Multiple sequence alignment - TraesCS1B01G129700

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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 TraesCS1B01G129700 chr1B 100.000 2595 0 0 1 2595 160016954 160019548 0.000000e+00 4793.0
1 TraesCS1B01G129700 chr1B 83.448 145 9 5 448 583 36924701 36924839 1.260000e-23 121.0
2 TraesCS1B01G129700 chr3D 90.685 1707 85 22 1 1678 347130974 347129313 0.000000e+00 2204.0
3 TraesCS1B01G129700 chr1D 90.237 1731 78 24 1 1682 182524994 182523306 0.000000e+00 2176.0
4 TraesCS1B01G129700 chr1D 88.235 51 1 3 494 539 409061005 409060955 3.610000e-04 56.5
5 TraesCS1B01G129700 chr6D 91.132 1590 62 18 138 1675 348104220 348102658 0.000000e+00 2082.0
6 TraesCS1B01G129700 chr6D 95.333 150 7 0 1 150 348105877 348105728 3.340000e-59 239.0
7 TraesCS1B01G129700 chr7D 88.113 1590 69 28 138 1675 498288616 498287095 0.000000e+00 1779.0
8 TraesCS1B01G129700 chr7D 96.220 926 31 2 1674 2595 595750663 595749738 0.000000e+00 1513.0
9 TraesCS1B01G129700 chr7D 86.047 559 28 11 1169 1677 498235749 498235191 2.920000e-154 555.0
10 TraesCS1B01G129700 chr7D 96.269 134 5 0 1 134 498290242 498290109 1.210000e-53 220.0
11 TraesCS1B01G129700 chr7D 100.000 28 0 0 1649 1676 4258692 4258665 5.000000e-03 52.8
12 TraesCS1B01G129700 chr2B 97.405 925 21 2 1674 2595 742354787 742353863 0.000000e+00 1572.0
13 TraesCS1B01G129700 chr2B 96.649 925 28 1 1674 2595 684001487 684000563 0.000000e+00 1533.0
14 TraesCS1B01G129700 chr2B 96.514 918 30 1 1674 2589 49036592 49037509 0.000000e+00 1517.0
15 TraesCS1B01G129700 chr2B 96.000 925 34 1 1674 2595 33602203 33603127 0.000000e+00 1500.0
16 TraesCS1B01G129700 chr2B 97.403 77 2 0 897 973 754629307 754629231 5.830000e-27 132.0
17 TraesCS1B01G129700 chr2B 100.000 29 0 0 1649 1677 752250799 752250771 1.000000e-03 54.7
18 TraesCS1B01G129700 chr3B 97.386 918 23 1 1 918 590829931 590829015 0.000000e+00 1561.0
19 TraesCS1B01G129700 chr3B 95.520 625 28 0 914 1538 590827269 590826645 0.000000e+00 1000.0
20 TraesCS1B01G129700 chr3B 96.269 134 5 0 1 134 739575258 739575125 1.210000e-53 220.0
21 TraesCS1B01G129700 chr3B 90.083 121 12 0 1555 1675 370263882 370263762 9.610000e-35 158.0
22 TraesCS1B01G129700 chr3B 100.000 29 0 0 1649 1677 336731506 336731534 1.000000e-03 54.7
23 TraesCS1B01G129700 chr6B 97.180 922 24 2 1674 2595 700765308 700764389 0.000000e+00 1557.0
24 TraesCS1B01G129700 chr6B 96.108 925 33 1 1674 2595 241432188 241433112 0.000000e+00 1506.0
25 TraesCS1B01G129700 chr6B 92.920 113 7 1 655 766 720407161 720407273 2.070000e-36 163.0
26 TraesCS1B01G129700 chr6B 85.401 137 4 6 840 975 720407270 720407391 7.540000e-26 128.0
27 TraesCS1B01G129700 chr7B 95.779 924 37 1 1674 2595 348750824 348749901 0.000000e+00 1489.0
28 TraesCS1B01G129700 chr7B 100.000 29 0 0 1649 1677 315574509 315574481 1.000000e-03 54.7
29 TraesCS1B01G129700 chr5D 95.788 926 32 5 1674 2595 551104388 551105310 0.000000e+00 1487.0
30 TraesCS1B01G129700 chr2D 88.293 1119 60 27 578 1676 542308714 542309781 0.000000e+00 1275.0
31 TraesCS1B01G129700 chr2D 94.400 250 11 2 1 248 542308467 542308715 5.240000e-102 381.0
32 TraesCS1B01G129700 chr2D 96.269 134 5 0 1 134 619210941 619210808 1.210000e-53 220.0
33 TraesCS1B01G129700 chrUn 89.252 428 26 15 1257 1664 476388571 476388998 3.830000e-143 518.0
34 TraesCS1B01G129700 chrUn 88.235 51 1 3 494 539 366669552 366669502 3.610000e-04 56.5
35 TraesCS1B01G129700 chrUn 88.235 51 1 3 494 539 479219017 479219067 3.610000e-04 56.5
36 TraesCS1B01G129700 chr5A 88.803 259 27 2 838 1095 214856113 214856370 1.500000e-82 316.0
37 TraesCS1B01G129700 chr5A 84.921 126 10 6 693 810 214856040 214856164 4.540000e-23 119.0
38 TraesCS1B01G129700 chr6A 87.645 259 30 2 838 1095 350126632 350126375 1.510000e-77 300.0
39 TraesCS1B01G129700 chr6A 84.291 261 30 3 1109 1358 350126276 350126016 7.170000e-61 244.0
40 TraesCS1B01G129700 chr6A 84.127 126 12 6 693 810 350126706 350126581 5.870000e-22 115.0
41 TraesCS1B01G129700 chr4D 88.136 177 15 4 1100 1270 667140 666964 3.380000e-49 206.0
42 TraesCS1B01G129700 chr4D 87.432 183 17 4 1094 1270 509503431 509503613 3.380000e-49 206.0
43 TraesCS1B01G129700 chr4D 94.444 36 1 1 1649 1683 290733145 290733180 1.000000e-03 54.7


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 TraesCS1B01G129700 chr1B 160016954 160019548 2594 False 4793.000000 4793 100.000000 1 2595 1 chr1B.!!$F2 2594
1 TraesCS1B01G129700 chr3D 347129313 347130974 1661 True 2204.000000 2204 90.685000 1 1678 1 chr3D.!!$R1 1677
2 TraesCS1B01G129700 chr1D 182523306 182524994 1688 True 2176.000000 2176 90.237000 1 1682 1 chr1D.!!$R1 1681
3 TraesCS1B01G129700 chr6D 348102658 348105877 3219 True 1160.500000 2082 93.232500 1 1675 2 chr6D.!!$R1 1674
4 TraesCS1B01G129700 chr7D 595749738 595750663 925 True 1513.000000 1513 96.220000 1674 2595 1 chr7D.!!$R3 921
5 TraesCS1B01G129700 chr7D 498287095 498290242 3147 True 999.500000 1779 92.191000 1 1675 2 chr7D.!!$R4 1674
6 TraesCS1B01G129700 chr7D 498235191 498235749 558 True 555.000000 555 86.047000 1169 1677 1 chr7D.!!$R2 508
7 TraesCS1B01G129700 chr2B 742353863 742354787 924 True 1572.000000 1572 97.405000 1674 2595 1 chr2B.!!$R2 921
8 TraesCS1B01G129700 chr2B 684000563 684001487 924 True 1533.000000 1533 96.649000 1674 2595 1 chr2B.!!$R1 921
9 TraesCS1B01G129700 chr2B 49036592 49037509 917 False 1517.000000 1517 96.514000 1674 2589 1 chr2B.!!$F2 915
10 TraesCS1B01G129700 chr2B 33602203 33603127 924 False 1500.000000 1500 96.000000 1674 2595 1 chr2B.!!$F1 921
11 TraesCS1B01G129700 chr3B 590826645 590829931 3286 True 1280.500000 1561 96.453000 1 1538 2 chr3B.!!$R3 1537
12 TraesCS1B01G129700 chr6B 700764389 700765308 919 True 1557.000000 1557 97.180000 1674 2595 1 chr6B.!!$R1 921
13 TraesCS1B01G129700 chr6B 241432188 241433112 924 False 1506.000000 1506 96.108000 1674 2595 1 chr6B.!!$F1 921
14 TraesCS1B01G129700 chr7B 348749901 348750824 923 True 1489.000000 1489 95.779000 1674 2595 1 chr7B.!!$R2 921
15 TraesCS1B01G129700 chr5D 551104388 551105310 922 False 1487.000000 1487 95.788000 1674 2595 1 chr5D.!!$F1 921
16 TraesCS1B01G129700 chr2D 542308467 542309781 1314 False 828.000000 1275 91.346500 1 1676 2 chr2D.!!$F1 1675
17 TraesCS1B01G129700 chr6A 350126016 350126706 690 True 219.666667 300 85.354333 693 1358 3 chr6A.!!$R1 665

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
984 4309 2.826128 ACCATCTTCTACAAGCGAGACA 59.174 45.455 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2491 6057 0.806884 GGTGTCGTGGTGTCAAACGA 60.807 55.0 7.7 7.7 45.86 3.85 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
90 91 4.081642 TGGAGTACTAGTCCATTGAAGTGC 60.082 45.833 8.39 0.00 42.54 4.40
164 1694 5.109210 TGCTCATAATTAAGTGTCGGAGTG 58.891 41.667 0.00 0.00 0.00 3.51
574 2134 6.227298 AGATTGCAAGCTACTGTAGTGTAT 57.773 37.500 17.09 6.00 0.00 2.29
772 2332 8.740123 TTTTGTACTTCAATTGTTCTACTCCA 57.260 30.769 5.13 0.00 35.84 3.86
984 4309 2.826128 ACCATCTTCTACAAGCGAGACA 59.174 45.455 0.00 0.00 0.00 3.41
1010 4335 1.943968 GCCGTTGTCAATGGTGAGCTA 60.944 52.381 22.22 0.00 39.84 3.32
1019 4344 5.656859 TGTCAATGGTGAGCTAGTACTACAT 59.343 40.000 0.00 0.00 33.27 2.29
1059 4384 2.191400 ACCTTCTGCTGCTCCTTATGA 58.809 47.619 0.00 0.00 0.00 2.15
1062 4387 3.456280 CTTCTGCTGCTCCTTATGAGTC 58.544 50.000 0.00 0.00 43.48 3.36
1072 4397 3.555966 TCCTTATGAGTCGCTGATCTGA 58.444 45.455 3.42 0.00 0.00 3.27
1104 4514 4.520179 TGTTGCTAATCTGATGATGCTGT 58.480 39.130 9.85 0.00 32.44 4.40
1129 4568 2.037121 TGTGAAACTACTGCTGCTGCTA 59.963 45.455 17.00 0.89 37.73 3.49
1167 4606 1.552337 CTGCTGTCATACTCCACCTGT 59.448 52.381 0.00 0.00 0.00 4.00
1321 4769 3.403558 GCCCTCAGGACCTGGGAC 61.404 72.222 23.91 10.72 43.47 4.46
1326 4774 2.363795 CAGGACCTGGGACCGCTA 60.364 66.667 14.26 0.00 35.21 4.26
1380 4918 1.903877 CTGGGAACTGGGATCGCTGT 61.904 60.000 15.27 15.27 0.00 4.40
1474 5012 4.075793 AGGACCTGGGAGCGCCTA 62.076 66.667 2.29 0.00 0.00 3.93
1573 5130 2.100087 GAGGATGGAGGAAGAAGACGAC 59.900 54.545 0.00 0.00 0.00 4.34
1582 5139 0.737219 AAGAAGACGACGGGGATACG 59.263 55.000 0.00 0.00 40.31 3.06
1602 5159 2.802719 GGATTCAAACTAGGGGCAACA 58.197 47.619 0.00 0.00 39.74 3.33
1626 5183 3.318557 TGTAAATTCCACCGTTTTCACCC 59.681 43.478 0.00 0.00 0.00 4.61
1628 5185 0.179012 ATTCCACCGTTTTCACCCGT 60.179 50.000 0.00 0.00 0.00 5.28
1659 5216 3.695830 TCCTCCAGCGACTTACATTTT 57.304 42.857 0.00 0.00 0.00 1.82
2244 5801 1.116308 TGGTCACTGTCGTTTCCTCA 58.884 50.000 0.00 0.00 0.00 3.86
2344 5901 5.583854 CAGCAGACAGACTATTTAAGTGCAT 59.416 40.000 0.00 0.00 39.07 3.96
2491 6057 7.639113 TTGCCGGATAGAATTTATCTTTGTT 57.361 32.000 5.05 0.00 39.71 2.83
2525 6091 2.122989 ACCCAGACACGACACCCT 60.123 61.111 0.00 0.00 0.00 4.34
2551 6117 1.587054 CGACACCTCTTCGGCTTCT 59.413 57.895 0.00 0.00 35.61 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
164 1694 2.983803 GACAGCGAACAGAGAAGAAGAC 59.016 50.000 0.00 0.00 0.00 3.01
521 2081 8.809066 TCTTGCAAATCCTACACTAAACTACTA 58.191 33.333 0.00 0.00 0.00 1.82
976 4301 2.357517 CGGCCTTGTTGTCTCGCT 60.358 61.111 0.00 0.00 0.00 4.93
984 4309 0.673437 CCATTGACAACGGCCTTGTT 59.327 50.000 17.93 6.17 43.60 2.83
1059 4384 4.456535 ACAGTAGTATCAGATCAGCGACT 58.543 43.478 0.00 0.00 0.00 4.18
1062 4387 4.926244 ACAACAGTAGTATCAGATCAGCG 58.074 43.478 0.00 0.00 0.00 5.18
1072 4397 8.478066 TCATCAGATTAGCAACAACAGTAGTAT 58.522 33.333 0.00 0.00 0.00 2.12
1104 4514 3.065233 CAGCAGCAGTAGTTTCACAACAA 59.935 43.478 0.00 0.00 35.05 2.83
1129 4568 4.692625 CAGCAGCAGTAGTAGTTTGACAAT 59.307 41.667 0.00 0.00 0.00 2.71
1167 4606 1.352083 ACAGCTGCTGGGTTCTTCTA 58.648 50.000 31.00 0.00 35.51 2.10
1326 4774 0.253160 TAGGTCCCAGGTCCAGCAAT 60.253 55.000 2.75 0.00 0.00 3.56
1539 5096 2.502492 ATCCTCCAGGCCATCGTCG 61.502 63.158 5.01 0.00 34.44 5.12
1541 5098 2.446848 CCATCCTCCAGGCCATCGT 61.447 63.158 5.01 0.00 34.44 3.73
1553 5110 2.104170 GTCGTCTTCTTCCTCCATCCT 58.896 52.381 0.00 0.00 0.00 3.24
1573 5130 2.614829 AGTTTGAATCCGTATCCCCG 57.385 50.000 0.00 0.00 0.00 5.73
1582 5139 2.802719 TGTTGCCCCTAGTTTGAATCC 58.197 47.619 0.00 0.00 0.00 3.01
1602 5159 5.510009 GGGTGAAAACGGTGGAATTTACATT 60.510 40.000 0.00 0.00 0.00 2.71
1659 5216 2.042162 ACTTACTACTCCCTCCGTTCCA 59.958 50.000 0.00 0.00 0.00 3.53
1924 5481 7.272037 AGTACTTGATTGTTTTCCAATTCGT 57.728 32.000 0.00 0.00 43.87 3.85
1985 5542 5.008712 ACCAGCACTAAACAGAAAAAGCTAC 59.991 40.000 0.00 0.00 0.00 3.58
2344 5901 7.817418 AGAAAAACTAACATGCCTTTCAGTA 57.183 32.000 0.00 0.00 0.00 2.74
2491 6057 0.806884 GGTGTCGTGGTGTCAAACGA 60.807 55.000 7.70 7.70 45.86 3.85
2525 6091 3.518552 AAGAGGTGTCGGGGGTCGA 62.519 63.158 0.00 0.00 46.77 4.20
2551 6117 5.802956 CGAAAAGCACCTTTTTAGTCAACAA 59.197 36.000 4.64 0.00 42.72 2.83


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

AutoCloner maintained by Alex Coulton.