Multiple sequence alignment - TraesCS6D01G031800

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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 TraesCS6D01G031800 chr6D 100.000 3357 0 0 1 3357 13475731 13479087 0.000000e+00 6200.0
1 TraesCS6D01G031800 chr6D 92.749 331 21 2 1168 1496 450188473 450188144 3.030000e-130 475.0
2 TraesCS6D01G031800 chr1D 97.560 3361 55 5 1 3357 62893680 62897017 0.000000e+00 5727.0
3 TraesCS6D01G031800 chr1D 86.842 684 56 8 182 863 60174599 60173948 0.000000e+00 734.0
4 TraesCS6D01G031800 chr1D 84.195 658 61 20 1498 2145 37568514 37569138 1.720000e-167 599.0
5 TraesCS6D01G031800 chr1D 85.185 324 29 9 860 1164 60173721 60173398 6.990000e-82 315.0
6 TraesCS6D01G031800 chr5D 97.478 3014 53 5 350 3357 14029653 14032649 0.000000e+00 5123.0
7 TraesCS6D01G031800 chr5D 92.565 1197 70 8 2146 3326 127938812 127937619 0.000000e+00 1700.0
8 TraesCS6D01G031800 chr5D 92.749 331 21 2 1168 1496 127939137 127938808 3.030000e-130 475.0
9 TraesCS6D01G031800 chr2D 93.141 1910 65 17 1432 3320 518814 520678 0.000000e+00 2741.0
10 TraesCS6D01G031800 chr2D 95.385 715 27 5 1432 2140 23116197 23115483 0.000000e+00 1133.0
11 TraesCS6D01G031800 chr2D 92.751 676 22 6 1 672 518166 518818 0.000000e+00 952.0
12 TraesCS6D01G031800 chr2D 92.377 669 27 4 1 668 23116844 23116199 0.000000e+00 931.0
13 TraesCS6D01G031800 chr2D 93.373 332 19 2 1168 1496 29095570 29095239 3.890000e-134 488.0
14 TraesCS6D01G031800 chr5A 97.222 1188 27 4 1837 3021 689190312 689189128 0.000000e+00 2006.0
15 TraesCS6D01G031800 chr5A 97.138 1188 29 3 1837 3021 707255988 707257173 0.000000e+00 2001.0
16 TraesCS6D01G031800 chr5A 95.732 1031 24 4 1 1028 707254971 707255984 0.000000e+00 1642.0
17 TraesCS6D01G031800 chr5A 94.995 939 19 4 92 1028 689191228 689190316 0.000000e+00 1448.0
18 TraesCS6D01G031800 chr5A 91.311 679 29 14 1 672 3949175 3948520 0.000000e+00 900.0
19 TraesCS6D01G031800 chr5A 93.898 590 29 5 1432 2014 3948524 3947935 0.000000e+00 883.0
20 TraesCS6D01G031800 chr6A 97.138 1188 29 3 1837 3021 540806189 540805004 0.000000e+00 2001.0
21 TraesCS6D01G031800 chr6A 96.465 1188 37 3 1837 3021 589345936 589347121 0.000000e+00 1956.0
22 TraesCS6D01G031800 chr6A 94.949 990 29 7 1 986 540818296 540817324 0.000000e+00 1531.0
23 TraesCS6D01G031800 chr6A 95.370 864 17 5 170 1028 589345087 589345932 0.000000e+00 1352.0
24 TraesCS6D01G031800 chr6A 97.143 175 4 1 1 174 589344664 589344838 9.110000e-76 294.0
25 TraesCS6D01G031800 chr4A 96.549 1188 36 3 1837 3021 637544917 637546102 0.000000e+00 1962.0
26 TraesCS6D01G031800 chr4A 94.700 566 9 10 465 1028 637544367 637544913 0.000000e+00 859.0
27 TraesCS6D01G031800 chr4A 97.619 42 1 0 3315 3356 31395528 31395487 4.650000e-09 73.1
28 TraesCS6D01G031800 chr7D 92.359 1191 72 8 2146 3320 340174822 340176009 0.000000e+00 1677.0
29 TraesCS6D01G031800 chr7D 93.051 331 20 2 1168 1496 530740077 530739748 6.510000e-132 481.0
30 TraesCS6D01G031800 chr7D 97.500 40 1 0 3318 3357 449501613 449501574 6.010000e-08 69.4
31 TraesCS6D01G031800 chr7D 97.500 40 1 0 3318 3357 621799234 621799273 6.010000e-08 69.4
32 TraesCS6D01G031800 chr2A 86.148 989 77 18 198 1164 3758373 3759323 0.000000e+00 1013.0
33 TraesCS6D01G031800 chr3B 92.806 417 27 2 1168 1581 775658635 775658219 4.790000e-168 601.0
34 TraesCS6D01G031800 chr3B 97.333 75 2 0 1 75 775659845 775659771 9.780000e-26 128.0
35 TraesCS6D01G031800 chr1B 91.388 418 32 2 1168 1581 289694130 289694547 1.350000e-158 569.0
36 TraesCS6D01G031800 chr1B 82.362 652 48 25 1503 2145 57499162 57499755 3.870000e-139 505.0
37 TraesCS6D01G031800 chr1B 95.714 70 3 0 6 75 289692962 289693031 2.740000e-21 113.0
38 TraesCS6D01G031800 chr1B 90.000 80 7 1 1907 1985 57499714 57499793 5.930000e-18 102.0
39 TraesCS6D01G031800 chr2B 87.665 454 41 11 661 1111 62444612 62445053 6.420000e-142 514.0
40 TraesCS6D01G031800 chr4D 92.793 333 20 3 1168 1496 85851013 85850681 2.340000e-131 479.0
41 TraesCS6D01G031800 chr1A 92.353 170 12 1 1528 1696 36778741 36778910 1.200000e-59 241.0
42 TraesCS6D01G031800 chr1A 82.143 224 17 5 1681 1902 36779014 36779216 1.600000e-38 171.0
43 TraesCS6D01G031800 chrUn 95.000 40 2 0 3318 3357 284055832 284055793 2.800000e-06 63.9
44 TraesCS6D01G031800 chrUn 97.297 37 1 0 3318 3354 284069456 284069492 2.800000e-06 63.9
45 TraesCS6D01G031800 chrUn 95.000 40 2 0 3318 3357 289948950 289948911 2.800000e-06 63.9
46 TraesCS6D01G031800 chrUn 97.297 37 1 0 3318 3354 289969793 289969829 2.800000e-06 63.9


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 TraesCS6D01G031800 chr6D 13475731 13479087 3356 False 6200.000000 6200 100.0000 1 3357 1 chr6D.!!$F1 3356
1 TraesCS6D01G031800 chr1D 62893680 62897017 3337 False 5727.000000 5727 97.5600 1 3357 1 chr1D.!!$F2 3356
2 TraesCS6D01G031800 chr1D 37568514 37569138 624 False 599.000000 599 84.1950 1498 2145 1 chr1D.!!$F1 647
3 TraesCS6D01G031800 chr1D 60173398 60174599 1201 True 524.500000 734 86.0135 182 1164 2 chr1D.!!$R1 982
4 TraesCS6D01G031800 chr5D 14029653 14032649 2996 False 5123.000000 5123 97.4780 350 3357 1 chr5D.!!$F1 3007
5 TraesCS6D01G031800 chr5D 127937619 127939137 1518 True 1087.500000 1700 92.6570 1168 3326 2 chr5D.!!$R1 2158
6 TraesCS6D01G031800 chr2D 518166 520678 2512 False 1846.500000 2741 92.9460 1 3320 2 chr2D.!!$F1 3319
7 TraesCS6D01G031800 chr2D 23115483 23116844 1361 True 1032.000000 1133 93.8810 1 2140 2 chr2D.!!$R2 2139
8 TraesCS6D01G031800 chr5A 707254971 707257173 2202 False 1821.500000 2001 96.4350 1 3021 2 chr5A.!!$F1 3020
9 TraesCS6D01G031800 chr5A 689189128 689191228 2100 True 1727.000000 2006 96.1085 92 3021 2 chr5A.!!$R2 2929
10 TraesCS6D01G031800 chr5A 3947935 3949175 1240 True 891.500000 900 92.6045 1 2014 2 chr5A.!!$R1 2013
11 TraesCS6D01G031800 chr6A 540805004 540806189 1185 True 2001.000000 2001 97.1380 1837 3021 1 chr6A.!!$R1 1184
12 TraesCS6D01G031800 chr6A 540817324 540818296 972 True 1531.000000 1531 94.9490 1 986 1 chr6A.!!$R2 985
13 TraesCS6D01G031800 chr6A 589344664 589347121 2457 False 1200.666667 1956 96.3260 1 3021 3 chr6A.!!$F1 3020
14 TraesCS6D01G031800 chr4A 637544367 637546102 1735 False 1410.500000 1962 95.6245 465 3021 2 chr4A.!!$F1 2556
15 TraesCS6D01G031800 chr7D 340174822 340176009 1187 False 1677.000000 1677 92.3590 2146 3320 1 chr7D.!!$F1 1174
16 TraesCS6D01G031800 chr2A 3758373 3759323 950 False 1013.000000 1013 86.1480 198 1164 1 chr2A.!!$F1 966
17 TraesCS6D01G031800 chr3B 775658219 775659845 1626 True 364.500000 601 95.0695 1 1581 2 chr3B.!!$R1 1580
18 TraesCS6D01G031800 chr1B 289692962 289694547 1585 False 341.000000 569 93.5510 6 1581 2 chr1B.!!$F2 1575
19 TraesCS6D01G031800 chr1B 57499162 57499793 631 False 303.500000 505 86.1810 1503 2145 2 chr1B.!!$F1 642

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
629 1181 2.159517 GCATTGGGAAAGCTCAAGTACG 60.16 50.0 0.0 0.0 38.04 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2358 4071 0.107508 CGGAGTTGGCCATGATGTCT 60.108 55.0 6.09 0.0 0.0 3.41 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
559 1102 7.491696 AGCCGCTTTTATCAGTTAGTTAGTTAG 59.508 37.037 0.00 0.0 0.00 2.34
560 1103 7.277319 GCCGCTTTTATCAGTTAGTTAGTTAGT 59.723 37.037 0.00 0.0 0.00 2.24
561 1104 9.148104 CCGCTTTTATCAGTTAGTTAGTTAGTT 57.852 33.333 0.00 0.0 0.00 2.24
629 1181 2.159517 GCATTGGGAAAGCTCAAGTACG 60.160 50.000 0.00 0.0 38.04 3.67
1007 2211 6.147821 CGACTTTGTTCCATTGATAGTGAGTT 59.852 38.462 0.00 0.0 0.00 3.01
1989 3677 8.542497 TTCTGAACTTGCATATTTAGTACGTT 57.458 30.769 0.00 0.0 0.00 3.99
2285 3978 3.542712 ACTAAGCTGCATTTGTTGACG 57.457 42.857 1.02 0.0 0.00 4.35
2296 3989 2.098215 TTGTTGACGCATTTCACACG 57.902 45.000 0.00 0.0 0.00 4.49
2419 4132 1.354337 CGAGTGGGTGCAGAACATCG 61.354 60.000 0.00 0.0 0.00 3.84
2689 4413 5.163513 CACAAATATGGAAAGAAGTGTGGC 58.836 41.667 0.00 0.0 33.22 5.01
2783 4507 7.819415 TCTGTTTGTTCTTCGATGATCTTATGT 59.181 33.333 1.37 0.0 0.00 2.29
2842 4566 9.463902 TCTAGTTAGTAAGCAGAACTCTGTTAT 57.536 33.333 8.46 0.0 45.45 1.89
2971 4696 3.742369 GCAAAACACAAGCTGCAATGTAT 59.258 39.130 10.18 0.0 34.87 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
384 921 2.048444 AGCACCACCATCATCATCAC 57.952 50.000 0.00 0.00 0.00 3.06
559 1102 6.543465 ACCAACCAACCAACTAACTAACTAAC 59.457 38.462 0.00 0.00 0.00 2.34
560 1103 6.661777 ACCAACCAACCAACTAACTAACTAA 58.338 36.000 0.00 0.00 0.00 2.24
561 1104 6.251255 ACCAACCAACCAACTAACTAACTA 57.749 37.500 0.00 0.00 0.00 2.24
562 1105 5.120054 ACCAACCAACCAACTAACTAACT 57.880 39.130 0.00 0.00 0.00 2.24
563 1106 5.450826 CCAACCAACCAACCAACTAACTAAC 60.451 44.000 0.00 0.00 0.00 2.34
564 1107 4.645588 CCAACCAACCAACCAACTAACTAA 59.354 41.667 0.00 0.00 0.00 2.24
565 1108 4.208746 CCAACCAACCAACCAACTAACTA 58.791 43.478 0.00 0.00 0.00 2.24
567 1110 2.761767 ACCAACCAACCAACCAACTAAC 59.238 45.455 0.00 0.00 0.00 2.34
569 1112 2.761208 CAACCAACCAACCAACCAACTA 59.239 45.455 0.00 0.00 0.00 2.24
570 1113 1.552792 CAACCAACCAACCAACCAACT 59.447 47.619 0.00 0.00 0.00 3.16
571 1114 1.406205 CCAACCAACCAACCAACCAAC 60.406 52.381 0.00 0.00 0.00 3.77
572 1115 0.905357 CCAACCAACCAACCAACCAA 59.095 50.000 0.00 0.00 0.00 3.67
573 1116 0.252284 ACCAACCAACCAACCAACCA 60.252 50.000 0.00 0.00 0.00 3.67
629 1181 6.096001 ACTGAATTTGCCTCATAACAATCTCC 59.904 38.462 0.00 0.00 0.00 3.71
1097 2533 5.734720 ACGAGGAACTATTGTGATGATGTT 58.265 37.500 0.00 0.00 41.55 2.71
1484 3157 3.004839 TGCCAAAATCCGAAAATCGAACA 59.995 39.130 0.58 0.00 43.74 3.18
1989 3677 3.513515 TGTGTGGACTGCTGATACATACA 59.486 43.478 0.00 5.23 32.11 2.29
2285 3978 6.165659 ACTATAAGTCAACGTGTGAAATGC 57.834 37.500 0.00 0.00 38.23 3.56
2358 4071 0.107508 CGGAGTTGGCCATGATGTCT 60.108 55.000 6.09 0.00 0.00 3.41
2419 4132 0.320374 TCGTCCCACATGAACACCTC 59.680 55.000 0.00 0.00 0.00 3.85
2689 4413 5.366768 TGACAGAGATGACTAAAATAGGGGG 59.633 44.000 0.00 0.00 0.00 5.40
2783 4507 1.614903 CAATGAGAACCAGGCAAGCAA 59.385 47.619 0.00 0.00 0.00 3.91
2842 4566 2.686915 GACGTCCCAGCTAGCTTTACTA 59.313 50.000 16.46 0.00 0.00 1.82
2971 4696 4.944619 AGACATGTCAGACAAGAGTTGA 57.055 40.909 27.02 0.00 0.00 3.18
3016 4741 5.809001 AGAAAGAATAGCATCAGGAACACA 58.191 37.500 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.