Multiple sequence alignment - TraesCS2D01G253600

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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 TraesCS2D01G253600 chr2D 100.000 4133 0 0 1 4133 305916665 305912533 0.000000e+00 7633.0
1 TraesCS2D01G253600 chr2A 91.762 1566 66 27 239 1786 384894689 384893169 0.000000e+00 2119.0
2 TraesCS2D01G253600 chr2A 96.883 1123 31 4 2590 3711 384892350 384891231 0.000000e+00 1877.0
3 TraesCS2D01G253600 chr2A 96.813 753 21 3 1840 2591 384893182 384892432 0.000000e+00 1254.0
4 TraesCS2D01G253600 chr2A 95.023 442 14 4 3694 4133 384891218 384890783 0.000000e+00 688.0
5 TraesCS2D01G253600 chr2B 95.788 1021 41 2 3002 4020 373998411 373997391 0.000000e+00 1646.0
6 TraesCS2D01G253600 chr2B 91.360 1169 95 5 1836 3002 373999615 373998451 0.000000e+00 1594.0
7 TraesCS2D01G253600 chr2B 92.763 608 15 10 696 1285 374000739 374000143 0.000000e+00 852.0
8 TraesCS2D01G253600 chr2B 97.590 332 7 1 366 696 374001114 374000783 6.000000e-158 568.0
9 TraesCS2D01G253600 chr2B 90.778 347 19 3 1 334 374001457 374001111 6.300000e-123 451.0
10 TraesCS2D01G253600 chr2B 94.138 290 11 1 1498 1787 373999881 373999598 1.760000e-118 436.0
11 TraesCS2D01G253600 chr2B 98.429 191 2 1 1311 1500 374000149 373999959 6.620000e-88 335.0
12 TraesCS2D01G253600 chr2B 93.966 116 4 3 4019 4133 373997327 373997214 5.490000e-39 172.0
13 TraesCS2D01G253600 chr7D 93.478 46 3 0 3415 3460 621646360 621646405 7.410000e-08 69.4
14 TraesCS2D01G253600 chr7A 91.489 47 4 0 3418 3464 254386164 254386118 9.590000e-07 65.8
15 TraesCS2D01G253600 chr1B 91.489 47 4 0 3418 3464 222308871 222308825 9.590000e-07 65.8
16 TraesCS2D01G253600 chr5A 90.000 50 4 1 3416 3464 143029025 143028976 3.450000e-06 63.9
17 TraesCS2D01G253600 chr1A 88.462 52 4 2 3414 3464 232340428 232340378 1.240000e-05 62.1
18 TraesCS2D01G253600 chr5B 88.235 51 4 2 3416 3465 295217261 295217310 4.460000e-05 60.2
19 TraesCS2D01G253600 chr7B 86.792 53 5 2 3414 3465 192854265 192854214 1.600000e-04 58.4


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 TraesCS2D01G253600 chr2D 305912533 305916665 4132 True 7633.00 7633 100.00000 1 4133 1 chr2D.!!$R1 4132
1 TraesCS2D01G253600 chr2A 384890783 384894689 3906 True 1484.50 2119 95.12025 239 4133 4 chr2A.!!$R1 3894
2 TraesCS2D01G253600 chr2B 373997214 374001457 4243 True 756.75 1646 94.35150 1 4133 8 chr2B.!!$R1 4132

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
363 410 0.043032 TGGTATGGTAACGGAGGGGT 59.957 55.0 0.00 0.0 42.51 4.95 F
368 415 0.397564 TGGTAACGGAGGGGTTTGAC 59.602 55.0 0.00 0.0 42.51 3.18 F
1264 1385 0.749454 ATCAACGCTGGCCTGGATTC 60.749 55.0 12.06 0.0 0.00 2.52 F
2844 3132 0.391263 CCCGAGGTGAGCCAAACTAC 60.391 60.0 0.00 0.0 37.19 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2345 2549 0.305922 GCGCCCAAGATTGATCTTCG 59.694 55.000 0.00 6.2 44.84 3.79 R
2495 2699 6.023603 AGTTCCTATTTCACCTTCTCCACTA 58.976 40.000 0.00 0.0 0.00 2.74 R
2879 3167 1.880027 GCGGGATCGGCAGAATATTTT 59.120 47.619 2.79 0.0 36.79 1.82 R
3683 4013 2.544721 TGTCTCTCTTTCAGGCATCCT 58.455 47.619 0.00 0.0 0.00 3.24 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
69 70 1.372087 CGATGAACTGGCAAGGAGGC 61.372 60.000 0.00 0.00 44.50 4.70
102 103 0.179108 GGTGGCATAGTCACGGAGTC 60.179 60.000 0.00 0.00 41.61 3.36
105 106 0.103208 GGCATAGTCACGGAGTCCAG 59.897 60.000 10.49 4.72 41.61 3.86
130 131 3.868754 GCGGGAGAGGTTAGTGTTCAATT 60.869 47.826 0.00 0.00 0.00 2.32
146 147 3.492337 TCAATTCCTAACAACCGCCTTT 58.508 40.909 0.00 0.00 0.00 3.11
160 161 1.064952 CGCCTTTTATAACCGCCCAAG 59.935 52.381 0.00 0.00 0.00 3.61
163 164 2.758423 CCTTTTATAACCGCCCAAGCTT 59.242 45.455 0.00 0.00 36.60 3.74
191 203 2.978824 CGAAAGGCCGAGGAGGAA 59.021 61.111 0.00 0.00 45.00 3.36
325 339 2.338620 GTTTGGGTTGCTTCGGGC 59.661 61.111 0.00 0.00 42.22 6.13
326 340 2.915137 TTTGGGTTGCTTCGGGCC 60.915 61.111 0.00 0.00 40.92 5.80
334 381 2.586357 GCTTCGGGCCGTCTGATC 60.586 66.667 27.32 6.72 34.27 2.92
335 382 2.892640 CTTCGGGCCGTCTGATCA 59.107 61.111 27.32 0.36 0.00 2.92
336 383 1.218047 CTTCGGGCCGTCTGATCAA 59.782 57.895 27.32 9.90 0.00 2.57
337 384 0.391130 CTTCGGGCCGTCTGATCAAA 60.391 55.000 27.32 9.10 0.00 2.69
338 385 0.391130 TTCGGGCCGTCTGATCAAAG 60.391 55.000 27.32 0.00 0.00 2.77
339 386 1.815421 CGGGCCGTCTGATCAAAGG 60.815 63.158 19.97 1.53 0.00 3.11
340 387 2.115291 GGGCCGTCTGATCAAAGGC 61.115 63.158 21.06 21.06 46.51 4.35
341 388 3.093278 GCCGTCTGATCAAAGGCG 58.907 61.111 16.65 10.29 44.78 5.52
342 389 1.741770 GCCGTCTGATCAAAGGCGT 60.742 57.895 16.65 0.00 43.70 5.68
343 390 1.298859 GCCGTCTGATCAAAGGCGTT 61.299 55.000 16.65 0.00 43.70 4.84
344 391 1.156736 CCGTCTGATCAAAGGCGTTT 58.843 50.000 7.99 0.00 43.70 3.60
345 392 1.135972 CCGTCTGATCAAAGGCGTTTG 60.136 52.381 22.69 22.69 43.70 2.93
346 393 1.135972 CGTCTGATCAAAGGCGTTTGG 60.136 52.381 26.60 13.82 42.98 3.28
347 394 1.880027 GTCTGATCAAAGGCGTTTGGT 59.120 47.619 26.60 22.33 42.98 3.67
348 395 3.071479 GTCTGATCAAAGGCGTTTGGTA 58.929 45.455 26.60 12.70 42.98 3.25
349 396 3.689649 GTCTGATCAAAGGCGTTTGGTAT 59.310 43.478 26.60 16.38 42.98 2.73
350 397 3.689161 TCTGATCAAAGGCGTTTGGTATG 59.311 43.478 26.60 17.38 42.98 2.39
351 398 2.752354 TGATCAAAGGCGTTTGGTATGG 59.248 45.455 26.60 5.35 42.98 2.74
352 399 2.279935 TCAAAGGCGTTTGGTATGGT 57.720 45.000 26.60 0.00 42.98 3.55
353 400 3.420300 TCAAAGGCGTTTGGTATGGTA 57.580 42.857 26.60 7.42 42.98 3.25
354 401 3.752665 TCAAAGGCGTTTGGTATGGTAA 58.247 40.909 26.60 6.76 42.98 2.85
355 402 3.502979 TCAAAGGCGTTTGGTATGGTAAC 59.497 43.478 26.60 0.00 42.98 2.50
356 403 1.729284 AGGCGTTTGGTATGGTAACG 58.271 50.000 0.00 0.00 45.31 3.18
357 404 0.728542 GGCGTTTGGTATGGTAACGG 59.271 55.000 0.00 0.00 43.41 4.44
358 405 1.675415 GGCGTTTGGTATGGTAACGGA 60.675 52.381 0.00 0.00 43.41 4.69
359 406 1.662122 GCGTTTGGTATGGTAACGGAG 59.338 52.381 0.00 0.00 43.41 4.63
360 407 2.273557 CGTTTGGTATGGTAACGGAGG 58.726 52.381 0.00 0.00 40.51 4.30
361 408 2.635714 GTTTGGTATGGTAACGGAGGG 58.364 52.381 0.00 0.00 42.51 4.30
362 409 1.205966 TTGGTATGGTAACGGAGGGG 58.794 55.000 0.00 0.00 42.51 4.79
363 410 0.043032 TGGTATGGTAACGGAGGGGT 59.957 55.000 0.00 0.00 42.51 4.95
364 411 1.206878 GGTATGGTAACGGAGGGGTT 58.793 55.000 0.00 0.00 42.51 4.11
365 412 1.561076 GGTATGGTAACGGAGGGGTTT 59.439 52.381 0.00 0.00 42.51 3.27
366 413 2.635714 GTATGGTAACGGAGGGGTTTG 58.364 52.381 0.00 0.00 42.51 2.93
367 414 1.364269 ATGGTAACGGAGGGGTTTGA 58.636 50.000 0.00 0.00 42.51 2.69
368 415 0.397564 TGGTAACGGAGGGGTTTGAC 59.602 55.000 0.00 0.00 42.51 3.18
397 444 3.594134 GAGAGATCAACAGGGTGAACAG 58.406 50.000 0.00 0.00 0.00 3.16
615 663 2.774439 AACTGTAACTTTTGGCAGCG 57.226 45.000 0.00 0.00 32.65 5.18
629 677 0.947180 GCAGCGAACTGTCCGGTAAA 60.947 55.000 0.00 0.00 46.30 2.01
677 725 3.811497 AGTAACGAACTGTAACTTTGGCC 59.189 43.478 0.00 0.00 36.93 5.36
707 799 9.539825 AATGACAAAGCACATAGATTACTAGAG 57.460 33.333 0.00 0.00 31.78 2.43
708 800 7.492524 TGACAAAGCACATAGATTACTAGAGG 58.507 38.462 0.00 0.00 31.78 3.69
709 801 7.342026 TGACAAAGCACATAGATTACTAGAGGA 59.658 37.037 0.00 0.00 31.78 3.71
710 802 7.721402 ACAAAGCACATAGATTACTAGAGGAG 58.279 38.462 0.00 0.00 31.78 3.69
811 903 1.078759 CCATGCGTCACCTTCGTCTC 61.079 60.000 0.00 0.00 0.00 3.36
826 918 1.230650 TCTCCCTCCTCCTCCTCCA 60.231 63.158 0.00 0.00 0.00 3.86
936 1035 2.856222 CATCATTTGGTAGGGAGAGCC 58.144 52.381 0.00 0.00 0.00 4.70
1261 1382 2.046023 CATCAACGCTGGCCTGGA 60.046 61.111 12.06 0.17 0.00 3.86
1262 1383 1.452651 CATCAACGCTGGCCTGGAT 60.453 57.895 12.06 2.69 0.00 3.41
1264 1385 0.749454 ATCAACGCTGGCCTGGATTC 60.749 55.000 12.06 0.00 0.00 2.52
1265 1386 2.044946 AACGCTGGCCTGGATTCC 60.045 61.111 12.06 0.00 0.00 3.01
1267 1388 2.825836 CGCTGGCCTGGATTCCAC 60.826 66.667 12.06 0.00 0.00 4.02
1278 1399 2.240667 CTGGATTCCACTTCCACCTGAT 59.759 50.000 0.00 0.00 38.35 2.90
1279 1400 3.455910 CTGGATTCCACTTCCACCTGATA 59.544 47.826 0.00 0.00 38.35 2.15
1280 1401 3.849574 TGGATTCCACTTCCACCTGATAA 59.150 43.478 0.00 0.00 38.35 1.75
1281 1402 4.080356 TGGATTCCACTTCCACCTGATAAG 60.080 45.833 0.00 0.00 38.35 1.73
1282 1403 4.080299 GGATTCCACTTCCACCTGATAAGT 60.080 45.833 0.00 0.00 33.82 2.24
1283 1404 4.993705 TTCCACTTCCACCTGATAAGTT 57.006 40.909 0.00 0.00 31.21 2.66
1284 1405 4.993705 TCCACTTCCACCTGATAAGTTT 57.006 40.909 0.00 0.00 31.21 2.66
1285 1406 4.906618 TCCACTTCCACCTGATAAGTTTC 58.093 43.478 0.00 0.00 31.21 2.78
1286 1407 3.684788 CCACTTCCACCTGATAAGTTTCG 59.315 47.826 0.00 0.00 31.21 3.46
1287 1408 4.562757 CCACTTCCACCTGATAAGTTTCGA 60.563 45.833 0.00 0.00 31.21 3.71
1288 1409 4.627467 CACTTCCACCTGATAAGTTTCGAG 59.373 45.833 0.00 0.00 31.21 4.04
1289 1410 4.527038 ACTTCCACCTGATAAGTTTCGAGA 59.473 41.667 0.00 0.00 29.25 4.04
1290 1411 5.187967 ACTTCCACCTGATAAGTTTCGAGAT 59.812 40.000 0.00 0.00 29.25 2.75
1291 1412 6.380274 ACTTCCACCTGATAAGTTTCGAGATA 59.620 38.462 0.00 0.00 29.25 1.98
1292 1413 6.145338 TCCACCTGATAAGTTTCGAGATAC 57.855 41.667 0.00 0.00 0.00 2.24
1293 1414 4.976731 CCACCTGATAAGTTTCGAGATACG 59.023 45.833 0.00 0.00 44.09 3.06
1306 1427 3.551890 TCGAGATACGATCAAAGCTTTGC 59.448 43.478 30.35 18.18 46.45 3.68
1307 1428 3.302740 CGAGATACGATCAAAGCTTTGCC 60.303 47.826 30.35 22.61 45.77 4.52
1308 1429 3.609853 AGATACGATCAAAGCTTTGCCA 58.390 40.909 30.35 17.33 38.05 4.92
1309 1430 4.202441 AGATACGATCAAAGCTTTGCCAT 58.798 39.130 30.35 20.97 38.05 4.40
1317 1439 6.957077 CGATCAAAGCTTTGCCATTAATTTTG 59.043 34.615 30.35 6.93 38.05 2.44
1543 1745 4.220602 GGGGAAGCTGAAATTAACATGTGT 59.779 41.667 0.00 0.00 0.00 3.72
1562 1766 4.145052 GTGTCTGTTCCAGGGAGATTTTT 58.855 43.478 0.00 0.00 31.51 1.94
1664 1868 2.725312 GCTCATCGCAGGGACAGGA 61.725 63.158 0.00 0.00 38.92 3.86
1750 1954 1.151413 AGGTGACTGGGGAAGGTTAGA 59.849 52.381 0.00 0.00 41.13 2.10
1751 1955 1.278413 GGTGACTGGGGAAGGTTAGAC 59.722 57.143 0.00 0.00 0.00 2.59
1752 1956 1.975680 GTGACTGGGGAAGGTTAGACA 59.024 52.381 0.00 0.00 0.00 3.41
1753 1957 1.975680 TGACTGGGGAAGGTTAGACAC 59.024 52.381 0.00 0.00 0.00 3.67
1780 1984 5.221342 ACACACACCTCTAACTTCTTCTCTG 60.221 44.000 0.00 0.00 0.00 3.35
1787 1991 7.713073 CACCTCTAACTTCTTCTCTGTCTTTTT 59.287 37.037 0.00 0.00 0.00 1.94
1814 2018 3.430333 TTTTTGCGGGTGAACTTCTTC 57.570 42.857 0.00 0.00 0.00 2.87
1815 2019 2.341846 TTTGCGGGTGAACTTCTTCT 57.658 45.000 0.00 0.00 0.00 2.85
1816 2020 1.878953 TTGCGGGTGAACTTCTTCTC 58.121 50.000 0.00 0.00 0.00 2.87
1817 2021 1.048601 TGCGGGTGAACTTCTTCTCT 58.951 50.000 0.00 0.00 0.00 3.10
1818 2022 1.270305 TGCGGGTGAACTTCTTCTCTG 60.270 52.381 0.00 0.00 0.00 3.35
1819 2023 1.270358 GCGGGTGAACTTCTTCTCTGT 60.270 52.381 0.00 0.00 0.00 3.41
1820 2024 2.678324 CGGGTGAACTTCTTCTCTGTC 58.322 52.381 0.00 0.00 0.00 3.51
1821 2025 2.297597 CGGGTGAACTTCTTCTCTGTCT 59.702 50.000 0.00 0.00 0.00 3.41
1822 2026 3.243907 CGGGTGAACTTCTTCTCTGTCTT 60.244 47.826 0.00 0.00 0.00 3.01
1823 2027 4.709250 GGGTGAACTTCTTCTCTGTCTTT 58.291 43.478 0.00 0.00 0.00 2.52
1824 2028 5.509163 CGGGTGAACTTCTTCTCTGTCTTTA 60.509 44.000 0.00 0.00 0.00 1.85
1825 2029 6.289064 GGGTGAACTTCTTCTCTGTCTTTAA 58.711 40.000 0.00 0.00 0.00 1.52
1826 2030 6.203145 GGGTGAACTTCTTCTCTGTCTTTAAC 59.797 42.308 0.00 0.00 0.00 2.01
1827 2031 6.987404 GGTGAACTTCTTCTCTGTCTTTAACT 59.013 38.462 0.00 0.00 0.00 2.24
1828 2032 7.170151 GGTGAACTTCTTCTCTGTCTTTAACTC 59.830 40.741 0.00 0.00 0.00 3.01
1829 2033 7.170151 GTGAACTTCTTCTCTGTCTTTAACTCC 59.830 40.741 0.00 0.00 0.00 3.85
1830 2034 6.732896 ACTTCTTCTCTGTCTTTAACTCCA 57.267 37.500 0.00 0.00 0.00 3.86
1831 2035 7.309770 ACTTCTTCTCTGTCTTTAACTCCAT 57.690 36.000 0.00 0.00 0.00 3.41
1832 2036 7.158021 ACTTCTTCTCTGTCTTTAACTCCATG 58.842 38.462 0.00 0.00 0.00 3.66
1833 2037 6.042638 TCTTCTCTGTCTTTAACTCCATGG 57.957 41.667 4.97 4.97 0.00 3.66
1834 2038 5.544176 TCTTCTCTGTCTTTAACTCCATGGT 59.456 40.000 12.58 0.00 0.00 3.55
1835 2039 6.724441 TCTTCTCTGTCTTTAACTCCATGGTA 59.276 38.462 12.58 0.00 0.00 3.25
1836 2040 6.282199 TCTCTGTCTTTAACTCCATGGTAC 57.718 41.667 12.58 0.00 0.00 3.34
1837 2041 6.017192 TCTCTGTCTTTAACTCCATGGTACT 58.983 40.000 12.58 0.00 0.00 2.73
1838 2042 6.497259 TCTCTGTCTTTAACTCCATGGTACTT 59.503 38.462 12.58 4.20 0.00 2.24
1839 2043 6.698380 TCTGTCTTTAACTCCATGGTACTTC 58.302 40.000 12.58 0.00 0.00 3.01
1840 2044 6.497259 TCTGTCTTTAACTCCATGGTACTTCT 59.503 38.462 12.58 0.00 0.00 2.85
1841 2045 7.016268 TCTGTCTTTAACTCCATGGTACTTCTT 59.984 37.037 12.58 0.00 0.00 2.52
1842 2046 7.159372 TGTCTTTAACTCCATGGTACTTCTTC 58.841 38.462 12.58 0.00 0.00 2.87
1843 2047 7.016268 TGTCTTTAACTCCATGGTACTTCTTCT 59.984 37.037 12.58 0.00 0.00 2.85
1844 2048 7.546316 GTCTTTAACTCCATGGTACTTCTTCTC 59.454 40.741 12.58 0.00 0.00 2.87
1845 2049 7.455008 TCTTTAACTCCATGGTACTTCTTCTCT 59.545 37.037 12.58 0.00 0.00 3.10
1867 2071 7.339721 TCTCTGTCTTTAACTCCATGGTACTAG 59.660 40.741 12.58 3.92 0.00 2.57
1900 2104 3.436243 AGTGGAGGAGACTGGTTAAGAG 58.564 50.000 0.00 0.00 44.43 2.85
1908 2112 6.565976 AGGAGACTGGTTAAGAGGCAACTAG 61.566 48.000 0.00 0.00 46.33 2.57
1922 2126 3.753272 GGCAACTAGTGAAGCTGATTTCA 59.247 43.478 13.00 0.00 34.83 2.69
1923 2127 4.216257 GGCAACTAGTGAAGCTGATTTCAA 59.784 41.667 13.00 0.00 38.69 2.69
1931 2135 5.126061 AGTGAAGCTGATTTCAAGTTGTTGT 59.874 36.000 2.11 0.00 38.69 3.32
1940 2144 4.566545 TTCAAGTTGTTGTGGCACTATG 57.433 40.909 19.83 6.25 34.98 2.23
1970 2174 1.952296 GGCTATGGGATTTCAGCACAG 59.048 52.381 0.00 0.00 35.69 3.66
2183 2387 5.870978 GCTTACAGAGTTCGGTTACCAATTA 59.129 40.000 1.13 0.00 0.00 1.40
2246 2450 6.258727 TGAGCTGAAGCATAATGTTAACTAGC 59.741 38.462 7.22 4.01 45.16 3.42
2345 2549 5.412526 TTTTTCACGACAGTTGGACATAC 57.587 39.130 0.00 0.00 0.00 2.39
2501 2705 1.067565 CAGAGACTTGCGCTTAGTGGA 60.068 52.381 18.24 0.00 0.00 4.02
2686 2974 5.362556 AGATTTCAACATGTTTCTGACCG 57.637 39.130 8.77 0.00 0.00 4.79
2844 3132 0.391263 CCCGAGGTGAGCCAAACTAC 60.391 60.000 0.00 0.00 37.19 2.73
2879 3167 4.347000 GGGTCTACCATAATGCCTAGTTGA 59.653 45.833 0.81 0.00 39.85 3.18
2895 3183 6.566753 GCCTAGTTGAAAATATTCTGCCGATC 60.567 42.308 0.00 0.00 36.48 3.69
2901 3189 1.194781 ATATTCTGCCGATCCCGCCT 61.195 55.000 0.00 0.00 0.00 5.52
2971 3259 8.492673 TGTAGTTGCATCAGGAATAAAGTTAG 57.507 34.615 0.00 0.00 0.00 2.34
3442 3772 3.452878 TCCCTCCGTCCCAAAATAAGTA 58.547 45.455 0.00 0.00 0.00 2.24
3451 3781 4.272748 GTCCCAAAATAAGTATCGCTGACC 59.727 45.833 0.00 0.00 0.00 4.02
3683 4013 9.255304 GAATTCTTGCAACAAAATACTTTACCA 57.745 29.630 0.00 0.00 0.00 3.25
3767 4127 0.313672 TTGCCTCAAATGCGGTCAAC 59.686 50.000 0.00 0.00 0.00 3.18
3906 4267 9.725019 TTCAATCATGACTAACAACTAGACAAT 57.275 29.630 0.00 0.00 36.18 2.71
4080 4505 5.197549 CCGCGTTTATGTATCTTGATGTTG 58.802 41.667 4.92 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.501222 CGTTCGTGAGGACCGACG 60.501 66.667 11.66 11.66 35.69 5.12
12 13 2.126580 CCGTTCGTGAGGACCGAC 60.127 66.667 0.00 0.00 35.69 4.79
42 43 2.182496 CCAGTTCATCGGCATTGCA 58.818 52.632 11.39 0.00 0.00 4.08
52 53 1.377725 CGCCTCCTTGCCAGTTCAT 60.378 57.895 0.00 0.00 0.00 2.57
69 70 2.591311 CCACCGACGAACAACCACG 61.591 63.158 0.00 0.00 0.00 4.94
102 103 1.381327 TAACCTCTCCCGCTCCTGG 60.381 63.158 0.00 0.00 0.00 4.45
105 106 0.971447 ACACTAACCTCTCCCGCTCC 60.971 60.000 0.00 0.00 0.00 4.70
130 131 4.943093 GGTTATAAAAGGCGGTTGTTAGGA 59.057 41.667 0.00 0.00 0.00 2.94
146 147 2.791347 TCAAGCTTGGGCGGTTATAA 57.209 45.000 25.73 0.00 44.37 0.98
163 164 4.794648 CCTTTCGGCGGCCCATCA 62.795 66.667 14.55 0.00 0.00 3.07
191 203 2.334023 GCCTCATGGGACTTATCTCCT 58.666 52.381 0.00 0.00 37.23 3.69
293 307 4.747583 ACCCAAACCATAGCCTAGTTTTT 58.252 39.130 0.00 0.00 31.54 1.94
325 339 1.135972 CAAACGCCTTTGATCAGACGG 60.136 52.381 2.36 7.79 39.43 4.79
326 340 1.135972 CCAAACGCCTTTGATCAGACG 60.136 52.381 9.43 1.43 39.43 4.18
334 381 3.668491 CGTTACCATACCAAACGCCTTTG 60.668 47.826 1.60 1.60 39.43 2.77
335 382 2.485038 CGTTACCATACCAAACGCCTTT 59.515 45.455 0.00 0.00 39.43 3.11
336 383 2.078392 CGTTACCATACCAAACGCCTT 58.922 47.619 0.00 0.00 39.43 4.35
337 384 1.676615 CCGTTACCATACCAAACGCCT 60.677 52.381 1.54 0.00 43.40 5.52
338 385 0.728542 CCGTTACCATACCAAACGCC 59.271 55.000 1.54 0.00 43.40 5.68
339 386 1.662122 CTCCGTTACCATACCAAACGC 59.338 52.381 1.54 0.00 43.40 4.84
340 387 2.273557 CCTCCGTTACCATACCAAACG 58.726 52.381 0.00 0.00 44.13 3.60
341 388 2.635714 CCCTCCGTTACCATACCAAAC 58.364 52.381 0.00 0.00 0.00 2.93
342 389 1.560611 CCCCTCCGTTACCATACCAAA 59.439 52.381 0.00 0.00 0.00 3.28
343 390 1.205966 CCCCTCCGTTACCATACCAA 58.794 55.000 0.00 0.00 0.00 3.67
344 391 0.043032 ACCCCTCCGTTACCATACCA 59.957 55.000 0.00 0.00 0.00 3.25
345 392 1.206878 AACCCCTCCGTTACCATACC 58.793 55.000 0.00 0.00 0.00 2.73
346 393 2.236893 TCAAACCCCTCCGTTACCATAC 59.763 50.000 0.00 0.00 0.00 2.39
347 394 2.236893 GTCAAACCCCTCCGTTACCATA 59.763 50.000 0.00 0.00 0.00 2.74
348 395 1.003928 GTCAAACCCCTCCGTTACCAT 59.996 52.381 0.00 0.00 0.00 3.55
349 396 0.397564 GTCAAACCCCTCCGTTACCA 59.602 55.000 0.00 0.00 0.00 3.25
350 397 0.671472 CGTCAAACCCCTCCGTTACC 60.671 60.000 0.00 0.00 0.00 2.85
351 398 1.293963 GCGTCAAACCCCTCCGTTAC 61.294 60.000 0.00 0.00 0.00 2.50
352 399 1.004679 GCGTCAAACCCCTCCGTTA 60.005 57.895 0.00 0.00 0.00 3.18
353 400 2.281276 GCGTCAAACCCCTCCGTT 60.281 61.111 0.00 0.00 0.00 4.44
354 401 4.675029 CGCGTCAAACCCCTCCGT 62.675 66.667 0.00 0.00 0.00 4.69
385 432 1.213296 AACACCTCTGTTCACCCTGT 58.787 50.000 0.00 0.00 35.57 4.00
397 444 3.424433 CGCTAATTGAACGGAAACACCTC 60.424 47.826 0.00 0.00 36.31 3.85
615 663 3.007635 CCTGGATTTTACCGGACAGTTC 58.992 50.000 9.46 0.00 38.49 3.01
629 677 3.527665 AGCACTGGTATAAACCCTGGATT 59.472 43.478 0.00 0.00 46.16 3.01
677 725 4.944962 TCTATGTGCTTTGTCATTTCCG 57.055 40.909 0.00 0.00 0.00 4.30
811 903 2.443016 CGTGGAGGAGGAGGAGGG 60.443 72.222 0.00 0.00 0.00 4.30
826 918 1.584380 CGTCGAGGAGAAAGGGACGT 61.584 60.000 0.00 0.00 43.81 4.34
936 1035 6.377146 GGTATATGCTCTTCTCCTCCTTCTAG 59.623 46.154 0.00 0.00 0.00 2.43
1218 1328 3.672503 GGATGCCAGGTGGGGGTT 61.673 66.667 0.00 0.00 37.04 4.11
1261 1382 5.520748 AACTTATCAGGTGGAAGTGGAAT 57.479 39.130 0.00 0.00 33.75 3.01
1262 1383 4.993705 AACTTATCAGGTGGAAGTGGAA 57.006 40.909 0.00 0.00 33.75 3.53
1264 1385 3.684788 CGAAACTTATCAGGTGGAAGTGG 59.315 47.826 0.00 0.00 33.75 4.00
1265 1386 4.566004 TCGAAACTTATCAGGTGGAAGTG 58.434 43.478 0.00 0.00 33.75 3.16
1267 1388 5.073311 TCTCGAAACTTATCAGGTGGAAG 57.927 43.478 0.00 0.00 0.00 3.46
1280 1401 9.455507 GCAAAGCTTTGATCGTATCTCGAAACT 62.456 40.741 37.14 0.00 43.73 2.66
1281 1402 7.417728 GCAAAGCTTTGATCGTATCTCGAAAC 61.418 42.308 37.14 13.59 43.73 2.78
1282 1403 5.445939 GCAAAGCTTTGATCGTATCTCGAAA 60.446 40.000 37.14 0.00 43.73 3.46
1283 1404 4.032900 GCAAAGCTTTGATCGTATCTCGAA 59.967 41.667 37.14 0.00 43.73 3.71
1284 1405 3.551890 GCAAAGCTTTGATCGTATCTCGA 59.448 43.478 37.14 0.00 44.17 4.04
1285 1406 3.302740 GGCAAAGCTTTGATCGTATCTCG 60.303 47.826 37.14 11.30 40.55 4.04
1286 1407 3.623060 TGGCAAAGCTTTGATCGTATCTC 59.377 43.478 37.14 18.47 40.55 2.75
1287 1408 3.609853 TGGCAAAGCTTTGATCGTATCT 58.390 40.909 37.14 0.00 40.55 1.98
1288 1409 4.558538 ATGGCAAAGCTTTGATCGTATC 57.441 40.909 37.14 19.77 40.55 2.24
1289 1410 4.989279 AATGGCAAAGCTTTGATCGTAT 57.011 36.364 37.14 20.75 40.55 3.06
1290 1411 5.888691 TTAATGGCAAAGCTTTGATCGTA 57.111 34.783 37.14 21.37 40.55 3.43
1291 1412 4.782019 TTAATGGCAAAGCTTTGATCGT 57.218 36.364 37.14 25.85 40.55 3.73
1292 1413 6.651755 AAATTAATGGCAAAGCTTTGATCG 57.348 33.333 37.14 15.67 40.55 3.69
1293 1414 7.809665 ACAAAATTAATGGCAAAGCTTTGATC 58.190 30.769 37.14 27.39 40.55 2.92
1294 1415 7.748691 ACAAAATTAATGGCAAAGCTTTGAT 57.251 28.000 37.14 22.30 40.55 2.57
1295 1416 7.416022 CAACAAAATTAATGGCAAAGCTTTGA 58.584 30.769 37.14 21.11 40.55 2.69
1296 1417 6.637658 CCAACAAAATTAATGGCAAAGCTTTG 59.362 34.615 30.70 30.70 41.03 2.77
1297 1418 6.737118 CCAACAAAATTAATGGCAAAGCTTT 58.263 32.000 5.69 5.69 0.00 3.51
1298 1419 6.316440 CCAACAAAATTAATGGCAAAGCTT 57.684 33.333 0.00 0.00 0.00 3.74
1299 1420 5.945466 CCAACAAAATTAATGGCAAAGCT 57.055 34.783 0.00 0.00 0.00 3.74
1306 1427 8.785946 AGAATTTCAAGCCAACAAAATTAATGG 58.214 29.630 0.00 0.00 32.90 3.16
1309 1430 9.388506 TGAAGAATTTCAAGCCAACAAAATTAA 57.611 25.926 0.00 0.00 40.26 1.40
1317 1439 4.520492 TCCTCTGAAGAATTTCAAGCCAAC 59.480 41.667 0.00 0.00 42.48 3.77
1562 1766 1.078918 CAGCTTCACATGGCTCGGA 60.079 57.895 0.00 0.00 36.59 4.55
1750 1954 2.500098 AGTTAGAGGTGTGTGTGTGTGT 59.500 45.455 0.00 0.00 0.00 3.72
1751 1955 3.179443 AGTTAGAGGTGTGTGTGTGTG 57.821 47.619 0.00 0.00 0.00 3.82
1752 1956 3.451178 AGAAGTTAGAGGTGTGTGTGTGT 59.549 43.478 0.00 0.00 0.00 3.72
1753 1957 4.060038 AGAAGTTAGAGGTGTGTGTGTG 57.940 45.455 0.00 0.00 0.00 3.82
1794 1998 3.020984 AGAAGAAGTTCACCCGCAAAAA 58.979 40.909 5.50 0.00 34.82 1.94
1795 1999 2.616842 GAGAAGAAGTTCACCCGCAAAA 59.383 45.455 5.50 0.00 34.82 2.44
1796 2000 2.158813 AGAGAAGAAGTTCACCCGCAAA 60.159 45.455 5.50 0.00 34.82 3.68
1797 2001 1.416401 AGAGAAGAAGTTCACCCGCAA 59.584 47.619 5.50 0.00 34.82 4.85
1798 2002 1.048601 AGAGAAGAAGTTCACCCGCA 58.951 50.000 5.50 0.00 34.82 5.69
1799 2003 1.270358 ACAGAGAAGAAGTTCACCCGC 60.270 52.381 5.50 0.00 34.82 6.13
1800 2004 2.297597 AGACAGAGAAGAAGTTCACCCG 59.702 50.000 5.50 0.00 34.82 5.28
1801 2005 4.344359 AAGACAGAGAAGAAGTTCACCC 57.656 45.455 5.50 0.00 34.82 4.61
1802 2006 6.987404 AGTTAAAGACAGAGAAGAAGTTCACC 59.013 38.462 5.50 0.00 34.82 4.02
1803 2007 7.170151 GGAGTTAAAGACAGAGAAGAAGTTCAC 59.830 40.741 5.50 0.00 34.82 3.18
1804 2008 7.147724 TGGAGTTAAAGACAGAGAAGAAGTTCA 60.148 37.037 5.50 0.00 34.82 3.18
1805 2009 7.210873 TGGAGTTAAAGACAGAGAAGAAGTTC 58.789 38.462 0.00 0.00 0.00 3.01
1806 2010 7.125792 TGGAGTTAAAGACAGAGAAGAAGTT 57.874 36.000 0.00 0.00 0.00 2.66
1807 2011 6.732896 TGGAGTTAAAGACAGAGAAGAAGT 57.267 37.500 0.00 0.00 0.00 3.01
1808 2012 6.593382 CCATGGAGTTAAAGACAGAGAAGAAG 59.407 42.308 5.56 0.00 0.00 2.85
1809 2013 6.043243 ACCATGGAGTTAAAGACAGAGAAGAA 59.957 38.462 21.47 0.00 0.00 2.52
1810 2014 5.544176 ACCATGGAGTTAAAGACAGAGAAGA 59.456 40.000 21.47 0.00 0.00 2.87
1811 2015 5.799213 ACCATGGAGTTAAAGACAGAGAAG 58.201 41.667 21.47 0.00 0.00 2.85
1812 2016 5.825593 ACCATGGAGTTAAAGACAGAGAA 57.174 39.130 21.47 0.00 0.00 2.87
1813 2017 6.017192 AGTACCATGGAGTTAAAGACAGAGA 58.983 40.000 21.47 0.00 0.00 3.10
1814 2018 6.287589 AGTACCATGGAGTTAAAGACAGAG 57.712 41.667 21.47 0.00 0.00 3.35
1815 2019 6.497259 AGAAGTACCATGGAGTTAAAGACAGA 59.503 38.462 21.47 0.00 0.00 3.41
1816 2020 6.702329 AGAAGTACCATGGAGTTAAAGACAG 58.298 40.000 21.47 0.00 0.00 3.51
1817 2021 6.681729 AGAAGTACCATGGAGTTAAAGACA 57.318 37.500 21.47 0.00 0.00 3.41
1818 2022 7.387643 AGAAGAAGTACCATGGAGTTAAAGAC 58.612 38.462 21.47 2.82 0.00 3.01
1819 2023 7.455008 AGAGAAGAAGTACCATGGAGTTAAAGA 59.545 37.037 21.47 0.00 0.00 2.52
1820 2024 7.547370 CAGAGAAGAAGTACCATGGAGTTAAAG 59.453 40.741 21.47 0.00 0.00 1.85
1821 2025 7.016268 ACAGAGAAGAAGTACCATGGAGTTAAA 59.984 37.037 21.47 0.00 0.00 1.52
1822 2026 6.497259 ACAGAGAAGAAGTACCATGGAGTTAA 59.503 38.462 21.47 0.00 0.00 2.01
1823 2027 6.017192 ACAGAGAAGAAGTACCATGGAGTTA 58.983 40.000 21.47 0.00 0.00 2.24
1824 2028 4.841246 ACAGAGAAGAAGTACCATGGAGTT 59.159 41.667 21.47 11.19 0.00 3.01
1825 2029 4.421131 ACAGAGAAGAAGTACCATGGAGT 58.579 43.478 21.47 0.00 0.00 3.85
1826 2030 4.709397 AGACAGAGAAGAAGTACCATGGAG 59.291 45.833 21.47 0.00 0.00 3.86
1827 2031 4.678256 AGACAGAGAAGAAGTACCATGGA 58.322 43.478 21.47 0.00 0.00 3.41
1828 2032 5.413309 AAGACAGAGAAGAAGTACCATGG 57.587 43.478 11.19 11.19 0.00 3.66
1829 2033 8.091449 AGTTAAAGACAGAGAAGAAGTACCATG 58.909 37.037 0.00 0.00 0.00 3.66
1830 2034 8.196378 AGTTAAAGACAGAGAAGAAGTACCAT 57.804 34.615 0.00 0.00 0.00 3.55
1831 2035 7.255871 GGAGTTAAAGACAGAGAAGAAGTACCA 60.256 40.741 0.00 0.00 0.00 3.25
1832 2036 7.092079 GGAGTTAAAGACAGAGAAGAAGTACC 58.908 42.308 0.00 0.00 0.00 3.34
1833 2037 7.659186 TGGAGTTAAAGACAGAGAAGAAGTAC 58.341 38.462 0.00 0.00 0.00 2.73
1834 2038 7.834881 TGGAGTTAAAGACAGAGAAGAAGTA 57.165 36.000 0.00 0.00 0.00 2.24
1835 2039 6.732896 TGGAGTTAAAGACAGAGAAGAAGT 57.267 37.500 0.00 0.00 0.00 3.01
1836 2040 6.593382 CCATGGAGTTAAAGACAGAGAAGAAG 59.407 42.308 5.56 0.00 0.00 2.85
1837 2041 6.043243 ACCATGGAGTTAAAGACAGAGAAGAA 59.957 38.462 21.47 0.00 0.00 2.52
1838 2042 5.544176 ACCATGGAGTTAAAGACAGAGAAGA 59.456 40.000 21.47 0.00 0.00 2.87
1839 2043 5.799213 ACCATGGAGTTAAAGACAGAGAAG 58.201 41.667 21.47 0.00 0.00 2.85
1840 2044 5.825593 ACCATGGAGTTAAAGACAGAGAA 57.174 39.130 21.47 0.00 0.00 2.87
1841 2045 6.017192 AGTACCATGGAGTTAAAGACAGAGA 58.983 40.000 21.47 0.00 0.00 3.10
1842 2046 6.287589 AGTACCATGGAGTTAAAGACAGAG 57.712 41.667 21.47 0.00 0.00 3.35
1843 2047 6.952358 ACTAGTACCATGGAGTTAAAGACAGA 59.048 38.462 21.47 0.00 0.00 3.41
1844 2048 7.171630 ACTAGTACCATGGAGTTAAAGACAG 57.828 40.000 21.47 3.83 0.00 3.51
1845 2049 8.834004 ATACTAGTACCATGGAGTTAAAGACA 57.166 34.615 21.47 0.00 0.00 3.41
1867 2071 8.145122 CCAGTCTCCTCCACTTAAAAGATATAC 58.855 40.741 0.00 0.00 0.00 1.47
1881 2085 2.821437 CCTCTTAACCAGTCTCCTCCA 58.179 52.381 0.00 0.00 0.00 3.86
1888 2092 4.021368 TCACTAGTTGCCTCTTAACCAGTC 60.021 45.833 0.00 0.00 29.61 3.51
1900 2104 3.753272 TGAAATCAGCTTCACTAGTTGCC 59.247 43.478 0.00 0.00 35.27 4.52
1908 2112 5.230726 CACAACAACTTGAAATCAGCTTCAC 59.769 40.000 0.00 0.00 35.07 3.18
1922 2126 5.564651 GCAATACATAGTGCCACAACAACTT 60.565 40.000 0.00 0.00 41.02 2.66
1923 2127 4.082787 GCAATACATAGTGCCACAACAACT 60.083 41.667 0.00 0.00 41.02 3.16
1931 2135 2.642427 CCACTGCAATACATAGTGCCA 58.358 47.619 8.70 0.00 45.74 4.92
1940 2144 2.638480 TCCCATAGCCACTGCAATAC 57.362 50.000 0.00 0.00 41.13 1.89
1970 2174 0.953727 TCACAACTGCTGTCAATGCC 59.046 50.000 0.00 0.00 35.47 4.40
2246 2450 3.922910 TCATTCTGTGCTCTCTTCACTG 58.077 45.455 0.00 0.00 35.58 3.66
2330 2534 3.211803 TCTTCGTATGTCCAACTGTCG 57.788 47.619 0.00 0.00 0.00 4.35
2345 2549 0.305922 GCGCCCAAGATTGATCTTCG 59.694 55.000 0.00 6.20 44.84 3.79
2495 2699 6.023603 AGTTCCTATTTCACCTTCTCCACTA 58.976 40.000 0.00 0.00 0.00 2.74
2686 2974 8.465201 AGATCTTTTCCATCTGCAAAATTAGAC 58.535 33.333 0.00 0.00 0.00 2.59
2719 3007 4.694037 AGAACTTTACCGACCATAACAAGC 59.306 41.667 0.00 0.00 0.00 4.01
2844 3132 2.104111 TGGTAGACCCACAGTGAGTTTG 59.896 50.000 0.62 0.00 38.72 2.93
2879 3167 1.880027 GCGGGATCGGCAGAATATTTT 59.120 47.619 2.79 0.00 36.79 1.82
2895 3183 7.488322 TCAATCATTTAATAAAAGAAGGCGGG 58.512 34.615 0.00 0.00 0.00 6.13
3002 3290 8.499403 AGCTTTCTATGAGAATTAGTTTGGAC 57.501 34.615 0.00 0.00 33.67 4.02
3151 3479 9.693739 ACATAATTTACATGAATGTGGTAGGAA 57.306 29.630 0.00 0.00 41.89 3.36
3442 3772 1.267121 AGTTGTACCAGGTCAGCGAT 58.733 50.000 0.00 0.00 0.00 4.58
3451 3781 2.358322 ACCACCCAAAGTTGTACCAG 57.642 50.000 0.00 0.00 0.00 4.00
3683 4013 2.544721 TGTCTCTCTTTCAGGCATCCT 58.455 47.619 0.00 0.00 0.00 3.24
4080 4505 5.326900 TGTTTATCCTGTAGTTTTTCCCCC 58.673 41.667 0.00 0.00 0.00 5.40


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

AutoCloner maintained by Alex Coulton.