Multiple sequence alignment - TraesCS2D01G530200

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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 TraesCS2D01G530200 chr2D 100.000 6093 0 0 1 6093 616941423 616947515 0.000000e+00 11252.0
1 TraesCS2D01G530200 chr2A 93.277 4611 209 47 879 5453 746938949 746943494 0.000000e+00 6704.0
2 TraesCS2D01G530200 chr2A 88.577 2924 245 46 1145 3991 746956270 746959181 0.000000e+00 3467.0
3 TraesCS2D01G530200 chr2A 86.120 915 111 12 4006 4909 746959563 746960472 0.000000e+00 972.0
4 TraesCS2D01G530200 chr2A 86.933 551 46 13 1 541 746938009 746938543 4.070000e-166 595.0
5 TraesCS2D01G530200 chr2A 79.102 646 67 24 5467 6080 746943641 746944250 3.450000e-102 383.0
6 TraesCS2D01G530200 chr2A 82.629 426 42 13 5466 5867 746961107 746961524 1.260000e-91 348.0
7 TraesCS2D01G530200 chr2A 80.894 246 19 13 5859 6080 746962768 746963009 1.050000e-37 169.0
8 TraesCS2D01G530200 chr2A 91.304 115 9 1 1 115 746953380 746953493 8.180000e-34 156.0
9 TraesCS2D01G530200 chr2A 87.931 116 9 3 5338 5453 746960434 746960544 1.380000e-26 132.0
10 TraesCS2D01G530200 chr2A 84.956 113 9 5 1 111 746945087 746945193 2.320000e-19 108.0
11 TraesCS2D01G530200 chr2A 100.000 32 0 0 1098 1129 746956177 746956208 6.600000e-05 60.2
12 TraesCS2D01G530200 chr2B 87.432 4201 416 63 1144 5277 752480125 752484280 0.000000e+00 4730.0
13 TraesCS2D01G530200 chr2B 88.312 3063 292 32 1741 4793 752411849 752414855 0.000000e+00 3613.0
14 TraesCS2D01G530200 chr2B 88.909 541 51 8 1160 1697 752410956 752411490 0.000000e+00 658.0
15 TraesCS2D01G530200 chr2B 79.672 610 70 29 5466 6047 752484824 752485407 2.060000e-104 390.0
16 TraesCS2D01G530200 chr2B 95.327 107 5 0 1 107 752408118 752408224 2.920000e-38 171.0
17 TraesCS2D01G530200 chr2B 90.351 114 10 1 2 115 752478600 752478712 1.370000e-31 148.0
18 TraesCS2D01G530200 chr2B 84.483 116 13 4 5338 5453 752484488 752484598 6.460000e-20 110.0
19 TraesCS2D01G530200 chr6D 77.979 2375 450 47 1745 4084 468872445 468874781 0.000000e+00 1421.0
20 TraesCS2D01G530200 chr6D 76.380 2409 470 60 1932 4292 468941591 468943948 0.000000e+00 1205.0
21 TraesCS2D01G530200 chr6D 78.237 1622 312 27 2433 4036 468588736 468587138 0.000000e+00 1002.0
22 TraesCS2D01G530200 chr6D 75.731 342 66 10 3212 3550 468860465 468860792 8.180000e-34 156.0
23 TraesCS2D01G530200 chr6D 75.000 264 56 10 1187 1445 468255954 468255696 4.990000e-21 113.0
24 TraesCS2D01G530200 chr6B 76.547 2601 510 58 1745 4292 715154735 715157288 0.000000e+00 1332.0
25 TraesCS2D01G530200 chrUn 100.000 388 0 0 2811 3198 480372188 480371801 0.000000e+00 717.0
26 TraesCS2D01G530200 chrUn 91.228 114 9 1 2 114 9576565 9576678 2.940000e-33 154.0
27 TraesCS2D01G530200 chrUn 75.704 284 59 10 1167 1445 75218285 75218563 3.830000e-27 134.0
28 TraesCS2D01G530200 chrUn 93.056 72 3 2 937 1006 9577458 9577529 3.000000e-18 104.0
29 TraesCS2D01G530200 chrUn 90.769 65 6 0 817 881 9577248 9577312 3.030000e-13 87.9
30 TraesCS2D01G530200 chr5B 82.212 208 22 11 5817 6009 61390138 61390345 1.360000e-36 165.0
31 TraesCS2D01G530200 chr5B 90.476 84 8 0 1 84 61391991 61392074 1.800000e-20 111.0


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 TraesCS2D01G530200 chr2D 616941423 616947515 6092 False 11252.000000 11252 100.000000 1 6093 1 chr2D.!!$F1 6092
1 TraesCS2D01G530200 chr2A 746938009 746945193 7184 False 1947.500000 6704 86.067000 1 6080 4 chr2A.!!$F1 6079
2 TraesCS2D01G530200 chr2A 746953380 746963009 9629 False 757.742857 3467 88.207857 1 6080 7 chr2A.!!$F2 6079
3 TraesCS2D01G530200 chr2B 752408118 752414855 6737 False 1480.666667 3613 90.849333 1 4793 3 chr2B.!!$F1 4792
4 TraesCS2D01G530200 chr2B 752478600 752485407 6807 False 1344.500000 4730 85.484500 2 6047 4 chr2B.!!$F2 6045
5 TraesCS2D01G530200 chr6D 468872445 468874781 2336 False 1421.000000 1421 77.979000 1745 4084 1 chr6D.!!$F2 2339
6 TraesCS2D01G530200 chr6D 468941591 468943948 2357 False 1205.000000 1205 76.380000 1932 4292 1 chr6D.!!$F3 2360
7 TraesCS2D01G530200 chr6D 468587138 468588736 1598 True 1002.000000 1002 78.237000 2433 4036 1 chr6D.!!$R2 1603
8 TraesCS2D01G530200 chr6B 715154735 715157288 2553 False 1332.000000 1332 76.547000 1745 4292 1 chr6B.!!$F1 2547

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
50 51 0.110486 GGCTCTTGTCCTGGGTGAAA 59.890 55.000 0.0 0.0 0.00 2.69 F
1184 5136 1.134401 GGAGATGAAGATGGCCGTCAA 60.134 52.381 26.7 12.2 36.87 3.18 F
1549 5528 1.217057 ATGCTTCACCCACCCAGGAT 61.217 55.000 0.0 0.0 41.22 3.24 F
2338 6671 1.076549 GGCCCCATTCACAACAGGA 59.923 57.895 0.0 0.0 0.00 3.86 F
3593 7950 0.671251 TGAAACCGTGGCATCCAAAC 59.329 50.000 0.0 0.0 34.18 2.93 F
4828 9567 0.320771 CCGCTTCACTGCTGGTACTT 60.321 55.000 0.0 0.0 0.00 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1549 5528 0.178767 CCTTGGTGCCATCGATCTCA 59.821 55.000 0.00 0.0 0.0 3.27 R
2338 6671 1.304713 CATGCTGCCCTTGGTTCCT 60.305 57.895 0.00 0.0 0.0 3.36 R
2795 7128 3.059352 ACTTGAGTCTACAATGCCCAC 57.941 47.619 0.00 0.0 0.0 4.61 R
3744 8101 0.032540 GCAAGGACCAGTGGCAAAAG 59.967 55.000 9.78 0.0 0.0 2.27 R
5075 9814 0.035820 TCTCACCGTGGCCAAATACC 60.036 55.000 7.24 0.0 0.0 2.73 R
5939 12677 0.601558 GGTAACTGCACGACCTCTGA 59.398 55.000 0.00 0.0 0.0 3.27 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
50 51 0.110486 GGCTCTTGTCCTGGGTGAAA 59.890 55.000 0.00 0.00 0.00 2.69
99 100 5.520748 ACCAGAACTATGTCCCATTTCTT 57.479 39.130 0.00 0.00 0.00 2.52
120 122 9.959721 TTTCTTGAATGGAGGTTATATATAGCC 57.040 33.333 15.87 15.87 34.24 3.93
121 123 8.679344 TCTTGAATGGAGGTTATATATAGCCA 57.321 34.615 23.14 14.89 36.24 4.75
123 125 9.911788 CTTGAATGGAGGTTATATATAGCCATT 57.088 33.333 23.14 21.29 44.67 3.16
129 131 9.739276 TGGAGGTTATATATAGCCATTTTCTTG 57.261 33.333 23.14 0.00 36.24 3.02
238 282 1.134877 CAGATCTGACACGGTGCTGAT 60.135 52.381 18.34 14.48 0.00 2.90
250 294 4.079253 ACGGTGCTGATTAACAAAAGGAT 58.921 39.130 0.00 0.00 0.00 3.24
254 298 5.869344 GGTGCTGATTAACAAAAGGATTTCC 59.131 40.000 0.00 0.00 37.28 3.13
272 598 4.640771 TTCCTCACTTAATGCAGGAACT 57.359 40.909 0.00 0.00 38.57 3.01
420 749 4.760715 AGCATCATTGACATTGGATAGCTC 59.239 41.667 0.00 0.00 0.00 4.09
450 779 3.126831 GACTCGGCAGTTGATTAGGATG 58.873 50.000 0.00 0.00 30.63 3.51
461 790 2.705658 TGATTAGGATGCCACACCCTAG 59.294 50.000 0.00 0.00 34.39 3.02
543 909 5.075858 TGAGTTTGCCCATTCATTCATTC 57.924 39.130 0.00 0.00 0.00 2.67
596 962 1.448985 TGCTGAATTGTTAGGGCGAC 58.551 50.000 0.00 0.00 0.00 5.19
640 1069 8.770438 TTTCAAACTTTGTTGCTTGATAGTTT 57.230 26.923 1.44 0.00 36.55 2.66
663 1092 5.966742 AGATATTGATAGTGCAGAGCGTA 57.033 39.130 0.00 0.00 0.00 4.42
720 1149 6.402983 CCTGAACATCTGCTCTATGAACAAAC 60.403 42.308 0.00 0.00 0.00 2.93
731 1160 7.443879 TGCTCTATGAACAAACTTGTGATGTAA 59.556 33.333 0.00 0.00 41.31 2.41
732 1161 8.454106 GCTCTATGAACAAACTTGTGATGTAAT 58.546 33.333 0.00 0.00 41.31 1.89
735 1164 9.897744 CTATGAACAAACTTGTGATGTAATTGT 57.102 29.630 0.00 0.00 41.31 2.71
737 1166 8.404889 TGAACAAACTTGTGATGTAATTGTTG 57.595 30.769 5.79 0.00 41.31 3.33
738 1167 6.826893 ACAAACTTGTGATGTAATTGTTGC 57.173 33.333 0.00 0.00 40.49 4.17
751 1180 5.427157 TGTAATTGTTGCTCATAGGGTCCTA 59.573 40.000 0.00 0.00 0.00 2.94
752 1181 4.696479 ATTGTTGCTCATAGGGTCCTAG 57.304 45.455 2.97 0.00 31.45 3.02
772 1207 1.271102 GCTAGCTAGGATTCCTCGTGG 59.729 57.143 22.10 0.00 34.61 4.94
775 1210 1.759459 GCTAGGATTCCTCGTGGGGG 61.759 65.000 8.94 0.00 34.61 5.40
777 1212 2.252012 TAGGATTCCTCGTGGGGGCT 62.252 60.000 8.94 0.00 34.61 5.19
779 1214 1.342672 GGATTCCTCGTGGGGGCTAA 61.343 60.000 3.23 0.00 35.33 3.09
782 1217 1.882308 TTCCTCGTGGGGGCTAATAA 58.118 50.000 3.23 0.00 35.33 1.40
822 1277 2.484287 CTTGCCCCGGACACCTTCAT 62.484 60.000 0.73 0.00 0.00 2.57
845 1307 3.016031 TGTTGTTCTTGCACACAGTCAT 58.984 40.909 0.00 0.00 0.00 3.06
847 1309 1.948834 TGTTCTTGCACACAGTCATGG 59.051 47.619 0.00 0.00 0.00 3.66
848 1310 1.949525 GTTCTTGCACACAGTCATGGT 59.050 47.619 0.00 0.00 0.00 3.55
849 1311 1.596603 TCTTGCACACAGTCATGGTG 58.403 50.000 0.00 0.00 41.95 4.17
881 1347 1.294041 TCCTGACATGGGTGCCATTA 58.706 50.000 0.00 0.00 42.23 1.90
1184 5136 1.134401 GGAGATGAAGATGGCCGTCAA 60.134 52.381 26.70 12.20 36.87 3.18
1533 5512 3.853671 CCGTTGTCTAAAATGCTTCATGC 59.146 43.478 0.00 0.00 43.25 4.06
1549 5528 1.217057 ATGCTTCACCCACCCAGGAT 61.217 55.000 0.00 0.00 41.22 3.24
1635 5614 3.372676 GACGCCATGTTGCTCGCTG 62.373 63.158 0.00 0.00 0.00 5.18
2338 6671 1.076549 GGCCCCATTCACAACAGGA 59.923 57.895 0.00 0.00 0.00 3.86
2795 7128 8.767478 AAAAATCACTAATTTCTGGATTGCAG 57.233 30.769 0.00 0.00 36.54 4.41
3449 7797 6.509523 AAGAATTCCATTCCCGTATTCCTA 57.490 37.500 0.65 0.00 40.13 2.94
3593 7950 0.671251 TGAAACCGTGGCATCCAAAC 59.329 50.000 0.00 0.00 34.18 2.93
3670 8027 2.059345 TTTGGGGTCGAGGGGAACAC 62.059 60.000 0.00 0.00 35.81 3.32
3679 8036 3.066481 GTCGAGGGGAACACACTATAGAC 59.934 52.174 6.78 0.00 0.00 2.59
3744 8101 8.976986 AGCAAGCTTAGCATTATAAATTATGC 57.023 30.769 18.74 5.94 45.77 3.14
3955 8315 4.452455 AGAAGTTTTATGCACCTGAAGACG 59.548 41.667 0.00 0.00 0.00 4.18
3961 8321 0.396435 TGCACCTGAAGACGGTTCAT 59.604 50.000 3.24 0.00 30.82 2.57
4116 8852 4.094887 CCTTTGTCGACTCCATATTGTTGG 59.905 45.833 17.92 0.00 38.18 3.77
4138 8874 4.327680 GTTGCCCAGAGTTATCTCAGTTT 58.672 43.478 3.70 0.00 42.66 2.66
4139 8875 3.942829 TGCCCAGAGTTATCTCAGTTTG 58.057 45.455 3.70 0.00 42.66 2.93
4211 8947 6.380846 AGGGTTATACACAGGTTTGACGTATA 59.619 38.462 0.00 0.00 32.59 1.47
4233 8969 2.722094 TGGAAAGTGTTTGACTGCTGT 58.278 42.857 0.00 0.00 34.02 4.40
4352 9088 4.006319 CCAAAAGATGAAGTCCCTGAGAC 58.994 47.826 0.00 0.00 46.71 3.36
4365 9101 2.158986 CCCTGAGACAACTAGATGCCAG 60.159 54.545 0.00 3.90 0.00 4.85
4367 9103 3.196469 CCTGAGACAACTAGATGCCAGAA 59.804 47.826 14.77 0.00 0.00 3.02
4373 9109 3.076621 CAACTAGATGCCAGAAGTTGCA 58.923 45.455 0.00 0.00 41.49 4.08
4440 9176 2.074099 TGGCAGCCCATGACAAGTA 58.926 52.632 9.64 0.00 46.85 2.24
4637 9376 2.900716 TGATGACGTGACTGAAACCA 57.099 45.000 0.00 0.00 0.00 3.67
4644 9383 1.156736 GTGACTGAAACCATCACGGG 58.843 55.000 0.00 0.00 40.22 5.28
4691 9430 2.498078 CTCACCTCCCTCCAAAGTCTAC 59.502 54.545 0.00 0.00 0.00 2.59
4692 9431 1.204941 CACCTCCCTCCAAAGTCTACG 59.795 57.143 0.00 0.00 0.00 3.51
4700 9439 4.689345 CCCTCCAAAGTCTACGTTTTACAG 59.311 45.833 0.00 0.00 0.00 2.74
4758 9497 5.336293 GCCTTTCTTCTCTCAGGGAATTTTG 60.336 44.000 0.00 0.00 0.00 2.44
4764 9503 5.108187 TCTCTCAGGGAATTTTGGATCAG 57.892 43.478 0.00 0.00 0.00 2.90
4766 9505 5.014544 TCTCTCAGGGAATTTTGGATCAGTT 59.985 40.000 0.00 0.00 0.00 3.16
4823 9562 3.965539 CTCCCCGCTTCACTGCTGG 62.966 68.421 0.00 0.00 37.13 4.85
4828 9567 0.320771 CCGCTTCACTGCTGGTACTT 60.321 55.000 0.00 0.00 0.00 2.24
4836 9575 3.257375 TCACTGCTGGTACTTGACGTAAT 59.743 43.478 0.00 0.00 0.00 1.89
4837 9576 3.367932 CACTGCTGGTACTTGACGTAATG 59.632 47.826 0.00 0.00 0.00 1.90
4846 9585 1.305219 TTGACGTAATGGGCTGCAGC 61.305 55.000 30.88 30.88 41.14 5.25
4868 9607 3.002791 CGTGAGATAAAAGAGCAAGCCA 58.997 45.455 0.00 0.00 0.00 4.75
4873 9612 5.948162 TGAGATAAAAGAGCAAGCCAAGAAT 59.052 36.000 0.00 0.00 0.00 2.40
4876 9615 7.341805 AGATAAAAGAGCAAGCCAAGAATCTA 58.658 34.615 0.00 0.00 0.00 1.98
4880 9619 6.655078 AAGAGCAAGCCAAGAATCTAAAAA 57.345 33.333 0.00 0.00 0.00 1.94
4904 9643 5.275067 AGCAAAGCCTTGTTTGATTGTTA 57.725 34.783 0.00 0.00 39.40 2.41
4906 9645 5.754890 AGCAAAGCCTTGTTTGATTGTTAAG 59.245 36.000 0.00 0.00 39.40 1.85
4908 9647 5.869649 AAGCCTTGTTTGATTGTTAAGGT 57.130 34.783 0.00 0.00 39.97 3.50
4910 9649 3.740832 GCCTTGTTTGATTGTTAAGGTGC 59.259 43.478 0.00 0.00 39.97 5.01
4911 9650 3.980775 CCTTGTTTGATTGTTAAGGTGCG 59.019 43.478 0.00 0.00 34.58 5.34
4912 9651 4.499019 CCTTGTTTGATTGTTAAGGTGCGT 60.499 41.667 0.00 0.00 34.58 5.24
4914 9653 3.628032 TGTTTGATTGTTAAGGTGCGTCA 59.372 39.130 0.00 0.00 0.00 4.35
4915 9654 3.889196 TTGATTGTTAAGGTGCGTCAC 57.111 42.857 1.92 1.92 0.00 3.67
4916 9655 3.120321 TGATTGTTAAGGTGCGTCACT 57.880 42.857 9.31 0.00 34.40 3.41
4917 9656 3.472652 TGATTGTTAAGGTGCGTCACTT 58.527 40.909 9.31 0.16 34.40 3.16
4920 9659 3.120321 TGTTAAGGTGCGTCACTTCAT 57.880 42.857 9.31 0.00 34.40 2.57
4922 9661 3.880490 TGTTAAGGTGCGTCACTTCATTT 59.120 39.130 9.31 1.90 34.40 2.32
4923 9662 4.336993 TGTTAAGGTGCGTCACTTCATTTT 59.663 37.500 9.31 0.62 34.40 1.82
5018 9757 8.807948 AAAAATAGGCTGCTTATCAGTTCTTA 57.192 30.769 4.66 0.00 44.66 2.10
5066 9805 6.546395 CAATTGCAAGTGACAGTCTTATACC 58.454 40.000 21.79 0.00 0.00 2.73
5075 9814 4.405680 TGACAGTCTTATACCATCCACAGG 59.594 45.833 1.31 0.00 0.00 4.00
5077 9816 3.711704 CAGTCTTATACCATCCACAGGGT 59.288 47.826 0.00 0.00 40.74 4.34
5078 9817 4.899457 CAGTCTTATACCATCCACAGGGTA 59.101 45.833 0.00 0.00 43.10 3.69
5082 9821 6.710744 GTCTTATACCATCCACAGGGTATTTG 59.289 42.308 8.47 3.45 45.63 2.32
5083 9822 2.826674 ACCATCCACAGGGTATTTGG 57.173 50.000 0.00 0.00 33.84 3.28
5084 9823 1.341976 ACCATCCACAGGGTATTTGGC 60.342 52.381 0.00 0.00 33.84 4.52
5085 9824 1.402787 CATCCACAGGGTATTTGGCC 58.597 55.000 0.00 0.00 34.93 5.36
5086 9825 1.006813 ATCCACAGGGTATTTGGCCA 58.993 50.000 0.00 0.00 34.93 5.36
5088 9827 1.312371 CCACAGGGTATTTGGCCACG 61.312 60.000 3.88 0.00 0.00 4.94
5089 9828 1.001393 ACAGGGTATTTGGCCACGG 60.001 57.895 3.88 0.00 0.00 4.94
5090 9829 1.001393 CAGGGTATTTGGCCACGGT 60.001 57.895 3.88 0.00 0.00 4.83
5091 9830 1.001393 AGGGTATTTGGCCACGGTG 60.001 57.895 3.88 0.00 0.00 4.94
5092 9831 1.001887 GGGTATTTGGCCACGGTGA 60.002 57.895 3.88 0.00 0.00 4.02
5094 9833 0.035820 GGTATTTGGCCACGGTGAGA 60.036 55.000 3.88 0.00 0.00 3.27
5095 9834 1.408266 GGTATTTGGCCACGGTGAGAT 60.408 52.381 3.88 0.00 0.00 2.75
5096 9835 2.365582 GTATTTGGCCACGGTGAGATT 58.634 47.619 3.88 0.00 0.00 2.40
5097 9836 1.463674 ATTTGGCCACGGTGAGATTC 58.536 50.000 3.88 0.00 0.00 2.52
5099 9838 1.773856 TTGGCCACGGTGAGATTCCA 61.774 55.000 3.88 5.91 0.00 3.53
5100 9839 1.002624 GGCCACGGTGAGATTCCAA 60.003 57.895 10.28 0.00 0.00 3.53
5101 9840 0.394352 GGCCACGGTGAGATTCCAAT 60.394 55.000 10.28 0.00 0.00 3.16
5102 9841 1.463674 GCCACGGTGAGATTCCAATT 58.536 50.000 10.28 0.00 0.00 2.32
5103 9842 1.818674 GCCACGGTGAGATTCCAATTT 59.181 47.619 10.28 0.00 0.00 1.82
5146 9885 2.428171 GCCATGATATTGTGCAGGTTGT 59.572 45.455 0.00 0.00 0.00 3.32
5150 9889 5.589855 CCATGATATTGTGCAGGTTGTCTTA 59.410 40.000 0.00 0.00 0.00 2.10
5282 10062 3.236816 GTCATTTTTGCTGACGTGATGG 58.763 45.455 0.00 0.00 34.24 3.51
5303 10083 2.622436 GCCCGTAAGAGATCCATATGC 58.378 52.381 0.00 0.00 43.02 3.14
5335 10225 0.602905 GGTCAGTTGCTTGTACGCCT 60.603 55.000 0.00 0.00 0.00 5.52
5336 10226 1.226746 GTCAGTTGCTTGTACGCCTT 58.773 50.000 0.00 0.00 0.00 4.35
5350 10240 6.680874 TGTACGCCTTGAAACTAAAAGAAA 57.319 33.333 0.00 0.00 0.00 2.52
5351 10241 6.721321 TGTACGCCTTGAAACTAAAAGAAAG 58.279 36.000 0.00 0.00 0.00 2.62
5352 10242 5.183014 ACGCCTTGAAACTAAAAGAAAGG 57.817 39.130 0.00 0.00 37.76 3.11
5355 10245 6.127563 ACGCCTTGAAACTAAAAGAAAGGAAA 60.128 34.615 3.49 0.00 37.02 3.13
5386 10276 7.658575 TGTTTATCTGTTGAGGTAAGTAACACC 59.341 37.037 0.00 0.00 36.22 4.16
5403 10293 4.994907 ACACCCACTTTTTGAAACCTAC 57.005 40.909 0.00 0.00 0.00 3.18
5407 10297 5.009310 CACCCACTTTTTGAAACCTACCTAC 59.991 44.000 0.00 0.00 0.00 3.18
5408 10298 4.521639 CCCACTTTTTGAAACCTACCTACC 59.478 45.833 0.00 0.00 0.00 3.18
5421 10311 6.301169 ACCTACCTACCTTTCTGAAATCTG 57.699 41.667 2.88 0.00 0.00 2.90
5423 10313 6.500751 ACCTACCTACCTTTCTGAAATCTGAA 59.499 38.462 2.88 0.00 33.02 3.02
5453 10343 4.193826 ACTCGTGTCATTGCAGAAGTAT 57.806 40.909 0.00 0.00 0.00 2.12
5455 10345 3.925379 TCGTGTCATTGCAGAAGTATGT 58.075 40.909 0.00 0.00 0.00 2.29
5456 10346 4.314961 TCGTGTCATTGCAGAAGTATGTT 58.685 39.130 0.00 0.00 0.00 2.71
5457 10347 4.388773 TCGTGTCATTGCAGAAGTATGTTC 59.611 41.667 0.00 0.00 0.00 3.18
5458 10348 4.641954 GTGTCATTGCAGAAGTATGTTCG 58.358 43.478 0.00 0.00 0.00 3.95
5459 10349 4.152402 GTGTCATTGCAGAAGTATGTTCGT 59.848 41.667 0.00 0.00 0.00 3.85
5462 10352 6.128661 TGTCATTGCAGAAGTATGTTCGTTAC 60.129 38.462 0.00 0.00 0.00 2.50
5463 10353 5.929415 TCATTGCAGAAGTATGTTCGTTACA 59.071 36.000 0.00 0.00 41.97 2.41
5534 10990 5.979517 GCAGTATTGTTTGCTTTTGTTCTCT 59.020 36.000 0.00 0.00 37.35 3.10
5541 10997 9.899226 ATTGTTTGCTTTTGTTCTCTCTAATAC 57.101 29.630 0.00 0.00 0.00 1.89
5548 11004 9.640963 GCTTTTGTTCTCTCTAATACTAGACAA 57.359 33.333 0.00 0.00 30.68 3.18
5555 11012 8.961294 TCTCTCTAATACTAGACAACACCTAC 57.039 38.462 0.00 0.00 30.68 3.18
5565 11023 8.747538 ACTAGACAACACCTACTTTTGAAATT 57.252 30.769 0.00 0.00 0.00 1.82
5617 11077 7.092079 TGCATGATTTCACCTTTGTAAATCTG 58.908 34.615 0.00 0.00 39.34 2.90
5640 11100 4.201576 GTCAAGTAAAAAGTTCGCTGTCG 58.798 43.478 0.00 0.00 0.00 4.35
5670 11130 6.157211 ACTAAGACTATATTTTCGGCCATCG 58.843 40.000 2.24 0.00 40.90 3.84
5690 11150 7.277981 GCCATCGTATTTTCAGAACTAGAAGAA 59.722 37.037 0.00 0.00 0.00 2.52
5714 11179 1.194781 AACCAGGTCGAGGACAGCAT 61.195 55.000 0.00 0.00 33.68 3.79
5730 11195 2.161012 CAGCATGTGCAACTTACTCTGG 59.839 50.000 7.83 0.00 45.16 3.86
5734 11217 4.201851 GCATGTGCAACTTACTCTGGTATG 60.202 45.833 0.00 0.00 41.59 2.39
5751 11234 4.142026 TGGTATGTTGGATAACCGTCTGAG 60.142 45.833 0.00 0.00 39.42 3.35
5758 11241 2.297597 GGATAACCGTCTGAGATCCAGG 59.702 54.545 10.23 0.00 43.12 4.45
5789 11272 2.427453 GCTAGTGAGTCGATTTCTCCCA 59.573 50.000 0.00 0.00 0.00 4.37
5810 11293 1.008403 TCCCAGCTACCCACTACTCT 58.992 55.000 0.00 0.00 0.00 3.24
5811 11294 1.115467 CCCAGCTACCCACTACTCTG 58.885 60.000 0.00 0.00 0.00 3.35
5812 11295 1.619977 CCCAGCTACCCACTACTCTGT 60.620 57.143 0.00 0.00 0.00 3.41
5813 11296 1.751924 CCAGCTACCCACTACTCTGTC 59.248 57.143 0.00 0.00 0.00 3.51
5814 11297 2.621929 CCAGCTACCCACTACTCTGTCT 60.622 54.545 0.00 0.00 0.00 3.41
5815 11298 2.685897 CAGCTACCCACTACTCTGTCTC 59.314 54.545 0.00 0.00 0.00 3.36
5870 12603 0.997196 GGGTTTAGTTGTAGCTCGCG 59.003 55.000 0.00 0.00 0.00 5.87
5899 12632 2.270205 CCTTGACTGGGATGCGCT 59.730 61.111 9.73 0.00 0.00 5.92
5917 12655 1.673033 GCTTGCACATACCGTCAGACT 60.673 52.381 0.00 0.00 0.00 3.24
5938 12676 3.260483 GACTGGATGCGCGCTCAG 61.260 66.667 31.67 31.67 0.00 3.35
5939 12677 3.997064 GACTGGATGCGCGCTCAGT 62.997 63.158 35.73 35.73 42.37 3.41
5958 12696 0.601558 TCAGAGGTCGTGCAGTTACC 59.398 55.000 4.24 4.24 0.00 2.85
5959 12697 0.603569 CAGAGGTCGTGCAGTTACCT 59.396 55.000 13.08 13.08 46.33 3.08
5961 12699 0.389948 GAGGTCGTGCAGTTACCTGG 60.390 60.000 17.05 0.00 43.69 4.45
5963 12701 2.033194 GTCGTGCAGTTACCTGGGC 61.033 63.158 0.00 0.00 39.22 5.36
6026 12778 8.641541 GCAAGATTATATTCTGAATTTTGGGGA 58.358 33.333 8.38 0.00 31.26 4.81
6055 12809 1.754803 AGCATACCTAGTTAGCGCACA 59.245 47.619 11.47 0.00 0.00 4.57
6067 12824 0.599558 AGCGCACATTGCTGACATTT 59.400 45.000 11.47 0.00 42.25 2.32
6082 13099 6.258287 TGCTGACATTTTTCAAGATTTGGTTG 59.742 34.615 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 7.341805 ACAAACAGCTATATGACCTTGAGAAT 58.658 34.615 0.00 0.00 0.00 2.40
120 122 9.393512 AGTTCTAGATCTCCATTCAAGAAAATG 57.606 33.333 0.00 0.00 36.57 2.32
162 189 9.696572 TTACCTGATGATTAAGTACTCACTACT 57.303 33.333 0.00 0.00 37.28 2.57
165 192 9.427821 AGATTACCTGATGATTAAGTACTCACT 57.572 33.333 0.00 0.00 36.19 3.41
195 237 3.551890 GCAGCATCAATGAGAAGCAAATG 59.448 43.478 7.63 0.21 43.20 2.32
250 294 4.985538 AGTTCCTGCATTAAGTGAGGAAA 58.014 39.130 11.54 0.00 41.51 3.13
254 298 6.204301 CCATGATAGTTCCTGCATTAAGTGAG 59.796 42.308 0.00 0.00 0.00 3.51
256 576 5.824624 ACCATGATAGTTCCTGCATTAAGTG 59.175 40.000 0.00 0.00 0.00 3.16
357 684 7.231925 ACTCTGGCAATCAATTGATGCATAATA 59.768 33.333 28.26 15.98 40.14 0.98
361 688 3.704566 ACTCTGGCAATCAATTGATGCAT 59.295 39.130 28.26 0.00 40.14 3.96
450 779 1.204941 CACTACAGTCTAGGGTGTGGC 59.795 57.143 7.85 0.00 0.00 5.01
461 790 6.313164 GCATTTCTAACTAACCCACTACAGTC 59.687 42.308 0.00 0.00 0.00 3.51
511 846 1.202348 GGGCAAACTCATACAACTGGC 59.798 52.381 0.00 0.00 0.00 4.85
543 909 3.270027 TGTACGCAAATGAATCCTCCAG 58.730 45.455 0.00 0.00 0.00 3.86
573 939 2.480073 CGCCCTAACAATTCAGCAATGG 60.480 50.000 0.00 0.00 0.00 3.16
640 1069 5.966742 ACGCTCTGCACTATCAATATCTA 57.033 39.130 0.00 0.00 0.00 1.98
645 1074 4.503910 TGTTTACGCTCTGCACTATCAAT 58.496 39.130 0.00 0.00 0.00 2.57
689 1118 1.872313 GAGCAGATGTTCAGGCATAGC 59.128 52.381 0.00 0.00 33.14 2.97
693 1122 2.767960 TCATAGAGCAGATGTTCAGGCA 59.232 45.455 0.00 0.00 0.00 4.75
720 1149 7.191551 CCTATGAGCAACAATTACATCACAAG 58.808 38.462 0.00 0.00 0.00 3.16
731 1160 3.181450 GCTAGGACCCTATGAGCAACAAT 60.181 47.826 4.82 0.00 0.00 2.71
732 1161 2.170607 GCTAGGACCCTATGAGCAACAA 59.829 50.000 4.82 0.00 0.00 2.83
733 1162 1.762957 GCTAGGACCCTATGAGCAACA 59.237 52.381 4.82 0.00 0.00 3.33
734 1163 2.043227 AGCTAGGACCCTATGAGCAAC 58.957 52.381 10.83 0.00 0.00 4.17
735 1164 2.478872 AGCTAGGACCCTATGAGCAA 57.521 50.000 10.83 0.00 0.00 3.91
736 1165 2.819726 GCTAGCTAGGACCCTATGAGCA 60.820 54.545 22.10 0.00 32.44 4.26
737 1166 1.822371 GCTAGCTAGGACCCTATGAGC 59.178 57.143 22.10 1.73 0.00 4.26
738 1167 3.449746 AGCTAGCTAGGACCCTATGAG 57.550 52.381 17.69 0.00 0.00 2.90
751 1180 2.235016 CACGAGGAATCCTAGCTAGCT 58.765 52.381 23.12 23.12 31.76 3.32
752 1181 1.271102 CCACGAGGAATCCTAGCTAGC 59.729 57.143 15.74 6.62 36.89 3.42
769 1204 2.932261 CAAGAGGTTATTAGCCCCCAC 58.068 52.381 0.00 0.00 0.00 4.61
772 1207 1.214424 TGGCAAGAGGTTATTAGCCCC 59.786 52.381 0.00 0.00 41.33 5.80
775 1210 2.683362 GTGGTGGCAAGAGGTTATTAGC 59.317 50.000 0.00 0.00 0.00 3.09
777 1212 2.303600 ACGTGGTGGCAAGAGGTTATTA 59.696 45.455 0.00 0.00 0.00 0.98
779 1214 0.690762 ACGTGGTGGCAAGAGGTTAT 59.309 50.000 0.00 0.00 0.00 1.89
782 1217 2.383245 CTGACGTGGTGGCAAGAGGT 62.383 60.000 0.00 0.00 0.00 3.85
822 1277 2.158559 ACTGTGTGCAAGAACAACACA 58.841 42.857 7.55 7.55 41.77 3.72
845 1307 3.396276 TCAGGAAATTTACACCTCCACCA 59.604 43.478 2.58 0.00 31.06 4.17
847 1309 4.394729 TGTCAGGAAATTTACACCTCCAC 58.605 43.478 2.58 0.62 31.06 4.02
848 1310 4.715534 TGTCAGGAAATTTACACCTCCA 57.284 40.909 2.58 0.00 31.06 3.86
849 1311 4.399303 CCATGTCAGGAAATTTACACCTCC 59.601 45.833 2.58 0.00 31.06 4.30
881 1347 2.039879 GGGACATTAGTGTGGGTCAAGT 59.960 50.000 0.00 0.00 39.09 3.16
1549 5528 0.178767 CCTTGGTGCCATCGATCTCA 59.821 55.000 0.00 0.00 0.00 3.27
1635 5614 2.436115 GGTAGTTGCCGAGGGTGC 60.436 66.667 0.00 0.00 0.00 5.01
2338 6671 1.304713 CATGCTGCCCTTGGTTCCT 60.305 57.895 0.00 0.00 0.00 3.36
2795 7128 3.059352 ACTTGAGTCTACAATGCCCAC 57.941 47.619 0.00 0.00 0.00 4.61
3350 7698 9.277783 CAAAATTACATTACATTCCCAACCAAA 57.722 29.630 0.00 0.00 0.00 3.28
3449 7797 4.034285 ACCATTTCATCTTTCCGACCTT 57.966 40.909 0.00 0.00 0.00 3.50
3593 7950 5.819379 TCAGTTTAGCATCATTAGCTTCCTG 59.181 40.000 0.00 0.00 43.25 3.86
3670 8027 5.891451 TCAAGAACATCACCGTCTATAGTG 58.109 41.667 0.00 0.00 35.24 2.74
3679 8036 1.276421 AGACCCTCAAGAACATCACCG 59.724 52.381 0.00 0.00 0.00 4.94
3744 8101 0.032540 GCAAGGACCAGTGGCAAAAG 59.967 55.000 9.78 0.00 0.00 2.27
3961 8321 6.012337 TCAAGTTCTGGCATATTCCCAATA 57.988 37.500 0.00 0.00 30.66 1.90
4000 8360 2.301583 TGAAAACAAAGGGCTATTGGGC 59.698 45.455 7.51 0.00 40.05 5.36
4037 8764 2.496899 AGGGGGCAATATAAGCATCG 57.503 50.000 2.92 0.00 0.00 3.84
4038 8765 3.760684 CAGAAGGGGGCAATATAAGCATC 59.239 47.826 2.92 0.00 0.00 3.91
4116 8852 3.618690 ACTGAGATAACTCTGGGCAAC 57.381 47.619 10.85 0.00 43.30 4.17
4138 8874 0.621571 AAGTATGAGGCAGAGGGGCA 60.622 55.000 0.00 0.00 46.44 5.36
4139 8875 0.107643 GAAGTATGAGGCAGAGGGGC 59.892 60.000 0.00 0.00 43.80 5.80
4211 8947 3.701040 ACAGCAGTCAAACACTTTCCATT 59.299 39.130 0.00 0.00 30.26 3.16
4233 8969 1.208535 CCAACGCACCCTCATACCTAA 59.791 52.381 0.00 0.00 0.00 2.69
4286 9022 5.873179 ACGTGTGGTGACCTATAAATTTG 57.127 39.130 2.11 0.00 0.00 2.32
4352 9088 3.076621 TGCAACTTCTGGCATCTAGTTG 58.923 45.455 22.06 22.06 46.31 3.16
4359 9095 1.874345 GCTGCTGCAACTTCTGGCAT 61.874 55.000 11.11 0.00 39.65 4.40
4591 9330 5.891551 ACAGAACTTTAATGTGTGAAGGGTT 59.108 36.000 9.75 0.00 0.00 4.11
4637 9376 1.260538 TGCTCTTGCTCTCCCGTGAT 61.261 55.000 0.00 0.00 40.48 3.06
4644 9383 2.783935 GCGCTTGCTCTTGCTCTC 59.216 61.111 0.00 0.00 40.48 3.20
4691 9430 2.384382 CAGTTTGCAGCCTGTAAAACG 58.616 47.619 9.61 0.66 33.94 3.60
4692 9431 2.127251 GCAGTTTGCAGCCTGTAAAAC 58.873 47.619 9.61 12.14 44.26 2.43
4700 9439 3.286751 TGACCGCAGTTTGCAGCC 61.287 61.111 1.69 0.00 45.36 4.85
4717 9456 0.905337 GGCCATATAGCCGAGGGAGT 60.905 60.000 0.00 0.00 44.57 3.85
4758 9497 5.059833 GGATTCCATCACAGTAACTGATCC 58.940 45.833 0.00 0.00 35.18 3.36
4764 9503 5.882557 AGTGATTGGATTCCATCACAGTAAC 59.117 40.000 29.54 15.23 40.75 2.50
4766 9505 5.430886 CAGTGATTGGATTCCATCACAGTA 58.569 41.667 29.54 10.68 40.75 2.74
4823 9562 1.664151 GCAGCCCATTACGTCAAGTAC 59.336 52.381 0.00 0.00 34.56 2.73
4828 9567 1.745115 GCTGCAGCCCATTACGTCA 60.745 57.895 28.76 0.00 34.31 4.35
4846 9585 2.352960 GGCTTGCTCTTTTATCTCACGG 59.647 50.000 0.00 0.00 0.00 4.94
4880 9619 4.516323 ACAATCAAACAAGGCTTTGCTTT 58.484 34.783 8.71 5.97 37.85 3.51
4888 9627 3.740832 GCACCTTAACAATCAAACAAGGC 59.259 43.478 0.00 0.00 39.53 4.35
4897 9636 3.496884 TGAAGTGACGCACCTTAACAATC 59.503 43.478 6.39 0.00 34.49 2.67
4898 9637 3.472652 TGAAGTGACGCACCTTAACAAT 58.527 40.909 6.39 0.00 34.49 2.71
4941 9680 6.296026 TCAGAAGCTAGCTAGGTTTCAAAAA 58.704 36.000 32.51 16.15 43.36 1.94
4942 9681 5.865085 TCAGAAGCTAGCTAGGTTTCAAAA 58.135 37.500 32.51 17.29 43.36 2.44
4943 9682 5.483685 TCAGAAGCTAGCTAGGTTTCAAA 57.516 39.130 32.51 18.73 43.36 2.69
4944 9683 5.483685 TTCAGAAGCTAGCTAGGTTTCAA 57.516 39.130 32.51 23.02 43.36 2.69
4945 9684 5.483685 TTTCAGAAGCTAGCTAGGTTTCA 57.516 39.130 32.51 19.46 43.36 2.69
4946 9685 6.345298 AGATTTCAGAAGCTAGCTAGGTTTC 58.655 40.000 32.51 24.94 43.36 2.78
5018 9757 5.767168 GCATGCATAATTTCTTAGGAGAGGT 59.233 40.000 14.21 0.00 32.44 3.85
5066 9805 1.341877 TGGCCAAATACCCTGTGGATG 60.342 52.381 0.61 0.00 34.05 3.51
5075 9814 0.035820 TCTCACCGTGGCCAAATACC 60.036 55.000 7.24 0.00 0.00 2.73
5077 9816 2.639065 GAATCTCACCGTGGCCAAATA 58.361 47.619 7.24 0.00 0.00 1.40
5078 9817 1.463674 GAATCTCACCGTGGCCAAAT 58.536 50.000 7.24 0.00 0.00 2.32
5079 9818 0.608035 GGAATCTCACCGTGGCCAAA 60.608 55.000 7.24 0.00 0.00 3.28
5082 9821 0.394352 ATTGGAATCTCACCGTGGCC 60.394 55.000 0.00 0.00 0.00 5.36
5083 9822 1.463674 AATTGGAATCTCACCGTGGC 58.536 50.000 0.00 0.00 0.00 5.01
5084 9823 4.142469 GGTTAAATTGGAATCTCACCGTGG 60.142 45.833 0.00 0.00 0.00 4.94
5085 9824 4.457603 TGGTTAAATTGGAATCTCACCGTG 59.542 41.667 0.00 0.00 0.00 4.94
5086 9825 4.457949 GTGGTTAAATTGGAATCTCACCGT 59.542 41.667 0.00 0.00 0.00 4.83
5088 9827 6.350194 GGAAGTGGTTAAATTGGAATCTCACC 60.350 42.308 0.00 0.00 0.00 4.02
5089 9828 6.621613 GGAAGTGGTTAAATTGGAATCTCAC 58.378 40.000 0.00 0.00 0.00 3.51
5090 9829 5.414454 CGGAAGTGGTTAAATTGGAATCTCA 59.586 40.000 0.00 0.00 0.00 3.27
5091 9830 5.646360 TCGGAAGTGGTTAAATTGGAATCTC 59.354 40.000 0.00 0.00 0.00 2.75
5092 9831 5.566469 TCGGAAGTGGTTAAATTGGAATCT 58.434 37.500 0.00 0.00 0.00 2.40
5094 9833 4.705023 CCTCGGAAGTGGTTAAATTGGAAT 59.295 41.667 0.00 0.00 39.82 3.01
5095 9834 4.076394 CCTCGGAAGTGGTTAAATTGGAA 58.924 43.478 0.00 0.00 39.82 3.53
5096 9835 3.560453 CCCTCGGAAGTGGTTAAATTGGA 60.560 47.826 0.00 0.00 43.06 3.53
5097 9836 2.752903 CCCTCGGAAGTGGTTAAATTGG 59.247 50.000 0.00 0.00 43.06 3.16
5099 9838 3.801307 ACCCTCGGAAGTGGTTAAATT 57.199 42.857 0.00 0.00 43.06 1.82
5100 9839 3.560668 GGAACCCTCGGAAGTGGTTAAAT 60.561 47.826 6.32 0.00 43.61 1.40
5101 9840 2.224597 GGAACCCTCGGAAGTGGTTAAA 60.225 50.000 6.32 0.00 43.61 1.52
5102 9841 1.348696 GGAACCCTCGGAAGTGGTTAA 59.651 52.381 6.32 0.00 43.61 2.01
5103 9842 0.978907 GGAACCCTCGGAAGTGGTTA 59.021 55.000 6.32 0.00 43.61 2.85
5185 9924 4.981806 TGCAGGATAACAAAACATAGCC 57.018 40.909 0.00 0.00 0.00 3.93
5237 9980 8.919777 ACCTGCTTCAAGTAAACTAACTAATT 57.080 30.769 0.00 0.00 0.00 1.40
5244 9987 7.817418 AAAATGACCTGCTTCAAGTAAACTA 57.183 32.000 0.00 0.00 0.00 2.24
5245 9988 6.715347 AAAATGACCTGCTTCAAGTAAACT 57.285 33.333 0.00 0.00 0.00 2.66
5249 9992 4.584325 AGCAAAAATGACCTGCTTCAAGTA 59.416 37.500 0.00 0.00 43.83 2.24
5257 10000 1.001378 ACGTCAGCAAAAATGACCTGC 60.001 47.619 0.82 0.00 43.36 4.85
5261 10004 3.236816 CCATCACGTCAGCAAAAATGAC 58.763 45.455 0.00 0.00 42.94 3.06
5282 10062 2.678190 GCATATGGATCTCTTACGGGCC 60.678 54.545 4.56 0.00 0.00 5.80
5287 10067 5.480073 AGAGGACAGCATATGGATCTCTTAC 59.520 44.000 4.56 0.00 33.07 2.34
5335 10225 9.855021 CAAGAGTTTCCTTTCTTTTAGTTTCAA 57.145 29.630 0.00 0.00 31.53 2.69
5336 10226 9.020731 ACAAGAGTTTCCTTTCTTTTAGTTTCA 57.979 29.630 0.00 0.00 31.53 2.69
5350 10240 6.712547 CCTCAACAGATAAACAAGAGTTTCCT 59.287 38.462 0.00 0.00 44.35 3.36
5351 10241 6.486993 ACCTCAACAGATAAACAAGAGTTTCC 59.513 38.462 0.00 0.00 44.35 3.13
5352 10242 7.497925 ACCTCAACAGATAAACAAGAGTTTC 57.502 36.000 0.00 0.00 44.35 2.78
5355 10245 7.736893 ACTTACCTCAACAGATAAACAAGAGT 58.263 34.615 0.00 0.00 0.00 3.24
5357 10247 9.485206 GTTACTTACCTCAACAGATAAACAAGA 57.515 33.333 0.00 0.00 0.00 3.02
5386 10276 5.382616 AGGTAGGTAGGTTTCAAAAAGTGG 58.617 41.667 0.00 0.00 0.00 4.00
5403 10293 7.390027 TCTTCTTCAGATTTCAGAAAGGTAGG 58.610 38.462 1.28 0.00 0.00 3.18
5421 10311 6.128553 TGCAATGACACGAGTAAATCTTCTTC 60.129 38.462 0.00 0.00 0.00 2.87
5423 10313 5.237815 TGCAATGACACGAGTAAATCTTCT 58.762 37.500 0.00 0.00 0.00 2.85
5453 10343 3.391965 AGCCGTGTAAATGTAACGAACA 58.608 40.909 0.00 0.00 43.86 3.18
5455 10345 4.309099 AGAAGCCGTGTAAATGTAACGAA 58.691 39.130 0.00 0.00 39.64 3.85
5456 10346 3.916761 AGAAGCCGTGTAAATGTAACGA 58.083 40.909 0.00 0.00 39.64 3.85
5457 10347 4.657075 AAGAAGCCGTGTAAATGTAACG 57.343 40.909 0.00 0.00 37.07 3.18
5487 10942 6.478344 TGCAAATGAAATTAACAGTTGTGACC 59.522 34.615 19.18 9.18 42.59 4.02
5521 10977 8.803235 TGTCTAGTATTAGAGAGAACAAAAGCA 58.197 33.333 0.00 0.00 36.61 3.91
5541 10997 7.591426 GCAATTTCAAAAGTAGGTGTTGTCTAG 59.409 37.037 0.00 0.00 0.00 2.43
5548 11004 5.590530 TGTGCAATTTCAAAAGTAGGTGT 57.409 34.783 0.00 0.00 0.00 4.16
5555 11012 3.810941 ACTGGCATGTGCAATTTCAAAAG 59.189 39.130 7.36 0.00 44.36 2.27
5565 11023 3.534941 TGCAAACTGGCATGTGCA 58.465 50.000 13.80 13.80 44.36 4.57
5617 11077 4.524749 GACAGCGAACTTTTTACTTGACC 58.475 43.478 0.00 0.00 0.00 4.02
5633 11093 2.358267 AGTCTTAGTATTCCCGACAGCG 59.642 50.000 0.00 0.00 37.24 5.18
5640 11100 7.548427 GGCCGAAAATATAGTCTTAGTATTCCC 59.452 40.741 0.00 0.00 0.00 3.97
5690 11150 0.685660 GTCCTCGACCTGGTTCCTTT 59.314 55.000 0.00 0.00 0.00 3.11
5692 11152 0.900647 CTGTCCTCGACCTGGTTCCT 60.901 60.000 0.00 0.00 0.00 3.36
5714 11179 4.617253 ACATACCAGAGTAAGTTGCACA 57.383 40.909 0.00 0.00 25.83 4.57
5730 11195 5.258456 TCTCAGACGGTTATCCAACATAC 57.742 43.478 0.00 0.00 36.29 2.39
5734 11217 3.132289 TGGATCTCAGACGGTTATCCAAC 59.868 47.826 0.00 0.00 42.33 3.77
5751 11234 1.228094 GCTTGGCTAGCCCTGGATC 60.228 63.158 30.81 10.17 44.48 3.36
5770 11253 3.695060 GAGTGGGAGAAATCGACTCACTA 59.305 47.826 5.56 0.00 39.00 2.74
5771 11254 2.494073 GAGTGGGAGAAATCGACTCACT 59.506 50.000 5.26 5.26 39.00 3.41
5789 11272 0.711184 AGTAGTGGGTAGCTGGGAGT 59.289 55.000 0.00 0.00 0.00 3.85
5810 11293 2.368548 AGCACCATGTAACACAGAGACA 59.631 45.455 0.00 0.00 0.00 3.41
5811 11294 3.045601 AGCACCATGTAACACAGAGAC 57.954 47.619 0.00 0.00 0.00 3.36
5812 11295 3.769739 AAGCACCATGTAACACAGAGA 57.230 42.857 0.00 0.00 0.00 3.10
5813 11296 5.237815 TCTAAAGCACCATGTAACACAGAG 58.762 41.667 0.00 0.00 0.00 3.35
5814 11297 5.222079 TCTAAAGCACCATGTAACACAGA 57.778 39.130 0.00 0.00 0.00 3.41
5815 11298 5.163723 CCATCTAAAGCACCATGTAACACAG 60.164 44.000 0.00 0.00 0.00 3.66
5899 12632 1.337728 CCAGTCTGACGGTATGTGCAA 60.338 52.381 0.00 0.00 0.00 4.08
5903 12636 2.093106 GTCTCCAGTCTGACGGTATGT 58.907 52.381 15.00 0.00 0.00 2.29
5907 12645 0.896019 CCAGTCTCCAGTCTGACGGT 60.896 60.000 15.00 0.00 38.16 4.83
5917 12655 4.819761 GCGCGCATCCAGTCTCCA 62.820 66.667 29.10 0.00 0.00 3.86
5938 12676 1.669211 GGTAACTGCACGACCTCTGAC 60.669 57.143 0.00 0.00 0.00 3.51
5939 12677 0.601558 GGTAACTGCACGACCTCTGA 59.398 55.000 0.00 0.00 0.00 3.27
5958 12696 1.615883 ACGAGTATCAGCTATGCCCAG 59.384 52.381 0.00 0.00 33.17 4.45
5959 12697 1.704641 ACGAGTATCAGCTATGCCCA 58.295 50.000 0.00 0.00 33.17 5.36
5961 12699 3.426963 GCTCTACGAGTATCAGCTATGCC 60.427 52.174 0.00 0.00 33.17 4.40
5963 12701 3.753797 TGGCTCTACGAGTATCAGCTATG 59.246 47.826 11.66 0.00 33.17 2.23
6026 12778 8.189460 GCGCTAACTAGGTATGCTATATACTTT 58.811 37.037 0.00 0.00 0.00 2.66
6035 12787 1.754803 TGTGCGCTAACTAGGTATGCT 59.245 47.619 9.73 0.00 0.00 3.79
6055 12809 6.993902 ACCAAATCTTGAAAAATGTCAGCAAT 59.006 30.769 0.00 0.00 0.00 3.56
6067 12824 1.410517 TGCGGCAACCAAATCTTGAAA 59.589 42.857 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.