Multiple sequence alignment - TraesCS6B01G414700

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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 TraesCS6B01G414700 chr6B 100.000 2178 0 0 582 2759 687526062 687523885 0.000000e+00 4023.0
1 TraesCS6B01G414700 chr6B 100.000 239 0 0 1 239 687526643 687526405 2.520000e-120 442.0
2 TraesCS6B01G414700 chr6B 86.534 401 50 4 1247 1645 460928705 460929103 3.260000e-119 438.0
3 TraesCS6B01G414700 chr6D 94.811 2197 63 22 582 2759 452722814 452720650 0.000000e+00 3378.0
4 TraesCS6B01G414700 chr6D 90.456 241 4 8 10 239 452723036 452722804 1.610000e-77 300.0
5 TraesCS6B01G414700 chr6A 93.524 2208 69 29 582 2759 598620375 598618212 0.000000e+00 3217.0
6 TraesCS6B01G414700 chr6A 86.386 404 51 4 1247 1648 422328663 422328262 3.260000e-119 438.0
7 TraesCS6B01G414700 chr6A 95.102 245 5 3 2517 2759 598616144 598615905 2.010000e-101 379.0
8 TraesCS6B01G414700 chr6A 89.744 234 4 9 10 239 598620582 598620365 5.820000e-72 281.0
9 TraesCS6B01G414700 chr4B 89.563 412 29 4 2074 2482 343861678 343862078 6.820000e-141 510.0
10 TraesCS6B01G414700 chr2D 86.861 411 52 2 1236 1645 483256320 483255911 2.500000e-125 459.0
11 TraesCS6B01G414700 chr2D 91.667 120 10 0 2202 2321 494965741 494965622 1.700000e-37 167.0
12 TraesCS6B01G414700 chr2D 90.588 85 2 2 2452 2534 494965618 494965538 1.040000e-19 108.0
13 TraesCS6B01G414700 chr2B 86.618 411 53 2 1236 1645 568275143 568275552 1.160000e-123 453.0
14 TraesCS6B01G414700 chr2A 86.375 411 54 2 1236 1645 626589676 626589267 5.420000e-122 448.0
15 TraesCS6B01G414700 chr1D 86.935 398 50 2 1243 1639 393750476 393750080 1.950000e-121 446.0
16 TraesCS6B01G414700 chr1B 86.967 399 48 4 1243 1639 422563208 422562812 1.950000e-121 446.0
17 TraesCS6B01G414700 chr1B 90.533 169 7 4 2452 2619 271233537 271233697 5.980000e-52 215.0
18 TraesCS6B01G414700 chr1B 92.241 116 8 1 2204 2318 271233415 271233530 2.200000e-36 163.0
19 TraesCS6B01G414700 chr1B 95.000 40 2 0 1988 2027 271221870 271221909 2.290000e-06 63.9
20 TraesCS6B01G414700 chr7D 93.820 178 6 3 2305 2482 609322023 609322195 2.110000e-66 263.0
21 TraesCS6B01G414700 chr7D 92.500 120 8 1 2199 2318 110150661 110150779 1.310000e-38 171.0
22 TraesCS6B01G414700 chr7D 88.596 114 8 3 2499 2612 57624012 57624120 1.720000e-27 134.0
23 TraesCS6B01G414700 chr4D 89.941 169 8 6 2452 2619 87148486 87148326 2.780000e-50 209.0
24 TraesCS6B01G414700 chr4D 95.000 120 6 0 2202 2321 87148609 87148490 3.630000e-44 189.0
25 TraesCS6B01G414700 chr4D 92.000 50 4 0 1988 2037 87148817 87148768 1.370000e-08 71.3
26 TraesCS6B01G414700 chr4A 89.412 170 8 5 2452 2619 286715007 286714846 3.600000e-49 206.0
27 TraesCS6B01G414700 chr4A 88.757 169 10 4 2452 2619 510344788 510344948 6.030000e-47 198.0
28 TraesCS6B01G414700 chr4A 93.333 120 8 0 2199 2318 510344662 510344781 7.850000e-41 178.0
29 TraesCS6B01G414700 chr4A 92.500 120 9 0 2202 2321 286715130 286715011 3.650000e-39 172.0
30 TraesCS6B01G414700 chr4A 96.000 50 2 0 1988 2037 510344457 510344506 6.330000e-12 82.4
31 TraesCS6B01G414700 chr4A 94.340 53 0 2 2089 2138 286715267 286715215 8.190000e-11 78.7
32 TraesCS6B01G414700 chr4A 95.652 46 2 0 1988 2033 286715328 286715283 1.060000e-09 75.0
33 TraesCS6B01G414700 chr1A 91.781 146 7 3 2475 2619 257948554 257948413 6.030000e-47 198.0
34 TraesCS6B01G414700 chr1A 94.340 53 0 2 2089 2138 257948740 257948688 8.190000e-11 78.7
35 TraesCS6B01G414700 chr5D 94.340 53 0 2 2089 2138 238202796 238202848 8.190000e-11 78.7
36 TraesCS6B01G414700 chr5D 94.340 53 0 1 2089 2138 346806540 346806592 8.190000e-11 78.7
37 TraesCS6B01G414700 chr5A 94.340 53 0 2 2089 2138 195255896 195255948 8.190000e-11 78.7
38 TraesCS6B01G414700 chr5A 94.340 53 0 1 2089 2138 216560875 216560927 8.190000e-11 78.7


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 TraesCS6B01G414700 chr6B 687523885 687526643 2758 True 2232.500000 4023 100.0000 1 2759 2 chr6B.!!$R1 2758
1 TraesCS6B01G414700 chr6D 452720650 452723036 2386 True 1839.000000 3378 92.6335 10 2759 2 chr6D.!!$R1 2749
2 TraesCS6B01G414700 chr6A 598615905 598620582 4677 True 1292.333333 3217 92.7900 10 2759 3 chr6A.!!$R2 2749

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
755 773 0.460987 CACTCCTGCCGAGATTCCAC 60.461 60.0 4.99 0.0 41.63 4.02 F
791 809 1.129326 CGCTACGGATTTCCATCGAC 58.871 55.0 0.00 0.0 35.14 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1740 1760 0.097674 GTCACGGCATGATGAAGTGC 59.902 55.0 13.38 7.29 40.28 4.40 R
2089 2130 0.905357 ATGGCTCACTGGTCACTACC 59.095 55.0 0.00 0.00 46.98 3.18 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
63 67 2.559231 GTCTAGAGCTATGCCCTACCAC 59.441 54.545 0.00 0.00 0.00 4.16
94 98 2.372172 CCATCACTATACCACCTTCCCC 59.628 54.545 0.00 0.00 0.00 4.81
168 184 4.928520 CCCATCCCCCTCCCCCTC 62.929 77.778 0.00 0.00 0.00 4.30
169 185 4.928520 CCATCCCCCTCCCCCTCC 62.929 77.778 0.00 0.00 0.00 4.30
170 186 4.928520 CATCCCCCTCCCCCTCCC 62.929 77.778 0.00 0.00 0.00 4.30
236 252 2.579873 CACTGTTCATCCATCCCCATC 58.420 52.381 0.00 0.00 0.00 3.51
237 253 2.174210 CACTGTTCATCCATCCCCATCT 59.826 50.000 0.00 0.00 0.00 2.90
238 254 2.441001 ACTGTTCATCCATCCCCATCTC 59.559 50.000 0.00 0.00 0.00 2.75
672 688 2.183555 GCAATCTTGGGCTGCTGC 59.816 61.111 7.10 7.10 38.76 5.25
673 689 2.348888 GCAATCTTGGGCTGCTGCT 61.349 57.895 15.64 0.00 39.59 4.24
674 690 1.511305 CAATCTTGGGCTGCTGCTG 59.489 57.895 15.64 0.77 39.59 4.41
719 735 1.153549 GATCAGTCCTCACCACCGC 60.154 63.158 0.00 0.00 0.00 5.68
755 773 0.460987 CACTCCTGCCGAGATTCCAC 60.461 60.000 4.99 0.00 41.63 4.02
791 809 1.129326 CGCTACGGATTTCCATCGAC 58.871 55.000 0.00 0.00 35.14 4.20
792 810 1.499049 GCTACGGATTTCCATCGACC 58.501 55.000 0.00 0.00 35.14 4.79
809 827 1.342174 GACCGACTACTGGTGAACCAA 59.658 52.381 3.33 0.00 46.97 3.67
826 844 5.822519 TGAACCAACAGATTCAGGTATATGC 59.177 40.000 0.00 0.00 33.15 3.14
847 865 1.714794 CATCTCAACGCGTCTCCTTT 58.285 50.000 14.44 0.00 0.00 3.11
848 866 1.391485 CATCTCAACGCGTCTCCTTTG 59.609 52.381 14.44 6.03 0.00 2.77
870 888 1.781786 TCCTTCCTCTCTTGGATCGG 58.218 55.000 0.00 0.00 35.83 4.18
905 923 3.306364 CCATAAATCTCCTGACCTAGCGG 60.306 52.174 0.00 0.00 0.00 5.52
975 995 3.277133 GCAATGCGCAGGGAAGAA 58.723 55.556 18.32 0.00 41.79 2.52
976 996 1.138247 GCAATGCGCAGGGAAGAAG 59.862 57.895 18.32 0.00 41.79 2.85
1032 1052 2.351924 ATCACCACCACCACCACCAC 62.352 60.000 0.00 0.00 0.00 4.16
1858 1891 1.538512 CCAGTGCTGGTTCATCAACTG 59.461 52.381 9.96 0.00 45.53 3.16
1931 1967 5.867903 TTTTGCAAAAGGATTTCTCTCCA 57.132 34.783 20.46 0.00 37.28 3.86
2027 2068 4.721776 TCTAGCTTGGGATCAATTGGTAGT 59.278 41.667 5.42 0.00 34.04 2.73
2028 2069 3.891049 AGCTTGGGATCAATTGGTAGTC 58.109 45.455 5.42 0.00 31.75 2.59
2048 2089 4.109050 GTCGTTTGATTTTGTTTCTGCCA 58.891 39.130 0.00 0.00 0.00 4.92
2056 2097 5.580297 TGATTTTGTTTCTGCCAGTTTCAAC 59.420 36.000 0.00 0.00 0.00 3.18
2089 2130 4.213270 CCTCGTGAGAATCTCTAGCTAGTG 59.787 50.000 20.10 17.58 41.32 2.74
2266 2315 0.319405 GTACTACTGCCGGTGGTTGT 59.681 55.000 1.90 11.72 40.18 3.32
2279 2328 3.492337 GGTGGTTGTCCATTGTTAGGAA 58.508 45.455 0.00 0.00 46.20 3.36
2405 2454 8.868103 TCCTTGAGCATCCATATGATCTATATC 58.132 37.037 3.65 0.00 46.49 1.63
2425 2474 4.508461 TCTTGTCCAATTGCAAGTCATG 57.492 40.909 19.15 1.39 41.83 3.07
2470 2520 7.713764 ATGGCTTGTTTCTTTTGATTTGTAC 57.286 32.000 0.00 0.00 0.00 2.90
2471 2521 6.872920 TGGCTTGTTTCTTTTGATTTGTACT 58.127 32.000 0.00 0.00 0.00 2.73
2472 2522 8.001881 TGGCTTGTTTCTTTTGATTTGTACTA 57.998 30.769 0.00 0.00 0.00 1.82
2519 2570 2.181954 ACTGCTTGCTCTTTCCTCAG 57.818 50.000 0.00 0.00 0.00 3.35
2531 2582 3.582647 TCTTTCCTCAGTATGCAAGGACA 59.417 43.478 3.48 0.00 34.76 4.02
2532 2583 4.225942 TCTTTCCTCAGTATGCAAGGACAT 59.774 41.667 3.48 0.00 34.76 3.06
2533 2584 3.548745 TCCTCAGTATGCAAGGACATG 57.451 47.619 0.00 0.00 34.76 3.21
2638 2689 1.419387 AGGGGCAACAGATAGATGAGC 59.581 52.381 0.00 0.00 39.74 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.035442 GGCAACAAGAGACGGCTCC 61.035 63.158 16.58 0.00 42.30 4.70
1 2 0.603975 AAGGCAACAAGAGACGGCTC 60.604 55.000 11.39 11.39 39.66 4.70
2 3 0.603975 GAAGGCAACAAGAGACGGCT 60.604 55.000 0.00 0.00 41.41 5.52
3 4 1.578206 GGAAGGCAACAAGAGACGGC 61.578 60.000 0.00 0.00 41.41 5.68
4 5 0.035458 AGGAAGGCAACAAGAGACGG 59.965 55.000 0.00 0.00 41.41 4.79
5 6 2.611518 CTAGGAAGGCAACAAGAGACG 58.388 52.381 0.00 0.00 41.41 4.18
6 7 2.351455 GCTAGGAAGGCAACAAGAGAC 58.649 52.381 0.00 0.00 41.41 3.36
7 8 2.770164 GCTAGGAAGGCAACAAGAGA 57.230 50.000 0.00 0.00 41.41 3.10
63 67 3.775316 GGTATAGTGATGGTGATAGGGGG 59.225 52.174 0.00 0.00 0.00 5.40
94 98 2.115266 GTGTGGTGTGGGAAGGGG 59.885 66.667 0.00 0.00 0.00 4.79
96 100 2.281484 CGGTGTGGTGTGGGAAGG 60.281 66.667 0.00 0.00 0.00 3.46
98 102 4.572571 GGCGGTGTGGTGTGGGAA 62.573 66.667 0.00 0.00 0.00 3.97
166 182 1.694525 GGAGGAAGGGGAAGGGGAG 60.695 68.421 0.00 0.00 0.00 4.30
167 183 2.191846 AGGAGGAAGGGGAAGGGGA 61.192 63.158 0.00 0.00 0.00 4.81
168 184 1.694525 GAGGAGGAAGGGGAAGGGG 60.695 68.421 0.00 0.00 0.00 4.79
169 185 1.694525 GGAGGAGGAAGGGGAAGGG 60.695 68.421 0.00 0.00 0.00 3.95
170 186 0.692756 GAGGAGGAGGAAGGGGAAGG 60.693 65.000 0.00 0.00 0.00 3.46
171 187 0.341609 AGAGGAGGAGGAAGGGGAAG 59.658 60.000 0.00 0.00 0.00 3.46
172 188 0.340208 GAGAGGAGGAGGAAGGGGAA 59.660 60.000 0.00 0.00 0.00 3.97
581 597 1.556561 GGGGGAGAGAGATGGGGAT 59.443 63.158 0.00 0.00 0.00 3.85
582 598 3.037715 GGGGGAGAGAGATGGGGA 58.962 66.667 0.00 0.00 0.00 4.81
672 688 3.371063 CCACCCAAGCAGCAGCAG 61.371 66.667 3.17 0.00 45.49 4.24
673 689 4.980702 CCCACCCAAGCAGCAGCA 62.981 66.667 3.17 0.00 45.49 4.41
719 735 2.127869 TGTGAGCCTAGCTAGCGGG 61.128 63.158 15.74 20.54 39.88 6.13
722 738 0.387565 GGAGTGTGAGCCTAGCTAGC 59.612 60.000 15.74 6.62 39.88 3.42
723 739 1.680735 CAGGAGTGTGAGCCTAGCTAG 59.319 57.143 14.20 14.20 39.88 3.42
724 740 1.769026 CAGGAGTGTGAGCCTAGCTA 58.231 55.000 0.00 0.00 39.88 3.32
725 741 1.612395 GCAGGAGTGTGAGCCTAGCT 61.612 60.000 0.00 0.00 43.88 3.32
746 764 1.815421 ATGCGCGTGGTGGAATCTC 60.815 57.895 8.43 0.00 0.00 2.75
785 803 1.092348 TCACCAGTAGTCGGTCGATG 58.908 55.000 0.00 0.00 33.25 3.84
809 827 3.751479 TGCGCATATACCTGAATCTGT 57.249 42.857 5.66 0.00 0.00 3.41
847 865 2.030027 TCCAAGAGAGGAAGGAAGCA 57.970 50.000 0.00 0.00 33.93 3.91
848 866 2.482839 CGATCCAAGAGAGGAAGGAAGC 60.483 54.545 0.00 0.00 41.92 3.86
905 923 2.529619 GCTCCGATTCAAGCGAGCC 61.530 63.158 0.00 0.00 0.00 4.70
1032 1052 1.491754 TGTCCAGGGATCATGTGATGG 59.508 52.381 0.00 0.00 34.37 3.51
1740 1760 0.097674 GTCACGGCATGATGAAGTGC 59.902 55.000 13.38 7.29 40.28 4.40
1816 1844 2.723530 TCCCAAGAAGGAGAGAACCT 57.276 50.000 0.00 0.00 41.22 3.50
1817 1845 2.682269 GCATCCCAAGAAGGAGAGAACC 60.682 54.545 0.00 0.00 39.95 3.62
1918 1954 6.011628 TGGAAATTAAGGTGGAGAGAAATCCT 60.012 38.462 0.00 0.00 40.29 3.24
1931 1967 8.482128 TGAAGTGAAACAAATGGAAATTAAGGT 58.518 29.630 0.00 0.00 41.43 3.50
2027 2068 4.142271 ACTGGCAGAAACAAAATCAAACGA 60.142 37.500 23.66 0.00 0.00 3.85
2028 2069 4.111916 ACTGGCAGAAACAAAATCAAACG 58.888 39.130 23.66 0.00 0.00 3.60
2048 2089 3.669536 GAGGAGCTAGCAAGTTGAAACT 58.330 45.455 18.83 0.89 42.04 2.66
2056 2097 1.098869 TCTCACGAGGAGCTAGCAAG 58.901 55.000 18.83 5.48 43.70 4.01
2089 2130 0.905357 ATGGCTCACTGGTCACTACC 59.095 55.000 0.00 0.00 46.98 3.18
2105 2154 5.620429 GCAATTTTCTCCAATGCCAAAATGG 60.620 40.000 0.00 0.00 41.55 3.16
2125 2174 5.048782 TCGATGCTAGTTTTGTTCTTGCAAT 60.049 36.000 0.00 0.00 43.74 3.56
2266 2315 6.295067 GCCTTTTTAGCTTTCCTAACAATGGA 60.295 38.462 0.00 0.00 35.80 3.41
2279 2328 2.887152 CTCCACTGTGCCTTTTTAGCTT 59.113 45.455 1.29 0.00 0.00 3.74
2344 2393 6.745159 TTTAAAGCAAGACAAGTACACACA 57.255 33.333 0.00 0.00 0.00 3.72
2345 2394 7.753580 ACTTTTTAAAGCAAGACAAGTACACAC 59.246 33.333 6.64 0.00 39.63 3.82
2405 2454 4.247267 ACATGACTTGCAATTGGACAAG 57.753 40.909 18.67 18.67 46.91 3.16
2442 2492 9.643693 ACAAATCAAAAGAAACAAGCCATATAG 57.356 29.630 0.00 0.00 0.00 1.31
2469 2519 6.990349 TGTAACTTTTTGACAAGCTAGCTAGT 59.010 34.615 19.70 12.16 0.00 2.57
2470 2520 7.421530 TGTAACTTTTTGACAAGCTAGCTAG 57.578 36.000 19.70 16.84 0.00 3.42
2471 2521 7.795482 TTGTAACTTTTTGACAAGCTAGCTA 57.205 32.000 19.70 0.00 0.00 3.32
2472 2522 6.693315 TTGTAACTTTTTGACAAGCTAGCT 57.307 33.333 12.68 12.68 0.00 3.32
2519 2570 4.024556 GCACTACATCATGTCCTTGCATAC 60.025 45.833 11.55 0.00 32.78 2.39
2531 2582 5.720202 TCGTTCAAACTAGCACTACATCAT 58.280 37.500 0.00 0.00 0.00 2.45
2532 2583 5.128992 TCGTTCAAACTAGCACTACATCA 57.871 39.130 0.00 0.00 0.00 3.07
2533 2584 7.435488 ACATATCGTTCAAACTAGCACTACATC 59.565 37.037 0.00 0.00 0.00 3.06
2638 2689 4.416505 TTTGCTTGGCTTTGTTTGTTTG 57.583 36.364 0.00 0.00 0.00 2.93


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

AutoCloner maintained by Alex Coulton.