Multiple sequence alignment - TraesCS3A01G197100

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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 TraesCS3A01G197100 chr3A 100.000 3091 0 0 1 3091 304892064 304888974 0.000000e+00 5709.0
1 TraesCS3A01G197100 chr3A 90.137 1673 164 1 728 2400 304883654 304881983 0.000000e+00 2174.0
2 TraesCS3A01G197100 chr3A 93.074 693 46 2 2399 3089 304873440 304872748 0.000000e+00 1013.0
3 TraesCS3A01G197100 chr3A 88.906 667 66 3 71 729 265533380 265532714 0.000000e+00 815.0
4 TraesCS3A01G197100 chr3A 88.788 660 72 2 71 729 274038492 274037834 0.000000e+00 808.0
5 TraesCS3A01G197100 chr3A 83.958 667 80 17 75 729 335382021 335382672 5.660000e-172 614.0
6 TraesCS3A01G197100 chr3A 83.333 606 71 23 2496 3089 313894755 313895342 1.630000e-147 532.0
7 TraesCS3A01G197100 chr3A 82.176 533 79 11 1104 1630 236351558 236351036 7.870000e-121 444.0
8 TraesCS3A01G197100 chr3A 84.000 450 61 10 1186 1630 236311143 236310700 3.690000e-114 422.0
9 TraesCS3A01G197100 chr3A 91.765 255 21 0 71 325 189483278 189483024 3.790000e-94 355.0
10 TraesCS3A01G197100 chr3A 86.818 220 23 4 2870 3089 418082075 418081862 1.110000e-59 241.0
11 TraesCS3A01G197100 chr3A 89.535 86 8 1 1301 1385 396592864 396592779 1.170000e-19 108.0
12 TraesCS3A01G197100 chr3A 98.246 57 1 0 1 57 209649244 209649300 1.960000e-17 100.0
13 TraesCS3A01G197100 chr3A 98.246 57 1 0 1 57 341021206 341021262 1.960000e-17 100.0
14 TraesCS3A01G197100 chr1D 82.386 1249 164 37 95 1313 69533849 69535071 0.000000e+00 1037.0
15 TraesCS3A01G197100 chr1D 82.338 804 107 22 89 871 138560392 138561181 0.000000e+00 665.0
16 TraesCS3A01G197100 chr1D 78.442 719 91 46 2285 2986 139714967 139714296 7.980000e-111 411.0
17 TraesCS3A01G197100 chr1D 87.166 187 9 8 2286 2458 317796312 317796127 6.760000e-47 198.0
18 TraesCS3A01G197100 chr1D 87.293 181 14 8 2286 2458 317800958 317800779 6.760000e-47 198.0
19 TraesCS3A01G197100 chr1D 84.146 82 9 1 1293 1374 271453429 271453352 3.310000e-10 76.8
20 TraesCS3A01G197100 chr1D 82.927 82 10 1 1293 1374 271460443 271460366 1.540000e-08 71.3
21 TraesCS3A01G197100 chr1D 85.965 57 6 2 1404 1458 195590033 195590089 3.330000e-05 60.2
22 TraesCS3A01G197100 chr6A 84.871 932 111 15 116 1025 229909603 229908680 0.000000e+00 913.0
23 TraesCS3A01G197100 chr6A 88.351 661 73 4 71 729 234208192 234207534 0.000000e+00 791.0
24 TraesCS3A01G197100 chr6A 81.790 961 130 32 741 1664 283375638 283374686 0.000000e+00 763.0
25 TraesCS3A01G197100 chr6A 81.693 874 113 32 829 1664 283299419 283298555 0.000000e+00 684.0
26 TraesCS3A01G197100 chr6A 82.545 613 69 32 2498 3089 364825007 364824412 3.560000e-139 505.0
27 TraesCS3A01G197100 chr6A 87.619 420 48 2 1671 2090 235257750 235258165 4.630000e-133 484.0
28 TraesCS3A01G197100 chr6A 86.190 420 57 1 1671 2090 235283677 235284095 1.310000e-123 453.0
29 TraesCS3A01G197100 chr6A 93.023 86 3 3 2410 2493 207244765 207244849 4.190000e-24 122.0
30 TraesCS3A01G197100 chr6A 98.246 57 1 0 1 57 299333602 299333658 1.960000e-17 100.0
31 TraesCS3A01G197100 chr6A 93.651 63 3 1 1 63 275564814 275564875 3.280000e-15 93.5
32 TraesCS3A01G197100 chr6A 100.000 31 0 0 2429 2459 406434920 406434890 1.200000e-04 58.4
33 TraesCS3A01G197100 chr4B 80.726 1240 164 48 101 1285 29547490 29546271 0.000000e+00 896.0
34 TraesCS3A01G197100 chr4B 79.777 717 117 26 2394 3089 213695987 213695278 2.140000e-136 496.0
35 TraesCS3A01G197100 chr5B 79.231 1300 185 62 75 1313 157796878 157798153 0.000000e+00 826.0
36 TraesCS3A01G197100 chr5B 81.288 652 98 21 2454 3089 258272963 258273606 9.890000e-140 507.0
37 TraesCS3A01G197100 chr4D 88.923 659 72 1 71 729 281280682 281281339 0.000000e+00 811.0
38 TraesCS3A01G197100 chr4D 82.080 798 99 31 101 871 61712918 61712138 2.600000e-180 641.0
39 TraesCS3A01G197100 chr4D 75.136 736 119 39 730 1433 250318645 250319348 1.400000e-73 287.0
40 TraesCS3A01G197100 chr4D 85.965 57 6 2 1404 1458 98471524 98471580 3.330000e-05 60.2
41 TraesCS3A01G197100 chr4D 85.965 57 6 2 1404 1458 98479402 98479458 3.330000e-05 60.2
42 TraesCS3A01G197100 chr4D 85.965 57 6 2 1404 1458 335434444 335434500 3.330000e-05 60.2
43 TraesCS3A01G197100 chr6D 88.720 656 69 5 75 729 254225128 254224477 0.000000e+00 797.0
44 TraesCS3A01G197100 chr6D 77.888 606 83 27 736 1304 81723255 81722664 2.300000e-86 329.0
45 TraesCS3A01G197100 chr6D 76.112 607 103 31 730 1308 125391401 125391993 2.350000e-71 279.0
46 TraesCS3A01G197100 chr6D 77.555 499 76 28 736 1207 125365396 125365885 5.080000e-68 268.0
47 TraesCS3A01G197100 chr6D 86.747 83 10 1 1293 1374 332965256 332965174 1.180000e-14 91.6
48 TraesCS3A01G197100 chr6D 86.747 83 10 1 1293 1374 332972138 332972056 1.180000e-14 91.6
49 TraesCS3A01G197100 chr6D 87.500 72 8 1 1362 1433 269328623 269328553 7.100000e-12 82.4
50 TraesCS3A01G197100 chr6D 87.500 72 8 1 1362 1433 269336238 269336168 7.100000e-12 82.4
51 TraesCS3A01G197100 chr6D 91.837 49 4 0 1326 1374 43365082 43365034 5.530000e-08 69.4
52 TraesCS3A01G197100 chr6D 91.837 49 4 0 1326 1374 43373254 43373206 5.530000e-08 69.4
53 TraesCS3A01G197100 chr6D 84.211 57 7 2 1404 1458 218003776 218003720 2.000000e-03 54.7
54 TraesCS3A01G197100 chr4A 86.357 733 97 3 1439 2169 402864812 402865543 0.000000e+00 797.0
55 TraesCS3A01G197100 chr4A 85.929 732 100 3 1439 2167 402856927 402857658 0.000000e+00 778.0
56 TraesCS3A01G197100 chr4A 83.571 420 57 6 1671 2090 137625558 137625151 1.740000e-102 383.0
57 TraesCS3A01G197100 chr4A 94.792 96 4 1 1535 1630 238450081 238449987 6.910000e-32 148.0
58 TraesCS3A01G197100 chr4A 91.579 95 7 1 1535 1629 238417296 238417203 2.500000e-26 130.0
59 TraesCS3A01G197100 chr4A 98.246 57 1 0 1 57 304102335 304102391 1.960000e-17 100.0
60 TraesCS3A01G197100 chr1A 88.386 663 74 3 68 729 287624614 287625274 0.000000e+00 795.0
61 TraesCS3A01G197100 chr1A 92.771 83 6 0 1303 1385 313635178 313635260 1.510000e-23 121.0
62 TraesCS3A01G197100 chr1A 89.412 85 7 2 1302 1385 247878484 247878401 4.220000e-19 106.0
63 TraesCS3A01G197100 chr1A 98.246 57 1 0 1 57 200474760 200474816 1.960000e-17 100.0
64 TraesCS3A01G197100 chr1A 98.246 57 1 0 1 57 201188857 201188913 1.960000e-17 100.0
65 TraesCS3A01G197100 chr2D 88.191 669 73 6 71 736 245525590 245524925 0.000000e+00 793.0
66 TraesCS3A01G197100 chr2D 85.034 588 63 22 737 1313 450430191 450429618 2.670000e-160 575.0
67 TraesCS3A01G197100 chr2D 95.000 60 3 0 1326 1385 347238180 347238239 9.120000e-16 95.3
68 TraesCS3A01G197100 chr7D 86.987 707 74 12 755 1451 321092292 321092990 0.000000e+00 780.0
69 TraesCS3A01G197100 chr7D 84.354 588 69 20 736 1313 302528037 302528611 3.480000e-154 555.0
70 TraesCS3A01G197100 chr7D 86.624 157 8 8 2281 2432 175982442 175982294 8.870000e-36 161.0
71 TraesCS3A01G197100 chr7D 86.624 157 8 8 2281 2432 175990590 175990442 8.870000e-36 161.0
72 TraesCS3A01G197100 chr5D 83.456 816 97 13 89 871 555856477 555857287 0.000000e+00 725.0
73 TraesCS3A01G197100 chr5D 90.850 153 13 1 1301 1453 322895115 322895266 1.450000e-48 204.0
74 TraesCS3A01G197100 chr5D 86.538 156 10 6 2281 2432 54154702 54154850 8.870000e-36 161.0
75 TraesCS3A01G197100 chr5D 88.000 75 8 1 1293 1366 421944537 421944611 1.530000e-13 87.9
76 TraesCS3A01G197100 chr5D 84.337 83 12 1 1293 1374 421936049 421936131 2.560000e-11 80.5
77 TraesCS3A01G197100 chr5D 91.892 37 3 0 1550 1586 322895265 322895301 6.000000e-03 52.8
78 TraesCS3A01G197100 chr2A 90.909 495 40 5 2594 3085 245029278 245029770 0.000000e+00 660.0
79 TraesCS3A01G197100 chr2A 81.898 801 108 21 92 871 315872750 315873534 2.600000e-180 641.0
80 TraesCS3A01G197100 chr2A 89.899 495 31 11 2594 3085 245037053 245037531 1.220000e-173 619.0
81 TraesCS3A01G197100 chr2A 86.706 504 57 10 2592 3089 312429684 312430183 4.500000e-153 551.0
82 TraesCS3A01G197100 chr2A 91.584 202 17 0 1784 1985 286553599 286553800 2.350000e-71 279.0
83 TraesCS3A01G197100 chr2A 85.475 179 25 1 1688 1866 416729095 416728918 5.260000e-43 185.0
84 TraesCS3A01G197100 chr2A 94.186 86 2 3 2410 2493 533140173 533140257 9.000000e-26 128.0
85 TraesCS3A01G197100 chr2B 81.011 811 120 25 75 865 118750983 118750187 5.660000e-172 614.0
86 TraesCS3A01G197100 chr1B 85.179 560 70 13 736 1291 572596129 572595579 2.080000e-156 562.0
87 TraesCS3A01G197100 chr7B 80.799 651 99 24 2454 3089 224734242 224733603 1.290000e-133 486.0
88 TraesCS3A01G197100 chr3D 78.445 733 103 34 736 1433 376745483 376744771 7.920000e-116 427.0
89 TraesCS3A01G197100 chr3D 78.748 687 93 24 781 1433 376751708 376751041 7.980000e-111 411.0
90 TraesCS3A01G197100 chr3D 86.624 157 8 8 2281 2432 291865063 291864915 8.870000e-36 161.0
91 TraesCS3A01G197100 chr3D 85.350 157 10 8 2281 2432 291857037 291856889 1.920000e-32 150.0
92 TraesCS3A01G197100 chr3D 86.747 83 10 1 1293 1374 460207437 460207519 1.180000e-14 91.6
93 TraesCS3A01G197100 chr5A 85.253 217 27 5 1876 2090 228303125 228303338 5.190000e-53 219.0
94 TraesCS3A01G197100 chr5A 85.976 164 13 7 2364 2522 215816342 215816184 1.910000e-37 167.0
95 TraesCS3A01G197100 chr5A 98.246 57 1 0 1 57 229031305 229031249 1.960000e-17 100.0
96 TraesCS3A01G197100 chrUn 75.349 430 78 22 1010 1433 27821772 27821365 6.810000e-42 182.0
97 TraesCS3A01G197100 chr3B 95.082 61 2 1 3 63 344832452 344832511 9.120000e-16 95.3


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 TraesCS3A01G197100 chr3A 304888974 304892064 3090 True 5709 5709 100.000 1 3091 1 chr3A.!!$R8 3090
1 TraesCS3A01G197100 chr3A 304881983 304883654 1671 True 2174 2174 90.137 728 2400 1 chr3A.!!$R7 1672
2 TraesCS3A01G197100 chr3A 304872748 304873440 692 True 1013 1013 93.074 2399 3089 1 chr3A.!!$R6 690
3 TraesCS3A01G197100 chr3A 265532714 265533380 666 True 815 815 88.906 71 729 1 chr3A.!!$R4 658
4 TraesCS3A01G197100 chr3A 274037834 274038492 658 True 808 808 88.788 71 729 1 chr3A.!!$R5 658
5 TraesCS3A01G197100 chr3A 335382021 335382672 651 False 614 614 83.958 75 729 1 chr3A.!!$F3 654
6 TraesCS3A01G197100 chr3A 313894755 313895342 587 False 532 532 83.333 2496 3089 1 chr3A.!!$F2 593
7 TraesCS3A01G197100 chr3A 236351036 236351558 522 True 444 444 82.176 1104 1630 1 chr3A.!!$R3 526
8 TraesCS3A01G197100 chr1D 69533849 69535071 1222 False 1037 1037 82.386 95 1313 1 chr1D.!!$F1 1218
9 TraesCS3A01G197100 chr1D 138560392 138561181 789 False 665 665 82.338 89 871 1 chr1D.!!$F2 782
10 TraesCS3A01G197100 chr1D 139714296 139714967 671 True 411 411 78.442 2285 2986 1 chr1D.!!$R1 701
11 TraesCS3A01G197100 chr6A 229908680 229909603 923 True 913 913 84.871 116 1025 1 chr6A.!!$R1 909
12 TraesCS3A01G197100 chr6A 234207534 234208192 658 True 791 791 88.351 71 729 1 chr6A.!!$R2 658
13 TraesCS3A01G197100 chr6A 283374686 283375638 952 True 763 763 81.790 741 1664 1 chr6A.!!$R4 923
14 TraesCS3A01G197100 chr6A 283298555 283299419 864 True 684 684 81.693 829 1664 1 chr6A.!!$R3 835
15 TraesCS3A01G197100 chr6A 364824412 364825007 595 True 505 505 82.545 2498 3089 1 chr6A.!!$R5 591
16 TraesCS3A01G197100 chr4B 29546271 29547490 1219 True 896 896 80.726 101 1285 1 chr4B.!!$R1 1184
17 TraesCS3A01G197100 chr4B 213695278 213695987 709 True 496 496 79.777 2394 3089 1 chr4B.!!$R2 695
18 TraesCS3A01G197100 chr5B 157796878 157798153 1275 False 826 826 79.231 75 1313 1 chr5B.!!$F1 1238
19 TraesCS3A01G197100 chr5B 258272963 258273606 643 False 507 507 81.288 2454 3089 1 chr5B.!!$F2 635
20 TraesCS3A01G197100 chr4D 281280682 281281339 657 False 811 811 88.923 71 729 1 chr4D.!!$F4 658
21 TraesCS3A01G197100 chr4D 61712138 61712918 780 True 641 641 82.080 101 871 1 chr4D.!!$R1 770
22 TraesCS3A01G197100 chr4D 250318645 250319348 703 False 287 287 75.136 730 1433 1 chr4D.!!$F3 703
23 TraesCS3A01G197100 chr6D 254224477 254225128 651 True 797 797 88.720 75 729 1 chr6D.!!$R5 654
24 TraesCS3A01G197100 chr6D 81722664 81723255 591 True 329 329 77.888 736 1304 1 chr6D.!!$R3 568
25 TraesCS3A01G197100 chr6D 125391401 125391993 592 False 279 279 76.112 730 1308 1 chr6D.!!$F2 578
26 TraesCS3A01G197100 chr4A 402864812 402865543 731 False 797 797 86.357 1439 2169 1 chr4A.!!$F3 730
27 TraesCS3A01G197100 chr4A 402856927 402857658 731 False 778 778 85.929 1439 2167 1 chr4A.!!$F2 728
28 TraesCS3A01G197100 chr1A 287624614 287625274 660 False 795 795 88.386 68 729 1 chr1A.!!$F3 661
29 TraesCS3A01G197100 chr2D 245524925 245525590 665 True 793 793 88.191 71 736 1 chr2D.!!$R1 665
30 TraesCS3A01G197100 chr2D 450429618 450430191 573 True 575 575 85.034 737 1313 1 chr2D.!!$R2 576
31 TraesCS3A01G197100 chr7D 321092292 321092990 698 False 780 780 86.987 755 1451 1 chr7D.!!$F2 696
32 TraesCS3A01G197100 chr7D 302528037 302528611 574 False 555 555 84.354 736 1313 1 chr7D.!!$F1 577
33 TraesCS3A01G197100 chr5D 555856477 555857287 810 False 725 725 83.456 89 871 1 chr5D.!!$F4 782
34 TraesCS3A01G197100 chr2A 315872750 315873534 784 False 641 641 81.898 92 871 1 chr2A.!!$F5 779
35 TraesCS3A01G197100 chr2B 118750187 118750983 796 True 614 614 81.011 75 865 1 chr2B.!!$R1 790
36 TraesCS3A01G197100 chr1B 572595579 572596129 550 True 562 562 85.179 736 1291 1 chr1B.!!$R1 555
37 TraesCS3A01G197100 chr7B 224733603 224734242 639 True 486 486 80.799 2454 3089 1 chr7B.!!$R1 635
38 TraesCS3A01G197100 chr3D 376744771 376745483 712 True 427 427 78.445 736 1433 1 chr3D.!!$R3 697
39 TraesCS3A01G197100 chr3D 376751041 376751708 667 True 411 411 78.748 781 1433 1 chr3D.!!$R4 652

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
51 52 0.099436 GCGGATGATGTGGTGAAAGC 59.901 55.0 0.00 0.00 0.00 3.51 F
690 739 0.106569 TGAGGGATGGCATCGCAATT 60.107 50.0 36.15 21.93 43.92 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1264 1399 0.250901 AACCGCTCCAAGAATGCACT 60.251 50.0 0.0 0.0 0.0 4.40 R
2386 2528 0.468029 CCCCTGCTCTCTCTCTCTCC 60.468 65.0 0.0 0.0 0.0 3.71 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
18 19 3.332706 TTGGTTAGGTTGCGGAAGG 57.667 52.632 0.00 0.00 0.00 3.46
19 20 0.891904 TTGGTTAGGTTGCGGAAGGC 60.892 55.000 0.00 0.00 43.96 4.35
20 21 1.002502 GGTTAGGTTGCGGAAGGCT 60.003 57.895 0.00 0.00 44.05 4.58
21 22 0.251073 GGTTAGGTTGCGGAAGGCTA 59.749 55.000 0.00 0.00 44.05 3.93
22 23 1.134189 GGTTAGGTTGCGGAAGGCTAT 60.134 52.381 0.00 0.00 44.05 2.97
23 24 1.940613 GTTAGGTTGCGGAAGGCTATG 59.059 52.381 0.00 0.00 44.05 2.23
24 25 0.468226 TAGGTTGCGGAAGGCTATGG 59.532 55.000 0.00 0.00 44.05 2.74
25 26 1.077716 GGTTGCGGAAGGCTATGGT 60.078 57.895 0.00 0.00 44.05 3.55
26 27 1.376609 GGTTGCGGAAGGCTATGGTG 61.377 60.000 0.00 0.00 44.05 4.17
27 28 1.077787 TTGCGGAAGGCTATGGTGG 60.078 57.895 0.00 0.00 44.05 4.61
28 29 1.847798 TTGCGGAAGGCTATGGTGGT 61.848 55.000 0.00 0.00 44.05 4.16
29 30 1.819632 GCGGAAGGCTATGGTGGTG 60.820 63.158 0.00 0.00 39.11 4.17
30 31 1.602237 CGGAAGGCTATGGTGGTGT 59.398 57.895 0.00 0.00 0.00 4.16
31 32 0.828022 CGGAAGGCTATGGTGGTGTA 59.172 55.000 0.00 0.00 0.00 2.90
32 33 1.202533 CGGAAGGCTATGGTGGTGTAG 60.203 57.143 0.00 0.00 0.00 2.74
33 34 1.475213 GGAAGGCTATGGTGGTGTAGC 60.475 57.143 0.00 0.00 41.95 3.58
34 35 0.178068 AAGGCTATGGTGGTGTAGCG 59.822 55.000 0.00 0.00 43.24 4.26
35 36 1.227556 GGCTATGGTGGTGTAGCGG 60.228 63.158 0.00 0.00 43.24 5.52
36 37 1.682451 GGCTATGGTGGTGTAGCGGA 61.682 60.000 0.00 0.00 43.24 5.54
37 38 0.393077 GCTATGGTGGTGTAGCGGAT 59.607 55.000 0.00 0.00 34.60 4.18
38 39 1.873903 GCTATGGTGGTGTAGCGGATG 60.874 57.143 0.00 0.00 34.60 3.51
39 40 1.686587 CTATGGTGGTGTAGCGGATGA 59.313 52.381 0.00 0.00 0.00 2.92
40 41 1.131638 ATGGTGGTGTAGCGGATGAT 58.868 50.000 0.00 0.00 0.00 2.45
41 42 0.177836 TGGTGGTGTAGCGGATGATG 59.822 55.000 0.00 0.00 0.00 3.07
42 43 0.178068 GGTGGTGTAGCGGATGATGT 59.822 55.000 0.00 0.00 0.00 3.06
43 44 1.290203 GTGGTGTAGCGGATGATGTG 58.710 55.000 0.00 0.00 0.00 3.21
44 45 0.177836 TGGTGTAGCGGATGATGTGG 59.822 55.000 0.00 0.00 0.00 4.17
45 46 0.178068 GGTGTAGCGGATGATGTGGT 59.822 55.000 0.00 0.00 0.00 4.16
46 47 1.290203 GTGTAGCGGATGATGTGGTG 58.710 55.000 0.00 0.00 0.00 4.17
47 48 1.134818 GTGTAGCGGATGATGTGGTGA 60.135 52.381 0.00 0.00 0.00 4.02
48 49 1.552792 TGTAGCGGATGATGTGGTGAA 59.447 47.619 0.00 0.00 0.00 3.18
49 50 2.027653 TGTAGCGGATGATGTGGTGAAA 60.028 45.455 0.00 0.00 0.00 2.69
50 51 1.742761 AGCGGATGATGTGGTGAAAG 58.257 50.000 0.00 0.00 0.00 2.62
51 52 0.099436 GCGGATGATGTGGTGAAAGC 59.901 55.000 0.00 0.00 0.00 3.51
52 53 0.734889 CGGATGATGTGGTGAAAGCC 59.265 55.000 0.00 0.00 0.00 4.35
53 54 1.106285 GGATGATGTGGTGAAAGCCC 58.894 55.000 0.00 0.00 0.00 5.19
54 55 1.341383 GGATGATGTGGTGAAAGCCCT 60.341 52.381 0.00 0.00 0.00 5.19
55 56 2.092429 GGATGATGTGGTGAAAGCCCTA 60.092 50.000 0.00 0.00 0.00 3.53
56 57 2.787473 TGATGTGGTGAAAGCCCTAG 57.213 50.000 0.00 0.00 0.00 3.02
57 58 2.265367 TGATGTGGTGAAAGCCCTAGA 58.735 47.619 0.00 0.00 0.00 2.43
58 59 2.642311 TGATGTGGTGAAAGCCCTAGAA 59.358 45.455 0.00 0.00 0.00 2.10
59 60 2.561478 TGTGGTGAAAGCCCTAGAAC 57.439 50.000 0.00 0.00 0.00 3.01
60 61 1.771854 TGTGGTGAAAGCCCTAGAACA 59.228 47.619 0.00 0.00 0.00 3.18
61 62 2.173782 TGTGGTGAAAGCCCTAGAACAA 59.826 45.455 0.00 0.00 0.00 2.83
62 63 3.219281 GTGGTGAAAGCCCTAGAACAAA 58.781 45.455 0.00 0.00 0.00 2.83
63 64 3.634910 GTGGTGAAAGCCCTAGAACAAAA 59.365 43.478 0.00 0.00 0.00 2.44
64 65 4.280929 GTGGTGAAAGCCCTAGAACAAAAT 59.719 41.667 0.00 0.00 0.00 1.82
65 66 4.898861 TGGTGAAAGCCCTAGAACAAAATT 59.101 37.500 0.00 0.00 0.00 1.82
66 67 5.365314 TGGTGAAAGCCCTAGAACAAAATTT 59.635 36.000 0.00 0.00 0.00 1.82
69 70 7.154656 GTGAAAGCCCTAGAACAAAATTTGAT 58.845 34.615 13.19 0.00 0.00 2.57
73 74 4.466015 GCCCTAGAACAAAATTTGATGGGA 59.534 41.667 13.19 0.00 33.14 4.37
82 83 7.315066 ACAAAATTTGATGGGACCATAAACT 57.685 32.000 13.19 0.00 36.70 2.66
122 123 6.403866 TGCAAAATCAAGGAACATAACACT 57.596 33.333 0.00 0.00 0.00 3.55
309 338 3.909086 GAGGGGCTGAGCAAAGCGT 62.909 63.158 6.82 0.00 44.52 5.07
313 342 0.169009 GGGCTGAGCAAAGCGTTAAG 59.831 55.000 6.82 0.00 44.52 1.85
325 354 4.680171 AAGCGTTAAGATAGCCAAACAC 57.320 40.909 0.00 0.00 0.00 3.32
329 358 4.671766 GCGTTAAGATAGCCAAACACCAAG 60.672 45.833 0.00 0.00 0.00 3.61
333 362 4.098914 AGATAGCCAAACACCAAGTTGA 57.901 40.909 3.87 0.00 41.19 3.18
344 373 1.428912 ACCAAGTTGATGGGATGGTGT 59.571 47.619 3.87 0.00 45.18 4.16
411 447 2.201732 AGTGGTATTTAGCGCGACATG 58.798 47.619 12.10 0.00 39.04 3.21
431 468 2.362397 TGGAGATAGCATCGAGACAACC 59.638 50.000 0.00 0.00 0.00 3.77
447 486 4.022849 AGACAACCAGCAAAGCAAAGATAC 60.023 41.667 0.00 0.00 0.00 2.24
488 527 2.357569 GGTCATCTTGCCTGAAATCCCT 60.358 50.000 0.00 0.00 0.00 4.20
549 588 3.549019 CGTAGTCGAATGGATCCTCACAG 60.549 52.174 14.23 0.97 39.71 3.66
597 640 1.515521 AAGCGCAACCGGAAAGAAGG 61.516 55.000 9.46 0.00 34.32 3.46
610 653 5.334879 CCGGAAAGAAGGAAACAACATAGTG 60.335 44.000 0.00 0.00 0.00 2.74
613 656 7.308589 CGGAAAGAAGGAAACAACATAGTGAAT 60.309 37.037 0.00 0.00 0.00 2.57
676 720 3.355378 TGCATGTCTGGTTTAATGAGGG 58.645 45.455 0.00 0.00 0.00 4.30
684 733 3.565307 TGGTTTAATGAGGGATGGCATC 58.435 45.455 19.23 19.23 0.00 3.91
690 739 0.106569 TGAGGGATGGCATCGCAATT 60.107 50.000 36.15 21.93 43.92 2.32
698 747 1.337917 TGGCATCGCAATTTGCAACAT 60.338 42.857 20.56 6.88 45.36 2.71
705 754 6.535811 CATCGCAATTTGCAACATACAAAAT 58.464 32.000 20.56 0.00 45.36 1.82
871 937 0.738389 CGGTAAATCCCCACATGCAC 59.262 55.000 0.00 0.00 0.00 4.57
891 958 5.904802 GCACTTAGCAAATAAAGCAAACAC 58.095 37.500 0.00 0.00 44.79 3.32
892 960 5.387342 GCACTTAGCAAATAAAGCAAACACG 60.387 40.000 0.00 0.00 44.79 4.49
1040 1156 2.888594 CCACGACAACATATCGGTTCT 58.111 47.619 0.00 0.00 43.95 3.01
1162 1289 1.534729 GTGGCAAGGAAACGAGGAAT 58.465 50.000 0.00 0.00 0.00 3.01
1222 1353 5.352293 GCATCTCATACAACACATCACAAGA 59.648 40.000 0.00 0.00 0.00 3.02
1236 1370 1.459592 CACAAGAATTCGTCCACGGTC 59.540 52.381 0.00 0.00 40.29 4.79
1264 1399 4.524802 TCCGTGGTTATACCTTCCTAGA 57.475 45.455 0.00 0.00 39.58 2.43
1335 1471 6.464222 TGTTCGTTTCAGATAGGAACTTGAT 58.536 36.000 20.30 0.00 41.75 2.57
1386 1522 2.232399 TGTACACGACAAGGCTAGTCA 58.768 47.619 0.00 0.00 34.15 3.41
1453 1590 1.142870 CTCTTGTGGTGGAACTTGGGA 59.857 52.381 0.00 0.00 36.74 4.37
1512 1649 3.299503 TGAGATGGTCTTGATGATCCGA 58.700 45.455 0.00 0.00 0.00 4.55
1521 1658 3.823304 TCTTGATGATCCGACGAGATGAT 59.177 43.478 0.00 0.00 0.00 2.45
1529 1666 1.135112 CCGACGAGATGATGTGGTTCA 60.135 52.381 0.00 0.00 0.00 3.18
1588 1725 0.108329 CGGGGTACTTGTCGCATTCT 60.108 55.000 0.00 0.00 0.00 2.40
1604 1741 4.181578 GCATTCTGGTTGTGTAGTCGTAT 58.818 43.478 0.00 0.00 0.00 3.06
1634 1772 0.239879 CGCGGTGTACTTGGCATTTT 59.760 50.000 0.00 0.00 0.00 1.82
1641 1779 1.000717 GTACTTGGCATTTTGGTGCGT 60.001 47.619 0.00 0.00 45.97 5.24
1686 1824 1.359475 GGTGGTCTAGACGATCCGC 59.641 63.158 16.56 9.22 0.00 5.54
1707 1845 3.512680 CGAGGAAGTAAACAGAGCGATT 58.487 45.455 0.00 0.00 0.00 3.34
1712 1850 2.766313 AGTAAACAGAGCGATTGTGCA 58.234 42.857 0.00 0.00 37.31 4.57
1714 1852 1.597742 AAACAGAGCGATTGTGCAGT 58.402 45.000 0.00 0.00 37.31 4.40
1773 1912 1.192146 ATGGTGCTCGTGGTAGTGGT 61.192 55.000 0.00 0.00 0.00 4.16
1783 1922 0.541063 TGGTAGTGGTCGGAGCAAGA 60.541 55.000 12.00 0.00 0.00 3.02
1831 1970 3.368571 GGCTGTGGTGGCTTGAGC 61.369 66.667 0.00 0.00 41.14 4.26
1910 2049 1.202330 CAACTGGAGGAGCAGAGGAT 58.798 55.000 0.00 0.00 0.00 3.24
1925 2064 1.077787 GGATGTCAACGGATGGGCA 60.078 57.895 0.00 0.00 0.00 5.36
1927 2066 1.392589 GATGTCAACGGATGGGCATT 58.607 50.000 0.00 0.00 0.00 3.56
2016 2155 1.450312 GGACCAATGCGGGAGACAG 60.450 63.158 0.00 0.00 40.22 3.51
2020 2159 0.107017 CCAATGCGGGAGACAGGAAT 60.107 55.000 0.00 0.00 0.00 3.01
2027 2166 1.274703 GGGAGACAGGAATGAGGCCA 61.275 60.000 5.01 0.00 0.00 5.36
2105 2244 0.462047 CCTGATTCACGGTGGTAGGC 60.462 60.000 8.50 0.00 0.00 3.93
2233 2372 1.679977 GAAAGCATGCTGGGCAGGA 60.680 57.895 23.48 0.00 43.36 3.86
2240 2379 4.459089 GCTGGGCAGGACGTCCTC 62.459 72.222 34.28 25.69 46.65 3.71
2241 2380 2.997315 CTGGGCAGGACGTCCTCA 60.997 66.667 34.28 26.11 46.65 3.86
2242 2381 2.525629 TGGGCAGGACGTCCTCAA 60.526 61.111 34.28 15.35 46.65 3.02
2243 2382 2.111999 CTGGGCAGGACGTCCTCAAA 62.112 60.000 34.28 18.21 46.65 2.69
2249 2388 1.993370 CAGGACGTCCTCAAATCGAAC 59.007 52.381 34.28 2.83 46.65 3.95
2252 2391 2.527100 GACGTCCTCAAATCGAACGAT 58.473 47.619 3.51 3.80 37.13 3.73
2253 2392 2.259618 ACGTCCTCAAATCGAACGATG 58.740 47.619 10.40 1.31 37.13 3.84
2254 2393 1.588404 CGTCCTCAAATCGAACGATGG 59.412 52.381 10.40 7.55 35.45 3.51
2323 2465 2.375345 GGGAAAGGGGATCGAGCCA 61.375 63.158 23.22 0.00 0.00 4.75
2386 2528 2.444256 GGAGGGGTCAAGGGATCGG 61.444 68.421 0.00 0.00 0.00 4.18
2673 2834 6.152379 GGTGAAGTTTGAATCCAACTCATTC 58.848 40.000 0.00 0.00 30.88 2.67
2681 2842 9.065871 GTTTGAATCCAACTCATTCGAATTTAG 57.934 33.333 8.21 11.41 36.47 1.85
2730 2893 5.494706 AGGTAATAGGGAGGTCCAAAAATGA 59.505 40.000 0.00 0.00 38.24 2.57
2949 3122 4.002906 TCCCTCGATTTAAATGGATCGG 57.997 45.455 12.58 14.03 43.85 4.18
2993 3167 5.104693 AGTTGAGTTTTTAAAAAGGGGGTGG 60.105 40.000 13.58 0.00 0.00 4.61
3066 3243 2.913777 AATCACACGACGAATCTCGA 57.086 45.000 0.00 0.00 43.74 4.04
3089 3266 3.334910 TCCATGGAAGGCATCTAGAGA 57.665 47.619 13.46 0.00 0.00 3.10
3090 3267 3.237746 TCCATGGAAGGCATCTAGAGAG 58.762 50.000 13.46 0.00 0.00 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.891904 GCCTTCCGCAACCTAACCAA 60.892 55.000 0.00 0.00 37.47 3.67
4 5 1.134220 CCATAGCCTTCCGCAACCTAA 60.134 52.381 0.00 0.00 41.38 2.69
5 6 0.468226 CCATAGCCTTCCGCAACCTA 59.532 55.000 0.00 0.00 41.38 3.08
7 8 1.077716 ACCATAGCCTTCCGCAACC 60.078 57.895 0.00 0.00 41.38 3.77
8 9 1.376609 CCACCATAGCCTTCCGCAAC 61.377 60.000 0.00 0.00 41.38 4.17
9 10 1.077787 CCACCATAGCCTTCCGCAA 60.078 57.895 0.00 0.00 41.38 4.85
10 11 2.297895 ACCACCATAGCCTTCCGCA 61.298 57.895 0.00 0.00 41.38 5.69
11 12 1.819632 CACCACCATAGCCTTCCGC 60.820 63.158 0.00 0.00 37.98 5.54
12 13 0.828022 TACACCACCATAGCCTTCCG 59.172 55.000 0.00 0.00 0.00 4.30
13 14 1.475213 GCTACACCACCATAGCCTTCC 60.475 57.143 0.00 0.00 38.29 3.46
14 15 1.806623 CGCTACACCACCATAGCCTTC 60.807 57.143 0.00 0.00 40.66 3.46
15 16 0.178068 CGCTACACCACCATAGCCTT 59.822 55.000 0.00 0.00 40.66 4.35
16 17 1.686325 CCGCTACACCACCATAGCCT 61.686 60.000 0.00 0.00 40.66 4.58
17 18 1.227556 CCGCTACACCACCATAGCC 60.228 63.158 0.00 0.00 40.66 3.93
18 19 0.393077 ATCCGCTACACCACCATAGC 59.607 55.000 0.00 0.00 40.40 2.97
19 20 1.686587 TCATCCGCTACACCACCATAG 59.313 52.381 0.00 0.00 0.00 2.23
20 21 1.783071 TCATCCGCTACACCACCATA 58.217 50.000 0.00 0.00 0.00 2.74
21 22 1.131638 ATCATCCGCTACACCACCAT 58.868 50.000 0.00 0.00 0.00 3.55
22 23 0.177836 CATCATCCGCTACACCACCA 59.822 55.000 0.00 0.00 0.00 4.17
23 24 0.178068 ACATCATCCGCTACACCACC 59.822 55.000 0.00 0.00 0.00 4.61
24 25 1.290203 CACATCATCCGCTACACCAC 58.710 55.000 0.00 0.00 0.00 4.16
25 26 0.177836 CCACATCATCCGCTACACCA 59.822 55.000 0.00 0.00 0.00 4.17
26 27 0.178068 ACCACATCATCCGCTACACC 59.822 55.000 0.00 0.00 0.00 4.16
27 28 1.134818 TCACCACATCATCCGCTACAC 60.135 52.381 0.00 0.00 0.00 2.90
28 29 1.190643 TCACCACATCATCCGCTACA 58.809 50.000 0.00 0.00 0.00 2.74
29 30 2.309528 TTCACCACATCATCCGCTAC 57.690 50.000 0.00 0.00 0.00 3.58
30 31 2.905075 CTTTCACCACATCATCCGCTA 58.095 47.619 0.00 0.00 0.00 4.26
31 32 1.742761 CTTTCACCACATCATCCGCT 58.257 50.000 0.00 0.00 0.00 5.52
32 33 0.099436 GCTTTCACCACATCATCCGC 59.901 55.000 0.00 0.00 0.00 5.54
33 34 0.734889 GGCTTTCACCACATCATCCG 59.265 55.000 0.00 0.00 0.00 4.18
34 35 1.106285 GGGCTTTCACCACATCATCC 58.894 55.000 0.00 0.00 0.00 3.51
35 36 2.134789 AGGGCTTTCACCACATCATC 57.865 50.000 0.00 0.00 0.00 2.92
36 37 2.846206 TCTAGGGCTTTCACCACATCAT 59.154 45.455 0.00 0.00 0.00 2.45
37 38 2.265367 TCTAGGGCTTTCACCACATCA 58.735 47.619 0.00 0.00 0.00 3.07
38 39 3.010420 GTTCTAGGGCTTTCACCACATC 58.990 50.000 0.00 0.00 0.00 3.06
39 40 2.375174 TGTTCTAGGGCTTTCACCACAT 59.625 45.455 0.00 0.00 0.00 3.21
40 41 1.771854 TGTTCTAGGGCTTTCACCACA 59.228 47.619 0.00 0.00 0.00 4.17
41 42 2.561478 TGTTCTAGGGCTTTCACCAC 57.439 50.000 0.00 0.00 0.00 4.16
42 43 3.586470 TTTGTTCTAGGGCTTTCACCA 57.414 42.857 0.00 0.00 0.00 4.17
43 44 5.468540 AATTTTGTTCTAGGGCTTTCACC 57.531 39.130 0.00 0.00 0.00 4.02
44 45 6.512297 TCAAATTTTGTTCTAGGGCTTTCAC 58.488 36.000 8.89 0.00 0.00 3.18
45 46 6.723298 TCAAATTTTGTTCTAGGGCTTTCA 57.277 33.333 8.89 0.00 0.00 2.69
46 47 6.591448 CCATCAAATTTTGTTCTAGGGCTTTC 59.409 38.462 8.89 0.00 0.00 2.62
47 48 6.466812 CCATCAAATTTTGTTCTAGGGCTTT 58.533 36.000 8.89 0.00 0.00 3.51
48 49 5.046376 CCCATCAAATTTTGTTCTAGGGCTT 60.046 40.000 8.89 0.00 0.00 4.35
49 50 4.467438 CCCATCAAATTTTGTTCTAGGGCT 59.533 41.667 8.89 0.00 0.00 5.19
50 51 4.466015 TCCCATCAAATTTTGTTCTAGGGC 59.534 41.667 8.89 0.00 32.63 5.19
51 52 5.105351 GGTCCCATCAAATTTTGTTCTAGGG 60.105 44.000 8.89 12.56 0.00 3.53
52 53 5.480073 TGGTCCCATCAAATTTTGTTCTAGG 59.520 40.000 8.89 5.01 0.00 3.02
53 54 6.588719 TGGTCCCATCAAATTTTGTTCTAG 57.411 37.500 8.89 0.00 0.00 2.43
54 55 8.657387 TTATGGTCCCATCAAATTTTGTTCTA 57.343 30.769 1.17 0.00 37.82 2.10
55 56 7.552050 TTATGGTCCCATCAAATTTTGTTCT 57.448 32.000 1.17 0.00 37.82 3.01
56 57 7.877612 AGTTTATGGTCCCATCAAATTTTGTTC 59.122 33.333 1.17 0.00 37.82 3.18
57 58 7.744733 AGTTTATGGTCCCATCAAATTTTGTT 58.255 30.769 1.17 0.00 37.82 2.83
58 59 7.235399 AGAGTTTATGGTCCCATCAAATTTTGT 59.765 33.333 1.17 0.00 37.82 2.83
59 60 7.614494 AGAGTTTATGGTCCCATCAAATTTTG 58.386 34.615 1.17 2.59 37.82 2.44
60 61 7.454380 TGAGAGTTTATGGTCCCATCAAATTTT 59.546 33.333 1.17 0.00 37.82 1.82
61 62 6.953520 TGAGAGTTTATGGTCCCATCAAATTT 59.046 34.615 1.17 0.00 37.82 1.82
62 63 6.493166 TGAGAGTTTATGGTCCCATCAAATT 58.507 36.000 1.17 0.25 37.82 1.82
63 64 6.078456 TGAGAGTTTATGGTCCCATCAAAT 57.922 37.500 1.17 0.00 37.82 2.32
64 65 5.512942 TGAGAGTTTATGGTCCCATCAAA 57.487 39.130 1.17 0.41 37.82 2.69
65 66 5.684704 GATGAGAGTTTATGGTCCCATCAA 58.315 41.667 1.17 0.00 37.82 2.57
66 67 4.202253 CGATGAGAGTTTATGGTCCCATCA 60.202 45.833 1.17 0.00 37.82 3.07
69 70 3.104512 ACGATGAGAGTTTATGGTCCCA 58.895 45.455 0.00 0.00 0.00 4.37
73 74 5.395324 CCCTAACACGATGAGAGTTTATGGT 60.395 44.000 0.00 0.00 35.35 3.55
82 83 2.107366 TGCATCCCTAACACGATGAGA 58.893 47.619 1.34 0.00 38.53 3.27
122 123 2.620115 CGCCCTAGTTTCCGTCATACTA 59.380 50.000 0.00 0.00 0.00 1.82
221 224 8.899887 TGTCATGGGATATCACAATATCTCTA 57.100 34.615 12.63 0.00 43.27 2.43
309 338 6.065374 TCAACTTGGTGTTTGGCTATCTTAA 58.935 36.000 0.00 0.00 36.63 1.85
313 342 4.380867 CCATCAACTTGGTGTTTGGCTATC 60.381 45.833 1.35 0.00 36.63 2.08
325 354 2.220653 ACACCATCCCATCAACTTGG 57.779 50.000 0.00 0.00 36.46 3.61
329 358 4.086457 ACCTTTTACACCATCCCATCAAC 58.914 43.478 0.00 0.00 0.00 3.18
333 362 5.340027 CCTCTAACCTTTTACACCATCCCAT 60.340 44.000 0.00 0.00 0.00 4.00
344 373 7.811282 TGCCATGATAATCCTCTAACCTTTTA 58.189 34.615 0.00 0.00 0.00 1.52
398 433 2.862530 GCTATCTCCATGTCGCGCTAAA 60.863 50.000 5.56 0.00 0.00 1.85
399 434 1.335964 GCTATCTCCATGTCGCGCTAA 60.336 52.381 5.56 0.00 0.00 3.09
411 447 2.362397 TGGTTGTCTCGATGCTATCTCC 59.638 50.000 0.00 0.00 0.00 3.71
431 468 4.697352 ACCACTAGTATCTTTGCTTTGCTG 59.303 41.667 0.00 0.00 0.00 4.41
447 486 4.205587 ACCGTTACTCTGGATACCACTAG 58.794 47.826 0.00 0.00 0.00 2.57
488 527 3.977312 TGGATTCGGTCTTCTTCCTAGA 58.023 45.455 0.00 0.00 0.00 2.43
549 588 2.358939 AGTTCCGGTTATGTCGTGAC 57.641 50.000 0.00 0.00 0.00 3.67
597 640 8.511321 TGTGATGGTTATTCACTATGTTGTTTC 58.489 33.333 5.52 0.00 43.12 2.78
610 653 7.218228 TGCCATGATTATGTGATGGTTATTC 57.782 36.000 0.00 0.00 42.91 1.75
613 656 6.305411 TCATGCCATGATTATGTGATGGTTA 58.695 36.000 2.53 0.00 42.91 2.85
627 670 2.379972 TGATTGTGCATCATGCCATGA 58.620 42.857 10.29 10.29 44.23 3.07
698 747 8.685838 AGCTCCACTAAACTTGTAATTTTGTA 57.314 30.769 0.00 0.00 0.00 2.41
705 754 8.154856 ACTTATTGAGCTCCACTAAACTTGTAA 58.845 33.333 12.15 0.00 0.00 2.41
714 763 7.415318 CGAGAGTTAACTTATTGAGCTCCACTA 60.415 40.741 12.15 0.00 0.00 2.74
871 937 6.984740 TTCGTGTTTGCTTTATTTGCTAAG 57.015 33.333 0.00 0.00 0.00 2.18
928 998 5.599242 TGCATCCAACCATGAATATGTCATT 59.401 36.000 0.00 0.00 45.13 2.57
1064 1180 4.274214 CACATCTGCACACTTCTCTTTTGA 59.726 41.667 0.00 0.00 0.00 2.69
1162 1289 2.083774 GTCCGAATTGATCCTTGCACA 58.916 47.619 0.00 0.00 0.00 4.57
1222 1353 3.044809 CGATGACCGTGGACGAATT 57.955 52.632 0.00 0.00 43.02 2.17
1243 1377 4.079558 ACTCTAGGAAGGTATAACCACGGA 60.080 45.833 0.00 0.00 41.95 4.69
1247 1381 4.616553 TGCACTCTAGGAAGGTATAACCA 58.383 43.478 0.00 0.00 41.95 3.67
1264 1399 0.250901 AACCGCTCCAAGAATGCACT 60.251 50.000 0.00 0.00 0.00 4.40
1335 1471 2.235402 GACCCCAAGTTACTCGGATTCA 59.765 50.000 0.00 0.00 0.00 2.57
1380 1516 3.187227 ACGCAAGCATCAAGTTTGACTAG 59.813 43.478 0.00 0.00 40.48 2.57
1386 1522 3.628017 GTGTAACGCAAGCATCAAGTTT 58.372 40.909 0.00 0.00 45.62 2.66
1433 1569 1.142870 TCCCAAGTTCCACCACAAGAG 59.857 52.381 0.00 0.00 0.00 2.85
1440 1576 2.302587 TTGGATTCCCAAGTTCCACC 57.697 50.000 0.00 0.00 46.94 4.61
1482 1619 0.453793 AGACCATCTCAGTTCTCGCG 59.546 55.000 0.00 0.00 0.00 5.87
1512 1649 1.208052 CCCTGAACCACATCATCTCGT 59.792 52.381 0.00 0.00 0.00 4.18
1521 1658 1.348064 CTAGACCACCCTGAACCACA 58.652 55.000 0.00 0.00 0.00 4.17
1529 1666 0.910088 GCCAAGACCTAGACCACCCT 60.910 60.000 0.00 0.00 0.00 4.34
1588 1725 3.068560 GCCAAATACGACTACACAACCA 58.931 45.455 0.00 0.00 0.00 3.67
1634 1772 1.493772 CAAGTTCGACTTACGCACCA 58.506 50.000 0.00 0.00 36.03 4.17
1641 1779 0.963962 AGACCGGCAAGTTCGACTTA 59.036 50.000 0.00 0.00 36.03 2.24
1686 1824 2.631418 TCGCTCTGTTTACTTCCTCG 57.369 50.000 0.00 0.00 0.00 4.63
1695 1833 1.265095 CACTGCACAATCGCTCTGTTT 59.735 47.619 0.00 0.00 0.00 2.83
1707 1845 2.595463 GCTGCTTCCCACTGCACA 60.595 61.111 0.00 0.00 35.20 4.57
1736 1874 3.181452 ACCATGTTTTCTTTGCTGCCATT 60.181 39.130 0.00 0.00 0.00 3.16
1738 1876 1.761784 ACCATGTTTTCTTTGCTGCCA 59.238 42.857 0.00 0.00 0.00 4.92
1773 1912 1.218047 CGGGATGTTCTTGCTCCGA 59.782 57.895 0.00 0.00 39.83 4.55
1783 1922 4.030913 TCTTGAACTCCTATCGGGATGTT 58.969 43.478 0.00 0.00 44.15 2.71
1874 2013 4.996434 GCAGAGCGCACCACCACT 62.996 66.667 11.47 0.00 41.79 4.00
1910 2049 0.964860 CCAATGCCCATCCGTTGACA 60.965 55.000 0.00 0.00 34.42 3.58
1925 2064 4.326766 GCGTGCGTGTGTGCCAAT 62.327 61.111 0.00 0.00 0.00 3.16
1954 2093 3.321648 ATGGACGCCACCTGCTCA 61.322 61.111 0.50 0.00 35.80 4.26
2011 2150 0.617413 CTGTGGCCTCATTCCTGTCT 59.383 55.000 8.18 0.00 0.00 3.41
2016 2155 1.225704 CTCCCTGTGGCCTCATTCC 59.774 63.158 8.18 0.00 0.00 3.01
2027 2166 4.361971 TCCTCGTCGCCTCCCTGT 62.362 66.667 0.00 0.00 0.00 4.00
2083 2222 1.195442 TACCACCGTGAATCAGGCCA 61.195 55.000 5.01 0.00 0.00 5.36
2105 2244 3.777925 CCTTTGTCGCAGTCGCCG 61.778 66.667 0.00 0.00 35.26 6.46
2216 2355 1.980772 GTCCTGCCCAGCATGCTTT 60.981 57.895 19.98 0.00 38.13 3.51
2233 2372 2.259618 CATCGTTCGATTTGAGGACGT 58.740 47.619 4.92 0.00 35.42 4.34
2240 2379 1.351707 CCCGCCATCGTTCGATTTG 59.648 57.895 4.92 1.74 0.00 2.32
2241 2380 1.817941 CCCCGCCATCGTTCGATTT 60.818 57.895 4.92 0.00 0.00 2.17
2242 2381 2.203015 CCCCGCCATCGTTCGATT 60.203 61.111 4.92 0.00 0.00 3.34
2243 2382 3.151710 TCCCCGCCATCGTTCGAT 61.152 61.111 1.68 1.68 0.00 3.59
2277 2416 4.521062 CTCCTTCCTCGCGCCAGG 62.521 72.222 15.77 15.77 34.40 4.45
2280 2419 4.856607 CGTCTCCTTCCTCGCGCC 62.857 72.222 0.00 0.00 0.00 6.53
2292 2431 1.107945 CTTTCCCCTCCTCTCGTCTC 58.892 60.000 0.00 0.00 0.00 3.36
2350 2492 2.283676 TCCTCGTTCCCTTCCGCT 60.284 61.111 0.00 0.00 0.00 5.52
2386 2528 0.468029 CCCCTGCTCTCTCTCTCTCC 60.468 65.000 0.00 0.00 0.00 3.71
2487 2635 1.986757 GAGAGAGAGCCTGCACCCA 60.987 63.158 0.00 0.00 0.00 4.51
2621 2779 8.995220 ACATGTTCATTTCATTTTTCTTGGATG 58.005 29.630 0.00 0.00 0.00 3.51
2730 2893 2.093447 CGAGCTCCACCTTAAACCTCAT 60.093 50.000 8.47 0.00 0.00 2.90
2993 3167 4.042398 GTGCATTGCATCATGTCATCTTC 58.958 43.478 15.49 0.00 41.91 2.87
3025 3199 2.164422 TGTTGGTTTGTTGCGTTCATCA 59.836 40.909 0.00 0.00 0.00 3.07
3066 3243 4.662179 TCTCTAGATGCCTTCCATGGATTT 59.338 41.667 17.06 0.00 33.29 2.17


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

AutoCloner maintained by Alex Coulton.