Multiple sequence alignment - TraesCS7A01G547400

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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 TraesCS7A01G547400 chr7A 100.000 2863 0 0 1 2863 722591136 722593998 0.000000e+00 5288.0
1 TraesCS7A01G547400 chr7A 87.363 182 21 2 276 455 722580606 722580787 1.040000e-49 207.0
2 TraesCS7A01G547400 chr7B 92.616 1246 67 9 869 2104 727639585 727638355 0.000000e+00 1768.0
3 TraesCS7A01G547400 chr7B 89.590 634 46 11 228 845 727640439 727639810 0.000000e+00 787.0
4 TraesCS7A01G547400 chr7B 86.408 309 34 6 222 528 727645364 727645062 5.910000e-87 331.0
5 TraesCS7A01G547400 chr7B 85.570 298 41 2 2535 2831 663491103 663490807 7.700000e-81 311.0
6 TraesCS7A01G547400 chr7B 82.124 386 47 14 2152 2529 742472164 742471793 7.700000e-81 311.0
7 TraesCS7A01G547400 chr7B 87.225 227 26 3 276 499 727649965 727649739 3.660000e-64 255.0
8 TraesCS7A01G547400 chr7B 82.295 305 43 9 2222 2520 702271100 702270801 1.320000e-63 254.0
9 TraesCS7A01G547400 chr7B 86.829 205 17 2 4 198 727640778 727640574 1.340000e-53 220.0
10 TraesCS7A01G547400 chr7B 81.319 91 9 2 27 117 727645672 727645590 1.840000e-07 67.6
11 TraesCS7A01G547400 chr7D 92.996 1128 63 7 869 1984 627085783 627086906 0.000000e+00 1631.0
12 TraesCS7A01G547400 chr7D 90.283 494 27 13 228 705 627084948 627085436 6.730000e-176 627.0
13 TraesCS7A01G547400 chr7D 94.675 169 9 0 1 169 627084594 627084762 2.190000e-66 263.0
14 TraesCS7A01G547400 chr7D 83.594 256 32 6 228 483 627080206 627080451 6.170000e-57 231.0
15 TraesCS7A01G547400 chr7D 91.429 70 4 2 2007 2076 627087024 627087091 8.440000e-16 95.3
16 TraesCS7A01G547400 chr7D 77.027 148 22 7 27 171 627079852 627079990 1.100000e-09 75.0
17 TraesCS7A01G547400 chr7D 89.130 46 3 2 21 64 626911290 626911335 3.980000e-04 56.5
18 TraesCS7A01G547400 chr4D 88.926 298 30 3 2535 2831 23267423 23267128 5.830000e-97 364.0
19 TraesCS7A01G547400 chr4D 82.383 386 46 12 2150 2529 419334005 419333636 1.660000e-82 316.0
20 TraesCS7A01G547400 chr6A 88.079 302 34 2 2535 2835 20278193 20277893 9.750000e-95 357.0
21 TraesCS7A01G547400 chr3D 87.869 305 35 2 2532 2835 449122256 449121953 9.750000e-95 357.0
22 TraesCS7A01G547400 chr3D 87.889 289 33 2 2535 2822 100546661 100546374 3.530000e-89 339.0
23 TraesCS7A01G547400 chr3D 93.617 47 3 0 2150 2196 100547282 100547236 1.420000e-08 71.3
24 TraesCS7A01G547400 chr2D 87.879 297 31 4 2529 2822 636235741 636236035 7.590000e-91 344.0
25 TraesCS7A01G547400 chr2D 82.741 394 46 13 2144 2530 636225186 636225564 5.910000e-87 331.0
26 TraesCS7A01G547400 chr2B 86.557 305 38 3 2529 2831 207723496 207723193 1.640000e-87 333.0
27 TraesCS7A01G547400 chr1B 86.379 301 39 2 2532 2831 669785063 669785362 7.650000e-86 327.0
28 TraesCS7A01G547400 chr1B 80.829 386 51 15 2150 2527 669784643 669785013 6.040000e-72 281.0
29 TraesCS7A01G547400 chr1B 79.634 383 54 16 2150 2527 390611359 390610996 1.320000e-63 254.0
30 TraesCS7A01G547400 chr3A 85.714 301 41 2 2532 2831 716994633 716994932 1.660000e-82 316.0
31 TraesCS7A01G547400 chr3A 80.457 394 53 16 2142 2527 716994206 716994583 2.170000e-71 279.0
32 TraesCS7A01G547400 chr3B 80.829 386 48 17 2150 2527 823318996 823319363 2.170000e-71 279.0
33 TraesCS7A01G547400 chr1A 80.362 387 56 10 2148 2529 492869122 492869493 2.810000e-70 276.0
34 TraesCS7A01G547400 chr2A 79.737 380 54 16 2154 2527 703112339 703112701 1.320000e-63 254.0
35 TraesCS7A01G547400 chr5A 79.948 384 40 20 2150 2529 436989530 436989180 6.130000e-62 248.0
36 TraesCS7A01G547400 chr4A 81.150 313 49 6 2219 2529 702260676 702260980 2.850000e-60 243.0
37 TraesCS7A01G547400 chr6B 78.866 388 52 18 2150 2527 690179124 690178757 4.770000e-58 235.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G547400 chr7A 722591136 722593998 2862 False 5288.000 5288 100.000000 1 2863 1 chr7A.!!$F2 2862
1 TraesCS7A01G547400 chr7B 727638355 727640778 2423 True 925.000 1768 89.678333 4 2104 3 chr7B.!!$R5 2100
2 TraesCS7A01G547400 chr7D 627084594 627087091 2497 False 654.075 1631 92.345750 1 2076 4 chr7D.!!$F3 2075
3 TraesCS7A01G547400 chr3D 100546374 100547282 908 True 205.150 339 90.753000 2150 2822 2 chr3D.!!$R2 672
4 TraesCS7A01G547400 chr1B 669784643 669785362 719 False 304.000 327 83.604000 2150 2831 2 chr1B.!!$F1 681
5 TraesCS7A01G547400 chr3A 716994206 716994932 726 False 297.500 316 83.085500 2142 2831 2 chr3A.!!$F1 689

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
322 471 0.248215 CGGCCACGAGATTTGCAATC 60.248 55.0 2.24 0.09 44.6 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2238 2758 0.106669 ATGACTCCCTCCGATGACGA 60.107 55.0 0.0 0.0 42.66 4.2 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 1.375396 TGCGGCGCTTGATAGTGTT 60.375 52.632 33.26 0.00 34.31 3.32
33 34 2.288025 TGTTGGTCGGCCTAGGGTC 61.288 63.158 11.72 0.00 35.27 4.46
41 46 1.043673 CGGCCTAGGGTCTTACAGCT 61.044 60.000 11.72 0.00 0.00 4.24
155 166 9.937175 GCTAGGTAGTTGCTCTATTTAATTTTG 57.063 33.333 0.00 0.00 0.00 2.44
198 232 2.485479 GGCTCTCAAGTGTTCAAGTGGA 60.485 50.000 0.00 0.00 0.00 4.02
199 233 3.406764 GCTCTCAAGTGTTCAAGTGGAT 58.593 45.455 0.00 0.00 0.00 3.41
200 234 3.434984 GCTCTCAAGTGTTCAAGTGGATC 59.565 47.826 0.00 0.00 0.00 3.36
201 235 4.635223 CTCTCAAGTGTTCAAGTGGATCA 58.365 43.478 0.00 0.00 0.00 2.92
202 236 5.233083 TCTCAAGTGTTCAAGTGGATCAT 57.767 39.130 0.00 0.00 0.00 2.45
203 237 5.624159 TCTCAAGTGTTCAAGTGGATCATT 58.376 37.500 0.00 0.00 0.00 2.57
204 238 5.471116 TCTCAAGTGTTCAAGTGGATCATTG 59.529 40.000 0.00 0.00 0.00 2.82
205 239 4.520111 TCAAGTGTTCAAGTGGATCATTGG 59.480 41.667 0.00 0.00 0.00 3.16
219 368 5.686159 GATCATTGGATCCAGTTGCTTAG 57.314 43.478 15.53 0.00 43.44 2.18
220 369 4.574674 TCATTGGATCCAGTTGCTTAGT 57.425 40.909 15.53 0.00 0.00 2.24
221 370 4.922206 TCATTGGATCCAGTTGCTTAGTT 58.078 39.130 15.53 0.00 0.00 2.24
222 371 5.324409 TCATTGGATCCAGTTGCTTAGTTT 58.676 37.500 15.53 0.00 0.00 2.66
223 372 5.183713 TCATTGGATCCAGTTGCTTAGTTTG 59.816 40.000 15.53 0.00 0.00 2.93
224 373 4.365514 TGGATCCAGTTGCTTAGTTTGA 57.634 40.909 11.44 0.00 0.00 2.69
225 374 4.922206 TGGATCCAGTTGCTTAGTTTGAT 58.078 39.130 11.44 0.00 0.00 2.57
226 375 4.943705 TGGATCCAGTTGCTTAGTTTGATC 59.056 41.667 11.44 0.00 0.00 2.92
232 381 5.455392 CAGTTGCTTAGTTTGATCCAGTTG 58.545 41.667 0.00 0.00 0.00 3.16
257 406 1.312371 TGGCAACTGGATAAAGCGCC 61.312 55.000 2.29 0.00 38.79 6.53
277 426 2.288729 CCAGGCATGTACGATGAATGTG 59.711 50.000 0.00 1.92 0.00 3.21
278 427 1.942657 AGGCATGTACGATGAATGTGC 59.057 47.619 8.81 0.00 0.00 4.57
282 431 3.002553 GCATGTACGATGAATGTGCATCA 59.997 43.478 0.00 0.00 43.76 3.07
322 471 0.248215 CGGCCACGAGATTTGCAATC 60.248 55.000 2.24 0.09 44.60 2.67
360 509 0.608130 TGAGGACCTGTCATGTTCCG 59.392 55.000 0.00 0.00 0.00 4.30
383 532 2.359850 GTGGACATTGCGAGGCCA 60.360 61.111 5.01 0.00 0.00 5.36
461 610 2.143122 GATCGGACAAGCAAGACACAA 58.857 47.619 0.00 0.00 0.00 3.33
475 624 1.269998 GACACAACGAGTAGGTCAGCT 59.730 52.381 0.00 0.00 0.00 4.24
506 655 0.753111 CATGGCCTGTAAGCTTCCCC 60.753 60.000 0.00 0.00 0.00 4.81
507 656 1.214305 ATGGCCTGTAAGCTTCCCCA 61.214 55.000 0.00 4.06 0.00 4.96
558 707 0.385751 TGTGATCGGAGAGATTCGCC 59.614 55.000 0.00 0.00 43.63 5.54
572 721 1.433053 TTCGCCCGTGCCGATTATTG 61.433 55.000 0.00 0.00 34.35 1.90
575 724 1.301423 GCCCGTGCCGATTATTGTAA 58.699 50.000 0.00 0.00 0.00 2.41
577 726 1.263217 CCCGTGCCGATTATTGTAAGC 59.737 52.381 0.00 0.00 0.00 3.09
578 727 1.070843 CCGTGCCGATTATTGTAAGCG 60.071 52.381 0.83 0.83 0.00 4.68
579 728 1.591158 CGTGCCGATTATTGTAAGCGT 59.409 47.619 6.62 0.00 0.00 5.07
580 729 2.347292 CGTGCCGATTATTGTAAGCGTC 60.347 50.000 6.62 0.00 0.00 5.19
582 731 1.856597 GCCGATTATTGTAAGCGTCGT 59.143 47.619 6.62 0.00 0.00 4.34
691 856 1.137513 GTCTTCACCAAAGTCGTCGG 58.862 55.000 0.00 0.00 36.31 4.79
706 888 1.527148 TCGGCCCTCTCGATCTCAG 60.527 63.158 0.00 0.00 0.00 3.35
966 1370 2.559668 AGTGCCATTCCAACATCACAAG 59.440 45.455 0.00 0.00 0.00 3.16
967 1371 2.557924 GTGCCATTCCAACATCACAAGA 59.442 45.455 0.00 0.00 0.00 3.02
969 1373 2.414559 GCCATTCCAACATCACAAGACG 60.415 50.000 0.00 0.00 0.00 4.18
1233 1649 2.507102 CACTCGTACCTGCCGCTG 60.507 66.667 0.00 0.00 0.00 5.18
1302 1718 2.512515 GCCTACGGCTGCTTCCTG 60.513 66.667 0.00 0.00 46.69 3.86
1473 1889 2.872388 CGTGCCAGTCCACACCTCT 61.872 63.158 0.00 0.00 35.47 3.69
1486 1905 2.042435 CCTCTTCCTCCTCCGCCT 60.042 66.667 0.00 0.00 0.00 5.52
1491 1910 4.816984 TCCTCCTCCGCCTCGTCC 62.817 72.222 0.00 0.00 0.00 4.79
1492 1911 4.824515 CCTCCTCCGCCTCGTCCT 62.825 72.222 0.00 0.00 0.00 3.85
1623 2042 3.386237 GCGTCCTCCTCTGCCACT 61.386 66.667 0.00 0.00 0.00 4.00
1636 2055 4.697756 CCACTTCGCCCAAGCCGA 62.698 66.667 0.00 0.00 35.17 5.54
1651 2070 3.043713 CGAGGCTTGCGCTTGTGA 61.044 61.111 9.73 0.00 36.09 3.58
1767 2186 2.048127 AGCGAGAAGGTGTTCCGC 60.048 61.111 10.89 10.89 45.26 5.54
1774 2193 3.883744 AAGGTGTTCCGCAGCCTCG 62.884 63.158 0.00 0.00 46.08 4.63
1813 2232 1.915614 GCTCAACATCCACACGCCAG 61.916 60.000 0.00 0.00 0.00 4.85
1822 2241 0.881118 CCACACGCCAGCAATTTAGT 59.119 50.000 0.00 0.00 0.00 2.24
1833 2252 5.119125 GCCAGCAATTTAGTTTCACATTGTC 59.881 40.000 0.00 0.00 0.00 3.18
1946 2368 2.159268 CGTGCAGTGATCTCATCTCAGT 60.159 50.000 0.00 0.00 0.00 3.41
1997 2435 4.327357 CACACACCAACGTTTTGCATTTTA 59.673 37.500 0.00 0.00 0.00 1.52
2000 2438 5.233050 CACACCAACGTTTTGCATTTTATGA 59.767 36.000 0.00 0.00 0.00 2.15
2062 2579 3.236816 GCCACAAATTTCAGTGTCATCG 58.763 45.455 7.61 0.00 33.99 3.84
2080 2597 7.111593 GTGTCATCGTAATTTCACTTCACAAAC 59.888 37.037 0.00 0.00 0.00 2.93
2091 2608 4.873259 TCACTTCACAAACGAGATTGACAA 59.127 37.500 0.00 0.00 34.38 3.18
2099 2616 7.431960 TCACAAACGAGATTGACAAAAGATTTG 59.568 33.333 0.00 1.47 34.38 2.32
2104 2621 8.827177 ACGAGATTGACAAAAGATTTGTACTA 57.173 30.769 8.34 1.74 31.96 1.82
2105 2622 9.436957 ACGAGATTGACAAAAGATTTGTACTAT 57.563 29.630 8.34 5.62 31.96 2.12
2117 2634 9.760077 AAAGATTTGTACTATACACTTATCCCG 57.240 33.333 0.00 0.00 38.63 5.14
2118 2635 8.701908 AGATTTGTACTATACACTTATCCCGA 57.298 34.615 0.00 0.00 38.63 5.14
2119 2636 9.139734 AGATTTGTACTATACACTTATCCCGAA 57.860 33.333 0.00 0.00 38.63 4.30
2120 2637 9.754382 GATTTGTACTATACACTTATCCCGAAA 57.246 33.333 0.00 0.00 38.63 3.46
2122 2639 8.931385 TTGTACTATACACTTATCCCGAAAAC 57.069 34.615 0.00 0.00 38.63 2.43
2123 2640 8.065473 TGTACTATACACTTATCCCGAAAACA 57.935 34.615 0.00 0.00 32.89 2.83
2124 2641 8.698210 TGTACTATACACTTATCCCGAAAACAT 58.302 33.333 0.00 0.00 32.89 2.71
2125 2642 9.538508 GTACTATACACTTATCCCGAAAACATT 57.461 33.333 0.00 0.00 0.00 2.71
2126 2643 8.658499 ACTATACACTTATCCCGAAAACATTC 57.342 34.615 0.00 0.00 0.00 2.67
2127 2644 8.262227 ACTATACACTTATCCCGAAAACATTCA 58.738 33.333 0.00 0.00 0.00 2.57
2128 2645 5.880054 ACACTTATCCCGAAAACATTCAG 57.120 39.130 0.00 0.00 0.00 3.02
2129 2646 4.700213 ACACTTATCCCGAAAACATTCAGG 59.300 41.667 0.00 0.00 0.00 3.86
2130 2647 4.700213 CACTTATCCCGAAAACATTCAGGT 59.300 41.667 0.00 0.00 0.00 4.00
2131 2648 5.183140 CACTTATCCCGAAAACATTCAGGTT 59.817 40.000 0.00 0.00 0.00 3.50
2132 2649 5.773176 ACTTATCCCGAAAACATTCAGGTTT 59.227 36.000 0.00 0.00 42.49 3.27
2140 2657 5.535753 AAAACATTCAGGTTTTGGGAGAG 57.464 39.130 1.68 0.00 46.19 3.20
2141 2658 4.453480 AACATTCAGGTTTTGGGAGAGA 57.547 40.909 0.00 0.00 0.00 3.10
2142 2659 4.453480 ACATTCAGGTTTTGGGAGAGAA 57.547 40.909 0.00 0.00 0.00 2.87
2143 2660 4.803452 ACATTCAGGTTTTGGGAGAGAAA 58.197 39.130 0.00 0.00 0.00 2.52
2144 2661 4.829492 ACATTCAGGTTTTGGGAGAGAAAG 59.171 41.667 0.00 0.00 0.00 2.62
2145 2662 2.863809 TCAGGTTTTGGGAGAGAAAGC 58.136 47.619 0.00 0.00 34.42 3.51
2146 2663 2.174639 TCAGGTTTTGGGAGAGAAAGCA 59.825 45.455 0.00 0.00 36.12 3.91
2147 2664 2.294512 CAGGTTTTGGGAGAGAAAGCAC 59.705 50.000 0.00 0.00 36.12 4.40
2148 2665 2.175715 AGGTTTTGGGAGAGAAAGCACT 59.824 45.455 0.00 0.00 36.12 4.40
2193 2710 3.224324 GCGACCCGAGAGCCCATA 61.224 66.667 0.00 0.00 0.00 2.74
2194 2711 3.043419 CGACCCGAGAGCCCATAG 58.957 66.667 0.00 0.00 0.00 2.23
2195 2712 2.565645 CGACCCGAGAGCCCATAGG 61.566 68.421 0.00 0.00 0.00 2.57
2218 2735 2.824489 GGTTTCCCTAGGCGCTGC 60.824 66.667 7.64 0.00 0.00 5.25
2236 2756 4.825679 CCCCTCCACTCCTCCCCC 62.826 77.778 0.00 0.00 0.00 5.40
2238 2758 4.400251 CCTCCACTCCTCCCCCGT 62.400 72.222 0.00 0.00 0.00 5.28
2244 2764 2.442272 CTCCTCCCCCGTCGTCAT 60.442 66.667 0.00 0.00 0.00 3.06
2246 2766 3.900892 CCTCCCCCGTCGTCATCG 61.901 72.222 0.00 0.00 38.55 3.84
2256 2776 1.030488 GTCGTCATCGGAGGGAGTCA 61.030 60.000 0.00 0.00 37.69 3.41
2262 2782 3.227276 CGGAGGGAGTCATCGGGG 61.227 72.222 0.00 0.00 0.00 5.73
2263 2783 2.041819 GGAGGGAGTCATCGGGGT 60.042 66.667 0.00 0.00 0.00 4.95
2264 2784 2.435693 GGAGGGAGTCATCGGGGTG 61.436 68.421 0.00 0.00 0.00 4.61
2265 2785 2.365635 AGGGAGTCATCGGGGTGG 60.366 66.667 0.00 0.00 0.00 4.61
2268 2788 4.530857 GAGTCATCGGGGTGGGCG 62.531 72.222 0.00 0.00 0.00 6.13
2270 2790 4.832608 GTCATCGGGGTGGGCGAC 62.833 72.222 0.00 0.00 0.00 5.19
2272 2792 4.838152 CATCGGGGTGGGCGACTG 62.838 72.222 0.00 0.00 0.00 3.51
2277 2797 3.998672 GGGTGGGCGACTGTCGAA 61.999 66.667 32.07 14.54 43.74 3.71
2278 2798 2.264794 GGTGGGCGACTGTCGAAT 59.735 61.111 32.07 0.00 43.74 3.34
2305 3019 2.046314 CGGTGATGACGGGGCTTT 60.046 61.111 0.00 0.00 0.00 3.51
2309 3023 0.953960 GTGATGACGGGGCTTTCGTT 60.954 55.000 3.17 0.00 41.22 3.85
2317 3032 2.617274 GGGCTTTCGTTGCTTCGCT 61.617 57.895 0.00 0.00 0.00 4.93
2318 3033 1.154395 GGCTTTCGTTGCTTCGCTC 60.154 57.895 0.00 0.00 0.00 5.03
2319 3034 1.507919 GCTTTCGTTGCTTCGCTCG 60.508 57.895 0.00 0.00 0.00 5.03
2320 3035 1.507919 CTTTCGTTGCTTCGCTCGC 60.508 57.895 0.00 0.00 0.00 5.03
2342 3059 2.056223 CGAAGGACCCCGGAGCTTA 61.056 63.158 0.73 0.00 0.00 3.09
2496 3214 2.024560 TCCTCTGCTCCAGATCTGAAGA 60.025 50.000 24.62 17.66 39.92 2.87
2497 3215 2.765135 CCTCTGCTCCAGATCTGAAGAA 59.235 50.000 24.62 6.92 39.92 2.52
2510 3229 4.086706 TCTGAAGAACAGGTTTTCCCTC 57.913 45.455 0.00 0.00 43.86 4.30
2511 3230 3.149981 CTGAAGAACAGGTTTTCCCTCC 58.850 50.000 0.00 0.00 43.86 4.30
2512 3231 2.158519 TGAAGAACAGGTTTTCCCTCCC 60.159 50.000 0.00 0.00 43.86 4.30
2513 3232 1.834540 AGAACAGGTTTTCCCTCCCT 58.165 50.000 0.00 0.00 43.86 4.20
2527 3246 0.468029 CTCCCTCTCTCTGCTCTCCC 60.468 65.000 0.00 0.00 0.00 4.30
2528 3247 0.923729 TCCCTCTCTCTGCTCTCCCT 60.924 60.000 0.00 0.00 0.00 4.20
2529 3248 0.468029 CCCTCTCTCTGCTCTCCCTC 60.468 65.000 0.00 0.00 0.00 4.30
2533 3297 3.898509 CTCTGCTCTCCCTCCGCG 61.899 72.222 0.00 0.00 0.00 6.46
2580 3344 2.035783 GAGCCCAGTGGAAACCCC 59.964 66.667 11.95 0.00 0.00 4.95
2591 3355 2.823747 GTGGAAACCCCTGTTGGTATTC 59.176 50.000 0.00 0.00 37.76 1.75
2601 3365 3.070676 TGGTATTCCCAACGCGGT 58.929 55.556 12.47 0.00 41.50 5.68
2602 3366 1.078988 TGGTATTCCCAACGCGGTC 60.079 57.895 12.47 0.00 41.50 4.79
2605 3369 3.298115 TATTCCCAACGCGGTCGCA 62.298 57.895 12.47 0.00 42.06 5.10
2632 3396 0.307760 CCTTTTGCGTCGTTCTGCTT 59.692 50.000 0.00 0.00 0.00 3.91
2646 3410 0.882042 CTGCTTGTTGGAGTCGCAGT 60.882 55.000 7.14 0.00 42.19 4.40
2683 3447 4.528039 CCCGGCCATGCTTCCCAT 62.528 66.667 2.24 0.00 33.39 4.00
2704 3468 1.153349 GAAAGCTCGAATCCCGGCT 60.153 57.895 0.00 0.00 43.26 5.52
2741 3505 3.533105 ACCTGGTGCGTCGTGTCA 61.533 61.111 0.00 0.00 0.00 3.58
2767 3531 4.699522 GGCGCCGTCTGGGAAAGT 62.700 66.667 12.58 0.00 38.47 2.66
2789 3553 2.498056 GGTGCTTTGGGGGTGTGTG 61.498 63.158 0.00 0.00 0.00 3.82
2797 3561 3.605664 GGGGTGTGTGGCAGTTGC 61.606 66.667 0.00 0.00 41.14 4.17
2822 3587 2.908073 CGCCTGGTGTTTGTGGAGC 61.908 63.158 0.00 0.00 0.00 4.70
2824 3589 1.151450 CCTGGTGTTTGTGGAGCCT 59.849 57.895 0.00 0.00 0.00 4.58
2845 3610 2.594592 GCGACCCAGCCACAAGTT 60.595 61.111 0.00 0.00 0.00 2.66
2846 3611 2.908073 GCGACCCAGCCACAAGTTG 61.908 63.158 0.00 0.00 0.00 3.16
2847 3612 2.908073 CGACCCAGCCACAAGTTGC 61.908 63.158 1.81 0.00 0.00 4.17
2848 3613 1.529244 GACCCAGCCACAAGTTGCT 60.529 57.895 1.81 0.00 38.67 3.91
2849 3614 0.250727 GACCCAGCCACAAGTTGCTA 60.251 55.000 1.81 0.00 35.69 3.49
2850 3615 0.405585 ACCCAGCCACAAGTTGCTAT 59.594 50.000 1.81 0.00 35.69 2.97
2851 3616 0.813184 CCCAGCCACAAGTTGCTATG 59.187 55.000 1.81 0.00 35.69 2.23
2852 3617 0.171903 CCAGCCACAAGTTGCTATGC 59.828 55.000 1.81 0.64 35.69 3.14
2853 3618 0.179181 CAGCCACAAGTTGCTATGCG 60.179 55.000 1.81 0.00 35.69 4.73
2854 3619 1.137404 GCCACAAGTTGCTATGCGG 59.863 57.895 1.81 0.00 0.00 5.69
2855 3620 1.586154 GCCACAAGTTGCTATGCGGT 61.586 55.000 1.81 0.00 0.00 5.68
2856 3621 0.168788 CCACAAGTTGCTATGCGGTG 59.831 55.000 1.81 0.00 0.00 4.94
2857 3622 0.168788 CACAAGTTGCTATGCGGTGG 59.831 55.000 1.81 0.00 0.00 4.61
2858 3623 0.250727 ACAAGTTGCTATGCGGTGGT 60.251 50.000 1.81 0.00 0.00 4.16
2859 3624 0.168788 CAAGTTGCTATGCGGTGGTG 59.831 55.000 0.00 0.00 0.00 4.17
2860 3625 0.250727 AAGTTGCTATGCGGTGGTGT 60.251 50.000 0.00 0.00 0.00 4.16
2861 3626 0.250727 AGTTGCTATGCGGTGGTGTT 60.251 50.000 0.00 0.00 0.00 3.32
2862 3627 0.109781 GTTGCTATGCGGTGGTGTTG 60.110 55.000 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.068741 CCTAGGCCGACCAACACTATC 59.931 57.143 0.00 0.00 39.06 2.08
18 19 0.685458 GTAAGACCCTAGGCCGACCA 60.685 60.000 2.05 0.00 39.06 4.02
33 34 6.785488 TTGACAGTGTTGATTAGCTGTAAG 57.215 37.500 0.00 0.00 41.59 2.34
73 78 7.148239 GGTTGTGCTGTTTAGATTAACTGCTAT 60.148 37.037 15.82 0.00 46.67 2.97
198 232 5.121380 ACTAAGCAACTGGATCCAATGAT 57.879 39.130 24.52 18.31 0.00 2.45
199 233 4.574674 ACTAAGCAACTGGATCCAATGA 57.425 40.909 24.52 8.49 0.00 2.57
200 234 5.183713 TCAAACTAAGCAACTGGATCCAATG 59.816 40.000 17.00 17.98 0.00 2.82
201 235 5.324409 TCAAACTAAGCAACTGGATCCAAT 58.676 37.500 17.00 1.69 0.00 3.16
202 236 4.724399 TCAAACTAAGCAACTGGATCCAA 58.276 39.130 17.00 0.00 0.00 3.53
203 237 4.365514 TCAAACTAAGCAACTGGATCCA 57.634 40.909 15.27 15.27 0.00 3.41
204 238 4.336713 GGATCAAACTAAGCAACTGGATCC 59.663 45.833 4.20 4.20 41.74 3.36
205 239 4.943705 TGGATCAAACTAAGCAACTGGATC 59.056 41.667 0.00 0.00 0.00 3.36
209 358 5.239306 TCAACTGGATCAAACTAAGCAACTG 59.761 40.000 0.00 0.00 0.00 3.16
232 381 4.614946 GCTTTATCCAGTTGCCATTGATC 58.385 43.478 0.00 0.00 0.00 2.92
250 399 2.398554 CGTACATGCCTGGCGCTTT 61.399 57.895 14.98 0.50 38.78 3.51
257 406 2.286595 GCACATTCATCGTACATGCCTG 60.287 50.000 0.00 0.00 0.00 4.85
268 417 4.473199 CGATCCATTGATGCACATTCATC 58.527 43.478 0.00 0.00 42.33 2.92
277 426 0.670162 CCCAACCGATCCATTGATGC 59.330 55.000 5.38 0.00 0.00 3.91
278 427 2.057137 ACCCAACCGATCCATTGATG 57.943 50.000 5.38 0.34 0.00 3.07
282 431 1.074727 TGACAACCCAACCGATCCATT 59.925 47.619 0.00 0.00 0.00 3.16
343 492 0.608640 GACGGAACATGACAGGTCCT 59.391 55.000 0.00 0.00 0.00 3.85
383 532 0.382515 GCTACATCGCTCGACCTTCT 59.617 55.000 0.00 0.00 0.00 2.85
493 642 0.678048 GTGCCTGGGGAAGCTTACAG 60.678 60.000 11.69 13.70 0.00 2.74
506 655 1.240641 TGGGTACATTTGCGTGCCTG 61.241 55.000 0.00 0.00 41.09 4.85
507 656 0.323360 ATGGGTACATTTGCGTGCCT 60.323 50.000 0.00 0.00 41.09 4.75
691 856 1.106351 TGAGCTGAGATCGAGAGGGC 61.106 60.000 0.00 0.00 0.00 5.19
706 888 0.249405 CCCGAGCTGAGAATCTGAGC 60.249 60.000 13.83 13.83 40.88 4.26
884 1288 0.677842 GGGGTATATATAGGCCGCCG 59.322 60.000 3.05 0.00 0.00 6.46
1255 1671 1.667830 CGAGGAAGCCGTCAAGCAA 60.668 57.895 0.00 0.00 34.23 3.91
1408 1824 3.706373 GCCAGCGAGGTCCTTGGA 61.706 66.667 11.73 0.00 40.61 3.53
1457 1873 1.754745 GAAGAGGTGTGGACTGGCA 59.245 57.895 0.00 0.00 0.00 4.92
1473 1889 2.754658 GACGAGGCGGAGGAGGAA 60.755 66.667 0.00 0.00 0.00 3.36
1557 1976 4.162690 GCGGCGACCTGGAGGAAT 62.163 66.667 12.98 0.00 38.94 3.01
1813 2232 8.741101 TGTATGACAATGTGAAACTAAATTGC 57.259 30.769 0.00 0.00 38.04 3.56
1822 2241 8.931775 GTGTGTATACTGTATGACAATGTGAAA 58.068 33.333 10.51 0.00 0.00 2.69
2062 2579 8.067784 TCAATCTCGTTTGTGAAGTGAAATTAC 58.932 33.333 0.00 0.00 0.00 1.89
2091 2608 9.760077 CGGGATAAGTGTATAGTACAAATCTTT 57.240 33.333 0.00 0.00 40.93 2.52
2099 2616 9.538508 AATGTTTTCGGGATAAGTGTATAGTAC 57.461 33.333 0.00 0.00 0.00 2.73
2104 2621 7.553881 CTGAATGTTTTCGGGATAAGTGTAT 57.446 36.000 0.00 0.00 35.02 2.29
2105 2622 6.978343 CTGAATGTTTTCGGGATAAGTGTA 57.022 37.500 0.00 0.00 35.02 2.90
2106 2623 5.880054 CTGAATGTTTTCGGGATAAGTGT 57.120 39.130 0.00 0.00 35.02 3.55
2115 2632 3.068873 TCCCAAAACCTGAATGTTTTCGG 59.931 43.478 6.68 6.68 44.38 4.30
2116 2633 4.037446 TCTCCCAAAACCTGAATGTTTTCG 59.963 41.667 0.00 0.00 44.38 3.46
2117 2634 5.301805 TCTCTCCCAAAACCTGAATGTTTTC 59.698 40.000 0.00 0.00 44.38 2.29
2118 2635 5.208121 TCTCTCCCAAAACCTGAATGTTTT 58.792 37.500 0.00 0.00 46.46 2.43
2119 2636 4.803452 TCTCTCCCAAAACCTGAATGTTT 58.197 39.130 0.00 0.00 40.05 2.83
2120 2637 4.453480 TCTCTCCCAAAACCTGAATGTT 57.547 40.909 0.00 0.00 0.00 2.71
2121 2638 4.453480 TTCTCTCCCAAAACCTGAATGT 57.547 40.909 0.00 0.00 0.00 2.71
2122 2639 4.321527 GCTTTCTCTCCCAAAACCTGAATG 60.322 45.833 0.00 0.00 0.00 2.67
2123 2640 3.829026 GCTTTCTCTCCCAAAACCTGAAT 59.171 43.478 0.00 0.00 0.00 2.57
2124 2641 3.222603 GCTTTCTCTCCCAAAACCTGAA 58.777 45.455 0.00 0.00 0.00 3.02
2125 2642 2.174639 TGCTTTCTCTCCCAAAACCTGA 59.825 45.455 0.00 0.00 0.00 3.86
2126 2643 2.294512 GTGCTTTCTCTCCCAAAACCTG 59.705 50.000 0.00 0.00 0.00 4.00
2127 2644 2.175715 AGTGCTTTCTCTCCCAAAACCT 59.824 45.455 0.00 0.00 0.00 3.50
2128 2645 2.554462 GAGTGCTTTCTCTCCCAAAACC 59.446 50.000 0.00 0.00 0.00 3.27
2129 2646 2.554462 GGAGTGCTTTCTCTCCCAAAAC 59.446 50.000 0.00 0.00 43.69 2.43
2130 2647 2.863809 GGAGTGCTTTCTCTCCCAAAA 58.136 47.619 0.00 0.00 43.69 2.44
2131 2648 2.568623 GGAGTGCTTTCTCTCCCAAA 57.431 50.000 0.00 0.00 43.69 3.28
2136 2653 0.539518 GGGAGGGAGTGCTTTCTCTC 59.460 60.000 8.81 8.81 42.79 3.20
2137 2654 0.912006 GGGGAGGGAGTGCTTTCTCT 60.912 60.000 0.00 0.00 35.11 3.10
2138 2655 0.912006 AGGGGAGGGAGTGCTTTCTC 60.912 60.000 0.00 0.00 0.00 2.87
2139 2656 0.912006 GAGGGGAGGGAGTGCTTTCT 60.912 60.000 0.00 0.00 0.00 2.52
2140 2657 1.604915 GAGGGGAGGGAGTGCTTTC 59.395 63.158 0.00 0.00 0.00 2.62
2141 2658 2.294078 CGAGGGGAGGGAGTGCTTT 61.294 63.158 0.00 0.00 0.00 3.51
2142 2659 2.685380 CGAGGGGAGGGAGTGCTT 60.685 66.667 0.00 0.00 0.00 3.91
2216 2733 4.741239 GGAGGAGTGGAGGGGGCA 62.741 72.222 0.00 0.00 0.00 5.36
2218 2735 4.825679 GGGGAGGAGTGGAGGGGG 62.826 77.778 0.00 0.00 0.00 5.40
2223 2740 4.753662 CGACGGGGGAGGAGTGGA 62.754 72.222 0.00 0.00 0.00 4.02
2228 2745 2.441532 GATGACGACGGGGGAGGA 60.442 66.667 0.00 0.00 0.00 3.71
2236 2756 2.049475 GACTCCCTCCGATGACGACG 62.049 65.000 0.00 0.00 42.66 5.12
2238 2758 0.106669 ATGACTCCCTCCGATGACGA 60.107 55.000 0.00 0.00 42.66 4.20
2244 2764 2.123854 CCCGATGACTCCCTCCGA 60.124 66.667 0.00 0.00 0.00 4.55
2246 2766 2.041819 ACCCCGATGACTCCCTCC 60.042 66.667 0.00 0.00 0.00 4.30
2262 2782 1.787847 CAATTCGACAGTCGCCCAC 59.212 57.895 18.62 0.00 40.21 4.61
2263 2783 2.032634 GCAATTCGACAGTCGCCCA 61.033 57.895 18.62 4.97 40.21 5.36
2264 2784 2.750888 GGCAATTCGACAGTCGCCC 61.751 63.158 18.62 8.98 40.21 6.13
2265 2785 2.785258 GGCAATTCGACAGTCGCC 59.215 61.111 18.62 9.31 40.21 5.54
2268 2788 1.324736 GTCATCGGCAATTCGACAGTC 59.675 52.381 0.00 0.00 42.21 3.51
2269 2789 1.359848 GTCATCGGCAATTCGACAGT 58.640 50.000 0.00 0.00 42.21 3.55
2270 2790 0.298707 CGTCATCGGCAATTCGACAG 59.701 55.000 0.00 0.00 42.21 3.51
2271 2791 2.368856 CGTCATCGGCAATTCGACA 58.631 52.632 0.00 0.00 42.21 4.35
2293 3007 2.332654 GCAACGAAAGCCCCGTCAT 61.333 57.895 0.00 0.00 39.57 3.06
2294 3008 2.951475 AAGCAACGAAAGCCCCGTCA 62.951 55.000 0.00 0.00 39.57 4.35
2296 3010 2.203294 AAGCAACGAAAGCCCCGT 60.203 55.556 0.00 0.00 42.61 5.28
2326 3042 1.689582 CCTAAGCTCCGGGGTCCTT 60.690 63.158 1.62 0.43 0.00 3.36
2327 3043 2.041819 CCTAAGCTCCGGGGTCCT 60.042 66.667 1.62 0.00 0.00 3.85
2333 3049 4.899239 CTGCCGCCTAAGCTCCGG 62.899 72.222 0.00 0.00 44.58 5.14
2359 3076 2.992689 TAGACGGTGCCGCCTCAA 60.993 61.111 10.87 0.00 44.19 3.02
2472 3190 0.105555 AGATCTGGAGCAGAGGAGGG 60.106 60.000 0.00 0.00 44.08 4.30
2509 3228 0.923729 AGGGAGAGCAGAGAGAGGGA 60.924 60.000 0.00 0.00 0.00 4.20
2510 3229 0.468029 GAGGGAGAGCAGAGAGAGGG 60.468 65.000 0.00 0.00 0.00 4.30
2511 3230 0.468029 GGAGGGAGAGCAGAGAGAGG 60.468 65.000 0.00 0.00 0.00 3.69
2512 3231 0.819259 CGGAGGGAGAGCAGAGAGAG 60.819 65.000 0.00 0.00 0.00 3.20
2513 3232 1.225983 CGGAGGGAGAGCAGAGAGA 59.774 63.158 0.00 0.00 0.00 3.10
2539 3303 0.975040 AGCACTACCAGCTCAGGGAG 60.975 60.000 0.59 0.59 45.75 4.30
2544 3308 1.877576 CGTCCAGCACTACCAGCTCA 61.878 60.000 0.00 0.00 41.14 4.26
2569 3333 1.525175 TACCAACAGGGGTTTCCACT 58.475 50.000 0.00 0.00 42.42 4.00
2571 3335 2.225167 GGAATACCAACAGGGGTTTCCA 60.225 50.000 15.29 0.00 42.00 3.53
2601 3365 4.947147 AAAAGGGTGCCGCTGCGA 62.947 61.111 25.45 0.32 41.78 5.10
2602 3366 4.705519 CAAAAGGGTGCCGCTGCG 62.706 66.667 16.34 16.34 41.78 5.18
2611 3375 1.782028 GCAGAACGACGCAAAAGGGT 61.782 55.000 0.00 0.00 0.00 4.34
2632 3396 1.299850 CACGACTGCGACTCCAACA 60.300 57.895 0.00 0.00 41.64 3.33
2646 3410 2.680352 GTGGAGGAGAGCCCACGA 60.680 66.667 0.00 0.00 42.73 4.35
2677 3441 0.321210 TTCGAGCTTTCGCATGGGAA 60.321 50.000 20.25 20.25 39.10 3.97
2683 3447 1.809619 CGGGATTCGAGCTTTCGCA 60.810 57.895 0.00 0.00 42.43 5.10
2724 3488 2.765250 GATGACACGACGCACCAGGT 62.765 60.000 0.00 0.00 0.00 4.00
2741 3505 4.162690 GACGGCGCCTCCAAGGAT 62.163 66.667 26.68 0.00 37.67 3.24
2763 3527 1.211703 CCCCCAAAGCACCAAAACTTT 59.788 47.619 0.00 0.00 36.56 2.66
2767 3531 0.618968 ACACCCCCAAAGCACCAAAA 60.619 50.000 0.00 0.00 0.00 2.44
2804 3569 2.908073 GCTCCACAAACACCAGGCG 61.908 63.158 0.00 0.00 0.00 5.52
2811 3576 1.827789 GCCACAGGCTCCACAAACA 60.828 57.895 0.00 0.00 46.69 2.83
2831 3596 0.405585 ATAGCAACTTGTGGCTGGGT 59.594 50.000 12.50 0.00 41.25 4.51
2832 3597 0.813184 CATAGCAACTTGTGGCTGGG 59.187 55.000 12.50 1.39 41.25 4.45
2833 3598 0.171903 GCATAGCAACTTGTGGCTGG 59.828 55.000 12.50 6.17 41.25 4.85
2834 3599 0.179181 CGCATAGCAACTTGTGGCTG 60.179 55.000 12.50 0.00 41.25 4.85
2835 3600 1.308069 CCGCATAGCAACTTGTGGCT 61.308 55.000 7.83 7.83 43.94 4.75
2836 3601 1.137404 CCGCATAGCAACTTGTGGC 59.863 57.895 0.00 0.00 36.76 5.01
2837 3602 0.168788 CACCGCATAGCAACTTGTGG 59.831 55.000 1.17 1.17 46.61 4.17
2838 3603 0.168788 CCACCGCATAGCAACTTGTG 59.831 55.000 0.00 0.00 0.00 3.33
2839 3604 0.250727 ACCACCGCATAGCAACTTGT 60.251 50.000 0.00 0.00 0.00 3.16
2840 3605 0.168788 CACCACCGCATAGCAACTTG 59.831 55.000 0.00 0.00 0.00 3.16
2841 3606 0.250727 ACACCACCGCATAGCAACTT 60.251 50.000 0.00 0.00 0.00 2.66
2842 3607 0.250727 AACACCACCGCATAGCAACT 60.251 50.000 0.00 0.00 0.00 3.16
2843 3608 0.109781 CAACACCACCGCATAGCAAC 60.110 55.000 0.00 0.00 0.00 4.17
2844 3609 2.252556 CAACACCACCGCATAGCAA 58.747 52.632 0.00 0.00 0.00 3.91
2845 3610 3.979789 CAACACCACCGCATAGCA 58.020 55.556 0.00 0.00 0.00 3.49


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

AutoCloner maintained by Alex Coulton.