Multiple sequence alignment - TraesCS5B01G352500

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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 TraesCS5B01G352500 chr5B 100.000 2294 0 0 1 2294 532239279 532241572 0.000000e+00 4237.0
1 TraesCS5B01G352500 chr5B 84.155 1319 178 21 1 1313 531817127 531818420 0.000000e+00 1249.0
2 TraesCS5B01G352500 chr5B 96.245 719 21 2 1581 2294 692132527 692133244 0.000000e+00 1173.0
3 TraesCS5B01G352500 chr5B 76.909 1113 213 33 129 1212 533035136 533034039 1.960000e-165 592.0
4 TraesCS5B01G352500 chr5D 96.441 1489 50 3 1 1488 437867336 437868822 0.000000e+00 2453.0
5 TraesCS5B01G352500 chr5D 77.453 479 99 8 129 603 438658171 438657698 6.240000e-71 278.0
6 TraesCS5B01G352500 chr5D 97.561 41 1 0 1542 1582 437868850 437868890 1.140000e-08 71.3
7 TraesCS5B01G352500 chr6B 96.379 718 21 1 1582 2294 13444822 13445539 0.000000e+00 1177.0
8 TraesCS5B01G352500 chr1B 96.250 720 22 1 1580 2294 654307746 654307027 0.000000e+00 1175.0
9 TraesCS5B01G352500 chr6A 96.095 717 23 1 1583 2294 617139935 617139219 0.000000e+00 1164.0
10 TraesCS5B01G352500 chr4B 96.095 717 23 1 1583 2294 19761811 19762527 0.000000e+00 1164.0
11 TraesCS5B01G352500 chr4B 95.961 718 24 1 1582 2294 670755772 670755055 0.000000e+00 1160.0
12 TraesCS5B01G352500 chr5A 95.955 717 24 1 1583 2294 15993715 15994431 0.000000e+00 1158.0
13 TraesCS5B01G352500 chr5A 76.295 772 164 16 129 894 554218378 554217620 5.940000e-106 394.0
14 TraesCS5B01G352500 chr2B 95.955 717 24 1 1583 2294 712823162 712822446 0.000000e+00 1158.0
15 TraesCS5B01G352500 chr2B 76.625 1108 215 37 129 1212 20146766 20147853 2.560000e-159 571.0
16 TraesCS5B01G352500 chr2B 75.970 1082 218 32 120 1179 65047756 65048817 9.390000e-144 520.0
17 TraesCS5B01G352500 chr4A 95.349 731 26 4 1570 2294 656578384 656579112 0.000000e+00 1155.0
18 TraesCS5B01G352500 chr7D 77.457 1211 237 32 103 1295 101738616 101739808 0.000000e+00 691.0
19 TraesCS5B01G352500 chr7D 80.066 913 163 15 1 905 101732835 101733736 0.000000e+00 660.0
20 TraesCS5B01G352500 chr7A 77.655 1177 225 32 103 1261 105512681 105513837 0.000000e+00 682.0
21 TraesCS5B01G352500 chr7A 77.985 913 172 20 1 905 105503988 105504879 1.550000e-151 545.0
22 TraesCS5B01G352500 chr7B 77.596 1098 215 28 103 1185 59072849 59073930 8.940000e-179 636.0
23 TraesCS5B01G352500 chr2A 76.805 1108 212 37 129 1212 14740371 14739285 4.250000e-162 580.0
24 TraesCS5B01G352500 chr2A 76.292 1122 209 41 129 1212 14703410 14702308 1.550000e-151 545.0
25 TraesCS5B01G352500 chr2D 78.491 795 144 22 112 894 12626459 12625680 1.580000e-136 496.0


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 TraesCS5B01G352500 chr5B 532239279 532241572 2293 False 4237.00 4237 100.000 1 2294 1 chr5B.!!$F2 2293
1 TraesCS5B01G352500 chr5B 531817127 531818420 1293 False 1249.00 1249 84.155 1 1313 1 chr5B.!!$F1 1312
2 TraesCS5B01G352500 chr5B 692132527 692133244 717 False 1173.00 1173 96.245 1581 2294 1 chr5B.!!$F3 713
3 TraesCS5B01G352500 chr5B 533034039 533035136 1097 True 592.00 592 76.909 129 1212 1 chr5B.!!$R1 1083
4 TraesCS5B01G352500 chr5D 437867336 437868890 1554 False 1262.15 2453 97.001 1 1582 2 chr5D.!!$F1 1581
5 TraesCS5B01G352500 chr6B 13444822 13445539 717 False 1177.00 1177 96.379 1582 2294 1 chr6B.!!$F1 712
6 TraesCS5B01G352500 chr1B 654307027 654307746 719 True 1175.00 1175 96.250 1580 2294 1 chr1B.!!$R1 714
7 TraesCS5B01G352500 chr6A 617139219 617139935 716 True 1164.00 1164 96.095 1583 2294 1 chr6A.!!$R1 711
8 TraesCS5B01G352500 chr4B 19761811 19762527 716 False 1164.00 1164 96.095 1583 2294 1 chr4B.!!$F1 711
9 TraesCS5B01G352500 chr4B 670755055 670755772 717 True 1160.00 1160 95.961 1582 2294 1 chr4B.!!$R1 712
10 TraesCS5B01G352500 chr5A 15993715 15994431 716 False 1158.00 1158 95.955 1583 2294 1 chr5A.!!$F1 711
11 TraesCS5B01G352500 chr5A 554217620 554218378 758 True 394.00 394 76.295 129 894 1 chr5A.!!$R1 765
12 TraesCS5B01G352500 chr2B 712822446 712823162 716 True 1158.00 1158 95.955 1583 2294 1 chr2B.!!$R1 711
13 TraesCS5B01G352500 chr2B 20146766 20147853 1087 False 571.00 571 76.625 129 1212 1 chr2B.!!$F1 1083
14 TraesCS5B01G352500 chr2B 65047756 65048817 1061 False 520.00 520 75.970 120 1179 1 chr2B.!!$F2 1059
15 TraesCS5B01G352500 chr4A 656578384 656579112 728 False 1155.00 1155 95.349 1570 2294 1 chr4A.!!$F1 724
16 TraesCS5B01G352500 chr7D 101738616 101739808 1192 False 691.00 691 77.457 103 1295 1 chr7D.!!$F2 1192
17 TraesCS5B01G352500 chr7D 101732835 101733736 901 False 660.00 660 80.066 1 905 1 chr7D.!!$F1 904
18 TraesCS5B01G352500 chr7A 105512681 105513837 1156 False 682.00 682 77.655 103 1261 1 chr7A.!!$F2 1158
19 TraesCS5B01G352500 chr7A 105503988 105504879 891 False 545.00 545 77.985 1 905 1 chr7A.!!$F1 904
20 TraesCS5B01G352500 chr7B 59072849 59073930 1081 False 636.00 636 77.596 103 1185 1 chr7B.!!$F1 1082
21 TraesCS5B01G352500 chr2A 14739285 14740371 1086 True 580.00 580 76.805 129 1212 1 chr2A.!!$R2 1083
22 TraesCS5B01G352500 chr2A 14702308 14703410 1102 True 545.00 545 76.292 129 1212 1 chr2A.!!$R1 1083
23 TraesCS5B01G352500 chr2D 12625680 12626459 779 True 496.00 496 78.491 112 894 1 chr2D.!!$R1 782

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
84 85 2.697431 TGTTGCTTTGTTCATACGGC 57.303 45.0 0.0 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1529 1581 0.108138 GGGTCACATGCTACTCGCTT 60.108 55.0 0.0 0.0 40.11 4.68 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
52 53 9.981460 AAAATAGTTTCCTCTTATTCACTCCAT 57.019 29.630 0.00 0.00 0.00 3.41
65 66 3.937814 TCACTCCATAATTGCTCACGTT 58.062 40.909 0.00 0.00 0.00 3.99
81 82 4.593157 TCACGTTGTTGCTTTGTTCATAC 58.407 39.130 0.00 0.00 0.00 2.39
83 84 2.970609 CGTTGTTGCTTTGTTCATACGG 59.029 45.455 0.00 0.00 0.00 4.02
84 85 2.697431 TGTTGCTTTGTTCATACGGC 57.303 45.000 0.00 0.00 0.00 5.68
171 172 5.013704 TGTCAAAAGGCTAAGTAGGGATTCA 59.986 40.000 0.00 0.00 0.00 2.57
251 252 4.435121 CCGTAATTTGGTTCGACTACTTGC 60.435 45.833 0.00 0.00 0.00 4.01
299 300 7.744087 AGTTGTTGATTTATGAGTACTTGCA 57.256 32.000 0.00 0.00 0.00 4.08
525 542 8.861086 TGACTATAATCCATAGAGACCTCAAAC 58.139 37.037 0.00 0.00 39.29 2.93
717 738 7.788026 TCCTGTTTCAGTAACTCTTGAAAGTA 58.212 34.615 0.33 0.00 37.64 2.24
785 807 3.845860 AGGTGTCTTCTCTACCAAGTCA 58.154 45.455 0.00 0.00 36.94 3.41
1013 1064 3.772572 TCGTGGAATATGTGGAAGGAAGA 59.227 43.478 0.00 0.00 0.00 2.87
1033 1084 5.956068 AGAGAAGACAAAAGATTTGGCTC 57.044 39.130 11.35 9.37 36.61 4.70
1115 1167 5.299279 CACTATTGTGTGTTCAGGAAAACCT 59.701 40.000 0.00 0.00 39.24 3.50
1346 1398 1.281419 TGTGTGGGTTCGGTGGATAT 58.719 50.000 0.00 0.00 0.00 1.63
1350 1402 0.834612 TGGGTTCGGTGGATATGGAC 59.165 55.000 0.00 0.00 0.00 4.02
1398 1450 9.495572 AACAAAATAAAGTCTTGACCAACAAAA 57.504 25.926 0.00 0.00 38.08 2.44
1415 1467 6.402766 CCAACAAAATGGTCATGCATCATTTC 60.403 38.462 19.44 1.54 39.34 2.17
1528 1580 7.732222 ACAAAGATAGAGAAGGAGATGAACT 57.268 36.000 0.00 0.00 0.00 3.01
1529 1581 8.830915 ACAAAGATAGAGAAGGAGATGAACTA 57.169 34.615 0.00 0.00 0.00 2.24
1530 1582 9.261035 ACAAAGATAGAGAAGGAGATGAACTAA 57.739 33.333 0.00 0.00 0.00 2.24
1531 1583 9.748708 CAAAGATAGAGAAGGAGATGAACTAAG 57.251 37.037 0.00 0.00 0.00 2.18
1532 1584 7.524717 AGATAGAGAAGGAGATGAACTAAGC 57.475 40.000 0.00 0.00 0.00 3.09
1533 1585 4.647424 AGAGAAGGAGATGAACTAAGCG 57.353 45.455 0.00 0.00 0.00 4.68
1534 1586 4.274147 AGAGAAGGAGATGAACTAAGCGA 58.726 43.478 0.00 0.00 0.00 4.93
1535 1587 4.338118 AGAGAAGGAGATGAACTAAGCGAG 59.662 45.833 0.00 0.00 0.00 5.03
1536 1588 4.020543 AGAAGGAGATGAACTAAGCGAGT 58.979 43.478 0.00 0.00 41.56 4.18
1537 1589 5.194432 AGAAGGAGATGAACTAAGCGAGTA 58.806 41.667 0.00 0.00 37.44 2.59
1538 1590 5.298276 AGAAGGAGATGAACTAAGCGAGTAG 59.702 44.000 0.00 0.00 37.44 2.57
1553 1605 2.680805 CGAGTAGCATGTGACCCCATTT 60.681 50.000 0.00 0.00 0.00 2.32
1610 1662 0.030603 AAAAGGGGGCAAAGGTCCAA 60.031 50.000 0.00 0.00 42.08 3.53
1910 1968 1.678269 GCGTAAGAGCAGAGCACACG 61.678 60.000 0.00 0.00 43.02 4.49
1987 2045 3.149196 CTCCTATGCACACAAGGTGTTT 58.851 45.455 0.00 0.00 45.08 2.83
2036 2094 1.277557 GCTTTCTCCTCTCCAAGCTCA 59.722 52.381 0.00 0.00 38.89 4.26
2038 2096 3.621958 GCTTTCTCCTCTCCAAGCTCAAT 60.622 47.826 0.00 0.00 38.89 2.57
2109 2167 3.307906 CCGTCCCCGTCTTCACCA 61.308 66.667 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 3.980646 AAGCAACAACGTGAGCAATTA 57.019 38.095 0.00 0.00 0.00 1.40
65 66 1.069568 CGCCGTATGAACAAAGCAACA 60.070 47.619 0.00 0.00 0.00 3.33
81 82 5.963586 GGAACTCATAAATTTTAGTTCGCCG 59.036 40.000 21.78 0.00 45.61 6.46
84 85 9.983804 GTAAGGGAACTCATAAATTTTAGTTCG 57.016 33.333 21.78 3.85 45.61 3.95
171 172 5.128499 TGTGAATTCAATTGTCCCTTGTTGT 59.872 36.000 10.35 0.00 0.00 3.32
226 227 5.643379 AGTAGTCGAACCAAATTACGGTA 57.357 39.130 0.09 0.00 34.99 4.02
251 252 0.107508 ATCTCCCTCGCCACAACATG 60.108 55.000 0.00 0.00 0.00 3.21
453 470 0.615827 AGCCCCCTTGCAATTCCTTC 60.616 55.000 0.00 0.00 0.00 3.46
525 542 4.427312 GCATCTAGCAAAACATTTCCAGG 58.573 43.478 0.00 0.00 44.79 4.45
671 689 7.390718 ACAGGATTTGAGTATAACCACAAGTTC 59.609 37.037 0.00 0.00 40.05 3.01
785 807 5.683876 ACACACCAAAGCTATAGATGTCT 57.316 39.130 3.21 0.00 0.00 3.41
1013 1064 6.266103 TGAATGAGCCAAATCTTTTGTCTTCT 59.734 34.615 0.00 0.00 0.00 2.85
1033 1084 9.498176 TGAACAAGTATCCATGATAGATGAATG 57.502 33.333 0.00 0.00 0.00 2.67
1060 1111 5.279156 GGATGCAAAGGAAAAGTTCATCTGT 60.279 40.000 0.00 0.00 32.03 3.41
1115 1167 3.395273 TGACATCAATGGCCTATCATCCA 59.605 43.478 3.32 0.00 33.92 3.41
1250 1302 8.717821 CAGTAACGGATAAAGAATTCACAAAGA 58.282 33.333 8.44 0.00 0.00 2.52
1253 1305 8.610248 TTCAGTAACGGATAAAGAATTCACAA 57.390 30.769 8.44 0.00 0.00 3.33
1322 1374 2.432874 TCCACCGAACCCACACATATAG 59.567 50.000 0.00 0.00 0.00 1.31
1333 1385 0.249741 CCGTCCATATCCACCGAACC 60.250 60.000 0.00 0.00 0.00 3.62
1346 1398 0.606944 GTAAATGGCACCACCGTCCA 60.607 55.000 0.00 0.00 43.94 4.02
1350 1402 4.637276 TGATATAGTAAATGGCACCACCG 58.363 43.478 0.00 0.00 43.94 4.94
1392 1444 6.469410 AGAAATGATGCATGACCATTTTGTT 58.531 32.000 19.90 10.47 39.67 2.83
1398 1450 7.070198 TCCAAATAAGAAATGATGCATGACCAT 59.930 33.333 2.46 0.00 0.00 3.55
1404 1456 8.070034 TGACTTCCAAATAAGAAATGATGCAT 57.930 30.769 0.00 0.00 0.00 3.96
1415 1467 8.960591 AGACCAATACAATGACTTCCAAATAAG 58.039 33.333 0.00 0.00 0.00 1.73
1502 1554 9.261035 AGTTCATCTCCTTCTCTATCTTTGTTA 57.739 33.333 0.00 0.00 0.00 2.41
1507 1559 7.255451 CGCTTAGTTCATCTCCTTCTCTATCTT 60.255 40.741 0.00 0.00 0.00 2.40
1508 1560 6.206634 CGCTTAGTTCATCTCCTTCTCTATCT 59.793 42.308 0.00 0.00 0.00 1.98
1509 1561 6.205853 TCGCTTAGTTCATCTCCTTCTCTATC 59.794 42.308 0.00 0.00 0.00 2.08
1510 1562 6.065374 TCGCTTAGTTCATCTCCTTCTCTAT 58.935 40.000 0.00 0.00 0.00 1.98
1511 1563 5.437946 TCGCTTAGTTCATCTCCTTCTCTA 58.562 41.667 0.00 0.00 0.00 2.43
1512 1564 4.274147 TCGCTTAGTTCATCTCCTTCTCT 58.726 43.478 0.00 0.00 0.00 3.10
1514 1566 4.020543 ACTCGCTTAGTTCATCTCCTTCT 58.979 43.478 0.00 0.00 33.35 2.85
1515 1567 4.379339 ACTCGCTTAGTTCATCTCCTTC 57.621 45.455 0.00 0.00 33.35 3.46
1516 1568 4.202070 GCTACTCGCTTAGTTCATCTCCTT 60.202 45.833 0.00 0.00 39.80 3.36
1517 1569 3.316868 GCTACTCGCTTAGTTCATCTCCT 59.683 47.826 0.00 0.00 39.80 3.69
1518 1570 3.066900 TGCTACTCGCTTAGTTCATCTCC 59.933 47.826 0.00 0.00 39.80 3.71
1519 1571 4.294416 TGCTACTCGCTTAGTTCATCTC 57.706 45.455 0.00 0.00 39.80 2.75
1520 1572 4.098654 ACATGCTACTCGCTTAGTTCATCT 59.901 41.667 0.00 0.00 39.80 2.90
1521 1573 4.208047 CACATGCTACTCGCTTAGTTCATC 59.792 45.833 0.00 0.00 39.80 2.92
1522 1574 4.115516 CACATGCTACTCGCTTAGTTCAT 58.884 43.478 0.00 0.00 39.80 2.57
1523 1575 3.192633 TCACATGCTACTCGCTTAGTTCA 59.807 43.478 0.00 0.00 39.80 3.18
1524 1576 3.548268 GTCACATGCTACTCGCTTAGTTC 59.452 47.826 0.00 0.00 39.80 3.01
1525 1577 3.512680 GTCACATGCTACTCGCTTAGTT 58.487 45.455 0.00 0.00 39.80 2.24
1526 1578 2.159226 GGTCACATGCTACTCGCTTAGT 60.159 50.000 0.00 0.00 42.62 2.24
1527 1579 2.464865 GGTCACATGCTACTCGCTTAG 58.535 52.381 0.00 0.00 40.11 2.18
1528 1580 1.136305 GGGTCACATGCTACTCGCTTA 59.864 52.381 0.00 0.00 40.11 3.09
1529 1581 0.108138 GGGTCACATGCTACTCGCTT 60.108 55.000 0.00 0.00 40.11 4.68
1530 1582 1.517832 GGGTCACATGCTACTCGCT 59.482 57.895 0.00 0.00 40.11 4.93
1531 1583 1.521681 GGGGTCACATGCTACTCGC 60.522 63.158 0.00 0.00 39.77 5.03
1532 1584 0.465705 ATGGGGTCACATGCTACTCG 59.534 55.000 0.00 0.00 0.00 4.18
1533 1585 2.717639 AATGGGGTCACATGCTACTC 57.282 50.000 0.00 0.00 0.00 2.59
1534 1586 3.371595 GGTAAATGGGGTCACATGCTACT 60.372 47.826 0.00 0.00 0.00 2.57
1535 1587 2.949644 GGTAAATGGGGTCACATGCTAC 59.050 50.000 0.00 0.00 0.00 3.58
1536 1588 2.092103 GGGTAAATGGGGTCACATGCTA 60.092 50.000 0.00 0.00 0.00 3.49
1537 1589 1.341976 GGGTAAATGGGGTCACATGCT 60.342 52.381 0.00 0.00 0.00 3.79
1538 1590 1.111277 GGGTAAATGGGGTCACATGC 58.889 55.000 0.00 0.00 0.00 4.06
1539 1591 2.523325 TGGGTAAATGGGGTCACATG 57.477 50.000 0.00 0.00 0.00 3.21
1540 1592 3.774842 AATGGGTAAATGGGGTCACAT 57.225 42.857 0.00 0.00 0.00 3.21
1553 1605 7.768807 AGTGTTTAAGTTGCAATAATGGGTA 57.231 32.000 0.59 0.00 0.00 3.69
1610 1662 0.916358 ACTAATGGGCTGACCTGGCT 60.916 55.000 0.00 0.00 41.11 4.75
1614 1666 1.338136 CGGGACTAATGGGCTGACCT 61.338 60.000 0.00 0.00 41.11 3.85
1665 1717 2.261671 CTCACGAACCGGGTCCAG 59.738 66.667 15.47 6.72 0.00 3.86
1716 1768 2.572284 GTCCAGACGAACCGGGAG 59.428 66.667 6.32 0.00 0.00 4.30
1787 1844 1.379843 ACCAACCGGGATCAATGGC 60.380 57.895 6.32 0.00 41.15 4.40
1794 1851 2.035626 CAAGCCACCAACCGGGAT 59.964 61.111 6.32 0.00 41.15 3.85
1987 2045 2.192979 GGCTCGGGCATTCCATCA 59.807 61.111 10.74 0.00 40.87 3.07
2036 2094 4.264083 TGAGGAAAATGGAGCTTGGAGATT 60.264 41.667 0.00 0.00 0.00 2.40
2038 2096 2.644299 TGAGGAAAATGGAGCTTGGAGA 59.356 45.455 0.00 0.00 0.00 3.71
2109 2167 4.831307 GCGCGAGTGATCGACGGT 62.831 66.667 12.10 0.00 34.88 4.83


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

AutoCloner maintained by Alex Coulton.