Multiple sequence alignment - TraesCS1A01G167400

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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 TraesCS1A01G167400 chr1A 100.000 6602 0 0 1 6602 300106108 300112709 0.000000e+00 12192.0
1 TraesCS1A01G167400 chr1A 93.209 751 40 10 5851 6593 234183773 234184520 0.000000e+00 1094.0
2 TraesCS1A01G167400 chr1A 87.273 110 11 3 3361 3469 300109384 300109491 8.990000e-24 122.0
3 TraesCS1A01G167400 chr1A 87.273 110 11 3 3277 3384 300109468 300109576 8.990000e-24 122.0
4 TraesCS1A01G167400 chr1A 100.000 32 0 0 4124 4155 300110204 300110235 7.150000e-05 60.2
5 TraesCS1A01G167400 chr1A 100.000 32 0 0 4097 4128 300110231 300110262 7.150000e-05 60.2
6 TraesCS1A01G167400 chr1B 96.774 3255 71 11 2145 5397 330506058 330509280 0.000000e+00 5398.0
7 TraesCS1A01G167400 chr1B 93.962 1590 67 11 1 1571 330503686 330505265 0.000000e+00 2377.0
8 TraesCS1A01G167400 chr1B 92.132 394 20 6 1766 2158 330505495 330505878 4.500000e-151 545.0
9 TraesCS1A01G167400 chr1B 84.871 271 23 9 5585 5853 330509538 330509792 2.360000e-64 257.0
10 TraesCS1A01G167400 chr1B 88.718 195 3 4 5398 5592 330509311 330509486 3.100000e-53 220.0
11 TraesCS1A01G167400 chr1B 88.550 131 6 4 1578 1706 330505315 330505438 4.120000e-32 150.0
12 TraesCS1A01G167400 chr1B 88.785 107 10 2 3277 3382 330507274 330507379 5.370000e-26 130.0
13 TraesCS1A01G167400 chr1B 89.655 58 6 0 3180 3237 330507221 330507278 2.550000e-09 75.0
14 TraesCS1A01G167400 chr1D 95.863 2973 66 18 1704 4673 247303086 247300168 0.000000e+00 4756.0
15 TraesCS1A01G167400 chr1D 94.817 1582 65 10 1 1571 247305029 247303454 0.000000e+00 2451.0
16 TraesCS1A01G167400 chr1D 97.678 732 14 1 4669 5397 247300089 247299358 0.000000e+00 1254.0
17 TraesCS1A01G167400 chr1D 96.923 195 6 0 5398 5592 247299327 247299133 1.780000e-85 327.0
18 TraesCS1A01G167400 chr1D 93.985 133 4 1 1578 1706 247303244 247303112 1.450000e-46 198.0
19 TraesCS1A01G167400 chr1D 90.411 146 11 1 5588 5730 247299079 247298934 8.740000e-44 189.0
20 TraesCS1A01G167400 chr1D 89.091 110 9 3 3361 3469 247301521 247301414 4.150000e-27 134.0
21 TraesCS1A01G167400 chr1D 87.273 110 11 3 3277 3384 247301437 247301329 8.990000e-24 122.0
22 TraesCS1A01G167400 chr1D 89.655 58 6 0 3180 3237 247301490 247301433 2.550000e-09 75.0
23 TraesCS1A01G167400 chrUn 97.851 698 15 0 5854 6551 806256 805559 0.000000e+00 1206.0
24 TraesCS1A01G167400 chr2A 93.017 759 42 9 5853 6602 631675261 631676017 0.000000e+00 1098.0
25 TraesCS1A01G167400 chr2A 92.074 757 49 9 5854 6602 556220567 556221320 0.000000e+00 1055.0
26 TraesCS1A01G167400 chr2A 92.102 747 51 7 5854 6596 278317959 278317217 0.000000e+00 1046.0
27 TraesCS1A01G167400 chr5A 92.473 744 53 3 5854 6595 497385869 497385127 0.000000e+00 1061.0
28 TraesCS1A01G167400 chr6A 92.493 746 46 7 5854 6592 403464984 403465726 0.000000e+00 1059.0
29 TraesCS1A01G167400 chr6A 89.051 137 12 2 5594 5730 9182136 9182003 4.090000e-37 167.0
30 TraesCS1A01G167400 chr7A 91.755 752 57 5 5854 6601 226974763 226975513 0.000000e+00 1040.0
31 TraesCS1A01G167400 chr4A 92.059 743 52 7 5855 6593 547851860 547852599 0.000000e+00 1038.0
32 TraesCS1A01G167400 chr4A 92.381 105 6 1 5642 5744 684503932 684503828 1.480000e-31 148.0
33 TraesCS1A01G167400 chr4A 92.063 63 4 1 5747 5808 684503805 684503743 3.280000e-13 87.9
34 TraesCS1A01G167400 chr4D 86.335 161 13 4 5642 5793 477578245 477578085 4.090000e-37 167.0
35 TraesCS1A01G167400 chr6D 83.969 131 19 1 5600 5730 8757714 8757842 2.500000e-24 124.0


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 TraesCS1A01G167400 chr1A 300106108 300112709 6601 False 2511.280000 12192 94.909200 1 6602 5 chr1A.!!$F2 6601
1 TraesCS1A01G167400 chr1A 234183773 234184520 747 False 1094.000000 1094 93.209000 5851 6593 1 chr1A.!!$F1 742
2 TraesCS1A01G167400 chr1B 330503686 330509792 6106 False 1144.000000 5398 90.430875 1 5853 8 chr1B.!!$F1 5852
3 TraesCS1A01G167400 chr1D 247298934 247305029 6095 True 1056.222222 4756 92.855111 1 5730 9 chr1D.!!$R1 5729
4 TraesCS1A01G167400 chrUn 805559 806256 697 True 1206.000000 1206 97.851000 5854 6551 1 chrUn.!!$R1 697
5 TraesCS1A01G167400 chr2A 631675261 631676017 756 False 1098.000000 1098 93.017000 5853 6602 1 chr2A.!!$F2 749
6 TraesCS1A01G167400 chr2A 556220567 556221320 753 False 1055.000000 1055 92.074000 5854 6602 1 chr2A.!!$F1 748
7 TraesCS1A01G167400 chr2A 278317217 278317959 742 True 1046.000000 1046 92.102000 5854 6596 1 chr2A.!!$R1 742
8 TraesCS1A01G167400 chr5A 497385127 497385869 742 True 1061.000000 1061 92.473000 5854 6595 1 chr5A.!!$R1 741
9 TraesCS1A01G167400 chr6A 403464984 403465726 742 False 1059.000000 1059 92.493000 5854 6592 1 chr6A.!!$F1 738
10 TraesCS1A01G167400 chr7A 226974763 226975513 750 False 1040.000000 1040 91.755000 5854 6601 1 chr7A.!!$F1 747
11 TraesCS1A01G167400 chr4A 547851860 547852599 739 False 1038.000000 1038 92.059000 5855 6593 1 chr4A.!!$F1 738

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
81 82 1.214175 TCCCCAAGAAGTCAGCAAACA 59.786 47.619 0.00 0.00 0.00 2.83 F
1017 1027 0.676736 TGGGGTCATTTTGAAACCGC 59.323 50.000 0.00 0.00 44.03 5.68 F
1018 1028 0.676736 GGGGTCATTTTGAAACCGCA 59.323 50.000 3.27 0.00 43.44 5.69 F
1277 1298 1.194896 CTTCGTCTCGTCGATTCGGC 61.195 60.000 6.18 2.87 39.57 5.54 F
1312 1333 1.368850 GTTTCGTGCGTTCTGTGGC 60.369 57.895 0.00 0.00 0.00 5.01 F
1332 1353 1.531677 CGTGCTATGTTTTGCATCCGG 60.532 52.381 0.00 0.00 41.45 5.14 F
1763 2020 1.533625 TATTTCTTTGCACAGCCGCT 58.466 45.000 0.00 0.00 0.00 5.52 F
2682 3135 1.732308 GCTGCCTAGCCTTGATTGC 59.268 57.895 0.00 0.00 44.33 3.56 F
3863 4316 0.743345 GATACTCCAAGCCGCCGTTT 60.743 55.000 0.00 0.00 0.00 3.60 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1316 1337 0.029300 CGCCCGGATGCAAAACATAG 59.971 55.000 0.73 0.0 39.84 2.23 R
2049 2308 1.209261 ACTGATGACACACACACACCA 59.791 47.619 0.00 0.0 0.00 4.17 R
2051 2310 5.673337 AATTACTGATGACACACACACAC 57.327 39.130 0.00 0.0 0.00 3.82 R
2311 2764 6.251549 GCATTTGATTAAGTCCTTTCTCGAC 58.748 40.000 0.00 0.0 0.00 4.20 R
2682 3135 6.677913 ACATTGTTAGAAAAAGAACGATGGG 58.322 36.000 15.79 0.0 45.72 4.00 R
3342 3795 1.629043 ACTGCGGTTCAGAGGTCTTA 58.371 50.000 0.00 0.0 45.72 2.10 R
3581 4034 3.405831 TGCAGTGCATCAAGATATAGCC 58.594 45.455 15.37 0.0 31.71 3.93 R
4131 4584 1.073923 GTCACCCCATCCTTGTCAAGT 59.926 52.381 11.61 0.0 0.00 3.16 R
5776 6407 0.666577 GCTCGTAGCACTTTGTCCGT 60.667 55.000 2.53 0.0 41.89 4.69 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
67 68 3.192944 AGTTCATCCTCATCTTCCCCAA 58.807 45.455 0.00 0.00 0.00 4.12
81 82 1.214175 TCCCCAAGAAGTCAGCAAACA 59.786 47.619 0.00 0.00 0.00 2.83
123 124 3.695825 TCCCCTCCTCCACCTCCC 61.696 72.222 0.00 0.00 0.00 4.30
143 153 1.743995 GAGCGGTGGCGGTAACAAT 60.744 57.895 0.00 0.00 46.35 2.71
256 266 2.182030 CTCCTTGTCGTCCTCGGC 59.818 66.667 0.00 0.00 42.45 5.54
455 465 4.323477 CGCGGGACCCACTGGAAA 62.323 66.667 12.15 0.00 34.81 3.13
458 468 2.439245 GGGACCCACTGGAAACCC 59.561 66.667 5.33 2.73 36.50 4.11
656 666 3.052181 GCTACTCGAGGCAAGGAAC 57.948 57.895 18.41 0.00 0.00 3.62
819 829 4.834892 CGGCCATTTTCGCTGCGG 62.835 66.667 23.03 5.75 0.00 5.69
846 856 1.908340 CTGCTCCAGGAACCAGGAGG 61.908 65.000 25.98 12.21 46.96 4.30
1013 1023 1.347062 GGGCTGGGGTCATTTTGAAA 58.653 50.000 0.00 0.00 0.00 2.69
1015 1025 1.001974 GGCTGGGGTCATTTTGAAACC 59.998 52.381 0.00 0.00 0.00 3.27
1016 1026 1.336795 GCTGGGGTCATTTTGAAACCG 60.337 52.381 0.00 0.00 33.69 4.44
1017 1027 0.676736 TGGGGTCATTTTGAAACCGC 59.323 50.000 0.00 0.00 44.03 5.68
1018 1028 0.676736 GGGGTCATTTTGAAACCGCA 59.323 50.000 3.27 0.00 43.44 5.69
1277 1298 1.194896 CTTCGTCTCGTCGATTCGGC 61.195 60.000 6.18 2.87 39.57 5.54
1309 1330 1.647346 TTCTGTTTCGTGCGTTCTGT 58.353 45.000 0.00 0.00 0.00 3.41
1312 1333 1.368850 GTTTCGTGCGTTCTGTGGC 60.369 57.895 0.00 0.00 0.00 5.01
1316 1337 4.666532 GTGCGTTCTGTGGCGTGC 62.667 66.667 0.00 0.00 0.00 5.34
1332 1353 1.531677 CGTGCTATGTTTTGCATCCGG 60.532 52.381 0.00 0.00 41.45 5.14
1470 1492 5.003402 CGTTTAAAATTGGAATGCTACGCTG 59.997 40.000 0.00 0.00 0.00 5.18
1541 1563 7.496263 GGTAGTTGTTGATATTTTCCCTCTCTC 59.504 40.741 0.00 0.00 0.00 3.20
1544 1566 7.609532 AGTTGTTGATATTTTCCCTCTCTCTTG 59.390 37.037 0.00 0.00 0.00 3.02
1551 1573 2.704190 TCCCTCTCTCTTGGTTCAGT 57.296 50.000 0.00 0.00 0.00 3.41
1571 1593 3.057734 GTTCTGGTTGTTCGTCTAGTGG 58.942 50.000 0.00 0.00 0.00 4.00
1572 1594 2.589720 TCTGGTTGTTCGTCTAGTGGA 58.410 47.619 0.00 0.00 0.00 4.02
1573 1595 3.162666 TCTGGTTGTTCGTCTAGTGGAT 58.837 45.455 0.00 0.00 0.00 3.41
1574 1596 4.338012 TCTGGTTGTTCGTCTAGTGGATA 58.662 43.478 0.00 0.00 0.00 2.59
1576 1598 6.124340 TCTGGTTGTTCGTCTAGTGGATATA 58.876 40.000 0.00 0.00 0.00 0.86
1579 1601 7.431249 TGGTTGTTCGTCTAGTGGATATATTC 58.569 38.462 0.00 0.00 0.00 1.75
1581 1603 8.790718 GGTTGTTCGTCTAGTGGATATATTCTA 58.209 37.037 0.00 0.00 0.00 2.10
1584 1606 9.175312 TGTTCGTCTAGTGGATATATTCTATCC 57.825 37.037 4.62 4.62 42.88 2.59
1585 1607 8.623030 GTTCGTCTAGTGGATATATTCTATCCC 58.377 40.741 8.43 1.73 42.10 3.85
1593 1818 7.342284 AGTGGATATATTCTATCCCGTGGTTAG 59.658 40.741 8.43 3.06 42.10 2.34
1763 2020 1.533625 TATTTCTTTGCACAGCCGCT 58.466 45.000 0.00 0.00 0.00 5.52
1768 2025 1.915614 CTTTGCACAGCCGCTACCTG 61.916 60.000 0.00 0.00 36.41 4.00
1892 2149 6.599986 TGGAACTTATATACCAAACCCCAT 57.400 37.500 0.00 0.00 0.00 4.00
1930 2189 2.694760 GCTGCAGTTGGGCTAGCAC 61.695 63.158 18.24 14.86 37.64 4.40
1953 2212 8.364129 CACAATTTGGTGCTAGTTTACATTTT 57.636 30.769 0.78 0.00 31.10 1.82
1986 2245 4.960938 ACACAAGTAGAGACTTTGCATCA 58.039 39.130 0.00 0.00 43.70 3.07
1994 2253 5.542616 AGAGACTTTGCATCAGAAATTCG 57.457 39.130 0.48 0.00 0.00 3.34
1998 2257 2.634982 TTGCATCAGAAATTCGGCAC 57.365 45.000 0.00 0.00 0.00 5.01
2028 2287 6.531503 TTGTAAAGATGGTTTGTGTTGGAA 57.468 33.333 0.00 0.00 0.00 3.53
2049 2308 7.872138 TGGAACCATGAGGACTAGATTTTATT 58.128 34.615 0.00 0.00 38.69 1.40
2051 2310 7.229506 GGAACCATGAGGACTAGATTTTATTGG 59.770 40.741 0.00 0.00 38.69 3.16
2052 2311 7.213178 ACCATGAGGACTAGATTTTATTGGT 57.787 36.000 0.00 0.00 38.69 3.67
2053 2312 7.056635 ACCATGAGGACTAGATTTTATTGGTG 58.943 38.462 0.00 0.00 38.69 4.17
2054 2313 7.056635 CCATGAGGACTAGATTTTATTGGTGT 58.943 38.462 0.00 0.00 36.89 4.16
2055 2314 7.012704 CCATGAGGACTAGATTTTATTGGTGTG 59.987 40.741 0.00 0.00 36.89 3.82
2056 2315 7.016153 TGAGGACTAGATTTTATTGGTGTGT 57.984 36.000 0.00 0.00 0.00 3.72
2311 2764 3.488553 GGGGAAAAGTGTTCAAGTTGACG 60.489 47.826 4.68 0.00 0.00 4.35
2682 3135 1.732308 GCTGCCTAGCCTTGATTGC 59.268 57.895 0.00 0.00 44.33 3.56
2847 3300 7.435488 CACTAAGAGGTATTAATGACAACGAGG 59.565 40.741 0.00 0.00 0.00 4.63
3286 3739 7.664318 TCCTCAAACTTACTTGGTTCCTTATTC 59.336 37.037 0.00 0.00 0.00 1.75
3641 4094 6.239148 GCTGAAGGAGTTCTTGAATTTTCCTT 60.239 38.462 18.07 18.07 45.15 3.36
3863 4316 0.743345 GATACTCCAAGCCGCCGTTT 60.743 55.000 0.00 0.00 0.00 3.60
4088 4541 3.008835 TGAAAGCCCTTCTGATCATGG 57.991 47.619 0.00 0.00 34.86 3.66
4122 4575 2.292828 AACTTGACAAGGATGGGGTG 57.707 50.000 19.16 0.00 0.00 4.61
4123 4576 1.444933 ACTTGACAAGGATGGGGTGA 58.555 50.000 19.16 0.00 0.00 4.02
4124 4577 1.073923 ACTTGACAAGGATGGGGTGAC 59.926 52.381 19.16 0.00 0.00 3.67
4125 4578 1.352352 CTTGACAAGGATGGGGTGACT 59.648 52.381 7.35 0.00 0.00 3.41
4126 4579 1.444933 TGACAAGGATGGGGTGACTT 58.555 50.000 0.00 0.00 0.00 3.01
4127 4580 1.351017 TGACAAGGATGGGGTGACTTC 59.649 52.381 0.00 0.00 0.00 3.01
4128 4581 1.351017 GACAAGGATGGGGTGACTTCA 59.649 52.381 0.00 0.00 0.00 3.02
4129 4582 1.780309 ACAAGGATGGGGTGACTTCAA 59.220 47.619 0.00 0.00 0.00 2.69
4130 4583 2.176798 ACAAGGATGGGGTGACTTCAAA 59.823 45.455 0.00 0.00 0.00 2.69
4131 4584 3.230134 CAAGGATGGGGTGACTTCAAAA 58.770 45.455 0.00 0.00 0.00 2.44
4132 4585 2.876581 AGGATGGGGTGACTTCAAAAC 58.123 47.619 0.00 0.00 0.00 2.43
4133 4586 2.447047 AGGATGGGGTGACTTCAAAACT 59.553 45.455 0.00 0.00 0.00 2.66
4134 4587 3.117131 AGGATGGGGTGACTTCAAAACTT 60.117 43.478 0.00 0.00 0.00 2.66
4135 4588 3.005791 GGATGGGGTGACTTCAAAACTTG 59.994 47.826 0.00 0.00 0.00 3.16
4136 4589 3.374042 TGGGGTGACTTCAAAACTTGA 57.626 42.857 0.00 0.00 38.04 3.02
4137 4590 3.020984 TGGGGTGACTTCAAAACTTGAC 58.979 45.455 0.00 0.00 39.87 3.18
4138 4591 3.020984 GGGGTGACTTCAAAACTTGACA 58.979 45.455 0.00 0.00 39.87 3.58
4139 4592 3.445805 GGGGTGACTTCAAAACTTGACAA 59.554 43.478 0.00 0.00 39.87 3.18
4140 4593 4.440112 GGGGTGACTTCAAAACTTGACAAG 60.440 45.833 13.77 13.77 39.87 3.16
4141 4594 4.440112 GGGTGACTTCAAAACTTGACAAGG 60.440 45.833 19.16 1.74 39.87 3.61
4142 4595 4.398044 GGTGACTTCAAAACTTGACAAGGA 59.602 41.667 19.16 4.14 39.87 3.36
4143 4596 5.067805 GGTGACTTCAAAACTTGACAAGGAT 59.932 40.000 19.16 5.13 39.87 3.24
4144 4597 5.973565 GTGACTTCAAAACTTGACAAGGATG 59.026 40.000 19.16 13.72 39.87 3.51
4145 4598 5.067674 TGACTTCAAAACTTGACAAGGATGG 59.932 40.000 19.16 5.48 39.87 3.51
4146 4599 4.342092 ACTTCAAAACTTGACAAGGATGGG 59.658 41.667 19.16 12.19 39.87 4.00
4147 4600 3.230134 TCAAAACTTGACAAGGATGGGG 58.770 45.455 19.16 4.23 34.08 4.96
4148 4601 2.965147 CAAAACTTGACAAGGATGGGGT 59.035 45.455 19.16 0.00 0.00 4.95
4292 4745 6.006449 GGGTTAATGCATACTGGAAGATGAT 58.994 40.000 0.00 0.00 37.43 2.45
4321 4774 4.595762 AATGCCATCAGGAATTGCATAC 57.404 40.909 0.00 0.00 43.86 2.39
4355 4808 6.417930 CAGATATGTTTGCTGCATTCTCATTG 59.582 38.462 1.84 0.00 0.00 2.82
4391 4844 5.055642 ACTGTGCAATGCATCATATATGC 57.944 39.130 12.38 11.07 41.91 3.14
4398 4851 7.546316 GTGCAATGCATCATATATGCCATTTTA 59.454 33.333 12.38 10.15 43.94 1.52
4528 4981 9.249053 TGAAGTAATGCCAAAAGGTATATTCAA 57.751 29.630 0.00 0.00 0.00 2.69
4535 4988 7.041107 TGCCAAAAGGTATATTCAATTGCTTC 58.959 34.615 0.00 0.00 0.00 3.86
4607 5062 7.225523 GCAGTAAAATGCCAATTATCTTGTG 57.774 36.000 0.00 0.00 40.43 3.33
4844 5382 4.256983 AGTCTGTGGTATCTCTGGATCA 57.743 45.455 0.00 0.00 33.71 2.92
5123 5662 0.819582 CTTTACAGGCAAGCCCCATG 59.180 55.000 7.62 2.23 36.58 3.66
5144 5683 7.063308 CCCATGTGATGTTTTGTTTATTAGCAC 59.937 37.037 0.00 0.00 0.00 4.40
5278 5817 6.429385 GGAAAGACTCACAGAAGTCATTTGAT 59.571 38.462 6.79 0.00 46.65 2.57
5455 6027 3.056607 ACCATTTGCTGAATGCTGTAACC 60.057 43.478 7.58 0.00 43.11 2.85
5496 6068 5.095145 AGAATCTCTTGCATGCTCTGTAA 57.905 39.130 20.33 3.02 0.00 2.41
5598 6229 7.138081 TGTGAATGATGTGTATGTTTTGTGTC 58.862 34.615 0.00 0.00 0.00 3.67
5645 6276 7.654923 CACTGCTCACTATTATATGCTTGAAGA 59.345 37.037 0.00 0.00 0.00 2.87
5650 6281 9.702494 CTCACTATTATATGCTTGAAGATCACA 57.298 33.333 0.00 0.00 0.00 3.58
5662 6293 6.017934 GCTTGAAGATCACACACAAGAACTTA 60.018 38.462 15.81 0.00 39.84 2.24
5664 6295 9.208022 CTTGAAGATCACACACAAGAACTTATA 57.792 33.333 0.00 0.00 39.84 0.98
5665 6296 8.763049 TGAAGATCACACACAAGAACTTATAG 57.237 34.615 0.00 0.00 28.67 1.31
5667 6298 8.764524 AAGATCACACACAAGAACTTATAGTC 57.235 34.615 0.00 0.00 0.00 2.59
5668 6299 7.030165 AGATCACACACAAGAACTTATAGTCG 58.970 38.462 0.00 0.00 0.00 4.18
5730 6361 7.832503 TCACGCAATCATATACATAATCTGG 57.167 36.000 0.00 0.00 0.00 3.86
5731 6362 6.313658 TCACGCAATCATATACATAATCTGGC 59.686 38.462 0.00 0.00 0.00 4.85
5732 6363 5.586243 ACGCAATCATATACATAATCTGGCC 59.414 40.000 0.00 0.00 0.00 5.36
5733 6364 5.819379 CGCAATCATATACATAATCTGGCCT 59.181 40.000 3.32 0.00 0.00 5.19
5734 6365 6.018425 CGCAATCATATACATAATCTGGCCTC 60.018 42.308 3.32 0.00 0.00 4.70
5735 6366 6.261826 GCAATCATATACATAATCTGGCCTCC 59.738 42.308 3.32 0.00 0.00 4.30
5736 6367 5.957771 TCATATACATAATCTGGCCTCCC 57.042 43.478 3.32 0.00 0.00 4.30
5737 6368 5.603750 TCATATACATAATCTGGCCTCCCT 58.396 41.667 3.32 0.00 0.00 4.20
5738 6369 6.752091 TCATATACATAATCTGGCCTCCCTA 58.248 40.000 3.32 0.00 0.00 3.53
5739 6370 7.373463 TCATATACATAATCTGGCCTCCCTAT 58.627 38.462 3.32 0.00 0.00 2.57
5740 6371 8.519597 TCATATACATAATCTGGCCTCCCTATA 58.480 37.037 3.32 0.00 0.00 1.31
5741 6372 8.811017 CATATACATAATCTGGCCTCCCTATAG 58.189 40.741 3.32 0.00 0.00 1.31
5742 6373 4.366267 ACATAATCTGGCCTCCCTATAGG 58.634 47.826 12.27 12.27 39.87 2.57
5743 6374 4.047265 ACATAATCTGGCCTCCCTATAGGA 59.953 45.833 21.07 5.61 44.91 2.94
5744 6375 2.632763 ATCTGGCCTCCCTATAGGAC 57.367 55.000 21.07 0.00 45.93 3.85
5752 6383 3.244249 GCCTCCCTATAGGACATGACAAC 60.244 52.174 21.07 0.00 40.93 3.32
5757 6388 5.188163 TCCCTATAGGACATGACAACGAAAA 59.812 40.000 21.07 0.00 40.93 2.29
5766 6397 9.607988 AGGACATGACAACGAAAATTATATACA 57.392 29.630 0.00 0.00 0.00 2.29
5778 6409 9.567917 CGAAAATTATATACATGACACTCAACG 57.432 33.333 0.00 0.00 0.00 4.10
5779 6410 9.864034 GAAAATTATATACATGACACTCAACGG 57.136 33.333 0.00 0.00 0.00 4.44
5780 6411 9.607988 AAAATTATATACATGACACTCAACGGA 57.392 29.630 0.00 0.00 0.00 4.69
5788 6420 1.003866 GACACTCAACGGACAAAGTGC 60.004 52.381 1.49 0.00 42.23 4.40
5905 6537 3.886505 TGTAATCCAACTCTTGCCGTTTT 59.113 39.130 0.00 0.00 0.00 2.43
6083 6715 2.341101 GCACTCCGTTCTCCTCCGA 61.341 63.158 0.00 0.00 0.00 4.55
6405 7038 6.694611 ACCTCTATATAAAGACCACCCTCTT 58.305 40.000 0.00 0.00 31.41 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 3.119137 GGGTTGTTTGTTTGCTGACTTCT 60.119 43.478 0.00 0.00 0.00 2.85
81 82 2.698274 GTGACCAATTGGAGGGTTGTTT 59.302 45.455 31.22 4.68 37.57 2.83
124 125 3.765660 TATTGTTACCGCCACCGCTCC 62.766 57.143 0.00 0.00 0.00 4.70
125 126 0.460635 TATTGTTACCGCCACCGCTC 60.461 55.000 0.00 0.00 0.00 5.03
143 153 1.349688 GTGGATGGTGGTGGTGAAGTA 59.650 52.381 0.00 0.00 0.00 2.24
194 204 2.887454 TCCACCCCAATGAGGAGATA 57.113 50.000 0.00 0.00 41.22 1.98
236 246 1.248785 CCGAGGACGACAAGGAGGAA 61.249 60.000 0.00 0.00 42.66 3.36
298 308 2.184322 GGCTCGCCGATGAGTTCA 59.816 61.111 0.00 0.00 38.28 3.18
819 829 4.527583 CCTGGAGCAGAGGAGCGC 62.528 72.222 0.00 0.00 40.15 5.92
948 958 2.504244 GCCAGAACGGACGACTCG 60.504 66.667 0.00 0.00 36.56 4.18
1013 1023 3.669344 CAAATGCCACGGTGCGGT 61.669 61.111 1.68 0.00 0.00 5.68
1015 1025 3.609214 GACCAAATGCCACGGTGCG 62.609 63.158 1.68 0.00 31.63 5.34
1016 1026 2.200170 GAGACCAAATGCCACGGTGC 62.200 60.000 1.68 0.00 31.63 5.01
1017 1027 0.606401 AGAGACCAAATGCCACGGTG 60.606 55.000 0.00 0.00 31.63 4.94
1018 1028 0.110486 AAGAGACCAAATGCCACGGT 59.890 50.000 0.00 0.00 35.12 4.83
1136 1157 3.219928 TCTCGGATCCAGCGAGGC 61.220 66.667 13.41 0.00 37.29 4.70
1204 1225 1.375326 GCGAAACCAAGGAGAGGGT 59.625 57.895 0.00 0.00 39.65 4.34
1309 1330 0.887247 ATGCAAAACATAGCACGCCA 59.113 45.000 0.00 0.00 44.49 5.69
1312 1333 1.531677 CCGGATGCAAAACATAGCACG 60.532 52.381 0.00 0.00 44.49 5.34
1316 1337 0.029300 CGCCCGGATGCAAAACATAG 59.971 55.000 0.73 0.00 39.84 2.23
1470 1492 8.797438 AGATTCAAAAGTTAGACAGGGAAATTC 58.203 33.333 0.00 0.00 0.00 2.17
1534 1556 3.306641 CCAGAACTGAACCAAGAGAGAGG 60.307 52.174 3.19 0.00 0.00 3.69
1541 1563 3.242739 CGAACAACCAGAACTGAACCAAG 60.243 47.826 3.19 0.00 0.00 3.61
1544 1566 2.285977 ACGAACAACCAGAACTGAACC 58.714 47.619 3.19 0.00 0.00 3.62
1551 1573 2.960384 TCCACTAGACGAACAACCAGAA 59.040 45.455 0.00 0.00 0.00 3.02
1571 1593 6.324254 AGGCTAACCACGGGATAGAATATATC 59.676 42.308 10.17 0.00 39.06 1.63
1572 1594 6.203072 AGGCTAACCACGGGATAGAATATAT 58.797 40.000 10.17 0.00 39.06 0.86
1573 1595 5.586877 AGGCTAACCACGGGATAGAATATA 58.413 41.667 10.17 0.00 39.06 0.86
1574 1596 4.426704 AGGCTAACCACGGGATAGAATAT 58.573 43.478 10.17 0.00 39.06 1.28
1576 1598 2.633481 GAGGCTAACCACGGGATAGAAT 59.367 50.000 10.17 0.25 39.06 2.40
1579 1601 0.314302 CGAGGCTAACCACGGGATAG 59.686 60.000 0.00 0.00 45.16 2.08
1581 1603 3.217231 CGAGGCTAACCACGGGAT 58.783 61.111 0.00 0.00 45.16 3.85
1763 2020 2.891580 GGAGTGACAGAGAACACAGGTA 59.108 50.000 0.00 0.00 39.18 3.08
1768 2025 4.218635 TGACTATGGAGTGACAGAGAACAC 59.781 45.833 0.00 0.00 35.45 3.32
1870 2127 6.370453 ACATGGGGTTTGGTATATAAGTTCC 58.630 40.000 0.00 0.00 0.00 3.62
1892 2149 2.191400 CAAGGATGGGAGAGAGGAACA 58.809 52.381 0.00 0.00 0.00 3.18
1930 2189 9.906660 TCTAAAATGTAAACTAGCACCAAATTG 57.093 29.630 0.00 0.00 0.00 2.32
1986 2245 4.754322 ACAAACAAAAGTGCCGAATTTCT 58.246 34.783 0.00 0.00 0.00 2.52
1994 2253 5.356426 ACCATCTTTACAAACAAAAGTGCC 58.644 37.500 0.00 0.00 35.79 5.01
1998 2257 8.250538 ACACAAACCATCTTTACAAACAAAAG 57.749 30.769 0.00 0.00 35.66 2.27
2028 2287 7.056635 CACCAATAAAATCTAGTCCTCATGGT 58.943 38.462 0.00 0.00 36.77 3.55
2049 2308 1.209261 ACTGATGACACACACACACCA 59.791 47.619 0.00 0.00 0.00 4.17
2051 2310 5.673337 AATTACTGATGACACACACACAC 57.327 39.130 0.00 0.00 0.00 3.82
2052 2311 6.989759 ACTAAATTACTGATGACACACACACA 59.010 34.615 0.00 0.00 0.00 3.72
2053 2312 7.421530 ACTAAATTACTGATGACACACACAC 57.578 36.000 0.00 0.00 0.00 3.82
2054 2313 9.549078 TTTACTAAATTACTGATGACACACACA 57.451 29.630 0.00 0.00 0.00 3.72
2055 2314 9.807386 GTTTACTAAATTACTGATGACACACAC 57.193 33.333 0.00 0.00 0.00 3.82
2056 2315 8.995220 GGTTTACTAAATTACTGATGACACACA 58.005 33.333 0.00 0.00 0.00 3.72
2084 2343 8.282982 TCAACCTCTTTAGTCATAGTATCTCCT 58.717 37.037 0.00 0.00 0.00 3.69
2122 2381 8.182881 ACAGTATAGCACTAAGAAAACGTAGAG 58.817 37.037 0.00 0.00 34.98 2.43
2311 2764 6.251549 GCATTTGATTAAGTCCTTTCTCGAC 58.748 40.000 0.00 0.00 0.00 4.20
2682 3135 6.677913 ACATTGTTAGAAAAAGAACGATGGG 58.322 36.000 15.79 0.00 45.72 4.00
3342 3795 1.629043 ACTGCGGTTCAGAGGTCTTA 58.371 50.000 0.00 0.00 45.72 2.10
3489 3942 8.767478 ATTCCAACAAGAATGCTAAGAAAATG 57.233 30.769 0.00 0.00 35.15 2.32
3581 4034 3.405831 TGCAGTGCATCAAGATATAGCC 58.594 45.455 15.37 0.00 31.71 3.93
3968 4421 4.130857 TGAGGTTTCATGTTTCGCAACTA 58.869 39.130 0.00 0.00 33.58 2.24
4088 4541 4.394920 TGTCAAGTTTTGAAGTGTCAGGAC 59.605 41.667 0.00 0.00 42.15 3.85
4122 4575 5.507985 CCCATCCTTGTCAAGTTTTGAAGTC 60.508 44.000 11.61 0.00 42.15 3.01
4123 4576 4.342092 CCCATCCTTGTCAAGTTTTGAAGT 59.658 41.667 11.61 0.00 42.15 3.01
4124 4577 4.262164 CCCCATCCTTGTCAAGTTTTGAAG 60.262 45.833 11.61 0.00 42.15 3.02
4125 4578 3.640967 CCCCATCCTTGTCAAGTTTTGAA 59.359 43.478 11.61 0.00 42.15 2.69
4126 4579 3.230134 CCCCATCCTTGTCAAGTTTTGA 58.770 45.455 11.61 2.14 37.33 2.69
4127 4580 2.965147 ACCCCATCCTTGTCAAGTTTTG 59.035 45.455 11.61 5.90 0.00 2.44
4128 4581 2.965147 CACCCCATCCTTGTCAAGTTTT 59.035 45.455 11.61 0.00 0.00 2.43
4129 4582 2.176798 TCACCCCATCCTTGTCAAGTTT 59.823 45.455 11.61 0.00 0.00 2.66
4130 4583 1.780309 TCACCCCATCCTTGTCAAGTT 59.220 47.619 11.61 0.00 0.00 2.66
4131 4584 1.073923 GTCACCCCATCCTTGTCAAGT 59.926 52.381 11.61 0.00 0.00 3.16
4132 4585 1.352352 AGTCACCCCATCCTTGTCAAG 59.648 52.381 5.53 5.53 0.00 3.02
4133 4586 1.444933 AGTCACCCCATCCTTGTCAA 58.555 50.000 0.00 0.00 0.00 3.18
4134 4587 1.351017 GAAGTCACCCCATCCTTGTCA 59.649 52.381 0.00 0.00 0.00 3.58
4135 4588 1.630878 AGAAGTCACCCCATCCTTGTC 59.369 52.381 0.00 0.00 0.00 3.18
4136 4589 1.747444 AGAAGTCACCCCATCCTTGT 58.253 50.000 0.00 0.00 0.00 3.16
4137 4590 3.455910 TGATAGAAGTCACCCCATCCTTG 59.544 47.826 0.00 0.00 0.00 3.61
4138 4591 3.456277 GTGATAGAAGTCACCCCATCCTT 59.544 47.826 0.00 0.00 42.04 3.36
4139 4592 3.041946 GTGATAGAAGTCACCCCATCCT 58.958 50.000 0.00 0.00 42.04 3.24
4140 4593 2.771943 TGTGATAGAAGTCACCCCATCC 59.228 50.000 4.75 0.00 46.17 3.51
4141 4594 3.706594 TCTGTGATAGAAGTCACCCCATC 59.293 47.826 4.75 0.00 46.17 3.51
4142 4595 3.724478 TCTGTGATAGAAGTCACCCCAT 58.276 45.455 4.75 0.00 46.17 4.00
4143 4596 3.184382 TCTGTGATAGAAGTCACCCCA 57.816 47.619 4.75 0.00 46.17 4.96
4144 4597 3.369576 GGTTCTGTGATAGAAGTCACCCC 60.370 52.174 4.75 0.00 45.71 4.95
4145 4598 3.515901 AGGTTCTGTGATAGAAGTCACCC 59.484 47.826 4.75 0.00 45.71 4.61
4146 4599 4.220821 TCAGGTTCTGTGATAGAAGTCACC 59.779 45.833 4.75 0.00 45.71 4.02
4147 4600 5.392767 TCAGGTTCTGTGATAGAAGTCAC 57.607 43.478 0.00 0.30 45.71 3.67
4148 4601 4.464244 CCTCAGGTTCTGTGATAGAAGTCA 59.536 45.833 0.00 0.00 45.71 3.41
4292 4745 6.594937 GCAATTCCTGATGGCATTTAAGAAAA 59.405 34.615 0.00 0.00 34.59 2.29
4355 4808 8.068977 TGCATTGCACAGTCAAAAATTTAAATC 58.931 29.630 7.38 0.00 31.71 2.17
4528 4981 7.887996 TCGAAGCATAAATTTTTGAAGCAAT 57.112 28.000 12.18 0.00 0.00 3.56
4607 5062 4.622695 GCCTCAGCTCAGGTTATGATATCC 60.623 50.000 5.21 0.00 37.28 2.59
4676 5214 6.588756 TGAAGACAATAACCAACGATGACTAC 59.411 38.462 0.00 0.00 0.00 2.73
4844 5382 9.349713 TGTTTAGTGATTAGTGAATTCTTGGTT 57.650 29.630 7.05 0.00 0.00 3.67
5278 5817 3.691118 GGCTTTGCACAGATTGTCTCATA 59.309 43.478 3.47 0.00 0.00 2.15
5387 5929 5.967674 CCATTCAGCAAAAGCTAGTATTTCG 59.032 40.000 0.00 0.00 0.00 3.46
5487 6059 6.734137 ACATTTTGTCGAATTTTACAGAGCA 58.266 32.000 0.00 0.00 0.00 4.26
5496 6068 8.977505 CACCATAGAAAACATTTTGTCGAATTT 58.022 29.630 0.00 0.00 0.00 1.82
5598 6229 5.047802 AGTGTGGTGCATAAAGAATTTGGAG 60.048 40.000 0.00 0.00 39.63 3.86
5645 6276 6.100004 CCGACTATAAGTTCTTGTGTGTGAT 58.900 40.000 0.00 0.00 0.00 3.06
5650 6281 4.021368 AGCACCGACTATAAGTTCTTGTGT 60.021 41.667 0.00 0.00 0.00 3.72
5716 6347 7.958583 CCTATAGGGAGGCCAGATTATGTATAT 59.041 40.741 11.33 0.00 37.23 0.86
5721 6352 4.407296 GTCCTATAGGGAGGCCAGATTATG 59.593 50.000 18.97 0.00 46.10 1.90
5722 6353 4.047265 TGTCCTATAGGGAGGCCAGATTAT 59.953 45.833 18.97 0.03 46.10 1.28
5723 6354 3.404769 TGTCCTATAGGGAGGCCAGATTA 59.595 47.826 18.97 0.00 46.10 1.75
5724 6355 2.182312 TGTCCTATAGGGAGGCCAGATT 59.818 50.000 18.97 0.00 46.10 2.40
5727 6358 1.905215 CATGTCCTATAGGGAGGCCAG 59.095 57.143 18.97 0.00 46.10 4.85
5728 6359 1.507742 TCATGTCCTATAGGGAGGCCA 59.492 52.381 18.97 8.38 46.10 5.36
5729 6360 1.903183 GTCATGTCCTATAGGGAGGCC 59.097 57.143 18.97 0.00 46.10 5.19
5730 6361 2.609747 TGTCATGTCCTATAGGGAGGC 58.390 52.381 18.97 8.36 46.10 4.70
5731 6362 3.005897 CGTTGTCATGTCCTATAGGGAGG 59.994 52.174 18.97 7.86 46.10 4.30
5732 6363 3.889538 TCGTTGTCATGTCCTATAGGGAG 59.110 47.826 18.97 6.64 46.10 4.30
5733 6364 3.905968 TCGTTGTCATGTCCTATAGGGA 58.094 45.455 18.97 5.18 42.77 4.20
5734 6365 4.665833 TTCGTTGTCATGTCCTATAGGG 57.334 45.455 18.97 2.67 35.41 3.53
5735 6366 7.553881 AATTTTCGTTGTCATGTCCTATAGG 57.446 36.000 13.07 13.07 0.00 2.57
5740 6371 9.607988 TGTATATAATTTTCGTTGTCATGTCCT 57.392 29.630 0.00 0.00 0.00 3.85
5752 6383 9.567917 CGTTGAGTGTCATGTATATAATTTTCG 57.432 33.333 0.00 0.00 0.00 3.46
5757 6388 7.722363 TGTCCGTTGAGTGTCATGTATATAAT 58.278 34.615 0.00 0.00 0.00 1.28
5764 6395 2.613026 TTGTCCGTTGAGTGTCATGT 57.387 45.000 0.00 0.00 0.00 3.21
5765 6396 2.872245 ACTTTGTCCGTTGAGTGTCATG 59.128 45.455 0.00 0.00 0.00 3.07
5766 6397 2.872245 CACTTTGTCCGTTGAGTGTCAT 59.128 45.455 0.00 0.00 35.84 3.06
5767 6398 2.276201 CACTTTGTCCGTTGAGTGTCA 58.724 47.619 0.00 0.00 35.84 3.58
5768 6399 1.003866 GCACTTTGTCCGTTGAGTGTC 60.004 52.381 4.52 0.00 41.11 3.67
5769 6400 1.014352 GCACTTTGTCCGTTGAGTGT 58.986 50.000 4.52 0.00 41.11 3.55
5770 6401 1.299541 AGCACTTTGTCCGTTGAGTG 58.700 50.000 0.00 0.00 41.76 3.51
5771 6402 2.480845 GTAGCACTTTGTCCGTTGAGT 58.519 47.619 0.00 0.00 0.00 3.41
5772 6403 1.455786 CGTAGCACTTTGTCCGTTGAG 59.544 52.381 0.00 0.00 0.00 3.02
5773 6404 1.067364 TCGTAGCACTTTGTCCGTTGA 59.933 47.619 0.00 0.00 0.00 3.18
5775 6406 1.779569 CTCGTAGCACTTTGTCCGTT 58.220 50.000 0.00 0.00 0.00 4.44
5776 6407 0.666577 GCTCGTAGCACTTTGTCCGT 60.667 55.000 2.53 0.00 41.89 4.69
5777 6408 2.070861 GCTCGTAGCACTTTGTCCG 58.929 57.895 2.53 0.00 41.89 4.79
5788 6420 1.374631 TTGCTGGCTGTGCTCGTAG 60.375 57.895 0.00 0.00 0.00 3.51
5815 6447 6.089685 GCACCTTCGTTTTCAAAACAAAAGTA 59.910 34.615 13.42 0.00 0.00 2.24
5818 6450 4.991687 AGCACCTTCGTTTTCAAAACAAAA 59.008 33.333 13.42 5.86 0.00 2.44
5905 6537 7.899330 CGAGAAAATAAAATAACTTAACGCCGA 59.101 33.333 0.00 0.00 0.00 5.54
6083 6715 7.610305 ACACGAAATAAAGGTAGAAATGACCAT 59.390 33.333 0.00 0.00 39.65 3.55
6405 7038 1.060163 GGAGGGGATCCGGGATTTCA 61.060 60.000 11.57 0.00 38.67 2.69
6495 7133 3.338126 CTGCTCGTTAGACGGCGGT 62.338 63.158 13.24 0.00 42.81 5.68
6504 7142 3.309436 ATGTGGCGGCTGCTCGTTA 62.309 57.895 18.85 0.09 42.25 3.18


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

AutoCloner maintained by Alex Coulton.