Multiple sequence alignment - TraesCS7D01G172100

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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 TraesCS7D01G172100 chr7D 100.000 3785 0 0 1 3785 124506378 124502594 0.000000e+00 6990.0
1 TraesCS7D01G172100 chr7D 96.466 566 16 2 3222 3785 279998 280561 0.000000e+00 931.0
2 TraesCS7D01G172100 chr7D 79.487 156 26 6 1609 1761 123739127 123738975 5.170000e-19 106.0
3 TraesCS7D01G172100 chr7B 93.776 2137 82 18 849 2969 86166417 86164316 0.000000e+00 3162.0
4 TraesCS7D01G172100 chr7B 84.268 642 36 34 1 612 86169662 86169056 1.970000e-157 566.0
5 TraesCS7D01G172100 chr7B 94.798 173 6 2 3534 3704 226614862 226614691 2.240000e-67 267.0
6 TraesCS7D01G172100 chr7B 91.150 113 5 3 717 828 86166511 86166403 8.470000e-32 148.0
7 TraesCS7D01G172100 chr7A 93.394 2074 84 22 849 2906 126919719 126917683 0.000000e+00 3022.0
8 TraesCS7D01G172100 chr7A 95.181 249 11 1 1 248 126926544 126926296 3.540000e-105 392.0
9 TraesCS7D01G172100 chr7A 85.496 393 25 12 242 606 126925737 126925349 7.670000e-102 381.0
10 TraesCS7D01G172100 chr7A 92.632 95 2 2 734 828 126919794 126919705 8.530000e-27 132.0
11 TraesCS7D01G172100 chr3D 96.643 566 15 2 3222 3785 382808502 382809065 0.000000e+00 937.0
12 TraesCS7D01G172100 chr4D 96.466 566 16 2 3222 3785 484192879 484193442 0.000000e+00 931.0
13 TraesCS7D01G172100 chr4D 75.377 1458 276 51 1395 2789 127928429 127929866 8.930000e-176 627.0
14 TraesCS7D01G172100 chr6D 96.466 566 15 3 3222 3785 108243929 108244491 0.000000e+00 929.0
15 TraesCS7D01G172100 chr6D 72.987 1366 303 59 1357 2698 410117387 410116064 5.850000e-113 418.0
16 TraesCS7D01G172100 chr4B 93.819 453 26 2 3236 3687 128948957 128948506 0.000000e+00 680.0
17 TraesCS7D01G172100 chr4B 74.425 1478 278 59 1397 2789 191788587 191790049 9.250000e-151 544.0
18 TraesCS7D01G172100 chr3A 75.787 1462 263 55 1395 2789 10290985 10292422 0.000000e+00 654.0
19 TraesCS7D01G172100 chr3A 98.851 87 1 0 3699 3785 94148456 94148542 5.060000e-34 156.0
20 TraesCS7D01G172100 chr4A 96.078 357 13 1 3222 3577 616659384 616659028 7.050000e-162 580.0
21 TraesCS7D01G172100 chr4A 74.816 1358 261 47 1397 2685 440254903 440253558 4.300000e-149 538.0
22 TraesCS7D01G172100 chr2B 94.783 345 14 3 3363 3704 717362711 717363054 5.570000e-148 534.0
23 TraesCS7D01G172100 chr2A 92.717 357 25 1 3222 3577 278541695 278542051 7.250000e-142 514.0
24 TraesCS7D01G172100 chr1A 90.936 342 29 2 3223 3564 492887964 492887625 3.450000e-125 459.0
25 TraesCS7D01G172100 chr6B 73.077 1352 296 59 1357 2683 616867592 616868900 5.850000e-113 418.0
26 TraesCS7D01G172100 chr3B 94.828 174 6 2 3534 3704 633396807 633396634 6.230000e-68 268.0
27 TraesCS7D01G172100 chr5D 98.864 88 0 1 3699 3785 539737775 539737862 5.060000e-34 156.0
28 TraesCS7D01G172100 chrUn 91.250 80 4 2 3704 3780 110795223 110795302 5.170000e-19 106.0
29 TraesCS7D01G172100 chr5A 89.610 77 4 2 3706 3778 701072528 701072604 1.120000e-15 95.3


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 TraesCS7D01G172100 chr7D 124502594 124506378 3784 True 6990.0 6990 100.000000 1 3785 1 chr7D.!!$R2 3784
1 TraesCS7D01G172100 chr7D 279998 280561 563 False 931.0 931 96.466000 3222 3785 1 chr7D.!!$F1 563
2 TraesCS7D01G172100 chr7B 86164316 86169662 5346 True 1292.0 3162 89.731333 1 2969 3 chr7B.!!$R2 2968
3 TraesCS7D01G172100 chr7A 126917683 126919794 2111 True 1577.0 3022 93.013000 734 2906 2 chr7A.!!$R1 2172
4 TraesCS7D01G172100 chr7A 126925349 126926544 1195 True 386.5 392 90.338500 1 606 2 chr7A.!!$R2 605
5 TraesCS7D01G172100 chr3D 382808502 382809065 563 False 937.0 937 96.643000 3222 3785 1 chr3D.!!$F1 563
6 TraesCS7D01G172100 chr4D 484192879 484193442 563 False 931.0 931 96.466000 3222 3785 1 chr4D.!!$F2 563
7 TraesCS7D01G172100 chr4D 127928429 127929866 1437 False 627.0 627 75.377000 1395 2789 1 chr4D.!!$F1 1394
8 TraesCS7D01G172100 chr6D 108243929 108244491 562 False 929.0 929 96.466000 3222 3785 1 chr6D.!!$F1 563
9 TraesCS7D01G172100 chr6D 410116064 410117387 1323 True 418.0 418 72.987000 1357 2698 1 chr6D.!!$R1 1341
10 TraesCS7D01G172100 chr4B 191788587 191790049 1462 False 544.0 544 74.425000 1397 2789 1 chr4B.!!$F1 1392
11 TraesCS7D01G172100 chr3A 10290985 10292422 1437 False 654.0 654 75.787000 1395 2789 1 chr3A.!!$F1 1394
12 TraesCS7D01G172100 chr4A 440253558 440254903 1345 True 538.0 538 74.816000 1397 2685 1 chr4A.!!$R1 1288
13 TraesCS7D01G172100 chr6B 616867592 616868900 1308 False 418.0 418 73.077000 1357 2683 1 chr6B.!!$F1 1326

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
970 4029 0.52847 CACTTGACCTCCTCGACCTC 59.472 60.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2881 6122 0.856641 TTCTTTTTGGCGACGACGAG 59.143 50.0 12.29 0.0 42.66 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
41 42 8.282455 TCTGTGGTTTGTTTTATGAACTTGTA 57.718 30.769 0.00 0.00 0.00 2.41
42 43 8.908903 TCTGTGGTTTGTTTTATGAACTTGTAT 58.091 29.630 0.00 0.00 0.00 2.29
149 154 2.332654 GGACACGCAACATGGGACC 61.333 63.158 0.00 0.00 34.12 4.46
203 208 3.524606 GCCGCTGTAGCCGGAGTA 61.525 66.667 5.05 0.00 37.05 2.59
275 845 6.707440 TCACTATTGGATTGTGTTGTGTTT 57.293 33.333 3.24 0.00 37.31 2.83
441 1041 2.821378 TCAGTTTGGTAGCGCTAGTACA 59.179 45.455 19.48 14.49 0.00 2.90
550 1150 6.168389 TCCTTCGAAAAATGGAACCTACTAC 58.832 40.000 0.00 0.00 0.00 2.73
551 1151 6.013984 TCCTTCGAAAAATGGAACCTACTACT 60.014 38.462 0.00 0.00 0.00 2.57
552 1152 7.178983 TCCTTCGAAAAATGGAACCTACTACTA 59.821 37.037 0.00 0.00 0.00 1.82
576 1176 4.335594 AGGTCTTCGTTGTTCAAAGGAAAG 59.664 41.667 0.00 0.00 34.13 2.62
609 1209 8.655935 AAATACATAGGAATTGGAATGGGATC 57.344 34.615 0.00 0.00 0.00 3.36
612 1212 7.406620 ACATAGGAATTGGAATGGGATCTTA 57.593 36.000 0.00 0.00 0.00 2.10
613 1213 7.825709 ACATAGGAATTGGAATGGGATCTTAA 58.174 34.615 0.00 0.00 0.00 1.85
614 1214 7.725844 ACATAGGAATTGGAATGGGATCTTAAC 59.274 37.037 0.00 0.00 0.00 2.01
626 1848 3.306502 GGGATCTTAACCGTGAAGTGACA 60.307 47.826 0.00 0.00 0.00 3.58
639 1861 6.367695 CCGTGAAGTGACATAACATGTAAGAA 59.632 38.462 0.00 0.00 45.03 2.52
702 3753 8.132362 AGATATAACATCGAACTCAGACAAGTC 58.868 37.037 0.00 0.00 0.00 3.01
703 3754 4.592485 AACATCGAACTCAGACAAGTCT 57.408 40.909 0.00 0.00 41.37 3.24
704 3755 4.167554 ACATCGAACTCAGACAAGTCTC 57.832 45.455 0.00 0.00 37.98 3.36
705 3756 3.570125 ACATCGAACTCAGACAAGTCTCA 59.430 43.478 0.00 0.00 37.98 3.27
706 3757 3.906014 TCGAACTCAGACAAGTCTCAG 57.094 47.619 0.00 0.00 37.98 3.35
707 3758 3.215151 TCGAACTCAGACAAGTCTCAGT 58.785 45.455 0.58 0.58 43.02 3.41
708 3759 3.251245 TCGAACTCAGACAAGTCTCAGTC 59.749 47.826 7.22 1.46 40.23 3.51
709 3760 3.560503 GAACTCAGACAAGTCTCAGTCG 58.439 50.000 7.22 0.00 40.23 4.18
710 3761 2.852449 ACTCAGACAAGTCTCAGTCGA 58.148 47.619 0.58 0.00 36.22 4.20
711 3762 2.550606 ACTCAGACAAGTCTCAGTCGAC 59.449 50.000 7.70 7.70 36.22 4.20
712 3763 1.880675 TCAGACAAGTCTCAGTCGACC 59.119 52.381 13.01 0.00 37.98 4.79
713 3764 1.609072 CAGACAAGTCTCAGTCGACCA 59.391 52.381 13.01 0.00 37.98 4.02
714 3765 2.034685 CAGACAAGTCTCAGTCGACCAA 59.965 50.000 13.01 0.00 37.98 3.67
715 3766 2.894126 AGACAAGTCTCAGTCGACCAAT 59.106 45.455 13.01 0.00 39.67 3.16
719 3770 3.753294 AGTCTCAGTCGACCAATGTTT 57.247 42.857 13.01 0.00 34.46 2.83
779 3831 3.648339 GTGTGTGCACAAGGAATCAAT 57.352 42.857 23.59 0.00 43.77 2.57
815 3868 3.797353 CAGCCACCCCGCCACTAT 61.797 66.667 0.00 0.00 0.00 2.12
816 3869 3.015145 AGCCACCCCGCCACTATT 61.015 61.111 0.00 0.00 0.00 1.73
817 3870 2.828549 GCCACCCCGCCACTATTG 60.829 66.667 0.00 0.00 0.00 1.90
905 3958 2.440627 TCTGGCATTCTACTCCATGCAT 59.559 45.455 6.48 0.00 46.53 3.96
968 4027 1.592223 CCACTTGACCTCCTCGACC 59.408 63.158 0.00 0.00 0.00 4.79
969 4028 0.900647 CCACTTGACCTCCTCGACCT 60.901 60.000 0.00 0.00 0.00 3.85
970 4029 0.528470 CACTTGACCTCCTCGACCTC 59.472 60.000 0.00 0.00 0.00 3.85
971 4030 0.961358 ACTTGACCTCCTCGACCTCG 60.961 60.000 0.00 0.00 41.45 4.63
973 4032 0.959372 TTGACCTCCTCGACCTCGAC 60.959 60.000 0.00 0.00 44.22 4.20
1311 4374 1.300311 CACAGGTCCACGTAACGCA 60.300 57.895 0.00 0.00 0.00 5.24
1470 4533 3.825833 CTCGCCGTATCTGGTCCGC 62.826 68.421 0.00 0.00 0.00 5.54
1620 4707 4.115199 GTCCAGGGCCTCGGCAAT 62.115 66.667 0.95 0.00 44.11 3.56
1818 4926 2.670635 CTACGTGAGCATGCTCCAC 58.329 57.895 37.92 31.59 42.09 4.02
1972 5158 1.796796 GACGGCTTCAACTGGATGC 59.203 57.895 0.00 0.00 43.87 3.91
2337 5559 2.556287 GCGAACAAGGTCAAGGCG 59.444 61.111 0.00 0.00 0.00 5.52
2793 6033 2.243407 CTCGTCGACTGAGTAACTTGC 58.757 52.381 21.52 0.00 0.00 4.01
2881 6122 4.764679 TTGTGGTCACTGAAATACATGC 57.235 40.909 0.00 0.00 0.00 4.06
2906 6147 3.481028 GTCGTCGCCAAAAAGAAAGAAAC 59.519 43.478 0.00 0.00 0.00 2.78
2907 6148 2.462565 CGTCGCCAAAAAGAAAGAAACG 59.537 45.455 0.00 0.00 0.00 3.60
2908 6149 3.687200 GTCGCCAAAAAGAAAGAAACGA 58.313 40.909 0.00 0.00 0.00 3.85
2909 6150 4.099824 GTCGCCAAAAAGAAAGAAACGAA 58.900 39.130 0.00 0.00 0.00 3.85
2910 6151 4.559643 GTCGCCAAAAAGAAAGAAACGAAA 59.440 37.500 0.00 0.00 0.00 3.46
2911 6152 4.796312 TCGCCAAAAAGAAAGAAACGAAAG 59.204 37.500 0.00 0.00 0.00 2.62
2912 6153 4.796312 CGCCAAAAAGAAAGAAACGAAAGA 59.204 37.500 0.00 0.00 0.00 2.52
2913 6154 5.287513 CGCCAAAAAGAAAGAAACGAAAGAA 59.712 36.000 0.00 0.00 0.00 2.52
2914 6155 6.183360 CGCCAAAAAGAAAGAAACGAAAGAAA 60.183 34.615 0.00 0.00 0.00 2.52
2915 6156 7.173419 GCCAAAAAGAAAGAAACGAAAGAAAG 58.827 34.615 0.00 0.00 0.00 2.62
2932 6173 3.583526 AGAAAGGAAGGGACTGACTAACC 59.416 47.826 0.00 0.00 40.86 2.85
2956 6197 4.147219 CAGTCGACTGAAAACCCAATTC 57.853 45.455 36.73 0.00 46.59 2.17
2969 6210 0.965439 CCAATTCGGGCCAGTCAAAA 59.035 50.000 4.39 0.00 0.00 2.44
2970 6211 1.342819 CCAATTCGGGCCAGTCAAAAA 59.657 47.619 4.39 0.00 0.00 1.94
2989 6230 2.097680 AAATTTCCTTTGCATGCGGG 57.902 45.000 14.09 14.78 0.00 6.13
2990 6231 0.391528 AATTTCCTTTGCATGCGGGC 60.392 50.000 14.09 0.00 0.00 6.13
2991 6232 1.259840 ATTTCCTTTGCATGCGGGCT 61.260 50.000 14.09 1.38 34.04 5.19
2992 6233 2.157305 TTTCCTTTGCATGCGGGCTG 62.157 55.000 14.09 0.27 34.04 4.85
2993 6234 4.807039 CCTTTGCATGCGGGCTGC 62.807 66.667 12.43 12.43 46.70 5.25
3002 6243 2.125147 GCGGGCTGCACATAGTCA 60.125 61.111 14.74 0.00 45.45 3.41
3003 6244 1.745115 GCGGGCTGCACATAGTCAA 60.745 57.895 14.74 0.00 45.45 3.18
3004 6245 1.097547 GCGGGCTGCACATAGTCAAT 61.098 55.000 14.74 0.00 45.45 2.57
3005 6246 1.382522 CGGGCTGCACATAGTCAATT 58.617 50.000 1.50 0.00 0.00 2.32
3006 6247 1.745087 CGGGCTGCACATAGTCAATTT 59.255 47.619 1.50 0.00 0.00 1.82
3007 6248 2.223340 CGGGCTGCACATAGTCAATTTC 60.223 50.000 1.50 0.00 0.00 2.17
3008 6249 2.099756 GGGCTGCACATAGTCAATTTCC 59.900 50.000 0.50 0.00 0.00 3.13
3009 6250 3.019564 GGCTGCACATAGTCAATTTCCT 58.980 45.455 0.50 0.00 0.00 3.36
3010 6251 3.065925 GGCTGCACATAGTCAATTTCCTC 59.934 47.826 0.50 0.00 0.00 3.71
3011 6252 3.944015 GCTGCACATAGTCAATTTCCTCT 59.056 43.478 0.00 0.00 0.00 3.69
3012 6253 4.397417 GCTGCACATAGTCAATTTCCTCTT 59.603 41.667 0.00 0.00 0.00 2.85
3013 6254 5.448360 GCTGCACATAGTCAATTTCCTCTTC 60.448 44.000 0.00 0.00 0.00 2.87
3014 6255 4.943705 TGCACATAGTCAATTTCCTCTTCC 59.056 41.667 0.00 0.00 0.00 3.46
3015 6256 4.336713 GCACATAGTCAATTTCCTCTTCCC 59.663 45.833 0.00 0.00 0.00 3.97
3016 6257 4.572389 CACATAGTCAATTTCCTCTTCCCG 59.428 45.833 0.00 0.00 0.00 5.14
3017 6258 2.789409 AGTCAATTTCCTCTTCCCGG 57.211 50.000 0.00 0.00 0.00 5.73
3018 6259 1.282157 AGTCAATTTCCTCTTCCCGGG 59.718 52.381 16.85 16.85 0.00 5.73
3019 6260 0.034477 TCAATTTCCTCTTCCCGGGC 60.034 55.000 18.49 0.00 0.00 6.13
3020 6261 1.037579 CAATTTCCTCTTCCCGGGCC 61.038 60.000 18.49 0.00 0.00 5.80
3021 6262 2.552231 AATTTCCTCTTCCCGGGCCG 62.552 60.000 21.46 21.46 0.00 6.13
3024 6265 4.468689 CCTCTTCCCGGGCCGTTC 62.469 72.222 26.32 0.00 0.00 3.95
3025 6266 3.702048 CTCTTCCCGGGCCGTTCA 61.702 66.667 26.32 4.71 0.00 3.18
3026 6267 3.243053 TCTTCCCGGGCCGTTCAA 61.243 61.111 26.32 12.87 0.00 2.69
3027 6268 2.746277 CTTCCCGGGCCGTTCAAG 60.746 66.667 26.32 18.34 0.00 3.02
3028 6269 4.338710 TTCCCGGGCCGTTCAAGG 62.339 66.667 26.32 18.34 0.00 3.61
3036 6277 2.361610 CCGTTCAAGGGCTGCCAT 60.362 61.111 22.05 11.43 0.00 4.40
3037 6278 2.409870 CCGTTCAAGGGCTGCCATC 61.410 63.158 22.05 3.63 0.00 3.51
3038 6279 1.377725 CGTTCAAGGGCTGCCATCT 60.378 57.895 22.05 6.30 0.00 2.90
3039 6280 1.372087 CGTTCAAGGGCTGCCATCTC 61.372 60.000 22.05 2.38 0.00 2.75
3040 6281 1.034292 GTTCAAGGGCTGCCATCTCC 61.034 60.000 22.05 1.96 0.00 3.71
3041 6282 2.123982 CAAGGGCTGCCATCTCCC 60.124 66.667 22.05 1.14 40.36 4.30
3042 6283 3.424105 AAGGGCTGCCATCTCCCC 61.424 66.667 22.05 0.33 40.97 4.81
3043 6284 4.444957 AGGGCTGCCATCTCCCCT 62.445 66.667 22.05 3.04 42.99 4.79
3044 6285 4.201122 GGGCTGCCATCTCCCCTG 62.201 72.222 22.05 0.00 34.59 4.45
3045 6286 4.891037 GGCTGCCATCTCCCCTGC 62.891 72.222 15.17 0.00 0.00 4.85
3046 6287 4.891037 GCTGCCATCTCCCCTGCC 62.891 72.222 0.00 0.00 0.00 4.85
3047 6288 3.095163 CTGCCATCTCCCCTGCCT 61.095 66.667 0.00 0.00 0.00 4.75
3048 6289 2.614969 TGCCATCTCCCCTGCCTT 60.615 61.111 0.00 0.00 0.00 4.35
3049 6290 2.123982 GCCATCTCCCCTGCCTTG 60.124 66.667 0.00 0.00 0.00 3.61
3050 6291 2.599597 CCATCTCCCCTGCCTTGG 59.400 66.667 0.00 0.00 0.00 3.61
3051 6292 2.123982 CATCTCCCCTGCCTTGGC 60.124 66.667 4.43 4.43 0.00 4.52
3052 6293 2.614969 ATCTCCCCTGCCTTGGCA 60.615 61.111 14.10 14.10 0.00 4.92
3053 6294 2.240918 ATCTCCCCTGCCTTGGCAA 61.241 57.895 15.63 0.00 0.00 4.52
3054 6295 2.220786 ATCTCCCCTGCCTTGGCAAG 62.221 60.000 20.31 20.31 0.00 4.01
3068 6309 3.297620 CAAGGCCGCCACAAAGCT 61.298 61.111 13.15 0.00 0.00 3.74
3069 6310 3.297620 AAGGCCGCCACAAAGCTG 61.298 61.111 13.15 0.00 0.00 4.24
3072 6313 4.712425 GCCGCCACAAAGCTGCTG 62.712 66.667 1.35 0.00 39.59 4.41
3073 6314 4.712425 CCGCCACAAAGCTGCTGC 62.712 66.667 1.35 7.62 40.05 5.25
3084 6325 2.667536 CTGCTGCTGCTGACCGTT 60.668 61.111 17.00 0.00 40.01 4.44
3085 6326 1.374631 CTGCTGCTGCTGACCGTTA 60.375 57.895 17.00 0.00 40.01 3.18
3086 6327 1.357258 CTGCTGCTGCTGACCGTTAG 61.357 60.000 17.00 0.00 40.01 2.34
3087 6328 1.374758 GCTGCTGCTGACCGTTAGT 60.375 57.895 10.92 0.00 36.03 2.24
3088 6329 1.355066 GCTGCTGCTGACCGTTAGTC 61.355 60.000 10.92 0.00 46.51 2.59
3097 6338 2.825861 GACCGTTAGTCAGTCCCAAA 57.174 50.000 0.00 0.00 45.55 3.28
3098 6339 3.116079 GACCGTTAGTCAGTCCCAAAA 57.884 47.619 0.00 0.00 45.55 2.44
3099 6340 3.469739 GACCGTTAGTCAGTCCCAAAAA 58.530 45.455 0.00 0.00 45.55 1.94
3100 6341 4.070009 GACCGTTAGTCAGTCCCAAAAAT 58.930 43.478 0.00 0.00 45.55 1.82
3101 6342 4.070009 ACCGTTAGTCAGTCCCAAAAATC 58.930 43.478 0.00 0.00 0.00 2.17
3102 6343 4.202430 ACCGTTAGTCAGTCCCAAAAATCT 60.202 41.667 0.00 0.00 0.00 2.40
3103 6344 4.154195 CCGTTAGTCAGTCCCAAAAATCTG 59.846 45.833 0.00 0.00 0.00 2.90
3104 6345 4.378459 CGTTAGTCAGTCCCAAAAATCTGC 60.378 45.833 0.00 0.00 0.00 4.26
3105 6346 3.515602 AGTCAGTCCCAAAAATCTGCT 57.484 42.857 0.00 0.00 0.00 4.24
3106 6347 3.152341 AGTCAGTCCCAAAAATCTGCTG 58.848 45.455 0.00 0.00 0.00 4.41
3107 6348 1.888512 TCAGTCCCAAAAATCTGCTGC 59.111 47.619 0.00 0.00 0.00 5.25
3108 6349 1.891150 CAGTCCCAAAAATCTGCTGCT 59.109 47.619 0.00 0.00 0.00 4.24
3109 6350 1.891150 AGTCCCAAAAATCTGCTGCTG 59.109 47.619 0.00 0.00 0.00 4.41
3110 6351 0.604578 TCCCAAAAATCTGCTGCTGC 59.395 50.000 8.89 8.89 40.20 5.25
3111 6352 0.390735 CCCAAAAATCTGCTGCTGCC 60.391 55.000 13.47 0.00 38.71 4.85
3112 6353 0.734942 CCAAAAATCTGCTGCTGCCG 60.735 55.000 13.47 6.90 38.71 5.69
3113 6354 0.241749 CAAAAATCTGCTGCTGCCGA 59.758 50.000 13.47 12.60 38.71 5.54
3114 6355 0.242017 AAAAATCTGCTGCTGCCGAC 59.758 50.000 13.47 0.00 35.36 4.79
3115 6356 0.607489 AAAATCTGCTGCTGCCGACT 60.607 50.000 13.47 0.00 35.36 4.18
3116 6357 0.607489 AAATCTGCTGCTGCCGACTT 60.607 50.000 13.47 5.49 35.36 3.01
3117 6358 0.607489 AATCTGCTGCTGCCGACTTT 60.607 50.000 13.47 1.84 35.36 2.66
3118 6359 0.607489 ATCTGCTGCTGCCGACTTTT 60.607 50.000 13.47 0.00 35.36 2.27
3119 6360 0.819259 TCTGCTGCTGCCGACTTTTT 60.819 50.000 13.47 0.00 38.71 1.94
3120 6361 0.662374 CTGCTGCTGCCGACTTTTTG 60.662 55.000 13.47 0.00 38.71 2.44
3121 6362 1.372128 GCTGCTGCCGACTTTTTGG 60.372 57.895 3.85 0.00 0.00 3.28
3126 6367 2.650778 GCCGACTTTTTGGCCCAG 59.349 61.111 0.00 0.00 45.93 4.45
3127 6368 2.650778 CCGACTTTTTGGCCCAGC 59.349 61.111 0.00 0.00 0.00 4.85
3128 6369 2.255252 CGACTTTTTGGCCCAGCG 59.745 61.111 0.00 0.00 0.00 5.18
3129 6370 2.258013 CGACTTTTTGGCCCAGCGA 61.258 57.895 0.00 0.00 0.00 4.93
3130 6371 1.791103 CGACTTTTTGGCCCAGCGAA 61.791 55.000 0.00 0.00 0.00 4.70
3131 6372 0.039165 GACTTTTTGGCCCAGCGAAG 60.039 55.000 0.00 0.00 0.00 3.79
3132 6373 0.755327 ACTTTTTGGCCCAGCGAAGT 60.755 50.000 0.00 0.51 0.00 3.01
3133 6374 1.243902 CTTTTTGGCCCAGCGAAGTA 58.756 50.000 0.00 0.00 0.00 2.24
3134 6375 1.818674 CTTTTTGGCCCAGCGAAGTAT 59.181 47.619 0.00 0.00 0.00 2.12
3135 6376 1.917872 TTTTGGCCCAGCGAAGTATT 58.082 45.000 0.00 0.00 0.00 1.89
3136 6377 1.917872 TTTGGCCCAGCGAAGTATTT 58.082 45.000 0.00 0.00 0.00 1.40
3137 6378 1.917872 TTGGCCCAGCGAAGTATTTT 58.082 45.000 0.00 0.00 0.00 1.82
3138 6379 1.917872 TGGCCCAGCGAAGTATTTTT 58.082 45.000 0.00 0.00 0.00 1.94
3163 6404 2.256117 AAAAAGTCGGCAGTAGCAGT 57.744 45.000 0.00 0.00 44.61 4.40
3164 6405 3.396260 AAAAAGTCGGCAGTAGCAGTA 57.604 42.857 0.00 0.00 44.61 2.74
3165 6406 3.611766 AAAAGTCGGCAGTAGCAGTAT 57.388 42.857 0.00 0.00 44.61 2.12
3166 6407 3.611766 AAAGTCGGCAGTAGCAGTATT 57.388 42.857 0.00 0.00 44.61 1.89
3167 6408 3.611766 AAGTCGGCAGTAGCAGTATTT 57.388 42.857 0.00 0.00 44.61 1.40
3168 6409 3.611766 AGTCGGCAGTAGCAGTATTTT 57.388 42.857 0.00 0.00 44.61 1.82
3169 6410 3.262420 AGTCGGCAGTAGCAGTATTTTG 58.738 45.455 0.00 0.00 44.61 2.44
3170 6411 2.351726 GTCGGCAGTAGCAGTATTTTGG 59.648 50.000 0.00 0.00 44.61 3.28
3171 6412 2.235155 TCGGCAGTAGCAGTATTTTGGA 59.765 45.455 0.00 0.00 44.61 3.53
3172 6413 3.006940 CGGCAGTAGCAGTATTTTGGAA 58.993 45.455 0.00 0.00 44.61 3.53
3173 6414 3.181510 CGGCAGTAGCAGTATTTTGGAAC 60.182 47.826 0.00 0.00 44.61 3.62
3174 6415 3.181510 GGCAGTAGCAGTATTTTGGAACG 60.182 47.826 0.00 0.00 44.61 3.95
3175 6416 3.682858 GCAGTAGCAGTATTTTGGAACGA 59.317 43.478 0.00 0.00 41.58 3.85
3176 6417 4.153475 GCAGTAGCAGTATTTTGGAACGAA 59.847 41.667 0.00 0.00 41.58 3.85
3177 6418 5.671329 GCAGTAGCAGTATTTTGGAACGAAG 60.671 44.000 0.00 0.00 41.58 3.79
3178 6419 4.935808 AGTAGCAGTATTTTGGAACGAAGG 59.064 41.667 0.00 0.00 0.00 3.46
3179 6420 3.081804 AGCAGTATTTTGGAACGAAGGG 58.918 45.455 0.00 0.00 0.00 3.95
3180 6421 3.078837 GCAGTATTTTGGAACGAAGGGA 58.921 45.455 0.00 0.00 0.00 4.20
3181 6422 3.127030 GCAGTATTTTGGAACGAAGGGAG 59.873 47.826 0.00 0.00 0.00 4.30
3182 6423 3.689649 CAGTATTTTGGAACGAAGGGAGG 59.310 47.826 0.00 0.00 0.00 4.30
3183 6424 3.585732 AGTATTTTGGAACGAAGGGAGGA 59.414 43.478 0.00 0.00 0.00 3.71
3184 6425 2.265589 TTTTGGAACGAAGGGAGGAC 57.734 50.000 0.00 0.00 0.00 3.85
3185 6426 0.034337 TTTGGAACGAAGGGAGGACG 59.966 55.000 0.00 0.00 0.00 4.79
3186 6427 0.828762 TTGGAACGAAGGGAGGACGA 60.829 55.000 0.00 0.00 0.00 4.20
3187 6428 0.828762 TGGAACGAAGGGAGGACGAA 60.829 55.000 0.00 0.00 0.00 3.85
3188 6429 0.319405 GGAACGAAGGGAGGACGAAA 59.681 55.000 0.00 0.00 0.00 3.46
3189 6430 1.066358 GGAACGAAGGGAGGACGAAAT 60.066 52.381 0.00 0.00 0.00 2.17
3190 6431 2.614734 GGAACGAAGGGAGGACGAAATT 60.615 50.000 0.00 0.00 0.00 1.82
3191 6432 3.368739 GGAACGAAGGGAGGACGAAATTA 60.369 47.826 0.00 0.00 0.00 1.40
3192 6433 3.967332 ACGAAGGGAGGACGAAATTAA 57.033 42.857 0.00 0.00 0.00 1.40
3193 6434 4.276058 ACGAAGGGAGGACGAAATTAAA 57.724 40.909 0.00 0.00 0.00 1.52
3194 6435 3.999001 ACGAAGGGAGGACGAAATTAAAC 59.001 43.478 0.00 0.00 0.00 2.01
3195 6436 3.373130 CGAAGGGAGGACGAAATTAAACC 59.627 47.826 0.00 0.00 0.00 3.27
3196 6437 4.329392 GAAGGGAGGACGAAATTAAACCA 58.671 43.478 0.00 0.00 0.00 3.67
3197 6438 3.951663 AGGGAGGACGAAATTAAACCAG 58.048 45.455 0.00 0.00 0.00 4.00
3198 6439 2.422479 GGGAGGACGAAATTAAACCAGC 59.578 50.000 0.00 0.00 0.00 4.85
3199 6440 2.095372 GGAGGACGAAATTAAACCAGCG 59.905 50.000 0.00 0.00 0.00 5.18
3200 6441 2.997986 GAGGACGAAATTAAACCAGCGA 59.002 45.455 0.00 0.00 0.00 4.93
3201 6442 3.404899 AGGACGAAATTAAACCAGCGAA 58.595 40.909 0.00 0.00 0.00 4.70
3202 6443 3.816523 AGGACGAAATTAAACCAGCGAAA 59.183 39.130 0.00 0.00 0.00 3.46
3203 6444 4.276431 AGGACGAAATTAAACCAGCGAAAA 59.724 37.500 0.00 0.00 0.00 2.29
3204 6445 4.977347 GGACGAAATTAAACCAGCGAAAAA 59.023 37.500 0.00 0.00 0.00 1.94
3205 6446 5.631929 GGACGAAATTAAACCAGCGAAAAAT 59.368 36.000 0.00 0.00 0.00 1.82
3206 6447 6.399564 GGACGAAATTAAACCAGCGAAAAATG 60.400 38.462 0.00 0.00 0.00 2.32
3207 6448 5.980715 ACGAAATTAAACCAGCGAAAAATGT 59.019 32.000 0.00 0.00 0.00 2.71
3208 6449 6.477360 ACGAAATTAAACCAGCGAAAAATGTT 59.523 30.769 0.00 0.00 0.00 2.71
3209 6450 7.001347 CGAAATTAAACCAGCGAAAAATGTTC 58.999 34.615 0.00 0.00 0.00 3.18
3210 6451 6.779115 AATTAAACCAGCGAAAAATGTTCC 57.221 33.333 0.00 0.00 0.00 3.62
3211 6452 3.810310 AAACCAGCGAAAAATGTTCCA 57.190 38.095 0.00 0.00 0.00 3.53
3212 6453 2.793278 ACCAGCGAAAAATGTTCCAC 57.207 45.000 0.00 0.00 0.00 4.02
3213 6454 2.306847 ACCAGCGAAAAATGTTCCACT 58.693 42.857 0.00 0.00 0.00 4.00
3214 6455 3.482436 ACCAGCGAAAAATGTTCCACTA 58.518 40.909 0.00 0.00 0.00 2.74
3215 6456 3.252458 ACCAGCGAAAAATGTTCCACTAC 59.748 43.478 0.00 0.00 0.00 2.73
3216 6457 3.502211 CCAGCGAAAAATGTTCCACTACT 59.498 43.478 0.00 0.00 0.00 2.57
3217 6458 4.378459 CCAGCGAAAAATGTTCCACTACTC 60.378 45.833 0.00 0.00 0.00 2.59
3218 6459 3.432252 AGCGAAAAATGTTCCACTACTCG 59.568 43.478 0.00 0.00 0.00 4.18
3219 6460 3.732943 CGAAAAATGTTCCACTACTCGC 58.267 45.455 0.00 0.00 0.00 5.03
3220 6461 3.185594 CGAAAAATGTTCCACTACTCGCA 59.814 43.478 0.00 0.00 0.00 5.10
3253 6494 1.380403 CGCTGTCGTCTCCCTCAGAT 61.380 60.000 0.00 0.00 32.08 2.90
3260 6501 1.002662 TCTCCCTCAGATGCAGCCT 59.997 57.895 0.00 0.00 0.00 4.58
3344 6585 4.598894 CTGCGGCGATGGAGGGAG 62.599 72.222 12.98 0.00 0.00 4.30
3389 6630 4.585526 GATGGACGCGCCGGATCA 62.586 66.667 5.05 0.00 40.66 2.92
3399 6640 2.861101 GCCGGATCATCGCTCCTCA 61.861 63.158 5.05 0.00 0.00 3.86
3521 6762 4.379243 CGCGGTGTGCTTCCCTCT 62.379 66.667 0.00 0.00 43.27 3.69
3553 6794 0.691078 TCCTCTCCCTCCCCAAATCG 60.691 60.000 0.00 0.00 0.00 3.34
3597 6838 1.075600 CCTCCTCTCCCTCCCTGAC 60.076 68.421 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 7.010091 CACGGCTCAAAAAGACTAAAAACAAAT 59.990 33.333 0.00 0.00 0.00 2.32
42 43 6.309251 CACGGCTCAAAAAGACTAAAAACAAA 59.691 34.615 0.00 0.00 0.00 2.83
45 46 4.206404 GCACGGCTCAAAAAGACTAAAAAC 59.794 41.667 0.00 0.00 0.00 2.43
52 54 0.040067 CCTGCACGGCTCAAAAAGAC 60.040 55.000 0.00 0.00 0.00 3.01
203 208 4.772231 TTCCTCCCGCGGGTAGCT 62.772 66.667 41.57 0.00 45.59 3.32
383 955 4.515191 GGCGCTTCAGTGGATTATCATTAA 59.485 41.667 7.64 0.00 0.00 1.40
384 956 4.065088 GGCGCTTCAGTGGATTATCATTA 58.935 43.478 7.64 0.00 0.00 1.90
388 960 1.953559 TGGCGCTTCAGTGGATTATC 58.046 50.000 7.64 0.00 0.00 1.75
441 1041 3.009723 CAGGTTCAACATTACCATCGCT 58.990 45.455 0.00 0.00 36.87 4.93
450 1050 8.421249 TTGAATCTTAATCCAGGTTCAACATT 57.579 30.769 5.24 0.00 45.15 2.71
509 1109 4.675114 CGAAGGAAACAAATGAAAACCTCG 59.325 41.667 0.00 0.00 0.00 4.63
550 1150 5.054477 TCCTTTGAACAACGAAGACCTTAG 58.946 41.667 0.00 0.00 41.25 2.18
551 1151 5.026038 TCCTTTGAACAACGAAGACCTTA 57.974 39.130 0.00 0.00 41.25 2.69
552 1152 3.881220 TCCTTTGAACAACGAAGACCTT 58.119 40.909 0.00 0.00 41.25 3.50
576 1176 9.841295 TTCCAATTCCTATGTATTTACTACACC 57.159 33.333 0.00 0.00 43.01 4.16
609 1209 6.147164 ACATGTTATGTCACTTCACGGTTAAG 59.853 38.462 0.00 0.65 39.92 1.85
612 1212 4.385825 ACATGTTATGTCACTTCACGGTT 58.614 39.130 0.00 0.00 39.92 4.44
613 1213 4.002906 ACATGTTATGTCACTTCACGGT 57.997 40.909 0.00 0.00 39.92 4.83
614 1214 5.867174 TCTTACATGTTATGTCACTTCACGG 59.133 40.000 2.30 0.00 43.67 4.94
677 1918 8.132362 AGACTTGTCTGAGTTCGATGTTATATC 58.868 37.037 2.11 0.00 0.00 1.63
686 3737 3.215151 ACTGAGACTTGTCTGAGTTCGA 58.785 45.455 15.25 0.00 30.12 3.71
691 3742 2.095466 GGTCGACTGAGACTTGTCTGAG 60.095 54.545 16.46 14.07 40.76 3.35
692 3743 1.880675 GGTCGACTGAGACTTGTCTGA 59.119 52.381 16.46 0.00 40.76 3.27
693 3744 1.609072 TGGTCGACTGAGACTTGTCTG 59.391 52.381 16.46 0.00 40.76 3.51
694 3745 1.982660 TGGTCGACTGAGACTTGTCT 58.017 50.000 16.46 2.59 40.76 3.41
695 3746 2.795175 TTGGTCGACTGAGACTTGTC 57.205 50.000 16.46 0.00 40.76 3.18
697 3748 3.032017 ACATTGGTCGACTGAGACTTG 57.968 47.619 16.46 6.58 40.76 3.16
698 3749 3.753294 AACATTGGTCGACTGAGACTT 57.247 42.857 16.46 0.00 40.76 3.01
700 3751 2.480419 CCAAACATTGGTCGACTGAGAC 59.520 50.000 16.46 0.00 45.93 3.36
712 3763 6.042143 AGTAAAACAGTCTTGCCAAACATTG 58.958 36.000 0.00 0.00 0.00 2.82
713 3764 6.220726 AGTAAAACAGTCTTGCCAAACATT 57.779 33.333 0.00 0.00 0.00 2.71
714 3765 5.852282 AGTAAAACAGTCTTGCCAAACAT 57.148 34.783 0.00 0.00 0.00 2.71
715 3766 6.376018 AGTTAGTAAAACAGTCTTGCCAAACA 59.624 34.615 0.00 0.00 0.00 2.83
719 3770 5.925509 AGAGTTAGTAAAACAGTCTTGCCA 58.074 37.500 0.00 0.00 0.00 4.92
723 3774 7.226918 GCTTGGAAGAGTTAGTAAAACAGTCTT 59.773 37.037 0.00 0.00 0.00 3.01
777 3829 4.520179 TGTCTGTGCTGCTCATCATTATT 58.480 39.130 4.73 0.00 0.00 1.40
778 3830 4.127907 CTGTCTGTGCTGCTCATCATTAT 58.872 43.478 4.73 0.00 0.00 1.28
779 3831 3.528532 CTGTCTGTGCTGCTCATCATTA 58.471 45.455 4.73 0.00 0.00 1.90
831 3884 6.102897 TCCAATATTCCCGCAAAAGAAAAA 57.897 33.333 0.00 0.00 0.00 1.94
832 3885 5.730296 TCCAATATTCCCGCAAAAGAAAA 57.270 34.783 0.00 0.00 0.00 2.29
833 3886 5.656416 AGATCCAATATTCCCGCAAAAGAAA 59.344 36.000 0.00 0.00 0.00 2.52
834 3887 5.200483 AGATCCAATATTCCCGCAAAAGAA 58.800 37.500 0.00 0.00 0.00 2.52
835 3888 4.792068 AGATCCAATATTCCCGCAAAAGA 58.208 39.130 0.00 0.00 0.00 2.52
836 3889 5.765182 AGTAGATCCAATATTCCCGCAAAAG 59.235 40.000 0.00 0.00 0.00 2.27
837 3890 5.690865 AGTAGATCCAATATTCCCGCAAAA 58.309 37.500 0.00 0.00 0.00 2.44
838 3891 5.071788 AGAGTAGATCCAATATTCCCGCAAA 59.928 40.000 0.00 0.00 0.00 3.68
839 3892 4.593206 AGAGTAGATCCAATATTCCCGCAA 59.407 41.667 0.00 0.00 0.00 4.85
840 3893 4.160329 AGAGTAGATCCAATATTCCCGCA 58.840 43.478 0.00 0.00 0.00 5.69
841 3894 4.810191 AGAGTAGATCCAATATTCCCGC 57.190 45.455 0.00 0.00 0.00 6.13
842 3895 5.246203 TCCAAGAGTAGATCCAATATTCCCG 59.754 44.000 0.00 0.00 0.00 5.14
843 3896 6.688073 TCCAAGAGTAGATCCAATATTCCC 57.312 41.667 0.00 0.00 0.00 3.97
844 3897 8.040132 CAGATCCAAGAGTAGATCCAATATTCC 58.960 40.741 0.00 0.00 39.83 3.01
845 3898 7.548780 GCAGATCCAAGAGTAGATCCAATATTC 59.451 40.741 0.00 0.00 39.83 1.75
846 3899 7.393216 GCAGATCCAAGAGTAGATCCAATATT 58.607 38.462 0.00 0.00 39.83 1.28
847 3900 6.070309 GGCAGATCCAAGAGTAGATCCAATAT 60.070 42.308 0.00 0.00 39.83 1.28
905 3958 7.068470 TGGATTGATATTTATGCAAAGCTGTCA 59.932 33.333 0.00 0.00 0.00 3.58
968 4027 4.165779 AGTGCTTGTTTTGTTTTGTCGAG 58.834 39.130 0.00 0.00 0.00 4.04
969 4028 4.167554 AGTGCTTGTTTTGTTTTGTCGA 57.832 36.364 0.00 0.00 0.00 4.20
970 4029 5.328691 TCTAGTGCTTGTTTTGTTTTGTCG 58.671 37.500 0.00 0.00 0.00 4.35
971 4030 7.612266 CAATCTAGTGCTTGTTTTGTTTTGTC 58.388 34.615 0.00 0.00 0.00 3.18
972 4031 6.035975 GCAATCTAGTGCTTGTTTTGTTTTGT 59.964 34.615 0.00 0.00 41.51 2.83
973 4032 6.413269 GCAATCTAGTGCTTGTTTTGTTTTG 58.587 36.000 0.00 0.00 41.51 2.44
1015 4074 1.382692 GCTCCAGCAGCTTCCATTCC 61.383 60.000 0.00 0.00 45.83 3.01
1016 4075 2.105124 GCTCCAGCAGCTTCCATTC 58.895 57.895 0.00 0.00 45.83 2.67
1017 4076 4.333417 GCTCCAGCAGCTTCCATT 57.667 55.556 0.00 0.00 45.83 3.16
1159 4218 1.827789 GCTGTTTCACCTGTGCCCA 60.828 57.895 0.00 0.00 0.00 5.36
1290 4353 1.346365 CGTTACGTGGACCTGTGATG 58.654 55.000 0.00 0.00 0.00 3.07
1470 4533 0.459237 CCTCGTACTGCCTCAGCTTG 60.459 60.000 0.00 0.00 40.80 4.01
1575 4641 1.374252 CACCACGTACCTGCACTCC 60.374 63.158 0.00 0.00 0.00 3.85
1620 4707 2.755876 ACGAGGCTGAGCATCCGA 60.756 61.111 13.90 0.00 35.86 4.55
1818 4926 1.771044 GTAGCGGACGACGTTGTTG 59.229 57.895 10.42 7.30 46.52 3.33
1873 5017 0.962356 AGGTGGAGGTACACGTACGG 60.962 60.000 21.06 11.05 42.23 4.02
2034 5220 2.825836 GGGAACATGCGCTCCAGG 60.826 66.667 14.61 0.00 32.95 4.45
2304 5502 4.347453 GCCTTGGCCGTGCTGTTG 62.347 66.667 0.00 0.00 0.00 3.33
2337 5559 2.203153 AACGACACCACCAGCACC 60.203 61.111 0.00 0.00 0.00 5.01
2701 5926 4.933064 CGGGTCGAGATCCTGCGC 62.933 72.222 0.00 0.00 0.00 6.09
2757 5997 0.917259 CGAGCTTGAGACCGAAATCG 59.083 55.000 0.00 0.00 39.44 3.34
2793 6033 3.385469 TCTGTGCAGAGAGCCAGG 58.615 61.111 9.94 0.00 44.83 4.45
2881 6122 0.856641 TTCTTTTTGGCGACGACGAG 59.143 50.000 12.29 0.00 42.66 4.18
2906 6147 3.067833 GTCAGTCCCTTCCTTTCTTTCG 58.932 50.000 0.00 0.00 0.00 3.46
2907 6148 4.359434 AGTCAGTCCCTTCCTTTCTTTC 57.641 45.455 0.00 0.00 0.00 2.62
2908 6149 5.456330 GGTTAGTCAGTCCCTTCCTTTCTTT 60.456 44.000 0.00 0.00 0.00 2.52
2909 6150 4.041815 GGTTAGTCAGTCCCTTCCTTTCTT 59.958 45.833 0.00 0.00 0.00 2.52
2910 6151 3.583526 GGTTAGTCAGTCCCTTCCTTTCT 59.416 47.826 0.00 0.00 0.00 2.52
2911 6152 3.616802 CGGTTAGTCAGTCCCTTCCTTTC 60.617 52.174 0.00 0.00 0.00 2.62
2912 6153 2.302157 CGGTTAGTCAGTCCCTTCCTTT 59.698 50.000 0.00 0.00 0.00 3.11
2913 6154 1.900486 CGGTTAGTCAGTCCCTTCCTT 59.100 52.381 0.00 0.00 0.00 3.36
2914 6155 1.203149 ACGGTTAGTCAGTCCCTTCCT 60.203 52.381 0.00 0.00 0.00 3.36
2915 6156 1.264295 ACGGTTAGTCAGTCCCTTCC 58.736 55.000 0.00 0.00 0.00 3.46
2939 6180 2.611974 CCGAATTGGGTTTTCAGTCG 57.388 50.000 0.00 0.00 0.00 4.18
2969 6210 2.425539 CCCGCATGCAAAGGAAATTTT 58.574 42.857 19.57 0.00 0.00 1.82
2970 6211 1.945355 GCCCGCATGCAAAGGAAATTT 60.945 47.619 19.57 0.00 0.00 1.82
2971 6212 0.391528 GCCCGCATGCAAAGGAAATT 60.392 50.000 19.57 0.00 0.00 1.82
2972 6213 1.218854 GCCCGCATGCAAAGGAAAT 59.781 52.632 19.57 0.00 0.00 2.17
2973 6214 1.907807 AGCCCGCATGCAAAGGAAA 60.908 52.632 19.57 0.00 0.00 3.13
2974 6215 2.283101 AGCCCGCATGCAAAGGAA 60.283 55.556 19.57 0.00 0.00 3.36
2975 6216 3.063704 CAGCCCGCATGCAAAGGA 61.064 61.111 19.57 0.00 0.00 3.36
2976 6217 4.807039 GCAGCCCGCATGCAAAGG 62.807 66.667 19.57 15.77 43.31 3.11
2985 6226 1.097547 ATTGACTATGTGCAGCCCGC 61.098 55.000 0.00 0.00 42.89 6.13
2986 6227 1.382522 AATTGACTATGTGCAGCCCG 58.617 50.000 0.00 0.00 0.00 6.13
2987 6228 2.099756 GGAAATTGACTATGTGCAGCCC 59.900 50.000 0.00 0.00 0.00 5.19
2988 6229 3.019564 AGGAAATTGACTATGTGCAGCC 58.980 45.455 0.00 0.00 0.00 4.85
2989 6230 3.944015 AGAGGAAATTGACTATGTGCAGC 59.056 43.478 0.00 0.00 0.00 5.25
2990 6231 5.065731 GGAAGAGGAAATTGACTATGTGCAG 59.934 44.000 0.00 0.00 0.00 4.41
2991 6232 4.943705 GGAAGAGGAAATTGACTATGTGCA 59.056 41.667 0.00 0.00 0.00 4.57
2992 6233 4.336713 GGGAAGAGGAAATTGACTATGTGC 59.663 45.833 0.00 0.00 0.00 4.57
2993 6234 4.572389 CGGGAAGAGGAAATTGACTATGTG 59.428 45.833 0.00 0.00 0.00 3.21
2994 6235 4.384208 CCGGGAAGAGGAAATTGACTATGT 60.384 45.833 0.00 0.00 0.00 2.29
2995 6236 4.130118 CCGGGAAGAGGAAATTGACTATG 58.870 47.826 0.00 0.00 0.00 2.23
2996 6237 3.136626 CCCGGGAAGAGGAAATTGACTAT 59.863 47.826 18.48 0.00 0.00 2.12
2997 6238 2.504175 CCCGGGAAGAGGAAATTGACTA 59.496 50.000 18.48 0.00 0.00 2.59
2998 6239 1.282157 CCCGGGAAGAGGAAATTGACT 59.718 52.381 18.48 0.00 0.00 3.41
2999 6240 1.751437 CCCGGGAAGAGGAAATTGAC 58.249 55.000 18.48 0.00 0.00 3.18
3000 6241 0.034477 GCCCGGGAAGAGGAAATTGA 60.034 55.000 29.31 0.00 0.00 2.57
3001 6242 1.037579 GGCCCGGGAAGAGGAAATTG 61.038 60.000 29.31 0.00 0.00 2.32
3002 6243 1.306633 GGCCCGGGAAGAGGAAATT 59.693 57.895 29.31 0.00 0.00 1.82
3003 6244 3.007542 GGCCCGGGAAGAGGAAAT 58.992 61.111 29.31 0.00 0.00 2.17
3004 6245 3.712907 CGGCCCGGGAAGAGGAAA 61.713 66.667 29.31 0.00 0.00 3.13
3007 6248 4.468689 GAACGGCCCGGGAAGAGG 62.469 72.222 29.31 10.05 0.00 3.69
3008 6249 3.248446 TTGAACGGCCCGGGAAGAG 62.248 63.158 29.31 14.21 0.00 2.85
3009 6250 3.243053 TTGAACGGCCCGGGAAGA 61.243 61.111 29.31 0.00 0.00 2.87
3010 6251 2.746277 CTTGAACGGCCCGGGAAG 60.746 66.667 29.31 19.96 0.00 3.46
3011 6252 4.338710 CCTTGAACGGCCCGGGAA 62.339 66.667 29.31 7.38 0.00 3.97
3019 6260 2.361610 ATGGCAGCCCTTGAACGG 60.362 61.111 9.64 0.00 0.00 4.44
3020 6261 1.372087 GAGATGGCAGCCCTTGAACG 61.372 60.000 9.64 0.00 0.00 3.95
3021 6262 1.034292 GGAGATGGCAGCCCTTGAAC 61.034 60.000 9.64 0.00 0.00 3.18
3022 6263 1.304282 GGAGATGGCAGCCCTTGAA 59.696 57.895 9.64 0.00 0.00 2.69
3023 6264 2.683465 GGGAGATGGCAGCCCTTGA 61.683 63.158 9.64 0.00 38.85 3.02
3024 6265 2.123982 GGGAGATGGCAGCCCTTG 60.124 66.667 9.64 0.00 38.85 3.61
3025 6266 3.424105 GGGGAGATGGCAGCCCTT 61.424 66.667 18.67 0.00 41.72 3.95
3026 6267 4.444957 AGGGGAGATGGCAGCCCT 62.445 66.667 18.67 0.00 41.72 5.19
3027 6268 4.201122 CAGGGGAGATGGCAGCCC 62.201 72.222 9.64 12.94 41.28 5.19
3028 6269 4.891037 GCAGGGGAGATGGCAGCC 62.891 72.222 3.66 3.66 0.00 4.85
3029 6270 4.891037 GGCAGGGGAGATGGCAGC 62.891 72.222 0.00 0.00 42.45 5.25
3030 6271 2.687610 AAGGCAGGGGAGATGGCAG 61.688 63.158 0.00 0.00 45.14 4.85
3031 6272 2.614969 AAGGCAGGGGAGATGGCA 60.615 61.111 0.00 0.00 45.14 4.92
3032 6273 2.123982 CAAGGCAGGGGAGATGGC 60.124 66.667 0.00 0.00 43.18 4.40
3033 6274 2.599597 CCAAGGCAGGGGAGATGG 59.400 66.667 0.00 0.00 0.00 3.51
3034 6275 2.123982 GCCAAGGCAGGGGAGATG 60.124 66.667 6.14 0.00 41.49 2.90
3051 6292 3.297620 AGCTTTGTGGCGGCCTTG 61.298 61.111 21.46 6.74 37.29 3.61
3052 6293 3.297620 CAGCTTTGTGGCGGCCTT 61.298 61.111 21.46 0.00 37.29 4.35
3056 6297 4.712425 GCAGCAGCTTTGTGGCGG 62.712 66.667 0.00 0.00 37.91 6.13
3067 6308 1.357258 CTAACGGTCAGCAGCAGCAG 61.357 60.000 3.17 0.00 45.49 4.24
3068 6309 1.374631 CTAACGGTCAGCAGCAGCA 60.375 57.895 3.17 0.00 45.49 4.41
3069 6310 1.355066 GACTAACGGTCAGCAGCAGC 61.355 60.000 0.00 0.00 43.94 5.25
3070 6311 2.743195 GACTAACGGTCAGCAGCAG 58.257 57.895 0.00 0.00 43.94 4.24
3071 6312 4.988065 GACTAACGGTCAGCAGCA 57.012 55.556 0.00 0.00 43.94 4.41
3079 6320 3.564053 TTTTTGGGACTGACTAACGGT 57.436 42.857 0.00 0.00 41.27 4.83
3080 6321 4.154195 CAGATTTTTGGGACTGACTAACGG 59.846 45.833 0.00 0.00 32.90 4.44
3081 6322 4.378459 GCAGATTTTTGGGACTGACTAACG 60.378 45.833 0.00 0.00 32.90 3.18
3082 6323 4.762251 AGCAGATTTTTGGGACTGACTAAC 59.238 41.667 0.00 0.00 32.90 2.34
3083 6324 4.761739 CAGCAGATTTTTGGGACTGACTAA 59.238 41.667 0.00 0.00 32.90 2.24
3084 6325 4.326826 CAGCAGATTTTTGGGACTGACTA 58.673 43.478 0.00 0.00 32.90 2.59
3085 6326 3.152341 CAGCAGATTTTTGGGACTGACT 58.848 45.455 0.00 0.00 32.90 3.41
3086 6327 2.352127 GCAGCAGATTTTTGGGACTGAC 60.352 50.000 0.00 0.00 32.90 3.51
3087 6328 1.888512 GCAGCAGATTTTTGGGACTGA 59.111 47.619 0.00 0.00 32.90 3.41
3088 6329 1.891150 AGCAGCAGATTTTTGGGACTG 59.109 47.619 0.00 0.00 0.00 3.51
3089 6330 1.891150 CAGCAGCAGATTTTTGGGACT 59.109 47.619 0.00 0.00 0.00 3.85
3090 6331 1.670967 GCAGCAGCAGATTTTTGGGAC 60.671 52.381 0.00 0.00 41.58 4.46
3091 6332 0.604578 GCAGCAGCAGATTTTTGGGA 59.395 50.000 0.00 0.00 41.58 4.37
3092 6333 0.390735 GGCAGCAGCAGATTTTTGGG 60.391 55.000 2.65 0.00 44.61 4.12
3093 6334 0.734942 CGGCAGCAGCAGATTTTTGG 60.735 55.000 2.65 0.00 44.61 3.28
3094 6335 0.241749 TCGGCAGCAGCAGATTTTTG 59.758 50.000 2.65 0.00 44.61 2.44
3095 6336 0.242017 GTCGGCAGCAGCAGATTTTT 59.758 50.000 7.26 0.00 46.35 1.94
3096 6337 0.607489 AGTCGGCAGCAGCAGATTTT 60.607 50.000 7.26 0.00 46.35 1.82
3097 6338 0.607489 AAGTCGGCAGCAGCAGATTT 60.607 50.000 7.26 6.68 46.35 2.17
3098 6339 0.607489 AAAGTCGGCAGCAGCAGATT 60.607 50.000 7.26 0.00 46.35 2.40
3099 6340 0.607489 AAAAGTCGGCAGCAGCAGAT 60.607 50.000 7.26 0.00 46.35 2.90
3100 6341 0.819259 AAAAAGTCGGCAGCAGCAGA 60.819 50.000 2.65 0.57 44.61 4.26
3101 6342 0.662374 CAAAAAGTCGGCAGCAGCAG 60.662 55.000 2.65 0.00 44.61 4.24
3102 6343 1.359833 CAAAAAGTCGGCAGCAGCA 59.640 52.632 2.65 0.00 44.61 4.41
3103 6344 1.372128 CCAAAAAGTCGGCAGCAGC 60.372 57.895 0.00 0.00 41.10 5.25
3104 6345 4.950744 CCAAAAAGTCGGCAGCAG 57.049 55.556 0.00 0.00 0.00 4.24
3110 6351 2.650778 GCTGGGCCAAAAAGTCGG 59.349 61.111 8.04 0.00 0.00 4.79
3111 6352 1.791103 TTCGCTGGGCCAAAAAGTCG 61.791 55.000 8.04 4.46 0.00 4.18
3112 6353 0.039165 CTTCGCTGGGCCAAAAAGTC 60.039 55.000 8.04 0.00 0.00 3.01
3113 6354 0.755327 ACTTCGCTGGGCCAAAAAGT 60.755 50.000 17.49 17.49 0.00 2.66
3114 6355 1.243902 TACTTCGCTGGGCCAAAAAG 58.756 50.000 8.04 13.57 0.00 2.27
3115 6356 1.917872 ATACTTCGCTGGGCCAAAAA 58.082 45.000 8.04 0.90 0.00 1.94
3116 6357 1.917872 AATACTTCGCTGGGCCAAAA 58.082 45.000 8.04 1.30 0.00 2.44
3117 6358 1.917872 AAATACTTCGCTGGGCCAAA 58.082 45.000 8.04 0.00 0.00 3.28
3118 6359 1.917872 AAAATACTTCGCTGGGCCAA 58.082 45.000 8.04 0.00 0.00 4.52
3119 6360 1.917872 AAAAATACTTCGCTGGGCCA 58.082 45.000 5.85 5.85 0.00 5.36
3144 6385 2.256117 ACTGCTACTGCCGACTTTTT 57.744 45.000 0.00 0.00 38.71 1.94
3145 6386 3.611766 ATACTGCTACTGCCGACTTTT 57.388 42.857 0.00 0.00 38.71 2.27
3146 6387 3.611766 AATACTGCTACTGCCGACTTT 57.388 42.857 0.00 0.00 38.71 2.66
3147 6388 3.611766 AAATACTGCTACTGCCGACTT 57.388 42.857 0.00 0.00 38.71 3.01
3148 6389 3.262420 CAAAATACTGCTACTGCCGACT 58.738 45.455 0.00 0.00 38.71 4.18
3149 6390 2.351726 CCAAAATACTGCTACTGCCGAC 59.648 50.000 0.00 0.00 38.71 4.79
3150 6391 2.235155 TCCAAAATACTGCTACTGCCGA 59.765 45.455 0.00 0.00 38.71 5.54
3151 6392 2.627945 TCCAAAATACTGCTACTGCCG 58.372 47.619 0.00 0.00 38.71 5.69
3152 6393 3.181510 CGTTCCAAAATACTGCTACTGCC 60.182 47.826 0.00 0.00 38.71 4.85
3153 6394 3.682858 TCGTTCCAAAATACTGCTACTGC 59.317 43.478 0.00 0.00 40.20 4.40
3154 6395 5.163854 CCTTCGTTCCAAAATACTGCTACTG 60.164 44.000 0.00 0.00 0.00 2.74
3155 6396 4.935808 CCTTCGTTCCAAAATACTGCTACT 59.064 41.667 0.00 0.00 0.00 2.57
3156 6397 4.094442 CCCTTCGTTCCAAAATACTGCTAC 59.906 45.833 0.00 0.00 0.00 3.58
3157 6398 4.020039 TCCCTTCGTTCCAAAATACTGCTA 60.020 41.667 0.00 0.00 0.00 3.49
3158 6399 3.081804 CCCTTCGTTCCAAAATACTGCT 58.918 45.455 0.00 0.00 0.00 4.24
3159 6400 3.078837 TCCCTTCGTTCCAAAATACTGC 58.921 45.455 0.00 0.00 0.00 4.40
3160 6401 3.689649 CCTCCCTTCGTTCCAAAATACTG 59.310 47.826 0.00 0.00 0.00 2.74
3161 6402 3.585732 TCCTCCCTTCGTTCCAAAATACT 59.414 43.478 0.00 0.00 0.00 2.12
3162 6403 3.688185 GTCCTCCCTTCGTTCCAAAATAC 59.312 47.826 0.00 0.00 0.00 1.89
3163 6404 3.618019 CGTCCTCCCTTCGTTCCAAAATA 60.618 47.826 0.00 0.00 0.00 1.40
3164 6405 2.791655 GTCCTCCCTTCGTTCCAAAAT 58.208 47.619 0.00 0.00 0.00 1.82
3165 6406 1.541670 CGTCCTCCCTTCGTTCCAAAA 60.542 52.381 0.00 0.00 0.00 2.44
3166 6407 0.034337 CGTCCTCCCTTCGTTCCAAA 59.966 55.000 0.00 0.00 0.00 3.28
3167 6408 0.828762 TCGTCCTCCCTTCGTTCCAA 60.829 55.000 0.00 0.00 0.00 3.53
3168 6409 0.828762 TTCGTCCTCCCTTCGTTCCA 60.829 55.000 0.00 0.00 0.00 3.53
3169 6410 0.319405 TTTCGTCCTCCCTTCGTTCC 59.681 55.000 0.00 0.00 0.00 3.62
3170 6411 2.381725 ATTTCGTCCTCCCTTCGTTC 57.618 50.000 0.00 0.00 0.00 3.95
3171 6412 2.853235 AATTTCGTCCTCCCTTCGTT 57.147 45.000 0.00 0.00 0.00 3.85
3172 6413 3.967332 TTAATTTCGTCCTCCCTTCGT 57.033 42.857 0.00 0.00 0.00 3.85
3173 6414 3.373130 GGTTTAATTTCGTCCTCCCTTCG 59.627 47.826 0.00 0.00 0.00 3.79
3174 6415 4.329392 TGGTTTAATTTCGTCCTCCCTTC 58.671 43.478 0.00 0.00 0.00 3.46
3175 6416 4.332828 CTGGTTTAATTTCGTCCTCCCTT 58.667 43.478 0.00 0.00 0.00 3.95
3176 6417 3.872630 GCTGGTTTAATTTCGTCCTCCCT 60.873 47.826 0.00 0.00 0.00 4.20
3177 6418 2.422479 GCTGGTTTAATTTCGTCCTCCC 59.578 50.000 0.00 0.00 0.00 4.30
3178 6419 2.095372 CGCTGGTTTAATTTCGTCCTCC 59.905 50.000 0.00 0.00 0.00 4.30
3179 6420 2.997986 TCGCTGGTTTAATTTCGTCCTC 59.002 45.455 0.00 0.00 0.00 3.71
3180 6421 3.048337 TCGCTGGTTTAATTTCGTCCT 57.952 42.857 0.00 0.00 0.00 3.85
3181 6422 3.817148 TTCGCTGGTTTAATTTCGTCC 57.183 42.857 0.00 0.00 0.00 4.79
3182 6423 6.143278 ACATTTTTCGCTGGTTTAATTTCGTC 59.857 34.615 0.00 0.00 0.00 4.20
3183 6424 5.980715 ACATTTTTCGCTGGTTTAATTTCGT 59.019 32.000 0.00 0.00 0.00 3.85
3184 6425 6.446659 ACATTTTTCGCTGGTTTAATTTCG 57.553 33.333 0.00 0.00 0.00 3.46
3185 6426 7.042389 TGGAACATTTTTCGCTGGTTTAATTTC 60.042 33.333 0.00 0.00 0.00 2.17
3186 6427 6.763610 TGGAACATTTTTCGCTGGTTTAATTT 59.236 30.769 0.00 0.00 0.00 1.82
3187 6428 6.201997 GTGGAACATTTTTCGCTGGTTTAATT 59.798 34.615 0.00 0.00 44.52 1.40
3188 6429 5.694458 GTGGAACATTTTTCGCTGGTTTAAT 59.306 36.000 0.00 0.00 44.52 1.40
3189 6430 5.044558 GTGGAACATTTTTCGCTGGTTTAA 58.955 37.500 0.00 0.00 44.52 1.52
3190 6431 4.339814 AGTGGAACATTTTTCGCTGGTTTA 59.660 37.500 0.00 0.00 44.52 2.01
3191 6432 3.132111 AGTGGAACATTTTTCGCTGGTTT 59.868 39.130 0.00 0.00 44.52 3.27
3192 6433 2.693074 AGTGGAACATTTTTCGCTGGTT 59.307 40.909 0.00 0.00 44.52 3.67
3193 6434 2.306847 AGTGGAACATTTTTCGCTGGT 58.693 42.857 0.00 0.00 44.52 4.00
3194 6435 3.502211 AGTAGTGGAACATTTTTCGCTGG 59.498 43.478 0.00 0.00 44.52 4.85
3195 6436 4.666655 CGAGTAGTGGAACATTTTTCGCTG 60.667 45.833 0.00 0.00 44.52 5.18
3196 6437 3.432252 CGAGTAGTGGAACATTTTTCGCT 59.568 43.478 0.00 0.00 44.52 4.93
3197 6438 3.732943 CGAGTAGTGGAACATTTTTCGC 58.267 45.455 0.00 0.00 44.52 4.70
3198 6439 3.185594 TGCGAGTAGTGGAACATTTTTCG 59.814 43.478 0.00 0.00 44.52 3.46
3199 6440 4.464112 GTGCGAGTAGTGGAACATTTTTC 58.536 43.478 0.00 0.00 44.52 2.29
3200 6441 3.059188 CGTGCGAGTAGTGGAACATTTTT 60.059 43.478 0.00 0.00 44.52 1.94
3201 6442 2.478894 CGTGCGAGTAGTGGAACATTTT 59.521 45.455 0.00 0.00 44.52 1.82
3202 6443 2.066262 CGTGCGAGTAGTGGAACATTT 58.934 47.619 0.00 0.00 44.52 2.32
3203 6444 1.271379 TCGTGCGAGTAGTGGAACATT 59.729 47.619 0.00 0.00 44.52 2.71
3204 6445 0.885879 TCGTGCGAGTAGTGGAACAT 59.114 50.000 0.00 0.00 44.52 2.71
3205 6446 0.240145 CTCGTGCGAGTAGTGGAACA 59.760 55.000 12.87 0.00 37.03 3.18
3206 6447 1.071567 GCTCGTGCGAGTAGTGGAAC 61.072 60.000 20.55 0.56 43.70 3.62
3207 6448 1.211969 GCTCGTGCGAGTAGTGGAA 59.788 57.895 20.55 0.00 43.70 3.53
3208 6449 2.875485 GCTCGTGCGAGTAGTGGA 59.125 61.111 20.55 0.00 43.70 4.02
3260 6501 1.591594 GCGATTCGATTCAGCGGGA 60.592 57.895 10.88 0.00 0.00 5.14
3266 6507 2.525248 GGCAGCGCGATTCGATTCA 61.525 57.895 12.10 0.00 41.67 2.57
3332 6573 3.474570 AGTGGCTCCCTCCATCGC 61.475 66.667 0.00 0.00 38.57 4.58
3389 6630 3.160047 CTGGCCCTGAGGAGCGAT 61.160 66.667 0.00 0.00 33.47 4.58
3520 6761 3.655810 GAGGAGCAGCGTGTGGGAG 62.656 68.421 0.00 0.00 0.00 4.30
3521 6762 3.695606 GAGGAGCAGCGTGTGGGA 61.696 66.667 0.00 0.00 0.00 4.37
3553 6794 2.593134 GCAGCGCGAGATCCATGTC 61.593 63.158 12.10 0.00 0.00 3.06
3597 6838 0.877071 AGCACAAGATTCACGGCAAG 59.123 50.000 0.00 0.00 0.00 4.01
3654 6895 2.512515 GATGGTGCCTGGCGAGAC 60.513 66.667 14.98 6.64 0.00 3.36


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

AutoCloner maintained by Alex Coulton.