Multiple sequence alignment - TraesCS2B01G475600

Loading Multiple Alignment...

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 TraesCS2B01G475600 chr2B 100.000 2297 0 0 1 2297 672744732 672747028 0.000000e+00 4242.0
1 TraesCS2B01G475600 chr2B 97.600 1375 12 4 1 1354 672860114 672858740 0.000000e+00 2337.0
2 TraesCS2B01G475600 chr2B 99.664 595 2 0 1349 1943 672854363 672853769 0.000000e+00 1088.0
3 TraesCS2B01G475600 chr2B 88.519 540 46 9 792 1328 672530641 672531167 6.920000e-180 640.0
4 TraesCS2B01G475600 chr2B 87.549 514 45 12 792 1300 672344891 672345390 5.500000e-161 577.0
5 TraesCS2B01G475600 chr2B 98.214 280 2 1 2018 2297 672853777 672853501 9.540000e-134 486.0
6 TraesCS2B01G475600 chr2B 88.235 340 24 5 998 1328 672646578 672646910 2.140000e-105 392.0
7 TraesCS2B01G475600 chr2B 90.476 168 12 2 593 759 672341387 672341551 3.840000e-53 219.0
8 TraesCS2B01G475600 chr2B 100.000 88 0 0 1934 2021 774106559 774106646 1.830000e-36 163.0
9 TraesCS2B01G475600 chr2B 90.164 122 11 1 634 755 672576087 672576207 8.500000e-35 158.0
10 TraesCS2B01G475600 chr2A 85.799 1345 102 46 634 1933 703110626 703111926 0.000000e+00 1343.0
11 TraesCS2B01G475600 chr2A 84.041 589 42 25 820 1374 703105600 703106170 9.410000e-144 520.0
12 TraesCS2B01G475600 chr2A 87.906 339 27 2 998 1328 703291240 703291572 9.950000e-104 387.0
13 TraesCS2B01G475600 chr2A 91.304 46 4 0 594 639 480153929 480153974 1.910000e-06 63.9
14 TraesCS2B01G475600 chr2A 100.000 28 0 0 612 639 33730504 33730531 4.000000e-03 52.8
15 TraesCS2B01G475600 chr2D 86.299 1051 79 26 634 1659 562580914 562581924 0.000000e+00 1083.0
16 TraesCS2B01G475600 chr2D 83.725 510 45 20 792 1300 562449082 562449554 4.500000e-122 448.0
17 TraesCS2B01G475600 chr2D 86.667 180 20 3 1754 1933 562582107 562582282 1.800000e-46 196.0
18 TraesCS2B01G475600 chr6B 97.302 593 14 2 1 592 548650296 548650887 0.000000e+00 1005.0
19 TraesCS2B01G475600 chr6B 96.801 594 16 3 1 592 679651991 679652583 0.000000e+00 989.0
20 TraesCS2B01G475600 chr6B 93.333 105 4 3 1920 2021 716607888 716607784 3.950000e-33 152.0
21 TraesCS2B01G475600 chr7A 96.500 600 16 3 1 596 399746601 399746003 0.000000e+00 987.0
22 TraesCS2B01G475600 chr7A 96.482 597 16 3 1 593 399780712 399781307 0.000000e+00 981.0
23 TraesCS2B01G475600 chr7A 96.477 596 15 4 1 592 30013006 30012413 0.000000e+00 979.0
24 TraesCS2B01G475600 chr7A 96.147 597 18 3 1 593 399781781 399782376 0.000000e+00 970.0
25 TraesCS2B01G475600 chr5B 96.160 599 18 3 1 595 60480347 60480944 0.000000e+00 974.0
26 TraesCS2B01G475600 chr5B 92.381 105 6 1 1919 2021 135750751 135750647 5.110000e-32 148.0
27 TraesCS2B01G475600 chr5A 96.147 597 19 2 1 593 689898323 689897727 0.000000e+00 972.0
28 TraesCS2B01G475600 chr5A 97.826 92 2 0 1930 2021 9508098 9508007 2.360000e-35 159.0
29 TraesCS2B01G475600 chr5A 94.118 51 2 1 594 644 580457007 580457056 2.450000e-10 76.8
30 TraesCS2B01G475600 chr5A 100.000 28 0 0 612 639 299771151 299771124 4.000000e-03 52.8
31 TraesCS2B01G475600 chr3B 87.805 246 20 5 2031 2267 746284795 746284551 1.740000e-71 279.0
32 TraesCS2B01G475600 chr3B 96.809 94 2 1 1927 2020 256530606 256530514 3.060000e-34 156.0
33 TraesCS2B01G475600 chr1B 100.000 88 0 0 1935 2022 513482622 513482709 1.830000e-36 163.0
34 TraesCS2B01G475600 chr4D 98.876 89 1 0 1932 2020 461574590 461574678 2.360000e-35 159.0
35 TraesCS2B01G475600 chr4B 98.876 89 1 0 1932 2020 103889966 103890054 2.360000e-35 159.0
36 TraesCS2B01G475600 chr1D 95.918 98 4 0 1924 2021 197821557 197821654 2.360000e-35 159.0
37 TraesCS2B01G475600 chr7B 88.333 60 5 2 2029 2087 41313183 41313125 1.140000e-08 71.3


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 TraesCS2B01G475600 chr2B 672744732 672747028 2296 False 4242.0 4242 100.0000 1 2297 1 chr2B.!!$F4 2296
1 TraesCS2B01G475600 chr2B 672858740 672860114 1374 True 2337.0 2337 97.6000 1 1354 1 chr2B.!!$R1 1353
2 TraesCS2B01G475600 chr2B 672853501 672854363 862 True 787.0 1088 98.9390 1349 2297 2 chr2B.!!$R2 948
3 TraesCS2B01G475600 chr2B 672530641 672531167 526 False 640.0 640 88.5190 792 1328 1 chr2B.!!$F1 536
4 TraesCS2B01G475600 chr2B 672341387 672345390 4003 False 398.0 577 89.0125 593 1300 2 chr2B.!!$F6 707
5 TraesCS2B01G475600 chr2A 703110626 703111926 1300 False 1343.0 1343 85.7990 634 1933 1 chr2A.!!$F4 1299
6 TraesCS2B01G475600 chr2A 703105600 703106170 570 False 520.0 520 84.0410 820 1374 1 chr2A.!!$F3 554
7 TraesCS2B01G475600 chr2D 562580914 562582282 1368 False 639.5 1083 86.4830 634 1933 2 chr2D.!!$F2 1299
8 TraesCS2B01G475600 chr6B 548650296 548650887 591 False 1005.0 1005 97.3020 1 592 1 chr6B.!!$F1 591
9 TraesCS2B01G475600 chr6B 679651991 679652583 592 False 989.0 989 96.8010 1 592 1 chr6B.!!$F2 591
10 TraesCS2B01G475600 chr7A 399746003 399746601 598 True 987.0 987 96.5000 1 596 1 chr7A.!!$R2 595
11 TraesCS2B01G475600 chr7A 30012413 30013006 593 True 979.0 979 96.4770 1 592 1 chr7A.!!$R1 591
12 TraesCS2B01G475600 chr7A 399780712 399782376 1664 False 975.5 981 96.3145 1 593 2 chr7A.!!$F1 592
13 TraesCS2B01G475600 chr5B 60480347 60480944 597 False 974.0 974 96.1600 1 595 1 chr5B.!!$F1 594
14 TraesCS2B01G475600 chr5A 689897727 689898323 596 True 972.0 972 96.1470 1 593 1 chr5A.!!$R3 592

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
1334 5764 5.943416 TGTTTGGATCGACAAGATAACCATT 59.057 36.0 0.0 0.0 40.26 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2246 6776 1.134995 TGGCGTCTGCTCTCTATTGTG 60.135 52.381 0.0 0.0 42.25 3.33 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
1334 5764 5.943416 TGTTTGGATCGACAAGATAACCATT 59.057 36.000 0.00 0.00 40.26 3.16
1943 6473 3.588569 ACCCTTGTGATATACTCCCTCC 58.411 50.000 0.00 0.00 0.00 4.30
1944 6474 2.563179 CCCTTGTGATATACTCCCTCCG 59.437 54.545 0.00 0.00 0.00 4.63
1945 6475 3.231818 CCTTGTGATATACTCCCTCCGT 58.768 50.000 0.00 0.00 0.00 4.69
1946 6476 4.404640 CCTTGTGATATACTCCCTCCGTA 58.595 47.826 0.00 0.00 0.00 4.02
1947 6477 4.831155 CCTTGTGATATACTCCCTCCGTAA 59.169 45.833 0.00 0.00 0.00 3.18
1948 6478 5.303589 CCTTGTGATATACTCCCTCCGTAAA 59.696 44.000 0.00 0.00 0.00 2.01
1949 6479 5.779529 TGTGATATACTCCCTCCGTAAAC 57.220 43.478 0.00 0.00 0.00 2.01
1950 6480 5.452255 TGTGATATACTCCCTCCGTAAACT 58.548 41.667 0.00 0.00 0.00 2.66
1951 6481 6.604171 TGTGATATACTCCCTCCGTAAACTA 58.396 40.000 0.00 0.00 0.00 2.24
1952 6482 7.062322 TGTGATATACTCCCTCCGTAAACTAA 58.938 38.462 0.00 0.00 0.00 2.24
1953 6483 7.727186 TGTGATATACTCCCTCCGTAAACTAAT 59.273 37.037 0.00 0.00 0.00 1.73
1954 6484 9.236006 GTGATATACTCCCTCCGTAAACTAATA 57.764 37.037 0.00 0.00 0.00 0.98
1955 6485 9.986157 TGATATACTCCCTCCGTAAACTAATAT 57.014 33.333 0.00 0.00 0.00 1.28
1961 6491 7.930325 ACTCCCTCCGTAAACTAATATAAAAGC 59.070 37.037 0.00 0.00 0.00 3.51
1962 6492 6.925165 TCCCTCCGTAAACTAATATAAAAGCG 59.075 38.462 0.00 0.00 0.00 4.68
1963 6493 6.703165 CCCTCCGTAAACTAATATAAAAGCGT 59.297 38.462 0.00 0.00 0.00 5.07
1964 6494 7.225341 CCCTCCGTAAACTAATATAAAAGCGTT 59.775 37.037 0.00 0.00 0.00 4.84
1965 6495 8.606602 CCTCCGTAAACTAATATAAAAGCGTTT 58.393 33.333 2.53 2.53 0.00 3.60
1983 6513 9.918630 AAAGCGTTTAGAATACTAAAGTAGTGA 57.081 29.630 0.00 0.00 45.42 3.41
1985 6515 9.733219 AGCGTTTAGAATACTAAAGTAGTGATC 57.267 33.333 0.00 0.00 45.42 2.92
1986 6516 9.733219 GCGTTTAGAATACTAAAGTAGTGATCT 57.267 33.333 0.00 4.67 45.42 2.75
1992 6522 9.733219 AGAATACTAAAGTAGTGATCTAAACGC 57.267 33.333 0.00 0.00 39.81 4.84
1993 6523 9.733219 GAATACTAAAGTAGTGATCTAAACGCT 57.267 33.333 0.00 0.00 39.81 5.07
1994 6524 9.733219 AATACTAAAGTAGTGATCTAAACGCTC 57.267 33.333 0.00 0.00 39.81 5.03
1995 6525 7.393841 ACTAAAGTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
1996 6526 7.828712 ACTAAAGTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
1997 6527 8.954350 ACTAAAGTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
1998 6528 9.953697 CTAAAGTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
2013 6543 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
2014 6544 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
2015 6545 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
2016 6546 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
2017 6547 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
2146 6676 3.451178 ACTATGTAACGTCCATTCAGGCT 59.549 43.478 6.05 0.00 37.29 4.58
2147 6677 4.647853 ACTATGTAACGTCCATTCAGGCTA 59.352 41.667 6.05 0.00 37.29 3.93
2148 6678 3.241067 TGTAACGTCCATTCAGGCTAC 57.759 47.619 0.00 0.00 37.29 3.58
2153 6683 3.097614 ACGTCCATTCAGGCTACTACTT 58.902 45.455 0.00 0.00 37.29 2.24
2246 6776 1.562575 CGTCTTGGTTGTACCGGCAC 61.563 60.000 0.00 0.00 42.58 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
358 367 8.771920 ACTGACTTCATCGACAACAATAATAA 57.228 30.769 0.00 0.00 0.00 1.40
376 385 9.533253 CAAATAAGAACCAAATTCAACTGACTT 57.467 29.630 0.00 0.00 40.09 3.01
1334 5764 5.336744 GGTCGTTTCTTCAAAACAACATCA 58.663 37.500 2.05 0.00 0.00 3.07
1824 6354 6.034898 GGATCAAACTGGTCAATTTAATTGCG 59.965 38.462 12.39 4.28 40.05 4.85
1957 6487 9.918630 TCACTACTTTAGTATTCTAAACGCTTT 57.081 29.630 0.76 0.00 40.05 3.51
1959 6489 9.733219 GATCACTACTTTAGTATTCTAAACGCT 57.267 33.333 0.76 0.00 40.05 5.07
1960 6490 9.733219 AGATCACTACTTTAGTATTCTAAACGC 57.267 33.333 0.76 0.00 40.05 4.84
1966 6496 9.733219 GCGTTTAGATCACTACTTTAGTATTCT 57.267 33.333 0.00 0.00 37.23 2.40
1967 6497 9.733219 AGCGTTTAGATCACTACTTTAGTATTC 57.267 33.333 0.00 0.00 37.23 1.75
1968 6498 9.733219 GAGCGTTTAGATCACTACTTTAGTATT 57.267 33.333 0.00 0.00 37.23 1.89
1969 6499 9.122779 AGAGCGTTTAGATCACTACTTTAGTAT 57.877 33.333 0.00 0.00 37.82 2.12
1970 6500 8.503458 AGAGCGTTTAGATCACTACTTTAGTA 57.497 34.615 0.00 0.00 37.82 1.82
1971 6501 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
1972 6502 9.953697 ATAAGAGCGTTTAGATCACTACTTTAG 57.046 33.333 0.00 0.00 37.82 1.85
1987 6517 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
1988 6518 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
1989 6519 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
1990 6520 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
1991 6521 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
1996 6526 9.804977 GGAGTACTCCCTCTGTAAACTAATATA 57.195 37.037 28.87 0.00 43.94 0.86
1997 6527 8.709272 GGAGTACTCCCTCTGTAAACTAATAT 57.291 38.462 28.87 0.00 43.94 1.28
2146 6676 4.921470 GCTTTTGCATCGACAAGTAGTA 57.079 40.909 0.00 0.00 46.58 1.82
2147 6677 3.813529 GCTTTTGCATCGACAAGTAGT 57.186 42.857 0.00 0.00 46.58 2.73
2196 6726 1.521010 CTCATCTCGCTGCAGGTGG 60.521 63.158 17.12 4.16 0.00 4.61
2246 6776 1.134995 TGGCGTCTGCTCTCTATTGTG 60.135 52.381 0.00 0.00 42.25 3.33


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

AutoCloner maintained by Alex Coulton.