 GCGCACTTACCCGTGTTTTAA 59.736 47.619 0.30 0.00 37.24 1.52 R
6887 8754 1.446791 GAGGCTGAGCTCCATGGAG 59.553 63.158 33.73 33.73 44.56 3.86 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
152 153 8.429641 GGATTACATGACTGATTTCCCTTAGTA 58.570 37.037 0.00 0.00 0.00 1.82
188 189 4.768807 ATATAGGAGGGCTGAGTTAGGT 57.231 45.455 0.00 0.00 0.00 3.08
197 198 2.289565 GCTGAGTTAGGTAACATGCCC 58.710 52.381 2.83 0.00 38.62 5.36
218 219 5.163713 GCCCGATTTCTGATGGCTATAAATC 60.164 44.000 6.68 6.68 39.05 2.17
224 225 7.444629 TTTCTGATGGCTATAAATCTGCATC 57.555 36.000 0.00 0.00 0.00 3.91
235 236 7.042187 GCTATAAATCTGCATCCTTGATATCCG 60.042 40.741 0.00 0.00 0.00 4.18
340 342 3.164268 CAACATCCCCACCTGATTGAAA 58.836 45.455 0.00 0.00 0.00 2.69
341 343 3.541242 ACATCCCCACCTGATTGAAAA 57.459 42.857 0.00 0.00 0.00 2.29
342 344 4.065214 ACATCCCCACCTGATTGAAAAT 57.935 40.909 0.00 0.00 0.00 1.82
343 345 3.770933 ACATCCCCACCTGATTGAAAATG 59.229 43.478 0.00 0.00 0.00 2.32
387 389 7.863901 AGAGGGCTGAATAAGATGTTATAGT 57.136 36.000 0.00 0.00 0.00 2.12
413 415 6.901887 CGTCTATGATTCAAAACTCGGATTTG 59.098 38.462 0.00 0.00 38.76 2.32
475 477 6.341316 AGCACTCTTCATAACACATTCGTAT 58.659 36.000 0.00 0.00 0.00 3.06
477 479 7.649705 AGCACTCTTCATAACACATTCGTATAG 59.350 37.037 0.00 0.00 0.00 1.31
558 560 9.798885 GATAATGTAAGCTAAAACGAGCAATAG 57.201 33.333 0.00 0.00 45.43 1.73
567 569 2.074729 ACGAGCAATAGCCCTAGTCT 57.925 50.000 0.00 0.00 43.56 3.24
568 570 2.389715 ACGAGCAATAGCCCTAGTCTT 58.610 47.619 0.00 0.00 43.56 3.01
574 576 3.318557 GCAATAGCCCTAGTCTTAGTCGT 59.681 47.826 0.00 0.00 33.58 4.34
584 586 6.264088 CCTAGTCTTAGTCGTGGTTTATCAC 58.736 44.000 0.00 0.00 0.00 3.06
594 596 0.655733 GGTTTATCACCGTCGGCATG 59.344 55.000 12.28 2.98 35.12 4.06
595 597 1.365699 GTTTATCACCGTCGGCATGT 58.634 50.000 12.28 0.00 0.00 3.21
631 633 2.586079 CGTCATAGGTGCCCTGCG 60.586 66.667 4.16 1.10 34.61 5.18
635 637 1.522355 CATAGGTGCCCTGCGACAG 60.522 63.158 4.16 0.00 34.61 3.51
662 664 1.800315 CGTCGCCGAAGTCGTCAAT 60.800 57.895 0.00 0.00 37.74 2.57
665 667 0.172578 TCGCCGAAGTCGTCAATGAT 59.827 50.000 0.00 0.00 37.74 2.45
671 673 1.732259 GAAGTCGTCAATGATGCGGTT 59.268 47.619 0.00 0.00 0.00 4.44
689 691 4.742201 GGCCTTCGCTCACGCTCA 62.742 66.667 0.00 0.00 39.84 4.26
693 695 1.226407 CTTCGCTCACGCTCATCGA 60.226 57.895 0.00 0.00 41.67 3.59
699 701 1.601412 GCTCACGCTCATCGATGATGA 60.601 52.381 27.43 24.53 45.35 2.92
716 718 9.025041 TCGATGATGACCAATAATATAGTCAGT 57.975 33.333 10.49 2.35 42.13 3.41
723 725 7.092623 TGACCAATAATATAGTCAGTTGGTGGT 60.093 37.037 17.08 7.03 46.61 4.16
735 737 8.262601 AGTCAGTTGGTGGTTATATGATATGA 57.737 34.615 0.00 0.00 0.00 2.15
737 739 8.367911 GTCAGTTGGTGGTTATATGATATGAGA 58.632 37.037 0.00 0.00 0.00 3.27
739 741 7.821359 CAGTTGGTGGTTATATGATATGAGAGG 59.179 40.741 0.00 0.00 0.00 3.69
763 765 2.805671 TCTACAATCAACACTTGTGGCG 59.194 45.455 5.72 0.00 37.41 5.69
769 771 1.939934 TCAACACTTGTGGCGAAAGAG 59.060 47.619 5.72 1.21 0.00 2.85
772 774 2.755650 ACACTTGTGGCGAAAGAGTAG 58.244 47.619 5.72 0.00 28.41 2.57
776 778 4.272504 CACTTGTGGCGAAAGAGTAGAAAA 59.727 41.667 6.04 0.00 0.00 2.29
778 780 6.147164 CACTTGTGGCGAAAGAGTAGAAAATA 59.853 38.462 6.04 0.00 0.00 1.40
784 786 6.876789 TGGCGAAAGAGTAGAAAATATCAACA 59.123 34.615 0.00 0.00 0.00 3.33
788 790 8.338259 CGAAAGAGTAGAAAATATCAACATGGG 58.662 37.037 0.00 0.00 0.00 4.00
790 792 6.904626 AGAGTAGAAAATATCAACATGGGCT 58.095 36.000 0.00 0.00 0.00 5.19
791 793 6.769822 AGAGTAGAAAATATCAACATGGGCTG 59.230 38.462 0.00 0.00 0.00 4.85
806 808 2.173356 TGGGCTGTTGGATTAGAGATGG 59.827 50.000 0.00 0.00 0.00 3.51
809 811 3.126831 GCTGTTGGATTAGAGATGGACG 58.873 50.000 0.00 0.00 0.00 4.79
811 813 4.615949 CTGTTGGATTAGAGATGGACGAG 58.384 47.826 0.00 0.00 0.00 4.18
820 822 0.904649 AGATGGACGAGGCACAATCA 59.095 50.000 0.00 0.00 0.00 2.57
823 825 2.198827 TGGACGAGGCACAATCATTT 57.801 45.000 0.00 0.00 0.00 2.32
828 830 2.890311 ACGAGGCACAATCATTTGGAAA 59.110 40.909 0.00 0.00 37.15 3.13
861 865 3.168292 ACATCTATGCCATCGATCTCCA 58.832 45.455 0.00 0.00 0.00 3.86
873 877 1.406887 CGATCTCCAATCCAACGGGTT 60.407 52.381 0.00 0.00 34.93 4.11
874 878 2.017049 GATCTCCAATCCAACGGGTTG 58.983 52.381 4.58 4.58 40.13 3.77
918 922 2.564771 TCACCACAAGCTCTGTTTCTG 58.435 47.619 0.00 0.00 35.47 3.02
943 947 0.458889 CAAAATAGTCGTCCGCCCGA 60.459 55.000 0.00 0.00 33.79 5.14
1170 1174 4.426313 CAGCCCGTTCCCCTTCCC 62.426 72.222 0.00 0.00 0.00 3.97
1173 1177 4.043100 CCCGTTCCCCTTCCCCAC 62.043 72.222 0.00 0.00 0.00 4.61
1176 1180 2.666098 CGTTCCCCTTCCCCACGAT 61.666 63.158 0.00 0.00 32.51 3.73
1393 1397 2.443390 TGGCGGTAGCTAGACCCC 60.443 66.667 0.00 0.00 44.37 4.95
1404 1408 2.005960 CTAGACCCCAAGACGAGGCG 62.006 65.000 0.00 0.00 0.00 5.52
1565 1569 3.956377 AGCCCTCGGGTCAGTATG 58.044 61.111 3.54 0.00 37.65 2.39
1582 1586 5.050634 TCAGTATGTTACACTTTGCAACGAC 60.051 40.000 10.27 0.00 37.40 4.34
1603 1607 5.678483 CGACACTGACTGAAAGAAATGTTTG 59.322 40.000 0.00 0.00 37.43 2.93
1604 1608 5.343249 ACACTGACTGAAAGAAATGTTTGC 58.657 37.500 0.00 0.00 37.43 3.68
1618 1622 7.319646 AGAAATGTTTGCTGTTGTTTACTTGA 58.680 30.769 0.00 0.00 0.00 3.02
1677 1681 3.055891 TCTTCTTTCTCGATGATGTGCCA 60.056 43.478 0.00 0.00 0.00 4.92
1680 1684 4.264253 TCTTTCTCGATGATGTGCCAAAT 58.736 39.130 0.00 0.00 0.00 2.32
1681 1685 4.701651 TCTTTCTCGATGATGTGCCAAATT 59.298 37.500 0.00 0.00 0.00 1.82
1682 1686 5.183713 TCTTTCTCGATGATGTGCCAAATTT 59.816 36.000 0.00 0.00 0.00 1.82
1684 1688 5.389859 TCTCGATGATGTGCCAAATTTTT 57.610 34.783 0.00 0.00 0.00 1.94
1708 1712 1.529244 GTTTGCAGGTCTGGGTGCT 60.529 57.895 0.00 0.00 40.54 4.40
1714 1718 4.416738 GGTCTGGGTGCTGGGCTC 62.417 72.222 0.00 0.00 0.00 4.70
1911 1915 2.436646 CGAATCGCTTGTGCCCCT 60.437 61.111 0.00 0.00 35.36 4.79
1925 1929 1.775459 TGCCCCTGCCGGTATTATTTA 59.225 47.619 1.90 0.00 36.33 1.40
1952 1956 5.681954 GCTGATGCTGCAATATTTTGGGTTA 60.682 40.000 6.36 0.00 36.03 2.85
1953 1957 5.904941 TGATGCTGCAATATTTTGGGTTAG 58.095 37.500 6.36 0.00 33.22 2.34
1959 1963 5.463154 TGCAATATTTTGGGTTAGGCCTAT 58.537 37.500 14.74 0.00 37.43 2.57
2004 2008 5.524646 CCACTGAATTTGTGTGCTGATTTTT 59.475 36.000 10.31 0.00 33.92 1.94
2045 2049 2.165641 TGATATCGTTCGTCAAGGTGCT 59.834 45.455 0.00 0.00 0.00 4.40
2101 2105 0.391661 GATGCCGAGCTTGGTCAAGA 60.392 55.000 21.55 1.41 40.79 3.02
2106 2110 0.449388 CGAGCTTGGTCAAGATTGGC 59.551 55.000 14.20 0.00 40.79 4.52
2256 2260 3.573967 GGTCATCAACATTTCAACACCCT 59.426 43.478 0.00 0.00 0.00 4.34
2263 2267 4.170468 ACATTTCAACACCCTCTGAAGT 57.830 40.909 0.00 0.00 33.30 3.01
2269 2273 7.739498 TTTCAACACCCTCTGAAGTTAATAC 57.261 36.000 0.00 0.00 33.30 1.89
2273 2277 5.794894 ACACCCTCTGAAGTTAATACACTG 58.205 41.667 0.00 0.00 0.00 3.66
2285 2289 2.649331 ATACACTGTTCGTTCCCTCG 57.351 50.000 0.00 0.00 0.00 4.63
2310 2314 4.096003 CAGGTCCATCGGGCGGTT 62.096 66.667 0.00 0.00 0.00 4.44
2421 2425 6.773638 ACTCCTGACTTACACAAATCTCATT 58.226 36.000 0.00 0.00 0.00 2.57
2436 2440 9.147732 ACAAATCTCATTCCTAAAGGTCTTTTT 57.852 29.630 1.04 0.00 36.34 1.94
2646 2656 3.452990 TGCACGGATAATTAACCAGAGGA 59.547 43.478 11.87 2.89 0.00 3.71
2647 2657 4.102524 TGCACGGATAATTAACCAGAGGAT 59.897 41.667 11.87 0.00 0.00 3.24
2679 2689 1.383943 TGGGGTAGCCATGGTCGAT 60.384 57.895 14.67 0.00 0.00 3.59
2680 2690 1.071471 GGGGTAGCCATGGTCGATG 59.929 63.158 14.67 0.00 0.00 3.84
2745 2757 3.866816 TCCAGAGAGCATATGGGAAGAT 58.133 45.455 4.56 0.00 40.95 2.40
2789 2801 5.796502 TTGTGGAAGGATTAAGGGAAGAT 57.203 39.130 0.00 0.00 0.00 2.40
2790 2802 5.116084 TGTGGAAGGATTAAGGGAAGATG 57.884 43.478 0.00 0.00 0.00 2.90
2791 2803 4.788075 TGTGGAAGGATTAAGGGAAGATGA 59.212 41.667 0.00 0.00 0.00 2.92
2792 2804 5.433051 TGTGGAAGGATTAAGGGAAGATGAT 59.567 40.000 0.00 0.00 0.00 2.45
2837 2850 1.076632 CCTGGACCTCTACCGCTCT 60.077 63.158 0.00 0.00 0.00 4.09
2840 2853 0.622136 TGGACCTCTACCGCTCTACA 59.378 55.000 0.00 0.00 0.00 2.74
2927 2940 9.547753 GGATAGTTGAGATCTGTTTATTGCTTA 57.452 33.333 0.00 0.00 0.00 3.09
2935 2948 9.162764 GAGATCTGTTTATTGCTTACCTGTAAA 57.837 33.333 0.00 0.00 0.00 2.01
3000 3013 4.162509 AGGCCTAAGTTCAGATCCTAACAC 59.837 45.833 1.29 0.00 0.00 3.32
3035 3049 5.578157 ACTCTAGAGAAGGATCCTACTCC 57.422 47.826 26.57 5.00 35.37 3.85
3058 3072 3.997021 CTCCATCCCATATTAACTGTCGC 59.003 47.826 0.00 0.00 0.00 5.19
3072 3086 2.094182 ACTGTCGCTCAAACGGATGTAT 60.094 45.455 0.00 0.00 0.00 2.29
3073 3087 2.535984 CTGTCGCTCAAACGGATGTATC 59.464 50.000 0.00 0.00 0.00 2.24
3074 3088 1.517276 GTCGCTCAAACGGATGTATCG 59.483 52.381 0.00 0.00 0.00 2.92
3075 3089 1.402613 TCGCTCAAACGGATGTATCGA 59.597 47.619 0.00 0.00 0.00 3.59
3077 3091 1.523095 GCTCAAACGGATGTATCGAGC 59.477 52.381 0.00 0.00 37.81 5.03
3078 3092 1.781429 CTCAAACGGATGTATCGAGCG 59.219 52.381 0.00 0.00 0.00 5.03
3079 3093 1.133598 TCAAACGGATGTATCGAGCGT 59.866 47.619 0.00 0.00 0.00 5.07
3081 3095 2.288961 AACGGATGTATCGAGCGTTT 57.711 45.000 0.00 0.00 31.47 3.60
3082 3096 1.556564 ACGGATGTATCGAGCGTTTG 58.443 50.000 0.00 0.00 0.00 2.93
3085 3099 1.523095 GGATGTATCGAGCGTTTGAGC 59.477 52.381 0.00 0.00 37.41 4.26
3086 3100 2.193447 GATGTATCGAGCGTTTGAGCA 58.807 47.619 0.00 0.00 40.15 4.26
3087 3101 2.073117 TGTATCGAGCGTTTGAGCAA 57.927 45.000 0.00 0.00 40.15 3.91
3089 3103 1.724623 GTATCGAGCGTTTGAGCAACA 59.275 47.619 0.00 0.00 40.15 3.33
3090 3104 0.792640 ATCGAGCGTTTGAGCAACAG 59.207 50.000 0.00 0.00 40.15 3.16
3091 3105 0.529773 TCGAGCGTTTGAGCAACAGT 60.530 50.000 0.00 0.00 40.15 3.55
3092 3106 1.136690 CGAGCGTTTGAGCAACAGTA 58.863 50.000 0.00 0.00 40.15 2.74
3255 4858 3.929002 GCATCATGCAGGCCTCAA 58.071 55.556 0.00 0.00 44.26 3.02
3256 4859 2.426651 GCATCATGCAGGCCTCAAT 58.573 52.632 0.00 0.00 44.26 2.57
3257 4860 0.750850 GCATCATGCAGGCCTCAATT 59.249 50.000 0.00 0.00 44.26 2.32
3258 4861 1.958579 GCATCATGCAGGCCTCAATTA 59.041 47.619 0.00 0.00 44.26 1.40
3259 4862 2.363038 GCATCATGCAGGCCTCAATTAA 59.637 45.455 0.00 0.00 44.26 1.40
3260 4863 3.181473 GCATCATGCAGGCCTCAATTAAA 60.181 43.478 0.00 0.00 44.26 1.52
3330 4947 4.536489 ACCTATAATTCCTATGTCTGGGCC 59.464 45.833 0.00 0.00 0.00 5.80
3362 4979 0.679002 GCTGCTCCTTGCTGAATCCA 60.679 55.000 0.00 0.00 42.27 3.41
3465 5086 9.453830 ACTCTTCCTTAACCTTATATTCCTGAT 57.546 33.333 0.00 0.00 0.00 2.90
3506 5128 4.055360 TGAACTACCTTGACATCACAACG 58.945 43.478 0.00 0.00 0.00 4.10
3510 5132 2.337583 ACCTTGACATCACAACGATCG 58.662 47.619 14.88 14.88 29.21 3.69
3523 5145 4.267690 CACAACGATCGTACAGCAATATGT 59.732 41.667 23.04 15.39 37.19 2.29
3526 5148 6.020121 ACAACGATCGTACAGCAATATGTTAC 60.020 38.462 23.04 0.00 34.56 2.50
3527 5149 5.584442 ACGATCGTACAGCAATATGTTACA 58.416 37.500 21.32 0.00 34.56 2.41
3528 5150 6.037726 ACGATCGTACAGCAATATGTTACAA 58.962 36.000 21.32 0.00 34.56 2.41
3555 5185 6.157211 GCTATGTGAAGTAGTGTACACAAGT 58.843 40.000 27.06 9.98 44.36 3.16
3574 5204 1.665679 GTGTATGCGAACACCATCTGG 59.334 52.381 9.61 0.00 43.23 3.86
3616 5250 2.555732 AATGATCAACCCAGGCCATT 57.444 45.000 5.01 0.00 0.00 3.16
3623 5257 2.026262 TCAACCCAGGCCATTCTTACTC 60.026 50.000 5.01 0.00 0.00 2.59
3671 5305 2.948979 ACGAAAACACTGAAGCCATGAA 59.051 40.909 0.00 0.00 0.00 2.57
3751 5386 6.432783 TGAACCGAAACAATGGTATTCTGAAT 59.567 34.615 8.14 8.14 37.54 2.57
3754 5389 6.127730 ACCGAAACAATGGTATTCTGAATTCC 60.128 38.462 16.52 16.52 36.50 3.01
3811 5448 3.264998 TGCGAATTCATGGATGACAGA 57.735 42.857 6.22 0.00 36.36 3.41
3812 5449 3.200483 TGCGAATTCATGGATGACAGAG 58.800 45.455 6.22 0.00 36.36 3.35
3954 5591 2.036862 GGGCTATTACGTCCCTAAGGTG 59.963 54.545 0.00 0.00 37.08 4.00
4035 5672 9.861138 TTTGATTTTTCATTCTGCGTATTTTTG 57.139 25.926 0.00 0.00 0.00 2.44
4060 5852 9.764363 TGGTCTATGATGTTATAGTTTGTGATC 57.236 33.333 0.00 0.00 33.38 2.92
4061 5853 9.988815 GGTCTATGATGTTATAGTTTGTGATCT 57.011 33.333 0.00 0.00 33.38 2.75
4174 5989 6.403333 TGAGAACTGTCGTTATATGCAAAC 57.597 37.500 0.00 0.00 32.39 2.93
4220 6038 5.048013 CCAGACCAAGAATTTGAAGTAACCC 60.048 44.000 0.00 0.00 36.36 4.11
4228 6046 7.476540 AGAATTTGAAGTAACCCCAAATACC 57.523 36.000 0.00 0.00 38.94 2.73
4323 6150 7.040755 CCGATAAATTGAAGTAACCATATGGCA 60.041 37.037 22.18 7.12 39.32 4.92
4481 6320 8.418662 TGAATAATTACTATGTCGGCTAAGTGT 58.581 33.333 5.28 0.00 0.00 3.55
4483 6322 4.644103 TTACTATGTCGGCTAAGTGTCC 57.356 45.455 5.28 0.00 0.00 4.02
4491 6330 0.320697 GGCTAAGTGTCCAGTCGGTT 59.679 55.000 0.00 0.00 0.00 4.44
4492 6331 1.270678 GGCTAAGTGTCCAGTCGGTTT 60.271 52.381 0.00 0.00 0.00 3.27
4493 6332 2.028748 GGCTAAGTGTCCAGTCGGTTTA 60.029 50.000 0.00 0.00 0.00 2.01
4494 6333 3.555586 GGCTAAGTGTCCAGTCGGTTTAA 60.556 47.826 0.00 0.00 0.00 1.52
4495 6334 3.431233 GCTAAGTGTCCAGTCGGTTTAAC 59.569 47.826 0.00 0.00 0.00 2.01
4496 6335 3.547054 AAGTGTCCAGTCGGTTTAACA 57.453 42.857 0.00 0.00 0.00 2.41
4498 6337 4.081322 AGTGTCCAGTCGGTTTAACATT 57.919 40.909 0.00 0.00 0.00 2.71
4499 6338 4.062991 AGTGTCCAGTCGGTTTAACATTC 58.937 43.478 0.00 0.00 0.00 2.67
4500 6339 3.810941 GTGTCCAGTCGGTTTAACATTCA 59.189 43.478 0.00 0.00 0.00 2.57
4501 6340 4.273969 GTGTCCAGTCGGTTTAACATTCAA 59.726 41.667 0.00 0.00 0.00 2.69
4503 6342 4.514066 GTCCAGTCGGTTTAACATTCAAGT 59.486 41.667 0.00 0.00 0.00 3.16
4509 6348 7.647715 CAGTCGGTTTAACATTCAAGTGAAAAT 59.352 33.333 0.00 0.00 37.61 1.82
4605 6444 5.359576 GGTTGCAAGTTATTGTGGATATGGA 59.640 40.000 0.00 0.00 38.76 3.41
4647 6486 2.031682 CGGCAAGCATATAAACTGGAGC 60.032 50.000 0.00 0.00 0.00 4.70
4852 6697 8.103305 ACACAAGTCCTCATATTCTGTGTAAAT 58.897 33.333 3.27 0.00 36.41 1.40
4910 6755 2.092968 GGGGACATGAGCACATCTTGTA 60.093 50.000 0.00 0.00 44.10 2.41
4980 6825 4.499183 GGGTCTTCTGACAACTACATCTG 58.501 47.826 0.00 0.00 44.61 2.90
5142 6987 8.579850 TGCTTCTCATACCATTTGTTTAATCT 57.420 30.769 0.00 0.00 0.00 2.40
5414 7259 2.041620 TCTTATTGACTTTGGGGCAGCT 59.958 45.455 0.00 0.00 32.68 4.24
5442 7287 7.281549 GTGAGTTCCCTAAAAAGTTTGTAGACA 59.718 37.037 13.55 0.00 0.00 3.41
5501 7346 8.274322 TCCTCATATCCAATACAAAATCTGTGT 58.726 33.333 0.00 0.00 39.20 3.72
5581 7426 1.939255 GCAAATAGAGACAGAGCTGGC 59.061 52.381 0.00 0.00 39.43 4.85
5659 7504 1.596477 GGATGCTCATGTCGAGGCC 60.596 63.158 0.00 0.00 42.55 5.19
5698 7543 1.675641 ATTCGCAACTCCTGGTGGC 60.676 57.895 0.33 0.00 41.31 5.01
5818 7663 2.559440 CTCCATAGAAAGCTGTCAGGC 58.441 52.381 6.68 0.00 0.00 4.85
5899 7744 4.563061 AGGTTTACGAGCAGTACGATTTT 58.437 39.130 0.00 0.00 34.56 1.82
5947 7792 2.423446 ACACTGGTTAAAACACGGGT 57.577 45.000 0.00 0.00 0.00 5.28
5976 7821 3.870299 GCCTTTACCCTCTTGTCCTGAAG 60.870 52.174 0.00 0.00 0.00 3.02
5978 7823 4.202472 CCTTTACCCTCTTGTCCTGAAGTT 60.202 45.833 0.00 0.00 0.00 2.66
6089 7934 8.859236 ATATTCTTCATGTCATGGAAATCGAT 57.141 30.769 12.90 0.00 0.00 3.59
6145 7990 3.297979 GCGTTTTCATTGTAATGTGAGCG 59.702 43.478 4.67 8.79 37.65 5.03
6226 8071 0.093705 GATGAGTTGCTGCGTTCGTC 59.906 55.000 0.00 0.04 0.00 4.20
6247 8092 5.346281 CGTCTGCTTCCACTAAGAAGTAAAG 59.654 44.000 3.47 0.50 44.27 1.85
6634 8483 3.503748 ACTGTGCAAGTAAAGAAGGATGC 59.496 43.478 0.00 0.00 37.36 3.91
6683 8532 3.109619 TGAAAAACGTTGAAATGCGACC 58.890 40.909 0.00 0.00 0.00 4.79
6733 8598 8.698973 TCATGTGTTAAAAAGTCCCAGATTTA 57.301 30.769 0.00 0.00 0.00 1.40
6762 8627 2.017049 GCATAGCCCTCATTTCAACGT 58.983 47.619 0.00 0.00 0.00 3.99
6773 8638 5.461032 TCATTTCAACGTATTTTGCCCTT 57.539 34.783 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.371176 TGGAAGTACATAGCATCCCCAAATA 59.629 40.000 0.00 0.00 0.00 1.40
1 2 4.167892 TGGAAGTACATAGCATCCCCAAAT 59.832 41.667 0.00 0.00 0.00 2.32
2 3 3.525609 TGGAAGTACATAGCATCCCCAAA 59.474 43.478 0.00 0.00 0.00 3.28
3 4 3.119319 TGGAAGTACATAGCATCCCCAA 58.881 45.455 0.00 0.00 0.00 4.12
4 5 2.705658 CTGGAAGTACATAGCATCCCCA 59.294 50.000 0.00 0.00 0.00 4.96
5 6 3.409026 CTGGAAGTACATAGCATCCCC 57.591 52.381 0.00 0.00 0.00 4.81
188 189 3.213506 CCATCAGAAATCGGGCATGTTA 58.786 45.455 0.00 0.00 0.00 2.41
197 198 6.148315 TGCAGATTTATAGCCATCAGAAATCG 59.852 38.462 0.00 0.00 40.07 3.34
218 219 2.174363 TGCGGATATCAAGGATGCAG 57.826 50.000 4.83 0.00 0.00 4.41
309 311 3.554934 GTGGGGATGTTGATATCAAGCA 58.445 45.455 18.47 17.79 36.39 3.91
340 342 3.562141 TGTACAAGTAACTTGCGCACATT 59.438 39.130 11.12 10.41 44.43 2.71
341 343 3.135225 TGTACAAGTAACTTGCGCACAT 58.865 40.909 11.12 0.89 44.43 3.21
342 344 2.552031 TGTACAAGTAACTTGCGCACA 58.448 42.857 11.12 0.00 44.43 4.57
343 345 3.246699 TCTTGTACAAGTAACTTGCGCAC 59.753 43.478 29.83 0.00 44.43 5.34
387 389 5.319140 TCCGAGTTTTGAATCATAGACGA 57.681 39.130 0.00 0.00 0.00 4.20
448 450 6.477033 ACGAATGTGTTATGAAGAGTGCTATC 59.523 38.462 0.00 0.00 0.00 2.08
533 535 8.283291 GCTATTGCTCGTTTTAGCTTACATTAT 58.717 33.333 0.00 0.00 43.19 1.28
534 536 7.254658 GGCTATTGCTCGTTTTAGCTTACATTA 60.255 37.037 0.00 0.00 43.19 1.90
536 538 5.007724 GGCTATTGCTCGTTTTAGCTTACAT 59.992 40.000 0.00 0.00 43.19 2.29
538 540 4.260661 GGGCTATTGCTCGTTTTAGCTTAC 60.261 45.833 0.00 0.00 43.19 2.34
558 560 1.472188 ACCACGACTAAGACTAGGGC 58.528 55.000 0.00 0.00 0.00 5.19
662 664 2.745884 CGAAGGCCAACCGCATCA 60.746 61.111 5.01 0.00 42.76 3.07
693 695 9.730705 CCAACTGACTATATTATTGGTCATCAT 57.269 33.333 10.48 1.89 37.92 2.45
716 718 6.574269 CGCCTCTCATATCATATAACCACCAA 60.574 42.308 0.00 0.00 0.00 3.67
723 725 8.575649 TTGTAGACGCCTCTCATATCATATAA 57.424 34.615 0.00 0.00 0.00 0.98
732 734 3.195610 TGTTGATTGTAGACGCCTCTCAT 59.804 43.478 0.00 0.00 0.00 2.90
735 737 2.563179 AGTGTTGATTGTAGACGCCTCT 59.437 45.455 0.00 0.00 0.00 3.69
737 739 3.067106 CAAGTGTTGATTGTAGACGCCT 58.933 45.455 0.00 0.00 0.00 5.52
739 741 3.363970 CCACAAGTGTTGATTGTAGACGC 60.364 47.826 0.00 0.00 38.80 5.19
763 765 8.131731 GCCCATGTTGATATTTTCTACTCTTTC 58.868 37.037 0.00 0.00 32.15 2.62
769 771 6.699575 ACAGCCCATGTTGATATTTTCTAC 57.300 37.500 0.00 0.00 39.96 2.59
784 786 3.181436 CCATCTCTAATCCAACAGCCCAT 60.181 47.826 0.00 0.00 0.00 4.00
788 790 3.126831 CGTCCATCTCTAATCCAACAGC 58.873 50.000 0.00 0.00 0.00 4.40
790 792 3.384789 CCTCGTCCATCTCTAATCCAACA 59.615 47.826 0.00 0.00 0.00 3.33
791 793 3.800604 GCCTCGTCCATCTCTAATCCAAC 60.801 52.174 0.00 0.00 0.00 3.77
793 795 1.964223 GCCTCGTCCATCTCTAATCCA 59.036 52.381 0.00 0.00 0.00 3.41
806 808 2.083774 TCCAAATGATTGTGCCTCGTC 58.916 47.619 0.00 0.00 34.60 4.20
809 811 9.598517 TTTATAATTTCCAAATGATTGTGCCTC 57.401 29.630 0.00 0.00 34.60 4.70
811 813 9.986833 GTTTTATAATTTCCAAATGATTGTGCC 57.013 29.630 0.00 0.00 34.60 5.01
854 858 2.017049 CAACCCGTTGGATTGGAGATC 58.983 52.381 0.00 0.00 36.95 2.75
886 890 6.205658 AGAGCTTGTGGTGAAAAATAGAAGAC 59.794 38.462 0.00 0.00 0.00 3.01
918 922 2.655001 GCGGACGACTATTTTGCAAAAC 59.345 45.455 26.05 12.75 0.00 2.43
943 947 0.912006 GGGACCAAGAAGAGGAGCCT 60.912 60.000 0.00 0.00 0.00 4.58
985 989 3.267860 CATGGCGAGCGAAGGAGC 61.268 66.667 0.00 0.00 37.41 4.70
1170 1174 3.385749 CTCGGGGTGGGAATCGTGG 62.386 68.421 0.00 0.00 0.00 4.94
1191 1195 2.107953 GGGCGAGATGAGTCTGCC 59.892 66.667 9.12 9.12 42.74 4.85
1404 1408 0.109039 GTGAGAGCTCAGGACGAACC 60.109 60.000 17.77 0.00 40.75 3.62
1410 1414 0.323816 ATGACGGTGAGAGCTCAGGA 60.324 55.000 17.77 0.00 40.75 3.86
1565 1569 3.062909 TCAGTGTCGTTGCAAAGTGTAAC 59.937 43.478 12.18 3.87 39.17 2.50
1582 1586 5.457799 CAGCAAACATTTCTTTCAGTCAGTG 59.542 40.000 0.00 0.00 0.00 3.66
1631 1635 9.323985 AGAAGATTTAGTCTGCATTCTATTCAC 57.676 33.333 0.00 0.00 37.23 3.18
1637 1641 8.860780 AAAGAAGAAGATTTAGTCTGCATTCT 57.139 30.769 0.00 0.00 37.23 2.40
1644 1648 8.744652 TCATCGAGAAAGAAGAAGATTTAGTCT 58.255 33.333 0.00 0.00 39.43 3.24
1645 1649 8.918961 TCATCGAGAAAGAAGAAGATTTAGTC 57.081 34.615 0.00 0.00 0.00 2.59
1682 1686 3.386402 CCCAGACCTGCAAACCTTAAAAA 59.614 43.478 0.00 0.00 0.00 1.94
1684 1688 2.091555 ACCCAGACCTGCAAACCTTAAA 60.092 45.455 0.00 0.00 0.00 1.52
1714 1718 1.443407 CTGTAGACCTCCCCATGCG 59.557 63.158 0.00 0.00 0.00 4.73
1753 1757 2.633692 TCCCCAACAGGTGTACCATAA 58.366 47.619 3.56 0.00 38.89 1.90
1837 1841 4.838152 CCCCGCATCCGACACAGG 62.838 72.222 0.00 0.00 36.29 4.00
1888 1892 1.291877 GCACAAGCGATTCGTCCTGT 61.292 55.000 8.03 6.04 0.00 4.00
1911 1915 5.278266 GCATCAGCTTTAAATAATACCGGCA 60.278 40.000 0.00 0.00 37.91 5.69
1925 1929 4.873827 CCAAAATATTGCAGCATCAGCTTT 59.126 37.500 0.00 0.00 40.94 3.51
1952 1956 3.696051 CACAAGCACATAACAATAGGCCT 59.304 43.478 11.78 11.78 0.00 5.19
1953 1957 3.694072 TCACAAGCACATAACAATAGGCC 59.306 43.478 0.00 0.00 0.00 5.19
1959 1963 3.305267 GGCACATCACAAGCACATAACAA 60.305 43.478 0.00 0.00 0.00 2.83
2004 2008 0.764890 AGAGCTGCCAACACCTACAA 59.235 50.000 0.00 0.00 0.00 2.41
2045 2049 1.209261 TGCTTCCTCGGCATAACATCA 59.791 47.619 0.00 0.00 34.56 3.07
2256 2260 6.643770 GGAACGAACAGTGTATTAACTTCAGA 59.356 38.462 0.00 0.00 0.00 3.27
2263 2267 4.022068 ACGAGGGAACGAACAGTGTATTAA 60.022 41.667 0.00 0.00 37.03 1.40
2269 2273 1.578583 AAACGAGGGAACGAACAGTG 58.421 50.000 0.00 0.00 37.03 3.66
2273 2277 4.142966 CCTGATAAAAACGAGGGAACGAAC 60.143 45.833 0.00 0.00 37.03 3.95
2285 2289 2.357952 GCCCGATGGACCTGATAAAAAC 59.642 50.000 0.00 0.00 0.00 2.43
2310 2314 3.433306 ACATCCGAACCATCCTTCAAA 57.567 42.857 0.00 0.00 0.00 2.69
2421 2425 7.824779 GCTCTATCAAGAAAAAGACCTTTAGGA 59.175 37.037 2.06 0.00 38.94 2.94
2554 2563 5.972107 ATTTTGAGAGACATGGTTTGGAG 57.028 39.130 0.00 0.00 0.00 3.86
2646 2656 4.483243 CCACACCGCCGGCCTTAT 62.483 66.667 23.46 0.50 0.00 1.73
2679 2689 0.618680 ATCTCCTGCTGCCTACCACA 60.619 55.000 0.00 0.00 0.00 4.17
2680 2690 0.543749 AATCTCCTGCTGCCTACCAC 59.456 55.000 0.00 0.00 0.00 4.16
2745 2757 2.452505 TCACCGACCATGTGACATCTA 58.547 47.619 0.00 0.00 37.80 1.98
2847 2860 4.845447 GCCCCATCATGGCTGGCA 62.845 66.667 16.97 6.31 42.31 4.92
2927 2940 5.195185 GACTACCTCTAGCTCTTTACAGGT 58.805 45.833 0.00 0.00 37.93 4.00
2935 2948 7.996644 GGCTATATAATGACTACCTCTAGCTCT 59.003 40.741 0.00 0.00 31.92 4.09
3000 3013 5.215252 TCTCTAGAGTTTGTTCCCAAGTG 57.785 43.478 19.21 0.00 0.00 3.16
3035 3049 4.569943 CGACAGTTAATATGGGATGGAGG 58.430 47.826 0.00 0.00 0.00 4.30
3058 3072 1.781429 CGCTCGATACATCCGTTTGAG 59.219 52.381 0.00 0.00 0.00 3.02
3072 3086 0.529773 ACTGTTGCTCAAACGCTCGA 60.530 50.000 0.00 0.00 42.10 4.04
3073 3087 1.136690 TACTGTTGCTCAAACGCTCG 58.863 50.000 0.00 0.00 42.10 5.03
3074 3088 3.813529 ATTACTGTTGCTCAAACGCTC 57.186 42.857 0.00 0.00 42.10 5.03
3075 3089 4.094887 CCATATTACTGTTGCTCAAACGCT 59.905 41.667 0.00 0.00 42.10 5.07
3077 3091 4.634004 TCCCATATTACTGTTGCTCAAACG 59.366 41.667 0.00 0.00 42.10 3.60
3078 3092 5.447279 CGTCCCATATTACTGTTGCTCAAAC 60.447 44.000 0.00 0.00 39.41 2.93
3079 3093 4.634004 CGTCCCATATTACTGTTGCTCAAA 59.366 41.667 0.00 0.00 0.00 2.69
3081 3095 3.431626 CCGTCCCATATTACTGTTGCTCA 60.432 47.826 0.00 0.00 0.00 4.26
3082 3096 3.131396 CCGTCCCATATTACTGTTGCTC 58.869 50.000 0.00 0.00 0.00 4.26
3085 3099 3.494398 CCCTCCGTCCCATATTACTGTTG 60.494 52.174 0.00 0.00 0.00 3.33
3086 3100 2.704065 CCCTCCGTCCCATATTACTGTT 59.296 50.000 0.00 0.00 0.00 3.16
3087 3101 2.090943 TCCCTCCGTCCCATATTACTGT 60.091 50.000 0.00 0.00 0.00 3.55
3089 3103 2.179424 ACTCCCTCCGTCCCATATTACT 59.821 50.000 0.00 0.00 0.00 2.24
3090 3104 2.606378 ACTCCCTCCGTCCCATATTAC 58.394 52.381 0.00 0.00 0.00 1.89
3091 3105 3.400322 AGTACTCCCTCCGTCCCATATTA 59.600 47.826 0.00 0.00 0.00 0.98
3092 3106 2.179424 AGTACTCCCTCCGTCCCATATT 59.821 50.000 0.00 0.00 0.00 1.28
3189 4792 5.555017 TCTGGATCAGGCAATAAGATAAGC 58.445 41.667 0.00 0.00 31.51 3.09
3200 4803 4.776435 TTGTATCATTCTGGATCAGGCA 57.224 40.909 0.00 0.00 31.51 4.75
3244 4847 3.265737 TCCTAGTTTAATTGAGGCCTGCA 59.734 43.478 12.00 5.19 0.00 4.41
3245 4848 3.628032 GTCCTAGTTTAATTGAGGCCTGC 59.372 47.826 12.00 1.89 0.00 4.85
3246 4849 5.104259 AGTCCTAGTTTAATTGAGGCCTG 57.896 43.478 12.00 0.00 0.00 4.85
3247 4850 5.033522 AGAGTCCTAGTTTAATTGAGGCCT 58.966 41.667 3.86 3.86 0.00 5.19
3248 4851 5.360649 AGAGTCCTAGTTTAATTGAGGCC 57.639 43.478 0.00 0.00 0.00 5.19
3249 4852 7.557724 AGTTAGAGTCCTAGTTTAATTGAGGC 58.442 38.462 0.00 0.00 0.00 4.70
3250 4853 9.372369 CAAGTTAGAGTCCTAGTTTAATTGAGG 57.628 37.037 0.00 0.00 0.00 3.86
3251 4854 8.874816 GCAAGTTAGAGTCCTAGTTTAATTGAG 58.125 37.037 0.00 0.00 0.00 3.02
3252 4855 7.822822 GGCAAGTTAGAGTCCTAGTTTAATTGA 59.177 37.037 0.00 0.00 0.00 2.57
3253 4856 7.606456 TGGCAAGTTAGAGTCCTAGTTTAATTG 59.394 37.037 0.00 0.00 0.00 2.32
3254 4857 7.686434 TGGCAAGTTAGAGTCCTAGTTTAATT 58.314 34.615 0.00 0.00 0.00 1.40
3255 4858 7.253905 TGGCAAGTTAGAGTCCTAGTTTAAT 57.746 36.000 0.00 0.00 0.00 1.40
3256 4859 6.675413 TGGCAAGTTAGAGTCCTAGTTTAA 57.325 37.500 0.00 0.00 0.00 1.52
3257 4860 6.295688 CCTTGGCAAGTTAGAGTCCTAGTTTA 60.296 42.308 24.57 0.00 0.00 2.01
3258 4861 5.513267 CCTTGGCAAGTTAGAGTCCTAGTTT 60.513 44.000 24.57 0.00 0.00 2.66
3259 4862 4.020128 CCTTGGCAAGTTAGAGTCCTAGTT 60.020 45.833 24.57 0.00 0.00 2.24
3260 4863 3.515901 CCTTGGCAAGTTAGAGTCCTAGT 59.484 47.826 24.57 0.00 0.00 2.57
3323 4940 2.240918 AATGCTTGAGGGGCCCAGA 61.241 57.895 27.72 7.53 0.00 3.86
3362 4979 1.818642 GCACAGGCAGAGATCAACTT 58.181 50.000 0.00 0.00 40.72 2.66
3385 5002 4.444876 GGGGCAGCTTAATGAATCTGACTA 60.445 45.833 0.00 0.00 37.07 2.59
3465 5086 7.496346 AGTTCAAAGATAGTCACATAAGGGA 57.504 36.000 0.00 0.00 0.00 4.20
3506 5128 8.699582 CAATTGTAACATATTGCTGTACGATC 57.300 34.615 0.00 0.00 0.00 3.69
3523 5145 9.146984 GTACACTACTTCACATAGCAATTGTAA 57.853 33.333 7.40 0.00 0.00 2.41
3526 5148 7.117667 TGTGTACACTACTTCACATAGCAATTG 59.882 37.037 25.60 0.00 36.17 2.32
3527 5149 7.158697 TGTGTACACTACTTCACATAGCAATT 58.841 34.615 25.60 0.00 36.17 2.32
3528 5150 6.697395 TGTGTACACTACTTCACATAGCAAT 58.303 36.000 25.60 0.00 36.17 3.56
3555 5185 1.552792 TCCAGATGGTGTTCGCATACA 59.447 47.619 0.00 0.00 36.34 2.29
3574 5204 3.129462 TCGCATATAGGCTACAGCATCTC 59.871 47.826 7.89 0.00 44.36 2.75
3644 5278 4.148891 GGCTTCAGTGTTTTCGTATTTCG 58.851 43.478 0.00 0.00 41.41 3.46
3683 5317 4.804139 ACGTGCGGAGAAAGACTATAAATG 59.196 41.667 0.00 0.00 0.00 2.32
3684 5318 5.007385 ACGTGCGGAGAAAGACTATAAAT 57.993 39.130 0.00 0.00 0.00 1.40
3685 5319 4.445452 ACGTGCGGAGAAAGACTATAAA 57.555 40.909 0.00 0.00 0.00 1.40
3764 5399 8.592809 ACAATTTTAGCTCAATATTGGAAACCA 58.407 29.630 15.36 0.00 38.90 3.67
3776 5411 6.212235 TGAATTCGCAACAATTTTAGCTCAA 58.788 32.000 0.04 0.00 0.00 3.02
3854 5491 2.833943 TCACATTCTCTTGCCAGCTCTA 59.166 45.455 0.00 0.00 0.00 2.43
3954 5591 4.668576 TTTGCTCGACAATTCATCAGTC 57.331 40.909 2.09 0.00 38.31 3.51
4035 5672 9.988815 AGATCACAAACTATAACATCATAGACC 57.011 33.333 0.00 0.00 33.49 3.85
4174 5989 7.706607 TCTGGCAATAGTATATAATGCTTAGCG 59.293 37.037 0.00 0.00 37.20 4.26
4220 6038 3.941483 AGCTTTCAGATGTCGGTATTTGG 59.059 43.478 0.00 0.00 0.00 3.28
4370 6197 7.050377 GGAATGATGTCAAGAGTCTTCCAATA 58.950 38.462 1.26 0.00 32.90 1.90
4375 6202 5.486526 ACTGGAATGATGTCAAGAGTCTTC 58.513 41.667 1.26 0.00 0.00 2.87
4414 6253 7.797121 ATTTCCCAAGGACAAATAATGAAGT 57.203 32.000 0.00 0.00 0.00 3.01
4481 6320 4.513692 CACTTGAATGTTAAACCGACTGGA 59.486 41.667 0.00 0.00 39.21 3.86
4483 6322 5.666969 TCACTTGAATGTTAAACCGACTG 57.333 39.130 0.00 0.00 0.00 3.51
4491 6330 9.598517 AGAGCAAAATTTTCACTTGAATGTTAA 57.401 25.926 0.00 0.00 33.54 2.01
4492 6331 9.598517 AAGAGCAAAATTTTCACTTGAATGTTA 57.401 25.926 0.00 0.00 33.54 2.41
4493 6332 8.496707 AAGAGCAAAATTTTCACTTGAATGTT 57.503 26.923 0.00 0.00 33.54 2.71
4494 6333 8.496707 AAAGAGCAAAATTTTCACTTGAATGT 57.503 26.923 0.00 0.00 33.54 2.71
4495 6334 8.823818 AGAAAGAGCAAAATTTTCACTTGAATG 58.176 29.630 0.00 0.00 34.18 2.67
4496 6335 8.953368 AGAAAGAGCAAAATTTTCACTTGAAT 57.047 26.923 0.00 0.00 34.18 2.57
4501 6340 8.768019 GCAATAAGAAAGAGCAAAATTTTCACT 58.232 29.630 0.00 1.47 34.18 3.41
4503 6342 8.891671 AGCAATAAGAAAGAGCAAAATTTTCA 57.108 26.923 0.00 0.00 34.18 2.69
4509 6348 5.769662 TCAGGAGCAATAAGAAAGAGCAAAA 59.230 36.000 0.00 0.00 0.00 2.44
4540 6379 4.978099 TCAGCTCAGTTCTCCAAGAAAAT 58.022 39.130 0.00 0.00 35.75 1.82
4542 6381 3.389329 ACTCAGCTCAGTTCTCCAAGAAA 59.611 43.478 0.00 0.00 35.75 2.52
4544 6383 2.603021 ACTCAGCTCAGTTCTCCAAGA 58.397 47.619 0.00 0.00 0.00 3.02
4605 6444 6.714810 TGCCGCTATTTAAGAAATGTATGGAT 59.285 34.615 0.00 0.00 32.38 3.41
4610 6449 5.355630 TGCTTGCCGCTATTTAAGAAATGTA 59.644 36.000 0.00 0.00 40.11 2.29
4626 6465 2.031682 GCTCCAGTTTATATGCTTGCCG 60.032 50.000 0.00 0.00 0.00 5.69
4647 6486 3.287867 AGCATATCTGGTTTGTCAGGG 57.712 47.619 0.00 0.00 35.58 4.45
4852 6697 8.378172 ACGATTAACTTTGAGTCAATCAGAAA 57.622 30.769 6.36 3.57 39.68 2.52
4876 6721 6.166982 GCTCATGTCCCCACTAAGATATAAC 58.833 44.000 0.00 0.00 0.00 1.89
4879 6724 4.040952 GTGCTCATGTCCCCACTAAGATAT 59.959 45.833 0.00 0.00 0.00 1.63
4883 6728 1.278985 TGTGCTCATGTCCCCACTAAG 59.721 52.381 0.00 0.00 0.00 2.18
4889 6734 1.340405 ACAAGATGTGCTCATGTCCCC 60.340 52.381 5.89 0.00 30.09 4.81
4933 6778 4.549458 CCATAAGAAAGTGGTTTGCACAG 58.451 43.478 0.00 0.00 0.00 3.66
4980 6825 3.317993 ACTCCTGTACAAAACCAACATGC 59.682 43.478 0.00 0.00 0.00 4.06
5414 7259 5.187687 ACAAACTTTTTAGGGAACTCACGA 58.812 37.500 0.00 0.00 43.67 4.35
5451 7296 8.682710 GGATAAGTTTTGATTGCTTACCATACA 58.317 33.333 0.00 0.00 0.00 2.29
5499 7344 8.673711 GCCATCTTGAATACAGTAAATAACACA 58.326 33.333 0.00 0.00 0.00 3.72
5501 7346 7.011950 CGGCCATCTTGAATACAGTAAATAACA 59.988 37.037 2.24 0.00 0.00 2.41
5581 7426 0.172578 TGCGGGACATCTCTAACACG 59.827 55.000 0.00 0.00 0.00 4.49
5659 7504 4.143333 ACCCCGACGATGAAGGCG 62.143 66.667 0.00 0.00 43.40 5.52
5698 7543 2.721274 TGTTTGCACGGAAATCATGG 57.279 45.000 0.00 0.00 0.00 3.66
5935 7780 1.263752 GCGCACTTACCCGTGTTTTAA 59.736 47.619 0.30 0.00 37.24 1.52
5947 7792 1.272807 AGAGGGTAAAGGCGCACTTA 58.727 50.000 10.83 2.61 38.85 2.24
5976 7821 5.334879 CCAGCCTGTGTAACTATTTGACAAC 60.335 44.000 0.00 0.00 38.04 3.32
5978 7823 4.202419 ACCAGCCTGTGTAACTATTTGACA 60.202 41.667 0.00 0.00 38.04 3.58
6089 7934 3.118592 GGACCCAACCAAACAAAATCACA 60.119 43.478 0.00 0.00 0.00 3.58
6226 8071 7.389053 ACATTCTTTACTTCTTAGTGGAAGCAG 59.611 37.037 4.42 0.10 44.51 4.24
6247 8092 9.573133 AAGCAAGCACAGTTTTTATATACATTC 57.427 29.630 0.00 0.00 0.00 2.67
6409 8254 3.053842 ACATGTCTTGCATCCTCCTCAAT 60.054 43.478 0.00 0.00 35.19 2.57
6613 8462 3.755378 AGCATCCTTCTTTACTTGCACAG 59.245 43.478 0.00 0.00 32.66 3.66
6625 8474 5.104776 ACACACATACACATAGCATCCTTCT 60.105 40.000 0.00 0.00 0.00 2.85
6626 8475 5.118990 ACACACATACACATAGCATCCTTC 58.881 41.667 0.00 0.00 0.00 3.46
6634 8483 9.773328 CCTGAAATTTTACACACATACACATAG 57.227 33.333 0.00 0.00 0.00 2.23
6701 8550 9.575868 TGGGACTTTTTAACACATGATACTAAA 57.424 29.630 0.00 0.00 0.00 1.85
6873 8740 2.295909 CCATGGAGCTCGGTTTTGAAAA 59.704 45.455 5.56 0.00 0.00 2.29
6887 8754 1.446791 GAGGCTGAGCTCCATGGAG 59.553 63.158 33.73 33.73 44.56 3.86
6900 8767 2.945668 GCGAATATTGTCTTTGGAGGCT 59.054 45.455 0.00 0.00 0.00 4.58


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

AutoCloner maintained by Alex Coulton.