Multiple sequence alignment - TraesCS2A01G234100

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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 TraesCS2A01G234100 chr2A 100.000 2375 0 0 1 2375 280109699 280107325 0.000000e+00 4386.0
1 TraesCS2A01G234100 chr2A 97.806 547 12 0 1829 2375 450037423 450037969 0.000000e+00 944.0
2 TraesCS2A01G234100 chr2A 97.806 547 11 1 1830 2375 147691730 147691184 0.000000e+00 942.0
3 TraesCS2A01G234100 chr2A 97.623 547 13 0 1829 2375 450045184 450045730 0.000000e+00 939.0
4 TraesCS2A01G234100 chr2A 95.811 549 19 4 1830 2375 295046425 295046972 0.000000e+00 883.0
5 TraesCS2A01G234100 chr1A 97.806 547 12 0 1829 2375 26005370 26005916 0.000000e+00 944.0
6 TraesCS2A01G234100 chr1A 97.619 546 12 1 1830 2375 25997581 25998125 0.000000e+00 935.0
7 TraesCS2A01G234100 chr5A 97.459 551 13 1 1825 2375 620946059 620946608 0.000000e+00 939.0
8 TraesCS2A01G234100 chr5A 97.258 547 14 1 1830 2375 204185973 204185427 0.000000e+00 926.0
9 TraesCS2A01G234100 chr2D 90.698 731 27 7 889 1617 247439167 247438476 0.000000e+00 935.0
10 TraesCS2A01G234100 chr2D 90.702 527 34 9 307 824 247441775 247441255 0.000000e+00 688.0
11 TraesCS2A01G234100 chr2D 91.667 300 23 2 1 300 247442055 247441758 4.720000e-112 414.0
12 TraesCS2A01G234100 chr2D 90.278 216 20 1 1615 1830 518802486 518802700 5.000000e-72 281.0
13 TraesCS2A01G234100 chr2D 89.815 216 22 0 1615 1830 2671070 2671285 6.470000e-71 278.0
14 TraesCS2A01G234100 chr2D 79.775 89 17 1 323 411 114826759 114826846 1.970000e-06 63.9
15 TraesCS2A01G234100 chr7A 96.892 547 16 1 1830 2375 607343345 607342799 0.000000e+00 915.0
16 TraesCS2A01G234100 chr7A 91.549 213 18 0 1618 1830 467785055 467784843 6.420000e-76 294.0
17 TraesCS2A01G234100 chr3D 90.610 213 20 0 1618 1830 441134678 441134890 1.390000e-72 283.0
18 TraesCS2A01G234100 chr3D 88.987 227 23 2 1605 1830 48628999 48628774 1.800000e-71 279.0
19 TraesCS2A01G234100 chr1D 90.610 213 20 0 1618 1830 163709475 163709263 1.390000e-72 283.0
20 TraesCS2A01G234100 chr1D 90.094 212 21 0 1619 1830 430106943 430107154 2.330000e-70 276.0
21 TraesCS2A01G234100 chr1D 81.513 119 11 5 327 442 292530808 292530918 1.170000e-13 87.9
22 TraesCS2A01G234100 chr5D 90.141 213 21 0 1618 1830 536698807 536699019 6.470000e-71 278.0
23 TraesCS2A01G234100 chr5D 84.444 90 12 2 354 442 514144636 514144724 1.170000e-13 87.9
24 TraesCS2A01G234100 chr6D 89.767 215 22 0 1616 1830 62136743 62136957 2.330000e-70 276.0
25 TraesCS2A01G234100 chr3A 86.777 121 15 1 323 442 505839923 505840043 1.480000e-27 134.0
26 TraesCS2A01G234100 chr4B 93.617 47 3 0 374 420 78602631 78602677 1.180000e-08 71.3


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G234100 chr2A 280107325 280109699 2374 True 4386 4386 100.000000 1 2375 1 chr2A.!!$R2 2374
1 TraesCS2A01G234100 chr2A 450037423 450037969 546 False 944 944 97.806000 1829 2375 1 chr2A.!!$F2 546
2 TraesCS2A01G234100 chr2A 147691184 147691730 546 True 942 942 97.806000 1830 2375 1 chr2A.!!$R1 545
3 TraesCS2A01G234100 chr2A 450045184 450045730 546 False 939 939 97.623000 1829 2375 1 chr2A.!!$F3 546
4 TraesCS2A01G234100 chr2A 295046425 295046972 547 False 883 883 95.811000 1830 2375 1 chr2A.!!$F1 545
5 TraesCS2A01G234100 chr1A 26005370 26005916 546 False 944 944 97.806000 1829 2375 1 chr1A.!!$F2 546
6 TraesCS2A01G234100 chr1A 25997581 25998125 544 False 935 935 97.619000 1830 2375 1 chr1A.!!$F1 545
7 TraesCS2A01G234100 chr5A 620946059 620946608 549 False 939 939 97.459000 1825 2375 1 chr5A.!!$F1 550
8 TraesCS2A01G234100 chr5A 204185427 204185973 546 True 926 926 97.258000 1830 2375 1 chr5A.!!$R1 545
9 TraesCS2A01G234100 chr2D 247438476 247442055 3579 True 679 935 91.022333 1 1617 3 chr2D.!!$R1 1616
10 TraesCS2A01G234100 chr7A 607342799 607343345 546 True 915 915 96.892000 1830 2375 1 chr7A.!!$R2 545

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
603 612 0.331616 ATAGCCAAGGAACACCACCC 59.668 55.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1818 3864 0.039798 GCTGTGACAAGTGGCATGTG 60.04 55.0 0.0 0.0 34.33 3.21 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
25 26 2.825836 GTCGCTGGGCTGGATTGG 60.826 66.667 0.00 0.00 0.00 3.16
34 35 3.515286 CTGGATTGGCGCTGGCAG 61.515 66.667 10.94 10.94 42.47 4.85
69 70 2.223377 GGTTCATGTGTTGACGTCCTTC 59.777 50.000 14.12 3.99 32.84 3.46
97 98 2.698797 GGTATTCACTGGCCTGTAGCTA 59.301 50.000 15.70 4.34 43.05 3.32
107 108 2.158813 GGCCTGTAGCTACCTTTGCATA 60.159 50.000 21.01 0.00 43.05 3.14
121 122 5.244626 ACCTTTGCATATTATCCAGCAATCC 59.755 40.000 0.00 0.00 45.23 3.01
161 162 3.287222 AGTTGGTGCCGCAATTATACAT 58.713 40.909 0.00 0.00 0.00 2.29
162 163 3.699038 AGTTGGTGCCGCAATTATACATT 59.301 39.130 0.00 0.00 0.00 2.71
232 233 9.609346 GTGTAGGTTGGCTAATAAAAGATAGAA 57.391 33.333 0.00 0.00 0.00 2.10
245 246 9.877178 AATAAAAGATAGAACTGTGAGGTACTG 57.123 33.333 0.00 0.00 41.55 2.74
273 274 2.305405 GCTCTTGCTCTATGGTGCG 58.695 57.895 0.00 0.00 35.02 5.34
279 280 4.320023 TCTTGCTCTATGGTGCGTAAAAA 58.680 39.130 0.00 0.00 35.02 1.94
281 282 3.670625 TGCTCTATGGTGCGTAAAAACT 58.329 40.909 0.00 0.00 35.02 2.66
293 294 6.457799 GGTGCGTAAAAACTGAAGAAGAAGAA 60.458 38.462 0.00 0.00 0.00 2.52
294 295 6.629252 GTGCGTAAAAACTGAAGAAGAAGAAG 59.371 38.462 0.00 0.00 0.00 2.85
295 296 6.537301 TGCGTAAAAACTGAAGAAGAAGAAGA 59.463 34.615 0.00 0.00 0.00 2.87
296 297 7.065324 TGCGTAAAAACTGAAGAAGAAGAAGAA 59.935 33.333 0.00 0.00 0.00 2.52
297 298 7.584485 GCGTAAAAACTGAAGAAGAAGAAGAAG 59.416 37.037 0.00 0.00 0.00 2.85
298 299 8.818057 CGTAAAAACTGAAGAAGAAGAAGAAGA 58.182 33.333 0.00 0.00 0.00 2.87
301 302 9.454859 AAAAACTGAAGAAGAAGAAGAAGAAGA 57.545 29.630 0.00 0.00 0.00 2.87
302 303 9.454859 AAAACTGAAGAAGAAGAAGAAGAAGAA 57.545 29.630 0.00 0.00 0.00 2.52
303 304 8.661352 AACTGAAGAAGAAGAAGAAGAAGAAG 57.339 34.615 0.00 0.00 0.00 2.85
304 305 8.017418 ACTGAAGAAGAAGAAGAAGAAGAAGA 57.983 34.615 0.00 0.00 0.00 2.87
305 306 8.482128 ACTGAAGAAGAAGAAGAAGAAGAAGAA 58.518 33.333 0.00 0.00 0.00 2.52
306 307 8.885494 TGAAGAAGAAGAAGAAGAAGAAGAAG 57.115 34.615 0.00 0.00 0.00 2.85
307 308 8.700051 TGAAGAAGAAGAAGAAGAAGAAGAAGA 58.300 33.333 0.00 0.00 0.00 2.87
308 309 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
309 310 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
310 311 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
311 312 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
312 313 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
313 314 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
314 315 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
315 316 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
316 317 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
317 318 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
318 319 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
321 322 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
564 565 2.305635 GGGGGCCAAAAATTGTCATTCT 59.694 45.455 4.39 0.00 0.00 2.40
566 567 4.503910 GGGGCCAAAAATTGTCATTCTAC 58.496 43.478 4.39 0.00 0.00 2.59
567 568 4.173256 GGGCCAAAAATTGTCATTCTACG 58.827 43.478 4.39 0.00 0.00 3.51
568 569 4.082463 GGGCCAAAAATTGTCATTCTACGA 60.082 41.667 4.39 0.00 0.00 3.43
570 571 5.344933 GGCCAAAAATTGTCATTCTACGAAC 59.655 40.000 0.00 0.00 0.00 3.95
571 572 5.918011 GCCAAAAATTGTCATTCTACGAACA 59.082 36.000 0.00 0.00 0.00 3.18
572 573 6.586082 GCCAAAAATTGTCATTCTACGAACAT 59.414 34.615 0.00 0.00 0.00 2.71
573 574 7.116233 GCCAAAAATTGTCATTCTACGAACATT 59.884 33.333 0.00 0.00 0.00 2.71
603 612 0.331616 ATAGCCAAGGAACACCACCC 59.668 55.000 0.00 0.00 0.00 4.61
606 615 1.228552 CCAAGGAACACCACCCTGG 60.229 63.158 0.00 0.00 45.02 4.45
618 627 1.693606 CCACCCTGGCAAAAATCAAGT 59.306 47.619 0.00 0.00 0.00 3.16
621 631 4.202305 CCACCCTGGCAAAAATCAAGTAAA 60.202 41.667 0.00 0.00 0.00 2.01
670 680 3.361786 TGACGAATGGACCATACTCAGA 58.638 45.455 7.59 0.00 0.00 3.27
692 702 2.429478 CAGCATGTGAAGACCATGTGA 58.571 47.619 0.00 0.00 41.38 3.58
695 705 2.416747 CATGTGAAGACCATGTGACGT 58.583 47.619 0.00 0.00 35.94 4.34
706 716 4.684877 ACCATGTGACGTATATGCGTTTA 58.315 39.130 19.91 9.82 45.79 2.01
749 759 5.766174 ACGTCAGGTAAACACATAAACCATT 59.234 36.000 0.00 0.00 34.29 3.16
765 775 3.813443 ACCATTCCAAGATCGAGATTGG 58.187 45.455 20.28 20.28 46.09 3.16
775 785 5.413309 AGATCGAGATTGGACAACTCTTT 57.587 39.130 0.00 0.00 0.00 2.52
786 796 9.317936 GATTGGACAACTCTTTTCAAGAAAAAT 57.682 29.630 9.05 0.00 39.49 1.82
824 842 1.651987 ATACACGCTTCAACCCATCG 58.348 50.000 0.00 0.00 0.00 3.84
836 854 3.438781 TCAACCCATCGTAAAAGCATGAC 59.561 43.478 0.00 0.00 0.00 3.06
841 2885 4.638421 CCCATCGTAAAAGCATGACCTAAA 59.362 41.667 0.00 0.00 0.00 1.85
847 2891 5.448632 CGTAAAAGCATGACCTAAATCCACC 60.449 44.000 0.00 0.00 0.00 4.61
855 2899 6.688922 GCATGACCTAAATCCACCTAGAATCA 60.689 42.308 0.00 0.00 0.00 2.57
885 2929 4.208686 GACGCTAGTCTGGCCCGG 62.209 72.222 0.00 0.00 43.80 5.73
905 2949 2.052766 GAGCGCGCCATTTCATCG 60.053 61.111 30.33 0.00 0.00 3.84
922 2966 3.317149 TCATCGTAGTTCCCGTTATCCTG 59.683 47.826 0.00 0.00 0.00 3.86
925 2969 2.547826 GTAGTTCCCGTTATCCTGTGC 58.452 52.381 0.00 0.00 0.00 4.57
926 2970 1.276622 AGTTCCCGTTATCCTGTGCT 58.723 50.000 0.00 0.00 0.00 4.40
927 2971 1.207329 AGTTCCCGTTATCCTGTGCTC 59.793 52.381 0.00 0.00 0.00 4.26
928 2972 1.207329 GTTCCCGTTATCCTGTGCTCT 59.793 52.381 0.00 0.00 0.00 4.09
929 2973 2.429610 GTTCCCGTTATCCTGTGCTCTA 59.570 50.000 0.00 0.00 0.00 2.43
930 2974 2.742348 TCCCGTTATCCTGTGCTCTAA 58.258 47.619 0.00 0.00 0.00 2.10
941 2985 2.747989 CTGTGCTCTAAGTCTACCGTCA 59.252 50.000 0.00 0.00 0.00 4.35
1057 3103 4.824515 CGTCCTCGCCCCTCCTCT 62.825 72.222 0.00 0.00 0.00 3.69
1058 3104 2.835895 GTCCTCGCCCCTCCTCTC 60.836 72.222 0.00 0.00 0.00 3.20
1059 3105 4.144727 TCCTCGCCCCTCCTCTCC 62.145 72.222 0.00 0.00 0.00 3.71
1060 3106 4.150454 CCTCGCCCCTCCTCTCCT 62.150 72.222 0.00 0.00 0.00 3.69
1061 3107 2.520741 CTCGCCCCTCCTCTCCTC 60.521 72.222 0.00 0.00 0.00 3.71
1062 3108 4.144727 TCGCCCCTCCTCTCCTCC 62.145 72.222 0.00 0.00 0.00 4.30
1064 3110 4.890306 GCCCCTCCTCTCCTCCCC 62.890 77.778 0.00 0.00 0.00 4.81
1065 3111 4.179599 CCCCTCCTCTCCTCCCCC 62.180 77.778 0.00 0.00 0.00 5.40
1066 3112 3.039526 CCCTCCTCTCCTCCCCCT 61.040 72.222 0.00 0.00 0.00 4.79
1067 3113 2.612251 CCTCCTCTCCTCCCCCTC 59.388 72.222 0.00 0.00 0.00 4.30
1068 3114 2.612251 CTCCTCTCCTCCCCCTCC 59.388 72.222 0.00 0.00 0.00 4.30
1069 3115 2.018086 CTCCTCTCCTCCCCCTCCT 61.018 68.421 0.00 0.00 0.00 3.69
1070 3116 2.015726 TCCTCTCCTCCCCCTCCTC 61.016 68.421 0.00 0.00 0.00 3.71
1253 3299 1.153549 CCTACTCCAAGCCTGTCGC 60.154 63.158 0.00 0.00 37.98 5.19
1387 3433 1.269723 TGCTGTAGTGTCTCCTTCACG 59.730 52.381 0.00 0.00 40.28 4.35
1392 3438 4.392047 TGTAGTGTCTCCTTCACGTTCTA 58.608 43.478 0.00 0.00 40.28 2.10
1415 3461 1.668793 TCGTCGTCGAGTACAGGCA 60.669 57.895 0.00 0.00 41.35 4.75
1465 3511 0.250640 GCAGGATGATGCGGGAGATT 60.251 55.000 0.00 0.00 39.69 2.40
1467 3513 0.250640 AGGATGATGCGGGAGATTGC 60.251 55.000 0.00 0.00 0.00 3.56
1498 3544 3.390135 CTCAGGTTCGTGTTTTGCTCTA 58.610 45.455 0.00 0.00 0.00 2.43
1518 3564 9.209048 TGCTCTATTCCTTCCAAATACTAAGTA 57.791 33.333 0.00 0.00 0.00 2.24
1607 3653 7.281774 CACATCAACTATCACCAGCTTTATTCT 59.718 37.037 0.00 0.00 0.00 2.40
1635 3681 4.825546 TTTACGAAAACATTAACGCCCA 57.174 36.364 0.00 0.00 0.00 5.36
1636 3682 5.373981 TTTACGAAAACATTAACGCCCAT 57.626 34.783 0.00 0.00 0.00 4.00
1637 3683 6.492007 TTTACGAAAACATTAACGCCCATA 57.508 33.333 0.00 0.00 0.00 2.74
1638 3684 6.492007 TTACGAAAACATTAACGCCCATAA 57.508 33.333 0.00 0.00 0.00 1.90
1639 3685 4.976987 ACGAAAACATTAACGCCCATAAG 58.023 39.130 0.00 0.00 0.00 1.73
1640 3686 4.456566 ACGAAAACATTAACGCCCATAAGT 59.543 37.500 0.00 0.00 0.00 2.24
1641 3687 4.791163 CGAAAACATTAACGCCCATAAGTG 59.209 41.667 0.00 0.00 0.00 3.16
1642 3688 5.618195 CGAAAACATTAACGCCCATAAGTGT 60.618 40.000 0.00 0.00 0.00 3.55
1643 3689 4.695217 AACATTAACGCCCATAAGTGTG 57.305 40.909 0.00 0.00 0.00 3.82
1644 3690 3.013921 ACATTAACGCCCATAAGTGTGG 58.986 45.455 0.00 0.00 39.05 4.17
1652 3698 0.109319 CCATAAGTGTGGGCGTTTGC 60.109 55.000 0.00 0.00 41.71 3.68
1653 3699 0.595588 CATAAGTGTGGGCGTTTGCA 59.404 50.000 0.00 0.00 45.35 4.08
1654 3700 1.202114 CATAAGTGTGGGCGTTTGCAT 59.798 47.619 0.00 0.00 45.35 3.96
1655 3701 0.878416 TAAGTGTGGGCGTTTGCATC 59.122 50.000 0.00 0.00 45.35 3.91
1656 3702 0.823356 AAGTGTGGGCGTTTGCATCT 60.823 50.000 0.00 0.00 45.35 2.90
1657 3703 1.210155 GTGTGGGCGTTTGCATCTC 59.790 57.895 0.00 0.00 45.35 2.75
1658 3704 2.324330 TGTGGGCGTTTGCATCTCG 61.324 57.895 0.00 0.00 45.35 4.04
1659 3705 2.745884 TGGGCGTTTGCATCTCGG 60.746 61.111 0.00 0.00 45.35 4.63
1660 3706 4.179579 GGGCGTTTGCATCTCGGC 62.180 66.667 18.47 18.47 45.35 5.54
1661 3707 4.179579 GGCGTTTGCATCTCGGCC 62.180 66.667 16.79 9.25 45.35 6.13
1662 3708 3.430862 GCGTTTGCATCTCGGCCA 61.431 61.111 2.24 0.00 42.15 5.36
1663 3709 2.480555 CGTTTGCATCTCGGCCAC 59.519 61.111 2.24 0.00 0.00 5.01
1664 3710 2.324330 CGTTTGCATCTCGGCCACA 61.324 57.895 2.24 0.00 0.00 4.17
1665 3711 1.210155 GTTTGCATCTCGGCCACAC 59.790 57.895 2.24 0.00 0.00 3.82
1666 3712 2.324330 TTTGCATCTCGGCCACACG 61.324 57.895 2.24 0.00 0.00 4.49
1682 3728 4.429212 CGCGTGGATCCGTGTCCA 62.429 66.667 7.39 2.15 45.78 4.02
1689 3735 3.704800 TGGATCCGTGTCCATTTGTAA 57.295 42.857 7.39 0.00 43.20 2.41
1690 3736 3.605634 TGGATCCGTGTCCATTTGTAAG 58.394 45.455 7.39 0.00 43.20 2.34
1691 3737 2.354821 GGATCCGTGTCCATTTGTAAGC 59.645 50.000 0.00 0.00 38.20 3.09
1692 3738 1.434555 TCCGTGTCCATTTGTAAGCG 58.565 50.000 0.00 0.00 0.00 4.68
1693 3739 0.179200 CCGTGTCCATTTGTAAGCGC 60.179 55.000 0.00 0.00 0.00 5.92
1694 3740 0.515127 CGTGTCCATTTGTAAGCGCA 59.485 50.000 11.47 0.00 0.00 6.09
1695 3741 1.724654 CGTGTCCATTTGTAAGCGCAC 60.725 52.381 11.47 0.00 0.00 5.34
1696 3742 0.515127 TGTCCATTTGTAAGCGCACG 59.485 50.000 11.47 0.00 0.00 5.34
1697 3743 0.793861 GTCCATTTGTAAGCGCACGA 59.206 50.000 11.47 0.00 0.00 4.35
1698 3744 1.195900 GTCCATTTGTAAGCGCACGAA 59.804 47.619 11.47 6.59 0.00 3.85
1699 3745 2.080693 TCCATTTGTAAGCGCACGAAT 58.919 42.857 11.47 8.93 33.59 3.34
1700 3746 2.095213 TCCATTTGTAAGCGCACGAATC 59.905 45.455 11.47 0.00 31.40 2.52
1701 3747 2.095853 CCATTTGTAAGCGCACGAATCT 59.904 45.455 11.47 0.00 31.40 2.40
1702 3748 3.426159 CCATTTGTAAGCGCACGAATCTT 60.426 43.478 11.47 0.00 31.40 2.40
1703 3749 2.873170 TTGTAAGCGCACGAATCTTG 57.127 45.000 11.47 0.00 0.00 3.02
1704 3750 1.075542 TGTAAGCGCACGAATCTTGG 58.924 50.000 11.47 0.00 0.00 3.61
1705 3751 0.247695 GTAAGCGCACGAATCTTGGC 60.248 55.000 11.47 0.00 0.00 4.52
1706 3752 0.672091 TAAGCGCACGAATCTTGGCA 60.672 50.000 11.47 0.00 0.00 4.92
1707 3753 1.308069 AAGCGCACGAATCTTGGCAT 61.308 50.000 11.47 0.00 0.00 4.40
1708 3754 1.584483 GCGCACGAATCTTGGCATG 60.584 57.895 0.30 0.00 0.00 4.06
1709 3755 1.796151 CGCACGAATCTTGGCATGT 59.204 52.632 0.00 0.00 0.00 3.21
1710 3756 0.168788 CGCACGAATCTTGGCATGTT 59.831 50.000 0.00 0.00 0.00 2.71
1711 3757 1.401409 CGCACGAATCTTGGCATGTTT 60.401 47.619 0.00 0.00 0.00 2.83
1712 3758 2.253603 GCACGAATCTTGGCATGTTTC 58.746 47.619 11.97 11.97 0.00 2.78
1713 3759 2.095059 GCACGAATCTTGGCATGTTTCT 60.095 45.455 17.10 6.52 0.00 2.52
1714 3760 3.126858 GCACGAATCTTGGCATGTTTCTA 59.873 43.478 17.10 0.00 0.00 2.10
1715 3761 4.728882 GCACGAATCTTGGCATGTTTCTAG 60.729 45.833 17.10 12.11 0.00 2.43
1716 3762 4.393062 CACGAATCTTGGCATGTTTCTAGT 59.607 41.667 17.10 9.33 0.00 2.57
1717 3763 4.393062 ACGAATCTTGGCATGTTTCTAGTG 59.607 41.667 17.10 8.13 0.00 2.74
1718 3764 4.666237 GAATCTTGGCATGTTTCTAGTGC 58.334 43.478 13.85 0.00 38.12 4.40
1722 3768 3.975992 GCATGTTTCTAGTGCCACG 57.024 52.632 0.00 0.00 32.88 4.94
1723 3769 1.156736 GCATGTTTCTAGTGCCACGT 58.843 50.000 0.00 0.00 32.88 4.49
1724 3770 2.343101 GCATGTTTCTAGTGCCACGTA 58.657 47.619 0.00 0.00 32.88 3.57
1725 3771 2.348666 GCATGTTTCTAGTGCCACGTAG 59.651 50.000 0.00 0.00 32.88 3.51
1726 3772 2.074547 TGTTTCTAGTGCCACGTAGC 57.925 50.000 0.00 0.00 0.00 3.58
1727 3773 1.341852 TGTTTCTAGTGCCACGTAGCA 59.658 47.619 4.01 4.01 41.46 3.49
1728 3774 2.028476 TGTTTCTAGTGCCACGTAGCAT 60.028 45.455 12.77 4.17 46.24 3.79
1729 3775 3.000727 GTTTCTAGTGCCACGTAGCATT 58.999 45.455 12.77 10.81 46.24 3.56
1730 3776 2.293677 TCTAGTGCCACGTAGCATTG 57.706 50.000 12.77 5.77 46.24 2.82
1731 3777 1.134818 TCTAGTGCCACGTAGCATTGG 60.135 52.381 12.77 10.30 46.24 3.16
1732 3778 0.107897 TAGTGCCACGTAGCATTGGG 60.108 55.000 12.77 0.00 46.24 4.12
1733 3779 2.749839 TGCCACGTAGCATTGGGC 60.750 61.111 4.01 3.99 44.82 5.36
1742 3788 2.652530 GCATTGGGCTGGTGTGTG 59.347 61.111 0.00 0.00 40.25 3.82
1743 3789 2.934570 GCATTGGGCTGGTGTGTGG 61.935 63.158 0.00 0.00 40.25 4.17
1744 3790 2.118076 ATTGGGCTGGTGTGTGGG 59.882 61.111 0.00 0.00 0.00 4.61
1745 3791 4.912395 TTGGGCTGGTGTGTGGGC 62.912 66.667 0.00 0.00 0.00 5.36
1747 3793 4.684134 GGGCTGGTGTGTGGGCAT 62.684 66.667 0.00 0.00 0.00 4.40
1748 3794 2.601367 GGCTGGTGTGTGGGCATT 60.601 61.111 0.00 0.00 0.00 3.56
1749 3795 2.639327 GGCTGGTGTGTGGGCATTC 61.639 63.158 0.00 0.00 0.00 2.67
1750 3796 1.902918 GCTGGTGTGTGGGCATTCA 60.903 57.895 0.00 0.00 0.00 2.57
1751 3797 1.959085 CTGGTGTGTGGGCATTCAC 59.041 57.895 0.00 0.00 38.09 3.18
1752 3798 3.365535 GGTGTGTGGGCATTCACC 58.634 61.111 0.00 0.00 42.40 4.02
1760 3806 4.778143 GGCATTCACCCGGTCGCT 62.778 66.667 0.00 0.00 0.00 4.93
1761 3807 3.195698 GCATTCACCCGGTCGCTC 61.196 66.667 0.00 0.00 0.00 5.03
1762 3808 2.264480 CATTCACCCGGTCGCTCA 59.736 61.111 0.00 0.00 0.00 4.26
1763 3809 2.100631 CATTCACCCGGTCGCTCAC 61.101 63.158 0.00 0.00 0.00 3.51
1764 3810 2.579657 ATTCACCCGGTCGCTCACA 61.580 57.895 0.00 0.00 0.00 3.58
1765 3811 2.781595 ATTCACCCGGTCGCTCACAC 62.782 60.000 0.00 0.00 0.00 3.82
1766 3812 4.293648 CACCCGGTCGCTCACACA 62.294 66.667 0.00 0.00 0.00 3.72
1767 3813 3.991051 ACCCGGTCGCTCACACAG 61.991 66.667 0.00 0.00 0.00 3.66
1770 3816 4.363990 CGGTCGCTCACACAGCCT 62.364 66.667 0.00 0.00 46.74 4.58
1771 3817 2.031163 GGTCGCTCACACAGCCTT 59.969 61.111 0.00 0.00 46.74 4.35
1772 3818 1.598130 GGTCGCTCACACAGCCTTT 60.598 57.895 0.00 0.00 46.74 3.11
1773 3819 1.166531 GGTCGCTCACACAGCCTTTT 61.167 55.000 0.00 0.00 46.74 2.27
1774 3820 0.235926 GTCGCTCACACAGCCTTTTC 59.764 55.000 0.00 0.00 46.74 2.29
1775 3821 0.179059 TCGCTCACACAGCCTTTTCA 60.179 50.000 0.00 0.00 46.74 2.69
1776 3822 0.040958 CGCTCACACAGCCTTTTCAC 60.041 55.000 0.00 0.00 46.74 3.18
1777 3823 0.312102 GCTCACACAGCCTTTTCACC 59.688 55.000 0.00 0.00 43.17 4.02
1778 3824 1.679139 CTCACACAGCCTTTTCACCA 58.321 50.000 0.00 0.00 0.00 4.17
1779 3825 1.334869 CTCACACAGCCTTTTCACCAC 59.665 52.381 0.00 0.00 0.00 4.16
1780 3826 1.102154 CACACAGCCTTTTCACCACA 58.898 50.000 0.00 0.00 0.00 4.17
1781 3827 1.682854 CACACAGCCTTTTCACCACAT 59.317 47.619 0.00 0.00 0.00 3.21
1782 3828 1.682854 ACACAGCCTTTTCACCACATG 59.317 47.619 0.00 0.00 0.00 3.21
1783 3829 1.000060 CACAGCCTTTTCACCACATGG 60.000 52.381 0.00 0.00 42.17 3.66
1784 3830 0.604578 CAGCCTTTTCACCACATGGG 59.395 55.000 2.32 0.00 44.81 4.00
1785 3831 0.482446 AGCCTTTTCACCACATGGGA 59.518 50.000 0.00 0.00 41.15 4.37
1786 3832 1.077663 AGCCTTTTCACCACATGGGAT 59.922 47.619 0.00 0.00 41.15 3.85
1787 3833 1.205417 GCCTTTTCACCACATGGGATG 59.795 52.381 0.00 0.00 41.15 3.51
1788 3834 1.826720 CCTTTTCACCACATGGGATGG 59.173 52.381 0.00 0.00 43.43 3.51
1789 3835 2.557229 CCTTTTCACCACATGGGATGGA 60.557 50.000 7.78 0.00 39.87 3.41
1790 3836 2.214376 TTTCACCACATGGGATGGAC 57.786 50.000 7.78 0.00 39.87 4.02
1791 3837 1.371467 TTCACCACATGGGATGGACT 58.629 50.000 7.78 0.00 39.87 3.85
1792 3838 0.620030 TCACCACATGGGATGGACTG 59.380 55.000 7.78 0.00 39.87 3.51
1793 3839 0.394762 CACCACATGGGATGGACTGG 60.395 60.000 7.78 0.75 39.87 4.00
1794 3840 0.846427 ACCACATGGGATGGACTGGT 60.846 55.000 7.78 1.38 39.87 4.00
1795 3841 0.394762 CCACATGGGATGGACTGGTG 60.395 60.000 0.00 0.00 39.87 4.17
1796 3842 0.329261 CACATGGGATGGACTGGTGT 59.671 55.000 0.00 0.00 33.60 4.16
1797 3843 0.329261 ACATGGGATGGACTGGTGTG 59.671 55.000 0.00 0.00 33.60 3.82
1798 3844 0.329261 CATGGGATGGACTGGTGTGT 59.671 55.000 0.00 0.00 0.00 3.72
1799 3845 0.329261 ATGGGATGGACTGGTGTGTG 59.671 55.000 0.00 0.00 0.00 3.82
1800 3846 1.002134 GGGATGGACTGGTGTGTGG 60.002 63.158 0.00 0.00 0.00 4.17
1801 3847 1.002134 GGATGGACTGGTGTGTGGG 60.002 63.158 0.00 0.00 0.00 4.61
1802 3848 1.675641 GATGGACTGGTGTGTGGGC 60.676 63.158 0.00 0.00 0.00 5.36
1803 3849 3.551496 ATGGACTGGTGTGTGGGCG 62.551 63.158 0.00 0.00 0.00 6.13
1804 3850 4.250305 GGACTGGTGTGTGGGCGT 62.250 66.667 0.00 0.00 0.00 5.68
1805 3851 2.203153 GACTGGTGTGTGGGCGTT 60.203 61.111 0.00 0.00 0.00 4.84
1806 3852 1.822186 GACTGGTGTGTGGGCGTTT 60.822 57.895 0.00 0.00 0.00 3.60
1807 3853 0.533308 GACTGGTGTGTGGGCGTTTA 60.533 55.000 0.00 0.00 0.00 2.01
1808 3854 0.534203 ACTGGTGTGTGGGCGTTTAG 60.534 55.000 0.00 0.00 0.00 1.85
1821 3867 1.493772 CGTTTAGCAGTTCGTCCACA 58.506 50.000 0.00 0.00 0.00 4.17
1822 3868 2.066262 CGTTTAGCAGTTCGTCCACAT 58.934 47.619 0.00 0.00 0.00 3.21
1823 3869 2.159841 CGTTTAGCAGTTCGTCCACATG 60.160 50.000 0.00 0.00 0.00 3.21
1824 3870 1.438651 TTAGCAGTTCGTCCACATGC 58.561 50.000 0.00 0.00 37.15 4.06
1825 3871 0.391130 TAGCAGTTCGTCCACATGCC 60.391 55.000 0.00 0.00 37.61 4.40
1826 3872 1.965930 GCAGTTCGTCCACATGCCA 60.966 57.895 0.00 0.00 0.00 4.92
1827 3873 1.868997 CAGTTCGTCCACATGCCAC 59.131 57.895 0.00 0.00 0.00 5.01
1964 4012 2.239400 GGCAAGAACCCTTAAGCTTGT 58.761 47.619 9.86 0.00 39.79 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.197790 CAATCCAGCCCAGCGACG 61.198 66.667 0.00 0.00 0.00 5.12
23 24 1.303561 AGAAAATCTGCCAGCGCCA 60.304 52.632 2.29 0.00 0.00 5.69
25 26 4.779819 CAGAAAATCTGCCAGCGC 57.220 55.556 0.00 0.00 37.72 5.92
34 35 4.682860 CACATGAACCAAGCACAGAAAATC 59.317 41.667 0.00 0.00 0.00 2.17
69 70 1.512926 GCCAGTGAATACCCTATGCG 58.487 55.000 0.00 0.00 0.00 4.73
97 98 5.244626 GGATTGCTGGATAATATGCAAAGGT 59.755 40.000 0.00 0.00 46.31 3.50
107 108 3.870538 TGAGCTGGATTGCTGGATAAT 57.129 42.857 0.00 0.00 44.17 1.28
138 139 3.508012 TGTATAATTGCGGCACCAACTTT 59.492 39.130 0.05 0.00 0.00 2.66
146 147 5.699001 CCTACAGTAATGTATAATTGCGGCA 59.301 40.000 3.10 0.00 0.00 5.69
147 148 5.699458 ACCTACAGTAATGTATAATTGCGGC 59.301 40.000 3.10 0.00 0.00 6.53
161 162 9.175312 CACTTCTCTCATAGTTACCTACAGTAA 57.825 37.037 0.00 0.00 38.65 2.24
162 163 8.327271 ACACTTCTCTCATAGTTACCTACAGTA 58.673 37.037 0.00 0.00 0.00 2.74
175 176 2.094182 GCGAACCCACACTTCTCTCATA 60.094 50.000 0.00 0.00 0.00 2.15
205 206 8.989131 TCTATCTTTTATTAGCCAACCTACACT 58.011 33.333 0.00 0.00 0.00 3.55
206 207 9.609346 TTCTATCTTTTATTAGCCAACCTACAC 57.391 33.333 0.00 0.00 0.00 2.90
207 208 9.609346 GTTCTATCTTTTATTAGCCAACCTACA 57.391 33.333 0.00 0.00 0.00 2.74
208 209 9.833917 AGTTCTATCTTTTATTAGCCAACCTAC 57.166 33.333 0.00 0.00 0.00 3.18
209 210 9.832445 CAGTTCTATCTTTTATTAGCCAACCTA 57.168 33.333 0.00 0.00 0.00 3.08
210 211 8.329502 ACAGTTCTATCTTTTATTAGCCAACCT 58.670 33.333 0.00 0.00 0.00 3.50
232 233 1.003580 CATTGGCCAGTACCTCACAGT 59.996 52.381 5.11 0.00 0.00 3.55
245 246 3.204418 GCAAGAGCTCCATTGGCC 58.796 61.111 10.93 0.00 37.91 5.36
279 280 8.017418 TCTTCTTCTTCTTCTTCTTCTTCAGT 57.983 34.615 0.00 0.00 0.00 3.41
281 282 8.700051 TCTTCTTCTTCTTCTTCTTCTTCTTCA 58.300 33.333 0.00 0.00 0.00 3.02
293 294 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
294 295 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
295 296 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
296 297 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
297 298 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
298 299 9.898152 TTTCTTCTTCTTCTTCTTCTTCTTCTT 57.102 29.630 0.00 0.00 0.00 2.52
299 300 9.898152 TTTTCTTCTTCTTCTTCTTCTTCTTCT 57.102 29.630 0.00 0.00 0.00 2.85
302 303 9.844257 TGATTTTCTTCTTCTTCTTCTTCTTCT 57.156 29.630 0.00 0.00 0.00 2.85
305 306 9.625747 ACTTGATTTTCTTCTTCTTCTTCTTCT 57.374 29.630 0.00 0.00 0.00 2.85
530 531 0.746923 GGCCCCCGAACAACATAGAC 60.747 60.000 0.00 0.00 0.00 2.59
538 539 0.394565 CAATTTTTGGCCCCCGAACA 59.605 50.000 0.00 0.00 0.00 3.18
540 541 0.682292 GACAATTTTTGGCCCCCGAA 59.318 50.000 0.00 0.00 30.38 4.30
573 574 9.515226 GGTGTTCCTTGGCTATATAATGAATTA 57.485 33.333 0.00 0.00 0.00 1.40
588 597 1.228552 CCAGGGTGGTGTTCCTTGG 60.229 63.158 0.00 0.00 43.77 3.61
593 602 0.827368 TTTTTGCCAGGGTGGTGTTC 59.173 50.000 0.00 0.00 40.46 3.18
595 604 1.047801 GATTTTTGCCAGGGTGGTGT 58.952 50.000 0.00 0.00 40.46 4.16
639 649 4.081365 TGGTCCATTCGTCAAAGCTACATA 60.081 41.667 0.00 0.00 0.00 2.29
654 664 3.264193 TGCTGTTCTGAGTATGGTCCATT 59.736 43.478 10.33 0.00 0.00 3.16
706 716 5.414765 TGACGTCAATATCTGATATAGGCGT 59.585 40.000 17.62 21.67 36.14 5.68
713 723 7.919091 GTGTTTACCTGACGTCAATATCTGATA 59.081 37.037 20.49 0.00 36.14 2.15
714 724 6.757010 GTGTTTACCTGACGTCAATATCTGAT 59.243 38.462 20.49 0.00 36.14 2.90
715 725 6.097356 GTGTTTACCTGACGTCAATATCTGA 58.903 40.000 20.49 0.00 0.00 3.27
749 759 3.515502 AGTTGTCCAATCTCGATCTTGGA 59.484 43.478 19.55 19.55 46.63 3.53
792 802 4.921470 AGCGTGTATTTGTGTGTATCAC 57.079 40.909 0.00 0.00 46.31 3.06
808 818 1.434555 TTACGATGGGTTGAAGCGTG 58.565 50.000 0.00 0.00 36.51 5.34
824 842 5.652452 AGGTGGATTTAGGTCATGCTTTTAC 59.348 40.000 0.00 0.00 0.00 2.01
836 854 5.471456 GCATGTGATTCTAGGTGGATTTAGG 59.529 44.000 0.00 0.00 0.00 2.69
841 2885 2.700371 TCGCATGTGATTCTAGGTGGAT 59.300 45.455 4.45 0.00 0.00 3.41
847 2891 5.276114 CGTCTTTCTTCGCATGTGATTCTAG 60.276 44.000 10.29 4.55 0.00 2.43
886 2930 3.512287 GATGAAATGGCGCGCTCCG 62.512 63.158 32.29 0.00 40.75 4.63
887 2931 2.329339 GATGAAATGGCGCGCTCC 59.671 61.111 32.29 16.28 0.00 4.70
905 2949 2.167900 AGCACAGGATAACGGGAACTAC 59.832 50.000 0.00 0.00 0.00 2.73
922 2966 2.159407 GGTGACGGTAGACTTAGAGCAC 60.159 54.545 0.00 0.00 0.00 4.40
925 2969 4.263435 AGAAGGTGACGGTAGACTTAGAG 58.737 47.826 0.00 0.00 0.00 2.43
926 2970 4.298103 AGAAGGTGACGGTAGACTTAGA 57.702 45.455 0.00 0.00 0.00 2.10
927 2971 4.734917 CAAGAAGGTGACGGTAGACTTAG 58.265 47.826 0.00 0.00 0.00 2.18
928 2972 3.057033 GCAAGAAGGTGACGGTAGACTTA 60.057 47.826 0.00 0.00 0.00 2.24
929 2973 2.288886 GCAAGAAGGTGACGGTAGACTT 60.289 50.000 0.00 0.00 0.00 3.01
930 2974 1.272769 GCAAGAAGGTGACGGTAGACT 59.727 52.381 0.00 0.00 0.00 3.24
941 2985 0.261696 AGGGTGTTTGGCAAGAAGGT 59.738 50.000 0.00 0.00 0.00 3.50
968 3012 6.830324 TGCGAACCCTAAGAGTAGTTCTATTA 59.170 38.462 0.00 0.00 37.15 0.98
969 3013 5.655532 TGCGAACCCTAAGAGTAGTTCTATT 59.344 40.000 0.00 0.00 37.15 1.73
971 3015 4.592942 TGCGAACCCTAAGAGTAGTTCTA 58.407 43.478 0.00 0.00 37.15 2.10
972 3016 3.428532 TGCGAACCCTAAGAGTAGTTCT 58.571 45.455 0.00 0.00 37.15 3.01
973 3017 3.863142 TGCGAACCCTAAGAGTAGTTC 57.137 47.619 0.00 0.00 36.19 3.01
974 3018 3.132467 GGATGCGAACCCTAAGAGTAGTT 59.868 47.826 0.00 0.00 0.00 2.24
976 3020 2.287668 CGGATGCGAACCCTAAGAGTAG 60.288 54.545 0.00 0.00 0.00 2.57
977 3021 1.679680 CGGATGCGAACCCTAAGAGTA 59.320 52.381 0.00 0.00 0.00 2.59
979 3023 0.876342 GCGGATGCGAACCCTAAGAG 60.876 60.000 12.10 0.00 0.00 2.85
980 3024 1.143183 GCGGATGCGAACCCTAAGA 59.857 57.895 12.10 0.00 0.00 2.10
1059 3105 4.862823 GTCGGGGAGGAGGGGGAG 62.863 77.778 0.00 0.00 0.00 4.30
1061 3107 4.499116 ATGTCGGGGAGGAGGGGG 62.499 72.222 0.00 0.00 0.00 5.40
1062 3108 2.844839 GATGTCGGGGAGGAGGGG 60.845 72.222 0.00 0.00 0.00 4.79
1063 3109 2.844839 GGATGTCGGGGAGGAGGG 60.845 72.222 0.00 0.00 0.00 4.30
1064 3110 2.844839 GGGATGTCGGGGAGGAGG 60.845 72.222 0.00 0.00 0.00 4.30
1065 3111 1.834822 GAGGGATGTCGGGGAGGAG 60.835 68.421 0.00 0.00 0.00 3.69
1066 3112 2.282446 GAGGGATGTCGGGGAGGA 59.718 66.667 0.00 0.00 0.00 3.71
1067 3113 3.227276 CGAGGGATGTCGGGGAGG 61.227 72.222 0.00 0.00 36.26 4.30
1068 3114 3.917760 GCGAGGGATGTCGGGGAG 61.918 72.222 0.00 0.00 40.44 4.30
1077 3123 2.831742 TTAGCCGTCGCGAGGGAT 60.832 61.111 42.80 39.63 41.18 3.85
1352 3398 4.097863 GCACGTAACCGGCAAGCC 62.098 66.667 0.00 0.00 38.78 4.35
1387 3433 0.247419 TCGACGACGACGCATAGAAC 60.247 55.000 14.67 0.00 43.81 3.01
1392 3438 1.059994 GTACTCGACGACGACGCAT 59.940 57.895 14.67 7.66 43.81 4.73
1440 3486 2.831366 CGCATCATCCTGCTGCACC 61.831 63.158 0.00 0.00 39.27 5.01
1465 3511 1.806542 GAACCTGAGCTTGAAATCGCA 59.193 47.619 0.00 0.00 0.00 5.10
1467 3513 2.069273 ACGAACCTGAGCTTGAAATCG 58.931 47.619 9.62 9.62 35.36 3.34
1574 3620 5.125356 TGGTGATAGTTGATGTGGCAATAG 58.875 41.667 0.00 0.00 0.00 1.73
1617 3663 4.456566 ACTTATGGGCGTTAATGTTTTCGT 59.543 37.500 0.00 0.00 0.00 3.85
1618 3664 4.791163 CACTTATGGGCGTTAATGTTTTCG 59.209 41.667 0.00 0.00 0.00 3.46
1619 3665 5.571357 CACACTTATGGGCGTTAATGTTTTC 59.429 40.000 0.00 0.00 0.00 2.29
1620 3666 5.465935 CACACTTATGGGCGTTAATGTTTT 58.534 37.500 0.00 0.00 0.00 2.43
1621 3667 4.082463 CCACACTTATGGGCGTTAATGTTT 60.082 41.667 0.00 0.00 35.95 2.83
1622 3668 3.442273 CCACACTTATGGGCGTTAATGTT 59.558 43.478 0.00 0.00 35.95 2.71
1623 3669 3.013921 CCACACTTATGGGCGTTAATGT 58.986 45.455 0.00 0.00 35.95 2.71
1624 3670 3.691049 CCACACTTATGGGCGTTAATG 57.309 47.619 0.00 0.00 35.95 1.90
1633 3679 0.109319 GCAAACGCCCACACTTATGG 60.109 55.000 0.00 0.00 39.71 2.74
1634 3680 0.595588 TGCAAACGCCCACACTTATG 59.404 50.000 0.00 0.00 0.00 1.90
1635 3681 1.472480 GATGCAAACGCCCACACTTAT 59.528 47.619 0.00 0.00 0.00 1.73
1636 3682 0.878416 GATGCAAACGCCCACACTTA 59.122 50.000 0.00 0.00 0.00 2.24
1637 3683 0.823356 AGATGCAAACGCCCACACTT 60.823 50.000 0.00 0.00 0.00 3.16
1638 3684 1.228245 AGATGCAAACGCCCACACT 60.228 52.632 0.00 0.00 0.00 3.55
1639 3685 1.210155 GAGATGCAAACGCCCACAC 59.790 57.895 0.00 0.00 0.00 3.82
1640 3686 2.324330 CGAGATGCAAACGCCCACA 61.324 57.895 0.00 0.00 0.00 4.17
1641 3687 2.480555 CGAGATGCAAACGCCCAC 59.519 61.111 0.00 0.00 0.00 4.61
1642 3688 2.745884 CCGAGATGCAAACGCCCA 60.746 61.111 0.00 0.00 0.00 5.36
1643 3689 4.179579 GCCGAGATGCAAACGCCC 62.180 66.667 0.00 0.00 0.00 6.13
1644 3690 4.179579 GGCCGAGATGCAAACGCC 62.180 66.667 0.00 0.00 0.00 5.68
1645 3691 3.430862 TGGCCGAGATGCAAACGC 61.431 61.111 0.00 0.00 0.00 4.84
1646 3692 2.324330 TGTGGCCGAGATGCAAACG 61.324 57.895 0.00 0.00 0.00 3.60
1647 3693 1.210155 GTGTGGCCGAGATGCAAAC 59.790 57.895 0.00 0.00 0.00 2.93
1648 3694 2.324330 CGTGTGGCCGAGATGCAAA 61.324 57.895 0.00 0.00 0.00 3.68
1649 3695 2.741985 CGTGTGGCCGAGATGCAA 60.742 61.111 0.00 0.00 0.00 4.08
1661 3707 3.478394 CACGGATCCACGCGTGTG 61.478 66.667 34.81 25.89 46.00 3.82
1662 3708 3.986006 ACACGGATCCACGCGTGT 61.986 61.111 34.81 20.11 44.64 4.49
1663 3709 3.179265 GACACGGATCCACGCGTG 61.179 66.667 31.77 31.77 43.39 5.34
1664 3710 4.430765 GGACACGGATCCACGCGT 62.431 66.667 5.58 5.58 38.77 6.01
1665 3711 4.429212 TGGACACGGATCCACGCG 62.429 66.667 13.41 3.53 44.14 6.01
1670 3716 2.354821 GCTTACAAATGGACACGGATCC 59.645 50.000 0.00 0.00 39.45 3.36
1671 3717 2.030457 CGCTTACAAATGGACACGGATC 59.970 50.000 0.00 0.00 0.00 3.36
1672 3718 2.006888 CGCTTACAAATGGACACGGAT 58.993 47.619 0.00 0.00 0.00 4.18
1673 3719 1.434555 CGCTTACAAATGGACACGGA 58.565 50.000 0.00 0.00 0.00 4.69
1674 3720 0.179200 GCGCTTACAAATGGACACGG 60.179 55.000 0.00 0.00 0.00 4.94
1675 3721 0.515127 TGCGCTTACAAATGGACACG 59.485 50.000 9.73 0.00 0.00 4.49
1676 3722 1.724654 CGTGCGCTTACAAATGGACAC 60.725 52.381 9.73 0.00 0.00 3.67
1677 3723 0.515127 CGTGCGCTTACAAATGGACA 59.485 50.000 9.73 0.00 0.00 4.02
1678 3724 0.793861 TCGTGCGCTTACAAATGGAC 59.206 50.000 9.73 0.00 0.00 4.02
1679 3725 1.514003 TTCGTGCGCTTACAAATGGA 58.486 45.000 9.73 0.00 0.00 3.41
1680 3726 2.095853 AGATTCGTGCGCTTACAAATGG 59.904 45.455 9.73 0.00 0.00 3.16
1681 3727 3.389687 AGATTCGTGCGCTTACAAATG 57.610 42.857 9.73 0.00 0.00 2.32
1682 3728 3.426159 CCAAGATTCGTGCGCTTACAAAT 60.426 43.478 9.73 0.00 0.00 2.32
1683 3729 2.095969 CCAAGATTCGTGCGCTTACAAA 60.096 45.455 9.73 0.00 0.00 2.83
1684 3730 1.463056 CCAAGATTCGTGCGCTTACAA 59.537 47.619 9.73 0.00 0.00 2.41
1685 3731 1.075542 CCAAGATTCGTGCGCTTACA 58.924 50.000 9.73 0.00 0.00 2.41
1686 3732 0.247695 GCCAAGATTCGTGCGCTTAC 60.248 55.000 9.73 0.00 0.00 2.34
1687 3733 0.672091 TGCCAAGATTCGTGCGCTTA 60.672 50.000 9.73 0.00 0.00 3.09
1688 3734 1.308069 ATGCCAAGATTCGTGCGCTT 61.308 50.000 9.73 0.00 0.00 4.68
1689 3735 1.746615 ATGCCAAGATTCGTGCGCT 60.747 52.632 9.73 0.00 0.00 5.92
1690 3736 1.584483 CATGCCAAGATTCGTGCGC 60.584 57.895 0.00 0.00 0.00 6.09
1691 3737 0.168788 AACATGCCAAGATTCGTGCG 59.831 50.000 0.00 0.00 0.00 5.34
1692 3738 2.095059 AGAAACATGCCAAGATTCGTGC 60.095 45.455 0.00 0.00 0.00 5.34
1693 3739 3.837213 AGAAACATGCCAAGATTCGTG 57.163 42.857 0.00 0.00 0.00 4.35
1694 3740 4.393062 CACTAGAAACATGCCAAGATTCGT 59.607 41.667 0.00 0.00 0.00 3.85
1695 3741 4.728882 GCACTAGAAACATGCCAAGATTCG 60.729 45.833 0.00 0.00 33.06 3.34
1696 3742 4.666237 GCACTAGAAACATGCCAAGATTC 58.334 43.478 0.00 0.00 33.06 2.52
1697 3743 4.708726 GCACTAGAAACATGCCAAGATT 57.291 40.909 0.00 0.00 33.06 2.40
1704 3750 1.156736 ACGTGGCACTAGAAACATGC 58.843 50.000 16.72 0.00 38.68 4.06
1705 3751 2.348666 GCTACGTGGCACTAGAAACATG 59.651 50.000 19.95 0.00 0.00 3.21
1706 3752 2.028476 TGCTACGTGGCACTAGAAACAT 60.028 45.455 23.68 0.00 37.29 2.71
1707 3753 1.341852 TGCTACGTGGCACTAGAAACA 59.658 47.619 23.68 0.00 37.29 2.83
1708 3754 2.074547 TGCTACGTGGCACTAGAAAC 57.925 50.000 23.68 0.87 37.29 2.78
1709 3755 3.000041 CAATGCTACGTGGCACTAGAAA 59.000 45.455 29.60 4.30 45.36 2.52
1710 3756 2.616960 CAATGCTACGTGGCACTAGAA 58.383 47.619 29.60 5.13 45.36 2.10
1711 3757 1.134818 CCAATGCTACGTGGCACTAGA 60.135 52.381 29.60 5.97 45.36 2.43
1712 3758 1.290203 CCAATGCTACGTGGCACTAG 58.710 55.000 29.60 19.89 45.36 2.57
1713 3759 0.107897 CCCAATGCTACGTGGCACTA 60.108 55.000 29.60 6.83 45.36 2.74
1714 3760 1.377202 CCCAATGCTACGTGGCACT 60.377 57.895 29.60 16.72 45.36 4.40
1715 3761 3.051392 GCCCAATGCTACGTGGCAC 62.051 63.158 29.60 12.25 45.36 5.01
1716 3762 2.749839 GCCCAATGCTACGTGGCA 60.750 61.111 29.17 29.17 46.63 4.92
1725 3771 2.652530 CACACACCAGCCCAATGC 59.347 61.111 0.00 0.00 41.71 3.56
1726 3772 2.277591 CCCACACACCAGCCCAATG 61.278 63.158 0.00 0.00 0.00 2.82
1727 3773 2.118076 CCCACACACCAGCCCAAT 59.882 61.111 0.00 0.00 0.00 3.16
1728 3774 4.912395 GCCCACACACCAGCCCAA 62.912 66.667 0.00 0.00 0.00 4.12
1730 3776 4.684134 ATGCCCACACACCAGCCC 62.684 66.667 0.00 0.00 0.00 5.19
1731 3777 2.601367 AATGCCCACACACCAGCC 60.601 61.111 0.00 0.00 0.00 4.85
1732 3778 1.902918 TGAATGCCCACACACCAGC 60.903 57.895 0.00 0.00 0.00 4.85
1733 3779 1.959085 GTGAATGCCCACACACCAG 59.041 57.895 0.00 0.00 37.04 4.00
1734 3780 4.172625 GTGAATGCCCACACACCA 57.827 55.556 0.00 0.00 37.04 4.17
1735 3781 3.365535 GGTGAATGCCCACACACC 58.634 61.111 0.00 0.00 44.23 4.16
1743 3789 4.778143 AGCGACCGGGTGAATGCC 62.778 66.667 3.30 0.00 0.00 4.40
1744 3790 3.195698 GAGCGACCGGGTGAATGC 61.196 66.667 3.30 3.08 0.00 3.56
1745 3791 2.100631 GTGAGCGACCGGGTGAATG 61.101 63.158 3.30 0.00 0.00 2.67
1746 3792 2.264794 GTGAGCGACCGGGTGAAT 59.735 61.111 3.30 0.00 0.00 2.57
1747 3793 3.228017 TGTGAGCGACCGGGTGAA 61.228 61.111 3.30 0.00 0.00 3.18
1748 3794 3.986006 GTGTGAGCGACCGGGTGA 61.986 66.667 3.30 0.00 0.00 4.02
1749 3795 4.293648 TGTGTGAGCGACCGGGTG 62.294 66.667 3.30 0.00 0.00 4.61
1750 3796 3.991051 CTGTGTGAGCGACCGGGT 61.991 66.667 6.32 0.00 0.00 5.28
1759 3805 1.334869 GTGGTGAAAAGGCTGTGTGAG 59.665 52.381 0.00 0.00 0.00 3.51
1760 3806 1.340502 TGTGGTGAAAAGGCTGTGTGA 60.341 47.619 0.00 0.00 0.00 3.58
1761 3807 1.102154 TGTGGTGAAAAGGCTGTGTG 58.898 50.000 0.00 0.00 0.00 3.82
1762 3808 1.682854 CATGTGGTGAAAAGGCTGTGT 59.317 47.619 0.00 0.00 0.00 3.72
1763 3809 1.000060 CCATGTGGTGAAAAGGCTGTG 60.000 52.381 0.00 0.00 0.00 3.66
1764 3810 1.331214 CCATGTGGTGAAAAGGCTGT 58.669 50.000 0.00 0.00 0.00 4.40
1765 3811 0.604578 CCCATGTGGTGAAAAGGCTG 59.395 55.000 0.00 0.00 0.00 4.85
1766 3812 0.482446 TCCCATGTGGTGAAAAGGCT 59.518 50.000 0.00 0.00 34.77 4.58
1767 3813 1.205417 CATCCCATGTGGTGAAAAGGC 59.795 52.381 0.00 0.00 34.77 4.35
1768 3814 1.826720 CCATCCCATGTGGTGAAAAGG 59.173 52.381 0.00 0.00 34.77 3.11
1769 3815 2.493278 GTCCATCCCATGTGGTGAAAAG 59.507 50.000 1.12 0.00 37.96 2.27
1770 3816 2.109834 AGTCCATCCCATGTGGTGAAAA 59.890 45.455 1.12 0.00 37.96 2.29
1771 3817 1.710244 AGTCCATCCCATGTGGTGAAA 59.290 47.619 1.12 0.00 37.96 2.69
1772 3818 1.004628 CAGTCCATCCCATGTGGTGAA 59.995 52.381 1.12 0.00 37.96 3.18
1773 3819 0.620030 CAGTCCATCCCATGTGGTGA 59.380 55.000 1.12 0.00 37.96 4.02
1774 3820 0.394762 CCAGTCCATCCCATGTGGTG 60.395 60.000 1.12 0.00 37.96 4.17
1775 3821 0.846427 ACCAGTCCATCCCATGTGGT 60.846 55.000 1.12 0.00 37.96 4.16
1776 3822 0.394762 CACCAGTCCATCCCATGTGG 60.395 60.000 0.00 0.00 38.11 4.17
1777 3823 0.329261 ACACCAGTCCATCCCATGTG 59.671 55.000 0.00 0.00 0.00 3.21
1778 3824 0.329261 CACACCAGTCCATCCCATGT 59.671 55.000 0.00 0.00 0.00 3.21
1779 3825 0.329261 ACACACCAGTCCATCCCATG 59.671 55.000 0.00 0.00 0.00 3.66
1780 3826 0.329261 CACACACCAGTCCATCCCAT 59.671 55.000 0.00 0.00 0.00 4.00
1781 3827 1.760527 CACACACCAGTCCATCCCA 59.239 57.895 0.00 0.00 0.00 4.37
1782 3828 1.002134 CCACACACCAGTCCATCCC 60.002 63.158 0.00 0.00 0.00 3.85
1783 3829 1.002134 CCCACACACCAGTCCATCC 60.002 63.158 0.00 0.00 0.00 3.51
1784 3830 1.675641 GCCCACACACCAGTCCATC 60.676 63.158 0.00 0.00 0.00 3.51
1785 3831 2.436109 GCCCACACACCAGTCCAT 59.564 61.111 0.00 0.00 0.00 3.41
1786 3832 4.248842 CGCCCACACACCAGTCCA 62.249 66.667 0.00 0.00 0.00 4.02
1787 3833 3.767630 AACGCCCACACACCAGTCC 62.768 63.158 0.00 0.00 0.00 3.85
1788 3834 0.533308 TAAACGCCCACACACCAGTC 60.533 55.000 0.00 0.00 0.00 3.51
1789 3835 0.534203 CTAAACGCCCACACACCAGT 60.534 55.000 0.00 0.00 0.00 4.00
1790 3836 1.852067 GCTAAACGCCCACACACCAG 61.852 60.000 0.00 0.00 0.00 4.00
1791 3837 1.894756 GCTAAACGCCCACACACCA 60.895 57.895 0.00 0.00 0.00 4.17
1792 3838 1.852067 CTGCTAAACGCCCACACACC 61.852 60.000 0.00 0.00 38.05 4.16
1793 3839 1.164041 ACTGCTAAACGCCCACACAC 61.164 55.000 0.00 0.00 38.05 3.82
1794 3840 0.464735 AACTGCTAAACGCCCACACA 60.465 50.000 0.00 0.00 38.05 3.72
1795 3841 0.237498 GAACTGCTAAACGCCCACAC 59.763 55.000 0.00 0.00 38.05 3.82
1796 3842 1.225376 CGAACTGCTAAACGCCCACA 61.225 55.000 0.00 0.00 38.05 4.17
1797 3843 1.226030 ACGAACTGCTAAACGCCCAC 61.226 55.000 0.00 0.00 38.05 4.61
1798 3844 0.947180 GACGAACTGCTAAACGCCCA 60.947 55.000 0.00 0.00 38.05 5.36
1799 3845 1.632948 GGACGAACTGCTAAACGCCC 61.633 60.000 0.00 0.00 38.05 6.13
1800 3846 0.947180 TGGACGAACTGCTAAACGCC 60.947 55.000 0.00 0.00 38.05 5.68
1801 3847 0.163146 GTGGACGAACTGCTAAACGC 59.837 55.000 0.00 0.00 39.77 4.84
1802 3848 1.493772 TGTGGACGAACTGCTAAACG 58.506 50.000 0.00 0.00 0.00 3.60
1803 3849 2.412847 GCATGTGGACGAACTGCTAAAC 60.413 50.000 0.00 0.00 0.00 2.01
1804 3850 1.804151 GCATGTGGACGAACTGCTAAA 59.196 47.619 0.00 0.00 0.00 1.85
1805 3851 1.438651 GCATGTGGACGAACTGCTAA 58.561 50.000 0.00 0.00 0.00 3.09
1806 3852 0.391130 GGCATGTGGACGAACTGCTA 60.391 55.000 0.00 0.00 33.43 3.49
1807 3853 1.672356 GGCATGTGGACGAACTGCT 60.672 57.895 0.00 0.00 33.43 4.24
1808 3854 1.965930 TGGCATGTGGACGAACTGC 60.966 57.895 0.00 0.00 0.00 4.40
1809 3855 0.603707 AGTGGCATGTGGACGAACTG 60.604 55.000 0.00 0.00 0.00 3.16
1810 3856 0.108585 AAGTGGCATGTGGACGAACT 59.891 50.000 0.00 0.00 0.00 3.01
1811 3857 0.238289 CAAGTGGCATGTGGACGAAC 59.762 55.000 0.00 0.00 0.00 3.95
1812 3858 0.179032 ACAAGTGGCATGTGGACGAA 60.179 50.000 0.00 0.00 0.00 3.85
1813 3859 0.602638 GACAAGTGGCATGTGGACGA 60.603 55.000 0.00 0.00 0.00 4.20
1814 3860 0.884259 TGACAAGTGGCATGTGGACG 60.884 55.000 0.00 0.00 0.00 4.79
1815 3861 0.593128 GTGACAAGTGGCATGTGGAC 59.407 55.000 0.00 0.00 34.33 4.02
1816 3862 0.182299 TGTGACAAGTGGCATGTGGA 59.818 50.000 0.00 0.00 34.33 4.02
1817 3863 0.594602 CTGTGACAAGTGGCATGTGG 59.405 55.000 0.00 0.00 34.33 4.17
1818 3864 0.039798 GCTGTGACAAGTGGCATGTG 60.040 55.000 0.00 0.00 34.33 3.21
1819 3865 1.174712 GGCTGTGACAAGTGGCATGT 61.175 55.000 0.00 0.00 34.33 3.21
1820 3866 1.582968 GGCTGTGACAAGTGGCATG 59.417 57.895 0.00 0.00 34.33 4.06
1821 3867 1.604593 GGGCTGTGACAAGTGGCAT 60.605 57.895 0.00 0.00 34.33 4.40
1822 3868 1.414866 TAGGGCTGTGACAAGTGGCA 61.415 55.000 0.00 0.00 0.00 4.92
1823 3869 0.674895 CTAGGGCTGTGACAAGTGGC 60.675 60.000 0.00 0.00 0.00 5.01
1824 3870 0.976641 TCTAGGGCTGTGACAAGTGG 59.023 55.000 0.00 0.00 0.00 4.00
1825 3871 2.839486 TTCTAGGGCTGTGACAAGTG 57.161 50.000 0.00 0.00 0.00 3.16
1826 3872 4.074970 CAAATTCTAGGGCTGTGACAAGT 58.925 43.478 0.00 0.00 0.00 3.16
1827 3873 4.326826 TCAAATTCTAGGGCTGTGACAAG 58.673 43.478 0.00 0.00 0.00 3.16
1909 3956 5.420725 AAGTTTTTGAGGCTTCCACTTTT 57.579 34.783 0.00 0.00 0.00 2.27
1964 4012 4.837860 AGGCCATTTTGGTTTCACTGAATA 59.162 37.500 5.01 0.00 40.46 1.75
2139 4188 7.215789 TCCAACAGCACATAAAACATTTCAAT 58.784 30.769 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.