Multiple sequence alignment - TraesCS3D01G043400

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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 TraesCS3D01G043400 chr3D 100.000 2732 0 0 1 2732 16513799 16516530 0.000000e+00 5046.0
1 TraesCS3D01G043400 chr3D 85.417 96 10 2 2553 2646 16516444 16516351 2.240000e-16 97.1
2 TraesCS3D01G043400 chr3B 90.010 1001 68 20 1749 2732 23957128 23958113 0.000000e+00 1266.0
3 TraesCS3D01G043400 chr3B 93.262 653 31 2 1104 1756 23956295 23956934 0.000000e+00 950.0
4 TraesCS3D01G043400 chr3B 92.105 190 11 4 922 1109 23956077 23956264 5.800000e-67 265.0
5 TraesCS3D01G043400 chr3A 88.671 918 51 24 1820 2711 20021203 20020313 0.000000e+00 1070.0
6 TraesCS3D01G043400 chr3A 91.908 692 39 4 1106 1784 20029114 20028427 0.000000e+00 952.0
7 TraesCS3D01G043400 chr3A 92.529 174 10 1 939 1109 20029326 20029153 2.100000e-61 246.0
8 TraesCS3D01G043400 chr3A 86.667 120 14 1 87 206 20030838 20030721 6.140000e-27 132.0
9 TraesCS3D01G043400 chr3A 94.828 58 1 2 844 899 20029895 20029838 3.750000e-14 89.8
10 TraesCS3D01G043400 chr7B 89.607 433 28 4 1335 1755 63391596 63392023 4.000000e-148 534.0
11 TraesCS3D01G043400 chr7B 95.588 68 3 0 1287 1354 63392102 63392035 2.880000e-20 110.0
12 TraesCS3D01G043400 chr7B 94.030 67 2 2 1023 1088 63391546 63391611 1.730000e-17 100.0
13 TraesCS3D01G043400 chr6D 89.450 436 29 4 1335 1758 137129265 137128835 4.000000e-148 534.0
14 TraesCS3D01G043400 chr6D 92.075 265 13 2 1094 1354 137128566 137128826 1.550000e-97 366.0
15 TraesCS3D01G043400 chr6D 91.860 258 13 4 1101 1354 137126893 137127146 1.200000e-93 353.0
16 TraesCS3D01G043400 chr6D 91.860 258 13 4 1101 1354 137127733 137127986 1.200000e-93 353.0
17 TraesCS3D01G043400 chr6D 94.030 67 2 2 1023 1088 137129315 137129250 1.730000e-17 100.0
18 TraesCS3D01G043400 chr6D 82.178 101 12 6 2551 2647 7460176 7460274 6.270000e-12 82.4
19 TraesCS3D01G043400 chr7D 89.078 293 15 8 1335 1615 482120745 482120458 5.600000e-92 348.0
20 TraesCS3D01G043400 chr7D 94.030 67 2 2 1023 1088 482120795 482120730 1.730000e-17 100.0
21 TraesCS3D01G043400 chr4D 96.552 58 0 1 2553 2610 504343764 504343819 8.050000e-16 95.3
22 TraesCS3D01G043400 chr4D 96.552 58 0 1 2553 2610 505192447 505192392 8.050000e-16 95.3
23 TraesCS3D01G043400 chr7A 82.828 99 12 2 2548 2646 730464788 730464695 1.740000e-12 84.2
24 TraesCS3D01G043400 chr1B 84.043 94 6 5 2553 2646 528379970 528380054 6.270000e-12 82.4
25 TraesCS3D01G043400 chr1A 81.905 105 10 8 2546 2646 566218074 566218173 2.260000e-11 80.5
26 TraesCS3D01G043400 chr6B 81.553 103 12 6 2549 2646 298287810 298287910 8.110000e-11 78.7
27 TraesCS3D01G043400 chr2B 79.808 104 12 8 2546 2645 164904152 164904250 1.760000e-07 67.6


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 TraesCS3D01G043400 chr3D 16513799 16516530 2731 False 5046.000000 5046 100.000000 1 2732 1 chr3D.!!$F1 2731
1 TraesCS3D01G043400 chr3B 23956077 23958113 2036 False 827.000000 1266 91.792333 922 2732 3 chr3B.!!$F1 1810
2 TraesCS3D01G043400 chr3A 20020313 20021203 890 True 1070.000000 1070 88.671000 1820 2711 1 chr3A.!!$R1 891
3 TraesCS3D01G043400 chr3A 20028427 20030838 2411 True 354.950000 952 91.483000 87 1784 4 chr3A.!!$R2 1697
4 TraesCS3D01G043400 chr6D 137126893 137128826 1933 False 357.333333 366 91.931667 1094 1354 3 chr6D.!!$F2 260

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
312 544 0.037882 ACAGTCTCGACAGTGCATGG 60.038 55.0 0.0 0.0 29.59 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1848 3674 0.533491 TGCAGCGGTAAATCGGTAGT 59.467 50.0 0.0 0.0 38.91 2.73 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
24 25 6.576662 TTAATTTGCCTGTACGATTTTCCA 57.423 33.333 0.00 0.00 0.00 3.53
26 27 4.920640 TTTGCCTGTACGATTTTCCAAA 57.079 36.364 0.00 0.00 0.00 3.28
27 28 3.907894 TGCCTGTACGATTTTCCAAAC 57.092 42.857 0.00 0.00 0.00 2.93
29 30 3.823873 TGCCTGTACGATTTTCCAAACAT 59.176 39.130 0.00 0.00 0.00 2.71
30 31 4.279671 TGCCTGTACGATTTTCCAAACATT 59.720 37.500 0.00 0.00 0.00 2.71
32 33 5.335661 GCCTGTACGATTTTCCAAACATTCT 60.336 40.000 0.00 0.00 0.00 2.40
34 35 6.072728 CCTGTACGATTTTCCAAACATTCTGA 60.073 38.462 0.00 0.00 0.00 3.27
36 37 7.708051 TGTACGATTTTCCAAACATTCTGAAA 58.292 30.769 0.00 0.00 0.00 2.69
37 38 7.860373 TGTACGATTTTCCAAACATTCTGAAAG 59.140 33.333 0.00 0.00 0.00 2.62
38 39 6.805713 ACGATTTTCCAAACATTCTGAAAGT 58.194 32.000 0.00 0.00 33.76 2.66
39 40 7.264947 ACGATTTTCCAAACATTCTGAAAGTT 58.735 30.769 5.27 5.27 33.76 2.66
41 42 7.357532 CGATTTTCCAAACATTCTGAAAGTTCG 60.358 37.037 10.96 5.02 32.84 3.95
42 43 6.443934 TTTCCAAACATTCTGAAAGTTCGA 57.556 33.333 10.96 7.54 33.76 3.71
43 44 6.443934 TTCCAAACATTCTGAAAGTTCGAA 57.556 33.333 10.96 12.08 33.76 3.71
44 45 6.633500 TCCAAACATTCTGAAAGTTCGAAT 57.367 33.333 10.96 5.74 33.78 3.34
47 48 7.227711 TCCAAACATTCTGAAAGTTCGAATGTA 59.772 33.333 26.10 16.87 46.97 2.29
48 49 7.323656 CCAAACATTCTGAAAGTTCGAATGTAC 59.676 37.037 26.10 0.00 46.97 2.90
49 50 7.730364 AACATTCTGAAAGTTCGAATGTACT 57.270 32.000 26.10 17.49 46.97 2.73
50 51 7.730364 ACATTCTGAAAGTTCGAATGTACTT 57.270 32.000 25.41 0.00 46.49 2.24
52 53 5.591643 TCTGAAAGTTCGAATGTACTTGC 57.408 39.130 0.00 0.00 36.07 4.01
53 54 5.053811 TCTGAAAGTTCGAATGTACTTGCA 58.946 37.500 0.00 4.62 38.35 4.08
55 56 4.572795 TGAAAGTTCGAATGTACTTGCACA 59.427 37.500 0.00 0.51 36.45 4.57
57 58 3.462982 AGTTCGAATGTACTTGCACACA 58.537 40.909 0.00 0.00 0.00 3.72
59 60 4.515191 AGTTCGAATGTACTTGCACACAAT 59.485 37.500 0.00 0.00 34.61 2.71
61 62 3.812609 TCGAATGTACTTGCACACAATGT 59.187 39.130 0.00 0.00 34.61 2.71
62 63 4.084066 TCGAATGTACTTGCACACAATGTC 60.084 41.667 0.00 0.00 34.61 3.06
63 64 4.475944 GAATGTACTTGCACACAATGTCC 58.524 43.478 0.00 0.00 34.61 4.02
64 65 3.207265 TGTACTTGCACACAATGTCCT 57.793 42.857 0.00 0.00 34.61 3.85
65 66 3.550820 TGTACTTGCACACAATGTCCTT 58.449 40.909 0.00 0.00 34.61 3.36
66 67 3.951037 TGTACTTGCACACAATGTCCTTT 59.049 39.130 0.00 0.00 34.61 3.11
67 68 4.400884 TGTACTTGCACACAATGTCCTTTT 59.599 37.500 0.00 0.00 34.61 2.27
68 69 4.470334 ACTTGCACACAATGTCCTTTTT 57.530 36.364 0.00 0.00 34.61 1.94
97 98 0.880441 TGCGCAACTGCATACAATGT 59.120 45.000 8.16 0.00 40.62 2.71
121 122 1.302511 CAAGCTTGCAGGGTACGGT 60.303 57.895 14.65 0.00 0.00 4.83
125 126 0.671796 GCTTGCAGGGTACGGTTTTT 59.328 50.000 0.00 0.00 0.00 1.94
172 173 8.441572 TCTCCGAAAATGTATATGGGGAAAATA 58.558 33.333 0.00 0.00 0.00 1.40
173 174 8.398878 TCCGAAAATGTATATGGGGAAAATAC 57.601 34.615 0.00 0.00 0.00 1.89
177 178 7.429636 AAATGTATATGGGGAAAATACGACG 57.570 36.000 0.00 0.00 0.00 5.12
257 484 3.254903 TCCCTTCGTATGTCATCGTATGG 59.745 47.826 0.00 0.00 0.00 2.74
264 491 4.143115 CGTATGTCATCGTATGGCCAATTC 60.143 45.833 10.96 1.83 32.84 2.17
268 495 0.944386 ATCGTATGGCCAATTCGTGC 59.056 50.000 10.96 0.00 31.57 5.34
293 525 7.117523 GCCAAAACAAATTGTAAGTATGCATCA 59.882 33.333 0.19 0.00 0.00 3.07
296 528 8.746922 AAACAAATTGTAAGTATGCATCACAG 57.253 30.769 0.19 0.00 0.00 3.66
299 531 7.391554 ACAAATTGTAAGTATGCATCACAGTCT 59.608 33.333 0.19 0.00 0.00 3.24
307 539 1.336240 TGCATCACAGTCTCGACAGTG 60.336 52.381 14.20 14.20 46.19 3.66
308 540 1.344458 CATCACAGTCTCGACAGTGC 58.656 55.000 15.20 0.00 44.99 4.40
309 541 0.961753 ATCACAGTCTCGACAGTGCA 59.038 50.000 15.20 7.22 44.99 4.57
310 542 0.961753 TCACAGTCTCGACAGTGCAT 59.038 50.000 15.20 0.00 44.99 3.96
311 543 1.066136 CACAGTCTCGACAGTGCATG 58.934 55.000 9.19 0.00 40.87 4.06
312 544 0.037882 ACAGTCTCGACAGTGCATGG 60.038 55.000 0.00 0.00 29.59 3.66
313 545 0.037882 CAGTCTCGACAGTGCATGGT 60.038 55.000 0.00 0.00 0.00 3.55
355 587 1.002366 CCGACCGCTCAAATCTCAAG 58.998 55.000 0.00 0.00 0.00 3.02
357 589 2.069273 CGACCGCTCAAATCTCAAGTT 58.931 47.619 0.00 0.00 0.00 2.66
367 608 5.436175 TCAAATCTCAAGTTGAACCTGTCA 58.564 37.500 7.06 0.00 36.61 3.58
389 639 1.670811 GCAATGGTACCATGAGAACCG 59.329 52.381 28.00 11.33 36.68 4.44
398 648 1.656652 CATGAGAACCGGCCACTAAG 58.343 55.000 0.00 0.00 0.00 2.18
402 652 2.304761 TGAGAACCGGCCACTAAGAAAT 59.695 45.455 0.00 0.00 0.00 2.17
456 706 9.847224 TTTCTTATCAAAACTTCTAGGTGACTT 57.153 29.630 0.00 0.00 43.67 3.01
462 712 6.761714 TCAAAACTTCTAGGTGACTTCTTGTC 59.238 38.462 0.00 0.00 45.54 3.18
472 722 3.731274 GACTTCTTGTCGGCATTTCTC 57.269 47.619 0.00 0.00 35.81 2.87
478 728 6.431234 ACTTCTTGTCGGCATTTCTCTTTATT 59.569 34.615 0.00 0.00 0.00 1.40
480 730 7.915293 TCTTGTCGGCATTTCTCTTTATTTA 57.085 32.000 0.00 0.00 0.00 1.40
538 788 2.358957 TCATTGCACCTGGATTTCGAG 58.641 47.619 0.00 0.00 0.00 4.04
556 806 0.898320 AGAACCCACTCTCCATGTCG 59.102 55.000 0.00 0.00 0.00 4.35
573 823 2.383527 CGCTCTCCTGGAACGTTGC 61.384 63.158 13.47 13.47 0.00 4.17
574 824 2.035442 GCTCTCCTGGAACGTTGCC 61.035 63.158 17.64 12.80 0.00 4.52
575 825 1.371183 CTCTCCTGGAACGTTGCCA 59.629 57.895 17.64 16.43 0.00 4.92
578 828 0.817634 CTCCTGGAACGTTGCCACAA 60.818 55.000 17.64 6.72 0.00 3.33
579 829 1.098712 TCCTGGAACGTTGCCACAAC 61.099 55.000 17.64 0.32 0.00 3.32
597 847 6.858478 GCCACAACTTTCTCTCTACAAATTTC 59.142 38.462 0.00 0.00 0.00 2.17
603 853 7.740805 ACTTTCTCTCTACAAATTTCTGAGGT 58.259 34.615 10.06 0.00 0.00 3.85
624 874 5.048013 AGGTGTGCCTGCTATTTCTTTTTAC 60.048 40.000 0.00 0.00 45.05 2.01
637 887 4.529716 TCTTTTTACAGTGGTTTCCCCT 57.470 40.909 0.00 0.00 0.00 4.79
660 910 6.093495 CCTTGTATTTATTTGACTTCTCCGCA 59.907 38.462 0.00 0.00 0.00 5.69
674 924 2.325082 CCGCACAGTTTTCCCTCCG 61.325 63.158 0.00 0.00 0.00 4.63
695 945 7.265647 TCCGAGAAAACAACATCAAATACAA 57.734 32.000 0.00 0.00 0.00 2.41
698 948 6.582295 CGAGAAAACAACATCAAATACAAGGG 59.418 38.462 0.00 0.00 0.00 3.95
705 955 7.535139 ACAACATCAAATACAAGGGAATTACG 58.465 34.615 0.00 0.00 0.00 3.18
723 973 2.999331 ACGTGGAGGGAATTGTAATGG 58.001 47.619 0.00 0.00 0.00 3.16
752 1002 2.315011 CATGTTGCAACGCGTTTATGT 58.685 42.857 24.21 0.00 0.00 2.29
768 1018 6.021468 GCGTTTATGTGCTGTGATAAAATGTC 60.021 38.462 0.00 0.00 0.00 3.06
775 1025 5.961843 GTGCTGTGATAAAATGTCGAGAATG 59.038 40.000 0.00 0.00 0.00 2.67
785 1035 6.633500 AAATGTCGAGAATGTCCAGAAAAA 57.367 33.333 0.00 0.00 0.00 1.94
787 1037 6.824305 ATGTCGAGAATGTCCAGAAAAATT 57.176 33.333 0.00 0.00 0.00 1.82
793 1043 6.470235 CGAGAATGTCCAGAAAAATTATGTGC 59.530 38.462 0.00 0.00 0.00 4.57
820 1070 4.635769 CCTAATGGCCGAGTTGCA 57.364 55.556 0.00 0.00 0.00 4.08
821 1071 2.866872 CCTAATGGCCGAGTTGCAA 58.133 52.632 0.00 0.00 0.00 4.08
822 1072 0.451783 CCTAATGGCCGAGTTGCAAC 59.548 55.000 22.17 22.17 0.00 4.17
823 1073 0.096976 CTAATGGCCGAGTTGCAACG 59.903 55.000 23.21 12.93 0.00 4.10
824 1074 0.320858 TAATGGCCGAGTTGCAACGA 60.321 50.000 23.21 5.56 0.00 3.85
825 1075 1.169661 AATGGCCGAGTTGCAACGAA 61.170 50.000 23.21 7.52 0.00 3.85
826 1076 1.852067 ATGGCCGAGTTGCAACGAAC 61.852 55.000 23.21 16.83 0.00 3.95
827 1077 2.127758 GCCGAGTTGCAACGAACG 60.128 61.111 26.71 26.71 0.00 3.95
828 1078 2.549282 CCGAGTTGCAACGAACGG 59.451 61.111 32.66 32.66 38.06 4.44
829 1079 1.952133 CCGAGTTGCAACGAACGGA 60.952 57.895 37.04 3.48 42.51 4.69
830 1080 1.200839 CGAGTTGCAACGAACGGAC 59.799 57.895 26.29 13.59 0.00 4.79
831 1081 1.213094 CGAGTTGCAACGAACGGACT 61.213 55.000 26.29 10.22 0.00 3.85
832 1082 0.232303 GAGTTGCAACGAACGGACTG 59.768 55.000 23.21 0.00 0.00 3.51
833 1083 0.461339 AGTTGCAACGAACGGACTGT 60.461 50.000 23.21 0.00 0.00 3.55
834 1084 0.042448 GTTGCAACGAACGGACTGTC 60.042 55.000 14.90 0.00 0.00 3.51
835 1085 0.460459 TTGCAACGAACGGACTGTCA 60.460 50.000 10.38 0.00 0.00 3.58
836 1086 0.460459 TGCAACGAACGGACTGTCAA 60.460 50.000 10.38 0.00 0.00 3.18
837 1087 0.232303 GCAACGAACGGACTGTCAAG 59.768 55.000 10.38 5.60 0.00 3.02
838 1088 0.232303 CAACGAACGGACTGTCAAGC 59.768 55.000 10.38 0.00 0.00 4.01
839 1089 0.878961 AACGAACGGACTGTCAAGCC 60.879 55.000 10.38 0.00 0.00 4.35
840 1090 1.300620 CGAACGGACTGTCAAGCCA 60.301 57.895 10.38 0.00 0.00 4.75
841 1091 1.557443 CGAACGGACTGTCAAGCCAC 61.557 60.000 10.38 0.00 0.00 5.01
842 1092 1.227853 AACGGACTGTCAAGCCACC 60.228 57.895 10.38 0.00 0.00 4.61
843 1093 1.696097 AACGGACTGTCAAGCCACCT 61.696 55.000 10.38 0.00 0.00 4.00
844 1094 1.071471 CGGACTGTCAAGCCACCTT 59.929 57.895 10.38 0.00 0.00 3.50
846 1096 0.890996 GGACTGTCAAGCCACCTTGG 60.891 60.000 10.38 0.00 46.69 3.61
847 1097 0.890996 GACTGTCAAGCCACCTTGGG 60.891 60.000 2.24 0.00 46.69 4.12
899 1149 7.789831 TCCTACCTACAAGATCCAGATACATTT 59.210 37.037 0.00 0.00 0.00 2.32
900 1150 8.091449 CCTACCTACAAGATCCAGATACATTTC 58.909 40.741 0.00 0.00 0.00 2.17
901 1151 6.831976 ACCTACAAGATCCAGATACATTTCC 58.168 40.000 0.00 0.00 0.00 3.13
902 1152 6.183361 ACCTACAAGATCCAGATACATTTCCC 60.183 42.308 0.00 0.00 0.00 3.97
903 1153 5.983333 ACAAGATCCAGATACATTTCCCT 57.017 39.130 0.00 0.00 0.00 4.20
904 1154 7.235606 CCTACAAGATCCAGATACATTTCCCTA 59.764 40.741 0.00 0.00 0.00 3.53
905 1155 7.451731 ACAAGATCCAGATACATTTCCCTAA 57.548 36.000 0.00 0.00 0.00 2.69
906 1156 7.872138 ACAAGATCCAGATACATTTCCCTAAA 58.128 34.615 0.00 0.00 0.00 1.85
907 1157 8.336235 ACAAGATCCAGATACATTTCCCTAAAA 58.664 33.333 0.00 0.00 0.00 1.52
908 1158 9.189156 CAAGATCCAGATACATTTCCCTAAAAA 57.811 33.333 0.00 0.00 0.00 1.94
935 1185 1.270305 ACAAGATCAGACACACCCACG 60.270 52.381 0.00 0.00 0.00 4.94
1018 1743 2.113433 ATGTCTCCGTCGTCCTCCG 61.113 63.158 0.00 0.00 38.13 4.63
1019 1744 2.435586 GTCTCCGTCGTCCTCCGA 60.436 66.667 0.00 0.00 45.00 4.55
1077 1802 2.265739 GACATCAGCCTGCCGTCA 59.734 61.111 8.05 0.00 0.00 4.35
1741 3367 5.954335 AGTTCATCGAATGATTTGGTTTCC 58.046 37.500 0.00 0.00 39.39 3.13
1743 3369 6.209391 AGTTCATCGAATGATTTGGTTTCCTT 59.791 34.615 0.00 0.00 39.39 3.36
1745 3371 5.125417 TCATCGAATGATTTGGTTTCCTTCC 59.875 40.000 0.00 0.00 33.59 3.46
1746 3372 4.402829 TCGAATGATTTGGTTTCCTTCCA 58.597 39.130 0.00 0.00 0.00 3.53
1747 3373 4.458989 TCGAATGATTTGGTTTCCTTCCAG 59.541 41.667 0.00 0.00 36.28 3.86
1785 3611 0.591170 TTTTCGTTGCTGGCAGTAGC 59.409 50.000 17.16 13.03 43.95 3.58
1806 3632 5.118990 AGCACTAGCACATGGTTATTACTG 58.881 41.667 0.00 0.00 45.49 2.74
1835 3661 9.820725 ACTGATTTCTCAAATGAAAAACATGAA 57.179 25.926 0.00 0.00 39.08 2.57
1837 3663 9.820725 TGATTTCTCAAATGAAAAACATGAAGT 57.179 25.926 0.00 0.00 39.08 3.01
1840 3666 6.514947 TCTCAAATGAAAAACATGAAGTGGG 58.485 36.000 0.00 0.00 39.39 4.61
1841 3667 6.323482 TCTCAAATGAAAAACATGAAGTGGGA 59.677 34.615 0.00 0.00 39.39 4.37
1842 3668 7.015487 TCTCAAATGAAAAACATGAAGTGGGAT 59.985 33.333 0.00 0.00 39.39 3.85
1843 3669 6.930164 TCAAATGAAAAACATGAAGTGGGATG 59.070 34.615 0.00 0.00 39.39 3.51
1845 3671 4.478203 TGAAAAACATGAAGTGGGATGGA 58.522 39.130 0.00 0.00 0.00 3.41
1846 3672 5.085920 TGAAAAACATGAAGTGGGATGGAT 58.914 37.500 0.00 0.00 0.00 3.41
1847 3673 5.543405 TGAAAAACATGAAGTGGGATGGATT 59.457 36.000 0.00 0.00 0.00 3.01
1848 3674 6.723515 TGAAAAACATGAAGTGGGATGGATTA 59.276 34.615 0.00 0.00 0.00 1.75
1849 3675 6.530019 AAAACATGAAGTGGGATGGATTAC 57.470 37.500 0.00 0.00 0.00 1.89
1917 3746 7.494922 AATAGGGCATTTTCAATTGGTAAGT 57.505 32.000 5.42 0.00 0.00 2.24
1918 3747 8.602472 AATAGGGCATTTTCAATTGGTAAGTA 57.398 30.769 5.42 0.00 0.00 2.24
1919 3748 6.926630 AGGGCATTTTCAATTGGTAAGTAA 57.073 33.333 5.42 0.00 0.00 2.24
1967 3796 7.977789 AATTCGGCAAATTGGAGTTTTATTT 57.022 28.000 0.00 0.00 36.20 1.40
1970 3799 5.011125 TCGGCAAATTGGAGTTTTATTTCCA 59.989 36.000 0.00 0.00 41.59 3.53
2035 3864 2.959030 TGACATCCGATCCAAGGACTAG 59.041 50.000 0.00 0.00 41.10 2.57
2040 3869 0.461548 CGATCCAAGGACTAGCAGCA 59.538 55.000 0.00 0.00 0.00 4.41
2071 3900 3.393472 GCACCTCCTGGAGCAATAG 57.607 57.895 18.51 6.77 46.92 1.73
2146 3975 2.111043 ACAACACCCTGAGCACCG 59.889 61.111 0.00 0.00 0.00 4.94
2223 4072 0.036010 AAGGCAGAGACAACATCCCG 60.036 55.000 0.00 0.00 0.00 5.14
2230 4079 1.153628 GACAACATCCCGAGGTCCG 60.154 63.158 0.00 0.00 38.18 4.79
2296 4151 4.637771 GCATCGGCTTTACTGGGT 57.362 55.556 0.00 0.00 36.96 4.51
2416 4271 1.359848 CCAAGTACACGGTGCTGATC 58.640 55.000 8.30 0.00 0.00 2.92
2464 4319 2.568623 ACAGGCCGATGAAGAAGTTT 57.431 45.000 0.00 0.00 0.00 2.66
2488 4343 6.061441 TGATACCTGCAAAGAGAAAGAACAA 58.939 36.000 0.00 0.00 0.00 2.83
2544 4400 4.478699 ACAGTGCAAAACATTGATCATCG 58.521 39.130 0.00 0.00 38.22 3.84
2548 4404 5.048504 AGTGCAAAACATTGATCATCGAAGT 60.049 36.000 0.00 0.00 0.00 3.01
2619 4507 9.887629 TCTTATATTATGGGACGTTACAAAACA 57.112 29.630 0.00 0.00 35.16 2.83
2622 4510 8.974060 ATATTATGGGACGTTACAAAACATCT 57.026 30.769 0.00 0.00 35.16 2.90
2623 4511 7.696992 ATTATGGGACGTTACAAAACATCTT 57.303 32.000 0.00 0.00 35.16 2.40
2624 4512 8.795842 ATTATGGGACGTTACAAAACATCTTA 57.204 30.769 0.00 0.00 35.16 2.10
2625 4513 8.795842 TTATGGGACGTTACAAAACATCTTAT 57.204 30.769 0.00 0.00 35.16 1.73
2626 4514 9.887629 TTATGGGACGTTACAAAACATCTTATA 57.112 29.630 0.00 0.00 35.16 0.98
2627 4515 8.974060 ATGGGACGTTACAAAACATCTTATAT 57.026 30.769 0.00 0.00 35.16 0.86
2628 4516 8.795842 TGGGACGTTACAAAACATCTTATATT 57.204 30.769 0.00 0.00 35.16 1.28
2629 4517 9.887629 TGGGACGTTACAAAACATCTTATATTA 57.112 29.630 0.00 0.00 35.16 0.98
2685 4573 9.640974 CTGTTACAGAATGCATTTTTCTTTTTG 57.359 29.630 14.33 0.00 42.53 2.44
2690 4578 8.949177 ACAGAATGCATTTTTCTTTTTGTTCTT 58.051 25.926 14.33 0.00 42.53 2.52
2713 4602 6.392625 TCTTCCAGTTTCATCTATCTACCG 57.607 41.667 0.00 0.00 0.00 4.02
2726 4615 4.882427 TCTATCTACCGAAGTGGACAGAAG 59.118 45.833 0.00 0.00 34.46 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.576662 TGGAAAATCGTACAGGCAAATTAA 57.423 33.333 0.00 0.00 0.00 1.40
2 3 6.576662 TTGGAAAATCGTACAGGCAAATTA 57.423 33.333 0.00 0.00 0.00 1.40
3 4 5.461032 TTGGAAAATCGTACAGGCAAATT 57.539 34.783 0.00 0.00 0.00 1.82
4 5 5.221342 TGTTTGGAAAATCGTACAGGCAAAT 60.221 36.000 0.00 0.00 0.00 2.32
5 6 4.098044 TGTTTGGAAAATCGTACAGGCAAA 59.902 37.500 0.00 0.00 0.00 3.68
6 7 3.632604 TGTTTGGAAAATCGTACAGGCAA 59.367 39.130 0.00 0.00 0.00 4.52
7 8 3.215151 TGTTTGGAAAATCGTACAGGCA 58.785 40.909 0.00 0.00 0.00 4.75
10 11 6.898041 TCAGAATGTTTGGAAAATCGTACAG 58.102 36.000 0.00 0.00 37.40 2.74
11 12 6.869315 TCAGAATGTTTGGAAAATCGTACA 57.131 33.333 0.00 0.00 37.40 2.90
12 13 7.860872 ACTTTCAGAATGTTTGGAAAATCGTAC 59.139 33.333 0.00 0.00 37.40 3.67
13 14 7.936584 ACTTTCAGAATGTTTGGAAAATCGTA 58.063 30.769 0.00 0.00 37.40 3.43
15 16 7.357532 CGAACTTTCAGAATGTTTGGAAAATCG 60.358 37.037 16.59 9.79 37.40 3.34
18 19 6.857956 TCGAACTTTCAGAATGTTTGGAAAA 58.142 32.000 21.16 6.71 37.40 2.29
19 20 6.443934 TCGAACTTTCAGAATGTTTGGAAA 57.556 33.333 21.16 6.97 37.40 3.13
20 21 6.443934 TTCGAACTTTCAGAATGTTTGGAA 57.556 33.333 21.16 18.85 37.40 3.53
21 22 6.039270 ACATTCGAACTTTCAGAATGTTTGGA 59.961 34.615 22.46 16.50 46.39 3.53
22 23 6.208644 ACATTCGAACTTTCAGAATGTTTGG 58.791 36.000 22.46 14.15 46.39 3.28
24 25 8.154649 AGTACATTCGAACTTTCAGAATGTTT 57.845 30.769 27.48 20.03 46.39 2.83
27 28 6.521133 GCAAGTACATTCGAACTTTCAGAATG 59.479 38.462 21.66 21.66 44.29 2.67
29 30 5.525745 TGCAAGTACATTCGAACTTTCAGAA 59.474 36.000 0.00 0.00 33.72 3.02
30 31 5.050363 GTGCAAGTACATTCGAACTTTCAGA 60.050 40.000 0.00 0.00 33.72 3.27
32 33 4.572795 TGTGCAAGTACATTCGAACTTTCA 59.427 37.500 0.00 0.00 33.72 2.69
34 35 4.334203 TGTGTGCAAGTACATTCGAACTTT 59.666 37.500 0.00 0.00 33.72 2.66
36 37 3.462982 TGTGTGCAAGTACATTCGAACT 58.537 40.909 0.00 0.00 32.43 3.01
37 38 3.870723 TGTGTGCAAGTACATTCGAAC 57.129 42.857 0.00 0.00 32.43 3.95
38 39 4.274705 ACATTGTGTGCAAGTACATTCGAA 59.725 37.500 0.00 0.00 38.10 3.71
39 40 3.812609 ACATTGTGTGCAAGTACATTCGA 59.187 39.130 0.00 0.00 38.10 3.71
41 42 4.216257 AGGACATTGTGTGCAAGTACATTC 59.784 41.667 4.47 0.00 41.46 2.67
42 43 4.144297 AGGACATTGTGTGCAAGTACATT 58.856 39.130 4.47 0.00 41.46 2.71
43 44 3.754965 AGGACATTGTGTGCAAGTACAT 58.245 40.909 4.47 0.00 41.46 2.29
44 45 3.207265 AGGACATTGTGTGCAAGTACA 57.793 42.857 4.47 0.00 41.46 2.90
46 47 5.590530 AAAAAGGACATTGTGTGCAAGTA 57.409 34.783 4.47 0.00 41.46 2.24
47 48 4.470334 AAAAAGGACATTGTGTGCAAGT 57.530 36.364 4.47 0.00 41.46 3.16
74 75 2.498807 TGTATGCAGTTGCGCAAAAA 57.501 40.000 26.87 11.06 46.87 1.94
75 76 2.498807 TTGTATGCAGTTGCGCAAAA 57.501 40.000 26.87 10.12 46.87 2.44
76 77 2.288091 ACATTGTATGCAGTTGCGCAAA 60.288 40.909 26.87 9.95 46.87 3.68
77 78 1.269174 ACATTGTATGCAGTTGCGCAA 59.731 42.857 21.02 21.02 46.87 4.85
80 81 1.739466 AGGACATTGTATGCAGTTGCG 59.261 47.619 0.00 0.00 45.83 4.85
81 82 3.242870 GCTAGGACATTGTATGCAGTTGC 60.243 47.826 0.00 0.00 42.50 4.17
82 83 3.940852 TGCTAGGACATTGTATGCAGTTG 59.059 43.478 0.00 0.00 0.00 3.16
83 84 4.220693 TGCTAGGACATTGTATGCAGTT 57.779 40.909 0.00 0.00 0.00 3.16
84 85 3.912496 TGCTAGGACATTGTATGCAGT 57.088 42.857 0.00 0.00 0.00 4.40
85 86 3.003068 GCTTGCTAGGACATTGTATGCAG 59.997 47.826 0.00 0.00 0.00 4.41
145 146 5.223449 TCCCCATATACATTTTCGGAGAC 57.777 43.478 0.00 0.00 34.32 3.36
147 148 6.952773 TTTTCCCCATATACATTTTCGGAG 57.047 37.500 0.00 0.00 0.00 4.63
149 150 7.173562 TCGTATTTTCCCCATATACATTTTCGG 59.826 37.037 0.00 0.00 0.00 4.30
153 154 7.218614 TCGTCGTATTTTCCCCATATACATTT 58.781 34.615 0.00 0.00 0.00 2.32
161 162 3.946606 AGTTTCGTCGTATTTTCCCCAT 58.053 40.909 0.00 0.00 0.00 4.00
162 163 3.405823 AGTTTCGTCGTATTTTCCCCA 57.594 42.857 0.00 0.00 0.00 4.96
163 164 4.328169 CAGTAGTTTCGTCGTATTTTCCCC 59.672 45.833 0.00 0.00 0.00 4.81
172 173 3.111098 GTGTGAACAGTAGTTTCGTCGT 58.889 45.455 0.00 0.00 38.30 4.34
173 174 3.369385 AGTGTGAACAGTAGTTTCGTCG 58.631 45.455 0.00 0.00 38.30 5.12
177 178 8.133627 TGTTACTAGAGTGTGAACAGTAGTTTC 58.866 37.037 0.00 0.00 38.30 2.78
220 447 4.331443 ACGAAGGGAAACAAAACAAATTGC 59.669 37.500 0.00 0.00 33.52 3.56
232 459 3.518590 ACGATGACATACGAAGGGAAAC 58.481 45.455 12.27 0.00 0.00 2.78
237 464 2.987149 GCCATACGATGACATACGAAGG 59.013 50.000 12.27 10.98 0.00 3.46
257 484 5.076098 CAATTTGTTTTGGCACGAATTGGC 61.076 41.667 16.13 0.00 46.35 4.52
264 491 6.615418 GCATACTTACAATTTGTTTTGGCACG 60.615 38.462 7.45 0.00 0.00 5.34
268 495 8.434661 GTGATGCATACTTACAATTTGTTTTGG 58.565 33.333 7.45 0.00 0.00 3.28
293 525 0.037882 CCATGCACTGTCGAGACTGT 60.038 55.000 9.48 9.48 42.93 3.55
296 528 1.071605 GAACCATGCACTGTCGAGAC 58.928 55.000 0.00 0.00 0.00 3.36
299 531 3.261580 CATTAGAACCATGCACTGTCGA 58.738 45.455 0.00 0.00 0.00 4.20
307 539 2.030457 CGTTCGGACATTAGAACCATGC 59.970 50.000 0.00 0.00 42.57 4.06
308 540 2.607635 CCGTTCGGACATTAGAACCATG 59.392 50.000 5.19 0.00 42.57 3.66
309 541 2.419574 CCCGTTCGGACATTAGAACCAT 60.420 50.000 13.08 0.00 42.57 3.55
310 542 1.066716 CCCGTTCGGACATTAGAACCA 60.067 52.381 13.08 0.00 42.57 3.67
311 543 1.648504 CCCGTTCGGACATTAGAACC 58.351 55.000 13.08 0.00 42.57 3.62
312 544 1.004595 GCCCGTTCGGACATTAGAAC 58.995 55.000 13.08 0.00 42.23 3.01
313 545 0.609151 TGCCCGTTCGGACATTAGAA 59.391 50.000 13.08 0.00 0.00 2.10
337 569 1.714794 ACTTGAGATTTGAGCGGTCG 58.285 50.000 10.46 0.00 0.00 4.79
346 578 5.278660 GCATGACAGGTTCAACTTGAGATTT 60.279 40.000 6.66 0.00 37.92 2.17
355 587 2.297033 ACCATTGCATGACAGGTTCAAC 59.703 45.455 0.00 0.00 37.92 3.18
357 589 2.291209 ACCATTGCATGACAGGTTCA 57.709 45.000 0.00 0.00 39.11 3.18
367 608 3.290710 GGTTCTCATGGTACCATTGCAT 58.709 45.455 25.25 1.15 33.90 3.96
433 683 9.495572 AAGAAGTCACCTAGAAGTTTTGATAAG 57.504 33.333 0.00 0.00 0.00 1.73
438 688 6.927294 ACAAGAAGTCACCTAGAAGTTTTG 57.073 37.500 0.00 0.00 0.00 2.44
456 706 6.817765 AAATAAAGAGAAATGCCGACAAGA 57.182 33.333 0.00 0.00 0.00 3.02
521 771 2.151202 GTTCTCGAAATCCAGGTGCAA 58.849 47.619 0.00 0.00 0.00 4.08
538 788 0.741221 GCGACATGGAGAGTGGGTTC 60.741 60.000 0.00 0.00 0.00 3.62
556 806 2.035442 GGCAACGTTCCAGGAGAGC 61.035 63.158 0.00 0.00 0.00 4.09
573 823 8.072567 CAGAAATTTGTAGAGAGAAAGTTGTGG 58.927 37.037 0.00 0.00 35.12 4.17
574 824 8.830580 TCAGAAATTTGTAGAGAGAAAGTTGTG 58.169 33.333 0.00 0.00 38.04 3.33
575 825 8.964476 TCAGAAATTTGTAGAGAGAAAGTTGT 57.036 30.769 0.00 0.00 27.59 3.32
578 828 7.659390 CACCTCAGAAATTTGTAGAGAGAAAGT 59.341 37.037 12.96 3.74 0.00 2.66
579 829 7.659390 ACACCTCAGAAATTTGTAGAGAGAAAG 59.341 37.037 12.96 3.11 0.00 2.62
597 847 2.012673 GAAATAGCAGGCACACCTCAG 58.987 52.381 0.00 0.00 46.34 3.35
603 853 5.534654 ACTGTAAAAAGAAATAGCAGGCACA 59.465 36.000 0.00 0.00 0.00 4.57
637 887 6.428465 TGTGCGGAGAAGTCAAATAAATACAA 59.572 34.615 0.00 0.00 0.00 2.41
660 910 3.570912 TTTTCTCGGAGGGAAAACTGT 57.429 42.857 4.96 0.00 37.63 3.55
674 924 7.657336 TCCCTTGTATTTGATGTTGTTTTCTC 58.343 34.615 0.00 0.00 0.00 2.87
681 931 7.484641 CACGTAATTCCCTTGTATTTGATGTTG 59.515 37.037 0.00 0.00 0.00 3.33
695 945 1.961133 TTCCCTCCACGTAATTCCCT 58.039 50.000 0.00 0.00 0.00 4.20
698 948 6.238648 CCATTACAATTCCCTCCACGTAATTC 60.239 42.308 0.00 0.00 29.48 2.17
705 955 2.031870 GGCCATTACAATTCCCTCCAC 58.968 52.381 0.00 0.00 0.00 4.02
744 994 6.192682 CGACATTTTATCACAGCACATAAACG 59.807 38.462 0.00 0.00 0.00 3.60
752 1002 5.643348 ACATTCTCGACATTTTATCACAGCA 59.357 36.000 0.00 0.00 0.00 4.41
768 1018 6.470235 GCACATAATTTTTCTGGACATTCTCG 59.530 38.462 0.00 0.00 0.00 4.04
810 1060 2.127758 CGTTCGTTGCAACTCGGC 60.128 61.111 26.09 12.78 0.00 5.54
811 1061 1.952133 TCCGTTCGTTGCAACTCGG 60.952 57.895 32.00 32.00 36.99 4.63
812 1062 1.200839 GTCCGTTCGTTGCAACTCG 59.799 57.895 26.09 23.82 0.00 4.18
813 1063 0.232303 CAGTCCGTTCGTTGCAACTC 59.768 55.000 26.09 15.15 0.00 3.01
814 1064 0.461339 ACAGTCCGTTCGTTGCAACT 60.461 50.000 26.09 2.60 0.00 3.16
815 1065 0.042448 GACAGTCCGTTCGTTGCAAC 60.042 55.000 19.89 19.89 0.00 4.17
816 1066 0.460459 TGACAGTCCGTTCGTTGCAA 60.460 50.000 0.00 0.00 0.00 4.08
817 1067 0.460459 TTGACAGTCCGTTCGTTGCA 60.460 50.000 0.00 0.00 0.00 4.08
818 1068 0.232303 CTTGACAGTCCGTTCGTTGC 59.768 55.000 0.00 0.00 0.00 4.17
819 1069 0.232303 GCTTGACAGTCCGTTCGTTG 59.768 55.000 0.00 0.00 0.00 4.10
820 1070 0.878961 GGCTTGACAGTCCGTTCGTT 60.879 55.000 0.00 0.00 0.00 3.85
821 1071 1.300697 GGCTTGACAGTCCGTTCGT 60.301 57.895 0.00 0.00 0.00 3.85
822 1072 1.300620 TGGCTTGACAGTCCGTTCG 60.301 57.895 0.00 0.00 0.00 3.95
823 1073 1.228657 GGTGGCTTGACAGTCCGTTC 61.229 60.000 0.00 0.00 0.00 3.95
824 1074 1.227853 GGTGGCTTGACAGTCCGTT 60.228 57.895 0.00 0.00 0.00 4.44
825 1075 1.696097 AAGGTGGCTTGACAGTCCGT 61.696 55.000 0.00 0.00 0.00 4.69
826 1076 1.071471 AAGGTGGCTTGACAGTCCG 59.929 57.895 0.00 0.00 0.00 4.79
827 1077 0.890996 CCAAGGTGGCTTGACAGTCC 60.891 60.000 0.00 0.00 36.50 3.85
828 1078 0.890996 CCCAAGGTGGCTTGACAGTC 60.891 60.000 0.00 0.00 35.79 3.51
829 1079 1.151450 CCCAAGGTGGCTTGACAGT 59.849 57.895 0.00 0.00 35.79 3.55
830 1080 4.085876 CCCAAGGTGGCTTGACAG 57.914 61.111 0.00 0.00 35.79 3.51
847 1097 2.365617 TGTAGCTCAACTGGGCTATAGC 59.634 50.000 16.78 16.78 42.01 2.97
848 1098 4.672587 TTGTAGCTCAACTGGGCTATAG 57.327 45.455 14.20 0.00 42.01 1.31
911 1161 4.097892 GTGGGTGTGTCTGATCTTGTTTTT 59.902 41.667 0.00 0.00 0.00 1.94
912 1162 3.632145 GTGGGTGTGTCTGATCTTGTTTT 59.368 43.478 0.00 0.00 0.00 2.43
913 1163 3.214328 GTGGGTGTGTCTGATCTTGTTT 58.786 45.455 0.00 0.00 0.00 2.83
914 1164 2.806745 CGTGGGTGTGTCTGATCTTGTT 60.807 50.000 0.00 0.00 0.00 2.83
915 1165 1.270305 CGTGGGTGTGTCTGATCTTGT 60.270 52.381 0.00 0.00 0.00 3.16
916 1166 1.000843 TCGTGGGTGTGTCTGATCTTG 59.999 52.381 0.00 0.00 0.00 3.02
917 1167 1.338107 TCGTGGGTGTGTCTGATCTT 58.662 50.000 0.00 0.00 0.00 2.40
918 1168 1.000955 GTTCGTGGGTGTGTCTGATCT 59.999 52.381 0.00 0.00 0.00 2.75
919 1169 1.000955 AGTTCGTGGGTGTGTCTGATC 59.999 52.381 0.00 0.00 0.00 2.92
920 1170 1.048601 AGTTCGTGGGTGTGTCTGAT 58.951 50.000 0.00 0.00 0.00 2.90
935 1185 0.741915 TTTGCCGGTTTGGACAGTTC 59.258 50.000 1.90 0.00 42.00 3.01
1597 3223 2.329690 CCTCTCGTCGCCGATCAG 59.670 66.667 0.00 0.00 43.27 2.90
1779 3605 2.680312 ACCATGTGCTAGTGCTACTG 57.320 50.000 0.00 0.00 40.48 2.74
1784 3610 4.876107 ACAGTAATAACCATGTGCTAGTGC 59.124 41.667 0.00 0.00 40.20 4.40
1785 3611 6.985188 AACAGTAATAACCATGTGCTAGTG 57.015 37.500 0.00 0.00 0.00 2.74
1786 3612 7.764443 CAGTAACAGTAATAACCATGTGCTAGT 59.236 37.037 0.00 0.00 0.00 2.57
1787 3613 7.979537 TCAGTAACAGTAATAACCATGTGCTAG 59.020 37.037 0.00 0.00 0.00 3.42
1827 3653 5.831103 AGTAATCCATCCCACTTCATGTTT 58.169 37.500 0.00 0.00 0.00 2.83
1829 3655 5.163195 GGTAGTAATCCATCCCACTTCATGT 60.163 44.000 0.00 0.00 0.00 3.21
1830 3656 5.308825 GGTAGTAATCCATCCCACTTCATG 58.691 45.833 0.00 0.00 0.00 3.07
1831 3657 4.040461 CGGTAGTAATCCATCCCACTTCAT 59.960 45.833 0.00 0.00 0.00 2.57
1832 3658 3.386726 CGGTAGTAATCCATCCCACTTCA 59.613 47.826 0.00 0.00 0.00 3.02
1833 3659 3.640029 TCGGTAGTAATCCATCCCACTTC 59.360 47.826 0.00 0.00 0.00 3.01
1835 3661 3.323774 TCGGTAGTAATCCATCCCACT 57.676 47.619 0.00 0.00 0.00 4.00
1836 3662 4.618920 AATCGGTAGTAATCCATCCCAC 57.381 45.455 0.00 0.00 0.00 4.61
1837 3663 5.012354 GGTAAATCGGTAGTAATCCATCCCA 59.988 44.000 0.00 0.00 0.00 4.37
1838 3664 5.485620 GGTAAATCGGTAGTAATCCATCCC 58.514 45.833 0.00 0.00 0.00 3.85
1840 3666 4.624452 GCGGTAAATCGGTAGTAATCCATC 59.376 45.833 0.00 0.00 0.00 3.51
1841 3667 4.282703 AGCGGTAAATCGGTAGTAATCCAT 59.717 41.667 0.00 0.00 39.18 3.41
1842 3668 3.638160 AGCGGTAAATCGGTAGTAATCCA 59.362 43.478 0.00 0.00 39.18 3.41
1843 3669 3.985925 CAGCGGTAAATCGGTAGTAATCC 59.014 47.826 0.00 0.00 38.91 3.01
1845 3671 3.181473 TGCAGCGGTAAATCGGTAGTAAT 60.181 43.478 0.00 0.00 38.91 1.89
1846 3672 2.166050 TGCAGCGGTAAATCGGTAGTAA 59.834 45.455 0.00 0.00 38.91 2.24
1847 3673 1.750206 TGCAGCGGTAAATCGGTAGTA 59.250 47.619 0.00 0.00 38.91 1.82
1848 3674 0.533491 TGCAGCGGTAAATCGGTAGT 59.467 50.000 0.00 0.00 38.91 2.73
1849 3675 1.792949 GATGCAGCGGTAAATCGGTAG 59.207 52.381 0.00 0.00 38.91 3.18
1967 3796 4.712829 TCCTTATATGTGTCGGAACTTGGA 59.287 41.667 0.00 0.00 0.00 3.53
1970 3799 5.934402 ACTCCTTATATGTGTCGGAACTT 57.066 39.130 0.00 0.00 0.00 2.66
2040 3869 2.310052 AGGAGGTGCAAGATTTAGGCTT 59.690 45.455 0.00 0.00 0.00 4.35
2071 3900 5.583854 TCTCAGAATCAAAGAGCTTATGTGC 59.416 40.000 0.00 0.00 0.00 4.57
2146 3975 3.336715 GACGCCATTCAAACCGGCC 62.337 63.158 0.00 0.00 43.17 6.13
2156 3985 3.254024 AAGGTCGCCTGACGCCATT 62.254 57.895 0.00 0.00 46.49 3.16
2182 4011 8.406297 GCCTTTTATGTAGTTCCTGAAATAAGG 58.594 37.037 0.00 0.00 38.84 2.69
2223 4072 0.666577 CACAAACGTCCTCGGACCTC 60.667 60.000 10.34 0.00 41.76 3.85
2230 4079 1.300697 ACCGAGCACAAACGTCCTC 60.301 57.895 0.00 0.00 0.00 3.71
2416 4271 0.316689 GCGTCGTCAACAAGTTTGGG 60.317 55.000 0.00 0.00 0.00 4.12
2464 4319 5.620206 TGTTCTTTCTCTTTGCAGGTATCA 58.380 37.500 0.00 0.00 0.00 2.15
2488 4343 3.021695 CTGGCACCAGTGAATCATCATT 58.978 45.455 8.61 0.00 38.01 2.57
2544 4400 2.687425 GGACGGAGGGAGTACTTACTTC 59.313 54.545 0.00 0.00 36.50 3.01
2548 4404 1.002069 TGGGACGGAGGGAGTACTTA 58.998 55.000 0.00 0.00 0.00 2.24
2611 4499 9.496873 CCGTCCCATAATATAAGATGTTTTGTA 57.503 33.333 0.00 0.00 0.00 2.41
2612 4500 8.215050 TCCGTCCCATAATATAAGATGTTTTGT 58.785 33.333 0.00 0.00 0.00 2.83
2613 4501 8.615878 TCCGTCCCATAATATAAGATGTTTTG 57.384 34.615 0.00 0.00 0.00 2.44
2614 4502 7.883311 CCTCCGTCCCATAATATAAGATGTTTT 59.117 37.037 0.00 0.00 0.00 2.43
2615 4503 7.236847 TCCTCCGTCCCATAATATAAGATGTTT 59.763 37.037 0.00 0.00 0.00 2.83
2616 4504 6.729100 TCCTCCGTCCCATAATATAAGATGTT 59.271 38.462 0.00 0.00 0.00 2.71
2617 4505 6.261435 TCCTCCGTCCCATAATATAAGATGT 58.739 40.000 0.00 0.00 0.00 3.06
2618 4506 6.791867 TCCTCCGTCCCATAATATAAGATG 57.208 41.667 0.00 0.00 0.00 2.90
2619 4507 6.960542 ACTTCCTCCGTCCCATAATATAAGAT 59.039 38.462 0.00 0.00 0.00 2.40
2620 4508 6.320518 ACTTCCTCCGTCCCATAATATAAGA 58.679 40.000 0.00 0.00 0.00 2.10
2621 4509 6.607004 ACTTCCTCCGTCCCATAATATAAG 57.393 41.667 0.00 0.00 0.00 1.73
2622 4510 7.472741 TCTACTTCCTCCGTCCCATAATATAA 58.527 38.462 0.00 0.00 0.00 0.98
2623 4511 7.036154 TCTACTTCCTCCGTCCCATAATATA 57.964 40.000 0.00 0.00 0.00 0.86
2624 4512 5.900437 TCTACTTCCTCCGTCCCATAATAT 58.100 41.667 0.00 0.00 0.00 1.28
2625 4513 5.329191 TCTACTTCCTCCGTCCCATAATA 57.671 43.478 0.00 0.00 0.00 0.98
2626 4514 4.194678 TCTACTTCCTCCGTCCCATAAT 57.805 45.455 0.00 0.00 0.00 1.28
2627 4515 3.675348 TCTACTTCCTCCGTCCCATAA 57.325 47.619 0.00 0.00 0.00 1.90
2628 4516 3.675348 TTCTACTTCCTCCGTCCCATA 57.325 47.619 0.00 0.00 0.00 2.74
2629 4517 2.544844 TTCTACTTCCTCCGTCCCAT 57.455 50.000 0.00 0.00 0.00 4.00
2630 4518 2.176889 CTTTCTACTTCCTCCGTCCCA 58.823 52.381 0.00 0.00 0.00 4.37
2685 4573 9.308318 GTAGATAGATGAAACTGGAAGAAGAAC 57.692 37.037 0.00 0.00 37.43 3.01
2690 4578 6.127101 TCGGTAGATAGATGAAACTGGAAGA 58.873 40.000 0.00 0.00 37.43 2.87


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

AutoCloner maintained by Alex Coulton.