Multiple sequence alignment - TraesCS2B01G488600

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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 TraesCS2B01G488600 chr2B 100.000 3341 0 0 1 3341 686044632 686047972 0.000000e+00 6170.0
1 TraesCS2B01G488600 chr2B 75.000 828 185 18 2524 3340 686455149 686455965 2.450000e-96 363.0
2 TraesCS2B01G488600 chr2B 77.021 631 106 21 1554 2168 686810642 686811249 3.210000e-85 326.0
3 TraesCS2B01G488600 chr2B 80.645 279 50 4 1002 1278 685265866 685266142 2.610000e-51 213.0
4 TraesCS2B01G488600 chr2B 70.611 1014 263 28 2343 3340 97342798 97341804 4.400000e-44 189.0
5 TraesCS2B01G488600 chr2B 77.863 262 56 2 1012 1272 686809428 686809688 9.590000e-36 161.0
6 TraesCS2B01G488600 chr2B 76.289 194 31 12 858 1038 685795249 685795440 4.590000e-14 89.8
7 TraesCS2B01G488600 chr2A 83.756 1459 197 21 1894 3341 711059068 711060497 0.000000e+00 1345.0
8 TraesCS2B01G488600 chr2A 89.928 417 32 5 856 1268 711035302 711035712 2.280000e-146 529.0
9 TraesCS2B01G488600 chr2A 73.429 1114 252 35 2244 3341 710756207 710757292 8.750000e-101 377.0
10 TraesCS2B01G488600 chr2A 88.535 314 32 2 955 1268 711058287 711058596 8.750000e-101 377.0
11 TraesCS2B01G488600 chr2A 74.632 816 181 19 2539 3341 710651314 710652116 1.490000e-88 337.0
12 TraesCS2B01G488600 chr2A 72.331 871 202 35 2494 3340 27726404 27727259 1.550000e-58 237.0
13 TraesCS2B01G488600 chr2A 79.938 324 61 2 955 1278 710755203 710755522 5.570000e-58 235.0
14 TraesCS2B01G488600 chr2A 91.566 166 13 1 602 766 711035091 711035256 9.330000e-56 228.0
15 TraesCS2B01G488600 chr2A 79.061 277 46 8 1002 1278 710648008 710648272 2.650000e-41 180.0
16 TraesCS2B01G488600 chr2A 88.435 147 17 0 1558 1704 710648502 710648648 9.530000e-41 178.0
17 TraesCS2B01G488600 chr2A 86.275 153 21 0 1558 1710 702084695 702084543 2.060000e-37 167.0
18 TraesCS2B01G488600 chr2A 88.235 119 14 0 1002 1120 710799487 710799605 3.470000e-30 143.0
19 TraesCS2B01G488600 chr2A 90.805 87 6 2 1689 1774 710649691 710649776 7.570000e-22 115.0
20 TraesCS2B01G488600 chr2A 84.259 108 14 2 1441 1548 711058653 711058757 5.900000e-18 102.0
21 TraesCS2B01G488600 chr2A 84.444 90 10 1 606 691 710965985 710966074 5.940000e-13 86.1
22 TraesCS2B01G488600 chr1B 96.812 596 18 1 1 595 72017353 72016758 0.000000e+00 994.0
23 TraesCS2B01G488600 chr3D 96.026 604 22 2 1 602 96389712 96390315 0.000000e+00 981.0
24 TraesCS2B01G488600 chr3D 70.028 714 201 11 2633 3341 554957046 554957751 1.630000e-23 121.0
25 TraesCS2B01G488600 chr5B 95.847 602 21 3 4 602 617667271 617666671 0.000000e+00 970.0
26 TraesCS2B01G488600 chr5B 86.758 438 43 4 178 602 520103989 520103554 1.080000e-129 473.0
27 TraesCS2B01G488600 chr6B 94.408 608 22 5 1 602 9361913 9361312 0.000000e+00 924.0
28 TraesCS2B01G488600 chr6B 88.584 438 36 3 178 602 652381994 652381558 1.370000e-143 520.0
29 TraesCS2B01G488600 chr3A 92.715 604 25 13 1 602 682273991 682274577 0.000000e+00 854.0
30 TraesCS2B01G488600 chr3A 70.490 715 196 13 2633 3341 691715196 691714491 1.620000e-28 137.0
31 TraesCS2B01G488600 chr4A 91.987 599 28 12 7 602 613746273 613745692 0.000000e+00 822.0
32 TraesCS2B01G488600 chr1A 90.099 606 32 14 1 602 545857245 545856664 0.000000e+00 761.0
33 TraesCS2B01G488600 chr2D 75.645 1511 319 34 1849 3329 572067148 572068639 0.000000e+00 706.0
34 TraesCS2B01G488600 chr2D 76.679 819 160 21 2538 3341 571877992 571878794 3.080000e-115 425.0
35 TraesCS2B01G488600 chr2D 80.000 270 50 4 1002 1268 572029940 572030208 2.630000e-46 196.0
36 TraesCS2B01G488600 chr2D 79.039 229 43 3 1558 1782 572030394 572030621 5.770000e-33 152.0
37 TraesCS2B01G488600 chr6D 86.469 606 60 9 5 592 110725523 110724922 0.000000e+00 645.0
38 TraesCS2B01G488600 chr5A 86.013 622 53 13 8 602 7572923 7572309 1.310000e-178 636.0
39 TraesCS2B01G488600 chr5A 86.738 558 50 8 1 534 672453223 672453780 1.720000e-167 599.0
40 TraesCS2B01G488600 chr5D 88.577 499 35 5 1 482 462039261 462039754 1.340000e-163 586.0
41 TraesCS2B01G488600 chr3B 87.215 438 41 4 178 602 741496396 741495961 5.010000e-133 484.0
42 TraesCS2B01G488600 chr3B 69.616 1119 285 43 2246 3341 737767386 737766300 7.520000e-27 132.0
43 TraesCS2B01G488600 chr7A 70.869 944 251 19 2410 3341 726737355 726738286 7.310000e-47 198.0
44 TraesCS2B01G488600 chr7D 74.272 412 101 3 2498 2905 631060436 631060026 5.730000e-38 169.0


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 TraesCS2B01G488600 chr2B 686044632 686047972 3340 False 6170.0 6170 100.000000 1 3341 1 chr2B.!!$F3 3340
1 TraesCS2B01G488600 chr2B 686455149 686455965 816 False 363.0 363 75.000000 2524 3340 1 chr2B.!!$F4 816
2 TraesCS2B01G488600 chr2B 686809428 686811249 1821 False 243.5 326 77.442000 1012 2168 2 chr2B.!!$F5 1156
3 TraesCS2B01G488600 chr2A 711058287 711060497 2210 False 608.0 1345 85.516667 955 3341 3 chr2A.!!$F7 2386
4 TraesCS2B01G488600 chr2A 711035091 711035712 621 False 378.5 529 90.747000 602 1268 2 chr2A.!!$F6 666
5 TraesCS2B01G488600 chr2A 710755203 710757292 2089 False 306.0 377 76.683500 955 3341 2 chr2A.!!$F5 2386
6 TraesCS2B01G488600 chr2A 27726404 27727259 855 False 237.0 237 72.331000 2494 3340 1 chr2A.!!$F1 846
7 TraesCS2B01G488600 chr2A 710648008 710652116 4108 False 202.5 337 83.233250 1002 3341 4 chr2A.!!$F4 2339
8 TraesCS2B01G488600 chr1B 72016758 72017353 595 True 994.0 994 96.812000 1 595 1 chr1B.!!$R1 594
9 TraesCS2B01G488600 chr3D 96389712 96390315 603 False 981.0 981 96.026000 1 602 1 chr3D.!!$F1 601
10 TraesCS2B01G488600 chr5B 617666671 617667271 600 True 970.0 970 95.847000 4 602 1 chr5B.!!$R2 598
11 TraesCS2B01G488600 chr6B 9361312 9361913 601 True 924.0 924 94.408000 1 602 1 chr6B.!!$R1 601
12 TraesCS2B01G488600 chr3A 682273991 682274577 586 False 854.0 854 92.715000 1 602 1 chr3A.!!$F1 601
13 TraesCS2B01G488600 chr4A 613745692 613746273 581 True 822.0 822 91.987000 7 602 1 chr4A.!!$R1 595
14 TraesCS2B01G488600 chr1A 545856664 545857245 581 True 761.0 761 90.099000 1 602 1 chr1A.!!$R1 601
15 TraesCS2B01G488600 chr2D 572067148 572068639 1491 False 706.0 706 75.645000 1849 3329 1 chr2D.!!$F2 1480
16 TraesCS2B01G488600 chr2D 571877992 571878794 802 False 425.0 425 76.679000 2538 3341 1 chr2D.!!$F1 803
17 TraesCS2B01G488600 chr6D 110724922 110725523 601 True 645.0 645 86.469000 5 592 1 chr6D.!!$R1 587
18 TraesCS2B01G488600 chr5A 7572309 7572923 614 True 636.0 636 86.013000 8 602 1 chr5A.!!$R1 594
19 TraesCS2B01G488600 chr5A 672453223 672453780 557 False 599.0 599 86.738000 1 534 1 chr5A.!!$F1 533

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
972 1016 0.036010 CTTCCTCCATTGACCACGCT 60.036 55.0 0.0 0.0 0.00 5.07 F
1941 4816 0.031721 GCTGAGCCTATTGCCATTGC 59.968 55.0 0.0 0.0 42.71 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2130 5008 0.105760 TGGTGGCTGGTCATTTGGTT 60.106 50.000 0.00 0.0 0.0 3.67 R
3097 6292 1.203287 TGATGCTCCTGACAGTTCTCG 59.797 52.381 0.93 0.0 0.0 4.04 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
138 146 2.181777 GCGATCAGAGACACGCCA 59.818 61.111 0.00 0.00 44.27 5.69
310 321 1.154016 GCTGCTTCTCGCTACGTCA 60.154 57.895 0.00 0.00 40.11 4.35
313 324 1.868251 GCTTCTCGCTACGTCACCG 60.868 63.158 0.00 0.00 36.38 4.94
385 400 6.006449 ACACATGTAGCAAGAAGGAATCTTT 58.994 36.000 0.00 0.00 46.39 2.52
513 549 9.558396 TTTCAGGCTTTATGACAAATCAAAATT 57.442 25.926 0.00 0.00 38.69 1.82
622 661 1.989706 AAAACTAGCCTCGCCCAAAA 58.010 45.000 0.00 0.00 0.00 2.44
630 669 2.068519 GCCTCGCCCAAAATTTTGAAG 58.931 47.619 28.44 20.29 40.55 3.02
633 672 4.176271 CCTCGCCCAAAATTTTGAAGATC 58.824 43.478 28.44 12.88 40.55 2.75
641 680 6.101997 CCAAAATTTTGAAGATCTACAGGCC 58.898 40.000 28.44 0.00 40.55 5.19
662 701 0.176680 AACTCACGCAGCCCATAGAG 59.823 55.000 0.00 0.00 0.00 2.43
680 719 4.109675 CTTCCCGGGCCCAACGAT 62.110 66.667 24.92 0.00 0.00 3.73
709 748 5.805486 TGAAAGCGTGTCTGTATAATCTCAC 59.195 40.000 0.00 0.00 0.00 3.51
710 749 4.308899 AGCGTGTCTGTATAATCTCACC 57.691 45.455 0.00 0.00 0.00 4.02
711 750 3.068307 AGCGTGTCTGTATAATCTCACCC 59.932 47.826 0.00 0.00 0.00 4.61
715 754 5.872617 CGTGTCTGTATAATCTCACCCAAAA 59.127 40.000 0.00 0.00 0.00 2.44
769 809 4.285291 GCATTCGGCGCATTGTAC 57.715 55.556 10.83 0.00 0.00 2.90
771 811 0.934496 GCATTCGGCGCATTGTACTA 59.066 50.000 10.83 0.00 0.00 1.82
772 812 1.332904 GCATTCGGCGCATTGTACTAC 60.333 52.381 10.83 0.00 0.00 2.73
773 813 2.201732 CATTCGGCGCATTGTACTACT 58.798 47.619 10.83 0.00 0.00 2.57
777 817 1.268184 CGGCGCATTGTACTACTCGTA 60.268 52.381 10.83 0.00 0.00 3.43
781 821 4.977963 GGCGCATTGTACTACTCGTATTTA 59.022 41.667 10.83 0.00 0.00 1.40
785 825 8.693504 GCGCATTGTACTACTCGTATTTATTTA 58.306 33.333 0.30 0.00 0.00 1.40
820 860 2.511145 CCTTCTGCTCGGCTGCTC 60.511 66.667 0.00 0.00 0.00 4.26
821 861 2.511145 CTTCTGCTCGGCTGCTCC 60.511 66.667 0.00 0.00 0.00 4.70
824 864 4.172512 CTGCTCGGCTGCTCCCAT 62.173 66.667 0.00 0.00 0.00 4.00
826 866 3.859414 GCTCGGCTGCTCCCATCT 61.859 66.667 0.00 0.00 0.00 2.90
828 868 2.685017 TCGGCTGCTCCCATCTGT 60.685 61.111 0.00 0.00 0.00 3.41
829 869 2.202987 CGGCTGCTCCCATCTGTC 60.203 66.667 0.00 0.00 0.00 3.51
830 870 2.202987 GGCTGCTCCCATCTGTCG 60.203 66.667 0.00 0.00 0.00 4.35
831 871 2.581354 GCTGCTCCCATCTGTCGT 59.419 61.111 0.00 0.00 0.00 4.34
832 872 1.520342 GCTGCTCCCATCTGTCGTC 60.520 63.158 0.00 0.00 0.00 4.20
833 873 1.226802 CTGCTCCCATCTGTCGTCG 60.227 63.158 0.00 0.00 0.00 5.12
834 874 1.938657 CTGCTCCCATCTGTCGTCGT 61.939 60.000 0.00 0.00 0.00 4.34
835 875 1.226717 GCTCCCATCTGTCGTCGTC 60.227 63.158 0.00 0.00 0.00 4.20
836 876 1.934220 GCTCCCATCTGTCGTCGTCA 61.934 60.000 0.00 0.00 0.00 4.35
837 877 0.179161 CTCCCATCTGTCGTCGTCAC 60.179 60.000 0.00 0.00 0.00 3.67
838 878 0.608308 TCCCATCTGTCGTCGTCACT 60.608 55.000 0.00 0.00 0.00 3.41
839 879 0.456824 CCCATCTGTCGTCGTCACTG 60.457 60.000 0.00 0.00 0.00 3.66
840 880 0.521735 CCATCTGTCGTCGTCACTGA 59.478 55.000 0.00 0.00 0.00 3.41
841 881 1.607713 CATCTGTCGTCGTCACTGAC 58.392 55.000 0.00 0.00 35.49 3.51
842 882 1.197949 CATCTGTCGTCGTCACTGACT 59.802 52.381 7.58 0.00 36.71 3.41
843 883 0.586802 TCTGTCGTCGTCACTGACTG 59.413 55.000 7.58 1.81 36.71 3.51
844 884 0.999228 CTGTCGTCGTCACTGACTGC 60.999 60.000 7.58 0.00 36.71 4.40
845 885 2.075489 GTCGTCGTCACTGACTGCG 61.075 63.158 7.58 10.74 36.71 5.18
846 886 2.801162 CGTCGTCACTGACTGCGG 60.801 66.667 7.58 0.00 36.71 5.69
847 887 3.106407 GTCGTCACTGACTGCGGC 61.106 66.667 7.58 0.00 35.95 6.53
848 888 3.601685 TCGTCACTGACTGCGGCA 61.602 61.111 1.29 1.29 0.00 5.69
849 889 2.433145 CGTCACTGACTGCGGCAT 60.433 61.111 1.75 0.00 0.00 4.40
850 890 2.029288 CGTCACTGACTGCGGCATT 61.029 57.895 1.75 0.00 0.00 3.56
851 891 1.499056 GTCACTGACTGCGGCATTG 59.501 57.895 1.75 0.00 0.00 2.82
852 892 1.071299 TCACTGACTGCGGCATTGT 59.929 52.632 1.75 0.00 0.00 2.71
853 893 0.320050 TCACTGACTGCGGCATTGTA 59.680 50.000 1.75 0.00 0.00 2.41
854 894 1.066215 TCACTGACTGCGGCATTGTAT 60.066 47.619 1.75 0.00 0.00 2.29
881 921 9.863845 TTGTATATCGTATTGTTCAGAGACAAA 57.136 29.630 0.00 0.00 42.29 2.83
894 934 3.057174 CAGAGACAAACGTCCTCTTAGCT 60.057 47.826 6.90 0.00 33.60 3.32
907 947 2.769095 CTCTTAGCTTTCCTACCTGCCT 59.231 50.000 0.00 0.00 0.00 4.75
909 949 1.112113 TAGCTTTCCTACCTGCCTCG 58.888 55.000 0.00 0.00 0.00 4.63
919 959 3.056749 CCTACCTGCCTCGTTGTATATCC 60.057 52.174 0.00 0.00 0.00 2.59
922 962 3.573110 ACCTGCCTCGTTGTATATCCTAC 59.427 47.826 0.00 0.00 0.00 3.18
952 992 4.925861 GCTCGGCTGCTCCCCATC 62.926 72.222 0.00 0.00 0.00 3.51
971 1015 1.026718 CCTTCCTCCATTGACCACGC 61.027 60.000 0.00 0.00 0.00 5.34
972 1016 0.036010 CTTCCTCCATTGACCACGCT 60.036 55.000 0.00 0.00 0.00 5.07
973 1017 0.036388 TTCCTCCATTGACCACGCTC 60.036 55.000 0.00 0.00 0.00 5.03
974 1018 1.811266 CCTCCATTGACCACGCTCG 60.811 63.158 0.00 0.00 0.00 5.03
975 1019 1.811266 CTCCATTGACCACGCTCGG 60.811 63.158 0.00 0.00 0.00 4.63
1116 1160 3.266636 TGACGTTGAAAAGCTCAAGTCA 58.733 40.909 11.69 11.69 44.83 3.41
1146 1190 1.821753 AGAGTCAAGATGGTGGTCTCG 59.178 52.381 0.00 0.00 0.00 4.04
1204 1248 3.554524 GATGAATCTCTCGCTCTTCTCG 58.445 50.000 0.00 0.00 0.00 4.04
1205 1249 2.360844 TGAATCTCTCGCTCTTCTCGT 58.639 47.619 0.00 0.00 0.00 4.18
1248 1292 2.885861 GTGGTCGACGAGCTGGAT 59.114 61.111 25.62 0.00 0.00 3.41
1278 1322 1.072965 CTCCAAGAGCTGGTTGAAGGT 59.927 52.381 6.93 0.00 46.51 3.50
1280 1324 0.595095 CAAGAGCTGGTTGAAGGTGC 59.405 55.000 0.00 0.00 0.00 5.01
1281 1325 0.538287 AAGAGCTGGTTGAAGGTGCC 60.538 55.000 0.00 0.00 0.00 5.01
1282 1326 1.973812 GAGCTGGTTGAAGGTGCCC 60.974 63.158 0.00 0.00 0.00 5.36
1284 1328 2.672996 CTGGTTGAAGGTGCCCGG 60.673 66.667 0.00 0.00 0.00 5.73
1285 1329 4.966787 TGGTTGAAGGTGCCCGGC 62.967 66.667 1.04 1.04 0.00 6.13
1307 1363 2.413142 GGCTGCCTGCAGATCCAAC 61.413 63.158 22.64 4.65 46.30 3.77
1308 1364 2.413142 GCTGCCTGCAGATCCAACC 61.413 63.158 22.64 0.00 46.30 3.77
1312 1368 2.401766 CCTGCAGATCCAACCGTGC 61.402 63.158 17.39 0.00 36.42 5.34
1314 1370 1.642037 CTGCAGATCCAACCGTGCTG 61.642 60.000 8.42 0.00 36.84 4.41
1327 1383 1.515521 CGTGCTGGTTCCTTCCAACC 61.516 60.000 0.00 0.00 45.54 3.77
1329 1385 0.178992 TGCTGGTTCCTTCCAACCTG 60.179 55.000 4.10 4.68 45.54 4.00
1330 1386 2.646121 CTGGTTCCTTCCAACCTGC 58.354 57.895 4.10 0.00 45.54 4.85
1332 1388 1.606601 GGTTCCTTCCAACCTGCCC 60.607 63.158 0.00 0.00 42.46 5.36
1333 1389 1.152830 GTTCCTTCCAACCTGCCCA 59.847 57.895 0.00 0.00 0.00 5.36
1337 1393 1.383799 CTTCCAACCTGCCCATCCA 59.616 57.895 0.00 0.00 0.00 3.41
1338 1394 0.251742 CTTCCAACCTGCCCATCCAA 60.252 55.000 0.00 0.00 0.00 3.53
1339 1395 0.251742 TTCCAACCTGCCCATCCAAG 60.252 55.000 0.00 0.00 0.00 3.61
1340 1396 1.683365 CCAACCTGCCCATCCAAGG 60.683 63.158 0.00 0.00 0.00 3.61
1341 1397 1.383799 CAACCTGCCCATCCAAGGA 59.616 57.895 0.00 0.00 0.00 3.36
1360 1416 2.694109 GGAGAAGGAGGTACGCATACTT 59.306 50.000 0.00 0.00 0.00 2.24
1379 1437 5.153950 ACTTCTTCCTGTAGATCCAACAC 57.846 43.478 0.00 0.00 0.00 3.32
1381 1439 5.071788 ACTTCTTCCTGTAGATCCAACACAA 59.928 40.000 0.00 0.00 0.00 3.33
1384 1442 4.974645 TCCTGTAGATCCAACACAAAGT 57.025 40.909 0.00 0.00 0.00 2.66
1386 1444 5.305585 TCCTGTAGATCCAACACAAAGTTC 58.694 41.667 0.00 0.00 38.74 3.01
1387 1445 5.071788 TCCTGTAGATCCAACACAAAGTTCT 59.928 40.000 0.00 0.00 38.74 3.01
1390 1448 7.259290 TGTAGATCCAACACAAAGTTCTTTC 57.741 36.000 0.00 0.00 38.74 2.62
1391 1449 6.826231 TGTAGATCCAACACAAAGTTCTTTCA 59.174 34.615 0.00 0.00 38.74 2.69
1394 1452 8.103948 AGATCCAACACAAAGTTCTTTCATAG 57.896 34.615 0.00 0.00 38.74 2.23
1395 1453 6.633500 TCCAACACAAAGTTCTTTCATAGG 57.367 37.500 0.00 0.00 38.74 2.57
1396 1454 5.009610 TCCAACACAAAGTTCTTTCATAGGC 59.990 40.000 0.00 0.00 38.74 3.93
1398 1456 3.502211 ACACAAAGTTCTTTCATAGGCCG 59.498 43.478 0.00 0.00 0.00 6.13
1399 1457 3.751175 CACAAAGTTCTTTCATAGGCCGA 59.249 43.478 0.00 0.00 0.00 5.54
1400 1458 4.003648 ACAAAGTTCTTTCATAGGCCGAG 58.996 43.478 0.00 0.00 0.00 4.63
1401 1459 3.983044 AAGTTCTTTCATAGGCCGAGT 57.017 42.857 0.00 0.00 0.00 4.18
1411 1469 2.154567 TAGGCCGAGTATCCAAGTGT 57.845 50.000 0.00 0.00 0.00 3.55
1413 1471 0.535335 GGCCGAGTATCCAAGTGTGA 59.465 55.000 0.00 0.00 0.00 3.58
1414 1472 1.641577 GCCGAGTATCCAAGTGTGAC 58.358 55.000 0.00 0.00 0.00 3.67
1420 1478 5.466819 CGAGTATCCAAGTGTGACAAACTA 58.533 41.667 0.00 0.00 0.00 2.24
1424 1482 7.603651 AGTATCCAAGTGTGACAAACTACTAG 58.396 38.462 0.00 0.00 0.00 2.57
1425 1483 5.864418 TCCAAGTGTGACAAACTACTAGT 57.136 39.130 0.00 0.00 0.00 2.57
1426 1484 6.964807 TCCAAGTGTGACAAACTACTAGTA 57.035 37.500 0.00 1.89 0.00 1.82
1427 1485 7.350744 TCCAAGTGTGACAAACTACTAGTAA 57.649 36.000 3.76 0.00 0.00 2.24
1428 1486 7.959175 TCCAAGTGTGACAAACTACTAGTAAT 58.041 34.615 3.76 0.00 0.00 1.89
1460 1518 8.736244 GTCTGATGATCCTATCTTACTTAGGAC 58.264 40.741 1.69 0.00 46.07 3.85
1522 2234 4.947645 TGCTTTTCTGGTCCATTTTTCTG 58.052 39.130 0.00 0.00 0.00 3.02
1539 2251 1.882912 CTGTTGGCACAGCTACAAGA 58.117 50.000 4.56 0.00 44.16 3.02
1571 2340 2.162681 AGGTAACAGTGCTGGCAAATC 58.837 47.619 4.11 0.00 41.41 2.17
1599 2368 3.207778 CGTGGTCTGGGAAAACTTTACA 58.792 45.455 0.00 0.00 0.00 2.41
1600 2369 3.250040 CGTGGTCTGGGAAAACTTTACAG 59.750 47.826 0.00 0.00 0.00 2.74
1610 2379 6.127842 TGGGAAAACTTTACAGTCACAGAAAC 60.128 38.462 0.00 0.00 30.45 2.78
1611 2380 6.095021 GGGAAAACTTTACAGTCACAGAAACT 59.905 38.462 0.00 0.00 30.45 2.66
1624 2393 5.122396 GTCACAGAAACTGTTGACAGAAAGT 59.878 40.000 17.42 6.05 42.59 2.66
1679 2448 6.025749 TGAGTTCAAGTGTGATACGAAGAT 57.974 37.500 0.00 0.00 32.48 2.40
1701 3528 7.374272 AGATCAACGGTACATCATCTATGAAG 58.626 38.462 0.00 0.00 40.69 3.02
1793 3635 6.825721 AGGTACCTAAAGAAGAATTGAGCATG 59.174 38.462 14.41 0.00 0.00 4.06
1794 3636 6.823689 GGTACCTAAAGAAGAATTGAGCATGA 59.176 38.462 4.06 0.00 0.00 3.07
1795 3637 6.998968 ACCTAAAGAAGAATTGAGCATGAG 57.001 37.500 0.00 0.00 0.00 2.90
1798 3640 2.652590 AGAAGAATTGAGCATGAGCCC 58.347 47.619 0.00 0.00 43.56 5.19
1799 3641 2.025605 AGAAGAATTGAGCATGAGCCCA 60.026 45.455 0.00 0.00 43.56 5.36
1800 3642 2.750141 AGAATTGAGCATGAGCCCAT 57.250 45.000 0.00 0.00 43.56 4.00
1801 3643 3.028094 AGAATTGAGCATGAGCCCATT 57.972 42.857 0.00 0.00 43.56 3.16
1802 3644 3.371965 AGAATTGAGCATGAGCCCATTT 58.628 40.909 0.00 0.00 43.56 2.32
1803 3645 4.539726 AGAATTGAGCATGAGCCCATTTA 58.460 39.130 0.00 0.00 43.56 1.40
1804 3646 4.957954 AGAATTGAGCATGAGCCCATTTAA 59.042 37.500 0.00 0.00 43.56 1.52
1805 3647 5.601313 AGAATTGAGCATGAGCCCATTTAAT 59.399 36.000 0.00 0.00 43.56 1.40
1806 3648 5.881923 ATTGAGCATGAGCCCATTTAATT 57.118 34.783 0.00 0.00 43.56 1.40
1807 3649 6.982160 ATTGAGCATGAGCCCATTTAATTA 57.018 33.333 0.00 0.00 43.56 1.40
1809 3651 5.693961 TGAGCATGAGCCCATTTAATTAGA 58.306 37.500 0.00 0.00 43.56 2.10
1811 3653 6.606796 TGAGCATGAGCCCATTTAATTAGAAA 59.393 34.615 0.00 0.00 43.56 2.52
1813 3655 7.664758 AGCATGAGCCCATTTAATTAGAAATC 58.335 34.615 0.00 0.00 43.56 2.17
1816 3658 7.639113 TGAGCCCATTTAATTAGAAATCGTT 57.361 32.000 0.00 0.00 0.00 3.85
1817 3659 8.062065 TGAGCCCATTTAATTAGAAATCGTTT 57.938 30.769 0.00 0.00 0.00 3.60
1870 3962 2.741759 TACATCTTCTTGACAGCGCA 57.258 45.000 11.47 0.00 0.00 6.09
1871 3963 1.151668 ACATCTTCTTGACAGCGCAC 58.848 50.000 11.47 0.51 0.00 5.34
1877 4749 4.065088 TCTTCTTGACAGCGCACTAATTT 58.935 39.130 11.47 0.00 0.00 1.82
1901 4773 1.562475 TCCTAATAGCCAACCCACCAC 59.438 52.381 0.00 0.00 0.00 4.16
1935 4810 0.747283 AGCACTGCTGAGCCTATTGC 60.747 55.000 1.67 5.26 37.57 3.56
1936 4811 1.722636 GCACTGCTGAGCCTATTGCC 61.723 60.000 0.23 0.00 42.71 4.52
1941 4816 0.031721 GCTGAGCCTATTGCCATTGC 59.968 55.000 0.00 0.00 42.71 3.56
1971 4846 3.052490 TCCAGGGGAAAAGGAAAGAAACA 60.052 43.478 0.00 0.00 0.00 2.83
1972 4847 3.321968 CCAGGGGAAAAGGAAAGAAACAG 59.678 47.826 0.00 0.00 0.00 3.16
2052 4930 6.379703 ACCAAAGCAATATGTAAATACTGCCA 59.620 34.615 2.72 0.00 0.00 4.92
2073 4951 2.027745 ACACAGAGATCAAGTGCGGAAT 60.028 45.455 10.83 0.00 36.76 3.01
2074 4952 2.350804 CACAGAGATCAAGTGCGGAATG 59.649 50.000 0.00 0.00 0.00 2.67
2089 4967 1.079127 AATGAAGACCGGGACAGCG 60.079 57.895 6.32 0.00 0.00 5.18
2098 4976 2.590092 GGGACAGCGGGTATGCTT 59.410 61.111 0.00 0.00 44.46 3.91
2116 4994 7.435192 GGTATGCTTAACCATAACAAGATTTGC 59.565 37.037 1.61 0.00 35.84 3.68
2130 5008 5.360714 ACAAGATTTGCAAGAAGAAACCTGA 59.639 36.000 0.00 0.00 0.00 3.86
2215 5314 6.760291 TGTTGTTTTATAAACAATCCCCACC 58.240 36.000 17.58 6.75 41.51 4.61
2231 5330 2.494059 CCACCATGGTTCTAATAGCCG 58.506 52.381 16.84 0.00 31.35 5.52
2238 5344 5.448632 CCATGGTTCTAATAGCCGTTTGTTC 60.449 44.000 2.57 0.00 0.00 3.18
2259 5409 7.939782 TGTTCATGATCTTTTTCTTACTGCAA 58.060 30.769 0.00 0.00 0.00 4.08
2262 5412 8.114331 TCATGATCTTTTTCTTACTGCAACAT 57.886 30.769 0.00 0.00 0.00 2.71
2263 5413 8.579006 TCATGATCTTTTTCTTACTGCAACATT 58.421 29.630 0.00 0.00 0.00 2.71
2295 5445 5.756195 ACTGCAAATGCGACATATATTGT 57.244 34.783 0.35 0.00 45.83 2.71
2296 5446 5.513376 ACTGCAAATGCGACATATATTGTG 58.487 37.500 0.35 0.00 45.83 3.33
2300 5450 5.748152 GCAAATGCGACATATATTGTGGTTT 59.252 36.000 0.00 0.00 39.18 3.27
2301 5451 6.915300 GCAAATGCGACATATATTGTGGTTTA 59.085 34.615 0.00 0.00 39.18 2.01
2302 5452 7.594758 GCAAATGCGACATATATTGTGGTTTAT 59.405 33.333 0.00 0.00 39.18 1.40
2303 5453 8.904712 CAAATGCGACATATATTGTGGTTTATG 58.095 33.333 0.00 0.00 39.18 1.90
2304 5454 7.977789 ATGCGACATATATTGTGGTTTATGA 57.022 32.000 0.00 0.00 39.18 2.15
2305 5455 7.184800 TGCGACATATATTGTGGTTTATGAC 57.815 36.000 0.00 0.00 39.18 3.06
2316 5478 4.868171 TGTGGTTTATGACGATTCAGCTAC 59.132 41.667 0.00 0.00 34.35 3.58
2317 5479 4.868171 GTGGTTTATGACGATTCAGCTACA 59.132 41.667 0.00 0.00 34.35 2.74
2351 5513 1.136695 GAGTGGATGAGGAGTCAGCAG 59.863 57.143 0.00 0.00 41.16 4.24
2378 5543 2.303022 ACTGCAGCTAATACACACACCT 59.697 45.455 15.27 0.00 0.00 4.00
2406 5571 6.045459 TGGGACAAGGCTACATTATCCAATAT 59.955 38.462 0.00 0.00 31.92 1.28
2447 5621 3.055094 TCAGTTACAAGAGATCCAAGGGC 60.055 47.826 0.00 0.00 0.00 5.19
2455 5629 0.622665 AGATCCAAGGGCAAGTGAGG 59.377 55.000 0.00 0.00 0.00 3.86
2462 5636 0.178873 AGGGCAAGTGAGGGAGGTTA 60.179 55.000 0.00 0.00 0.00 2.85
2468 5642 2.761208 CAAGTGAGGGAGGTTATCGAGT 59.239 50.000 0.00 0.00 0.00 4.18
2511 5688 6.323482 TCTTCCAGTTCAAATCACCATCAAAA 59.677 34.615 0.00 0.00 0.00 2.44
2522 5699 9.874205 CAAATCACCATCAAAATACAACCTTAT 57.126 29.630 0.00 0.00 0.00 1.73
2529 5706 8.017373 CCATCAAAATACAACCTTATATCAGCG 58.983 37.037 0.00 0.00 0.00 5.18
2534 5711 3.991367 ACAACCTTATATCAGCGCCTAC 58.009 45.455 2.29 0.00 0.00 3.18
2550 5727 2.893637 CCTACGGACATCAAGTCTTGG 58.106 52.381 12.66 0.24 46.72 3.61
2593 5770 5.136105 AGAGTTGCAGAAAAGAACTCCATT 58.864 37.500 8.48 0.00 44.46 3.16
2598 5778 6.317789 TGCAGAAAAGAACTCCATTGTAAG 57.682 37.500 0.00 0.00 0.00 2.34
2610 5790 6.595682 ACTCCATTGTAAGGATGATAACAGG 58.404 40.000 0.00 0.00 33.99 4.00
2702 5885 7.056006 TGCTCAACTTGTATACAATGATCCAT 58.944 34.615 18.35 0.00 35.02 3.41
2752 5935 0.893727 GGGTTTGGGTGTCTCGCAAT 60.894 55.000 5.37 0.00 45.76 3.56
2782 5965 5.544176 TGAAGTGAGACTAACAAGGGAGATT 59.456 40.000 0.00 0.00 0.00 2.40
2796 5985 7.060421 ACAAGGGAGATTTTGAACTCTGTTTA 58.940 34.615 0.00 0.00 34.11 2.01
2815 6004 7.613022 TCTGTTTATCAAGAAAGGCATGAAGAT 59.387 33.333 0.00 0.00 0.00 2.40
2857 6046 4.403585 TCAGGAGATCTTGAAGCATCAG 57.596 45.455 0.00 0.00 36.78 2.90
2867 6062 1.078848 AAGCATCAGGCCGACTCAC 60.079 57.895 0.00 0.00 46.50 3.51
2870 6065 1.812922 CATCAGGCCGACTCACAGC 60.813 63.158 0.00 0.00 0.00 4.40
2924 6119 7.148407 GGGATGACATGAACGATAATATCCAAC 60.148 40.741 0.00 0.00 34.64 3.77
2925 6120 7.387673 GGATGACATGAACGATAATATCCAACA 59.612 37.037 0.00 0.00 33.50 3.33
2926 6121 7.477144 TGACATGAACGATAATATCCAACAC 57.523 36.000 0.00 0.00 0.00 3.32
2927 6122 6.481976 TGACATGAACGATAATATCCAACACC 59.518 38.462 0.00 0.00 0.00 4.16
3013 6208 3.904136 AGTATGTCTGTTGCACAAAGC 57.096 42.857 0.00 0.00 45.96 3.51
3084 6279 8.253810 TGACTTTTGGTTATTGTTCAAATCACA 58.746 29.630 0.00 0.00 31.60 3.58
3085 6280 8.419076 ACTTTTGGTTATTGTTCAAATCACAC 57.581 30.769 0.00 0.00 31.60 3.82
3097 6292 4.541779 TCAAATCACACGCATTTGGTTAC 58.458 39.130 6.60 0.00 40.33 2.50
3107 6302 3.423123 CGCATTTGGTTACGAGAACTGTC 60.423 47.826 0.00 0.00 0.00 3.51
3189 6384 4.752101 CCCATTAGCAGTTGTATCTACAGC 59.248 45.833 0.00 0.00 37.52 4.40
3231 6426 8.575649 AAACTTAACACCGATTATTGGAGAAT 57.424 30.769 5.33 0.00 0.00 2.40
3258 6453 8.530269 GTTCTAAAGAACGAAGAGTGGAAATA 57.470 34.615 7.08 0.00 43.97 1.40
3267 6462 4.571984 CGAAGAGTGGAAATACATGCATCA 59.428 41.667 0.00 0.00 0.00 3.07
3277 6472 6.072286 GGAAATACATGCATCACAATAGAGGG 60.072 42.308 0.00 0.00 0.00 4.30
3330 6525 4.448395 TCAACTTCCGTACCATTTACAACG 59.552 41.667 0.00 0.00 35.20 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
138 146 4.986034 GCGTTTTATTGCCCACTTTTTAGT 59.014 37.500 0.00 0.00 0.00 2.24
385 400 2.115695 TTGTGCATCAGCCAGCCA 59.884 55.556 0.00 0.00 41.13 4.75
530 566 5.883115 TGATGTCATCGGCACCTTTTTATTA 59.117 36.000 8.29 0.00 0.00 0.98
614 653 5.708948 TGTAGATCTTCAAAATTTTGGGCG 58.291 37.500 26.45 16.37 38.66 6.13
622 661 4.487714 TCGGCCTGTAGATCTTCAAAAT 57.512 40.909 0.00 0.00 0.00 1.82
630 669 1.534175 CGTGAGTTCGGCCTGTAGATC 60.534 57.143 0.00 0.00 0.00 2.75
633 672 1.805945 GCGTGAGTTCGGCCTGTAG 60.806 63.158 0.00 0.00 0.00 2.74
641 680 1.148157 CTATGGGCTGCGTGAGTTCG 61.148 60.000 0.00 0.00 0.00 3.95
680 719 0.384309 ACAGACACGCTTTCAGTCGA 59.616 50.000 0.00 0.00 37.36 4.20
722 761 1.332904 CGGAGAAGAAAACACACACGC 60.333 52.381 0.00 0.00 0.00 5.34
723 762 1.332904 GCGGAGAAGAAAACACACACG 60.333 52.381 0.00 0.00 0.00 4.49
724 763 1.332904 CGCGGAGAAGAAAACACACAC 60.333 52.381 0.00 0.00 0.00 3.82
725 764 0.934496 CGCGGAGAAGAAAACACACA 59.066 50.000 0.00 0.00 0.00 3.72
731 771 1.891150 AGTAGGACGCGGAGAAGAAAA 59.109 47.619 12.47 0.00 0.00 2.29
796 836 0.533032 GCCGAGCAGAAGGAGTACTT 59.467 55.000 0.00 0.00 43.65 2.24
797 837 0.323908 AGCCGAGCAGAAGGAGTACT 60.324 55.000 0.00 0.00 0.00 2.73
798 838 0.179124 CAGCCGAGCAGAAGGAGTAC 60.179 60.000 0.00 0.00 0.00 2.73
799 839 1.949847 GCAGCCGAGCAGAAGGAGTA 61.950 60.000 0.00 0.00 0.00 2.59
800 840 2.977178 CAGCCGAGCAGAAGGAGT 59.023 61.111 0.00 0.00 0.00 3.85
801 841 2.511145 GCAGCCGAGCAGAAGGAG 60.511 66.667 0.00 0.00 0.00 3.69
802 842 2.999648 AGCAGCCGAGCAGAAGGA 61.000 61.111 0.00 0.00 36.85 3.36
803 843 2.511145 GAGCAGCCGAGCAGAAGG 60.511 66.667 0.00 0.00 36.85 3.46
804 844 2.511145 GGAGCAGCCGAGCAGAAG 60.511 66.667 0.00 0.00 36.85 2.85
805 845 4.087892 GGGAGCAGCCGAGCAGAA 62.088 66.667 0.00 0.00 37.63 3.02
820 860 0.456824 CAGTGACGACGACAGATGGG 60.457 60.000 0.00 0.00 0.00 4.00
821 861 0.521735 TCAGTGACGACGACAGATGG 59.478 55.000 0.00 0.00 0.00 3.51
824 864 0.586802 CAGTCAGTGACGACGACAGA 59.413 55.000 17.40 0.00 40.98 3.41
826 866 1.008881 GCAGTCAGTGACGACGACA 60.009 57.895 17.40 0.00 40.98 4.35
828 868 2.251371 CGCAGTCAGTGACGACGA 59.749 61.111 26.80 0.00 40.98 4.20
829 869 2.801162 CCGCAGTCAGTGACGACG 60.801 66.667 25.04 25.04 40.98 5.12
830 870 3.106407 GCCGCAGTCAGTGACGAC 61.106 66.667 17.40 12.31 37.67 4.34
831 871 2.434658 AATGCCGCAGTCAGTGACGA 62.435 55.000 17.40 0.00 37.67 4.20
832 872 2.029288 AATGCCGCAGTCAGTGACG 61.029 57.895 17.40 13.11 37.67 4.35
833 873 1.230635 ACAATGCCGCAGTCAGTGAC 61.231 55.000 15.78 15.78 31.29 3.67
834 874 0.320050 TACAATGCCGCAGTCAGTGA 59.680 50.000 0.00 0.00 31.29 3.41
835 875 1.372582 ATACAATGCCGCAGTCAGTG 58.627 50.000 0.00 0.00 37.54 3.66
836 876 2.113860 AATACAATGCCGCAGTCAGT 57.886 45.000 0.00 0.00 0.00 3.41
837 877 2.162208 ACAAATACAATGCCGCAGTCAG 59.838 45.455 0.00 0.00 0.00 3.51
838 878 2.158559 ACAAATACAATGCCGCAGTCA 58.841 42.857 0.00 0.00 0.00 3.41
839 879 2.919666 ACAAATACAATGCCGCAGTC 57.080 45.000 0.00 0.00 0.00 3.51
840 880 5.107104 CGATATACAAATACAATGCCGCAGT 60.107 40.000 0.00 0.00 0.00 4.40
841 881 5.107104 ACGATATACAAATACAATGCCGCAG 60.107 40.000 0.00 0.00 0.00 5.18
842 882 4.752604 ACGATATACAAATACAATGCCGCA 59.247 37.500 0.00 0.00 0.00 5.69
843 883 5.277601 ACGATATACAAATACAATGCCGC 57.722 39.130 0.00 0.00 0.00 6.53
844 884 8.440059 ACAATACGATATACAAATACAATGCCG 58.560 33.333 0.00 0.00 0.00 5.69
854 894 9.863845 TTGTCTCTGAACAATACGATATACAAA 57.136 29.630 0.00 0.00 34.31 2.83
872 912 3.057174 AGCTAAGAGGACGTTTGTCTCTG 60.057 47.826 10.78 3.68 44.83 3.35
881 921 2.759535 GGTAGGAAAGCTAAGAGGACGT 59.240 50.000 0.00 0.00 0.00 4.34
894 934 1.053424 ACAACGAGGCAGGTAGGAAA 58.947 50.000 0.00 0.00 0.00 3.13
907 947 6.127647 ACAAAAGACGGTAGGATATACAACGA 60.128 38.462 2.42 0.00 0.00 3.85
909 949 6.478016 GGACAAAAGACGGTAGGATATACAAC 59.522 42.308 0.00 0.00 0.00 3.32
919 959 1.347320 GAGCGGACAAAAGACGGTAG 58.653 55.000 0.00 0.00 38.55 3.18
922 962 2.380410 CCGAGCGGACAAAAGACGG 61.380 63.158 2.00 0.00 37.50 4.79
950 990 1.210478 CGTGGTCAATGGAGGAAGGAT 59.790 52.381 0.00 0.00 0.00 3.24
951 991 0.613260 CGTGGTCAATGGAGGAAGGA 59.387 55.000 0.00 0.00 0.00 3.36
952 992 1.026718 GCGTGGTCAATGGAGGAAGG 61.027 60.000 0.00 0.00 0.00 3.46
1116 1160 4.217510 CCATCTTGACTCTCCTGATCTCT 58.782 47.826 0.00 0.00 0.00 3.10
1146 1190 0.616111 TCCCTCTCTCCTTCACAGCC 60.616 60.000 0.00 0.00 0.00 4.85
1204 1248 0.523757 GCTTCGTAGAGTCGCTCCAC 60.524 60.000 0.00 0.45 38.43 4.02
1205 1249 1.654954 GGCTTCGTAGAGTCGCTCCA 61.655 60.000 0.00 0.00 38.43 3.86
1212 1256 1.792941 GTCGTCGGCTTCGTAGAGT 59.207 57.895 0.00 0.00 38.43 3.24
1307 1363 1.228124 TTGGAAGGAACCAGCACGG 60.228 57.895 0.00 0.00 41.19 4.94
1308 1364 1.515521 GGTTGGAAGGAACCAGCACG 61.516 60.000 0.00 0.00 44.34 5.34
1312 1368 0.895559 GGCAGGTTGGAAGGAACCAG 60.896 60.000 0.00 0.00 46.94 4.00
1314 1370 1.606601 GGGCAGGTTGGAAGGAACC 60.607 63.158 0.00 0.00 45.16 3.62
1327 1383 0.106819 CCTTCTCCTTGGATGGGCAG 60.107 60.000 0.00 0.00 0.00 4.85
1329 1385 0.182299 CTCCTTCTCCTTGGATGGGC 59.818 60.000 0.00 0.00 33.14 5.36
1330 1386 0.842635 CCTCCTTCTCCTTGGATGGG 59.157 60.000 0.00 0.00 33.14 4.00
1332 1388 2.101582 CGTACCTCCTTCTCCTTGGATG 59.898 54.545 0.00 0.00 0.00 3.51
1333 1389 2.389715 CGTACCTCCTTCTCCTTGGAT 58.610 52.381 0.00 0.00 0.00 3.41
1337 1393 1.867363 ATGCGTACCTCCTTCTCCTT 58.133 50.000 0.00 0.00 0.00 3.36
1338 1394 2.091775 AGTATGCGTACCTCCTTCTCCT 60.092 50.000 12.54 0.00 0.00 3.69
1339 1395 2.308690 AGTATGCGTACCTCCTTCTCC 58.691 52.381 12.54 0.00 0.00 3.71
1340 1396 3.633065 AGAAGTATGCGTACCTCCTTCTC 59.367 47.826 12.54 0.00 0.00 2.87
1341 1397 3.633418 AGAAGTATGCGTACCTCCTTCT 58.367 45.455 12.54 11.55 0.00 2.85
1360 1416 5.071788 ACTTTGTGTTGGATCTACAGGAAGA 59.928 40.000 19.02 0.00 0.00 2.87
1379 1437 4.003648 ACTCGGCCTATGAAAGAACTTTG 58.996 43.478 0.00 0.00 32.11 2.77
1381 1439 3.983044 ACTCGGCCTATGAAAGAACTT 57.017 42.857 0.00 0.00 0.00 2.66
1384 1442 3.964688 TGGATACTCGGCCTATGAAAGAA 59.035 43.478 0.00 0.00 37.61 2.52
1386 1444 4.202264 ACTTGGATACTCGGCCTATGAAAG 60.202 45.833 0.00 1.32 37.61 2.62
1387 1445 3.709653 ACTTGGATACTCGGCCTATGAAA 59.290 43.478 0.00 0.00 37.61 2.69
1390 1448 2.365617 ACACTTGGATACTCGGCCTATG 59.634 50.000 0.00 0.00 37.61 2.23
1391 1449 2.365617 CACACTTGGATACTCGGCCTAT 59.634 50.000 0.00 0.00 37.61 2.57
1394 1452 0.535335 TCACACTTGGATACTCGGCC 59.465 55.000 0.00 0.00 37.61 6.13
1395 1453 1.067142 TGTCACACTTGGATACTCGGC 60.067 52.381 0.00 0.00 37.61 5.54
1396 1454 3.313012 TTGTCACACTTGGATACTCGG 57.687 47.619 0.00 0.00 37.61 4.63
1398 1456 6.456501 AGTAGTTTGTCACACTTGGATACTC 58.543 40.000 0.00 0.00 37.61 2.59
1399 1457 6.420913 AGTAGTTTGTCACACTTGGATACT 57.579 37.500 0.00 0.00 37.61 2.12
1400 1458 7.376615 ACTAGTAGTTTGTCACACTTGGATAC 58.623 38.462 0.00 0.00 0.00 2.24
1401 1459 7.534723 ACTAGTAGTTTGTCACACTTGGATA 57.465 36.000 0.00 0.00 0.00 2.59
1420 1478 9.427821 AGGATCATCAGACTAACAATTACTAGT 57.572 33.333 0.00 0.00 0.00 2.57
1428 1486 9.647918 AGTAAGATAGGATCATCAGACTAACAA 57.352 33.333 0.00 0.00 0.00 2.83
1475 1533 8.470002 CATGGTCGTCCTTGATCAGATAATATA 58.530 37.037 8.58 0.00 40.11 0.86
1522 2234 2.602217 CGTTTCTTGTAGCTGTGCCAAC 60.602 50.000 0.00 0.00 0.00 3.77
1539 2251 0.393820 TGTTACCTTCGGGCTCGTTT 59.606 50.000 5.57 0.00 39.10 3.60
1562 2331 1.671054 ACGGACCGTGATTTGCCAG 60.671 57.895 21.02 0.00 39.18 4.85
1599 2368 4.471904 TCTGTCAACAGTTTCTGTGACT 57.528 40.909 20.76 2.24 44.62 3.41
1600 2369 5.122396 ACTTTCTGTCAACAGTTTCTGTGAC 59.878 40.000 9.82 17.06 44.62 3.67
1610 2379 3.320611 TTGGCGGACTTTCTGTCAACAG 61.321 50.000 3.69 3.69 41.90 3.16
1611 2380 1.407575 TTGGCGGACTTTCTGTCAACA 60.408 47.619 0.00 0.00 41.90 3.33
1618 2387 4.898607 TGCTTTGGCGGACTTTCT 57.101 50.000 0.00 0.00 42.25 2.52
1628 2397 4.389992 CACAGTGTCTACATACTGCTTTGG 59.610 45.833 0.00 0.00 46.27 3.28
1679 2448 6.709018 TCTTCATAGATGATGTACCGTTGA 57.291 37.500 5.58 0.00 36.56 3.18
1701 3528 5.298026 GGGATGCTCCTTCTCTAAATGTTTC 59.702 44.000 2.79 0.00 36.57 2.78
1710 3537 2.685106 TATCGGGATGCTCCTTCTCT 57.315 50.000 2.79 0.00 36.57 3.10
1843 3935 6.923508 CGCTGTCAAGAAGATGTATATAACCA 59.076 38.462 0.00 0.00 0.00 3.67
1844 3936 6.128795 GCGCTGTCAAGAAGATGTATATAACC 60.129 42.308 0.00 0.00 0.00 2.85
1845 3937 6.420903 TGCGCTGTCAAGAAGATGTATATAAC 59.579 38.462 9.73 0.00 0.00 1.89
1858 3950 3.058293 CCAAAATTAGTGCGCTGTCAAGA 60.058 43.478 10.80 0.00 0.00 3.02
1864 3956 1.812571 AGGACCAAAATTAGTGCGCTG 59.187 47.619 10.80 0.00 0.00 5.18
1870 3962 6.605995 GGTTGGCTATTAGGACCAAAATTAGT 59.394 38.462 4.84 0.00 44.67 2.24
1871 3963 6.040504 GGGTTGGCTATTAGGACCAAAATTAG 59.959 42.308 4.84 0.00 44.67 1.73
1877 4749 2.025699 GTGGGTTGGCTATTAGGACCAA 60.026 50.000 0.00 0.00 41.08 3.67
1923 4798 0.672342 GGCAATGGCAATAGGCTCAG 59.328 55.000 0.58 0.00 43.71 3.35
1935 4810 1.107538 CCTGGATGAGCTGGCAATGG 61.108 60.000 0.00 0.00 0.00 3.16
1936 4811 1.107538 CCCTGGATGAGCTGGCAATG 61.108 60.000 0.00 0.00 0.00 2.82
1941 4816 0.332632 TTTTCCCCTGGATGAGCTGG 59.667 55.000 0.00 0.00 0.00 4.85
2017 4895 0.685785 TTGCTTTGGTTGGCTGTCCA 60.686 50.000 0.00 0.00 41.55 4.02
2028 4906 6.697019 GTGGCAGTATTTACATATTGCTTTGG 59.303 38.462 13.91 0.00 44.35 3.28
2052 4930 0.969149 TCCGCACTTGATCTCTGTGT 59.031 50.000 12.35 0.00 34.52 3.72
2073 4951 3.691342 CCGCTGTCCCGGTCTTCA 61.691 66.667 0.00 0.00 43.24 3.02
2074 4952 4.452733 CCCGCTGTCCCGGTCTTC 62.453 72.222 0.00 0.00 46.71 2.87
2089 4967 7.582667 AATCTTGTTATGGTTAAGCATACCC 57.417 36.000 23.45 17.61 34.66 3.69
2098 4976 8.402798 TCTTCTTGCAAATCTTGTTATGGTTA 57.597 30.769 0.00 0.00 0.00 2.85
2116 4994 5.979517 GTCATTTGGTTCAGGTTTCTTCTTG 59.020 40.000 0.00 0.00 0.00 3.02
2130 5008 0.105760 TGGTGGCTGGTCATTTGGTT 60.106 50.000 0.00 0.00 0.00 3.67
2188 5244 7.547722 GTGGGGATTGTTTATAAAACAACATCC 59.452 37.037 20.01 20.01 42.18 3.51
2203 5259 1.432807 AGAACCATGGTGGGGATTGTT 59.567 47.619 20.60 0.00 43.37 2.83
2206 5262 4.447762 GCTATTAGAACCATGGTGGGGATT 60.448 45.833 20.60 0.00 43.37 3.01
2208 5264 2.441750 GCTATTAGAACCATGGTGGGGA 59.558 50.000 20.60 5.92 43.37 4.81
2215 5314 5.123186 TGAACAAACGGCTATTAGAACCATG 59.877 40.000 0.00 0.00 0.00 3.66
2231 5330 8.694394 GCAGTAAGAAAAAGATCATGAACAAAC 58.306 33.333 0.00 0.00 0.00 2.93
2238 5344 8.644619 CAATGTTGCAGTAAGAAAAAGATCATG 58.355 33.333 0.00 0.00 0.00 3.07
2289 5439 6.767902 AGCTGAATCGTCATAAACCACAATAT 59.232 34.615 0.00 0.00 31.85 1.28
2295 5445 5.079689 TGTAGCTGAATCGTCATAAACCA 57.920 39.130 0.00 0.00 31.85 3.67
2296 5446 5.810587 TCTTGTAGCTGAATCGTCATAAACC 59.189 40.000 0.00 0.00 31.85 3.27
2300 5450 7.817478 TCTTTTTCTTGTAGCTGAATCGTCATA 59.183 33.333 0.00 0.00 31.85 2.15
2301 5451 6.650807 TCTTTTTCTTGTAGCTGAATCGTCAT 59.349 34.615 0.00 0.00 31.85 3.06
2302 5452 5.989168 TCTTTTTCTTGTAGCTGAATCGTCA 59.011 36.000 0.00 0.00 0.00 4.35
2303 5453 6.467723 TCTTTTTCTTGTAGCTGAATCGTC 57.532 37.500 0.00 0.00 0.00 4.20
2304 5454 6.073003 CCTTCTTTTTCTTGTAGCTGAATCGT 60.073 38.462 0.00 0.00 0.00 3.73
2305 5455 6.147821 TCCTTCTTTTTCTTGTAGCTGAATCG 59.852 38.462 0.00 0.00 0.00 3.34
2312 5474 5.180304 CCACTCTCCTTCTTTTTCTTGTAGC 59.820 44.000 0.00 0.00 0.00 3.58
2316 5478 6.000219 TCATCCACTCTCCTTCTTTTTCTTG 59.000 40.000 0.00 0.00 0.00 3.02
2317 5479 6.192970 TCATCCACTCTCCTTCTTTTTCTT 57.807 37.500 0.00 0.00 0.00 2.52
2351 5513 5.122239 TGTGTGTATTAGCTGCAGTGATTTC 59.878 40.000 16.64 3.55 0.00 2.17
2378 5543 2.969821 AATGTAGCCTTGTCCCAACA 57.030 45.000 0.00 0.00 0.00 3.33
2437 5611 0.394899 CCCTCACTTGCCCTTGGATC 60.395 60.000 0.00 0.00 0.00 3.36
2447 5621 2.761208 ACTCGATAACCTCCCTCACTTG 59.239 50.000 0.00 0.00 0.00 3.16
2455 5629 4.931661 TCCATGTAACTCGATAACCTCC 57.068 45.455 0.00 0.00 0.00 4.30
2462 5636 5.860941 AAGTCTGATCCATGTAACTCGAT 57.139 39.130 0.00 0.00 0.00 3.59
2468 5642 7.345653 ACTGGAAGATAAGTCTGATCCATGTAA 59.654 37.037 0.00 0.00 39.49 2.41
2511 5688 4.891992 AGGCGCTGATATAAGGTTGTAT 57.108 40.909 7.64 0.00 0.00 2.29
2534 5711 1.001974 TGGACCAAGACTTGATGTCCG 59.998 52.381 25.84 10.66 46.46 4.79
2550 5727 5.998363 ACTCTTCCATACACTTTTCTTGGAC 59.002 40.000 0.00 0.00 36.25 4.02
2593 5770 7.918076 ACTTTTCTCCTGTTATCATCCTTACA 58.082 34.615 0.00 0.00 0.00 2.41
2598 5778 5.819901 CCAGACTTTTCTCCTGTTATCATCC 59.180 44.000 0.00 0.00 0.00 3.51
2610 5790 5.589050 ACAACTAAACCACCAGACTTTTCTC 59.411 40.000 0.00 0.00 0.00 2.87
2702 5885 8.259411 CCTTTGGTCAAAATGATCATCCAAATA 58.741 33.333 26.49 14.09 37.35 1.40
2705 5888 5.779260 TCCTTTGGTCAAAATGATCATCCAA 59.221 36.000 17.53 17.53 37.35 3.53
2710 5893 6.324512 CCCATATCCTTTGGTCAAAATGATCA 59.675 38.462 0.00 0.00 35.36 2.92
2716 5899 5.012561 CCAAACCCATATCCTTTGGTCAAAA 59.987 40.000 0.00 0.00 39.34 2.44
2752 5935 6.486657 CCCTTGTTAGTCTCACTTCATCAAAA 59.513 38.462 0.00 0.00 0.00 2.44
2782 5965 7.068103 TGCCTTTCTTGATAAACAGAGTTCAAA 59.932 33.333 0.00 0.00 0.00 2.69
2815 6004 6.806249 CCTGAAGCTTCGCAAAACATTTTATA 59.194 34.615 21.11 0.00 0.00 0.98
2821 6010 2.227388 CTCCTGAAGCTTCGCAAAACAT 59.773 45.455 21.11 0.00 0.00 2.71
2852 6041 1.812922 GCTGTGAGTCGGCCTGATG 60.813 63.158 0.00 0.00 42.19 3.07
2857 6046 3.575351 AAGTCGCTGTGAGTCGGCC 62.575 63.158 0.00 0.00 44.92 6.13
2867 6062 9.941664 ATCATCTAAAATGATTAAAAGTCGCTG 57.058 29.630 0.00 0.00 35.39 5.18
2925 6120 4.019174 CAGAGGAGCCAACATTTTATGGT 58.981 43.478 0.00 0.00 39.00 3.55
2926 6121 3.382546 CCAGAGGAGCCAACATTTTATGG 59.617 47.826 0.00 0.00 39.80 2.74
2927 6122 4.019174 ACCAGAGGAGCCAACATTTTATG 58.981 43.478 0.00 0.00 0.00 1.90
2994 6189 8.958417 GCCTAAGCTTTGTGCAACAGACATAC 62.958 46.154 3.20 0.00 42.34 2.39
3013 6208 4.645809 GGCTTGAGGGTGCCTAAG 57.354 61.111 0.00 0.00 45.26 2.18
3084 6279 2.478894 CAGTTCTCGTAACCAAATGCGT 59.521 45.455 0.76 0.00 0.00 5.24
3085 6280 2.478894 ACAGTTCTCGTAACCAAATGCG 59.521 45.455 0.76 0.00 0.00 4.73
3097 6292 1.203287 TGATGCTCCTGACAGTTCTCG 59.797 52.381 0.93 0.00 0.00 4.04
3107 6302 7.615582 TGATACTTAAACTTTGATGCTCCTG 57.384 36.000 0.00 0.00 0.00 3.86
3148 6343 1.810755 GGGTTGCCCTTTAACTTCTCG 59.189 52.381 0.00 0.00 41.34 4.04
3177 6372 7.283807 TCCGTAATAGTTCTGCTGTAGATACAA 59.716 37.037 0.00 0.00 35.50 2.41
3189 6384 9.199982 TGTTAAGTTTCTTCCGTAATAGTTCTG 57.800 33.333 0.00 0.00 0.00 3.02
3244 6439 4.571984 TGATGCATGTATTTCCACTCTTCG 59.428 41.667 2.46 0.00 0.00 3.79
3258 6453 4.103627 TGATCCCTCTATTGTGATGCATGT 59.896 41.667 2.46 0.00 0.00 3.21
3267 6462 2.224719 GCAGCCATGATCCCTCTATTGT 60.225 50.000 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.