Multiple sequence alignment - TraesCS4D01G248200

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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 TraesCS4D01G248200 chr4D 100.000 5229 0 0 1 5229 416942899 416937671 0.000000e+00 9657.0
1 TraesCS4D01G248200 chr4D 87.234 94 12 0 2868 2961 416939861 416939768 1.990000e-19 108.0
2 TraesCS4D01G248200 chr4D 87.234 94 12 0 3039 3132 416940032 416939939 1.990000e-19 108.0
3 TraesCS4D01G248200 chr4D 97.059 34 0 1 4020 4052 507484169 507484202 7.320000e-04 56.5
4 TraesCS4D01G248200 chr4B 94.473 3257 111 22 745 3968 514064282 514061062 0.000000e+00 4953.0
5 TraesCS4D01G248200 chr4B 89.916 595 49 10 115 701 514065554 514064963 0.000000e+00 756.0
6 TraesCS4D01G248200 chr4B 91.203 557 21 13 4074 4604 514061032 514060478 0.000000e+00 732.0
7 TraesCS4D01G248200 chr4B 90.230 348 24 9 4886 5229 514060329 514059988 3.720000e-121 446.0
8 TraesCS4D01G248200 chr4B 95.833 120 5 0 1 120 514417297 514417178 1.490000e-45 195.0
9 TraesCS4D01G248200 chr4B 91.667 84 7 0 3049 3132 514062143 514062060 3.310000e-22 117.0
10 TraesCS4D01G248200 chr4B 80.734 109 13 3 601 701 514064918 514064810 1.560000e-10 78.7
11 TraesCS4D01G248200 chr4A 91.984 2682 148 29 1 2634 47096402 47099064 0.000000e+00 3699.0
12 TraesCS4D01G248200 chr4A 95.527 1319 53 4 2636 3951 47099133 47100448 0.000000e+00 2104.0
13 TraesCS4D01G248200 chr4A 89.097 642 43 11 4074 4694 47100428 47101063 0.000000e+00 773.0
14 TraesCS4D01G248200 chr4A 79.714 350 45 14 4888 5229 47101066 47101397 4.070000e-56 230.0
15 TraesCS4D01G248200 chr4A 88.298 94 9 2 2868 2961 47099537 47099628 1.540000e-20 111.0
16 TraesCS4D01G248200 chr1D 93.452 168 10 1 4712 4879 481182285 481182119 1.120000e-61 248.0
17 TraesCS4D01G248200 chr1D 92.169 166 12 1 4714 4879 481319943 481319779 3.150000e-57 233.0
18 TraesCS4D01G248200 chr5D 92.353 170 10 3 4711 4879 537391482 537391315 6.770000e-59 239.0
19 TraesCS4D01G248200 chrUn 92.771 166 8 4 4714 4879 16723510 16723671 2.430000e-58 237.0
20 TraesCS4D01G248200 chrUn 92.262 168 5 5 4714 4879 16705761 16705922 1.130000e-56 231.0
21 TraesCS4D01G248200 chr5A 92.771 166 9 3 4714 4879 286058514 286058676 2.430000e-58 237.0
22 TraesCS4D01G248200 chr5A 93.506 154 9 1 4714 4867 6863796 6863644 1.460000e-55 228.0
23 TraesCS4D01G248200 chr5A 100.000 29 0 0 4020 4048 3424095 3424067 3.000000e-03 54.7
24 TraesCS4D01G248200 chr6B 92.169 166 12 1 4714 4879 127756207 127756371 3.150000e-57 233.0
25 TraesCS4D01G248200 chr3D 91.617 167 11 2 4713 4879 338296960 338297123 1.460000e-55 228.0
26 TraesCS4D01G248200 chr3D 100.000 28 0 0 4020 4047 123305956 123305929 9.000000e-03 52.8
27 TraesCS4D01G248200 chr2B 100.000 28 0 0 4020 4047 781580574 781580547 9.000000e-03 52.8


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 TraesCS4D01G248200 chr4D 416937671 416942899 5228 True 3291.00 9657 91.489333 1 5229 3 chr4D.!!$R1 5228
1 TraesCS4D01G248200 chr4B 514059988 514065554 5566 True 1180.45 4953 89.703833 115 5229 6 chr4B.!!$R2 5114
2 TraesCS4D01G248200 chr4A 47096402 47101397 4995 False 1383.40 3699 88.924000 1 5229 5 chr4A.!!$F1 5228

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
729 914 0.250727 CCACTCGAGCCCCTCAAAAA 60.251 55.000 13.61 0.00 0.00 1.94 F
1930 2626 1.069636 CCAGCAAGCAAACGAGAGAAC 60.070 52.381 0.00 0.00 0.00 3.01 F
3027 3792 2.361757 AGCTTGTTGTTTGTGCATGCTA 59.638 40.909 20.33 5.09 40.32 3.49 F
3682 4463 0.543749 ACCTGCTCTCTAATGGCACC 59.456 55.000 0.00 0.00 32.33 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2346 3044 0.250727 TGTTCTTTGGCTCTTCCCCG 60.251 55.000 0.00 0.00 0.00 5.73 R
3297 4064 1.143073 GTCCTTTCCTTGACTGGTGGT 59.857 52.381 0.00 0.00 0.00 4.16 R
3976 4761 0.033796 ATCGTTGGACGGAGGGAGTA 60.034 55.000 0.27 0.00 42.81 2.59 R
4850 5702 0.107654 AAGTTGAGCTACCCGGATGC 60.108 55.000 0.73 3.76 0.00 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
24 25 5.051891 AGAAAAATGAGAACATGCGAAGG 57.948 39.130 0.00 0.00 36.79 3.46
42 43 3.389741 GCAAAGACAATGCCTCGTG 57.610 52.632 0.00 0.00 37.85 4.35
59 60 1.334960 CGTGTCAGTTCATGTTTGGGC 60.335 52.381 0.00 0.00 0.00 5.36
99 100 8.355169 CAATTGGAGGAATATGTGATGGTTTAG 58.645 37.037 0.00 0.00 0.00 1.85
216 217 1.732941 TTTGAATCGTGGTAGCGCAT 58.267 45.000 11.47 0.00 0.00 4.73
218 219 2.812358 TGAATCGTGGTAGCGCATAT 57.188 45.000 11.47 0.00 0.00 1.78
281 283 3.896648 AATTGTCGCTGAAATGTCGTT 57.103 38.095 0.00 0.00 0.00 3.85
286 288 3.249799 TGTCGCTGAAATGTCGTTCAATT 59.750 39.130 0.00 0.00 37.08 2.32
347 356 3.591835 AGTGCCACCGGTTTTGCG 61.592 61.111 2.97 0.00 0.00 4.85
350 359 2.105328 GCCACCGGTTTTGCGTTT 59.895 55.556 2.97 0.00 0.00 3.60
406 415 6.910191 TCATATTCACTCATTGGTATTGGGT 58.090 36.000 0.00 0.00 0.00 4.51
408 417 4.380843 TTCACTCATTGGTATTGGGTGT 57.619 40.909 3.82 0.00 44.32 4.16
439 448 0.310854 ATCATCGCACGAGTCGCATA 59.689 50.000 13.59 0.00 0.00 3.14
452 461 1.924524 GTCGCATATACGCAACACACT 59.075 47.619 0.00 0.00 0.00 3.55
453 462 3.110358 GTCGCATATACGCAACACACTA 58.890 45.455 0.00 0.00 0.00 2.74
454 463 3.734231 GTCGCATATACGCAACACACTAT 59.266 43.478 0.00 0.00 0.00 2.12
505 530 2.125225 GACTCCCCAACCCCCTCT 59.875 66.667 0.00 0.00 0.00 3.69
535 560 0.389426 CCGGACGGACGATTTGACTT 60.389 55.000 4.40 0.00 37.50 3.01
542 567 5.338614 ACGGACGATTTGACTTGTAAAAG 57.661 39.130 0.00 0.00 0.00 2.27
553 582 9.849166 ATTTGACTTGTAAAAGAAAAACTCGAA 57.151 25.926 0.00 0.00 0.00 3.71
601 630 1.635817 ATGTCTGGGCTAACCGGCAT 61.636 55.000 0.00 0.00 45.92 4.40
641 670 1.880646 GCCTCCGTGCTGAACCTTTTA 60.881 52.381 0.00 0.00 0.00 1.52
652 681 4.805219 CTGAACCTTTTATTTTGACGGGG 58.195 43.478 0.00 0.00 0.00 5.73
653 682 4.216708 TGAACCTTTTATTTTGACGGGGT 58.783 39.130 0.00 0.00 0.00 4.95
654 683 5.383476 TGAACCTTTTATTTTGACGGGGTA 58.617 37.500 0.00 0.00 0.00 3.69
656 685 6.323225 TGAACCTTTTATTTTGACGGGGTAAA 59.677 34.615 0.00 0.00 0.00 2.01
657 686 6.728089 ACCTTTTATTTTGACGGGGTAAAA 57.272 33.333 0.00 0.00 0.00 1.52
658 687 7.122138 ACCTTTTATTTTGACGGGGTAAAAA 57.878 32.000 0.00 0.00 31.43 1.94
725 910 2.363018 CTCCACTCGAGCCCCTCA 60.363 66.667 13.61 0.00 0.00 3.86
726 911 1.984570 CTCCACTCGAGCCCCTCAA 60.985 63.158 13.61 0.00 0.00 3.02
727 912 1.535444 TCCACTCGAGCCCCTCAAA 60.535 57.895 13.61 0.00 0.00 2.69
729 914 0.250727 CCACTCGAGCCCCTCAAAAA 60.251 55.000 13.61 0.00 0.00 1.94
775 1455 1.283347 ACATCTGCACCCTCACTGAT 58.717 50.000 0.00 0.00 0.00 2.90
823 1503 4.113815 CCATGGGAGCAAGCCGGA 62.114 66.667 5.05 0.00 0.00 5.14
919 1600 1.745489 CTTTTCCTTCTCCGCCCGG 60.745 63.158 0.00 0.00 0.00 5.73
921 1602 2.059345 TTTTCCTTCTCCGCCCGGTT 62.059 55.000 6.61 0.00 36.47 4.44
1917 2613 4.579869 ACAGGTTAGTTGATACCAGCAAG 58.420 43.478 0.00 0.00 36.87 4.01
1930 2626 1.069636 CCAGCAAGCAAACGAGAGAAC 60.070 52.381 0.00 0.00 0.00 3.01
1937 2633 5.560953 GCAAGCAAACGAGAGAACTAATTGT 60.561 40.000 0.00 0.00 0.00 2.71
1938 2634 5.597813 AGCAAACGAGAGAACTAATTGTG 57.402 39.130 0.00 0.00 0.00 3.33
1939 2635 5.057149 AGCAAACGAGAGAACTAATTGTGT 58.943 37.500 0.00 0.00 0.00 3.72
1940 2636 5.050091 AGCAAACGAGAGAACTAATTGTGTG 60.050 40.000 0.00 0.00 0.00 3.82
2081 2777 5.885912 ACTACTGTTGACCATGTTTGTTCTT 59.114 36.000 0.00 0.00 0.00 2.52
2098 2794 7.426929 TTGTTCTTTACTCTCTGAATTCAGC 57.573 36.000 27.45 11.43 43.46 4.26
2101 2797 6.510879 TCTTTACTCTCTGAATTCAGCGTA 57.489 37.500 27.45 22.62 43.46 4.42
2329 3025 5.292589 TGCTATATTGTCTGATGCGCATATG 59.707 40.000 25.40 18.55 0.00 1.78
2346 3044 6.291585 GCGCATATGGTTTTTATAACAGCAAC 60.292 38.462 0.30 0.00 0.00 4.17
2664 3429 4.208460 AGCGACATATATTCGTTTGGTTCG 59.792 41.667 14.49 0.00 38.77 3.95
2675 3440 3.055963 TCGTTTGGTTCGGTATACCATGT 60.056 43.478 21.76 0.00 44.70 3.21
2713 3478 3.620821 GTGCTACTTCCAGATTGAAGCTC 59.379 47.826 0.90 0.00 44.50 4.09
2913 3678 8.407832 TGGACATGAATAGCAAAAATGACATAG 58.592 33.333 0.00 0.00 0.00 2.23
3004 3769 8.321353 AGATAAATGTGTGTTACTTCCAGATCA 58.679 33.333 0.00 0.00 0.00 2.92
3027 3792 2.361757 AGCTTGTTGTTTGTGCATGCTA 59.638 40.909 20.33 5.09 40.32 3.49
3225 3992 6.408548 GGTTCTCTTGGGAATCACTATGATGA 60.409 42.308 0.00 0.00 37.15 2.92
3354 4121 2.233676 TGTTCTCCATAGTGATGTGCGT 59.766 45.455 0.00 0.00 0.00 5.24
3498 4279 8.894768 AGTATTAACTATGGCTGTTTGAGATC 57.105 34.615 0.00 0.00 32.84 2.75
3600 4381 4.579869 TGATAAGGCAGTTGAGGAAAGAC 58.420 43.478 0.00 0.00 0.00 3.01
3672 4453 3.243201 CCAAAAAGTGAACACCTGCTCTC 60.243 47.826 1.11 0.00 0.00 3.20
3682 4463 0.543749 ACCTGCTCTCTAATGGCACC 59.456 55.000 0.00 0.00 32.33 5.01
3760 4541 7.787725 ACCTGTTTAGTTTTCACTAGTTGAG 57.212 36.000 0.00 0.00 36.81 3.02
3913 4697 3.818773 TCGAGACTGACTGAACATACACA 59.181 43.478 0.00 0.00 0.00 3.72
3968 4753 8.178313 TCATCTTTACAGTTCAAGAGTGACTA 57.822 34.615 0.00 0.00 32.53 2.59
3969 4754 8.807118 TCATCTTTACAGTTCAAGAGTGACTAT 58.193 33.333 0.00 0.00 32.53 2.12
3981 4766 9.871238 TTCAAGAGTGACTATAATTTGTACTCC 57.129 33.333 0.00 0.00 35.01 3.85
3982 4767 8.475639 TCAAGAGTGACTATAATTTGTACTCCC 58.524 37.037 0.00 0.00 35.01 4.30
3984 4769 8.240267 AGAGTGACTATAATTTGTACTCCCTC 57.760 38.462 0.00 0.00 35.01 4.30
3985 4770 7.288158 AGAGTGACTATAATTTGTACTCCCTCC 59.712 40.741 0.00 0.00 35.01 4.30
3986 4771 6.040616 AGTGACTATAATTTGTACTCCCTCCG 59.959 42.308 0.00 0.00 0.00 4.63
3988 4773 6.040166 TGACTATAATTTGTACTCCCTCCGTC 59.960 42.308 0.00 0.00 0.00 4.79
3989 4774 4.684484 ATAATTTGTACTCCCTCCGTCC 57.316 45.455 0.00 0.00 0.00 4.79
3990 4775 1.946984 ATTTGTACTCCCTCCGTCCA 58.053 50.000 0.00 0.00 0.00 4.02
3992 4777 0.971386 TTGTACTCCCTCCGTCCAAC 59.029 55.000 0.00 0.00 0.00 3.77
3993 4778 1.246056 TGTACTCCCTCCGTCCAACG 61.246 60.000 0.00 0.00 42.11 4.10
3994 4779 0.962356 GTACTCCCTCCGTCCAACGA 60.962 60.000 0.24 0.00 46.05 3.85
3995 4780 0.033796 TACTCCCTCCGTCCAACGAT 60.034 55.000 0.24 0.00 46.05 3.73
3996 4781 0.903454 ACTCCCTCCGTCCAACGATT 60.903 55.000 0.24 0.00 46.05 3.34
3997 4782 0.460284 CTCCCTCCGTCCAACGATTG 60.460 60.000 0.24 0.00 46.05 2.67
3998 4783 1.189524 TCCCTCCGTCCAACGATTGT 61.190 55.000 0.24 0.00 46.05 2.71
3999 4784 0.739813 CCCTCCGTCCAACGATTGTC 60.740 60.000 0.24 0.00 46.05 3.18
4000 4785 0.037697 CCTCCGTCCAACGATTGTCA 60.038 55.000 0.24 0.00 46.05 3.58
4001 4786 1.068474 CTCCGTCCAACGATTGTCAC 58.932 55.000 0.24 0.00 46.05 3.67
4002 4787 0.677288 TCCGTCCAACGATTGTCACT 59.323 50.000 0.24 0.00 46.05 3.41
4003 4788 0.790207 CCGTCCAACGATTGTCACTG 59.210 55.000 0.24 0.00 46.05 3.66
4004 4789 0.163788 CGTCCAACGATTGTCACTGC 59.836 55.000 0.00 0.00 46.05 4.40
4005 4790 1.512926 GTCCAACGATTGTCACTGCT 58.487 50.000 0.00 0.00 0.00 4.24
4006 4791 1.873591 GTCCAACGATTGTCACTGCTT 59.126 47.619 0.00 0.00 0.00 3.91
4007 4792 3.064207 GTCCAACGATTGTCACTGCTTA 58.936 45.455 0.00 0.00 0.00 3.09
4008 4793 3.496884 GTCCAACGATTGTCACTGCTTAA 59.503 43.478 0.00 0.00 0.00 1.85
4009 4794 4.154195 GTCCAACGATTGTCACTGCTTAAT 59.846 41.667 0.00 0.00 0.00 1.40
4010 4795 5.350365 GTCCAACGATTGTCACTGCTTAATA 59.650 40.000 0.00 0.00 0.00 0.98
4011 4796 5.580691 TCCAACGATTGTCACTGCTTAATAG 59.419 40.000 0.00 0.00 0.00 1.73
4012 4797 5.220662 CCAACGATTGTCACTGCTTAATAGG 60.221 44.000 0.00 0.00 0.00 2.57
4013 4798 4.442706 ACGATTGTCACTGCTTAATAGGG 58.557 43.478 0.00 0.00 0.00 3.53
4014 4799 3.248602 CGATTGTCACTGCTTAATAGGGC 59.751 47.826 0.00 0.00 0.00 5.19
4015 4800 2.309528 TGTCACTGCTTAATAGGGCG 57.690 50.000 0.00 0.00 0.00 6.13
4016 4801 1.828595 TGTCACTGCTTAATAGGGCGA 59.171 47.619 0.00 0.00 0.00 5.54
4017 4802 2.434336 TGTCACTGCTTAATAGGGCGAT 59.566 45.455 0.00 0.00 0.00 4.58
4018 4803 3.118408 TGTCACTGCTTAATAGGGCGATT 60.118 43.478 0.00 0.00 0.00 3.34
4019 4804 3.248602 GTCACTGCTTAATAGGGCGATTG 59.751 47.826 0.00 0.00 0.00 2.67
4020 4805 3.118408 TCACTGCTTAATAGGGCGATTGT 60.118 43.478 0.00 0.00 0.00 2.71
4021 4806 3.248602 CACTGCTTAATAGGGCGATTGTC 59.751 47.826 0.00 0.00 0.00 3.18
4022 4807 2.808543 CTGCTTAATAGGGCGATTGTCC 59.191 50.000 0.00 0.00 41.57 4.02
4023 4808 2.152016 GCTTAATAGGGCGATTGTCCC 58.848 52.381 0.00 2.00 42.57 4.46
4024 4809 2.486548 GCTTAATAGGGCGATTGTCCCA 60.487 50.000 13.18 0.00 46.36 4.37
4025 4810 2.922740 TAATAGGGCGATTGTCCCAC 57.077 50.000 13.18 0.00 46.36 4.61
4026 4811 0.916086 AATAGGGCGATTGTCCCACA 59.084 50.000 13.18 3.30 46.36 4.17
4027 4812 0.916086 ATAGGGCGATTGTCCCACAA 59.084 50.000 13.18 0.00 46.36 3.33
4044 4829 9.521841 TGTCCCACAATATAAGATGTTTTTACA 57.478 29.630 0.00 0.00 0.00 2.41
4068 4853 8.508875 ACAAGTAAAAACGTCTTATATTGTGGG 58.491 33.333 15.51 0.00 0.00 4.61
4069 4854 8.723311 CAAGTAAAAACGTCTTATATTGTGGGA 58.277 33.333 0.00 0.00 0.00 4.37
4070 4855 8.488651 AGTAAAAACGTCTTATATTGTGGGAG 57.511 34.615 0.00 0.00 0.00 4.30
4071 4856 6.753107 AAAAACGTCTTATATTGTGGGAGG 57.247 37.500 0.00 0.00 0.00 4.30
4072 4857 4.417426 AACGTCTTATATTGTGGGAGGG 57.583 45.455 0.00 0.00 0.00 4.30
4105 4890 5.047164 TGAATTCATCTTTCACCATGGGTTG 60.047 40.000 18.09 6.33 31.02 3.77
4195 4988 3.375299 GTGAATGATGGCTGACAGTTACC 59.625 47.826 3.99 0.00 0.00 2.85
4257 5050 1.079875 CCCGCAAGCAACATGAATGC 61.080 55.000 16.88 16.88 44.15 3.56
4291 5087 2.252346 GGAGCCGCAGAGCATCATG 61.252 63.158 0.00 0.00 37.82 3.07
4362 5158 1.803334 TAACGTCTCCATGTGCAACC 58.197 50.000 0.00 0.00 34.36 3.77
4410 5213 3.874543 ACTTTTGTTCTGTGTACATGCGA 59.125 39.130 0.00 0.00 0.00 5.10
4497 5300 1.476891 GTACAAGAGACCGCAGATGGA 59.523 52.381 0.00 0.00 0.00 3.41
4547 5350 6.816640 TCTTGTATTCCTAAGTTGATTGTCGG 59.183 38.462 0.00 0.00 0.00 4.79
4629 5481 6.578919 GCTGTTGCTGAATTTTACTGTTAGTC 59.421 38.462 0.00 0.00 36.03 2.59
4634 5486 5.220416 GCTGAATTTTACTGTTAGTCGCGAT 60.220 40.000 14.06 3.98 0.00 4.58
4654 5506 6.394867 GCGATCGAATTGAAAATAGTTTTGC 58.605 36.000 21.57 0.00 31.94 3.68
4663 5515 5.833082 TGAAAATAGTTTTGCGGCAAACTA 58.167 33.333 26.39 25.77 32.79 2.24
4680 5532 5.391523 GCAAACTAAAGTGCGTATGGAATGA 60.392 40.000 0.00 0.00 0.00 2.57
4694 5546 7.627088 GCGTATGGAATGAAATATGGATCAAGG 60.627 40.741 0.00 0.00 0.00 3.61
4701 5553 6.757897 TGAAATATGGATCAAGGTTGTCAC 57.242 37.500 0.00 0.00 0.00 3.67
4707 5559 1.227999 ATCAAGGTTGTCACGTGGCG 61.228 55.000 16.50 0.00 0.00 5.69
4729 5581 3.541713 GCAGGGGCGGACCTAGAG 61.542 72.222 0.00 0.00 39.34 2.43
4730 5582 2.279073 CAGGGGCGGACCTAGAGA 59.721 66.667 0.00 0.00 39.34 3.10
4731 5583 1.830408 CAGGGGCGGACCTAGAGAG 60.830 68.421 0.00 0.00 39.34 3.20
4732 5584 2.007568 AGGGGCGGACCTAGAGAGA 61.008 63.158 0.00 0.00 39.65 3.10
4733 5585 1.076192 GGGGCGGACCTAGAGAGAA 60.076 63.158 0.00 0.00 40.03 2.87
4734 5586 0.686769 GGGGCGGACCTAGAGAGAAA 60.687 60.000 0.00 0.00 40.03 2.52
4735 5587 1.192428 GGGCGGACCTAGAGAGAAAA 58.808 55.000 0.00 0.00 35.85 2.29
4736 5588 1.763545 GGGCGGACCTAGAGAGAAAAT 59.236 52.381 0.00 0.00 35.85 1.82
4737 5589 2.483889 GGGCGGACCTAGAGAGAAAATG 60.484 54.545 0.00 0.00 35.85 2.32
4738 5590 2.431057 GGCGGACCTAGAGAGAAAATGA 59.569 50.000 0.00 0.00 0.00 2.57
4739 5591 3.449632 GCGGACCTAGAGAGAAAATGAC 58.550 50.000 0.00 0.00 0.00 3.06
4740 5592 3.738590 GCGGACCTAGAGAGAAAATGACC 60.739 52.174 0.00 0.00 0.00 4.02
4741 5593 3.181474 CGGACCTAGAGAGAAAATGACCC 60.181 52.174 0.00 0.00 0.00 4.46
4742 5594 3.775316 GGACCTAGAGAGAAAATGACCCA 59.225 47.826 0.00 0.00 0.00 4.51
4743 5595 4.141824 GGACCTAGAGAGAAAATGACCCAG 60.142 50.000 0.00 0.00 0.00 4.45
4744 5596 4.430441 ACCTAGAGAGAAAATGACCCAGT 58.570 43.478 0.00 0.00 0.00 4.00
4745 5597 4.223923 ACCTAGAGAGAAAATGACCCAGTG 59.776 45.833 0.00 0.00 0.00 3.66
4746 5598 4.223923 CCTAGAGAGAAAATGACCCAGTGT 59.776 45.833 0.00 0.00 0.00 3.55
4747 5599 4.278975 AGAGAGAAAATGACCCAGTGTC 57.721 45.455 0.00 0.00 44.72 3.67
4748 5600 3.008485 AGAGAGAAAATGACCCAGTGTCC 59.992 47.826 0.00 0.00 43.78 4.02
4749 5601 2.982488 AGAGAAAATGACCCAGTGTCCT 59.018 45.455 0.00 0.00 43.78 3.85
4750 5602 4.168101 AGAGAAAATGACCCAGTGTCCTA 58.832 43.478 0.00 0.00 43.78 2.94
4751 5603 4.223923 AGAGAAAATGACCCAGTGTCCTAG 59.776 45.833 0.00 0.00 43.78 3.02
4752 5604 2.789409 AAATGACCCAGTGTCCTAGC 57.211 50.000 0.00 0.00 43.78 3.42
4753 5605 1.656587 AATGACCCAGTGTCCTAGCA 58.343 50.000 0.00 0.00 43.78 3.49
4754 5606 1.885049 ATGACCCAGTGTCCTAGCAT 58.115 50.000 0.00 0.00 43.78 3.79
4755 5607 2.543037 TGACCCAGTGTCCTAGCATA 57.457 50.000 0.00 0.00 43.78 3.14
4756 5608 3.046283 TGACCCAGTGTCCTAGCATAT 57.954 47.619 0.00 0.00 43.78 1.78
4757 5609 2.700371 TGACCCAGTGTCCTAGCATATG 59.300 50.000 0.00 0.00 43.78 1.78
4758 5610 2.965831 GACCCAGTGTCCTAGCATATGA 59.034 50.000 6.97 0.00 38.09 2.15
4759 5611 3.580458 GACCCAGTGTCCTAGCATATGAT 59.420 47.826 6.97 1.82 38.09 2.45
4760 5612 3.580458 ACCCAGTGTCCTAGCATATGATC 59.420 47.826 6.97 0.00 0.00 2.92
4761 5613 3.580022 CCCAGTGTCCTAGCATATGATCA 59.420 47.826 6.97 0.00 0.00 2.92
4762 5614 4.562347 CCCAGTGTCCTAGCATATGATCAC 60.562 50.000 6.97 4.65 0.00 3.06
4763 5615 4.282957 CCAGTGTCCTAGCATATGATCACT 59.717 45.833 6.97 7.05 32.51 3.41
4764 5616 5.468592 CAGTGTCCTAGCATATGATCACTC 58.531 45.833 6.97 0.00 31.20 3.51
4765 5617 5.010415 CAGTGTCCTAGCATATGATCACTCA 59.990 44.000 6.97 0.00 31.20 3.41
4766 5618 5.779260 AGTGTCCTAGCATATGATCACTCAT 59.221 40.000 6.97 0.00 44.39 2.90
4767 5619 6.950619 AGTGTCCTAGCATATGATCACTCATA 59.049 38.462 6.97 0.00 45.91 2.15
4793 5645 3.017048 CATCTTAAAGATGGGGTGGCA 57.983 47.619 0.00 0.00 46.34 4.92
4794 5646 2.507407 TCTTAAAGATGGGGTGGCAC 57.493 50.000 9.70 9.70 0.00 5.01
4795 5647 1.707989 TCTTAAAGATGGGGTGGCACA 59.292 47.619 20.82 0.00 0.00 4.57
4796 5648 3.877735 ATCTTAAAGATGGGGTGGCACAC 60.878 47.826 20.82 17.01 46.17 3.82
4813 5665 7.929941 TGGCACACACTATATTTTGTATGAA 57.070 32.000 0.14 0.00 0.00 2.57
4814 5666 8.341892 TGGCACACACTATATTTTGTATGAAA 57.658 30.769 0.14 0.00 0.00 2.69
4815 5667 8.240682 TGGCACACACTATATTTTGTATGAAAC 58.759 33.333 0.14 0.00 0.00 2.78
4816 5668 8.458843 GGCACACACTATATTTTGTATGAAACT 58.541 33.333 0.14 0.00 0.00 2.66
4817 5669 9.840427 GCACACACTATATTTTGTATGAAACTT 57.160 29.630 0.14 0.00 0.00 2.66
4841 5693 1.247567 AGAAAACATCTTGCACCCGG 58.752 50.000 0.00 0.00 33.39 5.73
4842 5694 0.958822 GAAAACATCTTGCACCCGGT 59.041 50.000 0.00 0.00 0.00 5.28
4843 5695 0.673437 AAAACATCTTGCACCCGGTG 59.327 50.000 13.71 13.71 36.51 4.94
4844 5696 0.467290 AAACATCTTGCACCCGGTGT 60.467 50.000 18.95 0.00 35.75 4.16
4845 5697 0.889186 AACATCTTGCACCCGGTGTC 60.889 55.000 18.95 11.53 35.75 3.67
4846 5698 2.040544 CATCTTGCACCCGGTGTCC 61.041 63.158 18.95 3.90 35.75 4.02
4847 5699 2.224159 ATCTTGCACCCGGTGTCCT 61.224 57.895 18.95 0.00 35.75 3.85
4848 5700 2.469465 ATCTTGCACCCGGTGTCCTG 62.469 60.000 18.95 7.40 35.75 3.86
4849 5701 3.476031 CTTGCACCCGGTGTCCTGT 62.476 63.158 18.95 0.00 35.75 4.00
4850 5702 3.765894 TTGCACCCGGTGTCCTGTG 62.766 63.158 18.95 0.62 35.75 3.66
4852 5704 4.248842 CACCCGGTGTCCTGTGCA 62.249 66.667 9.64 0.00 0.00 4.57
4853 5705 3.249189 ACCCGGTGTCCTGTGCAT 61.249 61.111 0.00 0.00 0.00 3.96
4854 5706 2.436646 CCCGGTGTCCTGTGCATC 60.437 66.667 0.00 0.00 0.00 3.91
4855 5707 2.436646 CCGGTGTCCTGTGCATCC 60.437 66.667 0.00 0.00 0.00 3.51
4856 5708 2.815211 CGGTGTCCTGTGCATCCG 60.815 66.667 0.00 0.00 0.00 4.18
4857 5709 2.436646 GGTGTCCTGTGCATCCGG 60.437 66.667 0.00 0.00 0.00 5.14
4858 5710 2.436646 GTGTCCTGTGCATCCGGG 60.437 66.667 0.00 0.00 0.00 5.73
4859 5711 2.927856 TGTCCTGTGCATCCGGGT 60.928 61.111 0.00 0.00 0.00 5.28
4860 5712 1.610967 TGTCCTGTGCATCCGGGTA 60.611 57.895 0.00 0.00 0.00 3.69
4861 5713 1.144057 GTCCTGTGCATCCGGGTAG 59.856 63.158 0.00 0.00 0.00 3.18
4862 5714 2.203070 CCTGTGCATCCGGGTAGC 60.203 66.667 0.00 3.91 0.00 3.58
4863 5715 2.735772 CCTGTGCATCCGGGTAGCT 61.736 63.158 0.00 0.00 0.00 3.32
4864 5716 1.227380 CTGTGCATCCGGGTAGCTC 60.227 63.158 0.00 5.22 0.00 4.09
4865 5717 1.960040 CTGTGCATCCGGGTAGCTCA 61.960 60.000 0.00 9.71 0.00 4.26
4866 5718 1.220749 GTGCATCCGGGTAGCTCAA 59.779 57.895 0.00 0.00 0.00 3.02
4867 5719 1.090052 GTGCATCCGGGTAGCTCAAC 61.090 60.000 0.00 0.00 0.00 3.18
4868 5720 1.264749 TGCATCCGGGTAGCTCAACT 61.265 55.000 0.00 0.00 0.00 3.16
4869 5721 0.107654 GCATCCGGGTAGCTCAACTT 60.108 55.000 0.00 0.00 0.00 2.66
4870 5722 1.656652 CATCCGGGTAGCTCAACTTG 58.343 55.000 0.00 0.00 0.00 3.16
4871 5723 0.541863 ATCCGGGTAGCTCAACTTGG 59.458 55.000 0.00 0.00 0.00 3.61
4872 5724 1.078426 CCGGGTAGCTCAACTTGGG 60.078 63.158 0.00 0.00 0.00 4.12
4873 5725 1.677552 CGGGTAGCTCAACTTGGGT 59.322 57.895 0.00 0.00 0.00 4.51
4874 5726 0.899720 CGGGTAGCTCAACTTGGGTA 59.100 55.000 0.00 0.00 0.00 3.69
4875 5727 1.405121 CGGGTAGCTCAACTTGGGTAC 60.405 57.143 0.00 9.42 36.19 3.34
4876 5728 1.405121 GGGTAGCTCAACTTGGGTACG 60.405 57.143 0.00 0.00 37.31 3.67
4877 5729 1.356938 GTAGCTCAACTTGGGTACGC 58.643 55.000 2.35 2.35 0.00 4.42
4878 5730 0.248289 TAGCTCAACTTGGGTACGCC 59.752 55.000 7.55 0.31 0.00 5.68
4879 5731 2.388232 GCTCAACTTGGGTACGCCG 61.388 63.158 7.55 1.27 34.97 6.46
4880 5732 2.357760 TCAACTTGGGTACGCCGC 60.358 61.111 7.55 0.00 34.97 6.53
4881 5733 3.784412 CAACTTGGGTACGCCGCG 61.784 66.667 12.14 12.14 34.97 6.46
4882 5734 4.303993 AACTTGGGTACGCCGCGT 62.304 61.111 23.72 23.72 44.35 6.01
4883 5735 2.929903 AACTTGGGTACGCCGCGTA 61.930 57.895 21.35 21.35 41.54 4.42
4884 5736 2.105528 CTTGGGTACGCCGCGTAT 59.894 61.111 27.02 4.95 44.12 3.06
4885 5737 1.359833 CTTGGGTACGCCGCGTATA 59.640 57.895 27.02 14.58 44.12 1.47
4886 5738 0.662374 CTTGGGTACGCCGCGTATAG 60.662 60.000 27.02 17.44 44.12 1.31
4900 5752 4.381863 CCGCGTATAGTAACTGTTATGCTG 59.618 45.833 4.92 0.00 0.00 4.41
4925 5778 2.356535 GCACACCAGATCCCTGAGAAAT 60.357 50.000 0.00 0.00 43.02 2.17
4948 5803 9.829507 AAATTGAGATGAGATAACAGTTAGAGG 57.170 33.333 0.00 0.00 0.00 3.69
4963 5818 0.106149 AGAGGTTCACGCCGAAGTTT 59.894 50.000 0.00 0.00 33.09 2.66
4968 5824 3.187842 AGGTTCACGCCGAAGTTTAAATC 59.812 43.478 0.00 0.00 33.09 2.17
5021 5879 4.633565 TGTGTGCGTATCATCTTGCAAATA 59.366 37.500 0.00 0.00 39.34 1.40
5028 5886 6.576313 GCGTATCATCTTGCAAATAGTCATTG 59.424 38.462 0.00 0.00 0.00 2.82
5060 5918 0.779997 AAACCAAGCCAGAGTGGGAT 59.220 50.000 0.00 0.00 39.39 3.85
5078 5936 7.072562 AGTGGGATAATATGACTTCTGTCTCT 58.927 38.462 0.00 0.00 43.29 3.10
5080 5938 7.014711 GTGGGATAATATGACTTCTGTCTCTGA 59.985 40.741 0.00 0.00 43.29 3.27
5097 5955 3.564264 TCTGAGGGACTGAGATGAGATG 58.436 50.000 0.00 0.00 45.39 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.536766 CTTTGCCTTCGCATGTTCTCA 59.463 47.619 0.00 0.00 46.67 3.27
24 25 0.593128 ACACGAGGCATTGTCTTTGC 59.407 50.000 0.00 0.00 39.41 3.68
42 43 0.951558 ACGCCCAAACATGAACTGAC 59.048 50.000 0.00 0.00 0.00 3.51
59 60 3.334691 TCCAATTGTGCCTTCTCTAACG 58.665 45.455 4.43 0.00 0.00 3.18
99 100 5.929697 TGACATGTTCTCACATCACTTTC 57.070 39.130 0.00 0.00 42.14 2.62
253 254 6.269315 ACATTTCAGCGACAATTTTGTGTTA 58.731 32.000 0.00 0.00 42.43 2.41
281 283 6.701841 GTCGAATGCTCCATTACTCTAATTGA 59.298 38.462 0.00 0.00 33.90 2.57
286 288 5.359860 TCTTGTCGAATGCTCCATTACTCTA 59.640 40.000 0.00 0.00 33.90 2.43
383 392 6.547141 ACACCCAATACCAATGAGTGAATATG 59.453 38.462 0.00 0.00 0.00 1.78
397 406 2.092323 GCTTGAGGAACACCCAATACC 58.908 52.381 0.00 0.00 37.41 2.73
406 415 2.349590 CGATGATGTGCTTGAGGAACA 58.650 47.619 0.00 0.00 37.96 3.18
408 417 1.338960 TGCGATGATGTGCTTGAGGAA 60.339 47.619 0.00 0.00 0.00 3.36
452 461 3.316868 TCTGATGCACCGAACATACGATA 59.683 43.478 0.00 0.00 35.09 2.92
453 462 2.100749 TCTGATGCACCGAACATACGAT 59.899 45.455 0.00 0.00 35.09 3.73
454 463 1.474879 TCTGATGCACCGAACATACGA 59.525 47.619 0.00 0.00 35.09 3.43
505 530 3.151710 CGTCCGGGCATGTAGGGA 61.152 66.667 6.96 0.00 0.00 4.20
527 552 9.849166 TTCGAGTTTTTCTTTTACAAGTCAAAT 57.151 25.926 0.00 0.00 0.00 2.32
535 560 7.701924 TCGTCTAGTTCGAGTTTTTCTTTTACA 59.298 33.333 8.23 0.00 33.38 2.41
542 567 5.306590 GCATTCGTCTAGTTCGAGTTTTTC 58.693 41.667 11.09 0.40 38.52 2.29
553 582 2.293677 CGGTATGAGGCATTCGTCTAGT 59.706 50.000 0.00 0.00 0.00 2.57
601 630 2.089201 CTGCTTCCAACAGATGATGCA 58.911 47.619 0.00 0.00 37.32 3.96
657 686 2.817844 GGGGCTGTCACGATAAGTTTTT 59.182 45.455 0.00 0.00 0.00 1.94
658 687 2.433436 GGGGCTGTCACGATAAGTTTT 58.567 47.619 0.00 0.00 0.00 2.43
659 688 1.674817 CGGGGCTGTCACGATAAGTTT 60.675 52.381 0.00 0.00 0.00 2.66
701 886 4.803426 CTCGAGTGGAGGCGTGGC 62.803 72.222 3.62 0.00 39.22 5.01
823 1503 1.956629 ATTTCGCACTCGATCCCGGT 61.957 55.000 0.00 0.00 45.04 5.28
896 1576 0.037734 GCGGAGAAGGAAAAGGGGAA 59.962 55.000 0.00 0.00 0.00 3.97
919 1600 2.322830 GGTGGAAGCGAACGGGAAC 61.323 63.158 0.00 0.00 0.00 3.62
921 1602 4.011517 GGGTGGAAGCGAACGGGA 62.012 66.667 0.00 0.00 33.03 5.14
929 1610 2.506472 GAGATCGGGGGTGGAAGC 59.494 66.667 0.00 0.00 0.00 3.86
1917 2613 5.140177 CACACAATTAGTTCTCTCGTTTGC 58.860 41.667 0.00 0.00 0.00 3.68
1930 2626 5.470098 AGCAACAACCTAGACACACAATTAG 59.530 40.000 0.00 0.00 0.00 1.73
1937 2633 3.070878 TGATCAGCAACAACCTAGACACA 59.929 43.478 0.00 0.00 0.00 3.72
1938 2634 3.664107 TGATCAGCAACAACCTAGACAC 58.336 45.455 0.00 0.00 0.00 3.67
1939 2635 4.350368 TTGATCAGCAACAACCTAGACA 57.650 40.909 0.00 0.00 0.00 3.41
1940 2636 4.757149 ACTTTGATCAGCAACAACCTAGAC 59.243 41.667 0.00 0.00 35.91 2.59
2081 2777 9.249457 CAAATATACGCTGAATTCAGAGAGTAA 57.751 33.333 36.16 23.17 46.59 2.24
2098 2794 5.237127 TGCCAGATCAAAGAGCAAATATACG 59.763 40.000 0.00 0.00 0.00 3.06
2101 2797 5.198965 ACTGCCAGATCAAAGAGCAAATAT 58.801 37.500 0.00 0.00 32.14 1.28
2329 3025 3.506844 TCCCCGTTGCTGTTATAAAAACC 59.493 43.478 0.00 0.00 0.00 3.27
2346 3044 0.250727 TGTTCTTTGGCTCTTCCCCG 60.251 55.000 0.00 0.00 0.00 5.73
2675 3440 7.769044 GGAAGTAGCACACATTTATCTTCCTTA 59.231 37.037 11.73 0.00 43.34 2.69
2713 3478 1.002576 TCACAGCATGCTCAAACAACG 60.003 47.619 19.68 6.54 42.53 4.10
2867 3632 8.129496 TGTCCAAGAACTAGTATGTTGTCATA 57.871 34.615 0.00 0.00 35.70 2.15
2891 3656 9.229784 GACACTATGTCATTTTTGCTATTCATG 57.770 33.333 4.08 0.00 46.22 3.07
3004 3769 2.352342 GCATGCACAAACAACAAGCTTT 59.648 40.909 14.21 0.00 0.00 3.51
3027 3792 4.142609 ACGATGCCATAAGAACAGTCAT 57.857 40.909 0.00 0.00 0.00 3.06
3297 4064 1.143073 GTCCTTTCCTTGACTGGTGGT 59.857 52.381 0.00 0.00 0.00 4.16
3354 4121 1.308047 ATTCAGCACGTTCAACTGCA 58.692 45.000 12.60 0.00 35.73 4.41
3408 4182 4.497300 GCTTCAAACCATGTGCAATGTAT 58.503 39.130 0.00 0.00 32.66 2.29
3473 4254 8.709308 AGATCTCAAACAGCCATAGTTAATACT 58.291 33.333 0.00 0.00 38.44 2.12
3498 4279 7.432869 CAAACTTGATCCTCTCTGATACCTAG 58.567 42.308 0.00 0.00 0.00 3.02
3600 4381 1.541588 GGCTGTGCTTTAGGAACAAGG 59.458 52.381 0.00 0.00 32.20 3.61
3672 4453 9.896645 AAATATCATCTATACAGGTGCCATTAG 57.103 33.333 0.00 0.00 32.46 1.73
3760 4541 9.048446 TGTTAGTTACTTGTAAATGGACAACTC 57.952 33.333 4.07 0.00 34.40 3.01
3968 4753 4.035112 TGGACGGAGGGAGTACAAATTAT 58.965 43.478 0.00 0.00 27.89 1.28
3969 4754 3.443052 TGGACGGAGGGAGTACAAATTA 58.557 45.455 0.00 0.00 27.89 1.40
3971 4756 1.946984 TGGACGGAGGGAGTACAAAT 58.053 50.000 0.00 0.00 27.89 2.32
3972 4757 1.345415 GTTGGACGGAGGGAGTACAAA 59.655 52.381 0.00 0.00 43.26 2.83
3973 4758 0.971386 GTTGGACGGAGGGAGTACAA 59.029 55.000 0.00 0.00 39.86 2.41
3974 4759 1.246056 CGTTGGACGGAGGGAGTACA 61.246 60.000 0.00 0.00 38.08 2.90
3975 4760 0.962356 TCGTTGGACGGAGGGAGTAC 60.962 60.000 0.27 0.00 42.81 2.73
3976 4761 0.033796 ATCGTTGGACGGAGGGAGTA 60.034 55.000 0.27 0.00 42.81 2.59
3977 4762 0.903454 AATCGTTGGACGGAGGGAGT 60.903 55.000 0.27 0.00 42.81 3.85
3978 4763 0.460284 CAATCGTTGGACGGAGGGAG 60.460 60.000 0.27 0.00 42.81 4.30
3979 4764 1.189524 ACAATCGTTGGACGGAGGGA 61.190 55.000 0.27 0.00 42.81 4.20
3980 4765 0.739813 GACAATCGTTGGACGGAGGG 60.740 60.000 0.27 0.00 42.81 4.30
3981 4766 0.037697 TGACAATCGTTGGACGGAGG 60.038 55.000 0.27 0.00 42.81 4.30
3982 4767 1.068474 GTGACAATCGTTGGACGGAG 58.932 55.000 0.27 0.00 42.81 4.63
3984 4769 0.790207 CAGTGACAATCGTTGGACGG 59.210 55.000 0.27 0.00 42.81 4.79
3985 4770 0.163788 GCAGTGACAATCGTTGGACG 59.836 55.000 0.00 0.00 44.19 4.79
3986 4771 1.512926 AGCAGTGACAATCGTTGGAC 58.487 50.000 0.00 0.56 34.12 4.02
3988 4773 4.685169 ATTAAGCAGTGACAATCGTTGG 57.315 40.909 0.00 0.00 34.12 3.77
3989 4774 5.220662 CCCTATTAAGCAGTGACAATCGTTG 60.221 44.000 0.00 0.00 0.00 4.10
3990 4775 4.876107 CCCTATTAAGCAGTGACAATCGTT 59.124 41.667 0.00 0.00 0.00 3.85
3992 4777 3.248602 GCCCTATTAAGCAGTGACAATCG 59.751 47.826 0.00 0.00 0.00 3.34
3993 4778 3.248602 CGCCCTATTAAGCAGTGACAATC 59.751 47.826 0.00 0.00 0.00 2.67
3994 4779 3.118408 TCGCCCTATTAAGCAGTGACAAT 60.118 43.478 0.00 0.00 0.00 2.71
3995 4780 2.235155 TCGCCCTATTAAGCAGTGACAA 59.765 45.455 0.00 0.00 0.00 3.18
3996 4781 1.828595 TCGCCCTATTAAGCAGTGACA 59.171 47.619 0.00 0.00 0.00 3.58
3997 4782 2.596904 TCGCCCTATTAAGCAGTGAC 57.403 50.000 0.00 0.00 0.00 3.67
3998 4783 3.118408 ACAATCGCCCTATTAAGCAGTGA 60.118 43.478 0.00 0.00 0.00 3.41
3999 4784 3.206150 ACAATCGCCCTATTAAGCAGTG 58.794 45.455 0.00 0.00 0.00 3.66
4000 4785 3.467803 GACAATCGCCCTATTAAGCAGT 58.532 45.455 0.00 0.00 0.00 4.40
4001 4786 2.808543 GGACAATCGCCCTATTAAGCAG 59.191 50.000 0.00 0.00 0.00 4.24
4002 4787 2.486548 GGGACAATCGCCCTATTAAGCA 60.487 50.000 0.00 0.00 42.56 3.91
4003 4788 2.152016 GGGACAATCGCCCTATTAAGC 58.848 52.381 0.00 0.00 42.56 3.09
4004 4789 3.139077 GTGGGACAATCGCCCTATTAAG 58.861 50.000 0.00 0.00 46.19 1.85
4005 4790 2.506231 TGTGGGACAATCGCCCTATTAA 59.494 45.455 0.00 0.00 46.19 1.40
4006 4791 2.120312 TGTGGGACAATCGCCCTATTA 58.880 47.619 0.00 0.00 46.19 0.98
4007 4792 0.916086 TGTGGGACAATCGCCCTATT 59.084 50.000 0.00 0.00 46.19 1.73
4008 4793 0.916086 TTGTGGGACAATCGCCCTAT 59.084 50.000 0.00 0.00 46.19 2.57
4009 4794 0.916086 ATTGTGGGACAATCGCCCTA 59.084 50.000 0.00 0.00 44.91 3.53
4010 4795 0.916086 TATTGTGGGACAATCGCCCT 59.084 50.000 5.24 0.00 44.91 5.19
4011 4796 1.981256 ATATTGTGGGACAATCGCCC 58.019 50.000 5.24 0.00 44.91 6.13
4012 4797 4.385825 TCTTATATTGTGGGACAATCGCC 58.614 43.478 5.24 0.00 44.91 5.54
4013 4798 5.470098 ACATCTTATATTGTGGGACAATCGC 59.530 40.000 5.24 0.00 44.91 4.58
4014 4799 7.496529 AACATCTTATATTGTGGGACAATCG 57.503 36.000 5.24 0.00 44.91 3.34
4018 4803 9.521841 TGTAAAAACATCTTATATTGTGGGACA 57.478 29.630 0.00 0.00 0.00 4.02
4042 4827 8.508875 CCCACAATATAAGACGTTTTTACTTGT 58.491 33.333 0.00 7.05 0.00 3.16
4043 4828 8.723311 TCCCACAATATAAGACGTTTTTACTTG 58.277 33.333 0.00 6.53 0.00 3.16
4044 4829 8.851541 TCCCACAATATAAGACGTTTTTACTT 57.148 30.769 0.00 0.00 0.00 2.24
4045 4830 7.551617 CCTCCCACAATATAAGACGTTTTTACT 59.448 37.037 0.00 0.00 0.00 2.24
4046 4831 7.201670 CCCTCCCACAATATAAGACGTTTTTAC 60.202 40.741 0.00 0.00 0.00 2.01
4047 4832 6.824704 CCCTCCCACAATATAAGACGTTTTTA 59.175 38.462 0.00 0.00 0.00 1.52
4048 4833 5.650703 CCCTCCCACAATATAAGACGTTTTT 59.349 40.000 0.00 0.00 0.00 1.94
4049 4834 5.045432 TCCCTCCCACAATATAAGACGTTTT 60.045 40.000 0.00 0.00 0.00 2.43
4050 4835 4.472108 TCCCTCCCACAATATAAGACGTTT 59.528 41.667 0.00 0.00 0.00 3.60
4051 4836 4.035112 TCCCTCCCACAATATAAGACGTT 58.965 43.478 0.00 0.00 0.00 3.99
4052 4837 3.387050 GTCCCTCCCACAATATAAGACGT 59.613 47.826 0.00 0.00 0.00 4.34
4053 4838 3.386726 TGTCCCTCCCACAATATAAGACG 59.613 47.826 0.00 0.00 0.00 4.18
4054 4839 5.123936 GTTGTCCCTCCCACAATATAAGAC 58.876 45.833 0.00 0.00 36.19 3.01
4055 4840 4.165372 GGTTGTCCCTCCCACAATATAAGA 59.835 45.833 0.00 0.00 36.19 2.10
4056 4841 4.080015 TGGTTGTCCCTCCCACAATATAAG 60.080 45.833 0.00 0.00 36.19 1.73
4057 4842 3.853181 TGGTTGTCCCTCCCACAATATAA 59.147 43.478 0.00 0.00 36.19 0.98
4058 4843 3.465832 TGGTTGTCCCTCCCACAATATA 58.534 45.455 0.00 0.00 36.19 0.86
4059 4844 2.283834 TGGTTGTCCCTCCCACAATAT 58.716 47.619 0.00 0.00 36.19 1.28
4060 4845 1.748732 TGGTTGTCCCTCCCACAATA 58.251 50.000 0.00 0.00 36.19 1.90
4061 4846 0.856982 TTGGTTGTCCCTCCCACAAT 59.143 50.000 0.00 0.00 36.19 2.71
4062 4847 0.856982 ATTGGTTGTCCCTCCCACAA 59.143 50.000 0.00 0.00 0.00 3.33
4063 4848 0.112218 CATTGGTTGTCCCTCCCACA 59.888 55.000 0.00 0.00 0.00 4.17
4064 4849 0.404040 TCATTGGTTGTCCCTCCCAC 59.596 55.000 0.00 0.00 0.00 4.61
4065 4850 1.153539 TTCATTGGTTGTCCCTCCCA 58.846 50.000 0.00 0.00 0.00 4.37
4066 4851 2.532250 ATTCATTGGTTGTCCCTCCC 57.468 50.000 0.00 0.00 0.00 4.30
4067 4852 3.430453 TGAATTCATTGGTTGTCCCTCC 58.570 45.455 3.38 0.00 0.00 4.30
4068 4853 4.952335 AGATGAATTCATTGGTTGTCCCTC 59.048 41.667 21.57 5.85 36.57 4.30
4069 4854 4.939255 AGATGAATTCATTGGTTGTCCCT 58.061 39.130 21.57 8.30 36.57 4.20
4070 4855 5.665916 AAGATGAATTCATTGGTTGTCCC 57.334 39.130 21.57 6.18 36.57 4.46
4071 4856 6.587608 GTGAAAGATGAATTCATTGGTTGTCC 59.412 38.462 21.57 6.86 38.89 4.02
4072 4857 6.587608 GGTGAAAGATGAATTCATTGGTTGTC 59.412 38.462 21.57 12.48 38.89 3.18
4105 4890 7.585286 ACACAACATGCATTTTATCAATCAC 57.415 32.000 0.00 0.00 0.00 3.06
4136 4925 5.762218 GGTGAGCATGCTTTGTATAGAGAAT 59.238 40.000 23.61 0.00 0.00 2.40
4273 5066 2.110627 ATGATGCTCTGCGGCTCC 59.889 61.111 0.00 0.00 0.00 4.70
4362 5158 2.163818 TCACCCAAGCTACAAAGACG 57.836 50.000 0.00 0.00 0.00 4.18
4410 5213 6.567321 GCACAGAGCTATCGAAATGCATAAAT 60.567 38.462 0.00 0.00 41.15 1.40
4629 5481 6.609212 CAAAACTATTTTCAATTCGATCGCG 58.391 36.000 11.09 0.00 39.35 5.87
4634 5486 4.619336 GCCGCAAAACTATTTTCAATTCGA 59.381 37.500 0.00 0.00 0.00 3.71
4639 5491 5.112686 AGTTTGCCGCAAAACTATTTTCAA 58.887 33.333 19.87 0.00 46.10 2.69
4654 5506 2.475519 CCATACGCACTTTAGTTTGCCG 60.476 50.000 0.00 0.00 35.14 5.69
4663 5515 6.545666 TCCATATTTCATTCCATACGCACTTT 59.454 34.615 0.00 0.00 0.00 2.66
4680 5532 5.123820 CACGTGACAACCTTGATCCATATTT 59.876 40.000 10.90 0.00 0.00 1.40
4694 5546 1.850640 CTGTACGCCACGTGACAAC 59.149 57.895 19.30 7.27 41.39 3.32
4707 5559 4.468689 GGTCCGCCCCTGCTGTAC 62.469 72.222 0.00 0.00 34.43 2.90
4713 5565 1.830408 CTCTCTAGGTCCGCCCCTG 60.830 68.421 1.64 0.00 35.97 4.45
4714 5566 1.581923 TTCTCTCTAGGTCCGCCCCT 61.582 60.000 0.00 0.00 38.70 4.79
4715 5567 0.686769 TTTCTCTCTAGGTCCGCCCC 60.687 60.000 0.00 0.00 34.57 5.80
4716 5568 1.192428 TTTTCTCTCTAGGTCCGCCC 58.808 55.000 0.00 0.00 34.57 6.13
4717 5569 2.431057 TCATTTTCTCTCTAGGTCCGCC 59.569 50.000 0.00 0.00 0.00 6.13
4718 5570 3.449632 GTCATTTTCTCTCTAGGTCCGC 58.550 50.000 0.00 0.00 0.00 5.54
4719 5571 3.181474 GGGTCATTTTCTCTCTAGGTCCG 60.181 52.174 0.00 0.00 0.00 4.79
4720 5572 3.775316 TGGGTCATTTTCTCTCTAGGTCC 59.225 47.826 0.00 0.00 0.00 4.46
4721 5573 4.468153 ACTGGGTCATTTTCTCTCTAGGTC 59.532 45.833 0.00 0.00 0.00 3.85
4722 5574 4.223923 CACTGGGTCATTTTCTCTCTAGGT 59.776 45.833 0.00 0.00 0.00 3.08
4723 5575 4.223923 ACACTGGGTCATTTTCTCTCTAGG 59.776 45.833 0.00 0.00 0.00 3.02
4724 5576 5.413309 ACACTGGGTCATTTTCTCTCTAG 57.587 43.478 0.00 0.00 0.00 2.43
4725 5577 5.407407 GACACTGGGTCATTTTCTCTCTA 57.593 43.478 4.91 0.00 46.19 2.43
4726 5578 4.278975 GACACTGGGTCATTTTCTCTCT 57.721 45.455 4.91 0.00 46.19 3.10
4737 5589 2.965831 TCATATGCTAGGACACTGGGTC 59.034 50.000 0.18 0.18 46.20 4.46
4738 5590 3.046283 TCATATGCTAGGACACTGGGT 57.954 47.619 0.00 0.00 0.00 4.51
4739 5591 3.580022 TGATCATATGCTAGGACACTGGG 59.420 47.826 0.00 0.00 0.00 4.45
4740 5592 4.282957 AGTGATCATATGCTAGGACACTGG 59.717 45.833 0.00 0.00 33.24 4.00
4741 5593 5.010415 TGAGTGATCATATGCTAGGACACTG 59.990 44.000 7.51 0.00 33.99 3.66
4742 5594 5.143369 TGAGTGATCATATGCTAGGACACT 58.857 41.667 0.00 3.12 35.34 3.55
4743 5595 5.459536 TGAGTGATCATATGCTAGGACAC 57.540 43.478 0.00 0.00 0.00 3.67
4744 5596 7.968014 ATATGAGTGATCATATGCTAGGACA 57.032 36.000 9.39 0.00 40.59 4.02
4745 5597 9.664332 AAAATATGAGTGATCATATGCTAGGAC 57.336 33.333 10.63 0.00 41.06 3.85
4774 5626 2.311542 TGTGCCACCCCATCTTTAAGAT 59.688 45.455 0.99 0.99 34.74 2.40
4775 5627 1.707989 TGTGCCACCCCATCTTTAAGA 59.292 47.619 0.00 0.00 0.00 2.10
4776 5628 1.818674 GTGTGCCACCCCATCTTTAAG 59.181 52.381 0.00 0.00 0.00 1.85
4777 5629 1.145945 TGTGTGCCACCCCATCTTTAA 59.854 47.619 0.00 0.00 32.73 1.52
4778 5630 0.774276 TGTGTGCCACCCCATCTTTA 59.226 50.000 0.00 0.00 32.73 1.85
4779 5631 0.827507 GTGTGTGCCACCCCATCTTT 60.828 55.000 0.00 0.00 38.18 2.52
4780 5632 1.228552 GTGTGTGCCACCCCATCTT 60.229 57.895 0.00 0.00 38.18 2.40
4781 5633 0.840288 TAGTGTGTGCCACCCCATCT 60.840 55.000 0.00 0.00 45.74 2.90
4782 5634 0.255890 ATAGTGTGTGCCACCCCATC 59.744 55.000 0.00 0.00 45.74 3.51
4783 5635 1.590591 TATAGTGTGTGCCACCCCAT 58.409 50.000 0.00 0.00 45.74 4.00
4784 5636 1.590591 ATATAGTGTGTGCCACCCCA 58.409 50.000 0.00 0.00 45.74 4.96
4785 5637 2.729028 AATATAGTGTGTGCCACCCC 57.271 50.000 0.00 0.00 45.74 4.95
4786 5638 3.761752 ACAAAATATAGTGTGTGCCACCC 59.238 43.478 0.00 0.00 45.74 4.61
4787 5639 6.317642 TCATACAAAATATAGTGTGTGCCACC 59.682 38.462 6.26 0.00 45.74 4.61
4788 5640 7.315247 TCATACAAAATATAGTGTGTGCCAC 57.685 36.000 6.26 0.00 44.89 5.01
4789 5641 7.929941 TTCATACAAAATATAGTGTGTGCCA 57.070 32.000 6.26 0.00 36.95 4.92
4790 5642 8.458843 AGTTTCATACAAAATATAGTGTGTGCC 58.541 33.333 6.26 0.00 36.95 5.01
4791 5643 9.840427 AAGTTTCATACAAAATATAGTGTGTGC 57.160 29.630 6.26 0.00 36.95 4.57
4809 5661 9.034544 GCAAGATGTTTTCTTTGTAAGTTTCAT 57.965 29.630 0.00 0.00 42.15 2.57
4810 5662 8.031864 TGCAAGATGTTTTCTTTGTAAGTTTCA 58.968 29.630 0.00 0.00 42.15 2.69
4811 5663 8.321005 GTGCAAGATGTTTTCTTTGTAAGTTTC 58.679 33.333 0.00 0.00 42.15 2.78
4812 5664 7.277760 GGTGCAAGATGTTTTCTTTGTAAGTTT 59.722 33.333 0.00 0.00 42.15 2.66
4813 5665 6.756542 GGTGCAAGATGTTTTCTTTGTAAGTT 59.243 34.615 0.00 0.00 42.15 2.66
4814 5666 6.273071 GGTGCAAGATGTTTTCTTTGTAAGT 58.727 36.000 0.00 0.00 42.15 2.24
4815 5667 5.691754 GGGTGCAAGATGTTTTCTTTGTAAG 59.308 40.000 0.00 0.00 42.15 2.34
4816 5668 5.596845 GGGTGCAAGATGTTTTCTTTGTAA 58.403 37.500 0.00 0.00 42.15 2.41
4817 5669 4.261405 CGGGTGCAAGATGTTTTCTTTGTA 60.261 41.667 0.00 0.00 42.15 2.41
4818 5670 3.490761 CGGGTGCAAGATGTTTTCTTTGT 60.491 43.478 0.00 0.00 42.15 2.83
4819 5671 3.052036 CGGGTGCAAGATGTTTTCTTTG 58.948 45.455 0.00 0.00 42.15 2.77
4820 5672 2.035832 CCGGGTGCAAGATGTTTTCTTT 59.964 45.455 0.00 0.00 42.15 2.52
4821 5673 1.613437 CCGGGTGCAAGATGTTTTCTT 59.387 47.619 0.00 0.00 45.83 2.52
4822 5674 1.247567 CCGGGTGCAAGATGTTTTCT 58.752 50.000 0.00 0.00 35.70 2.52
4823 5675 0.958822 ACCGGGTGCAAGATGTTTTC 59.041 50.000 6.32 0.00 0.00 2.29
4824 5676 0.673437 CACCGGGTGCAAGATGTTTT 59.327 50.000 15.29 0.00 0.00 2.43
4825 5677 0.467290 ACACCGGGTGCAAGATGTTT 60.467 50.000 26.62 0.92 36.98 2.83
4826 5678 0.889186 GACACCGGGTGCAAGATGTT 60.889 55.000 26.62 4.63 36.98 2.71
4827 5679 1.302511 GACACCGGGTGCAAGATGT 60.303 57.895 26.62 5.43 36.98 3.06
4828 5680 2.040544 GGACACCGGGTGCAAGATG 61.041 63.158 26.62 1.80 37.84 2.90
4829 5681 2.224159 AGGACACCGGGTGCAAGAT 61.224 57.895 26.62 7.03 40.89 2.40
4830 5682 2.847234 AGGACACCGGGTGCAAGA 60.847 61.111 26.62 0.00 40.89 3.02
4831 5683 2.669569 CAGGACACCGGGTGCAAG 60.670 66.667 26.62 10.70 40.89 4.01
4832 5684 3.484806 ACAGGACACCGGGTGCAA 61.485 61.111 26.62 0.00 40.89 4.08
4833 5685 4.248842 CACAGGACACCGGGTGCA 62.249 66.667 26.62 0.00 40.89 4.57
4835 5687 3.551496 ATGCACAGGACACCGGGTG 62.551 63.158 25.21 25.21 39.75 4.61
4836 5688 3.249189 ATGCACAGGACACCGGGT 61.249 61.111 6.32 0.00 0.00 5.28
4837 5689 2.436646 GATGCACAGGACACCGGG 60.437 66.667 6.32 0.00 0.00 5.73
4838 5690 2.436646 GGATGCACAGGACACCGG 60.437 66.667 0.00 0.00 0.00 5.28
4839 5691 2.815211 CGGATGCACAGGACACCG 60.815 66.667 0.00 0.00 34.77 4.94
4840 5692 2.436646 CCGGATGCACAGGACACC 60.437 66.667 0.00 0.00 35.91 4.16
4841 5693 1.895020 TACCCGGATGCACAGGACAC 61.895 60.000 0.73 0.00 35.91 3.67
4842 5694 1.610967 TACCCGGATGCACAGGACA 60.611 57.895 0.73 0.00 35.91 4.02
4843 5695 1.144057 CTACCCGGATGCACAGGAC 59.856 63.158 0.73 0.00 35.91 3.85
4844 5696 2.731571 GCTACCCGGATGCACAGGA 61.732 63.158 0.73 0.00 35.91 3.86
4845 5697 2.203070 GCTACCCGGATGCACAGG 60.203 66.667 0.73 0.00 0.00 4.00
4846 5698 1.227380 GAGCTACCCGGATGCACAG 60.227 63.158 0.73 0.00 0.00 3.66
4847 5699 1.549243 TTGAGCTACCCGGATGCACA 61.549 55.000 0.73 6.16 0.00 4.57
4848 5700 1.090052 GTTGAGCTACCCGGATGCAC 61.090 60.000 0.73 3.26 0.00 4.57
4849 5701 1.220749 GTTGAGCTACCCGGATGCA 59.779 57.895 0.73 0.00 0.00 3.96
4850 5702 0.107654 AAGTTGAGCTACCCGGATGC 60.108 55.000 0.73 3.76 0.00 3.91
4851 5703 1.656652 CAAGTTGAGCTACCCGGATG 58.343 55.000 0.73 0.00 0.00 3.51
4852 5704 0.541863 CCAAGTTGAGCTACCCGGAT 59.458 55.000 0.73 0.00 0.00 4.18
4853 5705 1.550130 CCCAAGTTGAGCTACCCGGA 61.550 60.000 0.73 0.00 0.00 5.14
4854 5706 1.078426 CCCAAGTTGAGCTACCCGG 60.078 63.158 3.87 0.00 0.00 5.73
4855 5707 0.899720 TACCCAAGTTGAGCTACCCG 59.100 55.000 3.87 0.00 0.00 5.28
4856 5708 1.405121 CGTACCCAAGTTGAGCTACCC 60.405 57.143 3.87 0.00 0.00 3.69
4857 5709 2.005560 GCGTACCCAAGTTGAGCTACC 61.006 57.143 3.87 0.00 0.00 3.18
4858 5710 1.356938 GCGTACCCAAGTTGAGCTAC 58.643 55.000 3.87 0.03 0.00 3.58
4859 5711 0.248289 GGCGTACCCAAGTTGAGCTA 59.752 55.000 3.87 0.00 0.00 3.32
4860 5712 1.003718 GGCGTACCCAAGTTGAGCT 60.004 57.895 3.87 0.00 0.00 4.09
4861 5713 2.388232 CGGCGTACCCAAGTTGAGC 61.388 63.158 3.87 1.93 0.00 4.26
4862 5714 2.388232 GCGGCGTACCCAAGTTGAG 61.388 63.158 9.37 0.00 0.00 3.02
4863 5715 2.357760 GCGGCGTACCCAAGTTGA 60.358 61.111 9.37 0.00 0.00 3.18
4864 5716 3.784412 CGCGGCGTACCCAAGTTG 61.784 66.667 15.36 0.00 0.00 3.16
4865 5717 2.229690 ATACGCGGCGTACCCAAGTT 62.230 55.000 34.25 16.18 45.07 2.66
4866 5718 1.383456 TATACGCGGCGTACCCAAGT 61.383 55.000 34.25 20.86 45.07 3.16
4867 5719 0.662374 CTATACGCGGCGTACCCAAG 60.662 60.000 34.25 23.82 45.07 3.61
4868 5720 1.359833 CTATACGCGGCGTACCCAA 59.640 57.895 34.25 17.11 45.07 4.12
4869 5721 0.533978 TACTATACGCGGCGTACCCA 60.534 55.000 34.25 21.49 45.07 4.51
4870 5722 0.591170 TTACTATACGCGGCGTACCC 59.409 55.000 34.25 0.00 45.07 3.69
4871 5723 1.264288 AGTTACTATACGCGGCGTACC 59.736 52.381 34.25 18.19 45.07 3.34
4872 5724 2.286418 ACAGTTACTATACGCGGCGTAC 60.286 50.000 34.25 23.73 45.07 3.67
4873 5725 1.939934 ACAGTTACTATACGCGGCGTA 59.060 47.619 33.74 33.74 46.28 4.42
4874 5726 0.734889 ACAGTTACTATACGCGGCGT 59.265 50.000 31.64 31.64 44.35 5.68
4875 5727 1.831343 AACAGTTACTATACGCGGCG 58.169 50.000 22.36 22.36 0.00 6.46
4876 5728 3.120782 GCATAACAGTTACTATACGCGGC 59.879 47.826 12.47 0.00 0.00 6.53
4877 5729 4.381863 CAGCATAACAGTTACTATACGCGG 59.618 45.833 12.47 0.00 0.00 6.46
4878 5730 5.209977 TCAGCATAACAGTTACTATACGCG 58.790 41.667 3.53 3.53 0.00 6.01
4879 5731 6.144080 CCTTCAGCATAACAGTTACTATACGC 59.856 42.308 0.00 0.00 0.00 4.42
4880 5732 6.144080 GCCTTCAGCATAACAGTTACTATACG 59.856 42.308 0.00 0.00 42.97 3.06
4881 5733 7.409465 GCCTTCAGCATAACAGTTACTATAC 57.591 40.000 0.00 0.00 42.97 1.47
4900 5752 0.393537 CAGGGATCTGGTGTGCCTTC 60.394 60.000 0.00 0.00 34.94 3.46
4911 5764 5.904169 TCTCATCTCAATTTCTCAGGGATCT 59.096 40.000 0.00 0.00 0.00 2.75
4925 5778 7.962995 ACCTCTAACTGTTATCTCATCTCAA 57.037 36.000 0.00 0.00 0.00 3.02
4948 5803 4.136517 TGATTTAAACTTCGGCGTGAAC 57.863 40.909 6.85 0.00 31.87 3.18
4963 5818 7.148573 GCATCGAAGAGTTTTCTGACTGATTTA 60.149 37.037 0.00 0.00 43.63 1.40
4968 5824 3.742882 TGCATCGAAGAGTTTTCTGACTG 59.257 43.478 0.00 0.00 43.63 3.51
5021 5879 3.111853 TCAGAACTTCGTGCAATGACT 57.888 42.857 0.00 0.00 0.00 3.41
5028 5886 2.854805 GCTTGGTTTCAGAACTTCGTGC 60.855 50.000 0.00 0.00 36.03 5.34
5029 5887 2.287009 GGCTTGGTTTCAGAACTTCGTG 60.287 50.000 0.00 0.00 36.03 4.35
5078 5936 3.029570 CACATCTCATCTCAGTCCCTCA 58.970 50.000 0.00 0.00 0.00 3.86
5080 5938 1.761784 GCACATCTCATCTCAGTCCCT 59.238 52.381 0.00 0.00 0.00 4.20
5097 5955 4.999751 AAAAAGAGATCTCGTTGAGCAC 57.000 40.909 22.19 0.00 32.67 4.40
5148 6006 9.659830 GTTTAAAGCGATTTTCTCTGTCTTAAA 57.340 29.630 3.03 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.