Multiple sequence alignment - TraesCS7B01G430200

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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 TraesCS7B01G430200 chr7B 100.000 4123 0 0 1 4123 698885007 698880885 0.000000e+00 7614.0
1 TraesCS7B01G430200 chr7B 99.484 3102 15 1 1 3101 693342384 693339283 0.000000e+00 5638.0
2 TraesCS7B01G430200 chr7B 97.559 1024 23 1 3102 4123 697606180 697605157 0.000000e+00 1751.0
3 TraesCS7B01G430200 chr7B 93.512 1156 66 7 1952 3101 697607400 697606248 0.000000e+00 1711.0
4 TraesCS7B01G430200 chr7B 86.803 1470 108 27 1 1422 695918408 695916977 0.000000e+00 1561.0
5 TraesCS7B01G430200 chr7B 89.571 1026 103 2 3102 4123 697519853 697520878 0.000000e+00 1299.0
6 TraesCS7B01G430200 chr7B 88.458 979 111 2 2124 3101 697114643 697115620 0.000000e+00 1181.0
7 TraesCS7B01G430200 chr7B 98.006 652 13 0 3472 4123 693338886 693338235 0.000000e+00 1133.0
8 TraesCS7B01G430200 chr7B 85.552 969 133 5 2140 3101 697430210 697429242 0.000000e+00 1007.0
9 TraesCS7B01G430200 chr7B 90.839 775 30 16 3 746 695828368 695829132 0.000000e+00 1000.0
10 TraesCS7B01G430200 chr7B 90.839 775 30 16 3 746 695850067 695850831 0.000000e+00 1000.0
11 TraesCS7B01G430200 chr7B 87.426 843 84 13 585 1422 697433173 697432348 0.000000e+00 950.0
12 TraesCS7B01G430200 chr7B 85.539 899 123 5 2145 3036 685079127 685078229 0.000000e+00 933.0
13 TraesCS7B01G430200 chr7B 83.954 966 148 5 2143 3101 695916333 695915368 0.000000e+00 918.0
14 TraesCS7B01G430200 chr7B 82.655 1032 152 15 3102 4123 697115688 697116702 0.000000e+00 889.0
15 TraesCS7B01G430200 chr7B 81.853 1036 153 24 3102 4123 685209675 685210689 0.000000e+00 839.0
16 TraesCS7B01G430200 chr7B 81.871 1026 157 18 3102 4123 697429174 697428174 0.000000e+00 837.0
17 TraesCS7B01G430200 chr7B 81.529 1007 134 32 3126 4123 695915276 695914313 0.000000e+00 782.0
18 TraesCS7B01G430200 chr7B 80.522 996 172 16 3102 4094 685072824 685071848 0.000000e+00 745.0
19 TraesCS7B01G430200 chr7B 85.221 521 62 11 957 1465 697608241 697607724 4.720000e-144 521.0
20 TraesCS7B01G430200 chr7B 85.089 503 67 6 932 1428 685087705 685087205 1.320000e-139 507.0
21 TraesCS7B01G430200 chr7B 83.368 487 68 3 994 1468 685207896 685208381 4.890000e-119 438.0
22 TraesCS7B01G430200 chr7B 100.000 178 0 0 3102 3279 693339215 693339038 3.070000e-86 329.0
23 TraesCS7B01G430200 chr7B 84.722 288 22 6 3 272 694271268 694271551 6.790000e-68 268.0
24 TraesCS7B01G430200 chr7B 81.034 290 21 9 1 259 697057267 697057553 2.510000e-47 200.0
25 TraesCS7B01G430200 chr7B 82.114 123 9 9 25 147 685118787 685118678 4.390000e-15 93.5
26 TraesCS7B01G430200 chr7B 91.304 69 4 2 177 245 693342644 693342578 4.390000e-15 93.5
27 TraesCS7B01G430200 chr7B 94.340 53 1 1 1497 1547 697607630 697607578 3.420000e-11 80.5
28 TraesCS7B01G430200 chrUn 99.436 1418 8 0 1684 3101 312471075 312469658 0.000000e+00 2575.0
29 TraesCS7B01G430200 chrUn 98.532 1022 15 0 3102 4123 312469590 312468569 0.000000e+00 1805.0
30 TraesCS7B01G430200 chrUn 98.006 652 13 0 3472 4123 289851615 289850964 0.000000e+00 1133.0
31 TraesCS7B01G430200 chr7D 89.808 991 98 3 2112 3101 608085455 608086443 0.000000e+00 1267.0
32 TraesCS7B01G430200 chr7D 87.875 734 62 18 994 1721 608082829 608083541 0.000000e+00 837.0
33 TraesCS7B01G430200 chr7D 82.519 778 95 11 3102 3875 608086511 608087251 0.000000e+00 645.0
34 TraesCS7B01G430200 chr7D 83.486 109 12 5 159 262 607985249 607985142 3.390000e-16 97.1
35 TraesCS7B01G430200 chr7A 83.333 1026 144 19 3102 4122 700085702 700086705 0.000000e+00 922.0
36 TraesCS7B01G430200 chr7A 83.954 966 148 5 2143 3101 700111213 700110248 0.000000e+00 918.0
37 TraesCS7B01G430200 chr7A 80.116 1031 177 16 3102 4122 700062792 700063804 0.000000e+00 743.0
38 TraesCS7B01G430200 chr7A 84.112 642 99 3 2461 3101 700062085 700062724 5.860000e-173 617.0
39 TraesCS7B01G430200 chr7A 85.680 419 58 1 1004 1422 700055266 700055682 1.360000e-119 440.0
40 TraesCS7B01G430200 chr7A 82.122 509 57 22 3519 4011 700031348 700030858 4.960000e-109 405.0
41 TraesCS7B01G430200 chr7A 85.358 321 47 0 994 1314 700082588 700082908 2.380000e-87 333.0
42 TraesCS7B01G430200 chr7A 85.135 296 17 2 1 272 700054880 700055172 1.130000e-70 278.0


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 TraesCS7B01G430200 chr7B 698880885 698885007 4122 True 7614.000000 7614 100.000000 1 4123 1 chr7B.!!$R5 4122
1 TraesCS7B01G430200 chr7B 693338235 693342644 4409 True 1798.375000 5638 97.198500 1 4123 4 chr7B.!!$R6 4122
2 TraesCS7B01G430200 chr7B 697519853 697520878 1025 False 1299.000000 1299 89.571000 3102 4123 1 chr7B.!!$F5 1021
3 TraesCS7B01G430200 chr7B 695914313 695918408 4095 True 1087.000000 1561 84.095333 1 4123 3 chr7B.!!$R7 4122
4 TraesCS7B01G430200 chr7B 697114643 697116702 2059 False 1035.000000 1181 85.556500 2124 4123 2 chr7B.!!$F7 1999
5 TraesCS7B01G430200 chr7B 697605157 697608241 3084 True 1015.875000 1751 92.658000 957 4123 4 chr7B.!!$R9 3166
6 TraesCS7B01G430200 chr7B 695828368 695829132 764 False 1000.000000 1000 90.839000 3 746 1 chr7B.!!$F2 743
7 TraesCS7B01G430200 chr7B 695850067 695850831 764 False 1000.000000 1000 90.839000 3 746 1 chr7B.!!$F3 743
8 TraesCS7B01G430200 chr7B 685078229 685079127 898 True 933.000000 933 85.539000 2145 3036 1 chr7B.!!$R2 891
9 TraesCS7B01G430200 chr7B 697428174 697433173 4999 True 931.333333 1007 84.949667 585 4123 3 chr7B.!!$R8 3538
10 TraesCS7B01G430200 chr7B 685071848 685072824 976 True 745.000000 745 80.522000 3102 4094 1 chr7B.!!$R1 992
11 TraesCS7B01G430200 chr7B 685207896 685210689 2793 False 638.500000 839 82.610500 994 4123 2 chr7B.!!$F6 3129
12 TraesCS7B01G430200 chr7B 685087205 685087705 500 True 507.000000 507 85.089000 932 1428 1 chr7B.!!$R3 496
13 TraesCS7B01G430200 chrUn 312468569 312471075 2506 True 2190.000000 2575 98.984000 1684 4123 2 chrUn.!!$R2 2439
14 TraesCS7B01G430200 chrUn 289850964 289851615 651 True 1133.000000 1133 98.006000 3472 4123 1 chrUn.!!$R1 651
15 TraesCS7B01G430200 chr7D 608082829 608087251 4422 False 916.333333 1267 86.734000 994 3875 3 chr7D.!!$F1 2881
16 TraesCS7B01G430200 chr7A 700110248 700111213 965 True 918.000000 918 83.954000 2143 3101 1 chr7A.!!$R2 958
17 TraesCS7B01G430200 chr7A 700062085 700063804 1719 False 680.000000 743 82.114000 2461 4122 2 chr7A.!!$F2 1661
18 TraesCS7B01G430200 chr7A 700082588 700086705 4117 False 627.500000 922 84.345500 994 4122 2 chr7A.!!$F3 3128
19 TraesCS7B01G430200 chr7A 700054880 700055682 802 False 359.000000 440 85.407500 1 1422 2 chr7A.!!$F1 1421

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
44 306 4.084380 GCCAAAGTTGCTCTTTTATGTTGC 60.084 41.667 5.08 0.0 42.95 4.17 F
263 558 7.452880 AGCTTGTGTTCAGCTCATTAATTAA 57.547 32.000 0.00 0.0 32.98 1.40 F
1022 1400 4.871871 TGGCAGATCCAATTACCCTTAA 57.128 40.909 0.00 0.0 43.21 1.85 F
2637 6985 3.315470 GGAAGTCTGCCCGGATTTTAATC 59.685 47.826 0.73 0.0 34.66 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1022 1400 1.842007 CCCCATCCTACAGCAGCAT 59.158 57.895 0.00 0.0 0.00 3.79 R
2637 6985 7.308435 AGATTTTCTTTTAAGGCATGAAGACG 58.692 34.615 0.00 0.0 0.00 4.18 R
2700 7048 4.041567 ACTGTTGTACCAGACATCATCCAA 59.958 41.667 6.18 0.0 37.19 3.53 R
4039 8471 0.343018 TCCCATCATCCCAGACCAGA 59.657 55.000 0.00 0.0 0.00 3.86 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
44 306 4.084380 GCCAAAGTTGCTCTTTTATGTTGC 60.084 41.667 5.08 0.0 42.95 4.17
263 558 7.452880 AGCTTGTGTTCAGCTCATTAATTAA 57.547 32.000 0.00 0.0 32.98 1.40
1022 1400 4.871871 TGGCAGATCCAATTACCCTTAA 57.128 40.909 0.00 0.0 43.21 1.85
2637 6985 3.315470 GGAAGTCTGCCCGGATTTTAATC 59.685 47.826 0.73 0.0 34.66 1.75
2700 7048 6.866248 GTGTGGAAAACGGATTTTGTTGATAT 59.134 34.615 0.00 0.0 38.17 1.63
3977 8409 3.040147 TCCACGGTCTTGAGAATGTTC 57.960 47.619 0.00 0.0 0.00 3.18
4012 8444 1.135170 GCTCTTGAAGCCAATCTTGCC 60.135 52.381 0.00 0.0 45.92 4.52
4039 8471 4.600062 AGGAAAAACTCACAGAACTGGTT 58.400 39.130 6.76 0.0 34.19 3.67
4099 8546 0.248843 CAGAGGTGCTTGAGGGTCTC 59.751 60.000 0.00 0.0 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 306 0.179166 AACAGCACAACACTGCAACG 60.179 50.000 0.00 0.0 39.86 4.10
263 558 6.098838 TCAGTATTAGTGGAGTCATGCTGAAT 59.901 38.462 5.94 0.0 0.00 2.57
1022 1400 1.842007 CCCCATCCTACAGCAGCAT 59.158 57.895 0.00 0.0 0.00 3.79
2637 6985 7.308435 AGATTTTCTTTTAAGGCATGAAGACG 58.692 34.615 0.00 0.0 0.00 4.18
2700 7048 4.041567 ACTGTTGTACCAGACATCATCCAA 59.958 41.667 6.18 0.0 37.19 3.53
3977 8409 3.457099 GAGCCTCTTCCTTGCTCTG 57.543 57.895 3.61 0.0 46.19 3.35
4012 8444 1.946768 TCTGTGAGTTTTTCCTTGCCG 59.053 47.619 0.00 0.0 0.00 5.69
4039 8471 0.343018 TCCCATCATCCCAGACCAGA 59.657 55.000 0.00 0.0 0.00 3.86


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

AutoCloner maintained by Alex Coulton.