Multiple sequence alignment - TraesCS4B01G316200

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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 TraesCS4B01G316200 chr4B 100.000 2867 0 0 1 2867 605694239 605691373 0.000000e+00 5295
1 TraesCS4B01G316200 chr4B 81.250 304 53 4 1137 1438 605682888 605683189 2.850000e-60 243
2 TraesCS4B01G316200 chr4D 95.045 2886 93 19 1 2867 479000351 478997497 0.000000e+00 4492
3 TraesCS4B01G316200 chr4D 84.328 268 34 6 1156 1419 382738013 382738276 3.670000e-64 255
4 TraesCS4B01G316200 chr4D 79.245 265 40 14 1154 1412 52763827 52764082 1.370000e-38 171
5 TraesCS4B01G316200 chr4A 90.824 2899 157 41 53 2867 685382574 685379701 0.000000e+00 3779
6 TraesCS4B01G316200 chr4A 82.566 304 49 4 1137 1438 685372125 685372426 6.090000e-67 265
7 TraesCS4B01G316200 chr4A 84.586 266 37 4 1156 1419 64956723 64956986 7.880000e-66 261
8 TraesCS4B01G316200 chr4A 100.000 57 0 0 2 58 685402995 685402939 3.910000e-19 106
9 TraesCS4B01G316200 chr6D 87.132 272 33 2 1150 1420 462273020 462272750 9.980000e-80 307
10 TraesCS4B01G316200 chr6A 87.085 271 35 0 1150 1420 609107553 609107283 9.980000e-80 307
11 TraesCS4B01G316200 chr6B 86.765 272 34 2 1150 1420 704751360 704751630 4.640000e-78 302
12 TraesCS4B01G316200 chr3D 75.000 260 41 22 1143 1392 511726697 511726452 6.540000e-17 99
13 TraesCS4B01G316200 chr3A 75.000 260 41 22 1143 1392 647755513 647755268 6.540000e-17 99


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 TraesCS4B01G316200 chr4B 605691373 605694239 2866 True 5295 5295 100.000 1 2867 1 chr4B.!!$R1 2866
1 TraesCS4B01G316200 chr4D 478997497 479000351 2854 True 4492 4492 95.045 1 2867 1 chr4D.!!$R1 2866
2 TraesCS4B01G316200 chr4A 685379701 685382574 2873 True 3779 3779 90.824 53 2867 1 chr4A.!!$R1 2814

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
985 1020 1.208293 CTCTTTCCCCCTTCCTCTTCG 59.792 57.143 0.0 0.0 0.0 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2404 2459 1.566703 ACTGGAGGAGCTAGCTAGTCA 59.433 52.381 19.38 12.56 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
54 55 4.982916 CCTACCTACACGATTTAGTCATGC 59.017 45.833 0.00 0.00 0.00 4.06
281 285 2.893489 GTTCCAATCTTTCCTGCAGGTT 59.107 45.455 31.58 15.93 36.34 3.50
531 550 4.437682 TTCCCATCACATATTGTCTCCC 57.562 45.455 0.00 0.00 0.00 4.30
623 642 5.722441 TGCTTGTATATGTATTATCCCCGGA 59.278 40.000 0.73 0.00 0.00 5.14
683 702 4.772100 ACCCATCCCAACTAATCACAAAAG 59.228 41.667 0.00 0.00 0.00 2.27
869 904 1.384989 CCTTAGCGGAAGAGGCGAGA 61.385 60.000 3.23 0.00 37.33 4.04
952 987 4.231890 TGTTTATTCCCTCAGGCCCTAATT 59.768 41.667 0.00 0.00 0.00 1.40
953 988 5.208890 GTTTATTCCCTCAGGCCCTAATTT 58.791 41.667 0.00 0.00 0.00 1.82
968 1003 4.019174 CCTAATTTCCAACCATGCACTCT 58.981 43.478 0.00 0.00 0.00 3.24
969 1004 4.463891 CCTAATTTCCAACCATGCACTCTT 59.536 41.667 0.00 0.00 0.00 2.85
985 1020 1.208293 CTCTTTCCCCCTTCCTCTTCG 59.792 57.143 0.00 0.00 0.00 3.79
1034 1069 1.548081 CCATTGCACTCCAACCATCA 58.452 50.000 0.00 0.00 35.99 3.07
1038 1073 2.812836 TGCACTCCAACCATCATCAT 57.187 45.000 0.00 0.00 0.00 2.45
1039 1074 2.646930 TGCACTCCAACCATCATCATC 58.353 47.619 0.00 0.00 0.00 2.92
1040 1075 2.026075 TGCACTCCAACCATCATCATCA 60.026 45.455 0.00 0.00 0.00 3.07
1041 1076 3.220110 GCACTCCAACCATCATCATCAT 58.780 45.455 0.00 0.00 0.00 2.45
1042 1077 3.252701 GCACTCCAACCATCATCATCATC 59.747 47.826 0.00 0.00 0.00 2.92
1043 1078 4.457466 CACTCCAACCATCATCATCATCA 58.543 43.478 0.00 0.00 0.00 3.07
1044 1079 5.070685 CACTCCAACCATCATCATCATCAT 58.929 41.667 0.00 0.00 0.00 2.45
1092 1137 4.636249 GGAGAGAGACAACACAATCAGTT 58.364 43.478 0.00 0.00 0.00 3.16
1094 1139 4.636249 AGAGAGACAACACAATCAGTTCC 58.364 43.478 0.00 0.00 0.00 3.62
1112 1157 1.300465 CATCACCGAGCGATCCAGG 60.300 63.158 0.00 0.00 0.00 4.45
1180 1225 0.524392 CGGTGCGTGCAAGTTTTTGA 60.524 50.000 0.59 0.00 36.36 2.69
1701 1749 0.806102 ACATGATGTACCACGCGCTC 60.806 55.000 5.73 0.00 0.00 5.03
1887 1935 6.128063 CGTAAGAACCACTACAACTAGCTAGT 60.128 42.308 20.95 20.95 43.02 2.57
1974 2025 2.487265 GGGCTTGAGAGTTTGAGTTGGA 60.487 50.000 0.00 0.00 0.00 3.53
2011 2062 9.882856 GTAATTTTTAAAGTCTACGTCGATCAG 57.117 33.333 0.00 0.00 0.00 2.90
2042 2093 4.610333 TCATGCTCAGGTTCTAGTCCTTA 58.390 43.478 6.52 0.21 32.37 2.69
2051 2102 4.028825 GGTTCTAGTCCTTACCTAGCCAA 58.971 47.826 0.00 0.00 33.43 4.52
2117 2168 4.159321 AGATCTATACATGATCACCGCAGG 59.841 45.833 0.00 0.00 45.07 4.85
2159 2210 4.620982 ACAGCAAAAATGCTTCTTGGTAC 58.379 39.130 0.00 0.00 43.52 3.34
2232 2284 7.948357 AGTTCTGTTCTGTATAGTTGTGTACA 58.052 34.615 0.00 0.00 0.00 2.90
2423 2478 2.356665 TGACTAGCTAGCTCCTCCAG 57.643 55.000 23.26 15.25 0.00 3.86
2424 2479 1.566703 TGACTAGCTAGCTCCTCCAGT 59.433 52.381 23.26 18.67 0.00 4.00
2494 2551 9.607333 TTCCTATGGATCTGATATTCAAGTACT 57.393 33.333 0.00 0.00 0.00 2.73
2506 2563 8.949177 TGATATTCAAGTACTAGTACGTGTTGA 58.051 33.333 33.53 28.05 43.05 3.18
2582 2665 7.806960 GCAATCCTTAATCATGATCTGCTTAAC 59.193 37.037 9.06 0.00 0.00 2.01
2587 2670 7.286316 CCTTAATCATGATCTGCTTAACCCTTT 59.714 37.037 9.06 0.00 0.00 3.11
2617 2701 5.537300 TTATGCTTAGACTGTGATCCTCC 57.463 43.478 0.00 0.00 0.00 4.30
2725 2809 8.015658 GCACTAAGATCGTATTGTTCTTGTTTT 58.984 33.333 7.61 0.00 37.25 2.43
2777 2861 5.589050 GTGGGGGTGATTAAGAACATAACTC 59.411 44.000 0.00 0.00 0.00 3.01
2778 2862 5.491078 TGGGGGTGATTAAGAACATAACTCT 59.509 40.000 0.00 0.00 0.00 3.24
2851 2940 0.893727 GTTGGGGCAGAACGGAACAT 60.894 55.000 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 7.806487 CCATGCTTATCACTAAATTACATGCAG 59.194 37.037 0.00 0.00 32.91 4.41
281 285 2.094182 CGGCTGCTCTAAACTAAGTGGA 60.094 50.000 0.00 0.00 0.00 4.02
531 550 3.045601 TCAGCTCCTTTCTTTTCCTCG 57.954 47.619 0.00 0.00 0.00 4.63
623 642 4.012374 CCAGCACAGTCCAGTTGATAAAT 58.988 43.478 0.00 0.00 0.00 1.40
662 681 6.588719 TTCTTTTGTGATTAGTTGGGATGG 57.411 37.500 0.00 0.00 0.00 3.51
683 702 1.468054 GCTTGCCCGTGTGATGATTTC 60.468 52.381 0.00 0.00 0.00 2.17
869 904 0.895100 TTTGAGCTTCCAATGGCGCT 60.895 50.000 14.15 14.15 33.33 5.92
912 947 1.079127 CAATTCCGGCGTGTCTCCT 60.079 57.895 6.01 0.00 0.00 3.69
941 976 2.230130 TGGTTGGAAATTAGGGCCTG 57.770 50.000 18.53 0.00 0.00 4.85
952 987 2.238521 GGAAAGAGTGCATGGTTGGAA 58.761 47.619 0.00 0.00 0.00 3.53
953 988 1.547675 GGGAAAGAGTGCATGGTTGGA 60.548 52.381 0.00 0.00 0.00 3.53
968 1003 0.981943 GACGAAGAGGAAGGGGGAAA 59.018 55.000 0.00 0.00 0.00 3.13
969 1004 0.116541 AGACGAAGAGGAAGGGGGAA 59.883 55.000 0.00 0.00 0.00 3.97
985 1020 2.224314 GCGCCATTGCTTATAAGGAGAC 59.776 50.000 14.28 1.93 34.43 3.36
1034 1069 2.155279 GCTGCTGCTGATGATGATGAT 58.845 47.619 10.92 0.00 36.03 2.45
1038 1073 0.106149 ATCGCTGCTGCTGATGATGA 59.894 50.000 14.03 1.95 36.97 2.92
1039 1074 0.513385 GATCGCTGCTGCTGATGATG 59.487 55.000 20.90 3.53 34.47 3.07
1040 1075 0.106149 TGATCGCTGCTGCTGATGAT 59.894 50.000 20.90 13.31 34.47 2.45
1041 1076 0.808847 GTGATCGCTGCTGCTGATGA 60.809 55.000 20.90 13.60 34.47 2.92
1042 1077 1.642215 GTGATCGCTGCTGCTGATG 59.358 57.895 20.90 5.08 34.47 3.07
1043 1078 1.523258 GGTGATCGCTGCTGCTGAT 60.523 57.895 17.71 17.71 36.02 2.90
1044 1079 2.125391 GGTGATCGCTGCTGCTGA 60.125 61.111 14.03 12.39 36.97 4.26
1092 1137 1.738346 CTGGATCGCTCGGTGATGGA 61.738 60.000 4.92 0.00 32.57 3.41
1094 1139 1.300465 CCTGGATCGCTCGGTGATG 60.300 63.158 4.92 0.00 32.57 3.07
1164 1209 0.527385 GCCTCAAAAACTTGCACGCA 60.527 50.000 0.00 0.00 0.00 5.24
1389 1434 1.639298 GGAGTGCGAAGATGTGTGCC 61.639 60.000 0.00 0.00 0.00 5.01
1404 1449 1.196766 TCATGACCTGCTGCTGGAGT 61.197 55.000 29.14 10.28 0.00 3.85
1479 1524 2.661537 TCGTTCTGGTGCTGCACG 60.662 61.111 24.86 13.54 34.83 5.34
1480 1525 2.939022 GTCGTTCTGGTGCTGCAC 59.061 61.111 24.02 24.02 0.00 4.57
1492 1537 1.080974 CGTAGCCCTTGACGTCGTT 60.081 57.895 11.62 0.00 34.39 3.85
1590 1638 4.662961 TACGCGCACTGCTGCTGT 62.663 61.111 5.73 6.33 41.77 4.40
1674 1722 3.004419 CGTGGTACATCATGTAGTCCGAT 59.996 47.826 0.00 0.00 44.52 4.18
1755 1803 3.264866 GAACGACGACTGGTCCGCT 62.265 63.158 0.00 0.00 42.99 5.52
1761 1809 2.126580 GTCCCGAACGACGACTGG 60.127 66.667 0.00 1.44 45.77 4.00
1986 2037 9.630098 ACTGATCGACGTAGACTTTAAAAATTA 57.370 29.630 0.00 0.00 0.00 1.40
2011 2062 2.831333 ACCTGAGCATGATTGATCGAC 58.169 47.619 0.00 0.00 41.23 4.20
2042 2093 8.233116 ACTAGGATTATTACTAGTTGGCTAGGT 58.767 37.037 0.00 0.00 45.57 3.08
2094 2145 4.159321 CCTGCGGTGATCATGTATAGATCT 59.841 45.833 0.00 0.00 41.85 2.75
2117 2168 5.449451 GCTGTCTAGTCAACTAGCTAGGTTC 60.449 48.000 24.35 13.22 44.24 3.62
2121 2172 5.568685 TTGCTGTCTAGTCAACTAGCTAG 57.431 43.478 19.44 19.44 44.24 3.42
2122 2173 5.977489 TTTGCTGTCTAGTCAACTAGCTA 57.023 39.130 11.56 0.00 44.24 3.32
2123 2174 4.873746 TTTGCTGTCTAGTCAACTAGCT 57.126 40.909 11.56 0.00 44.24 3.32
2124 2175 5.924475 TTTTTGCTGTCTAGTCAACTAGC 57.076 39.130 11.56 4.35 44.24 3.42
2232 2284 9.232473 TCGAATCATATACAGAATACTACTGCT 57.768 33.333 0.00 0.00 38.74 4.24
2404 2459 1.566703 ACTGGAGGAGCTAGCTAGTCA 59.433 52.381 19.38 12.56 0.00 3.41
2423 2478 7.770201 AGAGTAGATAGGTTCCGTAAAAGAAC 58.230 38.462 0.00 0.00 42.36 3.01
2424 2479 7.951347 AGAGTAGATAGGTTCCGTAAAAGAA 57.049 36.000 0.00 0.00 0.00 2.52
2582 2665 6.316390 AGTCTAAGCATAATTTCGTCAAAGGG 59.684 38.462 0.00 0.00 0.00 3.95
2587 2670 6.394809 TCACAGTCTAAGCATAATTTCGTCA 58.605 36.000 0.00 0.00 0.00 4.35
2675 2759 7.014134 TGCACATCAAATAGTCTCCAAGAAAAA 59.986 33.333 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.