Multiple sequence alignment - TraesCS3A01G356600

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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 TraesCS3A01G356600 chr3A 100.000 2576 0 0 1 2576 604324599 604327174 0.000000e+00 4758.0
1 TraesCS3A01G356600 chr3D 86.801 1879 85 68 71 1863 461950306 461952107 0.000000e+00 1945.0
2 TraesCS3A01G356600 chr3D 83.879 428 41 9 2025 2437 461952106 461952520 1.450000e-102 383.0
3 TraesCS3A01G356600 chr3D 91.124 169 14 1 1858 2026 580330942 580331109 7.170000e-56 228.0
4 TraesCS3A01G356600 chr3B 87.057 1468 61 59 476 1863 612799188 612800606 0.000000e+00 1539.0
5 TraesCS3A01G356600 chr3B 90.754 411 34 4 2168 2576 612802953 612803361 1.740000e-151 545.0
6 TraesCS3A01G356600 chr3B 88.259 247 15 4 13 255 612798454 612798690 1.510000e-72 283.0
7 TraesCS3A01G356600 chr3B 93.662 142 9 0 2025 2166 612800605 612800746 2.010000e-51 213.0
8 TraesCS3A01G356600 chr4D 91.908 173 14 0 1854 2026 62120463 62120635 2.560000e-60 243.0
9 TraesCS3A01G356600 chr2D 90.857 175 16 0 1858 2032 593801592 593801766 4.290000e-58 235.0
10 TraesCS3A01G356600 chr2D 92.121 165 13 0 1862 2026 134799977 134800141 1.540000e-57 233.0
11 TraesCS3A01G356600 chr5D 92.121 165 13 0 1862 2026 547239875 547239711 1.540000e-57 233.0
12 TraesCS3A01G356600 chr5D 87.671 146 13 4 2435 2576 339987572 339987716 5.700000e-37 165.0
13 TraesCS3A01G356600 chr5D 82.877 146 22 3 2434 2576 241959563 241959708 7.480000e-26 128.0
14 TraesCS3A01G356600 chr5D 75.207 242 41 15 1160 1390 525302710 525302943 2.110000e-16 97.1
15 TraesCS3A01G356600 chr5D 85.714 84 10 2 1158 1240 525154790 525154708 1.270000e-13 87.9
16 TraesCS3A01G356600 chr5D 74.104 251 45 17 1152 1390 525250416 525250658 4.570000e-13 86.1
17 TraesCS3A01G356600 chr6A 90.000 180 16 2 1851 2029 546930963 546931141 5.540000e-57 231.0
18 TraesCS3A01G356600 chr1D 91.071 168 15 0 1862 2029 140137145 140136978 7.170000e-56 228.0
19 TraesCS3A01G356600 chr1D 90.230 174 16 1 1858 2031 480757287 480757459 2.580000e-55 226.0
20 TraesCS3A01G356600 chr1D 97.143 70 2 0 1322 1391 383177970 383177901 4.500000e-23 119.0
21 TraesCS3A01G356600 chr1D 86.420 81 9 2 1162 1241 20061997 20062076 1.270000e-13 87.9
22 TraesCS3A01G356600 chr1D 86.250 80 9 2 1163 1241 20193515 20193593 4.570000e-13 86.1
23 TraesCS3A01G356600 chr7D 90.643 171 15 1 1858 2027 599810436 599810606 2.580000e-55 226.0
24 TraesCS3A01G356600 chr2A 86.207 145 17 3 2435 2576 727433745 727433601 1.230000e-33 154.0
25 TraesCS3A01G356600 chr5A 86.111 144 17 3 2435 2576 441169941 441170083 4.440000e-33 152.0
26 TraesCS3A01G356600 chr5A 75.207 242 42 11 1156 1390 651755174 651755404 5.870000e-17 99.0
27 TraesCS3A01G356600 chr5B 87.597 129 14 2 2450 2576 289658867 289658739 5.740000e-32 148.0
28 TraesCS3A01G356600 chr5B 75.200 250 47 14 1152 1390 659604768 659605013 1.260000e-18 104.0
29 TraesCS3A01G356600 chr6D 85.417 144 18 3 2436 2576 437661839 437661696 2.070000e-31 147.0
30 TraesCS3A01G356600 chr6B 87.903 124 13 2 2436 2557 710000326 710000203 7.430000e-31 145.0
31 TraesCS3A01G356600 chr1B 80.176 227 18 15 1165 1391 513481425 513481226 7.430000e-31 145.0
32 TraesCS3A01G356600 chr1B 85.366 82 10 2 1161 1241 33857284 33857204 1.640000e-12 84.2
33 TraesCS3A01G356600 chr7B 84.247 146 20 3 2434 2576 705329054 705329199 3.460000e-29 139.0
34 TraesCS3A01G356600 chr1A 97.143 70 2 0 1322 1391 482964107 482964038 4.500000e-23 119.0
35 TraesCS3A01G356600 chr1A 86.585 82 9 2 1161 1241 22282864 22282784 3.530000e-14 89.8


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 TraesCS3A01G356600 chr3A 604324599 604327174 2575 False 4758 4758 100.000 1 2576 1 chr3A.!!$F1 2575
1 TraesCS3A01G356600 chr3D 461950306 461952520 2214 False 1164 1945 85.340 71 2437 2 chr3D.!!$F2 2366
2 TraesCS3A01G356600 chr3B 612798454 612803361 4907 False 645 1539 89.933 13 2576 4 chr3B.!!$F1 2563

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
880 1230 0.037882 TGAGCAACTCCTTCTCTGCG 60.038 55.0 0.0 0.0 39.8 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1801 2217 0.177373 TGCTGATCTACAGGCTGCAG 59.823 55.0 15.89 11.99 45.82 4.41 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
193 194 2.202756 CCTCTAGCGTGCGGGAAC 60.203 66.667 0.00 0.00 0.00 3.62
218 219 0.449507 CTGCGCTTTTCGTTCGTCAG 60.450 55.000 9.73 0.00 41.07 3.51
288 534 1.370293 CGTACGTACGTGTGCACCA 60.370 57.895 33.95 5.88 44.13 4.17
289 535 1.599422 CGTACGTACGTGTGCACCAC 61.599 60.000 33.95 17.01 44.13 4.16
290 536 1.007502 TACGTACGTGTGCACCACC 60.008 57.895 30.25 0.98 41.26 4.61
291 537 2.730006 TACGTACGTGTGCACCACCG 62.730 60.000 30.25 15.96 41.26 4.94
292 538 3.039588 GTACGTGTGCACCACCGG 61.040 66.667 15.69 0.00 41.26 5.28
297 556 2.203139 TGTGCACCACCGGAACAG 60.203 61.111 15.69 0.00 32.73 3.16
324 583 3.291585 TCGACGAGAACAAGTAACGAAC 58.708 45.455 0.00 0.00 0.00 3.95
325 584 3.002656 TCGACGAGAACAAGTAACGAACT 59.997 43.478 0.00 0.00 41.49 3.01
327 586 4.905866 CGACGAGAACAAGTAACGAACTAA 59.094 41.667 0.00 0.00 37.50 2.24
328 587 5.566774 CGACGAGAACAAGTAACGAACTAAT 59.433 40.000 0.00 0.00 37.50 1.73
329 588 6.236889 CGACGAGAACAAGTAACGAACTAATC 60.237 42.308 0.00 0.00 37.50 1.75
337 596 4.507879 CGAACTAATCGCCGGGTT 57.492 55.556 2.18 0.00 45.89 4.11
338 597 2.294728 CGAACTAATCGCCGGGTTC 58.705 57.895 2.18 6.25 45.89 3.62
339 598 0.458889 CGAACTAATCGCCGGGTTCA 60.459 55.000 16.08 0.00 45.89 3.18
340 599 1.004595 GAACTAATCGCCGGGTTCAC 58.995 55.000 2.18 0.00 38.23 3.18
341 600 0.738412 AACTAATCGCCGGGTTCACG 60.738 55.000 2.18 0.00 0.00 4.35
350 609 3.998672 GGGTTCACGGCTCGTCCA 61.999 66.667 0.00 0.00 38.32 4.02
351 610 2.264794 GGTTCACGGCTCGTCCAT 59.735 61.111 0.00 0.00 38.32 3.41
352 611 2.100631 GGTTCACGGCTCGTCCATG 61.101 63.158 0.00 0.00 38.32 3.66
353 612 2.434185 TTCACGGCTCGTCCATGC 60.434 61.111 0.00 0.00 38.32 4.06
354 613 4.794439 TCACGGCTCGTCCATGCG 62.794 66.667 0.00 0.00 38.32 4.73
463 735 2.710724 AAGCAACCGTCGACCACTCC 62.711 60.000 10.58 0.00 0.00 3.85
468 740 1.663702 CCGTCGACCACTCCACAAC 60.664 63.158 10.58 0.00 0.00 3.32
469 741 1.362717 CGTCGACCACTCCACAACT 59.637 57.895 10.58 0.00 0.00 3.16
567 892 3.256936 CGTCAGTACGTGGGTCGA 58.743 61.111 0.00 0.00 44.21 4.20
630 964 2.356793 CCATCGCCATCGCTCTCC 60.357 66.667 0.00 0.00 35.26 3.71
636 970 3.133014 CCATCGCTCTCCCGTGAT 58.867 61.111 0.00 0.00 34.65 3.06
656 990 2.171003 TCTCGATCAGCTTCTGGAACA 58.829 47.619 0.00 0.00 31.51 3.18
657 991 5.028291 GATCTCGATCAGCTTCTGGAACAG 61.028 50.000 2.15 0.00 46.80 3.16
691 1034 5.530519 GCAAACTTTTTATTGCCTAAGCC 57.469 39.130 0.00 0.00 44.72 4.35
692 1035 5.237815 GCAAACTTTTTATTGCCTAAGCCT 58.762 37.500 0.00 0.00 44.72 4.58
693 1036 6.394809 GCAAACTTTTTATTGCCTAAGCCTA 58.605 36.000 0.00 0.00 44.72 3.93
694 1037 6.871492 GCAAACTTTTTATTGCCTAAGCCTAA 59.129 34.615 0.00 0.00 44.72 2.69
734 1077 2.787249 CCCATGCTTGAACGAGCG 59.213 61.111 9.13 0.00 45.64 5.03
864 1212 3.550656 GTCCGGCTTTGACGTGAG 58.449 61.111 0.00 0.00 28.54 3.51
878 1228 1.000283 ACGTGAGCAACTCCTTCTCTG 60.000 52.381 0.00 0.00 0.00 3.35
880 1230 0.037882 TGAGCAACTCCTTCTCTGCG 60.038 55.000 0.00 0.00 39.80 5.18
954 1304 0.179215 CGCGTGACTGGAATTTCAGC 60.179 55.000 14.03 7.37 38.26 4.26
959 1309 0.729690 GACTGGAATTTCAGCTCGCC 59.270 55.000 14.03 0.00 38.26 5.54
961 1311 1.709147 CTGGAATTTCAGCTCGCCGG 61.709 60.000 0.00 0.00 0.00 6.13
982 1350 3.572682 GGTGGGAAGAAAAGGGTTACAAG 59.427 47.826 0.00 0.00 0.00 3.16
1008 1376 0.521735 TCTCGACCGTGATGACACTG 59.478 55.000 0.00 0.00 43.99 3.66
1572 1976 2.027837 TCAGCTGCTTGATCTGCTTGTA 60.028 45.455 9.47 0.00 38.87 2.41
1591 1995 8.245701 GCTTGTATAGCCTCATAAGTCATAAC 57.754 38.462 0.00 0.00 44.48 1.89
1593 1997 9.416794 CTTGTATAGCCTCATAAGTCATAACAG 57.583 37.037 0.00 0.00 0.00 3.16
1594 1998 8.706322 TGTATAGCCTCATAAGTCATAACAGA 57.294 34.615 0.00 0.00 0.00 3.41
1595 1999 9.314133 TGTATAGCCTCATAAGTCATAACAGAT 57.686 33.333 0.00 0.00 0.00 2.90
1600 2004 9.553064 AGCCTCATAAGTCATAACAGATTAAAG 57.447 33.333 0.00 0.00 0.00 1.85
1601 2005 9.547753 GCCTCATAAGTCATAACAGATTAAAGA 57.452 33.333 0.00 0.00 0.00 2.52
1652 2062 4.934001 ACATGATGATAGATGATTCCGTGC 59.066 41.667 0.00 0.00 0.00 5.34
1654 2064 4.563061 TGATGATAGATGATTCCGTGCTG 58.437 43.478 0.00 0.00 0.00 4.41
1749 2165 8.844244 AGCTACATGATGATTGAGTAATTTTCC 58.156 33.333 0.00 0.00 0.00 3.13
1750 2166 8.623903 GCTACATGATGATTGAGTAATTTTCCA 58.376 33.333 0.00 0.00 0.00 3.53
1754 2170 8.689061 CATGATGATTGAGTAATTTTCCAGGAA 58.311 33.333 0.00 0.00 0.00 3.36
1756 2172 9.087871 TGATGATTGAGTAATTTTCCAGGAAAA 57.912 29.630 26.43 26.43 44.04 2.29
1774 2190 8.367156 CCAGGAAAAGATGGTTGAGAAATTTTA 58.633 33.333 0.00 0.00 0.00 1.52
1799 2215 5.063180 ACGTAATCCTTGACATGTCGTTA 57.937 39.130 20.54 11.12 0.00 3.18
1800 2216 5.100259 ACGTAATCCTTGACATGTCGTTAG 58.900 41.667 20.54 16.15 0.00 2.34
1801 2217 4.026804 CGTAATCCTTGACATGTCGTTAGC 60.027 45.833 20.54 5.57 0.00 3.09
1802 2218 3.895232 ATCCTTGACATGTCGTTAGCT 57.105 42.857 20.54 0.00 0.00 3.32
1803 2219 2.959516 TCCTTGACATGTCGTTAGCTG 58.040 47.619 20.54 6.81 0.00 4.24
1804 2220 1.394917 CCTTGACATGTCGTTAGCTGC 59.605 52.381 20.54 0.00 0.00 5.25
1868 2290 9.416284 TGTTGTTTTTATTCTCTTTTACTCCCT 57.584 29.630 0.00 0.00 0.00 4.20
1869 2291 9.894783 GTTGTTTTTATTCTCTTTTACTCCCTC 57.105 33.333 0.00 0.00 0.00 4.30
1870 2292 8.631480 TGTTTTTATTCTCTTTTACTCCCTCC 57.369 34.615 0.00 0.00 0.00 4.30
1871 2293 8.221944 TGTTTTTATTCTCTTTTACTCCCTCCA 58.778 33.333 0.00 0.00 0.00 3.86
1872 2294 9.244292 GTTTTTATTCTCTTTTACTCCCTCCAT 57.756 33.333 0.00 0.00 0.00 3.41
1873 2295 9.822727 TTTTTATTCTCTTTTACTCCCTCCATT 57.177 29.630 0.00 0.00 0.00 3.16
1874 2296 9.822727 TTTTATTCTCTTTTACTCCCTCCATTT 57.177 29.630 0.00 0.00 0.00 2.32
1875 2297 9.462606 TTTATTCTCTTTTACTCCCTCCATTTC 57.537 33.333 0.00 0.00 0.00 2.17
1876 2298 6.704056 TTCTCTTTTACTCCCTCCATTTCT 57.296 37.500 0.00 0.00 0.00 2.52
1877 2299 7.808279 TTCTCTTTTACTCCCTCCATTTCTA 57.192 36.000 0.00 0.00 0.00 2.10
1878 2300 7.808279 TCTCTTTTACTCCCTCCATTTCTAA 57.192 36.000 0.00 0.00 0.00 2.10
1879 2301 8.214721 TCTCTTTTACTCCCTCCATTTCTAAA 57.785 34.615 0.00 0.00 0.00 1.85
1880 2302 8.836735 TCTCTTTTACTCCCTCCATTTCTAAAT 58.163 33.333 0.00 0.00 0.00 1.40
1888 2310 9.453830 ACTCCCTCCATTTCTAAATATAAGTCT 57.546 33.333 0.00 0.00 0.00 3.24
1932 2354 9.955102 AGACTACAATATATGGACGTATGTAGA 57.045 33.333 18.70 0.00 33.24 2.59
1978 2400 9.767684 TCATTTATTTTGCTTTGTATGTAGTCG 57.232 29.630 0.00 0.00 0.00 4.18
1979 2401 8.523464 CATTTATTTTGCTTTGTATGTAGTCGC 58.477 33.333 0.00 0.00 0.00 5.19
1980 2402 5.880054 ATTTTGCTTTGTATGTAGTCGCT 57.120 34.783 0.00 0.00 0.00 4.93
1981 2403 5.682943 TTTTGCTTTGTATGTAGTCGCTT 57.317 34.783 0.00 0.00 0.00 4.68
1982 2404 4.661993 TTGCTTTGTATGTAGTCGCTTG 57.338 40.909 0.00 0.00 0.00 4.01
1983 2405 3.659786 TGCTTTGTATGTAGTCGCTTGT 58.340 40.909 0.00 0.00 0.00 3.16
1984 2406 4.062293 TGCTTTGTATGTAGTCGCTTGTT 58.938 39.130 0.00 0.00 0.00 2.83
1985 2407 4.084066 TGCTTTGTATGTAGTCGCTTGTTG 60.084 41.667 0.00 0.00 0.00 3.33
1986 2408 4.394795 CTTTGTATGTAGTCGCTTGTTGC 58.605 43.478 0.00 0.00 38.57 4.17
1987 2409 3.033368 TGTATGTAGTCGCTTGTTGCA 57.967 42.857 0.00 0.00 43.06 4.08
1988 2410 3.394719 TGTATGTAGTCGCTTGTTGCAA 58.605 40.909 0.00 0.00 43.06 4.08
1989 2411 4.000325 TGTATGTAGTCGCTTGTTGCAAT 59.000 39.130 0.59 0.00 43.06 3.56
1990 2412 3.747099 ATGTAGTCGCTTGTTGCAATC 57.253 42.857 0.59 0.00 43.06 2.67
1991 2413 2.766313 TGTAGTCGCTTGTTGCAATCT 58.234 42.857 0.59 0.00 43.06 2.40
1992 2414 2.736721 TGTAGTCGCTTGTTGCAATCTC 59.263 45.455 0.59 0.00 43.06 2.75
1993 2415 2.175878 AGTCGCTTGTTGCAATCTCT 57.824 45.000 0.59 0.00 43.06 3.10
1994 2416 3.319137 AGTCGCTTGTTGCAATCTCTA 57.681 42.857 0.59 0.00 43.06 2.43
1995 2417 3.257393 AGTCGCTTGTTGCAATCTCTAG 58.743 45.455 0.59 0.00 43.06 2.43
1996 2418 3.056536 AGTCGCTTGTTGCAATCTCTAGA 60.057 43.478 0.59 0.00 43.06 2.43
1997 2419 3.679980 GTCGCTTGTTGCAATCTCTAGAA 59.320 43.478 0.59 0.00 43.06 2.10
1998 2420 4.152402 GTCGCTTGTTGCAATCTCTAGAAA 59.848 41.667 0.59 0.00 43.06 2.52
1999 2421 4.389992 TCGCTTGTTGCAATCTCTAGAAAG 59.610 41.667 0.59 0.00 43.06 2.62
2000 2422 4.389992 CGCTTGTTGCAATCTCTAGAAAGA 59.610 41.667 0.59 0.00 43.06 2.52
2001 2423 5.626211 GCTTGTTGCAATCTCTAGAAAGAC 58.374 41.667 0.59 0.00 42.31 3.01
2002 2424 5.411053 GCTTGTTGCAATCTCTAGAAAGACT 59.589 40.000 0.59 0.00 42.31 3.24
2003 2425 6.072783 GCTTGTTGCAATCTCTAGAAAGACTT 60.073 38.462 0.59 0.00 42.31 3.01
2004 2426 7.118390 GCTTGTTGCAATCTCTAGAAAGACTTA 59.882 37.037 0.59 0.00 42.31 2.24
2005 2427 9.160496 CTTGTTGCAATCTCTAGAAAGACTTAT 57.840 33.333 0.59 0.00 0.00 1.73
2016 2438 9.250624 CTCTAGAAAGACTTATATTTGGGAACG 57.749 37.037 0.00 0.00 0.00 3.95
2017 2439 8.974238 TCTAGAAAGACTTATATTTGGGAACGA 58.026 33.333 0.00 0.00 0.00 3.85
2018 2440 9.595823 CTAGAAAGACTTATATTTGGGAACGAA 57.404 33.333 0.00 0.00 38.33 3.85
2019 2441 8.857694 AGAAAGACTTATATTTGGGAACGAAA 57.142 30.769 0.00 0.00 37.25 3.46
2020 2442 8.947115 AGAAAGACTTATATTTGGGAACGAAAG 58.053 33.333 0.00 0.00 37.25 2.62
2021 2443 7.625828 AAGACTTATATTTGGGAACGAAAGG 57.374 36.000 0.00 0.00 37.25 3.11
2022 2444 6.954232 AGACTTATATTTGGGAACGAAAGGA 58.046 36.000 0.00 0.00 37.25 3.36
2023 2445 7.048512 AGACTTATATTTGGGAACGAAAGGAG 58.951 38.462 0.00 0.00 37.25 3.69
2024 2446 6.718294 ACTTATATTTGGGAACGAAAGGAGT 58.282 36.000 0.00 0.00 37.25 3.85
2025 2447 7.854337 ACTTATATTTGGGAACGAAAGGAGTA 58.146 34.615 0.00 0.00 37.25 2.59
2090 2518 4.772434 CACAAACGGTGTCTAACTGAATG 58.228 43.478 0.00 0.00 42.75 2.67
2093 2521 2.960819 ACGGTGTCTAACTGAATGAGC 58.039 47.619 0.00 0.00 38.65 4.26
2096 2524 3.003480 GGTGTCTAACTGAATGAGCACC 58.997 50.000 0.00 0.00 38.37 5.01
2097 2525 2.668457 GTGTCTAACTGAATGAGCACCG 59.332 50.000 0.00 0.00 0.00 4.94
2122 2555 8.050750 CGACTACGTGATGATTGAGTAAAATTC 58.949 37.037 0.00 0.00 34.56 2.17
2153 2586 6.346359 CGATCATGACATACTATTGCACAGTG 60.346 42.308 9.86 0.00 0.00 3.66
2166 2599 8.774586 ACTATTGCACAGTGTTCTTTAAACTAG 58.225 33.333 1.61 0.00 0.00 2.57
2169 4807 7.189693 TGCACAGTGTTCTTTAAACTAGATG 57.810 36.000 1.61 0.00 0.00 2.90
2286 4924 2.857483 TCCATCGGAAAAACAAGCTCA 58.143 42.857 0.00 0.00 0.00 4.26
2318 4956 1.219393 CTCCTCCCTCAAACTCGGC 59.781 63.158 0.00 0.00 0.00 5.54
2319 4957 2.245438 CTCCTCCCTCAAACTCGGCC 62.245 65.000 0.00 0.00 0.00 6.13
2337 4975 1.007271 CGTGCCTCTCGTGTGAGTT 60.007 57.895 0.00 0.00 43.09 3.01
2342 4980 1.269831 GCCTCTCGTGTGAGTTTGTCT 60.270 52.381 0.00 0.00 43.09 3.41
2343 4981 2.803492 GCCTCTCGTGTGAGTTTGTCTT 60.803 50.000 0.00 0.00 43.09 3.01
2393 5035 4.746466 TGTAATGAAAAATCAGGTGGGGT 58.254 39.130 0.00 0.00 0.00 4.95
2413 5055 4.448210 GGTGATCGCCCTCTTGTATTTAA 58.552 43.478 14.81 0.00 0.00 1.52
2421 5063 6.148811 TCGCCCTCTTGTATTTAACTCAAAAG 59.851 38.462 0.00 0.00 0.00 2.27
2439 5081 3.538634 AAGGGATTACGGCTTGTACTC 57.461 47.619 0.00 0.00 33.25 2.59
2440 5082 2.748388 AGGGATTACGGCTTGTACTCT 58.252 47.619 0.00 0.00 34.19 3.24
2443 5085 3.243468 GGGATTACGGCTTGTACTCTCTC 60.243 52.174 0.00 0.00 32.06 3.20
2448 5090 1.067776 CGGCTTGTACTCTCTCCGTTT 60.068 52.381 0.00 0.00 32.93 3.60
2459 5101 5.221130 ACTCTCTCCGTTTCTTTTTAGTCG 58.779 41.667 0.00 0.00 0.00 4.18
2475 5117 9.274065 CTTTTTAGTCGGCATATAAGTTTTGTC 57.726 33.333 0.00 0.00 0.00 3.18
2476 5118 6.913873 TTAGTCGGCATATAAGTTTTGTCC 57.086 37.500 0.00 0.00 0.00 4.02
2481 5123 4.331717 CGGCATATAAGTTTTGTCCGAAGT 59.668 41.667 0.00 0.00 38.02 3.01
2487 5129 9.146984 CATATAAGTTTTGTCCGAAGTCAAGTA 57.853 33.333 0.00 0.00 0.00 2.24
2489 5131 6.541111 AAGTTTTGTCCGAAGTCAAGTATC 57.459 37.500 0.00 0.00 0.00 2.24
2494 5136 7.406031 TTTGTCCGAAGTCAAGTATCTCTAT 57.594 36.000 0.00 0.00 0.00 1.98
2497 5139 8.515695 TGTCCGAAGTCAAGTATCTCTATTTA 57.484 34.615 0.00 0.00 0.00 1.40
2498 5140 8.963725 TGTCCGAAGTCAAGTATCTCTATTTAA 58.036 33.333 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.758251 TCAGGTGTGATGCGCGGG 62.758 66.667 8.83 0.00 0.00 6.13
11 12 3.490759 GTCAGGTGTGATGCGCGG 61.491 66.667 8.83 0.00 34.36 6.46
15 16 1.741770 GGGACGTCAGGTGTGATGC 60.742 63.158 18.91 0.00 42.72 3.91
139 140 2.440247 GGACTGGGATTTGGGCGG 60.440 66.667 0.00 0.00 0.00 6.13
170 171 1.009449 CGCACGCTAGAGGCTAGAC 60.009 63.158 5.69 0.00 39.13 2.59
171 172 2.187493 CCGCACGCTAGAGGCTAGA 61.187 63.158 5.69 0.00 39.13 2.43
172 173 2.333225 CCGCACGCTAGAGGCTAG 59.667 66.667 0.00 0.00 39.13 3.42
173 174 3.217017 CCCGCACGCTAGAGGCTA 61.217 66.667 0.00 0.00 39.13 3.93
175 176 4.143333 TTCCCGCACGCTAGAGGC 62.143 66.667 0.00 0.00 37.64 4.70
176 177 2.202756 GTTCCCGCACGCTAGAGG 60.203 66.667 0.00 0.00 0.00 3.69
177 178 2.579787 CGTTCCCGCACGCTAGAG 60.580 66.667 0.00 0.00 32.43 2.43
193 194 4.741781 CGAAAAGCGCAGTGGCCG 62.742 66.667 11.47 0.90 36.38 6.13
218 219 2.585869 CGCGTGGACGTGCATATCC 61.586 63.158 14.45 11.38 43.06 2.59
288 534 1.608336 TCGATCCACCTGTTCCGGT 60.608 57.895 0.00 0.00 37.93 5.28
289 535 1.153628 GTCGATCCACCTGTTCCGG 60.154 63.158 0.00 0.00 0.00 5.14
290 536 1.516386 CGTCGATCCACCTGTTCCG 60.516 63.158 0.00 0.00 0.00 4.30
291 537 0.179134 CTCGTCGATCCACCTGTTCC 60.179 60.000 0.00 0.00 0.00 3.62
292 538 0.809385 TCTCGTCGATCCACCTGTTC 59.191 55.000 0.00 0.00 0.00 3.18
297 556 1.067776 ACTTGTTCTCGTCGATCCACC 60.068 52.381 0.00 0.00 0.00 4.61
324 583 1.881252 CCGTGAACCCGGCGATTAG 60.881 63.158 9.30 0.00 41.78 1.73
325 584 2.184836 CCGTGAACCCGGCGATTA 59.815 61.111 9.30 0.00 41.78 1.75
333 592 3.310860 ATGGACGAGCCGTGAACCC 62.311 63.158 4.94 1.40 41.37 4.11
334 593 2.264794 ATGGACGAGCCGTGAACC 59.735 61.111 4.94 1.73 41.37 3.62
357 616 3.282745 CTCCCCGTGACTCCGTGTG 62.283 68.421 0.00 0.00 0.00 3.82
358 617 2.989824 CTCCCCGTGACTCCGTGT 60.990 66.667 0.00 0.00 0.00 4.49
359 618 4.436998 GCTCCCCGTGACTCCGTG 62.437 72.222 0.00 0.00 0.00 4.94
372 631 0.179189 CCACATTTTTCGAGCGCTCC 60.179 55.000 30.66 13.79 0.00 4.70
449 721 2.129146 TTGTGGAGTGGTCGACGGT 61.129 57.895 9.92 0.00 34.25 4.83
463 735 3.627732 ACGTGACTGTAGAGAGTTGTG 57.372 47.619 0.00 0.00 0.00 3.33
468 740 1.062294 GGCGTACGTGACTGTAGAGAG 59.938 57.143 17.90 0.00 0.00 3.20
469 741 1.081892 GGCGTACGTGACTGTAGAGA 58.918 55.000 17.90 0.00 0.00 3.10
574 899 2.013483 CTCGCATCGCCATCTCGTC 61.013 63.158 0.00 0.00 0.00 4.20
578 903 2.419198 GACCTCGCATCGCCATCT 59.581 61.111 0.00 0.00 0.00 2.90
630 964 1.336440 AGAAGCTGATCGAGATCACGG 59.664 52.381 12.66 5.08 42.42 4.94
636 970 2.165234 CTGTTCCAGAAGCTGATCGAGA 59.835 50.000 0.00 0.00 32.44 4.04
656 990 0.746659 AGTTTGCTTGCTTTTCCGCT 59.253 45.000 0.00 0.00 0.00 5.52
657 991 1.570813 AAGTTTGCTTGCTTTTCCGC 58.429 45.000 0.00 0.00 32.92 5.54
661 1004 6.095300 AGGCAATAAAAAGTTTGCTTGCTTTT 59.905 30.769 20.39 6.80 45.81 2.27
689 1032 2.828549 CGGGGCACATGGTTAGGC 60.829 66.667 0.00 0.00 0.00 3.93
690 1033 1.451387 GTCGGGGCACATGGTTAGG 60.451 63.158 0.00 0.00 0.00 2.69
691 1034 1.813753 CGTCGGGGCACATGGTTAG 60.814 63.158 0.00 0.00 0.00 2.34
692 1035 2.266372 CGTCGGGGCACATGGTTA 59.734 61.111 0.00 0.00 0.00 2.85
864 1212 4.996976 TCGCAGAGAAGGAGTTGC 57.003 55.556 0.00 0.00 0.00 4.17
880 1230 2.109126 GTTGCGGGTGGCTGATCTC 61.109 63.158 0.00 0.00 44.05 2.75
954 1304 1.298859 CTTTTCTTCCCACCGGCGAG 61.299 60.000 9.30 0.06 0.00 5.03
959 1309 2.156917 GTAACCCTTTTCTTCCCACCG 58.843 52.381 0.00 0.00 0.00 4.94
961 1311 3.572682 CCTTGTAACCCTTTTCTTCCCAC 59.427 47.826 0.00 0.00 0.00 4.61
1193 1585 3.408851 GGAACGACGTGAACCGCC 61.409 66.667 0.00 0.00 41.42 6.13
1536 1937 4.519437 TGATGCTCGGAGCTGCGG 62.519 66.667 27.80 18.49 42.97 5.69
1596 2000 9.542462 GCACATCCTATACAAGTATGTTCTTTA 57.458 33.333 3.06 0.00 41.05 1.85
1597 2001 8.046708 TGCACATCCTATACAAGTATGTTCTTT 58.953 33.333 3.06 0.00 41.05 2.52
1599 2003 7.124573 TGCACATCCTATACAAGTATGTTCT 57.875 36.000 3.06 0.00 41.05 3.01
1600 2004 7.969536 ATGCACATCCTATACAAGTATGTTC 57.030 36.000 3.06 0.00 41.05 3.18
1601 2005 8.428852 TGTATGCACATCCTATACAAGTATGTT 58.571 33.333 3.06 0.00 41.05 2.71
1606 2010 7.962441 TGTATGTATGCACATCCTATACAAGT 58.038 34.615 0.00 0.00 44.42 3.16
1607 2011 8.876790 CATGTATGTATGCACATCCTATACAAG 58.123 37.037 13.66 8.97 44.42 3.16
1608 2012 8.592809 TCATGTATGTATGCACATCCTATACAA 58.407 33.333 13.66 2.83 44.42 2.41
1610 2014 9.038803 CATCATGTATGTATGCACATCCTATAC 57.961 37.037 0.00 0.00 44.42 1.47
1611 2015 8.980596 TCATCATGTATGTATGCACATCCTATA 58.019 33.333 0.00 0.00 44.42 1.31
1626 2036 7.254353 GCACGGAATCATCTATCATCATGTATG 60.254 40.741 0.00 0.00 36.88 2.39
1628 2038 6.071165 AGCACGGAATCATCTATCATCATGTA 60.071 38.462 0.00 0.00 0.00 2.29
1630 2040 5.063564 CAGCACGGAATCATCTATCATCATG 59.936 44.000 0.00 0.00 0.00 3.07
1631 2041 5.176592 CAGCACGGAATCATCTATCATCAT 58.823 41.667 0.00 0.00 0.00 2.45
1632 2042 4.039609 ACAGCACGGAATCATCTATCATCA 59.960 41.667 0.00 0.00 0.00 3.07
1633 2043 4.564041 ACAGCACGGAATCATCTATCATC 58.436 43.478 0.00 0.00 0.00 2.92
1636 2046 4.871513 TGTACAGCACGGAATCATCTATC 58.128 43.478 0.00 0.00 0.00 2.08
1637 2047 4.937201 TGTACAGCACGGAATCATCTAT 57.063 40.909 0.00 0.00 0.00 1.98
1638 2048 4.501400 CCATGTACAGCACGGAATCATCTA 60.501 45.833 0.33 0.00 30.69 1.98
1639 2049 3.461061 CATGTACAGCACGGAATCATCT 58.539 45.455 0.33 0.00 0.00 2.90
1652 2062 6.949352 ATAAATCAAGCCTTCCATGTACAG 57.051 37.500 0.33 0.00 0.00 2.74
1654 2064 7.547227 ACAAATAAATCAAGCCTTCCATGTAC 58.453 34.615 0.00 0.00 0.00 2.90
1749 2165 9.415544 CTAAAATTTCTCAACCATCTTTTCCTG 57.584 33.333 0.00 0.00 0.00 3.86
1750 2166 9.367160 TCTAAAATTTCTCAACCATCTTTTCCT 57.633 29.630 0.00 0.00 0.00 3.36
1751 2167 9.981114 TTCTAAAATTTCTCAACCATCTTTTCC 57.019 29.630 0.00 0.00 0.00 3.13
1754 2170 8.630037 ACGTTCTAAAATTTCTCAACCATCTTT 58.370 29.630 0.00 0.00 0.00 2.52
1756 2172 7.745620 ACGTTCTAAAATTTCTCAACCATCT 57.254 32.000 0.00 0.00 0.00 2.90
1774 2190 4.174009 CGACATGTCAAGGATTACGTTCT 58.826 43.478 24.93 0.00 0.00 3.01
1799 2215 0.464870 CTGATCTACAGGCTGCAGCT 59.535 55.000 35.82 20.59 42.39 4.24
1800 2216 1.159098 GCTGATCTACAGGCTGCAGC 61.159 60.000 30.88 30.88 45.82 5.25
1801 2217 0.177373 TGCTGATCTACAGGCTGCAG 59.823 55.000 15.89 11.99 45.82 4.41
1802 2218 0.177373 CTGCTGATCTACAGGCTGCA 59.823 55.000 15.89 0.00 45.82 4.41
1803 2219 0.532417 CCTGCTGATCTACAGGCTGC 60.532 60.000 15.89 0.00 46.50 5.25
1804 2220 3.682766 CCTGCTGATCTACAGGCTG 57.317 57.895 14.16 14.16 46.50 4.85
1906 2328 9.955102 TCTACATACGTCCATATATTGTAGTCT 57.045 33.333 14.02 0.00 0.00 3.24
1952 2374 9.767684 CGACTACATACAAAGCAAAATAAATGA 57.232 29.630 0.00 0.00 0.00 2.57
1953 2375 8.523464 GCGACTACATACAAAGCAAAATAAATG 58.477 33.333 0.00 0.00 0.00 2.32
1954 2376 8.458843 AGCGACTACATACAAAGCAAAATAAAT 58.541 29.630 0.00 0.00 0.00 1.40
1955 2377 7.812648 AGCGACTACATACAAAGCAAAATAAA 58.187 30.769 0.00 0.00 0.00 1.40
1956 2378 7.372451 AGCGACTACATACAAAGCAAAATAA 57.628 32.000 0.00 0.00 0.00 1.40
1957 2379 6.978343 AGCGACTACATACAAAGCAAAATA 57.022 33.333 0.00 0.00 0.00 1.40
1958 2380 5.880054 AGCGACTACATACAAAGCAAAAT 57.120 34.783 0.00 0.00 0.00 1.82
1959 2381 5.008217 ACAAGCGACTACATACAAAGCAAAA 59.992 36.000 0.00 0.00 0.00 2.44
1960 2382 4.513692 ACAAGCGACTACATACAAAGCAAA 59.486 37.500 0.00 0.00 0.00 3.68
1961 2383 4.062293 ACAAGCGACTACATACAAAGCAA 58.938 39.130 0.00 0.00 0.00 3.91
1962 2384 3.659786 ACAAGCGACTACATACAAAGCA 58.340 40.909 0.00 0.00 0.00 3.91
1963 2385 4.394795 CAACAAGCGACTACATACAAAGC 58.605 43.478 0.00 0.00 0.00 3.51
1964 2386 4.394795 GCAACAAGCGACTACATACAAAG 58.605 43.478 0.00 0.00 0.00 2.77
1965 2387 4.398549 GCAACAAGCGACTACATACAAA 57.601 40.909 0.00 0.00 0.00 2.83
1978 2400 5.411053 AGTCTTTCTAGAGATTGCAACAAGC 59.589 40.000 0.00 0.00 45.96 4.01
1979 2401 7.432350 AAGTCTTTCTAGAGATTGCAACAAG 57.568 36.000 0.00 0.00 0.00 3.16
1990 2412 9.250624 CGTTCCCAAATATAAGTCTTTCTAGAG 57.749 37.037 0.00 0.00 0.00 2.43
1991 2413 8.974238 TCGTTCCCAAATATAAGTCTTTCTAGA 58.026 33.333 0.00 0.00 0.00 2.43
1992 2414 9.595823 TTCGTTCCCAAATATAAGTCTTTCTAG 57.404 33.333 0.00 0.00 0.00 2.43
1993 2415 9.947433 TTTCGTTCCCAAATATAAGTCTTTCTA 57.053 29.630 0.00 0.00 0.00 2.10
1994 2416 8.857694 TTTCGTTCCCAAATATAAGTCTTTCT 57.142 30.769 0.00 0.00 0.00 2.52
1995 2417 8.182227 CCTTTCGTTCCCAAATATAAGTCTTTC 58.818 37.037 0.00 0.00 0.00 2.62
1996 2418 7.886446 TCCTTTCGTTCCCAAATATAAGTCTTT 59.114 33.333 0.00 0.00 0.00 2.52
1997 2419 7.399634 TCCTTTCGTTCCCAAATATAAGTCTT 58.600 34.615 0.00 0.00 0.00 3.01
1998 2420 6.954232 TCCTTTCGTTCCCAAATATAAGTCT 58.046 36.000 0.00 0.00 0.00 3.24
1999 2421 6.822170 ACTCCTTTCGTTCCCAAATATAAGTC 59.178 38.462 0.00 0.00 0.00 3.01
2000 2422 6.718294 ACTCCTTTCGTTCCCAAATATAAGT 58.282 36.000 0.00 0.00 0.00 2.24
2001 2423 8.202137 TCTACTCCTTTCGTTCCCAAATATAAG 58.798 37.037 0.00 0.00 0.00 1.73
2002 2424 8.081517 TCTACTCCTTTCGTTCCCAAATATAA 57.918 34.615 0.00 0.00 0.00 0.98
2003 2425 7.664552 TCTACTCCTTTCGTTCCCAAATATA 57.335 36.000 0.00 0.00 0.00 0.86
2004 2426 6.555463 TCTACTCCTTTCGTTCCCAAATAT 57.445 37.500 0.00 0.00 0.00 1.28
2005 2427 6.555463 ATCTACTCCTTTCGTTCCCAAATA 57.445 37.500 0.00 0.00 0.00 1.40
2006 2428 4.903045 TCTACTCCTTTCGTTCCCAAAT 57.097 40.909 0.00 0.00 0.00 2.32
2007 2429 4.903045 ATCTACTCCTTTCGTTCCCAAA 57.097 40.909 0.00 0.00 0.00 3.28
2008 2430 4.323257 GGAATCTACTCCTTTCGTTCCCAA 60.323 45.833 0.00 0.00 32.21 4.12
2009 2431 3.197116 GGAATCTACTCCTTTCGTTCCCA 59.803 47.826 0.00 0.00 32.21 4.37
2010 2432 3.197116 TGGAATCTACTCCTTTCGTTCCC 59.803 47.826 0.00 0.00 36.35 3.97
2011 2433 4.467198 TGGAATCTACTCCTTTCGTTCC 57.533 45.455 0.00 0.00 36.35 3.62
2012 2434 5.420409 ACATGGAATCTACTCCTTTCGTTC 58.580 41.667 0.00 0.00 36.35 3.95
2013 2435 5.422214 ACATGGAATCTACTCCTTTCGTT 57.578 39.130 0.00 0.00 36.35 3.85
2014 2436 5.187967 AGAACATGGAATCTACTCCTTTCGT 59.812 40.000 0.00 0.00 36.35 3.85
2015 2437 5.665459 AGAACATGGAATCTACTCCTTTCG 58.335 41.667 0.00 0.00 36.35 3.46
2016 2438 7.929941 AAAGAACATGGAATCTACTCCTTTC 57.070 36.000 0.00 0.00 36.35 2.62
2017 2439 9.981460 AATAAAGAACATGGAATCTACTCCTTT 57.019 29.630 0.00 0.00 36.35 3.11
2025 2447 8.897752 GCAAGACTAATAAAGAACATGGAATCT 58.102 33.333 0.00 0.00 0.00 2.40
2050 2472 6.464834 CGTTTGTGTCTTCGGAAATAAATAGC 59.535 38.462 0.00 0.00 27.85 2.97
2090 2518 0.450583 TCATCACGTAGTCGGTGCTC 59.549 55.000 0.00 0.00 41.61 4.26
2093 2521 3.108881 CTCAATCATCACGTAGTCGGTG 58.891 50.000 0.00 0.00 41.61 4.94
2096 2524 6.864560 TTTTACTCAATCATCACGTAGTCG 57.135 37.500 0.00 0.00 41.61 4.18
2097 2525 8.050750 CGAATTTTACTCAATCATCACGTAGTC 58.949 37.037 0.00 0.00 41.61 2.59
2122 2555 6.183359 GCAATAGTATGTCATGATCGTTCTCG 60.183 42.308 0.00 0.00 38.55 4.04
2166 2599 7.502177 GCATATATGTGCAAATACAAGCATC 57.498 36.000 18.51 0.00 44.43 3.91
2286 4924 1.757699 GGAGGAGAAGGTCAATACGCT 59.242 52.381 0.00 0.00 0.00 5.07
2318 4956 2.126307 CTCACACGAGAGGCACGG 60.126 66.667 0.00 0.00 42.34 4.94
2319 4957 0.597637 AAACTCACACGAGAGGCACG 60.598 55.000 0.00 0.00 42.34 5.34
2337 4975 4.642437 TGCACATCAACAAAGGTAAGACAA 59.358 37.500 0.00 0.00 0.00 3.18
2342 4980 5.068329 TGAACATGCACATCAACAAAGGTAA 59.932 36.000 0.00 0.00 0.00 2.85
2343 4981 4.582240 TGAACATGCACATCAACAAAGGTA 59.418 37.500 0.00 0.00 0.00 3.08
2393 5035 5.105106 TGAGTTAAATACAAGAGGGCGATCA 60.105 40.000 0.00 0.00 0.00 2.92
2413 5055 3.081804 CAAGCCGTAATCCCTTTTGAGT 58.918 45.455 0.00 0.00 0.00 3.41
2421 5063 2.694109 AGAGAGTACAAGCCGTAATCCC 59.306 50.000 7.50 0.00 44.50 3.85
2428 5070 0.526662 AACGGAGAGAGTACAAGCCG 59.473 55.000 0.00 0.00 43.95 5.52
2439 5081 3.123116 GCCGACTAAAAAGAAACGGAGAG 59.877 47.826 0.00 0.00 42.40 3.20
2440 5082 3.062042 GCCGACTAAAAAGAAACGGAGA 58.938 45.455 0.00 0.00 42.40 3.71
2443 5085 3.824414 ATGCCGACTAAAAAGAAACGG 57.176 42.857 0.00 0.00 42.63 4.44
2448 5090 9.005777 ACAAAACTTATATGCCGACTAAAAAGA 57.994 29.630 0.00 0.00 0.00 2.52
2459 5101 5.353123 TGACTTCGGACAAAACTTATATGCC 59.647 40.000 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.