Multiple sequence alignment - TraesCS2A01G590000

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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 TraesCS2A01G590000 chr2A 100.000 4358 0 0 1 4358 778429019 778424662 0.000000e+00 8048
1 TraesCS2A01G590000 chr2B 88.720 3617 236 60 806 4352 778851492 778847978 0.000000e+00 4261
2 TraesCS2A01G590000 chr2B 87.639 631 71 5 4 631 778852343 778851717 0.000000e+00 726
3 TraesCS2A01G590000 chr2D 91.864 2704 165 28 966 3636 634873651 634876332 0.000000e+00 3723
4 TraesCS2A01G590000 chr2D 89.698 563 32 11 3652 4191 634876385 634876944 0.000000e+00 695
5 TraesCS2A01G590000 chr2D 93.701 127 4 4 810 935 634873090 634873213 2.070000e-43 187
6 TraesCS2A01G590000 chr2D 91.765 85 5 1 4234 4318 634876949 634877031 2.750000e-22 117


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 TraesCS2A01G590000 chr2A 778424662 778429019 4357 True 8048.0 8048 100.0000 1 4358 1 chr2A.!!$R1 4357
1 TraesCS2A01G590000 chr2B 778847978 778852343 4365 True 2493.5 4261 88.1795 4 4352 2 chr2B.!!$R1 4348
2 TraesCS2A01G590000 chr2D 634873090 634877031 3941 False 1180.5 3723 91.7570 810 4318 4 chr2D.!!$F1 3508

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
669 673 0.109272 TAAGAAGCAGCCGACACGAG 60.109 55.0 0.0 0.0 0.0 4.18 F
1497 1988 0.749649 ACGCTCTCCTCCTGCTATTG 59.250 55.0 0.0 0.0 0.0 1.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2432 2968 1.560505 TGCCTAGATCACACAGAGCA 58.439 50.0 0.0 0.0 34.3 4.26 R
3422 3968 0.392060 GGCGACACTCCGGGTATTTT 60.392 55.0 0.0 0.0 0.0 1.82 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
28 29 7.184862 AGATTGGGTTTGGATACTTTGAAGAT 58.815 34.615 0.00 0.00 37.61 2.40
32 33 5.047377 GGGTTTGGATACTTTGAAGATGCAA 60.047 40.000 0.00 2.80 37.61 4.08
34 35 7.338440 GTTTGGATACTTTGAAGATGCAAAC 57.662 36.000 21.61 21.61 46.98 2.93
47 48 9.504710 TTGAAGATGCAAACAAAAATTCAAATG 57.495 25.926 0.00 0.00 33.75 2.32
77 78 7.184753 ACATAGGAAAGTCCTTTTATTCCCTCT 59.815 37.037 1.34 0.00 46.91 3.69
82 83 6.455690 AAGTCCTTTTATTCCCTCTGTCTT 57.544 37.500 0.00 0.00 0.00 3.01
130 131 6.615264 ATCCTCATCAAATTTGATCACTCG 57.385 37.500 27.08 17.12 45.62 4.18
133 134 5.220739 CCTCATCAAATTTGATCACTCGGAC 60.221 44.000 27.08 0.00 45.62 4.79
134 135 5.244755 TCATCAAATTTGATCACTCGGACA 58.755 37.500 27.08 0.78 45.62 4.02
146 147 5.614324 TCACTCGGACAATCATTCCTAAT 57.386 39.130 0.00 0.00 0.00 1.73
153 154 5.907391 CGGACAATCATTCCTAATTTTACGC 59.093 40.000 0.00 0.00 0.00 4.42
157 158 9.434559 GACAATCATTCCTAATTTTACGCTAAC 57.565 33.333 0.00 0.00 0.00 2.34
193 195 1.207791 CTGGGGATGTTACAGCCTCT 58.792 55.000 20.74 0.00 41.61 3.69
208 210 0.324091 CCTCTTTCCCCTGCTGCATT 60.324 55.000 1.31 0.00 0.00 3.56
216 218 1.364626 CCCTGCTGCATTCGACACTC 61.365 60.000 1.31 0.00 0.00 3.51
217 219 1.690283 CCTGCTGCATTCGACACTCG 61.690 60.000 1.31 0.00 42.10 4.18
260 263 4.002256 TCTAACCTCCACCACCATCATA 57.998 45.455 0.00 0.00 0.00 2.15
264 267 2.342659 CCTCCACCACCATCATATCCT 58.657 52.381 0.00 0.00 0.00 3.24
269 272 4.103153 TCCACCACCATCATATCCTTTCTC 59.897 45.833 0.00 0.00 0.00 2.87
272 275 3.071602 CCACCATCATATCCTTTCTCCGT 59.928 47.826 0.00 0.00 0.00 4.69
286 289 2.778299 TCTCCGTTCAATTCCACCAAG 58.222 47.619 0.00 0.00 0.00 3.61
288 291 0.887933 CCGTTCAATTCCACCAAGGG 59.112 55.000 0.00 0.00 38.24 3.95
311 314 1.144708 TCAAGGAAGCATGACCAACCA 59.855 47.619 0.00 0.00 0.00 3.67
313 316 0.606401 AGGAAGCATGACCAACCACG 60.606 55.000 0.00 0.00 0.00 4.94
314 317 1.210155 GAAGCATGACCAACCACGC 59.790 57.895 0.00 0.00 0.00 5.34
317 321 4.101790 CATGACCAACCACGCGCC 62.102 66.667 5.73 0.00 0.00 6.53
336 340 2.355209 GCCTCCACTTCCTCTCGAAATT 60.355 50.000 0.00 0.00 0.00 1.82
341 345 3.594134 CACTTCCTCTCGAAATTGAGCT 58.406 45.455 0.00 0.00 35.90 4.09
346 350 2.928757 CCTCTCGAAATTGAGCTCACAG 59.071 50.000 18.03 6.34 35.90 3.66
351 355 0.877071 AAATTGAGCTCACAGCACGG 59.123 50.000 18.03 0.00 45.56 4.94
370 374 2.851071 CGAGATCCTCCTCCACCGC 61.851 68.421 0.00 0.00 0.00 5.68
389 393 1.730121 GCGCAACCTCATCACACAATG 60.730 52.381 0.30 0.00 0.00 2.82
392 396 1.887854 CAACCTCATCACACAATGCCA 59.112 47.619 0.00 0.00 0.00 4.92
395 399 1.332686 CCTCATCACACAATGCCATCG 59.667 52.381 0.00 0.00 0.00 3.84
427 431 1.995376 ACCAACACCCCATGAAAGTC 58.005 50.000 0.00 0.00 0.00 3.01
428 432 0.881118 CCAACACCCCATGAAAGTCG 59.119 55.000 0.00 0.00 0.00 4.18
440 444 5.336372 CCCATGAAAGTCGCCTTAAAATGAA 60.336 40.000 0.00 0.00 0.00 2.57
445 449 3.000727 AGTCGCCTTAAAATGAACCTCG 58.999 45.455 0.00 0.00 0.00 4.63
453 457 6.322491 CCTTAAAATGAACCTCGAATGAACC 58.678 40.000 0.00 0.00 0.00 3.62
488 492 1.469767 CGTGATTCGTGCTCTCATGGA 60.470 52.381 0.00 0.00 34.52 3.41
501 505 4.497674 GCTCTCATGGAAAAAGCATGCTAG 60.498 45.833 23.00 11.33 33.21 3.42
524 528 2.557924 GGGCAACACTTGAATCATGTGA 59.442 45.455 28.42 0.00 40.46 3.58
526 530 4.501229 GGGCAACACTTGAATCATGTGAAA 60.501 41.667 28.42 0.00 40.46 2.69
527 531 5.049167 GGCAACACTTGAATCATGTGAAAA 58.951 37.500 28.42 0.00 40.46 2.29
535 539 8.017373 CACTTGAATCATGTGAAAAACGACTAT 58.983 33.333 20.45 0.00 40.46 2.12
536 540 8.017373 ACTTGAATCATGTGAAAAACGACTATG 58.983 33.333 0.72 0.00 0.00 2.23
537 541 7.665561 TGAATCATGTGAAAAACGACTATGA 57.334 32.000 0.00 0.00 0.00 2.15
538 542 7.742151 TGAATCATGTGAAAAACGACTATGAG 58.258 34.615 0.00 0.00 0.00 2.90
550 554 5.723672 ACGACTATGAGAAGGAGAAAACA 57.276 39.130 0.00 0.00 0.00 2.83
554 558 3.771577 ATGAGAAGGAGAAAACACGGT 57.228 42.857 0.00 0.00 0.00 4.83
558 562 5.962433 TGAGAAGGAGAAAACACGGTATAG 58.038 41.667 0.00 0.00 0.00 1.31
563 567 3.129287 GGAGAAAACACGGTATAGGACGA 59.871 47.826 0.00 0.00 0.00 4.20
573 577 2.484770 GGTATAGGACGAAGGCAATGCA 60.485 50.000 7.79 0.00 0.00 3.96
574 578 1.668419 ATAGGACGAAGGCAATGCAC 58.332 50.000 7.79 0.00 0.00 4.57
575 579 0.739462 TAGGACGAAGGCAATGCACG 60.739 55.000 7.79 11.94 0.00 5.34
576 580 2.325082 GGACGAAGGCAATGCACGT 61.325 57.895 19.48 19.48 37.17 4.49
592 596 2.855187 GCACGTATACGAGAGAGGCAAG 60.855 54.545 30.77 8.45 43.02 4.01
600 604 1.208052 CGAGAGAGGCAAGGAATTGGA 59.792 52.381 0.00 0.00 0.00 3.53
606 610 1.642762 AGGCAAGGAATTGGAGGATGT 59.357 47.619 0.00 0.00 0.00 3.06
611 615 1.202698 AGGAATTGGAGGATGTAGCGC 60.203 52.381 0.00 0.00 0.00 5.92
612 616 1.202698 GGAATTGGAGGATGTAGCGCT 60.203 52.381 17.26 17.26 0.00 5.92
621 625 2.556189 AGGATGTAGCGCTGTCAGATAG 59.444 50.000 22.90 0.00 0.00 2.08
631 635 1.365633 GTCAGATAGCTGCCGAGGG 59.634 63.158 2.24 0.00 42.01 4.30
632 636 1.075970 TCAGATAGCTGCCGAGGGT 60.076 57.895 2.24 0.00 42.01 4.34
635 639 3.030780 CAGATAGCTGCCGAGGGTACC 62.031 61.905 2.17 2.17 42.33 3.34
648 652 0.459078 GGGTACCGAGGTAGCTTGAC 59.541 60.000 24.93 9.68 45.28 3.18
650 654 0.807496 GTACCGAGGTAGCTTGACGT 59.193 55.000 10.90 3.78 0.00 4.34
651 655 2.009774 GTACCGAGGTAGCTTGACGTA 58.990 52.381 10.90 2.84 0.00 3.57
652 656 1.538047 ACCGAGGTAGCTTGACGTAA 58.462 50.000 10.90 0.00 0.00 3.18
653 657 6.494669 GGTACCGAGGTAGCTTGACGTAAG 62.495 54.167 20.56 0.00 43.38 2.34
655 659 2.163010 CCGAGGTAGCTTGACGTAAGAA 59.837 50.000 10.90 0.00 38.76 2.52
657 661 3.180613 GAGGTAGCTTGACGTAAGAAGC 58.819 50.000 15.30 15.30 44.79 3.86
659 663 2.924290 GGTAGCTTGACGTAAGAAGCAG 59.076 50.000 21.79 0.00 46.29 4.24
660 664 1.433534 AGCTTGACGTAAGAAGCAGC 58.566 50.000 21.79 7.20 46.29 5.25
661 665 0.444260 GCTTGACGTAAGAAGCAGCC 59.556 55.000 17.26 0.00 44.11 4.85
665 669 0.388134 GACGTAAGAAGCAGCCGACA 60.388 55.000 0.00 0.00 43.62 4.35
666 670 0.666577 ACGTAAGAAGCAGCCGACAC 60.667 55.000 0.00 0.00 43.62 3.67
667 671 1.674611 CGTAAGAAGCAGCCGACACG 61.675 60.000 0.00 0.00 43.02 4.49
668 672 0.388134 GTAAGAAGCAGCCGACACGA 60.388 55.000 0.00 0.00 0.00 4.35
669 673 0.109272 TAAGAAGCAGCCGACACGAG 60.109 55.000 0.00 0.00 0.00 4.18
671 675 4.299547 AAGCAGCCGACACGAGCA 62.300 61.111 0.00 0.00 0.00 4.26
672 676 4.731612 AGCAGCCGACACGAGCAG 62.732 66.667 0.00 0.00 0.00 4.24
700 704 2.038975 CGGAAGGAGAGGGGGTGA 59.961 66.667 0.00 0.00 0.00 4.02
708 734 1.280457 GAGAGGGGGTGACAGTGAAT 58.720 55.000 0.00 0.00 0.00 2.57
755 781 5.385396 CGAACGGTCGCTTTATAGATTTT 57.615 39.130 11.19 0.00 41.08 1.82
757 783 6.925600 CGAACGGTCGCTTTATAGATTTTTA 58.074 36.000 11.19 0.00 41.08 1.52
758 784 7.393327 CGAACGGTCGCTTTATAGATTTTTAA 58.607 34.615 11.19 0.00 41.08 1.52
759 785 7.899330 CGAACGGTCGCTTTATAGATTTTTAAA 59.101 33.333 11.19 0.00 41.08 1.52
760 786 9.545611 GAACGGTCGCTTTATAGATTTTTAAAA 57.454 29.630 0.00 0.00 0.00 1.52
872 926 5.379706 AAAATCCAAATCCAAAACCACCA 57.620 34.783 0.00 0.00 0.00 4.17
952 1012 2.951458 CGCCGACCAAAAACCTCC 59.049 61.111 0.00 0.00 0.00 4.30
984 1456 3.700350 CTCCCTCCCTCCCCACCT 61.700 72.222 0.00 0.00 0.00 4.00
1284 1774 2.585153 GCCTTCTTCCCCGACTCC 59.415 66.667 0.00 0.00 0.00 3.85
1356 1846 4.044390 ATGGGCAGGGAGGAGGGT 62.044 66.667 0.00 0.00 0.00 4.34
1388 1878 2.031163 GTGGCGCAGGTGAGAACT 59.969 61.111 10.83 0.00 0.00 3.01
1395 1885 3.322466 AGGTGAGAACTGCCCCCG 61.322 66.667 0.00 0.00 0.00 5.73
1410 1901 2.812178 CCGCCGATCCGTTTTCGT 60.812 61.111 0.00 0.00 42.35 3.85
1414 1905 1.708027 CCGATCCGTTTTCGTCTGC 59.292 57.895 0.00 0.00 42.35 4.26
1432 1923 1.686325 GCTGCTATCCGGTTCCTGGA 61.686 60.000 0.00 0.00 40.46 3.86
1497 1988 0.749649 ACGCTCTCCTCCTGCTATTG 59.250 55.000 0.00 0.00 0.00 1.90
1500 1991 1.069978 GCTCTCCTCCTGCTATTGTCC 59.930 57.143 0.00 0.00 0.00 4.02
1506 1997 2.104963 CCTCCTGCTATTGTCCCCTAAC 59.895 54.545 0.00 0.00 0.00 2.34
1587 2078 7.806014 GGAAACTCGTATTTTTATGTTTGCTCA 59.194 33.333 0.00 0.00 34.52 4.26
1615 2106 6.370442 TCGATTACGATTGAACTGGAAATTGT 59.630 34.615 0.00 0.00 43.81 2.71
1645 2136 6.630444 GATGATTGCATCTACCAAGTTCAT 57.370 37.500 0.00 0.00 45.93 2.57
1646 2137 6.630444 ATGATTGCATCTACCAAGTTCATC 57.370 37.500 0.00 0.00 0.00 2.92
1647 2138 5.748402 TGATTGCATCTACCAAGTTCATCT 58.252 37.500 0.00 0.00 0.00 2.90
1648 2139 6.182627 TGATTGCATCTACCAAGTTCATCTT 58.817 36.000 0.00 0.00 36.75 2.40
1659 2150 2.079158 AGTTCATCTTGCGTGTGGATG 58.921 47.619 0.00 0.00 38.41 3.51
1664 2155 3.118811 TCATCTTGCGTGTGGATGTATGA 60.119 43.478 0.00 0.00 38.28 2.15
1665 2156 2.616960 TCTTGCGTGTGGATGTATGAC 58.383 47.619 0.00 0.00 0.00 3.06
1666 2157 2.233676 TCTTGCGTGTGGATGTATGACT 59.766 45.455 0.00 0.00 0.00 3.41
1667 2158 2.760634 TGCGTGTGGATGTATGACTT 57.239 45.000 0.00 0.00 0.00 3.01
1668 2159 2.616960 TGCGTGTGGATGTATGACTTC 58.383 47.619 0.00 0.00 0.00 3.01
1669 2160 2.233676 TGCGTGTGGATGTATGACTTCT 59.766 45.455 0.00 0.00 0.00 2.85
1670 2161 2.860735 GCGTGTGGATGTATGACTTCTC 59.139 50.000 0.00 0.00 0.00 2.87
1671 2162 3.429547 GCGTGTGGATGTATGACTTCTCT 60.430 47.826 0.00 0.00 0.00 3.10
1672 2163 4.355437 CGTGTGGATGTATGACTTCTCTC 58.645 47.826 0.00 0.00 0.00 3.20
1673 2164 4.097135 CGTGTGGATGTATGACTTCTCTCT 59.903 45.833 0.00 0.00 0.00 3.10
1796 2320 8.993121 ACAGTTTACTGATTATCACTGAACTTG 58.007 33.333 16.31 9.94 46.59 3.16
1806 2330 3.305720 TCACTGAACTTGGAGTAGGTGT 58.694 45.455 0.00 0.00 0.00 4.16
1818 2342 4.007659 GGAGTAGGTGTTTACATGGTTGG 58.992 47.826 0.00 0.00 0.00 3.77
1831 2355 3.511146 ACATGGTTGGCATAGAAAAGTGG 59.489 43.478 0.00 0.00 0.00 4.00
1839 2363 3.129287 GGCATAGAAAAGTGGTGGATGTG 59.871 47.826 0.00 0.00 0.00 3.21
1852 2376 5.015515 TGGTGGATGTGCATTCATCTTTTA 58.984 37.500 14.82 0.99 42.45 1.52
1861 2385 6.038161 TGTGCATTCATCTTTTATTAGGGTCG 59.962 38.462 0.00 0.00 0.00 4.79
1879 2404 3.554337 GGTCGCTGTTCAGTTCCTTAGAA 60.554 47.826 1.78 0.00 0.00 2.10
1887 2412 7.303634 TGTTCAGTTCCTTAGAATAAATCGC 57.696 36.000 0.00 0.00 33.67 4.58
2006 2531 5.876460 ACGCTACCGATAGTTTGGTATTTTT 59.124 36.000 0.00 0.00 40.46 1.94
2028 2554 4.226384 TGTGATATCATGCTCAGTACCCT 58.774 43.478 9.02 0.00 0.00 4.34
2079 2605 3.099905 TCAGCTGCTTATGTCCTGTAGT 58.900 45.455 9.47 0.00 0.00 2.73
2280 2811 4.080919 AGTGGCATATTCTTGTACTCTGCA 60.081 41.667 0.00 0.00 0.00 4.41
2305 2836 4.695396 TGCATTGCTTTTCTGAACATGTT 58.305 34.783 11.78 11.78 0.00 2.71
2368 2904 9.384764 GGCAACTCTAATTCTGTATTTAAGACT 57.615 33.333 0.00 0.00 0.00 3.24
2431 2967 3.648067 TGATTTGGCCCAAATTTGTGGTA 59.352 39.130 22.11 8.46 43.05 3.25
2432 2968 4.288105 TGATTTGGCCCAAATTTGTGGTAT 59.712 37.500 22.11 0.00 43.05 2.73
2447 2983 4.023291 TGTGGTATGCTCTGTGTGATCTA 58.977 43.478 0.00 0.00 0.00 1.98
2460 2996 4.194640 GTGTGATCTAGGCATTGTGATGT 58.805 43.478 0.00 0.00 35.63 3.06
2505 3041 6.097412 TGCTGTGATAGTTGTCATACAGAGAT 59.903 38.462 0.00 0.00 28.75 2.75
2534 3070 8.730680 CAGTAAACTAGTTATGCAATGTCCTTT 58.269 33.333 8.92 0.00 0.00 3.11
2548 3084 4.046286 TGTCCTTTGATAATGGCCTTGT 57.954 40.909 3.32 0.00 0.00 3.16
2598 3134 0.616679 TGGCCTACCACAGTACCCTC 60.617 60.000 3.32 0.00 42.67 4.30
2672 3208 4.799564 TTCCCTTGCATGGTGTAAATTC 57.200 40.909 16.81 0.00 0.00 2.17
2899 3438 4.827284 CGTGAGGGGGCATTTCTTAATTAT 59.173 41.667 0.00 0.00 0.00 1.28
2961 3500 4.160252 ACTTGTGGTGTTCTGCAGATTTTT 59.840 37.500 19.04 0.00 0.00 1.94
3039 3578 0.249784 CGGAGCTCATCCCACATGAG 60.250 60.000 17.19 7.16 46.50 2.90
3165 3704 0.107945 GCCAGGTCCTAGTGAAGCTG 60.108 60.000 0.00 8.48 39.98 4.24
3177 3716 0.327259 TGAAGCTGAAGCATGCTCCT 59.673 50.000 22.93 6.03 45.16 3.69
3180 3719 1.077930 GCTGAAGCATGCTCCTCCA 60.078 57.895 22.93 15.06 41.59 3.86
3267 3806 2.922950 CGCACCAGCACCAGCAAAT 61.923 57.895 0.00 0.00 45.49 2.32
3303 3842 0.767375 TGGAGAGCAAAGAAGCACCT 59.233 50.000 0.00 0.00 36.85 4.00
3340 3879 0.329931 AGAGACGGAGAAGGAGCAGA 59.670 55.000 0.00 0.00 0.00 4.26
3389 3935 6.184789 TCTTTTTACAGAAACACCAGAACCT 58.815 36.000 0.00 0.00 0.00 3.50
3404 3950 5.248477 ACCAGAACCTTGACTATGCTTAGAA 59.752 40.000 13.22 0.00 0.00 2.10
3405 3951 5.814705 CCAGAACCTTGACTATGCTTAGAAG 59.185 44.000 13.22 7.23 0.00 2.85
3443 3989 0.396139 AATACCCGGAGTGTCGCCTA 60.396 55.000 0.73 0.00 0.00 3.93
3444 3990 1.105759 ATACCCGGAGTGTCGCCTAC 61.106 60.000 0.73 0.00 0.00 3.18
3500 4047 4.159321 CAGGATGGCTATGTATCGATCAGT 59.841 45.833 0.00 0.00 0.00 3.41
3544 4091 2.493278 ACAGCAAACAACTGCACTCTTT 59.507 40.909 0.00 0.00 45.18 2.52
3561 4108 5.467063 CACTCTTTACTGTTTTCTCCTGGTC 59.533 44.000 0.00 0.00 0.00 4.02
3569 4116 1.352083 TTTCTCCTGGTCCCAGACTG 58.648 55.000 14.98 0.00 46.30 3.51
3570 4117 0.545309 TTCTCCTGGTCCCAGACTGG 60.545 60.000 15.15 15.15 46.30 4.00
3571 4118 1.079256 CTCCTGGTCCCAGACTGGA 59.921 63.158 23.77 6.31 46.30 3.86
3573 4120 1.015609 TCCTGGTCCCAGACTGGATA 58.984 55.000 23.77 7.74 46.30 2.59
3622 4177 5.698545 AGCTGAGAAGTTAACTGAATGTGAC 59.301 40.000 9.34 0.00 0.00 3.67
3641 4196 1.202417 ACGACATGCCTGATTCTACCG 60.202 52.381 0.00 0.00 0.00 4.02
3647 4202 3.728076 TGCCTGATTCTACCGTCATAC 57.272 47.619 0.00 0.00 0.00 2.39
3712 4310 9.162764 TCTATCATTTACAACTTCTAACTTGCC 57.837 33.333 0.00 0.00 0.00 4.52
3713 4311 9.167311 CTATCATTTACAACTTCTAACTTGCCT 57.833 33.333 0.00 0.00 0.00 4.75
3714 4312 7.435068 TCATTTACAACTTCTAACTTGCCTC 57.565 36.000 0.00 0.00 0.00 4.70
3715 4313 6.995686 TCATTTACAACTTCTAACTTGCCTCA 59.004 34.615 0.00 0.00 0.00 3.86
3716 4314 6.613755 TTTACAACTTCTAACTTGCCTCAC 57.386 37.500 0.00 0.00 0.00 3.51
3717 4315 3.477530 ACAACTTCTAACTTGCCTCACC 58.522 45.455 0.00 0.00 0.00 4.02
3773 4392 5.895534 CCTCTATGGTACTGTAACCCTACAA 59.104 44.000 0.00 0.00 37.58 2.41
3781 4402 6.716173 GGTACTGTAACCCTACAAAATGGAAA 59.284 38.462 0.00 0.00 37.58 3.13
3798 4419 5.467035 TGGAAATAAAGGAACAAAGCAGG 57.533 39.130 0.00 0.00 0.00 4.85
3808 4430 2.860971 AAAGCAGGCCACCCTCCT 60.861 61.111 5.01 0.00 40.33 3.69
3926 4548 4.070552 GAGTCGCTGGAGGCCGTT 62.071 66.667 0.00 0.00 37.74 4.44
3971 4593 3.849951 CTGATGTACCCCGGCGCT 61.850 66.667 7.64 0.00 0.00 5.92
3983 4605 2.765356 CGGCGCTGTCAGCTCTCTA 61.765 63.158 22.13 0.00 39.60 2.43
4009 4631 0.331278 ATCCGGATTGGCTTGGACAA 59.669 50.000 12.38 0.00 37.80 3.18
4025 4647 2.487265 GGACAACATCTTCACCACCTGT 60.487 50.000 0.00 0.00 0.00 4.00
4172 4794 1.208052 TCATACAGCTCCCAAGTCTGC 59.792 52.381 0.00 0.00 32.93 4.26
4173 4795 0.176680 ATACAGCTCCCAAGTCTGCG 59.823 55.000 0.00 0.00 32.93 5.18
4176 4798 2.743928 GCTCCCAAGTCTGCGGTG 60.744 66.667 0.00 0.00 0.00 4.94
4187 4813 0.396435 TCTGCGGTGAATGTTCAGGT 59.604 50.000 0.00 0.00 37.98 4.00
4191 4817 3.215151 TGCGGTGAATGTTCAGGTTTAA 58.785 40.909 0.00 0.00 37.98 1.52
4192 4818 3.252215 TGCGGTGAATGTTCAGGTTTAAG 59.748 43.478 0.00 0.00 37.98 1.85
4193 4819 3.500680 GCGGTGAATGTTCAGGTTTAAGA 59.499 43.478 0.00 0.00 37.98 2.10
4194 4820 4.378459 GCGGTGAATGTTCAGGTTTAAGAG 60.378 45.833 0.00 0.00 37.98 2.85
4195 4821 4.755123 CGGTGAATGTTCAGGTTTAAGAGT 59.245 41.667 0.00 0.00 37.98 3.24
4196 4822 5.238650 CGGTGAATGTTCAGGTTTAAGAGTT 59.761 40.000 0.00 0.00 37.98 3.01
4197 4823 6.238648 CGGTGAATGTTCAGGTTTAAGAGTTT 60.239 38.462 0.00 0.00 37.98 2.66
4199 4825 8.290325 GGTGAATGTTCAGGTTTAAGAGTTTAG 58.710 37.037 0.00 0.00 37.98 1.85
4200 4826 9.052759 GTGAATGTTCAGGTTTAAGAGTTTAGA 57.947 33.333 0.00 0.00 37.98 2.10
4201 4827 9.052759 TGAATGTTCAGGTTTAAGAGTTTAGAC 57.947 33.333 0.00 0.00 32.50 2.59
4202 4828 9.274206 GAATGTTCAGGTTTAAGAGTTTAGACT 57.726 33.333 0.00 0.00 39.32 3.24
4210 4836 6.456501 GTTTAAGAGTTTAGACTGAGGCTGA 58.543 40.000 0.00 0.00 35.88 4.26
4223 4849 8.845413 AGACTGAGGCTGATATAAATCATTTC 57.155 34.615 0.00 0.00 41.29 2.17
4231 4857 8.086522 GGCTGATATAAATCATTTCATGCTTGT 58.913 33.333 0.00 0.00 41.29 3.16
4241 4867 9.932207 AATCATTTCATGCTTGTGAATCTTTTA 57.068 25.926 0.00 0.00 37.88 1.52
4242 4868 9.932207 ATCATTTCATGCTTGTGAATCTTTTAA 57.068 25.926 0.00 0.00 37.88 1.52
4327 4955 5.741011 AGTTTTACTGGACAGTCTTGTTGA 58.259 37.500 8.44 0.00 42.54 3.18
4339 4967 6.528321 ACAGTCTTGTTGATCTGATTTCTGA 58.472 36.000 0.00 0.00 32.28 3.27
4341 4969 7.172875 ACAGTCTTGTTGATCTGATTTCTGAAG 59.827 37.037 0.00 0.00 32.28 3.02
4343 4971 6.149142 GTCTTGTTGATCTGATTTCTGAAGCT 59.851 38.462 0.00 0.00 0.00 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.713708 TTCAAAGTATCCAAACCCAATCTTAA 57.286 30.769 0.00 0.00 0.00 1.85
1 2 8.167392 TCTTCAAAGTATCCAAACCCAATCTTA 58.833 33.333 0.00 0.00 0.00 2.10
2 3 7.010160 TCTTCAAAGTATCCAAACCCAATCTT 58.990 34.615 0.00 0.00 0.00 2.40
28 29 7.596494 TGTTTCCATTTGAATTTTTGTTTGCA 58.404 26.923 0.00 0.00 31.67 4.08
32 33 9.844257 TCCTATGTTTCCATTTGAATTTTTGTT 57.156 25.926 0.00 0.00 31.67 2.83
89 90 5.363580 TGAGGATTTCAGGCTTTTGAGTTTT 59.636 36.000 0.00 0.00 0.00 2.43
130 131 7.027778 AGCGTAAAATTAGGAATGATTGTCC 57.972 36.000 0.00 0.00 35.17 4.02
167 169 4.273318 GCTGTAACATCCCCAGATTTTCT 58.727 43.478 0.00 0.00 0.00 2.52
168 170 3.381590 GGCTGTAACATCCCCAGATTTTC 59.618 47.826 0.00 0.00 0.00 2.29
174 176 1.207791 AGAGGCTGTAACATCCCCAG 58.792 55.000 0.00 0.00 0.00 4.45
193 195 0.960364 GTCGAATGCAGCAGGGGAAA 60.960 55.000 0.00 0.00 0.00 3.13
234 237 0.527817 GTGGTGGAGGTTAGATCGCG 60.528 60.000 0.00 0.00 0.00 5.87
237 240 2.771943 TGATGGTGGTGGAGGTTAGATC 59.228 50.000 0.00 0.00 0.00 2.75
260 263 4.010349 GTGGAATTGAACGGAGAAAGGAT 58.990 43.478 0.00 0.00 0.00 3.24
264 267 3.216187 TGGTGGAATTGAACGGAGAAA 57.784 42.857 0.00 0.00 0.00 2.52
269 272 0.887933 CCCTTGGTGGAATTGAACGG 59.112 55.000 0.00 0.00 38.35 4.44
272 275 3.784429 CCCCCTTGGTGGAATTGAA 57.216 52.632 0.00 0.00 38.35 2.69
286 289 0.681243 GTCATGCTTCCTTGACCCCC 60.681 60.000 0.00 0.00 39.14 5.40
296 299 1.210155 GCGTGGTTGGTCATGCTTC 59.790 57.895 0.00 0.00 43.98 3.86
307 310 4.250305 AAGTGGAGGCGCGTGGTT 62.250 61.111 7.63 0.00 0.00 3.67
311 314 4.070552 GAGGAAGTGGAGGCGCGT 62.071 66.667 8.43 0.27 0.00 6.01
313 316 2.185608 GAGAGGAAGTGGAGGCGC 59.814 66.667 0.00 0.00 0.00 6.53
314 317 1.595993 TTCGAGAGGAAGTGGAGGCG 61.596 60.000 0.00 0.00 0.00 5.52
317 321 4.180057 CTCAATTTCGAGAGGAAGTGGAG 58.820 47.826 0.00 0.00 44.42 3.86
341 345 2.181777 GATCTCGCCGTGCTGTGA 59.818 61.111 0.00 0.00 0.00 3.58
346 350 3.492311 GAGGAGGATCTCGCCGTGC 62.492 68.421 0.00 0.00 40.51 5.34
351 355 2.851071 CGGTGGAGGAGGATCTCGC 61.851 68.421 0.00 0.00 34.74 5.03
370 374 1.730121 GCATTGTGTGATGAGGTTGCG 60.730 52.381 0.00 0.00 0.00 4.85
427 431 4.094294 TCATTCGAGGTTCATTTTAAGGCG 59.906 41.667 0.00 0.00 0.00 5.52
428 432 5.560966 TCATTCGAGGTTCATTTTAAGGC 57.439 39.130 0.00 0.00 0.00 4.35
440 444 0.249398 CCCTTCGGTTCATTCGAGGT 59.751 55.000 0.00 0.00 37.93 3.85
445 449 1.032114 CCTGCCCCTTCGGTTCATTC 61.032 60.000 0.00 0.00 0.00 2.67
464 468 0.802607 GAGAGCACGAATCACGACCC 60.803 60.000 0.00 0.00 45.77 4.46
470 474 3.333029 TTTCCATGAGAGCACGAATCA 57.667 42.857 0.00 0.00 0.00 2.57
488 492 1.631405 TGCCCACTAGCATGCTTTTT 58.369 45.000 28.02 7.60 38.00 1.94
501 505 2.297033 ACATGATTCAAGTGTTGCCCAC 59.703 45.455 0.00 0.00 44.89 4.61
524 528 7.497909 TGTTTTCTCCTTCTCATAGTCGTTTTT 59.502 33.333 0.00 0.00 0.00 1.94
526 530 6.424207 GTGTTTTCTCCTTCTCATAGTCGTTT 59.576 38.462 0.00 0.00 0.00 3.60
527 531 5.927115 GTGTTTTCTCCTTCTCATAGTCGTT 59.073 40.000 0.00 0.00 0.00 3.85
535 539 4.884668 ATACCGTGTTTTCTCCTTCTCA 57.115 40.909 0.00 0.00 0.00 3.27
536 540 5.126707 TCCTATACCGTGTTTTCTCCTTCTC 59.873 44.000 0.00 0.00 0.00 2.87
537 541 5.021458 TCCTATACCGTGTTTTCTCCTTCT 58.979 41.667 0.00 0.00 0.00 2.85
538 542 5.107824 GTCCTATACCGTGTTTTCTCCTTC 58.892 45.833 0.00 0.00 0.00 3.46
550 554 1.477553 TTGCCTTCGTCCTATACCGT 58.522 50.000 0.00 0.00 0.00 4.83
554 558 2.801699 CGTGCATTGCCTTCGTCCTATA 60.802 50.000 6.12 0.00 0.00 1.31
558 562 1.017177 TACGTGCATTGCCTTCGTCC 61.017 55.000 20.45 0.00 36.24 4.79
563 567 2.159156 TCTCGTATACGTGCATTGCCTT 60.159 45.455 23.67 0.00 40.80 4.35
573 577 1.948145 CCTTGCCTCTCTCGTATACGT 59.052 52.381 23.67 0.00 40.80 3.57
574 578 2.219458 TCCTTGCCTCTCTCGTATACG 58.781 52.381 19.23 19.23 41.45 3.06
575 579 4.857509 ATTCCTTGCCTCTCTCGTATAC 57.142 45.455 0.00 0.00 0.00 1.47
576 580 4.039245 CCAATTCCTTGCCTCTCTCGTATA 59.961 45.833 0.00 0.00 0.00 1.47
592 596 1.202698 AGCGCTACATCCTCCAATTCC 60.203 52.381 8.99 0.00 0.00 3.01
600 604 1.407936 ATCTGACAGCGCTACATCCT 58.592 50.000 10.99 0.00 0.00 3.24
606 610 0.031314 GCAGCTATCTGACAGCGCTA 59.969 55.000 10.99 0.00 43.97 4.26
621 625 4.208686 CTCGGTACCCTCGGCAGC 62.209 72.222 6.25 0.00 0.00 5.25
631 635 0.807496 ACGTCAAGCTACCTCGGTAC 59.193 55.000 0.00 0.00 0.00 3.34
632 636 2.401583 TACGTCAAGCTACCTCGGTA 57.598 50.000 0.00 0.00 0.00 4.02
635 639 3.427243 CTTCTTACGTCAAGCTACCTCG 58.573 50.000 0.00 0.00 33.94 4.63
636 640 3.180613 GCTTCTTACGTCAAGCTACCTC 58.819 50.000 15.91 0.00 41.61 3.85
637 641 2.561419 TGCTTCTTACGTCAAGCTACCT 59.439 45.455 21.02 0.00 44.59 3.08
638 642 2.924290 CTGCTTCTTACGTCAAGCTACC 59.076 50.000 21.02 1.33 44.59 3.18
640 644 2.607187 GCTGCTTCTTACGTCAAGCTA 58.393 47.619 21.02 11.05 44.59 3.32
643 647 0.716108 CGGCTGCTTCTTACGTCAAG 59.284 55.000 0.00 0.00 35.38 3.02
644 648 0.315886 TCGGCTGCTTCTTACGTCAA 59.684 50.000 0.00 0.00 0.00 3.18
645 649 0.388134 GTCGGCTGCTTCTTACGTCA 60.388 55.000 0.00 0.00 0.00 4.35
648 652 1.674611 CGTGTCGGCTGCTTCTTACG 61.675 60.000 0.00 1.36 0.00 3.18
650 654 0.109272 CTCGTGTCGGCTGCTTCTTA 60.109 55.000 0.00 0.00 0.00 2.10
651 655 1.373497 CTCGTGTCGGCTGCTTCTT 60.373 57.895 0.00 0.00 0.00 2.52
652 656 2.259818 CTCGTGTCGGCTGCTTCT 59.740 61.111 0.00 0.00 0.00 2.85
653 657 3.482783 GCTCGTGTCGGCTGCTTC 61.483 66.667 0.00 0.00 0.00 3.86
655 659 4.731612 CTGCTCGTGTCGGCTGCT 62.732 66.667 0.00 0.00 0.00 4.24
665 669 4.803426 GCTACGCTGCCTGCTCGT 62.803 66.667 12.73 12.73 40.11 4.18
673 677 4.143333 TCCTTCCGGCTACGCTGC 62.143 66.667 0.00 0.00 39.22 5.25
674 678 2.105128 CTCCTTCCGGCTACGCTG 59.895 66.667 0.00 0.00 39.22 5.18
675 679 2.044252 TCTCCTTCCGGCTACGCT 60.044 61.111 0.00 0.00 39.22 5.07
676 680 2.413765 CTCTCCTTCCGGCTACGC 59.586 66.667 0.00 0.00 39.22 4.42
678 682 2.134933 CCCCTCTCCTTCCGGCTAC 61.135 68.421 0.00 0.00 0.00 3.58
679 683 2.282446 CCCCTCTCCTTCCGGCTA 59.718 66.667 0.00 0.00 0.00 3.93
682 686 3.083997 CACCCCCTCTCCTTCCGG 61.084 72.222 0.00 0.00 0.00 5.14
683 687 2.038975 TCACCCCCTCTCCTTCCG 59.961 66.667 0.00 0.00 0.00 4.30
684 688 1.229529 TGTCACCCCCTCTCCTTCC 60.230 63.158 0.00 0.00 0.00 3.46
685 689 0.545548 ACTGTCACCCCCTCTCCTTC 60.546 60.000 0.00 0.00 0.00 3.46
686 690 0.838122 CACTGTCACCCCCTCTCCTT 60.838 60.000 0.00 0.00 0.00 3.36
687 691 1.229336 CACTGTCACCCCCTCTCCT 60.229 63.158 0.00 0.00 0.00 3.69
689 693 1.065854 CATTCACTGTCACCCCCTCTC 60.066 57.143 0.00 0.00 0.00 3.20
692 696 1.380302 GCATTCACTGTCACCCCCT 59.620 57.895 0.00 0.00 0.00 4.79
694 698 1.298859 GACGCATTCACTGTCACCCC 61.299 60.000 0.00 0.00 32.91 4.95
695 699 1.626654 CGACGCATTCACTGTCACCC 61.627 60.000 0.00 0.00 32.91 4.61
698 702 2.027073 GGCGACGCATTCACTGTCA 61.027 57.895 23.09 0.00 32.91 3.58
700 704 2.742372 GGGCGACGCATTCACTGT 60.742 61.111 23.09 0.00 0.00 3.55
768 800 8.822652 AACAGATTTTATGCTCTTTTCCTTTG 57.177 30.769 0.00 0.00 0.00 2.77
799 831 1.443802 GCGCTGCCTTACTCTCTTTT 58.556 50.000 0.00 0.00 0.00 2.27
801 833 1.153745 CGCGCTGCCTTACTCTCTT 60.154 57.895 5.56 0.00 0.00 2.85
805 837 3.188786 CCACGCGCTGCCTTACTC 61.189 66.667 5.73 0.00 0.00 2.59
853 907 2.637382 GGTGGTGGTTTTGGATTTGGAT 59.363 45.455 0.00 0.00 0.00 3.41
957 1017 4.890306 GGAGGGAGGGGGAGAGGC 62.890 77.778 0.00 0.00 0.00 4.70
958 1018 4.179599 GGGAGGGAGGGGGAGAGG 62.180 77.778 0.00 0.00 0.00 3.69
960 1020 3.036959 GAGGGAGGGAGGGGGAGA 61.037 72.222 0.00 0.00 0.00 3.71
1368 1858 3.240134 TTCTCACCTGCGCCACTCC 62.240 63.158 4.18 0.00 0.00 3.85
1410 1901 0.687757 AGGAACCGGATAGCAGCAGA 60.688 55.000 9.46 0.00 0.00 4.26
1414 1905 0.105039 GTCCAGGAACCGGATAGCAG 59.895 60.000 9.46 0.00 34.32 4.24
1432 1923 1.562783 GAACCCTAGCTCTGTCAGGT 58.437 55.000 0.00 0.00 36.55 4.00
1485 1976 2.103153 TAGGGGACAATAGCAGGAGG 57.897 55.000 0.00 0.00 0.00 4.30
1497 1988 5.240121 TGAATTAACTGAACGTTAGGGGAC 58.760 41.667 0.00 0.00 39.15 4.46
1500 1991 4.693566 TGCTGAATTAACTGAACGTTAGGG 59.306 41.667 0.00 0.00 39.15 3.53
1506 1997 4.466828 CAGGTTGCTGAATTAACTGAACG 58.533 43.478 0.00 0.00 0.00 3.95
1537 2028 5.514914 CGTACACAAAATTGCAACTTTGTCT 59.485 36.000 30.12 23.11 42.41 3.41
1538 2029 5.276161 CCGTACACAAAATTGCAACTTTGTC 60.276 40.000 30.12 20.19 42.41 3.18
1541 2032 5.000012 TCCGTACACAAAATTGCAACTTT 58.000 34.783 0.00 0.00 0.00 2.66
1542 2033 4.640789 TCCGTACACAAAATTGCAACTT 57.359 36.364 0.00 0.00 0.00 2.66
1543 2034 4.640789 TTCCGTACACAAAATTGCAACT 57.359 36.364 0.00 0.00 0.00 3.16
1597 2088 6.079763 CACTACACAATTTCCAGTTCAATCG 58.920 40.000 0.00 0.00 0.00 3.34
1601 2092 5.042463 TCCACTACACAATTTCCAGTTCA 57.958 39.130 0.00 0.00 0.00 3.18
1643 2134 3.001634 GTCATACATCCACACGCAAGATG 59.998 47.826 0.00 0.00 42.49 2.90
1644 2135 3.118629 AGTCATACATCCACACGCAAGAT 60.119 43.478 0.00 0.00 43.62 2.40
1645 2136 2.233676 AGTCATACATCCACACGCAAGA 59.766 45.455 0.00 0.00 43.62 3.02
1647 2138 2.760634 AGTCATACATCCACACGCAA 57.239 45.000 0.00 0.00 0.00 4.85
1648 2139 2.233676 AGAAGTCATACATCCACACGCA 59.766 45.455 0.00 0.00 0.00 5.24
1649 2140 2.860735 GAGAAGTCATACATCCACACGC 59.139 50.000 0.00 0.00 0.00 5.34
1659 2150 9.730420 GATTCAGTTCTAAGAGAGAAGTCATAC 57.270 37.037 0.00 0.00 44.63 2.39
1664 2155 6.437162 AGCAGATTCAGTTCTAAGAGAGAAGT 59.563 38.462 0.00 0.00 46.94 3.01
1665 2156 6.866480 AGCAGATTCAGTTCTAAGAGAGAAG 58.134 40.000 0.00 0.00 45.06 2.85
1666 2157 6.849085 AGCAGATTCAGTTCTAAGAGAGAA 57.151 37.500 0.00 0.00 42.13 2.87
1667 2158 7.946381 TTAGCAGATTCAGTTCTAAGAGAGA 57.054 36.000 0.00 0.00 0.00 3.10
1670 2161 9.809096 TGTAATTAGCAGATTCAGTTCTAAGAG 57.191 33.333 0.00 0.00 0.00 2.85
1671 2162 9.809096 CTGTAATTAGCAGATTCAGTTCTAAGA 57.191 33.333 8.52 0.00 36.12 2.10
1672 2163 9.593134 ACTGTAATTAGCAGATTCAGTTCTAAG 57.407 33.333 16.84 0.00 37.40 2.18
1673 2164 9.587772 GACTGTAATTAGCAGATTCAGTTCTAA 57.412 33.333 16.84 0.00 37.40 2.10
1796 2320 4.007659 CCAACCATGTAAACACCTACTCC 58.992 47.826 0.00 0.00 0.00 3.85
1806 2330 6.295011 CCACTTTTCTATGCCAACCATGTAAA 60.295 38.462 0.00 0.00 35.34 2.01
1818 2342 3.428045 GCACATCCACCACTTTTCTATGC 60.428 47.826 0.00 0.00 0.00 3.14
1831 2355 7.864379 CCTAATAAAAGATGAATGCACATCCAC 59.136 37.037 12.38 1.59 45.20 4.02
1839 2363 5.239525 AGCGACCCTAATAAAAGATGAATGC 59.760 40.000 0.00 0.00 0.00 3.56
1852 2376 2.354805 GGAACTGAACAGCGACCCTAAT 60.355 50.000 1.46 0.00 0.00 1.73
1861 2385 7.402640 CGATTTATTCTAAGGAACTGAACAGC 58.597 38.462 1.46 0.00 40.86 4.40
1879 2404 5.047872 ACCAAAAGGTTAAACCGCGATTTAT 60.048 36.000 8.23 0.00 44.90 1.40
1887 2412 2.159085 TGCCAACCAAAAGGTTAAACCG 60.159 45.455 0.00 0.00 44.90 4.44
1983 2508 5.978934 AAAATACCAAACTATCGGTAGCG 57.021 39.130 8.29 8.29 40.99 4.26
2006 2531 4.226384 AGGGTACTGAGCATGATATCACA 58.774 43.478 7.78 0.38 0.00 3.58
2028 2554 7.337942 AGACGATATGTACAGCTCATCATCATA 59.662 37.037 0.33 0.00 0.00 2.15
2139 2665 4.396166 ACTGATCGGTTTTAATGGAGCTTG 59.604 41.667 0.00 0.00 0.00 4.01
2280 2811 4.389890 TGTTCAGAAAAGCAATGCAAGT 57.610 36.364 8.35 0.00 0.00 3.16
2431 2967 2.113807 TGCCTAGATCACACAGAGCAT 58.886 47.619 0.00 0.00 34.30 3.79
2432 2968 1.560505 TGCCTAGATCACACAGAGCA 58.439 50.000 0.00 0.00 34.30 4.26
2447 2983 3.988976 ACTACTGACATCACAATGCCT 57.011 42.857 0.00 0.00 36.26 4.75
2460 2996 6.430925 ACAGCAAAAATGAAGCATACTACTGA 59.569 34.615 0.00 0.00 0.00 3.41
2505 3041 6.717289 ACATTGCATAACTAGTTTACTGGGA 58.283 36.000 14.49 0.00 0.00 4.37
2534 3070 3.495331 ACACAACACAAGGCCATTATCA 58.505 40.909 5.01 0.00 0.00 2.15
2548 3084 3.244422 GGTTCAGGTATCAGGACACAACA 60.244 47.826 0.00 0.00 0.00 3.33
2693 3229 3.715628 ACCACAATGAAGCTGTCAAAC 57.284 42.857 0.00 0.00 40.50 2.93
2694 3230 4.159321 TGAAACCACAATGAAGCTGTCAAA 59.841 37.500 0.00 0.00 40.50 2.69
2695 3231 3.698539 TGAAACCACAATGAAGCTGTCAA 59.301 39.130 0.00 0.00 40.50 3.18
2697 3233 3.304928 CCTGAAACCACAATGAAGCTGTC 60.305 47.826 0.00 0.00 0.00 3.51
2920 3459 2.708051 AGTCCACAGTGATCAATGCAG 58.292 47.619 22.33 14.88 0.00 4.41
2961 3500 4.042809 TGGAATTTCTCCTGGCTTTCTACA 59.957 41.667 0.00 0.00 45.64 2.74
3039 3578 1.692296 GCTTCTCGATGGTAGCGATC 58.308 55.000 0.00 0.00 37.13 3.69
3141 3680 0.396556 TCACTAGGACCTGGCGCATA 60.397 55.000 10.83 0.00 0.00 3.14
3165 3704 1.817099 CGGTGGAGGAGCATGCTTC 60.817 63.158 23.61 21.29 36.27 3.86
3240 3779 4.090057 GCTGGTGCGCCGTCTTTC 62.090 66.667 12.58 0.00 37.67 2.62
3284 3823 0.767375 AGGTGCTTCTTTGCTCTCCA 59.233 50.000 0.00 0.00 0.00 3.86
3285 3824 1.163554 CAGGTGCTTCTTTGCTCTCC 58.836 55.000 0.00 0.00 0.00 3.71
3340 3879 1.193323 AGCTACTCTGATGCTGCAGT 58.807 50.000 16.64 2.41 37.20 4.40
3389 3935 8.691661 AAAAGTTTCCTTCTAAGCATAGTCAA 57.308 30.769 0.00 0.00 0.00 3.18
3413 3959 7.527568 ACACTCCGGGTATTTTTGAAAATAA 57.472 32.000 0.00 0.00 41.14 1.40
3415 3961 5.335348 CGACACTCCGGGTATTTTTGAAAAT 60.335 40.000 0.00 6.88 41.24 1.82
3416 3962 4.023878 CGACACTCCGGGTATTTTTGAAAA 60.024 41.667 0.00 0.00 0.00 2.29
3418 3964 3.068560 CGACACTCCGGGTATTTTTGAA 58.931 45.455 0.00 0.00 0.00 2.69
3420 3966 1.129811 GCGACACTCCGGGTATTTTTG 59.870 52.381 0.00 0.00 0.00 2.44
3421 3967 1.445871 GCGACACTCCGGGTATTTTT 58.554 50.000 0.00 0.00 0.00 1.94
3422 3968 0.392060 GGCGACACTCCGGGTATTTT 60.392 55.000 0.00 0.00 0.00 1.82
3423 3969 1.219935 GGCGACACTCCGGGTATTT 59.780 57.895 0.00 0.00 0.00 1.40
3544 4091 2.637872 CTGGGACCAGGAGAAAACAGTA 59.362 50.000 10.55 0.00 40.17 2.74
3561 4108 7.461749 ACCATAATGTATTTATCCAGTCTGGG 58.538 38.462 19.11 0.53 38.32 4.45
3622 4177 1.202417 ACGGTAGAATCAGGCATGTCG 60.202 52.381 0.00 0.00 0.00 4.35
3641 4196 8.398491 CAATGTAAAATTGCTGGAAGTATGAC 57.602 34.615 0.00 0.00 35.30 3.06
3709 4307 2.297701 GAGTTTTGTCTTGGTGAGGCA 58.702 47.619 0.00 0.00 38.47 4.75
3710 4308 2.297701 TGAGTTTTGTCTTGGTGAGGC 58.702 47.619 0.00 0.00 0.00 4.70
3712 4310 4.320057 GCTCATGAGTTTTGTCTTGGTGAG 60.320 45.833 23.38 0.00 35.04 3.51
3713 4311 3.565482 GCTCATGAGTTTTGTCTTGGTGA 59.435 43.478 23.38 0.00 0.00 4.02
3714 4312 3.316029 TGCTCATGAGTTTTGTCTTGGTG 59.684 43.478 23.38 0.00 0.00 4.17
3715 4313 3.554934 TGCTCATGAGTTTTGTCTTGGT 58.445 40.909 23.38 0.00 0.00 3.67
3716 4314 3.817084 TCTGCTCATGAGTTTTGTCTTGG 59.183 43.478 23.38 0.00 0.00 3.61
3717 4315 4.274214 TGTCTGCTCATGAGTTTTGTCTTG 59.726 41.667 23.38 4.35 0.00 3.02
3773 4392 6.936335 CCTGCTTTGTTCCTTTATTTCCATTT 59.064 34.615 0.00 0.00 0.00 2.32
3781 4402 2.562738 GTGGCCTGCTTTGTTCCTTTAT 59.437 45.455 3.32 0.00 0.00 1.40
3887 4509 1.760613 AGGTTCAAGAACTCGACCACA 59.239 47.619 12.22 0.00 40.94 4.17
3926 4548 1.264749 ATAGCGGTGTCTCCAAGGCA 61.265 55.000 0.00 0.00 35.57 4.75
3971 4593 3.316588 GGATCAACGATAGAGAGCTGACA 59.683 47.826 0.00 0.00 41.38 3.58
3983 4605 0.469917 AGCCAATCCGGATCAACGAT 59.530 50.000 19.43 0.00 36.56 3.73
4009 4631 1.977854 TGCTACAGGTGGTGAAGATGT 59.022 47.619 0.00 0.00 0.00 3.06
4025 4647 4.585526 CGCCGCCCTTCGATGCTA 62.586 66.667 0.00 0.00 41.67 3.49
4058 4680 2.360475 GTGGCCCTCTTCTGCACC 60.360 66.667 0.00 0.00 0.00 5.01
4172 4794 4.755123 ACTCTTAAACCTGAACATTCACCG 59.245 41.667 0.00 0.00 32.90 4.94
4173 4795 6.635030 AACTCTTAAACCTGAACATTCACC 57.365 37.500 0.00 0.00 32.90 4.02
4176 4798 9.274206 AGTCTAAACTCTTAAACCTGAACATTC 57.726 33.333 0.00 0.00 0.00 2.67
4187 4813 6.665992 TCAGCCTCAGTCTAAACTCTTAAA 57.334 37.500 0.00 0.00 31.71 1.52
4191 4817 8.540507 TTTATATCAGCCTCAGTCTAAACTCT 57.459 34.615 0.00 0.00 31.71 3.24
4192 4818 9.418045 GATTTATATCAGCCTCAGTCTAAACTC 57.582 37.037 0.00 0.00 31.71 3.01
4193 4819 8.928448 TGATTTATATCAGCCTCAGTCTAAACT 58.072 33.333 0.00 0.00 35.87 2.66
4194 4820 9.717942 ATGATTTATATCAGCCTCAGTCTAAAC 57.282 33.333 2.30 0.00 43.70 2.01
4197 4823 9.935241 GAAATGATTTATATCAGCCTCAGTCTA 57.065 33.333 2.30 0.00 43.70 2.59
4199 4825 8.613060 TGAAATGATTTATATCAGCCTCAGTC 57.387 34.615 2.30 0.00 43.70 3.51
4202 4828 7.668469 AGCATGAAATGATTTATATCAGCCTCA 59.332 33.333 0.00 5.03 42.55 3.86
4223 4849 7.221452 GCCAGTATTAAAAGATTCACAAGCATG 59.779 37.037 0.00 0.00 0.00 4.06
4241 4867 7.607991 GCATATACCTGACTTTATGCCAGTATT 59.392 37.037 3.04 0.00 40.51 1.89
4242 4868 7.038017 AGCATATACCTGACTTTATGCCAGTAT 60.038 37.037 9.46 0.00 45.05 2.12
4261 4887 6.203530 GTGATGAACTTAGCTTGCAGCATATA 59.796 38.462 0.00 0.00 45.56 0.86
4263 4889 4.333649 GTGATGAACTTAGCTTGCAGCATA 59.666 41.667 0.00 0.00 45.56 3.14
4313 4941 5.936956 AGAAATCAGATCAACAAGACTGTCC 59.063 40.000 3.76 0.00 33.45 4.02
4318 4946 6.149142 AGCTTCAGAAATCAGATCAACAAGAC 59.851 38.462 0.00 0.00 0.00 3.01
4320 4948 6.072618 ACAGCTTCAGAAATCAGATCAACAAG 60.073 38.462 0.00 0.00 0.00 3.16
4327 4955 8.659925 CTGTAATACAGCTTCAGAAATCAGAT 57.340 34.615 7.55 0.00 39.62 2.90


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

AutoCloner maintained by Alex Coulton.