Multiple sequence alignment - TraesCS1A01G188600

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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 TraesCS1A01G188600 chr1A 100.000 4433 0 0 1 4433 340429701 340425269 0.000000e+00 8187.0
1 TraesCS1A01G188600 chr1D 92.625 1505 59 21 948 2442 260313231 260314693 0.000000e+00 2117.0
2 TraesCS1A01G188600 chr1D 91.940 1191 84 8 2540 3728 260316710 260317890 0.000000e+00 1657.0
3 TraesCS1A01G188600 chr1D 88.852 601 37 14 43 628 260289456 260290041 0.000000e+00 712.0
4 TraesCS1A01G188600 chr1D 82.244 704 108 14 3728 4424 56978948 56978255 3.820000e-165 592.0
5 TraesCS1A01G188600 chr1D 97.143 35 1 0 10 44 354536525 354536559 4.790000e-05 60.2
6 TraesCS1A01G188600 chr1D 97.059 34 1 0 895 928 260313202 260313235 1.720000e-04 58.4
7 TraesCS1A01G188600 chr1B 90.612 1406 109 15 2334 3728 352890028 352888635 0.000000e+00 1844.0
8 TraesCS1A01G188600 chr1B 91.057 1107 62 15 1248 2329 352891273 352890179 0.000000e+00 1461.0
9 TraesCS1A01G188600 chr1B 93.566 373 12 4 813 1185 352891991 352891631 3.020000e-151 545.0
10 TraesCS1A01G188600 chr1B 83.568 426 42 16 239 651 352892935 352892525 1.510000e-99 374.0
11 TraesCS1A01G188600 chr1B 96.117 103 4 0 651 753 633728070 633728172 7.630000e-38 169.0
12 TraesCS1A01G188600 chr1B 85.890 163 11 8 50 209 352893072 352892919 3.550000e-36 163.0
13 TraesCS1A01G188600 chr1B 92.537 67 4 1 751 816 352892527 352892461 1.310000e-15 95.3
14 TraesCS1A01G188600 chr7A 98.159 706 11 2 3729 4433 353610424 353609720 0.000000e+00 1230.0
15 TraesCS1A01G188600 chr7A 91.261 698 55 5 3729 4425 25377585 25378277 0.000000e+00 946.0
16 TraesCS1A01G188600 chr7A 87.135 171 15 6 3730 3899 537849364 537849200 2.110000e-43 187.0
17 TraesCS1A01G188600 chr4A 97.592 706 16 1 3729 4433 332330581 332331286 0.000000e+00 1208.0
18 TraesCS1A01G188600 chr4A 90.857 700 56 7 3728 4425 637673912 637673219 0.000000e+00 931.0
19 TraesCS1A01G188600 chr5A 89.407 708 63 9 3729 4431 515526988 515527688 0.000000e+00 881.0
20 TraesCS1A01G188600 chr5A 97.087 103 3 0 651 753 442271173 442271071 1.640000e-39 174.0
21 TraesCS1A01G188600 chr5A 97.143 35 1 0 10 44 236626152 236626186 4.790000e-05 60.2
22 TraesCS1A01G188600 chr5A 97.143 35 1 0 10 44 246444678 246444644 4.790000e-05 60.2
23 TraesCS1A01G188600 chr6B 84.777 716 90 15 3728 4431 152317117 152316409 0.000000e+00 701.0
24 TraesCS1A01G188600 chr5B 83.310 713 95 17 3730 4431 251007274 251007973 1.740000e-178 636.0
25 TraesCS1A01G188600 chr5B 97.143 35 1 0 10 44 77934056 77934090 4.790000e-05 60.2
26 TraesCS1A01G188600 chr2D 81.831 710 106 19 3729 4427 552955542 552954845 3.850000e-160 575.0
27 TraesCS1A01G188600 chr2D 98.058 103 2 0 651 753 33934610 33934508 3.520000e-41 180.0
28 TraesCS1A01G188600 chr2D 98.058 103 2 0 651 753 272800864 272800966 3.520000e-41 180.0
29 TraesCS1A01G188600 chr2D 98.058 103 2 0 651 753 630271087 630270985 3.520000e-41 180.0
30 TraesCS1A01G188600 chr2D 97.143 35 1 0 10 44 113428261 113428295 4.790000e-05 60.2
31 TraesCS1A01G188600 chr2D 97.143 35 1 0 10 44 379191509 379191475 4.790000e-05 60.2
32 TraesCS1A01G188600 chr4B 80.111 719 131 11 3721 4433 289830646 289831358 3.930000e-145 525.0
33 TraesCS1A01G188600 chr4B 97.143 35 1 0 10 44 456476489 456476523 4.790000e-05 60.2
34 TraesCS1A01G188600 chr3B 79.473 721 130 14 3729 4433 699714159 699714877 3.080000e-136 496.0
35 TraesCS1A01G188600 chr2A 86.239 218 24 6 3729 3945 371111167 371110955 9.590000e-57 231.0
36 TraesCS1A01G188600 chrUn 98.058 103 2 0 651 753 327662510 327662612 3.520000e-41 180.0
37 TraesCS1A01G188600 chr4D 98.058 103 2 0 651 753 245649477 245649375 3.520000e-41 180.0
38 TraesCS1A01G188600 chr3A 97.087 103 3 0 651 753 672877638 672877740 1.640000e-39 174.0
39 TraesCS1A01G188600 chr6D 96.117 103 4 0 651 753 202698370 202698268 7.630000e-38 169.0
40 TraesCS1A01G188600 chr6D 97.143 35 1 0 10 44 351687464 351687430 4.790000e-05 60.2
41 TraesCS1A01G188600 chr2B 91.111 45 3 1 1 44 666783104 666783060 4.790000e-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 TraesCS1A01G188600 chr1A 340425269 340429701 4432 True 8187.000000 8187 100.000000 1 4433 1 chr1A.!!$R1 4432
1 TraesCS1A01G188600 chr1D 260313202 260317890 4688 False 1277.466667 2117 93.874667 895 3728 3 chr1D.!!$F3 2833
2 TraesCS1A01G188600 chr1D 260289456 260290041 585 False 712.000000 712 88.852000 43 628 1 chr1D.!!$F1 585
3 TraesCS1A01G188600 chr1D 56978255 56978948 693 True 592.000000 592 82.244000 3728 4424 1 chr1D.!!$R1 696
4 TraesCS1A01G188600 chr1B 352888635 352893072 4437 True 747.050000 1844 89.538333 50 3728 6 chr1B.!!$R1 3678
5 TraesCS1A01G188600 chr7A 353609720 353610424 704 True 1230.000000 1230 98.159000 3729 4433 1 chr7A.!!$R1 704
6 TraesCS1A01G188600 chr7A 25377585 25378277 692 False 946.000000 946 91.261000 3729 4425 1 chr7A.!!$F1 696
7 TraesCS1A01G188600 chr4A 332330581 332331286 705 False 1208.000000 1208 97.592000 3729 4433 1 chr4A.!!$F1 704
8 TraesCS1A01G188600 chr4A 637673219 637673912 693 True 931.000000 931 90.857000 3728 4425 1 chr4A.!!$R1 697
9 TraesCS1A01G188600 chr5A 515526988 515527688 700 False 881.000000 881 89.407000 3729 4431 1 chr5A.!!$F2 702
10 TraesCS1A01G188600 chr6B 152316409 152317117 708 True 701.000000 701 84.777000 3728 4431 1 chr6B.!!$R1 703
11 TraesCS1A01G188600 chr5B 251007274 251007973 699 False 636.000000 636 83.310000 3730 4431 1 chr5B.!!$F2 701
12 TraesCS1A01G188600 chr2D 552954845 552955542 697 True 575.000000 575 81.831000 3729 4427 1 chr2D.!!$R3 698
13 TraesCS1A01G188600 chr4B 289830646 289831358 712 False 525.000000 525 80.111000 3721 4433 1 chr4B.!!$F1 712
14 TraesCS1A01G188600 chr3B 699714159 699714877 718 False 496.000000 496 79.473000 3729 4433 1 chr3B.!!$F1 704

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
226 231 0.035317 AAGCGCATCTGTGGTTCTCA 59.965 50.0 11.47 0.0 41.73 3.27 F
840 1334 0.035820 CTAAACCCAGCGCCCTAACA 60.036 55.0 2.29 0.0 0.00 2.41 F
1869 2660 0.035439 TTGAATTCTCGGTGGGAGCC 60.035 55.0 7.05 0.0 42.82 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1590 2379 1.063469 GCGAACCCAATGTACCATTCG 59.937 52.381 0.00 0.00 41.31 3.34 R
2353 3314 2.093816 TGACTTCCTAGAGTGCATGCAG 60.094 50.000 23.41 8.94 0.00 4.41 R
3673 6555 0.179045 CCCCAGCCTTACGAATCCAG 60.179 60.000 0.00 0.00 0.00 3.86 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
24 25 7.478520 CCCAATAACGTCTACCAGAATAAAG 57.521 40.000 0.00 0.00 0.00 1.85
25 26 7.046033 CCCAATAACGTCTACCAGAATAAAGT 58.954 38.462 0.00 0.00 0.00 2.66
26 27 7.224167 CCCAATAACGTCTACCAGAATAAAGTC 59.776 40.741 0.00 0.00 0.00 3.01
27 28 7.043590 CCAATAACGTCTACCAGAATAAAGTCG 60.044 40.741 0.00 0.00 0.00 4.18
28 29 3.767278 ACGTCTACCAGAATAAAGTCGC 58.233 45.455 0.00 0.00 0.00 5.19
29 30 2.782192 CGTCTACCAGAATAAAGTCGCG 59.218 50.000 0.00 0.00 0.00 5.87
30 31 3.730061 CGTCTACCAGAATAAAGTCGCGT 60.730 47.826 5.77 0.00 0.00 6.01
31 32 4.494690 CGTCTACCAGAATAAAGTCGCGTA 60.495 45.833 5.77 0.00 0.00 4.42
32 33 4.968788 GTCTACCAGAATAAAGTCGCGTAG 59.031 45.833 5.77 0.00 0.00 3.51
33 34 3.863142 ACCAGAATAAAGTCGCGTAGT 57.137 42.857 5.77 0.00 0.00 2.73
34 35 4.970662 ACCAGAATAAAGTCGCGTAGTA 57.029 40.909 5.77 0.00 0.00 1.82
35 36 4.918037 ACCAGAATAAAGTCGCGTAGTAG 58.082 43.478 5.77 0.00 0.00 2.57
36 37 4.637534 ACCAGAATAAAGTCGCGTAGTAGA 59.362 41.667 5.77 0.00 0.00 2.59
37 38 4.968788 CCAGAATAAAGTCGCGTAGTAGAC 59.031 45.833 5.77 0.00 37.51 2.59
38 39 5.448225 CCAGAATAAAGTCGCGTAGTAGACA 60.448 44.000 5.77 0.00 39.09 3.41
39 40 6.200100 CAGAATAAAGTCGCGTAGTAGACAT 58.800 40.000 5.77 0.00 39.09 3.06
40 41 6.357503 CAGAATAAAGTCGCGTAGTAGACATC 59.642 42.308 5.77 0.00 39.09 3.06
41 42 5.746307 ATAAAGTCGCGTAGTAGACATCA 57.254 39.130 5.77 0.00 39.09 3.07
46 47 4.335874 AGTCGCGTAGTAGACATCAAGAAT 59.664 41.667 5.77 0.00 39.09 2.40
54 55 8.808529 CGTAGTAGACATCAAGAATCGAAAAAT 58.191 33.333 0.00 0.00 0.00 1.82
135 140 0.539986 ACCCAGTAGTATGGTTGCGG 59.460 55.000 0.00 0.00 38.81 5.69
140 145 3.126343 CCAGTAGTATGGTTGCGGTTTTC 59.874 47.826 0.00 0.00 35.47 2.29
161 166 7.469537 TTTCACTTTTGTTTTGGAAGGACTA 57.530 32.000 0.00 0.00 0.00 2.59
204 209 3.879892 GAGTTCAAGGTTGTGCTTCTCTT 59.120 43.478 0.00 0.00 0.00 2.85
215 220 1.466167 TGCTTCTCTTGAAAGCGCATC 59.534 47.619 11.47 8.39 32.74 3.91
220 225 1.129998 CTCTTGAAAGCGCATCTGTGG 59.870 52.381 11.47 0.00 0.00 4.17
226 231 0.035317 AAGCGCATCTGTGGTTCTCA 59.965 50.000 11.47 0.00 41.73 3.27
244 249 5.164620 TCTCATAGAAGGACATTTGTGCA 57.835 39.130 5.00 0.00 38.96 4.57
258 263 2.014335 TGTGCATCTCGTGGAATCAG 57.986 50.000 0.00 0.00 0.00 2.90
370 376 5.221067 GCTTCTCGTGGATTCACAGTCTATA 60.221 44.000 4.68 0.00 43.79 1.31
379 385 9.330063 GTGGATTCACAGTCTATATTTTCATGA 57.670 33.333 0.00 0.00 43.13 3.07
420 428 5.007234 CACCAGAAACATGTTTGTTCTCGTA 59.993 40.000 27.85 0.00 45.30 3.43
429 437 3.554324 TGTTTGTTCTCGTAGAAGCACAC 59.446 43.478 0.00 0.00 34.42 3.82
434 442 5.534407 TGTTCTCGTAGAAGCACACATTTA 58.466 37.500 0.00 0.00 34.42 1.40
438 446 8.653338 GTTCTCGTAGAAGCACACATTTATTTA 58.347 33.333 0.00 0.00 34.42 1.40
439 447 8.942338 TCTCGTAGAAGCACACATTTATTTAT 57.058 30.769 0.00 0.00 34.09 1.40
440 448 9.378551 TCTCGTAGAAGCACACATTTATTTATT 57.621 29.630 0.00 0.00 34.09 1.40
441 449 9.988350 CTCGTAGAAGCACACATTTATTTATTT 57.012 29.630 0.00 0.00 34.09 1.40
530 549 5.833406 AAACCAGGCAAAAATCCAAAAAG 57.167 34.783 0.00 0.00 0.00 2.27
561 582 7.387265 AAAACCTCATCTAAAACCCCAAAAT 57.613 32.000 0.00 0.00 0.00 1.82
568 589 8.760980 TCATCTAAAACCCCAAAATACATAGG 57.239 34.615 0.00 0.00 0.00 2.57
620 641 2.766263 TCAGAAGGAGCGTCCAACATAT 59.234 45.455 6.78 0.00 39.61 1.78
630 651 3.242413 GCGTCCAACATATGACATGTGAC 60.242 47.826 17.98 12.27 31.80 3.67
632 653 4.180817 GTCCAACATATGACATGTGACGA 58.819 43.478 17.98 7.59 31.80 4.20
633 654 4.811024 GTCCAACATATGACATGTGACGAT 59.189 41.667 17.98 0.00 31.80 3.73
636 657 3.133691 ACATATGACATGTGACGATGGC 58.866 45.455 17.98 0.00 0.00 4.40
645 666 1.005037 TGACGATGGCTGGACACAC 60.005 57.895 0.00 0.00 0.00 3.82
646 667 1.293498 GACGATGGCTGGACACACT 59.707 57.895 0.00 0.00 0.00 3.55
648 669 1.137086 GACGATGGCTGGACACACTAT 59.863 52.381 0.00 0.00 0.00 2.12
649 670 1.555075 ACGATGGCTGGACACACTATT 59.445 47.619 0.00 0.00 0.00 1.73
650 671 2.027192 ACGATGGCTGGACACACTATTT 60.027 45.455 0.00 0.00 0.00 1.40
651 672 3.009723 CGATGGCTGGACACACTATTTT 58.990 45.455 0.00 0.00 0.00 1.82
652 673 3.440173 CGATGGCTGGACACACTATTTTT 59.560 43.478 0.00 0.00 0.00 1.94
717 738 9.893305 AAGACAAAATCAAAGTTTAGTAATCGG 57.107 29.630 0.00 0.00 0.00 4.18
718 739 9.063615 AGACAAAATCAAAGTTTAGTAATCGGT 57.936 29.630 0.00 0.00 0.00 4.69
723 744 7.982371 ATCAAAGTTTAGTAATCGGTAGTCG 57.018 36.000 0.00 0.00 40.90 4.18
724 745 6.913170 TCAAAGTTTAGTAATCGGTAGTCGT 58.087 36.000 0.00 0.00 40.32 4.34
725 746 7.370383 TCAAAGTTTAGTAATCGGTAGTCGTT 58.630 34.615 0.00 0.00 40.32 3.85
726 747 7.538678 TCAAAGTTTAGTAATCGGTAGTCGTTC 59.461 37.037 0.00 0.00 40.32 3.95
727 748 6.749923 AGTTTAGTAATCGGTAGTCGTTCT 57.250 37.500 0.00 0.00 40.32 3.01
728 749 7.150783 AGTTTAGTAATCGGTAGTCGTTCTT 57.849 36.000 0.00 0.00 40.32 2.52
729 750 7.025963 AGTTTAGTAATCGGTAGTCGTTCTTG 58.974 38.462 0.00 0.00 40.32 3.02
730 751 6.741992 TTAGTAATCGGTAGTCGTTCTTGA 57.258 37.500 0.00 0.00 40.32 3.02
731 752 5.633830 AGTAATCGGTAGTCGTTCTTGAA 57.366 39.130 0.00 0.00 40.32 2.69
732 753 6.205101 AGTAATCGGTAGTCGTTCTTGAAT 57.795 37.500 0.00 0.00 40.32 2.57
733 754 6.628185 AGTAATCGGTAGTCGTTCTTGAATT 58.372 36.000 0.00 0.00 40.32 2.17
734 755 6.750963 AGTAATCGGTAGTCGTTCTTGAATTC 59.249 38.462 0.00 0.00 40.32 2.17
735 756 3.495193 TCGGTAGTCGTTCTTGAATTCG 58.505 45.455 0.04 0.00 40.32 3.34
736 757 3.189080 TCGGTAGTCGTTCTTGAATTCGA 59.811 43.478 0.04 0.00 40.32 3.71
737 758 3.916172 CGGTAGTCGTTCTTGAATTCGAA 59.084 43.478 0.00 0.00 34.23 3.71
738 759 4.030306 CGGTAGTCGTTCTTGAATTCGAAG 59.970 45.833 3.35 6.19 34.23 3.79
739 760 5.159209 GGTAGTCGTTCTTGAATTCGAAGA 58.841 41.667 3.35 13.14 34.23 2.87
740 761 5.805994 GGTAGTCGTTCTTGAATTCGAAGAT 59.194 40.000 16.13 0.00 35.04 2.40
741 762 6.310711 GGTAGTCGTTCTTGAATTCGAAGATT 59.689 38.462 16.13 0.00 35.04 2.40
742 763 6.787085 AGTCGTTCTTGAATTCGAAGATTT 57.213 33.333 16.13 0.00 35.04 2.17
743 764 7.190920 AGTCGTTCTTGAATTCGAAGATTTT 57.809 32.000 16.13 0.00 35.04 1.82
744 765 7.639945 AGTCGTTCTTGAATTCGAAGATTTTT 58.360 30.769 16.13 0.00 35.04 1.94
745 766 7.798982 AGTCGTTCTTGAATTCGAAGATTTTTC 59.201 33.333 16.13 2.68 35.04 2.29
746 767 7.798982 GTCGTTCTTGAATTCGAAGATTTTTCT 59.201 33.333 16.13 0.00 35.04 2.52
747 768 8.342634 TCGTTCTTGAATTCGAAGATTTTTCTT 58.657 29.630 16.13 0.00 35.04 2.52
748 769 8.958043 CGTTCTTGAATTCGAAGATTTTTCTTT 58.042 29.630 16.13 0.00 35.04 2.52
789 811 2.403252 AATAAGTGACCCTTGCGGAG 57.597 50.000 0.00 0.00 34.46 4.63
799 821 2.609610 TTGCGGAGGCCCCTAGTT 60.610 61.111 0.00 0.00 38.85 2.24
801 823 3.400054 GCGGAGGCCCCTAGTTGT 61.400 66.667 0.00 0.00 0.00 3.32
806 828 1.631898 GGAGGCCCCTAGTTGTTAACA 59.368 52.381 3.59 3.59 0.00 2.41
816 838 7.166167 CCCCTAGTTGTTAACAGTTGATTAGT 58.834 38.462 8.56 0.00 0.00 2.24
817 839 7.664318 CCCCTAGTTGTTAACAGTTGATTAGTT 59.336 37.037 8.56 0.00 0.00 2.24
818 840 8.504005 CCCTAGTTGTTAACAGTTGATTAGTTG 58.496 37.037 8.56 0.00 0.00 3.16
821 1315 5.699097 TGTTAACAGTTGATTAGTTGGGC 57.301 39.130 3.59 0.00 0.00 5.36
823 1317 6.535540 TGTTAACAGTTGATTAGTTGGGCTA 58.464 36.000 3.59 0.00 0.00 3.93
836 1330 4.426313 GGCTAAACCCAGCGCCCT 62.426 66.667 2.29 0.00 42.76 5.19
839 1333 1.374343 GCTAAACCCAGCGCCCTAAC 61.374 60.000 2.29 0.00 0.00 2.34
840 1334 0.035820 CTAAACCCAGCGCCCTAACA 60.036 55.000 2.29 0.00 0.00 2.41
1011 1505 2.074948 ATCCGCCATGGCTCTCCTT 61.075 57.895 33.07 10.09 39.32 3.36
1090 1584 3.793775 TTCGTCCGGCAACTCGCAA 62.794 57.895 0.00 0.00 45.17 4.85
1255 2044 1.444553 GGTCGCTCTGAACCACTCG 60.445 63.158 0.00 0.00 0.00 4.18
1290 2079 3.350909 TTATCTCACACGCGGCGCT 62.351 57.895 30.54 14.21 0.00 5.92
1429 2218 1.336887 GCTCGTCTGTTACCTCTGCAA 60.337 52.381 0.00 0.00 0.00 4.08
1470 2259 1.672881 GCCATAACTCACATGCCTGAC 59.327 52.381 0.00 0.00 0.00 3.51
1589 2378 0.240678 GATGCGTCAATGTGTTGGCA 59.759 50.000 0.00 0.00 39.94 4.92
1590 2379 0.039256 ATGCGTCAATGTGTTGGCAC 60.039 50.000 0.00 0.00 39.94 5.01
1622 2411 2.175811 GTTCGCACGGTGAATGCC 59.824 61.111 13.29 0.00 40.09 4.40
1825 2616 6.489022 AGTGGTATGTTCTTTTAGGTGTTTCC 59.511 38.462 0.00 0.00 0.00 3.13
1869 2660 0.035439 TTGAATTCTCGGTGGGAGCC 60.035 55.000 7.05 0.00 42.82 4.70
1984 2787 5.227569 TCTTTGTGGCTTTGATAGTCTCA 57.772 39.130 0.00 0.00 30.60 3.27
2095 2899 3.324846 AGACATCACTAGGACTGTTGCAA 59.675 43.478 0.00 0.00 0.00 4.08
2128 2932 3.375642 GTTGAGTTTGCTTCTTTCTGGC 58.624 45.455 0.00 0.00 0.00 4.85
2133 2937 3.189287 AGTTTGCTTCTTTCTGGCGTATG 59.811 43.478 0.00 0.00 0.00 2.39
2144 2956 3.368248 TCTGGCGTATGTTTAGTACCCT 58.632 45.455 0.00 0.00 0.00 4.34
2145 2957 3.131577 TCTGGCGTATGTTTAGTACCCTG 59.868 47.826 0.00 0.00 0.00 4.45
2148 2960 3.451526 GCGTATGTTTAGTACCCTGTCC 58.548 50.000 0.00 0.00 0.00 4.02
2153 2965 2.964464 TGTTTAGTACCCTGTCCGTTCA 59.036 45.455 0.00 0.00 0.00 3.18
2177 2991 7.615757 TCAGAAATAGATGGTCTTAGACACTGA 59.384 37.037 14.72 10.18 33.68 3.41
2204 3019 6.119536 TGGTATCCAACATGTATCTTTGACC 58.880 40.000 0.00 2.18 0.00 4.02
2222 3037 3.496884 TGACCGTTTCTCTTTGTATGCAC 59.503 43.478 0.00 0.00 0.00 4.57
2223 3038 2.478894 ACCGTTTCTCTTTGTATGCACG 59.521 45.455 0.00 0.00 0.00 5.34
2230 3045 6.828502 TTCTCTTTGTATGCACGATATGTC 57.171 37.500 0.00 0.00 0.00 3.06
2237 3052 5.363939 TGTATGCACGATATGTCAATGGAA 58.636 37.500 0.00 0.00 0.00 3.53
2238 3053 5.997129 TGTATGCACGATATGTCAATGGAAT 59.003 36.000 0.00 0.00 0.00 3.01
2239 3054 6.486320 TGTATGCACGATATGTCAATGGAATT 59.514 34.615 0.00 0.00 36.63 2.17
2240 3055 7.659390 TGTATGCACGATATGTCAATGGAATTA 59.341 33.333 0.00 0.00 32.46 1.40
2241 3056 7.692460 ATGCACGATATGTCAATGGAATTAT 57.308 32.000 0.00 0.00 32.46 1.28
2242 3057 6.901265 TGCACGATATGTCAATGGAATTATG 58.099 36.000 0.00 0.00 32.46 1.90
2243 3058 6.709846 TGCACGATATGTCAATGGAATTATGA 59.290 34.615 0.00 0.00 32.46 2.15
2367 3328 4.510711 CAGGATTAACTGCATGCACTCTAG 59.489 45.833 18.46 9.49 0.00 2.43
2404 3365 4.385358 TTGGTTGAGGTTGCTTCTTTTC 57.615 40.909 0.00 0.00 0.00 2.29
2486 4785 9.575783 GGTACTATCTAGCAGTTAAAGATATGC 57.424 37.037 2.63 0.00 38.97 3.14
2510 4818 5.929058 TTATGAAGCAATTGCATGGGTAA 57.071 34.783 30.89 18.58 45.16 2.85
2537 4845 5.664457 TGTTTGGTTGTTATGCAATTGTCA 58.336 33.333 7.40 6.18 39.55 3.58
2563 5443 6.849588 TGTGTGATAATGTGTAGCATGATC 57.150 37.500 0.00 0.00 43.07 2.92
2622 5502 2.019249 GTGCCAGCTCATAGCAATTGA 58.981 47.619 10.34 0.00 45.56 2.57
2668 5548 3.979347 ACTGGAATCCTCCTGCAGATATT 59.021 43.478 17.39 8.78 42.93 1.28
2671 5551 4.202503 TGGAATCCTCCTGCAGATATTTCC 60.203 45.833 17.39 18.98 42.94 3.13
2747 5627 4.097741 ACAATTTGAGCAGTGCTTTGTACA 59.902 37.500 24.55 13.81 39.88 2.90
2774 5654 6.945435 TCCTAATTTTTCTGGTAAGTGCATCA 59.055 34.615 0.00 0.00 0.00 3.07
2790 5670 2.103771 GCATCATTCTCTCCTGCCTACA 59.896 50.000 0.00 0.00 0.00 2.74
2804 5684 3.754965 TGCCTACAAGAGCATGTTTCTT 58.245 40.909 8.30 8.30 35.34 2.52
2817 5697 5.300286 AGCATGTTTCTTCTAAGTTTGTGCT 59.700 36.000 0.00 0.00 33.64 4.40
2820 5700 7.647715 GCATGTTTCTTCTAAGTTTGTGCTAAA 59.352 33.333 0.00 0.00 0.00 1.85
2844 5724 6.252995 AGGTTTTGGTTTAGCTATCCAATCA 58.747 36.000 22.81 14.40 40.28 2.57
2863 5744 8.641541 TCCAATCAATATTATTTTCTTGCCCTC 58.358 33.333 0.00 0.00 0.00 4.30
2875 5756 1.136305 CTTGCCCTCATTGATTGCAGG 59.864 52.381 9.36 7.49 32.88 4.85
2876 5757 0.685131 TGCCCTCATTGATTGCAGGG 60.685 55.000 6.24 5.15 41.83 4.45
2881 5762 2.662866 CTCATTGATTGCAGGGGTCAT 58.337 47.619 0.00 0.00 0.00 3.06
2888 5769 0.255890 TTGCAGGGGTCATTCTAGGC 59.744 55.000 0.00 0.00 0.00 3.93
2927 5808 9.229784 GTATCAAGCATCAAAGATGTGTATTTG 57.770 33.333 8.60 6.48 37.77 2.32
2957 5838 8.486210 AGTTATTATAGTTCAGATGAAGCACCA 58.514 33.333 0.00 0.00 34.27 4.17
2962 5843 2.945668 GTTCAGATGAAGCACCATACCC 59.054 50.000 0.00 0.00 34.27 3.69
2963 5844 2.481441 TCAGATGAAGCACCATACCCT 58.519 47.619 0.00 0.00 0.00 4.34
2964 5845 2.435805 TCAGATGAAGCACCATACCCTC 59.564 50.000 0.00 0.00 0.00 4.30
2965 5846 2.437281 CAGATGAAGCACCATACCCTCT 59.563 50.000 0.00 0.00 0.00 3.69
2966 5847 3.118112 CAGATGAAGCACCATACCCTCTT 60.118 47.826 0.00 0.00 0.00 2.85
2967 5848 2.787473 TGAAGCACCATACCCTCTTG 57.213 50.000 0.00 0.00 0.00 3.02
2968 5849 1.985159 TGAAGCACCATACCCTCTTGT 59.015 47.619 0.00 0.00 0.00 3.16
2977 5858 2.327325 TACCCTCTTGTCTCTTGCCT 57.673 50.000 0.00 0.00 0.00 4.75
2985 5866 3.006859 TCTTGTCTCTTGCCTTCGATCAA 59.993 43.478 0.00 0.00 0.00 2.57
2992 5873 5.008019 TCTCTTGCCTTCGATCAATAATTGC 59.992 40.000 0.00 0.00 0.00 3.56
2994 5875 4.291540 TGCCTTCGATCAATAATTGCAC 57.708 40.909 0.00 0.00 0.00 4.57
3009 5890 3.815856 TTGCACTGAAATTCTTGGCAA 57.184 38.095 12.17 12.17 37.43 4.52
3020 5901 9.474920 CTGAAATTCTTGGCAACTTTTATAACA 57.525 29.630 0.00 0.00 37.61 2.41
3031 5912 8.495148 GGCAACTTTTATAACAATTGGTTTGAG 58.505 33.333 10.83 1.98 40.96 3.02
3103 5984 3.695060 ACTACCGGATGTCTAGTTGACTG 59.305 47.826 9.46 0.00 45.54 3.51
3106 5987 2.417379 CCGGATGTCTAGTTGACTGGTG 60.417 54.545 0.00 0.00 45.54 4.17
3178 6059 3.470709 TGTCTCACTGCTTTTCTCCTTG 58.529 45.455 0.00 0.00 0.00 3.61
3192 6073 9.260002 GCTTTTCTCCTTGTTTCATATTTTTCA 57.740 29.630 0.00 0.00 0.00 2.69
3240 6121 2.498167 GTGCTGGTTTCATCAGACACT 58.502 47.619 0.00 0.00 36.87 3.55
3366 6247 0.680618 TGTTGGCCTCCAATGCAAAG 59.319 50.000 3.32 0.00 45.80 2.77
3402 6283 7.500559 AGTGAGAAAGATATGGTTTGGATAAGC 59.499 37.037 0.00 0.00 0.00 3.09
3440 6321 4.577687 TTCGACTTGCGTAAATCATCAC 57.422 40.909 0.00 0.00 41.80 3.06
3524 6406 3.385193 AATGGTTTTGTACAAGCCAGC 57.615 42.857 26.82 17.62 33.19 4.85
3525 6407 1.769026 TGGTTTTGTACAAGCCAGCA 58.231 45.000 22.30 16.58 0.00 4.41
3535 6417 3.990318 ACAAGCCAGCAAGTAAACTTC 57.010 42.857 0.00 0.00 33.11 3.01
3581 6463 9.697250 CAATGCTGTTGCTGAAATATTTATTTG 57.303 29.630 0.00 0.00 40.48 2.32
3602 6484 4.454678 TGAGAGCTTGTATTGGCTAATGG 58.545 43.478 5.42 0.00 39.05 3.16
3616 6498 2.099756 GCTAATGGGCAATCAGTGAACC 59.900 50.000 0.00 0.00 0.00 3.62
3622 6504 1.620822 GCAATCAGTGAACCACCCTT 58.379 50.000 0.00 0.00 34.49 3.95
3639 6521 7.064229 ACCACCCTTAAAGTTTGACAGAAATA 58.936 34.615 0.00 0.00 0.00 1.40
3652 6534 3.543680 CAGAAATACTGTGGTCCGGAT 57.456 47.619 7.81 0.00 41.30 4.18
3658 6540 2.927856 TGTGGTCCGGATGGCAGT 60.928 61.111 7.81 0.00 34.14 4.40
3673 6555 6.391537 GGATGGCAGTATAGAACTACTAAGC 58.608 44.000 0.00 0.00 35.76 3.09
3688 6570 2.766828 ACTAAGCTGGATTCGTAAGGCT 59.233 45.455 0.00 0.00 38.47 4.58
3718 6600 5.685954 GTGAACAATAGAATGATGCATGCAG 59.314 40.000 26.69 10.47 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.046033 ACTTTATTCTGGTAGACGTTATTGGG 58.954 38.462 0.00 0.00 0.00 4.12
1 2 7.043590 CGACTTTATTCTGGTAGACGTTATTGG 60.044 40.741 0.00 0.00 0.00 3.16
2 3 7.514747 GCGACTTTATTCTGGTAGACGTTATTG 60.515 40.741 0.00 0.00 0.00 1.90
3 4 6.474751 GCGACTTTATTCTGGTAGACGTTATT 59.525 38.462 0.00 0.00 0.00 1.40
4 5 5.975939 GCGACTTTATTCTGGTAGACGTTAT 59.024 40.000 0.00 0.00 0.00 1.89
5 6 5.335127 GCGACTTTATTCTGGTAGACGTTA 58.665 41.667 0.00 0.00 0.00 3.18
6 7 4.171754 GCGACTTTATTCTGGTAGACGTT 58.828 43.478 0.00 0.00 0.00 3.99
7 8 3.730061 CGCGACTTTATTCTGGTAGACGT 60.730 47.826 0.00 0.00 0.00 4.34
8 9 2.782192 CGCGACTTTATTCTGGTAGACG 59.218 50.000 0.00 0.00 0.00 4.18
9 10 3.767278 ACGCGACTTTATTCTGGTAGAC 58.233 45.455 15.93 0.00 0.00 2.59
10 11 4.637534 ACTACGCGACTTTATTCTGGTAGA 59.362 41.667 15.93 0.00 32.57 2.59
11 12 4.918037 ACTACGCGACTTTATTCTGGTAG 58.082 43.478 15.93 1.00 33.99 3.18
12 13 4.970662 ACTACGCGACTTTATTCTGGTA 57.029 40.909 15.93 0.00 0.00 3.25
13 14 3.863142 ACTACGCGACTTTATTCTGGT 57.137 42.857 15.93 0.00 0.00 4.00
14 15 4.968788 GTCTACTACGCGACTTTATTCTGG 59.031 45.833 15.93 0.00 0.00 3.86
15 16 5.566623 TGTCTACTACGCGACTTTATTCTG 58.433 41.667 15.93 0.00 0.00 3.02
16 17 5.808042 TGTCTACTACGCGACTTTATTCT 57.192 39.130 15.93 0.00 0.00 2.40
17 18 6.197276 TGATGTCTACTACGCGACTTTATTC 58.803 40.000 15.93 0.00 0.00 1.75
18 19 6.127810 TGATGTCTACTACGCGACTTTATT 57.872 37.500 15.93 0.00 0.00 1.40
19 20 5.746307 TGATGTCTACTACGCGACTTTAT 57.254 39.130 15.93 0.00 0.00 1.40
20 21 5.352293 TCTTGATGTCTACTACGCGACTTTA 59.648 40.000 15.93 0.00 0.00 1.85
21 22 4.155462 TCTTGATGTCTACTACGCGACTTT 59.845 41.667 15.93 0.00 0.00 2.66
22 23 3.688185 TCTTGATGTCTACTACGCGACTT 59.312 43.478 15.93 0.00 0.00 3.01
23 24 3.268330 TCTTGATGTCTACTACGCGACT 58.732 45.455 15.93 0.00 0.00 4.18
24 25 3.670311 TCTTGATGTCTACTACGCGAC 57.330 47.619 15.93 0.00 0.00 5.19
25 26 4.552184 CGATTCTTGATGTCTACTACGCGA 60.552 45.833 15.93 0.00 0.00 5.87
26 27 3.659899 CGATTCTTGATGTCTACTACGCG 59.340 47.826 3.53 3.53 0.00 6.01
27 28 4.845387 TCGATTCTTGATGTCTACTACGC 58.155 43.478 0.00 0.00 0.00 4.42
28 29 7.736031 TTTTCGATTCTTGATGTCTACTACG 57.264 36.000 0.00 0.00 0.00 3.51
110 115 5.250982 GCAACCATACTACTGGGTTTAAGT 58.749 41.667 0.00 0.00 42.01 2.24
113 118 3.369681 CCGCAACCATACTACTGGGTTTA 60.370 47.826 0.00 0.00 42.01 2.01
116 121 0.539986 CCGCAACCATACTACTGGGT 59.460 55.000 0.00 0.00 40.85 4.51
135 140 6.649141 AGTCCTTCCAAAACAAAAGTGAAAAC 59.351 34.615 0.00 0.00 0.00 2.43
140 145 6.215845 CCATAGTCCTTCCAAAACAAAAGTG 58.784 40.000 0.00 0.00 0.00 3.16
161 166 6.784031 ACTCTACAAGAAATGTCTTTCCCAT 58.216 36.000 0.00 0.00 41.55 4.00
204 209 0.874390 GAACCACAGATGCGCTTTCA 59.126 50.000 9.73 0.00 0.00 2.69
215 220 4.808414 TGTCCTTCTATGAGAACCACAG 57.192 45.455 0.00 0.00 29.89 3.66
220 225 5.412594 TGCACAAATGTCCTTCTATGAGAAC 59.587 40.000 0.00 0.00 29.89 3.01
226 231 4.813161 CGAGATGCACAAATGTCCTTCTAT 59.187 41.667 0.00 0.00 0.00 1.98
244 249 0.824109 TTCCGCTGATTCCACGAGAT 59.176 50.000 0.00 0.00 0.00 2.75
258 263 3.240684 GCATAACATGTGCTTCCGC 57.759 52.632 0.00 0.00 39.45 5.54
300 306 1.334599 GGATGCGCTTCTACGAGAGAG 60.335 57.143 21.05 0.00 34.93 3.20
302 308 0.382158 TGGATGCGCTTCTACGAGAG 59.618 55.000 21.05 0.00 34.06 3.20
370 376 6.476243 GCACAGATTTGCTTTCATGAAAAT 57.524 33.333 20.82 11.87 39.59 1.82
438 446 8.034804 GTGAACCATAGCCATGTTTAGAAAAAT 58.965 33.333 0.00 0.00 0.00 1.82
439 447 7.014711 TGTGAACCATAGCCATGTTTAGAAAAA 59.985 33.333 0.00 0.00 0.00 1.94
440 448 6.491745 TGTGAACCATAGCCATGTTTAGAAAA 59.508 34.615 0.00 0.00 0.00 2.29
441 449 6.007076 TGTGAACCATAGCCATGTTTAGAAA 58.993 36.000 0.00 0.00 0.00 2.52
540 559 6.557568 TGTATTTTGGGGTTTTAGATGAGGT 58.442 36.000 0.00 0.00 0.00 3.85
583 604 8.996271 GCTCCTTCTGAATTTTGATTTTGATTT 58.004 29.630 0.00 0.00 0.00 2.17
584 605 7.330208 CGCTCCTTCTGAATTTTGATTTTGATT 59.670 33.333 0.00 0.00 0.00 2.57
585 606 6.810182 CGCTCCTTCTGAATTTTGATTTTGAT 59.190 34.615 0.00 0.00 0.00 2.57
620 641 0.391528 CCAGCCATCGTCACATGTCA 60.392 55.000 0.00 0.00 0.00 3.58
630 651 2.315925 AATAGTGTGTCCAGCCATCG 57.684 50.000 0.00 0.00 0.00 3.84
691 712 9.893305 CCGATTACTAAACTTTGATTTTGTCTT 57.107 29.630 0.00 0.00 31.43 3.01
692 713 9.063615 ACCGATTACTAAACTTTGATTTTGTCT 57.936 29.630 0.00 0.00 31.43 3.41
697 718 8.866956 CGACTACCGATTACTAAACTTTGATTT 58.133 33.333 0.00 0.00 41.76 2.17
698 719 8.031277 ACGACTACCGATTACTAAACTTTGATT 58.969 33.333 0.00 0.00 41.76 2.57
699 720 7.542025 ACGACTACCGATTACTAAACTTTGAT 58.458 34.615 0.00 0.00 41.76 2.57
700 721 6.913170 ACGACTACCGATTACTAAACTTTGA 58.087 36.000 0.00 0.00 41.76 2.69
701 722 7.540055 AGAACGACTACCGATTACTAAACTTTG 59.460 37.037 0.00 0.00 41.76 2.77
702 723 7.597386 AGAACGACTACCGATTACTAAACTTT 58.403 34.615 0.00 0.00 41.76 2.66
703 724 7.150783 AGAACGACTACCGATTACTAAACTT 57.849 36.000 0.00 0.00 41.76 2.66
704 725 6.749923 AGAACGACTACCGATTACTAAACT 57.250 37.500 0.00 0.00 41.76 2.66
705 726 7.023575 TCAAGAACGACTACCGATTACTAAAC 58.976 38.462 0.00 0.00 41.76 2.01
706 727 7.144722 TCAAGAACGACTACCGATTACTAAA 57.855 36.000 0.00 0.00 41.76 1.85
707 728 6.741992 TCAAGAACGACTACCGATTACTAA 57.258 37.500 0.00 0.00 41.76 2.24
708 729 6.741992 TTCAAGAACGACTACCGATTACTA 57.258 37.500 0.00 0.00 41.76 1.82
709 730 5.633830 TTCAAGAACGACTACCGATTACT 57.366 39.130 0.00 0.00 41.76 2.24
710 731 6.290956 CGAATTCAAGAACGACTACCGATTAC 60.291 42.308 6.22 0.00 41.76 1.89
711 732 5.740569 CGAATTCAAGAACGACTACCGATTA 59.259 40.000 6.22 0.00 41.76 1.75
712 733 4.561606 CGAATTCAAGAACGACTACCGATT 59.438 41.667 6.22 0.00 41.76 3.34
713 734 4.103357 CGAATTCAAGAACGACTACCGAT 58.897 43.478 6.22 0.00 41.76 4.18
714 735 3.189080 TCGAATTCAAGAACGACTACCGA 59.811 43.478 6.22 0.00 41.76 4.69
715 736 3.495193 TCGAATTCAAGAACGACTACCG 58.505 45.455 6.22 0.00 45.44 4.02
716 737 5.159209 TCTTCGAATTCAAGAACGACTACC 58.841 41.667 14.20 0.00 34.59 3.18
717 738 6.872670 ATCTTCGAATTCAAGAACGACTAC 57.127 37.500 18.12 0.00 33.57 2.73
718 739 7.884816 AAATCTTCGAATTCAAGAACGACTA 57.115 32.000 18.12 2.05 33.57 2.59
719 740 6.787085 AAATCTTCGAATTCAAGAACGACT 57.213 33.333 18.12 5.30 33.57 4.18
720 741 7.798982 AGAAAAATCTTCGAATTCAAGAACGAC 59.201 33.333 18.12 11.74 33.57 4.34
721 742 7.861630 AGAAAAATCTTCGAATTCAAGAACGA 58.138 30.769 18.12 3.21 33.57 3.85
722 743 8.494236 AAGAAAAATCTTCGAATTCAAGAACG 57.506 30.769 18.12 1.08 33.57 3.95
724 745 9.801873 ACAAAGAAAAATCTTCGAATTCAAGAA 57.198 25.926 18.12 9.11 33.57 2.52
725 746 9.801873 AACAAAGAAAAATCTTCGAATTCAAGA 57.198 25.926 17.13 17.13 34.37 3.02
728 749 9.579768 TCAAACAAAGAAAAATCTTCGAATTCA 57.420 25.926 6.22 0.00 0.00 2.57
731 752 8.490355 GCATCAAACAAAGAAAAATCTTCGAAT 58.510 29.630 0.00 0.00 0.00 3.34
732 753 7.490725 TGCATCAAACAAAGAAAAATCTTCGAA 59.509 29.630 0.00 0.00 0.00 3.71
733 754 6.977502 TGCATCAAACAAAGAAAAATCTTCGA 59.022 30.769 0.00 0.00 0.00 3.71
734 755 7.043192 AGTGCATCAAACAAAGAAAAATCTTCG 60.043 33.333 0.00 0.00 0.00 3.79
735 756 8.134905 AGTGCATCAAACAAAGAAAAATCTTC 57.865 30.769 0.00 0.00 0.00 2.87
736 757 7.983484 AGAGTGCATCAAACAAAGAAAAATCTT 59.017 29.630 0.00 0.00 0.00 2.40
737 758 7.495055 AGAGTGCATCAAACAAAGAAAAATCT 58.505 30.769 0.00 0.00 0.00 2.40
738 759 7.704789 AGAGTGCATCAAACAAAGAAAAATC 57.295 32.000 0.00 0.00 0.00 2.17
739 760 9.252962 CTTAGAGTGCATCAAACAAAGAAAAAT 57.747 29.630 0.00 0.00 0.00 1.82
740 761 8.465999 TCTTAGAGTGCATCAAACAAAGAAAAA 58.534 29.630 0.00 0.00 0.00 1.94
741 762 7.915397 GTCTTAGAGTGCATCAAACAAAGAAAA 59.085 33.333 0.00 0.00 0.00 2.29
742 763 7.283127 AGTCTTAGAGTGCATCAAACAAAGAAA 59.717 33.333 0.00 0.00 0.00 2.52
743 764 6.767902 AGTCTTAGAGTGCATCAAACAAAGAA 59.232 34.615 0.00 0.00 0.00 2.52
744 765 6.291377 AGTCTTAGAGTGCATCAAACAAAGA 58.709 36.000 0.00 0.00 0.00 2.52
745 766 6.551385 AGTCTTAGAGTGCATCAAACAAAG 57.449 37.500 0.00 0.00 0.00 2.77
746 767 8.445275 TTTAGTCTTAGAGTGCATCAAACAAA 57.555 30.769 0.00 0.00 0.00 2.83
747 768 8.621532 ATTTAGTCTTAGAGTGCATCAAACAA 57.378 30.769 0.00 0.00 0.00 2.83
748 769 9.719355 TTATTTAGTCTTAGAGTGCATCAAACA 57.281 29.630 0.00 0.00 0.00 2.83
789 811 2.817844 CAACTGTTAACAACTAGGGGCC 59.182 50.000 10.03 0.00 0.00 5.80
799 821 5.381757 AGCCCAACTAATCAACTGTTAACA 58.618 37.500 8.28 8.28 0.00 2.41
801 823 7.040271 GGTTTAGCCCAACTAATCAACTGTTAA 60.040 37.037 0.00 0.00 40.55 2.01
821 1315 0.035820 TGTTAGGGCGCTGGGTTTAG 60.036 55.000 14.51 0.00 0.00 1.85
823 1317 1.303317 CTGTTAGGGCGCTGGGTTT 60.303 57.895 14.51 0.00 0.00 3.27
836 1330 2.662596 CCACGAGGCCTGCTGTTA 59.337 61.111 12.00 0.00 0.00 2.41
876 1370 2.583143 GTACAACAAGTCCAAAGGGCT 58.417 47.619 0.00 0.00 0.00 5.19
1027 1521 2.167487 GAGGCTGTAGGTGGAGAAGAAG 59.833 54.545 0.00 0.00 0.00 2.85
1028 1522 2.180276 GAGGCTGTAGGTGGAGAAGAA 58.820 52.381 0.00 0.00 0.00 2.52
1029 1523 1.619977 GGAGGCTGTAGGTGGAGAAGA 60.620 57.143 0.00 0.00 0.00 2.87
1290 2079 1.748403 GGATCCCTGCGATAGTGCA 59.252 57.895 0.00 0.00 43.95 4.57
1295 2084 2.603473 CCGGGGATCCCTGCGATA 60.603 66.667 31.85 0.00 42.67 2.92
1429 2218 1.922447 TGGGCATTATCAGGGTGAAGT 59.078 47.619 0.00 0.00 0.00 3.01
1470 2259 1.253545 CGATTTCGCGTAACCGGTTAG 59.746 52.381 27.20 20.23 33.68 2.34
1589 2378 2.352388 CGAACCCAATGTACCATTCGT 58.648 47.619 0.00 0.00 35.43 3.85
1590 2379 1.063469 GCGAACCCAATGTACCATTCG 59.937 52.381 0.00 0.00 41.31 3.34
1622 2411 2.418746 CCCAAGTCATACTCACTTCCCG 60.419 54.545 0.00 0.00 31.40 5.14
1825 2616 4.141620 ACTGGTTCAAGTCTATATGGCTGG 60.142 45.833 0.00 0.00 0.00 4.85
1869 2660 2.594541 GCTTAAGGCATCTCGGTCG 58.405 57.895 4.29 0.00 41.35 4.79
1958 2761 7.882791 TGAGACTATCAAAGCCACAAAGATAAA 59.117 33.333 0.00 0.00 34.02 1.40
2063 2867 6.824704 AGTCCTAGTGATGTCTACAGTAACTC 59.175 42.308 0.00 0.00 0.00 3.01
2095 2899 4.644685 AGCAAACTCAACCAAACACTACAT 59.355 37.500 0.00 0.00 0.00 2.29
2128 2932 3.129287 ACGGACAGGGTACTAAACATACG 59.871 47.826 0.00 0.00 0.00 3.06
2133 2937 3.256631 TCTGAACGGACAGGGTACTAAAC 59.743 47.826 10.33 0.00 38.31 2.01
2144 2956 4.466370 AGACCATCTATTTCTGAACGGACA 59.534 41.667 0.00 0.00 0.00 4.02
2145 2957 5.012328 AGACCATCTATTTCTGAACGGAC 57.988 43.478 0.00 0.00 0.00 4.79
2148 2960 7.221067 GTGTCTAAGACCATCTATTTCTGAACG 59.779 40.741 0.00 0.00 0.00 3.95
2153 2965 7.397476 TGTCAGTGTCTAAGACCATCTATTTCT 59.603 37.037 0.00 0.00 0.00 2.52
2177 2991 7.283127 GTCAAAGATACATGTTGGATACCATGT 59.717 37.037 2.30 9.85 40.76 3.21
2204 3019 4.584029 ATCGTGCATACAAAGAGAAACG 57.416 40.909 0.00 0.00 0.00 3.60
2263 3078 9.823647 AATGTCAATATAGTTCTCGTTGAGATT 57.176 29.630 0.00 0.00 38.56 2.40
2350 3311 3.515502 ACTTCCTAGAGTGCATGCAGTTA 59.484 43.478 28.06 19.26 0.00 2.24
2353 3314 2.093816 TGACTTCCTAGAGTGCATGCAG 60.094 50.000 23.41 8.94 0.00 4.41
2358 3319 4.344978 AGTACATGACTTCCTAGAGTGCA 58.655 43.478 0.00 0.00 33.13 4.57
2389 3350 3.381590 ACACCAAGAAAAGAAGCAACCTC 59.618 43.478 0.00 0.00 0.00 3.85
2482 4781 5.929415 CCATGCAATTGCTTCATAATGCATA 59.071 36.000 29.37 6.35 39.36 3.14
2486 4785 4.699637 ACCCATGCAATTGCTTCATAATG 58.300 39.130 29.37 21.72 42.66 1.90
2493 4792 4.255301 CATTGTTACCCATGCAATTGCTT 58.745 39.130 29.37 21.33 42.66 3.91
2510 4818 6.541641 ACAATTGCATAACAACCAAACATTGT 59.458 30.769 5.05 0.00 42.27 2.71
2537 4845 7.628769 TCATGCTACACATTATCACACAATT 57.371 32.000 0.00 0.00 36.64 2.32
2563 5443 4.440802 GGTGAGACATCTAACCAGTAGCAG 60.441 50.000 10.24 0.00 45.30 4.24
2622 5502 7.827203 TATCCTCGGATGCACAACACATTGT 62.827 44.000 8.69 0.00 41.46 2.71
2651 5531 5.393068 TTGGAAATATCTGCAGGAGGATT 57.607 39.130 15.13 5.74 0.00 3.01
2668 5548 7.566569 ACCAATCAATCATTGCATATTTGGAA 58.433 30.769 16.27 0.00 40.75 3.53
2671 5551 8.426881 TGAACCAATCAATCATTGCATATTTG 57.573 30.769 0.00 0.00 40.75 2.32
2722 5602 3.130869 ACAAAGCACTGCTCAAATTGTCA 59.869 39.130 11.46 0.00 38.25 3.58
2729 5609 3.253188 GGAATGTACAAAGCACTGCTCAA 59.747 43.478 3.40 0.00 38.25 3.02
2747 5627 7.775053 TGCACTTACCAGAAAAATTAGGAAT 57.225 32.000 0.00 0.00 0.00 3.01
2790 5670 7.420800 CACAAACTTAGAAGAAACATGCTCTT 58.579 34.615 9.77 9.77 35.82 2.85
2804 5684 6.378848 ACCAAAACCTTTAGCACAAACTTAGA 59.621 34.615 0.00 0.00 0.00 2.10
2817 5697 8.658840 ATTGGATAGCTAAACCAAAACCTTTA 57.341 30.769 27.49 12.04 44.91 1.85
2820 5700 6.252995 TGATTGGATAGCTAAACCAAAACCT 58.747 36.000 27.49 17.33 44.91 3.50
2863 5744 3.028850 AGAATGACCCCTGCAATCAATG 58.971 45.455 0.00 0.00 0.00 2.82
2881 5762 2.151202 CAAGCAAAAGGTCGCCTAGAA 58.849 47.619 0.00 0.00 31.13 2.10
2888 5769 3.492313 GCTTGATACAAGCAAAAGGTCG 58.508 45.455 25.01 0.00 42.56 4.79
2949 5830 2.237392 AGACAAGAGGGTATGGTGCTTC 59.763 50.000 0.00 0.00 0.00 3.86
2957 5838 2.839228 AGGCAAGAGACAAGAGGGTAT 58.161 47.619 0.00 0.00 0.00 2.73
2959 5840 1.349357 GAAGGCAAGAGACAAGAGGGT 59.651 52.381 0.00 0.00 0.00 4.34
2962 5843 2.732412 TCGAAGGCAAGAGACAAGAG 57.268 50.000 0.00 0.00 0.00 2.85
2963 5844 2.562738 TGATCGAAGGCAAGAGACAAGA 59.437 45.455 0.00 0.00 0.00 3.02
2964 5845 2.964740 TGATCGAAGGCAAGAGACAAG 58.035 47.619 0.00 0.00 0.00 3.16
2965 5846 3.401033 TTGATCGAAGGCAAGAGACAA 57.599 42.857 0.00 0.00 0.00 3.18
2966 5847 3.616956 ATTGATCGAAGGCAAGAGACA 57.383 42.857 0.00 0.00 0.00 3.41
2967 5848 6.425504 CAATTATTGATCGAAGGCAAGAGAC 58.574 40.000 0.00 0.00 0.00 3.36
2968 5849 5.008019 GCAATTATTGATCGAAGGCAAGAGA 59.992 40.000 9.36 0.00 0.00 3.10
2977 5858 8.461222 AGAATTTCAGTGCAATTATTGATCGAA 58.539 29.630 9.36 2.82 0.00 3.71
2985 5866 6.040209 TGCCAAGAATTTCAGTGCAATTAT 57.960 33.333 0.48 0.00 0.00 1.28
2992 5873 7.951530 ATAAAAGTTGCCAAGAATTTCAGTG 57.048 32.000 0.00 0.00 0.00 3.66
2994 5875 9.474920 TGTTATAAAAGTTGCCAAGAATTTCAG 57.525 29.630 0.00 0.00 0.00 3.02
3009 5890 8.421002 AGCACTCAAACCAATTGTTATAAAAGT 58.579 29.630 4.43 0.00 40.11 2.66
3020 5901 8.367156 ACATATACAAAAGCACTCAAACCAATT 58.633 29.630 0.00 0.00 0.00 2.32
3031 5912 9.289303 CAAATAACCTCACATATACAAAAGCAC 57.711 33.333 0.00 0.00 0.00 4.40
3065 5946 4.701171 CCGGTAGTCCTATTCCTAAGCTAG 59.299 50.000 0.00 0.00 0.00 3.42
3066 5947 4.352001 TCCGGTAGTCCTATTCCTAAGCTA 59.648 45.833 0.00 0.00 0.00 3.32
3068 5949 3.494332 TCCGGTAGTCCTATTCCTAAGC 58.506 50.000 0.00 0.00 0.00 3.09
3079 5960 3.066481 GTCAACTAGACATCCGGTAGTCC 59.934 52.174 20.23 7.53 46.77 3.85
3103 5984 7.589395 AGGAAAACAAAAACACAATTTTCACC 58.411 30.769 9.28 0.00 39.79 4.02
3106 5987 9.457110 ACAAAGGAAAACAAAAACACAATTTTC 57.543 25.926 0.00 0.00 38.14 2.29
3162 6043 4.637483 TGAAACAAGGAGAAAAGCAGTG 57.363 40.909 0.00 0.00 0.00 3.66
3163 6044 7.530426 AATATGAAACAAGGAGAAAAGCAGT 57.470 32.000 0.00 0.00 0.00 4.40
3240 6121 4.473196 TGTGGTAGAATATTCCCAAGCTGA 59.527 41.667 11.92 0.00 0.00 4.26
3295 6176 0.322816 GCTGGATCAGGGTTGCTCAA 60.323 55.000 0.00 0.00 31.21 3.02
3366 6247 7.875041 ACCATATCTTTCTCACTGTATGCATAC 59.125 37.037 26.72 26.72 0.00 2.39
3402 6283 6.991485 AGTCGAAATTTATTTGCAACTGTG 57.009 33.333 0.00 0.00 0.00 3.66
3440 6321 2.899303 AACTGGAATACCTTGGGTGG 57.101 50.000 0.00 0.00 36.19 4.61
3501 6383 4.618227 GCTGGCTTGTACAAAACCATTAGG 60.618 45.833 23.42 15.68 42.21 2.69
3524 6406 4.995487 GTCTGGTACTGGGAAGTTTACTTG 59.005 45.833 0.00 0.00 36.11 3.16
3525 6407 4.657039 TGTCTGGTACTGGGAAGTTTACTT 59.343 41.667 0.00 0.00 39.23 2.24
3535 6417 1.812571 GTGCAAATGTCTGGTACTGGG 59.187 52.381 0.00 0.00 0.00 4.45
3581 6463 3.817647 CCCATTAGCCAATACAAGCTCTC 59.182 47.826 0.00 0.00 40.56 3.20
3593 6475 1.284491 TCACTGATTGCCCATTAGCCA 59.716 47.619 0.00 0.00 0.00 4.75
3602 6484 0.251341 AGGGTGGTTCACTGATTGCC 60.251 55.000 0.00 0.00 34.40 4.52
3608 6490 4.642885 TCAAACTTTAAGGGTGGTTCACTG 59.357 41.667 0.00 0.00 34.40 3.66
3616 6498 8.076178 CAGTATTTCTGTCAAACTTTAAGGGTG 58.924 37.037 0.00 0.00 39.17 4.61
3639 6521 2.927856 TGCCATCCGGACCACAGT 60.928 61.111 6.12 0.00 0.00 3.55
3648 6530 6.570672 TTAGTAGTTCTATACTGCCATCCG 57.429 41.667 0.00 0.00 40.02 4.18
3652 6534 5.302059 CCAGCTTAGTAGTTCTATACTGCCA 59.698 44.000 0.00 0.00 40.02 4.92
3658 6540 9.565090 TTACGAATCCAGCTTAGTAGTTCTATA 57.435 33.333 0.00 0.00 0.00 1.31
3673 6555 0.179045 CCCCAGCCTTACGAATCCAG 60.179 60.000 0.00 0.00 0.00 3.86
3688 6570 4.649267 TCATTCTATTGTTCACACCCCA 57.351 40.909 0.00 0.00 0.00 4.96


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

AutoCloner maintained by Alex Coulton.