Multiple sequence alignment - TraesCS4B01G317600

Loading Multiple Alignment...

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 TraesCS4B01G317600 chr4B 100.000 2715 0 0 1 2715 607287548 607290262 0.000000e+00 5014.0
1 TraesCS4B01G317600 chr4B 87.037 324 22 6 2152 2469 583072514 583072823 5.560000e-92 348.0
2 TraesCS4B01G317600 chr4B 89.759 166 17 0 1350 1515 607288798 607288963 2.120000e-51 213.0
3 TraesCS4B01G317600 chr4B 89.759 166 17 0 1251 1416 607288897 607289062 2.120000e-51 213.0
4 TraesCS4B01G317600 chr4B 93.798 129 8 0 1383 1511 607288798 607288926 7.670000e-46 195.0
5 TraesCS4B01G317600 chr4B 93.798 129 8 0 1251 1379 607288930 607289058 7.670000e-46 195.0
6 TraesCS4B01G317600 chr4D 87.199 1414 68 36 3 1379 479961897 479963234 0.000000e+00 1504.0
7 TraesCS4B01G317600 chr4D 92.898 352 14 2 1383 1734 479963106 479963446 4.040000e-138 501.0
8 TraesCS4B01G317600 chr4D 87.079 356 25 8 2201 2539 479963672 479964023 1.530000e-102 383.0
9 TraesCS4B01G317600 chr4D 88.211 246 18 5 2152 2391 465951724 465951964 1.590000e-72 283.0
10 TraesCS4B01G317600 chr4D 91.667 132 11 0 1322 1453 479963111 479963242 1.660000e-42 183.0
11 TraesCS4B01G317600 chr4D 93.043 115 8 0 1482 1596 465910045 465910159 4.650000e-38 169.0
12 TraesCS4B01G317600 chr4D 92.982 114 7 1 2565 2678 479966702 479966814 6.010000e-37 165.0
13 TraesCS4B01G317600 chr4D 94.118 68 4 0 1454 1521 479963111 479963178 1.330000e-18 104.0
14 TraesCS4B01G317600 chr4D 89.706 68 7 0 2142 2209 479963563 479963630 1.340000e-13 87.9
15 TraesCS4B01G317600 chr4D 94.444 54 3 0 2416 2469 465951963 465952016 1.730000e-12 84.2
16 TraesCS4B01G317600 chr6B 80.678 590 78 19 61 637 674935900 674935334 2.500000e-115 425.0
17 TraesCS4B01G317600 chr2B 81.781 494 65 12 158 637 572586851 572586369 9.110000e-105 390.0
18 TraesCS4B01G317600 chr2B 79.626 481 66 19 171 634 701490642 701491107 1.570000e-82 316.0
19 TraesCS4B01G317600 chr4A 79.727 587 71 34 61 626 686385145 686385704 5.490000e-102 381.0
20 TraesCS4B01G317600 chr4A 88.710 310 25 8 1030 1329 641601966 641601657 1.190000e-98 370.0
21 TraesCS4B01G317600 chr4A 78.208 413 28 26 2323 2715 641600820 641600450 9.850000e-50 207.0
22 TraesCS4B01G317600 chr4A 90.909 66 3 1 2201 2263 641600886 641600821 4.820000e-13 86.1
23 TraesCS4B01G317600 chr5B 86.647 337 24 8 2365 2684 42744042 42744374 1.200000e-93 353.0
24 TraesCS4B01G317600 chr5B 79.923 518 72 15 139 637 441446011 441446515 4.300000e-93 351.0
25 TraesCS4B01G317600 chr5B 80.272 441 56 16 160 584 448803608 448804033 1.220000e-78 303.0
26 TraesCS4B01G317600 chr2D 80.882 476 65 17 170 634 582494558 582495018 4.300000e-93 351.0
27 TraesCS4B01G317600 chr2D 80.444 450 48 19 169 599 488229528 488229100 9.440000e-80 307.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G317600 chr4B 607287548 607290262 2714 False 1166.000000 5014 93.422800 1 2715 5 chr4B.!!$F2 2714
1 TraesCS4B01G317600 chr4D 479961897 479966814 4917 False 418.271429 1504 90.807000 3 2678 7 chr4D.!!$F3 2675
2 TraesCS4B01G317600 chr6B 674935334 674935900 566 True 425.000000 425 80.678000 61 637 1 chr6B.!!$R1 576
3 TraesCS4B01G317600 chr4A 686385145 686385704 559 False 381.000000 381 79.727000 61 626 1 chr4A.!!$F1 565
4 TraesCS4B01G317600 chr4A 641600450 641601966 1516 True 221.033333 370 85.942333 1030 2715 3 chr4A.!!$R1 1685
5 TraesCS4B01G317600 chr5B 441446011 441446515 504 False 351.000000 351 79.923000 139 637 1 chr5B.!!$F2 498

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
554 606 0.179086 GGTTGTGTTGCTTTGGTGGG 60.179 55.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2013 2127 0.036164 AGCAATGCACGGTGGTAAGA 59.964 50.0 8.35 0.0 0.0 2.1 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
44 45 6.620877 TCCACAATATACAGTTCCTCAAGT 57.379 37.500 0.00 0.00 0.00 3.16
45 46 7.016153 TCCACAATATACAGTTCCTCAAGTT 57.984 36.000 0.00 0.00 0.00 2.66
46 47 7.458397 TCCACAATATACAGTTCCTCAAGTTT 58.542 34.615 0.00 0.00 0.00 2.66
47 48 8.598916 TCCACAATATACAGTTCCTCAAGTTTA 58.401 33.333 0.00 0.00 0.00 2.01
48 49 9.226606 CCACAATATACAGTTCCTCAAGTTTAA 57.773 33.333 0.00 0.00 0.00 1.52
53 54 9.838339 ATATACAGTTCCTCAAGTTTAATCCAG 57.162 33.333 0.00 0.00 0.00 3.86
79 80 6.472486 ACTTGAACATAATGACGACGATACAG 59.528 38.462 0.00 0.00 0.00 2.74
117 122 8.631480 ACTAAAAATAAGACCCAACCAACTAG 57.369 34.615 0.00 0.00 0.00 2.57
142 147 9.604569 AGTGATCCTCATAGAGTAGTAGTAGTA 57.395 37.037 0.00 0.00 0.00 1.82
183 201 0.919981 ATCTAGACGACGACGACGAC 59.080 55.000 25.15 18.88 42.66 4.34
196 217 1.195448 ACGACGACGACGATTTAGTGT 59.805 47.619 25.15 0.00 42.66 3.55
366 393 1.301293 GGTCCTTGGCCTTCTCCAG 59.699 63.158 3.32 0.00 37.44 3.86
426 471 2.182030 CGACTCCTTCTCCGGCAC 59.818 66.667 0.00 0.00 0.00 5.01
427 472 2.579738 GACTCCTTCTCCGGCACC 59.420 66.667 0.00 0.00 0.00 5.01
428 473 3.358076 GACTCCTTCTCCGGCACCG 62.358 68.421 1.02 1.02 39.44 4.94
461 506 4.785453 CCACCGGAGCCTCCTTGC 62.785 72.222 9.46 0.00 33.30 4.01
499 544 3.820777 AAGCTGAGATCGAAAACTTGC 57.179 42.857 0.00 0.00 0.00 4.01
501 546 1.131315 GCTGAGATCGAAAACTTGCCC 59.869 52.381 0.00 0.00 0.00 5.36
554 606 0.179086 GGTTGTGTTGCTTTGGTGGG 60.179 55.000 0.00 0.00 0.00 4.61
562 614 3.914713 CTTTGGTGGGCAGGGGGT 61.915 66.667 0.00 0.00 0.00 4.95
563 615 3.886550 CTTTGGTGGGCAGGGGGTC 62.887 68.421 0.00 0.00 0.00 4.46
596 649 2.237392 CCTACTTATATGCAGGGGAGGC 59.763 54.545 0.00 0.00 0.00 4.70
606 664 3.637273 GGGGAGGCCGTGTCTTGT 61.637 66.667 0.00 0.00 0.00 3.16
659 717 2.266279 TGGACTTGGAGTAGGGGAAAG 58.734 52.381 0.00 0.00 0.00 2.62
660 718 1.560146 GGACTTGGAGTAGGGGAAAGG 59.440 57.143 0.00 0.00 0.00 3.11
661 719 2.547990 GACTTGGAGTAGGGGAAAGGA 58.452 52.381 0.00 0.00 0.00 3.36
662 720 2.910977 GACTTGGAGTAGGGGAAAGGAA 59.089 50.000 0.00 0.00 0.00 3.36
663 721 3.329814 GACTTGGAGTAGGGGAAAGGAAA 59.670 47.826 0.00 0.00 0.00 3.13
664 722 3.330998 ACTTGGAGTAGGGGAAAGGAAAG 59.669 47.826 0.00 0.00 0.00 2.62
665 723 3.285290 TGGAGTAGGGGAAAGGAAAGA 57.715 47.619 0.00 0.00 0.00 2.52
666 724 3.604787 TGGAGTAGGGGAAAGGAAAGAA 58.395 45.455 0.00 0.00 0.00 2.52
667 725 3.329814 TGGAGTAGGGGAAAGGAAAGAAC 59.670 47.826 0.00 0.00 0.00 3.01
668 726 3.587951 GGAGTAGGGGAAAGGAAAGAACT 59.412 47.826 0.00 0.00 0.00 3.01
669 727 4.043059 GGAGTAGGGGAAAGGAAAGAACTT 59.957 45.833 0.00 0.00 0.00 2.66
670 728 4.986783 AGTAGGGGAAAGGAAAGAACTTG 58.013 43.478 0.00 0.00 0.00 3.16
671 729 3.244887 AGGGGAAAGGAAAGAACTTGG 57.755 47.619 0.00 0.00 0.00 3.61
672 730 2.789399 AGGGGAAAGGAAAGAACTTGGA 59.211 45.455 0.00 0.00 0.00 3.53
673 731 3.206639 AGGGGAAAGGAAAGAACTTGGAA 59.793 43.478 0.00 0.00 0.00 3.53
701 759 0.600255 AAAGAGAGCGTCCCGTTGTG 60.600 55.000 0.00 0.00 0.00 3.33
708 766 1.666872 CGTCCCGTTGTGAACCTCC 60.667 63.158 0.00 0.00 0.00 4.30
713 771 1.512926 CCGTTGTGAACCTCCTCTTG 58.487 55.000 0.00 0.00 0.00 3.02
714 772 1.512926 CGTTGTGAACCTCCTCTTGG 58.487 55.000 0.00 0.00 0.00 3.61
715 773 1.070134 CGTTGTGAACCTCCTCTTGGA 59.930 52.381 0.00 0.00 40.69 3.53
716 774 2.289694 CGTTGTGAACCTCCTCTTGGAT 60.290 50.000 0.00 0.00 42.29 3.41
717 775 3.056107 CGTTGTGAACCTCCTCTTGGATA 60.056 47.826 0.00 0.00 42.29 2.59
721 779 6.485830 TGTGAACCTCCTCTTGGATAATAG 57.514 41.667 0.00 0.00 42.29 1.73
761 819 4.345859 AATTGACCACACGAGGAAGTAA 57.654 40.909 0.00 0.00 0.00 2.24
767 825 3.118519 ACCACACGAGGAAGTAACACTTT 60.119 43.478 0.00 0.00 38.80 2.66
769 827 3.247648 CACACGAGGAAGTAACACTTTGG 59.752 47.826 0.00 0.00 38.80 3.28
770 828 3.133362 ACACGAGGAAGTAACACTTTGGA 59.867 43.478 0.00 0.00 38.80 3.53
771 829 3.741344 CACGAGGAAGTAACACTTTGGAG 59.259 47.826 0.00 0.00 38.80 3.86
772 830 3.387050 ACGAGGAAGTAACACTTTGGAGT 59.613 43.478 0.00 0.00 38.80 3.85
773 831 4.141779 ACGAGGAAGTAACACTTTGGAGTT 60.142 41.667 0.00 0.00 38.80 3.01
774 832 4.448060 CGAGGAAGTAACACTTTGGAGTTC 59.552 45.833 0.00 0.00 38.80 3.01
775 833 4.377897 AGGAAGTAACACTTTGGAGTTCG 58.622 43.478 0.00 0.00 38.80 3.95
776 834 3.497262 GGAAGTAACACTTTGGAGTTCGG 59.503 47.826 0.00 0.00 38.80 4.30
777 835 4.374399 GAAGTAACACTTTGGAGTTCGGA 58.626 43.478 0.00 0.00 38.80 4.55
778 836 4.618920 AGTAACACTTTGGAGTTCGGAT 57.381 40.909 0.00 0.00 32.54 4.18
779 837 4.566987 AGTAACACTTTGGAGTTCGGATC 58.433 43.478 0.00 0.00 32.54 3.36
780 838 3.485463 AACACTTTGGAGTTCGGATCA 57.515 42.857 0.00 0.00 32.54 2.92
781 839 3.045601 ACACTTTGGAGTTCGGATCAG 57.954 47.619 0.00 0.00 32.54 2.90
782 840 2.632996 ACACTTTGGAGTTCGGATCAGA 59.367 45.455 0.00 0.00 32.54 3.27
783 841 3.071023 ACACTTTGGAGTTCGGATCAGAA 59.929 43.478 4.00 4.00 32.54 3.02
784 842 3.681897 CACTTTGGAGTTCGGATCAGAAG 59.318 47.826 8.65 0.00 32.54 2.85
785 843 3.325135 ACTTTGGAGTTCGGATCAGAAGT 59.675 43.478 14.77 14.77 36.57 3.01
786 844 4.527038 ACTTTGGAGTTCGGATCAGAAGTA 59.473 41.667 14.82 0.00 34.24 2.24
787 845 4.720649 TTGGAGTTCGGATCAGAAGTAG 57.279 45.455 14.82 0.00 34.24 2.57
788 846 3.698289 TGGAGTTCGGATCAGAAGTAGT 58.302 45.455 14.82 0.00 34.24 2.73
789 847 4.851843 TGGAGTTCGGATCAGAAGTAGTA 58.148 43.478 14.82 3.52 34.24 1.82
790 848 5.258841 TGGAGTTCGGATCAGAAGTAGTAA 58.741 41.667 14.82 0.68 34.24 2.24
817 878 5.177696 ACGAACTCTTTTCTTTTCTGATCGG 59.822 40.000 0.00 0.00 0.00 4.18
826 887 7.928307 TTTCTTTTCTGATCGGATGAAGATT 57.072 32.000 21.97 0.00 0.00 2.40
831 892 9.270640 CTTTTCTGATCGGATGAAGATTATCTT 57.729 33.333 17.26 7.23 39.87 2.40
835 897 8.690884 TCTGATCGGATGAAGATTATCTTATCC 58.309 37.037 20.81 20.81 36.73 2.59
849 911 2.039216 TCTTATCCCAAGTGCAAACGGA 59.961 45.455 0.00 0.00 0.00 4.69
869 932 2.757917 GGGAGCTGCTCGTCCTCT 60.758 66.667 22.25 0.00 32.90 3.69
971 1049 2.111669 CCGCAGCAGCCATATCCA 59.888 61.111 0.00 0.00 37.52 3.41
974 1052 0.887836 CGCAGCAGCCATATCCACAT 60.888 55.000 0.00 0.00 37.52 3.21
984 1062 3.616076 GCCATATCCACATCTCTTCTCGG 60.616 52.174 0.00 0.00 0.00 4.63
1000 1078 0.959553 TCGGTCGATTCCCTAGCATC 59.040 55.000 0.00 0.00 0.00 3.91
1001 1079 0.038159 CGGTCGATTCCCTAGCATCC 60.038 60.000 0.00 0.00 0.00 3.51
1002 1080 1.343069 GGTCGATTCCCTAGCATCCT 58.657 55.000 0.00 0.00 0.00 3.24
1003 1081 1.694696 GGTCGATTCCCTAGCATCCTT 59.305 52.381 0.00 0.00 0.00 3.36
1004 1082 2.104963 GGTCGATTCCCTAGCATCCTTT 59.895 50.000 0.00 0.00 0.00 3.11
1005 1083 3.433740 GGTCGATTCCCTAGCATCCTTTT 60.434 47.826 0.00 0.00 0.00 2.27
1006 1084 4.200092 GTCGATTCCCTAGCATCCTTTTT 58.800 43.478 0.00 0.00 0.00 1.94
1281 1370 4.111016 CTGCCGGCGAGTACACGA 62.111 66.667 23.90 0.00 35.09 4.35
1282 1371 4.409218 TGCCGGCGAGTACACGAC 62.409 66.667 23.90 13.03 38.00 4.34
1286 1375 2.576317 GGCGAGTACACGACGAGC 60.576 66.667 17.12 0.00 35.47 5.03
1287 1376 2.175078 GCGAGTACACGACGAGCA 59.825 61.111 17.12 0.00 36.01 4.26
1288 1377 1.441515 GCGAGTACACGACGAGCAA 60.442 57.895 17.12 0.00 36.01 3.91
1289 1378 1.396543 GCGAGTACACGACGAGCAAG 61.397 60.000 17.12 0.00 36.01 4.01
1290 1379 0.793478 CGAGTACACGACGAGCAAGG 60.793 60.000 6.90 0.00 35.09 3.61
1291 1380 1.071567 GAGTACACGACGAGCAAGGC 61.072 60.000 0.00 0.00 0.00 4.35
1292 1381 2.092882 GTACACGACGAGCAAGGCC 61.093 63.158 0.00 0.00 0.00 5.19
1293 1382 3.291101 TACACGACGAGCAAGGCCC 62.291 63.158 0.00 0.00 0.00 5.80
1294 1383 4.680237 CACGACGAGCAAGGCCCA 62.680 66.667 0.00 0.00 0.00 5.36
1295 1384 4.681978 ACGACGAGCAAGGCCCAC 62.682 66.667 0.00 0.00 0.00 4.61
1314 1403 3.740397 CGGCCGGTGAGTACACGA 61.740 66.667 20.10 0.00 46.77 4.35
1315 1404 2.126189 GGCCGGTGAGTACACGAC 60.126 66.667 1.90 0.00 46.77 4.34
1316 1405 2.503375 GCCGGTGAGTACACGACG 60.503 66.667 1.90 0.00 46.77 5.12
1317 1406 2.503375 CCGGTGAGTACACGACGC 60.503 66.667 0.00 0.00 46.77 5.19
1318 1407 2.559840 CGGTGAGTACACGACGCT 59.440 61.111 0.00 0.00 46.77 5.07
1319 1408 1.511464 CGGTGAGTACACGACGCTC 60.511 63.158 0.00 0.00 46.77 5.03
1320 1409 1.577922 GGTGAGTACACGACGCTCA 59.422 57.895 0.00 0.00 46.77 4.26
1321 1410 0.039798 GGTGAGTACACGACGCTCAA 60.040 55.000 4.75 0.00 46.77 3.02
1322 1411 1.328439 GTGAGTACACGACGCTCAAG 58.672 55.000 4.75 0.00 40.40 3.02
1323 1412 0.240145 TGAGTACACGACGCTCAAGG 59.760 55.000 0.00 0.00 36.46 3.61
1324 1413 1.071567 GAGTACACGACGCTCAAGGC 61.072 60.000 0.00 0.00 37.64 4.35
1325 1414 2.092882 GTACACGACGCTCAAGGCC 61.093 63.158 0.00 0.00 37.74 5.19
1326 1415 3.291101 TACACGACGCTCAAGGCCC 62.291 63.158 0.00 0.00 37.74 5.80
1383 1472 4.111016 CCGGCGAGTACACTGCGA 62.111 66.667 9.30 0.00 0.00 5.10
1384 1473 2.577112 CGGCGAGTACACTGCGAG 60.577 66.667 0.00 0.00 0.00 5.03
1385 1474 2.881352 GGCGAGTACACTGCGAGC 60.881 66.667 0.00 0.00 0.00 5.03
1386 1475 2.126463 GCGAGTACACTGCGAGCA 60.126 61.111 0.00 0.00 0.00 4.26
1387 1476 1.733041 GCGAGTACACTGCGAGCAA 60.733 57.895 0.00 0.00 0.00 3.91
1388 1477 1.678269 GCGAGTACACTGCGAGCAAG 61.678 60.000 0.00 0.00 0.00 4.01
1389 1478 1.073216 CGAGTACACTGCGAGCAAGG 61.073 60.000 0.00 0.00 0.00 3.61
1390 1479 1.355066 GAGTACACTGCGAGCAAGGC 61.355 60.000 0.00 0.00 0.00 4.35
1391 1480 2.047274 TACACTGCGAGCAAGGCC 60.047 61.111 0.00 0.00 0.00 5.19
1392 1481 3.605749 TACACTGCGAGCAAGGCCC 62.606 63.158 0.00 0.00 0.00 5.80
1418 1507 2.202401 GGCGAGTACACGACGACC 60.202 66.667 17.12 4.19 35.09 4.79
1419 1508 2.557805 GCGAGTACACGACGACCA 59.442 61.111 17.12 0.00 35.09 4.02
1420 1509 1.081906 GCGAGTACACGACGACCAA 60.082 57.895 17.12 0.00 35.09 3.67
1421 1510 1.063951 GCGAGTACACGACGACCAAG 61.064 60.000 17.12 0.00 35.09 3.61
1422 1511 0.453950 CGAGTACACGACGACCAAGG 60.454 60.000 6.90 0.00 35.09 3.61
1423 1512 0.731855 GAGTACACGACGACCAAGGC 60.732 60.000 0.00 0.00 0.00 4.35
1424 1513 1.735559 GTACACGACGACCAAGGCC 60.736 63.158 0.00 0.00 0.00 5.19
1425 1514 2.934570 TACACGACGACCAAGGCCC 61.935 63.158 0.00 0.00 0.00 5.80
1453 1542 1.582968 GGGAGTACACGACGCTCAA 59.417 57.895 0.00 0.00 0.00 3.02
1459 1548 4.379243 CACGACGCTCAAGGCCCT 62.379 66.667 0.00 0.00 37.74 5.19
1523 1612 1.511464 GTACACGACGCTCAGGACG 60.511 63.158 0.00 0.00 0.00 4.79
1628 1720 3.133542 TGATGAGATGCCAGTAGGTTGAG 59.866 47.826 0.00 0.00 37.19 3.02
1629 1721 1.833630 TGAGATGCCAGTAGGTTGAGG 59.166 52.381 0.00 0.00 37.19 3.86
1630 1722 2.111384 GAGATGCCAGTAGGTTGAGGA 58.889 52.381 0.00 0.00 37.19 3.71
1631 1723 1.834263 AGATGCCAGTAGGTTGAGGAC 59.166 52.381 0.00 0.00 37.19 3.85
1632 1724 1.834263 GATGCCAGTAGGTTGAGGACT 59.166 52.381 0.00 0.00 37.19 3.85
1633 1725 1.729586 TGCCAGTAGGTTGAGGACTT 58.270 50.000 0.00 0.00 37.19 3.01
1634 1726 1.347707 TGCCAGTAGGTTGAGGACTTG 59.652 52.381 0.00 0.00 37.19 3.16
1635 1727 1.623811 GCCAGTAGGTTGAGGACTTGA 59.376 52.381 0.00 0.00 37.19 3.02
1657 1749 4.215109 AGGCTTTGTTGGTTACTGAATGT 58.785 39.130 0.00 0.00 0.00 2.71
1676 1768 8.437360 TGAATGTTTCTGTCGCTGATAATTAT 57.563 30.769 0.00 0.00 0.00 1.28
1741 1834 4.142687 GGCACAATATTGTCGCAGTTAGTT 60.143 41.667 28.27 3.99 39.91 2.24
1747 1840 6.985188 ATATTGTCGCAGTTAGTTGATGTT 57.015 33.333 0.00 0.00 0.00 2.71
1750 1843 3.493129 TGTCGCAGTTAGTTGATGTTGAC 59.507 43.478 0.00 0.00 0.00 3.18
1751 1844 3.741344 GTCGCAGTTAGTTGATGTTGACT 59.259 43.478 0.00 0.00 0.00 3.41
1752 1845 4.921515 GTCGCAGTTAGTTGATGTTGACTA 59.078 41.667 0.00 0.00 0.00 2.59
1753 1846 4.921515 TCGCAGTTAGTTGATGTTGACTAC 59.078 41.667 0.00 0.00 0.00 2.73
1754 1847 4.923871 CGCAGTTAGTTGATGTTGACTACT 59.076 41.667 0.00 0.00 0.00 2.57
1755 1848 5.164051 CGCAGTTAGTTGATGTTGACTACTG 60.164 44.000 0.00 0.00 34.41 2.74
1756 1849 5.926542 GCAGTTAGTTGATGTTGACTACTGA 59.073 40.000 0.00 0.00 33.85 3.41
1757 1850 6.423905 GCAGTTAGTTGATGTTGACTACTGAA 59.576 38.462 0.00 0.00 33.85 3.02
1758 1851 7.359598 GCAGTTAGTTGATGTTGACTACTGAAG 60.360 40.741 0.00 0.00 33.85 3.02
1759 1852 7.653713 CAGTTAGTTGATGTTGACTACTGAAGT 59.346 37.037 0.00 0.00 42.80 3.01
1760 1853 8.204836 AGTTAGTTGATGTTGACTACTGAAGTT 58.795 33.333 0.00 0.00 39.07 2.66
1761 1854 8.488764 GTTAGTTGATGTTGACTACTGAAGTTC 58.511 37.037 0.00 0.00 39.07 3.01
1762 1855 6.582636 AGTTGATGTTGACTACTGAAGTTCA 58.417 36.000 5.25 5.25 39.07 3.18
1763 1856 7.220030 AGTTGATGTTGACTACTGAAGTTCAT 58.780 34.615 5.91 0.00 39.07 2.57
1764 1857 8.367911 AGTTGATGTTGACTACTGAAGTTCATA 58.632 33.333 5.91 1.03 39.07 2.15
1765 1858 9.155975 GTTGATGTTGACTACTGAAGTTCATAT 57.844 33.333 5.91 0.47 39.07 1.78
1863 1963 2.655090 TGCATTGGACCTTCAACTCA 57.345 45.000 0.00 0.00 0.00 3.41
1891 2005 4.082625 CCACATCTTACAACACATGCATGT 60.083 41.667 26.61 26.61 42.84 3.21
1902 2016 4.334552 ACACATGCATGTAACCTGATTCA 58.665 39.130 30.92 0.00 39.39 2.57
1905 2019 6.071221 ACACATGCATGTAACCTGATTCATTT 60.071 34.615 30.92 0.51 39.39 2.32
1909 2023 8.573885 CATGCATGTAACCTGATTCATTTATCT 58.426 33.333 18.91 0.00 0.00 1.98
1910 2024 9.797642 ATGCATGTAACCTGATTCATTTATCTA 57.202 29.630 0.00 0.00 0.00 1.98
1911 2025 9.276590 TGCATGTAACCTGATTCATTTATCTAG 57.723 33.333 0.00 0.00 0.00 2.43
1912 2026 9.277783 GCATGTAACCTGATTCATTTATCTAGT 57.722 33.333 0.00 0.00 0.00 2.57
1919 2033 9.554053 ACCTGATTCATTTATCTAGTATAGCCT 57.446 33.333 0.00 0.00 38.99 4.58
1921 2035 9.729023 CTGATTCATTTATCTAGTATAGCCTCG 57.271 37.037 0.00 0.00 38.99 4.63
1922 2036 9.244292 TGATTCATTTATCTAGTATAGCCTCGT 57.756 33.333 0.00 0.00 38.99 4.18
1941 2055 2.203480 TTTTTGCGCCCTGGAGCT 60.203 55.556 13.11 0.00 41.45 4.09
1950 2064 2.362369 CCCTGGAGCTGGACGACAT 61.362 63.158 0.00 0.00 0.00 3.06
1955 2069 0.037326 GGAGCTGGACGACATCAACA 60.037 55.000 0.00 0.00 0.00 3.33
1958 2072 3.521995 CTGGACGACATCAACAGCT 57.478 52.632 0.00 0.00 0.00 4.24
1965 2079 5.163457 TGGACGACATCAACAGCTTGATATA 60.163 40.000 0.56 0.00 44.04 0.86
1967 2081 6.128715 GGACGACATCAACAGCTTGATATATG 60.129 42.308 0.56 0.00 44.04 1.78
1993 2107 7.850935 ATTCATAATCTTTGCCCTCAATCAT 57.149 32.000 0.00 0.00 31.33 2.45
1994 2108 7.664552 TTCATAATCTTTGCCCTCAATCATT 57.335 32.000 0.00 0.00 31.33 2.57
1995 2109 7.281040 TCATAATCTTTGCCCTCAATCATTC 57.719 36.000 0.00 0.00 31.33 2.67
1996 2110 6.266103 TCATAATCTTTGCCCTCAATCATTCC 59.734 38.462 0.00 0.00 31.33 3.01
1997 2111 2.368439 TCTTTGCCCTCAATCATTCCG 58.632 47.619 0.00 0.00 31.33 4.30
1998 2112 1.406539 CTTTGCCCTCAATCATTCCGG 59.593 52.381 0.00 0.00 31.33 5.14
1999 2113 0.623194 TTGCCCTCAATCATTCCGGA 59.377 50.000 0.00 0.00 0.00 5.14
2000 2114 0.107214 TGCCCTCAATCATTCCGGAC 60.107 55.000 1.83 0.00 0.00 4.79
2001 2115 0.107214 GCCCTCAATCATTCCGGACA 60.107 55.000 1.83 0.00 0.00 4.02
2002 2116 1.681780 GCCCTCAATCATTCCGGACAA 60.682 52.381 1.83 0.00 0.00 3.18
2003 2117 2.936202 CCCTCAATCATTCCGGACAAT 58.064 47.619 1.83 0.00 0.00 2.71
2013 2127 0.035152 TCCGGACAATGCTTGCATCT 60.035 50.000 0.00 0.00 0.00 2.90
2014 2128 0.379669 CCGGACAATGCTTGCATCTC 59.620 55.000 8.64 6.62 0.00 2.75
2016 2130 1.741706 CGGACAATGCTTGCATCTCTT 59.258 47.619 8.64 0.00 0.00 2.85
2019 2133 3.065925 GGACAATGCTTGCATCTCTTACC 59.934 47.826 8.64 4.14 0.00 2.85
2020 2134 3.689347 ACAATGCTTGCATCTCTTACCA 58.311 40.909 8.64 0.00 0.00 3.25
2021 2135 3.441572 ACAATGCTTGCATCTCTTACCAC 59.558 43.478 8.64 0.00 0.00 4.16
2022 2136 2.113860 TGCTTGCATCTCTTACCACC 57.886 50.000 0.00 0.00 0.00 4.61
2023 2137 1.009829 GCTTGCATCTCTTACCACCG 58.990 55.000 0.00 0.00 0.00 4.94
2024 2138 1.676014 GCTTGCATCTCTTACCACCGT 60.676 52.381 0.00 0.00 0.00 4.83
2025 2139 2.002586 CTTGCATCTCTTACCACCGTG 58.997 52.381 0.00 0.00 0.00 4.94
2026 2140 0.391130 TGCATCTCTTACCACCGTGC 60.391 55.000 0.00 0.00 0.00 5.34
2027 2141 0.391130 GCATCTCTTACCACCGTGCA 60.391 55.000 0.00 0.00 0.00 4.57
2029 2143 2.632377 CATCTCTTACCACCGTGCATT 58.368 47.619 0.00 0.00 0.00 3.56
2030 2144 2.093306 TCTCTTACCACCGTGCATTG 57.907 50.000 0.00 0.00 0.00 2.82
2031 2145 0.447801 CTCTTACCACCGTGCATTGC 59.552 55.000 0.46 0.46 0.00 3.56
2034 2226 0.958382 TTACCACCGTGCATTGCTCC 60.958 55.000 10.49 0.00 0.00 4.70
2036 2228 3.803082 CACCGTGCATTGCTCCGG 61.803 66.667 27.39 27.39 44.58 5.14
2039 2231 2.331893 CCGTGCATTGCTCCGGAAA 61.332 57.895 26.02 0.00 42.84 3.13
2041 2233 0.171007 CGTGCATTGCTCCGGAAAAT 59.829 50.000 5.23 5.87 0.00 1.82
2046 2238 3.761218 TGCATTGCTCCGGAAAATTCTAA 59.239 39.130 5.23 0.00 0.00 2.10
2047 2239 4.142403 TGCATTGCTCCGGAAAATTCTAAG 60.142 41.667 5.23 0.00 0.00 2.18
2049 2241 5.573146 CATTGCTCCGGAAAATTCTAAGTC 58.427 41.667 5.23 0.00 0.00 3.01
2050 2242 4.553330 TGCTCCGGAAAATTCTAAGTCT 57.447 40.909 5.23 0.00 0.00 3.24
2052 2244 5.661458 TGCTCCGGAAAATTCTAAGTCTAG 58.339 41.667 5.23 0.00 0.00 2.43
2054 2246 5.980715 GCTCCGGAAAATTCTAAGTCTAGAG 59.019 44.000 5.23 0.00 35.55 2.43
2056 2248 5.956563 TCCGGAAAATTCTAAGTCTAGAGGT 59.043 40.000 0.00 0.00 35.55 3.85
2057 2249 6.439692 TCCGGAAAATTCTAAGTCTAGAGGTT 59.560 38.462 0.00 0.00 35.55 3.50
2058 2250 6.757478 CCGGAAAATTCTAAGTCTAGAGGTTC 59.243 42.308 0.00 0.00 35.55 3.62
2067 2259 7.640313 TCTAAGTCTAGAGGTTCCTACATGAA 58.360 38.462 0.00 0.00 30.34 2.57
2069 2261 6.783708 AGTCTAGAGGTTCCTACATGAAAG 57.216 41.667 0.00 0.00 0.00 2.62
2070 2262 5.128008 AGTCTAGAGGTTCCTACATGAAAGC 59.872 44.000 0.00 0.00 0.00 3.51
2071 2263 5.023452 TCTAGAGGTTCCTACATGAAAGCA 58.977 41.667 0.00 0.00 0.00 3.91
2072 2264 4.213564 AGAGGTTCCTACATGAAAGCAG 57.786 45.455 0.00 0.00 0.00 4.24
2073 2265 2.680339 GAGGTTCCTACATGAAAGCAGC 59.320 50.000 0.00 0.00 0.00 5.25
2111 2303 6.259550 AGAATCAGTTTTCCTTGTATGCAC 57.740 37.500 0.00 0.00 0.00 4.57
2156 2400 7.333423 GCTTGTACTGTTGTAATCTGGATAACA 59.667 37.037 0.00 0.00 0.00 2.41
2157 2401 9.214957 CTTGTACTGTTGTAATCTGGATAACAA 57.785 33.333 0.00 0.00 31.67 2.83
2164 2408 8.530311 TGTTGTAATCTGGATAACAAAATGCAT 58.470 29.630 0.00 0.00 33.92 3.96
2166 2410 7.416817 TGTAATCTGGATAACAAAATGCATCG 58.583 34.615 0.00 0.00 0.00 3.84
2171 2415 7.995289 TCTGGATAACAAAATGCATCGTTATT 58.005 30.769 20.97 9.84 35.30 1.40
2209 2453 5.253330 ACACCGTGAATTCCAGTTATCATT 58.747 37.500 5.28 0.00 0.00 2.57
2211 2455 6.538742 ACACCGTGAATTCCAGTTATCATTAG 59.461 38.462 5.28 0.00 0.00 1.73
2213 2457 6.055588 CCGTGAATTCCAGTTATCATTAGGT 58.944 40.000 2.27 0.00 0.00 3.08
2215 2459 6.511767 CGTGAATTCCAGTTATCATTAGGTGC 60.512 42.308 2.27 0.00 0.00 5.01
2218 2462 4.835284 TCCAGTTATCATTAGGTGCACA 57.165 40.909 20.43 0.00 0.00 4.57
2220 2464 3.309682 CCAGTTATCATTAGGTGCACACG 59.690 47.826 20.43 1.43 0.00 4.49
2221 2465 4.180817 CAGTTATCATTAGGTGCACACGA 58.819 43.478 20.43 7.25 0.00 4.35
2297 2635 3.006112 TGGCCTTTGCGGTCATAATAA 57.994 42.857 3.32 0.00 44.09 1.40
2298 2636 3.561143 TGGCCTTTGCGGTCATAATAAT 58.439 40.909 3.32 0.00 44.09 1.28
2299 2637 4.720046 TGGCCTTTGCGGTCATAATAATA 58.280 39.130 3.32 0.00 44.09 0.98
2300 2638 5.321102 TGGCCTTTGCGGTCATAATAATAT 58.679 37.500 3.32 0.00 44.09 1.28
2339 2677 1.001815 CTCGCAAAACCGATGTTTGGT 60.002 47.619 7.30 0.00 43.80 3.67
2352 2690 6.887545 ACCGATGTTTGGTCTTTTATAATGGA 59.112 34.615 0.00 0.00 33.35 3.41
2363 2701 9.918630 GGTCTTTTATAATGGATCATCAAATGG 57.081 33.333 0.00 0.00 0.00 3.16
2460 2801 0.609131 ATGTTTTCAGGGGTGCGAGG 60.609 55.000 0.00 0.00 0.00 4.63
2465 2806 0.766131 TTCAGGGGTGCGAGGTTTTA 59.234 50.000 0.00 0.00 0.00 1.52
2510 2868 5.419542 GACATAGGAGTGTGTTGCTTATCA 58.580 41.667 0.00 0.00 31.16 2.15
2539 2897 1.731424 GCACTAGCAATGCACAGCTTG 60.731 52.381 18.52 18.05 42.88 4.01
2555 2913 3.117491 GCTTGCAGCTCCTATCATGTA 57.883 47.619 0.00 0.00 38.45 2.29
2556 2914 3.672808 GCTTGCAGCTCCTATCATGTAT 58.327 45.455 0.00 0.00 38.45 2.29
2557 2915 4.070716 GCTTGCAGCTCCTATCATGTATT 58.929 43.478 0.00 0.00 38.45 1.89
2559 2917 4.277515 TGCAGCTCCTATCATGTATTCC 57.722 45.455 0.00 0.00 0.00 3.01
2560 2918 3.906218 TGCAGCTCCTATCATGTATTCCT 59.094 43.478 0.00 0.00 0.00 3.36
2561 2919 5.086621 TGCAGCTCCTATCATGTATTCCTA 58.913 41.667 0.00 0.00 0.00 2.94
2562 2920 5.047021 TGCAGCTCCTATCATGTATTCCTAC 60.047 44.000 0.00 0.00 0.00 3.18
2563 2921 5.645624 CAGCTCCTATCATGTATTCCTACG 58.354 45.833 0.00 0.00 0.00 3.51
2564 2922 4.158764 AGCTCCTATCATGTATTCCTACGC 59.841 45.833 0.00 0.00 0.00 4.42
2565 2923 4.082190 GCTCCTATCATGTATTCCTACGCA 60.082 45.833 0.00 0.00 0.00 5.24
2566 2924 5.644977 TCCTATCATGTATTCCTACGCAG 57.355 43.478 0.00 0.00 0.00 5.18
2586 5602 8.001881 ACGCAGAATATGATAGTAATAGGGAG 57.998 38.462 0.00 0.00 0.00 4.30
2616 5632 8.868522 TCCAGTTTCAGATTCAATTCAATACT 57.131 30.769 0.00 0.00 0.00 2.12
2617 5633 8.950210 TCCAGTTTCAGATTCAATTCAATACTC 58.050 33.333 0.00 0.00 0.00 2.59
2618 5634 8.186821 CCAGTTTCAGATTCAATTCAATACTCC 58.813 37.037 0.00 0.00 0.00 3.85
2669 5685 6.630444 AATGCATCTCCATGAAGAACATAC 57.370 37.500 0.00 0.00 37.46 2.39
2692 5708 6.418101 ACCAATGCACTAAATCACTATCAGT 58.582 36.000 0.00 0.00 0.00 3.41
2693 5709 7.564793 ACCAATGCACTAAATCACTATCAGTA 58.435 34.615 0.00 0.00 0.00 2.74
2694 5710 7.495934 ACCAATGCACTAAATCACTATCAGTAC 59.504 37.037 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 8.739972 AGGAACTGTATATTGTGGATTTTTGAC 58.260 33.333 0.00 0.00 37.18 3.18
44 45 8.664798 CGTCATTATGTTCAAGTCTGGATTAAA 58.335 33.333 0.00 0.00 0.00 1.52
45 46 8.038351 TCGTCATTATGTTCAAGTCTGGATTAA 58.962 33.333 0.00 0.00 0.00 1.40
46 47 7.491372 GTCGTCATTATGTTCAAGTCTGGATTA 59.509 37.037 0.00 0.00 0.00 1.75
47 48 6.313905 GTCGTCATTATGTTCAAGTCTGGATT 59.686 38.462 0.00 0.00 0.00 3.01
48 49 5.812642 GTCGTCATTATGTTCAAGTCTGGAT 59.187 40.000 0.00 0.00 0.00 3.41
49 50 5.168569 GTCGTCATTATGTTCAAGTCTGGA 58.831 41.667 0.00 0.00 0.00 3.86
50 51 4.031765 CGTCGTCATTATGTTCAAGTCTGG 59.968 45.833 0.00 0.00 0.00 3.86
51 52 4.857037 TCGTCGTCATTATGTTCAAGTCTG 59.143 41.667 0.00 0.00 0.00 3.51
52 53 5.055642 TCGTCGTCATTATGTTCAAGTCT 57.944 39.130 0.00 0.00 0.00 3.24
53 54 5.950965 ATCGTCGTCATTATGTTCAAGTC 57.049 39.130 0.00 0.00 0.00 3.01
100 105 4.224370 GGATCACTAGTTGGTTGGGTCTTA 59.776 45.833 0.00 0.00 0.00 2.10
142 147 7.631933 AGATGGCCTATCGTTACTACTACTAT 58.368 38.462 3.32 0.00 40.86 2.12
183 201 2.839026 GTCGAGTCACACTAAATCGTCG 59.161 50.000 0.00 0.00 35.05 5.12
186 207 2.159612 TCCGTCGAGTCACACTAAATCG 60.160 50.000 0.00 0.00 34.80 3.34
190 211 0.514255 CGTCCGTCGAGTCACACTAA 59.486 55.000 0.00 0.00 42.86 2.24
461 506 1.137872 CTTTCGGGACCTGATGGAGAG 59.862 57.143 3.15 0.00 37.04 3.20
531 583 0.249405 CCAAAGCAACACAACCGCAT 60.249 50.000 0.00 0.00 0.00 4.73
596 649 0.951040 GCTTCCTCCACAAGACACGG 60.951 60.000 0.00 0.00 0.00 4.94
659 717 6.944234 TCTCTTTCTTTCCAAGTTCTTTCC 57.056 37.500 0.00 0.00 0.00 3.13
660 718 8.678199 TCTTTCTCTTTCTTTCCAAGTTCTTTC 58.322 33.333 0.00 0.00 0.00 2.62
661 719 8.581253 TCTTTCTCTTTCTTTCCAAGTTCTTT 57.419 30.769 0.00 0.00 0.00 2.52
662 720 8.049721 TCTCTTTCTCTTTCTTTCCAAGTTCTT 58.950 33.333 0.00 0.00 0.00 2.52
663 721 7.569240 TCTCTTTCTCTTTCTTTCCAAGTTCT 58.431 34.615 0.00 0.00 0.00 3.01
664 722 7.519809 GCTCTCTTTCTCTTTCTTTCCAAGTTC 60.520 40.741 0.00 0.00 0.00 3.01
665 723 6.262049 GCTCTCTTTCTCTTTCTTTCCAAGTT 59.738 38.462 0.00 0.00 0.00 2.66
666 724 5.762711 GCTCTCTTTCTCTTTCTTTCCAAGT 59.237 40.000 0.00 0.00 0.00 3.16
667 725 5.107143 CGCTCTCTTTCTCTTTCTTTCCAAG 60.107 44.000 0.00 0.00 0.00 3.61
668 726 4.752101 CGCTCTCTTTCTCTTTCTTTCCAA 59.248 41.667 0.00 0.00 0.00 3.53
669 727 4.202264 ACGCTCTCTTTCTCTTTCTTTCCA 60.202 41.667 0.00 0.00 0.00 3.53
670 728 4.311606 ACGCTCTCTTTCTCTTTCTTTCC 58.688 43.478 0.00 0.00 0.00 3.13
671 729 4.387559 GGACGCTCTCTTTCTCTTTCTTTC 59.612 45.833 0.00 0.00 0.00 2.62
672 730 4.311606 GGACGCTCTCTTTCTCTTTCTTT 58.688 43.478 0.00 0.00 0.00 2.52
673 731 3.306433 GGGACGCTCTCTTTCTCTTTCTT 60.306 47.826 0.00 0.00 0.00 2.52
721 779 9.353999 GGTCAATTTGTGTTCTTATCCAATTAC 57.646 33.333 0.00 0.00 0.00 1.89
744 802 2.035576 AGTGTTACTTCCTCGTGTGGTC 59.964 50.000 0.00 0.00 0.00 4.02
761 819 2.632996 TCTGATCCGAACTCCAAAGTGT 59.367 45.455 0.00 0.00 35.36 3.55
767 825 3.698289 ACTACTTCTGATCCGAACTCCA 58.302 45.455 0.00 0.00 0.00 3.86
769 827 7.201333 CGTTTTTACTACTTCTGATCCGAACTC 60.201 40.741 0.00 0.00 0.00 3.01
770 828 6.585322 CGTTTTTACTACTTCTGATCCGAACT 59.415 38.462 0.00 0.00 0.00 3.01
771 829 6.583806 TCGTTTTTACTACTTCTGATCCGAAC 59.416 38.462 0.00 0.00 0.00 3.95
772 830 6.680810 TCGTTTTTACTACTTCTGATCCGAA 58.319 36.000 0.00 0.00 0.00 4.30
773 831 6.258230 TCGTTTTTACTACTTCTGATCCGA 57.742 37.500 0.00 0.00 0.00 4.55
774 832 6.585322 AGTTCGTTTTTACTACTTCTGATCCG 59.415 38.462 0.00 0.00 0.00 4.18
775 833 7.813627 AGAGTTCGTTTTTACTACTTCTGATCC 59.186 37.037 0.00 0.00 0.00 3.36
776 834 8.745464 AGAGTTCGTTTTTACTACTTCTGATC 57.255 34.615 0.00 0.00 0.00 2.92
777 835 9.543783 AAAGAGTTCGTTTTTACTACTTCTGAT 57.456 29.630 0.00 0.00 0.00 2.90
778 836 8.937634 AAAGAGTTCGTTTTTACTACTTCTGA 57.062 30.769 0.00 0.00 0.00 3.27
779 837 9.634300 GAAAAGAGTTCGTTTTTACTACTTCTG 57.366 33.333 0.00 0.00 0.00 3.02
780 838 9.597170 AGAAAAGAGTTCGTTTTTACTACTTCT 57.403 29.630 0.00 0.00 0.00 2.85
786 844 9.556030 CAGAAAAGAAAAGAGTTCGTTTTTACT 57.444 29.630 2.38 0.00 32.01 2.24
787 845 9.550811 TCAGAAAAGAAAAGAGTTCGTTTTTAC 57.449 29.630 2.38 0.00 32.01 2.01
789 847 9.290483 GATCAGAAAAGAAAAGAGTTCGTTTTT 57.710 29.630 2.38 0.00 32.01 1.94
790 848 7.640240 CGATCAGAAAAGAAAAGAGTTCGTTTT 59.360 33.333 0.00 0.80 32.01 2.43
817 878 7.663081 TGCACTTGGGATAAGATAATCTTCATC 59.337 37.037 0.00 0.00 37.89 2.92
826 887 4.080807 TCCGTTTGCACTTGGGATAAGATA 60.081 41.667 0.00 0.00 0.00 1.98
831 892 2.570415 TTCCGTTTGCACTTGGGATA 57.430 45.000 0.00 0.00 0.00 2.59
835 897 0.031994 CCCTTTCCGTTTGCACTTGG 59.968 55.000 0.00 0.00 0.00 3.61
849 911 1.893919 GAGGACGAGCAGCTCCCTTT 61.894 60.000 18.45 3.24 0.00 3.11
869 932 1.677552 GGGACAAGGAAGAAGCGGA 59.322 57.895 0.00 0.00 0.00 5.54
903 966 3.753294 TTTCTTGTCGAGGAGAAAGCT 57.247 42.857 15.49 0.00 37.06 3.74
911 974 1.574702 GGGGCGTTTTCTTGTCGAGG 61.575 60.000 0.00 0.00 0.00 4.63
915 978 1.285950 GCAGGGGCGTTTTCTTGTC 59.714 57.895 0.00 0.00 0.00 3.18
964 1042 4.614764 CGACCGAGAAGAGATGTGGATATG 60.615 50.000 0.00 0.00 0.00 1.78
971 1049 2.359531 GGAATCGACCGAGAAGAGATGT 59.640 50.000 0.00 0.00 0.00 3.06
974 1052 1.064611 AGGGAATCGACCGAGAAGAGA 60.065 52.381 0.00 0.00 0.00 3.10
984 1062 3.477210 AAAGGATGCTAGGGAATCGAC 57.523 47.619 0.00 0.00 0.00 4.20
1006 1084 4.473444 AGAGAGATCAAAGTGGCCAAAAA 58.527 39.130 7.24 0.00 0.00 1.94
1007 1085 4.104383 AGAGAGATCAAAGTGGCCAAAA 57.896 40.909 7.24 0.00 0.00 2.44
1008 1086 3.795688 AGAGAGATCAAAGTGGCCAAA 57.204 42.857 7.24 0.00 0.00 3.28
1009 1087 3.055094 GGTAGAGAGATCAAAGTGGCCAA 60.055 47.826 7.24 0.00 0.00 4.52
1010 1088 2.501723 GGTAGAGAGATCAAAGTGGCCA 59.498 50.000 0.00 0.00 0.00 5.36
1011 1089 2.501723 TGGTAGAGAGATCAAAGTGGCC 59.498 50.000 0.00 0.00 0.00 5.36
1012 1090 3.895232 TGGTAGAGAGATCAAAGTGGC 57.105 47.619 0.00 0.00 0.00 5.01
1013 1091 4.187694 GCTTGGTAGAGAGATCAAAGTGG 58.812 47.826 0.00 0.00 0.00 4.00
1014 1092 4.187694 GGCTTGGTAGAGAGATCAAAGTG 58.812 47.826 0.00 0.00 0.00 3.16
1015 1093 3.198853 GGGCTTGGTAGAGAGATCAAAGT 59.801 47.826 0.00 0.00 0.00 2.66
1055 1136 1.450312 CGCTCCCTTGGTGTCCATC 60.450 63.158 0.00 0.00 31.53 3.51
1112 1193 3.160047 AGCATGGCCTCCTCCTCG 61.160 66.667 3.32 0.00 0.00 4.63
1267 1356 3.713615 CTCGTCGTGTACTCGCCGG 62.714 68.421 18.73 0.00 33.18 6.13
1268 1357 2.276493 CTCGTCGTGTACTCGCCG 60.276 66.667 13.81 13.81 33.62 6.46
1269 1358 2.576317 GCTCGTCGTGTACTCGCC 60.576 66.667 12.30 0.00 0.00 5.54
1270 1359 1.396543 CTTGCTCGTCGTGTACTCGC 61.397 60.000 12.30 7.00 0.00 5.03
1271 1360 0.793478 CCTTGCTCGTCGTGTACTCG 60.793 60.000 10.97 10.97 0.00 4.18
1272 1361 1.071567 GCCTTGCTCGTCGTGTACTC 61.072 60.000 0.00 0.00 0.00 2.59
1273 1362 1.080705 GCCTTGCTCGTCGTGTACT 60.081 57.895 0.00 0.00 0.00 2.73
1274 1363 2.092882 GGCCTTGCTCGTCGTGTAC 61.093 63.158 0.00 0.00 0.00 2.90
1275 1364 2.260434 GGCCTTGCTCGTCGTGTA 59.740 61.111 0.00 0.00 0.00 2.90
1276 1365 4.681978 GGGCCTTGCTCGTCGTGT 62.682 66.667 0.84 0.00 0.00 4.49
1277 1366 4.680237 TGGGCCTTGCTCGTCGTG 62.680 66.667 4.53 0.00 0.00 4.35
1278 1367 4.681978 GTGGGCCTTGCTCGTCGT 62.682 66.667 4.53 0.00 0.00 4.34
1297 1386 3.740397 TCGTGTACTCACCGGCCG 61.740 66.667 21.04 21.04 41.09 6.13
1298 1387 2.126189 GTCGTGTACTCACCGGCC 60.126 66.667 0.00 0.00 41.09 6.13
1299 1388 2.503375 CGTCGTGTACTCACCGGC 60.503 66.667 0.00 0.00 41.09 6.13
1300 1389 2.503375 GCGTCGTGTACTCACCGG 60.503 66.667 0.00 0.00 41.09 5.28
1301 1390 1.511464 GAGCGTCGTGTACTCACCG 60.511 63.158 0.00 0.00 41.09 4.94
1302 1391 0.039798 TTGAGCGTCGTGTACTCACC 60.040 55.000 0.47 0.00 40.03 4.02
1303 1392 1.328439 CTTGAGCGTCGTGTACTCAC 58.672 55.000 0.47 0.00 40.03 3.51
1304 1393 0.240145 CCTTGAGCGTCGTGTACTCA 59.760 55.000 0.00 0.00 38.62 3.41
1305 1394 1.071567 GCCTTGAGCGTCGTGTACTC 61.072 60.000 0.00 0.00 0.00 2.59
1306 1395 1.080705 GCCTTGAGCGTCGTGTACT 60.081 57.895 0.00 0.00 0.00 2.73
1307 1396 2.092882 GGCCTTGAGCGTCGTGTAC 61.093 63.158 0.00 0.00 45.17 2.90
1308 1397 2.260434 GGCCTTGAGCGTCGTGTA 59.740 61.111 0.00 0.00 45.17 2.90
1309 1398 4.681978 GGGCCTTGAGCGTCGTGT 62.682 66.667 0.84 0.00 45.17 4.49
1330 1419 3.511595 TAGTGTACTCGCCGGCGG 61.512 66.667 44.95 35.79 40.25 6.13
1331 1420 2.277756 GTAGTGTACTCGCCGGCG 60.278 66.667 42.13 42.13 41.35 6.46
1372 1461 1.374758 GCCTTGCTCGCAGTGTACT 60.375 57.895 0.00 0.00 0.00 2.73
1373 1462 2.391389 GGCCTTGCTCGCAGTGTAC 61.391 63.158 0.00 0.00 0.00 2.90
1374 1463 2.047274 GGCCTTGCTCGCAGTGTA 60.047 61.111 0.00 0.00 0.00 2.90
1399 1488 3.792047 TCGTCGTGTACTCGCCGG 61.792 66.667 18.73 0.00 33.18 6.13
1400 1489 2.572647 GTCGTCGTGTACTCGCCG 60.573 66.667 13.81 13.81 33.62 6.46
1401 1490 2.202401 GGTCGTCGTGTACTCGCC 60.202 66.667 12.30 0.00 0.00 5.54
1402 1491 1.063951 CTTGGTCGTCGTGTACTCGC 61.064 60.000 12.30 7.00 0.00 5.03
1403 1492 0.453950 CCTTGGTCGTCGTGTACTCG 60.454 60.000 10.97 10.97 0.00 4.18
1404 1493 0.731855 GCCTTGGTCGTCGTGTACTC 60.732 60.000 0.00 0.00 0.00 2.59
1405 1494 1.288127 GCCTTGGTCGTCGTGTACT 59.712 57.895 0.00 0.00 0.00 2.73
1406 1495 1.735559 GGCCTTGGTCGTCGTGTAC 60.736 63.158 0.00 0.00 0.00 2.90
1407 1496 2.652530 GGCCTTGGTCGTCGTGTA 59.347 61.111 0.00 0.00 0.00 2.90
1408 1497 4.309950 GGGCCTTGGTCGTCGTGT 62.310 66.667 0.84 0.00 0.00 4.49
1430 1519 4.139234 GTCGTGTACTCCCCGGCC 62.139 72.222 0.00 0.00 0.00 6.13
1431 1520 4.487412 CGTCGTGTACTCCCCGGC 62.487 72.222 0.00 0.00 0.00 6.13
1432 1521 4.487412 GCGTCGTGTACTCCCCGG 62.487 72.222 0.00 0.00 0.00 5.73
1433 1522 3.392595 GAGCGTCGTGTACTCCCCG 62.393 68.421 0.00 0.00 0.00 5.73
1434 1523 1.870055 TTGAGCGTCGTGTACTCCCC 61.870 60.000 0.00 0.00 0.00 4.81
1435 1524 0.456312 CTTGAGCGTCGTGTACTCCC 60.456 60.000 0.00 0.00 0.00 4.30
1436 1525 0.456312 CCTTGAGCGTCGTGTACTCC 60.456 60.000 0.00 0.00 0.00 3.85
1437 1526 1.071567 GCCTTGAGCGTCGTGTACTC 61.072 60.000 0.00 0.00 0.00 2.59
1628 1720 1.692411 ACCAACAAAGCCTCAAGTCC 58.308 50.000 0.00 0.00 0.00 3.85
1629 1721 3.883489 AGTAACCAACAAAGCCTCAAGTC 59.117 43.478 0.00 0.00 0.00 3.01
1630 1722 3.632145 CAGTAACCAACAAAGCCTCAAGT 59.368 43.478 0.00 0.00 0.00 3.16
1631 1723 3.882888 TCAGTAACCAACAAAGCCTCAAG 59.117 43.478 0.00 0.00 0.00 3.02
1632 1724 3.892284 TCAGTAACCAACAAAGCCTCAA 58.108 40.909 0.00 0.00 0.00 3.02
1633 1725 3.569194 TCAGTAACCAACAAAGCCTCA 57.431 42.857 0.00 0.00 0.00 3.86
1634 1726 4.278419 ACATTCAGTAACCAACAAAGCCTC 59.722 41.667 0.00 0.00 0.00 4.70
1635 1727 4.215109 ACATTCAGTAACCAACAAAGCCT 58.785 39.130 0.00 0.00 0.00 4.58
1657 1749 9.391006 ACCTAAAATAATTATCAGCGACAGAAA 57.609 29.630 0.00 0.00 0.00 2.52
1701 1793 1.765904 TGCCGGGATCAACAGCTAATA 59.234 47.619 2.18 0.00 0.00 0.98
1702 1794 0.546122 TGCCGGGATCAACAGCTAAT 59.454 50.000 2.18 0.00 0.00 1.73
1780 1873 9.403583 TGGAAAGCTTCTAGTAAAAGAAAGAAA 57.596 29.630 0.00 0.00 35.14 2.52
1838 1933 2.439409 TGAAGGTCCAATGCATGTCTG 58.561 47.619 0.00 0.00 0.00 3.51
1848 1943 3.073798 TGGCTAATGAGTTGAAGGTCCAA 59.926 43.478 0.00 0.00 0.00 3.53
1851 1946 3.674997 TGTGGCTAATGAGTTGAAGGTC 58.325 45.455 0.00 0.00 0.00 3.85
1863 1963 5.163622 GCATGTGTTGTAAGATGTGGCTAAT 60.164 40.000 0.00 0.00 0.00 1.73
1924 2038 2.203480 AGCTCCAGGGCGCAAAAA 60.203 55.556 10.83 0.00 37.29 1.94
1925 2039 2.985282 CAGCTCCAGGGCGCAAAA 60.985 61.111 10.83 0.00 37.29 2.44
1931 2045 4.459089 GTCGTCCAGCTCCAGGGC 62.459 72.222 0.00 0.00 0.00 5.19
1932 2046 2.303549 GATGTCGTCCAGCTCCAGGG 62.304 65.000 0.00 0.00 0.00 4.45
1933 2047 1.142748 GATGTCGTCCAGCTCCAGG 59.857 63.158 0.00 0.00 0.00 4.45
1934 2048 0.247460 TTGATGTCGTCCAGCTCCAG 59.753 55.000 0.00 0.00 0.00 3.86
1935 2049 0.037326 GTTGATGTCGTCCAGCTCCA 60.037 55.000 0.00 0.00 0.00 3.86
1936 2050 0.037326 TGTTGATGTCGTCCAGCTCC 60.037 55.000 0.00 0.00 0.00 4.70
1937 2051 1.354040 CTGTTGATGTCGTCCAGCTC 58.646 55.000 0.00 0.00 0.00 4.09
1938 2052 0.671781 GCTGTTGATGTCGTCCAGCT 60.672 55.000 13.23 0.00 43.89 4.24
1939 2053 0.671781 AGCTGTTGATGTCGTCCAGC 60.672 55.000 12.81 12.81 46.78 4.85
1940 2054 1.462283 CAAGCTGTTGATGTCGTCCAG 59.538 52.381 0.00 0.00 35.46 3.86
1941 2055 1.069978 TCAAGCTGTTGATGTCGTCCA 59.930 47.619 0.00 0.00 37.79 4.02
1965 2079 7.664552 TTGAGGGCAAAGATTATGAATTCAT 57.335 32.000 23.75 23.75 40.22 2.57
1967 2081 7.719483 TGATTGAGGGCAAAGATTATGAATTC 58.281 34.615 0.00 0.00 37.59 2.17
1982 2096 0.107214 TGTCCGGAATGATTGAGGGC 60.107 55.000 5.23 0.00 0.00 5.19
2001 2115 3.019564 GGTGGTAAGAGATGCAAGCATT 58.980 45.455 9.16 0.00 36.70 3.56
2002 2116 2.648059 GGTGGTAAGAGATGCAAGCAT 58.352 47.619 7.35 7.35 39.69 3.79
2003 2117 1.675714 CGGTGGTAAGAGATGCAAGCA 60.676 52.381 0.00 0.00 0.00 3.91
2013 2127 0.036164 AGCAATGCACGGTGGTAAGA 59.964 50.000 8.35 0.00 0.00 2.10
2014 2128 0.447801 GAGCAATGCACGGTGGTAAG 59.552 55.000 8.35 0.00 0.00 2.34
2016 2130 1.376683 GGAGCAATGCACGGTGGTA 60.377 57.895 8.35 0.00 0.00 3.25
2019 2133 3.803082 CCGGAGCAATGCACGGTG 61.803 66.667 25.81 3.15 42.95 4.94
2020 2134 3.545124 TTCCGGAGCAATGCACGGT 62.545 57.895 30.05 2.92 46.09 4.83
2021 2135 1.861542 TTTTCCGGAGCAATGCACGG 61.862 55.000 27.40 27.40 46.87 4.94
2022 2136 0.171007 ATTTTCCGGAGCAATGCACG 59.829 50.000 8.35 11.66 0.00 5.34
2023 2137 2.094545 AGAATTTTCCGGAGCAATGCAC 60.095 45.455 15.62 0.00 0.00 4.57
2024 2138 2.170166 AGAATTTTCCGGAGCAATGCA 58.830 42.857 15.62 0.00 0.00 3.96
2025 2139 2.947448 AGAATTTTCCGGAGCAATGC 57.053 45.000 3.34 6.28 0.00 3.56
2026 2140 5.355350 AGACTTAGAATTTTCCGGAGCAATG 59.645 40.000 3.34 0.00 0.00 2.82
2027 2141 5.501156 AGACTTAGAATTTTCCGGAGCAAT 58.499 37.500 3.34 4.57 0.00 3.56
2029 2143 4.553330 AGACTTAGAATTTTCCGGAGCA 57.447 40.909 3.34 0.00 0.00 4.26
2030 2144 5.903810 TCTAGACTTAGAATTTTCCGGAGC 58.096 41.667 3.34 0.00 33.01 4.70
2031 2145 6.097129 ACCTCTAGACTTAGAATTTTCCGGAG 59.903 42.308 3.34 0.00 35.55 4.63
2034 2226 6.757478 GGAACCTCTAGACTTAGAATTTTCCG 59.243 42.308 0.00 0.00 35.55 4.30
2036 2228 9.806203 GTAGGAACCTCTAGACTTAGAATTTTC 57.194 37.037 0.00 0.00 35.55 2.29
2039 2231 8.919145 CATGTAGGAACCTCTAGACTTAGAATT 58.081 37.037 0.00 0.00 35.55 2.17
2041 2233 7.640313 TCATGTAGGAACCTCTAGACTTAGAA 58.360 38.462 0.00 0.00 35.55 2.10
2046 2238 5.128008 GCTTTCATGTAGGAACCTCTAGACT 59.872 44.000 0.00 0.00 0.00 3.24
2047 2239 5.105310 TGCTTTCATGTAGGAACCTCTAGAC 60.105 44.000 0.00 0.00 0.00 2.59
2049 2241 5.344743 TGCTTTCATGTAGGAACCTCTAG 57.655 43.478 0.00 0.00 0.00 2.43
2050 2242 4.383118 GCTGCTTTCATGTAGGAACCTCTA 60.383 45.833 0.00 0.00 0.00 2.43
2052 2244 2.680339 GCTGCTTTCATGTAGGAACCTC 59.320 50.000 0.00 0.00 0.00 3.85
2054 2246 2.716217 AGCTGCTTTCATGTAGGAACC 58.284 47.619 0.00 0.00 0.00 3.62
2056 2248 2.489329 GCAAGCTGCTTTCATGTAGGAA 59.511 45.455 13.10 0.00 40.96 3.36
2057 2249 2.086869 GCAAGCTGCTTTCATGTAGGA 58.913 47.619 13.10 0.00 40.96 2.94
2058 2250 2.556534 GCAAGCTGCTTTCATGTAGG 57.443 50.000 13.10 0.00 40.96 3.18
2069 2261 2.489329 TCTTGTTCCATAAGCAAGCTGC 59.511 45.455 0.00 0.00 45.46 5.25
2070 2262 4.771590 TTCTTGTTCCATAAGCAAGCTG 57.228 40.909 0.00 0.00 39.36 4.24
2071 2263 5.012239 TGATTCTTGTTCCATAAGCAAGCT 58.988 37.500 0.00 0.00 39.36 3.74
2072 2264 5.105997 ACTGATTCTTGTTCCATAAGCAAGC 60.106 40.000 0.00 0.00 39.36 4.01
2073 2265 6.506500 ACTGATTCTTGTTCCATAAGCAAG 57.493 37.500 0.00 0.00 40.47 4.01
2111 2303 1.858798 GCTGCGCTGATGTTGCATAAG 60.859 52.381 19.32 0.00 38.07 1.73
2138 2367 7.890515 TGCATTTTGTTATCCAGATTACAACA 58.109 30.769 10.77 6.34 39.22 3.33
2139 2368 8.931385 ATGCATTTTGTTATCCAGATTACAAC 57.069 30.769 10.77 2.61 39.22 3.32
2156 2400 8.140628 TGCCATAATGTAATAACGATGCATTTT 58.859 29.630 0.00 0.00 32.79 1.82
2157 2401 7.656412 TGCCATAATGTAATAACGATGCATTT 58.344 30.769 0.00 0.00 32.79 2.32
2161 2405 6.480524 TCTGCCATAATGTAATAACGATGC 57.519 37.500 0.00 0.00 0.00 3.91
2164 2408 7.201661 GGTGTTTCTGCCATAATGTAATAACGA 60.202 37.037 0.00 0.00 0.00 3.85
2166 2410 6.910433 CGGTGTTTCTGCCATAATGTAATAAC 59.090 38.462 0.00 0.00 0.00 1.89
2171 2415 3.687212 CACGGTGTTTCTGCCATAATGTA 59.313 43.478 0.00 0.00 0.00 2.29
2209 2453 0.391130 GCTTGGATCGTGTGCACCTA 60.391 55.000 15.69 0.00 0.00 3.08
2211 2455 2.690778 GGCTTGGATCGTGTGCACC 61.691 63.158 15.69 4.74 0.00 5.01
2213 2457 1.073025 AAGGCTTGGATCGTGTGCA 59.927 52.632 0.00 0.00 0.00 4.57
2297 2635 6.092670 CGAGTGAAGATGTGTTGTTTCCATAT 59.907 38.462 0.00 0.00 0.00 1.78
2298 2636 5.408299 CGAGTGAAGATGTGTTGTTTCCATA 59.592 40.000 0.00 0.00 0.00 2.74
2299 2637 4.214119 CGAGTGAAGATGTGTTGTTTCCAT 59.786 41.667 0.00 0.00 0.00 3.41
2300 2638 3.559655 CGAGTGAAGATGTGTTGTTTCCA 59.440 43.478 0.00 0.00 0.00 3.53
2313 2651 1.798223 CATCGGTTTTGCGAGTGAAGA 59.202 47.619 0.00 0.00 0.00 2.87
2321 2659 1.001815 AGACCAAACATCGGTTTTGCG 60.002 47.619 0.00 0.00 44.63 4.85
2352 2690 7.959658 TGGATGTTAACTTCCATTTGATGAT 57.040 32.000 29.87 3.00 42.89 2.45
2363 2701 3.153919 TGGCCTGTTGGATGTTAACTTC 58.846 45.455 3.32 12.00 34.57 3.01
2460 2801 7.468141 AATTCTGAAGGGGTTCATCTAAAAC 57.532 36.000 0.00 0.00 0.00 2.43
2465 2806 4.044571 TCCAAATTCTGAAGGGGTTCATCT 59.955 41.667 0.00 0.00 0.00 2.90
2539 2897 4.550076 AGGAATACATGATAGGAGCTGC 57.450 45.455 0.00 0.00 0.00 5.25
2541 2899 4.158764 GCGTAGGAATACATGATAGGAGCT 59.841 45.833 0.00 0.00 0.00 4.09
2542 2900 4.082190 TGCGTAGGAATACATGATAGGAGC 60.082 45.833 0.00 0.00 0.00 4.70
2543 2901 5.416013 TCTGCGTAGGAATACATGATAGGAG 59.584 44.000 0.00 0.00 0.00 3.69
2544 2902 5.321927 TCTGCGTAGGAATACATGATAGGA 58.678 41.667 0.00 0.00 0.00 2.94
2545 2903 5.644977 TCTGCGTAGGAATACATGATAGG 57.355 43.478 0.00 0.00 0.00 2.57
2546 2904 9.242477 CATATTCTGCGTAGGAATACATGATAG 57.758 37.037 0.00 0.00 38.12 2.08
2547 2905 8.966868 TCATATTCTGCGTAGGAATACATGATA 58.033 33.333 0.00 0.00 38.12 2.15
2548 2906 7.840931 TCATATTCTGCGTAGGAATACATGAT 58.159 34.615 0.00 0.00 38.12 2.45
2550 2908 9.242477 CTATCATATTCTGCGTAGGAATACATG 57.758 37.037 0.00 0.00 38.12 3.21
2551 2909 8.972127 ACTATCATATTCTGCGTAGGAATACAT 58.028 33.333 0.00 3.51 38.12 2.29
2557 2915 9.121658 CCTATTACTATCATATTCTGCGTAGGA 57.878 37.037 0.00 0.00 0.00 2.94
2559 2917 9.121658 TCCCTATTACTATCATATTCTGCGTAG 57.878 37.037 0.00 0.00 0.00 3.51
2560 2918 9.121658 CTCCCTATTACTATCATATTCTGCGTA 57.878 37.037 0.00 0.00 0.00 4.42
2561 2919 7.616150 ACTCCCTATTACTATCATATTCTGCGT 59.384 37.037 0.00 0.00 0.00 5.24
2562 2920 8.001881 ACTCCCTATTACTATCATATTCTGCG 57.998 38.462 0.00 0.00 0.00 5.18
2580 5596 7.182026 TGAATCTGAAACTGGAATTACTCCCTA 59.818 37.037 0.00 0.00 44.69 3.53
2586 5602 9.912634 TTGAATTGAATCTGAAACTGGAATTAC 57.087 29.630 0.00 0.00 0.00 1.89
2618 5634 2.555757 CTGTTCTTGCCTTCCTTGGAAG 59.444 50.000 19.53 19.53 0.00 3.46
2669 5685 6.932356 ACTGATAGTGATTTAGTGCATTGG 57.068 37.500 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.