Multiple sequence alignment - TraesCS3D01G519900

Loading Multiple Alignment...

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 TraesCS3D01G519900 chr3D 100.000 4700 0 0 1 4700 602451095 602446396 0.000000e+00 8680.0
1 TraesCS3D01G519900 chr3D 94.963 1350 57 7 7 1354 602359363 602358023 0.000000e+00 2106.0
2 TraesCS3D01G519900 chr3D 90.500 1379 91 18 1986 3346 603634243 603632887 0.000000e+00 1784.0
3 TraesCS3D01G519900 chr3D 79.929 1410 194 57 2285 3640 602751183 602749809 0.000000e+00 953.0
4 TraesCS3D01G519900 chr3D 90.868 668 56 4 2282 2947 568495324 568495988 0.000000e+00 891.0
5 TraesCS3D01G519900 chr3D 79.161 1406 201 54 2282 3628 603867650 603869022 0.000000e+00 889.0
6 TraesCS3D01G519900 chr3D 81.557 1079 152 26 2282 3341 602656118 602657168 0.000000e+00 846.0
7 TraesCS3D01G519900 chr3D 81.027 896 129 26 2282 3166 602428996 602429861 0.000000e+00 675.0
8 TraesCS3D01G519900 chr3D 76.508 1111 182 48 1145 2217 602752473 602751404 2.490000e-147 532.0
9 TraesCS3D01G519900 chr3D 76.508 1111 182 48 1145 2217 603866363 603867432 2.490000e-147 532.0
10 TraesCS3D01G519900 chr3D 89.970 329 27 2 1605 1931 603634561 603634237 2.020000e-113 420.0
11 TraesCS3D01G519900 chr3D 86.486 370 30 7 3351 3700 603632143 603631774 5.700000e-104 388.0
12 TraesCS3D01G519900 chr3D 83.173 416 55 8 1178 1593 603635013 603634613 2.670000e-97 366.0
13 TraesCS3D01G519900 chr3D 86.076 316 31 8 3038 3341 568496043 568496357 1.260000e-85 327.0
14 TraesCS3D01G519900 chr3D 77.801 482 72 23 902 1362 602378983 602378516 1.000000e-66 265.0
15 TraesCS3D01G519900 chr3D 84.058 276 40 3 73 347 114334491 114334763 3.610000e-66 263.0
16 TraesCS3D01G519900 chr3D 78.711 357 52 15 902 1238 602460693 602460341 2.850000e-52 217.0
17 TraesCS3D01G519900 chr3A 89.232 1523 106 22 2091 3563 732420967 732422481 0.000000e+00 1851.0
18 TraesCS3D01G519900 chr3A 89.850 1202 96 15 1615 2802 732427512 732428701 0.000000e+00 1520.0
19 TraesCS3D01G519900 chr3A 92.907 1001 70 1 3699 4698 596352854 596353854 0.000000e+00 1454.0
20 TraesCS3D01G519900 chr3A 81.748 1030 151 24 2339 3346 732082193 732083207 0.000000e+00 826.0
21 TraesCS3D01G519900 chr3A 85.216 832 60 27 2923 3701 732428713 732429534 0.000000e+00 797.0
22 TraesCS3D01G519900 chr3A 81.419 888 117 24 2472 3341 731991683 731990826 0.000000e+00 682.0
23 TraesCS3D01G519900 chr3A 86.117 497 30 14 1615 2100 732419647 732420115 2.530000e-137 499.0
24 TraesCS3D01G519900 chr3A 75.292 1198 196 60 1045 2202 732099163 732100300 9.150000e-132 481.0
25 TraesCS3D01G519900 chr3A 82.775 418 54 12 1178 1592 732427039 732427441 1.610000e-94 357.0
26 TraesCS3D01G519900 chr3A 80.717 446 40 15 931 1354 732069267 732068846 5.910000e-79 305.0
27 TraesCS3D01G519900 chr3A 80.288 416 67 11 1178 1593 732419005 732419405 2.750000e-77 300.0
28 TraesCS3D01G519900 chr3A 90.654 214 14 2 3493 3700 732422484 732422697 3.580000e-71 279.0
29 TraesCS3D01G519900 chr3B 87.161 1659 133 38 2111 3701 810251604 810253250 0.000000e+00 1810.0
30 TraesCS3D01G519900 chr3B 80.872 826 118 28 2282 3094 809627228 809628026 8.640000e-172 614.0
31 TraesCS3D01G519900 chr3B 88.190 525 45 9 348 857 810249940 810250462 1.120000e-170 610.0
32 TraesCS3D01G519900 chr3B 76.270 1319 211 50 956 2218 809625740 809627012 4.020000e-170 608.0
33 TraesCS3D01G519900 chr3B 81.846 661 70 25 952 1593 810250515 810251144 1.170000e-140 510.0
34 TraesCS3D01G519900 chr3B 90.691 376 27 4 1653 2020 810251232 810251607 1.170000e-135 494.0
35 TraesCS3D01G519900 chr3B 95.455 44 2 0 1556 1599 28699259 28699302 2.350000e-08 71.3
36 TraesCS3D01G519900 chr6D 94.721 1004 51 2 3699 4700 192102107 192103110 0.000000e+00 1559.0
37 TraesCS3D01G519900 chr6D 89.442 1004 104 2 3699 4700 28278159 28277156 0.000000e+00 1266.0
38 TraesCS3D01G519900 chr2D 93.021 1003 69 1 3699 4700 214054525 214055527 0.000000e+00 1463.0
39 TraesCS3D01G519900 chr2D 92.331 1004 75 2 3699 4700 181583127 181582124 0.000000e+00 1426.0
40 TraesCS3D01G519900 chr4D 94.249 939 53 1 3704 4641 177114002 177113064 0.000000e+00 1434.0
41 TraesCS3D01G519900 chr4D 85.315 286 33 8 71 349 445107911 445107628 2.140000e-73 287.0
42 TraesCS3D01G519900 chr5A 91.532 992 82 2 3699 4689 454200072 454201062 0.000000e+00 1365.0
43 TraesCS3D01G519900 chr5A 76.354 1108 187 47 1145 2218 31571618 31572684 4.170000e-145 525.0
44 TraesCS3D01G519900 chr5A 84.859 284 35 6 71 347 573816534 573816252 3.580000e-71 279.0
45 TraesCS3D01G519900 chr5A 82.230 287 32 10 72 351 573806738 573807012 3.660000e-56 230.0
46 TraesCS3D01G519900 chr5B 89.542 1004 103 2 3699 4700 77615136 77614133 0.000000e+00 1271.0
47 TraesCS3D01G519900 chr2A 89.154 1005 108 1 3697 4700 565380004 565379000 0.000000e+00 1251.0
48 TraesCS3D01G519900 chrUn 79.096 1416 202 56 2285 3640 276043093 276041712 0.000000e+00 889.0
49 TraesCS3D01G519900 chrUn 76.508 1111 182 48 1145 2217 276044383 276043314 2.490000e-147 532.0
50 TraesCS3D01G519900 chrUn 78.846 104 16 4 1485 1585 96548937 96549037 1.090000e-06 65.8
51 TraesCS3D01G519900 chr5D 85.461 282 34 5 72 347 533556714 533556994 2.140000e-73 287.0
52 TraesCS3D01G519900 chr1B 83.039 283 41 5 74 349 278707118 278707400 2.810000e-62 250.0
53 TraesCS3D01G519900 chr1B 86.364 110 13 1 241 350 637516209 637516102 8.260000e-23 119.0
54 TraesCS3D01G519900 chr1B 78.302 106 17 4 1485 1587 13965200 13965302 3.930000e-06 63.9
55 TraesCS3D01G519900 chr6B 79.252 294 53 5 62 347 52471570 52471863 1.030000e-46 198.0
56 TraesCS3D01G519900 chr1D 81.443 97 14 2 1491 1585 9646361 9646267 5.040000e-10 76.8
57 TraesCS3D01G519900 chr1A 79.381 97 16 2 1491 1585 10972188 10972094 1.090000e-06 65.8


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 TraesCS3D01G519900 chr3D 602446396 602451095 4699 True 8680.000000 8680 100.00000 1 4700 1 chr3D.!!$R3 4699
1 TraesCS3D01G519900 chr3D 602358023 602359363 1340 True 2106.000000 2106 94.96300 7 1354 1 chr3D.!!$R1 1347
2 TraesCS3D01G519900 chr3D 602656118 602657168 1050 False 846.000000 846 81.55700 2282 3341 1 chr3D.!!$F3 1059
3 TraesCS3D01G519900 chr3D 602749809 602752473 2664 True 742.500000 953 78.21850 1145 3640 2 chr3D.!!$R5 2495
4 TraesCS3D01G519900 chr3D 603631774 603635013 3239 True 739.500000 1784 87.53225 1178 3700 4 chr3D.!!$R6 2522
5 TraesCS3D01G519900 chr3D 603866363 603869022 2659 False 710.500000 889 77.83450 1145 3628 2 chr3D.!!$F5 2483
6 TraesCS3D01G519900 chr3D 602428996 602429861 865 False 675.000000 675 81.02700 2282 3166 1 chr3D.!!$F2 884
7 TraesCS3D01G519900 chr3D 568495324 568496357 1033 False 609.000000 891 88.47200 2282 3341 2 chr3D.!!$F4 1059
8 TraesCS3D01G519900 chr3A 596352854 596353854 1000 False 1454.000000 1454 92.90700 3699 4698 1 chr3A.!!$F1 999
9 TraesCS3D01G519900 chr3A 732427039 732429534 2495 False 891.333333 1520 85.94700 1178 3701 3 chr3A.!!$F5 2523
10 TraesCS3D01G519900 chr3A 732082193 732083207 1014 False 826.000000 826 81.74800 2339 3346 1 chr3A.!!$F2 1007
11 TraesCS3D01G519900 chr3A 732419005 732422697 3692 False 732.250000 1851 86.57275 1178 3700 4 chr3A.!!$F4 2522
12 TraesCS3D01G519900 chr3A 731990826 731991683 857 True 682.000000 682 81.41900 2472 3341 1 chr3A.!!$R1 869
13 TraesCS3D01G519900 chr3A 732099163 732100300 1137 False 481.000000 481 75.29200 1045 2202 1 chr3A.!!$F3 1157
14 TraesCS3D01G519900 chr3B 810249940 810253250 3310 False 856.000000 1810 86.97200 348 3701 4 chr3B.!!$F3 3353
15 TraesCS3D01G519900 chr3B 809625740 809628026 2286 False 611.000000 614 78.57100 956 3094 2 chr3B.!!$F2 2138
16 TraesCS3D01G519900 chr6D 192102107 192103110 1003 False 1559.000000 1559 94.72100 3699 4700 1 chr6D.!!$F1 1001
17 TraesCS3D01G519900 chr6D 28277156 28278159 1003 True 1266.000000 1266 89.44200 3699 4700 1 chr6D.!!$R1 1001
18 TraesCS3D01G519900 chr2D 214054525 214055527 1002 False 1463.000000 1463 93.02100 3699 4700 1 chr2D.!!$F1 1001
19 TraesCS3D01G519900 chr2D 181582124 181583127 1003 True 1426.000000 1426 92.33100 3699 4700 1 chr2D.!!$R1 1001
20 TraesCS3D01G519900 chr4D 177113064 177114002 938 True 1434.000000 1434 94.24900 3704 4641 1 chr4D.!!$R1 937
21 TraesCS3D01G519900 chr5A 454200072 454201062 990 False 1365.000000 1365 91.53200 3699 4689 1 chr5A.!!$F2 990
22 TraesCS3D01G519900 chr5A 31571618 31572684 1066 False 525.000000 525 76.35400 1145 2218 1 chr5A.!!$F1 1073
23 TraesCS3D01G519900 chr5B 77614133 77615136 1003 True 1271.000000 1271 89.54200 3699 4700 1 chr5B.!!$R1 1001
24 TraesCS3D01G519900 chr2A 565379000 565380004 1004 True 1251.000000 1251 89.15400 3697 4700 1 chr2A.!!$R1 1003
25 TraesCS3D01G519900 chrUn 276041712 276044383 2671 True 710.500000 889 77.80200 1145 3640 2 chrUn.!!$R1 2495

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
618 621 1.364901 GGACGTCCGAACCAGTTCA 59.635 57.895 20.85 0.0 39.46 3.18 F
1612 1929 0.039978 AATGCTCTCGACTATCGCCG 60.040 55.000 0.00 0.0 40.21 6.46 F
2464 3866 0.108186 TGGTGCAACGATCAGCTAGG 60.108 55.000 0.00 0.0 38.12 3.02 F
2901 4316 0.320697 AAGGTCTTGACCGTGCCTAC 59.679 55.000 13.41 0.0 34.28 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2037 2399 0.250234 CTCGGGGATGCTCACTCAAA 59.750 55.0 0.00 0.00 0.00 2.69 R
3550 5860 0.036952 CCTTGAGCTTCTTCCTCGCA 60.037 55.0 0.00 0.00 31.98 5.10 R
3633 5949 0.107831 AGGAACCGCTAACAAGCACA 59.892 50.0 0.00 0.00 34.41 4.57 R
4392 6715 0.191064 ATCCTCGGAGGGGCTTATCA 59.809 55.0 23.39 2.17 35.59 2.15 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
183 184 5.510179 CGGTCCAATATAACGGTGTCCTAAT 60.510 44.000 0.00 0.00 0.00 1.73
239 240 5.291905 ACTTAACACTTCAGCAACTAGGT 57.708 39.130 0.00 0.00 0.00 3.08
599 602 3.795688 TTCTCTGGTCTGCAGGAAAAT 57.204 42.857 15.13 0.00 0.00 1.82
618 621 1.364901 GGACGTCCGAACCAGTTCA 59.635 57.895 20.85 0.00 39.46 3.18
693 706 4.527427 TCCACTTTGAATTGCATCCATGAA 59.473 37.500 0.00 0.00 0.00 2.57
1118 1188 2.901292 GCAGCAGCAGCACGACTTT 61.901 57.895 4.63 0.00 45.49 2.66
1204 1274 2.174854 TCGAGGTACCATGAGATCCTCA 59.825 50.000 15.94 0.00 44.99 3.86
1242 1312 2.436646 CAGTTACCAGCCTGCCCG 60.437 66.667 0.00 0.00 0.00 6.13
1243 1313 3.717294 AGTTACCAGCCTGCCCGG 61.717 66.667 0.00 0.00 0.00 5.73
1290 1363 5.587844 AGATCTTCCTTCGGATGAAATTGTG 59.412 40.000 0.00 0.00 38.93 3.33
1299 1372 2.167075 GGATGAAATTGTGGAAGCCCTG 59.833 50.000 0.00 0.00 0.00 4.45
1300 1373 2.673775 TGAAATTGTGGAAGCCCTGA 57.326 45.000 0.00 0.00 0.00 3.86
1302 1375 1.546029 GAAATTGTGGAAGCCCTGACC 59.454 52.381 0.00 0.00 0.00 4.02
1310 1383 0.745468 GAAGCCCTGACCCGTACTAG 59.255 60.000 0.00 0.00 0.00 2.57
1400 1473 1.986413 GACCAGATGTCCAGGCAGT 59.014 57.895 0.00 0.00 38.09 4.40
1433 1524 3.358076 GAGAGGACTCCGGCGTTGG 62.358 68.421 6.01 0.00 37.19 3.77
1443 1534 2.824041 GGCGTTGGCATCACCGAT 60.824 61.111 0.00 0.00 43.94 4.18
1447 1538 1.723870 GTTGGCATCACCGATGAGC 59.276 57.895 8.14 0.00 42.09 4.26
1458 1549 2.159430 CACCGATGAGCAATTCGTCAAA 59.841 45.455 0.00 0.00 41.13 2.69
1536 1627 4.707105 TGAATCAAGAGCAGTTCAACAGA 58.293 39.130 0.00 0.00 0.00 3.41
1596 1687 3.627577 GCCTGGTTAGTCACATACCAATG 59.372 47.826 2.99 0.00 41.15 2.82
1597 1688 3.627577 CCTGGTTAGTCACATACCAATGC 59.372 47.826 2.99 0.00 41.15 3.56
1598 1689 4.517285 CTGGTTAGTCACATACCAATGCT 58.483 43.478 2.99 0.00 41.15 3.79
1600 1691 4.225042 TGGTTAGTCACATACCAATGCTCT 59.775 41.667 0.00 0.00 38.92 4.09
1603 1742 2.760650 AGTCACATACCAATGCTCTCGA 59.239 45.455 0.00 0.00 36.50 4.04
1611 1928 1.413382 CAATGCTCTCGACTATCGCC 58.587 55.000 0.00 0.00 40.21 5.54
1612 1929 0.039978 AATGCTCTCGACTATCGCCG 60.040 55.000 0.00 0.00 40.21 6.46
1613 1930 2.427740 GCTCTCGACTATCGCCGC 60.428 66.667 0.00 0.00 40.21 6.53
1631 1948 3.374058 GCCGCCAATCATATACACATACC 59.626 47.826 0.00 0.00 0.00 2.73
1636 1953 7.652105 CCGCCAATCATATACACATACCTATAC 59.348 40.741 0.00 0.00 0.00 1.47
1637 1954 7.652105 CGCCAATCATATACACATACCTATACC 59.348 40.741 0.00 0.00 0.00 2.73
1638 1955 8.482943 GCCAATCATATACACATACCTATACCA 58.517 37.037 0.00 0.00 0.00 3.25
1649 1966 8.989131 ACACATACCTATACCATCTTTTGTACT 58.011 33.333 0.00 0.00 0.00 2.73
1671 1992 9.303537 GTACTTACTTACACATCTTTCCATCTC 57.696 37.037 0.00 0.00 0.00 2.75
1673 1994 9.256228 ACTTACTTACACATCTTTCCATCTCTA 57.744 33.333 0.00 0.00 0.00 2.43
1677 1998 8.364142 ACTTACACATCTTTCCATCTCTATAGC 58.636 37.037 0.00 0.00 0.00 2.97
1686 2007 7.766278 TCTTTCCATCTCTATAGCTGTTGAAAC 59.234 37.037 0.00 0.00 0.00 2.78
1713 2034 2.214387 TATCGACGAGCTAGACGACA 57.786 50.000 21.29 9.44 40.50 4.35
1716 2037 0.443088 CGACGAGCTAGACGACACTT 59.557 55.000 12.74 0.00 34.70 3.16
1853 2174 1.521681 GAGCGATTACCAGCGGCTT 60.522 57.895 0.00 0.00 38.61 4.35
1896 2238 2.545526 ACACTTTCAGTTCAGTGATGCG 59.454 45.455 6.32 0.00 42.74 4.73
1898 2240 2.545526 ACTTTCAGTTCAGTGATGCGTG 59.454 45.455 0.00 0.00 0.00 5.34
1899 2241 0.867746 TTCAGTTCAGTGATGCGTGC 59.132 50.000 0.00 0.00 0.00 5.34
1915 2257 0.727398 GTGCGGACTTAATCTGTGCC 59.273 55.000 0.00 0.00 35.91 5.01
1951 2301 6.934048 AACCAGTTTCTTCTTCTCTTCTTG 57.066 37.500 0.00 0.00 0.00 3.02
1984 2334 5.582689 GGTGACCCCAAATATTTCTCTTG 57.417 43.478 0.00 0.00 0.00 3.02
2027 2389 7.013274 ACTGCAATTTCTACTTCTTTTAGCACA 59.987 33.333 0.00 0.00 0.00 4.57
2035 2397 7.916552 TCTACTTCTTTTAGCACAGTTTTGAC 58.083 34.615 0.00 0.00 0.00 3.18
2036 2398 6.759497 ACTTCTTTTAGCACAGTTTTGACT 57.241 33.333 0.00 0.00 0.00 3.41
2037 2399 7.158099 ACTTCTTTTAGCACAGTTTTGACTT 57.842 32.000 0.00 0.00 0.00 3.01
2038 2400 7.602753 ACTTCTTTTAGCACAGTTTTGACTTT 58.397 30.769 0.00 0.00 0.00 2.66
2039 2401 8.088365 ACTTCTTTTAGCACAGTTTTGACTTTT 58.912 29.630 0.00 0.00 0.00 2.27
2040 2402 7.810766 TCTTTTAGCACAGTTTTGACTTTTG 57.189 32.000 0.00 0.00 0.00 2.44
2041 2403 7.598278 TCTTTTAGCACAGTTTTGACTTTTGA 58.402 30.769 0.00 0.00 0.00 2.69
2073 2441 2.205074 CGAGTTGTATGGACATGAGGC 58.795 52.381 0.00 0.00 34.86 4.70
2115 3347 9.875691 AAAAATTAAACTAGAATCCCATCTTGC 57.124 29.630 0.00 0.00 0.00 4.01
2180 3420 9.082313 AGATTGTGGAAAATCCCATAATATGTC 57.918 33.333 5.16 0.00 38.66 3.06
2225 3467 6.357367 ACAATTATACCTTCTTCGCCAAGAT 58.643 36.000 0.00 0.00 38.50 2.40
2296 3691 6.931838 AGTGATGCATTTTTCTCATGACAAT 58.068 32.000 0.00 0.00 28.87 2.71
2404 3806 7.158021 CCCCTGAAGTTGATAGAGATTATGTC 58.842 42.308 0.00 0.00 0.00 3.06
2419 3821 8.652290 AGAGATTATGTCCTATACTGGGAAAAC 58.348 37.037 0.00 0.00 34.35 2.43
2464 3866 0.108186 TGGTGCAACGATCAGCTAGG 60.108 55.000 0.00 0.00 38.12 3.02
2479 3881 5.871834 TCAGCTAGGCCAAGTTTAAAACTA 58.128 37.500 5.01 0.00 41.91 2.24
2488 3890 6.861572 GGCCAAGTTTAAAACTATGTTCAGTC 59.138 38.462 0.00 0.00 41.91 3.51
2519 3922 7.342026 AGAAATTGGACTAACAACCTTCTGTTT 59.658 33.333 0.00 0.00 40.08 2.83
2542 3945 9.255304 GTTTTTAACAGTGGCTTGAAAATCATA 57.745 29.630 0.00 0.00 0.00 2.15
2544 3947 9.995003 TTTTAACAGTGGCTTGAAAATCATATT 57.005 25.926 0.00 0.00 0.00 1.28
2620 4026 8.136165 GGAATGACAACTAATCTCTACGTATGT 58.864 37.037 0.00 0.00 0.00 2.29
2632 4038 6.656003 TCTCTACGTATGTGTTGTATCATCG 58.344 40.000 0.00 0.00 0.00 3.84
2676 4082 7.861629 ACTATTTAGTGGGATCAAATCTGTCA 58.138 34.615 0.00 0.00 34.72 3.58
2677 4083 7.770897 ACTATTTAGTGGGATCAAATCTGTCAC 59.229 37.037 0.00 0.00 34.72 3.67
2714 4120 3.351020 CAATTAGGATTGCTGCTGAGC 57.649 47.619 0.00 0.00 46.44 4.26
2726 4132 0.991146 TGCTGAGCTCCCCAACATTA 59.009 50.000 12.15 0.00 0.00 1.90
2779 4193 0.533951 GATTCCTTTGCCCCTTGCTG 59.466 55.000 0.00 0.00 42.00 4.41
2784 4198 1.348696 CCTTTGCCCCTTGCTGATTTT 59.651 47.619 0.00 0.00 42.00 1.82
2802 4216 5.877012 TGATTTTGATTGTCAGCTCTAGTCC 59.123 40.000 0.00 0.00 0.00 3.85
2901 4316 0.320697 AAGGTCTTGACCGTGCCTAC 59.679 55.000 13.41 0.00 34.28 3.18
2947 4362 1.386533 GCAGCAGGTCAGCATTGTAT 58.613 50.000 0.00 0.00 36.85 2.29
2951 4366 4.037208 GCAGCAGGTCAGCATTGTATATTT 59.963 41.667 0.00 0.00 36.85 1.40
2952 4367 5.516996 CAGCAGGTCAGCATTGTATATTTG 58.483 41.667 0.00 0.00 36.85 2.32
2953 4368 5.066893 CAGCAGGTCAGCATTGTATATTTGT 59.933 40.000 0.00 0.00 36.85 2.83
2954 4369 6.260714 CAGCAGGTCAGCATTGTATATTTGTA 59.739 38.462 0.00 0.00 36.85 2.41
2955 4370 7.000472 AGCAGGTCAGCATTGTATATTTGTAT 59.000 34.615 0.00 0.00 36.85 2.29
2956 4371 8.156820 AGCAGGTCAGCATTGTATATTTGTATA 58.843 33.333 0.00 0.00 36.85 1.47
2957 4372 8.230486 GCAGGTCAGCATTGTATATTTGTATAC 58.770 37.037 0.00 0.00 34.41 1.47
2958 4373 8.721478 CAGGTCAGCATTGTATATTTGTATACC 58.279 37.037 0.00 0.00 33.21 2.73
3180 4604 2.952714 CCTGGAGGGTTCTTGCAAG 58.047 57.895 20.81 20.81 0.00 4.01
3276 4712 6.197096 CCTTACGATGCAAATGCTTTAATCAC 59.803 38.462 6.97 0.00 42.66 3.06
3278 4714 4.082300 ACGATGCAAATGCTTTAATCACCA 60.082 37.500 6.97 0.00 42.66 4.17
3285 4726 3.872511 TGCTTTAATCACCATTGCAGG 57.127 42.857 0.00 0.00 0.00 4.85
3390 5573 1.542915 CCTGATGTTGCTCCTTTGTGG 59.457 52.381 0.00 0.00 37.10 4.17
3394 5577 1.604604 TGTTGCTCCTTTGTGGCTAC 58.395 50.000 0.00 0.00 35.26 3.58
3397 5588 1.055849 TGCTCCTTTGTGGCTACAGA 58.944 50.000 2.22 0.00 38.23 3.41
3489 5717 0.595588 CGCCCTGCATGTTTTGTGTA 59.404 50.000 0.00 0.00 0.00 2.90
3550 5860 2.549754 GCCAAAGACATATGCGCAGTAT 59.450 45.455 18.32 11.11 36.38 2.12
3604 5920 1.479389 GGATTGATTCCCAAGGCCGAT 60.479 52.381 0.00 0.00 38.75 4.18
3612 5928 1.056660 CCCAAGGCCGATATACCAGT 58.943 55.000 0.00 0.00 0.00 4.00
3622 5938 4.486090 CCGATATACCAGTGTAGATGTGC 58.514 47.826 0.00 0.00 29.25 4.57
3633 5949 2.154462 GTAGATGTGCTTGTTGCTGGT 58.846 47.619 0.00 0.00 43.37 4.00
3640 5956 0.872881 GCTTGTTGCTGGTGTGCTTG 60.873 55.000 0.00 0.00 38.95 4.01
3655 5971 0.803117 GCTTGTTAGCGGTTCCTTCC 59.197 55.000 0.00 0.00 37.71 3.46
3702 6022 5.798125 CTCCTATGGTCAGAGCATAAAGA 57.202 43.478 20.31 17.87 38.01 2.52
3760 6080 1.413517 GGGCCAATCTCCCCATTGATT 60.414 52.381 4.39 0.00 41.13 2.57
3868 6189 0.322546 GGAGGGCCAACTAACAGTGG 60.323 60.000 6.18 0.00 0.00 4.00
3952 6273 2.777692 TGGAGGACTTTGTGAAGGACTT 59.222 45.455 0.00 0.00 37.19 3.01
4042 6363 2.516225 GGGTCACCCTATTGGCGC 60.516 66.667 5.22 0.00 41.34 6.53
4392 6715 1.077265 CCAACAATCCAGGGCCAGT 59.923 57.895 6.18 0.00 0.00 4.00
4411 6734 0.191064 TGATAAGCCCCTCCGAGGAT 59.809 55.000 16.69 0.32 37.67 3.24
4412 6735 1.431633 TGATAAGCCCCTCCGAGGATA 59.568 52.381 16.69 4.14 37.67 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
139 140 3.611113 CCGTTAGTTGACCGTTATGTCAG 59.389 47.826 0.00 0.00 45.37 3.51
183 184 0.482887 TGACAGAGAGGGTCCACTCA 59.517 55.000 15.00 0.00 39.97 3.41
246 247 5.278604 ACTACAAAATTGGTTCGCTGTTTC 58.721 37.500 0.00 0.00 0.00 2.78
331 332 8.912988 CCCTTCAATTGGAGTATATAGCAAAAA 58.087 33.333 12.86 0.00 0.00 1.94
394 395 7.791029 ACAAGTTGAAACCCTTATCAAACATT 58.209 30.769 10.54 0.00 37.31 2.71
599 602 1.364901 GAACTGGTTCGGACGTCCA 59.635 57.895 32.80 17.85 35.14 4.02
618 621 3.791320 ACATGGTATCCTATCGGTCCAT 58.209 45.455 0.00 0.00 37.60 3.41
693 706 7.296856 TGAGAGAGAGAATATCAAGGAGTCAT 58.703 38.462 0.00 0.00 0.00 3.06
736 751 3.305398 TCTTCTCTCGCCAACTCTTTC 57.695 47.619 0.00 0.00 0.00 2.62
1245 1315 4.778415 CTGTCGCCGTCGTCCAGG 62.778 72.222 1.43 0.00 34.55 4.45
1256 1326 1.522580 GGAAGATCTGGGCTGTCGC 60.523 63.158 0.00 0.00 0.00 5.19
1290 1363 0.685458 TAGTACGGGTCAGGGCTTCC 60.685 60.000 0.00 0.00 0.00 3.46
1299 1372 6.630444 TCATCATAGAAACTAGTACGGGTC 57.370 41.667 0.00 0.00 0.00 4.46
1300 1373 6.776116 TCATCATCATAGAAACTAGTACGGGT 59.224 38.462 0.00 0.00 0.00 5.28
1302 1375 6.804295 GCTCATCATCATAGAAACTAGTACGG 59.196 42.308 0.00 0.00 0.00 4.02
1310 1383 3.186001 CCGCAGCTCATCATCATAGAAAC 59.814 47.826 0.00 0.00 0.00 2.78
1359 1432 1.271707 TGGGGTTCGACCAGGAATTTC 60.272 52.381 0.00 0.00 41.02 2.17
1362 1435 1.683441 GTGGGGTTCGACCAGGAAT 59.317 57.895 0.00 0.00 41.02 3.01
1369 1442 3.584868 CTGGTCCGTGGGGTTCGAC 62.585 68.421 0.00 0.00 33.83 4.20
1370 1443 3.307906 CTGGTCCGTGGGGTTCGA 61.308 66.667 0.00 0.00 33.83 3.71
1397 1470 4.523943 CCTCTCCAGAATCTCCATCTACTG 59.476 50.000 0.00 0.00 0.00 2.74
1400 1473 4.418526 AGTCCTCTCCAGAATCTCCATCTA 59.581 45.833 0.00 0.00 0.00 1.98
1430 1521 0.322366 TTGCTCATCGGTGATGCCAA 60.322 50.000 14.73 9.23 39.63 4.52
1433 1524 1.333524 CGAATTGCTCATCGGTGATGC 60.334 52.381 0.00 5.99 39.63 3.91
1434 1525 1.935873 ACGAATTGCTCATCGGTGATG 59.064 47.619 0.00 0.32 43.11 3.07
1443 1534 3.616821 CGGAGTATTTGACGAATTGCTCA 59.383 43.478 15.63 0.00 33.71 4.26
1447 1538 5.500931 GCTCTTCGGAGTATTTGACGAATTG 60.501 44.000 0.00 0.00 43.30 2.32
1458 1549 1.410882 GCCTTCAGCTCTTCGGAGTAT 59.589 52.381 0.00 0.00 43.59 2.12
1501 1592 5.065704 TCTTGATTCAGTCTAGTGTCAGC 57.934 43.478 0.00 0.00 32.43 4.26
1536 1627 7.010183 CGATAACGAATTAACTTGACATGGAGT 59.990 37.037 0.00 0.00 42.66 3.85
1550 1641 5.984233 AGCTTTGATGCGATAACGAATTA 57.016 34.783 0.00 0.00 37.97 1.40
1551 1642 4.882671 AGCTTTGATGCGATAACGAATT 57.117 36.364 0.00 0.00 37.97 2.17
1603 1742 3.194755 TGTATATGATTGGCGGCGATAGT 59.805 43.478 12.98 6.38 39.35 2.12
1611 1928 7.652105 GGTATAGGTATGTGTATATGATTGGCG 59.348 40.741 0.00 0.00 0.00 5.69
1612 1929 8.482943 TGGTATAGGTATGTGTATATGATTGGC 58.517 37.037 0.00 0.00 0.00 4.52
1636 1953 9.436957 AGATGTGTAAGTAAGTACAAAAGATGG 57.563 33.333 0.00 0.00 35.79 3.51
1642 1959 9.787435 ATGGAAAGATGTGTAAGTAAGTACAAA 57.213 29.630 0.00 0.00 35.79 2.83
1645 1962 9.303537 GAGATGGAAAGATGTGTAAGTAAGTAC 57.696 37.037 0.00 0.00 0.00 2.73
1647 1964 8.140112 AGAGATGGAAAGATGTGTAAGTAAGT 57.860 34.615 0.00 0.00 0.00 2.24
1657 1974 6.992664 ACAGCTATAGAGATGGAAAGATGT 57.007 37.500 7.63 0.00 43.70 3.06
1671 1992 5.530519 TGCTTTCGTTTCAACAGCTATAG 57.469 39.130 0.00 0.00 0.00 1.31
1673 1994 6.510157 CGATATGCTTTCGTTTCAACAGCTAT 60.510 38.462 0.00 0.00 32.08 2.97
1677 1998 5.015733 GTCGATATGCTTTCGTTTCAACAG 58.984 41.667 0.00 0.00 37.82 3.16
1686 2007 1.759994 AGCTCGTCGATATGCTTTCG 58.240 50.000 1.89 0.00 37.94 3.46
1713 2034 2.812011 GGTACTTGCGTTCCAATGAAGT 59.188 45.455 0.00 0.00 31.46 3.01
1716 2037 1.349688 AGGGTACTTGCGTTCCAATGA 59.650 47.619 0.00 0.00 32.65 2.57
1853 2174 5.834742 TGTACTTACACAGTTAGGAAGGACA 59.165 40.000 0.00 0.00 38.37 4.02
1896 2238 0.727398 GGCACAGATTAAGTCCGCAC 59.273 55.000 0.00 0.00 0.00 5.34
1898 2240 0.392461 TGGGCACAGATTAAGTCCGC 60.392 55.000 0.00 0.00 0.00 5.54
1899 2241 1.942657 CATGGGCACAGATTAAGTCCG 59.057 52.381 0.00 0.00 0.00 4.79
1915 2257 2.479566 ACTGGTTACTGTCTGCATGG 57.520 50.000 0.00 0.00 0.00 3.66
1951 2301 2.265904 GGGTCACCCGTTCAAAGGC 61.266 63.158 0.00 0.00 32.13 4.35
1984 2334 3.933155 CAGTCATGATTCCGTAACTGC 57.067 47.619 0.00 0.00 0.00 4.40
2027 2389 5.221126 GGATGCTCACTCAAAAGTCAAAACT 60.221 40.000 0.00 0.00 37.32 2.66
2035 2397 1.089920 CGGGGATGCTCACTCAAAAG 58.910 55.000 0.00 0.00 0.00 2.27
2036 2398 0.690192 TCGGGGATGCTCACTCAAAA 59.310 50.000 0.00 0.00 0.00 2.44
2037 2399 0.250234 CTCGGGGATGCTCACTCAAA 59.750 55.000 0.00 0.00 0.00 2.69
2038 2400 0.904865 ACTCGGGGATGCTCACTCAA 60.905 55.000 0.00 0.00 0.00 3.02
2039 2401 0.904865 AACTCGGGGATGCTCACTCA 60.905 55.000 0.00 0.00 0.00 3.41
2040 2402 0.460987 CAACTCGGGGATGCTCACTC 60.461 60.000 0.00 0.00 0.00 3.51
2041 2403 1.194781 ACAACTCGGGGATGCTCACT 61.195 55.000 0.00 0.00 0.00 3.41
2095 3324 4.407621 TCCGCAAGATGGGATTCTAGTTTA 59.592 41.667 0.00 0.00 43.02 2.01
2102 3331 2.557920 ATCTCCGCAAGATGGGATTC 57.442 50.000 0.00 0.00 43.35 2.52
2134 3366 8.875803 ACAATCTATTGCAAGCACAAATATTTG 58.124 29.630 23.60 23.60 41.38 2.32
2180 3420 5.070001 TGTTGTCATTTTCTTCTAGGGTGG 58.930 41.667 0.00 0.00 0.00 4.61
2225 3467 5.759506 TTGAAAAGCCGTTCTATCACAAA 57.240 34.783 0.00 0.00 0.00 2.83
2314 3710 3.152341 CCAAGTCTGCACCAGAAAAGAT 58.848 45.455 0.00 0.00 42.46 2.40
2404 3806 5.110814 TGACCATGTTTTCCCAGTATAGG 57.889 43.478 0.00 0.00 0.00 2.57
2419 3821 6.096705 TGCATACCTTAATTTCCTTGACCATG 59.903 38.462 0.00 0.00 0.00 3.66
2464 3866 7.422399 TGACTGAACATAGTTTTAAACTTGGC 58.578 34.615 15.83 10.34 42.81 4.52
2479 3881 7.785033 AGTCCAATTTCTTTTTGACTGAACAT 58.215 30.769 0.00 0.00 0.00 2.71
2488 3890 8.716646 AAGGTTGTTAGTCCAATTTCTTTTTG 57.283 30.769 0.00 0.00 0.00 2.44
2519 3922 9.638239 GAATATGATTTTCAAGCCACTGTTAAA 57.362 29.630 0.00 0.00 0.00 1.52
2542 3945 6.612049 ACCTCCGGAGTATCTTCTTTAAGAAT 59.388 38.462 29.25 0.00 44.75 2.40
2544 3947 5.516984 ACCTCCGGAGTATCTTCTTTAAGA 58.483 41.667 29.25 0.00 45.63 2.10
2620 4026 6.597672 AGGAAAGTTAATGCGATGATACAACA 59.402 34.615 0.00 0.00 0.00 3.33
2676 4082 7.672239 TCCTAATTGCTTGGTATAAACCTTTGT 59.328 33.333 0.00 0.00 46.91 2.83
2677 4083 8.062065 TCCTAATTGCTTGGTATAAACCTTTG 57.938 34.615 0.00 0.00 46.91 2.77
2714 4120 4.270008 AGACCGAAATTAATGTTGGGGAG 58.730 43.478 15.38 0.00 0.00 4.30
2726 4132 5.869579 ACCATGATATGCTAGACCGAAATT 58.130 37.500 0.00 0.00 0.00 1.82
2779 4193 6.036953 CAGGACTAGAGCTGACAATCAAAATC 59.963 42.308 0.00 0.00 0.00 2.17
2784 4198 2.762887 CCAGGACTAGAGCTGACAATCA 59.237 50.000 0.00 0.00 0.00 2.57
2856 4271 4.034742 ACAAACACGACATAAAAGCGAGTT 59.965 37.500 0.00 0.00 39.72 3.01
2901 4316 2.162681 ACCCGCTTCCAAATCTCAAAG 58.837 47.619 0.00 0.00 0.00 2.77
3173 4597 0.236711 CTTGTCGCTCCACTTGCAAG 59.763 55.000 24.84 24.84 0.00 4.01
3180 4604 1.272769 AGAACCTACTTGTCGCTCCAC 59.727 52.381 0.00 0.00 0.00 4.02
3247 4680 2.620115 AGCATTTGCATCGTAAGGGATG 59.380 45.455 5.20 0.00 45.23 3.51
3251 4684 6.197096 GTGATTAAAGCATTTGCATCGTAAGG 59.803 38.462 5.20 0.00 45.16 2.69
3370 5553 1.542915 CCACAAAGGAGCAACATCAGG 59.457 52.381 0.00 0.00 41.22 3.86
3390 5573 2.910688 TCCAATCCGGAATCTGTAGC 57.089 50.000 9.01 0.00 42.52 3.58
3421 5612 3.955650 TCTAACTTCCTGAGAAACCCG 57.044 47.619 0.00 0.00 0.00 5.28
3422 5613 5.805728 TGAATCTAACTTCCTGAGAAACCC 58.194 41.667 0.00 0.00 0.00 4.11
3424 5615 6.937465 ACCTTGAATCTAACTTCCTGAGAAAC 59.063 38.462 0.00 0.00 0.00 2.78
3465 5671 1.039856 AAAACATGCAGGGCGAAACT 58.960 45.000 2.31 0.00 0.00 2.66
3471 5699 3.443681 ACTATACACAAAACATGCAGGGC 59.556 43.478 2.31 0.00 0.00 5.19
3508 5818 1.273887 CGCGCGCTGAAATAGGAAG 59.726 57.895 30.48 4.48 0.00 3.46
3550 5860 0.036952 CCTTGAGCTTCTTCCTCGCA 60.037 55.000 0.00 0.00 31.98 5.10
3604 5920 5.932619 ACAAGCACATCTACACTGGTATA 57.067 39.130 0.00 0.00 0.00 1.47
3622 5938 0.457035 ACAAGCACACCAGCAACAAG 59.543 50.000 0.00 0.00 36.85 3.16
3633 5949 0.107831 AGGAACCGCTAACAAGCACA 59.892 50.000 0.00 0.00 34.41 4.57
3655 5971 4.132441 AACATGGCAATGGCGGCG 62.132 61.111 5.94 0.51 42.47 6.46
3760 6080 2.970324 GGTCGCACTGCCGTGAAA 60.970 61.111 12.93 0.00 43.97 2.69
3868 6189 3.674997 TCGATTTCCATAAGGCCTATGC 58.325 45.455 5.16 0.00 36.77 3.14
3952 6273 3.055167 CGATATATTCTGGATGGGGTGCA 60.055 47.826 0.00 0.00 0.00 4.57
4042 6363 0.527565 CGGATTCTGGCAAAAGGGTG 59.472 55.000 0.00 0.00 0.00 4.61
4271 6593 0.325296 AGGCATGAACCCTACCTCGA 60.325 55.000 0.00 0.00 0.00 4.04
4380 6703 0.475906 GCTTATCACTGGCCCTGGAT 59.524 55.000 0.00 2.52 0.00 3.41
4392 6715 0.191064 ATCCTCGGAGGGGCTTATCA 59.809 55.000 23.39 2.17 35.59 2.15
4401 6724 2.925262 CGCAGCCTATCCTCGGAGG 61.925 68.421 18.25 18.25 36.46 4.30
4411 6734 0.687757 AGATCCCTGTTCGCAGCCTA 60.688 55.000 0.00 0.00 43.67 3.93
4412 6735 0.687757 TAGATCCCTGTTCGCAGCCT 60.688 55.000 0.00 0.00 43.67 4.58
4598 6924 0.757188 CGATGAGGAGGCCTACTGGT 60.757 60.000 26.55 10.87 31.76 4.00
4654 6980 1.492133 CCTGAGGAGTGGCTTTCCCA 61.492 60.000 0.00 2.84 42.79 4.37


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

AutoCloner maintained by Alex Coulton.