Multiple sequence alignment - TraesCS6D01G032000

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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 TraesCS6D01G032000 chr6D 100.000 3548 0 0 1 3548 13497903 13494356 0.000000e+00 6553
1 TraesCS6D01G032000 chr6D 79.646 226 26 5 3316 3541 13559743 13559538 1.030000e-30 145
2 TraesCS6D01G032000 chr6B 91.627 2520 142 26 403 2890 25046700 25044218 0.000000e+00 3421
3 TraesCS6D01G032000 chr6B 97.052 916 23 2 2439 3350 182530942 182530027 0.000000e+00 1539
4 TraesCS6D01G032000 chr6B 96.616 916 27 2 2439 3350 496613695 496614610 0.000000e+00 1517
5 TraesCS6D01G032000 chr6B 93.314 344 21 2 4 347 25047043 25046702 1.140000e-139 507
6 TraesCS6D01G032000 chrUn 92.589 2267 118 19 397 2648 71370084 71372315 0.000000e+00 3210
7 TraesCS6D01G032000 chrUn 92.965 398 26 2 1 398 71368971 71369366 2.370000e-161 579
8 TraesCS6D01G032000 chr4A 97.052 916 23 2 2439 3350 659836045 659836960 0.000000e+00 1539
9 TraesCS6D01G032000 chr7A 96.943 916 24 2 2439 3350 164913535 164914450 0.000000e+00 1533
10 TraesCS6D01G032000 chr7A 96.507 916 28 2 2439 3350 56882344 56881429 0.000000e+00 1511
11 TraesCS6D01G032000 chr2B 96.943 916 24 2 2439 3350 132670352 132669437 0.000000e+00 1533
12 TraesCS6D01G032000 chr2B 96.616 916 27 2 2439 3350 122726294 122727209 0.000000e+00 1517
13 TraesCS6D01G032000 chr1B 96.834 916 25 2 2439 3350 67317722 67318637 0.000000e+00 1528
14 TraesCS6D01G032000 chr7B 96.507 916 28 2 2439 3350 591270046 591269131 0.000000e+00 1511


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 TraesCS6D01G032000 chr6D 13494356 13497903 3547 True 6553.0 6553 100.0000 1 3548 1 chr6D.!!$R1 3547
1 TraesCS6D01G032000 chr6B 25044218 25047043 2825 True 1964.0 3421 92.4705 4 2890 2 chr6B.!!$R2 2886
2 TraesCS6D01G032000 chr6B 182530027 182530942 915 True 1539.0 1539 97.0520 2439 3350 1 chr6B.!!$R1 911
3 TraesCS6D01G032000 chr6B 496613695 496614610 915 False 1517.0 1517 96.6160 2439 3350 1 chr6B.!!$F1 911
4 TraesCS6D01G032000 chrUn 71368971 71372315 3344 False 1894.5 3210 92.7770 1 2648 2 chrUn.!!$F1 2647
5 TraesCS6D01G032000 chr4A 659836045 659836960 915 False 1539.0 1539 97.0520 2439 3350 1 chr4A.!!$F1 911
6 TraesCS6D01G032000 chr7A 164913535 164914450 915 False 1533.0 1533 96.9430 2439 3350 1 chr7A.!!$F1 911
7 TraesCS6D01G032000 chr7A 56881429 56882344 915 True 1511.0 1511 96.5070 2439 3350 1 chr7A.!!$R1 911
8 TraesCS6D01G032000 chr2B 132669437 132670352 915 True 1533.0 1533 96.9430 2439 3350 1 chr2B.!!$R1 911
9 TraesCS6D01G032000 chr2B 122726294 122727209 915 False 1517.0 1517 96.6160 2439 3350 1 chr2B.!!$F1 911
10 TraesCS6D01G032000 chr1B 67317722 67318637 915 False 1528.0 1528 96.8340 2439 3350 1 chr1B.!!$F1 911
11 TraesCS6D01G032000 chr7B 591269131 591270046 915 True 1511.0 1511 96.5070 2439 3350 1 chr7B.!!$R1 911

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
906 1657 0.108138 ACATTCTGTACTCGCCTGCC 60.108 55.0 0.00 0.00 0.0 4.85 F
1632 2386 0.550147 ACCAAGGGCTGTACAGGGAT 60.550 55.0 23.95 5.03 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2278 3032 0.180406 ACGTCAGAGTTTGGCCTTGT 59.820 50.0 3.32 0.0 0.0 3.16 R
3480 4243 0.110688 CGCCGTATCATGCAATTCGG 60.111 55.0 11.00 11.0 41.1 4.30 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
33 34 1.104630 TGGACCGTTCAAAAACACCC 58.895 50.000 0.00 0.00 34.93 4.61
51 52 2.785258 GAACGCATCGACAAGGCC 59.215 61.111 0.00 0.00 0.00 5.19
67 68 2.932083 GCCGCGTACATGCTCGATG 61.932 63.158 4.92 5.43 38.15 3.84
108 109 2.031870 CATACGGTCTCCCATGTCTCA 58.968 52.381 0.00 0.00 0.00 3.27
159 160 1.079336 GGTGTTCACCGAGCTACCC 60.079 63.158 6.22 0.00 0.00 3.69
279 280 2.355837 TGCAGAAGCCGTGTCGAC 60.356 61.111 9.11 9.11 41.13 4.20
305 306 1.155042 GATGCATTCGGAGGATCAGC 58.845 55.000 0.00 0.00 36.25 4.26
347 348 2.957006 GAGGAGATTCGTAGGGTAGCAA 59.043 50.000 0.00 0.00 0.00 3.91
348 349 2.694109 AGGAGATTCGTAGGGTAGCAAC 59.306 50.000 0.00 0.00 0.00 4.17
369 370 4.112331 ACTGCTAACCCTAGGGAGATTTT 58.888 43.478 35.38 19.52 38.96 1.82
426 1146 0.736325 GCGTATGGTCGTTGCACTCT 60.736 55.000 0.00 0.00 0.00 3.24
456 1176 4.641645 CTGGCTGTGTTCGGGGCA 62.642 66.667 0.00 0.00 0.00 5.36
527 1247 2.420058 ATCTTCCTTTACCCCGCAAG 57.580 50.000 0.00 0.00 0.00 4.01
530 1250 2.084546 CTTCCTTTACCCCGCAAGAAG 58.915 52.381 0.00 0.00 43.02 2.85
569 1291 2.096013 GCGATTGCTCAAAGGAAGGTAC 59.904 50.000 0.00 0.00 38.39 3.34
595 1317 5.833667 TCGGACTACAATACCTGAAGATCAT 59.166 40.000 0.00 0.00 0.00 2.45
602 1324 5.821470 ACAATACCTGAAGATCATTCTGCTG 59.179 40.000 0.00 0.00 30.72 4.41
624 1346 3.714798 GGGGAGGAATACAATGTCCTACA 59.285 47.826 4.49 0.00 45.61 2.74
626 1348 5.546499 GGGGAGGAATACAATGTCCTACATA 59.454 44.000 4.49 0.00 45.61 2.29
642 1364 7.115553 GTCCTACATAAACGATTTTAAGTCGC 58.884 38.462 9.68 0.00 42.56 5.19
662 1384 5.865552 GTCGCGCCAATTCTATATACCTAAA 59.134 40.000 0.00 0.00 0.00 1.85
663 1385 6.534079 GTCGCGCCAATTCTATATACCTAAAT 59.466 38.462 0.00 0.00 0.00 1.40
664 1386 7.703621 GTCGCGCCAATTCTATATACCTAAATA 59.296 37.037 0.00 0.00 0.00 1.40
665 1387 8.252417 TCGCGCCAATTCTATATACCTAAATAA 58.748 33.333 0.00 0.00 0.00 1.40
666 1388 8.875803 CGCGCCAATTCTATATACCTAAATAAA 58.124 33.333 0.00 0.00 0.00 1.40
709 1431 7.772292 CACTAATTCCAATTCTCTCCATCTCAA 59.228 37.037 0.00 0.00 0.00 3.02
736 1465 1.154188 GAGTGTCGCGTCTCCACTC 60.154 63.158 23.69 23.69 45.69 3.51
737 1466 1.601197 AGTGTCGCGTCTCCACTCT 60.601 57.895 5.77 0.00 34.44 3.24
739 1468 2.333417 TGTCGCGTCTCCACTCTCC 61.333 63.158 5.77 0.00 0.00 3.71
740 1469 2.033602 TCGCGTCTCCACTCTCCA 59.966 61.111 5.77 0.00 0.00 3.86
741 1470 2.179517 CGCGTCTCCACTCTCCAC 59.820 66.667 0.00 0.00 0.00 4.02
742 1471 2.336478 CGCGTCTCCACTCTCCACT 61.336 63.158 0.00 0.00 0.00 4.00
743 1472 1.214062 GCGTCTCCACTCTCCACTG 59.786 63.158 0.00 0.00 0.00 3.66
744 1473 1.214062 CGTCTCCACTCTCCACTGC 59.786 63.158 0.00 0.00 0.00 4.40
745 1474 1.594310 GTCTCCACTCTCCACTGCC 59.406 63.158 0.00 0.00 0.00 4.85
746 1475 1.610673 TCTCCACTCTCCACTGCCC 60.611 63.158 0.00 0.00 0.00 5.36
765 1494 2.203252 CCAGGTCCATGATGGCGG 60.203 66.667 6.59 0.61 37.47 6.13
787 1516 2.605823 CGGACGGCTGAGATCTATTGAC 60.606 54.545 0.00 0.00 0.00 3.18
789 1518 1.338337 ACGGCTGAGATCTATTGACGG 59.662 52.381 17.71 3.21 0.00 4.79
791 1520 2.605823 CGGCTGAGATCTATTGACGGAC 60.606 54.545 0.00 0.00 0.00 4.79
793 1522 2.290916 GCTGAGATCTATTGACGGACGA 59.709 50.000 0.00 0.00 0.00 4.20
794 1523 3.850374 GCTGAGATCTATTGACGGACGAC 60.850 52.174 0.00 0.00 0.00 4.34
795 1524 3.542648 TGAGATCTATTGACGGACGACT 58.457 45.455 0.00 0.00 0.00 4.18
796 1525 3.945921 TGAGATCTATTGACGGACGACTT 59.054 43.478 0.00 0.00 0.00 3.01
798 1527 3.945921 AGATCTATTGACGGACGACTTGA 59.054 43.478 0.00 0.00 0.00 3.02
841 1592 5.056480 CCTGTGTGACAATTGAGTACTTGA 58.944 41.667 13.59 0.00 0.00 3.02
850 1601 7.552687 TGACAATTGAGTACTTGAACTGAACTT 59.447 33.333 13.59 0.00 0.00 2.66
861 1612 4.843728 TGAACTGAACTTCTGAAACCTGT 58.156 39.130 2.88 0.00 0.00 4.00
863 1614 5.815740 TGAACTGAACTTCTGAAACCTGTAC 59.184 40.000 2.88 0.00 0.00 2.90
883 1634 3.594134 ACGAGGCATCTCTGAAGAAAAG 58.406 45.455 0.00 0.00 37.86 2.27
884 1635 2.935201 CGAGGCATCTCTGAAGAAAAGG 59.065 50.000 0.00 0.00 37.86 3.11
885 1636 2.682352 GAGGCATCTCTGAAGAAAAGGC 59.318 50.000 0.00 0.00 37.07 4.35
886 1637 2.040813 AGGCATCTCTGAAGAAAAGGCA 59.959 45.455 0.00 0.00 34.49 4.75
887 1638 2.821969 GGCATCTCTGAAGAAAAGGCAA 59.178 45.455 0.00 0.00 34.49 4.52
888 1639 3.366781 GGCATCTCTGAAGAAAAGGCAAC 60.367 47.826 0.00 0.00 34.49 4.17
889 1640 3.254166 GCATCTCTGAAGAAAAGGCAACA 59.746 43.478 0.00 0.00 34.76 3.33
890 1641 4.082354 GCATCTCTGAAGAAAAGGCAACAT 60.082 41.667 0.00 0.00 34.76 2.71
891 1642 5.566230 GCATCTCTGAAGAAAAGGCAACATT 60.566 40.000 0.00 0.00 34.76 2.71
892 1643 5.695851 TCTCTGAAGAAAAGGCAACATTC 57.304 39.130 0.00 0.00 41.41 2.67
893 1644 5.380043 TCTCTGAAGAAAAGGCAACATTCT 58.620 37.500 0.00 0.00 44.05 2.40
894 1645 5.240183 TCTCTGAAGAAAAGGCAACATTCTG 59.760 40.000 0.00 0.00 42.16 3.02
906 1657 0.108138 ACATTCTGTACTCGCCTGCC 60.108 55.000 0.00 0.00 0.00 4.85
934 1685 2.357034 GCTGCCGGAGTTGTTCGA 60.357 61.111 5.05 0.00 0.00 3.71
935 1686 1.959226 GCTGCCGGAGTTGTTCGAA 60.959 57.895 5.05 0.00 0.00 3.71
938 1689 2.033194 GCCGGAGTTGTTCGAAGGG 61.033 63.158 5.05 0.00 0.00 3.95
1021 1775 2.733956 TGCAAGAAACAAACTCCCACT 58.266 42.857 0.00 0.00 0.00 4.00
1038 1792 2.751436 TGGCGCCATTCTTGCTCC 60.751 61.111 29.03 0.00 34.18 4.70
1045 1799 1.679032 GCCATTCTTGCTCCGTAACCT 60.679 52.381 0.00 0.00 0.00 3.50
1198 1952 2.341101 GCCGACCTCTCCGTCAAGA 61.341 63.158 0.00 0.00 32.74 3.02
1479 2233 3.628280 GAGGTCGCTCGCGGAGTTT 62.628 63.158 6.13 0.00 40.25 2.66
1492 2246 2.419297 GCGGAGTTTGATGACATCCTCT 60.419 50.000 12.90 8.13 0.00 3.69
1632 2386 0.550147 ACCAAGGGCTGTACAGGGAT 60.550 55.000 23.95 5.03 0.00 3.85
1926 2680 0.973632 ACATGTACTCCAAGTGCGGA 59.026 50.000 0.00 0.00 33.27 5.54
2606 3361 5.013079 GGGGATTTCCTTCCTTTGTTGATTT 59.987 40.000 0.00 0.00 35.97 2.17
2834 3593 5.549742 ACATACTCCTACTACGTAGCTCT 57.450 43.478 22.40 5.97 35.06 4.09
2999 3759 5.461078 GCTTGCATATAACCAGATTTTGCAG 59.539 40.000 0.00 0.00 39.49 4.41
3009 3769 5.717119 ACCAGATTTTGCAGATCATTGTTC 58.283 37.500 12.83 0.00 0.00 3.18
3092 3855 3.450457 AGTACTGATGGAGCTGAGAAAGG 59.550 47.826 0.00 0.00 0.00 3.11
3108 3871 2.887151 AAGGGAGTGGTTCATTCTGG 57.113 50.000 0.00 0.00 0.00 3.86
3145 3908 5.518865 ACAGGCAAATATTGTATTCCCTGT 58.481 37.500 19.00 19.00 44.97 4.00
3159 3922 6.661805 TGTATTCCCTGTGTAAATCCTTTTCC 59.338 38.462 0.00 0.00 0.00 3.13
3285 4048 9.006839 TCCAGATTGAATGTTATGCATATCTTC 57.993 33.333 7.36 10.94 36.67 2.87
3352 4115 2.938869 GCATCTTTGCTCTTGTTCCAC 58.061 47.619 0.00 0.00 45.77 4.02
3353 4116 2.666619 GCATCTTTGCTCTTGTTCCACG 60.667 50.000 0.00 0.00 45.77 4.94
3354 4117 2.613026 TCTTTGCTCTTGTTCCACGA 57.387 45.000 0.00 0.00 0.00 4.35
3355 4118 2.912771 TCTTTGCTCTTGTTCCACGAA 58.087 42.857 0.00 0.00 0.00 3.85
3356 4119 2.872245 TCTTTGCTCTTGTTCCACGAAG 59.128 45.455 0.00 0.00 0.00 3.79
3357 4120 0.944386 TTGCTCTTGTTCCACGAAGC 59.056 50.000 0.00 0.00 0.00 3.86
3358 4121 0.179059 TGCTCTTGTTCCACGAAGCA 60.179 50.000 0.00 0.00 0.00 3.91
3359 4122 0.235926 GCTCTTGTTCCACGAAGCAC 59.764 55.000 0.00 0.00 0.00 4.40
3360 4123 1.871080 CTCTTGTTCCACGAAGCACT 58.129 50.000 0.00 0.00 0.00 4.40
3361 4124 2.866460 GCTCTTGTTCCACGAAGCACTA 60.866 50.000 0.00 0.00 0.00 2.74
3362 4125 3.589988 CTCTTGTTCCACGAAGCACTAT 58.410 45.455 0.00 0.00 0.00 2.12
3363 4126 3.997021 CTCTTGTTCCACGAAGCACTATT 59.003 43.478 0.00 0.00 0.00 1.73
3364 4127 4.385825 TCTTGTTCCACGAAGCACTATTT 58.614 39.130 0.00 0.00 0.00 1.40
3365 4128 5.543714 TCTTGTTCCACGAAGCACTATTTA 58.456 37.500 0.00 0.00 0.00 1.40
3366 4129 6.170506 TCTTGTTCCACGAAGCACTATTTAT 58.829 36.000 0.00 0.00 0.00 1.40
3367 4130 7.324935 TCTTGTTCCACGAAGCACTATTTATA 58.675 34.615 0.00 0.00 0.00 0.98
3368 4131 7.491372 TCTTGTTCCACGAAGCACTATTTATAG 59.509 37.037 0.00 0.00 36.46 1.31
3369 4132 6.046593 TGTTCCACGAAGCACTATTTATAGG 58.953 40.000 0.00 0.00 34.69 2.57
3370 4133 5.864418 TCCACGAAGCACTATTTATAGGT 57.136 39.130 0.00 0.00 34.69 3.08
3371 4134 6.964807 TCCACGAAGCACTATTTATAGGTA 57.035 37.500 0.00 0.00 34.69 3.08
3372 4135 7.534723 TCCACGAAGCACTATTTATAGGTAT 57.465 36.000 0.00 0.00 34.69 2.73
3373 4136 7.600065 TCCACGAAGCACTATTTATAGGTATC 58.400 38.462 0.00 0.00 34.69 2.24
3374 4137 6.527023 CCACGAAGCACTATTTATAGGTATCG 59.473 42.308 0.00 7.83 34.69 2.92
3375 4138 7.082602 CACGAAGCACTATTTATAGGTATCGT 58.917 38.462 12.25 12.25 34.69 3.73
3376 4139 8.232513 CACGAAGCACTATTTATAGGTATCGTA 58.767 37.037 15.20 0.00 34.69 3.43
3377 4140 8.786898 ACGAAGCACTATTTATAGGTATCGTAA 58.213 33.333 14.57 0.00 34.69 3.18
3378 4141 9.784680 CGAAGCACTATTTATAGGTATCGTAAT 57.215 33.333 2.13 0.00 34.69 1.89
3380 4143 9.871238 AAGCACTATTTATAGGTATCGTAATGG 57.129 33.333 2.13 0.00 34.69 3.16
3381 4144 9.251440 AGCACTATTTATAGGTATCGTAATGGA 57.749 33.333 2.13 0.00 34.69 3.41
3382 4145 9.865321 GCACTATTTATAGGTATCGTAATGGAA 57.135 33.333 2.13 0.00 34.69 3.53
3392 4155 8.828688 AGGTATCGTAATGGAAATAACTAAGC 57.171 34.615 0.00 0.00 0.00 3.09
3393 4156 8.426489 AGGTATCGTAATGGAAATAACTAAGCA 58.574 33.333 0.00 0.00 0.00 3.91
3394 4157 9.048446 GGTATCGTAATGGAAATAACTAAGCAA 57.952 33.333 0.00 0.00 0.00 3.91
3398 4161 9.834628 TCGTAATGGAAATAACTAAGCAAAAAG 57.165 29.630 0.00 0.00 0.00 2.27
3399 4162 9.834628 CGTAATGGAAATAACTAAGCAAAAAGA 57.165 29.630 0.00 0.00 0.00 2.52
3401 4164 8.763049 AATGGAAATAACTAAGCAAAAAGAGC 57.237 30.769 0.00 0.00 0.00 4.09
3402 4165 7.283625 TGGAAATAACTAAGCAAAAAGAGCA 57.716 32.000 0.00 0.00 0.00 4.26
3403 4166 7.145323 TGGAAATAACTAAGCAAAAAGAGCAC 58.855 34.615 0.00 0.00 0.00 4.40
3404 4167 7.145323 GGAAATAACTAAGCAAAAAGAGCACA 58.855 34.615 0.00 0.00 0.00 4.57
3405 4168 7.651704 GGAAATAACTAAGCAAAAAGAGCACAA 59.348 33.333 0.00 0.00 0.00 3.33
3406 4169 7.930513 AATAACTAAGCAAAAAGAGCACAAC 57.069 32.000 0.00 0.00 0.00 3.32
3407 4170 5.582689 AACTAAGCAAAAAGAGCACAACT 57.417 34.783 0.00 0.00 0.00 3.16
3408 4171 4.925068 ACTAAGCAAAAAGAGCACAACTG 58.075 39.130 0.00 0.00 0.00 3.16
3409 4172 2.877043 AGCAAAAAGAGCACAACTGG 57.123 45.000 0.00 0.00 0.00 4.00
3410 4173 2.378038 AGCAAAAAGAGCACAACTGGA 58.622 42.857 0.00 0.00 0.00 3.86
3411 4174 2.360165 AGCAAAAAGAGCACAACTGGAG 59.640 45.455 0.00 0.00 0.00 3.86
3412 4175 2.544486 GCAAAAAGAGCACAACTGGAGG 60.544 50.000 0.00 0.00 0.00 4.30
3413 4176 2.689983 CAAAAAGAGCACAACTGGAGGT 59.310 45.455 0.00 0.00 0.00 3.85
3414 4177 3.857157 AAAAGAGCACAACTGGAGGTA 57.143 42.857 0.00 0.00 0.00 3.08
3415 4178 3.857157 AAAGAGCACAACTGGAGGTAA 57.143 42.857 0.00 0.00 0.00 2.85
3416 4179 2.841442 AGAGCACAACTGGAGGTAAC 57.159 50.000 0.00 0.00 0.00 2.50
3417 4180 2.047061 AGAGCACAACTGGAGGTAACA 58.953 47.619 0.00 0.00 41.41 2.41
3418 4181 2.143925 GAGCACAACTGGAGGTAACAC 58.856 52.381 0.00 0.00 41.41 3.32
3419 4182 1.768870 AGCACAACTGGAGGTAACACT 59.231 47.619 0.00 0.00 41.41 3.55
3420 4183 2.969950 AGCACAACTGGAGGTAACACTA 59.030 45.455 0.00 0.00 41.41 2.74
3421 4184 3.389983 AGCACAACTGGAGGTAACACTAA 59.610 43.478 0.00 0.00 41.41 2.24
3422 4185 4.041691 AGCACAACTGGAGGTAACACTAAT 59.958 41.667 0.00 0.00 41.41 1.73
3423 4186 4.760204 GCACAACTGGAGGTAACACTAATT 59.240 41.667 0.00 0.00 41.41 1.40
3424 4187 5.935789 GCACAACTGGAGGTAACACTAATTA 59.064 40.000 0.00 0.00 41.41 1.40
3425 4188 6.428771 GCACAACTGGAGGTAACACTAATTAA 59.571 38.462 0.00 0.00 41.41 1.40
3426 4189 7.572539 GCACAACTGGAGGTAACACTAATTAAC 60.573 40.741 0.00 0.00 41.41 2.01
3427 4190 7.442969 CACAACTGGAGGTAACACTAATTAACA 59.557 37.037 0.00 0.00 41.41 2.41
3428 4191 7.443272 ACAACTGGAGGTAACACTAATTAACAC 59.557 37.037 0.00 0.00 41.41 3.32
3429 4192 7.312415 ACTGGAGGTAACACTAATTAACACT 57.688 36.000 0.00 0.00 41.41 3.55
3430 4193 7.159372 ACTGGAGGTAACACTAATTAACACTG 58.841 38.462 0.00 0.00 41.41 3.66
3431 4194 6.469410 TGGAGGTAACACTAATTAACACTGG 58.531 40.000 0.00 0.00 41.41 4.00
3432 4195 6.043474 TGGAGGTAACACTAATTAACACTGGT 59.957 38.462 0.00 0.00 41.41 4.00
3433 4196 6.592994 GGAGGTAACACTAATTAACACTGGTC 59.407 42.308 0.00 0.00 41.41 4.02
3434 4197 7.069877 AGGTAACACTAATTAACACTGGTCA 57.930 36.000 0.00 0.00 41.41 4.02
3435 4198 7.686434 AGGTAACACTAATTAACACTGGTCAT 58.314 34.615 0.00 0.00 41.41 3.06
3436 4199 8.161425 AGGTAACACTAATTAACACTGGTCATT 58.839 33.333 0.00 0.00 41.41 2.57
3437 4200 8.234546 GGTAACACTAATTAACACTGGTCATTG 58.765 37.037 0.00 0.00 0.00 2.82
3438 4201 8.995220 GTAACACTAATTAACACTGGTCATTGA 58.005 33.333 0.00 0.00 0.00 2.57
3439 4202 8.635765 AACACTAATTAACACTGGTCATTGAT 57.364 30.769 0.00 0.00 0.00 2.57
3440 4203 9.733556 AACACTAATTAACACTGGTCATTGATA 57.266 29.630 0.00 0.00 0.00 2.15
3441 4204 9.905713 ACACTAATTAACACTGGTCATTGATAT 57.094 29.630 0.00 0.00 0.00 1.63
3450 4213 7.999679 ACACTGGTCATTGATATTTATGTTGG 58.000 34.615 0.00 0.00 0.00 3.77
3451 4214 7.833682 ACACTGGTCATTGATATTTATGTTGGA 59.166 33.333 0.00 0.00 0.00 3.53
3452 4215 8.685427 CACTGGTCATTGATATTTATGTTGGAA 58.315 33.333 0.00 0.00 0.00 3.53
3453 4216 9.253832 ACTGGTCATTGATATTTATGTTGGAAA 57.746 29.630 0.00 0.00 0.00 3.13
3455 4218 9.868277 TGGTCATTGATATTTATGTTGGAAAAC 57.132 29.630 0.00 0.00 0.00 2.43
3465 4228 8.650143 ATTTATGTTGGAAAACTGTCTATGGT 57.350 30.769 0.00 0.00 0.00 3.55
3466 4229 8.472007 TTTATGTTGGAAAACTGTCTATGGTT 57.528 30.769 0.00 0.00 0.00 3.67
3467 4230 9.575868 TTTATGTTGGAAAACTGTCTATGGTTA 57.424 29.630 0.00 0.00 0.00 2.85
3468 4231 7.687941 ATGTTGGAAAACTGTCTATGGTTAG 57.312 36.000 0.00 0.00 0.00 2.34
3469 4232 6.597562 TGTTGGAAAACTGTCTATGGTTAGT 58.402 36.000 0.00 0.00 0.00 2.24
3470 4233 7.057894 TGTTGGAAAACTGTCTATGGTTAGTT 58.942 34.615 0.00 0.00 35.06 2.24
3471 4234 8.212312 TGTTGGAAAACTGTCTATGGTTAGTTA 58.788 33.333 0.00 0.00 33.37 2.24
3472 4235 9.227777 GTTGGAAAACTGTCTATGGTTAGTTAT 57.772 33.333 0.00 0.00 33.37 1.89
3473 4236 9.444600 TTGGAAAACTGTCTATGGTTAGTTATC 57.555 33.333 0.00 0.00 33.37 1.75
3474 4237 8.822805 TGGAAAACTGTCTATGGTTAGTTATCT 58.177 33.333 0.00 0.00 33.37 1.98
3478 4241 7.507733 ACTGTCTATGGTTAGTTATCTACCG 57.492 40.000 0.00 0.00 0.00 4.02
3479 4242 7.059156 ACTGTCTATGGTTAGTTATCTACCGT 58.941 38.462 0.00 0.00 0.00 4.83
3480 4243 7.228308 ACTGTCTATGGTTAGTTATCTACCGTC 59.772 40.741 0.00 0.00 0.00 4.79
3481 4244 6.488006 TGTCTATGGTTAGTTATCTACCGTCC 59.512 42.308 0.00 0.00 0.00 4.79
3482 4245 4.843220 ATGGTTAGTTATCTACCGTCCG 57.157 45.455 0.00 0.00 0.00 4.79
3483 4246 3.884895 TGGTTAGTTATCTACCGTCCGA 58.115 45.455 0.00 0.00 0.00 4.55
3484 4247 4.269183 TGGTTAGTTATCTACCGTCCGAA 58.731 43.478 0.00 0.00 0.00 4.30
3485 4248 4.889409 TGGTTAGTTATCTACCGTCCGAAT 59.111 41.667 0.00 0.00 0.00 3.34
3486 4249 5.360714 TGGTTAGTTATCTACCGTCCGAATT 59.639 40.000 0.00 0.00 0.00 2.17
3487 4250 5.689068 GGTTAGTTATCTACCGTCCGAATTG 59.311 44.000 0.00 0.00 0.00 2.32
3488 4251 3.714391 AGTTATCTACCGTCCGAATTGC 58.286 45.455 0.00 0.00 0.00 3.56
3489 4252 3.131577 AGTTATCTACCGTCCGAATTGCA 59.868 43.478 0.00 0.00 0.00 4.08
3490 4253 2.910688 ATCTACCGTCCGAATTGCAT 57.089 45.000 0.00 0.00 0.00 3.96
3491 4254 1.934589 TCTACCGTCCGAATTGCATG 58.065 50.000 0.00 0.00 0.00 4.06
3492 4255 1.478916 TCTACCGTCCGAATTGCATGA 59.521 47.619 0.00 0.00 0.00 3.07
3493 4256 2.102420 TCTACCGTCCGAATTGCATGAT 59.898 45.455 0.00 0.00 0.00 2.45
3494 4257 2.613026 ACCGTCCGAATTGCATGATA 57.387 45.000 0.00 0.00 0.00 2.15
3495 4258 2.210116 ACCGTCCGAATTGCATGATAC 58.790 47.619 0.00 0.00 0.00 2.24
3496 4259 1.192312 CCGTCCGAATTGCATGATACG 59.808 52.381 0.00 0.00 0.00 3.06
3497 4260 1.192312 CGTCCGAATTGCATGATACGG 59.808 52.381 0.00 3.93 41.39 4.02
3498 4261 1.069906 GTCCGAATTGCATGATACGGC 60.070 52.381 0.00 0.00 40.12 5.68
3499 4262 0.110688 CCGAATTGCATGATACGGCG 60.111 55.000 4.80 4.80 34.36 6.46
3500 4263 0.110688 CGAATTGCATGATACGGCGG 60.111 55.000 13.24 0.00 0.00 6.13
3501 4264 0.944386 GAATTGCATGATACGGCGGT 59.056 50.000 13.24 1.39 0.00 5.68
3502 4265 2.139917 GAATTGCATGATACGGCGGTA 58.860 47.619 13.24 6.59 0.00 4.02
3503 4266 1.508632 ATTGCATGATACGGCGGTAC 58.491 50.000 13.24 1.88 0.00 3.34
3504 4267 0.175989 TTGCATGATACGGCGGTACA 59.824 50.000 13.24 8.27 0.00 2.90
3505 4268 0.391228 TGCATGATACGGCGGTACAT 59.609 50.000 13.24 10.36 0.00 2.29
3506 4269 1.614413 TGCATGATACGGCGGTACATA 59.386 47.619 13.24 0.00 0.00 2.29
3507 4270 2.259618 GCATGATACGGCGGTACATAG 58.740 52.381 13.24 9.02 0.00 2.23
3508 4271 2.094906 GCATGATACGGCGGTACATAGA 60.095 50.000 13.24 0.00 0.00 1.98
3509 4272 3.428999 GCATGATACGGCGGTACATAGAT 60.429 47.826 13.24 0.00 0.00 1.98
3510 4273 4.352039 CATGATACGGCGGTACATAGATC 58.648 47.826 13.24 1.28 0.00 2.75
3511 4274 3.682696 TGATACGGCGGTACATAGATCT 58.317 45.455 13.24 0.00 0.00 2.75
3512 4275 3.688185 TGATACGGCGGTACATAGATCTC 59.312 47.826 13.24 0.00 0.00 2.75
3513 4276 1.245732 ACGGCGGTACATAGATCTCC 58.754 55.000 13.24 0.00 0.00 3.71
3514 4277 1.202903 ACGGCGGTACATAGATCTCCT 60.203 52.381 13.24 0.00 0.00 3.69
3515 4278 1.887198 CGGCGGTACATAGATCTCCTT 59.113 52.381 0.00 0.00 0.00 3.36
3516 4279 2.296471 CGGCGGTACATAGATCTCCTTT 59.704 50.000 0.00 0.00 0.00 3.11
3517 4280 3.654414 GGCGGTACATAGATCTCCTTTG 58.346 50.000 0.00 0.00 0.00 2.77
3518 4281 3.321111 GGCGGTACATAGATCTCCTTTGA 59.679 47.826 0.00 0.00 0.00 2.69
3519 4282 4.021016 GGCGGTACATAGATCTCCTTTGAT 60.021 45.833 0.00 0.00 0.00 2.57
3520 4283 5.185249 GGCGGTACATAGATCTCCTTTGATA 59.815 44.000 0.00 0.00 0.00 2.15
3521 4284 6.094061 GCGGTACATAGATCTCCTTTGATAC 58.906 44.000 0.00 0.00 0.00 2.24
3522 4285 6.294564 GCGGTACATAGATCTCCTTTGATACA 60.295 42.308 0.00 0.00 0.00 2.29
3523 4286 7.085116 CGGTACATAGATCTCCTTTGATACAC 58.915 42.308 0.00 0.00 0.00 2.90
3524 4287 7.255486 CGGTACATAGATCTCCTTTGATACACA 60.255 40.741 0.00 0.00 0.00 3.72
3525 4288 8.421784 GGTACATAGATCTCCTTTGATACACAA 58.578 37.037 0.00 0.00 36.65 3.33
3526 4289 9.817809 GTACATAGATCTCCTTTGATACACAAA 57.182 33.333 0.00 0.00 44.79 2.83
3532 4295 9.911788 AGATCTCCTTTGATACACAAATAATGT 57.088 29.630 0.00 0.00 45.63 2.71
3542 4305 8.334632 TGATACACAAATAATGTATGAGTTGCG 58.665 33.333 2.50 0.00 42.11 4.85
3543 4306 6.735678 ACACAAATAATGTATGAGTTGCGA 57.264 33.333 0.00 0.00 41.46 5.10
3544 4307 6.542852 ACACAAATAATGTATGAGTTGCGAC 58.457 36.000 0.00 0.00 41.46 5.19
3545 4308 6.371548 ACACAAATAATGTATGAGTTGCGACT 59.628 34.615 6.22 6.22 41.46 4.18
3546 4309 7.547722 ACACAAATAATGTATGAGTTGCGACTA 59.452 33.333 6.58 0.00 41.46 2.59
3547 4310 7.846107 CACAAATAATGTATGAGTTGCGACTAC 59.154 37.037 6.58 2.33 41.46 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.385433 TGAACGGTCCAAAGTACTTGAGA 59.615 43.478 9.34 6.32 37.17 3.27
51 52 0.227234 GAACATCGAGCATGTACGCG 59.773 55.000 3.53 3.53 45.77 6.01
67 68 2.003301 GATCAAGCTTGTCGGAGGAAC 58.997 52.381 25.19 0.10 0.00 3.62
108 109 0.392193 CGATGAAGGGCTTGAGCTGT 60.392 55.000 0.00 0.00 41.70 4.40
159 160 1.439353 CTGCCAAATCCACCGGATCG 61.439 60.000 9.46 0.00 42.27 3.69
279 280 0.580578 CTCCGAATGCATCTTCAGCG 59.419 55.000 0.00 0.00 33.85 5.18
314 315 3.067320 CGAATCTCCTCTATGTGCACTCA 59.933 47.826 19.41 4.54 0.00 3.41
323 324 4.043059 TGCTACCCTACGAATCTCCTCTAT 59.957 45.833 0.00 0.00 0.00 1.98
347 348 3.423058 AATCTCCCTAGGGTTAGCAGT 57.577 47.619 27.58 5.56 36.47 4.40
348 349 4.779993 AAAATCTCCCTAGGGTTAGCAG 57.220 45.455 27.58 16.79 36.47 4.24
369 370 5.571741 CGCGAGTGACTAATGAGAGTAAAAA 59.428 40.000 0.00 0.00 0.00 1.94
456 1176 8.532819 CCTTAGACAAGTTTACAATAGAGTCCT 58.467 37.037 0.00 0.00 0.00 3.85
527 1247 3.675225 GCGGCATTTCTTTTCTTTCCTTC 59.325 43.478 0.00 0.00 0.00 3.46
530 1250 1.985684 CGCGGCATTTCTTTTCTTTCC 59.014 47.619 0.00 0.00 0.00 3.13
569 1291 3.376234 TCTTCAGGTATTGTAGTCCGACG 59.624 47.826 0.00 0.00 0.00 5.12
595 1317 1.965414 TGTATTCCTCCCCAGCAGAA 58.035 50.000 0.00 0.00 0.00 3.02
602 1324 3.714798 TGTAGGACATTGTATTCCTCCCC 59.285 47.826 0.00 0.00 41.63 4.81
624 1346 3.371591 TGGCGCGACTTAAAATCGTTTAT 59.628 39.130 15.80 0.00 41.68 1.40
626 1348 1.532007 TGGCGCGACTTAAAATCGTTT 59.468 42.857 15.80 0.00 41.68 3.60
636 1358 4.021368 AGGTATATAGAATTGGCGCGACTT 60.021 41.667 15.80 0.00 0.00 3.01
674 1396 8.501070 AGAGAATTGGAATTAGTGGAGATCAAT 58.499 33.333 0.00 0.00 0.00 2.57
681 1403 6.388100 AGATGGAGAGAATTGGAATTAGTGGA 59.612 38.462 0.00 0.00 0.00 4.02
683 1405 7.278135 TGAGATGGAGAGAATTGGAATTAGTG 58.722 38.462 0.00 0.00 0.00 2.74
688 1410 5.444176 GGTTGAGATGGAGAGAATTGGAAT 58.556 41.667 0.00 0.00 0.00 3.01
691 1413 3.201290 CGGTTGAGATGGAGAGAATTGG 58.799 50.000 0.00 0.00 0.00 3.16
736 1465 3.252284 ACCTGGTGGGCAGTGGAG 61.252 66.667 0.00 0.00 39.10 3.86
737 1466 3.249189 GACCTGGTGGGCAGTGGA 61.249 66.667 2.82 0.00 42.34 4.02
739 1468 2.910737 ATGGACCTGGTGGGCAGTG 61.911 63.158 2.82 0.00 45.45 3.66
740 1469 2.532715 ATGGACCTGGTGGGCAGT 60.533 61.111 2.82 0.00 45.45 4.40
741 1470 1.929860 ATCATGGACCTGGTGGGCAG 61.930 60.000 2.82 0.00 45.45 4.85
742 1471 1.930133 ATCATGGACCTGGTGGGCA 60.930 57.895 2.82 0.00 45.45 5.36
743 1472 1.454479 CATCATGGACCTGGTGGGC 60.454 63.158 2.82 0.00 41.93 5.36
744 1473 1.228228 CCATCATGGACCTGGTGGG 59.772 63.158 2.82 0.00 42.69 4.61
745 1474 4.993307 CCATCATGGACCTGGTGG 57.007 61.111 2.82 8.34 40.96 4.61
746 1475 1.820906 CGCCATCATGGACCTGGTG 60.821 63.158 8.30 0.00 40.96 4.17
765 1494 0.315568 AATAGATCTCAGCCGTCCGC 59.684 55.000 0.00 0.00 37.98 5.54
787 1516 2.014554 CACACCGTCAAGTCGTCCG 61.015 63.158 0.00 0.00 0.00 4.79
789 1518 0.309922 TCTCACACCGTCAAGTCGTC 59.690 55.000 0.00 0.00 0.00 4.20
791 1520 2.065993 AATCTCACACCGTCAAGTCG 57.934 50.000 0.00 0.00 0.00 4.18
793 1522 2.872245 CACAAATCTCACACCGTCAAGT 59.128 45.455 0.00 0.00 0.00 3.16
794 1523 3.130633 TCACAAATCTCACACCGTCAAG 58.869 45.455 0.00 0.00 0.00 3.02
795 1524 3.186702 TCACAAATCTCACACCGTCAA 57.813 42.857 0.00 0.00 0.00 3.18
796 1525 2.900716 TCACAAATCTCACACCGTCA 57.099 45.000 0.00 0.00 0.00 4.35
798 1527 2.616842 GGTTTCACAAATCTCACACCGT 59.383 45.455 0.00 0.00 0.00 4.83
841 1592 4.809426 CGTACAGGTTTCAGAAGTTCAGTT 59.191 41.667 5.50 0.00 0.00 3.16
850 1601 1.334160 TGCCTCGTACAGGTTTCAGA 58.666 50.000 11.47 0.00 45.61 3.27
861 1612 4.382040 CCTTTTCTTCAGAGATGCCTCGTA 60.382 45.833 0.00 0.00 44.08 3.43
863 1614 2.935201 CCTTTTCTTCAGAGATGCCTCG 59.065 50.000 0.00 0.00 44.08 4.63
888 1639 0.176680 AGGCAGGCGAGTACAGAATG 59.823 55.000 0.00 0.00 46.00 2.67
889 1640 0.461961 GAGGCAGGCGAGTACAGAAT 59.538 55.000 0.00 0.00 0.00 2.40
890 1641 0.612174 AGAGGCAGGCGAGTACAGAA 60.612 55.000 0.00 0.00 0.00 3.02
891 1642 1.000771 AGAGGCAGGCGAGTACAGA 60.001 57.895 0.00 0.00 0.00 3.41
892 1643 1.034838 AGAGAGGCAGGCGAGTACAG 61.035 60.000 0.00 0.00 0.00 2.74
893 1644 1.000771 AGAGAGGCAGGCGAGTACA 60.001 57.895 0.00 0.00 0.00 2.90
894 1645 1.731093 GAGAGAGGCAGGCGAGTAC 59.269 63.158 0.00 0.00 0.00 2.73
906 1657 2.578178 CGGCAGCGAACGAGAGAG 60.578 66.667 0.00 0.00 0.00 3.20
938 1689 1.603739 GGCCTTTGGGTGTGAGGAC 60.604 63.158 0.00 0.00 32.11 3.85
1038 1792 3.475774 GGCACGCGTGAGGTTACG 61.476 66.667 41.19 14.19 46.28 3.18
1198 1952 1.530771 GCAGGTGCAGGATGAGGAT 59.469 57.895 0.00 0.00 39.69 3.24
1477 2231 2.270923 CGCGAAGAGGATGTCATCAAA 58.729 47.619 14.72 0.00 0.00 2.69
1479 2233 3.648528 CGCGAAGAGGATGTCATCA 57.351 52.632 14.72 0.00 0.00 3.07
1632 2386 1.069090 GTCGAATATGGCCTCGGCA 59.931 57.895 11.44 0.00 44.11 5.69
1686 2440 1.271840 TGCTGTACCCCTCCACCATC 61.272 60.000 0.00 0.00 0.00 3.51
1926 2680 3.382832 CGCCCCTCCTCAACTCGT 61.383 66.667 0.00 0.00 0.00 4.18
2247 3001 3.270027 CCTGACAAAATCGTATGCCTGA 58.730 45.455 0.00 0.00 0.00 3.86
2262 3016 0.252330 TTGTCGGTATCCCCCTGACA 60.252 55.000 0.00 0.00 36.74 3.58
2278 3032 0.180406 ACGTCAGAGTTTGGCCTTGT 59.820 50.000 3.32 0.00 0.00 3.16
2280 3034 0.180406 ACACGTCAGAGTTTGGCCTT 59.820 50.000 3.32 0.00 0.00 4.35
2358 3112 5.749462 CTCAACTCAAATACCTCCCTTGAT 58.251 41.667 0.00 0.00 0.00 2.57
2606 3361 0.396974 AGCACCAAAGCCCAAGAACA 60.397 50.000 0.00 0.00 34.23 3.18
2691 3446 7.549488 ACTCTGCATTGTAAATAAGTGGACTAC 59.451 37.037 0.00 0.00 0.00 2.73
2692 3447 7.620880 ACTCTGCATTGTAAATAAGTGGACTA 58.379 34.615 0.00 0.00 0.00 2.59
2697 3452 7.278646 TGAGCTACTCTGCATTGTAAATAAGTG 59.721 37.037 0.00 0.00 34.99 3.16
2758 3514 7.639113 AAACCTCTTTGTTGTATTTCAGTGA 57.361 32.000 0.00 0.00 0.00 3.41
2834 3593 6.611642 AGGTCCTACAATCTGCTATTGAAGTA 59.388 38.462 16.20 1.93 33.51 2.24
2894 3654 2.153366 AAGCCAAATCTTTGTTGCCG 57.847 45.000 2.29 0.00 36.45 5.69
2999 3759 5.964958 TGGAAACAGAAGGAACAATGATC 57.035 39.130 0.00 0.00 35.01 2.92
3092 3855 3.244561 TGAGTTCCAGAATGAACCACTCC 60.245 47.826 0.59 0.00 44.55 3.85
3108 3871 2.494059 TGCCTGTTGCTAGTTGAGTTC 58.506 47.619 0.00 0.00 42.00 3.01
3145 3908 7.696992 ATTTTAGCTCGGAAAAGGATTTACA 57.303 32.000 0.00 0.00 37.28 2.41
3285 4048 7.549134 TGCTTTATGTCTAACACTCCTATGTTG 59.451 37.037 1.46 0.00 42.74 3.33
3350 4113 7.082602 ACGATACCTATAAATAGTGCTTCGTG 58.917 38.462 0.00 0.00 34.13 4.35
3351 4114 7.211966 ACGATACCTATAAATAGTGCTTCGT 57.788 36.000 0.00 0.00 0.00 3.85
3352 4115 9.784680 ATTACGATACCTATAAATAGTGCTTCG 57.215 33.333 0.00 0.00 0.00 3.79
3354 4117 9.871238 CCATTACGATACCTATAAATAGTGCTT 57.129 33.333 0.00 0.00 0.00 3.91
3355 4118 9.251440 TCCATTACGATACCTATAAATAGTGCT 57.749 33.333 0.00 0.00 0.00 4.40
3356 4119 9.865321 TTCCATTACGATACCTATAAATAGTGC 57.135 33.333 0.00 0.00 0.00 4.40
3366 4129 9.918630 GCTTAGTTATTTCCATTACGATACCTA 57.081 33.333 0.00 0.00 0.00 3.08
3367 4130 8.426489 TGCTTAGTTATTTCCATTACGATACCT 58.574 33.333 0.00 0.00 0.00 3.08
3368 4131 8.597662 TGCTTAGTTATTTCCATTACGATACC 57.402 34.615 0.00 0.00 0.00 2.73
3372 4135 9.834628 CTTTTTGCTTAGTTATTTCCATTACGA 57.165 29.630 0.00 0.00 0.00 3.43
3373 4136 9.834628 TCTTTTTGCTTAGTTATTTCCATTACG 57.165 29.630 0.00 0.00 0.00 3.18
3375 4138 9.855021 GCTCTTTTTGCTTAGTTATTTCCATTA 57.145 29.630 0.00 0.00 0.00 1.90
3376 4139 8.367156 TGCTCTTTTTGCTTAGTTATTTCCATT 58.633 29.630 0.00 0.00 0.00 3.16
3377 4140 7.814587 GTGCTCTTTTTGCTTAGTTATTTCCAT 59.185 33.333 0.00 0.00 0.00 3.41
3378 4141 7.145323 GTGCTCTTTTTGCTTAGTTATTTCCA 58.855 34.615 0.00 0.00 0.00 3.53
3379 4142 7.145323 TGTGCTCTTTTTGCTTAGTTATTTCC 58.855 34.615 0.00 0.00 0.00 3.13
3380 4143 8.480066 GTTGTGCTCTTTTTGCTTAGTTATTTC 58.520 33.333 0.00 0.00 0.00 2.17
3381 4144 8.197439 AGTTGTGCTCTTTTTGCTTAGTTATTT 58.803 29.630 0.00 0.00 0.00 1.40
3382 4145 7.649306 CAGTTGTGCTCTTTTTGCTTAGTTATT 59.351 33.333 0.00 0.00 0.00 1.40
3383 4146 7.141363 CAGTTGTGCTCTTTTTGCTTAGTTAT 58.859 34.615 0.00 0.00 0.00 1.89
3384 4147 6.459573 CCAGTTGTGCTCTTTTTGCTTAGTTA 60.460 38.462 0.00 0.00 0.00 2.24
3385 4148 5.343249 CAGTTGTGCTCTTTTTGCTTAGTT 58.657 37.500 0.00 0.00 0.00 2.24
3386 4149 4.202050 CCAGTTGTGCTCTTTTTGCTTAGT 60.202 41.667 0.00 0.00 0.00 2.24
3387 4150 4.036734 TCCAGTTGTGCTCTTTTTGCTTAG 59.963 41.667 0.00 0.00 0.00 2.18
3388 4151 3.951037 TCCAGTTGTGCTCTTTTTGCTTA 59.049 39.130 0.00 0.00 0.00 3.09
3389 4152 2.760092 TCCAGTTGTGCTCTTTTTGCTT 59.240 40.909 0.00 0.00 0.00 3.91
3390 4153 2.360165 CTCCAGTTGTGCTCTTTTTGCT 59.640 45.455 0.00 0.00 0.00 3.91
3391 4154 2.544486 CCTCCAGTTGTGCTCTTTTTGC 60.544 50.000 0.00 0.00 0.00 3.68
3392 4155 2.689983 ACCTCCAGTTGTGCTCTTTTTG 59.310 45.455 0.00 0.00 0.00 2.44
3393 4156 3.018423 ACCTCCAGTTGTGCTCTTTTT 57.982 42.857 0.00 0.00 0.00 1.94
3394 4157 2.736670 ACCTCCAGTTGTGCTCTTTT 57.263 45.000 0.00 0.00 0.00 2.27
3395 4158 3.118038 TGTTACCTCCAGTTGTGCTCTTT 60.118 43.478 0.00 0.00 0.00 2.52
3396 4159 2.438021 TGTTACCTCCAGTTGTGCTCTT 59.562 45.455 0.00 0.00 0.00 2.85
3397 4160 2.047061 TGTTACCTCCAGTTGTGCTCT 58.953 47.619 0.00 0.00 0.00 4.09
3398 4161 2.143925 GTGTTACCTCCAGTTGTGCTC 58.856 52.381 0.00 0.00 0.00 4.26
3399 4162 1.768870 AGTGTTACCTCCAGTTGTGCT 59.231 47.619 0.00 0.00 0.00 4.40
3400 4163 2.256117 AGTGTTACCTCCAGTTGTGC 57.744 50.000 0.00 0.00 0.00 4.57
3401 4164 7.442969 TGTTAATTAGTGTTACCTCCAGTTGTG 59.557 37.037 0.00 0.00 0.00 3.33
3402 4165 7.443272 GTGTTAATTAGTGTTACCTCCAGTTGT 59.557 37.037 0.00 0.00 0.00 3.32
3403 4166 7.660208 AGTGTTAATTAGTGTTACCTCCAGTTG 59.340 37.037 0.00 0.00 0.00 3.16
3404 4167 7.660208 CAGTGTTAATTAGTGTTACCTCCAGTT 59.340 37.037 0.00 0.00 0.00 3.16
3405 4168 7.159372 CAGTGTTAATTAGTGTTACCTCCAGT 58.841 38.462 0.00 0.00 0.00 4.00
3406 4169 6.594159 CCAGTGTTAATTAGTGTTACCTCCAG 59.406 42.308 0.00 0.00 0.00 3.86
3407 4170 6.043474 ACCAGTGTTAATTAGTGTTACCTCCA 59.957 38.462 0.00 0.00 0.00 3.86
3408 4171 6.470278 ACCAGTGTTAATTAGTGTTACCTCC 58.530 40.000 0.00 0.00 0.00 4.30
3409 4172 7.156673 TGACCAGTGTTAATTAGTGTTACCTC 58.843 38.462 0.00 0.00 0.00 3.85
3410 4173 7.069877 TGACCAGTGTTAATTAGTGTTACCT 57.930 36.000 0.00 0.00 0.00 3.08
3411 4174 7.916914 ATGACCAGTGTTAATTAGTGTTACC 57.083 36.000 0.00 0.00 0.00 2.85
3412 4175 8.995220 TCAATGACCAGTGTTAATTAGTGTTAC 58.005 33.333 0.00 0.00 0.00 2.50
3413 4176 9.733556 ATCAATGACCAGTGTTAATTAGTGTTA 57.266 29.630 0.00 0.00 0.00 2.41
3414 4177 8.635765 ATCAATGACCAGTGTTAATTAGTGTT 57.364 30.769 0.00 0.00 0.00 3.32
3415 4178 9.905713 ATATCAATGACCAGTGTTAATTAGTGT 57.094 29.630 0.00 0.00 0.00 3.55
3424 4187 8.469200 CCAACATAAATATCAATGACCAGTGTT 58.531 33.333 4.67 0.00 0.00 3.32
3425 4188 7.833682 TCCAACATAAATATCAATGACCAGTGT 59.166 33.333 4.67 0.00 0.00 3.55
3426 4189 8.224389 TCCAACATAAATATCAATGACCAGTG 57.776 34.615 4.67 0.00 0.00 3.66
3427 4190 8.821686 TTCCAACATAAATATCAATGACCAGT 57.178 30.769 4.67 0.00 0.00 4.00
3429 4192 9.868277 GTTTTCCAACATAAATATCAATGACCA 57.132 29.630 4.67 0.00 32.54 4.02
3439 4202 9.747898 ACCATAGACAGTTTTCCAACATAAATA 57.252 29.630 0.00 0.00 35.05 1.40
3440 4203 8.650143 ACCATAGACAGTTTTCCAACATAAAT 57.350 30.769 0.00 0.00 35.05 1.40
3441 4204 8.472007 AACCATAGACAGTTTTCCAACATAAA 57.528 30.769 0.00 0.00 35.05 1.40
3442 4205 9.226606 CTAACCATAGACAGTTTTCCAACATAA 57.773 33.333 0.00 0.00 35.05 1.90
3443 4206 8.380099 ACTAACCATAGACAGTTTTCCAACATA 58.620 33.333 0.00 0.00 32.68 2.29
3444 4207 7.231467 ACTAACCATAGACAGTTTTCCAACAT 58.769 34.615 0.00 0.00 32.68 2.71
3445 4208 6.597562 ACTAACCATAGACAGTTTTCCAACA 58.402 36.000 0.00 0.00 32.68 3.33
3446 4209 7.506328 AACTAACCATAGACAGTTTTCCAAC 57.494 36.000 0.00 0.00 33.15 3.77
3447 4210 9.444600 GATAACTAACCATAGACAGTTTTCCAA 57.555 33.333 0.00 0.00 33.47 3.53
3448 4211 8.822805 AGATAACTAACCATAGACAGTTTTCCA 58.177 33.333 0.00 0.00 32.63 3.53
3452 4215 8.411683 CGGTAGATAACTAACCATAGACAGTTT 58.588 37.037 0.00 0.00 33.13 2.66
3453 4216 7.559170 ACGGTAGATAACTAACCATAGACAGTT 59.441 37.037 0.00 0.00 33.13 3.16
3454 4217 7.059156 ACGGTAGATAACTAACCATAGACAGT 58.941 38.462 0.00 0.00 33.13 3.55
3455 4218 7.308469 GGACGGTAGATAACTAACCATAGACAG 60.308 44.444 0.00 0.00 33.13 3.51
3456 4219 6.488006 GGACGGTAGATAACTAACCATAGACA 59.512 42.308 0.00 0.00 33.13 3.41
3457 4220 6.348050 CGGACGGTAGATAACTAACCATAGAC 60.348 46.154 0.00 0.00 33.13 2.59
3458 4221 5.702670 CGGACGGTAGATAACTAACCATAGA 59.297 44.000 0.00 0.00 33.13 1.98
3459 4222 5.702670 TCGGACGGTAGATAACTAACCATAG 59.297 44.000 0.00 0.00 33.13 2.23
3460 4223 5.620206 TCGGACGGTAGATAACTAACCATA 58.380 41.667 0.00 0.00 33.13 2.74
3461 4224 4.464008 TCGGACGGTAGATAACTAACCAT 58.536 43.478 0.00 0.00 33.13 3.55
3462 4225 3.884895 TCGGACGGTAGATAACTAACCA 58.115 45.455 0.00 0.00 33.13 3.67
3463 4226 4.900635 TTCGGACGGTAGATAACTAACC 57.099 45.455 0.00 0.00 33.13 2.85
3464 4227 5.174579 GCAATTCGGACGGTAGATAACTAAC 59.825 44.000 0.00 0.00 33.37 2.34
3465 4228 5.163530 TGCAATTCGGACGGTAGATAACTAA 60.164 40.000 0.00 0.00 0.00 2.24
3466 4229 4.338964 TGCAATTCGGACGGTAGATAACTA 59.661 41.667 0.00 0.00 0.00 2.24
3467 4230 3.131577 TGCAATTCGGACGGTAGATAACT 59.868 43.478 0.00 0.00 0.00 2.24
3468 4231 3.450578 TGCAATTCGGACGGTAGATAAC 58.549 45.455 0.00 0.00 0.00 1.89
3469 4232 3.804786 TGCAATTCGGACGGTAGATAA 57.195 42.857 0.00 0.00 0.00 1.75
3470 4233 3.319689 TCATGCAATTCGGACGGTAGATA 59.680 43.478 0.00 0.00 0.00 1.98
3471 4234 2.102420 TCATGCAATTCGGACGGTAGAT 59.898 45.455 0.00 0.00 0.00 1.98
3472 4235 1.478916 TCATGCAATTCGGACGGTAGA 59.521 47.619 0.00 0.00 0.00 2.59
3473 4236 1.934589 TCATGCAATTCGGACGGTAG 58.065 50.000 0.00 0.00 0.00 3.18
3474 4237 2.613026 ATCATGCAATTCGGACGGTA 57.387 45.000 0.00 0.00 0.00 4.02
3475 4238 2.210116 GTATCATGCAATTCGGACGGT 58.790 47.619 0.00 0.00 0.00 4.83
3476 4239 1.192312 CGTATCATGCAATTCGGACGG 59.808 52.381 0.00 0.00 0.00 4.79
3477 4240 1.192312 CCGTATCATGCAATTCGGACG 59.808 52.381 10.05 6.46 40.76 4.79
3478 4241 1.069906 GCCGTATCATGCAATTCGGAC 60.070 52.381 17.56 7.53 40.76 4.79
3479 4242 1.225855 GCCGTATCATGCAATTCGGA 58.774 50.000 17.56 0.10 40.76 4.55
3480 4243 0.110688 CGCCGTATCATGCAATTCGG 60.111 55.000 11.00 11.00 41.10 4.30
3481 4244 0.110688 CCGCCGTATCATGCAATTCG 60.111 55.000 0.00 0.00 0.00 3.34
3482 4245 0.944386 ACCGCCGTATCATGCAATTC 59.056 50.000 0.00 0.00 0.00 2.17
3483 4246 1.871039 GTACCGCCGTATCATGCAATT 59.129 47.619 0.00 0.00 0.00 2.32
3484 4247 1.202592 TGTACCGCCGTATCATGCAAT 60.203 47.619 0.00 0.00 0.00 3.56
3485 4248 0.175989 TGTACCGCCGTATCATGCAA 59.824 50.000 0.00 0.00 0.00 4.08
3486 4249 0.391228 ATGTACCGCCGTATCATGCA 59.609 50.000 0.00 0.00 0.00 3.96
3487 4250 2.094906 TCTATGTACCGCCGTATCATGC 60.095 50.000 0.00 0.00 0.00 4.06
3488 4251 3.842732 TCTATGTACCGCCGTATCATG 57.157 47.619 0.00 0.00 0.00 3.07
3489 4252 4.270834 AGATCTATGTACCGCCGTATCAT 58.729 43.478 0.00 0.00 0.00 2.45
3490 4253 3.682696 AGATCTATGTACCGCCGTATCA 58.317 45.455 0.00 0.00 0.00 2.15
3491 4254 3.065095 GGAGATCTATGTACCGCCGTATC 59.935 52.174 0.00 0.00 0.00 2.24
3492 4255 3.015327 GGAGATCTATGTACCGCCGTAT 58.985 50.000 0.00 0.00 0.00 3.06
3493 4256 2.039480 AGGAGATCTATGTACCGCCGTA 59.961 50.000 0.00 0.00 0.00 4.02
3494 4257 1.202903 AGGAGATCTATGTACCGCCGT 60.203 52.381 0.00 0.00 0.00 5.68
3495 4258 1.535833 AGGAGATCTATGTACCGCCG 58.464 55.000 0.00 0.00 0.00 6.46
3496 4259 3.321111 TCAAAGGAGATCTATGTACCGCC 59.679 47.826 0.00 0.00 0.00 6.13
3497 4260 4.585955 TCAAAGGAGATCTATGTACCGC 57.414 45.455 0.00 0.00 0.00 5.68
3498 4261 7.085116 GTGTATCAAAGGAGATCTATGTACCG 58.915 42.308 0.00 0.00 0.00 4.02
3499 4262 7.952671 TGTGTATCAAAGGAGATCTATGTACC 58.047 38.462 0.00 0.00 0.00 3.34
3500 4263 9.817809 TTTGTGTATCAAAGGAGATCTATGTAC 57.182 33.333 0.00 0.00 40.56 2.90
3516 4279 8.334632 CGCAACTCATACATTATTTGTGTATCA 58.665 33.333 0.00 0.00 39.95 2.15
3517 4280 8.547894 TCGCAACTCATACATTATTTGTGTATC 58.452 33.333 0.00 0.00 39.95 2.24
3518 4281 8.335356 GTCGCAACTCATACATTATTTGTGTAT 58.665 33.333 0.00 0.00 42.01 2.29
3519 4282 7.547722 AGTCGCAACTCATACATTATTTGTGTA 59.452 33.333 0.00 0.00 39.48 2.90
3520 4283 6.371548 AGTCGCAACTCATACATTATTTGTGT 59.628 34.615 0.00 0.00 39.48 3.72
3521 4284 6.775088 AGTCGCAACTCATACATTATTTGTG 58.225 36.000 0.00 0.00 39.48 3.33
3522 4285 6.985188 AGTCGCAACTCATACATTATTTGT 57.015 33.333 0.00 0.00 42.62 2.83


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

AutoCloner maintained by Alex Coulton.