Multiple sequence alignment - TraesCS5D01G096800

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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 TraesCS5D01G096800 chr5D 100.000 4178 0 0 1 4178 107554936 107550759 0.000000e+00 7716.0
1 TraesCS5D01G096800 chr5D 80.720 472 69 12 3463 3922 35977186 35977647 8.600000e-92 348.0
2 TraesCS5D01G096800 chr5A 96.436 2329 75 5 869 3196 110354570 110352249 0.000000e+00 3834.0
3 TraesCS5D01G096800 chr5A 90.725 345 21 8 312 646 110355360 110355017 2.290000e-122 449.0
4 TraesCS5D01G096800 chr5A 88.298 188 11 2 3 179 110355669 110355482 9.100000e-52 215.0
5 TraesCS5D01G096800 chr5B 94.863 2375 116 3 819 3193 116831664 116829296 0.000000e+00 3705.0
6 TraesCS5D01G096800 chr5B 96.443 1012 35 1 3168 4178 116826155 116825144 0.000000e+00 1668.0
7 TraesCS5D01G096800 chr5B 89.213 343 25 9 311 646 116831993 116831656 6.460000e-113 418.0
8 TraesCS5D01G096800 chr5B 87.446 231 17 3 3 226 116832278 116832053 5.360000e-64 255.0
9 TraesCS5D01G096800 chr4B 91.879 2278 130 23 955 3204 28536527 28538777 0.000000e+00 3131.0
10 TraesCS5D01G096800 chr4B 86.395 147 10 4 37 179 28536368 28536508 7.230000e-33 152.0
11 TraesCS5D01G096800 chr7B 80.946 2262 329 56 968 3180 683105713 683107921 0.000000e+00 1696.0
12 TraesCS5D01G096800 chr7B 84.662 1154 162 8 2032 3173 683168298 683167148 0.000000e+00 1136.0
13 TraesCS5D01G096800 chr7B 83.993 1162 170 10 2032 3180 683230487 683229329 0.000000e+00 1101.0
14 TraesCS5D01G096800 chr7B 83.649 1162 167 15 2032 3173 683151510 683152668 0.000000e+00 1072.0
15 TraesCS5D01G096800 chr7B 78.991 852 153 17 965 1809 683243819 683242987 3.650000e-155 558.0
16 TraesCS5D01G096800 chr7B 83.871 62 5 3 4061 4119 748856739 748856798 2.000000e-03 54.7
17 TraesCS5D01G096800 chr7A 80.493 2230 335 52 999 3180 694254347 694252170 0.000000e+00 1616.0
18 TraesCS5D01G096800 chr7A 80.080 2264 342 64 968 3180 694196411 694198616 0.000000e+00 1581.0
19 TraesCS5D01G096800 chr7A 84.251 1162 167 8 2032 3180 694357196 694356038 0.000000e+00 1118.0
20 TraesCS5D01G096800 chr7A 78.580 859 151 30 965 1809 694375911 694375072 1.710000e-148 536.0
21 TraesCS5D01G096800 chr7A 83.562 73 12 0 559 631 331070360 331070288 7.500000e-08 69.4
22 TraesCS5D01G096800 chr7A 90.196 51 5 0 4092 4142 55393793 55393843 2.700000e-07 67.6
23 TraesCS5D01G096800 chr7D 79.840 2247 366 49 965 3176 602751530 602749336 0.000000e+00 1559.0
24 TraesCS5D01G096800 chr7D 85.758 976 133 4 2032 3001 602627491 602628466 0.000000e+00 1027.0
25 TraesCS5D01G096800 chr7D 78.989 752 140 10 1064 1809 602673492 602672753 8.070000e-137 497.0
26 TraesCS5D01G096800 chr7D 84.112 214 25 6 3622 3833 550978783 550978577 9.160000e-47 198.0
27 TraesCS5D01G096800 chr7D 80.071 281 41 8 3479 3751 142171911 142171638 1.190000e-45 195.0
28 TraesCS5D01G096800 chr7D 81.865 193 28 4 3645 3834 89310212 89310400 5.590000e-34 156.0
29 TraesCS5D01G096800 chr7D 92.157 51 4 0 4092 4142 53430647 53430697 5.790000e-09 73.1
30 TraesCS5D01G096800 chr7D 90.566 53 4 1 196 248 92796210 92796159 7.500000e-08 69.4
31 TraesCS5D01G096800 chr2D 77.167 473 63 25 3456 3903 346159885 346159433 2.510000e-57 233.0
32 TraesCS5D01G096800 chr6B 76.956 473 63 28 3415 3858 621055655 621056110 1.170000e-55 228.0
33 TraesCS5D01G096800 chr3A 81.340 209 30 6 3642 3848 662935809 662936010 1.200000e-35 161.0
34 TraesCS5D01G096800 chr3A 80.383 209 34 4 3642 3848 691737115 691736912 7.230000e-33 152.0
35 TraesCS5D01G096800 chr3A 90.698 43 1 3 4080 4119 82755877 82755835 2.000000e-03 54.7
36 TraesCS5D01G096800 chr1B 81.407 199 32 2 3661 3858 671261964 671261770 1.550000e-34 158.0
37 TraesCS5D01G096800 chr1A 91.935 62 3 2 571 631 515715544 515715484 7.440000e-13 86.1
38 TraesCS5D01G096800 chr4D 91.803 61 4 1 761 821 317203314 317203373 2.680000e-12 84.2
39 TraesCS5D01G096800 chr4A 78.226 124 18 9 4003 4118 492038856 492038734 2.080000e-08 71.3
40 TraesCS5D01G096800 chr1D 81.609 87 11 5 4035 4119 11975522 11975605 2.700000e-07 67.6
41 TraesCS5D01G096800 chr6D 90.698 43 1 3 4080 4119 445004210 445004252 2.000000e-03 54.7
42 TraesCS5D01G096800 chr3B 90.698 43 1 3 4080 4119 726749549 726749507 2.000000e-03 54.7


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 TraesCS5D01G096800 chr5D 107550759 107554936 4177 True 7716.000000 7716 100.000000 1 4178 1 chr5D.!!$R1 4177
1 TraesCS5D01G096800 chr5A 110352249 110355669 3420 True 1499.333333 3834 91.819667 3 3196 3 chr5A.!!$R1 3193
2 TraesCS5D01G096800 chr5B 116825144 116832278 7134 True 1511.500000 3705 91.991250 3 4178 4 chr5B.!!$R1 4175
3 TraesCS5D01G096800 chr4B 28536368 28538777 2409 False 1641.500000 3131 89.137000 37 3204 2 chr4B.!!$F1 3167
4 TraesCS5D01G096800 chr7B 683105713 683107921 2208 False 1696.000000 1696 80.946000 968 3180 1 chr7B.!!$F1 2212
5 TraesCS5D01G096800 chr7B 683167148 683168298 1150 True 1136.000000 1136 84.662000 2032 3173 1 chr7B.!!$R1 1141
6 TraesCS5D01G096800 chr7B 683229329 683230487 1158 True 1101.000000 1101 83.993000 2032 3180 1 chr7B.!!$R2 1148
7 TraesCS5D01G096800 chr7B 683151510 683152668 1158 False 1072.000000 1072 83.649000 2032 3173 1 chr7B.!!$F2 1141
8 TraesCS5D01G096800 chr7B 683242987 683243819 832 True 558.000000 558 78.991000 965 1809 1 chr7B.!!$R3 844
9 TraesCS5D01G096800 chr7A 694252170 694254347 2177 True 1616.000000 1616 80.493000 999 3180 1 chr7A.!!$R2 2181
10 TraesCS5D01G096800 chr7A 694196411 694198616 2205 False 1581.000000 1581 80.080000 968 3180 1 chr7A.!!$F2 2212
11 TraesCS5D01G096800 chr7A 694356038 694357196 1158 True 1118.000000 1118 84.251000 2032 3180 1 chr7A.!!$R3 1148
12 TraesCS5D01G096800 chr7A 694375072 694375911 839 True 536.000000 536 78.580000 965 1809 1 chr7A.!!$R4 844
13 TraesCS5D01G096800 chr7D 602749336 602751530 2194 True 1559.000000 1559 79.840000 965 3176 1 chr7D.!!$R5 2211
14 TraesCS5D01G096800 chr7D 602627491 602628466 975 False 1027.000000 1027 85.758000 2032 3001 1 chr7D.!!$F3 969
15 TraesCS5D01G096800 chr7D 602672753 602673492 739 True 497.000000 497 78.989000 1064 1809 1 chr7D.!!$R4 745

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
659 718 0.248289 TAGGACCGGCTTTGCTACAC 59.752 55.0 0.00 0.0 0.00 2.90 F
745 804 0.324275 CGGACCCACCCCATTCAAAT 60.324 55.0 0.00 0.0 34.64 2.32 F
2115 2671 0.601558 ACACGTACCATGAGCTCGTT 59.398 50.0 5.46 0.0 32.47 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1940 2487 0.179234 TACCATGGCCACACATACCG 59.821 55.0 8.16 0.00 0.00 4.02 R
2307 2882 0.744414 GGTTGCGATGCTTCAGCCTA 60.744 55.0 11.70 1.43 41.18 3.93 R
3212 6969 0.179111 CTCGGCGTGGCTATCTCAAA 60.179 55.0 6.85 0.00 0.00 2.69 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
34 36 5.010112 TCGGCTGGAAAATGTTGTTCATAAA 59.990 36.000 0.00 0.00 35.48 1.40
118 127 5.695816 CCATTTCAAATTTGACCGTGACAAT 59.304 36.000 20.35 12.29 36.83 2.71
125 134 5.607119 ATTTGACCGTGACAATTGACTAC 57.393 39.130 13.59 6.90 0.00 2.73
142 158 8.950208 ATTGACTACTCCACTAAGATTTTAGC 57.050 34.615 3.00 0.00 39.96 3.09
147 163 4.466726 ACTCCACTAAGATTTTAGCGACCT 59.533 41.667 3.00 0.00 39.96 3.85
179 195 4.476410 CTCAGCTACGCGCCGTCA 62.476 66.667 5.73 0.00 41.54 4.35
209 225 1.982073 GCCGGCCGTCAAAGATCTTG 61.982 60.000 26.12 4.68 0.00 3.02
348 407 3.049708 TGGAACAATGAGACAGAGCTG 57.950 47.619 0.00 0.00 31.92 4.24
349 408 2.634453 TGGAACAATGAGACAGAGCTGA 59.366 45.455 4.21 0.00 31.92 4.26
350 409 2.999355 GGAACAATGAGACAGAGCTGAC 59.001 50.000 4.21 0.00 0.00 3.51
351 410 2.360553 ACAATGAGACAGAGCTGACG 57.639 50.000 4.21 0.00 0.00 4.35
352 411 0.997932 CAATGAGACAGAGCTGACGC 59.002 55.000 4.21 0.63 0.00 5.19
375 434 4.680237 CGGCTGCGTCACCAAGGA 62.680 66.667 0.00 0.00 0.00 3.36
376 435 2.281484 GGCTGCGTCACCAAGGAA 60.281 61.111 0.00 0.00 0.00 3.36
377 436 2.328099 GGCTGCGTCACCAAGGAAG 61.328 63.158 0.00 0.00 0.00 3.46
378 437 1.301716 GCTGCGTCACCAAGGAAGA 60.302 57.895 0.00 0.00 0.00 2.87
379 438 0.884704 GCTGCGTCACCAAGGAAGAA 60.885 55.000 0.00 0.00 0.00 2.52
380 439 1.813513 CTGCGTCACCAAGGAAGAAT 58.186 50.000 0.00 0.00 0.00 2.40
381 440 1.466167 CTGCGTCACCAAGGAAGAATG 59.534 52.381 0.00 0.00 0.00 2.67
382 441 1.071542 TGCGTCACCAAGGAAGAATGA 59.928 47.619 0.00 0.00 0.00 2.57
383 442 1.734465 GCGTCACCAAGGAAGAATGAG 59.266 52.381 0.00 0.00 0.00 2.90
384 443 2.612972 GCGTCACCAAGGAAGAATGAGA 60.613 50.000 0.00 0.00 0.00 3.27
385 444 2.996621 CGTCACCAAGGAAGAATGAGAC 59.003 50.000 0.00 0.00 0.00 3.36
386 445 3.554960 CGTCACCAAGGAAGAATGAGACA 60.555 47.826 0.00 0.00 0.00 3.41
433 492 0.527565 GGCTGCGTCCAAACAATGAT 59.472 50.000 0.00 0.00 0.00 2.45
552 611 8.261522 ACCAACATATCCTAGAGAGAGAAAAAC 58.738 37.037 0.00 0.00 0.00 2.43
559 618 6.801953 TCCTAGAGAGAGAAAAACTAGGGAA 58.198 40.000 15.45 0.00 45.73 3.97
571 630 6.753107 AAAACTAGGGAACAATAATGACCG 57.247 37.500 0.00 0.00 0.00 4.79
583 642 6.563422 ACAATAATGACCGTTGGATCAATTG 58.437 36.000 0.00 0.00 32.75 2.32
636 695 9.990360 TGATGTACTGTAAAAAGTCTCAACATA 57.010 29.630 0.00 0.00 29.80 2.29
647 706 7.611213 AAAGTCTCAACATATTTTAGGACCG 57.389 36.000 0.00 0.00 0.00 4.79
648 707 5.671493 AGTCTCAACATATTTTAGGACCGG 58.329 41.667 0.00 0.00 0.00 5.28
649 708 4.272748 GTCTCAACATATTTTAGGACCGGC 59.727 45.833 0.00 0.00 0.00 6.13
650 709 4.163458 TCTCAACATATTTTAGGACCGGCT 59.837 41.667 0.00 0.00 0.00 5.52
651 710 4.850680 TCAACATATTTTAGGACCGGCTT 58.149 39.130 0.00 0.00 0.00 4.35
652 711 5.258051 TCAACATATTTTAGGACCGGCTTT 58.742 37.500 0.00 0.00 0.00 3.51
653 712 5.124776 TCAACATATTTTAGGACCGGCTTTG 59.875 40.000 0.00 0.00 0.00 2.77
654 713 3.380320 ACATATTTTAGGACCGGCTTTGC 59.620 43.478 0.00 0.00 0.00 3.68
655 714 2.215942 ATTTTAGGACCGGCTTTGCT 57.784 45.000 0.00 0.00 0.00 3.91
656 715 2.863132 TTTTAGGACCGGCTTTGCTA 57.137 45.000 0.00 0.00 0.00 3.49
657 716 2.103537 TTTAGGACCGGCTTTGCTAC 57.896 50.000 0.00 0.00 0.00 3.58
658 717 0.978151 TTAGGACCGGCTTTGCTACA 59.022 50.000 0.00 0.00 0.00 2.74
659 718 0.248289 TAGGACCGGCTTTGCTACAC 59.752 55.000 0.00 0.00 0.00 2.90
660 719 2.388232 GGACCGGCTTTGCTACACG 61.388 63.158 0.00 0.00 0.00 4.49
661 720 1.666872 GACCGGCTTTGCTACACGT 60.667 57.895 0.00 0.00 0.00 4.49
662 721 0.388907 GACCGGCTTTGCTACACGTA 60.389 55.000 0.00 0.00 0.00 3.57
663 722 0.668401 ACCGGCTTTGCTACACGTAC 60.668 55.000 0.00 0.00 0.00 3.67
664 723 0.668096 CCGGCTTTGCTACACGTACA 60.668 55.000 0.00 0.00 0.00 2.90
665 724 1.141645 CGGCTTTGCTACACGTACAA 58.858 50.000 0.00 0.00 0.00 2.41
666 725 1.126113 CGGCTTTGCTACACGTACAAG 59.874 52.381 0.00 0.00 0.00 3.16
667 726 2.409975 GGCTTTGCTACACGTACAAGA 58.590 47.619 0.00 0.00 0.00 3.02
668 727 3.000727 GGCTTTGCTACACGTACAAGAT 58.999 45.455 0.00 0.00 0.00 2.40
669 728 3.181520 GGCTTTGCTACACGTACAAGATG 60.182 47.826 0.00 0.00 0.00 2.90
670 729 3.432252 GCTTTGCTACACGTACAAGATGT 59.568 43.478 0.00 0.00 0.00 3.06
671 730 4.084013 GCTTTGCTACACGTACAAGATGTT 60.084 41.667 0.00 0.00 0.00 2.71
672 731 5.119588 GCTTTGCTACACGTACAAGATGTTA 59.880 40.000 0.00 0.00 0.00 2.41
673 732 6.669977 GCTTTGCTACACGTACAAGATGTTAG 60.670 42.308 0.00 0.00 0.00 2.34
674 733 4.740268 TGCTACACGTACAAGATGTTAGG 58.260 43.478 0.00 0.00 0.00 2.69
675 734 4.110482 GCTACACGTACAAGATGTTAGGG 58.890 47.826 0.00 0.00 0.00 3.53
676 735 4.142315 GCTACACGTACAAGATGTTAGGGA 60.142 45.833 0.00 0.00 0.00 4.20
677 736 4.451629 ACACGTACAAGATGTTAGGGAG 57.548 45.455 0.00 0.00 0.00 4.30
678 737 3.194968 ACACGTACAAGATGTTAGGGAGG 59.805 47.826 0.00 0.00 0.00 4.30
679 738 3.446161 CACGTACAAGATGTTAGGGAGGA 59.554 47.826 0.00 0.00 0.00 3.71
680 739 3.700038 ACGTACAAGATGTTAGGGAGGAG 59.300 47.826 0.00 0.00 0.00 3.69
681 740 3.952323 CGTACAAGATGTTAGGGAGGAGA 59.048 47.826 0.00 0.00 0.00 3.71
682 741 4.401519 CGTACAAGATGTTAGGGAGGAGAA 59.598 45.833 0.00 0.00 0.00 2.87
683 742 5.450688 CGTACAAGATGTTAGGGAGGAGAAG 60.451 48.000 0.00 0.00 0.00 2.85
684 743 4.689062 ACAAGATGTTAGGGAGGAGAAGA 58.311 43.478 0.00 0.00 0.00 2.87
685 744 5.284582 ACAAGATGTTAGGGAGGAGAAGAT 58.715 41.667 0.00 0.00 0.00 2.40
686 745 5.728741 ACAAGATGTTAGGGAGGAGAAGATT 59.271 40.000 0.00 0.00 0.00 2.40
687 746 6.903534 ACAAGATGTTAGGGAGGAGAAGATTA 59.096 38.462 0.00 0.00 0.00 1.75
688 747 6.987403 AGATGTTAGGGAGGAGAAGATTAC 57.013 41.667 0.00 0.00 0.00 1.89
689 748 6.444704 AGATGTTAGGGAGGAGAAGATTACA 58.555 40.000 0.00 0.00 0.00 2.41
690 749 6.553100 AGATGTTAGGGAGGAGAAGATTACAG 59.447 42.308 0.00 0.00 0.00 2.74
691 750 4.962995 TGTTAGGGAGGAGAAGATTACAGG 59.037 45.833 0.00 0.00 0.00 4.00
692 751 3.053359 AGGGAGGAGAAGATTACAGGG 57.947 52.381 0.00 0.00 0.00 4.45
693 752 2.319438 AGGGAGGAGAAGATTACAGGGT 59.681 50.000 0.00 0.00 0.00 4.34
694 753 2.436173 GGGAGGAGAAGATTACAGGGTG 59.564 54.545 0.00 0.00 0.00 4.61
695 754 3.375699 GGAGGAGAAGATTACAGGGTGA 58.624 50.000 0.00 0.00 0.00 4.02
696 755 3.970640 GGAGGAGAAGATTACAGGGTGAT 59.029 47.826 0.00 0.00 0.00 3.06
697 756 5.148502 GGAGGAGAAGATTACAGGGTGATA 58.851 45.833 0.00 0.00 0.00 2.15
698 757 5.782845 GGAGGAGAAGATTACAGGGTGATAT 59.217 44.000 0.00 0.00 0.00 1.63
699 758 6.295575 GGAGGAGAAGATTACAGGGTGATATG 60.296 46.154 0.00 0.00 0.00 1.78
700 759 6.146760 AGGAGAAGATTACAGGGTGATATGT 58.853 40.000 0.00 0.00 0.00 2.29
701 760 6.617371 AGGAGAAGATTACAGGGTGATATGTT 59.383 38.462 0.00 0.00 0.00 2.71
702 761 7.127955 AGGAGAAGATTACAGGGTGATATGTTT 59.872 37.037 0.00 0.00 0.00 2.83
703 762 7.775561 GGAGAAGATTACAGGGTGATATGTTTT 59.224 37.037 0.00 0.00 0.00 2.43
704 763 9.178758 GAGAAGATTACAGGGTGATATGTTTTT 57.821 33.333 0.00 0.00 0.00 1.94
711 770 7.790782 ACAGGGTGATATGTTTTTAATTGGT 57.209 32.000 0.00 0.00 0.00 3.67
712 771 7.610865 ACAGGGTGATATGTTTTTAATTGGTG 58.389 34.615 0.00 0.00 0.00 4.17
713 772 7.453126 ACAGGGTGATATGTTTTTAATTGGTGA 59.547 33.333 0.00 0.00 0.00 4.02
714 773 8.477256 CAGGGTGATATGTTTTTAATTGGTGAT 58.523 33.333 0.00 0.00 0.00 3.06
715 774 9.045745 AGGGTGATATGTTTTTAATTGGTGATT 57.954 29.630 0.00 0.00 0.00 2.57
721 780 7.832503 ATGTTTTTAATTGGTGATTAGCAGC 57.167 32.000 0.00 0.00 45.12 5.25
726 785 3.102097 GGTGATTAGCAGCGGCAC 58.898 61.111 12.44 0.00 44.61 5.01
740 799 4.360405 GCACGGACCCACCCCATT 62.360 66.667 0.00 0.00 34.64 3.16
741 800 2.045340 CACGGACCCACCCCATTC 60.045 66.667 0.00 0.00 34.64 2.67
742 801 2.530661 ACGGACCCACCCCATTCA 60.531 61.111 0.00 0.00 34.64 2.57
743 802 2.157452 ACGGACCCACCCCATTCAA 61.157 57.895 0.00 0.00 34.64 2.69
744 803 1.075836 CGGACCCACCCCATTCAAA 59.924 57.895 0.00 0.00 34.64 2.69
745 804 0.324275 CGGACCCACCCCATTCAAAT 60.324 55.000 0.00 0.00 34.64 2.32
746 805 1.485124 GGACCCACCCCATTCAAATC 58.515 55.000 0.00 0.00 0.00 2.17
747 806 1.272985 GGACCCACCCCATTCAAATCA 60.273 52.381 0.00 0.00 0.00 2.57
748 807 2.102578 GACCCACCCCATTCAAATCAG 58.897 52.381 0.00 0.00 0.00 2.90
749 808 1.273211 ACCCACCCCATTCAAATCAGG 60.273 52.381 0.00 0.00 0.00 3.86
750 809 1.006998 CCCACCCCATTCAAATCAGGA 59.993 52.381 0.00 0.00 0.00 3.86
751 810 2.381911 CCACCCCATTCAAATCAGGAG 58.618 52.381 0.00 0.00 0.00 3.69
752 811 2.381911 CACCCCATTCAAATCAGGAGG 58.618 52.381 0.00 0.00 0.00 4.30
753 812 2.025037 CACCCCATTCAAATCAGGAGGA 60.025 50.000 0.00 0.00 0.00 3.71
754 813 2.024941 ACCCCATTCAAATCAGGAGGAC 60.025 50.000 0.00 0.00 0.00 3.85
755 814 2.292267 CCCATTCAAATCAGGAGGACG 58.708 52.381 0.00 0.00 0.00 4.79
756 815 2.356125 CCCATTCAAATCAGGAGGACGT 60.356 50.000 0.00 0.00 0.00 4.34
757 816 3.347216 CCATTCAAATCAGGAGGACGTT 58.653 45.455 0.00 0.00 0.00 3.99
758 817 3.758554 CCATTCAAATCAGGAGGACGTTT 59.241 43.478 0.00 0.00 0.00 3.60
759 818 4.941263 CCATTCAAATCAGGAGGACGTTTA 59.059 41.667 0.00 0.00 0.00 2.01
760 819 5.065218 CCATTCAAATCAGGAGGACGTTTAG 59.935 44.000 0.00 0.00 0.00 1.85
761 820 5.477607 TTCAAATCAGGAGGACGTTTAGA 57.522 39.130 0.00 0.00 0.00 2.10
762 821 5.477607 TCAAATCAGGAGGACGTTTAGAA 57.522 39.130 0.00 0.00 0.00 2.10
763 822 5.860611 TCAAATCAGGAGGACGTTTAGAAA 58.139 37.500 0.00 0.00 0.00 2.52
764 823 5.932303 TCAAATCAGGAGGACGTTTAGAAAG 59.068 40.000 0.00 0.00 0.00 2.62
765 824 5.485209 AATCAGGAGGACGTTTAGAAAGT 57.515 39.130 0.00 0.00 0.00 2.66
766 825 4.950205 TCAGGAGGACGTTTAGAAAGTT 57.050 40.909 0.00 0.00 0.00 2.66
767 826 5.286267 TCAGGAGGACGTTTAGAAAGTTT 57.714 39.130 0.00 0.00 0.00 2.66
768 827 5.054477 TCAGGAGGACGTTTAGAAAGTTTG 58.946 41.667 0.00 0.00 0.00 2.93
769 828 5.054477 CAGGAGGACGTTTAGAAAGTTTGA 58.946 41.667 0.00 0.00 0.00 2.69
770 829 5.526111 CAGGAGGACGTTTAGAAAGTTTGAA 59.474 40.000 0.00 0.00 0.00 2.69
771 830 6.037830 CAGGAGGACGTTTAGAAAGTTTGAAA 59.962 38.462 0.00 0.00 0.00 2.69
772 831 6.260271 AGGAGGACGTTTAGAAAGTTTGAAAG 59.740 38.462 0.00 0.00 0.00 2.62
773 832 6.373186 AGGACGTTTAGAAAGTTTGAAAGG 57.627 37.500 0.00 2.21 0.00 3.11
774 833 6.117488 AGGACGTTTAGAAAGTTTGAAAGGA 58.883 36.000 14.56 0.00 0.00 3.36
775 834 6.260271 AGGACGTTTAGAAAGTTTGAAAGGAG 59.740 38.462 14.56 4.79 0.00 3.69
776 835 5.817988 ACGTTTAGAAAGTTTGAAAGGAGC 58.182 37.500 14.56 0.00 0.00 4.70
777 836 5.212934 CGTTTAGAAAGTTTGAAAGGAGCC 58.787 41.667 0.00 0.00 0.00 4.70
778 837 5.008712 CGTTTAGAAAGTTTGAAAGGAGCCT 59.991 40.000 0.00 0.00 0.00 4.58
779 838 6.209361 GTTTAGAAAGTTTGAAAGGAGCCTG 58.791 40.000 0.00 0.00 0.00 4.85
780 839 3.903467 AGAAAGTTTGAAAGGAGCCTGT 58.097 40.909 0.00 0.00 0.00 4.00
781 840 5.048846 AGAAAGTTTGAAAGGAGCCTGTA 57.951 39.130 0.00 0.00 0.00 2.74
782 841 5.066593 AGAAAGTTTGAAAGGAGCCTGTAG 58.933 41.667 0.00 0.00 0.00 2.74
783 842 4.706842 AAGTTTGAAAGGAGCCTGTAGA 57.293 40.909 0.00 0.00 0.00 2.59
784 843 4.706842 AGTTTGAAAGGAGCCTGTAGAA 57.293 40.909 0.00 0.00 0.00 2.10
785 844 4.390264 AGTTTGAAAGGAGCCTGTAGAAC 58.610 43.478 0.00 0.00 0.00 3.01
786 845 4.103311 AGTTTGAAAGGAGCCTGTAGAACT 59.897 41.667 0.00 0.00 0.00 3.01
787 846 4.706842 TTGAAAGGAGCCTGTAGAACTT 57.293 40.909 0.00 0.00 0.00 2.66
788 847 4.273148 TGAAAGGAGCCTGTAGAACTTC 57.727 45.455 0.00 0.00 0.00 3.01
789 848 3.904339 TGAAAGGAGCCTGTAGAACTTCT 59.096 43.478 0.00 0.00 0.00 2.85
790 849 3.971245 AAGGAGCCTGTAGAACTTCTG 57.029 47.619 1.17 0.00 0.00 3.02
791 850 2.896039 AGGAGCCTGTAGAACTTCTGT 58.104 47.619 1.17 0.00 0.00 3.41
792 851 4.048970 AGGAGCCTGTAGAACTTCTGTA 57.951 45.455 1.17 0.00 0.00 2.74
793 852 4.417437 AGGAGCCTGTAGAACTTCTGTAA 58.583 43.478 1.17 0.00 0.00 2.41
794 853 4.838986 AGGAGCCTGTAGAACTTCTGTAAA 59.161 41.667 1.17 0.00 0.00 2.01
795 854 5.307196 AGGAGCCTGTAGAACTTCTGTAAAA 59.693 40.000 1.17 0.00 0.00 1.52
796 855 5.639931 GGAGCCTGTAGAACTTCTGTAAAAG 59.360 44.000 1.17 0.00 0.00 2.27
797 856 6.176014 AGCCTGTAGAACTTCTGTAAAAGT 57.824 37.500 1.17 0.00 41.20 2.66
798 857 6.224584 AGCCTGTAGAACTTCTGTAAAAGTC 58.775 40.000 1.17 0.00 38.52 3.01
799 858 6.042208 AGCCTGTAGAACTTCTGTAAAAGTCT 59.958 38.462 1.17 0.00 38.52 3.24
800 859 6.146347 GCCTGTAGAACTTCTGTAAAAGTCTG 59.854 42.308 1.17 0.00 38.52 3.51
801 860 7.210873 CCTGTAGAACTTCTGTAAAAGTCTGT 58.789 38.462 1.17 0.00 38.52 3.41
802 861 8.358148 CCTGTAGAACTTCTGTAAAAGTCTGTA 58.642 37.037 1.17 0.00 38.52 2.74
803 862 9.182933 CTGTAGAACTTCTGTAAAAGTCTGTAC 57.817 37.037 1.17 0.00 38.52 2.90
804 863 7.859377 TGTAGAACTTCTGTAAAAGTCTGTACG 59.141 37.037 1.17 0.00 38.52 3.67
805 864 6.803642 AGAACTTCTGTAAAAGTCTGTACGT 58.196 36.000 0.00 0.00 38.52 3.57
806 865 6.916932 AGAACTTCTGTAAAAGTCTGTACGTC 59.083 38.462 0.00 0.00 38.52 4.34
807 866 6.388435 ACTTCTGTAAAAGTCTGTACGTCT 57.612 37.500 0.00 0.00 34.37 4.18
808 867 7.502120 ACTTCTGTAAAAGTCTGTACGTCTA 57.498 36.000 0.00 0.00 34.37 2.59
809 868 7.583230 ACTTCTGTAAAAGTCTGTACGTCTAG 58.417 38.462 0.00 0.00 34.37 2.43
810 869 5.936054 TCTGTAAAAGTCTGTACGTCTAGC 58.064 41.667 0.00 0.00 0.00 3.42
811 870 5.471116 TCTGTAAAAGTCTGTACGTCTAGCA 59.529 40.000 0.00 0.00 0.00 3.49
812 871 6.150641 TCTGTAAAAGTCTGTACGTCTAGCAT 59.849 38.462 0.00 0.00 0.00 3.79
813 872 6.684686 TGTAAAAGTCTGTACGTCTAGCATT 58.315 36.000 0.00 0.00 0.00 3.56
814 873 7.149973 TGTAAAAGTCTGTACGTCTAGCATTT 58.850 34.615 0.00 0.00 0.00 2.32
815 874 7.654520 TGTAAAAGTCTGTACGTCTAGCATTTT 59.345 33.333 0.00 5.47 0.00 1.82
816 875 7.492352 AAAAGTCTGTACGTCTAGCATTTTT 57.508 32.000 0.00 0.00 0.00 1.94
817 876 6.467723 AAGTCTGTACGTCTAGCATTTTTG 57.532 37.500 0.00 0.00 0.00 2.44
850 909 9.541143 GACGGAGGTAATATAGTAGTAGTATCC 57.459 40.741 0.55 0.00 0.00 2.59
887 1349 7.607223 AGTGAGTAGTAGTGGAGTAGTAAACTG 59.393 40.741 0.00 0.00 39.07 3.16
891 1353 8.386264 AGTAGTAGTGGAGTAGTAAACTGGTAA 58.614 37.037 0.00 0.00 39.07 2.85
894 1356 9.183368 AGTAGTGGAGTAGTAAACTGGTAATAC 57.817 37.037 0.00 0.00 39.07 1.89
910 1372 9.939802 ACTGGTAATACTAATAAATCGAATCCC 57.060 33.333 0.00 0.00 0.00 3.85
916 1378 5.488341 ACTAATAAATCGAATCCCATCCCG 58.512 41.667 0.00 0.00 0.00 5.14
970 1433 2.039879 TCTCCCCTTGTTTTCTAGTGCC 59.960 50.000 0.00 0.00 0.00 5.01
1040 1521 0.784495 AGTCTCACCACCCTAGTCCA 59.216 55.000 0.00 0.00 0.00 4.02
1174 1661 2.202492 CGTTCCTCAGCTCGTCCG 60.202 66.667 0.00 0.00 0.00 4.79
1643 2162 2.086869 CAAGTACCACAATGGCTCCAG 58.913 52.381 0.00 0.00 42.67 3.86
1741 2267 1.069935 GAGGAGGTTGCTATCGGCC 59.930 63.158 0.00 0.00 40.92 6.13
1940 2487 2.622436 AGTTCCGCTGCTATTTCTGTC 58.378 47.619 0.00 0.00 0.00 3.51
2115 2671 0.601558 ACACGTACCATGAGCTCGTT 59.398 50.000 5.46 0.00 32.47 3.85
3041 3619 0.175760 GTGCCGGAGCTTGAGTCATA 59.824 55.000 5.05 0.00 40.80 2.15
3105 3696 2.576615 GGCTCTTCTTTGGTCAACACT 58.423 47.619 0.00 0.00 0.00 3.55
3212 6969 3.390639 TGCCTTCCCATTGTTGATTGTTT 59.609 39.130 0.00 0.00 0.00 2.83
3252 7009 0.884704 GGTCGTCAGGTGTGCATTGT 60.885 55.000 0.00 0.00 0.00 2.71
3278 7035 9.719355 TCAGCTACAATTATTTTGAAGTACTGA 57.281 29.630 0.00 0.00 0.00 3.41
3330 7087 4.334203 TCATGGTCGGATTAATTTGGTTCG 59.666 41.667 0.00 0.00 0.00 3.95
3374 7131 3.314357 TCTGGTCGATCTTGTATGTACCG 59.686 47.826 0.00 0.00 0.00 4.02
3393 7150 1.849097 GACCGTGGATATTGTCGGAC 58.151 55.000 16.29 0.00 44.86 4.79
3442 7199 5.189934 TCTTTCCTCTTGAACTAGATTCCCC 59.810 44.000 0.00 0.00 36.36 4.81
3652 7409 2.796593 GTGCATGGCTCAAAACAAGTTC 59.203 45.455 0.00 0.00 0.00 3.01
3674 7431 8.023128 AGTTCCATAAACTTTCATCAATGTTCG 58.977 33.333 0.00 0.00 46.26 3.95
3704 7461 9.931210 AAGTTGTTTATAAAGTTCTTCTGTTCG 57.069 29.630 0.00 0.00 0.00 3.95
3779 7536 8.391106 CAGACCCACTAATAAGAAAATTCTTCG 58.609 37.037 11.46 3.19 43.72 3.79
3781 7538 9.110502 GACCCACTAATAAGAAAATTCTTCGAT 57.889 33.333 11.46 0.00 43.72 3.59
3811 7568 9.742144 TGATACTGTTTATTTAGCCCTTTACAA 57.258 29.630 0.00 0.00 0.00 2.41
3848 7605 2.550830 TCACTCCTTCCAGCAAAGTC 57.449 50.000 0.00 0.00 0.00 3.01
3868 7625 8.872845 CAAAGTCCACTAATTTAATGAAATGGC 58.127 33.333 0.00 0.00 35.38 4.40
3991 7748 4.646492 ACTCTGTTTTGGCTGAGTCAAAAT 59.354 37.500 25.33 8.65 46.31 1.82
4058 7816 7.397192 TGCCCTAATTTTAAAGCTCTCTCATTT 59.603 33.333 0.00 0.00 0.00 2.32
4141 7899 5.142061 TCAATCGACAACAACTAGCCTAA 57.858 39.130 0.00 0.00 0.00 2.69
4142 7900 5.730550 TCAATCGACAACAACTAGCCTAAT 58.269 37.500 0.00 0.00 0.00 1.73
4161 7919 3.515071 ATAAAACGTATCATTCCGCGC 57.485 42.857 0.00 0.00 0.00 6.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.604604 TTCCAGCCGAACTTTGGAAG 58.395 50.000 0.00 0.00 43.94 3.46
1 2 2.060050 TTTCCAGCCGAACTTTGGAA 57.940 45.000 0.00 1.27 46.33 3.53
34 36 8.621532 TGATGTAGCACAAGAAAGAAATTACT 57.378 30.769 0.00 0.00 0.00 2.24
118 127 7.033791 CGCTAAAATCTTAGTGGAGTAGTCAA 58.966 38.462 0.00 0.00 40.51 3.18
125 134 5.012328 AGGTCGCTAAAATCTTAGTGGAG 57.988 43.478 0.00 0.00 43.17 3.86
142 158 5.998553 TGAGCTCGTCTTTATATTAGGTCG 58.001 41.667 9.64 0.00 34.94 4.79
147 163 6.600350 CGTAGCTGAGCTCGTCTTTATATTA 58.400 40.000 11.68 0.00 40.44 0.98
179 195 2.123726 GGCCGGCCCAAGATCATT 60.124 61.111 36.64 0.00 0.00 2.57
251 267 4.767255 CAGTCGCCCCAGCAGTCC 62.767 72.222 0.00 0.00 39.83 3.85
326 385 3.374367 CAGCTCTGTCTCATTGTTCCATG 59.626 47.826 0.00 0.00 0.00 3.66
328 387 2.634453 TCAGCTCTGTCTCATTGTTCCA 59.366 45.455 0.00 0.00 0.00 3.53
358 417 4.680237 TCCTTGGTGACGCAGCCG 62.680 66.667 6.58 0.00 41.14 5.52
359 418 2.281484 TTCCTTGGTGACGCAGCC 60.281 61.111 6.58 0.00 0.00 4.85
360 419 0.884704 TTCTTCCTTGGTGACGCAGC 60.885 55.000 2.68 2.68 0.00 5.25
361 420 1.466167 CATTCTTCCTTGGTGACGCAG 59.534 52.381 0.00 0.00 0.00 5.18
362 421 1.071542 TCATTCTTCCTTGGTGACGCA 59.928 47.619 0.00 0.00 0.00 5.24
363 422 1.734465 CTCATTCTTCCTTGGTGACGC 59.266 52.381 0.00 0.00 0.00 5.19
364 423 2.996621 GTCTCATTCTTCCTTGGTGACG 59.003 50.000 0.00 0.00 0.00 4.35
365 424 4.008074 TGTCTCATTCTTCCTTGGTGAC 57.992 45.455 0.00 0.00 0.00 3.67
366 425 4.645535 CTTGTCTCATTCTTCCTTGGTGA 58.354 43.478 0.00 0.00 0.00 4.02
367 426 3.190118 GCTTGTCTCATTCTTCCTTGGTG 59.810 47.826 0.00 0.00 0.00 4.17
368 427 3.416156 GCTTGTCTCATTCTTCCTTGGT 58.584 45.455 0.00 0.00 0.00 3.67
369 428 2.417933 CGCTTGTCTCATTCTTCCTTGG 59.582 50.000 0.00 0.00 0.00 3.61
370 429 3.329386 TCGCTTGTCTCATTCTTCCTTG 58.671 45.455 0.00 0.00 0.00 3.61
371 430 3.685139 TCGCTTGTCTCATTCTTCCTT 57.315 42.857 0.00 0.00 0.00 3.36
372 431 3.594134 CTTCGCTTGTCTCATTCTTCCT 58.406 45.455 0.00 0.00 0.00 3.36
373 432 2.675348 CCTTCGCTTGTCTCATTCTTCC 59.325 50.000 0.00 0.00 0.00 3.46
374 433 2.675348 CCCTTCGCTTGTCTCATTCTTC 59.325 50.000 0.00 0.00 0.00 2.87
375 434 2.704572 CCCTTCGCTTGTCTCATTCTT 58.295 47.619 0.00 0.00 0.00 2.52
376 435 1.677217 GCCCTTCGCTTGTCTCATTCT 60.677 52.381 0.00 0.00 0.00 2.40
377 436 0.729690 GCCCTTCGCTTGTCTCATTC 59.270 55.000 0.00 0.00 0.00 2.67
378 437 0.036732 TGCCCTTCGCTTGTCTCATT 59.963 50.000 0.00 0.00 38.78 2.57
379 438 0.392193 CTGCCCTTCGCTTGTCTCAT 60.392 55.000 0.00 0.00 38.78 2.90
380 439 1.004560 CTGCCCTTCGCTTGTCTCA 60.005 57.895 0.00 0.00 38.78 3.27
381 440 2.394563 GCTGCCCTTCGCTTGTCTC 61.395 63.158 0.00 0.00 38.78 3.36
382 441 2.359230 GCTGCCCTTCGCTTGTCT 60.359 61.111 0.00 0.00 38.78 3.41
383 442 3.435186 GGCTGCCCTTCGCTTGTC 61.435 66.667 7.66 0.00 38.78 3.18
433 492 2.846206 AGCCCCATATCAGAACTGTTCA 59.154 45.455 21.50 3.25 0.00 3.18
484 543 7.875971 AGATTTGTCCTTTCTTGTGATGTTAC 58.124 34.615 0.00 0.00 0.00 2.50
552 611 4.574828 CCAACGGTCATTATTGTTCCCTAG 59.425 45.833 0.00 0.00 0.00 3.02
559 618 6.152661 ACAATTGATCCAACGGTCATTATTGT 59.847 34.615 13.59 0.00 33.91 2.71
571 630 7.936847 TGATGGGTAGTATACAATTGATCCAAC 59.063 37.037 13.59 3.93 45.43 3.77
636 695 2.215942 AGCAAAGCCGGTCCTAAAAT 57.784 45.000 1.90 0.00 0.00 1.82
637 696 2.224572 TGTAGCAAAGCCGGTCCTAAAA 60.225 45.455 1.90 0.00 0.00 1.52
638 697 1.348366 TGTAGCAAAGCCGGTCCTAAA 59.652 47.619 1.90 0.00 0.00 1.85
639 698 0.978151 TGTAGCAAAGCCGGTCCTAA 59.022 50.000 1.90 0.00 0.00 2.69
640 699 0.248289 GTGTAGCAAAGCCGGTCCTA 59.752 55.000 1.90 0.00 0.00 2.94
641 700 1.003718 GTGTAGCAAAGCCGGTCCT 60.004 57.895 1.90 0.00 0.00 3.85
642 701 2.388232 CGTGTAGCAAAGCCGGTCC 61.388 63.158 1.90 0.00 0.00 4.46
643 702 0.388907 TACGTGTAGCAAAGCCGGTC 60.389 55.000 1.90 0.00 0.00 4.79
644 703 0.668401 GTACGTGTAGCAAAGCCGGT 60.668 55.000 1.90 0.00 0.00 5.28
645 704 0.668096 TGTACGTGTAGCAAAGCCGG 60.668 55.000 0.00 0.00 0.00 6.13
646 705 1.126113 CTTGTACGTGTAGCAAAGCCG 59.874 52.381 0.00 0.00 0.00 5.52
647 706 2.409975 TCTTGTACGTGTAGCAAAGCC 58.590 47.619 0.00 0.00 0.00 4.35
648 707 3.432252 ACATCTTGTACGTGTAGCAAAGC 59.568 43.478 0.00 0.00 0.00 3.51
649 708 5.591643 AACATCTTGTACGTGTAGCAAAG 57.408 39.130 0.00 0.00 0.00 2.77
650 709 5.636121 CCTAACATCTTGTACGTGTAGCAAA 59.364 40.000 0.00 0.00 0.00 3.68
651 710 5.165676 CCTAACATCTTGTACGTGTAGCAA 58.834 41.667 0.00 0.00 0.00 3.91
652 711 4.381185 CCCTAACATCTTGTACGTGTAGCA 60.381 45.833 0.00 0.00 0.00 3.49
653 712 4.110482 CCCTAACATCTTGTACGTGTAGC 58.890 47.826 0.00 0.00 0.00 3.58
654 713 5.450137 CCTCCCTAACATCTTGTACGTGTAG 60.450 48.000 0.00 0.00 0.00 2.74
655 714 4.400251 CCTCCCTAACATCTTGTACGTGTA 59.600 45.833 0.00 0.00 0.00 2.90
656 715 3.194968 CCTCCCTAACATCTTGTACGTGT 59.805 47.826 0.00 0.00 0.00 4.49
657 716 3.446161 TCCTCCCTAACATCTTGTACGTG 59.554 47.826 0.00 0.00 0.00 4.49
658 717 3.700038 CTCCTCCCTAACATCTTGTACGT 59.300 47.826 0.00 0.00 0.00 3.57
659 718 3.952323 TCTCCTCCCTAACATCTTGTACG 59.048 47.826 0.00 0.00 0.00 3.67
660 719 5.657302 TCTTCTCCTCCCTAACATCTTGTAC 59.343 44.000 0.00 0.00 0.00 2.90
661 720 5.838955 TCTTCTCCTCCCTAACATCTTGTA 58.161 41.667 0.00 0.00 0.00 2.41
662 721 4.689062 TCTTCTCCTCCCTAACATCTTGT 58.311 43.478 0.00 0.00 0.00 3.16
663 722 5.885449 ATCTTCTCCTCCCTAACATCTTG 57.115 43.478 0.00 0.00 0.00 3.02
664 723 6.903534 TGTAATCTTCTCCTCCCTAACATCTT 59.096 38.462 0.00 0.00 0.00 2.40
665 724 6.444704 TGTAATCTTCTCCTCCCTAACATCT 58.555 40.000 0.00 0.00 0.00 2.90
666 725 6.239458 CCTGTAATCTTCTCCTCCCTAACATC 60.239 46.154 0.00 0.00 0.00 3.06
667 726 5.604650 CCTGTAATCTTCTCCTCCCTAACAT 59.395 44.000 0.00 0.00 0.00 2.71
668 727 4.962995 CCTGTAATCTTCTCCTCCCTAACA 59.037 45.833 0.00 0.00 0.00 2.41
669 728 4.345547 CCCTGTAATCTTCTCCTCCCTAAC 59.654 50.000 0.00 0.00 0.00 2.34
670 729 4.015541 ACCCTGTAATCTTCTCCTCCCTAA 60.016 45.833 0.00 0.00 0.00 2.69
671 730 3.536434 ACCCTGTAATCTTCTCCTCCCTA 59.464 47.826 0.00 0.00 0.00 3.53
672 731 2.319438 ACCCTGTAATCTTCTCCTCCCT 59.681 50.000 0.00 0.00 0.00 4.20
673 732 2.436173 CACCCTGTAATCTTCTCCTCCC 59.564 54.545 0.00 0.00 0.00 4.30
674 733 3.375699 TCACCCTGTAATCTTCTCCTCC 58.624 50.000 0.00 0.00 0.00 4.30
675 734 6.268847 ACATATCACCCTGTAATCTTCTCCTC 59.731 42.308 0.00 0.00 0.00 3.71
676 735 6.146760 ACATATCACCCTGTAATCTTCTCCT 58.853 40.000 0.00 0.00 0.00 3.69
677 736 6.426646 ACATATCACCCTGTAATCTTCTCC 57.573 41.667 0.00 0.00 0.00 3.71
678 737 8.738645 AAAACATATCACCCTGTAATCTTCTC 57.261 34.615 0.00 0.00 0.00 2.87
685 744 9.315363 ACCAATTAAAAACATATCACCCTGTAA 57.685 29.630 0.00 0.00 0.00 2.41
686 745 8.744652 CACCAATTAAAAACATATCACCCTGTA 58.255 33.333 0.00 0.00 0.00 2.74
687 746 7.453126 TCACCAATTAAAAACATATCACCCTGT 59.547 33.333 0.00 0.00 0.00 4.00
688 747 7.835822 TCACCAATTAAAAACATATCACCCTG 58.164 34.615 0.00 0.00 0.00 4.45
689 748 8.608185 ATCACCAATTAAAAACATATCACCCT 57.392 30.769 0.00 0.00 0.00 4.34
695 754 9.533253 GCTGCTAATCACCAATTAAAAACATAT 57.467 29.630 0.00 0.00 29.44 1.78
696 755 7.700234 CGCTGCTAATCACCAATTAAAAACATA 59.300 33.333 0.00 0.00 29.44 2.29
697 756 6.531240 CGCTGCTAATCACCAATTAAAAACAT 59.469 34.615 0.00 0.00 29.44 2.71
698 757 5.861251 CGCTGCTAATCACCAATTAAAAACA 59.139 36.000 0.00 0.00 29.44 2.83
699 758 5.288472 CCGCTGCTAATCACCAATTAAAAAC 59.712 40.000 0.00 0.00 29.44 2.43
700 759 5.406649 CCGCTGCTAATCACCAATTAAAAA 58.593 37.500 0.00 0.00 29.44 1.94
701 760 4.676723 GCCGCTGCTAATCACCAATTAAAA 60.677 41.667 0.00 0.00 29.44 1.52
702 761 3.181491 GCCGCTGCTAATCACCAATTAAA 60.181 43.478 0.00 0.00 29.44 1.52
703 762 2.357637 GCCGCTGCTAATCACCAATTAA 59.642 45.455 0.00 0.00 29.44 1.40
704 763 1.946768 GCCGCTGCTAATCACCAATTA 59.053 47.619 0.00 0.00 33.53 1.40
705 764 0.740737 GCCGCTGCTAATCACCAATT 59.259 50.000 0.00 0.00 33.53 2.32
706 765 0.394216 TGCCGCTGCTAATCACCAAT 60.394 50.000 0.70 0.00 38.71 3.16
707 766 1.002746 TGCCGCTGCTAATCACCAA 60.003 52.632 0.70 0.00 38.71 3.67
708 767 1.745115 GTGCCGCTGCTAATCACCA 60.745 57.895 0.70 0.00 38.71 4.17
709 768 2.813179 CGTGCCGCTGCTAATCACC 61.813 63.158 0.70 0.00 38.71 4.02
710 769 2.703409 CGTGCCGCTGCTAATCAC 59.297 61.111 0.70 0.00 38.71 3.06
711 770 2.511373 CCGTGCCGCTGCTAATCA 60.511 61.111 0.70 0.00 38.71 2.57
712 771 2.202878 TCCGTGCCGCTGCTAATC 60.203 61.111 0.70 0.00 38.71 1.75
713 772 2.511600 GTCCGTGCCGCTGCTAAT 60.512 61.111 0.70 0.00 38.71 1.73
714 773 4.752879 GGTCCGTGCCGCTGCTAA 62.753 66.667 0.70 0.00 38.71 3.09
723 782 4.360405 AATGGGGTGGGTCCGTGC 62.360 66.667 0.00 0.00 37.00 5.34
724 783 2.045340 GAATGGGGTGGGTCCGTG 60.045 66.667 0.00 0.00 37.00 4.94
725 784 1.721093 TTTGAATGGGGTGGGTCCGT 61.721 55.000 0.00 0.00 37.00 4.69
726 785 0.324275 ATTTGAATGGGGTGGGTCCG 60.324 55.000 0.00 0.00 37.00 4.79
727 786 1.272985 TGATTTGAATGGGGTGGGTCC 60.273 52.381 0.00 0.00 0.00 4.46
728 787 2.102578 CTGATTTGAATGGGGTGGGTC 58.897 52.381 0.00 0.00 0.00 4.46
729 788 1.273211 CCTGATTTGAATGGGGTGGGT 60.273 52.381 0.00 0.00 0.00 4.51
730 789 1.006998 TCCTGATTTGAATGGGGTGGG 59.993 52.381 0.00 0.00 0.00 4.61
731 790 2.381911 CTCCTGATTTGAATGGGGTGG 58.618 52.381 0.00 0.00 0.00 4.61
732 791 2.025037 TCCTCCTGATTTGAATGGGGTG 60.025 50.000 0.00 0.00 0.00 4.61
733 792 2.024941 GTCCTCCTGATTTGAATGGGGT 60.025 50.000 0.00 0.00 0.00 4.95
734 793 2.659428 GTCCTCCTGATTTGAATGGGG 58.341 52.381 0.00 0.00 0.00 4.96
735 794 2.292267 CGTCCTCCTGATTTGAATGGG 58.708 52.381 0.00 0.00 0.00 4.00
736 795 2.991250 ACGTCCTCCTGATTTGAATGG 58.009 47.619 0.00 0.00 0.00 3.16
737 796 5.874810 TCTAAACGTCCTCCTGATTTGAATG 59.125 40.000 0.00 0.00 0.00 2.67
738 797 6.049955 TCTAAACGTCCTCCTGATTTGAAT 57.950 37.500 0.00 0.00 0.00 2.57
739 798 5.477607 TCTAAACGTCCTCCTGATTTGAA 57.522 39.130 0.00 0.00 0.00 2.69
740 799 5.477607 TTCTAAACGTCCTCCTGATTTGA 57.522 39.130 0.00 0.00 0.00 2.69
741 800 5.701290 ACTTTCTAAACGTCCTCCTGATTTG 59.299 40.000 0.00 0.00 0.00 2.32
742 801 5.866207 ACTTTCTAAACGTCCTCCTGATTT 58.134 37.500 0.00 0.00 0.00 2.17
743 802 5.485209 ACTTTCTAAACGTCCTCCTGATT 57.515 39.130 0.00 0.00 0.00 2.57
744 803 5.485209 AACTTTCTAAACGTCCTCCTGAT 57.515 39.130 0.00 0.00 0.00 2.90
745 804 4.950205 AACTTTCTAAACGTCCTCCTGA 57.050 40.909 0.00 0.00 0.00 3.86
746 805 5.054477 TCAAACTTTCTAAACGTCCTCCTG 58.946 41.667 0.00 0.00 0.00 3.86
747 806 5.286267 TCAAACTTTCTAAACGTCCTCCT 57.714 39.130 0.00 0.00 0.00 3.69
748 807 5.996669 TTCAAACTTTCTAAACGTCCTCC 57.003 39.130 0.00 0.00 0.00 4.30
749 808 6.259387 TCCTTTCAAACTTTCTAAACGTCCTC 59.741 38.462 0.00 0.00 0.00 3.71
750 809 6.117488 TCCTTTCAAACTTTCTAAACGTCCT 58.883 36.000 0.00 0.00 0.00 3.85
751 810 6.367686 TCCTTTCAAACTTTCTAAACGTCC 57.632 37.500 0.00 0.00 0.00 4.79
752 811 5.907945 GCTCCTTTCAAACTTTCTAAACGTC 59.092 40.000 0.00 0.00 0.00 4.34
753 812 5.220989 GGCTCCTTTCAAACTTTCTAAACGT 60.221 40.000 0.00 0.00 0.00 3.99
754 813 5.008712 AGGCTCCTTTCAAACTTTCTAAACG 59.991 40.000 0.00 0.00 0.00 3.60
755 814 6.183360 ACAGGCTCCTTTCAAACTTTCTAAAC 60.183 38.462 0.00 0.00 0.00 2.01
756 815 5.891551 ACAGGCTCCTTTCAAACTTTCTAAA 59.108 36.000 0.00 0.00 0.00 1.85
757 816 5.445964 ACAGGCTCCTTTCAAACTTTCTAA 58.554 37.500 0.00 0.00 0.00 2.10
758 817 5.048846 ACAGGCTCCTTTCAAACTTTCTA 57.951 39.130 0.00 0.00 0.00 2.10
759 818 3.903467 ACAGGCTCCTTTCAAACTTTCT 58.097 40.909 0.00 0.00 0.00 2.52
760 819 5.063880 TCTACAGGCTCCTTTCAAACTTTC 58.936 41.667 0.00 0.00 0.00 2.62
761 820 5.048846 TCTACAGGCTCCTTTCAAACTTT 57.951 39.130 0.00 0.00 0.00 2.66
762 821 4.706842 TCTACAGGCTCCTTTCAAACTT 57.293 40.909 0.00 0.00 0.00 2.66
763 822 4.103311 AGTTCTACAGGCTCCTTTCAAACT 59.897 41.667 0.00 0.00 0.00 2.66
764 823 4.390264 AGTTCTACAGGCTCCTTTCAAAC 58.610 43.478 0.00 0.00 0.00 2.93
765 824 4.706842 AGTTCTACAGGCTCCTTTCAAA 57.293 40.909 0.00 0.00 0.00 2.69
766 825 4.348168 AGAAGTTCTACAGGCTCCTTTCAA 59.652 41.667 2.75 0.00 0.00 2.69
767 826 3.904339 AGAAGTTCTACAGGCTCCTTTCA 59.096 43.478 2.75 0.00 0.00 2.69
768 827 4.249661 CAGAAGTTCTACAGGCTCCTTTC 58.750 47.826 4.74 0.00 0.00 2.62
769 828 3.648545 ACAGAAGTTCTACAGGCTCCTTT 59.351 43.478 4.74 0.00 0.00 3.11
770 829 3.243724 ACAGAAGTTCTACAGGCTCCTT 58.756 45.455 4.74 0.00 0.00 3.36
771 830 2.896039 ACAGAAGTTCTACAGGCTCCT 58.104 47.619 4.74 0.00 0.00 3.69
772 831 4.803098 TTACAGAAGTTCTACAGGCTCC 57.197 45.455 4.74 0.00 0.00 4.70
773 832 6.224584 ACTTTTACAGAAGTTCTACAGGCTC 58.775 40.000 4.74 0.00 36.49 4.70
774 833 6.042208 AGACTTTTACAGAAGTTCTACAGGCT 59.958 38.462 4.74 0.00 39.84 4.58
775 834 6.146347 CAGACTTTTACAGAAGTTCTACAGGC 59.854 42.308 4.74 0.00 39.84 4.85
776 835 7.210873 ACAGACTTTTACAGAAGTTCTACAGG 58.789 38.462 4.74 0.00 39.84 4.00
777 836 9.182933 GTACAGACTTTTACAGAAGTTCTACAG 57.817 37.037 4.74 0.00 39.84 2.74
778 837 7.859377 CGTACAGACTTTTACAGAAGTTCTACA 59.141 37.037 4.74 0.00 39.84 2.74
779 838 7.859875 ACGTACAGACTTTTACAGAAGTTCTAC 59.140 37.037 4.74 0.00 39.84 2.59
780 839 7.934457 ACGTACAGACTTTTACAGAAGTTCTA 58.066 34.615 4.74 0.00 39.84 2.10
781 840 6.803642 ACGTACAGACTTTTACAGAAGTTCT 58.196 36.000 0.00 0.00 39.84 3.01
782 841 6.916932 AGACGTACAGACTTTTACAGAAGTTC 59.083 38.462 0.00 0.00 39.84 3.01
783 842 6.803642 AGACGTACAGACTTTTACAGAAGTT 58.196 36.000 0.00 0.00 39.84 2.66
784 843 6.388435 AGACGTACAGACTTTTACAGAAGT 57.612 37.500 0.00 0.00 42.31 3.01
785 844 6.523893 GCTAGACGTACAGACTTTTACAGAAG 59.476 42.308 0.00 0.00 0.00 2.85
786 845 6.016860 TGCTAGACGTACAGACTTTTACAGAA 60.017 38.462 0.00 0.00 0.00 3.02
787 846 5.471116 TGCTAGACGTACAGACTTTTACAGA 59.529 40.000 0.00 0.00 0.00 3.41
788 847 5.696822 TGCTAGACGTACAGACTTTTACAG 58.303 41.667 0.00 0.00 0.00 2.74
789 848 5.694231 TGCTAGACGTACAGACTTTTACA 57.306 39.130 0.00 0.00 0.00 2.41
790 849 7.578169 AAATGCTAGACGTACAGACTTTTAC 57.422 36.000 0.00 0.00 0.00 2.01
791 850 8.492748 CAAAAATGCTAGACGTACAGACTTTTA 58.507 33.333 0.00 0.00 0.00 1.52
792 851 7.012044 ACAAAAATGCTAGACGTACAGACTTTT 59.988 33.333 0.00 0.00 0.00 2.27
793 852 6.482308 ACAAAAATGCTAGACGTACAGACTTT 59.518 34.615 0.00 0.00 0.00 2.66
794 853 5.989777 ACAAAAATGCTAGACGTACAGACTT 59.010 36.000 0.00 0.00 0.00 3.01
795 854 5.539048 ACAAAAATGCTAGACGTACAGACT 58.461 37.500 0.00 0.00 0.00 3.24
796 855 5.840940 ACAAAAATGCTAGACGTACAGAC 57.159 39.130 0.00 0.00 0.00 3.51
797 856 6.854496 AAACAAAAATGCTAGACGTACAGA 57.146 33.333 0.00 0.00 0.00 3.41
798 857 7.744715 CCTAAAACAAAAATGCTAGACGTACAG 59.255 37.037 0.00 0.00 0.00 2.74
799 858 7.441760 TCCTAAAACAAAAATGCTAGACGTACA 59.558 33.333 0.00 0.00 0.00 2.90
800 859 7.743400 GTCCTAAAACAAAAATGCTAGACGTAC 59.257 37.037 0.00 0.00 0.00 3.67
801 860 7.359431 CGTCCTAAAACAAAAATGCTAGACGTA 60.359 37.037 0.00 0.00 0.00 3.57
802 861 6.565247 CGTCCTAAAACAAAAATGCTAGACGT 60.565 38.462 0.00 0.00 0.00 4.34
803 862 5.788531 CGTCCTAAAACAAAAATGCTAGACG 59.211 40.000 0.00 0.00 0.00 4.18
804 863 6.072893 TCCGTCCTAAAACAAAAATGCTAGAC 60.073 38.462 0.00 0.00 0.00 2.59
805 864 5.998981 TCCGTCCTAAAACAAAAATGCTAGA 59.001 36.000 0.00 0.00 0.00 2.43
806 865 6.249035 TCCGTCCTAAAACAAAAATGCTAG 57.751 37.500 0.00 0.00 0.00 3.42
807 866 5.182380 CCTCCGTCCTAAAACAAAAATGCTA 59.818 40.000 0.00 0.00 0.00 3.49
808 867 4.022329 CCTCCGTCCTAAAACAAAAATGCT 60.022 41.667 0.00 0.00 0.00 3.79
809 868 4.234574 CCTCCGTCCTAAAACAAAAATGC 58.765 43.478 0.00 0.00 0.00 3.56
810 869 5.447624 ACCTCCGTCCTAAAACAAAAATG 57.552 39.130 0.00 0.00 0.00 2.32
811 870 7.770366 ATTACCTCCGTCCTAAAACAAAAAT 57.230 32.000 0.00 0.00 0.00 1.82
812 871 8.866970 ATATTACCTCCGTCCTAAAACAAAAA 57.133 30.769 0.00 0.00 0.00 1.94
813 872 9.603921 CTATATTACCTCCGTCCTAAAACAAAA 57.396 33.333 0.00 0.00 0.00 2.44
814 873 8.761689 ACTATATTACCTCCGTCCTAAAACAAA 58.238 33.333 0.00 0.00 0.00 2.83
815 874 8.310122 ACTATATTACCTCCGTCCTAAAACAA 57.690 34.615 0.00 0.00 0.00 2.83
816 875 7.902920 ACTATATTACCTCCGTCCTAAAACA 57.097 36.000 0.00 0.00 0.00 2.83
817 876 9.072375 ACTACTATATTACCTCCGTCCTAAAAC 57.928 37.037 0.00 0.00 0.00 2.43
850 909 5.343593 CACTACTACTCACTCGCAGAAAAAG 59.656 44.000 0.00 0.00 34.09 2.27
891 1353 7.272978 CGGGATGGGATTCGATTTATTAGTAT 58.727 38.462 0.00 0.00 0.00 2.12
894 1356 4.876107 CCGGGATGGGATTCGATTTATTAG 59.124 45.833 0.00 0.00 0.00 1.73
916 1378 2.700773 GGACATTTCACGCCTGCCC 61.701 63.158 0.00 0.00 0.00 5.36
1174 1661 4.500116 GGTCGTCAGCTCGAGGGC 62.500 72.222 15.58 0.66 40.52 5.19
1643 2162 0.807496 GAGATCAACTGCCAGCAACC 59.193 55.000 0.00 0.00 0.00 3.77
1890 2437 5.340439 ACAGCAGGGTTACTACTAACATC 57.660 43.478 0.00 0.00 34.88 3.06
1940 2487 0.179234 TACCATGGCCACACATACCG 59.821 55.000 8.16 0.00 0.00 4.02
2235 2809 3.244078 ACTCTGCCGACAACATCTTTACA 60.244 43.478 0.00 0.00 0.00 2.41
2307 2882 0.744414 GGTTGCGATGCTTCAGCCTA 60.744 55.000 11.70 1.43 41.18 3.93
3004 3582 2.159014 GCACGGTCCTGTACATATGGAA 60.159 50.000 7.80 0.00 0.00 3.53
3030 3608 1.883084 CCGGCCGTATGACTCAAGC 60.883 63.158 26.12 0.00 0.00 4.01
3212 6969 0.179111 CTCGGCGTGGCTATCTCAAA 60.179 55.000 6.85 0.00 0.00 2.69
3252 7009 9.719355 TCAGTACTTCAAAATAATTGTAGCTGA 57.281 29.630 0.00 0.00 0.00 4.26
3278 7035 2.184322 CGGCATCAGTGTAGCGGT 59.816 61.111 0.00 0.00 0.00 5.68
3330 7087 5.582665 AGAGAAGTTAATCCAGCGAAATCAC 59.417 40.000 0.00 0.00 0.00 3.06
3374 7131 1.135527 TGTCCGACAATATCCACGGTC 59.864 52.381 0.00 0.00 44.72 4.79
3393 7150 4.761739 AGAATACATGCAATACCCCGAATG 59.238 41.667 0.00 0.00 0.00 2.67
3504 7261 7.901029 TGCACCAATTTATTTAAAGGTCATGA 58.099 30.769 0.00 0.00 0.00 3.07
3540 7297 8.730427 GCCGTGAGAAATTTAAATACATAAACG 58.270 33.333 0.01 7.89 0.00 3.60
3553 7310 1.250840 GGGCTGGCCGTGAGAAATTT 61.251 55.000 3.84 0.00 36.85 1.82
3609 7366 5.888161 CACAGTCTAATTTTATCTGGGGCTT 59.112 40.000 0.00 0.00 0.00 4.35
3627 7384 1.337703 TGTTTTGAGCCATGCACAGTC 59.662 47.619 0.00 0.00 30.09 3.51
3652 7409 6.747280 GTCCGAACATTGATGAAAGTTTATGG 59.253 38.462 0.00 0.00 0.00 2.74
3665 7422 4.974368 AAACAACTTGTCCGAACATTGA 57.026 36.364 0.00 0.00 34.73 2.57
3674 7431 9.665264 CAGAAGAACTTTATAAACAACTTGTCC 57.335 33.333 0.00 0.00 0.00 4.02
3779 7536 7.939588 AGGGCTAAATAAACAGTATCAGGAATC 59.060 37.037 0.00 0.00 0.00 2.52
3781 7538 7.208064 AGGGCTAAATAAACAGTATCAGGAA 57.792 36.000 0.00 0.00 0.00 3.36
3811 7568 7.840931 AGGAGTGAAGAACTTTTCATTTTTGT 58.159 30.769 0.00 0.00 40.07 2.83
3821 7578 3.117888 TGCTGGAAGGAGTGAAGAACTTT 60.118 43.478 0.00 0.00 40.07 2.66
3930 7687 2.995939 TCAACTGAATGTGATGTCTCGC 59.004 45.455 0.00 0.00 0.00 5.03
4077 7835 5.920273 CCAGTCAAAATGTGTACCAATTCAC 59.080 40.000 0.00 0.00 35.43 3.18
4141 7899 2.867368 TGCGCGGAATGATACGTTTTAT 59.133 40.909 8.83 0.00 0.00 1.40
4142 7900 2.029486 GTGCGCGGAATGATACGTTTTA 59.971 45.455 8.83 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.