Multiple sequence alignment - TraesCS3B01G133300

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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 TraesCS3B01G133300 chr3B 100.000 2450 0 0 1 2450 115675635 115673186 0 4525
1 TraesCS3B01G133300 chr3B 90.513 2456 174 33 1 2450 398773060 398775462 0 3190
2 TraesCS3B01G133300 chr3B 95.428 1028 45 2 495 1521 565180459 565181485 0 1637
3 TraesCS3B01G133300 chr3B 90.282 1204 114 3 1 1202 40495252 40496454 0 1572
4 TraesCS3B01G133300 chrUn 90.228 2456 182 33 1 2450 59444573 59442170 0 3153
5 TraesCS3B01G133300 chrUn 90.072 2347 193 30 1 2339 41661140 41663454 0 3007
6 TraesCS3B01G133300 chrUn 90.545 1523 139 5 1 1521 79020024 79018505 0 2010
7 TraesCS3B01G133300 chr1B 92.520 1524 107 7 1 1520 149476216 149474696 0 2176
8 TraesCS3B01G133300 chr7B 91.076 1524 129 5 1 1522 476087848 476086330 0 2054
9 TraesCS3B01G133300 chr7B 98.128 908 15 2 1542 2448 518304454 518303548 0 1581
10 TraesCS3B01G133300 chr7B 98.018 908 16 2 1542 2448 518288445 518287539 0 1576
11 TraesCS3B01G133300 chr7B 96.559 465 16 0 1 465 638611623 638611159 0 771
12 TraesCS3B01G133300 chr2B 91.018 1503 124 7 3 1500 298276000 298277496 0 2017
13 TraesCS3B01G133300 chr2B 95.996 1024 40 1 495 1517 762706717 762707740 0 1663
14 TraesCS3B01G133300 chr4B 88.852 1525 155 14 3 1519 155757745 155759262 0 1860
15 TraesCS3B01G133300 chr4B 98.570 909 12 1 1542 2450 485381422 485382329 0 1605
16 TraesCS3B01G133300 chr4B 96.370 909 32 1 1542 2450 165970089 165969182 0 1495
17 TraesCS3B01G133300 chr6B 84.138 1532 220 17 2 1521 314111581 314110061 0 1461
18 TraesCS3B01G133300 chr6B 94.298 912 47 4 1542 2450 144615794 144616703 0 1391
19 TraesCS3B01G133300 chr2A 94.633 913 39 9 1542 2450 82412971 82412065 0 1406
20 TraesCS3B01G133300 chr3A 94.085 913 44 9 1542 2450 167681899 167680993 0 1378


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 TraesCS3B01G133300 chr3B 115673186 115675635 2449 True 4525 4525 100.000 1 2450 1 chr3B.!!$R1 2449
1 TraesCS3B01G133300 chr3B 398773060 398775462 2402 False 3190 3190 90.513 1 2450 1 chr3B.!!$F2 2449
2 TraesCS3B01G133300 chr3B 565180459 565181485 1026 False 1637 1637 95.428 495 1521 1 chr3B.!!$F3 1026
3 TraesCS3B01G133300 chr3B 40495252 40496454 1202 False 1572 1572 90.282 1 1202 1 chr3B.!!$F1 1201
4 TraesCS3B01G133300 chrUn 59442170 59444573 2403 True 3153 3153 90.228 1 2450 1 chrUn.!!$R1 2449
5 TraesCS3B01G133300 chrUn 41661140 41663454 2314 False 3007 3007 90.072 1 2339 1 chrUn.!!$F1 2338
6 TraesCS3B01G133300 chrUn 79018505 79020024 1519 True 2010 2010 90.545 1 1521 1 chrUn.!!$R2 1520
7 TraesCS3B01G133300 chr1B 149474696 149476216 1520 True 2176 2176 92.520 1 1520 1 chr1B.!!$R1 1519
8 TraesCS3B01G133300 chr7B 476086330 476087848 1518 True 2054 2054 91.076 1 1522 1 chr7B.!!$R1 1521
9 TraesCS3B01G133300 chr7B 518303548 518304454 906 True 1581 1581 98.128 1542 2448 1 chr7B.!!$R3 906
10 TraesCS3B01G133300 chr7B 518287539 518288445 906 True 1576 1576 98.018 1542 2448 1 chr7B.!!$R2 906
11 TraesCS3B01G133300 chr2B 298276000 298277496 1496 False 2017 2017 91.018 3 1500 1 chr2B.!!$F1 1497
12 TraesCS3B01G133300 chr2B 762706717 762707740 1023 False 1663 1663 95.996 495 1517 1 chr2B.!!$F2 1022
13 TraesCS3B01G133300 chr4B 155757745 155759262 1517 False 1860 1860 88.852 3 1519 1 chr4B.!!$F1 1516
14 TraesCS3B01G133300 chr4B 485381422 485382329 907 False 1605 1605 98.570 1542 2450 1 chr4B.!!$F2 908
15 TraesCS3B01G133300 chr4B 165969182 165970089 907 True 1495 1495 96.370 1542 2450 1 chr4B.!!$R1 908
16 TraesCS3B01G133300 chr6B 314110061 314111581 1520 True 1461 1461 84.138 2 1521 1 chr6B.!!$R1 1519
17 TraesCS3B01G133300 chr6B 144615794 144616703 909 False 1391 1391 94.298 1542 2450 1 chr6B.!!$F1 908
18 TraesCS3B01G133300 chr2A 82412065 82412971 906 True 1406 1406 94.633 1542 2450 1 chr2A.!!$R1 908
19 TraesCS3B01G133300 chr3A 167680993 167681899 906 True 1378 1378 94.085 1542 2450 1 chr3A.!!$R1 908

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
568 569 0.318699 TCGAGTTCACTTGGAGTGCG 60.319 55.0 3.26 2.11 45.54 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1516 1529 0.250467 ATCGGTGGTATCATGCCTGC 60.25 55.0 0.0 0.0 0.0 4.85 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
45 46 3.266510 AGATGATTTAACTCGGCAGCA 57.733 42.857 0.00 0.00 0.00 4.41
97 98 8.397957 AGCTCTTATGATCCTTATTCTAGAGGA 58.602 37.037 1.21 1.21 45.57 3.71
139 140 4.776837 ACCTGCCATATTTGTGGATTTCAA 59.223 37.500 0.00 0.00 42.02 2.69
194 195 2.024414 CCCATCCTCCGGATTGTTTTC 58.976 52.381 3.57 0.00 39.79 2.29
320 321 7.016957 TCTCATCATTTGCCTCTAGTTATCCAT 59.983 37.037 0.00 0.00 0.00 3.41
331 332 5.869579 TCTAGTTATCCATTGCAGGGATTC 58.130 41.667 22.44 16.61 42.47 2.52
348 349 4.164221 GGGATTCAGGTACAATGAGGAGAA 59.836 45.833 0.00 0.00 0.00 2.87
399 400 9.775539 TTATTCAGCTCCTATTCATATACCTCT 57.224 33.333 0.00 0.00 0.00 3.69
568 569 0.318699 TCGAGTTCACTTGGAGTGCG 60.319 55.000 3.26 2.11 45.54 5.34
664 665 9.495572 GAAGAAGTAAGGAAGATTGAGAAGAAA 57.504 33.333 0.00 0.00 0.00 2.52
671 672 8.703378 AAGGAAGATTGAGAAGAAAATCAACT 57.297 30.769 0.00 0.00 38.19 3.16
695 696 5.102953 TGGCAGCACTATTTCTTCATAGT 57.897 39.130 0.00 0.00 40.08 2.12
766 767 1.357258 CGTCACATCCAGCTGAGCAC 61.357 60.000 17.39 4.61 0.00 4.40
837 841 5.241662 ACTAGAAGACAAGGAACAAGATGC 58.758 41.667 0.00 0.00 0.00 3.91
954 959 5.132648 ACCTGAGATTCATTGGCCTATTGTA 59.867 40.000 3.32 0.00 0.00 2.41
955 960 6.183361 ACCTGAGATTCATTGGCCTATTGTAT 60.183 38.462 3.32 0.00 0.00 2.29
1205 1210 4.514441 CCATGCTAGTCTTGAGCTTAATGG 59.486 45.833 0.00 0.00 40.76 3.16
1261 1266 7.801104 TGCTGATTTCTACCATCCTAAACATA 58.199 34.615 0.00 0.00 0.00 2.29
1343 1348 3.686726 CCTACCACTTGCATTGTCTCTTC 59.313 47.826 0.00 0.00 0.00 2.87
1389 1394 1.726791 CTTGTGCACGATCCACTACAC 59.273 52.381 13.13 0.00 34.38 2.90
1503 1516 1.346062 GGAGCAGGCATGAGGATAGA 58.654 55.000 0.62 0.00 0.00 1.98
1504 1517 1.275856 GGAGCAGGCATGAGGATAGAG 59.724 57.143 0.62 0.00 0.00 2.43
1505 1518 2.246469 GAGCAGGCATGAGGATAGAGA 58.754 52.381 0.62 0.00 0.00 3.10
1506 1519 2.632028 GAGCAGGCATGAGGATAGAGAA 59.368 50.000 0.62 0.00 0.00 2.87
1507 1520 2.633967 AGCAGGCATGAGGATAGAGAAG 59.366 50.000 0.62 0.00 0.00 2.85
1508 1521 2.871236 GCAGGCATGAGGATAGAGAAGC 60.871 54.545 0.62 0.00 0.00 3.86
1509 1522 2.367894 CAGGCATGAGGATAGAGAAGCA 59.632 50.000 0.00 0.00 0.00 3.91
1510 1523 3.044156 AGGCATGAGGATAGAGAAGCAA 58.956 45.455 0.00 0.00 0.00 3.91
1511 1524 3.457380 AGGCATGAGGATAGAGAAGCAAA 59.543 43.478 0.00 0.00 0.00 3.68
1512 1525 4.080129 AGGCATGAGGATAGAGAAGCAAAA 60.080 41.667 0.00 0.00 0.00 2.44
1513 1526 4.641989 GGCATGAGGATAGAGAAGCAAAAA 59.358 41.667 0.00 0.00 0.00 1.94
1514 1527 5.221009 GGCATGAGGATAGAGAAGCAAAAAG 60.221 44.000 0.00 0.00 0.00 2.27
1515 1528 5.587844 GCATGAGGATAGAGAAGCAAAAAGA 59.412 40.000 0.00 0.00 0.00 2.52
1516 1529 6.238429 GCATGAGGATAGAGAAGCAAAAAGAG 60.238 42.308 0.00 0.00 0.00 2.85
1517 1530 5.181748 TGAGGATAGAGAAGCAAAAAGAGC 58.818 41.667 0.00 0.00 0.00 4.09
1518 1531 5.171339 AGGATAGAGAAGCAAAAAGAGCA 57.829 39.130 0.00 0.00 0.00 4.26
1519 1532 5.184711 AGGATAGAGAAGCAAAAAGAGCAG 58.815 41.667 0.00 0.00 0.00 4.24
1520 1533 4.335037 GGATAGAGAAGCAAAAAGAGCAGG 59.665 45.833 0.00 0.00 0.00 4.85
1521 1534 1.885233 AGAGAAGCAAAAAGAGCAGGC 59.115 47.619 0.00 0.00 0.00 4.85
1522 1535 1.610522 GAGAAGCAAAAAGAGCAGGCA 59.389 47.619 0.00 0.00 0.00 4.75
1523 1536 2.230750 GAGAAGCAAAAAGAGCAGGCAT 59.769 45.455 0.00 0.00 0.00 4.40
1524 1537 2.029290 AGAAGCAAAAAGAGCAGGCATG 60.029 45.455 0.00 0.00 0.00 4.06
1525 1538 1.624336 AGCAAAAAGAGCAGGCATGA 58.376 45.000 0.62 0.00 0.00 3.07
1526 1539 2.176889 AGCAAAAAGAGCAGGCATGAT 58.823 42.857 0.62 0.00 0.00 2.45
1527 1540 3.359033 AGCAAAAAGAGCAGGCATGATA 58.641 40.909 0.62 0.00 0.00 2.15
1528 1541 3.129988 AGCAAAAAGAGCAGGCATGATAC 59.870 43.478 0.62 0.00 0.00 2.24
1529 1542 3.736126 GCAAAAAGAGCAGGCATGATACC 60.736 47.826 0.62 0.00 0.00 2.73
1530 1543 3.370840 AAAAGAGCAGGCATGATACCA 57.629 42.857 0.62 0.00 0.00 3.25
1531 1544 2.338577 AAGAGCAGGCATGATACCAC 57.661 50.000 0.62 0.00 0.00 4.16
1532 1545 0.471617 AGAGCAGGCATGATACCACC 59.528 55.000 0.62 0.00 0.00 4.61
1533 1546 0.882042 GAGCAGGCATGATACCACCG 60.882 60.000 0.62 0.00 0.00 4.94
1534 1547 1.146041 GCAGGCATGATACCACCGA 59.854 57.895 0.62 0.00 0.00 4.69
1535 1548 0.250467 GCAGGCATGATACCACCGAT 60.250 55.000 0.62 0.00 0.00 4.18
1536 1549 1.800805 CAGGCATGATACCACCGATC 58.199 55.000 0.00 0.00 0.00 3.69
1537 1550 0.687354 AGGCATGATACCACCGATCC 59.313 55.000 0.00 0.00 0.00 3.36
1538 1551 0.321653 GGCATGATACCACCGATCCC 60.322 60.000 0.00 0.00 0.00 3.85
1539 1552 0.396435 GCATGATACCACCGATCCCA 59.604 55.000 0.00 0.00 0.00 4.37
1540 1553 1.202758 GCATGATACCACCGATCCCAA 60.203 52.381 0.00 0.00 0.00 4.12
1764 1800 6.891361 AGGGTGATTGATGTGAATATGTGAAA 59.109 34.615 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 0.390472 GCTACTTCTTGCTGCCGAGT 60.390 55.000 0.00 0.0 0.00 4.18
45 46 5.432645 GCCTATCCTCAAAAGCTACTTCTT 58.567 41.667 0.00 0.0 0.00 2.52
320 321 3.010027 TCATTGTACCTGAATCCCTGCAA 59.990 43.478 0.00 0.0 0.00 4.08
331 332 3.007940 TGTGGTTCTCCTCATTGTACCTG 59.992 47.826 0.00 0.0 33.07 4.00
348 349 2.158682 TGTTGTGGAGCATAGTTGTGGT 60.159 45.455 0.00 0.0 0.00 4.16
568 569 5.346270 ACCTTCCTAATAGGATCATCCTCC 58.654 45.833 10.40 0.0 45.66 4.30
598 599 6.877855 CACTCTTGATCTTCTTCATTTCCTCA 59.122 38.462 0.00 0.0 0.00 3.86
664 665 3.641434 ATAGTGCTGCCAGAGTTGATT 57.359 42.857 0.00 0.0 0.00 2.57
671 672 3.701205 TGAAGAAATAGTGCTGCCAGA 57.299 42.857 0.00 0.0 0.00 3.86
695 696 6.183361 GGAATCCCAGAATTACTCAGCTCTAA 60.183 42.308 0.00 0.0 0.00 2.10
837 841 3.937706 CACTTGGGAATGTAGCTCTTGAG 59.062 47.826 0.00 0.0 0.00 3.02
847 851 4.728772 TCAACTTGATCACTTGGGAATGT 58.271 39.130 10.92 0.0 0.00 2.71
875 880 6.486056 ACTTCTTCAGGAGTAGTAGATGACA 58.514 40.000 0.00 0.0 34.62 3.58
954 959 3.860641 TGACACATCACGCTCATGTAAT 58.139 40.909 0.00 0.0 32.48 1.89
955 960 3.253230 CTGACACATCACGCTCATGTAA 58.747 45.455 0.00 0.0 32.48 2.41
1343 1348 2.787994 ACCTGAAAGAGCACTCAATGG 58.212 47.619 0.00 0.0 34.07 3.16
1389 1394 0.994995 CATCTCGAACTTGGTCAGCG 59.005 55.000 0.00 0.0 0.00 5.18
1503 1516 1.696063 TGCCTGCTCTTTTTGCTTCT 58.304 45.000 0.00 0.0 0.00 2.85
1504 1517 2.029649 TCATGCCTGCTCTTTTTGCTTC 60.030 45.455 0.00 0.0 0.00 3.86
1505 1518 1.965643 TCATGCCTGCTCTTTTTGCTT 59.034 42.857 0.00 0.0 0.00 3.91
1506 1519 1.624336 TCATGCCTGCTCTTTTTGCT 58.376 45.000 0.00 0.0 0.00 3.91
1507 1520 2.667473 ATCATGCCTGCTCTTTTTGC 57.333 45.000 0.00 0.0 0.00 3.68
1508 1521 3.444742 TGGTATCATGCCTGCTCTTTTTG 59.555 43.478 0.00 0.0 0.00 2.44
1509 1522 3.445096 GTGGTATCATGCCTGCTCTTTTT 59.555 43.478 0.00 0.0 0.00 1.94
1510 1523 3.019564 GTGGTATCATGCCTGCTCTTTT 58.980 45.455 0.00 0.0 0.00 2.27
1511 1524 2.648059 GTGGTATCATGCCTGCTCTTT 58.352 47.619 0.00 0.0 0.00 2.52
1512 1525 1.133976 GGTGGTATCATGCCTGCTCTT 60.134 52.381 0.00 0.0 0.00 2.85
1513 1526 0.471617 GGTGGTATCATGCCTGCTCT 59.528 55.000 0.00 0.0 0.00 4.09
1514 1527 0.882042 CGGTGGTATCATGCCTGCTC 60.882 60.000 0.00 0.0 0.00 4.26
1515 1528 1.146930 CGGTGGTATCATGCCTGCT 59.853 57.895 0.00 0.0 0.00 4.24
1516 1529 0.250467 ATCGGTGGTATCATGCCTGC 60.250 55.000 0.00 0.0 0.00 4.85
1517 1530 1.609061 GGATCGGTGGTATCATGCCTG 60.609 57.143 0.00 0.0 0.00 4.85
1518 1531 0.687354 GGATCGGTGGTATCATGCCT 59.313 55.000 0.00 0.0 0.00 4.75
1519 1532 0.321653 GGGATCGGTGGTATCATGCC 60.322 60.000 0.00 0.0 0.00 4.40
1520 1533 0.396435 TGGGATCGGTGGTATCATGC 59.604 55.000 0.00 0.0 0.00 4.06
1521 1534 2.928801 TTGGGATCGGTGGTATCATG 57.071 50.000 0.00 0.0 0.00 3.07
1522 1535 2.106511 CCTTTGGGATCGGTGGTATCAT 59.893 50.000 0.00 0.0 33.58 2.45
1523 1536 1.488812 CCTTTGGGATCGGTGGTATCA 59.511 52.381 0.00 0.0 33.58 2.15
1524 1537 1.766496 TCCTTTGGGATCGGTGGTATC 59.234 52.381 0.00 0.0 36.57 2.24
1525 1538 1.887797 TCCTTTGGGATCGGTGGTAT 58.112 50.000 0.00 0.0 36.57 2.73
1526 1539 1.557832 CTTCCTTTGGGATCGGTGGTA 59.442 52.381 0.00 0.0 41.87 3.25
1527 1540 0.328258 CTTCCTTTGGGATCGGTGGT 59.672 55.000 0.00 0.0 41.87 4.16
1528 1541 1.032114 GCTTCCTTTGGGATCGGTGG 61.032 60.000 0.00 0.0 41.87 4.61
1529 1542 0.322456 TGCTTCCTTTGGGATCGGTG 60.322 55.000 0.00 0.0 41.87 4.94
1530 1543 0.404040 TTGCTTCCTTTGGGATCGGT 59.596 50.000 0.00 0.0 41.87 4.69
1531 1544 1.544724 TTTGCTTCCTTTGGGATCGG 58.455 50.000 0.00 0.0 41.87 4.18
1532 1545 2.094545 CCTTTTGCTTCCTTTGGGATCG 60.095 50.000 0.00 0.0 41.87 3.69
1533 1546 3.165071 TCCTTTTGCTTCCTTTGGGATC 58.835 45.455 0.00 0.0 41.87 3.36
1534 1547 3.168292 CTCCTTTTGCTTCCTTTGGGAT 58.832 45.455 0.00 0.0 41.87 3.85
1535 1548 2.176798 TCTCCTTTTGCTTCCTTTGGGA 59.823 45.455 0.00 0.0 40.36 4.37
1536 1549 2.560105 CTCTCCTTTTGCTTCCTTTGGG 59.440 50.000 0.00 0.0 0.00 4.12
1537 1550 2.560105 CCTCTCCTTTTGCTTCCTTTGG 59.440 50.000 0.00 0.0 0.00 3.28
1538 1551 3.490348 TCCTCTCCTTTTGCTTCCTTTG 58.510 45.455 0.00 0.0 0.00 2.77
1539 1552 3.139211 ACTCCTCTCCTTTTGCTTCCTTT 59.861 43.478 0.00 0.0 0.00 3.11
1540 1553 2.713708 ACTCCTCTCCTTTTGCTTCCTT 59.286 45.455 0.00 0.0 0.00 3.36
1764 1800 5.536161 AGTTTACAAGGCATTCAACACTCAT 59.464 36.000 0.00 0.0 0.00 2.90
2027 2064 8.579850 AGCACAAAAATAGGAATCATCACTTA 57.420 30.769 0.00 0.0 0.00 2.24
2090 2127 5.754543 CTACTGTAGGTAGCCAGACTTAC 57.245 47.826 6.95 0.0 40.99 2.34
2193 2231 4.839121 GAACATGGTATACACCTGGTTCA 58.161 43.478 17.27 0.0 46.53 3.18


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

AutoCloner maintained by Alex Coulton.