Multiple sequence alignment - TraesCS7D01G209700

Loading Multiple Alignment...

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 TraesCS7D01G209700 chr7D 100.000 5369 0 0 1 5369 167569191 167563823 0.000000e+00 9915.0
1 TraesCS7D01G209700 chr7D 94.118 34 2 0 5190 5223 167575303 167575336 1.000000e-02 52.8
2 TraesCS7D01G209700 chr7A 93.883 2060 77 14 820 2832 169313389 169311332 0.000000e+00 3061.0
3 TraesCS7D01G209700 chr7A 93.535 1887 92 15 2820 4686 169311292 169309416 0.000000e+00 2782.0
4 TraesCS7D01G209700 chr7A 91.771 717 52 5 41 755 693355258 693355969 0.000000e+00 990.0
5 TraesCS7D01G209700 chr7A 91.492 717 54 5 41 755 693336873 693337584 0.000000e+00 979.0
6 TraesCS7D01G209700 chr7A 85.484 248 17 10 5105 5351 169308109 169307880 1.930000e-59 241.0
7 TraesCS7D01G209700 chr7A 92.086 139 8 2 4718 4855 169309417 169309281 5.490000e-45 193.0
8 TraesCS7D01G209700 chr7A 79.741 232 31 9 4842 5071 169305589 169305372 2.590000e-33 154.0
9 TraesCS7D01G209700 chr7A 94.286 70 1 1 4890 4959 169309283 169309217 2.650000e-18 104.0
10 TraesCS7D01G209700 chr7A 94.231 52 1 1 4971 5020 169309137 169309086 1.600000e-10 78.7
11 TraesCS7D01G209700 chr7B 93.008 1888 85 20 2820 4686 132135727 132133866 0.000000e+00 2712.0
12 TraesCS7D01G209700 chr7B 92.847 1468 54 23 1412 2832 132137230 132135767 0.000000e+00 2082.0
13 TraesCS7D01G209700 chr7B 94.048 588 25 5 786 1363 132138512 132137925 0.000000e+00 883.0
14 TraesCS7D01G209700 chr7B 94.203 138 6 1 4718 4855 132133867 132133732 5.450000e-50 209.0
15 TraesCS7D01G209700 chr7B 87.075 147 9 5 4890 5029 132133734 132133591 2.000000e-34 158.0
16 TraesCS7D01G209700 chr7B 88.525 61 7 0 4847 4907 132111469 132111409 2.070000e-09 75.0
17 TraesCS7D01G209700 chrUn 93.307 762 46 4 1 761 70162395 70161638 0.000000e+00 1120.0
18 TraesCS7D01G209700 chr5D 93.014 730 47 4 1 728 366786806 366786079 0.000000e+00 1062.0
19 TraesCS7D01G209700 chr3A 91.788 755 57 5 1 753 27683196 27683947 0.000000e+00 1046.0
20 TraesCS7D01G209700 chr3A 79.365 567 89 22 206 755 741440758 741440203 1.830000e-99 374.0
21 TraesCS7D01G209700 chr6A 91.579 760 56 7 1 755 520586901 520587657 0.000000e+00 1042.0
22 TraesCS7D01G209700 chr6A 91.149 757 62 5 1 755 410870547 410869794 0.000000e+00 1022.0
23 TraesCS7D01G209700 chr6A 93.139 685 43 4 1 683 591478817 591479499 0.000000e+00 1002.0
24 TraesCS7D01G209700 chr3D 91.667 756 58 5 1 755 580594284 580593533 0.000000e+00 1042.0
25 TraesCS7D01G209700 chr3D 97.619 42 1 0 5098 5139 575626085 575626044 7.460000e-09 73.1
26 TraesCS7D01G209700 chr4A 85.345 116 13 3 5095 5209 662428143 662428031 3.400000e-22 117.0
27 TraesCS7D01G209700 chr4A 86.813 91 10 1 5095 5185 662396486 662396398 3.420000e-17 100.0
28 TraesCS7D01G209700 chr1B 100.000 29 0 0 5023 5051 105294184 105294156 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 TraesCS7D01G209700 chr7D 167563823 167569191 5368 True 9915.000000 9915 100.000000 1 5369 1 chr7D.!!$R1 5368
1 TraesCS7D01G209700 chr7A 693355258 693355969 711 False 990.000000 990 91.771000 41 755 1 chr7A.!!$F2 714
2 TraesCS7D01G209700 chr7A 693336873 693337584 711 False 979.000000 979 91.492000 41 755 1 chr7A.!!$F1 714
3 TraesCS7D01G209700 chr7A 169305372 169313389 8017 True 944.814286 3061 90.463714 820 5351 7 chr7A.!!$R1 4531
4 TraesCS7D01G209700 chr7B 132133591 132138512 4921 True 1208.800000 2712 92.236200 786 5029 5 chr7B.!!$R2 4243
5 TraesCS7D01G209700 chrUn 70161638 70162395 757 True 1120.000000 1120 93.307000 1 761 1 chrUn.!!$R1 760
6 TraesCS7D01G209700 chr5D 366786079 366786806 727 True 1062.000000 1062 93.014000 1 728 1 chr5D.!!$R1 727
7 TraesCS7D01G209700 chr3A 27683196 27683947 751 False 1046.000000 1046 91.788000 1 753 1 chr3A.!!$F1 752
8 TraesCS7D01G209700 chr3A 741440203 741440758 555 True 374.000000 374 79.365000 206 755 1 chr3A.!!$R1 549
9 TraesCS7D01G209700 chr6A 520586901 520587657 756 False 1042.000000 1042 91.579000 1 755 1 chr6A.!!$F1 754
10 TraesCS7D01G209700 chr6A 410869794 410870547 753 True 1022.000000 1022 91.149000 1 755 1 chr6A.!!$R1 754
11 TraesCS7D01G209700 chr6A 591478817 591479499 682 False 1002.000000 1002 93.139000 1 683 1 chr6A.!!$F2 682
12 TraesCS7D01G209700 chr3D 580593533 580594284 751 True 1042.000000 1042 91.667000 1 755 1 chr3D.!!$R2 754

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
776 795 0.179097 TTTTGTTTTGACGGGCAGGC 60.179 50.000 0.00 0.00 0.00 4.85 F
1497 2176 0.031585 TCTTCGTGTGTCCTTCCGTG 59.968 55.000 0.00 0.00 0.00 4.94 F
2018 2702 1.222936 CTGAGTCCTGTGCCATCCC 59.777 63.158 0.00 0.00 0.00 3.85 F
2424 3140 1.435168 AGGAGGGGAGACTGGATATCC 59.565 57.143 15.39 15.39 38.06 2.59 F
3677 4465 0.374758 CCTCAAATGTCATGGTCGCG 59.625 55.000 0.00 0.00 0.00 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1819 2503 0.527565 ACATCGCCAATTTGCAGGTC 59.472 50.0 2.10 0.0 0.00 3.85 R
2933 3718 0.469892 TAGCATGCGGATCTGGAGGA 60.470 55.0 12.24 0.0 0.00 3.71 R
3166 3951 0.554305 TACCATCCTAGACCCGCAGA 59.446 55.0 0.00 0.0 0.00 4.26 R
3833 4621 0.670546 ATGACGTTGCCAGAGGTTCG 60.671 55.0 0.00 0.0 0.00 3.95 R
4859 5667 0.246635 AATAGTGCCAACGAGCGAGT 59.753 50.0 0.00 0.0 34.65 4.18 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
123 124 1.183030 GCCCCCGCCAACTAAAACTT 61.183 55.000 0.00 0.00 0.00 2.66
166 167 1.407437 GGGAAGGAGTTGCACATCGAT 60.407 52.381 0.00 0.00 0.00 3.59
170 171 4.394920 GGAAGGAGTTGCACATCGATTAAA 59.605 41.667 0.00 0.00 0.00 1.52
180 181 6.052360 TGCACATCGATTAAATAGGCAGTTA 58.948 36.000 0.00 0.00 0.00 2.24
199 200 7.361713 GGCAGTTAGCATGAACAACATACTAAA 60.362 37.037 0.00 0.00 42.71 1.85
215 216 7.109501 ACATACTAAATTGCACATACCACTGA 58.890 34.615 0.00 0.00 0.00 3.41
269 271 2.291800 ACTAGGTAGTTGGCCGAGGTAA 60.292 50.000 0.00 0.00 33.79 2.85
290 292 6.856938 GGTAATAGACTAGTTGCACGTCATAG 59.143 42.308 0.00 0.00 0.00 2.23
298 301 4.377021 AGTTGCACGTCATAGAAAGTTGA 58.623 39.130 0.00 0.00 0.00 3.18
310 313 7.965107 GTCATAGAAAGTTGATTGTCATGGTTC 59.035 37.037 0.00 0.00 0.00 3.62
472 480 2.088423 GTCAAAACATACCCATGCGGA 58.912 47.619 7.17 0.00 35.39 5.54
508 516 1.153901 TCGTCGCGAGGATTCCAAC 60.154 57.895 26.15 2.96 0.00 3.77
595 604 4.215399 CCCGAATAAATGGACATACGCATT 59.785 41.667 0.00 0.00 0.00 3.56
625 643 1.376683 GCGGTGTCTTGCCCATGTA 60.377 57.895 0.00 0.00 0.00 2.29
683 701 8.487313 AAAGACAAAATTTAGACCACAAAACC 57.513 30.769 0.00 0.00 0.00 3.27
689 707 6.478512 AATTTAGACCACAAAACCACATGT 57.521 33.333 0.00 0.00 0.00 3.21
694 712 2.298729 ACCACAAAACCACATGTATGCC 59.701 45.455 0.00 0.00 0.00 4.40
704 723 3.873361 CCACATGTATGCCTGTGTAAGAG 59.127 47.826 15.75 0.00 38.86 2.85
709 728 2.047274 GCCTGTGTAAGAGCGGCA 60.047 61.111 1.45 0.00 40.41 5.69
756 775 7.293018 CGTACGCACTTTTTAGAATTTAGGTT 58.707 34.615 0.52 0.00 0.00 3.50
775 794 2.301577 TTTTTGTTTTGACGGGCAGG 57.698 45.000 0.00 0.00 0.00 4.85
776 795 0.179097 TTTTGTTTTGACGGGCAGGC 60.179 50.000 0.00 0.00 0.00 4.85
777 796 1.323271 TTTGTTTTGACGGGCAGGCA 61.323 50.000 0.00 0.00 34.88 4.75
778 797 1.112315 TTGTTTTGACGGGCAGGCAT 61.112 50.000 0.00 0.00 37.96 4.40
779 798 1.112315 TGTTTTGACGGGCAGGCATT 61.112 50.000 0.00 0.00 37.96 3.56
780 799 0.667184 GTTTTGACGGGCAGGCATTG 60.667 55.000 0.00 0.00 37.96 2.82
781 800 1.112315 TTTTGACGGGCAGGCATTGT 61.112 50.000 0.00 0.00 37.96 2.71
782 801 1.523154 TTTGACGGGCAGGCATTGTC 61.523 55.000 0.00 1.29 37.96 3.18
794 813 4.579869 CAGGCATTGTCCTAGTTAACACT 58.420 43.478 8.61 0.00 33.95 3.55
877 896 5.047731 CGATCCAGATCTTGAGGCACTTATA 60.048 44.000 2.62 0.00 35.32 0.98
1217 1246 4.101448 ACATGCTCCGGTGCCCTC 62.101 66.667 24.73 0.00 0.00 4.30
1279 1308 4.701765 CTCAGGTATTCTGTTAGCTGCAT 58.298 43.478 1.02 0.00 43.89 3.96
1282 1311 6.830912 TCAGGTATTCTGTTAGCTGCATATT 58.169 36.000 1.02 0.00 43.89 1.28
1461 2140 3.878778 CTTCTACCCAGCTAGTGCAATT 58.121 45.455 0.00 0.00 42.74 2.32
1497 2176 0.031585 TCTTCGTGTGTCCTTCCGTG 59.968 55.000 0.00 0.00 0.00 4.94
1502 2181 1.872237 CGTGTGTCCTTCCGTGACAAT 60.872 52.381 0.00 0.00 43.82 2.71
1507 2186 1.535462 GTCCTTCCGTGACAATGTTGG 59.465 52.381 0.00 0.00 32.91 3.77
1597 2281 3.441572 GTGTTGCTGAGATGTAGGCATTT 59.558 43.478 0.00 0.00 35.07 2.32
1605 2289 2.751259 AGATGTAGGCATTTGTGCACTG 59.249 45.455 19.41 9.38 35.07 3.66
1614 2298 4.570369 GGCATTTGTGCACTGTTAGTTTTT 59.430 37.500 19.41 0.00 36.33 1.94
1819 2503 1.795286 GTGTCTTCAGGCAAGAACTCG 59.205 52.381 0.00 0.00 43.10 4.18
1961 2645 9.712305 AATGTAGCTTTAAGGTATAGCACTATG 57.288 33.333 7.16 0.00 35.55 2.23
1974 2658 9.331282 GGTATAGCACTATGACATTTCTCTTTT 57.669 33.333 0.00 0.00 0.00 2.27
2008 2692 5.495640 CTTTCAAATCCTAAGCTGAGTCCT 58.504 41.667 0.00 0.00 0.00 3.85
2009 2693 4.478206 TCAAATCCTAAGCTGAGTCCTG 57.522 45.455 0.00 0.00 0.00 3.86
2018 2702 1.222936 CTGAGTCCTGTGCCATCCC 59.777 63.158 0.00 0.00 0.00 3.85
2364 3056 4.272261 GCTTGGCTTCTTCTGCTAGTAATC 59.728 45.833 0.00 0.00 0.00 1.75
2424 3140 1.435168 AGGAGGGGAGACTGGATATCC 59.565 57.143 15.39 15.39 38.06 2.59
2460 3176 5.538067 AGTTCTATCTTTTCTTTGCGAGC 57.462 39.130 0.00 0.00 0.00 5.03
2461 3177 5.241662 AGTTCTATCTTTTCTTTGCGAGCT 58.758 37.500 0.00 0.00 0.00 4.09
2546 3275 8.171164 TGTGTAAATGAACCAAATGATGTACA 57.829 30.769 0.00 0.00 0.00 2.90
2573 3302 7.485913 ACAATCGTGCATTTTCTAAATAGCTTG 59.514 33.333 0.00 0.00 0.00 4.01
2576 3305 5.654497 GTGCATTTTCTAAATAGCTTGCCT 58.346 37.500 0.00 0.00 0.00 4.75
2581 3310 6.436843 TTTTCTAAATAGCTTGCCTGCTAC 57.563 37.500 9.47 0.00 46.60 3.58
2596 3325 5.163099 TGCCTGCTACCCATCTTTTGTATAT 60.163 40.000 0.00 0.00 0.00 0.86
2810 3543 8.523523 TCAGTTAAATCAGCATCATTTGTTTG 57.476 30.769 0.00 0.00 0.00 2.93
2838 3623 7.550196 TGCGTATCTGATATGAATGTAATGCAT 59.450 33.333 18.67 0.00 46.79 3.96
2897 3682 8.157476 GGCAGATATCTATTTACTCCTTCCAAA 58.843 37.037 4.54 0.00 0.00 3.28
2933 3718 9.981460 ATTATTGTTTACTCCTGATTCTCCTTT 57.019 29.630 0.00 0.00 0.00 3.11
3030 3815 2.625790 TGGTGATTTTAACAGCACACCC 59.374 45.455 11.72 0.00 44.58 4.61
3166 3951 7.559486 TCATGAGTGATAGTGCTTTAGATTGT 58.441 34.615 0.00 0.00 0.00 2.71
3256 4044 9.167311 GAAATGTGGTATCTTGTGATTTAGAGT 57.833 33.333 0.00 0.00 34.32 3.24
3334 4122 4.065088 GTGCCATCTACAAGTTCTTGTCA 58.935 43.478 19.37 9.24 36.44 3.58
3379 4167 7.066163 TGCATTAGATATTTCTTGCATATCCCG 59.934 37.037 8.05 0.00 39.59 5.14
3392 4180 6.413783 TGCATATCCCGAAAGTTATAGTGA 57.586 37.500 0.00 0.00 0.00 3.41
3535 4323 8.650143 AATTTGGTTTGTATTGTAGGTCAGAT 57.350 30.769 0.00 0.00 0.00 2.90
3537 4325 9.747898 ATTTGGTTTGTATTGTAGGTCAGATTA 57.252 29.630 0.00 0.00 0.00 1.75
3573 4361 7.981789 CAGATCTTAGTTGACCTAGCACATTTA 59.018 37.037 0.00 0.00 0.00 1.40
3677 4465 0.374758 CCTCAAATGTCATGGTCGCG 59.625 55.000 0.00 0.00 0.00 5.87
3765 4553 3.189702 ACTGAAGCACTCTCTTCGACTAC 59.810 47.826 0.00 0.00 44.01 2.73
3768 4556 3.060736 AGCACTCTCTTCGACTACTCA 57.939 47.619 0.00 0.00 0.00 3.41
3806 4594 4.642885 TGAAGTGCCGATTTATTTTAGGGG 59.357 41.667 0.00 0.00 0.00 4.79
3833 4621 1.202976 AGCAATAGGGGTCATCATGGC 60.203 52.381 0.00 0.00 0.00 4.40
3842 4630 1.293924 GTCATCATGGCGAACCTCTG 58.706 55.000 0.00 0.00 36.63 3.35
3917 4705 7.268586 ACGCTTCTAATCATGTCTGTATCTTT 58.731 34.615 0.00 0.00 0.00 2.52
3973 4761 5.531198 TGTTTAAGGTATACTCCTGGGCTA 58.469 41.667 2.25 0.00 37.93 3.93
4119 4907 9.596308 AAAGGACTATATGGTTTAAACTTTGGT 57.404 29.630 17.50 9.36 0.00 3.67
4120 4908 8.803397 AGGACTATATGGTTTAAACTTTGGTC 57.197 34.615 17.50 15.72 0.00 4.02
4121 4909 8.387813 AGGACTATATGGTTTAAACTTTGGTCA 58.612 33.333 17.50 6.72 0.00 4.02
4122 4910 9.185680 GGACTATATGGTTTAAACTTTGGTCAT 57.814 33.333 17.50 12.90 0.00 3.06
4124 4912 9.528489 ACTATATGGTTTAAACTTTGGTCATGT 57.472 29.630 17.50 11.44 0.00 3.21
4126 4914 6.723298 ATGGTTTAAACTTTGGTCATGTCA 57.277 33.333 17.50 3.53 0.00 3.58
4127 4915 6.723298 TGGTTTAAACTTTGGTCATGTCAT 57.277 33.333 17.50 0.00 0.00 3.06
4128 4916 6.511416 TGGTTTAAACTTTGGTCATGTCATG 58.489 36.000 17.50 6.47 0.00 3.07
4132 4922 7.581213 TTAAACTTTGGTCATGTCATGTTCT 57.419 32.000 12.54 0.00 0.00 3.01
4142 4932 4.458989 TCATGTCATGTTCTAGTTTTGGCC 59.541 41.667 12.54 0.00 0.00 5.36
4151 4941 6.440436 TGTTCTAGTTTTGGCCGTAAATTTC 58.560 36.000 0.00 0.00 0.00 2.17
4159 4949 7.177041 AGTTTTGGCCGTAAATTTCCTGTTATA 59.823 33.333 0.00 0.00 0.00 0.98
4162 4952 6.123651 TGGCCGTAAATTTCCTGTTATACAT 58.876 36.000 0.00 0.00 0.00 2.29
4362 5155 9.896645 AAACACATATATTTCTCAGACAGTGAT 57.103 29.630 0.00 0.00 33.51 3.06
4668 5475 1.082756 GCCAAACGCTCGAGTGTTG 60.083 57.895 37.14 29.09 46.75 3.33
4694 5501 5.864986 CGCAAGGTATACAAAACAAGTAGG 58.135 41.667 5.01 0.00 0.00 3.18
4695 5502 5.410439 CGCAAGGTATACAAAACAAGTAGGT 59.590 40.000 5.01 0.00 0.00 3.08
4696 5503 6.401796 CGCAAGGTATACAAAACAAGTAGGTC 60.402 42.308 5.01 0.00 0.00 3.85
4697 5504 6.428771 GCAAGGTATACAAAACAAGTAGGTCA 59.571 38.462 5.01 0.00 0.00 4.02
4698 5505 7.040961 GCAAGGTATACAAAACAAGTAGGTCAA 60.041 37.037 5.01 0.00 0.00 3.18
4699 5506 8.504005 CAAGGTATACAAAACAAGTAGGTCAAG 58.496 37.037 5.01 0.00 0.00 3.02
4700 5507 7.166167 AGGTATACAAAACAAGTAGGTCAAGG 58.834 38.462 5.01 0.00 0.00 3.61
4701 5508 7.016858 AGGTATACAAAACAAGTAGGTCAAGGA 59.983 37.037 5.01 0.00 0.00 3.36
4702 5509 7.118825 GGTATACAAAACAAGTAGGTCAAGGAC 59.881 40.741 5.01 0.00 0.00 3.85
4703 5510 4.850680 ACAAAACAAGTAGGTCAAGGACA 58.149 39.130 0.00 0.00 33.68 4.02
4704 5511 5.258051 ACAAAACAAGTAGGTCAAGGACAA 58.742 37.500 0.00 0.00 33.68 3.18
4705 5512 5.357032 ACAAAACAAGTAGGTCAAGGACAAG 59.643 40.000 0.00 0.00 33.68 3.16
4706 5513 3.771577 ACAAGTAGGTCAAGGACAAGG 57.228 47.619 0.00 0.00 33.68 3.61
4707 5514 3.314693 ACAAGTAGGTCAAGGACAAGGA 58.685 45.455 0.00 0.00 33.68 3.36
4708 5515 3.714798 ACAAGTAGGTCAAGGACAAGGAA 59.285 43.478 0.00 0.00 33.68 3.36
4709 5516 4.165372 ACAAGTAGGTCAAGGACAAGGAAA 59.835 41.667 0.00 0.00 33.68 3.13
4710 5517 4.625607 AGTAGGTCAAGGACAAGGAAAG 57.374 45.455 0.00 0.00 33.68 2.62
4711 5518 4.232091 AGTAGGTCAAGGACAAGGAAAGA 58.768 43.478 0.00 0.00 33.68 2.52
4712 5519 4.658901 AGTAGGTCAAGGACAAGGAAAGAA 59.341 41.667 0.00 0.00 33.68 2.52
4713 5520 4.519906 AGGTCAAGGACAAGGAAAGAAA 57.480 40.909 0.00 0.00 33.68 2.52
4714 5521 4.867086 AGGTCAAGGACAAGGAAAGAAAA 58.133 39.130 0.00 0.00 33.68 2.29
4715 5522 5.269189 AGGTCAAGGACAAGGAAAGAAAAA 58.731 37.500 0.00 0.00 33.68 1.94
4716 5523 5.899547 AGGTCAAGGACAAGGAAAGAAAAAT 59.100 36.000 0.00 0.00 33.68 1.82
4717 5524 7.066781 AGGTCAAGGACAAGGAAAGAAAAATA 58.933 34.615 0.00 0.00 33.68 1.40
4718 5525 7.563556 AGGTCAAGGACAAGGAAAGAAAAATAA 59.436 33.333 0.00 0.00 33.68 1.40
4752 5560 7.172532 CAGTTTAGCATTTGGTACTCAGTGTAA 59.827 37.037 0.00 0.00 32.25 2.41
4852 5660 5.715429 AGTGTACTCGTTCTGTCTATACG 57.285 43.478 0.00 0.00 36.67 3.06
4853 5661 4.033817 AGTGTACTCGTTCTGTCTATACGC 59.966 45.833 0.00 0.00 35.40 4.42
4854 5662 4.033817 GTGTACTCGTTCTGTCTATACGCT 59.966 45.833 0.00 0.00 35.40 5.07
4855 5663 5.233050 GTGTACTCGTTCTGTCTATACGCTA 59.767 44.000 0.00 0.00 35.40 4.26
4856 5664 5.987953 TGTACTCGTTCTGTCTATACGCTAT 59.012 40.000 0.00 0.00 35.40 2.97
4857 5665 7.115520 GTGTACTCGTTCTGTCTATACGCTATA 59.884 40.741 0.00 0.00 35.40 1.31
4858 5666 7.816513 TGTACTCGTTCTGTCTATACGCTATAT 59.183 37.037 0.00 0.00 35.40 0.86
4859 5667 9.295214 GTACTCGTTCTGTCTATACGCTATATA 57.705 37.037 0.00 0.00 35.40 0.86
4860 5668 8.183830 ACTCGTTCTGTCTATACGCTATATAC 57.816 38.462 0.00 0.00 35.40 1.47
4861 5669 8.034215 ACTCGTTCTGTCTATACGCTATATACT 58.966 37.037 0.00 0.00 35.40 2.12
4862 5670 8.404889 TCGTTCTGTCTATACGCTATATACTC 57.595 38.462 0.00 0.00 35.40 2.59
4863 5671 7.219726 TCGTTCTGTCTATACGCTATATACTCG 59.780 40.741 0.00 0.00 35.40 4.18
4864 5672 6.825284 TCTGTCTATACGCTATATACTCGC 57.175 41.667 0.91 0.00 0.00 5.03
4865 5673 6.571605 TCTGTCTATACGCTATATACTCGCT 58.428 40.000 0.91 0.00 0.00 4.93
4866 5674 6.696583 TCTGTCTATACGCTATATACTCGCTC 59.303 42.308 0.91 0.00 0.00 5.03
4867 5675 5.458126 TGTCTATACGCTATATACTCGCTCG 59.542 44.000 0.91 0.00 0.00 5.03
4868 5676 5.458452 GTCTATACGCTATATACTCGCTCGT 59.542 44.000 0.00 0.00 0.00 4.18
4869 5677 6.019961 GTCTATACGCTATATACTCGCTCGTT 60.020 42.308 0.00 0.00 0.00 3.85
4870 5678 3.184649 ACGCTATATACTCGCTCGTTG 57.815 47.619 0.91 0.00 0.00 4.10
4871 5679 2.095869 ACGCTATATACTCGCTCGTTGG 60.096 50.000 0.91 0.00 0.00 3.77
4872 5680 2.251893 GCTATATACTCGCTCGTTGGC 58.748 52.381 0.00 0.00 0.00 4.52
4873 5681 2.351447 GCTATATACTCGCTCGTTGGCA 60.351 50.000 0.00 0.00 0.00 4.92
4874 5682 2.135664 ATATACTCGCTCGTTGGCAC 57.864 50.000 0.00 0.00 0.00 5.01
4875 5683 1.100510 TATACTCGCTCGTTGGCACT 58.899 50.000 0.00 0.00 0.00 4.40
4876 5684 1.100510 ATACTCGCTCGTTGGCACTA 58.899 50.000 0.00 0.00 0.00 2.74
4877 5685 1.100510 TACTCGCTCGTTGGCACTAT 58.899 50.000 0.00 0.00 0.00 2.12
4878 5686 0.246635 ACTCGCTCGTTGGCACTATT 59.753 50.000 0.00 0.00 0.00 1.73
4879 5687 0.647410 CTCGCTCGTTGGCACTATTG 59.353 55.000 0.00 0.00 0.00 1.90
4907 5715 5.395768 GGTGATCCTGTGTTTAGACTGCTAT 60.396 44.000 0.00 0.00 0.00 2.97
4908 5716 6.183360 GGTGATCCTGTGTTTAGACTGCTATA 60.183 42.308 0.00 0.00 0.00 1.31
4911 5719 8.797438 TGATCCTGTGTTTAGACTGCTATATAG 58.203 37.037 5.30 5.30 0.00 1.31
4912 5720 7.526142 TCCTGTGTTTAGACTGCTATATAGG 57.474 40.000 11.72 0.00 0.00 2.57
4913 5721 7.295340 TCCTGTGTTTAGACTGCTATATAGGA 58.705 38.462 11.72 7.83 0.00 2.94
4914 5722 7.448777 TCCTGTGTTTAGACTGCTATATAGGAG 59.551 40.741 25.01 25.01 45.88 3.69
5016 5893 0.966920 AGTAGGGGAGTTGTGTGTCG 59.033 55.000 0.00 0.00 0.00 4.35
5019 5896 1.597027 GGGGAGTTGTGTGTCGGTG 60.597 63.158 0.00 0.00 0.00 4.94
5020 5897 1.145377 GGGAGTTGTGTGTCGGTGT 59.855 57.895 0.00 0.00 0.00 4.16
5021 5898 0.878961 GGGAGTTGTGTGTCGGTGTC 60.879 60.000 0.00 0.00 0.00 3.67
5022 5899 1.213094 GGAGTTGTGTGTCGGTGTCG 61.213 60.000 0.00 0.00 37.82 4.35
5024 5901 2.586635 TTGTGTGTCGGTGTCGGC 60.587 61.111 0.00 0.00 42.06 5.54
5025 5902 4.934942 TGTGTGTCGGTGTCGGCG 62.935 66.667 0.00 0.00 45.11 6.46
5034 5911 3.343421 GTGTCGGCGGCTCGTTTT 61.343 61.111 14.51 0.00 0.00 2.43
5036 5913 4.084888 GTCGGCGGCTCGTTTTGG 62.085 66.667 3.23 0.00 0.00 3.28
5037 5914 4.612412 TCGGCGGCTCGTTTTGGT 62.612 61.111 7.21 0.00 0.00 3.67
5038 5915 4.383602 CGGCGGCTCGTTTTGGTG 62.384 66.667 7.61 0.00 0.00 4.17
5039 5916 4.038080 GGCGGCTCGTTTTGGTGG 62.038 66.667 0.00 0.00 0.00 4.61
5041 5918 2.637025 CGGCTCGTTTTGGTGGTG 59.363 61.111 0.00 0.00 0.00 4.17
5043 5920 1.234615 CGGCTCGTTTTGGTGGTGAT 61.235 55.000 0.00 0.00 0.00 3.06
5045 5922 1.737793 GGCTCGTTTTGGTGGTGATAG 59.262 52.381 0.00 0.00 0.00 2.08
5046 5923 2.423577 GCTCGTTTTGGTGGTGATAGT 58.576 47.619 0.00 0.00 0.00 2.12
5048 5925 2.742053 CTCGTTTTGGTGGTGATAGTGG 59.258 50.000 0.00 0.00 0.00 4.00
5049 5926 2.105134 TCGTTTTGGTGGTGATAGTGGT 59.895 45.455 0.00 0.00 0.00 4.16
5052 5929 4.202070 CGTTTTGGTGGTGATAGTGGTTTT 60.202 41.667 0.00 0.00 0.00 2.43
5095 5972 8.785468 TCTTGTAACTTTTATTACGGTTTTGC 57.215 30.769 0.00 0.00 37.79 3.68
5096 5973 8.623030 TCTTGTAACTTTTATTACGGTTTTGCT 58.377 29.630 0.00 0.00 37.79 3.91
5097 5974 8.563289 TTGTAACTTTTATTACGGTTTTGCTG 57.437 30.769 0.00 0.00 37.79 4.41
5098 5975 7.928103 TGTAACTTTTATTACGGTTTTGCTGA 58.072 30.769 0.00 0.00 37.79 4.26
5099 5976 8.071368 TGTAACTTTTATTACGGTTTTGCTGAG 58.929 33.333 0.00 0.00 37.79 3.35
5100 5977 6.628919 ACTTTTATTACGGTTTTGCTGAGT 57.371 33.333 0.00 0.00 0.00 3.41
5101 5978 7.034685 ACTTTTATTACGGTTTTGCTGAGTT 57.965 32.000 0.00 0.00 0.00 3.01
5102 5979 7.485810 ACTTTTATTACGGTTTTGCTGAGTTT 58.514 30.769 0.00 0.00 0.00 2.66
5117 6890 6.166279 TGCTGAGTTTTAACTATGGTCTCAG 58.834 40.000 16.10 16.10 45.49 3.35
5118 6891 6.166982 GCTGAGTTTTAACTATGGTCTCAGT 58.833 40.000 19.38 0.00 44.92 3.41
5119 6892 6.311690 GCTGAGTTTTAACTATGGTCTCAGTC 59.688 42.308 19.38 11.87 44.92 3.51
5120 6893 7.297936 TGAGTTTTAACTATGGTCTCAGTCA 57.702 36.000 0.00 0.00 39.88 3.41
5121 6894 7.152645 TGAGTTTTAACTATGGTCTCAGTCAC 58.847 38.462 0.00 0.00 39.88 3.67
5122 6895 7.015292 TGAGTTTTAACTATGGTCTCAGTCACT 59.985 37.037 0.00 0.00 39.88 3.41
5136 6910 1.550976 AGTCACTTTTCTAGCCCTCCG 59.449 52.381 0.00 0.00 0.00 4.63
5139 6913 2.838202 TCACTTTTCTAGCCCTCCGATT 59.162 45.455 0.00 0.00 0.00 3.34
5144 6918 2.088104 TCTAGCCCTCCGATTGTCAT 57.912 50.000 0.00 0.00 0.00 3.06
5165 6939 3.198068 TGCTAAGATTCGTGATGGCTTC 58.802 45.455 0.00 0.00 0.00 3.86
5170 6944 3.005554 AGATTCGTGATGGCTTCTGTTG 58.994 45.455 1.86 0.00 0.00 3.33
5175 6949 3.009723 CGTGATGGCTTCTGTTGGTTAT 58.990 45.455 1.86 0.00 0.00 1.89
5177 6951 3.063997 GTGATGGCTTCTGTTGGTTATCG 59.936 47.826 1.86 0.00 0.00 2.92
5209 6983 1.084370 GTGCACGGCTCATCTGTACC 61.084 60.000 0.00 0.00 31.79 3.34
5210 6984 1.218047 GCACGGCTCATCTGTACCA 59.782 57.895 0.00 0.00 31.79 3.25
5214 6988 1.832912 GGCTCATCTGTACCAGGGG 59.167 63.158 0.00 0.00 31.51 4.79
5215 6989 1.147153 GCTCATCTGTACCAGGGGC 59.853 63.158 0.00 0.00 31.51 5.80
5216 6990 1.626356 GCTCATCTGTACCAGGGGCA 61.626 60.000 0.00 0.00 31.51 5.36
5217 6991 0.467384 CTCATCTGTACCAGGGGCAG 59.533 60.000 6.26 6.26 31.51 4.85
5219 6993 2.378634 ATCTGTACCAGGGGCAGCC 61.379 63.158 1.26 1.26 31.51 4.85
5220 6994 4.115199 CTGTACCAGGGGCAGCCC 62.115 72.222 24.23 24.23 44.51 5.19
5229 7003 2.753043 GGGCAGCCCATGTGTCTG 60.753 66.667 27.33 0.00 44.65 3.51
5230 7004 2.352422 GGCAGCCCATGTGTCTGA 59.648 61.111 0.00 0.00 0.00 3.27
5231 7005 1.748122 GGCAGCCCATGTGTCTGAG 60.748 63.158 0.00 0.00 0.00 3.35
5232 7006 1.002868 GCAGCCCATGTGTCTGAGT 60.003 57.895 9.43 0.00 0.00 3.41
5233 7007 1.023513 GCAGCCCATGTGTCTGAGTC 61.024 60.000 9.43 0.00 0.00 3.36
5234 7008 0.612229 CAGCCCATGTGTCTGAGTCT 59.388 55.000 0.00 0.00 0.00 3.24
5235 7009 1.002888 CAGCCCATGTGTCTGAGTCTT 59.997 52.381 0.00 0.00 0.00 3.01
5236 7010 2.234661 CAGCCCATGTGTCTGAGTCTTA 59.765 50.000 0.00 0.00 0.00 2.10
5237 7011 2.234908 AGCCCATGTGTCTGAGTCTTAC 59.765 50.000 0.00 0.00 0.00 2.34
5238 7012 2.678190 GCCCATGTGTCTGAGTCTTACC 60.678 54.545 0.00 0.00 0.00 2.85
5239 7013 2.417379 CCCATGTGTCTGAGTCTTACCG 60.417 54.545 0.00 0.00 0.00 4.02
5244 7018 2.553172 GTGTCTGAGTCTTACCGTCACT 59.447 50.000 0.00 0.00 0.00 3.41
5307 7081 1.078709 TTGCACGAGTTGAGCTATGC 58.921 50.000 1.30 0.00 38.93 3.14
5311 7085 2.240500 CGAGTTGAGCTATGCGGGC 61.241 63.158 0.00 0.00 0.00 6.13
5321 7095 1.332065 GCTATGCGGGCTTTCTTCTTC 59.668 52.381 0.00 0.00 0.00 2.87
5326 7161 2.293399 TGCGGGCTTTCTTCTTCTTTTC 59.707 45.455 0.00 0.00 0.00 2.29
5351 7186 2.890945 CCGACCAAAAAGGAAAGATGGT 59.109 45.455 0.00 0.00 46.63 3.55
5352 7187 3.320826 CCGACCAAAAAGGAAAGATGGTT 59.679 43.478 0.00 0.00 44.12 3.67
5353 7188 4.298332 CGACCAAAAAGGAAAGATGGTTG 58.702 43.478 0.00 0.00 44.12 3.77
5354 7189 4.058124 GACCAAAAAGGAAAGATGGTTGC 58.942 43.478 0.00 0.00 44.12 4.17
5356 7191 3.402110 CAAAAAGGAAAGATGGTTGCCC 58.598 45.455 0.00 0.00 0.00 5.36
5357 7192 6.264959 CCAAAAAGGAAAGATGGTTGCCCA 62.265 45.833 0.00 0.00 42.78 5.36
5358 7193 2.397044 AAGGAAAGATGGTTGCCCAA 57.603 45.000 0.00 0.00 46.04 4.12
5359 7194 2.397044 AGGAAAGATGGTTGCCCAAA 57.603 45.000 0.00 0.00 46.04 3.28
5360 7195 2.688477 AGGAAAGATGGTTGCCCAAAA 58.312 42.857 0.00 0.00 46.04 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
166 167 7.175816 TGTTGTTCATGCTAACTGCCTATTTAA 59.824 33.333 0.00 0.00 42.00 1.52
170 171 4.588899 TGTTGTTCATGCTAACTGCCTAT 58.411 39.130 0.00 0.00 42.00 2.57
183 184 9.787532 GTATGTGCAATTTAGTATGTTGTTCAT 57.212 29.630 0.00 0.00 40.25 2.57
193 194 7.931407 CCTATCAGTGGTATGTGCAATTTAGTA 59.069 37.037 0.00 0.00 0.00 1.82
199 200 3.181440 CCCCTATCAGTGGTATGTGCAAT 60.181 47.826 0.00 0.00 0.00 3.56
215 216 0.328548 CCCTTCCCCACTTCCCCTAT 60.329 60.000 0.00 0.00 0.00 2.57
269 271 6.694877 TTCTATGACGTGCAACTAGTCTAT 57.305 37.500 0.00 7.94 36.01 1.98
290 292 5.712152 AGGAACCATGACAATCAACTTTC 57.288 39.130 0.00 0.00 0.00 2.62
298 301 3.387374 TGCAACAAAGGAACCATGACAAT 59.613 39.130 0.00 0.00 0.00 2.71
310 313 9.037737 CCAATTCTTATGATATTGCAACAAAGG 57.962 33.333 0.00 0.00 0.00 3.11
369 376 6.350629 ACTTTAGTACCGGATTGTACAACT 57.649 37.500 9.46 4.87 42.84 3.16
374 381 4.931002 GTGCAACTTTAGTACCGGATTGTA 59.069 41.667 9.46 0.00 0.00 2.41
472 480 5.517054 GCGACGAGATCTTTGAAACTAGATT 59.483 40.000 0.00 0.00 31.46 2.40
569 578 4.319261 GCGTATGTCCATTTATTCGGGTTC 60.319 45.833 0.00 0.00 0.00 3.62
595 604 4.438608 GCAAGACACCGCATTATTTCATGA 60.439 41.667 0.00 0.00 0.00 3.07
625 643 5.671493 GTGGCATGTACTACTAGAATGGTT 58.329 41.667 0.00 0.00 0.00 3.67
689 707 0.179084 GCCGCTCTTACACAGGCATA 60.179 55.000 0.00 0.00 46.48 3.14
694 712 1.079543 AGCTGCCGCTCTTACACAG 60.080 57.895 0.00 0.00 45.15 3.66
704 723 0.806102 TAGATGAAACGAGCTGCCGC 60.806 55.000 9.82 0.00 0.00 6.53
709 728 4.504461 CGCACTAATTAGATGAAACGAGCT 59.496 41.667 19.38 0.00 0.00 4.09
756 775 1.740718 GCCTGCCCGTCAAAACAAAAA 60.741 47.619 0.00 0.00 0.00 1.94
761 780 0.667184 CAATGCCTGCCCGTCAAAAC 60.667 55.000 0.00 0.00 0.00 2.43
762 781 1.112315 ACAATGCCTGCCCGTCAAAA 61.112 50.000 0.00 0.00 0.00 2.44
763 782 1.523154 GACAATGCCTGCCCGTCAAA 61.523 55.000 0.00 0.00 0.00 2.69
764 783 1.971167 GACAATGCCTGCCCGTCAA 60.971 57.895 0.00 0.00 0.00 3.18
765 784 2.359850 GACAATGCCTGCCCGTCA 60.360 61.111 0.00 0.00 0.00 4.35
766 785 2.252072 TAGGACAATGCCTGCCCGTC 62.252 60.000 6.50 0.00 39.08 4.79
767 786 2.257409 CTAGGACAATGCCTGCCCGT 62.257 60.000 6.50 0.00 39.08 5.28
768 787 1.524621 CTAGGACAATGCCTGCCCG 60.525 63.158 6.50 0.00 39.08 6.13
769 788 0.034089 AACTAGGACAATGCCTGCCC 60.034 55.000 6.50 0.00 39.08 5.36
770 789 2.683362 GTTAACTAGGACAATGCCTGCC 59.317 50.000 0.00 0.00 39.08 4.85
771 790 3.127030 GTGTTAACTAGGACAATGCCTGC 59.873 47.826 7.22 0.00 39.08 4.85
772 791 4.579869 AGTGTTAACTAGGACAATGCCTG 58.420 43.478 7.22 0.97 39.08 4.85
773 792 4.910458 AGTGTTAACTAGGACAATGCCT 57.090 40.909 7.22 2.15 42.15 4.75
779 798 9.871175 TCCACATATATAGTGTTAACTAGGACA 57.129 33.333 7.22 0.00 42.16 4.02
782 801 9.622004 CGTTCCACATATATAGTGTTAACTAGG 57.378 37.037 7.22 0.00 42.16 3.02
783 802 9.622004 CCGTTCCACATATATAGTGTTAACTAG 57.378 37.037 7.22 0.00 42.16 2.57
784 803 9.135189 ACCGTTCCACATATATAGTGTTAACTA 57.865 33.333 7.22 0.00 43.04 2.24
794 813 7.600231 TCTTAACCACCGTTCCACATATATA 57.400 36.000 0.00 0.00 33.17 0.86
831 850 3.067106 GACGGTTCAGATGTGTTGTGAT 58.933 45.455 0.00 0.00 0.00 3.06
833 852 1.531149 GGACGGTTCAGATGTGTTGTG 59.469 52.381 0.00 0.00 0.00 3.33
877 896 7.358255 TCCTATATATGAGGGGTTGAGTACT 57.642 40.000 0.00 0.00 34.56 2.73
1123 1152 2.654877 GCGGTGGTCGAAAGGAGA 59.345 61.111 0.00 0.00 42.43 3.71
1244 1273 1.528542 CCTGAGCCCGAGGTCGATA 60.529 63.158 0.00 0.00 43.71 2.92
1279 1308 2.766263 ACCAATCTCCTCGACAGCAATA 59.234 45.455 0.00 0.00 0.00 1.90
1282 1311 0.976641 AACCAATCTCCTCGACAGCA 59.023 50.000 0.00 0.00 0.00 4.41
1461 2140 4.002982 CGAAGATCATGACTTTGTGGGAA 58.997 43.478 0.00 0.00 0.00 3.97
1497 2176 3.256631 AGCCAAACTGATCCAACATTGTC 59.743 43.478 0.00 0.00 0.00 3.18
1502 2181 2.665165 ACAAGCCAAACTGATCCAACA 58.335 42.857 0.00 0.00 0.00 3.33
1507 2186 1.615392 AGCCAACAAGCCAAACTGATC 59.385 47.619 0.00 0.00 0.00 2.92
1819 2503 0.527565 ACATCGCCAATTTGCAGGTC 59.472 50.000 2.10 0.00 0.00 3.85
1961 2645 7.150640 AGGCAGAAATTCAAAAGAGAAATGTC 58.849 34.615 0.00 0.00 0.00 3.06
1974 2658 7.537596 TTAGGATTTGAAAGGCAGAAATTCA 57.462 32.000 0.00 0.00 0.00 2.57
2030 2714 2.224621 ACATCCATCTTTAGCATCCCCG 60.225 50.000 0.00 0.00 0.00 5.73
2209 2893 7.061752 ACTTGAGCAACATTATTTCGTAGAC 57.938 36.000 0.00 0.00 34.32 2.59
2295 2980 8.260818 CCAGATGAATGAGAAACTACTCCTTAA 58.739 37.037 0.00 0.00 36.22 1.85
2305 2990 7.913674 AACTCTTACCAGATGAATGAGAAAC 57.086 36.000 0.00 0.00 0.00 2.78
2364 3056 4.089361 GGCCCATATCAAATAGGGAAAGG 58.911 47.826 0.00 0.00 44.30 3.11
2460 3176 6.147492 GCATGTTTCCAGATAGAGCTATTCAG 59.853 42.308 0.00 0.00 0.00 3.02
2461 3177 5.994054 GCATGTTTCCAGATAGAGCTATTCA 59.006 40.000 0.00 0.00 0.00 2.57
2546 3275 7.538575 AGCTATTTAGAAAATGCACGATTGTT 58.461 30.769 0.00 0.00 0.00 2.83
2573 3302 1.839424 ACAAAAGATGGGTAGCAGGC 58.161 50.000 0.00 0.00 0.00 4.85
2810 3543 8.060679 GCATTACATTCATATCAGATACGCATC 58.939 37.037 0.00 0.00 0.00 3.91
2838 3623 9.424319 GAAGTGATCAACAGTCATTTCTAACTA 57.576 33.333 0.00 0.00 38.52 2.24
2933 3718 0.469892 TAGCATGCGGATCTGGAGGA 60.470 55.000 12.24 0.00 0.00 3.71
3030 3815 4.446719 AGGAAGCAACTAAAACGTACTTCG 59.553 41.667 0.00 0.00 46.00 3.79
3166 3951 0.554305 TACCATCCTAGACCCGCAGA 59.446 55.000 0.00 0.00 0.00 4.26
3228 4016 9.513906 TCTAAATCACAAGATACCACATTTCAA 57.486 29.630 0.00 0.00 33.08 2.69
3334 4122 9.590451 CTAATGCAATATTTCACCTTCATTGTT 57.410 29.630 0.00 0.00 0.00 2.83
3409 4197 6.741109 TGTATGCATGGTCAATCAATCAATC 58.259 36.000 10.16 0.00 0.00 2.67
3410 4198 6.718522 TGTATGCATGGTCAATCAATCAAT 57.281 33.333 10.16 0.00 0.00 2.57
3411 4199 6.527057 TTGTATGCATGGTCAATCAATCAA 57.473 33.333 10.16 0.00 0.00 2.57
3412 4200 6.097129 ACATTGTATGCATGGTCAATCAATCA 59.903 34.615 10.16 0.00 0.00 2.57
3413 4201 6.419710 CACATTGTATGCATGGTCAATCAATC 59.580 38.462 10.16 0.00 0.00 2.67
3463 4251 4.766373 TGCCTTCTATCATGCAAAGAAACA 59.234 37.500 0.00 0.00 0.00 2.83
3535 4323 9.477484 GTCAACTAAGATCTGACAAGAAAGTAA 57.523 33.333 0.00 0.00 39.42 2.24
3537 4325 6.931840 GGTCAACTAAGATCTGACAAGAAAGT 59.068 38.462 12.51 0.00 41.03 2.66
3573 4361 9.939802 AAGGTAGATACAAGTCTTAAAACGAAT 57.060 29.630 0.00 0.00 0.00 3.34
3604 4392 5.730550 TCCATTCGCAGTTCAGTAAACTAT 58.269 37.500 0.00 0.00 46.69 2.12
3677 4465 2.165437 AGAGAGCTTCAACGGATGTCTC 59.835 50.000 0.00 0.00 32.24 3.36
3730 4518 2.872245 TGCTTCAGTTTCCACGAGAAAG 59.128 45.455 5.78 0.00 45.11 2.62
3736 4524 1.795286 GAGAGTGCTTCAGTTTCCACG 59.205 52.381 0.00 0.00 33.62 4.94
3737 4525 3.118905 AGAGAGTGCTTCAGTTTCCAC 57.881 47.619 0.00 0.00 0.00 4.02
3768 4556 6.597672 TCGGCACTTCATTTCAACTATATGTT 59.402 34.615 0.00 0.00 39.92 2.71
3806 4594 3.194005 TGACCCCTATTGCTCGAATTC 57.806 47.619 0.00 0.00 0.00 2.17
3833 4621 0.670546 ATGACGTTGCCAGAGGTTCG 60.671 55.000 0.00 0.00 0.00 3.95
3842 4630 2.609459 CCTCTTGTGATATGACGTTGCC 59.391 50.000 0.00 0.00 0.00 4.52
3917 4705 7.334858 TCAGCCACATTGTATATGTGTAGAAA 58.665 34.615 14.65 0.00 45.74 2.52
3954 4742 5.674799 TTCTAGCCCAGGAGTATACCTTA 57.325 43.478 0.00 0.00 38.32 2.69
3973 4761 3.181440 TGTCCAAAACTCTGGAGCATTCT 60.181 43.478 0.00 0.00 46.29 2.40
4119 4907 4.458989 GGCCAAAACTAGAACATGACATGA 59.541 41.667 22.19 0.00 0.00 3.07
4120 4908 4.672542 CGGCCAAAACTAGAACATGACATG 60.673 45.833 14.02 14.02 0.00 3.21
4121 4909 3.440173 CGGCCAAAACTAGAACATGACAT 59.560 43.478 2.24 0.00 0.00 3.06
4122 4910 2.811431 CGGCCAAAACTAGAACATGACA 59.189 45.455 2.24 0.00 0.00 3.58
4123 4911 2.812011 ACGGCCAAAACTAGAACATGAC 59.188 45.455 2.24 0.00 0.00 3.06
4124 4912 3.134574 ACGGCCAAAACTAGAACATGA 57.865 42.857 2.24 0.00 0.00 3.07
4125 4913 5.365403 TTTACGGCCAAAACTAGAACATG 57.635 39.130 2.24 0.00 0.00 3.21
4126 4914 6.584185 AATTTACGGCCAAAACTAGAACAT 57.416 33.333 2.24 0.00 0.00 2.71
4127 4915 6.394025 AAATTTACGGCCAAAACTAGAACA 57.606 33.333 2.24 0.00 0.00 3.18
4128 4916 5.860182 GGAAATTTACGGCCAAAACTAGAAC 59.140 40.000 2.24 0.00 0.00 3.01
4132 4922 4.828387 ACAGGAAATTTACGGCCAAAACTA 59.172 37.500 2.24 0.00 0.00 2.24
4362 5155 5.677319 ACTAACTTGCATCAGCCTAACTA 57.323 39.130 0.00 0.00 41.13 2.24
4447 5240 4.444838 TCACCGCCGCGCATACTT 62.445 61.111 8.75 0.00 0.00 2.24
4668 5475 4.214758 ACTTGTTTTGTATACCTTGCGGAC 59.785 41.667 0.00 0.00 0.00 4.79
4686 5493 3.314693 TCCTTGTCCTTGACCTACTTGT 58.685 45.455 0.00 0.00 0.00 3.16
4687 5494 4.351874 TTCCTTGTCCTTGACCTACTTG 57.648 45.455 0.00 0.00 0.00 3.16
4688 5495 4.658901 TCTTTCCTTGTCCTTGACCTACTT 59.341 41.667 0.00 0.00 0.00 2.24
4689 5496 4.232091 TCTTTCCTTGTCCTTGACCTACT 58.768 43.478 0.00 0.00 0.00 2.57
4690 5497 4.618920 TCTTTCCTTGTCCTTGACCTAC 57.381 45.455 0.00 0.00 0.00 3.18
4691 5498 5.640158 TTTCTTTCCTTGTCCTTGACCTA 57.360 39.130 0.00 0.00 0.00 3.08
4692 5499 4.519906 TTTCTTTCCTTGTCCTTGACCT 57.480 40.909 0.00 0.00 0.00 3.85
4693 5500 5.592104 TTTTTCTTTCCTTGTCCTTGACC 57.408 39.130 0.00 0.00 0.00 4.02
4714 5521 9.328845 CCAAATGCTAAACTGCCAAATATTATT 57.671 29.630 0.00 0.00 0.00 1.40
4715 5522 8.485392 ACCAAATGCTAAACTGCCAAATATTAT 58.515 29.630 0.00 0.00 0.00 1.28
4716 5523 7.846066 ACCAAATGCTAAACTGCCAAATATTA 58.154 30.769 0.00 0.00 0.00 0.98
4717 5524 6.710278 ACCAAATGCTAAACTGCCAAATATT 58.290 32.000 0.00 0.00 0.00 1.28
4718 5525 6.298441 ACCAAATGCTAAACTGCCAAATAT 57.702 33.333 0.00 0.00 0.00 1.28
4725 5532 4.455877 ACTGAGTACCAAATGCTAAACTGC 59.544 41.667 0.00 0.00 0.00 4.40
4752 5560 5.023533 TCTGCGCAAAATAGGAGAATAGT 57.976 39.130 13.05 0.00 31.95 2.12
4796 5604 8.192110 TCATGTACAGACTGCACGTTATAAATA 58.808 33.333 1.25 0.00 0.00 1.40
4800 5608 5.337554 GTCATGTACAGACTGCACGTTATA 58.662 41.667 14.48 0.00 33.29 0.98
4801 5609 4.174009 GTCATGTACAGACTGCACGTTAT 58.826 43.478 14.48 0.00 33.29 1.89
4852 5660 2.251893 GCCAACGAGCGAGTATATAGC 58.748 52.381 0.00 0.00 0.00 2.97
4853 5661 3.058155 AGTGCCAACGAGCGAGTATATAG 60.058 47.826 0.00 0.00 34.65 1.31
4854 5662 2.882761 AGTGCCAACGAGCGAGTATATA 59.117 45.455 0.00 0.00 34.65 0.86
4855 5663 1.681793 AGTGCCAACGAGCGAGTATAT 59.318 47.619 0.00 0.00 34.65 0.86
4856 5664 1.100510 AGTGCCAACGAGCGAGTATA 58.899 50.000 0.00 0.00 34.65 1.47
4857 5665 1.100510 TAGTGCCAACGAGCGAGTAT 58.899 50.000 0.00 0.00 34.65 2.12
4858 5666 1.100510 ATAGTGCCAACGAGCGAGTA 58.899 50.000 0.00 0.00 34.65 2.59
4859 5667 0.246635 AATAGTGCCAACGAGCGAGT 59.753 50.000 0.00 0.00 34.65 4.18
4860 5668 0.647410 CAATAGTGCCAACGAGCGAG 59.353 55.000 0.00 0.00 34.65 5.03
4861 5669 1.358725 GCAATAGTGCCAACGAGCGA 61.359 55.000 3.16 0.00 45.68 4.93
4862 5670 1.060937 GCAATAGTGCCAACGAGCG 59.939 57.895 3.16 0.00 45.68 5.03
4867 5675 6.458347 GGATCACCAAGCAATAGTGCCAAC 62.458 50.000 12.26 0.00 43.18 3.77
4868 5676 4.436006 GGATCACCAAGCAATAGTGCCAA 61.436 47.826 12.26 0.00 43.18 4.52
4869 5677 2.945440 GGATCACCAAGCAATAGTGCCA 60.945 50.000 12.26 0.00 43.18 4.92
4870 5678 1.678101 GGATCACCAAGCAATAGTGCC 59.322 52.381 12.26 0.00 43.18 5.01
4871 5679 2.357009 CAGGATCACCAAGCAATAGTGC 59.643 50.000 7.15 7.15 44.48 4.40
4872 5680 3.376234 CACAGGATCACCAAGCAATAGTG 59.624 47.826 0.00 0.00 38.94 2.74
4873 5681 3.009473 ACACAGGATCACCAAGCAATAGT 59.991 43.478 0.00 0.00 38.94 2.12
4874 5682 3.614092 ACACAGGATCACCAAGCAATAG 58.386 45.455 0.00 0.00 38.94 1.73
4875 5683 3.719268 ACACAGGATCACCAAGCAATA 57.281 42.857 0.00 0.00 38.94 1.90
4876 5684 2.592102 ACACAGGATCACCAAGCAAT 57.408 45.000 0.00 0.00 38.94 3.56
4877 5685 2.363306 AACACAGGATCACCAAGCAA 57.637 45.000 0.00 0.00 38.94 3.91
4878 5686 2.363306 AAACACAGGATCACCAAGCA 57.637 45.000 0.00 0.00 38.94 3.91
4879 5687 3.437049 GTCTAAACACAGGATCACCAAGC 59.563 47.826 0.00 0.00 38.94 4.01
4880 5688 4.692625 CAGTCTAAACACAGGATCACCAAG 59.307 45.833 0.00 0.00 38.94 3.61
4881 5689 4.641396 CAGTCTAAACACAGGATCACCAA 58.359 43.478 0.00 0.00 38.94 3.67
4882 5690 3.557054 GCAGTCTAAACACAGGATCACCA 60.557 47.826 0.00 0.00 38.94 4.17
4883 5691 3.003480 GCAGTCTAAACACAGGATCACC 58.997 50.000 0.00 0.00 0.00 4.02
4884 5692 3.931578 AGCAGTCTAAACACAGGATCAC 58.068 45.455 0.00 0.00 0.00 3.06
4885 5693 5.939764 ATAGCAGTCTAAACACAGGATCA 57.060 39.130 0.00 0.00 0.00 2.92
4886 5694 8.247562 CCTATATAGCAGTCTAAACACAGGATC 58.752 40.741 4.04 0.00 0.00 3.36
4887 5695 7.950684 TCCTATATAGCAGTCTAAACACAGGAT 59.049 37.037 4.04 0.00 0.00 3.24
4888 5696 7.295340 TCCTATATAGCAGTCTAAACACAGGA 58.705 38.462 4.04 0.00 0.00 3.86
4907 5715 6.769822 CGTTTGGTTAGTCTCCTACTCCTATA 59.230 42.308 0.00 0.00 39.80 1.31
4908 5716 5.593502 CGTTTGGTTAGTCTCCTACTCCTAT 59.406 44.000 0.00 0.00 39.80 2.57
4911 5719 3.509184 ACGTTTGGTTAGTCTCCTACTCC 59.491 47.826 0.00 0.00 39.80 3.85
4912 5720 4.780275 ACGTTTGGTTAGTCTCCTACTC 57.220 45.455 0.00 0.00 39.80 2.59
4913 5721 4.798593 GCAACGTTTGGTTAGTCTCCTACT 60.799 45.833 0.00 0.00 42.62 2.57
4914 5722 3.431233 GCAACGTTTGGTTAGTCTCCTAC 59.569 47.826 0.00 0.00 36.49 3.18
4915 5723 3.069872 TGCAACGTTTGGTTAGTCTCCTA 59.930 43.478 0.00 0.00 36.49 2.94
4959 5768 6.127647 GCCTCATCAATGACAACAATTCCTAA 60.128 38.462 0.00 0.00 32.50 2.69
5019 5896 4.084888 CCAAAACGAGCCGCCGAC 62.085 66.667 8.04 0.00 0.00 4.79
5020 5897 4.612412 ACCAAAACGAGCCGCCGA 62.612 61.111 8.04 0.00 0.00 5.54
5021 5898 4.383602 CACCAAAACGAGCCGCCG 62.384 66.667 0.00 0.44 0.00 6.46
5022 5899 4.038080 CCACCAAAACGAGCCGCC 62.038 66.667 0.00 0.00 0.00 6.13
5024 5901 1.234615 ATCACCACCAAAACGAGCCG 61.235 55.000 0.00 0.00 0.00 5.52
5025 5902 1.737793 CTATCACCACCAAAACGAGCC 59.262 52.381 0.00 0.00 0.00 4.70
5026 5903 2.159627 CACTATCACCACCAAAACGAGC 59.840 50.000 0.00 0.00 0.00 5.03
5028 5905 2.105134 ACCACTATCACCACCAAAACGA 59.895 45.455 0.00 0.00 0.00 3.85
5030 5907 4.929819 AAACCACTATCACCACCAAAAC 57.070 40.909 0.00 0.00 0.00 2.43
5071 5948 8.687301 CAGCAAAACCGTAATAAAAGTTACAAG 58.313 33.333 0.00 0.00 34.90 3.16
5072 5949 8.404000 TCAGCAAAACCGTAATAAAAGTTACAA 58.596 29.630 0.00 0.00 34.90 2.41
5073 5950 7.928103 TCAGCAAAACCGTAATAAAAGTTACA 58.072 30.769 0.00 0.00 34.90 2.41
5074 5951 8.071967 ACTCAGCAAAACCGTAATAAAAGTTAC 58.928 33.333 0.00 0.00 0.00 2.50
5075 5952 8.156994 ACTCAGCAAAACCGTAATAAAAGTTA 57.843 30.769 0.00 0.00 0.00 2.24
5079 5956 9.798994 TTAAAACTCAGCAAAACCGTAATAAAA 57.201 25.926 0.00 0.00 0.00 1.52
5080 5957 9.235537 GTTAAAACTCAGCAAAACCGTAATAAA 57.764 29.630 0.00 0.00 0.00 1.40
5081 5958 8.623030 AGTTAAAACTCAGCAAAACCGTAATAA 58.377 29.630 0.00 0.00 32.86 1.40
5082 5959 8.156994 AGTTAAAACTCAGCAAAACCGTAATA 57.843 30.769 0.00 0.00 32.86 0.98
5084 5961 6.439675 AGTTAAAACTCAGCAAAACCGTAA 57.560 33.333 0.00 0.00 32.86 3.18
5085 5962 7.308109 CCATAGTTAAAACTCAGCAAAACCGTA 60.308 37.037 0.00 0.00 40.37 4.02
5086 5963 4.976224 AGTTAAAACTCAGCAAAACCGT 57.024 36.364 0.00 0.00 32.86 4.83
5088 5965 6.745116 ACCATAGTTAAAACTCAGCAAAACC 58.255 36.000 0.00 0.00 40.37 3.27
5089 5966 7.649057 AGACCATAGTTAAAACTCAGCAAAAC 58.351 34.615 0.00 0.00 40.37 2.43
5090 5967 7.500892 TGAGACCATAGTTAAAACTCAGCAAAA 59.499 33.333 0.00 0.00 40.37 2.44
5091 5968 6.995686 TGAGACCATAGTTAAAACTCAGCAAA 59.004 34.615 0.00 0.00 40.37 3.68
5093 5970 6.109156 TGAGACCATAGTTAAAACTCAGCA 57.891 37.500 0.00 0.00 40.37 4.41
5094 5971 6.654793 CTGAGACCATAGTTAAAACTCAGC 57.345 41.667 0.00 0.00 41.63 4.26
5096 5973 7.015292 AGTGACTGAGACCATAGTTAAAACTCA 59.985 37.037 0.00 0.00 40.37 3.41
5097 5974 7.379750 AGTGACTGAGACCATAGTTAAAACTC 58.620 38.462 0.00 0.00 40.37 3.01
5098 5975 7.304497 AGTGACTGAGACCATAGTTAAAACT 57.696 36.000 0.39 0.39 42.91 2.66
5099 5976 7.964604 AAGTGACTGAGACCATAGTTAAAAC 57.035 36.000 0.00 0.00 0.00 2.43
5100 5977 8.974060 AAAAGTGACTGAGACCATAGTTAAAA 57.026 30.769 0.00 0.00 0.00 1.52
5101 5978 8.429641 AGAAAAGTGACTGAGACCATAGTTAAA 58.570 33.333 0.00 0.00 0.00 1.52
5102 5979 7.963532 AGAAAAGTGACTGAGACCATAGTTAA 58.036 34.615 0.00 0.00 0.00 2.01
5117 6890 1.549170 TCGGAGGGCTAGAAAAGTGAC 59.451 52.381 0.00 0.00 0.00 3.67
5118 6891 1.933021 TCGGAGGGCTAGAAAAGTGA 58.067 50.000 0.00 0.00 0.00 3.41
5119 6892 2.939103 CAATCGGAGGGCTAGAAAAGTG 59.061 50.000 0.00 0.00 0.00 3.16
5120 6893 2.572104 ACAATCGGAGGGCTAGAAAAGT 59.428 45.455 0.00 0.00 0.00 2.66
5121 6894 3.198872 GACAATCGGAGGGCTAGAAAAG 58.801 50.000 0.00 0.00 0.00 2.27
5122 6895 2.569853 TGACAATCGGAGGGCTAGAAAA 59.430 45.455 0.00 0.00 0.00 2.29
5136 6910 5.973651 TCACGAATCTTAGCATGACAATC 57.026 39.130 0.00 0.00 0.00 2.67
5139 6913 4.122046 CCATCACGAATCTTAGCATGACA 58.878 43.478 0.00 0.00 0.00 3.58
5144 6918 2.988010 AGCCATCACGAATCTTAGCA 57.012 45.000 0.00 0.00 0.00 3.49
5165 6939 1.429148 GCTCCCGCGATAACCAACAG 61.429 60.000 8.23 0.00 0.00 3.16
5187 6961 1.672030 CAGATGAGCCGTGCACCAA 60.672 57.895 12.15 0.00 0.00 3.67
5188 6962 1.540435 TACAGATGAGCCGTGCACCA 61.540 55.000 12.15 3.32 0.00 4.17
5214 6988 1.002868 ACTCAGACACATGGGCTGC 60.003 57.895 12.79 0.00 0.00 5.25
5215 6989 0.612229 AGACTCAGACACATGGGCTG 59.388 55.000 11.73 11.73 0.00 4.85
5216 6990 1.356124 AAGACTCAGACACATGGGCT 58.644 50.000 0.00 0.00 0.00 5.19
5217 6991 2.622436 GTAAGACTCAGACACATGGGC 58.378 52.381 0.00 0.00 0.00 5.36
5219 6993 2.231478 ACGGTAAGACTCAGACACATGG 59.769 50.000 0.00 0.00 0.00 3.66
5220 6994 3.057526 TGACGGTAAGACTCAGACACATG 60.058 47.826 0.00 0.00 0.00 3.21
5222 6996 2.292569 GTGACGGTAAGACTCAGACACA 59.707 50.000 0.00 0.00 0.00 3.72
5223 6997 2.553172 AGTGACGGTAAGACTCAGACAC 59.447 50.000 0.00 0.00 0.00 3.67
5224 6998 2.860009 AGTGACGGTAAGACTCAGACA 58.140 47.619 0.00 0.00 0.00 3.41
5225 6999 3.919223 AAGTGACGGTAAGACTCAGAC 57.081 47.619 0.00 0.00 0.00 3.51
5226 7000 4.583489 AGAAAAGTGACGGTAAGACTCAGA 59.417 41.667 0.00 0.00 0.00 3.27
5227 7001 4.872664 AGAAAAGTGACGGTAAGACTCAG 58.127 43.478 0.00 0.00 0.00 3.35
5228 7002 4.931661 AGAAAAGTGACGGTAAGACTCA 57.068 40.909 0.00 0.00 0.00 3.41
5229 7003 4.850470 CGTAGAAAAGTGACGGTAAGACTC 59.150 45.833 0.00 0.00 33.01 3.36
5230 7004 4.516698 TCGTAGAAAAGTGACGGTAAGACT 59.483 41.667 0.00 0.00 37.20 3.24
5231 7005 4.787598 TCGTAGAAAAGTGACGGTAAGAC 58.212 43.478 0.00 0.00 37.20 3.01
5232 7006 4.614535 GCTCGTAGAAAAGTGACGGTAAGA 60.615 45.833 0.00 0.00 37.20 2.10
5233 7007 3.607209 GCTCGTAGAAAAGTGACGGTAAG 59.393 47.826 0.00 0.00 37.20 2.34
5234 7008 3.568538 GCTCGTAGAAAAGTGACGGTAA 58.431 45.455 0.00 0.00 37.20 2.85
5235 7009 2.095059 GGCTCGTAGAAAAGTGACGGTA 60.095 50.000 0.00 0.00 37.20 4.02
5236 7010 1.336609 GGCTCGTAGAAAAGTGACGGT 60.337 52.381 0.00 0.00 37.20 4.83
5237 7011 1.347320 GGCTCGTAGAAAAGTGACGG 58.653 55.000 0.00 0.00 37.20 4.79
5238 7012 1.336517 TGGGCTCGTAGAAAAGTGACG 60.337 52.381 0.00 0.00 34.09 4.35
5239 7013 2.067013 GTGGGCTCGTAGAAAAGTGAC 58.933 52.381 0.00 0.00 34.09 3.67
5244 7018 1.689813 TGTCTGTGGGCTCGTAGAAAA 59.310 47.619 0.00 0.00 34.09 2.29
5307 7081 4.154375 GGTAGAAAAGAAGAAGAAAGCCCG 59.846 45.833 0.00 0.00 0.00 6.13
5311 7085 5.408909 GGTCGGGTAGAAAAGAAGAAGAAAG 59.591 44.000 0.00 0.00 0.00 2.62
5321 7095 4.139038 TCCTTTTTGGTCGGGTAGAAAAG 58.861 43.478 0.00 0.00 37.17 2.27
5326 7161 3.746940 TCTTTCCTTTTTGGTCGGGTAG 58.253 45.455 0.00 0.00 37.07 3.18


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

AutoCloner maintained by Alex Coulton.