Multiple sequence alignment - TraesCS6D01G099600

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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 TraesCS6D01G099600 chr6D 100.000 2547 0 0 1 2547 62798265 62795719 0.000000e+00 4704.0
1 TraesCS6D01G099600 chr6D 91.011 1157 60 16 564 1709 25857858 25858981 0.000000e+00 1520.0
2 TraesCS6D01G099600 chr6D 89.592 1153 82 10 569 1709 312544302 312543176 0.000000e+00 1430.0
3 TraesCS6D01G099600 chr6D 89.236 1152 84 17 569 1709 28981283 28980161 0.000000e+00 1404.0
4 TraesCS6D01G099600 chr6D 92.362 851 52 7 869 1709 329896504 329895657 0.000000e+00 1199.0
5 TraesCS6D01G099600 chr6D 92.169 332 16 1 586 917 14242655 14242976 6.420000e-126 460.0
6 TraesCS6D01G099600 chr6D 84.594 357 23 6 568 917 329896762 329896431 2.440000e-85 326.0
7 TraesCS6D01G099600 chr6D 79.062 320 38 13 7 307 6518479 6518788 2.590000e-45 193.0
8 TraesCS6D01G099600 chr3A 91.878 1145 65 9 569 1709 47284899 47286019 0.000000e+00 1574.0
9 TraesCS6D01G099600 chr3A 88.326 1165 103 14 565 1709 593512224 593513375 0.000000e+00 1367.0
10 TraesCS6D01G099600 chr3A 90.385 52 4 1 453 503 18650717 18650666 1.640000e-07 67.6
11 TraesCS6D01G099600 chr2D 91.376 1148 64 16 569 1709 590929802 590928683 0.000000e+00 1539.0
12 TraesCS6D01G099600 chr2D 91.154 1153 64 16 569 1709 12544104 12542978 0.000000e+00 1530.0
13 TraesCS6D01G099600 chr2D 90.862 1160 62 17 569 1709 614811165 614810031 0.000000e+00 1515.0
14 TraesCS6D01G099600 chr2D 89.881 840 65 16 1713 2547 472007033 472007857 0.000000e+00 1062.0
15 TraesCS6D01G099600 chr2D 89.362 846 72 12 1710 2547 53258266 53257431 0.000000e+00 1048.0
16 TraesCS6D01G099600 chr7B 91.092 1145 75 11 570 1709 685254374 685253252 0.000000e+00 1524.0
17 TraesCS6D01G099600 chr7B 88.102 353 28 2 569 917 643463723 643464065 8.480000e-110 407.0
18 TraesCS6D01G099600 chr5D 90.768 1159 66 17 569 1709 486728530 486727395 0.000000e+00 1509.0
19 TraesCS6D01G099600 chr5D 90.204 1174 62 18 569 1709 353835673 353834520 0.000000e+00 1482.0
20 TraesCS6D01G099600 chr5D 88.975 1161 80 19 569 1709 6910281 6909149 0.000000e+00 1391.0
21 TraesCS6D01G099600 chr5D 85.754 358 34 5 559 910 363887954 363888300 1.860000e-96 363.0
22 TraesCS6D01G099600 chr3D 89.939 1153 91 9 569 1709 370069643 370070782 0.000000e+00 1463.0
23 TraesCS6D01G099600 chr3D 87.955 1154 72 23 569 1709 527509677 527510776 0.000000e+00 1299.0
24 TraesCS6D01G099600 chr3D 88.967 852 70 19 1706 2547 531676669 531675832 0.000000e+00 1031.0
25 TraesCS6D01G099600 chr3D 81.443 97 15 2 415 510 886497 886591 2.720000e-10 76.8
26 TraesCS6D01G099600 chr7D 89.717 1167 87 17 561 1709 90563643 90562492 0.000000e+00 1459.0
27 TraesCS6D01G099600 chr7D 92.663 845 42 12 1710 2547 613189150 613188319 0.000000e+00 1199.0
28 TraesCS6D01G099600 chr7D 89.835 846 67 13 1710 2547 261030076 261030910 0.000000e+00 1068.0
29 TraesCS6D01G099600 chr2B 89.528 1165 93 12 560 1709 776222953 776224103 0.000000e+00 1448.0
30 TraesCS6D01G099600 chr2B 88.898 1162 102 15 569 1709 774565439 774566594 0.000000e+00 1406.0
31 TraesCS6D01G099600 chr6A 89.451 1166 93 13 560 1709 617222879 617221728 0.000000e+00 1445.0
32 TraesCS6D01G099600 chr6A 89.619 1156 90 13 569 1709 616131296 616132436 0.000000e+00 1443.0
33 TraesCS6D01G099600 chr6A 86.332 578 39 16 1 547 80092321 80091753 6.070000e-166 593.0
34 TraesCS6D01G099600 chr6A 83.505 97 7 4 417 504 498052333 498052429 5.840000e-12 82.4
35 TraesCS6D01G099600 chr3B 89.510 1163 93 12 562 1709 20305081 20306229 0.000000e+00 1445.0
36 TraesCS6D01G099600 chr3B 89.231 1170 97 12 555 1709 379294079 379295234 0.000000e+00 1435.0
37 TraesCS6D01G099600 chr3B 86.082 388 29 7 556 939 561238999 561239365 6.600000e-106 394.0
38 TraesCS6D01G099600 chrUn 89.384 1168 89 17 559 1709 43129537 43128388 0.000000e+00 1437.0
39 TraesCS6D01G099600 chrUn 89.298 1168 93 14 559 1709 175762104 175763256 0.000000e+00 1435.0
40 TraesCS6D01G099600 chrUn 89.280 1166 94 14 559 1709 231572783 231573932 0.000000e+00 1432.0
41 TraesCS6D01G099600 chrUn 88.366 1169 102 17 559 1709 87140317 87141469 0.000000e+00 1375.0
42 TraesCS6D01G099600 chrUn 89.119 1112 70 21 608 1709 43407879 43408949 0.000000e+00 1336.0
43 TraesCS6D01G099600 chrUn 87.713 1172 103 23 560 1709 60558702 60559854 0.000000e+00 1328.0
44 TraesCS6D01G099600 chrUn 87.692 1170 106 20 559 1709 88504303 88505453 0.000000e+00 1328.0
45 TraesCS6D01G099600 chrUn 85.948 1160 125 19 570 1709 37355777 37354636 0.000000e+00 1205.0
46 TraesCS6D01G099600 chrUn 89.037 675 56 6 718 1387 412767049 412767710 0.000000e+00 821.0
47 TraesCS6D01G099600 chrUn 86.453 561 52 9 560 1109 463206470 463205923 6.070000e-166 593.0
48 TraesCS6D01G099600 chrUn 83.380 355 28 10 569 917 355013877 355014206 1.480000e-77 300.0
49 TraesCS6D01G099600 chrUn 89.796 49 3 2 453 500 108755796 108755843 7.610000e-06 62.1
50 TraesCS6D01G099600 chrUn 89.796 49 3 2 453 500 108763426 108763473 7.610000e-06 62.1
51 TraesCS6D01G099600 chr4B 89.329 1162 94 14 563 1709 643548249 643547103 0.000000e+00 1432.0
52 TraesCS6D01G099600 chr4B 89.273 1156 95 12 569 1709 407108830 407107689 0.000000e+00 1421.0
53 TraesCS6D01G099600 chr4B 86.552 1160 87 22 569 1709 94513638 94514747 0.000000e+00 1214.0
54 TraesCS6D01G099600 chr4B 86.019 422 34 8 565 973 660380887 660380478 1.810000e-116 429.0
55 TraesCS6D01G099600 chr1D 89.329 1162 86 24 569 1709 451655793 451654649 0.000000e+00 1424.0
56 TraesCS6D01G099600 chr1D 89.583 1152 75 12 569 1709 347252964 347251847 0.000000e+00 1421.0
57 TraesCS6D01G099600 chr1D 89.227 1151 76 18 569 1709 25464319 25465431 0.000000e+00 1395.0
58 TraesCS6D01G099600 chr1D 87.263 1162 80 16 559 1709 464037584 464038688 0.000000e+00 1264.0
59 TraesCS6D01G099600 chr1A 89.373 1148 92 12 569 1709 2863286 2862162 0.000000e+00 1417.0
60 TraesCS6D01G099600 chr1A 88.764 1157 96 16 569 1709 462529533 462530671 0.000000e+00 1386.0
61 TraesCS6D01G099600 chr4D 88.660 1164 73 23 560 1709 50776925 50778043 0.000000e+00 1363.0
62 TraesCS6D01G099600 chr5B 87.900 1157 96 18 569 1709 680910064 680908936 0.000000e+00 1321.0
63 TraesCS6D01G099600 chr7A 90.769 845 59 12 1710 2547 169050276 169051108 0.000000e+00 1110.0
64 TraesCS6D01G099600 chr7A 80.986 142 24 3 368 508 3966950 3967089 2.680000e-20 110.0
65 TraesCS6D01G099600 chr5A 90.426 846 65 13 1707 2547 490367804 490368638 0.000000e+00 1099.0
66 TraesCS6D01G099600 chr5A 75.625 160 24 11 355 510 502882758 502882906 5.880000e-07 65.8
67 TraesCS6D01G099600 chr5A 97.436 39 0 1 462 500 704947026 704946989 5.880000e-07 65.8
68 TraesCS6D01G099600 chr4A 89.716 846 64 18 1709 2547 7735246 7734417 0.000000e+00 1059.0
69 TraesCS6D01G099600 chr4A 89.046 849 74 16 1710 2547 527057796 527056956 0.000000e+00 1035.0
70 TraesCS6D01G099600 chr4A 80.769 156 15 10 369 510 95179571 95179417 9.640000e-20 108.0
71 TraesCS6D01G099600 chr6B 83.366 505 34 11 1 487 136365683 136365211 3.030000e-114 422.0
72 TraesCS6D01G099600 chr6B 86.119 353 34 4 569 917 457214526 457214185 1.440000e-97 366.0


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 TraesCS6D01G099600 chr6D 62795719 62798265 2546 True 4704.0 4704 100.000 1 2547 1 chr6D.!!$R2 2546
1 TraesCS6D01G099600 chr6D 25857858 25858981 1123 False 1520.0 1520 91.011 564 1709 1 chr6D.!!$F3 1145
2 TraesCS6D01G099600 chr6D 312543176 312544302 1126 True 1430.0 1430 89.592 569 1709 1 chr6D.!!$R3 1140
3 TraesCS6D01G099600 chr6D 28980161 28981283 1122 True 1404.0 1404 89.236 569 1709 1 chr6D.!!$R1 1140
4 TraesCS6D01G099600 chr6D 329895657 329896762 1105 True 762.5 1199 88.478 568 1709 2 chr6D.!!$R4 1141
5 TraesCS6D01G099600 chr3A 47284899 47286019 1120 False 1574.0 1574 91.878 569 1709 1 chr3A.!!$F1 1140
6 TraesCS6D01G099600 chr3A 593512224 593513375 1151 False 1367.0 1367 88.326 565 1709 1 chr3A.!!$F2 1144
7 TraesCS6D01G099600 chr2D 590928683 590929802 1119 True 1539.0 1539 91.376 569 1709 1 chr2D.!!$R3 1140
8 TraesCS6D01G099600 chr2D 12542978 12544104 1126 True 1530.0 1530 91.154 569 1709 1 chr2D.!!$R1 1140
9 TraesCS6D01G099600 chr2D 614810031 614811165 1134 True 1515.0 1515 90.862 569 1709 1 chr2D.!!$R4 1140
10 TraesCS6D01G099600 chr2D 472007033 472007857 824 False 1062.0 1062 89.881 1713 2547 1 chr2D.!!$F1 834
11 TraesCS6D01G099600 chr2D 53257431 53258266 835 True 1048.0 1048 89.362 1710 2547 1 chr2D.!!$R2 837
12 TraesCS6D01G099600 chr7B 685253252 685254374 1122 True 1524.0 1524 91.092 570 1709 1 chr7B.!!$R1 1139
13 TraesCS6D01G099600 chr5D 486727395 486728530 1135 True 1509.0 1509 90.768 569 1709 1 chr5D.!!$R3 1140
14 TraesCS6D01G099600 chr5D 353834520 353835673 1153 True 1482.0 1482 90.204 569 1709 1 chr5D.!!$R2 1140
15 TraesCS6D01G099600 chr5D 6909149 6910281 1132 True 1391.0 1391 88.975 569 1709 1 chr5D.!!$R1 1140
16 TraesCS6D01G099600 chr3D 370069643 370070782 1139 False 1463.0 1463 89.939 569 1709 1 chr3D.!!$F2 1140
17 TraesCS6D01G099600 chr3D 527509677 527510776 1099 False 1299.0 1299 87.955 569 1709 1 chr3D.!!$F3 1140
18 TraesCS6D01G099600 chr3D 531675832 531676669 837 True 1031.0 1031 88.967 1706 2547 1 chr3D.!!$R1 841
19 TraesCS6D01G099600 chr7D 90562492 90563643 1151 True 1459.0 1459 89.717 561 1709 1 chr7D.!!$R1 1148
20 TraesCS6D01G099600 chr7D 613188319 613189150 831 True 1199.0 1199 92.663 1710 2547 1 chr7D.!!$R2 837
21 TraesCS6D01G099600 chr7D 261030076 261030910 834 False 1068.0 1068 89.835 1710 2547 1 chr7D.!!$F1 837
22 TraesCS6D01G099600 chr2B 776222953 776224103 1150 False 1448.0 1448 89.528 560 1709 1 chr2B.!!$F2 1149
23 TraesCS6D01G099600 chr2B 774565439 774566594 1155 False 1406.0 1406 88.898 569 1709 1 chr2B.!!$F1 1140
24 TraesCS6D01G099600 chr6A 617221728 617222879 1151 True 1445.0 1445 89.451 560 1709 1 chr6A.!!$R2 1149
25 TraesCS6D01G099600 chr6A 616131296 616132436 1140 False 1443.0 1443 89.619 569 1709 1 chr6A.!!$F2 1140
26 TraesCS6D01G099600 chr6A 80091753 80092321 568 True 593.0 593 86.332 1 547 1 chr6A.!!$R1 546
27 TraesCS6D01G099600 chr3B 20305081 20306229 1148 False 1445.0 1445 89.510 562 1709 1 chr3B.!!$F1 1147
28 TraesCS6D01G099600 chr3B 379294079 379295234 1155 False 1435.0 1435 89.231 555 1709 1 chr3B.!!$F2 1154
29 TraesCS6D01G099600 chrUn 43128388 43129537 1149 True 1437.0 1437 89.384 559 1709 1 chrUn.!!$R2 1150
30 TraesCS6D01G099600 chrUn 175762104 175763256 1152 False 1435.0 1435 89.298 559 1709 1 chrUn.!!$F7 1150
31 TraesCS6D01G099600 chrUn 231572783 231573932 1149 False 1432.0 1432 89.280 559 1709 1 chrUn.!!$F8 1150
32 TraesCS6D01G099600 chrUn 87140317 87141469 1152 False 1375.0 1375 88.366 559 1709 1 chrUn.!!$F3 1150
33 TraesCS6D01G099600 chrUn 43407879 43408949 1070 False 1336.0 1336 89.119 608 1709 1 chrUn.!!$F1 1101
34 TraesCS6D01G099600 chrUn 60558702 60559854 1152 False 1328.0 1328 87.713 560 1709 1 chrUn.!!$F2 1149
35 TraesCS6D01G099600 chrUn 88504303 88505453 1150 False 1328.0 1328 87.692 559 1709 1 chrUn.!!$F4 1150
36 TraesCS6D01G099600 chrUn 37354636 37355777 1141 True 1205.0 1205 85.948 570 1709 1 chrUn.!!$R1 1139
37 TraesCS6D01G099600 chrUn 412767049 412767710 661 False 821.0 821 89.037 718 1387 1 chrUn.!!$F10 669
38 TraesCS6D01G099600 chrUn 463205923 463206470 547 True 593.0 593 86.453 560 1109 1 chrUn.!!$R3 549
39 TraesCS6D01G099600 chr4B 643547103 643548249 1146 True 1432.0 1432 89.329 563 1709 1 chr4B.!!$R2 1146
40 TraesCS6D01G099600 chr4B 407107689 407108830 1141 True 1421.0 1421 89.273 569 1709 1 chr4B.!!$R1 1140
41 TraesCS6D01G099600 chr4B 94513638 94514747 1109 False 1214.0 1214 86.552 569 1709 1 chr4B.!!$F1 1140
42 TraesCS6D01G099600 chr1D 451654649 451655793 1144 True 1424.0 1424 89.329 569 1709 1 chr1D.!!$R2 1140
43 TraesCS6D01G099600 chr1D 347251847 347252964 1117 True 1421.0 1421 89.583 569 1709 1 chr1D.!!$R1 1140
44 TraesCS6D01G099600 chr1D 25464319 25465431 1112 False 1395.0 1395 89.227 569 1709 1 chr1D.!!$F1 1140
45 TraesCS6D01G099600 chr1D 464037584 464038688 1104 False 1264.0 1264 87.263 559 1709 1 chr1D.!!$F2 1150
46 TraesCS6D01G099600 chr1A 2862162 2863286 1124 True 1417.0 1417 89.373 569 1709 1 chr1A.!!$R1 1140
47 TraesCS6D01G099600 chr1A 462529533 462530671 1138 False 1386.0 1386 88.764 569 1709 1 chr1A.!!$F1 1140
48 TraesCS6D01G099600 chr4D 50776925 50778043 1118 False 1363.0 1363 88.660 560 1709 1 chr4D.!!$F1 1149
49 TraesCS6D01G099600 chr5B 680908936 680910064 1128 True 1321.0 1321 87.900 569 1709 1 chr5B.!!$R1 1140
50 TraesCS6D01G099600 chr7A 169050276 169051108 832 False 1110.0 1110 90.769 1710 2547 1 chr7A.!!$F2 837
51 TraesCS6D01G099600 chr5A 490367804 490368638 834 False 1099.0 1099 90.426 1707 2547 1 chr5A.!!$F1 840
52 TraesCS6D01G099600 chr4A 7734417 7735246 829 True 1059.0 1059 89.716 1709 2547 1 chr4A.!!$R1 838
53 TraesCS6D01G099600 chr4A 527056956 527057796 840 True 1035.0 1035 89.046 1710 2547 1 chr4A.!!$R3 837

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
556 598 1.062002 CACACACGTCTCAAAAACGCT 59.938 47.619 0.0 0.0 43.76 5.07 F
714 763 1.153127 AACGTTTTGACTCGGCCCA 60.153 52.632 0.0 0.0 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1499 1762 0.398696 ACACCCAGTGCGATTACCAA 59.601 50.0 0.0 0.0 36.98 3.67 R
1989 2306 0.461548 ATGATCACCGTCATCACGCT 59.538 50.0 0.0 0.0 45.29 5.07 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
69 70 2.143419 CCTGCCGCTCCCTCCTAAT 61.143 63.158 0.00 0.00 0.00 1.73
102 103 2.036256 GTGTTGCCTCTGCCCCAT 59.964 61.111 0.00 0.00 36.33 4.00
110 111 2.934932 TCTGCCCCATGGAGCACA 60.935 61.111 18.22 4.04 34.68 4.57
111 112 2.753043 CTGCCCCATGGAGCACAC 60.753 66.667 18.22 0.00 34.68 3.82
117 118 2.034532 CATGGAGCACACTGGGCA 59.965 61.111 5.94 0.00 0.00 5.36
123 124 4.927782 GCACACTGGGCACGTCCA 62.928 66.667 0.00 1.45 36.21 4.02
133 134 1.593209 GCACGTCCAACTTCGGTGA 60.593 57.895 0.00 0.00 0.00 4.02
170 183 3.648982 CAGCACACGCCGCTTTGA 61.649 61.111 0.00 0.00 37.72 2.69
171 184 3.649986 AGCACACGCCGCTTTGAC 61.650 61.111 0.00 0.00 35.82 3.18
173 186 3.334751 CACACGCCGCTTTGACGA 61.335 61.111 0.00 0.00 34.06 4.20
174 187 2.357034 ACACGCCGCTTTGACGAT 60.357 55.556 0.00 0.00 34.06 3.73
175 188 2.096406 CACGCCGCTTTGACGATG 59.904 61.111 0.00 0.00 34.06 3.84
176 189 2.357034 ACGCCGCTTTGACGATGT 60.357 55.556 0.00 0.00 34.06 3.06
177 190 2.380410 ACGCCGCTTTGACGATGTC 61.380 57.895 0.00 0.00 34.06 3.06
214 233 2.111999 CTCCACCAAGAAGGCCGACA 62.112 60.000 0.00 0.00 43.14 4.35
221 240 2.489971 CAAGAAGGCCGACACTGTTTA 58.510 47.619 0.00 0.00 0.00 2.01
222 241 2.875933 CAAGAAGGCCGACACTGTTTAA 59.124 45.455 0.00 0.00 0.00 1.52
223 242 3.202829 AGAAGGCCGACACTGTTTAAA 57.797 42.857 0.00 0.00 0.00 1.52
255 274 5.699001 TCAAATACTGTACAAGCGAACATGT 59.301 36.000 0.00 0.00 0.00 3.21
257 276 3.386768 ACTGTACAAGCGAACATGTCT 57.613 42.857 0.00 0.00 0.00 3.41
258 277 4.514781 ACTGTACAAGCGAACATGTCTA 57.485 40.909 0.00 0.00 0.00 2.59
259 278 4.486090 ACTGTACAAGCGAACATGTCTAG 58.514 43.478 0.00 0.00 0.00 2.43
264 283 1.460504 AGCGAACATGTCTAGTCCGA 58.539 50.000 0.00 0.00 0.00 4.55
274 293 8.441312 AACATGTCTAGTCCGAAAACTTTTAA 57.559 30.769 0.00 0.00 0.00 1.52
419 458 6.170675 GACTACTTGTCTGCGAAATTTCAT 57.829 37.500 17.99 0.00 42.21 2.57
420 459 5.931532 ACTACTTGTCTGCGAAATTTCATG 58.068 37.500 17.99 7.25 0.00 3.07
421 460 5.700832 ACTACTTGTCTGCGAAATTTCATGA 59.299 36.000 17.99 9.31 0.00 3.07
422 461 5.437289 ACTTGTCTGCGAAATTTCATGAA 57.563 34.783 17.99 3.38 0.00 2.57
475 515 6.393720 AAAATCACGATTTTTAGCACATGC 57.606 33.333 11.14 0.00 45.67 4.06
547 589 5.839262 TGATGAAATTACACACACGTCTC 57.161 39.130 0.00 0.00 0.00 3.36
548 590 5.293560 TGATGAAATTACACACACGTCTCA 58.706 37.500 0.00 0.00 0.00 3.27
549 591 5.755861 TGATGAAATTACACACACGTCTCAA 59.244 36.000 0.00 0.00 0.00 3.02
550 592 6.258947 TGATGAAATTACACACACGTCTCAAA 59.741 34.615 0.00 0.00 0.00 2.69
551 593 6.424176 TGAAATTACACACACGTCTCAAAA 57.576 33.333 0.00 0.00 0.00 2.44
552 594 6.843208 TGAAATTACACACACGTCTCAAAAA 58.157 32.000 0.00 0.00 0.00 1.94
553 595 6.743627 TGAAATTACACACACGTCTCAAAAAC 59.256 34.615 0.00 0.00 0.00 2.43
554 596 2.798834 ACACACACGTCTCAAAAACG 57.201 45.000 0.00 0.00 45.37 3.60
555 597 1.201987 ACACACACGTCTCAAAAACGC 60.202 47.619 0.00 0.00 43.76 4.84
556 598 1.062002 CACACACGTCTCAAAAACGCT 59.938 47.619 0.00 0.00 43.76 5.07
557 599 1.326548 ACACACGTCTCAAAAACGCTC 59.673 47.619 0.00 0.00 43.76 5.03
558 600 1.593006 CACACGTCTCAAAAACGCTCT 59.407 47.619 0.00 0.00 43.76 4.09
613 659 2.429971 TGTCCATTTGCTCAGTTTTGCA 59.570 40.909 0.00 0.00 37.42 4.08
684 733 1.467883 CGTTCCGTGAATACTGCCGTA 60.468 52.381 0.00 0.00 0.00 4.02
714 763 1.153127 AACGTTTTGACTCGGCCCA 60.153 52.632 0.00 0.00 0.00 5.36
817 912 3.184683 GCAGAGAGCCGTTGCGAG 61.185 66.667 0.00 0.00 44.33 5.03
818 913 3.184683 CAGAGAGCCGTTGCGAGC 61.185 66.667 0.00 0.00 44.33 5.03
819 914 4.443266 AGAGAGCCGTTGCGAGCC 62.443 66.667 0.00 0.00 44.33 4.70
938 1173 4.544689 CGGCGACAGAGAGAGCGG 62.545 72.222 0.00 0.00 0.00 5.52
948 1183 4.162690 GAGAGCGGCGGTGGGAAT 62.163 66.667 19.47 0.00 0.00 3.01
1065 1300 1.289066 GCGCGTGGAGATGCCTATA 59.711 57.895 8.43 0.00 37.63 1.31
1104 1358 4.814294 GCGGGCGTTGATCGGAGT 62.814 66.667 0.00 0.00 40.26 3.85
1314 1571 3.072944 ACTGCAAGAAGAGCATGAAGAC 58.927 45.455 0.00 0.00 41.82 3.01
1498 1761 5.461032 TTACTTTTGGGCATTTGTAGGTG 57.539 39.130 0.00 0.00 0.00 4.00
1499 1762 3.304829 ACTTTTGGGCATTTGTAGGTGT 58.695 40.909 0.00 0.00 0.00 4.16
1523 1786 1.094785 AATCGCACTGGGTGTAATGC 58.905 50.000 0.00 0.00 35.75 3.56
1552 1829 7.658525 ATTGTATGGAAAGGCATGAATTACA 57.341 32.000 0.00 0.00 0.00 2.41
1713 2022 9.603921 AATTCAGAAACTTTGATCAATGTGTTT 57.396 25.926 23.26 23.05 0.00 2.83
1757 2067 0.037697 TTCCTACGCACACGCAAGAT 60.038 50.000 0.00 0.00 45.53 2.40
1758 2068 0.457853 TCCTACGCACACGCAAGATC 60.458 55.000 0.00 0.00 45.53 2.75
1759 2069 0.458543 CCTACGCACACGCAAGATCT 60.459 55.000 0.00 0.00 45.53 2.75
1760 2070 1.202256 CCTACGCACACGCAAGATCTA 60.202 52.381 0.00 0.00 45.53 1.98
1796 2111 2.111384 GCAATGAGAGGGGAGAGTGTA 58.889 52.381 0.00 0.00 0.00 2.90
1823 2138 3.118261 ACGTACCCTCATAGACCGTAAGA 60.118 47.826 0.00 0.00 43.02 2.10
1842 2157 2.029290 AGAGGAAGCGTTATGACAACGT 60.029 45.455 10.77 0.00 44.69 3.99
1892 2208 2.947652 CTGACCGATCCTAGTACCGAAA 59.052 50.000 0.00 0.00 0.00 3.46
1934 2250 3.598715 ACGTTCGGCTCGGTGACA 61.599 61.111 0.00 0.00 0.00 3.58
2097 2415 1.609580 GGAACCGCACATGGTAAGACA 60.610 52.381 0.00 0.00 42.89 3.41
2100 2418 1.071699 ACCGCACATGGTAAGACAACT 59.928 47.619 0.00 0.00 41.55 3.16
2101 2419 1.464608 CCGCACATGGTAAGACAACTG 59.535 52.381 0.00 0.00 0.00 3.16
2102 2420 1.135972 CGCACATGGTAAGACAACTGC 60.136 52.381 0.00 0.00 0.00 4.40
2533 2876 5.366477 TGACTATGAGATTATGCAACTCCCA 59.634 40.000 0.00 0.00 0.00 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 2.363711 GATAGCGACGCCATGGACCA 62.364 60.000 18.40 0.00 0.00 4.02
102 103 4.624364 CGTGCCCAGTGTGCTCCA 62.624 66.667 0.00 0.00 0.00 3.86
110 111 1.227853 GAAGTTGGACGTGCCCAGT 60.228 57.895 4.04 0.00 37.53 4.00
111 112 2.317609 CGAAGTTGGACGTGCCCAG 61.318 63.158 4.04 0.00 37.53 4.45
117 118 1.366366 CCTCACCGAAGTTGGACGT 59.634 57.895 0.00 0.00 0.00 4.34
165 178 1.382419 GTCGTCGTGACATCGTCAAAG 59.618 52.381 0.00 0.00 44.49 2.77
166 179 1.401530 GTCGTCGTGACATCGTCAAA 58.598 50.000 0.00 0.00 44.49 2.69
167 180 3.081741 GTCGTCGTGACATCGTCAA 57.918 52.632 0.00 0.00 44.49 3.18
189 208 1.349357 GCCTTCTTGGTGGAGAGACTT 59.651 52.381 0.00 0.00 38.35 3.01
242 261 2.671351 CGGACTAGACATGTTCGCTTGT 60.671 50.000 0.00 0.00 38.06 3.16
258 277 9.244799 GTGATTTTGATTAAAAGTTTTCGGACT 57.755 29.630 3.60 0.00 39.01 3.85
259 278 8.484799 GGTGATTTTGATTAAAAGTTTTCGGAC 58.515 33.333 3.60 0.00 39.01 4.79
274 293 6.379417 GGAGAGGATTTTCTGGTGATTTTGAT 59.621 38.462 0.00 0.00 0.00 2.57
281 300 4.722526 TTTGGAGAGGATTTTCTGGTGA 57.277 40.909 0.00 0.00 0.00 4.02
320 339 9.482175 TTTTAAATAAAGGGCTTTATGGAGCTA 57.518 29.630 0.00 0.00 42.91 3.32
465 505 8.956533 TTTATAGTGAATAGTGCATGTGCTAA 57.043 30.769 6.55 0.00 42.66 3.09
510 552 5.509716 TTTCATCATGAGATACGTACCGT 57.490 39.130 0.09 0.00 44.35 4.83
511 553 7.593644 TGTAATTTCATCATGAGATACGTACCG 59.406 37.037 0.09 0.00 31.88 4.02
515 557 7.763985 TGTGTGTAATTTCATCATGAGATACGT 59.236 33.333 0.09 0.00 31.88 3.57
516 558 8.058328 GTGTGTGTAATTTCATCATGAGATACG 58.942 37.037 0.09 0.00 31.88 3.06
524 566 5.931724 TGAGACGTGTGTGTAATTTCATCAT 59.068 36.000 0.00 0.00 0.00 2.45
535 577 1.201987 GCGTTTTTGAGACGTGTGTGT 60.202 47.619 0.00 0.00 42.22 3.72
547 589 7.272037 ACCCCATAATATAAGAGCGTTTTTG 57.728 36.000 0.00 0.00 0.00 2.44
548 590 7.891498 AACCCCATAATATAAGAGCGTTTTT 57.109 32.000 0.00 0.00 0.00 1.94
549 591 8.983702 TTAACCCCATAATATAAGAGCGTTTT 57.016 30.769 0.00 0.00 0.00 2.43
550 592 9.582648 AATTAACCCCATAATATAAGAGCGTTT 57.417 29.630 0.00 0.00 0.00 3.60
613 659 2.224042 TGAGCACGATTCACAACTGAGT 60.224 45.455 0.00 0.00 0.00 3.41
684 733 1.871039 CAAAACGTTGACCTGACGGAT 59.129 47.619 0.00 0.00 44.34 4.18
714 763 2.367202 CGCCTGGTCCCACCTGTAT 61.367 63.158 0.00 0.00 39.58 2.29
819 914 2.143008 TATATAGCACACCCGCAACG 57.857 50.000 0.00 0.00 0.00 4.10
938 1173 1.512926 CACAGCTATATTCCCACCGC 58.487 55.000 0.00 0.00 0.00 5.68
948 1183 0.396556 TCGTGCCCTCCACAGCTATA 60.397 55.000 0.00 0.00 44.91 1.31
1065 1300 2.126071 CACCGCGGACAGACGAAT 60.126 61.111 35.90 1.64 35.47 3.34
1104 1358 3.807622 GGTTCTTCGATGTGTGAGAAACA 59.192 43.478 5.63 0.00 36.04 2.83
1498 1761 0.802494 CACCCAGTGCGATTACCAAC 59.198 55.000 0.00 0.00 0.00 3.77
1499 1762 0.398696 ACACCCAGTGCGATTACCAA 59.601 50.000 0.00 0.00 36.98 3.67
1523 1786 6.211587 TCATGCCTTTCCATACAATTTCAG 57.788 37.500 0.00 0.00 0.00 3.02
1552 1829 7.955918 ACAATTTCAAGCTTACAAATTCCTCT 58.044 30.769 18.79 3.25 29.17 3.69
1757 2067 4.895668 TGCTATGCATCACCATGATAGA 57.104 40.909 0.19 0.00 34.28 1.98
1758 2068 5.646360 TCATTGCTATGCATCACCATGATAG 59.354 40.000 0.19 0.00 38.76 2.08
1759 2069 5.562635 TCATTGCTATGCATCACCATGATA 58.437 37.500 0.19 0.00 38.76 2.15
1760 2070 4.403734 TCATTGCTATGCATCACCATGAT 58.596 39.130 0.19 0.00 38.76 2.45
1796 2111 2.652590 GTCTATGAGGGTACGTGGACT 58.347 52.381 0.00 0.00 35.44 3.85
1823 2138 2.066262 CACGTTGTCATAACGCTTCCT 58.934 47.619 6.59 0.00 46.58 3.36
1842 2157 3.076621 AGACGTACGACTACATCAACCA 58.923 45.455 24.41 0.00 0.00 3.67
1872 2188 2.715749 TTCGGTACTAGGATCGGTCA 57.284 50.000 8.01 0.00 0.00 4.02
1934 2250 1.033574 GGATCGAGAGTTCGTGGGAT 58.966 55.000 0.00 0.00 46.72 3.85
1989 2306 0.461548 ATGATCACCGTCATCACGCT 59.538 50.000 0.00 0.00 45.29 5.07
2006 2323 0.999406 CCTGCGTCGGTAACTTCATG 59.001 55.000 0.00 0.00 0.00 3.07
2079 2397 1.877443 GTTGTCTTACCATGTGCGGTT 59.123 47.619 0.00 0.00 40.67 4.44
2092 2410 2.164219 CACACAAGTTGGCAGTTGTCTT 59.836 45.455 12.82 3.05 43.59 3.01
2097 2415 2.128771 AGACACACAAGTTGGCAGTT 57.871 45.000 7.96 0.00 0.00 3.16
2100 2418 2.503331 CCATAGACACACAAGTTGGCA 58.497 47.619 7.96 0.00 0.00 4.92
2101 2419 1.812571 CCCATAGACACACAAGTTGGC 59.187 52.381 7.96 0.00 0.00 4.52
2102 2420 2.224769 ACCCCATAGACACACAAGTTGG 60.225 50.000 7.96 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.