Multiple sequence alignment - TraesCS4A01G102000

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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 TraesCS4A01G102000 chr4A 100.000 3252 0 0 1 3252 114587236 114590487 0.000000e+00 6006
1 TraesCS4A01G102000 chr4B 96.960 987 29 1 2267 3252 433644282 433643296 0.000000e+00 1655
2 TraesCS4A01G102000 chr4B 85.541 1238 77 24 1021 2225 433645551 433644383 0.000000e+00 1201
3 TraesCS4A01G102000 chr4B 94.892 372 19 0 1 372 433646780 433646409 1.680000e-162 582
4 TraesCS4A01G102000 chr4D 96.667 990 28 2 2267 3252 350499714 350498726 0.000000e+00 1640
5 TraesCS4A01G102000 chr4D 86.800 1250 79 27 1021 2225 350501017 350499809 0.000000e+00 1315
6 TraesCS4A01G102000 chr4D 97.312 372 10 0 1 372 350502257 350501886 1.650000e-177 632
7 TraesCS4A01G102000 chr2A 98.864 88 1 0 689 776 10197768 10197681 1.210000e-34 158
8 TraesCS4A01G102000 chr7A 97.802 91 1 1 690 780 646081324 646081413 4.340000e-34 156
9 TraesCS4A01G102000 chr3B 95.833 96 4 0 689 784 200482330 200482425 4.340000e-34 156
10 TraesCS4A01G102000 chr3B 94.845 97 4 1 686 782 683391960 683392055 2.020000e-32 150
11 TraesCS4A01G102000 chrUn 95.745 94 4 0 689 782 37289164 37289257 5.620000e-33 152
12 TraesCS4A01G102000 chrUn 95.745 94 4 0 689 782 37292340 37292433 5.620000e-33 152
13 TraesCS4A01G102000 chr6B 94.792 96 4 1 680 775 238140895 238140989 7.270000e-32 148
14 TraesCS4A01G102000 chr5B 94.792 96 3 1 682 777 509185797 509185704 7.270000e-32 148
15 TraesCS4A01G102000 chr2D 92.308 104 6 2 682 783 419675515 419675618 2.610000e-31 147


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 TraesCS4A01G102000 chr4A 114587236 114590487 3251 False 6006.000000 6006 100.000000 1 3252 1 chr4A.!!$F1 3251
1 TraesCS4A01G102000 chr4B 433643296 433646780 3484 True 1146.000000 1655 92.464333 1 3252 3 chr4B.!!$R1 3251
2 TraesCS4A01G102000 chr4D 350498726 350502257 3531 True 1195.666667 1640 93.593000 1 3252 3 chr4D.!!$R1 3251

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
819 1059 0.032952 TCCCTCGTTTGTCCGACAAG 59.967 55.0 13.51 4.36 39.53 3.16 F
1067 1377 0.105658 AAGGGGGCGCTCTACATCTA 60.106 55.0 7.48 0.00 0.00 1.98 F
2098 2462 0.038166 TTTGTGATGTCCTGGCCTCC 59.962 55.0 3.32 0.00 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2093 2457 0.038166 TTTCATGTGACCCAGGAGGC 59.962 55.000 0.0 0.0 40.58 4.70 R
2199 2586 1.691434 TCCTGGCACCCATTTGTTTTC 59.309 47.619 0.0 0.0 30.82 2.29 R
2990 3442 2.076100 TGTCTAAATGTGGAAGCAGCG 58.924 47.619 0.0 0.0 0.00 5.18 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
35 36 2.029073 ATTCTATGGCCGGCGTCG 59.971 61.111 22.54 0.29 0.00 5.12
71 72 1.013596 TTGAGCTCACAAACACCGTG 58.986 50.000 18.03 0.00 35.63 4.94
264 265 1.597302 CATGGCTCTGAGGATGGCG 60.597 63.158 6.83 0.00 0.00 5.69
275 276 0.103208 AGGATGGCGTCGATCTTGTC 59.897 55.000 0.00 0.00 0.00 3.18
287 288 1.342819 GATCTTGTCGGGAGGGAGATG 59.657 57.143 0.00 0.00 0.00 2.90
368 369 6.375455 CAGGATAATCTGGTGTAGCTTTTGTT 59.625 38.462 0.00 0.00 0.00 2.83
372 373 2.878406 TCTGGTGTAGCTTTTGTTGCTC 59.122 45.455 0.00 0.00 41.46 4.26
373 374 1.953686 TGGTGTAGCTTTTGTTGCTCC 59.046 47.619 0.00 0.00 41.46 4.70
375 376 2.558359 GGTGTAGCTTTTGTTGCTCCAT 59.442 45.455 0.00 0.00 41.46 3.41
380 390 2.435437 AGCTTTTGTTGCTCCATGGTTT 59.565 40.909 12.58 0.00 35.67 3.27
384 394 0.675083 TGTTGCTCCATGGTTTGCAG 59.325 50.000 21.66 10.46 36.75 4.41
386 396 2.144833 TTGCTCCATGGTTTGCAGCG 62.145 55.000 21.66 2.79 36.75 5.18
400 410 2.953669 CAGCGATTGCCATTTGAGC 58.046 52.632 0.00 0.00 44.31 4.26
401 411 0.171679 CAGCGATTGCCATTTGAGCA 59.828 50.000 0.00 0.00 44.31 4.26
403 413 1.143969 GCGATTGCCATTTGAGCAGC 61.144 55.000 0.00 0.00 42.17 5.25
405 415 1.797713 CGATTGCCATTTGAGCAGCTG 60.798 52.381 10.11 10.11 42.17 4.24
406 416 1.475280 GATTGCCATTTGAGCAGCTGA 59.525 47.619 20.43 0.00 42.17 4.26
408 418 0.037160 TGCCATTTGAGCAGCTGAGA 59.963 50.000 20.43 0.00 34.69 3.27
409 419 1.340697 TGCCATTTGAGCAGCTGAGAT 60.341 47.619 20.43 1.27 34.69 2.75
410 420 1.065701 GCCATTTGAGCAGCTGAGATG 59.934 52.381 20.43 12.23 0.00 2.90
411 421 1.065701 CCATTTGAGCAGCTGAGATGC 59.934 52.381 20.43 15.86 44.18 3.91
412 422 1.065701 CATTTGAGCAGCTGAGATGCC 59.934 52.381 20.09 11.40 44.97 4.40
413 423 1.022982 TTTGAGCAGCTGAGATGCCG 61.023 55.000 20.09 0.00 44.97 5.69
414 424 2.176314 TTGAGCAGCTGAGATGCCGT 62.176 55.000 20.09 0.67 44.97 5.68
415 425 1.322538 TGAGCAGCTGAGATGCCGTA 61.323 55.000 20.09 2.88 44.97 4.02
416 426 0.597118 GAGCAGCTGAGATGCCGTAG 60.597 60.000 20.09 0.00 44.97 3.51
433 443 3.432782 CGTAGGTTCGTTGTAGTGGATC 58.567 50.000 0.00 0.00 0.00 3.36
436 446 4.124851 AGGTTCGTTGTAGTGGATCATC 57.875 45.455 0.00 0.00 0.00 2.92
437 447 3.513912 AGGTTCGTTGTAGTGGATCATCA 59.486 43.478 0.00 0.00 0.00 3.07
438 448 4.162320 AGGTTCGTTGTAGTGGATCATCAT 59.838 41.667 0.00 0.00 0.00 2.45
439 449 5.362717 AGGTTCGTTGTAGTGGATCATCATA 59.637 40.000 0.00 0.00 0.00 2.15
440 450 5.462398 GGTTCGTTGTAGTGGATCATCATAC 59.538 44.000 0.00 0.00 0.00 2.39
442 452 5.831997 TCGTTGTAGTGGATCATCATACAG 58.168 41.667 0.00 0.00 0.00 2.74
443 453 5.592688 TCGTTGTAGTGGATCATCATACAGA 59.407 40.000 0.00 0.00 0.00 3.41
444 454 5.687730 CGTTGTAGTGGATCATCATACAGAC 59.312 44.000 0.00 0.34 0.00 3.51
446 456 6.396829 TGTAGTGGATCATCATACAGACAG 57.603 41.667 0.00 0.00 0.00 3.51
447 457 6.129179 TGTAGTGGATCATCATACAGACAGA 58.871 40.000 0.00 0.00 0.00 3.41
448 458 5.787953 AGTGGATCATCATACAGACAGAG 57.212 43.478 0.00 0.00 0.00 3.35
452 523 5.301298 TGGATCATCATACAGACAGAGACAG 59.699 44.000 0.00 0.00 0.00 3.51
463 534 1.905215 ACAGAGACAGGTGAAGGGATG 59.095 52.381 0.00 0.00 0.00 3.51
473 547 2.817844 GGTGAAGGGATGTGGTTGTAAC 59.182 50.000 0.00 0.00 0.00 2.50
480 554 6.886178 AGGGATGTGGTTGTAACTATTAGT 57.114 37.500 0.00 0.00 0.00 2.24
504 578 3.646736 AATAACTGTGGCCTAGGGTTC 57.353 47.619 11.72 0.00 0.00 3.62
542 627 1.862602 AACCAGTGGATTTTCGGCGC 61.863 55.000 18.40 0.00 0.00 6.53
543 628 2.098298 CAGTGGATTTTCGGCGCG 59.902 61.111 0.00 0.00 0.00 6.86
544 629 3.124921 AGTGGATTTTCGGCGCGG 61.125 61.111 8.83 8.94 0.00 6.46
545 630 3.122323 GTGGATTTTCGGCGCGGA 61.122 61.111 14.27 14.27 0.00 5.54
557 642 0.601558 GGCGCGGAGATGGAGTATAA 59.398 55.000 8.83 0.00 0.00 0.98
565 650 5.934625 GCGGAGATGGAGTATAAATGTGAAT 59.065 40.000 0.00 0.00 0.00 2.57
581 666 8.606040 AAATGTGAATTTTTGGTATGAACTGG 57.394 30.769 0.00 0.00 0.00 4.00
583 668 7.118496 TGTGAATTTTTGGTATGAACTGGTT 57.882 32.000 0.00 0.00 0.00 3.67
584 669 6.983307 TGTGAATTTTTGGTATGAACTGGTTG 59.017 34.615 0.00 0.00 0.00 3.77
585 670 7.147828 TGTGAATTTTTGGTATGAACTGGTTGA 60.148 33.333 0.00 0.00 0.00 3.18
586 671 7.872483 GTGAATTTTTGGTATGAACTGGTTGAT 59.128 33.333 0.00 0.00 0.00 2.57
587 672 9.083422 TGAATTTTTGGTATGAACTGGTTGATA 57.917 29.630 0.00 0.00 0.00 2.15
591 676 8.642935 TTTTGGTATGAACTGGTTGATAATCA 57.357 30.769 0.00 0.00 0.00 2.57
592 677 8.821686 TTTGGTATGAACTGGTTGATAATCAT 57.178 30.769 0.00 0.00 0.00 2.45
593 678 7.806409 TGGTATGAACTGGTTGATAATCATG 57.194 36.000 0.00 0.00 0.00 3.07
594 679 6.262944 TGGTATGAACTGGTTGATAATCATGC 59.737 38.462 0.00 0.00 31.71 4.06
597 682 5.255687 TGAACTGGTTGATAATCATGCAGT 58.744 37.500 0.00 0.00 0.00 4.40
598 683 5.711506 TGAACTGGTTGATAATCATGCAGTT 59.288 36.000 8.64 8.64 33.72 3.16
599 684 5.571784 ACTGGTTGATAATCATGCAGTTG 57.428 39.130 0.00 0.00 0.00 3.16
620 715 5.344743 TGCCTTGTTTGGTATGTTTTGAA 57.655 34.783 0.00 0.00 0.00 2.69
655 750 7.792374 ATGAAATGATGCTTATGTTAGTCGT 57.208 32.000 0.00 0.00 0.00 4.34
656 751 7.609760 TGAAATGATGCTTATGTTAGTCGTT 57.390 32.000 0.00 0.00 0.00 3.85
657 752 7.463544 TGAAATGATGCTTATGTTAGTCGTTG 58.536 34.615 0.00 0.00 0.00 4.10
658 753 4.857871 TGATGCTTATGTTAGTCGTTGC 57.142 40.909 0.00 0.00 0.00 4.17
659 754 4.503910 TGATGCTTATGTTAGTCGTTGCT 58.496 39.130 0.00 0.00 0.00 3.91
660 755 4.566759 TGATGCTTATGTTAGTCGTTGCTC 59.433 41.667 0.00 0.00 0.00 4.26
661 756 4.188247 TGCTTATGTTAGTCGTTGCTCT 57.812 40.909 0.00 0.00 0.00 4.09
662 757 4.566004 TGCTTATGTTAGTCGTTGCTCTT 58.434 39.130 0.00 0.00 0.00 2.85
663 758 4.625742 TGCTTATGTTAGTCGTTGCTCTTC 59.374 41.667 0.00 0.00 0.00 2.87
664 759 4.625742 GCTTATGTTAGTCGTTGCTCTTCA 59.374 41.667 0.00 0.00 0.00 3.02
665 760 5.220303 GCTTATGTTAGTCGTTGCTCTTCAG 60.220 44.000 0.00 0.00 0.00 3.02
674 769 4.116878 GCTCTTCAGCGGCTTAGG 57.883 61.111 0.00 0.00 35.39 2.69
675 770 1.517832 GCTCTTCAGCGGCTTAGGA 59.482 57.895 0.00 0.00 35.39 2.94
676 771 0.105778 GCTCTTCAGCGGCTTAGGAT 59.894 55.000 0.00 0.00 35.39 3.24
677 772 1.863267 CTCTTCAGCGGCTTAGGATG 58.137 55.000 0.00 0.00 0.00 3.51
678 773 1.137872 CTCTTCAGCGGCTTAGGATGT 59.862 52.381 0.00 0.00 0.00 3.06
679 774 1.134699 TCTTCAGCGGCTTAGGATGTG 60.135 52.381 0.00 0.00 0.00 3.21
680 775 0.107703 TTCAGCGGCTTAGGATGTGG 60.108 55.000 0.00 0.00 0.00 4.17
681 776 0.975556 TCAGCGGCTTAGGATGTGGA 60.976 55.000 0.00 0.00 0.00 4.02
682 777 0.107703 CAGCGGCTTAGGATGTGGAA 60.108 55.000 0.00 0.00 0.00 3.53
683 778 0.618458 AGCGGCTTAGGATGTGGAAA 59.382 50.000 0.00 0.00 0.00 3.13
684 779 1.212935 AGCGGCTTAGGATGTGGAAAT 59.787 47.619 0.00 0.00 0.00 2.17
685 780 2.024414 GCGGCTTAGGATGTGGAAATT 58.976 47.619 0.00 0.00 0.00 1.82
686 781 2.223572 GCGGCTTAGGATGTGGAAATTG 60.224 50.000 0.00 0.00 0.00 2.32
687 782 2.223572 CGGCTTAGGATGTGGAAATTGC 60.224 50.000 0.00 0.00 0.00 3.56
688 783 2.760092 GGCTTAGGATGTGGAAATTGCA 59.240 45.455 0.00 0.00 0.00 4.08
689 784 3.385755 GGCTTAGGATGTGGAAATTGCAT 59.614 43.478 0.00 0.00 0.00 3.96
690 785 4.584325 GGCTTAGGATGTGGAAATTGCATA 59.416 41.667 0.00 0.00 0.00 3.14
691 786 5.507985 GGCTTAGGATGTGGAAATTGCATAC 60.508 44.000 0.00 0.00 0.00 2.39
692 787 5.300286 GCTTAGGATGTGGAAATTGCATACT 59.700 40.000 0.00 0.00 37.53 2.12
693 788 6.514048 GCTTAGGATGTGGAAATTGCATACTC 60.514 42.308 0.00 0.00 35.59 2.59
694 789 4.210331 AGGATGTGGAAATTGCATACTCC 58.790 43.478 0.00 0.00 28.26 3.85
695 790 3.319122 GGATGTGGAAATTGCATACTCCC 59.681 47.826 6.13 0.00 0.00 4.30
696 791 3.737559 TGTGGAAATTGCATACTCCCT 57.262 42.857 6.13 0.00 0.00 4.20
697 792 3.620488 TGTGGAAATTGCATACTCCCTC 58.380 45.455 6.13 1.78 0.00 4.30
698 793 2.952310 GTGGAAATTGCATACTCCCTCC 59.048 50.000 6.13 0.00 0.00 4.30
699 794 2.222027 GGAAATTGCATACTCCCTCCG 58.778 52.381 0.00 0.00 0.00 4.63
702 797 2.622064 ATTGCATACTCCCTCCGTTC 57.378 50.000 0.00 0.00 0.00 3.95
708 803 3.886123 CATACTCCCTCCGTTCCAAAAT 58.114 45.455 0.00 0.00 0.00 1.82
712 807 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
718 813 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
761 857 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
762 858 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
763 859 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
765 861 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
766 862 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
767 863 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
768 864 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
769 865 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
771 867 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
773 869 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
775 871 3.629142 ATTTTGGAACGGAGGGAGTAG 57.371 47.619 0.00 0.00 0.00 2.57
777 873 2.314071 TTGGAACGGAGGGAGTAGAA 57.686 50.000 0.00 0.00 0.00 2.10
778 874 1.848652 TGGAACGGAGGGAGTAGAAG 58.151 55.000 0.00 0.00 0.00 2.85
782 878 2.830651 ACGGAGGGAGTAGAAGTCAT 57.169 50.000 0.00 0.00 0.00 3.06
790 886 2.696187 GGAGTAGAAGTCATCCCACTCC 59.304 54.545 9.50 9.50 45.89 3.85
791 887 2.696187 GAGTAGAAGTCATCCCACTCCC 59.304 54.545 0.00 0.00 35.81 4.30
792 888 1.763545 GTAGAAGTCATCCCACTCCCC 59.236 57.143 0.00 0.00 0.00 4.81
810 1050 1.408266 CCCCCAACTATCCCTCGTTTG 60.408 57.143 0.00 0.00 0.00 2.93
814 1054 2.268298 CAACTATCCCTCGTTTGTCCG 58.732 52.381 0.00 0.00 0.00 4.79
815 1055 1.843368 ACTATCCCTCGTTTGTCCGA 58.157 50.000 0.00 0.00 35.22 4.55
816 1056 1.475682 ACTATCCCTCGTTTGTCCGAC 59.524 52.381 0.00 0.00 32.57 4.79
818 1058 0.682852 ATCCCTCGTTTGTCCGACAA 59.317 50.000 9.99 9.99 36.11 3.18
819 1059 0.032952 TCCCTCGTTTGTCCGACAAG 59.967 55.000 13.51 4.36 39.53 3.16
820 1060 1.566018 CCCTCGTTTGTCCGACAAGC 61.566 60.000 15.94 15.94 39.53 4.01
821 1061 0.600255 CCTCGTTTGTCCGACAAGCT 60.600 55.000 21.35 0.00 39.53 3.74
822 1062 1.217882 CTCGTTTGTCCGACAAGCTT 58.782 50.000 21.35 0.00 39.53 3.74
828 1068 4.524749 GTTTGTCCGACAAGCTTTTAGAC 58.475 43.478 18.00 2.20 39.53 2.59
829 1069 3.462483 TGTCCGACAAGCTTTTAGACA 57.538 42.857 11.86 11.86 0.00 3.41
840 1082 2.489971 CTTTTAGACACCTTGGACGCA 58.510 47.619 0.00 0.00 0.00 5.24
845 1087 1.072331 AGACACCTTGGACGCAATCTT 59.928 47.619 0.00 0.00 0.00 2.40
856 1098 3.302480 GGACGCAATCTTATGCAACTACG 60.302 47.826 0.00 0.00 46.76 3.51
861 1103 4.498009 GCAATCTTATGCAACTACGGCAAT 60.498 41.667 0.00 0.00 45.60 3.56
863 1105 6.568462 GCAATCTTATGCAACTACGGCAATAT 60.568 38.462 0.00 0.00 45.60 1.28
870 1112 3.374058 GCAACTACGGCAATATCACAAGT 59.626 43.478 0.00 0.00 0.00 3.16
872 1114 3.531538 ACTACGGCAATATCACAAGTGG 58.468 45.455 0.00 0.00 0.00 4.00
873 1115 2.489938 ACGGCAATATCACAAGTGGT 57.510 45.000 0.00 0.00 0.00 4.16
876 1118 2.746904 CGGCAATATCACAAGTGGTTCA 59.253 45.455 0.00 0.00 0.00 3.18
877 1119 3.181507 CGGCAATATCACAAGTGGTTCAG 60.182 47.826 0.00 0.00 0.00 3.02
879 1121 3.758554 GCAATATCACAAGTGGTTCAGGT 59.241 43.478 0.00 0.00 0.00 4.00
880 1122 4.941263 GCAATATCACAAGTGGTTCAGGTA 59.059 41.667 0.00 0.00 0.00 3.08
881 1123 5.163754 GCAATATCACAAGTGGTTCAGGTAC 60.164 44.000 0.00 0.00 0.00 3.34
882 1124 2.519377 TCACAAGTGGTTCAGGTACG 57.481 50.000 0.00 0.00 0.00 3.67
883 1125 1.069513 TCACAAGTGGTTCAGGTACGG 59.930 52.381 0.00 0.00 0.00 4.02
901 1143 3.094386 GAGCAACAACTCCACACCA 57.906 52.632 0.00 0.00 0.00 4.17
902 1144 0.663153 GAGCAACAACTCCACACCAC 59.337 55.000 0.00 0.00 0.00 4.16
903 1145 0.751643 AGCAACAACTCCACACCACC 60.752 55.000 0.00 0.00 0.00 4.61
904 1146 1.734388 GCAACAACTCCACACCACCC 61.734 60.000 0.00 0.00 0.00 4.61
905 1147 1.153046 AACAACTCCACACCACCCG 60.153 57.895 0.00 0.00 0.00 5.28
906 1148 1.917336 AACAACTCCACACCACCCGT 61.917 55.000 0.00 0.00 0.00 5.28
936 1178 2.778679 GCACCTGCAACGTCGATC 59.221 61.111 0.00 0.00 41.59 3.69
937 1179 2.027073 GCACCTGCAACGTCGATCA 61.027 57.895 0.00 0.00 41.59 2.92
938 1180 1.959899 GCACCTGCAACGTCGATCAG 61.960 60.000 0.00 2.84 41.59 2.90
939 1181 0.667487 CACCTGCAACGTCGATCAGT 60.667 55.000 0.00 0.00 0.00 3.41
940 1182 0.667487 ACCTGCAACGTCGATCAGTG 60.667 55.000 0.00 0.00 0.00 3.66
941 1183 1.417592 CTGCAACGTCGATCAGTGC 59.582 57.895 0.00 0.00 0.00 4.40
942 1184 2.271024 CTGCAACGTCGATCAGTGCG 62.271 60.000 0.00 0.00 0.00 5.34
945 1187 0.506932 CAACGTCGATCAGTGCGTTT 59.493 50.000 6.51 0.00 43.69 3.60
946 1188 0.506932 AACGTCGATCAGTGCGTTTG 59.493 50.000 0.00 0.00 43.69 2.93
948 1190 0.992072 CGTCGATCAGTGCGTTTGAT 59.008 50.000 0.00 0.00 37.96 2.57
949 1191 1.390123 CGTCGATCAGTGCGTTTGATT 59.610 47.619 0.00 0.00 35.50 2.57
951 1193 3.155998 GTCGATCAGTGCGTTTGATTTG 58.844 45.455 0.00 0.00 35.50 2.32
952 1194 1.906966 CGATCAGTGCGTTTGATTTGC 59.093 47.619 0.00 0.00 35.50 3.68
953 1195 2.665245 CGATCAGTGCGTTTGATTTGCA 60.665 45.455 0.00 0.00 35.50 4.08
958 1200 0.249238 TGCGTTTGATTTGCACACCC 60.249 50.000 0.00 0.00 32.86 4.61
962 1204 2.932614 CGTTTGATTTGCACACCCAAAA 59.067 40.909 4.45 0.00 38.12 2.44
977 1219 7.470009 GCACACCCAAAACCCTATATAAATCTG 60.470 40.741 0.00 0.00 0.00 2.90
980 1222 6.125890 ACCCAAAACCCTATATAAATCTGGCT 60.126 38.462 0.00 0.00 0.00 4.75
989 1237 7.066284 CCCTATATAAATCTGGCTAACATGCAC 59.934 40.741 0.00 0.00 34.04 4.57
990 1238 4.818534 ATAAATCTGGCTAACATGCACG 57.181 40.909 0.00 0.00 34.04 5.34
991 1239 2.113860 AATCTGGCTAACATGCACGT 57.886 45.000 0.00 0.00 34.04 4.49
992 1240 2.979814 ATCTGGCTAACATGCACGTA 57.020 45.000 0.00 0.00 34.04 3.57
993 1241 2.753055 TCTGGCTAACATGCACGTAA 57.247 45.000 0.00 0.00 34.04 3.18
995 1243 1.060553 CTGGCTAACATGCACGTAACG 59.939 52.381 0.00 0.00 34.04 3.18
1015 1273 3.360340 GCACACCAGCAGCACTCC 61.360 66.667 0.00 0.00 0.00 3.85
1063 1373 3.399181 CCAAGGGGGCGCTCTACA 61.399 66.667 7.48 0.00 0.00 2.74
1064 1374 2.746375 CCAAGGGGGCGCTCTACAT 61.746 63.158 7.48 0.00 0.00 2.29
1065 1375 1.227674 CAAGGGGGCGCTCTACATC 60.228 63.158 7.48 0.00 0.00 3.06
1066 1376 1.383248 AAGGGGGCGCTCTACATCT 60.383 57.895 7.48 0.00 0.00 2.90
1067 1377 0.105658 AAGGGGGCGCTCTACATCTA 60.106 55.000 7.48 0.00 0.00 1.98
1086 1396 1.135108 CATGATGTTCGCGCTTGCA 59.865 52.632 5.56 0.90 39.07 4.08
1102 1412 3.771491 CACTGACGAGCTGCGCAC 61.771 66.667 5.66 3.54 46.04 5.34
1134 1444 2.885644 CTCAACGACCATCCCGCG 60.886 66.667 0.00 0.00 0.00 6.46
1206 1516 2.722201 CCCAGAGGTAGTGCCGGTC 61.722 68.421 1.90 0.00 43.70 4.79
1240 1559 2.929903 GCGTTGCCTTTGCCATCCA 61.930 57.895 0.00 0.00 36.33 3.41
1335 1672 1.679944 CCCCTGACGTTCTTCATGCAT 60.680 52.381 0.00 0.00 0.00 3.96
1349 1686 0.816825 ATGCATGACATCCTCGGCAC 60.817 55.000 0.00 0.00 35.37 5.01
1452 1789 2.183046 GACAGCCTCGTCCAGAGC 59.817 66.667 0.00 0.00 45.54 4.09
1453 1790 2.601666 ACAGCCTCGTCCAGAGCA 60.602 61.111 0.00 0.00 45.54 4.26
1454 1791 2.159819 GACAGCCTCGTCCAGAGCAA 62.160 60.000 0.00 0.00 45.54 3.91
1455 1792 1.739562 CAGCCTCGTCCAGAGCAAC 60.740 63.158 0.00 0.00 45.54 4.17
1456 1793 2.811317 GCCTCGTCCAGAGCAACG 60.811 66.667 0.00 0.00 45.54 4.10
1457 1794 2.125912 CCTCGTCCAGAGCAACGG 60.126 66.667 0.00 0.00 45.54 4.44
1458 1795 2.636412 CCTCGTCCAGAGCAACGGA 61.636 63.158 0.00 0.00 45.54 4.69
1459 1796 1.289066 CTCGTCCAGAGCAACGGAA 59.711 57.895 0.00 0.00 40.54 4.30
1460 1797 0.319555 CTCGTCCAGAGCAACGGAAA 60.320 55.000 0.00 0.00 40.54 3.13
1461 1798 0.599204 TCGTCCAGAGCAACGGAAAC 60.599 55.000 0.00 0.00 39.31 2.78
1733 2086 2.429930 CTTCTTCGGGGTGCACCA 59.570 61.111 35.78 14.62 42.91 4.17
1735 2088 2.397413 CTTCTTCGGGGTGCACCAGT 62.397 60.000 35.78 0.00 42.91 4.00
1736 2089 1.990160 TTCTTCGGGGTGCACCAGTT 61.990 55.000 35.78 0.00 42.91 3.16
1767 2120 4.155733 TCCCGCATCGCCGTCATT 62.156 61.111 0.00 0.00 0.00 2.57
1913 2271 3.738590 GCTGCTTCCCTAACTAGTGCTAC 60.739 52.174 0.00 0.00 0.00 3.58
1914 2272 2.764572 TGCTTCCCTAACTAGTGCTACC 59.235 50.000 0.00 0.00 0.00 3.18
1915 2273 2.764572 GCTTCCCTAACTAGTGCTACCA 59.235 50.000 0.00 0.00 0.00 3.25
1916 2274 3.430513 GCTTCCCTAACTAGTGCTACCAC 60.431 52.174 0.00 0.00 42.39 4.16
1918 2276 3.990369 TCCCTAACTAGTGCTACCACAT 58.010 45.455 0.00 0.00 44.53 3.21
1920 2278 4.404715 TCCCTAACTAGTGCTACCACATTC 59.595 45.833 0.00 0.00 44.53 2.67
1921 2279 4.443034 CCCTAACTAGTGCTACCACATTCC 60.443 50.000 0.00 0.00 44.53 3.01
1922 2280 4.161565 CCTAACTAGTGCTACCACATTCCA 59.838 45.833 0.00 0.00 44.53 3.53
1923 2281 4.634012 AACTAGTGCTACCACATTCCAA 57.366 40.909 0.00 0.00 44.53 3.53
1924 2282 4.207891 ACTAGTGCTACCACATTCCAAG 57.792 45.455 0.00 0.00 44.53 3.61
1925 2283 3.583086 ACTAGTGCTACCACATTCCAAGT 59.417 43.478 0.00 0.00 44.53 3.16
1926 2284 2.783135 AGTGCTACCACATTCCAAGTG 58.217 47.619 0.00 0.00 44.53 3.16
1927 2285 2.106511 AGTGCTACCACATTCCAAGTGT 59.893 45.455 0.00 0.00 44.53 3.55
1928 2286 2.884639 GTGCTACCACATTCCAAGTGTT 59.115 45.455 0.00 0.00 41.67 3.32
1929 2287 3.317993 GTGCTACCACATTCCAAGTGTTT 59.682 43.478 0.00 0.00 41.67 2.83
1930 2288 3.317711 TGCTACCACATTCCAAGTGTTTG 59.682 43.478 0.00 0.00 35.24 2.93
1931 2289 3.317993 GCTACCACATTCCAAGTGTTTGT 59.682 43.478 0.00 0.00 35.24 2.83
1932 2290 4.556699 GCTACCACATTCCAAGTGTTTGTC 60.557 45.833 0.00 0.00 35.24 3.18
1933 2291 2.693074 ACCACATTCCAAGTGTTTGTCC 59.307 45.455 0.00 0.00 35.24 4.02
1934 2292 2.958355 CCACATTCCAAGTGTTTGTCCT 59.042 45.455 0.00 0.00 35.24 3.85
1935 2293 3.384467 CCACATTCCAAGTGTTTGTCCTT 59.616 43.478 0.00 0.00 35.24 3.36
1936 2294 4.499696 CCACATTCCAAGTGTTTGTCCTTC 60.500 45.833 0.00 0.00 35.24 3.46
1995 2353 3.689161 TGTAATCTGAATTTCACGGCCTG 59.311 43.478 0.00 0.00 0.00 4.85
2041 2399 8.082852 ACTCCTATATGTAATGCGAACTAAGTG 58.917 37.037 0.00 0.00 0.00 3.16
2042 2400 7.948357 TCCTATATGTAATGCGAACTAAGTGT 58.052 34.615 0.00 0.00 0.00 3.55
2093 2457 8.964476 AACTAAGTATATTTGTGATGTCCTGG 57.036 34.615 0.00 0.00 0.00 4.45
2094 2458 6.992715 ACTAAGTATATTTGTGATGTCCTGGC 59.007 38.462 0.00 0.00 0.00 4.85
2096 2460 3.959495 ATATTTGTGATGTCCTGGCCT 57.041 42.857 3.32 0.00 0.00 5.19
2097 2461 2.134789 ATTTGTGATGTCCTGGCCTC 57.865 50.000 3.32 0.00 0.00 4.70
2098 2462 0.038166 TTTGTGATGTCCTGGCCTCC 59.962 55.000 3.32 0.00 0.00 4.30
2099 2463 0.842030 TTGTGATGTCCTGGCCTCCT 60.842 55.000 3.32 0.00 0.00 3.69
2146 2533 6.978080 TGAAAAACTTAACTGTTTGGATGAGC 59.022 34.615 0.00 0.00 39.71 4.26
2157 2544 5.316167 TGTTTGGATGAGCTTACAGAACAT 58.684 37.500 0.00 0.00 0.00 2.71
2167 2554 4.451096 AGCTTACAGAACATAAACCACACG 59.549 41.667 0.00 0.00 0.00 4.49
2179 2566 1.299541 ACCACACGAAAAGCAGAGTG 58.700 50.000 0.00 0.00 40.17 3.51
2186 2573 3.062763 ACGAAAAGCAGAGTGTCATGAG 58.937 45.455 0.00 0.00 0.00 2.90
2193 2580 2.481104 GCAGAGTGTCATGAGCTCCTAC 60.481 54.545 12.15 7.24 0.00 3.18
2199 2586 3.681897 GTGTCATGAGCTCCTACAAACAG 59.318 47.826 12.15 0.00 0.00 3.16
2218 2605 1.693606 AGAAAACAAATGGGTGCCAGG 59.306 47.619 0.00 0.00 36.75 4.45
2279 2730 9.442047 AACTCTCTATTCATGTACTTTGAAAGG 57.558 33.333 10.02 10.13 36.72 3.11
2388 2839 4.702831 TGTCATGTCACTAAAGAGTTGCA 58.297 39.130 0.00 0.00 31.73 4.08
2552 3003 2.472695 TCTGGAAGTCCGAAACCATG 57.527 50.000 0.00 0.00 39.43 3.66
2800 3252 1.784525 GTGGAGGTCACTCAGTTTCG 58.215 55.000 0.00 0.00 45.81 3.46
3041 3493 7.823745 AATGAACAAGTCAAGTACCAAATCT 57.176 32.000 0.00 0.00 40.50 2.40
3095 3547 2.088423 TCACCATAAACCGTCATTGGC 58.912 47.619 0.00 0.00 0.00 4.52
3098 3550 1.202290 CCATAAACCGTCATTGGCTGC 60.202 52.381 0.00 0.00 0.00 5.25
3100 3552 1.448985 TAAACCGTCATTGGCTGCTC 58.551 50.000 0.00 0.00 0.00 4.26
3136 3588 6.774170 TGGAAATGAGAGACAATGGATATTGG 59.226 38.462 5.17 0.00 46.33 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 4.221262 AGAGAGGCTATCAGATCTGCAATC 59.779 45.833 18.36 8.19 0.00 2.67
254 255 0.103026 CAAGATCGACGCCATCCTCA 59.897 55.000 0.00 0.00 0.00 3.86
275 276 1.532794 CCTCTCCATCTCCCTCCCG 60.533 68.421 0.00 0.00 0.00 5.14
279 280 2.406559 CAACATCCTCTCCATCTCCCT 58.593 52.381 0.00 0.00 0.00 4.20
281 282 1.767681 AGCAACATCCTCTCCATCTCC 59.232 52.381 0.00 0.00 0.00 3.71
287 288 3.914426 TCCTTAAGCAACATCCTCTCC 57.086 47.619 0.00 0.00 0.00 3.71
345 346 6.555315 CAACAAAAGCTACACCAGATTATCC 58.445 40.000 0.00 0.00 31.02 2.59
372 373 3.038946 CAATCGCTGCAAACCATGG 57.961 52.632 11.19 11.19 0.00 3.66
384 394 1.143969 GCTGCTCAAATGGCAATCGC 61.144 55.000 0.00 0.00 39.30 4.58
386 396 1.475280 TCAGCTGCTCAAATGGCAATC 59.525 47.619 9.47 0.00 39.30 2.67
398 408 1.440893 CTACGGCATCTCAGCTGCT 59.559 57.895 9.47 0.00 44.76 4.24
400 410 0.176680 AACCTACGGCATCTCAGCTG 59.823 55.000 7.63 7.63 46.31 4.24
401 411 0.461961 GAACCTACGGCATCTCAGCT 59.538 55.000 0.00 0.00 34.17 4.24
403 413 0.456221 ACGAACCTACGGCATCTCAG 59.544 55.000 0.00 0.00 37.61 3.35
405 415 1.278238 CAACGAACCTACGGCATCTC 58.722 55.000 0.00 0.00 37.61 2.75
406 416 0.606604 ACAACGAACCTACGGCATCT 59.393 50.000 0.00 0.00 37.61 2.90
408 418 1.547372 ACTACAACGAACCTACGGCAT 59.453 47.619 0.00 0.00 37.61 4.40
409 419 0.961019 ACTACAACGAACCTACGGCA 59.039 50.000 0.00 0.00 37.61 5.69
410 420 1.343506 CACTACAACGAACCTACGGC 58.656 55.000 0.00 0.00 37.61 5.68
411 421 1.541147 TCCACTACAACGAACCTACGG 59.459 52.381 0.00 0.00 37.61 4.02
412 422 2.995466 TCCACTACAACGAACCTACG 57.005 50.000 0.00 0.00 39.31 3.51
413 423 4.445452 TGATCCACTACAACGAACCTAC 57.555 45.455 0.00 0.00 0.00 3.18
414 424 4.707934 TGATGATCCACTACAACGAACCTA 59.292 41.667 0.00 0.00 0.00 3.08
415 425 3.513912 TGATGATCCACTACAACGAACCT 59.486 43.478 0.00 0.00 0.00 3.50
416 426 3.857052 TGATGATCCACTACAACGAACC 58.143 45.455 0.00 0.00 0.00 3.62
418 428 6.096282 TCTGTATGATGATCCACTACAACGAA 59.904 38.462 0.00 0.00 0.00 3.85
420 430 5.687730 GTCTGTATGATGATCCACTACAACG 59.312 44.000 0.00 0.00 0.00 4.10
421 431 6.573434 TGTCTGTATGATGATCCACTACAAC 58.427 40.000 0.00 0.00 0.00 3.32
422 432 6.607198 TCTGTCTGTATGATGATCCACTACAA 59.393 38.462 0.00 0.00 0.00 2.41
423 433 6.129179 TCTGTCTGTATGATGATCCACTACA 58.871 40.000 0.00 0.00 0.00 2.74
425 435 6.488344 GTCTCTGTCTGTATGATGATCCACTA 59.512 42.308 0.00 0.00 0.00 2.74
426 436 5.301551 GTCTCTGTCTGTATGATGATCCACT 59.698 44.000 0.00 0.00 0.00 4.00
428 438 5.203528 TGTCTCTGTCTGTATGATGATCCA 58.796 41.667 0.00 0.00 0.00 3.41
429 439 5.278907 CCTGTCTCTGTCTGTATGATGATCC 60.279 48.000 0.00 0.00 0.00 3.36
430 440 5.301551 ACCTGTCTCTGTCTGTATGATGATC 59.698 44.000 0.00 0.00 0.00 2.92
433 443 4.400567 TCACCTGTCTCTGTCTGTATGATG 59.599 45.833 0.00 0.00 0.00 3.07
436 446 4.381398 CCTTCACCTGTCTCTGTCTGTATG 60.381 50.000 0.00 0.00 0.00 2.39
437 447 3.766591 CCTTCACCTGTCTCTGTCTGTAT 59.233 47.826 0.00 0.00 0.00 2.29
438 448 3.157881 CCTTCACCTGTCTCTGTCTGTA 58.842 50.000 0.00 0.00 0.00 2.74
439 449 1.967066 CCTTCACCTGTCTCTGTCTGT 59.033 52.381 0.00 0.00 0.00 3.41
440 450 1.274728 CCCTTCACCTGTCTCTGTCTG 59.725 57.143 0.00 0.00 0.00 3.51
442 452 1.633774 TCCCTTCACCTGTCTCTGTC 58.366 55.000 0.00 0.00 0.00 3.51
443 453 1.905215 CATCCCTTCACCTGTCTCTGT 59.095 52.381 0.00 0.00 0.00 3.41
444 454 1.905215 ACATCCCTTCACCTGTCTCTG 59.095 52.381 0.00 0.00 0.00 3.35
446 456 1.065854 CCACATCCCTTCACCTGTCTC 60.066 57.143 0.00 0.00 0.00 3.36
447 457 0.987294 CCACATCCCTTCACCTGTCT 59.013 55.000 0.00 0.00 0.00 3.41
448 458 0.693049 ACCACATCCCTTCACCTGTC 59.307 55.000 0.00 0.00 0.00 3.51
452 523 2.817844 GTTACAACCACATCCCTTCACC 59.182 50.000 0.00 0.00 0.00 4.02
473 547 9.477484 CTAGGCCACAGTTATTACAACTAATAG 57.523 37.037 5.01 0.00 0.00 1.73
480 554 3.847780 ACCCTAGGCCACAGTTATTACAA 59.152 43.478 5.01 0.00 0.00 2.41
520 605 2.544903 CGCCGAAAATCCACTGGTTTTT 60.545 45.455 14.30 14.30 37.32 1.94
542 627 7.969536 AATTCACATTTATACTCCATCTCCG 57.030 36.000 0.00 0.00 0.00 4.63
557 642 7.734942 ACCAGTTCATACCAAAAATTCACATT 58.265 30.769 0.00 0.00 0.00 2.71
565 650 9.083422 TGATTATCAACCAGTTCATACCAAAAA 57.917 29.630 0.00 0.00 0.00 1.94
578 663 4.357142 GCAACTGCATGATTATCAACCAG 58.643 43.478 17.79 17.79 41.59 4.00
597 682 5.344743 TCAAAACATACCAAACAAGGCAA 57.655 34.783 0.00 0.00 0.00 4.52
598 683 5.344743 TTCAAAACATACCAAACAAGGCA 57.655 34.783 0.00 0.00 0.00 4.75
599 684 5.757808 ACATTCAAAACATACCAAACAAGGC 59.242 36.000 0.00 0.00 0.00 4.35
643 738 4.625742 GCTGAAGAGCAACGACTAACATAA 59.374 41.667 0.00 0.00 45.46 1.90
645 740 2.996621 GCTGAAGAGCAACGACTAACAT 59.003 45.455 0.00 0.00 45.46 2.71
652 747 2.715532 AAGCCGCTGAAGAGCAACGA 62.716 55.000 0.00 0.00 46.62 3.85
653 748 1.014044 TAAGCCGCTGAAGAGCAACG 61.014 55.000 0.00 0.00 46.62 4.10
654 749 0.723981 CTAAGCCGCTGAAGAGCAAC 59.276 55.000 0.00 0.00 46.62 4.17
655 750 0.391661 CCTAAGCCGCTGAAGAGCAA 60.392 55.000 0.00 0.00 46.62 3.91
656 751 1.219124 CCTAAGCCGCTGAAGAGCA 59.781 57.895 0.00 0.00 46.62 4.26
657 752 0.105778 ATCCTAAGCCGCTGAAGAGC 59.894 55.000 0.00 0.00 42.37 4.09
658 753 1.137872 ACATCCTAAGCCGCTGAAGAG 59.862 52.381 0.00 0.00 0.00 2.85
659 754 1.134699 CACATCCTAAGCCGCTGAAGA 60.135 52.381 0.00 0.00 0.00 2.87
660 755 1.293924 CACATCCTAAGCCGCTGAAG 58.706 55.000 0.00 0.00 0.00 3.02
661 756 0.107703 CCACATCCTAAGCCGCTGAA 60.108 55.000 0.00 0.00 0.00 3.02
662 757 0.975556 TCCACATCCTAAGCCGCTGA 60.976 55.000 0.00 0.00 0.00 4.26
663 758 0.107703 TTCCACATCCTAAGCCGCTG 60.108 55.000 0.00 0.00 0.00 5.18
664 759 0.618458 TTTCCACATCCTAAGCCGCT 59.382 50.000 0.00 0.00 0.00 5.52
665 760 1.680338 ATTTCCACATCCTAAGCCGC 58.320 50.000 0.00 0.00 0.00 6.53
666 761 2.223572 GCAATTTCCACATCCTAAGCCG 60.224 50.000 0.00 0.00 0.00 5.52
667 762 2.760092 TGCAATTTCCACATCCTAAGCC 59.240 45.455 0.00 0.00 0.00 4.35
668 763 4.660789 ATGCAATTTCCACATCCTAAGC 57.339 40.909 0.00 0.00 0.00 3.09
669 764 6.016777 GGAGTATGCAATTTCCACATCCTAAG 60.017 42.308 8.40 0.00 31.41 2.18
670 765 5.827797 GGAGTATGCAATTTCCACATCCTAA 59.172 40.000 8.40 0.00 31.41 2.69
671 766 5.376625 GGAGTATGCAATTTCCACATCCTA 58.623 41.667 8.40 0.00 31.41 2.94
672 767 4.210331 GGAGTATGCAATTTCCACATCCT 58.790 43.478 8.40 0.00 31.41 3.24
673 768 3.319122 GGGAGTATGCAATTTCCACATCC 59.681 47.826 13.63 2.33 32.35 3.51
674 769 4.210331 AGGGAGTATGCAATTTCCACATC 58.790 43.478 13.63 0.00 32.35 3.06
675 770 4.210331 GAGGGAGTATGCAATTTCCACAT 58.790 43.478 13.63 2.08 32.35 3.21
676 771 3.620488 GAGGGAGTATGCAATTTCCACA 58.380 45.455 13.63 0.00 32.35 4.17
677 772 2.952310 GGAGGGAGTATGCAATTTCCAC 59.048 50.000 13.63 8.14 32.35 4.02
678 773 2.421388 CGGAGGGAGTATGCAATTTCCA 60.421 50.000 13.63 0.00 32.35 3.53
679 774 2.222027 CGGAGGGAGTATGCAATTTCC 58.778 52.381 0.00 0.00 0.00 3.13
680 775 2.919228 ACGGAGGGAGTATGCAATTTC 58.081 47.619 0.00 0.00 0.00 2.17
681 776 3.279434 GAACGGAGGGAGTATGCAATTT 58.721 45.455 0.00 0.00 0.00 1.82
682 777 2.421529 GGAACGGAGGGAGTATGCAATT 60.422 50.000 0.00 0.00 0.00 2.32
683 778 1.141053 GGAACGGAGGGAGTATGCAAT 59.859 52.381 0.00 0.00 0.00 3.56
684 779 0.539986 GGAACGGAGGGAGTATGCAA 59.460 55.000 0.00 0.00 0.00 4.08
685 780 0.616395 TGGAACGGAGGGAGTATGCA 60.616 55.000 0.00 0.00 0.00 3.96
686 781 0.539986 TTGGAACGGAGGGAGTATGC 59.460 55.000 0.00 0.00 0.00 3.14
687 782 3.343941 TTTTGGAACGGAGGGAGTATG 57.656 47.619 0.00 0.00 0.00 2.39
688 783 4.966805 TCTATTTTGGAACGGAGGGAGTAT 59.033 41.667 0.00 0.00 0.00 2.12
689 784 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
690 785 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
691 786 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
692 787 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
693 788 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
694 789 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
695 790 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
696 791 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
697 792 6.683974 ATTGAGTCATCTATTTTGGAACGG 57.316 37.500 0.00 0.00 0.00 4.44
698 793 8.970691 AAAATTGAGTCATCTATTTTGGAACG 57.029 30.769 11.47 0.00 44.08 3.95
735 831 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
736 832 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
738 834 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
739 835 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
740 836 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
741 837 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
742 838 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
743 839 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
744 840 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
745 841 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
746 842 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
747 843 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
748 844 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
750 846 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
751 847 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
752 848 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
753 849 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
754 850 4.355549 TCTACTCCCTCCGTTCCAAAATA 58.644 43.478 0.00 0.00 0.00 1.40
755 851 3.178865 TCTACTCCCTCCGTTCCAAAAT 58.821 45.455 0.00 0.00 0.00 1.82
756 852 2.612000 TCTACTCCCTCCGTTCCAAAA 58.388 47.619 0.00 0.00 0.00 2.44
757 853 2.314071 TCTACTCCCTCCGTTCCAAA 57.686 50.000 0.00 0.00 0.00 3.28
761 857 2.444421 TGACTTCTACTCCCTCCGTTC 58.556 52.381 0.00 0.00 0.00 3.95
762 858 2.599408 TGACTTCTACTCCCTCCGTT 57.401 50.000 0.00 0.00 0.00 4.44
763 859 2.657143 GATGACTTCTACTCCCTCCGT 58.343 52.381 0.00 0.00 0.00 4.69
765 861 2.321719 GGGATGACTTCTACTCCCTCC 58.678 57.143 0.00 0.00 43.45 4.30
766 862 2.696187 GTGGGATGACTTCTACTCCCTC 59.304 54.545 7.90 0.88 46.37 4.30
767 863 2.316372 AGTGGGATGACTTCTACTCCCT 59.684 50.000 7.90 0.00 46.37 4.20
768 864 2.696187 GAGTGGGATGACTTCTACTCCC 59.304 54.545 0.00 0.00 46.41 4.30
769 865 2.696187 GGAGTGGGATGACTTCTACTCC 59.304 54.545 19.49 19.49 44.08 3.85
771 867 2.627217 GGGGAGTGGGATGACTTCTACT 60.627 54.545 0.00 0.00 0.00 2.57
773 869 1.344087 GGGGGAGTGGGATGACTTCTA 60.344 57.143 0.00 0.00 0.00 2.10
775 871 1.915983 GGGGGAGTGGGATGACTTC 59.084 63.158 0.00 0.00 0.00 3.01
790 886 0.916809 AAACGAGGGATAGTTGGGGG 59.083 55.000 0.00 0.00 0.00 5.40
791 887 1.280998 ACAAACGAGGGATAGTTGGGG 59.719 52.381 0.00 0.00 0.00 4.96
792 888 2.629051 GACAAACGAGGGATAGTTGGG 58.371 52.381 0.00 0.00 0.00 4.12
799 1039 0.682852 TTGTCGGACAAACGAGGGAT 59.317 50.000 20.52 0.00 44.42 3.85
801 1041 1.566018 GCTTGTCGGACAAACGAGGG 61.566 60.000 22.60 12.01 44.42 4.30
810 1050 2.479275 GGTGTCTAAAAGCTTGTCGGAC 59.521 50.000 0.00 7.67 0.00 4.79
814 1054 4.023963 GTCCAAGGTGTCTAAAAGCTTGTC 60.024 45.833 0.00 4.23 46.68 3.18
815 1055 3.883489 GTCCAAGGTGTCTAAAAGCTTGT 59.117 43.478 0.00 0.00 46.68 3.16
818 1058 2.767505 CGTCCAAGGTGTCTAAAAGCT 58.232 47.619 0.00 0.00 0.00 3.74
819 1059 1.197036 GCGTCCAAGGTGTCTAAAAGC 59.803 52.381 0.00 0.00 0.00 3.51
820 1060 2.489971 TGCGTCCAAGGTGTCTAAAAG 58.510 47.619 0.00 0.00 0.00 2.27
821 1061 2.623878 TGCGTCCAAGGTGTCTAAAA 57.376 45.000 0.00 0.00 0.00 1.52
822 1062 2.623878 TTGCGTCCAAGGTGTCTAAA 57.376 45.000 0.00 0.00 0.00 1.85
828 1068 2.223340 GCATAAGATTGCGTCCAAGGTG 60.223 50.000 0.00 0.00 33.80 4.00
829 1069 2.017049 GCATAAGATTGCGTCCAAGGT 58.983 47.619 0.00 0.00 33.80 3.50
840 1082 6.710295 TGATATTGCCGTAGTTGCATAAGATT 59.290 34.615 0.00 0.00 38.76 2.40
845 1087 4.698575 TGTGATATTGCCGTAGTTGCATA 58.301 39.130 0.00 0.00 38.76 3.14
856 1098 3.129287 CCTGAACCACTTGTGATATTGCC 59.871 47.826 1.89 0.00 0.00 4.52
861 1103 3.056393 CCGTACCTGAACCACTTGTGATA 60.056 47.826 1.89 0.00 0.00 2.15
863 1105 1.069513 CCGTACCTGAACCACTTGTGA 59.930 52.381 1.89 0.00 0.00 3.58
870 1112 0.034337 GTTGCTCCGTACCTGAACCA 59.966 55.000 0.00 0.00 0.00 3.67
872 1114 1.529865 GTTGTTGCTCCGTACCTGAAC 59.470 52.381 0.00 0.00 0.00 3.18
873 1115 1.414919 AGTTGTTGCTCCGTACCTGAA 59.585 47.619 0.00 0.00 0.00 3.02
876 1118 0.320697 GGAGTTGTTGCTCCGTACCT 59.679 55.000 0.00 0.00 44.64 3.08
877 1119 2.836944 GGAGTTGTTGCTCCGTACC 58.163 57.895 0.00 0.00 44.64 3.34
883 1125 0.663153 GTGGTGTGGAGTTGTTGCTC 59.337 55.000 0.00 0.00 34.89 4.26
930 1172 3.155998 CAAATCAAACGCACTGATCGAC 58.844 45.455 0.00 0.00 32.26 4.20
931 1173 2.412716 GCAAATCAAACGCACTGATCGA 60.413 45.455 0.00 0.00 32.26 3.59
933 1175 2.932498 TGCAAATCAAACGCACTGATC 58.068 42.857 0.00 0.00 32.26 2.92
939 1181 0.249238 GGGTGTGCAAATCAAACGCA 60.249 50.000 0.00 0.00 43.28 5.24
940 1182 0.249238 TGGGTGTGCAAATCAAACGC 60.249 50.000 0.00 0.00 43.86 4.84
941 1183 2.215907 TTGGGTGTGCAAATCAAACG 57.784 45.000 0.00 0.00 33.58 3.60
942 1184 3.064682 GGTTTTGGGTGTGCAAATCAAAC 59.935 43.478 7.57 2.16 31.94 2.93
945 1187 1.139853 GGGTTTTGGGTGTGCAAATCA 59.860 47.619 0.00 0.00 0.00 2.57
946 1188 1.416030 AGGGTTTTGGGTGTGCAAATC 59.584 47.619 0.00 0.00 0.00 2.17
948 1190 2.160721 TAGGGTTTTGGGTGTGCAAA 57.839 45.000 0.00 0.00 0.00 3.68
949 1191 2.390225 ATAGGGTTTTGGGTGTGCAA 57.610 45.000 0.00 0.00 0.00 4.08
951 1193 6.549736 AGATTTATATAGGGTTTTGGGTGTGC 59.450 38.462 0.00 0.00 0.00 4.57
952 1194 7.014230 CCAGATTTATATAGGGTTTTGGGTGTG 59.986 40.741 0.00 0.00 0.00 3.82
953 1195 7.066781 CCAGATTTATATAGGGTTTTGGGTGT 58.933 38.462 0.00 0.00 0.00 4.16
954 1196 6.015434 GCCAGATTTATATAGGGTTTTGGGTG 60.015 42.308 0.00 0.00 0.00 4.61
955 1197 6.075315 GCCAGATTTATATAGGGTTTTGGGT 58.925 40.000 0.00 0.00 0.00 4.51
958 1200 9.349713 TGTTAGCCAGATTTATATAGGGTTTTG 57.650 33.333 0.00 0.00 0.00 2.44
962 1204 7.112779 GCATGTTAGCCAGATTTATATAGGGT 58.887 38.462 0.00 0.00 0.00 4.34
977 1219 1.352114 TCGTTACGTGCATGTTAGCC 58.648 50.000 18.34 2.13 0.00 3.93
980 1222 2.338500 TGCATCGTTACGTGCATGTTA 58.662 42.857 23.04 5.03 45.60 2.41
989 1237 1.288419 TGCTGGTGTGCATCGTTACG 61.288 55.000 0.00 0.00 38.12 3.18
990 1238 0.443869 CTGCTGGTGTGCATCGTTAC 59.556 55.000 0.00 0.00 42.48 2.50
991 1239 1.298157 GCTGCTGGTGTGCATCGTTA 61.298 55.000 0.00 0.00 42.48 3.18
992 1240 2.620112 GCTGCTGGTGTGCATCGTT 61.620 57.895 0.00 0.00 42.48 3.85
993 1241 3.052082 GCTGCTGGTGTGCATCGT 61.052 61.111 0.00 0.00 42.48 3.73
995 1243 1.919956 GAGTGCTGCTGGTGTGCATC 61.920 60.000 0.00 0.00 42.48 3.91
1052 1362 1.613925 TCATGTAGATGTAGAGCGCCC 59.386 52.381 2.29 0.00 0.00 6.13
1063 1373 2.515926 AGCGCGAACATCATGTAGAT 57.484 45.000 12.10 0.00 37.48 1.98
1064 1374 1.926510 CAAGCGCGAACATCATGTAGA 59.073 47.619 12.10 0.00 0.00 2.59
1065 1375 1.593070 GCAAGCGCGAACATCATGTAG 60.593 52.381 12.10 0.00 0.00 2.74
1066 1376 0.373370 GCAAGCGCGAACATCATGTA 59.627 50.000 12.10 0.00 0.00 2.29
1067 1377 1.135315 GCAAGCGCGAACATCATGT 59.865 52.632 12.10 0.00 0.00 3.21
1075 1385 3.701530 CGTCAGTGCAAGCGCGAA 61.702 61.111 12.10 0.00 42.97 4.70
1150 1460 4.189580 CCCCGGCAATGGATCGGT 62.190 66.667 0.00 0.00 41.98 4.69
1226 1536 1.597989 GCATTGGATGGCAAAGGCA 59.402 52.632 2.48 0.00 43.71 4.75
1317 1654 2.094894 GTCATGCATGAAGAACGTCAGG 59.905 50.000 30.24 0.00 38.75 3.86
1335 1672 2.710902 CGAGGTGCCGAGGATGTCA 61.711 63.158 0.00 0.00 0.00 3.58
1414 1751 2.438951 TAGGGGACGACGTTGTTGCC 62.439 60.000 10.42 7.51 0.00 4.52
1464 1801 2.726691 CTTGTAGCCGCCGTTGACG 61.727 63.158 0.00 0.00 39.44 4.35
1465 1802 0.947180 TTCTTGTAGCCGCCGTTGAC 60.947 55.000 0.00 0.00 0.00 3.18
1466 1803 0.947180 GTTCTTGTAGCCGCCGTTGA 60.947 55.000 0.00 0.00 0.00 3.18
1505 1857 4.980805 TGTCGCCACCGCCAGAAC 62.981 66.667 0.00 0.00 0.00 3.01
1506 1858 4.980805 GTGTCGCCACCGCCAGAA 62.981 66.667 0.00 0.00 35.44 3.02
1520 1872 4.954118 TCTGGGTCTGGGGCGTGT 62.954 66.667 0.00 0.00 0.00 4.49
1526 1878 1.229658 AGGAGGTTCTGGGTCTGGG 60.230 63.158 0.00 0.00 0.00 4.45
1527 1879 1.268283 GGAGGAGGTTCTGGGTCTGG 61.268 65.000 0.00 0.00 0.00 3.86
1528 1880 0.252467 AGGAGGAGGTTCTGGGTCTG 60.252 60.000 0.00 0.00 0.00 3.51
1529 1881 0.041982 GAGGAGGAGGTTCTGGGTCT 59.958 60.000 0.00 0.00 0.00 3.85
1530 1882 1.324005 CGAGGAGGAGGTTCTGGGTC 61.324 65.000 0.00 0.00 0.00 4.46
1531 1883 1.305381 CGAGGAGGAGGTTCTGGGT 60.305 63.158 0.00 0.00 0.00 4.51
1767 2120 2.925706 TACTTCCCTGTGCCGCCA 60.926 61.111 0.00 0.00 0.00 5.69
1913 2271 2.958355 AGGACAAACACTTGGAATGTGG 59.042 45.455 0.00 0.00 45.37 4.17
1914 2272 4.499696 GGAAGGACAAACACTTGGAATGTG 60.500 45.833 0.00 0.00 46.39 3.21
1915 2273 3.636764 GGAAGGACAAACACTTGGAATGT 59.363 43.478 0.00 0.00 36.82 2.71
1916 2274 3.636300 TGGAAGGACAAACACTTGGAATG 59.364 43.478 0.00 0.00 36.82 2.67
1918 2276 3.287222 CTGGAAGGACAAACACTTGGAA 58.713 45.455 0.00 0.00 36.82 3.53
1933 2291 4.694509 GCAGAGCATCATATAACCTGGAAG 59.305 45.833 0.00 0.00 37.82 3.46
1934 2292 4.505566 GGCAGAGCATCATATAACCTGGAA 60.506 45.833 0.00 0.00 37.82 3.53
1935 2293 3.008375 GGCAGAGCATCATATAACCTGGA 59.992 47.826 0.00 0.00 37.82 3.86
1936 2294 3.341823 GGCAGAGCATCATATAACCTGG 58.658 50.000 0.00 0.00 37.82 4.45
1995 2353 8.904099 AGGAGTATTATGGTAGTAAAATGCAC 57.096 34.615 0.00 0.00 0.00 4.57
2082 2446 1.222936 CAGGAGGCCAGGACATCAC 59.777 63.158 5.01 0.00 0.00 3.06
2085 2449 2.693864 CCCAGGAGGCCAGGACAT 60.694 66.667 5.01 0.00 31.24 3.06
2086 2450 4.270153 ACCCAGGAGGCCAGGACA 62.270 66.667 5.01 0.00 40.58 4.02
2087 2451 3.403558 GACCCAGGAGGCCAGGAC 61.404 72.222 5.01 0.00 40.58 3.85
2088 2452 3.940480 TGACCCAGGAGGCCAGGA 61.940 66.667 5.01 0.00 40.58 3.86
2089 2453 3.721706 GTGACCCAGGAGGCCAGG 61.722 72.222 5.01 0.22 40.58 4.45
2090 2454 2.304056 ATGTGACCCAGGAGGCCAG 61.304 63.158 5.01 0.00 40.58 4.85
2092 2456 1.852157 TTCATGTGACCCAGGAGGCC 61.852 60.000 0.00 0.00 40.58 5.19
2093 2457 0.038166 TTTCATGTGACCCAGGAGGC 59.962 55.000 0.00 0.00 40.58 4.70
2094 2458 2.025981 TCATTTCATGTGACCCAGGAGG 60.026 50.000 0.00 0.00 43.78 4.30
2096 2460 3.805066 TTCATTTCATGTGACCCAGGA 57.195 42.857 0.00 0.00 30.65 3.86
2097 2461 4.142093 GGATTTCATTTCATGTGACCCAGG 60.142 45.833 0.00 0.00 0.00 4.45
2098 2462 4.708421 AGGATTTCATTTCATGTGACCCAG 59.292 41.667 0.00 0.00 0.00 4.45
2099 2463 4.463539 CAGGATTTCATTTCATGTGACCCA 59.536 41.667 0.00 0.00 0.00 4.51
2130 2517 6.109156 TCTGTAAGCTCATCCAAACAGTTA 57.891 37.500 0.00 0.00 36.56 2.24
2138 2525 5.880332 GGTTTATGTTCTGTAAGCTCATCCA 59.120 40.000 0.00 0.00 31.73 3.41
2146 2533 6.533819 TTCGTGTGGTTTATGTTCTGTAAG 57.466 37.500 0.00 0.00 0.00 2.34
2157 2544 3.311322 CACTCTGCTTTTCGTGTGGTTTA 59.689 43.478 0.00 0.00 0.00 2.01
2167 2554 3.072944 AGCTCATGACACTCTGCTTTTC 58.927 45.455 0.00 0.00 0.00 2.29
2179 2566 4.193826 TCTGTTTGTAGGAGCTCATGAC 57.806 45.455 17.19 10.29 0.00 3.06
2186 2573 5.691754 CCATTTGTTTTCTGTTTGTAGGAGC 59.308 40.000 0.00 0.00 0.00 4.70
2193 2580 3.312146 GGCACCCATTTGTTTTCTGTTTG 59.688 43.478 0.00 0.00 0.00 2.93
2199 2586 1.691434 TCCTGGCACCCATTTGTTTTC 59.309 47.619 0.00 0.00 30.82 2.29
2259 2694 8.616076 CCTTAGCCTTTCAAAGTACATGAATAG 58.384 37.037 12.99 12.33 36.72 1.73
2264 2699 5.940470 ACTCCTTAGCCTTTCAAAGTACATG 59.060 40.000 0.00 0.00 0.00 3.21
2272 2723 4.431416 TGTCAACTCCTTAGCCTTTCAA 57.569 40.909 0.00 0.00 0.00 2.69
2279 2730 4.997395 TCATGTTCTTGTCAACTCCTTAGC 59.003 41.667 0.00 0.00 0.00 3.09
2357 2808 2.346803 AGTGACATGACATGCGTTACC 58.653 47.619 15.49 0.00 0.00 2.85
2388 2839 4.385754 GCTTACCCAGGATTCTTCTTCCAT 60.386 45.833 0.00 0.00 35.59 3.41
2458 2909 1.992170 ATACTTCACACGGAGCGTTC 58.008 50.000 0.00 0.00 38.32 3.95
2933 3385 7.985634 GCCTTATGCATTCGAATCTTAAAAA 57.014 32.000 7.92 0.00 40.77 1.94
2988 3440 2.939103 GTCTAAATGTGGAAGCAGCGAT 59.061 45.455 0.00 0.00 0.00 4.58
2990 3442 2.076100 TGTCTAAATGTGGAAGCAGCG 58.924 47.619 0.00 0.00 0.00 5.18
3041 3493 9.033481 CAAACAAGAAGCTTTCAATATGTTTCA 57.967 29.630 0.00 0.00 34.92 2.69
3098 3550 3.329386 TCATTTCCAGACTTTGCGAGAG 58.671 45.455 0.00 0.00 0.00 3.20
3100 3552 3.329386 TCTCATTTCCAGACTTTGCGAG 58.671 45.455 0.00 0.00 0.00 5.03
3136 3588 7.255486 GGACTACCATAGAAATTTGGCATTACC 60.255 40.741 0.00 0.00 36.41 2.85


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

AutoCloner maintained by Alex Coulton.