Multiple sequence alignment - TraesCS6B01G078600

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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 TraesCS6B01G078600 chr6B 100.000 2312 0 0 1 2312 55120832 55123143 0.000000e+00 4270.0
1 TraesCS6B01G078600 chr6B 88.416 587 47 8 1694 2263 54662112 54661530 0.000000e+00 688.0
2 TraesCS6B01G078600 chr6B 87.416 596 54 18 838 1418 54663118 54662529 0.000000e+00 665.0
3 TraesCS6B01G078600 chr6B 87.415 588 60 12 839 1418 54877137 54876556 0.000000e+00 664.0
4 TraesCS6B01G078600 chr6B 87.805 492 44 11 838 1315 60928250 60928739 1.550000e-156 562.0
5 TraesCS6B01G078600 chr6B 82.524 721 46 37 767 1411 55651516 55650800 5.580000e-156 560.0
6 TraesCS6B01G078600 chr6B 90.191 418 31 8 1001 1414 58057663 58057252 9.400000e-149 536.0
7 TraesCS6B01G078600 chr5D 96.318 679 15 7 1 676 50970637 50971308 0.000000e+00 1107.0
8 TraesCS6B01G078600 chr2B 94.845 679 25 8 1 676 310513111 310513782 0.000000e+00 1051.0
9 TraesCS6B01G078600 chr4A 94.006 634 31 6 45 676 632242279 632241651 0.000000e+00 953.0
10 TraesCS6B01G078600 chr4A 79.252 294 36 11 1723 1997 676923366 676923079 5.070000e-42 182.0
11 TraesCS6B01G078600 chrUn 88.889 594 50 13 838 1418 103527627 103527037 0.000000e+00 717.0
12 TraesCS6B01G078600 chrUn 79.310 261 24 12 755 986 103670312 103670571 3.080000e-34 156.0
13 TraesCS6B01G078600 chr6A 86.984 630 64 9 1694 2312 28772436 28771814 0.000000e+00 693.0
14 TraesCS6B01G078600 chr6A 84.746 649 59 21 796 1418 29081740 29082374 4.220000e-172 614.0
15 TraesCS6B01G078600 chr6A 88.613 483 42 11 838 1310 33547935 33548414 1.990000e-160 575.0
16 TraesCS6B01G078600 chr6A 87.476 511 31 10 838 1319 31264641 31264135 2.010000e-155 558.0
17 TraesCS6B01G078600 chr6A 84.922 577 49 22 779 1319 28640790 28641364 1.210000e-152 549.0
18 TraesCS6B01G078600 chr6D 88.525 488 36 15 838 1310 28992837 28992355 7.170000e-160 573.0
19 TraesCS6B01G078600 chr7A 89.948 388 33 5 996 1378 628483781 628484167 1.600000e-136 496.0
20 TraesCS6B01G078600 chr5B 88.000 400 37 9 1 397 197631915 197631524 1.620000e-126 462.0
21 TraesCS6B01G078600 chr1D 94.275 262 13 2 416 676 333332810 333332550 1.290000e-107 399.0
22 TraesCS6B01G078600 chr7D 93.156 263 15 3 416 676 410091339 410091078 1.300000e-102 383.0
23 TraesCS6B01G078600 chr3D 85.603 257 27 9 1 257 231320151 231319905 6.340000e-66 261.0
24 TraesCS6B01G078600 chr3D 97.115 104 3 0 397 500 17426564 17426667 2.360000e-40 176.0
25 TraesCS6B01G078600 chr3D 97.115 104 3 0 397 500 17428187 17428290 2.360000e-40 176.0
26 TraesCS6B01G078600 chr1B 98.077 104 2 0 397 500 54332516 54332619 5.070000e-42 182.0
27 TraesCS6B01G078600 chr2D 97.143 105 3 0 396 500 200951185 200951081 6.560000e-41 178.0
28 TraesCS6B01G078600 chr4D 93.333 45 2 1 494 537 394294793 394294749 5.330000e-07 65.8


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 TraesCS6B01G078600 chr6B 55120832 55123143 2311 False 4270.0 4270 100.000 1 2312 1 chr6B.!!$F1 2311
1 TraesCS6B01G078600 chr6B 54661530 54663118 1588 True 676.5 688 87.916 838 2263 2 chr6B.!!$R4 1425
2 TraesCS6B01G078600 chr6B 54876556 54877137 581 True 664.0 664 87.415 839 1418 1 chr6B.!!$R1 579
3 TraesCS6B01G078600 chr6B 55650800 55651516 716 True 560.0 560 82.524 767 1411 1 chr6B.!!$R2 644
4 TraesCS6B01G078600 chr5D 50970637 50971308 671 False 1107.0 1107 96.318 1 676 1 chr5D.!!$F1 675
5 TraesCS6B01G078600 chr2B 310513111 310513782 671 False 1051.0 1051 94.845 1 676 1 chr2B.!!$F1 675
6 TraesCS6B01G078600 chr4A 632241651 632242279 628 True 953.0 953 94.006 45 676 1 chr4A.!!$R1 631
7 TraesCS6B01G078600 chrUn 103527037 103527627 590 True 717.0 717 88.889 838 1418 1 chrUn.!!$R1 580
8 TraesCS6B01G078600 chr6A 28771814 28772436 622 True 693.0 693 86.984 1694 2312 1 chr6A.!!$R1 618
9 TraesCS6B01G078600 chr6A 29081740 29082374 634 False 614.0 614 84.746 796 1418 1 chr6A.!!$F2 622
10 TraesCS6B01G078600 chr6A 31264135 31264641 506 True 558.0 558 87.476 838 1319 1 chr6A.!!$R2 481
11 TraesCS6B01G078600 chr6A 28640790 28641364 574 False 549.0 549 84.922 779 1319 1 chr6A.!!$F1 540

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
758 766 0.237498 GCCCAAAACAGTAGCGACAC 59.763 55.0 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2278 2564 1.269723 GGGTGGCTGTAAAGCAAACTC 59.73 52.381 7.33 0.35 36.33 3.01 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
345 352 5.493250 TGGGGCTTAGGTTCCTAAAAGAATA 59.507 40.000 11.71 0.00 0.00 1.75
346 353 6.161526 TGGGGCTTAGGTTCCTAAAAGAATAT 59.838 38.462 11.71 0.00 0.00 1.28
410 417 9.936329 AATGCTAAAAATCCCCTTTAGAGATAA 57.064 29.630 6.53 0.00 38.21 1.75
442 449 3.288964 TCTCTAAGCTAGCTAAACGCCT 58.711 45.455 19.70 2.44 40.39 5.52
482 489 2.418197 CCTCCGTCGATTTAGCCAAAGA 60.418 50.000 0.00 0.00 0.00 2.52
618 626 9.168451 TGAATAAAATGAACTAAAGCGGATGTA 57.832 29.630 0.00 0.00 0.00 2.29
637 645 0.540365 ATAATGCTTGCCATCCCCCG 60.540 55.000 0.00 0.00 31.43 5.73
644 652 2.759560 GCCATCCCCCGCAAACAT 60.760 61.111 0.00 0.00 0.00 2.71
682 690 8.480643 AAAATGTTTTGATTTACCAAACACGA 57.519 26.923 0.00 0.00 35.95 4.35
683 691 7.692908 AATGTTTTGATTTACCAAACACGAG 57.307 32.000 0.00 0.00 35.95 4.18
684 692 5.583495 TGTTTTGATTTACCAAACACGAGG 58.417 37.500 0.00 0.00 35.95 4.63
685 693 5.125739 TGTTTTGATTTACCAAACACGAGGT 59.874 36.000 0.00 0.00 41.89 3.85
686 694 5.838531 TTTGATTTACCAAACACGAGGTT 57.161 34.783 0.00 0.00 42.98 3.50
699 707 6.655078 AACACGAGGTTTTACTAGTAGGAA 57.345 37.500 2.23 0.00 35.82 3.36
700 708 6.655078 ACACGAGGTTTTACTAGTAGGAAA 57.345 37.500 3.23 3.23 0.00 3.13
701 709 7.237209 ACACGAGGTTTTACTAGTAGGAAAT 57.763 36.000 8.41 0.00 0.00 2.17
702 710 8.353423 ACACGAGGTTTTACTAGTAGGAAATA 57.647 34.615 8.41 0.00 0.00 1.40
703 711 8.975295 ACACGAGGTTTTACTAGTAGGAAATAT 58.025 33.333 8.41 0.00 0.00 1.28
704 712 9.245962 CACGAGGTTTTACTAGTAGGAAATATG 57.754 37.037 8.41 1.09 0.00 1.78
705 713 8.419442 ACGAGGTTTTACTAGTAGGAAATATGG 58.581 37.037 8.41 2.58 0.00 2.74
706 714 8.636213 CGAGGTTTTACTAGTAGGAAATATGGA 58.364 37.037 8.41 0.00 0.00 3.41
707 715 9.984190 GAGGTTTTACTAGTAGGAAATATGGAG 57.016 37.037 8.41 0.00 0.00 3.86
708 716 9.503369 AGGTTTTACTAGTAGGAAATATGGAGT 57.497 33.333 8.41 0.00 0.00 3.85
715 723 9.571816 ACTAGTAGGAAATATGGAGTACTACAC 57.428 37.037 10.81 0.00 33.60 2.90
716 724 7.507733 AGTAGGAAATATGGAGTACTACACG 57.492 40.000 10.81 0.00 33.60 4.49
717 725 7.059156 AGTAGGAAATATGGAGTACTACACGT 58.941 38.462 10.81 0.00 33.60 4.49
718 726 6.145338 AGGAAATATGGAGTACTACACGTG 57.855 41.667 10.81 15.48 0.00 4.49
719 727 5.889853 AGGAAATATGGAGTACTACACGTGA 59.110 40.000 25.01 4.97 0.00 4.35
720 728 6.379133 AGGAAATATGGAGTACTACACGTGAA 59.621 38.462 25.01 1.24 0.00 3.18
721 729 7.037438 GGAAATATGGAGTACTACACGTGAAA 58.963 38.462 25.01 8.93 0.00 2.69
722 730 7.222224 GGAAATATGGAGTACTACACGTGAAAG 59.778 40.741 25.01 20.28 0.00 2.62
723 731 3.293311 TGGAGTACTACACGTGAAAGC 57.707 47.619 25.01 8.08 0.00 3.51
724 732 2.889045 TGGAGTACTACACGTGAAAGCT 59.111 45.455 25.01 12.81 0.00 3.74
725 733 3.243336 GGAGTACTACACGTGAAAGCTG 58.757 50.000 25.01 7.52 0.00 4.24
726 734 2.662156 GAGTACTACACGTGAAAGCTGC 59.338 50.000 25.01 12.22 0.00 5.25
727 735 2.296471 AGTACTACACGTGAAAGCTGCT 59.704 45.455 25.01 13.95 0.00 4.24
728 736 3.504906 AGTACTACACGTGAAAGCTGCTA 59.495 43.478 25.01 0.00 0.00 3.49
729 737 3.594603 ACTACACGTGAAAGCTGCTAT 57.405 42.857 25.01 0.00 0.00 2.97
730 738 3.512680 ACTACACGTGAAAGCTGCTATC 58.487 45.455 25.01 0.00 0.00 2.08
731 739 2.751166 ACACGTGAAAGCTGCTATCT 57.249 45.000 25.01 0.00 0.00 1.98
732 740 2.341257 ACACGTGAAAGCTGCTATCTG 58.659 47.619 25.01 0.00 0.00 2.90
733 741 1.061711 CACGTGAAAGCTGCTATCTGC 59.938 52.381 10.90 0.00 43.25 4.26
735 743 2.166459 ACGTGAAAGCTGCTATCTGCTA 59.834 45.455 0.90 0.00 45.11 3.49
736 744 3.181471 ACGTGAAAGCTGCTATCTGCTAT 60.181 43.478 0.90 0.00 45.11 2.97
737 745 4.038042 ACGTGAAAGCTGCTATCTGCTATA 59.962 41.667 0.90 0.00 45.11 1.31
738 746 4.620609 CGTGAAAGCTGCTATCTGCTATAG 59.379 45.833 0.90 0.00 45.11 1.31
739 747 4.928615 GTGAAAGCTGCTATCTGCTATAGG 59.071 45.833 0.90 0.00 45.11 2.57
740 748 3.608316 AAGCTGCTATCTGCTATAGGC 57.392 47.619 0.90 0.00 45.11 3.93
741 749 1.830477 AGCTGCTATCTGCTATAGGCC 59.170 52.381 0.00 0.00 44.22 5.19
742 750 1.134551 GCTGCTATCTGCTATAGGCCC 60.135 57.143 0.00 0.00 43.37 5.80
743 751 2.182827 CTGCTATCTGCTATAGGCCCA 58.817 52.381 0.00 0.00 43.37 5.36
744 752 2.568956 CTGCTATCTGCTATAGGCCCAA 59.431 50.000 0.00 0.00 43.37 4.12
745 753 2.978978 TGCTATCTGCTATAGGCCCAAA 59.021 45.455 0.00 0.00 43.37 3.28
746 754 3.394274 TGCTATCTGCTATAGGCCCAAAA 59.606 43.478 0.00 0.00 43.37 2.44
747 755 3.753797 GCTATCTGCTATAGGCCCAAAAC 59.246 47.826 0.00 0.00 40.92 2.43
748 756 3.951563 ATCTGCTATAGGCCCAAAACA 57.048 42.857 0.00 0.00 40.92 2.83
749 757 3.281727 TCTGCTATAGGCCCAAAACAG 57.718 47.619 0.00 2.28 40.92 3.16
750 758 2.576191 TCTGCTATAGGCCCAAAACAGT 59.424 45.455 0.00 0.00 40.92 3.55
751 759 3.778075 TCTGCTATAGGCCCAAAACAGTA 59.222 43.478 0.00 0.00 40.92 2.74
752 760 4.130118 CTGCTATAGGCCCAAAACAGTAG 58.870 47.826 0.00 0.00 40.92 2.57
753 761 2.879026 GCTATAGGCCCAAAACAGTAGC 59.121 50.000 0.00 0.00 34.27 3.58
754 762 2.038387 ATAGGCCCAAAACAGTAGCG 57.962 50.000 0.00 0.00 0.00 4.26
755 763 0.978151 TAGGCCCAAAACAGTAGCGA 59.022 50.000 0.00 0.00 0.00 4.93
756 764 0.605589 AGGCCCAAAACAGTAGCGAC 60.606 55.000 0.00 0.00 0.00 5.19
757 765 0.887387 GGCCCAAAACAGTAGCGACA 60.887 55.000 0.00 0.00 0.00 4.35
758 766 0.237498 GCCCAAAACAGTAGCGACAC 59.763 55.000 0.00 0.00 0.00 3.67
759 767 1.588674 CCCAAAACAGTAGCGACACA 58.411 50.000 0.00 0.00 0.00 3.72
760 768 1.263217 CCCAAAACAGTAGCGACACAC 59.737 52.381 0.00 0.00 0.00 3.82
761 769 1.263217 CCAAAACAGTAGCGACACACC 59.737 52.381 0.00 0.00 0.00 4.16
762 770 1.937223 CAAAACAGTAGCGACACACCA 59.063 47.619 0.00 0.00 0.00 4.17
763 771 1.865865 AAACAGTAGCGACACACCAG 58.134 50.000 0.00 0.00 0.00 4.00
764 772 0.750850 AACAGTAGCGACACACCAGT 59.249 50.000 0.00 0.00 0.00 4.00
841 862 4.891727 GTCACCGATCCGCGCCAT 62.892 66.667 0.00 0.00 39.11 4.40
853 899 1.153289 GCGCCATCCTGTCACATCT 60.153 57.895 0.00 0.00 0.00 2.90
924 970 2.037251 GACCTCGCAGCTATAAATCCCA 59.963 50.000 0.00 0.00 0.00 4.37
925 971 2.438021 ACCTCGCAGCTATAAATCCCAA 59.562 45.455 0.00 0.00 0.00 4.12
926 972 3.070018 CCTCGCAGCTATAAATCCCAAG 58.930 50.000 0.00 0.00 0.00 3.61
936 983 2.992817 AAATCCCAAGCACGCCACCA 62.993 55.000 0.00 0.00 0.00 4.17
954 1015 4.980805 CCGTCCACCACACCACCG 62.981 72.222 0.00 0.00 0.00 4.94
986 1047 1.727511 CCACCACCAGCAACACACAG 61.728 60.000 0.00 0.00 0.00 3.66
988 1049 2.120282 CCACCAGCAACACACAGCA 61.120 57.895 0.00 0.00 0.00 4.41
1104 1194 1.227527 CATCACCAAGCCGGCGATA 60.228 57.895 23.20 5.02 34.10 2.92
1230 1320 2.989824 ACCTACACCGAGCACGCT 60.990 61.111 0.00 0.00 38.29 5.07
1326 1426 3.559657 CTAGGCCCCGCGAATCGAG 62.560 68.421 8.23 2.18 41.67 4.04
1336 1437 2.435938 GAATCGAGCCCACGCCAA 60.436 61.111 0.00 0.00 34.57 4.52
1343 1444 0.392461 GAGCCCACGCCAACAGATTA 60.392 55.000 0.00 0.00 34.57 1.75
1346 1447 1.821216 CCCACGCCAACAGATTAGTT 58.179 50.000 0.00 0.00 0.00 2.24
1387 1490 5.029807 TGTGTAGTGTTCATGGTCTTTGA 57.970 39.130 0.00 0.00 0.00 2.69
1391 1499 5.469760 TGTAGTGTTCATGGTCTTTGATGTG 59.530 40.000 0.00 0.00 0.00 3.21
1392 1500 3.822735 AGTGTTCATGGTCTTTGATGTGG 59.177 43.478 0.00 0.00 0.00 4.17
1413 1521 2.402388 CCGCATCTCGCTGCTTTG 59.598 61.111 0.00 0.00 40.06 2.77
1414 1522 2.102438 CCGCATCTCGCTGCTTTGA 61.102 57.895 0.00 0.00 40.06 2.69
1415 1523 1.434622 CCGCATCTCGCTGCTTTGAT 61.435 55.000 0.00 0.00 40.06 2.57
1416 1524 0.315951 CGCATCTCGCTGCTTTGATG 60.316 55.000 16.42 16.42 40.06 3.07
1417 1525 0.731417 GCATCTCGCTGCTTTGATGT 59.269 50.000 19.47 0.00 39.12 3.06
1418 1526 1.531264 GCATCTCGCTGCTTTGATGTG 60.531 52.381 19.47 6.10 39.12 3.21
1419 1527 2.004733 CATCTCGCTGCTTTGATGTGA 58.995 47.619 14.04 0.00 33.65 3.58
1420 1528 2.391616 TCTCGCTGCTTTGATGTGAT 57.608 45.000 0.00 0.00 0.00 3.06
1421 1529 2.703416 TCTCGCTGCTTTGATGTGATT 58.297 42.857 0.00 0.00 0.00 2.57
1422 1530 3.076621 TCTCGCTGCTTTGATGTGATTT 58.923 40.909 0.00 0.00 0.00 2.17
1469 1681 3.849911 TGGTCTCTCGCTCTGTAATTTG 58.150 45.455 0.00 0.00 0.00 2.32
1470 1682 3.258372 TGGTCTCTCGCTCTGTAATTTGT 59.742 43.478 0.00 0.00 0.00 2.83
1471 1683 3.860536 GGTCTCTCGCTCTGTAATTTGTC 59.139 47.826 0.00 0.00 0.00 3.18
1478 1690 2.678190 GCTCTGTAATTTGTCGCCTCCT 60.678 50.000 0.00 0.00 0.00 3.69
1479 1691 3.190874 CTCTGTAATTTGTCGCCTCCTC 58.809 50.000 0.00 0.00 0.00 3.71
1486 1698 2.099141 TTGTCGCCTCCTCAAATCAG 57.901 50.000 0.00 0.00 0.00 2.90
1487 1699 0.976641 TGTCGCCTCCTCAAATCAGT 59.023 50.000 0.00 0.00 0.00 3.41
1504 1720 0.464036 AGTCGTGTTGGCTTCAGTGA 59.536 50.000 0.00 0.00 0.00 3.41
1505 1721 1.070758 AGTCGTGTTGGCTTCAGTGAT 59.929 47.619 0.00 0.00 0.00 3.06
1506 1722 1.873591 GTCGTGTTGGCTTCAGTGATT 59.126 47.619 0.00 0.00 0.00 2.57
1507 1723 2.096218 GTCGTGTTGGCTTCAGTGATTC 60.096 50.000 0.00 0.00 0.00 2.52
1508 1724 2.146342 CGTGTTGGCTTCAGTGATTCT 58.854 47.619 0.00 0.00 0.00 2.40
1509 1725 3.006430 TCGTGTTGGCTTCAGTGATTCTA 59.994 43.478 0.00 0.00 0.00 2.10
1510 1726 3.369147 CGTGTTGGCTTCAGTGATTCTAG 59.631 47.826 0.00 0.00 0.00 2.43
1511 1727 3.126000 GTGTTGGCTTCAGTGATTCTAGC 59.874 47.826 6.06 6.06 0.00 3.42
1512 1728 2.680339 GTTGGCTTCAGTGATTCTAGCC 59.320 50.000 21.82 21.82 44.17 3.93
1513 1729 2.698855 GGCTTCAGTGATTCTAGCCA 57.301 50.000 23.11 0.00 43.66 4.75
1516 1732 3.137533 GCTTCAGTGATTCTAGCCATCC 58.862 50.000 3.54 0.00 0.00 3.51
1517 1733 3.737850 CTTCAGTGATTCTAGCCATCCC 58.262 50.000 0.00 0.00 0.00 3.85
1518 1734 3.051940 TCAGTGATTCTAGCCATCCCT 57.948 47.619 0.00 0.00 0.00 4.20
1519 1735 2.702478 TCAGTGATTCTAGCCATCCCTG 59.298 50.000 7.49 7.49 29.87 4.45
1520 1736 1.419387 AGTGATTCTAGCCATCCCTGC 59.581 52.381 0.00 0.00 0.00 4.85
1521 1737 1.141657 GTGATTCTAGCCATCCCTGCA 59.858 52.381 0.00 0.00 0.00 4.41
1522 1738 2.060275 TGATTCTAGCCATCCCTGCAT 58.940 47.619 0.00 0.00 0.00 3.96
1523 1739 2.444388 TGATTCTAGCCATCCCTGCATT 59.556 45.455 0.00 0.00 0.00 3.56
1524 1740 3.117398 TGATTCTAGCCATCCCTGCATTT 60.117 43.478 0.00 0.00 0.00 2.32
1525 1741 3.386932 TTCTAGCCATCCCTGCATTTT 57.613 42.857 0.00 0.00 0.00 1.82
1526 1742 3.386932 TCTAGCCATCCCTGCATTTTT 57.613 42.857 0.00 0.00 0.00 1.94
1527 1743 3.025978 TCTAGCCATCCCTGCATTTTTG 58.974 45.455 0.00 0.00 0.00 2.44
1528 1744 1.648116 AGCCATCCCTGCATTTTTGT 58.352 45.000 0.00 0.00 0.00 2.83
1535 1751 5.511202 CCATCCCTGCATTTTTGTACTTTGT 60.511 40.000 0.00 0.00 0.00 2.83
1548 1764 5.682943 TGTACTTTGTTTCTCCAAATCCG 57.317 39.130 0.00 0.00 34.07 4.18
1557 1773 1.586154 CTCCAAATCCGCGGCTGTTT 61.586 55.000 23.51 17.90 0.00 2.83
1562 1779 1.084289 AATCCGCGGCTGTTTACTTC 58.916 50.000 23.51 0.00 0.00 3.01
1580 1797 2.574006 TCTGCTCTGCCAATTGAACT 57.426 45.000 7.12 0.00 0.00 3.01
1617 1834 1.512734 GCGCTGCCAATTTCAGACG 60.513 57.895 0.00 10.78 35.66 4.18
1638 1855 3.062763 GTGAGTGTCTGACCTGAACATG 58.937 50.000 5.17 0.00 0.00 3.21
1650 1893 6.295249 TGACCTGAACATGTGAACAAATAGA 58.705 36.000 0.00 0.00 0.00 1.98
1655 1898 7.539710 CCTGAACATGTGAACAAATAGATGTTG 59.460 37.037 0.00 0.00 43.31 3.33
1659 1902 6.489700 ACATGTGAACAAATAGATGTTGACCA 59.510 34.615 0.00 0.00 43.83 4.02
1669 1912 3.965292 GATGTTGACCATCTGATGCTG 57.035 47.619 12.17 2.46 45.50 4.41
1670 1913 3.538591 GATGTTGACCATCTGATGCTGA 58.461 45.455 12.17 0.00 45.50 4.26
1671 1914 3.421919 TGTTGACCATCTGATGCTGAA 57.578 42.857 12.17 0.00 0.00 3.02
1673 1916 5.101648 TGTTGACCATCTGATGCTGAATA 57.898 39.130 12.17 0.00 0.00 1.75
1674 1917 5.499313 TGTTGACCATCTGATGCTGAATAA 58.501 37.500 12.17 0.00 0.00 1.40
1675 1918 5.355071 TGTTGACCATCTGATGCTGAATAAC 59.645 40.000 12.17 10.42 0.00 1.89
1676 1919 4.454678 TGACCATCTGATGCTGAATAACC 58.545 43.478 12.17 0.00 0.00 2.85
1678 1921 4.458397 ACCATCTGATGCTGAATAACCTG 58.542 43.478 12.17 0.00 0.00 4.00
1680 1923 4.514441 CCATCTGATGCTGAATAACCTGAC 59.486 45.833 12.17 0.00 0.00 3.51
1682 1925 5.426689 TCTGATGCTGAATAACCTGACTT 57.573 39.130 0.00 0.00 0.00 3.01
1684 1927 6.240894 TCTGATGCTGAATAACCTGACTTTT 58.759 36.000 0.00 0.00 0.00 2.27
1685 1928 6.149973 TCTGATGCTGAATAACCTGACTTTTG 59.850 38.462 0.00 0.00 0.00 2.44
1686 1929 6.003326 TGATGCTGAATAACCTGACTTTTGA 58.997 36.000 0.00 0.00 0.00 2.69
1687 1930 5.689383 TGCTGAATAACCTGACTTTTGAC 57.311 39.130 0.00 0.00 0.00 3.18
1688 1931 4.518970 TGCTGAATAACCTGACTTTTGACC 59.481 41.667 0.00 0.00 0.00 4.02
1691 1934 5.369833 TGAATAACCTGACTTTTGACCGAA 58.630 37.500 0.00 0.00 0.00 4.30
1692 1935 6.001460 TGAATAACCTGACTTTTGACCGAAT 58.999 36.000 0.00 0.00 0.00 3.34
1698 1958 2.803956 TGACTTTTGACCGAATCGAACC 59.196 45.455 3.36 0.00 29.73 3.62
1699 1959 2.803956 GACTTTTGACCGAATCGAACCA 59.196 45.455 3.36 0.00 29.73 3.67
1713 1973 7.295201 CGAATCGAACCAAGATTTTTGACTAA 58.705 34.615 0.00 0.00 38.32 2.24
1714 1974 7.801315 CGAATCGAACCAAGATTTTTGACTAAA 59.199 33.333 0.00 0.00 38.32 1.85
1736 1997 6.461110 AATAACCTGCTTTCTGAATCATGG 57.539 37.500 0.00 0.00 0.00 3.66
1738 1999 3.087031 ACCTGCTTTCTGAATCATGGTG 58.913 45.455 0.00 0.00 0.00 4.17
1790 2065 7.614974 AGATAGATATGAGCTGAGTGCAGATTA 59.385 37.037 0.00 0.00 41.63 1.75
1843 2118 2.084546 GCAGTAGTCACAATTCCCCAC 58.915 52.381 0.00 0.00 0.00 4.61
1871 2147 1.527370 GCTCGGTAATTCCCTGCCT 59.473 57.895 0.00 0.00 0.00 4.75
1903 2180 3.426568 GCTCGCTTCAGTGTGCCC 61.427 66.667 3.52 0.00 38.62 5.36
1929 2206 6.094881 TGGATTCGAACCAAATCAAATACTCC 59.905 38.462 14.54 7.21 35.30 3.85
1935 2212 4.289245 ACCAAATCAAATACTCCCCATGG 58.711 43.478 4.14 4.14 0.00 3.66
1981 2264 3.108144 CAAAAACTTGCTGACCTGAACG 58.892 45.455 0.00 0.00 0.00 3.95
2020 2303 3.366374 GGCGAGCTGCTGACTTTTTATTT 60.366 43.478 7.01 0.00 45.43 1.40
2024 2307 5.382618 AGCTGCTGACTTTTTATTTCAGG 57.617 39.130 0.00 0.00 37.77 3.86
2026 2309 4.321527 GCTGCTGACTTTTTATTTCAGGCT 60.322 41.667 0.00 0.00 37.77 4.58
2069 2352 1.938577 CCATCTGATGCGTCTTTCTGG 59.061 52.381 12.17 5.39 0.00 3.86
2082 2365 5.334879 GCGTCTTTCTGGTTTGTGATAACAT 60.335 40.000 0.00 0.00 0.00 2.71
2093 2376 4.888038 TGTGATAACATGCAGCAGATTC 57.112 40.909 0.00 0.00 0.00 2.52
2116 2399 0.933097 CGGCTGAACATGGATTCTCG 59.067 55.000 0.00 0.00 0.00 4.04
2120 2403 2.606725 GCTGAACATGGATTCTCGACTG 59.393 50.000 0.00 0.00 0.00 3.51
2163 2446 9.798994 GAAATTTGAGTCATGATAAGAAGCAAT 57.201 29.630 0.00 0.00 0.00 3.56
2169 2452 8.618677 TGAGTCATGATAAGAAGCAATTGATTC 58.381 33.333 25.27 25.27 40.47 2.52
2212 2495 6.476243 GGTACGAAGCAACTGATTTCTTTA 57.524 37.500 0.00 0.00 0.00 1.85
2214 2497 6.961554 GGTACGAAGCAACTGATTTCTTTATG 59.038 38.462 0.00 0.00 0.00 1.90
2239 2524 6.728200 ACAACATACATATGAGCCAAATTCG 58.272 36.000 10.38 0.00 37.15 3.34
2248 2533 2.754552 TGAGCCAAATTCGGATGGAAAG 59.245 45.455 0.31 0.00 39.12 2.62
2259 2545 4.905429 TCGGATGGAAAGAAGACATGAAA 58.095 39.130 0.00 0.00 0.00 2.69
2278 2564 8.515473 CATGAAATGGCTCATACATATGTTTG 57.485 34.615 14.77 16.29 41.79 2.93
2279 2565 7.878547 TGAAATGGCTCATACATATGTTTGA 57.121 32.000 22.53 22.53 35.34 2.69
2294 2580 4.040445 TGTTTGAGTTTGCTTTACAGCC 57.960 40.909 0.00 0.00 46.74 4.85
2301 2587 2.008242 TTGCTTTACAGCCACCCATT 57.992 45.000 0.00 0.00 46.74 3.16
2304 2590 3.088532 TGCTTTACAGCCACCCATTTAG 58.911 45.455 0.00 0.00 46.74 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
288 293 4.040217 TCTGTTTTATGCAGCCACCATTTT 59.960 37.500 0.00 0.00 34.21 1.82
345 352 5.774498 TCAACATCTCTAGTATGCGACAT 57.226 39.130 7.48 0.00 0.00 3.06
346 353 5.340803 GTTCAACATCTCTAGTATGCGACA 58.659 41.667 7.48 0.00 0.00 4.35
442 449 5.758296 CGGAGGCTTAGCTTATTATGTTTCA 59.242 40.000 3.59 0.00 0.00 2.69
482 489 3.344515 GACGTTATTTTCTCCAGGCCTT 58.655 45.455 0.00 0.00 0.00 4.35
554 562 4.751098 TCGTAAACTAAAAGTGCCATCGTT 59.249 37.500 0.00 0.00 0.00 3.85
618 626 0.540365 CGGGGGATGGCAAGCATTAT 60.540 55.000 0.00 0.00 0.00 1.28
620 628 2.442643 CGGGGGATGGCAAGCATT 60.443 61.111 0.00 0.00 0.00 3.56
663 671 5.838531 ACCTCGTGTTTGGTAAATCAAAA 57.161 34.783 0.00 0.00 38.21 2.44
676 684 6.655078 TTCCTACTAGTAAAACCTCGTGTT 57.345 37.500 3.76 0.00 39.43 3.32
677 685 6.655078 TTTCCTACTAGTAAAACCTCGTGT 57.345 37.500 3.76 0.00 0.00 4.49
678 686 9.245962 CATATTTCCTACTAGTAAAACCTCGTG 57.754 37.037 3.76 0.00 0.00 4.35
679 687 8.419442 CCATATTTCCTACTAGTAAAACCTCGT 58.581 37.037 3.76 0.00 0.00 4.18
680 688 8.636213 TCCATATTTCCTACTAGTAAAACCTCG 58.364 37.037 3.76 0.00 0.00 4.63
681 689 9.984190 CTCCATATTTCCTACTAGTAAAACCTC 57.016 37.037 3.76 0.00 0.00 3.85
682 690 9.503369 ACTCCATATTTCCTACTAGTAAAACCT 57.497 33.333 3.76 0.00 0.00 3.50
689 697 9.571816 GTGTAGTACTCCATATTTCCTACTAGT 57.428 37.037 0.00 0.00 0.00 2.57
690 698 8.719648 CGTGTAGTACTCCATATTTCCTACTAG 58.280 40.741 0.00 0.00 0.00 2.57
691 699 8.213679 ACGTGTAGTACTCCATATTTCCTACTA 58.786 37.037 0.00 0.00 0.00 1.82
692 700 7.013083 CACGTGTAGTACTCCATATTTCCTACT 59.987 40.741 7.58 0.00 0.00 2.57
693 701 7.012704 TCACGTGTAGTACTCCATATTTCCTAC 59.987 40.741 16.51 0.00 0.00 3.18
694 702 7.056006 TCACGTGTAGTACTCCATATTTCCTA 58.944 38.462 16.51 0.00 0.00 2.94
695 703 5.889853 TCACGTGTAGTACTCCATATTTCCT 59.110 40.000 16.51 0.00 0.00 3.36
696 704 6.140303 TCACGTGTAGTACTCCATATTTCC 57.860 41.667 16.51 0.00 0.00 3.13
697 705 7.254017 GCTTTCACGTGTAGTACTCCATATTTC 60.254 40.741 16.51 0.00 0.00 2.17
698 706 6.534079 GCTTTCACGTGTAGTACTCCATATTT 59.466 38.462 16.51 0.00 0.00 1.40
699 707 6.040878 GCTTTCACGTGTAGTACTCCATATT 58.959 40.000 16.51 0.00 0.00 1.28
700 708 5.360144 AGCTTTCACGTGTAGTACTCCATAT 59.640 40.000 16.51 0.00 0.00 1.78
701 709 4.703575 AGCTTTCACGTGTAGTACTCCATA 59.296 41.667 16.51 0.00 0.00 2.74
702 710 3.510360 AGCTTTCACGTGTAGTACTCCAT 59.490 43.478 16.51 0.00 0.00 3.41
703 711 2.889045 AGCTTTCACGTGTAGTACTCCA 59.111 45.455 16.51 0.00 0.00 3.86
704 712 3.243336 CAGCTTTCACGTGTAGTACTCC 58.757 50.000 16.51 0.00 0.00 3.85
705 713 2.662156 GCAGCTTTCACGTGTAGTACTC 59.338 50.000 16.51 0.00 0.00 2.59
706 714 2.296471 AGCAGCTTTCACGTGTAGTACT 59.704 45.455 16.51 0.00 0.00 2.73
707 715 2.673833 AGCAGCTTTCACGTGTAGTAC 58.326 47.619 16.51 8.04 0.00 2.73
708 716 4.398358 AGATAGCAGCTTTCACGTGTAGTA 59.602 41.667 16.51 3.70 0.00 1.82
709 717 3.193691 AGATAGCAGCTTTCACGTGTAGT 59.806 43.478 16.51 3.20 0.00 2.73
710 718 3.549471 CAGATAGCAGCTTTCACGTGTAG 59.451 47.826 16.51 14.78 0.00 2.74
711 719 3.511699 CAGATAGCAGCTTTCACGTGTA 58.488 45.455 16.51 2.27 0.00 2.90
712 720 2.341257 CAGATAGCAGCTTTCACGTGT 58.659 47.619 16.51 0.00 0.00 4.49
713 721 1.061711 GCAGATAGCAGCTTTCACGTG 59.938 52.381 9.94 9.94 44.79 4.49
714 722 1.363744 GCAGATAGCAGCTTTCACGT 58.636 50.000 14.53 0.00 44.79 4.49
725 733 3.703001 TTTGGGCCTATAGCAGATAGC 57.297 47.619 4.53 0.00 46.50 2.97
726 734 4.973168 TGTTTTGGGCCTATAGCAGATAG 58.027 43.478 4.53 0.00 46.50 2.08
727 735 4.412199 ACTGTTTTGGGCCTATAGCAGATA 59.588 41.667 24.68 0.00 46.50 1.98
728 736 3.203040 ACTGTTTTGGGCCTATAGCAGAT 59.797 43.478 24.68 10.26 46.50 2.90
729 737 2.576191 ACTGTTTTGGGCCTATAGCAGA 59.424 45.455 24.68 0.00 46.50 4.26
730 738 3.004752 ACTGTTTTGGGCCTATAGCAG 57.995 47.619 18.49 18.49 46.50 4.24
731 739 3.684413 GCTACTGTTTTGGGCCTATAGCA 60.684 47.826 11.14 4.39 46.50 3.49
732 740 2.879026 GCTACTGTTTTGGGCCTATAGC 59.121 50.000 4.53 1.51 42.60 2.97
733 741 3.131396 CGCTACTGTTTTGGGCCTATAG 58.869 50.000 4.53 0.52 0.00 1.31
734 742 2.767394 TCGCTACTGTTTTGGGCCTATA 59.233 45.455 4.53 0.00 0.00 1.31
735 743 1.557832 TCGCTACTGTTTTGGGCCTAT 59.442 47.619 4.53 0.00 0.00 2.57
736 744 0.978151 TCGCTACTGTTTTGGGCCTA 59.022 50.000 4.53 0.00 0.00 3.93
737 745 0.605589 GTCGCTACTGTTTTGGGCCT 60.606 55.000 4.53 0.00 0.00 5.19
738 746 0.887387 TGTCGCTACTGTTTTGGGCC 60.887 55.000 0.00 0.00 0.00 5.80
739 747 0.237498 GTGTCGCTACTGTTTTGGGC 59.763 55.000 0.00 0.00 0.00 5.36
740 748 1.263217 GTGTGTCGCTACTGTTTTGGG 59.737 52.381 0.00 0.00 0.00 4.12
741 749 1.263217 GGTGTGTCGCTACTGTTTTGG 59.737 52.381 0.00 0.00 0.00 3.28
742 750 1.937223 TGGTGTGTCGCTACTGTTTTG 59.063 47.619 0.00 0.00 0.00 2.44
743 751 2.210116 CTGGTGTGTCGCTACTGTTTT 58.790 47.619 0.00 0.00 0.00 2.43
744 752 1.138266 ACTGGTGTGTCGCTACTGTTT 59.862 47.619 0.00 0.00 0.00 2.83
745 753 0.750850 ACTGGTGTGTCGCTACTGTT 59.249 50.000 0.00 0.00 0.00 3.16
746 754 0.032130 CACTGGTGTGTCGCTACTGT 59.968 55.000 0.00 0.00 39.24 3.55
747 755 0.667487 CCACTGGTGTGTCGCTACTG 60.667 60.000 0.00 0.00 42.34 2.74
748 756 1.666011 CCACTGGTGTGTCGCTACT 59.334 57.895 0.00 0.00 42.34 2.57
749 757 2.027625 GCCACTGGTGTGTCGCTAC 61.028 63.158 0.00 0.00 42.34 3.58
750 758 2.342279 GCCACTGGTGTGTCGCTA 59.658 61.111 0.00 0.00 42.34 4.26
751 759 4.969196 CGCCACTGGTGTGTCGCT 62.969 66.667 0.00 0.00 38.67 4.93
759 767 4.299796 AATTGCCCCGCCACTGGT 62.300 61.111 0.00 0.00 0.00 4.00
760 768 3.451894 GAATTGCCCCGCCACTGG 61.452 66.667 0.00 0.00 0.00 4.00
761 769 3.814268 CGAATTGCCCCGCCACTG 61.814 66.667 0.00 0.00 0.00 3.66
762 770 4.344865 ACGAATTGCCCCGCCACT 62.345 61.111 0.00 0.00 0.00 4.00
763 771 4.114997 CACGAATTGCCCCGCCAC 62.115 66.667 0.00 0.00 0.00 5.01
764 772 4.337177 TCACGAATTGCCCCGCCA 62.337 61.111 0.00 0.00 0.00 5.69
765 773 3.508840 CTCACGAATTGCCCCGCC 61.509 66.667 0.00 0.00 0.00 6.13
775 783 3.869065 AGGAGTTGTGTTTTCTCACGAA 58.131 40.909 0.00 0.00 40.74 3.85
809 830 4.436998 GACGTGGAGTGGAGCGGG 62.437 72.222 0.00 0.00 0.00 6.13
810 831 3.680786 TGACGTGGAGTGGAGCGG 61.681 66.667 0.00 0.00 0.00 5.52
811 832 2.430921 GTGACGTGGAGTGGAGCG 60.431 66.667 0.00 0.00 0.00 5.03
812 833 2.048127 GGTGACGTGGAGTGGAGC 60.048 66.667 0.00 0.00 0.00 4.70
936 983 3.868985 GGTGGTGTGGTGGACGGT 61.869 66.667 0.00 0.00 0.00 4.83
966 1027 2.832661 TGTGTTGCTGGTGGTGGC 60.833 61.111 0.00 0.00 0.00 5.01
986 1047 1.427020 GACATCTTCGCTTGGCTGC 59.573 57.895 0.00 0.00 0.00 5.25
988 1049 4.192000 CGACATCTTCGCTTGGCT 57.808 55.556 0.00 0.00 41.87 4.75
1059 1149 2.319136 TGTTGTCACGTAGCACCTTT 57.681 45.000 0.00 0.00 0.00 3.11
1068 1158 1.302511 GCCCTGGATGTTGTCACGT 60.303 57.895 0.00 0.00 0.00 4.49
1071 1161 0.697658 TGATGCCCTGGATGTTGTCA 59.302 50.000 0.00 0.00 0.00 3.58
1326 1426 0.676782 ACTAATCTGTTGGCGTGGGC 60.677 55.000 0.00 0.00 38.90 5.36
1330 1430 1.806542 CAGCAACTAATCTGTTGGCGT 59.193 47.619 9.04 0.00 45.19 5.68
1336 1437 4.404073 AGCTAGCTACAGCAACTAATCTGT 59.596 41.667 17.69 0.00 44.35 3.41
1343 1444 3.034635 ACCATAGCTAGCTACAGCAACT 58.965 45.455 26.41 6.27 44.35 3.16
1346 1447 2.766263 ACAACCATAGCTAGCTACAGCA 59.234 45.455 26.41 6.60 44.35 4.41
1387 1490 2.124570 GAGATGCGGCCACCACAT 60.125 61.111 2.24 0.00 0.00 3.21
1411 1519 8.849168 AGTAACATCTGACAAAAATCACATCAA 58.151 29.630 0.00 0.00 0.00 2.57
1444 1656 1.846007 ACAGAGCGAGAGACCAATCT 58.154 50.000 0.00 0.00 38.15 2.40
1446 1658 4.744795 AATTACAGAGCGAGAGACCAAT 57.255 40.909 0.00 0.00 0.00 3.16
1449 1661 3.851098 ACAAATTACAGAGCGAGAGACC 58.149 45.455 0.00 0.00 0.00 3.85
1469 1681 1.646189 GACTGATTTGAGGAGGCGAC 58.354 55.000 0.00 0.00 0.00 5.19
1470 1682 0.173481 CGACTGATTTGAGGAGGCGA 59.827 55.000 0.00 0.00 40.90 5.54
1471 1683 0.108615 ACGACTGATTTGAGGAGGCG 60.109 55.000 0.00 0.00 44.13 5.52
1478 1690 2.254546 AGCCAACACGACTGATTTGA 57.745 45.000 0.00 0.00 0.00 2.69
1479 1691 2.290367 TGAAGCCAACACGACTGATTTG 59.710 45.455 0.00 0.00 0.00 2.32
1486 1698 1.512926 ATCACTGAAGCCAACACGAC 58.487 50.000 0.00 0.00 0.00 4.34
1487 1699 2.143122 GAATCACTGAAGCCAACACGA 58.857 47.619 0.00 0.00 0.00 4.35
1504 1720 3.607490 AAATGCAGGGATGGCTAGAAT 57.393 42.857 0.00 0.00 0.00 2.40
1505 1721 3.386932 AAAATGCAGGGATGGCTAGAA 57.613 42.857 0.00 0.00 0.00 2.10
1506 1722 3.025978 CAAAAATGCAGGGATGGCTAGA 58.974 45.455 0.00 0.00 0.00 2.43
1507 1723 2.762327 ACAAAAATGCAGGGATGGCTAG 59.238 45.455 0.00 0.00 0.00 3.42
1508 1724 2.818921 ACAAAAATGCAGGGATGGCTA 58.181 42.857 0.00 0.00 0.00 3.93
1509 1725 1.648116 ACAAAAATGCAGGGATGGCT 58.352 45.000 0.00 0.00 0.00 4.75
1510 1726 2.497273 AGTACAAAAATGCAGGGATGGC 59.503 45.455 0.00 0.00 0.00 4.40
1511 1727 4.806640 AAGTACAAAAATGCAGGGATGG 57.193 40.909 0.00 0.00 0.00 3.51
1512 1728 5.540911 ACAAAGTACAAAAATGCAGGGATG 58.459 37.500 0.00 0.00 0.00 3.51
1513 1729 5.806654 ACAAAGTACAAAAATGCAGGGAT 57.193 34.783 0.00 0.00 0.00 3.85
1516 1732 6.200854 GGAGAAACAAAGTACAAAAATGCAGG 59.799 38.462 0.00 0.00 0.00 4.85
1517 1733 6.756074 TGGAGAAACAAAGTACAAAAATGCAG 59.244 34.615 0.00 0.00 0.00 4.41
1518 1734 6.634805 TGGAGAAACAAAGTACAAAAATGCA 58.365 32.000 0.00 0.00 0.00 3.96
1519 1735 7.532682 TTGGAGAAACAAAGTACAAAAATGC 57.467 32.000 0.00 0.00 0.00 3.56
1521 1737 9.325198 GGATTTGGAGAAACAAAGTACAAAAAT 57.675 29.630 0.00 0.00 42.91 1.82
1522 1738 7.489757 CGGATTTGGAGAAACAAAGTACAAAAA 59.510 33.333 0.00 0.00 42.91 1.94
1523 1739 6.975772 CGGATTTGGAGAAACAAAGTACAAAA 59.024 34.615 0.00 0.00 42.91 2.44
1524 1740 6.500041 CGGATTTGGAGAAACAAAGTACAAA 58.500 36.000 0.00 0.00 42.91 2.83
1525 1741 5.506649 GCGGATTTGGAGAAACAAAGTACAA 60.507 40.000 0.00 0.00 42.91 2.41
1526 1742 4.023536 GCGGATTTGGAGAAACAAAGTACA 60.024 41.667 0.00 0.00 42.91 2.90
1527 1743 4.473199 GCGGATTTGGAGAAACAAAGTAC 58.527 43.478 0.00 0.00 42.91 2.73
1528 1744 3.187637 CGCGGATTTGGAGAAACAAAGTA 59.812 43.478 0.00 0.00 42.91 2.24
1535 1751 1.002624 AGCCGCGGATTTGGAGAAA 60.003 52.632 33.48 0.00 0.00 2.52
1548 1764 0.444260 GAGCAGAAGTAAACAGCCGC 59.556 55.000 0.00 0.00 0.00 6.53
1557 1773 3.701205 TCAATTGGCAGAGCAGAAGTA 57.299 42.857 5.42 0.00 0.00 2.24
1562 1779 3.755378 ACTTAGTTCAATTGGCAGAGCAG 59.245 43.478 5.42 0.00 0.00 4.24
1580 1797 4.103357 GCGCGTCTCTTATCTGAAACTTA 58.897 43.478 8.43 0.00 0.00 2.24
1598 1815 1.512734 GTCTGAAATTGGCAGCGCG 60.513 57.895 0.00 0.00 33.45 6.86
1617 1834 2.890808 TGTTCAGGTCAGACACTCAC 57.109 50.000 2.17 0.00 0.00 3.51
1650 1893 3.639672 TCAGCATCAGATGGTCAACAT 57.360 42.857 12.37 0.00 44.18 2.71
1655 1898 4.514441 CAGGTTATTCAGCATCAGATGGTC 59.486 45.833 12.37 0.46 39.29 4.02
1659 1902 5.627182 AGTCAGGTTATTCAGCATCAGAT 57.373 39.130 0.00 0.00 0.00 2.90
1669 1912 5.934935 TTCGGTCAAAAGTCAGGTTATTC 57.065 39.130 0.00 0.00 0.00 1.75
1670 1913 5.121768 CGATTCGGTCAAAAGTCAGGTTATT 59.878 40.000 0.00 0.00 0.00 1.40
1671 1914 4.630069 CGATTCGGTCAAAAGTCAGGTTAT 59.370 41.667 0.00 0.00 0.00 1.89
1673 1916 2.806244 CGATTCGGTCAAAAGTCAGGTT 59.194 45.455 0.00 0.00 0.00 3.50
1674 1917 2.036733 TCGATTCGGTCAAAAGTCAGGT 59.963 45.455 6.18 0.00 0.00 4.00
1675 1918 2.683968 TCGATTCGGTCAAAAGTCAGG 58.316 47.619 6.18 0.00 0.00 3.86
1676 1919 3.120649 GGTTCGATTCGGTCAAAAGTCAG 60.121 47.826 6.18 0.00 0.00 3.51
1678 1921 2.803956 TGGTTCGATTCGGTCAAAAGTC 59.196 45.455 6.18 0.00 0.00 3.01
1680 1923 3.496884 TCTTGGTTCGATTCGGTCAAAAG 59.503 43.478 6.18 4.98 0.00 2.27
1682 1925 3.114668 TCTTGGTTCGATTCGGTCAAA 57.885 42.857 6.18 0.00 0.00 2.69
1684 1927 3.328382 AATCTTGGTTCGATTCGGTCA 57.672 42.857 6.18 0.00 0.00 4.02
1685 1928 4.680171 AAAATCTTGGTTCGATTCGGTC 57.320 40.909 6.18 0.00 31.12 4.79
1686 1929 4.517453 TCAAAAATCTTGGTTCGATTCGGT 59.483 37.500 6.18 0.00 31.12 4.69
1687 1930 4.851558 GTCAAAAATCTTGGTTCGATTCGG 59.148 41.667 6.18 0.00 31.12 4.30
1688 1931 5.689819 AGTCAAAAATCTTGGTTCGATTCG 58.310 37.500 0.00 0.00 31.12 3.34
1692 1935 9.887406 GTTATTTAGTCAAAAATCTTGGTTCGA 57.113 29.630 0.00 0.00 31.63 3.71
1698 1958 9.696917 AAGCAGGTTATTTAGTCAAAAATCTTG 57.303 29.630 0.00 0.00 31.63 3.02
1713 1973 5.954150 ACCATGATTCAGAAAGCAGGTTATT 59.046 36.000 0.00 0.00 33.62 1.40
1714 1974 5.359009 CACCATGATTCAGAAAGCAGGTTAT 59.641 40.000 0.00 0.00 33.62 1.89
1720 1980 4.290711 TCTCACCATGATTCAGAAAGCA 57.709 40.909 0.00 0.00 34.83 3.91
1736 1997 1.731720 AGAAATCGGCTGCTTCTCAC 58.268 50.000 0.00 0.00 0.00 3.51
1738 1999 3.496155 CAAAAGAAATCGGCTGCTTCTC 58.504 45.455 9.40 0.00 0.00 2.87
1790 2065 2.031682 GCAACTGACTGCAGACGAATTT 60.032 45.455 23.35 3.22 45.17 1.82
1843 2118 2.279582 ATTACCGAGCGAGACAACAG 57.720 50.000 0.00 0.00 0.00 3.16
1871 2147 2.092968 AGCGAGCACCATTAGATTTGGA 60.093 45.455 0.00 0.00 37.69 3.53
1903 2180 7.088589 AGTATTTGATTTGGTTCGAATCCAG 57.911 36.000 5.84 0.00 34.34 3.86
1929 2206 2.292828 CCCAATTAGTAGCCCATGGG 57.707 55.000 27.87 27.87 41.38 4.00
1935 2212 4.081087 TGTCAAGAGTCCCAATTAGTAGCC 60.081 45.833 0.00 0.00 0.00 3.93
1981 2264 2.095969 TCGCCGTCATCACAATTCAAAC 60.096 45.455 0.00 0.00 0.00 2.93
2020 2303 5.393866 ACTCCCTATTTTCAAAAAGCCTGA 58.606 37.500 0.00 0.00 0.00 3.86
2024 2307 7.759886 GGTCAATACTCCCTATTTTCAAAAAGC 59.240 37.037 0.00 0.00 0.00 3.51
2026 2309 8.713708 TGGTCAATACTCCCTATTTTCAAAAA 57.286 30.769 0.00 0.00 0.00 1.94
2069 2352 4.424061 TCTGCTGCATGTTATCACAAAC 57.576 40.909 1.31 0.00 36.16 2.93
2116 2399 4.585879 TCAAATAGTTGGGTTAGGCAGTC 58.414 43.478 2.65 0.00 35.29 3.51
2120 2403 7.382898 TCAAATTTCAAATAGTTGGGTTAGGC 58.617 34.615 2.65 0.00 35.29 3.93
2163 2446 9.345517 CGCATAAAGAAAAAGAGAATGAATCAA 57.654 29.630 0.00 0.00 0.00 2.57
2169 2452 6.682863 CGTACCGCATAAAGAAAAAGAGAATG 59.317 38.462 0.00 0.00 0.00 2.67
2212 2495 7.828508 ATTTGGCTCATATGTATGTTGTCAT 57.171 32.000 1.90 0.00 38.00 3.06
2214 2497 6.852853 CGAATTTGGCTCATATGTATGTTGTC 59.147 38.462 1.90 0.00 35.26 3.18
2239 2524 5.680665 GCCATTTCATGTCTTCTTTCCATCC 60.681 44.000 0.00 0.00 0.00 3.51
2248 2533 6.630444 ATGTATGAGCCATTTCATGTCTTC 57.370 37.500 0.00 0.00 38.25 2.87
2259 2545 7.682741 GCAAACTCAAACATATGTATGAGCCAT 60.683 37.037 9.21 0.00 42.34 4.40
2268 2554 6.863126 GCTGTAAAGCAAACTCAAACATATGT 59.137 34.615 1.41 1.41 34.41 2.29
2269 2555 6.308766 GGCTGTAAAGCAAACTCAAACATATG 59.691 38.462 7.33 0.00 36.33 1.78
2270 2556 6.015519 TGGCTGTAAAGCAAACTCAAACATAT 60.016 34.615 7.33 0.00 36.33 1.78
2271 2557 5.300539 TGGCTGTAAAGCAAACTCAAACATA 59.699 36.000 7.33 0.00 36.33 2.29
2272 2558 4.099266 TGGCTGTAAAGCAAACTCAAACAT 59.901 37.500 7.33 0.00 36.33 2.71
2273 2559 3.445450 TGGCTGTAAAGCAAACTCAAACA 59.555 39.130 7.33 0.00 36.33 2.83
2274 2560 3.796717 GTGGCTGTAAAGCAAACTCAAAC 59.203 43.478 7.33 0.00 36.33 2.93
2275 2561 3.181480 GGTGGCTGTAAAGCAAACTCAAA 60.181 43.478 7.33 0.00 36.33 2.69
2276 2562 2.360801 GGTGGCTGTAAAGCAAACTCAA 59.639 45.455 7.33 0.00 36.33 3.02
2277 2563 1.953686 GGTGGCTGTAAAGCAAACTCA 59.046 47.619 7.33 0.00 36.33 3.41
2278 2564 1.269723 GGGTGGCTGTAAAGCAAACTC 59.730 52.381 7.33 0.35 36.33 3.01
2279 2565 1.328279 GGGTGGCTGTAAAGCAAACT 58.672 50.000 7.33 0.00 36.33 2.66


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

AutoCloner maintained by Alex Coulton.