Multiple sequence alignment - TraesCS1B01G403800

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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 TraesCS1B01G403800 chr1B 100.000 2585 0 0 1 2585 633173004 633175588 0 4774
1 TraesCS1B01G403800 chr1B 95.273 1629 74 2 957 2585 570458142 570456517 0 2579
2 TraesCS1B01G403800 chr1B 94.148 957 52 4 3 955 633156749 633157705 0 1454
3 TraesCS1B01G403800 chr7B 95.221 1632 72 4 957 2585 49223257 49221629 0 2577
4 TraesCS1B01G403800 chr7B 94.966 1629 81 1 957 2585 377024296 377022669 0 2553
5 TraesCS1B01G403800 chr7B 94.792 1632 80 3 957 2585 442358189 442359818 0 2538
6 TraesCS1B01G403800 chr7D 95.101 1633 75 3 957 2585 85019866 85021497 0 2567
7 TraesCS1B01G403800 chr3D 94.840 1628 84 0 957 2584 515672555 515674182 0 2542
8 TraesCS1B01G403800 chr2B 94.717 1628 86 0 957 2584 518051550 518053177 0 2531
9 TraesCS1B01G403800 chr2B 93.750 960 54 6 3 958 148312018 148311061 0 1435
10 TraesCS1B01G403800 chr6A 94.721 1629 82 3 957 2585 53152425 53154049 0 2529
11 TraesCS1B01G403800 chr5D 94.618 1635 82 1 957 2585 544615772 544617406 0 2527
12 TraesCS1B01G403800 chr5B 94.289 963 48 6 3 959 606009259 606010220 0 1467
13 TraesCS1B01G403800 chr5B 94.271 960 49 6 3 958 122615 123572 0 1463
14 TraesCS1B01G403800 chr5B 93.854 960 49 10 3 958 694193874 694194827 0 1437
15 TraesCS1B01G403800 chr6B 94.069 961 49 8 3 957 674707924 674708882 0 1452
16 TraesCS1B01G403800 chr6B 93.646 960 53 7 5 958 530703651 530702694 0 1428
17 TraesCS1B01G403800 chr4B 93.965 961 52 6 3 958 67051746 67050787 0 1448
18 TraesCS1B01G403800 chr4B 93.757 961 54 6 3 958 582048592 582049551 0 1437


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 TraesCS1B01G403800 chr1B 633173004 633175588 2584 False 4774 4774 100.000 1 2585 1 chr1B.!!$F2 2584
1 TraesCS1B01G403800 chr1B 570456517 570458142 1625 True 2579 2579 95.273 957 2585 1 chr1B.!!$R1 1628
2 TraesCS1B01G403800 chr1B 633156749 633157705 956 False 1454 1454 94.148 3 955 1 chr1B.!!$F1 952
3 TraesCS1B01G403800 chr7B 49221629 49223257 1628 True 2577 2577 95.221 957 2585 1 chr7B.!!$R1 1628
4 TraesCS1B01G403800 chr7B 377022669 377024296 1627 True 2553 2553 94.966 957 2585 1 chr7B.!!$R2 1628
5 TraesCS1B01G403800 chr7B 442358189 442359818 1629 False 2538 2538 94.792 957 2585 1 chr7B.!!$F1 1628
6 TraesCS1B01G403800 chr7D 85019866 85021497 1631 False 2567 2567 95.101 957 2585 1 chr7D.!!$F1 1628
7 TraesCS1B01G403800 chr3D 515672555 515674182 1627 False 2542 2542 94.840 957 2584 1 chr3D.!!$F1 1627
8 TraesCS1B01G403800 chr2B 518051550 518053177 1627 False 2531 2531 94.717 957 2584 1 chr2B.!!$F1 1627
9 TraesCS1B01G403800 chr2B 148311061 148312018 957 True 1435 1435 93.750 3 958 1 chr2B.!!$R1 955
10 TraesCS1B01G403800 chr6A 53152425 53154049 1624 False 2529 2529 94.721 957 2585 1 chr6A.!!$F1 1628
11 TraesCS1B01G403800 chr5D 544615772 544617406 1634 False 2527 2527 94.618 957 2585 1 chr5D.!!$F1 1628
12 TraesCS1B01G403800 chr5B 606009259 606010220 961 False 1467 1467 94.289 3 959 1 chr5B.!!$F2 956
13 TraesCS1B01G403800 chr5B 122615 123572 957 False 1463 1463 94.271 3 958 1 chr5B.!!$F1 955
14 TraesCS1B01G403800 chr5B 694193874 694194827 953 False 1437 1437 93.854 3 958 1 chr5B.!!$F3 955
15 TraesCS1B01G403800 chr6B 674707924 674708882 958 False 1452 1452 94.069 3 957 1 chr6B.!!$F1 954
16 TraesCS1B01G403800 chr6B 530702694 530703651 957 True 1428 1428 93.646 5 958 1 chr6B.!!$R1 953
17 TraesCS1B01G403800 chr4B 67050787 67051746 959 True 1448 1448 93.965 3 958 1 chr4B.!!$R1 955
18 TraesCS1B01G403800 chr4B 582048592 582049551 959 False 1437 1437 93.757 3 958 1 chr4B.!!$F1 955

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
706 711 0.318441 TGCTGACGGAACTCTCCTTG 59.682 55.0 0.0 0.0 39.93 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1667 1846 0.178903 TGTGTAGTGCTTCCTCCCCT 60.179 55.0 0.0 0.0 0.0 4.79 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
209 211 6.620877 TGGAAGCCTATATTTGGATATCGT 57.379 37.500 0.00 0.00 31.09 3.73
318 320 2.791868 GGAGAAGAGGAGAGGCGGC 61.792 68.421 0.00 0.00 0.00 6.53
357 360 1.550409 CCCTCCCCCTAGTCCGAATAG 60.550 61.905 0.00 0.00 0.00 1.73
409 412 2.140224 CCTTCCTCTCTCTCCCTCCTA 58.860 57.143 0.00 0.00 0.00 2.94
433 436 0.912486 CCCCCTTCTCGAAGTCCAAT 59.088 55.000 5.99 0.00 36.72 3.16
531 535 4.019231 CCTCCCCCTTGCTCCTTTATATAC 60.019 50.000 0.00 0.00 0.00 1.47
536 540 3.581332 CCTTGCTCCTTTATATACGGGGA 59.419 47.826 2.01 0.79 0.00 4.81
582 586 9.381033 CAACAATTGATCTCTTGATCTCTTAGT 57.619 33.333 13.59 0.00 46.84 2.24
625 629 5.125739 CCACCATAGTCCTCCTCGATAATAC 59.874 48.000 0.00 0.00 0.00 1.89
631 636 2.998670 TCCTCCTCGATAATACGTAGCG 59.001 50.000 0.08 2.67 43.02 4.26
665 670 0.742505 CCCTGCGACGGTAGAACATA 59.257 55.000 0.00 0.00 0.00 2.29
672 677 3.421231 GCGACGGTAGAACATAAAGATCG 59.579 47.826 0.00 0.00 0.00 3.69
681 686 5.734720 AGAACATAAAGATCGTCACCATGT 58.265 37.500 0.00 0.00 0.00 3.21
706 711 0.318441 TGCTGACGGAACTCTCCTTG 59.682 55.000 0.00 0.00 39.93 3.61
722 727 0.460987 CTTGGACACTCGGCTGGATC 60.461 60.000 0.00 0.00 0.00 3.36
743 748 1.269309 GGAGTTCGAGGGATGTCATCG 60.269 57.143 6.74 0.00 37.79 3.84
746 751 1.405821 GTTCGAGGGATGTCATCGAGT 59.594 52.381 6.74 0.00 45.23 4.18
793 798 2.073816 CCGTAGTTTCGGTGCTTGATT 58.926 47.619 0.00 0.00 44.77 2.57
802 807 2.361104 TGCTTGATTGGTCGGGCC 60.361 61.111 0.00 0.00 37.90 5.80
810 815 2.668632 TGGTCGGGCCATGAAGAC 59.331 61.111 4.39 5.54 43.61 3.01
827 832 3.754188 AGACGTACGACTACATCAACC 57.246 47.619 24.41 0.00 0.00 3.77
833 838 1.199789 ACGACTACATCAACCGCGTTA 59.800 47.619 4.92 0.00 0.00 3.18
840 845 7.398834 ACTACATCAACCGCGTTATTATAAC 57.601 36.000 4.92 5.11 0.00 1.89
855 860 2.467566 ATAACGCTTCCACTTTCGGT 57.532 45.000 0.00 0.00 0.00 4.69
879 884 1.538047 GAGGGTACGTGGACACACTA 58.462 55.000 0.00 0.00 45.50 2.74
927 932 0.973632 ATCCTGTGTGTGCGTAGGAA 59.026 50.000 0.00 0.00 42.20 3.36
1005 1010 5.282510 GTCGATGTTGACTAGGTTATGGAG 58.717 45.833 0.00 0.00 35.95 3.86
1031 1036 2.641815 GGATGAGGCTGATAATCCAGGT 59.358 50.000 0.00 0.00 38.78 4.00
1074 1079 1.679680 CAGGCATGGGTCATGTTCATC 59.320 52.381 9.28 0.00 43.10 2.92
1087 1092 2.820178 TGTTCATCCACCAGAGAGCTA 58.180 47.619 0.00 0.00 0.00 3.32
1125 1130 2.222027 CCTTTGATTCGCTATGGTCCC 58.778 52.381 0.00 0.00 0.00 4.46
1136 1141 1.638589 CTATGGTCCCTTGTTTCCCCA 59.361 52.381 0.00 0.00 0.00 4.96
1278 1283 3.319122 GGGGGCTTTTACAAGATAGCATG 59.681 47.826 0.00 0.00 35.36 4.06
1341 1346 2.158385 TGTTGGCCATAACCAGAGGTTT 60.158 45.455 6.09 0.00 44.33 3.27
1660 1839 2.009681 TCCTAGGTCACAGTCTGCAA 57.990 50.000 9.08 0.00 0.00 4.08
1667 1846 3.138304 GGTCACAGTCTGCAACATACAA 58.862 45.455 0.00 0.00 0.00 2.41
1783 1962 4.746611 CGCATGATGCTAACATTCTCACTA 59.253 41.667 16.17 0.00 42.25 2.74
1789 1968 4.253685 TGCTAACATTCTCACTAACAGCC 58.746 43.478 0.00 0.00 0.00 4.85
1847 2027 3.445008 AGTTCTACCTTGGAGATGCTGA 58.555 45.455 0.00 0.00 0.00 4.26
1864 2044 1.067416 GACTATGCATGTCGGCCGA 59.933 57.895 27.28 27.28 0.00 5.54
1913 2093 3.193691 AGGTACCATCTCAACGAGTTCTG 59.806 47.826 15.94 0.00 0.00 3.02
2216 2396 4.853924 ATGACGCTTGGAAGAACAAAAT 57.146 36.364 0.00 0.00 0.00 1.82
2232 2412 2.564062 CAAAATGTTGGAGTGGGCAGAT 59.436 45.455 0.00 0.00 0.00 2.90
2324 2510 5.510520 GCACAGAAGAAGAGGAAGAAGAAGA 60.511 44.000 0.00 0.00 0.00 2.87
2419 2631 7.072177 TGGCTCTTAATAATTTGAACTGTCG 57.928 36.000 0.00 0.00 0.00 4.35
2441 2653 7.822334 TGTCGTTTGATTGTAGTTAGGATGAAT 59.178 33.333 0.00 0.00 0.00 2.57
2483 2695 5.159273 TGGCACTATGTTCAGATTGTGTA 57.841 39.130 0.00 0.00 33.29 2.90
2487 2699 5.008019 GCACTATGTTCAGATTGTGTATGGG 59.992 44.000 0.00 0.00 33.29 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.031585 TGACCGAGACACGTTTCCAG 59.968 55.000 0.00 0.00 40.78 3.86
1 2 0.677288 ATGACCGAGACACGTTTCCA 59.323 50.000 0.00 0.00 40.78 3.53
47 48 1.084289 GAAACCTTAAGCGTGCGGAT 58.916 50.000 0.00 0.00 0.00 4.18
95 96 4.377022 CGAACAACCTTCGGTACATCAAAG 60.377 45.833 0.00 0.00 38.19 2.77
128 129 3.578688 CTCGTCATGTCTGTGATCACAA 58.421 45.455 27.63 14.98 41.33 3.33
209 211 2.690786 CGATTTCACCCGGAACACTTA 58.309 47.619 0.73 0.00 34.56 2.24
284 286 2.398588 TCTCCACTAAGGCCCACTATG 58.601 52.381 0.00 0.00 37.29 2.23
424 427 4.227527 TCCCTCCTTTCCTTATTGGACTTC 59.772 45.833 0.00 0.00 46.14 3.01
509 513 4.322801 CGTATATAAAGGAGCAAGGGGGAG 60.323 50.000 0.00 0.00 0.00 4.30
536 540 1.306226 GTCTAGAGGTGCCCCCTGT 60.306 63.158 0.00 0.00 46.51 4.00
625 629 2.877360 TTCGCCTAAGCACCGCTACG 62.877 60.000 0.00 0.00 38.25 3.51
655 660 5.657474 TGGTGACGATCTTTATGTTCTACC 58.343 41.667 0.00 0.00 0.00 3.18
665 670 2.607187 GACGACATGGTGACGATCTTT 58.393 47.619 8.61 0.00 37.72 2.52
672 677 1.372997 AGCACGACGACATGGTGAC 60.373 57.895 0.00 0.00 39.28 3.67
694 699 1.067495 CGAGTGTCCAAGGAGAGTTCC 60.067 57.143 0.00 0.00 44.39 3.62
706 711 2.105128 CGATCCAGCCGAGTGTCC 59.895 66.667 0.00 0.00 0.00 4.02
722 727 0.747255 ATGACATCCCTCGAACTCCG 59.253 55.000 0.00 0.00 40.25 4.63
736 741 2.124122 CACACGTTCAACTCGATGACA 58.876 47.619 0.00 0.00 0.00 3.58
743 748 3.381949 AGTTCTAGCACACGTTCAACTC 58.618 45.455 0.00 0.00 0.00 3.01
746 751 2.390938 CGAGTTCTAGCACACGTTCAA 58.609 47.619 4.36 0.00 0.00 2.69
778 783 1.399727 CGACCAATCAAGCACCGAAAC 60.400 52.381 0.00 0.00 0.00 2.78
802 807 4.905269 TGATGTAGTCGTACGTCTTCATG 58.095 43.478 28.66 0.00 43.23 3.07
803 808 5.330295 GTTGATGTAGTCGTACGTCTTCAT 58.670 41.667 25.67 25.67 43.23 2.57
810 815 1.186030 GCGGTTGATGTAGTCGTACG 58.814 55.000 9.53 9.53 30.95 3.67
833 838 4.510571 ACCGAAAGTGGAAGCGTTATAAT 58.489 39.130 0.00 0.00 0.00 1.28
840 845 1.347320 GTAGACCGAAAGTGGAAGCG 58.653 55.000 0.00 0.00 0.00 4.68
847 852 2.087646 GTACCCTCGTAGACCGAAAGT 58.912 52.381 0.00 0.00 46.75 2.66
855 860 0.324614 TGTCCACGTACCCTCGTAGA 59.675 55.000 0.00 0.00 42.27 2.59
879 884 0.394565 GCATAGCAACGAGAGGGGAT 59.605 55.000 0.00 0.00 0.00 3.85
946 951 4.962362 GGGAAATCAATCCTGTTGGGTAAT 59.038 41.667 0.00 0.00 39.57 1.89
955 960 3.127548 CGTTCAGTGGGAAATCAATCCTG 59.872 47.826 0.00 0.00 39.57 3.86
990 995 1.754803 CGTGCCTCCATAACCTAGTCA 59.245 52.381 0.00 0.00 0.00 3.41
1005 1010 0.106708 TTATCAGCCTCATCCGTGCC 59.893 55.000 0.00 0.00 0.00 5.01
1074 1079 1.268794 CGACGAATAGCTCTCTGGTGG 60.269 57.143 0.00 0.00 0.00 4.61
1087 1092 0.389948 GGTCTTCCAGCACGACGAAT 60.390 55.000 0.00 0.00 0.00 3.34
1125 1130 1.144913 TCCTGTTCCTGGGGAAACAAG 59.855 52.381 0.19 0.48 43.86 3.16
1136 1141 2.649742 TTGGATCCTCTCCTGTTCCT 57.350 50.000 14.23 0.00 45.21 3.36
1159 1164 9.419297 GTCATTGTAGTTGTAGATGTAGTTCAA 57.581 33.333 0.00 0.00 0.00 2.69
1178 1183 1.460504 TAGAGCCTCGACGTCATTGT 58.539 50.000 17.16 0.00 0.00 2.71
1263 1268 6.149308 CACTGGTGTTCATGCTATCTTGTAAA 59.851 38.462 0.00 0.00 0.00 2.01
1278 1283 1.140816 GCTCTTCGACACTGGTGTTC 58.859 55.000 7.82 1.51 45.05 3.18
1341 1346 4.979335 TGAACATGTTGTGAATGACCCTA 58.021 39.130 17.58 0.00 0.00 3.53
1660 1839 1.282157 GTGCTTCCTCCCCTTGTATGT 59.718 52.381 0.00 0.00 0.00 2.29
1667 1846 0.178903 TGTGTAGTGCTTCCTCCCCT 60.179 55.000 0.00 0.00 0.00 4.79
1783 1962 0.827925 TCAGGTCGACTCAGGCTGTT 60.828 55.000 16.46 2.42 0.00 3.16
1789 1968 1.339610 GATCCCATCAGGTCGACTCAG 59.660 57.143 16.46 5.83 36.75 3.35
1847 2027 1.068083 CTCGGCCGACATGCATAGT 59.932 57.895 27.28 0.00 0.00 2.12
1864 2044 3.803340 TCCTGAAGGGTGGAAGAATACT 58.197 45.455 0.00 0.00 36.25 2.12
2216 2396 1.303561 GCATCTGCCCACTCCAACA 60.304 57.895 0.00 0.00 34.31 3.33
2232 2412 2.697751 ACCTTTGTTAAGCCACATTGCA 59.302 40.909 0.00 0.00 0.00 4.08
2324 2510 2.701780 GCTGCTGCTGCTGATGCTT 61.702 57.895 23.39 0.00 40.01 3.91
2419 2631 9.774742 GACAATTCATCCTAACTACAATCAAAC 57.225 33.333 0.00 0.00 0.00 2.93
2441 2653 6.644592 GTGCCAGCTAAATAAACAAATGACAA 59.355 34.615 0.00 0.00 0.00 3.18
2455 2667 4.551702 TCTGAACATAGTGCCAGCTAAA 57.448 40.909 0.00 0.00 0.00 1.85
2456 2668 4.760530 ATCTGAACATAGTGCCAGCTAA 57.239 40.909 0.00 0.00 0.00 3.09
2483 2695 2.344093 ACTAGTGGTGACCTTCCCAT 57.656 50.000 2.11 0.00 32.32 4.00
2487 2699 5.471257 CACTTCTAACTAGTGGTGACCTTC 58.529 45.833 2.11 0.00 39.42 3.46


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

AutoCloner maintained by Alex Coulton.