Multiple sequence alignment - TraesCS2A01G100700

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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 TraesCS2A01G100700 chr2A 100.000 4101 0 0 1 4101 53781698 53785798 0.000000e+00 7574
1 TraesCS2A01G100700 chr2D 90.181 4196 190 88 4 4101 52226313 52230384 0.000000e+00 5262
2 TraesCS2A01G100700 chr2B 90.403 1761 79 39 62 1782 81754691 81756401 0.000000e+00 2233
3 TraesCS2A01G100700 chr2B 93.531 912 36 15 2104 3005 81756874 81757772 0.000000e+00 1336
4 TraesCS2A01G100700 chr2B 89.483 1103 50 34 3024 4100 81757948 81759010 0.000000e+00 1334
5 TraesCS2A01G100700 chr2B 87.261 314 22 6 1789 2102 81756384 81756679 3.930000e-90 342
6 TraesCS2A01G100700 chr4B 93.805 226 13 1 1038 1262 382692079 382692304 5.080000e-89 339
7 TraesCS2A01G100700 chr4D 93.421 228 14 1 1038 1264 306795482 306795709 1.830000e-88 337
8 TraesCS2A01G100700 chr4A 92.920 226 15 1 1038 1262 170710869 170710644 1.100000e-85 327
9 TraesCS2A01G100700 chr4A 93.814 97 3 2 75 168 67571165 67571261 4.270000e-30 143
10 TraesCS2A01G100700 chr3B 91.584 202 15 2 1052 1252 56055981 56056181 1.120000e-70 278
11 TraesCS2A01G100700 chr3D 90.594 202 17 2 1052 1252 33294996 33295196 2.430000e-67 267
12 TraesCS2A01G100700 chr3A 90.050 201 20 0 1052 1252 45776244 45776444 1.130000e-65 261
13 TraesCS2A01G100700 chr1B 93.878 98 5 1 75 171 491444015 491443918 3.300000e-31 147
14 TraesCS2A01G100700 chr1B 79.141 163 30 4 1056 1216 652782346 652782506 4.330000e-20 110
15 TraesCS2A01G100700 chr1D 94.681 94 4 1 75 168 351073936 351074028 1.190000e-30 145
16 TraesCS2A01G100700 chr7A 93.000 100 4 2 75 171 563588687 563588588 4.270000e-30 143
17 TraesCS2A01G100700 chr5B 93.000 100 4 2 75 171 34071694 34071595 4.270000e-30 143
18 TraesCS2A01G100700 chrUn 93.750 96 3 2 75 167 86446086 86445991 1.540000e-29 141
19 TraesCS2A01G100700 chrUn 92.000 100 5 2 75 171 446319763 446319664 1.990000e-28 137


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 TraesCS2A01G100700 chr2A 53781698 53785798 4100 False 7574.00 7574 100.0000 1 4101 1 chr2A.!!$F1 4100
1 TraesCS2A01G100700 chr2D 52226313 52230384 4071 False 5262.00 5262 90.1810 4 4101 1 chr2D.!!$F1 4097
2 TraesCS2A01G100700 chr2B 81754691 81759010 4319 False 1311.25 2233 90.1695 62 4100 4 chr2B.!!$F1 4038

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
419 421 0.043822 CGCGCGCTAACTCAATTCTC 60.044 55.0 30.48 0.00 0.00 2.87 F
836 883 0.468648 CCGAGGAATGTTACCCCCTC 59.531 60.0 0.00 0.00 41.25 4.30 F
1707 1759 0.591488 CGCACATGCATGCAAGCTAG 60.591 55.0 26.68 14.63 46.47 3.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1733 1785 0.108138 ACCGATCAAGGAAGAAGCCG 60.108 55.0 0.0 0.0 34.73 5.52 R
2569 2901 0.230515 CGCGTGCGTCGACTATAGTA 59.769 55.0 14.7 0.0 42.86 1.82 R
3224 3746 0.111832 TCCACTCCACAGTACGTCCT 59.888 55.0 0.0 0.0 0.00 3.85 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
41 42 3.813166 TGAAGAAAACTTCACGTCATCCC 59.187 43.478 8.32 0.00 38.30 3.85
42 43 3.771577 AGAAAACTTCACGTCATCCCT 57.228 42.857 0.00 0.00 0.00 4.20
48 49 0.681887 TTCACGTCATCCCTCGCCTA 60.682 55.000 0.00 0.00 0.00 3.93
50 51 0.527817 CACGTCATCCCTCGCCTAAC 60.528 60.000 0.00 0.00 0.00 2.34
134 135 3.988517 GGAAGAAGTTGTTCCACTCGTAG 59.011 47.826 23.37 0.00 42.79 3.51
172 173 5.140747 AGCTTAACTCACATTTCGAGACT 57.859 39.130 0.00 0.00 34.47 3.24
203 205 3.297134 AAGGAATGTACCATTGCCGAT 57.703 42.857 5.05 0.00 0.00 4.18
231 233 2.812011 GCGGTTATGGAGTGAACAAAGT 59.188 45.455 0.00 0.00 0.00 2.66
238 240 8.793592 GGTTATGGAGTGAACAAAGTTTAGATT 58.206 33.333 0.00 0.00 0.00 2.40
250 252 9.482627 AACAAAGTTTAGATTTTTGTGTGTTGA 57.517 25.926 2.97 0.00 42.40 3.18
292 294 7.029563 TCTATATGAAGCACAGTACATATGCG 58.970 38.462 1.58 0.00 44.25 4.73
297 299 6.223120 TGAAGCACAGTACATATGCGATATT 58.777 36.000 1.58 0.87 44.25 1.28
301 303 5.863935 GCACAGTACATATGCGATATTGAGA 59.136 40.000 1.58 0.00 0.00 3.27
343 345 2.086054 AGAGTTGCTCTAAGTTGGCG 57.914 50.000 0.00 0.00 39.28 5.69
376 378 2.202946 GCGTAGGCAGCTCCTTCC 60.203 66.667 9.58 0.00 44.75 3.46
379 381 1.826709 GTAGGCAGCTCCTTCCTCC 59.173 63.158 9.58 0.00 44.75 4.30
393 395 3.995048 CCTTCCTCCGAGAACAAACTAAC 59.005 47.826 0.00 0.00 0.00 2.34
394 396 4.502604 CCTTCCTCCGAGAACAAACTAACA 60.503 45.833 0.00 0.00 0.00 2.41
419 421 0.043822 CGCGCGCTAACTCAATTCTC 60.044 55.000 30.48 0.00 0.00 2.87
425 427 5.670341 GCGCGCTAACTCAATTCTCTTTTTA 60.670 40.000 26.67 0.00 0.00 1.52
427 429 6.246540 CGCGCTAACTCAATTCTCTTTTTAAC 59.753 38.462 5.56 0.00 0.00 2.01
428 430 6.523546 GCGCTAACTCAATTCTCTTTTTAACC 59.476 38.462 0.00 0.00 0.00 2.85
433 435 5.472478 ACTCAATTCTCTTTTTAACCCGGAC 59.528 40.000 0.73 0.00 0.00 4.79
441 443 4.043184 TCTTTTTAACCCGGACATAACCCT 59.957 41.667 0.73 0.00 0.00 4.34
501 510 6.448369 TCCATAACCAGAGAAGAAAAAGGA 57.552 37.500 0.00 0.00 0.00 3.36
503 512 7.294584 TCCATAACCAGAGAAGAAAAAGGAAA 58.705 34.615 0.00 0.00 0.00 3.13
548 566 2.325583 ACTCAGTTCAACGCTCCAAA 57.674 45.000 0.00 0.00 0.00 3.28
555 573 3.253432 AGTTCAACGCTCCAAATTTCTCC 59.747 43.478 0.00 0.00 0.00 3.71
579 597 2.581208 ATATCCGACGGCCGCAAACA 62.581 55.000 28.58 6.74 36.84 2.83
592 610 0.526739 GCAAACAAACGGTGACACCC 60.527 55.000 19.11 1.61 33.75 4.61
674 710 1.153168 CACCGTCATGTCATCCCCC 60.153 63.158 0.00 0.00 0.00 5.40
714 750 3.744719 CGGGACACGGCGAGAGAA 61.745 66.667 16.62 0.00 39.42 2.87
715 751 2.126031 GGGACACGGCGAGAGAAC 60.126 66.667 16.62 0.51 0.00 3.01
716 752 2.504244 GGACACGGCGAGAGAACG 60.504 66.667 16.62 0.00 38.63 3.95
717 753 2.504244 GACACGGCGAGAGAACGG 60.504 66.667 16.62 0.00 37.33 4.44
718 754 3.264866 GACACGGCGAGAGAACGGT 62.265 63.158 16.62 0.00 37.33 4.83
719 755 2.805353 CACGGCGAGAGAACGGTG 60.805 66.667 16.62 0.00 37.33 4.94
720 756 4.719369 ACGGCGAGAGAACGGTGC 62.719 66.667 16.62 0.00 37.33 5.01
834 881 1.276859 ACCCGAGGAATGTTACCCCC 61.277 60.000 0.00 0.00 0.00 5.40
835 882 0.986550 CCCGAGGAATGTTACCCCCT 60.987 60.000 0.00 0.00 0.00 4.79
836 883 0.468648 CCGAGGAATGTTACCCCCTC 59.531 60.000 0.00 0.00 41.25 4.30
837 884 1.497161 CGAGGAATGTTACCCCCTCT 58.503 55.000 0.00 0.00 42.20 3.69
838 885 1.413077 CGAGGAATGTTACCCCCTCTC 59.587 57.143 0.00 0.00 42.20 3.20
839 886 2.478292 GAGGAATGTTACCCCCTCTCA 58.522 52.381 0.00 0.00 41.40 3.27
840 887 2.170817 GAGGAATGTTACCCCCTCTCAC 59.829 54.545 0.00 0.00 41.40 3.51
841 888 2.197465 GGAATGTTACCCCCTCTCACT 58.803 52.381 0.00 0.00 0.00 3.41
842 889 2.170817 GGAATGTTACCCCCTCTCACTC 59.829 54.545 0.00 0.00 0.00 3.51
843 890 1.486211 ATGTTACCCCCTCTCACTCG 58.514 55.000 0.00 0.00 0.00 4.18
888 937 3.975670 GCCATCGACACTATATATAGCGC 59.024 47.826 18.00 0.00 33.68 5.92
953 1002 0.738975 TCTCGCCTCATAGTCCAACG 59.261 55.000 0.00 0.00 0.00 4.10
974 1024 1.829533 CCAATTCCCGGCCATCCTG 60.830 63.158 2.24 0.00 0.00 3.86
975 1025 2.123726 AATTCCCGGCCATCCTGC 60.124 61.111 2.24 0.00 0.00 4.85
976 1026 2.693871 AATTCCCGGCCATCCTGCT 61.694 57.895 2.24 0.00 0.00 4.24
977 1027 1.352622 AATTCCCGGCCATCCTGCTA 61.353 55.000 2.24 0.00 0.00 3.49
1359 1409 2.507324 GCCTCTTCCACGTCGCTC 60.507 66.667 0.00 0.00 0.00 5.03
1404 1454 1.025113 CGTACAGCTCGTCCTCCTCA 61.025 60.000 0.00 0.00 0.00 3.86
1602 1652 2.093106 CTCTACTACTCGTGCCAACCT 58.907 52.381 0.00 0.00 0.00 3.50
1684 1736 5.693104 CCAAGTTCTCAACCATGAACAATTG 59.307 40.000 3.24 3.24 43.38 2.32
1707 1759 0.591488 CGCACATGCATGCAAGCTAG 60.591 55.000 26.68 14.63 46.47 3.42
1765 1817 3.751479 TGATCGGTCGATGGAATTCAT 57.249 42.857 10.77 0.00 39.13 2.57
1766 1818 4.071961 TGATCGGTCGATGGAATTCATT 57.928 40.909 10.77 0.00 35.97 2.57
1767 1819 4.058124 TGATCGGTCGATGGAATTCATTC 58.942 43.478 10.77 2.45 35.97 2.67
1768 1820 3.535280 TCGGTCGATGGAATTCATTCA 57.465 42.857 7.93 0.00 38.53 2.57
1769 1821 4.071961 TCGGTCGATGGAATTCATTCAT 57.928 40.909 7.93 1.49 38.53 2.57
1770 1822 4.450976 TCGGTCGATGGAATTCATTCATT 58.549 39.130 7.93 0.00 38.53 2.57
1771 1823 4.511454 TCGGTCGATGGAATTCATTCATTC 59.489 41.667 7.93 0.00 38.53 2.67
1772 1824 4.273235 CGGTCGATGGAATTCATTCATTCA 59.727 41.667 7.93 0.00 38.53 2.57
1773 1825 5.049198 CGGTCGATGGAATTCATTCATTCAT 60.049 40.000 7.93 0.00 38.53 2.57
1774 1826 6.513884 CGGTCGATGGAATTCATTCATTCATT 60.514 38.462 7.93 0.00 38.53 2.57
1775 1827 6.860023 GGTCGATGGAATTCATTCATTCATTC 59.140 38.462 7.93 0.00 38.53 2.67
1776 1828 7.255381 GGTCGATGGAATTCATTCATTCATTCT 60.255 37.037 7.93 0.00 38.53 2.40
1777 1829 8.133627 GTCGATGGAATTCATTCATTCATTCTT 58.866 33.333 7.93 0.00 38.53 2.52
1778 1830 8.347771 TCGATGGAATTCATTCATTCATTCTTC 58.652 33.333 7.93 0.00 38.53 2.87
1779 1831 8.350722 CGATGGAATTCATTCATTCATTCTTCT 58.649 33.333 7.93 0.00 38.53 2.85
1782 1834 9.251440 TGGAATTCATTCATTCATTCTTCTTCT 57.749 29.630 7.93 0.00 38.53 2.85
1842 1894 8.437742 CGGTACAAGAAAATCGTATTGTTTACT 58.562 33.333 0.00 0.00 37.15 2.24
1859 1911 9.719355 ATTGTTTACTTTTTCACCTCTTGTTTT 57.281 25.926 0.00 0.00 0.00 2.43
1864 1916 6.946340 ACTTTTTCACCTCTTGTTTTGGATT 58.054 32.000 0.00 0.00 0.00 3.01
1869 1921 9.974980 TTTTCACCTCTTGTTTTGGATTATAAC 57.025 29.630 0.00 0.00 0.00 1.89
1903 1955 8.371571 AGAGATACCTCATGCATCATACATAA 57.628 34.615 0.00 0.00 41.87 1.90
1907 1959 6.732531 ACCTCATGCATCATACATAAATCG 57.267 37.500 0.00 0.00 0.00 3.34
1916 1968 6.676456 GCATCATACATAAATCGGAGGCAATC 60.676 42.308 0.00 0.00 32.88 2.67
1920 1972 4.389374 ACATAAATCGGAGGCAATCGAAT 58.611 39.130 0.00 0.00 38.92 3.34
1922 1974 5.639506 ACATAAATCGGAGGCAATCGAATAG 59.360 40.000 0.00 0.00 38.92 1.73
1950 2002 3.701040 ACCAGAAGTTGCATTGTCTTTGT 59.299 39.130 0.00 0.00 0.00 2.83
2096 2148 8.893219 TCTATCTGGTAAATAGAGCACAATTG 57.107 34.615 3.24 3.24 32.18 2.32
2183 2457 3.810743 GCCACTTCTAAGGCCAAAAGAGA 60.811 47.826 5.01 0.00 45.18 3.10
2237 2511 6.619329 ATTAGCAACAAACAACCCCATTAT 57.381 33.333 0.00 0.00 0.00 1.28
2240 2514 5.976458 AGCAACAAACAACCCCATTATATG 58.024 37.500 0.00 0.00 0.00 1.78
2242 2516 6.665680 AGCAACAAACAACCCCATTATATGTA 59.334 34.615 0.00 0.00 0.00 2.29
2243 2517 6.754675 GCAACAAACAACCCCATTATATGTAC 59.245 38.462 0.00 0.00 0.00 2.90
2244 2518 7.363443 GCAACAAACAACCCCATTATATGTACT 60.363 37.037 0.00 0.00 0.00 2.73
2245 2519 7.875327 ACAAACAACCCCATTATATGTACTC 57.125 36.000 0.00 0.00 0.00 2.59
2246 2520 6.831868 ACAAACAACCCCATTATATGTACTCC 59.168 38.462 0.00 0.00 0.00 3.85
2340 2614 7.483307 ACCATTAATCTATGTGCAAACATGTC 58.517 34.615 0.00 0.00 0.00 3.06
2348 2622 1.069906 GTGCAAACATGTCGTCTCACC 60.070 52.381 0.00 0.00 0.00 4.02
2417 2727 9.754382 AGTAAATATCAATTTCATTGCATGGAC 57.246 29.630 0.00 0.00 40.05 4.02
2418 2728 7.703298 AAATATCAATTTCATTGCATGGACG 57.297 32.000 0.00 0.00 40.05 4.79
2419 2729 2.878580 TCAATTTCATTGCATGGACGC 58.121 42.857 0.00 0.00 40.05 5.19
2420 2730 2.492881 TCAATTTCATTGCATGGACGCT 59.507 40.909 0.00 0.00 40.05 5.07
2421 2731 3.056678 TCAATTTCATTGCATGGACGCTT 60.057 39.130 0.00 0.00 40.05 4.68
2422 2732 2.350899 TTTCATTGCATGGACGCTTG 57.649 45.000 0.00 0.00 0.00 4.01
2423 2733 1.246649 TTCATTGCATGGACGCTTGT 58.753 45.000 0.00 0.00 0.00 3.16
2424 2734 2.106477 TCATTGCATGGACGCTTGTA 57.894 45.000 0.00 0.00 0.00 2.41
2425 2735 1.737236 TCATTGCATGGACGCTTGTAC 59.263 47.619 0.00 0.00 0.00 2.90
2426 2736 1.739466 CATTGCATGGACGCTTGTACT 59.261 47.619 0.00 0.00 0.00 2.73
2427 2737 2.753055 TTGCATGGACGCTTGTACTA 57.247 45.000 0.00 0.00 0.00 1.82
2428 2738 2.293677 TGCATGGACGCTTGTACTAG 57.706 50.000 0.00 0.00 0.00 2.57
2429 2739 1.548719 TGCATGGACGCTTGTACTAGT 59.451 47.619 0.00 0.00 0.00 2.57
2481 2813 1.148867 TCCATTTTGGATGGGTGTGGT 59.851 47.619 5.30 0.00 42.67 4.16
2497 2829 5.474189 GGGTGTGGTGCTTAATTAACTGTAA 59.526 40.000 0.00 0.00 0.00 2.41
2515 2847 8.630054 AACTGTAACTAATTTAGCCATGTTGA 57.370 30.769 3.28 0.00 0.00 3.18
2524 2856 5.643379 TTTAGCCATGTTGAACTCATTCC 57.357 39.130 0.00 0.00 33.49 3.01
2633 2968 2.494870 GCCTGCTCTGAATTTTCCACAT 59.505 45.455 0.00 0.00 0.00 3.21
2994 3353 2.532723 CGCTGAAAATGCATGCACATAC 59.467 45.455 25.37 15.31 0.00 2.39
2995 3354 2.532723 GCTGAAAATGCATGCACATACG 59.467 45.455 25.37 11.17 0.00 3.06
2996 3355 3.761657 CTGAAAATGCATGCACATACGT 58.238 40.909 25.37 2.19 0.00 3.57
3010 3369 6.311723 TGCACATACGTATATGATAGACACG 58.688 40.000 17.81 0.00 40.75 4.49
3022 3381 2.624316 TAGACACGTCCGATCAACAC 57.376 50.000 0.00 0.00 0.00 3.32
3029 3545 3.001070 CACGTCCGATCAACACTAATTCG 60.001 47.826 0.00 0.00 0.00 3.34
3032 3548 2.927477 TCCGATCAACACTAATTCGTGC 59.073 45.455 9.85 0.00 38.45 5.34
3054 3570 5.817616 CAAAATGTGTCTTCTCATTGTGC 57.182 39.130 0.00 0.00 36.58 4.57
3217 3739 1.197721 CGATGCAAACGGAAGCTTCTT 59.802 47.619 25.05 10.59 34.03 2.52
3218 3740 2.726066 CGATGCAAACGGAAGCTTCTTC 60.726 50.000 25.05 9.37 34.03 2.87
3219 3741 1.967319 TGCAAACGGAAGCTTCTTCT 58.033 45.000 25.05 7.57 0.00 2.85
3221 3743 3.472652 TGCAAACGGAAGCTTCTTCTAA 58.527 40.909 25.05 3.89 0.00 2.10
3223 3745 4.518970 TGCAAACGGAAGCTTCTTCTAATT 59.481 37.500 25.05 9.81 0.00 1.40
3224 3746 5.703592 TGCAAACGGAAGCTTCTTCTAATTA 59.296 36.000 25.05 4.61 0.00 1.40
3226 3748 6.675728 GCAAACGGAAGCTTCTTCTAATTAGG 60.676 42.308 25.05 6.90 0.00 2.69
3227 3749 5.934402 ACGGAAGCTTCTTCTAATTAGGA 57.066 39.130 25.05 2.70 0.00 2.94
3228 3750 5.662456 ACGGAAGCTTCTTCTAATTAGGAC 58.338 41.667 25.05 3.66 0.00 3.85
3263 3796 4.758251 TGGCGACTGCACGATGGG 62.758 66.667 0.24 0.00 45.35 4.00
3299 3832 1.023502 CCATCAACCGTGCATGCATA 58.976 50.000 25.64 0.00 0.00 3.14
3300 3833 1.268692 CCATCAACCGTGCATGCATAC 60.269 52.381 25.64 11.18 0.00 2.39
3316 3849 2.964438 ATACGCCATGCCCGTACGTG 62.964 60.000 15.21 3.42 43.02 4.49
3321 3854 4.467084 ATGCCCGTACGTGCCTGG 62.467 66.667 19.95 11.43 0.00 4.45
3325 3858 3.740397 CCGTACGTGCCTGGTCGA 61.740 66.667 15.21 0.00 0.00 4.20
3327 3860 1.153901 CGTACGTGCCTGGTCGATT 60.154 57.895 7.22 2.37 0.00 3.34
3425 3959 7.178573 TCCACCTATGTAATCAATCAACCAAA 58.821 34.615 0.00 0.00 0.00 3.28
3457 3991 3.138304 GCATACCACTGTCACTGTGAAA 58.862 45.455 15.98 6.24 35.76 2.69
3478 4012 1.810755 CAGCATTGCAGCCGATGATAT 59.189 47.619 11.91 0.00 35.24 1.63
3506 4040 4.756502 AGCGTAGTCCTAAATTTCACCTC 58.243 43.478 0.00 0.00 0.00 3.85
3591 4127 6.874134 AGATCAATGTAACGCCAGATAATACC 59.126 38.462 0.00 0.00 0.00 2.73
3606 4142 3.550437 AATACCACAGAGGAGATGTGC 57.450 47.619 0.58 0.00 45.37 4.57
3648 4184 3.112580 ACGTACAAAAATGTTGCTGTGC 58.887 40.909 0.00 0.00 0.00 4.57
3649 4185 3.111838 CGTACAAAAATGTTGCTGTGCA 58.888 40.909 0.00 0.00 36.47 4.57
3671 4207 4.493747 GCCGAACCGTAGCTCGCT 62.494 66.667 0.00 0.00 38.35 4.93
3672 4208 2.278013 CCGAACCGTAGCTCGCTC 60.278 66.667 0.00 0.00 38.35 5.03
3673 4209 2.648102 CGAACCGTAGCTCGCTCG 60.648 66.667 0.00 1.96 37.16 5.03
3674 4210 2.484203 GAACCGTAGCTCGCTCGT 59.516 61.111 0.00 0.00 38.35 4.18
3675 4211 1.717937 GAACCGTAGCTCGCTCGTA 59.282 57.895 0.00 0.00 38.35 3.43
3677 4213 1.712977 AACCGTAGCTCGCTCGTAGG 61.713 60.000 0.00 0.00 38.35 3.18
3678 4214 2.052060 CGTAGCTCGCTCGTAGGC 60.052 66.667 0.00 0.00 0.00 3.93
3695 4233 4.891727 CGCGGAGATTCCCCCACG 62.892 72.222 0.00 0.00 31.13 4.94
3696 4234 4.547367 GCGGAGATTCCCCCACGG 62.547 72.222 0.00 0.00 31.13 4.94
3697 4235 4.547367 CGGAGATTCCCCCACGGC 62.547 72.222 0.00 0.00 31.13 5.68
3698 4236 4.191015 GGAGATTCCCCCACGGCC 62.191 72.222 0.00 0.00 0.00 6.13
3699 4237 3.407967 GAGATTCCCCCACGGCCA 61.408 66.667 2.24 0.00 0.00 5.36
3700 4238 3.699134 GAGATTCCCCCACGGCCAC 62.699 68.421 2.24 0.00 0.00 5.01
3823 4361 3.306225 GCACACATGTCATTTTCCACCAT 60.306 43.478 0.00 0.00 0.00 3.55
3824 4362 4.082300 GCACACATGTCATTTTCCACCATA 60.082 41.667 0.00 0.00 0.00 2.74
3825 4363 5.401550 CACACATGTCATTTTCCACCATAC 58.598 41.667 0.00 0.00 0.00 2.39
3827 4365 5.774690 ACACATGTCATTTTCCACCATACTT 59.225 36.000 0.00 0.00 0.00 2.24
3828 4366 6.267471 ACACATGTCATTTTCCACCATACTTT 59.733 34.615 0.00 0.00 0.00 2.66
3830 4368 7.329226 CACATGTCATTTTCCACCATACTTTTC 59.671 37.037 0.00 0.00 0.00 2.29
3914 4457 3.194719 GCATGCACTTGCTCCTCC 58.805 61.111 14.21 0.00 42.66 4.30
3915 4458 1.378250 GCATGCACTTGCTCCTCCT 60.378 57.895 14.21 0.00 42.66 3.69
3916 4459 1.375098 GCATGCACTTGCTCCTCCTC 61.375 60.000 14.21 0.00 42.66 3.71
3917 4460 0.747283 CATGCACTTGCTCCTCCTCC 60.747 60.000 2.33 0.00 42.66 4.30
3918 4461 0.913451 ATGCACTTGCTCCTCCTCCT 60.913 55.000 2.33 0.00 42.66 3.69
3919 4462 1.220477 GCACTTGCTCCTCCTCCTC 59.780 63.158 0.00 0.00 38.21 3.71
3923 4466 1.002274 TTGCTCCTCCTCCTCCTCC 59.998 63.158 0.00 0.00 0.00 4.30
4003 4546 2.191128 AGCTCATGGACTTTGGTCAC 57.809 50.000 0.00 0.00 43.77 3.67
4025 4568 1.668294 CAGCCTACCCTAGCCGATG 59.332 63.158 0.00 0.00 0.00 3.84
4076 4619 1.328680 CTGTGGCGTGCATTATCAGTC 59.671 52.381 0.00 0.00 0.00 3.51
4089 4633 5.473931 CATTATCAGTCAGGAATCTACCCG 58.526 45.833 0.00 0.00 0.00 5.28
4090 4634 1.112113 TCAGTCAGGAATCTACCCGC 58.888 55.000 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.048509 TCTTCACGTCACATGCAATATATGT 58.951 36.000 0.00 0.00 39.23 2.29
1 2 6.529463 TCTTCACGTCACATGCAATATATG 57.471 37.500 0.00 0.00 0.00 1.78
2 3 7.552458 TTTCTTCACGTCACATGCAATATAT 57.448 32.000 0.00 0.00 0.00 0.86
5 6 5.238432 AGTTTTCTTCACGTCACATGCAATA 59.762 36.000 0.00 0.00 0.00 1.90
34 35 1.001597 CTACGTTAGGCGAGGGATGAC 60.002 57.143 0.00 0.00 44.77 3.06
37 38 0.184451 TCCTACGTTAGGCGAGGGAT 59.816 55.000 0.00 0.00 45.82 3.85
41 42 1.030457 ACCATCCTACGTTAGGCGAG 58.970 55.000 0.00 0.00 45.82 5.03
42 43 2.224606 CTACCATCCTACGTTAGGCGA 58.775 52.381 0.00 0.00 45.82 5.54
48 49 3.097342 ACCTCACTACCATCCTACGTT 57.903 47.619 0.00 0.00 0.00 3.99
50 51 2.100916 CCAACCTCACTACCATCCTACG 59.899 54.545 0.00 0.00 0.00 3.51
134 135 8.129211 TGAGTTAAGCTTTAAACAAAGAAGAGC 58.871 33.333 3.20 0.00 31.58 4.09
203 205 0.892755 ACTCCATAACCGCGAGTCAA 59.107 50.000 8.23 0.00 31.15 3.18
231 233 7.397892 TGAGGTCAACACACAAAAATCTAAA 57.602 32.000 0.00 0.00 0.00 1.85
238 240 5.680619 AGACTATGAGGTCAACACACAAAA 58.319 37.500 0.00 0.00 38.57 2.44
297 299 4.223700 AGAGTTGGCATATTGACAGTCTCA 59.776 41.667 15.04 0.00 36.33 3.27
301 303 5.683876 AGTAGAGTTGGCATATTGACAGT 57.316 39.130 0.00 0.00 36.33 3.55
343 345 2.150397 ACGCCAGTGAAGTAACTGTC 57.850 50.000 3.85 0.00 45.08 3.51
366 368 0.174617 GTTCTCGGAGGAAGGAGCTG 59.825 60.000 4.96 0.00 0.00 4.24
376 378 6.399669 CGTGTAATGTTAGTTTGTTCTCGGAG 60.400 42.308 0.00 0.00 0.00 4.63
379 381 5.070862 GCGTGTAATGTTAGTTTGTTCTCG 58.929 41.667 0.00 0.00 0.00 4.04
393 395 0.044161 GAGTTAGCGCGCGTGTAATG 60.044 55.000 32.35 0.92 0.00 1.90
394 396 0.457166 TGAGTTAGCGCGCGTGTAAT 60.457 50.000 32.35 15.51 0.00 1.89
419 421 4.338012 AGGGTTATGTCCGGGTTAAAAAG 58.662 43.478 0.00 0.00 0.00 2.27
425 427 2.984435 AAAAGGGTTATGTCCGGGTT 57.016 45.000 0.00 0.00 0.00 4.11
427 429 2.797786 TGAAAAAGGGTTATGTCCGGG 58.202 47.619 0.00 0.00 0.00 5.73
428 430 6.518208 TTAATGAAAAAGGGTTATGTCCGG 57.482 37.500 0.00 0.00 0.00 5.14
463 465 9.379770 TCTGGTTATGGATAGATGTATTTCAGA 57.620 33.333 0.00 0.00 0.00 3.27
465 467 9.379770 TCTCTGGTTATGGATAGATGTATTTCA 57.620 33.333 0.00 0.00 0.00 2.69
501 510 1.203523 TGGTGCGTTGAACTTGCTTTT 59.796 42.857 0.00 0.00 0.00 2.27
503 512 0.100503 GTGGTGCGTTGAACTTGCTT 59.899 50.000 0.00 0.00 0.00 3.91
548 566 3.393800 CGTCGGATATGCAAGGAGAAAT 58.606 45.455 0.00 0.00 0.00 2.17
555 573 2.310233 CGGCCGTCGGATATGCAAG 61.310 63.158 19.50 0.00 34.75 4.01
579 597 1.679153 GTGAATTGGGTGTCACCGTTT 59.321 47.619 15.93 8.91 39.83 3.60
592 610 1.539827 GACCGAAACCAGGGTGAATTG 59.460 52.381 0.00 0.00 36.46 2.32
600 618 3.244112 ACTTTCTACTGACCGAAACCAGG 60.244 47.826 0.00 0.00 34.85 4.45
635 670 4.069232 TTGACTCGCGAGGGGCTG 62.069 66.667 36.93 15.00 43.59 4.85
674 710 1.676006 GAAGGTGAGGTTGTGTGTTGG 59.324 52.381 0.00 0.00 0.00 3.77
723 759 4.704833 TGTCAGCTTGGCGCCTCC 62.705 66.667 29.70 15.50 40.39 4.30
724 760 3.426568 GTGTCAGCTTGGCGCCTC 61.427 66.667 29.70 16.55 40.39 4.70
834 881 2.579249 GCTGCGAGCGAGTGAGAG 60.579 66.667 0.00 0.00 0.00 3.20
835 882 2.919494 TTGCTGCGAGCGAGTGAGA 61.919 57.895 0.00 0.00 46.26 3.27
836 883 2.431430 TTGCTGCGAGCGAGTGAG 60.431 61.111 0.00 0.00 46.26 3.51
837 884 2.734723 GTTGCTGCGAGCGAGTGA 60.735 61.111 0.00 0.00 46.26 3.41
838 885 3.782244 GGTTGCTGCGAGCGAGTG 61.782 66.667 2.94 0.00 46.26 3.51
868 915 3.659899 GCGCGCTATATATAGTGTCGATG 59.340 47.826 31.47 19.72 41.65 3.84
953 1002 2.123726 ATGGCCGGGAATTGGAGC 60.124 61.111 2.18 0.00 0.00 4.70
1579 1629 1.095600 TGGCACGAGTAGTAGAGCTG 58.904 55.000 0.00 0.00 0.00 4.24
1580 1630 1.473278 GTTGGCACGAGTAGTAGAGCT 59.527 52.381 0.00 0.00 0.00 4.09
1581 1631 1.469423 GGTTGGCACGAGTAGTAGAGC 60.469 57.143 0.00 0.00 0.00 4.09
1733 1785 0.108138 ACCGATCAAGGAAGAAGCCG 60.108 55.000 0.00 0.00 34.73 5.52
1774 1826 9.898152 AGAAGAAGAAGAAGAAAAAGAAGAAGA 57.102 29.630 0.00 0.00 0.00 2.87
1777 1829 9.898152 AGAAGAAGAAGAAGAAGAAAAAGAAGA 57.102 29.630 0.00 0.00 0.00 2.87
1780 1832 8.821894 CGAAGAAGAAGAAGAAGAAGAAAAAGA 58.178 33.333 0.00 0.00 0.00 2.52
1781 1833 7.585936 GCGAAGAAGAAGAAGAAGAAGAAAAAG 59.414 37.037 0.00 0.00 0.00 2.27
1782 1834 7.281100 AGCGAAGAAGAAGAAGAAGAAGAAAAA 59.719 33.333 0.00 0.00 0.00 1.94
1783 1835 6.763610 AGCGAAGAAGAAGAAGAAGAAGAAAA 59.236 34.615 0.00 0.00 0.00 2.29
1784 1836 6.284459 AGCGAAGAAGAAGAAGAAGAAGAAA 58.716 36.000 0.00 0.00 0.00 2.52
1785 1837 5.848406 AGCGAAGAAGAAGAAGAAGAAGAA 58.152 37.500 0.00 0.00 0.00 2.52
1786 1838 5.461032 AGCGAAGAAGAAGAAGAAGAAGA 57.539 39.130 0.00 0.00 0.00 2.87
1787 1839 8.402472 TCTATAGCGAAGAAGAAGAAGAAGAAG 58.598 37.037 0.00 0.00 0.00 2.85
1864 1916 8.996651 TGAGGTATCTCTTCACTGATGTTATA 57.003 34.615 4.28 0.00 40.58 0.98
1869 1921 4.989797 GCATGAGGTATCTCTTCACTGATG 59.010 45.833 4.28 0.00 40.58 3.07
1903 1955 3.753294 ACTATTCGATTGCCTCCGATT 57.247 42.857 0.00 0.00 34.58 3.34
1907 1959 4.201920 GGTTGAAACTATTCGATTGCCTCC 60.202 45.833 0.00 0.00 38.46 4.30
1950 2002 5.781210 TGTCCATACATGCAAGAACAAAA 57.219 34.783 0.00 0.00 0.00 2.44
1994 2046 3.489785 GGCGATGATCCAAAAGTAGTACG 59.510 47.826 0.00 0.00 0.00 3.67
2146 2391 4.757149 AGAAGTGGCTGAAAACATGTACTC 59.243 41.667 0.00 0.00 0.00 2.59
2183 2457 0.392863 TATGCCTGACTTGCGCATGT 60.393 50.000 26.87 26.87 42.93 3.21
2237 2511 5.661312 ACCAGAACAAGCATAGGAGTACATA 59.339 40.000 0.00 0.00 0.00 2.29
2240 2514 4.434520 GACCAGAACAAGCATAGGAGTAC 58.565 47.826 0.00 0.00 0.00 2.73
2242 2516 2.237392 GGACCAGAACAAGCATAGGAGT 59.763 50.000 0.00 0.00 0.00 3.85
2243 2517 2.237143 TGGACCAGAACAAGCATAGGAG 59.763 50.000 0.00 0.00 0.00 3.69
2244 2518 2.265367 TGGACCAGAACAAGCATAGGA 58.735 47.619 0.00 0.00 0.00 2.94
2245 2519 2.787473 TGGACCAGAACAAGCATAGG 57.213 50.000 0.00 0.00 0.00 2.57
2246 2520 5.649782 ATTTTGGACCAGAACAAGCATAG 57.350 39.130 0.00 0.00 0.00 2.23
2312 2586 7.087409 TGTTTGCACATAGATTAATGGTCAG 57.913 36.000 0.00 0.00 0.00 3.51
2406 2716 1.739466 AGTACAAGCGTCCATGCAATG 59.261 47.619 0.00 0.00 46.21 2.82
2407 2717 2.113860 AGTACAAGCGTCCATGCAAT 57.886 45.000 0.00 0.00 37.31 3.56
2408 2718 2.028476 ACTAGTACAAGCGTCCATGCAA 60.028 45.455 0.00 0.00 37.31 4.08
2409 2719 1.548719 ACTAGTACAAGCGTCCATGCA 59.451 47.619 0.00 0.00 37.31 3.96
2410 2720 2.295253 ACTAGTACAAGCGTCCATGC 57.705 50.000 0.00 0.00 0.00 4.06
2411 2721 4.111375 AGAACTAGTACAAGCGTCCATG 57.889 45.455 0.00 0.00 0.00 3.66
2412 2722 4.803098 AAGAACTAGTACAAGCGTCCAT 57.197 40.909 0.00 0.00 0.00 3.41
2413 2723 4.280174 AGAAAGAACTAGTACAAGCGTCCA 59.720 41.667 0.00 0.00 0.00 4.02
2414 2724 4.807443 AGAAAGAACTAGTACAAGCGTCC 58.193 43.478 0.00 0.00 0.00 4.79
2415 2725 6.766452 AAAGAAAGAACTAGTACAAGCGTC 57.234 37.500 0.00 0.00 0.00 5.19
2416 2726 8.546244 GTTTAAAGAAAGAACTAGTACAAGCGT 58.454 33.333 0.00 0.00 0.00 5.07
2417 2727 8.762426 AGTTTAAAGAAAGAACTAGTACAAGCG 58.238 33.333 0.00 0.00 32.22 4.68
2497 2829 7.944729 ATGAGTTCAACATGGCTAAATTAGT 57.055 32.000 0.00 0.00 0.00 2.24
2515 2847 5.654650 TGTGGTTACAAACTTGGAATGAGTT 59.345 36.000 0.00 0.00 38.92 3.01
2524 2856 6.803320 CAGCATAGAATGTGGTTACAAACTTG 59.197 38.462 0.00 0.00 40.84 3.16
2569 2901 0.230515 CGCGTGCGTCGACTATAGTA 59.769 55.000 14.70 0.00 42.86 1.82
2570 2902 1.011463 CGCGTGCGTCGACTATAGT 60.011 57.895 14.70 4.68 42.86 2.12
2571 2903 3.798029 CGCGTGCGTCGACTATAG 58.202 61.111 14.70 0.00 42.86 1.31
2633 2968 2.885894 TGAACATGCATGAGCTGTTTGA 59.114 40.909 32.75 7.10 40.04 2.69
2994 3353 4.916099 TCGGACGTGTCTATCATATACG 57.084 45.455 0.00 0.00 40.30 3.06
2995 3354 6.418585 TGATCGGACGTGTCTATCATATAC 57.581 41.667 0.00 0.00 31.76 1.47
2996 3355 6.428771 TGTTGATCGGACGTGTCTATCATATA 59.571 38.462 14.74 3.63 34.47 0.86
3010 3369 3.241995 GCACGAATTAGTGTTGATCGGAC 60.242 47.826 18.28 0.00 43.61 4.79
3022 3381 6.373779 AGAAGACACATTTTGCACGAATTAG 58.626 36.000 0.00 0.00 0.00 1.73
3029 3545 5.174398 CACAATGAGAAGACACATTTTGCAC 59.826 40.000 0.00 0.00 35.73 4.57
3032 3548 5.401376 CAGCACAATGAGAAGACACATTTTG 59.599 40.000 0.00 0.00 37.61 2.44
3054 3570 6.402550 CCAATCGTCAGGAAATTACAAGACAG 60.403 42.308 2.61 0.00 0.00 3.51
3217 3739 5.356190 CACTCCACAGTACGTCCTAATTAGA 59.644 44.000 14.28 0.00 0.00 2.10
3218 3740 5.450137 CCACTCCACAGTACGTCCTAATTAG 60.450 48.000 5.43 5.43 0.00 1.73
3219 3741 4.400251 CCACTCCACAGTACGTCCTAATTA 59.600 45.833 0.00 0.00 0.00 1.40
3221 3743 2.758979 CCACTCCACAGTACGTCCTAAT 59.241 50.000 0.00 0.00 0.00 1.73
3223 3745 1.352017 TCCACTCCACAGTACGTCCTA 59.648 52.381 0.00 0.00 0.00 2.94
3224 3746 0.111832 TCCACTCCACAGTACGTCCT 59.888 55.000 0.00 0.00 0.00 3.85
3226 3748 1.612463 AGTTCCACTCCACAGTACGTC 59.388 52.381 0.00 0.00 0.00 4.34
3227 3749 1.340248 CAGTTCCACTCCACAGTACGT 59.660 52.381 0.00 0.00 0.00 3.57
3228 3750 1.336887 CCAGTTCCACTCCACAGTACG 60.337 57.143 0.00 0.00 0.00 3.67
3263 3796 1.446966 GGACTGCTTGCCTCTCGAC 60.447 63.158 0.00 0.00 0.00 4.20
3309 3842 1.153901 AATCGACCAGGCACGTACG 60.154 57.895 15.01 15.01 0.00 3.67
3316 3849 3.257393 CTGCTATATCAATCGACCAGGC 58.743 50.000 0.00 0.00 0.00 4.85
3318 3851 3.917988 TGCTGCTATATCAATCGACCAG 58.082 45.455 0.00 0.00 0.00 4.00
3321 3854 3.987807 GCTGCTGCTATATCAATCGAC 57.012 47.619 8.53 0.00 36.03 4.20
3367 3900 2.419436 CCGGACACATGGTGCACTATAA 60.419 50.000 15.99 0.00 37.78 0.98
3417 3951 2.830321 TGCATGCATATGGTTTGGTTGA 59.170 40.909 18.46 0.00 34.79 3.18
3420 3954 3.321682 GGTATGCATGCATATGGTTTGGT 59.678 43.478 36.01 14.95 40.49 3.67
3421 3955 3.321396 TGGTATGCATGCATATGGTTTGG 59.679 43.478 36.01 0.00 40.49 3.28
3425 3959 3.151554 CAGTGGTATGCATGCATATGGT 58.848 45.455 36.01 21.33 40.49 3.55
3457 3991 0.750546 ATCATCGGCTGCAATGCTGT 60.751 50.000 13.44 0.00 40.06 4.40
3460 3994 2.539346 GATATCATCGGCTGCAATGC 57.461 50.000 0.00 0.00 0.00 3.56
3555 4091 2.534298 ACATTGATCTCGACGAAGCAG 58.466 47.619 0.00 0.00 0.00 4.24
3591 4127 1.001746 ACAGTGCACATCTCCTCTGTG 59.998 52.381 21.04 6.74 45.39 3.66
3606 4142 0.386352 CGTGCCATGCAGAAACAGTG 60.386 55.000 0.00 0.00 40.08 3.66
3648 4184 2.514013 GCTACGGTTCGGCGATGTG 61.514 63.158 11.76 5.78 0.00 3.21
3649 4185 2.202703 GCTACGGTTCGGCGATGT 60.203 61.111 11.76 12.68 0.00 3.06
3670 4206 1.370657 GAATCTCCGCGCCTACGAG 60.371 63.158 0.00 0.98 43.93 4.18
3671 4207 2.719979 GAATCTCCGCGCCTACGA 59.280 61.111 0.00 0.00 43.93 3.43
3672 4208 2.354773 GGAATCTCCGCGCCTACG 60.355 66.667 0.00 0.00 44.07 3.51
3673 4209 2.029221 GGGAATCTCCGCGCCTAC 59.971 66.667 0.00 0.00 37.43 3.18
3674 4210 3.231736 GGGGAATCTCCGCGCCTA 61.232 66.667 0.00 0.00 39.75 3.93
3681 4219 4.191015 GGCCGTGGGGGAATCTCC 62.191 72.222 0.00 0.00 38.47 3.71
3823 4361 1.893168 GCGCGCGTTGGAGAAAAGTA 61.893 55.000 32.35 0.00 0.00 2.24
3824 4362 2.935955 CGCGCGTTGGAGAAAAGT 59.064 55.556 24.19 0.00 0.00 2.66
3825 4363 2.499732 GCGCGCGTTGGAGAAAAG 60.500 61.111 32.35 0.00 0.00 2.27
3862 4402 1.077429 GGTCACCAGATCCAAGGCC 60.077 63.158 0.00 0.00 0.00 5.19
3911 4454 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
3912 4455 1.087725 AGGAGGAGGAGGAGGAGGA 59.912 63.158 0.00 0.00 0.00 3.71
3913 4456 1.232792 CAGGAGGAGGAGGAGGAGG 59.767 68.421 0.00 0.00 0.00 4.30
3914 4457 1.457455 GCAGGAGGAGGAGGAGGAG 60.457 68.421 0.00 0.00 0.00 3.69
3915 4458 1.522917 AAGCAGGAGGAGGAGGAGGA 61.523 60.000 0.00 0.00 0.00 3.71
3916 4459 0.620121 AAAGCAGGAGGAGGAGGAGG 60.620 60.000 0.00 0.00 0.00 4.30
3917 4460 0.540923 CAAAGCAGGAGGAGGAGGAG 59.459 60.000 0.00 0.00 0.00 3.69
3918 4461 0.911525 CCAAAGCAGGAGGAGGAGGA 60.912 60.000 0.00 0.00 0.00 3.71
3919 4462 1.606531 CCAAAGCAGGAGGAGGAGG 59.393 63.158 0.00 0.00 0.00 4.30
3923 4466 0.914644 TGATCCCAAAGCAGGAGGAG 59.085 55.000 0.00 0.00 36.67 3.69
4003 4546 3.930012 GCTAGGGTAGGCTGCGGG 61.930 72.222 0.00 0.00 0.00 6.13
4025 4568 0.801067 GCACCACTCGACCGACATAC 60.801 60.000 0.00 0.00 0.00 2.39
4076 4619 1.749033 GGGAGCGGGTAGATTCCTG 59.251 63.158 0.00 0.00 36.96 3.86


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

AutoCloner maintained by Alex Coulton.