Multiple sequence alignment - TraesCS1D01G373900

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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 TraesCS1D01G373900 chr1D 100.000 3181 0 0 1 3181 451624086 451627266 0.000000e+00 5875.0
1 TraesCS1D01G373900 chr1D 88.862 835 75 13 905 1729 446434638 446435464 0.000000e+00 1011.0
2 TraesCS1D01G373900 chr1D 92.126 635 21 17 1076 1698 451524632 451525249 0.000000e+00 869.0
3 TraesCS1D01G373900 chr1D 86.170 188 18 3 3002 3181 451526833 451527020 2.500000e-46 196.0
4 TraesCS1D01G373900 chr1D 100.000 45 0 0 317 361 451624356 451624400 2.030000e-12 84.2
5 TraesCS1D01G373900 chr1D 100.000 45 0 0 271 315 451624402 451624446 2.030000e-12 84.2
6 TraesCS1D01G373900 chr1A 91.557 1741 112 19 317 2029 546215694 546217427 0.000000e+00 2368.0
7 TraesCS1D01G373900 chr1A 89.757 781 47 16 975 1729 542167879 542168652 0.000000e+00 968.0
8 TraesCS1D01G373900 chr1A 96.335 382 11 1 2803 3181 546217991 546218372 2.690000e-175 625.0
9 TraesCS1D01G373900 chr1A 86.701 579 43 14 2305 2875 546217468 546218020 2.100000e-171 612.0
10 TraesCS1D01G373900 chr1A 95.570 316 13 1 1 315 546215423 546215738 3.660000e-139 505.0
11 TraesCS1D01G373900 chr1A 78.667 225 14 20 1517 1736 557098441 557098246 5.570000e-23 119.0
12 TraesCS1D01G373900 chr1B 89.554 1771 109 31 318 2029 620785381 620787134 0.000000e+00 2176.0
13 TraesCS1D01G373900 chr1B 88.401 1388 128 19 317 1699 621058581 621059940 0.000000e+00 1640.0
14 TraesCS1D01G373900 chr1B 90.595 840 42 14 905 1737 621272360 621271551 0.000000e+00 1079.0
15 TraesCS1D01G373900 chr1B 93.252 652 33 7 905 1552 620899932 620900576 0.000000e+00 950.0
16 TraesCS1D01G373900 chr1B 88.000 825 67 18 905 1726 610558246 610559041 0.000000e+00 946.0
17 TraesCS1D01G373900 chr1B 91.710 386 22 4 2805 3181 621270550 621270166 7.820000e-146 527.0
18 TraesCS1D01G373900 chr1B 86.422 464 47 10 2422 2874 621270982 621270524 7.930000e-136 494.0
19 TraesCS1D01G373900 chr1B 85.808 458 63 2 318 774 621273097 621272641 4.770000e-133 484.0
20 TraesCS1D01G373900 chr1B 86.076 316 43 1 1 315 620785109 620785424 3.930000e-89 339.0
21 TraesCS1D01G373900 chr1B 85.862 290 39 2 1 289 621273368 621273080 1.110000e-79 307.0
22 TraesCS1D01G373900 chr1B 83.036 336 37 9 2861 3181 620901895 620902225 1.440000e-73 287.0
23 TraesCS1D01G373900 chr1B 86.614 254 31 3 37 289 621058348 621058599 8.690000e-71 278.0
24 TraesCS1D01G373900 chr1B 81.402 328 29 12 1729 2029 621271517 621271195 4.100000e-59 239.0
25 TraesCS1D01G373900 chr1B 90.698 172 14 2 2024 2193 620787211 620787382 8.880000e-56 228.0
26 TraesCS1D01G373900 chr1B 81.588 277 37 7 2861 3128 620553259 620553530 1.920000e-52 217.0
27 TraesCS1D01G373900 chr5B 81.955 266 26 10 1466 1726 436562604 436562852 4.160000e-49 206.0
28 TraesCS1D01G373900 chr4A 81.818 264 26 10 1466 1724 666809644 666809398 5.380000e-48 202.0
29 TraesCS1D01G373900 chr4A 85.030 167 15 2 1466 1632 632724336 632724492 9.130000e-36 161.0
30 TraesCS1D01G373900 chr3D 82.213 253 23 10 1466 1714 118253860 118254094 6.960000e-47 198.0
31 TraesCS1D01G373900 chr2B 79.924 264 31 10 1468 1726 439691732 439691978 1.170000e-39 174.0
32 TraesCS1D01G373900 chr3B 85.030 167 15 4 1466 1632 131500363 131500207 9.130000e-36 161.0


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 TraesCS1D01G373900 chr1D 451624086 451627266 3180 False 2014.466667 5875 100.00000 1 3181 3 chr1D.!!$F3 3180
1 TraesCS1D01G373900 chr1D 446434638 446435464 826 False 1011.000000 1011 88.86200 905 1729 1 chr1D.!!$F1 824
2 TraesCS1D01G373900 chr1D 451524632 451527020 2388 False 532.500000 869 89.14800 1076 3181 2 chr1D.!!$F2 2105
3 TraesCS1D01G373900 chr1A 546215423 546218372 2949 False 1027.500000 2368 92.54075 1 3181 4 chr1A.!!$F2 3180
4 TraesCS1D01G373900 chr1A 542167879 542168652 773 False 968.000000 968 89.75700 975 1729 1 chr1A.!!$F1 754
5 TraesCS1D01G373900 chr1B 621058348 621059940 1592 False 959.000000 1640 87.50750 37 1699 2 chr1B.!!$F5 1662
6 TraesCS1D01G373900 chr1B 610558246 610559041 795 False 946.000000 946 88.00000 905 1726 1 chr1B.!!$F1 821
7 TraesCS1D01G373900 chr1B 620785109 620787382 2273 False 914.333333 2176 88.77600 1 2193 3 chr1B.!!$F3 2192
8 TraesCS1D01G373900 chr1B 620899932 620902225 2293 False 618.500000 950 88.14400 905 3181 2 chr1B.!!$F4 2276
9 TraesCS1D01G373900 chr1B 621270166 621273368 3202 True 521.666667 1079 86.96650 1 3181 6 chr1B.!!$R1 3180

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
627 629 0.035056 CAAGCCTGACCCGAAATCCT 60.035 55.0 0.0 0.0 0.0 3.24 F
634 636 0.181350 GACCCGAAATCCTGGCATCT 59.819 55.0 0.0 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1746 2036 1.004745 GGGCCAGACATTTCAGAAGGA 59.995 52.381 4.39 0.0 0.0 3.36 R
2219 2692 1.021390 ATGAAACTGAGAAGCGCCGG 61.021 55.000 2.29 0.0 0.0 6.13 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
54 55 1.742880 CACGATGCCACCACTCCTG 60.743 63.158 0.00 0.00 0.00 3.86
119 120 4.331108 TGTAGTGAAATATGCTTGCCACA 58.669 39.130 0.00 0.00 0.00 4.17
121 122 3.156293 AGTGAAATATGCTTGCCACACA 58.844 40.909 0.00 0.00 0.00 3.72
158 159 1.674359 TTGCATAAGTATGTGGCCGG 58.326 50.000 0.00 0.00 36.11 6.13
242 244 1.729470 CGATGGTCGGAGGTCCAGAG 61.729 65.000 0.00 0.00 36.00 3.35
264 266 5.109903 AGTCGGTATTGAATAGCAAGTCAC 58.890 41.667 13.96 3.26 40.42 3.67
283 285 8.980610 CAAGTCACATGAAGATTTTGCATTTAA 58.019 29.630 0.00 0.00 0.00 1.52
284 286 8.752766 AGTCACATGAAGATTTTGCATTTAAG 57.247 30.769 0.00 0.00 0.00 1.85
285 287 7.330208 AGTCACATGAAGATTTTGCATTTAAGC 59.670 33.333 0.00 0.00 0.00 3.09
286 288 6.308524 TCACATGAAGATTTTGCATTTAAGCG 59.691 34.615 0.00 0.00 37.31 4.68
287 289 5.577945 ACATGAAGATTTTGCATTTAAGCGG 59.422 36.000 0.00 0.00 37.31 5.52
288 290 3.925913 TGAAGATTTTGCATTTAAGCGGC 59.074 39.130 0.00 0.00 37.31 6.53
289 291 3.591196 AGATTTTGCATTTAAGCGGCA 57.409 38.095 1.45 0.00 37.31 5.69
290 292 3.253230 AGATTTTGCATTTAAGCGGCAC 58.747 40.909 1.45 0.00 37.26 5.01
291 293 1.789506 TTTTGCATTTAAGCGGCACC 58.210 45.000 1.45 0.00 37.26 5.01
292 294 0.676184 TTTGCATTTAAGCGGCACCA 59.324 45.000 1.45 0.00 37.26 4.17
293 295 0.676184 TTGCATTTAAGCGGCACCAA 59.324 45.000 1.45 0.00 37.26 3.67
294 296 0.243365 TGCATTTAAGCGGCACCAAG 59.757 50.000 1.45 0.00 37.31 3.61
295 297 1.078201 GCATTTAAGCGGCACCAAGC 61.078 55.000 1.45 0.00 44.65 4.01
296 298 0.527565 CATTTAAGCGGCACCAAGCT 59.472 50.000 1.45 0.00 46.97 3.74
300 302 3.537388 AGCGGCACCAAGCTTTTT 58.463 50.000 1.45 0.00 41.52 1.94
301 303 1.363807 AGCGGCACCAAGCTTTTTC 59.636 52.632 1.45 0.00 41.52 2.29
302 304 1.067250 GCGGCACCAAGCTTTTTCA 59.933 52.632 0.00 0.00 44.79 2.69
303 305 0.940991 GCGGCACCAAGCTTTTTCAG 60.941 55.000 0.00 0.00 44.79 3.02
304 306 0.667993 CGGCACCAAGCTTTTTCAGA 59.332 50.000 0.00 0.00 44.79 3.27
305 307 1.270550 CGGCACCAAGCTTTTTCAGAT 59.729 47.619 0.00 0.00 44.79 2.90
306 308 2.487762 CGGCACCAAGCTTTTTCAGATA 59.512 45.455 0.00 0.00 44.79 1.98
307 309 3.129287 CGGCACCAAGCTTTTTCAGATAT 59.871 43.478 0.00 0.00 44.79 1.63
308 310 4.335315 CGGCACCAAGCTTTTTCAGATATA 59.665 41.667 0.00 0.00 44.79 0.86
309 311 5.504665 CGGCACCAAGCTTTTTCAGATATAG 60.505 44.000 0.00 0.00 44.79 1.31
310 312 5.358160 GGCACCAAGCTTTTTCAGATATAGT 59.642 40.000 0.00 0.00 44.79 2.12
311 313 6.261118 GCACCAAGCTTTTTCAGATATAGTG 58.739 40.000 0.00 0.00 41.15 2.74
312 314 6.094048 GCACCAAGCTTTTTCAGATATAGTGA 59.906 38.462 0.00 0.00 41.15 3.41
313 315 7.678218 GCACCAAGCTTTTTCAGATATAGTGAG 60.678 40.741 0.00 0.00 41.15 3.51
314 316 6.317391 ACCAAGCTTTTTCAGATATAGTGAGC 59.683 38.462 0.00 0.00 0.00 4.26
315 317 6.417327 CAAGCTTTTTCAGATATAGTGAGCG 58.583 40.000 0.00 0.00 0.00 5.03
316 318 5.053145 AGCTTTTTCAGATATAGTGAGCGG 58.947 41.667 0.00 0.00 0.00 5.52
317 319 5.050490 GCTTTTTCAGATATAGTGAGCGGA 58.950 41.667 0.00 0.00 0.00 5.54
318 320 5.698545 GCTTTTTCAGATATAGTGAGCGGAT 59.301 40.000 0.00 0.00 0.00 4.18
319 321 6.203723 GCTTTTTCAGATATAGTGAGCGGATT 59.796 38.462 0.00 0.00 0.00 3.01
320 322 7.254932 GCTTTTTCAGATATAGTGAGCGGATTT 60.255 37.037 0.00 0.00 0.00 2.17
321 323 8.506168 TTTTTCAGATATAGTGAGCGGATTTT 57.494 30.769 0.00 0.00 0.00 1.82
322 324 7.482654 TTTCAGATATAGTGAGCGGATTTTG 57.517 36.000 0.00 0.00 0.00 2.44
323 325 4.991056 TCAGATATAGTGAGCGGATTTTGC 59.009 41.667 0.00 0.00 0.00 3.68
324 326 4.751600 CAGATATAGTGAGCGGATTTTGCA 59.248 41.667 0.00 0.00 33.85 4.08
325 327 5.410746 CAGATATAGTGAGCGGATTTTGCAT 59.589 40.000 0.00 0.00 33.85 3.96
326 328 6.000219 AGATATAGTGAGCGGATTTTGCATT 59.000 36.000 0.00 0.00 33.85 3.56
327 329 4.989279 ATAGTGAGCGGATTTTGCATTT 57.011 36.364 0.00 0.00 33.85 2.32
328 330 7.661437 AGATATAGTGAGCGGATTTTGCATTTA 59.339 33.333 0.00 0.00 33.85 1.40
413 415 2.772077 TTTGTAGGTAGATTGCGCCA 57.228 45.000 4.18 0.00 0.00 5.69
414 416 3.275617 TTTGTAGGTAGATTGCGCCAT 57.724 42.857 4.18 0.00 0.00 4.40
528 530 1.045407 TGTTGTAGACCTTGCGGACT 58.955 50.000 0.00 0.00 38.80 3.85
529 531 1.000506 TGTTGTAGACCTTGCGGACTC 59.999 52.381 0.00 0.00 36.67 3.36
566 568 5.513233 AGAACACTATTCAATTGGCATCCT 58.487 37.500 5.42 0.00 0.00 3.24
577 579 2.341846 TGGCATCCTATCCGTTTTCC 57.658 50.000 0.00 0.00 0.00 3.13
581 583 3.460103 GCATCCTATCCGTTTTCCGTAA 58.540 45.455 0.00 0.00 33.66 3.18
602 604 1.233285 CCTATTCATGAGCAGCCCGC 61.233 60.000 0.00 0.00 42.91 6.13
624 626 0.400213 TGACAAGCCTGACCCGAAAT 59.600 50.000 0.00 0.00 0.00 2.17
627 629 0.035056 CAAGCCTGACCCGAAATCCT 60.035 55.000 0.00 0.00 0.00 3.24
634 636 0.181350 GACCCGAAATCCTGGCATCT 59.819 55.000 0.00 0.00 0.00 2.90
655 657 2.134287 TCTAGGCATGGGCTCGACC 61.134 63.158 0.00 0.00 39.70 4.79
671 673 0.320508 GACCTTTTCGTCCGAAGCCT 60.321 55.000 2.12 0.00 35.38 4.58
677 679 0.319555 TTCGTCCGAAGCCTGAACAG 60.320 55.000 0.00 0.00 0.00 3.16
789 858 7.624360 AGAAGTGTACTGTTCAAATGTTTCA 57.376 32.000 9.54 0.00 0.00 2.69
821 890 4.266714 GAATACGGGTTTGGGATTCTTGA 58.733 43.478 0.00 0.00 0.00 3.02
860 930 4.864334 CCCGTCCAGAGGGCATGC 62.864 72.222 9.90 9.90 42.77 4.06
872 942 2.413142 GGCATGCTCTGGTTCCAGC 61.413 63.158 18.92 5.20 34.33 4.85
921 1096 1.299165 GTCCACGTCATCGATCCGG 60.299 63.158 15.95 0.00 40.62 5.14
930 1105 1.838846 ATCGATCCGGGGCACTCAT 60.839 57.895 0.00 0.00 0.00 2.90
1004 1179 1.152830 GCTCCTTTCCCCACACCAA 59.847 57.895 0.00 0.00 0.00 3.67
1014 1189 1.418908 CCCACACCAACTCAGTCCCT 61.419 60.000 0.00 0.00 0.00 4.20
1027 1208 1.207329 CAGTCCCTACCTTTCCCTTCG 59.793 57.143 0.00 0.00 0.00 3.79
1036 1217 1.807142 CCTTTCCCTTCGAGCAAACTC 59.193 52.381 0.00 0.00 39.75 3.01
1037 1218 2.494059 CTTTCCCTTCGAGCAAACTCA 58.506 47.619 0.00 0.00 43.66 3.41
1042 1223 1.939934 CCTTCGAGCAAACTCACACAA 59.060 47.619 0.00 0.00 43.66 3.33
1046 1227 1.388547 GAGCAAACTCACACAACCCA 58.611 50.000 0.00 0.00 42.93 4.51
1055 1236 3.591835 CACAACCCACACCACCGC 61.592 66.667 0.00 0.00 0.00 5.68
1078 1259 4.278513 CCAACCCCACCCGAAGCA 62.279 66.667 0.00 0.00 0.00 3.91
1612 1821 8.116651 TGTTGACTCTGCTTATCTATCTATCC 57.883 38.462 0.00 0.00 0.00 2.59
1636 1873 4.734108 GCAAGTAGTGGTAGCAGTAGTAGC 60.734 50.000 15.70 12.49 0.00 3.58
1707 1951 5.062569 AACTGAAGTTGCTGCTTTGGCAT 62.063 43.478 0.00 0.00 41.35 4.40
1709 1953 7.734287 AACTGAAGTTGCTGCTTTGGCATAC 62.734 44.000 0.00 0.00 41.35 2.39
1766 2056 1.004745 TCCTTCTGAAATGTCTGGCCC 59.995 52.381 0.00 0.00 0.00 5.80
1768 2058 2.363683 CTTCTGAAATGTCTGGCCCTC 58.636 52.381 0.00 0.00 0.00 4.30
1770 2060 1.988107 TCTGAAATGTCTGGCCCTCTT 59.012 47.619 0.00 0.00 0.00 2.85
1771 2061 2.089980 CTGAAATGTCTGGCCCTCTTG 58.910 52.381 0.00 0.00 0.00 3.02
1772 2062 1.272092 TGAAATGTCTGGCCCTCTTGG 60.272 52.381 0.00 0.00 37.09 3.61
1774 2064 1.668826 AATGTCTGGCCCTCTTGGTA 58.331 50.000 0.00 0.00 36.04 3.25
1775 2065 0.912486 ATGTCTGGCCCTCTTGGTAC 59.088 55.000 0.00 0.00 36.04 3.34
1776 2066 1.198759 TGTCTGGCCCTCTTGGTACC 61.199 60.000 4.43 4.43 36.04 3.34
1852 2179 8.561738 TGGAATTTGGTAGTAAGAACTGAATC 57.438 34.615 0.00 0.00 36.36 2.52
1866 2193 2.233271 CTGAATCCAGTGGTGCAAACT 58.767 47.619 9.54 0.00 35.70 2.66
1938 2275 1.147153 GCTAGTCCCTGCCATGTCC 59.853 63.158 0.00 0.00 0.00 4.02
1950 2287 1.064060 GCCATGTCCGTGCTTTCATAC 59.936 52.381 0.00 0.00 0.00 2.39
1981 2328 7.424803 CAGTGTAATTTGTGTTTCCAGATTCA 58.575 34.615 0.00 0.00 0.00 2.57
1985 2332 8.081633 TGTAATTTGTGTTTCCAGATTCATGAC 58.918 33.333 0.00 0.00 0.00 3.06
2010 2357 5.407407 TCCATCAGTAGGTTCTGTTTCTC 57.593 43.478 0.00 0.00 36.85 2.87
2053 2515 2.488153 GTTTGCCTTACCATGTCCTGTC 59.512 50.000 0.00 0.00 0.00 3.51
2109 2571 2.732658 GCTGGCAGCAGCAGTTTT 59.267 55.556 33.33 0.00 46.73 2.43
2116 2578 2.119457 GCAGCAGCAGTTTTGTGTTAC 58.881 47.619 0.00 0.00 41.58 2.50
2156 2628 4.573900 TGGCAAATGTGAGTTGTTTTTGT 58.426 34.783 0.00 0.00 31.56 2.83
2168 2641 9.261318 GTGAGTTGTTTTTGTGAAAAATTAAGC 57.739 29.630 0.00 0.00 41.85 3.09
2179 2652 9.601971 TTGTGAAAAATTAAGCGTATGTTACTC 57.398 29.630 0.00 0.00 0.00 2.59
2193 2666 7.096966 GCGTATGTTACTCTCGATTTCTTGTAG 60.097 40.741 0.00 0.00 0.00 2.74
2197 2670 8.961294 TGTTACTCTCGATTTCTTGTAGTAAC 57.039 34.615 13.01 13.01 43.89 2.50
2198 2671 8.790718 TGTTACTCTCGATTTCTTGTAGTAACT 58.209 33.333 18.08 0.00 43.93 2.24
2218 2691 5.606348 ACTAAACAAGATGAGGCTCTAGG 57.394 43.478 16.72 3.60 0.00 3.02
2219 2692 2.998316 AACAAGATGAGGCTCTAGGC 57.002 50.000 16.72 2.41 41.43 3.93
2230 2703 3.492311 CTCTAGGCCGGCGCTTCTC 62.492 68.421 22.54 4.96 34.44 2.87
2231 2704 3.838271 CTAGGCCGGCGCTTCTCA 61.838 66.667 22.54 2.73 34.44 3.27
2236 2709 3.028366 GCCGGCGCTTCTCAGTTTC 62.028 63.158 12.58 0.00 0.00 2.78
2240 2713 1.464687 CGGCGCTTCTCAGTTTCATTG 60.465 52.381 7.64 0.00 0.00 2.82
2244 2717 3.002791 CGCTTCTCAGTTTCATTGCCTA 58.997 45.455 0.00 0.00 0.00 3.93
2249 2724 5.682234 TCTCAGTTTCATTGCCTATCTGA 57.318 39.130 0.00 0.00 0.00 3.27
2251 2726 5.046376 TCTCAGTTTCATTGCCTATCTGACA 60.046 40.000 0.00 0.00 0.00 3.58
2264 2739 5.551233 CCTATCTGACAACTGAAGAAACCA 58.449 41.667 0.00 0.00 0.00 3.67
2266 2741 5.954296 ATCTGACAACTGAAGAAACCATG 57.046 39.130 0.00 0.00 0.00 3.66
2277 2752 3.370840 AGAAACCATGCATGCCTTCTA 57.629 42.857 27.24 0.00 30.35 2.10
2299 2774 2.344535 ACATTTGGTGTGCTGCTCC 58.655 52.632 0.00 1.75 40.28 4.70
2300 2775 0.178981 ACATTTGGTGTGCTGCTCCT 60.179 50.000 0.00 0.00 40.28 3.69
2301 2776 0.963962 CATTTGGTGTGCTGCTCCTT 59.036 50.000 0.00 0.00 0.00 3.36
2302 2777 0.963962 ATTTGGTGTGCTGCTCCTTG 59.036 50.000 0.00 0.00 0.00 3.61
2303 2778 0.395586 TTTGGTGTGCTGCTCCTTGT 60.396 50.000 0.00 0.00 0.00 3.16
2340 2815 3.414700 CTGGCGTGCGTTCTGACC 61.415 66.667 0.00 0.00 0.00 4.02
2362 2837 7.118245 TGACCATGTTATCATATCGCAAGAATC 59.882 37.037 0.00 0.00 40.62 2.52
2370 2845 3.874873 CGCAAGAATCGTGCTGGA 58.125 55.556 18.05 0.00 39.95 3.86
2375 2850 2.733227 GCAAGAATCGTGCTGGAATTGG 60.733 50.000 13.67 0.00 39.00 3.16
2377 2852 2.636830 AGAATCGTGCTGGAATTGGAG 58.363 47.619 0.00 0.00 0.00 3.86
2380 2855 0.396435 TCGTGCTGGAATTGGAGTGT 59.604 50.000 0.00 0.00 0.00 3.55
2381 2856 1.202758 TCGTGCTGGAATTGGAGTGTT 60.203 47.619 0.00 0.00 0.00 3.32
2384 2859 0.961019 GCTGGAATTGGAGTGTTGCA 59.039 50.000 0.00 0.00 0.00 4.08
2413 2888 6.061022 AGTGTTTTTGGTTTCAAATTCCCT 57.939 33.333 0.00 0.00 41.84 4.20
2420 2895 5.269554 TGGTTTCAAATTCCCTGGATACT 57.730 39.130 0.00 0.00 37.61 2.12
2426 2901 6.139679 TCAAATTCCCTGGATACTCAAACT 57.860 37.500 0.00 0.00 37.61 2.66
2429 2904 7.508977 TCAAATTCCCTGGATACTCAAACTTTT 59.491 33.333 0.00 0.00 37.61 2.27
2481 2956 3.084039 CAAATCTGGTTCCAAGCTGCTA 58.916 45.455 0.90 0.00 0.00 3.49
2523 2998 5.702209 GGATGAAAATGCACATGAAAAACCT 59.298 36.000 0.00 0.00 0.00 3.50
2557 3042 2.442413 TGCATTACCAAACCTACCTGC 58.558 47.619 0.00 0.00 0.00 4.85
2562 3047 2.767644 ACCAAACCTACCTGCCTTTT 57.232 45.000 0.00 0.00 0.00 2.27
2565 3050 2.558359 CCAAACCTACCTGCCTTTTCTG 59.442 50.000 0.00 0.00 0.00 3.02
2621 3108 8.631480 AAACCTTCGATCAAATACTAAAAGGT 57.369 30.769 0.00 0.00 45.32 3.50
2642 3129 5.072741 GGTCAATACAAGGCATGTGGATAT 58.927 41.667 5.49 0.00 43.77 1.63
2645 3134 7.148188 GGTCAATACAAGGCATGTGGATATATG 60.148 40.741 5.49 0.00 43.77 1.78
2646 3135 6.885918 TCAATACAAGGCATGTGGATATATGG 59.114 38.462 5.49 0.00 43.77 2.74
2674 3163 1.153489 CAGGAGTGATGCAGACGGG 60.153 63.158 0.00 0.00 0.00 5.28
2677 3166 0.741221 GGAGTGATGCAGACGGGAAC 60.741 60.000 0.00 0.00 0.00 3.62
2678 3167 0.247736 GAGTGATGCAGACGGGAACT 59.752 55.000 0.00 0.00 0.00 3.01
2681 3170 0.684535 TGATGCAGACGGGAACTTGA 59.315 50.000 0.00 0.00 0.00 3.02
2702 3193 7.283354 ACTTGACTCTATCAACGATATCTCACA 59.717 37.037 0.34 0.00 42.62 3.58
2721 3212 5.301555 TCACATTGTCACTGACGGAAAATA 58.698 37.500 4.71 0.00 34.95 1.40
2837 3705 4.890158 TGCACATGAAGAACTTAGGAGA 57.110 40.909 0.00 0.00 0.00 3.71
2860 3728 4.283363 AGCTGAGACAGACATCACATTT 57.717 40.909 2.81 0.00 32.44 2.32
3075 4287 1.882912 TGAATCAAGCAACAGACGCT 58.117 45.000 0.00 0.00 42.98 5.07
3076 4288 3.038788 TGAATCAAGCAACAGACGCTA 57.961 42.857 0.00 0.00 39.29 4.26
3157 4375 4.937620 GCCTCTGAATCTGTTGAACATACA 59.062 41.667 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 120 4.475028 CAATGTGTTTATGCACGACATGT 58.525 39.130 0.00 0.00 41.94 3.21
121 122 3.057666 TGCAATGTGTTTATGCACGACAT 60.058 39.130 0.00 0.00 44.52 3.06
242 244 4.868171 TGTGACTTGCTATTCAATACCGAC 59.132 41.667 0.00 0.00 33.57 4.79
264 266 5.501252 GCCGCTTAAATGCAAAATCTTCATG 60.501 40.000 0.00 0.00 0.00 3.07
283 285 1.363807 GAAAAAGCTTGGTGCCGCT 59.636 52.632 0.00 0.00 44.23 5.52
284 286 0.940991 CTGAAAAAGCTTGGTGCCGC 60.941 55.000 0.00 0.00 44.23 6.53
285 287 0.667993 TCTGAAAAAGCTTGGTGCCG 59.332 50.000 0.00 0.00 44.23 5.69
286 288 4.725790 ATATCTGAAAAAGCTTGGTGCC 57.274 40.909 0.00 0.00 44.23 5.01
287 289 6.094048 TCACTATATCTGAAAAAGCTTGGTGC 59.906 38.462 0.00 0.00 43.29 5.01
288 290 7.615582 TCACTATATCTGAAAAAGCTTGGTG 57.384 36.000 0.00 0.00 0.00 4.17
289 291 6.317391 GCTCACTATATCTGAAAAAGCTTGGT 59.683 38.462 0.00 0.00 0.00 3.67
290 292 6.510799 CGCTCACTATATCTGAAAAAGCTTGG 60.511 42.308 0.00 0.00 0.00 3.61
291 293 6.417327 CGCTCACTATATCTGAAAAAGCTTG 58.583 40.000 0.00 0.00 0.00 4.01
292 294 5.525378 CCGCTCACTATATCTGAAAAAGCTT 59.475 40.000 0.00 0.00 0.00 3.74
293 295 5.053145 CCGCTCACTATATCTGAAAAAGCT 58.947 41.667 0.00 0.00 0.00 3.74
294 296 5.050490 TCCGCTCACTATATCTGAAAAAGC 58.950 41.667 0.00 0.00 0.00 3.51
295 297 7.721286 AATCCGCTCACTATATCTGAAAAAG 57.279 36.000 0.00 0.00 0.00 2.27
296 298 8.397906 CAAAATCCGCTCACTATATCTGAAAAA 58.602 33.333 0.00 0.00 0.00 1.94
297 299 7.467267 GCAAAATCCGCTCACTATATCTGAAAA 60.467 37.037 0.00 0.00 0.00 2.29
298 300 6.017934 GCAAAATCCGCTCACTATATCTGAAA 60.018 38.462 0.00 0.00 0.00 2.69
299 301 5.466728 GCAAAATCCGCTCACTATATCTGAA 59.533 40.000 0.00 0.00 0.00 3.02
300 302 4.991056 GCAAAATCCGCTCACTATATCTGA 59.009 41.667 0.00 0.00 0.00 3.27
301 303 4.751600 TGCAAAATCCGCTCACTATATCTG 59.248 41.667 0.00 0.00 0.00 2.90
302 304 4.960938 TGCAAAATCCGCTCACTATATCT 58.039 39.130 0.00 0.00 0.00 1.98
303 305 5.869753 ATGCAAAATCCGCTCACTATATC 57.130 39.130 0.00 0.00 0.00 1.63
304 306 6.639632 AAATGCAAAATCCGCTCACTATAT 57.360 33.333 0.00 0.00 0.00 0.86
305 307 7.561021 TTAAATGCAAAATCCGCTCACTATA 57.439 32.000 0.00 0.00 0.00 1.31
306 308 4.989279 AAATGCAAAATCCGCTCACTAT 57.011 36.364 0.00 0.00 0.00 2.12
307 309 5.676079 GCTTAAATGCAAAATCCGCTCACTA 60.676 40.000 0.00 0.00 0.00 2.74
308 310 4.737054 CTTAAATGCAAAATCCGCTCACT 58.263 39.130 0.00 0.00 0.00 3.41
309 311 3.304293 GCTTAAATGCAAAATCCGCTCAC 59.696 43.478 0.00 0.00 0.00 3.51
310 312 3.510719 GCTTAAATGCAAAATCCGCTCA 58.489 40.909 0.00 0.00 0.00 4.26
311 313 2.531508 CGCTTAAATGCAAAATCCGCTC 59.468 45.455 0.00 0.00 0.00 5.03
312 314 2.529151 CGCTTAAATGCAAAATCCGCT 58.471 42.857 0.00 0.00 0.00 5.52
313 315 1.587946 CCGCTTAAATGCAAAATCCGC 59.412 47.619 0.00 0.00 0.00 5.54
314 316 1.587946 GCCGCTTAAATGCAAAATCCG 59.412 47.619 0.00 0.00 0.00 4.18
315 317 2.348362 GTGCCGCTTAAATGCAAAATCC 59.652 45.455 0.00 0.00 36.65 3.01
316 318 2.348362 GGTGCCGCTTAAATGCAAAATC 59.652 45.455 0.00 0.00 36.65 2.17
317 319 2.289320 TGGTGCCGCTTAAATGCAAAAT 60.289 40.909 0.00 0.00 36.65 1.82
318 320 1.069204 TGGTGCCGCTTAAATGCAAAA 59.931 42.857 0.00 0.00 36.65 2.44
319 321 0.676184 TGGTGCCGCTTAAATGCAAA 59.324 45.000 0.00 0.00 36.65 3.68
320 322 0.676184 TTGGTGCCGCTTAAATGCAA 59.324 45.000 0.00 0.00 36.65 4.08
321 323 0.243365 CTTGGTGCCGCTTAAATGCA 59.757 50.000 0.00 0.00 0.00 3.96
322 324 1.078201 GCTTGGTGCCGCTTAAATGC 61.078 55.000 0.00 0.00 35.15 3.56
323 325 0.527565 AGCTTGGTGCCGCTTAAATG 59.472 50.000 0.00 0.00 44.23 2.32
324 326 1.256812 AAGCTTGGTGCCGCTTAAAT 58.743 45.000 0.00 0.00 44.05 1.40
325 327 1.036707 AAAGCTTGGTGCCGCTTAAA 58.963 45.000 0.00 0.00 45.03 1.52
326 328 1.036707 AAAAGCTTGGTGCCGCTTAA 58.963 45.000 0.00 0.00 45.03 1.85
327 329 1.000717 GAAAAAGCTTGGTGCCGCTTA 60.001 47.619 0.00 0.00 45.03 3.09
413 415 2.492484 GGAGTTCGACTGGACAGTACAT 59.508 50.000 4.73 0.00 42.66 2.29
414 416 1.884579 GGAGTTCGACTGGACAGTACA 59.115 52.381 4.73 0.00 42.66 2.90
528 530 2.798364 TTCTTCCACGTGGGTGCGA 61.798 57.895 33.40 20.46 43.00 5.10
529 531 2.280524 TTCTTCCACGTGGGTGCG 60.281 61.111 33.40 18.63 43.00 5.34
577 579 2.478134 GCTGCTCATGAATAGGCTTACG 59.522 50.000 0.00 0.00 0.00 3.18
581 583 0.110104 GGGCTGCTCATGAATAGGCT 59.890 55.000 23.12 0.00 36.16 4.58
602 604 2.352805 GGGTCAGGCTTGTCAGGG 59.647 66.667 0.00 0.00 0.00 4.45
605 607 0.400213 ATTTCGGGTCAGGCTTGTCA 59.600 50.000 0.00 0.00 0.00 3.58
624 626 1.050988 GCCTAGACCAGATGCCAGGA 61.051 60.000 0.00 0.00 0.00 3.86
627 629 0.471191 CATGCCTAGACCAGATGCCA 59.529 55.000 0.00 0.00 0.00 4.92
634 636 2.434843 CGAGCCCATGCCTAGACCA 61.435 63.158 0.00 0.00 38.69 4.02
655 657 1.194772 GTTCAGGCTTCGGACGAAAAG 59.805 52.381 8.59 0.00 33.34 2.27
671 673 0.976641 ACTCATTCGGCCTCTGTTCA 59.023 50.000 0.00 0.00 0.00 3.18
677 679 7.973944 ACAATTATTTAAAACTCATTCGGCCTC 59.026 33.333 0.00 0.00 0.00 4.70
860 930 1.471684 GCATTCTTGCTGGAACCAGAG 59.528 52.381 22.96 12.86 46.30 3.35
872 942 1.068748 ACTGCAAAGCGAGCATTCTTG 60.069 47.619 0.00 0.00 41.82 3.02
921 1096 2.592308 GTGGAGGGATGAGTGCCC 59.408 66.667 0.00 0.00 46.40 5.36
930 1105 2.989639 CGCTGATTGGTGGAGGGA 59.010 61.111 0.00 0.00 0.00 4.20
1004 1179 1.437547 AGGGAAAGGTAGGGACTGAGT 59.562 52.381 0.00 0.00 41.52 3.41
1014 1189 2.370849 AGTTTGCTCGAAGGGAAAGGTA 59.629 45.455 0.00 0.00 0.00 3.08
1027 1208 1.065551 GTGGGTTGTGTGAGTTTGCTC 59.934 52.381 0.00 0.00 41.97 4.26
1036 1217 2.477176 CGGTGGTGTGGGTTGTGTG 61.477 63.158 0.00 0.00 0.00 3.82
1037 1218 2.124487 CGGTGGTGTGGGTTGTGT 60.124 61.111 0.00 0.00 0.00 3.72
1059 1240 4.360405 CTTCGGGTGGGGTTGGGG 62.360 72.222 0.00 0.00 0.00 4.96
1588 1788 7.247728 CGGATAGATAGATAAGCAGAGTCAAC 58.752 42.308 0.00 0.00 0.00 3.18
1612 1821 2.163815 ACTACTGCTACCACTACTTGCG 59.836 50.000 0.00 0.00 0.00 4.85
1746 2036 1.004745 GGGCCAGACATTTCAGAAGGA 59.995 52.381 4.39 0.00 0.00 3.36
1766 2056 2.154462 CAGCAACCAAGGTACCAAGAG 58.846 52.381 15.94 2.03 0.00 2.85
1768 2058 2.270352 TCAGCAACCAAGGTACCAAG 57.730 50.000 15.94 5.60 0.00 3.61
1770 2060 1.493022 AGTTCAGCAACCAAGGTACCA 59.507 47.619 15.94 0.00 32.22 3.25
1771 2061 2.152016 GAGTTCAGCAACCAAGGTACC 58.848 52.381 2.73 2.73 32.22 3.34
1772 2062 2.808543 CAGAGTTCAGCAACCAAGGTAC 59.191 50.000 0.00 0.00 32.22 3.34
1774 2064 1.477558 CCAGAGTTCAGCAACCAAGGT 60.478 52.381 0.00 0.00 32.22 3.50
1775 2065 1.242076 CCAGAGTTCAGCAACCAAGG 58.758 55.000 0.00 0.00 32.22 3.61
1776 2066 1.972872 ACCAGAGTTCAGCAACCAAG 58.027 50.000 0.00 0.00 32.22 3.61
1852 2179 1.901591 ATCTCAGTTTGCACCACTGG 58.098 50.000 20.30 13.27 41.83 4.00
1938 2275 1.588404 CTGCTACGGTATGAAAGCACG 59.412 52.381 0.00 0.00 39.92 5.34
1950 2287 4.742438 AACACAAATTACACTGCTACGG 57.258 40.909 0.00 0.00 0.00 4.02
1981 2328 2.877154 ACCTACTGATGGAGGGTCAT 57.123 50.000 0.00 0.00 37.14 3.06
1985 2332 2.472029 ACAGAACCTACTGATGGAGGG 58.528 52.381 0.00 0.00 40.63 4.30
2010 2357 1.818674 GTTGGGTTCTGTGCCTAATGG 59.181 52.381 0.00 0.00 0.00 3.16
2053 2515 7.034397 GCAGAGTAAACTACTGTACCTTAAGG 58.966 42.308 20.42 20.42 39.59 2.69
2109 2571 5.560722 TTCAGAATTCAGAGGGTAACACA 57.439 39.130 8.44 0.00 39.74 3.72
2116 2578 3.765511 TGCCATTTTCAGAATTCAGAGGG 59.234 43.478 8.44 6.85 0.00 4.30
2156 2628 8.377681 CGAGAGTAACATACGCTTAATTTTTCA 58.622 33.333 0.00 0.00 38.97 2.69
2168 2641 7.909121 ACTACAAGAAATCGAGAGTAACATACG 59.091 37.037 0.00 0.00 0.00 3.06
2176 2649 9.623350 GTTTAGTTACTACAAGAAATCGAGAGT 57.377 33.333 0.00 0.00 0.00 3.24
2193 2666 6.981559 CCTAGAGCCTCATCTTGTTTAGTTAC 59.018 42.308 0.00 0.00 0.00 2.50
2195 2668 5.627968 GCCTAGAGCCTCATCTTGTTTAGTT 60.628 44.000 0.00 0.00 34.35 2.24
2196 2669 4.141824 GCCTAGAGCCTCATCTTGTTTAGT 60.142 45.833 0.00 0.00 34.35 2.24
2197 2670 4.376146 GCCTAGAGCCTCATCTTGTTTAG 58.624 47.826 0.00 0.00 34.35 1.85
2198 2671 4.408182 GCCTAGAGCCTCATCTTGTTTA 57.592 45.455 0.00 0.00 34.35 2.01
2199 2672 3.274095 GCCTAGAGCCTCATCTTGTTT 57.726 47.619 0.00 0.00 34.35 2.83
2218 2691 3.028366 GAAACTGAGAAGCGCCGGC 62.028 63.158 19.07 19.07 40.37 6.13
2219 2692 1.021390 ATGAAACTGAGAAGCGCCGG 61.021 55.000 2.29 0.00 0.00 6.13
2222 2695 1.611043 GCAATGAAACTGAGAAGCGC 58.389 50.000 0.00 0.00 0.00 5.92
2223 2696 1.808945 AGGCAATGAAACTGAGAAGCG 59.191 47.619 0.00 0.00 0.00 4.68
2230 2703 5.413833 AGTTGTCAGATAGGCAATGAAACTG 59.586 40.000 0.00 0.00 44.87 3.16
2231 2704 5.413833 CAGTTGTCAGATAGGCAATGAAACT 59.586 40.000 0.00 0.00 44.87 2.66
2236 2709 5.181009 TCTTCAGTTGTCAGATAGGCAATG 58.819 41.667 0.00 0.00 44.87 2.82
2240 2713 4.393371 GGTTTCTTCAGTTGTCAGATAGGC 59.607 45.833 0.00 0.00 0.00 3.93
2244 2717 4.217118 GCATGGTTTCTTCAGTTGTCAGAT 59.783 41.667 0.00 0.00 0.00 2.90
2249 2724 3.553508 GCATGCATGGTTTCTTCAGTTGT 60.554 43.478 27.34 0.00 0.00 3.32
2251 2726 2.028748 GGCATGCATGGTTTCTTCAGTT 60.029 45.455 27.34 0.00 0.00 3.16
2296 2771 4.744795 AACTATAGAGCACCACAAGGAG 57.255 45.455 6.78 0.00 38.69 3.69
2297 2772 5.516044 TCTAACTATAGAGCACCACAAGGA 58.484 41.667 6.78 0.00 34.35 3.36
2298 2773 5.854010 TCTAACTATAGAGCACCACAAGG 57.146 43.478 6.78 0.00 35.55 3.61
2299 2774 5.694006 GCATCTAACTATAGAGCACCACAAG 59.306 44.000 6.78 0.00 41.36 3.16
2300 2775 5.363868 AGCATCTAACTATAGAGCACCACAA 59.636 40.000 6.78 0.00 41.36 3.33
2301 2776 4.895889 AGCATCTAACTATAGAGCACCACA 59.104 41.667 6.78 0.00 41.36 4.17
2302 2777 5.226396 CAGCATCTAACTATAGAGCACCAC 58.774 45.833 6.78 0.00 41.36 4.16
2303 2778 4.281941 CCAGCATCTAACTATAGAGCACCA 59.718 45.833 6.78 0.00 41.36 4.17
2340 2815 6.952083 CACGATTCTTGCGATATGATAACATG 59.048 38.462 0.00 0.00 37.87 3.21
2362 2837 1.069022 CAACACTCCAATTCCAGCACG 60.069 52.381 0.00 0.00 0.00 5.34
2368 2843 3.940209 TGATTGCAACACTCCAATTCC 57.060 42.857 0.00 0.00 32.20 3.01
2370 2845 5.477984 ACACTATGATTGCAACACTCCAATT 59.522 36.000 0.00 0.00 32.20 2.32
2375 2850 6.144402 CCAAAAACACTATGATTGCAACACTC 59.856 38.462 0.00 0.00 0.00 3.51
2377 2852 5.752955 ACCAAAAACACTATGATTGCAACAC 59.247 36.000 0.00 0.00 0.00 3.32
2380 2855 7.044181 TGAAACCAAAAACACTATGATTGCAA 58.956 30.769 0.00 0.00 0.00 4.08
2381 2856 6.577103 TGAAACCAAAAACACTATGATTGCA 58.423 32.000 0.00 0.00 0.00 4.08
2413 2888 4.469657 ACTGCCAAAAGTTTGAGTATCCA 58.530 39.130 5.34 0.00 40.55 3.41
2481 2956 3.645975 CAACGTCCTTTGCGCCGT 61.646 61.111 4.18 2.43 34.56 5.68
2551 3036 3.137544 TCCAAGAACAGAAAAGGCAGGTA 59.862 43.478 0.00 0.00 0.00 3.08
2557 3042 4.038402 AGTGCAATCCAAGAACAGAAAAGG 59.962 41.667 0.00 0.00 0.00 3.11
2562 3047 6.899393 AAATAAGTGCAATCCAAGAACAGA 57.101 33.333 0.00 0.00 0.00 3.41
2565 3050 6.691508 AGGAAAATAAGTGCAATCCAAGAAC 58.308 36.000 0.00 0.00 0.00 3.01
2607 3094 8.519526 TGCCTTGTATTGACCTTTTAGTATTTG 58.480 33.333 0.00 0.00 0.00 2.32
2621 3108 6.885918 CCATATATCCACATGCCTTGTATTGA 59.114 38.462 0.00 0.00 36.57 2.57
2629 3116 2.355108 GCGTCCATATATCCACATGCCT 60.355 50.000 0.00 0.00 0.00 4.75
2642 3129 3.449377 TCACTCCTGTTTATGCGTCCATA 59.551 43.478 0.00 0.00 32.85 2.74
2645 3134 2.380084 TCACTCCTGTTTATGCGTCC 57.620 50.000 0.00 0.00 0.00 4.79
2646 3135 2.030946 GCATCACTCCTGTTTATGCGTC 59.969 50.000 0.00 0.00 35.01 5.19
2674 3163 8.346300 TGAGATATCGTTGATAGAGTCAAGTTC 58.654 37.037 0.00 0.00 46.99 3.01
2677 3166 7.643579 TGTGAGATATCGTTGATAGAGTCAAG 58.356 38.462 0.00 0.00 46.99 3.02
2678 3167 7.568199 TGTGAGATATCGTTGATAGAGTCAA 57.432 36.000 0.00 0.00 44.36 3.18
2681 3170 7.946207 ACAATGTGAGATATCGTTGATAGAGT 58.054 34.615 0.00 0.00 35.39 3.24
2702 3193 5.182950 TGCATTATTTTCCGTCAGTGACAAT 59.817 36.000 22.66 15.84 32.09 2.71
2721 3212 5.817816 GCTACTACACTAAGTGGATTGCATT 59.182 40.000 0.00 0.00 37.94 3.56
2837 3705 3.758755 TGTGATGTCTGTCTCAGCTTT 57.241 42.857 0.00 0.00 0.00 3.51
2860 3728 2.160205 CTGTACGAGTTCCTCCTGTGA 58.840 52.381 0.00 0.00 0.00 3.58
3075 4287 1.191535 ACTAGCGAATGGGTGCAGTA 58.808 50.000 0.00 0.00 0.00 2.74
3076 4288 1.134788 GTACTAGCGAATGGGTGCAGT 60.135 52.381 0.00 0.00 0.00 4.40
3157 4375 0.613260 TGCCGTCCATGCTAACTCTT 59.387 50.000 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.