Multiple sequence alignment - TraesCS3A01G507100

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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 TraesCS3A01G507100 chr3A 100.000 3278 0 0 1 3278 728257606 728254329 0.000000e+00 6054.0
1 TraesCS3A01G507100 chr3A 92.634 2335 100 24 1 2288 728107927 728105618 0.000000e+00 3293.0
2 TraesCS3A01G507100 chr3A 83.569 992 141 20 2297 3278 728105556 728104577 0.000000e+00 909.0
3 TraesCS3A01G507100 chr3D 96.607 1061 23 5 746 1804 598097761 598096712 0.000000e+00 1748.0
4 TraesCS3A01G507100 chr3D 94.411 662 37 0 1806 2467 598096683 598096022 0.000000e+00 1018.0
5 TraesCS3A01G507100 chr3D 91.713 724 41 12 1 718 598098542 598097832 0.000000e+00 987.0
6 TraesCS3A01G507100 chr3D 82.780 813 121 13 2473 3278 598085505 598084705 0.000000e+00 708.0
7 TraesCS3A01G507100 chr3D 80.325 615 104 12 1190 1796 551574848 551575453 1.790000e-122 449.0
8 TraesCS3A01G507100 chr3D 77.820 789 134 23 1014 1787 551624367 551625129 1.790000e-122 449.0
9 TraesCS3A01G507100 chr3D 80.392 612 91 18 1014 1605 586035810 586036412 3.880000e-119 438.0
10 TraesCS3A01G507100 chr3D 79.333 600 112 12 2441 3033 452654950 452655544 8.470000e-111 411.0
11 TraesCS3A01G507100 chr3D 87.879 330 37 3 2877 3204 598085959 598085631 5.130000e-103 385.0
12 TraesCS3A01G507100 chr3D 86.598 194 20 6 147 338 598098186 598097997 3.310000e-50 209.0
13 TraesCS3A01G507100 chr3D 81.633 245 40 3 1561 1804 582044725 582044965 7.170000e-47 198.0
14 TraesCS3A01G507100 chr7D 90.857 1225 49 10 811 2007 555404745 555403556 0.000000e+00 1583.0
15 TraesCS3A01G507100 chr7D 91.264 435 37 1 2004 2438 555394734 555394301 2.820000e-165 592.0
16 TraesCS3A01G507100 chr7D 81.698 530 89 7 2446 2971 635663617 635663092 5.020000e-118 435.0
17 TraesCS3A01G507100 chr7D 95.968 124 5 0 685 808 555422959 555422836 5.550000e-48 202.0
18 TraesCS3A01G507100 chr3B 90.000 840 57 11 1201 2013 805042042 805041203 0.000000e+00 1061.0
19 TraesCS3A01G507100 chr3B 91.115 529 29 5 1801 2329 805038224 805037714 0.000000e+00 701.0
20 TraesCS3A01G507100 chr3B 81.694 803 123 12 1014 1795 782677386 782678185 0.000000e+00 647.0
21 TraesCS3A01G507100 chr3B 89.979 469 28 7 1861 2329 805022598 805022149 3.640000e-164 588.0
22 TraesCS3A01G507100 chr3B 94.690 339 16 1 866 1202 805042424 805042086 2.900000e-145 525.0
23 TraesCS3A01G507100 chr3B 88.981 363 13 13 539 896 805022138 805021798 1.090000e-114 424.0
24 TraesCS3A01G507100 chr3B 88.556 367 15 13 539 900 805037703 805037359 1.410000e-113 420.0
25 TraesCS3A01G507100 chr5B 84.753 892 108 18 936 1804 636901996 636901110 0.000000e+00 869.0
26 TraesCS3A01G507100 chr5D 83.896 888 112 17 935 1799 506163364 506162485 0.000000e+00 819.0
27 TraesCS3A01G507100 chr4B 80.136 589 113 4 2446 3032 4541217 4541803 1.400000e-118 436.0
28 TraesCS3A01G507100 chr4D 79.700 601 114 8 2446 3042 425695118 425694522 8.410000e-116 427.0
29 TraesCS3A01G507100 chr1D 81.559 526 90 7 2446 2969 472292443 472291923 8.410000e-116 427.0
30 TraesCS3A01G507100 chr6A 80.292 548 101 6 2446 2990 608656056 608656599 1.100000e-109 407.0
31 TraesCS3A01G507100 chr2A 80.000 560 102 10 2446 3001 175388001 175387448 3.940000e-109 405.0
32 TraesCS3A01G507100 chr2A 76.975 595 111 22 2446 3033 49759969 49759394 1.900000e-82 316.0
33 TraesCS3A01G507100 chr6D 78.571 112 14 6 371 482 173913453 173913352 7.590000e-07 65.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G507100 chr3A 728254329 728257606 3277 True 6054.00 6054 100.00000 1 3278 1 chr3A.!!$R1 3277
1 TraesCS3A01G507100 chr3A 728104577 728107927 3350 True 2101.00 3293 88.10150 1 3278 2 chr3A.!!$R2 3277
2 TraesCS3A01G507100 chr3D 598096022 598098542 2520 True 990.50 1748 92.33225 1 2467 4 chr3D.!!$R2 2466
3 TraesCS3A01G507100 chr3D 598084705 598085959 1254 True 546.50 708 85.32950 2473 3278 2 chr3D.!!$R1 805
4 TraesCS3A01G507100 chr3D 551574848 551575453 605 False 449.00 449 80.32500 1190 1796 1 chr3D.!!$F2 606
5 TraesCS3A01G507100 chr3D 551624367 551625129 762 False 449.00 449 77.82000 1014 1787 1 chr3D.!!$F3 773
6 TraesCS3A01G507100 chr3D 586035810 586036412 602 False 438.00 438 80.39200 1014 1605 1 chr3D.!!$F5 591
7 TraesCS3A01G507100 chr3D 452654950 452655544 594 False 411.00 411 79.33300 2441 3033 1 chr3D.!!$F1 592
8 TraesCS3A01G507100 chr7D 555403556 555404745 1189 True 1583.00 1583 90.85700 811 2007 1 chr7D.!!$R2 1196
9 TraesCS3A01G507100 chr7D 635663092 635663617 525 True 435.00 435 81.69800 2446 2971 1 chr7D.!!$R4 525
10 TraesCS3A01G507100 chr3B 805037359 805042424 5065 True 676.75 1061 91.09025 539 2329 4 chr3B.!!$R2 1790
11 TraesCS3A01G507100 chr3B 782677386 782678185 799 False 647.00 647 81.69400 1014 1795 1 chr3B.!!$F1 781
12 TraesCS3A01G507100 chr3B 805021798 805022598 800 True 506.00 588 89.48000 539 2329 2 chr3B.!!$R1 1790
13 TraesCS3A01G507100 chr5B 636901110 636901996 886 True 869.00 869 84.75300 936 1804 1 chr5B.!!$R1 868
14 TraesCS3A01G507100 chr5D 506162485 506163364 879 True 819.00 819 83.89600 935 1799 1 chr5D.!!$R1 864
15 TraesCS3A01G507100 chr4B 4541217 4541803 586 False 436.00 436 80.13600 2446 3032 1 chr4B.!!$F1 586
16 TraesCS3A01G507100 chr4D 425694522 425695118 596 True 427.00 427 79.70000 2446 3042 1 chr4D.!!$R1 596
17 TraesCS3A01G507100 chr1D 472291923 472292443 520 True 427.00 427 81.55900 2446 2969 1 chr1D.!!$R1 523
18 TraesCS3A01G507100 chr6A 608656056 608656599 543 False 407.00 407 80.29200 2446 2990 1 chr6A.!!$F1 544
19 TraesCS3A01G507100 chr2A 175387448 175388001 553 True 405.00 405 80.00000 2446 3001 1 chr2A.!!$R2 555
20 TraesCS3A01G507100 chr2A 49759394 49759969 575 True 316.00 316 76.97500 2446 3033 1 chr2A.!!$R1 587

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
145 153 0.109319 GCACATTTGCGACCGGAATT 60.109 50.0 9.46 0.00 39.50 2.17 F
774 799 0.311790 AAGCCGACACAATGCAAGTG 59.688 50.0 17.96 17.96 42.56 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1666 1851 0.620556 ACGAAAGCCTGGGTGATGAT 59.379 50.0 0.0 0.0 0.0 2.45 R
2583 6036 0.107214 ATGGGGTGTTAGCATGACGG 60.107 55.0 0.0 0.0 0.0 4.79 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
81 89 4.794334 ACATTGTAGGACGGAGAGAGTAT 58.206 43.478 0.00 0.00 0.00 2.12
145 153 0.109319 GCACATTTGCGACCGGAATT 60.109 50.000 9.46 0.00 39.50 2.17
188 197 3.317109 GGGCTAACCGGGCTAACT 58.683 61.111 6.32 0.00 36.48 2.24
219 236 8.608185 AAAAGGAATTATGCTAGAAAATCCCA 57.392 30.769 0.00 0.00 0.00 4.37
220 237 7.588497 AAGGAATTATGCTAGAAAATCCCAC 57.412 36.000 0.00 0.00 0.00 4.61
221 238 6.672593 AGGAATTATGCTAGAAAATCCCACA 58.327 36.000 0.00 0.00 0.00 4.17
222 239 6.774656 AGGAATTATGCTAGAAAATCCCACAG 59.225 38.462 0.00 0.00 0.00 3.66
223 240 6.547510 GGAATTATGCTAGAAAATCCCACAGT 59.452 38.462 0.00 0.00 0.00 3.55
233 250 6.473758 AGAAAATCCCACAGTAACTAGGAAC 58.526 40.000 0.00 0.00 0.00 3.62
236 253 5.615925 ATCCCACAGTAACTAGGAACATC 57.384 43.478 0.00 0.00 0.00 3.06
237 254 3.446161 TCCCACAGTAACTAGGAACATCG 59.554 47.826 0.00 0.00 0.00 3.84
252 269 5.817816 AGGAACATCGTCTAGCCTTTAATTG 59.182 40.000 0.00 0.00 0.00 2.32
276 293 1.336755 ACATCAGAAAACCACAACCGC 59.663 47.619 0.00 0.00 0.00 5.68
339 356 6.595716 GCCATCTTCACTACATTTGAAGTACT 59.404 38.462 10.94 0.00 46.81 2.73
340 357 7.764443 GCCATCTTCACTACATTTGAAGTACTA 59.236 37.037 10.94 0.00 46.81 1.82
342 359 8.812329 CATCTTCACTACATTTGAAGTACTAGC 58.188 37.037 10.94 0.00 46.81 3.42
486 511 7.922505 TCATTTTAAACATCAGAAAACCACG 57.077 32.000 0.00 0.00 0.00 4.94
490 515 2.631160 ACATCAGAAAACCACGACCA 57.369 45.000 0.00 0.00 0.00 4.02
549 574 6.238731 CCAATGCCATCTTCGCTAGATTTTAA 60.239 38.462 0.00 0.00 41.78 1.52
600 625 4.590647 TCAGATCTATCCCACAGATTCACC 59.409 45.833 0.00 0.00 36.33 4.02
601 626 4.346127 CAGATCTATCCCACAGATTCACCA 59.654 45.833 0.00 0.00 36.33 4.17
602 627 4.592351 AGATCTATCCCACAGATTCACCAG 59.408 45.833 0.00 0.00 36.33 4.00
603 628 3.724478 TCTATCCCACAGATTCACCAGT 58.276 45.455 0.00 0.00 36.33 4.00
604 629 2.795231 ATCCCACAGATTCACCAGTG 57.205 50.000 0.00 0.00 0.00 3.66
605 630 1.434188 TCCCACAGATTCACCAGTGT 58.566 50.000 0.00 0.00 0.00 3.55
606 631 1.347707 TCCCACAGATTCACCAGTGTC 59.652 52.381 0.00 0.00 0.00 3.67
608 633 1.072173 CCACAGATTCACCAGTGTCCA 59.928 52.381 0.00 0.00 0.00 4.02
609 634 2.290514 CCACAGATTCACCAGTGTCCAT 60.291 50.000 0.00 0.00 0.00 3.41
610 635 3.055167 CCACAGATTCACCAGTGTCCATA 60.055 47.826 0.00 0.00 0.00 2.74
611 636 3.935203 CACAGATTCACCAGTGTCCATAC 59.065 47.826 0.00 0.00 0.00 2.39
612 637 3.582647 ACAGATTCACCAGTGTCCATACA 59.417 43.478 0.00 0.00 0.00 2.29
613 638 4.186926 CAGATTCACCAGTGTCCATACAG 58.813 47.826 0.00 0.00 35.91 2.74
614 639 4.081476 CAGATTCACCAGTGTCCATACAGA 60.081 45.833 0.00 0.00 35.91 3.41
618 643 4.385825 TCACCAGTGTCCATACAGAAAAC 58.614 43.478 0.00 0.00 35.91 2.43
620 645 3.137544 ACCAGTGTCCATACAGAAAACCA 59.862 43.478 0.00 0.00 35.91 3.67
621 646 4.202567 ACCAGTGTCCATACAGAAAACCAT 60.203 41.667 0.00 0.00 35.91 3.55
623 648 5.106157 CCAGTGTCCATACAGAAAACCATTC 60.106 44.000 0.00 0.00 35.91 2.67
626 651 4.202620 TGTCCATACAGAAAACCATTCCCA 60.203 41.667 0.00 0.00 0.00 4.37
628 653 5.016173 TCCATACAGAAAACCATTCCCAAG 58.984 41.667 0.00 0.00 0.00 3.61
629 654 4.381932 CCATACAGAAAACCATTCCCAAGC 60.382 45.833 0.00 0.00 0.00 4.01
631 656 1.969923 CAGAAAACCATTCCCAAGCCA 59.030 47.619 0.00 0.00 0.00 4.75
632 657 2.568509 CAGAAAACCATTCCCAAGCCAT 59.431 45.455 0.00 0.00 0.00 4.40
633 658 2.833943 AGAAAACCATTCCCAAGCCATC 59.166 45.455 0.00 0.00 0.00 3.51
634 659 2.629017 AAACCATTCCCAAGCCATCT 57.371 45.000 0.00 0.00 0.00 2.90
635 660 3.756082 AAACCATTCCCAAGCCATCTA 57.244 42.857 0.00 0.00 0.00 1.98
636 661 3.979501 AACCATTCCCAAGCCATCTAT 57.020 42.857 0.00 0.00 0.00 1.98
637 662 3.515602 ACCATTCCCAAGCCATCTATC 57.484 47.619 0.00 0.00 0.00 2.08
638 663 3.059097 ACCATTCCCAAGCCATCTATCT 58.941 45.455 0.00 0.00 0.00 1.98
639 664 3.073650 ACCATTCCCAAGCCATCTATCTC 59.926 47.826 0.00 0.00 0.00 2.75
640 665 3.073503 CCATTCCCAAGCCATCTATCTCA 59.926 47.826 0.00 0.00 0.00 3.27
641 666 3.845781 TTCCCAAGCCATCTATCTCAC 57.154 47.619 0.00 0.00 0.00 3.51
642 667 3.051940 TCCCAAGCCATCTATCTCACT 57.948 47.619 0.00 0.00 0.00 3.41
644 669 3.389329 TCCCAAGCCATCTATCTCACTTC 59.611 47.826 0.00 0.00 0.00 3.01
645 670 3.135348 CCCAAGCCATCTATCTCACTTCA 59.865 47.826 0.00 0.00 0.00 3.02
646 671 4.202440 CCCAAGCCATCTATCTCACTTCAT 60.202 45.833 0.00 0.00 0.00 2.57
647 672 5.012458 CCCAAGCCATCTATCTCACTTCATA 59.988 44.000 0.00 0.00 0.00 2.15
648 673 6.296317 CCCAAGCCATCTATCTCACTTCATAT 60.296 42.308 0.00 0.00 0.00 1.78
651 676 9.716531 CAAGCCATCTATCTCACTTCATATTTA 57.283 33.333 0.00 0.00 0.00 1.40
652 677 9.941325 AAGCCATCTATCTCACTTCATATTTAG 57.059 33.333 0.00 0.00 0.00 1.85
653 678 9.319060 AGCCATCTATCTCACTTCATATTTAGA 57.681 33.333 0.00 0.00 0.00 2.10
654 679 9.585099 GCCATCTATCTCACTTCATATTTAGAG 57.415 37.037 0.00 0.00 0.00 2.43
661 686 9.875708 ATCTCACTTCATATTTAGAGGTCTACT 57.124 33.333 0.00 0.00 0.00 2.57
699 724 7.484035 TTTTTGCAAAACAGTTTACACAAGT 57.516 28.000 23.79 0.00 0.00 3.16
701 726 5.637006 TGCAAAACAGTTTACACAAGTCT 57.363 34.783 0.00 0.00 0.00 3.24
702 727 6.019779 TGCAAAACAGTTTACACAAGTCTT 57.980 33.333 0.00 0.00 0.00 3.01
703 728 6.451393 TGCAAAACAGTTTACACAAGTCTTT 58.549 32.000 0.00 0.00 0.00 2.52
707 732 9.834628 CAAAACAGTTTACACAAGTCTTTTCTA 57.165 29.630 0.00 0.00 0.00 2.10
709 734 7.787725 ACAGTTTACACAAGTCTTTTCTAGG 57.212 36.000 0.00 0.00 0.00 3.02
710 735 7.562135 ACAGTTTACACAAGTCTTTTCTAGGA 58.438 34.615 0.00 0.00 0.00 2.94
711 736 8.044908 ACAGTTTACACAAGTCTTTTCTAGGAA 58.955 33.333 0.00 0.00 0.00 3.36
712 737 8.336080 CAGTTTACACAAGTCTTTTCTAGGAAC 58.664 37.037 0.00 0.00 0.00 3.62
713 738 8.044908 AGTTTACACAAGTCTTTTCTAGGAACA 58.955 33.333 0.00 0.00 0.00 3.18
715 740 8.974060 TTACACAAGTCTTTTCTAGGAACAAT 57.026 30.769 0.00 0.00 0.00 2.71
716 741 7.881775 ACACAAGTCTTTTCTAGGAACAATT 57.118 32.000 0.00 0.00 0.00 2.32
717 742 8.293699 ACACAAGTCTTTTCTAGGAACAATTT 57.706 30.769 0.00 0.00 0.00 1.82
718 743 8.190784 ACACAAGTCTTTTCTAGGAACAATTTG 58.809 33.333 0.00 0.00 0.00 2.32
720 745 8.966868 ACAAGTCTTTTCTAGGAACAATTTGAA 58.033 29.630 2.79 0.00 0.00 2.69
724 749 9.965824 GTCTTTTCTAGGAACAATTTGAATTGA 57.034 29.630 20.04 0.35 46.72 2.57
727 752 9.541143 TTTTCTAGGAACAATTTGAATTGAACC 57.459 29.630 20.04 19.23 46.72 3.62
728 753 7.831691 TCTAGGAACAATTTGAATTGAACCA 57.168 32.000 20.04 12.25 46.72 3.67
730 755 8.306038 TCTAGGAACAATTTGAATTGAACCATG 58.694 33.333 20.04 16.21 46.72 3.66
731 756 7.065120 AGGAACAATTTGAATTGAACCATGA 57.935 32.000 20.04 0.00 46.72 3.07
732 757 7.682628 AGGAACAATTTGAATTGAACCATGAT 58.317 30.769 20.04 6.80 46.72 2.45
734 759 9.434420 GGAACAATTTGAATTGAACCATGATAA 57.566 29.630 20.04 0.00 46.72 1.75
740 765 7.587037 TTGAATTGAACCATGATAATCTCCC 57.413 36.000 0.00 0.00 0.00 4.30
741 766 6.914665 TGAATTGAACCATGATAATCTCCCT 58.085 36.000 0.00 0.00 0.00 4.20
742 767 6.774170 TGAATTGAACCATGATAATCTCCCTG 59.226 38.462 0.00 0.00 0.00 4.45
743 768 5.715439 TTGAACCATGATAATCTCCCTGT 57.285 39.130 0.00 0.00 0.00 4.00
744 769 5.715439 TGAACCATGATAATCTCCCTGTT 57.285 39.130 0.00 0.00 0.00 3.16
745 770 6.078456 TGAACCATGATAATCTCCCTGTTT 57.922 37.500 0.00 0.00 0.00 2.83
746 771 7.206789 TGAACCATGATAATCTCCCTGTTTA 57.793 36.000 0.00 0.00 0.00 2.01
747 772 7.638444 TGAACCATGATAATCTCCCTGTTTAA 58.362 34.615 0.00 0.00 0.00 1.52
748 773 7.775093 TGAACCATGATAATCTCCCTGTTTAAG 59.225 37.037 0.00 0.00 0.00 1.85
766 791 3.009612 GGGTACAAAGCCGACACAA 57.990 52.632 0.00 0.00 32.57 3.33
767 792 1.530323 GGGTACAAAGCCGACACAAT 58.470 50.000 0.00 0.00 32.57 2.71
768 793 1.199097 GGGTACAAAGCCGACACAATG 59.801 52.381 0.00 0.00 32.57 2.82
770 795 1.265635 GTACAAAGCCGACACAATGCA 59.734 47.619 0.00 0.00 0.00 3.96
771 796 0.743688 ACAAAGCCGACACAATGCAA 59.256 45.000 0.00 0.00 0.00 4.08
772 797 1.269206 ACAAAGCCGACACAATGCAAG 60.269 47.619 0.00 0.00 0.00 4.01
773 798 1.032014 AAAGCCGACACAATGCAAGT 58.968 45.000 0.00 0.00 0.00 3.16
774 799 0.311790 AAGCCGACACAATGCAAGTG 59.688 50.000 17.96 17.96 42.56 3.16
775 800 1.081242 GCCGACACAATGCAAGTGG 60.081 57.895 21.90 9.47 41.21 4.00
776 801 1.580942 CCGACACAATGCAAGTGGG 59.419 57.895 21.90 13.21 43.85 4.61
778 803 0.950836 CGACACAATGCAAGTGGGAA 59.049 50.000 21.90 0.00 37.67 3.97
779 804 1.334960 CGACACAATGCAAGTGGGAAC 60.335 52.381 21.90 11.79 37.67 3.62
781 806 2.297033 GACACAATGCAAGTGGGAACAT 59.703 45.455 21.90 4.73 37.67 2.71
782 807 2.297033 ACACAATGCAAGTGGGAACATC 59.703 45.455 21.90 0.00 37.67 3.06
783 808 1.895131 ACAATGCAAGTGGGAACATCC 59.105 47.619 0.00 0.00 46.14 3.51
784 809 1.894466 CAATGCAAGTGGGAACATCCA 59.106 47.619 0.00 0.00 46.14 3.41
792 817 2.806945 TGGGAACATCCACATCCTTC 57.193 50.000 0.00 0.00 38.64 3.46
793 818 1.284785 TGGGAACATCCACATCCTTCC 59.715 52.381 0.00 0.00 38.64 3.46
794 819 1.410224 GGGAACATCCACATCCTTCCC 60.410 57.143 0.00 0.00 42.58 3.97
796 821 2.091665 GGAACATCCACATCCTTCCCAT 60.092 50.000 0.00 0.00 36.28 4.00
797 822 3.217626 GAACATCCACATCCTTCCCATC 58.782 50.000 0.00 0.00 0.00 3.51
798 823 2.207988 ACATCCACATCCTTCCCATCA 58.792 47.619 0.00 0.00 0.00 3.07
799 824 2.092212 ACATCCACATCCTTCCCATCAC 60.092 50.000 0.00 0.00 0.00 3.06
800 825 1.971149 TCCACATCCTTCCCATCACT 58.029 50.000 0.00 0.00 0.00 3.41
801 826 3.129262 TCCACATCCTTCCCATCACTA 57.871 47.619 0.00 0.00 0.00 2.74
802 827 3.668821 TCCACATCCTTCCCATCACTAT 58.331 45.455 0.00 0.00 0.00 2.12
803 828 3.648067 TCCACATCCTTCCCATCACTATC 59.352 47.826 0.00 0.00 0.00 2.08
804 829 3.244700 CCACATCCTTCCCATCACTATCC 60.245 52.174 0.00 0.00 0.00 2.59
805 830 3.392285 CACATCCTTCCCATCACTATCCA 59.608 47.826 0.00 0.00 0.00 3.41
806 831 4.047166 ACATCCTTCCCATCACTATCCAA 58.953 43.478 0.00 0.00 0.00 3.53
807 832 4.666907 ACATCCTTCCCATCACTATCCAAT 59.333 41.667 0.00 0.00 0.00 3.16
808 833 5.135020 ACATCCTTCCCATCACTATCCAATT 59.865 40.000 0.00 0.00 0.00 2.32
809 834 5.310409 TCCTTCCCATCACTATCCAATTC 57.690 43.478 0.00 0.00 0.00 2.17
810 835 4.726317 TCCTTCCCATCACTATCCAATTCA 59.274 41.667 0.00 0.00 0.00 2.57
812 837 5.893255 CCTTCCCATCACTATCCAATTCAAA 59.107 40.000 0.00 0.00 0.00 2.69
813 838 6.552350 CCTTCCCATCACTATCCAATTCAAAT 59.448 38.462 0.00 0.00 0.00 2.32
814 839 7.070322 CCTTCCCATCACTATCCAATTCAAATT 59.930 37.037 0.00 0.00 0.00 1.82
853 927 2.354328 AGAACATAAACCCCTGGACCA 58.646 47.619 0.00 0.00 0.00 4.02
865 939 1.293963 CTGGACCATGTGCACGTCTG 61.294 60.000 18.75 13.13 29.42 3.51
1012 1099 2.073056 CGACGAAAATGGATGTGGACA 58.927 47.619 0.00 0.00 0.00 4.02
1250 1394 4.552365 CCTCGGCATGGACGGCAT 62.552 66.667 0.00 0.00 33.33 4.40
1435 1586 1.490490 AGGTGACCTTCTTGAAGTGCA 59.510 47.619 0.00 4.50 0.00 4.57
1458 1609 2.516225 GTGGCATTAGGGACGGCC 60.516 66.667 0.00 0.00 46.58 6.13
1605 1775 2.531685 TCCCCACCCTTGGTCCAG 60.532 66.667 0.00 0.00 42.10 3.86
1812 2027 1.663702 CGTCGTCCGCTTCACCTTT 60.664 57.895 0.00 0.00 0.00 3.11
2028 5428 0.453793 ACTTCGAGCTCACCGAGATG 59.546 55.000 15.40 7.16 37.35 2.90
2042 5442 2.045926 GATGGACAGCAAGCCGGT 60.046 61.111 1.90 0.00 0.00 5.28
2225 5625 0.806102 GTGCGCGTCCTCATGTGTAT 60.806 55.000 8.43 0.00 0.00 2.29
2230 5630 1.409064 GCGTCCTCATGTGTATGGAGA 59.591 52.381 0.00 0.00 34.97 3.71
2231 5631 2.036475 GCGTCCTCATGTGTATGGAGAT 59.964 50.000 0.00 0.00 34.97 2.75
2251 5651 0.227234 CGCGATCCTCAACGATTTCG 59.773 55.000 0.00 0.00 46.33 3.46
2283 5683 2.187163 GCCCGGTTCTAGCTCCAC 59.813 66.667 0.00 0.00 0.00 4.02
2289 5689 3.378602 TTCTAGCTCCACGCGCCA 61.379 61.111 5.73 0.00 45.59 5.69
2295 5695 4.457496 CTCCACGCGCCACCTGAT 62.457 66.667 5.73 0.00 0.00 2.90
2299 5752 1.068083 CACGCGCCACCTGATATCT 59.932 57.895 5.73 0.00 0.00 1.98
2360 5813 1.075482 CTCCACTGCCACCACCATT 59.925 57.895 0.00 0.00 0.00 3.16
2403 5856 1.419374 GAGCCACGTCAGTGTTGTAG 58.581 55.000 0.00 0.00 46.56 2.74
2439 5892 2.639065 TGTTGGCGTGAGAAACTTTCT 58.361 42.857 3.55 3.55 44.21 2.52
2493 5946 3.364764 GGACCATGTAGCGACGACTATAC 60.365 52.174 0.00 0.00 0.00 1.47
2494 5947 3.208594 ACCATGTAGCGACGACTATACA 58.791 45.455 0.00 2.12 33.04 2.29
2518 5971 1.021202 TGAGTGAGCCAAAAACACGG 58.979 50.000 0.00 0.00 39.19 4.94
2540 5993 0.108138 CCGTCATCGCTCCTCCTTTT 60.108 55.000 0.00 0.00 35.54 2.27
2583 6036 3.398954 TGTTGTGAACAGTCGAAAAGC 57.601 42.857 0.00 0.00 36.25 3.51
2595 6048 1.730064 TCGAAAAGCCGTCATGCTAAC 59.270 47.619 0.00 0.00 41.80 2.34
2608 6061 1.959710 TGCTAACACCCCATAGGACA 58.040 50.000 0.00 0.00 39.89 4.02
2618 6071 1.271871 CCCATAGGACAAGTGCACCAA 60.272 52.381 14.63 0.00 33.47 3.67
2650 6104 1.469703 TCGCCGATGAGAAAGTCGTAA 59.530 47.619 0.00 0.00 36.17 3.18
2710 6169 0.683504 ACGTAGACCGGATCCAAGCT 60.684 55.000 9.46 7.49 42.24 3.74
2759 6219 1.801913 CGCAAGTTCCGACGGAGAG 60.802 63.158 17.51 9.34 31.21 3.20
2788 6376 1.079819 ACGTCCTCCAACGATGCTG 60.080 57.895 3.16 0.00 45.37 4.41
2879 6468 1.187567 AGCCCCAACCAAGACATTGC 61.188 55.000 0.00 0.00 34.91 3.56
2897 6486 6.888430 ACATTGCACGTAAAAAGAACTAGAG 58.112 36.000 0.00 0.00 0.00 2.43
2972 6562 2.918248 CCATCGGAGATGGGGCAA 59.082 61.111 18.63 0.00 45.12 4.52
2980 6570 2.359478 GATGGGGCAAACCGACGT 60.359 61.111 0.00 0.00 41.60 4.34
2991 6581 4.858433 CCGACGTTGGCGCCGATA 62.858 66.667 21.90 5.49 46.48 2.92
3033 6624 4.080072 GGATCTTTTCTTGTGGAGGAGGAT 60.080 45.833 0.00 0.00 0.00 3.24
3044 6635 3.070302 GTGGAGGAGGATGTATTGTCTCC 59.930 52.174 0.00 0.00 44.46 3.71
3063 6654 9.990360 TTGTCTCCGATATATTAGCAAATGTAA 57.010 29.630 0.00 0.00 0.00 2.41
3096 6688 3.578688 GGTCAATCACCAATTGCAGTTC 58.421 45.455 0.00 0.00 45.98 3.01
3101 6693 1.955778 TCACCAATTGCAGTTCCACAG 59.044 47.619 0.00 0.00 0.00 3.66
3176 6770 7.866393 AGTCCCTTCGATAAATATTACTTGTCG 59.134 37.037 0.00 0.00 38.35 4.35
3184 6778 8.757789 CGATAAATATTACTTGTCGCTGGTTTA 58.242 33.333 0.00 0.00 32.04 2.01
3189 6783 5.766702 TTACTTGTCGCTGGTTTAATACG 57.233 39.130 0.00 0.00 0.00 3.06
3231 6830 9.811995 TGTACTAAACCAGCTACAAGTAATATG 57.188 33.333 0.00 0.00 0.00 1.78
3236 6835 6.747414 ACCAGCTACAAGTAATATGGATCA 57.253 37.500 10.32 0.00 0.00 2.92
3240 6839 6.589523 CAGCTACAAGTAATATGGATCAGAGC 59.410 42.308 0.00 0.00 0.00 4.09
3249 6848 5.991933 ATATGGATCAGAGCGAGTACAAT 57.008 39.130 0.00 0.00 0.00 2.71
3252 6851 4.433615 TGGATCAGAGCGAGTACAATTTC 58.566 43.478 0.00 0.00 0.00 2.17
3254 6853 5.112686 GGATCAGAGCGAGTACAATTTCTT 58.887 41.667 0.00 0.00 0.00 2.52
3257 6856 6.861065 TCAGAGCGAGTACAATTTCTTTTT 57.139 33.333 0.00 0.00 0.00 1.94
3258 6857 7.956420 TCAGAGCGAGTACAATTTCTTTTTA 57.044 32.000 0.00 0.00 0.00 1.52
3259 6858 8.018677 TCAGAGCGAGTACAATTTCTTTTTAG 57.981 34.615 0.00 0.00 0.00 1.85
3260 6859 7.870954 TCAGAGCGAGTACAATTTCTTTTTAGA 59.129 33.333 0.00 0.00 0.00 2.10
3261 6860 8.660373 CAGAGCGAGTACAATTTCTTTTTAGAT 58.340 33.333 0.00 0.00 0.00 1.98
3262 6861 9.871238 AGAGCGAGTACAATTTCTTTTTAGATA 57.129 29.630 0.00 0.00 0.00 1.98
3264 6863 9.099454 AGCGAGTACAATTTCTTTTTAGATAGG 57.901 33.333 0.00 0.00 0.00 2.57
3265 6864 7.851472 GCGAGTACAATTTCTTTTTAGATAGGC 59.149 37.037 0.00 0.00 0.00 3.93
3266 6865 9.099454 CGAGTACAATTTCTTTTTAGATAGGCT 57.901 33.333 0.00 0.00 0.00 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 89 3.535561 GGCAAGTGAGCTAGCTAAATGA 58.464 45.455 19.38 0.00 34.17 2.57
197 206 6.672593 TGTGGGATTTTCTAGCATAATTCCT 58.327 36.000 8.96 0.00 29.75 3.36
216 233 3.194968 ACGATGTTCCTAGTTACTGTGGG 59.805 47.826 0.00 0.00 0.00 4.61
217 234 4.158025 AGACGATGTTCCTAGTTACTGTGG 59.842 45.833 0.00 0.00 0.00 4.17
218 235 5.312120 AGACGATGTTCCTAGTTACTGTG 57.688 43.478 0.00 0.00 0.00 3.66
219 236 5.066246 GCTAGACGATGTTCCTAGTTACTGT 59.934 44.000 0.00 0.00 34.06 3.55
220 237 5.505985 GGCTAGACGATGTTCCTAGTTACTG 60.506 48.000 0.00 0.00 34.06 2.74
221 238 4.579753 GGCTAGACGATGTTCCTAGTTACT 59.420 45.833 0.00 0.00 34.06 2.24
222 239 4.579753 AGGCTAGACGATGTTCCTAGTTAC 59.420 45.833 0.00 0.00 34.06 2.50
223 240 4.789807 AGGCTAGACGATGTTCCTAGTTA 58.210 43.478 0.00 0.00 34.06 2.24
233 250 7.970384 TGTTTACAATTAAAGGCTAGACGATG 58.030 34.615 0.00 0.00 0.00 3.84
236 253 7.970384 TGATGTTTACAATTAAAGGCTAGACG 58.030 34.615 0.00 0.00 0.00 4.18
237 254 9.162764 TCTGATGTTTACAATTAAAGGCTAGAC 57.837 33.333 0.00 0.00 0.00 2.59
252 269 4.973663 CGGTTGTGGTTTTCTGATGTTTAC 59.026 41.667 0.00 0.00 0.00 2.01
486 511 9.974980 TTTTGTTTTAAAGTGGATCTAATGGTC 57.025 29.630 0.00 0.00 0.00 4.02
549 574 8.157476 AGGATATGTTTTTCACAGTTCACTACT 58.843 33.333 0.00 0.00 39.40 2.57
600 625 5.106157 GGAATGGTTTTCTGTATGGACACTG 60.106 44.000 0.00 0.00 0.00 3.66
601 626 5.010282 GGAATGGTTTTCTGTATGGACACT 58.990 41.667 0.00 0.00 0.00 3.55
602 627 4.157840 GGGAATGGTTTTCTGTATGGACAC 59.842 45.833 0.00 0.00 0.00 3.67
603 628 4.202620 TGGGAATGGTTTTCTGTATGGACA 60.203 41.667 0.00 0.00 0.00 4.02
604 629 4.340617 TGGGAATGGTTTTCTGTATGGAC 58.659 43.478 0.00 0.00 0.00 4.02
605 630 4.666412 TGGGAATGGTTTTCTGTATGGA 57.334 40.909 0.00 0.00 0.00 3.41
606 631 4.381932 GCTTGGGAATGGTTTTCTGTATGG 60.382 45.833 0.00 0.00 0.00 2.74
608 633 3.769300 GGCTTGGGAATGGTTTTCTGTAT 59.231 43.478 0.00 0.00 0.00 2.29
609 634 3.161866 GGCTTGGGAATGGTTTTCTGTA 58.838 45.455 0.00 0.00 0.00 2.74
610 635 1.970640 GGCTTGGGAATGGTTTTCTGT 59.029 47.619 0.00 0.00 0.00 3.41
611 636 1.969923 TGGCTTGGGAATGGTTTTCTG 59.030 47.619 0.00 0.00 0.00 3.02
612 637 2.397044 TGGCTTGGGAATGGTTTTCT 57.603 45.000 0.00 0.00 0.00 2.52
613 638 2.833943 AGATGGCTTGGGAATGGTTTTC 59.166 45.455 0.00 0.00 0.00 2.29
614 639 2.906568 AGATGGCTTGGGAATGGTTTT 58.093 42.857 0.00 0.00 0.00 2.43
618 643 3.073503 TGAGATAGATGGCTTGGGAATGG 59.926 47.826 0.00 0.00 0.00 3.16
620 645 3.979347 AGTGAGATAGATGGCTTGGGAAT 59.021 43.478 0.00 0.00 0.00 3.01
621 646 3.387962 AGTGAGATAGATGGCTTGGGAA 58.612 45.455 0.00 0.00 0.00 3.97
623 648 3.135348 TGAAGTGAGATAGATGGCTTGGG 59.865 47.826 0.00 0.00 0.00 4.12
626 651 9.941325 CTAAATATGAAGTGAGATAGATGGCTT 57.059 33.333 0.00 0.00 0.00 4.35
628 653 9.585099 CTCTAAATATGAAGTGAGATAGATGGC 57.415 37.037 0.00 0.00 0.00 4.40
635 660 9.875708 AGTAGACCTCTAAATATGAAGTGAGAT 57.124 33.333 0.00 0.00 0.00 2.75
636 661 9.702253 AAGTAGACCTCTAAATATGAAGTGAGA 57.298 33.333 0.00 0.00 0.00 3.27
680 705 6.944557 AAAGACTTGTGTAAACTGTTTTGC 57.055 33.333 11.48 5.92 0.00 3.68
681 706 8.742554 AGAAAAGACTTGTGTAAACTGTTTTG 57.257 30.769 11.48 0.00 0.00 2.44
683 708 8.674607 CCTAGAAAAGACTTGTGTAAACTGTTT 58.325 33.333 10.98 10.98 0.00 2.83
684 709 8.044908 TCCTAGAAAAGACTTGTGTAAACTGTT 58.955 33.333 0.00 0.00 0.00 3.16
685 710 7.562135 TCCTAGAAAAGACTTGTGTAAACTGT 58.438 34.615 0.00 0.00 0.00 3.55
688 713 8.205131 TGTTCCTAGAAAAGACTTGTGTAAAC 57.795 34.615 0.00 0.00 0.00 2.01
689 714 8.795842 TTGTTCCTAGAAAAGACTTGTGTAAA 57.204 30.769 0.00 0.00 0.00 2.01
690 715 8.974060 ATTGTTCCTAGAAAAGACTTGTGTAA 57.026 30.769 0.00 0.00 0.00 2.41
691 716 8.974060 AATTGTTCCTAGAAAAGACTTGTGTA 57.026 30.769 0.00 0.00 0.00 2.90
692 717 7.881775 AATTGTTCCTAGAAAAGACTTGTGT 57.118 32.000 0.00 0.00 0.00 3.72
693 718 8.405531 TCAAATTGTTCCTAGAAAAGACTTGTG 58.594 33.333 0.00 0.00 0.00 3.33
694 719 8.519799 TCAAATTGTTCCTAGAAAAGACTTGT 57.480 30.769 0.00 0.00 0.00 3.16
695 720 9.971922 ATTCAAATTGTTCCTAGAAAAGACTTG 57.028 29.630 0.00 0.00 0.00 3.16
698 723 9.965824 TCAATTCAAATTGTTCCTAGAAAAGAC 57.034 29.630 13.57 0.00 44.66 3.01
701 726 9.541143 GGTTCAATTCAAATTGTTCCTAGAAAA 57.459 29.630 13.57 0.00 44.66 2.29
702 727 8.700051 TGGTTCAATTCAAATTGTTCCTAGAAA 58.300 29.630 20.38 5.94 44.66 2.52
703 728 8.243961 TGGTTCAATTCAAATTGTTCCTAGAA 57.756 30.769 20.38 6.43 44.66 2.10
707 732 7.065120 TCATGGTTCAATTCAAATTGTTCCT 57.935 32.000 20.38 11.23 44.66 3.36
708 733 7.910441 ATCATGGTTCAATTCAAATTGTTCC 57.090 32.000 13.57 15.38 44.66 3.62
715 740 7.840716 AGGGAGATTATCATGGTTCAATTCAAA 59.159 33.333 0.00 0.00 0.00 2.69
716 741 7.286087 CAGGGAGATTATCATGGTTCAATTCAA 59.714 37.037 0.00 0.00 0.00 2.69
717 742 6.774170 CAGGGAGATTATCATGGTTCAATTCA 59.226 38.462 0.00 0.00 0.00 2.57
718 743 6.774656 ACAGGGAGATTATCATGGTTCAATTC 59.225 38.462 0.00 0.00 0.00 2.17
720 745 6.271585 ACAGGGAGATTATCATGGTTCAAT 57.728 37.500 0.00 0.00 0.00 2.57
723 748 7.229506 CCTTAAACAGGGAGATTATCATGGTTC 59.770 40.741 0.00 0.00 39.39 3.62
724 749 7.062957 CCTTAAACAGGGAGATTATCATGGTT 58.937 38.462 0.00 0.00 39.39 3.67
725 750 6.605119 CCTTAAACAGGGAGATTATCATGGT 58.395 40.000 0.00 0.00 39.39 3.55
739 764 2.486592 CGGCTTTGTACCCTTAAACAGG 59.513 50.000 0.00 0.00 43.49 4.00
740 765 3.187842 GTCGGCTTTGTACCCTTAAACAG 59.812 47.826 0.00 0.00 0.00 3.16
741 766 3.140623 GTCGGCTTTGTACCCTTAAACA 58.859 45.455 0.00 0.00 0.00 2.83
742 767 3.058708 GTGTCGGCTTTGTACCCTTAAAC 60.059 47.826 0.00 0.00 0.00 2.01
743 768 3.140623 GTGTCGGCTTTGTACCCTTAAA 58.859 45.455 0.00 0.00 0.00 1.52
744 769 2.104451 TGTGTCGGCTTTGTACCCTTAA 59.896 45.455 0.00 0.00 0.00 1.85
745 770 1.693062 TGTGTCGGCTTTGTACCCTTA 59.307 47.619 0.00 0.00 0.00 2.69
746 771 0.470766 TGTGTCGGCTTTGTACCCTT 59.529 50.000 0.00 0.00 0.00 3.95
747 772 0.470766 TTGTGTCGGCTTTGTACCCT 59.529 50.000 0.00 0.00 0.00 4.34
748 773 1.199097 CATTGTGTCGGCTTTGTACCC 59.801 52.381 0.00 0.00 0.00 3.69
750 775 1.265635 TGCATTGTGTCGGCTTTGTAC 59.734 47.619 0.00 0.00 0.00 2.90
751 776 1.598882 TGCATTGTGTCGGCTTTGTA 58.401 45.000 0.00 0.00 0.00 2.41
752 777 0.743688 TTGCATTGTGTCGGCTTTGT 59.256 45.000 0.00 0.00 0.00 2.83
753 778 1.269206 ACTTGCATTGTGTCGGCTTTG 60.269 47.619 0.00 0.00 0.00 2.77
754 779 1.032014 ACTTGCATTGTGTCGGCTTT 58.968 45.000 0.00 0.00 0.00 3.51
757 782 1.081242 CCACTTGCATTGTGTCGGC 60.081 57.895 15.95 0.00 33.92 5.54
759 784 0.950836 TTCCCACTTGCATTGTGTCG 59.049 50.000 15.95 8.26 33.92 4.35
760 785 1.680735 TGTTCCCACTTGCATTGTGTC 59.319 47.619 15.95 7.11 33.92 3.67
761 786 1.774110 TGTTCCCACTTGCATTGTGT 58.226 45.000 15.95 0.00 33.92 3.72
762 787 2.353011 GGATGTTCCCACTTGCATTGTG 60.353 50.000 11.90 11.90 35.39 3.33
763 788 1.895131 GGATGTTCCCACTTGCATTGT 59.105 47.619 0.00 0.00 0.00 2.71
764 789 1.894466 TGGATGTTCCCACTTGCATTG 59.106 47.619 0.00 0.00 35.03 2.82
773 798 1.284785 GGAAGGATGTGGATGTTCCCA 59.715 52.381 0.00 0.00 35.03 4.37
774 799 2.058593 GGAAGGATGTGGATGTTCCC 57.941 55.000 0.00 0.00 35.03 3.97
775 800 1.284785 TGGGAAGGATGTGGATGTTCC 59.715 52.381 0.00 0.00 36.68 3.62
776 801 2.806945 TGGGAAGGATGTGGATGTTC 57.193 50.000 0.00 0.00 0.00 3.18
778 803 2.092212 GTGATGGGAAGGATGTGGATGT 60.092 50.000 0.00 0.00 0.00 3.06
779 804 2.174210 AGTGATGGGAAGGATGTGGATG 59.826 50.000 0.00 0.00 0.00 3.51
781 806 1.971149 AGTGATGGGAAGGATGTGGA 58.029 50.000 0.00 0.00 0.00 4.02
782 807 3.244700 GGATAGTGATGGGAAGGATGTGG 60.245 52.174 0.00 0.00 0.00 4.17
783 808 3.392285 TGGATAGTGATGGGAAGGATGTG 59.608 47.826 0.00 0.00 0.00 3.21
784 809 3.668821 TGGATAGTGATGGGAAGGATGT 58.331 45.455 0.00 0.00 0.00 3.06
786 811 5.373555 TGAATTGGATAGTGATGGGAAGGAT 59.626 40.000 0.00 0.00 0.00 3.24
787 812 4.726317 TGAATTGGATAGTGATGGGAAGGA 59.274 41.667 0.00 0.00 0.00 3.36
788 813 5.052693 TGAATTGGATAGTGATGGGAAGG 57.947 43.478 0.00 0.00 0.00 3.46
789 814 7.592885 ATTTGAATTGGATAGTGATGGGAAG 57.407 36.000 0.00 0.00 0.00 3.46
826 900 7.616542 GGTCCAGGGGTTTATGTTCTTAATTAA 59.383 37.037 0.00 0.00 0.00 1.40
827 901 7.120716 GGTCCAGGGGTTTATGTTCTTAATTA 58.879 38.462 0.00 0.00 0.00 1.40
828 902 5.955959 GGTCCAGGGGTTTATGTTCTTAATT 59.044 40.000 0.00 0.00 0.00 1.40
829 903 5.015817 TGGTCCAGGGGTTTATGTTCTTAAT 59.984 40.000 0.00 0.00 0.00 1.40
865 939 7.217200 TCTCCCATTTTATAGTCTACATGCAC 58.783 38.462 0.00 0.00 0.00 4.57
1012 1099 1.073706 ACTCCACCACCTCCACCTT 60.074 57.895 0.00 0.00 0.00 3.50
1435 1586 3.809013 CCCTAATGCCACCCCGCT 61.809 66.667 0.00 0.00 0.00 5.52
1666 1851 0.620556 ACGAAAGCCTGGGTGATGAT 59.379 50.000 0.00 0.00 0.00 2.45
1669 1854 1.079127 CGACGAAAGCCTGGGTGAT 60.079 57.895 0.00 0.00 0.00 3.06
1799 1987 2.345991 CCGGAAAGGTGAAGCGGA 59.654 61.111 0.00 0.00 34.51 5.54
1804 1992 2.282180 GCTGGCCGGAAAGGTGAA 60.282 61.111 18.31 0.00 43.70 3.18
2002 5402 2.676839 CGGTGAGCTCGAAGTAGTCTAA 59.323 50.000 9.64 0.00 0.00 2.10
2106 5506 4.029809 CCCCACCCGAAGTCCACC 62.030 72.222 0.00 0.00 0.00 4.61
2225 5625 0.385751 GTTGAGGATCGCGATCTCCA 59.614 55.000 39.13 32.63 38.61 3.86
2231 5631 1.556564 GAAATCGTTGAGGATCGCGA 58.443 50.000 13.09 13.09 45.83 5.87
2247 5647 0.179181 CGTACAGTAGGCGCTCGAAA 60.179 55.000 7.64 0.00 0.00 3.46
2283 5683 0.665670 CTCAGATATCAGGTGGCGCG 60.666 60.000 0.00 0.00 0.00 6.86
2289 5689 4.524714 CCAATCCGTACTCAGATATCAGGT 59.475 45.833 5.32 3.30 0.00 4.00
2295 5695 1.968493 GGCCCAATCCGTACTCAGATA 59.032 52.381 0.00 0.00 0.00 1.98
2299 5752 0.988832 AAAGGCCCAATCCGTACTCA 59.011 50.000 0.00 0.00 0.00 3.41
2397 5850 9.221775 CAACAAAAGATACTGACAAACTACAAC 57.778 33.333 0.00 0.00 0.00 3.32
2403 5856 4.675114 CGCCAACAAAAGATACTGACAAAC 59.325 41.667 0.00 0.00 0.00 2.93
2439 5892 9.661563 CCTGGTTGTAAGTTGTATTACTTGATA 57.338 33.333 0.00 0.00 38.72 2.15
2451 5904 1.871039 CACGGACCTGGTTGTAAGTTG 59.129 52.381 0.00 0.00 0.00 3.16
2454 5907 0.682852 TCCACGGACCTGGTTGTAAG 59.317 55.000 0.00 0.00 32.50 2.34
2478 5931 3.940657 AGTGTGTATAGTCGTCGCTAC 57.059 47.619 0.00 0.00 0.00 3.58
2493 5946 3.119531 TGTTTTTGGCTCACTCAAGTGTG 60.120 43.478 9.82 8.67 45.76 3.82
2494 5947 3.088532 TGTTTTTGGCTCACTCAAGTGT 58.911 40.909 9.82 0.00 45.76 3.55
2540 5993 2.503382 GGTTTGCCCGGCTCCAAAA 61.503 57.895 11.61 0.00 33.25 2.44
2542 5995 2.937959 AAAGGTTTGCCCGGCTCCAA 62.938 55.000 11.61 0.00 38.74 3.53
2583 6036 0.107214 ATGGGGTGTTAGCATGACGG 60.107 55.000 0.00 0.00 0.00 4.79
2595 6048 0.327924 TGCACTTGTCCTATGGGGTG 59.672 55.000 0.00 0.00 36.25 4.61
2608 6061 3.221771 TGATTGCTACTTTGGTGCACTT 58.778 40.909 17.98 0.00 36.37 3.16
2618 6071 2.138320 CATCGGCGATGATTGCTACTT 58.862 47.619 39.06 4.57 42.09 2.24
2650 6104 8.345565 GTGTTTATAGATTTGATGCTTCCGATT 58.654 33.333 0.00 0.00 0.00 3.34
2710 6169 0.770499 TGCTGGTCTTTGGTGGATCA 59.230 50.000 0.00 0.00 0.00 2.92
2759 6219 1.289380 GAGGACGTGTGGAGGTGTC 59.711 63.158 0.00 0.00 0.00 3.67
2788 6376 0.673644 CCCGTCTGAATGGTGTGTCC 60.674 60.000 0.00 0.00 0.00 4.02
2879 6468 3.367025 CCCGCTCTAGTTCTTTTTACGTG 59.633 47.826 0.00 0.00 0.00 4.49
2980 6570 1.040893 TCTTCCTCTATCGGCGCCAA 61.041 55.000 28.98 9.13 0.00 4.52
2991 6581 3.327439 TCCCAAACTTTCCTCTTCCTCT 58.673 45.455 0.00 0.00 0.00 3.69
3044 6635 7.910162 GCCATGGTTACATTTGCTAATATATCG 59.090 37.037 14.67 0.00 34.35 2.92
3046 6637 7.673504 TGGCCATGGTTACATTTGCTAATATAT 59.326 33.333 14.67 0.00 34.35 0.86
3080 6671 2.559668 CTGTGGAACTGCAATTGGTGAT 59.440 45.455 7.72 0.00 38.04 3.06
3129 6721 9.482627 GGGACTATCATACTTATTTGAGAGTTG 57.517 37.037 2.21 0.00 42.67 3.16
3130 6722 9.440761 AGGGACTATCATACTTATTTGAGAGTT 57.559 33.333 2.21 0.00 42.67 3.01
3132 6724 9.921637 GAAGGGACTATCATACTTATTTGAGAG 57.078 37.037 0.00 0.00 38.49 3.20
3133 6725 8.577296 CGAAGGGACTATCATACTTATTTGAGA 58.423 37.037 0.00 0.00 38.49 3.27
3134 6726 8.577296 TCGAAGGGACTATCATACTTATTTGAG 58.423 37.037 0.00 0.00 38.49 3.02
3135 6727 8.473358 TCGAAGGGACTATCATACTTATTTGA 57.527 34.615 0.00 0.00 38.49 2.69
3151 6745 7.359014 GCGACAAGTAATATTTATCGAAGGGAC 60.359 40.741 0.44 0.00 0.00 4.46
3163 6757 8.545420 CGTATTAAACCAGCGACAAGTAATATT 58.455 33.333 0.00 0.00 0.00 1.28
3219 6818 6.490381 ACTCGCTCTGATCCATATTACTTGTA 59.510 38.462 0.00 0.00 0.00 2.41
3231 6830 4.688021 AGAAATTGTACTCGCTCTGATCC 58.312 43.478 0.00 0.00 0.00 3.36
3236 6835 8.779354 ATCTAAAAAGAAATTGTACTCGCTCT 57.221 30.769 0.00 0.00 0.00 4.09
3240 6839 9.099454 AGCCTATCTAAAAAGAAATTGTACTCG 57.901 33.333 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.