Multiple sequence alignment - TraesCS1A01G153800

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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 TraesCS1A01G153800 chr1A 100.000 3944 0 0 1 3944 267357227 267353284 0.000000e+00 7284.0
1 TraesCS1A01G153800 chr1B 94.089 2081 93 13 867 2936 304783954 304786015 0.000000e+00 3134.0
2 TraesCS1A01G153800 chr1D 92.672 2006 95 19 745 2733 211804830 211802860 0.000000e+00 2843.0
3 TraesCS1A01G153800 chr1D 85.809 303 23 7 409 691 211805645 211805343 1.780000e-78 303.0
4 TraesCS1A01G153800 chr1D 82.510 263 26 5 409 651 395852058 395852320 3.090000e-51 213.0
5 TraesCS1A01G153800 chr7A 95.732 820 27 5 3128 3944 552452738 552451924 0.000000e+00 1314.0
6 TraesCS1A01G153800 chr7A 94.844 834 29 11 3115 3944 690375894 690375071 0.000000e+00 1290.0
7 TraesCS1A01G153800 chr7A 94.424 807 38 4 3142 3944 684924564 684925367 0.000000e+00 1234.0
8 TraesCS1A01G153800 chr7A 96.577 409 13 1 1 408 560839624 560839216 0.000000e+00 676.0
9 TraesCS1A01G153800 chr7A 85.217 575 72 6 1 573 22746699 22747262 2.640000e-161 579.0
10 TraesCS1A01G153800 chr7A 89.796 49 3 2 3013 3060 6840509 6840462 1.180000e-05 62.1
11 TraesCS1A01G153800 chr6A 95.155 805 34 3 3141 3944 303629809 303630609 0.000000e+00 1266.0
12 TraesCS1A01G153800 chr6A 94.507 801 37 4 3146 3944 563480014 563480809 0.000000e+00 1229.0
13 TraesCS1A01G153800 chr6A 96.577 409 13 1 1 408 147838054 147837646 0.000000e+00 676.0
14 TraesCS1A01G153800 chr6A 96.107 411 15 1 1 410 506361141 506361551 0.000000e+00 669.0
15 TraesCS1A01G153800 chr4A 95.043 807 33 4 3141 3944 44442392 44441590 0.000000e+00 1262.0
16 TraesCS1A01G153800 chr4A 96.577 409 12 2 1 408 150333136 150332729 0.000000e+00 676.0
17 TraesCS1A01G153800 chr4A 96.341 410 13 2 1 408 54412955 54412546 0.000000e+00 673.0
18 TraesCS1A01G153800 chr5A 94.417 806 38 5 3142 3944 493508478 493507677 0.000000e+00 1232.0
19 TraesCS1A01G153800 chr2A 94.417 806 37 5 3141 3944 591577526 591576727 0.000000e+00 1232.0
20 TraesCS1A01G153800 chr2A 94.183 808 37 7 3140 3944 591576596 591575796 0.000000e+00 1223.0
21 TraesCS1A01G153800 chr2A 96.333 409 14 1 1 408 240371613 240371205 0.000000e+00 671.0
22 TraesCS1A01G153800 chr2A 87.097 155 19 1 2942 3095 504067961 504067807 1.460000e-39 174.0
23 TraesCS1A01G153800 chr3A 96.577 409 13 1 1 408 46277036 46277444 0.000000e+00 676.0
24 TraesCS1A01G153800 chr3A 96.341 410 13 2 1 408 64237798 64237389 0.000000e+00 673.0
25 TraesCS1A01G153800 chr3A 96.333 409 14 1 1 408 63319476 63319884 0.000000e+00 671.0
26 TraesCS1A01G153800 chr5D 88.710 248 26 2 409 656 55588550 55588795 6.400000e-78 302.0
27 TraesCS1A01G153800 chr4D 85.317 252 32 3 409 660 59621063 59621309 5.060000e-64 255.0
28 TraesCS1A01G153800 chr7B 89.231 195 20 1 462 656 708062656 708062463 3.940000e-60 243.0
29 TraesCS1A01G153800 chr6B 86.697 218 29 0 409 626 661481094 661481311 3.940000e-60 243.0
30 TraesCS1A01G153800 chr6B 89.222 167 14 3 409 573 449450067 449450231 5.170000e-49 206.0
31 TraesCS1A01G153800 chr2D 82.890 263 25 4 409 651 644242951 644242689 6.640000e-53 219.0
32 TraesCS1A01G153800 chr7D 82.463 268 26 2 409 656 414101905 414101639 8.580000e-52 215.0
33 TraesCS1A01G153800 chr3D 82.061 262 27 4 409 650 608806459 608806720 5.170000e-49 206.0
34 TraesCS1A01G153800 chr3D 78.113 265 36 11 408 651 127248062 127247799 8.830000e-32 148.0
35 TraesCS1A01G153800 chr6D 81.343 268 28 3 409 656 402358047 402357782 8.640000e-47 198.0
36 TraesCS1A01G153800 chr3B 81.343 268 23 9 409 656 188485448 188485188 4.020000e-45 193.0
37 TraesCS1A01G153800 chr2B 86.777 121 14 2 2942 3060 61472117 61471997 2.470000e-27 134.0
38 TraesCS1A01G153800 chr5B 83.607 122 13 4 2942 3060 707443748 707443865 1.500000e-19 108.0


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 TraesCS1A01G153800 chr1A 267353284 267357227 3943 True 7284.0 7284 100.0000 1 3944 1 chr1A.!!$R1 3943
1 TraesCS1A01G153800 chr1B 304783954 304786015 2061 False 3134.0 3134 94.0890 867 2936 1 chr1B.!!$F1 2069
2 TraesCS1A01G153800 chr1D 211802860 211805645 2785 True 1573.0 2843 89.2405 409 2733 2 chr1D.!!$R1 2324
3 TraesCS1A01G153800 chr7A 552451924 552452738 814 True 1314.0 1314 95.7320 3128 3944 1 chr7A.!!$R2 816
4 TraesCS1A01G153800 chr7A 690375071 690375894 823 True 1290.0 1290 94.8440 3115 3944 1 chr7A.!!$R4 829
5 TraesCS1A01G153800 chr7A 684924564 684925367 803 False 1234.0 1234 94.4240 3142 3944 1 chr7A.!!$F2 802
6 TraesCS1A01G153800 chr7A 22746699 22747262 563 False 579.0 579 85.2170 1 573 1 chr7A.!!$F1 572
7 TraesCS1A01G153800 chr6A 303629809 303630609 800 False 1266.0 1266 95.1550 3141 3944 1 chr6A.!!$F1 803
8 TraesCS1A01G153800 chr6A 563480014 563480809 795 False 1229.0 1229 94.5070 3146 3944 1 chr6A.!!$F3 798
9 TraesCS1A01G153800 chr4A 44441590 44442392 802 True 1262.0 1262 95.0430 3141 3944 1 chr4A.!!$R1 803
10 TraesCS1A01G153800 chr5A 493507677 493508478 801 True 1232.0 1232 94.4170 3142 3944 1 chr5A.!!$R1 802
11 TraesCS1A01G153800 chr2A 591575796 591577526 1730 True 1227.5 1232 94.3000 3140 3944 2 chr2A.!!$R3 804

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
743 766 0.108615 ACGTCGGAAGCCATCAAGAG 60.109 55.0 0.0 0.0 0.0 2.85 F
843 1325 0.326618 GGGGAGAGGAGGGTTGATGA 60.327 60.0 0.0 0.0 0.0 2.92 F
1616 2120 0.034896 GTTCCTGGCTTCTCCGAACA 59.965 55.0 0.0 0.0 36.1 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1596 2100 0.034896 GTTCGGAGAAGCCAGGAACA 59.965 55.0 0.00 0.00 45.90 3.18 R
2327 2836 0.105039 CTGACTACCCAAGGATCGCC 59.895 60.0 0.00 0.00 0.00 5.54 R
2994 3504 0.252239 AAAAAGGGTGGGCCATCTCC 60.252 55.0 17.95 15.32 36.17 3.71 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
32 33 3.215975 CAAAGTTTTACCCAGGTTCGGA 58.784 45.455 0.00 0.00 0.00 4.55
44 45 1.035932 GGTTCGGACCCTCTCGATGA 61.036 60.000 0.00 0.00 40.25 2.92
77 79 6.147821 CCCTACGTCCTGCTTGATTAATATTG 59.852 42.308 0.00 0.00 0.00 1.90
110 112 7.147177 TGGGTAGTACAAGAGTAGATCTACCAT 60.147 40.741 25.93 14.15 43.02 3.55
134 136 4.479158 AGATCAGAGAGGCTAAACCCTAG 58.521 47.826 0.00 0.00 40.58 3.02
158 160 5.832539 AGCTAGCCTATGGTATGATTGTT 57.167 39.130 12.13 0.00 0.00 2.83
159 161 5.555017 AGCTAGCCTATGGTATGATTGTTG 58.445 41.667 12.13 0.00 0.00 3.33
160 162 5.307976 AGCTAGCCTATGGTATGATTGTTGA 59.692 40.000 12.13 0.00 0.00 3.18
161 163 6.013032 AGCTAGCCTATGGTATGATTGTTGAT 60.013 38.462 12.13 0.00 0.00 2.57
162 164 6.093219 GCTAGCCTATGGTATGATTGTTGATG 59.907 42.308 2.29 0.00 0.00 3.07
163 165 5.945310 AGCCTATGGTATGATTGTTGATGT 58.055 37.500 0.00 0.00 0.00 3.06
164 166 5.766670 AGCCTATGGTATGATTGTTGATGTG 59.233 40.000 0.00 0.00 0.00 3.21
165 167 5.532406 GCCTATGGTATGATTGTTGATGTGT 59.468 40.000 0.00 0.00 0.00 3.72
190 192 2.068915 TCCTACGGACAAAACCCCC 58.931 57.895 0.00 0.00 0.00 5.40
209 211 4.267349 CCCCCGGTTTATATAGACACTG 57.733 50.000 0.00 0.00 0.00 3.66
213 215 4.831155 CCCGGTTTATATAGACACTGGAGA 59.169 45.833 12.23 0.00 37.83 3.71
215 217 5.047943 CCGGTTTATATAGACACTGGAGAGG 60.048 48.000 5.71 0.00 37.83 3.69
217 219 5.839606 GGTTTATATAGACACTGGAGAGGGT 59.160 44.000 5.83 0.00 39.16 4.34
228 230 3.246387 ACTGGAGAGGGTTAGGGTTACAT 60.246 47.826 0.00 0.00 0.00 2.29
230 232 4.553678 TGGAGAGGGTTAGGGTTACATAG 58.446 47.826 0.00 0.00 0.00 2.23
231 233 4.233521 TGGAGAGGGTTAGGGTTACATAGA 59.766 45.833 0.00 0.00 0.00 1.98
243 245 5.659971 AGGGTTACATAGAGTCGGTTACAAT 59.340 40.000 4.88 0.00 0.00 2.71
246 248 6.335777 GTTACATAGAGTCGGTTACAATGGT 58.664 40.000 0.00 0.00 0.00 3.55
254 256 4.341520 AGTCGGTTACAATGGTAGGAGATC 59.658 45.833 0.00 0.00 0.00 2.75
256 258 4.341235 TCGGTTACAATGGTAGGAGATCTG 59.659 45.833 0.00 0.00 0.00 2.90
257 259 4.341235 CGGTTACAATGGTAGGAGATCTGA 59.659 45.833 0.00 0.00 0.00 3.27
267 269 6.732487 TGGTAGGAGATCTGAATATCCGTAT 58.268 40.000 0.00 0.00 46.12 3.06
268 270 6.829298 TGGTAGGAGATCTGAATATCCGTATC 59.171 42.308 0.00 0.00 46.12 2.24
272 274 4.017126 AGATCTGAATATCCGTATCGCCA 58.983 43.478 0.00 0.00 0.00 5.69
279 281 1.160329 ATCCGTATCGCCAAGCTTGC 61.160 55.000 21.43 14.85 0.00 4.01
287 289 2.202395 GCCAAGCTTGCCTTCCACA 61.202 57.895 21.43 0.00 0.00 4.17
293 295 1.809567 GCTTGCCTTCCACACCAAGG 61.810 60.000 0.00 0.00 43.13 3.61
295 297 0.260230 TTGCCTTCCACACCAAGGAA 59.740 50.000 2.52 0.00 42.94 3.36
302 304 0.478507 CCACACCAAGGAAAGTCCCT 59.521 55.000 0.00 0.00 37.19 4.20
336 338 3.265791 ACGGAGTCTTCAATCTTGCATC 58.734 45.455 0.00 0.00 29.74 3.91
346 348 7.495279 GTCTTCAATCTTGCATCTTCATAGTCT 59.505 37.037 0.00 0.00 0.00 3.24
348 350 8.883954 TTCAATCTTGCATCTTCATAGTCTAG 57.116 34.615 0.00 0.00 0.00 2.43
349 351 7.440198 TCAATCTTGCATCTTCATAGTCTAGG 58.560 38.462 0.00 0.00 0.00 3.02
358 360 1.775459 TCATAGTCTAGGAGTCCGGCT 59.225 52.381 2.76 0.00 0.00 5.52
359 361 1.883275 CATAGTCTAGGAGTCCGGCTG 59.117 57.143 2.76 0.00 0.00 4.85
361 363 0.331954 AGTCTAGGAGTCCGGCTGAA 59.668 55.000 2.76 0.00 0.00 3.02
370 373 2.694109 GAGTCCGGCTGAAGGTATAGTT 59.306 50.000 0.00 0.00 0.00 2.24
417 420 0.468226 GACTCCCTCACACCAACACA 59.532 55.000 0.00 0.00 0.00 3.72
432 435 1.859302 ACACAAGGCCAAAAAGACCA 58.141 45.000 5.01 0.00 0.00 4.02
433 436 2.183679 ACACAAGGCCAAAAAGACCAA 58.816 42.857 5.01 0.00 0.00 3.67
437 440 3.517500 ACAAGGCCAAAAAGACCAAAGAA 59.482 39.130 5.01 0.00 0.00 2.52
499 502 3.637273 GGAACCACCTCCACCGCT 61.637 66.667 0.00 0.00 35.36 5.52
500 503 2.288025 GGAACCACCTCCACCGCTA 61.288 63.158 0.00 0.00 35.36 4.26
506 509 1.681327 ACCTCCACCGCTATCGTGT 60.681 57.895 0.00 0.00 0.00 4.49
579 602 1.377987 GCATACCAGGCCCGAAACA 60.378 57.895 0.00 0.00 0.00 2.83
694 717 4.124351 CGGGTCAGTCGCCGCTTA 62.124 66.667 0.00 0.00 0.00 3.09
695 718 2.202756 GGGTCAGTCGCCGCTTAG 60.203 66.667 0.00 0.00 0.00 2.18
696 719 2.202756 GGTCAGTCGCCGCTTAGG 60.203 66.667 0.00 0.00 44.97 2.69
697 720 2.707849 GGTCAGTCGCCGCTTAGGA 61.708 63.158 0.00 0.00 45.00 2.94
698 721 1.226717 GTCAGTCGCCGCTTAGGAG 60.227 63.158 0.00 0.00 45.00 3.69
699 722 2.583593 CAGTCGCCGCTTAGGAGC 60.584 66.667 0.00 0.00 45.00 4.70
718 741 4.106925 CCCTCCTGGTGCAGCTCC 62.107 72.222 18.08 6.55 0.00 4.70
719 742 4.463879 CCTCCTGGTGCAGCTCCG 62.464 72.222 18.08 5.51 0.00 4.63
720 743 3.699894 CTCCTGGTGCAGCTCCGT 61.700 66.667 18.08 0.00 0.00 4.69
721 744 3.655810 CTCCTGGTGCAGCTCCGTC 62.656 68.421 18.08 0.00 0.00 4.79
722 745 4.767255 CCTGGTGCAGCTCCGTCC 62.767 72.222 18.08 0.00 0.00 4.79
723 746 4.767255 CTGGTGCAGCTCCGTCCC 62.767 72.222 18.08 0.00 0.00 4.46
729 752 4.778415 CAGCTCCGTCCCACGTCG 62.778 72.222 0.00 0.00 40.58 5.12
736 759 3.998672 GTCCCACGTCGGAAGCCA 61.999 66.667 2.52 0.00 36.56 4.75
737 760 3.000819 TCCCACGTCGGAAGCCAT 61.001 61.111 0.00 0.00 36.56 4.40
738 761 2.511600 CCCACGTCGGAAGCCATC 60.512 66.667 0.00 0.00 36.56 3.51
739 762 2.264480 CCACGTCGGAAGCCATCA 59.736 61.111 0.00 0.00 36.56 3.07
740 763 1.375396 CCACGTCGGAAGCCATCAA 60.375 57.895 0.00 0.00 36.56 2.57
741 764 1.361668 CCACGTCGGAAGCCATCAAG 61.362 60.000 0.00 0.00 36.56 3.02
742 765 0.389817 CACGTCGGAAGCCATCAAGA 60.390 55.000 0.00 0.00 0.00 3.02
743 766 0.108615 ACGTCGGAAGCCATCAAGAG 60.109 55.000 0.00 0.00 0.00 2.85
759 1241 3.552911 AGGGGAAGGTCAGGGGGT 61.553 66.667 0.00 0.00 0.00 4.95
837 1319 1.869452 AGGAAGGGGAGAGGAGGGT 60.869 63.158 0.00 0.00 0.00 4.34
843 1325 0.326618 GGGGAGAGGAGGGTTGATGA 60.327 60.000 0.00 0.00 0.00 2.92
858 1340 2.907897 GATGAAGTGGGAGGCCGACG 62.908 65.000 0.00 0.00 37.32 5.12
885 1369 3.532232 AGGAGACTTCCCCATAGACTACA 59.468 47.826 0.00 0.00 45.24 2.74
987 1486 5.652994 ATAAAAGCATGTAAAAAGCCCGA 57.347 34.783 0.00 0.00 0.00 5.14
988 1487 3.297830 AAAGCATGTAAAAAGCCCGAC 57.702 42.857 0.00 0.00 0.00 4.79
989 1488 0.802494 AGCATGTAAAAAGCCCGACG 59.198 50.000 0.00 0.00 0.00 5.12
990 1489 0.519961 GCATGTAAAAAGCCCGACGT 59.480 50.000 0.00 0.00 0.00 4.34
992 1491 2.073816 CATGTAAAAAGCCCGACGTCT 58.926 47.619 14.70 0.00 0.00 4.18
993 1492 1.504359 TGTAAAAAGCCCGACGTCTG 58.496 50.000 14.70 7.04 0.00 3.51
994 1493 0.794473 GTAAAAAGCCCGACGTCTGG 59.206 55.000 20.63 20.63 0.00 3.86
996 1495 1.164041 AAAAAGCCCGACGTCTGGTG 61.164 55.000 24.57 15.65 0.00 4.17
1222 1726 1.450312 CTCCCCGCGCAAGAAGATT 60.450 57.895 8.75 0.00 43.02 2.40
1616 2120 0.034896 GTTCCTGGCTTCTCCGAACA 59.965 55.000 0.00 0.00 36.10 3.18
1643 2147 1.002659 TCGGGCGGAAAGATTCTTCAA 59.997 47.619 0.00 0.00 0.00 2.69
1663 2167 3.785982 TCTGCGGCAGACAAGGTA 58.214 55.556 27.76 4.83 35.39 3.08
2050 2554 3.308438 TCTTCGCCTGTTACTGGTAAC 57.692 47.619 14.51 14.51 44.16 2.50
2217 2721 2.046892 GCTGGAGAAGGCGAGCAA 60.047 61.111 0.00 0.00 39.14 3.91
2235 2739 0.331616 AAGCGGGTAAGCCATTTCCT 59.668 50.000 0.00 0.00 38.01 3.36
2243 2747 3.696548 GGTAAGCCATTTCCTCTTTCCTG 59.303 47.826 0.00 0.00 34.09 3.86
2274 2778 4.921547 TGTTCTCTCTGTTAATCCGATCG 58.078 43.478 8.51 8.51 0.00 3.69
2327 2836 3.804518 TCACCATGATCGTTTTGTTCG 57.195 42.857 0.00 0.00 0.00 3.95
2339 2848 0.958382 TTTGTTCGGCGATCCTTGGG 60.958 55.000 11.76 0.00 0.00 4.12
2342 2851 0.529992 GTTCGGCGATCCTTGGGTAG 60.530 60.000 11.76 0.00 0.00 3.18
2358 2867 4.326826 TGGGTAGTCAGAAAAATGAGCAG 58.673 43.478 0.00 0.00 0.00 4.24
2376 2885 2.472488 GCAGTTTCATTTTGTTCAGCGG 59.528 45.455 0.00 0.00 0.00 5.52
2379 2888 4.911610 CAGTTTCATTTTGTTCAGCGGTAG 59.088 41.667 0.00 0.00 0.00 3.18
2398 2907 3.616956 AGGAAATCACTCGAGAATGCA 57.383 42.857 21.68 0.00 0.00 3.96
2399 2908 3.942829 AGGAAATCACTCGAGAATGCAA 58.057 40.909 21.68 0.00 0.00 4.08
2400 2909 3.686726 AGGAAATCACTCGAGAATGCAAC 59.313 43.478 21.68 4.39 0.00 4.17
2401 2910 3.436704 GGAAATCACTCGAGAATGCAACA 59.563 43.478 21.68 0.00 0.00 3.33
2492 3001 1.424493 CGCGGCCTCTTTCTGTCATC 61.424 60.000 0.00 0.00 0.00 2.92
2521 3031 5.531659 TGGTTTGCCTTAACGAAATCTACAA 59.468 36.000 0.00 0.00 35.27 2.41
2712 3222 1.271543 TGGGTTGCTTCATCAGTCTGG 60.272 52.381 0.00 0.00 0.00 3.86
2754 3264 0.167470 CTGCATTGTGCTCGGAACTG 59.833 55.000 3.41 0.00 45.31 3.16
2763 3273 0.810031 GCTCGGAACTGTGTGTGTGT 60.810 55.000 0.00 0.00 0.00 3.72
2802 3312 2.872732 TGGACGGTTCTCTCTGTAGTT 58.127 47.619 0.00 0.00 0.00 2.24
2807 3317 2.561419 CGGTTCTCTCTGTAGTTTCCCA 59.439 50.000 0.00 0.00 0.00 4.37
2815 3325 4.137543 CTCTGTAGTTTCCCAGCTGTTTT 58.862 43.478 13.81 0.00 0.00 2.43
2833 3343 6.292008 GCTGTTTTCTTCTTGATTTGAACTGC 60.292 38.462 0.00 0.00 34.99 4.40
2846 3356 3.354089 TGAACTGCAAAGTGCTAAAGC 57.646 42.857 1.43 0.00 45.31 3.51
2867 3377 0.934496 TCAAAGACGCTTGTGTTCCG 59.066 50.000 0.00 0.00 0.00 4.30
2889 3399 2.743664 GGTAAATGTACGCCGTTCCTTT 59.256 45.455 0.00 0.00 0.00 3.11
2890 3400 3.932089 GGTAAATGTACGCCGTTCCTTTA 59.068 43.478 0.00 0.00 0.00 1.85
2891 3401 4.033243 GGTAAATGTACGCCGTTCCTTTAG 59.967 45.833 0.00 0.00 0.00 1.85
2892 3402 3.323751 AATGTACGCCGTTCCTTTAGT 57.676 42.857 0.00 0.00 0.00 2.24
2893 3403 2.818130 TGTACGCCGTTCCTTTAGTT 57.182 45.000 0.00 0.00 0.00 2.24
2924 3434 3.193479 GGTGATCTCCGCCATTTTCTTTT 59.807 43.478 0.00 0.00 44.82 2.27
2962 3472 9.575868 TCAATAAATGAGTTACAGGGTTTTACA 57.424 29.630 0.00 0.00 33.04 2.41
2995 3505 6.806668 AATTTGATTGGTTAATAGGTGGGG 57.193 37.500 0.00 0.00 0.00 4.96
2996 3506 5.538082 TTTGATTGGTTAATAGGTGGGGA 57.462 39.130 0.00 0.00 0.00 4.81
2997 3507 4.788925 TGATTGGTTAATAGGTGGGGAG 57.211 45.455 0.00 0.00 0.00 4.30
2998 3508 4.376223 TGATTGGTTAATAGGTGGGGAGA 58.624 43.478 0.00 0.00 0.00 3.71
2999 3509 4.981647 TGATTGGTTAATAGGTGGGGAGAT 59.018 41.667 0.00 0.00 0.00 2.75
3000 3510 4.788925 TTGGTTAATAGGTGGGGAGATG 57.211 45.455 0.00 0.00 0.00 2.90
3001 3511 3.053077 TGGTTAATAGGTGGGGAGATGG 58.947 50.000 0.00 0.00 0.00 3.51
3002 3512 2.224793 GGTTAATAGGTGGGGAGATGGC 60.225 54.545 0.00 0.00 0.00 4.40
3003 3513 1.742308 TAATAGGTGGGGAGATGGCC 58.258 55.000 0.00 0.00 0.00 5.36
3011 3521 3.100111 GGAGATGGCCCACCCTTT 58.900 61.111 0.00 0.00 33.59 3.11
3012 3522 1.388133 GGAGATGGCCCACCCTTTT 59.612 57.895 0.00 0.00 33.59 2.27
3013 3523 0.252239 GGAGATGGCCCACCCTTTTT 60.252 55.000 0.00 0.00 33.59 1.94
3014 3524 0.897621 GAGATGGCCCACCCTTTTTG 59.102 55.000 0.00 0.00 33.59 2.44
3015 3525 0.486879 AGATGGCCCACCCTTTTTGA 59.513 50.000 0.00 0.00 33.59 2.69
3016 3526 1.132881 AGATGGCCCACCCTTTTTGAA 60.133 47.619 0.00 0.00 33.59 2.69
3017 3527 1.696884 GATGGCCCACCCTTTTTGAAA 59.303 47.619 0.00 0.00 33.59 2.69
3018 3528 1.584724 TGGCCCACCCTTTTTGAAAA 58.415 45.000 0.00 0.00 33.59 2.29
3019 3529 2.131023 TGGCCCACCCTTTTTGAAAAT 58.869 42.857 0.00 0.00 33.59 1.82
3020 3530 2.105649 TGGCCCACCCTTTTTGAAAATC 59.894 45.455 0.00 0.00 33.59 2.17
3021 3531 2.105649 GGCCCACCCTTTTTGAAAATCA 59.894 45.455 0.00 0.00 0.00 2.57
3022 3532 3.434310 GGCCCACCCTTTTTGAAAATCAA 60.434 43.478 0.00 0.00 34.03 2.57
3023 3533 3.814842 GCCCACCCTTTTTGAAAATCAAG 59.185 43.478 0.00 0.00 37.70 3.02
3024 3534 4.388485 CCCACCCTTTTTGAAAATCAAGG 58.612 43.478 0.87 0.87 37.70 3.61
3027 3537 4.019792 CCCTTTTTGAAAATCAAGGGGG 57.980 45.455 15.18 7.78 46.15 5.40
3028 3538 3.650461 CCCTTTTTGAAAATCAAGGGGGA 59.350 43.478 15.18 0.00 46.15 4.81
3029 3539 4.263025 CCCTTTTTGAAAATCAAGGGGGAG 60.263 45.833 15.18 0.00 46.15 4.30
3030 3540 4.347876 CCTTTTTGAAAATCAAGGGGGAGT 59.652 41.667 0.00 0.00 37.70 3.85
3031 3541 5.542251 CCTTTTTGAAAATCAAGGGGGAGTA 59.458 40.000 0.00 0.00 37.70 2.59
3032 3542 6.042666 CCTTTTTGAAAATCAAGGGGGAGTAA 59.957 38.462 0.00 0.00 37.70 2.24
3033 3543 6.664428 TTTTGAAAATCAAGGGGGAGTAAG 57.336 37.500 0.00 0.00 37.70 2.34
3034 3544 5.333566 TTGAAAATCAAGGGGGAGTAAGT 57.666 39.130 0.00 0.00 31.83 2.24
3035 3545 5.333566 TGAAAATCAAGGGGGAGTAAGTT 57.666 39.130 0.00 0.00 0.00 2.66
3036 3546 5.711698 TGAAAATCAAGGGGGAGTAAGTTT 58.288 37.500 0.00 0.00 0.00 2.66
3037 3547 5.538433 TGAAAATCAAGGGGGAGTAAGTTTG 59.462 40.000 0.00 0.00 0.00 2.93
3038 3548 4.741928 AATCAAGGGGGAGTAAGTTTGT 57.258 40.909 0.00 0.00 0.00 2.83
3039 3549 5.853572 AATCAAGGGGGAGTAAGTTTGTA 57.146 39.130 0.00 0.00 0.00 2.41
3040 3550 5.853572 ATCAAGGGGGAGTAAGTTTGTAA 57.146 39.130 0.00 0.00 0.00 2.41
3041 3551 5.853572 TCAAGGGGGAGTAAGTTTGTAAT 57.146 39.130 0.00 0.00 0.00 1.89
3042 3552 6.208840 TCAAGGGGGAGTAAGTTTGTAATT 57.791 37.500 0.00 0.00 0.00 1.40
3043 3553 6.007703 TCAAGGGGGAGTAAGTTTGTAATTG 58.992 40.000 0.00 0.00 0.00 2.32
3044 3554 4.930696 AGGGGGAGTAAGTTTGTAATTGG 58.069 43.478 0.00 0.00 0.00 3.16
3045 3555 4.355889 AGGGGGAGTAAGTTTGTAATTGGT 59.644 41.667 0.00 0.00 0.00 3.67
3046 3556 5.081728 GGGGGAGTAAGTTTGTAATTGGTT 58.918 41.667 0.00 0.00 0.00 3.67
3047 3557 6.045813 AGGGGGAGTAAGTTTGTAATTGGTTA 59.954 38.462 0.00 0.00 0.00 2.85
3048 3558 6.376299 GGGGGAGTAAGTTTGTAATTGGTTAG 59.624 42.308 0.00 0.00 0.00 2.34
3049 3559 6.944290 GGGGAGTAAGTTTGTAATTGGTTAGT 59.056 38.462 0.00 0.00 0.00 2.24
3050 3560 8.102676 GGGGAGTAAGTTTGTAATTGGTTAGTA 58.897 37.037 0.00 0.00 0.00 1.82
3051 3561 9.159364 GGGAGTAAGTTTGTAATTGGTTAGTAG 57.841 37.037 0.00 0.00 0.00 2.57
3052 3562 9.933723 GGAGTAAGTTTGTAATTGGTTAGTAGA 57.066 33.333 0.00 0.00 0.00 2.59
3094 3604 8.883731 ACTCATGTATTTGTTTGTATGTCTAGC 58.116 33.333 0.00 0.00 0.00 3.42
3095 3605 8.208718 TCATGTATTTGTTTGTATGTCTAGCC 57.791 34.615 0.00 0.00 0.00 3.93
3096 3606 6.656314 TGTATTTGTTTGTATGTCTAGCCG 57.344 37.500 0.00 0.00 0.00 5.52
3097 3607 6.399743 TGTATTTGTTTGTATGTCTAGCCGA 58.600 36.000 0.00 0.00 0.00 5.54
3098 3608 6.533723 TGTATTTGTTTGTATGTCTAGCCGAG 59.466 38.462 0.00 0.00 0.00 4.63
3099 3609 4.794278 TTGTTTGTATGTCTAGCCGAGA 57.206 40.909 0.00 0.00 0.00 4.04
3100 3610 5.339008 TTGTTTGTATGTCTAGCCGAGAT 57.661 39.130 0.00 0.00 36.29 2.75
3101 3611 5.339008 TGTTTGTATGTCTAGCCGAGATT 57.661 39.130 0.00 0.00 36.29 2.40
3102 3612 5.109210 TGTTTGTATGTCTAGCCGAGATTG 58.891 41.667 0.00 0.00 36.29 2.67
3103 3613 3.371102 TGTATGTCTAGCCGAGATTGC 57.629 47.619 0.00 0.00 36.29 3.56
3104 3614 2.693074 TGTATGTCTAGCCGAGATTGCA 59.307 45.455 0.00 0.00 36.29 4.08
3105 3615 2.988010 ATGTCTAGCCGAGATTGCAA 57.012 45.000 0.00 0.00 36.29 4.08
3106 3616 2.760634 TGTCTAGCCGAGATTGCAAA 57.239 45.000 1.71 0.00 36.29 3.68
3107 3617 3.052455 TGTCTAGCCGAGATTGCAAAA 57.948 42.857 1.71 0.00 36.29 2.44
3108 3618 3.407698 TGTCTAGCCGAGATTGCAAAAA 58.592 40.909 1.71 0.00 36.29 1.94
3109 3619 4.009675 TGTCTAGCCGAGATTGCAAAAAT 58.990 39.130 1.71 0.00 36.29 1.82
3110 3620 4.094887 TGTCTAGCCGAGATTGCAAAAATC 59.905 41.667 1.71 0.00 36.29 2.17
3111 3621 4.333926 GTCTAGCCGAGATTGCAAAAATCT 59.666 41.667 1.71 1.08 39.53 2.40
3112 3622 4.943705 TCTAGCCGAGATTGCAAAAATCTT 59.056 37.500 1.71 0.00 37.14 2.40
3113 3623 4.525912 AGCCGAGATTGCAAAAATCTTT 57.474 36.364 1.71 0.00 37.14 2.52
3114 3624 5.643379 AGCCGAGATTGCAAAAATCTTTA 57.357 34.783 1.71 0.00 37.14 1.85
3115 3625 6.212888 AGCCGAGATTGCAAAAATCTTTAT 57.787 33.333 1.71 0.00 37.14 1.40
3116 3626 6.268566 AGCCGAGATTGCAAAAATCTTTATC 58.731 36.000 1.71 0.00 37.14 1.75
3117 3627 6.096001 AGCCGAGATTGCAAAAATCTTTATCT 59.904 34.615 1.71 0.00 37.14 1.98
3118 3628 6.753744 GCCGAGATTGCAAAAATCTTTATCTT 59.246 34.615 1.71 0.00 37.14 2.40
3119 3629 7.276438 GCCGAGATTGCAAAAATCTTTATCTTT 59.724 33.333 1.71 0.00 37.14 2.52
3120 3630 9.787532 CCGAGATTGCAAAAATCTTTATCTTTA 57.212 29.630 1.71 0.00 37.14 1.85
3254 3770 7.064847 CCGCAGTACATGTTTAAGTTATAACCA 59.935 37.037 12.05 3.20 0.00 3.67
3264 3781 9.866798 TGTTTAAGTTATAACCAAACCGTTTTT 57.133 25.926 25.63 10.72 35.30 1.94
3339 3857 6.238374 CCGTTCATATTTAAGTCAGCCGAAAT 60.238 38.462 0.00 0.00 0.00 2.17
3673 4194 6.908825 TGCATACACAACTATGAAAAACCTC 58.091 36.000 0.00 0.00 0.00 3.85
3819 4343 2.546368 GTCACTGTCGGCAACACAAATA 59.454 45.455 0.00 0.00 33.24 1.40
3825 4349 3.755905 TGTCGGCAACACAAATATGATGT 59.244 39.130 0.00 0.00 31.20 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.562182 CTGGGTAAAACTTTGTGTCCCT 58.438 45.455 0.00 0.00 35.00 4.20
14 15 1.072806 GGTCCGAACCTGGGTAAAACT 59.927 52.381 0.00 0.00 42.80 2.66
77 79 8.865420 TCTACTCTTGTACTACCCATATCATC 57.135 38.462 0.00 0.00 0.00 2.92
110 112 3.034635 GGGTTTAGCCTCTCTGATCTCA 58.965 50.000 0.00 0.00 37.43 3.27
134 136 5.799213 ACAATCATACCATAGGCTAGCTTC 58.201 41.667 15.72 0.00 0.00 3.86
189 191 3.899360 TCCAGTGTCTATATAAACCGGGG 59.101 47.826 6.32 0.00 0.00 5.73
190 192 4.831155 TCTCCAGTGTCTATATAAACCGGG 59.169 45.833 6.32 0.00 0.00 5.73
208 210 3.502051 ATGTAACCCTAACCCTCTCCA 57.498 47.619 0.00 0.00 0.00 3.86
209 211 4.812653 TCTATGTAACCCTAACCCTCTCC 58.187 47.826 0.00 0.00 0.00 3.71
213 215 4.213513 CGACTCTATGTAACCCTAACCCT 58.786 47.826 0.00 0.00 0.00 4.34
215 217 3.956848 ACCGACTCTATGTAACCCTAACC 59.043 47.826 0.00 0.00 0.00 2.85
217 219 6.186957 TGTAACCGACTCTATGTAACCCTAA 58.813 40.000 0.00 0.00 0.00 2.69
228 230 4.858850 TCCTACCATTGTAACCGACTCTA 58.141 43.478 0.00 0.00 0.00 2.43
230 232 3.698040 TCTCCTACCATTGTAACCGACTC 59.302 47.826 0.00 0.00 0.00 3.36
231 233 3.705051 TCTCCTACCATTGTAACCGACT 58.295 45.455 0.00 0.00 0.00 4.18
243 245 4.999310 ACGGATATTCAGATCTCCTACCA 58.001 43.478 0.00 0.00 0.00 3.25
246 248 5.527951 GCGATACGGATATTCAGATCTCCTA 59.472 44.000 0.00 0.00 0.00 2.94
254 256 2.668457 GCTTGGCGATACGGATATTCAG 59.332 50.000 0.00 0.00 0.00 3.02
256 258 2.960819 AGCTTGGCGATACGGATATTC 58.039 47.619 0.00 0.00 0.00 1.75
257 259 3.067106 CAAGCTTGGCGATACGGATATT 58.933 45.455 19.14 0.00 0.00 1.28
272 274 0.396974 TTGGTGTGGAAGGCAAGCTT 60.397 50.000 0.00 0.00 0.00 3.74
279 281 2.230660 GACTTTCCTTGGTGTGGAAGG 58.769 52.381 0.00 0.00 43.48 3.46
308 310 2.126031 GAAGACTCCGTCCCGTGC 60.126 66.667 0.00 0.00 32.18 5.34
311 313 0.818296 AGATTGAAGACTCCGTCCCG 59.182 55.000 0.00 0.00 32.18 5.14
318 320 6.680874 ATGAAGATGCAAGATTGAAGACTC 57.319 37.500 0.00 0.00 0.00 3.36
319 321 7.337167 ACTATGAAGATGCAAGATTGAAGACT 58.663 34.615 0.00 0.00 0.00 3.24
333 335 4.457603 CCGGACTCCTAGACTATGAAGATG 59.542 50.000 0.00 0.00 0.00 2.90
336 338 2.554893 GCCGGACTCCTAGACTATGAAG 59.445 54.545 5.05 0.00 0.00 3.02
346 348 0.627451 TACCTTCAGCCGGACTCCTA 59.373 55.000 5.05 0.00 0.00 2.94
348 350 1.614413 CTATACCTTCAGCCGGACTCC 59.386 57.143 5.05 0.00 0.00 3.85
349 351 2.308690 ACTATACCTTCAGCCGGACTC 58.691 52.381 5.05 0.00 0.00 3.36
376 379 2.170607 CTGGATTAGGTGGTGTTCGGAT 59.829 50.000 0.00 0.00 0.00 4.18
405 408 0.323816 TTGGCCTTGTGTTGGTGTGA 60.324 50.000 3.32 0.00 0.00 3.58
417 420 4.835284 TTTCTTTGGTCTTTTTGGCCTT 57.165 36.364 3.32 0.00 42.07 4.35
432 435 1.268539 CGTCGCTTGGCACTTTTCTTT 60.269 47.619 0.00 0.00 0.00 2.52
433 436 0.307760 CGTCGCTTGGCACTTTTCTT 59.692 50.000 0.00 0.00 0.00 2.52
437 440 2.978010 CCCGTCGCTTGGCACTTT 60.978 61.111 0.00 0.00 0.00 2.66
457 460 1.003839 CTCGGCCTTGGTGCTGTTA 60.004 57.895 0.00 0.00 38.77 2.41
499 502 2.782222 GCGGGCCTCTCACACGATA 61.782 63.158 0.84 0.00 0.00 2.92
500 503 4.148825 GCGGGCCTCTCACACGAT 62.149 66.667 0.84 0.00 0.00 3.73
678 701 2.202756 CTAAGCGGCGACTGACCC 60.203 66.667 12.98 0.00 0.00 4.46
679 702 2.202756 CCTAAGCGGCGACTGACC 60.203 66.667 12.98 0.00 0.00 4.02
701 724 4.106925 GGAGCTGCACCAGGAGGG 62.107 72.222 11.41 0.00 44.81 4.30
702 725 4.463879 CGGAGCTGCACCAGGAGG 62.464 72.222 16.29 0.00 42.21 4.30
703 726 3.655810 GACGGAGCTGCACCAGGAG 62.656 68.421 16.29 2.33 36.10 3.69
704 727 3.695606 GACGGAGCTGCACCAGGA 61.696 66.667 16.29 0.00 31.21 3.86
705 728 4.767255 GGACGGAGCTGCACCAGG 62.767 72.222 16.29 3.39 31.21 4.45
706 729 4.767255 GGGACGGAGCTGCACCAG 62.767 72.222 16.29 10.86 34.12 4.00
719 742 3.310860 ATGGCTTCCGACGTGGGAC 62.311 63.158 19.87 8.73 38.76 4.46
720 743 3.000819 ATGGCTTCCGACGTGGGA 61.001 61.111 16.10 16.10 38.76 4.37
721 744 2.511600 GATGGCTTCCGACGTGGG 60.512 66.667 10.85 10.85 38.76 4.61
722 745 1.361668 CTTGATGGCTTCCGACGTGG 61.362 60.000 0.00 0.00 40.09 4.94
723 746 0.389817 TCTTGATGGCTTCCGACGTG 60.390 55.000 0.00 0.00 0.00 4.49
724 747 0.108615 CTCTTGATGGCTTCCGACGT 60.109 55.000 0.00 0.00 0.00 4.34
725 748 0.807667 CCTCTTGATGGCTTCCGACG 60.808 60.000 0.00 0.00 0.00 5.12
726 749 0.462759 CCCTCTTGATGGCTTCCGAC 60.463 60.000 0.00 0.00 0.00 4.79
727 750 1.626356 CCCCTCTTGATGGCTTCCGA 61.626 60.000 0.00 0.00 0.00 4.55
728 751 1.153086 CCCCTCTTGATGGCTTCCG 60.153 63.158 0.00 0.00 0.00 4.30
729 752 0.625849 TTCCCCTCTTGATGGCTTCC 59.374 55.000 0.00 0.00 0.00 3.46
730 753 1.409381 CCTTCCCCTCTTGATGGCTTC 60.409 57.143 0.00 0.00 0.00 3.86
731 754 0.627986 CCTTCCCCTCTTGATGGCTT 59.372 55.000 0.00 0.00 0.00 4.35
732 755 0.551131 ACCTTCCCCTCTTGATGGCT 60.551 55.000 0.00 0.00 31.87 4.75
733 756 0.106967 GACCTTCCCCTCTTGATGGC 60.107 60.000 0.00 0.00 31.87 4.40
734 757 1.211457 CTGACCTTCCCCTCTTGATGG 59.789 57.143 0.00 0.00 34.20 3.51
735 758 1.211457 CCTGACCTTCCCCTCTTGATG 59.789 57.143 0.00 0.00 0.00 3.07
736 759 1.589414 CCTGACCTTCCCCTCTTGAT 58.411 55.000 0.00 0.00 0.00 2.57
737 760 0.547712 CCCTGACCTTCCCCTCTTGA 60.548 60.000 0.00 0.00 0.00 3.02
738 761 1.566298 CCCCTGACCTTCCCCTCTTG 61.566 65.000 0.00 0.00 0.00 3.02
739 762 1.229984 CCCCTGACCTTCCCCTCTT 60.230 63.158 0.00 0.00 0.00 2.85
740 763 2.456840 CCCCTGACCTTCCCCTCT 59.543 66.667 0.00 0.00 0.00 3.69
741 764 2.692741 CCCCCTGACCTTCCCCTC 60.693 72.222 0.00 0.00 0.00 4.30
742 765 3.552911 ACCCCCTGACCTTCCCCT 61.553 66.667 0.00 0.00 0.00 4.79
743 766 3.015753 GACCCCCTGACCTTCCCC 61.016 72.222 0.00 0.00 0.00 4.81
794 1276 4.802051 ATCGTTGCTGGCGCCCAT 62.802 61.111 26.77 1.02 30.82 4.00
813 1295 4.798682 TCTCCCCTTCCTCCCCGC 62.799 72.222 0.00 0.00 0.00 6.13
837 1319 1.198094 TCGGCCTCCCACTTCATCAA 61.198 55.000 0.00 0.00 0.00 2.57
858 1340 3.471806 GGGGAAGTCTCCTCCCGC 61.472 72.222 3.87 0.00 44.46 6.13
859 1341 0.105658 TATGGGGAAGTCTCCTCCCG 60.106 60.000 3.87 0.00 42.35 5.14
861 1343 2.090999 AGTCTATGGGGAAGTCTCCTCC 60.091 54.545 0.00 0.00 42.35 4.30
864 1346 3.637694 GTGTAGTCTATGGGGAAGTCTCC 59.362 52.174 0.00 0.00 41.59 3.71
865 1347 3.315749 CGTGTAGTCTATGGGGAAGTCTC 59.684 52.174 0.00 0.00 0.00 3.36
885 1369 0.462403 ACTGCGGTAAACACCAACGT 60.462 50.000 0.00 0.00 0.00 3.99
901 1385 3.550678 GCCTTTTCTCGAATACGGTACTG 59.449 47.826 0.00 0.00 40.21 2.74
959 1458 9.516314 GGGCTTTTTACATGCTTTTATAGTAAG 57.484 33.333 0.00 0.00 0.00 2.34
960 1459 8.185505 CGGGCTTTTTACATGCTTTTATAGTAA 58.814 33.333 0.00 0.00 0.00 2.24
961 1460 7.553402 TCGGGCTTTTTACATGCTTTTATAGTA 59.447 33.333 0.00 0.00 0.00 1.82
962 1461 6.376018 TCGGGCTTTTTACATGCTTTTATAGT 59.624 34.615 0.00 0.00 0.00 2.12
963 1462 6.691388 GTCGGGCTTTTTACATGCTTTTATAG 59.309 38.462 0.00 0.00 0.00 1.31
964 1463 6.557110 GTCGGGCTTTTTACATGCTTTTATA 58.443 36.000 0.00 0.00 0.00 0.98
996 1495 3.951663 AGGCAGTTATTAGGTGGTGAAC 58.048 45.455 0.00 0.00 0.00 3.18
1078 1582 1.228124 CTGCGGGGTGTGGAAGAAA 60.228 57.895 0.00 0.00 0.00 2.52
1145 1649 3.155167 GGGGTCGGAGAAGGCGAT 61.155 66.667 0.00 0.00 39.69 4.58
1369 1873 3.338250 TTGGAGCCCTTGGGCGAT 61.338 61.111 23.26 8.57 40.23 4.58
1596 2100 0.034896 GTTCGGAGAAGCCAGGAACA 59.965 55.000 0.00 0.00 45.90 3.18
2137 2641 1.600663 GGTGACTGATACGGCGATGAG 60.601 57.143 16.62 9.04 0.00 2.90
2217 2721 0.107165 GAGGAAATGGCTTACCCGCT 60.107 55.000 0.00 0.00 35.87 5.52
2243 2747 3.409026 ACAGAGAGAACATGGACAACC 57.591 47.619 0.00 0.00 0.00 3.77
2274 2778 2.537730 GCGAACTTCGAATGATTCAGGC 60.538 50.000 15.43 0.46 43.74 4.85
2327 2836 0.105039 CTGACTACCCAAGGATCGCC 59.895 60.000 0.00 0.00 0.00 5.54
2339 2848 6.959361 TGAAACTGCTCATTTTTCTGACTAC 58.041 36.000 0.00 0.00 31.68 2.73
2342 2851 7.704789 AAATGAAACTGCTCATTTTTCTGAC 57.295 32.000 10.79 0.00 45.36 3.51
2358 2867 4.023536 TCCTACCGCTGAACAAAATGAAAC 60.024 41.667 0.00 0.00 0.00 2.78
2376 2885 4.433615 TGCATTCTCGAGTGATTTCCTAC 58.566 43.478 13.13 0.00 0.00 3.18
2379 2888 3.436704 TGTTGCATTCTCGAGTGATTTCC 59.563 43.478 13.13 0.00 0.00 3.13
2398 2907 5.461737 ACAAAATGATCGCGATTTGTTTGTT 59.538 32.000 31.08 22.41 41.75 2.83
2399 2908 4.981674 ACAAAATGATCGCGATTTGTTTGT 59.018 33.333 31.08 31.08 41.75 2.83
2400 2909 5.499268 ACAAAATGATCGCGATTTGTTTG 57.501 34.783 30.25 30.25 41.75 2.93
2492 3001 1.950909 TCGTTAAGGCAAACCACCAAG 59.049 47.619 0.00 0.00 39.06 3.61
2521 3031 0.820074 CCCTCGCTCTCCTGTACGAT 60.820 60.000 0.00 0.00 33.53 3.73
2754 3264 4.552166 ACAGCTTTCATAACACACACAC 57.448 40.909 0.00 0.00 0.00 3.82
2763 3273 4.570772 GTCCATTCGCTACAGCTTTCATAA 59.429 41.667 0.00 0.00 39.32 1.90
2779 3289 3.444388 ACTACAGAGAGAACCGTCCATTC 59.556 47.826 0.00 0.00 0.00 2.67
2781 3291 3.088789 ACTACAGAGAGAACCGTCCAT 57.911 47.619 0.00 0.00 0.00 3.41
2802 3312 3.897239 TCAAGAAGAAAACAGCTGGGAA 58.103 40.909 19.93 0.00 0.00 3.97
2807 3317 6.976925 CAGTTCAAATCAAGAAGAAAACAGCT 59.023 34.615 0.00 0.00 0.00 4.24
2815 3325 6.267817 CACTTTGCAGTTCAAATCAAGAAGA 58.732 36.000 0.00 0.00 43.14 2.87
2833 3343 3.968724 GTCTTTGACGCTTTAGCACTTTG 59.031 43.478 2.29 0.00 42.21 2.77
2867 3377 1.009078 GGAACGGCGTACATTTACCC 58.991 55.000 15.20 1.00 0.00 3.69
2889 3399 4.202151 CGGAGATCACCATCACATCAACTA 60.202 45.833 9.99 0.00 0.00 2.24
2890 3400 3.431346 CGGAGATCACCATCACATCAACT 60.431 47.826 9.99 0.00 0.00 3.16
2891 3401 2.868583 CGGAGATCACCATCACATCAAC 59.131 50.000 9.99 0.00 0.00 3.18
2892 3402 2.742856 GCGGAGATCACCATCACATCAA 60.743 50.000 9.99 0.00 0.00 2.57
2893 3403 1.202568 GCGGAGATCACCATCACATCA 60.203 52.381 9.99 0.00 0.00 3.07
2936 3446 9.575868 TGTAAAACCCTGTAACTCATTTATTGA 57.424 29.630 0.00 0.00 0.00 2.57
2969 3479 8.933653 CCCCACCTATTAACCAATCAAATTAAT 58.066 33.333 0.00 0.00 33.97 1.40
2970 3480 8.123130 TCCCCACCTATTAACCAATCAAATTAA 58.877 33.333 0.00 0.00 0.00 1.40
2971 3481 7.653503 TCCCCACCTATTAACCAATCAAATTA 58.346 34.615 0.00 0.00 0.00 1.40
2972 3482 6.507568 TCCCCACCTATTAACCAATCAAATT 58.492 36.000 0.00 0.00 0.00 1.82
2973 3483 6.068498 TCTCCCCACCTATTAACCAATCAAAT 60.068 38.462 0.00 0.00 0.00 2.32
2974 3484 5.254267 TCTCCCCACCTATTAACCAATCAAA 59.746 40.000 0.00 0.00 0.00 2.69
2975 3485 4.791334 TCTCCCCACCTATTAACCAATCAA 59.209 41.667 0.00 0.00 0.00 2.57
2976 3486 4.376223 TCTCCCCACCTATTAACCAATCA 58.624 43.478 0.00 0.00 0.00 2.57
2977 3487 5.316987 CATCTCCCCACCTATTAACCAATC 58.683 45.833 0.00 0.00 0.00 2.67
2978 3488 4.106341 CCATCTCCCCACCTATTAACCAAT 59.894 45.833 0.00 0.00 0.00 3.16
2979 3489 3.461831 CCATCTCCCCACCTATTAACCAA 59.538 47.826 0.00 0.00 0.00 3.67
2980 3490 3.053077 CCATCTCCCCACCTATTAACCA 58.947 50.000 0.00 0.00 0.00 3.67
2981 3491 2.224793 GCCATCTCCCCACCTATTAACC 60.225 54.545 0.00 0.00 0.00 2.85
2982 3492 2.224793 GGCCATCTCCCCACCTATTAAC 60.225 54.545 0.00 0.00 0.00 2.01
2983 3493 2.062636 GGCCATCTCCCCACCTATTAA 58.937 52.381 0.00 0.00 0.00 1.40
2984 3494 1.742308 GGCCATCTCCCCACCTATTA 58.258 55.000 0.00 0.00 0.00 0.98
2985 3495 1.068352 GGGCCATCTCCCCACCTATT 61.068 60.000 4.39 0.00 42.36 1.73
2986 3496 1.464198 GGGCCATCTCCCCACCTAT 60.464 63.158 4.39 0.00 42.36 2.57
2987 3497 2.039831 GGGCCATCTCCCCACCTA 60.040 66.667 4.39 0.00 42.36 3.08
2993 3503 2.168272 AAAAGGGTGGGCCATCTCCC 62.168 60.000 20.49 20.49 46.73 4.30
2994 3504 0.252239 AAAAAGGGTGGGCCATCTCC 60.252 55.000 17.95 15.32 36.17 3.71
2995 3505 0.897621 CAAAAAGGGTGGGCCATCTC 59.102 55.000 17.95 7.33 36.17 2.75
2996 3506 0.486879 TCAAAAAGGGTGGGCCATCT 59.513 50.000 17.95 11.59 36.17 2.90
2997 3507 1.347062 TTCAAAAAGGGTGGGCCATC 58.653 50.000 10.70 9.68 36.17 3.51
2998 3508 1.813102 TTTCAAAAAGGGTGGGCCAT 58.187 45.000 10.70 0.00 36.17 4.40
2999 3509 1.584724 TTTTCAAAAAGGGTGGGCCA 58.415 45.000 0.00 0.00 36.17 5.36
3000 3510 2.105649 TGATTTTCAAAAAGGGTGGGCC 59.894 45.455 0.00 0.00 0.00 5.80
3001 3511 3.483808 TGATTTTCAAAAAGGGTGGGC 57.516 42.857 0.00 0.00 0.00 5.36
3002 3512 4.388485 CCTTGATTTTCAAAAAGGGTGGG 58.612 43.478 0.00 0.00 35.73 4.61
3007 3517 4.347876 ACTCCCCCTTGATTTTCAAAAAGG 59.652 41.667 0.00 0.00 35.73 3.11
3008 3518 5.551305 ACTCCCCCTTGATTTTCAAAAAG 57.449 39.130 0.00 0.00 35.73 2.27
3009 3519 6.613679 ACTTACTCCCCCTTGATTTTCAAAAA 59.386 34.615 0.00 0.00 35.73 1.94
3010 3520 6.140377 ACTTACTCCCCCTTGATTTTCAAAA 58.860 36.000 0.00 0.00 35.73 2.44
3011 3521 5.711698 ACTTACTCCCCCTTGATTTTCAAA 58.288 37.500 0.00 0.00 35.73 2.69
3012 3522 5.333566 ACTTACTCCCCCTTGATTTTCAA 57.666 39.130 0.00 0.00 34.79 2.69
3013 3523 5.333566 AACTTACTCCCCCTTGATTTTCA 57.666 39.130 0.00 0.00 0.00 2.69
3014 3524 5.538813 ACAAACTTACTCCCCCTTGATTTTC 59.461 40.000 0.00 0.00 0.00 2.29
3015 3525 5.464069 ACAAACTTACTCCCCCTTGATTTT 58.536 37.500 0.00 0.00 0.00 1.82
3016 3526 5.074746 ACAAACTTACTCCCCCTTGATTT 57.925 39.130 0.00 0.00 0.00 2.17
3017 3527 4.741928 ACAAACTTACTCCCCCTTGATT 57.258 40.909 0.00 0.00 0.00 2.57
3018 3528 5.853572 TTACAAACTTACTCCCCCTTGAT 57.146 39.130 0.00 0.00 0.00 2.57
3019 3529 5.853572 ATTACAAACTTACTCCCCCTTGA 57.146 39.130 0.00 0.00 0.00 3.02
3020 3530 5.185056 CCAATTACAAACTTACTCCCCCTTG 59.815 44.000 0.00 0.00 0.00 3.61
3021 3531 5.162914 ACCAATTACAAACTTACTCCCCCTT 60.163 40.000 0.00 0.00 0.00 3.95
3022 3532 4.355889 ACCAATTACAAACTTACTCCCCCT 59.644 41.667 0.00 0.00 0.00 4.79
3023 3533 4.669700 ACCAATTACAAACTTACTCCCCC 58.330 43.478 0.00 0.00 0.00 5.40
3024 3534 6.944290 ACTAACCAATTACAAACTTACTCCCC 59.056 38.462 0.00 0.00 0.00 4.81
3025 3535 7.991084 ACTAACCAATTACAAACTTACTCCC 57.009 36.000 0.00 0.00 0.00 4.30
3026 3536 9.933723 TCTACTAACCAATTACAAACTTACTCC 57.066 33.333 0.00 0.00 0.00 3.85
3068 3578 8.883731 GCTAGACATACAAACAAATACATGAGT 58.116 33.333 0.00 0.00 0.00 3.41
3069 3579 8.338259 GGCTAGACATACAAACAAATACATGAG 58.662 37.037 0.00 0.00 0.00 2.90
3070 3580 7.011016 CGGCTAGACATACAAACAAATACATGA 59.989 37.037 0.00 0.00 0.00 3.07
3071 3581 7.011016 TCGGCTAGACATACAAACAAATACATG 59.989 37.037 0.00 0.00 0.00 3.21
3072 3582 7.045416 TCGGCTAGACATACAAACAAATACAT 58.955 34.615 0.00 0.00 0.00 2.29
3073 3583 6.399743 TCGGCTAGACATACAAACAAATACA 58.600 36.000 0.00 0.00 0.00 2.29
3074 3584 6.755141 TCTCGGCTAGACATACAAACAAATAC 59.245 38.462 0.00 0.00 0.00 1.89
3075 3585 6.869695 TCTCGGCTAGACATACAAACAAATA 58.130 36.000 0.00 0.00 0.00 1.40
3076 3586 5.730550 TCTCGGCTAGACATACAAACAAAT 58.269 37.500 0.00 0.00 0.00 2.32
3077 3587 5.142061 TCTCGGCTAGACATACAAACAAA 57.858 39.130 0.00 0.00 0.00 2.83
3078 3588 4.794278 TCTCGGCTAGACATACAAACAA 57.206 40.909 0.00 0.00 0.00 2.83
3079 3589 5.109210 CAATCTCGGCTAGACATACAAACA 58.891 41.667 0.00 0.00 36.93 2.83
3080 3590 4.025647 GCAATCTCGGCTAGACATACAAAC 60.026 45.833 0.00 0.00 36.93 2.93
3081 3591 4.119862 GCAATCTCGGCTAGACATACAAA 58.880 43.478 0.00 0.00 36.93 2.83
3082 3592 3.132111 TGCAATCTCGGCTAGACATACAA 59.868 43.478 0.00 0.00 36.93 2.41
3083 3593 2.693074 TGCAATCTCGGCTAGACATACA 59.307 45.455 0.00 0.00 36.93 2.29
3084 3594 3.371102 TGCAATCTCGGCTAGACATAC 57.629 47.619 0.00 0.00 36.93 2.39
3085 3595 4.400529 TTTGCAATCTCGGCTAGACATA 57.599 40.909 0.00 0.00 36.93 2.29
3086 3596 2.988010 TTGCAATCTCGGCTAGACAT 57.012 45.000 0.00 0.00 36.93 3.06
3087 3597 2.760634 TTTGCAATCTCGGCTAGACA 57.239 45.000 0.00 0.00 36.93 3.41
3088 3598 4.333926 AGATTTTTGCAATCTCGGCTAGAC 59.666 41.667 0.00 0.00 36.93 2.59
3089 3599 4.517285 AGATTTTTGCAATCTCGGCTAGA 58.483 39.130 0.00 0.00 39.02 2.43
3090 3600 4.889832 AGATTTTTGCAATCTCGGCTAG 57.110 40.909 0.00 0.00 31.78 3.42
3091 3601 5.643379 AAAGATTTTTGCAATCTCGGCTA 57.357 34.783 0.00 0.00 36.07 3.93
3092 3602 4.525912 AAAGATTTTTGCAATCTCGGCT 57.474 36.364 0.00 0.00 36.07 5.52
3093 3603 6.268566 AGATAAAGATTTTTGCAATCTCGGC 58.731 36.000 0.00 0.00 36.07 5.54
3094 3604 8.693542 AAAGATAAAGATTTTTGCAATCTCGG 57.306 30.769 0.00 0.00 36.07 4.63
3181 3697 7.259161 GGGTTTATTTATAAAATGGCGTGACA 58.741 34.615 1.21 0.00 34.36 3.58
3196 3712 9.643735 TTTACAGAAAACTGAGGGGTTTATTTA 57.356 29.630 0.00 0.00 38.30 1.40
3286 3803 4.710324 TGATTGTCTAAAACGTCAGGGTT 58.290 39.130 0.00 0.00 0.00 4.11
3287 3804 4.345859 TGATTGTCTAAAACGTCAGGGT 57.654 40.909 0.00 0.00 0.00 4.34
3366 3886 6.548441 AGATTGATTAACCGAAACGTCAAA 57.452 33.333 0.00 0.00 0.00 2.69
3819 4343 7.173218 ACGTCTTTTAGTTTCACATGACATCAT 59.827 33.333 0.00 0.00 36.96 2.45
3825 4349 4.513692 CCCACGTCTTTTAGTTTCACATGA 59.486 41.667 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.