Multiple sequence alignment - TraesCS4A01G206400

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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 TraesCS4A01G206400 chr4A 100.000 4550 0 0 1 4550 499353369 499357918 0.000000e+00 8403.0
1 TraesCS4A01G206400 chr4A 100.000 62 0 0 580 641 499353886 499353947 1.030000e-21 115.0
2 TraesCS4A01G206400 chr4A 100.000 62 0 0 518 579 499353948 499354009 1.030000e-21 115.0
3 TraesCS4A01G206400 chr4D 92.926 3308 159 40 580 3853 85590515 85593781 0.000000e+00 4743.0
4 TraesCS4A01G206400 chr4D 84.424 443 55 12 4113 4550 475131804 475131371 1.510000e-114 424.0
5 TraesCS4A01G206400 chr4D 90.520 327 17 4 1 313 85589913 85590239 1.960000e-113 420.0
6 TraesCS4A01G206400 chr4D 91.923 260 20 1 320 579 85590317 85590575 3.350000e-96 363.0
7 TraesCS4A01G206400 chr4D 83.810 105 16 1 3852 3955 108913339 108913235 1.040000e-16 99.0
8 TraesCS4A01G206400 chr4D 83.908 87 11 3 3869 3953 368508360 368508275 3.770000e-11 80.5
9 TraesCS4A01G206400 chr4B 88.905 1406 96 31 942 2326 122563128 122564494 0.000000e+00 1677.0
10 TraesCS4A01G206400 chr4B 95.960 792 25 2 2321 3105 122564519 122565310 0.000000e+00 1279.0
11 TraesCS4A01G206400 chr4B 91.460 644 38 12 3220 3859 122565394 122566024 0.000000e+00 869.0
12 TraesCS4A01G206400 chr4B 96.337 273 7 3 580 852 122562661 122562930 3.230000e-121 446.0
13 TraesCS4A01G206400 chr4B 96.744 215 7 0 362 576 122562505 122562719 4.330000e-95 359.0
14 TraesCS4A01G206400 chr4B 88.809 277 17 9 1 263 122561971 122562247 1.220000e-85 327.0
15 TraesCS4A01G206400 chr7A 81.063 734 84 37 3865 4550 704326044 704325318 6.700000e-148 534.0
16 TraesCS4A01G206400 chr7A 80.822 730 85 36 3865 4547 69885038 69885759 5.220000e-144 521.0
17 TraesCS4A01G206400 chr7A 79.561 729 76 46 3864 4547 510896065 510896765 1.930000e-123 453.0
18 TraesCS4A01G206400 chr3B 80.000 740 91 34 3865 4550 812601665 812600929 1.140000e-135 494.0
19 TraesCS4A01G206400 chr6D 91.389 360 24 3 4191 4550 328740995 328740643 1.900000e-133 486.0
20 TraesCS4A01G206400 chr6D 83.146 445 60 12 4113 4550 4788995 4789431 4.270000e-105 392.0
21 TraesCS4A01G206400 chr6D 91.667 144 12 0 3865 4008 328744059 328743916 2.780000e-47 200.0
22 TraesCS4A01G206400 chr6D 92.233 103 8 0 4009 4111 328741481 328741379 3.670000e-31 147.0
23 TraesCS4A01G206400 chr5D 86.783 401 46 7 4152 4550 481124362 481123967 1.500000e-119 440.0
24 TraesCS4A01G206400 chr5D 82.183 449 51 19 4113 4550 70154169 70153739 4.330000e-95 359.0
25 TraesCS4A01G206400 chr5D 81.651 218 21 10 3857 4056 481127427 481127211 3.640000e-36 163.0
26 TraesCS4A01G206400 chr2A 82.727 440 57 14 4115 4544 35944352 35944782 1.550000e-99 374.0
27 TraesCS4A01G206400 chr1A 82.727 440 55 16 4115 4544 70917154 70917582 5.560000e-99 372.0
28 TraesCS4A01G206400 chr3A 83.122 237 36 4 3268 3502 11941535 11941769 3.570000e-51 213.0
29 TraesCS4A01G206400 chr3D 80.795 151 27 2 3852 4001 91808390 91808539 2.880000e-22 117.0
30 TraesCS4A01G206400 chr5B 90.000 80 8 0 3867 3946 9444220 9444141 2.240000e-18 104.0
31 TraesCS4A01G206400 chr5B 84.783 92 10 3 3865 3953 488213740 488213830 6.270000e-14 89.8
32 TraesCS4A01G206400 chr6A 82.243 107 14 5 3850 3955 616233222 616233120 2.250000e-13 87.9


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 TraesCS4A01G206400 chr4A 499353369 499357918 4549 False 8403.000000 8403 100.000000 1 4550 1 chr4A.!!$F1 4549
1 TraesCS4A01G206400 chr4D 85589913 85593781 3868 False 1842.000000 4743 91.789667 1 3853 3 chr4D.!!$F1 3852
2 TraesCS4A01G206400 chr4B 122561971 122566024 4053 False 826.166667 1677 93.035833 1 3859 6 chr4B.!!$F1 3858
3 TraesCS4A01G206400 chr7A 704325318 704326044 726 True 534.000000 534 81.063000 3865 4550 1 chr7A.!!$R1 685
4 TraesCS4A01G206400 chr7A 69885038 69885759 721 False 521.000000 521 80.822000 3865 4547 1 chr7A.!!$F1 682
5 TraesCS4A01G206400 chr7A 510896065 510896765 700 False 453.000000 453 79.561000 3864 4547 1 chr7A.!!$F2 683
6 TraesCS4A01G206400 chr3B 812600929 812601665 736 True 494.000000 494 80.000000 3865 4550 1 chr3B.!!$R1 685
7 TraesCS4A01G206400 chr6D 328740643 328744059 3416 True 277.666667 486 91.763000 3865 4550 3 chr6D.!!$R1 685
8 TraesCS4A01G206400 chr5D 481123967 481127427 3460 True 301.500000 440 84.217000 3857 4550 2 chr5D.!!$R2 693

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
354 557 0.172352 GGAGAAGCAGGACTCTGTCG 59.828 60.0 0.00 0.00 42.78 4.35 F
360 563 0.319900 GCAGGACTCTGTCGCAGAAA 60.320 55.0 10.12 0.00 40.18 2.52 F
616 819 0.527565 AAATGCACCCACAGAATCGC 59.472 50.0 0.00 0.00 0.00 4.58 F
617 820 0.608856 AATGCACCCACAGAATCGCA 60.609 50.0 0.00 0.00 0.00 5.10 F
622 825 0.670546 ACCCACAGAATCGCAGAACG 60.671 55.0 0.00 0.00 43.58 3.95 F
624 827 0.670546 CCACAGAATCGCAGAACGGT 60.671 55.0 0.00 0.00 43.58 4.83 F
1735 2080 0.729116 CATGTGTCCGGCTTAAGCTG 59.271 55.0 26.53 26.53 46.63 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2043 2388 0.764369 AGCCTGGTGGAGTGACAAGA 60.764 55.000 0.00 0.00 34.57 3.02 R
2103 2448 1.540267 TCAACAGTCGACTGGTAGAGC 59.460 52.381 40.23 3.04 43.10 4.09 R
2445 2840 0.320683 CTTGGCACCACGACTCATCA 60.321 55.000 0.00 0.00 0.00 3.07 R
2454 2849 1.021390 CATCGAGACCTTGGCACCAC 61.021 60.000 0.00 0.00 0.00 4.16 R
2741 3142 6.263842 ACATATCCATTAGAATGTTGTGCCTG 59.736 38.462 1.78 0.00 34.60 4.85 R
2909 3310 3.559655 CCTCAAACATGACGTTGTTCTGA 59.440 43.478 6.11 10.37 38.85 3.27 R
3999 4423 0.251077 ACCTCGACCAGTAACGACCT 60.251 55.000 0.00 0.00 34.82 3.85 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
91 92 5.163364 TGCCAAATTCCTTTTCTGCTTTACA 60.163 36.000 0.00 0.00 0.00 2.41
137 148 9.585369 TCTGGAAAATATGCATATTTGTATCCA 57.415 29.630 35.21 35.21 40.88 3.41
176 187 0.685097 TAGCCAGTGTGACACTTCCC 59.315 55.000 16.79 7.18 42.59 3.97
201 212 8.562892 CCAGTTCCTACTAATGCATTTTGATAG 58.437 37.037 18.75 10.85 31.96 2.08
295 310 5.910355 TCATATCAAGATTCATGGGGTCA 57.090 39.130 0.00 0.00 0.00 4.02
302 317 2.176364 AGATTCATGGGGTCAAGGGATG 59.824 50.000 0.00 0.00 0.00 3.51
306 321 2.711009 TCATGGGGTCAAGGGATGATAC 59.289 50.000 0.00 0.00 40.97 2.24
308 323 2.567862 TGGGGTCAAGGGATGATACAA 58.432 47.619 0.00 0.00 40.97 2.41
309 324 2.509548 TGGGGTCAAGGGATGATACAAG 59.490 50.000 0.00 0.00 40.97 3.16
311 326 3.395941 GGGGTCAAGGGATGATACAAGAT 59.604 47.826 0.00 0.00 40.97 2.40
312 327 4.141158 GGGGTCAAGGGATGATACAAGATT 60.141 45.833 0.00 0.00 40.97 2.40
313 328 4.823989 GGGTCAAGGGATGATACAAGATTG 59.176 45.833 0.00 0.00 40.97 2.67
314 329 5.440610 GGTCAAGGGATGATACAAGATTGT 58.559 41.667 3.37 3.37 40.97 2.71
315 330 5.888161 GGTCAAGGGATGATACAAGATTGTT 59.112 40.000 3.14 0.00 40.97 2.83
316 331 7.054124 GGTCAAGGGATGATACAAGATTGTTA 58.946 38.462 3.14 0.00 40.97 2.41
317 332 7.012421 GGTCAAGGGATGATACAAGATTGTTAC 59.988 40.741 3.14 0.00 40.97 2.50
318 333 7.552687 GTCAAGGGATGATACAAGATTGTTACA 59.447 37.037 3.14 5.44 40.97 2.41
345 548 1.676967 GGGCACAAGGAGAAGCAGG 60.677 63.158 0.00 0.00 0.00 4.85
354 557 0.172352 GGAGAAGCAGGACTCTGTCG 59.828 60.000 0.00 0.00 42.78 4.35
355 558 0.457681 GAGAAGCAGGACTCTGTCGC 60.458 60.000 0.00 0.00 42.78 5.19
359 562 1.181741 AGCAGGACTCTGTCGCAGAA 61.182 55.000 10.12 0.00 40.18 3.02
360 563 0.319900 GCAGGACTCTGTCGCAGAAA 60.320 55.000 10.12 0.00 40.18 2.52
364 567 1.269831 GGACTCTGTCGCAGAAACAGT 60.270 52.381 10.12 5.46 43.68 3.55
432 635 5.355350 CACCAAAAGACTGACTGAGAAAACT 59.645 40.000 0.00 0.00 0.00 2.66
577 780 2.409870 CGGTTCATCAGCCAAGGCC 61.410 63.158 7.62 0.00 43.17 5.19
578 781 1.304381 GGTTCATCAGCCAAGGCCA 60.304 57.895 5.01 0.00 43.17 5.36
579 782 1.318158 GGTTCATCAGCCAAGGCCAG 61.318 60.000 5.01 0.84 43.17 4.85
580 783 1.000521 TTCATCAGCCAAGGCCAGG 60.001 57.895 5.01 7.88 43.17 4.45
581 784 2.441532 CATCAGCCAAGGCCAGGG 60.442 66.667 15.27 11.95 43.17 4.45
586 789 4.189580 GCCAAGGCCAGGGCGATA 62.190 66.667 20.29 0.00 40.93 2.92
587 790 2.595095 CCAAGGCCAGGGCGATAA 59.405 61.111 5.01 0.00 43.06 1.75
588 791 1.823899 CCAAGGCCAGGGCGATAAC 60.824 63.158 5.01 0.00 43.06 1.89
589 792 1.823899 CAAGGCCAGGGCGATAACC 60.824 63.158 5.01 0.00 43.06 2.85
598 801 3.562397 GGCGATAACCCTTGGTGAA 57.438 52.632 0.00 0.00 35.34 3.18
599 802 1.828979 GGCGATAACCCTTGGTGAAA 58.171 50.000 0.00 0.00 35.34 2.69
600 803 2.375146 GGCGATAACCCTTGGTGAAAT 58.625 47.619 0.00 0.00 35.34 2.17
601 804 2.099098 GGCGATAACCCTTGGTGAAATG 59.901 50.000 0.00 0.00 35.34 2.32
602 805 2.479560 GCGATAACCCTTGGTGAAATGC 60.480 50.000 0.00 0.00 35.34 3.56
603 806 2.752354 CGATAACCCTTGGTGAAATGCA 59.248 45.455 0.00 0.00 35.34 3.96
604 807 3.427503 CGATAACCCTTGGTGAAATGCAC 60.428 47.826 0.00 0.00 46.98 4.57
614 817 3.221964 GTGAAATGCACCCACAGAATC 57.778 47.619 9.30 0.00 41.78 2.52
615 818 1.811965 TGAAATGCACCCACAGAATCG 59.188 47.619 0.00 0.00 0.00 3.34
616 819 0.527565 AAATGCACCCACAGAATCGC 59.472 50.000 0.00 0.00 0.00 4.58
617 820 0.608856 AATGCACCCACAGAATCGCA 60.609 50.000 0.00 0.00 0.00 5.10
618 821 1.028330 ATGCACCCACAGAATCGCAG 61.028 55.000 0.00 0.00 32.10 5.18
619 822 1.375908 GCACCCACAGAATCGCAGA 60.376 57.895 0.00 0.00 45.75 4.26
620 823 0.955428 GCACCCACAGAATCGCAGAA 60.955 55.000 0.00 0.00 43.58 3.02
621 824 0.798776 CACCCACAGAATCGCAGAAC 59.201 55.000 0.00 0.00 43.58 3.01
622 825 0.670546 ACCCACAGAATCGCAGAACG 60.671 55.000 0.00 0.00 43.58 3.95
623 826 1.361668 CCCACAGAATCGCAGAACGG 61.362 60.000 0.00 0.00 43.58 4.44
624 827 0.670546 CCACAGAATCGCAGAACGGT 60.671 55.000 0.00 0.00 43.58 4.83
630 833 2.093306 AATCGCAGAACGGTTCATCA 57.907 45.000 21.86 4.27 42.96 3.07
631 834 1.645034 ATCGCAGAACGGTTCATCAG 58.355 50.000 21.86 10.57 43.58 2.90
632 835 1.014044 TCGCAGAACGGTTCATCAGC 61.014 55.000 21.86 17.19 43.89 4.26
633 836 1.796796 GCAGAACGGTTCATCAGCC 59.203 57.895 21.86 1.15 0.00 4.85
634 837 0.955428 GCAGAACGGTTCATCAGCCA 60.955 55.000 21.86 0.00 0.00 4.75
635 838 1.522668 CAGAACGGTTCATCAGCCAA 58.477 50.000 21.86 0.00 0.00 4.52
636 839 1.466167 CAGAACGGTTCATCAGCCAAG 59.534 52.381 21.86 0.00 0.00 3.61
637 840 0.804989 GAACGGTTCATCAGCCAAGG 59.195 55.000 15.70 0.00 0.00 3.61
638 841 1.244019 AACGGTTCATCAGCCAAGGC 61.244 55.000 2.02 2.02 42.33 4.35
639 842 2.409870 CGGTTCATCAGCCAAGGCC 61.410 63.158 7.62 0.00 43.17 5.19
640 843 1.304381 GGTTCATCAGCCAAGGCCA 60.304 57.895 5.01 0.00 43.17 5.36
701 904 3.959609 GCATAGCGCAAACAAGAAAAG 57.040 42.857 11.47 0.00 41.79 2.27
705 908 5.051106 GCATAGCGCAAACAAGAAAAGAAAA 60.051 36.000 11.47 0.00 41.79 2.29
877 1080 2.352651 CACAACTCATATCCCTTGTGCG 59.647 50.000 0.00 0.00 37.69 5.34
953 1264 2.610433 GAAAGGCTGCAATTGTAAGGC 58.390 47.619 21.49 21.49 36.79 4.35
989 1300 0.907486 TAGCACCTGATCTGCTTGCT 59.093 50.000 22.16 22.16 42.54 3.91
1211 1522 4.916983 ATGCATATGCGTGTATTGGTTT 57.083 36.364 21.52 0.00 45.83 3.27
1212 1523 4.026293 TGCATATGCGTGTATTGGTTTG 57.974 40.909 22.21 0.00 45.83 2.93
1213 1524 3.691609 TGCATATGCGTGTATTGGTTTGA 59.308 39.130 22.21 0.00 45.83 2.69
1214 1525 4.337836 TGCATATGCGTGTATTGGTTTGAT 59.662 37.500 22.21 0.00 45.83 2.57
1215 1526 4.911610 GCATATGCGTGTATTGGTTTGATC 59.088 41.667 12.82 0.00 0.00 2.92
1216 1527 5.451908 CATATGCGTGTATTGGTTTGATCC 58.548 41.667 0.00 0.00 0.00 3.36
1238 1549 1.985159 TGATGGGCAGTAACTTCTGGT 59.015 47.619 0.00 0.00 36.12 4.00
1304 1626 8.372459 TGTATTGTCAATACAGAAACTACCAGT 58.628 33.333 27.25 0.00 46.43 4.00
1310 1632 9.431887 GTCAATACAGAAACTACCAGTGATAAA 57.568 33.333 0.00 0.00 0.00 1.40
1353 1682 3.174375 CGAACAGTTAACCTAGTACCGC 58.826 50.000 0.88 0.00 0.00 5.68
1366 1695 5.421374 ACCTAGTACCGCTTATCATAATCCC 59.579 44.000 0.00 0.00 0.00 3.85
1369 1698 6.038997 AGTACCGCTTATCATAATCCCTTC 57.961 41.667 0.00 0.00 0.00 3.46
1373 1702 4.556233 CGCTTATCATAATCCCTTCGACA 58.444 43.478 0.00 0.00 0.00 4.35
1380 1709 5.769367 TCATAATCCCTTCGACATAAGACG 58.231 41.667 0.00 0.00 0.00 4.18
1381 1710 3.454371 AATCCCTTCGACATAAGACGG 57.546 47.619 0.00 0.00 33.79 4.79
1393 1722 5.607119 ACATAAGACGGATGTTTTGTCAC 57.393 39.130 0.00 0.00 33.70 3.67
1406 1736 3.624326 TTTGTCACGCAGAGGAAATTG 57.376 42.857 0.00 0.00 0.00 2.32
1425 1755 3.096489 TGTTTGGCTGCTTTTGATCAC 57.904 42.857 0.00 0.00 0.00 3.06
1443 1773 7.239763 TGATCACACCAAAATCACTAGTCTA 57.760 36.000 0.00 0.00 0.00 2.59
1447 1777 8.322906 TCACACCAAAATCACTAGTCTAAATG 57.677 34.615 0.00 0.00 0.00 2.32
1453 1783 9.778993 CCAAAATCACTAGTCTAAATGAACATG 57.221 33.333 0.00 0.00 0.00 3.21
1470 1800 7.967771 TGAACATGCATAACATATGTTTTCG 57.032 32.000 25.31 14.90 43.03 3.46
1505 1849 9.485206 TTGGTACAGTAACTTTTCTATCTTCAC 57.515 33.333 0.00 0.00 42.39 3.18
1509 1853 5.637810 CAGTAACTTTTCTATCTTCACCGCA 59.362 40.000 0.00 0.00 0.00 5.69
1512 1856 1.640428 TTTCTATCTTCACCGCAGCG 58.360 50.000 8.18 8.18 0.00 5.18
1584 1928 7.380870 TGTGAAAATCCAAACATAAACGTGATG 59.619 33.333 8.73 8.73 0.00 3.07
1592 1936 6.359617 CCAAACATAAACGTGATGTGTTTCTC 59.640 38.462 19.60 0.00 40.02 2.87
1622 1966 2.946564 TCTGCAGTAAGACATGACACG 58.053 47.619 14.67 0.00 0.00 4.49
1633 1978 2.676342 GACATGACACGGGTTAATCACC 59.324 50.000 0.00 0.00 46.46 4.02
1649 1994 7.871463 GGTTAATCACCACTAGCTTAACGATAT 59.129 37.037 0.00 0.00 46.42 1.63
1725 2070 3.913548 TTGTTTGAATCCATGTGTCCG 57.086 42.857 0.00 0.00 0.00 4.79
1735 2080 0.729116 CATGTGTCCGGCTTAAGCTG 59.271 55.000 26.53 26.53 46.63 4.24
1773 2118 9.349713 TGAAGGTTCATAAGTCATAACAAAACT 57.650 29.630 0.00 0.00 31.01 2.66
1852 2197 6.665465 ACAGTAAAATTTCTACCAAACGAGC 58.335 36.000 0.00 0.00 0.00 5.03
1857 2202 4.766404 ATTTCTACCAAACGAGCAAAGG 57.234 40.909 0.00 0.00 0.00 3.11
1866 2211 2.969443 ACGAGCAAAGGTTTCATTCG 57.031 45.000 0.00 0.00 0.00 3.34
1868 2213 1.535462 CGAGCAAAGGTTTCATTCGGT 59.465 47.619 0.00 0.00 0.00 4.69
1869 2214 2.031157 CGAGCAAAGGTTTCATTCGGTT 60.031 45.455 0.00 0.00 0.00 4.44
1870 2215 3.187637 CGAGCAAAGGTTTCATTCGGTTA 59.812 43.478 0.00 0.00 0.00 2.85
1871 2216 4.142687 CGAGCAAAGGTTTCATTCGGTTAT 60.143 41.667 0.00 0.00 0.00 1.89
1872 2217 5.059404 AGCAAAGGTTTCATTCGGTTATG 57.941 39.130 0.00 0.00 0.00 1.90
1873 2218 4.082245 AGCAAAGGTTTCATTCGGTTATGG 60.082 41.667 0.00 0.00 0.00 2.74
1874 2219 4.082463 GCAAAGGTTTCATTCGGTTATGGA 60.082 41.667 0.00 0.00 0.00 3.41
1875 2220 5.399013 CAAAGGTTTCATTCGGTTATGGAC 58.601 41.667 0.00 0.00 0.00 4.02
1905 2250 7.335422 TGGTTCAGAAGATCTCAAGCTTTATTC 59.665 37.037 0.00 0.00 29.40 1.75
2013 2358 0.804989 CGATTGGCCTTGAGAACACC 59.195 55.000 3.32 0.00 0.00 4.16
2043 2388 2.298661 CCAGGCTTACCGGACCCTT 61.299 63.158 9.46 0.00 42.76 3.95
2127 2472 1.338107 ACCAGTCGACTGTTGATGGA 58.662 50.000 36.37 0.00 42.27 3.41
2242 2606 3.314635 CACATGCATTCCCTTCTTAGAGC 59.685 47.826 0.00 0.00 0.00 4.09
2243 2607 2.717639 TGCATTCCCTTCTTAGAGCC 57.282 50.000 0.00 0.00 0.00 4.70
2454 2849 3.073678 TGTTGGTTCCAATGATGAGTCG 58.926 45.455 7.56 0.00 0.00 4.18
2566 2967 4.286291 CCTACAAGGACAGTTTACCTTCCT 59.714 45.833 0.00 0.00 43.54 3.36
2570 2971 6.296803 ACAAGGACAGTTTACCTTCCTTTAG 58.703 40.000 9.01 4.09 44.54 1.85
2741 3142 4.320494 CCAAACTTCTACAGCACAATGGTC 60.320 45.833 0.00 0.00 0.00 4.02
2757 3158 3.500448 TGGTCAGGCACAACATTCTAA 57.500 42.857 0.00 0.00 0.00 2.10
2909 3310 3.301274 GGAGACCTTCTACTACATGGCT 58.699 50.000 0.00 0.00 0.00 4.75
2969 3370 2.532715 ATGGTGACCCCTGGTGCT 60.533 61.111 0.00 0.00 35.25 4.40
3090 3491 0.698818 AGCACCCTCCCAAACCTAAG 59.301 55.000 0.00 0.00 0.00 2.18
3136 3537 4.174411 TGTTGACAAGACACTATCCTCG 57.826 45.455 0.00 0.00 0.00 4.63
3144 3545 3.162666 AGACACTATCCTCGACAACCAA 58.837 45.455 0.00 0.00 0.00 3.67
3204 3605 7.428826 CCAAAATAGTATGCCTTCAGAAATCC 58.571 38.462 0.00 0.00 0.00 3.01
3208 3609 5.121380 AGTATGCCTTCAGAAATCCACAT 57.879 39.130 0.00 0.00 0.00 3.21
3297 3698 3.692406 GGCGGTCAGTCGGAGGTT 61.692 66.667 0.00 0.00 0.00 3.50
3303 3704 1.533033 TCAGTCGGAGGTTGAGGCA 60.533 57.895 0.00 0.00 0.00 4.75
3315 3716 3.567473 GAGGCAACGCTGAACCTC 58.433 61.111 0.00 0.00 41.81 3.85
3564 3965 4.193334 TGATCCGTCGGCGAGCTG 62.193 66.667 12.93 2.86 41.33 4.24
3575 3976 3.436015 GTCGGCGAGCTGTCTATCTAATA 59.564 47.826 11.20 0.00 0.00 0.98
3583 3984 7.403421 CGAGCTGTCTATCTAATAATCTACCG 58.597 42.308 0.00 0.00 0.00 4.02
3584 3985 7.090953 AGCTGTCTATCTAATAATCTACCGC 57.909 40.000 0.00 0.00 0.00 5.68
3585 3986 6.659668 AGCTGTCTATCTAATAATCTACCGCA 59.340 38.462 0.00 0.00 0.00 5.69
3586 3987 7.340743 AGCTGTCTATCTAATAATCTACCGCAT 59.659 37.037 0.00 0.00 0.00 4.73
3587 3988 7.646130 GCTGTCTATCTAATAATCTACCGCATC 59.354 40.741 0.00 0.00 0.00 3.91
3589 3990 8.459635 TGTCTATCTAATAATCTACCGCATCAC 58.540 37.037 0.00 0.00 0.00 3.06
3590 3991 8.679100 GTCTATCTAATAATCTACCGCATCACT 58.321 37.037 0.00 0.00 0.00 3.41
3592 3993 6.650427 TCTAATAATCTACCGCATCACTGT 57.350 37.500 0.00 0.00 0.00 3.55
3593 3994 6.678878 TCTAATAATCTACCGCATCACTGTC 58.321 40.000 0.00 0.00 0.00 3.51
3596 3997 0.173481 TCTACCGCATCACTGTCAGC 59.827 55.000 0.00 0.00 0.00 4.26
3597 3998 0.807667 CTACCGCATCACTGTCAGCC 60.808 60.000 0.00 0.00 0.00 4.85
3624 4027 2.359107 TTGAGCAGCTTGAGGGCG 60.359 61.111 0.00 0.00 37.29 6.13
3689 4092 2.433604 GCTCTGATGGAAGAGATGGACA 59.566 50.000 5.42 0.00 45.59 4.02
3741 4145 8.265165 CTAAGTAAACTACTTTGGAATGGTCC 57.735 38.462 4.50 0.00 46.27 4.46
3747 4151 4.844655 ACTACTTTGGAATGGTCCTACTGT 59.155 41.667 0.00 0.00 45.22 3.55
3761 4165 3.196901 TCCTACTGTTGTATTCGCATGGT 59.803 43.478 0.00 0.00 0.00 3.55
3792 4197 1.941975 GCATTGTTGCCTTTGTTTGCT 59.058 42.857 0.00 0.00 43.38 3.91
3796 4201 1.066303 TGTTGCCTTTGTTTGCTACCG 59.934 47.619 0.00 0.00 33.24 4.02
3813 4218 6.040247 TGCTACCGTAAGTATGAACAATCTG 58.960 40.000 0.00 0.00 0.00 2.90
3823 4228 1.657751 GAACAATCTGAAGCGCCCCC 61.658 60.000 2.29 0.00 0.00 5.40
3840 4245 1.302671 CCCCTTTGGAACGCGGTAA 60.303 57.895 12.47 0.00 35.39 2.85
3849 4254 3.139850 TGGAACGCGGTAATTTTTCTGA 58.860 40.909 12.47 0.00 0.00 3.27
3853 4258 5.292589 GGAACGCGGTAATTTTTCTGAGATA 59.707 40.000 12.47 0.00 0.00 1.98
3854 4259 6.018180 GGAACGCGGTAATTTTTCTGAGATAT 60.018 38.462 12.47 0.00 0.00 1.63
3858 4263 9.052759 ACGCGGTAATTTTTCTGAGATATTATT 57.947 29.630 12.47 0.00 0.00 1.40
3930 4335 8.070171 CGCATTTAAATCTAGAATCGTTGGATT 58.930 33.333 0.00 0.00 45.43 3.01
4032 6890 0.531090 CGAGGTTGGTCCGTTGTTGA 60.531 55.000 0.00 0.00 41.99 3.18
4078 9672 0.745128 TCGTTGTTGGTGCGAGGTTT 60.745 50.000 0.00 0.00 0.00 3.27
4091 9685 3.319405 TGCGAGGTTTGATTGCCTTTTTA 59.681 39.130 0.00 0.00 34.81 1.52
4128 9767 4.168101 AGTCTGTCCCATTTGACTTCCTA 58.832 43.478 0.00 0.00 36.50 2.94
4129 9768 4.223923 AGTCTGTCCCATTTGACTTCCTAG 59.776 45.833 0.00 0.00 36.50 3.02
4130 9769 4.020128 GTCTGTCCCATTTGACTTCCTAGT 60.020 45.833 0.00 0.00 36.21 2.57
4131 9770 4.020218 TCTGTCCCATTTGACTTCCTAGTG 60.020 45.833 0.00 0.00 36.21 2.74
4135 9774 5.535030 GTCCCATTTGACTTCCTAGTGTTTT 59.465 40.000 0.00 0.00 33.84 2.43
4362 10265 8.659925 TTAAATGTTGTGCAAATCTTGATTGT 57.340 26.923 0.00 0.00 0.00 2.71
4379 10282 4.580995 TGATTGTGGGTTATTTTGTCACGT 59.419 37.500 0.00 0.00 0.00 4.49
4394 10297 2.658268 CGTGTGCTCTGTGTCGCA 60.658 61.111 0.00 0.00 0.00 5.10
4405 10308 0.579630 TGTGTCGCATCGTGTGTTTC 59.420 50.000 0.00 0.00 0.00 2.78
4406 10309 0.579630 GTGTCGCATCGTGTGTTTCA 59.420 50.000 0.00 0.00 0.00 2.69
4431 10335 2.572191 TCTTGTCGACTTGTTCACGT 57.428 45.000 17.92 0.00 0.00 4.49
4451 10355 3.562141 CGTATGTGTCTTTTGTTGGACCA 59.438 43.478 0.00 0.00 0.00 4.02
4456 10360 6.531503 TGTGTCTTTTGTTGGACCATTTTA 57.468 33.333 0.00 0.00 0.00 1.52
4479 10384 1.139095 CGCGGTCTAGGTCCTGTTC 59.861 63.158 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 92 5.221661 CCAGACTGGAGGTGTAGTTTAAAGT 60.222 44.000 17.22 0.37 40.96 2.66
137 148 7.633789 TGGCTAGGAGAAAAACAGAGAAATAT 58.366 34.615 0.00 0.00 0.00 1.28
139 150 5.880901 TGGCTAGGAGAAAAACAGAGAAAT 58.119 37.500 0.00 0.00 0.00 2.17
176 187 8.562892 CCTATCAAAATGCATTAGTAGGAACTG 58.437 37.037 22.37 8.63 41.52 3.16
218 231 7.066307 AGCCTTACCAAAATGTCTGAATTTT 57.934 32.000 5.36 5.36 39.71 1.82
228 241 5.656416 TGATTTCCCTAGCCTTACCAAAATG 59.344 40.000 0.00 0.00 0.00 2.32
234 247 6.791867 AAAAATGATTTCCCTAGCCTTACC 57.208 37.500 0.00 0.00 0.00 2.85
264 279 8.523658 CCATGAATCTTGATATGATGCTTTCAT 58.476 33.333 0.00 7.67 46.86 2.57
274 289 5.475909 CCTTGACCCCATGAATCTTGATATG 59.524 44.000 0.00 0.00 0.00 1.78
295 310 7.557719 CCTTGTAACAATCTTGTATCATCCCTT 59.442 37.037 0.00 0.00 41.31 3.95
302 317 6.403636 CCAGTGCCTTGTAACAATCTTGTATC 60.404 42.308 0.00 0.00 41.31 2.24
306 321 3.057315 CCCAGTGCCTTGTAACAATCTTG 60.057 47.826 0.00 0.00 0.00 3.02
308 323 2.555227 CCCCAGTGCCTTGTAACAATCT 60.555 50.000 0.00 0.00 0.00 2.40
309 324 1.818674 CCCCAGTGCCTTGTAACAATC 59.181 52.381 0.00 0.00 0.00 2.67
311 326 0.825840 GCCCCAGTGCCTTGTAACAA 60.826 55.000 0.00 0.00 0.00 2.83
312 327 1.228429 GCCCCAGTGCCTTGTAACA 60.228 57.895 0.00 0.00 0.00 2.41
313 328 1.228429 TGCCCCAGTGCCTTGTAAC 60.228 57.895 0.00 0.00 0.00 2.50
314 329 1.228429 GTGCCCCAGTGCCTTGTAA 60.228 57.895 0.00 0.00 0.00 2.41
315 330 2.000825 TTGTGCCCCAGTGCCTTGTA 62.001 55.000 0.00 0.00 0.00 2.41
316 331 3.372422 TTGTGCCCCAGTGCCTTGT 62.372 57.895 0.00 0.00 0.00 3.16
317 332 2.521465 TTGTGCCCCAGTGCCTTG 60.521 61.111 0.00 0.00 0.00 3.61
318 333 2.203538 CTTGTGCCCCAGTGCCTT 60.204 61.111 0.00 0.00 0.00 4.35
345 548 2.141535 ACTGTTTCTGCGACAGAGTC 57.858 50.000 10.87 7.12 45.72 3.36
354 557 5.215160 CACCATTCTTTGTACTGTTTCTGC 58.785 41.667 0.00 0.00 0.00 4.26
355 558 6.201517 CACACCATTCTTTGTACTGTTTCTG 58.798 40.000 0.00 0.00 0.00 3.02
359 562 3.317993 GGCACACCATTCTTTGTACTGTT 59.682 43.478 0.00 0.00 35.26 3.16
360 563 2.884639 GGCACACCATTCTTTGTACTGT 59.115 45.455 0.00 0.00 35.26 3.55
388 591 2.299013 TGATAACAACTCGAGCTGTGGT 59.701 45.455 21.41 13.78 0.00 4.16
432 635 4.334203 CCGTTGATTCCGTGGAATAAATCA 59.666 41.667 13.92 6.36 43.98 2.57
580 783 1.828979 TTTCACCAAGGGTTATCGCC 58.171 50.000 0.00 0.00 31.02 5.54
581 784 2.479560 GCATTTCACCAAGGGTTATCGC 60.480 50.000 0.00 0.00 31.02 4.58
582 785 2.752354 TGCATTTCACCAAGGGTTATCG 59.248 45.455 0.00 0.00 31.02 2.92
583 786 4.110036 GTGCATTTCACCAAGGGTTATC 57.890 45.455 0.00 0.00 39.79 1.75
594 797 2.414559 CGATTCTGTGGGTGCATTTCAC 60.415 50.000 9.22 9.22 44.90 3.18
595 798 1.811965 CGATTCTGTGGGTGCATTTCA 59.188 47.619 0.00 0.00 0.00 2.69
596 799 1.468054 GCGATTCTGTGGGTGCATTTC 60.468 52.381 0.00 0.00 0.00 2.17
597 800 0.527565 GCGATTCTGTGGGTGCATTT 59.472 50.000 0.00 0.00 0.00 2.32
598 801 0.608856 TGCGATTCTGTGGGTGCATT 60.609 50.000 0.00 0.00 0.00 3.56
599 802 1.002257 TGCGATTCTGTGGGTGCAT 60.002 52.632 0.00 0.00 0.00 3.96
600 803 1.672030 CTGCGATTCTGTGGGTGCA 60.672 57.895 0.00 0.00 0.00 4.57
601 804 0.955428 TTCTGCGATTCTGTGGGTGC 60.955 55.000 0.00 0.00 0.00 5.01
602 805 0.798776 GTTCTGCGATTCTGTGGGTG 59.201 55.000 0.00 0.00 0.00 4.61
603 806 0.670546 CGTTCTGCGATTCTGTGGGT 60.671 55.000 0.00 0.00 44.77 4.51
604 807 1.361668 CCGTTCTGCGATTCTGTGGG 61.362 60.000 0.00 0.00 44.77 4.61
605 808 0.670546 ACCGTTCTGCGATTCTGTGG 60.671 55.000 0.00 0.00 44.77 4.17
606 809 1.126846 GAACCGTTCTGCGATTCTGTG 59.873 52.381 3.88 0.00 39.91 3.66
607 810 1.270094 TGAACCGTTCTGCGATTCTGT 60.270 47.619 12.43 0.00 43.34 3.41
608 811 1.428448 TGAACCGTTCTGCGATTCTG 58.572 50.000 12.43 0.00 43.34 3.02
609 812 2.271800 GATGAACCGTTCTGCGATTCT 58.728 47.619 12.43 0.00 43.34 2.40
610 813 1.999735 TGATGAACCGTTCTGCGATTC 59.000 47.619 12.43 0.00 43.24 2.52
611 814 2.002586 CTGATGAACCGTTCTGCGATT 58.997 47.619 12.43 0.00 44.77 3.34
612 815 1.645034 CTGATGAACCGTTCTGCGAT 58.355 50.000 12.43 0.00 44.77 4.58
613 816 1.014044 GCTGATGAACCGTTCTGCGA 61.014 55.000 12.43 0.00 44.77 5.10
614 817 1.421485 GCTGATGAACCGTTCTGCG 59.579 57.895 12.43 0.59 40.95 5.18
615 818 0.955428 TGGCTGATGAACCGTTCTGC 60.955 55.000 12.43 10.49 36.44 4.26
616 819 1.466167 CTTGGCTGATGAACCGTTCTG 59.534 52.381 12.43 2.25 0.00 3.02
617 820 1.611673 CCTTGGCTGATGAACCGTTCT 60.612 52.381 12.43 0.00 0.00 3.01
618 821 0.804989 CCTTGGCTGATGAACCGTTC 59.195 55.000 4.18 4.18 0.00 3.95
619 822 1.244019 GCCTTGGCTGATGAACCGTT 61.244 55.000 4.11 0.00 0.00 4.44
620 823 1.675641 GCCTTGGCTGATGAACCGT 60.676 57.895 4.11 0.00 0.00 4.83
621 824 2.409870 GGCCTTGGCTGATGAACCG 61.410 63.158 11.71 0.00 0.00 4.44
622 825 0.899717 TTGGCCTTGGCTGATGAACC 60.900 55.000 11.71 0.00 0.00 3.62
623 826 1.135721 GATTGGCCTTGGCTGATGAAC 59.864 52.381 11.71 0.00 0.00 3.18
624 827 1.477553 GATTGGCCTTGGCTGATGAA 58.522 50.000 11.71 0.00 0.00 2.57
625 828 0.396139 GGATTGGCCTTGGCTGATGA 60.396 55.000 11.71 0.00 0.00 2.92
626 829 2.121645 GGATTGGCCTTGGCTGATG 58.878 57.895 11.71 0.00 0.00 3.07
627 830 4.692930 GGATTGGCCTTGGCTGAT 57.307 55.556 11.71 5.88 0.00 2.90
637 840 2.143876 TCTTGGCCTTAAGGATTGGC 57.856 50.000 26.21 9.99 45.42 4.52
638 841 3.430453 TGTTCTTGGCCTTAAGGATTGG 58.570 45.455 26.21 11.49 37.39 3.16
639 842 5.185635 TGAATGTTCTTGGCCTTAAGGATTG 59.814 40.000 26.21 11.19 37.39 2.67
640 843 5.332743 TGAATGTTCTTGGCCTTAAGGATT 58.667 37.500 26.21 12.58 37.39 3.01
705 908 8.220559 ACCATGTAAAACCTCTATAATGCTGAT 58.779 33.333 0.00 0.00 0.00 2.90
717 920 6.870971 TTTCTGTGTACCATGTAAAACCTC 57.129 37.500 0.00 0.00 0.00 3.85
789 992 0.622665 CCAATCCTCTTGCCACCTCT 59.377 55.000 0.00 0.00 0.00 3.69
852 1055 3.209410 CAAGGGATATGAGTTGTGAGGC 58.791 50.000 0.00 0.00 0.00 4.70
953 1264 2.288825 TGCTACCCTCTTCTTTGACACG 60.289 50.000 0.00 0.00 0.00 4.49
989 1300 1.879380 CAGACGCCATTGTTTCTGGAA 59.121 47.619 0.00 0.00 35.70 3.53
1119 1430 0.459899 TGACAAGCTCATCGGCGTAT 59.540 50.000 6.85 0.00 37.29 3.06
1180 1491 3.310227 CACGCATATGCATGGCAAAATTT 59.690 39.130 26.52 0.00 43.62 1.82
1207 1518 1.753073 CTGCCCATCAAGGATCAAACC 59.247 52.381 0.00 0.00 41.22 3.27
1210 1521 3.266772 AGTTACTGCCCATCAAGGATCAA 59.733 43.478 0.00 0.00 41.22 2.57
1211 1522 2.846206 AGTTACTGCCCATCAAGGATCA 59.154 45.455 0.00 0.00 41.22 2.92
1212 1523 3.567478 AGTTACTGCCCATCAAGGATC 57.433 47.619 0.00 0.00 41.22 3.36
1213 1524 3.525199 AGAAGTTACTGCCCATCAAGGAT 59.475 43.478 0.00 0.00 41.22 3.24
1214 1525 2.912956 AGAAGTTACTGCCCATCAAGGA 59.087 45.455 0.00 0.00 41.22 3.36
1215 1526 3.012518 CAGAAGTTACTGCCCATCAAGG 58.987 50.000 0.00 0.00 37.03 3.61
1216 1527 3.012518 CCAGAAGTTACTGCCCATCAAG 58.987 50.000 0.00 0.00 36.67 3.02
1238 1549 5.104776 CCCACTGATGTAAAGAGGATTCTCA 60.105 44.000 3.21 0.00 42.34 3.27
1332 1661 3.119708 AGCGGTACTAGGTTAACTGTTCG 60.120 47.826 5.42 10.28 0.00 3.95
1342 1671 5.421374 GGGATTATGATAAGCGGTACTAGGT 59.579 44.000 0.00 0.00 0.00 3.08
1353 1682 9.360093 GTCTTATGTCGAAGGGATTATGATAAG 57.640 37.037 0.00 0.00 0.00 1.73
1366 1695 5.120208 ACAAAACATCCGTCTTATGTCGAAG 59.880 40.000 0.00 0.00 36.56 3.79
1369 1698 4.387559 TGACAAAACATCCGTCTTATGTCG 59.612 41.667 0.00 0.00 38.93 4.35
1373 1702 3.124636 GCGTGACAAAACATCCGTCTTAT 59.875 43.478 0.00 0.00 0.00 1.73
1380 1709 1.197721 CCTCTGCGTGACAAAACATCC 59.802 52.381 0.00 0.00 0.00 3.51
1381 1710 2.143122 TCCTCTGCGTGACAAAACATC 58.857 47.619 0.00 0.00 0.00 3.06
1393 1722 1.270550 AGCCAAACAATTTCCTCTGCG 59.729 47.619 0.00 0.00 0.00 5.18
1406 1736 2.796593 GTGTGATCAAAAGCAGCCAAAC 59.203 45.455 0.00 0.00 0.00 2.93
1425 1755 8.783093 TGTTCATTTAGACTAGTGATTTTGGTG 58.217 33.333 0.00 0.00 0.00 4.17
1447 1777 8.786937 ATCGAAAACATATGTTATGCATGTTC 57.213 30.769 21.07 16.49 40.94 3.18
1453 1783 8.726650 TGCAATATCGAAAACATATGTTATGC 57.273 30.769 21.07 18.25 37.25 3.14
1470 1800 9.503427 GAAAAGTTACTGTACCAATGCAATATC 57.497 33.333 0.00 0.00 0.00 1.63
1509 1853 8.256605 ACATCAATCATATCTATTTAGCTCGCT 58.743 33.333 0.00 0.00 0.00 4.93
1565 1909 5.957842 ACACATCACGTTTATGTTTGGAT 57.042 34.783 9.96 0.00 35.39 3.41
1584 1928 4.864806 TGCAGATGTCTAATCGAGAAACAC 59.135 41.667 0.00 0.00 35.37 3.32
1592 1936 5.582550 TGTCTTACTGCAGATGTCTAATCG 58.417 41.667 23.35 0.00 0.00 3.34
1633 1978 3.990469 CCTGCCATATCGTTAAGCTAGTG 59.010 47.826 0.00 0.00 0.00 2.74
1634 1979 3.895656 TCCTGCCATATCGTTAAGCTAGT 59.104 43.478 0.00 0.00 0.00 2.57
1635 1980 4.521130 TCCTGCCATATCGTTAAGCTAG 57.479 45.455 0.00 0.00 0.00 3.42
1636 1981 4.820897 CATCCTGCCATATCGTTAAGCTA 58.179 43.478 0.00 0.00 0.00 3.32
1637 1982 3.668447 CATCCTGCCATATCGTTAAGCT 58.332 45.455 0.00 0.00 0.00 3.74
1638 1983 2.160417 GCATCCTGCCATATCGTTAAGC 59.840 50.000 0.00 0.00 37.42 3.09
1639 1984 3.402110 TGCATCCTGCCATATCGTTAAG 58.598 45.455 0.00 0.00 44.23 1.85
1640 1985 3.483808 TGCATCCTGCCATATCGTTAA 57.516 42.857 0.00 0.00 44.23 2.01
1644 1989 2.103537 TGATGCATCCTGCCATATCG 57.896 50.000 23.67 0.00 44.23 2.92
1649 1994 1.830847 GCCATGATGCATCCTGCCA 60.831 57.895 23.67 5.84 44.23 4.92
1725 2070 1.755179 TGGATTGCTCAGCTTAAGCC 58.245 50.000 23.71 9.07 43.38 4.35
1735 2080 3.614092 TGAACCTTCAGATGGATTGCTC 58.386 45.455 9.37 0.00 32.50 4.26
1852 2197 5.183140 AGTCCATAACCGAATGAAACCTTTG 59.817 40.000 0.00 0.00 0.00 2.77
1857 2202 6.317893 ACCATAAGTCCATAACCGAATGAAAC 59.682 38.462 0.00 0.00 0.00 2.78
1866 2211 6.650120 TCTTCTGAACCATAAGTCCATAACC 58.350 40.000 0.00 0.00 0.00 2.85
1868 2213 8.324191 AGATCTTCTGAACCATAAGTCCATAA 57.676 34.615 0.00 0.00 0.00 1.90
1869 2214 7.565029 TGAGATCTTCTGAACCATAAGTCCATA 59.435 37.037 0.00 0.00 0.00 2.74
1870 2215 6.385176 TGAGATCTTCTGAACCATAAGTCCAT 59.615 38.462 0.00 0.00 0.00 3.41
1871 2216 5.721480 TGAGATCTTCTGAACCATAAGTCCA 59.279 40.000 0.00 0.00 0.00 4.02
1872 2217 6.227298 TGAGATCTTCTGAACCATAAGTCC 57.773 41.667 0.00 0.00 0.00 3.85
1873 2218 6.257630 GCTTGAGATCTTCTGAACCATAAGTC 59.742 42.308 0.00 0.00 0.00 3.01
1874 2219 6.070309 AGCTTGAGATCTTCTGAACCATAAGT 60.070 38.462 0.00 0.00 0.00 2.24
1875 2220 6.347696 AGCTTGAGATCTTCTGAACCATAAG 58.652 40.000 0.00 0.00 0.00 1.73
1905 2250 1.321474 TGGTTTTCTGCAGCAGGAAG 58.679 50.000 22.62 0.00 29.95 3.46
2043 2388 0.764369 AGCCTGGTGGAGTGACAAGA 60.764 55.000 0.00 0.00 34.57 3.02
2103 2448 1.540267 TCAACAGTCGACTGGTAGAGC 59.460 52.381 40.23 3.04 43.10 4.09
2127 2472 6.966534 ACAAGGATGTCAACAATCTTCTTT 57.033 33.333 0.00 0.00 33.41 2.52
2445 2840 0.320683 CTTGGCACCACGACTCATCA 60.321 55.000 0.00 0.00 0.00 3.07
2454 2849 1.021390 CATCGAGACCTTGGCACCAC 61.021 60.000 0.00 0.00 0.00 4.16
2741 3142 6.263842 ACATATCCATTAGAATGTTGTGCCTG 59.736 38.462 1.78 0.00 34.60 4.85
2909 3310 3.559655 CCTCAAACATGACGTTGTTCTGA 59.440 43.478 6.11 10.37 38.85 3.27
2969 3370 2.431683 GCCCTGTCCTTGCACTCA 59.568 61.111 0.00 0.00 0.00 3.41
3136 3537 3.059166 GTCACCATGCAAATTGGTTGTC 58.941 45.455 7.76 0.00 45.19 3.18
3144 3545 7.829211 AGTTAGTTACTATGTCACCATGCAAAT 59.171 33.333 0.00 0.00 34.56 2.32
3154 3555 7.386848 GGCACTTTTGAGTTAGTTACTATGTCA 59.613 37.037 0.00 0.00 37.17 3.58
3155 3556 7.386848 TGGCACTTTTGAGTTAGTTACTATGTC 59.613 37.037 0.00 0.00 37.17 3.06
3157 3558 7.667043 TGGCACTTTTGAGTTAGTTACTATG 57.333 36.000 0.00 0.00 37.17 2.23
3158 3559 8.685838 TTTGGCACTTTTGAGTTAGTTACTAT 57.314 30.769 0.00 0.00 37.17 2.12
3159 3560 8.508883 TTTTGGCACTTTTGAGTTAGTTACTA 57.491 30.769 0.00 0.00 37.17 1.82
3160 3561 7.399245 TTTTGGCACTTTTGAGTTAGTTACT 57.601 32.000 0.00 0.00 40.71 2.24
3161 3562 9.394477 CTATTTTGGCACTTTTGAGTTAGTTAC 57.606 33.333 0.00 0.00 0.00 2.50
3162 3563 9.127277 ACTATTTTGGCACTTTTGAGTTAGTTA 57.873 29.630 0.00 0.00 0.00 2.24
3163 3564 8.007405 ACTATTTTGGCACTTTTGAGTTAGTT 57.993 30.769 0.00 0.00 0.00 2.24
3165 3566 9.559958 CATACTATTTTGGCACTTTTGAGTTAG 57.440 33.333 0.00 0.00 0.00 2.34
3297 3698 1.301716 GAGGTTCAGCGTTGCCTCA 60.302 57.895 17.14 0.00 45.00 3.86
3315 3716 2.480555 GCCTGGTTCATCGCGTTG 59.519 61.111 10.93 10.93 0.00 4.10
3564 3965 8.679100 AGTGATGCGGTAGATTATTAGATAGAC 58.321 37.037 0.00 0.00 0.00 2.59
3575 3976 2.739932 GCTGACAGTGATGCGGTAGATT 60.740 50.000 3.99 0.00 0.00 2.40
3590 3991 2.583441 AAGGCGCTACTGGCTGACA 61.583 57.895 7.64 0.00 45.07 3.58
3592 3993 2.230994 CTCAAGGCGCTACTGGCTGA 62.231 60.000 7.64 0.00 45.07 4.26
3593 3994 1.812922 CTCAAGGCGCTACTGGCTG 60.813 63.158 7.64 0.00 45.07 4.85
3596 3997 1.812922 CTGCTCAAGGCGCTACTGG 60.813 63.158 7.64 0.00 45.43 4.00
3597 3998 2.459442 GCTGCTCAAGGCGCTACTG 61.459 63.158 7.64 2.11 45.43 2.74
3641 4044 1.412387 GACCTGTAACAACGACGACC 58.588 55.000 0.00 0.00 0.00 4.79
3689 4092 7.042335 GTGGCAAAACACAGTATATACTCTCT 58.958 38.462 12.62 0.00 40.99 3.10
3740 4144 3.531538 ACCATGCGAATACAACAGTAGG 58.468 45.455 0.00 0.00 0.00 3.18
3741 4145 5.545658 AAACCATGCGAATACAACAGTAG 57.454 39.130 0.00 0.00 0.00 2.57
3792 4197 6.755141 GCTTCAGATTGTTCATACTTACGGTA 59.245 38.462 0.00 0.00 34.62 4.02
3796 4201 5.493735 GCGCTTCAGATTGTTCATACTTAC 58.506 41.667 0.00 0.00 0.00 2.34
3823 4228 1.170442 AATTACCGCGTTCCAAAGGG 58.830 50.000 4.92 0.00 0.00 3.95
3824 4229 3.291809 AAAATTACCGCGTTCCAAAGG 57.708 42.857 4.92 0.00 0.00 3.11
3825 4230 4.381566 CAGAAAAATTACCGCGTTCCAAAG 59.618 41.667 4.92 0.00 0.00 2.77
3853 4258 9.349713 TGAAATAGCAAACCCGATAGAAATAAT 57.650 29.630 0.00 0.00 39.76 1.28
3854 4259 8.617809 GTGAAATAGCAAACCCGATAGAAATAA 58.382 33.333 0.00 0.00 39.76 1.40
3858 4263 5.492895 TGTGAAATAGCAAACCCGATAGAA 58.507 37.500 0.00 0.00 39.76 2.10
3860 4265 5.760253 AGATGTGAAATAGCAAACCCGATAG 59.240 40.000 0.00 0.00 0.00 2.08
3861 4266 5.680619 AGATGTGAAATAGCAAACCCGATA 58.319 37.500 0.00 0.00 0.00 2.92
3862 4267 4.526970 AGATGTGAAATAGCAAACCCGAT 58.473 39.130 0.00 0.00 0.00 4.18
3956 4363 3.118775 AGCGCATCAACTAGACCATTGTA 60.119 43.478 11.47 0.00 0.00 2.41
3999 4423 0.251077 ACCTCGACCAGTAACGACCT 60.251 55.000 0.00 0.00 34.82 3.85
4091 9685 8.477419 TGGGACAGACTTTTGAAAAGAAATAT 57.523 30.769 23.14 1.05 0.00 1.28
4362 10265 2.033550 GCACACGTGACAAAATAACCCA 59.966 45.455 25.01 0.00 0.00 4.51
4379 10282 1.734117 CGATGCGACACAGAGCACA 60.734 57.895 0.00 0.00 46.83 4.57
4394 10297 6.035005 CGACAAGAAGATATGAAACACACGAT 59.965 38.462 0.00 0.00 0.00 3.73
4405 10308 6.453003 CGTGAACAAGTCGACAAGAAGATATG 60.453 42.308 19.50 4.82 0.00 1.78
4406 10309 5.573282 CGTGAACAAGTCGACAAGAAGATAT 59.427 40.000 19.50 0.00 0.00 1.63
4431 10335 6.723298 AAATGGTCCAACAAAAGACACATA 57.277 33.333 0.00 0.00 34.58 2.29
4451 10355 1.535437 CCTAGACCGCGTCGCTAAAAT 60.535 52.381 16.36 0.00 37.67 1.82
4456 10360 3.507009 GACCTAGACCGCGTCGCT 61.507 66.667 16.36 1.15 37.67 4.93
4479 10384 8.110860 AGATAATAATTAGCAAACCAATCCCG 57.889 34.615 0.00 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.