Multiple sequence alignment - TraesCS2A01G232900

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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 TraesCS2A01G232900 chr2A 100.000 6141 0 0 1 6141 277597757 277603897 0.000000e+00 11341.0
1 TraesCS2A01G232900 chr2D 92.455 5474 204 59 764 6141 205623301 205617941 0.000000e+00 7627.0
2 TraesCS2A01G232900 chr2D 88.809 697 17 17 1 646 205624067 205623381 0.000000e+00 798.0
3 TraesCS2A01G232900 chr2D 94.231 52 3 0 713 764 205623373 205623322 5.100000e-11 80.5
4 TraesCS2A01G232900 chr2B 94.066 2528 113 17 2711 5236 259784496 259782004 0.000000e+00 3803.0
5 TraesCS2A01G232900 chr2B 89.171 1773 75 37 994 2707 259786271 259784557 0.000000e+00 2102.0
6 TraesCS2A01G232900 chr2B 93.164 907 37 15 5234 6135 259781755 259780869 0.000000e+00 1308.0
7 TraesCS2A01G232900 chr2B 85.788 387 32 10 1 380 259787285 259786915 7.460000e-104 388.0
8 TraesCS2A01G232900 chr2B 82.710 214 15 5 676 871 259786602 259786393 2.940000e-38 171.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G232900 chr2A 277597757 277603897 6140 False 11341.000000 11341 100.000000 1 6141 1 chr2A.!!$F1 6140
1 TraesCS2A01G232900 chr2D 205617941 205624067 6126 True 2835.166667 7627 91.831667 1 6141 3 chr2D.!!$R1 6140
2 TraesCS2A01G232900 chr2B 259780869 259787285 6416 True 1554.400000 3803 88.979800 1 6135 5 chr2B.!!$R1 6134

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
723 825 0.393808 GTCTGGTGTGGTGTGGTGTT 60.394 55.0 0.00 0.00 0.00 3.32 F
1185 1356 0.103208 ATCCTTCTTCCTGCGCTACG 59.897 55.0 9.73 0.00 0.00 3.51 F
2211 2446 0.108472 TCCAGCTCTCTTCATGTGCG 60.108 55.0 0.00 0.00 0.00 5.34 F
3958 4257 0.463654 TGGAGCTCGCGGCAAAATAT 60.464 50.0 19.30 0.21 44.79 1.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2249 2484 0.239347 CAAAAGACTGCAAGCGAGGG 59.761 55.000 0.0 0.0 37.60 4.30 R
2513 2754 1.517242 CTGTTGTCCTGTGCTTCCTC 58.483 55.000 0.0 0.0 0.00 3.71 R
4015 4314 0.025001 CGCTGTATTTTCTGGCGTCG 59.975 55.000 0.0 0.0 40.78 5.12 R
5872 6428 1.407989 GGAAGGAACTCAGATGGCTGG 60.408 57.143 0.0 0.0 42.53 4.85 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
209 210 3.595758 GCCAGGCCACACACACAC 61.596 66.667 5.01 0.00 0.00 3.82
210 211 2.124362 CCAGGCCACACACACACA 60.124 61.111 5.01 0.00 0.00 3.72
373 382 2.423446 CCACCATAGGCTCGCCTC 59.577 66.667 14.75 0.00 44.43 4.70
374 383 2.028190 CACCATAGGCTCGCCTCG 59.972 66.667 14.75 7.00 44.43 4.63
402 450 1.339535 GGGTCCAAGAGCAAGGAGAAG 60.340 57.143 0.00 0.00 33.85 2.85
509 594 1.552792 CCTGGACTTTCCTCTCTCCAC 59.447 57.143 0.00 0.00 37.46 4.02
566 651 6.710744 CAGGAGGTAGTAGTTTTGAATTGTGT 59.289 38.462 0.00 0.00 0.00 3.72
630 715 6.849502 CATCAAGTGATGCAGTATTTGTCTT 58.150 36.000 8.29 0.00 44.44 3.01
631 716 6.486253 TCAAGTGATGCAGTATTTGTCTTC 57.514 37.500 0.00 0.00 0.00 2.87
632 717 6.233434 TCAAGTGATGCAGTATTTGTCTTCT 58.767 36.000 0.00 0.00 0.00 2.85
633 718 6.712095 TCAAGTGATGCAGTATTTGTCTTCTT 59.288 34.615 0.00 0.00 0.00 2.52
634 719 6.734104 AGTGATGCAGTATTTGTCTTCTTC 57.266 37.500 0.00 0.00 0.00 2.87
635 720 6.471146 AGTGATGCAGTATTTGTCTTCTTCT 58.529 36.000 0.00 0.00 0.00 2.85
636 721 6.939163 AGTGATGCAGTATTTGTCTTCTTCTT 59.061 34.615 0.00 0.00 0.00 2.52
637 722 7.118971 AGTGATGCAGTATTTGTCTTCTTCTTC 59.881 37.037 0.00 0.00 0.00 2.87
638 723 7.118971 GTGATGCAGTATTTGTCTTCTTCTTCT 59.881 37.037 0.00 0.00 0.00 2.85
639 724 7.663081 TGATGCAGTATTTGTCTTCTTCTTCTT 59.337 33.333 0.00 0.00 0.00 2.52
640 725 7.426929 TGCAGTATTTGTCTTCTTCTTCTTC 57.573 36.000 0.00 0.00 0.00 2.87
641 726 7.220030 TGCAGTATTTGTCTTCTTCTTCTTCT 58.780 34.615 0.00 0.00 0.00 2.85
642 727 7.716998 TGCAGTATTTGTCTTCTTCTTCTTCTT 59.283 33.333 0.00 0.00 0.00 2.52
643 728 8.227119 GCAGTATTTGTCTTCTTCTTCTTCTTC 58.773 37.037 0.00 0.00 0.00 2.87
644 729 9.487790 CAGTATTTGTCTTCTTCTTCTTCTTCT 57.512 33.333 0.00 0.00 0.00 2.85
648 733 9.625747 ATTTGTCTTCTTCTTCTTCTTCTTCTT 57.374 29.630 0.00 0.00 0.00 2.52
649 734 8.655651 TTGTCTTCTTCTTCTTCTTCTTCTTC 57.344 34.615 0.00 0.00 0.00 2.87
650 735 8.017418 TGTCTTCTTCTTCTTCTTCTTCTTCT 57.983 34.615 0.00 0.00 0.00 2.85
651 736 8.482128 TGTCTTCTTCTTCTTCTTCTTCTTCTT 58.518 33.333 0.00 0.00 0.00 2.52
652 737 8.978539 GTCTTCTTCTTCTTCTTCTTCTTCTTC 58.021 37.037 0.00 0.00 0.00 2.87
653 738 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
654 739 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
655 740 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
656 741 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
657 742 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
658 743 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
659 744 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
660 745 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
661 746 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
662 747 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
663 748 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
664 749 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
665 750 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
666 751 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
667 752 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
668 753 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
704 806 0.896019 AGTCGTCTGGTCTGGTCTGG 60.896 60.000 0.00 0.00 0.00 3.86
711 813 1.121407 TGGTCTGGTCTGGTCTGGTG 61.121 60.000 0.00 0.00 0.00 4.17
718 820 0.532862 GTCTGGTCTGGTGTGGTGTG 60.533 60.000 0.00 0.00 0.00 3.82
719 821 1.227943 CTGGTCTGGTGTGGTGTGG 60.228 63.158 0.00 0.00 0.00 4.17
720 822 1.983119 CTGGTCTGGTGTGGTGTGGT 61.983 60.000 0.00 0.00 0.00 4.16
721 823 1.525995 GGTCTGGTGTGGTGTGGTG 60.526 63.158 0.00 0.00 0.00 4.17
722 824 1.223487 GTCTGGTGTGGTGTGGTGT 59.777 57.895 0.00 0.00 0.00 4.16
723 825 0.393808 GTCTGGTGTGGTGTGGTGTT 60.394 55.000 0.00 0.00 0.00 3.32
725 827 1.560146 TCTGGTGTGGTGTGGTGTTTA 59.440 47.619 0.00 0.00 0.00 2.01
726 828 2.026169 TCTGGTGTGGTGTGGTGTTTAA 60.026 45.455 0.00 0.00 0.00 1.52
727 829 2.955660 CTGGTGTGGTGTGGTGTTTAAT 59.044 45.455 0.00 0.00 0.00 1.40
805 928 1.856597 GAATTGCTGGAATTCGCATGC 59.143 47.619 16.98 7.91 40.43 4.06
818 941 1.135315 TCGCATGCTTCTTGCCAATTC 60.135 47.619 17.13 0.00 42.00 2.17
819 942 1.403116 CGCATGCTTCTTGCCAATTCA 60.403 47.619 17.13 0.00 42.00 2.57
868 994 3.309138 CCTAATCGAGCTGATATGCATGC 59.691 47.826 11.82 11.82 35.84 4.06
869 995 2.467566 ATCGAGCTGATATGCATGCA 57.532 45.000 25.04 25.04 34.83 3.96
870 996 2.467566 TCGAGCTGATATGCATGCAT 57.532 45.000 33.92 33.92 40.19 3.96
871 997 2.774687 TCGAGCTGATATGCATGCATT 58.225 42.857 36.23 23.51 37.82 3.56
872 998 2.482721 TCGAGCTGATATGCATGCATTG 59.517 45.455 36.23 23.33 37.82 2.82
873 999 2.414161 CGAGCTGATATGCATGCATTGG 60.414 50.000 36.23 22.91 37.82 3.16
874 1000 1.893137 AGCTGATATGCATGCATTGGG 59.107 47.619 36.23 23.21 37.82 4.12
896 1038 7.181361 TGGGATTGGATTGATTCAAGTTTCTA 58.819 34.615 5.21 0.00 0.00 2.10
937 1079 4.590850 AAACTGCAATCTGTCCCTTTTC 57.409 40.909 0.00 0.00 0.00 2.29
953 1095 6.978659 GTCCCTTTTCCTTGTCTAAACTTTTG 59.021 38.462 0.00 0.00 0.00 2.44
964 1117 4.280929 GTCTAAACTTTTGGGTGGATTGCT 59.719 41.667 0.00 0.00 0.00 3.91
965 1118 3.473923 AAACTTTTGGGTGGATTGCTG 57.526 42.857 0.00 0.00 0.00 4.41
966 1119 2.380064 ACTTTTGGGTGGATTGCTGA 57.620 45.000 0.00 0.00 0.00 4.26
967 1120 2.676748 ACTTTTGGGTGGATTGCTGAA 58.323 42.857 0.00 0.00 0.00 3.02
968 1121 2.629617 ACTTTTGGGTGGATTGCTGAAG 59.370 45.455 0.00 0.00 0.00 3.02
1024 1177 3.954904 CAAGGGTGTAGAGAGCTAGCTAA 59.045 47.826 19.38 0.39 0.00 3.09
1032 1187 2.436542 AGAGAGCTAGCTAACTCGAGGA 59.563 50.000 19.38 3.03 37.99 3.71
1153 1314 6.591935 ACTTTAACTGATGAACAGGTGAGAA 58.408 36.000 0.00 0.00 46.95 2.87
1154 1315 6.483640 ACTTTAACTGATGAACAGGTGAGAAC 59.516 38.462 0.00 0.00 46.95 3.01
1180 1351 3.861840 TCTTGTTATCCTTCTTCCTGCG 58.138 45.455 0.00 0.00 0.00 5.18
1185 1356 0.103208 ATCCTTCTTCCTGCGCTACG 59.897 55.000 9.73 0.00 0.00 3.51
1194 1365 1.695893 CCTGCGCTACGTTGATGGTG 61.696 60.000 9.73 0.00 0.00 4.17
1201 1372 2.351726 GCTACGTTGATGGTGTCCATTC 59.648 50.000 0.00 0.00 45.26 2.67
1220 1391 1.512734 CTGCGATTTTGCGGCACTC 60.513 57.895 0.05 0.00 37.81 3.51
1225 1396 0.371645 GATTTTGCGGCACTCTCTCG 59.628 55.000 0.05 0.00 0.00 4.04
1249 1420 3.254411 TGTTCGCCTTGCATGATTTAACA 59.746 39.130 0.00 3.95 0.00 2.41
1255 1426 5.861251 CGCCTTGCATGATTTAACAAACTAA 59.139 36.000 0.00 0.00 0.00 2.24
1256 1427 6.033831 CGCCTTGCATGATTTAACAAACTAAG 59.966 38.462 0.00 0.00 0.00 2.18
1257 1428 6.868339 GCCTTGCATGATTTAACAAACTAAGT 59.132 34.615 0.00 0.00 0.00 2.24
1258 1429 8.026607 GCCTTGCATGATTTAACAAACTAAGTA 58.973 33.333 0.00 0.00 0.00 2.24
1279 1450 0.895530 TAACGGGTCAGAGGAGCAAG 59.104 55.000 0.00 0.00 43.32 4.01
1304 1475 6.987403 AAAGGAAATTGGCCTACAGTAAAA 57.013 33.333 3.32 0.00 33.76 1.52
1305 1476 6.987403 AAGGAAATTGGCCTACAGTAAAAA 57.013 33.333 3.32 0.00 33.76 1.94
1306 1477 6.590234 AGGAAATTGGCCTACAGTAAAAAG 57.410 37.500 3.32 0.00 32.92 2.27
1308 1479 6.954102 AGGAAATTGGCCTACAGTAAAAAGAT 59.046 34.615 3.32 0.00 32.92 2.40
1309 1480 7.454694 AGGAAATTGGCCTACAGTAAAAAGATT 59.545 33.333 3.32 0.00 32.92 2.40
1310 1481 7.759886 GGAAATTGGCCTACAGTAAAAAGATTC 59.240 37.037 3.32 0.00 0.00 2.52
1351 1544 5.186996 AGGAGTGTTTTACAAGCATGTTG 57.813 39.130 0.00 0.53 41.05 3.33
1381 1586 1.602920 CCTTTTCTTTTGCGGTGGAGC 60.603 52.381 0.00 0.00 37.71 4.70
1390 1595 1.598130 GCGGTGGAGCAAGTTCAGT 60.598 57.895 0.00 0.00 37.05 3.41
1391 1596 1.166531 GCGGTGGAGCAAGTTCAGTT 61.167 55.000 0.00 0.00 37.05 3.16
1392 1597 0.868406 CGGTGGAGCAAGTTCAGTTC 59.132 55.000 0.00 0.00 0.00 3.01
1393 1598 1.810031 CGGTGGAGCAAGTTCAGTTCA 60.810 52.381 0.00 0.00 0.00 3.18
1394 1599 1.876156 GGTGGAGCAAGTTCAGTTCAG 59.124 52.381 0.00 0.00 0.00 3.02
1395 1600 1.876156 GTGGAGCAAGTTCAGTTCAGG 59.124 52.381 0.00 0.00 0.00 3.86
1396 1601 0.877743 GGAGCAAGTTCAGTTCAGGC 59.122 55.000 0.00 0.00 0.00 4.85
1397 1602 1.597742 GAGCAAGTTCAGTTCAGGCA 58.402 50.000 0.00 0.00 0.00 4.75
1398 1603 2.157738 GAGCAAGTTCAGTTCAGGCAT 58.842 47.619 0.00 0.00 0.00 4.40
1399 1604 1.884579 AGCAAGTTCAGTTCAGGCATG 59.115 47.619 0.00 0.00 0.00 4.06
1400 1605 1.610522 GCAAGTTCAGTTCAGGCATGT 59.389 47.619 0.00 0.00 0.00 3.21
1401 1606 2.035066 GCAAGTTCAGTTCAGGCATGTT 59.965 45.455 0.00 0.00 0.00 2.71
1402 1607 3.635331 CAAGTTCAGTTCAGGCATGTTG 58.365 45.455 0.00 0.00 0.00 3.33
1403 1608 3.213206 AGTTCAGTTCAGGCATGTTGA 57.787 42.857 0.00 0.00 0.00 3.18
1404 1609 3.759581 AGTTCAGTTCAGGCATGTTGAT 58.240 40.909 0.00 0.00 0.00 2.57
1405 1610 3.504906 AGTTCAGTTCAGGCATGTTGATG 59.495 43.478 0.00 0.00 0.00 3.07
1406 1611 2.439409 TCAGTTCAGGCATGTTGATGG 58.561 47.619 0.00 0.00 0.00 3.51
1407 1612 1.475280 CAGTTCAGGCATGTTGATGGG 59.525 52.381 0.00 0.00 0.00 4.00
1441 1646 0.394625 GAGAGTCCTACACGCCTCCT 60.395 60.000 0.00 0.00 0.00 3.69
1480 1686 0.539438 ATGTGCCGCCCAGAGAAAAA 60.539 50.000 0.00 0.00 0.00 1.94
1484 1690 0.171231 GCCGCCCAGAGAAAAATGAC 59.829 55.000 0.00 0.00 0.00 3.06
1660 1866 7.201626 GCTGGATCAGAATTCATCAGCATATAC 60.202 40.741 21.88 3.98 32.44 1.47
1661 1867 7.914859 TGGATCAGAATTCATCAGCATATACT 58.085 34.615 8.44 0.00 0.00 2.12
1662 1868 7.822822 TGGATCAGAATTCATCAGCATATACTG 59.177 37.037 8.44 0.00 39.12 2.74
1663 1869 7.823310 GGATCAGAATTCATCAGCATATACTGT 59.177 37.037 8.44 0.00 38.84 3.55
1664 1870 9.866798 GATCAGAATTCATCAGCATATACTGTA 57.133 33.333 8.44 0.00 38.84 2.74
1694 1900 4.082354 AGCCAGATTGCTTGTCATTCTTTC 60.082 41.667 0.00 0.00 38.85 2.62
1695 1901 4.082354 GCCAGATTGCTTGTCATTCTTTCT 60.082 41.667 0.00 0.00 34.24 2.52
1702 1908 7.707624 TTGCTTGTCATTCTTTCTGGAATAT 57.292 32.000 0.00 0.00 34.59 1.28
1703 1909 7.707624 TGCTTGTCATTCTTTCTGGAATATT 57.292 32.000 0.00 0.00 34.59 1.28
1705 1911 9.241919 TGCTTGTCATTCTTTCTGGAATATTAA 57.758 29.630 0.00 0.00 34.59 1.40
1750 1958 5.105567 TGTCTTAGTCTCCTCTCTGGTAG 57.894 47.826 0.00 0.00 37.07 3.18
1825 2040 5.163723 CCATGTTAGTAGAGGCACACAATTG 60.164 44.000 3.24 3.24 0.00 2.32
1913 2136 4.724074 TGACCAATCTTCATGGCAATTC 57.276 40.909 0.00 0.00 41.89 2.17
1972 2195 2.047830 GGGGTCCTATTGTCCCTGTAG 58.952 57.143 0.00 0.00 40.88 2.74
2211 2446 0.108472 TCCAGCTCTCTTCATGTGCG 60.108 55.000 0.00 0.00 0.00 5.34
2241 2476 1.176619 TTGATTGTGCTGCTGCTGCT 61.177 50.000 27.67 11.28 40.48 4.24
2242 2477 1.154016 GATTGTGCTGCTGCTGCTG 60.154 57.895 27.67 16.73 40.48 4.41
2320 2559 5.316167 TCTAATGCAACAGTGAGGAACAAT 58.684 37.500 0.00 0.00 0.00 2.71
2451 2692 6.318648 ACAACAATTTTGACTCTGCTTGTCTA 59.681 34.615 0.00 0.00 35.63 2.59
2500 2741 1.818363 GAGTTCCCCGAAATCGCCC 60.818 63.158 0.00 0.00 38.18 6.13
2608 2849 1.514811 CGTGCGAAAGATGATCTCGTC 59.485 52.381 0.00 0.00 35.06 4.20
2649 2890 3.771798 CCGAAGAAGCTGTTCTAGGTAC 58.228 50.000 7.33 0.00 42.59 3.34
2702 2943 8.200792 ACAAGATTAAGCACCACACAAAAATTA 58.799 29.630 0.00 0.00 0.00 1.40
2703 2944 8.487176 CAAGATTAAGCACCACACAAAAATTAC 58.513 33.333 0.00 0.00 0.00 1.89
2704 2945 7.951591 AGATTAAGCACCACACAAAAATTACT 58.048 30.769 0.00 0.00 0.00 2.24
2705 2946 9.073475 AGATTAAGCACCACACAAAAATTACTA 57.927 29.630 0.00 0.00 0.00 1.82
2742 3041 8.697846 ATTGAACATTATTCACAAGCAGATTG 57.302 30.769 0.00 0.00 45.01 2.67
3054 3353 3.726144 GCTCCAGGCTGGCCTCTT 61.726 66.667 29.02 0.00 46.28 2.85
3152 3451 4.785453 CTCAACAGGAGGGCGGCC 62.785 72.222 22.67 22.67 40.13 6.13
3237 3536 2.880890 AGAAAACTGCAGGTGATGACAC 59.119 45.455 19.93 0.00 45.27 3.67
3286 3585 6.203808 CCATTGGAGGCATCATATTATGTG 57.796 41.667 0.00 3.49 0.00 3.21
3287 3586 5.947566 CCATTGGAGGCATCATATTATGTGA 59.052 40.000 0.00 0.00 0.00 3.58
3288 3587 6.605995 CCATTGGAGGCATCATATTATGTGAT 59.394 38.462 0.00 0.00 36.79 3.06
3308 3607 2.036387 TGTGAAGAGGACGGTTCTTGA 58.964 47.619 0.01 0.00 35.14 3.02
3315 3614 0.685660 GGACGGTTCTTGACCTCCTT 59.314 55.000 0.00 0.00 46.92 3.36
3344 3643 4.338379 AGCTAACGTCTCTGGAGTTTTT 57.662 40.909 0.00 0.00 0.00 1.94
3364 3663 4.994471 CAGGCCACTGCACGCAGA 62.994 66.667 25.09 0.00 46.30 4.26
3499 3798 0.879765 ACCAGTACAAGACCGAGACG 59.120 55.000 0.00 0.00 0.00 4.18
3603 3902 2.101965 CGTCTCGAGGAGCAGCAG 59.898 66.667 13.56 0.00 0.00 4.24
3749 4048 3.609256 TGGTAGCAGAGGAGAGATCAT 57.391 47.619 0.00 0.00 0.00 2.45
3750 4049 3.229293 TGGTAGCAGAGGAGAGATCATG 58.771 50.000 0.00 0.00 0.00 3.07
3847 4146 1.045911 AGAGGAACGATCTGGAGGGC 61.046 60.000 0.00 0.00 0.00 5.19
3884 4183 2.959071 GCGAGATCACGAGCCTGC 60.959 66.667 17.02 0.00 35.09 4.85
3958 4257 0.463654 TGGAGCTCGCGGCAAAATAT 60.464 50.000 19.30 0.21 44.79 1.28
4015 4314 2.202544 CGTGCTCAGCTCGAGTCC 60.203 66.667 16.06 0.00 46.28 3.85
4077 4376 0.034670 AGGCTCACAGAGAAATGCCC 60.035 55.000 0.00 0.00 41.08 5.36
4147 4446 1.742268 GAGCTGGCAGGACAAGAAATC 59.258 52.381 17.64 0.00 0.00 2.17
4293 4592 2.123428 AGGCCGCCAATTCAGATGC 61.123 57.895 13.15 0.00 0.00 3.91
4320 4619 3.440522 GCCCTGAATGAGAAGGTTAACAC 59.559 47.826 8.10 0.00 0.00 3.32
4423 4722 1.379642 GCTTGAAGGAGAATGCCGGG 61.380 60.000 2.18 0.00 0.00 5.73
4525 4824 2.172851 ACAAAATGACGAGCCGGTTA 57.827 45.000 1.90 0.00 0.00 2.85
4668 4967 2.436292 GTGCAGCAGAGCTCCAGG 60.436 66.667 10.93 1.26 36.40 4.45
4738 5037 6.266558 ACCTGCACATCACAAAGGTAAATTTA 59.733 34.615 0.00 0.00 39.48 1.40
4768 5068 6.698380 TCTCTTAACTATCACAACCAAGTCC 58.302 40.000 0.00 0.00 0.00 3.85
4826 5126 9.567776 TTATGTTTTTCTGATGAGTAACTGGAA 57.432 29.630 0.00 0.00 0.00 3.53
4854 5154 5.871396 TCACTTTGTACAGGAGAAAGAGT 57.129 39.130 9.29 0.00 40.15 3.24
4964 5264 1.738474 TCATCATCCCTGATCCTGGG 58.262 55.000 13.16 13.16 40.20 4.45
5060 5360 2.336088 CAGTTGGGCTGTTTGGCG 59.664 61.111 0.00 0.00 42.84 5.69
5070 5370 1.597797 CTGTTTGGCGGCCACATGAT 61.598 55.000 23.78 0.00 30.78 2.45
5090 5390 6.899393 TGATTGTGGTAGCAAAGAAAGATT 57.101 33.333 0.00 0.00 31.63 2.40
5117 5417 5.893255 AGAAAATTATATGGCTTGGCTGTCA 59.107 36.000 0.00 0.00 0.00 3.58
5150 5450 6.388100 AGATTGACAGAATCCTTCCCTGATTA 59.612 38.462 0.00 0.00 32.74 1.75
5253 5805 6.615726 AGATGAAGTGTATAGCCTTAAGGGAA 59.384 38.462 23.06 0.00 37.23 3.97
5326 5880 4.855531 GTTTTTAACCTCGTCTGCAACAT 58.144 39.130 0.00 0.00 0.00 2.71
5345 5899 6.183360 GCAACATGACTCCGTATCTTATATGC 60.183 42.308 0.00 0.00 0.00 3.14
5443 5997 6.752168 AGTTCAAATTTCAAATGTCCAGGAG 58.248 36.000 0.00 0.00 0.00 3.69
5533 6087 4.630069 CGGTACAAACTAACCAAGATGAGG 59.370 45.833 0.00 0.00 35.35 3.86
5594 6148 8.889849 ACCGTTCAAGTTTGATAATATTTTCG 57.110 30.769 0.00 0.00 37.00 3.46
5644 6199 8.088365 ACAGCAGGTAATATTTCAAGGAAAAAC 58.912 33.333 0.00 0.00 35.11 2.43
5847 6403 7.503566 TCAGATTTTATTCTCTTTGGGGCATAG 59.496 37.037 0.00 0.00 0.00 2.23
5872 6428 3.687572 CAGCATCACTGTCATTAAGGC 57.312 47.619 0.00 0.00 41.86 4.35
5911 6467 1.005215 CCTCATCCTCTGCAACCCTTT 59.995 52.381 0.00 0.00 0.00 3.11
5965 6521 3.002791 GTTTCAGCATCGTCTTCATCCA 58.997 45.455 0.00 0.00 0.00 3.41
5979 6535 0.734889 CATCCAGGTCGACCATTTGC 59.265 55.000 35.00 8.29 38.89 3.68
5998 6554 4.736126 TGCGTTTCTTCATCATCCTCTA 57.264 40.909 0.00 0.00 0.00 2.43
6009 6565 9.823647 TCTTCATCATCCTCTATAACAGTTTTC 57.176 33.333 0.00 0.00 0.00 2.29
6010 6566 9.829507 CTTCATCATCCTCTATAACAGTTTTCT 57.170 33.333 0.00 0.00 0.00 2.52
6012 6568 9.823647 TCATCATCCTCTATAACAGTTTTCTTC 57.176 33.333 0.00 0.00 0.00 2.87
6013 6569 9.829507 CATCATCCTCTATAACAGTTTTCTTCT 57.170 33.333 0.00 0.00 0.00 2.85
6015 6571 9.877178 TCATCCTCTATAACAGTTTTCTTCTTC 57.123 33.333 0.00 0.00 0.00 2.87
6016 6572 9.883142 CATCCTCTATAACAGTTTTCTTCTTCT 57.117 33.333 0.00 0.00 0.00 2.85
6018 6574 9.930693 TCCTCTATAACAGTTTTCTTCTTCTTC 57.069 33.333 0.00 0.00 0.00 2.87
6019 6575 9.936759 CCTCTATAACAGTTTTCTTCTTCTTCT 57.063 33.333 0.00 0.00 0.00 2.85
6036 6592 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
6045 6601 8.885494 TCTTCTTCTTCTTCTTCTTCTTCTTG 57.115 34.615 0.00 0.00 0.00 3.02
6106 6665 3.755378 CACCATTTGAGTTCCTTCCTCAG 59.245 47.826 0.00 0.00 39.91 3.35
6117 6676 1.339535 CCTTCCTCAGCCTCTTCAACC 60.340 57.143 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.729882 GGCACGTTCATATCATCGTACC 59.270 50.000 0.00 0.00 35.13 3.34
13 14 2.413112 GGATGGCACGTTCATATCATCG 59.587 50.000 0.00 0.00 33.79 3.84
100 101 0.820891 ATGGGATTGATCGTGCTGCC 60.821 55.000 0.00 0.00 0.00 4.85
201 202 0.167908 GGTGTGTGTGTGTGTGTGTG 59.832 55.000 0.00 0.00 0.00 3.82
202 203 0.250510 TGGTGTGTGTGTGTGTGTGT 60.251 50.000 0.00 0.00 0.00 3.72
203 204 1.093972 ATGGTGTGTGTGTGTGTGTG 58.906 50.000 0.00 0.00 0.00 3.82
204 205 1.093972 CATGGTGTGTGTGTGTGTGT 58.906 50.000 0.00 0.00 0.00 3.72
205 206 0.248580 GCATGGTGTGTGTGTGTGTG 60.249 55.000 0.00 0.00 0.00 3.82
206 207 0.394216 AGCATGGTGTGTGTGTGTGT 60.394 50.000 0.00 0.00 0.00 3.72
207 208 0.740149 AAGCATGGTGTGTGTGTGTG 59.260 50.000 0.00 0.00 0.00 3.82
208 209 1.024271 GAAGCATGGTGTGTGTGTGT 58.976 50.000 0.00 0.00 0.00 3.72
209 210 1.311859 AGAAGCATGGTGTGTGTGTG 58.688 50.000 0.00 0.00 0.00 3.82
210 211 2.057137 AAGAAGCATGGTGTGTGTGT 57.943 45.000 0.00 0.00 0.00 3.72
371 380 3.551496 TTGGACCCAAGCAGGCGAG 62.551 63.158 0.00 0.00 35.39 5.03
372 381 3.551496 CTTGGACCCAAGCAGGCGA 62.551 63.158 15.04 0.00 45.38 5.54
373 382 3.058160 CTTGGACCCAAGCAGGCG 61.058 66.667 15.04 0.00 45.38 5.52
380 389 0.401738 CTCCTTGCTCTTGGACCCAA 59.598 55.000 1.11 1.11 0.00 4.12
382 391 0.693049 TTCTCCTTGCTCTTGGACCC 59.307 55.000 0.00 0.00 0.00 4.46
419 467 2.303022 CAGCAAGACCCAGGAAGTAAGA 59.697 50.000 0.00 0.00 0.00 2.10
509 594 3.864686 CGCCGCAAATCACCGAGG 61.865 66.667 0.00 0.00 0.00 4.63
566 651 3.476552 AGCCGAGTTCATCAAGAAACAA 58.523 40.909 0.00 0.00 38.13 2.83
630 715 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
631 716 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
632 717 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
633 718 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
634 719 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
635 720 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
636 721 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
637 722 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
638 723 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
639 724 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
640 725 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
641 726 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
642 727 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
643 728 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
644 729 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
645 730 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
646 731 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
647 732 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
648 733 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
649 734 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
650 735 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
651 736 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
652 737 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
653 738 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
654 739 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
655 740 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
656 741 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
657 742 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
658 743 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
661 746 9.981114 ACTAAGAAGAAGAAGAAGAAGAAGAAG 57.019 33.333 0.00 0.00 0.00 2.85
662 747 9.974980 GACTAAGAAGAAGAAGAAGAAGAAGAA 57.025 33.333 0.00 0.00 0.00 2.52
663 748 8.293867 CGACTAAGAAGAAGAAGAAGAAGAAGA 58.706 37.037 0.00 0.00 0.00 2.87
664 749 8.079809 ACGACTAAGAAGAAGAAGAAGAAGAAG 58.920 37.037 0.00 0.00 0.00 2.85
665 750 7.942990 ACGACTAAGAAGAAGAAGAAGAAGAA 58.057 34.615 0.00 0.00 0.00 2.52
666 751 7.446013 AGACGACTAAGAAGAAGAAGAAGAAGA 59.554 37.037 0.00 0.00 0.00 2.87
667 752 7.537306 CAGACGACTAAGAAGAAGAAGAAGAAG 59.463 40.741 0.00 0.00 0.00 2.85
668 753 7.364200 CAGACGACTAAGAAGAAGAAGAAGAA 58.636 38.462 0.00 0.00 0.00 2.52
704 806 0.393808 AACACCACACCACACCAGAC 60.394 55.000 0.00 0.00 0.00 3.51
711 813 5.063880 AGAAGAGATTAAACACCACACCAC 58.936 41.667 0.00 0.00 0.00 4.16
718 820 5.745227 TCCATGGAGAAGAGATTAAACACC 58.255 41.667 11.44 0.00 0.00 4.16
719 821 7.256756 CATCCATGGAGAAGAGATTAAACAC 57.743 40.000 21.33 0.00 0.00 3.32
805 928 5.810587 CCATTCTGAATGAATTGGCAAGAAG 59.189 40.000 27.42 6.10 43.00 2.85
818 941 2.485426 AGTGTTGCGTCCATTCTGAATG 59.515 45.455 20.79 20.79 38.63 2.67
819 942 2.485426 CAGTGTTGCGTCCATTCTGAAT 59.515 45.455 0.00 0.00 0.00 2.57
868 994 6.229936 ACTTGAATCAATCCAATCCCAATG 57.770 37.500 0.00 0.00 0.00 2.82
869 995 6.879367 AACTTGAATCAATCCAATCCCAAT 57.121 33.333 0.00 0.00 0.00 3.16
870 996 6.497954 AGAAACTTGAATCAATCCAATCCCAA 59.502 34.615 0.00 0.00 0.00 4.12
871 997 6.018469 AGAAACTTGAATCAATCCAATCCCA 58.982 36.000 0.00 0.00 0.00 4.37
872 998 6.535963 AGAAACTTGAATCAATCCAATCCC 57.464 37.500 0.00 0.00 0.00 3.85
873 999 9.741647 GAATAGAAACTTGAATCAATCCAATCC 57.258 33.333 0.00 0.00 0.00 3.01
896 1038 7.281100 GCAGTTTAGGCAGTATACTTGAAGAAT 59.719 37.037 1.56 0.00 0.00 2.40
937 1079 4.211920 TCCACCCAAAAGTTTAGACAAGG 58.788 43.478 0.00 0.00 0.00 3.61
953 1095 1.541588 GTTCACTTCAGCAATCCACCC 59.458 52.381 0.00 0.00 0.00 4.61
964 1117 2.281484 GCGCCCCTGTTCACTTCA 60.281 61.111 0.00 0.00 0.00 3.02
965 1118 0.392461 TATGCGCCCCTGTTCACTTC 60.392 55.000 4.18 0.00 0.00 3.01
966 1119 0.037590 TTATGCGCCCCTGTTCACTT 59.962 50.000 4.18 0.00 0.00 3.16
967 1120 0.392998 CTTATGCGCCCCTGTTCACT 60.393 55.000 4.18 0.00 0.00 3.41
968 1121 1.993369 GCTTATGCGCCCCTGTTCAC 61.993 60.000 4.18 0.00 0.00 3.18
1024 1177 1.742768 GGCGATCCATTCCTCGAGT 59.257 57.895 12.31 0.00 37.05 4.18
1032 1187 2.109799 CAGCTCCGGCGATCCATT 59.890 61.111 9.30 0.00 44.37 3.16
1153 1314 5.189934 AGGAAGAAGGATAACAAGAATCCGT 59.810 40.000 0.00 0.00 46.37 4.69
1154 1315 5.525378 CAGGAAGAAGGATAACAAGAATCCG 59.475 44.000 0.00 0.00 46.37 4.18
1180 1351 2.024176 ATGGACACCATCAACGTAGC 57.976 50.000 0.00 0.00 40.74 3.58
1185 1356 1.474077 GCAGGAATGGACACCATCAAC 59.526 52.381 3.69 0.00 44.40 3.18
1194 1365 1.795162 CGCAAAATCGCAGGAATGGAC 60.795 52.381 0.00 0.00 0.00 4.02
1201 1372 2.504681 GTGCCGCAAAATCGCAGG 60.505 61.111 0.00 0.00 0.00 4.85
1249 1420 6.438425 TCCTCTGACCCGTTAATACTTAGTTT 59.562 38.462 0.00 0.00 0.00 2.66
1255 1426 2.694109 GCTCCTCTGACCCGTTAATACT 59.306 50.000 0.00 0.00 0.00 2.12
1256 1427 2.429610 TGCTCCTCTGACCCGTTAATAC 59.570 50.000 0.00 0.00 0.00 1.89
1257 1428 2.742348 TGCTCCTCTGACCCGTTAATA 58.258 47.619 0.00 0.00 0.00 0.98
1258 1429 1.568504 TGCTCCTCTGACCCGTTAAT 58.431 50.000 0.00 0.00 0.00 1.40
1279 1450 6.584185 TTACTGTAGGCCAATTTCCTTTTC 57.416 37.500 5.01 0.00 35.21 2.29
1304 1475 4.507710 ACACTACACATGCATCGAATCTT 58.492 39.130 0.00 0.00 0.00 2.40
1305 1476 4.115516 GACACTACACATGCATCGAATCT 58.884 43.478 0.00 0.00 0.00 2.40
1306 1477 3.865164 TGACACTACACATGCATCGAATC 59.135 43.478 0.00 0.00 0.00 2.52
1308 1479 3.311486 TGACACTACACATGCATCGAA 57.689 42.857 0.00 0.00 0.00 3.71
1309 1480 3.253230 CTTGACACTACACATGCATCGA 58.747 45.455 0.00 0.00 0.00 3.59
1310 1481 2.349580 CCTTGACACTACACATGCATCG 59.650 50.000 0.00 0.00 0.00 3.84
1351 1544 5.149977 CGCAAAAGAAAAGGAAGATGTCTC 58.850 41.667 0.00 0.00 0.00 3.36
1381 1586 3.316029 TCAACATGCCTGAACTGAACTTG 59.684 43.478 0.00 0.00 0.00 3.16
1390 1595 1.203038 ACACCCATCAACATGCCTGAA 60.203 47.619 2.46 0.00 0.00 3.02
1391 1596 0.405198 ACACCCATCAACATGCCTGA 59.595 50.000 0.00 0.00 0.00 3.86
1392 1597 1.259609 AACACCCATCAACATGCCTG 58.740 50.000 0.00 0.00 0.00 4.85
1393 1598 2.014010 AAACACCCATCAACATGCCT 57.986 45.000 0.00 0.00 0.00 4.75
1394 1599 4.081752 TCAATAAACACCCATCAACATGCC 60.082 41.667 0.00 0.00 0.00 4.40
1395 1600 4.864247 GTCAATAAACACCCATCAACATGC 59.136 41.667 0.00 0.00 0.00 4.06
1396 1601 6.271488 AGTCAATAAACACCCATCAACATG 57.729 37.500 0.00 0.00 0.00 3.21
1397 1602 6.916360 AAGTCAATAAACACCCATCAACAT 57.084 33.333 0.00 0.00 0.00 2.71
1398 1603 6.322456 TCAAAGTCAATAAACACCCATCAACA 59.678 34.615 0.00 0.00 0.00 3.33
1399 1604 6.744112 TCAAAGTCAATAAACACCCATCAAC 58.256 36.000 0.00 0.00 0.00 3.18
1400 1605 6.775142 TCTCAAAGTCAATAAACACCCATCAA 59.225 34.615 0.00 0.00 0.00 2.57
1401 1606 6.303054 TCTCAAAGTCAATAAACACCCATCA 58.697 36.000 0.00 0.00 0.00 3.07
1402 1607 6.431234 ACTCTCAAAGTCAATAAACACCCATC 59.569 38.462 0.00 0.00 30.02 3.51
1403 1608 6.306987 ACTCTCAAAGTCAATAAACACCCAT 58.693 36.000 0.00 0.00 30.02 4.00
1404 1609 5.690865 ACTCTCAAAGTCAATAAACACCCA 58.309 37.500 0.00 0.00 30.02 4.51
1441 1646 5.124297 CACATGTTGCATGATCTGTTAAGGA 59.876 40.000 15.03 0.00 0.00 3.36
1660 1866 5.212532 AGCAATCTGGCTCTCTTATACAG 57.787 43.478 0.00 0.00 41.05 2.74
1661 1867 5.104776 ACAAGCAATCTGGCTCTCTTATACA 60.105 40.000 0.00 0.00 45.07 2.29
1662 1868 5.363939 ACAAGCAATCTGGCTCTCTTATAC 58.636 41.667 0.00 0.00 45.07 1.47
1663 1869 5.129320 TGACAAGCAATCTGGCTCTCTTATA 59.871 40.000 0.00 0.00 45.07 0.98
1664 1870 4.080695 TGACAAGCAATCTGGCTCTCTTAT 60.081 41.667 0.00 0.00 45.07 1.73
1750 1958 6.128634 GCGTGCATCCTAGTATTACCATTTAC 60.129 42.308 0.00 0.00 0.00 2.01
1825 2040 5.048921 CCATTATTGTCATGTGGCTGAGATC 60.049 44.000 0.00 0.00 0.00 2.75
1913 2136 2.159028 GCTTCAGTTGGAGGCCTACTAG 60.159 54.545 18.18 7.97 42.44 2.57
1972 2195 0.321671 TGTCCTGTTAGCCACTCTGC 59.678 55.000 0.00 0.00 0.00 4.26
2098 2321 0.482446 TGGAGTGGCCACCAGAAAAT 59.518 50.000 32.29 12.16 43.33 1.82
2211 2446 1.135575 GCACAATCAAGTAGCAGTGGC 60.136 52.381 0.00 0.00 41.61 5.01
2247 2482 2.680974 AAAGACTGCAAGCGAGGGCA 62.681 55.000 0.00 0.00 43.41 5.36
2248 2483 1.518903 AAAAGACTGCAAGCGAGGGC 61.519 55.000 0.00 0.00 37.60 5.19
2249 2484 0.239347 CAAAAGACTGCAAGCGAGGG 59.761 55.000 0.00 0.00 37.60 4.30
2422 2663 3.552890 GCAGAGTCAAAATTGTTGTCCCC 60.553 47.826 0.00 0.00 0.00 4.81
2451 2692 6.271159 GGTGGTATCCTAATCAAAGAGGAGAT 59.729 42.308 0.00 0.00 45.03 2.75
2500 2741 2.669808 CTTCCTCGGATGCGACCTCG 62.670 65.000 4.75 0.00 43.27 4.63
2513 2754 1.517242 CTGTTGTCCTGTGCTTCCTC 58.483 55.000 0.00 0.00 0.00 3.71
2566 2807 4.379603 CGAATATCCGATACCACAGAGGAC 60.380 50.000 0.00 0.00 41.22 3.85
2608 2849 1.796459 GCAACTTTGGAATGCTGCTTG 59.204 47.619 0.00 0.00 37.12 4.01
2649 2890 2.224079 AGTCATGTTTAACTGCACTGCG 59.776 45.455 0.00 0.00 0.00 5.18
2702 2943 5.499004 TGTTCAATCAAAGGCTACCTAGT 57.501 39.130 0.00 0.00 31.13 2.57
2703 2944 8.682936 ATAATGTTCAATCAAAGGCTACCTAG 57.317 34.615 0.00 0.00 31.13 3.02
2704 2945 9.120538 GAATAATGTTCAATCAAAGGCTACCTA 57.879 33.333 0.00 0.00 31.13 3.08
2705 2946 7.615365 TGAATAATGTTCAATCAAAGGCTACCT 59.385 33.333 0.00 0.00 33.87 3.08
2742 3041 1.737236 TGGTACGAGAAATGCATGCAC 59.263 47.619 25.37 10.95 0.00 4.57
2808 3107 2.950975 TCTTGACAGTTGCAGCATTCAA 59.049 40.909 13.65 13.65 0.00 2.69
3054 3353 1.909302 AGCCGAATTCTCCTTCTCCAA 59.091 47.619 3.52 0.00 0.00 3.53
3237 3536 0.035458 AGCACACGAAGAAGGAAGGG 59.965 55.000 0.00 0.00 0.00 3.95
3243 3542 0.384725 CGCCAAAGCACACGAAGAAG 60.385 55.000 0.00 0.00 39.83 2.85
3284 3583 2.028930 AGAACCGTCCTCTTCACATCAC 60.029 50.000 0.00 0.00 0.00 3.06
3285 3584 2.248248 AGAACCGTCCTCTTCACATCA 58.752 47.619 0.00 0.00 0.00 3.07
3286 3585 2.996621 CAAGAACCGTCCTCTTCACATC 59.003 50.000 0.00 0.00 30.58 3.06
3287 3586 2.632996 TCAAGAACCGTCCTCTTCACAT 59.367 45.455 0.00 0.00 30.58 3.21
3288 3587 2.036387 TCAAGAACCGTCCTCTTCACA 58.964 47.619 0.00 0.00 30.58 3.58
3308 3607 3.487372 GTTAGCTTCCAACAAAGGAGGT 58.513 45.455 0.00 0.00 39.25 3.85
3315 3614 3.390135 CAGAGACGTTAGCTTCCAACAA 58.610 45.455 0.00 0.00 0.00 2.83
3361 3660 1.078567 GCTGCTGAAGGAGGGTCTG 60.079 63.158 0.78 0.00 33.79 3.51
3364 3663 2.604686 TCGCTGCTGAAGGAGGGT 60.605 61.111 14.09 0.00 44.58 4.34
3394 3693 4.154347 GCACAGAGGGAGCTCGGG 62.154 72.222 7.83 0.00 0.00 5.14
3499 3798 0.036010 TTGCTAGGCTTGCACTCCTC 60.036 55.000 22.86 0.00 40.40 3.71
3603 3902 1.520787 CCGGTGTCCTCGGCATAAC 60.521 63.158 0.00 0.00 41.07 1.89
3733 4032 2.960384 CTCACATGATCTCTCCTCTGCT 59.040 50.000 0.00 0.00 0.00 4.24
3769 4068 3.431486 GCCTCTCTCCATTGACGAGATTT 60.431 47.826 0.00 0.00 35.85 2.17
3847 4146 1.030488 CATGGGCCAGCTCAAGTCTG 61.030 60.000 13.78 0.00 0.00 3.51
3884 4183 2.825836 GATGCGCCCCTTGTCCAG 60.826 66.667 4.18 0.00 0.00 3.86
3958 4257 0.388294 CGAGCTCATCCATCTGCTGA 59.612 55.000 15.40 0.00 35.76 4.26
3972 4271 0.954449 TTTCGTCTCCGACTCGAGCT 60.954 55.000 13.61 0.00 44.13 4.09
4015 4314 0.025001 CGCTGTATTTTCTGGCGTCG 59.975 55.000 0.00 0.00 40.78 5.12
4077 4376 2.584418 CCAGAGCATCGACGGCAG 60.584 66.667 12.80 3.16 42.67 4.85
4147 4446 3.853307 GCACCTTCTTTTGGAATGACACG 60.853 47.826 0.00 0.00 33.01 4.49
4293 4592 2.097825 CCTTCTCATTCAGGGCAAAGG 58.902 52.381 0.00 0.00 0.00 3.11
4320 4619 1.815613 TCTCCAGAGTCTCTTCAAGCG 59.184 52.381 0.00 0.00 0.00 4.68
4423 4722 4.925646 GTCTCCAATTTCATTTCCAACTGC 59.074 41.667 0.00 0.00 0.00 4.40
4525 4824 4.040217 TCTGCTTCTTTCTCTTTGAGCTCT 59.960 41.667 16.19 0.00 0.00 4.09
4624 4923 3.006110 CCTGTTTCAAGTCATGGCATTGT 59.994 43.478 0.00 0.00 0.00 2.71
4668 4967 2.562298 TCCATTGGTTTTGGCTGATGAC 59.438 45.455 1.86 0.00 34.06 3.06
4738 5037 8.375493 TGGTTGTGATAGTTAAGAGATACCTT 57.625 34.615 0.00 0.00 0.00 3.50
4768 5068 3.403038 AGTCCTCAACTTTTCATCACCG 58.597 45.455 0.00 0.00 33.03 4.94
4798 5098 9.994432 CCAGTTACTCATCAGAAAAACATAATC 57.006 33.333 0.00 0.00 0.00 1.75
4826 5126 3.264193 TCTCCTGTACAAAGTGATGGCAT 59.736 43.478 0.00 0.00 0.00 4.40
4964 5264 2.289002 GGCGATGTCATGATTCTCAACC 59.711 50.000 0.00 0.00 0.00 3.77
5070 5370 4.870363 GCAATCTTTCTTTGCTACCACAA 58.130 39.130 1.36 0.00 44.71 3.33
5090 5390 4.650588 AGCCAAGCCATATAATTTTCTGCA 59.349 37.500 0.00 0.00 0.00 4.41
5093 5393 5.893255 TGACAGCCAAGCCATATAATTTTCT 59.107 36.000 0.00 0.00 0.00 2.52
5117 5417 9.566432 GGAAGGATTCTGTCAATCTTATTATGT 57.434 33.333 0.00 0.00 46.56 2.29
5150 5450 5.670485 TCGCATTAACTTGTCTCCATATGT 58.330 37.500 1.24 0.00 0.00 2.29
5170 5470 3.117046 GCTCTCACCTGTATAAACTCGC 58.883 50.000 0.00 0.00 0.00 5.03
5172 5472 5.582665 CCTTTGCTCTCACCTGTATAAACTC 59.417 44.000 0.00 0.00 0.00 3.01
5253 5805 8.878769 GTTGACCAAAATTGATTTTTACACAGT 58.121 29.630 0.00 0.00 37.86 3.55
5281 5835 8.511604 AACCATTTCGATAATTTCATGAGACT 57.488 30.769 0.00 0.00 0.00 3.24
5326 5880 5.183331 GGTGAGCATATAAGATACGGAGTCA 59.817 44.000 0.00 0.00 43.93 3.41
5345 5899 2.503331 TGTATGCAAGTGTTGGGTGAG 58.497 47.619 0.00 0.00 0.00 3.51
5384 5938 4.785346 ATGTGTAGGATCTCTGCCAATT 57.215 40.909 0.00 0.00 0.00 2.32
5443 5997 5.708948 TGGTGTAGTGAAATTAATGCAAGC 58.291 37.500 0.00 0.00 0.00 4.01
5487 6041 6.331061 CGAAGTAGCAATGGTCTAGTTTAGT 58.669 40.000 0.00 0.00 31.75 2.24
5533 6087 7.744087 ATACTATCTCATCTGACTCTGTGTC 57.256 40.000 3.03 3.03 45.54 3.67
5548 6102 9.924650 AACGGTATGGTTCATTTATACTATCTC 57.075 33.333 0.00 0.00 0.00 2.75
5549 6103 9.924650 GAACGGTATGGTTCATTTATACTATCT 57.075 33.333 0.88 0.00 44.44 1.98
5872 6428 1.407989 GGAAGGAACTCAGATGGCTGG 60.408 57.143 0.00 0.00 42.53 4.85
5956 6512 1.866015 ATGGTCGACCTGGATGAAGA 58.134 50.000 33.39 11.97 36.82 2.87
5965 6521 0.872388 GAAACGCAAATGGTCGACCT 59.128 50.000 33.39 17.38 36.82 3.85
5979 6535 7.923344 ACTGTTATAGAGGATGATGAAGAAACG 59.077 37.037 0.00 0.00 0.00 3.60
6007 6563 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
6008 6564 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
6009 6565 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
6010 6566 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
6011 6567 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
6012 6568 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
6013 6569 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
6014 6570 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
6015 6571 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
6016 6572 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
6017 6573 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
6018 6574 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
6019 6575 9.323985 CAAGAAGAAGAAGAAGAAGAAGAAGAA 57.676 33.333 0.00 0.00 0.00 2.52
6020 6576 8.482128 ACAAGAAGAAGAAGAAGAAGAAGAAGA 58.518 33.333 0.00 0.00 0.00 2.87
6021 6577 8.661352 ACAAGAAGAAGAAGAAGAAGAAGAAG 57.339 34.615 0.00 0.00 0.00 2.85
6022 6578 7.713073 GGACAAGAAGAAGAAGAAGAAGAAGAA 59.287 37.037 0.00 0.00 0.00 2.52
6023 6579 7.070571 AGGACAAGAAGAAGAAGAAGAAGAAGA 59.929 37.037 0.00 0.00 0.00 2.87
6024 6580 7.216494 AGGACAAGAAGAAGAAGAAGAAGAAG 58.784 38.462 0.00 0.00 0.00 2.85
6036 6592 4.213059 GCAGTCAGAAAGGACAAGAAGAAG 59.787 45.833 0.00 0.00 40.29 2.85
6106 6665 5.649831 AGAAGAATGTATTGGTTGAAGAGGC 59.350 40.000 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.