Multiple sequence alignment - TraesCS4B01G393900

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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 TraesCS4B01G393900 chr4B 100.000 3305 0 0 1 3305 668007666 668004362 0.000000e+00 6104
1 TraesCS4B01G393900 chr4B 91.168 736 53 8 2545 3270 300807737 300808470 0.000000e+00 989
2 TraesCS4B01G393900 chr4B 90.557 646 53 6 1 644 603184402 603183763 0.000000e+00 848
3 TraesCS4B01G393900 chr5A 97.200 1500 35 4 771 2266 683946333 683944837 0.000000e+00 2531
4 TraesCS4B01G393900 chr5A 83.047 814 79 24 2544 3305 149406969 149406163 0.000000e+00 684
5 TraesCS4B01G393900 chr5A 83.582 134 7 6 2383 2508 683944729 683944603 9.690000e-21 111
6 TraesCS4B01G393900 chrUn 94.299 1526 45 15 871 2386 29715855 29717348 0.000000e+00 2298
7 TraesCS4B01G393900 chr2A 91.576 736 51 6 2545 3270 1950405 1951139 0.000000e+00 1005
8 TraesCS4B01G393900 chr2A 91.440 736 52 6 2545 3270 2079741 2080475 0.000000e+00 1000
9 TraesCS4B01G393900 chr2A 86.979 791 71 14 2545 3305 116069884 116070672 0.000000e+00 861
10 TraesCS4B01G393900 chr2D 91.180 737 54 5 2544 3270 536442865 536442130 0.000000e+00 990
11 TraesCS4B01G393900 chr7A 91.168 736 54 6 2545 3270 47453390 47454124 0.000000e+00 989
12 TraesCS4B01G393900 chr7A 90.796 641 55 2 1 641 540868618 540869254 0.000000e+00 854
13 TraesCS4B01G393900 chr5B 91.168 736 54 7 2545 3270 634342213 634341479 0.000000e+00 989
14 TraesCS4B01G393900 chr5B 90.824 643 54 3 1 643 403154729 403154092 0.000000e+00 856
15 TraesCS4B01G393900 chr5B 90.698 645 55 3 1 645 614364728 614364089 0.000000e+00 854
16 TraesCS4B01G393900 chr4D 91.168 736 54 7 2545 3270 175703584 175702850 0.000000e+00 989
17 TraesCS4B01G393900 chr3B 91.168 736 54 6 2545 3270 29602593 29603327 0.000000e+00 989
18 TraesCS4B01G393900 chr1D 91.168 736 54 6 2545 3270 394834062 394833328 0.000000e+00 989
19 TraesCS4B01G393900 chr1B 91.163 645 51 3 1 644 589975621 589976260 0.000000e+00 870
20 TraesCS4B01G393900 chr2B 90.867 646 53 4 1 644 651134165 651134806 0.000000e+00 861
21 TraesCS4B01G393900 chr6B 90.683 644 56 2 1 644 679677030 679677669 0.000000e+00 854
22 TraesCS4B01G393900 chr6B 90.654 642 56 2 3 644 719752295 719751658 0.000000e+00 850
23 TraesCS4B01G393900 chr6B 90.543 645 56 3 1 644 101274254 101274894 0.000000e+00 848


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 TraesCS4B01G393900 chr4B 668004362 668007666 3304 True 6104 6104 100.000 1 3305 1 chr4B.!!$R2 3304
1 TraesCS4B01G393900 chr4B 300807737 300808470 733 False 989 989 91.168 2545 3270 1 chr4B.!!$F1 725
2 TraesCS4B01G393900 chr4B 603183763 603184402 639 True 848 848 90.557 1 644 1 chr4B.!!$R1 643
3 TraesCS4B01G393900 chr5A 683944603 683946333 1730 True 1321 2531 90.391 771 2508 2 chr5A.!!$R2 1737
4 TraesCS4B01G393900 chr5A 149406163 149406969 806 True 684 684 83.047 2544 3305 1 chr5A.!!$R1 761
5 TraesCS4B01G393900 chrUn 29715855 29717348 1493 False 2298 2298 94.299 871 2386 1 chrUn.!!$F1 1515
6 TraesCS4B01G393900 chr2A 1950405 1951139 734 False 1005 1005 91.576 2545 3270 1 chr2A.!!$F1 725
7 TraesCS4B01G393900 chr2A 2079741 2080475 734 False 1000 1000 91.440 2545 3270 1 chr2A.!!$F2 725
8 TraesCS4B01G393900 chr2A 116069884 116070672 788 False 861 861 86.979 2545 3305 1 chr2A.!!$F3 760
9 TraesCS4B01G393900 chr2D 536442130 536442865 735 True 990 990 91.180 2544 3270 1 chr2D.!!$R1 726
10 TraesCS4B01G393900 chr7A 47453390 47454124 734 False 989 989 91.168 2545 3270 1 chr7A.!!$F1 725
11 TraesCS4B01G393900 chr7A 540868618 540869254 636 False 854 854 90.796 1 641 1 chr7A.!!$F2 640
12 TraesCS4B01G393900 chr5B 634341479 634342213 734 True 989 989 91.168 2545 3270 1 chr5B.!!$R3 725
13 TraesCS4B01G393900 chr5B 403154092 403154729 637 True 856 856 90.824 1 643 1 chr5B.!!$R1 642
14 TraesCS4B01G393900 chr5B 614364089 614364728 639 True 854 854 90.698 1 645 1 chr5B.!!$R2 644
15 TraesCS4B01G393900 chr4D 175702850 175703584 734 True 989 989 91.168 2545 3270 1 chr4D.!!$R1 725
16 TraesCS4B01G393900 chr3B 29602593 29603327 734 False 989 989 91.168 2545 3270 1 chr3B.!!$F1 725
17 TraesCS4B01G393900 chr1D 394833328 394834062 734 True 989 989 91.168 2545 3270 1 chr1D.!!$R1 725
18 TraesCS4B01G393900 chr1B 589975621 589976260 639 False 870 870 91.163 1 644 1 chr1B.!!$F1 643
19 TraesCS4B01G393900 chr2B 651134165 651134806 641 False 861 861 90.867 1 644 1 chr2B.!!$F1 643
20 TraesCS4B01G393900 chr6B 679677030 679677669 639 False 854 854 90.683 1 644 1 chr6B.!!$F2 643
21 TraesCS4B01G393900 chr6B 719751658 719752295 637 True 850 850 90.654 3 644 1 chr6B.!!$R1 641
22 TraesCS4B01G393900 chr6B 101274254 101274894 640 False 848 848 90.543 1 644 1 chr6B.!!$F1 643

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
648 651 0.03831 GCTAGGGTTCCAGCCAGTTT 59.962 55.0 0.0 0.0 38.48 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2517 2544 0.033601 ACACAAGGCACAGGGAAACA 60.034 50.0 0.0 0.0 0.0 2.83 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.202348 CGCGGCTCCATCACTGATATA 59.798 52.381 0.00 0.00 0.00 0.86
74 75 2.091555 ACCAAAAGTGAAGCCCTTACCA 60.092 45.455 0.00 0.00 0.00 3.25
91 92 2.711542 ACCATTGAACGAATCAGACCC 58.288 47.619 0.00 0.00 39.77 4.46
123 124 2.126071 ACACGCCATCGAACTCCG 60.126 61.111 0.00 0.00 39.41 4.63
130 131 1.032794 CCATCGAACTCCGGATCTGA 58.967 55.000 3.57 3.38 39.14 3.27
141 142 1.987855 GGATCTGACACCCCACCGA 60.988 63.158 0.00 0.00 0.00 4.69
170 171 2.093658 ACGTCGCAGAAGGAAACCATAT 60.094 45.455 0.00 0.00 41.22 1.78
207 208 0.240945 CGAACCCAGCACATGTTTCC 59.759 55.000 0.00 0.00 0.00 3.13
215 216 2.886523 CAGCACATGTTTCCTCTTCCAA 59.113 45.455 0.00 0.00 0.00 3.53
224 225 2.762535 TCCTCTTCCAAATGTCGTCC 57.237 50.000 0.00 0.00 0.00 4.79
252 253 1.153086 ACAATCTGCATCCGCTCCC 60.153 57.895 0.00 0.00 39.64 4.30
267 268 1.856629 CTCCCGGACTACCTACCAAA 58.143 55.000 0.73 0.00 0.00 3.28
318 319 1.762460 AACGATGGAGCCCGAGGAT 60.762 57.895 0.00 0.00 0.00 3.24
340 341 1.074775 GGTCCACCACAAGGATGCA 59.925 57.895 0.00 0.00 37.52 3.96
392 393 4.482990 ACAGACTGGTTTCCAAATCCATT 58.517 39.130 7.51 0.00 30.80 3.16
395 396 4.089361 GACTGGTTTCCAAATCCATTCCT 58.911 43.478 0.00 0.00 30.80 3.36
427 428 2.028112 CCGATGGTCTTGTCAAGGAAGA 60.028 50.000 12.66 0.00 0.00 2.87
462 463 0.108662 ATTCAGCGCTGTCATCGTCA 60.109 50.000 34.70 12.25 0.00 4.35
471 472 2.158959 GTCATCGTCACCGCCGAAG 61.159 63.158 0.00 0.00 37.93 3.79
496 497 5.358298 AAGACGATGAACAGCCTAAAAAC 57.642 39.130 0.00 0.00 0.00 2.43
501 503 4.201822 CGATGAACAGCCTAAAAACCTAGC 60.202 45.833 0.00 0.00 0.00 3.42
509 511 3.455327 CCTAAAAACCTAGCCTACGAGC 58.545 50.000 0.00 0.00 0.00 5.03
514 517 0.394080 ACCTAGCCTACGAGCGAGTT 60.394 55.000 0.00 0.00 38.01 3.01
521 524 1.916000 CCTACGAGCGAGTTAAAACGG 59.084 52.381 0.00 0.00 0.00 4.44
615 618 3.521796 GGCGCTGGAAGATTGGGC 61.522 66.667 7.64 0.00 34.07 5.36
645 648 1.222936 CAGCTAGGGTTCCAGCCAG 59.777 63.158 0.00 0.00 38.48 4.85
646 649 1.229658 AGCTAGGGTTCCAGCCAGT 60.230 57.895 0.00 0.00 38.48 4.00
647 650 0.842467 AGCTAGGGTTCCAGCCAGTT 60.842 55.000 0.00 0.00 38.48 3.16
648 651 0.038310 GCTAGGGTTCCAGCCAGTTT 59.962 55.000 0.00 0.00 38.48 2.66
649 652 1.826385 CTAGGGTTCCAGCCAGTTTG 58.174 55.000 0.00 0.00 38.48 2.93
650 653 1.351017 CTAGGGTTCCAGCCAGTTTGA 59.649 52.381 0.00 0.00 38.48 2.69
651 654 0.779997 AGGGTTCCAGCCAGTTTGAT 59.220 50.000 0.00 0.00 38.48 2.57
652 655 1.177401 GGGTTCCAGCCAGTTTGATC 58.823 55.000 0.00 0.00 35.40 2.92
653 656 1.272147 GGGTTCCAGCCAGTTTGATCT 60.272 52.381 0.00 0.00 35.40 2.75
654 657 1.815003 GGTTCCAGCCAGTTTGATCTG 59.185 52.381 0.00 0.00 35.45 2.90
655 658 1.200948 GTTCCAGCCAGTTTGATCTGC 59.799 52.381 0.00 0.00 34.47 4.26
656 659 0.694771 TCCAGCCAGTTTGATCTGCT 59.305 50.000 0.00 0.00 34.47 4.24
657 660 1.093159 CCAGCCAGTTTGATCTGCTC 58.907 55.000 0.00 0.00 34.47 4.26
658 661 1.339824 CCAGCCAGTTTGATCTGCTCT 60.340 52.381 0.00 0.00 34.47 4.09
659 662 2.008329 CAGCCAGTTTGATCTGCTCTC 58.992 52.381 0.00 0.00 34.47 3.20
660 663 1.065564 AGCCAGTTTGATCTGCTCTCC 60.066 52.381 0.00 0.00 34.47 3.71
661 664 1.065564 GCCAGTTTGATCTGCTCTCCT 60.066 52.381 0.00 0.00 34.47 3.69
662 665 2.630158 CCAGTTTGATCTGCTCTCCTG 58.370 52.381 0.00 0.00 34.47 3.86
663 666 2.630158 CAGTTTGATCTGCTCTCCTGG 58.370 52.381 0.00 0.00 0.00 4.45
664 667 1.558756 AGTTTGATCTGCTCTCCTGGG 59.441 52.381 0.00 0.00 0.00 4.45
665 668 0.914644 TTTGATCTGCTCTCCTGGGG 59.085 55.000 0.00 0.00 0.00 4.96
666 669 0.252881 TTGATCTGCTCTCCTGGGGT 60.253 55.000 0.00 0.00 0.00 4.95
667 670 0.252881 TGATCTGCTCTCCTGGGGTT 60.253 55.000 0.00 0.00 0.00 4.11
668 671 0.915364 GATCTGCTCTCCTGGGGTTT 59.085 55.000 0.00 0.00 0.00 3.27
669 672 1.283321 GATCTGCTCTCCTGGGGTTTT 59.717 52.381 0.00 0.00 0.00 2.43
670 673 1.149101 TCTGCTCTCCTGGGGTTTTT 58.851 50.000 0.00 0.00 0.00 1.94
689 692 4.571375 TTTTCATCGTATTGTTCCGTCG 57.429 40.909 0.00 0.00 0.00 5.12
690 693 2.925578 TCATCGTATTGTTCCGTCGT 57.074 45.000 0.00 0.00 0.00 4.34
691 694 2.521996 TCATCGTATTGTTCCGTCGTG 58.478 47.619 0.00 0.00 0.00 4.35
692 695 2.095110 TCATCGTATTGTTCCGTCGTGT 60.095 45.455 0.00 0.00 0.00 4.49
693 696 3.126686 TCATCGTATTGTTCCGTCGTGTA 59.873 43.478 0.00 0.00 0.00 2.90
694 697 2.850321 TCGTATTGTTCCGTCGTGTAC 58.150 47.619 0.00 0.00 0.00 2.90
695 698 1.913403 CGTATTGTTCCGTCGTGTACC 59.087 52.381 0.00 0.00 0.00 3.34
696 699 2.414559 CGTATTGTTCCGTCGTGTACCT 60.415 50.000 0.00 0.00 0.00 3.08
697 700 2.825861 ATTGTTCCGTCGTGTACCTT 57.174 45.000 0.00 0.00 0.00 3.50
698 701 1.855513 TTGTTCCGTCGTGTACCTTG 58.144 50.000 0.00 0.00 0.00 3.61
699 702 0.598158 TGTTCCGTCGTGTACCTTGC 60.598 55.000 0.00 0.00 0.00 4.01
700 703 0.319297 GTTCCGTCGTGTACCTTGCT 60.319 55.000 0.00 0.00 0.00 3.91
701 704 0.390124 TTCCGTCGTGTACCTTGCTT 59.610 50.000 0.00 0.00 0.00 3.91
702 705 0.390124 TCCGTCGTGTACCTTGCTTT 59.610 50.000 0.00 0.00 0.00 3.51
703 706 1.612950 TCCGTCGTGTACCTTGCTTTA 59.387 47.619 0.00 0.00 0.00 1.85
704 707 2.231964 TCCGTCGTGTACCTTGCTTTAT 59.768 45.455 0.00 0.00 0.00 1.40
705 708 2.997986 CCGTCGTGTACCTTGCTTTATT 59.002 45.455 0.00 0.00 0.00 1.40
706 709 4.082300 TCCGTCGTGTACCTTGCTTTATTA 60.082 41.667 0.00 0.00 0.00 0.98
707 710 4.032104 CCGTCGTGTACCTTGCTTTATTAC 59.968 45.833 0.00 0.00 0.00 1.89
708 711 4.860907 CGTCGTGTACCTTGCTTTATTACT 59.139 41.667 0.00 0.00 0.00 2.24
709 712 5.004156 CGTCGTGTACCTTGCTTTATTACTC 59.996 44.000 0.00 0.00 0.00 2.59
710 713 6.098017 GTCGTGTACCTTGCTTTATTACTCT 58.902 40.000 0.00 0.00 0.00 3.24
711 714 6.034683 GTCGTGTACCTTGCTTTATTACTCTG 59.965 42.308 0.00 0.00 0.00 3.35
712 715 5.867716 CGTGTACCTTGCTTTATTACTCTGT 59.132 40.000 0.00 0.00 0.00 3.41
713 716 7.031372 CGTGTACCTTGCTTTATTACTCTGTA 58.969 38.462 0.00 0.00 0.00 2.74
714 717 7.705325 CGTGTACCTTGCTTTATTACTCTGTAT 59.295 37.037 0.00 0.00 0.00 2.29
715 718 8.818057 GTGTACCTTGCTTTATTACTCTGTATG 58.182 37.037 0.00 0.00 0.00 2.39
716 719 8.537016 TGTACCTTGCTTTATTACTCTGTATGT 58.463 33.333 0.00 0.00 0.00 2.29
719 722 9.547753 ACCTTGCTTTATTACTCTGTATGTATG 57.452 33.333 0.00 0.00 0.00 2.39
720 723 9.547753 CCTTGCTTTATTACTCTGTATGTATGT 57.452 33.333 0.00 0.00 0.00 2.29
734 737 9.932207 TCTGTATGTATGTATATAAAAACGGGG 57.068 33.333 0.00 0.00 0.00 5.73
735 738 8.550710 TGTATGTATGTATATAAAAACGGGGC 57.449 34.615 0.00 0.00 0.00 5.80
736 739 6.730960 ATGTATGTATATAAAAACGGGGCG 57.269 37.500 0.00 0.00 0.00 6.13
737 740 5.851720 TGTATGTATATAAAAACGGGGCGA 58.148 37.500 0.00 0.00 0.00 5.54
738 741 6.286758 TGTATGTATATAAAAACGGGGCGAA 58.713 36.000 0.00 0.00 0.00 4.70
739 742 6.765036 TGTATGTATATAAAAACGGGGCGAAA 59.235 34.615 0.00 0.00 0.00 3.46
740 743 5.738118 TGTATATAAAAACGGGGCGAAAG 57.262 39.130 0.00 0.00 0.00 2.62
804 807 6.938596 TGTACATGTACTCCGTATATGCTACT 59.061 38.462 30.69 0.00 39.91 2.57
868 871 6.594159 CGGGTTGAGACTTTGTATCTTGTAAT 59.406 38.462 0.00 0.00 0.00 1.89
869 872 7.762615 CGGGTTGAGACTTTGTATCTTGTAATA 59.237 37.037 0.00 0.00 0.00 0.98
1119 1132 3.901797 CTTCGAGGCCACCACCACC 62.902 68.421 5.01 0.00 0.00 4.61
1269 1282 2.344203 CGACAACCCGGAGAGAGCT 61.344 63.158 0.73 0.00 0.00 4.09
1305 1318 3.607987 GCCGTTCTCGATCGCACG 61.608 66.667 20.62 20.62 39.71 5.34
1470 1483 1.374252 GCGGGAAGAGCTCGACAAA 60.374 57.895 8.37 0.00 45.56 2.83
1488 1501 4.210331 ACAAAGACAAGGACTTGCTCAAT 58.790 39.130 11.73 0.00 44.03 2.57
1496 1509 0.445436 GACTTGCTCAATGACGGCAG 59.555 55.000 0.00 0.00 37.28 4.85
1530 1543 0.889186 GGTGCAACGTCATGGTCCTT 60.889 55.000 0.00 0.00 38.12 3.36
1599 1612 2.267006 CTGCGTGACCTCCTGCAT 59.733 61.111 0.00 0.00 36.64 3.96
1828 1847 2.805353 CGGAGCACCAAGACGACG 60.805 66.667 0.00 0.00 35.59 5.12
1829 1848 2.649034 GGAGCACCAAGACGACGA 59.351 61.111 0.00 0.00 35.97 4.20
1830 1849 1.215647 GGAGCACCAAGACGACGAT 59.784 57.895 0.00 0.00 35.97 3.73
2142 2161 3.004734 AGCATGCCGCCATTTATTCTAAC 59.995 43.478 15.66 0.00 44.04 2.34
2184 2203 5.302357 AGAAATCGCTTCCTTCATCAAAC 57.698 39.130 0.00 0.00 34.21 2.93
2306 2325 1.291877 CGCCGTCTTCTTGGTTGAGG 61.292 60.000 0.00 0.00 0.00 3.86
2307 2326 0.034896 GCCGTCTTCTTGGTTGAGGA 59.965 55.000 0.00 0.00 0.00 3.71
2308 2327 1.941668 GCCGTCTTCTTGGTTGAGGAG 60.942 57.143 0.00 0.00 0.00 3.69
2309 2328 1.618837 CCGTCTTCTTGGTTGAGGAGA 59.381 52.381 0.00 0.00 0.00 3.71
2310 2329 2.037251 CCGTCTTCTTGGTTGAGGAGAA 59.963 50.000 0.00 0.00 33.12 2.87
2311 2330 3.321497 CGTCTTCTTGGTTGAGGAGAAG 58.679 50.000 6.10 6.10 44.82 2.85
2312 2331 3.669536 GTCTTCTTGGTTGAGGAGAAGG 58.330 50.000 11.19 0.00 44.03 3.46
2313 2332 3.325135 GTCTTCTTGGTTGAGGAGAAGGA 59.675 47.826 11.19 0.00 44.03 3.36
2314 2333 3.580458 TCTTCTTGGTTGAGGAGAAGGAG 59.420 47.826 11.19 0.00 44.03 3.69
2315 2334 2.260822 TCTTGGTTGAGGAGAAGGAGG 58.739 52.381 0.00 0.00 0.00 4.30
2316 2335 2.158158 TCTTGGTTGAGGAGAAGGAGGA 60.158 50.000 0.00 0.00 0.00 3.71
2320 2339 2.169561 GGTTGAGGAGAAGGAGGATGAC 59.830 54.545 0.00 0.00 0.00 3.06
2332 2351 0.466372 AGGATGACGAGGAGATGCGA 60.466 55.000 0.00 0.00 0.00 5.10
2355 2374 3.069318 ACGGCGGAAGAGGAGGAC 61.069 66.667 13.24 0.00 0.00 3.85
2356 2375 3.068691 CGGCGGAAGAGGAGGACA 61.069 66.667 0.00 0.00 0.00 4.02
2358 2377 1.079057 GGCGGAAGAGGAGGACAAC 60.079 63.158 0.00 0.00 0.00 3.32
2359 2378 1.446272 GCGGAAGAGGAGGACAACG 60.446 63.158 0.00 0.00 0.00 4.10
2404 2423 6.249893 CACATCATGTTTAAACATCTTCGCAG 59.750 38.462 27.12 15.96 46.10 5.18
2467 2494 8.562892 AGTACATGCAATATAATTGAGCTCAAC 58.437 33.333 30.66 15.75 38.86 3.18
2480 2507 2.560105 GAGCTCAACTTCTTGCCCATTT 59.440 45.455 9.40 0.00 0.00 2.32
2481 2508 2.298163 AGCTCAACTTCTTGCCCATTTG 59.702 45.455 0.00 0.00 0.00 2.32
2482 2509 2.611224 GCTCAACTTCTTGCCCATTTGG 60.611 50.000 0.00 0.00 37.09 3.28
2483 2510 2.629617 CTCAACTTCTTGCCCATTTGGT 59.370 45.455 0.00 0.00 36.04 3.67
2484 2511 3.826157 CTCAACTTCTTGCCCATTTGGTA 59.174 43.478 0.00 0.00 36.04 3.25
2485 2512 4.415596 TCAACTTCTTGCCCATTTGGTAT 58.584 39.130 0.00 0.00 36.04 2.73
2486 2513 4.837860 TCAACTTCTTGCCCATTTGGTATT 59.162 37.500 0.00 0.00 36.04 1.89
2487 2514 6.013379 TCAACTTCTTGCCCATTTGGTATTA 58.987 36.000 0.00 0.00 36.04 0.98
2488 2515 5.914898 ACTTCTTGCCCATTTGGTATTAC 57.085 39.130 0.00 0.00 36.04 1.89
2508 2535 3.334691 ACATTGGGATGTCGTGTAAGTG 58.665 45.455 0.00 0.00 42.83 3.16
2509 2536 2.465860 TTGGGATGTCGTGTAAGTGG 57.534 50.000 0.00 0.00 0.00 4.00
2510 2537 0.611200 TGGGATGTCGTGTAAGTGGG 59.389 55.000 0.00 0.00 0.00 4.61
2511 2538 0.611714 GGGATGTCGTGTAAGTGGGT 59.388 55.000 0.00 0.00 0.00 4.51
2512 2539 1.826720 GGGATGTCGTGTAAGTGGGTA 59.173 52.381 0.00 0.00 0.00 3.69
2513 2540 2.433239 GGGATGTCGTGTAAGTGGGTAT 59.567 50.000 0.00 0.00 0.00 2.73
2514 2541 3.118519 GGGATGTCGTGTAAGTGGGTATT 60.119 47.826 0.00 0.00 0.00 1.89
2515 2542 4.117685 GGATGTCGTGTAAGTGGGTATTC 58.882 47.826 0.00 0.00 0.00 1.75
2516 2543 4.382254 GGATGTCGTGTAAGTGGGTATTCA 60.382 45.833 0.00 0.00 0.00 2.57
2517 2544 4.811969 TGTCGTGTAAGTGGGTATTCAT 57.188 40.909 0.00 0.00 0.00 2.57
2518 2545 4.500127 TGTCGTGTAAGTGGGTATTCATG 58.500 43.478 0.00 0.00 0.00 3.07
2519 2546 4.020928 TGTCGTGTAAGTGGGTATTCATGT 60.021 41.667 0.00 0.00 0.00 3.21
2520 2547 4.933400 GTCGTGTAAGTGGGTATTCATGTT 59.067 41.667 0.00 0.00 0.00 2.71
2521 2548 5.410439 GTCGTGTAAGTGGGTATTCATGTTT 59.590 40.000 0.00 0.00 0.00 2.83
2522 2549 5.640357 TCGTGTAAGTGGGTATTCATGTTTC 59.360 40.000 0.00 0.00 0.00 2.78
2523 2550 5.163794 CGTGTAAGTGGGTATTCATGTTTCC 60.164 44.000 0.00 0.00 0.00 3.13
2524 2551 5.124936 GTGTAAGTGGGTATTCATGTTTCCC 59.875 44.000 9.73 9.73 38.68 3.97
2525 2552 4.675063 AAGTGGGTATTCATGTTTCCCT 57.325 40.909 14.94 0.00 38.95 4.20
2526 2553 3.968265 AGTGGGTATTCATGTTTCCCTG 58.032 45.455 14.94 0.00 38.95 4.45
2527 2554 3.333680 AGTGGGTATTCATGTTTCCCTGT 59.666 43.478 14.94 4.40 38.95 4.00
2528 2555 3.443681 GTGGGTATTCATGTTTCCCTGTG 59.556 47.826 14.94 0.00 38.95 3.66
2529 2556 2.427095 GGGTATTCATGTTTCCCTGTGC 59.573 50.000 0.00 0.00 35.63 4.57
2530 2557 2.427095 GGTATTCATGTTTCCCTGTGCC 59.573 50.000 0.00 0.00 0.00 5.01
2531 2558 2.610438 ATTCATGTTTCCCTGTGCCT 57.390 45.000 0.00 0.00 0.00 4.75
2532 2559 2.380064 TTCATGTTTCCCTGTGCCTT 57.620 45.000 0.00 0.00 0.00 4.35
2533 2560 1.619654 TCATGTTTCCCTGTGCCTTG 58.380 50.000 0.00 0.00 0.00 3.61
2534 2561 1.133513 TCATGTTTCCCTGTGCCTTGT 60.134 47.619 0.00 0.00 0.00 3.16
2535 2562 1.000060 CATGTTTCCCTGTGCCTTGTG 60.000 52.381 0.00 0.00 0.00 3.33
2536 2563 0.033601 TGTTTCCCTGTGCCTTGTGT 60.034 50.000 0.00 0.00 0.00 3.72
2537 2564 1.111277 GTTTCCCTGTGCCTTGTGTT 58.889 50.000 0.00 0.00 0.00 3.32
2538 2565 1.480545 GTTTCCCTGTGCCTTGTGTTT 59.519 47.619 0.00 0.00 0.00 2.83
2539 2566 1.110442 TTCCCTGTGCCTTGTGTTTG 58.890 50.000 0.00 0.00 0.00 2.93
2540 2567 0.033601 TCCCTGTGCCTTGTGTTTGT 60.034 50.000 0.00 0.00 0.00 2.83
2541 2568 1.213182 TCCCTGTGCCTTGTGTTTGTA 59.787 47.619 0.00 0.00 0.00 2.41
2542 2569 1.336755 CCCTGTGCCTTGTGTTTGTAC 59.663 52.381 0.00 0.00 0.00 2.90
2566 2593 3.129113 TGCCATCAAACATCTTGATTCGG 59.871 43.478 0.00 0.00 37.06 4.30
2571 2599 3.947196 TCAAACATCTTGATTCGGATGGG 59.053 43.478 17.64 10.42 42.34 4.00
2582 2610 0.485543 TCGGATGGGACCTATGCCTA 59.514 55.000 3.70 0.00 37.19 3.93
2604 2632 7.143340 CCTACAATCTTGCATGGTGAATTATG 58.857 38.462 9.98 0.00 0.00 1.90
2617 2645 6.889198 TGGTGAATTATGAAAACCCAAAACA 58.111 32.000 0.00 0.00 0.00 2.83
2623 2651 7.575414 ATTATGAAAACCCAAAACAAAACCC 57.425 32.000 0.00 0.00 0.00 4.11
2704 2732 2.079158 CATGCAGTGTCAAGTACCCAG 58.921 52.381 0.00 0.00 0.00 4.45
2739 2767 4.018490 TCAGCACATCCAGCAATAACAAT 58.982 39.130 0.00 0.00 0.00 2.71
2742 2770 6.152492 TCAGCACATCCAGCAATAACAATAAA 59.848 34.615 0.00 0.00 0.00 1.40
2783 2811 2.736721 TCACGAGCAACATTAGCAGAAC 59.263 45.455 0.00 0.00 0.00 3.01
2793 2821 5.948992 ACATTAGCAGAACTTTCACCTTC 57.051 39.130 0.00 0.00 0.00 3.46
2839 2886 4.574599 ATTCTGCAACTTGAAACACTCC 57.425 40.909 0.00 0.00 0.00 3.85
2851 2898 3.006859 TGAAACACTCCGAGATGTCATGT 59.993 43.478 1.33 0.00 0.00 3.21
2870 2917 2.826128 TGTCCGTCTCTCTTGCAATACT 59.174 45.455 0.00 0.00 0.00 2.12
2871 2918 3.182967 GTCCGTCTCTCTTGCAATACTG 58.817 50.000 0.00 0.00 0.00 2.74
2879 2935 5.180117 TCTCTCTTGCAATACTGTTTCTTGC 59.820 40.000 0.00 12.60 44.25 4.01
2950 3006 8.378565 TCTCTTTCCATTATGTGAGTTCTTCTT 58.621 33.333 0.00 0.00 0.00 2.52
2963 3019 4.884247 AGTTCTTCTTCTTTGTCCTACCG 58.116 43.478 0.00 0.00 0.00 4.02
2965 3021 2.631062 TCTTCTTCTTTGTCCTACCGCA 59.369 45.455 0.00 0.00 0.00 5.69
2977 3033 4.161565 TGTCCTACCGCAAACAGATAATCT 59.838 41.667 0.00 0.00 0.00 2.40
2988 3044 3.300388 ACAGATAATCTCTCGGCTTGGA 58.700 45.455 0.00 0.00 29.16 3.53
3004 3060 4.262592 GGCTTGGAATGAACTTGAACCATT 60.263 41.667 0.00 0.00 33.66 3.16
3016 3072 2.722094 TGAACCATTATGAGGCACCAC 58.278 47.619 0.00 0.00 0.00 4.16
3036 3092 7.336931 GCACCACTAATTTCATCTTCTCCTTAA 59.663 37.037 0.00 0.00 0.00 1.85
3100 3156 6.544564 TCACGACTGTATAATATGGTGTCTCA 59.455 38.462 0.00 0.00 0.00 3.27
3144 3205 9.405587 GCAGTGAATAAAGTAACATTAAAGCAA 57.594 29.630 0.00 0.00 0.00 3.91
3164 3225 8.674263 AAGCAATATCTTCCTCTTCATACTTG 57.326 34.615 0.00 0.00 0.00 3.16
3265 3328 6.458210 ACCTGTCAGGAATAATTTTTGCTTG 58.542 36.000 26.18 0.00 37.67 4.01
3295 3376 4.025040 TGTCATGCAAATCTCTTCCAGT 57.975 40.909 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 2.032681 GGAGGTCCGCAAAGCTGT 59.967 61.111 0.00 0.00 0.00 4.40
74 75 1.406887 CCCGGGTCTGATTCGTTCAAT 60.407 52.381 14.18 0.00 32.78 2.57
123 124 1.961180 CTCGGTGGGGTGTCAGATCC 61.961 65.000 0.00 0.00 0.00 3.36
130 131 0.113776 TCTTAGTCTCGGTGGGGTGT 59.886 55.000 0.00 0.00 0.00 4.16
141 142 1.469308 CCTTCTGCGACGTCTTAGTCT 59.531 52.381 14.70 0.00 38.90 3.24
170 171 0.038618 CGTGGTTCGTGGATGACAGA 60.039 55.000 0.00 0.00 34.52 3.41
207 208 2.096496 GCATGGACGACATTTGGAAGAG 59.904 50.000 0.00 0.00 37.84 2.85
215 216 0.324614 TGGTCTGCATGGACGACATT 59.675 50.000 15.03 0.00 37.84 2.71
252 253 1.133790 CGGAGTTTGGTAGGTAGTCCG 59.866 57.143 0.00 0.00 45.24 4.79
262 263 4.612412 TTCGGCGCGGAGTTTGGT 62.612 61.111 17.51 0.00 0.00 3.67
304 305 0.833834 CCTGTATCCTCGGGCTCCAT 60.834 60.000 0.00 0.00 0.00 3.41
318 319 1.628340 CATCCTTGTGGTGGACCTGTA 59.372 52.381 0.00 0.00 36.30 2.74
348 349 3.443045 GCAAGGATGGCGTGGTGG 61.443 66.667 0.00 0.00 0.00 4.61
349 350 1.973281 AAGCAAGGATGGCGTGGTG 60.973 57.895 0.00 0.00 42.81 4.17
350 351 1.973281 CAAGCAAGGATGGCGTGGT 60.973 57.895 0.00 0.00 42.81 4.16
413 414 4.563580 CCTTCGGATTCTTCCTTGACAAGA 60.564 45.833 16.99 0.20 40.17 3.02
427 428 4.200092 GCTGAATAAAGACCCTTCGGATT 58.800 43.478 0.00 0.00 0.00 3.01
437 438 3.302092 CGATGACAGCGCTGAATAAAGAC 60.302 47.826 42.03 21.24 0.00 3.01
462 463 1.885163 ATCGTCTTTCCTTCGGCGGT 61.885 55.000 7.21 0.00 0.00 5.68
471 472 2.100605 AGGCTGTTCATCGTCTTTCC 57.899 50.000 0.00 0.00 0.00 3.13
472 473 5.607119 TTTTAGGCTGTTCATCGTCTTTC 57.393 39.130 0.00 0.00 0.00 2.62
496 497 1.590932 TAACTCGCTCGTAGGCTAGG 58.409 55.000 7.90 7.90 30.65 3.02
501 503 1.916000 CCGTTTTAACTCGCTCGTAGG 59.084 52.381 0.00 0.00 0.00 3.18
509 511 1.190763 CGTGTGGACCGTTTTAACTCG 59.809 52.381 0.00 0.00 0.00 4.18
514 517 1.227205 ACGCGTGTGGACCGTTTTA 60.227 52.632 12.93 0.00 0.00 1.52
547 550 3.300765 GGTCGTCGGTGGTGAGGT 61.301 66.667 0.00 0.00 0.00 3.85
595 598 2.040544 CCAATCTTCCAGCGCCGTT 61.041 57.895 2.29 0.00 0.00 4.44
615 618 1.227205 CTAGCTGCCGCCAGAAGAG 60.227 63.158 0.00 0.00 41.77 2.85
628 631 0.842467 AACTGGCTGGAACCCTAGCT 60.842 55.000 0.00 0.00 39.80 3.32
645 648 1.407989 CCCCAGGAGAGCAGATCAAAC 60.408 57.143 0.00 0.00 0.00 2.93
646 649 0.914644 CCCCAGGAGAGCAGATCAAA 59.085 55.000 0.00 0.00 0.00 2.69
647 650 0.252881 ACCCCAGGAGAGCAGATCAA 60.253 55.000 0.00 0.00 0.00 2.57
648 651 0.252881 AACCCCAGGAGAGCAGATCA 60.253 55.000 0.00 0.00 0.00 2.92
649 652 0.915364 AAACCCCAGGAGAGCAGATC 59.085 55.000 0.00 0.00 0.00 2.75
650 653 1.376649 AAAACCCCAGGAGAGCAGAT 58.623 50.000 0.00 0.00 0.00 2.90
651 654 1.149101 AAAAACCCCAGGAGAGCAGA 58.851 50.000 0.00 0.00 0.00 4.26
652 655 3.753787 AAAAACCCCAGGAGAGCAG 57.246 52.632 0.00 0.00 0.00 4.24
667 670 4.448395 ACGACGGAACAATACGATGAAAAA 59.552 37.500 0.00 0.00 0.00 1.94
668 671 3.989167 ACGACGGAACAATACGATGAAAA 59.011 39.130 0.00 0.00 0.00 2.29
669 672 3.365520 CACGACGGAACAATACGATGAAA 59.634 43.478 0.00 0.00 0.00 2.69
670 673 2.918600 CACGACGGAACAATACGATGAA 59.081 45.455 0.00 0.00 0.00 2.57
671 674 2.095110 ACACGACGGAACAATACGATGA 60.095 45.455 0.00 0.00 0.00 2.92
672 675 2.256174 ACACGACGGAACAATACGATG 58.744 47.619 0.00 0.00 0.00 3.84
673 676 2.642139 ACACGACGGAACAATACGAT 57.358 45.000 0.00 0.00 0.00 3.73
674 677 2.414029 GGTACACGACGGAACAATACGA 60.414 50.000 0.00 0.00 0.00 3.43
675 678 1.913403 GGTACACGACGGAACAATACG 59.087 52.381 0.00 0.00 0.00 3.06
676 679 3.221964 AGGTACACGACGGAACAATAC 57.778 47.619 0.00 0.00 0.00 1.89
677 680 3.577667 CAAGGTACACGACGGAACAATA 58.422 45.455 0.00 0.00 0.00 1.90
678 681 2.409975 CAAGGTACACGACGGAACAAT 58.590 47.619 0.00 0.00 0.00 2.71
679 682 1.855513 CAAGGTACACGACGGAACAA 58.144 50.000 0.00 0.00 0.00 2.83
680 683 0.598158 GCAAGGTACACGACGGAACA 60.598 55.000 0.00 0.00 0.00 3.18
681 684 0.319297 AGCAAGGTACACGACGGAAC 60.319 55.000 0.00 0.00 0.00 3.62
682 685 0.390124 AAGCAAGGTACACGACGGAA 59.610 50.000 0.00 0.00 0.00 4.30
683 686 0.390124 AAAGCAAGGTACACGACGGA 59.610 50.000 0.00 0.00 0.00 4.69
684 687 2.068837 TAAAGCAAGGTACACGACGG 57.931 50.000 0.00 0.00 0.00 4.79
685 688 4.860907 AGTAATAAAGCAAGGTACACGACG 59.139 41.667 0.00 0.00 0.00 5.12
686 689 6.034683 CAGAGTAATAAAGCAAGGTACACGAC 59.965 42.308 0.00 0.00 0.00 4.34
687 690 6.097356 CAGAGTAATAAAGCAAGGTACACGA 58.903 40.000 0.00 0.00 0.00 4.35
688 691 5.867716 ACAGAGTAATAAAGCAAGGTACACG 59.132 40.000 0.00 0.00 0.00 4.49
689 692 8.818057 CATACAGAGTAATAAAGCAAGGTACAC 58.182 37.037 0.00 0.00 0.00 2.90
690 693 8.537016 ACATACAGAGTAATAAAGCAAGGTACA 58.463 33.333 0.00 0.00 0.00 2.90
691 694 8.943909 ACATACAGAGTAATAAAGCAAGGTAC 57.056 34.615 0.00 0.00 0.00 3.34
693 696 9.547753 CATACATACAGAGTAATAAAGCAAGGT 57.452 33.333 0.00 0.00 0.00 3.50
694 697 9.547753 ACATACATACAGAGTAATAAAGCAAGG 57.452 33.333 0.00 0.00 0.00 3.61
708 711 9.932207 CCCCGTTTTTATATACATACATACAGA 57.068 33.333 0.00 0.00 0.00 3.41
709 712 8.662141 GCCCCGTTTTTATATACATACATACAG 58.338 37.037 0.00 0.00 0.00 2.74
710 713 7.331440 CGCCCCGTTTTTATATACATACATACA 59.669 37.037 0.00 0.00 0.00 2.29
711 714 7.545265 TCGCCCCGTTTTTATATACATACATAC 59.455 37.037 0.00 0.00 0.00 2.39
712 715 7.609960 TCGCCCCGTTTTTATATACATACATA 58.390 34.615 0.00 0.00 0.00 2.29
713 716 6.465948 TCGCCCCGTTTTTATATACATACAT 58.534 36.000 0.00 0.00 0.00 2.29
714 717 5.851720 TCGCCCCGTTTTTATATACATACA 58.148 37.500 0.00 0.00 0.00 2.29
715 718 6.783892 TTCGCCCCGTTTTTATATACATAC 57.216 37.500 0.00 0.00 0.00 2.39
716 719 6.073112 GCTTTCGCCCCGTTTTTATATACATA 60.073 38.462 0.00 0.00 0.00 2.29
717 720 5.278120 GCTTTCGCCCCGTTTTTATATACAT 60.278 40.000 0.00 0.00 0.00 2.29
718 721 4.035441 GCTTTCGCCCCGTTTTTATATACA 59.965 41.667 0.00 0.00 0.00 2.29
719 722 4.530388 GCTTTCGCCCCGTTTTTATATAC 58.470 43.478 0.00 0.00 0.00 1.47
720 723 4.816786 GCTTTCGCCCCGTTTTTATATA 57.183 40.909 0.00 0.00 0.00 0.86
721 724 3.703286 GCTTTCGCCCCGTTTTTATAT 57.297 42.857 0.00 0.00 0.00 0.86
758 761 9.268268 TGTACAACGATAAGATCTGTTTTTCTT 57.732 29.630 0.00 0.00 36.26 2.52
759 762 8.827177 TGTACAACGATAAGATCTGTTTTTCT 57.173 30.769 0.00 0.00 0.00 2.52
760 763 9.478019 CATGTACAACGATAAGATCTGTTTTTC 57.522 33.333 0.00 0.00 0.00 2.29
761 764 8.999431 ACATGTACAACGATAAGATCTGTTTTT 58.001 29.630 0.00 0.00 0.00 1.94
762 765 8.547967 ACATGTACAACGATAAGATCTGTTTT 57.452 30.769 0.00 0.00 0.00 2.43
763 766 9.084164 GTACATGTACAACGATAAGATCTGTTT 57.916 33.333 27.37 0.00 36.15 2.83
764 767 8.467598 AGTACATGTACAACGATAAGATCTGTT 58.532 33.333 32.02 7.55 38.48 3.16
765 768 7.997482 AGTACATGTACAACGATAAGATCTGT 58.003 34.615 32.02 7.90 38.48 3.41
766 769 7.591795 GGAGTACATGTACAACGATAAGATCTG 59.408 40.741 32.02 0.00 38.48 2.90
767 770 7.520131 CGGAGTACATGTACAACGATAAGATCT 60.520 40.741 31.52 13.56 38.67 2.75
768 771 6.577800 CGGAGTACATGTACAACGATAAGATC 59.422 42.308 31.52 19.74 38.67 2.75
769 772 6.039047 ACGGAGTACATGTACAACGATAAGAT 59.961 38.462 36.81 22.13 41.94 2.40
804 807 1.753930 TCGGACAGCCACTCGTATTA 58.246 50.000 0.00 0.00 0.00 0.98
869 872 8.749354 TGATGTGGTGAGCTATTTATCGTATAT 58.251 33.333 0.00 0.00 0.00 0.86
1269 1282 1.492319 CGAAAACGGACACGAAGCCA 61.492 55.000 0.00 0.00 44.60 4.75
1470 1483 3.406764 GTCATTGAGCAAGTCCTTGTCT 58.593 45.455 8.69 6.35 42.31 3.41
1488 1501 2.640302 GGAGAGAGCACTGCCGTCA 61.640 63.158 0.00 0.00 0.00 4.35
1496 1509 1.214062 CACCTGACGGAGAGAGCAC 59.786 63.158 0.00 0.00 0.00 4.40
1530 1543 2.360191 GGGGCTGCCAGGAAATCA 59.640 61.111 22.05 0.00 0.00 2.57
1582 1595 0.529337 CTATGCAGGAGGTCACGCAG 60.529 60.000 0.00 0.00 37.88 5.18
1704 1717 3.018019 CCCTCCATCATTGGGCCA 58.982 61.111 0.00 0.00 43.81 5.36
1809 1822 1.733399 GTCGTCTTGGTGCTCCGAC 60.733 63.158 0.00 1.83 40.71 4.79
2142 2161 1.885887 TCCGGCTTTTCATTGTTGAGG 59.114 47.619 0.00 0.00 32.27 3.86
2184 2203 2.481952 CGGTGCTCTTCTCCTTTTTCTG 59.518 50.000 0.00 0.00 0.00 3.02
2306 2325 1.953686 CTCCTCGTCATCCTCCTTCTC 59.046 57.143 0.00 0.00 0.00 2.87
2307 2326 1.566703 TCTCCTCGTCATCCTCCTTCT 59.433 52.381 0.00 0.00 0.00 2.85
2308 2327 2.060050 TCTCCTCGTCATCCTCCTTC 57.940 55.000 0.00 0.00 0.00 3.46
2309 2328 2.315176 CATCTCCTCGTCATCCTCCTT 58.685 52.381 0.00 0.00 0.00 3.36
2310 2329 1.993956 CATCTCCTCGTCATCCTCCT 58.006 55.000 0.00 0.00 0.00 3.69
2311 2330 0.316841 GCATCTCCTCGTCATCCTCC 59.683 60.000 0.00 0.00 0.00 4.30
2312 2331 0.039617 CGCATCTCCTCGTCATCCTC 60.040 60.000 0.00 0.00 0.00 3.71
2313 2332 0.466372 TCGCATCTCCTCGTCATCCT 60.466 55.000 0.00 0.00 0.00 3.24
2314 2333 0.039617 CTCGCATCTCCTCGTCATCC 60.040 60.000 0.00 0.00 0.00 3.51
2315 2334 0.039617 CCTCGCATCTCCTCGTCATC 60.040 60.000 0.00 0.00 0.00 2.92
2316 2335 2.037053 CCTCGCATCTCCTCGTCAT 58.963 57.895 0.00 0.00 0.00 3.06
2320 2339 2.279120 GTGCCTCGCATCTCCTCG 60.279 66.667 0.00 0.00 41.91 4.63
2332 2351 4.379243 CTCTTCCGCCGTGTGCCT 62.379 66.667 0.00 0.00 36.24 4.75
2355 2374 2.664851 TGCCGTCTCCTTGCGTTG 60.665 61.111 0.00 0.00 0.00 4.10
2356 2375 2.357517 CTGCCGTCTCCTTGCGTT 60.358 61.111 0.00 0.00 0.00 4.84
2440 2459 8.315391 TGAGCTCAATTATATTGCATGTACTC 57.685 34.615 15.67 0.00 0.00 2.59
2444 2463 7.578310 AGTTGAGCTCAATTATATTGCATGT 57.422 32.000 30.65 0.00 38.24 3.21
2446 2465 8.461249 AGAAGTTGAGCTCAATTATATTGCAT 57.539 30.769 30.65 10.08 38.24 3.96
2447 2466 7.870509 AGAAGTTGAGCTCAATTATATTGCA 57.129 32.000 30.65 2.63 38.24 4.08
2449 2468 7.646922 GGCAAGAAGTTGAGCTCAATTATATTG 59.353 37.037 30.65 27.57 38.24 1.90
2450 2469 7.201857 GGGCAAGAAGTTGAGCTCAATTATATT 60.202 37.037 30.65 19.30 38.24 1.28
2451 2470 6.264067 GGGCAAGAAGTTGAGCTCAATTATAT 59.736 38.462 30.65 12.99 38.24 0.86
2467 2494 5.913137 TGTAATACCAAATGGGCAAGAAG 57.087 39.130 4.17 0.00 42.05 2.85
2480 2507 4.080807 ACACGACATCCCAATGTAATACCA 60.081 41.667 0.00 0.00 46.20 3.25
2481 2508 4.448210 ACACGACATCCCAATGTAATACC 58.552 43.478 0.00 0.00 46.20 2.73
2482 2509 6.759827 ACTTACACGACATCCCAATGTAATAC 59.240 38.462 0.00 0.00 46.20 1.89
2483 2510 6.759356 CACTTACACGACATCCCAATGTAATA 59.241 38.462 0.00 0.00 46.20 0.98
2484 2511 5.584649 CACTTACACGACATCCCAATGTAAT 59.415 40.000 0.00 0.00 46.20 1.89
2485 2512 4.932799 CACTTACACGACATCCCAATGTAA 59.067 41.667 0.00 0.00 46.20 2.41
2486 2513 4.500127 CACTTACACGACATCCCAATGTA 58.500 43.478 0.00 0.00 46.20 2.29
2488 2515 2.677836 CCACTTACACGACATCCCAATG 59.322 50.000 0.00 0.00 38.93 2.82
2516 2543 1.331214 CACAAGGCACAGGGAAACAT 58.669 50.000 0.00 0.00 0.00 2.71
2517 2544 0.033601 ACACAAGGCACAGGGAAACA 60.034 50.000 0.00 0.00 0.00 2.83
2518 2545 1.111277 AACACAAGGCACAGGGAAAC 58.889 50.000 0.00 0.00 0.00 2.78
2519 2546 1.480137 CAAACACAAGGCACAGGGAAA 59.520 47.619 0.00 0.00 0.00 3.13
2520 2547 1.110442 CAAACACAAGGCACAGGGAA 58.890 50.000 0.00 0.00 0.00 3.97
2521 2548 0.033601 ACAAACACAAGGCACAGGGA 60.034 50.000 0.00 0.00 0.00 4.20
2522 2549 1.336755 GTACAAACACAAGGCACAGGG 59.663 52.381 0.00 0.00 0.00 4.45
2523 2550 1.002900 CGTACAAACACAAGGCACAGG 60.003 52.381 0.00 0.00 0.00 4.00
2524 2551 1.668751 ACGTACAAACACAAGGCACAG 59.331 47.619 0.00 0.00 0.00 3.66
2525 2552 1.398739 CACGTACAAACACAAGGCACA 59.601 47.619 0.00 0.00 0.00 4.57
2526 2553 1.858399 GCACGTACAAACACAAGGCAC 60.858 52.381 0.00 0.00 0.00 5.01
2527 2554 0.378962 GCACGTACAAACACAAGGCA 59.621 50.000 0.00 0.00 0.00 4.75
2528 2555 0.317519 GGCACGTACAAACACAAGGC 60.318 55.000 0.00 0.00 0.00 4.35
2529 2556 1.018148 TGGCACGTACAAACACAAGG 58.982 50.000 0.00 0.00 0.00 3.61
2530 2557 2.289274 TGATGGCACGTACAAACACAAG 59.711 45.455 0.00 0.00 0.00 3.16
2531 2558 2.289565 TGATGGCACGTACAAACACAA 58.710 42.857 0.00 0.00 0.00 3.33
2532 2559 1.954927 TGATGGCACGTACAAACACA 58.045 45.000 0.00 0.00 0.00 3.72
2533 2560 3.040099 GTTTGATGGCACGTACAAACAC 58.960 45.455 23.29 9.07 46.04 3.32
2534 2561 3.341857 GTTTGATGGCACGTACAAACA 57.658 42.857 23.29 11.22 46.04 2.83
2535 2562 3.341857 TGTTTGATGGCACGTACAAAC 57.658 42.857 22.33 22.33 46.57 2.93
2536 2563 3.818210 AGATGTTTGATGGCACGTACAAA 59.182 39.130 0.00 0.00 0.00 2.83
2537 2564 3.407698 AGATGTTTGATGGCACGTACAA 58.592 40.909 0.00 0.00 0.00 2.41
2538 2565 3.052455 AGATGTTTGATGGCACGTACA 57.948 42.857 0.00 0.00 0.00 2.90
2539 2566 3.435327 TCAAGATGTTTGATGGCACGTAC 59.565 43.478 0.00 0.00 0.00 3.67
2540 2567 3.669536 TCAAGATGTTTGATGGCACGTA 58.330 40.909 0.00 0.00 0.00 3.57
2541 2568 2.503331 TCAAGATGTTTGATGGCACGT 58.497 42.857 0.00 0.00 0.00 4.49
2542 2569 3.770263 ATCAAGATGTTTGATGGCACG 57.230 42.857 1.86 0.00 37.71 5.34
2566 2593 3.584848 AGATTGTAGGCATAGGTCCCATC 59.415 47.826 0.00 0.00 0.00 3.51
2571 2599 3.808728 TGCAAGATTGTAGGCATAGGTC 58.191 45.455 0.00 0.00 0.00 3.85
2582 2610 6.778834 TCATAATTCACCATGCAAGATTGT 57.221 33.333 0.00 0.00 0.00 2.71
2604 2632 2.096174 GCGGGTTTTGTTTTGGGTTTTC 59.904 45.455 0.00 0.00 0.00 2.29
2617 2645 1.621814 TCTACTACTGCTGCGGGTTTT 59.378 47.619 13.87 0.00 0.00 2.43
2623 2651 4.627467 ACTTTTGATTCTACTACTGCTGCG 59.373 41.667 0.00 0.00 0.00 5.18
2663 2691 3.687212 TGTACTTTTCATATGTGCCCACG 59.313 43.478 1.90 0.00 0.00 4.94
2704 2732 2.703416 TGTGCTGAGACCAATGATGAC 58.297 47.619 0.00 0.00 0.00 3.06
2739 2767 7.171508 GTGATGATAGTTCCGATGATGCTTTTA 59.828 37.037 0.00 0.00 0.00 1.52
2742 2770 4.993584 GTGATGATAGTTCCGATGATGCTT 59.006 41.667 0.00 0.00 0.00 3.91
2783 2811 8.637196 AGGAAAGGTAATAAAGAAGGTGAAAG 57.363 34.615 0.00 0.00 0.00 2.62
2839 2886 1.673400 AGAGACGGACATGACATCTCG 59.327 52.381 16.91 6.55 40.62 4.04
2851 2898 2.826128 ACAGTATTGCAAGAGAGACGGA 59.174 45.455 4.94 0.00 0.00 4.69
2870 2917 1.888512 GCAATCCAGAGGCAAGAAACA 59.111 47.619 0.00 0.00 0.00 2.83
2871 2918 1.135575 CGCAATCCAGAGGCAAGAAAC 60.136 52.381 0.00 0.00 0.00 2.78
2879 2935 2.202932 CCGGTCGCAATCCAGAGG 60.203 66.667 0.00 0.00 0.00 3.69
2922 2978 7.487822 AGAACTCACATAATGGAAAGAGAGA 57.512 36.000 0.00 0.00 0.00 3.10
2927 2983 8.558973 AGAAGAAGAACTCACATAATGGAAAG 57.441 34.615 0.00 0.00 0.00 2.62
2950 3006 2.103432 TCTGTTTGCGGTAGGACAAAGA 59.897 45.455 0.00 0.00 36.50 2.52
2963 3019 3.462021 AGCCGAGAGATTATCTGTTTGC 58.538 45.455 0.00 2.87 38.84 3.68
2965 3021 4.162320 TCCAAGCCGAGAGATTATCTGTTT 59.838 41.667 0.00 0.00 38.84 2.83
2977 3033 2.038426 TCAAGTTCATTCCAAGCCGAGA 59.962 45.455 0.00 0.00 0.00 4.04
2988 3044 5.716228 TGCCTCATAATGGTTCAAGTTCATT 59.284 36.000 0.00 0.00 35.57 2.57
3004 3060 6.252599 AGATGAAATTAGTGGTGCCTCATA 57.747 37.500 0.00 0.00 0.00 2.15
3144 3205 8.592809 GGATGTCAAGTATGAAGAGGAAGATAT 58.407 37.037 0.00 0.00 37.30 1.63
3164 3225 3.736720 TGATCTAGCTGCAATGGATGTC 58.263 45.455 1.02 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.