Multiple sequence alignment - TraesCS3B01G476500

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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 TraesCS3B01G476500 chr3B 100.000 3397 0 0 1 3397 725119880 725116484 0.000000e+00 6274.0
1 TraesCS3B01G476500 chr3B 85.647 1477 141 26 1041 2493 779567882 779569311 0.000000e+00 1487.0
2 TraesCS3B01G476500 chr3B 94.698 811 41 2 1 811 493862106 493861298 0.000000e+00 1258.0
3 TraesCS3B01G476500 chr3B 94.355 496 20 4 2893 3384 779569645 779570136 0.000000e+00 754.0
4 TraesCS3B01G476500 chr3B 75.920 897 153 40 1549 2425 779510659 779511512 5.280000e-108 401.0
5 TraesCS3B01G476500 chr3B 75.626 878 156 42 1539 2398 778490669 778489832 1.910000e-102 383.0
6 TraesCS3B01G476500 chr3B 93.860 228 12 2 2494 2720 779569372 779569598 3.250000e-90 342.0
7 TraesCS3B01G476500 chr3B 83.106 367 49 3 1174 1540 779510231 779510584 4.230000e-84 322.0
8 TraesCS3B01G476500 chr3B 85.650 223 32 0 1307 1529 778490964 778490742 5.670000e-58 235.0
9 TraesCS3B01G476500 chr3D 87.256 1483 139 23 1043 2502 581989673 581988218 0.000000e+00 1646.0
10 TraesCS3B01G476500 chr3D 89.963 807 57 11 2494 3294 581986259 581985471 0.000000e+00 1020.0
11 TraesCS3B01G476500 chr3D 77.015 918 151 37 1538 2431 582622780 582623661 3.970000e-129 472.0
12 TraesCS3B01G476500 chr3D 75.870 920 168 37 1531 2431 582793046 582793930 1.460000e-113 420.0
13 TraesCS3B01G476500 chr3D 76.392 826 142 38 1602 2406 582107703 582106910 2.460000e-106 396.0
14 TraesCS3B01G476500 chr3D 85.373 335 43 6 1196 1527 582108157 582107826 3.250000e-90 342.0
15 TraesCS3B01G476500 chr3D 87.603 242 30 0 1288 1529 580368044 580368285 7.180000e-72 281.0
16 TraesCS3B01G476500 chr3D 88.688 221 25 0 1303 1523 582792761 582792981 1.550000e-68 270.0
17 TraesCS3B01G476500 chr3D 83.636 220 36 0 1304 1523 582733820 582734039 1.240000e-49 207.0
18 TraesCS3B01G476500 chr3D 90.647 139 12 1 857 994 581989821 581989683 2.080000e-42 183.0
19 TraesCS3B01G476500 chr3D 79.545 132 20 4 2893 3017 582106050 582105919 1.680000e-13 87.9
20 TraesCS3B01G476500 chr3D 96.000 50 1 1 811 859 581989918 581989869 2.810000e-11 80.5
21 TraesCS3B01G476500 chr2A 94.588 813 39 3 1 812 592831357 592830549 0.000000e+00 1253.0
22 TraesCS3B01G476500 chr2A 94.268 820 43 2 1 820 641598953 641599768 0.000000e+00 1251.0
23 TraesCS3B01G476500 chr2A 75.448 391 77 13 1530 1917 747135912 747136286 4.510000e-39 172.0
24 TraesCS3B01G476500 chr1B 94.783 805 39 3 1 805 490456561 490455760 0.000000e+00 1251.0
25 TraesCS3B01G476500 chr1B 94.554 808 38 2 1 808 636032831 636032030 0.000000e+00 1243.0
26 TraesCS3B01G476500 chr1B 94.541 806 39 3 1 806 141756974 141756174 0.000000e+00 1240.0
27 TraesCS3B01G476500 chr1B 94.335 812 40 4 1 812 340460430 340459625 0.000000e+00 1240.0
28 TraesCS3B01G476500 chr1B 94.205 811 44 1 1 811 670408234 670407427 0.000000e+00 1234.0
29 TraesCS3B01G476500 chr4A 94.451 811 40 3 1 811 583935024 583935829 0.000000e+00 1243.0
30 TraesCS3B01G476500 chrUn 76.061 919 161 31 1538 2431 41505957 41506841 1.130000e-114 424.0
31 TraesCS3B01G476500 chrUn 75.399 878 158 42 1539 2398 41525511 41526348 4.140000e-99 372.0
32 TraesCS3B01G476500 chrUn 86.364 220 30 0 1304 1523 41525213 41525432 1.220000e-59 241.0
33 TraesCS3B01G476500 chr7B 100.000 30 0 0 873 902 171985457 171985428 4.740000e-04 56.5


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 TraesCS3B01G476500 chr3B 725116484 725119880 3396 True 6274.000 6274 100.000000 1 3397 1 chr3B.!!$R2 3396
1 TraesCS3B01G476500 chr3B 493861298 493862106 808 True 1258.000 1258 94.698000 1 811 1 chr3B.!!$R1 810
2 TraesCS3B01G476500 chr3B 779567882 779570136 2254 False 861.000 1487 91.287333 1041 3384 3 chr3B.!!$F2 2343
3 TraesCS3B01G476500 chr3B 779510231 779511512 1281 False 361.500 401 79.513000 1174 2425 2 chr3B.!!$F1 1251
4 TraesCS3B01G476500 chr3B 778489832 778490964 1132 True 309.000 383 80.638000 1307 2398 2 chr3B.!!$R3 1091
5 TraesCS3B01G476500 chr3D 581985471 581989918 4447 True 732.375 1646 90.966500 811 3294 4 chr3D.!!$R1 2483
6 TraesCS3B01G476500 chr3D 582622780 582623661 881 False 472.000 472 77.015000 1538 2431 1 chr3D.!!$F2 893
7 TraesCS3B01G476500 chr3D 582792761 582793930 1169 False 345.000 420 82.279000 1303 2431 2 chr3D.!!$F4 1128
8 TraesCS3B01G476500 chr3D 582105919 582108157 2238 True 275.300 396 80.436667 1196 3017 3 chr3D.!!$R2 1821
9 TraesCS3B01G476500 chr2A 592830549 592831357 808 True 1253.000 1253 94.588000 1 812 1 chr2A.!!$R1 811
10 TraesCS3B01G476500 chr2A 641598953 641599768 815 False 1251.000 1251 94.268000 1 820 1 chr2A.!!$F1 819
11 TraesCS3B01G476500 chr1B 490455760 490456561 801 True 1251.000 1251 94.783000 1 805 1 chr1B.!!$R3 804
12 TraesCS3B01G476500 chr1B 636032030 636032831 801 True 1243.000 1243 94.554000 1 808 1 chr1B.!!$R4 807
13 TraesCS3B01G476500 chr1B 141756174 141756974 800 True 1240.000 1240 94.541000 1 806 1 chr1B.!!$R1 805
14 TraesCS3B01G476500 chr1B 340459625 340460430 805 True 1240.000 1240 94.335000 1 812 1 chr1B.!!$R2 811
15 TraesCS3B01G476500 chr1B 670407427 670408234 807 True 1234.000 1234 94.205000 1 811 1 chr1B.!!$R5 810
16 TraesCS3B01G476500 chr4A 583935024 583935829 805 False 1243.000 1243 94.451000 1 811 1 chr4A.!!$F1 810
17 TraesCS3B01G476500 chrUn 41505957 41506841 884 False 424.000 424 76.061000 1538 2431 1 chrUn.!!$F1 893
18 TraesCS3B01G476500 chrUn 41525213 41526348 1135 False 306.500 372 80.881500 1304 2398 2 chrUn.!!$F2 1094

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
268 269 0.322456 CTGGCCGTTTGGATCCTCAA 60.322 55.000 14.23 2.90 37.49 3.02 F
432 433 0.523546 CGGTCGGATGACTCGAGTTG 60.524 60.000 21.08 7.84 44.83 3.16 F
465 466 0.611714 AGGGACACTTTTCGCGGTAT 59.388 50.000 6.13 0.00 33.74 2.73 F
668 669 1.412710 GATGATAACACAGGGCTCCGA 59.587 52.381 0.00 0.00 0.00 4.55 F
1285 1391 0.401395 ACCTCCTCCTCCACAAACCA 60.401 55.000 0.00 0.00 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1264 1334 0.036875 GTTTGTGGAGGAGGAGGTGG 59.963 60.0 0.0 0.0 0.00 4.61 R
1265 1335 0.036875 GGTTTGTGGAGGAGGAGGTG 59.963 60.0 0.0 0.0 0.00 4.00 R
1267 1337 0.036875 GTGGTTTGTGGAGGAGGAGG 59.963 60.0 0.0 0.0 0.00 4.30 R
2268 2507 0.260230 TGCTTGGAAGGACCCAAACA 59.740 50.0 0.0 0.0 44.78 2.83 R
3225 5878 0.327259 GAACGGCCCCTATAATCCCC 59.673 60.0 0.0 0.0 0.00 4.81 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
50 51 2.841317 GGAACCCCGGGTCTGTTT 59.159 61.111 21.85 3.84 33.12 2.83
136 137 2.613691 GCGTCGGAATAAGTTTCTCCA 58.386 47.619 0.00 0.00 0.00 3.86
148 149 1.469335 TTTCTCCAGGCTCCGTTCGT 61.469 55.000 0.00 0.00 0.00 3.85
161 162 2.599281 TTCGTGGTCAGGCGAGGA 60.599 61.111 0.00 0.00 38.40 3.71
268 269 0.322456 CTGGCCGTTTGGATCCTCAA 60.322 55.000 14.23 2.90 37.49 3.02
274 275 2.446435 CGTTTGGATCCTCAAATGGGT 58.554 47.619 14.23 0.00 38.98 4.51
349 350 2.810852 GCTGTTGTTCTTCTCCTTCCTG 59.189 50.000 0.00 0.00 0.00 3.86
373 374 1.129917 CTGATGCTGGTGGGAGATCT 58.870 55.000 0.00 0.00 0.00 2.75
384 385 1.004745 TGGGAGATCTTGCTTTGTCCC 59.995 52.381 0.00 0.59 43.57 4.46
432 433 0.523546 CGGTCGGATGACTCGAGTTG 60.524 60.000 21.08 7.84 44.83 3.16
465 466 0.611714 AGGGACACTTTTCGCGGTAT 59.388 50.000 6.13 0.00 33.74 2.73
472 473 3.810941 ACACTTTTCGCGGTATTCAAAGA 59.189 39.130 6.13 0.00 0.00 2.52
515 516 3.148412 CAGGTGTGTTGGATTGATGTCA 58.852 45.455 0.00 0.00 0.00 3.58
527 528 3.657398 TTGATGTCAATGCCCTCTCAT 57.343 42.857 0.00 0.00 0.00 2.90
654 655 7.015098 GTCTTCTCTCAAGATTCAGGGATGATA 59.985 40.741 0.00 0.00 28.87 2.15
668 669 1.412710 GATGATAACACAGGGCTCCGA 59.587 52.381 0.00 0.00 0.00 4.55
713 714 5.014966 TGTCTTAGGGTACTCTAGGTGTTCT 59.985 44.000 11.36 0.00 0.00 3.01
729 730 4.399934 GGTGTTCTTGGTCCTTTGTGTTTA 59.600 41.667 0.00 0.00 0.00 2.01
752 753 3.604772 CGTTTCAGTGTGCTTGTAAGAGC 60.605 47.826 0.00 0.00 43.00 4.09
912 964 8.867097 TGATACAGAGGAAGTACTAGTGTTTTT 58.133 33.333 5.39 0.00 0.00 1.94
936 988 5.762825 TTTACGCTCATACCCTGTACTAG 57.237 43.478 0.00 0.00 0.00 2.57
946 998 8.915057 TCATACCCTGTACTAGTAGATTACAC 57.085 38.462 1.87 0.00 0.00 2.90
953 1005 7.342769 TGTACTAGTAGATTACACCACATGG 57.657 40.000 1.87 0.00 42.17 3.66
960 1012 2.897271 TTACACCACATGGATTGCCT 57.103 45.000 4.53 0.00 38.94 4.75
1079 1134 6.797454 AGATATCACCTCGTCAACTTCTAAC 58.203 40.000 5.32 0.00 0.00 2.34
1090 1145 5.152804 GTCAACTTCTAACAGTAGACGACC 58.847 45.833 0.00 0.00 36.03 4.79
1094 1149 4.586001 ACTTCTAACAGTAGACGACCCAAA 59.414 41.667 0.00 0.00 36.03 3.28
1136 1191 2.034999 GGCCCGGACCATCAACAA 59.965 61.111 0.73 0.00 0.00 2.83
1146 1201 3.010420 GACCATCAACAAGCCTCCTAAC 58.990 50.000 0.00 0.00 0.00 2.34
1147 1202 2.644798 ACCATCAACAAGCCTCCTAACT 59.355 45.455 0.00 0.00 0.00 2.24
1148 1203 3.274288 CCATCAACAAGCCTCCTAACTC 58.726 50.000 0.00 0.00 0.00 3.01
1149 1204 3.274288 CATCAACAAGCCTCCTAACTCC 58.726 50.000 0.00 0.00 0.00 3.85
1150 1205 2.621070 TCAACAAGCCTCCTAACTCCT 58.379 47.619 0.00 0.00 0.00 3.69
1151 1206 3.786553 TCAACAAGCCTCCTAACTCCTA 58.213 45.455 0.00 0.00 0.00 2.94
1175 1233 3.370527 GCCTCTAACCCTAGCATTCACAA 60.371 47.826 0.00 0.00 0.00 3.33
1269 1339 3.498071 CCACCACCACCACCACCT 61.498 66.667 0.00 0.00 0.00 4.00
1285 1391 0.401395 ACCTCCTCCTCCACAAACCA 60.401 55.000 0.00 0.00 0.00 3.67
1297 1403 2.107546 AAACCACGCCTCGTCGTT 59.892 55.556 0.00 0.00 42.20 3.85
1299 1405 4.657824 ACCACGCCTCGTCGTTGG 62.658 66.667 0.00 0.00 41.21 3.77
1535 1641 4.394712 CTCCCCTGCACGGACCAC 62.395 72.222 2.94 0.00 33.16 4.16
1556 1743 1.174783 GCCTCACCGAGTTCTACTCA 58.825 55.000 7.52 0.00 45.30 3.41
1583 1782 4.592192 CGCGTCGCCATCCAGGAT 62.592 66.667 12.44 0.00 41.22 3.24
1585 1784 2.355126 CGTCGCCATCCAGGATCG 60.355 66.667 0.00 1.13 41.22 3.69
1586 1785 2.663188 GTCGCCATCCAGGATCGC 60.663 66.667 8.96 8.96 41.22 4.58
1589 1788 2.663188 GCCATCCAGGATCGCGAC 60.663 66.667 12.93 5.43 41.22 5.19
1590 1789 2.029666 CCATCCAGGATCGCGACC 59.970 66.667 12.93 15.45 41.22 4.79
1591 1790 2.355126 CATCCAGGATCGCGACCG 60.355 66.667 12.93 11.04 0.00 4.79
1592 1791 4.286320 ATCCAGGATCGCGACCGC 62.286 66.667 12.93 3.53 37.85 5.68
1594 1793 3.592814 CCAGGATCGCGACCGCTA 61.593 66.667 12.93 1.64 39.32 4.26
1595 1794 2.645567 CAGGATCGCGACCGCTAT 59.354 61.111 12.93 6.98 39.32 2.97
1596 1795 1.442857 CAGGATCGCGACCGCTATC 60.443 63.158 12.93 17.10 40.98 2.08
1597 1796 1.897137 AGGATCGCGACCGCTATCA 60.897 57.895 23.59 3.68 42.71 2.15
1600 1799 1.269444 GATCGCGACCGCTATCACAC 61.269 60.000 12.93 0.00 41.24 3.82
1663 1883 3.801997 CCGCCTGCCTGATCCCTT 61.802 66.667 0.00 0.00 0.00 3.95
1665 1885 3.001514 GCCTGCCTGATCCCTTGA 58.998 61.111 0.00 0.00 0.00 3.02
1668 1888 0.750911 CCTGCCTGATCCCTTGAAGC 60.751 60.000 0.00 0.00 0.00 3.86
1670 1890 1.304282 GCCTGATCCCTTGAAGCCA 59.696 57.895 0.00 0.00 0.00 4.75
1680 1900 2.167487 CCCTTGAAGCCAGAGAGACTAC 59.833 54.545 0.00 0.00 0.00 2.73
1727 1947 1.269621 CGTCGTCACCTTCAGGAAACT 60.270 52.381 0.00 0.00 46.44 2.66
1738 1958 3.479269 GGAAACTCTGCCGCGTCG 61.479 66.667 4.92 0.00 0.00 5.12
1928 2148 7.129109 TGTCGTTTCTTGGAGATAAATTGAC 57.871 36.000 0.00 0.00 0.00 3.18
1942 2162 2.568623 ATTGACTCTGCCGGAAGTTT 57.431 45.000 9.98 0.00 0.00 2.66
1944 2164 3.695830 TTGACTCTGCCGGAAGTTTAT 57.304 42.857 9.98 0.00 0.00 1.40
1987 2216 0.802494 GCGGTGTGGTGAGTTATTGG 59.198 55.000 0.00 0.00 0.00 3.16
1995 2224 5.703592 GTGTGGTGAGTTATTGGTCATTGTA 59.296 40.000 0.00 0.00 0.00 2.41
2006 2235 3.522759 TGGTCATTGTAAGGGTGGAGTA 58.477 45.455 0.00 0.00 0.00 2.59
2008 2237 3.262405 GGTCATTGTAAGGGTGGAGTACA 59.738 47.826 0.00 0.00 0.00 2.90
2023 2252 3.199071 GGAGTACAATCCATGGGTGTACA 59.801 47.826 35.80 18.46 46.52 2.90
2024 2253 4.141482 GGAGTACAATCCATGGGTGTACAT 60.141 45.833 35.80 27.54 46.52 2.29
2229 2462 5.991606 TGATGGGTCTTATCATGAATTCGTC 59.008 40.000 0.00 0.00 30.03 4.20
2237 2470 6.638468 TCTTATCATGAATTCGTCATCGACTG 59.362 38.462 0.00 0.00 44.01 3.51
2268 2507 3.127791 ACAGAGGATTGTGGATCTCCT 57.872 47.619 0.19 0.19 42.12 3.69
2310 2549 1.027357 GCTGATGCAGTACAATGGGG 58.973 55.000 0.00 0.00 39.41 4.96
2311 2550 1.683011 GCTGATGCAGTACAATGGGGT 60.683 52.381 0.00 0.00 39.41 4.95
2313 2552 3.091545 CTGATGCAGTACAATGGGGTTT 58.908 45.455 0.00 0.00 0.00 3.27
2314 2553 3.088532 TGATGCAGTACAATGGGGTTTC 58.911 45.455 0.00 0.00 0.00 2.78
2315 2554 2.666272 TGCAGTACAATGGGGTTTCA 57.334 45.000 0.00 0.00 0.00 2.69
2316 2555 3.168035 TGCAGTACAATGGGGTTTCAT 57.832 42.857 0.00 0.00 0.00 2.57
2339 2578 2.952310 ACTGTCCAGAAGTTTTCAAGGC 59.048 45.455 0.40 0.00 0.00 4.35
2359 2602 2.002586 CACATTTGCTCCCTAGTGACG 58.997 52.381 0.00 0.00 0.00 4.35
2367 2612 2.159407 GCTCCCTAGTGACGAGTTACAC 60.159 54.545 0.00 0.00 37.30 2.90
2442 2698 3.599343 AGCAGCAAATTCAGTACGATGA 58.401 40.909 0.00 0.00 0.00 2.92
2451 3085 8.080417 GCAAATTCAGTACGATGAGTATACCTA 58.920 37.037 0.00 0.00 37.69 3.08
2474 3108 2.012673 CCTCTTACAATGCTCTGGTGC 58.987 52.381 0.00 0.00 0.00 5.01
2475 3109 2.355513 CCTCTTACAATGCTCTGGTGCT 60.356 50.000 0.00 0.00 0.00 4.40
2485 3119 1.943507 GCTCTGGTGCTTGGTCTCTTC 60.944 57.143 0.00 0.00 0.00 2.87
2508 5109 0.822164 ATCTGGCCTGAAAGCAATGC 59.178 50.000 17.04 0.00 0.00 3.56
2513 5114 0.461339 GCCTGAAAGCAATGCCATGG 60.461 55.000 7.63 7.63 0.00 3.66
2538 5149 2.504175 GAGGTGGATGTTTGGGCTAGTA 59.496 50.000 0.00 0.00 0.00 1.82
2544 5155 4.781087 TGGATGTTTGGGCTAGTAAGTACT 59.219 41.667 0.00 0.00 40.24 2.73
2667 5293 5.595133 TGGTTTTTATTCGTGAAGGAAGGTT 59.405 36.000 0.00 0.00 0.00 3.50
2708 5336 4.171005 CCATTGTTTAGCTAAGTCGTCGA 58.829 43.478 6.24 0.00 0.00 4.20
2747 5375 5.241064 GCTCAATCATGCTTGGATAAGTGAT 59.759 40.000 9.29 0.00 33.49 3.06
2754 5382 6.433716 TCATGCTTGGATAAGTGATTGTGAAA 59.566 34.615 0.00 0.00 36.27 2.69
2800 5428 0.749049 GCTGCAAAGATTCCATCCCC 59.251 55.000 0.00 0.00 0.00 4.81
2924 5571 1.915489 TGTGCATGGATTACCCTGTCT 59.085 47.619 0.00 0.00 34.90 3.41
2955 5602 1.922447 AGGATTTATGTGCCTGGGTGA 59.078 47.619 0.00 0.00 0.00 4.02
3048 5701 4.637534 TGAAGTCAGGAATAATGCTTGCTC 59.362 41.667 0.00 0.00 0.00 4.26
3294 5953 6.694877 ACATGATGATGAAGAGAATTGTGG 57.305 37.500 0.00 0.00 33.36 4.17
3312 5971 4.355437 TGTGGTATTTTTGTTGTGCTTCG 58.645 39.130 0.00 0.00 0.00 3.79
3320 5979 1.206072 GTTGTGCTTCGCTCAGCTG 59.794 57.895 7.63 7.63 40.79 4.24
3321 5980 2.610694 TTGTGCTTCGCTCAGCTGC 61.611 57.895 9.47 0.00 40.79 5.25
3322 5981 2.741598 GTGCTTCGCTCAGCTGCT 60.742 61.111 9.47 0.00 40.79 4.24
3380 6039 5.798434 ACGTTTTTGCTTAAGTGAACAACTC 59.202 36.000 4.02 0.00 38.56 3.01
3381 6040 6.027749 CGTTTTTGCTTAAGTGAACAACTCT 58.972 36.000 4.02 0.00 38.56 3.24
3382 6041 6.021468 CGTTTTTGCTTAAGTGAACAACTCTG 60.021 38.462 4.02 0.00 38.56 3.35
3383 6042 6.509418 TTTTGCTTAAGTGAACAACTCTGT 57.491 33.333 4.02 0.00 38.56 3.41
3384 6043 5.484173 TTGCTTAAGTGAACAACTCTGTG 57.516 39.130 4.02 0.00 38.56 3.66
3385 6044 4.513442 TGCTTAAGTGAACAACTCTGTGT 58.487 39.130 4.02 0.00 38.56 3.72
3386 6045 4.570772 TGCTTAAGTGAACAACTCTGTGTC 59.429 41.667 4.02 0.00 38.56 3.67
3387 6046 4.811557 GCTTAAGTGAACAACTCTGTGTCT 59.188 41.667 4.02 0.00 38.56 3.41
3388 6047 5.983720 GCTTAAGTGAACAACTCTGTGTCTA 59.016 40.000 4.02 0.00 38.56 2.59
3389 6048 6.647067 GCTTAAGTGAACAACTCTGTGTCTAT 59.353 38.462 4.02 0.00 38.56 1.98
3390 6049 7.359598 GCTTAAGTGAACAACTCTGTGTCTATG 60.360 40.741 4.02 0.00 38.56 2.23
3391 6050 5.791336 AGTGAACAACTCTGTGTCTATGA 57.209 39.130 0.00 0.00 31.64 2.15
3392 6051 6.161855 AGTGAACAACTCTGTGTCTATGAA 57.838 37.500 0.00 0.00 31.64 2.57
3393 6052 6.219473 AGTGAACAACTCTGTGTCTATGAAG 58.781 40.000 0.00 0.00 31.64 3.02
3394 6053 5.986135 GTGAACAACTCTGTGTCTATGAAGT 59.014 40.000 0.00 0.00 35.37 3.01
3395 6054 5.985530 TGAACAACTCTGTGTCTATGAAGTG 59.014 40.000 0.00 0.00 35.37 3.16
3396 6055 5.537300 ACAACTCTGTGTCTATGAAGTGT 57.463 39.130 0.00 0.00 33.30 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 4.735599 GTTCCCCCTCCCTCCCGT 62.736 72.222 0.00 0.00 0.00 5.28
50 51 0.472161 TACCACACACCCACCTAGCA 60.472 55.000 0.00 0.00 0.00 3.49
136 137 2.915659 TGACCACGAACGGAGCCT 60.916 61.111 0.00 0.00 0.00 4.58
148 149 0.960364 GCAAAATCCTCGCCTGACCA 60.960 55.000 0.00 0.00 0.00 4.02
161 162 2.633488 GCTCCTAGACGAAGGCAAAAT 58.367 47.619 0.00 0.00 36.51 1.82
209 210 2.597805 ATAGCCCGCGACCTCGAT 60.598 61.111 8.23 0.00 43.02 3.59
268 269 0.105862 CCCTGCATCCATCACCCATT 60.106 55.000 0.00 0.00 0.00 3.16
274 275 0.687427 TCGTCTCCCTGCATCCATCA 60.687 55.000 0.00 0.00 0.00 3.07
373 374 4.257654 TCCGCCGGGACAAAGCAA 62.258 61.111 1.90 0.00 37.43 3.91
465 466 2.223144 CGTCGCCATCTTTGTCTTTGAA 59.777 45.455 0.00 0.00 0.00 2.69
472 473 2.034879 CAGCCGTCGCCATCTTTGT 61.035 57.895 0.00 0.00 34.57 2.83
515 516 1.147824 CCAGCGATGAGAGGGCATT 59.852 57.895 0.06 0.00 0.00 3.56
527 528 0.756294 TCCTTTCTTGACACCAGCGA 59.244 50.000 0.00 0.00 0.00 4.93
654 655 0.250513 GATCTTCGGAGCCCTGTGTT 59.749 55.000 0.00 0.00 0.00 3.32
713 714 4.458295 TGAAACGTAAACACAAAGGACCAA 59.542 37.500 0.00 0.00 0.00 3.67
729 730 3.527533 TCTTACAAGCACACTGAAACGT 58.472 40.909 0.00 0.00 0.00 3.99
752 753 3.498397 ACGAATCAGTACAAAGCAGTTGG 59.502 43.478 0.00 0.00 41.97 3.77
912 964 5.410355 AGTACAGGGTATGAGCGTAAAAA 57.590 39.130 0.00 0.00 0.00 1.94
922 974 7.722728 TGGTGTAATCTACTAGTACAGGGTATG 59.277 40.741 0.00 0.00 39.19 2.39
930 982 7.578310 TCCATGTGGTGTAATCTACTAGTAC 57.422 40.000 0.00 0.00 36.34 2.73
936 988 4.275936 GGCAATCCATGTGGTGTAATCTAC 59.724 45.833 0.00 0.00 36.34 2.59
946 998 1.683943 CCTGTAGGCAATCCATGTGG 58.316 55.000 0.00 0.00 33.74 4.17
953 1005 4.489306 AGAAACTACCCTGTAGGCAATC 57.511 45.455 6.25 0.00 40.58 2.67
960 1012 8.877195 AGACATCTAAAAAGAAACTACCCTGTA 58.123 33.333 0.00 0.00 0.00 2.74
1068 1120 4.217118 GGGTCGTCTACTGTTAGAAGTTGA 59.783 45.833 0.00 0.00 36.03 3.18
1079 1134 0.682852 TGGGTTTGGGTCGTCTACTG 59.317 55.000 0.00 0.00 0.00 2.74
1136 1191 1.292546 AGGCTTAGGAGTTAGGAGGCT 59.707 52.381 0.00 0.00 38.27 4.58
1146 1201 2.894765 GCTAGGGTTAGAGGCTTAGGAG 59.105 54.545 0.00 0.00 0.00 3.69
1147 1202 2.246588 TGCTAGGGTTAGAGGCTTAGGA 59.753 50.000 0.00 0.00 0.00 2.94
1148 1203 2.679082 TGCTAGGGTTAGAGGCTTAGG 58.321 52.381 0.00 0.00 0.00 2.69
1149 1204 4.345257 TGAATGCTAGGGTTAGAGGCTTAG 59.655 45.833 0.00 0.00 0.00 2.18
1150 1205 4.101119 GTGAATGCTAGGGTTAGAGGCTTA 59.899 45.833 0.00 0.00 0.00 3.09
1151 1206 3.115390 TGAATGCTAGGGTTAGAGGCTT 58.885 45.455 0.00 0.00 0.00 4.35
1261 1331 2.122729 TGGAGGAGGAGGTGGTGG 59.877 66.667 0.00 0.00 0.00 4.61
1263 1333 0.401395 TTTGTGGAGGAGGAGGTGGT 60.401 55.000 0.00 0.00 0.00 4.16
1264 1334 0.036875 GTTTGTGGAGGAGGAGGTGG 59.963 60.000 0.00 0.00 0.00 4.61
1265 1335 0.036875 GGTTTGTGGAGGAGGAGGTG 59.963 60.000 0.00 0.00 0.00 4.00
1266 1336 0.401395 TGGTTTGTGGAGGAGGAGGT 60.401 55.000 0.00 0.00 0.00 3.85
1267 1337 0.036875 GTGGTTTGTGGAGGAGGAGG 59.963 60.000 0.00 0.00 0.00 4.30
1268 1338 0.320771 CGTGGTTTGTGGAGGAGGAG 60.321 60.000 0.00 0.00 0.00 3.69
1269 1339 1.752198 CGTGGTTTGTGGAGGAGGA 59.248 57.895 0.00 0.00 0.00 3.71
1297 1403 1.536907 TCCGGCAGGAAGTAACCCA 60.537 57.895 1.89 0.00 45.12 4.51
1547 1734 1.291132 GGCAGCCGAATGAGTAGAAC 58.709 55.000 0.00 0.00 0.00 3.01
1585 1784 2.585247 GGGTGTGATAGCGGTCGC 60.585 66.667 7.32 7.32 42.33 5.19
1586 1785 2.278596 CGGGTGTGATAGCGGTCG 60.279 66.667 0.00 0.00 0.00 4.79
1587 1786 2.585247 GCGGGTGTGATAGCGGTC 60.585 66.667 0.00 0.00 0.00 4.79
1588 1787 4.157120 GGCGGGTGTGATAGCGGT 62.157 66.667 0.00 0.00 0.00 5.68
1592 1791 4.201679 TCGCGGCGGGTGTGATAG 62.202 66.667 23.46 0.00 0.00 2.08
1593 1792 4.201679 CTCGCGGCGGGTGTGATA 62.202 66.667 23.46 2.08 0.00 2.15
1662 1882 2.791655 TCGTAGTCTCTCTGGCTTCAA 58.208 47.619 0.00 0.00 0.00 2.69
1663 1883 2.491675 TCGTAGTCTCTCTGGCTTCA 57.508 50.000 0.00 0.00 0.00 3.02
1665 1885 2.797786 ACTTCGTAGTCTCTCTGGCTT 58.202 47.619 0.00 0.00 0.00 4.35
1680 1900 2.877335 CCGGAAAAGAGGACTACTTCG 58.123 52.381 0.00 0.00 0.00 3.79
1685 1905 0.529378 GTCGCCGGAAAAGAGGACTA 59.471 55.000 5.05 0.00 0.00 2.59
1727 1947 1.448365 TAGTAGACGACGCGGCAGA 60.448 57.895 14.85 0.00 37.34 4.26
1738 1958 2.420129 CCCCAATGTGGCAGTAGTAGAC 60.420 54.545 0.00 0.00 35.79 2.59
1928 2148 2.678336 GGACAATAAACTTCCGGCAGAG 59.322 50.000 8.52 2.75 0.00 3.35
1942 2162 3.370527 GCTAGCCAGAACCTTGGACAATA 60.371 47.826 2.29 0.00 40.87 1.90
1944 2164 1.271379 GCTAGCCAGAACCTTGGACAA 60.271 52.381 2.29 0.00 40.87 3.18
1971 2200 4.518970 ACAATGACCAATAACTCACCACAC 59.481 41.667 0.00 0.00 0.00 3.82
1972 2201 4.724399 ACAATGACCAATAACTCACCACA 58.276 39.130 0.00 0.00 0.00 4.17
1987 2216 4.546829 TGTACTCCACCCTTACAATGAC 57.453 45.455 0.00 0.00 0.00 3.06
2006 2235 4.046286 ACAATGTACACCCATGGATTGT 57.954 40.909 15.22 16.53 33.12 2.71
2008 2237 5.779771 AGAAAACAATGTACACCCATGGATT 59.220 36.000 15.22 0.05 0.00 3.01
2023 2252 4.339247 CCCGGATTGCAGATAGAAAACAAT 59.661 41.667 0.73 0.00 33.82 2.71
2024 2253 3.694072 CCCGGATTGCAGATAGAAAACAA 59.306 43.478 0.73 0.00 0.00 2.83
2237 2470 4.785453 CCTCTGTTCGCCCTGGGC 62.785 72.222 28.17 28.17 46.75 5.36
2268 2507 0.260230 TGCTTGGAAGGACCCAAACA 59.740 50.000 0.00 0.00 44.78 2.83
2308 2547 4.652822 ACTTCTGGACAGTTATGAAACCC 58.347 43.478 0.00 0.00 36.15 4.11
2310 2549 7.703328 TGAAAACTTCTGGACAGTTATGAAAC 58.297 34.615 0.00 0.00 33.12 2.78
2311 2550 7.873719 TGAAAACTTCTGGACAGTTATGAAA 57.126 32.000 0.00 0.00 33.12 2.69
2313 2552 6.486657 CCTTGAAAACTTCTGGACAGTTATGA 59.513 38.462 0.00 0.00 33.12 2.15
2314 2553 6.672147 CCTTGAAAACTTCTGGACAGTTATG 58.328 40.000 0.00 0.00 33.12 1.90
2315 2554 5.241728 GCCTTGAAAACTTCTGGACAGTTAT 59.758 40.000 0.00 0.00 33.12 1.89
2316 2555 4.578928 GCCTTGAAAACTTCTGGACAGTTA 59.421 41.667 0.00 0.00 33.12 2.24
2339 2578 2.002586 CGTCACTAGGGAGCAAATGTG 58.997 52.381 0.00 0.00 0.00 3.21
2442 2698 7.299134 AGCATTGTAAGAGGAGTAGGTATACT 58.701 38.462 2.25 0.00 45.16 2.12
2451 3085 3.055530 CACCAGAGCATTGTAAGAGGAGT 60.056 47.826 0.00 0.00 0.00 3.85
2456 3090 3.076621 CAAGCACCAGAGCATTGTAAGA 58.923 45.455 0.00 0.00 36.85 2.10
2474 3108 3.069443 GGCCAGATAGAGAAGAGACCAAG 59.931 52.174 0.00 0.00 0.00 3.61
2475 3109 3.034635 GGCCAGATAGAGAAGAGACCAA 58.965 50.000 0.00 0.00 0.00 3.67
2485 3119 2.996249 TGCTTTCAGGCCAGATAGAG 57.004 50.000 17.84 9.01 0.00 2.43
2508 5109 1.152819 CATCCACCTCTGCCCATGG 60.153 63.158 4.14 4.14 0.00 3.66
2513 5114 0.967380 CCCAAACATCCACCTCTGCC 60.967 60.000 0.00 0.00 0.00 4.85
2538 5149 5.367302 CGAGTCTAGGGCTACTAAGTACTT 58.633 45.833 13.68 13.68 0.00 2.24
2544 5155 2.776536 AGTCCGAGTCTAGGGCTACTAA 59.223 50.000 4.00 0.00 42.78 2.24
2667 5293 1.026182 GCATCGGCATTGGACTCACA 61.026 55.000 0.00 0.00 40.72 3.58
2708 5336 4.828939 TGATTGAGCAAAGTTCCAAGACAT 59.171 37.500 0.00 0.00 0.00 3.06
2747 5375 4.638421 ACATTTCTCGTCAACCTTTCACAA 59.362 37.500 0.00 0.00 0.00 3.33
2754 5382 7.712797 ACAAAAATTACATTTCTCGTCAACCT 58.287 30.769 0.00 0.00 0.00 3.50
2779 5407 1.826720 GGGATGGAATCTTTGCAGCAA 59.173 47.619 2.83 2.83 44.71 3.91
2924 5571 7.067372 CAGGCACATAAATCCTCATCTTAACAA 59.933 37.037 0.00 0.00 0.00 2.83
2955 5602 2.557452 CCCCTGCCCACTTAAAACTCAT 60.557 50.000 0.00 0.00 0.00 2.90
3009 5662 2.093128 ACTTCACAACGAGTCCCAAAGT 60.093 45.455 0.00 0.00 0.00 2.66
3048 5701 6.267928 AGGTTTAGCAGGATACATACTACTGG 59.732 42.308 0.00 0.00 41.41 4.00
3225 5878 0.327259 GAACGGCCCCTATAATCCCC 59.673 60.000 0.00 0.00 0.00 4.81
3320 5979 0.175989 GACACTAGTACCAGCCCAGC 59.824 60.000 0.00 0.00 0.00 4.85
3321 5980 1.751924 GAGACACTAGTACCAGCCCAG 59.248 57.143 0.00 0.00 0.00 4.45
3322 5981 1.358103 AGAGACACTAGTACCAGCCCA 59.642 52.381 0.00 0.00 0.00 5.36
3328 5987 3.995048 GCAAACCAAGAGACACTAGTACC 59.005 47.826 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.