Multiple sequence alignment - TraesCS7D01G023400

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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 TraesCS7D01G023400 chr7D 100.000 3209 0 0 1 3209 10964660 10961452 0.000000e+00 5927.0
1 TraesCS7D01G023400 chr7D 85.461 1410 133 37 1815 3202 10972505 10971146 0.000000e+00 1402.0
2 TraesCS7D01G023400 chr7D 83.723 1370 177 25 1092 2427 10910344 10908987 0.000000e+00 1253.0
3 TraesCS7D01G023400 chr7D 90.372 779 49 16 2450 3209 10903402 10902631 0.000000e+00 1000.0
4 TraesCS7D01G023400 chr7D 77.159 1725 271 75 930 2605 10151177 10149527 0.000000e+00 889.0
5 TraesCS7D01G023400 chr7D 78.723 1363 222 37 1095 2438 10465539 10464226 0.000000e+00 848.0
6 TraesCS7D01G023400 chr7D 78.109 1407 234 37 1028 2412 8870162 8871516 0.000000e+00 824.0
7 TraesCS7D01G023400 chr7D 73.992 769 106 55 2446 3194 9382242 9382936 3.220000e-55 226.0
8 TraesCS7D01G023400 chr7A 91.368 2398 146 35 855 3200 10092196 10089808 0.000000e+00 3225.0
9 TraesCS7D01G023400 chr7A 79.540 1828 242 60 999 2805 10157673 10155957 0.000000e+00 1182.0
10 TraesCS7D01G023400 chr7A 79.901 1612 256 39 1009 2604 10169953 10168394 0.000000e+00 1120.0
11 TraesCS7D01G023400 chr7A 90.283 813 71 6 1817 2628 10168224 10167419 0.000000e+00 1057.0
12 TraesCS7D01G023400 chr7A 79.012 1620 271 46 1009 2605 114414390 114412817 0.000000e+00 1044.0
13 TraesCS7D01G023400 chr7A 77.059 1809 316 64 1009 2770 114688758 114687002 0.000000e+00 950.0
14 TraesCS7D01G023400 chr7A 89.228 557 46 7 2666 3209 10167418 10166863 0.000000e+00 684.0
15 TraesCS7D01G023400 chr7A 98.438 64 1 0 799 862 10092277 10092214 2.620000e-21 113.0
16 TraesCS7D01G023400 chr7B 79.975 1618 263 39 1006 2604 68223641 68222066 0.000000e+00 1136.0
17 TraesCS7D01G023400 chr7B 89.735 565 54 3 58 621 197038887 197039448 0.000000e+00 719.0
18 TraesCS7D01G023400 chr4B 81.505 1395 220 24 1001 2378 654201948 654203321 0.000000e+00 1112.0
19 TraesCS7D01G023400 chr4B 89.261 568 50 9 58 621 666750282 666750842 0.000000e+00 701.0
20 TraesCS7D01G023400 chr4D 80.569 1477 234 32 930 2378 507352313 507350862 0.000000e+00 1088.0
21 TraesCS7D01G023400 chr4A 78.110 1640 274 58 1003 2602 728645443 728643849 0.000000e+00 961.0
22 TraesCS7D01G023400 chr4A 77.213 1830 298 62 999 2794 729157300 729159044 0.000000e+00 959.0
23 TraesCS7D01G023400 chr4A 78.678 1543 252 54 1092 2603 729819319 729820815 0.000000e+00 955.0
24 TraesCS7D01G023400 chr4A 77.551 1715 286 49 1091 2778 729880945 729882587 0.000000e+00 942.0
25 TraesCS7D01G023400 chr4A 81.066 1220 192 27 999 2209 728353077 728351888 0.000000e+00 937.0
26 TraesCS7D01G023400 chr4A 85.141 922 78 25 2304 3209 727412179 727413057 0.000000e+00 889.0
27 TraesCS7D01G023400 chr4A 77.649 1548 264 41 1057 2579 730456111 730457601 0.000000e+00 867.0
28 TraesCS7D01G023400 chr4A 77.326 1548 277 38 1057 2579 729972612 729971114 0.000000e+00 846.0
29 TraesCS7D01G023400 chr4A 79.481 1272 186 51 985 2222 731097636 731098866 0.000000e+00 833.0
30 TraesCS7D01G023400 chr4A 78.100 1379 233 43 1005 2351 729827486 729828827 0.000000e+00 809.0
31 TraesCS7D01G023400 chr4A 76.538 1560 274 42 1057 2579 730509840 730511344 0.000000e+00 769.0
32 TraesCS7D01G023400 chr4A 77.830 1069 168 35 1731 2778 729678548 729679568 5.930000e-167 597.0
33 TraesCS7D01G023400 chr4A 88.000 250 16 5 2970 3209 727413222 727413467 1.880000e-72 283.0
34 TraesCS7D01G023400 chr4A 86.842 114 11 3 3089 3200 727131553 727131664 1.210000e-24 124.0
35 TraesCS7D01G023400 chr4A 96.970 33 0 1 624 655 192738650 192738682 2.000000e-03 54.7
36 TraesCS7D01G023400 chr3B 90.813 566 46 5 58 621 557941458 557942019 0.000000e+00 752.0
37 TraesCS7D01G023400 chr3B 89.242 567 51 9 58 621 408314482 408313923 0.000000e+00 701.0
38 TraesCS7D01G023400 chr1D 89.894 564 47 9 58 617 402717711 402718268 0.000000e+00 717.0
39 TraesCS7D01G023400 chr2A 89.613 568 52 4 58 621 141092036 141092600 0.000000e+00 715.0
40 TraesCS7D01G023400 chr6A 89.594 567 50 8 58 621 516011520 516010960 0.000000e+00 712.0
41 TraesCS7D01G023400 chr5B 89.418 567 51 8 58 621 74020634 74021194 0.000000e+00 706.0
42 TraesCS7D01G023400 chr5B 89.418 567 51 8 58 621 74026158 74026718 0.000000e+00 706.0
43 TraesCS7D01G023400 chr6D 76.771 607 84 33 2218 2813 84281277 84281837 1.460000e-73 287.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G023400 chr7D 10961452 10964660 3208 True 5927.000000 5927 100.000000 1 3209 1 chr7D.!!$R5 3208
1 TraesCS7D01G023400 chr7D 10971146 10972505 1359 True 1402.000000 1402 85.461000 1815 3202 1 chr7D.!!$R6 1387
2 TraesCS7D01G023400 chr7D 10908987 10910344 1357 True 1253.000000 1253 83.723000 1092 2427 1 chr7D.!!$R4 1335
3 TraesCS7D01G023400 chr7D 10902631 10903402 771 True 1000.000000 1000 90.372000 2450 3209 1 chr7D.!!$R3 759
4 TraesCS7D01G023400 chr7D 10149527 10151177 1650 True 889.000000 889 77.159000 930 2605 1 chr7D.!!$R1 1675
5 TraesCS7D01G023400 chr7D 10464226 10465539 1313 True 848.000000 848 78.723000 1095 2438 1 chr7D.!!$R2 1343
6 TraesCS7D01G023400 chr7D 8870162 8871516 1354 False 824.000000 824 78.109000 1028 2412 1 chr7D.!!$F1 1384
7 TraesCS7D01G023400 chr7D 9382242 9382936 694 False 226.000000 226 73.992000 2446 3194 1 chr7D.!!$F2 748
8 TraesCS7D01G023400 chr7A 10089808 10092277 2469 True 1669.000000 3225 94.903000 799 3200 2 chr7A.!!$R4 2401
9 TraesCS7D01G023400 chr7A 10155957 10157673 1716 True 1182.000000 1182 79.540000 999 2805 1 chr7A.!!$R1 1806
10 TraesCS7D01G023400 chr7A 114412817 114414390 1573 True 1044.000000 1044 79.012000 1009 2605 1 chr7A.!!$R2 1596
11 TraesCS7D01G023400 chr7A 10166863 10169953 3090 True 953.666667 1120 86.470667 1009 3209 3 chr7A.!!$R5 2200
12 TraesCS7D01G023400 chr7A 114687002 114688758 1756 True 950.000000 950 77.059000 1009 2770 1 chr7A.!!$R3 1761
13 TraesCS7D01G023400 chr7B 68222066 68223641 1575 True 1136.000000 1136 79.975000 1006 2604 1 chr7B.!!$R1 1598
14 TraesCS7D01G023400 chr7B 197038887 197039448 561 False 719.000000 719 89.735000 58 621 1 chr7B.!!$F1 563
15 TraesCS7D01G023400 chr4B 654201948 654203321 1373 False 1112.000000 1112 81.505000 1001 2378 1 chr4B.!!$F1 1377
16 TraesCS7D01G023400 chr4B 666750282 666750842 560 False 701.000000 701 89.261000 58 621 1 chr4B.!!$F2 563
17 TraesCS7D01G023400 chr4D 507350862 507352313 1451 True 1088.000000 1088 80.569000 930 2378 1 chr4D.!!$R1 1448
18 TraesCS7D01G023400 chr4A 728643849 728645443 1594 True 961.000000 961 78.110000 1003 2602 1 chr4A.!!$R2 1599
19 TraesCS7D01G023400 chr4A 729157300 729159044 1744 False 959.000000 959 77.213000 999 2794 1 chr4A.!!$F3 1795
20 TraesCS7D01G023400 chr4A 729819319 729820815 1496 False 955.000000 955 78.678000 1092 2603 1 chr4A.!!$F5 1511
21 TraesCS7D01G023400 chr4A 729880945 729882587 1642 False 942.000000 942 77.551000 1091 2778 1 chr4A.!!$F7 1687
22 TraesCS7D01G023400 chr4A 728351888 728353077 1189 True 937.000000 937 81.066000 999 2209 1 chr4A.!!$R1 1210
23 TraesCS7D01G023400 chr4A 730456111 730457601 1490 False 867.000000 867 77.649000 1057 2579 1 chr4A.!!$F8 1522
24 TraesCS7D01G023400 chr4A 729971114 729972612 1498 True 846.000000 846 77.326000 1057 2579 1 chr4A.!!$R3 1522
25 TraesCS7D01G023400 chr4A 731097636 731098866 1230 False 833.000000 833 79.481000 985 2222 1 chr4A.!!$F10 1237
26 TraesCS7D01G023400 chr4A 729827486 729828827 1341 False 809.000000 809 78.100000 1005 2351 1 chr4A.!!$F6 1346
27 TraesCS7D01G023400 chr4A 730509840 730511344 1504 False 769.000000 769 76.538000 1057 2579 1 chr4A.!!$F9 1522
28 TraesCS7D01G023400 chr4A 729678548 729679568 1020 False 597.000000 597 77.830000 1731 2778 1 chr4A.!!$F4 1047
29 TraesCS7D01G023400 chr4A 727412179 727413467 1288 False 586.000000 889 86.570500 2304 3209 2 chr4A.!!$F11 905
30 TraesCS7D01G023400 chr3B 557941458 557942019 561 False 752.000000 752 90.813000 58 621 1 chr3B.!!$F1 563
31 TraesCS7D01G023400 chr3B 408313923 408314482 559 True 701.000000 701 89.242000 58 621 1 chr3B.!!$R1 563
32 TraesCS7D01G023400 chr1D 402717711 402718268 557 False 717.000000 717 89.894000 58 617 1 chr1D.!!$F1 559
33 TraesCS7D01G023400 chr2A 141092036 141092600 564 False 715.000000 715 89.613000 58 621 1 chr2A.!!$F1 563
34 TraesCS7D01G023400 chr6A 516010960 516011520 560 True 712.000000 712 89.594000 58 621 1 chr6A.!!$R1 563
35 TraesCS7D01G023400 chr5B 74020634 74021194 560 False 706.000000 706 89.418000 58 621 1 chr5B.!!$F1 563
36 TraesCS7D01G023400 chr5B 74026158 74026718 560 False 706.000000 706 89.418000 58 621 1 chr5B.!!$F2 563
37 TraesCS7D01G023400 chr6D 84281277 84281837 560 False 287.000000 287 76.771000 2218 2813 1 chr6D.!!$F1 595

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
460 471 0.105658 AGGCGGCTAGACTTCCCATA 60.106 55.0 11.03 0.00 30.6 2.74 F
649 660 0.108756 GTGGCTAGGTCTCGGTCAAC 60.109 60.0 0.00 0.00 0.0 3.18 F
1742 1904 0.035534 ATGTACGTGATTGGCAGCCA 60.036 50.0 11.22 11.22 0.0 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1631 1772 0.111832 ACACCAGTCTCCTGTCCGTA 59.888 55.0 0.00 0.0 36.95 4.02 R
1924 3037 0.250234 CGATCCTTGAGCCACCAGAA 59.750 55.0 0.00 0.0 0.00 3.02 R
3024 4298 0.108186 TCTGCTGCATTACCCTGACG 60.108 55.0 1.31 0.0 0.00 4.35 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 35 3.626154 CGACTTCGCTAGGGAGTTC 57.374 57.895 9.68 9.15 0.00 3.01
35 36 1.096416 CGACTTCGCTAGGGAGTTCT 58.904 55.000 9.68 0.00 0.00 3.01
36 37 1.473278 CGACTTCGCTAGGGAGTTCTT 59.527 52.381 9.68 0.00 0.00 2.52
37 38 2.732597 CGACTTCGCTAGGGAGTTCTTG 60.733 54.545 9.68 1.18 0.00 3.02
38 39 2.492484 GACTTCGCTAGGGAGTTCTTGA 59.508 50.000 9.68 0.00 0.00 3.02
39 40 2.231721 ACTTCGCTAGGGAGTTCTTGAC 59.768 50.000 9.68 0.00 0.00 3.18
40 41 1.183549 TCGCTAGGGAGTTCTTGACC 58.816 55.000 5.20 0.00 0.00 4.02
41 42 0.179134 CGCTAGGGAGTTCTTGACCG 60.179 60.000 0.00 0.00 0.00 4.79
42 43 0.460459 GCTAGGGAGTTCTTGACCGC 60.460 60.000 0.00 0.00 0.00 5.68
43 44 0.175989 CTAGGGAGTTCTTGACCGCC 59.824 60.000 0.00 0.00 0.00 6.13
44 45 0.543410 TAGGGAGTTCTTGACCGCCA 60.543 55.000 0.00 0.00 0.00 5.69
45 46 1.072505 GGGAGTTCTTGACCGCCAA 59.927 57.895 0.00 0.00 0.00 4.52
46 47 0.536460 GGGAGTTCTTGACCGCCAAA 60.536 55.000 0.00 0.00 33.76 3.28
47 48 1.314730 GGAGTTCTTGACCGCCAAAA 58.685 50.000 0.00 0.00 33.76 2.44
48 49 1.679153 GGAGTTCTTGACCGCCAAAAA 59.321 47.619 0.00 0.00 33.76 1.94
68 69 4.864334 GATGCACCCCAGCGGAGG 62.864 72.222 0.00 0.00 37.31 4.30
127 128 3.072468 CCTCCAACGCCGAGGGTA 61.072 66.667 0.00 0.00 42.85 3.69
144 145 1.446907 GTAATGCACTGCAGCTCACT 58.553 50.000 15.27 4.20 43.65 3.41
205 207 2.690778 GCGGGCGCTTTTGATGACT 61.691 57.895 7.64 0.00 38.26 3.41
214 216 2.412847 GCTTTTGATGACTCGAAACCCG 60.413 50.000 0.00 0.00 40.25 5.28
224 226 1.068417 CGAAACCCGATATGCCCGA 59.932 57.895 0.00 0.00 41.76 5.14
243 245 1.997874 GAGGGACCACATCAGGGCT 60.998 63.158 0.00 0.00 36.69 5.19
245 247 2.300967 GGGACCACATCAGGGCTCA 61.301 63.158 0.00 0.00 37.02 4.26
301 303 1.381327 CCTAGGGCCTCGAGGTTCA 60.381 63.158 31.43 14.05 37.57 3.18
345 347 2.726832 ACGAAGAACGAGGAAGAAGG 57.273 50.000 0.00 0.00 45.77 3.46
347 349 2.626743 ACGAAGAACGAGGAAGAAGGAA 59.373 45.455 0.00 0.00 45.77 3.36
360 366 4.893524 GGAAGAAGGAAAACAAGGGAGAAA 59.106 41.667 0.00 0.00 0.00 2.52
449 460 3.767673 CCTTGGTATATAAGAGGCGGCTA 59.232 47.826 13.24 0.00 0.00 3.93
460 471 0.105658 AGGCGGCTAGACTTCCCATA 60.106 55.000 11.03 0.00 30.60 2.74
465 476 2.693591 CGGCTAGACTTCCCATACAAGA 59.306 50.000 0.00 0.00 0.00 3.02
547 558 8.989653 ACTTTCCAAAACTGTTCGATTTAAAA 57.010 26.923 0.00 0.00 0.00 1.52
548 559 9.425577 ACTTTCCAAAACTGTTCGATTTAAAAA 57.574 25.926 0.00 0.00 0.00 1.94
565 576 7.519032 TTTAAAAACTAGCTGCACCTTGTAT 57.481 32.000 1.02 0.00 0.00 2.29
568 579 3.703001 ACTAGCTGCACCTTGTATGTT 57.297 42.857 1.02 0.00 0.00 2.71
621 632 1.541588 ACGAGCCCAAAAGCAATCTTC 59.458 47.619 0.00 0.00 34.23 2.87
622 633 1.815003 CGAGCCCAAAAGCAATCTTCT 59.185 47.619 0.00 0.00 34.23 2.85
623 634 3.009723 CGAGCCCAAAAGCAATCTTCTA 58.990 45.455 0.00 0.00 34.23 2.10
624 635 3.629398 CGAGCCCAAAAGCAATCTTCTAT 59.371 43.478 0.00 0.00 34.23 1.98
625 636 4.816385 CGAGCCCAAAAGCAATCTTCTATA 59.184 41.667 0.00 0.00 34.23 1.31
626 637 5.049818 CGAGCCCAAAAGCAATCTTCTATAG 60.050 44.000 0.00 0.00 34.23 1.31
627 638 5.136105 AGCCCAAAAGCAATCTTCTATAGG 58.864 41.667 0.00 0.00 34.23 2.57
628 639 5.103940 AGCCCAAAAGCAATCTTCTATAGGA 60.104 40.000 0.00 0.00 34.23 2.94
629 640 5.772169 GCCCAAAAGCAATCTTCTATAGGAT 59.228 40.000 0.00 0.00 0.00 3.24
630 641 6.294397 GCCCAAAAGCAATCTTCTATAGGATG 60.294 42.308 0.00 0.00 0.00 3.51
631 642 6.774656 CCCAAAAGCAATCTTCTATAGGATGT 59.225 38.462 0.00 0.00 0.00 3.06
632 643 7.255381 CCCAAAAGCAATCTTCTATAGGATGTG 60.255 40.741 0.00 0.10 0.00 3.21
633 644 7.255381 CCAAAAGCAATCTTCTATAGGATGTGG 60.255 40.741 0.00 0.00 0.00 4.17
634 645 4.904241 AGCAATCTTCTATAGGATGTGGC 58.096 43.478 0.00 2.20 0.00 5.01
635 646 4.596643 AGCAATCTTCTATAGGATGTGGCT 59.403 41.667 0.00 4.19 0.00 4.75
636 647 5.782331 AGCAATCTTCTATAGGATGTGGCTA 59.218 40.000 0.00 0.00 0.00 3.93
637 648 6.070881 AGCAATCTTCTATAGGATGTGGCTAG 60.071 42.308 0.00 0.00 0.00 3.42
638 649 6.638610 CAATCTTCTATAGGATGTGGCTAGG 58.361 44.000 0.00 0.00 0.00 3.02
639 650 5.340891 TCTTCTATAGGATGTGGCTAGGT 57.659 43.478 0.00 0.00 0.00 3.08
640 651 5.326069 TCTTCTATAGGATGTGGCTAGGTC 58.674 45.833 0.00 0.00 0.00 3.85
641 652 5.075205 TCTTCTATAGGATGTGGCTAGGTCT 59.925 44.000 0.00 0.00 0.00 3.85
642 653 4.924625 TCTATAGGATGTGGCTAGGTCTC 58.075 47.826 0.00 0.00 0.00 3.36
643 654 1.982660 TAGGATGTGGCTAGGTCTCG 58.017 55.000 0.00 0.00 0.00 4.04
644 655 0.757188 AGGATGTGGCTAGGTCTCGG 60.757 60.000 0.00 0.00 0.00 4.63
645 656 1.043673 GGATGTGGCTAGGTCTCGGT 61.044 60.000 0.00 0.00 0.00 4.69
646 657 0.386113 GATGTGGCTAGGTCTCGGTC 59.614 60.000 0.00 0.00 0.00 4.79
647 658 0.324368 ATGTGGCTAGGTCTCGGTCA 60.324 55.000 0.00 0.00 0.00 4.02
648 659 0.541063 TGTGGCTAGGTCTCGGTCAA 60.541 55.000 0.00 0.00 0.00 3.18
649 660 0.108756 GTGGCTAGGTCTCGGTCAAC 60.109 60.000 0.00 0.00 0.00 3.18
650 661 0.251653 TGGCTAGGTCTCGGTCAACT 60.252 55.000 0.00 0.00 0.00 3.16
651 662 1.005097 TGGCTAGGTCTCGGTCAACTA 59.995 52.381 0.00 0.00 0.00 2.24
652 663 2.097825 GGCTAGGTCTCGGTCAACTAA 58.902 52.381 0.00 0.00 0.00 2.24
653 664 2.099427 GGCTAGGTCTCGGTCAACTAAG 59.901 54.545 0.00 0.00 0.00 2.18
654 665 3.015327 GCTAGGTCTCGGTCAACTAAGA 58.985 50.000 0.00 0.00 0.00 2.10
655 666 3.633065 GCTAGGTCTCGGTCAACTAAGAT 59.367 47.826 0.00 0.00 0.00 2.40
656 667 4.098196 GCTAGGTCTCGGTCAACTAAGATT 59.902 45.833 0.00 0.00 0.00 2.40
657 668 5.298777 GCTAGGTCTCGGTCAACTAAGATTA 59.701 44.000 0.00 0.00 0.00 1.75
658 669 6.183360 GCTAGGTCTCGGTCAACTAAGATTAA 60.183 42.308 0.00 0.00 0.00 1.40
659 670 5.963594 AGGTCTCGGTCAACTAAGATTAAC 58.036 41.667 0.00 0.00 0.00 2.01
660 671 5.105432 AGGTCTCGGTCAACTAAGATTAACC 60.105 44.000 0.00 0.00 0.00 2.85
661 672 5.337009 GGTCTCGGTCAACTAAGATTAACCA 60.337 44.000 0.00 0.00 0.00 3.67
662 673 6.161381 GTCTCGGTCAACTAAGATTAACCAA 58.839 40.000 0.00 0.00 0.00 3.67
663 674 6.310711 GTCTCGGTCAACTAAGATTAACCAAG 59.689 42.308 0.00 0.00 0.00 3.61
664 675 6.209986 TCTCGGTCAACTAAGATTAACCAAGA 59.790 38.462 0.00 0.00 0.00 3.02
665 676 6.161381 TCGGTCAACTAAGATTAACCAAGAC 58.839 40.000 0.00 0.00 0.00 3.01
666 677 6.014840 TCGGTCAACTAAGATTAACCAAGACT 60.015 38.462 0.00 0.00 0.00 3.24
667 678 6.310711 CGGTCAACTAAGATTAACCAAGACTC 59.689 42.308 0.00 0.00 0.00 3.36
668 679 7.159372 GGTCAACTAAGATTAACCAAGACTCA 58.841 38.462 0.00 0.00 0.00 3.41
669 680 7.332182 GGTCAACTAAGATTAACCAAGACTCAG 59.668 40.741 0.00 0.00 0.00 3.35
670 681 7.873505 GTCAACTAAGATTAACCAAGACTCAGT 59.126 37.037 0.00 0.00 0.00 3.41
671 682 8.088981 TCAACTAAGATTAACCAAGACTCAGTC 58.911 37.037 0.00 0.00 0.00 3.51
672 683 7.540474 ACTAAGATTAACCAAGACTCAGTCA 57.460 36.000 7.77 0.00 34.60 3.41
673 684 7.963532 ACTAAGATTAACCAAGACTCAGTCAA 58.036 34.615 7.77 0.00 34.60 3.18
674 685 8.091449 ACTAAGATTAACCAAGACTCAGTCAAG 58.909 37.037 7.77 0.00 34.60 3.02
675 686 6.426646 AGATTAACCAAGACTCAGTCAAGT 57.573 37.500 7.77 0.00 34.60 3.16
676 687 6.831976 AGATTAACCAAGACTCAGTCAAGTT 58.168 36.000 7.77 9.64 34.60 2.66
677 688 7.963532 AGATTAACCAAGACTCAGTCAAGTTA 58.036 34.615 7.77 8.67 34.60 2.24
678 689 8.598041 AGATTAACCAAGACTCAGTCAAGTTAT 58.402 33.333 7.77 2.92 34.60 1.89
679 690 9.871238 GATTAACCAAGACTCAGTCAAGTTATA 57.129 33.333 7.77 4.05 34.60 0.98
733 744 9.945904 AAAGGAAAAACCAAAAATAACTACACA 57.054 25.926 0.00 0.00 42.04 3.72
734 745 9.945904 AAGGAAAAACCAAAAATAACTACACAA 57.054 25.926 0.00 0.00 42.04 3.33
735 746 9.594478 AGGAAAAACCAAAAATAACTACACAAG 57.406 29.630 0.00 0.00 42.04 3.16
736 747 9.373603 GGAAAAACCAAAAATAACTACACAAGT 57.626 29.630 0.00 0.00 38.24 3.16
740 751 8.936070 AACCAAAAATAACTACACAAGTTTCC 57.064 30.769 0.00 0.00 46.61 3.13
741 752 8.068892 ACCAAAAATAACTACACAAGTTTCCA 57.931 30.769 0.00 0.00 46.61 3.53
742 753 7.977293 ACCAAAAATAACTACACAAGTTTCCAC 59.023 33.333 0.00 0.00 46.61 4.02
743 754 7.166804 CCAAAAATAACTACACAAGTTTCCACG 59.833 37.037 0.00 0.00 46.61 4.94
744 755 6.930667 AAATAACTACACAAGTTTCCACGT 57.069 33.333 0.00 0.00 46.61 4.49
745 756 8.436046 AAAATAACTACACAAGTTTCCACGTA 57.564 30.769 0.00 0.00 46.61 3.57
746 757 8.436046 AAATAACTACACAAGTTTCCACGTAA 57.564 30.769 0.00 0.00 46.61 3.18
747 758 5.978934 AACTACACAAGTTTCCACGTAAG 57.021 39.130 0.00 0.00 46.61 2.34
748 759 5.266733 ACTACACAAGTTTCCACGTAAGA 57.733 39.130 0.00 0.00 36.13 2.10
749 760 5.850614 ACTACACAAGTTTCCACGTAAGAT 58.149 37.500 0.00 0.00 36.13 2.40
750 761 5.924825 ACTACACAAGTTTCCACGTAAGATC 59.075 40.000 0.00 0.00 36.13 2.75
751 762 3.739300 ACACAAGTTTCCACGTAAGATCG 59.261 43.478 0.00 0.00 43.62 3.69
752 763 3.985279 CACAAGTTTCCACGTAAGATCGA 59.015 43.478 0.00 0.00 43.62 3.59
753 764 4.625742 CACAAGTTTCCACGTAAGATCGAT 59.374 41.667 0.00 0.00 43.62 3.59
754 765 4.863131 ACAAGTTTCCACGTAAGATCGATC 59.137 41.667 17.91 17.91 43.62 3.69
755 766 3.692576 AGTTTCCACGTAAGATCGATCG 58.307 45.455 19.33 9.36 43.62 3.69
756 767 2.768833 TTCCACGTAAGATCGATCGG 57.231 50.000 19.33 13.22 43.62 4.18
757 768 1.957668 TCCACGTAAGATCGATCGGA 58.042 50.000 19.33 15.24 43.62 4.55
758 769 1.600957 TCCACGTAAGATCGATCGGAC 59.399 52.381 19.33 18.45 43.62 4.79
759 770 1.602851 CCACGTAAGATCGATCGGACT 59.397 52.381 19.33 11.86 43.62 3.85
760 771 2.602456 CCACGTAAGATCGATCGGACTG 60.602 54.545 19.33 17.32 43.62 3.51
761 772 1.602851 ACGTAAGATCGATCGGACTGG 59.397 52.381 19.33 11.47 43.62 4.00
762 773 1.602851 CGTAAGATCGATCGGACTGGT 59.397 52.381 19.33 3.95 43.02 4.00
763 774 2.804527 CGTAAGATCGATCGGACTGGTA 59.195 50.000 19.33 3.04 43.02 3.25
764 775 3.436015 CGTAAGATCGATCGGACTGGTAT 59.564 47.826 19.33 0.00 43.02 2.73
765 776 4.083431 CGTAAGATCGATCGGACTGGTATT 60.083 45.833 19.33 7.73 43.02 1.89
766 777 4.939052 AAGATCGATCGGACTGGTATTT 57.061 40.909 19.33 1.81 0.00 1.40
767 778 6.347969 CGTAAGATCGATCGGACTGGTATTTA 60.348 42.308 19.33 6.11 43.02 1.40
768 779 6.401047 AAGATCGATCGGACTGGTATTTAA 57.599 37.500 19.33 0.00 0.00 1.52
769 780 5.770417 AGATCGATCGGACTGGTATTTAAC 58.230 41.667 19.33 0.00 0.00 2.01
770 781 4.987408 TCGATCGGACTGGTATTTAACA 57.013 40.909 16.41 0.00 0.00 2.41
771 782 5.327616 TCGATCGGACTGGTATTTAACAA 57.672 39.130 16.41 0.00 0.00 2.83
772 783 5.345702 TCGATCGGACTGGTATTTAACAAG 58.654 41.667 16.41 0.00 34.98 3.16
773 784 5.105635 TCGATCGGACTGGTATTTAACAAGT 60.106 40.000 16.41 0.00 45.67 3.16
783 794 9.574516 ACTGGTATTTAACAAGTCTCAAATCTT 57.425 29.630 0.00 0.00 37.95 2.40
796 807 5.944013 TCTCAAATCTTAGACTGAGACGTG 58.056 41.667 17.08 1.44 39.43 4.49
797 808 5.060662 TCAAATCTTAGACTGAGACGTGG 57.939 43.478 0.00 0.00 0.00 4.94
834 845 0.172803 ATCGTACCCTCGTTGACTGC 59.827 55.000 0.00 0.00 0.00 4.40
888 925 2.444700 AAACCAGGTACGCTCCACCG 62.445 60.000 0.00 0.00 41.21 4.94
922 959 1.065928 CGACGATTTCCTCTCCCCG 59.934 63.158 0.00 0.00 0.00 5.73
924 961 0.535797 GACGATTTCCTCTCCCCGTT 59.464 55.000 0.00 0.00 0.00 4.44
976 1027 2.365635 GGCCTGACCTCCAGCCTA 60.366 66.667 0.00 0.00 41.57 3.93
996 1051 0.390866 CGCAGCACTCCAGATTCAGT 60.391 55.000 0.00 0.00 0.00 3.41
997 1052 1.085091 GCAGCACTCCAGATTCAGTG 58.915 55.000 0.00 0.00 42.61 3.66
1334 1443 2.187946 CCTCCCTTACCTGCAGCG 59.812 66.667 8.66 4.27 0.00 5.18
1339 1448 3.490759 CTTACCTGCAGCGTGGCG 61.491 66.667 8.66 0.00 36.28 5.69
1388 1500 2.158842 CCTGTAATGGCCTCCTTCTCTG 60.159 54.545 3.32 0.00 0.00 3.35
1416 1537 0.750182 ACAACAACAAGGTGACCCCG 60.750 55.000 0.00 0.00 36.95 5.73
1417 1538 1.826487 AACAACAAGGTGACCCCGC 60.826 57.895 0.00 0.00 38.74 6.13
1503 1636 1.294659 CTCAGCCTCAAACGCAGGAC 61.295 60.000 0.00 0.00 31.91 3.85
1600 1741 1.662438 CGAGCAGACCTCTCCAGGAC 61.662 65.000 0.00 0.00 43.65 3.85
1601 1742 0.324275 GAGCAGACCTCTCCAGGACT 60.324 60.000 0.00 0.00 44.75 3.85
1631 1772 3.827302 ACAGGAGTGAACATCTACTCGTT 59.173 43.478 0.00 0.00 43.24 3.85
1742 1904 0.035534 ATGTACGTGATTGGCAGCCA 60.036 50.000 11.22 11.22 0.00 4.75
1743 1905 0.673333 TGTACGTGATTGGCAGCCAG 60.673 55.000 15.50 5.03 33.81 4.85
1907 3020 4.460731 TGCCGATGATAACAACAAAATCCA 59.539 37.500 0.00 0.00 0.00 3.41
1924 3037 1.902508 TCCAGTTTTCCGAGAGAGCAT 59.097 47.619 0.00 0.00 0.00 3.79
2771 4035 4.946784 AACCACAGAGAAATCGCATAAC 57.053 40.909 0.00 0.00 0.00 1.89
3024 4298 3.188667 GTGCACTCTTAACTTAACAGCCC 59.811 47.826 10.32 0.00 0.00 5.19
3025 4299 2.415512 GCACTCTTAACTTAACAGCCCG 59.584 50.000 0.00 0.00 0.00 6.13
3026 4300 3.660865 CACTCTTAACTTAACAGCCCGT 58.339 45.455 0.00 0.00 0.00 5.28
3027 4301 3.678548 CACTCTTAACTTAACAGCCCGTC 59.321 47.826 0.00 0.00 0.00 4.79
3041 4324 1.078497 CCGTCAGGGTAATGCAGCA 60.078 57.895 0.00 0.00 0.00 4.41
3043 4326 0.108186 CGTCAGGGTAATGCAGCAGA 60.108 55.000 0.00 0.00 0.00 4.26
3046 4329 2.615912 GTCAGGGTAATGCAGCAGAATC 59.384 50.000 0.00 0.00 0.00 2.52
3075 4358 1.000233 GCTGTACGCGTCGAAACTGA 61.000 55.000 18.63 0.00 0.00 3.41
3076 4359 0.701303 CTGTACGCGTCGAAACTGAC 59.299 55.000 18.63 6.25 35.49 3.51
3079 4362 2.784957 TACGCGTCGAAACTGACCCG 62.785 60.000 18.63 0.00 43.72 5.28
3080 4363 2.355481 GCGTCGAAACTGACCCGT 60.355 61.111 0.00 0.00 35.40 5.28
3203 4914 6.959639 AACCTGCAAGTTTGAGAATCTTAA 57.040 33.333 0.00 0.00 34.92 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.096416 AGAACTCCCTAGCGAAGTCG 58.904 55.000 0.00 0.00 43.27 4.18
17 18 2.492484 TCAAGAACTCCCTAGCGAAGTC 59.508 50.000 0.00 0.00 0.00 3.01
18 19 2.231721 GTCAAGAACTCCCTAGCGAAGT 59.768 50.000 0.00 0.00 0.00 3.01
19 20 2.417515 GGTCAAGAACTCCCTAGCGAAG 60.418 54.545 0.00 0.00 0.00 3.79
20 21 1.549170 GGTCAAGAACTCCCTAGCGAA 59.451 52.381 0.00 0.00 0.00 4.70
21 22 1.183549 GGTCAAGAACTCCCTAGCGA 58.816 55.000 0.00 0.00 0.00 4.93
22 23 0.179134 CGGTCAAGAACTCCCTAGCG 60.179 60.000 0.00 0.00 0.00 4.26
23 24 0.460459 GCGGTCAAGAACTCCCTAGC 60.460 60.000 0.00 0.00 0.00 3.42
24 25 0.175989 GGCGGTCAAGAACTCCCTAG 59.824 60.000 0.00 0.00 0.00 3.02
25 26 0.543410 TGGCGGTCAAGAACTCCCTA 60.543 55.000 0.00 0.00 0.00 3.53
26 27 1.415672 TTGGCGGTCAAGAACTCCCT 61.416 55.000 0.00 0.00 0.00 4.20
27 28 0.536460 TTTGGCGGTCAAGAACTCCC 60.536 55.000 0.00 0.00 36.62 4.30
28 29 1.314730 TTTTGGCGGTCAAGAACTCC 58.685 50.000 0.00 0.00 36.62 3.85
45 46 0.247185 CGCTGGGGTGCATCATTTTT 59.753 50.000 0.00 0.00 0.00 1.94
46 47 1.606885 CCGCTGGGGTGCATCATTTT 61.607 55.000 0.00 0.00 0.00 1.82
47 48 2.053865 CCGCTGGGGTGCATCATTT 61.054 57.895 0.00 0.00 0.00 2.32
48 49 2.440796 CCGCTGGGGTGCATCATT 60.441 61.111 0.00 0.00 0.00 2.57
49 50 3.410628 TCCGCTGGGGTGCATCAT 61.411 61.111 10.81 0.00 37.00 2.45
50 51 4.100084 CTCCGCTGGGGTGCATCA 62.100 66.667 10.81 0.00 37.00 3.07
51 52 4.864334 CCTCCGCTGGGGTGCATC 62.864 72.222 10.81 0.00 37.00 3.91
127 128 0.879765 GAAGTGAGCTGCAGTGCATT 59.120 50.000 20.10 8.82 38.13 3.56
144 145 2.338015 CGGACGGGTCTCCTTCGAA 61.338 63.158 0.00 0.00 32.58 3.71
224 226 1.997874 GCCCTGATGTGGTCCCTCT 60.998 63.158 0.00 0.00 0.00 3.69
233 235 4.457496 CGCCGTGAGCCCTGATGT 62.457 66.667 0.00 0.00 38.78 3.06
282 284 1.076192 GAACCTCGAGGCCCTAGGA 60.076 63.158 31.56 2.91 39.32 2.94
301 303 1.906574 TCTTCTTCATTACAGGGCGGT 59.093 47.619 0.00 0.00 0.00 5.68
449 460 4.767409 GCCTTTTTCTTGTATGGGAAGTCT 59.233 41.667 0.00 0.00 0.00 3.24
460 471 5.070847 ACATGAATCCAAGCCTTTTTCTTGT 59.929 36.000 0.00 7.00 39.30 3.16
465 476 3.903090 TGGACATGAATCCAAGCCTTTTT 59.097 39.130 0.00 0.00 46.08 1.94
547 558 3.703001 ACATACAAGGTGCAGCTAGTT 57.297 42.857 20.51 8.88 0.00 2.24
548 559 3.703001 AACATACAAGGTGCAGCTAGT 57.297 42.857 20.51 10.09 0.00 2.57
621 632 3.692101 CGAGACCTAGCCACATCCTATAG 59.308 52.174 0.00 0.00 0.00 1.31
622 633 3.561528 CCGAGACCTAGCCACATCCTATA 60.562 52.174 0.00 0.00 0.00 1.31
623 634 2.520069 CGAGACCTAGCCACATCCTAT 58.480 52.381 0.00 0.00 0.00 2.57
624 635 1.478837 CCGAGACCTAGCCACATCCTA 60.479 57.143 0.00 0.00 0.00 2.94
625 636 0.757188 CCGAGACCTAGCCACATCCT 60.757 60.000 0.00 0.00 0.00 3.24
626 637 1.043673 ACCGAGACCTAGCCACATCC 61.044 60.000 0.00 0.00 0.00 3.51
627 638 0.386113 GACCGAGACCTAGCCACATC 59.614 60.000 0.00 0.00 0.00 3.06
628 639 0.324368 TGACCGAGACCTAGCCACAT 60.324 55.000 0.00 0.00 0.00 3.21
629 640 0.541063 TTGACCGAGACCTAGCCACA 60.541 55.000 0.00 0.00 0.00 4.17
630 641 0.108756 GTTGACCGAGACCTAGCCAC 60.109 60.000 0.00 0.00 0.00 5.01
631 642 0.251653 AGTTGACCGAGACCTAGCCA 60.252 55.000 0.00 0.00 0.00 4.75
632 643 1.760192 TAGTTGACCGAGACCTAGCC 58.240 55.000 0.00 0.00 0.00 3.93
633 644 3.015327 TCTTAGTTGACCGAGACCTAGC 58.985 50.000 0.00 0.00 0.00 3.42
634 645 5.838531 AATCTTAGTTGACCGAGACCTAG 57.161 43.478 0.00 0.00 0.00 3.02
635 646 6.096001 GGTTAATCTTAGTTGACCGAGACCTA 59.904 42.308 0.00 0.00 29.59 3.08
636 647 5.105432 GGTTAATCTTAGTTGACCGAGACCT 60.105 44.000 0.00 0.00 29.59 3.85
637 648 5.107824 GGTTAATCTTAGTTGACCGAGACC 58.892 45.833 0.00 0.00 29.59 3.85
638 649 5.717119 TGGTTAATCTTAGTTGACCGAGAC 58.283 41.667 0.00 0.00 39.79 3.36
639 650 5.988310 TGGTTAATCTTAGTTGACCGAGA 57.012 39.130 0.00 0.00 39.79 4.04
640 651 6.310711 GTCTTGGTTAATCTTAGTTGACCGAG 59.689 42.308 13.99 13.99 44.62 4.63
641 652 6.014840 AGTCTTGGTTAATCTTAGTTGACCGA 60.015 38.462 0.00 0.00 39.79 4.69
642 653 6.164176 AGTCTTGGTTAATCTTAGTTGACCG 58.836 40.000 0.00 0.00 39.79 4.79
643 654 7.159372 TGAGTCTTGGTTAATCTTAGTTGACC 58.841 38.462 0.00 0.00 38.02 4.02
644 655 7.873505 ACTGAGTCTTGGTTAATCTTAGTTGAC 59.126 37.037 0.00 0.00 0.00 3.18
645 656 7.963532 ACTGAGTCTTGGTTAATCTTAGTTGA 58.036 34.615 0.00 0.00 0.00 3.18
646 657 7.872993 TGACTGAGTCTTGGTTAATCTTAGTTG 59.127 37.037 14.42 0.00 33.15 3.16
647 658 7.963532 TGACTGAGTCTTGGTTAATCTTAGTT 58.036 34.615 14.42 0.00 33.15 2.24
648 659 7.540474 TGACTGAGTCTTGGTTAATCTTAGT 57.460 36.000 14.42 0.00 33.15 2.24
649 660 8.091449 ACTTGACTGAGTCTTGGTTAATCTTAG 58.909 37.037 14.42 0.00 33.15 2.18
650 661 7.963532 ACTTGACTGAGTCTTGGTTAATCTTA 58.036 34.615 14.42 0.00 33.15 2.10
651 662 6.831976 ACTTGACTGAGTCTTGGTTAATCTT 58.168 36.000 14.42 0.00 33.15 2.40
652 663 6.426646 ACTTGACTGAGTCTTGGTTAATCT 57.573 37.500 14.42 0.00 33.15 2.40
653 664 8.779354 ATAACTTGACTGAGTCTTGGTTAATC 57.221 34.615 14.42 0.00 31.74 1.75
707 718 9.945904 TGTGTAGTTATTTTTGGTTTTTCCTTT 57.054 25.926 0.00 0.00 37.07 3.11
708 719 9.945904 TTGTGTAGTTATTTTTGGTTTTTCCTT 57.054 25.926 0.00 0.00 37.07 3.36
709 720 9.594478 CTTGTGTAGTTATTTTTGGTTTTTCCT 57.406 29.630 0.00 0.00 37.07 3.36
710 721 9.373603 ACTTGTGTAGTTATTTTTGGTTTTTCC 57.626 29.630 0.00 0.00 31.29 3.13
714 725 9.373603 GGAAACTTGTGTAGTTATTTTTGGTTT 57.626 29.630 0.00 0.00 46.34 3.27
715 726 8.532819 TGGAAACTTGTGTAGTTATTTTTGGTT 58.467 29.630 0.00 0.00 46.34 3.67
716 727 7.977293 GTGGAAACTTGTGTAGTTATTTTTGGT 59.023 33.333 0.00 0.00 46.34 3.67
717 728 7.166804 CGTGGAAACTTGTGTAGTTATTTTTGG 59.833 37.037 0.00 0.00 46.34 3.28
718 729 7.698970 ACGTGGAAACTTGTGTAGTTATTTTTG 59.301 33.333 0.00 0.00 46.34 2.44
719 730 7.764331 ACGTGGAAACTTGTGTAGTTATTTTT 58.236 30.769 0.00 0.00 46.34 1.94
720 731 7.324354 ACGTGGAAACTTGTGTAGTTATTTT 57.676 32.000 0.00 0.00 46.34 1.82
721 732 6.930667 ACGTGGAAACTTGTGTAGTTATTT 57.069 33.333 0.00 0.00 46.34 1.40
722 733 7.927629 TCTTACGTGGAAACTTGTGTAGTTATT 59.072 33.333 0.00 0.00 46.34 1.40
723 734 7.436118 TCTTACGTGGAAACTTGTGTAGTTAT 58.564 34.615 0.00 0.00 46.34 1.89
724 735 6.804677 TCTTACGTGGAAACTTGTGTAGTTA 58.195 36.000 0.00 0.00 46.34 2.24
726 737 5.266733 TCTTACGTGGAAACTTGTGTAGT 57.733 39.130 0.00 0.00 39.32 2.73
727 738 5.060569 CGATCTTACGTGGAAACTTGTGTAG 59.939 44.000 0.00 0.00 0.00 2.74
728 739 4.919168 CGATCTTACGTGGAAACTTGTGTA 59.081 41.667 0.00 0.00 0.00 2.90
729 740 3.739300 CGATCTTACGTGGAAACTTGTGT 59.261 43.478 0.00 0.00 0.00 3.72
730 741 3.985279 TCGATCTTACGTGGAAACTTGTG 59.015 43.478 0.00 0.00 34.70 3.33
731 742 4.247267 TCGATCTTACGTGGAAACTTGT 57.753 40.909 0.00 0.00 34.70 3.16
732 743 4.027621 CGATCGATCTTACGTGGAAACTTG 60.028 45.833 22.43 0.00 34.70 3.16
733 744 4.103357 CGATCGATCTTACGTGGAAACTT 58.897 43.478 22.43 0.00 34.70 2.66
734 745 3.488721 CCGATCGATCTTACGTGGAAACT 60.489 47.826 22.43 0.00 34.70 2.66
735 746 2.787680 CCGATCGATCTTACGTGGAAAC 59.212 50.000 22.43 0.00 34.70 2.78
736 747 2.684374 TCCGATCGATCTTACGTGGAAA 59.316 45.455 22.43 0.00 31.76 3.13
737 748 2.032550 GTCCGATCGATCTTACGTGGAA 59.967 50.000 22.43 3.95 34.41 3.53
738 749 1.600957 GTCCGATCGATCTTACGTGGA 59.399 52.381 22.43 16.77 34.70 4.02
739 750 1.602851 AGTCCGATCGATCTTACGTGG 59.397 52.381 22.43 14.83 34.70 4.94
740 751 2.602456 CCAGTCCGATCGATCTTACGTG 60.602 54.545 22.43 16.67 34.70 4.49
741 752 1.602851 CCAGTCCGATCGATCTTACGT 59.397 52.381 22.43 0.00 34.70 3.57
742 753 1.602851 ACCAGTCCGATCGATCTTACG 59.397 52.381 22.43 10.30 0.00 3.18
743 754 5.373981 AATACCAGTCCGATCGATCTTAC 57.626 43.478 22.43 18.52 0.00 2.34
744 755 7.013559 TGTTAAATACCAGTCCGATCGATCTTA 59.986 37.037 22.43 8.05 0.00 2.10
745 756 4.939052 AAATACCAGTCCGATCGATCTT 57.061 40.909 22.43 4.54 0.00 2.40
746 757 5.301045 TGTTAAATACCAGTCCGATCGATCT 59.699 40.000 22.43 11.30 0.00 2.75
747 758 5.526115 TGTTAAATACCAGTCCGATCGATC 58.474 41.667 18.66 15.68 0.00 3.69
748 759 5.524971 TGTTAAATACCAGTCCGATCGAT 57.475 39.130 18.66 0.00 0.00 3.59
749 760 4.987408 TGTTAAATACCAGTCCGATCGA 57.013 40.909 18.66 0.00 0.00 3.59
750 761 5.107133 ACTTGTTAAATACCAGTCCGATCG 58.893 41.667 8.51 8.51 26.84 3.69
751 762 6.338937 AGACTTGTTAAATACCAGTCCGATC 58.661 40.000 5.76 0.00 45.91 3.69
752 763 6.070995 TGAGACTTGTTAAATACCAGTCCGAT 60.071 38.462 5.76 0.00 45.91 4.18
753 764 5.244402 TGAGACTTGTTAAATACCAGTCCGA 59.756 40.000 5.76 0.00 45.91 4.55
754 765 5.475719 TGAGACTTGTTAAATACCAGTCCG 58.524 41.667 5.76 0.00 45.91 4.79
755 766 7.739498 TTTGAGACTTGTTAAATACCAGTCC 57.261 36.000 5.76 0.54 45.91 3.85
756 767 9.220767 AGATTTGAGACTTGTTAAATACCAGTC 57.779 33.333 0.00 0.00 45.39 3.51
757 768 9.574516 AAGATTTGAGACTTGTTAAATACCAGT 57.425 29.630 0.00 0.00 35.57 4.00
773 784 5.106118 CCACGTCTCAGTCTAAGATTTGAGA 60.106 44.000 8.19 8.19 42.61 3.27
774 785 5.098893 CCACGTCTCAGTCTAAGATTTGAG 58.901 45.833 0.00 0.00 38.67 3.02
775 786 4.618460 GCCACGTCTCAGTCTAAGATTTGA 60.618 45.833 0.00 0.00 0.00 2.69
776 787 3.614616 GCCACGTCTCAGTCTAAGATTTG 59.385 47.826 0.00 0.00 0.00 2.32
777 788 3.673594 CGCCACGTCTCAGTCTAAGATTT 60.674 47.826 0.00 0.00 0.00 2.17
778 789 2.159366 CGCCACGTCTCAGTCTAAGATT 60.159 50.000 0.00 0.00 0.00 2.40
779 790 1.402259 CGCCACGTCTCAGTCTAAGAT 59.598 52.381 0.00 0.00 0.00 2.40
780 791 0.803117 CGCCACGTCTCAGTCTAAGA 59.197 55.000 0.00 0.00 0.00 2.10
781 792 0.522180 ACGCCACGTCTCAGTCTAAG 59.478 55.000 0.00 0.00 33.69 2.18
782 793 1.812235 TACGCCACGTCTCAGTCTAA 58.188 50.000 0.00 0.00 41.54 2.10
783 794 2.034104 ATACGCCACGTCTCAGTCTA 57.966 50.000 0.00 0.00 41.54 2.59
784 795 2.034104 TATACGCCACGTCTCAGTCT 57.966 50.000 0.00 0.00 41.54 3.24
785 796 3.043586 CAATATACGCCACGTCTCAGTC 58.956 50.000 0.00 0.00 41.54 3.51
786 797 2.223735 CCAATATACGCCACGTCTCAGT 60.224 50.000 0.00 0.00 41.54 3.41
787 798 2.394708 CCAATATACGCCACGTCTCAG 58.605 52.381 0.00 0.00 41.54 3.35
788 799 1.537348 GCCAATATACGCCACGTCTCA 60.537 52.381 0.00 0.00 41.54 3.27
789 800 1.137513 GCCAATATACGCCACGTCTC 58.862 55.000 0.00 0.00 41.54 3.36
790 801 0.462375 TGCCAATATACGCCACGTCT 59.538 50.000 0.00 0.00 41.54 4.18
791 802 1.260561 CTTGCCAATATACGCCACGTC 59.739 52.381 0.00 0.00 41.54 4.34
792 803 1.295792 CTTGCCAATATACGCCACGT 58.704 50.000 0.00 0.00 44.35 4.49
793 804 1.260561 GACTTGCCAATATACGCCACG 59.739 52.381 0.00 0.00 0.00 4.94
794 805 1.602377 GGACTTGCCAATATACGCCAC 59.398 52.381 0.00 0.00 36.34 5.01
795 806 1.210722 TGGACTTGCCAATATACGCCA 59.789 47.619 0.00 0.00 45.87 5.69
796 807 1.961793 TGGACTTGCCAATATACGCC 58.038 50.000 0.00 0.00 45.87 5.68
834 845 2.097038 CGCTTCGCACCTTGGAGAG 61.097 63.158 0.00 0.00 0.00 3.20
862 873 2.360726 GTACCTGGTTTGGGGCGG 60.361 66.667 3.84 0.00 0.00 6.13
868 905 0.953960 GGTGGAGCGTACCTGGTTTG 60.954 60.000 3.84 0.00 35.30 2.93
871 908 3.379445 CGGTGGAGCGTACCTGGT 61.379 66.667 4.05 4.05 36.03 4.00
918 955 0.811281 GAGGAAATCTGCAAACGGGG 59.189 55.000 0.00 0.00 0.00 5.73
922 959 3.679389 TGGAGAGAGGAAATCTGCAAAC 58.321 45.455 0.00 0.00 41.46 2.93
969 1020 2.510238 GAGTGCTGCGTAGGCTGG 60.510 66.667 14.89 6.53 40.82 4.85
971 1022 2.997315 TGGAGTGCTGCGTAGGCT 60.997 61.111 9.11 0.00 40.82 4.58
972 1023 2.303549 ATCTGGAGTGCTGCGTAGGC 62.304 60.000 1.76 0.00 40.52 3.93
976 1027 0.390866 CTGAATCTGGAGTGCTGCGT 60.391 55.000 0.00 0.00 0.00 5.24
1270 1379 0.535102 CCGGAGACACCAGCAAAGTT 60.535 55.000 0.00 0.00 38.90 2.66
1334 1443 1.641577 GATGTCCTTGTACTCGCCAC 58.358 55.000 0.00 0.00 0.00 5.01
1339 1448 2.480416 CCTGAGCGATGTCCTTGTACTC 60.480 54.545 0.00 0.00 0.00 2.59
1371 1483 0.839946 GGCAGAGAAGGAGGCCATTA 59.160 55.000 5.01 0.00 45.70 1.90
1388 1500 0.385974 CTTGTTGTTGTAGCAGCGGC 60.386 55.000 0.00 0.00 41.61 6.53
1416 1537 1.239347 GGAAATAATCCTCTGCCCGC 58.761 55.000 0.00 0.00 45.56 6.13
1417 1538 1.202651 ACGGAAATAATCCTCTGCCCG 60.203 52.381 0.00 0.00 46.98 6.13
1429 1550 1.987770 GCAGACGACGAAACGGAAATA 59.012 47.619 0.00 0.00 37.61 1.40
1503 1636 1.889829 TGGTTATTTCTGTTTGCCGGG 59.110 47.619 2.18 0.00 0.00 5.73
1631 1772 0.111832 ACACCAGTCTCCTGTCCGTA 59.888 55.000 0.00 0.00 36.95 4.02
1742 1904 2.434884 CGTTCATGCGGTCCAGCT 60.435 61.111 7.14 0.00 38.13 4.24
1743 1905 2.740714 GACGTTCATGCGGTCCAGC 61.741 63.158 0.00 0.00 35.98 4.85
1907 3020 3.594134 CAGAATGCTCTCTCGGAAAACT 58.406 45.455 0.00 0.00 0.00 2.66
1924 3037 0.250234 CGATCCTTGAGCCACCAGAA 59.750 55.000 0.00 0.00 0.00 3.02
2211 3373 3.612479 GCACATGCTTGGTTTGAAGGTAG 60.612 47.826 4.44 0.00 38.21 3.18
2545 3752 3.879295 CAGGTTGACAATATGCACTAGGG 59.121 47.826 0.00 0.00 0.00 3.53
2771 4035 9.384682 GCATTTTTATTTCAGTTTTGGACATTG 57.615 29.630 0.00 0.00 0.00 2.82
2888 4159 2.760650 CCCCTTTTTCATAGGTGAAGCC 59.239 50.000 0.00 0.00 44.62 4.35
3024 4298 0.108186 TCTGCTGCATTACCCTGACG 60.108 55.000 1.31 0.00 0.00 4.35
3025 4299 2.113860 TTCTGCTGCATTACCCTGAC 57.886 50.000 1.31 0.00 0.00 3.51
3026 4300 2.507058 AGATTCTGCTGCATTACCCTGA 59.493 45.455 1.31 0.00 0.00 3.86
3027 4301 2.617308 CAGATTCTGCTGCATTACCCTG 59.383 50.000 1.31 3.99 0.00 4.45
3051 4334 3.467119 CGACGCGTACAGCCACAC 61.467 66.667 13.97 0.00 44.76 3.82
3075 4358 3.568430 GTGATTTTTCTTCCTTGACGGGT 59.432 43.478 0.00 0.00 0.00 5.28
3076 4359 3.057526 GGTGATTTTTCTTCCTTGACGGG 60.058 47.826 0.00 0.00 0.00 5.28
3079 4362 4.036380 ACACGGTGATTTTTCTTCCTTGAC 59.964 41.667 16.29 0.00 0.00 3.18
3080 4363 4.204012 ACACGGTGATTTTTCTTCCTTGA 58.796 39.130 16.29 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.