Multiple sequence alignment - TraesCS4A01G129900

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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 TraesCS4A01G129900 chr4A 100.000 4913 0 0 344 5256 170171952 170167040 0.000000e+00 9073.0
1 TraesCS4A01G129900 chr4A 100.000 128 0 0 1 128 170172295 170172168 2.450000e-58 237.0
2 TraesCS4A01G129900 chr4A 82.624 282 26 7 4998 5256 17097217 17097498 1.470000e-55 228.0
3 TraesCS4A01G129900 chr4A 84.783 138 21 0 3667 3804 33622970 33622833 7.100000e-29 139.0
4 TraesCS4A01G129900 chr4D 95.805 1931 43 14 2848 4755 307148464 307150379 0.000000e+00 3083.0
5 TraesCS4A01G129900 chr4D 89.407 944 44 20 1329 2245 307146086 307147000 0.000000e+00 1138.0
6 TraesCS4A01G129900 chr4D 93.844 731 17 8 639 1344 307145342 307146069 0.000000e+00 1075.0
7 TraesCS4A01G129900 chr4D 89.344 366 22 7 2495 2852 307148062 307148418 1.340000e-120 444.0
8 TraesCS4A01G129900 chr4D 94.059 202 10 1 348 547 307144912 307145113 6.610000e-79 305.0
9 TraesCS4A01G129900 chr4D 86.071 280 18 7 4998 5256 307150783 307151062 1.110000e-71 281.0
10 TraesCS4A01G129900 chr4D 92.810 153 6 4 2241 2390 307147680 307147830 3.190000e-52 217.0
11 TraesCS4A01G129900 chr4D 100.000 32 0 0 592 623 307145123 307145154 5.680000e-05 60.2
12 TraesCS4A01G129900 chr4B 96.685 1659 39 8 2848 4498 383098094 383099744 0.000000e+00 2745.0
13 TraesCS4A01G129900 chr4B 90.128 2107 96 42 344 2390 383095261 383097315 0.000000e+00 2636.0
14 TraesCS4A01G129900 chr4B 89.615 260 15 6 2495 2751 383097546 383097796 2.360000e-83 320.0
15 TraesCS4A01G129900 chr1D 84.091 264 29 8 4998 5256 51918547 51918292 5.260000e-60 243.0
16 TraesCS4A01G129900 chrUn 82.624 282 26 7 4998 5256 397078622 397078341 1.470000e-55 228.0
17 TraesCS4A01G129900 chrUn 82.437 279 26 7 5001 5256 455551577 455551855 6.850000e-54 222.0
18 TraesCS4A01G129900 chrUn 91.083 157 14 0 5100 5256 424751348 424751192 4.120000e-51 213.0
19 TraesCS4A01G129900 chr6D 82.437 279 26 7 5001 5256 389248060 389248338 6.850000e-54 222.0
20 TraesCS4A01G129900 chr2D 85.068 221 29 4 3714 3931 554076572 554076791 6.850000e-54 222.0
21 TraesCS4A01G129900 chr5D 91.250 160 14 0 5097 5256 503269491 503269332 8.860000e-53 219.0
22 TraesCS4A01G129900 chr7B 90.244 164 16 0 5093 5256 662722205 662722368 1.150000e-51 215.0
23 TraesCS4A01G129900 chr2A 91.176 68 4 1 4866 4933 38810287 38810352 2.020000e-14 91.6
24 TraesCS4A01G129900 chr1A 90.909 66 4 1 4868 4933 430630249 430630186 2.610000e-13 87.9
25 TraesCS4A01G129900 chr3B 88.710 62 7 0 4867 4928 507490828 507490767 5.640000e-10 76.8
26 TraesCS4A01G129900 chr5B 85.075 67 6 2 4867 4933 30845132 30845194 1.220000e-06 65.8
27 TraesCS4A01G129900 chr3D 96.875 32 1 0 1001 1032 77351800 77351831 3.000000e-03 54.7


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 TraesCS4A01G129900 chr4A 170167040 170172295 5255 True 4655.000000 9073 100.000000 1 5256 2 chr4A.!!$R2 5255
1 TraesCS4A01G129900 chr4D 307144912 307151062 6150 False 825.400000 3083 92.667500 348 5256 8 chr4D.!!$F1 4908
2 TraesCS4A01G129900 chr4B 383095261 383099744 4483 False 1900.333333 2745 92.142667 344 4498 3 chr4B.!!$F1 4154

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
555 558 0.317160 CCGTATTGGCTCGCTATGGA 59.683 55.0 0.0 0.0 0.00 3.41 F
2141 2429 0.394938 TCCGCAAAAGAGGCAGTGTA 59.605 50.0 0.0 0.0 0.00 2.90 F
2168 2456 0.037512 CGGGTGCCATGCAATTCAAA 60.038 50.0 0.0 0.0 41.47 2.69 F
2508 3609 0.039346 CGTGCAATGACCAATGTGCA 60.039 50.0 0.0 0.0 44.36 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2149 2437 0.037512 TTTGAATTGCATGGCACCCG 60.038 50.000 0.00 0.0 38.71 5.28 R
4081 5390 0.323302 TAGCGGCACTCAACATTGGA 59.677 50.000 1.45 0.0 0.00 3.53 R
4177 5486 3.777106 ACTGAATCTCCTGACTTGCAA 57.223 42.857 0.00 0.0 0.00 4.08 R
4256 5565 1.053835 TGAGCCAACCTCACCTGACA 61.054 55.000 0.00 0.0 45.44 3.58 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
25 26 2.793278 GTTGCGACCAACTTCCATTT 57.207 45.000 0.00 0.00 46.13 2.32
26 27 2.393764 GTTGCGACCAACTTCCATTTG 58.606 47.619 0.00 0.00 46.13 2.32
27 28 2.862140 GTTGCGACCAACTTCCATTTGG 60.862 50.000 0.00 0.00 46.13 3.28
28 29 1.243902 GCGACCAACTTCCATTTGGA 58.756 50.000 8.10 0.00 45.69 3.53
29 30 1.818674 GCGACCAACTTCCATTTGGAT 59.181 47.619 8.10 0.00 45.69 3.41
30 31 2.415893 GCGACCAACTTCCATTTGGATG 60.416 50.000 8.10 10.14 45.69 3.51
36 37 3.814504 ACTTCCATTTGGATGTCCTGT 57.185 42.857 11.29 0.00 45.95 4.00
37 38 4.118168 ACTTCCATTTGGATGTCCTGTT 57.882 40.909 11.29 0.00 45.95 3.16
38 39 4.482990 ACTTCCATTTGGATGTCCTGTTT 58.517 39.130 11.29 0.00 45.95 2.83
39 40 4.281688 ACTTCCATTTGGATGTCCTGTTTG 59.718 41.667 11.29 0.00 45.95 2.93
40 41 4.111255 TCCATTTGGATGTCCTGTTTGA 57.889 40.909 0.00 0.00 39.78 2.69
41 42 4.676109 TCCATTTGGATGTCCTGTTTGAT 58.324 39.130 0.00 0.00 39.78 2.57
42 43 5.085920 TCCATTTGGATGTCCTGTTTGATT 58.914 37.500 0.00 0.00 39.78 2.57
43 44 6.252233 TCCATTTGGATGTCCTGTTTGATTA 58.748 36.000 0.00 0.00 39.78 1.75
44 45 6.723515 TCCATTTGGATGTCCTGTTTGATTAA 59.276 34.615 0.00 0.00 39.78 1.40
45 46 7.399765 TCCATTTGGATGTCCTGTTTGATTAAT 59.600 33.333 0.00 0.00 39.78 1.40
46 47 7.707893 CCATTTGGATGTCCTGTTTGATTAATC 59.292 37.037 8.60 8.60 37.39 1.75
47 48 7.773489 TTTGGATGTCCTGTTTGATTAATCA 57.227 32.000 14.23 14.23 36.82 2.57
48 49 6.757897 TGGATGTCCTGTTTGATTAATCAC 57.242 37.500 17.76 8.24 35.02 3.06
49 50 5.652014 TGGATGTCCTGTTTGATTAATCACC 59.348 40.000 17.76 11.60 35.02 4.02
50 51 5.652014 GGATGTCCTGTTTGATTAATCACCA 59.348 40.000 17.76 15.26 36.36 4.17
51 52 5.957842 TGTCCTGTTTGATTAATCACCAC 57.042 39.130 17.76 16.53 36.36 4.16
52 53 5.630121 TGTCCTGTTTGATTAATCACCACT 58.370 37.500 17.76 0.00 36.36 4.00
53 54 5.705441 TGTCCTGTTTGATTAATCACCACTC 59.295 40.000 17.76 7.41 36.36 3.51
54 55 5.940470 GTCCTGTTTGATTAATCACCACTCT 59.060 40.000 17.76 0.00 36.36 3.24
55 56 7.103641 GTCCTGTTTGATTAATCACCACTCTA 58.896 38.462 17.76 0.00 36.36 2.43
56 57 7.278868 GTCCTGTTTGATTAATCACCACTCTAG 59.721 40.741 17.76 10.45 36.36 2.43
57 58 7.180229 TCCTGTTTGATTAATCACCACTCTAGA 59.820 37.037 17.76 9.85 36.36 2.43
58 59 7.278868 CCTGTTTGATTAATCACCACTCTAGAC 59.721 40.741 17.76 6.45 36.36 2.59
59 60 7.676004 TGTTTGATTAATCACCACTCTAGACA 58.324 34.615 17.76 8.54 36.36 3.41
60 61 8.321353 TGTTTGATTAATCACCACTCTAGACAT 58.679 33.333 17.76 0.00 36.36 3.06
61 62 9.167311 GTTTGATTAATCACCACTCTAGACATT 57.833 33.333 17.76 0.00 36.36 2.71
71 72 9.599866 TCACCACTCTAGACATTATTTGTATTG 57.400 33.333 0.00 0.00 39.18 1.90
72 73 9.599866 CACCACTCTAGACATTATTTGTATTGA 57.400 33.333 0.00 0.00 39.18 2.57
539 542 4.743955 GCCTATATTTGAAGAGAAGCCCGT 60.744 45.833 0.00 0.00 0.00 5.28
554 557 0.670546 CCCGTATTGGCTCGCTATGG 60.671 60.000 0.00 0.00 35.87 2.74
555 558 0.317160 CCGTATTGGCTCGCTATGGA 59.683 55.000 0.00 0.00 0.00 3.41
556 559 1.419374 CGTATTGGCTCGCTATGGAC 58.581 55.000 0.00 0.00 0.00 4.02
557 560 1.797025 GTATTGGCTCGCTATGGACC 58.203 55.000 0.00 0.00 0.00 4.46
558 561 1.344763 GTATTGGCTCGCTATGGACCT 59.655 52.381 0.00 0.00 0.00 3.85
559 562 0.839946 ATTGGCTCGCTATGGACCTT 59.160 50.000 0.00 0.00 0.00 3.50
571 574 4.202161 GCTATGGACCTTCTTCTGAATCGA 60.202 45.833 0.00 0.00 0.00 3.59
572 575 4.826274 ATGGACCTTCTTCTGAATCGAA 57.174 40.909 0.00 0.00 0.00 3.71
579 582 5.189934 ACCTTCTTCTGAATCGAATTAGGGT 59.810 40.000 0.00 0.00 32.20 4.34
582 585 5.844004 TCTTCTGAATCGAATTAGGGTAGC 58.156 41.667 0.00 0.00 0.00 3.58
586 589 7.540474 TCTGAATCGAATTAGGGTAGCTAAT 57.460 36.000 0.00 0.00 0.00 1.73
590 593 7.872993 TGAATCGAATTAGGGTAGCTAATCAAG 59.127 37.037 0.00 0.00 0.00 3.02
765 945 2.352651 AGACGCGTATGTACACACGTAT 59.647 45.455 25.86 15.33 40.25 3.06
766 946 3.555547 AGACGCGTATGTACACACGTATA 59.444 43.478 25.86 0.00 40.25 1.47
890 1080 0.681733 ATATTCTCTCGCACCGCCAT 59.318 50.000 0.00 0.00 0.00 4.40
1268 1477 0.916358 AAGGTCTGCATGCCCCTACT 60.916 55.000 16.68 4.18 0.00 2.57
1278 1487 3.954258 GCATGCCCCTACTTCTTGTATTT 59.046 43.478 6.36 0.00 0.00 1.40
1292 1501 5.194199 CTTGTATTTCAAGCCAATTTGCG 57.806 39.130 0.00 0.00 45.37 4.85
1300 1509 1.297893 GCCAATTTGCGCGCTCTAG 60.298 57.895 33.29 17.34 0.00 2.43
1301 1510 1.353103 CCAATTTGCGCGCTCTAGG 59.647 57.895 33.29 22.16 0.00 3.02
1379 1643 6.610741 TTTTTGTGCGCATATTTTCCTTTT 57.389 29.167 15.91 0.00 0.00 2.27
1380 1644 5.837586 TTTGTGCGCATATTTTCCTTTTC 57.162 34.783 15.91 0.00 0.00 2.29
1387 1651 6.035843 GCGCATATTTTCCTTTTCATTCTGA 58.964 36.000 0.30 0.00 0.00 3.27
1421 1685 6.841119 TGCGTAAAATAGCTTATATGCATGG 58.159 36.000 10.16 0.00 35.86 3.66
1422 1686 6.652900 TGCGTAAAATAGCTTATATGCATGGA 59.347 34.615 10.16 0.00 35.86 3.41
1423 1687 7.174080 TGCGTAAAATAGCTTATATGCATGGAA 59.826 33.333 10.16 2.05 35.86 3.53
1424 1688 8.020819 GCGTAAAATAGCTTATATGCATGGAAA 58.979 33.333 10.16 0.00 34.99 3.13
1433 1697 9.971922 AGCTTATATGCATGGAAAGTAAATTTC 57.028 29.630 10.16 0.00 39.98 2.17
1452 1716 3.237268 TCCAATTGTGCCTGTACCTTT 57.763 42.857 4.43 0.00 0.00 3.11
1492 1756 3.300009 CAATGAGCACAAAACTTCGTCC 58.700 45.455 0.00 0.00 0.00 4.79
1498 1762 2.737252 GCACAAAACTTCGTCCTAGAGG 59.263 50.000 0.00 0.00 0.00 3.69
1522 1786 8.982723 AGGTCTTACATTGTCATACAGATAGTT 58.017 33.333 0.00 0.00 0.00 2.24
1523 1787 9.250624 GGTCTTACATTGTCATACAGATAGTTC 57.749 37.037 0.00 0.00 0.00 3.01
1524 1788 9.250624 GTCTTACATTGTCATACAGATAGTTCC 57.749 37.037 0.00 0.00 0.00 3.62
1564 1828 2.287188 CCAGCTTGCATACAATTAGGCG 60.287 50.000 0.00 0.00 37.85 5.52
1642 1906 7.950512 TGAACAATGTGAATTTGTATTGTCCT 58.049 30.769 12.50 2.88 41.43 3.85
1677 1941 4.272489 TCCTTCATGGATTGGTAGCTTTG 58.728 43.478 0.00 0.00 40.56 2.77
1751 2015 5.981315 GTGTCCAAATTGGCAGATCATAATG 59.019 40.000 7.24 0.00 37.47 1.90
1752 2016 5.657745 TGTCCAAATTGGCAGATCATAATGT 59.342 36.000 7.24 0.00 37.47 2.71
1753 2017 5.981315 GTCCAAATTGGCAGATCATAATGTG 59.019 40.000 7.24 0.00 37.47 3.21
1758 2022 2.146342 GGCAGATCATAATGTGTCCCG 58.854 52.381 0.00 0.00 0.00 5.14
1768 2033 3.478857 AATGTGTCCCGTTCACAGTTA 57.521 42.857 9.59 0.00 46.54 2.24
1819 2084 5.869649 TGCTATATAAGGTTGCTGTCAGA 57.130 39.130 3.32 0.00 0.00 3.27
1830 2095 5.530171 AGGTTGCTGTCAGATGCATTAATAG 59.470 40.000 3.32 0.00 39.07 1.73
1927 2200 6.002704 AGAAGTCCTTTTCTGTAGTCGACTA 58.997 40.000 21.25 21.25 36.12 2.59
1982 2255 7.096436 GCAAGATTGTATAGTCGACTACACATG 60.096 40.741 31.18 26.26 35.97 3.21
2090 2378 6.455360 TTTGTGGGCTGAAGAAATATGATC 57.545 37.500 0.00 0.00 0.00 2.92
2123 2411 3.356290 ACACCCAGAAACATATGCCTTC 58.644 45.455 1.58 6.34 0.00 3.46
2125 2413 1.949525 CCCAGAAACATATGCCTTCCG 59.050 52.381 1.58 0.00 0.00 4.30
2141 2429 0.394938 TCCGCAAAAGAGGCAGTGTA 59.605 50.000 0.00 0.00 0.00 2.90
2142 2430 1.202710 TCCGCAAAAGAGGCAGTGTAA 60.203 47.619 0.00 0.00 0.00 2.41
2148 2436 3.508845 AAAGAGGCAGTGTAACACCAT 57.491 42.857 0.00 0.00 41.43 3.55
2149 2437 2.770164 AGAGGCAGTGTAACACCATC 57.230 50.000 0.00 0.00 41.43 3.51
2150 2438 1.066858 AGAGGCAGTGTAACACCATCG 60.067 52.381 0.00 0.00 41.43 3.84
2168 2456 0.037512 CGGGTGCCATGCAATTCAAA 60.038 50.000 0.00 0.00 41.47 2.69
2236 2524 8.459635 GCGTCTGTGATAGTTCAGGATATATAA 58.540 37.037 0.00 0.00 30.85 0.98
2324 3298 6.650807 CACACCTCTAAGAAGAAATGCTGTTA 59.349 38.462 0.00 0.00 0.00 2.41
2327 3301 9.553064 CACCTCTAAGAAGAAATGCTGTTATAT 57.447 33.333 0.00 0.00 0.00 0.86
2477 3547 6.942532 AAGTCTAAACATCAAGAAACTGCA 57.057 33.333 0.00 0.00 0.00 4.41
2478 3548 6.305693 AGTCTAAACATCAAGAAACTGCAC 57.694 37.500 0.00 0.00 0.00 4.57
2508 3609 0.039346 CGTGCAATGACCAATGTGCA 60.039 50.000 0.00 0.00 44.36 4.57
2520 3621 3.701040 ACCAATGTGCAATTCACCTATCC 59.299 43.478 0.00 0.00 45.03 2.59
2574 3675 9.726438 GTGGCTCTATATTATTGGTCTGTTTAT 57.274 33.333 0.00 0.00 0.00 1.40
2620 3722 6.978659 GGTGAGTGATTTTGTGATCGATAGTA 59.021 38.462 0.00 0.00 37.40 1.82
2624 3726 9.171701 GAGTGATTTTGTGATCGATAGTAGTAC 57.828 37.037 0.00 0.00 37.40 2.73
2643 3746 3.646736 ACTGGCCTGGATTTTAGTACC 57.353 47.619 14.82 0.00 0.00 3.34
2644 3747 3.190439 ACTGGCCTGGATTTTAGTACCT 58.810 45.455 14.82 0.00 0.00 3.08
2690 3794 9.555727 AAGATATAATTTACTTGTGGCATACGT 57.444 29.630 0.00 0.00 0.00 3.57
2694 3798 8.682128 ATAATTTACTTGTGGCATACGTTTTG 57.318 30.769 0.00 0.00 0.00 2.44
2702 3806 2.017049 GGCATACGTTTTGCAGGATCT 58.983 47.619 20.45 0.00 41.95 2.75
2703 3807 3.202906 GGCATACGTTTTGCAGGATCTA 58.797 45.455 20.45 0.00 41.95 1.98
2704 3808 3.248602 GGCATACGTTTTGCAGGATCTAG 59.751 47.826 20.45 0.00 41.95 2.43
2705 3809 3.303395 GCATACGTTTTGCAGGATCTAGC 60.303 47.826 15.79 0.00 39.90 3.42
2706 3810 1.739067 ACGTTTTGCAGGATCTAGCC 58.261 50.000 7.32 0.00 0.00 3.93
2707 3811 1.003118 ACGTTTTGCAGGATCTAGCCA 59.997 47.619 7.32 0.00 0.00 4.75
2708 3812 2.083774 CGTTTTGCAGGATCTAGCCAA 58.916 47.619 7.32 1.03 0.00 4.52
2709 3813 2.096496 CGTTTTGCAGGATCTAGCCAAG 59.904 50.000 7.32 0.00 0.00 3.61
2740 3844 4.751600 TGCACTAGATATTCATTCGCTTGG 59.248 41.667 0.00 0.00 0.00 3.61
2831 4089 3.996150 AACTGCTTTCATGACCTTGTG 57.004 42.857 0.00 0.00 0.00 3.33
2839 4097 4.365514 TTCATGACCTTGTGCCTAGAAA 57.634 40.909 0.00 0.00 0.00 2.52
2848 4106 5.888161 ACCTTGTGCCTAGAAATCTATTTGG 59.112 40.000 0.00 0.00 0.00 3.28
2893 4201 6.054860 ACTATGCCAATCTACTGTCTTTGT 57.945 37.500 0.00 0.00 0.00 2.83
2992 4300 6.779860 ACCATAACCACAGATTATACCATCC 58.220 40.000 0.00 0.00 0.00 3.51
3042 4350 4.515567 AGCTACAAAAAGTTGGCTGTAGAC 59.484 41.667 17.31 11.26 42.47 2.59
3279 4587 3.188254 AGATCGACATGATAGCACTCTCG 59.812 47.826 0.00 0.00 37.47 4.04
3378 4686 3.381272 CCAAGGTATGTTTATGCCCACAG 59.619 47.826 0.00 0.00 39.66 3.66
3394 4703 3.685756 CCCACAGGCTTGCATTTTATTTG 59.314 43.478 0.00 0.00 0.00 2.32
3535 4844 2.639839 AGATTTGGGTATGGAGATCCCG 59.360 50.000 0.00 0.00 43.75 5.14
3759 5068 2.182827 TCCAGAGTTAGCAGTGCAGAT 58.817 47.619 19.20 0.00 0.00 2.90
4021 5330 4.074970 AGCTGAAGACCGACAATGATTTT 58.925 39.130 0.00 0.00 0.00 1.82
4078 5387 2.894765 GAGTCTCATAGTTAGGGGCCTC 59.105 54.545 0.84 0.00 0.00 4.70
4081 5390 3.648545 GTCTCATAGTTAGGGGCCTCATT 59.351 47.826 4.79 0.00 0.00 2.57
4177 5486 2.360475 GCCAAGAAGCTCGGCCTT 60.360 61.111 0.00 0.00 40.07 4.35
4186 5495 2.260869 GCTCGGCCTTTGCAAGTCA 61.261 57.895 0.00 0.00 40.13 3.41
4228 5537 0.672889 ATCGTCTCAGCGCATCATCT 59.327 50.000 11.47 0.00 0.00 2.90
4250 5559 2.489722 CTCGTCAGGATCTTGACAGTGA 59.510 50.000 30.37 20.68 46.11 3.41
4256 5565 6.402222 GTCAGGATCTTGACAGTGAATTAGT 58.598 40.000 27.74 0.00 45.32 2.24
4281 5590 1.541118 TGAGGTTGGCTCATGGGGA 60.541 57.895 0.00 0.00 0.00 4.81
4411 5720 2.808543 GTGTCGCCCATTCTGAATATCC 59.191 50.000 1.98 0.00 0.00 2.59
4412 5721 2.705658 TGTCGCCCATTCTGAATATCCT 59.294 45.455 1.98 0.00 0.00 3.24
4435 5744 9.998106 TCCTTTGCTAAATAATACATACTCTCC 57.002 33.333 0.00 0.00 0.00 3.71
4477 5786 3.889196 TCGTTCAGTATGTTGTTTGGC 57.111 42.857 0.00 0.00 37.40 4.52
4478 5787 3.472652 TCGTTCAGTATGTTGTTTGGCT 58.527 40.909 0.00 0.00 37.40 4.75
4479 5788 3.249799 TCGTTCAGTATGTTGTTTGGCTG 59.750 43.478 0.00 0.00 37.40 4.85
4481 5790 1.885887 TCAGTATGTTGTTTGGCTGCC 59.114 47.619 12.87 12.87 37.40 4.85
4500 5816 7.175467 TGGCTGCCTTTATACAAAGATCATATG 59.825 37.037 21.03 0.00 43.32 1.78
4504 5820 8.352201 TGCCTTTATACAAAGATCATATGTTGC 58.648 33.333 1.90 0.00 43.32 4.17
4583 5910 4.329462 AGAGTTTTGTGACAGAGACCTC 57.671 45.455 0.00 0.00 0.00 3.85
4584 5911 3.964031 AGAGTTTTGTGACAGAGACCTCT 59.036 43.478 0.00 0.00 41.37 3.69
4585 5912 4.407296 AGAGTTTTGTGACAGAGACCTCTT 59.593 41.667 0.00 0.00 37.98 2.85
4586 5913 4.446371 AGTTTTGTGACAGAGACCTCTTG 58.554 43.478 0.00 0.00 37.98 3.02
4587 5914 2.533266 TTGTGACAGAGACCTCTTGC 57.467 50.000 0.00 0.00 37.98 4.01
4589 5916 1.973515 TGTGACAGAGACCTCTTGCAT 59.026 47.619 0.00 0.00 37.98 3.96
4590 5917 2.369860 TGTGACAGAGACCTCTTGCATT 59.630 45.455 0.00 0.00 37.98 3.56
4664 5991 3.057734 AGGCGACAAAACTTAACTCTCG 58.942 45.455 0.00 0.00 0.00 4.04
4725 6057 4.204012 AGAAAGACTCTATGGTCGAGAGG 58.796 47.826 4.79 0.00 44.06 3.69
4726 6058 3.935818 AAGACTCTATGGTCGAGAGGA 57.064 47.619 4.79 0.00 44.06 3.71
4727 6059 3.935818 AGACTCTATGGTCGAGAGGAA 57.064 47.619 4.79 0.00 44.06 3.36
4728 6060 4.447138 AGACTCTATGGTCGAGAGGAAT 57.553 45.455 4.79 0.00 44.06 3.01
4729 6061 4.798882 AGACTCTATGGTCGAGAGGAATT 58.201 43.478 4.79 0.00 44.06 2.17
4734 6066 7.007723 ACTCTATGGTCGAGAGGAATTAGAAT 58.992 38.462 4.79 0.00 44.06 2.40
4736 6068 9.184523 CTCTATGGTCGAGAGGAATTAGAATAT 57.815 37.037 0.00 0.00 37.40 1.28
4737 6069 9.535170 TCTATGGTCGAGAGGAATTAGAATATT 57.465 33.333 0.00 0.00 0.00 1.28
4760 6092 8.996651 ATTAACCTCTTGAAAGAAAGGAAGAA 57.003 30.769 5.58 0.00 34.03 2.52
4761 6093 8.996651 TTAACCTCTTGAAAGAAAGGAAGAAT 57.003 30.769 5.58 0.00 34.03 2.40
4763 6095 5.242615 ACCTCTTGAAAGAAAGGAAGAATGC 59.757 40.000 5.58 0.00 34.03 3.56
4764 6096 5.476254 CCTCTTGAAAGAAAGGAAGAATGCT 59.524 40.000 0.00 0.00 34.03 3.79
4768 6100 5.248640 TGAAAGAAAGGAAGAATGCTCGAT 58.751 37.500 0.00 0.00 0.00 3.59
4770 6102 7.050377 TGAAAGAAAGGAAGAATGCTCGATAT 58.950 34.615 0.00 0.00 0.00 1.63
4771 6103 8.204160 TGAAAGAAAGGAAGAATGCTCGATATA 58.796 33.333 0.00 0.00 0.00 0.86
4772 6104 8.964476 AAAGAAAGGAAGAATGCTCGATATAA 57.036 30.769 0.00 0.00 0.00 0.98
4773 6105 7.954788 AGAAAGGAAGAATGCTCGATATAAC 57.045 36.000 0.00 0.00 0.00 1.89
4831 6283 4.200827 CGTGTACATCACAAAACTTCGTG 58.799 43.478 0.00 0.00 46.44 4.35
4832 6284 3.966218 GTGTACATCACAAAACTTCGTGC 59.034 43.478 0.00 0.00 45.51 5.34
4838 6290 0.248054 ACAAAACTTCGTGCGCACAG 60.248 50.000 37.03 29.32 0.00 3.66
4840 6292 0.730265 AAAACTTCGTGCGCACAGAA 59.270 45.000 37.03 33.40 0.00 3.02
4841 6293 0.304705 AAACTTCGTGCGCACAGAAG 59.695 50.000 40.73 40.73 42.22 2.85
4842 6294 1.498865 AACTTCGTGCGCACAGAAGG 61.499 55.000 42.32 33.22 41.56 3.46
4844 6296 1.498865 CTTCGTGCGCACAGAAGGTT 61.499 55.000 38.31 0.00 37.81 3.50
4845 6297 1.771073 TTCGTGCGCACAGAAGGTTG 61.771 55.000 37.03 19.77 0.00 3.77
4846 6298 2.243957 CGTGCGCACAGAAGGTTGA 61.244 57.895 37.03 0.00 0.00 3.18
4849 6301 2.009774 GTGCGCACAGAAGGTTGATAT 58.990 47.619 34.52 0.00 0.00 1.63
4852 6304 2.223112 GCGCACAGAAGGTTGATATGTG 60.223 50.000 0.30 0.00 43.18 3.21
4856 6308 3.127548 CACAGAAGGTTGATATGTGCACC 59.872 47.826 15.69 0.00 35.35 5.01
4857 6309 2.684881 CAGAAGGTTGATATGTGCACCC 59.315 50.000 15.69 6.14 0.00 4.61
4911 6363 3.332706 TTTTTACCGGTGGCAGGAG 57.667 52.632 19.93 0.00 0.00 3.69
4912 6364 0.891904 TTTTTACCGGTGGCAGGAGC 60.892 55.000 19.93 0.00 41.10 4.70
4913 6365 2.058125 TTTTACCGGTGGCAGGAGCA 62.058 55.000 19.93 0.00 44.61 4.26
4914 6366 1.847798 TTTACCGGTGGCAGGAGCAT 61.848 55.000 19.93 0.00 44.61 3.79
4915 6367 0.978667 TTACCGGTGGCAGGAGCATA 60.979 55.000 19.93 0.00 44.61 3.14
4916 6368 0.762842 TACCGGTGGCAGGAGCATAT 60.763 55.000 19.93 0.00 44.61 1.78
4917 6369 1.598962 CCGGTGGCAGGAGCATATG 60.599 63.158 0.00 0.00 44.61 1.78
4918 6370 2.256591 CGGTGGCAGGAGCATATGC 61.257 63.158 20.36 20.36 44.61 3.14
4930 6382 1.971481 GCATATGCTCCCATGTGTCA 58.029 50.000 20.64 0.00 41.17 3.58
4931 6383 2.300433 GCATATGCTCCCATGTGTCAA 58.700 47.619 20.64 0.00 41.17 3.18
4932 6384 2.689471 GCATATGCTCCCATGTGTCAAA 59.311 45.455 20.64 0.00 41.17 2.69
4933 6385 3.319972 GCATATGCTCCCATGTGTCAAAT 59.680 43.478 20.64 0.00 41.17 2.32
4944 6396 5.451659 CCCATGTGTCAAATGTCAAAGTGAA 60.452 40.000 2.27 0.00 0.00 3.18
4982 6434 9.995003 AAAATGTTCTTATAAAACCAATCTGCA 57.005 25.926 0.00 0.00 0.00 4.41
4983 6435 9.995003 AAATGTTCTTATAAAACCAATCTGCAA 57.005 25.926 0.00 0.00 0.00 4.08
4984 6436 8.986477 ATGTTCTTATAAAACCAATCTGCAAC 57.014 30.769 0.00 0.00 0.00 4.17
4986 6438 6.524101 TCTTATAAAACCAATCTGCAACCC 57.476 37.500 0.00 0.00 0.00 4.11
4988 6440 6.377146 TCTTATAAAACCAATCTGCAACCCTC 59.623 38.462 0.00 0.00 0.00 4.30
4990 6442 2.380064 AACCAATCTGCAACCCTCAA 57.620 45.000 0.00 0.00 0.00 3.02
4991 6443 1.620822 ACCAATCTGCAACCCTCAAC 58.379 50.000 0.00 0.00 0.00 3.18
4992 6444 0.890683 CCAATCTGCAACCCTCAACC 59.109 55.000 0.00 0.00 0.00 3.77
4993 6445 0.890683 CAATCTGCAACCCTCAACCC 59.109 55.000 0.00 0.00 0.00 4.11
4994 6446 0.779997 AATCTGCAACCCTCAACCCT 59.220 50.000 0.00 0.00 0.00 4.34
4995 6447 0.038744 ATCTGCAACCCTCAACCCTG 59.961 55.000 0.00 0.00 0.00 4.45
4996 6448 1.059584 TCTGCAACCCTCAACCCTGA 61.060 55.000 0.00 0.00 0.00 3.86
4997 6449 0.178992 CTGCAACCCTCAACCCTGAA 60.179 55.000 0.00 0.00 0.00 3.02
4999 6451 1.177401 GCAACCCTCAACCCTGAATC 58.823 55.000 0.00 0.00 0.00 2.52
5000 6452 1.839424 CAACCCTCAACCCTGAATCC 58.161 55.000 0.00 0.00 0.00 3.01
5008 6558 4.411013 CTCAACCCTGAATCCTTTTCCTT 58.589 43.478 0.00 0.00 0.00 3.36
5014 6564 3.191371 CCTGAATCCTTTTCCTTGTTCGG 59.809 47.826 0.00 0.00 0.00 4.30
5021 6571 3.498777 CCTTTTCCTTGTTCGGAAGTCTC 59.501 47.826 0.00 0.00 43.49 3.36
5023 6573 1.712056 TCCTTGTTCGGAAGTCTCCA 58.288 50.000 0.00 0.00 42.58 3.86
5026 6576 1.344763 CTTGTTCGGAAGTCTCCACCT 59.655 52.381 0.00 0.00 42.58 4.00
5055 6609 4.082136 CCACTCCACCAGACTAACTAAGAC 60.082 50.000 0.00 0.00 0.00 3.01
5059 6613 5.091552 TCCACCAGACTAACTAAGACCAAT 58.908 41.667 0.00 0.00 0.00 3.16
5064 6618 6.497259 ACCAGACTAACTAAGACCAATTGAGA 59.503 38.462 7.12 0.00 0.00 3.27
5065 6619 7.181125 ACCAGACTAACTAAGACCAATTGAGAT 59.819 37.037 7.12 0.00 0.00 2.75
5130 6700 7.601886 TGTCCTTTTACCAAACATATGCAAATG 59.398 33.333 1.58 0.00 0.00 2.32
5176 6746 6.292150 AGAAATCTTTCTCGGTATCAATCCC 58.708 40.000 0.00 0.00 43.72 3.85
5237 6808 9.796120 TTTTCGACTTAACATTTCTTCATTTGT 57.204 25.926 0.00 0.00 0.00 2.83
5247 6818 8.000780 ACATTTCTTCATTTGTAATCTAGGCC 57.999 34.615 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.234884 GAAGTTGGTCGCAACCTTCG 59.765 55.000 0.00 0.00 46.60 3.79
2 3 0.591659 GGAAGTTGGTCGCAACCTTC 59.408 55.000 0.00 0.00 46.60 3.46
3 4 0.106918 TGGAAGTTGGTCGCAACCTT 60.107 50.000 0.00 0.00 46.60 3.50
4 5 0.110486 ATGGAAGTTGGTCGCAACCT 59.890 50.000 0.00 0.00 46.60 3.50
5 6 0.958822 AATGGAAGTTGGTCGCAACC 59.041 50.000 2.74 0.00 46.66 3.77
6 7 2.393764 CAAATGGAAGTTGGTCGCAAC 58.606 47.619 0.00 0.00 38.43 4.17
7 8 2.791383 CAAATGGAAGTTGGTCGCAA 57.209 45.000 0.00 0.00 38.43 4.85
20 21 5.410355 AATCAAACAGGACATCCAAATGG 57.590 39.130 0.00 0.00 37.19 3.16
21 22 8.252417 TGATTAATCAAACAGGACATCCAAATG 58.748 33.333 15.82 0.00 34.18 2.32
22 23 8.253113 GTGATTAATCAAACAGGACATCCAAAT 58.747 33.333 19.55 0.00 38.75 2.32
23 24 7.309744 GGTGATTAATCAAACAGGACATCCAAA 60.310 37.037 19.55 0.00 38.75 3.28
24 25 6.152661 GGTGATTAATCAAACAGGACATCCAA 59.847 38.462 19.55 0.00 38.75 3.53
25 26 5.652014 GGTGATTAATCAAACAGGACATCCA 59.348 40.000 19.55 0.00 38.75 3.41
26 27 5.652014 TGGTGATTAATCAAACAGGACATCC 59.348 40.000 19.55 12.42 38.75 3.51
27 28 6.375455 AGTGGTGATTAATCAAACAGGACATC 59.625 38.462 19.55 8.84 38.75 3.06
28 29 6.248433 AGTGGTGATTAATCAAACAGGACAT 58.752 36.000 19.55 2.63 38.75 3.06
29 30 5.630121 AGTGGTGATTAATCAAACAGGACA 58.370 37.500 19.55 7.73 38.75 4.02
30 31 5.940470 AGAGTGGTGATTAATCAAACAGGAC 59.060 40.000 19.55 13.79 38.75 3.85
31 32 6.126863 AGAGTGGTGATTAATCAAACAGGA 57.873 37.500 19.55 0.00 38.75 3.86
32 33 7.278868 GTCTAGAGTGGTGATTAATCAAACAGG 59.721 40.741 19.55 11.49 38.75 4.00
33 34 7.819415 TGTCTAGAGTGGTGATTAATCAAACAG 59.181 37.037 19.55 13.37 38.75 3.16
34 35 7.676004 TGTCTAGAGTGGTGATTAATCAAACA 58.324 34.615 19.55 17.55 38.75 2.83
35 36 8.723942 ATGTCTAGAGTGGTGATTAATCAAAC 57.276 34.615 19.55 18.91 38.75 2.93
45 46 9.599866 CAATACAAATAATGTCTAGAGTGGTGA 57.400 33.333 0.00 0.00 42.70 4.02
46 47 9.599866 TCAATACAAATAATGTCTAGAGTGGTG 57.400 33.333 0.00 0.00 42.70 4.17
347 348 6.398918 ACGAGTTGCTAAGTAGATTGTTCAT 58.601 36.000 0.00 0.00 0.00 2.57
400 401 5.648092 ACATTCCACTAGACCTAAAATGTGC 59.352 40.000 0.00 0.00 35.27 4.57
539 542 1.717032 AGGTCCATAGCGAGCCAATA 58.283 50.000 0.00 0.00 0.00 1.90
549 552 5.521906 TCGATTCAGAAGAAGGTCCATAG 57.478 43.478 0.00 0.00 37.14 2.23
552 555 4.826274 ATTCGATTCAGAAGAAGGTCCA 57.174 40.909 0.00 0.00 37.14 4.02
554 557 5.755861 CCCTAATTCGATTCAGAAGAAGGTC 59.244 44.000 13.83 0.00 37.14 3.85
555 558 5.189934 ACCCTAATTCGATTCAGAAGAAGGT 59.810 40.000 13.83 0.00 37.14 3.50
556 559 5.675538 ACCCTAATTCGATTCAGAAGAAGG 58.324 41.667 0.00 10.93 37.14 3.46
557 560 6.422400 GCTACCCTAATTCGATTCAGAAGAAG 59.578 42.308 0.00 0.00 37.14 2.85
558 561 6.098409 AGCTACCCTAATTCGATTCAGAAGAA 59.902 38.462 0.00 0.00 38.31 2.52
559 562 5.598830 AGCTACCCTAATTCGATTCAGAAGA 59.401 40.000 0.00 0.00 33.19 2.87
571 574 8.562949 TTAGACCTTGATTAGCTACCCTAATT 57.437 34.615 0.00 0.00 44.72 1.40
572 575 8.562949 TTTAGACCTTGATTAGCTACCCTAAT 57.437 34.615 0.00 0.00 46.77 1.73
579 582 8.090788 AGGACAATTTAGACCTTGATTAGCTA 57.909 34.615 0.00 0.00 29.23 3.32
582 585 9.667107 TTGTAGGACAATTTAGACCTTGATTAG 57.333 33.333 0.00 0.00 32.34 1.73
586 589 7.074653 ACTTGTAGGACAATTTAGACCTTGA 57.925 36.000 0.00 0.00 37.48 3.02
628 631 7.618019 TGCAGAGGAAGTATTGGAGTATTAT 57.382 36.000 0.00 0.00 0.00 1.28
634 637 2.941720 GCTTGCAGAGGAAGTATTGGAG 59.058 50.000 0.42 0.00 0.00 3.86
635 638 2.573462 AGCTTGCAGAGGAAGTATTGGA 59.427 45.455 0.42 0.00 0.00 3.53
636 639 2.996631 AGCTTGCAGAGGAAGTATTGG 58.003 47.619 0.42 0.00 0.00 3.16
637 640 6.500684 TTTAAGCTTGCAGAGGAAGTATTG 57.499 37.500 9.86 0.00 0.00 1.90
732 912 2.507324 GCGTCTGGCCTTCTCGTC 60.507 66.667 3.32 0.00 34.80 4.20
890 1080 1.610554 GGTTGGATCGGAAGGGACGA 61.611 60.000 0.00 0.00 45.19 4.20
1278 1487 2.430582 GCGCGCAAATTGGCTTGA 60.431 55.556 29.10 0.00 0.00 3.02
1300 1509 3.320826 ACAAGCCAATCACAAGGTAAACC 59.679 43.478 0.00 0.00 0.00 3.27
1301 1510 4.037446 TGACAAGCCAATCACAAGGTAAAC 59.963 41.667 0.00 0.00 0.00 2.01
1421 1685 6.705825 ACAGGCACAATTGGAAATTTACTTTC 59.294 34.615 10.83 0.00 42.18 2.62
1422 1686 6.591001 ACAGGCACAATTGGAAATTTACTTT 58.409 32.000 10.83 0.00 0.00 2.66
1423 1687 6.173427 ACAGGCACAATTGGAAATTTACTT 57.827 33.333 10.83 0.00 0.00 2.24
1424 1688 5.806654 ACAGGCACAATTGGAAATTTACT 57.193 34.783 10.83 0.00 0.00 2.24
1426 1690 5.777732 AGGTACAGGCACAATTGGAAATTTA 59.222 36.000 10.83 0.00 0.00 1.40
1427 1691 4.592778 AGGTACAGGCACAATTGGAAATTT 59.407 37.500 10.83 0.00 0.00 1.82
1428 1692 4.159557 AGGTACAGGCACAATTGGAAATT 58.840 39.130 10.83 0.00 0.00 1.82
1429 1693 3.778265 AGGTACAGGCACAATTGGAAAT 58.222 40.909 10.83 0.00 0.00 2.17
1430 1694 3.237268 AGGTACAGGCACAATTGGAAA 57.763 42.857 10.83 0.00 0.00 3.13
1431 1695 2.969821 AGGTACAGGCACAATTGGAA 57.030 45.000 10.83 0.00 0.00 3.53
1432 1696 2.969821 AAGGTACAGGCACAATTGGA 57.030 45.000 10.83 0.00 0.00 3.53
1433 1697 4.335400 AAAAAGGTACAGGCACAATTGG 57.665 40.909 10.83 0.00 0.00 3.16
1459 1723 1.756375 GCTCATTGCTACGCCTGTCG 61.756 60.000 0.00 0.00 40.65 4.35
1460 1724 0.740868 TGCTCATTGCTACGCCTGTC 60.741 55.000 0.00 0.00 43.37 3.51
1489 1753 5.916661 TGACAATGTAAGACCTCTAGGAC 57.083 43.478 2.23 0.00 38.94 3.85
1492 1756 8.226819 TCTGTATGACAATGTAAGACCTCTAG 57.773 38.462 0.00 0.00 0.00 2.43
1498 1762 9.250624 GGAACTATCTGTATGACAATGTAAGAC 57.749 37.037 0.00 0.00 0.00 3.01
1522 1786 3.572255 GGCACAACAAATCCAAACTAGGA 59.428 43.478 0.00 0.00 43.01 2.94
1523 1787 3.320541 TGGCACAACAAATCCAAACTAGG 59.679 43.478 0.00 0.00 31.92 3.02
1524 1788 4.549458 CTGGCACAACAAATCCAAACTAG 58.451 43.478 0.00 0.00 38.70 2.57
1640 1904 3.754965 TGAAGGAACAATTGTCCAGAGG 58.245 45.455 21.54 0.00 0.00 3.69
1642 1906 4.081406 CCATGAAGGAACAATTGTCCAGA 58.919 43.478 21.54 10.37 41.22 3.86
1708 1972 5.988561 GGACACCAACATTTAGCATGAAAAA 59.011 36.000 0.00 0.00 0.00 1.94
1709 1973 5.069648 TGGACACCAACATTTAGCATGAAAA 59.930 36.000 0.00 0.00 0.00 2.29
1751 2015 2.521105 AGTAACTGTGAACGGGACAC 57.479 50.000 0.00 0.00 38.55 3.67
1752 2016 2.544277 CGAAGTAACTGTGAACGGGACA 60.544 50.000 0.00 0.00 0.00 4.02
1753 2017 2.056577 CGAAGTAACTGTGAACGGGAC 58.943 52.381 0.00 0.00 0.00 4.46
1758 2022 6.367969 ACCATACATTCGAAGTAACTGTGAAC 59.632 38.462 10.78 0.00 0.00 3.18
1768 2033 4.222145 ACCAGTACACCATACATTCGAAGT 59.778 41.667 3.35 4.82 0.00 3.01
1819 2084 5.765182 GGAGTGGTTAGCACTATTAATGCAT 59.235 40.000 17.36 0.00 45.92 3.96
1830 2095 2.789409 AATCAGGGAGTGGTTAGCAC 57.211 50.000 6.42 6.42 0.00 4.40
1917 2190 9.557338 GGATGATTTATATGTGTAGTCGACTAC 57.443 37.037 37.47 37.47 46.78 2.73
1982 2255 3.449018 AGGGCGAGATGGTGATATGATAC 59.551 47.826 0.00 0.00 0.00 2.24
2090 2378 3.899052 TCTGGGTGTTATAAAGGTCCG 57.101 47.619 0.00 0.00 0.00 4.79
2123 2411 1.069227 GTTACACTGCCTCTTTTGCGG 60.069 52.381 0.00 0.00 40.98 5.69
2125 2413 2.287608 GGTGTTACACTGCCTCTTTTGC 60.288 50.000 15.44 0.00 34.40 3.68
2148 2436 0.897401 TTGAATTGCATGGCACCCGA 60.897 50.000 0.00 0.00 38.71 5.14
2149 2437 0.037512 TTTGAATTGCATGGCACCCG 60.038 50.000 0.00 0.00 38.71 5.28
2150 2438 1.676615 CCTTTGAATTGCATGGCACCC 60.677 52.381 0.00 0.00 38.71 4.61
2236 2524 8.470002 GGAACCTACAAAGCATCAAGAATATTT 58.530 33.333 0.00 0.00 0.00 1.40
2451 3499 8.898761 TGCAGTTTCTTGATGTTTAGACTTTTA 58.101 29.630 0.00 0.00 0.00 1.52
2478 3548 3.602062 GGTCATTGCACGTTTTTATGACG 59.398 43.478 15.59 0.00 43.65 4.35
2492 3562 3.123959 GTGAATTGCACATTGGTCATTGC 59.876 43.478 0.00 0.00 46.91 3.56
2493 3563 4.914312 GTGAATTGCACATTGGTCATTG 57.086 40.909 0.00 0.00 46.91 2.82
2508 3609 4.677182 ACAAGCCAAAGGATAGGTGAATT 58.323 39.130 0.00 0.00 0.00 2.17
2520 3621 7.894376 ATGAAACATGAATAACAAGCCAAAG 57.106 32.000 0.00 0.00 0.00 2.77
2574 3675 5.069781 CACCTTCAAAGTCAACCCCAATTTA 59.930 40.000 0.00 0.00 0.00 1.40
2578 3679 2.024846 TCACCTTCAAAGTCAACCCCAA 60.025 45.455 0.00 0.00 0.00 4.12
2580 3681 2.230660 CTCACCTTCAAAGTCAACCCC 58.769 52.381 0.00 0.00 0.00 4.95
2620 3722 4.163649 GGTACTAAAATCCAGGCCAGTACT 59.836 45.833 19.42 0.00 38.77 2.73
2624 3726 3.199946 TCAGGTACTAAAATCCAGGCCAG 59.800 47.826 5.01 0.00 36.02 4.85
2690 3794 3.439857 ACTTGGCTAGATCCTGCAAAA 57.560 42.857 2.20 3.36 0.00 2.44
2694 3798 1.270571 GGCTACTTGGCTAGATCCTGC 60.271 57.143 2.20 0.00 38.32 4.85
2702 3806 1.281867 AGTGCATTGGCTACTTGGCTA 59.718 47.619 0.00 0.00 41.91 3.93
2703 3807 0.038744 AGTGCATTGGCTACTTGGCT 59.961 50.000 0.00 0.00 41.91 4.75
2704 3808 1.672881 CTAGTGCATTGGCTACTTGGC 59.327 52.381 0.00 0.00 41.91 4.52
2705 3809 3.266510 TCTAGTGCATTGGCTACTTGG 57.733 47.619 0.00 0.00 41.91 3.61
2706 3810 6.707608 TGAATATCTAGTGCATTGGCTACTTG 59.292 38.462 0.00 0.00 41.91 3.16
2707 3811 6.830912 TGAATATCTAGTGCATTGGCTACTT 58.169 36.000 0.00 0.00 41.91 2.24
2708 3812 6.425210 TGAATATCTAGTGCATTGGCTACT 57.575 37.500 0.00 0.00 41.91 2.57
2709 3813 7.412346 CGAATGAATATCTAGTGCATTGGCTAC 60.412 40.741 0.00 0.00 41.91 3.58
2756 3986 5.418524 TGCAAGCTGGAAAGCTAATAATTCA 59.581 36.000 0.00 0.00 45.54 2.57
2757 3987 5.894807 TGCAAGCTGGAAAGCTAATAATTC 58.105 37.500 0.00 0.00 45.54 2.17
2772 4002 5.761726 TGAAGTAATCCTGATATGCAAGCTG 59.238 40.000 0.00 0.00 0.00 4.24
2773 4003 5.933617 TGAAGTAATCCTGATATGCAAGCT 58.066 37.500 0.00 0.00 0.00 3.74
2812 4070 1.610522 GCACAAGGTCATGAAAGCAGT 59.389 47.619 0.00 0.00 0.00 4.40
2819 4077 4.225942 AGATTTCTAGGCACAAGGTCATGA 59.774 41.667 0.00 0.00 0.00 3.07
2831 4089 5.126067 TGCTGTCCAAATAGATTTCTAGGC 58.874 41.667 0.00 0.00 0.00 3.93
2893 4201 2.039216 TGCGAATTTCTGGTCCCTGTAA 59.961 45.455 0.00 0.00 0.00 2.41
2992 4300 3.572632 AATCATGGTCTCATCACCCTG 57.427 47.619 0.00 0.00 35.26 4.45
3042 4350 1.888436 TAGTGCTCCCAGGCTTCACG 61.888 60.000 0.00 0.00 33.28 4.35
3087 4395 0.385223 CACAAGAAAGCGCTGTGAGC 60.385 55.000 18.81 0.00 38.02 4.26
3279 4587 3.683340 GGTCTGATCCTTTCCGTACAAAC 59.317 47.826 0.00 0.00 0.00 2.93
3378 4686 4.996758 ACAACCTCAAATAAAATGCAAGCC 59.003 37.500 0.00 0.00 0.00 4.35
3394 4703 5.831997 AGACAACAGCAATAAAACAACCTC 58.168 37.500 0.00 0.00 0.00 3.85
3451 4760 5.863935 GTCATCAAAATTAGCAACACCTTCC 59.136 40.000 0.00 0.00 0.00 3.46
3535 4844 7.814642 TCTGAGCAAAGAAAATCTTCTCAATC 58.185 34.615 10.74 1.11 41.23 2.67
4021 5330 1.300931 GTCGCTGCAAGTCCAGTCA 60.301 57.895 0.00 0.00 35.30 3.41
4062 5371 2.979678 GGAATGAGGCCCCTAACTATGA 59.020 50.000 0.00 0.00 0.00 2.15
4063 5372 2.711009 TGGAATGAGGCCCCTAACTATG 59.289 50.000 0.00 0.00 0.00 2.23
4066 5375 1.681229 TTGGAATGAGGCCCCTAACT 58.319 50.000 0.00 0.00 0.00 2.24
4078 5387 1.733389 GCGGCACTCAACATTGGAATG 60.733 52.381 0.00 0.00 42.10 2.67
4081 5390 0.323302 TAGCGGCACTCAACATTGGA 59.677 50.000 1.45 0.00 0.00 3.53
4177 5486 3.777106 ACTGAATCTCCTGACTTGCAA 57.223 42.857 0.00 0.00 0.00 4.08
4186 5495 1.072331 ACCGCAACAACTGAATCTCCT 59.928 47.619 0.00 0.00 0.00 3.69
4250 5559 3.810743 GCCAACCTCACCTGACACTAATT 60.811 47.826 0.00 0.00 0.00 1.40
4256 5565 1.053835 TGAGCCAACCTCACCTGACA 61.054 55.000 0.00 0.00 45.44 3.58
4433 5742 7.147897 CGAACTGGCATATATATTGAGTAGGGA 60.148 40.741 0.00 0.00 0.00 4.20
4434 5743 6.980978 CGAACTGGCATATATATTGAGTAGGG 59.019 42.308 0.00 0.00 0.00 3.53
4435 5744 7.548097 ACGAACTGGCATATATATTGAGTAGG 58.452 38.462 0.00 0.00 0.00 3.18
4477 5786 9.888878 CAACATATGATCTTTGTATAAAGGCAG 57.111 33.333 10.38 3.28 42.81 4.85
4478 5787 8.352201 GCAACATATGATCTTTGTATAAAGGCA 58.648 33.333 10.38 10.40 42.81 4.75
4479 5788 7.535258 CGCAACATATGATCTTTGTATAAAGGC 59.465 37.037 10.38 5.69 42.81 4.35
4481 5790 7.535258 GCCGCAACATATGATCTTTGTATAAAG 59.465 37.037 10.38 5.65 43.72 1.85
4500 5816 4.250431 ACAGCACAACGCCGCAAC 62.250 61.111 0.00 0.00 44.04 4.17
4504 5820 1.573829 ATAACCACAGCACAACGCCG 61.574 55.000 0.00 0.00 44.04 6.46
4546 5873 4.837896 AACTCTTCTAAAAGCAACCTGC 57.162 40.909 0.00 0.00 45.46 4.85
4560 5887 4.698575 AGGTCTCTGTCACAAAACTCTTC 58.301 43.478 0.00 0.00 0.00 2.87
4583 5910 9.136952 CAAATCCTCTTCTTTTCTTAATGCAAG 57.863 33.333 0.00 0.00 35.38 4.01
4584 5911 8.641541 ACAAATCCTCTTCTTTTCTTAATGCAA 58.358 29.630 0.00 0.00 0.00 4.08
4585 5912 8.181904 ACAAATCCTCTTCTTTTCTTAATGCA 57.818 30.769 0.00 0.00 0.00 3.96
4629 5956 2.100631 CGCCTTGACTAACGCCCTG 61.101 63.158 0.00 0.00 0.00 4.45
4658 5985 7.039223 TCCTAGGTTATTCAAAGTTTCGAGAGT 60.039 37.037 9.08 0.00 0.00 3.24
4664 5991 8.847196 ACAAAGTCCTAGGTTATTCAAAGTTTC 58.153 33.333 9.08 0.00 0.00 2.78
4715 6047 8.365647 GGTTAATATTCTAATTCCTCTCGACCA 58.634 37.037 0.00 0.00 0.00 4.02
4736 6068 8.850156 CATTCTTCCTTTCTTTCAAGAGGTTAA 58.150 33.333 0.00 0.00 36.22 2.01
4737 6069 7.040409 GCATTCTTCCTTTCTTTCAAGAGGTTA 60.040 37.037 0.00 0.00 36.22 2.85
4755 6087 9.517361 CAAAATACGTTATATCGAGCATTCTTC 57.483 33.333 10.08 0.00 34.70 2.87
4757 6089 8.812147 TCAAAATACGTTATATCGAGCATTCT 57.188 30.769 10.08 0.00 34.70 2.40
4758 6090 9.858247 TTTCAAAATACGTTATATCGAGCATTC 57.142 29.630 10.08 0.00 34.70 2.67
4760 6092 9.811655 CATTTCAAAATACGTTATATCGAGCAT 57.188 29.630 10.08 0.00 34.70 3.79
4761 6093 8.822855 ACATTTCAAAATACGTTATATCGAGCA 58.177 29.630 10.08 0.00 34.70 4.26
4771 6103 8.967218 CAGAATTGTGACATTTCAAAATACGTT 58.033 29.630 18.79 0.00 38.55 3.99
4772 6104 8.349245 TCAGAATTGTGACATTTCAAAATACGT 58.651 29.630 18.79 0.00 38.55 3.57
4773 6105 8.629986 GTCAGAATTGTGACATTTCAAAATACG 58.370 33.333 26.12 0.00 45.34 3.06
4806 6180 6.420030 ACGAAGTTTTGTGATGTACACGGAA 61.420 40.000 0.00 0.00 46.75 4.30
4808 6182 3.246699 ACGAAGTTTTGTGATGTACACGG 59.753 43.478 0.00 0.00 46.75 4.94
4809 6183 4.446857 ACGAAGTTTTGTGATGTACACG 57.553 40.909 0.00 0.00 46.75 4.49
4813 6187 2.349060 GCGCACGAAGTTTTGTGATGTA 60.349 45.455 14.85 0.00 43.74 2.29
4814 6188 1.596954 GCGCACGAAGTTTTGTGATGT 60.597 47.619 14.85 0.00 43.74 3.06
4815 6189 1.044725 GCGCACGAAGTTTTGTGATG 58.955 50.000 14.85 8.04 43.74 3.07
4817 6191 0.247894 GTGCGCACGAAGTTTTGTGA 60.248 50.000 26.77 0.00 43.74 3.58
4818 6192 0.522286 TGTGCGCACGAAGTTTTGTG 60.522 50.000 33.22 7.70 41.61 3.33
4831 6283 2.009774 ACATATCAACCTTCTGTGCGC 58.990 47.619 0.00 0.00 0.00 6.09
4832 6284 3.663464 CACATATCAACCTTCTGTGCG 57.337 47.619 0.00 0.00 31.81 5.34
4838 6290 2.024414 GGGGTGCACATATCAACCTTC 58.976 52.381 20.43 0.00 41.04 3.46
4840 6292 0.998928 TGGGGTGCACATATCAACCT 59.001 50.000 20.43 0.00 41.04 3.50
4841 6293 1.064758 TCTGGGGTGCACATATCAACC 60.065 52.381 20.43 8.37 40.54 3.77
4842 6294 2.418368 TCTGGGGTGCACATATCAAC 57.582 50.000 20.43 0.00 0.00 3.18
4844 6296 3.668141 AATTCTGGGGTGCACATATCA 57.332 42.857 20.43 9.55 0.00 2.15
4845 6297 3.068590 CCAAATTCTGGGGTGCACATATC 59.931 47.826 20.43 0.00 42.17 1.63
4846 6298 3.033184 CCAAATTCTGGGGTGCACATAT 58.967 45.455 20.43 0.00 42.17 1.78
4849 6301 0.187117 TCCAAATTCTGGGGTGCACA 59.813 50.000 20.43 0.00 46.44 4.57
4852 6304 3.701205 AAATTCCAAATTCTGGGGTGC 57.299 42.857 6.77 0.00 46.44 5.01
4893 6345 0.891904 GCTCCTGCCACCGGTAAAAA 60.892 55.000 6.87 0.00 0.00 1.94
4894 6346 1.302993 GCTCCTGCCACCGGTAAAA 60.303 57.895 6.87 0.00 0.00 1.52
4895 6347 1.847798 ATGCTCCTGCCACCGGTAAA 61.848 55.000 6.87 0.00 38.71 2.01
4896 6348 0.978667 TATGCTCCTGCCACCGGTAA 60.979 55.000 6.87 0.00 38.71 2.85
4897 6349 0.762842 ATATGCTCCTGCCACCGGTA 60.763 55.000 6.87 0.00 38.71 4.02
4898 6350 2.072487 ATATGCTCCTGCCACCGGT 61.072 57.895 0.00 0.00 38.71 5.28
4899 6351 1.598962 CATATGCTCCTGCCACCGG 60.599 63.158 0.00 0.00 38.71 5.28
4900 6352 2.256591 GCATATGCTCCTGCCACCG 61.257 63.158 20.64 0.00 38.71 4.94
4901 6353 3.755434 GCATATGCTCCTGCCACC 58.245 61.111 20.64 0.00 38.71 4.61
4911 6363 1.971481 TGACACATGGGAGCATATGC 58.029 50.000 20.36 20.36 42.49 3.14
4912 6364 4.340097 ACATTTGACACATGGGAGCATATG 59.660 41.667 0.00 12.31 0.00 1.78
4913 6365 4.539726 ACATTTGACACATGGGAGCATAT 58.460 39.130 0.00 0.00 0.00 1.78
4914 6366 3.947196 GACATTTGACACATGGGAGCATA 59.053 43.478 0.00 0.00 0.00 3.14
4915 6367 2.756760 GACATTTGACACATGGGAGCAT 59.243 45.455 0.00 0.00 0.00 3.79
4916 6368 2.161855 GACATTTGACACATGGGAGCA 58.838 47.619 0.00 0.00 0.00 4.26
4917 6369 2.161855 TGACATTTGACACATGGGAGC 58.838 47.619 0.00 0.00 0.00 4.70
4918 6370 4.279169 ACTTTGACATTTGACACATGGGAG 59.721 41.667 0.00 0.00 0.00 4.30
4919 6371 4.037803 CACTTTGACATTTGACACATGGGA 59.962 41.667 0.00 0.00 0.00 4.37
4920 6372 4.037803 TCACTTTGACATTTGACACATGGG 59.962 41.667 6.54 0.00 0.00 4.00
4921 6373 5.185668 TCACTTTGACATTTGACACATGG 57.814 39.130 6.54 0.00 0.00 3.66
4922 6374 7.703298 AATTCACTTTGACATTTGACACATG 57.297 32.000 0.00 0.00 0.00 3.21
4923 6375 7.980662 TGAAATTCACTTTGACATTTGACACAT 59.019 29.630 0.00 0.00 0.00 3.21
4924 6376 7.318893 TGAAATTCACTTTGACATTTGACACA 58.681 30.769 0.00 0.00 0.00 3.72
4925 6377 7.754069 TGAAATTCACTTTGACATTTGACAC 57.246 32.000 0.00 0.00 0.00 3.67
4926 6378 8.945481 ATTGAAATTCACTTTGACATTTGACA 57.055 26.923 0.00 0.00 0.00 3.58
4957 6409 9.995003 TTGCAGATTGGTTTTATAAGAACATTT 57.005 25.926 0.00 0.00 0.00 2.32
4960 6412 7.375053 GGTTGCAGATTGGTTTTATAAGAACA 58.625 34.615 10.59 2.14 0.00 3.18
4964 6416 6.152661 TGAGGGTTGCAGATTGGTTTTATAAG 59.847 38.462 0.00 0.00 0.00 1.73
4965 6417 6.013379 TGAGGGTTGCAGATTGGTTTTATAA 58.987 36.000 0.00 0.00 0.00 0.98
4967 6419 4.415596 TGAGGGTTGCAGATTGGTTTTAT 58.584 39.130 0.00 0.00 0.00 1.40
4968 6420 3.838565 TGAGGGTTGCAGATTGGTTTTA 58.161 40.909 0.00 0.00 0.00 1.52
4969 6421 2.676748 TGAGGGTTGCAGATTGGTTTT 58.323 42.857 0.00 0.00 0.00 2.43
4971 6423 1.963515 GTTGAGGGTTGCAGATTGGTT 59.036 47.619 0.00 0.00 0.00 3.67
4972 6424 1.620822 GTTGAGGGTTGCAGATTGGT 58.379 50.000 0.00 0.00 0.00 3.67
4974 6426 0.890683 GGGTTGAGGGTTGCAGATTG 59.109 55.000 0.00 0.00 0.00 2.67
4975 6427 0.779997 AGGGTTGAGGGTTGCAGATT 59.220 50.000 0.00 0.00 0.00 2.40
4976 6428 0.038744 CAGGGTTGAGGGTTGCAGAT 59.961 55.000 0.00 0.00 0.00 2.90
4977 6429 1.059584 TCAGGGTTGAGGGTTGCAGA 61.060 55.000 0.00 0.00 0.00 4.26
4978 6430 0.178992 TTCAGGGTTGAGGGTTGCAG 60.179 55.000 0.00 0.00 34.15 4.41
4979 6431 0.482446 ATTCAGGGTTGAGGGTTGCA 59.518 50.000 0.00 0.00 34.15 4.08
4980 6432 1.177401 GATTCAGGGTTGAGGGTTGC 58.823 55.000 0.00 0.00 34.15 4.17
4981 6433 1.355720 AGGATTCAGGGTTGAGGGTTG 59.644 52.381 0.00 0.00 34.15 3.77
4982 6434 1.760405 AGGATTCAGGGTTGAGGGTT 58.240 50.000 0.00 0.00 34.15 4.11
4983 6435 1.760405 AAGGATTCAGGGTTGAGGGT 58.240 50.000 0.00 0.00 34.15 4.34
4984 6436 2.907458 AAAGGATTCAGGGTTGAGGG 57.093 50.000 0.00 0.00 34.15 4.30
4986 6438 4.039603 AGGAAAAGGATTCAGGGTTGAG 57.960 45.455 0.00 0.00 34.15 3.02
4988 6440 3.897505 ACAAGGAAAAGGATTCAGGGTTG 59.102 43.478 0.00 0.00 0.00 3.77
4990 6442 3.903530 ACAAGGAAAAGGATTCAGGGT 57.096 42.857 0.00 0.00 0.00 4.34
4991 6443 3.191371 CGAACAAGGAAAAGGATTCAGGG 59.809 47.826 0.00 0.00 0.00 4.45
4992 6444 3.191371 CCGAACAAGGAAAAGGATTCAGG 59.809 47.826 0.00 0.00 0.00 3.86
4993 6445 4.072131 TCCGAACAAGGAAAAGGATTCAG 58.928 43.478 0.00 0.00 37.36 3.02
4994 6446 4.093472 TCCGAACAAGGAAAAGGATTCA 57.907 40.909 0.00 0.00 37.36 2.57
5040 6590 6.936279 TCTCAATTGGTCTTAGTTAGTCTGG 58.064 40.000 5.42 0.00 0.00 3.86
5099 6653 8.034804 GCATATGTTTGGTAAAAGGACAATCTT 58.965 33.333 4.29 0.00 0.00 2.40
5100 6654 7.178274 TGCATATGTTTGGTAAAAGGACAATCT 59.822 33.333 4.29 0.00 0.00 2.40
5101 6655 7.319646 TGCATATGTTTGGTAAAAGGACAATC 58.680 34.615 4.29 0.00 0.00 2.67
5102 6656 7.238486 TGCATATGTTTGGTAAAAGGACAAT 57.762 32.000 4.29 0.00 0.00 2.71
5104 6658 6.656632 TTGCATATGTTTGGTAAAAGGACA 57.343 33.333 4.29 0.00 0.00 4.02
5105 6659 7.816995 TCATTTGCATATGTTTGGTAAAAGGAC 59.183 33.333 15.51 0.00 0.00 3.85
5106 6660 7.901029 TCATTTGCATATGTTTGGTAAAAGGA 58.099 30.769 15.51 0.00 0.00 3.36
5107 6661 8.545229 TTCATTTGCATATGTTTGGTAAAAGG 57.455 30.769 15.51 0.00 0.00 3.11
5109 6663 8.502387 GCTTTCATTTGCATATGTTTGGTAAAA 58.498 29.630 15.51 7.20 0.00 1.52
5176 6746 2.220653 TCAAAGAATGAGGGGCAAGG 57.779 50.000 0.00 0.00 33.04 3.61


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

AutoCloner maintained by Alex Coulton.