Multiple sequence alignment - TraesCS2D01G177700

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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 TraesCS2D01G177700 chr2D 100.000 3866 0 0 1 3866 121062687 121058822 0.000000e+00 7140
1 TraesCS2D01G177700 chr2D 80.229 875 117 27 1814 2649 121355276 121354419 1.190000e-169 606
2 TraesCS2D01G177700 chr2D 85.208 480 46 17 1066 1534 121356109 121355644 1.630000e-128 470
3 TraesCS2D01G177700 chr2B 88.091 2032 127 42 857 2832 174593915 174591943 0.000000e+00 2305
4 TraesCS2D01G177700 chr2B 87.443 661 38 20 2849 3498 174591988 174591362 0.000000e+00 719
5 TraesCS2D01G177700 chr2B 93.317 404 26 1 1 404 174596239 174595837 2.570000e-166 595
6 TraesCS2D01G177700 chr2B 89.486 428 27 12 397 820 174594921 174594508 3.420000e-145 525
7 TraesCS2D01G177700 chr2B 78.190 862 150 28 1813 2657 174663515 174662675 2.060000e-142 516
8 TraesCS2D01G177700 chr2B 91.343 335 21 4 3540 3866 174591182 174590848 5.890000e-123 451
9 TraesCS2D01G177700 chr2B 84.049 489 48 20 1066 1529 174664207 174663724 9.860000e-121 444
10 TraesCS2D01G177700 chr2A 92.493 1492 68 19 834 2292 125253319 125251839 0.000000e+00 2095
11 TraesCS2D01G177700 chr2A 89.104 670 43 13 2849 3505 125251095 125250443 0.000000e+00 806
12 TraesCS2D01G177700 chr2A 90.295 577 48 6 4 573 125267664 125267089 0.000000e+00 749
13 TraesCS2D01G177700 chr2A 91.071 448 23 9 2347 2786 125251814 125251376 1.200000e-164 590
14 TraesCS2D01G177700 chr2A 79.392 888 129 29 1812 2657 125458875 125458000 9.310000e-161 577
15 TraesCS2D01G177700 chr2A 89.706 340 22 5 3540 3866 125250293 125249954 4.620000e-114 422
16 TraesCS2D01G177700 chr2A 88.968 281 26 4 1303 1580 125459448 125459170 3.700000e-90 342
17 TraesCS2D01G177700 chr5A 78.636 220 40 6 49 265 415348097 415347882 5.210000e-29 139
18 TraesCS2D01G177700 chr6A 87.879 66 4 3 62 125 427081010 427081073 1.490000e-09 75


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 TraesCS2D01G177700 chr2D 121058822 121062687 3865 True 7140.00 7140 100.0000 1 3866 1 chr2D.!!$R1 3865
1 TraesCS2D01G177700 chr2D 121354419 121356109 1690 True 538.00 606 82.7185 1066 2649 2 chr2D.!!$R2 1583
2 TraesCS2D01G177700 chr2B 174590848 174596239 5391 True 919.00 2305 89.9360 1 3866 5 chr2B.!!$R1 3865
3 TraesCS2D01G177700 chr2B 174662675 174664207 1532 True 480.00 516 81.1195 1066 2657 2 chr2B.!!$R2 1591
4 TraesCS2D01G177700 chr2A 125249954 125253319 3365 True 978.25 2095 90.5935 834 3866 4 chr2A.!!$R2 3032
5 TraesCS2D01G177700 chr2A 125267089 125267664 575 True 749.00 749 90.2950 4 573 1 chr2A.!!$R1 569
6 TraesCS2D01G177700 chr2A 125458000 125459448 1448 True 459.50 577 84.1800 1303 2657 2 chr2A.!!$R3 1354

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
674 1604 0.179062 GAATCTGCACCTCGCTCCAT 60.179 55.0 0.0 0.0 43.06 3.41 F
895 2382 0.317854 GGCTGCGAAACCTGTTGAAC 60.318 55.0 0.0 0.0 0.00 3.18 F
2718 4524 0.036952 ATCATCCATCGCCATCGGAC 60.037 55.0 0.0 0.0 36.13 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1706 3385 0.179097 GAACCTGATCGTGGAGCCTC 60.179 60.0 10.99 0.0 0.00 4.70 R
2729 4535 0.179000 ACAGTGAGATTCCCGATGCC 59.821 55.0 0.00 0.0 0.00 4.40 R
3843 6096 0.895530 CCAGCGTAGGTCTCAAGGAA 59.104 55.0 0.00 0.0 33.74 3.36 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
37 38 2.423185 TGATTGGGCATTTACAAGAGCG 59.577 45.455 0.00 0.00 0.00 5.03
198 199 3.447950 AGTTATTTCGGAGTACCAGGGT 58.552 45.455 0.00 0.00 35.59 4.34
199 200 4.613437 AGTTATTTCGGAGTACCAGGGTA 58.387 43.478 0.00 0.00 35.59 3.69
203 204 3.287867 TTCGGAGTACCAGGGTAGTAG 57.712 52.381 5.82 4.34 34.71 2.57
215 217 5.222068 ACCAGGGTAGTAGAAAAGGAAAAGG 60.222 44.000 0.00 0.00 0.00 3.11
248 250 2.546778 GGCGGACGTTTGATGAATAGA 58.453 47.619 0.00 0.00 0.00 1.98
272 274 1.063764 GGATGACCGACTCTCGTACAC 59.936 57.143 0.00 0.00 38.40 2.90
274 276 1.436600 TGACCGACTCTCGTACACTC 58.563 55.000 0.00 0.00 38.40 3.51
336 338 2.838202 TCGGAGATGCCTTTAAGACCTT 59.162 45.455 0.00 0.00 0.00 3.50
357 359 5.048782 CCTTCGATTTTGACACATTGGAGAA 60.049 40.000 0.00 0.00 0.00 2.87
442 1369 3.442977 AGCAAAGAGAGGTTGATTGATGC 59.557 43.478 0.00 0.00 0.00 3.91
444 1371 3.616956 AAGAGAGGTTGATTGATGCGA 57.383 42.857 0.00 0.00 0.00 5.10
448 1375 3.726607 AGAGGTTGATTGATGCGAGATC 58.273 45.455 0.00 0.00 0.00 2.75
494 1422 2.806198 CGCGTGGCCTGCAAATTG 60.806 61.111 18.58 0.00 0.00 2.32
500 1428 0.978151 TGGCCTGCAAATTGAGCATT 59.022 45.000 3.32 0.00 41.82 3.56
530 1458 1.740025 GTCATAGCTTTCTGGCACCAC 59.260 52.381 0.00 0.00 34.17 4.16
668 1598 1.291184 TGCAACGAATCTGCACCTCG 61.291 55.000 5.94 5.94 44.67 4.63
669 1599 1.421485 CAACGAATCTGCACCTCGC 59.579 57.895 7.13 0.00 42.89 5.03
674 1604 0.179062 GAATCTGCACCTCGCTCCAT 60.179 55.000 0.00 0.00 43.06 3.41
733 1664 0.595310 GCCTAGCTAGCTTCCGAACG 60.595 60.000 24.88 3.95 0.00 3.95
736 1667 2.357009 CCTAGCTAGCTTCCGAACGTTA 59.643 50.000 24.88 0.00 0.00 3.18
737 1668 2.274920 AGCTAGCTTCCGAACGTTAC 57.725 50.000 12.68 0.00 0.00 2.50
739 1670 1.918609 GCTAGCTTCCGAACGTTACAG 59.081 52.381 7.70 0.00 0.00 2.74
740 1671 2.415090 GCTAGCTTCCGAACGTTACAGA 60.415 50.000 7.70 0.00 0.00 3.41
741 1672 2.806608 AGCTTCCGAACGTTACAGAA 57.193 45.000 0.00 3.87 0.00 3.02
742 1673 2.401351 AGCTTCCGAACGTTACAGAAC 58.599 47.619 0.00 0.83 0.00 3.01
745 1676 3.001533 GCTTCCGAACGTTACAGAACAAA 59.998 43.478 0.00 0.00 35.06 2.83
747 1678 3.519579 TCCGAACGTTACAGAACAAACA 58.480 40.909 0.00 0.00 35.06 2.83
748 1679 4.121317 TCCGAACGTTACAGAACAAACAT 58.879 39.130 0.00 0.00 35.06 2.71
749 1680 4.571580 TCCGAACGTTACAGAACAAACATT 59.428 37.500 0.00 0.00 35.06 2.71
750 1681 4.668837 CCGAACGTTACAGAACAAACATTG 59.331 41.667 0.00 0.00 35.06 2.82
752 1683 5.502706 CGAACGTTACAGAACAAACATTGGA 60.503 40.000 0.00 0.00 35.06 3.53
754 1685 5.997385 ACGTTACAGAACAAACATTGGATC 58.003 37.500 0.00 0.00 35.06 3.36
755 1686 5.763204 ACGTTACAGAACAAACATTGGATCT 59.237 36.000 0.00 0.00 35.06 2.75
756 1687 6.932400 ACGTTACAGAACAAACATTGGATCTA 59.068 34.615 0.00 0.00 35.06 1.98
757 1688 7.095355 ACGTTACAGAACAAACATTGGATCTAC 60.095 37.037 0.00 0.00 35.06 2.59
758 1689 7.117812 CGTTACAGAACAAACATTGGATCTACT 59.882 37.037 0.00 0.00 35.06 2.57
759 1690 8.443937 GTTACAGAACAAACATTGGATCTACTC 58.556 37.037 0.00 0.00 35.48 2.59
760 1691 6.533730 ACAGAACAAACATTGGATCTACTCA 58.466 36.000 0.00 0.00 32.14 3.41
761 1692 6.428159 ACAGAACAAACATTGGATCTACTCAC 59.572 38.462 0.00 0.00 32.14 3.51
762 1693 6.427853 CAGAACAAACATTGGATCTACTCACA 59.572 38.462 0.00 0.00 32.14 3.58
763 1694 6.652481 AGAACAAACATTGGATCTACTCACAG 59.348 38.462 0.00 0.00 31.77 3.66
764 1695 4.697352 ACAAACATTGGATCTACTCACAGC 59.303 41.667 0.00 0.00 34.12 4.40
765 1696 4.833478 AACATTGGATCTACTCACAGCT 57.167 40.909 0.00 0.00 0.00 4.24
766 1697 5.939764 AACATTGGATCTACTCACAGCTA 57.060 39.130 0.00 0.00 0.00 3.32
767 1698 5.528043 ACATTGGATCTACTCACAGCTAG 57.472 43.478 0.00 0.00 0.00 3.42
813 1744 1.154093 GTACGTAGCAGCAGCGACA 60.154 57.895 14.24 0.00 45.32 4.35
816 1747 1.807165 CGTAGCAGCAGCGACACAT 60.807 57.895 14.24 0.00 45.32 3.21
824 2060 1.492873 CAGCGACACATTGACACGG 59.507 57.895 0.00 0.00 0.00 4.94
826 2062 2.860293 CGACACATTGACACGGGC 59.140 61.111 0.00 0.00 0.00 6.13
895 2382 0.317854 GGCTGCGAAACCTGTTGAAC 60.318 55.000 0.00 0.00 0.00 3.18
896 2383 0.380378 GCTGCGAAACCTGTTGAACA 59.620 50.000 0.00 0.00 0.00 3.18
911 2398 2.587322 GAACATGACCCATCCCGCGA 62.587 60.000 8.23 0.00 0.00 5.87
933 2420 3.202706 GAGGCGCAAACCCCGATC 61.203 66.667 10.83 0.00 0.00 3.69
936 2423 2.125106 GCGCAAACCCCGATCTCT 60.125 61.111 0.30 0.00 0.00 3.10
1220 2752 1.770294 CCTCCTCCAGGTCAGTAGTC 58.230 60.000 0.00 0.00 37.53 2.59
1223 2755 1.668101 CCTCCAGGTCAGTAGTCCGC 61.668 65.000 0.00 0.00 0.00 5.54
1531 3100 2.202703 GCGACGCCGACAAGGTAT 60.203 61.111 9.14 0.00 43.70 2.73
1535 3104 1.268896 CGACGCCGACAAGGTATGTAT 60.269 52.381 0.00 0.00 44.12 2.29
1548 3122 6.984474 ACAAGGTATGTATGTAAACAGGATCG 59.016 38.462 0.00 0.00 41.63 3.69
1553 3138 4.295870 TGTATGTAAACAGGATCGATCGC 58.704 43.478 18.81 11.84 0.00 4.58
1591 3179 3.902063 CGCCGCGTGACAGAATCG 61.902 66.667 4.92 0.00 0.00 3.34
1656 3335 2.917227 GTGTGGGTTTGGCAGGGG 60.917 66.667 0.00 0.00 0.00 4.79
1671 3350 1.130054 AGGGGCTGCTGAGAGTTGAA 61.130 55.000 0.00 0.00 0.00 2.69
1706 3385 4.796231 CCTCGCCTCAACGGTCGG 62.796 72.222 0.00 0.00 34.48 4.79
1740 3493 0.780596 GGTTCGGTTCGTCTTCGTTC 59.219 55.000 0.00 0.00 38.33 3.95
1741 3494 0.428618 GTTCGGTTCGTCTTCGTTCG 59.571 55.000 0.00 0.00 38.33 3.95
1765 3519 1.400494 GTGGAGAAAACTGCAACGTGT 59.600 47.619 0.00 0.00 0.00 4.49
1787 3541 2.686405 CCTGTGGCTGTACGTACTGATA 59.314 50.000 29.87 17.35 0.00 2.15
1793 3547 5.061808 GTGGCTGTACGTACTGATAGTTTTG 59.938 44.000 29.87 8.78 0.00 2.44
1796 3550 4.497300 TGTACGTACTGATAGTTTTGCCC 58.503 43.478 25.12 0.00 0.00 5.36
1797 3551 2.981898 ACGTACTGATAGTTTTGCCCC 58.018 47.619 0.00 0.00 0.00 5.80
1808 3562 3.835790 TTTGCCCCGTTCCTCCACG 62.836 63.158 0.00 0.00 40.02 4.94
2172 3958 3.938637 GAAAGGGGACAAGGCCGGG 62.939 68.421 2.18 0.00 0.00 5.73
2294 4095 2.438021 ACCTCAGCTCACCAACTTGTAA 59.562 45.455 0.00 0.00 0.00 2.41
2295 4096 2.808543 CCTCAGCTCACCAACTTGTAAC 59.191 50.000 0.00 0.00 0.00 2.50
2317 4118 3.542648 GGAGGCCAGTTTAACCATCTAC 58.457 50.000 5.01 0.00 0.00 2.59
2318 4119 3.200165 GGAGGCCAGTTTAACCATCTACT 59.800 47.826 5.01 0.00 0.00 2.57
2319 4120 4.407945 GGAGGCCAGTTTAACCATCTACTA 59.592 45.833 5.01 0.00 0.00 1.82
2334 4139 5.689514 CCATCTACTATCTGACGAAAAGCAG 59.310 44.000 0.00 0.00 0.00 4.24
2362 4167 5.245531 TCGTAATTCTTGGTTGCTCAATCT 58.754 37.500 0.00 0.00 0.00 2.40
2363 4168 5.122239 TCGTAATTCTTGGTTGCTCAATCTG 59.878 40.000 0.00 0.00 0.00 2.90
2367 4172 7.707624 AATTCTTGGTTGCTCAATCTGAATA 57.292 32.000 11.69 0.00 31.05 1.75
2427 4232 0.883833 GGACGTTCACGAAGAGGGTA 59.116 55.000 6.30 0.00 43.02 3.69
2689 4494 4.024670 GGCTTCTTCCTAGTTCCTAGACA 58.975 47.826 0.00 0.00 36.26 3.41
2692 4497 5.186215 GCTTCTTCCTAGTTCCTAGACAGTT 59.814 44.000 0.00 0.00 36.26 3.16
2695 4501 5.887035 TCTTCCTAGTTCCTAGACAGTTAGC 59.113 44.000 0.00 0.00 36.26 3.09
2718 4524 0.036952 ATCATCCATCGCCATCGGAC 60.037 55.000 0.00 0.00 36.13 4.79
2721 4527 0.891373 ATCCATCGCCATCGGACTAG 59.109 55.000 0.00 0.00 36.13 2.57
2725 4531 2.231478 CCATCGCCATCGGACTAGTAAT 59.769 50.000 0.00 0.00 36.13 1.89
2727 4533 4.082408 CCATCGCCATCGGACTAGTAATAA 60.082 45.833 0.00 0.00 36.13 1.40
2728 4534 5.466819 CATCGCCATCGGACTAGTAATAAA 58.533 41.667 0.00 0.00 36.13 1.40
2729 4535 5.117355 TCGCCATCGGACTAGTAATAAAG 57.883 43.478 0.00 0.00 36.13 1.85
2731 4537 3.995048 GCCATCGGACTAGTAATAAAGGC 59.005 47.826 0.00 2.05 0.00 4.35
2732 4538 4.502604 GCCATCGGACTAGTAATAAAGGCA 60.503 45.833 15.69 0.00 37.23 4.75
2733 4539 5.794894 CCATCGGACTAGTAATAAAGGCAT 58.205 41.667 0.00 0.00 0.00 4.40
2734 4540 5.869888 CCATCGGACTAGTAATAAAGGCATC 59.130 44.000 0.00 0.00 0.00 3.91
2736 4542 4.022589 TCGGACTAGTAATAAAGGCATCGG 60.023 45.833 0.00 0.00 0.00 4.18
2737 4543 4.566987 GGACTAGTAATAAAGGCATCGGG 58.433 47.826 0.00 0.00 0.00 5.14
2749 4559 1.293924 GCATCGGGAATCTCACTGTG 58.706 55.000 0.17 0.17 0.00 3.66
2751 4561 0.833287 ATCGGGAATCTCACTGTGGG 59.167 55.000 8.11 4.27 0.00 4.61
2806 4893 3.607310 CGCCGTAAGCAGTCAGATAGTAG 60.607 52.174 0.00 0.00 44.04 2.57
2807 4894 3.315749 GCCGTAAGCAGTCAGATAGTAGT 59.684 47.826 0.00 0.00 42.97 2.73
2808 4895 4.514441 GCCGTAAGCAGTCAGATAGTAGTA 59.486 45.833 0.00 0.00 42.97 1.82
2809 4896 5.181622 GCCGTAAGCAGTCAGATAGTAGTAT 59.818 44.000 0.00 0.00 42.97 2.12
2810 4897 6.621164 GCCGTAAGCAGTCAGATAGTAGTATC 60.621 46.154 9.25 9.25 42.97 2.24
2811 4898 6.427242 CCGTAAGCAGTCAGATAGTAGTATCA 59.573 42.308 17.87 0.00 38.04 2.15
2812 4899 7.360522 CCGTAAGCAGTCAGATAGTAGTATCAG 60.361 44.444 17.87 11.12 38.04 2.90
2813 4900 7.171848 CGTAAGCAGTCAGATAGTAGTATCAGT 59.828 40.741 17.87 0.89 38.04 3.41
2814 4901 7.504924 AAGCAGTCAGATAGTAGTATCAGTC 57.495 40.000 17.87 9.08 38.04 3.51
2815 4902 6.596621 AGCAGTCAGATAGTAGTATCAGTCA 58.403 40.000 17.87 0.00 38.04 3.41
2816 4903 7.230747 AGCAGTCAGATAGTAGTATCAGTCAT 58.769 38.462 17.87 0.00 38.04 3.06
2817 4904 7.174772 AGCAGTCAGATAGTAGTATCAGTCATG 59.825 40.741 17.87 8.40 38.04 3.07
2818 4905 7.574779 GCAGTCAGATAGTAGTATCAGTCATGG 60.575 44.444 17.87 4.53 38.04 3.66
2819 4906 7.446931 CAGTCAGATAGTAGTATCAGTCATGGT 59.553 40.741 17.87 0.00 38.04 3.55
2820 4907 8.001875 AGTCAGATAGTAGTATCAGTCATGGTT 58.998 37.037 17.87 0.00 38.04 3.67
2821 4908 8.634444 GTCAGATAGTAGTATCAGTCATGGTTT 58.366 37.037 17.87 0.00 38.04 3.27
2822 4909 8.851145 TCAGATAGTAGTATCAGTCATGGTTTC 58.149 37.037 17.87 0.00 38.04 2.78
2823 4910 8.633561 CAGATAGTAGTATCAGTCATGGTTTCA 58.366 37.037 17.87 0.00 38.04 2.69
2824 4911 8.855110 AGATAGTAGTATCAGTCATGGTTTCAG 58.145 37.037 17.87 0.00 38.04 3.02
2825 4912 8.768501 ATAGTAGTATCAGTCATGGTTTCAGA 57.231 34.615 0.00 0.00 0.00 3.27
2826 4913 7.482169 AGTAGTATCAGTCATGGTTTCAGAA 57.518 36.000 0.00 0.00 0.00 3.02
2827 4914 8.083828 AGTAGTATCAGTCATGGTTTCAGAAT 57.916 34.615 0.00 0.00 0.00 2.40
2828 4915 8.543774 AGTAGTATCAGTCATGGTTTCAGAATT 58.456 33.333 0.00 0.00 0.00 2.17
2829 4916 7.856145 AGTATCAGTCATGGTTTCAGAATTC 57.144 36.000 0.00 0.00 0.00 2.17
2830 4917 7.397221 AGTATCAGTCATGGTTTCAGAATTCA 58.603 34.615 8.44 0.00 0.00 2.57
2831 4918 6.754702 ATCAGTCATGGTTTCAGAATTCAG 57.245 37.500 8.44 0.00 0.00 3.02
2832 4919 4.456911 TCAGTCATGGTTTCAGAATTCAGC 59.543 41.667 8.44 0.00 0.00 4.26
2833 4920 4.216902 CAGTCATGGTTTCAGAATTCAGCA 59.783 41.667 8.44 3.02 0.00 4.41
2834 4921 5.014858 AGTCATGGTTTCAGAATTCAGCAT 58.985 37.500 8.44 5.36 0.00 3.79
2835 4922 5.479375 AGTCATGGTTTCAGAATTCAGCATT 59.521 36.000 8.44 0.00 0.00 3.56
2836 4923 5.575606 GTCATGGTTTCAGAATTCAGCATTG 59.424 40.000 8.44 0.00 0.00 2.82
2837 4924 5.244402 TCATGGTTTCAGAATTCAGCATTGT 59.756 36.000 8.44 0.00 0.00 2.71
2838 4925 4.873817 TGGTTTCAGAATTCAGCATTGTG 58.126 39.130 8.44 0.00 37.47 3.33
2839 4926 4.341806 TGGTTTCAGAATTCAGCATTGTGT 59.658 37.500 8.44 0.00 37.41 3.72
2840 4927 4.919754 GGTTTCAGAATTCAGCATTGTGTC 59.080 41.667 8.44 0.00 37.41 3.67
2841 4928 5.507817 GGTTTCAGAATTCAGCATTGTGTCA 60.508 40.000 8.44 0.00 37.41 3.58
2842 4929 5.970317 TTCAGAATTCAGCATTGTGTCAT 57.030 34.783 8.44 0.00 37.41 3.06
2843 4930 5.556355 TCAGAATTCAGCATTGTGTCATC 57.444 39.130 8.44 0.00 37.41 2.92
2844 4931 5.005094 TCAGAATTCAGCATTGTGTCATCA 58.995 37.500 8.44 0.00 37.41 3.07
2845 4932 5.123344 TCAGAATTCAGCATTGTGTCATCAG 59.877 40.000 8.44 0.00 37.41 2.90
2846 4933 5.123344 CAGAATTCAGCATTGTGTCATCAGA 59.877 40.000 8.44 0.00 32.51 3.27
2847 4934 5.708697 AGAATTCAGCATTGTGTCATCAGAA 59.291 36.000 8.44 0.00 0.00 3.02
2848 4935 6.377429 AGAATTCAGCATTGTGTCATCAGAAT 59.623 34.615 8.44 0.00 37.92 2.40
2849 4936 7.555195 AGAATTCAGCATTGTGTCATCAGAATA 59.445 33.333 8.44 0.00 35.77 1.75
2850 4937 7.634671 ATTCAGCATTGTGTCATCAGAATAA 57.365 32.000 0.00 0.00 35.77 1.40
2851 4938 6.673154 TCAGCATTGTGTCATCAGAATAAG 57.327 37.500 0.00 0.00 35.77 1.73
2852 4939 5.065602 TCAGCATTGTGTCATCAGAATAAGC 59.934 40.000 0.00 0.00 35.77 3.09
2853 4940 4.945543 AGCATTGTGTCATCAGAATAAGCA 59.054 37.500 0.00 0.00 35.77 3.91
2854 4941 5.066117 AGCATTGTGTCATCAGAATAAGCAG 59.934 40.000 0.00 0.00 35.77 4.24
2855 4942 5.163683 GCATTGTGTCATCAGAATAAGCAGT 60.164 40.000 0.00 0.00 35.77 4.40
2856 4943 6.484540 CATTGTGTCATCAGAATAAGCAGTC 58.515 40.000 0.00 0.00 35.77 3.51
2857 4944 5.151297 TGTGTCATCAGAATAAGCAGTCA 57.849 39.130 0.00 0.00 0.00 3.41
2858 4945 5.173664 TGTGTCATCAGAATAAGCAGTCAG 58.826 41.667 0.00 0.00 0.00 3.51
2859 4946 4.569966 GTGTCATCAGAATAAGCAGTCAGG 59.430 45.833 0.00 0.00 0.00 3.86
2860 4947 4.223700 TGTCATCAGAATAAGCAGTCAGGT 59.776 41.667 0.00 0.00 0.00 4.00
2861 4948 5.422012 TGTCATCAGAATAAGCAGTCAGGTA 59.578 40.000 0.00 0.00 0.00 3.08
2862 4949 5.982516 GTCATCAGAATAAGCAGTCAGGTAG 59.017 44.000 0.00 0.00 0.00 3.18
2874 4961 5.358442 AGCAGTCAGGTAGTACTATCAGTTG 59.642 44.000 15.51 10.88 0.00 3.16
2902 4989 8.188139 GGTTTCAGAGTTCAGTGATTTGTAAAA 58.812 33.333 0.00 0.00 0.00 1.52
2903 4990 9.226345 GTTTCAGAGTTCAGTGATTTGTAAAAG 57.774 33.333 0.00 0.00 0.00 2.27
2904 4991 7.496529 TCAGAGTTCAGTGATTTGTAAAAGG 57.503 36.000 0.00 0.00 0.00 3.11
2963 5051 1.702182 TGTGGCTGCCTGATTGAAAA 58.298 45.000 21.03 0.00 0.00 2.29
2964 5052 2.250031 TGTGGCTGCCTGATTGAAAAT 58.750 42.857 21.03 0.00 0.00 1.82
2965 5053 2.633967 TGTGGCTGCCTGATTGAAAATT 59.366 40.909 21.03 0.00 0.00 1.82
2966 5054 3.071312 TGTGGCTGCCTGATTGAAAATTT 59.929 39.130 21.03 0.00 0.00 1.82
2967 5055 3.434299 GTGGCTGCCTGATTGAAAATTTG 59.566 43.478 21.03 0.00 0.00 2.32
2968 5056 3.324268 TGGCTGCCTGATTGAAAATTTGA 59.676 39.130 21.03 0.00 0.00 2.69
2969 5057 4.202336 TGGCTGCCTGATTGAAAATTTGAA 60.202 37.500 21.03 0.00 0.00 2.69
2970 5058 4.756135 GGCTGCCTGATTGAAAATTTGAAA 59.244 37.500 12.43 0.00 0.00 2.69
2976 5064 8.098286 TGCCTGATTGAAAATTTGAAATGAGAT 58.902 29.630 11.64 0.00 0.00 2.75
3025 5113 5.824624 GGAGAAATTGCAGTCCTATCAATCA 59.175 40.000 0.00 0.00 30.84 2.57
3026 5114 6.319658 GGAGAAATTGCAGTCCTATCAATCAA 59.680 38.462 0.00 0.00 30.84 2.57
3051 5140 4.887071 TGACAAATCACATATTACTGGCCC 59.113 41.667 0.00 0.00 0.00 5.80
3057 5146 1.971357 ACATATTACTGGCCCTCTCCG 59.029 52.381 0.00 0.00 0.00 4.63
3080 5169 0.610232 AGGATGTTCTGCCCTGCAAC 60.610 55.000 0.00 0.00 38.41 4.17
3085 5174 3.842925 TTCTGCCCTGCAACCGGAC 62.843 63.158 9.46 0.00 38.41 4.79
3103 5192 1.666189 GACTTTTGTAGATGCGCCTCC 59.334 52.381 4.18 0.00 0.00 4.30
3117 5206 1.230324 GCCTCCACACAGTTCTGAAC 58.770 55.000 12.54 12.54 0.00 3.18
3119 5208 0.861837 CTCCACACAGTTCTGAACGC 59.138 55.000 14.35 0.00 36.23 4.84
3120 5209 0.464036 TCCACACAGTTCTGAACGCT 59.536 50.000 14.35 1.42 36.23 5.07
3172 5261 7.167924 TGGAGCATAAATTTCACTTGCATTA 57.832 32.000 14.09 0.00 35.79 1.90
3178 5267 7.970061 GCATAAATTTCACTTGCATTACTCAGA 59.030 33.333 0.00 0.00 33.58 3.27
3179 5268 9.499585 CATAAATTTCACTTGCATTACTCAGAG 57.500 33.333 0.00 0.00 0.00 3.35
3201 5290 4.095483 AGAAAGGAGATGCGCAAAATACAG 59.905 41.667 17.11 0.00 0.00 2.74
3220 5309 4.082845 ACAGCAGCATATCCGTAGATACT 58.917 43.478 0.00 0.00 37.80 2.12
3221 5310 4.082517 ACAGCAGCATATCCGTAGATACTG 60.083 45.833 0.00 0.00 37.80 2.74
3284 5373 5.241506 CGATGTCATGGCCTTGGTTATTATT 59.758 40.000 17.95 0.00 0.00 1.40
3355 5445 4.218312 AGGAAGATAAATCACAATGGGCC 58.782 43.478 0.00 0.00 0.00 5.80
3385 5480 4.797275 GCCACTGATTCAGGAAAACTTTGG 60.797 45.833 17.66 13.36 35.51 3.28
3492 5589 2.556144 TGAGTTCAAGATGCTGCTGT 57.444 45.000 0.00 0.00 0.00 4.40
3519 5745 6.753279 CAGACAAATATTGACCGCATGATTTT 59.247 34.615 0.00 0.00 0.00 1.82
3522 5748 7.322664 ACAAATATTGACCGCATGATTTTCTT 58.677 30.769 0.00 0.00 0.00 2.52
3527 5753 3.191162 TGACCGCATGATTTTCTTGGAAG 59.809 43.478 0.00 0.00 0.00 3.46
3599 5841 8.979574 GGCAGTACTGTTAATAATATGTCAGAC 58.020 37.037 23.44 0.00 0.00 3.51
3654 5896 5.474876 AGGCTTTGTGAAAAGACATTAGGAG 59.525 40.000 6.81 0.00 40.26 3.69
3674 5923 3.680525 CGATCAACTCGCAGACCG 58.319 61.111 0.00 0.00 41.14 4.79
3686 5935 2.933906 TCGCAGACCGTCATTTTTATCC 59.066 45.455 0.40 0.00 38.35 2.59
3691 5940 3.682858 AGACCGTCATTTTTATCCGTGTG 59.317 43.478 0.40 0.00 0.00 3.82
3843 6096 4.379339 GAGAAACTCGATAGCTTCCTGT 57.621 45.455 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
198 199 4.659115 GCCCACCTTTTCCTTTTCTACTA 58.341 43.478 0.00 0.00 0.00 1.82
199 200 3.497332 GCCCACCTTTTCCTTTTCTACT 58.503 45.455 0.00 0.00 0.00 2.57
203 204 0.317160 CCGCCCACCTTTTCCTTTTC 59.683 55.000 0.00 0.00 0.00 2.29
248 250 0.811915 CGAGAGTCGGTCATCCAACT 59.188 55.000 0.00 0.00 36.00 3.16
272 274 2.159819 CTATCCGGCCGTGGATGGAG 62.160 65.000 26.12 11.56 46.76 3.86
313 315 2.552031 GTCTTAAAGGCATCTCCGACC 58.448 52.381 0.00 0.00 40.77 4.79
336 338 4.819088 TGTTCTCCAATGTGTCAAAATCGA 59.181 37.500 0.00 0.00 0.00 3.59
357 359 8.049721 AGAAAGGAAAATCGAGAAATATCCTGT 58.950 33.333 5.95 1.66 36.03 4.00
442 1369 5.122396 CCTTTTGGGTGTAGAAAAGATCTCG 59.878 44.000 0.00 0.00 40.25 4.04
444 1371 6.004574 GTCCTTTTGGGTGTAGAAAAGATCT 58.995 40.000 0.00 0.00 40.25 2.75
448 1375 5.130350 TCTGTCCTTTTGGGTGTAGAAAAG 58.870 41.667 0.00 0.00 40.87 2.27
494 1422 4.730521 GCTATGACTTTTACGCAAATGCTC 59.269 41.667 3.63 0.00 39.32 4.26
500 1428 5.106712 CCAGAAAGCTATGACTTTTACGCAA 60.107 40.000 0.00 0.00 39.93 4.85
530 1458 4.659088 ACATCGACGTGTATGTACTTCTG 58.341 43.478 9.94 0.00 34.61 3.02
668 1598 2.494870 AGCAACAAAATGGAGATGGAGC 59.505 45.455 0.00 0.00 0.00 4.70
669 1599 4.096984 GGTAGCAACAAAATGGAGATGGAG 59.903 45.833 0.00 0.00 0.00 3.86
674 1604 4.202461 ACTGAGGTAGCAACAAAATGGAGA 60.202 41.667 0.00 0.00 0.00 3.71
733 1664 8.324163 AGTAGATCCAATGTTTGTTCTGTAAC 57.676 34.615 0.00 0.00 36.07 2.50
736 1667 6.428159 GTGAGTAGATCCAATGTTTGTTCTGT 59.572 38.462 0.00 0.00 0.00 3.41
737 1668 6.427853 TGTGAGTAGATCCAATGTTTGTTCTG 59.572 38.462 0.00 0.00 0.00 3.02
739 1670 6.621596 GCTGTGAGTAGATCCAATGTTTGTTC 60.622 42.308 0.00 0.00 0.00 3.18
740 1671 5.182001 GCTGTGAGTAGATCCAATGTTTGTT 59.818 40.000 0.00 0.00 0.00 2.83
741 1672 4.697352 GCTGTGAGTAGATCCAATGTTTGT 59.303 41.667 0.00 0.00 0.00 2.83
742 1673 4.940046 AGCTGTGAGTAGATCCAATGTTTG 59.060 41.667 0.00 0.00 0.00 2.93
745 1676 4.202202 GCTAGCTGTGAGTAGATCCAATGT 60.202 45.833 7.70 0.00 0.00 2.71
747 1678 3.323403 GGCTAGCTGTGAGTAGATCCAAT 59.677 47.826 15.72 0.00 0.00 3.16
748 1679 2.695666 GGCTAGCTGTGAGTAGATCCAA 59.304 50.000 15.72 0.00 0.00 3.53
749 1680 2.311463 GGCTAGCTGTGAGTAGATCCA 58.689 52.381 15.72 0.00 0.00 3.41
750 1681 2.295909 CTGGCTAGCTGTGAGTAGATCC 59.704 54.545 15.72 0.00 0.00 3.36
752 1683 2.315176 CCTGGCTAGCTGTGAGTAGAT 58.685 52.381 15.72 0.00 0.00 1.98
754 1685 0.103937 GCCTGGCTAGCTGTGAGTAG 59.896 60.000 15.72 2.36 0.00 2.57
755 1686 0.614697 TGCCTGGCTAGCTGTGAGTA 60.615 55.000 21.03 0.00 0.00 2.59
756 1687 1.897225 CTGCCTGGCTAGCTGTGAGT 61.897 60.000 21.03 0.00 0.00 3.41
757 1688 1.153409 CTGCCTGGCTAGCTGTGAG 60.153 63.158 21.03 1.84 0.00 3.51
758 1689 2.984623 CTGCCTGGCTAGCTGTGA 59.015 61.111 21.03 0.00 0.00 3.58
759 1690 2.823147 GCTGCCTGGCTAGCTGTG 60.823 66.667 25.72 4.14 36.99 3.66
760 1691 2.898933 TTGCTGCCTGGCTAGCTGT 61.899 57.895 29.71 0.00 40.52 4.40
761 1692 2.045634 TTGCTGCCTGGCTAGCTG 60.046 61.111 29.71 7.95 40.52 4.24
762 1693 2.045536 GTTGCTGCCTGGCTAGCT 60.046 61.111 29.71 0.00 40.52 3.32
763 1694 3.503363 CGTTGCTGCCTGGCTAGC 61.503 66.667 26.04 26.04 40.29 3.42
764 1695 3.503363 GCGTTGCTGCCTGGCTAG 61.503 66.667 21.03 15.83 0.00 3.42
784 1715 3.003482 GCTGCTACGTACAGTACTAGCAT 59.997 47.826 27.42 8.47 40.78 3.79
790 1721 1.546834 GCTGCTGCTACGTACAGTAC 58.453 55.000 19.43 0.00 37.47 2.73
824 2060 4.195334 ATGGATGGTCAGCCGGCC 62.195 66.667 26.15 8.39 40.42 6.13
826 2062 2.903855 GCATGGATGGTCAGCCGG 60.904 66.667 0.00 0.00 40.42 6.13
875 2362 0.749818 TTCAACAGGTTTCGCAGCCA 60.750 50.000 0.00 0.00 0.00 4.75
877 2364 0.380378 TGTTCAACAGGTTTCGCAGC 59.620 50.000 0.00 0.00 0.00 5.25
895 2382 2.588877 GTCGCGGGATGGGTCATG 60.589 66.667 6.13 0.00 0.00 3.07
896 2383 4.221422 CGTCGCGGGATGGGTCAT 62.221 66.667 13.60 0.00 0.00 3.06
920 2407 1.784525 GATAGAGATCGGGGTTTGCG 58.215 55.000 0.00 0.00 0.00 4.85
933 2420 5.004448 TGTACTTATCCTGAGCCGATAGAG 58.996 45.833 0.00 0.00 39.76 2.43
936 2423 4.726583 ACTGTACTTATCCTGAGCCGATA 58.273 43.478 0.00 0.00 0.00 2.92
1013 2536 1.664321 GGCGATCGAGTGGTACTGGT 61.664 60.000 21.57 0.00 0.00 4.00
1241 2773 2.282820 GCAAGATTACTCTAGCACACGC 59.717 50.000 0.00 0.00 38.99 5.34
1531 3100 4.295870 GCGATCGATCCTGTTTACATACA 58.704 43.478 21.57 0.00 0.00 2.29
1535 3104 1.202486 GGGCGATCGATCCTGTTTACA 60.202 52.381 21.57 0.00 0.00 2.41
1591 3179 6.202937 TGAAATGATTGTTCGTGGTACAAAC 58.797 36.000 0.00 0.00 44.16 2.93
1656 3335 1.675415 CCCTCTTCAACTCTCAGCAGC 60.675 57.143 0.00 0.00 0.00 5.25
1706 3385 0.179097 GAACCTGATCGTGGAGCCTC 60.179 60.000 10.99 0.00 0.00 4.70
1740 3493 1.428448 TGCAGTTTTCTCCACGATCG 58.572 50.000 14.88 14.88 0.00 3.69
1741 3494 2.411547 CGTTGCAGTTTTCTCCACGATC 60.412 50.000 0.00 0.00 0.00 3.69
1765 3519 0.885879 CAGTACGTACAGCCACAGGA 59.114 55.000 26.55 0.00 0.00 3.86
1787 3541 1.228459 GGAGGAACGGGGCAAAACT 60.228 57.895 0.00 0.00 0.00 2.66
1797 3551 4.351938 TGACCGCGTGGAGGAACG 62.352 66.667 24.59 0.00 46.30 3.95
1978 3732 2.048127 GCGAAGGCGAGGTTGTCT 60.048 61.111 0.00 0.00 40.82 3.41
2079 3833 0.814457 AGCAAGACTGAGTAGAGCGG 59.186 55.000 0.00 0.00 0.00 5.52
2172 3958 4.719369 ACGAACGTCTCCGCCTGC 62.719 66.667 0.00 0.00 37.70 4.85
2294 4095 0.696501 ATGGTTAAACTGGCCTCCGT 59.303 50.000 3.32 0.00 0.00 4.69
2295 4096 1.065418 AGATGGTTAAACTGGCCTCCG 60.065 52.381 3.32 0.00 0.00 4.63
2317 4118 2.263077 ACGCTGCTTTTCGTCAGATAG 58.737 47.619 0.00 0.00 33.09 2.08
2318 4119 2.363788 ACGCTGCTTTTCGTCAGATA 57.636 45.000 0.00 0.00 33.09 1.98
2319 4120 3.217242 ACGCTGCTTTTCGTCAGAT 57.783 47.368 0.00 0.00 33.09 2.90
2334 4139 2.474032 GCAACCAAGAATTACGAGACGC 60.474 50.000 0.00 0.00 0.00 5.19
2362 4167 2.486918 CGACCTCTGCATGCATATTCA 58.513 47.619 22.97 2.09 0.00 2.57
2363 4168 1.196354 GCGACCTCTGCATGCATATTC 59.804 52.381 22.97 13.86 0.00 1.75
2367 4172 2.515523 GGCGACCTCTGCATGCAT 60.516 61.111 22.97 5.92 0.00 3.96
2689 4494 3.397482 GCGATGGATGATGAAGCTAACT 58.603 45.455 0.00 0.00 0.00 2.24
2692 4497 1.693606 TGGCGATGGATGATGAAGCTA 59.306 47.619 0.00 0.00 0.00 3.32
2695 4501 1.730612 CGATGGCGATGGATGATGAAG 59.269 52.381 0.00 0.00 40.82 3.02
2718 4524 6.702329 AGATTCCCGATGCCTTTATTACTAG 58.298 40.000 0.00 0.00 0.00 2.57
2721 4527 5.179555 GTGAGATTCCCGATGCCTTTATTAC 59.820 44.000 0.00 0.00 0.00 1.89
2725 4531 2.771943 AGTGAGATTCCCGATGCCTTTA 59.228 45.455 0.00 0.00 0.00 1.85
2727 4533 1.134280 CAGTGAGATTCCCGATGCCTT 60.134 52.381 0.00 0.00 0.00 4.35
2728 4534 0.467384 CAGTGAGATTCCCGATGCCT 59.533 55.000 0.00 0.00 0.00 4.75
2729 4535 0.179000 ACAGTGAGATTCCCGATGCC 59.821 55.000 0.00 0.00 0.00 4.40
2731 4537 1.473965 CCCACAGTGAGATTCCCGATG 60.474 57.143 0.62 0.00 0.00 3.84
2732 4538 0.833287 CCCACAGTGAGATTCCCGAT 59.167 55.000 0.62 0.00 0.00 4.18
2733 4539 0.544357 ACCCACAGTGAGATTCCCGA 60.544 55.000 0.62 0.00 0.00 5.14
2734 4540 1.983224 ACCCACAGTGAGATTCCCG 59.017 57.895 0.62 0.00 0.00 5.14
2749 4559 1.271054 ACAGTGCTGAATCTGTCACCC 60.271 52.381 6.17 0.00 40.28 4.61
2751 4561 4.058124 TGTTACAGTGCTGAATCTGTCAC 58.942 43.478 6.17 2.53 42.77 3.67
2806 4893 7.615582 TGAATTCTGAAACCATGACTGATAC 57.384 36.000 7.05 0.00 0.00 2.24
2807 4894 6.317140 GCTGAATTCTGAAACCATGACTGATA 59.683 38.462 15.79 0.00 0.00 2.15
2808 4895 5.125097 GCTGAATTCTGAAACCATGACTGAT 59.875 40.000 15.79 0.00 0.00 2.90
2809 4896 4.456911 GCTGAATTCTGAAACCATGACTGA 59.543 41.667 15.79 0.00 0.00 3.41
2810 4897 4.216902 TGCTGAATTCTGAAACCATGACTG 59.783 41.667 15.79 0.00 0.00 3.51
2811 4898 4.401022 TGCTGAATTCTGAAACCATGACT 58.599 39.130 15.79 0.00 0.00 3.41
2812 4899 4.771590 TGCTGAATTCTGAAACCATGAC 57.228 40.909 15.79 0.00 0.00 3.06
2813 4900 5.244402 ACAATGCTGAATTCTGAAACCATGA 59.756 36.000 15.79 0.00 0.00 3.07
2814 4901 5.347635 CACAATGCTGAATTCTGAAACCATG 59.652 40.000 15.79 6.81 0.00 3.66
2815 4902 5.011329 ACACAATGCTGAATTCTGAAACCAT 59.989 36.000 15.79 6.88 0.00 3.55
2816 4903 4.341806 ACACAATGCTGAATTCTGAAACCA 59.658 37.500 15.79 4.93 0.00 3.67
2817 4904 4.874970 ACACAATGCTGAATTCTGAAACC 58.125 39.130 15.79 0.00 0.00 3.27
2818 4905 5.522456 TGACACAATGCTGAATTCTGAAAC 58.478 37.500 15.79 0.00 0.00 2.78
2819 4906 5.771153 TGACACAATGCTGAATTCTGAAA 57.229 34.783 15.79 3.91 0.00 2.69
2820 4907 5.474189 TGATGACACAATGCTGAATTCTGAA 59.526 36.000 15.79 5.99 0.00 3.02
2821 4908 5.005094 TGATGACACAATGCTGAATTCTGA 58.995 37.500 15.79 2.39 0.00 3.27
2822 4909 5.123344 TCTGATGACACAATGCTGAATTCTG 59.877 40.000 7.05 7.51 0.00 3.02
2823 4910 5.250982 TCTGATGACACAATGCTGAATTCT 58.749 37.500 7.05 0.00 0.00 2.40
2824 4911 5.556355 TCTGATGACACAATGCTGAATTC 57.444 39.130 0.00 0.00 0.00 2.17
2825 4912 5.970317 TTCTGATGACACAATGCTGAATT 57.030 34.783 0.00 0.00 0.00 2.17
2826 4913 7.634671 TTATTCTGATGACACAATGCTGAAT 57.365 32.000 0.00 0.00 33.62 2.57
2827 4914 6.403964 GCTTATTCTGATGACACAATGCTGAA 60.404 38.462 0.00 0.00 0.00 3.02
2828 4915 5.065602 GCTTATTCTGATGACACAATGCTGA 59.934 40.000 0.00 0.00 0.00 4.26
2829 4916 5.163693 TGCTTATTCTGATGACACAATGCTG 60.164 40.000 0.00 0.00 0.00 4.41
2830 4917 4.945543 TGCTTATTCTGATGACACAATGCT 59.054 37.500 0.00 0.00 0.00 3.79
2831 4918 5.163683 ACTGCTTATTCTGATGACACAATGC 60.164 40.000 0.00 0.00 0.00 3.56
2832 4919 6.093082 TGACTGCTTATTCTGATGACACAATG 59.907 38.462 0.00 0.00 0.00 2.82
2833 4920 6.175471 TGACTGCTTATTCTGATGACACAAT 58.825 36.000 0.00 0.00 0.00 2.71
2834 4921 5.550290 TGACTGCTTATTCTGATGACACAA 58.450 37.500 0.00 0.00 0.00 3.33
2835 4922 5.151297 TGACTGCTTATTCTGATGACACA 57.849 39.130 0.00 0.00 0.00 3.72
2836 4923 4.569966 CCTGACTGCTTATTCTGATGACAC 59.430 45.833 0.00 0.00 0.00 3.67
2837 4924 4.223700 ACCTGACTGCTTATTCTGATGACA 59.776 41.667 0.00 0.00 0.00 3.58
2838 4925 4.764172 ACCTGACTGCTTATTCTGATGAC 58.236 43.478 0.00 0.00 0.00 3.06
2839 4926 5.658634 ACTACCTGACTGCTTATTCTGATGA 59.341 40.000 0.00 0.00 0.00 2.92
2840 4927 5.911752 ACTACCTGACTGCTTATTCTGATG 58.088 41.667 0.00 0.00 0.00 3.07
2841 4928 6.836527 AGTACTACCTGACTGCTTATTCTGAT 59.163 38.462 0.00 0.00 0.00 2.90
2842 4929 6.188407 AGTACTACCTGACTGCTTATTCTGA 58.812 40.000 0.00 0.00 0.00 3.27
2843 4930 6.458232 AGTACTACCTGACTGCTTATTCTG 57.542 41.667 0.00 0.00 0.00 3.02
2844 4931 7.999545 TGATAGTACTACCTGACTGCTTATTCT 59.000 37.037 4.31 0.00 0.00 2.40
2845 4932 8.167605 TGATAGTACTACCTGACTGCTTATTC 57.832 38.462 4.31 0.00 0.00 1.75
2846 4933 7.780745 ACTGATAGTACTACCTGACTGCTTATT 59.219 37.037 4.31 0.00 0.00 1.40
2847 4934 7.291566 ACTGATAGTACTACCTGACTGCTTAT 58.708 38.462 4.31 0.00 0.00 1.73
2848 4935 6.660800 ACTGATAGTACTACCTGACTGCTTA 58.339 40.000 4.31 0.00 0.00 3.09
2849 4936 5.511363 ACTGATAGTACTACCTGACTGCTT 58.489 41.667 4.31 0.00 0.00 3.91
2850 4937 5.118729 ACTGATAGTACTACCTGACTGCT 57.881 43.478 4.31 0.00 0.00 4.24
2851 4938 5.125739 ACAACTGATAGTACTACCTGACTGC 59.874 44.000 4.31 0.00 0.00 4.40
2852 4939 6.404844 CCACAACTGATAGTACTACCTGACTG 60.405 46.154 4.31 5.75 0.00 3.51
2853 4940 5.652891 CCACAACTGATAGTACTACCTGACT 59.347 44.000 4.31 0.00 0.00 3.41
2854 4941 5.418209 ACCACAACTGATAGTACTACCTGAC 59.582 44.000 4.31 0.00 0.00 3.51
2855 4942 5.577100 ACCACAACTGATAGTACTACCTGA 58.423 41.667 4.31 0.00 0.00 3.86
2856 4943 5.916661 ACCACAACTGATAGTACTACCTG 57.083 43.478 4.31 1.75 0.00 4.00
2857 4944 6.495872 TGAAACCACAACTGATAGTACTACCT 59.504 38.462 4.31 0.00 0.00 3.08
2858 4945 6.694447 TGAAACCACAACTGATAGTACTACC 58.306 40.000 4.31 0.00 0.00 3.18
2859 4946 7.600065 TCTGAAACCACAACTGATAGTACTAC 58.400 38.462 4.31 0.35 0.00 2.73
2860 4947 7.450634 ACTCTGAAACCACAACTGATAGTACTA 59.549 37.037 4.77 4.77 0.00 1.82
2861 4948 6.267928 ACTCTGAAACCACAACTGATAGTACT 59.732 38.462 0.00 0.00 0.00 2.73
2862 4949 6.456501 ACTCTGAAACCACAACTGATAGTAC 58.543 40.000 0.00 0.00 0.00 2.73
2874 4961 5.066505 ACAAATCACTGAACTCTGAAACCAC 59.933 40.000 0.00 0.00 0.00 4.16
2902 4989 1.079127 CCGTCGGTCATTTGAGCCT 60.079 57.895 2.08 0.00 39.23 4.58
2903 4990 0.462047 ATCCGTCGGTCATTTGAGCC 60.462 55.000 11.88 0.00 39.23 4.70
2904 4991 0.652592 CATCCGTCGGTCATTTGAGC 59.347 55.000 11.88 0.00 39.04 4.26
2963 5051 3.624777 AGCGTGGGATCTCATTTCAAAT 58.375 40.909 0.00 0.00 0.00 2.32
2964 5052 3.071874 AGCGTGGGATCTCATTTCAAA 57.928 42.857 0.00 0.00 0.00 2.69
2965 5053 2.787473 AGCGTGGGATCTCATTTCAA 57.213 45.000 0.00 0.00 0.00 2.69
2966 5054 3.904800 TTAGCGTGGGATCTCATTTCA 57.095 42.857 0.00 0.00 0.00 2.69
2967 5055 4.494199 CGTTTTAGCGTGGGATCTCATTTC 60.494 45.833 0.00 0.00 0.00 2.17
2968 5056 3.374058 CGTTTTAGCGTGGGATCTCATTT 59.626 43.478 0.00 0.00 0.00 2.32
2969 5057 2.936498 CGTTTTAGCGTGGGATCTCATT 59.064 45.455 0.00 0.00 0.00 2.57
2970 5058 2.550978 CGTTTTAGCGTGGGATCTCAT 58.449 47.619 0.00 0.00 0.00 2.90
2976 5064 0.390209 GGTAGCGTTTTAGCGTGGGA 60.390 55.000 0.00 0.00 43.00 4.37
3025 5113 7.417797 GGGCCAGTAATATGTGATTTGTCATTT 60.418 37.037 4.39 0.00 0.00 2.32
3026 5114 6.040842 GGGCCAGTAATATGTGATTTGTCATT 59.959 38.462 4.39 0.00 0.00 2.57
3057 5146 0.393537 CAGGGCAGAACATCCTGGAC 60.394 60.000 0.00 0.00 43.09 4.02
3080 5169 0.373716 GCGCATCTACAAAAGTCCGG 59.626 55.000 0.30 0.00 0.00 5.14
3085 5174 1.398390 GTGGAGGCGCATCTACAAAAG 59.602 52.381 29.77 0.00 31.48 2.27
3103 5192 0.583438 CCAGCGTTCAGAACTGTGTG 59.417 55.000 11.60 3.49 0.00 3.82
3117 5206 3.797039 TGTCAGGAAGAATTATCCAGCG 58.203 45.455 11.31 1.64 39.55 5.18
3119 5208 5.819901 GGAGTTGTCAGGAAGAATTATCCAG 59.180 44.000 11.31 4.63 39.55 3.86
3120 5209 5.339200 GGGAGTTGTCAGGAAGAATTATCCA 60.339 44.000 11.31 0.00 39.55 3.41
3157 5246 7.750229 TTCTCTGAGTAATGCAAGTGAAATT 57.250 32.000 4.32 0.00 0.00 1.82
3172 5261 1.134848 GCGCATCTCCTTTCTCTGAGT 60.135 52.381 0.30 0.00 0.00 3.41
3178 5267 4.009675 TGTATTTTGCGCATCTCCTTTCT 58.990 39.130 12.75 0.00 0.00 2.52
3179 5268 4.346129 CTGTATTTTGCGCATCTCCTTTC 58.654 43.478 12.75 0.00 0.00 2.62
3201 5290 4.442375 ACAGTATCTACGGATATGCTGC 57.558 45.455 10.44 0.00 36.88 5.25
3242 5331 5.640732 ACATCGAGGTAATGCAATTGAAAC 58.359 37.500 10.34 0.00 36.99 2.78
3284 5373 2.596338 TGCGACACGTCCTGGAGA 60.596 61.111 0.00 0.00 0.00 3.71
3355 5445 2.082231 CCTGAATCAGTGGCACTTCAG 58.918 52.381 28.75 28.75 42.61 3.02
3385 5480 2.919228 CTGGCCTATTTGACTGTACCC 58.081 52.381 3.32 0.00 0.00 3.69
3470 5567 2.097629 CAGCAGCATCTTGAACTCATGG 59.902 50.000 0.00 0.00 0.00 3.66
3492 5589 5.423886 TCATGCGGTCAATATTTGTCTGTA 58.576 37.500 0.00 0.00 0.00 2.74
3498 5595 7.254185 CCAAGAAAATCATGCGGTCAATATTTG 60.254 37.037 0.00 0.00 0.00 2.32
3499 5596 6.757947 CCAAGAAAATCATGCGGTCAATATTT 59.242 34.615 0.00 0.00 0.00 1.40
3500 5597 6.096705 TCCAAGAAAATCATGCGGTCAATATT 59.903 34.615 0.00 0.00 0.00 1.28
3501 5598 5.593909 TCCAAGAAAATCATGCGGTCAATAT 59.406 36.000 0.00 0.00 0.00 1.28
3503 5600 3.763360 TCCAAGAAAATCATGCGGTCAAT 59.237 39.130 0.00 0.00 0.00 2.57
3519 5745 2.303022 CTCCTACTTGTGGCTTCCAAGA 59.697 50.000 15.58 3.25 41.44 3.02
3522 5748 1.729586 ACTCCTACTTGTGGCTTCCA 58.270 50.000 0.00 0.00 0.00 3.53
3527 5753 1.429463 CGTCAACTCCTACTTGTGGC 58.571 55.000 0.00 0.00 0.00 5.01
3607 5849 7.467623 CCTGTAGCTTGTTCAGTTGATTTATC 58.532 38.462 0.00 0.00 0.00 1.75
3668 5917 3.682858 ACACGGATAAAAATGACGGTCTG 59.317 43.478 9.88 0.00 0.00 3.51
3669 5918 3.682858 CACACGGATAAAAATGACGGTCT 59.317 43.478 9.88 0.00 0.00 3.85
3674 5923 5.048991 ACAAGGACACACGGATAAAAATGAC 60.049 40.000 0.00 0.00 0.00 3.06
3686 5935 3.192844 ACCTCATACTACAAGGACACACG 59.807 47.826 0.00 0.00 34.16 4.49
3736 5989 9.448438 AAGTGCAGAACATTAACAGTATTATCA 57.552 29.630 0.00 0.00 0.00 2.15
3843 6096 0.895530 CCAGCGTAGGTCTCAAGGAA 59.104 55.000 0.00 0.00 33.74 3.36


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

AutoCloner maintained by Alex Coulton.