Multiple sequence alignment - TraesCS2D01G119400

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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 TraesCS2D01G119400 chr2D 100.000 3332 0 0 1 3332 68797125 68800456 0.000000e+00 6154.0
1 TraesCS2D01G119400 chr2D 91.765 340 21 3 2125 2461 68811694 68812029 1.810000e-127 466.0
2 TraesCS2D01G119400 chr2D 90.588 340 13 6 2255 2580 68810755 68811089 1.840000e-117 433.0
3 TraesCS2D01G119400 chr2D 87.405 262 14 10 2337 2584 69030198 69029942 1.960000e-72 283.0
4 TraesCS2D01G119400 chr2A 93.621 2414 120 20 726 3111 66087979 66085572 0.000000e+00 3574.0
5 TraesCS2D01G119400 chr2A 91.922 1894 110 17 725 2584 65997872 65995988 0.000000e+00 2610.0
6 TraesCS2D01G119400 chr2A 91.327 196 11 3 758 947 66088249 66088054 2.550000e-66 263.0
7 TraesCS2D01G119400 chr2A 91.237 194 13 3 24 217 65999265 65999076 9.170000e-66 261.0
8 TraesCS2D01G119400 chr2A 92.265 181 11 3 2258 2437 66079380 66079202 1.530000e-63 254.0
9 TraesCS2D01G119400 chr2A 90.977 133 7 4 769 901 66088325 66088198 1.230000e-39 174.0
10 TraesCS2D01G119400 chr2A 85.294 136 10 8 2435 2566 66006060 66005931 7.500000e-27 132.0
11 TraesCS2D01G119400 chr2A 81.102 127 22 2 541 666 5112185 5112060 2.120000e-17 100.0
12 TraesCS2D01G119400 chr2B 93.721 2389 105 16 758 3111 101976481 101974103 0.000000e+00 3539.0
13 TraesCS2D01G119400 chr2B 96.190 315 10 2 24 338 101979654 101979342 6.370000e-142 514.0
14 TraesCS2D01G119400 chr2B 92.722 316 19 2 24 338 101977418 101977106 1.410000e-123 453.0
15 TraesCS2D01G119400 chr2B 88.953 344 11 5 2255 2584 101544898 101544568 1.860000e-107 399.0
16 TraesCS2D01G119400 chr2B 93.258 267 18 0 1416 1682 101979117 101978851 8.660000e-106 394.0
17 TraesCS2D01G119400 chr2B 94.118 187 10 1 341 526 101979305 101979119 1.960000e-72 283.0
18 TraesCS2D01G119400 chr2B 91.542 201 13 3 701 897 101976629 101976429 1.180000e-69 274.0
19 TraesCS2D01G119400 chr2B 95.575 113 5 0 344 456 101977065 101976953 7.340000e-42 182.0
20 TraesCS2D01G119400 chr2B 97.778 90 2 0 455 544 101976715 101976626 4.450000e-34 156.0
21 TraesCS2D01G119400 chr3D 84.167 240 21 11 3104 3330 96440347 96440582 2.010000e-52 217.0
22 TraesCS2D01G119400 chr3D 81.818 132 22 1 537 666 47349713 47349844 3.510000e-20 110.0
23 TraesCS2D01G119400 chr3D 83.333 96 11 5 574 666 395904326 395904233 2.130000e-12 84.2
24 TraesCS2D01G119400 chr3D 94.595 37 1 1 666 701 482502765 482502801 4.640000e-04 56.5
25 TraesCS2D01G119400 chr4D 83.258 221 16 13 3106 3311 214937933 214937719 2.040000e-42 183.0
26 TraesCS2D01G119400 chr5B 81.974 233 25 15 3105 3330 45821329 45821107 7.340000e-42 182.0
27 TraesCS2D01G119400 chr5B 97.222 36 1 0 666 701 304688397 304688432 9.980000e-06 62.1
28 TraesCS2D01G119400 chr1B 81.773 203 21 10 3105 3297 630741600 630741404 4.450000e-34 156.0
29 TraesCS2D01G119400 chr5D 78.764 259 33 15 3088 3330 565268264 565268516 1.600000e-33 154.0
30 TraesCS2D01G119400 chr5D 82.979 94 13 3 574 666 205127262 205127353 7.660000e-12 82.4
31 TraesCS2D01G119400 chr5D 90.741 54 5 0 2218 2271 554516694 554516747 4.610000e-09 73.1
32 TraesCS2D01G119400 chr3A 79.747 237 26 15 3104 3327 615644 615871 5.760000e-33 152.0
33 TraesCS2D01G119400 chr3A 81.188 202 17 13 3105 3293 552539228 552539421 3.470000e-30 143.0
34 TraesCS2D01G119400 chr6B 95.402 87 2 2 3104 3189 688064602 688064687 1.610000e-28 137.0
35 TraesCS2D01G119400 chr7B 95.294 85 3 1 3105 3189 559527130 559527047 2.090000e-27 134.0
36 TraesCS2D01G119400 chr1D 84.848 132 17 3 536 666 54972585 54972456 2.700000e-26 130.0
37 TraesCS2D01G119400 chr1D 82.308 130 17 5 540 666 26370094 26369968 1.260000e-19 108.0
38 TraesCS2D01G119400 chr1D 90.698 43 2 2 666 708 385050912 385050872 4.640000e-04 56.5
39 TraesCS2D01G119400 chr4B 91.111 45 2 2 666 710 580771937 580771895 3.590000e-05 60.2


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 TraesCS2D01G119400 chr2D 68797125 68800456 3331 False 6154.000 6154 100.0000 1 3332 1 chr2D.!!$F1 3331
1 TraesCS2D01G119400 chr2D 68810755 68812029 1274 False 449.500 466 91.1765 2125 2580 2 chr2D.!!$F2 455
2 TraesCS2D01G119400 chr2A 65995988 65999265 3277 True 1435.500 2610 91.5795 24 2584 2 chr2A.!!$R4 2560
3 TraesCS2D01G119400 chr2A 66085572 66088325 2753 True 1337.000 3574 91.9750 726 3111 3 chr2A.!!$R5 2385
4 TraesCS2D01G119400 chr2B 101974103 101979654 5551 True 724.375 3539 94.3630 24 3111 8 chr2B.!!$R2 3087

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
551 3727 0.034477 CGGACCCATTAAGGCCTTGT 60.034 55.0 28.77 16.69 35.39 3.16 F
1140 4639 0.034574 TGTCCAACCACAACACTGCT 60.035 50.0 0.00 0.00 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1426 4925 1.192146 TAGAAGCTGCACCGGTTCCT 61.192 55.0 2.97 0.0 41.12 3.36 R
3126 6933 0.034477 AAGTAATGGAACCGGGGCAG 60.034 55.0 6.32 0.0 0.00 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
161 162 8.167392 TGGGGAAATTAGACTGAATTTTGTCTA 58.833 33.333 13.85 13.85 42.67 2.59
214 215 6.476706 GCTCTTTGTGATTTTGCTTTTGTAGT 59.523 34.615 0.00 0.00 0.00 2.73
217 218 9.296400 TCTTTGTGATTTTGCTTTTGTAGTAAC 57.704 29.630 0.00 0.00 0.00 2.50
242 243 0.250081 GCAGATGGGCTGTACCTAGC 60.250 60.000 0.00 0.00 46.62 3.42
293 294 1.040646 CTGCCCGATAAGCCAGTAGA 58.959 55.000 0.00 0.00 0.00 2.59
334 335 5.566032 CGTTCAATGTGTACTGGTTCCTAGA 60.566 44.000 0.00 0.00 0.00 2.43
338 339 1.134560 GTGTACTGGTTCCTAGAGCGG 59.865 57.143 0.00 0.00 0.00 5.52
339 340 1.272313 TGTACTGGTTCCTAGAGCGGT 60.272 52.381 0.00 0.00 39.70 5.68
341 342 1.313812 ACTGGTTCCTAGAGCGGTCG 61.314 60.000 9.28 0.00 31.32 4.79
342 343 1.001764 TGGTTCCTAGAGCGGTCGA 60.002 57.895 9.28 2.62 0.00 4.20
381 2653 0.405585 CCCACATCCAGGGTCAGTTT 59.594 55.000 0.00 0.00 41.61 2.66
490 3045 8.617809 TCAAATTGTTAATCTAAAGGATACGCC 58.382 33.333 0.00 0.00 46.39 5.68
540 3716 2.160721 ACACTACTGATCGGACCCAT 57.839 50.000 9.00 0.00 0.00 4.00
541 3717 2.467880 ACACTACTGATCGGACCCATT 58.532 47.619 9.00 0.00 0.00 3.16
542 3718 3.638860 ACACTACTGATCGGACCCATTA 58.361 45.455 9.00 0.00 0.00 1.90
543 3719 4.028131 ACACTACTGATCGGACCCATTAA 58.972 43.478 9.00 0.00 0.00 1.40
544 3720 4.099573 ACACTACTGATCGGACCCATTAAG 59.900 45.833 9.00 0.00 0.00 1.85
545 3721 3.641906 ACTACTGATCGGACCCATTAAGG 59.358 47.826 9.00 0.00 37.03 2.69
546 3722 1.141053 ACTGATCGGACCCATTAAGGC 59.859 52.381 9.00 0.00 35.39 4.35
547 3723 0.472471 TGATCGGACCCATTAAGGCC 59.528 55.000 0.00 0.00 35.39 5.19
548 3724 0.765510 GATCGGACCCATTAAGGCCT 59.234 55.000 0.00 0.00 35.39 5.19
549 3725 1.143073 GATCGGACCCATTAAGGCCTT 59.857 52.381 24.18 24.18 35.39 4.35
550 3726 0.254747 TCGGACCCATTAAGGCCTTG 59.745 55.000 28.77 12.40 35.39 3.61
551 3727 0.034477 CGGACCCATTAAGGCCTTGT 60.034 55.000 28.77 16.69 35.39 3.16
552 3728 1.210967 CGGACCCATTAAGGCCTTGTA 59.789 52.381 28.77 16.03 35.39 2.41
553 3729 2.651455 GGACCCATTAAGGCCTTGTAC 58.349 52.381 28.77 13.75 35.39 2.90
554 3730 2.025699 GGACCCATTAAGGCCTTGTACA 60.026 50.000 28.77 4.66 35.39 2.90
555 3731 3.562609 GGACCCATTAAGGCCTTGTACAA 60.563 47.826 28.77 14.62 35.39 2.41
556 3732 4.278310 GACCCATTAAGGCCTTGTACAAT 58.722 43.478 28.77 16.33 35.39 2.71
557 3733 4.278310 ACCCATTAAGGCCTTGTACAATC 58.722 43.478 28.77 4.19 35.39 2.67
558 3734 3.636764 CCCATTAAGGCCTTGTACAATCC 59.363 47.826 28.77 13.07 35.39 3.01
559 3735 4.277476 CCATTAAGGCCTTGTACAATCCA 58.723 43.478 28.77 0.77 0.00 3.41
560 3736 4.709397 CCATTAAGGCCTTGTACAATCCAA 59.291 41.667 28.77 11.10 0.00 3.53
561 3737 5.163519 CCATTAAGGCCTTGTACAATCCAAG 60.164 44.000 28.77 7.41 39.19 3.61
568 3744 4.853924 CTTGTACAATCCAAGGTGCTTT 57.146 40.909 9.13 0.00 36.50 3.51
569 3745 4.549458 CTTGTACAATCCAAGGTGCTTTG 58.451 43.478 9.13 0.00 36.50 2.77
570 3746 2.295909 TGTACAATCCAAGGTGCTTTGC 59.704 45.455 0.00 0.00 0.00 3.68
571 3747 0.314935 ACAATCCAAGGTGCTTTGCG 59.685 50.000 0.00 0.00 0.00 4.85
572 3748 0.388907 CAATCCAAGGTGCTTTGCGG 60.389 55.000 0.00 0.00 0.00 5.69
573 3749 0.539438 AATCCAAGGTGCTTTGCGGA 60.539 50.000 0.00 0.00 0.00 5.54
574 3750 0.962356 ATCCAAGGTGCTTTGCGGAG 60.962 55.000 0.00 0.00 0.00 4.63
575 3751 2.629656 CCAAGGTGCTTTGCGGAGG 61.630 63.158 0.00 0.00 0.00 4.30
576 3752 1.898574 CAAGGTGCTTTGCGGAGGT 60.899 57.895 0.00 0.00 0.00 3.85
577 3753 1.898574 AAGGTGCTTTGCGGAGGTG 60.899 57.895 0.00 0.00 0.00 4.00
578 3754 4.043200 GGTGCTTTGCGGAGGTGC 62.043 66.667 0.00 0.00 0.00 5.01
579 3755 2.980233 GTGCTTTGCGGAGGTGCT 60.980 61.111 0.00 0.00 35.36 4.40
580 3756 2.203337 TGCTTTGCGGAGGTGCTT 60.203 55.556 0.00 0.00 35.36 3.91
581 3757 1.072332 TGCTTTGCGGAGGTGCTTA 59.928 52.632 0.00 0.00 35.36 3.09
582 3758 0.955428 TGCTTTGCGGAGGTGCTTAG 60.955 55.000 0.00 0.00 35.36 2.18
583 3759 0.673644 GCTTTGCGGAGGTGCTTAGA 60.674 55.000 0.00 0.00 35.36 2.10
584 3760 1.363744 CTTTGCGGAGGTGCTTAGAG 58.636 55.000 0.00 0.00 35.36 2.43
585 3761 0.973632 TTTGCGGAGGTGCTTAGAGA 59.026 50.000 0.00 0.00 35.36 3.10
586 3762 0.973632 TTGCGGAGGTGCTTAGAGAA 59.026 50.000 0.00 0.00 35.36 2.87
587 3763 0.973632 TGCGGAGGTGCTTAGAGAAA 59.026 50.000 0.00 0.00 35.36 2.52
588 3764 1.555075 TGCGGAGGTGCTTAGAGAAAT 59.445 47.619 0.00 0.00 35.36 2.17
589 3765 2.764010 TGCGGAGGTGCTTAGAGAAATA 59.236 45.455 0.00 0.00 35.36 1.40
590 3766 3.196901 TGCGGAGGTGCTTAGAGAAATAA 59.803 43.478 0.00 0.00 35.36 1.40
591 3767 4.189231 GCGGAGGTGCTTAGAGAAATAAA 58.811 43.478 0.00 0.00 0.00 1.40
592 3768 4.816925 GCGGAGGTGCTTAGAGAAATAAAT 59.183 41.667 0.00 0.00 0.00 1.40
593 3769 5.050023 GCGGAGGTGCTTAGAGAAATAAATC 60.050 44.000 0.00 0.00 0.00 2.17
594 3770 6.049149 CGGAGGTGCTTAGAGAAATAAATCA 58.951 40.000 0.00 0.00 0.00 2.57
595 3771 6.538742 CGGAGGTGCTTAGAGAAATAAATCAA 59.461 38.462 0.00 0.00 0.00 2.57
596 3772 7.254590 CGGAGGTGCTTAGAGAAATAAATCAAG 60.255 40.741 0.00 0.00 0.00 3.02
597 3773 7.770897 GGAGGTGCTTAGAGAAATAAATCAAGA 59.229 37.037 0.00 0.00 0.00 3.02
598 3774 9.336171 GAGGTGCTTAGAGAAATAAATCAAGAT 57.664 33.333 0.00 0.00 0.00 2.40
599 3775 9.692325 AGGTGCTTAGAGAAATAAATCAAGATT 57.308 29.630 0.00 0.00 0.00 2.40
611 3787 9.875691 AAATAAATCAAGATTTTCCTAAGCACC 57.124 29.630 12.73 0.00 40.99 5.01
612 3788 5.567138 AATCAAGATTTTCCTAAGCACCG 57.433 39.130 0.00 0.00 0.00 4.94
613 3789 3.343617 TCAAGATTTTCCTAAGCACCGG 58.656 45.455 0.00 0.00 0.00 5.28
614 3790 3.081804 CAAGATTTTCCTAAGCACCGGT 58.918 45.455 0.00 0.00 0.00 5.28
615 3791 2.711542 AGATTTTCCTAAGCACCGGTG 58.288 47.619 30.66 30.66 0.00 4.94
628 3804 3.634568 CACCGGTGCTTATTTGTTCAA 57.365 42.857 24.02 0.00 0.00 2.69
629 3805 3.564511 CACCGGTGCTTATTTGTTCAAG 58.435 45.455 24.02 0.00 0.00 3.02
630 3806 2.556622 ACCGGTGCTTATTTGTTCAAGG 59.443 45.455 6.12 0.00 0.00 3.61
631 3807 2.556622 CCGGTGCTTATTTGTTCAAGGT 59.443 45.455 0.00 0.00 0.00 3.50
632 3808 3.754323 CCGGTGCTTATTTGTTCAAGGTA 59.246 43.478 0.00 0.00 0.00 3.08
633 3809 4.142687 CCGGTGCTTATTTGTTCAAGGTAG 60.143 45.833 0.00 0.00 0.00 3.18
634 3810 4.693566 CGGTGCTTATTTGTTCAAGGTAGA 59.306 41.667 0.00 0.00 0.00 2.59
635 3811 5.354234 CGGTGCTTATTTGTTCAAGGTAGAT 59.646 40.000 0.00 0.00 0.00 1.98
636 3812 6.555315 GGTGCTTATTTGTTCAAGGTAGATG 58.445 40.000 0.00 0.00 0.00 2.90
637 3813 6.030228 GTGCTTATTTGTTCAAGGTAGATGC 58.970 40.000 0.00 0.00 0.00 3.91
638 3814 5.945784 TGCTTATTTGTTCAAGGTAGATGCT 59.054 36.000 0.00 0.00 0.00 3.79
639 3815 6.434028 TGCTTATTTGTTCAAGGTAGATGCTT 59.566 34.615 0.00 0.00 0.00 3.91
640 3816 7.609918 TGCTTATTTGTTCAAGGTAGATGCTTA 59.390 33.333 0.00 0.00 0.00 3.09
641 3817 8.458843 GCTTATTTGTTCAAGGTAGATGCTTAA 58.541 33.333 0.00 0.00 0.00 1.85
646 3822 9.733556 TTTGTTCAAGGTAGATGCTTAATTAGA 57.266 29.630 0.00 0.00 0.00 2.10
647 3823 9.905713 TTGTTCAAGGTAGATGCTTAATTAGAT 57.094 29.630 0.00 0.00 0.00 1.98
648 3824 9.330063 TGTTCAAGGTAGATGCTTAATTAGATG 57.670 33.333 0.00 0.00 0.00 2.90
649 3825 9.331282 GTTCAAGGTAGATGCTTAATTAGATGT 57.669 33.333 0.00 0.00 0.00 3.06
650 3826 9.547753 TTCAAGGTAGATGCTTAATTAGATGTC 57.452 33.333 0.00 0.00 0.00 3.06
651 3827 8.928448 TCAAGGTAGATGCTTAATTAGATGTCT 58.072 33.333 0.00 0.00 0.00 3.41
652 3828 9.202273 CAAGGTAGATGCTTAATTAGATGTCTC 57.798 37.037 0.00 0.00 0.00 3.36
653 3829 8.719645 AGGTAGATGCTTAATTAGATGTCTCT 57.280 34.615 0.00 0.00 35.39 3.10
654 3830 9.153479 AGGTAGATGCTTAATTAGATGTCTCTT 57.847 33.333 0.00 0.00 32.66 2.85
655 3831 9.418045 GGTAGATGCTTAATTAGATGTCTCTTC 57.582 37.037 0.00 0.00 32.66 2.87
658 3834 8.703743 AGATGCTTAATTAGATGTCTCTTCTGT 58.296 33.333 0.00 0.00 32.66 3.41
659 3835 9.973450 GATGCTTAATTAGATGTCTCTTCTGTA 57.027 33.333 0.00 0.00 32.66 2.74
660 3836 9.979578 ATGCTTAATTAGATGTCTCTTCTGTAG 57.020 33.333 0.00 0.00 32.66 2.74
661 3837 9.190317 TGCTTAATTAGATGTCTCTTCTGTAGA 57.810 33.333 0.00 0.00 32.66 2.59
673 3849 9.698309 TGTCTCTTCTGTAGAAATAAAACTCAG 57.302 33.333 0.00 0.00 33.07 3.35
674 3850 9.699703 GTCTCTTCTGTAGAAATAAAACTCAGT 57.300 33.333 0.00 0.00 33.07 3.41
691 3867 9.529325 AAAACTCAGTTTATTTTTCTAAGCACC 57.471 29.630 2.38 0.00 34.43 5.01
692 3868 8.465273 AACTCAGTTTATTTTTCTAAGCACCT 57.535 30.769 0.00 0.00 0.00 4.00
693 3869 9.569122 AACTCAGTTTATTTTTCTAAGCACCTA 57.431 29.630 0.00 0.00 0.00 3.08
694 3870 9.220767 ACTCAGTTTATTTTTCTAAGCACCTAG 57.779 33.333 0.00 0.00 0.00 3.02
695 3871 8.040716 TCAGTTTATTTTTCTAAGCACCTAGC 57.959 34.615 0.00 0.00 46.19 3.42
717 3893 5.470098 AGCATTGTTAACAAGACTGTTCGAT 59.530 36.000 24.22 2.87 42.25 3.59
743 3929 7.716560 TGAATCAGTATCATTTCAACCATCGAT 59.283 33.333 0.00 0.00 0.00 3.59
761 4252 2.798145 CGATATACTTGCACGCCTCACA 60.798 50.000 0.00 0.00 0.00 3.58
765 4256 1.032014 ACTTGCACGCCTCACAAATT 58.968 45.000 0.00 0.00 0.00 1.82
790 4281 8.462589 TCATGCATATCCATCTAGAGATACTC 57.537 38.462 0.00 0.00 32.63 2.59
803 4298 9.827198 ATCTAGAGATACTCAAGAGATGGATTT 57.173 33.333 3.73 0.00 30.83 2.17
804 4299 9.076781 TCTAGAGATACTCAAGAGATGGATTTG 57.923 37.037 3.73 0.00 32.06 2.32
815 4310 7.833682 TCAAGAGATGGATTTGTTAATTAGCCA 59.166 33.333 0.00 0.00 0.00 4.75
819 4314 4.027437 TGGATTTGTTAATTAGCCACCCC 58.973 43.478 0.00 0.00 0.00 4.95
871 4366 3.257127 CACCAATGCATGCATATCCATCA 59.743 43.478 32.36 1.82 35.31 3.07
947 4446 3.712881 GGACACACGCTCAACCGC 61.713 66.667 0.00 0.00 0.00 5.68
984 4483 4.942483 TCGAACATAGCCCTAGTATAGAGC 59.058 45.833 0.00 0.00 43.50 4.09
1063 4562 1.675310 CTGAATTCGGCCAGCCACA 60.675 57.895 9.78 0.00 35.37 4.17
1137 4636 0.250793 TCGTGTCCAACCACAACACT 59.749 50.000 3.69 0.00 40.84 3.55
1140 4639 0.034574 TGTCCAACCACAACACTGCT 60.035 50.000 0.00 0.00 0.00 4.24
1145 4644 0.756442 AACCACAACACTGCTGGCAT 60.756 50.000 0.00 0.00 30.91 4.40
1282 4781 4.671590 TCGGGCTGGACCTCGTCA 62.672 66.667 0.00 0.00 39.10 4.35
1357 4856 1.080434 GCCGTCTTCGACTCTGCTT 60.080 57.895 0.00 0.00 39.71 3.91
1358 4857 0.667792 GCCGTCTTCGACTCTGCTTT 60.668 55.000 0.00 0.00 39.71 3.51
1405 4904 0.320421 CACAGACCCCAAGTGTACGG 60.320 60.000 0.00 0.00 0.00 4.02
1423 4922 4.033251 CCCCCTACACCCCCTCCA 62.033 72.222 0.00 0.00 0.00 3.86
1426 4925 2.285368 CCTACACCCCCTCCAGCA 60.285 66.667 0.00 0.00 0.00 4.41
1506 5005 2.876879 CGACACGTTTGCCTTCGCA 61.877 57.895 0.00 0.00 45.49 5.10
1579 5081 4.649954 GCTGCGCACACACGACAC 62.650 66.667 5.66 0.00 34.06 3.67
1707 5209 2.945668 GCGGTTCTCATATTGCCTCTTT 59.054 45.455 0.00 0.00 0.00 2.52
1729 5231 2.829384 GGACAGAGCCACCCCAACA 61.829 63.158 0.00 0.00 0.00 3.33
1779 5281 2.764128 ATCCCGAGGCACGACCAT 60.764 61.111 5.74 0.00 45.77 3.55
2133 5635 0.109873 ACCTGTACGAAGAAGCGACG 60.110 55.000 0.00 0.00 34.83 5.12
2224 5726 1.030488 GGACGAGGAGATGACGGTGA 61.030 60.000 0.00 0.00 0.00 4.02
2584 6109 4.336889 TTTATACTCCCTCCGATGCAAG 57.663 45.455 0.00 0.00 0.00 4.01
2769 6301 1.929836 CTGTGCGCTAGATCAGTTTCC 59.070 52.381 9.73 0.00 0.00 3.13
2888 6689 1.942657 TGCTAGCCGATGATTTTCAGC 59.057 47.619 13.29 0.00 0.00 4.26
3108 6915 8.002459 TGGGGTTAAGAAAGTCTAGACATTTTT 58.998 33.333 24.44 20.44 0.00 1.94
3127 6934 4.741928 TTTTTAGAGGAAAAGGGCTCCT 57.258 40.909 0.00 0.00 46.40 3.69
3128 6935 3.721087 TTTAGAGGAAAAGGGCTCCTG 57.279 47.619 0.00 0.00 43.65 3.86
3129 6936 0.912486 TAGAGGAAAAGGGCTCCTGC 59.088 55.000 0.00 0.00 43.65 4.85
3130 6937 6.882412 TTTTAGAGGAAAAGGGCTCCTGCC 62.882 50.000 0.00 0.00 43.65 4.85
3140 6947 3.411517 CTCCTGCCCCGGTTCCAT 61.412 66.667 0.00 0.00 0.00 3.41
3141 6948 2.938798 TCCTGCCCCGGTTCCATT 60.939 61.111 0.00 0.00 0.00 3.16
3143 6950 1.453197 CCTGCCCCGGTTCCATTAC 60.453 63.158 0.00 0.00 0.00 1.89
3144 6951 1.607612 CTGCCCCGGTTCCATTACT 59.392 57.895 0.00 0.00 0.00 2.24
3145 6952 0.034477 CTGCCCCGGTTCCATTACTT 60.034 55.000 0.00 0.00 0.00 2.24
3147 6954 1.634459 TGCCCCGGTTCCATTACTTAA 59.366 47.619 0.00 0.00 0.00 1.85
3148 6955 2.041350 TGCCCCGGTTCCATTACTTAAA 59.959 45.455 0.00 0.00 0.00 1.52
3149 6956 3.090790 GCCCCGGTTCCATTACTTAAAA 58.909 45.455 0.00 0.00 0.00 1.52
3150 6957 3.702548 GCCCCGGTTCCATTACTTAAAAT 59.297 43.478 0.00 0.00 0.00 1.82
3151 6958 4.440940 GCCCCGGTTCCATTACTTAAAATG 60.441 45.833 0.00 0.00 36.74 2.32
3152 6959 4.951094 CCCCGGTTCCATTACTTAAAATGA 59.049 41.667 0.00 0.00 38.84 2.57
3154 6961 6.071278 CCCCGGTTCCATTACTTAAAATGAAA 60.071 38.462 0.00 0.00 38.84 2.69
3155 6962 6.809689 CCCGGTTCCATTACTTAAAATGAAAC 59.190 38.462 0.00 0.00 38.84 2.78
3156 6963 6.809689 CCGGTTCCATTACTTAAAATGAAACC 59.190 38.462 9.75 9.75 45.66 3.27
3161 6968 8.698973 TCCATTACTTAAAATGAAACCACAGA 57.301 30.769 2.09 0.00 38.84 3.41
3162 6969 9.137459 TCCATTACTTAAAATGAAACCACAGAA 57.863 29.630 2.09 0.00 38.84 3.02
3163 6970 9.927668 CCATTACTTAAAATGAAACCACAGAAT 57.072 29.630 2.09 0.00 38.84 2.40
3166 6973 7.595819 ACTTAAAATGAAACCACAGAATCCA 57.404 32.000 0.00 0.00 0.00 3.41
3167 6974 7.661040 ACTTAAAATGAAACCACAGAATCCAG 58.339 34.615 0.00 0.00 0.00 3.86
3168 6975 7.287696 ACTTAAAATGAAACCACAGAATCCAGT 59.712 33.333 0.00 0.00 0.00 4.00
3169 6976 5.712152 AAATGAAACCACAGAATCCAGTC 57.288 39.130 0.00 0.00 0.00 3.51
3170 6977 4.647564 ATGAAACCACAGAATCCAGTCT 57.352 40.909 0.00 0.00 0.00 3.24
3171 6978 4.008074 TGAAACCACAGAATCCAGTCTC 57.992 45.455 0.00 0.00 0.00 3.36
3172 6979 3.390967 TGAAACCACAGAATCCAGTCTCA 59.609 43.478 0.00 0.00 0.00 3.27
3173 6980 4.042062 TGAAACCACAGAATCCAGTCTCAT 59.958 41.667 0.00 0.00 0.00 2.90
3174 6981 4.647564 AACCACAGAATCCAGTCTCATT 57.352 40.909 0.00 0.00 0.00 2.57
3175 6982 5.762179 AACCACAGAATCCAGTCTCATTA 57.238 39.130 0.00 0.00 0.00 1.90
3176 6983 5.091261 ACCACAGAATCCAGTCTCATTAC 57.909 43.478 0.00 0.00 0.00 1.89
3177 6984 4.532126 ACCACAGAATCCAGTCTCATTACA 59.468 41.667 0.00 0.00 0.00 2.41
3178 6985 5.114780 CCACAGAATCCAGTCTCATTACAG 58.885 45.833 0.00 0.00 0.00 2.74
3179 6986 4.569966 CACAGAATCCAGTCTCATTACAGC 59.430 45.833 0.00 0.00 0.00 4.40
3180 6987 4.125703 CAGAATCCAGTCTCATTACAGCC 58.874 47.826 0.00 0.00 0.00 4.85
3181 6988 3.135530 AGAATCCAGTCTCATTACAGCCC 59.864 47.826 0.00 0.00 0.00 5.19
3182 6989 0.824109 TCCAGTCTCATTACAGCCCG 59.176 55.000 0.00 0.00 0.00 6.13
3183 6990 0.811616 CCAGTCTCATTACAGCCCGC 60.812 60.000 0.00 0.00 0.00 6.13
3184 6991 1.141881 AGTCTCATTACAGCCCGCG 59.858 57.895 0.00 0.00 0.00 6.46
3185 6992 1.883084 GTCTCATTACAGCCCGCGG 60.883 63.158 21.04 21.04 0.00 6.46
3186 6993 2.588877 CTCATTACAGCCCGCGGG 60.589 66.667 40.26 40.26 38.57 6.13
3213 7020 0.606673 GCTCCCTCCGGCATAAATCC 60.607 60.000 0.00 0.00 0.00 3.01
3214 7021 0.764890 CTCCCTCCGGCATAAATCCA 59.235 55.000 0.00 0.00 0.00 3.41
3216 7023 0.537371 CCCTCCGGCATAAATCCACC 60.537 60.000 0.00 0.00 0.00 4.61
3217 7024 0.474184 CCTCCGGCATAAATCCACCT 59.526 55.000 0.00 0.00 0.00 4.00
3218 7025 1.697432 CCTCCGGCATAAATCCACCTA 59.303 52.381 0.00 0.00 0.00 3.08
3219 7026 2.105821 CCTCCGGCATAAATCCACCTAA 59.894 50.000 0.00 0.00 0.00 2.69
3221 7028 3.547746 TCCGGCATAAATCCACCTAAAC 58.452 45.455 0.00 0.00 0.00 2.01
3222 7029 3.054287 TCCGGCATAAATCCACCTAAACA 60.054 43.478 0.00 0.00 0.00 2.83
3223 7030 3.066203 CCGGCATAAATCCACCTAAACAC 59.934 47.826 0.00 0.00 0.00 3.32
3225 7032 4.438200 CGGCATAAATCCACCTAAACACAC 60.438 45.833 0.00 0.00 0.00 3.82
3226 7033 4.438200 GGCATAAATCCACCTAAACACACG 60.438 45.833 0.00 0.00 0.00 4.49
3227 7034 4.393680 GCATAAATCCACCTAAACACACGA 59.606 41.667 0.00 0.00 0.00 4.35
3228 7035 5.672819 GCATAAATCCACCTAAACACACGAC 60.673 44.000 0.00 0.00 0.00 4.34
3229 7036 3.764237 AATCCACCTAAACACACGACT 57.236 42.857 0.00 0.00 0.00 4.18
3230 7037 3.764237 ATCCACCTAAACACACGACTT 57.236 42.857 0.00 0.00 0.00 3.01
3231 7038 3.547054 TCCACCTAAACACACGACTTT 57.453 42.857 0.00 0.00 0.00 2.66
3233 7040 5.021033 TCCACCTAAACACACGACTTTAA 57.979 39.130 0.00 0.00 0.00 1.52
3236 7043 5.967088 CCACCTAAACACACGACTTTAAAAC 59.033 40.000 0.00 0.00 0.00 2.43
3237 7044 5.967088 CACCTAAACACACGACTTTAAAACC 59.033 40.000 0.00 0.00 0.00 3.27
3238 7045 5.882000 ACCTAAACACACGACTTTAAAACCT 59.118 36.000 0.00 0.00 0.00 3.50
3239 7046 6.037500 ACCTAAACACACGACTTTAAAACCTC 59.962 38.462 0.00 0.00 0.00 3.85
3243 7050 6.594284 ACACACGACTTTAAAACCTCTTAC 57.406 37.500 0.00 0.00 0.00 2.34
3246 7053 7.069569 CACACGACTTTAAAACCTCTTACATG 58.930 38.462 0.00 0.00 0.00 3.21
3248 7055 5.761234 ACGACTTTAAAACCTCTTACATGCA 59.239 36.000 0.00 0.00 0.00 3.96
3250 7057 6.961554 CGACTTTAAAACCTCTTACATGCATC 59.038 38.462 0.00 0.00 0.00 3.91
3253 7060 8.462016 ACTTTAAAACCTCTTACATGCATCATC 58.538 33.333 0.00 0.00 0.00 2.92
3254 7061 8.579850 TTTAAAACCTCTTACATGCATCATCT 57.420 30.769 0.00 0.00 0.00 2.90
3255 7062 9.679661 TTTAAAACCTCTTACATGCATCATCTA 57.320 29.630 0.00 0.00 0.00 1.98
3257 7064 7.559590 AAACCTCTTACATGCATCATCTAAC 57.440 36.000 0.00 0.00 0.00 2.34
3258 7065 5.292765 ACCTCTTACATGCATCATCTAACG 58.707 41.667 0.00 0.00 0.00 3.18
3259 7066 5.069119 ACCTCTTACATGCATCATCTAACGA 59.931 40.000 0.00 0.00 0.00 3.85
3260 7067 5.985530 CCTCTTACATGCATCATCTAACGAA 59.014 40.000 0.00 0.00 0.00 3.85
3262 7069 7.359849 CCTCTTACATGCATCATCTAACGAATG 60.360 40.741 0.00 0.00 0.00 2.67
3263 7070 6.986231 TCTTACATGCATCATCTAACGAATGT 59.014 34.615 0.00 0.00 0.00 2.71
3264 7071 5.663795 ACATGCATCATCTAACGAATGTC 57.336 39.130 0.00 0.00 0.00 3.06
3266 7073 6.515832 ACATGCATCATCTAACGAATGTCTA 58.484 36.000 0.00 0.00 0.00 2.59
3267 7074 6.422100 ACATGCATCATCTAACGAATGTCTAC 59.578 38.462 0.00 0.00 0.00 2.59
3268 7075 6.149129 TGCATCATCTAACGAATGTCTACT 57.851 37.500 0.00 0.00 0.00 2.57
3269 7076 5.979517 TGCATCATCTAACGAATGTCTACTG 59.020 40.000 0.00 0.00 0.00 2.74
3270 7077 6.183360 TGCATCATCTAACGAATGTCTACTGA 60.183 38.462 0.00 0.00 0.00 3.41
3271 7078 6.143118 GCATCATCTAACGAATGTCTACTGAC 59.857 42.308 0.00 0.00 43.20 3.51
3285 7092 6.410243 GTCTACTGACAGAACATAAAAGGC 57.590 41.667 10.08 0.00 42.48 4.35
3286 7093 6.166982 GTCTACTGACAGAACATAAAAGGCT 58.833 40.000 10.08 0.00 42.48 4.58
3287 7094 7.321153 GTCTACTGACAGAACATAAAAGGCTA 58.679 38.462 10.08 0.00 42.48 3.93
3288 7095 7.817962 GTCTACTGACAGAACATAAAAGGCTAA 59.182 37.037 10.08 0.00 42.48 3.09
3289 7096 8.540388 TCTACTGACAGAACATAAAAGGCTAAT 58.460 33.333 10.08 0.00 0.00 1.73
3290 7097 7.383102 ACTGACAGAACATAAAAGGCTAATG 57.617 36.000 10.08 0.00 0.00 1.90
3291 7098 6.127897 ACTGACAGAACATAAAAGGCTAATGC 60.128 38.462 10.08 0.00 38.76 3.56
3316 7123 2.687566 AGGAAGGCCTGGTACCCG 60.688 66.667 5.69 2.14 44.90 5.28
3317 7124 2.686106 GGAAGGCCTGGTACCCGA 60.686 66.667 5.69 0.00 0.00 5.14
3318 7125 2.070650 GGAAGGCCTGGTACCCGAT 61.071 63.158 5.69 0.00 0.00 4.18
3319 7126 0.761702 GGAAGGCCTGGTACCCGATA 60.762 60.000 5.69 0.00 0.00 2.92
3320 7127 1.349067 GAAGGCCTGGTACCCGATAT 58.651 55.000 5.69 0.00 0.00 1.63
3321 7128 1.275573 GAAGGCCTGGTACCCGATATC 59.724 57.143 5.69 0.00 0.00 1.63
3322 7129 0.487772 AGGCCTGGTACCCGATATCT 59.512 55.000 3.11 0.00 0.00 1.98
3323 7130 1.714787 AGGCCTGGTACCCGATATCTA 59.285 52.381 3.11 0.00 0.00 1.98
3324 7131 2.315155 AGGCCTGGTACCCGATATCTAT 59.685 50.000 3.11 0.00 0.00 1.98
3325 7132 2.694109 GGCCTGGTACCCGATATCTATC 59.306 54.545 10.07 0.00 0.00 2.08
3326 7133 3.627747 GGCCTGGTACCCGATATCTATCT 60.628 52.174 10.07 0.00 0.00 1.98
3327 7134 3.633065 GCCTGGTACCCGATATCTATCTC 59.367 52.174 10.07 0.00 0.00 2.75
3328 7135 4.629204 GCCTGGTACCCGATATCTATCTCT 60.629 50.000 10.07 0.00 0.00 3.10
3329 7136 5.511363 CCTGGTACCCGATATCTATCTCTT 58.489 45.833 10.07 0.00 0.00 2.85
3330 7137 5.591067 CCTGGTACCCGATATCTATCTCTTC 59.409 48.000 10.07 0.00 0.00 2.87
3331 7138 6.390048 TGGTACCCGATATCTATCTCTTCT 57.610 41.667 10.07 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.827177 AGAGAGTAGAGACTAGATTATGTTCG 57.173 38.462 0.00 0.00 35.45 3.95
7 8 9.312904 GGGTAGTAGAGAGTAGAGACTAGATTA 57.687 40.741 0.00 0.00 35.45 1.75
8 9 7.790798 TGGGTAGTAGAGAGTAGAGACTAGATT 59.209 40.741 0.00 0.00 35.45 2.40
15 16 5.278873 TCTGTGGGTAGTAGAGAGTAGAGA 58.721 45.833 0.00 0.00 0.00 3.10
16 17 5.617528 TCTGTGGGTAGTAGAGAGTAGAG 57.382 47.826 0.00 0.00 0.00 2.43
17 18 6.409464 GGATTCTGTGGGTAGTAGAGAGTAGA 60.409 46.154 0.00 0.00 0.00 2.59
18 19 5.766174 GGATTCTGTGGGTAGTAGAGAGTAG 59.234 48.000 0.00 0.00 0.00 2.57
19 20 5.193124 TGGATTCTGTGGGTAGTAGAGAGTA 59.807 44.000 0.00 0.00 0.00 2.59
20 21 4.017407 TGGATTCTGTGGGTAGTAGAGAGT 60.017 45.833 0.00 0.00 0.00 3.24
21 22 4.537751 TGGATTCTGTGGGTAGTAGAGAG 58.462 47.826 0.00 0.00 0.00 3.20
22 23 4.603094 TGGATTCTGTGGGTAGTAGAGA 57.397 45.455 0.00 0.00 0.00 3.10
105 106 0.521735 GGGGCATCGAGAACAAACAC 59.478 55.000 0.00 0.00 0.00 3.32
214 215 1.134007 CAGCCCATCTGCATCCTGTTA 60.134 52.381 0.00 0.00 35.78 2.41
217 218 0.471191 TACAGCCCATCTGCATCCTG 59.529 55.000 0.00 0.00 46.76 3.86
293 294 4.385825 TGAACGTTTCCTGCTATCTGTTT 58.614 39.130 0.46 0.00 0.00 2.83
342 343 2.820787 GGTAGATCCCAGATCGAACGAT 59.179 50.000 9.46 9.46 37.59 3.73
370 2642 3.945285 ACCGCAATATTAAACTGACCCTG 59.055 43.478 0.00 0.00 0.00 4.45
372 2644 3.314357 GGACCGCAATATTAAACTGACCC 59.686 47.826 0.00 0.00 0.00 4.46
381 2653 9.733556 AGTCATATAATTTGGACCGCAATATTA 57.266 29.630 0.00 0.00 0.00 0.98
490 3045 5.890334 TCTTTTCAATTTATTAGGGCTGCG 58.110 37.500 0.00 0.00 0.00 5.18
547 3723 4.549458 CAAAGCACCTTGGATTGTACAAG 58.451 43.478 14.65 1.64 43.73 3.16
548 3724 3.243704 GCAAAGCACCTTGGATTGTACAA 60.244 43.478 11.41 11.41 0.00 2.41
549 3725 2.295909 GCAAAGCACCTTGGATTGTACA 59.704 45.455 0.00 0.00 0.00 2.90
550 3726 2.668279 CGCAAAGCACCTTGGATTGTAC 60.668 50.000 0.00 0.00 0.00 2.90
551 3727 1.539388 CGCAAAGCACCTTGGATTGTA 59.461 47.619 0.00 0.00 0.00 2.41
552 3728 0.314935 CGCAAAGCACCTTGGATTGT 59.685 50.000 0.00 0.00 0.00 2.71
553 3729 0.388907 CCGCAAAGCACCTTGGATTG 60.389 55.000 0.00 0.00 0.00 2.67
554 3730 0.539438 TCCGCAAAGCACCTTGGATT 60.539 50.000 0.00 0.00 0.00 3.01
555 3731 0.962356 CTCCGCAAAGCACCTTGGAT 60.962 55.000 0.00 0.00 0.00 3.41
556 3732 1.600636 CTCCGCAAAGCACCTTGGA 60.601 57.895 0.00 0.00 0.00 3.53
557 3733 2.629656 CCTCCGCAAAGCACCTTGG 61.630 63.158 0.00 0.00 0.00 3.61
558 3734 1.898574 ACCTCCGCAAAGCACCTTG 60.899 57.895 0.00 0.00 0.00 3.61
559 3735 1.898574 CACCTCCGCAAAGCACCTT 60.899 57.895 0.00 0.00 0.00 3.50
560 3736 2.281761 CACCTCCGCAAAGCACCT 60.282 61.111 0.00 0.00 0.00 4.00
561 3737 4.043200 GCACCTCCGCAAAGCACC 62.043 66.667 0.00 0.00 0.00 5.01
562 3738 1.234615 TAAGCACCTCCGCAAAGCAC 61.235 55.000 0.00 0.00 0.00 4.40
563 3739 0.955428 CTAAGCACCTCCGCAAAGCA 60.955 55.000 0.00 0.00 0.00 3.91
564 3740 0.673644 TCTAAGCACCTCCGCAAAGC 60.674 55.000 0.00 0.00 0.00 3.51
565 3741 1.066858 TCTCTAAGCACCTCCGCAAAG 60.067 52.381 0.00 0.00 0.00 2.77
566 3742 0.973632 TCTCTAAGCACCTCCGCAAA 59.026 50.000 0.00 0.00 0.00 3.68
567 3743 0.973632 TTCTCTAAGCACCTCCGCAA 59.026 50.000 0.00 0.00 0.00 4.85
568 3744 0.973632 TTTCTCTAAGCACCTCCGCA 59.026 50.000 0.00 0.00 0.00 5.69
569 3745 2.317530 ATTTCTCTAAGCACCTCCGC 57.682 50.000 0.00 0.00 0.00 5.54
570 3746 6.049149 TGATTTATTTCTCTAAGCACCTCCG 58.951 40.000 0.00 0.00 0.00 4.63
571 3747 7.770897 TCTTGATTTATTTCTCTAAGCACCTCC 59.229 37.037 0.00 0.00 0.00 4.30
572 3748 8.723942 TCTTGATTTATTTCTCTAAGCACCTC 57.276 34.615 0.00 0.00 0.00 3.85
573 3749 9.692325 AATCTTGATTTATTTCTCTAAGCACCT 57.308 29.630 0.00 0.00 0.00 4.00
585 3761 9.875691 GGTGCTTAGGAAAATCTTGATTTATTT 57.124 29.630 8.75 0.00 0.00 1.40
586 3762 8.190784 CGGTGCTTAGGAAAATCTTGATTTATT 58.809 33.333 8.75 0.00 0.00 1.40
587 3763 7.201821 CCGGTGCTTAGGAAAATCTTGATTTAT 60.202 37.037 8.75 2.53 0.00 1.40
588 3764 6.094881 CCGGTGCTTAGGAAAATCTTGATTTA 59.905 38.462 8.75 0.00 0.00 1.40
589 3765 5.105756 CCGGTGCTTAGGAAAATCTTGATTT 60.106 40.000 0.00 3.04 0.00 2.17
590 3766 4.399303 CCGGTGCTTAGGAAAATCTTGATT 59.601 41.667 0.00 0.00 0.00 2.57
591 3767 3.947834 CCGGTGCTTAGGAAAATCTTGAT 59.052 43.478 0.00 0.00 0.00 2.57
592 3768 3.244770 ACCGGTGCTTAGGAAAATCTTGA 60.245 43.478 6.12 0.00 0.00 3.02
593 3769 3.081804 ACCGGTGCTTAGGAAAATCTTG 58.918 45.455 6.12 0.00 0.00 3.02
594 3770 3.081804 CACCGGTGCTTAGGAAAATCTT 58.918 45.455 24.02 0.00 0.00 2.40
595 3771 2.711542 CACCGGTGCTTAGGAAAATCT 58.288 47.619 24.02 0.00 0.00 2.40
608 3784 3.564511 CTTGAACAAATAAGCACCGGTG 58.435 45.455 30.66 30.66 0.00 4.94
609 3785 2.556622 CCTTGAACAAATAAGCACCGGT 59.443 45.455 0.00 0.00 0.00 5.28
610 3786 2.556622 ACCTTGAACAAATAAGCACCGG 59.443 45.455 0.00 0.00 0.00 5.28
611 3787 3.915437 ACCTTGAACAAATAAGCACCG 57.085 42.857 0.00 0.00 0.00 4.94
612 3788 6.555315 CATCTACCTTGAACAAATAAGCACC 58.445 40.000 0.00 0.00 0.00 5.01
613 3789 6.030228 GCATCTACCTTGAACAAATAAGCAC 58.970 40.000 0.00 0.00 0.00 4.40
614 3790 5.945784 AGCATCTACCTTGAACAAATAAGCA 59.054 36.000 0.00 0.00 0.00 3.91
615 3791 6.442513 AGCATCTACCTTGAACAAATAAGC 57.557 37.500 0.00 0.00 0.00 3.09
620 3796 9.733556 TCTAATTAAGCATCTACCTTGAACAAA 57.266 29.630 0.00 0.00 0.00 2.83
621 3797 9.905713 ATCTAATTAAGCATCTACCTTGAACAA 57.094 29.630 0.00 0.00 0.00 2.83
622 3798 9.330063 CATCTAATTAAGCATCTACCTTGAACA 57.670 33.333 0.00 0.00 0.00 3.18
623 3799 9.331282 ACATCTAATTAAGCATCTACCTTGAAC 57.669 33.333 0.00 0.00 0.00 3.18
624 3800 9.547753 GACATCTAATTAAGCATCTACCTTGAA 57.452 33.333 0.00 0.00 0.00 2.69
625 3801 8.928448 AGACATCTAATTAAGCATCTACCTTGA 58.072 33.333 0.00 0.00 0.00 3.02
626 3802 9.202273 GAGACATCTAATTAAGCATCTACCTTG 57.798 37.037 0.00 0.00 0.00 3.61
627 3803 9.153479 AGAGACATCTAATTAAGCATCTACCTT 57.847 33.333 0.00 0.00 32.54 3.50
628 3804 8.719645 AGAGACATCTAATTAAGCATCTACCT 57.280 34.615 0.00 0.00 32.54 3.08
629 3805 9.418045 GAAGAGACATCTAATTAAGCATCTACC 57.582 37.037 0.00 0.00 33.45 3.18
632 3808 8.703743 ACAGAAGAGACATCTAATTAAGCATCT 58.296 33.333 0.00 0.00 33.45 2.90
633 3809 8.885494 ACAGAAGAGACATCTAATTAAGCATC 57.115 34.615 0.00 0.00 33.45 3.91
634 3810 9.979578 CTACAGAAGAGACATCTAATTAAGCAT 57.020 33.333 0.00 0.00 33.45 3.79
635 3811 9.190317 TCTACAGAAGAGACATCTAATTAAGCA 57.810 33.333 0.00 0.00 33.45 3.91
647 3823 9.698309 CTGAGTTTTATTTCTACAGAAGAGACA 57.302 33.333 0.00 0.00 35.05 3.41
648 3824 9.699703 ACTGAGTTTTATTTCTACAGAAGAGAC 57.300 33.333 0.00 0.00 35.05 3.36
665 3841 9.529325 GGTGCTTAGAAAAATAAACTGAGTTTT 57.471 29.630 16.49 0.00 37.01 2.43
666 3842 8.914011 AGGTGCTTAGAAAAATAAACTGAGTTT 58.086 29.630 15.57 15.57 39.24 2.66
667 3843 8.465273 AGGTGCTTAGAAAAATAAACTGAGTT 57.535 30.769 0.00 0.00 0.00 3.01
668 3844 9.220767 CTAGGTGCTTAGAAAAATAAACTGAGT 57.779 33.333 0.00 0.00 0.00 3.41
669 3845 8.178313 GCTAGGTGCTTAGAAAAATAAACTGAG 58.822 37.037 0.00 0.00 38.95 3.35
670 3846 7.663905 TGCTAGGTGCTTAGAAAAATAAACTGA 59.336 33.333 0.00 0.00 43.37 3.41
671 3847 7.816640 TGCTAGGTGCTTAGAAAAATAAACTG 58.183 34.615 0.00 0.00 43.37 3.16
672 3848 7.996098 TGCTAGGTGCTTAGAAAAATAAACT 57.004 32.000 0.00 0.00 43.37 2.66
673 3849 9.076596 CAATGCTAGGTGCTTAGAAAAATAAAC 57.923 33.333 0.00 0.00 43.37 2.01
674 3850 8.802267 ACAATGCTAGGTGCTTAGAAAAATAAA 58.198 29.630 0.00 0.00 43.37 1.40
675 3851 8.348285 ACAATGCTAGGTGCTTAGAAAAATAA 57.652 30.769 0.00 0.00 43.37 1.40
676 3852 7.938140 ACAATGCTAGGTGCTTAGAAAAATA 57.062 32.000 0.00 0.00 43.37 1.40
677 3853 6.840780 ACAATGCTAGGTGCTTAGAAAAAT 57.159 33.333 0.00 0.00 43.37 1.82
678 3854 6.648879 AACAATGCTAGGTGCTTAGAAAAA 57.351 33.333 0.00 0.00 43.37 1.94
679 3855 7.229707 TGTTAACAATGCTAGGTGCTTAGAAAA 59.770 33.333 5.64 0.00 43.37 2.29
680 3856 6.712998 TGTTAACAATGCTAGGTGCTTAGAAA 59.287 34.615 5.64 0.00 43.37 2.52
681 3857 6.234920 TGTTAACAATGCTAGGTGCTTAGAA 58.765 36.000 5.64 0.00 43.37 2.10
682 3858 5.800296 TGTTAACAATGCTAGGTGCTTAGA 58.200 37.500 5.64 0.00 43.37 2.10
683 3859 6.371548 TCTTGTTAACAATGCTAGGTGCTTAG 59.628 38.462 20.83 4.83 43.37 2.18
684 3860 6.148811 GTCTTGTTAACAATGCTAGGTGCTTA 59.851 38.462 20.83 0.00 43.37 3.09
685 3861 5.048713 GTCTTGTTAACAATGCTAGGTGCTT 60.049 40.000 20.83 0.00 43.37 3.91
686 3862 4.455877 GTCTTGTTAACAATGCTAGGTGCT 59.544 41.667 20.83 0.00 43.37 4.40
687 3863 4.455877 AGTCTTGTTAACAATGCTAGGTGC 59.544 41.667 20.83 6.80 43.25 5.01
688 3864 5.470098 ACAGTCTTGTTAACAATGCTAGGTG 59.530 40.000 20.83 13.20 32.28 4.00
689 3865 5.621193 ACAGTCTTGTTAACAATGCTAGGT 58.379 37.500 20.83 13.08 32.28 3.08
690 3866 6.560253 AACAGTCTTGTTAACAATGCTAGG 57.440 37.500 20.83 8.82 45.45 3.02
717 3893 7.047271 TCGATGGTTGAAATGATACTGATTCA 58.953 34.615 0.00 0.00 0.00 2.57
743 3929 2.753055 TTGTGAGGCGTGCAAGTATA 57.247 45.000 0.59 0.00 0.00 1.47
765 4256 8.057623 TGAGTATCTCTAGATGGATATGCATGA 58.942 37.037 15.13 5.59 36.05 3.07
790 4281 7.917505 GTGGCTAATTAACAAATCCATCTCTTG 59.082 37.037 0.00 0.00 0.00 3.02
803 4298 3.712733 AGATACGGGGTGGCTAATTAACA 59.287 43.478 0.00 0.00 0.00 2.41
804 4299 4.347360 AGATACGGGGTGGCTAATTAAC 57.653 45.455 0.00 0.00 0.00 2.01
815 4310 2.355986 TGCAGCGAAGATACGGGGT 61.356 57.895 0.00 0.00 0.00 4.95
819 4314 2.798680 ACTTAGTGCAGCGAAGATACG 58.201 47.619 13.18 0.00 34.51 3.06
947 4446 2.426522 TGTTCGATGAAGCCAGAAAGG 58.573 47.619 0.00 0.00 41.84 3.11
984 4483 2.169352 AGACATGGTTGATTCCTCCGAG 59.831 50.000 0.00 0.00 0.00 4.63
1030 4529 2.847327 TTCAGCAGAACAAGGAGGAG 57.153 50.000 0.00 0.00 0.00 3.69
1101 4600 1.689273 ACGATAGGCAGACTGAATCCC 59.311 52.381 6.65 0.00 43.77 3.85
1156 4655 3.777925 CGTGAGGTTCGCGCCAAG 61.778 66.667 0.00 0.00 43.59 3.61
1282 4781 2.290768 ACTGCATCCAAGTCAGATTGCT 60.291 45.455 0.00 0.00 0.00 3.91
1357 4856 1.295423 GCTTGTAGCGAGGGGACAA 59.705 57.895 0.00 0.00 0.00 3.18
1358 4857 1.911269 TGCTTGTAGCGAGGGGACA 60.911 57.895 0.00 0.00 46.26 4.02
1426 4925 1.192146 TAGAAGCTGCACCGGTTCCT 61.192 55.000 2.97 0.00 41.12 3.36
1516 5015 3.386237 GTGTCCTCCTCCTGCGCT 61.386 66.667 9.73 0.00 0.00 5.92
1680 5182 2.128035 CAATATGAGAACCGCGAGTCC 58.872 52.381 8.23 0.00 0.00 3.85
1729 5231 3.637273 GAGGAACCCGTGCCTGGT 61.637 66.667 0.00 0.00 37.85 4.00
2318 5820 4.479056 TCTCTAGGATCTAGACAGTTGGGT 59.521 45.833 0.00 0.00 0.00 4.51
2584 6109 3.891049 ACATGGCTTTCCTCCAGATAAC 58.109 45.455 0.00 0.00 36.98 1.89
2741 6273 4.112634 TGATCTAGCGCACAGTAATGTTC 58.887 43.478 11.47 0.00 0.00 3.18
2831 6363 4.079253 AGGGATGTTTTGACATTTAGCGT 58.921 39.130 0.00 0.00 0.00 5.07
2888 6689 2.363680 CCTGACACTGGATAGCCTACAG 59.636 54.545 0.00 1.04 38.19 2.74
2962 6763 3.608796 ACAAAAATTGCACCACTGCTTT 58.391 36.364 0.00 0.00 44.57 3.51
3022 6823 1.337071 CTATAAGCGGCCTGAGAACGA 59.663 52.381 0.00 0.00 0.00 3.85
3108 6915 2.290960 GCAGGAGCCCTTTTCCTCTAAA 60.291 50.000 0.00 0.00 43.17 1.85
3111 6918 1.688211 GCAGGAGCCCTTTTCCTCT 59.312 57.895 0.00 0.00 43.17 3.69
3112 6919 4.328041 GCAGGAGCCCTTTTCCTC 57.672 61.111 0.00 0.00 43.17 3.71
3125 6932 1.453197 GTAATGGAACCGGGGCAGG 60.453 63.158 6.32 0.00 37.30 4.85
3126 6933 0.034477 AAGTAATGGAACCGGGGCAG 60.034 55.000 6.32 0.00 0.00 4.85
3127 6934 1.287217 TAAGTAATGGAACCGGGGCA 58.713 50.000 6.32 0.00 0.00 5.36
3128 6935 2.423446 TTAAGTAATGGAACCGGGGC 57.577 50.000 6.32 0.00 0.00 5.80
3129 6936 4.951094 TCATTTTAAGTAATGGAACCGGGG 59.049 41.667 6.32 0.00 36.41 5.73
3130 6937 6.518208 TTCATTTTAAGTAATGGAACCGGG 57.482 37.500 6.32 0.00 36.41 5.73
3131 6938 7.806149 GTTTCATTTTAAGTAATGGAACCGG 57.194 36.000 10.96 0.00 43.55 5.28
3134 6941 9.191995 CTGTGGTTTCATTTTAAGTAATGGAAC 57.808 33.333 12.75 12.75 46.41 3.62
3135 6942 9.137459 TCTGTGGTTTCATTTTAAGTAATGGAA 57.863 29.630 1.08 0.00 36.41 3.53
3136 6943 8.698973 TCTGTGGTTTCATTTTAAGTAATGGA 57.301 30.769 1.08 0.00 36.41 3.41
3137 6944 9.927668 ATTCTGTGGTTTCATTTTAAGTAATGG 57.072 29.630 1.08 0.00 36.41 3.16
3140 6947 9.137459 TGGATTCTGTGGTTTCATTTTAAGTAA 57.863 29.630 0.00 0.00 0.00 2.24
3141 6948 8.698973 TGGATTCTGTGGTTTCATTTTAAGTA 57.301 30.769 0.00 0.00 0.00 2.24
3143 6950 7.661040 ACTGGATTCTGTGGTTTCATTTTAAG 58.339 34.615 0.00 0.00 0.00 1.85
3144 6951 7.505585 AGACTGGATTCTGTGGTTTCATTTTAA 59.494 33.333 0.00 0.00 0.00 1.52
3145 6952 7.004086 AGACTGGATTCTGTGGTTTCATTTTA 58.996 34.615 0.00 0.00 0.00 1.52
3147 6954 5.388654 AGACTGGATTCTGTGGTTTCATTT 58.611 37.500 0.00 0.00 0.00 2.32
3148 6955 4.990526 AGACTGGATTCTGTGGTTTCATT 58.009 39.130 0.00 0.00 0.00 2.57
3149 6956 4.042062 TGAGACTGGATTCTGTGGTTTCAT 59.958 41.667 0.00 0.00 0.00 2.57
3150 6957 3.390967 TGAGACTGGATTCTGTGGTTTCA 59.609 43.478 0.00 0.00 0.00 2.69
3151 6958 4.008074 TGAGACTGGATTCTGTGGTTTC 57.992 45.455 0.00 0.00 0.00 2.78
3152 6959 4.647564 ATGAGACTGGATTCTGTGGTTT 57.352 40.909 0.00 0.00 0.00 3.27
3154 6961 4.532126 TGTAATGAGACTGGATTCTGTGGT 59.468 41.667 0.00 0.00 0.00 4.16
3155 6962 5.089970 TGTAATGAGACTGGATTCTGTGG 57.910 43.478 0.00 0.00 0.00 4.17
3156 6963 4.569966 GCTGTAATGAGACTGGATTCTGTG 59.430 45.833 0.00 0.00 0.00 3.66
3157 6964 4.383552 GGCTGTAATGAGACTGGATTCTGT 60.384 45.833 0.00 0.00 0.00 3.41
3158 6965 4.125703 GGCTGTAATGAGACTGGATTCTG 58.874 47.826 0.00 0.00 0.00 3.02
3159 6966 3.135530 GGGCTGTAATGAGACTGGATTCT 59.864 47.826 0.00 0.00 0.00 2.40
3161 6968 2.158900 CGGGCTGTAATGAGACTGGATT 60.159 50.000 0.00 0.00 0.00 3.01
3162 6969 1.414181 CGGGCTGTAATGAGACTGGAT 59.586 52.381 0.00 0.00 0.00 3.41
3163 6970 0.824109 CGGGCTGTAATGAGACTGGA 59.176 55.000 0.00 0.00 0.00 3.86
3164 6971 0.811616 GCGGGCTGTAATGAGACTGG 60.812 60.000 0.00 0.00 0.00 4.00
3165 6972 1.148157 CGCGGGCTGTAATGAGACTG 61.148 60.000 0.00 0.00 0.00 3.51
3166 6973 1.141881 CGCGGGCTGTAATGAGACT 59.858 57.895 0.00 0.00 0.00 3.24
3167 6974 1.883084 CCGCGGGCTGTAATGAGAC 60.883 63.158 20.10 0.00 0.00 3.36
3168 6975 2.499205 CCGCGGGCTGTAATGAGA 59.501 61.111 20.10 0.00 0.00 3.27
3169 6976 2.588877 CCCGCGGGCTGTAATGAG 60.589 66.667 34.96 3.26 0.00 2.90
3170 6977 3.078196 TCCCGCGGGCTGTAATGA 61.078 61.111 39.89 17.41 34.68 2.57
3171 6978 2.588877 CTCCCGCGGGCTGTAATG 60.589 66.667 39.89 17.51 34.68 1.90
3172 6979 4.547367 GCTCCCGCGGGCTGTAAT 62.547 66.667 39.89 0.00 34.68 1.89
3199 7006 3.485463 TTAGGTGGATTTATGCCGGAG 57.515 47.619 5.05 0.00 0.00 4.63
3200 7007 3.054287 TGTTTAGGTGGATTTATGCCGGA 60.054 43.478 5.05 0.00 0.00 5.14
3201 7008 3.066203 GTGTTTAGGTGGATTTATGCCGG 59.934 47.826 0.00 0.00 0.00 6.13
3202 7009 3.692101 TGTGTTTAGGTGGATTTATGCCG 59.308 43.478 0.00 0.00 0.00 5.69
3203 7010 4.438200 CGTGTGTTTAGGTGGATTTATGCC 60.438 45.833 0.00 0.00 0.00 4.40
3213 7020 5.967088 GGTTTTAAAGTCGTGTGTTTAGGTG 59.033 40.000 0.00 0.00 0.00 4.00
3214 7021 5.882000 AGGTTTTAAAGTCGTGTGTTTAGGT 59.118 36.000 0.00 0.00 0.00 3.08
3216 7023 7.242914 AGAGGTTTTAAAGTCGTGTGTTTAG 57.757 36.000 0.00 0.00 0.00 1.85
3217 7024 7.614124 AAGAGGTTTTAAAGTCGTGTGTTTA 57.386 32.000 0.00 0.00 0.00 2.01
3218 7025 6.505044 AAGAGGTTTTAAAGTCGTGTGTTT 57.495 33.333 0.00 0.00 0.00 2.83
3219 7026 6.594937 TGTAAGAGGTTTTAAAGTCGTGTGTT 59.405 34.615 0.00 0.00 0.00 3.32
3221 7028 6.592798 TGTAAGAGGTTTTAAAGTCGTGTG 57.407 37.500 0.00 0.00 0.00 3.82
3222 7029 6.293244 GCATGTAAGAGGTTTTAAAGTCGTGT 60.293 38.462 0.00 0.00 0.00 4.49
3223 7030 6.077838 GCATGTAAGAGGTTTTAAAGTCGTG 58.922 40.000 0.00 0.00 0.00 4.35
3225 7032 6.236017 TGCATGTAAGAGGTTTTAAAGTCG 57.764 37.500 0.00 0.00 0.00 4.18
3226 7033 7.816640 TGATGCATGTAAGAGGTTTTAAAGTC 58.183 34.615 2.46 0.00 0.00 3.01
3227 7034 7.759489 TGATGCATGTAAGAGGTTTTAAAGT 57.241 32.000 2.46 0.00 0.00 2.66
3228 7035 8.680903 AGATGATGCATGTAAGAGGTTTTAAAG 58.319 33.333 2.46 0.00 0.00 1.85
3229 7036 8.579850 AGATGATGCATGTAAGAGGTTTTAAA 57.420 30.769 2.46 0.00 0.00 1.52
3230 7037 9.679661 TTAGATGATGCATGTAAGAGGTTTTAA 57.320 29.630 2.46 0.00 28.68 1.52
3231 7038 9.109393 GTTAGATGATGCATGTAAGAGGTTTTA 57.891 33.333 2.46 0.00 31.81 1.52
3233 7040 6.258727 CGTTAGATGATGCATGTAAGAGGTTT 59.741 38.462 2.46 0.00 31.81 3.27
3236 7043 5.532557 TCGTTAGATGATGCATGTAAGAGG 58.467 41.667 2.46 0.00 31.81 3.69
3237 7044 7.170489 ACATTCGTTAGATGATGCATGTAAGAG 59.830 37.037 2.46 0.00 31.81 2.85
3238 7045 6.986231 ACATTCGTTAGATGATGCATGTAAGA 59.014 34.615 2.46 0.00 31.81 2.10
3239 7046 7.170489 AGACATTCGTTAGATGATGCATGTAAG 59.830 37.037 2.46 0.00 31.81 2.34
3243 7050 5.919272 AGACATTCGTTAGATGATGCATG 57.081 39.130 2.46 0.00 0.00 4.06
3246 7053 6.143118 GTCAGTAGACATTCGTTAGATGATGC 59.857 42.308 0.00 0.00 44.34 3.91
3262 7069 6.166982 AGCCTTTTATGTTCTGTCAGTAGAC 58.833 40.000 0.00 0.00 45.19 2.59
3263 7070 6.360370 AGCCTTTTATGTTCTGTCAGTAGA 57.640 37.500 0.00 0.00 0.00 2.59
3264 7071 8.607459 CATTAGCCTTTTATGTTCTGTCAGTAG 58.393 37.037 0.00 0.00 0.00 2.57
3266 7073 6.127897 GCATTAGCCTTTTATGTTCTGTCAGT 60.128 38.462 0.00 0.00 33.58 3.41
3267 7074 6.261118 GCATTAGCCTTTTATGTTCTGTCAG 58.739 40.000 0.00 0.00 33.58 3.51
3268 7075 6.194796 GCATTAGCCTTTTATGTTCTGTCA 57.805 37.500 0.00 0.00 33.58 3.58
3291 7098 3.655211 AGGCCTTCCTGCTGGTGG 61.655 66.667 0.00 13.48 42.34 4.61


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

AutoCloner maintained by Alex Coulton.