Multiple sequence alignment - TraesCS5A01G204600

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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 TraesCS5A01G204600 chr5A 100.000 8406 0 0 1 8406 414159998 414168403 0.000000e+00 15524.0
1 TraesCS5A01G204600 chr5D 98.338 7100 88 13 760 7837 320315711 320308620 0.000000e+00 12430.0
2 TraesCS5A01G204600 chr5D 89.892 831 28 22 4 799 320316535 320315726 0.000000e+00 1018.0
3 TraesCS5A01G204600 chr5D 82.258 372 16 17 7935 8296 320308623 320308292 8.310000e-70 276.0
4 TraesCS5A01G204600 chr5D 93.269 104 7 0 7837 7940 9936715 9936612 4.060000e-33 154.0
5 TraesCS5A01G204600 chr5D 95.556 45 1 1 8363 8406 320236900 320236856 4.210000e-08 71.3
6 TraesCS5A01G204600 chr5B 96.774 6788 160 18 1092 7837 371193949 371187179 0.000000e+00 11267.0
7 TraesCS5A01G204600 chr5B 87.486 919 42 33 4 879 371194837 371193949 0.000000e+00 992.0
8 TraesCS5A01G204600 chr5B 87.069 232 15 7 7945 8171 371187180 371186959 1.810000e-61 248.0
9 TraesCS5A01G204600 chrUn 100.000 411 0 0 3880 4290 477678615 477679025 0.000000e+00 760.0
10 TraesCS5A01G204600 chrUn 93.000 100 7 0 7837 7936 94188019 94187920 6.800000e-31 147.0
11 TraesCS5A01G204600 chr2D 75.097 1036 204 29 5298 6303 146306152 146307163 1.300000e-117 435.0
12 TraesCS5A01G204600 chr2D 78.462 585 106 17 3672 4253 146304563 146305130 1.720000e-96 364.0
13 TraesCS5A01G204600 chr2B 75.097 1036 204 29 5298 6303 206373815 206374826 1.300000e-117 435.0
14 TraesCS5A01G204600 chr2B 77.949 585 109 16 3672 4253 206372226 206372793 1.740000e-91 348.0
15 TraesCS5A01G204600 chr2B 83.465 127 10 6 8265 8381 392526265 392526140 3.210000e-19 108.0
16 TraesCS5A01G204600 chr2A 74.903 1032 207 28 5301 6303 155944083 155943075 2.800000e-114 424.0
17 TraesCS5A01G204600 chr2A 78.462 585 106 17 3672 4253 155945679 155945112 1.720000e-96 364.0
18 TraesCS5A01G204600 chr2A 94.231 104 6 0 7837 7940 603930737 603930840 8.730000e-35 159.0
19 TraesCS5A01G204600 chr7B 94.059 101 6 0 7837 7937 562125542 562125442 4.060000e-33 154.0
20 TraesCS5A01G204600 chr6A 93.269 104 7 0 7837 7940 592211597 592211700 4.060000e-33 154.0
21 TraesCS5A01G204600 chr3D 92.233 103 8 0 7837 7939 360863834 360863732 6.800000e-31 147.0
22 TraesCS5A01G204600 chr6D 92.079 101 8 0 7837 7937 436847061 436847161 8.800000e-30 143.0
23 TraesCS5A01G204600 chr7D 91.346 104 8 1 7837 7940 104093649 104093547 3.160000e-29 141.0
24 TraesCS5A01G204600 chr1A 100.000 31 0 0 7910 7940 403387151 403387121 3.280000e-04 58.4


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 TraesCS5A01G204600 chr5A 414159998 414168403 8405 False 15524.000000 15524 100.000000 1 8406 1 chr5A.!!$F1 8405
1 TraesCS5A01G204600 chr5D 320308292 320316535 8243 True 4574.666667 12430 90.162667 4 8296 3 chr5D.!!$R3 8292
2 TraesCS5A01G204600 chr5B 371186959 371194837 7878 True 4169.000000 11267 90.443000 4 8171 3 chr5B.!!$R1 8167
3 TraesCS5A01G204600 chr2D 146304563 146307163 2600 False 399.500000 435 76.779500 3672 6303 2 chr2D.!!$F1 2631
4 TraesCS5A01G204600 chr2B 206372226 206374826 2600 False 391.500000 435 76.523000 3672 6303 2 chr2B.!!$F1 2631
5 TraesCS5A01G204600 chr2A 155943075 155945679 2604 True 394.000000 424 76.682500 3672 6303 2 chr2A.!!$R1 2631

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
279 290 0.309612 GGTTCCGCACGTTCATGTTT 59.690 50.000 0.00 0.0 0.00 2.83 F
1514 1630 0.308993 GATGGACGCTTATGGCTTGC 59.691 55.000 0.00 0.0 39.13 4.01 F
1520 1636 1.502231 CGCTTATGGCTTGCGTAGAT 58.498 50.000 0.00 0.0 44.00 1.98 F
3380 3513 0.393537 CCGCTGAAGAGAAATGGCCT 60.394 55.000 3.32 0.0 0.00 5.19 F
3637 3770 0.318762 GCAGGAGGCCTAGATAACCG 59.681 60.000 4.42 0.0 36.11 4.44 F
3803 3936 1.831736 CCACTTGGGAGATACCTTCGT 59.168 52.381 0.00 0.0 40.01 3.85 F
4290 4424 4.462508 TGTTTCAGCTCTCTGTATCCAG 57.537 45.455 0.00 0.0 41.10 3.86 F
4998 5238 4.410099 TGCCAGAACTGATTCTTCCAATT 58.590 39.130 3.19 0.0 42.91 2.32 F
5270 5516 2.872245 CAGTGTGTCTGAAAATGGACGT 59.128 45.455 0.00 0.0 46.27 4.34 F
7009 7294 0.391661 TCTCCACAAAGATGGCTCGC 60.392 55.000 0.00 0.0 39.85 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1520 1636 0.888619 CCAGAGCTCGACAACCTACA 59.111 55.000 8.37 0.0 0.00 2.74 R
3380 3513 0.811219 GCGTGATGGCAGCAGTATGA 60.811 55.000 5.29 0.0 39.69 2.15 R
3490 3623 6.095860 CAGAGAATTGGCATGATTAACAGGAA 59.904 38.462 0.00 0.0 31.40 3.36 R
4378 4512 1.278413 GAGGGTGGGAGGTTAACTGAC 59.722 57.143 5.42 0.0 0.00 3.51 R
4614 4845 1.548719 CGTCCAAGGTGGTGATACTCA 59.451 52.381 0.00 0.0 39.03 3.41 R
4998 5238 2.108075 TGGTGGCTTGGAGATTTTCTGA 59.892 45.455 0.00 0.0 0.00 3.27 R
5270 5516 4.058124 CGATAGAATTCATGGAAAGGCGA 58.942 43.478 8.44 0.0 39.76 5.54 R
6855 7130 3.252215 TCCAGTAAAAACGGTGCATTGAG 59.748 43.478 0.00 0.0 0.00 3.02 R
7237 7522 0.955919 GCTTGTCCCAGGTGTACTGC 60.956 60.000 0.00 0.0 46.14 4.40 R
7843 8131 0.034670 AGGGCAAATGAGGAGCAGAC 60.035 55.000 0.00 0.0 0.00 3.51 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
67 68 5.776716 TCATTGATCTTTCCCAAGCTTTCTT 59.223 36.000 0.00 0.00 0.00 2.52
124 125 5.705609 AAAACCCGACATTATATGCCATC 57.294 39.130 0.00 0.00 0.00 3.51
132 133 6.701400 CCGACATTATATGCCATCGATAATGA 59.299 38.462 19.79 0.00 42.38 2.57
156 157 6.630071 ACCCATTATCAACAACTGCAAATAC 58.370 36.000 0.00 0.00 0.00 1.89
194 196 5.594724 TTTCATTTTAAGTACCGTCCACG 57.405 39.130 0.00 0.00 39.44 4.94
275 286 1.671054 CCTGGTTCCGCACGTTCAT 60.671 57.895 0.00 0.00 0.00 2.57
277 288 1.227704 TGGTTCCGCACGTTCATGT 60.228 52.632 0.00 0.00 0.00 3.21
279 290 0.309612 GGTTCCGCACGTTCATGTTT 59.690 50.000 0.00 0.00 0.00 2.83
281 292 2.456010 GTTCCGCACGTTCATGTTTTT 58.544 42.857 0.00 0.00 0.00 1.94
282 293 3.548415 GGTTCCGCACGTTCATGTTTTTA 60.548 43.478 0.00 0.00 0.00 1.52
287 307 4.262045 CCGCACGTTCATGTTTTTAATAGC 59.738 41.667 0.00 0.00 0.00 2.97
290 310 6.083630 GCACGTTCATGTTTTTAATAGCAGA 58.916 36.000 0.00 0.00 0.00 4.26
295 315 9.128107 CGTTCATGTTTTTAATAGCAGACAATT 57.872 29.630 0.00 0.00 0.00 2.32
321 341 1.003928 GGAGTATTTCACAACCGGGGT 59.996 52.381 6.32 0.00 0.00 4.95
463 484 6.355805 AGGTACTCCTATATGGATATCCACCC 60.356 46.154 26.82 12.47 45.42 4.61
477 498 1.079127 CACCCTACACAAGGCGAGG 60.079 63.158 0.00 0.00 45.03 4.63
655 681 4.479993 CCGCCTTCCCCTGCTCTG 62.480 72.222 0.00 0.00 0.00 3.35
657 683 3.726144 GCCTTCCCCTGCTCTGCT 61.726 66.667 0.00 0.00 0.00 4.24
661 687 0.977108 CTTCCCCTGCTCTGCTCTCT 60.977 60.000 0.00 0.00 0.00 3.10
662 688 0.975040 TTCCCCTGCTCTGCTCTCTC 60.975 60.000 0.00 0.00 0.00 3.20
663 689 2.433994 CCCCTGCTCTGCTCTCTCC 61.434 68.421 0.00 0.00 0.00 3.71
664 690 1.381599 CCCTGCTCTGCTCTCTCCT 60.382 63.158 0.00 0.00 0.00 3.69
666 692 1.394266 CCTGCTCTGCTCTCTCCTCC 61.394 65.000 0.00 0.00 0.00 4.30
676 725 0.633921 TCTCTCCTCCCTCCTCCAAG 59.366 60.000 0.00 0.00 0.00 3.61
758 810 0.749091 CTCCCGCATTGGCTGAATCA 60.749 55.000 0.00 0.00 38.10 2.57
766 818 2.892425 GGCTGAATCACCGCTCCG 60.892 66.667 0.00 0.00 0.00 4.63
1022 1135 2.031919 TGTGCTGGATTTCGCGGT 59.968 55.556 6.13 0.00 0.00 5.68
1303 1416 5.060569 CGCGATATTAGGTAACGGAAATCTG 59.939 44.000 0.00 0.00 46.39 2.90
1305 1418 6.089150 GCGATATTAGGTAACGGAAATCTGTC 59.911 42.308 0.00 0.00 46.39 3.51
1309 1422 4.457834 AGGTAACGGAAATCTGTCTCTG 57.542 45.455 0.00 0.00 46.39 3.35
1311 1424 4.082136 AGGTAACGGAAATCTGTCTCTGTC 60.082 45.833 0.00 0.00 46.39 3.51
1312 1425 3.320673 AACGGAAATCTGTCTCTGTCC 57.679 47.619 0.00 0.00 33.61 4.02
1394 1509 9.877178 ATGGAAGTGAACTAGTAAATCAGTTAG 57.123 33.333 13.61 0.00 36.98 2.34
1395 1510 8.867097 TGGAAGTGAACTAGTAAATCAGTTAGT 58.133 33.333 13.61 0.00 36.98 2.24
1438 1553 6.749118 CCTTCTAATAAGTGCAAAATGTCTGC 59.251 38.462 0.00 0.00 40.35 4.26
1505 1621 1.623811 AGTAGTGGTTGATGGACGCTT 59.376 47.619 0.00 0.00 0.00 4.68
1514 1630 0.308993 GATGGACGCTTATGGCTTGC 59.691 55.000 0.00 0.00 39.13 4.01
1520 1636 1.502231 CGCTTATGGCTTGCGTAGAT 58.498 50.000 0.00 0.00 44.00 1.98
1531 1647 2.554806 TGCGTAGATGTAGGTTGTCG 57.445 50.000 0.00 0.00 0.00 4.35
1649 1766 5.880887 CCAGGGACTTACTTCTTAAATGACC 59.119 44.000 0.00 0.00 34.60 4.02
1696 1813 9.136952 GTTAGTGTTAGTAACTCAACATACAGG 57.863 37.037 14.00 0.00 37.04 4.00
2018 2147 7.005709 ACTAATAGAGCAACTGGTGTTAGTT 57.994 36.000 0.00 0.00 41.37 2.24
2055 2184 2.289320 CCCACCAAGAGAGTGTTCAGAG 60.289 54.545 0.00 0.00 33.20 3.35
3006 3135 6.582636 TGGTTTGTTGGCATTTATTTACACA 58.417 32.000 0.00 0.00 0.00 3.72
3282 3415 6.426937 ACGAGTTATTTCAGTAACTGCAATGT 59.573 34.615 4.22 0.00 43.13 2.71
3334 3467 3.126514 CACATTTCTGCTAAGTCTGCTGG 59.873 47.826 0.00 0.00 0.00 4.85
3380 3513 0.393537 CCGCTGAAGAGAAATGGCCT 60.394 55.000 3.32 0.00 0.00 5.19
3490 3623 4.223032 ACCTGAGTGTACCGAATCTGAATT 59.777 41.667 0.00 0.00 0.00 2.17
3637 3770 0.318762 GCAGGAGGCCTAGATAACCG 59.681 60.000 4.42 0.00 36.11 4.44
3803 3936 1.831736 CCACTTGGGAGATACCTTCGT 59.168 52.381 0.00 0.00 40.01 3.85
4290 4424 4.462508 TGTTTCAGCTCTCTGTATCCAG 57.537 45.455 0.00 0.00 41.10 3.86
4378 4512 5.479306 CATTATAGTCCCATGGTTACTCGG 58.521 45.833 17.77 0.00 0.00 4.63
4998 5238 4.410099 TGCCAGAACTGATTCTTCCAATT 58.590 39.130 3.19 0.00 42.91 2.32
5270 5516 2.872245 CAGTGTGTCTGAAAATGGACGT 59.128 45.455 0.00 0.00 46.27 4.34
5875 6121 8.731605 TGTTACGCATAAACTGGATTCAAAATA 58.268 29.630 0.00 0.00 0.00 1.40
5903 6149 6.810182 GCTTTCAACATATGTCAAATTGCTCT 59.190 34.615 9.23 0.00 0.00 4.09
6017 6284 7.750903 GCAGATAATACAAAGTTTTCAGTGACC 59.249 37.037 0.00 0.00 0.00 4.02
6655 6930 9.110986 TGATACATCAATTCTTGCGGTATGCAG 62.111 40.741 0.00 0.00 44.12 4.41
6855 7130 4.009002 AGGAGCAAGAAGAAGCATCTTTC 58.991 43.478 5.55 0.00 45.91 2.62
7009 7294 0.391661 TCTCCACAAAGATGGCTCGC 60.392 55.000 0.00 0.00 39.85 5.03
7237 7522 1.493950 GCATCATCGACTTCCTGCGG 61.494 60.000 0.00 0.00 0.00 5.69
7306 7591 2.124695 CTAGGCGGCCCCAAGAAC 60.125 66.667 17.02 0.00 35.39 3.01
7843 8131 9.877178 AATAGGATCTGTTAGTCTTACAAGTTG 57.123 33.333 0.00 0.00 0.00 3.16
7844 8132 7.304497 AGGATCTGTTAGTCTTACAAGTTGT 57.696 36.000 14.05 14.05 0.00 3.32
7845 8133 7.379750 AGGATCTGTTAGTCTTACAAGTTGTC 58.620 38.462 12.82 0.00 0.00 3.18
7846 8134 7.233757 AGGATCTGTTAGTCTTACAAGTTGTCT 59.766 37.037 12.82 5.98 0.00 3.41
7847 8135 7.329717 GGATCTGTTAGTCTTACAAGTTGTCTG 59.670 40.741 12.82 6.80 0.00 3.51
7848 8136 5.983720 TCTGTTAGTCTTACAAGTTGTCTGC 59.016 40.000 12.82 1.95 0.00 4.26
7849 8137 5.914033 TGTTAGTCTTACAAGTTGTCTGCT 58.086 37.500 12.82 9.25 0.00 4.24
7850 8138 5.983720 TGTTAGTCTTACAAGTTGTCTGCTC 59.016 40.000 12.82 1.29 0.00 4.26
7851 8139 3.996480 AGTCTTACAAGTTGTCTGCTCC 58.004 45.455 12.82 0.00 0.00 4.70
7852 8140 3.643792 AGTCTTACAAGTTGTCTGCTCCT 59.356 43.478 12.82 0.00 0.00 3.69
7853 8141 3.991121 GTCTTACAAGTTGTCTGCTCCTC 59.009 47.826 12.82 0.00 0.00 3.71
7854 8142 3.641436 TCTTACAAGTTGTCTGCTCCTCA 59.359 43.478 12.82 0.00 0.00 3.86
7855 8143 4.284490 TCTTACAAGTTGTCTGCTCCTCAT 59.716 41.667 12.82 0.00 0.00 2.90
7856 8144 3.498774 ACAAGTTGTCTGCTCCTCATT 57.501 42.857 1.64 0.00 0.00 2.57
7857 8145 3.825328 ACAAGTTGTCTGCTCCTCATTT 58.175 40.909 1.64 0.00 0.00 2.32
7858 8146 3.567164 ACAAGTTGTCTGCTCCTCATTTG 59.433 43.478 1.64 0.00 0.00 2.32
7859 8147 2.157738 AGTTGTCTGCTCCTCATTTGC 58.842 47.619 0.00 0.00 0.00 3.68
7860 8148 1.200948 GTTGTCTGCTCCTCATTTGCC 59.799 52.381 0.00 0.00 0.00 4.52
7861 8149 0.322816 TGTCTGCTCCTCATTTGCCC 60.323 55.000 0.00 0.00 0.00 5.36
7862 8150 0.034670 GTCTGCTCCTCATTTGCCCT 60.035 55.000 0.00 0.00 0.00 5.19
7863 8151 0.034767 TCTGCTCCTCATTTGCCCTG 60.035 55.000 0.00 0.00 0.00 4.45
7864 8152 1.000521 TGCTCCTCATTTGCCCTGG 60.001 57.895 0.00 0.00 0.00 4.45
7865 8153 1.755783 GCTCCTCATTTGCCCTGGG 60.756 63.158 8.86 8.86 0.00 4.45
7866 8154 1.076485 CTCCTCATTTGCCCTGGGG 60.076 63.158 16.03 4.75 35.41 4.96
7867 8155 1.543642 TCCTCATTTGCCCTGGGGA 60.544 57.895 16.03 9.43 41.06 4.81
7868 8156 1.076485 CCTCATTTGCCCTGGGGAG 60.076 63.158 16.03 11.62 36.24 4.30
7869 8157 1.755783 CTCATTTGCCCTGGGGAGC 60.756 63.158 16.03 0.00 37.50 4.70
7870 8158 2.761213 CATTTGCCCTGGGGAGCC 60.761 66.667 16.03 0.00 37.50 4.70
7871 8159 3.275271 ATTTGCCCTGGGGAGCCA 61.275 61.111 16.03 0.01 37.50 4.75
7872 8160 3.307089 ATTTGCCCTGGGGAGCCAG 62.307 63.158 16.03 0.00 37.50 4.85
7876 8164 4.748144 CCCTGGGGAGCCAGCAAC 62.748 72.222 4.27 0.00 36.57 4.17
7877 8165 4.748144 CCTGGGGAGCCAGCAACC 62.748 72.222 0.00 0.00 36.57 3.77
7878 8166 3.655211 CTGGGGAGCCAGCAACCT 61.655 66.667 0.00 0.00 0.00 3.50
7879 8167 2.204074 TGGGGAGCCAGCAACCTA 60.204 61.111 6.00 0.00 0.00 3.08
7880 8168 2.262774 CTGGGGAGCCAGCAACCTAG 62.263 65.000 0.00 2.54 0.00 3.02
7881 8169 2.592308 GGGAGCCAGCAACCTAGG 59.408 66.667 7.41 7.41 0.00 3.02
7882 8170 1.995626 GGGAGCCAGCAACCTAGGA 60.996 63.158 17.98 0.00 0.00 2.94
7883 8171 1.524482 GGAGCCAGCAACCTAGGAG 59.476 63.158 17.98 8.77 0.00 3.69
7884 8172 1.153269 GAGCCAGCAACCTAGGAGC 60.153 63.158 17.98 18.63 0.00 4.70
7885 8173 1.614824 AGCCAGCAACCTAGGAGCT 60.615 57.895 22.23 22.23 39.63 4.09
7888 8176 3.732938 AGCAACCTAGGAGCTGGG 58.267 61.111 25.52 7.08 38.14 4.45
7889 8177 1.081092 AGCAACCTAGGAGCTGGGA 59.919 57.895 25.52 0.00 35.58 4.37
7890 8178 0.980231 AGCAACCTAGGAGCTGGGAG 60.980 60.000 25.52 5.31 35.58 4.30
7891 8179 1.268283 GCAACCTAGGAGCTGGGAGT 61.268 60.000 17.98 0.00 35.58 3.85
7892 8180 0.539051 CAACCTAGGAGCTGGGAGTG 59.461 60.000 17.98 0.00 35.58 3.51
7893 8181 0.618968 AACCTAGGAGCTGGGAGTGG 60.619 60.000 17.98 0.00 35.58 4.00
7894 8182 1.311403 CCTAGGAGCTGGGAGTGGA 59.689 63.158 1.05 0.00 33.74 4.02
7895 8183 0.758685 CCTAGGAGCTGGGAGTGGAG 60.759 65.000 1.05 0.00 33.74 3.86
7896 8184 1.381872 TAGGAGCTGGGAGTGGAGC 60.382 63.158 0.00 0.00 35.28 4.70
7898 8186 1.381872 GGAGCTGGGAGTGGAGCTA 60.382 63.158 0.00 0.00 45.72 3.32
7899 8187 0.978146 GGAGCTGGGAGTGGAGCTAA 60.978 60.000 0.00 0.00 45.72 3.09
7900 8188 0.463620 GAGCTGGGAGTGGAGCTAAG 59.536 60.000 0.00 0.00 45.72 2.18
7901 8189 0.980231 AGCTGGGAGTGGAGCTAAGG 60.980 60.000 0.00 0.00 43.88 2.69
7902 8190 0.978146 GCTGGGAGTGGAGCTAAGGA 60.978 60.000 0.00 0.00 32.12 3.36
7903 8191 1.799933 CTGGGAGTGGAGCTAAGGAT 58.200 55.000 0.00 0.00 0.00 3.24
7904 8192 2.122768 CTGGGAGTGGAGCTAAGGATT 58.877 52.381 0.00 0.00 0.00 3.01
7905 8193 2.507471 CTGGGAGTGGAGCTAAGGATTT 59.493 50.000 0.00 0.00 0.00 2.17
7906 8194 2.239654 TGGGAGTGGAGCTAAGGATTTG 59.760 50.000 0.00 0.00 0.00 2.32
7907 8195 2.505819 GGGAGTGGAGCTAAGGATTTGA 59.494 50.000 0.00 0.00 0.00 2.69
7908 8196 3.432890 GGGAGTGGAGCTAAGGATTTGAG 60.433 52.174 0.00 0.00 0.00 3.02
7909 8197 3.432890 GGAGTGGAGCTAAGGATTTGAGG 60.433 52.174 0.00 0.00 0.00 3.86
7910 8198 2.507471 AGTGGAGCTAAGGATTTGAGGG 59.493 50.000 0.00 0.00 0.00 4.30
7911 8199 2.505819 GTGGAGCTAAGGATTTGAGGGA 59.494 50.000 0.00 0.00 0.00 4.20
7912 8200 2.774234 TGGAGCTAAGGATTTGAGGGAG 59.226 50.000 0.00 0.00 0.00 4.30
7913 8201 2.774809 GGAGCTAAGGATTTGAGGGAGT 59.225 50.000 0.00 0.00 0.00 3.85
7914 8202 3.432890 GGAGCTAAGGATTTGAGGGAGTG 60.433 52.174 0.00 0.00 0.00 3.51
7915 8203 2.507471 AGCTAAGGATTTGAGGGAGTGG 59.493 50.000 0.00 0.00 0.00 4.00
7916 8204 2.505819 GCTAAGGATTTGAGGGAGTGGA 59.494 50.000 0.00 0.00 0.00 4.02
7917 8205 3.432890 GCTAAGGATTTGAGGGAGTGGAG 60.433 52.174 0.00 0.00 0.00 3.86
7918 8206 2.350863 AGGATTTGAGGGAGTGGAGT 57.649 50.000 0.00 0.00 0.00 3.85
7919 8207 1.912043 AGGATTTGAGGGAGTGGAGTG 59.088 52.381 0.00 0.00 0.00 3.51
7920 8208 1.065126 GGATTTGAGGGAGTGGAGTGG 60.065 57.143 0.00 0.00 0.00 4.00
7921 8209 1.909302 GATTTGAGGGAGTGGAGTGGA 59.091 52.381 0.00 0.00 0.00 4.02
7922 8210 2.044793 TTTGAGGGAGTGGAGTGGAT 57.955 50.000 0.00 0.00 0.00 3.41
7923 8211 1.573108 TTGAGGGAGTGGAGTGGATC 58.427 55.000 0.00 0.00 0.00 3.36
7932 8220 1.153349 GGAGTGGATCCGAACAGGC 60.153 63.158 7.39 0.00 38.67 4.85
7933 8221 1.153349 GAGTGGATCCGAACAGGCC 60.153 63.158 7.39 0.00 40.77 5.19
7934 8222 2.124695 GTGGATCCGAACAGGCCC 60.125 66.667 7.39 0.00 40.77 5.80
7935 8223 2.285368 TGGATCCGAACAGGCCCT 60.285 61.111 7.39 0.00 40.77 5.19
7936 8224 1.923395 TGGATCCGAACAGGCCCTT 60.923 57.895 7.39 0.00 40.77 3.95
7937 8225 0.619255 TGGATCCGAACAGGCCCTTA 60.619 55.000 7.39 0.00 40.77 2.69
7938 8226 0.106894 GGATCCGAACAGGCCCTTAG 59.893 60.000 0.00 0.00 40.77 2.18
7939 8227 0.831307 GATCCGAACAGGCCCTTAGT 59.169 55.000 0.00 0.00 40.77 2.24
7940 8228 0.831307 ATCCGAACAGGCCCTTAGTC 59.169 55.000 0.00 0.00 40.77 2.59
7941 8229 1.153628 CCGAACAGGCCCTTAGTCG 60.154 63.158 0.00 1.64 0.00 4.18
7942 8230 1.810030 CGAACAGGCCCTTAGTCGC 60.810 63.158 0.00 0.00 0.00 5.19
7943 8231 1.449778 GAACAGGCCCTTAGTCGCC 60.450 63.158 0.00 0.00 46.09 5.54
7985 8288 6.842437 AGACTTAGCTATGTCTCAGTCAAA 57.158 37.500 27.96 0.00 38.91 2.69
7986 8289 7.416964 AGACTTAGCTATGTCTCAGTCAAAT 57.583 36.000 27.96 10.28 38.91 2.32
7987 8290 7.264221 AGACTTAGCTATGTCTCAGTCAAATG 58.736 38.462 27.96 0.00 38.91 2.32
7988 8291 7.123397 AGACTTAGCTATGTCTCAGTCAAATGA 59.877 37.037 27.96 0.00 38.91 2.57
7989 8292 7.790027 ACTTAGCTATGTCTCAGTCAAATGAT 58.210 34.615 6.46 0.00 0.00 2.45
7990 8293 7.710044 ACTTAGCTATGTCTCAGTCAAATGATG 59.290 37.037 6.46 0.00 0.00 3.07
7991 8294 5.987098 AGCTATGTCTCAGTCAAATGATGT 58.013 37.500 0.00 0.00 0.00 3.06
7992 8295 6.047870 AGCTATGTCTCAGTCAAATGATGTC 58.952 40.000 0.00 0.00 0.00 3.06
7993 8296 5.814188 GCTATGTCTCAGTCAAATGATGTCA 59.186 40.000 0.00 0.00 0.00 3.58
8102 8408 0.177836 GTTGGGCTTGTTTGTGGCTT 59.822 50.000 0.00 0.00 0.00 4.35
8103 8409 0.177604 TTGGGCTTGTTTGTGGCTTG 59.822 50.000 0.00 0.00 0.00 4.01
8146 8452 0.325933 TGTGATGGGCTTGACTGAGG 59.674 55.000 0.00 0.00 0.00 3.86
8148 8454 1.067295 TGATGGGCTTGACTGAGGTT 58.933 50.000 0.00 0.00 0.00 3.50
8250 8563 9.457110 AGGAATGACAAAAACAAAAACAAAAAC 57.543 25.926 0.00 0.00 0.00 2.43
8251 8564 9.237846 GGAATGACAAAAACAAAAACAAAAACA 57.762 25.926 0.00 0.00 0.00 2.83
8284 8597 0.966179 GGAAAAGGGAACATGCCGTT 59.034 50.000 0.00 0.00 41.86 4.44
8296 8609 2.589442 GCCGTTCCACGTGACCAA 60.589 61.111 19.30 3.64 40.58 3.67
8297 8610 2.604174 GCCGTTCCACGTGACCAAG 61.604 63.158 19.30 3.72 40.58 3.61
8298 8611 1.068417 CCGTTCCACGTGACCAAGA 59.932 57.895 19.30 1.61 40.58 3.02
8299 8612 0.531090 CCGTTCCACGTGACCAAGAA 60.531 55.000 19.30 8.67 40.58 2.52
8300 8613 1.292061 CGTTCCACGTGACCAAGAAA 58.708 50.000 19.30 0.00 36.74 2.52
8301 8614 1.260561 CGTTCCACGTGACCAAGAAAG 59.739 52.381 19.30 9.85 36.74 2.62
8302 8615 1.602377 GTTCCACGTGACCAAGAAAGG 59.398 52.381 19.30 0.00 0.00 3.11
8303 8616 0.107831 TCCACGTGACCAAGAAAGGG 59.892 55.000 19.30 0.00 0.00 3.95
8304 8617 0.889186 CCACGTGACCAAGAAAGGGG 60.889 60.000 19.30 0.00 0.00 4.79
8305 8618 0.107831 CACGTGACCAAGAAAGGGGA 59.892 55.000 10.90 0.00 0.00 4.81
8306 8619 0.841289 ACGTGACCAAGAAAGGGGAA 59.159 50.000 0.00 0.00 0.00 3.97
8307 8620 1.423921 ACGTGACCAAGAAAGGGGAAT 59.576 47.619 0.00 0.00 0.00 3.01
8308 8621 1.812571 CGTGACCAAGAAAGGGGAATG 59.187 52.381 0.00 0.00 0.00 2.67
8309 8622 2.171003 GTGACCAAGAAAGGGGAATGG 58.829 52.381 0.00 0.00 37.19 3.16
8310 8623 1.786441 TGACCAAGAAAGGGGAATGGT 59.214 47.619 0.00 0.00 46.63 3.55
8311 8624 2.990284 TGACCAAGAAAGGGGAATGGTA 59.010 45.455 0.00 0.00 44.12 3.25
8312 8625 3.010138 TGACCAAGAAAGGGGAATGGTAG 59.990 47.826 0.00 0.00 44.12 3.18
8313 8626 2.993863 ACCAAGAAAGGGGAATGGTAGT 59.006 45.455 0.00 0.00 42.38 2.73
8314 8627 3.245264 ACCAAGAAAGGGGAATGGTAGTG 60.245 47.826 0.00 0.00 42.38 2.74
8315 8628 3.245264 CCAAGAAAGGGGAATGGTAGTGT 60.245 47.826 0.00 0.00 0.00 3.55
8316 8629 4.407365 CAAGAAAGGGGAATGGTAGTGTT 58.593 43.478 0.00 0.00 0.00 3.32
8317 8630 5.515886 CCAAGAAAGGGGAATGGTAGTGTTA 60.516 44.000 0.00 0.00 0.00 2.41
8318 8631 5.175388 AGAAAGGGGAATGGTAGTGTTAC 57.825 43.478 0.00 0.00 0.00 2.50
8319 8632 3.622166 AAGGGGAATGGTAGTGTTACG 57.378 47.619 0.00 0.00 0.00 3.18
8320 8633 1.208776 AGGGGAATGGTAGTGTTACGC 59.791 52.381 0.00 0.00 0.00 4.42
8321 8634 1.065998 GGGGAATGGTAGTGTTACGCA 60.066 52.381 0.00 0.00 0.00 5.24
8332 8645 3.515071 GTGTTACGCACAAACCAGTAG 57.485 47.619 0.00 0.00 46.91 2.57
8333 8646 3.125316 GTGTTACGCACAAACCAGTAGA 58.875 45.455 0.00 0.00 46.91 2.59
8334 8647 3.060070 GTGTTACGCACAAACCAGTAGAC 60.060 47.826 0.00 0.00 46.91 2.59
8335 8648 3.125316 GTTACGCACAAACCAGTAGACA 58.875 45.455 0.00 0.00 0.00 3.41
8336 8649 1.578583 ACGCACAAACCAGTAGACAC 58.421 50.000 0.00 0.00 0.00 3.67
8337 8650 1.134640 ACGCACAAACCAGTAGACACA 60.135 47.619 0.00 0.00 0.00 3.72
8338 8651 1.260561 CGCACAAACCAGTAGACACAC 59.739 52.381 0.00 0.00 0.00 3.82
8339 8652 2.285083 GCACAAACCAGTAGACACACA 58.715 47.619 0.00 0.00 0.00 3.72
8340 8653 2.287915 GCACAAACCAGTAGACACACAG 59.712 50.000 0.00 0.00 0.00 3.66
8341 8654 2.872245 CACAAACCAGTAGACACACAGG 59.128 50.000 0.00 0.00 0.00 4.00
8342 8655 1.873591 CAAACCAGTAGACACACAGGC 59.126 52.381 0.00 0.00 0.00 4.85
8343 8656 1.424638 AACCAGTAGACACACAGGCT 58.575 50.000 0.00 0.00 40.36 4.58
8344 8657 2.304221 ACCAGTAGACACACAGGCTA 57.696 50.000 0.00 0.00 36.54 3.93
8345 8658 2.605257 ACCAGTAGACACACAGGCTAA 58.395 47.619 0.00 0.00 40.29 3.09
8346 8659 2.563179 ACCAGTAGACACACAGGCTAAG 59.437 50.000 0.00 0.00 40.29 2.18
8347 8660 2.826128 CCAGTAGACACACAGGCTAAGA 59.174 50.000 0.00 0.00 40.29 2.10
8348 8661 3.258372 CCAGTAGACACACAGGCTAAGAA 59.742 47.826 0.00 0.00 40.29 2.52
8349 8662 4.262463 CCAGTAGACACACAGGCTAAGAAA 60.262 45.833 0.00 0.00 40.29 2.52
8350 8663 5.297547 CAGTAGACACACAGGCTAAGAAAA 58.702 41.667 0.00 0.00 40.29 2.29
8351 8664 5.177696 CAGTAGACACACAGGCTAAGAAAAC 59.822 44.000 0.00 0.00 40.29 2.43
8352 8665 4.150897 AGACACACAGGCTAAGAAAACA 57.849 40.909 0.00 0.00 29.36 2.83
8353 8666 4.523083 AGACACACAGGCTAAGAAAACAA 58.477 39.130 0.00 0.00 29.36 2.83
8354 8667 4.947388 AGACACACAGGCTAAGAAAACAAA 59.053 37.500 0.00 0.00 29.36 2.83
8355 8668 5.417580 AGACACACAGGCTAAGAAAACAAAA 59.582 36.000 0.00 0.00 29.36 2.44
8356 8669 6.096846 AGACACACAGGCTAAGAAAACAAAAT 59.903 34.615 0.00 0.00 29.36 1.82
8357 8670 7.284489 AGACACACAGGCTAAGAAAACAAAATA 59.716 33.333 0.00 0.00 29.36 1.40
8358 8671 7.777095 ACACACAGGCTAAGAAAACAAAATAA 58.223 30.769 0.00 0.00 0.00 1.40
8359 8672 7.704899 ACACACAGGCTAAGAAAACAAAATAAC 59.295 33.333 0.00 0.00 0.00 1.89
8360 8673 7.920682 CACACAGGCTAAGAAAACAAAATAACT 59.079 33.333 0.00 0.00 0.00 2.24
8361 8674 9.127277 ACACAGGCTAAGAAAACAAAATAACTA 57.873 29.630 0.00 0.00 0.00 2.24
8362 8675 9.612620 CACAGGCTAAGAAAACAAAATAACTAG 57.387 33.333 0.00 0.00 0.00 2.57
8363 8676 9.569122 ACAGGCTAAGAAAACAAAATAACTAGA 57.431 29.630 0.00 0.00 0.00 2.43
8376 8689 8.870879 ACAAAATAACTAGAAGTGATAGAACGC 58.129 33.333 0.00 0.00 0.00 4.84
8377 8690 9.088512 CAAAATAACTAGAAGTGATAGAACGCT 57.911 33.333 0.00 0.00 0.00 5.07
8379 8692 9.953697 AAATAACTAGAAGTGATAGAACGCTAG 57.046 33.333 0.00 0.00 36.67 3.42
8380 8693 8.905660 ATAACTAGAAGTGATAGAACGCTAGA 57.094 34.615 0.00 0.00 35.40 2.43
8381 8694 7.627298 AACTAGAAGTGATAGAACGCTAGAA 57.373 36.000 0.00 0.00 35.40 2.10
8382 8695 7.811117 ACTAGAAGTGATAGAACGCTAGAAT 57.189 36.000 0.00 0.00 35.40 2.40
8383 8696 8.228035 ACTAGAAGTGATAGAACGCTAGAATT 57.772 34.615 0.00 0.00 35.40 2.17
8384 8697 8.132362 ACTAGAAGTGATAGAACGCTAGAATTG 58.868 37.037 0.00 0.00 35.40 2.32
8385 8698 6.276847 AGAAGTGATAGAACGCTAGAATTGG 58.723 40.000 0.00 0.00 0.00 3.16
8386 8699 5.599999 AGTGATAGAACGCTAGAATTGGT 57.400 39.130 0.00 0.00 0.00 3.67
8387 8700 6.710597 AGTGATAGAACGCTAGAATTGGTA 57.289 37.500 0.00 0.00 0.00 3.25
8388 8701 6.740110 AGTGATAGAACGCTAGAATTGGTAG 58.260 40.000 0.00 0.00 0.00 3.18
8389 8702 6.321690 AGTGATAGAACGCTAGAATTGGTAGT 59.678 38.462 0.00 0.00 0.00 2.73
8390 8703 7.501559 AGTGATAGAACGCTAGAATTGGTAGTA 59.498 37.037 0.00 0.00 0.00 1.82
8391 8704 8.298140 GTGATAGAACGCTAGAATTGGTAGTAT 58.702 37.037 0.00 0.00 0.00 2.12
8392 8705 8.297426 TGATAGAACGCTAGAATTGGTAGTATG 58.703 37.037 0.00 0.00 0.00 2.39
8393 8706 5.844004 AGAACGCTAGAATTGGTAGTATGG 58.156 41.667 0.00 0.00 0.00 2.74
8394 8707 5.597182 AGAACGCTAGAATTGGTAGTATGGA 59.403 40.000 0.00 0.00 0.00 3.41
8395 8708 6.267928 AGAACGCTAGAATTGGTAGTATGGAT 59.732 38.462 0.00 0.00 0.00 3.41
8396 8709 7.450634 AGAACGCTAGAATTGGTAGTATGGATA 59.549 37.037 0.00 0.00 0.00 2.59
8397 8710 7.719871 ACGCTAGAATTGGTAGTATGGATAT 57.280 36.000 0.00 0.00 0.00 1.63
8398 8711 8.135382 ACGCTAGAATTGGTAGTATGGATATT 57.865 34.615 0.00 0.00 0.00 1.28
8399 8712 8.035394 ACGCTAGAATTGGTAGTATGGATATTG 58.965 37.037 0.00 0.00 0.00 1.90
8400 8713 7.010552 CGCTAGAATTGGTAGTATGGATATTGC 59.989 40.741 0.00 0.00 0.00 3.56
8401 8714 8.043710 GCTAGAATTGGTAGTATGGATATTGCT 58.956 37.037 0.00 0.00 0.00 3.91
8404 8717 9.326489 AGAATTGGTAGTATGGATATTGCTAGA 57.674 33.333 0.00 0.00 0.00 2.43
8405 8718 9.593134 GAATTGGTAGTATGGATATTGCTAGAG 57.407 37.037 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.066291 TGCCTTACAATTCATGACGGT 57.934 42.857 0.00 0.00 0.00 4.83
1 2 5.702670 AGATATGCCTTACAATTCATGACGG 59.297 40.000 0.00 0.00 0.00 4.79
2 3 6.791887 AGATATGCCTTACAATTCATGACG 57.208 37.500 0.00 0.00 0.00 4.35
108 109 7.306807 GGTCATTATCGATGGCATATAATGTCG 60.307 40.741 26.79 16.44 42.28 4.35
110 111 6.767902 GGGTCATTATCGATGGCATATAATGT 59.232 38.462 26.79 6.59 42.28 2.71
132 133 5.743636 ATTTGCAGTTGTTGATAATGGGT 57.256 34.783 0.00 0.00 0.00 4.51
251 262 1.012486 CGTGCGGAACCAGGTCTTAC 61.012 60.000 0.00 0.00 0.00 2.34
295 315 6.350906 CCCGGTTGTGAAATACTCCTAATTA 58.649 40.000 0.00 0.00 0.00 1.40
301 321 1.003928 ACCCCGGTTGTGAAATACTCC 59.996 52.381 0.00 0.00 0.00 3.85
302 322 2.484742 ACCCCGGTTGTGAAATACTC 57.515 50.000 0.00 0.00 0.00 2.59
303 323 2.963599 AACCCCGGTTGTGAAATACT 57.036 45.000 0.00 0.00 36.91 2.12
452 473 2.224548 GCCTTGTGTAGGGTGGATATCC 60.225 54.545 15.39 15.39 44.91 2.59
477 498 1.166129 GTTTCCTTCCTCCTTTCGGC 58.834 55.000 0.00 0.00 0.00 5.54
638 662 4.479993 CAGAGCAGGGGAAGGCGG 62.480 72.222 0.00 0.00 34.54 6.13
655 681 1.152546 GGAGGAGGGAGGAGAGAGC 60.153 68.421 0.00 0.00 0.00 4.09
656 682 0.633921 TTGGAGGAGGGAGGAGAGAG 59.366 60.000 0.00 0.00 0.00 3.20
657 683 0.633921 CTTGGAGGAGGGAGGAGAGA 59.366 60.000 0.00 0.00 0.00 3.10
661 687 2.041265 GGCTTGGAGGAGGGAGGA 59.959 66.667 0.00 0.00 0.00 3.71
662 688 2.041928 AGGCTTGGAGGAGGGAGG 59.958 66.667 0.00 0.00 0.00 4.30
663 689 2.069430 GGAGGCTTGGAGGAGGGAG 61.069 68.421 0.00 0.00 0.00 4.30
664 690 2.041265 GGAGGCTTGGAGGAGGGA 59.959 66.667 0.00 0.00 0.00 4.20
666 692 1.500783 TTTGGGAGGCTTGGAGGAGG 61.501 60.000 0.00 0.00 0.00 4.30
676 725 0.899717 TGGTTGCAGATTTGGGAGGC 60.900 55.000 0.00 0.00 0.00 4.70
1033 1146 0.397816 AGGGATCTGGTCTTCTCCGG 60.398 60.000 0.00 0.00 35.33 5.14
1303 1416 2.433868 TTTGCACTACGGACAGAGAC 57.566 50.000 0.00 0.00 0.00 3.36
1305 1418 5.856126 TTAATTTTGCACTACGGACAGAG 57.144 39.130 0.00 0.00 0.00 3.35
1309 1422 5.705902 ACCAATTAATTTTGCACTACGGAC 58.294 37.500 0.00 0.00 0.00 4.79
1311 1424 5.575218 GGAACCAATTAATTTTGCACTACGG 59.425 40.000 0.00 0.00 0.00 4.02
1312 1425 6.386654 AGGAACCAATTAATTTTGCACTACG 58.613 36.000 0.00 0.00 0.00 3.51
1505 1621 2.963101 ACCTACATCTACGCAAGCCATA 59.037 45.455 0.00 0.00 45.62 2.74
1514 1630 2.355132 AGCTCGACAACCTACATCTACG 59.645 50.000 0.00 0.00 0.00 3.51
1520 1636 0.888619 CCAGAGCTCGACAACCTACA 59.111 55.000 8.37 0.00 0.00 2.74
1531 1647 0.952984 GTCAACAGTGGCCAGAGCTC 60.953 60.000 5.11 5.27 39.73 4.09
1696 1813 2.124695 GGGCTTGGGGTCATCGAC 60.125 66.667 0.00 0.00 0.00 4.20
2055 2184 6.266330 AGCTTGAAAATGCCTAAATAGATCCC 59.734 38.462 0.00 0.00 0.00 3.85
2498 2627 4.367386 AACCTGTTCGAGTATAGTTCCG 57.633 45.455 0.00 0.00 0.00 4.30
3006 3135 6.183810 TGAGCACATCAAATGATAGGAGAT 57.816 37.500 0.00 0.00 34.02 2.75
3018 3147 2.259266 TCAACAGCTGAGCACATCAA 57.741 45.000 23.35 0.00 37.52 2.57
3282 3415 0.953727 GTCCATGCTTCTTGTGCACA 59.046 50.000 17.42 17.42 43.59 4.57
3334 3467 7.112528 CTGAGACTATCAGTAGTATCACGAC 57.887 44.000 8.39 0.00 46.61 4.34
3362 3495 1.012841 GAGGCCATTTCTCTTCAGCG 58.987 55.000 5.01 0.00 0.00 5.18
3380 3513 0.811219 GCGTGATGGCAGCAGTATGA 60.811 55.000 5.29 0.00 39.69 2.15
3490 3623 6.095860 CAGAGAATTGGCATGATTAACAGGAA 59.904 38.462 0.00 0.00 31.40 3.36
3637 3770 2.716217 AGCTACATGAAAGCCTGTTCC 58.284 47.619 17.39 0.00 41.02 3.62
3803 3936 7.942341 AGATGTACCTGGTCAAATAAGTTTTCA 59.058 33.333 0.63 0.00 0.00 2.69
4290 4424 5.525378 AGCAGATTCAATTTCACGATAGGAC 59.475 40.000 0.00 0.00 43.77 3.85
4378 4512 1.278413 GAGGGTGGGAGGTTAACTGAC 59.722 57.143 5.42 0.00 0.00 3.51
4614 4845 1.548719 CGTCCAAGGTGGTGATACTCA 59.451 52.381 0.00 0.00 39.03 3.41
4633 4864 4.266976 CGTATACCTGTTTTTACTGGCTCG 59.733 45.833 0.00 0.00 32.74 5.03
4998 5238 2.108075 TGGTGGCTTGGAGATTTTCTGA 59.892 45.455 0.00 0.00 0.00 3.27
5270 5516 4.058124 CGATAGAATTCATGGAAAGGCGA 58.942 43.478 8.44 0.00 39.76 5.54
5875 6121 6.366877 GCAATTTGACATATGTTGAAAGCTGT 59.633 34.615 10.30 0.00 0.00 4.40
6017 6284 5.333046 CAAACTGCCTTGCAAAATAACAG 57.667 39.130 0.00 6.46 38.41 3.16
6855 7130 3.252215 TCCAGTAAAAACGGTGCATTGAG 59.748 43.478 0.00 0.00 0.00 3.02
7009 7294 5.874093 AGGCCTGGTAGAAGATAATGAATG 58.126 41.667 3.11 0.00 0.00 2.67
7237 7522 0.955919 GCTTGTCCCAGGTGTACTGC 60.956 60.000 0.00 0.00 46.14 4.40
7306 7591 2.543861 CGATATGACAGTTGGGGTCTCG 60.544 54.545 0.00 0.00 36.26 4.04
7725 8012 5.012239 AGACCACAATGCAAATGTACAGAT 58.988 37.500 8.04 0.00 0.00 2.90
7829 8117 4.833380 AGGAGCAGACAACTTGTAAGACTA 59.167 41.667 0.00 0.00 0.00 2.59
7830 8118 3.643792 AGGAGCAGACAACTTGTAAGACT 59.356 43.478 0.00 0.00 0.00 3.24
7831 8119 3.991121 GAGGAGCAGACAACTTGTAAGAC 59.009 47.826 0.00 0.00 0.00 3.01
7832 8120 3.641436 TGAGGAGCAGACAACTTGTAAGA 59.359 43.478 0.00 0.00 0.00 2.10
7833 8121 3.995199 TGAGGAGCAGACAACTTGTAAG 58.005 45.455 0.00 0.00 0.00 2.34
7836 8124 3.498774 AATGAGGAGCAGACAACTTGT 57.501 42.857 0.00 0.00 0.00 3.16
7837 8125 3.611057 GCAAATGAGGAGCAGACAACTTG 60.611 47.826 0.00 0.00 0.00 3.16
7838 8126 2.555757 GCAAATGAGGAGCAGACAACTT 59.444 45.455 0.00 0.00 0.00 2.66
7839 8127 2.157738 GCAAATGAGGAGCAGACAACT 58.842 47.619 0.00 0.00 0.00 3.16
7840 8128 1.200948 GGCAAATGAGGAGCAGACAAC 59.799 52.381 0.00 0.00 0.00 3.32
7841 8129 1.538047 GGCAAATGAGGAGCAGACAA 58.462 50.000 0.00 0.00 0.00 3.18
7843 8131 0.034670 AGGGCAAATGAGGAGCAGAC 60.035 55.000 0.00 0.00 0.00 3.51
7844 8132 0.034767 CAGGGCAAATGAGGAGCAGA 60.035 55.000 0.00 0.00 0.00 4.26
7845 8133 1.035932 CCAGGGCAAATGAGGAGCAG 61.036 60.000 0.00 0.00 0.00 4.24
7846 8134 1.000521 CCAGGGCAAATGAGGAGCA 60.001 57.895 0.00 0.00 0.00 4.26
7847 8135 1.755783 CCCAGGGCAAATGAGGAGC 60.756 63.158 0.00 0.00 0.00 4.70
7848 8136 1.076485 CCCCAGGGCAAATGAGGAG 60.076 63.158 0.00 0.00 0.00 3.69
7849 8137 1.543642 TCCCCAGGGCAAATGAGGA 60.544 57.895 0.00 0.00 34.68 3.71
7850 8138 1.076485 CTCCCCAGGGCAAATGAGG 60.076 63.158 0.00 0.00 34.68 3.86
7851 8139 1.755783 GCTCCCCAGGGCAAATGAG 60.756 63.158 0.00 1.73 34.68 2.90
7852 8140 2.360191 GCTCCCCAGGGCAAATGA 59.640 61.111 0.00 0.00 34.68 2.57
7853 8141 2.761213 GGCTCCCCAGGGCAAATG 60.761 66.667 0.00 0.00 34.68 2.32
7854 8142 3.275271 TGGCTCCCCAGGGCAAAT 61.275 61.111 0.00 0.00 35.79 2.32
7862 8150 2.204074 TAGGTTGCTGGCTCCCCA 60.204 61.111 0.00 0.00 39.32 4.96
7863 8151 2.592308 CTAGGTTGCTGGCTCCCC 59.408 66.667 0.00 0.00 0.00 4.81
7864 8152 1.977293 CTCCTAGGTTGCTGGCTCCC 61.977 65.000 9.08 0.00 0.00 4.30
7865 8153 1.524482 CTCCTAGGTTGCTGGCTCC 59.476 63.158 9.08 0.00 0.00 4.70
7866 8154 1.153269 GCTCCTAGGTTGCTGGCTC 60.153 63.158 17.86 0.00 0.00 4.70
7867 8155 1.614824 AGCTCCTAGGTTGCTGGCT 60.615 57.895 23.95 15.01 35.54 4.75
7868 8156 2.993853 AGCTCCTAGGTTGCTGGC 59.006 61.111 23.95 13.44 35.54 4.85
7871 8159 0.980231 CTCCCAGCTCCTAGGTTGCT 60.980 60.000 20.72 20.72 37.56 3.91
7872 8160 1.268283 ACTCCCAGCTCCTAGGTTGC 61.268 60.000 17.58 17.58 0.00 4.17
7873 8161 0.539051 CACTCCCAGCTCCTAGGTTG 59.461 60.000 9.08 6.22 0.00 3.77
7874 8162 0.618968 CCACTCCCAGCTCCTAGGTT 60.619 60.000 9.08 0.00 0.00 3.50
7875 8163 1.002274 CCACTCCCAGCTCCTAGGT 59.998 63.158 9.08 0.00 0.00 3.08
7876 8164 0.758685 CTCCACTCCCAGCTCCTAGG 60.759 65.000 0.82 0.82 0.00 3.02
7877 8165 1.398958 GCTCCACTCCCAGCTCCTAG 61.399 65.000 0.00 0.00 32.48 3.02
7878 8166 1.381872 GCTCCACTCCCAGCTCCTA 60.382 63.158 0.00 0.00 32.48 2.94
7879 8167 1.879927 TAGCTCCACTCCCAGCTCCT 61.880 60.000 0.00 0.00 42.60 3.69
7880 8168 0.978146 TTAGCTCCACTCCCAGCTCC 60.978 60.000 0.00 0.00 42.60 4.70
7881 8169 0.463620 CTTAGCTCCACTCCCAGCTC 59.536 60.000 0.00 0.00 42.60 4.09
7883 8171 0.978146 TCCTTAGCTCCACTCCCAGC 60.978 60.000 0.00 0.00 35.73 4.85
7884 8172 1.799933 ATCCTTAGCTCCACTCCCAG 58.200 55.000 0.00 0.00 0.00 4.45
7885 8173 2.239654 CAAATCCTTAGCTCCACTCCCA 59.760 50.000 0.00 0.00 0.00 4.37
7886 8174 2.505819 TCAAATCCTTAGCTCCACTCCC 59.494 50.000 0.00 0.00 0.00 4.30
7887 8175 3.432890 CCTCAAATCCTTAGCTCCACTCC 60.433 52.174 0.00 0.00 0.00 3.85
7888 8176 3.432890 CCCTCAAATCCTTAGCTCCACTC 60.433 52.174 0.00 0.00 0.00 3.51
7889 8177 2.507471 CCCTCAAATCCTTAGCTCCACT 59.493 50.000 0.00 0.00 0.00 4.00
7890 8178 2.505819 TCCCTCAAATCCTTAGCTCCAC 59.494 50.000 0.00 0.00 0.00 4.02
7891 8179 2.774234 CTCCCTCAAATCCTTAGCTCCA 59.226 50.000 0.00 0.00 0.00 3.86
7892 8180 2.774809 ACTCCCTCAAATCCTTAGCTCC 59.225 50.000 0.00 0.00 0.00 4.70
7893 8181 3.432890 CCACTCCCTCAAATCCTTAGCTC 60.433 52.174 0.00 0.00 0.00 4.09
7894 8182 2.507471 CCACTCCCTCAAATCCTTAGCT 59.493 50.000 0.00 0.00 0.00 3.32
7895 8183 2.505819 TCCACTCCCTCAAATCCTTAGC 59.494 50.000 0.00 0.00 0.00 3.09
7896 8184 3.777522 ACTCCACTCCCTCAAATCCTTAG 59.222 47.826 0.00 0.00 0.00 2.18
7897 8185 3.519510 CACTCCACTCCCTCAAATCCTTA 59.480 47.826 0.00 0.00 0.00 2.69
7898 8186 2.307098 CACTCCACTCCCTCAAATCCTT 59.693 50.000 0.00 0.00 0.00 3.36
7899 8187 1.912043 CACTCCACTCCCTCAAATCCT 59.088 52.381 0.00 0.00 0.00 3.24
7900 8188 1.065126 CCACTCCACTCCCTCAAATCC 60.065 57.143 0.00 0.00 0.00 3.01
7901 8189 1.909302 TCCACTCCACTCCCTCAAATC 59.091 52.381 0.00 0.00 0.00 2.17
7902 8190 2.044793 TCCACTCCACTCCCTCAAAT 57.955 50.000 0.00 0.00 0.00 2.32
7903 8191 1.909302 GATCCACTCCACTCCCTCAAA 59.091 52.381 0.00 0.00 0.00 2.69
7904 8192 1.573108 GATCCACTCCACTCCCTCAA 58.427 55.000 0.00 0.00 0.00 3.02
7905 8193 0.325671 GGATCCACTCCACTCCCTCA 60.326 60.000 6.95 0.00 44.26 3.86
7906 8194 1.395826 CGGATCCACTCCACTCCCTC 61.396 65.000 13.41 0.00 45.24 4.30
7907 8195 1.381872 CGGATCCACTCCACTCCCT 60.382 63.158 13.41 0.00 45.24 4.20
7908 8196 0.976073 TTCGGATCCACTCCACTCCC 60.976 60.000 13.41 0.00 45.24 4.30
7909 8197 0.175989 GTTCGGATCCACTCCACTCC 59.824 60.000 13.41 0.00 45.24 3.85
7910 8198 0.895530 TGTTCGGATCCACTCCACTC 59.104 55.000 13.41 0.00 45.24 3.51
7911 8199 0.898320 CTGTTCGGATCCACTCCACT 59.102 55.000 13.41 0.00 45.24 4.00
7912 8200 0.108138 CCTGTTCGGATCCACTCCAC 60.108 60.000 13.41 0.80 45.24 4.02
7913 8201 1.899437 GCCTGTTCGGATCCACTCCA 61.899 60.000 13.41 1.43 45.24 3.86
7914 8202 1.153349 GCCTGTTCGGATCCACTCC 60.153 63.158 13.41 0.00 41.07 3.85
7915 8203 1.153349 GGCCTGTTCGGATCCACTC 60.153 63.158 13.41 1.28 33.16 3.51
7916 8204 2.670148 GGGCCTGTTCGGATCCACT 61.670 63.158 13.41 0.00 33.16 4.00
7917 8205 2.124695 GGGCCTGTTCGGATCCAC 60.125 66.667 13.41 3.70 33.16 4.02
7918 8206 0.619255 TAAGGGCCTGTTCGGATCCA 60.619 55.000 6.92 0.00 32.17 3.41
7919 8207 0.106894 CTAAGGGCCTGTTCGGATCC 59.893 60.000 6.92 0.00 33.16 3.36
7920 8208 0.831307 ACTAAGGGCCTGTTCGGATC 59.169 55.000 6.92 0.00 33.16 3.36
7921 8209 0.831307 GACTAAGGGCCTGTTCGGAT 59.169 55.000 6.92 0.00 33.16 4.18
7922 8210 1.601419 CGACTAAGGGCCTGTTCGGA 61.601 60.000 19.04 0.00 33.16 4.55
7923 8211 1.153628 CGACTAAGGGCCTGTTCGG 60.154 63.158 19.04 6.81 0.00 4.30
7924 8212 1.810030 GCGACTAAGGGCCTGTTCG 60.810 63.158 21.34 21.34 0.00 3.95
7925 8213 1.449778 GGCGACTAAGGGCCTGTTC 60.450 63.158 6.92 2.66 45.93 3.18
7926 8214 2.669240 GGCGACTAAGGGCCTGTT 59.331 61.111 6.92 0.00 45.93 3.16
7931 8219 1.099879 TCGACTAGGCGACTAAGGGC 61.100 60.000 18.89 0.00 43.83 5.19
7932 8220 3.091318 TCGACTAGGCGACTAAGGG 57.909 57.895 18.89 0.00 43.83 3.95
7939 8227 0.249676 AGTCTCAGTCGACTAGGCGA 59.750 55.000 18.89 18.89 42.19 5.54
7940 8228 1.088306 AAGTCTCAGTCGACTAGGCG 58.912 55.000 19.57 13.16 43.14 5.52
7941 8229 1.133407 CCAAGTCTCAGTCGACTAGGC 59.867 57.143 19.57 16.58 43.14 3.93
7942 8230 2.680841 CTCCAAGTCTCAGTCGACTAGG 59.319 54.545 19.57 13.71 43.14 3.02
7943 8231 3.372822 GTCTCCAAGTCTCAGTCGACTAG 59.627 52.174 19.57 15.41 43.14 2.57
7985 8288 5.532557 ACGATCGTACATGAATGACATCAT 58.467 37.500 21.32 0.00 40.64 2.45
7986 8289 4.932146 ACGATCGTACATGAATGACATCA 58.068 39.130 21.32 0.00 37.07 3.07
7987 8290 4.383052 GGACGATCGTACATGAATGACATC 59.617 45.833 25.52 5.47 37.07 3.06
7988 8291 4.299155 GGACGATCGTACATGAATGACAT 58.701 43.478 25.52 0.00 40.17 3.06
7989 8292 3.702330 GGACGATCGTACATGAATGACA 58.298 45.455 25.52 0.00 0.00 3.58
7990 8293 2.719556 CGGACGATCGTACATGAATGAC 59.280 50.000 28.94 9.29 0.00 3.06
7991 8294 2.287368 CCGGACGATCGTACATGAATGA 60.287 50.000 28.94 0.00 0.00 2.57
7992 8295 2.051423 CCGGACGATCGTACATGAATG 58.949 52.381 28.94 12.07 0.00 2.67
7993 8296 1.679680 ACCGGACGATCGTACATGAAT 59.320 47.619 28.94 7.16 0.00 2.57
8050 8353 9.903682 ACATCACAAAATCATCTCAAAAAGTAG 57.096 29.630 0.00 0.00 0.00 2.57
8052 8355 9.603921 AAACATCACAAAATCATCTCAAAAAGT 57.396 25.926 0.00 0.00 0.00 2.66
8059 8362 6.643770 ACAAGCAAACATCACAAAATCATCTC 59.356 34.615 0.00 0.00 0.00 2.75
8102 8408 1.340211 ACAACGGACAAAGGACAACCA 60.340 47.619 0.00 0.00 38.94 3.67
8103 8409 1.385528 ACAACGGACAAAGGACAACC 58.614 50.000 0.00 0.00 0.00 3.77
8146 8452 2.146073 ATCAACGCAAGCCAGCCAAC 62.146 55.000 0.00 0.00 45.62 3.77
8148 8454 1.462731 AAATCAACGCAAGCCAGCCA 61.463 50.000 0.00 0.00 45.62 4.75
8252 8565 6.780522 TGTTCCCTTTTCCATAGCTAGTTTTT 59.219 34.615 0.00 0.00 0.00 1.94
8253 8566 6.311735 TGTTCCCTTTTCCATAGCTAGTTTT 58.688 36.000 0.00 0.00 0.00 2.43
8254 8567 5.887754 TGTTCCCTTTTCCATAGCTAGTTT 58.112 37.500 0.00 0.00 0.00 2.66
8255 8568 5.514500 TGTTCCCTTTTCCATAGCTAGTT 57.486 39.130 0.00 0.00 0.00 2.24
8284 8597 0.107831 CCCTTTCTTGGTCACGTGGA 59.892 55.000 17.00 0.96 0.00 4.02
8296 8609 4.323257 CGTAACACTACCATTCCCCTTTCT 60.323 45.833 0.00 0.00 0.00 2.52
8297 8610 3.937079 CGTAACACTACCATTCCCCTTTC 59.063 47.826 0.00 0.00 0.00 2.62
8298 8611 3.871074 GCGTAACACTACCATTCCCCTTT 60.871 47.826 0.00 0.00 0.00 3.11
8299 8612 2.355412 GCGTAACACTACCATTCCCCTT 60.355 50.000 0.00 0.00 0.00 3.95
8300 8613 1.208776 GCGTAACACTACCATTCCCCT 59.791 52.381 0.00 0.00 0.00 4.79
8301 8614 1.065998 TGCGTAACACTACCATTCCCC 60.066 52.381 0.00 0.00 0.00 4.81
8302 8615 2.004733 GTGCGTAACACTACCATTCCC 58.995 52.381 0.00 0.00 46.41 3.97
8313 8626 3.125316 GTCTACTGGTTTGTGCGTAACA 58.875 45.455 0.00 0.00 36.85 2.41
8314 8627 3.060070 GTGTCTACTGGTTTGTGCGTAAC 60.060 47.826 0.00 0.00 0.00 2.50
8315 8628 3.125316 GTGTCTACTGGTTTGTGCGTAA 58.875 45.455 0.00 0.00 0.00 3.18
8316 8629 2.101082 TGTGTCTACTGGTTTGTGCGTA 59.899 45.455 0.00 0.00 0.00 4.42
8317 8630 1.134640 TGTGTCTACTGGTTTGTGCGT 60.135 47.619 0.00 0.00 0.00 5.24
8318 8631 1.260561 GTGTGTCTACTGGTTTGTGCG 59.739 52.381 0.00 0.00 0.00 5.34
8319 8632 2.285083 TGTGTGTCTACTGGTTTGTGC 58.715 47.619 0.00 0.00 0.00 4.57
8320 8633 2.872245 CCTGTGTGTCTACTGGTTTGTG 59.128 50.000 0.00 0.00 35.60 3.33
8321 8634 2.745152 GCCTGTGTGTCTACTGGTTTGT 60.745 50.000 0.00 0.00 40.58 2.83
8322 8635 1.873591 GCCTGTGTGTCTACTGGTTTG 59.126 52.381 0.00 0.00 40.58 2.93
8323 8636 1.768870 AGCCTGTGTGTCTACTGGTTT 59.231 47.619 0.00 0.00 40.58 3.27
8324 8637 1.424638 AGCCTGTGTGTCTACTGGTT 58.575 50.000 0.00 0.00 40.58 3.67
8325 8638 2.304221 TAGCCTGTGTGTCTACTGGT 57.696 50.000 0.00 0.00 40.58 4.00
8326 8639 2.826128 TCTTAGCCTGTGTGTCTACTGG 59.174 50.000 0.00 0.00 41.18 4.00
8327 8640 4.521130 TTCTTAGCCTGTGTGTCTACTG 57.479 45.455 0.00 0.00 0.00 2.74
8328 8641 5.163343 TGTTTTCTTAGCCTGTGTGTCTACT 60.163 40.000 0.00 0.00 0.00 2.57
8329 8642 5.054477 TGTTTTCTTAGCCTGTGTGTCTAC 58.946 41.667 0.00 0.00 0.00 2.59
8330 8643 5.284861 TGTTTTCTTAGCCTGTGTGTCTA 57.715 39.130 0.00 0.00 0.00 2.59
8331 8644 4.150897 TGTTTTCTTAGCCTGTGTGTCT 57.849 40.909 0.00 0.00 0.00 3.41
8332 8645 4.893424 TTGTTTTCTTAGCCTGTGTGTC 57.107 40.909 0.00 0.00 0.00 3.67
8333 8646 5.652994 TTTTGTTTTCTTAGCCTGTGTGT 57.347 34.783 0.00 0.00 0.00 3.72
8334 8647 7.920682 AGTTATTTTGTTTTCTTAGCCTGTGTG 59.079 33.333 0.00 0.00 0.00 3.82
8335 8648 8.007405 AGTTATTTTGTTTTCTTAGCCTGTGT 57.993 30.769 0.00 0.00 0.00 3.72
8336 8649 9.612620 CTAGTTATTTTGTTTTCTTAGCCTGTG 57.387 33.333 0.00 0.00 0.00 3.66
8337 8650 9.569122 TCTAGTTATTTTGTTTTCTTAGCCTGT 57.431 29.630 0.00 0.00 0.00 4.00
8350 8663 8.870879 GCGTTCTATCACTTCTAGTTATTTTGT 58.129 33.333 0.00 0.00 0.00 2.83
8351 8664 9.088512 AGCGTTCTATCACTTCTAGTTATTTTG 57.911 33.333 0.00 0.00 0.00 2.44
8353 8666 9.953697 CTAGCGTTCTATCACTTCTAGTTATTT 57.046 33.333 0.00 0.00 0.00 1.40
8354 8667 9.339850 TCTAGCGTTCTATCACTTCTAGTTATT 57.660 33.333 0.00 0.00 0.00 1.40
8355 8668 8.905660 TCTAGCGTTCTATCACTTCTAGTTAT 57.094 34.615 0.00 0.00 0.00 1.89
8356 8669 8.728337 TTCTAGCGTTCTATCACTTCTAGTTA 57.272 34.615 0.00 0.00 0.00 2.24
8357 8670 7.627298 TTCTAGCGTTCTATCACTTCTAGTT 57.373 36.000 0.00 0.00 0.00 2.24
8358 8671 7.811117 ATTCTAGCGTTCTATCACTTCTAGT 57.189 36.000 0.00 0.00 0.00 2.57
8359 8672 7.593273 CCAATTCTAGCGTTCTATCACTTCTAG 59.407 40.741 0.00 0.00 0.00 2.43
8360 8673 7.068348 ACCAATTCTAGCGTTCTATCACTTCTA 59.932 37.037 0.00 0.00 0.00 2.10
8361 8674 6.127310 ACCAATTCTAGCGTTCTATCACTTCT 60.127 38.462 0.00 0.00 0.00 2.85
8362 8675 6.043411 ACCAATTCTAGCGTTCTATCACTTC 58.957 40.000 0.00 0.00 0.00 3.01
8363 8676 5.978814 ACCAATTCTAGCGTTCTATCACTT 58.021 37.500 0.00 0.00 0.00 3.16
8364 8677 5.599999 ACCAATTCTAGCGTTCTATCACT 57.400 39.130 0.00 0.00 0.00 3.41
8365 8678 6.505272 ACTACCAATTCTAGCGTTCTATCAC 58.495 40.000 0.00 0.00 0.00 3.06
8366 8679 6.710597 ACTACCAATTCTAGCGTTCTATCA 57.289 37.500 0.00 0.00 0.00 2.15
8367 8680 7.755822 CCATACTACCAATTCTAGCGTTCTATC 59.244 40.741 0.00 0.00 0.00 2.08
8368 8681 7.450634 TCCATACTACCAATTCTAGCGTTCTAT 59.549 37.037 0.00 0.00 0.00 1.98
8369 8682 6.774170 TCCATACTACCAATTCTAGCGTTCTA 59.226 38.462 0.00 0.00 0.00 2.10
8370 8683 5.597182 TCCATACTACCAATTCTAGCGTTCT 59.403 40.000 0.00 0.00 0.00 3.01
8371 8684 5.839621 TCCATACTACCAATTCTAGCGTTC 58.160 41.667 0.00 0.00 0.00 3.95
8372 8685 5.864418 TCCATACTACCAATTCTAGCGTT 57.136 39.130 0.00 0.00 0.00 4.84
8373 8686 7.719871 ATATCCATACTACCAATTCTAGCGT 57.280 36.000 0.00 0.00 0.00 5.07
8374 8687 7.010552 GCAATATCCATACTACCAATTCTAGCG 59.989 40.741 0.00 0.00 0.00 4.26
8375 8688 8.043710 AGCAATATCCATACTACCAATTCTAGC 58.956 37.037 0.00 0.00 0.00 3.42
8378 8691 9.326489 TCTAGCAATATCCATACTACCAATTCT 57.674 33.333 0.00 0.00 0.00 2.40
8379 8692 9.593134 CTCTAGCAATATCCATACTACCAATTC 57.407 37.037 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.