Multiple sequence alignment - TraesCS2A01G307900

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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 TraesCS2A01G307900 chr2A 100.000 7223 0 0 1 7223 528904426 528911648 0.000000e+00 13339.0
1 TraesCS2A01G307900 chr2A 90.700 2699 157 39 4198 6829 529694574 529697245 0.000000e+00 3507.0
2 TraesCS2A01G307900 chr2A 90.935 2471 149 36 1694 4148 529792464 529794875 0.000000e+00 3253.0
3 TraesCS2A01G307900 chr2A 88.963 2546 163 45 1620 4148 529692131 529694575 0.000000e+00 3037.0
4 TraesCS2A01G307900 chr2A 92.614 2112 119 17 4198 6287 529794874 529796970 0.000000e+00 3001.0
5 TraesCS2A01G307900 chr2A 83.876 645 44 24 846 1475 529791492 529792091 1.760000e-155 560.0
6 TraesCS2A01G307900 chr2A 84.584 493 46 23 1144 1618 529691604 529692084 5.100000e-126 462.0
7 TraesCS2A01G307900 chr2D 96.515 5624 123 33 684 6285 391849716 391855288 0.000000e+00 9232.0
8 TraesCS2A01G307900 chr2D 91.923 2402 143 26 1764 4148 392052528 392054895 0.000000e+00 3314.0
9 TraesCS2A01G307900 chr2D 92.891 2110 98 19 4198 6285 392054894 392056973 0.000000e+00 3018.0
10 TraesCS2A01G307900 chr2D 89.400 783 61 3 6442 7223 391863153 391863914 0.000000e+00 966.0
11 TraesCS2A01G307900 chr2D 89.020 510 50 5 1 505 391847670 391848178 1.710000e-175 627.0
12 TraesCS2A01G307900 chr2D 84.729 609 39 16 877 1473 392051780 392052346 1.760000e-155 560.0
13 TraesCS2A01G307900 chr2D 87.218 133 11 2 584 716 391849655 391849781 5.840000e-31 147.0
14 TraesCS2A01G307900 chr2B 96.286 5628 157 23 668 6285 463765496 463771081 0.000000e+00 9188.0
15 TraesCS2A01G307900 chr2B 93.011 2232 129 11 1928 4147 464021518 464023734 0.000000e+00 3232.0
16 TraesCS2A01G307900 chr2B 90.532 2461 154 42 1704 4148 463856119 463858516 0.000000e+00 3181.0
17 TraesCS2A01G307900 chr2B 94.104 2086 109 7 4200 6285 464023736 464025807 0.000000e+00 3158.0
18 TraesCS2A01G307900 chr2B 93.067 2106 108 18 4198 6285 463858515 463860600 0.000000e+00 3046.0
19 TraesCS2A01G307900 chr2B 89.880 919 51 11 6312 7223 463771158 463772041 0.000000e+00 1144.0
20 TraesCS2A01G307900 chr2B 81.541 1051 101 52 858 1876 464020301 464021290 0.000000e+00 780.0
21 TraesCS2A01G307900 chr2B 88.762 525 43 7 6312 6829 463860684 463861199 4.760000e-176 628.0
22 TraesCS2A01G307900 chr2B 81.258 779 58 37 877 1618 463855299 463856026 3.810000e-152 549.0
23 TraesCS2A01G307900 chr2B 82.752 487 75 8 1 481 463764531 463765014 6.700000e-115 425.0
24 TraesCS2A01G307900 chr2B 84.314 153 13 5 6312 6453 464025885 464026037 9.770000e-29 139.0
25 TraesCS2A01G307900 chr6D 85.714 119 17 0 4335 4453 128257908 128258026 7.610000e-25 126.0
26 TraesCS2A01G307900 chr6B 78.756 193 37 4 4335 4525 227096126 227096316 7.610000e-25 126.0
27 TraesCS2A01G307900 chr5B 87.692 65 8 0 2283 2347 62958514 62958578 7.770000e-10 76.8
28 TraesCS2A01G307900 chr5A 97.143 35 1 0 2578 2612 444923497 444923531 7.830000e-05 60.2


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 TraesCS2A01G307900 chr2A 528904426 528911648 7222 False 13339.000000 13339 100.000000 1 7223 1 chr2A.!!$F1 7222
1 TraesCS2A01G307900 chr2A 529691604 529697245 5641 False 2335.333333 3507 88.082333 1144 6829 3 chr2A.!!$F2 5685
2 TraesCS2A01G307900 chr2A 529791492 529796970 5478 False 2271.333333 3253 89.141667 846 6287 3 chr2A.!!$F3 5441
3 TraesCS2A01G307900 chr2D 391847670 391855288 7618 False 3335.333333 9232 90.917667 1 6285 3 chr2D.!!$F2 6284
4 TraesCS2A01G307900 chr2D 392051780 392056973 5193 False 2297.333333 3314 89.847667 877 6285 3 chr2D.!!$F3 5408
5 TraesCS2A01G307900 chr2D 391863153 391863914 761 False 966.000000 966 89.400000 6442 7223 1 chr2D.!!$F1 781
6 TraesCS2A01G307900 chr2B 463764531 463772041 7510 False 3585.666667 9188 89.639333 1 7223 3 chr2B.!!$F1 7222
7 TraesCS2A01G307900 chr2B 463855299 463861199 5900 False 1851.000000 3181 88.404750 877 6829 4 chr2B.!!$F2 5952
8 TraesCS2A01G307900 chr2B 464020301 464026037 5736 False 1827.250000 3232 88.242500 858 6453 4 chr2B.!!$F3 5595

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
630 2207 0.732538 CGCGTATGCATGCTCCGATA 60.733 55.000 20.33 5.26 42.97 2.92 F
1736 3674 0.106149 GAAGTTGGTCTCACGGGTGT 59.894 55.000 0.00 0.00 0.00 4.16 F
2280 4441 1.536766 TGTTTCTCTGCAGCAATTCCG 59.463 47.619 9.47 0.00 0.00 4.30 F
2797 4959 0.740516 GCAGCCAGAGAGAAGCAGAC 60.741 60.000 0.00 0.00 0.00 3.51 F
4322 6488 1.207089 TGCTCGTACCATTGAGAAGGG 59.793 52.381 0.24 0.00 38.57 3.95 F
4813 6979 0.512952 GCTCGTTCGTCATTGCTGTT 59.487 50.000 0.00 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2611 4773 1.877576 ATGTCGCCTTCTGCACGAGA 61.878 55.000 0.00 0.0 41.33 4.04 R
2724 4886 2.185608 GAGCACGAGCCTTCCTCC 59.814 66.667 0.00 0.0 43.56 4.30 R
4322 6488 3.551846 TCCCTCACTTTGTCTTGGAAAC 58.448 45.455 0.00 0.0 0.00 2.78 R
4813 6979 0.326595 TGAAACGCAGGCCCTTGATA 59.673 50.000 0.00 0.0 0.00 2.15 R
5785 8003 1.079127 CCTGAATCTTGGCGTCCGT 60.079 57.895 0.00 0.0 0.00 4.69 R
6805 9121 0.690744 ACAGTTTTGGGGCCTTTGCT 60.691 50.000 0.84 0.0 37.74 3.91 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
29 30 1.471287 CCTCATGTTGTGCCAGTCATG 59.529 52.381 0.00 0.00 38.96 3.07
55 56 0.950836 TTGCAACAATGGTGTCTCCG 59.049 50.000 0.00 0.00 36.80 4.63
85 86 1.149401 GCATAGGGAGGAGGTTGCC 59.851 63.158 0.00 0.00 0.00 4.52
89 90 2.449967 TAGGGAGGAGGTTGCCGACA 62.450 60.000 0.00 0.00 33.14 4.35
142 143 1.396996 CGGGCGATTAAGTTGGTCAAG 59.603 52.381 0.00 0.00 0.00 3.02
151 152 6.523201 CGATTAAGTTGGTCAAGTTACAATGC 59.477 38.462 9.69 0.00 36.32 3.56
152 153 6.952773 TTAAGTTGGTCAAGTTACAATGCT 57.047 33.333 9.69 0.00 36.32 3.79
162 163 2.226437 AGTTACAATGCTGTCCTTTGCG 59.774 45.455 0.00 0.00 36.96 4.85
178 179 1.961277 GCGGGGTTGCTATCCATCG 60.961 63.158 0.00 0.00 0.00 3.84
223 224 1.353103 GCGTTGGATCAATCGGCTG 59.647 57.895 2.85 0.00 0.00 4.85
293 296 6.127451 CCCCTGTTTTTAGGATGGTAATTCAC 60.127 42.308 0.00 0.00 40.42 3.18
320 323 6.726258 TCTAGTTGTACAATCAGCAATGTG 57.274 37.500 12.26 0.00 0.00 3.21
324 327 4.424061 TGTACAATCAGCAATGTGAAGC 57.576 40.909 0.00 0.00 0.00 3.86
335 338 4.095483 AGCAATGTGAAGCTGTAATACTGC 59.905 41.667 13.37 13.37 42.43 4.40
338 341 6.558009 CAATGTGAAGCTGTAATACTGCAAT 58.442 36.000 21.27 11.46 44.20 3.56
359 362 9.449550 TGCAATGTTATTTTATCGCAAAGATAG 57.550 29.630 0.00 0.00 42.29 2.08
404 407 2.270275 TGTTGGTCAACACAAAAGCG 57.730 45.000 11.95 0.00 45.42 4.68
414 418 2.227194 ACACAAAAGCGGTCCCTAAAG 58.773 47.619 0.00 0.00 0.00 1.85
416 420 3.081804 CACAAAAGCGGTCCCTAAAGAT 58.918 45.455 0.00 0.00 0.00 2.40
423 427 7.793948 AAAGCGGTCCCTAAAGATATATACT 57.206 36.000 0.00 0.00 0.00 2.12
424 428 8.890410 AAAGCGGTCCCTAAAGATATATACTA 57.110 34.615 0.00 0.00 0.00 1.82
467 474 8.638685 ATCACATTTTCAAGTCAAACTCAAAG 57.361 30.769 0.00 0.00 0.00 2.77
474 481 7.391148 TTCAAGTCAAACTCAAAGCTAACTT 57.609 32.000 0.00 0.00 37.90 2.66
481 488 8.799091 GTCAAACTCAAAGCTAACTTCTTTTTC 58.201 33.333 0.00 0.00 34.05 2.29
482 489 7.973944 TCAAACTCAAAGCTAACTTCTTTTTCC 59.026 33.333 0.00 0.00 34.05 3.13
484 491 8.747538 AACTCAAAGCTAACTTCTTTTTCCTA 57.252 30.769 0.00 0.00 34.05 2.94
494 501 6.846325 ACTTCTTTTTCCTAGTTGAACTCG 57.154 37.500 0.00 0.00 0.00 4.18
495 502 6.346896 ACTTCTTTTTCCTAGTTGAACTCGT 58.653 36.000 0.00 0.00 0.00 4.18
500 507 8.145767 TCTTTTTCCTAGTTGAACTCGTATCAA 58.854 33.333 0.00 0.00 34.56 2.57
501 508 8.665643 TTTTTCCTAGTTGAACTCGTATCAAA 57.334 30.769 0.00 0.00 38.44 2.69
537 544 6.147328 AGCTTTAACTCGTATCAAACTTGACC 59.853 38.462 0.00 0.00 40.49 4.02
550 557 2.322658 ACTTGACCGAACTGGGAAGTA 58.677 47.619 0.00 0.00 40.76 2.24
558 565 3.443681 CCGAACTGGGAAGTAAAATGCAT 59.556 43.478 0.00 0.00 0.00 3.96
560 567 5.299279 CCGAACTGGGAAGTAAAATGCATAT 59.701 40.000 0.00 0.00 0.00 1.78
561 568 6.201517 CGAACTGGGAAGTAAAATGCATATG 58.798 40.000 0.00 0.00 0.00 1.78
562 569 5.520376 ACTGGGAAGTAAAATGCATATGC 57.480 39.130 21.09 21.09 42.50 3.14
595 2172 9.950680 CGATTGTAATATGCTAAGAAAACCATT 57.049 29.630 0.00 0.00 0.00 3.16
608 2185 6.773976 AGAAAACCATTGAAAACAGTCTCA 57.226 33.333 0.00 0.00 0.00 3.27
612 2189 5.862924 ACCATTGAAAACAGTCTCATACG 57.137 39.130 0.00 0.00 0.00 3.06
614 2191 4.326205 CATTGAAAACAGTCTCATACGCG 58.674 43.478 3.53 3.53 0.00 6.01
618 2195 4.561213 TGAAAACAGTCTCATACGCGTATG 59.439 41.667 40.41 40.41 43.16 2.39
621 2198 2.034685 ACAGTCTCATACGCGTATGCAT 59.965 45.455 40.92 27.40 41.92 3.96
630 2207 0.732538 CGCGTATGCATGCTCCGATA 60.733 55.000 20.33 5.26 42.97 2.92
632 2209 1.126846 GCGTATGCATGCTCCGATAAC 59.873 52.381 20.33 5.53 42.15 1.89
634 2211 1.726791 GTATGCATGCTCCGATAACCG 59.273 52.381 20.33 0.00 38.18 4.44
667 2245 3.056821 TCACATTTCCGAGTCGAACTCAT 60.057 43.478 15.64 0.00 45.30 2.90
668 2246 4.157105 TCACATTTCCGAGTCGAACTCATA 59.843 41.667 15.64 0.00 45.30 2.15
669 2247 5.043903 CACATTTCCGAGTCGAACTCATAT 58.956 41.667 15.64 0.00 45.30 1.78
670 2248 5.174035 CACATTTCCGAGTCGAACTCATATC 59.826 44.000 15.64 0.00 45.30 1.63
671 2249 4.976224 TTTCCGAGTCGAACTCATATCA 57.024 40.909 15.64 0.00 45.30 2.15
672 2250 4.976224 TTCCGAGTCGAACTCATATCAA 57.024 40.909 15.64 0.00 45.30 2.57
673 2251 4.976224 TCCGAGTCGAACTCATATCAAA 57.024 40.909 15.64 0.00 45.30 2.69
674 2252 4.669318 TCCGAGTCGAACTCATATCAAAC 58.331 43.478 15.64 0.00 45.30 2.93
675 2253 3.797256 CCGAGTCGAACTCATATCAAACC 59.203 47.826 15.64 0.00 45.30 3.27
676 2254 4.440250 CCGAGTCGAACTCATATCAAACCT 60.440 45.833 15.64 0.00 45.30 3.50
677 2255 5.103000 CGAGTCGAACTCATATCAAACCTT 58.897 41.667 6.73 0.00 45.30 3.50
678 2256 5.577164 CGAGTCGAACTCATATCAAACCTTT 59.423 40.000 6.73 0.00 45.30 3.11
679 2257 6.237595 CGAGTCGAACTCATATCAAACCTTTC 60.238 42.308 6.73 0.00 45.30 2.62
680 2258 6.702329 AGTCGAACTCATATCAAACCTTTCT 58.298 36.000 0.00 0.00 0.00 2.52
681 2259 7.162082 AGTCGAACTCATATCAAACCTTTCTT 58.838 34.615 0.00 0.00 0.00 2.52
682 2260 8.311836 AGTCGAACTCATATCAAACCTTTCTTA 58.688 33.333 0.00 0.00 0.00 2.10
683 2261 8.932791 GTCGAACTCATATCAAACCTTTCTTAA 58.067 33.333 0.00 0.00 0.00 1.85
684 2262 9.667107 TCGAACTCATATCAAACCTTTCTTAAT 57.333 29.630 0.00 0.00 0.00 1.40
695 2273 9.635404 TCAAACCTTTCTTAATTTTCTAGTGGA 57.365 29.630 0.00 0.00 0.00 4.02
717 2296 7.391833 GTGGAACTCAAATCAAACCTTCTCTAT 59.608 37.037 0.00 0.00 0.00 1.98
758 2337 1.602377 CAAACTTGTCTGAACCCGGAC 59.398 52.381 0.73 0.00 46.43 4.79
775 2354 1.578206 GACACGGAGAAGCAAAGCCC 61.578 60.000 0.00 0.00 0.00 5.19
776 2355 2.358737 ACGGAGAAGCAAAGCCCG 60.359 61.111 0.00 0.00 45.09 6.13
777 2356 3.127533 CGGAGAAGCAAAGCCCGG 61.128 66.667 0.00 0.00 36.81 5.73
779 2358 2.351276 GAGAAGCAAAGCCCGGGA 59.649 61.111 29.31 0.00 0.00 5.14
1087 2671 2.437359 CGCAAGCAAGGGAGGGAG 60.437 66.667 0.00 0.00 0.00 4.30
1088 2672 2.044551 GCAAGCAAGGGAGGGAGG 60.045 66.667 0.00 0.00 0.00 4.30
1365 2961 1.003233 GGTCCCTGTCTGGTACCTTTG 59.997 57.143 14.36 3.66 0.00 2.77
1383 2979 5.221641 ACCTTTGGTTTTCCTGCCTTTATTC 60.222 40.000 0.00 0.00 41.38 1.75
1384 2980 4.882842 TTGGTTTTCCTGCCTTTATTCC 57.117 40.909 0.00 0.00 41.38 3.01
1385 2981 3.169908 TGGTTTTCCTGCCTTTATTCCC 58.830 45.455 0.00 0.00 41.38 3.97
1465 3063 1.629043 ACTCGAAGTGTTGAGGCCTA 58.371 50.000 4.42 0.00 36.53 3.93
1469 3067 2.029290 TCGAAGTGTTGAGGCCTACTTC 60.029 50.000 26.45 26.45 43.32 3.01
1475 3074 3.502595 GTGTTGAGGCCTACTTCTTTTCC 59.497 47.826 4.42 0.00 0.00 3.13
1476 3075 3.082548 GTTGAGGCCTACTTCTTTTCCC 58.917 50.000 4.42 0.00 0.00 3.97
1539 3171 1.002366 GATAGTTGCGTGTCCTGCTG 58.998 55.000 0.00 0.00 0.00 4.41
1541 3173 0.963225 TAGTTGCGTGTCCTGCTGTA 59.037 50.000 0.00 0.00 0.00 2.74
1545 3177 0.319555 TGCGTGTCCTGCTGTAGAAC 60.320 55.000 0.00 0.00 0.00 3.01
1552 3184 3.195610 TGTCCTGCTGTAGAACTGGTATG 59.804 47.826 0.00 0.00 0.00 2.39
1650 3332 3.011566 TCTTTTGGTTGAGCCTGTTCA 57.988 42.857 0.00 0.00 38.35 3.18
1662 3344 1.221840 CTGTTCATGGGGGAGTCGG 59.778 63.158 0.00 0.00 0.00 4.79
1665 3347 0.976073 GTTCATGGGGGAGTCGGAGA 60.976 60.000 0.00 0.00 0.00 3.71
1736 3674 0.106149 GAAGTTGGTCTCACGGGTGT 59.894 55.000 0.00 0.00 0.00 4.16
2250 4411 7.645340 GCGATACATGCTTGATCAAATTAACTT 59.355 33.333 9.88 0.00 0.00 2.66
2280 4441 1.536766 TGTTTCTCTGCAGCAATTCCG 59.463 47.619 9.47 0.00 0.00 4.30
2724 4886 1.996191 GGCGTTGTTAGAAGCTGAGAG 59.004 52.381 0.00 0.00 0.00 3.20
2797 4959 0.740516 GCAGCCAGAGAGAAGCAGAC 60.741 60.000 0.00 0.00 0.00 3.51
2851 5013 4.008074 ACTTCAGAGGGTATGTGTTGTG 57.992 45.455 0.00 0.00 0.00 3.33
2966 5130 1.807573 GAAGCAGCGAGGAAGTCCG 60.808 63.158 0.00 0.00 42.08 4.79
3624 5790 6.127535 TGTTAGTTAAGACAATACTCGAGGGG 60.128 42.308 18.41 5.40 0.00 4.79
3969 6135 3.080319 AGAGAAGGTTCAGCATTTGAGC 58.920 45.455 0.00 0.00 37.07 4.26
4008 6174 1.606668 CGTATGGACTCTGCTCTCTCC 59.393 57.143 0.00 0.00 0.00 3.71
4322 6488 1.207089 TGCTCGTACCATTGAGAAGGG 59.793 52.381 0.24 0.00 38.57 3.95
4446 6612 3.913799 TGGTAAAGGAAGTGAGGGATTCA 59.086 43.478 0.00 0.00 0.00 2.57
4487 6653 4.516652 AGGAATGGAAGGAGGAAATCTG 57.483 45.455 0.00 0.00 0.00 2.90
4628 6794 6.183361 TGTTCCTGTACAAATGAAGGTACTCA 60.183 38.462 0.00 0.00 38.49 3.41
4813 6979 0.512952 GCTCGTTCGTCATTGCTGTT 59.487 50.000 0.00 0.00 0.00 3.16
4899 7065 8.863872 AAACTTGTCCTATAATTAACTGCAGT 57.136 30.769 15.25 15.25 0.00 4.40
4900 7066 8.863872 AACTTGTCCTATAATTAACTGCAGTT 57.136 30.769 32.97 32.97 41.73 3.16
4901 7067 8.268850 ACTTGTCCTATAATTAACTGCAGTTG 57.731 34.615 36.50 20.33 38.90 3.16
4902 7068 7.883311 ACTTGTCCTATAATTAACTGCAGTTGT 59.117 33.333 36.50 23.93 38.90 3.32
4903 7069 8.630054 TTGTCCTATAATTAACTGCAGTTGTT 57.370 30.769 36.50 30.12 38.90 2.83
4904 7070 8.630054 TGTCCTATAATTAACTGCAGTTGTTT 57.370 30.769 36.50 29.16 38.90 2.83
4905 7071 9.073475 TGTCCTATAATTAACTGCAGTTGTTTT 57.927 29.630 36.50 27.11 38.90 2.43
4906 7072 9.908152 GTCCTATAATTAACTGCAGTTGTTTTT 57.092 29.630 36.50 25.03 38.90 1.94
5207 7424 4.445453 TCTAACAACATCAGCAGCATAGG 58.555 43.478 0.00 0.00 0.00 2.57
5211 7428 1.964891 CATCAGCAGCATAGGGGCG 60.965 63.158 0.00 0.00 39.27 6.13
5707 7925 2.594592 GCGCCCTGGTGAAGTTGT 60.595 61.111 0.00 0.00 0.00 3.32
5785 8003 2.048222 CGTCAGCCGGCTCTTTGA 60.048 61.111 30.29 19.87 0.00 2.69
6067 8285 2.357760 GCCCGTGGTACAAAGCGA 60.358 61.111 0.00 0.00 44.16 4.93
6355 8652 4.997395 TGAGCAGTTGGATGTTAAACTCTC 59.003 41.667 0.00 0.00 34.41 3.20
6378 8678 5.639506 TCGAATCACTGATTCTGAAAAGGAC 59.360 40.000 23.42 1.39 44.22 3.85
6429 8738 9.034800 TGGATTTTATCTGTTAAAGGCTCAAAT 57.965 29.630 0.00 0.00 31.57 2.32
6468 8779 2.533266 TGCTTCAGAACAGACCTCAC 57.467 50.000 0.00 0.00 0.00 3.51
6757 9072 2.649331 GCGAGGACTTACTTGCAGTA 57.351 50.000 0.00 0.00 45.33 2.74
6829 9145 4.038080 GCCCCAAAACTGTCGGCG 62.038 66.667 0.00 0.00 0.00 6.46
6846 9162 1.866925 CGAAGGCCTCAAAACCGTC 59.133 57.895 5.23 0.00 0.00 4.79
6885 9201 4.289672 TCTTTGATTCCCTCAGTAAAGCCT 59.710 41.667 0.00 0.00 34.68 4.58
6915 9231 1.612950 TCGGTGTACAAAAGCCGTAGA 59.387 47.619 18.74 1.48 44.07 2.59
6938 9254 1.935933 AGAAACATATGCCGACGGTC 58.064 50.000 16.73 8.54 0.00 4.79
6966 9283 1.940613 GCCATCGGCGAAAAAGTAGAT 59.059 47.619 15.93 0.00 39.62 1.98
6983 9300 2.962786 TGACACGGCCGTCAAACG 60.963 61.111 31.80 19.99 42.82 3.60
6991 9308 1.495951 GCCGTCAAACGTCATCCAC 59.504 57.895 0.00 0.00 40.58 4.02
7008 9325 3.582120 CACACGTGCCGGTTTGCT 61.582 61.111 17.22 0.00 0.00 3.91
7104 9421 3.945285 TGGCCGAAGATTCCAACTTTATC 59.055 43.478 0.00 0.00 0.00 1.75
7107 9424 5.506317 GGCCGAAGATTCCAACTTTATCATG 60.506 44.000 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 0.104671 ACCATTGTTGCAAGCCACAC 59.895 50.000 0.00 0.00 0.00 3.82
55 56 3.594134 CTCCCTATGCTATGCTACAAGC 58.406 50.000 0.00 0.00 42.82 4.01
89 90 5.419155 TGAATACTCTTGACCAGTCGATCTT 59.581 40.000 0.00 0.00 0.00 2.40
142 143 2.584791 CGCAAAGGACAGCATTGTAAC 58.415 47.619 0.00 0.00 37.76 2.50
151 152 2.919494 GCAACCCCGCAAAGGACAG 61.919 63.158 0.00 0.00 45.00 3.51
152 153 2.058125 TAGCAACCCCGCAAAGGACA 62.058 55.000 0.00 0.00 45.00 4.02
162 163 0.693049 ATCCGATGGATAGCAACCCC 59.307 55.000 0.00 0.00 41.16 4.95
178 179 1.135046 CATCGATCGCACACTCATCC 58.865 55.000 11.09 0.00 0.00 3.51
260 261 2.356330 CCTAAAAACAGGGGCCGATACA 60.356 50.000 0.00 0.00 31.47 2.29
265 266 1.102978 CATCCTAAAAACAGGGGCCG 58.897 55.000 0.00 0.00 36.26 6.13
293 296 8.239314 ACATTGCTGATTGTACAACTAGAAATG 58.761 33.333 30.66 30.66 37.94 2.32
320 323 9.573133 AAAATAACATTGCAGTATTACAGCTTC 57.427 29.630 11.80 0.00 31.40 3.86
335 338 9.669353 AGCTATCTTTGCGATAAAATAACATTG 57.331 29.630 0.00 0.00 34.32 2.82
386 389 1.135228 ACCGCTTTTGTGTTGACCAAC 60.135 47.619 5.97 5.97 41.50 3.77
389 392 0.030235 GGACCGCTTTTGTGTTGACC 59.970 55.000 0.00 0.00 0.00 4.02
396 399 2.943036 TCTTTAGGGACCGCTTTTGT 57.057 45.000 0.00 0.00 0.00 2.83
467 474 8.155821 AGTTCAACTAGGAAAAAGAAGTTAGC 57.844 34.615 0.00 0.00 31.20 3.09
474 481 7.663827 TGATACGAGTTCAACTAGGAAAAAGA 58.336 34.615 2.47 0.00 0.00 2.52
481 488 7.653767 AAAGTTTGATACGAGTTCAACTAGG 57.346 36.000 2.47 0.00 33.03 3.02
508 515 7.724305 AGTTTGATACGAGTTAAAGCTCAAA 57.276 32.000 0.00 0.00 35.33 2.69
509 516 7.439955 TCAAGTTTGATACGAGTTAAAGCTCAA 59.560 33.333 0.00 0.00 31.99 3.02
510 517 6.926826 TCAAGTTTGATACGAGTTAAAGCTCA 59.073 34.615 0.00 0.00 31.99 4.26
511 518 7.228150 GTCAAGTTTGATACGAGTTAAAGCTC 58.772 38.462 0.00 0.00 39.73 4.09
514 521 6.364165 TCGGTCAAGTTTGATACGAGTTAAAG 59.636 38.462 15.66 0.00 41.24 1.85
515 522 6.215121 TCGGTCAAGTTTGATACGAGTTAAA 58.785 36.000 15.66 0.00 41.24 1.52
516 523 5.771469 TCGGTCAAGTTTGATACGAGTTAA 58.229 37.500 15.66 0.94 41.24 2.01
517 524 5.375417 TCGGTCAAGTTTGATACGAGTTA 57.625 39.130 15.66 1.20 41.24 2.24
537 544 4.701956 ATGCATTTTACTTCCCAGTTCG 57.298 40.909 0.00 0.00 34.06 3.95
558 565 6.372381 AGCATATTACAATCGAAGCATGCATA 59.628 34.615 21.98 4.99 39.91 3.14
560 567 4.516321 AGCATATTACAATCGAAGCATGCA 59.484 37.500 21.98 0.00 39.91 3.96
561 568 5.039480 AGCATATTACAATCGAAGCATGC 57.961 39.130 10.51 10.51 38.20 4.06
562 569 8.021955 TCTTAGCATATTACAATCGAAGCATG 57.978 34.615 0.00 0.00 0.00 4.06
563 570 8.607441 TTCTTAGCATATTACAATCGAAGCAT 57.393 30.769 0.00 0.00 0.00 3.79
565 572 9.159470 GTTTTCTTAGCATATTACAATCGAAGC 57.841 33.333 0.00 0.00 0.00 3.86
566 573 9.651718 GGTTTTCTTAGCATATTACAATCGAAG 57.348 33.333 0.00 0.00 0.00 3.79
568 575 8.725405 TGGTTTTCTTAGCATATTACAATCGA 57.275 30.769 0.00 0.00 0.00 3.59
569 576 9.950680 AATGGTTTTCTTAGCATATTACAATCG 57.049 29.630 0.00 0.00 35.33 3.34
578 922 8.637986 ACTGTTTTCAATGGTTTTCTTAGCATA 58.362 29.630 0.00 0.00 35.33 3.14
595 2172 3.021269 ACGCGTATGAGACTGTTTTCA 57.979 42.857 11.67 0.00 0.00 2.69
608 2185 1.008875 CGGAGCATGCATACGCGTAT 61.009 55.000 25.54 25.54 42.97 3.06
612 2189 1.126846 GTTATCGGAGCATGCATACGC 59.873 52.381 21.98 0.00 39.24 4.42
614 2191 1.726791 CGGTTATCGGAGCATGCATAC 59.273 52.381 21.98 10.59 34.75 2.39
618 2195 0.582005 GTTCGGTTATCGGAGCATGC 59.418 55.000 10.51 10.51 39.77 4.06
621 2198 1.822990 AGAAGTTCGGTTATCGGAGCA 59.177 47.619 0.00 0.00 39.77 4.26
630 2207 3.703001 ATGTGATCCAGAAGTTCGGTT 57.297 42.857 11.74 5.65 0.00 4.44
632 2209 3.375299 GGAAATGTGATCCAGAAGTTCGG 59.625 47.826 7.25 7.25 36.92 4.30
634 2211 4.253685 TCGGAAATGTGATCCAGAAGTTC 58.746 43.478 0.00 0.00 36.74 3.01
669 2247 9.635404 TCCACTAGAAAATTAAGAAAGGTTTGA 57.365 29.630 0.00 0.00 0.00 2.69
672 2250 9.642343 AGTTCCACTAGAAAATTAAGAAAGGTT 57.358 29.630 0.00 0.00 35.85 3.50
673 2251 9.286170 GAGTTCCACTAGAAAATTAAGAAAGGT 57.714 33.333 0.00 0.00 35.85 3.50
674 2252 9.284968 TGAGTTCCACTAGAAAATTAAGAAAGG 57.715 33.333 0.00 0.00 35.85 3.11
682 2260 9.750125 GTTTGATTTGAGTTCCACTAGAAAATT 57.250 29.630 0.00 0.00 35.85 1.82
683 2261 8.360390 GGTTTGATTTGAGTTCCACTAGAAAAT 58.640 33.333 0.00 0.00 35.85 1.82
684 2262 7.559897 AGGTTTGATTTGAGTTCCACTAGAAAA 59.440 33.333 0.00 0.00 35.85 2.29
685 2263 7.060421 AGGTTTGATTTGAGTTCCACTAGAAA 58.940 34.615 0.00 0.00 35.85 2.52
686 2264 6.601332 AGGTTTGATTTGAGTTCCACTAGAA 58.399 36.000 0.00 0.00 0.00 2.10
687 2265 6.187727 AGGTTTGATTTGAGTTCCACTAGA 57.812 37.500 0.00 0.00 0.00 2.43
688 2266 6.712547 AGAAGGTTTGATTTGAGTTCCACTAG 59.287 38.462 0.00 0.00 0.00 2.57
689 2267 6.601332 AGAAGGTTTGATTTGAGTTCCACTA 58.399 36.000 0.00 0.00 0.00 2.74
690 2268 5.449553 AGAAGGTTTGATTTGAGTTCCACT 58.550 37.500 0.00 0.00 0.00 4.00
691 2269 5.532779 AGAGAAGGTTTGATTTGAGTTCCAC 59.467 40.000 0.00 0.00 0.00 4.02
692 2270 5.694995 AGAGAAGGTTTGATTTGAGTTCCA 58.305 37.500 0.00 0.00 0.00 3.53
693 2271 7.929941 ATAGAGAAGGTTTGATTTGAGTTCC 57.070 36.000 0.00 0.00 0.00 3.62
717 2296 8.966868 AGTTTGATTTGAGTTCCACTAGAAAAA 58.033 29.630 0.00 0.00 35.85 1.94
758 2337 2.680913 CGGGCTTTGCTTCTCCGTG 61.681 63.158 0.00 0.00 36.38 4.94
775 2354 2.513897 GACCGAATTGCCCTCCCG 60.514 66.667 0.00 0.00 0.00 5.14
776 2355 1.001393 TTGACCGAATTGCCCTCCC 60.001 57.895 0.00 0.00 0.00 4.30
777 2356 1.313091 GGTTGACCGAATTGCCCTCC 61.313 60.000 0.00 0.00 0.00 4.30
779 2358 1.304134 GGGTTGACCGAATTGCCCT 60.304 57.895 0.00 0.00 36.71 5.19
1085 2669 0.744281 CTCGCTTTCTCCTCCTCCTC 59.256 60.000 0.00 0.00 0.00 3.71
1086 2670 0.686112 CCTCGCTTTCTCCTCCTCCT 60.686 60.000 0.00 0.00 0.00 3.69
1087 2671 1.819905 CCTCGCTTTCTCCTCCTCC 59.180 63.158 0.00 0.00 0.00 4.30
1088 2672 1.142965 GCCTCGCTTTCTCCTCCTC 59.857 63.158 0.00 0.00 0.00 3.71
1365 2961 2.500098 GGGGAATAAAGGCAGGAAAACC 59.500 50.000 0.00 0.00 0.00 3.27
1385 2981 0.851332 AGGAAGAAGGGGAAAGGGGG 60.851 60.000 0.00 0.00 0.00 5.40
1465 3063 8.422566 CGAGTATAATAGAAGGGGAAAAGAAGT 58.577 37.037 0.00 0.00 0.00 3.01
1469 3067 6.862090 CGACGAGTATAATAGAAGGGGAAAAG 59.138 42.308 0.00 0.00 0.00 2.27
1475 3074 4.082895 CCACCGACGAGTATAATAGAAGGG 60.083 50.000 0.00 0.00 0.00 3.95
1476 3075 4.518211 ACCACCGACGAGTATAATAGAAGG 59.482 45.833 0.00 0.00 0.00 3.46
1563 3195 7.277396 ACAGCACCACTTTCTTACTAAAGTAA 58.723 34.615 1.96 2.76 45.59 2.24
1566 3198 6.619801 AACAGCACCACTTTCTTACTAAAG 57.380 37.500 0.00 0.00 41.35 1.85
1568 3200 7.121463 TCAAAAACAGCACCACTTTCTTACTAA 59.879 33.333 0.00 0.00 0.00 2.24
1569 3201 6.600032 TCAAAAACAGCACCACTTTCTTACTA 59.400 34.615 0.00 0.00 0.00 1.82
1570 3202 5.417580 TCAAAAACAGCACCACTTTCTTACT 59.582 36.000 0.00 0.00 0.00 2.24
1571 3203 5.646606 TCAAAAACAGCACCACTTTCTTAC 58.353 37.500 0.00 0.00 0.00 2.34
1650 3332 3.110552 AGTCTCCGACTCCCCCAT 58.889 61.111 0.00 0.00 38.71 4.00
1662 3344 5.872070 CCCAAAGAATGTAACTCTGAGTCTC 59.128 44.000 11.31 7.86 0.00 3.36
1665 3347 5.825593 TCCCAAAGAATGTAACTCTGAGT 57.174 39.130 4.06 4.06 0.00 3.41
1666 3348 7.175641 ACAATTCCCAAAGAATGTAACTCTGAG 59.824 37.037 2.45 2.45 44.75 3.35
1667 3349 7.004086 ACAATTCCCAAAGAATGTAACTCTGA 58.996 34.615 0.00 0.00 44.75 3.27
1668 3350 7.219484 ACAATTCCCAAAGAATGTAACTCTG 57.781 36.000 0.00 0.00 44.75 3.35
1669 3351 7.839680 AACAATTCCCAAAGAATGTAACTCT 57.160 32.000 0.00 0.00 44.75 3.24
1670 3352 7.326063 CGAAACAATTCCCAAAGAATGTAACTC 59.674 37.037 0.00 0.00 44.75 3.01
1671 3353 7.145323 CGAAACAATTCCCAAAGAATGTAACT 58.855 34.615 0.00 0.00 44.75 2.24
1672 3354 6.364976 CCGAAACAATTCCCAAAGAATGTAAC 59.635 38.462 0.00 0.00 44.75 2.50
1673 3355 6.451393 CCGAAACAATTCCCAAAGAATGTAA 58.549 36.000 0.00 0.00 44.75 2.41
1674 3356 5.565834 GCCGAAACAATTCCCAAAGAATGTA 60.566 40.000 0.00 0.00 44.75 2.29
1736 3674 3.629855 TCCAACAGAAAAGCAATTCGTGA 59.370 39.130 0.00 0.00 34.46 4.35
2200 4360 9.233232 CGCTAATTCACTTCAAACTTACTTTTT 57.767 29.630 0.00 0.00 0.00 1.94
2250 4411 6.747125 TGCTGCAGAGAAACAATTGAAAATA 58.253 32.000 20.43 0.00 0.00 1.40
2280 4441 2.796032 GCTTTGCAGGATAACCAATCGC 60.796 50.000 0.00 0.00 38.94 4.58
2611 4773 1.877576 ATGTCGCCTTCTGCACGAGA 61.878 55.000 0.00 0.00 41.33 4.04
2724 4886 2.185608 GAGCACGAGCCTTCCTCC 59.814 66.667 0.00 0.00 43.56 4.30
2797 4959 8.742777 TCCAGATGTTCTTTCAATTTAATCCTG 58.257 33.333 0.00 0.00 0.00 3.86
3069 5233 9.773328 ACTCGAACATACAAATACAATCAAATG 57.227 29.630 0.00 0.00 0.00 2.32
4322 6488 3.551846 TCCCTCACTTTGTCTTGGAAAC 58.448 45.455 0.00 0.00 0.00 2.78
4446 6612 1.675641 GGGAGCCAAGTCGTGCAAT 60.676 57.895 0.00 0.00 0.00 3.56
4487 6653 5.409826 AGAATTTCGAGGTCAATGTTCTCAC 59.590 40.000 6.47 0.00 0.00 3.51
4628 6794 1.152030 TGTCCTGGGAGCCTGACTT 60.152 57.895 0.00 0.00 30.99 3.01
4813 6979 0.326595 TGAAACGCAGGCCCTTGATA 59.673 50.000 0.00 0.00 0.00 2.15
4897 7063 7.054491 AGAATTCCACTGCATAAAAACAACT 57.946 32.000 0.65 0.00 0.00 3.16
4898 7064 8.699749 GTTAGAATTCCACTGCATAAAAACAAC 58.300 33.333 0.65 0.00 0.00 3.32
4899 7065 8.417106 TGTTAGAATTCCACTGCATAAAAACAA 58.583 29.630 0.65 0.00 0.00 2.83
4900 7066 7.946207 TGTTAGAATTCCACTGCATAAAAACA 58.054 30.769 0.65 0.00 0.00 2.83
4901 7067 8.986477 ATGTTAGAATTCCACTGCATAAAAAC 57.014 30.769 0.65 0.00 0.00 2.43
4902 7068 9.995003 AAATGTTAGAATTCCACTGCATAAAAA 57.005 25.926 0.65 0.00 0.00 1.94
4903 7069 9.995003 AAAATGTTAGAATTCCACTGCATAAAA 57.005 25.926 0.65 0.00 0.00 1.52
4904 7070 9.995003 AAAAATGTTAGAATTCCACTGCATAAA 57.005 25.926 0.65 0.00 0.00 1.40
4905 7071 9.638239 GAAAAATGTTAGAATTCCACTGCATAA 57.362 29.630 0.65 0.00 0.00 1.90
4906 7072 9.023962 AGAAAAATGTTAGAATTCCACTGCATA 57.976 29.630 0.65 0.00 0.00 3.14
4907 7073 7.816031 CAGAAAAATGTTAGAATTCCACTGCAT 59.184 33.333 0.65 0.00 0.00 3.96
5207 7424 4.196971 ACCAGATAACAAATAGAACGCCC 58.803 43.478 0.00 0.00 0.00 6.13
5211 7428 7.606456 TGTCAGGAACCAGATAACAAATAGAAC 59.394 37.037 0.00 0.00 0.00 3.01
5704 7922 1.149627 CCGGGGAGTTGTCCAACAA 59.850 57.895 12.32 0.00 46.07 2.83
5707 7925 2.221299 CCTCCGGGGAGTTGTCCAA 61.221 63.158 0.37 0.00 46.07 3.53
5730 7948 1.205893 GCCTCCACGATCTCTTCAGTT 59.794 52.381 0.00 0.00 0.00 3.16
5769 7987 2.383527 CGTCAAAGAGCCGGCTGAC 61.384 63.158 38.41 31.85 35.82 3.51
5785 8003 1.079127 CCTGAATCTTGGCGTCCGT 60.079 57.895 0.00 0.00 0.00 4.69
5818 8036 1.833787 TTCAGGAGCACCCGGGTTAC 61.834 60.000 27.83 20.12 40.87 2.50
6067 8285 6.515272 AAACTAAATTCACATTCAGGCGAT 57.485 33.333 0.00 0.00 0.00 4.58
6315 8612 8.817100 CAACTGCTCAAACAAACGAGATATATA 58.183 33.333 0.00 0.00 0.00 0.86
6468 8779 1.098050 CAGGGCTTTTTCTCCATCCG 58.902 55.000 0.00 0.00 0.00 4.18
6757 9072 1.153524 TTTCCTGTGGTGCTGGCAT 59.846 52.632 0.00 0.00 36.29 4.40
6761 9076 1.525995 ACCGTTTCCTGTGGTGCTG 60.526 57.895 0.00 0.00 33.91 4.41
6762 9077 1.525995 CACCGTTTCCTGTGGTGCT 60.526 57.895 0.00 0.00 45.85 4.40
6805 9121 0.690744 ACAGTTTTGGGGCCTTTGCT 60.691 50.000 0.84 0.00 37.74 3.91
6829 9145 1.574702 CCGACGGTTTTGAGGCCTTC 61.575 60.000 6.77 0.10 0.00 3.46
6861 9177 4.396478 GGCTTTACTGAGGGAATCAAAGAC 59.604 45.833 0.00 0.00 37.52 3.01
6885 9201 2.680707 TACACCGACGGCCATCCA 60.681 61.111 15.39 0.00 0.00 3.41
6899 9215 5.648178 TCTATGTCTACGGCTTTTGTACA 57.352 39.130 0.00 0.00 0.00 2.90
6915 9231 3.181469 ACCGTCGGCATATGTTTCTATGT 60.181 43.478 12.28 0.00 32.69 2.29
6955 9271 2.093783 CGGCCGTGTCATCTACTTTTTC 59.906 50.000 19.50 0.00 0.00 2.29
6966 9283 2.962786 CGTTTGACGGCCGTGTCA 60.963 61.111 39.65 26.23 46.63 3.58
6983 9300 3.253955 GGCACGTGTGTGGATGAC 58.746 61.111 18.38 0.00 46.51 3.06
7040 9357 1.208165 ATGACCACCAAGAGGACCCC 61.208 60.000 0.00 0.00 38.69 4.95
7079 9396 1.025041 GTTGGAATCTTCGGCCATCC 58.975 55.000 2.24 0.43 0.00 3.51


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

AutoCloner maintained by Alex Coulton.