Multiple sequence alignment - TraesCS6D01G117100

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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 TraesCS6D01G117100 chr6D 100.000 2909 0 0 1 2909 83103628 83100720 0.000000e+00 5373.0
1 TraesCS6D01G117100 chr6D 83.571 2313 175 74 96 2323 84029940 84032132 0.000000e+00 1977.0
2 TraesCS6D01G117100 chr6D 89.744 1482 122 11 850 2323 83550019 83551478 0.000000e+00 1868.0
3 TraesCS6D01G117100 chr6D 78.958 499 49 31 1 453 83544350 83544838 3.670000e-74 289.0
4 TraesCS6D01G117100 chr6D 87.395 119 8 5 591 704 83112632 83112516 2.350000e-26 130.0
5 TraesCS6D01G117100 chr6D 82.209 163 9 7 291 453 83112853 83112711 3.940000e-24 122.0
6 TraesCS6D01G117100 chr6D 92.208 77 3 2 96 169 83114411 83114335 3.960000e-19 106.0
7 TraesCS6D01G117100 chr6D 77.202 193 27 15 520 703 83549677 83549861 2.390000e-16 97.1
8 TraesCS6D01G117100 chr6D 94.118 51 3 0 2583 2633 83551619 83551669 8.640000e-11 78.7
9 TraesCS6D01G117100 chr6A 86.422 2099 177 52 609 2664 100181557 100179524 0.000000e+00 2198.0
10 TraesCS6D01G117100 chr6A 88.660 1508 123 16 849 2323 100811585 100813077 0.000000e+00 1794.0
11 TraesCS6D01G117100 chr6A 84.502 1826 164 41 661 2450 100764692 100766434 0.000000e+00 1694.0
12 TraesCS6D01G117100 chr6A 85.053 475 25 23 1 453 100764106 100764556 2.660000e-120 442.0
13 TraesCS6D01G117100 chr6A 83.951 405 31 26 235 619 100810967 100811357 9.910000e-95 357.0
14 TraesCS6D01G117100 chr6A 83.239 352 15 17 90 397 100182015 100181664 1.710000e-72 283.0
15 TraesCS6D01G117100 chr6A 85.520 221 23 7 2696 2909 100179532 100179314 3.770000e-54 222.0
16 TraesCS6D01G117100 chr6A 82.447 188 9 6 1 168 100810742 100810925 3.020000e-30 143.0
17 TraesCS6D01G117100 chr6A 96.491 57 2 0 653 709 100811364 100811420 8.580000e-16 95.3
18 TraesCS6D01G117100 chr6A 92.593 54 4 0 988 1041 100811765 100811818 8.640000e-11 78.7
19 TraesCS6D01G117100 chr6B 87.500 1680 120 23 659 2285 158145986 158144344 0.000000e+00 1857.0
20 TraesCS6D01G117100 chr6B 85.892 1687 148 34 840 2482 159598751 159600391 0.000000e+00 1714.0
21 TraesCS6D01G117100 chr6B 85.554 1696 154 31 836 2482 159407165 159408818 0.000000e+00 1690.0
22 TraesCS6D01G117100 chr6B 84.502 271 23 9 675 934 159598538 159598800 1.730000e-62 250.0
23 TraesCS6D01G117100 chr6B 92.727 110 8 0 235 344 158146364 158146255 3.000000e-35 159.0
24 TraesCS6D01G117100 chr6B 78.889 180 20 14 96 266 159405919 159406089 3.960000e-19 106.0
25 TraesCS6D01G117100 chr6B 95.385 65 3 0 428 492 158146214 158146150 1.430000e-18 104.0
26 TraesCS6D01G117100 chr6B 97.368 38 1 0 533 570 158146139 158146102 6.730000e-07 65.8
27 TraesCS6D01G117100 chr7D 85.057 174 21 4 270 438 254142741 254142568 3.850000e-39 172.0
28 TraesCS6D01G117100 chr7B 82.432 148 20 5 267 408 231322556 231322409 1.090000e-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 TraesCS6D01G117100 chr6D 83100720 83103628 2908 True 5373.000000 5373 100.000000 1 2909 1 chr6D.!!$R1 2908
1 TraesCS6D01G117100 chr6D 84029940 84032132 2192 False 1977.000000 1977 83.571000 96 2323 1 chr6D.!!$F2 2227
2 TraesCS6D01G117100 chr6D 83549677 83551669 1992 False 681.266667 1868 87.021333 520 2633 3 chr6D.!!$F3 2113
3 TraesCS6D01G117100 chr6A 100764106 100766434 2328 False 1068.000000 1694 84.777500 1 2450 2 chr6A.!!$F1 2449
4 TraesCS6D01G117100 chr6A 100179314 100182015 2701 True 901.000000 2198 85.060333 90 2909 3 chr6A.!!$R1 2819
5 TraesCS6D01G117100 chr6A 100810742 100813077 2335 False 493.600000 1794 88.828400 1 2323 5 chr6A.!!$F2 2322
6 TraesCS6D01G117100 chr6B 159598538 159600391 1853 False 982.000000 1714 85.197000 675 2482 2 chr6B.!!$F2 1807
7 TraesCS6D01G117100 chr6B 159405919 159408818 2899 False 898.000000 1690 82.221500 96 2482 2 chr6B.!!$F1 2386
8 TraesCS6D01G117100 chr6B 158144344 158146364 2020 True 546.450000 1857 93.245000 235 2285 4 chr6B.!!$R1 2050

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
502 1143 0.036022 GCAAAGACCAGCTGTCCTCT 59.964 55.0 13.81 6.48 45.68 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1967 3046 0.104304 CGACCTAACAATCCGGGGAG 59.896 60.0 0.0 0.0 0.0 4.3 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
53 54 2.905415 TCCAACTTGGCCTGAATCAT 57.095 45.000 3.32 0.00 37.47 2.45
54 55 4.314522 TTCCAACTTGGCCTGAATCATA 57.685 40.909 3.32 0.00 37.47 2.15
55 56 3.620488 TCCAACTTGGCCTGAATCATAC 58.380 45.455 3.32 0.00 37.47 2.39
56 57 2.355756 CCAACTTGGCCTGAATCATACG 59.644 50.000 3.32 0.00 0.00 3.06
94 111 2.715737 TTGGTTGGCGTAAAAGATGC 57.284 45.000 0.00 0.00 39.59 3.91
126 147 4.019174 ACCTTCCACTTGCATAATTCCAG 58.981 43.478 0.00 0.00 0.00 3.86
148 171 1.197036 TCGCAGTGTTAGTGAGAGACG 59.803 52.381 0.00 0.00 0.00 4.18
168 199 1.956477 GTTGATTCAACAGGCTGGTGT 59.044 47.619 30.19 14.02 43.09 4.16
180 211 1.097232 GCTGGTGTGCATGCTATTGA 58.903 50.000 20.33 0.00 0.00 2.57
187 235 2.925578 TGCATGCTATTGAAGTGCAC 57.074 45.000 20.33 9.40 40.51 4.57
475 1116 2.218934 GAGGCGTTTCGTCGAACAA 58.781 52.632 7.29 0.00 36.23 2.83
497 1138 2.926250 TGGGCAAAGACCAGCTGT 59.074 55.556 13.81 0.11 34.69 4.40
498 1139 1.228245 TGGGCAAAGACCAGCTGTC 60.228 57.895 13.81 10.34 34.69 3.51
499 1140 1.973812 GGGCAAAGACCAGCTGTCC 60.974 63.158 13.81 3.60 45.68 4.02
500 1141 1.073897 GGCAAAGACCAGCTGTCCT 59.926 57.895 13.81 6.11 45.68 3.85
501 1142 0.957888 GGCAAAGACCAGCTGTCCTC 60.958 60.000 13.81 4.10 45.68 3.71
502 1143 0.036022 GCAAAGACCAGCTGTCCTCT 59.964 55.000 13.81 6.48 45.68 3.69
503 1144 1.943507 GCAAAGACCAGCTGTCCTCTC 60.944 57.143 13.81 0.00 45.68 3.20
504 1145 0.980423 AAAGACCAGCTGTCCTCTCC 59.020 55.000 13.81 0.00 45.68 3.71
505 1146 0.907230 AAGACCAGCTGTCCTCTCCC 60.907 60.000 13.81 0.00 45.68 4.30
506 1147 1.610673 GACCAGCTGTCCTCTCCCA 60.611 63.158 13.81 0.00 38.09 4.37
507 1148 1.893919 GACCAGCTGTCCTCTCCCAC 61.894 65.000 13.81 0.00 38.09 4.61
508 1149 1.915266 CCAGCTGTCCTCTCCCACA 60.915 63.158 13.81 0.00 0.00 4.17
509 1150 1.294780 CAGCTGTCCTCTCCCACAC 59.705 63.158 5.25 0.00 0.00 3.82
600 1352 2.487918 TGGCAACACGTCAAAGCTT 58.512 47.368 0.00 0.00 46.17 3.74
601 1353 1.669604 TGGCAACACGTCAAAGCTTA 58.330 45.000 0.00 0.00 46.17 3.09
602 1354 1.601903 TGGCAACACGTCAAAGCTTAG 59.398 47.619 0.00 0.00 46.17 2.18
603 1355 1.602377 GGCAACACGTCAAAGCTTAGT 59.398 47.619 0.00 0.00 0.00 2.24
604 1356 2.349532 GGCAACACGTCAAAGCTTAGTC 60.350 50.000 0.00 0.00 0.00 2.59
605 1357 2.286833 GCAACACGTCAAAGCTTAGTCA 59.713 45.455 0.00 0.00 0.00 3.41
606 1358 3.844943 GCAACACGTCAAAGCTTAGTCAC 60.845 47.826 0.00 0.00 0.00 3.67
607 1359 2.480845 ACACGTCAAAGCTTAGTCACC 58.519 47.619 0.00 0.00 0.00 4.02
608 1360 2.159014 ACACGTCAAAGCTTAGTCACCA 60.159 45.455 0.00 0.00 0.00 4.17
609 1361 2.221055 CACGTCAAAGCTTAGTCACCAC 59.779 50.000 0.00 0.00 0.00 4.16
704 1530 6.198687 CGAAAATGTCTCTGTTTGCACTTTA 58.801 36.000 0.00 0.00 0.00 1.85
725 1569 1.474478 CAGAGTATGCCGTGTCTGTCT 59.526 52.381 0.00 0.00 33.20 3.41
726 1570 1.746220 AGAGTATGCCGTGTCTGTCTC 59.254 52.381 0.00 0.00 0.00 3.36
737 1581 2.668457 GTGTCTGTCTCACGCCTATTTG 59.332 50.000 0.00 0.00 0.00 2.32
754 1598 6.576185 CCTATTTGCCTTATTTGCAGAATGT 58.424 36.000 4.89 0.00 40.35 2.71
782 1637 2.164017 CCATCATTTCACGCCATCACAA 59.836 45.455 0.00 0.00 0.00 3.33
808 1663 0.319900 TCAGTGCCAAGCTCGAGAAC 60.320 55.000 18.75 0.00 0.00 3.01
818 1674 1.347707 AGCTCGAGAACAAATGGTGGA 59.652 47.619 18.75 0.00 0.00 4.02
820 1676 1.734465 CTCGAGAACAAATGGTGGAGC 59.266 52.381 6.58 0.00 0.00 4.70
821 1677 1.347707 TCGAGAACAAATGGTGGAGCT 59.652 47.619 0.00 0.00 0.00 4.09
822 1678 1.734465 CGAGAACAAATGGTGGAGCTC 59.266 52.381 4.71 4.71 0.00 4.09
823 1679 2.613977 CGAGAACAAATGGTGGAGCTCT 60.614 50.000 14.64 0.00 0.00 4.09
824 1680 3.416156 GAGAACAAATGGTGGAGCTCTT 58.584 45.455 14.64 0.00 0.00 2.85
827 1683 4.651045 AGAACAAATGGTGGAGCTCTTTTT 59.349 37.500 14.64 4.17 0.00 1.94
944 1982 2.607631 TGCTGATCAATGAGCATCGA 57.392 45.000 0.29 0.00 42.02 3.59
1130 2177 2.043664 ACTCCTCCATCTTGGTCAGAGA 59.956 50.000 13.35 0.00 39.03 3.10
1132 2179 1.135915 CCTCCATCTTGGTCAGAGACG 59.864 57.143 0.00 0.00 39.03 4.18
1136 2183 0.171455 ATCTTGGTCAGAGACGTCGC 59.829 55.000 11.72 11.72 33.87 5.19
1154 2201 1.972978 CCTTCTTCTCGGACCGGTT 59.027 57.895 15.25 0.00 0.00 4.44
1261 2308 1.671379 GGGCCAACGAAGAGTGTCC 60.671 63.158 4.39 0.00 0.00 4.02
1286 2342 2.202544 CGAGTCTGCCTCAGTCGC 60.203 66.667 0.00 0.00 40.48 5.19
1292 2348 3.602513 CTGCCTCAGTCGCAGGCTT 62.603 63.158 12.74 0.00 45.33 4.35
1296 2352 1.670406 CTCAGTCGCAGGCTTTGCT 60.670 57.895 11.04 0.00 45.33 3.91
1297 2353 1.227943 TCAGTCGCAGGCTTTGCTT 60.228 52.632 11.04 0.00 45.33 3.91
1298 2354 0.819259 TCAGTCGCAGGCTTTGCTTT 60.819 50.000 11.04 0.00 45.33 3.51
1344 2403 4.802051 GGGCCAGCGAAGGATGCA 62.802 66.667 4.39 0.00 33.85 3.96
1355 2414 0.110486 AAGGATGCAACCACCGAGTT 59.890 50.000 16.21 0.00 0.00 3.01
1372 2431 0.798776 GTTTGCCACCATCTCAGTCG 59.201 55.000 0.00 0.00 0.00 4.18
1453 2512 4.100084 CCGAGGCTGCCACCATCA 62.100 66.667 22.65 0.00 0.00 3.07
1488 2547 1.587054 CTTCTTCTCGCACCGGTCT 59.413 57.895 2.59 0.00 0.00 3.85
1532 2591 1.623811 CCTCTTCCAGTTTTCCCTCGA 59.376 52.381 0.00 0.00 0.00 4.04
1536 2595 1.619654 TCCAGTTTTCCCTCGACGTA 58.380 50.000 0.00 0.00 0.00 3.57
1575 2634 1.579429 GATGCCGCCGTTCAAAGTT 59.421 52.632 0.00 0.00 0.00 2.66
1681 2740 1.446792 CTGCTCATCGAGGCACGTT 60.447 57.895 3.89 0.00 43.13 3.99
1703 2762 1.458639 GGCTGCTGCTTCTTGGTGTT 61.459 55.000 15.64 0.00 39.59 3.32
1715 2774 0.254462 TTGGTGTTCAGCTCCACACA 59.746 50.000 21.23 9.66 44.40 3.72
1840 2899 4.485163 ACAAAGAACACAGCAAAGAACAC 58.515 39.130 0.00 0.00 0.00 3.32
1842 2901 4.782019 AAGAACACAGCAAAGAACACAA 57.218 36.364 0.00 0.00 0.00 3.33
1877 2938 3.127895 TGCACAAGCGAAACAAGTAAACT 59.872 39.130 0.00 0.00 46.23 2.66
1903 2968 4.989797 ACAATTGCGATGCTGAAATTCAAA 59.010 33.333 5.05 0.00 0.00 2.69
1904 2969 5.466058 ACAATTGCGATGCTGAAATTCAAAA 59.534 32.000 5.05 0.00 0.00 2.44
1957 3036 2.563086 GATTGTTTGCTCGCCGTCGG 62.563 60.000 6.99 6.99 36.13 4.79
1968 3047 3.816524 CCGTCGGCGAGAGAAGCT 61.817 66.667 12.93 0.00 41.33 3.74
1969 3048 2.277628 CGTCGGCGAGAGAAGCTC 60.278 66.667 11.20 0.00 41.33 4.09
1970 3049 2.103340 GTCGGCGAGAGAAGCTCC 59.897 66.667 11.20 0.00 40.70 4.70
1975 3054 2.440430 CGAGAGAAGCTCCCCGGA 60.440 66.667 0.73 0.00 40.70 5.14
1991 3070 0.174845 CGGATTGTTAGGTCGCCAGA 59.825 55.000 0.00 0.00 0.00 3.86
2008 3094 0.793478 AGAAGAACGTCGCGTGATCG 60.793 55.000 5.77 15.86 39.99 3.69
2064 3170 2.803956 ACCCGGCTGATATAGATCGAA 58.196 47.619 0.00 0.00 34.49 3.71
2386 3548 1.000486 CCCGGAGAGGACCAGAAGA 60.000 63.158 0.73 0.00 45.00 2.87
2389 3551 0.820871 CGGAGAGGACCAGAAGAAGG 59.179 60.000 0.00 0.00 0.00 3.46
2392 3554 1.219393 GAGGACCAGAAGAAGGGCG 59.781 63.158 0.00 0.00 33.83 6.13
2530 3693 1.601412 GCGACGAGATCAGCATCATCA 60.601 52.381 0.00 0.00 0.00 3.07
2532 3695 3.671702 GCGACGAGATCAGCATCATCATA 60.672 47.826 0.00 0.00 0.00 2.15
2564 3727 0.901114 TTCGTGGGATTCCTCGTGGA 60.901 55.000 14.00 1.10 46.55 4.02
2644 3807 7.123355 AGAAGAAGCTACAGATTGAAGCTAT 57.877 36.000 0.00 0.00 45.61 2.97
2646 3809 5.852827 AGAAGCTACAGATTGAAGCTATCC 58.147 41.667 0.00 0.00 45.61 2.59
2662 3825 1.602311 ATCCCAGCATGAAATCGCTC 58.398 50.000 0.00 0.00 39.69 5.03
2663 3826 0.464373 TCCCAGCATGAAATCGCTCC 60.464 55.000 0.00 0.00 39.69 4.70
2664 3827 0.465097 CCCAGCATGAAATCGCTCCT 60.465 55.000 0.00 0.00 39.69 3.69
2665 3828 1.386533 CCAGCATGAAATCGCTCCTT 58.613 50.000 0.00 0.00 39.69 3.36
2666 3829 1.332997 CCAGCATGAAATCGCTCCTTC 59.667 52.381 0.00 0.00 39.69 3.46
2667 3830 2.011947 CAGCATGAAATCGCTCCTTCA 58.988 47.619 0.00 0.00 39.69 3.02
2668 3831 2.421073 CAGCATGAAATCGCTCCTTCAA 59.579 45.455 0.00 0.00 39.69 2.69
2669 3832 3.084039 AGCATGAAATCGCTCCTTCAAA 58.916 40.909 0.00 0.00 35.31 2.69
2670 3833 3.128242 AGCATGAAATCGCTCCTTCAAAG 59.872 43.478 0.00 0.00 35.31 2.77
2671 3834 7.880695 CAGCATGAAATCGCTCCTTCAAAGG 62.881 48.000 0.00 2.15 43.58 3.11
2672 3835 2.436417 TGAAATCGCTCCTTCAAAGGG 58.564 47.619 8.89 1.60 46.47 3.95
2673 3836 2.039746 TGAAATCGCTCCTTCAAAGGGA 59.960 45.455 8.89 0.00 46.47 4.20
2682 3845 2.206576 CTTCAAAGGGAGAAGGGTGG 57.793 55.000 0.00 0.00 38.99 4.61
2683 3846 1.425448 CTTCAAAGGGAGAAGGGTGGT 59.575 52.381 0.00 0.00 38.99 4.16
2684 3847 1.529744 TCAAAGGGAGAAGGGTGGTT 58.470 50.000 0.00 0.00 0.00 3.67
2685 3848 1.144913 TCAAAGGGAGAAGGGTGGTTG 59.855 52.381 0.00 0.00 0.00 3.77
2686 3849 1.144913 CAAAGGGAGAAGGGTGGTTGA 59.855 52.381 0.00 0.00 0.00 3.18
2687 3850 1.068121 AAGGGAGAAGGGTGGTTGAG 58.932 55.000 0.00 0.00 0.00 3.02
2688 3851 0.842467 AGGGAGAAGGGTGGTTGAGG 60.842 60.000 0.00 0.00 0.00 3.86
2689 3852 1.134438 GGGAGAAGGGTGGTTGAGGT 61.134 60.000 0.00 0.00 0.00 3.85
2690 3853 0.771755 GGAGAAGGGTGGTTGAGGTT 59.228 55.000 0.00 0.00 0.00 3.50
2691 3854 1.145119 GGAGAAGGGTGGTTGAGGTTT 59.855 52.381 0.00 0.00 0.00 3.27
2692 3855 2.424379 GGAGAAGGGTGGTTGAGGTTTT 60.424 50.000 0.00 0.00 0.00 2.43
2693 3856 3.296854 GAGAAGGGTGGTTGAGGTTTTT 58.703 45.455 0.00 0.00 0.00 1.94
2694 3857 3.031013 AGAAGGGTGGTTGAGGTTTTTG 58.969 45.455 0.00 0.00 0.00 2.44
2695 3858 2.838637 AGGGTGGTTGAGGTTTTTGA 57.161 45.000 0.00 0.00 0.00 2.69
2696 3859 3.108847 AGGGTGGTTGAGGTTTTTGAA 57.891 42.857 0.00 0.00 0.00 2.69
2697 3860 3.653164 AGGGTGGTTGAGGTTTTTGAAT 58.347 40.909 0.00 0.00 0.00 2.57
2698 3861 4.037222 AGGGTGGTTGAGGTTTTTGAATT 58.963 39.130 0.00 0.00 0.00 2.17
2699 3862 4.473196 AGGGTGGTTGAGGTTTTTGAATTT 59.527 37.500 0.00 0.00 0.00 1.82
2700 3863 4.814234 GGGTGGTTGAGGTTTTTGAATTTC 59.186 41.667 0.00 0.00 0.00 2.17
2701 3864 5.396324 GGGTGGTTGAGGTTTTTGAATTTCT 60.396 40.000 0.00 0.00 0.00 2.52
2702 3865 5.753438 GGTGGTTGAGGTTTTTGAATTTCTC 59.247 40.000 0.00 0.00 0.00 2.87
2709 3872 6.991531 TGAGGTTTTTGAATTTCTCCCATTTG 59.008 34.615 0.00 0.00 0.00 2.32
2721 3884 2.036217 CTCCCATTTGTTTGCTTGCAGA 59.964 45.455 0.00 0.00 0.00 4.26
2742 3905 5.119588 CAGATGTTTCAAATGTTCCATGTGC 59.880 40.000 0.00 0.00 0.00 4.57
2748 3911 2.299582 CAAATGTTCCATGTGCCCTTGA 59.700 45.455 0.00 0.00 0.00 3.02
2750 3913 0.478072 TGTTCCATGTGCCCTTGACT 59.522 50.000 0.00 0.00 0.00 3.41
2751 3914 1.702401 TGTTCCATGTGCCCTTGACTA 59.298 47.619 0.00 0.00 0.00 2.59
2752 3915 2.290260 TGTTCCATGTGCCCTTGACTAG 60.290 50.000 0.00 0.00 0.00 2.57
2753 3916 1.951209 TCCATGTGCCCTTGACTAGA 58.049 50.000 0.00 0.00 0.00 2.43
2754 3917 1.555075 TCCATGTGCCCTTGACTAGAC 59.445 52.381 0.00 0.00 0.00 2.59
2755 3918 1.556911 CCATGTGCCCTTGACTAGACT 59.443 52.381 0.00 0.00 0.00 3.24
2756 3919 2.026822 CCATGTGCCCTTGACTAGACTT 60.027 50.000 0.00 0.00 0.00 3.01
2760 3923 3.006537 TGTGCCCTTGACTAGACTTACAC 59.993 47.826 0.00 0.00 0.00 2.90
2762 3925 3.644265 TGCCCTTGACTAGACTTACACAA 59.356 43.478 0.00 0.00 0.00 3.33
2763 3926 4.101898 TGCCCTTGACTAGACTTACACAAA 59.898 41.667 0.00 0.00 0.00 2.83
2764 3927 4.691216 GCCCTTGACTAGACTTACACAAAG 59.309 45.833 0.00 0.00 41.33 2.77
2765 3928 5.510861 GCCCTTGACTAGACTTACACAAAGA 60.511 44.000 0.00 0.00 38.67 2.52
2766 3929 6.522054 CCCTTGACTAGACTTACACAAAGAA 58.478 40.000 0.00 0.00 38.67 2.52
2767 3930 7.162082 CCCTTGACTAGACTTACACAAAGAAT 58.838 38.462 0.00 0.00 38.67 2.40
2768 3931 7.332182 CCCTTGACTAGACTTACACAAAGAATC 59.668 40.741 0.00 0.00 38.67 2.52
2769 3932 7.332182 CCTTGACTAGACTTACACAAAGAATCC 59.668 40.741 0.00 0.00 38.67 3.01
2771 3934 7.732025 TGACTAGACTTACACAAAGAATCCAA 58.268 34.615 0.00 0.00 38.67 3.53
2772 3935 8.208224 TGACTAGACTTACACAAAGAATCCAAA 58.792 33.333 0.00 0.00 38.67 3.28
2773 3936 8.379457 ACTAGACTTACACAAAGAATCCAAAC 57.621 34.615 0.00 0.00 38.67 2.93
2774 3937 6.300354 AGACTTACACAAAGAATCCAAACG 57.700 37.500 0.00 0.00 38.67 3.60
2775 3938 6.053005 AGACTTACACAAAGAATCCAAACGA 58.947 36.000 0.00 0.00 38.67 3.85
2777 3940 6.725246 ACTTACACAAAGAATCCAAACGAAG 58.275 36.000 0.00 0.00 38.67 3.79
2778 3941 6.317893 ACTTACACAAAGAATCCAAACGAAGT 59.682 34.615 0.00 0.00 40.20 3.01
2779 3942 7.148137 ACTTACACAAAGAATCCAAACGAAGTT 60.148 33.333 0.00 0.00 46.01 2.66
2849 4018 6.455647 TCAATATTTGAGGTGCTACGATAGG 58.544 40.000 0.00 0.00 35.69 2.57
2863 4032 1.221414 GATAGGCGTTCATCCAGTGC 58.779 55.000 0.00 0.00 0.00 4.40
2865 4034 2.045926 GGCGTTCATCCAGTGCCT 60.046 61.111 0.00 0.00 42.44 4.75
2880 4049 2.259204 CCTTGTTGCATGCCCACG 59.741 61.111 16.68 9.42 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 5.835280 CAGGCCAAGTTGGAATTAGGATATT 59.165 40.000 26.52 0.00 40.96 1.28
32 33 3.173953 TGATTCAGGCCAAGTTGGAAT 57.826 42.857 26.52 15.44 40.96 3.01
35 36 2.355756 CGTATGATTCAGGCCAAGTTGG 59.644 50.000 18.17 18.17 41.55 3.77
38 39 4.689612 ATACGTATGATTCAGGCCAAGT 57.310 40.909 7.41 0.00 0.00 3.16
40 41 6.353404 TCATATACGTATGATTCAGGCCAA 57.647 37.500 18.37 0.00 41.28 4.52
94 111 3.857010 GCAAGTGGAAGGTGAATTTTCCG 60.857 47.826 2.90 0.00 44.66 4.30
126 147 2.981140 GTCTCTCACTAACACTGCGAAC 59.019 50.000 0.00 0.00 0.00 3.95
148 171 1.956477 ACACCAGCCTGTTGAATCAAC 59.044 47.619 18.42 18.42 43.78 3.18
168 199 1.473677 GGTGCACTTCAATAGCATGCA 59.526 47.619 21.98 6.36 43.70 3.96
180 211 3.292936 GCTGCTGCTGGTGCACTT 61.293 61.111 17.98 0.00 45.31 3.16
233 281 3.907260 CTGACCCGTGGCAGTGCAT 62.907 63.158 18.61 0.00 0.00 3.96
296 363 3.160047 CCAGCGGCCAGATCTCCT 61.160 66.667 2.24 0.00 0.00 3.69
492 1133 1.915769 GGTGTGGGAGAGGACAGCT 60.916 63.158 0.00 0.00 37.56 4.24
493 1134 2.217038 TGGTGTGGGAGAGGACAGC 61.217 63.158 0.00 0.00 40.29 4.40
494 1135 1.121407 TGTGGTGTGGGAGAGGACAG 61.121 60.000 0.00 0.00 0.00 3.51
495 1136 1.074850 TGTGGTGTGGGAGAGGACA 60.075 57.895 0.00 0.00 0.00 4.02
496 1137 1.371558 GTGTGGTGTGGGAGAGGAC 59.628 63.158 0.00 0.00 0.00 3.85
497 1138 1.841556 GGTGTGGTGTGGGAGAGGA 60.842 63.158 0.00 0.00 0.00 3.71
498 1139 2.750350 GGTGTGGTGTGGGAGAGG 59.250 66.667 0.00 0.00 0.00 3.69
499 1140 2.343758 CGGTGTGGTGTGGGAGAG 59.656 66.667 0.00 0.00 0.00 3.20
500 1141 3.936203 GCGGTGTGGTGTGGGAGA 61.936 66.667 0.00 0.00 0.00 3.71
501 1142 3.941188 AGCGGTGTGGTGTGGGAG 61.941 66.667 0.00 0.00 0.00 4.30
502 1143 4.248842 CAGCGGTGTGGTGTGGGA 62.249 66.667 6.41 0.00 41.21 4.37
704 1530 1.202582 GACAGACACGGCATACTCTGT 59.797 52.381 6.15 6.15 44.81 3.41
730 1574 6.576185 ACATTCTGCAAATAAGGCAAATAGG 58.424 36.000 0.00 0.00 41.39 2.57
733 1577 6.934056 TGTACATTCTGCAAATAAGGCAAAT 58.066 32.000 0.00 0.00 41.39 2.32
737 1581 5.572896 GTGTTGTACATTCTGCAAATAAGGC 59.427 40.000 0.00 0.00 0.00 4.35
754 1598 2.486203 GGCGTGAAATGATGGTGTTGTA 59.514 45.455 0.00 0.00 0.00 2.41
782 1637 3.118629 TCGAGCTTGGCACTGATCTTATT 60.119 43.478 0.00 0.00 0.00 1.40
885 1858 6.770746 TTTTAGTGTAGCTAGGTGGAGTAG 57.229 41.667 4.27 0.00 0.00 2.57
944 1982 4.263435 AGTGTTAGCTAGACTAGTCGCTT 58.737 43.478 24.41 9.06 34.14 4.68
1109 2156 2.043664 TCTCTGACCAAGATGGAGGAGT 59.956 50.000 2.85 0.00 40.96 3.85
1130 2177 1.970114 TCCGAGAAGAAGGCGACGT 60.970 57.895 0.00 0.00 0.00 4.34
1132 2179 1.153804 GGTCCGAGAAGAAGGCGAC 60.154 63.158 0.00 0.00 0.00 5.19
1136 2183 0.389948 CAACCGGTCCGAGAAGAAGG 60.390 60.000 14.39 0.00 0.00 3.46
1154 2201 3.889044 GCCTCGCTCCGTCGATCA 61.889 66.667 0.00 0.00 37.87 2.92
1174 2221 2.032860 ATGGAGGCATCGTCCTTCGG 62.033 60.000 7.03 0.00 38.97 4.30
1181 2228 2.298158 GACCGTGATGGAGGCATCGT 62.298 60.000 0.00 0.00 42.00 3.73
1286 2342 1.198637 CGGAGAAGAAAGCAAAGCCTG 59.801 52.381 0.00 0.00 0.00 4.85
1292 2348 0.320421 CCGGTCGGAGAAGAAAGCAA 60.320 55.000 2.83 0.00 39.69 3.91
1321 2380 4.093291 CTTCGCTGGCCCTGCTCT 62.093 66.667 11.07 0.00 0.00 4.09
1344 2403 1.826487 GGTGGCAAACTCGGTGGTT 60.826 57.895 0.00 0.00 0.00 3.67
1355 2414 1.204704 CTACGACTGAGATGGTGGCAA 59.795 52.381 0.00 0.00 0.00 4.52
1506 2565 3.569200 AAACTGGAAGAGGCCGGCC 62.569 63.158 39.29 39.29 37.87 6.13
1559 2618 2.548295 GGAACTTTGAACGGCGGCA 61.548 57.895 13.24 6.19 0.00 5.69
1681 2740 1.303074 CCAAGAAGCAGCAGCCTGA 60.303 57.895 0.00 0.00 41.77 3.86
1703 2762 2.031012 CGGCTTGTGTGGAGCTGA 59.969 61.111 0.00 0.00 46.98 4.26
1840 2899 3.713858 TGTGCAATCACTTGGTCTTTG 57.286 42.857 0.00 0.00 43.49 2.77
1842 2901 2.035066 GCTTGTGCAATCACTTGGTCTT 59.965 45.455 0.00 0.00 43.49 3.01
1877 2938 3.639716 TTTCAGCATCGCAATTGTTCA 57.360 38.095 7.40 0.00 0.00 3.18
1903 2968 6.054295 CCTCTTTCTTCTCCGATCATCATTT 58.946 40.000 0.00 0.00 0.00 2.32
1904 2969 5.365025 TCCTCTTTCTTCTCCGATCATCATT 59.635 40.000 0.00 0.00 0.00 2.57
1958 3037 1.395826 AATCCGGGGAGCTTCTCTCG 61.396 60.000 0.00 0.00 42.82 4.04
1959 3038 0.105778 CAATCCGGGGAGCTTCTCTC 59.894 60.000 0.00 0.00 41.15 3.20
1960 3039 0.618968 ACAATCCGGGGAGCTTCTCT 60.619 55.000 0.00 0.00 0.00 3.10
1961 3040 0.253327 AACAATCCGGGGAGCTTCTC 59.747 55.000 0.00 0.00 0.00 2.87
1962 3041 1.486726 CTAACAATCCGGGGAGCTTCT 59.513 52.381 0.00 0.00 0.00 2.85
1963 3042 1.475213 CCTAACAATCCGGGGAGCTTC 60.475 57.143 0.00 0.00 0.00 3.86
1964 3043 0.546598 CCTAACAATCCGGGGAGCTT 59.453 55.000 0.00 0.00 0.00 3.74
1965 3044 0.620700 ACCTAACAATCCGGGGAGCT 60.621 55.000 0.00 0.00 0.00 4.09
1966 3045 0.179054 GACCTAACAATCCGGGGAGC 60.179 60.000 0.00 0.00 0.00 4.70
1967 3046 0.104304 CGACCTAACAATCCGGGGAG 59.896 60.000 0.00 0.00 0.00 4.30
1968 3047 1.963464 GCGACCTAACAATCCGGGGA 61.963 60.000 0.00 0.00 0.00 4.81
1969 3048 1.523032 GCGACCTAACAATCCGGGG 60.523 63.158 0.00 0.00 0.00 5.73
1970 3049 1.523032 GGCGACCTAACAATCCGGG 60.523 63.158 0.00 0.00 0.00 5.73
1975 3054 3.335579 GTTCTTCTGGCGACCTAACAAT 58.664 45.455 0.00 0.00 0.00 2.71
1991 3070 0.179171 ATCGATCACGCGACGTTCTT 60.179 50.000 15.93 0.00 43.79 2.52
2008 3094 2.933260 GCACTTTTCCTTCTCCTCGATC 59.067 50.000 0.00 0.00 0.00 3.69
2356 3517 3.327404 TCCGGGGTTCTTCCAGCC 61.327 66.667 0.00 0.00 38.11 4.85
2443 3605 4.537433 GCAGCGGCCGAGGAAGAT 62.537 66.667 33.48 1.03 0.00 2.40
2530 3693 3.833070 CCCACGAATAGGAAGTAGGCTAT 59.167 47.826 0.00 0.00 0.00 2.97
2532 3695 2.040178 CCCACGAATAGGAAGTAGGCT 58.960 52.381 0.00 0.00 0.00 4.58
2564 3727 5.363580 CCAATTGCCTTACCTTTGTCCATAT 59.636 40.000 0.00 0.00 0.00 1.78
2644 3807 0.464373 GGAGCGATTTCATGCTGGGA 60.464 55.000 0.00 0.00 42.60 4.37
2646 3809 1.332997 GAAGGAGCGATTTCATGCTGG 59.667 52.381 0.00 0.00 42.60 4.85
2663 3826 1.425448 ACCACCCTTCTCCCTTTGAAG 59.575 52.381 0.00 0.00 40.23 3.02
2664 3827 1.529744 ACCACCCTTCTCCCTTTGAA 58.470 50.000 0.00 0.00 0.00 2.69
2665 3828 1.144913 CAACCACCCTTCTCCCTTTGA 59.855 52.381 0.00 0.00 0.00 2.69
2666 3829 1.144913 TCAACCACCCTTCTCCCTTTG 59.855 52.381 0.00 0.00 0.00 2.77
2667 3830 1.425448 CTCAACCACCCTTCTCCCTTT 59.575 52.381 0.00 0.00 0.00 3.11
2668 3831 1.068121 CTCAACCACCCTTCTCCCTT 58.932 55.000 0.00 0.00 0.00 3.95
2669 3832 0.842467 CCTCAACCACCCTTCTCCCT 60.842 60.000 0.00 0.00 0.00 4.20
2670 3833 1.134438 ACCTCAACCACCCTTCTCCC 61.134 60.000 0.00 0.00 0.00 4.30
2671 3834 0.771755 AACCTCAACCACCCTTCTCC 59.228 55.000 0.00 0.00 0.00 3.71
2672 3835 2.658807 AAACCTCAACCACCCTTCTC 57.341 50.000 0.00 0.00 0.00 2.87
2673 3836 3.031013 CAAAAACCTCAACCACCCTTCT 58.969 45.455 0.00 0.00 0.00 2.85
2674 3837 3.028130 TCAAAAACCTCAACCACCCTTC 58.972 45.455 0.00 0.00 0.00 3.46
2675 3838 3.108847 TCAAAAACCTCAACCACCCTT 57.891 42.857 0.00 0.00 0.00 3.95
2676 3839 2.838637 TCAAAAACCTCAACCACCCT 57.161 45.000 0.00 0.00 0.00 4.34
2677 3840 4.415881 AATTCAAAAACCTCAACCACCC 57.584 40.909 0.00 0.00 0.00 4.61
2678 3841 5.670485 AGAAATTCAAAAACCTCAACCACC 58.330 37.500 0.00 0.00 0.00 4.61
2679 3842 5.753438 GGAGAAATTCAAAAACCTCAACCAC 59.247 40.000 0.00 0.00 0.00 4.16
2680 3843 5.163353 GGGAGAAATTCAAAAACCTCAACCA 60.163 40.000 0.00 0.00 0.00 3.67
2681 3844 5.163353 TGGGAGAAATTCAAAAACCTCAACC 60.163 40.000 0.00 0.00 0.00 3.77
2682 3845 5.912892 TGGGAGAAATTCAAAAACCTCAAC 58.087 37.500 0.00 0.00 0.00 3.18
2683 3846 6.745794 ATGGGAGAAATTCAAAAACCTCAA 57.254 33.333 0.00 0.00 0.00 3.02
2684 3847 6.745794 AATGGGAGAAATTCAAAAACCTCA 57.254 33.333 0.00 0.00 0.00 3.86
2685 3848 6.992123 ACAAATGGGAGAAATTCAAAAACCTC 59.008 34.615 0.00 0.00 0.00 3.85
2686 3849 6.899089 ACAAATGGGAGAAATTCAAAAACCT 58.101 32.000 0.00 0.00 0.00 3.50
2687 3850 7.566760 AACAAATGGGAGAAATTCAAAAACC 57.433 32.000 0.00 0.00 0.00 3.27
2688 3851 7.431960 GCAAACAAATGGGAGAAATTCAAAAAC 59.568 33.333 0.00 0.00 0.00 2.43
2689 3852 7.338957 AGCAAACAAATGGGAGAAATTCAAAAA 59.661 29.630 0.00 0.00 0.00 1.94
2690 3853 6.827762 AGCAAACAAATGGGAGAAATTCAAAA 59.172 30.769 0.00 0.00 0.00 2.44
2691 3854 6.355747 AGCAAACAAATGGGAGAAATTCAAA 58.644 32.000 0.00 0.00 0.00 2.69
2692 3855 5.927819 AGCAAACAAATGGGAGAAATTCAA 58.072 33.333 0.00 0.00 0.00 2.69
2693 3856 5.549742 AGCAAACAAATGGGAGAAATTCA 57.450 34.783 0.00 0.00 0.00 2.57
2694 3857 5.334337 GCAAGCAAACAAATGGGAGAAATTC 60.334 40.000 0.00 0.00 0.00 2.17
2695 3858 4.516321 GCAAGCAAACAAATGGGAGAAATT 59.484 37.500 0.00 0.00 0.00 1.82
2696 3859 4.067192 GCAAGCAAACAAATGGGAGAAAT 58.933 39.130 0.00 0.00 0.00 2.17
2697 3860 3.118482 TGCAAGCAAACAAATGGGAGAAA 60.118 39.130 0.00 0.00 0.00 2.52
2698 3861 2.433604 TGCAAGCAAACAAATGGGAGAA 59.566 40.909 0.00 0.00 0.00 2.87
2699 3862 2.036217 CTGCAAGCAAACAAATGGGAGA 59.964 45.455 0.00 0.00 0.00 3.71
2700 3863 2.036217 TCTGCAAGCAAACAAATGGGAG 59.964 45.455 0.00 0.00 0.00 4.30
2701 3864 2.037901 TCTGCAAGCAAACAAATGGGA 58.962 42.857 0.00 0.00 0.00 4.37
2702 3865 2.529780 TCTGCAAGCAAACAAATGGG 57.470 45.000 0.00 0.00 0.00 4.00
2709 3872 5.006941 ACATTTGAAACATCTGCAAGCAAAC 59.993 36.000 0.00 0.00 0.00 2.93
2742 3905 6.097915 TCTTTGTGTAAGTCTAGTCAAGGG 57.902 41.667 0.00 0.00 35.28 3.95
2748 3911 7.170998 CGTTTGGATTCTTTGTGTAAGTCTAGT 59.829 37.037 0.00 0.00 35.28 2.57
2750 3913 7.211573 TCGTTTGGATTCTTTGTGTAAGTCTA 58.788 34.615 0.00 0.00 35.28 2.59
2751 3914 6.053005 TCGTTTGGATTCTTTGTGTAAGTCT 58.947 36.000 0.00 0.00 35.28 3.24
2752 3915 6.295039 TCGTTTGGATTCTTTGTGTAAGTC 57.705 37.500 0.00 0.00 35.28 3.01
2753 3916 6.317893 ACTTCGTTTGGATTCTTTGTGTAAGT 59.682 34.615 0.00 0.00 35.28 2.24
2754 3917 6.725246 ACTTCGTTTGGATTCTTTGTGTAAG 58.275 36.000 0.00 0.00 35.04 2.34
2755 3918 6.687081 ACTTCGTTTGGATTCTTTGTGTAA 57.313 33.333 0.00 0.00 0.00 2.41
2756 3919 6.687081 AACTTCGTTTGGATTCTTTGTGTA 57.313 33.333 0.00 0.00 0.00 2.90
2760 3923 8.507249 AGAGATAAACTTCGTTTGGATTCTTTG 58.493 33.333 2.46 0.00 36.37 2.77
2762 3925 7.878127 TCAGAGATAAACTTCGTTTGGATTCTT 59.122 33.333 2.46 0.00 36.37 2.52
2763 3926 7.386851 TCAGAGATAAACTTCGTTTGGATTCT 58.613 34.615 2.46 0.72 36.37 2.40
2764 3927 7.596749 TCAGAGATAAACTTCGTTTGGATTC 57.403 36.000 2.46 0.00 36.37 2.52
2765 3928 7.979444 TTCAGAGATAAACTTCGTTTGGATT 57.021 32.000 2.46 0.00 36.37 3.01
2766 3929 7.979444 TTTCAGAGATAAACTTCGTTTGGAT 57.021 32.000 2.46 0.00 36.37 3.41
2767 3930 7.659799 TCATTTCAGAGATAAACTTCGTTTGGA 59.340 33.333 2.46 0.00 36.37 3.53
2768 3931 7.806690 TCATTTCAGAGATAAACTTCGTTTGG 58.193 34.615 2.46 0.00 36.37 3.28
2769 3932 9.322776 CTTCATTTCAGAGATAAACTTCGTTTG 57.677 33.333 2.46 0.00 36.37 2.93
2771 3934 8.608844 ACTTCATTTCAGAGATAAACTTCGTT 57.391 30.769 0.00 0.00 0.00 3.85
2772 3935 8.608844 AACTTCATTTCAGAGATAAACTTCGT 57.391 30.769 0.00 0.00 0.00 3.85
2781 3944 8.877779 CAAGACGATAAACTTCATTTCAGAGAT 58.122 33.333 0.00 0.00 0.00 2.75
2785 3948 9.483062 GATTCAAGACGATAAACTTCATTTCAG 57.517 33.333 0.00 0.00 0.00 3.02
2786 3949 9.219603 AGATTCAAGACGATAAACTTCATTTCA 57.780 29.630 0.00 0.00 0.00 2.69
2849 4018 1.237285 ACAAGGCACTGGATGAACGC 61.237 55.000 0.00 0.00 40.86 4.84
2851 4020 1.336240 GCAACAAGGCACTGGATGAAC 60.336 52.381 0.00 0.00 40.86 3.18
2863 4032 1.240641 TACGTGGGCATGCAACAAGG 61.241 55.000 21.36 14.52 0.00 3.61
2865 4034 1.201181 GAATACGTGGGCATGCAACAA 59.799 47.619 21.36 8.44 0.00 2.83


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

AutoCloner maintained by Alex Coulton.