Multiple sequence alignment - TraesCS3D01G210400

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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 TraesCS3D01G210400 chr3D 100.000 3237 0 0 1 3237 278800654 278803890 0.000000e+00 5978.0
1 TraesCS3D01G210400 chr3D 94.515 237 12 1 3002 3237 363925998 363926234 6.600000e-97 364.0
2 TraesCS3D01G210400 chr3D 89.130 46 4 1 758 802 278801603 278801648 4.510000e-04 56.5
3 TraesCS3D01G210400 chr3A 94.028 1976 38 28 837 2764 360518612 360516669 0.000000e+00 2922.0
4 TraesCS3D01G210400 chr3A 92.135 178 12 1 2748 2923 360516626 360516449 1.930000e-62 250.0
5 TraesCS3D01G210400 chr3A 96.970 33 1 0 770 802 360518484 360518452 4.510000e-04 56.5
6 TraesCS3D01G210400 chr3B 94.549 1706 34 18 1081 2764 371978729 371977061 0.000000e+00 2580.0
7 TraesCS3D01G210400 chr3B 85.458 557 68 7 1 548 669742712 669743264 4.690000e-158 568.0
8 TraesCS3D01G210400 chr3B 92.424 198 14 1 586 782 371979499 371979302 6.840000e-72 281.0
9 TraesCS3D01G210400 chr3B 93.220 177 10 2 2748 2923 371977018 371976843 3.200000e-65 259.0
10 TraesCS3D01G210400 chr3B 91.061 179 13 3 829 1006 371979295 371979119 4.170000e-59 239.0
11 TraesCS3D01G210400 chr3B 89.130 46 4 1 758 802 371979175 371979130 4.510000e-04 56.5
12 TraesCS3D01G210400 chr4D 89.219 538 57 1 2 538 249365332 249364795 0.000000e+00 671.0
13 TraesCS3D01G210400 chr4D 94.468 235 13 0 3000 3234 240269206 240269440 2.370000e-96 363.0
14 TraesCS3D01G210400 chr4A 87.387 555 59 5 3 548 656904194 656904746 7.620000e-176 627.0
15 TraesCS3D01G210400 chr4A 89.549 488 50 1 2 488 36654877 36655364 4.590000e-173 617.0
16 TraesCS3D01G210400 chr1D 87.250 549 64 6 2 548 204993115 204992571 3.550000e-174 621.0
17 TraesCS3D01G210400 chr1D 93.361 241 14 2 2999 3237 124705572 124705332 3.970000e-94 355.0
18 TraesCS3D01G210400 chr5A 85.949 548 74 3 2 547 20894869 20895415 1.670000e-162 582.0
19 TraesCS3D01G210400 chr4B 85.870 552 68 3 1 545 31530625 31530077 2.170000e-161 579.0
20 TraesCS3D01G210400 chr6A 84.843 541 64 5 3 541 560812362 560811838 2.210000e-146 529.0
21 TraesCS3D01G210400 chr1B 83.957 561 70 14 1 548 363558788 363558235 1.330000e-143 520.0
22 TraesCS3D01G210400 chr6D 94.958 238 11 1 3001 3237 259884298 259884535 3.940000e-99 372.0
23 TraesCS3D01G210400 chr6D 94.492 236 12 1 3003 3237 236428821 236428586 2.370000e-96 363.0
24 TraesCS3D01G210400 chr5D 94.538 238 12 1 3001 3237 51032824 51032587 1.840000e-97 366.0
25 TraesCS3D01G210400 chr5D 94.538 238 12 1 3001 3237 203383951 203384188 1.840000e-97 366.0
26 TraesCS3D01G210400 chr2D 94.118 238 13 1 3001 3237 198911812 198912049 8.540000e-96 361.0
27 TraesCS3D01G210400 chr2D 94.118 238 13 1 3001 3237 295019821 295019584 8.540000e-96 361.0


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 TraesCS3D01G210400 chr3D 278800654 278803890 3236 False 3017.250000 5978 94.565000 1 3237 2 chr3D.!!$F2 3236
1 TraesCS3D01G210400 chr3A 360516449 360518612 2163 True 1076.166667 2922 94.377667 770 2923 3 chr3A.!!$R1 2153
2 TraesCS3D01G210400 chr3B 371976843 371979499 2656 True 683.100000 2580 92.076800 586 2923 5 chr3B.!!$R1 2337
3 TraesCS3D01G210400 chr3B 669742712 669743264 552 False 568.000000 568 85.458000 1 548 1 chr3B.!!$F1 547
4 TraesCS3D01G210400 chr4D 249364795 249365332 537 True 671.000000 671 89.219000 2 538 1 chr4D.!!$R1 536
5 TraesCS3D01G210400 chr4A 656904194 656904746 552 False 627.000000 627 87.387000 3 548 1 chr4A.!!$F2 545
6 TraesCS3D01G210400 chr1D 204992571 204993115 544 True 621.000000 621 87.250000 2 548 1 chr1D.!!$R2 546
7 TraesCS3D01G210400 chr5A 20894869 20895415 546 False 582.000000 582 85.949000 2 547 1 chr5A.!!$F1 545
8 TraesCS3D01G210400 chr4B 31530077 31530625 548 True 579.000000 579 85.870000 1 545 1 chr4B.!!$R1 544
9 TraesCS3D01G210400 chr6A 560811838 560812362 524 True 529.000000 529 84.843000 3 541 1 chr6A.!!$R1 538
10 TraesCS3D01G210400 chr1B 363558235 363558788 553 True 520.000000 520 83.957000 1 548 1 chr1B.!!$R1 547

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
800 821 0.098728 AATGCGTCCACTTATTGCGC 59.901 50.0 0.00 0.0 47.0 6.09 F
805 826 0.459585 GTCCACTTATTGCGCCTCGA 60.460 55.0 4.18 0.0 0.0 4.04 F
806 827 0.459585 TCCACTTATTGCGCCTCGAC 60.460 55.0 4.18 0.0 0.0 4.20 F
809 830 0.460284 ACTTATTGCGCCTCGACCAG 60.460 55.0 4.18 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2139 2480 0.107066 TATGCCCGACTCCGACTGTA 60.107 55.000 0.00 0.0 38.22 2.74 R
2141 2482 0.389391 ATTATGCCCGACTCCGACTG 59.611 55.000 0.00 0.0 38.22 3.51 R
2188 2535 0.751643 AGGTTTCACTGTGGTGTGGC 60.752 55.000 8.11 0.0 43.41 5.01 R
2362 2710 1.153147 GCCCCGGATGAGAGGAAAC 60.153 63.158 0.73 0.0 0.00 2.78 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
199 201 4.308458 CCCGACCCGCAACAGTGA 62.308 66.667 0.00 0.00 0.00 3.41
286 300 2.463620 GCACGATGATGGAGCGCAA 61.464 57.895 11.47 0.00 36.77 4.85
330 344 2.125350 GAGCAGAAGGACCGGCAG 60.125 66.667 0.00 0.00 0.00 4.85
331 345 2.604686 AGCAGAAGGACCGGCAGA 60.605 61.111 0.00 0.00 0.00 4.26
401 419 3.899545 AAGGGAGGACGCGGAGGAA 62.900 63.158 12.47 0.00 0.00 3.36
411 429 3.049080 GCGGAGGAAATGGAGCCCT 62.049 63.158 0.00 0.00 0.00 5.19
416 434 2.119495 GAGGAAATGGAGCCCTACAGA 58.881 52.381 0.00 0.00 0.00 3.41
554 574 2.498726 AGCGCTAGAGCTCAAGGC 59.501 61.111 15.92 15.03 45.67 4.35
555 575 2.587473 GCGCTAGAGCTCAAGGCC 60.587 66.667 17.77 0.00 43.05 5.19
556 576 2.279120 CGCTAGAGCTCAAGGCCG 60.279 66.667 17.77 7.16 43.05 6.13
557 577 2.775856 CGCTAGAGCTCAAGGCCGA 61.776 63.158 17.77 0.00 43.05 5.54
558 578 1.067250 GCTAGAGCTCAAGGCCGAG 59.933 63.158 17.77 0.00 43.05 4.63
559 579 1.388065 GCTAGAGCTCAAGGCCGAGA 61.388 60.000 17.77 5.95 43.05 4.04
560 580 1.107114 CTAGAGCTCAAGGCCGAGAA 58.893 55.000 17.77 0.00 43.05 2.87
561 581 1.686052 CTAGAGCTCAAGGCCGAGAAT 59.314 52.381 17.77 0.00 43.05 2.40
562 582 0.908198 AGAGCTCAAGGCCGAGAATT 59.092 50.000 17.77 0.00 43.05 2.17
563 583 1.012841 GAGCTCAAGGCCGAGAATTG 58.987 55.000 9.40 3.66 43.05 2.32
564 584 0.615331 AGCTCAAGGCCGAGAATTGA 59.385 50.000 11.49 7.89 43.05 2.57
565 585 0.729690 GCTCAAGGCCGAGAATTGAC 59.270 55.000 11.49 1.37 34.79 3.18
566 586 1.945819 GCTCAAGGCCGAGAATTGACA 60.946 52.381 11.49 0.00 34.79 3.58
567 587 2.636830 CTCAAGGCCGAGAATTGACAT 58.363 47.619 1.57 0.00 34.79 3.06
568 588 2.353889 CTCAAGGCCGAGAATTGACATG 59.646 50.000 1.57 0.00 34.79 3.21
569 589 1.098050 AAGGCCGAGAATTGACATGC 58.902 50.000 0.00 0.00 0.00 4.06
570 590 1.091771 AGGCCGAGAATTGACATGCG 61.092 55.000 0.00 0.00 0.00 4.73
571 591 1.369091 GGCCGAGAATTGACATGCGT 61.369 55.000 0.00 0.00 0.00 5.24
572 592 1.286501 GCCGAGAATTGACATGCGTA 58.713 50.000 0.00 0.00 0.00 4.42
573 593 1.004927 GCCGAGAATTGACATGCGTAC 60.005 52.381 0.00 0.00 0.00 3.67
574 594 1.255342 CCGAGAATTGACATGCGTACG 59.745 52.381 11.84 11.84 0.00 3.67
575 595 1.917955 CGAGAATTGACATGCGTACGT 59.082 47.619 17.90 0.00 0.00 3.57
576 596 2.284457 CGAGAATTGACATGCGTACGTG 60.284 50.000 17.90 10.72 38.85 4.49
577 597 2.921121 GAGAATTGACATGCGTACGTGA 59.079 45.455 17.90 4.24 36.58 4.35
578 598 2.666508 AGAATTGACATGCGTACGTGAC 59.333 45.455 17.90 9.08 36.58 3.67
579 599 2.073117 ATTGACATGCGTACGTGACA 57.927 45.000 17.90 11.61 36.01 3.58
580 600 2.073117 TTGACATGCGTACGTGACAT 57.927 45.000 17.90 9.03 37.33 3.06
581 601 1.345410 TGACATGCGTACGTGACATG 58.655 50.000 23.94 23.94 45.28 3.21
663 683 9.868277 AAATAACAACACAATGACTTTCTTGAA 57.132 25.926 0.00 0.00 0.00 2.69
708 728 7.230849 TGTTGAGCATCTGAATTTAAACCAT 57.769 32.000 0.00 0.00 34.92 3.55
709 729 8.347004 TGTTGAGCATCTGAATTTAAACCATA 57.653 30.769 0.00 0.00 34.92 2.74
712 732 9.638239 TTGAGCATCTGAATTTAAACCATAAAC 57.362 29.630 0.00 0.00 34.92 2.01
727 747 4.082571 ACCATAAACATTTCAGCAGAGCAC 60.083 41.667 0.00 0.00 0.00 4.40
729 749 2.283145 AACATTTCAGCAGAGCACCT 57.717 45.000 0.00 0.00 0.00 4.00
737 757 1.952296 CAGCAGAGCACCTTTCAAAGT 59.048 47.619 0.00 0.00 0.00 2.66
760 781 5.511088 ACATTAGTACGTTGAGAAAAGCG 57.489 39.130 0.00 0.00 0.00 4.68
770 791 3.338818 TGAGAAAAGCGCAAACAAGAG 57.661 42.857 11.47 0.00 0.00 2.85
778 799 9.542462 AGAAAAGCGCAAACAAGAGTATATATA 57.458 29.630 11.47 0.00 0.00 0.86
799 820 2.542766 AAATGCGTCCACTTATTGCG 57.457 45.000 0.00 0.00 0.00 4.85
800 821 0.098728 AATGCGTCCACTTATTGCGC 59.901 50.000 0.00 0.00 47.00 6.09
801 822 1.714899 ATGCGTCCACTTATTGCGCC 61.715 55.000 4.18 0.00 46.39 6.53
802 823 2.106683 GCGTCCACTTATTGCGCCT 61.107 57.895 4.18 0.00 41.93 5.52
803 824 2.006772 CGTCCACTTATTGCGCCTC 58.993 57.895 4.18 0.00 0.00 4.70
804 825 1.752501 CGTCCACTTATTGCGCCTCG 61.753 60.000 4.18 0.00 0.00 4.63
805 826 0.459585 GTCCACTTATTGCGCCTCGA 60.460 55.000 4.18 0.00 0.00 4.04
806 827 0.459585 TCCACTTATTGCGCCTCGAC 60.460 55.000 4.18 0.00 0.00 4.20
807 828 1.429148 CCACTTATTGCGCCTCGACC 61.429 60.000 4.18 0.00 0.00 4.79
808 829 0.739462 CACTTATTGCGCCTCGACCA 60.739 55.000 4.18 0.00 0.00 4.02
809 830 0.460284 ACTTATTGCGCCTCGACCAG 60.460 55.000 4.18 0.00 0.00 4.00
810 831 1.766143 CTTATTGCGCCTCGACCAGC 61.766 60.000 4.18 0.00 0.00 4.85
811 832 2.514510 TTATTGCGCCTCGACCAGCA 62.515 55.000 4.18 0.47 37.89 4.41
812 833 4.617520 TTGCGCCTCGACCAGCAA 62.618 61.111 4.18 11.22 45.79 3.91
813 834 4.617520 TGCGCCTCGACCAGCAAA 62.618 61.111 4.18 0.00 36.60 3.68
814 835 3.353836 GCGCCTCGACCAGCAAAA 61.354 61.111 0.00 0.00 0.00 2.44
815 836 2.903547 GCGCCTCGACCAGCAAAAA 61.904 57.895 0.00 0.00 0.00 1.94
839 860 6.767524 AAAGTGAGTGACCATAACAAAACA 57.232 33.333 0.00 0.00 0.00 2.83
848 869 9.965824 AGTGACCATAACAAAACAAAAAGATAG 57.034 29.630 0.00 0.00 0.00 2.08
894 915 2.259917 AGGGGGAAATCCTTGCAAAAG 58.740 47.619 0.00 0.00 35.95 2.27
905 926 3.381272 TCCTTGCAAAAGAAAGTGAGTGG 59.619 43.478 0.00 0.00 0.00 4.00
1013 1036 1.351153 CCCTCTTCTTCGCGTTTCTC 58.649 55.000 5.77 0.00 0.00 2.87
1060 1086 1.980772 CCTTCCCCAAGCCAAGCAG 60.981 63.158 0.00 0.00 0.00 4.24
1062 1088 0.540365 CTTCCCCAAGCCAAGCAGAA 60.540 55.000 0.00 0.00 0.00 3.02
2100 2441 4.276678 TCATCCTTTCTTTGTCACAAGCAG 59.723 41.667 0.00 0.00 0.00 4.24
2130 2471 3.181515 CCGAGTACGCTGCATAGATCTAG 60.182 52.174 8.70 0.00 38.29 2.43
2132 2473 4.004314 GAGTACGCTGCATAGATCTAGGA 58.996 47.826 18.28 6.00 0.00 2.94
2133 2474 4.006989 AGTACGCTGCATAGATCTAGGAG 58.993 47.826 18.28 15.09 0.00 3.69
2134 2475 2.870175 ACGCTGCATAGATCTAGGAGT 58.130 47.619 18.28 8.61 0.00 3.85
2135 2476 4.022413 ACGCTGCATAGATCTAGGAGTA 57.978 45.455 18.28 4.70 0.00 2.59
2136 2477 4.594970 ACGCTGCATAGATCTAGGAGTAT 58.405 43.478 18.28 6.01 0.00 2.12
2137 2478 4.397730 ACGCTGCATAGATCTAGGAGTATG 59.602 45.833 18.28 7.50 0.00 2.39
2138 2479 4.681744 GCTGCATAGATCTAGGAGTATGC 58.318 47.826 18.28 16.91 45.30 3.14
2139 2480 4.402155 GCTGCATAGATCTAGGAGTATGCT 59.598 45.833 18.28 0.00 45.30 3.79
2140 2481 5.592282 GCTGCATAGATCTAGGAGTATGCTA 59.408 44.000 18.28 7.85 45.30 3.49
2141 2482 6.459573 GCTGCATAGATCTAGGAGTATGCTAC 60.460 46.154 18.28 9.88 45.30 3.58
2142 2483 6.485171 TGCATAGATCTAGGAGTATGCTACA 58.515 40.000 18.28 0.51 45.30 2.74
2143 2484 6.601217 TGCATAGATCTAGGAGTATGCTACAG 59.399 42.308 18.28 0.00 45.30 2.74
2144 2485 6.601613 GCATAGATCTAGGAGTATGCTACAGT 59.398 42.308 18.28 0.00 42.91 3.55
2145 2486 7.201696 GCATAGATCTAGGAGTATGCTACAGTC 60.202 44.444 18.28 0.00 42.91 3.51
2146 2487 5.242434 AGATCTAGGAGTATGCTACAGTCG 58.758 45.833 0.00 0.00 38.32 4.18
2147 2488 3.741249 TCTAGGAGTATGCTACAGTCGG 58.259 50.000 0.00 0.00 38.32 4.79
2188 2535 8.461249 TGCAAGAAGGGTATACTACTAGTTAG 57.539 38.462 0.00 0.00 0.00 2.34
2243 2591 1.445582 GAGGTGAACTGGGTACGCG 60.446 63.158 3.53 3.53 0.00 6.01
2244 2592 1.870055 GAGGTGAACTGGGTACGCGA 61.870 60.000 15.93 0.00 0.00 5.87
2245 2593 1.445582 GGTGAACTGGGTACGCGAG 60.446 63.158 15.93 0.36 0.00 5.03
2246 2594 2.092882 GTGAACTGGGTACGCGAGC 61.093 63.158 15.93 6.12 0.00 5.03
2333 2681 4.536295 TCCTTTTTGGTTTCTCTCCCTT 57.464 40.909 0.00 0.00 37.07 3.95
2362 2710 3.565482 CCTCAATCTCTCTTCTCCTCTCG 59.435 52.174 0.00 0.00 0.00 4.04
2364 2712 4.594970 TCAATCTCTCTTCTCCTCTCGTT 58.405 43.478 0.00 0.00 0.00 3.85
2488 2846 1.680314 GGCTGGGCCTGGAAAGAAG 60.680 63.158 12.70 0.00 46.69 2.85
2489 2847 1.380302 GCTGGGCCTGGAAAGAAGA 59.620 57.895 12.70 0.00 0.00 2.87
2490 2848 0.251341 GCTGGGCCTGGAAAGAAGAA 60.251 55.000 12.70 0.00 0.00 2.52
2513 2871 1.294857 AAATGCCGTTGGTTTTGTGC 58.705 45.000 0.00 0.00 0.00 4.57
2514 2872 0.873743 AATGCCGTTGGTTTTGTGCG 60.874 50.000 0.00 0.00 0.00 5.34
2515 2873 2.010582 ATGCCGTTGGTTTTGTGCGT 62.011 50.000 0.00 0.00 0.00 5.24
2516 2874 2.227568 GCCGTTGGTTTTGTGCGTG 61.228 57.895 0.00 0.00 0.00 5.34
2517 2875 1.587613 CCGTTGGTTTTGTGCGTGG 60.588 57.895 0.00 0.00 0.00 4.94
2518 2876 2.227568 CGTTGGTTTTGTGCGTGGC 61.228 57.895 0.00 0.00 0.00 5.01
2519 2877 2.103143 TTGGTTTTGTGCGTGGCG 59.897 55.556 0.00 0.00 0.00 5.69
2520 2878 2.407428 TTGGTTTTGTGCGTGGCGA 61.407 52.632 0.00 0.00 0.00 5.54
2521 2879 2.051345 GGTTTTGTGCGTGGCGAG 60.051 61.111 0.00 0.00 0.00 5.03
2522 2880 2.051345 GTTTTGTGCGTGGCGAGG 60.051 61.111 0.00 0.00 0.00 4.63
2523 2881 3.283684 TTTTGTGCGTGGCGAGGG 61.284 61.111 0.00 0.00 0.00 4.30
2594 2952 2.098680 GACGTCACTCTCGCTCCG 59.901 66.667 11.55 0.00 0.00 4.63
2595 2953 4.104417 ACGTCACTCTCGCTCCGC 62.104 66.667 0.00 0.00 0.00 5.54
2861 3301 2.421619 GGAAGAAGCGGGATGATCATC 58.578 52.381 24.90 24.90 37.11 2.92
2864 3304 0.318441 GAAGCGGGATGATCATCGGA 59.682 55.000 25.60 0.00 38.69 4.55
2947 3387 3.422417 TTCTGAGCATAGTACAGACGC 57.578 47.619 0.00 0.00 39.80 5.19
2948 3388 1.676529 TCTGAGCATAGTACAGACGCC 59.323 52.381 0.00 0.00 36.04 5.68
2949 3389 0.380733 TGAGCATAGTACAGACGCCG 59.619 55.000 0.00 0.00 0.00 6.46
2950 3390 0.661552 GAGCATAGTACAGACGCCGA 59.338 55.000 0.00 0.00 0.00 5.54
2951 3391 0.381089 AGCATAGTACAGACGCCGAC 59.619 55.000 0.00 0.00 0.00 4.79
2953 3393 0.928908 CATAGTACAGACGCCGACGC 60.929 60.000 0.00 0.00 45.53 5.19
2954 3394 1.094073 ATAGTACAGACGCCGACGCT 61.094 55.000 0.00 0.00 45.53 5.07
2955 3395 1.699656 TAGTACAGACGCCGACGCTC 61.700 60.000 0.00 0.00 45.53 5.03
2956 3396 4.156622 TACAGACGCCGACGCTCG 62.157 66.667 0.00 6.26 45.53 5.03
2958 3398 4.156622 CAGACGCCGACGCTCGTA 62.157 66.667 12.16 0.00 45.53 3.43
2959 3399 3.200593 AGACGCCGACGCTCGTAT 61.201 61.111 12.16 7.58 45.53 3.06
2960 3400 1.884464 AGACGCCGACGCTCGTATA 60.884 57.895 12.16 0.00 45.53 1.47
2961 3401 1.206072 GACGCCGACGCTCGTATAT 59.794 57.895 12.16 0.00 45.53 0.86
2962 3402 0.439985 GACGCCGACGCTCGTATATA 59.560 55.000 12.16 0.00 45.53 0.86
2963 3403 0.164647 ACGCCGACGCTCGTATATAC 59.835 55.000 10.82 2.53 45.53 1.47
2964 3404 0.164432 CGCCGACGCTCGTATATACA 59.836 55.000 13.22 0.11 38.40 2.29
2965 3405 1.599992 GCCGACGCTCGTATATACAC 58.400 55.000 13.22 1.21 38.40 2.90
2966 3406 1.069703 GCCGACGCTCGTATATACACA 60.070 52.381 13.22 0.00 38.40 3.72
2967 3407 2.568100 CCGACGCTCGTATATACACAC 58.432 52.381 13.22 0.54 38.40 3.82
2968 3408 2.032636 CCGACGCTCGTATATACACACA 60.033 50.000 13.22 0.00 38.40 3.72
2969 3409 3.364664 CCGACGCTCGTATATACACACAT 60.365 47.826 13.22 0.00 38.40 3.21
2970 3410 4.143052 CCGACGCTCGTATATACACACATA 60.143 45.833 13.22 0.00 38.40 2.29
2971 3411 5.446875 CCGACGCTCGTATATACACACATAT 60.447 44.000 13.22 0.00 38.40 1.78
2972 3412 6.237915 CCGACGCTCGTATATACACACATATA 60.238 42.308 13.22 0.00 38.40 0.86
2973 3413 6.622572 CGACGCTCGTATATACACACATATAC 59.377 42.308 13.22 4.04 39.46 1.47
2974 3414 7.463780 CGACGCTCGTATATACACACATATACT 60.464 40.741 13.22 0.00 40.17 2.12
2975 3415 7.682824 ACGCTCGTATATACACACATATACTC 58.317 38.462 13.22 1.93 40.17 2.59
2976 3416 7.332678 ACGCTCGTATATACACACATATACTCA 59.667 37.037 13.22 0.00 40.17 3.41
2977 3417 8.336080 CGCTCGTATATACACACATATACTCAT 58.664 37.037 13.22 0.00 40.17 2.90
2988 3428 9.692749 ACACACATATACTCATTCCTATTAACG 57.307 33.333 0.00 0.00 0.00 3.18
2989 3429 9.692749 CACACATATACTCATTCCTATTAACGT 57.307 33.333 0.00 0.00 0.00 3.99
2990 3430 9.692749 ACACATATACTCATTCCTATTAACGTG 57.307 33.333 0.00 0.00 0.00 4.49
2991 3431 8.648097 CACATATACTCATTCCTATTAACGTGC 58.352 37.037 0.00 0.00 0.00 5.34
2992 3432 7.541091 ACATATACTCATTCCTATTAACGTGCG 59.459 37.037 0.00 0.00 0.00 5.34
2993 3433 2.864343 ACTCATTCCTATTAACGTGCGC 59.136 45.455 0.00 0.00 0.00 6.09
2994 3434 2.863740 CTCATTCCTATTAACGTGCGCA 59.136 45.455 5.66 5.66 0.00 6.09
2995 3435 2.605818 TCATTCCTATTAACGTGCGCAC 59.394 45.455 30.42 30.42 0.00 5.34
3013 3453 4.681978 GCCCACTGTCGGCGTTCT 62.682 66.667 6.85 0.00 36.47 3.01
3014 3454 2.738521 CCCACTGTCGGCGTTCTG 60.739 66.667 6.85 8.33 0.00 3.02
3015 3455 2.738521 CCACTGTCGGCGTTCTGG 60.739 66.667 6.85 4.02 0.00 3.86
3016 3456 2.738521 CACTGTCGGCGTTCTGGG 60.739 66.667 6.85 3.25 0.00 4.45
3017 3457 2.915659 ACTGTCGGCGTTCTGGGA 60.916 61.111 6.85 0.00 0.00 4.37
3018 3458 2.342279 CTGTCGGCGTTCTGGGAA 59.658 61.111 6.85 0.00 0.00 3.97
3019 3459 2.027625 CTGTCGGCGTTCTGGGAAC 61.028 63.158 6.85 0.00 0.00 3.62
3020 3460 3.110178 GTCGGCGTTCTGGGAACG 61.110 66.667 22.95 22.95 45.56 3.95
3021 3461 4.367023 TCGGCGTTCTGGGAACGG 62.367 66.667 26.41 15.26 43.25 4.44
3024 3464 4.324991 GCGTTCTGGGAACGGGGT 62.325 66.667 26.41 0.00 43.25 4.95
3025 3465 2.047560 CGTTCTGGGAACGGGGTC 60.048 66.667 20.56 0.00 39.73 4.46
3026 3466 2.350134 GTTCTGGGAACGGGGTCC 59.650 66.667 0.00 0.00 37.31 4.46
3038 3478 3.984732 GGGTCCCCAGGCTTGCTT 61.985 66.667 0.00 0.00 35.81 3.91
3039 3479 2.677875 GGTCCCCAGGCTTGCTTG 60.678 66.667 0.00 0.00 0.00 4.01
3040 3480 3.376918 GTCCCCAGGCTTGCTTGC 61.377 66.667 0.00 0.00 0.00 4.01
3078 3518 4.814294 CCACTCGCGGCCCTGTAC 62.814 72.222 6.13 0.00 0.00 2.90
3087 3527 3.391382 GCCCTGTACGGCCTGTCT 61.391 66.667 0.00 0.00 43.66 3.41
3088 3528 2.955881 GCCCTGTACGGCCTGTCTT 61.956 63.158 0.00 0.00 43.66 3.01
3089 3529 1.218316 CCCTGTACGGCCTGTCTTC 59.782 63.158 0.00 0.00 0.00 2.87
3090 3530 1.541310 CCCTGTACGGCCTGTCTTCA 61.541 60.000 0.00 1.35 0.00 3.02
3091 3531 0.389948 CCTGTACGGCCTGTCTTCAC 60.390 60.000 0.00 0.00 0.00 3.18
3092 3532 0.389948 CTGTACGGCCTGTCTTCACC 60.390 60.000 0.00 0.00 0.00 4.02
3093 3533 1.116536 TGTACGGCCTGTCTTCACCA 61.117 55.000 0.00 0.00 0.00 4.17
3094 3534 0.034337 GTACGGCCTGTCTTCACCAA 59.966 55.000 0.00 0.00 0.00 3.67
3095 3535 0.034337 TACGGCCTGTCTTCACCAAC 59.966 55.000 0.00 0.00 0.00 3.77
3096 3536 1.227823 CGGCCTGTCTTCACCAACA 60.228 57.895 0.00 0.00 0.00 3.33
3097 3537 0.817634 CGGCCTGTCTTCACCAACAA 60.818 55.000 0.00 0.00 0.00 2.83
3098 3538 1.398692 GGCCTGTCTTCACCAACAAA 58.601 50.000 0.00 0.00 0.00 2.83
3099 3539 1.067060 GGCCTGTCTTCACCAACAAAC 59.933 52.381 0.00 0.00 0.00 2.93
3100 3540 1.268539 GCCTGTCTTCACCAACAAACG 60.269 52.381 0.00 0.00 0.00 3.60
3101 3541 1.268539 CCTGTCTTCACCAACAAACGC 60.269 52.381 0.00 0.00 0.00 4.84
3102 3542 1.670811 CTGTCTTCACCAACAAACGCT 59.329 47.619 0.00 0.00 0.00 5.07
3103 3543 2.088423 TGTCTTCACCAACAAACGCTT 58.912 42.857 0.00 0.00 0.00 4.68
3104 3544 3.271729 TGTCTTCACCAACAAACGCTTA 58.728 40.909 0.00 0.00 0.00 3.09
3105 3545 3.690139 TGTCTTCACCAACAAACGCTTAA 59.310 39.130 0.00 0.00 0.00 1.85
3106 3546 4.201871 TGTCTTCACCAACAAACGCTTAAG 60.202 41.667 0.00 0.00 0.00 1.85
3107 3547 4.034742 GTCTTCACCAACAAACGCTTAAGA 59.965 41.667 6.67 0.00 0.00 2.10
3108 3548 3.955771 TCACCAACAAACGCTTAAGAC 57.044 42.857 6.67 0.00 0.00 3.01
3109 3549 2.614983 TCACCAACAAACGCTTAAGACC 59.385 45.455 6.67 0.00 0.00 3.85
3110 3550 1.951602 ACCAACAAACGCTTAAGACCC 59.048 47.619 6.67 0.00 0.00 4.46
3111 3551 2.227194 CCAACAAACGCTTAAGACCCT 58.773 47.619 6.67 0.00 0.00 4.34
3112 3552 2.225727 CCAACAAACGCTTAAGACCCTC 59.774 50.000 6.67 0.00 0.00 4.30
3113 3553 1.792006 ACAAACGCTTAAGACCCTCG 58.208 50.000 6.67 2.11 0.00 4.63
3114 3554 0.442699 CAAACGCTTAAGACCCTCGC 59.557 55.000 6.67 0.00 0.00 5.03
3116 3556 1.870055 AACGCTTAAGACCCTCGCGA 61.870 55.000 9.26 9.26 45.99 5.87
3117 3557 1.586564 CGCTTAAGACCCTCGCGAG 60.587 63.158 29.06 29.06 45.99 5.03
3118 3558 2.938539 CGCTTAAGACCCTCGCGAGG 62.939 65.000 41.90 41.90 45.99 4.63
3148 3588 2.805353 CGAGGCGGACGACACAAG 60.805 66.667 0.00 0.00 0.00 3.16
3149 3589 2.649034 GAGGCGGACGACACAAGA 59.351 61.111 0.00 0.00 0.00 3.02
3150 3590 1.733399 GAGGCGGACGACACAAGAC 60.733 63.158 0.00 0.00 0.00 3.01
3151 3591 2.737376 GGCGGACGACACAAGACC 60.737 66.667 0.00 0.00 0.00 3.85
3152 3592 2.338984 GCGGACGACACAAGACCT 59.661 61.111 0.00 0.00 0.00 3.85
3153 3593 1.733399 GCGGACGACACAAGACCTC 60.733 63.158 0.00 0.00 0.00 3.85
3154 3594 1.080705 CGGACGACACAAGACCTCC 60.081 63.158 0.00 0.00 0.00 4.30
3155 3595 1.524863 CGGACGACACAAGACCTCCT 61.525 60.000 0.00 0.00 0.00 3.69
3156 3596 0.038159 GGACGACACAAGACCTCCTG 60.038 60.000 0.00 0.00 0.00 3.86
3157 3597 0.038159 GACGACACAAGACCTCCTGG 60.038 60.000 0.00 0.00 39.83 4.45
3158 3598 1.293498 CGACACAAGACCTCCTGGG 59.707 63.158 0.00 0.00 41.89 4.45
3159 3599 1.679898 GACACAAGACCTCCTGGGG 59.320 63.158 0.00 0.00 40.03 4.96
3160 3600 1.842381 GACACAAGACCTCCTGGGGG 61.842 65.000 12.23 12.23 40.03 5.40
3174 3614 4.748144 GGGGGCAGCCTCACCAAG 62.748 72.222 15.19 0.00 0.00 3.61
3176 3616 4.357279 GGGCAGCCTCACCAAGCT 62.357 66.667 12.43 0.00 40.89 3.74
3181 3621 2.749441 GCCTCACCAAGCTGGCTC 60.749 66.667 3.33 0.00 42.67 4.70
3182 3622 2.435586 CCTCACCAAGCTGGCTCG 60.436 66.667 0.00 0.00 42.67 5.03
3183 3623 3.123620 CTCACCAAGCTGGCTCGC 61.124 66.667 0.00 0.00 42.67 5.03
3186 3626 4.749310 ACCAAGCTGGCTCGCGAG 62.749 66.667 31.37 31.37 42.67 5.03
3199 3639 3.984749 GCGAGGGGCGGAGAGATC 61.985 72.222 0.00 0.00 41.29 2.75
3200 3640 2.519541 CGAGGGGCGGAGAGATCA 60.520 66.667 0.00 0.00 36.03 2.92
3201 3641 2.127869 CGAGGGGCGGAGAGATCAA 61.128 63.158 0.00 0.00 36.03 2.57
3202 3642 1.745264 GAGGGGCGGAGAGATCAAG 59.255 63.158 0.00 0.00 0.00 3.02
3203 3643 1.753368 GAGGGGCGGAGAGATCAAGG 61.753 65.000 0.00 0.00 0.00 3.61
3204 3644 2.110006 GGGCGGAGAGATCAAGGC 59.890 66.667 0.00 0.00 0.00 4.35
3205 3645 2.735772 GGGCGGAGAGATCAAGGCA 61.736 63.158 0.00 0.00 0.00 4.75
3206 3646 1.221840 GGCGGAGAGATCAAGGCAA 59.778 57.895 0.00 0.00 0.00 4.52
3207 3647 0.813210 GGCGGAGAGATCAAGGCAAG 60.813 60.000 0.00 0.00 0.00 4.01
3208 3648 0.813210 GCGGAGAGATCAAGGCAAGG 60.813 60.000 0.00 0.00 0.00 3.61
3209 3649 0.813210 CGGAGAGATCAAGGCAAGGC 60.813 60.000 0.00 0.00 0.00 4.35
3210 3650 0.813210 GGAGAGATCAAGGCAAGGCG 60.813 60.000 0.00 0.00 0.00 5.52
3211 3651 0.176680 GAGAGATCAAGGCAAGGCGA 59.823 55.000 0.00 0.00 0.00 5.54
3212 3652 0.615331 AGAGATCAAGGCAAGGCGAA 59.385 50.000 0.00 0.00 0.00 4.70
3213 3653 0.729690 GAGATCAAGGCAAGGCGAAC 59.270 55.000 0.00 0.00 0.00 3.95
3214 3654 0.678048 AGATCAAGGCAAGGCGAACC 60.678 55.000 0.00 0.00 0.00 3.62
3230 3670 3.799753 CCTCGCGAGGTTCCAATG 58.200 61.111 40.77 17.62 43.61 2.82
3231 3671 1.218047 CCTCGCGAGGTTCCAATGA 59.782 57.895 40.77 0.75 43.61 2.57
3232 3672 1.084370 CCTCGCGAGGTTCCAATGAC 61.084 60.000 40.77 0.00 43.61 3.06
3233 3673 1.413767 CTCGCGAGGTTCCAATGACG 61.414 60.000 28.40 0.00 0.00 4.35
3234 3674 1.736645 CGCGAGGTTCCAATGACGT 60.737 57.895 0.00 0.00 0.00 4.34
3235 3675 0.457166 CGCGAGGTTCCAATGACGTA 60.457 55.000 0.00 0.00 0.00 3.57
3236 3676 1.717194 GCGAGGTTCCAATGACGTAA 58.283 50.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
229 243 1.076559 TTCGGCCCTATCGTCCAGA 60.077 57.895 0.00 0.00 0.00 3.86
307 321 0.539051 CGGTCCTTCTGCTCCATCTT 59.461 55.000 0.00 0.00 0.00 2.40
311 325 3.706373 GCCGGTCCTTCTGCTCCA 61.706 66.667 1.90 0.00 0.00 3.86
330 344 4.779733 TCCCCTGCCTCCTCCGTC 62.780 72.222 0.00 0.00 0.00 4.79
331 345 4.095400 ATCCCCTGCCTCCTCCGT 62.095 66.667 0.00 0.00 0.00 4.69
401 419 2.023501 AGTCTCTCTGTAGGGCTCCATT 60.024 50.000 0.00 0.00 0.00 3.16
416 434 1.686355 CTATGGCGTCCAGAGTCTCT 58.314 55.000 11.02 0.00 37.99 3.10
520 539 2.683572 TCCCCTGCTCTAGCGCAA 60.684 61.111 11.47 0.00 45.83 4.85
521 540 3.150335 CTCCCCTGCTCTAGCGCA 61.150 66.667 11.47 7.28 45.83 6.09
548 568 2.358957 CATGTCAATTCTCGGCCTTGA 58.641 47.619 0.00 0.00 0.00 3.02
549 569 1.202222 GCATGTCAATTCTCGGCCTTG 60.202 52.381 0.00 0.00 0.00 3.61
550 570 1.098050 GCATGTCAATTCTCGGCCTT 58.902 50.000 0.00 0.00 0.00 4.35
551 571 1.091771 CGCATGTCAATTCTCGGCCT 61.092 55.000 0.00 0.00 0.00 5.19
552 572 1.353103 CGCATGTCAATTCTCGGCC 59.647 57.895 0.00 0.00 0.00 6.13
553 573 1.004927 GTACGCATGTCAATTCTCGGC 60.005 52.381 0.00 0.00 0.00 5.54
554 574 1.255342 CGTACGCATGTCAATTCTCGG 59.745 52.381 0.52 0.00 0.00 4.63
555 575 1.917955 ACGTACGCATGTCAATTCTCG 59.082 47.619 16.72 0.00 0.00 4.04
556 576 2.921121 TCACGTACGCATGTCAATTCTC 59.079 45.455 16.72 0.00 0.00 2.87
557 577 2.666508 GTCACGTACGCATGTCAATTCT 59.333 45.455 16.72 0.00 0.00 2.40
558 578 2.410392 TGTCACGTACGCATGTCAATTC 59.590 45.455 16.72 0.00 0.00 2.17
559 579 2.409012 TGTCACGTACGCATGTCAATT 58.591 42.857 16.72 0.00 0.00 2.32
560 580 2.073117 TGTCACGTACGCATGTCAAT 57.927 45.000 16.72 0.00 0.00 2.57
561 581 1.724082 CATGTCACGTACGCATGTCAA 59.276 47.619 16.72 0.00 36.28 3.18
562 582 1.336424 ACATGTCACGTACGCATGTCA 60.336 47.619 24.94 17.11 46.93 3.58
563 583 1.346365 ACATGTCACGTACGCATGTC 58.654 50.000 24.94 12.96 46.93 3.06
564 584 3.507597 ACATGTCACGTACGCATGT 57.492 47.368 24.94 24.94 45.56 3.21
565 585 5.822584 ATTATACATGTCACGTACGCATG 57.177 39.130 23.94 23.94 43.84 4.06
566 586 6.838198 AAATTATACATGTCACGTACGCAT 57.162 33.333 16.72 8.14 0.00 4.73
567 587 7.648510 TCATAAATTATACATGTCACGTACGCA 59.351 33.333 16.72 5.79 0.00 5.24
568 588 7.999213 TCATAAATTATACATGTCACGTACGC 58.001 34.615 16.72 0.00 0.00 4.42
685 705 9.638239 TTTATGGTTTAAATTCAGATGCTCAAC 57.362 29.630 0.00 0.00 0.00 3.18
708 728 3.754965 AGGTGCTCTGCTGAAATGTTTA 58.245 40.909 0.00 0.00 0.00 2.01
709 729 2.590821 AGGTGCTCTGCTGAAATGTTT 58.409 42.857 0.00 0.00 0.00 2.83
712 732 2.555325 TGAAAGGTGCTCTGCTGAAATG 59.445 45.455 0.00 0.00 0.00 2.32
719 739 2.878406 TGTACTTTGAAAGGTGCTCTGC 59.122 45.455 10.02 0.00 0.00 4.26
737 757 5.061311 GCGCTTTTCTCAACGTACTAATGTA 59.939 40.000 0.00 0.00 0.00 2.29
750 770 2.682856 ACTCTTGTTTGCGCTTTTCTCA 59.317 40.909 9.73 0.00 0.00 3.27
751 771 3.340337 ACTCTTGTTTGCGCTTTTCTC 57.660 42.857 9.73 0.00 0.00 2.87
778 799 4.209452 CGCAATAAGTGGACGCATTTAT 57.791 40.909 0.00 0.00 0.00 1.40
785 806 1.752501 CGAGGCGCAATAAGTGGACG 61.753 60.000 10.83 0.00 0.00 4.79
786 807 0.459585 TCGAGGCGCAATAAGTGGAC 60.460 55.000 10.83 0.00 0.00 4.02
789 810 0.739462 TGGTCGAGGCGCAATAAGTG 60.739 55.000 10.83 0.00 0.00 3.16
790 811 0.460284 CTGGTCGAGGCGCAATAAGT 60.460 55.000 10.83 0.00 0.00 2.24
791 812 1.766143 GCTGGTCGAGGCGCAATAAG 61.766 60.000 10.83 0.00 0.00 1.73
792 813 1.813753 GCTGGTCGAGGCGCAATAA 60.814 57.895 10.83 0.00 0.00 1.40
793 814 2.202878 GCTGGTCGAGGCGCAATA 60.203 61.111 10.83 0.00 0.00 1.90
795 816 4.617520 TTGCTGGTCGAGGCGCAA 62.618 61.111 10.83 10.14 39.77 4.85
796 817 4.617520 TTTGCTGGTCGAGGCGCA 62.618 61.111 10.83 0.00 0.00 6.09
814 835 7.607250 TGTTTTGTTATGGTCACTCACTTTTT 58.393 30.769 0.00 0.00 0.00 1.94
815 836 7.164230 TGTTTTGTTATGGTCACTCACTTTT 57.836 32.000 0.00 0.00 0.00 2.27
816 837 6.767524 TGTTTTGTTATGGTCACTCACTTT 57.232 33.333 0.00 0.00 0.00 2.66
817 838 6.767524 TTGTTTTGTTATGGTCACTCACTT 57.232 33.333 0.00 0.00 0.00 3.16
818 839 6.767524 TTTGTTTTGTTATGGTCACTCACT 57.232 33.333 0.00 0.00 0.00 3.41
819 840 7.757624 TCTTTTTGTTTTGTTATGGTCACTCAC 59.242 33.333 0.00 0.00 0.00 3.51
820 841 7.831753 TCTTTTTGTTTTGTTATGGTCACTCA 58.168 30.769 0.00 0.00 0.00 3.41
821 842 8.871686 ATCTTTTTGTTTTGTTATGGTCACTC 57.128 30.769 0.00 0.00 0.00 3.51
822 843 9.965824 CTATCTTTTTGTTTTGTTATGGTCACT 57.034 29.630 0.00 0.00 0.00 3.41
823 844 9.959749 TCTATCTTTTTGTTTTGTTATGGTCAC 57.040 29.630 0.00 0.00 0.00 3.67
830 851 9.810545 CACCCTTTCTATCTTTTTGTTTTGTTA 57.189 29.630 0.00 0.00 0.00 2.41
831 852 8.536175 TCACCCTTTCTATCTTTTTGTTTTGTT 58.464 29.630 0.00 0.00 0.00 2.83
832 853 8.073467 TCACCCTTTCTATCTTTTTGTTTTGT 57.927 30.769 0.00 0.00 0.00 2.83
833 854 8.940768 TTCACCCTTTCTATCTTTTTGTTTTG 57.059 30.769 0.00 0.00 0.00 2.44
834 855 9.952030 TTTTCACCCTTTCTATCTTTTTGTTTT 57.048 25.926 0.00 0.00 0.00 2.43
835 856 9.599866 CTTTTCACCCTTTCTATCTTTTTGTTT 57.400 29.630 0.00 0.00 0.00 2.83
836 857 8.977412 TCTTTTCACCCTTTCTATCTTTTTGTT 58.023 29.630 0.00 0.00 0.00 2.83
837 858 8.533569 TCTTTTCACCCTTTCTATCTTTTTGT 57.466 30.769 0.00 0.00 0.00 2.83
838 859 9.816354 TTTCTTTTCACCCTTTCTATCTTTTTG 57.184 29.630 0.00 0.00 0.00 2.44
839 860 9.817809 GTTTCTTTTCACCCTTTCTATCTTTTT 57.182 29.630 0.00 0.00 0.00 1.94
894 915 5.415701 TCAATTTCTATGGCCACTCACTTTC 59.584 40.000 8.16 0.00 0.00 2.62
905 926 6.000219 TCTAGGCATTCTCAATTTCTATGGC 59.000 40.000 0.00 0.00 40.76 4.40
1060 1086 0.607489 TTCTTGGCCTCTGCTGCTTC 60.607 55.000 3.32 0.00 37.74 3.86
1062 1088 0.039326 ATTTCTTGGCCTCTGCTGCT 59.961 50.000 3.32 0.00 37.74 4.24
2100 2441 0.438830 CAGCGTACTCGGCTTGTTTC 59.561 55.000 0.00 0.00 37.56 2.78
2130 2471 2.291190 GACTCCGACTGTAGCATACTCC 59.709 54.545 0.00 0.00 43.54 3.85
2132 2473 1.941294 CGACTCCGACTGTAGCATACT 59.059 52.381 0.00 0.00 39.39 2.12
2133 2474 1.002684 CCGACTCCGACTGTAGCATAC 60.003 57.143 0.00 0.00 39.20 2.39
2134 2475 1.306148 CCGACTCCGACTGTAGCATA 58.694 55.000 0.00 0.00 38.22 3.14
2135 2476 1.384989 CCCGACTCCGACTGTAGCAT 61.385 60.000 0.00 0.00 38.22 3.79
2136 2477 2.044555 CCCGACTCCGACTGTAGCA 61.045 63.158 0.00 0.00 38.22 3.49
2137 2478 2.799371 CCCGACTCCGACTGTAGC 59.201 66.667 0.00 0.00 38.22 3.58
2138 2479 1.384989 ATGCCCGACTCCGACTGTAG 61.385 60.000 0.00 0.00 38.22 2.74
2139 2480 0.107066 TATGCCCGACTCCGACTGTA 60.107 55.000 0.00 0.00 38.22 2.74
2140 2481 0.968901 TTATGCCCGACTCCGACTGT 60.969 55.000 0.00 0.00 38.22 3.55
2141 2482 0.389391 ATTATGCCCGACTCCGACTG 59.611 55.000 0.00 0.00 38.22 3.51
2142 2483 1.068741 GAATTATGCCCGACTCCGACT 59.931 52.381 0.00 0.00 38.22 4.18
2143 2484 1.068741 AGAATTATGCCCGACTCCGAC 59.931 52.381 0.00 0.00 38.22 4.79
2144 2485 1.068588 CAGAATTATGCCCGACTCCGA 59.931 52.381 0.00 0.00 38.22 4.55
2145 2486 1.502231 CAGAATTATGCCCGACTCCG 58.498 55.000 0.00 0.00 0.00 4.63
2146 2487 1.230324 GCAGAATTATGCCCGACTCC 58.770 55.000 14.15 0.00 40.43 3.85
2147 2488 1.953559 TGCAGAATTATGCCCGACTC 58.046 50.000 21.56 0.00 45.91 3.36
2188 2535 0.751643 AGGTTTCACTGTGGTGTGGC 60.752 55.000 8.11 0.00 43.41 5.01
2243 2591 2.617762 CGAATCGCTCGCTTGCTC 59.382 61.111 0.00 0.00 41.49 4.26
2244 2592 2.887568 CCGAATCGCTCGCTTGCT 60.888 61.111 0.00 0.00 46.71 3.91
2245 2593 4.581648 GCCGAATCGCTCGCTTGC 62.582 66.667 0.00 0.00 46.71 4.01
2246 2594 4.271170 CGCCGAATCGCTCGCTTG 62.271 66.667 0.00 0.00 46.71 4.01
2333 2681 4.090090 AGAAGAGAGATTGAGGAAACGGA 58.910 43.478 0.00 0.00 0.00 4.69
2362 2710 1.153147 GCCCCGGATGAGAGGAAAC 60.153 63.158 0.73 0.00 0.00 2.78
2364 2712 2.040442 TGCCCCGGATGAGAGGAA 59.960 61.111 0.73 0.00 0.00 3.36
2594 2952 2.749441 GAGCCAAGGCACTGGAGC 60.749 66.667 14.40 0.00 44.88 4.70
2595 2953 2.435586 CGAGCCAAGGCACTGGAG 60.436 66.667 14.40 0.00 44.88 3.86
2622 2981 3.097614 TGTTCACTTAGGACTAGGAGCC 58.902 50.000 0.00 0.00 0.00 4.70
2924 3364 4.625742 GCGTCTGTACTATGCTCAGAAAAA 59.374 41.667 0.00 0.00 39.42 1.94
2925 3365 4.174009 GCGTCTGTACTATGCTCAGAAAA 58.826 43.478 0.00 0.00 39.42 2.29
2926 3366 3.428999 GGCGTCTGTACTATGCTCAGAAA 60.429 47.826 11.23 0.00 39.42 2.52
2931 3371 0.661552 TCGGCGTCTGTACTATGCTC 59.338 55.000 6.85 3.56 0.00 4.26
2935 3375 1.094073 AGCGTCGGCGTCTGTACTAT 61.094 55.000 12.58 0.00 46.35 2.12
2941 3381 2.097661 TATACGAGCGTCGGCGTCTG 62.098 60.000 12.58 3.00 45.59 3.51
2944 3384 0.164647 GTATATACGAGCGTCGGCGT 59.835 55.000 12.58 0.00 45.59 5.68
2945 3385 0.164432 TGTATATACGAGCGTCGGCG 59.836 55.000 4.29 4.29 45.59 6.46
2946 3386 1.069703 TGTGTATATACGAGCGTCGGC 60.070 52.381 8.33 0.00 45.59 5.54
2947 3387 2.032636 TGTGTGTATATACGAGCGTCGG 60.033 50.000 8.33 0.00 45.59 4.79
2948 3388 3.243226 TGTGTGTATATACGAGCGTCG 57.757 47.619 8.33 5.97 46.93 5.12
2949 3389 7.682824 AGTATATGTGTGTATATACGAGCGTC 58.317 38.462 8.33 1.05 45.05 5.19
2950 3390 7.332678 TGAGTATATGTGTGTATATACGAGCGT 59.667 37.037 8.33 0.00 45.05 5.07
2951 3391 7.681903 TGAGTATATGTGTGTATATACGAGCG 58.318 38.462 8.33 0.00 45.05 5.03
2962 3402 9.692749 CGTTAATAGGAATGAGTATATGTGTGT 57.307 33.333 0.00 0.00 0.00 3.72
2963 3403 9.692749 ACGTTAATAGGAATGAGTATATGTGTG 57.307 33.333 0.00 0.00 0.00 3.82
2964 3404 9.692749 CACGTTAATAGGAATGAGTATATGTGT 57.307 33.333 0.00 0.00 0.00 3.72
2965 3405 8.648097 GCACGTTAATAGGAATGAGTATATGTG 58.352 37.037 0.00 0.00 0.00 3.21
2966 3406 7.541091 CGCACGTTAATAGGAATGAGTATATGT 59.459 37.037 0.00 0.00 0.00 2.29
2967 3407 7.462856 GCGCACGTTAATAGGAATGAGTATATG 60.463 40.741 0.30 0.00 0.00 1.78
2968 3408 6.530534 GCGCACGTTAATAGGAATGAGTATAT 59.469 38.462 0.30 0.00 0.00 0.86
2969 3409 5.860182 GCGCACGTTAATAGGAATGAGTATA 59.140 40.000 0.30 0.00 0.00 1.47
2970 3410 4.684703 GCGCACGTTAATAGGAATGAGTAT 59.315 41.667 0.30 0.00 0.00 2.12
2971 3411 4.046462 GCGCACGTTAATAGGAATGAGTA 58.954 43.478 0.30 0.00 0.00 2.59
2972 3412 2.864343 GCGCACGTTAATAGGAATGAGT 59.136 45.455 0.30 0.00 0.00 3.41
2973 3413 2.863740 TGCGCACGTTAATAGGAATGAG 59.136 45.455 5.66 0.00 0.00 2.90
2974 3414 2.605818 GTGCGCACGTTAATAGGAATGA 59.394 45.455 26.77 0.00 0.00 2.57
2975 3415 2.969055 GTGCGCACGTTAATAGGAATG 58.031 47.619 26.77 0.00 0.00 2.67
2997 3437 2.738521 CAGAACGCCGACAGTGGG 60.739 66.667 0.00 0.00 0.00 4.61
2998 3438 2.738521 CCAGAACGCCGACAGTGG 60.739 66.667 0.00 0.00 0.00 4.00
2999 3439 2.709125 TTCCCAGAACGCCGACAGTG 62.709 60.000 0.00 0.00 0.00 3.66
3000 3440 2.504274 TTCCCAGAACGCCGACAGT 61.504 57.895 0.00 0.00 0.00 3.55
3001 3441 2.027625 GTTCCCAGAACGCCGACAG 61.028 63.158 0.00 0.00 0.00 3.51
3002 3442 2.029964 GTTCCCAGAACGCCGACA 59.970 61.111 0.00 0.00 0.00 4.35
3003 3443 3.110178 CGTTCCCAGAACGCCGAC 61.110 66.667 15.91 0.00 36.82 4.79
3004 3444 4.367023 CCGTTCCCAGAACGCCGA 62.367 66.667 21.18 0.00 41.85 5.54
3007 3447 4.324991 ACCCCGTTCCCAGAACGC 62.325 66.667 21.18 0.00 41.85 4.84
3008 3448 2.047560 GACCCCGTTCCCAGAACG 60.048 66.667 19.99 19.99 42.74 3.95
3009 3449 2.350134 GGACCCCGTTCCCAGAAC 59.650 66.667 0.00 0.00 0.00 3.01
3023 3463 3.376918 GCAAGCAAGCCTGGGGAC 61.377 66.667 0.00 0.00 0.00 4.46
3061 3501 4.814294 GTACAGGGCCGCGAGTGG 62.814 72.222 8.23 0.00 0.00 4.00
3071 3511 1.218316 GAAGACAGGCCGTACAGGG 59.782 63.158 0.00 0.00 41.48 4.45
3072 3512 0.389948 GTGAAGACAGGCCGTACAGG 60.390 60.000 0.00 0.00 44.97 4.00
3073 3513 0.389948 GGTGAAGACAGGCCGTACAG 60.390 60.000 0.00 0.00 0.00 2.74
3074 3514 1.116536 TGGTGAAGACAGGCCGTACA 61.117 55.000 0.00 0.00 0.00 2.90
3075 3515 0.034337 TTGGTGAAGACAGGCCGTAC 59.966 55.000 0.00 0.00 0.00 3.67
3076 3516 0.034337 GTTGGTGAAGACAGGCCGTA 59.966 55.000 0.00 0.00 0.00 4.02
3077 3517 1.227853 GTTGGTGAAGACAGGCCGT 60.228 57.895 0.00 0.00 0.00 5.68
3078 3518 0.817634 TTGTTGGTGAAGACAGGCCG 60.818 55.000 0.00 0.00 0.00 6.13
3079 3519 1.067060 GTTTGTTGGTGAAGACAGGCC 59.933 52.381 0.00 0.00 0.00 5.19
3080 3520 1.268539 CGTTTGTTGGTGAAGACAGGC 60.269 52.381 0.00 0.00 0.00 4.85
3081 3521 1.268539 GCGTTTGTTGGTGAAGACAGG 60.269 52.381 0.00 0.00 0.00 4.00
3082 3522 1.670811 AGCGTTTGTTGGTGAAGACAG 59.329 47.619 0.00 0.00 0.00 3.51
3083 3523 1.745232 AGCGTTTGTTGGTGAAGACA 58.255 45.000 0.00 0.00 0.00 3.41
3084 3524 2.844122 AAGCGTTTGTTGGTGAAGAC 57.156 45.000 0.00 0.00 0.00 3.01
3085 3525 4.034742 GTCTTAAGCGTTTGTTGGTGAAGA 59.965 41.667 0.00 0.00 33.09 2.87
3086 3526 4.279659 GTCTTAAGCGTTTGTTGGTGAAG 58.720 43.478 0.00 0.00 0.00 3.02
3087 3527 3.065648 GGTCTTAAGCGTTTGTTGGTGAA 59.934 43.478 0.00 0.00 0.00 3.18
3088 3528 2.614983 GGTCTTAAGCGTTTGTTGGTGA 59.385 45.455 0.00 0.00 0.00 4.02
3089 3529 2.287368 GGGTCTTAAGCGTTTGTTGGTG 60.287 50.000 0.00 0.00 0.00 4.17
3090 3530 1.951602 GGGTCTTAAGCGTTTGTTGGT 59.048 47.619 0.00 0.00 0.00 3.67
3091 3531 2.225727 GAGGGTCTTAAGCGTTTGTTGG 59.774 50.000 0.00 0.00 0.00 3.77
3092 3532 2.096417 CGAGGGTCTTAAGCGTTTGTTG 60.096 50.000 0.00 0.00 0.00 3.33
3093 3533 2.140717 CGAGGGTCTTAAGCGTTTGTT 58.859 47.619 0.00 0.00 0.00 2.83
3094 3534 1.792006 CGAGGGTCTTAAGCGTTTGT 58.208 50.000 0.00 0.00 0.00 2.83
3095 3535 0.442699 GCGAGGGTCTTAAGCGTTTG 59.557 55.000 0.00 0.00 0.00 2.93
3096 3536 1.012486 CGCGAGGGTCTTAAGCGTTT 61.012 55.000 0.00 0.00 44.96 3.60
3097 3537 1.445582 CGCGAGGGTCTTAAGCGTT 60.446 57.895 0.00 0.00 44.96 4.84
3098 3538 2.181021 CGCGAGGGTCTTAAGCGT 59.819 61.111 0.00 0.00 44.96 5.07
3100 3540 1.227002 CCTCGCGAGGGTCTTAAGC 60.227 63.158 41.47 0.00 44.87 3.09
3131 3571 2.805353 CTTGTGTCGTCCGCCTCG 60.805 66.667 0.00 0.00 0.00 4.63
3132 3572 1.733399 GTCTTGTGTCGTCCGCCTC 60.733 63.158 0.00 0.00 0.00 4.70
3133 3573 2.338984 GTCTTGTGTCGTCCGCCT 59.661 61.111 0.00 0.00 0.00 5.52
3134 3574 2.737376 GGTCTTGTGTCGTCCGCC 60.737 66.667 0.00 0.00 0.00 6.13
3135 3575 1.733399 GAGGTCTTGTGTCGTCCGC 60.733 63.158 0.00 0.00 0.00 5.54
3136 3576 1.080705 GGAGGTCTTGTGTCGTCCG 60.081 63.158 0.00 0.00 29.79 4.79
3137 3577 0.038159 CAGGAGGTCTTGTGTCGTCC 60.038 60.000 0.00 0.00 36.83 4.79
3138 3578 0.038159 CCAGGAGGTCTTGTGTCGTC 60.038 60.000 0.00 0.00 0.00 4.20
3139 3579 1.472662 CCCAGGAGGTCTTGTGTCGT 61.473 60.000 0.00 0.00 0.00 4.34
3140 3580 1.293498 CCCAGGAGGTCTTGTGTCG 59.707 63.158 0.00 0.00 0.00 4.35
3141 3581 1.679898 CCCCAGGAGGTCTTGTGTC 59.320 63.158 0.00 0.00 0.00 3.67
3142 3582 1.847968 CCCCCAGGAGGTCTTGTGT 60.848 63.158 0.00 0.00 33.47 3.72
3143 3583 3.081554 CCCCCAGGAGGTCTTGTG 58.918 66.667 0.00 0.00 33.47 3.33
3157 3597 4.748144 CTTGGTGAGGCTGCCCCC 62.748 72.222 16.57 13.61 0.00 5.40
3159 3599 4.357279 AGCTTGGTGAGGCTGCCC 62.357 66.667 16.57 7.66 37.41 5.36
3165 3605 2.435586 CGAGCCAGCTTGGTGAGG 60.436 66.667 0.00 0.00 40.46 3.86
3166 3606 3.123620 GCGAGCCAGCTTGGTGAG 61.124 66.667 8.93 0.00 40.46 3.51
3169 3609 4.749310 CTCGCGAGCCAGCTTGGT 62.749 66.667 25.07 0.00 40.46 3.67
3182 3622 3.984749 GATCTCTCCGCCCCTCGC 61.985 72.222 0.00 0.00 36.73 5.03
3183 3623 2.081425 CTTGATCTCTCCGCCCCTCG 62.081 65.000 0.00 0.00 38.08 4.63
3184 3624 1.745264 CTTGATCTCTCCGCCCCTC 59.255 63.158 0.00 0.00 0.00 4.30
3185 3625 1.764054 CCTTGATCTCTCCGCCCCT 60.764 63.158 0.00 0.00 0.00 4.79
3186 3626 2.825264 CCTTGATCTCTCCGCCCC 59.175 66.667 0.00 0.00 0.00 5.80
3187 3627 2.110006 GCCTTGATCTCTCCGCCC 59.890 66.667 0.00 0.00 0.00 6.13
3188 3628 0.813210 CTTGCCTTGATCTCTCCGCC 60.813 60.000 0.00 0.00 0.00 6.13
3189 3629 0.813210 CCTTGCCTTGATCTCTCCGC 60.813 60.000 0.00 0.00 0.00 5.54
3190 3630 0.813210 GCCTTGCCTTGATCTCTCCG 60.813 60.000 0.00 0.00 0.00 4.63
3191 3631 0.813210 CGCCTTGCCTTGATCTCTCC 60.813 60.000 0.00 0.00 0.00 3.71
3192 3632 0.176680 TCGCCTTGCCTTGATCTCTC 59.823 55.000 0.00 0.00 0.00 3.20
3193 3633 0.615331 TTCGCCTTGCCTTGATCTCT 59.385 50.000 0.00 0.00 0.00 3.10
3194 3634 0.729690 GTTCGCCTTGCCTTGATCTC 59.270 55.000 0.00 0.00 0.00 2.75
3195 3635 0.678048 GGTTCGCCTTGCCTTGATCT 60.678 55.000 0.00 0.00 0.00 2.75
3196 3636 1.803289 GGTTCGCCTTGCCTTGATC 59.197 57.895 0.00 0.00 0.00 2.92
3197 3637 4.002797 GGTTCGCCTTGCCTTGAT 57.997 55.556 0.00 0.00 0.00 2.57
3214 3654 1.413767 CGTCATTGGAACCTCGCGAG 61.414 60.000 29.06 29.06 0.00 5.03
3215 3655 1.445410 CGTCATTGGAACCTCGCGA 60.445 57.895 9.26 9.26 0.00 5.87
3216 3656 0.457166 TACGTCATTGGAACCTCGCG 60.457 55.000 0.00 0.00 0.00 5.87
3217 3657 1.717194 TTACGTCATTGGAACCTCGC 58.283 50.000 0.00 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.