Multiple sequence alignment - TraesCS7A01G474300

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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 TraesCS7A01G474300 chr7A 100.000 3483 0 0 1 3483 669738537 669735055 0.000000e+00 6433.0
1 TraesCS7A01G474300 chr7A 98.519 1148 12 3 1 1148 11214771 11215913 0.000000e+00 2021.0
2 TraesCS7A01G474300 chr7A 97.952 830 17 0 2654 3483 513204228 513205057 0.000000e+00 1439.0
3 TraesCS7A01G474300 chr7A 97.590 830 19 1 2654 3483 193116746 193117574 0.000000e+00 1421.0
4 TraesCS7A01G474300 chr1B 96.906 1293 23 9 1 1290 252588420 252587142 0.000000e+00 2150.0
5 TraesCS7A01G474300 chr1B 96.829 1293 26 6 1 1291 52695976 52697255 0.000000e+00 2146.0
6 TraesCS7A01G474300 chr1B 96.599 147 3 2 1148 1292 546912325 546912179 3.470000e-60 243.0
7 TraesCS7A01G474300 chr5B 98.868 1148 12 1 1 1148 225927590 225928736 0.000000e+00 2047.0
8 TraesCS7A01G474300 chr5B 98.258 1148 14 4 1 1148 118344106 118345247 0.000000e+00 2004.0
9 TraesCS7A01G474300 chr5B 95.542 830 37 0 2654 3483 275056072 275055243 0.000000e+00 1328.0
10 TraesCS7A01G474300 chr5B 91.523 696 22 9 633 1295 624694970 624694279 0.000000e+00 924.0
11 TraesCS7A01G474300 chr5B 91.248 697 22 8 633 1295 628281014 628280323 0.000000e+00 913.0
12 TraesCS7A01G474300 chr1A 98.606 1148 14 1 1 1148 8620449 8621594 0.000000e+00 2030.0
13 TraesCS7A01G474300 chr1A 98.077 832 16 0 2652 3483 543651843 543651012 0.000000e+00 1448.0
14 TraesCS7A01G474300 chr4B 94.591 1331 34 8 1 1298 202062704 202061379 0.000000e+00 2025.0
15 TraesCS7A01G474300 chr7B 98.345 1148 15 2 1 1148 680937952 680936809 0.000000e+00 2012.0
16 TraesCS7A01G474300 chr7B 97.279 147 2 1 1148 1292 680936779 680936633 7.470000e-62 248.0
17 TraesCS7A01G474300 chr2A 94.033 1324 28 9 1 1291 626132358 626133663 0.000000e+00 1960.0
18 TraesCS7A01G474300 chr2A 89.444 180 11 5 2439 2617 105851334 105851162 1.630000e-53 220.0
19 TraesCS7A01G474300 chr3B 97.387 1148 27 1 1 1148 569694874 569693730 0.000000e+00 1951.0
20 TraesCS7A01G474300 chr3B 95.904 830 34 0 2654 3483 416805558 416804729 0.000000e+00 1345.0
21 TraesCS7A01G474300 chrUn 95.328 1220 21 8 105 1291 55070999 55072215 0.000000e+00 1905.0
22 TraesCS7A01G474300 chrUn 72.208 788 188 27 2651 3425 341236048 341235279 2.720000e-51 213.0
23 TraesCS7A01G474300 chrUn 95.200 125 6 0 2654 2778 9951270 9951146 7.630000e-47 198.0
24 TraesCS7A01G474300 chrUn 94.828 116 6 0 2654 2769 162556217 162556102 7.680000e-42 182.0
25 TraesCS7A01G474300 chrUn 94.167 120 5 2 2650 2769 192581955 192582072 7.680000e-42 182.0
26 TraesCS7A01G474300 chrUn 93.548 62 4 0 2654 2715 254087836 254087775 3.700000e-15 93.5
27 TraesCS7A01G474300 chrUn 93.548 62 4 0 2654 2715 424926523 424926462 3.700000e-15 93.5
28 TraesCS7A01G474300 chrUn 88.406 69 2 4 2654 2722 103116585 103116523 1.040000e-10 78.7
29 TraesCS7A01G474300 chrUn 87.671 73 1 6 2650 2722 171657942 171657878 1.040000e-10 78.7
30 TraesCS7A01G474300 chrUn 87.671 73 2 5 2650 2722 171659982 171659917 1.040000e-10 78.7
31 TraesCS7A01G474300 chr3A 98.072 830 15 1 2654 3483 502504922 502504094 0.000000e+00 1443.0
32 TraesCS7A01G474300 chr3A 97.839 833 14 2 2652 3483 648371257 648372086 0.000000e+00 1435.0
33 TraesCS7A01G474300 chr2D 95.918 833 33 1 2651 3483 179127588 179128419 0.000000e+00 1349.0
34 TraesCS7A01G474300 chr2D 95.663 830 36 0 2654 3483 603523552 603522723 0.000000e+00 1334.0
35 TraesCS7A01G474300 chr3D 95.558 833 37 0 2651 3483 223480054 223479222 0.000000e+00 1334.0
36 TraesCS7A01G474300 chr3D 95.553 832 37 0 2652 3483 91808626 91809457 0.000000e+00 1332.0
37 TraesCS7A01G474300 chr3D 95.000 840 36 2 2650 3483 553902304 553901465 0.000000e+00 1314.0
38 TraesCS7A01G474300 chr3D 95.181 830 38 2 2654 3483 11348135 11347308 0.000000e+00 1310.0
39 TraesCS7A01G474300 chr1D 95.542 830 35 1 2654 3483 388964871 388965698 0.000000e+00 1327.0
40 TraesCS7A01G474300 chr1D 73.324 731 174 18 2654 3375 60310688 60309970 2.080000e-62 250.0
41 TraesCS7A01G474300 chr7D 95.324 834 38 1 2650 3483 511081352 511080520 0.000000e+00 1323.0
42 TraesCS7A01G474300 chr7D 96.557 610 20 1 2662 3271 38864514 38865122 0.000000e+00 1009.0
43 TraesCS7A01G474300 chr7D 89.295 766 41 8 1292 2037 577621642 577620898 0.000000e+00 922.0
44 TraesCS7A01G474300 chr7D 88.424 622 38 13 2056 2651 577620912 577620299 0.000000e+00 719.0
45 TraesCS7A01G474300 chr5D 95.324 834 38 1 2650 3483 349376330 349375498 0.000000e+00 1323.0
46 TraesCS7A01G474300 chr5D 85.321 436 60 4 2654 3088 374250382 374249950 6.860000e-122 448.0
47 TraesCS7A01G474300 chr5D 82.960 223 29 6 2653 2871 322000336 322000119 3.550000e-45 193.0
48 TraesCS7A01G474300 chr5D 92.424 132 10 0 2638 2769 471989512 471989381 4.590000e-44 189.0
49 TraesCS7A01G474300 chr4D 95.113 839 34 3 2650 3483 15922320 15921484 0.000000e+00 1315.0
50 TraesCS7A01G474300 chr4D 84.515 691 102 4 2665 3353 464846604 464845917 0.000000e+00 678.0
51 TraesCS7A01G474300 chr4D 75.434 749 162 18 2656 3396 97493675 97492941 9.260000e-91 344.0
52 TraesCS7A01G474300 chr4D 76.596 282 53 12 2650 2927 227305430 227305158 3.620000e-30 143.0
53 TraesCS7A01G474300 chr4D 81.325 166 17 8 2646 2807 205984030 205983875 4.720000e-24 122.0
54 TraesCS7A01G474300 chr5A 92.063 693 18 8 633 1292 181399691 181399003 0.000000e+00 941.0
55 TraesCS7A01G474300 chr6D 85.978 813 109 4 2648 3456 328979838 328980649 0.000000e+00 865.0
56 TraesCS7A01G474300 chr6D 74.608 638 147 15 2650 3281 439599430 439598802 2.060000e-67 267.0
57 TraesCS7A01G474300 chr6D 76.619 278 53 11 2654 2927 29291212 29291481 3.620000e-30 143.0
58 TraesCS7A01G474300 chr6D 83.784 148 11 7 2664 2807 117432301 117432163 1.010000e-25 128.0
59 TraesCS7A01G474300 chr6D 81.325 166 16 9 2646 2807 193466654 193466500 1.700000e-23 121.0
60 TraesCS7A01G474300 chr6D 84.685 111 11 5 2656 2762 309794137 309794029 4.750000e-19 106.0
61 TraesCS7A01G474300 chr4A 96.599 147 3 1 1148 1292 613932644 613932790 3.470000e-60 243.0


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 TraesCS7A01G474300 chr7A 669735055 669738537 3482 True 6433.0 6433 100.0000 1 3483 1 chr7A.!!$R1 3482
1 TraesCS7A01G474300 chr7A 11214771 11215913 1142 False 2021.0 2021 98.5190 1 1148 1 chr7A.!!$F1 1147
2 TraesCS7A01G474300 chr7A 513204228 513205057 829 False 1439.0 1439 97.9520 2654 3483 1 chr7A.!!$F3 829
3 TraesCS7A01G474300 chr7A 193116746 193117574 828 False 1421.0 1421 97.5900 2654 3483 1 chr7A.!!$F2 829
4 TraesCS7A01G474300 chr1B 252587142 252588420 1278 True 2150.0 2150 96.9060 1 1290 1 chr1B.!!$R1 1289
5 TraesCS7A01G474300 chr1B 52695976 52697255 1279 False 2146.0 2146 96.8290 1 1291 1 chr1B.!!$F1 1290
6 TraesCS7A01G474300 chr5B 225927590 225928736 1146 False 2047.0 2047 98.8680 1 1148 1 chr5B.!!$F2 1147
7 TraesCS7A01G474300 chr5B 118344106 118345247 1141 False 2004.0 2004 98.2580 1 1148 1 chr5B.!!$F1 1147
8 TraesCS7A01G474300 chr5B 275055243 275056072 829 True 1328.0 1328 95.5420 2654 3483 1 chr5B.!!$R1 829
9 TraesCS7A01G474300 chr5B 624694279 624694970 691 True 924.0 924 91.5230 633 1295 1 chr5B.!!$R2 662
10 TraesCS7A01G474300 chr5B 628280323 628281014 691 True 913.0 913 91.2480 633 1295 1 chr5B.!!$R3 662
11 TraesCS7A01G474300 chr1A 8620449 8621594 1145 False 2030.0 2030 98.6060 1 1148 1 chr1A.!!$F1 1147
12 TraesCS7A01G474300 chr1A 543651012 543651843 831 True 1448.0 1448 98.0770 2652 3483 1 chr1A.!!$R1 831
13 TraesCS7A01G474300 chr4B 202061379 202062704 1325 True 2025.0 2025 94.5910 1 1298 1 chr4B.!!$R1 1297
14 TraesCS7A01G474300 chr7B 680936633 680937952 1319 True 1130.0 2012 97.8120 1 1292 2 chr7B.!!$R1 1291
15 TraesCS7A01G474300 chr2A 626132358 626133663 1305 False 1960.0 1960 94.0330 1 1291 1 chr2A.!!$F1 1290
16 TraesCS7A01G474300 chr3B 569693730 569694874 1144 True 1951.0 1951 97.3870 1 1148 1 chr3B.!!$R2 1147
17 TraesCS7A01G474300 chr3B 416804729 416805558 829 True 1345.0 1345 95.9040 2654 3483 1 chr3B.!!$R1 829
18 TraesCS7A01G474300 chrUn 55070999 55072215 1216 False 1905.0 1905 95.3280 105 1291 1 chrUn.!!$F1 1186
19 TraesCS7A01G474300 chrUn 341235279 341236048 769 True 213.0 213 72.2080 2651 3425 1 chrUn.!!$R5 774
20 TraesCS7A01G474300 chr3A 502504094 502504922 828 True 1443.0 1443 98.0720 2654 3483 1 chr3A.!!$R1 829
21 TraesCS7A01G474300 chr3A 648371257 648372086 829 False 1435.0 1435 97.8390 2652 3483 1 chr3A.!!$F1 831
22 TraesCS7A01G474300 chr2D 179127588 179128419 831 False 1349.0 1349 95.9180 2651 3483 1 chr2D.!!$F1 832
23 TraesCS7A01G474300 chr2D 603522723 603523552 829 True 1334.0 1334 95.6630 2654 3483 1 chr2D.!!$R1 829
24 TraesCS7A01G474300 chr3D 223479222 223480054 832 True 1334.0 1334 95.5580 2651 3483 1 chr3D.!!$R2 832
25 TraesCS7A01G474300 chr3D 91808626 91809457 831 False 1332.0 1332 95.5530 2652 3483 1 chr3D.!!$F1 831
26 TraesCS7A01G474300 chr3D 553901465 553902304 839 True 1314.0 1314 95.0000 2650 3483 1 chr3D.!!$R3 833
27 TraesCS7A01G474300 chr3D 11347308 11348135 827 True 1310.0 1310 95.1810 2654 3483 1 chr3D.!!$R1 829
28 TraesCS7A01G474300 chr1D 388964871 388965698 827 False 1327.0 1327 95.5420 2654 3483 1 chr1D.!!$F1 829
29 TraesCS7A01G474300 chr1D 60309970 60310688 718 True 250.0 250 73.3240 2654 3375 1 chr1D.!!$R1 721
30 TraesCS7A01G474300 chr7D 511080520 511081352 832 True 1323.0 1323 95.3240 2650 3483 1 chr7D.!!$R1 833
31 TraesCS7A01G474300 chr7D 38864514 38865122 608 False 1009.0 1009 96.5570 2662 3271 1 chr7D.!!$F1 609
32 TraesCS7A01G474300 chr7D 577620299 577621642 1343 True 820.5 922 88.8595 1292 2651 2 chr7D.!!$R2 1359
33 TraesCS7A01G474300 chr5D 349375498 349376330 832 True 1323.0 1323 95.3240 2650 3483 1 chr5D.!!$R2 833
34 TraesCS7A01G474300 chr4D 15921484 15922320 836 True 1315.0 1315 95.1130 2650 3483 1 chr4D.!!$R1 833
35 TraesCS7A01G474300 chr4D 464845917 464846604 687 True 678.0 678 84.5150 2665 3353 1 chr4D.!!$R5 688
36 TraesCS7A01G474300 chr4D 97492941 97493675 734 True 344.0 344 75.4340 2656 3396 1 chr4D.!!$R2 740
37 TraesCS7A01G474300 chr5A 181399003 181399691 688 True 941.0 941 92.0630 633 1292 1 chr5A.!!$R1 659
38 TraesCS7A01G474300 chr6D 328979838 328980649 811 False 865.0 865 85.9780 2648 3456 1 chr6D.!!$F2 808
39 TraesCS7A01G474300 chr6D 439598802 439599430 628 True 267.0 267 74.6080 2650 3281 1 chr6D.!!$R4 631

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
658 659 5.289675 GTCGATGATTAGTGTTGAACCTCAG 59.710 44.0 0.0 0.0 0.00 3.35 F
1540 1578 0.033504 GAGCTCGTGTTCCTCACCAA 59.966 55.0 0.0 0.0 43.51 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1655 1693 0.034896 GAAGCGAACAGTCCTTGGGA 59.965 55.0 0.00 0.0 0.0 4.37 R
2627 2710 0.466543 AACATATAAGGGCACGGCGA 59.533 50.0 16.62 0.0 0.0 5.54 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
177 178 8.199449 CCAAAAGGTTATGCATTTACTCATGAT 58.801 33.333 3.54 0.00 30.21 2.45
658 659 5.289675 GTCGATGATTAGTGTTGAACCTCAG 59.710 44.000 0.00 0.00 0.00 3.35
1015 1018 9.679661 AGGTTGTTTTCTGTAAAATTGGATTTT 57.320 25.926 4.32 4.32 44.13 1.82
1057 1063 5.183228 ACATTACTAGTGGCGCATTTAAGT 58.817 37.500 10.83 8.29 0.00 2.24
1098 1104 4.682778 TCCTTTATTACTAGTGGCGCAT 57.317 40.909 10.83 0.00 0.00 4.73
1251 1287 1.948834 CCACTGATGCGCCATTAATGA 59.051 47.619 17.23 0.00 0.00 2.57
1261 1297 5.555966 TGCGCCATTAATGACCATATTAGA 58.444 37.500 17.23 0.00 0.00 2.10
1302 1340 0.242825 TAGTAGTGACGCTGCACACC 59.757 55.000 18.48 8.45 41.19 4.16
1313 1351 4.314440 GCACACCGGCTCTGTCCA 62.314 66.667 0.00 0.00 0.00 4.02
1323 1361 3.865929 CTCTGTCCACGCGGCTGTT 62.866 63.158 12.47 0.00 0.00 3.16
1331 1369 1.741770 ACGCGGCTGTTCAAGATCC 60.742 57.895 12.47 0.00 0.00 3.36
1339 1377 2.095718 GCTGTTCAAGATCCACGTTTCC 60.096 50.000 0.00 0.00 0.00 3.13
1366 1404 2.357517 CACCTGCACGGTCCTCAC 60.358 66.667 5.02 0.00 44.93 3.51
1398 1436 2.684843 GCCGTGAAGCTGCTCAAGG 61.685 63.158 20.68 20.68 44.91 3.61
1519 1557 4.760047 GACAGCGATGGCACCGGT 62.760 66.667 0.00 0.00 43.41 5.28
1539 1577 1.666011 GAGCTCGTGTTCCTCACCA 59.334 57.895 0.00 0.00 43.51 4.17
1540 1578 0.033504 GAGCTCGTGTTCCTCACCAA 59.966 55.000 0.00 0.00 43.51 3.67
1541 1579 0.468226 AGCTCGTGTTCCTCACCAAA 59.532 50.000 0.00 0.00 43.51 3.28
1542 1580 1.134220 AGCTCGTGTTCCTCACCAAAA 60.134 47.619 0.00 0.00 43.51 2.44
1543 1581 1.002792 GCTCGTGTTCCTCACCAAAAC 60.003 52.381 0.00 0.00 43.51 2.43
1544 1582 2.561569 CTCGTGTTCCTCACCAAAACT 58.438 47.619 0.00 0.00 43.51 2.66
1545 1583 2.285083 TCGTGTTCCTCACCAAAACTG 58.715 47.619 0.00 0.00 43.51 3.16
1546 1584 1.268539 CGTGTTCCTCACCAAAACTGC 60.269 52.381 0.00 0.00 43.51 4.40
1547 1585 1.748493 GTGTTCCTCACCAAAACTGCA 59.252 47.619 0.00 0.00 40.84 4.41
1548 1586 2.165437 GTGTTCCTCACCAAAACTGCAA 59.835 45.455 0.00 0.00 40.84 4.08
1549 1587 2.426738 TGTTCCTCACCAAAACTGCAAG 59.573 45.455 0.00 0.00 42.29 4.01
1550 1588 1.032014 TCCTCACCAAAACTGCAAGC 58.968 50.000 0.00 0.00 37.60 4.01
1551 1589 0.746063 CCTCACCAAAACTGCAAGCA 59.254 50.000 0.00 0.00 37.60 3.91
1552 1590 1.536709 CCTCACCAAAACTGCAAGCAC 60.537 52.381 0.00 0.00 37.60 4.40
1553 1591 0.459489 TCACCAAAACTGCAAGCACC 59.541 50.000 0.00 0.00 37.60 5.01
1577 1615 3.435186 GTGAGGGCGAGCTTTGGC 61.435 66.667 5.06 5.06 39.06 4.52
1589 1627 0.324943 GCTTTGGCTGTCTCCTGGTA 59.675 55.000 0.00 0.00 35.22 3.25
1601 1639 2.579201 CTGGTACACCCGAGGCTG 59.421 66.667 0.00 0.00 35.15 4.85
1604 1642 4.814294 GTACACCCGAGGCTGCCG 62.814 72.222 13.96 1.76 0.00 5.69
1652 1690 0.040157 CCGTGTGGCATGTGTTCAAG 60.040 55.000 0.00 0.00 0.00 3.02
1654 1692 0.385029 GTGTGGCATGTGTTCAAGCA 59.615 50.000 0.00 0.00 39.63 3.91
1655 1693 1.000060 GTGTGGCATGTGTTCAAGCAT 60.000 47.619 0.00 0.00 39.63 3.79
1661 1699 2.673043 GCATGTGTTCAAGCATCCCAAG 60.673 50.000 0.00 0.00 38.05 3.61
1664 1702 1.541588 GTGTTCAAGCATCCCAAGGAC 59.458 52.381 0.00 0.00 32.98 3.85
1672 1710 0.036010 CATCCCAAGGACTGTTCGCT 60.036 55.000 0.00 0.00 32.98 4.93
1743 1799 1.626654 CCAGTGCACCGTCACGATTC 61.627 60.000 14.63 0.00 41.61 2.52
1752 1808 1.272781 CGTCACGATTCTGAAGGAGC 58.727 55.000 0.00 0.00 0.00 4.70
1753 1809 1.135257 CGTCACGATTCTGAAGGAGCT 60.135 52.381 0.00 0.00 0.00 4.09
1817 1875 2.125350 CAGCACTTCCGGGAGCTC 60.125 66.667 10.62 4.71 34.61 4.09
1822 1880 4.521062 CTTCCGGGAGCTCCTGCG 62.521 72.222 33.02 26.49 45.42 5.18
1866 1924 2.646175 TTCCTCGTCTCCGGCAAGG 61.646 63.158 0.00 0.00 42.97 3.61
1983 2041 1.918262 AGATCAAGGACATGGAGGCAA 59.082 47.619 0.00 0.00 0.00 4.52
2024 2082 5.661458 CTGGAGTTTATCTACACCGACAAT 58.339 41.667 0.00 0.00 32.86 2.71
2025 2083 5.416083 TGGAGTTTATCTACACCGACAATG 58.584 41.667 0.00 0.00 31.03 2.82
2026 2084 5.046878 TGGAGTTTATCTACACCGACAATGT 60.047 40.000 0.00 0.00 31.03 2.71
2027 2085 5.873164 GGAGTTTATCTACACCGACAATGTT 59.127 40.000 0.00 0.00 0.00 2.71
2028 2086 6.035758 GGAGTTTATCTACACCGACAATGTTC 59.964 42.308 0.00 0.00 0.00 3.18
2029 2087 5.873164 AGTTTATCTACACCGACAATGTTCC 59.127 40.000 0.00 0.00 0.00 3.62
2030 2088 5.670792 TTATCTACACCGACAATGTTCCT 57.329 39.130 0.00 0.00 0.00 3.36
2031 2089 3.313012 TCTACACCGACAATGTTCCTG 57.687 47.619 0.00 0.00 0.00 3.86
2032 2090 2.894765 TCTACACCGACAATGTTCCTGA 59.105 45.455 0.00 0.00 0.00 3.86
2033 2091 2.631160 ACACCGACAATGTTCCTGAA 57.369 45.000 0.00 0.00 0.00 3.02
2034 2092 2.218603 ACACCGACAATGTTCCTGAAC 58.781 47.619 3.07 3.07 41.50 3.18
2035 2093 2.158813 ACACCGACAATGTTCCTGAACT 60.159 45.455 11.03 0.00 41.67 3.01
2036 2094 2.878406 CACCGACAATGTTCCTGAACTT 59.122 45.455 11.03 2.46 41.67 2.66
2037 2095 3.058914 CACCGACAATGTTCCTGAACTTC 60.059 47.826 11.03 2.68 41.67 3.01
2038 2096 2.484264 CCGACAATGTTCCTGAACTTCC 59.516 50.000 11.03 0.00 41.67 3.46
2039 2097 3.403038 CGACAATGTTCCTGAACTTCCT 58.597 45.455 11.03 0.00 41.67 3.36
2040 2098 3.815401 CGACAATGTTCCTGAACTTCCTT 59.185 43.478 11.03 0.00 41.67 3.36
2041 2099 4.083802 CGACAATGTTCCTGAACTTCCTTC 60.084 45.833 11.03 2.82 41.67 3.46
2042 2100 3.815401 ACAATGTTCCTGAACTTCCTTCG 59.185 43.478 11.03 0.00 41.67 3.79
2043 2101 1.878953 TGTTCCTGAACTTCCTTCGC 58.121 50.000 11.03 0.00 41.67 4.70
2044 2102 1.140052 TGTTCCTGAACTTCCTTCGCA 59.860 47.619 11.03 0.00 41.67 5.10
2045 2103 2.218603 GTTCCTGAACTTCCTTCGCAA 58.781 47.619 2.80 0.00 38.25 4.85
2046 2104 2.616842 GTTCCTGAACTTCCTTCGCAAA 59.383 45.455 2.80 0.00 38.25 3.68
2047 2105 2.925724 TCCTGAACTTCCTTCGCAAAA 58.074 42.857 0.00 0.00 0.00 2.44
2048 2106 3.283751 TCCTGAACTTCCTTCGCAAAAA 58.716 40.909 0.00 0.00 0.00 1.94
2084 2142 1.831652 AACTTGACCGGGAGCTGGAG 61.832 60.000 6.32 0.00 33.36 3.86
2136 2194 3.066190 CGGCTGACAGGTACGGGA 61.066 66.667 4.26 0.00 0.00 5.14
2138 2196 1.905512 GGCTGACAGGTACGGGATT 59.094 57.895 4.26 0.00 0.00 3.01
2156 2214 5.594926 GGGATTGACAGGCTCAAAATTATG 58.405 41.667 0.00 0.00 42.37 1.90
2186 2252 1.153289 GCTCATCGGTGGCATCACT 60.153 57.895 0.00 0.00 43.17 3.41
2192 2258 2.094659 CGGTGGCATCACTGTCGAC 61.095 63.158 9.11 9.11 43.44 4.20
2219 2285 1.234821 CGACTACTTTGGCTTTGGCA 58.765 50.000 0.00 0.00 40.87 4.92
2248 2314 2.424842 AATTGCCCGCACCTCAAGGA 62.425 55.000 2.30 0.00 38.94 3.36
2255 2321 0.034059 CGCACCTCAAGGAGAAGTGT 59.966 55.000 2.30 0.00 38.94 3.55
2256 2322 1.517242 GCACCTCAAGGAGAAGTGTG 58.483 55.000 2.30 0.00 38.94 3.82
2258 2324 2.760374 CACCTCAAGGAGAAGTGTGTC 58.240 52.381 2.30 0.00 38.94 3.67
2291 2357 1.751924 AGTACTCCTGCGATCCTTGAC 59.248 52.381 0.00 0.00 0.00 3.18
2323 2389 0.032017 ACGGAGGGGTCTAAGCATCT 60.032 55.000 0.00 0.00 0.00 2.90
2416 2496 3.368236 GCTAGTCGCTAAAGTCCAAGTTG 59.632 47.826 0.00 0.00 35.14 3.16
2458 2538 5.604758 TGCATGATCTAGCAGAACTTAGT 57.395 39.130 8.30 0.00 35.51 2.24
2486 2568 6.003950 GCCTGTCTTTGGCCTAATATAATGA 58.996 40.000 3.32 0.00 44.32 2.57
2519 2601 6.609237 TGCTACATCAATCATCTTGTAAGC 57.391 37.500 0.00 0.00 0.00 3.09
2525 2607 3.197766 TCAATCATCTTGTAAGCCCGAGT 59.802 43.478 0.00 0.00 0.00 4.18
2537 2619 0.801067 GCCCGAGTAACTAGTGTGCG 60.801 60.000 0.00 0.00 0.00 5.34
2539 2621 0.801067 CCGAGTAACTAGTGTGCGCC 60.801 60.000 4.18 0.00 0.00 6.53
2540 2622 0.170561 CGAGTAACTAGTGTGCGCCT 59.829 55.000 4.18 0.00 0.00 5.52
2542 2624 0.531200 AGTAACTAGTGTGCGCCTCC 59.469 55.000 4.18 0.00 0.00 4.30
2543 2625 0.245539 GTAACTAGTGTGCGCCTCCA 59.754 55.000 4.18 0.00 0.00 3.86
2545 2627 1.191535 AACTAGTGTGCGCCTCCATA 58.808 50.000 4.18 0.00 0.00 2.74
2546 2628 1.414158 ACTAGTGTGCGCCTCCATAT 58.586 50.000 4.18 0.00 0.00 1.78
2547 2629 1.762957 ACTAGTGTGCGCCTCCATATT 59.237 47.619 4.18 0.00 0.00 1.28
2559 2641 4.823989 CGCCTCCATATTCTCCTTGAATTT 59.176 41.667 0.00 0.00 42.28 1.82
2585 2667 3.065371 GGATCTAGTTTCGTGCCAAATGG 59.935 47.826 0.00 0.00 38.53 3.16
2589 2671 2.306847 AGTTTCGTGCCAAATGGTTCT 58.693 42.857 0.71 0.00 37.57 3.01
2598 2681 1.205417 CCAAATGGTTCTGGATGTGGC 59.795 52.381 0.00 0.00 34.35 5.01
2605 2688 2.762327 GGTTCTGGATGTGGCAAATCAT 59.238 45.455 19.01 4.34 0.00 2.45
2606 2689 3.196254 GGTTCTGGATGTGGCAAATCATT 59.804 43.478 19.01 0.00 0.00 2.57
2607 2690 4.427312 GTTCTGGATGTGGCAAATCATTC 58.573 43.478 19.01 4.05 0.00 2.67
2619 2702 4.826733 GGCAAATCATTCCTTTTTGGGTTT 59.173 37.500 0.00 0.00 36.20 3.27
2625 2708 6.993786 TCATTCCTTTTTGGGTTTGTTTTC 57.006 33.333 0.00 0.00 36.20 2.29
2626 2709 6.476378 TCATTCCTTTTTGGGTTTGTTTTCA 58.524 32.000 0.00 0.00 36.20 2.69
2627 2710 7.115414 TCATTCCTTTTTGGGTTTGTTTTCAT 58.885 30.769 0.00 0.00 36.20 2.57
2628 2711 6.993786 TTCCTTTTTGGGTTTGTTTTCATC 57.006 33.333 0.00 0.00 36.20 2.92
2629 2712 5.112686 TCCTTTTTGGGTTTGTTTTCATCG 58.887 37.500 0.00 0.00 36.20 3.84
2630 2713 4.260579 CCTTTTTGGGTTTGTTTTCATCGC 60.261 41.667 0.00 0.00 0.00 4.58
2631 2714 2.517650 TTGGGTTTGTTTTCATCGCC 57.482 45.000 0.00 0.00 0.00 5.54
2632 2715 0.312416 TGGGTTTGTTTTCATCGCCG 59.688 50.000 0.00 0.00 0.00 6.46
2633 2716 0.312729 GGGTTTGTTTTCATCGCCGT 59.687 50.000 0.00 0.00 0.00 5.68
2634 2717 1.404477 GGTTTGTTTTCATCGCCGTG 58.596 50.000 0.00 0.00 0.00 4.94
2635 2718 0.775861 GTTTGTTTTCATCGCCGTGC 59.224 50.000 0.00 0.00 0.00 5.34
2636 2719 0.318275 TTTGTTTTCATCGCCGTGCC 60.318 50.000 0.00 0.00 0.00 5.01
2637 2720 2.136196 TTGTTTTCATCGCCGTGCCC 62.136 55.000 0.00 0.00 0.00 5.36
2638 2721 2.033448 TTTTCATCGCCGTGCCCT 59.967 55.556 0.00 0.00 0.00 5.19
2639 2722 1.602323 TTTTCATCGCCGTGCCCTT 60.602 52.632 0.00 0.00 0.00 3.95
2640 2723 0.321741 TTTTCATCGCCGTGCCCTTA 60.322 50.000 0.00 0.00 0.00 2.69
2641 2724 0.107410 TTTCATCGCCGTGCCCTTAT 60.107 50.000 0.00 0.00 0.00 1.73
2642 2725 0.753867 TTCATCGCCGTGCCCTTATA 59.246 50.000 0.00 0.00 0.00 0.98
2643 2726 0.973632 TCATCGCCGTGCCCTTATAT 59.026 50.000 0.00 0.00 0.00 0.86
2644 2727 1.078709 CATCGCCGTGCCCTTATATG 58.921 55.000 0.00 0.00 0.00 1.78
2645 2728 0.685097 ATCGCCGTGCCCTTATATGT 59.315 50.000 0.00 0.00 0.00 2.29
2646 2729 0.466543 TCGCCGTGCCCTTATATGTT 59.533 50.000 0.00 0.00 0.00 2.71
2876 2968 1.796459 CTTGTTACGAAACACCCTCGG 59.204 52.381 0.00 0.00 45.18 4.63
2970 3062 3.820557 CATGTCGGTCCTTTTATCCCAT 58.179 45.455 0.00 0.00 0.00 4.00
2976 3068 4.080015 TCGGTCCTTTTATCCCATCATTGT 60.080 41.667 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
238 239 7.444183 TCCGAGACACATCAAAACTAAAGATTT 59.556 33.333 0.00 0.00 0.00 2.17
262 263 9.959749 TCATCACAACTTAACAAAAGTAAATCC 57.040 29.630 0.00 0.00 0.00 3.01
658 659 4.400251 TGGAAATGAATTGCAGAGGACATC 59.600 41.667 0.00 0.00 34.05 3.06
1057 1063 1.200519 AGGTGCGCCACTAATAAGGA 58.799 50.000 20.59 0.00 37.19 3.36
1098 1104 5.510179 GGTGCGCCACTAATAACCTTATAGA 60.510 44.000 12.58 0.00 34.40 1.98
1251 1287 5.165961 ACTAATGGCGCATCTAATATGGT 57.834 39.130 10.83 0.00 0.00 3.55
1261 1297 2.729028 AAACCCTACTAATGGCGCAT 57.271 45.000 10.83 0.00 0.00 4.73
1313 1351 1.741770 GGATCTTGAACAGCCGCGT 60.742 57.895 4.92 0.00 0.00 6.01
1323 1361 2.710377 CATGGGAAACGTGGATCTTGA 58.290 47.619 0.00 0.00 32.27 3.02
1331 1369 2.686816 GGTCGCCATGGGAAACGTG 61.687 63.158 15.13 0.00 35.80 4.49
1339 1377 4.720902 TGCAGGTGGTCGCCATGG 62.721 66.667 7.63 7.63 35.28 3.66
1398 1436 2.027625 CCAGGCGGAAACTGTCGAC 61.028 63.158 9.11 9.11 34.16 4.20
1509 1547 4.148825 GAGCTCGACCGGTGCCAT 62.149 66.667 14.63 0.00 0.00 4.40
1518 1556 0.729816 GTGAGGAACACGAGCTCGAC 60.730 60.000 40.58 25.46 43.02 4.20
1519 1557 1.579932 GTGAGGAACACGAGCTCGA 59.420 57.895 40.58 14.59 43.02 4.04
1545 1583 2.353839 CACGTTGCAGGTGCTTGC 60.354 61.111 6.99 0.00 44.33 4.01
1546 1584 1.280746 CTCACGTTGCAGGTGCTTG 59.719 57.895 13.43 4.77 42.66 4.01
1547 1585 1.893808 CCTCACGTTGCAGGTGCTT 60.894 57.895 13.43 0.00 42.66 3.91
1548 1586 2.281070 CCTCACGTTGCAGGTGCT 60.281 61.111 13.43 0.00 42.66 4.40
1549 1587 3.357079 CCCTCACGTTGCAGGTGC 61.357 66.667 13.43 0.00 42.50 5.01
1550 1588 3.357079 GCCCTCACGTTGCAGGTG 61.357 66.667 12.36 12.36 35.48 4.00
1551 1589 4.988598 CGCCCTCACGTTGCAGGT 62.989 66.667 4.63 0.00 0.00 4.00
1552 1590 4.680237 TCGCCCTCACGTTGCAGG 62.680 66.667 0.00 0.00 0.00 4.85
1553 1591 3.114616 CTCGCCCTCACGTTGCAG 61.115 66.667 0.00 0.00 0.00 4.41
1577 1615 0.611062 TCGGGTGTACCAGGAGACAG 60.611 60.000 3.11 0.00 40.22 3.51
1608 1646 1.442520 CTTCGTTGCCATTGTGCGG 60.443 57.895 0.00 0.00 0.00 5.69
1609 1647 0.040514 TTCTTCGTTGCCATTGTGCG 60.041 50.000 0.00 0.00 0.00 5.34
1610 1648 2.132740 TTTCTTCGTTGCCATTGTGC 57.867 45.000 0.00 0.00 0.00 4.57
1611 1649 3.730715 GTCTTTTCTTCGTTGCCATTGTG 59.269 43.478 0.00 0.00 0.00 3.33
1612 1650 3.243401 GGTCTTTTCTTCGTTGCCATTGT 60.243 43.478 0.00 0.00 0.00 2.71
1613 1651 3.308530 GGTCTTTTCTTCGTTGCCATTG 58.691 45.455 0.00 0.00 0.00 2.82
1614 1652 2.031157 CGGTCTTTTCTTCGTTGCCATT 60.031 45.455 0.00 0.00 0.00 3.16
1615 1653 1.535462 CGGTCTTTTCTTCGTTGCCAT 59.465 47.619 0.00 0.00 0.00 4.40
1616 1654 0.941542 CGGTCTTTTCTTCGTTGCCA 59.058 50.000 0.00 0.00 0.00 4.92
1617 1655 0.942252 ACGGTCTTTTCTTCGTTGCC 59.058 50.000 0.00 0.00 31.38 4.52
1618 1656 1.329599 ACACGGTCTTTTCTTCGTTGC 59.670 47.619 0.00 0.00 33.31 4.17
1652 1690 1.648467 GCGAACAGTCCTTGGGATGC 61.648 60.000 0.00 0.00 32.73 3.91
1654 1692 0.693049 AAGCGAACAGTCCTTGGGAT 59.307 50.000 0.00 0.00 32.73 3.85
1655 1693 0.034896 GAAGCGAACAGTCCTTGGGA 59.965 55.000 0.00 0.00 0.00 4.37
1661 1699 0.241481 AGACTCGAAGCGAACAGTCC 59.759 55.000 0.00 0.00 34.74 3.85
1664 1702 1.399504 GCGAGACTCGAAGCGAACAG 61.400 60.000 28.43 0.00 43.74 3.16
1672 1710 0.039437 GTCCACAAGCGAGACTCGAA 60.039 55.000 28.43 1.31 43.74 3.71
1743 1799 2.290916 TCGTATAAGCGAGCTCCTTCAG 59.709 50.000 17.42 9.91 35.83 3.02
1752 1808 1.766301 CGTCGTTGTCGTATAAGCGAG 59.234 52.381 0.00 0.00 41.85 5.03
1753 1809 1.529622 CCGTCGTTGTCGTATAAGCGA 60.530 52.381 0.00 0.00 38.68 4.93
1822 1880 4.452733 CTGCTCCCGTCCCGTTCC 62.453 72.222 0.00 0.00 0.00 3.62
1907 1965 0.250513 AGAACTCGGCCATGAAGACC 59.749 55.000 2.24 0.00 0.00 3.85
1910 1968 1.002366 CGAAGAACTCGGCCATGAAG 58.998 55.000 2.24 0.00 44.20 3.02
1931 1989 3.177997 GAGCTCTTCTCCTTCATGTCC 57.822 52.381 6.43 0.00 35.77 4.02
1953 2011 3.257561 CTTGATCTCCACGCGCCG 61.258 66.667 5.73 0.00 0.00 6.46
1956 2014 0.179100 ATGTCCTTGATCTCCACGCG 60.179 55.000 3.53 3.53 0.00 6.01
1957 2015 1.293924 CATGTCCTTGATCTCCACGC 58.706 55.000 0.00 0.00 0.00 5.34
2024 2082 1.140052 TGCGAAGGAAGTTCAGGAACA 59.860 47.619 14.06 0.00 43.47 3.18
2025 2083 1.878953 TGCGAAGGAAGTTCAGGAAC 58.121 50.000 5.01 4.00 41.45 3.62
2026 2084 2.631160 TTGCGAAGGAAGTTCAGGAA 57.369 45.000 5.01 0.00 34.44 3.36
2027 2085 2.631160 TTTGCGAAGGAAGTTCAGGA 57.369 45.000 5.01 0.00 40.30 3.86
2028 2086 3.708563 TTTTTGCGAAGGAAGTTCAGG 57.291 42.857 5.01 0.00 40.30 3.86
2052 2110 4.202111 CCGGTCAAGTTCAGGAACATTTTT 60.202 41.667 14.06 0.00 43.47 1.94
2053 2111 3.317993 CCGGTCAAGTTCAGGAACATTTT 59.682 43.478 14.06 0.00 43.47 1.82
2054 2112 2.884639 CCGGTCAAGTTCAGGAACATTT 59.115 45.455 14.06 0.00 43.47 2.32
2055 2113 2.504367 CCGGTCAAGTTCAGGAACATT 58.496 47.619 14.06 3.64 43.47 2.71
2056 2114 1.271379 CCCGGTCAAGTTCAGGAACAT 60.271 52.381 14.06 0.00 43.47 2.71
2093 2151 1.497223 GCAGATGCTGAGCCATCGTC 61.497 60.000 0.23 0.00 44.86 4.20
2136 2194 5.413499 GCACATAATTTTGAGCCTGTCAAT 58.587 37.500 6.98 0.00 44.89 2.57
2138 2196 3.119884 CGCACATAATTTTGAGCCTGTCA 60.120 43.478 11.43 0.00 30.55 3.58
2172 2230 1.153568 CGACAGTGATGCCACCGAT 60.154 57.895 0.00 0.00 44.22 4.18
2192 2258 2.431942 AAAGTAGTCGCCGCCGTG 60.432 61.111 0.00 0.00 35.54 4.94
2234 2300 1.078848 CTTCTCCTTGAGGTGCGGG 60.079 63.158 0.00 0.00 36.34 6.13
2248 2314 6.025749 TGATGATAAACTCGACACACTTCT 57.974 37.500 0.00 0.00 0.00 2.85
2255 2321 5.886474 AGGAGTACTGATGATAAACTCGACA 59.114 40.000 0.00 0.00 37.93 4.35
2256 2322 6.380095 AGGAGTACTGATGATAAACTCGAC 57.620 41.667 0.00 0.00 37.93 4.20
2314 2380 1.134159 AGCTTGCCTCCAGATGCTTAG 60.134 52.381 0.00 0.00 0.00 2.18
2433 2513 3.651206 AGTTCTGCTAGATCATGCATCG 58.349 45.455 12.01 3.75 38.59 3.84
2505 2587 3.914426 ACTCGGGCTTACAAGATGATT 57.086 42.857 0.00 0.00 0.00 2.57
2508 2590 4.124851 AGTTACTCGGGCTTACAAGATG 57.875 45.455 0.00 0.00 0.00 2.90
2509 2591 4.954826 ACTAGTTACTCGGGCTTACAAGAT 59.045 41.667 0.00 0.00 0.00 2.40
2510 2592 4.157289 CACTAGTTACTCGGGCTTACAAGA 59.843 45.833 0.00 0.00 0.00 3.02
2511 2593 4.082354 ACACTAGTTACTCGGGCTTACAAG 60.082 45.833 0.00 0.00 0.00 3.16
2512 2594 3.828451 ACACTAGTTACTCGGGCTTACAA 59.172 43.478 0.00 0.00 0.00 2.41
2513 2595 3.192001 CACACTAGTTACTCGGGCTTACA 59.808 47.826 0.00 0.00 0.00 2.41
2514 2596 3.767278 CACACTAGTTACTCGGGCTTAC 58.233 50.000 0.00 0.00 0.00 2.34
2517 2599 0.531200 GCACACTAGTTACTCGGGCT 59.469 55.000 0.00 0.00 0.00 5.19
2519 2601 0.801067 GCGCACACTAGTTACTCGGG 60.801 60.000 0.30 0.00 0.00 5.14
2525 2607 1.191535 ATGGAGGCGCACACTAGTTA 58.808 50.000 10.83 0.00 0.00 2.24
2537 2619 5.829924 TCAAATTCAAGGAGAATATGGAGGC 59.170 40.000 0.00 0.00 46.09 4.70
2539 2621 7.722728 TCCATCAAATTCAAGGAGAATATGGAG 59.277 37.037 13.07 0.00 45.61 3.86
2540 2622 7.585440 TCCATCAAATTCAAGGAGAATATGGA 58.415 34.615 13.07 13.07 46.89 3.41
2542 2624 9.298250 AGATCCATCAAATTCAAGGAGAATATG 57.702 33.333 0.00 0.00 46.09 1.78
2546 2628 7.865820 ACTAGATCCATCAAATTCAAGGAGAA 58.134 34.615 0.00 0.00 41.28 2.87
2547 2629 7.443302 ACTAGATCCATCAAATTCAAGGAGA 57.557 36.000 0.00 0.00 0.00 3.71
2559 2641 2.499693 TGGCACGAAACTAGATCCATCA 59.500 45.455 0.00 0.00 0.00 3.07
2585 2667 4.427312 GAATGATTTGCCACATCCAGAAC 58.573 43.478 0.00 0.00 0.00 3.01
2589 2671 3.104519 AGGAATGATTTGCCACATCCA 57.895 42.857 0.00 0.00 0.00 3.41
2598 2681 6.940831 ACAAACCCAAAAAGGAATGATTTG 57.059 33.333 0.00 0.00 41.22 2.32
2605 2688 5.582665 CGATGAAAACAAACCCAAAAAGGAA 59.417 36.000 0.00 0.00 41.22 3.36
2606 2689 5.112686 CGATGAAAACAAACCCAAAAAGGA 58.887 37.500 0.00 0.00 41.22 3.36
2607 2690 4.260579 GCGATGAAAACAAACCCAAAAAGG 60.261 41.667 0.00 0.00 37.03 3.11
2619 2702 2.622011 GGGCACGGCGATGAAAACA 61.622 57.895 16.62 0.00 0.00 2.83
2625 2708 1.078709 CATATAAGGGCACGGCGATG 58.921 55.000 16.62 9.66 0.00 3.84
2626 2709 0.685097 ACATATAAGGGCACGGCGAT 59.315 50.000 16.62 0.00 0.00 4.58
2627 2710 0.466543 AACATATAAGGGCACGGCGA 59.533 50.000 16.62 0.00 0.00 5.54
2628 2711 1.263217 GAAACATATAAGGGCACGGCG 59.737 52.381 4.80 4.80 0.00 6.46
2629 2712 2.294074 TGAAACATATAAGGGCACGGC 58.706 47.619 0.00 0.00 0.00 5.68
2630 2713 6.817765 ATAATGAAACATATAAGGGCACGG 57.182 37.500 0.00 0.00 0.00 4.94
2631 2714 9.528018 AAAAATAATGAAACATATAAGGGCACG 57.472 29.630 0.00 0.00 0.00 5.34
2876 2968 4.630505 GGACTATTTGGAACGAGAGAAACC 59.369 45.833 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.