Multiple sequence alignment - TraesCS4A01G025100

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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 TraesCS4A01G025100 chr4A 100.000 4373 0 0 1 4373 17262765 17258393 0.000000e+00 8076.0
1 TraesCS4A01G025100 chr4A 94.545 55 1 2 4217 4269 121501272 121501326 2.800000e-12 84.2
2 TraesCS4A01G025100 chr4D 95.862 2803 84 6 922 3715 449731672 449734451 0.000000e+00 4505.0
3 TraesCS4A01G025100 chr4D 91.139 474 28 9 3741 4206 449734448 449734915 7.980000e-177 630.0
4 TraesCS4A01G025100 chr4D 85.175 371 16 16 11 368 449730649 449730993 1.160000e-90 344.0
5 TraesCS4A01G025100 chr4D 76.638 458 64 24 473 904 449731170 449731610 3.430000e-51 213.0
6 TraesCS4A01G025100 chr4D 93.750 112 5 2 4264 4373 449734914 449735025 2.710000e-37 167.0
7 TraesCS4A01G025100 chr4B 95.860 2802 86 6 900 3693 562355779 562358558 0.000000e+00 4505.0
8 TraesCS4A01G025100 chr4B 87.431 541 31 16 3689 4206 562358618 562359144 4.870000e-164 588.0
9 TraesCS4A01G025100 chr4B 76.251 939 104 61 42 904 562354717 562355612 5.300000e-104 388.0
10 TraesCS4A01G025100 chr4B 95.495 111 4 1 4264 4373 562359143 562359253 4.490000e-40 176.0
11 TraesCS4A01G025100 chr3A 95.522 67 3 0 3999 4065 30397390 30397456 1.660000e-19 108.0
12 TraesCS4A01G025100 chr7B 94.737 57 1 2 4220 4275 304527225 304527170 2.170000e-13 87.9
13 TraesCS4A01G025100 chr7B 92.727 55 4 0 4220 4274 670232207 670232261 3.630000e-11 80.5
14 TraesCS4A01G025100 chr2D 100.000 47 0 0 4222 4268 596007853 596007807 2.170000e-13 87.9
15 TraesCS4A01G025100 chr2D 94.444 54 1 2 4221 4274 35588359 35588308 1.010000e-11 82.4
16 TraesCS4A01G025100 chr1B 96.078 51 2 0 4220 4270 451733225 451733175 2.800000e-12 84.2
17 TraesCS4A01G025100 chr6A 92.727 55 4 0 4220 4274 447635245 447635299 3.630000e-11 80.5
18 TraesCS4A01G025100 chr5B 88.889 63 6 1 4220 4281 316712651 316712589 4.690000e-10 76.8
19 TraesCS4A01G025100 chr5A 90.164 61 3 3 4220 4277 476099431 476099371 4.690000e-10 76.8


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 TraesCS4A01G025100 chr4A 17258393 17262765 4372 True 8076.00 8076 100.00000 1 4373 1 chr4A.!!$R1 4372
1 TraesCS4A01G025100 chr4D 449730649 449735025 4376 False 1171.80 4505 88.51280 11 4373 5 chr4D.!!$F1 4362
2 TraesCS4A01G025100 chr4B 562354717 562359253 4536 False 1414.25 4505 88.75925 42 4373 4 chr4B.!!$F1 4331

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
721 856 0.109412 GATCGGACTGGTTTCGTCGT 60.109 55.000 0.00 0.00 32.24 4.34 F
734 869 0.167470 TCGTCGTTCTGGTGATCGTC 59.833 55.000 0.00 0.00 36.91 4.20 F
901 1210 1.134175 CCCCGCGTCAATTTGCTTTAT 59.866 47.619 4.92 0.00 0.00 1.40 F
2812 3122 1.007734 GTGCTCTTGGACGACGTCA 60.008 57.895 27.77 12.43 33.68 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2686 2996 0.171455 AAAGTAGCGCGAGACCTCTG 59.829 55.000 12.10 0.0 0.00 3.35 R
2697 3007 1.263776 CTCGAGCAGTCAAAGTAGCG 58.736 55.000 0.00 0.0 0.00 4.26 R
2895 3205 2.987232 AGTGGTAAAATCTCCGAAGCC 58.013 47.619 0.00 0.0 0.00 4.35 R
3796 4193 1.658095 GCTTGTCTCTGCAAGTCGATC 59.342 52.381 7.51 0.0 45.47 3.69 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
20 21 0.741915 CGGAGGGAGTAGAAGCTGAC 59.258 60.000 0.00 0.00 0.00 3.51
23 24 1.142097 GGGAGTAGAAGCTGACGGC 59.858 63.158 0.00 0.00 42.19 5.68
62 63 1.002624 GACCCTGATCGCACCCAAA 60.003 57.895 0.00 0.00 0.00 3.28
64 65 1.750399 CCCTGATCGCACCCAAAGG 60.750 63.158 0.00 0.00 40.04 3.11
71 72 2.421314 GCACCCAAAGGCACCAAC 59.579 61.111 0.00 0.00 36.11 3.77
77 78 1.300080 CAAAGGCACCAACCGCTTG 60.300 57.895 0.00 0.00 33.69 4.01
83 84 1.912371 GCACCAACCGCTTGAGTAGC 61.912 60.000 0.00 0.00 46.83 3.58
96 97 2.031163 GTAGCTAGCCGGCATGGG 59.969 66.667 31.54 15.94 38.63 4.00
102 103 2.650813 CTAGCCGGCATGGGAGTCAC 62.651 65.000 31.54 0.00 38.63 3.67
142 144 1.305802 ACATCGTACTCCCCAGCCA 60.306 57.895 0.00 0.00 0.00 4.75
143 145 1.330655 ACATCGTACTCCCCAGCCAG 61.331 60.000 0.00 0.00 0.00 4.85
144 146 2.435693 ATCGTACTCCCCAGCCAGC 61.436 63.158 0.00 0.00 0.00 4.85
145 147 4.162690 CGTACTCCCCAGCCAGCC 62.163 72.222 0.00 0.00 0.00 4.85
146 148 3.009115 GTACTCCCCAGCCAGCCA 61.009 66.667 0.00 0.00 0.00 4.75
147 149 2.688666 TACTCCCCAGCCAGCCAG 60.689 66.667 0.00 0.00 0.00 4.85
175 177 3.055963 CAGCATGGTTCTCACTTCTCTCT 60.056 47.826 0.00 0.00 0.00 3.10
176 178 3.582208 AGCATGGTTCTCACTTCTCTCTT 59.418 43.478 0.00 0.00 0.00 2.85
177 179 3.932089 GCATGGTTCTCACTTCTCTCTTC 59.068 47.826 0.00 0.00 0.00 2.87
178 180 4.322650 GCATGGTTCTCACTTCTCTCTTCT 60.323 45.833 0.00 0.00 0.00 2.85
179 181 4.862902 TGGTTCTCACTTCTCTCTTCTG 57.137 45.455 0.00 0.00 0.00 3.02
180 182 4.219115 TGGTTCTCACTTCTCTCTTCTGT 58.781 43.478 0.00 0.00 0.00 3.41
181 183 4.279671 TGGTTCTCACTTCTCTCTTCTGTC 59.720 45.833 0.00 0.00 0.00 3.51
190 192 4.592485 TCTCTCTTCTGTCCTTCAACAC 57.408 45.455 0.00 0.00 0.00 3.32
212 214 1.302993 ATCCAACCCAACCGAACCG 60.303 57.895 0.00 0.00 0.00 4.44
381 414 4.933064 GCCGATCTCCTCCGCACG 62.933 72.222 0.00 0.00 0.00 5.34
382 415 4.271816 CCGATCTCCTCCGCACGG 62.272 72.222 1.73 1.73 34.77 4.94
425 479 1.205893 CCGACTCCTTCCCTTCTCTTG 59.794 57.143 0.00 0.00 0.00 3.02
434 488 1.470098 TCCCTTCTCTTGTACGTACGC 59.530 52.381 20.18 0.00 0.00 4.42
435 489 1.200716 CCCTTCTCTTGTACGTACGCA 59.799 52.381 20.18 9.01 0.00 5.24
436 490 2.248487 CCTTCTCTTGTACGTACGCAC 58.752 52.381 20.18 14.06 0.00 5.34
462 516 2.264794 GCCGTGGACCAACTCGAT 59.735 61.111 0.00 0.00 0.00 3.59
465 519 1.472728 GCCGTGGACCAACTCGATAAT 60.473 52.381 0.00 0.00 0.00 1.28
466 520 2.201732 CCGTGGACCAACTCGATAATG 58.798 52.381 0.00 0.00 0.00 1.90
467 521 1.593006 CGTGGACCAACTCGATAATGC 59.407 52.381 0.00 0.00 0.00 3.56
468 522 2.627945 GTGGACCAACTCGATAATGCA 58.372 47.619 0.00 0.00 0.00 3.96
470 524 1.593006 GGACCAACTCGATAATGCACG 59.407 52.381 0.00 0.00 0.00 5.34
480 593 1.056700 ATAATGCACGCCCCTCTCCT 61.057 55.000 0.00 0.00 0.00 3.69
484 597 2.046892 CACGCCCCTCTCCTTGTG 60.047 66.667 0.00 0.00 0.00 3.33
485 598 2.203788 ACGCCCCTCTCCTTGTGA 60.204 61.111 0.00 0.00 0.00 3.58
491 605 1.144936 CCTCTCCTTGTGATCCCGC 59.855 63.158 0.00 0.00 0.00 6.13
493 607 1.612146 TCTCCTTGTGATCCCGCCA 60.612 57.895 0.00 0.00 0.00 5.69
494 608 0.982852 TCTCCTTGTGATCCCGCCAT 60.983 55.000 0.00 0.00 0.00 4.40
497 611 1.153369 CTTGTGATCCCGCCATCGT 60.153 57.895 0.00 0.00 0.00 3.73
511 625 3.082579 ATCGTCTTCTCCGCCTGCC 62.083 63.158 0.00 0.00 0.00 4.85
514 628 2.604686 TCTTCTCCGCCTGCCACT 60.605 61.111 0.00 0.00 0.00 4.00
516 630 2.922503 TTCTCCGCCTGCCACTGA 60.923 61.111 0.00 0.00 0.00 3.41
565 683 1.886542 GGAAGGGCCCGCTATTATTTG 59.113 52.381 18.44 0.00 0.00 2.32
566 684 2.488347 GGAAGGGCCCGCTATTATTTGA 60.488 50.000 18.44 0.00 0.00 2.69
586 704 1.758906 CGGGGAAGGGAGGAGAGAC 60.759 68.421 0.00 0.00 0.00 3.36
588 706 1.000612 GGGAAGGGAGGAGAGACGT 59.999 63.158 0.00 0.00 0.00 4.34
601 719 1.819903 AGAGACGTTAGACAAGGGAGC 59.180 52.381 0.00 0.00 0.00 4.70
619 741 2.663188 GGCCACCTGCGATCGATC 60.663 66.667 21.57 15.68 42.61 3.69
620 742 2.663188 GCCACCTGCGATCGATCC 60.663 66.667 21.57 12.54 0.00 3.36
629 759 3.369147 CCTGCGATCGATCCATGTAAATC 59.631 47.826 21.57 0.00 0.00 2.17
636 766 2.806745 CGATCCATGTAAATCCACCGCT 60.807 50.000 0.00 0.00 0.00 5.52
646 776 0.322546 ATCCACCGCTGGTTTCCTTC 60.323 55.000 0.00 0.00 38.90 3.46
650 780 1.741770 CCGCTGGTTTCCTTCTCCG 60.742 63.158 0.00 0.00 0.00 4.63
656 786 1.982226 TGGTTTCCTTCTCCGATGGAA 59.018 47.619 7.02 7.02 41.83 3.53
662 792 4.417426 TCCTTCTCCGATGGAAATTACC 57.583 45.455 0.00 0.00 33.79 2.85
663 793 3.778075 TCCTTCTCCGATGGAAATTACCA 59.222 43.478 0.00 0.00 44.41 3.25
680 815 0.179103 CCATTTGCGATTTCCCTGCC 60.179 55.000 0.00 0.00 0.00 4.85
684 819 3.439540 GCGATTTCCCTGCCGCAA 61.440 61.111 0.00 0.00 46.04 4.85
695 830 1.538276 CTGCCGCAACGATTTGAATC 58.462 50.000 0.00 0.00 34.24 2.52
699 834 0.808125 CGCAACGATTTGAATCCCCA 59.192 50.000 0.00 0.00 34.24 4.96
701 836 2.352225 CGCAACGATTTGAATCCCCAAA 60.352 45.455 0.00 0.00 39.93 3.28
705 840 5.343249 CAACGATTTGAATCCCCAAAGATC 58.657 41.667 0.00 0.00 39.13 2.75
706 841 3.627577 ACGATTTGAATCCCCAAAGATCG 59.372 43.478 0.00 0.00 40.98 3.69
708 843 3.730215 TTTGAATCCCCAAAGATCGGA 57.270 42.857 0.00 0.00 32.77 4.55
709 844 2.710096 TGAATCCCCAAAGATCGGAC 57.290 50.000 0.00 0.00 0.00 4.79
714 849 0.328258 CCCCAAAGATCGGACTGGTT 59.672 55.000 5.18 0.00 0.00 3.67
716 851 2.084546 CCCAAAGATCGGACTGGTTTC 58.915 52.381 5.18 0.00 0.00 2.78
717 852 1.732259 CCAAAGATCGGACTGGTTTCG 59.268 52.381 0.00 0.00 0.00 3.46
718 853 2.413837 CAAAGATCGGACTGGTTTCGT 58.586 47.619 0.00 0.00 0.00 3.85
719 854 2.365408 AAGATCGGACTGGTTTCGTC 57.635 50.000 0.00 0.00 0.00 4.20
720 855 0.170561 AGATCGGACTGGTTTCGTCG 59.829 55.000 0.00 0.00 32.24 5.12
721 856 0.109412 GATCGGACTGGTTTCGTCGT 60.109 55.000 0.00 0.00 32.24 4.34
724 859 0.318445 CGGACTGGTTTCGTCGTTCT 60.318 55.000 0.00 0.00 32.24 3.01
734 869 0.167470 TCGTCGTTCTGGTGATCGTC 59.833 55.000 0.00 0.00 36.91 4.20
739 874 1.828832 GTTCTGGTGATCGTCTAGCG 58.171 55.000 0.83 0.83 43.01 4.26
763 898 5.673337 TTTGGTCGAGTGATTCTTTCTTG 57.327 39.130 0.00 0.00 0.00 3.02
769 904 4.755123 TCGAGTGATTCTTTCTTGGTTTCC 59.245 41.667 0.00 0.00 0.00 3.13
771 906 5.932303 CGAGTGATTCTTTCTTGGTTTCCTA 59.068 40.000 0.00 0.00 0.00 2.94
776 911 4.903045 TCTTTCTTGGTTTCCTATCGGT 57.097 40.909 0.00 0.00 0.00 4.69
778 913 5.001232 TCTTTCTTGGTTTCCTATCGGTTG 58.999 41.667 0.00 0.00 0.00 3.77
780 915 3.934068 TCTTGGTTTCCTATCGGTTGTC 58.066 45.455 0.00 0.00 0.00 3.18
783 918 4.360951 TGGTTTCCTATCGGTTGTCTTT 57.639 40.909 0.00 0.00 0.00 2.52
784 919 4.721132 TGGTTTCCTATCGGTTGTCTTTT 58.279 39.130 0.00 0.00 0.00 2.27
785 920 4.517453 TGGTTTCCTATCGGTTGTCTTTTG 59.483 41.667 0.00 0.00 0.00 2.44
786 921 4.082949 GGTTTCCTATCGGTTGTCTTTTGG 60.083 45.833 0.00 0.00 0.00 3.28
787 922 3.343941 TCCTATCGGTTGTCTTTTGGG 57.656 47.619 0.00 0.00 0.00 4.12
788 923 2.640826 TCCTATCGGTTGTCTTTTGGGT 59.359 45.455 0.00 0.00 0.00 4.51
789 924 3.839490 TCCTATCGGTTGTCTTTTGGGTA 59.161 43.478 0.00 0.00 0.00 3.69
790 925 4.472108 TCCTATCGGTTGTCTTTTGGGTAT 59.528 41.667 0.00 0.00 0.00 2.73
791 926 4.574828 CCTATCGGTTGTCTTTTGGGTATG 59.425 45.833 0.00 0.00 0.00 2.39
792 927 2.156098 TCGGTTGTCTTTTGGGTATGC 58.844 47.619 0.00 0.00 0.00 3.14
793 928 1.883275 CGGTTGTCTTTTGGGTATGCA 59.117 47.619 0.00 0.00 0.00 3.96
794 929 2.294791 CGGTTGTCTTTTGGGTATGCAA 59.705 45.455 0.00 0.00 0.00 4.08
795 930 3.243569 CGGTTGTCTTTTGGGTATGCAAA 60.244 43.478 0.00 0.00 0.00 3.68
796 931 4.560513 CGGTTGTCTTTTGGGTATGCAAAT 60.561 41.667 0.00 0.00 0.00 2.32
802 937 8.076910 TGTCTTTTGGGTATGCAAATAATCAT 57.923 30.769 0.00 0.00 0.00 2.45
846 981 8.442605 TTTTATTTTCGCTACTGCATTTGTAC 57.557 30.769 0.00 0.00 39.64 2.90
851 986 1.401905 GCTACTGCATTTGTACCAGGC 59.598 52.381 0.00 0.00 39.41 4.85
856 991 1.617850 TGCATTTGTACCAGGCAAAGG 59.382 47.619 0.00 1.07 38.91 3.11
857 992 1.892474 GCATTTGTACCAGGCAAAGGA 59.108 47.619 8.02 0.00 39.17 3.36
859 994 3.429410 GCATTTGTACCAGGCAAAGGATC 60.429 47.826 8.02 0.00 39.17 3.36
871 1009 7.147846 ACCAGGCAAAGGATCATTACAAATAAG 60.148 37.037 0.00 0.00 0.00 1.73
882 1020 7.246674 TCATTACAAATAAGCTCGTGAATCC 57.753 36.000 0.00 0.00 0.00 3.01
901 1210 1.134175 CCCCGCGTCAATTTGCTTTAT 59.866 47.619 4.92 0.00 0.00 1.40
918 1227 9.762933 TTTGCTTTATTTCTTTGTTGCTTCTAT 57.237 25.926 0.00 0.00 0.00 1.98
919 1228 9.762933 TTGCTTTATTTCTTTGTTGCTTCTATT 57.237 25.926 0.00 0.00 0.00 1.73
920 1229 9.762933 TGCTTTATTTCTTTGTTGCTTCTATTT 57.237 25.926 0.00 0.00 0.00 1.40
970 1280 2.187707 CCATAACTGCGCTGAAATTGC 58.812 47.619 21.92 0.00 0.00 3.56
990 1300 4.136796 TGCACATCTGCTCTTTTTACAGT 58.863 39.130 0.00 0.00 44.57 3.55
991 1301 4.580167 TGCACATCTGCTCTTTTTACAGTT 59.420 37.500 0.00 0.00 44.57 3.16
992 1302 5.762711 TGCACATCTGCTCTTTTTACAGTTA 59.237 36.000 0.00 0.00 44.57 2.24
1134 1444 1.531739 GGTTTGATTCCGGCAAGCCA 61.532 55.000 17.35 4.96 43.51 4.75
1260 1570 3.179265 CGCGGTGTGATGGTCGAC 61.179 66.667 7.13 7.13 0.00 4.20
1404 1714 4.573900 AGGCCATGACGATATTGAAGATC 58.426 43.478 5.01 0.00 0.00 2.75
1530 1840 5.125100 TGCAAAACATTCCTGTGAAGATC 57.875 39.130 0.00 0.00 35.22 2.75
1560 1870 1.134788 GTGGTTGGGAGACAGATACCG 60.135 57.143 0.00 0.00 0.00 4.02
1561 1871 1.192428 GGTTGGGAGACAGATACCGT 58.808 55.000 0.00 0.00 0.00 4.83
1947 2257 1.737008 GCAACCGTTCCTCGAGTCC 60.737 63.158 12.31 0.00 42.86 3.85
1959 2269 1.144936 CGAGTCCCATCAGCCCTTC 59.855 63.158 0.00 0.00 0.00 3.46
2083 2393 3.553511 CGTTGCCAAGATGACATCTCTAC 59.446 47.826 18.21 11.52 39.08 2.59
2247 2557 1.692411 ACCACCAACTGCTTCTTTCC 58.308 50.000 0.00 0.00 0.00 3.13
2289 2599 6.629128 AGATGATATCCTTGCTAATGACTCG 58.371 40.000 0.00 0.00 0.00 4.18
2292 2602 6.678878 TGATATCCTTGCTAATGACTCGTAC 58.321 40.000 0.00 0.00 0.00 3.67
2544 2854 3.932710 TGATTGAGGTATTGAACGACTGC 59.067 43.478 0.00 0.00 0.00 4.40
2812 3122 1.007734 GTGCTCTTGGACGACGTCA 60.008 57.895 27.77 12.43 33.68 4.35
3111 3421 2.222027 GCAGATATGGGGAAGGAAACG 58.778 52.381 0.00 0.00 0.00 3.60
3120 3430 1.145803 GGAAGGAAACGACGTTCAGG 58.854 55.000 14.58 0.00 36.70 3.86
3213 3523 2.102084 GGTGATACGGGGGAAGAACTAC 59.898 54.545 0.00 0.00 0.00 2.73
3521 3839 9.557338 CTGTTTATCAGTTACAGTACAGTAGTC 57.443 37.037 0.00 0.00 39.17 2.59
3556 3874 8.437360 AATTTTCAATTTTCTCTGGTCCAAAC 57.563 30.769 0.00 0.00 0.00 2.93
3647 3965 9.267084 GAGTTTTGAGATTCTCTGTCTTTTAGT 57.733 33.333 14.54 0.00 0.00 2.24
3776 4173 0.034337 GGTAGTGGTTCAACCTGCGA 59.966 55.000 8.40 0.00 39.58 5.10
3779 4176 0.249911 AGTGGTTCAACCTGCGACTC 60.250 55.000 8.40 0.00 39.58 3.36
3915 4315 1.120530 GCCCCGTCTTTCTGGAGATA 58.879 55.000 0.00 0.00 0.00 1.98
3946 4346 4.464112 GAACATGTACGGCTTTTTCAGTC 58.536 43.478 0.00 0.00 0.00 3.51
3960 4360 5.651172 TTTTCAGTCTGAATACGTGTGTG 57.349 39.130 15.95 0.00 36.11 3.82
4030 4436 6.429385 AGCTGTCAACCTAAAAGATTTGAGAG 59.571 38.462 3.62 3.62 40.55 3.20
4086 4492 4.677378 GCGTAATATACAGCTCTGTCTGTG 59.323 45.833 5.72 0.00 45.95 3.66
4096 4502 1.446792 CTGTCTGTGTAGGCTGGCG 60.447 63.158 0.00 0.00 0.00 5.69
4118 4524 1.610522 GCAGCACCAAGTCAATTCTGT 59.389 47.619 0.00 0.00 0.00 3.41
4122 4528 3.503748 AGCACCAAGTCAATTCTGTAAGC 59.496 43.478 0.00 0.00 0.00 3.09
4136 4542 4.385825 TCTGTAAGCACGATTCCTTTTGT 58.614 39.130 0.00 0.00 0.00 2.83
4137 4543 4.451096 TCTGTAAGCACGATTCCTTTTGTC 59.549 41.667 0.00 0.00 0.00 3.18
4149 4555 3.084039 TCCTTTTGTCCAATGCTAGCTG 58.916 45.455 17.23 6.64 0.00 4.24
4150 4556 3.084039 CCTTTTGTCCAATGCTAGCTGA 58.916 45.455 17.23 4.57 0.00 4.26
4151 4557 3.128242 CCTTTTGTCCAATGCTAGCTGAG 59.872 47.826 17.23 5.12 0.00 3.35
4152 4558 3.423539 TTTGTCCAATGCTAGCTGAGT 57.576 42.857 17.23 0.00 0.00 3.41
4153 4559 4.551702 TTTGTCCAATGCTAGCTGAGTA 57.448 40.909 17.23 0.00 0.00 2.59
4154 4560 3.526931 TGTCCAATGCTAGCTGAGTAC 57.473 47.619 17.23 9.40 0.00 2.73
4155 4561 3.099905 TGTCCAATGCTAGCTGAGTACT 58.900 45.455 17.23 0.00 0.00 2.73
4156 4562 4.278310 TGTCCAATGCTAGCTGAGTACTA 58.722 43.478 17.23 0.00 0.00 1.82
4157 4563 4.339530 TGTCCAATGCTAGCTGAGTACTAG 59.660 45.833 17.23 0.00 40.13 2.57
4177 4583 5.948162 ACTAGTACTGTAGATCGGAAACCAA 59.052 40.000 5.39 0.00 0.00 3.67
4180 4586 6.164176 AGTACTGTAGATCGGAAACCAAAAG 58.836 40.000 0.00 0.00 0.00 2.27
4194 4600 7.255346 CGGAAACCAAAAGTTACTTGGAGTAAT 60.255 37.037 12.37 0.00 45.31 1.89
4204 4610 8.553459 AGTTACTTGGAGTAATCAAATGACTG 57.447 34.615 4.08 0.00 42.06 3.51
4205 4611 8.157476 AGTTACTTGGAGTAATCAAATGACTGT 58.843 33.333 4.08 0.00 42.06 3.55
4206 4612 8.443937 GTTACTTGGAGTAATCAAATGACTGTC 58.556 37.037 0.00 0.00 42.06 3.51
4207 4613 6.773638 ACTTGGAGTAATCAAATGACTGTCT 58.226 36.000 9.51 0.00 0.00 3.41
4208 4614 6.652481 ACTTGGAGTAATCAAATGACTGTCTG 59.348 38.462 9.51 0.00 0.00 3.51
4209 4615 6.358974 TGGAGTAATCAAATGACTGTCTGA 57.641 37.500 9.51 5.08 0.00 3.27
4210 4616 6.950842 TGGAGTAATCAAATGACTGTCTGAT 58.049 36.000 9.51 7.22 0.00 2.90
4211 4617 7.397221 TGGAGTAATCAAATGACTGTCTGATT 58.603 34.615 20.51 20.51 40.62 2.57
4212 4618 7.550551 TGGAGTAATCAAATGACTGTCTGATTC 59.449 37.037 20.37 14.44 38.91 2.52
4213 4619 7.768120 GGAGTAATCAAATGACTGTCTGATTCT 59.232 37.037 20.37 17.34 38.91 2.40
4214 4620 8.489990 AGTAATCAAATGACTGTCTGATTCTG 57.510 34.615 20.37 9.92 38.91 3.02
4215 4621 5.814764 ATCAAATGACTGTCTGATTCTGC 57.185 39.130 9.51 0.00 0.00 4.26
4216 4622 3.681417 TCAAATGACTGTCTGATTCTGCG 59.319 43.478 9.51 0.00 0.00 5.18
4217 4623 3.325293 AATGACTGTCTGATTCTGCGT 57.675 42.857 9.51 0.00 0.00 5.24
4218 4624 2.070262 TGACTGTCTGATTCTGCGTG 57.930 50.000 9.51 0.00 0.00 5.34
4219 4625 1.341209 TGACTGTCTGATTCTGCGTGT 59.659 47.619 9.51 0.00 0.00 4.49
4220 4626 2.556622 TGACTGTCTGATTCTGCGTGTA 59.443 45.455 9.51 0.00 0.00 2.90
4221 4627 3.005367 TGACTGTCTGATTCTGCGTGTAA 59.995 43.478 9.51 0.00 0.00 2.41
4222 4628 3.987868 GACTGTCTGATTCTGCGTGTAAA 59.012 43.478 0.00 0.00 0.00 2.01
4223 4629 3.990469 ACTGTCTGATTCTGCGTGTAAAG 59.010 43.478 0.00 0.00 0.00 1.85
4224 4630 3.990092 TGTCTGATTCTGCGTGTAAAGT 58.010 40.909 0.00 0.00 0.00 2.66
4225 4631 4.377021 TGTCTGATTCTGCGTGTAAAGTT 58.623 39.130 0.00 0.00 0.00 2.66
4226 4632 5.534407 TGTCTGATTCTGCGTGTAAAGTTA 58.466 37.500 0.00 0.00 0.00 2.24
4227 4633 5.633601 TGTCTGATTCTGCGTGTAAAGTTAG 59.366 40.000 0.00 0.00 0.00 2.34
4228 4634 5.634020 GTCTGATTCTGCGTGTAAAGTTAGT 59.366 40.000 0.00 0.00 0.00 2.24
4229 4635 6.805271 GTCTGATTCTGCGTGTAAAGTTAGTA 59.195 38.462 0.00 0.00 0.00 1.82
4230 4636 7.488471 GTCTGATTCTGCGTGTAAAGTTAGTAT 59.512 37.037 0.00 0.00 0.00 2.12
4231 4637 8.680001 TCTGATTCTGCGTGTAAAGTTAGTATA 58.320 33.333 0.00 0.00 0.00 1.47
4232 4638 9.297586 CTGATTCTGCGTGTAAAGTTAGTATAA 57.702 33.333 0.00 0.00 0.00 0.98
4233 4639 9.642327 TGATTCTGCGTGTAAAGTTAGTATAAA 57.358 29.630 0.00 0.00 0.00 1.40
4235 4641 9.649167 ATTCTGCGTGTAAAGTTAGTATAAAGT 57.351 29.630 0.00 0.00 0.00 2.66
4236 4642 9.480053 TTCTGCGTGTAAAGTTAGTATAAAGTT 57.520 29.630 0.00 0.00 0.00 2.66
4237 4643 8.918658 TCTGCGTGTAAAGTTAGTATAAAGTTG 58.081 33.333 0.00 0.00 0.00 3.16
4238 4644 8.815141 TGCGTGTAAAGTTAGTATAAAGTTGA 57.185 30.769 0.00 0.00 0.00 3.18
4239 4645 8.918658 TGCGTGTAAAGTTAGTATAAAGTTGAG 58.081 33.333 0.00 0.00 0.00 3.02
4240 4646 9.132521 GCGTGTAAAGTTAGTATAAAGTTGAGA 57.867 33.333 0.00 0.00 0.00 3.27
4257 4663 7.653767 AGTTGAGACACTTATTTTAAGACGG 57.346 36.000 1.47 0.00 0.00 4.79
4258 4664 7.439381 AGTTGAGACACTTATTTTAAGACGGA 58.561 34.615 1.47 0.00 0.00 4.69
4259 4665 7.599245 AGTTGAGACACTTATTTTAAGACGGAG 59.401 37.037 1.47 0.00 0.00 4.63
4260 4666 6.395629 TGAGACACTTATTTTAAGACGGAGG 58.604 40.000 1.47 0.00 0.00 4.30
4261 4667 5.731591 AGACACTTATTTTAAGACGGAGGG 58.268 41.667 1.47 0.00 0.00 4.30
4262 4668 5.482878 AGACACTTATTTTAAGACGGAGGGA 59.517 40.000 1.47 0.00 0.00 4.20
4361 4769 0.392998 GTGCGGTTGATCAGGTCCAT 60.393 55.000 12.04 0.00 0.00 3.41
4362 4770 0.107703 TGCGGTTGATCAGGTCCATC 60.108 55.000 12.04 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.395862 TCAGCTTCTACTCCCTCCGG 60.396 60.000 0.00 0.00 0.00 5.14
1 2 0.741915 GTCAGCTTCTACTCCCTCCG 59.258 60.000 0.00 0.00 0.00 4.63
2 3 0.741915 CGTCAGCTTCTACTCCCTCC 59.258 60.000 0.00 0.00 0.00 4.30
3 4 0.741915 CCGTCAGCTTCTACTCCCTC 59.258 60.000 0.00 0.00 0.00 4.30
4 5 1.324005 GCCGTCAGCTTCTACTCCCT 61.324 60.000 0.00 0.00 38.99 4.20
5 6 1.142097 GCCGTCAGCTTCTACTCCC 59.858 63.158 0.00 0.00 38.99 4.30
6 7 1.226717 CGCCGTCAGCTTCTACTCC 60.227 63.158 0.00 0.00 40.39 3.85
7 8 1.874466 GCGCCGTCAGCTTCTACTC 60.874 63.158 0.00 0.00 40.39 2.59
8 9 2.182030 GCGCCGTCAGCTTCTACT 59.818 61.111 0.00 0.00 40.39 2.57
9 10 3.248171 CGCGCCGTCAGCTTCTAC 61.248 66.667 0.00 0.00 40.39 2.59
20 21 4.838486 GACTCTGGAGACGCGCCG 62.838 72.222 5.73 0.00 0.00 6.46
23 24 2.041115 TCTGGACTCTGGAGACGCG 61.041 63.158 3.53 3.53 0.00 6.01
24 25 1.244697 TGTCTGGACTCTGGAGACGC 61.245 60.000 4.49 0.00 39.23 5.19
62 63 1.764571 TACTCAAGCGGTTGGTGCCT 61.765 55.000 25.70 7.72 34.09 4.75
64 65 1.912371 GCTACTCAAGCGGTTGGTGC 61.912 60.000 25.70 20.58 42.53 5.01
77 78 1.005630 CCATGCCGGCTAGCTACTC 60.006 63.158 29.70 2.44 0.00 2.59
83 84 2.423446 GACTCCCATGCCGGCTAG 59.577 66.667 29.70 19.52 0.00 3.42
86 87 2.650813 CTAGTGACTCCCATGCCGGC 62.651 65.000 22.73 22.73 0.00 6.13
102 103 2.413502 GCGTGAGTGAGTGACTGACTAG 60.414 54.545 4.31 1.32 36.70 2.57
144 146 4.753662 ACCATGCTGGCTGGCTGG 62.754 66.667 9.98 7.83 42.67 4.85
145 147 2.678934 AACCATGCTGGCTGGCTG 60.679 61.111 2.00 2.91 42.67 4.85
146 148 2.362120 GAACCATGCTGGCTGGCT 60.362 61.111 2.00 0.69 42.67 4.75
147 149 2.362120 AGAACCATGCTGGCTGGC 60.362 61.111 9.70 0.00 42.67 4.85
148 150 1.001764 TGAGAACCATGCTGGCTGG 60.002 57.895 2.50 8.67 42.67 4.85
149 151 0.322277 AGTGAGAACCATGCTGGCTG 60.322 55.000 2.50 0.00 42.67 4.85
150 152 0.403271 AAGTGAGAACCATGCTGGCT 59.597 50.000 2.50 0.00 42.67 4.75
151 153 0.807496 GAAGTGAGAACCATGCTGGC 59.193 55.000 2.50 0.00 42.67 4.85
152 154 2.027377 AGAGAAGTGAGAACCATGCTGG 60.027 50.000 1.16 1.16 45.02 4.85
153 155 3.055963 AGAGAGAAGTGAGAACCATGCTG 60.056 47.826 0.00 0.00 0.00 4.41
154 156 3.172339 AGAGAGAAGTGAGAACCATGCT 58.828 45.455 0.00 0.00 0.00 3.79
175 177 1.124780 TCCGGTGTTGAAGGACAGAA 58.875 50.000 0.00 0.00 0.00 3.02
176 178 1.275291 GATCCGGTGTTGAAGGACAGA 59.725 52.381 0.00 0.00 36.81 3.41
177 179 1.676014 GGATCCGGTGTTGAAGGACAG 60.676 57.143 0.00 0.00 36.81 3.51
178 180 0.323629 GGATCCGGTGTTGAAGGACA 59.676 55.000 0.00 0.00 36.81 4.02
179 181 0.323629 TGGATCCGGTGTTGAAGGAC 59.676 55.000 7.39 0.00 36.81 3.85
180 182 1.060729 TTGGATCCGGTGTTGAAGGA 58.939 50.000 7.39 0.00 38.56 3.36
181 183 1.165270 GTTGGATCCGGTGTTGAAGG 58.835 55.000 7.39 0.00 0.00 3.46
190 192 2.437716 CGGTTGGGTTGGATCCGG 60.438 66.667 7.39 0.00 37.92 5.14
212 214 2.067013 GTCTACAGCTCCGTTTGGTTC 58.933 52.381 0.00 0.00 36.30 3.62
321 354 0.036010 AATGGAACCTCTGGCGAGTG 60.036 55.000 0.00 0.00 35.43 3.51
402 435 3.372554 GAAGGGAAGGAGTCGGGCG 62.373 68.421 0.00 0.00 0.00 6.13
403 436 1.962321 GAGAAGGGAAGGAGTCGGGC 61.962 65.000 0.00 0.00 0.00 6.13
409 463 2.826725 ACGTACAAGAGAAGGGAAGGAG 59.173 50.000 0.00 0.00 0.00 3.69
442 496 3.998672 GAGTTGGTCCACGGCGGA 61.999 66.667 13.24 0.00 43.61 5.54
444 498 2.274232 TATCGAGTTGGTCCACGGCG 62.274 60.000 4.80 4.80 0.00 6.46
445 499 0.108520 TTATCGAGTTGGTCCACGGC 60.109 55.000 0.00 0.00 0.00 5.68
446 500 2.201732 CATTATCGAGTTGGTCCACGG 58.798 52.381 0.00 0.00 0.00 4.94
462 516 1.271840 AAGGAGAGGGGCGTGCATTA 61.272 55.000 0.00 0.00 0.00 1.90
465 519 4.020617 CAAGGAGAGGGGCGTGCA 62.021 66.667 0.00 0.00 0.00 4.57
466 520 4.021925 ACAAGGAGAGGGGCGTGC 62.022 66.667 0.00 0.00 0.00 5.34
467 521 1.903877 ATCACAAGGAGAGGGGCGTG 61.904 60.000 0.00 0.00 0.00 5.34
468 522 1.613630 ATCACAAGGAGAGGGGCGT 60.614 57.895 0.00 0.00 0.00 5.68
470 524 1.529309 GGATCACAAGGAGAGGGGC 59.471 63.158 0.00 0.00 0.00 5.80
480 593 1.153449 GACGATGGCGGGATCACAA 60.153 57.895 0.00 0.00 43.17 3.33
484 597 0.319125 GAGAAGACGATGGCGGGATC 60.319 60.000 0.00 0.00 43.17 3.36
485 598 1.742768 GAGAAGACGATGGCGGGAT 59.257 57.895 0.00 0.00 43.17 3.85
491 605 1.227089 CAGGCGGAGAAGACGATGG 60.227 63.158 0.00 0.00 0.00 3.51
493 607 2.496817 GCAGGCGGAGAAGACGAT 59.503 61.111 0.00 0.00 0.00 3.73
494 608 3.760035 GGCAGGCGGAGAAGACGA 61.760 66.667 0.00 0.00 0.00 4.20
497 611 2.604686 AGTGGCAGGCGGAGAAGA 60.605 61.111 0.00 0.00 0.00 2.87
511 625 1.679898 GTCCCCTCCCTTGTCAGTG 59.320 63.158 0.00 0.00 0.00 3.66
514 628 2.606519 CCGTCCCCTCCCTTGTCA 60.607 66.667 0.00 0.00 0.00 3.58
516 630 2.284699 CTCCGTCCCCTCCCTTGT 60.285 66.667 0.00 0.00 0.00 3.16
551 669 2.681152 CCGTTCAAATAATAGCGGGC 57.319 50.000 0.00 0.00 36.05 6.13
556 674 5.043737 TCCCTTCCCCGTTCAAATAATAG 57.956 43.478 0.00 0.00 0.00 1.73
565 683 1.305887 TCTCCTCCCTTCCCCGTTC 60.306 63.158 0.00 0.00 0.00 3.95
566 684 1.306226 CTCTCCTCCCTTCCCCGTT 60.306 63.158 0.00 0.00 0.00 4.44
586 704 1.810030 GCCGCTCCCTTGTCTAACG 60.810 63.158 0.00 0.00 0.00 3.18
588 706 1.916273 TGGCCGCTCCCTTGTCTAA 60.916 57.895 0.00 0.00 0.00 2.10
601 719 4.592192 ATCGATCGCAGGTGGCCG 62.592 66.667 11.09 0.00 40.31 6.13
613 735 3.664107 CGGTGGATTTACATGGATCGAT 58.336 45.455 0.00 0.00 0.00 3.59
616 738 2.549754 CAGCGGTGGATTTACATGGATC 59.450 50.000 6.74 0.00 0.00 3.36
646 776 4.610945 GCAAATGGTAATTTCCATCGGAG 58.389 43.478 16.10 8.33 46.14 4.63
650 780 7.165427 GAAATCGCAAATGGTAATTTCCATC 57.835 36.000 16.10 4.49 46.14 3.51
656 786 4.680440 GCAGGGAAATCGCAAATGGTAATT 60.680 41.667 0.14 0.00 0.00 1.40
662 792 0.526096 CGGCAGGGAAATCGCAAATG 60.526 55.000 0.14 0.00 0.00 2.32
663 793 1.809207 CGGCAGGGAAATCGCAAAT 59.191 52.632 0.14 0.00 0.00 2.32
665 795 3.439540 GCGGCAGGGAAATCGCAA 61.440 61.111 0.00 0.00 46.33 4.85
669 804 1.376609 ATCGTTGCGGCAGGGAAATC 61.377 55.000 1.67 0.00 0.00 2.17
680 815 0.808125 TGGGGATTCAAATCGTTGCG 59.192 50.000 0.00 0.00 36.27 4.85
684 819 3.627577 CGATCTTTGGGGATTCAAATCGT 59.372 43.478 0.00 0.00 35.84 3.73
695 830 0.328258 AACCAGTCCGATCTTTGGGG 59.672 55.000 0.00 0.00 34.99 4.96
699 834 2.685100 GACGAAACCAGTCCGATCTTT 58.315 47.619 0.00 0.00 32.78 2.52
701 836 0.170561 CGACGAAACCAGTCCGATCT 59.829 55.000 0.00 0.00 35.33 2.75
705 840 0.318445 AGAACGACGAAACCAGTCCG 60.318 55.000 0.00 0.00 35.33 4.79
706 841 1.137513 CAGAACGACGAAACCAGTCC 58.862 55.000 0.00 0.00 35.33 3.85
708 843 0.462789 ACCAGAACGACGAAACCAGT 59.537 50.000 0.00 0.00 0.00 4.00
709 844 0.859232 CACCAGAACGACGAAACCAG 59.141 55.000 0.00 0.00 0.00 4.00
714 849 0.594602 ACGATCACCAGAACGACGAA 59.405 50.000 0.00 0.00 41.92 3.85
716 851 0.168348 AGACGATCACCAGAACGACG 59.832 55.000 2.23 0.00 41.92 5.12
717 852 2.791849 GCTAGACGATCACCAGAACGAC 60.792 54.545 0.00 0.00 41.92 4.34
718 853 1.400846 GCTAGACGATCACCAGAACGA 59.599 52.381 0.00 0.00 41.92 3.85
719 854 1.828832 GCTAGACGATCACCAGAACG 58.171 55.000 0.00 0.00 44.48 3.95
739 874 6.310197 CAAGAAAGAATCACTCGACCAAATC 58.690 40.000 0.00 0.00 0.00 2.17
747 882 4.757149 AGGAAACCAAGAAAGAATCACTCG 59.243 41.667 0.00 0.00 0.00 4.18
751 886 6.985188 CGATAGGAAACCAAGAAAGAATCA 57.015 37.500 0.00 0.00 0.00 2.57
769 904 4.035208 GCATACCCAAAAGACAACCGATAG 59.965 45.833 0.00 0.00 0.00 2.08
771 906 2.752903 GCATACCCAAAAGACAACCGAT 59.247 45.455 0.00 0.00 0.00 4.18
776 911 7.901029 TGATTATTTGCATACCCAAAAGACAA 58.099 30.769 0.00 0.00 38.12 3.18
778 913 7.439056 CCATGATTATTTGCATACCCAAAAGAC 59.561 37.037 0.00 0.00 38.12 3.01
780 915 7.499292 TCCATGATTATTTGCATACCCAAAAG 58.501 34.615 0.00 0.00 38.12 2.27
783 918 7.289549 TCATTCCATGATTATTTGCATACCCAA 59.710 33.333 0.00 0.00 33.59 4.12
784 919 6.781507 TCATTCCATGATTATTTGCATACCCA 59.218 34.615 0.00 0.00 33.59 4.51
785 920 7.230849 TCATTCCATGATTATTTGCATACCC 57.769 36.000 0.00 0.00 33.59 3.69
821 956 7.539366 GGTACAAATGCAGTAGCGAAAATAAAA 59.461 33.333 0.00 0.00 46.23 1.52
822 957 7.024768 GGTACAAATGCAGTAGCGAAAATAAA 58.975 34.615 0.00 0.00 46.23 1.40
825 960 4.457603 TGGTACAAATGCAGTAGCGAAAAT 59.542 37.500 8.65 0.00 41.52 1.82
828 963 3.000041 CTGGTACAAATGCAGTAGCGAA 59.000 45.455 8.65 0.00 41.13 4.70
830 965 1.665679 CCTGGTACAAATGCAGTAGCG 59.334 52.381 8.65 4.79 41.13 4.26
846 981 5.603170 ATTTGTAATGATCCTTTGCCTGG 57.397 39.130 0.00 0.00 0.00 4.45
851 986 7.641411 CACGAGCTTATTTGTAATGATCCTTTG 59.359 37.037 0.00 0.00 0.00 2.77
856 991 8.012241 GGATTCACGAGCTTATTTGTAATGATC 58.988 37.037 0.00 0.00 0.00 2.92
857 992 7.041098 GGGATTCACGAGCTTATTTGTAATGAT 60.041 37.037 0.00 0.00 0.00 2.45
859 994 6.430451 GGGATTCACGAGCTTATTTGTAATG 58.570 40.000 0.00 0.00 0.00 1.90
871 1009 4.814294 ACGCGGGGATTCACGAGC 62.814 66.667 12.47 0.26 33.14 5.03
882 1020 2.559998 ATAAAGCAAATTGACGCGGG 57.440 45.000 12.47 0.00 0.00 6.13
1134 1444 1.144936 GCTATGCGTGAGGGCTTCT 59.855 57.895 0.00 0.00 0.00 2.85
1260 1570 2.103934 CTCTTGAGCTCCTCGGCG 59.896 66.667 12.15 0.00 37.29 6.46
1284 1594 1.215647 GTGCGAGTTCTCACCGGAT 59.784 57.895 9.46 0.00 0.00 4.18
1330 1640 5.065731 ACTCAAGAAGTTTGTCAAGCTTCAG 59.934 40.000 31.48 24.69 40.57 3.02
1362 1672 3.467803 CTCTCCCACGTTTTTCTTGACT 58.532 45.455 0.00 0.00 0.00 3.41
1404 1714 2.416547 CAGGGTAATGACTTTGACGCAG 59.583 50.000 0.00 0.00 0.00 5.18
1442 1752 4.335594 GGAACTTAGCTTCGGCAATGTAAT 59.664 41.667 0.00 0.00 44.74 1.89
1452 1762 1.936547 GCAGGATGGAACTTAGCTTCG 59.063 52.381 0.00 0.00 35.86 3.79
1530 1840 4.586841 TGTCTCCCAACCACCTTTTTAATG 59.413 41.667 0.00 0.00 0.00 1.90
1560 1870 3.618594 TCTCGATGTGCAGCTTTATCAAC 59.381 43.478 0.00 0.00 0.00 3.18
1561 1871 3.860641 TCTCGATGTGCAGCTTTATCAA 58.139 40.909 0.00 0.00 0.00 2.57
1947 2257 1.000521 TGCAAGGAAGGGCTGATGG 60.001 57.895 0.00 0.00 0.00 3.51
2289 2599 6.421202 CCTTCTTTATAACCATCTGCTCGTAC 59.579 42.308 0.00 0.00 0.00 3.67
2292 2602 5.601662 TCCTTCTTTATAACCATCTGCTCG 58.398 41.667 0.00 0.00 0.00 5.03
2544 2854 4.125703 GAGCATACATCCTGTTGAGAAGG 58.874 47.826 0.00 0.00 36.02 3.46
2685 2995 2.272918 AAGTAGCGCGAGACCTCTGC 62.273 60.000 12.10 0.00 0.00 4.26
2686 2996 0.171455 AAAGTAGCGCGAGACCTCTG 59.829 55.000 12.10 0.00 0.00 3.35
2697 3007 1.263776 CTCGAGCAGTCAAAGTAGCG 58.736 55.000 0.00 0.00 0.00 4.26
2812 3122 4.652822 GGTGTTTCTTCCACTATCCAGTT 58.347 43.478 0.00 0.00 30.46 3.16
2895 3205 2.987232 AGTGGTAAAATCTCCGAAGCC 58.013 47.619 0.00 0.00 0.00 4.35
3111 3421 0.804989 CCAAGCAATCCCTGAACGTC 59.195 55.000 0.00 0.00 0.00 4.34
3120 3430 3.067320 GCCTTATCTCAACCAAGCAATCC 59.933 47.826 0.00 0.00 0.00 3.01
3213 3523 0.738975 TCTTGTAGTCCAGCGATCCG 59.261 55.000 0.00 0.00 0.00 4.18
3457 3767 0.319297 AGACGCGTCTTGTAACCACC 60.319 55.000 34.98 7.02 36.31 4.61
3513 3831 7.466804 TGAAAATTATTTGAGGGGACTACTGT 58.533 34.615 0.00 0.00 44.43 3.55
3521 3839 9.948964 AGAGAAAATTGAAAATTATTTGAGGGG 57.051 29.630 0.00 0.00 0.00 4.79
3552 3870 3.627577 GTGTGCCTATATCACAGGGTTTG 59.372 47.826 7.87 0.00 44.11 2.93
3556 3874 3.558931 TTGTGTGCCTATATCACAGGG 57.441 47.619 7.87 0.00 44.11 4.45
3647 3965 9.868160 TTCAAACTATGTCCTCTGAGAGATATA 57.132 33.333 11.82 8.79 0.00 0.86
3648 3966 8.774546 TTCAAACTATGTCCTCTGAGAGATAT 57.225 34.615 11.82 8.15 0.00 1.63
3733 4115 8.270030 ACCGTATGCTAGTAGTATATACCATCA 58.730 37.037 10.67 0.78 0.00 3.07
3737 4119 9.039870 CACTACCGTATGCTAGTAGTATATACC 57.960 40.741 10.67 0.00 43.65 2.73
3743 4125 5.296151 ACCACTACCGTATGCTAGTAGTA 57.704 43.478 11.37 0.00 43.65 1.82
3744 4126 4.162040 ACCACTACCGTATGCTAGTAGT 57.838 45.455 7.42 7.42 45.77 2.73
3745 4127 4.577693 TGAACCACTACCGTATGCTAGTAG 59.422 45.833 6.40 6.40 39.50 2.57
3796 4193 1.658095 GCTTGTCTCTGCAAGTCGATC 59.342 52.381 7.51 0.00 45.47 3.69
3859 4258 4.237349 AGCACAGGAATTTTTACCGTTG 57.763 40.909 0.00 0.00 0.00 4.10
3860 4259 4.929819 AAGCACAGGAATTTTTACCGTT 57.070 36.364 0.00 0.00 0.00 4.44
3861 4260 6.094464 GGTATAAGCACAGGAATTTTTACCGT 59.906 38.462 0.00 0.00 0.00 4.83
3862 4261 6.094325 TGGTATAAGCACAGGAATTTTTACCG 59.906 38.462 0.00 0.00 32.92 4.02
3907 4307 6.118170 ACATGTTCCATGTCTTTATCTCCAG 58.882 40.000 4.08 0.00 0.00 3.86
3915 4315 2.747446 GCCGTACATGTTCCATGTCTTT 59.253 45.455 12.75 0.00 33.76 2.52
3939 4339 4.689071 ACACACACGTATTCAGACTGAAA 58.311 39.130 21.29 8.65 40.12 2.69
3946 4346 4.523813 GAACCAAACACACACGTATTCAG 58.476 43.478 0.00 0.00 0.00 3.02
3960 4360 5.637006 TTACATGTATGCAGGAACCAAAC 57.363 39.130 6.36 0.00 0.00 2.93
4030 4436 2.930826 TTCAGTCTTCCAGGTTGACC 57.069 50.000 9.83 0.00 0.00 4.02
4096 4502 2.095364 CAGAATTGACTTGGTGCTGCTC 60.095 50.000 0.00 0.00 0.00 4.26
4118 4524 3.745799 TGGACAAAAGGAATCGTGCTTA 58.254 40.909 0.00 0.00 33.69 3.09
4122 4528 3.057315 AGCATTGGACAAAAGGAATCGTG 60.057 43.478 0.00 0.00 0.00 4.35
4136 4542 4.537751 ACTAGTACTCAGCTAGCATTGGA 58.462 43.478 18.83 7.80 39.48 3.53
4137 4543 4.927978 ACTAGTACTCAGCTAGCATTGG 57.072 45.455 18.83 6.48 39.48 3.16
4149 4555 7.042119 GGTTTCCGATCTACAGTACTAGTACTC 60.042 44.444 28.86 17.26 43.98 2.59
4150 4556 6.765512 GGTTTCCGATCTACAGTACTAGTACT 59.234 42.308 26.61 26.61 46.52 2.73
4151 4557 6.540189 TGGTTTCCGATCTACAGTACTAGTAC 59.460 42.308 23.03 23.03 36.35 2.73
4152 4558 6.653020 TGGTTTCCGATCTACAGTACTAGTA 58.347 40.000 0.00 0.00 0.00 1.82
4153 4559 5.503927 TGGTTTCCGATCTACAGTACTAGT 58.496 41.667 0.00 0.00 0.00 2.57
4154 4560 6.446781 TTGGTTTCCGATCTACAGTACTAG 57.553 41.667 0.00 0.00 0.00 2.57
4155 4561 6.839124 TTTGGTTTCCGATCTACAGTACTA 57.161 37.500 0.00 0.00 0.00 1.82
4156 4562 5.733620 TTTGGTTTCCGATCTACAGTACT 57.266 39.130 0.00 0.00 0.00 2.73
4157 4563 5.930569 ACTTTTGGTTTCCGATCTACAGTAC 59.069 40.000 0.00 0.00 0.00 2.73
4177 4583 9.574516 AGTCATTTGATTACTCCAAGTAACTTT 57.425 29.630 1.85 0.00 42.78 2.66
4180 4586 8.324163 ACAGTCATTTGATTACTCCAAGTAAC 57.676 34.615 1.85 0.00 42.78 2.50
4194 4600 3.681417 CGCAGAATCAGACAGTCATTTGA 59.319 43.478 2.66 0.00 0.00 2.69
4204 4610 4.992381 AACTTTACACGCAGAATCAGAC 57.008 40.909 0.00 0.00 0.00 3.51
4205 4611 5.779922 ACTAACTTTACACGCAGAATCAGA 58.220 37.500 0.00 0.00 0.00 3.27
4206 4612 7.757097 ATACTAACTTTACACGCAGAATCAG 57.243 36.000 0.00 0.00 0.00 2.90
4207 4613 9.642327 TTTATACTAACTTTACACGCAGAATCA 57.358 29.630 0.00 0.00 0.00 2.57
4209 4615 9.649167 ACTTTATACTAACTTTACACGCAGAAT 57.351 29.630 0.00 0.00 0.00 2.40
4210 4616 9.480053 AACTTTATACTAACTTTACACGCAGAA 57.520 29.630 0.00 0.00 0.00 3.02
4211 4617 8.918658 CAACTTTATACTAACTTTACACGCAGA 58.081 33.333 0.00 0.00 0.00 4.26
4212 4618 8.918658 TCAACTTTATACTAACTTTACACGCAG 58.081 33.333 0.00 0.00 0.00 5.18
4213 4619 8.815141 TCAACTTTATACTAACTTTACACGCA 57.185 30.769 0.00 0.00 0.00 5.24
4214 4620 9.132521 TCTCAACTTTATACTAACTTTACACGC 57.867 33.333 0.00 0.00 0.00 5.34
4231 4637 8.557029 CCGTCTTAAAATAAGTGTCTCAACTTT 58.443 33.333 0.00 0.00 40.77 2.66
4232 4638 7.929785 TCCGTCTTAAAATAAGTGTCTCAACTT 59.070 33.333 0.00 0.00 42.89 2.66
4233 4639 7.439381 TCCGTCTTAAAATAAGTGTCTCAACT 58.561 34.615 0.00 0.00 0.00 3.16
4234 4640 7.148623 CCTCCGTCTTAAAATAAGTGTCTCAAC 60.149 40.741 0.00 0.00 0.00 3.18
4235 4641 6.872020 CCTCCGTCTTAAAATAAGTGTCTCAA 59.128 38.462 0.00 0.00 0.00 3.02
4236 4642 6.395629 CCTCCGTCTTAAAATAAGTGTCTCA 58.604 40.000 0.00 0.00 0.00 3.27
4237 4643 5.811100 CCCTCCGTCTTAAAATAAGTGTCTC 59.189 44.000 0.00 0.00 0.00 3.36
4238 4644 5.482878 TCCCTCCGTCTTAAAATAAGTGTCT 59.517 40.000 0.00 0.00 0.00 3.41
4239 4645 5.727434 TCCCTCCGTCTTAAAATAAGTGTC 58.273 41.667 0.00 0.00 0.00 3.67
4240 4646 5.247792 ACTCCCTCCGTCTTAAAATAAGTGT 59.752 40.000 0.00 0.00 0.00 3.55
4241 4647 5.731591 ACTCCCTCCGTCTTAAAATAAGTG 58.268 41.667 0.00 0.00 0.00 3.16
4242 4648 7.486407 TTACTCCCTCCGTCTTAAAATAAGT 57.514 36.000 0.00 0.00 0.00 2.24
4243 4649 8.827677 CAATTACTCCCTCCGTCTTAAAATAAG 58.172 37.037 0.00 0.00 0.00 1.73
4244 4650 8.542080 TCAATTACTCCCTCCGTCTTAAAATAA 58.458 33.333 0.00 0.00 0.00 1.40
4245 4651 8.081517 TCAATTACTCCCTCCGTCTTAAAATA 57.918 34.615 0.00 0.00 0.00 1.40
4246 4652 6.954232 TCAATTACTCCCTCCGTCTTAAAAT 58.046 36.000 0.00 0.00 0.00 1.82
4247 4653 6.363167 TCAATTACTCCCTCCGTCTTAAAA 57.637 37.500 0.00 0.00 0.00 1.52
4248 4654 6.555463 ATCAATTACTCCCTCCGTCTTAAA 57.445 37.500 0.00 0.00 0.00 1.52
4249 4655 6.555463 AATCAATTACTCCCTCCGTCTTAA 57.445 37.500 0.00 0.00 0.00 1.85
4250 4656 6.239232 GCTAATCAATTACTCCCTCCGTCTTA 60.239 42.308 0.00 0.00 0.00 2.10
4251 4657 5.453480 GCTAATCAATTACTCCCTCCGTCTT 60.453 44.000 0.00 0.00 0.00 3.01
4252 4658 4.039366 GCTAATCAATTACTCCCTCCGTCT 59.961 45.833 0.00 0.00 0.00 4.18
4253 4659 4.202223 TGCTAATCAATTACTCCCTCCGTC 60.202 45.833 0.00 0.00 0.00 4.79
4254 4660 3.709653 TGCTAATCAATTACTCCCTCCGT 59.290 43.478 0.00 0.00 0.00 4.69
4255 4661 4.310769 CTGCTAATCAATTACTCCCTCCG 58.689 47.826 0.00 0.00 0.00 4.63
4256 4662 4.103311 ACCTGCTAATCAATTACTCCCTCC 59.897 45.833 0.00 0.00 0.00 4.30
4257 4663 5.163301 TGACCTGCTAATCAATTACTCCCTC 60.163 44.000 0.00 0.00 0.00 4.30
4258 4664 4.721776 TGACCTGCTAATCAATTACTCCCT 59.278 41.667 0.00 0.00 0.00 4.20
4259 4665 5.036117 TGACCTGCTAATCAATTACTCCC 57.964 43.478 0.00 0.00 0.00 4.30
4260 4666 5.297029 GGTTGACCTGCTAATCAATTACTCC 59.703 44.000 0.00 0.00 37.19 3.85
4261 4667 5.880332 TGGTTGACCTGCTAATCAATTACTC 59.120 40.000 1.34 0.00 37.19 2.59
4262 4668 5.815581 TGGTTGACCTGCTAATCAATTACT 58.184 37.500 1.34 0.00 37.19 2.24


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

AutoCloner maintained by Alex Coulton.