Multiple sequence alignment - TraesCS1A01G053200

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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 TraesCS1A01G053200 chr1A 100.000 2947 0 0 1 2947 35298561 35295615 0.000000e+00 5443
1 TraesCS1A01G053200 chr1A 94.444 234 7 6 2718 2947 414759712 414759943 3.610000e-94 355
2 TraesCS1A01G053200 chr1B 91.235 1563 87 20 656 2193 55462876 55461339 0.000000e+00 2082
3 TraesCS1A01G053200 chr1B 90.783 651 56 4 1 650 50533722 50533075 0.000000e+00 867
4 TraesCS1A01G053200 chr3A 93.789 644 38 2 6 649 546398695 546398054 0.000000e+00 966
5 TraesCS1A01G053200 chr4A 98.182 550 10 0 2194 2743 628000640 628000091 0.000000e+00 961
6 TraesCS1A01G053200 chr5A 97.636 550 13 0 2194 2743 40623115 40622566 0.000000e+00 944
7 TraesCS1A01G053200 chr5A 97.273 550 14 1 2195 2743 23919565 23920114 0.000000e+00 931
8 TraesCS1A01G053200 chr5A 94.737 228 9 3 2720 2947 596176921 596176697 4.670000e-93 351
9 TraesCS1A01G053200 chr7A 96.175 549 20 1 2195 2743 48842811 48842264 0.000000e+00 896
10 TraesCS1A01G053200 chr7A 78.571 182 32 6 1264 1441 78451786 78451964 2.400000e-21 113
11 TraesCS1A01G053200 chr2D 90.601 649 55 3 1 649 528522921 528522279 0.000000e+00 856
12 TraesCS1A01G053200 chr2D 94.516 547 30 0 2197 2743 531768424 531767878 0.000000e+00 845
13 TraesCS1A01G053200 chr2D 95.089 224 9 2 2725 2947 206213706 206213928 4.670000e-93 351
14 TraesCS1A01G053200 chr4B 94.161 548 32 0 2196 2743 339494805 339494258 0.000000e+00 835
15 TraesCS1A01G053200 chr2B 93.478 552 32 3 2193 2743 94864130 94863582 0.000000e+00 817
16 TraesCS1A01G053200 chr2B 76.513 413 88 8 240 648 67787176 67786769 1.780000e-52 217
17 TraesCS1A01G053200 chr3B 93.443 549 36 0 2195 2743 27472177 27471629 0.000000e+00 815
18 TraesCS1A01G053200 chr3B 96.313 217 8 0 2731 2947 333637122 333637338 1.000000e-94 357
19 TraesCS1A01G053200 chr7B 93.248 548 37 0 2196 2743 541954238 541953691 0.000000e+00 808
20 TraesCS1A01G053200 chr7B 95.909 220 9 0 2728 2947 570597634 570597853 1.000000e-94 357
21 TraesCS1A01G053200 chr6D 89.127 653 63 3 1 653 186785286 186784642 0.000000e+00 806
22 TraesCS1A01G053200 chr5B 86.957 644 83 1 6 649 399028021 399027379 0.000000e+00 723
23 TraesCS1A01G053200 chr6A 81.510 649 106 7 2 650 34701261 34700627 3.370000e-144 521
24 TraesCS1A01G053200 chr2A 97.630 211 5 0 2737 2947 414524349 414524559 2.160000e-96 363
25 TraesCS1A01G053200 chr2A 95.089 224 9 2 2725 2947 682583373 682583595 4.670000e-93 351
26 TraesCS1A01G053200 chr6B 97.619 210 5 0 2738 2947 510902431 510902222 7.760000e-96 361
27 TraesCS1A01G053200 chr6B 94.760 229 8 4 2722 2947 347247387 347247614 1.300000e-93 353
28 TraesCS1A01G053200 chrUn 76.755 413 87 7 240 649 320108342 320107936 3.820000e-54 222
29 TraesCS1A01G053200 chrUn 76.570 414 86 9 240 649 362522709 362522303 1.780000e-52 217


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 TraesCS1A01G053200 chr1A 35295615 35298561 2946 True 5443 5443 100.000 1 2947 1 chr1A.!!$R1 2946
1 TraesCS1A01G053200 chr1B 55461339 55462876 1537 True 2082 2082 91.235 656 2193 1 chr1B.!!$R2 1537
2 TraesCS1A01G053200 chr1B 50533075 50533722 647 True 867 867 90.783 1 650 1 chr1B.!!$R1 649
3 TraesCS1A01G053200 chr3A 546398054 546398695 641 True 966 966 93.789 6 649 1 chr3A.!!$R1 643
4 TraesCS1A01G053200 chr4A 628000091 628000640 549 True 961 961 98.182 2194 2743 1 chr4A.!!$R1 549
5 TraesCS1A01G053200 chr5A 40622566 40623115 549 True 944 944 97.636 2194 2743 1 chr5A.!!$R1 549
6 TraesCS1A01G053200 chr5A 23919565 23920114 549 False 931 931 97.273 2195 2743 1 chr5A.!!$F1 548
7 TraesCS1A01G053200 chr7A 48842264 48842811 547 True 896 896 96.175 2195 2743 1 chr7A.!!$R1 548
8 TraesCS1A01G053200 chr2D 528522279 528522921 642 True 856 856 90.601 1 649 1 chr2D.!!$R1 648
9 TraesCS1A01G053200 chr2D 531767878 531768424 546 True 845 845 94.516 2197 2743 1 chr2D.!!$R2 546
10 TraesCS1A01G053200 chr4B 339494258 339494805 547 True 835 835 94.161 2196 2743 1 chr4B.!!$R1 547
11 TraesCS1A01G053200 chr2B 94863582 94864130 548 True 817 817 93.478 2193 2743 1 chr2B.!!$R2 550
12 TraesCS1A01G053200 chr3B 27471629 27472177 548 True 815 815 93.443 2195 2743 1 chr3B.!!$R1 548
13 TraesCS1A01G053200 chr7B 541953691 541954238 547 True 808 808 93.248 2196 2743 1 chr7B.!!$R1 547
14 TraesCS1A01G053200 chr6D 186784642 186785286 644 True 806 806 89.127 1 653 1 chr6D.!!$R1 652
15 TraesCS1A01G053200 chr5B 399027379 399028021 642 True 723 723 86.957 6 649 1 chr5B.!!$R1 643
16 TraesCS1A01G053200 chr6A 34700627 34701261 634 True 521 521 81.510 2 650 1 chr6A.!!$R1 648

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
848 855 0.108138 CCAGACCAATCGGACCTCAC 60.108 60.0 0.0 0.0 35.59 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2780 2811 0.023732 CTTGATCGTACACGCTTGCG 59.976 55.0 13.7 13.7 39.6 4.85 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
42 43 3.429492 TGCAATCACTAGATTTGGCCAA 58.571 40.909 16.05 16.05 42.46 4.52
61 62 5.193679 GCCAAGAGGTATACAACAAAGGAT 58.806 41.667 5.01 0.00 37.19 3.24
250 251 0.955428 GGAGTGTCATCTTTGCGGCA 60.955 55.000 0.00 0.00 0.00 5.69
345 346 5.256474 AGCTATTCAACATTGCACCTTACT 58.744 37.500 0.00 0.00 0.00 2.24
346 347 5.711976 AGCTATTCAACATTGCACCTTACTT 59.288 36.000 0.00 0.00 0.00 2.24
348 349 7.557719 AGCTATTCAACATTGCACCTTACTTAT 59.442 33.333 0.00 0.00 0.00 1.73
349 350 7.857885 GCTATTCAACATTGCACCTTACTTATC 59.142 37.037 0.00 0.00 0.00 1.75
350 351 5.794687 TCAACATTGCACCTTACTTATCG 57.205 39.130 0.00 0.00 0.00 2.92
351 352 5.242434 TCAACATTGCACCTTACTTATCGT 58.758 37.500 0.00 0.00 0.00 3.73
352 353 5.350365 TCAACATTGCACCTTACTTATCGTC 59.650 40.000 0.00 0.00 0.00 4.20
353 354 3.863424 ACATTGCACCTTACTTATCGTCG 59.137 43.478 0.00 0.00 0.00 5.12
362 368 4.494764 CCTTACTTATCGTCGTTTCAGTCG 59.505 45.833 0.00 0.00 0.00 4.18
421 427 1.001120 TCACCAGGTCGGCCTATGA 59.999 57.895 9.07 13.68 44.97 2.15
514 520 4.058817 CAAAATAGGGTAGCAGATCGGTC 58.941 47.826 0.00 0.00 0.00 4.79
591 597 5.476599 CCACCTTGTGTTGAGGATTTATTGA 59.523 40.000 0.00 0.00 37.72 2.57
613 619 3.568853 ACTCTCGATTGTAACCCTATCCG 59.431 47.826 0.00 0.00 0.00 4.18
615 621 3.956199 TCTCGATTGTAACCCTATCCGTT 59.044 43.478 0.00 0.00 0.00 4.44
704 710 3.771568 TTTGCGCTTGTGCTGGTGC 62.772 57.895 9.73 0.00 39.13 5.01
711 717 0.461135 CTTGTGCTGGTGCTGGTTTT 59.539 50.000 0.00 0.00 40.48 2.43
723 729 1.269257 GCTGGTTTTGGACTGCACTTC 60.269 52.381 0.00 0.00 0.00 3.01
731 737 2.203788 ACTGCACTTCTCCCCCGA 60.204 61.111 0.00 0.00 0.00 5.14
763 770 6.768381 GGATGGATTTCTCTTTCGAATACCTT 59.232 38.462 0.00 0.00 0.00 3.50
848 855 0.108138 CCAGACCAATCGGACCTCAC 60.108 60.000 0.00 0.00 35.59 3.51
855 862 2.227089 AATCGGACCTCACGCACCTC 62.227 60.000 0.00 0.00 0.00 3.85
864 871 1.300620 CACGCACCTCGAGGACAAA 60.301 57.895 37.69 0.00 41.67 2.83
884 895 4.644103 AAAGTACCGACGCACAGTATAT 57.356 40.909 0.00 0.00 0.00 0.86
885 896 5.756195 AAAGTACCGACGCACAGTATATA 57.244 39.130 0.00 0.00 0.00 0.86
886 897 5.954296 AAGTACCGACGCACAGTATATAT 57.046 39.130 0.00 0.00 0.00 0.86
887 898 7.439157 AAAGTACCGACGCACAGTATATATA 57.561 36.000 0.00 0.00 0.00 0.86
888 899 6.414408 AGTACCGACGCACAGTATATATAC 57.586 41.667 14.05 14.05 0.00 1.47
889 900 6.169094 AGTACCGACGCACAGTATATATACT 58.831 40.000 18.01 18.01 44.03 2.12
890 901 5.542616 ACCGACGCACAGTATATATACTC 57.457 43.478 20.38 10.33 41.44 2.59
923 934 4.954970 CGCACACCCAACCCAGCT 62.955 66.667 0.00 0.00 0.00 4.24
925 936 2.515398 CACACCCAACCCAGCTCA 59.485 61.111 0.00 0.00 0.00 4.26
934 945 4.760047 CCCAGCTCAACCGGACCG 62.760 72.222 9.46 6.99 0.00 4.79
940 951 3.605749 CTCAACCGGACCGCACCAT 62.606 63.158 9.46 0.00 0.00 3.55
977 988 1.506718 CGCCTCACGTAGCTCTTGA 59.493 57.895 0.00 0.00 36.87 3.02
986 997 1.343069 GTAGCTCTTGATCCCCGGAT 58.657 55.000 0.73 0.00 37.59 4.18
990 1001 1.811941 GCTCTTGATCCCCGGATTGTC 60.812 57.143 0.73 0.00 34.60 3.18
997 1008 1.521681 CCCCGGATTGTCGAAGAGC 60.522 63.158 0.73 0.00 36.95 4.09
1058 1069 1.218316 GGCGACCTGTCTCCGATTT 59.782 57.895 0.00 0.00 0.00 2.17
1061 1072 1.939838 GCGACCTGTCTCCGATTTTGT 60.940 52.381 0.00 0.00 0.00 2.83
1133 1144 4.566360 GGGTTTCGTTGATATGCCAAATTG 59.434 41.667 0.00 0.00 0.00 2.32
1143 1154 7.770366 TGATATGCCAAATTGATAATCAGCT 57.230 32.000 0.00 0.00 0.00 4.24
1145 1156 9.299465 TGATATGCCAAATTGATAATCAGCTAA 57.701 29.630 0.00 0.00 0.00 3.09
1160 1171 3.062763 CAGCTAATCGCCTGACCATTAG 58.937 50.000 0.00 0.00 40.39 1.73
1168 1179 3.318275 TCGCCTGACCATTAGTTAGCTAG 59.682 47.826 0.00 0.00 30.73 3.42
1169 1180 3.068307 CGCCTGACCATTAGTTAGCTAGT 59.932 47.826 0.00 0.00 30.73 2.57
1170 1181 4.277672 CGCCTGACCATTAGTTAGCTAGTA 59.722 45.833 0.00 0.00 30.73 1.82
1171 1182 5.530712 GCCTGACCATTAGTTAGCTAGTAC 58.469 45.833 0.00 0.00 30.73 2.73
1172 1183 5.302313 GCCTGACCATTAGTTAGCTAGTACT 59.698 44.000 0.00 0.00 30.73 2.73
1173 1184 6.515365 GCCTGACCATTAGTTAGCTAGTACTC 60.515 46.154 0.00 0.00 30.73 2.59
1174 1185 6.293516 CCTGACCATTAGTTAGCTAGTACTCG 60.294 46.154 0.00 0.00 30.73 4.18
1175 1186 6.118170 TGACCATTAGTTAGCTAGTACTCGT 58.882 40.000 0.00 0.00 0.00 4.18
1176 1187 7.275183 TGACCATTAGTTAGCTAGTACTCGTA 58.725 38.462 0.00 0.00 0.00 3.43
1177 1188 7.225538 TGACCATTAGTTAGCTAGTACTCGTAC 59.774 40.741 0.00 0.00 36.35 3.67
1178 1189 7.050377 ACCATTAGTTAGCTAGTACTCGTACA 58.950 38.462 0.00 0.00 38.48 2.90
1179 1190 7.718753 ACCATTAGTTAGCTAGTACTCGTACAT 59.281 37.037 0.00 0.00 38.48 2.29
1180 1191 9.212641 CCATTAGTTAGCTAGTACTCGTACATA 57.787 37.037 0.00 0.00 38.48 2.29
1187 1198 7.747155 AGCTAGTACTCGTACATATCATGTT 57.253 36.000 0.00 0.00 41.63 2.71
1199 1210 4.100035 ACATATCATGTTCTTCGAGCCTCA 59.900 41.667 0.00 0.00 41.63 3.86
1242 1253 5.094812 GCTTTTGCATATTGATTCACGTGA 58.905 37.500 15.76 15.76 46.58 4.35
1246 1257 5.081888 TGCATATTGATTCACGTGATTCG 57.918 39.130 26.58 17.00 46.00 3.34
1258 1269 2.899339 GATTCGCAGAGGCCAGCC 60.899 66.667 5.01 0.00 38.43 4.85
1278 1289 1.578926 CGCGTCAGATTTTTGGGCA 59.421 52.632 0.00 0.00 0.00 5.36
1282 1293 1.994779 CGTCAGATTTTTGGGCAATGC 59.005 47.619 0.00 0.00 0.00 3.56
1294 1305 3.399879 GCAATGCCAAATCGAACGT 57.600 47.368 0.00 0.00 0.00 3.99
1295 1306 1.696988 GCAATGCCAAATCGAACGTT 58.303 45.000 0.00 0.00 0.00 3.99
1320 1331 1.876799 TCATGGTAACCTGTGTTTGCG 59.123 47.619 0.00 0.00 35.87 4.85
1332 1343 0.107643 TGTTTGCGGTGGATGACAGA 59.892 50.000 0.00 0.00 0.00 3.41
1359 1370 2.764314 GCGAGCATGGCAAATCCGT 61.764 57.895 0.00 0.00 40.68 4.69
1360 1371 1.802636 CGAGCATGGCAAATCCGTT 59.197 52.632 0.00 0.00 37.80 4.44
1426 1440 7.994425 AATTTGCCATCGTCATACCAATATA 57.006 32.000 0.00 0.00 0.00 0.86
1528 1542 8.209584 AGACATAATGCCATGATCAGATATACC 58.790 37.037 0.09 0.00 0.00 2.73
1533 1547 4.223700 TGCCATGATCAGATATACCCAGAC 59.776 45.833 0.09 0.00 0.00 3.51
1570 1584 7.359262 TCGTGAGACGATGAATTACAAAAAT 57.641 32.000 0.00 0.00 46.73 1.82
1571 1585 8.468720 TCGTGAGACGATGAATTACAAAAATA 57.531 30.769 0.00 0.00 46.73 1.40
1573 1587 9.702726 CGTGAGACGATGAATTACAAAAATAAT 57.297 29.630 0.00 0.00 46.05 1.28
1617 1632 4.385825 TCTTGCTCAAAATTCAGTACGGT 58.614 39.130 0.00 0.00 0.00 4.83
1676 1691 2.821969 GGCCCGAGCATTATGATGAAAT 59.178 45.455 0.85 0.00 42.56 2.17
1691 1706 1.009829 GAAATTGGATGAGCGCGACT 58.990 50.000 12.10 6.51 0.00 4.18
1701 1716 0.867753 GAGCGCGACTGTATCCTGTG 60.868 60.000 12.10 0.00 0.00 3.66
1725 1740 6.729187 GTGAAGCTCACAAAGACATTAAAGT 58.271 36.000 10.30 0.00 46.22 2.66
1727 1742 8.507249 GTGAAGCTCACAAAGACATTAAAGTAT 58.493 33.333 10.30 0.00 46.22 2.12
1785 1800 4.586001 AGCAACCAGTTCATTGTTCTCAAT 59.414 37.500 0.00 0.00 44.02 2.57
1788 1803 6.506147 CAACCAGTTCATTGTTCTCAATTCA 58.494 36.000 0.00 0.00 41.66 2.57
1792 1807 9.028284 ACCAGTTCATTGTTCTCAATTCATATT 57.972 29.630 0.00 0.00 41.66 1.28
1797 1812 9.970395 TTCATTGTTCTCAATTCATATTATGGC 57.030 29.630 3.89 0.00 41.66 4.40
1798 1813 8.579006 TCATTGTTCTCAATTCATATTATGGCC 58.421 33.333 0.00 0.00 41.66 5.36
1914 1944 2.508526 CCTTTTGGAAGACAGGACAGG 58.491 52.381 0.00 0.00 44.07 4.00
1984 2014 5.861787 GTGGCATTGGTGTTATGACTTTTAC 59.138 40.000 0.00 0.00 32.07 2.01
2002 2032 8.683550 ACTTTTACTTTTTGCTTGTACTGAAC 57.316 30.769 0.00 0.00 0.00 3.18
2031 2061 4.431416 TGGACCTGAGTTGTAAATGTGT 57.569 40.909 0.00 0.00 0.00 3.72
2055 2085 1.073284 GTTGGAAACTAGGCTGTGGGA 59.927 52.381 0.00 0.00 45.32 4.37
2131 2161 2.561478 TAGCCCGCTTTTCAGACTTT 57.439 45.000 0.00 0.00 0.00 2.66
2342 2372 0.035598 TGACCACCATACCCAACACG 59.964 55.000 0.00 0.00 0.00 4.49
2751 2782 2.301505 CGAAGGATCATGTGACGCC 58.698 57.895 0.00 0.00 0.00 5.68
2752 2783 1.154205 CGAAGGATCATGTGACGCCC 61.154 60.000 0.00 0.00 0.00 6.13
2753 2784 0.815615 GAAGGATCATGTGACGCCCC 60.816 60.000 0.00 0.00 0.00 5.80
2754 2785 2.203209 GGATCATGTGACGCCCCC 60.203 66.667 0.00 0.00 0.00 5.40
2755 2786 2.588877 GATCATGTGACGCCCCCG 60.589 66.667 0.00 0.00 41.14 5.73
2756 2787 3.080765 ATCATGTGACGCCCCCGA 61.081 61.111 0.00 0.00 38.29 5.14
2757 2788 2.383245 GATCATGTGACGCCCCCGAT 62.383 60.000 0.00 0.00 38.29 4.18
2758 2789 2.383245 ATCATGTGACGCCCCCGATC 62.383 60.000 0.00 0.00 38.29 3.69
2759 2790 3.861797 ATGTGACGCCCCCGATCC 61.862 66.667 0.00 0.00 38.29 3.36
2761 2792 4.090588 GTGACGCCCCCGATCCAA 62.091 66.667 0.00 0.00 38.29 3.53
2762 2793 3.087253 TGACGCCCCCGATCCAAT 61.087 61.111 0.00 0.00 38.29 3.16
2763 2794 2.280865 GACGCCCCCGATCCAATC 60.281 66.667 0.00 0.00 38.29 2.67
2778 2809 6.158175 GATCCAATCGTACACTAATCATGC 57.842 41.667 0.00 0.00 0.00 4.06
2779 2810 5.017294 TCCAATCGTACACTAATCATGCA 57.983 39.130 0.00 0.00 0.00 3.96
2780 2811 4.808895 TCCAATCGTACACTAATCATGCAC 59.191 41.667 0.00 0.00 0.00 4.57
2781 2812 4.318050 CCAATCGTACACTAATCATGCACG 60.318 45.833 0.00 0.00 38.02 5.34
2782 2813 2.190161 TCGTACACTAATCATGCACGC 58.810 47.619 0.00 0.00 36.88 5.34
2783 2814 1.923864 CGTACACTAATCATGCACGCA 59.076 47.619 0.00 0.00 30.70 5.24
2784 2815 2.347150 CGTACACTAATCATGCACGCAA 59.653 45.455 0.00 0.00 30.70 4.85
2785 2816 5.720340 TCGTACACTAATCATGCACGCAAG 61.720 45.833 0.00 0.00 36.88 4.01
2786 2817 1.131126 ACACTAATCATGCACGCAAGC 59.869 47.619 0.00 0.00 45.62 4.01
2787 2818 0.374758 ACTAATCATGCACGCAAGCG 59.625 50.000 13.50 13.50 46.03 4.68
2797 2828 3.761995 CGCAAGCGTGTACGATCA 58.238 55.556 8.82 0.00 43.02 2.92
2798 2829 2.066807 CGCAAGCGTGTACGATCAA 58.933 52.632 8.82 0.00 43.02 2.57
2799 2830 0.023732 CGCAAGCGTGTACGATCAAG 59.976 55.000 8.82 0.00 43.02 3.02
2800 2831 1.346365 GCAAGCGTGTACGATCAAGA 58.654 50.000 8.82 0.00 43.02 3.02
2801 2832 1.927174 GCAAGCGTGTACGATCAAGAT 59.073 47.619 8.82 0.00 43.02 2.40
2802 2833 2.034507 GCAAGCGTGTACGATCAAGATC 60.035 50.000 8.82 0.00 43.02 2.75
2803 2834 3.179048 CAAGCGTGTACGATCAAGATCA 58.821 45.455 8.82 0.00 43.02 2.92
2804 2835 3.071786 AGCGTGTACGATCAAGATCAG 57.928 47.619 8.82 5.82 43.02 2.90
2805 2836 2.120232 GCGTGTACGATCAAGATCAGG 58.880 52.381 8.82 0.00 43.02 3.86
2806 2837 2.732366 CGTGTACGATCAAGATCAGGG 58.268 52.381 10.39 0.00 43.02 4.45
2807 2838 2.357952 CGTGTACGATCAAGATCAGGGA 59.642 50.000 10.39 0.00 43.02 4.20
2808 2839 3.707793 GTGTACGATCAAGATCAGGGAC 58.292 50.000 10.39 2.84 37.69 4.46
2809 2840 3.381908 GTGTACGATCAAGATCAGGGACT 59.618 47.826 10.39 0.00 43.88 3.85
2810 2841 3.632604 TGTACGATCAAGATCAGGGACTC 59.367 47.826 10.39 0.00 34.60 3.36
2811 2842 2.739943 ACGATCAAGATCAGGGACTCA 58.260 47.619 10.39 0.00 34.60 3.41
2812 2843 2.428890 ACGATCAAGATCAGGGACTCAC 59.571 50.000 10.39 0.00 34.60 3.51
2813 2844 2.542618 CGATCAAGATCAGGGACTCACG 60.543 54.545 10.39 0.00 34.60 4.35
2814 2845 1.186200 TCAAGATCAGGGACTCACGG 58.814 55.000 0.00 0.00 34.60 4.94
2815 2846 0.176680 CAAGATCAGGGACTCACGGG 59.823 60.000 0.00 0.00 34.60 5.28
2816 2847 0.041238 AAGATCAGGGACTCACGGGA 59.959 55.000 0.00 0.00 34.60 5.14
2817 2848 0.041238 AGATCAGGGACTCACGGGAA 59.959 55.000 0.00 0.00 34.60 3.97
2818 2849 0.461961 GATCAGGGACTCACGGGAAG 59.538 60.000 0.00 0.00 34.60 3.46
2819 2850 0.041238 ATCAGGGACTCACGGGAAGA 59.959 55.000 0.00 0.00 34.60 2.87
2820 2851 0.041238 TCAGGGACTCACGGGAAGAT 59.959 55.000 0.00 0.00 34.60 2.40
2821 2852 1.286849 TCAGGGACTCACGGGAAGATA 59.713 52.381 0.00 0.00 34.60 1.98
2822 2853 2.091278 TCAGGGACTCACGGGAAGATAT 60.091 50.000 0.00 0.00 34.60 1.63
2823 2854 2.297597 CAGGGACTCACGGGAAGATATC 59.702 54.545 0.00 0.00 34.60 1.63
2824 2855 2.091278 AGGGACTCACGGGAAGATATCA 60.091 50.000 5.32 0.00 0.00 2.15
2825 2856 2.036089 GGGACTCACGGGAAGATATCAC 59.964 54.545 5.32 0.00 0.00 3.06
2826 2857 2.693591 GGACTCACGGGAAGATATCACA 59.306 50.000 5.32 0.00 0.00 3.58
2827 2858 3.132289 GGACTCACGGGAAGATATCACAA 59.868 47.826 5.32 0.00 0.00 3.33
2828 2859 4.113354 GACTCACGGGAAGATATCACAAC 58.887 47.826 5.32 0.00 0.00 3.32
2829 2860 3.513912 ACTCACGGGAAGATATCACAACA 59.486 43.478 5.32 0.00 0.00 3.33
2830 2861 3.857052 TCACGGGAAGATATCACAACAC 58.143 45.455 5.32 0.00 0.00 3.32
2831 2862 3.259625 TCACGGGAAGATATCACAACACA 59.740 43.478 5.32 0.00 0.00 3.72
2832 2863 4.000325 CACGGGAAGATATCACAACACAA 59.000 43.478 5.32 0.00 0.00 3.33
2833 2864 4.000988 ACGGGAAGATATCACAACACAAC 58.999 43.478 5.32 0.00 0.00 3.32
2834 2865 4.253685 CGGGAAGATATCACAACACAACT 58.746 43.478 5.32 0.00 0.00 3.16
2835 2866 4.330074 CGGGAAGATATCACAACACAACTC 59.670 45.833 5.32 0.00 0.00 3.01
2836 2867 5.491982 GGGAAGATATCACAACACAACTCT 58.508 41.667 5.32 0.00 0.00 3.24
2837 2868 6.627287 CGGGAAGATATCACAACACAACTCTA 60.627 42.308 5.32 0.00 0.00 2.43
2838 2869 7.103641 GGGAAGATATCACAACACAACTCTAA 58.896 38.462 5.32 0.00 0.00 2.10
2839 2870 7.606456 GGGAAGATATCACAACACAACTCTAAA 59.394 37.037 5.32 0.00 0.00 1.85
2840 2871 8.999431 GGAAGATATCACAACACAACTCTAAAA 58.001 33.333 5.32 0.00 0.00 1.52
2841 2872 9.813080 GAAGATATCACAACACAACTCTAAAAC 57.187 33.333 5.32 0.00 0.00 2.43
2842 2873 8.902540 AGATATCACAACACAACTCTAAAACA 57.097 30.769 5.32 0.00 0.00 2.83
2843 2874 9.507329 AGATATCACAACACAACTCTAAAACAT 57.493 29.630 5.32 0.00 0.00 2.71
2864 2895 8.978874 AACATAAATAAGTCATACAGGCATCA 57.021 30.769 0.00 0.00 0.00 3.07
2865 2896 9.578576 AACATAAATAAGTCATACAGGCATCAT 57.421 29.630 0.00 0.00 0.00 2.45
2873 2904 8.613060 AAGTCATACAGGCATCATAATACAAG 57.387 34.615 0.00 0.00 0.00 3.16
2874 2905 6.652481 AGTCATACAGGCATCATAATACAAGC 59.348 38.462 0.00 0.00 0.00 4.01
2875 2906 5.939883 TCATACAGGCATCATAATACAAGCC 59.060 40.000 0.00 0.00 42.31 4.35
2876 2907 4.169059 ACAGGCATCATAATACAAGCCA 57.831 40.909 0.00 0.00 44.34 4.75
2877 2908 4.139786 ACAGGCATCATAATACAAGCCAG 58.860 43.478 0.00 0.00 44.34 4.85
2878 2909 3.504906 CAGGCATCATAATACAAGCCAGG 59.495 47.826 0.00 0.00 44.34 4.45
2879 2910 2.821969 GGCATCATAATACAAGCCAGGG 59.178 50.000 0.00 0.00 41.63 4.45
2880 2911 2.821969 GCATCATAATACAAGCCAGGGG 59.178 50.000 0.00 0.00 0.00 4.79
2904 2935 1.291132 GAGGGCTCGAATACAAGTGC 58.709 55.000 0.00 0.00 0.00 4.40
2905 2936 0.905357 AGGGCTCGAATACAAGTGCT 59.095 50.000 0.00 0.00 0.00 4.40
2906 2937 1.134670 AGGGCTCGAATACAAGTGCTC 60.135 52.381 0.00 0.00 0.00 4.26
2907 2938 0.924090 GGCTCGAATACAAGTGCTCG 59.076 55.000 0.00 0.00 0.00 5.03
2908 2939 1.469251 GGCTCGAATACAAGTGCTCGA 60.469 52.381 7.80 7.80 37.95 4.04
2909 2940 2.464865 GCTCGAATACAAGTGCTCGAT 58.535 47.619 8.31 0.00 39.39 3.59
2910 2941 2.469516 GCTCGAATACAAGTGCTCGATC 59.530 50.000 8.31 2.80 39.39 3.69
2911 2942 3.695816 CTCGAATACAAGTGCTCGATCA 58.304 45.455 8.31 0.00 39.39 2.92
2912 2943 4.294232 CTCGAATACAAGTGCTCGATCAT 58.706 43.478 8.31 0.00 39.39 2.45
2913 2944 5.432885 TCGAATACAAGTGCTCGATCATA 57.567 39.130 0.00 0.00 35.52 2.15
2914 2945 5.452777 TCGAATACAAGTGCTCGATCATAG 58.547 41.667 0.00 0.00 35.52 2.23
2915 2946 5.238650 TCGAATACAAGTGCTCGATCATAGA 59.761 40.000 0.00 0.00 35.52 1.98
2916 2947 5.340932 CGAATACAAGTGCTCGATCATAGAC 59.659 44.000 0.00 0.00 33.13 2.59
2917 2948 3.071786 ACAAGTGCTCGATCATAGACG 57.928 47.619 0.00 0.00 0.00 4.18
2918 2949 2.683362 ACAAGTGCTCGATCATAGACGA 59.317 45.455 0.00 0.00 37.03 4.20
2925 2956 3.727518 CTCGATCATAGACGAGTTAGCG 58.272 50.000 0.00 0.00 46.90 4.26
2926 2957 2.479275 TCGATCATAGACGAGTTAGCGG 59.521 50.000 0.00 0.00 34.49 5.52
2927 2958 2.479275 CGATCATAGACGAGTTAGCGGA 59.521 50.000 0.00 0.00 35.12 5.54
2928 2959 3.059120 CGATCATAGACGAGTTAGCGGAA 60.059 47.826 0.00 0.00 35.12 4.30
2929 2960 3.965292 TCATAGACGAGTTAGCGGAAG 57.035 47.619 0.00 0.00 35.12 3.46
2946 2977 5.643339 CGGAAGCAACAATATCTGAGTAC 57.357 43.478 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 4.104102 ACCGGCATCTTCCCTTTTATGATA 59.896 41.667 0.00 0.00 0.00 2.15
229 230 0.321564 CCGCAAAGATGACACTCCCA 60.322 55.000 0.00 0.00 0.00 4.37
250 251 3.443329 TGCAGTTGAAAATGCATCGGTAT 59.557 39.130 13.60 0.00 46.97 2.73
345 346 2.485426 AGTCCGACTGAAACGACGATAA 59.515 45.455 0.00 0.00 0.00 1.75
346 347 2.079158 AGTCCGACTGAAACGACGATA 58.921 47.619 0.00 0.00 0.00 2.92
348 349 0.236711 GAGTCCGACTGAAACGACGA 59.763 55.000 5.57 0.00 0.00 4.20
349 350 0.728466 GGAGTCCGACTGAAACGACG 60.728 60.000 5.57 0.00 0.00 5.12
350 351 0.597072 AGGAGTCCGACTGAAACGAC 59.403 55.000 5.57 0.00 0.00 4.34
351 352 0.879765 GAGGAGTCCGACTGAAACGA 59.120 55.000 5.57 0.00 0.00 3.85
352 353 0.454620 CGAGGAGTCCGACTGAAACG 60.455 60.000 5.57 3.06 0.00 3.60
353 354 0.109226 CCGAGGAGTCCGACTGAAAC 60.109 60.000 5.57 0.00 0.00 2.78
362 368 2.997897 AGTGCCACCGAGGAGTCC 60.998 66.667 0.00 0.00 41.22 3.85
421 427 3.118884 ACGTATTTCCGCTACCAGATGTT 60.119 43.478 0.00 0.00 0.00 2.71
487 493 4.778213 TCTGCTACCCTATTTTGCTCAT 57.222 40.909 0.00 0.00 0.00 2.90
514 520 2.032054 TCCGTACGACTATACAAAGCCG 59.968 50.000 18.76 0.00 0.00 5.52
547 553 2.275318 GTCCTCTTGCTAGTCATGCAC 58.725 52.381 0.00 0.00 40.40 4.57
591 597 3.568853 CGGATAGGGTTACAATCGAGAGT 59.431 47.826 0.00 0.00 0.00 3.24
613 619 9.076596 CGATGGAGAAAGATTTTTATTCCAAAC 57.923 33.333 14.59 11.72 40.55 2.93
615 621 7.093988 TGCGATGGAGAAAGATTTTTATTCCAA 60.094 33.333 14.59 1.44 40.55 3.53
650 656 1.338973 CATATGCAAAATCGGCAGGCT 59.661 47.619 0.00 0.00 45.68 4.58
651 657 1.067516 ACATATGCAAAATCGGCAGGC 59.932 47.619 1.58 0.00 45.68 4.85
652 658 2.544277 CCACATATGCAAAATCGGCAGG 60.544 50.000 1.58 0.00 45.68 4.85
653 659 2.099592 ACCACATATGCAAAATCGGCAG 59.900 45.455 1.58 0.00 45.68 4.85
654 660 2.098614 ACCACATATGCAAAATCGGCA 58.901 42.857 1.58 0.00 46.66 5.69
698 704 0.670162 CAGTCCAAAACCAGCACCAG 59.330 55.000 0.00 0.00 0.00 4.00
704 710 2.291741 GAGAAGTGCAGTCCAAAACCAG 59.708 50.000 0.00 0.00 0.00 4.00
711 717 2.224159 GGGGGAGAAGTGCAGTCCA 61.224 63.158 0.00 0.00 31.31 4.02
723 729 1.995626 ATCCAACACCTCGGGGGAG 60.996 63.158 6.13 0.00 38.76 4.30
731 737 4.664688 AAGAGAAATCCATCCAACACCT 57.335 40.909 0.00 0.00 0.00 4.00
767 774 6.395629 AGGTATTCGAAAGATTGTCTTCGAA 58.604 36.000 18.46 18.46 43.14 3.71
769 776 6.020281 CAGAGGTATTCGAAAGATTGTCTTCG 60.020 42.308 0.00 0.00 41.60 3.79
770 777 7.009723 GTCAGAGGTATTCGAAAGATTGTCTTC 59.990 40.741 0.00 0.00 41.60 2.87
771 778 6.814146 GTCAGAGGTATTCGAAAGATTGTCTT 59.186 38.462 0.00 0.00 41.60 3.01
776 783 5.450688 CCGAGTCAGAGGTATTCGAAAGATT 60.451 44.000 0.00 0.00 41.60 2.40
777 784 4.036971 CCGAGTCAGAGGTATTCGAAAGAT 59.963 45.833 0.00 0.00 41.60 2.40
848 855 0.600255 ACTTTTGTCCTCGAGGTGCG 60.600 55.000 30.17 15.71 42.69 5.34
855 862 1.334054 CGTCGGTACTTTTGTCCTCG 58.666 55.000 0.00 0.00 0.00 4.63
864 871 5.954296 ATATATACTGTGCGTCGGTACTT 57.046 39.130 0.00 0.00 40.22 2.24
884 895 5.349543 GCGTTCTTTTCTTTTCGGGAGTATA 59.650 40.000 0.00 0.00 0.00 1.47
885 896 4.153655 GCGTTCTTTTCTTTTCGGGAGTAT 59.846 41.667 0.00 0.00 0.00 2.12
886 897 3.495753 GCGTTCTTTTCTTTTCGGGAGTA 59.504 43.478 0.00 0.00 0.00 2.59
887 898 2.289820 GCGTTCTTTTCTTTTCGGGAGT 59.710 45.455 0.00 0.00 0.00 3.85
888 899 2.289547 TGCGTTCTTTTCTTTTCGGGAG 59.710 45.455 0.00 0.00 0.00 4.30
889 900 2.032426 GTGCGTTCTTTTCTTTTCGGGA 59.968 45.455 0.00 0.00 0.00 5.14
890 901 2.223386 TGTGCGTTCTTTTCTTTTCGGG 60.223 45.455 0.00 0.00 0.00 5.14
923 934 3.599285 GATGGTGCGGTCCGGTTGA 62.599 63.158 14.38 0.00 0.00 3.18
925 936 4.404098 GGATGGTGCGGTCCGGTT 62.404 66.667 14.38 0.00 0.00 4.44
934 945 2.969238 CCTCGATGCGGATGGTGC 60.969 66.667 0.00 0.00 0.00 5.01
940 951 2.798689 CTTCGTCCTCGATGCGGA 59.201 61.111 0.00 0.00 45.65 5.54
963 974 1.112113 GGGGATCAAGAGCTACGTGA 58.888 55.000 0.00 0.00 40.75 4.35
977 988 0.753262 CTCTTCGACAATCCGGGGAT 59.247 55.000 0.00 0.00 36.23 3.85
986 997 2.543578 GCCATGTGCTCTTCGACAA 58.456 52.632 0.00 0.00 36.87 3.18
997 1008 2.608752 GGAGCACAAAAGAAGCCATGTG 60.609 50.000 0.00 0.00 44.55 3.21
1009 1020 2.435938 GGCGGATCGGAGCACAAA 60.436 61.111 4.16 0.00 34.54 2.83
1047 1058 2.940994 TCCCAACAAAATCGGAGACA 57.059 45.000 0.00 0.00 42.51 3.41
1048 1059 3.408634 TCTTCCCAACAAAATCGGAGAC 58.591 45.455 0.00 0.00 42.51 3.36
1058 1069 0.326927 GGGTCGGATCTTCCCAACAA 59.673 55.000 12.94 0.00 40.79 2.83
1061 1072 4.571236 TGGGTCGGATCTTCCCAA 57.429 55.556 16.49 5.20 46.78 4.12
1123 1134 7.310664 CGATTAGCTGATTATCAATTTGGCAT 58.689 34.615 0.00 0.00 0.00 4.40
1143 1154 4.344102 AGCTAACTAATGGTCAGGCGATTA 59.656 41.667 0.00 0.00 0.00 1.75
1145 1156 2.700897 AGCTAACTAATGGTCAGGCGAT 59.299 45.455 0.00 0.00 0.00 4.58
1160 1171 8.719648 ACATGATATGTACGAGTACTAGCTAAC 58.280 37.037 13.67 0.49 42.78 2.34
1168 1179 7.350467 TCGAAGAACATGATATGTACGAGTAC 58.650 38.462 0.00 6.46 44.07 2.73
1169 1180 7.486802 TCGAAGAACATGATATGTACGAGTA 57.513 36.000 0.00 0.00 44.07 2.59
1170 1181 6.373186 TCGAAGAACATGATATGTACGAGT 57.627 37.500 0.00 0.00 44.07 4.18
1171 1182 5.340932 GCTCGAAGAACATGATATGTACGAG 59.659 44.000 21.38 21.38 44.07 4.18
1172 1183 5.212934 GCTCGAAGAACATGATATGTACGA 58.787 41.667 0.00 1.22 44.07 3.43
1173 1184 4.383052 GGCTCGAAGAACATGATATGTACG 59.617 45.833 0.00 0.00 44.07 3.67
1174 1185 5.533482 AGGCTCGAAGAACATGATATGTAC 58.467 41.667 0.00 0.00 44.07 2.90
1175 1186 5.301805 TGAGGCTCGAAGAACATGATATGTA 59.698 40.000 10.42 0.00 44.07 2.29
1177 1188 4.625028 TGAGGCTCGAAGAACATGATATG 58.375 43.478 10.42 0.00 34.09 1.78
1178 1189 4.343526 ACTGAGGCTCGAAGAACATGATAT 59.656 41.667 10.42 0.00 34.09 1.63
1179 1190 3.701542 ACTGAGGCTCGAAGAACATGATA 59.298 43.478 10.42 0.00 34.09 2.15
1180 1191 2.499289 ACTGAGGCTCGAAGAACATGAT 59.501 45.455 10.42 0.00 34.09 2.45
1181 1192 1.895798 ACTGAGGCTCGAAGAACATGA 59.104 47.619 10.42 0.00 34.09 3.07
1187 1198 3.056749 GGAAACTTACTGAGGCTCGAAGA 60.057 47.826 22.80 5.69 0.00 2.87
1199 1210 4.781934 AGCTCAAACACAGGAAACTTACT 58.218 39.130 0.00 0.00 40.21 2.24
1236 1247 2.456119 GGCCTCTGCGAATCACGTG 61.456 63.158 9.94 9.94 44.60 4.49
1242 1253 4.496336 GGGCTGGCCTCTGCGAAT 62.496 66.667 13.80 0.00 38.51 3.34
1258 1269 1.506262 CCCAAAAATCTGACGCGGG 59.494 57.895 12.47 0.00 0.00 6.13
1305 1316 0.309612 CCACCGCAAACACAGGTTAC 59.690 55.000 0.00 0.00 35.82 2.50
1308 1319 1.150536 ATCCACCGCAAACACAGGT 59.849 52.632 0.00 0.00 39.12 4.00
1309 1320 0.888736 TCATCCACCGCAAACACAGG 60.889 55.000 0.00 0.00 0.00 4.00
1310 1321 0.238289 GTCATCCACCGCAAACACAG 59.762 55.000 0.00 0.00 0.00 3.66
1317 1328 2.236146 ACTAAATCTGTCATCCACCGCA 59.764 45.455 0.00 0.00 0.00 5.69
1320 1331 4.437390 CGCAAACTAAATCTGTCATCCACC 60.437 45.833 0.00 0.00 0.00 4.61
1332 1343 1.818060 TGCCATGCTCGCAAACTAAAT 59.182 42.857 0.00 0.00 32.05 1.40
1374 1385 1.000385 CAAGCACGGCAATTTCCTGAA 60.000 47.619 0.00 0.00 0.00 3.02
1377 1391 1.290009 GCAAGCACGGCAATTTCCT 59.710 52.632 0.00 0.00 0.00 3.36
1418 1432 9.921637 ACGTTTTTCATGTCAATTTATATTGGT 57.078 25.926 6.12 0.00 41.23 3.67
1426 1440 8.542132 CAGATCAAACGTTTTTCATGTCAATTT 58.458 29.630 11.66 0.00 0.00 1.82
1450 1464 5.531659 AGAGATGCTAAAAATCTGATGGCAG 59.468 40.000 0.00 0.00 43.67 4.85
1489 1503 5.822519 GGCATTATGTCTGATACAGGTCAAA 59.177 40.000 0.00 0.00 42.70 2.69
1494 1508 5.554070 TCATGGCATTATGTCTGATACAGG 58.446 41.667 0.00 0.00 42.70 4.00
1495 1509 6.877322 TGATCATGGCATTATGTCTGATACAG 59.123 38.462 0.00 0.00 42.70 2.74
1496 1510 6.771573 TGATCATGGCATTATGTCTGATACA 58.228 36.000 0.00 8.35 43.86 2.29
1497 1511 7.101700 TCTGATCATGGCATTATGTCTGATAC 58.898 38.462 0.00 6.69 0.00 2.24
1498 1512 7.248743 TCTGATCATGGCATTATGTCTGATA 57.751 36.000 0.00 0.00 0.00 2.15
1499 1513 6.123045 TCTGATCATGGCATTATGTCTGAT 57.877 37.500 0.00 10.05 0.00 2.90
1500 1514 5.556006 TCTGATCATGGCATTATGTCTGA 57.444 39.130 0.00 0.26 0.00 3.27
1501 1515 9.043079 GTATATCTGATCATGGCATTATGTCTG 57.957 37.037 0.00 0.00 0.00 3.51
1502 1516 8.209584 GGTATATCTGATCATGGCATTATGTCT 58.790 37.037 0.00 0.00 0.00 3.41
1503 1517 7.443575 GGGTATATCTGATCATGGCATTATGTC 59.556 40.741 0.00 0.00 0.00 3.06
1528 1542 5.410924 TCACGAATTTACATCTCAGTCTGG 58.589 41.667 0.00 0.00 0.00 3.86
1533 1547 5.612435 CGTCTCACGAATTTACATCTCAG 57.388 43.478 0.00 0.00 46.05 3.35
1617 1632 6.703319 TCTTCCTTGATATGTTTTCCGTGTA 58.297 36.000 0.00 0.00 0.00 2.90
1676 1691 0.459899 ATACAGTCGCGCTCATCCAA 59.540 50.000 5.56 0.00 0.00 3.53
1691 1706 3.319137 GTGAGCTTCACACAGGATACA 57.681 47.619 10.30 0.00 46.22 2.29
1785 1800 4.865905 ACAACCACAGGCCATAATATGAA 58.134 39.130 5.01 0.00 0.00 2.57
1788 1803 9.243105 GAATAATACAACCACAGGCCATAATAT 57.757 33.333 5.01 0.00 0.00 1.28
1792 1807 6.260700 AGAATAATACAACCACAGGCCATA 57.739 37.500 5.01 0.00 0.00 2.74
1793 1808 5.129368 AGAATAATACAACCACAGGCCAT 57.871 39.130 5.01 0.00 0.00 4.40
1794 1809 4.584638 AGAATAATACAACCACAGGCCA 57.415 40.909 5.01 0.00 0.00 5.36
1795 1810 7.582667 AATAAGAATAATACAACCACAGGCC 57.417 36.000 0.00 0.00 0.00 5.19
1825 1855 3.237268 TGTCCCTGCAGGTTAAAACAT 57.763 42.857 30.63 0.00 36.75 2.71
1914 1944 6.239036 GGAGGTATATTTTCCACAGGCATTTC 60.239 42.308 0.00 0.00 0.00 2.17
1952 1982 8.359642 GTCATAACACCAATGCCACATTAATAT 58.640 33.333 0.00 0.00 0.00 1.28
1957 1987 4.088634 AGTCATAACACCAATGCCACATT 58.911 39.130 0.00 0.00 0.00 2.71
1963 1993 8.587952 AAAAGTAAAAGTCATAACACCAATGC 57.412 30.769 0.00 0.00 0.00 3.56
1965 1995 9.040939 GCAAAAAGTAAAAGTCATAACACCAAT 57.959 29.630 0.00 0.00 0.00 3.16
1984 2014 5.591099 ACATGGTTCAGTACAAGCAAAAAG 58.409 37.500 0.00 0.00 37.32 2.27
2031 2061 2.948979 CACAGCCTAGTTTCCAACACAA 59.051 45.455 0.00 0.00 0.00 3.33
2131 2161 7.824289 CCATGTACATCTTCTCCTTCAGTAAAA 59.176 37.037 5.07 0.00 0.00 1.52
2136 2166 5.604758 TCCATGTACATCTTCTCCTTCAG 57.395 43.478 5.07 0.00 0.00 3.02
2175 2205 6.436843 AAAAATAATCCTCGCTAGGTGTTG 57.563 37.500 3.89 0.00 44.09 3.33
2342 2372 2.319841 GCGGGTTGGTGGACGTTAC 61.320 63.158 0.00 0.00 0.00 2.50
2744 2775 3.400599 ATTGGATCGGGGGCGTCAC 62.401 63.158 0.00 0.00 0.00 3.67
2745 2776 3.087253 ATTGGATCGGGGGCGTCA 61.087 61.111 0.00 0.00 0.00 4.35
2746 2777 2.280865 GATTGGATCGGGGGCGTC 60.281 66.667 0.00 0.00 0.00 5.19
2755 2786 5.696270 TGCATGATTAGTGTACGATTGGATC 59.304 40.000 0.00 0.00 0.00 3.36
2756 2787 5.466728 GTGCATGATTAGTGTACGATTGGAT 59.533 40.000 0.00 0.00 0.00 3.41
2757 2788 4.808895 GTGCATGATTAGTGTACGATTGGA 59.191 41.667 0.00 0.00 0.00 3.53
2758 2789 5.083136 GTGCATGATTAGTGTACGATTGG 57.917 43.478 0.00 0.00 0.00 3.16
2764 2795 3.785505 GCTTGCGTGCATGATTAGTGTAC 60.786 47.826 10.93 0.00 0.00 2.90
2765 2796 2.351418 GCTTGCGTGCATGATTAGTGTA 59.649 45.455 10.93 0.00 0.00 2.90
2766 2797 1.131126 GCTTGCGTGCATGATTAGTGT 59.869 47.619 10.93 0.00 0.00 3.55
2767 2798 1.818850 GCTTGCGTGCATGATTAGTG 58.181 50.000 10.93 0.00 0.00 2.74
2768 2799 0.374758 CGCTTGCGTGCATGATTAGT 59.625 50.000 10.93 0.00 0.00 2.24
2769 2800 0.374758 ACGCTTGCGTGCATGATTAG 59.625 50.000 20.01 4.13 0.00 1.73
2770 2801 0.096802 CACGCTTGCGTGCATGATTA 59.903 50.000 30.14 0.00 32.99 1.75
2771 2802 1.154169 CACGCTTGCGTGCATGATT 60.154 52.632 30.14 0.04 32.99 2.57
2772 2803 1.018752 TACACGCTTGCGTGCATGAT 61.019 50.000 37.08 24.34 42.99 2.45
2773 2804 1.666234 TACACGCTTGCGTGCATGA 60.666 52.632 37.08 22.35 42.99 3.07
2774 2805 1.509787 GTACACGCTTGCGTGCATG 60.510 57.895 37.08 20.93 42.99 4.06
2775 2806 2.860293 GTACACGCTTGCGTGCAT 59.140 55.556 37.08 25.54 42.99 3.96
2776 2807 3.697444 CGTACACGCTTGCGTGCA 61.697 61.111 37.08 27.44 42.99 4.57
2777 2808 2.597650 GATCGTACACGCTTGCGTGC 62.598 60.000 37.08 24.91 42.99 5.34
2778 2809 1.340465 GATCGTACACGCTTGCGTG 59.660 57.895 36.03 36.03 44.56 5.34
2779 2810 0.665068 TTGATCGTACACGCTTGCGT 60.665 50.000 15.19 15.19 39.60 5.24
2780 2811 0.023732 CTTGATCGTACACGCTTGCG 59.976 55.000 13.70 13.70 39.60 4.85
2781 2812 1.346365 TCTTGATCGTACACGCTTGC 58.654 50.000 0.00 0.00 39.60 4.01
2782 2813 3.179048 TGATCTTGATCGTACACGCTTG 58.821 45.455 6.19 0.00 39.60 4.01
2783 2814 3.439293 CTGATCTTGATCGTACACGCTT 58.561 45.455 6.19 0.00 39.60 4.68
2784 2815 2.223595 CCTGATCTTGATCGTACACGCT 60.224 50.000 6.19 0.00 39.60 5.07
2785 2816 2.120232 CCTGATCTTGATCGTACACGC 58.880 52.381 6.19 0.00 39.60 5.34
2786 2817 2.357952 TCCCTGATCTTGATCGTACACG 59.642 50.000 6.19 0.00 41.45 4.49
2787 2818 3.381908 AGTCCCTGATCTTGATCGTACAC 59.618 47.826 6.19 1.73 0.00 2.90
2788 2819 3.632333 AGTCCCTGATCTTGATCGTACA 58.368 45.455 6.19 0.00 0.00 2.90
2789 2820 3.632604 TGAGTCCCTGATCTTGATCGTAC 59.367 47.826 6.19 2.53 0.00 3.67
2790 2821 3.632604 GTGAGTCCCTGATCTTGATCGTA 59.367 47.826 6.19 0.00 0.00 3.43
2791 2822 2.428890 GTGAGTCCCTGATCTTGATCGT 59.571 50.000 6.19 0.00 0.00 3.73
2792 2823 2.542618 CGTGAGTCCCTGATCTTGATCG 60.543 54.545 6.19 2.03 0.00 3.69
2793 2824 2.223923 CCGTGAGTCCCTGATCTTGATC 60.224 54.545 3.82 3.82 0.00 2.92
2794 2825 1.759445 CCGTGAGTCCCTGATCTTGAT 59.241 52.381 0.00 0.00 0.00 2.57
2795 2826 1.186200 CCGTGAGTCCCTGATCTTGA 58.814 55.000 0.00 0.00 0.00 3.02
2796 2827 0.176680 CCCGTGAGTCCCTGATCTTG 59.823 60.000 0.00 0.00 0.00 3.02
2797 2828 0.041238 TCCCGTGAGTCCCTGATCTT 59.959 55.000 0.00 0.00 0.00 2.40
2798 2829 0.041238 TTCCCGTGAGTCCCTGATCT 59.959 55.000 0.00 0.00 0.00 2.75
2799 2830 0.461961 CTTCCCGTGAGTCCCTGATC 59.538 60.000 0.00 0.00 0.00 2.92
2800 2831 0.041238 TCTTCCCGTGAGTCCCTGAT 59.959 55.000 0.00 0.00 0.00 2.90
2801 2832 0.041238 ATCTTCCCGTGAGTCCCTGA 59.959 55.000 0.00 0.00 0.00 3.86
2802 2833 1.776662 TATCTTCCCGTGAGTCCCTG 58.223 55.000 0.00 0.00 0.00 4.45
2803 2834 2.091278 TGATATCTTCCCGTGAGTCCCT 60.091 50.000 3.98 0.00 0.00 4.20
2804 2835 2.036089 GTGATATCTTCCCGTGAGTCCC 59.964 54.545 3.98 0.00 0.00 4.46
2805 2836 2.693591 TGTGATATCTTCCCGTGAGTCC 59.306 50.000 3.98 0.00 0.00 3.85
2806 2837 4.113354 GTTGTGATATCTTCCCGTGAGTC 58.887 47.826 3.98 0.00 0.00 3.36
2807 2838 3.513912 TGTTGTGATATCTTCCCGTGAGT 59.486 43.478 3.98 0.00 0.00 3.41
2808 2839 3.865745 GTGTTGTGATATCTTCCCGTGAG 59.134 47.826 3.98 0.00 0.00 3.51
2809 2840 3.259625 TGTGTTGTGATATCTTCCCGTGA 59.740 43.478 3.98 0.00 0.00 4.35
2810 2841 3.595173 TGTGTTGTGATATCTTCCCGTG 58.405 45.455 3.98 0.00 0.00 4.94
2811 2842 3.973206 TGTGTTGTGATATCTTCCCGT 57.027 42.857 3.98 0.00 0.00 5.28
2812 2843 4.253685 AGTTGTGTTGTGATATCTTCCCG 58.746 43.478 3.98 0.00 0.00 5.14
2813 2844 5.491982 AGAGTTGTGTTGTGATATCTTCCC 58.508 41.667 3.98 0.00 0.00 3.97
2814 2845 8.547967 TTTAGAGTTGTGTTGTGATATCTTCC 57.452 34.615 3.98 0.00 0.00 3.46
2815 2846 9.813080 GTTTTAGAGTTGTGTTGTGATATCTTC 57.187 33.333 3.98 0.00 0.00 2.87
2816 2847 9.337396 TGTTTTAGAGTTGTGTTGTGATATCTT 57.663 29.630 3.98 0.00 0.00 2.40
2817 2848 8.902540 TGTTTTAGAGTTGTGTTGTGATATCT 57.097 30.769 3.98 0.00 0.00 1.98
2838 2869 9.407380 TGATGCCTGTATGACTTATTTATGTTT 57.593 29.630 0.00 0.00 0.00 2.83
2839 2870 8.978874 TGATGCCTGTATGACTTATTTATGTT 57.021 30.769 0.00 0.00 0.00 2.71
2847 2878 9.710900 CTTGTATTATGATGCCTGTATGACTTA 57.289 33.333 0.00 0.00 0.00 2.24
2848 2879 7.173907 GCTTGTATTATGATGCCTGTATGACTT 59.826 37.037 0.00 0.00 0.00 3.01
2849 2880 6.652481 GCTTGTATTATGATGCCTGTATGACT 59.348 38.462 0.00 0.00 0.00 3.41
2850 2881 6.128172 GGCTTGTATTATGATGCCTGTATGAC 60.128 42.308 0.00 0.00 37.58 3.06
2851 2882 5.939883 GGCTTGTATTATGATGCCTGTATGA 59.060 40.000 0.00 0.00 37.58 2.15
2852 2883 5.706833 TGGCTTGTATTATGATGCCTGTATG 59.293 40.000 0.00 0.00 40.82 2.39
2853 2884 5.879763 TGGCTTGTATTATGATGCCTGTAT 58.120 37.500 0.00 0.00 40.82 2.29
2854 2885 5.303259 TGGCTTGTATTATGATGCCTGTA 57.697 39.130 0.00 0.00 40.82 2.74
2855 2886 4.139786 CTGGCTTGTATTATGATGCCTGT 58.860 43.478 0.00 0.00 40.82 4.00
2856 2887 3.504906 CCTGGCTTGTATTATGATGCCTG 59.495 47.826 0.00 0.00 40.82 4.85
2857 2888 3.499202 CCCTGGCTTGTATTATGATGCCT 60.499 47.826 0.00 0.00 40.82 4.75
2858 2889 2.821969 CCCTGGCTTGTATTATGATGCC 59.178 50.000 0.00 0.00 40.62 4.40
2859 2890 2.821969 CCCCTGGCTTGTATTATGATGC 59.178 50.000 0.00 0.00 0.00 3.91
2860 2891 2.821969 GCCCCTGGCTTGTATTATGATG 59.178 50.000 0.00 0.00 46.69 3.07
2861 2892 3.160679 GCCCCTGGCTTGTATTATGAT 57.839 47.619 0.00 0.00 46.69 2.45
2862 2893 2.656947 GCCCCTGGCTTGTATTATGA 57.343 50.000 0.00 0.00 46.69 2.15
2885 2916 1.134670 AGCACTTGTATTCGAGCCCTC 60.135 52.381 0.00 0.00 0.00 4.30
2886 2917 0.905357 AGCACTTGTATTCGAGCCCT 59.095 50.000 0.00 0.00 0.00 5.19
2887 2918 1.291132 GAGCACTTGTATTCGAGCCC 58.709 55.000 0.00 0.00 0.00 5.19
2888 2919 0.924090 CGAGCACTTGTATTCGAGCC 59.076 55.000 0.00 0.00 35.19 4.70
2889 2920 1.909376 TCGAGCACTTGTATTCGAGC 58.091 50.000 5.19 0.00 37.18 5.03
2890 2921 3.695816 TGATCGAGCACTTGTATTCGAG 58.304 45.455 0.00 0.00 44.14 4.04
2891 2922 3.775661 TGATCGAGCACTTGTATTCGA 57.224 42.857 0.00 9.86 44.88 3.71
2892 2923 5.340932 GTCTATGATCGAGCACTTGTATTCG 59.659 44.000 5.03 0.00 34.56 3.34
2893 2924 5.340932 CGTCTATGATCGAGCACTTGTATTC 59.659 44.000 5.03 0.00 0.00 1.75
2894 2925 5.008712 TCGTCTATGATCGAGCACTTGTATT 59.991 40.000 5.03 0.00 0.00 1.89
2895 2926 4.515567 TCGTCTATGATCGAGCACTTGTAT 59.484 41.667 5.03 0.00 0.00 2.29
2896 2927 3.875134 TCGTCTATGATCGAGCACTTGTA 59.125 43.478 5.03 0.00 0.00 2.41
2897 2928 2.683362 TCGTCTATGATCGAGCACTTGT 59.317 45.455 5.03 0.00 0.00 3.16
2898 2929 3.295785 CTCGTCTATGATCGAGCACTTG 58.704 50.000 5.03 0.00 44.82 3.16
2899 2930 3.617540 CTCGTCTATGATCGAGCACTT 57.382 47.619 5.03 0.00 44.82 3.16
2905 2936 2.479275 CCGCTAACTCGTCTATGATCGA 59.521 50.000 0.00 0.00 34.88 3.59
2906 2937 2.479275 TCCGCTAACTCGTCTATGATCG 59.521 50.000 0.00 0.00 0.00 3.69
2907 2938 4.468643 CTTCCGCTAACTCGTCTATGATC 58.531 47.826 0.00 0.00 0.00 2.92
2908 2939 3.304794 GCTTCCGCTAACTCGTCTATGAT 60.305 47.826 0.00 0.00 0.00 2.45
2909 2940 2.033049 GCTTCCGCTAACTCGTCTATGA 59.967 50.000 0.00 0.00 0.00 2.15
2910 2941 2.223502 TGCTTCCGCTAACTCGTCTATG 60.224 50.000 0.00 0.00 36.97 2.23
2911 2942 2.022195 TGCTTCCGCTAACTCGTCTAT 58.978 47.619 0.00 0.00 36.97 1.98
2912 2943 1.456296 TGCTTCCGCTAACTCGTCTA 58.544 50.000 0.00 0.00 36.97 2.59
2913 2944 0.601558 TTGCTTCCGCTAACTCGTCT 59.398 50.000 0.00 0.00 36.97 4.18
2914 2945 0.714439 GTTGCTTCCGCTAACTCGTC 59.286 55.000 0.00 0.00 36.97 4.20
2915 2946 0.032952 TGTTGCTTCCGCTAACTCGT 59.967 50.000 0.00 0.00 36.97 4.18
2916 2947 1.144969 TTGTTGCTTCCGCTAACTCG 58.855 50.000 0.00 0.00 36.97 4.18
2917 2948 4.811557 AGATATTGTTGCTTCCGCTAACTC 59.188 41.667 0.00 0.00 36.97 3.01
2918 2949 4.572389 CAGATATTGTTGCTTCCGCTAACT 59.428 41.667 0.00 0.00 36.97 2.24
2919 2950 4.570772 TCAGATATTGTTGCTTCCGCTAAC 59.429 41.667 0.00 0.00 36.97 2.34
2920 2951 4.765273 TCAGATATTGTTGCTTCCGCTAA 58.235 39.130 0.00 0.00 36.97 3.09
2921 2952 4.141937 ACTCAGATATTGTTGCTTCCGCTA 60.142 41.667 0.00 0.00 36.97 4.26
2922 2953 3.201290 CTCAGATATTGTTGCTTCCGCT 58.799 45.455 0.00 0.00 36.97 5.52
2923 2954 2.939103 ACTCAGATATTGTTGCTTCCGC 59.061 45.455 0.00 0.00 0.00 5.54
2924 2955 5.643339 GTACTCAGATATTGTTGCTTCCG 57.357 43.478 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.