Multiple sequence alignment - TraesCS3B01G244500

Loading Multiple Alignment...

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 TraesCS3B01G244500 chr3B 100.000 3756 0 0 1 3756 387182430 387186185 0.000000e+00 6937.0
1 TraesCS3B01G244500 chr3D 94.390 2941 78 23 859 3741 293609613 293612524 0.000000e+00 4436.0
2 TraesCS3B01G244500 chr3D 92.716 659 46 2 1 657 293608964 293609622 0.000000e+00 950.0
3 TraesCS3B01G244500 chr3D 86.207 203 18 7 658 852 587551290 587551090 1.060000e-50 211.0
4 TraesCS3B01G244500 chr6A 86.792 212 18 7 658 860 86280008 86279798 1.050000e-55 228.0
5 TraesCS3B01G244500 chr4A 86.765 204 18 5 657 852 609797875 609798077 6.320000e-53 219.0
6 TraesCS3B01G244500 chr4A 80.571 175 33 1 1096 1270 488249117 488249290 2.350000e-27 134.0
7 TraesCS3B01G244500 chr4A 73.498 283 60 13 1131 1409 478209783 478210054 3.990000e-15 93.5
8 TraesCS3B01G244500 chr2A 85.581 215 21 9 655 860 210465100 210465313 2.270000e-52 217.0
9 TraesCS3B01G244500 chr2A 85.024 207 23 6 658 857 757966248 757966453 1.770000e-48 204.0
10 TraesCS3B01G244500 chr7A 85.507 207 20 6 658 855 632633941 632633736 1.370000e-49 207.0
11 TraesCS3B01G244500 chr6B 84.977 213 22 7 657 860 506027909 506027698 1.370000e-49 207.0
12 TraesCS3B01G244500 chr6B 84.270 89 13 1 173 261 673855551 673855464 6.680000e-13 86.1
13 TraesCS3B01G244500 chr2B 86.070 201 19 4 659 851 53663400 53663599 1.370000e-49 207.0
14 TraesCS3B01G244500 chr2B 84.146 82 13 0 173 254 614412672 614412591 3.110000e-11 80.5
15 TraesCS3B01G244500 chr2B 84.416 77 12 0 173 249 614307244 614307168 4.020000e-10 76.8
16 TraesCS3B01G244500 chrUn 85.096 208 22 6 658 857 74669686 74669480 1.770000e-48 204.0
17 TraesCS3B01G244500 chr5D 84.768 151 23 0 1117 1267 58677822 58677972 6.500000e-33 152.0
18 TraesCS3B01G244500 chr5D 85.714 112 16 0 1117 1228 58947094 58947205 6.590000e-23 119.0
19 TraesCS3B01G244500 chr5D 80.132 151 27 3 1117 1266 58659227 58659375 3.970000e-20 110.0
20 TraesCS3B01G244500 chr5B 82.877 146 25 0 1121 1266 63632076 63632221 8.470000e-27 132.0
21 TraesCS3B01G244500 chr5B 80.537 149 27 2 1120 1267 72631215 72631068 3.070000e-21 113.0
22 TraesCS3B01G244500 chr4D 79.188 197 35 4 1080 1276 93612610 93612420 8.470000e-27 132.0
23 TraesCS3B01G244500 chr4D 85.263 95 14 0 1134 1228 97962210 97962116 8.590000e-17 99.0
24 TraesCS3B01G244500 chr4B 86.316 95 13 0 1134 1228 139548990 139548896 1.850000e-18 104.0
25 TraesCS3B01G244500 chr3A 81.102 127 24 0 129 255 710799004 710798878 6.640000e-18 102.0
26 TraesCS3B01G244500 chr6D 77.632 152 32 2 1120 1270 380576959 380576809 1.440000e-14 91.6
27 TraesCS3B01G244500 chr7B 85.366 82 12 0 173 254 242667035 242666954 6.680000e-13 86.1
28 TraesCS3B01G244500 chr1B 85.366 82 12 0 173 254 11863598 11863517 6.680000e-13 86.1


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 TraesCS3B01G244500 chr3B 387182430 387186185 3755 False 6937 6937 100.000 1 3756 1 chr3B.!!$F1 3755
1 TraesCS3B01G244500 chr3D 293608964 293612524 3560 False 2693 4436 93.553 1 3741 2 chr3D.!!$F1 3740

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
716 719 0.038343 GCTCCCGTGTACGTGGTTTA 60.038 55.0 0.0 0.0 37.74 2.01 F
762 765 0.041982 GCCCCACCCCCTTAAAATCA 59.958 55.0 0.0 0.0 0.00 2.57 F
852 855 0.185901 TGGAAAGGAAGCAGGCAAGT 59.814 50.0 0.0 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2530 2539 0.248565 GCTGTGCTCTCTCCATGACA 59.751 55.000 0.0 0.0 0.00 3.58 R
2534 2543 1.207570 CAGAAGCTGTGCTCTCTCCAT 59.792 52.381 0.0 0.0 38.25 3.41 R
2804 2813 1.501169 AGCAAAAGAAACGGCAATGC 58.499 45.000 0.0 0.0 0.00 3.56 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
20 21 2.462723 GTCCTCTAGGCAGAAGAACCT 58.537 52.381 0.00 0.00 40.24 3.50
31 32 4.498345 GGCAGAAGAACCTGAGAGTATACG 60.498 50.000 0.00 0.00 36.29 3.06
42 43 6.608002 ACCTGAGAGTATACGGATTTTCTTCT 59.392 38.462 0.00 0.00 0.00 2.85
43 44 7.142680 CCTGAGAGTATACGGATTTTCTTCTC 58.857 42.308 0.00 2.12 0.00 2.87
145 146 3.094062 ATGTGGACCCTGGCGATCG 62.094 63.158 11.69 11.69 0.00 3.69
214 215 4.394300 CCACATCATCCAAGTCTTCTTCAC 59.606 45.833 0.00 0.00 0.00 3.18
234 235 3.065371 CACGCAACCCTAATTCCTTCATC 59.935 47.826 0.00 0.00 0.00 2.92
237 238 4.438744 CGCAACCCTAATTCCTTCATCAAC 60.439 45.833 0.00 0.00 0.00 3.18
246 247 2.616960 TCCTTCATCAACGATTCCACG 58.383 47.619 0.00 0.00 39.31 4.94
258 259 1.719780 GATTCCACGTCGTTGACTGTC 59.280 52.381 0.00 0.00 0.00 3.51
259 260 0.456628 TTCCACGTCGTTGACTGTCA 59.543 50.000 6.36 6.36 0.00 3.58
272 273 0.895530 ACTGTCATTGATCCCGACGT 59.104 50.000 0.00 0.00 32.17 4.34
273 274 1.135083 ACTGTCATTGATCCCGACGTC 60.135 52.381 5.18 5.18 32.17 4.34
394 396 0.736325 GATGTGTCCCGACCAAGACG 60.736 60.000 0.00 0.00 35.71 4.18
428 430 1.814169 GGATCGCCCCGTTTCAGTC 60.814 63.158 0.00 0.00 0.00 3.51
429 431 1.814169 GATCGCCCCGTTTCAGTCC 60.814 63.158 0.00 0.00 0.00 3.85
484 486 0.452585 GAAGAAGCGAGCTCTACGGT 59.547 55.000 12.85 1.63 43.08 4.83
489 491 2.991076 GCGAGCTCTACGGTGGTGT 61.991 63.158 12.85 0.00 0.00 4.16
493 495 1.401199 GAGCTCTACGGTGGTGTAGTC 59.599 57.143 6.43 0.00 42.01 2.59
498 500 1.308069 TACGGTGGTGTAGTCGCCTC 61.308 60.000 0.00 0.00 43.94 4.70
509 511 1.066587 GTCGCCTCCGAGAGAATGG 59.933 63.158 0.00 0.00 45.38 3.16
520 522 3.055385 CCGAGAGAATGGAAACCCTAACA 60.055 47.826 0.00 0.00 0.00 2.41
553 555 1.173913 GGCAGGGACAAGCGTATTTT 58.826 50.000 0.00 0.00 32.45 1.82
628 631 1.111715 GGAAATCATCTGCTGGGCCC 61.112 60.000 17.59 17.59 0.00 5.80
638 641 4.143740 CTGGGCCCAGAAGAGAGT 57.856 61.111 44.19 0.00 46.30 3.24
646 649 1.349026 CCCAGAAGAGAGTTTGCTCCA 59.651 52.381 0.00 0.00 42.59 3.86
647 650 2.421619 CCAGAAGAGAGTTTGCTCCAC 58.578 52.381 0.00 0.00 42.59 4.02
648 651 2.064762 CAGAAGAGAGTTTGCTCCACG 58.935 52.381 0.00 0.00 42.59 4.94
649 652 1.964223 AGAAGAGAGTTTGCTCCACGA 59.036 47.619 0.00 0.00 42.59 4.35
650 653 2.062519 GAAGAGAGTTTGCTCCACGAC 58.937 52.381 0.00 0.00 42.59 4.34
651 654 1.040646 AGAGAGTTTGCTCCACGACA 58.959 50.000 0.00 0.00 42.59 4.35
652 655 1.620819 AGAGAGTTTGCTCCACGACAT 59.379 47.619 0.00 0.00 42.59 3.06
653 656 2.037772 AGAGAGTTTGCTCCACGACATT 59.962 45.455 0.00 0.00 42.59 2.71
654 657 2.413453 GAGAGTTTGCTCCACGACATTC 59.587 50.000 0.00 0.00 42.59 2.67
655 658 1.126846 GAGTTTGCTCCACGACATTCG 59.873 52.381 0.00 0.00 39.67 3.34
656 659 0.165944 GTTTGCTCCACGACATTCGG 59.834 55.000 0.03 0.00 45.59 4.30
657 660 0.953471 TTTGCTCCACGACATTCGGG 60.953 55.000 0.03 0.00 45.59 5.14
663 666 2.977700 CACGACATTCGGGGATGAG 58.022 57.895 0.03 0.00 45.59 2.90
664 667 0.459899 CACGACATTCGGGGATGAGA 59.540 55.000 0.03 0.00 45.59 3.27
665 668 0.460311 ACGACATTCGGGGATGAGAC 59.540 55.000 0.03 0.00 45.59 3.36
666 669 0.747255 CGACATTCGGGGATGAGACT 59.253 55.000 0.00 0.00 36.00 3.24
667 670 1.137086 CGACATTCGGGGATGAGACTT 59.863 52.381 0.00 0.00 36.00 3.01
668 671 2.555199 GACATTCGGGGATGAGACTTG 58.445 52.381 0.00 0.00 0.00 3.16
669 672 1.909302 ACATTCGGGGATGAGACTTGT 59.091 47.619 0.00 0.00 0.00 3.16
670 673 2.093447 ACATTCGGGGATGAGACTTGTC 60.093 50.000 0.00 0.00 0.00 3.18
671 674 1.938585 TTCGGGGATGAGACTTGTCT 58.061 50.000 2.59 2.59 0.00 3.41
672 675 1.186200 TCGGGGATGAGACTTGTCTG 58.814 55.000 8.11 0.00 0.00 3.51
673 676 0.460987 CGGGGATGAGACTTGTCTGC 60.461 60.000 8.11 1.41 0.00 4.26
674 677 0.908198 GGGGATGAGACTTGTCTGCT 59.092 55.000 8.11 0.00 0.00 4.24
675 678 1.134551 GGGGATGAGACTTGTCTGCTC 60.135 57.143 8.11 4.65 0.00 4.26
676 679 1.134551 GGGATGAGACTTGTCTGCTCC 60.135 57.143 8.11 12.35 0.00 4.70
677 680 1.134551 GGATGAGACTTGTCTGCTCCC 60.135 57.143 8.11 1.08 0.00 4.30
678 681 0.908198 ATGAGACTTGTCTGCTCCCC 59.092 55.000 8.11 0.00 0.00 4.81
679 682 1.194781 TGAGACTTGTCTGCTCCCCC 61.195 60.000 8.11 0.00 0.00 5.40
680 683 2.232298 GAGACTTGTCTGCTCCCCCG 62.232 65.000 8.11 0.00 0.00 5.73
681 684 3.316573 GACTTGTCTGCTCCCCCGG 62.317 68.421 0.00 0.00 0.00 5.73
682 685 4.785453 CTTGTCTGCTCCCCCGGC 62.785 72.222 0.00 0.00 0.00 6.13
697 700 3.490759 GGCGTGTGCTCATCCGTG 61.491 66.667 0.00 0.00 42.25 4.94
698 701 4.152625 GCGTGTGCTCATCCGTGC 62.153 66.667 0.00 0.00 38.39 5.34
699 702 2.433145 CGTGTGCTCATCCGTGCT 60.433 61.111 0.00 0.00 32.76 4.40
700 703 2.447887 CGTGTGCTCATCCGTGCTC 61.448 63.158 0.00 0.00 32.76 4.26
701 704 2.103042 GTGTGCTCATCCGTGCTCC 61.103 63.158 0.00 0.00 32.76 4.70
702 705 2.512515 GTGCTCATCCGTGCTCCC 60.513 66.667 0.00 0.00 32.76 4.30
703 706 4.147449 TGCTCATCCGTGCTCCCG 62.147 66.667 0.00 0.00 32.76 5.14
704 707 4.148825 GCTCATCCGTGCTCCCGT 62.149 66.667 0.00 0.00 0.00 5.28
705 708 2.202797 CTCATCCGTGCTCCCGTG 60.203 66.667 0.00 0.00 0.00 4.94
706 709 2.994995 TCATCCGTGCTCCCGTGT 60.995 61.111 0.00 0.00 0.00 4.49
707 710 1.663379 CTCATCCGTGCTCCCGTGTA 61.663 60.000 0.00 0.00 0.00 2.90
708 711 1.518572 CATCCGTGCTCCCGTGTAC 60.519 63.158 0.00 0.00 0.00 2.90
709 712 3.060020 ATCCGTGCTCCCGTGTACG 62.060 63.158 0.00 0.00 43.66 3.67
710 713 4.047059 CCGTGCTCCCGTGTACGT 62.047 66.667 3.57 0.00 42.78 3.57
711 714 2.803670 CGTGCTCCCGTGTACGTG 60.804 66.667 0.00 0.00 40.25 4.49
712 715 2.431942 GTGCTCCCGTGTACGTGG 60.432 66.667 0.00 4.86 37.74 4.94
713 716 2.913578 TGCTCCCGTGTACGTGGT 60.914 61.111 0.00 0.00 37.74 4.16
714 717 2.341176 GCTCCCGTGTACGTGGTT 59.659 61.111 0.00 0.00 37.74 3.67
715 718 1.301165 GCTCCCGTGTACGTGGTTT 60.301 57.895 0.00 0.00 37.74 3.27
716 719 0.038343 GCTCCCGTGTACGTGGTTTA 60.038 55.000 0.00 0.00 37.74 2.01
717 720 1.404583 GCTCCCGTGTACGTGGTTTAT 60.405 52.381 0.00 0.00 37.74 1.40
718 721 2.932187 GCTCCCGTGTACGTGGTTTATT 60.932 50.000 0.00 0.00 37.74 1.40
719 722 3.328505 CTCCCGTGTACGTGGTTTATTT 58.671 45.455 0.00 0.00 37.74 1.40
720 723 3.324993 TCCCGTGTACGTGGTTTATTTC 58.675 45.455 0.00 0.00 37.74 2.17
721 724 2.092524 CCCGTGTACGTGGTTTATTTCG 59.907 50.000 0.00 0.00 37.74 3.46
722 725 2.985809 CCGTGTACGTGGTTTATTTCGA 59.014 45.455 0.00 0.00 37.74 3.71
723 726 3.613737 CCGTGTACGTGGTTTATTTCGAT 59.386 43.478 0.00 0.00 37.74 3.59
724 727 4.091800 CCGTGTACGTGGTTTATTTCGATT 59.908 41.667 0.00 0.00 37.74 3.34
725 728 5.010749 CGTGTACGTGGTTTATTTCGATTG 58.989 41.667 0.00 0.00 34.11 2.67
726 729 5.318349 GTGTACGTGGTTTATTTCGATTGG 58.682 41.667 0.00 0.00 0.00 3.16
727 730 5.120519 GTGTACGTGGTTTATTTCGATTGGA 59.879 40.000 0.00 0.00 0.00 3.53
728 731 5.699915 TGTACGTGGTTTATTTCGATTGGAA 59.300 36.000 0.00 0.00 0.00 3.53
729 732 5.038247 ACGTGGTTTATTTCGATTGGAAC 57.962 39.130 0.00 0.00 33.42 3.62
730 733 4.515944 ACGTGGTTTATTTCGATTGGAACA 59.484 37.500 0.00 0.00 33.42 3.18
744 747 1.899142 TGGAACAAAATAAGGCCCAGC 59.101 47.619 0.00 0.00 31.92 4.85
745 748 3.413952 TGGAACAAAATAAGGCCCAGCC 61.414 50.000 0.00 0.00 43.28 4.85
757 760 2.944390 CCAGCCCCACCCCCTTAA 60.944 66.667 0.00 0.00 0.00 1.85
758 761 2.553330 CCAGCCCCACCCCCTTAAA 61.553 63.158 0.00 0.00 0.00 1.52
759 762 1.467432 CAGCCCCACCCCCTTAAAA 59.533 57.895 0.00 0.00 0.00 1.52
760 763 0.042581 CAGCCCCACCCCCTTAAAAT 59.957 55.000 0.00 0.00 0.00 1.82
761 764 0.338467 AGCCCCACCCCCTTAAAATC 59.662 55.000 0.00 0.00 0.00 2.17
762 765 0.041982 GCCCCACCCCCTTAAAATCA 59.958 55.000 0.00 0.00 0.00 2.57
763 766 1.964830 GCCCCACCCCCTTAAAATCAG 60.965 57.143 0.00 0.00 0.00 2.90
764 767 1.342975 CCCCACCCCCTTAAAATCAGG 60.343 57.143 0.00 0.00 0.00 3.86
821 824 3.357166 CGTAGGATGAAGTAGGAGCAC 57.643 52.381 0.00 0.00 0.00 4.40
822 825 2.688446 CGTAGGATGAAGTAGGAGCACA 59.312 50.000 0.00 0.00 0.00 4.57
823 826 3.319405 CGTAGGATGAAGTAGGAGCACAT 59.681 47.826 0.00 0.00 0.00 3.21
824 827 4.519350 CGTAGGATGAAGTAGGAGCACATA 59.481 45.833 0.00 0.00 0.00 2.29
825 828 5.184096 CGTAGGATGAAGTAGGAGCACATAT 59.816 44.000 0.00 0.00 0.00 1.78
826 829 5.480642 AGGATGAAGTAGGAGCACATATG 57.519 43.478 0.00 0.00 0.00 1.78
827 830 4.285517 AGGATGAAGTAGGAGCACATATGG 59.714 45.833 7.80 0.00 0.00 2.74
828 831 4.564406 GGATGAAGTAGGAGCACATATGGG 60.564 50.000 7.80 3.61 0.00 4.00
829 832 3.653164 TGAAGTAGGAGCACATATGGGA 58.347 45.455 9.80 0.00 0.00 4.37
830 833 3.643320 TGAAGTAGGAGCACATATGGGAG 59.357 47.826 9.80 0.00 0.00 4.30
831 834 1.974236 AGTAGGAGCACATATGGGAGC 59.026 52.381 9.80 8.99 0.00 4.70
832 835 1.694150 GTAGGAGCACATATGGGAGCA 59.306 52.381 9.80 0.00 0.00 4.26
833 836 1.442773 AGGAGCACATATGGGAGCAT 58.557 50.000 9.80 0.00 0.00 3.79
834 837 1.073444 AGGAGCACATATGGGAGCATG 59.927 52.381 9.80 0.00 0.00 4.06
835 838 1.531423 GAGCACATATGGGAGCATGG 58.469 55.000 9.80 0.00 0.00 3.66
836 839 1.072806 GAGCACATATGGGAGCATGGA 59.927 52.381 9.80 0.00 0.00 3.41
837 840 1.496001 AGCACATATGGGAGCATGGAA 59.504 47.619 9.80 0.00 0.00 3.53
838 841 2.091720 AGCACATATGGGAGCATGGAAA 60.092 45.455 9.80 0.00 0.00 3.13
839 842 2.295349 GCACATATGGGAGCATGGAAAG 59.705 50.000 9.80 0.00 0.00 2.62
840 843 2.889045 CACATATGGGAGCATGGAAAGG 59.111 50.000 7.80 0.00 0.00 3.11
841 844 2.785269 ACATATGGGAGCATGGAAAGGA 59.215 45.455 7.80 0.00 0.00 3.36
842 845 3.205056 ACATATGGGAGCATGGAAAGGAA 59.795 43.478 7.80 0.00 0.00 3.36
843 846 2.449137 ATGGGAGCATGGAAAGGAAG 57.551 50.000 0.00 0.00 0.00 3.46
844 847 0.323725 TGGGAGCATGGAAAGGAAGC 60.324 55.000 0.00 0.00 0.00 3.86
845 848 0.323725 GGGAGCATGGAAAGGAAGCA 60.324 55.000 0.00 0.00 0.00 3.91
846 849 1.101331 GGAGCATGGAAAGGAAGCAG 58.899 55.000 0.00 0.00 0.00 4.24
847 850 1.101331 GAGCATGGAAAGGAAGCAGG 58.899 55.000 0.00 0.00 0.00 4.85
848 851 0.969409 AGCATGGAAAGGAAGCAGGC 60.969 55.000 0.00 0.00 0.00 4.85
849 852 1.252904 GCATGGAAAGGAAGCAGGCA 61.253 55.000 0.00 0.00 0.00 4.75
850 853 1.259609 CATGGAAAGGAAGCAGGCAA 58.740 50.000 0.00 0.00 0.00 4.52
851 854 1.203994 CATGGAAAGGAAGCAGGCAAG 59.796 52.381 0.00 0.00 0.00 4.01
852 855 0.185901 TGGAAAGGAAGCAGGCAAGT 59.814 50.000 0.00 0.00 0.00 3.16
853 856 0.884514 GGAAAGGAAGCAGGCAAGTC 59.115 55.000 0.00 0.00 0.00 3.01
854 857 0.519077 GAAAGGAAGCAGGCAAGTCG 59.481 55.000 0.00 0.00 0.00 4.18
855 858 0.890996 AAAGGAAGCAGGCAAGTCGG 60.891 55.000 0.00 0.00 0.00 4.79
856 859 1.768684 AAGGAAGCAGGCAAGTCGGA 61.769 55.000 0.00 0.00 0.00 4.55
857 860 2.035442 GGAAGCAGGCAAGTCGGAC 61.035 63.158 0.00 0.00 0.00 4.79
948 954 2.039624 TCTCCACCTGCTCCCTCC 59.960 66.667 0.00 0.00 0.00 4.30
1036 1042 2.596631 GCATCATGCGGGCCATCT 60.597 61.111 4.39 0.00 31.71 2.90
1101 1107 3.423162 CTCCGCTGCCTTCTCCTCG 62.423 68.421 0.00 0.00 0.00 4.63
1482 1491 2.815647 CTCTTCGCCGCCAAGTCC 60.816 66.667 0.00 0.00 0.00 3.85
1620 1629 1.165270 CGGACACAAATGACCTTCCC 58.835 55.000 0.00 0.00 38.39 3.97
1647 1656 2.432628 CACGTCTTCCCGCACCTC 60.433 66.667 0.00 0.00 0.00 3.85
1692 1701 2.704572 GACATCAAGACCAAGGACCTG 58.295 52.381 0.00 0.00 0.00 4.00
1701 1710 1.987855 CAAGGACCTGGACCGCCTA 60.988 63.158 9.53 0.00 34.31 3.93
2007 2016 1.352156 GCAACACCGTCATCGAGGTC 61.352 60.000 0.00 0.00 39.00 3.85
2018 2027 4.066490 GTCATCGAGGTCTAGCTAGCTTA 58.934 47.826 24.88 9.09 0.00 3.09
2019 2028 4.515944 GTCATCGAGGTCTAGCTAGCTTAA 59.484 45.833 24.88 8.70 0.00 1.85
2154 2163 0.961019 CACCACCACCATTCCAAGTG 59.039 55.000 0.00 0.00 0.00 3.16
2168 2177 1.271543 CCAAGTGTCAAGATCCTGGCA 60.272 52.381 0.00 0.00 0.00 4.92
2205 2214 0.321671 AGTGCGCAAAGAGGCTAAGA 59.678 50.000 14.00 0.00 0.00 2.10
2243 2252 1.134280 AGATGCTTCCCCAATGTCGAG 60.134 52.381 0.00 0.00 0.00 4.04
2273 2282 5.588240 CATGTCATGGTGAGATTCCATTTG 58.412 41.667 4.78 0.00 42.92 2.32
2310 2319 3.746492 AGCATTTTACACCGTCTCAACTC 59.254 43.478 0.00 0.00 0.00 3.01
2311 2320 3.496884 GCATTTTACACCGTCTCAACTCA 59.503 43.478 0.00 0.00 0.00 3.41
2312 2321 4.024387 GCATTTTACACCGTCTCAACTCAA 60.024 41.667 0.00 0.00 0.00 3.02
2313 2322 5.440685 CATTTTACACCGTCTCAACTCAAC 58.559 41.667 0.00 0.00 0.00 3.18
2314 2323 4.395959 TTTACACCGTCTCAACTCAACT 57.604 40.909 0.00 0.00 0.00 3.16
2335 2344 9.034544 TCAACTTATTATCTGATGATTGTGTCG 57.965 33.333 0.00 0.00 34.32 4.35
2337 2346 6.931281 ACTTATTATCTGATGATTGTGTCGGG 59.069 38.462 0.00 0.00 34.32 5.14
2340 2349 0.392863 CTGATGATTGTGTCGGGGCA 60.393 55.000 0.00 0.00 0.00 5.36
2530 2539 1.129058 AGGTCGTGTTCCTCAGGTTT 58.871 50.000 0.00 0.00 34.10 3.27
2534 2543 1.483004 TCGTGTTCCTCAGGTTTGTCA 59.517 47.619 0.00 0.00 34.10 3.58
2662 2671 2.653115 CGTGCCAGCAGAGACTCA 59.347 61.111 5.02 0.00 0.00 3.41
2804 2813 6.183359 GCTGATATGTTTCGATCGTGATACAG 60.183 42.308 15.94 14.82 34.16 2.74
2812 2821 1.193203 GATCGTGATACAGCATTGCCG 59.807 52.381 4.70 0.00 0.00 5.69
2826 2835 3.492756 GCATTGCCGTTTCTTTTGCTAAA 59.507 39.130 0.00 0.00 0.00 1.85
2870 2886 0.744414 GTTATCCGCTGGCAAGAGCA 60.744 55.000 0.00 0.00 44.61 4.26
2964 2982 2.094675 GCCAGTAGTCCATGCAATGTT 58.905 47.619 0.00 0.00 44.81 2.71
3012 3030 3.368843 GGCTAAATTGCAGACATTTGTGC 59.631 43.478 5.31 8.55 40.29 4.57
3026 3044 5.049167 ACATTTGTGCGTTTCATGTGATTT 58.951 33.333 0.00 0.00 0.00 2.17
3069 3092 3.367992 TTCGTTTCATGTGCTGCATTT 57.632 38.095 5.27 0.00 35.19 2.32
3072 3095 4.864633 TCGTTTCATGTGCTGCATTTTTA 58.135 34.783 5.27 0.00 35.19 1.52
3083 3106 6.200665 TGTGCTGCATTTTTAGTTGAAATGTC 59.799 34.615 5.27 4.96 43.20 3.06
3136 3159 7.895759 AGTACAGGTGATATTTGCAAATTTGT 58.104 30.769 28.45 21.60 0.00 2.83
3137 3160 7.814107 AGTACAGGTGATATTTGCAAATTTGTG 59.186 33.333 28.45 18.33 0.00 3.33
3138 3161 5.409214 ACAGGTGATATTTGCAAATTTGTGC 59.591 36.000 28.45 15.04 45.15 4.57
3139 3162 5.640357 CAGGTGATATTTGCAAATTTGTGCT 59.360 36.000 28.45 7.20 45.17 4.40
3180 3203 9.970395 GTAATTTTCTGCAATGATGATCCATTA 57.030 29.630 0.00 0.00 35.20 1.90
3185 3208 9.749340 TTTCTGCAATGATGATCCATTATATCT 57.251 29.630 0.00 0.00 35.20 1.98
3186 3209 8.959705 TCTGCAATGATGATCCATTATATCTC 57.040 34.615 0.00 0.00 35.20 2.75
3187 3210 8.545472 TCTGCAATGATGATCCATTATATCTCA 58.455 33.333 0.00 0.00 35.20 3.27
3188 3211 8.732746 TGCAATGATGATCCATTATATCTCAG 57.267 34.615 0.00 0.00 35.20 3.35
3189 3212 8.545472 TGCAATGATGATCCATTATATCTCAGA 58.455 33.333 0.00 0.00 35.20 3.27
3190 3213 9.392259 GCAATGATGATCCATTATATCTCAGAA 57.608 33.333 0.00 0.00 35.20 3.02
3222 3245 9.929180 ATTGAAGCATACTATGTATTGTATCGT 57.071 29.630 0.00 0.00 28.64 3.73
3238 3261 6.793492 TGTATCGTTCATGTGATTTGTCAA 57.207 33.333 0.00 0.00 0.00 3.18
3257 3280 3.066621 TCAATTTGTGATTATCTGCGGCC 59.933 43.478 0.00 0.00 0.00 6.13
3273 3296 2.798009 CCTTTGGTATTGCCGGCG 59.202 61.111 23.90 0.00 41.21 6.46
3283 3306 2.490328 ATTGCCGGCGTTTAATGATG 57.510 45.000 23.90 0.00 0.00 3.07
3306 3329 5.107133 GGAATTGAAGAATGAAGGTGCATG 58.893 41.667 0.00 0.00 0.00 4.06
3313 3336 1.747709 ATGAAGGTGCATGTGCTCTC 58.252 50.000 6.55 0.00 42.66 3.20
3330 3353 0.537188 CTCCCGGATGTGCTGTAAGT 59.463 55.000 0.73 0.00 35.30 2.24
3379 3410 5.375417 TGAACTTATGTTGAAGGTGCATG 57.625 39.130 0.00 0.00 36.39 4.06
3380 3411 4.826733 TGAACTTATGTTGAAGGTGCATGT 59.173 37.500 0.00 0.00 36.39 3.21
3381 3412 6.000840 TGAACTTATGTTGAAGGTGCATGTA 58.999 36.000 0.00 0.00 36.39 2.29
3382 3413 6.149308 TGAACTTATGTTGAAGGTGCATGTAG 59.851 38.462 0.00 0.00 36.39 2.74
3383 3414 5.804639 ACTTATGTTGAAGGTGCATGTAGA 58.195 37.500 0.00 0.00 0.00 2.59
3434 3467 2.303175 GGTGTTGCCACTGAAAGGTTA 58.697 47.619 0.00 0.00 41.53 2.85
3441 3474 3.084786 GCCACTGAAAGGTTAAGCTGAT 58.915 45.455 8.16 0.11 39.30 2.90
3464 3497 2.289547 GCACAAACTAGTCCGCTTTTCA 59.710 45.455 0.00 0.00 0.00 2.69
3465 3498 3.607078 GCACAAACTAGTCCGCTTTTCAG 60.607 47.826 0.00 0.00 0.00 3.02
3479 3512 7.275560 GTCCGCTTTTCAGTAATTGCAATAATT 59.724 33.333 13.39 0.03 0.00 1.40
3508 3541 4.402793 TGTTGATTCCTTCCGTTTTTGGAA 59.597 37.500 0.00 0.00 45.62 3.53
3524 3557 6.642707 TTTTGGAAGTAACCATGAATCGTT 57.357 33.333 0.00 0.00 39.82 3.85
3536 3569 8.757164 AACCATGAATCGTTTTAATTCCTTTC 57.243 30.769 0.00 0.00 33.13 2.62
3541 3574 8.859517 TGAATCGTTTTAATTCCTTTCGTTTT 57.140 26.923 0.00 0.00 33.13 2.43
3599 3632 3.253188 TGAGTGTTGCTGGCTTATTTGTC 59.747 43.478 0.00 0.00 0.00 3.18
3629 3662 7.792374 AATTTGATAGTGTATGCGATTGACT 57.208 32.000 0.00 0.00 0.00 3.41
3676 3735 8.806429 TCTTTATCACTAAAATGATTGCCTGA 57.194 30.769 0.00 0.00 39.97 3.86
3737 3798 5.531122 AATAAGACTCGCCTGTTAGCATA 57.469 39.130 0.00 0.00 0.00 3.14
3739 3800 4.408182 AAGACTCGCCTGTTAGCATATT 57.592 40.909 0.00 0.00 0.00 1.28
3740 3801 3.983741 AGACTCGCCTGTTAGCATATTC 58.016 45.455 0.00 0.00 0.00 1.75
3741 3802 3.060602 GACTCGCCTGTTAGCATATTCC 58.939 50.000 0.00 0.00 0.00 3.01
3742 3803 2.434336 ACTCGCCTGTTAGCATATTCCA 59.566 45.455 0.00 0.00 0.00 3.53
3743 3804 3.071602 ACTCGCCTGTTAGCATATTCCAT 59.928 43.478 0.00 0.00 0.00 3.41
3744 3805 4.283467 ACTCGCCTGTTAGCATATTCCATA 59.717 41.667 0.00 0.00 0.00 2.74
3745 3806 5.046304 ACTCGCCTGTTAGCATATTCCATAT 60.046 40.000 0.00 0.00 0.00 1.78
3746 3807 5.804639 TCGCCTGTTAGCATATTCCATATT 58.195 37.500 0.00 0.00 0.00 1.28
3747 3808 5.643348 TCGCCTGTTAGCATATTCCATATTG 59.357 40.000 0.00 0.00 0.00 1.90
3748 3809 5.163723 CGCCTGTTAGCATATTCCATATTGG 60.164 44.000 0.00 0.00 39.43 3.16
3749 3810 5.711976 GCCTGTTAGCATATTCCATATTGGT 59.288 40.000 0.00 0.00 39.03 3.67
3750 3811 6.127897 GCCTGTTAGCATATTCCATATTGGTC 60.128 42.308 0.00 0.00 39.03 4.02
3751 3812 6.942005 CCTGTTAGCATATTCCATATTGGTCA 59.058 38.462 0.00 0.00 39.03 4.02
3752 3813 7.094634 CCTGTTAGCATATTCCATATTGGTCAC 60.095 40.741 0.00 0.00 39.03 3.67
3753 3814 7.517320 TGTTAGCATATTCCATATTGGTCACT 58.483 34.615 0.00 0.00 39.03 3.41
3754 3815 7.661437 TGTTAGCATATTCCATATTGGTCACTC 59.339 37.037 0.00 0.00 39.03 3.51
3755 3816 5.564550 AGCATATTCCATATTGGTCACTCC 58.435 41.667 0.00 0.00 39.03 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.245443 ACTCTCAGGTTCTTCTGCCTAGA 60.245 47.826 0.00 0.00 34.91 2.43
5 6 3.096092 ACTCTCAGGTTCTTCTGCCTAG 58.904 50.000 0.00 0.00 34.91 3.02
20 21 7.201830 CCTGAGAAGAAAATCCGTATACTCTCA 60.202 40.741 12.43 12.43 0.00 3.27
31 32 2.816777 AGGCCCTGAGAAGAAAATCC 57.183 50.000 0.00 0.00 0.00 3.01
42 43 4.526970 GAGATGTGAAATTTAGGCCCTGA 58.473 43.478 0.00 0.00 0.00 3.86
43 44 3.313526 CGAGATGTGAAATTTAGGCCCTG 59.686 47.826 0.00 0.00 0.00 4.45
167 168 1.590259 GATGAGAAGGAGGCGTCGC 60.590 63.158 9.22 9.22 0.00 5.19
214 215 3.278574 TGATGAAGGAATTAGGGTTGCG 58.721 45.455 0.00 0.00 0.00 4.85
237 238 0.708370 CAGTCAACGACGTGGAATCG 59.292 55.000 6.65 0.00 45.17 3.34
246 247 2.673368 GGGATCAATGACAGTCAACGAC 59.327 50.000 7.50 2.80 0.00 4.34
250 251 2.673893 CGTCGGGATCAATGACAGTCAA 60.674 50.000 7.50 0.00 32.91 3.18
258 259 1.200483 CTTCGACGTCGGGATCAATG 58.800 55.000 35.05 14.63 40.29 2.82
259 260 0.527817 GCTTCGACGTCGGGATCAAT 60.528 55.000 35.05 0.00 40.29 2.57
298 299 0.107945 AACCAGATGGAGAAGAGCGC 60.108 55.000 5.72 0.00 38.94 5.92
360 362 4.203076 ATCGGGGCTACGACGTGC 62.203 66.667 11.56 11.93 46.64 5.34
367 369 2.504519 GGGACACATCGGGGCTAC 59.495 66.667 0.00 0.00 0.00 3.58
406 408 2.750237 AAACGGGGCGATCCTTGC 60.750 61.111 0.00 0.00 35.33 4.01
415 417 0.958876 AATTCGGACTGAAACGGGGC 60.959 55.000 0.00 0.00 40.71 5.80
419 421 2.668457 CCTCTCAATTCGGACTGAAACG 59.332 50.000 0.00 0.00 40.71 3.60
428 430 2.749621 CCCTTGTTTCCTCTCAATTCGG 59.250 50.000 0.00 0.00 0.00 4.30
429 431 2.749621 CCCCTTGTTTCCTCTCAATTCG 59.250 50.000 0.00 0.00 0.00 3.34
452 454 1.378514 TTCTTCCCTGCCGCCATTC 60.379 57.895 0.00 0.00 0.00 2.67
460 462 1.813337 GAGCTCGCTTCTTCCCTGC 60.813 63.158 0.00 0.00 0.00 4.85
484 486 2.034532 TCGGAGGCGACTACACCA 59.965 61.111 0.00 0.00 43.79 4.17
489 491 1.309950 CATTCTCTCGGAGGCGACTA 58.690 55.000 4.96 0.00 44.43 2.59
493 495 0.175760 TTTCCATTCTCTCGGAGGCG 59.824 55.000 4.96 0.00 31.51 5.52
498 500 3.055385 TGTTAGGGTTTCCATTCTCTCGG 60.055 47.826 0.00 0.00 34.83 4.63
520 522 1.566231 CCCTGCCAATAGTTCCCTCTT 59.434 52.381 0.00 0.00 0.00 2.85
606 608 1.303309 CCCAGCAGATGATTTCCGTC 58.697 55.000 0.00 0.00 0.00 4.79
628 631 2.064762 CGTGGAGCAAACTCTCTTCTG 58.935 52.381 0.00 0.00 42.98 3.02
637 640 0.165944 CCGAATGTCGTGGAGCAAAC 59.834 55.000 0.00 0.00 38.40 2.93
638 641 0.953471 CCCGAATGTCGTGGAGCAAA 60.953 55.000 0.00 0.00 38.40 3.68
646 649 0.460311 GTCTCATCCCCGAATGTCGT 59.540 55.000 0.00 0.00 38.40 4.34
647 650 0.747255 AGTCTCATCCCCGAATGTCG 59.253 55.000 0.00 0.00 40.07 4.35
648 651 2.093447 ACAAGTCTCATCCCCGAATGTC 60.093 50.000 0.00 0.00 0.00 3.06
649 652 1.909302 ACAAGTCTCATCCCCGAATGT 59.091 47.619 0.00 0.00 0.00 2.71
650 653 2.169352 AGACAAGTCTCATCCCCGAATG 59.831 50.000 0.00 0.00 34.17 2.67
651 654 2.169352 CAGACAAGTCTCATCCCCGAAT 59.831 50.000 0.00 0.00 37.98 3.34
652 655 1.550524 CAGACAAGTCTCATCCCCGAA 59.449 52.381 0.00 0.00 37.98 4.30
653 656 1.186200 CAGACAAGTCTCATCCCCGA 58.814 55.000 0.00 0.00 37.98 5.14
654 657 0.460987 GCAGACAAGTCTCATCCCCG 60.461 60.000 0.00 0.00 37.98 5.73
655 658 0.908198 AGCAGACAAGTCTCATCCCC 59.092 55.000 0.00 0.00 37.98 4.81
656 659 1.134551 GGAGCAGACAAGTCTCATCCC 60.135 57.143 14.91 5.71 37.98 3.85
657 660 1.134551 GGGAGCAGACAAGTCTCATCC 60.135 57.143 16.54 16.54 39.17 3.51
658 661 1.134551 GGGGAGCAGACAAGTCTCATC 60.135 57.143 0.00 1.67 37.98 2.92
659 662 0.908198 GGGGAGCAGACAAGTCTCAT 59.092 55.000 0.00 0.00 37.98 2.90
660 663 1.194781 GGGGGAGCAGACAAGTCTCA 61.195 60.000 0.00 0.00 37.98 3.27
661 664 1.599576 GGGGGAGCAGACAAGTCTC 59.400 63.158 0.00 0.00 37.98 3.36
662 665 2.286523 CGGGGGAGCAGACAAGTCT 61.287 63.158 0.00 0.00 41.37 3.24
663 666 2.266055 CGGGGGAGCAGACAAGTC 59.734 66.667 0.00 0.00 0.00 3.01
664 667 3.322466 CCGGGGGAGCAGACAAGT 61.322 66.667 0.00 0.00 0.00 3.16
665 668 4.785453 GCCGGGGGAGCAGACAAG 62.785 72.222 2.18 0.00 0.00 3.16
680 683 3.490759 CACGGATGAGCACACGCC 61.491 66.667 0.00 0.00 39.83 5.68
681 684 4.152625 GCACGGATGAGCACACGC 62.153 66.667 0.00 0.00 38.99 5.34
682 685 2.433145 AGCACGGATGAGCACACG 60.433 61.111 0.00 0.00 33.73 4.49
683 686 2.103042 GGAGCACGGATGAGCACAC 61.103 63.158 0.00 0.00 33.73 3.82
684 687 2.265739 GGAGCACGGATGAGCACA 59.734 61.111 0.00 0.00 33.73 4.57
685 688 2.512515 GGGAGCACGGATGAGCAC 60.513 66.667 0.00 0.00 33.73 4.40
686 689 4.147449 CGGGAGCACGGATGAGCA 62.147 66.667 0.00 0.00 33.73 4.26
687 690 4.148825 ACGGGAGCACGGATGAGC 62.149 66.667 0.00 0.00 38.39 4.26
688 691 1.663379 TACACGGGAGCACGGATGAG 61.663 60.000 0.00 0.00 38.39 2.90
689 692 1.679641 TACACGGGAGCACGGATGA 60.680 57.895 0.00 0.00 38.39 2.92
690 693 1.518572 GTACACGGGAGCACGGATG 60.519 63.158 0.00 0.00 38.39 3.51
691 694 2.890371 GTACACGGGAGCACGGAT 59.110 61.111 0.00 0.00 38.39 4.18
692 695 3.740397 CGTACACGGGAGCACGGA 61.740 66.667 0.00 0.00 38.39 4.69
693 696 4.047059 ACGTACACGGGAGCACGG 62.047 66.667 13.82 0.00 44.95 4.94
700 703 2.092524 CGAAATAAACCACGTACACGGG 59.907 50.000 6.72 1.25 44.95 5.28
701 704 2.985809 TCGAAATAAACCACGTACACGG 59.014 45.455 6.72 0.00 44.95 4.94
702 705 4.828291 ATCGAAATAAACCACGTACACG 57.172 40.909 0.00 0.00 46.33 4.49
703 706 5.120519 TCCAATCGAAATAAACCACGTACAC 59.879 40.000 0.00 0.00 0.00 2.90
704 707 5.236282 TCCAATCGAAATAAACCACGTACA 58.764 37.500 0.00 0.00 0.00 2.90
705 708 5.783100 TCCAATCGAAATAAACCACGTAC 57.217 39.130 0.00 0.00 0.00 3.67
706 709 5.699915 TGTTCCAATCGAAATAAACCACGTA 59.300 36.000 0.00 0.00 30.39 3.57
707 710 4.515944 TGTTCCAATCGAAATAAACCACGT 59.484 37.500 0.00 0.00 30.39 4.49
708 711 5.037015 TGTTCCAATCGAAATAAACCACG 57.963 39.130 0.00 0.00 30.39 4.94
709 712 7.701809 TTTTGTTCCAATCGAAATAAACCAC 57.298 32.000 0.00 0.00 30.39 4.16
710 713 9.982651 TTATTTTGTTCCAATCGAAATAAACCA 57.017 25.926 0.00 0.00 37.78 3.67
713 716 9.145865 GCCTTATTTTGTTCCAATCGAAATAAA 57.854 29.630 0.00 0.00 39.01 1.40
714 717 7.762159 GGCCTTATTTTGTTCCAATCGAAATAA 59.238 33.333 0.00 0.00 38.10 1.40
715 718 7.262048 GGCCTTATTTTGTTCCAATCGAAATA 58.738 34.615 0.00 0.00 32.97 1.40
716 719 6.106003 GGCCTTATTTTGTTCCAATCGAAAT 58.894 36.000 0.00 0.00 34.51 2.17
717 720 5.474825 GGCCTTATTTTGTTCCAATCGAAA 58.525 37.500 0.00 0.00 30.39 3.46
718 721 4.081917 GGGCCTTATTTTGTTCCAATCGAA 60.082 41.667 0.84 0.00 0.00 3.71
719 722 3.445805 GGGCCTTATTTTGTTCCAATCGA 59.554 43.478 0.84 0.00 0.00 3.59
720 723 3.194542 TGGGCCTTATTTTGTTCCAATCG 59.805 43.478 4.53 0.00 0.00 3.34
721 724 4.758688 CTGGGCCTTATTTTGTTCCAATC 58.241 43.478 4.53 0.00 0.00 2.67
722 725 3.055167 GCTGGGCCTTATTTTGTTCCAAT 60.055 43.478 4.53 0.00 0.00 3.16
723 726 2.301583 GCTGGGCCTTATTTTGTTCCAA 59.698 45.455 4.53 0.00 0.00 3.53
724 727 1.899142 GCTGGGCCTTATTTTGTTCCA 59.101 47.619 4.53 0.00 0.00 3.53
725 728 1.207089 GGCTGGGCCTTATTTTGTTCC 59.793 52.381 4.53 0.00 46.69 3.62
726 729 2.672961 GGCTGGGCCTTATTTTGTTC 57.327 50.000 4.53 0.00 46.69 3.18
740 743 2.100525 TTTTAAGGGGGTGGGGCTGG 62.101 60.000 0.00 0.00 0.00 4.85
741 744 0.042581 ATTTTAAGGGGGTGGGGCTG 59.957 55.000 0.00 0.00 0.00 4.85
742 745 0.338467 GATTTTAAGGGGGTGGGGCT 59.662 55.000 0.00 0.00 0.00 5.19
743 746 0.041982 TGATTTTAAGGGGGTGGGGC 59.958 55.000 0.00 0.00 0.00 5.80
744 747 1.342975 CCTGATTTTAAGGGGGTGGGG 60.343 57.143 0.00 0.00 0.00 4.96
745 748 2.159179 CCTGATTTTAAGGGGGTGGG 57.841 55.000 0.00 0.00 0.00 4.61
790 793 5.374071 ACTTCATCCTACGGTTGTCTTTTT 58.626 37.500 0.00 0.00 0.00 1.94
791 794 4.969484 ACTTCATCCTACGGTTGTCTTTT 58.031 39.130 0.00 0.00 0.00 2.27
792 795 4.618920 ACTTCATCCTACGGTTGTCTTT 57.381 40.909 0.00 0.00 0.00 2.52
793 796 4.159879 CCTACTTCATCCTACGGTTGTCTT 59.840 45.833 0.00 0.00 0.00 3.01
794 797 3.700038 CCTACTTCATCCTACGGTTGTCT 59.300 47.826 0.00 0.00 0.00 3.41
795 798 3.698040 TCCTACTTCATCCTACGGTTGTC 59.302 47.826 0.00 0.00 0.00 3.18
796 799 3.700038 CTCCTACTTCATCCTACGGTTGT 59.300 47.826 0.00 0.00 0.00 3.32
797 800 3.491104 GCTCCTACTTCATCCTACGGTTG 60.491 52.174 0.00 0.00 0.00 3.77
798 801 2.694109 GCTCCTACTTCATCCTACGGTT 59.306 50.000 0.00 0.00 0.00 4.44
799 802 2.308690 GCTCCTACTTCATCCTACGGT 58.691 52.381 0.00 0.00 0.00 4.83
800 803 2.034812 GTGCTCCTACTTCATCCTACGG 59.965 54.545 0.00 0.00 0.00 4.02
801 804 2.688446 TGTGCTCCTACTTCATCCTACG 59.312 50.000 0.00 0.00 0.00 3.51
802 805 4.946478 ATGTGCTCCTACTTCATCCTAC 57.054 45.455 0.00 0.00 0.00 3.18
803 806 5.481824 CCATATGTGCTCCTACTTCATCCTA 59.518 44.000 1.24 0.00 0.00 2.94
804 807 4.285517 CCATATGTGCTCCTACTTCATCCT 59.714 45.833 1.24 0.00 0.00 3.24
805 808 4.564406 CCCATATGTGCTCCTACTTCATCC 60.564 50.000 1.24 0.00 0.00 3.51
806 809 4.284490 TCCCATATGTGCTCCTACTTCATC 59.716 45.833 1.24 0.00 0.00 2.92
807 810 4.234550 TCCCATATGTGCTCCTACTTCAT 58.765 43.478 1.24 0.00 0.00 2.57
808 811 3.643320 CTCCCATATGTGCTCCTACTTCA 59.357 47.826 1.24 0.00 0.00 3.02
809 812 3.556004 GCTCCCATATGTGCTCCTACTTC 60.556 52.174 1.24 0.00 0.00 3.01
810 813 2.370189 GCTCCCATATGTGCTCCTACTT 59.630 50.000 1.24 0.00 0.00 2.24
811 814 1.974236 GCTCCCATATGTGCTCCTACT 59.026 52.381 1.24 0.00 0.00 2.57
812 815 1.694150 TGCTCCCATATGTGCTCCTAC 59.306 52.381 1.24 0.00 0.00 3.18
813 816 2.101640 TGCTCCCATATGTGCTCCTA 57.898 50.000 1.24 0.00 0.00 2.94
814 817 1.073444 CATGCTCCCATATGTGCTCCT 59.927 52.381 1.24 0.00 0.00 3.69
815 818 1.531423 CATGCTCCCATATGTGCTCC 58.469 55.000 1.24 0.00 0.00 4.70
816 819 1.072806 TCCATGCTCCCATATGTGCTC 59.927 52.381 1.24 0.00 0.00 4.26
817 820 1.142936 TCCATGCTCCCATATGTGCT 58.857 50.000 1.24 0.00 0.00 4.40
818 821 1.985473 TTCCATGCTCCCATATGTGC 58.015 50.000 1.24 4.02 0.00 4.57
819 822 2.889045 CCTTTCCATGCTCCCATATGTG 59.111 50.000 1.24 0.00 0.00 3.21
820 823 2.785269 TCCTTTCCATGCTCCCATATGT 59.215 45.455 1.24 0.00 0.00 2.29
821 824 3.513909 TCCTTTCCATGCTCCCATATG 57.486 47.619 0.00 0.00 0.00 1.78
822 825 3.753193 GCTTCCTTTCCATGCTCCCATAT 60.753 47.826 0.00 0.00 0.00 1.78
823 826 2.423373 GCTTCCTTTCCATGCTCCCATA 60.423 50.000 0.00 0.00 0.00 2.74
824 827 1.687368 GCTTCCTTTCCATGCTCCCAT 60.687 52.381 0.00 0.00 0.00 4.00
825 828 0.323725 GCTTCCTTTCCATGCTCCCA 60.324 55.000 0.00 0.00 0.00 4.37
826 829 0.323725 TGCTTCCTTTCCATGCTCCC 60.324 55.000 0.00 0.00 0.00 4.30
827 830 1.101331 CTGCTTCCTTTCCATGCTCC 58.899 55.000 0.00 0.00 0.00 4.70
828 831 1.101331 CCTGCTTCCTTTCCATGCTC 58.899 55.000 0.00 0.00 0.00 4.26
829 832 0.969409 GCCTGCTTCCTTTCCATGCT 60.969 55.000 0.00 0.00 0.00 3.79
830 833 1.252904 TGCCTGCTTCCTTTCCATGC 61.253 55.000 0.00 0.00 0.00 4.06
831 834 1.203994 CTTGCCTGCTTCCTTTCCATG 59.796 52.381 0.00 0.00 0.00 3.66
832 835 1.203100 ACTTGCCTGCTTCCTTTCCAT 60.203 47.619 0.00 0.00 0.00 3.41
833 836 0.185901 ACTTGCCTGCTTCCTTTCCA 59.814 50.000 0.00 0.00 0.00 3.53
834 837 0.884514 GACTTGCCTGCTTCCTTTCC 59.115 55.000 0.00 0.00 0.00 3.13
835 838 0.519077 CGACTTGCCTGCTTCCTTTC 59.481 55.000 0.00 0.00 0.00 2.62
836 839 0.890996 CCGACTTGCCTGCTTCCTTT 60.891 55.000 0.00 0.00 0.00 3.11
837 840 1.302832 CCGACTTGCCTGCTTCCTT 60.303 57.895 0.00 0.00 0.00 3.36
838 841 2.217038 TCCGACTTGCCTGCTTCCT 61.217 57.895 0.00 0.00 0.00 3.36
839 842 2.035442 GTCCGACTTGCCTGCTTCC 61.035 63.158 0.00 0.00 0.00 3.46
840 843 2.035442 GGTCCGACTTGCCTGCTTC 61.035 63.158 0.00 0.00 0.00 3.86
841 844 2.032681 GGTCCGACTTGCCTGCTT 59.967 61.111 0.00 0.00 0.00 3.91
842 845 4.379243 CGGTCCGACTTGCCTGCT 62.379 66.667 4.91 0.00 0.00 4.24
843 846 4.373116 TCGGTCCGACTTGCCTGC 62.373 66.667 10.71 0.00 0.00 4.85
948 954 1.981495 AGAGGGTTTTCAGGAGTGAGG 59.019 52.381 0.00 0.00 32.98 3.86
995 1001 1.002257 ATGGTTGCTGGCATCGTCA 60.002 52.632 0.00 0.00 0.00 4.35
1089 1095 2.650116 GCAGGTCGAGGAGAAGGCA 61.650 63.158 0.00 0.00 0.00 4.75
1398 1407 2.669569 CAAGCCGTGGTGAGGTGG 60.670 66.667 0.00 0.00 0.00 4.61
1692 1701 1.448013 GCACTGAAGTAGGCGGTCC 60.448 63.158 0.00 0.00 0.00 4.46
1701 1710 3.537206 GACGGGGCTGCACTGAAGT 62.537 63.158 19.31 5.13 0.00 3.01
1971 1980 1.953138 GCCGATCTCGAGCACATGG 60.953 63.158 7.81 6.13 43.02 3.66
2007 2016 8.994170 GTCCATTAAAGGAATTAAGCTAGCTAG 58.006 37.037 19.70 16.84 39.92 3.42
2138 2147 1.979855 TGACACTTGGAATGGTGGTG 58.020 50.000 0.00 0.00 37.72 4.17
2154 2163 3.217626 CCCTTAATGCCAGGATCTTGAC 58.782 50.000 6.37 0.00 32.41 3.18
2168 2177 3.016736 CACTCCAAATCGCACCCTTAAT 58.983 45.455 0.00 0.00 0.00 1.40
2205 2214 0.835941 CTGAGGAAGGTAGGCAGCAT 59.164 55.000 0.00 0.00 0.00 3.79
2273 2282 9.237846 GTGTAAAATGCTAAATTAGGAGATTGC 57.762 33.333 1.88 3.39 0.00 3.56
2283 2292 6.811253 TGAGACGGTGTAAAATGCTAAATT 57.189 33.333 0.00 0.00 0.00 1.82
2310 2319 8.278408 CCGACACAATCATCAGATAATAAGTTG 58.722 37.037 0.00 0.00 33.08 3.16
2311 2320 7.442364 CCCGACACAATCATCAGATAATAAGTT 59.558 37.037 0.00 0.00 33.08 2.66
2312 2321 6.931281 CCCGACACAATCATCAGATAATAAGT 59.069 38.462 0.00 0.00 33.08 2.24
2313 2322 6.369890 CCCCGACACAATCATCAGATAATAAG 59.630 42.308 0.00 0.00 33.08 1.73
2314 2323 6.230472 CCCCGACACAATCATCAGATAATAA 58.770 40.000 0.00 0.00 33.08 1.40
2335 2344 0.393537 CAGATCAACCAGACTGCCCC 60.394 60.000 0.00 0.00 0.00 5.80
2337 2346 2.559440 GATCAGATCAACCAGACTGCC 58.441 52.381 5.44 0.00 0.00 4.85
2340 2349 3.843027 AGTTGGATCAGATCAACCAGACT 59.157 43.478 12.66 0.00 42.87 3.24
2450 2459 0.670162 GTGTGTGACTGCAGGCATTT 59.330 50.000 28.33 0.00 0.00 2.32
2530 2539 0.248565 GCTGTGCTCTCTCCATGACA 59.751 55.000 0.00 0.00 0.00 3.58
2534 2543 1.207570 CAGAAGCTGTGCTCTCTCCAT 59.792 52.381 0.00 0.00 38.25 3.41
2662 2671 3.005684 TGCGCACCAAGATTGAGAATTTT 59.994 39.130 5.66 0.00 0.00 1.82
2804 2813 1.501169 AGCAAAAGAAACGGCAATGC 58.499 45.000 0.00 0.00 0.00 3.56
2870 2886 8.870075 AAGCCAAGAATTCAGTCTAAATAAGT 57.130 30.769 8.44 0.00 0.00 2.24
2945 2963 4.100707 CAAACATTGCATGGACTACTGG 57.899 45.455 0.00 0.00 33.60 4.00
2964 2982 2.436417 GGTACAATTCAGCAGGAGCAA 58.564 47.619 0.00 0.00 45.49 3.91
2967 2985 2.749621 GTTGGGTACAATTCAGCAGGAG 59.250 50.000 0.00 0.00 39.13 3.69
3012 3030 3.182173 GGCACACAAAATCACATGAAACG 59.818 43.478 0.00 0.00 0.00 3.60
3026 3044 1.336440 CACGAGAAAATGGGCACACAA 59.664 47.619 0.00 0.00 0.00 3.33
3083 3106 6.588756 TCGGCACAAGTAAGAAATACAGTAAG 59.411 38.462 0.00 0.00 36.94 2.34
3098 3121 2.565834 ACCTGTACTAATCGGCACAAGT 59.434 45.455 0.00 0.00 0.00 3.16
3154 3177 8.882415 AATGGATCATCATTGCAGAAAATTAC 57.118 30.769 0.00 0.00 36.16 1.89
3181 3204 9.534565 GTATGCTTCAATGTAAGTTCTGAGATA 57.465 33.333 0.00 0.00 0.00 1.98
3182 3205 8.263640 AGTATGCTTCAATGTAAGTTCTGAGAT 58.736 33.333 0.00 0.00 0.00 2.75
3183 3206 7.615403 AGTATGCTTCAATGTAAGTTCTGAGA 58.385 34.615 0.00 0.00 0.00 3.27
3184 3207 7.840342 AGTATGCTTCAATGTAAGTTCTGAG 57.160 36.000 0.00 0.00 0.00 3.35
3185 3208 9.317936 CATAGTATGCTTCAATGTAAGTTCTGA 57.682 33.333 0.00 0.00 0.00 3.27
3186 3209 9.102757 ACATAGTATGCTTCAATGTAAGTTCTG 57.897 33.333 10.16 0.00 0.00 3.02
3196 3219 9.929180 ACGATACAATACATAGTATGCTTCAAT 57.071 29.630 10.16 0.00 31.45 2.57
3197 3220 9.758651 AACGATACAATACATAGTATGCTTCAA 57.241 29.630 10.16 0.00 31.45 2.69
3198 3221 9.406828 GAACGATACAATACATAGTATGCTTCA 57.593 33.333 10.16 0.00 31.45 3.02
3222 3245 8.890124 AATCACAAATTGACAAATCACATGAA 57.110 26.923 0.00 0.00 36.92 2.57
3238 3261 2.936202 AGGCCGCAGATAATCACAAAT 58.064 42.857 0.00 0.00 0.00 2.32
3251 3274 2.347322 GGCAATACCAAAGGCCGCA 61.347 57.895 0.00 0.00 38.86 5.69
3257 3280 0.242555 AAACGCCGGCAATACCAAAG 59.757 50.000 28.98 9.11 39.03 2.77
3283 3306 4.789012 TGCACCTTCATTCTTCAATTCC 57.211 40.909 0.00 0.00 0.00 3.01
3306 3329 2.512515 GCACATCCGGGAGAGCAC 60.513 66.667 0.00 0.00 0.00 4.40
3313 3336 0.249120 TGACTTACAGCACATCCGGG 59.751 55.000 0.00 0.00 0.00 5.73
3379 3410 3.127548 TCAATTCCGGTGACTACGTCTAC 59.872 47.826 0.00 0.00 33.15 2.59
3380 3411 3.346315 TCAATTCCGGTGACTACGTCTA 58.654 45.455 0.00 0.00 33.15 2.59
3381 3412 2.165167 TCAATTCCGGTGACTACGTCT 58.835 47.619 0.00 0.00 33.15 4.18
3382 3413 2.642139 TCAATTCCGGTGACTACGTC 57.358 50.000 0.00 0.00 0.00 4.34
3383 3414 2.559668 TCTTCAATTCCGGTGACTACGT 59.440 45.455 0.00 0.00 0.00 3.57
3400 3433 4.546570 GGCAACACCAACATAAGTTCTTC 58.453 43.478 0.00 0.00 38.86 2.87
3434 3467 3.077359 GACTAGTTTGTGCCATCAGCTT 58.923 45.455 0.00 0.00 44.23 3.74
3441 3474 0.107831 AAGCGGACTAGTTTGTGCCA 59.892 50.000 0.00 0.00 0.00 4.92
3455 3488 7.524294 AATTATTGCAATTACTGAAAAGCGG 57.476 32.000 18.75 0.00 0.00 5.52
3479 3512 7.519032 AAAACGGAAGGAATCAACAAGATTA 57.481 32.000 0.00 0.00 46.76 1.75
3508 3541 8.575649 AGGAATTAAAACGATTCATGGTTACT 57.424 30.769 0.00 0.00 35.66 2.24
3513 3546 7.027161 ACGAAAGGAATTAAAACGATTCATGG 58.973 34.615 0.00 0.00 35.66 3.66
3536 3569 5.219633 CCTTCATGGTTACTTCCAAAAACG 58.780 41.667 0.00 0.00 41.09 3.60
3599 3632 4.437495 CGCATACACTATCAAATTTTGGCG 59.563 41.667 9.18 8.76 0.00 5.69
3609 3642 5.901552 TCAAGTCAATCGCATACACTATCA 58.098 37.500 0.00 0.00 0.00 2.15
3629 3662 1.134580 GCAGCAGCTCTATGACCTCAA 60.135 52.381 0.00 0.00 37.91 3.02
3655 3714 8.415553 CCAAATCAGGCAATCATTTTAGTGATA 58.584 33.333 0.00 0.00 37.85 2.15
3676 3735 4.466015 CCTAACCACATACAAAGCCCAAAT 59.534 41.667 0.00 0.00 0.00 2.32
3683 3742 8.465999 TCAATTTATGCCTAACCACATACAAAG 58.534 33.333 0.00 0.00 0.00 2.77


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

AutoCloner maintained by Alex Coulton.