Multiple sequence alignment - TraesCS2A01G243200

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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 TraesCS2A01G243200 chr2A 100.000 4580 0 0 1 4580 341624310 341628889 0.000000e+00 8458.0
1 TraesCS2A01G243200 chr2A 85.913 575 61 13 3170 3733 118783003 118783568 3.050000e-166 595.0
2 TraesCS2A01G243200 chr2A 79.803 203 18 8 4227 4416 36128200 36128392 4.810000e-25 126.0
3 TraesCS2A01G243200 chr2A 87.629 97 12 0 548 644 304657571 304657667 3.750000e-21 113.0
4 TraesCS2A01G243200 chr2A 87.629 97 12 0 548 644 304685403 304685499 3.750000e-21 113.0
5 TraesCS2A01G243200 chr2A 84.000 125 7 5 1845 1958 341625884 341626006 1.740000e-19 108.0
6 TraesCS2A01G243200 chr2A 84.000 125 7 5 1575 1697 341626154 341626267 1.740000e-19 108.0
7 TraesCS2A01G243200 chr2A 92.105 76 4 2 2715 2790 118782713 118782786 6.270000e-19 106.0
8 TraesCS2A01G243200 chr2D 93.533 1639 56 20 1310 2937 274408017 274406418 0.000000e+00 2394.0
9 TraesCS2A01G243200 chr2D 95.874 1018 35 6 3170 4184 274405718 274404705 0.000000e+00 1640.0
10 TraesCS2A01G243200 chr2D 93.759 673 33 7 640 1310 274408711 274408046 0.000000e+00 1002.0
11 TraesCS2A01G243200 chr2D 92.083 240 17 2 2935 3173 274405991 274405753 2.040000e-88 337.0
12 TraesCS2A01G243200 chr2D 89.655 87 9 0 4492 4578 274404389 274404303 1.350000e-20 111.0
13 TraesCS2A01G243200 chr2D 92.308 52 3 1 1584 1634 274407471 274407420 6.360000e-09 73.1
14 TraesCS2A01G243200 chr2B 87.984 1032 48 17 705 1703 329141188 329140200 0.000000e+00 1149.0
15 TraesCS2A01G243200 chr2B 94.795 634 31 2 3205 3838 329138531 329137900 0.000000e+00 987.0
16 TraesCS2A01G243200 chr2B 98.025 557 10 1 1 556 347420062 347419506 0.000000e+00 966.0
17 TraesCS2A01G243200 chr2B 91.045 536 31 6 1820 2344 329139985 329139456 0.000000e+00 708.0
18 TraesCS2A01G243200 chr2B 91.463 492 23 5 2380 2859 329139189 329138705 0.000000e+00 658.0
19 TraesCS2A01G243200 chr2B 92.857 98 3 2 1697 1792 329140076 329139981 6.180000e-29 139.0
20 TraesCS2A01G243200 chr2B 80.576 139 17 7 4286 4424 521916998 521917126 1.050000e-16 99.0
21 TraesCS2A01G243200 chr2B 83.478 115 8 4 1854 1958 329140319 329140206 3.770000e-16 97.1
22 TraesCS2A01G243200 chrUn 98.205 557 9 1 1 556 176918352 176917796 0.000000e+00 972.0
23 TraesCS2A01G243200 chrUn 98.025 557 10 1 1 556 161832648 161833204 0.000000e+00 966.0
24 TraesCS2A01G243200 chrUn 98.025 557 10 1 1 556 232582278 232582834 0.000000e+00 966.0
25 TraesCS2A01G243200 chrUn 98.025 557 10 1 1 556 313773801 313774357 0.000000e+00 966.0
26 TraesCS2A01G243200 chr7A 98.205 557 9 1 1 556 352967362 352967918 0.000000e+00 972.0
27 TraesCS2A01G243200 chr7A 98.025 557 10 1 1 556 368228598 368229154 0.000000e+00 966.0
28 TraesCS2A01G243200 chr7A 90.977 133 8 4 3920 4049 46900829 46900698 4.710000e-40 176.0
29 TraesCS2A01G243200 chr7A 87.097 93 10 2 557 648 29056382 29056473 2.250000e-18 104.0
30 TraesCS2A01G243200 chr7A 80.741 135 17 3 4286 4420 69846061 69846186 3.770000e-16 97.1
31 TraesCS2A01G243200 chr7A 80.142 141 19 5 4288 4428 150584807 150584676 3.770000e-16 97.1
32 TraesCS2A01G243200 chr6B 98.025 557 10 1 1 556 325384268 325384824 0.000000e+00 966.0
33 TraesCS2A01G243200 chr3B 98.025 557 10 1 1 556 330839668 330839112 0.000000e+00 966.0
34 TraesCS2A01G243200 chr3B 87.197 289 29 8 3922 4205 28319237 28319522 5.720000e-84 322.0
35 TraesCS2A01G243200 chr3B 81.905 105 18 1 548 652 824163838 824163941 2.270000e-13 87.9
36 TraesCS2A01G243200 chr3A 86.038 573 60 12 3170 3731 368363634 368363071 8.480000e-167 597.0
37 TraesCS2A01G243200 chr4A 91.873 283 17 6 3923 4202 565745688 565745409 1.540000e-104 390.0
38 TraesCS2A01G243200 chr5A 93.233 133 5 4 3920 4049 299619420 299619289 4.680000e-45 193.0
39 TraesCS2A01G243200 chr5A 91.250 80 3 4 2711 2790 3607136 3607211 6.270000e-19 106.0
40 TraesCS2A01G243200 chr5A 85.437 103 13 2 551 653 10814272 10814172 6.270000e-19 106.0
41 TraesCS2A01G243200 chr5A 78.621 145 22 6 4286 4430 519850874 519851009 2.270000e-13 87.9
42 TraesCS2A01G243200 chr5A 83.158 95 15 1 551 644 81473350 81473256 8.160000e-13 86.1
43 TraesCS2A01G243200 chr5A 82.524 103 8 6 4303 4404 452707352 452707259 1.060000e-11 82.4
44 TraesCS2A01G243200 chr7D 91.729 133 7 4 3920 4049 32512986 32512855 1.010000e-41 182.0
45 TraesCS2A01G243200 chr7D 83.505 97 15 1 548 643 594945987 594946083 6.310000e-14 89.8
46 TraesCS2A01G243200 chr3D 90.226 133 9 4 3920 4049 146283399 146283268 2.190000e-38 171.0
47 TraesCS2A01G243200 chr3D 81.188 101 19 0 548 648 3769549 3769649 1.060000e-11 82.4
48 TraesCS2A01G243200 chr4D 81.313 198 15 8 4228 4412 399536022 399535834 1.720000e-29 141.0
49 TraesCS2A01G243200 chr4D 84.783 92 14 0 557 648 270644680 270644771 4.880000e-15 93.5
50 TraesCS2A01G243200 chr5D 80.808 198 19 5 4228 4412 217976549 217976740 2.220000e-28 137.0
51 TraesCS2A01G243200 chr6D 76.619 278 35 17 2515 2773 417506468 417506734 4.810000e-25 126.0
52 TraesCS2A01G243200 chr6A 82.443 131 14 3 4286 4416 4727518 4727639 6.270000e-19 106.0
53 TraesCS2A01G243200 chr6A 92.105 76 4 2 2715 2790 206140283 206140356 6.270000e-19 106.0
54 TraesCS2A01G243200 chr6A 90.000 80 4 4 2711 2790 68352080 68352005 2.920000e-17 100.0
55 TraesCS2A01G243200 chr1D 94.118 51 3 0 4228 4278 465892400 465892450 1.370000e-10 78.7


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 TraesCS2A01G243200 chr2A 341624310 341628889 4579 False 2891.333333 8458 89.333333 1 4580 3 chr2A.!!$F5 4579
1 TraesCS2A01G243200 chr2A 118782713 118783568 855 False 350.500000 595 89.009000 2715 3733 2 chr2A.!!$F4 1018
2 TraesCS2A01G243200 chr2D 274404303 274408711 4408 True 926.183333 2394 92.868667 640 4578 6 chr2D.!!$R1 3938
3 TraesCS2A01G243200 chr2B 347419506 347420062 556 True 966.000000 966 98.025000 1 556 1 chr2B.!!$R1 555
4 TraesCS2A01G243200 chr2B 329137900 329141188 3288 True 623.016667 1149 90.270333 705 3838 6 chr2B.!!$R2 3133
5 TraesCS2A01G243200 chrUn 176917796 176918352 556 True 972.000000 972 98.205000 1 556 1 chrUn.!!$R1 555
6 TraesCS2A01G243200 chrUn 161832648 161833204 556 False 966.000000 966 98.025000 1 556 1 chrUn.!!$F1 555
7 TraesCS2A01G243200 chrUn 232582278 232582834 556 False 966.000000 966 98.025000 1 556 1 chrUn.!!$F2 555
8 TraesCS2A01G243200 chrUn 313773801 313774357 556 False 966.000000 966 98.025000 1 556 1 chrUn.!!$F3 555
9 TraesCS2A01G243200 chr7A 352967362 352967918 556 False 972.000000 972 98.205000 1 556 1 chr7A.!!$F3 555
10 TraesCS2A01G243200 chr7A 368228598 368229154 556 False 966.000000 966 98.025000 1 556 1 chr7A.!!$F4 555
11 TraesCS2A01G243200 chr6B 325384268 325384824 556 False 966.000000 966 98.025000 1 556 1 chr6B.!!$F1 555
12 TraesCS2A01G243200 chr3B 330839112 330839668 556 True 966.000000 966 98.025000 1 556 1 chr3B.!!$R1 555
13 TraesCS2A01G243200 chr3A 368363071 368363634 563 True 597.000000 597 86.038000 3170 3731 1 chr3A.!!$R1 561

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
840 841 0.118346 ACATGACACCCCTGACCCTA 59.882 55.0 0.00 0.0 0.00 3.53 F
1772 1967 0.181350 CAGGATTACCAGGTGAGGGC 59.819 60.0 0.76 0.0 38.94 5.19 F
2897 3347 0.105039 GGAAGCGGAGAGGTGGTATG 59.895 60.0 0.00 0.0 0.00 2.39 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2375 2581 0.734889 GCGGATGAAGACAATGGTGG 59.265 55.0 0.0 0.0 0.00 4.61 R
2900 3350 0.394899 CTGAAACCCATCCCCAGCTC 60.395 60.0 0.0 0.0 0.00 4.09 R
4310 5371 0.036306 ACCCTTTTGCTACCGTCAGG 59.964 55.0 0.0 0.0 45.13 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
50 51 2.750237 GGTTGCCGATCACCACCC 60.750 66.667 0.00 0.00 0.00 4.61
55 56 4.082523 CCGATCACCACCCGCTGT 62.083 66.667 0.00 0.00 0.00 4.40
123 124 4.348461 TGATACACCACCACCACTTCTTAA 59.652 41.667 0.00 0.00 0.00 1.85
484 485 1.273327 CAGGACAAAATTCTGGTGCCC 59.727 52.381 0.00 0.00 0.00 5.36
536 537 0.809241 GCTACTGCTGCTGCTGGTAG 60.809 60.000 27.26 27.26 42.63 3.18
555 556 7.437713 TGGTAGCCAGGAGGATATATTTATG 57.562 40.000 0.00 0.00 38.22 1.90
556 557 7.196187 TGGTAGCCAGGAGGATATATTTATGA 58.804 38.462 0.00 0.00 38.22 2.15
557 558 7.851451 TGGTAGCCAGGAGGATATATTTATGAT 59.149 37.037 0.00 0.00 38.22 2.45
558 559 8.718656 GGTAGCCAGGAGGATATATTTATGATT 58.281 37.037 0.00 0.00 38.22 2.57
562 563 9.905713 GCCAGGAGGATATATTTATGATTAACA 57.094 33.333 0.00 0.00 36.89 2.41
585 586 9.713684 AACATAAAATCAATGGATCTAAAGGGA 57.286 29.630 0.00 0.00 31.88 4.20
586 587 9.136323 ACATAAAATCAATGGATCTAAAGGGAC 57.864 33.333 0.00 0.00 31.88 4.46
587 588 6.699575 AAAATCAATGGATCTAAAGGGACG 57.300 37.500 0.00 0.00 31.88 4.79
588 589 5.630415 AATCAATGGATCTAAAGGGACGA 57.370 39.130 0.00 0.00 31.88 4.20
589 590 4.402056 TCAATGGATCTAAAGGGACGAC 57.598 45.455 0.00 0.00 0.00 4.34
590 591 3.123804 CAATGGATCTAAAGGGACGACG 58.876 50.000 0.00 0.00 0.00 5.12
591 592 1.843368 TGGATCTAAAGGGACGACGT 58.157 50.000 0.00 0.00 0.00 4.34
592 593 3.003394 TGGATCTAAAGGGACGACGTA 57.997 47.619 0.00 0.00 0.00 3.57
593 594 3.559069 TGGATCTAAAGGGACGACGTAT 58.441 45.455 0.00 0.00 0.00 3.06
594 595 4.717877 TGGATCTAAAGGGACGACGTATA 58.282 43.478 0.00 0.00 0.00 1.47
595 596 4.758674 TGGATCTAAAGGGACGACGTATAG 59.241 45.833 0.00 0.00 0.00 1.31
596 597 4.999950 GGATCTAAAGGGACGACGTATAGA 59.000 45.833 0.00 5.10 0.00 1.98
597 598 5.471456 GGATCTAAAGGGACGACGTATAGAA 59.529 44.000 0.00 0.00 0.00 2.10
598 599 6.016777 GGATCTAAAGGGACGACGTATAGAAA 60.017 42.308 0.00 0.00 0.00 2.52
599 600 6.757897 TCTAAAGGGACGACGTATAGAAAA 57.242 37.500 0.00 0.00 0.00 2.29
600 601 6.555315 TCTAAAGGGACGACGTATAGAAAAC 58.445 40.000 0.00 0.00 0.00 2.43
601 602 5.397142 AAAGGGACGACGTATAGAAAACT 57.603 39.130 0.00 0.00 0.00 2.66
602 603 6.515272 AAAGGGACGACGTATAGAAAACTA 57.485 37.500 0.00 0.00 0.00 2.24
603 604 6.705863 AAGGGACGACGTATAGAAAACTAT 57.294 37.500 0.00 0.00 0.00 2.12
604 605 6.069684 AGGGACGACGTATAGAAAACTATG 57.930 41.667 0.00 0.00 0.00 2.23
605 606 5.824624 AGGGACGACGTATAGAAAACTATGA 59.175 40.000 0.00 0.00 0.00 2.15
606 607 6.319658 AGGGACGACGTATAGAAAACTATGAA 59.680 38.462 0.00 0.00 0.00 2.57
607 608 6.974622 GGGACGACGTATAGAAAACTATGAAA 59.025 38.462 0.00 0.00 0.00 2.69
608 609 7.489113 GGGACGACGTATAGAAAACTATGAAAA 59.511 37.037 0.00 0.00 0.00 2.29
609 610 8.316753 GGACGACGTATAGAAAACTATGAAAAC 58.683 37.037 0.00 0.00 0.00 2.43
610 611 8.976986 ACGACGTATAGAAAACTATGAAAACT 57.023 30.769 0.00 0.00 0.00 2.66
611 612 9.415544 ACGACGTATAGAAAACTATGAAAACTT 57.584 29.630 0.00 0.00 0.00 2.66
719 720 1.693083 GGACGAGCAAAATCGACGGG 61.693 60.000 2.78 0.00 45.56 5.28
840 841 0.118346 ACATGACACCCCTGACCCTA 59.882 55.000 0.00 0.00 0.00 3.53
863 864 0.889186 GCACCCCAGTCATTTCACGT 60.889 55.000 0.00 0.00 0.00 4.49
888 889 8.827677 GTCAAATTCTGTTCTATAAATACGCCT 58.172 33.333 0.00 0.00 0.00 5.52
912 914 0.656259 CTGTGCCATCAATCTCGCAG 59.344 55.000 0.00 0.00 0.00 5.18
946 948 4.441495 CCCCAAAGACAACAGAAAACCTTC 60.441 45.833 0.00 0.00 0.00 3.46
977 979 0.591170 ACGCACCAAAATCACCTTCG 59.409 50.000 0.00 0.00 0.00 3.79
990 992 0.747255 ACCTTCGATCTCATCACCGG 59.253 55.000 0.00 0.00 0.00 5.28
1115 1119 0.955919 GAATGCGATTCCCGATCCCC 60.956 60.000 0.00 0.00 41.76 4.81
1131 1135 1.383248 CCCGTCCCAATCCTCCTCT 60.383 63.158 0.00 0.00 0.00 3.69
1197 1202 0.731417 CATCTCCGGTTCGTCGTAGT 59.269 55.000 0.00 0.00 0.00 2.73
1199 1204 1.645034 TCTCCGGTTCGTCGTAGTAG 58.355 55.000 0.00 0.00 0.00 2.57
1340 1403 1.338674 CGGAACCTGGATTGCACAGTA 60.339 52.381 0.00 0.00 34.16 2.74
1341 1404 2.790433 GGAACCTGGATTGCACAGTAA 58.210 47.619 0.00 0.00 34.16 2.24
1497 1560 2.997986 GTCAGGTGTTACGTATGGTTGG 59.002 50.000 0.00 0.00 0.00 3.77
1515 1578 6.001460 TGGTTGGTCTTAATCTGTGGTTAAG 58.999 40.000 4.47 4.47 39.41 1.85
1527 1590 6.428083 TCTGTGGTTAAGTTGTTCAGGATA 57.572 37.500 0.00 0.00 0.00 2.59
1772 1967 0.181350 CAGGATTACCAGGTGAGGGC 59.819 60.000 0.76 0.00 38.94 5.19
2086 2289 3.244044 GGCAACTTTTGGAGCCAATGTTA 60.244 43.478 15.67 0.00 46.26 2.41
2119 2322 7.301868 TGAAATTCAGGTCCTTTTTAATGCT 57.698 32.000 0.00 0.00 0.00 3.79
2120 2323 7.734942 TGAAATTCAGGTCCTTTTTAATGCTT 58.265 30.769 0.00 0.00 0.00 3.91
2313 2516 0.883833 ATTGCTCCCGCTTGTTTCTG 59.116 50.000 0.00 0.00 36.97 3.02
2344 2550 9.720769 AACTATCATATTTCTTATAACCACCCG 57.279 33.333 0.00 0.00 0.00 5.28
2358 2564 3.292460 ACCACCCGAAAAGACAAAATGA 58.708 40.909 0.00 0.00 0.00 2.57
2362 2568 4.917415 CACCCGAAAAGACAAAATGACATC 59.083 41.667 0.00 0.00 0.00 3.06
2396 2833 0.620556 ACCATTGTCTTCATCCGCCT 59.379 50.000 0.00 0.00 0.00 5.52
2454 2891 3.057315 CACCTCCTTACAATTGCTTGTGG 60.057 47.826 5.05 4.07 45.16 4.17
2625 3075 6.725246 ACGGAAATATAGAATTTGAAAGGCG 58.275 36.000 0.00 0.00 0.00 5.52
2680 3130 2.089980 GATGAGGCACATGCACTTCTT 58.910 47.619 1.04 0.00 44.36 2.52
2830 3280 7.712639 TCATCCATCTATTTAGCAGTGAAAGAC 59.287 37.037 0.00 0.00 0.00 3.01
2896 3346 0.325296 TGGAAGCGGAGAGGTGGTAT 60.325 55.000 0.00 0.00 0.00 2.73
2897 3347 0.105039 GGAAGCGGAGAGGTGGTATG 59.895 60.000 0.00 0.00 0.00 2.39
2898 3348 0.105039 GAAGCGGAGAGGTGGTATGG 59.895 60.000 0.00 0.00 0.00 2.74
2899 3349 1.338136 AAGCGGAGAGGTGGTATGGG 61.338 60.000 0.00 0.00 0.00 4.00
2900 3350 2.808206 GCGGAGAGGTGGTATGGGG 61.808 68.421 0.00 0.00 0.00 4.96
2901 3351 1.075525 CGGAGAGGTGGTATGGGGA 60.076 63.158 0.00 0.00 0.00 4.81
2902 3352 1.115930 CGGAGAGGTGGTATGGGGAG 61.116 65.000 0.00 0.00 0.00 4.30
2903 3353 1.411651 GGAGAGGTGGTATGGGGAGC 61.412 65.000 0.00 0.00 0.00 4.70
2951 3830 2.124860 GGCGCACGAGGGGTTAAT 60.125 61.111 10.83 0.00 0.00 1.40
2965 3844 3.835395 GGGGTTAATGAACAACATTGGGA 59.165 43.478 0.00 0.00 46.93 4.37
2975 3854 2.652348 ACAACATTGGGAATAGGGGTGA 59.348 45.455 0.00 0.00 0.00 4.02
3059 3938 1.353394 GGGTGGGGAGGAATCGGAAT 61.353 60.000 0.00 0.00 0.00 3.01
3068 3947 3.063588 GGAGGAATCGGAATGAACGAAAC 59.936 47.826 0.00 0.00 44.20 2.78
3069 3948 3.670625 AGGAATCGGAATGAACGAAACA 58.329 40.909 0.00 0.00 44.20 2.83
3604 4535 1.407989 GGAAGAGTGATGCCCCTCTTG 60.408 57.143 6.64 0.00 45.57 3.02
3750 4681 9.787435 TTGTTCTGAATTACAGTACCTAATGTT 57.213 29.630 0.00 0.00 43.20 2.71
3807 4738 7.559590 AACTATCCTGTCTGAATGTTAATGC 57.440 36.000 0.00 0.00 0.00 3.56
3872 4803 2.406596 TTGCTGAGCATATCACTGCA 57.593 45.000 8.44 0.00 44.77 4.41
3910 4841 4.614284 CACATGCACATCGAAGTTTCTTTC 59.386 41.667 0.00 0.00 0.00 2.62
3911 4842 3.896648 TGCACATCGAAGTTTCTTTCC 57.103 42.857 0.00 0.00 0.00 3.13
3914 4845 3.125316 GCACATCGAAGTTTCTTTCCGAT 59.875 43.478 0.00 0.00 0.00 4.18
3915 4846 4.641954 CACATCGAAGTTTCTTTCCGATG 58.358 43.478 20.93 20.93 40.18 3.84
3920 4851 4.927425 TCGAAGTTTCTTTCCGATGGTTAG 59.073 41.667 0.00 0.00 0.00 2.34
3977 4908 6.871844 TCTCATTGATGAAGTGGTAGAAGAG 58.128 40.000 0.00 0.00 36.18 2.85
3991 4922 4.771054 GGTAGAAGAGAACAGTTACAGGGA 59.229 45.833 0.00 0.00 0.00 4.20
4024 4955 6.589139 GGAAAAGAAGAAAGAATCCATGCAAG 59.411 38.462 0.00 0.00 0.00 4.01
4054 4985 1.209128 CCTCGCTATAAACACTGGCG 58.791 55.000 0.00 0.00 45.93 5.69
4077 5008 4.170468 AGATCACAACTCAAGGTGGTTT 57.830 40.909 0.00 0.00 35.74 3.27
4083 5014 7.176589 TCACAACTCAAGGTGGTTTAAAAAT 57.823 32.000 0.00 0.00 35.74 1.82
4138 5070 2.363680 ACTCTGGCCTCGTCTATGATTG 59.636 50.000 3.32 0.00 0.00 2.67
4140 5072 2.101415 TCTGGCCTCGTCTATGATTGTG 59.899 50.000 3.32 0.00 0.00 3.33
4151 5083 5.419542 GTCTATGATTGTGGAGTGCACTTA 58.580 41.667 22.65 10.82 0.00 2.24
4159 5091 1.592223 GAGTGCACTTAGGGACGCT 59.408 57.895 22.65 0.00 33.93 5.07
4184 5116 2.358267 CTGGCTCTTGCATTGAAGATCC 59.642 50.000 0.00 0.00 38.31 3.36
4185 5117 1.332997 GGCTCTTGCATTGAAGATCCG 59.667 52.381 0.00 0.00 41.91 4.18
4186 5118 2.283298 GCTCTTGCATTGAAGATCCGA 58.717 47.619 0.00 0.00 39.41 4.55
4187 5119 2.877168 GCTCTTGCATTGAAGATCCGAT 59.123 45.455 0.00 0.00 39.41 4.18
4190 5122 2.602257 TGCATTGAAGATCCGATCGT 57.398 45.000 15.09 0.00 0.00 3.73
4193 5125 2.221981 GCATTGAAGATCCGATCGTTCC 59.778 50.000 15.09 2.07 0.00 3.62
4194 5126 3.457234 CATTGAAGATCCGATCGTTCCA 58.543 45.455 15.09 3.51 0.00 3.53
4195 5127 2.579207 TGAAGATCCGATCGTTCCAC 57.421 50.000 15.09 8.03 0.00 4.02
4196 5128 2.100197 TGAAGATCCGATCGTTCCACT 58.900 47.619 15.09 3.28 0.00 4.00
4197 5129 2.099263 TGAAGATCCGATCGTTCCACTC 59.901 50.000 15.09 8.12 0.00 3.51
4198 5130 2.060050 AGATCCGATCGTTCCACTCT 57.940 50.000 15.09 3.75 0.00 3.24
4199 5131 2.379972 AGATCCGATCGTTCCACTCTT 58.620 47.619 15.09 0.00 0.00 2.85
4200 5132 2.761208 AGATCCGATCGTTCCACTCTTT 59.239 45.455 15.09 0.00 0.00 2.52
4201 5133 2.649331 TCCGATCGTTCCACTCTTTC 57.351 50.000 15.09 0.00 0.00 2.62
4202 5134 1.890489 TCCGATCGTTCCACTCTTTCA 59.110 47.619 15.09 0.00 0.00 2.69
4203 5135 2.496070 TCCGATCGTTCCACTCTTTCAT 59.504 45.455 15.09 0.00 0.00 2.57
4205 5137 3.797256 CCGATCGTTCCACTCTTTCATAC 59.203 47.826 15.09 0.00 0.00 2.39
4206 5138 4.440250 CCGATCGTTCCACTCTTTCATACT 60.440 45.833 15.09 0.00 0.00 2.12
4207 5139 4.735822 CGATCGTTCCACTCTTTCATACTC 59.264 45.833 7.03 0.00 0.00 2.59
4208 5140 5.449314 CGATCGTTCCACTCTTTCATACTCT 60.449 44.000 7.03 0.00 0.00 3.24
4211 5143 6.157211 TCGTTCCACTCTTTCATACTCTTTC 58.843 40.000 0.00 0.00 0.00 2.62
4212 5144 5.926542 CGTTCCACTCTTTCATACTCTTTCA 59.073 40.000 0.00 0.00 0.00 2.69
4241 5302 3.057019 TGCTCGACACTGTGTTCAATAC 58.943 45.455 15.54 0.00 0.00 1.89
4247 5308 5.242171 TCGACACTGTGTTCAATACTTAGGA 59.758 40.000 15.54 0.00 0.00 2.94
4248 5309 5.573282 CGACACTGTGTTCAATACTTAGGAG 59.427 44.000 15.54 0.00 0.00 3.69
4249 5310 5.794894 ACACTGTGTTCAATACTTAGGAGG 58.205 41.667 7.80 0.00 0.00 4.30
4251 5312 6.213600 ACACTGTGTTCAATACTTAGGAGGAT 59.786 38.462 7.80 0.00 0.00 3.24
4252 5313 7.106239 CACTGTGTTCAATACTTAGGAGGATT 58.894 38.462 0.00 0.00 36.87 3.01
4254 5315 8.164070 ACTGTGTTCAATACTTAGGAGGATTTT 58.836 33.333 0.00 0.00 34.05 1.82
4255 5316 8.335532 TGTGTTCAATACTTAGGAGGATTTTG 57.664 34.615 0.00 0.00 34.05 2.44
4257 5318 6.093495 TGTTCAATACTTAGGAGGATTTTGCG 59.907 38.462 0.00 0.00 34.05 4.85
4258 5319 5.123227 TCAATACTTAGGAGGATTTTGCGG 58.877 41.667 0.00 0.00 34.05 5.69
4259 5320 4.772886 ATACTTAGGAGGATTTTGCGGT 57.227 40.909 0.00 0.00 0.00 5.68
4260 5321 5.881923 ATACTTAGGAGGATTTTGCGGTA 57.118 39.130 0.00 0.00 0.00 4.02
4261 5322 4.138487 ACTTAGGAGGATTTTGCGGTAG 57.862 45.455 0.00 0.00 0.00 3.18
4262 5323 3.118371 ACTTAGGAGGATTTTGCGGTAGG 60.118 47.826 0.00 0.00 0.00 3.18
4263 5324 0.546598 AGGAGGATTTTGCGGTAGGG 59.453 55.000 0.00 0.00 0.00 3.53
4264 5325 0.255033 GGAGGATTTTGCGGTAGGGT 59.745 55.000 0.00 0.00 0.00 4.34
4265 5326 1.487558 GGAGGATTTTGCGGTAGGGTA 59.512 52.381 0.00 0.00 0.00 3.69
4266 5327 2.105993 GGAGGATTTTGCGGTAGGGTAT 59.894 50.000 0.00 0.00 0.00 2.73
4267 5328 3.139077 GAGGATTTTGCGGTAGGGTATG 58.861 50.000 0.00 0.00 0.00 2.39
4268 5329 1.607148 GGATTTTGCGGTAGGGTATGC 59.393 52.381 0.00 0.00 0.00 3.14
4269 5330 2.294074 GATTTTGCGGTAGGGTATGCA 58.706 47.619 0.00 0.00 35.15 3.96
4270 5331 2.201921 TTTTGCGGTAGGGTATGCAA 57.798 45.000 0.00 0.00 44.81 4.08
4271 5332 1.455248 TTTGCGGTAGGGTATGCAAC 58.545 50.000 0.00 0.00 46.00 4.17
4272 5333 1.951424 TTTGCGGTAGGGTATGCAACC 60.951 52.381 8.94 8.94 46.00 3.77
4283 5344 3.279434 GGTATGCAACCTTACCTCTTGG 58.721 50.000 6.93 0.00 45.75 3.61
4284 5345 3.308188 GGTATGCAACCTTACCTCTTGGT 60.308 47.826 6.93 0.00 46.51 3.67
4285 5346 5.400589 GGTATGCAACCTTACCTCTTGGTG 61.401 50.000 6.93 0.00 45.35 4.17
4295 5356 3.629142 ACCTCTTGGTGCTGTTATACC 57.371 47.619 0.00 0.00 46.51 2.73
4296 5357 2.238898 ACCTCTTGGTGCTGTTATACCC 59.761 50.000 0.00 0.00 46.51 3.69
4297 5358 2.505819 CCTCTTGGTGCTGTTATACCCT 59.494 50.000 0.00 0.00 36.10 4.34
4298 5359 3.709653 CCTCTTGGTGCTGTTATACCCTA 59.290 47.826 0.00 0.00 36.10 3.53
4299 5360 4.443034 CCTCTTGGTGCTGTTATACCCTAC 60.443 50.000 0.00 0.00 36.10 3.18
4300 5361 3.453353 TCTTGGTGCTGTTATACCCTACC 59.547 47.826 0.00 0.00 36.10 3.18
4301 5362 1.758280 TGGTGCTGTTATACCCTACCG 59.242 52.381 0.00 0.00 36.10 4.02
4302 5363 1.758862 GGTGCTGTTATACCCTACCGT 59.241 52.381 0.00 0.00 0.00 4.83
4303 5364 2.223900 GGTGCTGTTATACCCTACCGTC 60.224 54.545 0.00 0.00 0.00 4.79
4304 5365 2.428171 GTGCTGTTATACCCTACCGTCA 59.572 50.000 0.00 0.00 0.00 4.35
4305 5366 3.069158 GTGCTGTTATACCCTACCGTCAT 59.931 47.826 0.00 0.00 0.00 3.06
4306 5367 3.069016 TGCTGTTATACCCTACCGTCATG 59.931 47.826 0.00 0.00 0.00 3.07
4307 5368 3.554337 GCTGTTATACCCTACCGTCATGG 60.554 52.174 0.00 0.00 46.41 3.66
4308 5369 3.893200 CTGTTATACCCTACCGTCATGGA 59.107 47.826 0.00 0.00 42.00 3.41
4309 5370 3.638160 TGTTATACCCTACCGTCATGGAC 59.362 47.826 0.00 0.00 42.00 4.02
4310 5371 1.713297 ATACCCTACCGTCATGGACC 58.287 55.000 0.00 0.00 42.00 4.46
4311 5372 0.397535 TACCCTACCGTCATGGACCC 60.398 60.000 0.00 0.00 42.00 4.46
4312 5373 1.382695 CCCTACCGTCATGGACCCT 60.383 63.158 0.00 0.00 42.00 4.34
4313 5374 1.686325 CCCTACCGTCATGGACCCTG 61.686 65.000 0.00 0.00 42.00 4.45
4314 5375 0.686441 CCTACCGTCATGGACCCTGA 60.686 60.000 0.00 0.00 42.00 3.86
4315 5376 0.460311 CTACCGTCATGGACCCTGAC 59.540 60.000 17.43 17.43 42.00 3.51
4326 5387 3.625745 ACCCTGACGGTAGCAAAAG 57.374 52.632 0.00 0.00 45.97 2.27
4327 5388 0.036306 ACCCTGACGGTAGCAAAAGG 59.964 55.000 0.00 0.00 45.97 3.11
4328 5389 0.676782 CCCTGACGGTAGCAAAAGGG 60.677 60.000 8.06 8.06 38.56 3.95
4329 5390 0.036306 CCTGACGGTAGCAAAAGGGT 59.964 55.000 0.00 0.00 0.00 4.34
4330 5391 1.544759 CCTGACGGTAGCAAAAGGGTT 60.545 52.381 0.00 0.00 0.00 4.11
4331 5392 2.289819 CCTGACGGTAGCAAAAGGGTTA 60.290 50.000 0.00 0.00 0.00 2.85
4332 5393 3.000727 CTGACGGTAGCAAAAGGGTTAG 58.999 50.000 0.00 0.00 0.00 2.34
4333 5394 2.633967 TGACGGTAGCAAAAGGGTTAGA 59.366 45.455 0.00 0.00 0.00 2.10
4334 5395 3.262405 TGACGGTAGCAAAAGGGTTAGAT 59.738 43.478 0.00 0.00 0.00 1.98
4335 5396 3.869832 GACGGTAGCAAAAGGGTTAGATC 59.130 47.826 0.00 0.00 0.00 2.75
4336 5397 3.518303 ACGGTAGCAAAAGGGTTAGATCT 59.482 43.478 0.00 0.00 0.00 2.75
4337 5398 4.019591 ACGGTAGCAAAAGGGTTAGATCTT 60.020 41.667 0.00 0.00 0.00 2.40
4338 5399 4.332819 CGGTAGCAAAAGGGTTAGATCTTG 59.667 45.833 0.00 0.00 0.00 3.02
4339 5400 5.497474 GGTAGCAAAAGGGTTAGATCTTGA 58.503 41.667 0.00 0.00 0.00 3.02
4340 5401 5.944007 GGTAGCAAAAGGGTTAGATCTTGAA 59.056 40.000 0.00 0.00 0.00 2.69
4343 5404 7.544804 AGCAAAAGGGTTAGATCTTGAAAAT 57.455 32.000 0.00 0.00 0.00 1.82
4346 5407 9.875691 GCAAAAGGGTTAGATCTTGAAAATAAT 57.124 29.630 0.00 0.00 0.00 1.28
4398 5459 6.827641 TCGAATAGGTTTCAGAAAAATGTCG 58.172 36.000 0.00 4.39 0.00 4.35
4429 5490 0.991146 TTAGCCTCCAGATGCACCAA 59.009 50.000 0.00 0.00 0.00 3.67
4460 5521 4.648007 AGGTGGACCTGCAGAGAA 57.352 55.556 17.39 0.00 46.55 2.87
4461 5522 2.854253 AGGTGGACCTGCAGAGAAA 58.146 52.632 17.39 0.00 46.55 2.52
4462 5523 1.140312 AGGTGGACCTGCAGAGAAAA 58.860 50.000 17.39 0.00 46.55 2.29
4463 5524 1.202818 AGGTGGACCTGCAGAGAAAAC 60.203 52.381 17.39 6.63 46.55 2.43
4464 5525 0.868406 GTGGACCTGCAGAGAAAACG 59.132 55.000 17.39 0.00 0.00 3.60
4465 5526 0.250295 TGGACCTGCAGAGAAAACGG 60.250 55.000 17.39 0.00 0.00 4.44
4466 5527 0.955919 GGACCTGCAGAGAAAACGGG 60.956 60.000 17.39 0.00 35.85 5.28
4467 5528 1.578206 GACCTGCAGAGAAAACGGGC 61.578 60.000 17.39 0.00 32.75 6.13
4468 5529 1.600636 CCTGCAGAGAAAACGGGCA 60.601 57.895 17.39 0.00 0.00 5.36
4469 5530 1.871772 CTGCAGAGAAAACGGGCAG 59.128 57.895 8.42 0.00 44.91 4.85
4470 5531 1.580845 CTGCAGAGAAAACGGGCAGG 61.581 60.000 8.42 0.00 46.10 4.85
4471 5532 2.982744 GCAGAGAAAACGGGCAGGC 61.983 63.158 0.00 0.00 0.00 4.85
4472 5533 2.034221 AGAGAAAACGGGCAGGCC 59.966 61.111 1.81 1.81 0.00 5.19
4473 5534 3.431725 GAGAAAACGGGCAGGCCG 61.432 66.667 32.71 32.71 36.85 6.13
4474 5535 4.265056 AGAAAACGGGCAGGCCGT 62.265 61.111 34.22 34.22 46.18 5.68
4475 5536 4.038080 GAAAACGGGCAGGCCGTG 62.038 66.667 39.04 19.14 43.33 4.94
4476 5537 4.572571 AAAACGGGCAGGCCGTGA 62.573 61.111 39.04 0.00 43.33 4.35
4477 5538 3.860930 AAAACGGGCAGGCCGTGAT 62.861 57.895 39.04 27.94 43.33 3.06
4481 5542 4.864334 GGGCAGGCCGTGATGAGG 62.864 72.222 3.89 0.00 36.85 3.86
4482 5543 4.101448 GGCAGGCCGTGATGAGGT 62.101 66.667 0.00 0.00 0.00 3.85
4483 5544 2.821366 GCAGGCCGTGATGAGGTG 60.821 66.667 0.00 0.00 0.00 4.00
4484 5545 2.665000 CAGGCCGTGATGAGGTGT 59.335 61.111 0.00 0.00 0.00 4.16
4485 5546 1.003355 CAGGCCGTGATGAGGTGTT 60.003 57.895 0.00 0.00 0.00 3.32
4486 5547 1.003355 AGGCCGTGATGAGGTGTTG 60.003 57.895 0.00 0.00 0.00 3.33
4487 5548 2.690778 GGCCGTGATGAGGTGTTGC 61.691 63.158 0.00 0.00 0.00 4.17
4488 5549 1.965930 GCCGTGATGAGGTGTTGCA 60.966 57.895 0.00 0.00 0.00 4.08
4489 5550 1.868997 CCGTGATGAGGTGTTGCAC 59.131 57.895 0.00 0.00 0.00 4.57
4536 5597 1.021390 GCAGATCGGGTTGTGAGGTG 61.021 60.000 0.00 0.00 0.00 4.00
4549 5610 1.373748 GAGGTGTTTGTCGGCGCTA 60.374 57.895 7.64 0.00 0.00 4.26
4578 5639 3.603365 CCGTCAGGCATTTTCCCC 58.397 61.111 0.00 0.00 0.00 4.81
4579 5640 2.406616 CCGTCAGGCATTTTCCCCG 61.407 63.158 0.00 0.00 0.00 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 1.156736 CCAGTTCTTACCCAACAGCG 58.843 55.000 0.00 0.00 0.00 5.18
55 56 7.291566 TCAAATTCTTACCAGTTCTTACCCAA 58.708 34.615 0.00 0.00 0.00 4.12
123 124 9.373450 ACACAAGAATATGATCCTACAGACTAT 57.627 33.333 0.00 0.00 0.00 2.12
484 485 1.580845 GCACCAACAGCAGTAGCAGG 61.581 60.000 0.00 0.00 45.49 4.85
536 537 9.905713 TGTTAATCATAAATATATCCTCCTGGC 57.094 33.333 0.00 0.00 0.00 4.85
559 560 9.713684 TCCCTTTAGATCCATTGATTTTATGTT 57.286 29.630 0.00 0.00 0.00 2.71
560 561 9.136323 GTCCCTTTAGATCCATTGATTTTATGT 57.864 33.333 0.00 0.00 0.00 2.29
561 562 8.292448 CGTCCCTTTAGATCCATTGATTTTATG 58.708 37.037 0.00 0.00 0.00 1.90
562 563 8.217799 TCGTCCCTTTAGATCCATTGATTTTAT 58.782 33.333 0.00 0.00 0.00 1.40
563 564 7.497909 GTCGTCCCTTTAGATCCATTGATTTTA 59.502 37.037 0.00 0.00 0.00 1.52
564 565 6.318900 GTCGTCCCTTTAGATCCATTGATTTT 59.681 38.462 0.00 0.00 0.00 1.82
565 566 5.823045 GTCGTCCCTTTAGATCCATTGATTT 59.177 40.000 0.00 0.00 0.00 2.17
566 567 5.368989 GTCGTCCCTTTAGATCCATTGATT 58.631 41.667 0.00 0.00 0.00 2.57
567 568 4.501571 CGTCGTCCCTTTAGATCCATTGAT 60.502 45.833 0.00 0.00 0.00 2.57
568 569 3.181479 CGTCGTCCCTTTAGATCCATTGA 60.181 47.826 0.00 0.00 0.00 2.57
569 570 3.123804 CGTCGTCCCTTTAGATCCATTG 58.876 50.000 0.00 0.00 0.00 2.82
570 571 2.764572 ACGTCGTCCCTTTAGATCCATT 59.235 45.455 0.00 0.00 0.00 3.16
571 572 2.385803 ACGTCGTCCCTTTAGATCCAT 58.614 47.619 0.00 0.00 0.00 3.41
572 573 1.843368 ACGTCGTCCCTTTAGATCCA 58.157 50.000 0.00 0.00 0.00 3.41
573 574 4.999950 TCTATACGTCGTCCCTTTAGATCC 59.000 45.833 0.00 0.00 0.00 3.36
574 575 6.551385 TTCTATACGTCGTCCCTTTAGATC 57.449 41.667 0.00 0.00 0.00 2.75
575 576 6.949352 TTTCTATACGTCGTCCCTTTAGAT 57.051 37.500 0.00 0.00 0.00 1.98
576 577 6.375455 AGTTTTCTATACGTCGTCCCTTTAGA 59.625 38.462 0.00 0.00 0.00 2.10
577 578 6.558909 AGTTTTCTATACGTCGTCCCTTTAG 58.441 40.000 0.00 0.00 0.00 1.85
578 579 6.515272 AGTTTTCTATACGTCGTCCCTTTA 57.485 37.500 0.00 0.00 0.00 1.85
579 580 5.397142 AGTTTTCTATACGTCGTCCCTTT 57.603 39.130 0.00 0.00 0.00 3.11
580 581 6.319658 TCATAGTTTTCTATACGTCGTCCCTT 59.680 38.462 0.00 0.00 40.73 3.95
581 582 5.824624 TCATAGTTTTCTATACGTCGTCCCT 59.175 40.000 0.00 0.00 40.73 4.20
582 583 6.064846 TCATAGTTTTCTATACGTCGTCCC 57.935 41.667 0.00 0.00 40.73 4.46
583 584 7.975866 TTTCATAGTTTTCTATACGTCGTCC 57.024 36.000 0.00 0.00 40.73 4.79
584 585 9.070149 AGTTTTCATAGTTTTCTATACGTCGTC 57.930 33.333 0.00 0.00 40.73 4.20
585 586 8.976986 AGTTTTCATAGTTTTCTATACGTCGT 57.023 30.769 2.21 2.21 40.73 4.34
712 713 0.883153 TTCTCGAATGTTCCCGTCGA 59.117 50.000 0.00 0.00 41.22 4.20
719 720 1.719780 ACGCGTTCTTCTCGAATGTTC 59.280 47.619 5.58 0.00 40.14 3.18
840 841 0.251787 GAAATGACTGGGGTGCCCTT 60.252 55.000 7.26 0.00 45.70 3.95
863 864 8.958119 AGGCGTATTTATAGAACAGAATTTGA 57.042 30.769 0.00 0.00 0.00 2.69
912 914 2.834549 TGTCTTTGGGGTGAGAGAGATC 59.165 50.000 0.00 0.00 0.00 2.75
977 979 0.394565 CCTTCCCCGGTGATGAGATC 59.605 60.000 0.00 0.00 0.00 2.75
1077 1081 2.813908 CGTACCAGCTTGCCGGTC 60.814 66.667 1.90 0.00 36.69 4.79
1115 1119 1.834263 AGAAAGAGGAGGATTGGGACG 59.166 52.381 0.00 0.00 0.00 4.79
1145 1149 5.224135 CCACAAACACCTAAAATTTACGGG 58.776 41.667 9.66 6.56 0.00 5.28
1197 1202 4.801891 AGTTTCTCAACATCGCGTTACTA 58.198 39.130 5.77 0.00 35.52 1.82
1199 1204 4.084745 TCAAGTTTCTCAACATCGCGTTAC 60.085 41.667 5.77 0.00 35.52 2.50
1340 1403 9.558396 AGTAGTAATACTAAGCTACAGATCGTT 57.442 33.333 0.00 0.00 37.02 3.85
1497 1560 8.149973 TGAACAACTTAACCACAGATTAAGAC 57.850 34.615 10.62 0.36 40.59 3.01
1515 1578 4.003648 CTCACCTGGTTATCCTGAACAAC 58.996 47.826 0.00 0.00 35.11 3.32
1527 1590 2.509964 GGATATCAACCCTCACCTGGTT 59.490 50.000 4.83 0.00 46.92 3.67
1772 1967 6.206048 TCAATCATGCATAACTAAGGCATCAG 59.794 38.462 0.00 0.00 45.81 2.90
2094 2297 7.910584 AGCATTAAAAAGGACCTGAATTTCAT 58.089 30.769 0.00 0.00 0.00 2.57
2108 2311 9.478019 CACGTTATCTCAGTAAGCATTAAAAAG 57.522 33.333 0.00 0.00 28.70 2.27
2119 2322 5.403166 CCGTTTCAACACGTTATCTCAGTAA 59.597 40.000 0.00 0.00 38.57 2.24
2120 2323 4.919168 CCGTTTCAACACGTTATCTCAGTA 59.081 41.667 0.00 0.00 38.57 2.74
2145 2348 8.734386 GTTGATTCAACAGACCTGAATTCTATT 58.266 33.333 21.75 0.00 42.27 1.73
2307 2510 8.443953 AGAAATATGATAGTTGCCTCAGAAAC 57.556 34.615 0.00 0.00 0.00 2.78
2344 2550 4.820897 GGGGGATGTCATTTTGTCTTTTC 58.179 43.478 0.00 0.00 0.00 2.29
2375 2581 0.734889 GCGGATGAAGACAATGGTGG 59.265 55.000 0.00 0.00 0.00 4.61
2396 2833 8.725405 TTGAAGTGTCAACAATACTGAGTAAA 57.275 30.769 0.00 0.00 38.88 2.01
2556 2994 4.572985 GCTTGTTGCAAGATATGGCATA 57.427 40.909 10.07 10.07 40.17 3.14
2625 3075 4.327680 ACCTCAACCACAATCTTTAGAGC 58.672 43.478 0.00 0.00 0.00 4.09
2680 3130 2.514896 TGCAGGACATGGTGCACA 59.485 55.556 20.43 5.24 44.70 4.57
2898 3348 2.573893 GAAACCCATCCCCAGCTCCC 62.574 65.000 0.00 0.00 0.00 4.30
2899 3349 1.076705 GAAACCCATCCCCAGCTCC 60.077 63.158 0.00 0.00 0.00 4.70
2900 3350 0.394899 CTGAAACCCATCCCCAGCTC 60.395 60.000 0.00 0.00 0.00 4.09
2901 3351 0.846427 TCTGAAACCCATCCCCAGCT 60.846 55.000 0.00 0.00 0.00 4.24
2902 3352 0.394899 CTCTGAAACCCATCCCCAGC 60.395 60.000 0.00 0.00 0.00 4.85
2903 3353 0.995024 ACTCTGAAACCCATCCCCAG 59.005 55.000 0.00 0.00 0.00 4.45
2951 3830 3.076785 ACCCCTATTCCCAATGTTGTTCA 59.923 43.478 0.00 0.00 0.00 3.18
2965 3844 3.245264 CCAGAAAACTGGTCACCCCTATT 60.245 47.826 7.96 0.00 39.56 1.73
3028 3907 3.402681 CCACCCTCCCACGATGCT 61.403 66.667 0.00 0.00 0.00 3.79
3059 3938 5.339348 CGTAGTACGTACATTGTTTCGTTCA 59.661 40.000 26.55 5.69 36.74 3.18
3604 4535 1.740025 GGTGCTGGCTCTTATTGACAC 59.260 52.381 0.00 0.00 0.00 3.67
3750 4681 2.680841 ACAACGAAGCAACTGTAGCAAA 59.319 40.909 0.00 0.00 0.00 3.68
3807 4738 0.740149 TCAGCGGCATATTGGCTTTG 59.260 50.000 1.45 0.00 41.25 2.77
3856 4787 4.377897 TGAAGATGCAGTGATATGCTCAG 58.622 43.478 0.00 0.00 46.63 3.35
3872 4803 0.679002 ATGTGCTGCGGCTTGAAGAT 60.679 50.000 20.27 0.00 39.59 2.40
3954 4885 6.871844 TCTCTTCTACCACTTCATCAATGAG 58.128 40.000 0.00 0.00 38.19 2.90
3991 4922 7.014711 GGATTCTTTCTTCTTTTCCTTCCAGTT 59.985 37.037 0.00 0.00 0.00 3.16
4054 4985 3.744660 ACCACCTTGAGTTGTGATCTTC 58.255 45.455 0.00 0.00 34.37 2.87
4077 5008 1.202330 CCCCATGGCCAGCATTTTTA 58.798 50.000 13.05 0.00 0.00 1.52
4138 5070 0.389948 CGTCCCTAAGTGCACTCCAC 60.390 60.000 21.95 11.12 45.01 4.02
4140 5072 1.448013 GCGTCCCTAAGTGCACTCC 60.448 63.158 21.95 3.37 0.00 3.85
4159 5091 0.537828 TCAATGCAAGAGCCAGCACA 60.538 50.000 0.00 0.00 44.49 4.57
4184 5116 4.673441 AGTATGAAAGAGTGGAACGATCG 58.327 43.478 14.88 14.88 45.86 3.69
4185 5117 5.897050 AGAGTATGAAAGAGTGGAACGATC 58.103 41.667 0.00 0.00 45.86 3.69
4186 5118 5.923733 AGAGTATGAAAGAGTGGAACGAT 57.076 39.130 0.00 0.00 45.86 3.73
4187 5119 5.723672 AAGAGTATGAAAGAGTGGAACGA 57.276 39.130 0.00 0.00 45.86 3.85
4190 5122 8.156820 TCAATGAAAGAGTATGAAAGAGTGGAA 58.843 33.333 0.00 0.00 0.00 3.53
4193 5125 8.449397 CCTTCAATGAAAGAGTATGAAAGAGTG 58.551 37.037 0.00 0.00 30.37 3.51
4194 5126 8.160106 ACCTTCAATGAAAGAGTATGAAAGAGT 58.840 33.333 0.00 0.00 30.37 3.24
4195 5127 8.449397 CACCTTCAATGAAAGAGTATGAAAGAG 58.551 37.037 0.00 0.00 30.37 2.85
4196 5128 7.094634 GCACCTTCAATGAAAGAGTATGAAAGA 60.095 37.037 0.00 0.00 30.37 2.52
4197 5129 7.025963 GCACCTTCAATGAAAGAGTATGAAAG 58.974 38.462 0.00 0.00 30.37 2.62
4198 5130 6.716628 AGCACCTTCAATGAAAGAGTATGAAA 59.283 34.615 0.00 0.00 30.37 2.69
4199 5131 6.240894 AGCACCTTCAATGAAAGAGTATGAA 58.759 36.000 0.00 0.00 0.00 2.57
4200 5132 5.809001 AGCACCTTCAATGAAAGAGTATGA 58.191 37.500 0.00 0.00 0.00 2.15
4201 5133 5.220548 CGAGCACCTTCAATGAAAGAGTATG 60.221 44.000 0.00 0.00 0.00 2.39
4202 5134 4.872691 CGAGCACCTTCAATGAAAGAGTAT 59.127 41.667 0.00 0.00 0.00 2.12
4203 5135 4.021456 TCGAGCACCTTCAATGAAAGAGTA 60.021 41.667 0.00 0.00 0.00 2.59
4205 5137 3.124297 GTCGAGCACCTTCAATGAAAGAG 59.876 47.826 0.00 0.00 0.00 2.85
4206 5138 3.067106 GTCGAGCACCTTCAATGAAAGA 58.933 45.455 0.00 0.00 0.00 2.52
4207 5139 2.807967 TGTCGAGCACCTTCAATGAAAG 59.192 45.455 0.00 0.00 0.00 2.62
4208 5140 2.548057 GTGTCGAGCACCTTCAATGAAA 59.452 45.455 0.00 0.00 42.10 2.69
4231 5292 7.251281 GCAAAATCCTCCTAAGTATTGAACAC 58.749 38.462 0.00 0.00 0.00 3.32
4241 5302 3.467803 CCTACCGCAAAATCCTCCTAAG 58.532 50.000 0.00 0.00 0.00 2.18
4247 5308 2.748465 GCATACCCTACCGCAAAATCCT 60.748 50.000 0.00 0.00 0.00 3.24
4248 5309 1.607148 GCATACCCTACCGCAAAATCC 59.393 52.381 0.00 0.00 0.00 3.01
4249 5310 2.294074 TGCATACCCTACCGCAAAATC 58.706 47.619 0.00 0.00 0.00 2.17
4251 5312 1.813786 GTTGCATACCCTACCGCAAAA 59.186 47.619 0.00 0.00 45.19 2.44
4252 5313 1.455248 GTTGCATACCCTACCGCAAA 58.545 50.000 0.00 0.00 45.19 3.68
4254 5315 1.222387 GGTTGCATACCCTACCGCA 59.778 57.895 6.76 0.00 41.43 5.69
4255 5316 4.136250 GGTTGCATACCCTACCGC 57.864 61.111 6.76 0.00 41.43 5.68
4276 5337 2.505819 AGGGTATAACAGCACCAAGAGG 59.494 50.000 0.00 0.00 36.48 3.69
4277 5338 3.914426 AGGGTATAACAGCACCAAGAG 57.086 47.619 0.00 0.00 36.48 2.85
4278 5339 3.453353 GGTAGGGTATAACAGCACCAAGA 59.547 47.826 0.00 0.00 36.48 3.02
4279 5340 3.740141 CGGTAGGGTATAACAGCACCAAG 60.740 52.174 5.76 0.00 36.48 3.61
4280 5341 2.168936 CGGTAGGGTATAACAGCACCAA 59.831 50.000 5.76 0.00 36.48 3.67
4281 5342 1.758280 CGGTAGGGTATAACAGCACCA 59.242 52.381 5.76 0.00 36.48 4.17
4282 5343 1.758862 ACGGTAGGGTATAACAGCACC 59.241 52.381 0.00 0.00 0.00 5.01
4283 5344 2.428171 TGACGGTAGGGTATAACAGCAC 59.572 50.000 0.00 0.00 0.00 4.40
4284 5345 2.737544 TGACGGTAGGGTATAACAGCA 58.262 47.619 0.00 0.00 0.00 4.41
4285 5346 3.554337 CCATGACGGTAGGGTATAACAGC 60.554 52.174 0.00 0.00 0.00 4.40
4286 5347 3.893200 TCCATGACGGTAGGGTATAACAG 59.107 47.826 0.00 0.00 35.57 3.16
4287 5348 3.638160 GTCCATGACGGTAGGGTATAACA 59.362 47.826 0.00 0.00 35.57 2.41
4288 5349 3.006217 GGTCCATGACGGTAGGGTATAAC 59.994 52.174 0.00 0.00 35.57 1.89
4289 5350 3.233507 GGTCCATGACGGTAGGGTATAA 58.766 50.000 0.00 0.00 35.57 0.98
4290 5351 2.491455 GGGTCCATGACGGTAGGGTATA 60.491 54.545 0.00 0.00 35.57 1.47
4291 5352 1.713297 GGTCCATGACGGTAGGGTAT 58.287 55.000 0.00 0.00 35.57 2.73
4292 5353 0.397535 GGGTCCATGACGGTAGGGTA 60.398 60.000 0.00 0.00 35.57 3.69
4293 5354 1.688187 GGGTCCATGACGGTAGGGT 60.688 63.158 0.00 0.00 35.57 4.34
4294 5355 1.382695 AGGGTCCATGACGGTAGGG 60.383 63.158 0.00 0.00 35.57 3.53
4295 5356 0.686441 TCAGGGTCCATGACGGTAGG 60.686 60.000 1.03 0.00 35.57 3.18
4296 5357 0.460311 GTCAGGGTCCATGACGGTAG 59.540 60.000 20.14 0.00 37.88 3.18
4297 5358 2.587080 GTCAGGGTCCATGACGGTA 58.413 57.895 20.14 0.00 37.88 4.02
4298 5359 3.388841 GTCAGGGTCCATGACGGT 58.611 61.111 20.14 0.00 37.88 4.83
4309 5370 0.676782 CCCTTTTGCTACCGTCAGGG 60.677 60.000 0.00 0.00 43.47 4.45
4310 5371 0.036306 ACCCTTTTGCTACCGTCAGG 59.964 55.000 0.00 0.00 45.13 3.86
4311 5372 1.892209 AACCCTTTTGCTACCGTCAG 58.108 50.000 0.00 0.00 0.00 3.51
4312 5373 2.633967 TCTAACCCTTTTGCTACCGTCA 59.366 45.455 0.00 0.00 0.00 4.35
4313 5374 3.323751 TCTAACCCTTTTGCTACCGTC 57.676 47.619 0.00 0.00 0.00 4.79
4314 5375 3.518303 AGATCTAACCCTTTTGCTACCGT 59.482 43.478 0.00 0.00 0.00 4.83
4315 5376 4.138487 AGATCTAACCCTTTTGCTACCG 57.862 45.455 0.00 0.00 0.00 4.02
4316 5377 5.497474 TCAAGATCTAACCCTTTTGCTACC 58.503 41.667 0.00 0.00 0.00 3.18
4317 5378 7.448748 TTTCAAGATCTAACCCTTTTGCTAC 57.551 36.000 0.00 0.00 0.00 3.58
4318 5379 8.650143 ATTTTCAAGATCTAACCCTTTTGCTA 57.350 30.769 0.00 0.00 0.00 3.49
4319 5380 6.976934 TTTTCAAGATCTAACCCTTTTGCT 57.023 33.333 0.00 0.00 0.00 3.91
4320 5381 9.875691 ATTATTTTCAAGATCTAACCCTTTTGC 57.124 29.630 0.00 0.00 0.00 3.68
4370 5431 8.630037 ACATTTTTCTGAAACCTATTCGAGTTT 58.370 29.630 1.58 0.59 38.85 2.66
4371 5432 8.166422 ACATTTTTCTGAAACCTATTCGAGTT 57.834 30.769 1.58 0.00 0.00 3.01
4372 5433 7.360101 CGACATTTTTCTGAAACCTATTCGAGT 60.360 37.037 1.58 0.00 0.00 4.18
4373 5434 6.955963 CGACATTTTTCTGAAACCTATTCGAG 59.044 38.462 1.58 0.00 0.00 4.04
4374 5435 6.647481 TCGACATTTTTCTGAAACCTATTCGA 59.353 34.615 1.58 9.85 0.00 3.71
4375 5436 6.827641 TCGACATTTTTCTGAAACCTATTCG 58.172 36.000 1.58 7.89 0.00 3.34
4381 5442 6.695278 TCATGTTTCGACATTTTTCTGAAACC 59.305 34.615 1.58 0.00 44.71 3.27
4393 5454 6.404734 GGAGGCTAAATTTCATGTTTCGACAT 60.405 38.462 0.00 0.00 0.00 3.06
4394 5455 5.106317 GGAGGCTAAATTTCATGTTTCGACA 60.106 40.000 0.00 0.00 0.00 4.35
4398 5459 6.515272 TCTGGAGGCTAAATTTCATGTTTC 57.485 37.500 0.00 0.00 0.00 2.78
4404 5465 3.696051 GTGCATCTGGAGGCTAAATTTCA 59.304 43.478 8.63 0.00 39.14 2.69
4429 5490 1.757306 CACCTGCCTGTTGGTCTCT 59.243 57.895 0.00 0.00 33.75 3.10
4449 5510 1.600916 GCCCGTTTTCTCTGCAGGT 60.601 57.895 15.13 0.00 0.00 4.00
4453 5514 2.982744 GCCTGCCCGTTTTCTCTGC 61.983 63.158 0.00 0.00 0.00 4.26
4464 5525 4.864334 CCTCATCACGGCCTGCCC 62.864 72.222 0.00 0.00 0.00 5.36
4465 5526 4.101448 ACCTCATCACGGCCTGCC 62.101 66.667 0.00 0.00 0.00 4.85
4466 5527 2.821366 CACCTCATCACGGCCTGC 60.821 66.667 0.00 0.00 0.00 4.85
4467 5528 1.003355 AACACCTCATCACGGCCTG 60.003 57.895 0.00 0.00 0.00 4.85
4468 5529 1.003355 CAACACCTCATCACGGCCT 60.003 57.895 0.00 0.00 0.00 5.19
4469 5530 2.690778 GCAACACCTCATCACGGCC 61.691 63.158 0.00 0.00 0.00 6.13
4470 5531 1.965930 TGCAACACCTCATCACGGC 60.966 57.895 0.00 0.00 0.00 5.68
4471 5532 1.868997 GTGCAACACCTCATCACGG 59.131 57.895 0.00 0.00 36.32 4.94
4481 5542 2.978010 CCTGGGACGGTGCAACAC 60.978 66.667 0.98 0.00 39.98 3.32
4482 5543 4.947147 GCCTGGGACGGTGCAACA 62.947 66.667 0.98 0.00 39.98 3.33
4507 5568 2.101185 CGATCTGCTCGTCGTGCT 59.899 61.111 18.94 0.20 42.56 4.40
4512 5573 1.078759 CACAACCCGATCTGCTCGTC 61.079 60.000 0.00 0.00 46.18 4.20
4513 5574 1.079819 CACAACCCGATCTGCTCGT 60.080 57.895 0.00 0.00 46.18 4.18
4528 5589 1.885388 CGCCGACAAACACCTCACA 60.885 57.895 0.00 0.00 0.00 3.58
4529 5590 2.935955 CGCCGACAAACACCTCAC 59.064 61.111 0.00 0.00 0.00 3.51
4536 5597 0.589708 AACCTTTAGCGCCGACAAAC 59.410 50.000 2.29 0.00 0.00 2.93
4549 5610 0.535102 CCTGACGGCAGACAACCTTT 60.535 55.000 23.07 0.00 45.17 3.11


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

AutoCloner maintained by Alex Coulton.