Multiple sequence alignment - TraesCS4A01G030500

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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 TraesCS4A01G030500 chr4A 100.000 2465 0 0 1 2465 23845008 23842544 0.000000e+00 4553
1 TraesCS4A01G030500 chr4A 94.084 1724 76 16 760 2465 23614743 23613028 0.000000e+00 2595
2 TraesCS4A01G030500 chr4A 95.600 250 9 2 204 453 23615016 23614769 1.370000e-107 399
3 TraesCS4A01G030500 chr4A 86.822 129 10 2 4 132 23615594 23615473 1.190000e-28 137
4 TraesCS4A01G030500 chr4D 93.716 1480 61 14 1003 2464 444173942 444175407 0.000000e+00 2189
5 TraesCS4A01G030500 chr4D 91.083 157 9 3 768 924 444173418 444173569 8.930000e-50 207
6 TraesCS4A01G030500 chr4B 90.795 1119 52 8 888 1991 553863652 553864734 0.000000e+00 1448
7 TraesCS4A01G030500 chr4B 95.376 173 7 1 2088 2260 553864735 553864906 8.680000e-70 274
8 TraesCS4A01G030500 chr4B 93.893 131 8 0 760 890 553862935 553863065 5.380000e-47 198
9 TraesCS4A01G030500 chr4B 83.871 124 16 1 1499 1622 625595274 625595393 5.570000e-22 115
10 TraesCS4A01G030500 chr1B 97.495 479 9 1 991 1469 344375648 344375173 0.000000e+00 815
11 TraesCS4A01G030500 chr1B 94.949 495 19 2 989 1483 434335383 434335871 0.000000e+00 771
12 TraesCS4A01G030500 chr1B 85.321 109 12 3 15 120 298165340 298165447 2.590000e-20 110
13 TraesCS4A01G030500 chr1A 87.677 706 68 14 770 1469 344190014 344189322 0.000000e+00 804
14 TraesCS4A01G030500 chr2B 94.567 497 21 2 988 1484 473299911 473300401 0.000000e+00 763
15 TraesCS4A01G030500 chr2A 94.567 497 21 2 988 1484 537003389 537003879 0.000000e+00 763
16 TraesCS4A01G030500 chr2A 91.509 212 15 3 508 717 723881550 723881340 3.100000e-74 289
17 TraesCS4A01G030500 chr2D 94.366 497 22 2 988 1484 399347615 399348105 0.000000e+00 758
18 TraesCS4A01G030500 chr5A 91.270 252 16 5 506 753 40028895 40029144 3.040000e-89 339
19 TraesCS4A01G030500 chr5A 90.654 214 15 4 508 717 480495192 480494980 1.870000e-71 279
20 TraesCS4A01G030500 chr7A 92.130 216 15 2 504 717 148983511 148983726 1.110000e-78 303
21 TraesCS4A01G030500 chr6A 91.905 210 15 2 508 715 585107213 585107004 2.400000e-75 292
22 TraesCS4A01G030500 chr6A 91.038 212 14 4 508 717 553185028 553185236 5.190000e-72 281
23 TraesCS4A01G030500 chr3A 91.038 212 16 3 505 714 22828370 22828580 1.440000e-72 283
24 TraesCS4A01G030500 chr3A 90.952 210 16 3 508 714 532344692 532344483 1.870000e-71 279
25 TraesCS4A01G030500 chr3A 90.566 212 17 3 506 714 358900511 358900722 6.710000e-71 278
26 TraesCS4A01G030500 chr7B 85.830 247 23 8 1384 1622 648782922 648782680 4.070000e-63 252
27 TraesCS4A01G030500 chr6B 83.871 124 16 4 10 132 173028879 173028999 5.570000e-22 115


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 TraesCS4A01G030500 chr4A 23842544 23845008 2464 True 4553.000000 4553 100.000000 1 2465 1 chr4A.!!$R1 2464
1 TraesCS4A01G030500 chr4A 23613028 23615594 2566 True 1043.666667 2595 92.168667 4 2465 3 chr4A.!!$R2 2461
2 TraesCS4A01G030500 chr4D 444173418 444175407 1989 False 1198.000000 2189 92.399500 768 2464 2 chr4D.!!$F1 1696
3 TraesCS4A01G030500 chr4B 553862935 553864906 1971 False 640.000000 1448 93.354667 760 2260 3 chr4B.!!$F2 1500
4 TraesCS4A01G030500 chr1A 344189322 344190014 692 True 804.000000 804 87.677000 770 1469 1 chr1A.!!$R1 699

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
489 875 0.032615 TGTTTTTCCCCACCACAGCT 60.033 50.0 0.0 0.0 0.0 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2329 3665 0.181824 ACTTGCCACGGTTAACAGGT 59.818 50.0 10.55 3.36 0.0 4.0 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
27 28 1.767759 CCTTCATGGAGGCCGATTTT 58.232 50.000 7.24 0.00 38.35 1.82
28 29 2.102578 CCTTCATGGAGGCCGATTTTT 58.897 47.619 7.24 0.00 38.35 1.94
120 121 4.256110 AGGATGTGATGTGTATGTGTGTG 58.744 43.478 0.00 0.00 0.00 3.82
129 130 5.733226 TGTGTATGTGTGTGAAACTTCAG 57.267 39.130 0.00 0.00 37.98 3.02
132 133 6.037062 TGTGTATGTGTGTGAAACTTCAGAAG 59.963 38.462 8.77 8.77 37.98 2.85
133 134 4.558538 ATGTGTGTGAAACTTCAGAAGC 57.441 40.909 10.33 0.00 37.98 3.86
134 135 2.682856 TGTGTGTGAAACTTCAGAAGCC 59.317 45.455 10.33 0.85 37.98 4.35
136 137 3.316308 GTGTGTGAAACTTCAGAAGCCAT 59.684 43.478 10.33 0.00 37.98 4.40
137 138 3.316029 TGTGTGAAACTTCAGAAGCCATG 59.684 43.478 10.33 0.00 37.98 3.66
138 139 2.886523 TGTGAAACTTCAGAAGCCATGG 59.113 45.455 7.63 7.63 37.98 3.66
139 140 3.149196 GTGAAACTTCAGAAGCCATGGA 58.851 45.455 18.40 0.00 37.98 3.41
140 141 3.760684 GTGAAACTTCAGAAGCCATGGAT 59.239 43.478 18.40 6.18 37.98 3.41
141 142 4.943705 GTGAAACTTCAGAAGCCATGGATA 59.056 41.667 18.40 0.00 37.98 2.59
142 143 4.943705 TGAAACTTCAGAAGCCATGGATAC 59.056 41.667 18.40 5.10 32.50 2.24
145 146 2.890808 TCAGAAGCCATGGATACGAC 57.109 50.000 18.40 1.95 42.51 4.34
146 147 1.412710 TCAGAAGCCATGGATACGACC 59.587 52.381 18.40 0.00 42.51 4.79
147 148 1.138859 CAGAAGCCATGGATACGACCA 59.861 52.381 18.40 0.00 44.41 4.02
148 149 1.837439 AGAAGCCATGGATACGACCAA 59.163 47.619 18.40 0.00 43.47 3.67
150 151 0.180406 AGCCATGGATACGACCAACC 59.820 55.000 18.40 0.00 43.47 3.77
152 153 1.663695 CCATGGATACGACCAACCAC 58.336 55.000 5.56 0.00 43.47 4.16
153 154 1.286501 CATGGATACGACCAACCACG 58.713 55.000 0.00 0.00 43.47 4.94
154 155 0.461339 ATGGATACGACCAACCACGC 60.461 55.000 0.00 0.00 43.47 5.34
155 156 1.079681 GGATACGACCAACCACGCA 60.080 57.895 0.00 0.00 0.00 5.24
157 158 1.365699 GATACGACCAACCACGCATT 58.634 50.000 0.00 0.00 0.00 3.56
158 159 1.062002 GATACGACCAACCACGCATTG 59.938 52.381 0.00 0.00 0.00 2.82
159 160 1.570347 TACGACCAACCACGCATTGC 61.570 55.000 0.00 0.00 0.00 3.56
160 161 2.258286 GACCAACCACGCATTGCC 59.742 61.111 2.41 0.00 0.00 4.52
161 162 3.281359 GACCAACCACGCATTGCCC 62.281 63.158 2.41 0.00 0.00 5.36
163 164 2.049248 CAACCACGCATTGCCCAC 60.049 61.111 2.41 0.00 0.00 4.61
167 168 4.041917 CACGCATTGCCCACGCTT 62.042 61.111 2.41 0.00 35.36 4.68
169 170 2.100216 CGCATTGCCCACGCTTAC 59.900 61.111 2.41 0.00 35.36 2.34
170 171 2.489751 GCATTGCCCACGCTTACC 59.510 61.111 0.00 0.00 35.36 2.85
171 172 2.339556 GCATTGCCCACGCTTACCA 61.340 57.895 0.00 0.00 35.36 3.25
172 173 1.802636 CATTGCCCACGCTTACCAG 59.197 57.895 0.00 0.00 35.36 4.00
173 174 1.378514 ATTGCCCACGCTTACCAGG 60.379 57.895 0.00 0.00 35.36 4.45
174 175 2.837031 ATTGCCCACGCTTACCAGGG 62.837 60.000 0.00 0.00 44.37 4.45
179 265 0.322322 CCACGCTTACCAGGGTACAA 59.678 55.000 0.00 0.00 44.20 2.41
180 266 1.674817 CCACGCTTACCAGGGTACAAG 60.675 57.143 0.00 0.00 44.20 3.16
185 271 2.423577 CTTACCAGGGTACAAGCACAC 58.576 52.381 0.00 0.00 0.00 3.82
186 272 1.425694 TACCAGGGTACAAGCACACA 58.574 50.000 0.00 0.00 0.00 3.72
187 273 0.548989 ACCAGGGTACAAGCACACAA 59.451 50.000 0.00 0.00 0.00 3.33
191 277 2.290641 CAGGGTACAAGCACACAAGTTC 59.709 50.000 0.00 0.00 0.00 3.01
192 278 1.263217 GGGTACAAGCACACAAGTTCG 59.737 52.381 0.00 0.00 0.00 3.95
193 279 1.937899 GGTACAAGCACACAAGTTCGT 59.062 47.619 0.00 0.00 0.00 3.85
196 282 0.042188 CAAGCACACAAGTTCGTCCG 60.042 55.000 0.00 0.00 0.00 4.79
202 288 0.790207 CACAAGTTCGTCCGTCATGG 59.210 55.000 0.00 0.00 40.09 3.66
226 612 2.511900 TGGTGTCCCCACGGTTTC 59.488 61.111 0.00 0.00 42.80 2.78
421 807 2.960384 TCTGCCGTTCCGATATCCTTTA 59.040 45.455 0.00 0.00 0.00 1.85
428 814 5.451520 CCGTTCCGATATCCTTTACTTGTCT 60.452 44.000 0.00 0.00 0.00 3.41
489 875 0.032615 TGTTTTTCCCCACCACAGCT 60.033 50.000 0.00 0.00 0.00 4.24
490 876 1.215673 TGTTTTTCCCCACCACAGCTA 59.784 47.619 0.00 0.00 0.00 3.32
491 877 2.158385 TGTTTTTCCCCACCACAGCTAT 60.158 45.455 0.00 0.00 0.00 2.97
492 878 3.074687 TGTTTTTCCCCACCACAGCTATA 59.925 43.478 0.00 0.00 0.00 1.31
493 879 4.264172 TGTTTTTCCCCACCACAGCTATAT 60.264 41.667 0.00 0.00 0.00 0.86
494 880 5.044772 TGTTTTTCCCCACCACAGCTATATA 60.045 40.000 0.00 0.00 0.00 0.86
495 881 4.699925 TTTCCCCACCACAGCTATATAC 57.300 45.455 0.00 0.00 0.00 1.47
496 882 2.244695 TCCCCACCACAGCTATATACG 58.755 52.381 0.00 0.00 0.00 3.06
497 883 1.337823 CCCCACCACAGCTATATACGC 60.338 57.143 0.00 0.00 0.00 4.42
498 884 1.343142 CCCACCACAGCTATATACGCA 59.657 52.381 0.00 0.00 0.00 5.24
499 885 2.224185 CCCACCACAGCTATATACGCAA 60.224 50.000 0.00 0.00 0.00 4.85
500 886 3.462982 CCACCACAGCTATATACGCAAA 58.537 45.455 0.00 0.00 0.00 3.68
501 887 3.247648 CCACCACAGCTATATACGCAAAC 59.752 47.826 0.00 0.00 0.00 2.93
502 888 3.247648 CACCACAGCTATATACGCAAACC 59.752 47.826 0.00 0.00 0.00 3.27
503 889 2.806244 CCACAGCTATATACGCAAACCC 59.194 50.000 0.00 0.00 0.00 4.11
504 890 2.806244 CACAGCTATATACGCAAACCCC 59.194 50.000 0.00 0.00 0.00 4.95
505 891 2.704065 ACAGCTATATACGCAAACCCCT 59.296 45.455 0.00 0.00 0.00 4.79
506 892 3.067106 CAGCTATATACGCAAACCCCTG 58.933 50.000 0.00 0.00 0.00 4.45
507 893 2.969950 AGCTATATACGCAAACCCCTGA 59.030 45.455 0.00 0.00 0.00 3.86
508 894 3.006967 AGCTATATACGCAAACCCCTGAG 59.993 47.826 0.00 0.00 0.00 3.35
509 895 2.930826 ATATACGCAAACCCCTGAGG 57.069 50.000 0.00 0.00 43.78 3.86
510 896 0.179468 TATACGCAAACCCCTGAGGC 59.821 55.000 0.00 0.00 40.58 4.70
511 897 1.562672 ATACGCAAACCCCTGAGGCT 61.563 55.000 0.00 0.00 40.58 4.58
512 898 0.905809 TACGCAAACCCCTGAGGCTA 60.906 55.000 0.00 0.00 40.58 3.93
513 899 1.450312 CGCAAACCCCTGAGGCTAG 60.450 63.158 0.00 0.00 40.58 3.42
514 900 1.685820 GCAAACCCCTGAGGCTAGT 59.314 57.895 0.00 0.00 40.58 2.57
515 901 0.393132 GCAAACCCCTGAGGCTAGTC 60.393 60.000 0.00 0.00 40.58 2.59
516 902 0.984230 CAAACCCCTGAGGCTAGTCA 59.016 55.000 0.00 0.00 40.58 3.41
517 903 1.561542 CAAACCCCTGAGGCTAGTCAT 59.438 52.381 0.00 0.00 40.58 3.06
518 904 2.771943 CAAACCCCTGAGGCTAGTCATA 59.228 50.000 0.00 0.00 40.58 2.15
519 905 2.390225 ACCCCTGAGGCTAGTCATAG 57.610 55.000 0.00 0.00 40.58 2.23
520 906 1.576272 ACCCCTGAGGCTAGTCATAGT 59.424 52.381 0.00 0.00 40.58 2.12
521 907 1.967066 CCCCTGAGGCTAGTCATAGTG 59.033 57.143 0.00 0.00 0.00 2.74
522 908 2.424957 CCCCTGAGGCTAGTCATAGTGA 60.425 54.545 0.00 0.00 0.00 3.41
523 909 2.890311 CCCTGAGGCTAGTCATAGTGAG 59.110 54.545 0.00 0.00 0.00 3.51
524 910 2.890311 CCTGAGGCTAGTCATAGTGAGG 59.110 54.545 0.00 0.00 0.00 3.86
525 911 2.890311 CTGAGGCTAGTCATAGTGAGGG 59.110 54.545 0.00 0.00 0.00 4.30
526 912 2.245028 TGAGGCTAGTCATAGTGAGGGT 59.755 50.000 0.00 0.00 0.00 4.34
527 913 3.462205 TGAGGCTAGTCATAGTGAGGGTA 59.538 47.826 0.00 0.00 0.00 3.69
528 914 4.079385 TGAGGCTAGTCATAGTGAGGGTAA 60.079 45.833 0.00 0.00 0.00 2.85
529 915 4.216708 AGGCTAGTCATAGTGAGGGTAAC 58.783 47.826 0.00 0.00 0.00 2.50
530 916 4.079096 AGGCTAGTCATAGTGAGGGTAACT 60.079 45.833 0.00 0.00 0.00 2.24
531 917 4.650131 GGCTAGTCATAGTGAGGGTAACTT 59.350 45.833 0.00 0.00 0.00 2.66
532 918 5.832060 GGCTAGTCATAGTGAGGGTAACTTA 59.168 44.000 0.00 0.00 0.00 2.24
533 919 6.016108 GGCTAGTCATAGTGAGGGTAACTTAG 60.016 46.154 0.00 0.00 0.00 2.18
534 920 6.771749 GCTAGTCATAGTGAGGGTAACTTAGA 59.228 42.308 0.00 0.00 0.00 2.10
535 921 7.449086 GCTAGTCATAGTGAGGGTAACTTAGAT 59.551 40.741 0.00 0.00 0.00 1.98
538 924 9.710818 AGTCATAGTGAGGGTAACTTAGATAAA 57.289 33.333 0.00 0.00 0.00 1.40
581 967 8.900983 ACAATTTTGTTTATGTGGCAAGTATT 57.099 26.923 0.00 0.00 38.47 1.89
582 968 9.336171 ACAATTTTGTTTATGTGGCAAGTATTT 57.664 25.926 0.00 0.00 38.47 1.40
593 979 8.682936 ATGTGGCAAGTATTTAATAAGGAGAG 57.317 34.615 0.00 0.00 0.00 3.20
594 980 7.857456 TGTGGCAAGTATTTAATAAGGAGAGA 58.143 34.615 0.00 0.00 0.00 3.10
595 981 7.987458 TGTGGCAAGTATTTAATAAGGAGAGAG 59.013 37.037 0.00 0.00 0.00 3.20
596 982 7.442666 GTGGCAAGTATTTAATAAGGAGAGAGG 59.557 40.741 0.00 0.00 0.00 3.69
597 983 7.127339 TGGCAAGTATTTAATAAGGAGAGAGGT 59.873 37.037 0.00 0.00 0.00 3.85
598 984 7.442666 GGCAAGTATTTAATAAGGAGAGAGGTG 59.557 40.741 0.00 0.00 0.00 4.00
599 985 7.041712 GCAAGTATTTAATAAGGAGAGAGGTGC 60.042 40.741 0.00 0.00 0.00 5.01
600 986 7.922699 AGTATTTAATAAGGAGAGAGGTGCT 57.077 36.000 0.00 0.00 0.00 4.40
601 987 8.325477 AGTATTTAATAAGGAGAGAGGTGCTT 57.675 34.615 0.00 0.00 32.20 3.91
602 988 8.207545 AGTATTTAATAAGGAGAGAGGTGCTTG 58.792 37.037 0.00 0.00 29.82 4.01
603 989 6.620877 TTTAATAAGGAGAGAGGTGCTTGA 57.379 37.500 0.00 0.00 29.82 3.02
604 990 6.620877 TTAATAAGGAGAGAGGTGCTTGAA 57.379 37.500 0.00 0.00 29.82 2.69
605 991 4.751767 ATAAGGAGAGAGGTGCTTGAAG 57.248 45.455 0.00 0.00 29.82 3.02
606 992 2.022718 AGGAGAGAGGTGCTTGAAGT 57.977 50.000 0.00 0.00 0.00 3.01
607 993 3.176924 AGGAGAGAGGTGCTTGAAGTA 57.823 47.619 0.00 0.00 0.00 2.24
608 994 3.511477 AGGAGAGAGGTGCTTGAAGTAA 58.489 45.455 0.00 0.00 0.00 2.24
609 995 3.259625 AGGAGAGAGGTGCTTGAAGTAAC 59.740 47.826 0.00 0.00 0.00 2.50
610 996 3.006967 GGAGAGAGGTGCTTGAAGTAACA 59.993 47.826 0.30 0.00 0.00 2.41
611 997 4.323104 GGAGAGAGGTGCTTGAAGTAACAT 60.323 45.833 0.30 0.00 0.00 2.71
612 998 5.105310 GGAGAGAGGTGCTTGAAGTAACATA 60.105 44.000 0.30 0.00 0.00 2.29
613 999 6.360370 AGAGAGGTGCTTGAAGTAACATAA 57.640 37.500 0.30 0.00 0.00 1.90
614 1000 6.951971 AGAGAGGTGCTTGAAGTAACATAAT 58.048 36.000 0.30 0.00 0.00 1.28
615 1001 8.079211 AGAGAGGTGCTTGAAGTAACATAATA 57.921 34.615 0.30 0.00 0.00 0.98
616 1002 8.709308 AGAGAGGTGCTTGAAGTAACATAATAT 58.291 33.333 0.30 0.00 0.00 1.28
617 1003 8.668510 AGAGGTGCTTGAAGTAACATAATATG 57.331 34.615 0.30 0.00 0.00 1.78
633 1019 8.520835 ACATAATATGTTACTGTCACATAGCG 57.479 34.615 17.03 9.61 41.63 4.26
634 1020 5.907197 AATATGTTACTGTCACATAGCGC 57.093 39.130 17.03 0.00 39.83 5.92
635 1021 3.526931 ATGTTACTGTCACATAGCGCT 57.473 42.857 17.26 17.26 32.88 5.92
636 1022 3.313012 TGTTACTGTCACATAGCGCTT 57.687 42.857 18.68 0.00 0.00 4.68
637 1023 3.250744 TGTTACTGTCACATAGCGCTTC 58.749 45.455 18.68 0.18 0.00 3.86
638 1024 2.579207 TACTGTCACATAGCGCTTCC 57.421 50.000 18.68 0.00 0.00 3.46
639 1025 0.108138 ACTGTCACATAGCGCTTCCC 60.108 55.000 18.68 0.00 0.00 3.97
640 1026 1.148157 CTGTCACATAGCGCTTCCCG 61.148 60.000 18.68 4.15 40.75 5.14
641 1027 1.141019 GTCACATAGCGCTTCCCGA 59.859 57.895 18.68 5.06 40.02 5.14
642 1028 0.872021 GTCACATAGCGCTTCCCGAG 60.872 60.000 18.68 1.08 40.02 4.63
643 1029 1.141881 CACATAGCGCTTCCCGAGT 59.858 57.895 18.68 2.50 40.02 4.18
644 1030 0.384309 CACATAGCGCTTCCCGAGTA 59.616 55.000 18.68 0.00 40.02 2.59
645 1031 1.108776 ACATAGCGCTTCCCGAGTAA 58.891 50.000 18.68 0.00 40.02 2.24
646 1032 1.479323 ACATAGCGCTTCCCGAGTAAA 59.521 47.619 18.68 0.00 40.02 2.01
647 1033 2.093869 ACATAGCGCTTCCCGAGTAAAA 60.094 45.455 18.68 0.00 40.02 1.52
648 1034 2.973694 TAGCGCTTCCCGAGTAAAAT 57.026 45.000 18.68 0.00 40.02 1.82
649 1035 1.369625 AGCGCTTCCCGAGTAAAATG 58.630 50.000 2.64 0.00 40.02 2.32
650 1036 1.066430 AGCGCTTCCCGAGTAAAATGA 60.066 47.619 2.64 0.00 40.02 2.57
651 1037 1.327764 GCGCTTCCCGAGTAAAATGAG 59.672 52.381 0.00 0.00 40.02 2.90
652 1038 2.618053 CGCTTCCCGAGTAAAATGAGT 58.382 47.619 0.00 0.00 40.02 3.41
653 1039 2.603560 CGCTTCCCGAGTAAAATGAGTC 59.396 50.000 0.00 0.00 40.02 3.36
654 1040 3.676324 CGCTTCCCGAGTAAAATGAGTCT 60.676 47.826 0.00 0.00 40.02 3.24
655 1041 4.439700 CGCTTCCCGAGTAAAATGAGTCTA 60.440 45.833 0.00 0.00 40.02 2.59
656 1042 5.602628 GCTTCCCGAGTAAAATGAGTCTAT 58.397 41.667 0.00 0.00 0.00 1.98
657 1043 6.514541 CGCTTCCCGAGTAAAATGAGTCTATA 60.515 42.308 0.00 0.00 40.02 1.31
658 1044 7.208080 GCTTCCCGAGTAAAATGAGTCTATAA 58.792 38.462 0.00 0.00 0.00 0.98
659 1045 7.382759 GCTTCCCGAGTAAAATGAGTCTATAAG 59.617 40.741 0.00 0.00 0.00 1.73
660 1046 8.529424 TTCCCGAGTAAAATGAGTCTATAAGA 57.471 34.615 0.00 0.00 0.00 2.10
661 1047 7.938715 TCCCGAGTAAAATGAGTCTATAAGAC 58.061 38.462 0.00 0.00 45.38 3.01
719 1105 9.656323 AAGATACTTTGTACTATGAGGGTATGA 57.344 33.333 0.00 0.00 0.00 2.15
720 1106 9.080097 AGATACTTTGTACTATGAGGGTATGAC 57.920 37.037 0.00 0.00 0.00 3.06
721 1107 8.777578 ATACTTTGTACTATGAGGGTATGACA 57.222 34.615 0.00 0.00 0.00 3.58
722 1108 6.875076 ACTTTGTACTATGAGGGTATGACAC 58.125 40.000 0.00 0.00 0.00 3.67
723 1109 6.668283 ACTTTGTACTATGAGGGTATGACACT 59.332 38.462 0.00 0.00 32.13 3.55
724 1110 7.837689 ACTTTGTACTATGAGGGTATGACACTA 59.162 37.037 0.00 0.00 27.47 2.74
725 1111 7.818997 TTGTACTATGAGGGTATGACACTAG 57.181 40.000 0.00 0.00 27.47 2.57
726 1112 6.907961 TGTACTATGAGGGTATGACACTAGT 58.092 40.000 0.00 0.00 27.47 2.57
727 1113 6.996879 TGTACTATGAGGGTATGACACTAGTC 59.003 42.308 0.00 0.00 45.19 2.59
728 1114 6.268855 ACTATGAGGGTATGACACTAGTCT 57.731 41.667 0.00 0.00 45.20 3.24
729 1115 7.390013 ACTATGAGGGTATGACACTAGTCTA 57.610 40.000 0.00 0.00 45.20 2.59
730 1116 7.813331 ACTATGAGGGTATGACACTAGTCTAA 58.187 38.462 0.00 0.00 45.20 2.10
731 1117 7.940137 ACTATGAGGGTATGACACTAGTCTAAG 59.060 40.741 0.00 0.00 45.20 2.18
732 1118 6.075949 TGAGGGTATGACACTAGTCTAAGT 57.924 41.667 0.00 0.00 45.20 2.24
733 1119 6.491383 TGAGGGTATGACACTAGTCTAAGTT 58.509 40.000 0.00 0.00 45.20 2.66
734 1120 6.952358 TGAGGGTATGACACTAGTCTAAGTTT 59.048 38.462 0.00 0.00 45.20 2.66
735 1121 7.122353 TGAGGGTATGACACTAGTCTAAGTTTC 59.878 40.741 0.00 0.00 45.20 2.78
736 1122 6.380560 AGGGTATGACACTAGTCTAAGTTTCC 59.619 42.308 0.00 0.00 45.20 3.13
737 1123 6.406737 GGGTATGACACTAGTCTAAGTTTCCC 60.407 46.154 0.00 0.00 45.20 3.97
738 1124 5.678955 ATGACACTAGTCTAAGTTTCCCC 57.321 43.478 0.00 0.00 45.20 4.81
739 1125 4.485875 TGACACTAGTCTAAGTTTCCCCA 58.514 43.478 0.00 0.00 45.20 4.96
740 1126 4.282703 TGACACTAGTCTAAGTTTCCCCAC 59.717 45.833 0.00 0.00 45.20 4.61
741 1127 4.490706 ACACTAGTCTAAGTTTCCCCACT 58.509 43.478 0.00 0.00 0.00 4.00
742 1128 5.648247 ACACTAGTCTAAGTTTCCCCACTA 58.352 41.667 0.00 0.00 0.00 2.74
743 1129 6.262207 ACACTAGTCTAAGTTTCCCCACTAT 58.738 40.000 0.00 0.00 0.00 2.12
744 1130 6.154706 ACACTAGTCTAAGTTTCCCCACTATG 59.845 42.308 0.00 0.00 0.00 2.23
745 1131 6.380274 CACTAGTCTAAGTTTCCCCACTATGA 59.620 42.308 0.00 0.00 0.00 2.15
746 1132 5.678955 AGTCTAAGTTTCCCCACTATGAC 57.321 43.478 0.00 0.00 33.10 3.06
747 1133 4.470304 AGTCTAAGTTTCCCCACTATGACC 59.530 45.833 0.00 0.00 33.24 4.02
748 1134 4.224370 GTCTAAGTTTCCCCACTATGACCA 59.776 45.833 0.00 0.00 0.00 4.02
749 1135 3.721087 AAGTTTCCCCACTATGACCAG 57.279 47.619 0.00 0.00 0.00 4.00
750 1136 1.282157 AGTTTCCCCACTATGACCAGC 59.718 52.381 0.00 0.00 0.00 4.85
751 1137 0.623723 TTTCCCCACTATGACCAGCC 59.376 55.000 0.00 0.00 0.00 4.85
752 1138 0.253160 TTCCCCACTATGACCAGCCT 60.253 55.000 0.00 0.00 0.00 4.58
753 1139 0.639943 TCCCCACTATGACCAGCCTA 59.360 55.000 0.00 0.00 0.00 3.93
754 1140 1.009060 TCCCCACTATGACCAGCCTAA 59.991 52.381 0.00 0.00 0.00 2.69
755 1141 1.843851 CCCCACTATGACCAGCCTAAA 59.156 52.381 0.00 0.00 0.00 1.85
756 1142 2.241176 CCCCACTATGACCAGCCTAAAA 59.759 50.000 0.00 0.00 0.00 1.52
757 1143 3.308832 CCCCACTATGACCAGCCTAAAAA 60.309 47.826 0.00 0.00 0.00 1.94
845 1234 3.458163 ATGTCACGGATCCGCGGT 61.458 61.111 33.62 12.40 44.19 5.68
1507 2787 0.392461 GCTGTTCGCCCTGGTTATCA 60.392 55.000 0.00 0.00 0.00 2.15
1532 2812 5.336849 CCAAGTAGAAGTAGTGCTAGTGCTT 60.337 44.000 0.25 0.00 40.48 3.91
1551 2831 2.885135 TGATGGGAGTTGCTGAATGT 57.115 45.000 0.00 0.00 0.00 2.71
1647 2928 1.783711 CGTCGCTTATGATCTGACTGC 59.216 52.381 0.00 0.00 0.00 4.40
1661 2943 2.357009 CTGACTGCTGTTGCTTTTCTGT 59.643 45.455 0.00 0.00 40.48 3.41
1663 2945 3.181497 TGACTGCTGTTGCTTTTCTGTTC 60.181 43.478 0.00 0.00 40.48 3.18
1699 2981 0.888736 TGCCACGGGACTGAACATTG 60.889 55.000 0.00 0.00 0.00 2.82
1702 2984 1.604604 CACGGGACTGAACATTGGTT 58.395 50.000 0.00 0.00 40.76 3.67
1717 2999 5.838529 ACATTGGTTTTGTTAGTGTTAGGC 58.161 37.500 0.00 0.00 0.00 3.93
1751 3033 3.744238 AACTTATTGGGTTGGTTGCAC 57.256 42.857 0.00 0.00 0.00 4.57
1855 3150 3.067461 TGCTCGTGCTTTTGGTTTGTAAT 59.933 39.130 11.19 0.00 40.48 1.89
2049 3369 8.225107 TGCTGTTTATCGAACATAAGTTACAAC 58.775 33.333 0.00 0.00 46.58 3.32
2120 3440 3.804036 CCTGTAGTTGTTGACTTGGTGA 58.196 45.455 0.00 0.00 39.86 4.02
2137 3457 2.484417 GGTGAGCCAGTATCATGGACTG 60.484 54.545 17.21 17.21 43.57 3.51
2211 3534 4.024556 GGAATGTGAAATATCCGCACTGAG 60.025 45.833 0.00 0.00 33.83 3.35
2252 3575 5.196341 TGTGACTTGAGACGACAGTATTT 57.804 39.130 0.00 0.00 0.00 1.40
2297 3633 5.135508 AGCAGTAACGAACTAATCTGTGT 57.864 39.130 0.00 0.00 35.76 3.72
2329 3665 2.698274 TCACTTCAGAAGTACTGGCACA 59.302 45.455 15.73 0.00 45.76 4.57
2347 3684 0.591170 CACCTGTTAACCGTGGCAAG 59.409 55.000 12.80 0.00 0.00 4.01
2349 3686 1.314730 CCTGTTAACCGTGGCAAGTT 58.685 50.000 2.48 8.93 0.00 2.66
2374 3711 9.823647 TTTTATAGCCACAACAAAAGAAATTGA 57.176 25.926 0.00 0.00 34.38 2.57
2377 3714 3.060339 GCCACAACAAAAGAAATTGAGCG 60.060 43.478 0.00 0.00 34.38 5.03
2378 3715 4.111916 CCACAACAAAAGAAATTGAGCGT 58.888 39.130 0.00 0.00 34.38 5.07
2379 3716 4.026640 CCACAACAAAAGAAATTGAGCGTG 60.027 41.667 0.00 0.00 34.38 5.34
2380 3717 4.562394 CACAACAAAAGAAATTGAGCGTGT 59.438 37.500 0.00 0.00 34.38 4.49
2420 3757 7.715657 TGGTGCTAAAATTTCATATCCATGAC 58.284 34.615 0.00 0.00 40.94 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.035530 CCTCCATGAAGGCTGAGTTC 57.964 55.000 0.00 0.00 37.29 3.01
79 80 7.814107 CACATCCTTGTGTGCTTGTATAATTTT 59.186 33.333 0.00 0.00 46.68 1.82
80 81 7.315142 CACATCCTTGTGTGCTTGTATAATTT 58.685 34.615 0.00 0.00 46.68 1.82
81 82 6.855836 CACATCCTTGTGTGCTTGTATAATT 58.144 36.000 0.00 0.00 46.68 1.40
82 83 6.441093 CACATCCTTGTGTGCTTGTATAAT 57.559 37.500 0.00 0.00 46.68 1.28
83 84 5.878332 CACATCCTTGTGTGCTTGTATAA 57.122 39.130 0.00 0.00 46.68 0.98
120 121 4.034510 CGTATCCATGGCTTCTGAAGTTTC 59.965 45.833 17.97 9.26 0.00 2.78
129 130 1.940613 GTTGGTCGTATCCATGGCTTC 59.059 52.381 6.96 0.00 37.33 3.86
132 133 0.107410 TGGTTGGTCGTATCCATGGC 60.107 55.000 6.96 0.00 37.33 4.40
133 134 1.663695 GTGGTTGGTCGTATCCATGG 58.336 55.000 4.97 4.97 37.33 3.66
134 135 1.286501 CGTGGTTGGTCGTATCCATG 58.713 55.000 0.00 0.00 37.33 3.66
136 137 1.079681 GCGTGGTTGGTCGTATCCA 60.080 57.895 0.00 0.00 35.49 3.41
137 138 0.461339 ATGCGTGGTTGGTCGTATCC 60.461 55.000 0.00 0.00 0.00 2.59
138 139 1.062002 CAATGCGTGGTTGGTCGTATC 59.938 52.381 0.00 0.00 32.02 2.24
139 140 1.083489 CAATGCGTGGTTGGTCGTAT 58.917 50.000 0.00 0.00 34.31 3.06
140 141 1.570347 GCAATGCGTGGTTGGTCGTA 61.570 55.000 0.00 0.00 0.00 3.43
141 142 2.903547 GCAATGCGTGGTTGGTCGT 61.904 57.895 0.00 0.00 0.00 4.34
142 143 2.126888 GCAATGCGTGGTTGGTCG 60.127 61.111 0.00 0.00 0.00 4.79
145 146 3.301554 TGGGCAATGCGTGGTTGG 61.302 61.111 0.00 0.00 0.00 3.77
146 147 2.049248 GTGGGCAATGCGTGGTTG 60.049 61.111 0.00 0.00 0.00 3.77
147 148 3.669344 CGTGGGCAATGCGTGGTT 61.669 61.111 0.00 0.00 0.00 3.67
150 151 2.685829 TAAGCGTGGGCAATGCGTG 61.686 57.895 4.66 0.00 46.14 5.34
152 153 2.100216 GTAAGCGTGGGCAATGCG 59.900 61.111 0.00 0.00 46.14 4.73
153 154 2.270297 CTGGTAAGCGTGGGCAATGC 62.270 60.000 0.00 0.00 43.41 3.56
154 155 1.656818 CCTGGTAAGCGTGGGCAATG 61.657 60.000 0.00 0.00 43.41 2.82
155 156 1.378514 CCTGGTAAGCGTGGGCAAT 60.379 57.895 0.00 0.00 43.41 3.56
157 158 4.028490 CCCTGGTAAGCGTGGGCA 62.028 66.667 0.00 0.00 43.41 5.36
158 159 2.662070 TACCCTGGTAAGCGTGGGC 61.662 63.158 0.00 0.00 43.25 5.36
159 160 1.219935 GTACCCTGGTAAGCGTGGG 59.780 63.158 0.00 0.00 44.89 4.61
160 161 0.322322 TTGTACCCTGGTAAGCGTGG 59.678 55.000 0.00 0.00 31.86 4.94
161 162 1.722011 CTTGTACCCTGGTAAGCGTG 58.278 55.000 0.00 0.00 31.86 5.34
163 164 0.036765 TGCTTGTACCCTGGTAAGCG 60.037 55.000 15.51 2.38 37.30 4.68
165 166 2.224426 TGTGTGCTTGTACCCTGGTAAG 60.224 50.000 0.00 0.00 31.86 2.34
166 167 1.769465 TGTGTGCTTGTACCCTGGTAA 59.231 47.619 0.00 0.00 31.86 2.85
167 168 1.425694 TGTGTGCTTGTACCCTGGTA 58.574 50.000 0.00 0.00 0.00 3.25
169 170 1.238439 CTTGTGTGCTTGTACCCTGG 58.762 55.000 0.00 0.00 0.00 4.45
170 171 1.967319 ACTTGTGTGCTTGTACCCTG 58.033 50.000 0.00 0.00 0.00 4.45
171 172 2.572290 GAACTTGTGTGCTTGTACCCT 58.428 47.619 0.00 0.00 0.00 4.34
172 173 1.263217 CGAACTTGTGTGCTTGTACCC 59.737 52.381 0.00 0.00 0.00 3.69
173 174 1.937899 ACGAACTTGTGTGCTTGTACC 59.062 47.619 0.00 0.00 0.00 3.34
174 175 2.033151 GGACGAACTTGTGTGCTTGTAC 60.033 50.000 0.00 0.00 0.00 2.90
179 265 0.874607 GACGGACGAACTTGTGTGCT 60.875 55.000 0.00 0.00 0.00 4.40
180 266 1.149361 TGACGGACGAACTTGTGTGC 61.149 55.000 0.00 0.00 0.00 4.57
185 271 1.336887 ACTCCATGACGGACGAACTTG 60.337 52.381 0.00 1.47 39.64 3.16
186 272 0.966920 ACTCCATGACGGACGAACTT 59.033 50.000 0.00 0.00 39.64 2.66
187 273 0.966920 AACTCCATGACGGACGAACT 59.033 50.000 0.00 0.00 39.64 3.01
191 277 3.741029 ATGAACTCCATGACGGACG 57.259 52.632 0.00 0.00 39.64 4.79
221 607 4.187694 TGTGGCACAAAATTGAAGAAACC 58.812 39.130 19.74 0.00 44.16 3.27
294 680 8.969121 TTTGAATTTTATGCATGTGAGTACTG 57.031 30.769 10.16 0.00 0.00 2.74
337 723 9.549078 TTTTTCCATATACGCATACTCATGTTA 57.451 29.630 0.00 0.00 34.40 2.41
456 842 6.110033 GGGGAAAAACATATACGGCATTTTT 58.890 36.000 0.00 0.00 35.68 1.94
457 843 5.187967 TGGGGAAAAACATATACGGCATTTT 59.812 36.000 0.00 0.00 0.00 1.82
468 854 2.158385 AGCTGTGGTGGGGAAAAACATA 60.158 45.455 0.00 0.00 0.00 2.29
470 856 0.032615 AGCTGTGGTGGGGAAAAACA 60.033 50.000 0.00 0.00 0.00 2.83
472 858 2.990740 ATAGCTGTGGTGGGGAAAAA 57.009 45.000 0.00 0.00 0.00 1.94
477 863 1.337823 GCGTATATAGCTGTGGTGGGG 60.338 57.143 0.00 0.00 0.00 4.96
478 864 1.343142 TGCGTATATAGCTGTGGTGGG 59.657 52.381 0.00 0.00 35.28 4.61
489 875 2.038033 GCCTCAGGGGTTTGCGTATATA 59.962 50.000 0.00 0.00 37.43 0.86
490 876 1.202770 GCCTCAGGGGTTTGCGTATAT 60.203 52.381 0.00 0.00 37.43 0.86
491 877 0.179468 GCCTCAGGGGTTTGCGTATA 59.821 55.000 0.00 0.00 37.43 1.47
492 878 1.077716 GCCTCAGGGGTTTGCGTAT 60.078 57.895 0.00 0.00 37.43 3.06
493 879 0.905809 TAGCCTCAGGGGTTTGCGTA 60.906 55.000 0.00 0.00 43.77 4.42
494 880 2.185310 CTAGCCTCAGGGGTTTGCGT 62.185 60.000 0.00 0.00 43.77 5.24
495 881 1.450312 CTAGCCTCAGGGGTTTGCG 60.450 63.158 0.00 0.00 43.77 4.85
496 882 0.393132 GACTAGCCTCAGGGGTTTGC 60.393 60.000 0.00 0.00 43.77 3.68
497 883 0.984230 TGACTAGCCTCAGGGGTTTG 59.016 55.000 0.00 0.00 43.77 2.93
498 884 1.972588 ATGACTAGCCTCAGGGGTTT 58.027 50.000 0.00 0.00 43.77 3.27
499 885 2.022918 ACTATGACTAGCCTCAGGGGTT 60.023 50.000 0.00 0.00 43.77 4.11
500 886 1.576272 ACTATGACTAGCCTCAGGGGT 59.424 52.381 0.00 0.00 46.15 4.95
501 887 1.967066 CACTATGACTAGCCTCAGGGG 59.033 57.143 0.00 0.00 38.36 4.79
502 888 2.890311 CTCACTATGACTAGCCTCAGGG 59.110 54.545 0.00 0.00 0.00 4.45
503 889 2.890311 CCTCACTATGACTAGCCTCAGG 59.110 54.545 0.00 0.00 0.00 3.86
504 890 2.890311 CCCTCACTATGACTAGCCTCAG 59.110 54.545 0.00 0.00 0.00 3.35
505 891 2.245028 ACCCTCACTATGACTAGCCTCA 59.755 50.000 0.00 0.00 0.00 3.86
506 892 2.952116 ACCCTCACTATGACTAGCCTC 58.048 52.381 0.00 0.00 0.00 4.70
507 893 4.079096 AGTTACCCTCACTATGACTAGCCT 60.079 45.833 0.00 0.00 0.00 4.58
508 894 4.216708 AGTTACCCTCACTATGACTAGCC 58.783 47.826 0.00 0.00 0.00 3.93
509 895 5.855740 AAGTTACCCTCACTATGACTAGC 57.144 43.478 0.00 0.00 0.00 3.42
510 896 8.927675 ATCTAAGTTACCCTCACTATGACTAG 57.072 38.462 0.00 0.00 0.00 2.57
512 898 9.710818 TTTATCTAAGTTACCCTCACTATGACT 57.289 33.333 0.00 0.00 0.00 3.41
556 942 8.900983 AATACTTGCCACATAAACAAAATTGT 57.099 26.923 0.00 0.00 44.72 2.71
567 953 9.778741 CTCTCCTTATTAAATACTTGCCACATA 57.221 33.333 0.00 0.00 0.00 2.29
568 954 8.494433 TCTCTCCTTATTAAATACTTGCCACAT 58.506 33.333 0.00 0.00 0.00 3.21
569 955 7.857456 TCTCTCCTTATTAAATACTTGCCACA 58.143 34.615 0.00 0.00 0.00 4.17
570 956 7.442666 CCTCTCTCCTTATTAAATACTTGCCAC 59.557 40.741 0.00 0.00 0.00 5.01
571 957 7.127339 ACCTCTCTCCTTATTAAATACTTGCCA 59.873 37.037 0.00 0.00 0.00 4.92
572 958 7.442666 CACCTCTCTCCTTATTAAATACTTGCC 59.557 40.741 0.00 0.00 0.00 4.52
573 959 7.041712 GCACCTCTCTCCTTATTAAATACTTGC 60.042 40.741 0.00 0.00 0.00 4.01
574 960 8.207545 AGCACCTCTCTCCTTATTAAATACTTG 58.792 37.037 0.00 0.00 0.00 3.16
575 961 8.325477 AGCACCTCTCTCCTTATTAAATACTT 57.675 34.615 0.00 0.00 0.00 2.24
576 962 7.922699 AGCACCTCTCTCCTTATTAAATACT 57.077 36.000 0.00 0.00 0.00 2.12
577 963 8.204836 TCAAGCACCTCTCTCCTTATTAAATAC 58.795 37.037 0.00 0.00 0.00 1.89
578 964 8.319057 TCAAGCACCTCTCTCCTTATTAAATA 57.681 34.615 0.00 0.00 0.00 1.40
579 965 7.200434 TCAAGCACCTCTCTCCTTATTAAAT 57.800 36.000 0.00 0.00 0.00 1.40
580 966 6.620877 TCAAGCACCTCTCTCCTTATTAAA 57.379 37.500 0.00 0.00 0.00 1.52
581 967 6.213600 ACTTCAAGCACCTCTCTCCTTATTAA 59.786 38.462 0.00 0.00 0.00 1.40
582 968 5.721960 ACTTCAAGCACCTCTCTCCTTATTA 59.278 40.000 0.00 0.00 0.00 0.98
583 969 4.534103 ACTTCAAGCACCTCTCTCCTTATT 59.466 41.667 0.00 0.00 0.00 1.40
584 970 4.100373 ACTTCAAGCACCTCTCTCCTTAT 58.900 43.478 0.00 0.00 0.00 1.73
585 971 3.511477 ACTTCAAGCACCTCTCTCCTTA 58.489 45.455 0.00 0.00 0.00 2.69
586 972 2.334023 ACTTCAAGCACCTCTCTCCTT 58.666 47.619 0.00 0.00 0.00 3.36
587 973 2.022718 ACTTCAAGCACCTCTCTCCT 57.977 50.000 0.00 0.00 0.00 3.69
588 974 3.006967 TGTTACTTCAAGCACCTCTCTCC 59.993 47.826 0.00 0.00 0.00 3.71
589 975 4.258702 TGTTACTTCAAGCACCTCTCTC 57.741 45.455 0.00 0.00 0.00 3.20
590 976 4.899352 ATGTTACTTCAAGCACCTCTCT 57.101 40.909 0.00 0.00 0.00 3.10
591 977 8.768955 CATATTATGTTACTTCAAGCACCTCTC 58.231 37.037 0.00 0.00 0.00 3.20
592 978 8.267894 ACATATTATGTTACTTCAAGCACCTCT 58.732 33.333 3.40 0.00 41.63 3.69
593 979 8.438676 ACATATTATGTTACTTCAAGCACCTC 57.561 34.615 3.40 0.00 41.63 3.85
609 995 7.329471 AGCGCTATGTGACAGTAACATATTATG 59.671 37.037 8.99 2.03 39.23 1.90
610 996 7.378966 AGCGCTATGTGACAGTAACATATTAT 58.621 34.615 8.99 0.00 39.23 1.28
611 997 6.745116 AGCGCTATGTGACAGTAACATATTA 58.255 36.000 8.99 0.00 39.23 0.98
612 998 5.601662 AGCGCTATGTGACAGTAACATATT 58.398 37.500 8.99 0.00 39.23 1.28
613 999 5.201713 AGCGCTATGTGACAGTAACATAT 57.798 39.130 8.99 0.00 39.23 1.78
614 1000 4.649088 AGCGCTATGTGACAGTAACATA 57.351 40.909 8.99 10.04 39.05 2.29
615 1001 3.526931 AGCGCTATGTGACAGTAACAT 57.473 42.857 8.99 8.71 41.14 2.71
616 1002 3.250744 GAAGCGCTATGTGACAGTAACA 58.749 45.455 12.05 0.00 0.00 2.41
617 1003 2.603560 GGAAGCGCTATGTGACAGTAAC 59.396 50.000 12.05 0.00 0.00 2.50
618 1004 2.418197 GGGAAGCGCTATGTGACAGTAA 60.418 50.000 12.05 0.00 0.00 2.24
619 1005 1.136305 GGGAAGCGCTATGTGACAGTA 59.864 52.381 12.05 0.00 0.00 2.74
620 1006 0.108138 GGGAAGCGCTATGTGACAGT 60.108 55.000 12.05 0.00 0.00 3.55
621 1007 1.148157 CGGGAAGCGCTATGTGACAG 61.148 60.000 12.05 0.00 0.00 3.51
622 1008 1.153647 CGGGAAGCGCTATGTGACA 60.154 57.895 12.05 0.00 0.00 3.58
623 1009 0.872021 CTCGGGAAGCGCTATGTGAC 60.872 60.000 12.05 0.00 0.00 3.67
624 1010 1.320344 ACTCGGGAAGCGCTATGTGA 61.320 55.000 12.05 6.23 0.00 3.58
625 1011 0.384309 TACTCGGGAAGCGCTATGTG 59.616 55.000 12.05 1.10 0.00 3.21
626 1012 1.108776 TTACTCGGGAAGCGCTATGT 58.891 50.000 12.05 6.23 0.00 2.29
627 1013 2.218953 TTTACTCGGGAAGCGCTATG 57.781 50.000 12.05 0.24 0.00 2.23
628 1014 2.973694 TTTTACTCGGGAAGCGCTAT 57.026 45.000 12.05 0.00 0.00 2.97
629 1015 2.166870 TCATTTTACTCGGGAAGCGCTA 59.833 45.455 12.05 0.00 0.00 4.26
630 1016 1.066430 TCATTTTACTCGGGAAGCGCT 60.066 47.619 2.64 2.64 0.00 5.92
631 1017 1.327764 CTCATTTTACTCGGGAAGCGC 59.672 52.381 0.00 0.00 0.00 5.92
632 1018 2.603560 GACTCATTTTACTCGGGAAGCG 59.396 50.000 0.00 0.00 0.00 4.68
633 1019 3.863041 AGACTCATTTTACTCGGGAAGC 58.137 45.455 0.00 0.00 0.00 3.86
634 1020 8.630917 TCTTATAGACTCATTTTACTCGGGAAG 58.369 37.037 0.00 0.00 0.00 3.46
635 1021 8.411683 GTCTTATAGACTCATTTTACTCGGGAA 58.588 37.037 0.00 0.00 41.88 3.97
636 1022 7.558807 TGTCTTATAGACTCATTTTACTCGGGA 59.441 37.037 8.18 0.00 45.27 5.14
637 1023 7.713750 TGTCTTATAGACTCATTTTACTCGGG 58.286 38.462 8.18 0.00 45.27 5.14
638 1024 9.751542 ATTGTCTTATAGACTCATTTTACTCGG 57.248 33.333 8.18 0.00 45.27 4.63
693 1079 9.656323 TCATACCCTCATAGTACAAAGTATCTT 57.344 33.333 0.00 0.00 0.00 2.40
694 1080 9.080097 GTCATACCCTCATAGTACAAAGTATCT 57.920 37.037 0.00 0.00 0.00 1.98
695 1081 8.857098 TGTCATACCCTCATAGTACAAAGTATC 58.143 37.037 0.00 0.00 0.00 2.24
696 1082 8.639761 GTGTCATACCCTCATAGTACAAAGTAT 58.360 37.037 0.00 0.00 0.00 2.12
697 1083 7.837689 AGTGTCATACCCTCATAGTACAAAGTA 59.162 37.037 0.00 0.00 0.00 2.24
698 1084 6.668283 AGTGTCATACCCTCATAGTACAAAGT 59.332 38.462 0.00 0.00 0.00 2.66
699 1085 7.113658 AGTGTCATACCCTCATAGTACAAAG 57.886 40.000 0.00 0.00 0.00 2.77
700 1086 7.837689 ACTAGTGTCATACCCTCATAGTACAAA 59.162 37.037 0.00 0.00 0.00 2.83
701 1087 7.351952 ACTAGTGTCATACCCTCATAGTACAA 58.648 38.462 0.00 0.00 0.00 2.41
702 1088 6.907961 ACTAGTGTCATACCCTCATAGTACA 58.092 40.000 0.00 0.00 0.00 2.90
703 1089 7.225725 AGACTAGTGTCATACCCTCATAGTAC 58.774 42.308 0.00 0.00 45.20 2.73
704 1090 7.390013 AGACTAGTGTCATACCCTCATAGTA 57.610 40.000 0.00 0.00 45.20 1.82
705 1091 6.268855 AGACTAGTGTCATACCCTCATAGT 57.731 41.667 0.00 0.00 45.20 2.12
706 1092 7.940137 ACTTAGACTAGTGTCATACCCTCATAG 59.060 40.741 0.00 0.00 45.20 2.23
707 1093 7.813331 ACTTAGACTAGTGTCATACCCTCATA 58.187 38.462 0.00 0.00 45.20 2.15
708 1094 6.674573 ACTTAGACTAGTGTCATACCCTCAT 58.325 40.000 0.00 0.00 45.20 2.90
709 1095 6.075949 ACTTAGACTAGTGTCATACCCTCA 57.924 41.667 0.00 0.00 45.20 3.86
710 1096 7.407393 AAACTTAGACTAGTGTCATACCCTC 57.593 40.000 0.00 0.00 45.20 4.30
711 1097 6.380560 GGAAACTTAGACTAGTGTCATACCCT 59.619 42.308 0.00 0.00 45.20 4.34
712 1098 6.406737 GGGAAACTTAGACTAGTGTCATACCC 60.407 46.154 0.00 2.33 45.20 3.69
713 1099 6.406737 GGGGAAACTTAGACTAGTGTCATACC 60.407 46.154 0.00 0.00 45.20 2.73
714 1100 6.154021 TGGGGAAACTTAGACTAGTGTCATAC 59.846 42.308 0.00 0.00 45.20 2.39
715 1101 6.154021 GTGGGGAAACTTAGACTAGTGTCATA 59.846 42.308 0.00 0.00 45.20 2.15
716 1102 5.046520 GTGGGGAAACTTAGACTAGTGTCAT 60.047 44.000 0.00 0.00 45.20 3.06
717 1103 4.282703 GTGGGGAAACTTAGACTAGTGTCA 59.717 45.833 0.00 0.00 45.20 3.58
718 1104 4.527427 AGTGGGGAAACTTAGACTAGTGTC 59.473 45.833 0.00 0.00 43.22 3.67
719 1105 4.490706 AGTGGGGAAACTTAGACTAGTGT 58.509 43.478 0.00 0.00 0.00 3.55
720 1106 6.380274 TCATAGTGGGGAAACTTAGACTAGTG 59.620 42.308 0.00 0.00 0.00 2.74
721 1107 6.380560 GTCATAGTGGGGAAACTTAGACTAGT 59.619 42.308 0.00 0.00 33.47 2.57
722 1108 6.183360 GGTCATAGTGGGGAAACTTAGACTAG 60.183 46.154 0.00 0.00 35.13 2.57
723 1109 5.659971 GGTCATAGTGGGGAAACTTAGACTA 59.340 44.000 0.00 0.00 35.13 2.59
724 1110 4.470304 GGTCATAGTGGGGAAACTTAGACT 59.530 45.833 0.00 0.00 35.13 3.24
725 1111 4.224370 TGGTCATAGTGGGGAAACTTAGAC 59.776 45.833 0.00 0.00 34.54 2.59
726 1112 4.431378 TGGTCATAGTGGGGAAACTTAGA 58.569 43.478 0.00 0.00 0.00 2.10
727 1113 4.770795 CTGGTCATAGTGGGGAAACTTAG 58.229 47.826 0.00 0.00 0.00 2.18
728 1114 3.054655 GCTGGTCATAGTGGGGAAACTTA 60.055 47.826 0.00 0.00 0.00 2.24
729 1115 2.290960 GCTGGTCATAGTGGGGAAACTT 60.291 50.000 0.00 0.00 0.00 2.66
730 1116 1.282157 GCTGGTCATAGTGGGGAAACT 59.718 52.381 0.00 0.00 0.00 2.66
731 1117 1.682087 GGCTGGTCATAGTGGGGAAAC 60.682 57.143 0.00 0.00 0.00 2.78
732 1118 0.623723 GGCTGGTCATAGTGGGGAAA 59.376 55.000 0.00 0.00 0.00 3.13
733 1119 0.253160 AGGCTGGTCATAGTGGGGAA 60.253 55.000 0.00 0.00 0.00 3.97
734 1120 0.639943 TAGGCTGGTCATAGTGGGGA 59.360 55.000 0.00 0.00 0.00 4.81
735 1121 1.507140 TTAGGCTGGTCATAGTGGGG 58.493 55.000 0.00 0.00 0.00 4.96
736 1122 3.644966 TTTTAGGCTGGTCATAGTGGG 57.355 47.619 0.00 0.00 0.00 4.61
755 1141 4.134563 CTGCGGTGGGTATATAGCTTTTT 58.865 43.478 11.53 0.00 0.00 1.94
756 1142 3.740115 CTGCGGTGGGTATATAGCTTTT 58.260 45.455 11.53 0.00 0.00 2.27
757 1143 2.550208 GCTGCGGTGGGTATATAGCTTT 60.550 50.000 11.53 0.00 0.00 3.51
758 1144 1.002087 GCTGCGGTGGGTATATAGCTT 59.998 52.381 11.53 0.00 0.00 3.74
766 1152 0.676466 CAGATTTGCTGCGGTGGGTA 60.676 55.000 0.00 0.00 37.90 3.69
845 1234 1.909986 TGATTGGTGGATTCGTGGGTA 59.090 47.619 0.00 0.00 0.00 3.69
1440 2712 1.694696 GAGGAGGTGAACTTGGTGACT 59.305 52.381 0.00 0.00 0.00 3.41
1507 2787 4.082136 GCACTAGCACTACTTCTACTTGGT 60.082 45.833 0.00 0.00 41.58 3.67
1532 2812 2.885135 ACATTCAGCAACTCCCATCA 57.115 45.000 0.00 0.00 0.00 3.07
1647 2928 4.336433 TCAGAAGGAACAGAAAAGCAACAG 59.664 41.667 0.00 0.00 0.00 3.16
1661 2943 2.833794 CACAGTTCGGTTCAGAAGGAA 58.166 47.619 0.00 0.00 0.00 3.36
1663 2945 0.868406 GCACAGTTCGGTTCAGAAGG 59.132 55.000 0.00 0.00 0.00 3.46
1699 2981 5.298527 ACTGAAGCCTAACACTAACAAAACC 59.701 40.000 0.00 0.00 0.00 3.27
1702 2984 6.354130 AGAACTGAAGCCTAACACTAACAAA 58.646 36.000 0.00 0.00 0.00 2.83
1751 3033 7.106239 ACTCATAAACTCATAACCTGAAGTGG 58.894 38.462 0.00 0.00 32.14 4.00
1753 3035 8.258708 GGTACTCATAAACTCATAACCTGAAGT 58.741 37.037 0.00 0.00 32.14 3.01
1755 3037 7.262772 CGGTACTCATAAACTCATAACCTGAA 58.737 38.462 0.00 0.00 32.14 3.02
1970 3289 6.487299 AGGAACCAACTTCTAGATGATACC 57.513 41.667 12.31 6.74 0.00 2.73
2062 3382 7.615403 TGCTTGAATAGATTCACTAACAGTCT 58.385 34.615 4.42 0.00 45.63 3.24
2252 3575 5.543507 ATCCCAAATGCAAAACTGTACAA 57.456 34.783 0.00 0.00 0.00 2.41
2297 3633 5.026121 ACTTCTGAAGTGATGATGGAGGTA 58.974 41.667 21.47 0.00 41.01 3.08
2329 3665 0.181824 ACTTGCCACGGTTAACAGGT 59.818 50.000 10.55 3.36 0.00 4.00
2347 3684 9.862585 CAATTTCTTTTGTTGTGGCTATAAAAC 57.137 29.630 0.00 0.00 0.00 2.43
2349 3686 9.474920 CTCAATTTCTTTTGTTGTGGCTATAAA 57.525 29.630 0.00 0.00 0.00 1.40
2361 3698 6.720012 AAAAACACGCTCAATTTCTTTTGT 57.280 29.167 0.00 0.00 0.00 2.83
2396 3733 7.147976 GGTCATGGATATGAAATTTTAGCACC 58.852 38.462 0.00 0.00 44.49 5.01
2420 3757 4.331968 TCTTGCTACCCATACTTTTGTGG 58.668 43.478 0.00 0.00 33.72 4.17


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

AutoCloner maintained by Alex Coulton.