Multiple sequence alignment - TraesCS6D01G104400

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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 TraesCS6D01G104400 chr6D 100.000 2378 0 0 1 2378 68080632 68083009 0.000000e+00 4392.0
1 TraesCS6D01G104400 chr6D 84.848 66 10 0 2313 2378 433714508 433714443 1.530000e-07 67.6
2 TraesCS6D01G104400 chr6A 93.419 2249 98 20 1 2230 85572014 85574231 0.000000e+00 3288.0
3 TraesCS6D01G104400 chr6B 92.760 1464 51 17 154 1589 142990901 142992337 0.000000e+00 2065.0
4 TraesCS6D01G104400 chr6B 91.935 620 34 7 1614 2228 142992321 142992929 0.000000e+00 854.0
5 TraesCS6D01G104400 chr6B 91.358 162 4 3 1 159 142990719 142990873 1.850000e-51 213.0
6 TraesCS6D01G104400 chr6B 93.243 74 4 1 2157 2230 142993116 142993188 8.990000e-20 108.0
7 TraesCS6D01G104400 chr3D 97.849 93 2 0 2222 2314 224304659 224304751 6.800000e-36 161.0
8 TraesCS6D01G104400 chr7D 94.286 105 5 1 2224 2328 10560702 10560599 2.450000e-35 159.0
9 TraesCS6D01G104400 chr7D 94.949 99 5 0 2230 2328 52840534 52840436 3.160000e-34 156.0
10 TraesCS6D01G104400 chr7D 95.876 97 3 1 2230 2326 53485586 53485491 3.160000e-34 156.0
11 TraesCS6D01G104400 chr7D 91.743 109 6 3 2230 2337 34845641 34845535 5.300000e-32 148.0
12 TraesCS6D01G104400 chr5D 95.876 97 3 1 2228 2324 37920306 37920401 3.160000e-34 156.0
13 TraesCS6D01G104400 chr5B 94.175 103 5 1 2230 2332 492096689 492096588 3.160000e-34 156.0
14 TraesCS6D01G104400 chr1B 90.179 112 9 2 2206 2317 636840283 636840174 6.850000e-31 145.0
15 TraesCS6D01G104400 chr1B 88.430 121 11 3 2230 2349 47517346 47517464 2.460000e-30 143.0
16 TraesCS6D01G104400 chr2A 93.220 59 2 2 2321 2377 221203204 221203146 4.210000e-13 86.1
17 TraesCS6D01G104400 chr2B 89.552 67 5 2 2313 2377 377102731 377102665 1.510000e-12 84.2


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 TraesCS6D01G104400 chr6D 68080632 68083009 2377 False 4392 4392 100.000 1 2378 1 chr6D.!!$F1 2377
1 TraesCS6D01G104400 chr6A 85572014 85574231 2217 False 3288 3288 93.419 1 2230 1 chr6A.!!$F1 2229
2 TraesCS6D01G104400 chr6B 142990719 142993188 2469 False 810 2065 92.324 1 2230 4 chr6B.!!$F1 2229

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
424 461 0.815213 CACCGTCCCCTACATGCATG 60.815 60.0 25.09 25.09 0.0 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2079 2153 0.178301 GTTAGTGTGGGGGCTAGCTC 59.822 60.0 15.72 11.22 0.0 4.09 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
27 28 3.391506 AACCAAAGATGCCTTGAAAGC 57.608 42.857 0.00 0.00 31.91 3.51
181 218 4.221703 CACACCTTAACTCTCCAGATCTGT 59.778 45.833 21.11 4.30 0.00 3.41
187 224 6.098982 CCTTAACTCTCCAGATCTGTGGTTAT 59.901 42.308 21.11 6.28 38.88 1.89
236 273 6.870971 TTAGTCGGTGAATTTAAAAGCAGT 57.129 33.333 0.00 0.00 0.00 4.40
243 280 6.531240 CGGTGAATTTAAAAGCAGTTGCATAT 59.469 34.615 6.90 0.00 45.16 1.78
332 369 4.461781 GGTGGAAGAACAGCTAGTACACTA 59.538 45.833 0.00 0.00 36.03 2.74
421 458 1.045407 TATCACCGTCCCCTACATGC 58.955 55.000 0.00 0.00 0.00 4.06
422 459 0.980754 ATCACCGTCCCCTACATGCA 60.981 55.000 0.00 0.00 0.00 3.96
423 460 0.980754 TCACCGTCCCCTACATGCAT 60.981 55.000 0.00 0.00 0.00 3.96
424 461 0.815213 CACCGTCCCCTACATGCATG 60.815 60.000 25.09 25.09 0.00 4.06
433 470 1.884579 CCTACATGCATGGATCCAAGC 59.115 52.381 30.50 30.50 40.56 4.01
483 520 1.745232 TATGAACACACGCCATTCCC 58.255 50.000 0.00 0.00 0.00 3.97
523 562 4.083324 ACGCTTTCATTACACTGTCAATGG 60.083 41.667 10.24 0.39 33.77 3.16
542 581 1.012486 GCAGCCAGCTGAACATTTGC 61.012 55.000 23.40 8.12 46.30 3.68
558 597 8.763356 TGAACATTTGCACAATAATCAAGAAAC 58.237 29.630 0.00 0.00 0.00 2.78
812 861 2.040545 CCACCCCGCCCATAATATACAA 59.959 50.000 0.00 0.00 0.00 2.41
888 952 1.291335 TCCTCCTCCTCTTAACCTCCC 59.709 57.143 0.00 0.00 0.00 4.30
950 1014 1.372582 TCGCAAGATCATCAACCAGC 58.627 50.000 0.00 0.00 45.01 4.85
951 1015 1.065926 TCGCAAGATCATCAACCAGCT 60.066 47.619 0.00 0.00 45.01 4.24
1390 1458 2.225727 CCATGGTGATTGATCATGCTCG 59.774 50.000 2.57 0.00 39.30 5.03
1408 1476 1.708027 GTGCATGGCGACGTAGAAC 59.292 57.895 0.00 0.00 0.00 3.01
1544 1612 5.350365 GCCAGTAGATAGATAGTCTCTCACG 59.650 48.000 0.00 0.00 35.28 4.35
1545 1613 6.693466 CCAGTAGATAGATAGTCTCTCACGA 58.307 44.000 0.00 0.00 35.28 4.35
1558 1628 0.724549 CTCACGAGTCTCGAGTCTGG 59.275 60.000 28.33 17.24 43.74 3.86
1559 1629 0.320697 TCACGAGTCTCGAGTCTGGA 59.679 55.000 28.33 12.90 43.74 3.86
1560 1630 1.157585 CACGAGTCTCGAGTCTGGAA 58.842 55.000 28.33 0.00 43.74 3.53
1561 1631 1.740585 CACGAGTCTCGAGTCTGGAAT 59.259 52.381 28.33 4.27 43.74 3.01
1564 1634 2.616376 CGAGTCTCGAGTCTGGAATGAT 59.384 50.000 17.52 0.00 43.74 2.45
1586 1658 7.520798 TGATTAATGATGATCTTGTAAGGGCT 58.479 34.615 0.00 0.00 0.00 5.19
1591 1663 3.914426 TGATCTTGTAAGGGCTCTTCC 57.086 47.619 0.00 0.00 34.59 3.46
1673 1745 7.292713 TGATTTTGATTCCCATGATACATGG 57.707 36.000 19.97 19.97 38.88 3.66
1674 1746 5.534207 TTTTGATTCCCATGATACATGGC 57.466 39.130 21.09 10.79 37.85 4.40
1686 1758 3.583966 TGATACATGGCTGCATCCTCATA 59.416 43.478 8.29 0.00 0.00 2.15
1738 1810 8.055181 AGCCAGATATTGTTCTCCAGAAATTAA 58.945 33.333 0.00 0.00 35.58 1.40
1740 1812 8.844244 CCAGATATTGTTCTCCAGAAATTAAGG 58.156 37.037 0.00 0.00 35.58 2.69
1741 1813 8.844244 CAGATATTGTTCTCCAGAAATTAAGGG 58.156 37.037 0.00 0.00 35.58 3.95
1744 1817 7.855784 ATTGTTCTCCAGAAATTAAGGGTTT 57.144 32.000 0.00 0.00 35.58 3.27
1960 2033 2.040278 AGATACTTGCAGCTGGGACAAA 59.960 45.455 17.12 0.00 38.70 2.83
1984 2057 1.243902 ACAGGTGGCACAATTAACCG 58.756 50.000 20.82 0.47 44.16 4.44
2003 2076 2.104792 CCGCATAATTCCTGGGAGAGAA 59.895 50.000 0.00 0.00 0.00 2.87
2068 2142 7.971183 AGAGAAACACAACCTTCTAATCTTC 57.029 36.000 0.00 0.00 32.01 2.87
2072 2146 7.775561 AGAAACACAACCTTCTAATCTTCTGTT 59.224 33.333 0.00 0.00 30.05 3.16
2107 2181 4.480908 AGCCCCCACACTAACCTATTTATT 59.519 41.667 0.00 0.00 0.00 1.40
2112 2186 7.147966 CCCCCACACTAACCTATTTATTTCAAC 60.148 40.741 0.00 0.00 0.00 3.18
2141 2215 2.400962 GCCACATCAGCATGCGACA 61.401 57.895 13.01 0.00 34.76 4.35
2240 2572 7.741554 AGAATTTACATTCTACTCCCTCTGT 57.258 36.000 2.19 0.00 46.33 3.41
2241 2573 8.840200 AGAATTTACATTCTACTCCCTCTGTA 57.160 34.615 2.19 0.00 46.33 2.74
2242 2574 9.268282 AGAATTTACATTCTACTCCCTCTGTAA 57.732 33.333 2.19 0.00 46.33 2.41
2243 2575 9.886132 GAATTTACATTCTACTCCCTCTGTAAA 57.114 33.333 7.80 7.80 40.95 2.01
2244 2576 9.668497 AATTTACATTCTACTCCCTCTGTAAAC 57.332 33.333 7.58 0.00 40.08 2.01
2245 2577 8.431910 TTTACATTCTACTCCCTCTGTAAACT 57.568 34.615 0.00 0.00 35.38 2.66
2246 2578 9.537852 TTTACATTCTACTCCCTCTGTAAACTA 57.462 33.333 0.00 0.00 35.38 2.24
2247 2579 9.537852 TTACATTCTACTCCCTCTGTAAACTAA 57.462 33.333 0.00 0.00 0.00 2.24
2248 2580 8.611051 ACATTCTACTCCCTCTGTAAACTAAT 57.389 34.615 0.00 0.00 0.00 1.73
2249 2581 9.710818 ACATTCTACTCCCTCTGTAAACTAATA 57.289 33.333 0.00 0.00 0.00 0.98
2256 2588 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
2257 2589 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
2258 2590 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
2259 2591 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
2260 2592 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
2308 2640 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
2309 2641 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
2310 2642 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
2311 2643 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
2312 2644 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
2320 2652 8.548880 TTAGTTTACAGAGGGAGTATTATGCT 57.451 34.615 0.00 0.00 0.00 3.79
2321 2653 9.650714 TTAGTTTACAGAGGGAGTATTATGCTA 57.349 33.333 0.00 0.00 0.00 3.49
2322 2654 8.728596 AGTTTACAGAGGGAGTATTATGCTAT 57.271 34.615 0.00 0.00 0.00 2.97
2323 2655 9.160412 AGTTTACAGAGGGAGTATTATGCTATT 57.840 33.333 0.00 0.00 0.00 1.73
2324 2656 9.780186 GTTTACAGAGGGAGTATTATGCTATTT 57.220 33.333 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 6.764877 ACCGCTATTGTATCATAAAGTTCG 57.235 37.500 0.00 0.00 0.00 3.95
155 159 2.037251 TCTGGAGAGTTAAGGTGTGTGC 59.963 50.000 0.00 0.00 0.00 4.57
172 209 6.878317 TCAGTCTAAATAACCACAGATCTGG 58.122 40.000 26.08 13.28 37.33 3.86
181 218 8.736244 GCTGGTTAATTTCAGTCTAAATAACCA 58.264 33.333 11.86 11.86 38.46 3.67
187 224 8.911918 TGTTAGCTGGTTAATTTCAGTCTAAA 57.088 30.769 0.00 0.00 34.64 1.85
236 273 8.415950 TTTCAGAAAGGGAGTAAAATATGCAA 57.584 30.769 0.00 0.00 0.00 4.08
243 280 6.010219 CCCATCTTTCAGAAAGGGAGTAAAA 58.990 40.000 20.70 1.61 42.80 1.52
247 284 2.989571 ACCCATCTTTCAGAAAGGGAGT 59.010 45.455 20.70 12.90 42.80 3.85
304 341 2.736670 AGCTGTTCTTCCACCAGTTT 57.263 45.000 0.00 0.00 0.00 2.66
421 458 1.479389 GGTTAGGGGCTTGGATCCATG 60.479 57.143 17.06 19.20 0.00 3.66
422 459 0.853530 GGTTAGGGGCTTGGATCCAT 59.146 55.000 17.06 1.24 0.00 3.41
423 460 0.551377 TGGTTAGGGGCTTGGATCCA 60.551 55.000 11.44 11.44 0.00 3.41
424 461 0.629058 TTGGTTAGGGGCTTGGATCC 59.371 55.000 4.20 4.20 0.00 3.36
433 470 2.831526 CTCCAATGGTTTTGGTTAGGGG 59.168 50.000 0.00 0.00 40.40 4.79
483 520 2.427453 AGCGTATGTGGAGTAGGTCAAG 59.573 50.000 0.00 0.00 0.00 3.02
523 562 1.012486 GCAAATGTTCAGCTGGCTGC 61.012 55.000 15.13 8.47 43.31 5.25
542 581 7.403312 TGGGTATGGTTTCTTGATTATTGTG 57.597 36.000 0.00 0.00 0.00 3.33
558 597 8.163408 TGTATTATTTCTCTTGGATGGGTATGG 58.837 37.037 0.00 0.00 0.00 2.74
812 861 4.699522 GGTTCTTGCGAGGGCGGT 62.700 66.667 0.00 0.00 44.10 5.68
938 1002 0.330604 AGTGGCAGCTGGTTGATGAT 59.669 50.000 17.12 0.00 33.12 2.45
941 1005 0.403271 AAGAGTGGCAGCTGGTTGAT 59.597 50.000 17.12 0.00 0.00 2.57
942 1006 0.250467 GAAGAGTGGCAGCTGGTTGA 60.250 55.000 17.12 0.00 0.00 3.18
944 1008 1.302033 CGAAGAGTGGCAGCTGGTT 60.302 57.895 17.12 0.00 0.00 3.67
946 1010 3.123620 GCGAAGAGTGGCAGCTGG 61.124 66.667 17.12 0.00 0.00 4.85
948 1012 4.749310 CGGCGAAGAGTGGCAGCT 62.749 66.667 0.00 0.00 0.00 4.24
950 1014 1.901650 GAAACGGCGAAGAGTGGCAG 61.902 60.000 16.62 0.00 0.00 4.85
951 1015 1.959226 GAAACGGCGAAGAGTGGCA 60.959 57.895 16.62 0.00 0.00 4.92
1349 1417 4.704833 TGGCGTTGCTCCTGCTCC 62.705 66.667 0.00 0.00 40.48 4.70
1390 1458 1.011968 TGTTCTACGTCGCCATGCAC 61.012 55.000 0.00 0.00 0.00 4.57
1544 1612 4.647424 AATCATTCCAGACTCGAGACTC 57.353 45.455 21.68 7.24 0.00 3.36
1545 1613 6.322456 TCATTAATCATTCCAGACTCGAGACT 59.678 38.462 21.68 16.39 0.00 3.24
1559 1629 8.800332 GCCCTTACAAGATCATCATTAATCATT 58.200 33.333 0.00 0.00 0.00 2.57
1560 1630 8.168725 AGCCCTTACAAGATCATCATTAATCAT 58.831 33.333 0.00 0.00 0.00 2.45
1561 1631 7.520798 AGCCCTTACAAGATCATCATTAATCA 58.479 34.615 0.00 0.00 0.00 2.57
1564 1634 7.141758 AGAGCCCTTACAAGATCATCATTAA 57.858 36.000 0.00 0.00 0.00 1.40
1586 1658 4.974368 TGCTCGAAAACAAAAAGGAAGA 57.026 36.364 0.00 0.00 0.00 2.87
1591 1663 4.732923 TCGATGTTGCTCGAAAACAAAAAG 59.267 37.500 15.09 8.59 44.14 2.27
1673 1745 2.039480 TGGAGGAATATGAGGATGCAGC 59.961 50.000 0.00 0.00 0.00 5.25
1674 1746 3.869140 GCTGGAGGAATATGAGGATGCAG 60.869 52.174 0.00 0.00 0.00 4.41
1686 1758 3.382278 TCTTCTGATCAGCTGGAGGAAT 58.618 45.455 18.36 0.00 0.00 3.01
1763 1836 9.352191 GAGTAGACATAAATAAGAGGACACCTA 57.648 37.037 0.00 0.00 31.76 3.08
1960 2033 4.262420 GGTTAATTGTGCCACCTGTTTCAT 60.262 41.667 0.00 0.00 0.00 2.57
1984 2057 4.102367 AGTCTTCTCTCCCAGGAATTATGC 59.898 45.833 0.00 0.00 0.00 3.14
2003 2076 8.809468 AAAAACAGTAAAAGAAGGAGAAGTCT 57.191 30.769 0.00 0.00 0.00 3.24
2035 2109 5.720202 AGGTTGTGTTTCTCTTGGTTTTTC 58.280 37.500 0.00 0.00 0.00 2.29
2044 2118 7.659390 CAGAAGATTAGAAGGTTGTGTTTCTCT 59.341 37.037 0.00 0.00 35.42 3.10
2068 2142 3.471680 GGGGCTAGCTCTTCATAAACAG 58.528 50.000 15.73 0.00 0.00 3.16
2072 2146 1.768870 GTGGGGGCTAGCTCTTCATAA 59.231 52.381 15.73 0.00 0.00 1.90
2079 2153 0.178301 GTTAGTGTGGGGGCTAGCTC 59.822 60.000 15.72 11.22 0.00 4.09
2086 2160 6.428295 TGAAATAAATAGGTTAGTGTGGGGG 58.572 40.000 0.00 0.00 0.00 5.40
2116 2190 1.191535 ATGCTGATGTGGCATGCTTT 58.808 45.000 18.92 0.00 46.85 3.51
2230 2562 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
2231 2563 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
2232 2564 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
2233 2565 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
2234 2566 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
2282 2614 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
2283 2615 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
2284 2616 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
2285 2617 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
2286 2618 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
2294 2626 9.160412 AGCATAATACTCCCTCTGTAAACTAAT 57.840 33.333 0.00 0.00 0.00 1.73
2295 2627 8.548880 AGCATAATACTCCCTCTGTAAACTAA 57.451 34.615 0.00 0.00 0.00 2.24
2296 2628 9.824216 ATAGCATAATACTCCCTCTGTAAACTA 57.176 33.333 0.00 0.00 0.00 2.24
2297 2629 8.728596 ATAGCATAATACTCCCTCTGTAAACT 57.271 34.615 0.00 0.00 0.00 2.66
2298 2630 9.780186 AAATAGCATAATACTCCCTCTGTAAAC 57.220 33.333 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.