Multiple sequence alignment - TraesCS5A01G043100

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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 TraesCS5A01G043100 chr5A 100.000 3787 0 0 2799 6585 38802842 38806628 0.000000e+00 6994.0
1 TraesCS5A01G043100 chr5A 100.000 2575 0 0 1 2575 38800044 38802618 0.000000e+00 4756.0
2 TraesCS5A01G043100 chr5A 100.000 30 0 0 5591 5620 38804145 38804116 1.000000e-03 56.5
3 TraesCS5A01G043100 chr5A 100.000 30 0 0 4073 4102 38805663 38805634 1.000000e-03 56.5
4 TraesCS5A01G043100 chr5D 94.458 2833 113 19 2799 5594 49477140 49479965 0.000000e+00 4322.0
5 TraesCS5A01G043100 chr5D 93.234 1685 72 19 922 2575 49475082 49476755 0.000000e+00 2442.0
6 TraesCS5A01G043100 chr5D 99.286 560 4 0 5789 6348 49480449 49481008 0.000000e+00 1013.0
7 TraesCS5A01G043100 chr5D 97.844 371 8 0 6215 6585 49480943 49481313 5.570000e-180 641.0
8 TraesCS5A01G043100 chr5D 89.807 363 32 3 1 358 49473845 49474207 1.670000e-125 460.0
9 TraesCS5A01G043100 chr5D 98.830 171 2 0 5619 5789 49480244 49480414 8.300000e-79 305.0
10 TraesCS5A01G043100 chr5D 97.015 134 4 0 6215 6348 49480909 49481042 6.640000e-55 226.0
11 TraesCS5A01G043100 chr5D 95.000 100 5 0 6249 6348 49480875 49480974 2.460000e-34 158.0
12 TraesCS5A01G043100 chr5D 94.737 38 1 1 5583 5620 49478480 49478444 2.560000e-04 58.4
13 TraesCS5A01G043100 chr5D 100.000 28 0 0 607 634 49474599 49474626 1.200000e-02 52.8
14 TraesCS5A01G043100 chr5B 92.297 2817 112 39 2821 5571 52001323 52004100 0.000000e+00 3903.0
15 TraesCS5A01G043100 chr5B 93.209 1502 62 18 1086 2554 51999497 52000991 0.000000e+00 2172.0
16 TraesCS5A01G043100 chr5B 96.931 554 17 0 5795 6348 52004590 52005143 0.000000e+00 929.0
17 TraesCS5A01G043100 chr5B 96.226 371 14 0 6215 6585 52005146 52005516 5.650000e-170 608.0
18 TraesCS5A01G043100 chr5B 96.269 134 5 0 6215 6348 52005078 52005211 3.090000e-53 220.0
19 TraesCS5A01G043100 chr5B 95.522 134 6 0 6215 6348 52005112 52005245 1.440000e-51 215.0
20 TraesCS5A01G043100 chr5B 86.432 199 19 4 845 1041 51998809 51999001 1.860000e-50 211.0
21 TraesCS5A01G043100 chr5B 94.776 134 7 0 6215 6348 52005044 52005177 6.690000e-50 209.0
22 TraesCS5A01G043100 chr5B 86.224 196 22 2 167 358 51997947 51998141 2.410000e-49 207.0
23 TraesCS5A01G043100 chr5B 95.283 106 5 0 5684 5789 52004449 52004554 1.140000e-37 169.0
24 TraesCS5A01G043100 chr5B 88.372 129 12 2 1 127 51997822 51997949 1.140000e-32 152.0
25 TraesCS5A01G043100 chr5B 89.076 119 13 0 360 478 51998249 51998367 1.480000e-31 148.0
26 TraesCS5A01G043100 chr5B 97.778 45 1 0 5619 5663 52004407 52004451 1.970000e-10 78.7
27 TraesCS5A01G043100 chr5B 94.737 38 1 1 5583 5620 52002639 52002603 2.560000e-04 58.4
28 TraesCS5A01G043100 chrUn 100.000 390 0 0 5789 6178 480013863 480013474 0.000000e+00 721.0
29 TraesCS5A01G043100 chr3B 91.544 272 22 1 4517 4788 70844443 70844713 2.240000e-99 374.0
30 TraesCS5A01G043100 chr3B 95.217 230 11 0 4292 4521 70828420 70828649 1.350000e-96 364.0
31 TraesCS5A01G043100 chr3B 92.424 66 5 0 674 739 546195849 546195914 1.950000e-15 95.3
32 TraesCS5A01G043100 chr3D 87.500 48 4 2 1379 1425 118592028 118591982 3.000000e-03 54.7


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 TraesCS5A01G043100 chr5A 38800044 38806628 6584 False 5875.000000 6994 100.000000 1 6585 2 chr5A.!!$F1 6584
1 TraesCS5A01G043100 chr5D 49473845 49481313 7468 False 1068.866667 4322 96.163778 1 6585 9 chr5D.!!$F1 6584
2 TraesCS5A01G043100 chr5B 51997822 52005516 7694 False 709.361538 3903 92.953462 1 6585 13 chr5B.!!$F1 6584

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
911 1215 0.404426 GGTGAAAGTGGGCCTAGGTT 59.596 55.000 11.31 0.0 0.00 3.50 F
1580 2595 0.178987 TTGCCACCCGGTTGTATTGT 60.179 50.000 0.00 0.0 33.28 2.71 F
2210 3244 0.250295 TCCCGACAGAAGCAAACCAG 60.250 55.000 0.00 0.0 0.00 4.00 F
3385 4742 0.321671 CTTTCGGCCTGGACTCTTCA 59.678 55.000 0.00 0.0 0.00 3.02 F
3635 4992 2.163613 ACGATCAGATAACGCTGTGTGA 59.836 45.455 0.00 0.0 37.20 3.58 F
3656 5040 2.235845 TCATCTGCATGTCTAGCTGC 57.764 50.000 0.00 0.0 38.87 5.25 F
5033 6428 0.101219 GGGTTGCAATTCATCGGCTC 59.899 55.000 0.59 0.0 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2183 3217 0.247736 CTTCTGTCGGGACCTTCTGG 59.752 60.000 0.00 0.00 39.83 3.86 R
3370 4727 1.515020 CTCTGAAGAGTCCAGGCCG 59.485 63.158 0.00 0.00 37.40 6.13 R
3900 5284 1.131638 ACTCCAAAGACACAGCAGGA 58.868 50.000 0.00 0.00 0.00 3.86 R
4694 6084 0.877071 CAGCAACAATGAAGCGTCCT 59.123 50.000 0.00 0.00 0.00 3.85 R
4994 6389 1.267806 CCATTCTTTGCTGTTGCGACT 59.732 47.619 5.50 0.00 43.34 4.18 R
5157 6552 1.592081 CTGTATCTTTCAGCTGCGAGC 59.408 52.381 9.47 3.87 42.84 5.03 R
6395 8262 4.227864 AGCTATAAAGGCTTGTCTTGCT 57.772 40.909 0.00 4.90 36.56 3.91 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
26 27 1.418264 TCGGGGTGAAAATCAGTGACA 59.582 47.619 0.00 0.00 0.00 3.58
28 29 2.819608 CGGGGTGAAAATCAGTGACAAT 59.180 45.455 0.00 0.00 0.00 2.71
29 30 4.006989 CGGGGTGAAAATCAGTGACAATA 58.993 43.478 0.00 0.00 0.00 1.90
83 85 1.377994 CAGCCAGGGGATCCTATGC 59.622 63.158 12.58 9.62 42.67 3.14
135 137 5.185454 TCTGTTGGTGGTCATTATAGCAAG 58.815 41.667 0.00 0.00 33.14 4.01
144 146 4.445735 GGTCATTATAGCAAGGGGTAAGCA 60.446 45.833 0.00 0.00 0.00 3.91
159 161 0.621571 AAGCAGGATGGCTAGGTGGA 60.622 55.000 0.00 0.00 45.07 4.02
170 172 2.324541 GCTAGGTGGATGGTCTCATCT 58.675 52.381 6.37 0.00 46.70 2.90
191 193 6.406692 TCTAGGAAATCTATTGACGGGAAG 57.593 41.667 0.00 0.00 0.00 3.46
192 194 5.897824 TCTAGGAAATCTATTGACGGGAAGT 59.102 40.000 0.00 0.00 0.00 3.01
218 220 5.709164 GGTATCATTCTCTAGTAAGCGGGTA 59.291 44.000 0.00 0.00 0.00 3.69
293 295 8.907222 ACAAATCATTTACCTTTTTGAGCAAT 57.093 26.923 0.00 0.00 32.88 3.56
313 315 6.483640 AGCAATTGTCCGGACTTAAGATATTC 59.516 38.462 33.39 12.79 0.00 1.75
314 316 6.260050 GCAATTGTCCGGACTTAAGATATTCA 59.740 38.462 33.39 7.53 0.00 2.57
423 536 6.587273 TGATGTAATATGGTGGACGATTTGA 58.413 36.000 0.00 0.00 0.00 2.69
425 538 7.719193 TGATGTAATATGGTGGACGATTTGATT 59.281 33.333 0.00 0.00 0.00 2.57
426 539 7.873719 TGTAATATGGTGGACGATTTGATTT 57.126 32.000 0.00 0.00 0.00 2.17
471 584 2.640989 CCACTGGAACGACGACGA 59.359 61.111 15.32 0.00 42.66 4.20
515 810 1.944430 GCTGGGTTTGGAGGTTCGTAG 60.944 57.143 0.00 0.00 0.00 3.51
519 823 2.007608 GGTTTGGAGGTTCGTAGATGC 58.992 52.381 0.00 0.00 35.04 3.91
532 836 3.321968 TCGTAGATGCTTGAGCCATGTAT 59.678 43.478 0.00 0.00 41.18 2.29
535 839 5.335976 CGTAGATGCTTGAGCCATGTATAGA 60.336 44.000 0.00 0.00 41.18 1.98
543 847 6.039717 GCTTGAGCCATGTATAGAAAAATCCA 59.960 38.462 0.00 0.00 34.31 3.41
546 850 7.944061 TGAGCCATGTATAGAAAAATCCATTG 58.056 34.615 0.00 0.00 0.00 2.82
559 863 8.165397 AGAAAAATCCATTGGATGTCCATTTTT 58.835 29.630 18.87 18.58 46.97 1.94
585 889 3.937814 TGGACCATGTACAGATTGTGTC 58.062 45.455 0.33 5.14 40.94 3.67
586 890 3.582647 TGGACCATGTACAGATTGTGTCT 59.417 43.478 0.33 0.00 40.94 3.41
587 891 4.041567 TGGACCATGTACAGATTGTGTCTT 59.958 41.667 0.33 0.00 40.94 3.01
588 892 5.003804 GGACCATGTACAGATTGTGTCTTT 58.996 41.667 0.33 0.00 40.94 2.52
589 893 5.473504 GGACCATGTACAGATTGTGTCTTTT 59.526 40.000 0.33 0.00 40.94 2.27
590 894 6.348540 GGACCATGTACAGATTGTGTCTTTTC 60.349 42.308 0.33 0.00 40.94 2.29
591 895 6.299141 ACCATGTACAGATTGTGTCTTTTCT 58.701 36.000 0.33 0.00 40.94 2.52
592 896 7.450074 ACCATGTACAGATTGTGTCTTTTCTA 58.550 34.615 0.33 0.00 40.94 2.10
593 897 7.604164 ACCATGTACAGATTGTGTCTTTTCTAG 59.396 37.037 0.33 0.00 40.94 2.43
594 898 7.065085 CCATGTACAGATTGTGTCTTTTCTAGG 59.935 40.741 0.33 0.00 40.94 3.02
595 899 6.464222 TGTACAGATTGTGTCTTTTCTAGGG 58.536 40.000 0.00 0.00 40.94 3.53
596 900 5.825593 ACAGATTGTGTCTTTTCTAGGGA 57.174 39.130 0.00 0.00 31.90 4.20
598 902 6.601332 ACAGATTGTGTCTTTTCTAGGGAAA 58.399 36.000 0.00 0.00 35.62 3.13
600 904 7.175641 ACAGATTGTGTCTTTTCTAGGGAAATG 59.824 37.037 0.00 0.00 36.66 2.32
601 905 7.175641 CAGATTGTGTCTTTTCTAGGGAAATGT 59.824 37.037 0.00 0.00 40.57 2.71
602 906 6.877611 TTGTGTCTTTTCTAGGGAAATGTC 57.122 37.500 0.00 0.00 40.57 3.06
603 907 6.187727 TGTGTCTTTTCTAGGGAAATGTCT 57.812 37.500 0.00 0.00 40.57 3.41
604 908 5.997746 TGTGTCTTTTCTAGGGAAATGTCTG 59.002 40.000 0.00 0.00 40.57 3.51
605 909 6.183361 TGTGTCTTTTCTAGGGAAATGTCTGA 60.183 38.462 0.00 0.00 40.57 3.27
634 938 1.358787 TGGACAATTGGGGAAGAGCAT 59.641 47.619 10.83 0.00 0.00 3.79
635 939 2.225343 TGGACAATTGGGGAAGAGCATT 60.225 45.455 10.83 0.00 0.00 3.56
636 940 2.167075 GGACAATTGGGGAAGAGCATTG 59.833 50.000 10.83 0.00 0.00 2.82
637 941 2.827921 GACAATTGGGGAAGAGCATTGT 59.172 45.455 10.83 0.00 40.07 2.71
638 942 3.242011 ACAATTGGGGAAGAGCATTGTT 58.758 40.909 10.83 0.00 35.05 2.83
639 943 3.007182 ACAATTGGGGAAGAGCATTGTTG 59.993 43.478 10.83 0.00 35.05 3.33
641 945 0.776810 TGGGGAAGAGCATTGTTGGA 59.223 50.000 0.00 0.00 0.00 3.53
642 946 1.358787 TGGGGAAGAGCATTGTTGGAT 59.641 47.619 0.00 0.00 0.00 3.41
643 947 2.580322 TGGGGAAGAGCATTGTTGGATA 59.420 45.455 0.00 0.00 0.00 2.59
644 948 2.952310 GGGGAAGAGCATTGTTGGATAC 59.048 50.000 0.00 0.00 0.00 2.24
660 964 5.899631 TGGATACACCCCCTAGTTTTATC 57.100 43.478 0.00 0.00 46.17 1.75
661 965 5.544682 TGGATACACCCCCTAGTTTTATCT 58.455 41.667 0.00 0.00 46.17 1.98
662 966 6.695624 TGGATACACCCCCTAGTTTTATCTA 58.304 40.000 0.00 0.00 46.17 1.98
663 967 6.556116 TGGATACACCCCCTAGTTTTATCTAC 59.444 42.308 0.00 0.00 46.17 2.59
664 968 6.556116 GGATACACCCCCTAGTTTTATCTACA 59.444 42.308 0.00 0.00 0.00 2.74
665 969 7.071572 GGATACACCCCCTAGTTTTATCTACAA 59.928 40.741 0.00 0.00 0.00 2.41
666 970 6.309389 ACACCCCCTAGTTTTATCTACAAG 57.691 41.667 0.00 0.00 0.00 3.16
667 971 5.123936 CACCCCCTAGTTTTATCTACAAGC 58.876 45.833 0.00 0.00 0.00 4.01
668 972 5.037598 ACCCCCTAGTTTTATCTACAAGCT 58.962 41.667 0.00 0.00 0.00 3.74
669 973 5.130643 ACCCCCTAGTTTTATCTACAAGCTC 59.869 44.000 0.00 0.00 0.00 4.09
670 974 5.367060 CCCCCTAGTTTTATCTACAAGCTCT 59.633 44.000 0.00 0.00 0.00 4.09
671 975 6.126739 CCCCCTAGTTTTATCTACAAGCTCTT 60.127 42.308 0.00 0.00 0.00 2.85
672 976 7.070821 CCCCCTAGTTTTATCTACAAGCTCTTA 59.929 40.741 0.00 0.00 0.00 2.10
673 977 8.145122 CCCCTAGTTTTATCTACAAGCTCTTAG 58.855 40.741 0.00 0.00 0.00 2.18
674 978 8.697292 CCCTAGTTTTATCTACAAGCTCTTAGT 58.303 37.037 0.00 0.00 0.00 2.24
682 986 9.731819 TTATCTACAAGCTCTTAGTTAACGATG 57.268 33.333 0.00 0.00 0.00 3.84
683 987 7.154435 TCTACAAGCTCTTAGTTAACGATGT 57.846 36.000 0.00 0.00 0.00 3.06
684 988 8.272545 TCTACAAGCTCTTAGTTAACGATGTA 57.727 34.615 0.00 0.00 0.00 2.29
685 989 8.733458 TCTACAAGCTCTTAGTTAACGATGTAA 58.267 33.333 0.00 0.00 0.00 2.41
686 990 7.813852 ACAAGCTCTTAGTTAACGATGTAAG 57.186 36.000 0.00 3.29 0.00 2.34
687 991 7.376615 ACAAGCTCTTAGTTAACGATGTAAGT 58.623 34.615 10.46 0.00 0.00 2.24
688 992 7.871463 ACAAGCTCTTAGTTAACGATGTAAGTT 59.129 33.333 10.46 0.00 35.75 2.66
689 993 8.709646 CAAGCTCTTAGTTAACGATGTAAGTTT 58.290 33.333 10.46 3.51 33.42 2.66
690 994 8.240883 AGCTCTTAGTTAACGATGTAAGTTTG 57.759 34.615 10.46 5.82 33.42 2.93
691 995 8.086522 AGCTCTTAGTTAACGATGTAAGTTTGA 58.913 33.333 10.46 0.00 33.42 2.69
692 996 8.870879 GCTCTTAGTTAACGATGTAAGTTTGAT 58.129 33.333 10.46 0.00 33.42 2.57
698 1002 9.268268 AGTTAACGATGTAAGTTTGATTTGAGA 57.732 29.630 0.00 0.00 33.42 3.27
701 1005 7.905604 ACGATGTAAGTTTGATTTGAGATGA 57.094 32.000 0.00 0.00 0.00 2.92
702 1006 8.322906 ACGATGTAAGTTTGATTTGAGATGAA 57.677 30.769 0.00 0.00 0.00 2.57
703 1007 8.950210 ACGATGTAAGTTTGATTTGAGATGAAT 58.050 29.630 0.00 0.00 0.00 2.57
714 1018 8.806429 TGATTTGAGATGAATAAAACTAGCCA 57.194 30.769 0.00 0.00 0.00 4.75
715 1019 9.412460 TGATTTGAGATGAATAAAACTAGCCAT 57.588 29.630 0.00 0.00 0.00 4.40
716 1020 9.674824 GATTTGAGATGAATAAAACTAGCCATG 57.325 33.333 0.00 0.00 0.00 3.66
717 1021 8.806429 TTTGAGATGAATAAAACTAGCCATGA 57.194 30.769 0.00 0.00 0.00 3.07
718 1022 8.806429 TTGAGATGAATAAAACTAGCCATGAA 57.194 30.769 0.00 0.00 0.00 2.57
719 1023 8.442632 TGAGATGAATAAAACTAGCCATGAAG 57.557 34.615 0.00 0.00 0.00 3.02
720 1024 7.500227 TGAGATGAATAAAACTAGCCATGAAGG 59.500 37.037 0.00 0.00 41.84 3.46
731 1035 2.205022 CCATGAAGGCCTTCTTGTCA 57.795 50.000 38.85 26.64 40.82 3.58
732 1036 2.517959 CCATGAAGGCCTTCTTGTCAA 58.482 47.619 38.85 25.07 40.82 3.18
733 1037 2.892852 CCATGAAGGCCTTCTTGTCAAA 59.107 45.455 38.85 24.48 40.82 2.69
734 1038 3.321682 CCATGAAGGCCTTCTTGTCAAAA 59.678 43.478 38.85 23.89 40.82 2.44
735 1039 4.202243 CCATGAAGGCCTTCTTGTCAAAAA 60.202 41.667 38.85 23.31 40.82 1.94
792 1096 6.408107 TTTTTAGGGGAATTGTTTTAGCGT 57.592 33.333 0.00 0.00 0.00 5.07
803 1107 2.809696 TGTTTTAGCGTTAGTTGCTCCC 59.190 45.455 0.00 0.00 42.85 4.30
839 1143 7.517614 AAATTTTGAGAAGAGAAGAACTCCC 57.482 36.000 0.00 0.00 45.96 4.30
840 1144 3.944055 TTGAGAAGAGAAGAACTCCCG 57.056 47.619 0.00 0.00 45.96 5.14
841 1145 1.546476 TGAGAAGAGAAGAACTCCCGC 59.454 52.381 0.00 0.00 45.96 6.13
842 1146 1.546476 GAGAAGAGAAGAACTCCCGCA 59.454 52.381 0.00 0.00 45.96 5.69
843 1147 2.167487 GAGAAGAGAAGAACTCCCGCAT 59.833 50.000 0.00 0.00 45.96 4.73
847 1151 4.762289 AGAGAAGAACTCCCGCATAAAT 57.238 40.909 0.00 0.00 45.96 1.40
884 1188 1.549950 CCACACAAATGGGCCTAGGTT 60.550 52.381 11.31 0.00 35.95 3.50
886 1190 2.632512 CACACAAATGGGCCTAGGTTTT 59.367 45.455 11.31 3.22 0.00 2.43
887 1191 3.070878 CACACAAATGGGCCTAGGTTTTT 59.929 43.478 11.31 2.87 0.00 1.94
907 1211 4.456662 TTTTTAGGTGAAAGTGGGCCTA 57.543 40.909 4.53 0.00 32.90 3.93
908 1212 3.713826 TTTAGGTGAAAGTGGGCCTAG 57.286 47.619 4.53 0.00 35.33 3.02
909 1213 1.580059 TAGGTGAAAGTGGGCCTAGG 58.420 55.000 3.67 3.67 32.90 3.02
910 1214 0.475828 AGGTGAAAGTGGGCCTAGGT 60.476 55.000 11.31 0.00 0.00 3.08
911 1215 0.404426 GGTGAAAGTGGGCCTAGGTT 59.596 55.000 11.31 0.00 0.00 3.50
912 1216 1.203013 GGTGAAAGTGGGCCTAGGTTT 60.203 52.381 11.31 2.02 0.00 3.27
953 1507 2.439104 GGCCCACAAAAAGCCCACA 61.439 57.895 0.00 0.00 41.00 4.17
978 1532 4.832608 GCTAACTGGGCGGTCGGG 62.833 72.222 0.00 0.00 0.00 5.14
1010 1564 2.671619 CCCGCCGCAGAAAGGAAA 60.672 61.111 0.00 0.00 0.00 3.13
1027 1582 6.971726 AAGGAAACCTAAAACCCTAACTTG 57.028 37.500 0.00 0.00 31.13 3.16
1030 1585 2.786777 ACCTAAAACCCTAACTTGCCG 58.213 47.619 0.00 0.00 0.00 5.69
1237 2243 4.034258 GGGACAGCGACGACGACA 62.034 66.667 12.29 0.00 42.66 4.35
1285 2291 1.152139 GGGGATGAGGAGGAGGAGG 60.152 68.421 0.00 0.00 0.00 4.30
1293 2299 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
1294 2300 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
1295 2301 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
1296 2302 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
1297 2303 0.996762 GGAGGAGGAGGAGGAGGAGA 60.997 65.000 0.00 0.00 0.00 3.71
1298 2304 0.930726 GAGGAGGAGGAGGAGGAGAA 59.069 60.000 0.00 0.00 0.00 2.87
1354 2360 1.144093 AGGAGTACCTGGAGAGGATCG 59.856 57.143 0.00 0.00 45.92 3.69
1395 2401 0.634465 AGGAGGAAGAGGAGGAGGAC 59.366 60.000 0.00 0.00 0.00 3.85
1538 2544 3.064545 GCAGCAATTCTCTGCGAGTTTAT 59.935 43.478 11.96 0.00 45.99 1.40
1540 2546 5.220662 GCAGCAATTCTCTGCGAGTTTATTA 60.221 40.000 11.96 0.00 45.99 0.98
1541 2547 6.675486 GCAGCAATTCTCTGCGAGTTTATTAA 60.675 38.462 11.96 0.00 45.99 1.40
1545 2551 9.076596 GCAATTCTCTGCGAGTTTATTAATTTT 57.923 29.630 0.00 0.00 31.50 1.82
1548 2554 8.447787 TTCTCTGCGAGTTTATTAATTTTTGC 57.552 30.769 0.00 0.00 0.00 3.68
1565 2580 0.968405 TGCTGTCCTTCCATTTTGCC 59.032 50.000 0.00 0.00 0.00 4.52
1576 2591 0.962489 CATTTTGCCACCCGGTTGTA 59.038 50.000 0.00 0.00 33.28 2.41
1580 2595 0.178987 TTGCCACCCGGTTGTATTGT 60.179 50.000 0.00 0.00 33.28 2.71
1595 2626 4.253685 TGTATTGTTGCTTAGACTGCCTC 58.746 43.478 0.00 0.00 0.00 4.70
1608 2639 2.421424 GACTGCCTCGCTCAAATCAAAT 59.579 45.455 0.00 0.00 0.00 2.32
1610 2641 4.009675 ACTGCCTCGCTCAAATCAAATTA 58.990 39.130 0.00 0.00 0.00 1.40
1614 2645 4.741676 GCCTCGCTCAAATCAAATTAATGG 59.258 41.667 0.00 0.00 0.00 3.16
1674 2705 1.342819 GCAATTTGCAGGGTGTTACCA 59.657 47.619 16.35 0.00 44.26 3.25
1738 2769 1.893808 CCAGTGACTGCCGTTGCTT 60.894 57.895 7.16 0.00 38.71 3.91
1770 2801 1.894756 CGACAAGGGGTTTTCGGCA 60.895 57.895 0.00 0.00 0.00 5.69
1813 2844 4.222847 GGGATGTCGAGACCGGGC 62.223 72.222 6.32 0.52 36.24 6.13
1857 2888 5.072040 CAACTGAAAAGGTGTTGGTTTCT 57.928 39.130 0.00 0.00 37.85 2.52
1878 2909 2.169352 TCACCATGCTAAAGCTCCTCTC 59.831 50.000 3.26 0.00 42.66 3.20
1884 2915 5.509501 CCATGCTAAAGCTCCTCTCTCTAAG 60.510 48.000 3.26 0.00 42.66 2.18
1984 3015 3.364460 TCCATTTGTGGGATGTTCGAT 57.636 42.857 0.00 0.00 0.00 3.59
2179 3213 4.418013 AAACAAGGCAAACAAAAACTGC 57.582 36.364 0.00 0.00 35.28 4.40
2183 3217 4.157649 CAAGGCAAACAAAAACTGCAAAC 58.842 39.130 0.00 0.00 37.83 2.93
2210 3244 0.250295 TCCCGACAGAAGCAAACCAG 60.250 55.000 0.00 0.00 0.00 4.00
2220 3254 4.921515 CAGAAGCAAACCAGAACAATGATG 59.078 41.667 0.00 0.00 0.00 3.07
2236 3270 9.801714 GAACAATGATGAAAAGCAAAATTGTAG 57.198 29.630 0.00 0.00 41.70 2.74
2280 3315 7.763172 TCGTGCTTGTAAAATTGAAAATTGT 57.237 28.000 0.00 0.00 0.00 2.71
2319 3354 2.093869 TGTGACGGAATGGGTAGCTTAC 60.094 50.000 0.00 0.00 0.00 2.34
2335 3370 9.953565 GGGTAGCTTACATTATTTCCATGTATA 57.046 33.333 0.00 0.00 37.05 1.47
2361 3396 6.015434 TGTGTTGTATGTCAGAGTCATACTGT 60.015 38.462 14.28 0.00 44.35 3.55
2406 3441 6.067217 AGGCAAACCACTTATAGTTCATCT 57.933 37.500 0.00 0.00 39.06 2.90
2897 4249 3.314080 GGTCAATTCACACGGAACTTGAA 59.686 43.478 0.00 0.00 38.60 2.69
2939 4291 7.693120 CGTTTACAAGTGTAAGCTGTTTGTTTA 59.307 33.333 13.82 0.00 41.03 2.01
2948 4300 7.538678 GTGTAAGCTGTTTGTTTATGATTCAGG 59.461 37.037 0.00 0.00 0.00 3.86
3014 4370 5.411361 CAGTGTGTATAGCTTACTTTTGCCA 59.589 40.000 0.00 0.00 0.00 4.92
3030 4386 7.538575 ACTTTTGCCATGTAATATTCTGTCAC 58.461 34.615 0.00 0.00 0.00 3.67
3085 4441 3.918294 ATTGCCCAATGCTAAATTGCT 57.082 38.095 0.00 0.00 42.00 3.91
3093 4449 6.739286 GCCCAATGCTAAATTGCTAATGATGA 60.739 38.462 0.00 0.00 36.87 2.92
3147 4503 0.761802 GCCCCTGCACTAGCTTATCT 59.238 55.000 0.00 0.00 42.74 1.98
3241 4597 2.812591 CACTATTGATGCCCTCATGAGC 59.187 50.000 17.76 8.63 32.72 4.26
3352 4709 0.691078 TCAGTGGACATAGAGGGCCC 60.691 60.000 16.46 16.46 0.00 5.80
3370 4727 2.280628 CCCGTATCCTGTCTTGCTTTC 58.719 52.381 0.00 0.00 0.00 2.62
3385 4742 0.321671 CTTTCGGCCTGGACTCTTCA 59.678 55.000 0.00 0.00 0.00 3.02
3472 4829 3.244318 TGCACTGCCTATATGGTCATCAG 60.244 47.826 0.00 0.00 38.35 2.90
3493 4850 5.705441 TCAGGGTGAAATATTGACAACTGAC 59.295 40.000 17.39 4.12 30.66 3.51
3582 4939 2.800544 GCACTTAGCTCTGTTTCGTTCA 59.199 45.455 0.00 0.00 41.15 3.18
3600 4957 4.259451 CGTTCATTGTAGCTTCTACGCTTC 60.259 45.833 0.00 0.00 41.30 3.86
3612 4969 5.063438 GCTTCTACGCTTCATATGTTTGTGA 59.937 40.000 1.90 0.00 0.00 3.58
3616 4973 5.389642 ACGCTTCATATGTTTGTGATACG 57.610 39.130 1.90 0.00 32.01 3.06
3634 4991 2.530177 ACGATCAGATAACGCTGTGTG 58.470 47.619 0.00 0.00 37.20 3.82
3635 4992 2.163613 ACGATCAGATAACGCTGTGTGA 59.836 45.455 0.00 0.00 37.20 3.58
3656 5040 2.235845 TCATCTGCATGTCTAGCTGC 57.764 50.000 0.00 0.00 38.87 5.25
3674 5058 8.924303 TCTAGCTGCTTTCAATAAATAGGTAGA 58.076 33.333 7.79 0.00 41.02 2.59
3689 5073 8.840200 AAATAGGTAGACTGATAAGACCTCAA 57.160 34.615 0.00 0.00 40.92 3.02
3693 5077 7.057894 AGGTAGACTGATAAGACCTCAAGTAG 58.942 42.308 0.00 0.00 35.57 2.57
3713 5097 4.654091 AGGGTTTTCAACAATGTGTGAG 57.346 40.909 0.00 0.00 0.00 3.51
3736 5120 7.081526 AGCATGTAAATGACACTTTCATCTC 57.918 36.000 0.00 0.00 44.86 2.75
3809 5193 6.881602 CCTTTCTCTGTTAAGAAATGTAGGCT 59.118 38.462 0.00 0.00 42.68 4.58
3825 5209 9.523168 AAATGTAGGCTAAAACCTTGTAATGTA 57.477 29.630 0.00 0.00 41.50 2.29
3900 5284 3.068307 AGTCACAGTTAGTCTTTCGTGCT 59.932 43.478 0.00 0.00 0.00 4.40
3966 5350 7.986704 AGGAATATTTGTCTGGATCAGATGAT 58.013 34.615 0.72 0.00 42.73 2.45
4002 5386 6.772716 AGCTTTGGAGTGTTATGAGAAAGAAA 59.227 34.615 0.00 0.00 0.00 2.52
4106 5490 6.822170 GGTAAAAGATACTTTCTCAATCCCGT 59.178 38.462 0.00 0.00 31.78 5.28
4199 5589 4.762251 AGCTTCTTGTAGTGATTGGAAACC 59.238 41.667 0.00 0.00 0.00 3.27
4203 5593 5.630121 TCTTGTAGTGATTGGAAACCATGT 58.370 37.500 0.00 0.00 31.53 3.21
4288 5678 2.504367 GGTACTTGTGGTCAATGCAGT 58.496 47.619 0.00 0.00 32.82 4.40
4341 5731 8.853077 TCATTTCAACAACTGAGATTATGTCT 57.147 30.769 0.00 0.00 40.81 3.41
4353 5743 9.965902 ACTGAGATTATGTCTTGTTTATTCCTT 57.034 29.630 0.00 0.00 37.29 3.36
4569 5959 8.766000 TTTAACTCGCATTATTCTACTTCACA 57.234 30.769 0.00 0.00 0.00 3.58
4572 5962 5.079689 TCGCATTATTCTACTTCACACCA 57.920 39.130 0.00 0.00 0.00 4.17
4591 5981 5.778750 ACACCAGTGGTCATTACTTACTACT 59.221 40.000 13.31 0.00 37.86 2.57
4606 5996 7.878547 ACTTACTACTGTAATGACTACCCTC 57.121 40.000 0.00 0.00 37.92 4.30
4614 6004 6.070710 ACTGTAATGACTACCCTCTCTTTTCC 60.071 42.308 0.00 0.00 0.00 3.13
4654 6044 4.103357 GTCTGATCTGCAATTTGTCATGC 58.897 43.478 0.00 0.00 42.86 4.06
4768 6158 5.606348 TTTAGCTGGTGAAATTTGGTTGT 57.394 34.783 0.00 0.00 0.00 3.32
4776 6166 5.053145 GGTGAAATTTGGTTGTGTGCATAA 58.947 37.500 0.00 0.00 0.00 1.90
4791 6181 3.944015 GTGCATAATATGATCCAGAGGCC 59.056 47.826 4.14 0.00 0.00 5.19
4792 6182 3.588396 TGCATAATATGATCCAGAGGCCA 59.412 43.478 5.01 0.00 0.00 5.36
4796 6186 6.479006 CATAATATGATCCAGAGGCCAAGAA 58.521 40.000 5.01 0.00 0.00 2.52
4808 6198 3.481453 AGGCCAAGAAAGTTGTCTCTTC 58.519 45.455 5.01 0.00 29.29 2.87
4810 6200 3.885901 GGCCAAGAAAGTTGTCTCTTCTT 59.114 43.478 0.00 0.00 29.29 2.52
4811 6201 5.063880 GGCCAAGAAAGTTGTCTCTTCTTA 58.936 41.667 0.00 0.00 29.29 2.10
4850 6240 8.213518 TCTCAAGAAATGCTAACATGATAACC 57.786 34.615 0.00 0.00 36.36 2.85
4855 6250 8.438676 AGAAATGCTAACATGATAACCACTAC 57.561 34.615 0.00 0.00 36.36 2.73
4874 6269 5.744345 CACTACTGATGGTCGTTCTTATGTC 59.256 44.000 0.00 0.00 0.00 3.06
4886 6281 5.048013 TCGTTCTTATGTCTGCTCTCAAGAA 60.048 40.000 0.00 0.00 31.48 2.52
4890 6285 7.840342 TCTTATGTCTGCTCTCAAGAAATTC 57.160 36.000 0.00 0.00 0.00 2.17
4897 6292 3.994392 TGCTCTCAAGAAATTCCGTGTAC 59.006 43.478 0.00 0.00 0.00 2.90
4912 6307 2.981875 GTGTACCAGCACGAAACAAAG 58.018 47.619 0.00 0.00 0.00 2.77
4914 6309 2.353269 TGTACCAGCACGAAACAAAGTG 59.647 45.455 0.00 0.00 41.01 3.16
4982 6377 3.165087 TCTTAGGAACCTCGTCTTGGA 57.835 47.619 0.00 0.00 0.00 3.53
4994 6389 0.610785 GTCTTGGAAAATGGGGCCGA 60.611 55.000 0.00 0.00 0.00 5.54
5033 6428 0.101219 GGGTTGCAATTCATCGGCTC 59.899 55.000 0.59 0.00 0.00 4.70
5190 6585 4.993705 AAGATACAGGAAGGTTGAACCA 57.006 40.909 17.83 0.00 41.95 3.67
5369 6764 0.036388 CCATTGTAGACGGCAGGTGT 60.036 55.000 0.00 0.00 0.00 4.16
5427 6847 7.147312 TGAAATGATTGTCACAGGAAATTGTC 58.853 34.615 0.00 0.00 0.00 3.18
5594 7016 9.734984 TGGTAGATATATCTCAGACGTAATTGA 57.265 33.333 18.59 0.00 38.32 2.57
5605 7027 8.740906 TCTCAGACGTAATTGAGAAAGTATCTT 58.259 33.333 18.95 0.00 44.92 2.40
5606 7028 9.360093 CTCAGACGTAATTGAGAAAGTATCTTT 57.640 33.333 15.42 0.00 42.67 2.52
5607 7029 9.706691 TCAGACGTAATTGAGAAAGTATCTTTT 57.293 29.630 0.00 0.00 38.96 2.27
5616 7038 7.996098 TGAGAAAGTATCTTTTACCTTTGGG 57.004 36.000 0.00 0.00 38.96 4.12
5617 7039 6.433093 TGAGAAAGTATCTTTTACCTTTGGGC 59.567 38.462 0.00 0.00 38.96 5.36
6395 8262 3.973458 TGGTTGTCCGGTTCCAGA 58.027 55.556 0.00 0.00 36.30 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.039746 TGTCACTGATTTTCACCCCGAT 59.960 45.455 0.00 0.00 0.00 4.18
26 27 9.457436 AGGTTTTAAAATAGTGGTCGATGTATT 57.543 29.630 3.52 0.00 0.00 1.89
28 29 9.590451 CTAGGTTTTAAAATAGTGGTCGATGTA 57.410 33.333 3.52 0.00 0.00 2.29
29 30 7.551617 CCTAGGTTTTAAAATAGTGGTCGATGT 59.448 37.037 3.52 0.00 0.00 3.06
53 55 3.185203 TGGCTGCAACCCCTTCCT 61.185 61.111 3.10 0.00 0.00 3.36
83 85 3.381272 ACAATGTTGAATAGGATTGGCGG 59.619 43.478 0.00 0.00 31.34 6.13
135 137 0.398318 CTAGCCATCCTGCTTACCCC 59.602 60.000 0.00 0.00 42.75 4.95
144 146 0.029681 ACCATCCACCTAGCCATCCT 60.030 55.000 0.00 0.00 0.00 3.24
159 161 8.592809 GTCAATAGATTTCCTAGATGAGACCAT 58.407 37.037 0.00 0.00 31.71 3.55
170 172 5.163343 CCACTTCCCGTCAATAGATTTCCTA 60.163 44.000 0.00 0.00 0.00 2.94
191 193 5.462405 CGCTTACTAGAGAATGATACCCAC 58.538 45.833 0.00 0.00 0.00 4.61
192 194 4.523173 CCGCTTACTAGAGAATGATACCCA 59.477 45.833 0.00 0.00 0.00 4.51
226 228 3.749088 TCACGTCGTGCTCCATAAAAATT 59.251 39.130 20.56 0.00 32.98 1.82
279 281 2.035832 CCGGACAATTGCTCAAAAAGGT 59.964 45.455 5.05 0.00 0.00 3.50
286 288 3.007506 TCTTAAGTCCGGACAATTGCTCA 59.992 43.478 35.00 9.16 0.00 4.26
293 295 9.893634 TTTTATGAATATCTTAAGTCCGGACAA 57.106 29.630 35.00 20.76 0.00 3.18
314 316 9.578439 GCTCAAAGCAGAATAATTCACTTTTAT 57.422 29.630 0.00 0.00 41.89 1.40
342 349 6.650120 ACTTGTTTACTCTTCCTCTTTGACA 58.350 36.000 0.00 0.00 0.00 3.58
376 489 4.583073 AGTTTTCCTTTACAACGGCTGAAT 59.417 37.500 0.00 0.00 0.00 2.57
382 495 5.432885 ACATCAGTTTTCCTTTACAACGG 57.567 39.130 0.00 0.00 0.00 4.44
388 501 9.184523 CCACCATATTACATCAGTTTTCCTTTA 57.815 33.333 0.00 0.00 0.00 1.85
457 570 1.002250 CCTTGTCGTCGTCGTTCCAG 61.002 60.000 1.33 0.00 38.33 3.86
487 782 0.606604 TCCAAACCCAGCTCGTCTAC 59.393 55.000 0.00 0.00 0.00 2.59
492 787 0.955919 GAACCTCCAAACCCAGCTCG 60.956 60.000 0.00 0.00 0.00 5.03
493 788 0.955919 CGAACCTCCAAACCCAGCTC 60.956 60.000 0.00 0.00 0.00 4.09
494 789 1.073199 CGAACCTCCAAACCCAGCT 59.927 57.895 0.00 0.00 0.00 4.24
515 810 6.624352 TTTTCTATACATGGCTCAAGCATC 57.376 37.500 4.13 0.00 44.36 3.91
519 823 7.572523 TGGATTTTTCTATACATGGCTCAAG 57.427 36.000 0.00 0.00 0.00 3.02
559 863 6.945435 ACACAATCTGTACATGGTCCAAATAA 59.055 34.615 0.00 0.00 0.00 1.40
564 868 3.582647 AGACACAATCTGTACATGGTCCA 59.417 43.478 0.00 0.00 35.81 4.02
565 869 4.207891 AGACACAATCTGTACATGGTCC 57.792 45.455 0.00 0.00 35.81 4.46
566 870 6.428159 AGAAAAGACACAATCTGTACATGGTC 59.572 38.462 0.00 2.73 37.88 4.02
574 878 5.825593 TCCCTAGAAAAGACACAATCTGT 57.174 39.130 0.00 0.00 37.88 3.41
575 879 7.175641 ACATTTCCCTAGAAAAGACACAATCTG 59.824 37.037 0.00 0.00 44.91 2.90
585 889 7.391554 TCAACATCAGACATTTCCCTAGAAAAG 59.608 37.037 0.00 0.00 44.91 2.27
586 890 7.230747 TCAACATCAGACATTTCCCTAGAAAA 58.769 34.615 0.00 0.00 44.91 2.29
587 891 6.778821 TCAACATCAGACATTTCCCTAGAAA 58.221 36.000 0.00 0.00 45.78 2.52
588 892 6.213397 TCTCAACATCAGACATTTCCCTAGAA 59.787 38.462 0.00 0.00 0.00 2.10
589 893 5.721480 TCTCAACATCAGACATTTCCCTAGA 59.279 40.000 0.00 0.00 0.00 2.43
590 894 5.982356 TCTCAACATCAGACATTTCCCTAG 58.018 41.667 0.00 0.00 0.00 3.02
591 895 6.351711 CATCTCAACATCAGACATTTCCCTA 58.648 40.000 0.00 0.00 0.00 3.53
592 896 4.916041 TCTCAACATCAGACATTTCCCT 57.084 40.909 0.00 0.00 0.00 4.20
593 897 4.337555 CCATCTCAACATCAGACATTTCCC 59.662 45.833 0.00 0.00 0.00 3.97
594 898 5.065731 GTCCATCTCAACATCAGACATTTCC 59.934 44.000 0.00 0.00 0.00 3.13
595 899 5.645067 TGTCCATCTCAACATCAGACATTTC 59.355 40.000 0.00 0.00 0.00 2.17
596 900 5.563592 TGTCCATCTCAACATCAGACATTT 58.436 37.500 0.00 0.00 0.00 2.32
598 902 4.831674 TGTCCATCTCAACATCAGACAT 57.168 40.909 0.00 0.00 0.00 3.06
600 904 5.163683 CCAATTGTCCATCTCAACATCAGAC 60.164 44.000 4.43 0.00 0.00 3.51
601 905 4.945543 CCAATTGTCCATCTCAACATCAGA 59.054 41.667 4.43 0.00 0.00 3.27
602 906 4.097437 CCCAATTGTCCATCTCAACATCAG 59.903 45.833 4.43 0.00 0.00 2.90
603 907 4.018490 CCCAATTGTCCATCTCAACATCA 58.982 43.478 4.43 0.00 0.00 3.07
604 908 3.382546 CCCCAATTGTCCATCTCAACATC 59.617 47.826 4.43 0.00 0.00 3.06
605 909 3.011595 TCCCCAATTGTCCATCTCAACAT 59.988 43.478 4.43 0.00 0.00 2.71
634 938 2.923908 ACTAGGGGGTGTATCCAACAA 58.076 47.619 0.00 0.00 40.63 2.83
635 939 2.653543 ACTAGGGGGTGTATCCAACA 57.346 50.000 0.00 0.00 38.11 3.33
636 940 4.311520 AAAACTAGGGGGTGTATCCAAC 57.688 45.455 0.00 0.00 38.11 3.77
637 941 5.974370 AGATAAAACTAGGGGGTGTATCCAA 59.026 40.000 0.00 0.00 38.11 3.53
638 942 5.544682 AGATAAAACTAGGGGGTGTATCCA 58.455 41.667 0.00 0.00 38.11 3.41
639 943 6.556116 TGTAGATAAAACTAGGGGGTGTATCC 59.444 42.308 0.00 0.00 0.00 2.59
641 945 7.419865 GCTTGTAGATAAAACTAGGGGGTGTAT 60.420 40.741 0.00 0.00 0.00 2.29
642 946 6.126968 GCTTGTAGATAAAACTAGGGGGTGTA 60.127 42.308 0.00 0.00 0.00 2.90
643 947 5.338953 GCTTGTAGATAAAACTAGGGGGTGT 60.339 44.000 0.00 0.00 0.00 4.16
644 948 5.104485 AGCTTGTAGATAAAACTAGGGGGTG 60.104 44.000 0.00 0.00 0.00 4.61
645 949 5.037598 AGCTTGTAGATAAAACTAGGGGGT 58.962 41.667 0.00 0.00 0.00 4.95
656 960 9.731819 CATCGTTAACTAAGAGCTTGTAGATAA 57.268 33.333 10.66 7.22 0.00 1.75
657 961 8.900781 ACATCGTTAACTAAGAGCTTGTAGATA 58.099 33.333 10.66 2.18 0.00 1.98
658 962 7.773149 ACATCGTTAACTAAGAGCTTGTAGAT 58.227 34.615 10.66 3.00 0.00 1.98
659 963 7.154435 ACATCGTTAACTAAGAGCTTGTAGA 57.846 36.000 10.66 0.00 0.00 2.59
660 964 8.906636 TTACATCGTTAACTAAGAGCTTGTAG 57.093 34.615 3.71 0.00 0.00 2.74
661 965 8.517878 ACTTACATCGTTAACTAAGAGCTTGTA 58.482 33.333 15.49 3.23 0.00 2.41
662 966 7.376615 ACTTACATCGTTAACTAAGAGCTTGT 58.623 34.615 15.49 4.02 0.00 3.16
663 967 7.813852 ACTTACATCGTTAACTAAGAGCTTG 57.186 36.000 15.49 0.00 0.00 4.01
664 968 8.709646 CAAACTTACATCGTTAACTAAGAGCTT 58.290 33.333 15.49 6.42 0.00 3.74
665 969 8.086522 TCAAACTTACATCGTTAACTAAGAGCT 58.913 33.333 15.49 0.00 0.00 4.09
666 970 8.236084 TCAAACTTACATCGTTAACTAAGAGC 57.764 34.615 15.49 0.00 0.00 4.09
672 976 9.268268 TCTCAAATCAAACTTACATCGTTAACT 57.732 29.630 3.71 0.00 0.00 2.24
675 979 9.430623 TCATCTCAAATCAAACTTACATCGTTA 57.569 29.630 0.00 0.00 0.00 3.18
676 980 8.322906 TCATCTCAAATCAAACTTACATCGTT 57.677 30.769 0.00 0.00 0.00 3.85
677 981 7.905604 TCATCTCAAATCAAACTTACATCGT 57.094 32.000 0.00 0.00 0.00 3.73
688 992 9.241919 TGGCTAGTTTTATTCATCTCAAATCAA 57.758 29.630 0.00 0.00 0.00 2.57
689 993 8.806429 TGGCTAGTTTTATTCATCTCAAATCA 57.194 30.769 0.00 0.00 0.00 2.57
690 994 9.674824 CATGGCTAGTTTTATTCATCTCAAATC 57.325 33.333 0.00 0.00 0.00 2.17
691 995 9.412460 TCATGGCTAGTTTTATTCATCTCAAAT 57.588 29.630 0.00 0.00 0.00 2.32
692 996 8.806429 TCATGGCTAGTTTTATTCATCTCAAA 57.194 30.769 0.00 0.00 0.00 2.69
693 997 8.806429 TTCATGGCTAGTTTTATTCATCTCAA 57.194 30.769 0.00 0.00 0.00 3.02
694 998 7.500227 CCTTCATGGCTAGTTTTATTCATCTCA 59.500 37.037 0.00 0.00 0.00 3.27
695 999 7.869800 CCTTCATGGCTAGTTTTATTCATCTC 58.130 38.462 0.00 0.00 0.00 2.75
696 1000 7.814264 CCTTCATGGCTAGTTTTATTCATCT 57.186 36.000 0.00 0.00 0.00 2.90
712 1016 2.205022 TGACAAGAAGGCCTTCATGG 57.795 50.000 39.46 30.91 41.14 3.66
713 1017 4.589216 TTTTGACAAGAAGGCCTTCATG 57.411 40.909 39.84 38.37 42.16 3.07
816 1120 5.703130 CGGGAGTTCTTCTCTTCTCAAAATT 59.297 40.000 0.00 0.00 42.40 1.82
818 1122 4.632153 CGGGAGTTCTTCTCTTCTCAAAA 58.368 43.478 0.00 0.00 42.40 2.44
819 1123 3.555168 GCGGGAGTTCTTCTCTTCTCAAA 60.555 47.826 0.00 0.00 42.40 2.69
820 1124 2.028930 GCGGGAGTTCTTCTCTTCTCAA 60.029 50.000 0.00 0.00 42.40 3.02
822 1126 1.546476 TGCGGGAGTTCTTCTCTTCTC 59.454 52.381 0.00 0.00 42.40 2.87
823 1127 1.633774 TGCGGGAGTTCTTCTCTTCT 58.366 50.000 0.00 0.00 42.40 2.85
825 1129 4.553330 TTTATGCGGGAGTTCTTCTCTT 57.447 40.909 0.00 0.00 42.40 2.85
826 1130 4.762289 ATTTATGCGGGAGTTCTTCTCT 57.238 40.909 0.00 0.00 42.40 3.10
827 1131 6.920569 TTTATTTATGCGGGAGTTCTTCTC 57.079 37.500 0.00 0.00 42.07 2.87
828 1132 7.110155 TCTTTTATTTATGCGGGAGTTCTTCT 58.890 34.615 0.00 0.00 0.00 2.85
829 1133 7.280205 TCTCTTTTATTTATGCGGGAGTTCTTC 59.720 37.037 0.00 0.00 0.00 2.87
830 1134 7.110155 TCTCTTTTATTTATGCGGGAGTTCTT 58.890 34.615 0.00 0.00 0.00 2.52
831 1135 6.650120 TCTCTTTTATTTATGCGGGAGTTCT 58.350 36.000 0.00 0.00 0.00 3.01
834 1138 7.227512 CAGATTCTCTTTTATTTATGCGGGAGT 59.772 37.037 0.00 0.00 0.00 3.85
835 1139 7.227512 ACAGATTCTCTTTTATTTATGCGGGAG 59.772 37.037 0.00 0.00 0.00 4.30
836 1140 7.054124 ACAGATTCTCTTTTATTTATGCGGGA 58.946 34.615 0.00 0.00 0.00 5.14
837 1141 7.264373 ACAGATTCTCTTTTATTTATGCGGG 57.736 36.000 0.00 0.00 0.00 6.13
838 1142 9.651718 GTTACAGATTCTCTTTTATTTATGCGG 57.348 33.333 0.00 0.00 0.00 5.69
839 1143 9.651718 GGTTACAGATTCTCTTTTATTTATGCG 57.348 33.333 0.00 0.00 0.00 4.73
847 1151 8.740123 TTTGTGTGGTTACAGATTCTCTTTTA 57.260 30.769 0.00 0.00 37.52 1.52
886 1190 3.322191 AGGCCCACTTTCACCTAAAAA 57.678 42.857 0.00 0.00 0.00 1.94
887 1191 3.245122 CCTAGGCCCACTTTCACCTAAAA 60.245 47.826 0.00 0.00 34.44 1.52
888 1192 2.307686 CCTAGGCCCACTTTCACCTAAA 59.692 50.000 0.00 0.00 34.44 1.85
889 1193 1.913419 CCTAGGCCCACTTTCACCTAA 59.087 52.381 0.00 0.00 34.44 2.69
890 1194 1.203389 ACCTAGGCCCACTTTCACCTA 60.203 52.381 9.30 0.00 33.60 3.08
891 1195 0.475828 ACCTAGGCCCACTTTCACCT 60.476 55.000 9.30 0.00 36.27 4.00
892 1196 0.404426 AACCTAGGCCCACTTTCACC 59.596 55.000 9.30 0.00 0.00 4.02
893 1197 2.287977 AAACCTAGGCCCACTTTCAC 57.712 50.000 9.30 0.00 0.00 3.18
894 1198 3.322191 AAAAACCTAGGCCCACTTTCA 57.678 42.857 9.30 0.00 0.00 2.69
911 1215 1.412343 GTTGAAGCTGGGCAGGAAAAA 59.588 47.619 0.00 0.00 0.00 1.94
912 1216 1.039856 GTTGAAGCTGGGCAGGAAAA 58.960 50.000 0.00 0.00 0.00 2.29
926 1230 1.561643 TTTTGTGGGCCAGTGTTGAA 58.438 45.000 6.40 0.00 0.00 2.69
953 1507 1.512156 CGCCCAGTTAGCACCGTTTT 61.512 55.000 0.00 0.00 0.00 2.43
1010 1564 2.786777 CGGCAAGTTAGGGTTTTAGGT 58.213 47.619 0.00 0.00 0.00 3.08
1047 1602 2.258013 CGCCATTGGTCGGTGTTGT 61.258 57.895 4.26 0.00 0.00 3.32
1048 1603 2.560861 CGCCATTGGTCGGTGTTG 59.439 61.111 4.26 0.00 0.00 3.33
1049 1604 3.361977 GCGCCATTGGTCGGTGTT 61.362 61.111 17.24 0.00 36.37 3.32
1268 2274 0.178935 CTCCTCCTCCTCCTCATCCC 60.179 65.000 0.00 0.00 0.00 3.85
1285 2291 1.749286 CGTCTCCTTCTCCTCCTCCTC 60.749 61.905 0.00 0.00 0.00 3.71
1293 2299 3.839432 CCGGCCGTCTCCTTCTCC 61.839 72.222 26.12 0.00 0.00 3.71
1294 2300 3.839432 CCCGGCCGTCTCCTTCTC 61.839 72.222 26.12 0.00 0.00 2.87
1395 2401 1.180315 CGTCGTCATCTTCGTCGTCG 61.180 60.000 0.00 0.00 35.85 5.12
1533 2539 8.825667 TGGAAGGACAGCAAAAATTAATAAAC 57.174 30.769 0.00 0.00 0.00 2.01
1538 2544 7.255070 GCAAAATGGAAGGACAGCAAAAATTAA 60.255 33.333 0.00 0.00 0.00 1.40
1540 2546 5.008911 GCAAAATGGAAGGACAGCAAAAATT 59.991 36.000 0.00 0.00 0.00 1.82
1541 2547 4.516321 GCAAAATGGAAGGACAGCAAAAAT 59.484 37.500 0.00 0.00 0.00 1.82
1545 2551 1.344114 GGCAAAATGGAAGGACAGCAA 59.656 47.619 0.00 0.00 0.00 3.91
1547 2553 0.968405 TGGCAAAATGGAAGGACAGC 59.032 50.000 0.00 0.00 0.00 4.40
1548 2554 1.273327 GGTGGCAAAATGGAAGGACAG 59.727 52.381 0.00 0.00 0.00 3.51
1565 2580 1.243902 AGCAACAATACAACCGGGTG 58.756 50.000 20.60 20.60 0.00 4.61
1576 2591 2.350522 CGAGGCAGTCTAAGCAACAAT 58.649 47.619 0.00 0.00 0.00 2.71
1580 2595 0.108615 GAGCGAGGCAGTCTAAGCAA 60.109 55.000 4.95 0.00 33.44 3.91
1595 2626 7.012327 TCCTACTCCATTAATTTGATTTGAGCG 59.988 37.037 0.00 0.00 0.00 5.03
1628 2659 3.619733 GCCTTGTCACATACATGAGGTGA 60.620 47.826 0.00 7.22 46.27 4.02
1630 2661 2.305635 TGCCTTGTCACATACATGAGGT 59.694 45.455 0.00 0.00 38.08 3.85
1631 2662 2.989909 TGCCTTGTCACATACATGAGG 58.010 47.619 0.00 0.00 38.61 3.86
1632 2663 4.732647 GCAATGCCTTGTCACATACATGAG 60.733 45.833 0.00 0.00 38.10 2.90
1633 2664 3.129113 GCAATGCCTTGTCACATACATGA 59.871 43.478 0.00 0.00 38.10 3.07
1634 2665 3.119424 TGCAATGCCTTGTCACATACATG 60.119 43.478 1.53 0.00 38.10 3.21
1677 2708 1.228228 GAATCCATCCTGCTGGCCA 59.772 57.895 4.71 4.71 36.16 5.36
1680 2711 4.748277 AAATTTGAATCCATCCTGCTGG 57.252 40.909 2.58 2.58 37.66 4.85
1813 2844 3.492313 GCCACAAATACTTCTCGCTTTG 58.508 45.455 0.00 0.00 35.30 2.77
1857 2888 2.169352 GAGAGGAGCTTTAGCATGGTGA 59.831 50.000 7.89 0.00 45.16 4.02
1878 2909 5.895362 ACCTGCTGGCTTCTCTTCTTAGAG 61.895 50.000 9.95 0.00 42.28 2.43
1884 2915 1.304509 GCACCTGCTGGCTTCTCTTC 61.305 60.000 9.95 0.00 38.21 2.87
1984 3015 0.902984 ACCTGTATGTGCTCCCGTGA 60.903 55.000 0.00 0.00 0.00 4.35
2010 3041 9.981114 TTAGCTCTTATATCATCGACAAATGAA 57.019 29.630 0.00 0.00 39.04 2.57
2045 3076 4.500603 AACTTGCAAGCATTTCTCTGAG 57.499 40.909 26.27 0.00 0.00 3.35
2133 3167 0.885196 GGGCCGTTACAAATTCTGCA 59.115 50.000 0.00 0.00 0.00 4.41
2183 3217 0.247736 CTTCTGTCGGGACCTTCTGG 59.752 60.000 0.00 0.00 39.83 3.86
2210 3244 9.801714 CTACAATTTTGCTTTTCATCATTGTTC 57.198 29.630 0.00 0.00 38.08 3.18
2220 3254 6.616017 AGCTAGCTCTACAATTTTGCTTTTC 58.384 36.000 12.68 0.00 35.47 2.29
2335 3370 7.038048 CAGTATGACTCTGACATACAACACAT 58.962 38.462 16.22 0.00 46.96 3.21
2346 3381 7.068348 TGGGTTATTAGACAGTATGACTCTGAC 59.932 40.741 0.00 0.00 40.99 3.51
2361 3396 7.015682 TGCCTTGATTTGTTTTGGGTTATTAGA 59.984 33.333 0.00 0.00 0.00 2.10
2406 3441 4.613925 ACAGCTCAAGAGAAACATCTCA 57.386 40.909 8.42 0.00 39.12 3.27
2862 4214 7.492669 CGTGTGAATTGACCTAAGAATACATCT 59.507 37.037 0.00 0.00 41.32 2.90
2897 4249 6.433847 TGTAAACGGATCCTGATATGGAAT 57.566 37.500 10.75 0.00 39.85 3.01
2939 4291 2.750141 AATGCTGCTCCCTGAATCAT 57.250 45.000 0.00 0.00 0.00 2.45
2948 4300 1.888512 TCCAACTGAAAATGCTGCTCC 59.111 47.619 0.00 0.00 0.00 4.70
3069 4425 6.643770 GTCATCATTAGCAATTTAGCATTGGG 59.356 38.462 0.00 0.00 36.85 4.12
3085 4441 5.951747 CCAAAAGAGGGAAAGGTCATCATTA 59.048 40.000 0.00 0.00 0.00 1.90
3147 4503 3.565764 AAAGGATCATGGATCTTGCGA 57.434 42.857 6.22 0.00 38.91 5.10
3352 4709 1.927174 CCGAAAGCAAGACAGGATACG 59.073 52.381 0.00 0.00 46.39 3.06
3370 4727 1.515020 CTCTGAAGAGTCCAGGCCG 59.485 63.158 0.00 0.00 37.40 6.13
3472 4829 4.671766 GCGTCAGTTGTCAATATTTCACCC 60.672 45.833 0.00 0.00 0.00 4.61
3493 4850 2.886081 AGTCTATCTTTGCTGAGTGCG 58.114 47.619 0.00 0.00 46.63 5.34
3612 4969 4.036380 TCACACAGCGTTATCTGATCGTAT 59.964 41.667 0.00 0.00 37.51 3.06
3616 4973 4.805719 TGAATCACACAGCGTTATCTGATC 59.194 41.667 0.00 0.00 37.51 2.92
3634 4991 3.186817 GCAGCTAGACATGCAGATGAATC 59.813 47.826 10.88 0.00 42.11 2.52
3635 4992 3.139850 GCAGCTAGACATGCAGATGAAT 58.860 45.455 10.88 0.00 42.11 2.57
3674 5058 4.949121 ACCCTACTTGAGGTCTTATCAGT 58.051 43.478 0.00 0.00 45.03 3.41
3700 5084 6.088483 GTCATTTACATGCTCACACATTGTTG 59.912 38.462 0.00 0.00 0.00 3.33
3736 5120 2.886523 TCTCCTTGGTTGCATGAAACAG 59.113 45.455 18.45 7.82 31.08 3.16
3809 5193 9.506018 GGTAAGTCCTTACATTACAAGGTTTTA 57.494 33.333 16.65 0.35 45.32 1.52
3854 5238 2.503765 TCCGGTATCTGCCAAGAAATGA 59.496 45.455 0.00 0.00 35.59 2.57
3900 5284 1.131638 ACTCCAAAGACACAGCAGGA 58.868 50.000 0.00 0.00 0.00 3.86
4102 5486 1.630244 CGCAGAAAGAGAGCAACGGG 61.630 60.000 0.00 0.00 0.00 5.28
4106 5490 5.940192 TTTTTATCGCAGAAAGAGAGCAA 57.060 34.783 0.00 0.00 43.58 3.91
4140 5524 5.765510 TCCTACCATACCTTGCATCAAAAT 58.234 37.500 0.00 0.00 0.00 1.82
4184 5574 7.681939 TCTTTACATGGTTTCCAATCACTAC 57.318 36.000 0.00 0.00 36.95 2.73
4211 5601 5.414454 TGACTAATGTTGCCTGGTCAAATAC 59.586 40.000 5.35 0.00 31.99 1.89
4217 5607 6.238759 GGAAATATGACTAATGTTGCCTGGTC 60.239 42.308 0.00 0.00 33.19 4.02
4227 5617 8.748412 TGGTGAAAAAGGGAAATATGACTAATG 58.252 33.333 0.00 0.00 0.00 1.90
4267 5657 1.464608 CTGCATTGACCACAAGTACCG 59.535 52.381 0.00 0.00 39.46 4.02
4288 5678 2.957402 ACAGGAAGGCAATGTTCTCA 57.043 45.000 0.00 0.00 0.00 3.27
4468 5858 2.294791 CCAAAGGCGAACAACACCATTA 59.705 45.455 0.00 0.00 0.00 1.90
4569 5959 5.778750 ACAGTAGTAAGTAATGACCACTGGT 59.221 40.000 10.41 0.00 39.44 4.00
4591 5981 5.105473 CGGAAAAGAGAGGGTAGTCATTACA 60.105 44.000 0.00 0.00 33.73 2.41
4592 5982 5.105432 ACGGAAAAGAGAGGGTAGTCATTAC 60.105 44.000 0.00 0.00 0.00 1.89
4606 5996 3.611766 ACAGGGTCATACGGAAAAGAG 57.388 47.619 0.00 0.00 0.00 2.85
4614 6004 4.082408 TCAGACTTACAACAGGGTCATACG 60.082 45.833 0.00 0.00 0.00 3.06
4654 6044 3.508793 AGAATTGACAAAGCCATCCTGTG 59.491 43.478 0.00 0.00 34.75 3.66
4655 6045 3.760684 GAGAATTGACAAAGCCATCCTGT 59.239 43.478 0.00 0.00 0.00 4.00
4694 6084 0.877071 CAGCAACAATGAAGCGTCCT 59.123 50.000 0.00 0.00 0.00 3.85
4768 6158 4.566278 GGCCTCTGGATCATATTATGCACA 60.566 45.833 0.00 0.00 0.00 4.57
4776 6166 4.414846 ACTTTCTTGGCCTCTGGATCATAT 59.585 41.667 3.32 0.00 0.00 1.78
4826 6216 7.912250 GTGGTTATCATGTTAGCATTTCTTGAG 59.088 37.037 0.00 0.00 31.99 3.02
4830 6220 8.267894 AGTAGTGGTTATCATGTTAGCATTTCT 58.732 33.333 0.00 0.00 31.99 2.52
4833 6223 7.564793 TCAGTAGTGGTTATCATGTTAGCATT 58.435 34.615 0.00 0.00 31.99 3.56
4849 6239 3.594603 AAGAACGACCATCAGTAGTGG 57.405 47.619 0.00 0.00 42.55 4.00
4850 6240 5.651530 ACATAAGAACGACCATCAGTAGTG 58.348 41.667 0.00 0.00 34.18 2.74
4855 6250 3.553511 GCAGACATAAGAACGACCATCAG 59.446 47.826 0.00 0.00 0.00 2.90
4864 6259 7.608308 ATTTCTTGAGAGCAGACATAAGAAC 57.392 36.000 0.00 0.00 34.87 3.01
4874 6269 3.070018 ACACGGAATTTCTTGAGAGCAG 58.930 45.455 0.00 0.00 0.00 4.24
4897 6292 1.400142 TGACACTTTGTTTCGTGCTGG 59.600 47.619 0.00 0.00 34.58 4.85
4982 6377 2.750237 GCGACTCGGCCCCATTTT 60.750 61.111 0.00 0.00 0.00 1.82
4994 6389 1.267806 CCATTCTTTGCTGTTGCGACT 59.732 47.619 5.50 0.00 43.34 4.18
5033 6428 6.507958 TCTTCAGAGTCATCTTGTAGACTG 57.492 41.667 0.00 0.00 44.61 3.51
5157 6552 1.592081 CTGTATCTTTCAGCTGCGAGC 59.408 52.381 9.47 3.87 42.84 5.03
5160 6555 2.299993 TCCTGTATCTTTCAGCTGCG 57.700 50.000 9.47 0.00 0.00 5.18
5594 7016 6.311735 TGCCCAAAGGTAAAAGATACTTTCT 58.688 36.000 0.00 0.00 33.19 2.52
5596 7018 6.987403 TTGCCCAAAGGTAAAAGATACTTT 57.013 33.333 0.00 0.00 34.42 2.66
5597 7019 6.987403 TTTGCCCAAAGGTAAAAGATACTT 57.013 33.333 0.00 0.00 43.80 2.24
5610 7032 3.828875 TGGTTTACCTTTTGCCCAAAG 57.171 42.857 0.00 0.00 41.64 2.77
5615 7037 2.929161 GCCGATTGGTTTACCTTTTGCC 60.929 50.000 0.00 0.00 37.67 4.52
5616 7038 2.333926 GCCGATTGGTTTACCTTTTGC 58.666 47.619 0.00 0.00 37.67 3.68
5617 7039 2.297597 TGGCCGATTGGTTTACCTTTTG 59.702 45.455 0.00 0.00 37.67 2.44
5623 7319 2.156098 TCTGTTGGCCGATTGGTTTAC 58.844 47.619 0.00 0.00 37.67 2.01
6395 8262 4.227864 AGCTATAAAGGCTTGTCTTGCT 57.772 40.909 0.00 4.90 36.56 3.91


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

AutoCloner maintained by Alex Coulton.