Multiple sequence alignment - TraesCS5A01G364300

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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 TraesCS5A01G364300 chr5A 100.000 6861 0 0 1 6861 564601331 564594471 0.000000e+00 12670.0
1 TraesCS5A01G364300 chr5A 87.607 234 26 3 5716 5949 564536138 564535908 1.130000e-67 268.0
2 TraesCS5A01G364300 chr5A 82.186 247 39 5 5880 6123 564589693 564589449 2.510000e-49 207.0
3 TraesCS5A01G364300 chr5A 90.226 133 13 0 5735 5867 564582687 564582555 2.540000e-39 174.0
4 TraesCS5A01G364300 chr5D 90.463 2244 125 29 4 2182 446760233 446758014 0.000000e+00 2876.0
5 TraesCS5A01G364300 chr5D 91.625 1779 100 23 4880 6610 446757480 446755703 0.000000e+00 2414.0
6 TraesCS5A01G364300 chr5D 89.953 1503 150 1 3360 4861 87177906 87179408 0.000000e+00 1938.0
7 TraesCS5A01G364300 chr5D 79.209 1289 179 47 4892 6124 446574040 446572785 0.000000e+00 813.0
8 TraesCS5A01G364300 chr5D 94.048 252 14 1 6610 6861 446755476 446755226 1.400000e-101 381.0
9 TraesCS5A01G364300 chr5D 87.984 258 18 9 3093 3343 446757746 446757495 6.730000e-75 292.0
10 TraesCS5A01G364300 chr5D 79.532 171 25 6 6237 6401 446572639 446572473 5.620000e-21 113.0
11 TraesCS5A01G364300 chr1A 97.961 1520 29 2 3363 4881 104245623 104247141 0.000000e+00 2634.0
12 TraesCS5A01G364300 chr6A 97.188 1529 37 4 3354 4881 391043908 391045431 0.000000e+00 2580.0
13 TraesCS5A01G364300 chr6A 81.136 440 67 5 6438 6861 44977136 44977575 8.520000e-89 339.0
14 TraesCS5A01G364300 chr2A 97.041 1521 41 2 3362 4881 603536551 603538068 0.000000e+00 2556.0
15 TraesCS5A01G364300 chr2A 80.952 441 66 7 6438 6861 489637043 489636604 3.970000e-87 333.0
16 TraesCS5A01G364300 chr2A 80.455 440 70 5 6438 6861 649702139 649702578 8.580000e-84 322.0
17 TraesCS5A01G364300 chr5B 91.197 1579 95 10 4880 6438 544907242 544905688 0.000000e+00 2106.0
18 TraesCS5A01G364300 chr5B 95.479 1283 40 10 4 1274 544910568 544909292 0.000000e+00 2032.0
19 TraesCS5A01G364300 chr5B 90.670 1522 140 2 3361 4881 563523998 563522478 0.000000e+00 2023.0
20 TraesCS5A01G364300 chr5B 93.868 1109 54 12 2263 3360 544908347 544907242 0.000000e+00 1659.0
21 TraesCS5A01G364300 chr5B 79.297 1251 160 48 4945 6127 544767407 544766188 0.000000e+00 784.0
22 TraesCS5A01G364300 chr5B 88.565 446 30 7 6434 6861 544905656 544905214 7.890000e-144 521.0
23 TraesCS5A01G364300 chr5B 83.260 227 33 5 5880 6103 544813029 544812805 3.240000e-48 204.0
24 TraesCS5A01G364300 chr5B 80.702 171 26 4 6237 6401 544766050 544765881 7.220000e-25 126.0
25 TraesCS5A01G364300 chr4D 91.132 1466 129 1 3397 4861 12292800 12291335 0.000000e+00 1986.0
26 TraesCS5A01G364300 chr1B 90.191 1519 147 2 3365 4881 284378353 284379871 0.000000e+00 1978.0
27 TraesCS5A01G364300 chr1B 81.132 424 65 7 6451 6861 557440587 557441008 6.640000e-85 326.0
28 TraesCS5A01G364300 chr1B 89.655 87 7 2 1857 1942 653049108 653049193 7.280000e-20 110.0
29 TraesCS5A01G364300 chr6D 90.200 1500 146 1 3363 4861 50572431 50570932 0.000000e+00 1954.0
30 TraesCS5A01G364300 chr6D 92.857 70 5 0 1576 1645 40663121 40663052 1.220000e-17 102.0
31 TraesCS5A01G364300 chr6D 92.857 70 5 0 1576 1645 468741296 468741227 1.220000e-17 102.0
32 TraesCS5A01G364300 chr7A 89.960 1514 151 1 3369 4881 69627871 69626358 0.000000e+00 1953.0
33 TraesCS5A01G364300 chr2B 85.437 412 41 6 1777 2187 103485845 103486238 1.780000e-110 411.0
34 TraesCS5A01G364300 chr2B 83.777 413 47 6 1777 2187 472575851 472576245 2.340000e-99 374.0
35 TraesCS5A01G364300 chr2B 89.950 199 7 7 2263 2456 103486372 103486562 1.910000e-60 244.0
36 TraesCS5A01G364300 chr2B 88.945 199 9 7 2263 2456 472576379 472576569 4.140000e-57 233.0
37 TraesCS5A01G364300 chr2B 91.667 60 5 0 2988 3047 472576328 472576387 4.410000e-12 84.2
38 TraesCS5A01G364300 chr2D 83.827 439 55 3 6437 6859 106377379 106376941 2.980000e-108 403.0
39 TraesCS5A01G364300 chr6B 85.024 414 40 10 1777 2187 655218193 655217799 1.070000e-107 401.0
40 TraesCS5A01G364300 chr6B 84.262 413 45 6 1777 2187 380971824 380972218 1.080000e-102 385.0
41 TraesCS5A01G364300 chr6B 89.109 202 9 7 2263 2459 655217665 655217472 8.890000e-59 239.0
42 TraesCS5A01G364300 chr6B 88.945 199 9 7 2263 2456 380972352 380972542 4.140000e-57 233.0
43 TraesCS5A01G364300 chr6B 91.667 60 5 0 2988 3047 380972301 380972360 4.410000e-12 84.2
44 TraesCS5A01G364300 chr6B 92.982 57 4 0 2991 3047 655217713 655217657 4.410000e-12 84.2
45 TraesCS5A01G364300 chr3D 83.258 442 58 4 6434 6859 136751035 136751476 6.450000e-105 392.0
46 TraesCS5A01G364300 chr3D 92.857 70 5 0 1576 1645 24924182 24924251 1.220000e-17 102.0
47 TraesCS5A01G364300 chr3D 92.857 70 5 0 1576 1645 525208604 525208535 1.220000e-17 102.0
48 TraesCS5A01G364300 chr3B 84.504 413 43 8 1777 2187 778613750 778613357 8.340000e-104 388.0
49 TraesCS5A01G364300 chr3B 83.014 418 58 3 6455 6859 726991887 726992304 3.910000e-97 366.0
50 TraesCS5A01G364300 chr3B 88.119 202 11 7 2263 2459 778613223 778613030 1.930000e-55 228.0
51 TraesCS5A01G364300 chr3B 92.982 57 4 0 2991 3047 778613271 778613215 4.410000e-12 84.2
52 TraesCS5A01G364300 chr4A 80.272 441 73 9 6434 6861 252715951 252716390 3.090000e-83 320.0
53 TraesCS5A01G364300 chr4B 89.950 199 7 7 2263 2456 630238246 630238436 1.910000e-60 244.0
54 TraesCS5A01G364300 chr4B 90.000 60 6 0 2988 3047 630238195 630238254 2.050000e-10 78.7
55 TraesCS5A01G364300 chr1D 93.671 79 4 1 1861 1938 470413476 470413554 4.350000e-22 117.0
56 TraesCS5A01G364300 chr1D 92.857 70 5 0 1576 1645 187584809 187584878 1.220000e-17 102.0
57 TraesCS5A01G364300 chr1D 92.857 70 5 0 1576 1645 392821902 392821833 1.220000e-17 102.0
58 TraesCS5A01G364300 chr1D 92.857 70 5 0 1576 1645 470413218 470413287 1.220000e-17 102.0
59 TraesCS5A01G364300 chrUn 92.857 70 5 0 1576 1645 377157925 377157994 1.220000e-17 102.0


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 TraesCS5A01G364300 chr5A 564594471 564601331 6860 True 12670.000000 12670 100.000000 1 6861 1 chr5A.!!$R4 6860
1 TraesCS5A01G364300 chr5D 87177906 87179408 1502 False 1938.000000 1938 89.953000 3360 4861 1 chr5D.!!$F1 1501
2 TraesCS5A01G364300 chr5D 446755226 446760233 5007 True 1490.750000 2876 91.030000 4 6861 4 chr5D.!!$R2 6857
3 TraesCS5A01G364300 chr5D 446572473 446574040 1567 True 463.000000 813 79.370500 4892 6401 2 chr5D.!!$R1 1509
4 TraesCS5A01G364300 chr1A 104245623 104247141 1518 False 2634.000000 2634 97.961000 3363 4881 1 chr1A.!!$F1 1518
5 TraesCS5A01G364300 chr6A 391043908 391045431 1523 False 2580.000000 2580 97.188000 3354 4881 1 chr6A.!!$F2 1527
6 TraesCS5A01G364300 chr2A 603536551 603538068 1517 False 2556.000000 2556 97.041000 3362 4881 1 chr2A.!!$F1 1519
7 TraesCS5A01G364300 chr5B 563522478 563523998 1520 True 2023.000000 2023 90.670000 3361 4881 1 chr5B.!!$R2 1520
8 TraesCS5A01G364300 chr5B 544905214 544910568 5354 True 1579.500000 2106 92.277250 4 6861 4 chr5B.!!$R4 6857
9 TraesCS5A01G364300 chr5B 544765881 544767407 1526 True 455.000000 784 79.999500 4945 6401 2 chr5B.!!$R3 1456
10 TraesCS5A01G364300 chr4D 12291335 12292800 1465 True 1986.000000 1986 91.132000 3397 4861 1 chr4D.!!$R1 1464
11 TraesCS5A01G364300 chr1B 284378353 284379871 1518 False 1978.000000 1978 90.191000 3365 4881 1 chr1B.!!$F1 1516
12 TraesCS5A01G364300 chr6D 50570932 50572431 1499 True 1954.000000 1954 90.200000 3363 4861 1 chr6D.!!$R2 1498
13 TraesCS5A01G364300 chr7A 69626358 69627871 1513 True 1953.000000 1953 89.960000 3369 4881 1 chr7A.!!$R1 1512
14 TraesCS5A01G364300 chr2B 103485845 103486562 717 False 327.500000 411 87.693500 1777 2456 2 chr2B.!!$F1 679
15 TraesCS5A01G364300 chr2B 472575851 472576569 718 False 230.400000 374 88.129667 1777 3047 3 chr2B.!!$F2 1270
16 TraesCS5A01G364300 chr6B 655217472 655218193 721 True 241.400000 401 89.038333 1777 3047 3 chr6B.!!$R1 1270
17 TraesCS5A01G364300 chr6B 380971824 380972542 718 False 234.066667 385 88.291333 1777 3047 3 chr6B.!!$F1 1270
18 TraesCS5A01G364300 chr3B 778613030 778613750 720 True 233.400000 388 88.535000 1777 3047 3 chr3B.!!$R1 1270

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
862 872 1.352687 GAGGGAAGGAAGGAAGCAACT 59.647 52.381 0.00 0.0 0.00 3.16 F
1466 1497 1.148273 TTGGGGTGTGTGCTGAGAC 59.852 57.895 0.00 0.0 0.00 3.36 F
2547 2709 0.332632 TATGAGCTGCTGCCCCTTTT 59.667 50.000 7.01 0.0 40.80 2.27 F
3603 3830 0.608130 CCTCGTCCTTGATGGTGTCA 59.392 55.000 0.00 0.0 37.07 3.58 F
4512 4740 0.465097 GATACCGAGACCACCGAGGA 60.465 60.000 0.00 0.0 41.22 3.71 F
5121 5353 1.068055 ACTTACAGGAGTTGCGTACCG 60.068 52.381 0.00 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1728 1802 1.039856 ACCAAACATGGCTGGAACAC 58.960 50.000 19.20 0.00 36.49 3.32 R
2611 2773 1.806542 CTTGCACAGCGGTAACTGAAT 59.193 47.619 0.00 0.00 40.25 2.57 R
4512 4740 0.033504 CGTGTATGCCGGCCTATCTT 59.966 55.000 26.77 4.09 0.00 2.40 R
4974 5203 0.948678 GCAAACGGTAGCCAGTTTCA 59.051 50.000 0.00 0.00 38.37 2.69 R
5743 6041 0.547471 TTCCAGCCATGAGGACCTGA 60.547 55.000 0.00 0.00 36.89 3.86 R
6362 6801 0.880278 GTTGTCTCTTGCGAGTGCCA 60.880 55.000 0.00 0.00 41.78 4.92 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
862 872 1.352687 GAGGGAAGGAAGGAAGCAACT 59.647 52.381 0.00 0.00 0.00 3.16
863 873 2.572104 GAGGGAAGGAAGGAAGCAACTA 59.428 50.000 0.00 0.00 0.00 2.24
864 874 2.573915 AGGGAAGGAAGGAAGCAACTAG 59.426 50.000 0.00 0.00 0.00 2.57
995 1012 4.883354 GGAGGCATCTTGGGGGCG 62.883 72.222 0.00 0.00 34.32 6.13
1188 1205 2.732619 GGGCAACTCCTCCTACCGG 61.733 68.421 0.00 0.00 34.39 5.28
1266 1286 4.179599 CCTCCCCTCCCCTCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
1288 1308 3.234630 TTCCAGCCGGTTCTCCACG 62.235 63.158 1.90 0.00 0.00 4.94
1308 1328 2.704719 GGATTACCCACCCTGACCA 58.295 57.895 0.00 0.00 34.14 4.02
1344 1366 2.671896 AATGGATCTTGGGAGGATGC 57.328 50.000 0.00 0.00 33.20 3.91
1415 1442 4.865925 TGATTCCGTTGGTTTAGATGTACG 59.134 41.667 0.00 0.00 0.00 3.67
1419 1446 4.699735 TCCGTTGGTTTAGATGTACGTAGA 59.300 41.667 0.00 0.00 0.00 2.59
1452 1479 2.572290 GATCCGAGTTATTGGGTTGGG 58.428 52.381 0.00 0.00 0.00 4.12
1466 1497 1.148273 TTGGGGTGTGTGCTGAGAC 59.852 57.895 0.00 0.00 0.00 3.36
1522 1580 4.460731 AGCCCTTTTTGCTCTGAAGTTATC 59.539 41.667 0.00 0.00 32.41 1.75
1574 1633 2.699954 ACGTAGGCATTTTGAGTCAGG 58.300 47.619 0.00 0.00 0.00 3.86
1624 1692 5.070313 AGTGCCCACATCAATTTGTTAGTTT 59.930 36.000 0.82 0.00 0.00 2.66
1670 1744 5.407084 GCAAACTTGTGGTGTTGTTAGTTTT 59.593 36.000 0.00 0.00 34.59 2.43
1671 1745 6.073494 GCAAACTTGTGGTGTTGTTAGTTTTT 60.073 34.615 0.00 0.00 34.59 1.94
1707 1781 2.744202 CAAACTCTGCTGCCTACGAATT 59.256 45.455 0.00 0.00 0.00 2.17
1708 1782 3.887621 AACTCTGCTGCCTACGAATTA 57.112 42.857 0.00 0.00 0.00 1.40
1709 1783 4.408182 AACTCTGCTGCCTACGAATTAT 57.592 40.909 0.00 0.00 0.00 1.28
1712 1786 3.982475 TCTGCTGCCTACGAATTATCTG 58.018 45.455 0.00 0.00 0.00 2.90
1717 1791 4.390297 GCTGCCTACGAATTATCTGAATCC 59.610 45.833 0.00 0.00 0.00 3.01
1718 1792 4.556233 TGCCTACGAATTATCTGAATCCG 58.444 43.478 0.00 0.00 0.00 4.18
1728 1802 9.066939 CGAATTATCTGAATCCGTTATACTCTG 57.933 37.037 0.00 0.00 0.00 3.35
1740 1816 4.680708 CGTTATACTCTGTGTTCCAGCCAT 60.681 45.833 0.00 0.00 41.25 4.40
1761 1843 1.615392 GTTTGGTTGGCATGAAGAGCT 59.385 47.619 0.00 0.00 0.00 4.09
1840 1938 1.644786 GAGGGCATTTTGTCGGGTCG 61.645 60.000 0.00 0.00 0.00 4.79
1959 2057 4.142513 GGATCAGCAAATGACCTTGAAGTC 60.143 45.833 0.00 0.00 41.91 3.01
1975 2073 5.405935 TGAAGTCTGCTATCTTTGTGCTA 57.594 39.130 0.00 0.00 0.00 3.49
1976 2074 5.982356 TGAAGTCTGCTATCTTTGTGCTAT 58.018 37.500 0.00 0.00 0.00 2.97
1977 2075 7.112452 TGAAGTCTGCTATCTTTGTGCTATA 57.888 36.000 0.00 0.00 0.00 1.31
1978 2076 6.980978 TGAAGTCTGCTATCTTTGTGCTATAC 59.019 38.462 0.00 0.00 0.00 1.47
1979 2077 5.524284 AGTCTGCTATCTTTGTGCTATACG 58.476 41.667 0.00 0.00 0.00 3.06
1980 2078 4.681942 GTCTGCTATCTTTGTGCTATACGG 59.318 45.833 0.00 0.00 0.00 4.02
1981 2079 4.583073 TCTGCTATCTTTGTGCTATACGGA 59.417 41.667 0.00 0.00 0.00 4.69
1995 2093 2.667473 TACGGAGTAGAAGCCAAAGC 57.333 50.000 0.00 0.00 45.11 3.51
2033 2131 5.363005 TGGAAACTGACCCTTCTATAGCTAC 59.637 44.000 0.00 0.00 0.00 3.58
2163 2266 4.677673 ATTGCCCAAATTTATCTGCCTC 57.322 40.909 0.00 0.00 0.00 4.70
2169 2272 4.530875 CCAAATTTATCTGCCTCTGGTCT 58.469 43.478 0.00 0.00 0.00 3.85
2201 2326 9.871238 TGACTAAATAATTTGAGACAGAGTACC 57.129 33.333 0.00 0.00 0.00 3.34
2224 2359 4.517285 TGGCTAGTTCATTGGTCTGAATC 58.483 43.478 0.00 0.00 37.47 2.52
2226 2361 4.384647 GGCTAGTTCATTGGTCTGAATCCT 60.385 45.833 0.00 0.00 37.47 3.24
2231 2366 6.962182 AGTTCATTGGTCTGAATCCTCATTA 58.038 36.000 0.00 0.00 37.47 1.90
2244 2379 6.443849 TGAATCCTCATTACCAAACTCCTAGT 59.556 38.462 0.00 0.00 0.00 2.57
2264 2406 6.656693 CCTAGTTTCTGTCCACTCAATTGATT 59.343 38.462 8.96 0.00 0.00 2.57
2270 2412 3.996363 TGTCCACTCAATTGATTGACTCG 59.004 43.478 23.26 9.60 41.51 4.18
2271 2413 3.372206 GTCCACTCAATTGATTGACTCGG 59.628 47.826 23.26 9.42 41.51 4.63
2272 2414 3.260632 TCCACTCAATTGATTGACTCGGA 59.739 43.478 23.26 11.35 41.51 4.55
2273 2415 4.080919 TCCACTCAATTGATTGACTCGGAT 60.081 41.667 23.26 0.00 41.51 4.18
2399 2561 2.265589 AACAGTACCGTTTTCCTGGG 57.734 50.000 0.00 0.00 0.00 4.45
2492 2654 6.422776 TTTTCTAGAAAATAGCTTCCGCAG 57.577 37.500 23.65 0.00 35.56 5.18
2506 2668 3.795623 TCCGCAGTTACAGAGTATTCC 57.204 47.619 0.00 0.00 0.00 3.01
2547 2709 0.332632 TATGAGCTGCTGCCCCTTTT 59.667 50.000 7.01 0.00 40.80 2.27
2576 2738 6.176975 TGCCTGACAAACTTAATGTAATCG 57.823 37.500 0.00 0.00 0.00 3.34
2594 2756 7.970384 TGTAATCGAACACTTGATAAATGTCC 58.030 34.615 0.00 0.00 0.00 4.02
2611 2773 0.685785 TCCAGCTTGGGTGCAAAACA 60.686 50.000 0.00 0.00 38.32 2.83
2621 2783 3.068873 TGGGTGCAAAACATTCAGTTACC 59.931 43.478 0.00 0.00 40.26 2.85
2668 2830 8.615211 TCAAATACTGAAATGACATGTGCTATC 58.385 33.333 1.15 0.00 0.00 2.08
2669 2831 8.618677 CAAATACTGAAATGACATGTGCTATCT 58.381 33.333 1.15 0.00 0.00 1.98
2701 2863 2.586648 AGCCAAAAGTTCCTACTGGG 57.413 50.000 0.00 0.00 34.01 4.45
2704 2866 3.076032 AGCCAAAAGTTCCTACTGGGATT 59.924 43.478 0.00 0.00 44.66 3.01
2719 2881 4.467438 ACTGGGATTGGAAAATGACCATTC 59.533 41.667 0.00 0.00 37.26 2.67
2737 2899 9.588096 TGACCATTCTATAGCTAGAAATACTGA 57.412 33.333 3.10 0.00 44.91 3.41
2749 2911 7.984617 AGCTAGAAATACTGAATCTGTTCCTTC 59.015 37.037 0.00 0.51 33.26 3.46
2770 2932 8.585881 TCCTTCCATAATCTTATAGTAGTGTGC 58.414 37.037 0.00 0.00 0.00 4.57
2772 2934 6.920817 TCCATAATCTTATAGTAGTGTGCGG 58.079 40.000 0.00 0.00 0.00 5.69
2775 2937 7.702772 CCATAATCTTATAGTAGTGTGCGGATC 59.297 40.741 0.00 0.00 0.00 3.36
2776 2938 4.744136 TCTTATAGTAGTGTGCGGATCG 57.256 45.455 0.00 0.00 0.00 3.69
2872 3034 4.091800 CAGCCTTTTGTTGTTGTTTGACTG 59.908 41.667 0.00 0.00 0.00 3.51
2898 3060 4.593956 ACAAGGAATTGGTCTTCCATCTC 58.406 43.478 5.70 0.00 46.02 2.75
3057 3265 4.345859 ACATTTCTTGGTCAGACGGTTA 57.654 40.909 0.00 0.00 0.00 2.85
3081 3293 4.568152 TTGAACTTAGCTTTGGACTTGC 57.432 40.909 0.00 0.00 0.00 4.01
3104 3323 6.206048 TGCAGATGCTGGATAATATTCAGTTG 59.794 38.462 10.06 5.60 42.66 3.16
3168 3387 6.957020 ACCATTTTTCTGGACCATGGTTTATA 59.043 34.615 20.85 2.66 44.32 0.98
3197 3420 6.966534 TCTGATGATCACATAGCTTGACTA 57.033 37.500 0.00 0.00 36.82 2.59
3200 3423 7.450944 TCTGATGATCACATAGCTTGACTAGAT 59.549 37.037 0.00 0.00 36.82 1.98
3229 3454 8.430801 TTCTAGAAGATAGCTTTTCTGCAATC 57.569 34.615 14.52 0.53 35.42 2.67
3242 3467 3.264947 TCTGCAATCACAGAGAATTCCG 58.735 45.455 0.65 0.00 41.72 4.30
3250 3475 5.160607 TCACAGAGAATTCCGTTACCAAT 57.839 39.130 0.65 0.00 0.00 3.16
3331 3557 5.163258 TGGGTGCAAAACTTCAAATTACCAT 60.163 36.000 0.00 0.00 0.00 3.55
3340 3566 7.856145 AACTTCAAATTACCATTTGTGCAAA 57.144 28.000 7.40 0.00 46.61 3.68
3603 3830 0.608130 CCTCGTCCTTGATGGTGTCA 59.392 55.000 0.00 0.00 37.07 3.58
4418 4646 1.296715 GACGTGAAGGTGGCTCCAT 59.703 57.895 8.51 0.00 39.02 3.41
4512 4740 0.465097 GATACCGAGACCACCGAGGA 60.465 60.000 0.00 0.00 41.22 3.71
5064 5296 4.706962 ACAAAGGATAGAAAGATGTTGGCC 59.293 41.667 0.00 0.00 0.00 5.36
5115 5347 7.611213 ACATTATGTTACTTACAGGAGTTGC 57.389 36.000 0.00 0.00 40.83 4.17
5121 5353 1.068055 ACTTACAGGAGTTGCGTACCG 60.068 52.381 0.00 0.00 0.00 4.02
5221 5460 7.312657 AGTATAAAGTTGCATGATGTGTCAG 57.687 36.000 0.00 0.00 37.87 3.51
5271 5512 8.035394 TGTTGCATTTGGTTCTTACTTACAAAA 58.965 29.630 0.00 0.00 35.06 2.44
5380 5665 2.783510 ACCTTCTCTTCAAAAGTGGGGA 59.216 45.455 0.00 0.00 0.00 4.81
5396 5681 6.678568 AGTGGGGAATTATCTCAGATGTAG 57.321 41.667 0.00 0.00 0.00 2.74
5437 5722 5.936956 AGATTTTGTTTTCAGTTTGTGGCAA 59.063 32.000 0.00 0.00 0.00 4.52
5461 5746 2.354003 GGTGTCTGGGCCATGAAATTTG 60.354 50.000 6.72 0.00 0.00 2.32
5472 5757 5.922544 GGCCATGAAATTTGTACTGATATGC 59.077 40.000 0.00 0.00 0.00 3.14
5553 5843 3.243724 AGGCTGCTTATCTACCCTTAGG 58.756 50.000 0.00 0.00 40.04 2.69
5686 5983 4.314096 ACGTCTTGACGTTGTCCG 57.686 55.556 21.04 0.00 44.63 4.79
5703 6001 2.470286 GAGGCGAGTTTTGCGTCG 59.530 61.111 0.00 0.00 38.59 5.12
5743 6041 4.347583 TGAATCCCAAAGCAATGTCCTTTT 59.652 37.500 0.00 0.00 30.52 2.27
5836 6135 4.980339 AATGCAAGGGGTTTCAAGAATT 57.020 36.364 0.00 0.00 0.00 2.17
5920 6219 1.067516 GATCCGTCATGCCATTTTGGG 59.932 52.381 0.00 0.00 38.19 4.12
6125 6429 1.005924 AGCACCGGAATTTCCCTGATT 59.994 47.619 9.46 0.00 31.13 2.57
6205 6509 6.774656 AGTCTTGAATTTTCTTCATCACACCT 59.225 34.615 0.00 0.00 0.00 4.00
6299 6732 2.969821 AACTCTTACCAATGGGCACA 57.030 45.000 3.55 0.00 37.90 4.57
6336 6775 8.478066 GGGATTTTTATTTAGAAGAACAGCCAT 58.522 33.333 0.00 0.00 0.00 4.40
6362 6801 6.042781 TGGCCTACTAAATGAACCGATAATCT 59.957 38.462 3.32 0.00 0.00 2.40
6388 6827 1.571460 GCAAGAGACAACGGCACTG 59.429 57.895 0.00 0.00 0.00 3.66
6408 6847 4.080919 ACTGCATAAGTAATCTGGCACTCA 60.081 41.667 0.00 0.00 37.36 3.41
6447 6922 1.732732 CGGAGCGACCTAGTGAAACAG 60.733 57.143 0.00 0.00 36.21 3.16
6462 6941 9.261180 CTAGTGAAACAGACTTTGAAGTTGATA 57.739 33.333 0.00 0.00 41.43 2.15
6497 6976 7.437713 TCTTGCTATCCCTTTATCTTCTTCA 57.562 36.000 0.00 0.00 0.00 3.02
6549 7028 4.823442 TGACTCGTACAACCACTTTCTCTA 59.177 41.667 0.00 0.00 0.00 2.43
6552 7031 5.068234 TCGTACAACCACTTTCTCTATGG 57.932 43.478 0.00 0.00 39.57 2.74
6584 7063 2.431954 ATGCTGAATGGGAAGGACAG 57.568 50.000 0.00 0.00 0.00 3.51
6672 7391 1.333177 TGTGCCGGCAAAGGTTAAAT 58.667 45.000 34.66 0.00 0.00 1.40
6673 7392 1.689273 TGTGCCGGCAAAGGTTAAATT 59.311 42.857 34.66 0.00 0.00 1.82
6699 7418 8.887036 TTTTCTTTCGAGAGCTATGCATAATA 57.113 30.769 8.00 0.00 0.00 0.98
6710 7429 7.768120 AGAGCTATGCATAATACTATTCCTTGC 59.232 37.037 8.00 2.97 0.00 4.01
6758 7477 0.606401 AAGTGAGTGGACAATGCCCG 60.606 55.000 0.00 0.00 0.00 6.13
6776 7495 1.678970 GGTGTGTGGGATTGGAGCC 60.679 63.158 0.00 0.00 0.00 4.70
6838 7557 1.888512 GCATGTTTGGAAAGCTCTGGA 59.111 47.619 0.00 0.00 0.00 3.86
6846 7565 5.441718 TTGGAAAGCTCTGGATATTCACT 57.558 39.130 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 6.912591 CACAGAATCAGGTTGTTTGTAACTTC 59.087 38.462 0.00 0.00 0.00 3.01
48 49 2.126734 GTGCACATTGCCACGAGC 60.127 61.111 13.17 0.00 44.23 5.03
87 88 1.532868 CTGTTGCCGAGGAAAGTGAAG 59.467 52.381 0.00 0.00 0.00 3.02
288 291 1.001641 GGCACTCCCACATTGCTCT 60.002 57.895 0.00 0.00 36.46 4.09
844 854 2.306219 ACTAGTTGCTTCCTTCCTTCCC 59.694 50.000 0.00 0.00 0.00 3.97
862 872 5.104444 AGCTTCTGTGCTCCTACTACTACTA 60.104 44.000 0.00 0.00 39.34 1.82
863 873 3.949113 GCTTCTGTGCTCCTACTACTACT 59.051 47.826 0.00 0.00 0.00 2.57
864 874 3.949113 AGCTTCTGTGCTCCTACTACTAC 59.051 47.826 0.00 0.00 39.34 2.73
1258 1275 2.069430 GCTGGAAGGAGGGAGAGGG 61.069 68.421 0.00 0.00 0.00 4.30
1266 1286 1.219393 GAGAACCGGCTGGAAGGAG 59.781 63.158 21.41 0.00 39.21 3.69
1303 1323 8.306038 CCATTTTGTTTTCTCTTCATATGGTCA 58.694 33.333 2.13 0.00 0.00 4.02
1304 1324 8.522830 TCCATTTTGTTTTCTCTTCATATGGTC 58.477 33.333 2.13 0.00 0.00 4.02
1305 1325 8.421249 TCCATTTTGTTTTCTCTTCATATGGT 57.579 30.769 2.13 0.00 0.00 3.55
1344 1366 4.798263 GCCCCAGCATAATCAATCATGTTG 60.798 45.833 0.00 0.00 39.53 3.33
1452 1479 0.179045 ACCTTGTCTCAGCACACACC 60.179 55.000 0.00 0.00 0.00 4.16
1466 1497 2.821969 CTGTTCCAAGATCCCAACCTTG 59.178 50.000 0.00 0.00 39.43 3.61
1513 1571 8.463930 AAATTGTGACCTTTCTGATAACTTCA 57.536 30.769 0.00 0.00 0.00 3.02
1517 1575 8.451748 GGACTAAATTGTGACCTTTCTGATAAC 58.548 37.037 0.00 0.00 0.00 1.89
1522 1580 4.755123 ACGGACTAAATTGTGACCTTTCTG 59.245 41.667 0.00 0.00 0.00 3.02
1534 1592 4.483476 GTTGCTCACAACGGACTAAATT 57.517 40.909 0.00 0.00 46.20 1.82
1549 1607 2.484264 ACTCAAAATGCCTACGTTGCTC 59.516 45.455 10.56 0.00 0.00 4.26
1574 1633 2.660189 TCTGGTTCGGACGGTAAATC 57.340 50.000 0.00 0.00 0.00 2.17
1624 1692 4.024387 GCGAAACTGTCAAACTGGAACATA 60.024 41.667 0.00 0.00 38.20 2.29
1702 1776 9.066939 CAGAGTATAACGGATTCAGATAATTCG 57.933 37.037 0.00 0.00 34.90 3.34
1707 1781 7.818997 ACACAGAGTATAACGGATTCAGATA 57.181 36.000 0.00 0.00 0.00 1.98
1708 1782 6.716934 ACACAGAGTATAACGGATTCAGAT 57.283 37.500 0.00 0.00 0.00 2.90
1709 1783 6.405508 GGAACACAGAGTATAACGGATTCAGA 60.406 42.308 0.00 0.00 0.00 3.27
1712 1786 5.657474 TGGAACACAGAGTATAACGGATTC 58.343 41.667 0.00 0.00 0.00 2.52
1728 1802 1.039856 ACCAAACATGGCTGGAACAC 58.960 50.000 19.20 0.00 36.49 3.32
1740 1816 1.340889 GCTCTTCATGCCAACCAAACA 59.659 47.619 0.00 0.00 0.00 2.83
1761 1843 7.944000 TGCAGCCTTTATGATAATTATCTGGAA 59.056 33.333 22.77 12.84 33.88 3.53
1798 1893 7.311092 TCCTTCTCCAAAACACACTTCTATA 57.689 36.000 0.00 0.00 0.00 1.31
1845 1943 3.581024 TGGCACAAAAGATCTGCATTC 57.419 42.857 0.00 0.00 31.92 2.67
1917 2015 4.235079 TCCACAACATAAAGATGGGAGG 57.765 45.455 0.00 0.00 37.39 4.30
1959 2057 4.871513 TCCGTATAGCACAAAGATAGCAG 58.128 43.478 0.00 0.00 0.00 4.24
1975 2073 3.180891 GCTTTGGCTTCTACTCCGTAT 57.819 47.619 0.00 0.00 35.22 3.06
1976 2074 2.667473 GCTTTGGCTTCTACTCCGTA 57.333 50.000 0.00 0.00 35.22 4.02
1977 2075 3.534721 GCTTTGGCTTCTACTCCGT 57.465 52.632 0.00 0.00 35.22 4.69
2015 2113 4.342378 TGCTTGTAGCTATAGAAGGGTCAG 59.658 45.833 3.21 0.00 42.97 3.51
2110 2213 8.776376 AACGAATTGCTAATTCAAATGGAAAT 57.224 26.923 16.55 0.00 45.94 2.17
2133 2236 8.829612 CAGATAAATTTGGGCAATTATGGAAAC 58.170 33.333 0.00 0.00 33.60 2.78
2201 2326 3.616956 TCAGACCAATGAACTAGCCAG 57.383 47.619 0.00 0.00 0.00 4.85
2205 2330 5.982356 TGAGGATTCAGACCAATGAACTAG 58.018 41.667 0.00 0.00 41.76 2.57
2244 2379 6.064060 AGTCAATCAATTGAGTGGACAGAAA 58.936 36.000 29.58 10.80 46.44 2.52
2264 2406 4.788679 TCTCAGGTACATAATCCGAGTCA 58.211 43.478 0.00 0.00 0.00 3.41
2270 2412 5.128827 TGACCACTTCTCAGGTACATAATCC 59.871 44.000 0.00 0.00 38.50 3.01
2271 2413 6.096987 TCTGACCACTTCTCAGGTACATAATC 59.903 42.308 0.00 0.00 38.50 1.75
2272 2414 5.958380 TCTGACCACTTCTCAGGTACATAAT 59.042 40.000 0.00 0.00 38.50 1.28
2273 2415 5.185249 GTCTGACCACTTCTCAGGTACATAA 59.815 44.000 0.00 0.00 38.50 1.90
2366 2528 5.645929 ACGGTACTGTTATGCAATCATCAAA 59.354 36.000 0.04 0.00 34.22 2.69
2399 2561 3.305335 CCTTATGCCGAATAAACCATGGC 60.305 47.826 13.04 0.00 45.91 4.40
2492 2654 4.811557 GCTGGTGATGGAATACTCTGTAAC 59.188 45.833 0.00 0.00 0.00 2.50
2506 2668 2.225019 GTCAACAAGTCTGCTGGTGATG 59.775 50.000 0.00 0.00 0.00 3.07
2573 2735 5.065218 GCTGGACATTTATCAAGTGTTCGAT 59.935 40.000 0.00 0.00 0.00 3.59
2576 2738 5.886960 AGCTGGACATTTATCAAGTGTTC 57.113 39.130 0.00 0.00 0.00 3.18
2594 2756 2.137523 GAATGTTTTGCACCCAAGCTG 58.862 47.619 0.00 0.00 34.99 4.24
2611 2773 1.806542 CTTGCACAGCGGTAACTGAAT 59.193 47.619 0.00 0.00 40.25 2.57
2621 2783 2.065993 AGTGTAGTACTTGCACAGCG 57.934 50.000 23.33 0.00 35.67 5.18
2669 2831 7.418483 AGGAACTTTTGGCTTTTATAGCACAAA 60.418 33.333 0.00 0.00 45.78 2.83
2696 2858 3.541242 TGGTCATTTTCCAATCCCAGT 57.459 42.857 0.00 0.00 31.50 4.00
2701 2863 8.401490 AGCTATAGAATGGTCATTTTCCAATC 57.599 34.615 3.21 0.00 38.52 2.67
2704 2866 8.262601 TCTAGCTATAGAATGGTCATTTTCCA 57.737 34.615 3.21 0.00 35.03 3.53
2732 2894 8.324191 AGATTATGGAAGGAACAGATTCAGTA 57.676 34.615 0.00 0.00 36.46 2.74
2749 2911 6.920817 TCCGCACACTACTATAAGATTATGG 58.079 40.000 0.00 0.00 0.00 2.74
2770 2932 7.861372 ACACTATTAATGTTTAGAGACGATCCG 59.139 37.037 0.00 0.00 0.00 4.18
2800 2962 9.796180 AGGAGTCACTAATATAGATAGAAACGT 57.204 33.333 0.00 0.00 0.00 3.99
2837 2999 3.454082 ACAAAAGGCTGACAATTTTGGGA 59.546 39.130 17.61 0.00 44.39 4.37
2872 3034 4.972514 GGAAGACCAATTCCTTGTCATC 57.027 45.455 0.00 0.00 44.57 2.92
2898 3060 5.704888 AGTTCTTTCATGTACTCTGTCTCG 58.295 41.667 0.00 0.00 0.00 4.04
3057 3265 6.434028 TGCAAGTCCAAAGCTAAGTTCAATAT 59.566 34.615 0.00 0.00 0.00 1.28
3081 3293 7.974482 TCAACTGAATATTATCCAGCATCTG 57.026 36.000 3.23 0.00 0.00 2.90
3168 3387 4.040584 AGCTATGTGATCATCAGATGCTGT 59.959 41.667 16.02 0.00 35.22 4.40
3229 3454 5.006746 GCTATTGGTAACGGAATTCTCTGTG 59.993 44.000 5.23 0.00 40.49 3.66
3242 3467 6.765989 TCATAGTCAACATGGCTATTGGTAAC 59.234 38.462 1.87 0.00 42.13 2.50
3250 3475 3.432186 GCAGGTCATAGTCAACATGGCTA 60.432 47.826 0.00 0.00 39.11 3.93
3340 3566 6.709018 AAAAAGTATTTGGTAGTGCAGTGT 57.291 33.333 3.69 0.00 39.02 3.55
3603 3830 1.759445 CCATCGATCACCTTCACCTCT 59.241 52.381 0.00 0.00 0.00 3.69
4150 4378 2.046411 CGGCCATGGTGCAGTACA 60.046 61.111 14.67 0.00 0.00 2.90
4178 4406 1.110518 TACAGGATATCCGCGGTGCA 61.111 55.000 27.15 11.93 42.08 4.57
4243 4471 3.901797 CTCGTCCCAAGGCGCCTTT 62.902 63.158 38.60 21.25 33.42 3.11
4301 4529 1.677637 GGACCGACCACTGGATCTCC 61.678 65.000 0.71 0.00 38.79 3.71
4402 4630 1.746615 CCATGGAGCCACCTTCACG 60.747 63.158 5.56 0.00 39.86 4.35
4418 4646 2.758327 ACCGATGCTACTCGCCCA 60.758 61.111 0.00 0.00 37.33 5.36
4512 4740 0.033504 CGTGTATGCCGGCCTATCTT 59.966 55.000 26.77 4.09 0.00 2.40
4762 4990 1.808945 CCTCTTTGACGAGCTTGCAAT 59.191 47.619 0.00 0.00 0.00 3.56
4974 5203 0.948678 GCAAACGGTAGCCAGTTTCA 59.051 50.000 0.00 0.00 38.37 2.69
5064 5296 1.079819 AGTTGGCGTGGATGTCTCG 60.080 57.895 0.00 0.00 0.00 4.04
5121 5353 6.883744 AGATAGTTTCTCTTCATCCTCCAAC 58.116 40.000 0.00 0.00 0.00 3.77
5217 5456 2.097825 AGAAATTGATGGCAGGCTGAC 58.902 47.619 20.86 18.07 0.00 3.51
5221 5460 6.579666 TGATATTAGAAATTGATGGCAGGC 57.420 37.500 0.00 0.00 0.00 4.85
5271 5512 6.993902 AGGAAACAAGAAAACATCATGCAATT 59.006 30.769 0.00 0.00 29.77 2.32
5339 5600 7.706607 AGAAGGTTACAAAAGATTCTTTGCAAC 59.293 33.333 12.27 14.35 39.94 4.17
5342 5603 7.652727 AGAGAAGGTTACAAAAGATTCTTTGC 58.347 34.615 12.27 2.04 39.46 3.68
5360 5639 3.508845 TCCCCACTTTTGAAGAGAAGG 57.491 47.619 0.00 0.00 0.00 3.46
5374 5659 5.799213 CCTACATCTGAGATAATTCCCCAC 58.201 45.833 0.00 0.00 0.00 4.61
5380 5665 7.372260 ACTCTTGCCTACATCTGAGATAATT 57.628 36.000 0.00 0.00 0.00 1.40
5396 5681 6.480320 ACAAAATCTATGTATCGACTCTTGCC 59.520 38.462 0.00 0.00 0.00 4.52
5437 5722 1.508667 TTCATGGCCCAGACACCCAT 61.509 55.000 0.00 0.00 39.86 4.00
5472 5757 4.701956 AAAGTAATTGGGATTCGCACTG 57.298 40.909 2.45 0.00 0.00 3.66
5476 5761 5.949735 TCTTCAAAAGTAATTGGGATTCGC 58.050 37.500 0.00 0.00 0.00 4.70
5477 5762 8.243426 TCAATCTTCAAAAGTAATTGGGATTCG 58.757 33.333 0.00 0.00 34.39 3.34
5586 5881 7.757097 AGTCGATTAGTGACAATCATGTAAC 57.243 36.000 0.00 0.00 40.74 2.50
5686 5983 1.828331 AACGACGCAAAACTCGCCTC 61.828 55.000 0.00 0.00 32.98 4.70
5703 6001 5.278022 GGGATTCAGAGTCACAGACAAAAAC 60.278 44.000 0.00 0.00 34.60 2.43
5743 6041 0.547471 TTCCAGCCATGAGGACCTGA 60.547 55.000 0.00 0.00 36.89 3.86
5836 6135 0.896940 ACCTAGGAGCGTTTGTCGGA 60.897 55.000 17.98 0.00 40.26 4.55
5920 6219 1.337167 GCACAGGGGAAATCAGCAAAC 60.337 52.381 0.00 0.00 0.00 2.93
5988 6288 3.071023 CCACTGTGGTTTTCTAGTCCTGA 59.929 47.826 18.76 0.00 31.35 3.86
6082 6386 6.089954 GCTGTGATAAAGAAAAAGGCACAATC 59.910 38.462 0.00 0.00 34.80 2.67
6125 6429 7.716123 AGCATGAAAATTTCAAGAATTCAACCA 59.284 29.630 12.75 0.00 43.95 3.67
6336 6775 3.985019 TCGGTTCATTTAGTAGGCCAA 57.015 42.857 5.01 0.00 0.00 4.52
6362 6801 0.880278 GTTGTCTCTTGCGAGTGCCA 60.880 55.000 0.00 0.00 41.78 4.92
6388 6827 7.496529 TTTATGAGTGCCAGATTACTTATGC 57.503 36.000 0.00 0.00 0.00 3.14
6408 6847 6.451393 GCTCCGTAGACTTCTCATCATTTAT 58.549 40.000 0.00 0.00 0.00 1.40
6462 6941 7.968014 AAGGGATAGCAAGAATTCTTTGAAT 57.032 32.000 18.16 11.05 33.11 2.57
6497 6976 1.269936 GCAACAAAGTCTTGCATGCCT 60.270 47.619 16.68 1.12 43.04 4.75
6584 7063 5.655090 ACCTATGTTTAACCTTTGGCCATAC 59.345 40.000 6.09 0.00 0.00 2.39
6673 7392 7.609760 TTATGCATAGCTCTCGAAAGAAAAA 57.390 32.000 6.50 0.00 41.32 1.94
6699 7418 1.211212 GGTAACCCGGCAAGGAATAGT 59.789 52.381 0.00 0.00 45.00 2.12
6725 7444 3.440173 CACTCACTTTGATATGGCGGTTT 59.560 43.478 0.00 0.00 0.00 3.27
6758 7477 1.678970 GGCTCCAATCCCACACACC 60.679 63.158 0.00 0.00 0.00 4.16
6776 7495 3.252974 AGGAGGTGCTTAATGTCTTCG 57.747 47.619 0.00 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.