Multiple sequence alignment - TraesCS2B01G476800

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 TraesCS2B01G476800 chr2B 100.000 2535 0 0 1 2535 673710480 673713014 0.000000e+00 4682
1 TraesCS2B01G476800 chr2D 89.220 1846 100 38 726 2532 563153035 563154820 0.000000e+00 2215
2 TraesCS2B01G476800 chr2D 90.640 609 40 11 1 600 563145449 563146049 0.000000e+00 793
3 TraesCS2B01G476800 chr2A 88.863 1697 104 40 726 2398 703553532 703555167 0.000000e+00 2008
4 TraesCS2B01G476800 chr2A 89.513 267 12 4 1 260 703547931 703548188 8.750000e-85 324
5 TraesCS2B01G476800 chr2A 94.286 140 8 0 2396 2535 703555404 703555543 5.490000e-52 215


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 TraesCS2B01G476800 chr2B 673710480 673713014 2534 False 4682.0 4682 100.0000 1 2535 1 chr2B.!!$F1 2534
1 TraesCS2B01G476800 chr2D 563153035 563154820 1785 False 2215.0 2215 89.2200 726 2532 1 chr2D.!!$F2 1806
2 TraesCS2B01G476800 chr2D 563145449 563146049 600 False 793.0 793 90.6400 1 600 1 chr2D.!!$F1 599
3 TraesCS2B01G476800 chr2A 703553532 703555543 2011 False 1111.5 2008 91.5745 726 2535 2 chr2A.!!$F2 1809

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
705 714 0.179156 CCATGTGCAAAGGTCGATGC 60.179 55.0 1.74 1.74 42.86 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1575 1585 0.039798 ACTGTACGTACGTGTGCCAG 60.04 55.0 30.25 26.78 0.0 4.85 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.511403 TGCTGTGGCACCGGTTAA 59.489 55.556 16.26 0.00 44.28 2.01
42 43 1.392510 GTTAATGTCTCGGCGTTGGTC 59.607 52.381 6.85 0.00 0.00 4.02
52 53 3.708734 CGTTGGTCGCCGTGAACC 61.709 66.667 0.00 0.00 31.20 3.62
76 77 2.355363 TACGGCGTGTCACTGTGC 60.355 61.111 24.86 0.00 0.00 4.57
79 80 3.349006 GGCGTGTCACTGTGCCAG 61.349 66.667 13.65 1.16 46.76 4.85
80 81 2.280119 GCGTGTCACTGTGCCAGA 60.280 61.111 2.12 0.00 35.18 3.86
85 86 1.070134 GTGTCACTGTGCCAGAGGTTA 59.930 52.381 2.12 0.00 35.18 2.85
91 92 2.639839 ACTGTGCCAGAGGTTAATGTCT 59.360 45.455 8.91 0.00 35.18 3.41
96 97 1.560923 CAGAGGTTAATGTCTCGGCG 58.439 55.000 0.00 0.00 35.34 6.46
124 125 2.031870 GGCCTGGAGTGTTGTTTTCTT 58.968 47.619 0.00 0.00 0.00 2.52
125 126 2.034685 GGCCTGGAGTGTTGTTTTCTTC 59.965 50.000 0.00 0.00 0.00 2.87
126 127 2.687935 GCCTGGAGTGTTGTTTTCTTCA 59.312 45.455 0.00 0.00 0.00 3.02
127 128 3.130340 GCCTGGAGTGTTGTTTTCTTCAA 59.870 43.478 0.00 0.00 0.00 2.69
137 138 5.073428 GTTGTTTTCTTCAAGGAGGAGGAT 58.927 41.667 0.00 0.00 0.00 3.24
142 143 2.316067 TCTTCAAGGAGGAGGATGAGGA 59.684 50.000 0.00 0.00 0.00 3.71
251 252 1.069924 CGCTCTTGTCGTGCTCTGAG 61.070 60.000 0.00 0.00 0.00 3.35
285 286 2.097038 CGAAGGCGACAAGAGCTGG 61.097 63.158 0.00 0.00 40.82 4.85
339 340 2.358615 TGCTCATTCCGCGCTGTT 60.359 55.556 5.56 0.00 0.00 3.16
347 348 1.803334 TTCCGCGCTGTTAAGACAAT 58.197 45.000 5.56 0.00 34.85 2.71
356 358 1.979308 TGTTAAGACAATGACCCCCGA 59.021 47.619 0.00 0.00 31.49 5.14
386 389 5.804692 TGTACACGGGTTGCATAATTTAG 57.195 39.130 0.00 0.00 0.00 1.85
387 390 4.636648 TGTACACGGGTTGCATAATTTAGG 59.363 41.667 0.00 0.00 0.00 2.69
401 404 1.234821 TTTAGGTGCAACTTCGCAGG 58.765 50.000 10.94 0.00 44.05 4.85
405 408 0.383949 GGTGCAACTTCGCAGGAAAA 59.616 50.000 0.00 0.00 44.05 2.29
406 409 1.477105 GTGCAACTTCGCAGGAAAAC 58.523 50.000 0.00 0.00 44.05 2.43
410 413 2.926838 GCAACTTCGCAGGAAAACAAAA 59.073 40.909 0.00 0.00 0.00 2.44
414 417 4.561105 ACTTCGCAGGAAAACAAAACAAA 58.439 34.783 0.00 0.00 0.00 2.83
415 418 5.175127 ACTTCGCAGGAAAACAAAACAAAT 58.825 33.333 0.00 0.00 0.00 2.32
416 419 6.334202 ACTTCGCAGGAAAACAAAACAAATA 58.666 32.000 0.00 0.00 0.00 1.40
417 420 6.814146 ACTTCGCAGGAAAACAAAACAAATAA 59.186 30.769 0.00 0.00 0.00 1.40
418 421 7.494298 ACTTCGCAGGAAAACAAAACAAATAAT 59.506 29.630 0.00 0.00 0.00 1.28
419 422 8.873215 TTCGCAGGAAAACAAAACAAATAATA 57.127 26.923 0.00 0.00 0.00 0.98
440 448 0.329596 GGGAGGTGCTGTCATTTCCT 59.670 55.000 0.00 0.00 31.88 3.36
445 453 2.040278 AGGTGCTGTCATTTCCTTGCTA 59.960 45.455 0.00 0.00 0.00 3.49
450 458 5.528690 GTGCTGTCATTTCCTTGCTATCATA 59.471 40.000 0.00 0.00 0.00 2.15
477 485 3.149196 TCTGAATTGGTCCAAGCAAGAC 58.851 45.455 10.72 0.00 39.11 3.01
489 497 2.673368 CAAGCAAGACCGTATTCAGTCC 59.327 50.000 0.00 0.00 33.29 3.85
577 585 6.373495 ACATGGATGATGGATCATGTTTATCG 59.627 38.462 6.85 0.00 46.84 2.92
587 595 5.357032 GGATCATGTTTATCGAACCCAAGTT 59.643 40.000 0.00 0.00 39.54 2.66
590 598 7.315247 TCATGTTTATCGAACCCAAGTTATG 57.685 36.000 0.00 0.00 35.94 1.90
600 609 5.644644 GAACCCAAGTTATGAAGCATCTTG 58.355 41.667 0.00 0.00 35.94 3.02
601 610 4.666512 ACCCAAGTTATGAAGCATCTTGT 58.333 39.130 0.00 0.00 35.26 3.16
602 611 5.815581 ACCCAAGTTATGAAGCATCTTGTA 58.184 37.500 0.00 0.00 35.26 2.41
603 612 5.648092 ACCCAAGTTATGAAGCATCTTGTAC 59.352 40.000 0.00 0.00 35.26 2.90
604 613 5.647658 CCCAAGTTATGAAGCATCTTGTACA 59.352 40.000 0.00 0.00 35.26 2.90
605 614 6.150976 CCCAAGTTATGAAGCATCTTGTACAA 59.849 38.462 8.28 8.28 35.26 2.41
606 615 7.148018 CCCAAGTTATGAAGCATCTTGTACAAT 60.148 37.037 9.13 0.00 35.26 2.71
607 616 7.912250 CCAAGTTATGAAGCATCTTGTACAATC 59.088 37.037 9.13 3.23 35.26 2.67
608 617 8.671921 CAAGTTATGAAGCATCTTGTACAATCT 58.328 33.333 9.13 1.72 33.27 2.40
609 618 9.890629 AAGTTATGAAGCATCTTGTACAATCTA 57.109 29.630 9.13 0.00 0.00 1.98
610 619 9.890629 AGTTATGAAGCATCTTGTACAATCTAA 57.109 29.630 9.13 1.81 0.00 2.10
613 622 7.977789 TGAAGCATCTTGTACAATCTAAACA 57.022 32.000 9.13 2.55 0.00 2.83
614 623 8.032952 TGAAGCATCTTGTACAATCTAAACAG 57.967 34.615 9.13 0.00 0.00 3.16
615 624 6.428385 AGCATCTTGTACAATCTAAACAGC 57.572 37.500 9.13 5.46 0.00 4.40
616 625 5.939883 AGCATCTTGTACAATCTAAACAGCA 59.060 36.000 9.13 0.00 0.00 4.41
617 626 6.430925 AGCATCTTGTACAATCTAAACAGCAA 59.569 34.615 9.13 0.00 0.00 3.91
618 627 7.040478 AGCATCTTGTACAATCTAAACAGCAAA 60.040 33.333 9.13 0.00 0.00 3.68
619 628 7.756722 GCATCTTGTACAATCTAAACAGCAAAT 59.243 33.333 9.13 0.00 0.00 2.32
620 629 9.069078 CATCTTGTACAATCTAAACAGCAAATG 57.931 33.333 9.13 0.00 0.00 2.32
621 630 7.592938 TCTTGTACAATCTAAACAGCAAATGG 58.407 34.615 9.13 0.00 0.00 3.16
622 631 5.708948 TGTACAATCTAAACAGCAAATGGC 58.291 37.500 0.00 0.00 45.30 4.40
636 645 5.880054 GCAAATGGCTGTTAAGAGTAAGA 57.120 39.130 1.12 0.00 40.25 2.10
637 646 6.254281 GCAAATGGCTGTTAAGAGTAAGAA 57.746 37.500 1.12 0.00 40.25 2.52
638 647 6.856895 GCAAATGGCTGTTAAGAGTAAGAAT 58.143 36.000 1.12 0.00 40.25 2.40
639 648 7.985476 GCAAATGGCTGTTAAGAGTAAGAATA 58.015 34.615 1.12 0.00 40.25 1.75
640 649 7.910683 GCAAATGGCTGTTAAGAGTAAGAATAC 59.089 37.037 1.12 0.00 40.25 1.89
641 650 9.167311 CAAATGGCTGTTAAGAGTAAGAATACT 57.833 33.333 1.12 0.00 45.10 2.12
642 651 8.723942 AATGGCTGTTAAGAGTAAGAATACTG 57.276 34.615 1.12 0.00 42.47 2.74
643 652 7.241042 TGGCTGTTAAGAGTAAGAATACTGT 57.759 36.000 1.12 0.00 42.47 3.55
644 653 8.357290 TGGCTGTTAAGAGTAAGAATACTGTA 57.643 34.615 1.12 0.00 42.47 2.74
645 654 8.248945 TGGCTGTTAAGAGTAAGAATACTGTAC 58.751 37.037 1.12 0.00 42.47 2.90
646 655 7.705752 GGCTGTTAAGAGTAAGAATACTGTACC 59.294 40.741 1.12 0.00 42.47 3.34
647 656 8.248945 GCTGTTAAGAGTAAGAATACTGTACCA 58.751 37.037 1.12 0.00 42.47 3.25
652 661 7.973048 AGAGTAAGAATACTGTACCAATGGA 57.027 36.000 6.16 0.00 42.47 3.41
653 662 8.012957 AGAGTAAGAATACTGTACCAATGGAG 57.987 38.462 6.16 0.00 42.47 3.86
654 663 7.839705 AGAGTAAGAATACTGTACCAATGGAGA 59.160 37.037 6.16 0.00 42.47 3.71
655 664 8.375493 AGTAAGAATACTGTACCAATGGAGAA 57.625 34.615 6.16 0.00 40.88 2.87
656 665 8.478877 AGTAAGAATACTGTACCAATGGAGAAG 58.521 37.037 6.16 2.19 40.88 2.85
657 666 6.875972 AGAATACTGTACCAATGGAGAAGT 57.124 37.500 6.16 8.41 0.00 3.01
658 667 7.973048 AGAATACTGTACCAATGGAGAAGTA 57.027 36.000 6.16 10.37 0.00 2.24
659 668 8.554490 AGAATACTGTACCAATGGAGAAGTAT 57.446 34.615 6.16 12.15 31.65 2.12
660 669 8.993424 AGAATACTGTACCAATGGAGAAGTATT 58.007 33.333 24.06 24.06 37.45 1.89
677 686 9.921637 GAGAAGTATTATCCGATTCATTTCTCT 57.078 33.333 0.00 0.00 35.91 3.10
678 687 9.703892 AGAAGTATTATCCGATTCATTTCTCTG 57.296 33.333 0.00 0.00 0.00 3.35
679 688 7.897575 AGTATTATCCGATTCATTTCTCTGC 57.102 36.000 0.00 0.00 0.00 4.26
680 689 5.852738 ATTATCCGATTCATTTCTCTGCG 57.147 39.130 0.00 0.00 0.00 5.18
681 690 2.959507 TCCGATTCATTTCTCTGCGA 57.040 45.000 0.00 0.00 0.00 5.10
682 691 3.459232 TCCGATTCATTTCTCTGCGAT 57.541 42.857 0.00 0.00 0.00 4.58
683 692 3.797039 TCCGATTCATTTCTCTGCGATT 58.203 40.909 0.00 0.00 0.00 3.34
684 693 4.191544 TCCGATTCATTTCTCTGCGATTT 58.808 39.130 0.00 0.00 0.00 2.17
685 694 5.356426 TCCGATTCATTTCTCTGCGATTTA 58.644 37.500 0.00 0.00 0.00 1.40
686 695 5.234329 TCCGATTCATTTCTCTGCGATTTAC 59.766 40.000 0.00 0.00 0.00 2.01
687 696 5.435557 CGATTCATTTCTCTGCGATTTACC 58.564 41.667 0.00 0.00 0.00 2.85
688 697 5.006649 CGATTCATTTCTCTGCGATTTACCA 59.993 40.000 0.00 0.00 0.00 3.25
689 698 6.293081 CGATTCATTTCTCTGCGATTTACCAT 60.293 38.462 0.00 0.00 0.00 3.55
690 699 5.739752 TCATTTCTCTGCGATTTACCATG 57.260 39.130 0.00 0.00 0.00 3.66
691 700 5.185454 TCATTTCTCTGCGATTTACCATGT 58.815 37.500 0.00 0.00 0.00 3.21
692 701 4.944962 TTTCTCTGCGATTTACCATGTG 57.055 40.909 0.00 0.00 0.00 3.21
693 702 2.279741 TCTCTGCGATTTACCATGTGC 58.720 47.619 0.00 0.00 0.00 4.57
694 703 2.009051 CTCTGCGATTTACCATGTGCA 58.991 47.619 0.00 0.00 0.00 4.57
695 704 2.419673 CTCTGCGATTTACCATGTGCAA 59.580 45.455 0.00 0.00 31.16 4.08
696 705 2.816672 TCTGCGATTTACCATGTGCAAA 59.183 40.909 0.00 0.00 31.16 3.68
697 706 3.119884 TCTGCGATTTACCATGTGCAAAG 60.120 43.478 0.00 0.00 31.16 2.77
698 707 2.094803 TGCGATTTACCATGTGCAAAGG 60.095 45.455 0.00 0.00 0.00 3.11
699 708 2.094752 GCGATTTACCATGTGCAAAGGT 60.095 45.455 10.40 10.40 39.41 3.50
700 709 3.758300 CGATTTACCATGTGCAAAGGTC 58.242 45.455 9.04 0.00 36.87 3.85
701 710 3.727673 CGATTTACCATGTGCAAAGGTCG 60.728 47.826 9.04 4.14 36.87 4.79
702 711 2.552599 TTACCATGTGCAAAGGTCGA 57.447 45.000 9.04 0.00 36.87 4.20
703 712 2.779755 TACCATGTGCAAAGGTCGAT 57.220 45.000 9.04 0.00 36.87 3.59
704 713 1.167851 ACCATGTGCAAAGGTCGATG 58.832 50.000 0.00 0.00 0.00 3.84
705 714 0.179156 CCATGTGCAAAGGTCGATGC 60.179 55.000 1.74 1.74 42.86 3.91
709 718 2.845019 TGCAAAGGTCGATGCAGAG 58.155 52.632 7.31 0.00 46.87 3.35
710 719 0.321346 TGCAAAGGTCGATGCAGAGA 59.679 50.000 7.31 0.00 46.87 3.10
711 720 1.005340 GCAAAGGTCGATGCAGAGAG 58.995 55.000 3.89 0.00 42.12 3.20
712 721 1.674221 GCAAAGGTCGATGCAGAGAGT 60.674 52.381 3.89 0.00 42.12 3.24
713 722 1.998315 CAAAGGTCGATGCAGAGAGTG 59.002 52.381 0.00 0.00 0.00 3.51
714 723 0.534412 AAGGTCGATGCAGAGAGTGG 59.466 55.000 0.00 0.00 0.00 4.00
715 724 0.613292 AGGTCGATGCAGAGAGTGGT 60.613 55.000 0.00 0.00 0.00 4.16
716 725 0.247736 GGTCGATGCAGAGAGTGGTT 59.752 55.000 0.00 0.00 0.00 3.67
717 726 1.634702 GTCGATGCAGAGAGTGGTTC 58.365 55.000 0.00 0.00 0.00 3.62
718 727 1.203523 GTCGATGCAGAGAGTGGTTCT 59.796 52.381 0.00 0.00 39.43 3.01
719 728 1.895798 TCGATGCAGAGAGTGGTTCTT 59.104 47.619 0.00 0.00 35.87 2.52
720 729 1.998315 CGATGCAGAGAGTGGTTCTTG 59.002 52.381 0.00 0.00 35.87 3.02
721 730 2.354259 GATGCAGAGAGTGGTTCTTGG 58.646 52.381 0.00 0.00 35.87 3.61
722 731 1.131638 TGCAGAGAGTGGTTCTTGGT 58.868 50.000 0.00 0.00 35.87 3.67
723 732 1.202687 TGCAGAGAGTGGTTCTTGGTG 60.203 52.381 0.00 0.00 35.87 4.17
724 733 1.517242 CAGAGAGTGGTTCTTGGTGC 58.483 55.000 0.00 0.00 35.87 5.01
745 754 1.065701 AGAATCGATCGTTCAGGACCG 59.934 52.381 23.10 0.00 0.00 4.79
813 823 3.025978 CCTTTGGCTTCTATTCATGGCA 58.974 45.455 0.00 0.00 0.00 4.92
836 846 1.480954 GCTCTCCTCCGGTGTGAATTA 59.519 52.381 0.00 0.00 0.00 1.40
847 857 2.355108 GGTGTGAATTAGCAGCCTCTCA 60.355 50.000 0.00 0.00 0.00 3.27
848 858 3.338249 GTGTGAATTAGCAGCCTCTCAA 58.662 45.455 0.00 0.00 0.00 3.02
856 866 1.618640 GCAGCCTCTCAACGTTCGTC 61.619 60.000 0.00 0.00 0.00 4.20
874 884 1.671328 GTCGGAGGCTAAAAATGGAGC 59.329 52.381 0.00 0.00 38.00 4.70
1055 1065 2.185867 GCCGTCATCGCCCTTGTA 59.814 61.111 0.00 0.00 35.54 2.41
1058 1068 0.742505 CCGTCATCGCCCTTGTACTA 59.257 55.000 0.00 0.00 35.54 1.82
1064 1074 0.608856 TCGCCCTTGTACTACGTCCA 60.609 55.000 0.00 0.00 0.00 4.02
1156 1166 2.521126 TCTTCATGTACAGGTCCGTCA 58.479 47.619 7.49 0.00 0.00 4.35
1157 1167 2.894765 TCTTCATGTACAGGTCCGTCAA 59.105 45.455 7.49 0.00 0.00 3.18
1158 1168 3.513912 TCTTCATGTACAGGTCCGTCAAT 59.486 43.478 7.49 0.00 0.00 2.57
1159 1169 3.520290 TCATGTACAGGTCCGTCAATC 57.480 47.619 7.49 0.00 0.00 2.67
1160 1170 2.159296 TCATGTACAGGTCCGTCAATCG 60.159 50.000 7.49 0.00 39.52 3.34
1172 1182 2.745884 CAATCGGCCAGGCGTTCA 60.746 61.111 13.55 0.00 0.00 3.18
1185 1195 1.597854 CGTTCAGTCCCAGCTGCAA 60.598 57.895 8.66 0.00 36.49 4.08
1186 1196 0.957395 CGTTCAGTCCCAGCTGCAAT 60.957 55.000 8.66 0.00 36.49 3.56
1187 1197 0.524862 GTTCAGTCCCAGCTGCAATG 59.475 55.000 8.66 6.60 36.49 2.82
1188 1198 1.246056 TTCAGTCCCAGCTGCAATGC 61.246 55.000 8.66 0.00 36.49 3.56
1189 1199 2.749044 AGTCCCAGCTGCAATGCG 60.749 61.111 8.66 0.00 38.13 4.73
1190 1200 2.747460 GTCCCAGCTGCAATGCGA 60.747 61.111 8.66 0.00 38.13 5.10
1191 1201 2.117156 GTCCCAGCTGCAATGCGAT 61.117 57.895 8.66 0.00 38.13 4.58
1192 1202 1.378911 TCCCAGCTGCAATGCGATT 60.379 52.632 8.66 0.00 38.13 3.34
1194 1204 0.956633 CCCAGCTGCAATGCGATTAT 59.043 50.000 8.66 0.00 38.13 1.28
1211 1221 2.602257 TATGCGACCATCTTGTCTGG 57.398 50.000 0.00 0.00 39.80 3.86
1213 1223 1.191489 TGCGACCATCTTGTCTGGGA 61.191 55.000 0.00 0.00 38.14 4.37
1214 1224 0.741221 GCGACCATCTTGTCTGGGAC 60.741 60.000 0.00 0.00 38.14 4.46
1215 1225 0.898320 CGACCATCTTGTCTGGGACT 59.102 55.000 0.00 0.00 38.14 3.85
1216 1226 1.134965 CGACCATCTTGTCTGGGACTC 60.135 57.143 0.00 0.00 38.14 3.36
1219 1229 1.209019 CCATCTTGTCTGGGACTCTGG 59.791 57.143 0.00 0.00 33.15 3.86
1220 1230 2.182827 CATCTTGTCTGGGACTCTGGA 58.817 52.381 0.00 0.00 33.15 3.86
1227 1237 1.283905 TCTGGGACTCTGGATACGTGA 59.716 52.381 0.00 0.00 42.51 4.35
1228 1238 1.405821 CTGGGACTCTGGATACGTGAC 59.594 57.143 0.00 0.00 42.51 3.67
1230 1240 2.240414 TGGGACTCTGGATACGTGACTA 59.760 50.000 0.00 0.00 42.51 2.59
1231 1241 2.617774 GGGACTCTGGATACGTGACTAC 59.382 54.545 0.00 0.00 42.51 2.73
1405 1415 1.383799 CCACCACCACCACCATCAT 59.616 57.895 0.00 0.00 0.00 2.45
1426 1436 3.349006 CACCGTCAGCACCAGCAC 61.349 66.667 0.00 0.00 45.49 4.40
1427 1437 4.626081 ACCGTCAGCACCAGCACC 62.626 66.667 0.00 0.00 45.49 5.01
1428 1438 4.624364 CCGTCAGCACCAGCACCA 62.624 66.667 0.00 0.00 45.49 4.17
1429 1439 3.046087 CGTCAGCACCAGCACCAG 61.046 66.667 0.00 0.00 45.49 4.00
1430 1440 3.360340 GTCAGCACCAGCACCAGC 61.360 66.667 0.00 0.00 45.49 4.85
1431 1441 3.876236 TCAGCACCAGCACCAGCA 61.876 61.111 0.00 0.00 45.49 4.41
1432 1442 3.667282 CAGCACCAGCACCAGCAC 61.667 66.667 0.00 0.00 45.49 4.40
1433 1443 4.962836 AGCACCAGCACCAGCACC 62.963 66.667 0.00 0.00 45.49 5.01
1546 1556 1.374125 CGTGTGACGCTCCCATCAA 60.374 57.895 0.00 0.00 33.65 2.57
1561 1571 0.035439 ATCAAACCGCACCCGATCTT 60.035 50.000 0.00 0.00 36.29 2.40
1575 1585 0.248702 GATCTTCGGCGACCTCAGTC 60.249 60.000 10.16 1.39 39.83 3.51
1651 1661 1.582937 CTACGACTACACGCGCCAG 60.583 63.158 5.73 2.87 36.70 4.85
1681 1695 3.756933 TTAGGGACCGGTTGCATATAC 57.243 47.619 9.42 0.00 0.00 1.47
1692 1706 4.980434 CGGTTGCATATACTAGTGGTGTAC 59.020 45.833 5.39 4.73 0.00 2.90
1711 1725 0.922560 CGTACGTACACGCCTGATCG 60.923 60.000 24.50 3.65 44.43 3.69
1850 1869 1.759881 CATGGGCTCCCTCTCCATC 59.240 63.158 6.50 0.00 39.07 3.51
1988 2009 2.140717 CTTGTACACGTTCCTGAACCC 58.859 52.381 0.00 0.00 38.03 4.11
1991 2012 1.342174 GTACACGTTCCTGAACCCTGA 59.658 52.381 4.54 0.00 38.03 3.86
1995 2016 1.271379 ACGTTCCTGAACCCTGAATGG 60.271 52.381 4.54 0.00 38.03 3.16
2007 2028 1.466167 CCTGAATGGAAGTGCAACGAG 59.534 52.381 0.00 0.00 39.56 4.18
2039 2060 4.038522 AGTGTGGCTGCATGATACTACTAG 59.961 45.833 0.50 0.00 0.00 2.57
2040 2061 3.243873 TGTGGCTGCATGATACTACTAGC 60.244 47.826 0.50 0.00 0.00 3.42
2054 2075 8.202137 TGATACTACTAGCATGTAGGAAAAACC 58.798 37.037 16.76 0.00 42.92 3.27
2060 2081 4.079253 AGCATGTAGGAAAAACCGAACAT 58.921 39.130 0.00 0.00 44.73 2.71
2063 2084 6.377146 AGCATGTAGGAAAAACCGAACATAAT 59.623 34.615 0.00 0.00 43.27 1.28
2064 2085 7.554835 AGCATGTAGGAAAAACCGAACATAATA 59.445 33.333 0.00 0.00 43.27 0.98
2065 2086 7.855904 GCATGTAGGAAAAACCGAACATAATAG 59.144 37.037 0.00 0.00 43.27 1.73
2070 2095 6.598064 AGGAAAAACCGAACATAATAGTCAGG 59.402 38.462 0.00 0.00 44.74 3.86
2141 2166 1.084370 GTTTCTGTAGCAGCGCCGAT 61.084 55.000 2.29 0.00 0.00 4.18
2171 2196 2.679837 GGATTTGACAGTGTCATCGCAT 59.320 45.455 25.97 15.28 42.40 4.73
2173 2198 1.349234 TTGACAGTGTCATCGCATCG 58.651 50.000 25.97 0.00 42.40 3.84
2174 2199 1.078201 TGACAGTGTCATCGCATCGC 61.078 55.000 22.06 0.00 37.67 4.58
2233 2266 2.278857 CGGACCAAGGCGATCTCG 60.279 66.667 0.00 0.00 43.27 4.04
2235 2268 1.742768 GGACCAAGGCGATCTCGAT 59.257 57.895 3.33 0.00 43.02 3.59
2239 2272 1.212616 CCAAGGCGATCTCGATTCAC 58.787 55.000 3.33 0.00 43.02 3.18
2240 2273 1.202463 CCAAGGCGATCTCGATTCACT 60.202 52.381 3.33 0.00 43.02 3.41
2256 2289 9.743057 CTCGATTCACTATGAAAGATTAGTTCT 57.257 33.333 0.00 0.00 40.12 3.01
2278 2314 9.262358 GTTCTGTAATCAAGTATCCCAATACTC 57.738 37.037 0.00 0.00 45.92 2.59
2282 2318 5.730296 ATCAAGTATCCCAATACTCCGAG 57.270 43.478 0.00 0.00 45.92 4.63
2315 2352 1.296715 GACGGCCAATGGAGTCACT 59.703 57.895 18.70 0.00 34.03 3.41
2465 2753 3.264897 CCCGGCATCTTCTTCGCG 61.265 66.667 0.00 0.00 0.00 5.87
2487 2775 2.280524 CCGACAAGCACAACGGGA 60.281 61.111 0.00 0.00 41.41 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.241315 ACATTAACCGGTGCCACAGC 61.241 55.000 8.52 0.00 40.48 4.40
26 27 2.126071 CGACCAACGCCGAGACAT 60.126 61.111 0.00 0.00 34.51 3.06
42 43 1.153647 TAGCATCTGGTTCACGGCG 60.154 57.895 4.80 4.80 0.00 6.46
52 53 1.153842 TGACACGCCGTAGCATCTG 60.154 57.895 0.00 0.00 39.83 2.90
76 77 1.802880 CGCCGAGACATTAACCTCTGG 60.803 57.143 0.00 0.00 0.00 3.86
79 80 1.659098 CAACGCCGAGACATTAACCTC 59.341 52.381 0.00 0.00 0.00 3.85
80 81 1.674817 CCAACGCCGAGACATTAACCT 60.675 52.381 0.00 0.00 0.00 3.50
85 86 0.670546 CAGTCCAACGCCGAGACATT 60.671 55.000 0.00 0.00 32.82 2.71
96 97 1.302832 CACTCCAGGCCAGTCCAAC 60.303 63.158 5.01 0.00 37.29 3.77
124 125 1.686428 CGTCCTCATCCTCCTCCTTGA 60.686 57.143 0.00 0.00 0.00 3.02
125 126 0.749649 CGTCCTCATCCTCCTCCTTG 59.250 60.000 0.00 0.00 0.00 3.61
126 127 0.631753 TCGTCCTCATCCTCCTCCTT 59.368 55.000 0.00 0.00 0.00 3.36
127 128 0.106419 GTCGTCCTCATCCTCCTCCT 60.106 60.000 0.00 0.00 0.00 3.69
142 143 4.731503 CGTCTTCGCCGTCGTCGT 62.732 66.667 0.71 0.00 36.96 4.34
183 184 5.931146 CCATTAAAACCATTGTAAGCAAGCA 59.069 36.000 0.00 0.00 38.10 3.91
231 232 1.372251 CAGAGCACGACAAGAGCGT 60.372 57.895 0.00 0.00 43.67 5.07
251 252 1.296056 TTCGCAGGCGTCCTTTTAGC 61.296 55.000 13.83 0.00 40.74 3.09
339 340 2.169769 GTCATCGGGGGTCATTGTCTTA 59.830 50.000 0.00 0.00 0.00 2.10
347 348 1.801242 ACATATGTCATCGGGGGTCA 58.199 50.000 1.41 0.00 0.00 4.02
356 358 3.202906 GCAACCCGTGTACATATGTCAT 58.797 45.455 12.68 0.00 0.00 3.06
386 389 0.383949 TTTTCCTGCGAAGTTGCACC 59.616 50.000 0.00 0.00 40.62 5.01
387 390 1.202245 TGTTTTCCTGCGAAGTTGCAC 60.202 47.619 0.00 0.00 40.62 4.57
396 399 8.167985 CCATATTATTTGTTTTGTTTTCCTGCG 58.832 33.333 0.00 0.00 0.00 5.18
401 404 9.719355 ACCTCCCATATTATTTGTTTTGTTTTC 57.281 29.630 0.00 0.00 0.00 2.29
405 408 6.440328 AGCACCTCCCATATTATTTGTTTTGT 59.560 34.615 0.00 0.00 0.00 2.83
406 409 6.757947 CAGCACCTCCCATATTATTTGTTTTG 59.242 38.462 0.00 0.00 0.00 2.44
410 413 5.129368 ACAGCACCTCCCATATTATTTGT 57.871 39.130 0.00 0.00 0.00 2.83
414 417 5.589367 AATGACAGCACCTCCCATATTAT 57.411 39.130 0.00 0.00 0.00 1.28
415 418 5.376625 GAAATGACAGCACCTCCCATATTA 58.623 41.667 0.00 0.00 0.00 0.98
416 419 3.959495 AATGACAGCACCTCCCATATT 57.041 42.857 0.00 0.00 0.00 1.28
417 420 3.435601 GGAAATGACAGCACCTCCCATAT 60.436 47.826 0.00 0.00 0.00 1.78
418 421 2.092429 GGAAATGACAGCACCTCCCATA 60.092 50.000 0.00 0.00 0.00 2.74
419 422 1.341383 GGAAATGACAGCACCTCCCAT 60.341 52.381 0.00 0.00 0.00 4.00
440 448 7.231925 ACCAATTCAGATGCAATATGATAGCAA 59.768 33.333 0.00 0.00 45.03 3.91
445 453 6.072649 TGGACCAATTCAGATGCAATATGAT 58.927 36.000 0.00 0.00 45.03 2.45
450 458 3.118884 GCTTGGACCAATTCAGATGCAAT 60.119 43.478 7.54 0.00 0.00 3.56
477 485 1.066858 ACTGCACTGGACTGAATACGG 60.067 52.381 0.00 0.00 0.00 4.02
489 497 1.208358 CCATTGACGCACTGCACTG 59.792 57.895 1.11 0.00 0.00 3.66
538 546 6.061022 TCATCCATGTGTTTACCACTGTAT 57.939 37.500 0.00 0.00 44.81 2.29
542 550 4.018506 TCCATCATCCATGTGTTTACCACT 60.019 41.667 0.00 0.00 44.81 4.00
551 559 5.784578 AAACATGATCCATCATCCATGTG 57.215 39.130 0.00 0.00 45.23 3.21
559 567 5.063204 GGGTTCGATAAACATGATCCATCA 58.937 41.667 0.00 0.00 39.81 3.07
560 568 5.063204 TGGGTTCGATAAACATGATCCATC 58.937 41.667 0.00 0.00 39.81 3.51
561 569 5.047566 TGGGTTCGATAAACATGATCCAT 57.952 39.130 0.00 0.00 39.81 3.41
569 577 6.128117 GCTTCATAACTTGGGTTCGATAAACA 60.128 38.462 0.00 0.00 39.81 2.83
577 585 5.183904 ACAAGATGCTTCATAACTTGGGTTC 59.816 40.000 0.00 0.00 41.15 3.62
587 595 9.665719 TGTTTAGATTGTACAAGATGCTTCATA 57.334 29.630 14.65 0.00 0.00 2.15
590 598 6.963805 GCTGTTTAGATTGTACAAGATGCTTC 59.036 38.462 14.65 5.53 0.00 3.86
614 623 5.880054 TCTTACTCTTAACAGCCATTTGC 57.120 39.130 0.00 0.00 41.71 3.68
615 624 9.167311 AGTATTCTTACTCTTAACAGCCATTTG 57.833 33.333 0.00 0.00 33.18 2.32
616 625 9.167311 CAGTATTCTTACTCTTAACAGCCATTT 57.833 33.333 0.00 0.00 36.50 2.32
617 626 8.322091 ACAGTATTCTTACTCTTAACAGCCATT 58.678 33.333 0.00 0.00 36.50 3.16
618 627 7.852263 ACAGTATTCTTACTCTTAACAGCCAT 58.148 34.615 0.00 0.00 36.50 4.40
619 628 7.241042 ACAGTATTCTTACTCTTAACAGCCA 57.759 36.000 0.00 0.00 36.50 4.75
620 629 7.705752 GGTACAGTATTCTTACTCTTAACAGCC 59.294 40.741 0.00 0.00 36.50 4.85
621 630 8.248945 TGGTACAGTATTCTTACTCTTAACAGC 58.751 37.037 0.00 0.00 36.50 4.40
626 635 9.483489 TCCATTGGTACAGTATTCTTACTCTTA 57.517 33.333 1.86 0.00 42.39 2.10
627 636 8.375493 TCCATTGGTACAGTATTCTTACTCTT 57.625 34.615 1.86 0.00 42.39 2.85
628 637 7.839705 TCTCCATTGGTACAGTATTCTTACTCT 59.160 37.037 1.86 0.00 42.39 3.24
629 638 8.008513 TCTCCATTGGTACAGTATTCTTACTC 57.991 38.462 1.86 0.00 42.39 2.59
630 639 7.973048 TCTCCATTGGTACAGTATTCTTACT 57.027 36.000 1.86 0.00 42.39 2.24
631 640 8.258708 ACTTCTCCATTGGTACAGTATTCTTAC 58.741 37.037 1.86 0.00 42.39 2.34
632 641 8.375493 ACTTCTCCATTGGTACAGTATTCTTA 57.625 34.615 1.86 0.00 42.39 2.10
633 642 7.259088 ACTTCTCCATTGGTACAGTATTCTT 57.741 36.000 1.86 0.00 42.39 2.52
634 643 6.875972 ACTTCTCCATTGGTACAGTATTCT 57.124 37.500 1.86 0.00 42.39 2.40
638 647 8.867097 GGATAATACTTCTCCATTGGTACAGTA 58.133 37.037 1.86 7.64 42.39 2.74
639 648 7.471539 CGGATAATACTTCTCCATTGGTACAGT 60.472 40.741 1.86 5.75 42.39 3.55
640 649 6.868864 CGGATAATACTTCTCCATTGGTACAG 59.131 42.308 1.86 0.00 42.39 2.74
641 650 6.551975 TCGGATAATACTTCTCCATTGGTACA 59.448 38.462 1.86 0.00 0.00 2.90
642 651 6.989659 TCGGATAATACTTCTCCATTGGTAC 58.010 40.000 1.86 0.00 0.00 3.34
643 652 7.792364 ATCGGATAATACTTCTCCATTGGTA 57.208 36.000 1.86 0.00 0.00 3.25
644 653 6.688073 ATCGGATAATACTTCTCCATTGGT 57.312 37.500 1.86 0.00 0.00 3.67
645 654 7.161404 TGAATCGGATAATACTTCTCCATTGG 58.839 38.462 0.00 0.00 0.00 3.16
646 655 8.783833 ATGAATCGGATAATACTTCTCCATTG 57.216 34.615 0.00 0.00 0.00 2.82
647 656 9.799106 AAATGAATCGGATAATACTTCTCCATT 57.201 29.630 0.00 0.00 0.00 3.16
648 657 9.442047 GAAATGAATCGGATAATACTTCTCCAT 57.558 33.333 0.00 0.00 0.00 3.41
649 658 8.651389 AGAAATGAATCGGATAATACTTCTCCA 58.349 33.333 0.00 0.00 0.00 3.86
650 659 9.145865 GAGAAATGAATCGGATAATACTTCTCC 57.854 37.037 13.42 0.00 32.55 3.71
651 660 9.921637 AGAGAAATGAATCGGATAATACTTCTC 57.078 33.333 15.13 15.13 36.77 2.87
652 661 9.703892 CAGAGAAATGAATCGGATAATACTTCT 57.296 33.333 0.00 0.00 0.00 2.85
653 662 8.439286 GCAGAGAAATGAATCGGATAATACTTC 58.561 37.037 0.00 0.00 0.00 3.01
654 663 7.116948 CGCAGAGAAATGAATCGGATAATACTT 59.883 37.037 0.00 0.00 0.00 2.24
655 664 6.587990 CGCAGAGAAATGAATCGGATAATACT 59.412 38.462 0.00 0.00 0.00 2.12
656 665 6.586463 TCGCAGAGAAATGAATCGGATAATAC 59.414 38.462 0.00 0.00 0.00 1.89
657 666 6.687604 TCGCAGAGAAATGAATCGGATAATA 58.312 36.000 0.00 0.00 0.00 0.98
658 667 5.541845 TCGCAGAGAAATGAATCGGATAAT 58.458 37.500 0.00 0.00 0.00 1.28
659 668 4.944048 TCGCAGAGAAATGAATCGGATAA 58.056 39.130 0.00 0.00 0.00 1.75
660 669 4.584327 TCGCAGAGAAATGAATCGGATA 57.416 40.909 0.00 0.00 0.00 2.59
661 670 3.459232 TCGCAGAGAAATGAATCGGAT 57.541 42.857 0.00 0.00 0.00 4.18
662 671 2.959507 TCGCAGAGAAATGAATCGGA 57.040 45.000 0.00 0.00 0.00 4.55
663 672 4.542662 AAATCGCAGAGAAATGAATCGG 57.457 40.909 0.00 0.00 43.63 4.18
664 673 5.006649 TGGTAAATCGCAGAGAAATGAATCG 59.993 40.000 0.00 0.00 43.63 3.34
665 674 6.363577 TGGTAAATCGCAGAGAAATGAATC 57.636 37.500 0.00 0.00 43.63 2.52
666 675 6.319658 ACATGGTAAATCGCAGAGAAATGAAT 59.680 34.615 0.00 0.00 43.63 2.57
667 676 5.647658 ACATGGTAAATCGCAGAGAAATGAA 59.352 36.000 0.00 0.00 43.63 2.57
668 677 5.065090 CACATGGTAAATCGCAGAGAAATGA 59.935 40.000 0.00 0.00 43.63 2.57
669 678 5.268544 CACATGGTAAATCGCAGAGAAATG 58.731 41.667 0.00 0.00 43.63 2.32
670 679 4.201950 GCACATGGTAAATCGCAGAGAAAT 60.202 41.667 0.00 0.00 43.63 2.17
671 680 3.126858 GCACATGGTAAATCGCAGAGAAA 59.873 43.478 0.00 0.00 43.63 2.52
672 681 2.677836 GCACATGGTAAATCGCAGAGAA 59.322 45.455 0.00 0.00 43.63 2.87
673 682 2.279741 GCACATGGTAAATCGCAGAGA 58.720 47.619 0.00 0.00 43.63 3.10
674 683 2.009051 TGCACATGGTAAATCGCAGAG 58.991 47.619 0.00 0.00 43.63 3.35
675 684 2.106477 TGCACATGGTAAATCGCAGA 57.894 45.000 0.00 0.00 45.75 4.26
676 685 2.917701 TTGCACATGGTAAATCGCAG 57.082 45.000 0.00 0.00 0.00 5.18
677 686 2.094803 CCTTTGCACATGGTAAATCGCA 60.095 45.455 0.00 0.00 30.46 5.10
678 687 2.094752 ACCTTTGCACATGGTAAATCGC 60.095 45.455 0.00 0.00 30.46 4.58
679 688 3.727673 CGACCTTTGCACATGGTAAATCG 60.728 47.826 0.00 2.72 33.74 3.34
680 689 3.438781 TCGACCTTTGCACATGGTAAATC 59.561 43.478 0.00 0.00 33.74 2.17
681 690 3.417101 TCGACCTTTGCACATGGTAAAT 58.583 40.909 0.00 0.00 33.74 1.40
682 691 2.852449 TCGACCTTTGCACATGGTAAA 58.148 42.857 0.00 0.00 33.74 2.01
683 692 2.552599 TCGACCTTTGCACATGGTAA 57.447 45.000 0.00 0.00 33.74 2.85
684 693 2.355197 CATCGACCTTTGCACATGGTA 58.645 47.619 0.00 0.00 33.74 3.25
685 694 1.167851 CATCGACCTTTGCACATGGT 58.832 50.000 4.36 4.36 36.70 3.55
686 695 0.179156 GCATCGACCTTTGCACATGG 60.179 55.000 3.89 0.00 38.72 3.66
687 696 0.522626 TGCATCGACCTTTGCACATG 59.477 50.000 7.31 0.00 43.54 3.21
688 697 0.806868 CTGCATCGACCTTTGCACAT 59.193 50.000 7.31 0.00 43.54 3.21
689 698 0.250252 TCTGCATCGACCTTTGCACA 60.250 50.000 7.31 0.00 43.54 4.57
690 699 0.445436 CTCTGCATCGACCTTTGCAC 59.555 55.000 7.31 0.00 43.54 4.57
691 700 0.321346 TCTCTGCATCGACCTTTGCA 59.679 50.000 10.73 10.73 46.03 4.08
692 701 1.005340 CTCTCTGCATCGACCTTTGC 58.995 55.000 1.74 1.74 39.33 3.68
693 702 1.998315 CACTCTCTGCATCGACCTTTG 59.002 52.381 0.00 0.00 0.00 2.77
694 703 1.066573 CCACTCTCTGCATCGACCTTT 60.067 52.381 0.00 0.00 0.00 3.11
695 704 0.534412 CCACTCTCTGCATCGACCTT 59.466 55.000 0.00 0.00 0.00 3.50
696 705 0.613292 ACCACTCTCTGCATCGACCT 60.613 55.000 0.00 0.00 0.00 3.85
697 706 0.247736 AACCACTCTCTGCATCGACC 59.752 55.000 0.00 0.00 0.00 4.79
698 707 1.203523 AGAACCACTCTCTGCATCGAC 59.796 52.381 0.00 0.00 0.00 4.20
699 708 1.550327 AGAACCACTCTCTGCATCGA 58.450 50.000 0.00 0.00 0.00 3.59
700 709 1.998315 CAAGAACCACTCTCTGCATCG 59.002 52.381 0.00 0.00 31.02 3.84
701 710 2.289945 ACCAAGAACCACTCTCTGCATC 60.290 50.000 0.00 0.00 31.02 3.91
702 711 1.701847 ACCAAGAACCACTCTCTGCAT 59.298 47.619 0.00 0.00 31.02 3.96
703 712 1.131638 ACCAAGAACCACTCTCTGCA 58.868 50.000 0.00 0.00 31.02 4.41
704 713 1.517242 CACCAAGAACCACTCTCTGC 58.483 55.000 0.00 0.00 31.02 4.26
705 714 1.202687 TGCACCAAGAACCACTCTCTG 60.203 52.381 0.00 0.00 31.02 3.35
706 715 1.071385 CTGCACCAAGAACCACTCTCT 59.929 52.381 0.00 0.00 31.02 3.10
707 716 1.070758 TCTGCACCAAGAACCACTCTC 59.929 52.381 0.00 0.00 31.02 3.20
708 717 1.131638 TCTGCACCAAGAACCACTCT 58.868 50.000 0.00 0.00 35.13 3.24
709 718 1.967319 TTCTGCACCAAGAACCACTC 58.033 50.000 0.00 0.00 31.19 3.51
710 719 2.508526 GATTCTGCACCAAGAACCACT 58.491 47.619 0.00 0.00 38.95 4.00
711 720 1.197721 CGATTCTGCACCAAGAACCAC 59.802 52.381 0.00 0.00 38.95 4.16
712 721 1.071542 TCGATTCTGCACCAAGAACCA 59.928 47.619 0.00 0.00 38.95 3.67
713 722 1.808411 TCGATTCTGCACCAAGAACC 58.192 50.000 0.00 0.00 38.95 3.62
714 723 2.029728 CGATCGATTCTGCACCAAGAAC 59.970 50.000 10.26 0.00 38.95 3.01
715 724 2.270923 CGATCGATTCTGCACCAAGAA 58.729 47.619 10.26 0.00 40.36 2.52
716 725 1.204704 ACGATCGATTCTGCACCAAGA 59.795 47.619 24.34 0.00 0.00 3.02
717 726 1.645034 ACGATCGATTCTGCACCAAG 58.355 50.000 24.34 0.00 0.00 3.61
718 727 1.999735 GAACGATCGATTCTGCACCAA 59.000 47.619 24.34 0.00 0.00 3.67
719 728 1.067213 TGAACGATCGATTCTGCACCA 60.067 47.619 24.34 0.00 0.00 4.17
720 729 1.590238 CTGAACGATCGATTCTGCACC 59.410 52.381 24.34 0.00 0.00 5.01
721 730 1.590238 CCTGAACGATCGATTCTGCAC 59.410 52.381 24.34 0.00 0.00 4.57
722 731 1.476488 TCCTGAACGATCGATTCTGCA 59.524 47.619 24.34 9.14 0.00 4.41
723 732 1.855360 GTCCTGAACGATCGATTCTGC 59.145 52.381 24.34 9.69 0.00 4.26
724 733 2.464865 GGTCCTGAACGATCGATTCTG 58.535 52.381 24.34 21.46 0.00 3.02
745 754 6.976636 TTTTGTTTTTGGTCTGATGGAAAC 57.023 33.333 0.00 0.00 0.00 2.78
776 786 2.034221 GGCAAGGAACCGGAGCTT 59.966 61.111 9.46 0.00 0.00 3.74
836 846 1.373497 CGAACGTTGAGAGGCTGCT 60.373 57.895 5.00 0.00 0.00 4.24
847 857 0.314935 TTTAGCCTCCGACGAACGTT 59.685 50.000 0.00 0.00 40.78 3.99
848 858 0.314935 TTTTAGCCTCCGACGAACGT 59.685 50.000 0.00 0.00 40.78 3.99
856 866 1.672881 CAGCTCCATTTTTAGCCTCCG 59.327 52.381 0.00 0.00 39.64 4.63
1156 1166 2.436646 CTGAACGCCTGGCCGATT 60.437 61.111 14.12 5.08 0.00 3.34
1157 1167 3.665675 GACTGAACGCCTGGCCGAT 62.666 63.158 14.12 2.94 0.00 4.18
1158 1168 4.373116 GACTGAACGCCTGGCCGA 62.373 66.667 14.12 0.00 0.00 5.54
1161 1171 4.329545 TGGGACTGAACGCCTGGC 62.330 66.667 9.11 9.11 0.00 4.85
1162 1172 2.046892 CTGGGACTGAACGCCTGG 60.047 66.667 0.00 0.00 0.00 4.45
1163 1173 2.743928 GCTGGGACTGAACGCCTG 60.744 66.667 0.00 0.00 0.00 4.85
1164 1174 2.925170 AGCTGGGACTGAACGCCT 60.925 61.111 0.00 0.00 0.00 5.52
1165 1175 2.743928 CAGCTGGGACTGAACGCC 60.744 66.667 5.57 0.00 40.25 5.68
1166 1176 3.426568 GCAGCTGGGACTGAACGC 61.427 66.667 17.12 0.00 40.25 4.84
1167 1177 0.957395 ATTGCAGCTGGGACTGAACG 60.957 55.000 17.12 0.00 40.25 3.95
1172 1182 2.547640 ATCGCATTGCAGCTGGGACT 62.548 55.000 17.12 7.14 38.24 3.85
1185 1195 2.462456 AGATGGTCGCATAATCGCAT 57.538 45.000 0.00 0.00 0.00 4.73
1186 1196 1.866601 CAAGATGGTCGCATAATCGCA 59.133 47.619 0.00 0.00 0.00 5.10
1187 1197 1.867233 ACAAGATGGTCGCATAATCGC 59.133 47.619 0.00 0.00 0.00 4.58
1188 1198 3.183172 CAGACAAGATGGTCGCATAATCG 59.817 47.826 0.00 0.00 42.62 3.34
1189 1199 3.496130 CCAGACAAGATGGTCGCATAATC 59.504 47.826 0.00 0.00 42.62 1.75
1190 1200 3.470709 CCAGACAAGATGGTCGCATAAT 58.529 45.455 0.00 0.00 42.62 1.28
1191 1201 2.419990 CCCAGACAAGATGGTCGCATAA 60.420 50.000 0.00 0.00 42.62 1.90
1192 1202 1.138859 CCCAGACAAGATGGTCGCATA 59.861 52.381 0.00 0.00 42.62 3.14
1194 1204 1.191489 TCCCAGACAAGATGGTCGCA 61.191 55.000 0.00 0.00 42.62 5.10
1211 1221 2.287373 CGTAGTCACGTATCCAGAGTCC 59.713 54.545 0.00 0.00 43.31 3.85
1228 1238 1.450533 CTGCACAACACACGTACGTAG 59.549 52.381 22.34 18.51 0.00 3.51
1230 1240 1.149361 CCTGCACAACACACGTACGT 61.149 55.000 16.72 16.72 0.00 3.57
1231 1241 1.562691 CCTGCACAACACACGTACG 59.437 57.895 15.01 15.01 0.00 3.67
1236 1246 1.453015 TCACCCCTGCACAACACAC 60.453 57.895 0.00 0.00 0.00 3.82
1387 1397 0.680921 GATGATGGTGGTGGTGGTGG 60.681 60.000 0.00 0.00 0.00 4.61
1405 1415 1.293179 CTGGTGCTGACGGTGATGA 59.707 57.895 0.00 0.00 0.00 2.92
1541 1551 0.744414 AGATCGGGTGCGGTTTGATG 60.744 55.000 0.00 0.00 0.00 3.07
1546 1556 2.125673 CGAAGATCGGGTGCGGTT 60.126 61.111 0.00 0.00 36.00 4.44
1561 1571 3.062466 CCAGACTGAGGTCGCCGA 61.062 66.667 3.32 0.00 46.29 5.54
1575 1585 0.039798 ACTGTACGTACGTGTGCCAG 60.040 55.000 30.25 26.78 0.00 4.85
1638 1648 1.518572 GTATGCTGGCGCGTGTAGT 60.519 57.895 8.43 0.00 39.65 2.73
1651 1661 0.531311 CGGTCCCTAAACCCGTATGC 60.531 60.000 0.00 0.00 37.00 3.14
1692 1706 0.922560 CGATCAGGCGTGTACGTACG 60.923 60.000 20.18 15.01 46.28 3.67
1711 1725 1.302271 GTGGAACAACGGGACCCTC 60.302 63.158 9.41 0.00 44.16 4.30
1805 1819 0.388778 TTGCATGCAACAATGGCTCG 60.389 50.000 28.80 0.00 0.00 5.03
1850 1869 3.268023 AGTTAATCTGGGGCGAGAAAG 57.732 47.619 0.00 0.00 0.00 2.62
1960 1980 4.093703 CAGGAACGTGTACAAGAAAACACA 59.906 41.667 16.00 0.00 44.98 3.72
1961 1981 4.330620 TCAGGAACGTGTACAAGAAAACAC 59.669 41.667 16.00 0.00 42.04 3.32
1968 1988 2.140717 GGGTTCAGGAACGTGTACAAG 58.859 52.381 7.29 7.29 42.02 3.16
1972 1992 1.707106 TCAGGGTTCAGGAACGTGTA 58.293 50.000 6.12 0.00 42.02 2.90
1974 1994 1.806542 CATTCAGGGTTCAGGAACGTG 59.193 52.381 6.12 6.48 42.02 4.49
1976 1996 1.003118 TCCATTCAGGGTTCAGGAACG 59.997 52.381 6.12 0.00 42.02 3.95
1988 2009 2.158449 GTCTCGTTGCACTTCCATTCAG 59.842 50.000 0.00 0.00 0.00 3.02
1991 2012 2.146342 CTGTCTCGTTGCACTTCCATT 58.854 47.619 0.00 0.00 0.00 3.16
1995 2016 2.423926 TCTCTGTCTCGTTGCACTTC 57.576 50.000 0.00 0.00 0.00 3.01
2007 2028 0.871057 GCAGCCACACTTTCTCTGTC 59.129 55.000 0.00 0.00 0.00 3.51
2039 2060 3.907894 TGTTCGGTTTTTCCTACATGC 57.092 42.857 0.00 0.00 0.00 4.06
2040 2061 8.889717 ACTATTATGTTCGGTTTTTCCTACATG 58.110 33.333 0.00 0.00 38.57 3.21
2054 2075 6.565234 ACTCTGAACCTGACTATTATGTTCG 58.435 40.000 0.00 0.00 38.46 3.95
2060 2081 6.948886 ACTCTGAACTCTGAACCTGACTATTA 59.051 38.462 0.00 0.00 0.00 0.98
2063 2084 4.520874 CACTCTGAACTCTGAACCTGACTA 59.479 45.833 0.00 0.00 0.00 2.59
2064 2085 3.320541 CACTCTGAACTCTGAACCTGACT 59.679 47.826 0.00 0.00 0.00 3.41
2065 2086 3.553922 CCACTCTGAACTCTGAACCTGAC 60.554 52.174 0.00 0.00 0.00 3.51
2070 2095 3.735237 TCACCACTCTGAACTCTGAAC 57.265 47.619 0.00 0.00 0.00 3.18
2124 2149 0.806102 GAATCGGCGCTGCTACAGAA 60.806 55.000 12.58 0.00 32.44 3.02
2141 2166 6.833027 GACACTGTCAAATCCACTCCGGAA 62.833 50.000 5.23 0.00 38.87 4.30
2147 2172 3.329386 CGATGACACTGTCAAATCCACT 58.671 45.455 15.80 0.00 45.96 4.00
2149 2174 2.076100 GCGATGACACTGTCAAATCCA 58.924 47.619 15.80 0.00 45.96 3.41
2174 2199 1.811266 CTCACGTCGCCATCCTTGG 60.811 63.158 0.00 0.00 46.66 3.61
2217 2250 0.105039 AATCGAGATCGCCTTGGTCC 59.895 55.000 0.00 0.00 39.60 4.46
2256 2289 6.551975 TCGGAGTATTGGGATACTTGATTACA 59.448 38.462 1.06 0.00 46.53 2.41
2259 2292 5.839063 TCTCGGAGTATTGGGATACTTGATT 59.161 40.000 4.69 0.00 46.53 2.57
2270 2303 3.710326 TGATTCGTCTCGGAGTATTGG 57.290 47.619 4.69 0.00 0.00 3.16
2274 2307 4.868171 CCAATTTTGATTCGTCTCGGAGTA 59.132 41.667 4.69 0.00 0.00 2.59
2278 2314 3.483574 CGTCCAATTTTGATTCGTCTCGG 60.484 47.826 0.00 0.00 0.00 4.63
2282 2318 2.515912 GCCGTCCAATTTTGATTCGTC 58.484 47.619 0.00 0.00 0.00 4.20
2465 2753 2.970324 TTGTGCTTGTCGGGCGTC 60.970 61.111 0.00 0.00 0.00 5.19
2487 2775 1.160329 GCTCGCGGGAATATGCACTT 61.160 55.000 12.03 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.