Multiple sequence alignment - TraesCS1A01G277000

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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 TraesCS1A01G277000 chr1A 100.000 4429 0 0 1 4429 472139908 472144336 0.000000e+00 8179.0
1 TraesCS1A01G277000 chr1A 78.595 911 144 33 1985 2869 472080954 472081839 5.010000e-154 555.0
2 TraesCS1A01G277000 chr1A 76.097 866 128 47 1940 2796 472167489 472168284 3.230000e-101 379.0
3 TraesCS1A01G277000 chr1A 83.256 430 49 15 3103 3518 472082331 472082751 1.500000e-99 374.0
4 TraesCS1A01G277000 chr1A 83.492 315 40 7 2197 2508 526909125 526909430 2.610000e-72 283.0
5 TraesCS1A01G277000 chr1A 87.013 231 30 0 1518 1748 472080451 472080681 1.220000e-65 261.0
6 TraesCS1A01G277000 chr1A 83.673 147 18 4 988 1131 472164522 472164665 2.780000e-27 134.0
7 TraesCS1A01G277000 chr1B 92.767 2765 132 29 1701 4429 497780053 497782785 0.000000e+00 3936.0
8 TraesCS1A01G277000 chr1B 88.431 1625 116 34 306 1901 497778443 497780024 0.000000e+00 1893.0
9 TraesCS1A01G277000 chr1B 78.271 856 149 27 1985 2821 497471869 497472706 2.360000e-142 516.0
10 TraesCS1A01G277000 chr1B 80.038 521 63 21 3105 3593 497473328 497473839 9.120000e-92 348.0
11 TraesCS1A01G277000 chr1B 78.547 592 82 30 2888 3460 497821459 497822024 9.120000e-92 348.0
12 TraesCS1A01G277000 chr1B 80.230 435 77 9 1940 2371 497820523 497820951 7.150000e-83 318.0
13 TraesCS1A01G277000 chr1B 81.527 406 55 12 1362 1748 497471192 497471596 2.570000e-82 316.0
14 TraesCS1A01G277000 chr1B 77.758 553 84 22 1219 1738 497799604 497800150 2.000000e-78 303.0
15 TraesCS1A01G277000 chr1D 93.349 2556 119 25 1897 4429 372861189 372863716 0.000000e+00 3731.0
16 TraesCS1A01G277000 chr1D 87.018 1895 166 41 1 1849 372859247 372861107 0.000000e+00 2063.0
17 TraesCS1A01G277000 chr1D 79.162 955 155 27 1940 2869 372836067 372837002 4.870000e-174 621.0
18 TraesCS1A01G277000 chr1D 83.641 434 47 10 3101 3518 372837485 372837910 1.930000e-103 387.0
19 TraesCS1A01G277000 chr1D 80.080 502 70 19 2918 3401 372876849 372877338 3.280000e-91 346.0
20 TraesCS1A01G277000 chr1D 88.186 237 27 1 1513 1748 372835507 372835743 9.380000e-72 281.0
21 TraesCS1A01G277000 chr1D 82.986 288 35 5 2509 2796 372876319 372876592 9.510000e-62 248.0
22 TraesCS1A01G277000 chr1D 86.538 208 20 5 2885 3091 372837129 372837329 5.770000e-54 222.0
23 TraesCS1A01G277000 chr1D 75.087 574 75 40 988 1515 372874623 372875174 5.810000e-49 206.0
24 TraesCS1A01G277000 chr6D 83.796 216 28 4 1801 2014 421040514 421040304 9.720000e-47 198.0
25 TraesCS1A01G277000 chr2A 82.028 217 31 5 1801 2014 86671897 86671686 1.270000e-40 178.0
26 TraesCS1A01G277000 chr2A 86.667 90 7 4 2222 2311 576657767 576657683 1.310000e-15 95.3
27 TraesCS1A01G277000 chr3A 86.667 90 7 4 2222 2311 705929338 705929254 1.310000e-15 95.3
28 TraesCS1A01G277000 chr7B 92.308 52 3 1 4099 4149 706222172 706222223 6.140000e-09 73.1


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 TraesCS1A01G277000 chr1A 472139908 472144336 4428 False 8179.000000 8179 100.000000 1 4429 1 chr1A.!!$F1 4428
1 TraesCS1A01G277000 chr1A 472080451 472082751 2300 False 396.666667 555 82.954667 1518 3518 3 chr1A.!!$F3 2000
2 TraesCS1A01G277000 chr1A 472164522 472168284 3762 False 256.500000 379 79.885000 988 2796 2 chr1A.!!$F4 1808
3 TraesCS1A01G277000 chr1B 497778443 497782785 4342 False 2914.500000 3936 90.599000 306 4429 2 chr1B.!!$F3 4123
4 TraesCS1A01G277000 chr1B 497471192 497473839 2647 False 393.333333 516 79.945333 1362 3593 3 chr1B.!!$F2 2231
5 TraesCS1A01G277000 chr1B 497820523 497822024 1501 False 333.000000 348 79.388500 1940 3460 2 chr1B.!!$F4 1520
6 TraesCS1A01G277000 chr1B 497799604 497800150 546 False 303.000000 303 77.758000 1219 1738 1 chr1B.!!$F1 519
7 TraesCS1A01G277000 chr1D 372859247 372863716 4469 False 2897.000000 3731 90.183500 1 4429 2 chr1D.!!$F2 4428
8 TraesCS1A01G277000 chr1D 372835507 372837910 2403 False 377.750000 621 84.381750 1513 3518 4 chr1D.!!$F1 2005
9 TraesCS1A01G277000 chr1D 372874623 372877338 2715 False 266.666667 346 79.384333 988 3401 3 chr1D.!!$F3 2413

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
64 65 0.044092 TCTTGGGGGTAGCCAGATCA 59.956 55.000 14.06 2.48 0.00 2.92 F
432 433 0.186386 ACGGCTAGTCAGGCCTCTAT 59.814 55.000 0.00 0.00 46.73 1.98 F
743 769 0.246360 TATCATATCCAGGCGCGTGG 59.754 55.000 37.06 37.06 39.19 4.94 F
989 1025 0.321122 GAGGCTTGGTGGTCAGACAG 60.321 60.000 2.17 0.00 0.00 3.51 F
1468 1591 0.470341 GGGAACTATCTGGGTGAGCC 59.530 60.000 0.00 0.00 0.00 4.70 F
1474 1597 0.761187 TATCTGGGTGAGCCATGAGC 59.239 55.000 2.84 0.00 44.25 4.26 F
2001 4566 3.002791 AGGTGTATGACGTGCTCAAATG 58.997 45.455 0.00 0.00 30.60 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1468 1591 0.530744 ATTGCCTGCTTGTGCTCATG 59.469 50.000 0.00 0.0 40.48 3.07 R
1473 1596 0.597568 TGTGTATTGCCTGCTTGTGC 59.402 50.000 0.00 0.0 40.20 4.57 R
2056 4622 0.984230 AGCTGCTAGCACTTACCCAA 59.016 50.000 14.93 0.0 45.56 4.12 R
2782 5393 1.825090 CTGCCTAACATGTTGCAGGA 58.175 50.000 29.81 16.5 45.69 3.86 R
3275 6384 3.063485 GGCTGAAGAACTCTCACTTCAC 58.937 50.000 0.00 0.0 44.59 3.18 R
3390 6502 3.068732 GCTCCTTCCAGTTGCTTCTTTTT 59.931 43.478 0.00 0.0 0.00 1.94 R
3830 6965 1.108727 TTCAGGCTGTGGGCAGTTTG 61.109 55.000 15.27 0.0 44.32 2.93 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
18 19 3.231734 CATTGAGGCGACCTTGACA 57.768 52.632 0.00 0.00 31.76 3.58
19 20 1.081892 CATTGAGGCGACCTTGACAG 58.918 55.000 0.00 0.00 31.76 3.51
29 30 3.748568 GCGACCTTGACAGATTTCTTCTT 59.251 43.478 0.00 0.00 29.93 2.52
31 32 4.991056 CGACCTTGACAGATTTCTTCTTGA 59.009 41.667 0.00 0.00 29.93 3.02
39 40 7.397221 TGACAGATTTCTTCTTGATGGTATGT 58.603 34.615 0.00 0.00 29.93 2.29
41 42 7.170965 ACAGATTTCTTCTTGATGGTATGTGT 58.829 34.615 0.00 0.00 29.93 3.72
51 52 0.695924 TGGTATGTGTGGGTCTTGGG 59.304 55.000 0.00 0.00 0.00 4.12
58 59 2.612746 TGGGTCTTGGGGGTAGCC 60.613 66.667 1.07 1.07 0.00 3.93
63 64 0.470341 GTCTTGGGGGTAGCCAGATC 59.530 60.000 14.06 0.00 0.00 2.75
64 65 0.044092 TCTTGGGGGTAGCCAGATCA 59.956 55.000 14.06 2.48 0.00 2.92
69 70 1.335132 GGGGTAGCCAGATCAACCGA 61.335 60.000 14.06 0.00 32.53 4.69
79 80 0.322546 GATCAACCGAGGTGCCCTTT 60.323 55.000 0.00 0.00 31.76 3.11
111 112 8.480643 AATGTGTTTTAACATTTTTCGTCCAA 57.519 26.923 0.00 0.00 46.19 3.53
127 128 7.743520 TTCGTCCAAGTTTTTGTCAATTAAC 57.256 32.000 3.91 3.91 32.21 2.01
129 130 5.172411 CGTCCAAGTTTTTGTCAATTAACCG 59.828 40.000 7.21 2.13 32.21 4.44
140 141 4.039245 TGTCAATTAACCGGGCAATTTTCA 59.961 37.500 6.32 9.07 0.00 2.69
148 149 3.117512 ACCGGGCAATTTTCATCTATCCT 60.118 43.478 6.32 0.00 0.00 3.24
152 153 6.340522 CGGGCAATTTTCATCTATCCTTTTT 58.659 36.000 0.00 0.00 0.00 1.94
153 154 7.417342 CCGGGCAATTTTCATCTATCCTTTTTA 60.417 37.037 0.00 0.00 0.00 1.52
173 174 9.860898 CTTTTTAATAAATCAGACTTCCAAGGG 57.139 33.333 0.00 0.00 0.00 3.95
191 192 4.038271 AGGGCATCATGACTTGAGAAAA 57.962 40.909 0.00 0.00 37.89 2.29
194 195 4.096081 GGGCATCATGACTTGAGAAAAGAG 59.904 45.833 0.00 0.00 37.89 2.85
238 239 0.532862 GGTACCATGTGATGAGCCCG 60.533 60.000 7.15 0.00 0.00 6.13
257 258 2.282039 CCGGCCCCAAGCATCAAAA 61.282 57.895 0.00 0.00 46.50 2.44
258 259 1.616091 CCGGCCCCAAGCATCAAAAT 61.616 55.000 0.00 0.00 46.50 1.82
331 332 7.330208 GGAATTTTGTTTCTGAACATGATCAGG 59.670 37.037 27.00 5.68 44.71 3.86
373 374 4.296593 TGCCCGTACGCAACCGAA 62.297 61.111 10.49 0.00 35.32 4.30
374 375 3.043121 GCCCGTACGCAACCGAAA 61.043 61.111 10.49 0.00 38.29 3.46
407 408 0.751452 TATATAACCGTGCCACGCCA 59.249 50.000 12.68 0.00 40.91 5.69
421 422 4.767255 GCCAGCAGCACGGCTAGT 62.767 66.667 16.75 0.00 43.68 2.57
422 423 2.510238 CCAGCAGCACGGCTAGTC 60.510 66.667 0.00 0.00 43.68 2.59
423 424 2.262603 CAGCAGCACGGCTAGTCA 59.737 61.111 0.00 0.00 43.68 3.41
424 425 1.808799 CAGCAGCACGGCTAGTCAG 60.809 63.158 0.00 0.00 43.68 3.51
425 426 2.510238 GCAGCACGGCTAGTCAGG 60.510 66.667 0.00 0.00 36.40 3.86
426 427 2.510238 CAGCACGGCTAGTCAGGC 60.510 66.667 0.00 0.00 43.81 4.85
427 428 3.775654 AGCACGGCTAGTCAGGCC 61.776 66.667 0.00 0.00 44.39 5.19
428 429 3.775654 GCACGGCTAGTCAGGCCT 61.776 66.667 0.00 0.00 46.73 5.19
429 430 2.496817 CACGGCTAGTCAGGCCTC 59.503 66.667 0.00 0.00 46.73 4.70
430 431 2.055042 CACGGCTAGTCAGGCCTCT 61.055 63.158 0.00 0.00 46.73 3.69
431 432 0.752009 CACGGCTAGTCAGGCCTCTA 60.752 60.000 0.00 0.72 46.73 2.43
432 433 0.186386 ACGGCTAGTCAGGCCTCTAT 59.814 55.000 0.00 0.00 46.73 1.98
433 434 0.885196 CGGCTAGTCAGGCCTCTATC 59.115 60.000 0.00 0.00 46.73 2.08
434 435 1.262417 GGCTAGTCAGGCCTCTATCC 58.738 60.000 0.00 3.68 45.57 2.59
435 436 1.481428 GGCTAGTCAGGCCTCTATCCA 60.481 57.143 0.00 0.00 45.57 3.41
436 437 2.320781 GCTAGTCAGGCCTCTATCCAA 58.679 52.381 0.00 0.00 0.00 3.53
437 438 2.700897 GCTAGTCAGGCCTCTATCCAAA 59.299 50.000 0.00 0.00 0.00 3.28
438 439 3.493524 GCTAGTCAGGCCTCTATCCAAAC 60.494 52.174 0.00 0.00 0.00 2.93
439 440 2.551270 AGTCAGGCCTCTATCCAAACA 58.449 47.619 0.00 0.00 0.00 2.83
440 441 2.503356 AGTCAGGCCTCTATCCAAACAG 59.497 50.000 0.00 0.00 0.00 3.16
441 442 1.839994 TCAGGCCTCTATCCAAACAGG 59.160 52.381 0.00 0.00 39.47 4.00
443 444 3.102090 GCCTCTATCCAAACAGGCC 57.898 57.895 0.00 0.00 45.04 5.19
444 445 0.815615 GCCTCTATCCAAACAGGCCG 60.816 60.000 0.00 0.00 45.04 6.13
457 458 1.078708 AGGCCGTAAATCCACACCG 60.079 57.895 0.00 0.00 0.00 4.94
472 473 0.317770 CACCGCACATCACAACAACC 60.318 55.000 0.00 0.00 0.00 3.77
488 495 3.770040 CCGACTGCATCCGGTCCA 61.770 66.667 16.12 0.00 43.11 4.02
489 496 2.202797 CGACTGCATCCGGTCCAG 60.203 66.667 0.00 9.20 43.11 3.86
493 518 3.391665 CTGCATCCGGTCCAGTCCC 62.392 68.421 0.00 0.00 0.00 4.46
556 581 2.125753 GCACGGAGCAGAGGTGAG 60.126 66.667 0.00 0.00 44.79 3.51
584 609 1.314534 TGGGCTGCCATGATTTGTCG 61.315 55.000 22.05 0.00 0.00 4.35
588 614 1.742831 GCTGCCATGATTTGTCGGTTA 59.257 47.619 0.00 0.00 0.00 2.85
594 620 2.396590 TGATTTGTCGGTTAGGCCTC 57.603 50.000 9.68 0.00 34.25 4.70
600 626 1.381327 TCGGTTAGGCCTCCTCTGG 60.381 63.158 9.68 0.00 34.61 3.86
624 650 4.322804 CAGATGCAAGAGCGAATCAAAAAC 59.677 41.667 0.00 0.00 46.23 2.43
633 659 4.754322 AGCGAATCAAAAACCAAAACAGT 58.246 34.783 0.00 0.00 0.00 3.55
637 663 4.856115 ATCAAAAACCAAAACAGTTGCG 57.144 36.364 0.00 0.00 0.00 4.85
651 677 0.524414 GTTGCGGGACCCACAATTAC 59.476 55.000 16.93 1.71 0.00 1.89
654 680 1.029947 GCGGGACCCACAATTACAGG 61.030 60.000 12.15 0.00 0.00 4.00
715 741 1.137675 CAAGAGGCAGATCCGATCACA 59.862 52.381 11.01 0.00 40.77 3.58
724 750 5.413833 GGCAGATCCGATCACATAATCAATT 59.586 40.000 11.01 0.00 0.00 2.32
743 769 0.246360 TATCATATCCAGGCGCGTGG 59.754 55.000 37.06 37.06 39.19 4.94
744 770 3.349006 CATATCCAGGCGCGTGGC 61.349 66.667 37.72 15.67 37.53 5.01
850 877 2.093500 TGCCACACTCAGCTAACCATAG 60.093 50.000 0.00 0.00 0.00 2.23
988 1024 1.754745 GAGGCTTGGTGGTCAGACA 59.245 57.895 2.17 0.00 0.00 3.41
989 1025 0.321122 GAGGCTTGGTGGTCAGACAG 60.321 60.000 2.17 0.00 0.00 3.51
990 1026 1.302832 GGCTTGGTGGTCAGACAGG 60.303 63.158 2.17 0.00 0.00 4.00
991 1027 1.302832 GCTTGGTGGTCAGACAGGG 60.303 63.158 2.17 0.00 0.00 4.45
1149 1194 3.090037 TCACTGTCTCTGTAGCCTAACC 58.910 50.000 0.00 0.00 0.00 2.85
1173 1219 5.219468 TCCAAATTATCATTTCCCCCAGT 57.781 39.130 0.00 0.00 29.41 4.00
1176 1222 5.304357 CCAAATTATCATTTCCCCCAGTACC 59.696 44.000 0.00 0.00 29.41 3.34
1179 1225 2.053747 TCATTTCCCCCAGTACCTGT 57.946 50.000 0.00 0.00 0.00 4.00
1191 1237 5.178797 CCCAGTACCTGTGAATCTTTGTAG 58.821 45.833 0.00 0.00 0.00 2.74
1192 1238 5.046591 CCCAGTACCTGTGAATCTTTGTAGA 60.047 44.000 0.00 0.00 34.21 2.59
1193 1239 6.464222 CCAGTACCTGTGAATCTTTGTAGAA 58.536 40.000 0.00 0.00 33.20 2.10
1194 1240 6.369065 CCAGTACCTGTGAATCTTTGTAGAAC 59.631 42.308 0.00 0.00 33.20 3.01
1209 1255 8.922676 TCTTTGTAGAACACTCAATTACGAATC 58.077 33.333 0.00 0.00 0.00 2.52
1247 1336 4.634012 TTATGCAGGAGTTAACACACCT 57.366 40.909 8.61 10.33 44.34 4.00
1358 1481 5.986501 TGAAACTTACCTTGTGTGGTTTT 57.013 34.783 0.00 0.00 41.22 2.43
1382 1505 1.214062 CACACGCCTCCTCACTCTC 59.786 63.158 0.00 0.00 0.00 3.20
1468 1591 0.470341 GGGAACTATCTGGGTGAGCC 59.530 60.000 0.00 0.00 0.00 4.70
1469 1592 1.204146 GGAACTATCTGGGTGAGCCA 58.796 55.000 2.31 2.31 36.17 4.75
1470 1593 1.771255 GGAACTATCTGGGTGAGCCAT 59.229 52.381 2.84 0.00 36.17 4.40
1471 1594 2.486191 GGAACTATCTGGGTGAGCCATG 60.486 54.545 2.84 0.00 36.17 3.66
1472 1595 2.180946 ACTATCTGGGTGAGCCATGA 57.819 50.000 2.84 4.53 36.17 3.07
1473 1596 2.045524 ACTATCTGGGTGAGCCATGAG 58.954 52.381 2.84 4.48 36.17 2.90
1474 1597 0.761187 TATCTGGGTGAGCCATGAGC 59.239 55.000 2.84 0.00 44.25 4.26
1680 1863 3.299524 CTGGCAATTTGTGGGGGCG 62.300 63.158 0.00 0.00 0.00 6.13
1732 1915 5.124457 GTGCTCCTTTCAGATGCAAAATCTA 59.876 40.000 0.00 0.00 35.34 1.98
1795 4049 8.429493 AGTTTAATTAGAATGCCGGTTAGTAC 57.571 34.615 1.90 0.00 0.00 2.73
1796 4050 8.262933 AGTTTAATTAGAATGCCGGTTAGTACT 58.737 33.333 1.90 0.00 0.00 2.73
1802 4056 9.623000 ATTAGAATGCCGGTTAGTACTAAAAAT 57.377 29.630 16.82 4.38 0.00 1.82
1811 4065 7.980099 CCGGTTAGTACTAAAAATCTCAGTGAT 59.020 37.037 16.82 0.00 36.89 3.06
1924 4488 5.215069 AGTCCAGGAGATCATATTCACTGT 58.785 41.667 0.00 0.00 0.00 3.55
2001 4566 3.002791 AGGTGTATGACGTGCTCAAATG 58.997 45.455 0.00 0.00 30.60 2.32
2042 4608 3.430790 CCATACAAGCTGGAATCGTCTCA 60.431 47.826 0.00 0.00 35.70 3.27
2052 4618 5.525378 GCTGGAATCGTCTCACAATTTCTAT 59.475 40.000 0.00 0.00 0.00 1.98
2056 4622 6.926272 GGAATCGTCTCACAATTTCTATAGCT 59.074 38.462 0.00 0.00 0.00 3.32
2060 4627 5.235186 CGTCTCACAATTTCTATAGCTTGGG 59.765 44.000 0.00 8.87 0.00 4.12
2201 4770 6.488006 AGAGGTTTGTGATGCCATTATATGTC 59.512 38.462 0.00 0.00 0.00 3.06
2443 5033 8.696043 ATTGCCATCTATAAATTTGCTCTGTA 57.304 30.769 0.00 0.00 0.00 2.74
2447 5037 8.786898 GCCATCTATAAATTTGCTCTGTAATCA 58.213 33.333 0.00 0.00 0.00 2.57
2518 5121 5.012046 ACCATACTCTTCTGTTCATGTGACA 59.988 40.000 0.00 0.00 0.00 3.58
2669 5276 3.797039 TGTCTTGACAGGAAACTCACAG 58.203 45.455 0.00 0.00 40.21 3.66
2719 5330 8.429739 TTTATTTTCAGATAAGTTTGTTCGCG 57.570 30.769 0.00 0.00 0.00 5.87
2782 5393 6.192044 TCCTTTTGTCCTCAAGGTTAAGTTT 58.808 36.000 0.00 0.00 40.59 2.66
2786 5397 4.714632 TGTCCTCAAGGTTAAGTTTCCTG 58.285 43.478 0.00 0.00 33.97 3.86
3092 6018 6.899089 TCCTTTGCAGGAGATCATAAATACA 58.101 36.000 0.00 0.00 45.20 2.29
3093 6019 6.994496 TCCTTTGCAGGAGATCATAAATACAG 59.006 38.462 0.00 0.00 45.20 2.74
3094 6020 6.769822 CCTTTGCAGGAGATCATAAATACAGT 59.230 38.462 0.00 0.00 44.19 3.55
3095 6021 7.255035 CCTTTGCAGGAGATCATAAATACAGTG 60.255 40.741 0.00 0.00 44.19 3.66
3217 6310 5.117355 TGAAGTAAGTTCGTTCGAGTCAT 57.883 39.130 0.00 0.00 38.09 3.06
3218 6311 5.526115 TGAAGTAAGTTCGTTCGAGTCATT 58.474 37.500 0.00 0.00 38.09 2.57
3219 6312 6.671190 TGAAGTAAGTTCGTTCGAGTCATTA 58.329 36.000 0.00 0.00 38.09 1.90
3220 6313 7.310664 TGAAGTAAGTTCGTTCGAGTCATTAT 58.689 34.615 0.00 0.00 38.09 1.28
3221 6314 8.453320 TGAAGTAAGTTCGTTCGAGTCATTATA 58.547 33.333 0.00 0.00 38.09 0.98
3222 6315 8.612233 AAGTAAGTTCGTTCGAGTCATTATAC 57.388 34.615 0.00 0.00 0.00 1.47
3229 6322 9.327529 GTTCGTTCGAGTCATTATACTTATAGG 57.672 37.037 0.00 0.00 0.00 2.57
3268 6377 4.816925 GTGAGAACCTAACACTTTGCTTCT 59.183 41.667 0.00 0.00 0.00 2.85
3269 6378 5.989777 GTGAGAACCTAACACTTTGCTTCTA 59.010 40.000 0.00 0.00 0.00 2.10
3275 6384 6.970484 ACCTAACACTTTGCTTCTAAATGTG 58.030 36.000 0.00 0.00 0.00 3.21
3692 6826 9.745018 ACTACTTGTAGTAAGGTAATACAGACA 57.255 33.333 11.27 0.00 39.90 3.41
3759 6894 8.095452 ACTTACCTCCTTCATGAATCATTAGT 57.905 34.615 8.96 5.11 0.00 2.24
3822 6957 8.217111 TCATTACAGCATGGACCAAGATATTTA 58.783 33.333 0.00 0.00 43.62 1.40
3830 6965 9.196552 GCATGGACCAAGATATTTAAAAATAGC 57.803 33.333 0.00 3.13 37.50 2.97
3878 7013 4.870426 TCTGAACAACAGTGAACTTCTGAC 59.130 41.667 0.00 0.00 45.86 3.51
3954 7089 4.628333 CCAATTTCATGTGTCAAAGATGCC 59.372 41.667 0.00 0.00 29.55 4.40
4031 7166 7.167535 TCTCCATCGCATTTATCATTCCATTA 58.832 34.615 0.00 0.00 0.00 1.90
4096 7231 5.832595 TGAATTCAGTCAAGAAAACATCCCA 59.167 36.000 3.38 0.00 0.00 4.37
4097 7232 6.323482 TGAATTCAGTCAAGAAAACATCCCAA 59.677 34.615 3.38 0.00 0.00 4.12
4098 7233 6.923199 ATTCAGTCAAGAAAACATCCCAAT 57.077 33.333 0.00 0.00 0.00 3.16
4199 7352 1.273041 ACATGGGGAAAAACCTAGGCC 60.273 52.381 9.30 0.00 38.98 5.19
4291 7445 3.077359 CTCCTTTCAACGGCATCTTCTT 58.923 45.455 0.00 0.00 0.00 2.52
4345 7499 4.929819 TGAATAGGCGACAGTAATAGCA 57.070 40.909 0.00 0.00 0.00 3.49
4346 7500 5.468540 TGAATAGGCGACAGTAATAGCAT 57.531 39.130 0.00 0.00 0.00 3.79
4390 7544 3.557054 CCATTCCGACAGTTCTTCCTCAA 60.557 47.826 0.00 0.00 0.00 3.02
4413 7567 1.745115 GCACATTACCCGAGCAGCA 60.745 57.895 0.00 0.00 0.00 4.41
4414 7568 1.709147 GCACATTACCCGAGCAGCAG 61.709 60.000 0.00 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 7.335171 CACATACCATCAAGAAGAAATCTGTCA 59.665 37.037 0.00 0.00 38.79 3.58
18 19 6.600822 CCACACATACCATCAAGAAGAAATCT 59.399 38.462 0.00 0.00 41.32 2.40
19 20 6.183360 CCCACACATACCATCAAGAAGAAATC 60.183 42.308 0.00 0.00 0.00 2.17
29 30 2.026356 CCAAGACCCACACATACCATCA 60.026 50.000 0.00 0.00 0.00 3.07
31 32 1.284785 CCCAAGACCCACACATACCAT 59.715 52.381 0.00 0.00 0.00 3.55
39 40 2.228480 GCTACCCCCAAGACCCACA 61.228 63.158 0.00 0.00 0.00 4.17
41 42 2.612746 GGCTACCCCCAAGACCCA 60.613 66.667 0.00 0.00 0.00 4.51
51 52 0.105039 CTCGGTTGATCTGGCTACCC 59.895 60.000 0.00 0.00 31.19 3.69
58 59 4.208632 GGCACCTCGGTTGATCTG 57.791 61.111 0.00 0.00 0.00 2.90
88 89 7.091443 ACTTGGACGAAAAATGTTAAAACACA 58.909 30.769 0.00 0.00 42.51 3.72
94 95 8.535690 ACAAAAACTTGGACGAAAAATGTTAA 57.464 26.923 0.00 0.00 0.00 2.01
107 108 5.452077 CCCGGTTAATTGACAAAAACTTGGA 60.452 40.000 18.91 0.00 0.00 3.53
109 110 4.210328 GCCCGGTTAATTGACAAAAACTTG 59.790 41.667 0.00 8.52 0.00 3.16
111 112 3.385111 TGCCCGGTTAATTGACAAAAACT 59.615 39.130 0.00 0.00 0.00 2.66
127 128 3.490348 AGGATAGATGAAAATTGCCCGG 58.510 45.455 0.00 0.00 0.00 5.73
129 130 9.836864 ATTAAAAAGGATAGATGAAAATTGCCC 57.163 29.630 0.00 0.00 0.00 5.36
148 149 8.311109 GCCCTTGGAAGTCTGATTTATTAAAAA 58.689 33.333 0.00 0.00 0.00 1.94
152 153 6.073447 TGCCCTTGGAAGTCTGATTTATTA 57.927 37.500 0.00 0.00 0.00 0.98
153 154 4.934356 TGCCCTTGGAAGTCTGATTTATT 58.066 39.130 0.00 0.00 0.00 1.40
164 165 2.426024 CAAGTCATGATGCCCTTGGAAG 59.574 50.000 13.42 0.00 32.57 3.46
173 174 6.492007 TTCTCTTTTCTCAAGTCATGATGC 57.508 37.500 0.00 0.00 37.44 3.91
194 195 5.718146 TGGCATTATCGATGAGAGAGATTC 58.282 41.667 8.54 0.00 38.03 2.52
243 244 1.003349 TGCCAATTTTGATGCTTGGGG 59.997 47.619 3.01 0.00 39.85 4.96
275 276 3.088552 CTCAACACGACACGTTTTGTTC 58.911 45.455 17.92 0.00 44.45 3.18
294 295 2.344025 ACAAAATTCCTACGGACGCTC 58.656 47.619 0.00 0.00 0.00 5.03
331 332 1.594331 GTGAAATGGGTATCTCGGCC 58.406 55.000 0.00 0.00 0.00 6.13
389 390 0.531974 CTGGCGTGGCACGGTTATAT 60.532 55.000 37.33 0.00 42.82 0.86
407 408 2.575993 CTGACTAGCCGTGCTGCT 59.424 61.111 8.44 0.00 45.38 4.24
420 421 2.420687 CCTGTTTGGATAGAGGCCTGAC 60.421 54.545 12.00 0.00 38.35 3.51
421 422 1.839994 CCTGTTTGGATAGAGGCCTGA 59.160 52.381 12.00 0.00 38.35 3.86
422 423 1.748591 GCCTGTTTGGATAGAGGCCTG 60.749 57.143 12.00 0.00 44.54 4.85
423 424 0.548510 GCCTGTTTGGATAGAGGCCT 59.451 55.000 3.86 3.86 44.54 5.19
424 425 3.102090 GCCTGTTTGGATAGAGGCC 57.898 57.895 0.00 0.00 44.54 5.19
426 427 0.541863 ACGGCCTGTTTGGATAGAGG 59.458 55.000 0.00 0.00 38.35 3.69
427 428 3.536956 TTACGGCCTGTTTGGATAGAG 57.463 47.619 0.00 0.00 38.35 2.43
428 429 3.985019 TTTACGGCCTGTTTGGATAGA 57.015 42.857 0.00 0.00 38.35 1.98
429 430 3.564225 GGATTTACGGCCTGTTTGGATAG 59.436 47.826 0.00 0.00 38.35 2.08
430 431 3.054287 TGGATTTACGGCCTGTTTGGATA 60.054 43.478 0.00 0.00 38.35 2.59
431 432 2.291282 TGGATTTACGGCCTGTTTGGAT 60.291 45.455 0.00 0.00 38.35 3.41
432 433 1.074084 TGGATTTACGGCCTGTTTGGA 59.926 47.619 0.00 0.00 38.35 3.53
433 434 1.201414 GTGGATTTACGGCCTGTTTGG 59.799 52.381 0.00 0.00 39.35 3.28
434 435 1.883275 TGTGGATTTACGGCCTGTTTG 59.117 47.619 0.00 0.00 0.00 2.93
435 436 1.883926 GTGTGGATTTACGGCCTGTTT 59.116 47.619 0.00 0.00 0.00 2.83
436 437 1.530323 GTGTGGATTTACGGCCTGTT 58.470 50.000 0.00 0.00 0.00 3.16
437 438 0.322187 GGTGTGGATTTACGGCCTGT 60.322 55.000 0.00 2.95 0.00 4.00
438 439 1.366111 CGGTGTGGATTTACGGCCTG 61.366 60.000 0.00 0.00 0.00 4.85
439 440 1.078708 CGGTGTGGATTTACGGCCT 60.079 57.895 0.00 0.00 0.00 5.19
440 441 2.757056 GCGGTGTGGATTTACGGCC 61.757 63.158 0.00 0.00 37.22 6.13
441 442 2.036006 TGCGGTGTGGATTTACGGC 61.036 57.895 0.00 0.00 41.67 5.68
442 443 0.951525 TGTGCGGTGTGGATTTACGG 60.952 55.000 0.00 0.00 0.00 4.02
443 444 1.062002 GATGTGCGGTGTGGATTTACG 59.938 52.381 0.00 0.00 0.00 3.18
444 445 2.080693 TGATGTGCGGTGTGGATTTAC 58.919 47.619 0.00 0.00 0.00 2.01
457 458 0.944386 AGTCGGTTGTTGTGATGTGC 59.056 50.000 0.00 0.00 0.00 4.57
472 473 2.202797 CTGGACCGGATGCAGTCG 60.203 66.667 9.46 0.00 41.70 4.18
488 495 2.224159 ATGGCGACTTGTGGGGACT 61.224 57.895 0.00 0.00 0.00 3.85
489 496 2.040544 CATGGCGACTTGTGGGGAC 61.041 63.158 0.00 0.00 0.00 4.46
556 581 2.520260 GGCAGCCCATGTCCCATC 60.520 66.667 0.00 0.00 0.00 3.51
580 605 0.970937 CAGAGGAGGCCTAACCGACA 60.971 60.000 4.42 0.00 46.52 4.35
600 626 1.012086 TGATTCGCTCTTGCATCTGC 58.988 50.000 0.00 0.00 39.64 4.26
624 650 1.362355 GGTCCCGCAACTGTTTTGG 59.638 57.895 0.00 0.00 0.00 3.28
637 663 0.039035 TGCCTGTAATTGTGGGTCCC 59.961 55.000 0.00 0.00 0.00 4.46
675 701 4.924305 TGCAAATAGTAGTACTACCCCG 57.076 45.455 25.97 13.34 36.75 5.73
678 704 5.984323 GCCTCTTGCAAATAGTAGTACTACC 59.016 44.000 25.97 12.37 40.77 3.18
715 741 6.203530 CGCGCCTGGATATGATAATTGATTAT 59.796 38.462 0.00 0.00 35.77 1.28
724 750 0.246360 CCACGCGCCTGGATATGATA 59.754 55.000 19.37 0.00 32.30 2.15
729 755 4.830765 GTGCCACGCGCCTGGATA 62.831 66.667 26.87 13.05 36.24 2.59
743 769 2.358898 TGTTTTCTTCTTCCTGCTGTGC 59.641 45.455 0.00 0.00 0.00 4.57
744 770 4.843220 ATGTTTTCTTCTTCCTGCTGTG 57.157 40.909 0.00 0.00 0.00 3.66
850 877 1.912371 GCTGGGCTCGTGCAGTAAAC 61.912 60.000 12.07 0.00 41.91 2.01
927 963 5.394333 GCAGGGGAGAGATAATATACGGTTC 60.394 48.000 0.00 0.00 0.00 3.62
938 974 1.548809 CGGAGATGCAGGGGAGAGATA 60.549 57.143 0.00 0.00 0.00 1.98
990 1026 0.325671 TGGTCTCCATGGGTCTCTCC 60.326 60.000 13.02 7.08 0.00 3.71
991 1027 1.484240 CTTGGTCTCCATGGGTCTCTC 59.516 57.143 13.02 0.00 31.53 3.20
1041 1084 2.038007 AGCTGGCCGAGGAAGAGA 59.962 61.111 0.00 0.00 0.00 3.10
1122 1165 2.165437 GCTACAGAGACAGTGAGAAGGG 59.835 54.545 0.00 0.00 0.00 3.95
1149 1194 5.603813 ACTGGGGGAAATGATAATTTGGATG 59.396 40.000 0.00 0.00 0.00 3.51
1173 1219 7.062749 AGTGTTCTACAAAGATTCACAGGTA 57.937 36.000 11.15 0.00 38.39 3.08
1176 1222 7.482654 TTGAGTGTTCTACAAAGATTCACAG 57.517 36.000 11.15 0.00 38.39 3.66
1179 1225 8.708742 CGTAATTGAGTGTTCTACAAAGATTCA 58.291 33.333 0.00 0.00 0.00 2.57
1191 1237 4.693566 TGGGTGATTCGTAATTGAGTGTTC 59.306 41.667 0.00 0.00 0.00 3.18
1192 1238 4.647611 TGGGTGATTCGTAATTGAGTGTT 58.352 39.130 0.00 0.00 0.00 3.32
1193 1239 4.280436 TGGGTGATTCGTAATTGAGTGT 57.720 40.909 0.00 0.00 0.00 3.55
1194 1240 4.025730 CGATGGGTGATTCGTAATTGAGTG 60.026 45.833 0.00 0.00 0.00 3.51
1209 1255 5.160699 GCATAATATACATGCGATGGGTG 57.839 43.478 6.49 0.00 39.43 4.61
1247 1336 2.612972 GGCGAAGAAGGATTGTGTGAGA 60.613 50.000 0.00 0.00 0.00 3.27
1358 1481 1.000506 GTGAGGAGGCGTGTGAAACTA 59.999 52.381 0.00 0.00 38.04 2.24
1369 1492 1.730451 GGCGTAGAGAGTGAGGAGGC 61.730 65.000 0.00 0.00 0.00 4.70
1382 1505 0.737715 GCAAGACAGGAGTGGCGTAG 60.738 60.000 0.00 0.00 36.45 3.51
1468 1591 0.530744 ATTGCCTGCTTGTGCTCATG 59.469 50.000 0.00 0.00 40.48 3.07
1469 1592 1.747355 GTATTGCCTGCTTGTGCTCAT 59.253 47.619 0.00 0.00 40.48 2.90
1470 1593 1.167851 GTATTGCCTGCTTGTGCTCA 58.832 50.000 0.00 0.00 40.48 4.26
1471 1594 1.135575 GTGTATTGCCTGCTTGTGCTC 60.136 52.381 0.00 0.00 40.48 4.26
1472 1595 0.883833 GTGTATTGCCTGCTTGTGCT 59.116 50.000 0.00 0.00 40.48 4.40
1473 1596 0.597568 TGTGTATTGCCTGCTTGTGC 59.402 50.000 0.00 0.00 40.20 4.57
1474 1597 3.581024 AATGTGTATTGCCTGCTTGTG 57.419 42.857 0.00 0.00 0.00 3.33
1704 1887 1.471684 GCATCTGAAAGGAGCACAAGG 59.528 52.381 0.00 0.00 34.90 3.61
1732 1915 7.789202 ACTCATATATACCTTGCTCATCTGT 57.211 36.000 0.00 0.00 0.00 3.41
1802 4056 9.916360 TGTATCTTACTAGGTTTATCACTGAGA 57.084 33.333 0.00 0.00 0.00 3.27
1811 4065 8.692710 CATCCTGTGTGTATCTTACTAGGTTTA 58.307 37.037 0.00 0.00 0.00 2.01
1888 4142 1.002684 CCTGGACTACTGTACGATCGC 60.003 57.143 16.60 0.00 0.00 4.58
1924 4488 9.598517 AGCTGTAAATTTTTGAACAAGATTCAA 57.401 25.926 0.00 0.00 36.71 2.69
2001 4566 7.718525 TGTATGGGTCTTAAAGTTTGGTTTTC 58.281 34.615 0.00 0.00 0.00 2.29
2042 4608 6.318900 GCACTTACCCAAGCTATAGAAATTGT 59.681 38.462 3.21 0.00 34.94 2.71
2052 4618 2.168521 CTGCTAGCACTTACCCAAGCTA 59.831 50.000 14.93 0.00 38.47 3.32
2056 4622 0.984230 AGCTGCTAGCACTTACCCAA 59.016 50.000 14.93 0.00 45.56 4.12
2060 4627 5.383130 GTTTTGTAAGCTGCTAGCACTTAC 58.617 41.667 34.31 34.31 45.56 2.34
2201 4770 9.213799 GAAAATATTGCTGGATAGTAGGAAGAG 57.786 37.037 0.00 0.00 0.00 2.85
2248 4827 6.636454 TTCCTACATATTCAAGGGAAGTGT 57.364 37.500 0.00 0.00 38.53 3.55
2251 4831 8.432805 ACAGTATTCCTACATATTCAAGGGAAG 58.567 37.037 0.00 0.00 36.49 3.46
2431 5015 8.542497 TTAACTACGTGATTACAGAGCAAATT 57.458 30.769 0.00 0.00 0.00 1.82
2496 5088 6.648310 AGTTGTCACATGAACAGAAGAGTATG 59.352 38.462 0.00 0.00 0.00 2.39
2518 5121 7.823745 ATCTGATGTTTTGTCAGGTTAAGTT 57.176 32.000 3.58 0.00 42.58 2.66
2782 5393 1.825090 CTGCCTAACATGTTGCAGGA 58.175 50.000 29.81 16.50 45.69 3.86
2786 5397 5.289434 GCTTATTTTCTGCCTAACATGTTGC 59.711 40.000 21.42 16.62 0.00 4.17
3217 6310 7.849322 TCTGCACATGGACCTATAAGTATAA 57.151 36.000 0.00 0.00 0.00 0.98
3218 6311 9.715119 ATATCTGCACATGGACCTATAAGTATA 57.285 33.333 0.00 0.00 0.00 1.47
3219 6312 6.942163 ATCTGCACATGGACCTATAAGTAT 57.058 37.500 0.00 0.00 0.00 2.12
3220 6313 7.454694 ACATATCTGCACATGGACCTATAAGTA 59.545 37.037 0.00 0.00 0.00 2.24
3221 6314 6.270927 ACATATCTGCACATGGACCTATAAGT 59.729 38.462 0.00 0.00 0.00 2.24
3222 6315 6.592994 CACATATCTGCACATGGACCTATAAG 59.407 42.308 0.00 0.00 0.00 1.73
3229 6322 4.063998 TCTCACATATCTGCACATGGAC 57.936 45.455 0.00 0.00 0.00 4.02
3268 6377 7.272244 TGAAGAACTCTCACTTCACACATTTA 58.728 34.615 0.00 0.00 44.59 1.40
3269 6378 6.115446 TGAAGAACTCTCACTTCACACATTT 58.885 36.000 0.00 0.00 44.59 2.32
3275 6384 3.063485 GGCTGAAGAACTCTCACTTCAC 58.937 50.000 0.00 0.00 44.59 3.18
3390 6502 3.068732 GCTCCTTCCAGTTGCTTCTTTTT 59.931 43.478 0.00 0.00 0.00 1.94
3542 6671 7.432252 CCATCCTAACACAAAATATTCTTTCGC 59.568 37.037 0.00 0.00 0.00 4.70
3594 6724 6.032956 TGTTACCAAGTATGTACTGGACTG 57.967 41.667 5.17 1.05 36.50 3.51
3692 6826 5.721480 CCTGTTTTCCCCTCTCCATATTTTT 59.279 40.000 0.00 0.00 0.00 1.94
3759 6894 5.005740 CCAGTGATGAATTTCTGTGGAGAA 58.994 41.667 0.00 0.00 36.36 2.87
3822 6957 3.803368 GCTGTGGGCAGTTTGCTATTTTT 60.803 43.478 0.67 0.00 44.28 1.94
3830 6965 1.108727 TTCAGGCTGTGGGCAGTTTG 61.109 55.000 15.27 0.00 44.32 2.93
4037 7172 8.801299 TGATGTTTCAAGTTGCATATCCTTTTA 58.199 29.630 0.00 0.00 0.00 1.52
4038 7173 7.669427 TGATGTTTCAAGTTGCATATCCTTTT 58.331 30.769 0.00 0.00 0.00 2.27
4199 7352 6.407202 ACTAGTGTTTACTGGATAGCCTTTG 58.593 40.000 0.00 0.00 37.58 2.77
4213 7367 7.416438 GCTCCTACTCAATGCTACTAGTGTTTA 60.416 40.741 5.39 0.00 0.00 2.01
4291 7445 5.125356 CACACAATATGGTCTGATTGCCTA 58.875 41.667 0.00 0.00 36.67 3.93
4390 7544 1.065491 TGCTCGGGTAATGTGCAAGAT 60.065 47.619 0.00 0.00 33.39 2.40


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

AutoCloner maintained by Alex Coulton.