Multiple sequence alignment - TraesCS6A01G195300

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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 TraesCS6A01G195300 chr6A 100.000 3223 0 0 1 3223 279285602 279288824 0.000000e+00 5952
1 TraesCS6A01G195300 chr6D 93.852 2212 111 6 340 2529 83696932 83694724 0.000000e+00 3308
2 TraesCS6A01G195300 chr6D 97.353 529 13 1 2528 3056 83694682 83694155 0.000000e+00 898
3 TraesCS6A01G195300 chr6D 92.727 220 8 4 27 238 83697621 83697402 8.680000e-81 311
4 TraesCS6A01G195300 chr6D 96.407 167 6 0 3057 3223 83694051 83693885 3.170000e-70 276
5 TraesCS6A01G195300 chr2B 91.837 2401 147 25 170 2529 81025281 81027673 0.000000e+00 3302
6 TraesCS6A01G195300 chr2B 95.624 1097 42 4 1439 2529 47556967 47555871 0.000000e+00 1755
7 TraesCS6A01G195300 chr2B 94.986 1097 49 2 1439 2529 576816301 576817397 0.000000e+00 1716
8 TraesCS6A01G195300 chr2B 97.164 529 13 1 2528 3056 576817439 576817965 0.000000e+00 893
9 TraesCS6A01G195300 chr2B 96.226 530 19 1 2528 3056 81027715 81028244 0.000000e+00 867
10 TraesCS6A01G195300 chr2B 96.219 529 20 0 2528 3056 766616392 766615864 0.000000e+00 867
11 TraesCS6A01G195300 chr2B 83.011 465 25 22 28 444 47558445 47557987 3.930000e-99 372
12 TraesCS6A01G195300 chr2B 97.605 167 4 0 3057 3223 81028348 81028514 1.460000e-73 287
13 TraesCS6A01G195300 chr2B 96.407 167 6 0 3057 3223 766615760 766615594 3.170000e-70 276
14 TraesCS6A01G195300 chr2B 88.710 186 9 8 29 207 73850023 73849843 1.950000e-52 217
15 TraesCS6A01G195300 chr2B 91.139 158 5 4 28 176 80995400 80995557 4.210000e-49 206
16 TraesCS6A01G195300 chr5A 93.750 1328 62 10 1223 2529 639743848 639745175 0.000000e+00 1973
17 TraesCS6A01G195300 chr5A 89.118 1213 108 15 27 1227 639715529 639716729 0.000000e+00 1487
18 TraesCS6A01G195300 chr4B 94.513 1221 59 6 1316 2529 365508360 365509579 0.000000e+00 1877
19 TraesCS6A01G195300 chr4B 94.986 1097 49 4 1439 2529 636233499 636234595 0.000000e+00 1716
20 TraesCS6A01G195300 chr3B 95.624 1097 42 4 1439 2529 755582449 755583545 0.000000e+00 1755
21 TraesCS6A01G195300 chr3B 84.739 249 21 1 28 276 357049495 357049264 1.930000e-57 233
22 TraesCS6A01G195300 chr7B 95.077 1097 48 4 1439 2529 348043773 348044869 0.000000e+00 1722
23 TraesCS6A01G195300 chr7B 95.980 199 7 1 1316 1514 669608304 669608107 4.010000e-84 322
24 TraesCS6A01G195300 chr6B 89.234 1254 69 29 28 1241 697548689 697549916 0.000000e+00 1507
25 TraesCS6A01G195300 chr6B 97.353 529 12 1 2528 3056 47007653 47008179 0.000000e+00 898
26 TraesCS6A01G195300 chr6B 97.164 529 15 0 2528 3056 697573245 697573773 0.000000e+00 894
27 TraesCS6A01G195300 chr6B 97.164 529 15 0 2528 3056 697597265 697597793 0.000000e+00 894
28 TraesCS6A01G195300 chr6B 95.984 249 10 0 1233 1481 697570186 697570434 3.870000e-109 405
29 TraesCS6A01G195300 chr6B 95.984 249 10 0 1233 1481 697594206 697594454 3.870000e-109 405
30 TraesCS6A01G195300 chr6B 96.407 167 6 0 3057 3223 697573877 697574043 3.170000e-70 276
31 TraesCS6A01G195300 chr6B 96.407 167 6 0 3057 3223 697597897 697598063 3.170000e-70 276
32 TraesCS6A01G195300 chr7A 85.026 955 99 15 668 1608 59390592 59389668 0.000000e+00 931
33 TraesCS6A01G195300 chr7A 86.232 414 50 5 254 667 552752129 552751723 2.950000e-120 442
34 TraesCS6A01G195300 chr5B 97.164 529 13 1 2528 3056 662918160 662918686 0.000000e+00 893
35 TraesCS6A01G195300 chr1B 96.408 529 17 1 2528 3056 103073970 103073444 0.000000e+00 870
36 TraesCS6A01G195300 chr4A 82.714 995 110 27 662 1608 671651169 671650189 0.000000e+00 828
37 TraesCS6A01G195300 chr4A 97.605 167 4 0 3057 3223 667274468 667274634 1.460000e-73 287
38 TraesCS6A01G195300 chr4A 97.006 167 5 0 3057 3223 667252410 667252576 6.810000e-72 281
39 TraesCS6A01G195300 chr4A 96.407 167 6 0 3057 3223 667297993 667298159 3.170000e-70 276
40 TraesCS6A01G195300 chr7D 88.077 671 73 3 662 1331 55399792 55399128 0.000000e+00 789
41 TraesCS6A01G195300 chr2D 95.783 166 6 1 3057 3221 94909382 94909547 1.910000e-67 267


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 TraesCS6A01G195300 chr6A 279285602 279288824 3222 False 5952.000000 5952 100.000000 1 3223 1 chr6A.!!$F1 3222
1 TraesCS6A01G195300 chr6D 83693885 83697621 3736 True 1198.250000 3308 95.084750 27 3223 4 chr6D.!!$R1 3196
2 TraesCS6A01G195300 chr2B 81025281 81028514 3233 False 1485.333333 3302 95.222667 170 3223 3 chr2B.!!$F2 3053
3 TraesCS6A01G195300 chr2B 576816301 576817965 1664 False 1304.500000 1716 96.075000 1439 3056 2 chr2B.!!$F3 1617
4 TraesCS6A01G195300 chr2B 47555871 47558445 2574 True 1063.500000 1755 89.317500 28 2529 2 chr2B.!!$R2 2501
5 TraesCS6A01G195300 chr2B 766615594 766616392 798 True 571.500000 867 96.313000 2528 3223 2 chr2B.!!$R3 695
6 TraesCS6A01G195300 chr5A 639743848 639745175 1327 False 1973.000000 1973 93.750000 1223 2529 1 chr5A.!!$F2 1306
7 TraesCS6A01G195300 chr5A 639715529 639716729 1200 False 1487.000000 1487 89.118000 27 1227 1 chr5A.!!$F1 1200
8 TraesCS6A01G195300 chr4B 365508360 365509579 1219 False 1877.000000 1877 94.513000 1316 2529 1 chr4B.!!$F1 1213
9 TraesCS6A01G195300 chr4B 636233499 636234595 1096 False 1716.000000 1716 94.986000 1439 2529 1 chr4B.!!$F2 1090
10 TraesCS6A01G195300 chr3B 755582449 755583545 1096 False 1755.000000 1755 95.624000 1439 2529 1 chr3B.!!$F1 1090
11 TraesCS6A01G195300 chr7B 348043773 348044869 1096 False 1722.000000 1722 95.077000 1439 2529 1 chr7B.!!$F1 1090
12 TraesCS6A01G195300 chr6B 697548689 697549916 1227 False 1507.000000 1507 89.234000 28 1241 1 chr6B.!!$F2 1213
13 TraesCS6A01G195300 chr6B 47007653 47008179 526 False 898.000000 898 97.353000 2528 3056 1 chr6B.!!$F1 528
14 TraesCS6A01G195300 chr6B 697570186 697574043 3857 False 525.000000 894 96.518333 1233 3223 3 chr6B.!!$F3 1990
15 TraesCS6A01G195300 chr6B 697594206 697598063 3857 False 525.000000 894 96.518333 1233 3223 3 chr6B.!!$F4 1990
16 TraesCS6A01G195300 chr7A 59389668 59390592 924 True 931.000000 931 85.026000 668 1608 1 chr7A.!!$R1 940
17 TraesCS6A01G195300 chr5B 662918160 662918686 526 False 893.000000 893 97.164000 2528 3056 1 chr5B.!!$F1 528
18 TraesCS6A01G195300 chr1B 103073444 103073970 526 True 870.000000 870 96.408000 2528 3056 1 chr1B.!!$R1 528
19 TraesCS6A01G195300 chr4A 671650189 671651169 980 True 828.000000 828 82.714000 662 1608 1 chr4A.!!$R1 946
20 TraesCS6A01G195300 chr7D 55399128 55399792 664 True 789.000000 789 88.077000 662 1331 1 chr7D.!!$R1 669

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
359 756 0.030705 CCCTCTCATCCTCTTCCCCA 60.031 60.0 0.0 0.0 0.0 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2270 4933 0.40404 AAGGGGCGAACATGGAAAGA 59.596 50.0 0.0 0.0 0.0 2.52 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
354 751 1.047002 CGATGCCCTCTCATCCTCTT 58.953 55.000 0.00 0.00 39.64 2.85
359 756 0.030705 CCCTCTCATCCTCTTCCCCA 60.031 60.000 0.00 0.00 0.00 4.96
463 910 2.512515 CTACGGCTGGCTTGCTCC 60.513 66.667 0.00 0.00 0.00 4.70
494 941 1.131126 CGTGCATGCTTCGAATCCTTT 59.869 47.619 23.69 0.00 0.00 3.11
525 972 3.747579 CCCTTGGGCTGGCTGGAT 61.748 66.667 0.00 0.00 0.00 3.41
585 1032 2.335011 CTGCACGTCGTGTCTCCA 59.665 61.111 25.18 14.00 35.75 3.86
589 1036 2.597805 ACGTCGTGTCTCCAGCCT 60.598 61.111 0.00 0.00 0.00 4.58
637 1084 3.622826 CCGTTGTCCACCTCCCGT 61.623 66.667 0.00 0.00 0.00 5.28
804 1569 1.690633 GTCTCCCTCCATGCCTCCA 60.691 63.158 0.00 0.00 0.00 3.86
866 1631 5.588648 TCTCCTCCACGCATATTTTTAAAGG 59.411 40.000 0.00 0.00 0.00 3.11
884 1650 7.852971 TTAAAGGGAAATACGTAGGATTGTG 57.147 36.000 0.08 0.00 0.00 3.33
926 1692 1.209504 CGAATCCCCTTGCCAGACTTA 59.790 52.381 0.00 0.00 0.00 2.24
944 1727 4.957296 ACTTATTCTGTTGTGAGAACCGT 58.043 39.130 0.00 0.00 34.79 4.83
965 1748 4.446385 CGTTAAAATGAAGCCGGATCGATA 59.554 41.667 5.05 0.00 0.00 2.92
992 1783 5.751680 AGTTGCATACGATGTGAAATATGC 58.248 37.500 7.89 7.89 46.59 3.14
1013 1809 2.448542 AGCGATGGCCATAGGGGT 60.449 61.111 25.04 16.86 41.24 4.95
1093 1891 2.821378 CAATTGGAGATTGGTGAGTGCA 59.179 45.455 0.00 0.00 0.00 4.57
1099 1897 4.883585 TGGAGATTGGTGAGTGCATAATTC 59.116 41.667 0.00 0.00 0.00 2.17
1160 1984 2.095718 GCTAGTAGCTTGTGTGCCAAAC 60.096 50.000 15.16 0.00 38.45 2.93
1186 2014 5.398695 GGTTGTCCCCACTAGGCTTATAATT 60.399 44.000 0.00 0.00 0.00 1.40
1221 2049 4.635223 TCCTAATTGCAGATCTTCCATCG 58.365 43.478 0.00 0.00 0.00 3.84
1298 2156 3.636153 AGGCAATCCTACTTCTGGTTC 57.364 47.619 0.00 0.00 42.06 3.62
1352 2210 0.663688 TTACGCGTGTGGCATGTTTT 59.336 45.000 24.59 0.00 43.84 2.43
1388 2287 2.364970 TGGCATTCTGGAGTTTGTTTGG 59.635 45.455 0.00 0.00 0.00 3.28
1393 2292 3.374042 TCTGGAGTTTGTTTGGACCAA 57.626 42.857 1.69 1.69 0.00 3.67
1538 4197 2.627933 AGGTACTTAGGCCTTGGTTGA 58.372 47.619 12.58 0.00 27.25 3.18
1561 4222 1.376649 ATTCCTATCCATCCAGGGGC 58.623 55.000 0.00 0.00 38.24 5.80
1748 4409 1.523758 GACGCATCCAAGGTTGAGTT 58.476 50.000 7.76 0.00 30.30 3.01
1773 4434 0.613260 TGTGGAACCCCTTCAGATCG 59.387 55.000 0.00 0.00 34.36 3.69
1842 4503 1.152860 TCCTTTTTGTGCCTCCGCA 60.153 52.632 0.00 0.00 44.78 5.69
1891 4554 8.870160 CTTGTTTTGTCAAGGATGTAATTCAA 57.130 30.769 0.00 0.00 40.49 2.69
1950 4613 0.329596 GGTTCAGGCTCCTGGAACAT 59.670 55.000 21.39 0.00 39.05 2.71
1980 4643 1.449246 CTCGGAGCTGCCTTTGGAG 60.449 63.158 0.00 0.00 0.00 3.86
2043 4706 3.508762 TCTCGTCGCTATTTCCTTTGTC 58.491 45.455 0.00 0.00 0.00 3.18
2085 4748 6.649141 TGCTTAATGTGAGTTGTCTTAACGAT 59.351 34.615 0.00 0.00 0.00 3.73
2102 4765 2.942376 ACGATGTCTTGTCACTTTGCAA 59.058 40.909 0.00 0.00 0.00 4.08
2165 4828 1.637553 AGGGATCTTGTCAACATGGCT 59.362 47.619 0.00 0.00 0.00 4.75
2192 4855 1.932338 AGGACCAATGTCATCCCCATT 59.068 47.619 0.00 0.00 43.65 3.16
2213 4876 1.306911 TGAGGATGCTAGGCACCCA 60.307 57.895 5.66 3.13 46.70 4.51
2270 4933 5.426833 AGCTGTACCAGATCAAGGTATCTTT 59.573 40.000 17.02 5.11 43.08 2.52
2346 5009 4.906618 TCGGTTTCTTCTGCTCCTAATTT 58.093 39.130 0.00 0.00 0.00 1.82
2362 5025 1.033746 ATTTAGTGCCGCAGCTGCAT 61.034 50.000 36.03 17.84 41.46 3.96
2372 5035 1.671979 GCAGCTGCATCTCATTGGTA 58.328 50.000 33.36 0.00 41.59 3.25
2374 5037 2.915349 CAGCTGCATCTCATTGGTAGT 58.085 47.619 0.00 0.00 0.00 2.73
2499 5167 3.362706 AGCTGGTTCACTCGGATTAGTA 58.637 45.455 0.00 0.00 0.00 1.82
2847 5559 6.254281 TCCTTTTTCATGCTTTGCTACTAC 57.746 37.500 0.00 0.00 0.00 2.73
2928 5640 0.892755 ATTGTTGCAGCATGACCCAG 59.107 50.000 3.36 0.00 39.69 4.45
2988 5700 4.900054 AGTGTGGTGTTACCTCTCTTTACT 59.100 41.667 0.00 0.00 39.58 2.24
3019 5732 4.895297 TGGGCTGAAGAAATTTGAAGAAGT 59.105 37.500 0.00 0.00 0.00 3.01
3215 6031 2.092323 GAATGTAAAAAGGCCGAGGCT 58.908 47.619 14.33 0.00 41.24 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 5.480073 CCATGGGAAGAGTTTTGATTGGTTA 59.520 40.000 2.85 0.00 0.00 2.85
157 174 4.003648 CTGCGGGTATCTCTTTTTCTTGT 58.996 43.478 0.00 0.00 0.00 3.16
158 175 3.181506 GCTGCGGGTATCTCTTTTTCTTG 60.182 47.826 0.00 0.00 0.00 3.02
159 176 3.010420 GCTGCGGGTATCTCTTTTTCTT 58.990 45.455 0.00 0.00 0.00 2.52
160 177 2.633488 GCTGCGGGTATCTCTTTTTCT 58.367 47.619 0.00 0.00 0.00 2.52
161 178 1.671328 GGCTGCGGGTATCTCTTTTTC 59.329 52.381 0.00 0.00 0.00 2.29
171 195 4.354162 GGGTTTGGGCTGCGGGTA 62.354 66.667 0.00 0.00 0.00 3.69
354 751 1.209504 GTGGTCGATCTGAATTGGGGA 59.790 52.381 0.00 0.00 0.00 4.81
359 756 1.134788 GGACGGTGGTCGATCTGAATT 60.135 52.381 0.00 0.00 44.39 2.17
510 957 2.515523 CGATCCAGCCAGCCCAAG 60.516 66.667 0.00 0.00 0.00 3.61
512 959 4.100084 CACGATCCAGCCAGCCCA 62.100 66.667 0.00 0.00 0.00 5.36
575 1022 2.117423 TGGAGGCTGGAGACACGA 59.883 61.111 0.00 0.00 35.60 4.35
604 1051 3.745803 GGTCTCCGAGGTTCGCGT 61.746 66.667 5.77 0.00 38.82 6.01
796 1561 4.889112 CTGGCGGCATGGAGGCAT 62.889 66.667 13.85 0.00 44.47 4.40
866 1631 8.548721 CAAGATAACACAATCCTACGTATTTCC 58.451 37.037 0.00 0.00 0.00 3.13
881 1647 6.373005 TCTGAATCCTTCCAAGATAACACA 57.627 37.500 0.00 0.00 0.00 3.72
884 1650 6.516718 TCGATCTGAATCCTTCCAAGATAAC 58.483 40.000 0.00 0.00 0.00 1.89
926 1692 6.687081 TTTTAACGGTTCTCACAACAGAAT 57.313 33.333 0.00 0.00 34.86 2.40
944 1727 4.446385 CGTATCGATCCGGCTTCATTTTAA 59.554 41.667 0.00 0.00 0.00 1.52
965 1748 3.497297 TCACATCGTATGCAACTACGT 57.503 42.857 16.96 0.00 43.74 3.57
979 1765 2.288729 TCGCTGCTGCATATTTCACATC 59.711 45.455 16.29 0.00 39.64 3.06
991 1782 2.592574 TATGGCCATCGCTGCTGC 60.593 61.111 24.80 5.34 34.44 5.25
992 1783 1.964891 CCTATGGCCATCGCTGCTG 60.965 63.158 24.80 0.00 34.44 4.41
993 1784 2.429058 CCTATGGCCATCGCTGCT 59.571 61.111 24.80 0.00 34.44 4.24
1013 1809 2.905075 CCACCGCTACATCAAGATCAA 58.095 47.619 0.00 0.00 0.00 2.57
1160 1984 1.201429 AGCCTAGTGGGGACAACCAG 61.201 60.000 0.00 0.00 46.06 4.00
1186 2014 0.830444 ATTAGGATGGGGTCGCGCTA 60.830 55.000 5.56 0.00 0.00 4.26
1221 2049 7.550196 TGTCTAAATTGTTTAATAGGGGTCGTC 59.450 37.037 0.00 0.00 0.00 4.20
1298 2156 3.576118 CCCACCTGATAGACTGATACTGG 59.424 52.174 0.00 0.00 0.00 4.00
1352 2210 3.777106 ATGCCACAGAGAAGAGAACAA 57.223 42.857 0.00 0.00 0.00 2.83
1538 4197 4.017130 GCCCCTGGATGGATAGGAATAATT 60.017 45.833 0.00 0.00 38.35 1.40
1561 4222 9.478019 CTTATAACGACAACATCTTTGCTTAAG 57.522 33.333 0.00 0.00 35.04 1.85
1842 4503 6.381994 AGGTATTCAAACAATCCAGAATGCAT 59.618 34.615 0.00 0.00 35.62 3.96
1891 4554 4.760204 GCTACTACAACAATGGTTCCAGTT 59.240 41.667 2.13 0.00 34.21 3.16
1950 4613 1.964448 CTCCGAGGTACAGCACACA 59.036 57.895 0.00 0.00 0.00 3.72
1980 4643 0.512952 GACACATGAGACACGGTTGC 59.487 55.000 0.00 0.00 0.00 4.17
2043 4706 7.972277 ACATTAAGCAGCATTCACTTGAAATAG 59.028 33.333 0.00 0.00 37.61 1.73
2085 4748 3.119531 CCAGTTTGCAAAGTGACAAGACA 60.120 43.478 37.17 1.76 40.88 3.41
2102 4765 0.480690 TGGCATACACCAACCCAGTT 59.519 50.000 0.00 0.00 36.55 3.16
2165 4828 4.164221 GGGATGACATTGGTCCTCTTCTTA 59.836 45.833 0.00 0.00 43.65 2.10
2192 4855 1.414158 GGTGCCTAGCATCCTCAGTA 58.586 55.000 0.00 0.00 41.91 2.74
2213 4876 2.484264 GACCAGCATTCGTTACTTTGCT 59.516 45.455 0.00 0.00 45.86 3.91
2270 4933 0.404040 AAGGGGCGAACATGGAAAGA 59.596 50.000 0.00 0.00 0.00 2.52
2346 5009 2.512286 GATGCAGCTGCGGCACTA 60.512 61.111 32.11 15.38 45.23 2.74
2362 5025 4.341235 CCGAAGACCATACTACCAATGAGA 59.659 45.833 0.00 0.00 0.00 3.27
2372 5035 4.274950 CACAACAAAACCGAAGACCATACT 59.725 41.667 0.00 0.00 0.00 2.12
2374 5037 3.003897 GCACAACAAAACCGAAGACCATA 59.996 43.478 0.00 0.00 0.00 2.74
2499 5167 9.938280 TCTTGCTAACTTACTATGTTAACACAT 57.062 29.630 11.22 0.00 46.07 3.21
2847 5559 5.874895 TCTCAGTTCAAGCAAATCATCTG 57.125 39.130 0.00 0.00 0.00 2.90
2928 5640 5.238214 TCAAGGCACAAAATGTTTATTTGGC 59.762 36.000 4.29 4.58 41.08 4.52
3019 5732 4.200874 TCTTTACTTTGTCGGGCTTCAAA 58.799 39.130 0.00 0.00 33.44 2.69
3121 5937 9.653287 TTTCTATTTCTCACACTTTCACGATAT 57.347 29.630 0.00 0.00 0.00 1.63
3125 5941 7.408132 TCTTTCTATTTCTCACACTTTCACG 57.592 36.000 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.