Multiple sequence alignment - TraesCS2D01G346200

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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 TraesCS2D01G346200 chr2D 100.000 8561 0 0 1 8561 442981574 442990134 0.000000e+00 15810
1 TraesCS2D01G346200 chr2D 80.173 807 121 17 1 787 381219010 381219797 1.250000e-157 568
2 TraesCS2D01G346200 chr2D 91.129 124 8 2 5604 5724 256675160 256675283 1.910000e-36 165
3 TraesCS2D01G346200 chr2A 92.983 7567 292 72 790 8248 586450070 586457505 0.000000e+00 10811
4 TraesCS2D01G346200 chr2A 95.890 292 11 1 8271 8561 586457494 586457785 1.010000e-128 472
5 TraesCS2D01G346200 chr2A 84.393 173 25 2 4669 4840 450883934 450884105 1.480000e-37 169
6 TraesCS2D01G346200 chr2B 92.884 6802 271 80 828 7563 522083382 522090036 0.000000e+00 9683
7 TraesCS2D01G346200 chr2B 97.260 292 7 1 8271 8561 522091016 522091307 2.150000e-135 494
8 TraesCS2D01G346200 chr2B 94.079 304 18 0 7591 7894 522090125 522090428 6.050000e-126 462
9 TraesCS2D01G346200 chr2B 94.737 152 3 3 7980 8126 522090628 522090779 1.860000e-56 231
10 TraesCS2D01G346200 chr2B 92.366 131 9 1 8119 8248 522090897 522091027 1.470000e-42 185
11 TraesCS2D01G346200 chr2B 91.935 124 7 2 5604 5724 288943595 288943718 4.110000e-38 171
12 TraesCS2D01G346200 chr5D 83.929 728 78 17 4 712 563981629 563980922 0.000000e+00 660
13 TraesCS2D01G346200 chr5D 82.414 580 81 14 221 787 105615374 105615945 3.590000e-133 486
14 TraesCS2D01G346200 chr5B 81.605 810 103 14 1 787 492442468 492441682 5.640000e-176 628
15 TraesCS2D01G346200 chr4D 82.749 713 96 16 1 702 455656990 455657686 2.040000e-170 610
16 TraesCS2D01G346200 chr5A 83.758 628 79 12 1 618 503232296 503232910 2.680000e-159 573
17 TraesCS2D01G346200 chr5A 81.406 683 83 21 2 664 461272411 461271753 1.270000e-142 518
18 TraesCS2D01G346200 chr5A 82.407 216 31 6 4669 4883 340133365 340133574 1.900000e-41 182
19 TraesCS2D01G346200 chr4A 82.815 611 80 15 111 704 69829515 69830117 2.740000e-144 523
20 TraesCS2D01G346200 chr4B 81.785 549 77 12 111 642 476839182 476839724 1.020000e-118 438
21 TraesCS2D01G346200 chr7D 81.325 498 73 16 220 707 126510307 126509820 3.750000e-103 387
22 TraesCS2D01G346200 chr3A 79.720 286 50 4 4670 4953 550435005 550434726 5.240000e-47 200
23 TraesCS2D01G346200 chr3A 92.683 123 6 3 5604 5723 464907578 464907700 3.180000e-39 174
24 TraesCS2D01G346200 chr6A 91.473 129 8 2 5599 5724 506642961 506642833 3.180000e-39 174
25 TraesCS2D01G346200 chr6A 91.870 123 8 1 5604 5724 127884442 127884564 4.110000e-38 171
26 TraesCS2D01G346200 chr6D 91.870 123 8 1 5604 5724 105578904 105579026 4.110000e-38 171
27 TraesCS2D01G346200 chr6D 91.129 124 8 2 5604 5724 365847011 365846888 1.910000e-36 165
28 TraesCS2D01G346200 chr1D 86.093 151 20 1 4669 4819 267794485 267794634 2.470000e-35 161
29 TraesCS2D01G346200 chr1D 87.500 120 12 3 4632 4749 389800795 389800913 1.500000e-27 135
30 TraesCS2D01G346200 chr1A 86.093 151 19 2 4669 4819 335028704 335028556 2.470000e-35 161
31 TraesCS2D01G346200 chr1B 85.430 151 21 1 4669 4819 345320609 345320460 1.150000e-33 156


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 TraesCS2D01G346200 chr2D 442981574 442990134 8560 False 15810.0 15810 100.0000 1 8561 1 chr2D.!!$F3 8560
1 TraesCS2D01G346200 chr2D 381219010 381219797 787 False 568.0 568 80.1730 1 787 1 chr2D.!!$F2 786
2 TraesCS2D01G346200 chr2A 586450070 586457785 7715 False 5641.5 10811 94.4365 790 8561 2 chr2A.!!$F2 7771
3 TraesCS2D01G346200 chr2B 522083382 522091307 7925 False 2211.0 9683 94.2652 828 8561 5 chr2B.!!$F2 7733
4 TraesCS2D01G346200 chr5D 563980922 563981629 707 True 660.0 660 83.9290 4 712 1 chr5D.!!$R1 708
5 TraesCS2D01G346200 chr5D 105615374 105615945 571 False 486.0 486 82.4140 221 787 1 chr5D.!!$F1 566
6 TraesCS2D01G346200 chr5B 492441682 492442468 786 True 628.0 628 81.6050 1 787 1 chr5B.!!$R1 786
7 TraesCS2D01G346200 chr4D 455656990 455657686 696 False 610.0 610 82.7490 1 702 1 chr4D.!!$F1 701
8 TraesCS2D01G346200 chr5A 503232296 503232910 614 False 573.0 573 83.7580 1 618 1 chr5A.!!$F2 617
9 TraesCS2D01G346200 chr5A 461271753 461272411 658 True 518.0 518 81.4060 2 664 1 chr5A.!!$R1 662
10 TraesCS2D01G346200 chr4A 69829515 69830117 602 False 523.0 523 82.8150 111 704 1 chr4A.!!$F1 593
11 TraesCS2D01G346200 chr4B 476839182 476839724 542 False 438.0 438 81.7850 111 642 1 chr4B.!!$F1 531

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
719 763 0.038892 AAGCGGACGTACATGTTCGT 60.039 50.000 27.39 27.39 42.88 3.85 F
760 804 0.108804 AGACAAATCGCACGGATCGT 60.109 50.000 0.00 0.00 42.36 3.73 F
767 811 0.179156 TCGCACGGATCGTTTAGGTC 60.179 55.000 0.00 0.00 38.32 3.85 F
898 942 0.599558 CGGTTTCGACCCACTGACTA 59.400 55.000 1.55 0.00 39.00 2.59 F
1463 1520 0.677731 GCTGCCTCTGTATGCCACAA 60.678 55.000 0.00 0.00 36.48 3.33 F
1490 1547 1.009078 CGAATGCTGGAGCGAATTGA 58.991 50.000 0.00 0.00 45.83 2.57 F
3304 3382 1.001181 TGCATTGCTTTCTTGCCTTCC 59.999 47.619 10.49 0.00 35.51 3.46 F
3305 3383 1.274447 GCATTGCTTTCTTGCCTTCCT 59.726 47.619 0.16 0.00 0.00 3.36 F
4424 4515 2.352651 TCGCTGCTGATTTCTGTATTGC 59.647 45.455 0.00 0.00 0.00 3.56 F
5334 5426 0.938713 TGAACGTAGGGCACAAAACG 59.061 50.000 6.93 6.93 40.99 3.60 F
5651 5747 0.888736 CCACGTGCCAGAACCATGAA 60.889 55.000 10.91 0.00 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1854 1913 1.078143 GTGCTGGGAGTTAGGCTGG 60.078 63.158 0.00 0.00 0.00 4.85 R
2549 2616 2.104281 CCTTTCCCCTACATAAGACCGG 59.896 54.545 0.00 0.00 0.00 5.28 R
2682 2756 5.244178 TCTGTAAGGAAAGAACTCACCTCTC 59.756 44.000 0.00 0.00 31.89 3.20 R
2872 2946 4.077063 TGCTGTTTGTGCACATAATACG 57.923 40.909 22.39 12.79 35.31 3.06 R
3305 3383 0.036732 CAAGCTAACAGCAGGACCCA 59.963 55.000 0.38 0.00 45.56 4.51 R
3306 3384 0.036875 ACAAGCTAACAGCAGGACCC 59.963 55.000 0.38 0.00 45.56 4.46 R
4225 4316 0.612732 TGCAGCTCTTCCAAATGGGG 60.613 55.000 0.00 0.00 37.22 4.96 R
4820 4911 1.944430 GCCTAAACGTGGACAGAAGGG 60.944 57.143 0.00 0.00 0.00 3.95 R
5628 5724 0.036765 TGGTTCTGGCACGTGGATAC 60.037 55.000 18.88 0.00 0.00 2.24 R
6968 7104 1.382420 ACAAAAGTTGGCTGCCCCA 60.382 52.632 17.53 0.00 43.51 4.96 R
7601 7805 2.754552 TGCCAACCACTGCTATCATTTC 59.245 45.455 0.00 0.00 0.00 2.17 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
28 29 3.130160 GAAGGCCGAAGCAGCAGG 61.130 66.667 0.00 0.00 42.56 4.85
65 66 4.899239 CAGGCGGAGATGGCGGTC 62.899 72.222 0.00 0.00 39.82 4.79
139 140 2.499685 GCGGCTAACCCTGACGAT 59.500 61.111 0.00 0.00 38.36 3.73
142 143 1.522569 GGCTAACCCTGACGATGCT 59.477 57.895 0.00 0.00 0.00 3.79
453 475 0.747255 CCCGTCTTCATCGACCTCAT 59.253 55.000 0.00 0.00 0.00 2.90
504 538 1.924320 GACGTCTAGGACTGCGTGCT 61.924 60.000 8.70 7.70 37.71 4.40
628 667 1.069358 TGTTATCTGTGCCACGTGTGA 59.931 47.619 15.65 4.99 0.00 3.58
665 709 0.465460 ATGCGCATATTTGGGTCCGT 60.465 50.000 24.02 0.00 38.05 4.69
666 710 0.678366 TGCGCATATTTGGGTCCGTT 60.678 50.000 5.66 0.00 38.05 4.44
668 712 1.135228 GCGCATATTTGGGTCCGTTTT 60.135 47.619 0.30 0.00 38.05 2.43
669 713 2.672760 GCGCATATTTGGGTCCGTTTTT 60.673 45.455 0.30 0.00 38.05 1.94
694 738 1.723870 GCGCTCAAGCCGATTCATT 59.276 52.632 0.00 0.00 37.91 2.57
709 753 3.701532 TTCATTTGAAAAAGCGGACGT 57.298 38.095 0.00 0.00 0.00 4.34
710 754 4.815040 TTCATTTGAAAAAGCGGACGTA 57.185 36.364 0.00 0.00 0.00 3.57
713 757 4.214545 TCATTTGAAAAAGCGGACGTACAT 59.785 37.500 0.00 0.00 0.00 2.29
716 760 2.873472 TGAAAAAGCGGACGTACATGTT 59.127 40.909 2.30 0.00 0.00 2.71
717 761 3.059461 TGAAAAAGCGGACGTACATGTTC 60.059 43.478 2.30 0.00 0.00 3.18
718 762 1.065358 AAAGCGGACGTACATGTTCG 58.935 50.000 21.39 21.39 43.78 3.95
719 763 0.038892 AAGCGGACGTACATGTTCGT 60.039 50.000 27.39 27.39 42.88 3.85
725 769 1.645751 GACGTACATGTTCGTCGAACC 59.354 52.381 32.54 16.99 44.70 3.62
726 770 0.631745 CGTACATGTTCGTCGAACCG 59.368 55.000 29.85 23.57 41.35 4.44
727 771 1.689959 GTACATGTTCGTCGAACCGT 58.310 50.000 29.85 26.97 41.35 4.83
728 772 1.645751 GTACATGTTCGTCGAACCGTC 59.354 52.381 29.85 17.77 41.35 4.79
729 773 0.665369 ACATGTTCGTCGAACCGTCC 60.665 55.000 29.85 10.13 41.35 4.79
730 774 1.443194 ATGTTCGTCGAACCGTCCG 60.443 57.895 29.85 0.00 41.35 4.79
731 775 2.802414 GTTCGTCGAACCGTCCGG 60.802 66.667 24.47 3.76 36.65 5.14
732 776 2.977456 TTCGTCGAACCGTCCGGA 60.977 61.111 13.54 0.00 38.96 5.14
733 777 3.254014 TTCGTCGAACCGTCCGGAC 62.254 63.158 25.28 25.28 38.96 4.79
745 789 1.574134 GTCCGGACGAAAAACAGACA 58.426 50.000 20.85 0.00 0.00 3.41
746 790 1.935199 GTCCGGACGAAAAACAGACAA 59.065 47.619 20.85 0.00 0.00 3.18
747 791 2.352342 GTCCGGACGAAAAACAGACAAA 59.648 45.455 20.85 0.00 0.00 2.83
748 792 3.002965 GTCCGGACGAAAAACAGACAAAT 59.997 43.478 20.85 0.00 0.00 2.32
749 793 3.249080 TCCGGACGAAAAACAGACAAATC 59.751 43.478 0.00 0.00 0.00 2.17
750 794 3.215244 CGGACGAAAAACAGACAAATCG 58.785 45.455 0.00 0.00 36.45 3.34
751 795 2.971261 GGACGAAAAACAGACAAATCGC 59.029 45.455 0.00 0.00 33.88 4.58
752 796 3.547214 GGACGAAAAACAGACAAATCGCA 60.547 43.478 0.00 0.00 33.88 5.10
753 797 3.359654 ACGAAAAACAGACAAATCGCAC 58.640 40.909 0.00 0.00 33.88 5.34
754 798 2.397154 CGAAAAACAGACAAATCGCACG 59.603 45.455 0.00 0.00 0.00 5.34
755 799 2.399396 AAAACAGACAAATCGCACGG 57.601 45.000 0.00 0.00 0.00 4.94
756 800 1.588674 AAACAGACAAATCGCACGGA 58.411 45.000 0.00 0.00 0.00 4.69
757 801 1.808411 AACAGACAAATCGCACGGAT 58.192 45.000 0.00 0.00 36.78 4.18
758 802 1.359848 ACAGACAAATCGCACGGATC 58.640 50.000 0.00 0.00 33.02 3.36
759 803 0.298707 CAGACAAATCGCACGGATCG 59.701 55.000 0.00 0.00 33.02 3.69
760 804 0.108804 AGACAAATCGCACGGATCGT 60.109 50.000 0.00 0.00 42.36 3.73
761 805 0.719465 GACAAATCGCACGGATCGTT 59.281 50.000 0.00 0.00 38.32 3.85
762 806 1.127951 GACAAATCGCACGGATCGTTT 59.872 47.619 0.00 0.00 38.32 3.60
763 807 2.339418 ACAAATCGCACGGATCGTTTA 58.661 42.857 0.00 0.00 38.32 2.01
764 808 2.347452 ACAAATCGCACGGATCGTTTAG 59.653 45.455 0.00 0.00 38.32 1.85
765 809 1.567504 AATCGCACGGATCGTTTAGG 58.432 50.000 0.00 0.00 38.32 2.69
766 810 0.458669 ATCGCACGGATCGTTTAGGT 59.541 50.000 0.00 0.00 38.32 3.08
767 811 0.179156 TCGCACGGATCGTTTAGGTC 60.179 55.000 0.00 0.00 38.32 3.85
768 812 1.469126 CGCACGGATCGTTTAGGTCG 61.469 60.000 0.00 0.00 38.32 4.79
769 813 1.749609 GCACGGATCGTTTAGGTCGC 61.750 60.000 0.00 0.00 38.32 5.19
770 814 1.226491 ACGGATCGTTTAGGTCGCG 60.226 57.895 0.00 0.00 36.35 5.87
771 815 1.942712 CGGATCGTTTAGGTCGCGG 60.943 63.158 6.13 0.00 0.00 6.46
772 816 2.235699 GGATCGTTTAGGTCGCGGC 61.236 63.158 6.13 3.04 0.00 6.53
773 817 2.574222 GATCGTTTAGGTCGCGGCG 61.574 63.158 17.70 17.70 0.00 6.46
774 818 3.346631 ATCGTTTAGGTCGCGGCGT 62.347 57.895 22.90 11.84 0.00 5.68
775 819 2.824071 ATCGTTTAGGTCGCGGCGTT 62.824 55.000 22.90 11.64 0.00 4.84
776 820 2.472934 GTTTAGGTCGCGGCGTTG 59.527 61.111 22.90 1.13 0.00 4.10
777 821 2.739287 TTTAGGTCGCGGCGTTGG 60.739 61.111 22.90 0.00 0.00 3.77
778 822 3.223710 TTTAGGTCGCGGCGTTGGA 62.224 57.895 22.90 0.00 0.00 3.53
779 823 3.636313 TTAGGTCGCGGCGTTGGAG 62.636 63.158 22.90 0.00 0.00 3.86
782 826 4.072088 GTCGCGGCGTTGGAGTTG 62.072 66.667 22.90 0.00 0.00 3.16
785 829 4.090057 GCGGCGTTGGAGTTGCTC 62.090 66.667 9.37 0.00 0.00 4.26
786 830 2.357517 CGGCGTTGGAGTTGCTCT 60.358 61.111 0.00 0.00 0.00 4.09
787 831 1.961277 CGGCGTTGGAGTTGCTCTT 60.961 57.895 0.00 0.00 0.00 2.85
788 832 1.576421 GGCGTTGGAGTTGCTCTTG 59.424 57.895 0.00 0.00 0.00 3.02
803 847 1.966451 CTTGGTGCTCCCGGAACAC 60.966 63.158 11.92 11.92 35.15 3.32
820 864 0.603707 CACCCGATGGCATAGCGATT 60.604 55.000 9.85 0.00 41.60 3.34
832 876 2.052766 GCGATTGCGAAGGCGATG 60.053 61.111 0.00 0.00 43.46 3.84
833 877 2.525248 GCGATTGCGAAGGCGATGA 61.525 57.895 0.00 0.00 43.46 2.92
898 942 0.599558 CGGTTTCGACCCACTGACTA 59.400 55.000 1.55 0.00 39.00 2.59
912 956 1.288335 CTGACTAGTCTACCCACCCCT 59.712 57.143 23.01 0.00 0.00 4.79
913 957 1.006758 TGACTAGTCTACCCACCCCTG 59.993 57.143 23.01 0.00 0.00 4.45
933 978 1.839598 CTACCTACTACTCCGCGGCG 61.840 65.000 23.51 19.05 0.00 6.46
959 1004 2.437343 GCGACAGCGACGGAGAAAG 61.437 63.158 0.00 0.00 40.82 2.62
1032 1077 4.824515 ACCGCTCCCTCCTCCTCG 62.825 72.222 0.00 0.00 0.00 4.63
1039 1093 2.272797 CCTCCTCCTCGTCGTCCT 59.727 66.667 0.00 0.00 0.00 3.85
1040 1094 2.115911 CCTCCTCCTCGTCGTCCTG 61.116 68.421 0.00 0.00 0.00 3.86
1187 1241 2.425592 CGTCAGGTGAGGCCACAA 59.574 61.111 3.76 0.00 44.93 3.33
1249 1306 2.489971 GTCAGGTGTTTGACGGAATGA 58.510 47.619 0.00 0.00 38.23 2.57
1256 1313 2.039746 TGTTTGACGGAATGATGGGTCT 59.960 45.455 0.00 0.00 0.00 3.85
1462 1519 1.078214 GCTGCCTCTGTATGCCACA 60.078 57.895 0.00 0.00 35.30 4.17
1463 1520 0.677731 GCTGCCTCTGTATGCCACAA 60.678 55.000 0.00 0.00 36.48 3.33
1468 1525 2.736400 GCCTCTGTATGCCACAAATTGC 60.736 50.000 0.00 0.00 36.48 3.56
1477 1534 1.685640 CCACAAATTGCGGCGAATGC 61.686 55.000 12.98 0.00 41.71 3.56
1488 1545 1.718757 GGCGAATGCTGGAGCGAATT 61.719 55.000 0.00 0.00 45.83 2.17
1490 1547 1.009078 CGAATGCTGGAGCGAATTGA 58.991 50.000 0.00 0.00 45.83 2.57
1521 1578 5.579119 TGTGTACATTATGGTTTAGTGCTCG 59.421 40.000 0.00 0.00 0.00 5.03
1569 1628 4.916983 ATAAGCATGTGTTTGTGTGTGT 57.083 36.364 0.00 0.00 0.00 3.72
1570 1629 2.565210 AGCATGTGTTTGTGTGTGTG 57.435 45.000 0.00 0.00 0.00 3.82
1612 1671 2.158696 GGCATGCACTCCTCTCCTTATT 60.159 50.000 21.36 0.00 0.00 1.40
1613 1672 3.071602 GGCATGCACTCCTCTCCTTATTA 59.928 47.826 21.36 0.00 0.00 0.98
1708 1767 1.765314 AGTGCATTGGAGGCTAGTAGG 59.235 52.381 0.00 0.00 0.00 3.18
1777 1836 6.798959 GTGCCAATGCTATCTTCGAATAATTC 59.201 38.462 0.00 0.00 38.71 2.17
1802 1861 8.511321 TCGTTATTCTTTGCATTCTGTATTGTT 58.489 29.630 0.00 0.00 0.00 2.83
1821 1880 5.508200 TGTTGTCTGTAAATTGTTCCCAC 57.492 39.130 0.00 0.00 0.00 4.61
1953 2012 5.969423 TCATGCATCTCCTTTTCCATTTTC 58.031 37.500 0.00 0.00 0.00 2.29
2035 2094 2.900122 TGCGCTAATGAAAAGCACTC 57.100 45.000 9.73 0.00 40.08 3.51
2276 2343 7.984050 TGACAATTTGTAGATTCTCCAGATCTC 59.016 37.037 1.15 0.00 0.00 2.75
2442 2509 2.865551 CACTTGGTGTTTTGCATTGGTC 59.134 45.455 0.00 0.00 0.00 4.02
2445 2512 4.588528 ACTTGGTGTTTTGCATTGGTCTAT 59.411 37.500 0.00 0.00 0.00 1.98
2504 2571 6.954232 TCCCGTATGAAGTTTTTAGGATTCT 58.046 36.000 0.00 0.00 0.00 2.40
2509 2576 9.804758 CGTATGAAGTTTTTAGGATTCTAGAGT 57.195 33.333 0.00 0.00 0.00 3.24
2530 2597 5.728471 AGTCTGTCTAGTACGCTAGTGTTA 58.272 41.667 15.28 0.80 43.86 2.41
2549 2616 5.064071 GTGTTACTTAAGCCTCATCTGCTTC 59.936 44.000 1.29 0.00 45.58 3.86
2554 2621 1.522580 GCCTCATCTGCTTCCGGTC 60.523 63.158 0.00 0.00 0.00 4.79
2580 2647 8.927059 TTATGTAGGGGAAAGGCATATATAGT 57.073 34.615 0.00 0.00 0.00 2.12
2589 2656 3.614092 AGGCATATATAGTGCACCATGC 58.386 45.455 14.63 18.66 44.25 4.06
2682 2756 2.810439 TTTGAACGCCATTTTGGGAG 57.190 45.000 0.00 0.00 38.19 4.30
2799 2873 5.957842 TTCCATGTTGATTACAGGTTGTC 57.042 39.130 0.00 0.00 40.83 3.18
2872 2946 9.953697 CTGAGTCATTATCTGTAAGTTACTACC 57.046 37.037 14.00 0.00 33.76 3.18
2874 2948 8.517062 AGTCATTATCTGTAAGTTACTACCGT 57.483 34.615 14.00 0.00 33.76 4.83
2914 2988 5.241064 AGCATATGAGCTTTTCCATGTGATC 59.759 40.000 6.97 0.00 43.70 2.92
2919 2993 3.760684 GAGCTTTTCCATGTGATCCTTGT 59.239 43.478 0.00 0.00 0.00 3.16
3299 3377 3.556775 TGTTTCTTGCATTGCTTTCTTGC 59.443 39.130 10.49 0.00 36.91 4.01
3300 3378 2.443887 TCTTGCATTGCTTTCTTGCC 57.556 45.000 10.49 0.00 35.51 4.52
3301 3379 1.965643 TCTTGCATTGCTTTCTTGCCT 59.034 42.857 10.49 0.00 35.51 4.75
3302 3380 2.366266 TCTTGCATTGCTTTCTTGCCTT 59.634 40.909 10.49 0.00 35.51 4.35
3303 3381 2.443887 TGCATTGCTTTCTTGCCTTC 57.556 45.000 10.49 0.00 35.51 3.46
3304 3382 1.001181 TGCATTGCTTTCTTGCCTTCC 59.999 47.619 10.49 0.00 35.51 3.46
3305 3383 1.274447 GCATTGCTTTCTTGCCTTCCT 59.726 47.619 0.16 0.00 0.00 3.36
3306 3384 2.929592 GCATTGCTTTCTTGCCTTCCTG 60.930 50.000 0.16 0.00 0.00 3.86
3443 3521 8.095169 TCTATCTCCTTGTGTTTTCCTCTTTAC 58.905 37.037 0.00 0.00 0.00 2.01
3456 3534 7.865706 TTTCCTCTTTACTTGATATTCTGCC 57.134 36.000 0.00 0.00 0.00 4.85
3886 3970 4.973663 CGGTTTCAACTTGTCATTTACACC 59.026 41.667 0.00 0.00 38.00 4.16
3896 3980 5.119931 TGTCATTTACACCAAAGCATGTC 57.880 39.130 0.00 0.00 31.43 3.06
3920 4004 4.678509 TGTCGTAAATTTGGCTAGCAAG 57.321 40.909 18.24 0.00 0.00 4.01
4028 4112 8.299570 CAAAACTAACAGCTAAAGGTGATTCAT 58.700 33.333 15.62 0.00 45.66 2.57
4115 4199 4.335594 GTGGTATGCAGGTATTCCTTCAAC 59.664 45.833 0.00 0.00 43.07 3.18
4121 4205 3.000727 CAGGTATTCCTTCAACGGTGTC 58.999 50.000 0.00 0.00 43.07 3.67
4122 4206 2.635915 AGGTATTCCTTCAACGGTGTCA 59.364 45.455 0.00 0.00 42.12 3.58
4169 4254 7.042658 TGTCAACAACATAAAAATAAAACCCGC 60.043 33.333 0.00 0.00 31.20 6.13
4273 4364 5.255397 TGGTCACTGAAGGAATGGTTATT 57.745 39.130 0.00 0.00 0.00 1.40
4396 4487 2.622064 AGCGATCCATTTACACCCTC 57.378 50.000 0.00 0.00 0.00 4.30
4424 4515 2.352651 TCGCTGCTGATTTCTGTATTGC 59.647 45.455 0.00 0.00 0.00 3.56
4469 4560 6.721571 TGCGGATATTAGTTAAAGCTATGC 57.278 37.500 0.00 0.00 0.00 3.14
4527 4618 8.991243 TGAATATGTTTAGCTACGTAGTTGTT 57.009 30.769 22.98 9.72 37.78 2.83
4576 4667 4.408182 AAGTCAAAGGCAGCTACGATAT 57.592 40.909 0.00 0.00 0.00 1.63
4718 4809 5.302823 CCTTCTCCATCAGTTTGGACTTTTT 59.697 40.000 0.00 0.00 40.90 1.94
4794 4885 5.319453 TGGATTCAAGTCTCAGATTTTGCT 58.681 37.500 0.00 0.00 0.00 3.91
4806 4897 9.508567 GTCTCAGATTTTGCTATTTAAATGGAC 57.491 33.333 15.09 7.24 0.00 4.02
4820 4911 1.708341 ATGGACATATTGCTTGCCCC 58.292 50.000 0.00 0.00 0.00 5.80
4841 4932 1.002087 CCTTCTGTCCACGTTTAGGCT 59.998 52.381 0.00 0.00 0.00 4.58
4851 4942 3.187700 CACGTTTAGGCTTTATCGAGCT 58.812 45.455 0.00 0.00 42.32 4.09
4984 5075 8.344831 TCTGTTTTTGAGAAGTCATATGTTGTG 58.655 33.333 1.90 0.00 30.85 3.33
5241 5333 7.383102 AGTTCATTTGATACACAATCTGGTC 57.617 36.000 0.00 0.00 38.36 4.02
5325 5417 8.308931 TGGCTATTATAACTATTGAACGTAGGG 58.691 37.037 0.00 0.00 0.00 3.53
5334 5426 0.938713 TGAACGTAGGGCACAAAACG 59.061 50.000 6.93 6.93 40.99 3.60
5544 5637 5.336770 GGGAAATTTGTCTCAATCCCTTCAC 60.337 44.000 0.00 0.00 42.64 3.18
5617 5713 1.974265 TTTTTCCATGGACGAGTGCA 58.026 45.000 15.91 0.00 34.81 4.57
5628 5724 2.271800 GACGAGTGCATGGAAGTTAGG 58.728 52.381 0.00 0.00 0.00 2.69
5651 5747 0.888736 CCACGTGCCAGAACCATGAA 60.889 55.000 10.91 0.00 0.00 2.57
5742 5851 8.183536 TGTTGTTGCTTCTACATTTGCATATAG 58.816 33.333 0.00 0.00 35.27 1.31
5775 5884 1.990563 CGTACCTTGTCACGAATGGAC 59.009 52.381 0.00 0.00 40.56 4.02
5787 5896 7.279615 TGTCACGAATGGACCTATGAAAATAT 58.720 34.615 0.00 0.00 34.36 1.28
5788 5897 7.441157 TGTCACGAATGGACCTATGAAAATATC 59.559 37.037 0.00 0.00 34.36 1.63
5933 6046 6.241207 TGCTTTTGCTAGCACTTTAAGTAG 57.759 37.500 19.17 5.62 45.72 2.57
5939 6052 4.223032 TGCTAGCACTTTAAGTAGCTCCTT 59.777 41.667 14.93 0.00 35.39 3.36
5973 6086 8.084073 ACAAAATGAGTGACACATATTTTGGAG 58.916 33.333 34.04 23.20 41.95 3.86
6051 6164 9.941664 GACATGAATACATAATTGAAGTGAAGG 57.058 33.333 0.00 0.00 35.09 3.46
6142 6270 6.595326 CACATTTCCACTGTTAAGATGCTCTA 59.405 38.462 0.00 0.00 0.00 2.43
6242 6370 6.183360 CCGTACTAAGTGTTGTTAGAGCCTAT 60.183 42.308 0.00 0.00 34.58 2.57
6247 6375 6.852420 AAGTGTTGTTAGAGCCTATGAGTA 57.148 37.500 0.00 0.00 0.00 2.59
6256 6387 4.701765 AGAGCCTATGAGTAATTGCACAG 58.298 43.478 0.00 0.00 0.00 3.66
6301 6432 5.765182 AGATGTGGACTGATTTCGTTCTTTT 59.235 36.000 0.00 0.00 0.00 2.27
6302 6433 6.934645 AGATGTGGACTGATTTCGTTCTTTTA 59.065 34.615 0.00 0.00 0.00 1.52
6399 6530 9.935241 GTAGCAGAATCTCATCTTAATCCATAA 57.065 33.333 0.00 0.00 0.00 1.90
6565 6696 5.354513 GGTTCCTCAGCTTTATACTTGAACC 59.645 44.000 0.00 0.00 0.00 3.62
6567 6698 4.222145 TCCTCAGCTTTATACTTGAACCGT 59.778 41.667 0.00 0.00 0.00 4.83
6727 6861 5.177881 TCATTAATACGTGCGTGACTGTTTT 59.822 36.000 7.55 0.00 0.00 2.43
6911 7047 9.076596 GCACATTATTCCAATTTTGTACTTCTC 57.923 33.333 0.00 0.00 0.00 2.87
6933 7069 4.949856 TCCAGGGCTATCTTGAAACAATTC 59.050 41.667 0.00 0.00 36.04 2.17
6958 7094 6.109359 GTGACATCTGACCTTACAAAGCTAT 58.891 40.000 0.00 0.00 0.00 2.97
6968 7104 4.079958 CCTTACAAAGCTATTGGGGGTAGT 60.080 45.833 11.59 0.00 0.00 2.73
7052 7188 1.145162 GCTTGTGTTGTGGTTTGCCG 61.145 55.000 0.00 0.00 37.67 5.69
7118 7254 8.777413 TGTCTCATGCTCATGTAATTTATTAGC 58.223 33.333 9.41 0.00 39.72 3.09
7263 7399 1.135402 GGCAAGTCAATAAAGCCACCG 60.135 52.381 0.00 0.00 44.59 4.94
7318 7457 2.957402 TGGTCTGCTGGAAATGAAGT 57.043 45.000 0.00 0.00 0.00 3.01
7583 7751 7.693969 AATAGCATTGGCAGACTATATTTCC 57.306 36.000 6.48 0.00 44.61 3.13
7669 7873 1.952296 CAGGCATCCAGTATTCAAGCC 59.048 52.381 0.00 0.00 40.85 4.35
7756 7960 6.326375 TGTTTTGAACAGTAACCATTGACAC 58.674 36.000 0.00 0.00 36.25 3.67
7891 8096 5.339008 TCACACTTCTGTTGAGTTACAGT 57.661 39.130 0.00 0.00 44.62 3.55
7892 8097 5.109210 TCACACTTCTGTTGAGTTACAGTG 58.891 41.667 0.00 0.00 44.62 3.66
7955 8190 2.159448 TCAAGCCGTGGAATTATTTGCG 60.159 45.455 0.00 0.00 0.00 4.85
8154 8605 3.260632 TGTAAGAGGCACAGTTCAGCATA 59.739 43.478 0.00 0.00 0.00 3.14
8188 8639 1.615502 GTCTGTAGGTCGAAGCGAAC 58.384 55.000 0.00 0.00 44.66 3.95
8194 8645 2.446341 GGTCGAAGCGAACTGGAAG 58.554 57.895 0.00 0.00 40.75 3.46
8216 8668 3.190118 GTCTTGTGAGAATCCAGGCAAAG 59.810 47.826 0.00 0.00 32.66 2.77
8238 8690 1.405872 TATCCTTGTACGGGATGCGT 58.594 50.000 22.61 6.97 42.79 5.24
8239 8691 0.179084 ATCCTTGTACGGGATGCGTG 60.179 55.000 16.29 0.00 41.50 5.34
8240 8692 2.461110 CCTTGTACGGGATGCGTGC 61.461 63.158 0.00 0.00 0.00 5.34
8241 8693 1.447838 CTTGTACGGGATGCGTGCT 60.448 57.895 0.00 0.00 0.00 4.40
8242 8694 1.421410 CTTGTACGGGATGCGTGCTC 61.421 60.000 0.00 0.00 0.00 4.26
8243 8695 2.585247 GTACGGGATGCGTGCTCC 60.585 66.667 0.00 0.00 0.00 4.70
8244 8696 3.071837 TACGGGATGCGTGCTCCA 61.072 61.111 0.00 0.00 34.24 3.86
8245 8697 3.365291 TACGGGATGCGTGCTCCAC 62.365 63.158 0.00 0.00 34.24 4.02
8246 8698 4.457496 CGGGATGCGTGCTCCACT 62.457 66.667 0.00 0.00 34.24 4.00
8247 8699 2.045926 GGGATGCGTGCTCCACTT 60.046 61.111 0.00 0.00 34.24 3.16
8248 8700 1.675641 GGGATGCGTGCTCCACTTT 60.676 57.895 0.00 0.00 34.24 2.66
8249 8701 1.244019 GGGATGCGTGCTCCACTTTT 61.244 55.000 0.00 0.00 34.24 2.27
8250 8702 0.598065 GGATGCGTGCTCCACTTTTT 59.402 50.000 0.00 0.00 32.72 1.94
8414 8866 5.105595 GCTTCAAGCTTAGGTTTGGATCATT 60.106 40.000 0.71 0.00 38.45 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 120 4.078516 GTCAGGGTTAGCCGCGGT 62.079 66.667 28.70 16.08 34.97 5.68
179 188 3.319198 GGGGGCTGACGAACTCCA 61.319 66.667 0.00 0.00 0.00 3.86
248 270 3.567797 GTCGCCAATGCTCGAGGC 61.568 66.667 15.58 8.66 44.89 4.70
291 313 0.179145 ACATGCGCTACTCCGTGTAC 60.179 55.000 9.73 0.00 29.93 2.90
292 314 1.332686 CTACATGCGCTACTCCGTGTA 59.667 52.381 9.73 5.78 33.57 2.90
297 319 0.315568 CCCTCTACATGCGCTACTCC 59.684 60.000 9.73 0.00 0.00 3.85
397 419 1.518572 CGAAGGCGGCTTGATACGT 60.519 57.895 30.59 2.02 0.00 3.57
453 475 2.097728 CGTCGTCATCGTCGCTGA 59.902 61.111 0.00 0.00 40.72 4.26
504 538 2.028020 ACAAAAACAAAAGTTCCCGCCA 60.028 40.909 0.00 0.00 0.00 5.69
603 641 4.037446 ACACGTGGCACAGATAACAAAAAT 59.963 37.500 21.57 0.00 41.80 1.82
640 684 3.023119 ACCCAAATATGCGCATGAAGAA 58.977 40.909 32.48 13.04 0.00 2.52
641 685 2.618241 GACCCAAATATGCGCATGAAGA 59.382 45.455 32.48 13.46 0.00 2.87
646 690 0.465460 ACGGACCCAAATATGCGCAT 60.465 50.000 28.23 28.23 0.00 4.73
647 691 0.678366 AACGGACCCAAATATGCGCA 60.678 50.000 14.96 14.96 0.00 6.09
666 710 1.067213 GGCTTGAGCGCCCAATAAAAA 60.067 47.619 4.31 0.00 44.41 1.94
668 712 2.188912 GGCTTGAGCGCCCAATAAA 58.811 52.632 4.31 0.00 44.41 1.40
669 713 3.918544 GGCTTGAGCGCCCAATAA 58.081 55.556 4.31 0.00 44.41 1.40
690 734 3.560481 TGTACGTCCGCTTTTTCAAATGA 59.440 39.130 0.00 0.00 0.00 2.57
694 738 2.873472 ACATGTACGTCCGCTTTTTCAA 59.127 40.909 0.00 0.00 0.00 2.69
709 753 1.401409 GGACGGTTCGACGAACATGTA 60.401 52.381 34.34 1.65 43.54 2.29
710 754 0.665369 GGACGGTTCGACGAACATGT 60.665 55.000 34.34 30.63 43.54 3.21
713 757 2.051076 CGGACGGTTCGACGAACA 60.051 61.111 34.34 3.99 43.54 3.18
716 760 3.726517 GTCCGGACGGTTCGACGA 61.727 66.667 20.85 0.00 37.61 4.20
726 770 1.574134 TGTCTGTTTTTCGTCCGGAC 58.426 50.000 25.28 25.28 35.51 4.79
727 771 2.312722 TTGTCTGTTTTTCGTCCGGA 57.687 45.000 0.00 0.00 0.00 5.14
728 772 3.551551 GATTTGTCTGTTTTTCGTCCGG 58.448 45.455 0.00 0.00 0.00 5.14
729 773 3.215244 CGATTTGTCTGTTTTTCGTCCG 58.785 45.455 0.00 0.00 0.00 4.79
730 774 2.971261 GCGATTTGTCTGTTTTTCGTCC 59.029 45.455 0.00 0.00 0.00 4.79
731 775 3.417645 GTGCGATTTGTCTGTTTTTCGTC 59.582 43.478 0.00 0.00 0.00 4.20
732 776 3.359654 GTGCGATTTGTCTGTTTTTCGT 58.640 40.909 0.00 0.00 0.00 3.85
733 777 2.397154 CGTGCGATTTGTCTGTTTTTCG 59.603 45.455 0.00 0.00 0.00 3.46
734 778 2.719046 CCGTGCGATTTGTCTGTTTTTC 59.281 45.455 0.00 0.00 0.00 2.29
735 779 2.356382 TCCGTGCGATTTGTCTGTTTTT 59.644 40.909 0.00 0.00 0.00 1.94
736 780 1.944024 TCCGTGCGATTTGTCTGTTTT 59.056 42.857 0.00 0.00 0.00 2.43
737 781 1.588674 TCCGTGCGATTTGTCTGTTT 58.411 45.000 0.00 0.00 0.00 2.83
738 782 1.732259 GATCCGTGCGATTTGTCTGTT 59.268 47.619 0.00 0.00 0.00 3.16
739 783 1.359848 GATCCGTGCGATTTGTCTGT 58.640 50.000 0.00 0.00 0.00 3.41
740 784 0.298707 CGATCCGTGCGATTTGTCTG 59.701 55.000 0.00 0.00 0.00 3.51
741 785 0.108804 ACGATCCGTGCGATTTGTCT 60.109 50.000 0.00 0.00 39.18 3.41
742 786 0.719465 AACGATCCGTGCGATTTGTC 59.281 50.000 0.00 0.00 39.99 3.18
743 787 1.153353 AAACGATCCGTGCGATTTGT 58.847 45.000 0.00 0.00 39.99 2.83
744 788 2.285602 CCTAAACGATCCGTGCGATTTG 60.286 50.000 0.00 0.00 39.99 2.32
745 789 1.931172 CCTAAACGATCCGTGCGATTT 59.069 47.619 0.00 0.00 39.99 2.17
746 790 1.134907 ACCTAAACGATCCGTGCGATT 60.135 47.619 0.00 0.00 39.99 3.34
747 791 0.458669 ACCTAAACGATCCGTGCGAT 59.541 50.000 0.00 0.00 39.99 4.58
748 792 0.179156 GACCTAAACGATCCGTGCGA 60.179 55.000 0.00 0.00 39.99 5.10
749 793 1.469126 CGACCTAAACGATCCGTGCG 61.469 60.000 0.00 0.00 39.99 5.34
750 794 1.749609 GCGACCTAAACGATCCGTGC 61.750 60.000 0.00 0.00 39.99 5.34
751 795 1.469126 CGCGACCTAAACGATCCGTG 61.469 60.000 0.00 0.00 39.99 4.94
752 796 1.226491 CGCGACCTAAACGATCCGT 60.226 57.895 0.00 0.00 43.97 4.69
753 797 1.942712 CCGCGACCTAAACGATCCG 60.943 63.158 8.23 0.00 0.00 4.18
754 798 2.235699 GCCGCGACCTAAACGATCC 61.236 63.158 8.23 0.00 0.00 3.36
755 799 2.574222 CGCCGCGACCTAAACGATC 61.574 63.158 8.23 0.00 0.00 3.69
756 800 2.581409 CGCCGCGACCTAAACGAT 60.581 61.111 8.23 0.00 0.00 3.73
757 801 3.556543 AACGCCGCGACCTAAACGA 62.557 57.895 21.79 0.00 0.00 3.85
758 802 3.107661 AACGCCGCGACCTAAACG 61.108 61.111 21.79 1.78 0.00 3.60
759 803 2.472934 CAACGCCGCGACCTAAAC 59.527 61.111 21.79 0.00 0.00 2.01
760 804 2.739287 CCAACGCCGCGACCTAAA 60.739 61.111 21.79 0.00 0.00 1.85
761 805 3.636313 CTCCAACGCCGCGACCTAA 62.636 63.158 21.79 0.00 0.00 2.69
762 806 4.124351 CTCCAACGCCGCGACCTA 62.124 66.667 21.79 1.10 0.00 3.08
765 809 4.072088 CAACTCCAACGCCGCGAC 62.072 66.667 21.79 0.00 0.00 5.19
768 812 4.090057 GAGCAACTCCAACGCCGC 62.090 66.667 0.00 0.00 0.00 6.53
769 813 1.961277 AAGAGCAACTCCAACGCCG 60.961 57.895 0.00 0.00 0.00 6.46
770 814 1.576421 CAAGAGCAACTCCAACGCC 59.424 57.895 0.00 0.00 0.00 5.68
771 815 1.166531 ACCAAGAGCAACTCCAACGC 61.167 55.000 0.00 0.00 0.00 4.84
772 816 0.588252 CACCAAGAGCAACTCCAACG 59.412 55.000 0.00 0.00 0.00 4.10
773 817 0.312102 GCACCAAGAGCAACTCCAAC 59.688 55.000 0.00 0.00 0.00 3.77
774 818 0.183492 AGCACCAAGAGCAACTCCAA 59.817 50.000 0.00 0.00 0.00 3.53
775 819 0.250467 GAGCACCAAGAGCAACTCCA 60.250 55.000 0.00 0.00 0.00 3.86
776 820 0.957888 GGAGCACCAAGAGCAACTCC 60.958 60.000 0.00 0.00 37.17 3.85
777 821 0.957888 GGGAGCACCAAGAGCAACTC 60.958 60.000 1.58 0.00 39.85 3.01
778 822 1.073897 GGGAGCACCAAGAGCAACT 59.926 57.895 1.58 0.00 39.85 3.16
779 823 2.328099 CGGGAGCACCAAGAGCAAC 61.328 63.158 1.58 0.00 40.22 4.17
780 824 2.032528 CGGGAGCACCAAGAGCAA 59.967 61.111 1.58 0.00 40.22 3.91
781 825 4.020617 CCGGGAGCACCAAGAGCA 62.021 66.667 1.58 0.00 40.22 4.26
782 826 3.254024 TTCCGGGAGCACCAAGAGC 62.254 63.158 0.00 0.00 40.22 4.09
783 827 1.376037 GTTCCGGGAGCACCAAGAG 60.376 63.158 0.00 0.00 40.22 2.85
784 828 2.144078 TGTTCCGGGAGCACCAAGA 61.144 57.895 9.73 0.00 40.22 3.02
785 829 1.966451 GTGTTCCGGGAGCACCAAG 60.966 63.158 27.76 0.00 37.72 3.61
786 830 2.112297 GTGTTCCGGGAGCACCAA 59.888 61.111 27.76 0.00 37.72 3.67
803 847 1.915614 GCAATCGCTATGCCATCGGG 61.916 60.000 0.00 0.00 37.85 5.14
828 872 4.829518 TCTGCGTCGGCGTCATCG 62.830 66.667 12.58 9.27 44.10 3.84
829 873 2.951745 CTCTGCGTCGGCGTCATC 60.952 66.667 12.58 0.00 44.10 2.92
898 942 0.325390 GTAGCAGGGGTGGGTAGACT 60.325 60.000 0.00 0.00 0.00 3.24
912 956 0.816825 CCGCGGAGTAGTAGGTAGCA 60.817 60.000 24.07 0.00 0.00 3.49
913 957 1.947760 CCGCGGAGTAGTAGGTAGC 59.052 63.158 24.07 0.00 0.00 3.58
1249 1306 2.759114 CCCACTGCACAGACCCAT 59.241 61.111 4.31 0.00 0.00 4.00
1256 1313 4.624364 CCACGAGCCCACTGCACA 62.624 66.667 0.00 0.00 44.83 4.57
1448 1505 2.478370 CGCAATTTGTGGCATACAGAGG 60.478 50.000 1.90 0.00 41.10 3.69
1462 1519 1.153784 CCAGCATTCGCCGCAATTT 60.154 52.632 0.00 0.00 39.83 1.82
1463 1520 1.996786 CTCCAGCATTCGCCGCAATT 61.997 55.000 0.00 0.00 39.83 2.32
1477 1534 1.424493 GGTCGCTCAATTCGCTCCAG 61.424 60.000 0.00 0.00 0.00 3.86
1488 1545 3.430236 CCATAATGTACACAGGTCGCTCA 60.430 47.826 0.00 0.00 0.00 4.26
1490 1547 2.500098 ACCATAATGTACACAGGTCGCT 59.500 45.455 0.00 0.00 0.00 4.93
1544 1603 7.060979 CACACACACAAACACATGCTTATATTC 59.939 37.037 0.00 0.00 0.00 1.75
1546 1605 6.380995 CACACACACAAACACATGCTTATAT 58.619 36.000 0.00 0.00 0.00 0.86
1547 1606 5.756849 CACACACACAAACACATGCTTATA 58.243 37.500 0.00 0.00 0.00 0.98
1549 1608 3.733380 GCACACACACAAACACATGCTTA 60.733 43.478 0.00 0.00 0.00 3.09
1569 1628 2.289882 CCATCAAGAGAGACCAACAGCA 60.290 50.000 0.00 0.00 0.00 4.41
1570 1629 2.354259 CCATCAAGAGAGACCAACAGC 58.646 52.381 0.00 0.00 0.00 4.40
1613 1672 9.093458 AGGTTCCATTTCAGTTTTGAATTCTAT 57.907 29.630 7.05 0.00 42.60 1.98
1708 1767 3.357166 AGACCAAGATCGTCGATTAGC 57.643 47.619 9.52 0.00 35.33 3.09
1777 1836 8.577939 CAACAATACAGAATGCAAAGAATAACG 58.422 33.333 0.00 0.00 42.53 3.18
1783 1842 6.262944 ACAGACAACAATACAGAATGCAAAGA 59.737 34.615 0.00 0.00 42.53 2.52
1784 1843 6.441274 ACAGACAACAATACAGAATGCAAAG 58.559 36.000 0.00 0.00 42.53 2.77
1802 1861 4.171878 TGGTGGGAACAATTTACAGACA 57.828 40.909 0.00 0.00 46.06 3.41
1854 1913 1.078143 GTGCTGGGAGTTAGGCTGG 60.078 63.158 0.00 0.00 0.00 4.85
1953 2012 4.446371 CTCAAGGGTGAGCTACAATAAGG 58.554 47.826 0.00 0.00 44.74 2.69
2070 2129 7.769970 ACTGTAGGCTGAAGTAGTTAGTACTAG 59.230 40.741 2.23 0.00 41.50 2.57
2276 2343 8.700644 CAGAGCAGAATCAAATTTGAAAGAAAG 58.299 33.333 23.91 12.95 41.13 2.62
2481 2548 8.202137 TCTAGAATCCTAAAAACTTCATACGGG 58.798 37.037 0.00 0.00 0.00 5.28
2521 2588 5.751028 CAGATGAGGCTTAAGTAACACTAGC 59.249 44.000 4.02 0.00 30.88 3.42
2549 2616 2.104281 CCTTTCCCCTACATAAGACCGG 59.896 54.545 0.00 0.00 0.00 5.28
2554 2621 8.993424 ACTATATATGCCTTTCCCCTACATAAG 58.007 37.037 0.00 0.00 0.00 1.73
2682 2756 5.244178 TCTGTAAGGAAAGAACTCACCTCTC 59.756 44.000 0.00 0.00 31.89 3.20
2719 2793 8.830580 TGCAGAGCTTTTAACTGTATATGATTC 58.169 33.333 0.00 0.00 34.60 2.52
2799 2873 8.651588 GCTACAAATGGATCAATAAGATAGTCG 58.348 37.037 0.00 0.00 37.00 4.18
2872 2946 4.077063 TGCTGTTTGTGCACATAATACG 57.923 40.909 22.39 12.79 35.31 3.06
2874 2948 7.565323 TCATATGCTGTTTGTGCACATAATA 57.435 32.000 22.39 14.23 43.59 0.98
2962 3040 6.952773 AGCCAACACAGTTAATTAACAAGA 57.047 33.333 26.06 0.00 38.62 3.02
2979 3057 4.632538 ACAGTTGTTACTCAAAGCCAAC 57.367 40.909 0.00 0.00 37.81 3.77
2980 3058 5.652994 AAACAGTTGTTACTCAAAGCCAA 57.347 34.783 0.00 0.00 37.25 4.52
3224 3302 9.530129 GACATCTTCACTTGTAGAATTTTTACG 57.470 33.333 0.00 0.00 0.00 3.18
3267 3345 5.975939 GCAATGCAAGAAACAAGGATATCTC 59.024 40.000 0.00 0.00 0.00 2.75
3299 3377 1.783250 AACAGCAGGACCCAGGAAGG 61.783 60.000 0.00 0.00 37.03 3.46
3300 3378 0.984230 TAACAGCAGGACCCAGGAAG 59.016 55.000 0.00 0.00 0.00 3.46
3301 3379 0.984230 CTAACAGCAGGACCCAGGAA 59.016 55.000 0.00 0.00 0.00 3.36
3302 3380 1.553690 GCTAACAGCAGGACCCAGGA 61.554 60.000 0.00 0.00 41.89 3.86
3303 3381 1.078143 GCTAACAGCAGGACCCAGG 60.078 63.158 0.00 0.00 41.89 4.45
3304 3382 0.326264 AAGCTAACAGCAGGACCCAG 59.674 55.000 0.38 0.00 45.56 4.45
3305 3383 0.036732 CAAGCTAACAGCAGGACCCA 59.963 55.000 0.38 0.00 45.56 4.51
3306 3384 0.036875 ACAAGCTAACAGCAGGACCC 59.963 55.000 0.38 0.00 45.56 4.46
3443 3521 6.764308 TTTGGAGAAAGGCAGAATATCAAG 57.236 37.500 0.00 0.00 0.00 3.02
3483 3561 3.007635 GTCCAACTCCATCGGTAAAAGG 58.992 50.000 0.00 0.00 0.00 3.11
3491 3569 2.614057 GCCAATTAGTCCAACTCCATCG 59.386 50.000 0.00 0.00 0.00 3.84
3886 3970 3.513462 TTACGACAACGACATGCTTTG 57.487 42.857 0.00 0.00 42.66 2.77
3896 3980 3.120477 TGCTAGCCAAATTTACGACAACG 60.120 43.478 13.29 0.00 45.75 4.10
4028 4112 1.523758 GAAGCGCCTCCTTTCTTTGA 58.476 50.000 2.29 0.00 0.00 2.69
4115 4199 2.426522 AGGAAATGACATGTGACACCG 58.573 47.619 1.15 0.00 0.00 4.94
4121 4205 6.738114 ACACTAACAAAGGAAATGACATGTG 58.262 36.000 1.15 0.00 0.00 3.21
4122 4206 6.545666 TGACACTAACAAAGGAAATGACATGT 59.454 34.615 0.00 0.00 0.00 3.21
4160 4245 1.025647 GGGCACATACGCGGGTTTTA 61.026 55.000 11.50 0.00 0.00 1.52
4169 4254 4.330944 TGGAGTTAATAGGGCACATACG 57.669 45.455 0.00 0.00 0.00 3.06
4225 4316 0.612732 TGCAGCTCTTCCAAATGGGG 60.613 55.000 0.00 0.00 37.22 4.96
4315 4406 9.290988 TGGCTTGTGAAACTTAAAATAGTGATA 57.709 29.630 0.00 0.00 38.04 2.15
4396 4487 3.059529 CAGAAATCAGCAGCGATCATGAG 60.060 47.826 0.09 0.00 0.00 2.90
4424 4515 5.163513 CAAGCTAATAAACTTGTGCCAAGG 58.836 41.667 16.21 0.00 38.75 3.61
4469 4560 6.538381 GGTCATATATTTGGGCTTTTGTTTGG 59.462 38.462 0.00 0.00 0.00 3.28
4527 4618 7.926674 TCTCATCTTGCAATATTGTTTCTCA 57.073 32.000 16.61 3.21 0.00 3.27
4718 4809 4.594123 TCATGTACCAACGAGAAGAACA 57.406 40.909 0.00 0.00 0.00 3.18
4794 4885 7.441017 GGGCAAGCAATATGTCCATTTAAATA 58.559 34.615 0.00 0.00 42.25 1.40
4820 4911 1.944430 GCCTAAACGTGGACAGAAGGG 60.944 57.143 0.00 0.00 0.00 3.95
4851 4942 3.066190 CACCCCCTCTCACGCGTA 61.066 66.667 13.44 0.00 0.00 4.42
4901 4992 6.429385 AGAATCAAAAGTCTGAACTGATGGAC 59.571 38.462 0.00 0.00 35.36 4.02
4957 5048 8.345565 ACAACATATGACTTCTCAAAAACAGAC 58.654 33.333 10.38 0.00 0.00 3.51
4967 5058 5.587844 AGCATTCCACAACATATGACTTCTC 59.412 40.000 10.38 0.00 0.00 2.87
4984 5075 6.398918 TCTACTAGTGTCTGAAAAGCATTCC 58.601 40.000 5.39 0.00 0.00 3.01
5060 5151 2.287308 GCAGTTACACGCCAATGACAAA 60.287 45.455 0.00 0.00 0.00 2.83
5241 5333 8.706492 TTTATAGATTGGCAGAAAGCAAATTG 57.294 30.769 0.00 0.00 46.94 2.32
5289 5381 2.847327 ATAATAGCCAGTCATGCGCT 57.153 45.000 9.73 0.00 36.99 5.92
5290 5382 3.997021 AGTTATAATAGCCAGTCATGCGC 59.003 43.478 0.00 0.00 0.00 6.09
5325 5417 6.608610 AGAGGTACATAATTTCGTTTTGTGC 58.391 36.000 0.00 0.00 34.47 4.57
5334 5426 7.706607 GGGAAAATGCAAGAGGTACATAATTTC 59.293 37.037 0.00 0.00 0.00 2.17
5611 5705 4.141711 TGGATACCTAACTTCCATGCACTC 60.142 45.833 0.00 0.00 34.65 3.51
5612 5706 3.780294 TGGATACCTAACTTCCATGCACT 59.220 43.478 0.00 0.00 34.65 4.40
5617 5713 3.431766 GCACGTGGATACCTAACTTCCAT 60.432 47.826 18.88 0.00 41.37 3.41
5628 5724 0.036765 TGGTTCTGGCACGTGGATAC 60.037 55.000 18.88 0.00 0.00 2.24
5651 5747 9.265862 TGAAACCCATAAGATATCAAAACCAAT 57.734 29.630 5.32 0.00 0.00 3.16
5659 5755 8.150945 GCTAGAGTTGAAACCCATAAGATATCA 58.849 37.037 5.32 0.00 0.00 2.15
5742 5851 4.451900 ACAAGGTACGGGAATGAATCATC 58.548 43.478 0.00 0.00 0.00 2.92
5787 5896 8.768501 AATAGACCATATCACTGAACTACTGA 57.231 34.615 0.00 0.00 0.00 3.41
5788 5897 9.469807 GAAATAGACCATATCACTGAACTACTG 57.530 37.037 0.00 0.00 0.00 2.74
5933 6046 5.200368 TCATTTTGTCCAGAAAAAGGAGC 57.800 39.130 0.00 0.00 33.72 4.70
5939 6052 5.417266 TGTGTCACTCATTTTGTCCAGAAAA 59.583 36.000 4.27 0.00 0.00 2.29
5997 6110 2.955660 ACAGAGCAGAGTATGTCTAGCC 59.044 50.000 0.00 0.00 32.51 3.93
6012 6125 7.364522 TGTATTCATGTCAGTAAAACAGAGC 57.635 36.000 0.00 0.00 0.00 4.09
6051 6164 9.494271 TTGATGATGGAGAAGCAATATAACTAC 57.506 33.333 0.00 0.00 0.00 2.73
6242 6370 6.513806 AATGTAATGCTGTGCAATTACTCA 57.486 33.333 16.19 2.53 43.62 3.41
6247 6375 6.757947 GGTCATAAATGTAATGCTGTGCAATT 59.242 34.615 0.00 0.00 43.62 2.32
6256 6387 9.224267 ACATCTCATAGGTCATAAATGTAATGC 57.776 33.333 0.00 0.00 0.00 3.56
6399 6530 8.004215 TGGCAGATAATCCACCTACAAATTAAT 58.996 33.333 0.00 0.00 0.00 1.40
6565 6696 8.901748 CAATGGTACTTCTGTAAATTGAAAACG 58.098 33.333 0.00 0.00 37.27 3.60
6567 6698 8.417106 TGCAATGGTACTTCTGTAAATTGAAAA 58.583 29.630 12.82 0.00 37.27 2.29
6708 6842 3.955771 AAAAACAGTCACGCACGTATT 57.044 38.095 0.00 0.00 0.00 1.89
6727 6861 7.415086 AGAGGAGAAGAGAGTTCCTATACAAA 58.585 38.462 0.00 0.00 41.32 2.83
6903 7039 3.961408 TCAAGATAGCCCTGGAGAAGTAC 59.039 47.826 0.00 0.00 0.00 2.73
6911 7047 4.201950 CGAATTGTTTCAAGATAGCCCTGG 60.202 45.833 0.00 0.00 0.00 4.45
6933 7069 3.123621 GCTTTGTAAGGTCAGATGTCACG 59.876 47.826 0.00 0.00 0.00 4.35
6958 7094 2.938798 CTGCCCCACTACCCCCAA 60.939 66.667 0.00 0.00 0.00 4.12
6968 7104 1.382420 ACAAAAGTTGGCTGCCCCA 60.382 52.632 17.53 0.00 43.51 4.96
7052 7188 6.183360 GCACATTCTGAAATTCCCTAGAAGAC 60.183 42.308 0.00 0.00 34.86 3.01
7357 7496 5.626955 GCTTGCTCTACAAATTTCTGACAAC 59.373 40.000 0.00 0.00 37.96 3.32
7363 7502 5.068987 TGGTTTGCTTGCTCTACAAATTTCT 59.931 36.000 0.00 0.00 37.96 2.52
7601 7805 2.754552 TGCCAACCACTGCTATCATTTC 59.245 45.455 0.00 0.00 0.00 2.17
7669 7873 1.737793 GTCCTTGCCCATCTTTACACG 59.262 52.381 0.00 0.00 0.00 4.49
7891 8096 4.650734 TCATTATTGTTCAGAGCCACACA 58.349 39.130 0.00 0.00 0.00 3.72
7892 8097 5.587844 AGATCATTATTGTTCAGAGCCACAC 59.412 40.000 0.00 0.00 0.00 3.82
7933 8168 3.438360 GCAAATAATTCCACGGCTTGAG 58.562 45.455 0.00 0.00 0.00 3.02
7955 8190 0.936600 AGCAAAACGCAAAATGGCAC 59.063 45.000 0.00 0.00 46.13 5.01
8179 8630 1.457303 CAAGACTTCCAGTTCGCTTCG 59.543 52.381 0.00 0.00 0.00 3.79
8188 8639 4.252073 CTGGATTCTCACAAGACTTCCAG 58.748 47.826 14.47 14.47 46.03 3.86
8189 8640 3.008375 CCTGGATTCTCACAAGACTTCCA 59.992 47.826 0.00 6.28 39.82 3.53
8190 8641 3.604582 CCTGGATTCTCACAAGACTTCC 58.395 50.000 0.00 0.00 35.77 3.46
8192 8643 2.373169 TGCCTGGATTCTCACAAGACTT 59.627 45.455 0.00 0.00 0.00 3.01
8194 8645 2.479566 TGCCTGGATTCTCACAAGAC 57.520 50.000 0.00 0.00 0.00 3.01
8195 8646 3.415212 CTTTGCCTGGATTCTCACAAGA 58.585 45.455 0.00 0.00 0.00 3.02
8196 8647 2.490903 CCTTTGCCTGGATTCTCACAAG 59.509 50.000 0.00 0.00 0.00 3.16
8197 8648 2.108075 TCCTTTGCCTGGATTCTCACAA 59.892 45.455 0.00 0.00 0.00 3.33
8216 8668 2.674177 CGCATCCCGTACAAGGATATCC 60.674 54.545 14.41 14.41 42.41 2.59
8256 8708 3.191581 TGGAGCACGTCTTGTTTCAAAAA 59.808 39.130 0.00 0.00 0.00 1.94
8257 8709 2.750166 TGGAGCACGTCTTGTTTCAAAA 59.250 40.909 0.00 0.00 0.00 2.44
8258 8710 2.096819 GTGGAGCACGTCTTGTTTCAAA 59.903 45.455 0.00 0.00 0.00 2.69
8259 8711 1.668751 GTGGAGCACGTCTTGTTTCAA 59.331 47.619 0.00 0.00 0.00 2.69
8260 8712 1.134521 AGTGGAGCACGTCTTGTTTCA 60.135 47.619 0.00 0.00 39.64 2.69
8261 8713 1.583054 AGTGGAGCACGTCTTGTTTC 58.417 50.000 0.00 0.00 39.64 2.78
8262 8714 1.670811 CAAGTGGAGCACGTCTTGTTT 59.329 47.619 4.68 0.00 39.64 2.83
8263 8715 1.299541 CAAGTGGAGCACGTCTTGTT 58.700 50.000 4.68 0.00 39.64 2.83
8264 8716 1.160329 GCAAGTGGAGCACGTCTTGT 61.160 55.000 12.34 0.00 39.64 3.16
8265 8717 1.159713 TGCAAGTGGAGCACGTCTTG 61.160 55.000 7.79 7.79 39.64 3.02
8266 8718 0.463654 TTGCAAGTGGAGCACGTCTT 60.464 50.000 0.00 0.00 42.54 3.01
8267 8719 1.146041 TTGCAAGTGGAGCACGTCT 59.854 52.632 0.00 0.00 42.54 4.18
8268 8720 1.279840 GTTGCAAGTGGAGCACGTC 59.720 57.895 0.00 0.00 42.54 4.34
8269 8721 2.534019 CGTTGCAAGTGGAGCACGT 61.534 57.895 0.00 0.00 42.54 4.49
8270 8722 2.249309 CGTTGCAAGTGGAGCACG 59.751 61.111 0.00 0.00 42.54 5.34
8271 8723 1.009675 CACGTTGCAAGTGGAGCAC 60.010 57.895 16.58 0.00 42.54 4.40
8414 8866 3.103742 TGTGCACCACATATGTAGGAGA 58.896 45.455 23.07 9.37 39.62 3.71


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

AutoCloner maintained by Alex Coulton.